Multiple sequence alignment - TraesCS2A01G499100

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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 TraesCS2A01G499100 chr2A 100.000 2300 0 0 1 2300 729061062 729058763 0.000000e+00 4248
1 TraesCS2A01G499100 chr2A 88.968 562 40 5 1761 2300 75303695 75303134 0.000000e+00 675
2 TraesCS2A01G499100 chr2A 88.770 561 42 3 1761 2300 53451200 53451760 0.000000e+00 667
3 TraesCS2A01G499100 chr2A 86.455 347 40 6 191 533 729119930 729119587 7.760000e-100 374
4 TraesCS2A01G499100 chr2B 86.021 1445 119 54 203 1604 721726956 721725552 0.000000e+00 1472
5 TraesCS2A01G499100 chr2B 87.921 356 36 6 182 533 721902210 721901858 1.640000e-111 412
6 TraesCS2A01G499100 chr2B 85.119 168 18 6 1 166 721902358 721902196 5.080000e-37 165
7 TraesCS2A01G499100 chr2D 91.500 800 52 12 536 1327 594457009 594456218 0.000000e+00 1086
8 TraesCS2A01G499100 chr2D 93.554 543 24 8 1 538 594457624 594457088 0.000000e+00 798
9 TraesCS2A01G499100 chr2D 89.502 562 37 4 1760 2300 101695736 101696296 0.000000e+00 691
10 TraesCS2A01G499100 chr2D 88.968 562 39 5 1761 2300 567084569 567085129 0.000000e+00 673
11 TraesCS2A01G499100 chr2D 89.051 548 51 7 1761 2300 522887278 522886732 0.000000e+00 671
12 TraesCS2A01G499100 chr2D 82.909 275 23 19 1223 1485 594456228 594455966 2.300000e-55 226
13 TraesCS2A01G499100 chr2D 78.596 285 33 11 1502 1760 594455733 594455451 1.830000e-36 163
14 TraesCS2A01G499100 chr1D 90.792 543 41 7 1761 2300 100640974 100640438 0.000000e+00 717
15 TraesCS2A01G499100 chr1A 89.399 566 36 6 1757 2300 446514569 446514006 0.000000e+00 691
16 TraesCS2A01G499100 chr4D 89.046 566 39 5 1756 2300 482523734 482524297 0.000000e+00 680
17 TraesCS2A01G499100 chr7D 88.869 566 40 6 1756 2300 614643032 614642469 0.000000e+00 675
18 TraesCS2A01G499100 chr7D 88.434 562 41 5 1761 2300 579534897 579534338 0.000000e+00 656
19 TraesCS2A01G499100 chr3D 88.693 566 40 7 1756 2300 335847181 335847743 0.000000e+00 669
20 TraesCS2A01G499100 chr3D 88.770 561 41 4 1761 2300 483197131 483197690 0.000000e+00 667
21 TraesCS2A01G499100 chr3D 88.339 566 43 5 1756 2300 16644885 16645448 0.000000e+00 658
22 TraesCS2A01G499100 chr6A 88.277 563 43 6 1761 2300 616465267 616465829 0.000000e+00 652
23 TraesCS2A01G499100 chr6B 85.952 541 61 12 1761 2292 426457880 426458414 4.290000e-157 564
24 TraesCS2A01G499100 chr7A 85.870 276 18 6 1761 2015 500124565 500124290 8.100000e-70 274


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 TraesCS2A01G499100 chr2A 729058763 729061062 2299 True 4248.00 4248 100.00000 1 2300 1 chr2A.!!$R2 2299
1 TraesCS2A01G499100 chr2A 75303134 75303695 561 True 675.00 675 88.96800 1761 2300 1 chr2A.!!$R1 539
2 TraesCS2A01G499100 chr2A 53451200 53451760 560 False 667.00 667 88.77000 1761 2300 1 chr2A.!!$F1 539
3 TraesCS2A01G499100 chr2B 721725552 721726956 1404 True 1472.00 1472 86.02100 203 1604 1 chr2B.!!$R1 1401
4 TraesCS2A01G499100 chr2B 721901858 721902358 500 True 288.50 412 86.52000 1 533 2 chr2B.!!$R2 532
5 TraesCS2A01G499100 chr2D 101695736 101696296 560 False 691.00 691 89.50200 1760 2300 1 chr2D.!!$F1 540
6 TraesCS2A01G499100 chr2D 567084569 567085129 560 False 673.00 673 88.96800 1761 2300 1 chr2D.!!$F2 539
7 TraesCS2A01G499100 chr2D 522886732 522887278 546 True 671.00 671 89.05100 1761 2300 1 chr2D.!!$R1 539
8 TraesCS2A01G499100 chr2D 594455451 594457624 2173 True 568.25 1086 86.63975 1 1760 4 chr2D.!!$R2 1759
9 TraesCS2A01G499100 chr1D 100640438 100640974 536 True 717.00 717 90.79200 1761 2300 1 chr1D.!!$R1 539
10 TraesCS2A01G499100 chr1A 446514006 446514569 563 True 691.00 691 89.39900 1757 2300 1 chr1A.!!$R1 543
11 TraesCS2A01G499100 chr4D 482523734 482524297 563 False 680.00 680 89.04600 1756 2300 1 chr4D.!!$F1 544
12 TraesCS2A01G499100 chr7D 614642469 614643032 563 True 675.00 675 88.86900 1756 2300 1 chr7D.!!$R2 544
13 TraesCS2A01G499100 chr7D 579534338 579534897 559 True 656.00 656 88.43400 1761 2300 1 chr7D.!!$R1 539
14 TraesCS2A01G499100 chr3D 335847181 335847743 562 False 669.00 669 88.69300 1756 2300 1 chr3D.!!$F2 544
15 TraesCS2A01G499100 chr3D 483197131 483197690 559 False 667.00 667 88.77000 1761 2300 1 chr3D.!!$F3 539
16 TraesCS2A01G499100 chr3D 16644885 16645448 563 False 658.00 658 88.33900 1756 2300 1 chr3D.!!$F1 544
17 TraesCS2A01G499100 chr6A 616465267 616465829 562 False 652.00 652 88.27700 1761 2300 1 chr6A.!!$F1 539
18 TraesCS2A01G499100 chr6B 426457880 426458414 534 False 564.00 564 85.95200 1761 2292 1 chr6B.!!$F1 531


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
690 791 0.036105 TGCGTCGTCCTACTGGTAGA 60.036 55.0 9.11 0.0 35.21 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 2171 0.032267 GATGCGTAGGTACAGAGGCC 59.968 60.0 0.0 0.0 0.0 5.19 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
90 91 0.817654 TCAGACCATCCAGTACAGCG 59.182 55.000 0.00 0.00 0.00 5.18
108 109 3.385079 GCGCGACAGCTAAAATACTTT 57.615 42.857 12.10 0.00 42.32 2.66
109 110 3.743886 GCGCGACAGCTAAAATACTTTT 58.256 40.909 12.10 0.00 42.32 2.27
172 173 4.177026 CACGAAACCACAACATTTTTCCA 58.823 39.130 0.00 0.00 0.00 3.53
207 212 8.816640 AGAAACCACAACATTTAGCAAATTAG 57.183 30.769 0.00 0.00 0.00 1.73
268 273 8.734386 CAGTAAACAAGAGCAAATTCCTTCTAT 58.266 33.333 0.00 0.00 0.00 1.98
269 274 8.734386 AGTAAACAAGAGCAAATTCCTTCTATG 58.266 33.333 0.00 0.00 0.00 2.23
391 404 1.405526 GGCCTTCACGCTCTTATCACA 60.406 52.381 0.00 0.00 0.00 3.58
690 791 0.036105 TGCGTCGTCCTACTGGTAGA 60.036 55.000 9.11 0.00 35.21 2.59
724 828 0.036732 CTGGCTAACTTCCAGTGGCA 59.963 55.000 3.51 0.00 44.62 4.92
725 829 0.250727 TGGCTAACTTCCAGTGGCAC 60.251 55.000 10.29 10.29 32.12 5.01
785 892 1.361668 AAATCGCAGCAGGCTACACG 61.362 55.000 0.00 0.00 41.67 4.49
830 937 6.070194 TCCTCACCTACTTAATTTGCTAAGCT 60.070 38.462 0.00 0.00 32.97 3.74
834 941 8.482943 TCACCTACTTAATTTGCTAAGCTGATA 58.517 33.333 0.00 0.00 32.97 2.15
838 945 6.122277 ACTTAATTTGCTAAGCTGATAGCCA 58.878 36.000 13.59 1.53 46.19 4.75
904 1015 2.796593 GGTCACACAGCAAAGCAAATTC 59.203 45.455 0.00 0.00 0.00 2.17
946 1057 5.163602 CGAAAGATCCAACAGAGCTACTAGT 60.164 44.000 0.00 0.00 41.49 2.57
981 1092 1.005630 GCAGAGCCGAACAGAGTGT 60.006 57.895 0.00 0.00 0.00 3.55
1206 1327 2.318224 CATCAGGAAGGCGCTGATG 58.682 57.895 18.47 18.47 45.27 3.07
1209 1330 1.817099 CAGGAAGGCGCTGATGGAC 60.817 63.158 7.64 0.00 0.00 4.02
1308 1522 2.049063 GTTGCCTGACGCGAGACT 60.049 61.111 15.93 0.00 42.08 3.24
1377 1619 0.608130 CGATGTGGAGTCCTTGTCCA 59.392 55.000 11.33 0.00 42.06 4.02
1378 1620 1.404717 CGATGTGGAGTCCTTGTCCAG 60.405 57.143 11.33 0.00 45.00 3.86
1382 1624 1.067776 GTGGAGTCCTTGTCCAGTACG 60.068 57.143 11.33 0.00 45.00 3.67
1385 1627 0.113776 AGTCCTTGTCCAGTACGGGA 59.886 55.000 11.03 11.03 34.36 5.14
1390 1632 1.553248 CTTGTCCAGTACGGGATTGGA 59.447 52.381 18.11 7.36 41.48 3.53
1391 1633 1.191535 TGTCCAGTACGGGATTGGAG 58.808 55.000 18.11 0.00 44.17 3.86
1392 1634 1.192428 GTCCAGTACGGGATTGGAGT 58.808 55.000 18.11 0.00 44.17 3.85
1393 1635 1.553704 GTCCAGTACGGGATTGGAGTT 59.446 52.381 18.11 0.00 44.17 3.01
1394 1636 1.553248 TCCAGTACGGGATTGGAGTTG 59.447 52.381 11.03 0.00 38.96 3.16
1395 1637 1.406887 CCAGTACGGGATTGGAGTTGG 60.407 57.143 6.11 0.00 37.08 3.77
1396 1638 1.553248 CAGTACGGGATTGGAGTTGGA 59.447 52.381 0.00 0.00 0.00 3.53
1397 1639 1.831736 AGTACGGGATTGGAGTTGGAG 59.168 52.381 0.00 0.00 0.00 3.86
1398 1640 0.539986 TACGGGATTGGAGTTGGAGC 59.460 55.000 0.00 0.00 0.00 4.70
1399 1641 1.452108 CGGGATTGGAGTTGGAGCC 60.452 63.158 0.00 0.00 0.00 4.70
1400 1642 1.915078 CGGGATTGGAGTTGGAGCCT 61.915 60.000 0.00 0.00 0.00 4.58
1401 1643 0.332972 GGGATTGGAGTTGGAGCCTT 59.667 55.000 0.00 0.00 0.00 4.35
1402 1644 1.467920 GGATTGGAGTTGGAGCCTTG 58.532 55.000 0.00 0.00 0.00 3.61
1403 1645 1.467920 GATTGGAGTTGGAGCCTTGG 58.532 55.000 0.00 0.00 0.00 3.61
1404 1646 1.004745 GATTGGAGTTGGAGCCTTGGA 59.995 52.381 0.00 0.00 0.00 3.53
1405 1647 0.401738 TTGGAGTTGGAGCCTTGGAG 59.598 55.000 0.00 0.00 0.00 3.86
1406 1648 1.301293 GGAGTTGGAGCCTTGGAGG 59.699 63.158 0.00 0.00 38.80 4.30
1415 1657 2.276740 CCTTGGAGGCCATCACCC 59.723 66.667 5.01 0.00 31.53 4.61
1425 1667 1.625818 GGCCATCACCCAGTAGGATAG 59.374 57.143 0.00 0.00 39.89 2.08
1429 1671 3.833070 CCATCACCCAGTAGGATAGGTAC 59.167 52.174 0.00 0.00 39.89 3.34
1442 1684 5.395611 AGGATAGGTACTGGCTAGTTTAGG 58.604 45.833 8.46 0.00 41.52 2.69
1443 1685 5.103172 AGGATAGGTACTGGCTAGTTTAGGT 60.103 44.000 8.46 0.00 41.52 3.08
1447 1689 3.773667 GGTACTGGCTAGTTTAGGTTCCT 59.226 47.826 8.46 0.00 38.36 3.36
1485 1730 2.551287 CCCCGTGTAAACAACCAGATCA 60.551 50.000 0.00 0.00 0.00 2.92
1486 1731 3.142951 CCCGTGTAAACAACCAGATCAA 58.857 45.455 0.00 0.00 0.00 2.57
1487 1732 3.756434 CCCGTGTAAACAACCAGATCAAT 59.244 43.478 0.00 0.00 0.00 2.57
1488 1733 4.142687 CCCGTGTAAACAACCAGATCAATC 60.143 45.833 0.00 0.00 0.00 2.67
1490 1735 5.049060 CCGTGTAAACAACCAGATCAATCAA 60.049 40.000 0.00 0.00 0.00 2.57
1491 1736 6.349280 CCGTGTAAACAACCAGATCAATCAAT 60.349 38.462 0.00 0.00 0.00 2.57
1492 1737 6.742718 CGTGTAAACAACCAGATCAATCAATC 59.257 38.462 0.00 0.00 0.00 2.67
1493 1738 7.572910 CGTGTAAACAACCAGATCAATCAATCA 60.573 37.037 0.00 0.00 0.00 2.57
1494 1739 8.081633 GTGTAAACAACCAGATCAATCAATCAA 58.918 33.333 0.00 0.00 0.00 2.57
1495 1740 8.637099 TGTAAACAACCAGATCAATCAATCAAA 58.363 29.630 0.00 0.00 0.00 2.69
1496 1741 9.132521 GTAAACAACCAGATCAATCAATCAAAG 57.867 33.333 0.00 0.00 0.00 2.77
1497 1742 5.717119 ACAACCAGATCAATCAATCAAAGC 58.283 37.500 0.00 0.00 0.00 3.51
1498 1743 5.244402 ACAACCAGATCAATCAATCAAAGCA 59.756 36.000 0.00 0.00 0.00 3.91
1512 1980 9.768662 ATCAATCAAAGCAAATAATATTCCCAC 57.231 29.630 0.00 0.00 0.00 4.61
1516 1984 6.826231 TCAAAGCAAATAATATTCCCACGAGA 59.174 34.615 0.00 0.00 0.00 4.04
1519 1987 6.226787 AGCAAATAATATTCCCACGAGAGAG 58.773 40.000 0.00 0.00 0.00 3.20
1522 1990 3.992260 AATATTCCCACGAGAGAGACG 57.008 47.619 0.00 0.00 0.00 4.18
1526 1994 2.408241 CCCACGAGAGAGACGGTCC 61.408 68.421 4.14 0.00 34.93 4.46
1536 2004 1.078759 GAGACGGTCCTGTTGCGATG 61.079 60.000 4.14 0.00 0.00 3.84
1619 2112 4.337145 TCTAGTAGCTAGGCCTTGATAGC 58.663 47.826 19.07 17.52 43.85 2.97
1648 2141 0.798776 GCAGCTTGCGTATTGTGTCT 59.201 50.000 0.00 0.00 31.71 3.41
1649 2142 1.201965 GCAGCTTGCGTATTGTGTCTC 60.202 52.381 0.00 0.00 31.71 3.36
1650 2143 1.394917 CAGCTTGCGTATTGTGTCTCC 59.605 52.381 0.00 0.00 0.00 3.71
1651 2144 1.001974 AGCTTGCGTATTGTGTCTCCA 59.998 47.619 0.00 0.00 0.00 3.86
1653 2146 2.159653 GCTTGCGTATTGTGTCTCCAAG 60.160 50.000 0.00 0.00 33.32 3.61
1654 2147 3.325870 CTTGCGTATTGTGTCTCCAAGA 58.674 45.455 0.00 0.00 32.22 3.02
1656 2149 3.937814 TGCGTATTGTGTCTCCAAGAAT 58.062 40.909 0.00 0.00 0.00 2.40
1658 2151 5.483811 TGCGTATTGTGTCTCCAAGAATAA 58.516 37.500 0.00 0.00 0.00 1.40
1659 2152 6.112734 TGCGTATTGTGTCTCCAAGAATAAT 58.887 36.000 0.00 0.00 0.00 1.28
1660 2153 6.257849 TGCGTATTGTGTCTCCAAGAATAATC 59.742 38.462 0.00 0.00 0.00 1.75
1661 2154 6.562270 GCGTATTGTGTCTCCAAGAATAATCG 60.562 42.308 0.00 0.00 0.00 3.34
1662 2155 6.695713 CGTATTGTGTCTCCAAGAATAATCGA 59.304 38.462 0.00 0.00 0.00 3.59
1663 2156 7.382488 CGTATTGTGTCTCCAAGAATAATCGAT 59.618 37.037 0.00 0.00 0.00 3.59
1664 2157 7.721286 ATTGTGTCTCCAAGAATAATCGATC 57.279 36.000 0.00 0.00 0.00 3.69
1666 2159 6.639563 TGTGTCTCCAAGAATAATCGATCAA 58.360 36.000 0.00 0.00 0.00 2.57
1667 2160 7.275183 TGTGTCTCCAAGAATAATCGATCAAT 58.725 34.615 0.00 0.00 0.00 2.57
1669 2162 6.707608 TGTCTCCAAGAATAATCGATCAATGG 59.292 38.462 0.00 2.51 0.00 3.16
1670 2163 6.708054 GTCTCCAAGAATAATCGATCAATGGT 59.292 38.462 0.00 0.00 0.00 3.55
1671 2164 6.707608 TCTCCAAGAATAATCGATCAATGGTG 59.292 38.462 0.00 3.78 0.00 4.17
1672 2165 5.764686 TCCAAGAATAATCGATCAATGGTGG 59.235 40.000 0.00 3.63 0.00 4.61
1673 2166 5.048504 CCAAGAATAATCGATCAATGGTGGG 60.049 44.000 0.00 0.00 0.00 4.61
1674 2167 4.074970 AGAATAATCGATCAATGGTGGGC 58.925 43.478 0.00 0.00 0.00 5.36
1675 2168 1.877637 TAATCGATCAATGGTGGGCG 58.122 50.000 0.00 0.00 0.00 6.13
1676 2169 0.819259 AATCGATCAATGGTGGGCGG 60.819 55.000 0.00 0.00 0.00 6.13
1677 2170 1.983119 ATCGATCAATGGTGGGCGGT 61.983 55.000 0.00 0.00 0.00 5.68
1678 2171 2.472059 CGATCAATGGTGGGCGGTG 61.472 63.158 0.00 0.00 0.00 4.94
1679 2172 2.044053 ATCAATGGTGGGCGGTGG 60.044 61.111 0.00 0.00 0.00 4.61
1693 2186 1.814527 GGTGGCCTCTGTACCTACG 59.185 63.158 3.32 0.00 0.00 3.51
1701 2194 0.661552 TCTGTACCTACGCATCTCGC 59.338 55.000 0.00 0.00 43.23 5.03
1740 2233 1.267732 CCGTAGTACGTACTTGAGCCG 60.268 57.143 31.58 22.73 40.58 5.52
1743 2236 0.445436 AGTACGTACTTGAGCCGACG 59.555 55.000 22.45 0.00 41.02 5.12
1747 2240 0.860618 CGTACTTGAGCCGACGTAGC 60.861 60.000 1.85 1.85 0.00 3.58
1750 2243 0.450983 ACTTGAGCCGACGTAGCTAC 59.549 55.000 14.19 14.19 41.75 3.58
1911 2425 2.764010 GGTTTCTGGTTTCCCTTTGTGT 59.236 45.455 0.00 0.00 0.00 3.72
2029 2560 1.270550 TCGTGGAGTACCGTTCTTTCC 59.729 52.381 0.00 0.00 39.42 3.13
2048 2579 0.167470 CTTGCCGTCGTCTTCGTCTA 59.833 55.000 0.00 0.00 38.33 2.59
2053 2584 0.301088 CGTCGTCTTCGTCTATCGCT 59.699 55.000 0.00 0.00 39.67 4.93
2068 2599 2.980233 GCTGCCGCCACTCTTGTT 60.980 61.111 0.00 0.00 0.00 2.83
2120 2651 2.653115 GCTTGTTGCCTGCCCTTC 59.347 61.111 0.00 0.00 35.15 3.46
2122 2653 1.228675 CTTGTTGCCTGCCCTTCCT 60.229 57.895 0.00 0.00 0.00 3.36
2137 2669 3.587506 CCCTTCCTTGGTCCTTCTTTAGA 59.412 47.826 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.960689 TGATGATTGGAGCCATGCATG 59.039 47.619 20.19 20.19 0.00 4.06
72 73 0.807667 GCGCTGTACTGGATGGTCTG 60.808 60.000 0.00 0.00 0.00 3.51
191 196 9.573133 GTGATTAGTGCTAATTTGCTAAATGTT 57.427 29.630 12.99 0.00 36.02 2.71
200 205 7.290857 AGTACGTGTGATTAGTGCTAATTTG 57.709 36.000 0.00 0.00 36.02 2.32
207 212 5.389516 CCTTTCAAGTACGTGTGATTAGTGC 60.390 44.000 8.68 0.00 0.00 4.40
268 273 1.668826 AAGGTTATCTGGACCCTGCA 58.331 50.000 0.00 0.00 37.93 4.41
269 274 4.439253 AATAAGGTTATCTGGACCCTGC 57.561 45.455 0.00 0.00 37.93 4.85
305 314 1.763770 GGGGCATGTCCTATGAGGG 59.236 63.158 17.62 0.00 35.59 4.30
422 435 6.529220 ACATGGCCAATTGCTTAACTTTAAA 58.471 32.000 10.96 0.00 40.92 1.52
676 777 1.134560 GCAAGGTCTACCAGTAGGACG 59.865 57.143 5.04 0.00 38.89 4.79
679 780 2.362717 GCTAGCAAGGTCTACCAGTAGG 59.637 54.545 10.63 0.00 38.89 3.18
722 826 0.378257 ATGGCGTGATGATTTCGTGC 59.622 50.000 0.00 0.00 0.00 5.34
724 828 2.022764 TGATGGCGTGATGATTTCGT 57.977 45.000 0.00 0.00 0.00 3.85
725 829 2.545106 TGATGATGGCGTGATGATTTCG 59.455 45.455 0.00 0.00 0.00 3.46
830 937 2.293170 CGTGAGAGAGAGTGGCTATCA 58.707 52.381 0.00 0.00 37.31 2.15
834 941 1.304052 AGCGTGAGAGAGAGTGGCT 60.304 57.895 0.00 0.00 0.00 4.75
838 945 1.366111 GAGCGAGCGTGAGAGAGAGT 61.366 60.000 0.00 0.00 0.00 3.24
904 1015 1.073964 CGAGTGGTGTGCAAGAGATG 58.926 55.000 0.00 0.00 0.00 2.90
956 1067 4.457603 ACTCTGTTCGGCTCTGCTATATAG 59.542 45.833 5.30 5.30 0.00 1.31
957 1068 4.216472 CACTCTGTTCGGCTCTGCTATATA 59.784 45.833 0.00 0.00 0.00 0.86
958 1069 3.005261 CACTCTGTTCGGCTCTGCTATAT 59.995 47.826 0.00 0.00 0.00 0.86
981 1092 3.196901 ACATGCCGAGAAATACACTACCA 59.803 43.478 0.00 0.00 0.00 3.25
1293 1507 4.056125 CCAGTCTCGCGTCAGGCA 62.056 66.667 5.77 0.00 43.84 4.75
1340 1554 0.993251 CGTCGTTACACGTGAAGCGA 60.993 55.000 25.01 22.72 43.14 4.93
1341 1555 0.993251 TCGTCGTTACACGTGAAGCG 60.993 55.000 25.01 20.90 43.14 4.68
1342 1556 1.057285 CATCGTCGTTACACGTGAAGC 59.943 52.381 25.01 10.06 43.14 3.86
1356 1594 1.404315 GGACAAGGACTCCACATCGTC 60.404 57.143 0.00 0.00 0.00 4.20
1361 1599 1.968493 GTACTGGACAAGGACTCCACA 59.032 52.381 0.00 0.00 36.71 4.17
1377 1619 1.831736 CTCCAACTCCAATCCCGTACT 59.168 52.381 0.00 0.00 0.00 2.73
1378 1620 1.742750 GCTCCAACTCCAATCCCGTAC 60.743 57.143 0.00 0.00 0.00 3.67
1382 1624 0.332972 AAGGCTCCAACTCCAATCCC 59.667 55.000 0.00 0.00 0.00 3.85
1385 1627 1.005215 CTCCAAGGCTCCAACTCCAAT 59.995 52.381 0.00 0.00 0.00 3.16
1398 1640 2.276740 GGGTGATGGCCTCCAAGG 59.723 66.667 3.32 0.00 36.95 3.61
1399 1641 1.077212 CTGGGTGATGGCCTCCAAG 60.077 63.158 3.32 0.39 36.95 3.61
1400 1642 0.548926 TACTGGGTGATGGCCTCCAA 60.549 55.000 3.32 0.00 36.95 3.53
1401 1643 0.982852 CTACTGGGTGATGGCCTCCA 60.983 60.000 3.32 0.00 38.19 3.86
1402 1644 1.700042 CCTACTGGGTGATGGCCTCC 61.700 65.000 3.32 0.99 0.00 4.30
1403 1645 0.691078 TCCTACTGGGTGATGGCCTC 60.691 60.000 3.32 0.00 36.25 4.70
1404 1646 0.029681 ATCCTACTGGGTGATGGCCT 60.030 55.000 3.32 0.00 36.25 5.19
1405 1647 1.625818 CTATCCTACTGGGTGATGGCC 59.374 57.143 0.00 0.00 36.25 5.36
1406 1648 1.625818 CCTATCCTACTGGGTGATGGC 59.374 57.143 0.00 0.00 36.25 4.40
1407 1649 2.977808 ACCTATCCTACTGGGTGATGG 58.022 52.381 0.00 0.00 36.25 3.51
1408 1650 4.524714 CAGTACCTATCCTACTGGGTGATG 59.475 50.000 0.00 0.00 38.20 3.07
1415 1657 4.988029 ACTAGCCAGTACCTATCCTACTG 58.012 47.826 0.00 0.00 40.54 2.74
1425 1667 3.773667 AGGAACCTAAACTAGCCAGTACC 59.226 47.826 0.00 0.00 33.48 3.34
1429 1671 9.708092 GTATAAATAGGAACCTAAACTAGCCAG 57.292 37.037 4.63 0.00 31.73 4.85
1442 1684 7.654923 CGGGGTTACAAGAGTATAAATAGGAAC 59.345 40.741 0.00 0.00 0.00 3.62
1443 1685 7.345392 ACGGGGTTACAAGAGTATAAATAGGAA 59.655 37.037 0.00 0.00 0.00 3.36
1447 1689 7.422465 ACACGGGGTTACAAGAGTATAAATA 57.578 36.000 0.00 0.00 0.00 1.40
1486 1731 9.768662 GTGGGAATATTATTTGCTTTGATTGAT 57.231 29.630 0.00 0.00 0.00 2.57
1487 1732 7.920151 CGTGGGAATATTATTTGCTTTGATTGA 59.080 33.333 0.00 0.00 0.00 2.57
1488 1733 7.920151 TCGTGGGAATATTATTTGCTTTGATTG 59.080 33.333 0.00 0.00 0.00 2.67
1490 1735 7.502226 TCTCGTGGGAATATTATTTGCTTTGAT 59.498 33.333 0.00 0.00 0.00 2.57
1491 1736 6.826231 TCTCGTGGGAATATTATTTGCTTTGA 59.174 34.615 0.00 0.00 0.00 2.69
1492 1737 7.012327 TCTCTCGTGGGAATATTATTTGCTTTG 59.988 37.037 0.00 0.00 0.00 2.77
1493 1738 7.054124 TCTCTCGTGGGAATATTATTTGCTTT 58.946 34.615 0.00 0.00 0.00 3.51
1494 1739 6.591935 TCTCTCGTGGGAATATTATTTGCTT 58.408 36.000 0.00 0.00 0.00 3.91
1495 1740 6.042093 TCTCTCTCGTGGGAATATTATTTGCT 59.958 38.462 0.00 0.00 0.00 3.91
1496 1741 6.146347 GTCTCTCTCGTGGGAATATTATTTGC 59.854 42.308 0.00 0.00 0.00 3.68
1497 1742 6.363626 CGTCTCTCTCGTGGGAATATTATTTG 59.636 42.308 0.00 0.00 0.00 2.32
1498 1743 6.448006 CGTCTCTCTCGTGGGAATATTATTT 58.552 40.000 0.00 0.00 0.00 1.40
1509 1977 1.377463 AGGACCGTCTCTCTCGTGG 60.377 63.158 0.00 0.00 0.00 4.94
1512 1980 0.169230 CAACAGGACCGTCTCTCTCG 59.831 60.000 0.00 0.00 0.00 4.04
1516 1984 1.251527 ATCGCAACAGGACCGTCTCT 61.252 55.000 0.00 0.00 0.00 3.10
1519 1987 2.740714 GCATCGCAACAGGACCGTC 61.741 63.158 0.00 0.00 0.00 4.79
1522 1990 3.667087 TTGCATCGCAACAGGACC 58.333 55.556 0.00 0.00 43.99 4.46
1604 2072 1.141858 ACCAAGCTATCAAGGCCTAGC 59.858 52.381 16.20 16.20 40.52 3.42
1605 2073 2.843701 CACCAAGCTATCAAGGCCTAG 58.156 52.381 5.16 0.00 0.00 3.02
1606 2074 1.134098 GCACCAAGCTATCAAGGCCTA 60.134 52.381 5.16 0.00 41.15 3.93
1607 2075 0.394899 GCACCAAGCTATCAAGGCCT 60.395 55.000 0.00 0.00 41.15 5.19
1608 2076 2.110296 GCACCAAGCTATCAAGGCC 58.890 57.895 0.00 0.00 41.15 5.19
1641 2134 6.639563 TGATCGATTATTCTTGGAGACACAA 58.360 36.000 0.00 0.00 42.67 3.33
1645 2138 6.708054 ACCATTGATCGATTATTCTTGGAGAC 59.292 38.462 0.00 0.00 0.00 3.36
1648 2141 5.764686 CCACCATTGATCGATTATTCTTGGA 59.235 40.000 0.00 0.00 0.00 3.53
1649 2142 5.048504 CCCACCATTGATCGATTATTCTTGG 60.049 44.000 0.00 3.33 0.00 3.61
1650 2143 5.563475 GCCCACCATTGATCGATTATTCTTG 60.563 44.000 0.00 0.00 0.00 3.02
1651 2144 4.520492 GCCCACCATTGATCGATTATTCTT 59.480 41.667 0.00 0.00 0.00 2.52
1653 2146 3.120199 CGCCCACCATTGATCGATTATTC 60.120 47.826 0.00 0.00 0.00 1.75
1654 2147 2.813754 CGCCCACCATTGATCGATTATT 59.186 45.455 0.00 0.00 0.00 1.40
1656 2149 1.542328 CCGCCCACCATTGATCGATTA 60.542 52.381 0.00 0.00 0.00 1.75
1658 2151 1.227943 CCGCCCACCATTGATCGAT 60.228 57.895 0.00 0.00 0.00 3.59
1659 2152 2.189257 CCGCCCACCATTGATCGA 59.811 61.111 0.00 0.00 0.00 3.59
1660 2153 2.124736 ACCGCCCACCATTGATCG 60.125 61.111 0.00 0.00 0.00 3.69
1661 2154 2.120909 CCACCGCCCACCATTGATC 61.121 63.158 0.00 0.00 0.00 2.92
1662 2155 2.044053 CCACCGCCCACCATTGAT 60.044 61.111 0.00 0.00 0.00 2.57
1673 2166 2.056223 TAGGTACAGAGGCCACCGC 61.056 63.158 5.01 0.00 37.42 5.68
1674 2167 1.814527 GTAGGTACAGAGGCCACCG 59.185 63.158 5.01 0.00 37.42 4.94
1675 2168 1.814527 CGTAGGTACAGAGGCCACC 59.185 63.158 5.01 2.56 0.00 4.61
1676 2169 1.141234 GCGTAGGTACAGAGGCCAC 59.859 63.158 5.01 0.00 0.00 5.01
1677 2170 0.686441 ATGCGTAGGTACAGAGGCCA 60.686 55.000 5.01 0.00 0.00 5.36
1678 2171 0.032267 GATGCGTAGGTACAGAGGCC 59.968 60.000 0.00 0.00 0.00 5.19
1679 2172 1.001158 GAGATGCGTAGGTACAGAGGC 60.001 57.143 0.00 0.00 0.00 4.70
1693 2186 1.527311 GATTACTTTCCGGCGAGATGC 59.473 52.381 9.30 0.00 45.38 3.91
1729 2222 0.450983 AGCTACGTCGGCTCAAGTAC 59.549 55.000 9.69 0.00 34.70 2.73
1743 2236 1.089920 TCGGAGGAACACGTAGCTAC 58.910 55.000 14.19 14.19 33.03 3.58
1747 2240 2.921754 GTGATTTCGGAGGAACACGTAG 59.078 50.000 0.00 0.00 33.03 3.51
1750 2243 2.080286 AGTGATTTCGGAGGAACACG 57.920 50.000 0.00 0.00 35.46 4.49
1844 2337 0.247301 GCGCATCGAAAAAGTCTCCG 60.247 55.000 0.30 0.00 0.00 4.63
1981 2511 3.686016 GCCCACACCAGAGAGAAAATAA 58.314 45.455 0.00 0.00 0.00 1.40
1983 2513 1.611673 CGCCCACACCAGAGAGAAAAT 60.612 52.381 0.00 0.00 0.00 1.82
2017 2548 0.393820 ACGGCAAGGAAAGAACGGTA 59.606 50.000 0.00 0.00 0.00 4.02
2029 2560 0.167470 TAGACGAAGACGACGGCAAG 59.833 55.000 2.19 0.00 41.61 4.01
2048 2579 4.087892 AAGAGTGGCGGCAGCGAT 62.088 61.111 13.91 0.00 46.35 4.58
2053 2584 3.286751 GCAACAAGAGTGGCGGCA 61.287 61.111 7.97 7.97 34.42 5.69
2116 2647 4.287326 ACTCTAAAGAAGGACCAAGGAAGG 59.713 45.833 0.00 0.00 0.00 3.46
2120 2651 3.510360 TCGACTCTAAAGAAGGACCAAGG 59.490 47.826 0.00 0.00 0.00 3.61
2122 2653 3.257624 GGTCGACTCTAAAGAAGGACCAA 59.742 47.826 16.46 0.00 38.42 3.67



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

AutoCloner maintained by Alex Coulton.