Multiple sequence alignment - TraesCS5D01G484600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G484600 chr5D 100.000 2437 0 0 1 2437 520724356 520721920 0.000000e+00 4501
1 TraesCS5D01G484600 chr5D 94.400 125 7 0 1550 1674 341036470 341036346 2.470000e-45 193
2 TraesCS5D01G484600 chr5B 92.496 1346 71 10 230 1555 656233215 656231880 0.000000e+00 1899
3 TraesCS5D01G484600 chr5B 91.045 737 43 13 1673 2396 656231881 656231155 0.000000e+00 974
4 TraesCS5D01G484600 chr5B 89.000 200 7 3 7 205 656233466 656233281 1.460000e-57 233
5 TraesCS5D01G484600 chr5A 90.929 1345 76 16 224 1554 649192107 649190795 0.000000e+00 1766
6 TraesCS5D01G484600 chr5A 94.009 434 13 5 1675 2096 649190793 649190361 0.000000e+00 645
7 TraesCS5D01G484600 chr5A 96.100 359 13 1 2080 2437 649190345 649189987 3.490000e-163 584
8 TraesCS5D01G484600 chr5A 94.472 199 11 0 7 205 649192362 649192164 8.460000e-80 307
9 TraesCS5D01G484600 chr1D 91.096 146 9 4 1541 1684 441002259 441002402 6.880000e-46 195
10 TraesCS5D01G484600 chr3A 90.845 142 9 3 1543 1681 171206131 171206271 1.150000e-43 187
11 TraesCS5D01G484600 chr3D 93.651 126 5 2 1554 1676 412412859 412412984 4.140000e-43 185
12 TraesCS5D01G484600 chr3B 93.548 124 8 0 1551 1674 284421934 284422057 4.140000e-43 185
13 TraesCS5D01G484600 chr4B 93.600 125 5 2 1550 1674 128024818 128024697 1.490000e-42 183
14 TraesCS5D01G484600 chr2A 92.366 131 4 2 1554 1678 630094622 630094752 5.350000e-42 182
15 TraesCS5D01G484600 chr1B 92.366 131 4 2 1550 1674 683747956 683748086 5.350000e-42 182
16 TraesCS5D01G484600 chr1A 87.662 154 11 4 1535 1682 52557789 52557638 3.220000e-39 172


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G484600 chr5D 520721920 520724356 2436 True 4501.000000 4501 100.0000 1 2437 1 chr5D.!!$R2 2436
1 TraesCS5D01G484600 chr5B 656231155 656233466 2311 True 1035.333333 1899 90.8470 7 2396 3 chr5B.!!$R1 2389
2 TraesCS5D01G484600 chr5A 649189987 649192362 2375 True 825.500000 1766 93.8775 7 2437 4 chr5A.!!$R1 2430

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
218 265 0.392193 CCTCCAGGATGTGCACACTC 60.392 60.0 24.37 19.32 37.39 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 1752 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.0 0.0 0.0 0.0 3.28 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 0.532862 CCAGGAGCGTCAGTGTTTGT 60.533 55.000 0.00 0.00 0.00 2.83
74 75 2.124983 CCAGCATCACAGGTCCCG 60.125 66.667 0.00 0.00 0.00 5.14
173 174 5.232838 GCACAATTCTTTTCAAGTGAACTGG 59.767 40.000 0.00 0.00 33.13 4.00
183 184 2.426738 CAAGTGAACTGGTTGGCTTTCA 59.573 45.455 0.00 0.00 0.00 2.69
217 264 1.681666 CCTCCAGGATGTGCACACT 59.318 57.895 24.37 13.33 37.39 3.55
218 265 0.392193 CCTCCAGGATGTGCACACTC 60.392 60.000 24.37 19.32 37.39 3.51
219 266 0.392193 CTCCAGGATGTGCACACTCC 60.392 60.000 27.40 27.40 0.00 3.85
220 267 1.377725 CCAGGATGTGCACACTCCC 60.378 63.158 29.30 25.47 32.58 4.30
221 268 1.377725 CAGGATGTGCACACTCCCC 60.378 63.158 29.30 23.63 32.58 4.81
222 269 1.847506 AGGATGTGCACACTCCCCA 60.848 57.895 29.30 8.62 32.58 4.96
223 270 1.074775 GGATGTGCACACTCCCCAA 59.925 57.895 24.37 0.00 0.00 4.12
224 271 1.244019 GGATGTGCACACTCCCCAAC 61.244 60.000 24.37 6.18 0.00 3.77
261 311 9.612066 AAACTAAAAGCTGAAATGAATTTTCCA 57.388 25.926 0.00 0.00 42.63 3.53
269 319 9.122779 AGCTGAAATGAATTTTCCAAAATTTCA 57.877 25.926 10.59 9.89 45.70 2.69
272 322 8.351461 TGAAATGAATTTTCCAAAATTTCAGCC 58.649 29.630 10.59 0.55 45.70 4.85
285 335 4.085876 CAGCCCTTTCAGTGGGTG 57.914 61.111 0.00 0.00 46.22 4.61
287 337 2.116125 GCCCTTTCAGTGGGTGCT 59.884 61.111 0.00 0.00 46.22 4.40
350 401 7.710475 CCTCAAAATTTCAAGCTAGGTTCAAAA 59.290 33.333 7.82 10.23 0.00 2.44
363 414 9.710900 AGCTAGGTTCAAAATAATTTCAAAAGG 57.289 29.630 0.00 0.00 0.00 3.11
364 415 9.705290 GCTAGGTTCAAAATAATTTCAAAAGGA 57.295 29.630 0.00 0.00 0.00 3.36
513 582 8.549338 TGTTTTCAAAATTTAAAACCTCGGTT 57.451 26.923 19.43 0.00 42.32 4.44
590 660 4.821805 TGTTTGAGAACCAAAGTCATCTCC 59.178 41.667 0.00 0.00 44.64 3.71
775 847 1.614241 GGAAGCCTTCTGACGCCCTA 61.614 60.000 4.15 0.00 0.00 3.53
780 852 1.403814 CCTTCTGACGCCCTATCTGA 58.596 55.000 0.00 0.00 0.00 3.27
877 958 3.442273 GGCGGTTCACTGGAAATGAATAA 59.558 43.478 0.00 0.00 38.31 1.40
901 982 2.834689 CATTTCCAACGAACGCTACAC 58.165 47.619 0.00 0.00 0.00 2.90
916 997 7.692291 CGAACGCTACACAAATCTTATCAAATT 59.308 33.333 0.00 0.00 0.00 1.82
1086 1167 1.434188 TTCTGGGCAGAACAAGAGGA 58.566 50.000 0.00 0.00 42.06 3.71
1131 1212 6.656314 AATACAACGCGATGTCTAAATTGA 57.344 33.333 25.82 6.03 34.75 2.57
1132 1213 6.844696 ATACAACGCGATGTCTAAATTGAT 57.155 33.333 25.82 8.24 34.75 2.57
1160 1241 5.611374 GGTGAGCTAGGAAGTAAATATGCA 58.389 41.667 0.00 0.00 0.00 3.96
1179 1260 3.113322 GCATGCGTACTGAATCGAAGTA 58.887 45.455 0.00 0.00 0.00 2.24
1331 1415 6.508920 TGGAAGGCTATAATGGATCCCTATTT 59.491 38.462 9.90 0.48 0.00 1.40
1332 1416 7.019558 TGGAAGGCTATAATGGATCCCTATTTT 59.980 37.037 9.90 1.32 0.00 1.82
1362 1446 1.993956 TTTTGCAAGCAAGAGGCCTA 58.006 45.000 4.42 0.00 46.50 3.93
1389 1473 1.755380 AGGTGTACGTTGGAGCCTATC 59.245 52.381 0.00 0.00 0.00 2.08
1434 1518 3.455910 TGTGCTCTACCCTGCATTTATCT 59.544 43.478 0.00 0.00 41.45 1.98
1483 1567 6.424812 CGAATCAGTGATCTGCAAATGGTATA 59.575 38.462 5.98 0.00 41.10 1.47
1484 1568 7.502120 AATCAGTGATCTGCAAATGGTATAC 57.498 36.000 5.98 0.00 41.10 1.47
1520 1616 2.414824 GCACGGCAACCAAATCGATTTA 60.415 45.455 22.33 0.00 0.00 1.40
1563 1659 9.683870 ACTTATAGTAAGATATTACTCCCTCCG 57.316 37.037 15.76 4.80 38.56 4.63
1564 1660 9.683870 CTTATAGTAAGATATTACTCCCTCCGT 57.316 37.037 15.76 0.00 38.56 4.69
1565 1661 9.678260 TTATAGTAAGATATTACTCCCTCCGTC 57.322 37.037 15.76 0.00 38.56 4.79
1566 1662 5.323581 AGTAAGATATTACTCCCTCCGTCC 58.676 45.833 6.94 0.00 32.66 4.79
1567 1663 3.172471 AGATATTACTCCCTCCGTCCC 57.828 52.381 0.00 0.00 0.00 4.46
1568 1664 2.449730 AGATATTACTCCCTCCGTCCCA 59.550 50.000 0.00 0.00 0.00 4.37
1569 1665 2.852714 TATTACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
1570 1666 1.961133 ATTACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
1571 1667 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
1572 1668 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
1573 1669 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
1574 1670 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
1575 1671 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
1576 1672 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
1577 1673 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
1578 1674 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
1579 1675 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
1580 1676 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
1581 1677 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
1582 1678 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
1583 1679 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
1584 1680 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
1585 1681 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
1586 1682 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
1587 1683 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
1588 1684 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
1589 1685 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
1590 1686 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
1591 1687 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
1599 1695 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
1600 1696 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
1601 1697 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
1602 1698 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
1603 1699 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
1604 1700 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
1620 1716 7.539712 ACGGATGTATCAAGTCATGTTTTAG 57.460 36.000 0.00 0.00 0.00 1.85
1621 1717 7.327975 ACGGATGTATCAAGTCATGTTTTAGA 58.672 34.615 0.00 0.00 0.00 2.10
1622 1718 7.987458 ACGGATGTATCAAGTCATGTTTTAGAT 59.013 33.333 0.00 0.00 0.00 1.98
1623 1719 9.476202 CGGATGTATCAAGTCATGTTTTAGATA 57.524 33.333 0.00 0.00 0.00 1.98
1629 1725 7.770801 TCAAGTCATGTTTTAGATACATCCG 57.229 36.000 0.00 0.00 34.11 4.18
1630 1726 6.761242 TCAAGTCATGTTTTAGATACATCCGG 59.239 38.462 0.00 0.00 34.11 5.14
1631 1727 6.479972 AGTCATGTTTTAGATACATCCGGA 57.520 37.500 6.61 6.61 34.11 5.14
1632 1728 7.067496 AGTCATGTTTTAGATACATCCGGAT 57.933 36.000 12.38 12.38 34.11 4.18
1633 1729 7.509546 AGTCATGTTTTAGATACATCCGGATT 58.490 34.615 16.19 9.22 34.11 3.01
1634 1730 7.993183 AGTCATGTTTTAGATACATCCGGATTT 59.007 33.333 16.19 11.96 34.11 2.17
1635 1731 9.268268 GTCATGTTTTAGATACATCCGGATTTA 57.732 33.333 16.19 14.15 34.11 1.40
1636 1732 9.489084 TCATGTTTTAGATACATCCGGATTTAG 57.511 33.333 16.19 6.45 34.11 1.85
1637 1733 9.489084 CATGTTTTAGATACATCCGGATTTAGA 57.511 33.333 16.19 0.00 34.11 2.10
1638 1734 8.882415 TGTTTTAGATACATCCGGATTTAGAC 57.118 34.615 16.19 11.28 0.00 2.59
1639 1735 8.479689 TGTTTTAGATACATCCGGATTTAGACA 58.520 33.333 16.19 9.30 0.00 3.41
1640 1736 9.321562 GTTTTAGATACATCCGGATTTAGACAA 57.678 33.333 16.19 5.44 0.00 3.18
1641 1737 9.893634 TTTTAGATACATCCGGATTTAGACAAA 57.106 29.630 16.19 10.90 0.00 2.83
1643 1739 9.706691 TTAGATACATCCGGATTTAGACAAATC 57.293 33.333 16.19 7.41 46.30 2.17
1644 1740 7.967908 AGATACATCCGGATTTAGACAAATCT 58.032 34.615 16.19 9.67 46.26 2.40
1645 1741 9.090103 AGATACATCCGGATTTAGACAAATCTA 57.910 33.333 16.19 0.00 46.26 1.98
1646 1742 9.706691 GATACATCCGGATTTAGACAAATCTAA 57.293 33.333 16.19 0.00 46.26 2.10
1647 1743 9.712305 ATACATCCGGATTTAGACAAATCTAAG 57.288 33.333 16.19 0.00 45.93 2.18
1648 1744 7.792032 ACATCCGGATTTAGACAAATCTAAGA 58.208 34.615 16.19 5.41 45.93 2.10
1649 1745 7.711339 ACATCCGGATTTAGACAAATCTAAGAC 59.289 37.037 16.19 0.00 45.93 3.01
1650 1746 7.177832 TCCGGATTTAGACAAATCTAAGACA 57.822 36.000 0.00 0.00 45.93 3.41
1651 1747 7.617225 TCCGGATTTAGACAAATCTAAGACAA 58.383 34.615 0.00 0.00 45.93 3.18
1652 1748 7.764443 TCCGGATTTAGACAAATCTAAGACAAG 59.236 37.037 0.00 0.00 45.93 3.16
1653 1749 7.764443 CCGGATTTAGACAAATCTAAGACAAGA 59.236 37.037 0.00 0.00 45.93 3.02
1654 1750 9.151471 CGGATTTAGACAAATCTAAGACAAGAA 57.849 33.333 9.31 0.00 45.93 2.52
1661 1757 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
1662 1758 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
1663 1759 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
1664 1760 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
1665 1761 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
1666 1762 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
1667 1763 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
1668 1764 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
1669 1765 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
1670 1766 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
1671 1767 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
1672 1768 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
1673 1769 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
1894 1990 4.765273 TCGGTTTGCTAGCATCATAGAAA 58.235 39.130 20.13 4.81 0.00 2.52
1916 2012 3.503748 ACTGAACTTTGAAGGCTGCATAC 59.496 43.478 0.00 0.00 0.00 2.39
1928 2031 5.258456 AGGCTGCATACAAAAAGATGATG 57.742 39.130 0.50 0.00 0.00 3.07
1938 2041 9.507280 CATACAAAAAGATGATGACATGTTACC 57.493 33.333 0.00 0.00 38.71 2.85
2217 2362 5.278512 GGAAAAGAAGGGCAAAGACTGTAAG 60.279 44.000 0.00 0.00 42.29 2.34
2355 2500 9.288576 CCAGTAATCATTGAAAAGATATGCCTA 57.711 33.333 0.00 0.00 0.00 3.93
2388 2533 8.484641 AAATATTAGATACCAGCGACATCATG 57.515 34.615 0.00 0.00 0.00 3.07
2397 2542 1.276138 AGCGACATCATGTGGAAGTCA 59.724 47.619 3.58 0.00 42.85 3.41
2433 2579 7.974675 ACATCATATGAAAGTTCAGGTTTACG 58.025 34.615 9.99 0.00 41.08 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.317020 GGCAACAAACACTGACGCTC 60.317 55.000 0.00 0.00 0.00 5.03
38 39 0.600782 GGCATGGGCAACAAACACTG 60.601 55.000 0.00 0.00 43.71 3.66
74 75 4.120331 GCACTGCCACGCCATTCC 62.120 66.667 0.00 0.00 0.00 3.01
173 174 4.467735 GAAGTTCGAAGATGAAAGCCAAC 58.532 43.478 0.00 0.00 35.04 3.77
183 184 2.112190 GGAGGGAGGAAGTTCGAAGAT 58.888 52.381 0.00 0.00 35.04 2.40
255 305 5.749462 TGAAAGGGCTGAAATTTTGGAAAA 58.251 33.333 0.00 0.00 0.00 2.29
260 310 4.060205 CCACTGAAAGGGCTGAAATTTTG 58.940 43.478 0.00 0.00 34.45 2.44
261 311 3.071457 CCCACTGAAAGGGCTGAAATTTT 59.929 43.478 0.00 0.00 39.96 1.82
469 538 7.556275 TGAAAACAGAAAACTTCAGTACCTCAT 59.444 33.333 0.00 0.00 0.00 2.90
473 542 8.751302 TTTTGAAAACAGAAAACTTCAGTACC 57.249 30.769 0.00 0.00 0.00 3.34
536 605 7.598278 TGTCGTATCACCAAATTGCTTTAAAT 58.402 30.769 0.00 0.00 0.00 1.40
590 660 5.297776 CCCTGAAAATGCTCCTTGTGTATAG 59.702 44.000 0.00 0.00 0.00 1.31
775 847 2.171448 GCAGGGTGTACAGGAATCAGAT 59.829 50.000 0.00 0.00 0.00 2.90
780 852 2.375174 TCTTTGCAGGGTGTACAGGAAT 59.625 45.455 0.00 0.00 0.00 3.01
877 958 2.356135 AGCGTTCGTTGGAAATGCTAT 58.644 42.857 0.93 0.00 41.60 2.97
887 968 3.788434 AGATTTGTGTAGCGTTCGTTG 57.212 42.857 0.00 0.00 0.00 4.10
888 969 5.636121 TGATAAGATTTGTGTAGCGTTCGTT 59.364 36.000 0.00 0.00 0.00 3.85
916 997 2.775418 TGATCCCCCAATCTTGCTCTA 58.225 47.619 0.00 0.00 0.00 2.43
924 1005 3.515602 ACAAGCTATGATCCCCCAATC 57.484 47.619 0.00 0.00 0.00 2.67
1086 1167 9.209175 GTATTACTCTTGTCTGACAAATGTCTT 57.791 33.333 22.25 15.42 44.99 3.01
1153 1234 4.306600 TCGATTCAGTACGCATGCATATT 58.693 39.130 19.57 0.00 0.00 1.28
1160 1241 5.833082 AGAATACTTCGATTCAGTACGCAT 58.167 37.500 0.00 0.00 38.14 4.73
1226 1307 8.868522 TTTCTATGAAACTGACATGGAAAGAT 57.131 30.769 12.71 0.00 44.16 2.40
1331 1415 8.206325 TCTTGCTTGCAAAAATCATAAACAAA 57.794 26.923 9.39 0.00 0.00 2.83
1332 1416 7.041916 CCTCTTGCTTGCAAAAATCATAAACAA 60.042 33.333 9.39 0.00 0.00 2.83
1341 1425 1.695788 AGGCCTCTTGCTTGCAAAAAT 59.304 42.857 0.00 0.00 40.92 1.82
1434 1518 6.262944 CGATCATTTCCCATGGATGTTTCTTA 59.737 38.462 15.22 0.00 0.00 2.10
1483 1567 1.072332 TGCCGCCTAACATGTGTGT 59.928 52.632 0.00 0.00 41.28 3.72
1484 1568 1.501741 GTGCCGCCTAACATGTGTG 59.498 57.895 0.00 0.00 0.00 3.82
1555 1651 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
1556 1652 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
1557 1653 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
1558 1654 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
1559 1655 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
1560 1656 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
1561 1657 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
1562 1658 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
1563 1659 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
1564 1660 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
1565 1661 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
1573 1669 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
1574 1670 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
1575 1671 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
1576 1672 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
1577 1673 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
1578 1674 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
1594 1690 9.261180 CTAAAACATGACTTGATACATCCGTAT 57.739 33.333 0.00 0.00 41.16 3.06
1595 1691 8.471609 TCTAAAACATGACTTGATACATCCGTA 58.528 33.333 0.00 0.00 0.00 4.02
1596 1692 7.327975 TCTAAAACATGACTTGATACATCCGT 58.672 34.615 0.00 0.00 0.00 4.69
1597 1693 7.770801 TCTAAAACATGACTTGATACATCCG 57.229 36.000 0.00 0.00 0.00 4.18
1603 1699 9.476202 CGGATGTATCTAAAACATGACTTGATA 57.524 33.333 0.00 0.00 37.69 2.15
1604 1700 7.442364 CCGGATGTATCTAAAACATGACTTGAT 59.558 37.037 0.00 0.00 37.69 2.57
1605 1701 6.761242 CCGGATGTATCTAAAACATGACTTGA 59.239 38.462 0.00 0.00 37.69 3.02
1606 1702 6.761242 TCCGGATGTATCTAAAACATGACTTG 59.239 38.462 0.00 0.00 37.69 3.16
1607 1703 6.884832 TCCGGATGTATCTAAAACATGACTT 58.115 36.000 0.00 0.00 37.69 3.01
1608 1704 6.479972 TCCGGATGTATCTAAAACATGACT 57.520 37.500 0.00 0.00 37.69 3.41
1609 1705 7.730364 AATCCGGATGTATCTAAAACATGAC 57.270 36.000 19.95 0.00 37.69 3.06
1610 1706 9.489084 CTAAATCCGGATGTATCTAAAACATGA 57.511 33.333 19.95 0.00 37.69 3.07
1611 1707 9.489084 TCTAAATCCGGATGTATCTAAAACATG 57.511 33.333 19.95 0.73 37.69 3.21
1612 1708 9.490379 GTCTAAATCCGGATGTATCTAAAACAT 57.510 33.333 19.95 0.00 40.23 2.71
1613 1709 8.479689 TGTCTAAATCCGGATGTATCTAAAACA 58.520 33.333 19.95 10.91 0.00 2.83
1614 1710 8.882415 TGTCTAAATCCGGATGTATCTAAAAC 57.118 34.615 19.95 8.66 0.00 2.43
1615 1711 9.893634 TTTGTCTAAATCCGGATGTATCTAAAA 57.106 29.630 19.95 11.76 0.00 1.52
1617 1713 9.706691 GATTTGTCTAAATCCGGATGTATCTAA 57.293 33.333 19.95 14.90 44.08 2.10
1635 1731 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
1636 1732 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
1637 1733 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
1638 1734 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
1639 1735 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
1640 1736 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
1641 1737 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
1642 1738 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
1643 1739 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
1644 1740 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
1645 1741 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
1646 1742 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
1647 1743 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
1648 1744 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
1649 1745 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
1650 1746 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
1651 1747 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
1652 1748 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
1653 1749 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
1654 1750 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
1655 1751 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
1656 1752 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
1657 1753 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
1658 1754 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
1659 1755 1.064091 AGTTACTACTCCCTCCGTCCC 60.064 57.143 0.00 0.00 0.00 4.46
1660 1756 2.433662 AGTTACTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
1661 1757 3.882288 CCTTAGTTACTACTCCCTCCGTC 59.118 52.174 0.00 0.00 35.78 4.79
1662 1758 3.372458 CCCTTAGTTACTACTCCCTCCGT 60.372 52.174 0.00 0.00 35.78 4.69
1663 1759 3.220940 CCCTTAGTTACTACTCCCTCCG 58.779 54.545 0.00 0.00 35.78 4.63
1664 1760 3.959449 CACCCTTAGTTACTACTCCCTCC 59.041 52.174 0.00 0.00 35.78 4.30
1665 1761 3.384146 GCACCCTTAGTTACTACTCCCTC 59.616 52.174 0.00 0.00 35.78 4.30
1666 1762 3.245875 TGCACCCTTAGTTACTACTCCCT 60.246 47.826 0.00 0.00 35.78 4.20
1667 1763 3.102204 TGCACCCTTAGTTACTACTCCC 58.898 50.000 0.00 0.00 35.78 4.30
1668 1764 4.813750 TTGCACCCTTAGTTACTACTCC 57.186 45.455 0.00 0.00 35.78 3.85
1669 1765 5.176592 CCTTTGCACCCTTAGTTACTACTC 58.823 45.833 0.00 0.00 35.78 2.59
1670 1766 4.565028 GCCTTTGCACCCTTAGTTACTACT 60.565 45.833 0.00 0.00 36.52 2.57
1671 1767 3.688185 GCCTTTGCACCCTTAGTTACTAC 59.312 47.826 0.00 0.00 37.47 2.73
1672 1768 3.328343 TGCCTTTGCACCCTTAGTTACTA 59.672 43.478 0.00 0.00 44.23 1.82
1673 1769 2.107552 TGCCTTTGCACCCTTAGTTACT 59.892 45.455 0.00 0.00 44.23 2.24
1894 1990 2.057137 TGCAGCCTTCAAAGTTCAGT 57.943 45.000 0.00 0.00 0.00 3.41
2048 2157 5.536161 ACACTTTACAAGGTGCAAGAATCAT 59.464 36.000 4.31 0.00 36.99 2.45
2050 2159 5.008613 TGACACTTTACAAGGTGCAAGAATC 59.991 40.000 4.31 0.00 36.99 2.52
2160 2305 7.822822 ACTATGTTATTGGTTCTGGTGTTAGTC 59.177 37.037 0.00 0.00 0.00 2.59
2217 2362 5.050023 GCTGCCTCTTTATTTCGTTATCCTC 60.050 44.000 0.00 0.00 0.00 3.71
2255 2400 3.468071 ACAGGTATGGGTAGTCTGTGA 57.532 47.619 0.00 0.00 37.31 3.58
2360 2505 9.990360 TGATGTCGCTGGTATCTAATATTTAAA 57.010 29.630 0.00 0.00 0.00 1.52
2377 2522 1.276138 TGACTTCCACATGATGTCGCT 59.724 47.619 0.00 0.00 46.16 4.93


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.