Supplementary material 4. Fold-back structures for known miRNA from precocious trifoliate orange.Precursor secondary structures and dG value were produced using the mfold software. rpi.edu/.miRNA and miRNA* sequences are highlighted in red and blue,respectively. The numbers along the structure are nucleotide sites from the 5’ end of the pre-miRNA sequence.
Pt-miR473, scaffold_10:4756825:4756992,dG = -61.10
10 20 30 40 50 60
GA CGAC U - C U CG-- | UCCU
UGGAU GC GAAGCCCUU AGGG AGAGUGA CGACUC GCUUU--CUCAUUU \
ACCUA CG CUUCGGGAA UCCC UCUCACU GCUGAG CGAAA GAGUGAG U
AA ACC- - C - U AUGA \ ^ CUUU
160 150 140 130 120 70
80 90
UGUAUC----- AC- CAAC
UACA UAAG \
GUGU GUUC A
CCAAAGAAACA GCA UAAG
110 100
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:ACUCUCCCUCAAGGGCUUCGC
Pt-miR396g, scaffold_10:5361338:5361471,dG = -46.60
10 20 30 40 50 60 70
U| G C U A AAUUA - UUUU C CAA
CUUUU CAUG UUUUCCACGGC UUCUUGA CUU GUAC GGUUAA UUUGUG UAUUAA \
GGAAA GUAC AAAGGGUGCCG AAGAACU GAA CGUG CUAAUU AAACGU AUAAUU G
-^ - A U C A---- A UCU- - AAC
130 120 110 100 90 80
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUCCACGGCUUUCUUGAACUU
Pt-miR172a-2, scaffold_11:3936497:3936667,dG = -72.40
10 20 30 40 50
AAC-- CGU A A | U
AGUCAU UUGC GAUGCAGCAUCAUCAAGAUUC CAUG--UAUAUAUAUAUA A
UCAGUA AGCG CUACGUCGUAGUAGUUCUAAG GUAC AUAUAUAUAUAU U
ACUAA AAU A A \ ^ A
. 160 150 140 130 70 60
80 90 100
GAUAUAGAUAUAU UAAU- UG G
GC GG GAAAGAU U
CG UC UUUUCUA U
UUC------UUAUU GU U
120 110
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:AGAAUCUUGAUGAUGCUGCAU
Pt-miR172e, scaffold_8:1444339:1444460, dG = -57.00
10 20 30
A GGU A .-A| U
AUAUUUGC UGCGGCAUCAUCAAGAUUC CA GC U
UAUAAACG ACGUCGUAGUAGUUCUAAG GU CG U
- ACU G \ -^ A
120 110 100 90 40
50 60
A------CA G
AGGGAAUU UUGAAUA G
UUCCUUGA AACUUAU C
AAUAAACC A- C
8070
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:GAAUCUUGAUGAUGCUGCAU
Pt-miR530b, scaffold_12:3298202:3298355, dG = -68.40
10 20 30 40 50
AUUC C U .-UA -| C CG
UUUAUCUGCAUUUGCA CUGCAUCUUG UGCGU CUUG GUU UGGUU U
AAGUAGACGUGAACGU GACGUGGAAC ACGUA GAAC CGA ACCGA A
CCGU U U \ -- A^ A AA
150 140 130 120 70 60
80 90
AAGA- AUA A G G
GCCA GC GUCG CA A
UGGU CG CGGU GU U
UAUUG A-- A G A
110 100
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGCAUUUGCACCUGCAUCUUG
Pt-miR166a-1, scaffold_12:4684033:4684234,dG = -61.70
10 20 30 40 50 60 70 80 90
---- UUUUUCUU A- UU CU GGC ------UU UUA- -| CA U GUUUCAUUU
GGAAGC UUG GGGGAAUG GUCUGG CGA CACUAACU AGAUC UGAU AUCUCAGU UGAU UA AUUU \
UCUUCG AAC CCCCUUAC CGGACC GCU GUGAUUGA UCUAG ACUA UAGAGUUA AUUA AU UAAA U
UCUA UUAAU--- CC UU AG GCA AUUAAUAGAAU UU CCCA U^ -- U AUACCUUCU
200 190 180 170 160 150 140 130 120 110 100
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UCGGACCAGGCUUCAUUCCCC
Pt-miR319, scaffold_12:3883419:3883521,dG = -31.30
10 20 30 40 50
- AG-| G AC UC AA A AAAGG GA
AGGAUUUAAUU CU CUG UCAUUCA CA UACUG GU GUC A
UUCUAAGUUAA GA GGC AGUAAGU GU AUGAC CA UAG A
A ACA^ G GU GA AA C ----- GU
100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UAGCUGCUGACUCAUUCAUCCA
Pt-miR160a*, scaffold_15:3899913:3900035,dG = -57.70
10 20 30 40 50 60
--- U AUU--| GU C C A A A- GC
AAGG GAA AAUGG UAUGC UGGCUCC UGUAUGCCGC AGCAG CG CAAUCU \
UUCC CUU UUAUC AUACG ACCGAGG GCAUGCGGUG UCGUU GC GUUAGA C
UCU - CCUUC^ -- A A G - CG GG
120 110 100 90 80 70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:GCGUACGAGGAGCCAAGCAUA
Pt-miR167d*, scaffold_15:4341089:4341447,dG = -101.60
10 20 30 40 50 60 70 80 90
GAU U-- A C C AAUC .-UUU AUAU UU .-UUA| UUU UUU
AUGUUGGU UGAG GAUUGAAGCUGC AG AUGAUCUGGU AACC UUGUAU AUAUA AAUUCC UAGUU AGA \
UACAACCA ACUC UUAACUUCGACG UC UACUGGACUA UUGG AACGUG UAUAU UUGGGG AUUAA UCU A
AUU CUU A U - CC-- \ --- CUUU U- \ ---^ UUU UUA
350 340 330 320 310 160 150 100
110 120
GAU GGU U
CCAU UUCAAU \
GGUA AAGUUA C
U-- AAU U
140 130
170 180 190 200 210 220 230 240
-- AA- AUA AUA U UCCAAUC GUUU U UUU CCUAA
UUAUU GAGG GAUGGA GCGCCUU AAA ACUUUUUUA UAU UUGAUCUU UGCCC \
AGUAG CUUC UUAUUU UGUGGGA UUU UGAGAGAAU GUA AAUUGGAA AUGGG A
UA AUG GA- AG------U --- AAUUA
300 290 280 270 260 250
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:AGGUCAUCUUGCAGCUUCAAU
Pt-miR172c, scaffold_16:3593805:3593951,dG = -59.30
10 20 30 40 50 60 70
UGU| A G C A C UU UAG- - A U U UUUUA
UUGC GUUG AGCA CAUCAAGAUUC CAAA UA AGGGU UGA GUGGAG UAA GG GGCUA U
AGCG CGAC UCGU GUAGUUCUAAG GUUU GU UCUCG ACU CACUUC GUU CC CCGGU U
AAU^ A G A - U U- UUAA U - - - UUUUU
140 130 120 110 100 90 80
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGGAAUCUUGAUGAUGCUGCA
Pt-miR393a*, scaffold_16:4058214:4058319,dG = -43.20
10 20 30 40 50
A UA UA C U AA---| C U AAU
C GAGGA AAUCCAAAGGGAU GCA UGAUCCU GC UUAA UAU \
G UUCCU UUAGGUUUCCCUA CGU ACUAGGA UG AAUU AUA U
- GC CC U - GUACU^ U C CUC
100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:AUCAUGCUAUCCCUUUGGAUU
Pt-miR396c, scaffold_19:651626:651754,dG = -41.40
10 20 30 40 50 60 70
UUGC| GCCAUGG C .-UUCCUUCUUCUUCUUCUCUAAUUAUA UAU
CCA CCACAG UUUCUUGAACUUCU GGCUAC U
GGU GGUGUC AAAGAACUUGAAGA UCGGUG U
CCUA^ AAAGAAG U \ ------UAG
120 110 100 80
--- U
AGC G
UCG C
CUA A
90
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUCAAGAAAUCUGUGGGAAG
Pt-miR171b, scaffold_19:1002411:1002509,dG = -49.70
10 20 30 40
A AU-| A UGAG U AAAGU
GC ACG GAUAUUGGCGCGGUUCAAUC AGCAG GCUC C
UG UGC CUAUAACCGUGCCGAGUUAG UUGUC CGAG U
G CAC^ A UUUA C AAGAA
90 80 70 60 50
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGAUUGAGCCGUGCCAAUAUC
Pt-miR399l , scaffold_19:1984362:1984491,dG = -62.60
10 20 30 40 50
GGA UC AGA ------AC-- -| A
GAAU CAGGGCAAUUCUCCUUUGGC AAAUAUU GCGCUUGU GUAC ACGC \
CUUA GUCCCGUUAAGAGGAAACCG UUUAUAA CGCGGACA CAUG UGUG C
CAA CC CCG UAUAUAAUAU CGUU A^ G
. 120 110 100 90 80 70 60
miRNA (5’ to 3’)mapped to this predicted precursor hairpin:CGCCAAAGGAGAAUUGCCCU
Pt-miR397a, scaffold_19:3674664:3674776,dG = -41.90
10 20 30 40 50
GA C A UAUUU| GGU UUGCCAAUAU
AAAAAACAU AUUGAGUGCAGCGUUG UGAA GUC GCU \
UUUUUUGUA UAGCUCACGUCGCGAC ACUU UAG CGA U
GA C C UCU--^ GAC UCAUAUCUCU
110 100 90 80 70 60
miRNA(5’ to 3’) mapped to this predicted precursor hairpin:UCAUUGAGUGCAGCGUUGAUG
Pt-miR164a, scaffold_3:4619018:4619126,dG = -42.80
10 20 30 40 50
-| U U C CA A CACCACUU UCCU GGU
AGC CC UG UGGAGAAG GGGC CGUGCAAA UGGC UUC \
UUG GG AC ACCUCUUC CUCG GCACGUUU ACCG AAG U
C^ - U A CC C CCUAAAUC UU-- ACU
100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGGAGAAGCAGGGCACGUGCA
Pt-miR168a*, scaffold_1:4611422:4611604,dG = -68.50
10 20 30 40 50 60 70 80
AG--- GG UA C U A UG G UA ------| AUUUUU AGCGAG UG C
UUACC CGGUCUC AUUCG UUGGUGCAGG CGGGA C AUU GC GUUUUUUU UUUGAA UGAC G G G
AGUGG GCCAGAG UAAGU AACUACGUUC GCCCU G UAA CG UAAAAAAG AAAUUU GCUG U U U
UAGAG A- GC C C A GU G -- UUAGUAAUU^ GCAAU- GUUAA- GU G
180 170 160 150 140 130 120 110 100 90
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:CCCGCCUUGCAUCAACUGAAU
Pt-miR157d, scaffold_1:12925733:12925833,dG = -37.70
10 20 30 40 50
GAAAUU U G UAAA-| CAUUA
UUG UGACAGAA AUAGAGAGCGCA UUAAAAUGC A
AAC ACUGUCUU UGUCUCUCGUGU AAUUUUAUG G
ACGUGC U A UUCUA^ CAAAC
. 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGACAGAAGAUAGAGAGCGC
Pt-miR472, scaffold_1:13057711:13057804,dG = -40.10
10 20 30 40
G| A UGA - U AA CA
GGAAGUCUUGG GAUGGG GU UGGGAAAA AAU CUUUCUU \
CUUUUAGAAUC CUACCC CA ACCCUUUU UUA GAAAGAA C
-^ C UC- C U AC AG
90 80 70 60 50
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUUUCCCACACCUCCCAUCCC
Pt-miR482a, scaffold_1:13073631:13073724,dG = -44.20
10 20 30 40
G UC -| C A AAAAAGAA
GGAAAUU GGGAAUGGGU GCAUGGG AAGAGA GGAG \
CCUUUAG UCCUUACCCA CGUAUCC UUCUUU CCUU A
- UU C^ A - CAUAUAUA
90 80 70 60 50
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UCUUACCUAUGCCACCCAUUCC
Pt-miR482a-1, scaffold_1:13076870:13077015,dG = -63.50
10 20 30 40 50
UGAA--- G U - U - | CGU
GC AGGAAGUU UGGGAGUGGGA GCGUGGGG AAGAAG UGAA--GAAAA A
CG UCCUUUAG AUCCUUACCCU CGUAUCCC UUCUUU ACUU CUUUU U
UCCUUGA - U C - A \ ^ UAA
140 130 120 110 100 60
70
U------A
UUUCUUUUUC A
AAAGAAAGAG U
AAACAUUA U
90 80
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UCUUCCCUAUGCCUCCCAUUCC
Pt-miR482c, scaffold_1:13091685:13091786,dG = -39.60
10 20 30 40
G U UUU U- UG UU---- -| UU
CUG AAAAUU GGAAU GGG CUAGGGAAGGUU GUU UGAC G
GAC UUUUAG CCUUA CCC GAUCCCUUUUAA CAA ACUG U
- - UAU UC CU UUAAAU U^ UC
100 90 80 70 60 50
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUCCCUAGUCCCCCUAUUCCUA
Pt-miR398b-1, scaffold_20:1575655:1575774,dG = -69.90
10 20 30 40 50 60
G A U GC-| UU - AA U AU
AGAAGUCCCGCAGGGGCGAC UGAGA CACAU AACGCA GC CU UGCC AUAC \
UCUUUAGGGUGUCCCCGCUG ACUCU GUGUG UUGUGU UG GA GUGG UGUG U
- G U UAU^ U- U GG - GU
. 110 100 90 80 70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGUGUUCUCAGGUCGCCCCUG
Pt-miR1515, scaffold_23:3493103:3493277,dG = -46.30
10 20 30 40 50 60 70
- UG ------C .-C GCUC-| CUCAAC UUU UU AAU
UCGAUU C AUCAUUUUUGCGUG AAUGAUCC GAAUUU UCUUA UUUC UUAAU ACA A
GGUUGA G UAGUAAAAACGCAC UUACUAGG CUUAAA AGGAU AAAG GGUUA UGU U
C GU CUCAGUU - \ - AAAAA^ AA---- UUU UU ACU
170 160 150 140 110 100 90 80
120
UA U
AUUUUUG U
UAGGGGC A
UC A
130
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UCAUUUUUGCGUGCAAUGAUCC
Pt-miR172a-1, scaffold_25:2292234:2292378,dG = -65.40
10 20 30 40 50 60 70
AAC-- C A C A -- UCUA-| AA C UUU
AGUCGUUG UCGCUGU GCAGCGUC UCAAGAUUC CAU GCAG AAGGCA AGCAG AAU U
UCAGUAAU AGCGGCA CGUCGUAG AGUUCUAAG GUG UGUU UUCCGU UCGUU UUA C
AUCGA U A U A AC UUUGG^ -- U CUU
140 130 120 110 100 90 80
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:AGAAUCUUGAUGAUGCUGCAA
Pt-miR390a, scaffold_2:2007999:2008137,dG = -62.60
10 20 30 40 50 60
AA--- A U U G AUG ------UA--| AA
AGU AAGAAGAA CUGU AAGCUCAGGA GGAUAGCGCC GGUGCC AUGAA UGGG \
UCA UUCUUCUU GGUA UUUGAGUCCU CCUAUCGCGG UCACGG UACUU AUCU U
CUCUC - C C A --- GUAAUAAAUAG UGGG^ AG
130 120 110 100 90 80 70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:AAGCUCAGGAGGGAUAGCGCC
Pt-miR399j, scaffold_2:6285487:6285642,dG = -66.10
10
A .-AA GA
GAAGCAGU GC U
CUUCGUCA UG U
- \ -- AU
150 20
30 40 50 60 70
UU G ------|GC ------AAGA UAU
UGUAGGGC CUCUCCUUUGGCAGGU AU G CAA GGGCA UCAUAUAA \
AUAUCCCG GAGAGGAAACCGUCCA UA C GUU UCCGU GGUAUAUU A
UU G ACUUUUUUAU^UU AUUAAUCUUA ---- UAU
140 130 120 110 100 90 80 miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGCCAAAGGAGAGUUGCCCUA
Pt-miR2111a, scaffold_2:79290:79377,dG = -50.70
10 20 30 40
- C C U -| UGU
GAGGAU AGGUAAUCUG AUCCUGAGG UUGGAU CAGCA A
UUCCUA UCCAUUAGGC UAGGACUCC GAUCUA GUUGU C
A U A U U^ UUG
80 70 60 50
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UAAUCUGCAUCCUGAGGUUUG
Pt-miR159b, scaffold_3:1984099:1984287,dG = -90.90
10 20 30 40 50 60 70 80 90
G U--| GA GU UG GGUGAU G A G G C AAC GU- GU AG UCA
GUUU AAUGGAGCUCUCU ACUCCAA C AAAGGA GGUAG CC CG CU CUAGU CAUG ACCC G UGCGC AC A
CAGG UUACCUCGAGGGA UGAGGUU G UUUUCU CCAUC GG GC GA GGUCA GUAC UGGG C ACGCG UG U
A UAC^ AG AU GU AGUU-- - A A G A GUU AAU UG G- UCA
180 170 160 150 140 130 120 110 100
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:AUUGGAGUGAAGGGAGCUCCA
Pt-miR408-5p, scaffold_3:3435390:3435510,dG = -55.30
10 20 30 40 50 60
CAA------| CA CAAAAGA C A AU A UU GU
GAAG AGAGA CGGGGAA AGGCAG GCAUGG GGA CCA AACAG \
CUUC UCUCU GUCCCUU UCCGUC CGUACC CCU GGU UUGUC U
UUUCUGCUC^ CG CG----- C A CU C U- UC
. 110 100 90 80 70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:AUGCACUGCCUCUUCCCUGGC
Pt-miR167b* , scaffold_3:6400060:6400206,dG = -55.20
10 20 30 40 50 60 70
CA- UA - AA A C --| U CGCAUUU AAA AUAAAUAA
GUC CAAG GGGAA AGUGA GCUG C AGCAUGAUCUA CUAG GGUUAGUG GUA \
CAG GUUC UCCUU UCACU CGAC G UCGUACUGGAU GAUC CCAAUCAU CAU A
ACC GC A CC C A UC^ C ------AG- GAACGAAG
140 130 120 110 100 90 80
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:GGUCAUGCUCUGACAGCCUCACU
Pt-miR159a, scaffold_3:7579845:7580074,dG = -87.40
10 20 30 40 50 60 70 80 90 100 110
G------| A UUAAGGA GA UUCU -- UA U G - C GAUC U G GAUU-- UU
GUA GAGGG GUGGAGCUCCUU AGUCCAAAAGAGG AGC AAGGG AAU GAGCU CU GAG UAUG CCACAG CCUAU UAUCA UUAGGG \
CAU CUCUC CAUCUCGAGGGA UUAGGUUUUUUCC UUG UUCCC UUA UUCGA GG CUU AUAC GGUGUU GGAUA GUAGU AGUCUU U
CACUCAUCACA^ ------AG CAUU AA CA C - U U GUUC U - GGUAGU UG
. 220 210 200 190 180 170 160 150 140 130 120
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUUGGAUUGAAGGGAGCUCUA
Pt-miR156k*, scaffold_4:1239035:1239155,dG = -53.40
10 20 30 40 50
- AA- AGCUA -| A AG UU A
AAACAU CGAGAG CUGACAGAAGA GAGUGAGCAC CGC GUAA GUAUU G
UUUGUG GUUUUU GACUGUCUUCU CUCGCUCGUG GUG CGUU UAUAA A
U AAC ACUGC C^ C GA UC A
. 110 100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGCUCGCUCCUCUUCUGUCAGC
Pt-miR396b*-1, scaffold_4:4045476:4045588,dG = -58.90
10 20 30 40 50
U| C C U UCUU AUGAG CA
CCU UUUGUAUUUUUCCACAGCUUU UUGAACUGCA CA UGC GCCA G
GGA AAACAUAGAAGGGUGUCGAAA AACUUGGCGU GU ACG CGGU A
-^ C U U UU-- GUA-- UC
110 100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUCAAUAAAGCUGUGGGAAGA
Pt-miR396b*, scaffold_4:4051058:4051191,dG = -63.70
10 20 30 40 50 60
CUG C A CU U --| A A C U CU
GUCAUG UUUUCCACAGCUUUCUUGA CUUCCA GU UGC UG UU AUA ACGGC CUUG \
CGGUAC AGAGGGUGUCGAAAGAACU GAGGGU CG GCG AC AG UGU UGCCG GGAU A
ACA A C AC C CC^ - A A C CG
130 120 110 100 90 80 70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:GCUCAAGAAAGCUGUGGGAGA
Pt-miR171f, scaffold_4:4081925:4082032,dG = -38.90
10 20 30 40 50
AAAAAACGA C A C A - GA- -| AU
AAG GAUAUUGGUG GGUUCAAUC G AGA CG UUUAC AC U
UUC CUAUAACCGC CCGAGUUAG C UCU GC AAAUG UG G
AAUAUUUAA A G A - A AGA U^ AA
100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUGAGCCGCGCCAAUAUCACU
Pt-miR156c, scaffold_4:6319480:6319583,dG = -47.80
10 20 30 40 50
GCU GG UG A - A-| C UU U A
U UU AUGACAG AG AGAGAGAGUACA CCCG CA AGC AAAG \
A GA UACUGUC UC UCUCUCUCGUGU GGGU GU UCG UUUC G
UUU UU GU C U GA^ U UU - U
100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:AUGACAGAAGAGAGAGAGUAC
Pt-miR399b, scaffold_6:3262495:3262624,dG = -55.80
10 20 30 40 50 60
A U C AC - A U UUAU| CAA--- CAU
AAGCAGUU UAGGGCA CUCUU UUGGCAUG CA UGG GAU UGGUG UAAUCAG \
UUCGUCAG GUCCCGU GAGAG AACCGUAU GU ACC CUA ACCAU AUUGGUU U
C U U GA A C - ----^ AUCUUA AUA
. 120 110 100 90 80 70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGCCAAAGGAGAGUUGCCCUG
Pt-miR166g, scaffold_9:4701713:4701907,dG = -52.70
10 20 30 40 50 60 70 80 90 100
AAAG| AG GA UUCC AAAUUAAAC - A UA CUUUUCAUUUUGUU U UC UGA UC
AU CUUUG CCAGGC UUCCUCUCA ACCUA UCU UUAU AAUGGCUC AAUUU UUUGCU UGAU UC \
UA GGAAC GGUCUG AAGGAGAGU UGGAU AGG AGUG UUAUUGAG UUAAA GAACGG GUUA AG A
GAGG^ CU UC UUGU ------U - -- UUAUUUUCUU---- C GU UG- AU
190 180 170 160 150 140 130 120 110
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUGGACCAGGCUUCCUUCCUC
Pt-miR166a-2, scaffold_9:4701627:4701969,dG = -29.10
10 20 30 40
UG------A UU CU UC-| GG AAGA A
AG GGAAUG GUCUGG CAAGG AU AGG AUA A
UC CCUUAC CGGACC GUUCU UA UCC UAU U
UCAACCAAA A UU AG UAU^ AA CGAG A
90 80 70 60 50
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUGGACCAGGCUUCAUUCCAC
Pt-miR319e, scaffold_9:2325653:2325746,dG = -36.20
10 20 30 40
U U A G C GUU------| UAA
GG AGAA UAGGGGUUCCUU CGG CCAAAACA GGC \
UC UCUU AUCCUCGAGGGA GUC GGUUUUGU UCG C
C U A A A AUCUCUCUUC^ UCU
90 80 70 60 50
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUGGACUGAAGGGAGCUCCU
Pt-miR169i*, scaffold_95:635990:636122,dG = -51.90
10 20 30 40 50 60
-- U -| AA UUUG U U - UGCAAU UU G
AAGA AAG AGU UU UUAGCCAAGGA GACU GCCUG CGGCU AUAA AGGUUUCAA \
UUCU UUC UCG AG AAUCGGUUCCU CUGA CGGAC GUUGG UGUU UCCGAAGUU C
CU C U^ AC UCG- - - C UU---- U- U
130 120 110 100 90 80 70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:AGGCAGUCUCCUUGGCUAAG
Pt-miR166b*, scaffold_37:1227102:1227234,dG = -51.40
10 20 30 40 50 60
AAA -- U C UU CU AUUA-----| A A
AAUGA UUG UUCUGAGGGGA UG GUCUGG CGAUGC AU AUAAUUAUAAUU U
UUACU AAC AAGACUUCCCU AC CGGACC GCUAUG UA UAUUAAUAUUAA A
UUG UA U U UU AG GGAAAAAAG^ C U
130 120 110 100 90 80 70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:GGACUGUUGUCUGGCUCGAUG
Pt-miR162a*, scaffold_29:814051:814181,dG = -52.20
10 20 30 40 50 60
-- A--| A CA G C C AC UG CAA U GAA
AUAGAG GAGUGA GU CUGGA GCAG GGUU AUCGAUC UU UG AUUUUGU GU A
UAUCUC CUCACU CG GACCU CGUC CCAA UAGCUAG AA AC UAAAACA CA A
CU AAC^ - C- A U A CU GU A-- - AUA
. 120 110 100 90 80 70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UCGAUAAACCUCUGCAUCCAG
Pt-miR535,scaffold_49:246193:246291,dG = -39.90
10 20 30 40
- GCU AG .-ACC ---| U
CAAAUUU UGACAAUG AGAGAGCAC UGUCA GCA U
GUUUAAA ACUGUUAC UCUCUCGUG ACGGU CGU C
C AU- CA \ --- AAA^ G
90 80 50
60
AG UC
GCUG \
CGAU U
-- CA
70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGACAAUGAGAGAGAGCACAC
Pt-miR396a, scaffold_82:283600:283711,dG = -41.10
10 20 30 40 50
C U AUC C C .-AAUUUU| AUC
CUCUU GUG UUCCACAGCUUUCUUGAA UGU UUG CCG G
GAGAA CAU AAGGUGUCGAAAGAACUU ACA AAC GGC A
- U CAA A C \ ------^ CAU
110 100 90 80
60
UGCAU UU
GA \
CU A
C---- UA
70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:AUUCAAGAAAGCUGUGGAAAA
Pt-miR396b, scaffold_147:517:694,dG = -50.00
10 20 30 40 50 60 70 80 90 100 110 120
CC| G C .-UUCUUUCUUCUUCUUCUUCUUCUUCUUCUUCUUCUUCUUCUUCUUCUUCUUCUUCUUCUUCUUCCUCUAAUAAUA AU
UGUCAU UUUUUCCACAG UUUCUUGAACUUCU GGCUACG U
ACGGUA AGAAGGGUGUC AAAGAACUUGAAGA UCGGUGU U
AA^ A U \ ------AG
170 160 150 130
--- U
AGC G
UCG C
UUA A
140
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUCAAGAAAUCUGUGGGAAG
Pt-miR390a*, scaffold_107:123167:123406,dG = -62.40
10 20 30 40
.-CGUUAAC| CUU CA C G GAC G UG
UG GGA GAGAAAU AC GUCAA UC UCU \
AC UCU UUCUUUA UG UAGUU AG AGA C
\ ------^ AU- AC A G --- A CU
70 60 50
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUGGACAGAGAAAUCACGGUCA
Pt-miR479, scaffold_109:458201:458338,dG = -49.20
10 20 30 40 50 60 70
GAUU--| G U U A UAAUUAAU UC UUC---- CU
GGAGAAGUA ACA GG GUGAUAUUGGUUCGGCUC UCU AGAU AUAU AGCC \
UUUCUUCGU UGU UC CACUAUAACUAAGCCGAG AGA UCUA UAUG UUGG U
GUUUUC^ A - U C ------UA UACAUUC AA
130 120 110 100 90 80
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:CGAGCCGAAUCAAUAUCACUC
Pt-miR4414, scaffold_56:1113165:1113272,dG = -43.00
10 20 30 40 50
------| U G AC U AG U A AAAAU
GC UGAC AC CAGCU CUG UCGUUGG UCA AGC CAUCA UGG \
CG ACUG UG GUCGA GAC AGCAACC AGU UUG GUAGU ACU G
U GU AUU^ C G GA U CU U - AAGAU
100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:AGCUGCUGACUCGUUGGUUCA
Pt-miR482b-2, scaffold_138:158623:158752,dG = -53.00
10 20 30 40 50 60
G G U ------| AAC - A UCACUU
GGAAG UU UGGUAUGGGU GAGUAGGGAAGAUA AUUU UAAGUAA UA UAAUA \
CCUUU GA ACCGUACCCA CUCAUCCCUUCUAU UAAG AUUCAUU AU AUUAU U
- G U C AUGUU^ GA- U C UACUUU
. 120 110 100 90 80 70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UCUUCCCUACUCCACCCAUGCC
Pt-miR3951, scaffold_64:293141:293268,dG = -51.40
10 20 30 40 50 60
-| U A UAU - C AAUUUGUUCCCU
GUGCU GGCAUAGAUAA GAUGAGAGAAAAA GAGAGAA AGA GAGAGA C
UACGA UCGUGUCUAUU CUAUUCUCUUUUU UUCUUUU UCU CUCUCU U
U^ U G C-- C U CACCCACCCACC
120 110 100 90 80 70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UAGAUAAAGAUGAGAGAAAAA
Pt-miR171i*, scaffold_39:428372:428489,dG = -47.00
10 20 30 40 50
GUUGAAAUUUAAAAC-- A C UAU --| A
GGAGAUGUUGG ACGGCUCAAUCAAAU AAA CCUA UG A
CCUCUAUAACC UGCCGAGUUAGUUUA UUU GGGU AC A
UCGCUUUCUUCUGCUCU G A CCU UA^ U
110 100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGAUUGAGCCGUGCCAAUAUC
Pt-miR3952,scaffold_38:199544:199712,dG = -56.70
10 20 30 40 50 60
UAUUC U G U CCCUC .-CCAUGG| GGAA GGG
UUUCA GUGCU UAGAAAG CCCUUCA GGAAACGUCA ACU CU G
AAGGU CACGA AUCUUUC GGGAAGU CUUUUGCGGU UGA GA G
UACCU - G C UGAAA \ ------^ AA-- AGC
160 150 140 130 70
80 90
GAGA--- A - G UG
UCUG UGGUU G CAU \
AGAC GUCGA C GUG A
AGAAAGA - A G GA
120 110 100
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGAAGGGCCUUUCUAGAGCAC
Pt-miR2275a, scaffold_53:854317:854538,dG = -57.90
10 20 30 40 50 60 70
UCAGU C C A CUC C .-CUAUAUAUAAA| C G UG AGG
UG UGUUUAGUUUCCUC AAU UCUUAU CAGCUU UAAA ACAAGUU UGA U C G
AC ACAGAUCGAAGGAG UUA AGAAUG GUUGAA AUUU UGUUCAA ACU A G A
UGAUU - U - AAU C \ ------^ A A GU GUU
220 210 200 190 180 90 80
100 110 120 130
-- UUUUU .-CAAU UU -- CUU
GCUUGG ACUC AUCU UC UUCAG C
CGGACU UGAG UAGA AG AAGUC A
UA ----- \ ---- U- CA AAA
170 150 140
160
CUUCA A
GC \
CG A
A---- A
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUUAGUUUCCUCCAAUAUCUUA
Pt-miR166g*, scaffold_37:1226929:1227092:-,dG = -67.50
10 20 30 40 50 60 70 80
UU GG A- UU CU G C UUU---| A UC CUUUCUUUCU
GAGA UU UGGUUGAUGGGAAUG GUUUGG CGA GGUCAU UAGGU CA AAUUUUC GGA U
CUCU GG GCCAACUGCCCUUAC CGGACC GCU CUAGUG AUCCG GU UUAAAAG CCU G
U- UU CA UU AG - U UUUAUU^ A GA UUUUAUUUUC
160 150 140 130 120 110 100 90
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:GGAAUGUUGUUUGGCUCGAGGG
Pt-miR156f*, scaffold_4:4121679:4121793,dG = -60.70
10 20 30 40
AAA AAGA A - A .-G| UU
GGGU GG GGUGACAGA AGAGAGUGAGCAC CAU GUA U
CCCA CC CCACUGUCU UCUCUCACUCGUG GUA CGU U
CCC A--- - A C \ -^ UC
110 100 90 80 50
60
AU UG AU
GCUU AG C
CGAA UC C
U- GU GU
70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:GCUCACUCUCUAUCUGUCACC
Pt-miR167a-1, scaffold_1:5093826:5093941,dG = -60.10
10 20 30 40 50
AU- -| G U C AA - CCU
UCGUGC ACUA UAGUAG UGAAGCUGCCAG AUGAUCUG CUUUCCUU GA C
GGUACG UGGU GUUAUC ACUUUGACGGUC UACUAGAC GAAAGGGA CU C
ACC A^ A C - CG U CUA
110 100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGAAGCUGCCAGCAUGAUCUGA
Pt-miR167a-2, scaffold_3:6403390:6403476,dG = -42.30
10 20 30 40
CAG| U G AAA - CAC
CAGCAG UGAAGCUGCCA CAUGAUCU CU UCCUU \
GUUGUC ACUUCGAUGGU GUACUAGG GA AGGAA U
CUA^ C - CUA U CUG
80 70 60 50
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGAAGCUGCCAGCAUGAUCUA
Pt-miR167a-3, scaffold_27:527022:527133,dG = -51.80
10 20 30 40 50
UA G - -| UAU A A UAACU- CUU
UCG GC ACC AC CAG UGAAGCUGCC GCAUGAUCU UUCCUC U
AGC CG UGG UG GUC ACUUUGACGG CGUACUAGA AAGGAG G
AA A U U^ CUU C - CAUAGU CUC
110 100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGAAGCUGCCAGCAUGAUCUUA
Pt-miR3954-1, scaffold_27:1236405:1236538,dG = -46.70
10 20 30 40 50 60
U U A U CAU-- UGA-| U U CUG AAU U
UAUAUUUG UUGG CAGAGAAA CACGGU GAGA GUU UC AAU UACUGU CUG A
AUAUAGAC AACC GUCUCUUU GUGCCA CUCU CAG AG UUA GUGGUA GGC U
U U C - UCUUU UAGG^ C - UAA GU- A
130 120 110 100 90 80 70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUGGACAGAGAAAUCACGGUCA
Pt-miR3954-2, scaffold_61:672044:672130,dG = -20.80
10 20 30 40
- C G UG C-- - -| AA C CUU
UUUA UU GC GA AG AGAAAUCA CGGUC GU UCUU \
AGGU AG UG CU UC UCUUUAGU GUUAG CA AGGA G
A - G GU ACU U A^ -- A CUU
80 70 60 50
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGGACAGAGAAAUCACGGUCA
Pt-miR482a*, scaffold_1:13076870:13077015,dG = -20.80
10 20 30 40 50
UGAA--- G U - U - | CGU
GC AGGAAGUU UGGGAGUGGGA GCGUGGGG AAGAAG UGAA--GAAAA A
CG UCCUUUAG AUCCUUACCCU CGUAUCCC UUCUUU ACUU CUUUU U
UCCUUGA - U C - A \ ^ UAA
140 130 120 110 100 60
70
U------A
UUUCUUUUUC A
AAAGAAAGAG U
AAACAUUA U
90 80
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:AGUGGGAGCGUGGGGUAAGAAG
Pt-miR482b-1, scaffold_1:13086687:13086795,dG = -44.20
10 20 30 40 50
A CU CUU-| CGAUCUA U GUUCA
GGAAAUUU GGAAUGGGAGG GGCAAGAAG UUU UCUU \
CCUUUAGG CCUUACCCUCC CCGUUCUUU AAA AGAA A
- UU CCAC^ UUAAAAG U AAAAU
100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UCUUGCCCACCCCUCCCAUUCC
Pt-miR477a, scaffold_84:465243:465346,dG = -48.90
10 20 30 40
G CCA GAA C A------| UCA
AAGCUU ACCUCCCUC GG UUCCAAUAU CCAUGCUU CC \
UUCGAA UGGAGGGGG CC AAGGUUGUA GGUACGAA GG A
A AGC AUC A AG UGUUCC^ UUA
100 90 80 70 60 50
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:ACCUCCCUCGAAGGCUUCCAA
Pt-miR477e, scaffold_12:4089366:4089472,dG = -49.20
10 20 30 40
UUGG CU U G U .-GUUA| C
UUG CACUCUCCC CAA GGCUUC GGC AUUAAUGA \
AAC GUGAGAGGG GUU CCGGAG CCG UAAUUAUU A
UGAA AG - G U \ ----^ A
100 90 80 50
60
G U C
CU GCAG U
GA CGUC G
- C C
70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:ACUCUCCCUCAAGGGCUUCU
Pt-miR396b-1, scaffold_4:4051058:4051191,dG = -63.70
10 20 30 40 50 60
GAC-- GU G A - AAAUACACG -| U GU
AGUCGCU UUGC GGUGUAGCAUCAUCAAGAUUC CA UGC GC AG GAU G
UCGGCGA AACG CUACGUCGUAGUAGUUCUAAG GU ACG CG UC CUA A
AAAAU AU A A C AAG------U^ U AU
120 110 100 90 80 70 miRNA (5’ to 3’) mapped to this predicted precursor hairpin:AGAAUCUUGAUGAUGCUGCA
Pt-miR393a-3p, scaffold_2:2007999:2008137,dG = -61.10
10 20 30 40 50 60 70
AA--- A U U G AUG AUGAAUAUGGGA| UCUA
AGU AAGAAGAA CUGU AAGCUCAGGA GGAUAGCGCC GGUGCC AUGA \
UCA UUCUUCUU GGUA UUUGAGUCCU CCUAUCGCGG UCACGG UACU G
CUCUC - C C A --- GUAAUAAAUAG-^ UUGG
130 120 110 100 90 80
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:CGCUAUCCAUCCUGAGUUUC
Pt-miR169b, scaffold_53:553044:553203,dG = -60.30
10 20 30 40 50
---- U G U G C AG | CAU GC UU
GGGAA GA GGUA GUG UG AGCCA GAUGACUUGCCG--GCAA UG GUG \
CUCUU CU CCGU CAU AC UCGGU CUGCUGAACGGC CGUU AC CAC G
UACU C - - A A CU \ ^ UUU UA UA
. 150 140 130 120 70 60
80 90
UUC- AUA UACUA
AUUAG UGACAC C
UGAUC AUUGUG A
UACU A-- UAAAU
110 100
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:CAGCCAAGGAUGACUUGCCGG
Pt-miR169g, scaffold_95:631652:631790,dG = -57.40
10 20 30 40 50 60 70
AAUAUAAUAUCAUU ----| U U - - UUGAUU C G AG
GUUUGU UAGCCAAGGA GACU GCCUG CA CC GCAAGA GAGG UUUCA U
CGGACA AUCGGUUCCU CUGA CGGAC GU GG UGUUCU CUCC AAGGU G
ACUUUCUAUUCU-- CUGA^ - - C U UU---- - G CG
130 120 110 100 90 80
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UAGCCAAGGAUGACUUGCCUGC
Pt-miR168a, scaffold_1:4611422:4611604,dG = -67.60
10 20 30 40 50 60 70 80 90
AG--- GG UA C U A UG G UA UUUGAA| UU GAC AG GUGUU
UUACC CGGUCUC AUUCG UUGGUGCAGG CGGGA C AUU GC GUUUUUUU AUU UU AGCG GUGGC G
AGUGG GCCAGAG UAAGU AACUACGUUC GCCCU G UAA CG UAAAAAAG UAA AA UUGC UGCUG U
UAGAG A- GC C C A GU G -- UUAG--^ UU AU- AA GUUAA
180 170 160 150 140 130 120 110 100
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UCGCUUGGUGCAGGUCGGGAA
Pt-miR167d-1, scaffold_1:5093826:5093941,dG = -61.10
10 20 30 40 50
AU- -| G U C AA - CCU
UCGUGC ACUA UAGUAG UGAAGCUGCCAG AUGAUCUG CUUUCCUU GA C
GGUACG UGGU GUUAUC ACUUUGACGGUC UACUAGAC GAAAGGGA CU C
ACC A^ A C - CG U CUA
110 100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGAAGCUGCCAGCAUGAUCUG
Pt-miR167d, scaffold_15:4341089:4341447,dG = -102
10 20 30 40 50 60 70 80 90
GAU U-- A C C AAUC .-UUU AUAU UU .-UUA| UUU UUU
AUGUUGGU UGAG GAUUGAAGCUGC AG AUGAUCUGGU AACC UUGUAU AUAUA AAUUCC UAGUU AGA \
UACAACCA ACUC UUAACUUCGACG UC UACUGGACUA UUGG AACGUG UAUAU UUGGGG AUUAA UCU A
AUU CUU A U - CC-- \ --- CUUU U- \ ---^ UUU UUA
350 340 330 320 310 160 150 100
110 120
GAU GGU U
CCAU UUCAAU \
GGUA AAGUUA C
U-- AAU U
140 130
170 180 190 200 210 220 230 240
-- AA- AUA AUA U UCCAAUC GUUU U UUU CCUAA
UUAUU GAGG GAUGGA GCGCCUU AAA ACUUUUUUA UAU UUGAUCUU UGCCC \
AGUAG CUUC UUAUUU UGUGGGA UUU UGAGAGAAU GUA AAUUGGAA AUGGG A
UA AUG GA- AG------U --- AAUUA
300 290 280 270 260 250
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UGAAGCUGCCAGCAUGAUCUGG
Pt-miR166m, scaffold_37:1227102:1227234,dG = -51.40
10 20 30 40 50 60
AAA -- U C UU CU AUUA-----| A A
AAUGA UUG UUCUGAGGGGA UG GUCUGG CGAUGC AU AUAAUUAUAAUU U
UUACU AAC AAGACUUCCCU AC CGGACC GCUAUG UA UAUUAAUAUUAA A
UUG UA U U UU AG GGAAAAAAG^ C U
130 120 110 100 90 80 70
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UCGGACCAGGCUUCAUUCCCU
Pt-miR157a-1, scaffold_80:25066:25172,dG = -48.60
10 20 30 40
------| U CUGU - U - A UGG
GA GAUG UGACGGAAGA UAGAGAGCACAGA GA UGA AUGCG \
CU CUAC ACUGUCUUCU AUCUCUCGUGUUU CU ACU UACGU A
CCUCUCCGA^ U U--- U C C C UCG
100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin: UUGACGGAAGAUAGAGAGCAC
Pt-miR157a-2, scaffold_56:1364213:1364315,dG = -40.10
10 20 30 40 50
UGAAAUU U G UAAA-| CAUUA
UUG UGACAGAA AUAGAGAGCACA UUAAAAUGC A
AAC ACUGUCUU UAUCUCUCGUGU AAUUUUACG U
GACGCGC U A UUCUA^ CAAAC
100 90 80 70 60
miRNA (5’ to 3’) mapped to this predicted precursor hairpin:UUGACAGAAGAUAGAGAGCAC