Multiple sequence alignment - TraesCS3A01G323300

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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 TraesCS3A01G323300 chr3A 100.000 2545 0 0 1 2545 567981426 567978882 0 4700
1 TraesCS3A01G323300 chr3A 85.053 1405 202 7 160 1562 388951181 388952579 0 1424
2 TraesCS3A01G323300 chr3A 82.211 787 120 12 1769 2545 568021966 568021190 0 660
3 TraesCS3A01G323300 chr3D 85.273 1426 183 18 161 1573 177031899 177030488 0 1445
4 TraesCS3A01G323300 chr3D 94.349 814 32 6 1737 2545 429728103 429727299 0 1236
5 TraesCS3A01G323300 chr3D 78.286 1575 325 10 2 1562 348148748 348147177 0 998
6 TraesCS3A01G323300 chr3D 81.611 832 115 19 1729 2545 429790930 429790122 0 654
7 TraesCS3A01G323300 chr3B 85.014 1408 181 15 160 1562 387913060 387914442 0 1404
8 TraesCS3A01G323300 chr3B 94.725 891 22 9 1673 2545 561974727 561973844 0 1362
9 TraesCS3A01G323300 chr3B 83.557 821 107 17 1737 2545 562276662 562275858 0 743
10 TraesCS3A01G323300 chr2B 83.549 1465 235 6 1 1462 534375434 534373973 0 1365
11 TraesCS3A01G323300 chr2B 78.175 1567 333 8 11 1571 506150207 506148644 0 990
12 TraesCS3A01G323300 chr5D 80.392 1581 296 12 2 1573 193141189 193142764 0 1190
13 TraesCS3A01G323300 chr7B 79.494 1580 303 16 2 1571 15584474 15582906 0 1103
14 TraesCS3A01G323300 chr1D 78.653 1574 329 7 2 1571 113842080 113840510 0 1038


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 TraesCS3A01G323300 chr3A 567978882 567981426 2544 True 4700 4700 100.000 1 2545 1 chr3A.!!$R1 2544
1 TraesCS3A01G323300 chr3A 388951181 388952579 1398 False 1424 1424 85.053 160 1562 1 chr3A.!!$F1 1402
2 TraesCS3A01G323300 chr3A 568021190 568021966 776 True 660 660 82.211 1769 2545 1 chr3A.!!$R2 776
3 TraesCS3A01G323300 chr3D 177030488 177031899 1411 True 1445 1445 85.273 161 1573 1 chr3D.!!$R1 1412
4 TraesCS3A01G323300 chr3D 429727299 429728103 804 True 1236 1236 94.349 1737 2545 1 chr3D.!!$R3 808
5 TraesCS3A01G323300 chr3D 348147177 348148748 1571 True 998 998 78.286 2 1562 1 chr3D.!!$R2 1560
6 TraesCS3A01G323300 chr3D 429790122 429790930 808 True 654 654 81.611 1729 2545 1 chr3D.!!$R4 816
7 TraesCS3A01G323300 chr3B 387913060 387914442 1382 False 1404 1404 85.014 160 1562 1 chr3B.!!$F1 1402
8 TraesCS3A01G323300 chr3B 561973844 561974727 883 True 1362 1362 94.725 1673 2545 1 chr3B.!!$R1 872
9 TraesCS3A01G323300 chr3B 562275858 562276662 804 True 743 743 83.557 1737 2545 1 chr3B.!!$R2 808
10 TraesCS3A01G323300 chr2B 534373973 534375434 1461 True 1365 1365 83.549 1 1462 1 chr2B.!!$R2 1461
11 TraesCS3A01G323300 chr2B 506148644 506150207 1563 True 990 990 78.175 11 1571 1 chr2B.!!$R1 1560
12 TraesCS3A01G323300 chr5D 193141189 193142764 1575 False 1190 1190 80.392 2 1573 1 chr5D.!!$F1 1571
13 TraesCS3A01G323300 chr7B 15582906 15584474 1568 True 1103 1103 79.494 2 1571 1 chr7B.!!$R1 1569
14 TraesCS3A01G323300 chr1D 113840510 113842080 1570 True 1038 1038 78.653 2 1571 1 chr1D.!!$R1 1569

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
174 176 0.751643 GGCCAAGCATTATGTCGGGT 60.752 55.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 1614 0.042131 TACTCCCTCCGTCCCATTGT 59.958 55.0 0.0 0.0 0.0 2.71 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
66 67 2.288518 GCGTCTCCTGGATAATCCTGAC 60.289 54.545 0.00 0.00 37.65 3.51
68 69 3.639094 CGTCTCCTGGATAATCCTGACTT 59.361 47.826 0.00 0.00 37.65 3.01
80 81 4.760530 ATCCTGACTTGCTATGTGCTAA 57.239 40.909 0.00 0.00 43.37 3.09
82 83 4.507710 TCCTGACTTGCTATGTGCTAAAG 58.492 43.478 0.00 0.00 43.37 1.85
84 85 4.697352 CCTGACTTGCTATGTGCTAAAGTT 59.303 41.667 0.00 0.00 37.82 2.66
96 97 6.458232 TGTGCTAAAGTTTTAAGAGCCAAA 57.542 33.333 5.80 0.00 0.00 3.28
123 124 2.698855 CGGAAGGTGACCTGATGAAT 57.301 50.000 4.15 0.00 32.13 2.57
129 130 3.878778 AGGTGACCTGATGAATACAAGC 58.121 45.455 1.77 0.00 29.57 4.01
158 160 1.248486 GGTTCTTCCTTCACTTGGCC 58.752 55.000 0.00 0.00 0.00 5.36
169 171 2.806434 TCACTTGGCCAAGCATTATGT 58.194 42.857 39.52 20.45 41.99 2.29
174 176 0.751643 GGCCAAGCATTATGTCGGGT 60.752 55.000 0.00 0.00 0.00 5.28
207 209 9.040259 TCTCTCAGAAATGGTTATATATGGAGG 57.960 37.037 0.00 0.00 0.00 4.30
208 210 7.624549 TCTCAGAAATGGTTATATATGGAGGC 58.375 38.462 0.00 0.00 0.00 4.70
252 254 6.540083 TGACATATTGAGAGATGCATGGATT 58.460 36.000 2.46 0.00 0.00 3.01
261 263 4.056050 GAGATGCATGGATTCCAAATTGC 58.944 43.478 18.72 18.72 37.50 3.56
297 299 7.235812 AGGATTATTACTCCTAGATGTGGGAAC 59.764 40.741 0.89 0.00 41.42 3.62
298 300 7.016268 GGATTATTACTCCTAGATGTGGGAACA 59.984 40.741 0.00 0.00 31.78 3.18
340 342 6.319048 ACCTAATTGATCCAGTCATGAACT 57.681 37.500 0.00 0.00 39.44 3.01
372 374 6.272318 TGAAGATTTGGTGACACAAACATTC 58.728 36.000 8.08 12.50 42.51 2.67
389 391 3.118884 ACATTCTGGCCAATTGATGCTTC 60.119 43.478 7.01 0.00 0.00 3.86
403 405 1.103803 TGCTTCTAGAGTACTGGCGG 58.896 55.000 0.00 0.00 0.00 6.13
406 408 2.645802 CTTCTAGAGTACTGGCGGTCT 58.354 52.381 0.06 0.00 0.00 3.85
417 419 2.317040 CTGGCGGTCTTTCTCCCTATA 58.683 52.381 0.00 0.00 0.00 1.31
422 424 4.082136 GGCGGTCTTTCTCCCTATACATAG 60.082 50.000 0.00 0.00 0.00 2.23
593 598 7.765695 AGAAGATTTGGAATTTAGCTTGTCA 57.234 32.000 0.00 0.00 0.00 3.58
594 599 8.181904 AGAAGATTTGGAATTTAGCTTGTCAA 57.818 30.769 0.00 0.00 0.00 3.18
615 620 9.221933 TGTCAAGCGAAGGTAAAAATCTTTATA 57.778 29.630 0.00 0.00 37.06 0.98
676 681 4.025396 CGCTGGCTAATAGACACATGAAAG 60.025 45.833 0.00 0.00 0.00 2.62
691 696 3.316071 TGAAAGTTTCGCCCGTATACA 57.684 42.857 10.92 0.00 0.00 2.29
726 733 1.383523 GGCCAGAAGATACCAAGCAC 58.616 55.000 0.00 0.00 0.00 4.40
738 745 9.109393 GAAGATACCAAGCACATGTTATTTCTA 57.891 33.333 0.00 0.00 0.00 2.10
779 786 5.341169 AGTGTGGGATAAATTGGGAATGTT 58.659 37.500 0.00 0.00 0.00 2.71
812 819 4.874970 AGAAAAGCATGTGTTGTTGATCC 58.125 39.130 0.00 0.00 0.00 3.36
823 830 0.904865 TGTTGATCCTGCGGGAGAGT 60.905 55.000 21.28 2.52 45.86 3.24
891 898 1.974265 TGGGTTTTCAGAATGCACGA 58.026 45.000 0.00 0.00 34.76 4.35
915 922 5.069119 AGAGATGATTGCTATAACCGTGTGA 59.931 40.000 0.00 0.00 0.00 3.58
934 941 7.824289 CCGTGTGATATTTATGGTGGAATAGAT 59.176 37.037 0.00 0.00 0.00 1.98
953 960 5.246981 AGATGAAACTTGGTTCATGAGGA 57.753 39.130 17.34 0.00 45.98 3.71
978 985 1.689813 TCTCAAGAGGCGTACCAAACA 59.310 47.619 0.00 0.00 39.06 2.83
981 988 1.737793 CAAGAGGCGTACCAAACATCC 59.262 52.381 0.00 0.00 39.06 3.51
1044 1051 5.239306 CCACTCACACAATGCTAAGAGAAAA 59.761 40.000 0.00 0.00 0.00 2.29
1078 1085 1.152701 ACACACCTCCTAGGGGGTTTA 59.847 52.381 32.26 0.00 45.32 2.01
1110 1118 4.707030 TGTGGATGCTTCATTTGATCAC 57.293 40.909 0.00 0.00 0.00 3.06
1195 1205 5.106197 GGTGGAAATTGGAAAATTGAATGGC 60.106 40.000 0.00 0.00 0.00 4.40
1200 1210 1.337635 TGGAAAATTGAATGGCGTGCC 60.338 47.619 3.30 3.30 0.00 5.01
1207 1217 1.240641 TGAATGGCGTGCCGATGTTT 61.241 50.000 6.37 0.00 39.42 2.83
1281 1291 4.021456 ACGGGATGCAATCGTCTCATTATA 60.021 41.667 6.54 0.00 46.86 0.98
1328 1345 1.128692 CGCAATGAAGAACGAAGGACC 59.871 52.381 0.00 0.00 0.00 4.46
1389 1406 3.509575 ACTTTATGGCTTGCGATTTTCCA 59.490 39.130 0.00 0.00 0.00 3.53
1484 1510 3.186909 CGTGACAAGCGATTGGATAGAA 58.813 45.455 18.84 0.00 0.00 2.10
1590 1616 7.681939 AAAAACTGAACTACAAGAACAGACA 57.318 32.000 0.00 0.00 33.53 3.41
1591 1617 7.681939 AAAACTGAACTACAAGAACAGACAA 57.318 32.000 0.00 0.00 33.53 3.18
1592 1618 7.865706 AAACTGAACTACAAGAACAGACAAT 57.134 32.000 0.00 0.00 33.53 2.71
1593 1619 6.851222 ACTGAACTACAAGAACAGACAATG 57.149 37.500 0.00 0.00 33.53 2.82
1594 1620 5.760253 ACTGAACTACAAGAACAGACAATGG 59.240 40.000 0.00 0.00 33.53 3.16
1595 1621 5.063204 TGAACTACAAGAACAGACAATGGG 58.937 41.667 0.00 0.00 0.00 4.00
1596 1622 4.974645 ACTACAAGAACAGACAATGGGA 57.025 40.909 0.00 0.00 0.00 4.37
1597 1623 4.642429 ACTACAAGAACAGACAATGGGAC 58.358 43.478 0.00 0.00 0.00 4.46
1598 1624 2.494059 ACAAGAACAGACAATGGGACG 58.506 47.619 0.00 0.00 0.00 4.79
1599 1625 1.806542 CAAGAACAGACAATGGGACGG 59.193 52.381 0.00 0.00 0.00 4.79
1600 1626 1.348064 AGAACAGACAATGGGACGGA 58.652 50.000 0.00 0.00 0.00 4.69
1601 1627 1.276421 AGAACAGACAATGGGACGGAG 59.724 52.381 0.00 0.00 0.00 4.63
1602 1628 0.324943 AACAGACAATGGGACGGAGG 59.675 55.000 0.00 0.00 0.00 4.30
1603 1629 1.221840 CAGACAATGGGACGGAGGG 59.778 63.158 0.00 0.00 0.00 4.30
1604 1630 1.080354 AGACAATGGGACGGAGGGA 59.920 57.895 0.00 0.00 0.00 4.20
1605 1631 0.978146 AGACAATGGGACGGAGGGAG 60.978 60.000 0.00 0.00 0.00 4.30
1606 1632 1.229529 ACAATGGGACGGAGGGAGT 60.230 57.895 0.00 0.00 0.00 3.85
1607 1633 0.042131 ACAATGGGACGGAGGGAGTA 59.958 55.000 0.00 0.00 0.00 2.59
1608 1634 0.753262 CAATGGGACGGAGGGAGTAG 59.247 60.000 0.00 0.00 0.00 2.57
1609 1635 0.338814 AATGGGACGGAGGGAGTAGT 59.661 55.000 0.00 0.00 0.00 2.73
1610 1636 0.338814 ATGGGACGGAGGGAGTAGTT 59.661 55.000 0.00 0.00 0.00 2.24
1611 1637 0.324091 TGGGACGGAGGGAGTAGTTC 60.324 60.000 0.00 0.00 0.00 3.01
1612 1638 0.324091 GGGACGGAGGGAGTAGTTCA 60.324 60.000 0.00 0.00 0.00 3.18
1613 1639 0.816373 GGACGGAGGGAGTAGTTCAC 59.184 60.000 0.00 0.00 0.00 3.18
1614 1640 1.616456 GGACGGAGGGAGTAGTTCACT 60.616 57.143 0.00 0.00 44.17 3.41
1615 1641 2.356535 GGACGGAGGGAGTAGTTCACTA 60.357 54.545 0.00 0.00 40.54 2.74
1616 1642 2.682352 GACGGAGGGAGTAGTTCACTAC 59.318 54.545 8.82 8.82 40.54 2.73
1625 1651 2.400399 GTAGTTCACTACAAGCGCACA 58.600 47.619 11.47 0.00 46.08 4.57
1626 1652 2.169832 AGTTCACTACAAGCGCACAT 57.830 45.000 11.47 0.00 0.00 3.21
1627 1653 1.800586 AGTTCACTACAAGCGCACATG 59.199 47.619 11.47 8.37 0.00 3.21
1628 1654 1.531149 GTTCACTACAAGCGCACATGT 59.469 47.619 11.47 14.37 0.00 3.21
1629 1655 1.877637 TCACTACAAGCGCACATGTT 58.122 45.000 11.47 0.00 0.00 2.71
1630 1656 2.217750 TCACTACAAGCGCACATGTTT 58.782 42.857 11.47 0.00 0.00 2.83
1631 1657 3.394719 TCACTACAAGCGCACATGTTTA 58.605 40.909 11.47 0.00 0.00 2.01
1632 1658 4.000325 TCACTACAAGCGCACATGTTTAT 59.000 39.130 11.47 0.00 0.00 1.40
1633 1659 5.172205 TCACTACAAGCGCACATGTTTATA 58.828 37.500 11.47 0.00 0.00 0.98
1634 1660 5.815222 TCACTACAAGCGCACATGTTTATAT 59.185 36.000 11.47 0.00 0.00 0.86
1635 1661 6.981559 TCACTACAAGCGCACATGTTTATATA 59.018 34.615 11.47 0.00 0.00 0.86
1636 1662 7.492994 TCACTACAAGCGCACATGTTTATATAA 59.507 33.333 11.47 0.00 0.00 0.98
1637 1663 8.282592 CACTACAAGCGCACATGTTTATATAAT 58.717 33.333 11.47 0.00 0.00 1.28
1638 1664 8.282592 ACTACAAGCGCACATGTTTATATAATG 58.717 33.333 11.47 0.00 0.00 1.90
1639 1665 7.258022 ACAAGCGCACATGTTTATATAATGA 57.742 32.000 11.47 0.00 0.00 2.57
1640 1666 7.874940 ACAAGCGCACATGTTTATATAATGAT 58.125 30.769 11.47 0.00 0.00 2.45
1641 1667 7.804600 ACAAGCGCACATGTTTATATAATGATG 59.195 33.333 11.47 10.58 0.00 3.07
1642 1668 7.439157 AGCGCACATGTTTATATAATGATGT 57.561 32.000 11.47 11.49 0.00 3.06
1643 1669 8.546597 AGCGCACATGTTTATATAATGATGTA 57.453 30.769 11.47 0.00 0.00 2.29
1644 1670 8.659491 AGCGCACATGTTTATATAATGATGTAG 58.341 33.333 11.47 13.35 0.00 2.74
1645 1671 7.426456 GCGCACATGTTTATATAATGATGTAGC 59.574 37.037 0.30 16.90 0.00 3.58
1646 1672 8.659491 CGCACATGTTTATATAATGATGTAGCT 58.341 33.333 21.04 0.00 0.00 3.32
1647 1673 9.979270 GCACATGTTTATATAATGATGTAGCTC 57.021 33.333 14.84 6.23 0.00 4.09
1661 1687 9.624373 AATGATGTAGCTCTTTGATGAGTAATT 57.376 29.630 0.00 0.00 36.51 1.40
1666 1692 9.719355 TGTAGCTCTTTGATGAGTAATTAAACA 57.281 29.630 0.00 0.00 36.51 2.83
1670 1696 8.801913 GCTCTTTGATGAGTAATTAAACATTGC 58.198 33.333 6.96 0.00 36.51 3.56
1739 1782 2.817258 TGCCTATGCTGTACAAACCAAC 59.183 45.455 0.00 0.00 38.71 3.77
1764 1807 7.286775 ACAAAGCAACAAGAATTTCTACCCTTA 59.713 33.333 0.00 0.00 0.00 2.69
1765 1808 7.833285 AAGCAACAAGAATTTCTACCCTTAA 57.167 32.000 0.00 0.00 0.00 1.85
1766 1809 8.422577 AAGCAACAAGAATTTCTACCCTTAAT 57.577 30.769 0.00 0.00 0.00 1.40
1767 1810 8.422577 AGCAACAAGAATTTCTACCCTTAATT 57.577 30.769 0.00 0.00 0.00 1.40
1848 1891 4.322080 TTCAGTGTCAGACGTGATCTTT 57.678 40.909 0.00 0.00 34.41 2.52
2247 2299 3.833650 TCACCAGGACACCGAAACTATAA 59.166 43.478 0.00 0.00 0.00 0.98
2304 2356 4.503817 GCATATTCTGGAGACATGTAGCCA 60.504 45.833 15.97 15.97 41.51 4.75
2461 2526 2.202610 CTCGCGATGCCGAAGTCA 60.203 61.111 10.36 0.00 36.72 3.41
2512 2577 2.736144 ACACATTGCTTGCCTTCATG 57.264 45.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.701539 ACAATGCCAGATTGAAACAGTATAA 57.298 32.000 2.51 0.00 33.51 0.98
7 8 6.349280 GCTAACAATGCCAGATTGAAACAGTA 60.349 38.462 2.51 0.00 33.51 2.74
42 43 1.001406 GGATTATCCAGGAGACGCCAG 59.999 57.143 6.34 0.00 40.02 4.85
80 81 7.320399 CGGGAAATATTTGGCTCTTAAAACTT 58.680 34.615 5.17 0.00 0.00 2.66
82 83 6.040247 CCGGGAAATATTTGGCTCTTAAAAC 58.960 40.000 5.17 0.00 0.00 2.43
84 85 5.511363 TCCGGGAAATATTTGGCTCTTAAA 58.489 37.500 5.17 0.00 0.00 1.52
96 97 2.172717 CAGGTCACCTTCCGGGAAATAT 59.827 50.000 11.24 0.00 38.76 1.28
144 146 0.106268 TGCTTGGCCAAGTGAAGGAA 60.106 50.000 38.87 17.86 40.45 3.36
158 160 2.746904 TCAACACCCGACATAATGCTTG 59.253 45.455 0.00 0.00 0.00 4.01
169 171 2.525368 TCTGAGAGATTCAACACCCGA 58.475 47.619 0.00 0.00 34.81 5.14
207 209 6.873076 TGTCAATATTTTGTCCATTTCCAAGC 59.127 34.615 0.00 0.00 34.32 4.01
236 238 3.937778 TTGGAATCCATGCATCTCTCA 57.062 42.857 1.39 0.00 31.53 3.27
252 254 1.939934 CTCCTATTCGCGCAATTTGGA 59.060 47.619 8.75 14.76 0.00 3.53
261 263 5.341617 GGAGTAATAATCCTCCTATTCGCG 58.658 45.833 0.00 0.00 43.29 5.87
289 291 2.920724 TTCGTCAGAATGTTCCCACA 57.079 45.000 0.00 0.00 37.40 4.17
291 293 3.071023 AGACTTTCGTCAGAATGTTCCCA 59.929 43.478 2.19 0.00 42.48 4.37
297 299 5.715070 AGGTTAGAGACTTTCGTCAGAATG 58.285 41.667 0.00 0.00 42.73 2.67
298 300 5.986501 AGGTTAGAGACTTTCGTCAGAAT 57.013 39.130 0.00 0.00 42.73 2.40
316 318 6.725364 AGTTCATGACTGGATCAATTAGGTT 58.275 36.000 0.00 0.00 41.93 3.50
321 323 6.295462 CCCAAAAGTTCATGACTGGATCAATT 60.295 38.462 0.00 0.00 41.93 2.32
340 342 4.898265 TGTCACCAAATCTTCATCCCAAAA 59.102 37.500 0.00 0.00 0.00 2.44
372 374 3.548770 TCTAGAAGCATCAATTGGCCAG 58.451 45.455 5.11 0.00 0.00 4.85
389 391 3.018149 AGAAAGACCGCCAGTACTCTAG 58.982 50.000 0.00 0.00 0.00 2.43
403 405 8.452534 CGACATACTATGTATAGGGAGAAAGAC 58.547 40.741 1.45 0.00 45.03 3.01
406 408 7.464273 TCCGACATACTATGTATAGGGAGAAA 58.536 38.462 1.45 0.00 45.03 2.52
422 424 3.003689 CCAGGCAATGAAATCCGACATAC 59.996 47.826 0.00 0.00 0.00 2.39
458 463 4.567971 TGGTCGTACGGTAAACAAATCAT 58.432 39.130 16.52 0.00 0.00 2.45
461 466 2.738314 GCTGGTCGTACGGTAAACAAAT 59.262 45.455 16.52 0.00 0.00 2.32
471 476 2.858344 CTCCAAATAAGCTGGTCGTACG 59.142 50.000 9.53 9.53 35.30 3.67
593 598 8.135529 GCCATATAAAGATTTTTACCTTCGCTT 58.864 33.333 0.00 0.00 31.90 4.68
594 599 7.284489 TGCCATATAAAGATTTTTACCTTCGCT 59.716 33.333 0.00 0.00 31.90 4.93
615 620 0.473755 TCCCATGAAGCGTATGCCAT 59.526 50.000 2.51 0.00 44.31 4.40
676 681 0.648958 GCTGTGTATACGGGCGAAAC 59.351 55.000 0.20 0.00 33.62 2.78
691 696 1.244019 GGCCCATTCGAACAAGCTGT 61.244 55.000 0.00 0.00 0.00 4.40
747 754 6.458210 CAATTTATCCCACACTTCTTTTGCT 58.542 36.000 0.00 0.00 0.00 3.91
779 786 6.815089 ACACATGCTTTTCTAATTGTTCCAA 58.185 32.000 0.00 0.00 0.00 3.53
791 798 4.682860 CAGGATCAACAACACATGCTTTTC 59.317 41.667 0.00 0.00 0.00 2.29
812 819 1.878656 AAAGACCGACTCTCCCGCAG 61.879 60.000 0.00 0.00 0.00 5.18
823 830 5.677319 AGGAGTAATGATTCAAAGACCGA 57.323 39.130 0.00 0.00 0.00 4.69
891 898 5.069119 TCACACGGTTATAGCAATCATCTCT 59.931 40.000 0.00 0.00 0.00 3.10
934 941 5.656416 ACTTTTCCTCATGAACCAAGTTTCA 59.344 36.000 0.00 0.00 39.79 2.69
953 960 2.367567 TGGTACGCCTCTTGAGACTTTT 59.632 45.455 0.00 0.00 35.27 2.27
981 988 4.082787 GCCATTATAACACGAATCCCCATG 60.083 45.833 0.00 0.00 0.00 3.66
1019 1026 3.578282 TCTCTTAGCATTGTGTGAGTGGA 59.422 43.478 0.00 0.00 0.00 4.02
1044 1051 3.636764 GAGGTGTGTTCCATCCTTTGTTT 59.363 43.478 0.00 0.00 0.00 2.83
1047 1054 2.162681 GGAGGTGTGTTCCATCCTTTG 58.837 52.381 0.00 0.00 34.74 2.77
1048 1055 2.065799 AGGAGGTGTGTTCCATCCTTT 58.934 47.619 0.00 0.00 37.18 3.11
1058 1065 0.104090 AAACCCCCTAGGAGGTGTGT 60.104 55.000 16.99 1.53 39.89 3.72
1078 1085 4.951715 TGAAGCATCCACATTCAGCTTAAT 59.048 37.500 0.00 0.00 44.73 1.40
1110 1118 2.125106 GTGCCCCTTAGCAGGTCG 60.125 66.667 0.00 0.00 45.14 4.79
1195 1205 1.196808 AGCTGTTAAAACATCGGCACG 59.803 47.619 7.89 0.00 44.07 5.34
1200 1210 4.145876 TGCTTCAGCTGTTAAAACATCG 57.854 40.909 14.67 0.00 42.66 3.84
1207 1217 4.326826 AGTGCTAATGCTTCAGCTGTTAA 58.673 39.130 14.67 0.00 42.66 2.01
1352 1369 6.604795 AGCCATAAAGTAGCAGTCATCAAAAT 59.395 34.615 0.00 0.00 0.00 1.82
1418 1436 2.808543 CTCATGGGCTACTTTATTCGCC 59.191 50.000 0.00 0.00 41.75 5.54
1571 1597 5.180117 CCCATTGTCTGTTCTTGTAGTTCAG 59.820 44.000 0.00 0.00 0.00 3.02
1572 1598 5.063204 CCCATTGTCTGTTCTTGTAGTTCA 58.937 41.667 0.00 0.00 0.00 3.18
1573 1599 5.179555 GTCCCATTGTCTGTTCTTGTAGTTC 59.820 44.000 0.00 0.00 0.00 3.01
1574 1600 5.063880 GTCCCATTGTCTGTTCTTGTAGTT 58.936 41.667 0.00 0.00 0.00 2.24
1575 1601 4.642429 GTCCCATTGTCTGTTCTTGTAGT 58.358 43.478 0.00 0.00 0.00 2.73
1576 1602 3.679980 CGTCCCATTGTCTGTTCTTGTAG 59.320 47.826 0.00 0.00 0.00 2.74
1577 1603 3.556213 CCGTCCCATTGTCTGTTCTTGTA 60.556 47.826 0.00 0.00 0.00 2.41
1578 1604 2.494059 CGTCCCATTGTCTGTTCTTGT 58.506 47.619 0.00 0.00 0.00 3.16
1579 1605 1.806542 CCGTCCCATTGTCTGTTCTTG 59.193 52.381 0.00 0.00 0.00 3.02
1580 1606 1.697432 TCCGTCCCATTGTCTGTTCTT 59.303 47.619 0.00 0.00 0.00 2.52
1581 1607 1.276421 CTCCGTCCCATTGTCTGTTCT 59.724 52.381 0.00 0.00 0.00 3.01
1582 1608 1.676014 CCTCCGTCCCATTGTCTGTTC 60.676 57.143 0.00 0.00 0.00 3.18
1583 1609 0.324943 CCTCCGTCCCATTGTCTGTT 59.675 55.000 0.00 0.00 0.00 3.16
1584 1610 1.553690 CCCTCCGTCCCATTGTCTGT 61.554 60.000 0.00 0.00 0.00 3.41
1585 1611 1.221840 CCCTCCGTCCCATTGTCTG 59.778 63.158 0.00 0.00 0.00 3.51
1586 1612 0.978146 CTCCCTCCGTCCCATTGTCT 60.978 60.000 0.00 0.00 0.00 3.41
1587 1613 1.265454 ACTCCCTCCGTCCCATTGTC 61.265 60.000 0.00 0.00 0.00 3.18
1588 1614 0.042131 TACTCCCTCCGTCCCATTGT 59.958 55.000 0.00 0.00 0.00 2.71
1589 1615 0.753262 CTACTCCCTCCGTCCCATTG 59.247 60.000 0.00 0.00 0.00 2.82
1590 1616 0.338814 ACTACTCCCTCCGTCCCATT 59.661 55.000 0.00 0.00 0.00 3.16
1591 1617 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
1592 1618 0.324091 GAACTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
1593 1619 0.324091 TGAACTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
1594 1620 0.816373 GTGAACTACTCCCTCCGTCC 59.184 60.000 0.00 0.00 0.00 4.79
1595 1621 1.836802 AGTGAACTACTCCCTCCGTC 58.163 55.000 0.00 0.00 33.17 4.79
1596 1622 2.040813 TGTAGTGAACTACTCCCTCCGT 59.959 50.000 18.74 0.00 46.74 4.69
1597 1623 2.719739 TGTAGTGAACTACTCCCTCCG 58.280 52.381 18.74 0.00 46.74 4.63
1598 1624 3.119065 GCTTGTAGTGAACTACTCCCTCC 60.119 52.174 18.74 2.00 46.74 4.30
1599 1625 3.427773 CGCTTGTAGTGAACTACTCCCTC 60.428 52.174 18.74 5.84 46.74 4.30
1600 1626 2.492484 CGCTTGTAGTGAACTACTCCCT 59.508 50.000 18.74 0.00 46.74 4.20
1601 1627 2.877335 CGCTTGTAGTGAACTACTCCC 58.123 52.381 18.74 8.00 46.74 4.30
1602 1628 2.260481 GCGCTTGTAGTGAACTACTCC 58.740 52.381 18.74 8.27 46.74 3.85
1603 1629 2.662156 GTGCGCTTGTAGTGAACTACTC 59.338 50.000 18.74 9.10 46.74 2.59
1604 1630 2.035449 TGTGCGCTTGTAGTGAACTACT 59.965 45.455 18.74 0.00 46.74 2.57
1605 1631 2.400399 TGTGCGCTTGTAGTGAACTAC 58.600 47.619 9.73 12.72 46.78 2.73
1606 1632 2.804697 TGTGCGCTTGTAGTGAACTA 57.195 45.000 9.73 0.00 35.29 2.24
1607 1633 1.800586 CATGTGCGCTTGTAGTGAACT 59.199 47.619 9.73 0.00 35.29 3.01
1608 1634 1.531149 ACATGTGCGCTTGTAGTGAAC 59.469 47.619 16.37 0.00 34.82 3.18
1609 1635 1.877637 ACATGTGCGCTTGTAGTGAA 58.122 45.000 16.37 0.00 32.19 3.18
1610 1636 1.877637 AACATGTGCGCTTGTAGTGA 58.122 45.000 17.95 0.00 33.39 3.41
1611 1637 2.686558 AAACATGTGCGCTTGTAGTG 57.313 45.000 17.95 1.57 33.39 2.74
1612 1638 7.780008 TTATATAAACATGTGCGCTTGTAGT 57.220 32.000 17.95 11.99 33.39 2.73
1613 1639 8.495148 TCATTATATAAACATGTGCGCTTGTAG 58.505 33.333 17.95 0.00 33.39 2.74
1614 1640 8.371770 TCATTATATAAACATGTGCGCTTGTA 57.628 30.769 17.95 5.35 33.39 2.41
1615 1641 7.258022 TCATTATATAAACATGTGCGCTTGT 57.742 32.000 9.73 12.62 34.93 3.16
1616 1642 7.804600 ACATCATTATATAAACATGTGCGCTTG 59.195 33.333 9.73 11.29 0.00 4.01
1617 1643 7.874940 ACATCATTATATAAACATGTGCGCTT 58.125 30.769 9.73 0.00 0.00 4.68
1618 1644 7.439157 ACATCATTATATAAACATGTGCGCT 57.561 32.000 9.73 0.00 0.00 5.92
1619 1645 7.426456 GCTACATCATTATATAAACATGTGCGC 59.574 37.037 21.87 19.83 0.00 6.09
1620 1646 8.659491 AGCTACATCATTATATAAACATGTGCG 58.341 33.333 21.87 16.49 31.01 5.34
1621 1647 9.979270 GAGCTACATCATTATATAAACATGTGC 57.021 33.333 21.87 20.98 0.00 4.57
1635 1661 9.624373 AATTACTCATCAAAGAGCTACATCATT 57.376 29.630 0.00 0.00 39.26 2.57
1640 1666 9.719355 TGTTTAATTACTCATCAAAGAGCTACA 57.281 29.630 0.00 0.00 39.26 2.74
1644 1670 8.801913 GCAATGTTTAATTACTCATCAAAGAGC 58.198 33.333 0.00 0.00 39.26 4.09
1648 1674 9.979578 ACAAGCAATGTTTAATTACTCATCAAA 57.020 25.926 0.00 0.00 40.06 2.69
1682 1708 7.234355 ACCTAGTGTCAAAAGATCTTGGATTT 58.766 34.615 9.17 0.00 0.00 2.17
1684 1710 6.380079 ACCTAGTGTCAAAAGATCTTGGAT 57.620 37.500 9.17 0.00 0.00 3.41
1696 1722 8.107095 AGGCATTTCTATTTTACCTAGTGTCAA 58.893 33.333 0.00 0.00 0.00 3.18
1702 1728 8.725148 CAGCATAGGCATTTCTATTTTACCTAG 58.275 37.037 0.67 0.00 44.61 3.02
1714 1740 4.157656 TGGTTTGTACAGCATAGGCATTTC 59.842 41.667 0.67 0.00 44.61 2.17
1739 1782 6.089249 AGGGTAGAAATTCTTGTTGCTTTG 57.911 37.500 0.00 0.00 0.00 2.77
1848 1891 3.071892 ACGAACCTGGAGTAAACATTGGA 59.928 43.478 0.00 0.00 0.00 3.53
2247 2299 7.251994 GCGTATTCTCTATGAAGTCCGATATT 58.748 38.462 0.00 0.00 38.18 1.28
2268 2320 2.139917 GAATATGCAATGGACGGCGTA 58.860 47.619 14.74 0.00 36.09 4.42
2304 2356 3.576078 TGTGAGATGGTGGTTTTCAGT 57.424 42.857 0.00 0.00 0.00 3.41
2373 2432 5.381757 GGACATAGTGAGTACCATCTCTCT 58.618 45.833 0.00 0.00 40.11 3.10


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

AutoCloner maintained by Alex Coulton.