***** Conserved Regions - Zebrafish Mar. 2006 chr7 (Human Mar. 2006 chr7) *****
49526334 (155297577) to 49526633 (155297278) = 300bp at 74.7% exon
49528383 (155294212) to 49528475 (155294121) = 93bp at 79.6% intron
49529943 (155292012) to 49530204 (155291751) = 262bp at 77.9% exon
49531626 (155289179) to 49531808 (155288999) = 187bp at 69.5% exon
49532789 (155287807) to 49532899 (155287688) = 121bp at 76.9% UTR
49533106 (155287387) to 49533229 (155287281) = 124bp at 70.2% UTR
Total 1087bp at 74.7%
chr7:49,528,206-49,528,595 è full text ... need more nucleic acids
chr7:49,527,642-49,529,324 è full text
>danRer4_dna range=chr7:49527642-49529324 5'pad=0 3'pad=0 strand=+ repeatMasking=none
CCCTTTGCCAATGCTAAGGAAGAATAACATGCAGCTTACTAAGTGCATCG
AAAATATGTTTGCAGTGCAAATTAGCCTCTATTGAAGTGTTTCCGTGTAA
TTTACAAAGTGATTATCCCGAGCATAATTTTTATTAGGCTGTTTTGAACG
TGCCTCTGTTAAATAGCTTTTAGGTTCAAAGTCTAAGTCATGACCGGTTA
TAGCAAGGTTTGCTGAAGCATTGCGAATAATGTCCGCCAAAGTCAATTTA
CACGCGCCGCGCAGGTGCATTATAAAGTTTCCCTTTTACCGGTCCTTAAA
AAAGATGAAACCCGTGTCTGGTGTGGTTTTCTCAGATGTATATCAAGCTC
TACTTAAGGTGAATGTGATTATAAGTGTGCAGTGACCCGCGGGCACACAC
GCTGCTATAAGCTACCCTTGCAATCTAGTAACATCAAATGAACGTCTCAG
TCTTTCAAAGGGAGTTAACGAGGTGTCCTGTTGACAAATGTTTTGGAGAA
GCGCATCCGAGTGTAAGACAGGGTTTGTTGGTTGAACACGCTGTGCGGTG
AATTGGACTTAACGGTGAAGCTCGCGAAATTAGGCGCAACTGCGAGGGTA
TCCAGGAGGCTGTTTGCTCTGACAGGTAGCTGATAAGTGTTTCCTCTAAA
ACAGTTCATTTTGGGGGGAGATTAGTTGCTGACTGTGACTAGGCGGCTTG
TTGAACAAACCTCGTGTGGAGCACAAAGCGGCG[GCACAGGGGGTTCCCGC
TGCGCTTCATGGTGGCTGAACAGAATTTGGCTTGATTTGCGGCACACGAC
TCAATGAATTAATAAAGAGTTCAGGCT]TCACGGCTCATCAATCCCCGGTA
GTTTTGCTTAGGATGTGCTAGGTTGCATCTTTATGTCGCTTGCTTGTGGT
TTACTCTATCAATCAACAGCCACAAGTGTTGTAGAGCTAAAAGGCAGCAA
TTTAAAATATAGTAGTTAGGGGGTCTGTTTTATTTACTTTTGATTAAAGT
ACCATTTTGCTACATTCCATTCAGTGTACAGATATTCCAAAAAGGCATCA
TCCAGAGGATGCATCTGTGAAGTTTTTGCAATTTATTTCATTAGACTATA
TCGTTTGTATAATAGACTCTAGAAACACAATGAAGTGAACTGAACAGTTT
CATACATTCAGATATAATTCAGTGTAGTTTATAATTGACTAAACATTATT
TTTCTGATATACAATAAAGTGCAATTCAGCTTAGTAAAGTGCATATGGTC
TTCACTGCTGACATGAAAATTAGAGGGTCAAGCAGATCAGTAGGAAGTGG
GGCGATAGTCTGCTGGAGAAATTTATGTGGATGTTAGAGGCTAAGGATGT
GTGTGTGTGTGTGTGTGTATAAGGGGGGAGAGTCAGAGAAAGCGAGCAAG
TGAGTCAAAGCTAGGAGGGTATGTGTGTGAATTATTACAGGTATTAATTT
GGCTTAGTGTCACAATTTGCCAGCATATTTTGAATAGATTTTATATAACC
TCTGAAAGACCGTCAGTTAAGCAATCACATCACGTCCCTTGAGCAAACCT
GTGCTGCAAGAATAATGAGTAGTTGCTTCTCCTCTTGGACGCAGTGAAAG
AGTCTTTTGTGGTGTTTTATTTGACATATTGGTTAAGTGTTGGGAAGAGT
TGTCCTGGTGAAGGCCAAGCATCTCAAAGCAAG
chr7:49,528,375-49,528,468 è just CNS
>danRer4_dna range=chr7:49528375-49528468 5'pad=0 3'pad=0 strand=+ repeatMasking=none
GCACAGGGGGTTCCCGCTGCGCTTCATGGTGGCTGAACAGAATTTGGCTT
GATTTGCGGCACACGACTCAATGAATTAATAAAGAGTTCAGGCT
Primer 3 Design:
Primer3 Output
No mispriming library specified
Using 1-based sequence positions
OLIGO start len tm gc% any 3' seq
LEFT PRIMER 701 20 60.13 45.00 4.00 0.00 TTGAACAAACCTCGTGTGGA
RIGHT PRIMER 899 20 59.87 45.00 2.00 0.00 CCACAAGCAAGCGACATAAA
SEQUENCE SIZE: 1683
INCLUDED REGION SIZE: 1683
PRODUCT SIZE: 199, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 1.00
TARGETS (start, len)*: 734,94
1 CCCTTTGCCAATGCTAAGGAAGAATAACATGCAGCTTACTAAGTGCATCGAAAATATGTT
61 TGCAGTGCAAATTAGCCTCTATTGAAGTGTTTCCGTGTAATTTACAAAGTGATTATCCCG
121 AGCATAATTTTTATTAGGCTGTTTTGAACGTGCCTCTGTTAAATAGCTTTTAGGTTCAAA
181 GTCTAAGTCATGACCGGTTATAGCAAGGTTTGCTGAAGCATTGCGAATAATGTCCGCCAA
241 AGTCAATTTACACGCGCCGCGCAGGTGCATTATAAAGTTTCCCTTTTACCGGTCCTTAAA
301 AAAGATGAAACCCGTGTCTGGTGTGGTTTTCTCAGATGTATATCAAGCTCTACTTAAGGT
361 GAATGTGATTATAAGTGTGCAGTGACCCGCGGGCACACACGCTGCTATAAGCTACCCTTG
421 CAATCTAGTAACATCAAATGAACGTCTCAGTCTTTCAAAGGGAGTTAACGAGGTGTCCTG
481 TTGACAAATGTTTTGGAGAAGCGCATCCGAGTGTAAGACAGGGTTTGTTGGTTGAACACG
541 CTGTGCGGTGAATTGGACTTAACGGTGAAGCTCGCGAAATTAGGCGCAACTGCGAGGGTA
601 TCCAGGAGGCTGTTTGCTCTGACAGGTAGCTGATAAGTGTTTCCTCTAAAACAGTTCATT
661 TTGGGGGGAGATTAGTTGCTGACTGTGACTAGGCGGCTTGTTGAACAAACCTCGTGTGGA
>
721 GCACAAAGCGGCGGCACAGGGGGTTCCCGCTGCGCTTCATGGTGGCTGAACAGAATTTGG
***********************************************
781 CTTGATTTGCGGCACACGACTCAATGAATTAATAAAGAGTTCAGGCTTCACGGCTCATCA
***********************************************
841 ATCCCCGGTAGTTTTGCTTAGGATGTGCTAGGTTGCATCTTTATGTCGCTTGCTTGTGGT
<
901 TTACTCTATCAATCAACAGCCACAAGTGTTGTAGAGCTAAAAGGCAGCAATTTAAAATAT
961 AGTAGTTAGGGGGTCTGTTTTATTTACTTTTGATTAAAGTACCATTTTGCTACATTCCAT
1021 TCAGTGTACAGATATTCCAAAAAGGCATCATCCAGAGGATGCATCTGTGAAGTTTTTGCA
1081 ATTTATTTCATTAGACTATATCGTTTGTATAATAGACTCTAGAAACACAATGAAGTGAAC
1141 TGAACAGTTTCATACATTCAGATATAATTCAGTGTAGTTTATAATTGACTAAACATTATT
1201 TTTCTGATATACAATAAAGTGCAATTCAGCTTAGTAAAGTGCATATGGTCTTCACTGCTG
1261 ACATGAAAATTAGAGGGTCAAGCAGATCAGTAGGAAGTGGGGCGATAGTCTGCTGGAGAA
1321 ATTTATGTGGATGTTAGAGGCTAAGGATGTGTGTGTGTGTGTGTGTGTATAAGGGGGGAG
1381 AGTCAGAGAAAGCGAGCAAGTGAGTCAAAGCTAGGAGGGTATGTGTGTGAATTATTACAG
1441 GTATTAATTTGGCTTAGTGTCACAATTTGCCAGCATATTTTGAATAGATTTTATATAACC
1501 TCTGAAAGACCGTCAGTTAAGCAATCACATCACGTCCCTTGAGCAAACCTGTGCTGCAAG
1561 AATAATGAGTAGTTGCTTCTCCTCTTGGACGCAGTGAAAGAGTCTTTTGTGGTGTTTTAT
1621 TTGACATATTGGTTAAGTGTTGGGAAGAGTTGTCCTGGTGAAGGCCAAGCATCTCAAAGC
1681 AAG
KEYS (in order of precedence):
****** target
> left primer
< right primer
ADDITIONAL OLIGOS
start len tm gc% any 3' seq
1 LEFT PRIMER 701 20 60.13 45.00 4.00 0.00 TTGAACAAACCTCGTGTGGA
RIGHT PRIMER 859 20 59.84 45.00 4.00 3.00 AAGCAAAACTACCGGGGATT
PRODUCT SIZE: 159, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 3.00
2 LEFT PRIMER 702 20 59.72 50.00 3.00 1.00 TGAACAAACCTCGTGTGGAG
RIGHT PRIMER 899 20 59.87 45.00 2.00 0.00 CCACAAGCAAGCGACATAAA
PRODUCT SIZE: 198, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 0.00
3 LEFT PRIMER 702 20 59.72 50.00 3.00 1.00 TGAACAAACCTCGTGTGGAG
RIGHT PRIMER 859 20 59.84 45.00 4.00 3.00 AAGCAAAACTACCGGGGATT
PRODUCT SIZE: 158, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 2.00
4 LEFT PRIMER 701 20 60.13 45.00 4.00 0.00 TTGAACAAACCTCGTGTGGA
RIGHT PRIMER 903 20 60.44 45.00 2.00 0.00 TAAACCACAAGCAAGCGACA
PRODUCT SIZE: 203, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 2.00
Statistics
con too in in no tm tm high high high
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Left 6154 0 0 0 8 0 2453 1938 1 7 44 92 1611
Right 7779 0 0 0 495 0 3948 1261 0 1 22 66 1986
Pair Stats:
considered 10178, unacceptable product size 10167, ok 11
primer3 release 1.1.4
(primer3_results.cgi release 0.4.0)