Multiple sequence alignment - TraesCS2D01G375200

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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 TraesCS2D01G375200 chr2D 100.000 3195 0 0 1 3195 478875857 478872663 0.000000e+00 5901
1 TraesCS2D01G375200 chr2D 96.386 166 6 0 1565 1730 352876554 352876719 1.130000e-69 274
2 TraesCS2D01G375200 chr2B 93.522 1590 76 9 4 1588 561284776 561283209 0.000000e+00 2340
3 TraesCS2D01G375200 chr2B 95.129 698 25 3 1715 2406 561283114 561282420 0.000000e+00 1092
4 TraesCS2D01G375200 chr2B 91.211 512 16 5 2490 2998 561282410 561281925 0.000000e+00 669
5 TraesCS2D01G375200 chr2B 96.985 199 6 0 2997 3195 561281842 561281644 5.110000e-88 335
6 TraesCS2D01G375200 chr2A 92.502 1507 75 14 1723 3195 621566444 621564942 0.000000e+00 2122
7 TraesCS2D01G375200 chr2A 88.825 1575 118 27 4 1567 621567968 621566441 0.000000e+00 1881
8 TraesCS2D01G375200 chr3D 97.661 171 3 1 1557 1726 211947742 211947572 3.120000e-75 292
9 TraesCS2D01G375200 chr3D 97.516 161 4 0 1566 1726 536788497 536788337 3.140000e-70 276
10 TraesCS2D01G375200 chr6D 98.171 164 3 0 1565 1728 72143275 72143438 1.450000e-73 287
11 TraesCS2D01G375200 chr5D 98.160 163 3 0 1566 1728 476192534 476192372 5.220000e-73 285
12 TraesCS2D01G375200 chr5D 98.718 156 2 0 1566 1721 552059769 552059924 8.730000e-71 278
13 TraesCS2D01G375200 chr4D 97.561 164 4 0 1564 1727 38450778 38450615 6.750000e-72 281
14 TraesCS2D01G375200 chr1B 97.531 162 4 0 1565 1726 626072057 626071896 8.730000e-71 278
15 TraesCS2D01G375200 chr5B 91.935 186 11 4 1545 1727 409866823 409867007 1.140000e-64 257


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 TraesCS2D01G375200 chr2D 478872663 478875857 3194 True 5901.0 5901 100.00000 1 3195 1 chr2D.!!$R1 3194
1 TraesCS2D01G375200 chr2B 561281644 561284776 3132 True 1109.0 2340 94.21175 4 3195 4 chr2B.!!$R1 3191
2 TraesCS2D01G375200 chr2A 621564942 621567968 3026 True 2001.5 2122 90.66350 4 3195 2 chr2A.!!$R1 3191


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
462 466 0.035317 TGATCTTTCGTGCTGCCTGT 59.965 50.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 2254 0.944386 TGCTTCCAAGAACTGCGAAC 59.056 50.0 0.0 0.0 0.0 3.95 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
80 81 2.237392 CCTAAAACTACAGCTGGGCTCT 59.763 50.000 19.93 0.00 36.40 4.09
81 82 2.959465 AAAACTACAGCTGGGCTCTT 57.041 45.000 19.93 2.68 36.40 2.85
82 83 2.481289 AAACTACAGCTGGGCTCTTC 57.519 50.000 19.93 0.00 36.40 2.87
83 84 0.615850 AACTACAGCTGGGCTCTTCC 59.384 55.000 19.93 0.00 36.40 3.46
84 85 0.545309 ACTACAGCTGGGCTCTTCCA 60.545 55.000 19.93 0.00 36.40 3.53
206 209 2.167861 CCGAGCTTTAGCAGGCGAC 61.168 63.158 4.33 0.00 45.16 5.19
462 466 0.035317 TGATCTTTCGTGCTGCCTGT 59.965 50.000 0.00 0.00 0.00 4.00
466 470 0.040958 CTTTCGTGCTGCCTGTTCAC 60.041 55.000 0.00 0.00 0.00 3.18
476 480 3.492011 GCTGCCTGTTCACTGAATTTTTG 59.508 43.478 0.00 0.00 0.00 2.44
502 506 7.572523 TCTTTTCCTGCGAATTGATGAATAT 57.427 32.000 0.00 0.00 0.00 1.28
563 570 4.157472 TGTTGAGTTGTTGTCATTGCTTGA 59.843 37.500 0.00 0.00 0.00 3.02
667 674 3.181483 CCTGTCTGCAATTTCTTATGGCC 60.181 47.826 0.00 0.00 0.00 5.36
699 706 2.302260 CACCTCTCTTGCTCTCCGATA 58.698 52.381 0.00 0.00 0.00 2.92
847 854 1.443802 GACACCTGCTGCTTCCTTAC 58.556 55.000 0.00 0.00 0.00 2.34
881 888 4.133078 CAGCAGTTTCCTTTCACTTCTCT 58.867 43.478 0.00 0.00 0.00 3.10
919 926 3.053095 TCCCCTCGTTCCTGAATACTACT 60.053 47.826 0.00 0.00 0.00 2.57
923 930 5.508153 CCCTCGTTCCTGAATACTACTCATG 60.508 48.000 0.00 0.00 0.00 3.07
928 935 6.584184 CGTTCCTGAATACTACTCATGCTATG 59.416 42.308 0.00 0.00 0.00 2.23
968 976 7.693969 AGGTTTTGATCTTTCCATACAGAAG 57.306 36.000 0.00 0.00 0.00 2.85
974 982 3.437213 TCTTTCCATACAGAAGTCGGGA 58.563 45.455 0.00 0.00 0.00 5.14
1018 1026 2.423538 CCGATGGATTTTGGGACTGAAC 59.576 50.000 0.00 0.00 0.00 3.18
1256 1264 2.768527 ACTTCATGGACGAGGTGATGAT 59.231 45.455 0.00 0.00 0.00 2.45
1258 1266 3.912496 TCATGGACGAGGTGATGATTT 57.088 42.857 0.00 0.00 0.00 2.17
1261 1269 3.251479 TGGACGAGGTGATGATTTCTG 57.749 47.619 0.00 0.00 0.00 3.02
1279 1287 2.158667 TCTGTCTTCCCCTTGTTTGGTC 60.159 50.000 0.00 0.00 0.00 4.02
1280 1288 1.566703 TGTCTTCCCCTTGTTTGGTCA 59.433 47.619 0.00 0.00 0.00 4.02
1281 1289 2.024846 TGTCTTCCCCTTGTTTGGTCAA 60.025 45.455 0.00 0.00 0.00 3.18
1295 1303 1.566018 GGTCAACAACCTTCGGCTCG 61.566 60.000 0.00 0.00 45.45 5.03
1317 1325 3.088194 AGCATGCCTTATTTCATTGCG 57.912 42.857 15.66 0.00 0.00 4.85
1339 1347 5.670097 CGAATTCACATGACGAATCATACC 58.330 41.667 13.15 3.85 44.13 2.73
1356 1364 7.914427 ATCATACCTACACAAGTTATCAGGA 57.086 36.000 0.00 0.00 0.00 3.86
1365 1373 5.882557 ACACAAGTTATCAGGATTCATGGAC 59.117 40.000 0.00 0.00 0.00 4.02
1389 1397 5.745294 CGCCCTTGATTATCAAATTTCACAG 59.255 40.000 9.05 0.00 35.73 3.66
1441 1453 3.876914 TGCAATTGCGTCCTAATAAGAGG 59.123 43.478 24.58 0.00 45.83 3.69
1552 1565 7.763528 CCTATGTGGACTATTCTGATCTTATGC 59.236 40.741 0.00 0.00 38.35 3.14
1577 1590 5.079643 TGTTTAGTAAGTACTCCCTCCGTT 58.920 41.667 0.00 0.00 37.73 4.44
1579 1592 2.732763 AGTAAGTACTCCCTCCGTTCC 58.267 52.381 0.00 0.00 0.00 3.62
1580 1593 2.311243 AGTAAGTACTCCCTCCGTTCCT 59.689 50.000 0.00 0.00 0.00 3.36
1586 1599 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
1587 1600 6.856757 AGTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
1588 1601 7.300658 AGTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
1592 1605 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1594 1607 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
1595 1608 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
1596 1609 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
1612 1625 8.567285 AAGTCTTTGTAGAGGTTTCATTATGG 57.433 34.615 0.00 0.00 0.00 2.74
1613 1626 7.918076 AGTCTTTGTAGAGGTTTCATTATGGA 58.082 34.615 0.00 0.00 0.00 3.41
1614 1627 7.824779 AGTCTTTGTAGAGGTTTCATTATGGAC 59.175 37.037 0.00 0.00 0.00 4.02
1615 1628 7.824779 GTCTTTGTAGAGGTTTCATTATGGACT 59.175 37.037 0.00 0.00 0.00 3.85
1616 1629 9.042450 TCTTTGTAGAGGTTTCATTATGGACTA 57.958 33.333 0.00 0.00 0.00 2.59
1617 1630 9.099454 CTTTGTAGAGGTTTCATTATGGACTAC 57.901 37.037 0.00 0.00 0.00 2.73
1618 1631 7.727578 TGTAGAGGTTTCATTATGGACTACA 57.272 36.000 0.00 0.00 36.46 2.74
1619 1632 8.319057 TGTAGAGGTTTCATTATGGACTACAT 57.681 34.615 0.00 0.00 43.68 2.29
1620 1633 9.429109 TGTAGAGGTTTCATTATGGACTACATA 57.571 33.333 0.00 0.00 41.03 2.29
1621 1634 9.694137 GTAGAGGTTTCATTATGGACTACATAC 57.306 37.037 0.00 0.00 41.61 2.39
1622 1635 7.434492 AGAGGTTTCATTATGGACTACATACG 58.566 38.462 0.00 0.00 41.61 3.06
1623 1636 6.522054 AGGTTTCATTATGGACTACATACGG 58.478 40.000 0.00 0.00 41.61 4.02
1624 1637 6.325545 AGGTTTCATTATGGACTACATACGGA 59.674 38.462 0.00 0.00 41.61 4.69
1625 1638 6.645415 GGTTTCATTATGGACTACATACGGAG 59.355 42.308 0.00 0.00 41.61 4.63
1626 1639 5.386958 TCATTATGGACTACATACGGAGC 57.613 43.478 0.00 0.00 41.61 4.70
1627 1640 4.830600 TCATTATGGACTACATACGGAGCA 59.169 41.667 0.00 0.00 41.61 4.26
1628 1641 5.303333 TCATTATGGACTACATACGGAGCAA 59.697 40.000 0.00 0.00 41.61 3.91
1629 1642 5.601583 TTATGGACTACATACGGAGCAAA 57.398 39.130 0.00 0.00 41.61 3.68
1630 1643 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
1631 1644 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
1632 1645 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
1633 1646 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
1634 1647 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
1637 1650 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
1643 1656 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
1644 1657 4.872691 CGGAGCAAAATGAGTGAATCTACT 59.127 41.667 0.00 0.00 0.00 2.57
1646 1659 6.456181 CGGAGCAAAATGAGTGAATCTACTTC 60.456 42.308 0.00 0.00 0.00 3.01
1649 1662 9.155975 GAGCAAAATGAGTGAATCTACTTCTAA 57.844 33.333 0.00 0.00 34.75 2.10
1650 1663 9.507329 AGCAAAATGAGTGAATCTACTTCTAAA 57.493 29.630 0.00 0.00 34.75 1.85
1655 1668 9.453572 AATGAGTGAATCTACTTCTAAAATGCA 57.546 29.630 0.00 0.00 34.75 3.96
1657 1670 9.102757 TGAGTGAATCTACTTCTAAAATGCATC 57.897 33.333 0.00 0.00 34.75 3.91
1676 1689 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
1677 1690 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
1678 1691 7.093509 TGCATCTATATACATCCGTATGTGGTT 60.094 37.037 3.56 0.00 45.99 3.67
1679 1692 7.435488 GCATCTATATACATCCGTATGTGGTTC 59.565 40.741 3.56 0.00 45.99 3.62
1680 1693 8.466798 CATCTATATACATCCGTATGTGGTTCA 58.533 37.037 3.56 0.00 45.99 3.18
1682 1695 9.689501 TCTATATACATCCGTATGTGGTTCATA 57.310 33.333 3.56 0.00 45.99 2.15
1683 1696 9.952188 CTATATACATCCGTATGTGGTTCATAG 57.048 37.037 3.56 0.80 45.99 2.23
1684 1697 6.665992 ATACATCCGTATGTGGTTCATAGT 57.334 37.500 3.56 0.00 45.99 2.12
1685 1698 4.693283 ACATCCGTATGTGGTTCATAGTG 58.307 43.478 0.00 0.00 44.79 2.74
1686 1699 4.404394 ACATCCGTATGTGGTTCATAGTGA 59.596 41.667 0.00 0.00 44.79 3.41
1687 1700 5.105106 ACATCCGTATGTGGTTCATAGTGAA 60.105 40.000 0.00 0.00 44.79 3.18
1689 1702 5.984725 TCCGTATGTGGTTCATAGTGAAAT 58.015 37.500 0.00 0.00 38.22 2.17
1690 1703 6.046593 TCCGTATGTGGTTCATAGTGAAATC 58.953 40.000 0.00 0.00 38.22 2.17
1691 1704 6.049149 CCGTATGTGGTTCATAGTGAAATCT 58.951 40.000 0.00 0.00 38.22 2.40
1692 1705 6.201044 CCGTATGTGGTTCATAGTGAAATCTC 59.799 42.308 0.00 0.00 38.22 2.75
1695 1708 9.250624 GTATGTGGTTCATAGTGAAATCTCTAC 57.749 37.037 0.00 0.00 38.22 2.59
1696 1709 7.239763 TGTGGTTCATAGTGAAATCTCTACA 57.760 36.000 0.00 0.00 38.22 2.74
1697 1710 7.676004 TGTGGTTCATAGTGAAATCTCTACAA 58.324 34.615 0.00 0.00 38.22 2.41
1698 1711 8.154203 TGTGGTTCATAGTGAAATCTCTACAAA 58.846 33.333 0.00 0.00 38.22 2.83
1699 1712 8.660373 GTGGTTCATAGTGAAATCTCTACAAAG 58.340 37.037 0.00 0.00 38.22 2.77
1700 1713 8.593679 TGGTTCATAGTGAAATCTCTACAAAGA 58.406 33.333 0.00 0.00 38.22 2.52
1701 1714 8.874816 GGTTCATAGTGAAATCTCTACAAAGAC 58.125 37.037 0.00 0.00 38.22 3.01
1702 1715 9.646427 GTTCATAGTGAAATCTCTACAAAGACT 57.354 33.333 0.00 0.00 38.22 3.24
1798 1811 0.321298 TCCCCACTTAAGCAAGTCGC 60.321 55.000 1.29 0.00 43.30 5.19
1813 1826 1.954382 AGTCGCTTTCACCTTTTTCCC 59.046 47.619 0.00 0.00 0.00 3.97
1866 1879 0.674581 TCATGACTGGGCTTTCGCTG 60.675 55.000 0.00 0.00 36.09 5.18
1890 1903 4.889832 AGAGTTCAAAGTGCTTGTTCAG 57.110 40.909 0.00 0.00 36.34 3.02
1920 1933 2.540265 AGGAACTCAGTCAAGTGCAG 57.460 50.000 0.00 0.00 0.00 4.41
2040 2053 4.580167 TCTGGGCAATTTAGCATGATGTAC 59.420 41.667 0.00 0.00 35.83 2.90
2233 2254 3.454082 AGAAAGCTGTAAGATCTGGGAGG 59.546 47.826 0.00 0.00 34.07 4.30
2308 2347 1.774254 CCAACATGAGGGGCCTATGTA 59.226 52.381 17.45 0.00 34.18 2.29
2337 2376 0.947180 TCGTTAAACGGCTGTGGAGC 60.947 55.000 0.00 0.00 42.81 4.70
2346 2385 2.042831 GCTGTGGAGCCGAAGCAAT 61.043 57.895 8.01 0.00 43.56 3.56
2463 2503 2.615747 GGTAAAAGACCTCCTGGAGTGC 60.616 54.545 21.70 13.00 45.89 4.40
2539 2582 2.412525 CTTGCGTGCAAGTTGGCA 59.587 55.556 23.06 3.02 45.91 4.92
2641 2684 3.072915 TGTCTCCACCATGTGATTGAGTT 59.927 43.478 0.00 0.00 35.23 3.01
2642 2685 4.285775 TGTCTCCACCATGTGATTGAGTTA 59.714 41.667 0.00 0.00 35.23 2.24
2643 2686 5.045651 TGTCTCCACCATGTGATTGAGTTAT 60.046 40.000 0.00 0.00 35.23 1.89
2644 2687 5.882557 GTCTCCACCATGTGATTGAGTTATT 59.117 40.000 0.00 0.00 35.23 1.40
2645 2688 7.047891 GTCTCCACCATGTGATTGAGTTATTA 58.952 38.462 0.00 0.00 35.23 0.98
2646 2689 7.716998 GTCTCCACCATGTGATTGAGTTATTAT 59.283 37.037 0.00 0.00 35.23 1.28
2647 2690 8.274322 TCTCCACCATGTGATTGAGTTATTATT 58.726 33.333 0.00 0.00 35.23 1.40
2648 2691 9.559732 CTCCACCATGTGATTGAGTTATTATTA 57.440 33.333 0.00 0.00 35.23 0.98
2897 2965 8.497554 GTTTGATCTCTCATCTATTCTGCATTC 58.502 37.037 0.00 0.00 0.00 2.67
2924 2992 8.801299 CAGTAGATCTATGTCAACCTATGTCAT 58.199 37.037 5.57 0.00 40.27 3.06
3052 3204 1.207488 TGGGGTAATGCTGTGAGGCT 61.207 55.000 0.00 0.00 0.00 4.58
3094 3246 2.241941 TGGCACAAGATACCACATGGAT 59.758 45.455 4.53 0.00 34.98 3.41
3157 3309 9.477484 GAGTTTCAACTTAAGACACTCTTATGA 57.523 33.333 10.09 2.34 38.60 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.056005 AGATGTAATTTCTATTGCTATTGCGAA 57.944 29.630 0.00 0.00 43.34 4.70
1 2 8.498358 CAGATGTAATTTCTATTGCTATTGCGA 58.502 33.333 0.00 0.00 43.34 5.10
2 3 8.498358 TCAGATGTAATTTCTATTGCTATTGCG 58.502 33.333 0.00 0.00 43.34 4.85
80 81 1.681666 CTGAAGAGCCCAGCTGGAA 59.318 57.895 34.91 9.01 39.88 3.53
81 82 2.296365 CCTGAAGAGCCCAGCTGGA 61.296 63.158 34.91 11.29 39.88 3.86
82 83 2.271497 CCTGAAGAGCCCAGCTGG 59.729 66.667 26.87 26.87 39.88 4.85
83 84 1.633915 ATCCCTGAAGAGCCCAGCTG 61.634 60.000 6.78 6.78 39.88 4.24
84 85 0.030705 TATCCCTGAAGAGCCCAGCT 60.031 55.000 0.00 0.00 43.88 4.24
416 420 1.144936 GGAGTGGGCCAAGAGATCG 59.855 63.158 8.40 0.00 0.00 3.69
462 466 7.064490 GCAGGAAAAGAACAAAAATTCAGTGAA 59.936 33.333 8.27 8.27 0.00 3.18
466 470 5.748152 TCGCAGGAAAAGAACAAAAATTCAG 59.252 36.000 0.00 0.00 0.00 3.02
476 480 5.046910 TCATCAATTCGCAGGAAAAGAAC 57.953 39.130 0.00 0.00 35.40 3.01
502 506 7.675062 TGCCTTTTCCATTTTAGCAATAAGAA 58.325 30.769 0.00 0.00 0.00 2.52
541 545 4.671377 TCAAGCAATGACAACAACTCAAC 58.329 39.130 0.00 0.00 31.50 3.18
667 674 0.108233 GAGAGGTGGCAGCAGAGAAG 60.108 60.000 20.04 0.00 0.00 2.85
699 706 1.152694 TGCCTTGCAGCCTTGAAGT 60.153 52.632 0.00 0.00 33.32 3.01
804 811 5.288232 CGACAAGTGCATGAAAAAGACAAAA 59.712 36.000 0.00 0.00 0.00 2.44
847 854 3.190118 GGAAACTGCTGATTCTTGGACAG 59.810 47.826 12.22 0.00 35.14 3.51
881 888 1.573108 GGGAGGACACATGAAGGAGA 58.427 55.000 0.00 0.00 0.00 3.71
941 948 9.753674 TTCTGTATGGAAAGATCAAAACCTATT 57.246 29.630 0.00 0.00 0.00 1.73
958 965 1.137086 CTGGTCCCGACTTCTGTATGG 59.863 57.143 0.00 0.00 0.00 2.74
968 976 2.232298 CTGCTTCCTCTGGTCCCGAC 62.232 65.000 0.00 0.00 0.00 4.79
974 982 4.373156 AATTTGTACTGCTTCCTCTGGT 57.627 40.909 0.00 0.00 0.00 4.00
1018 1026 0.523072 CGGCAAACACATCCCTTCAG 59.477 55.000 0.00 0.00 0.00 3.02
1147 1155 3.388024 ACACGGCTGAGGTCAATATACAT 59.612 43.478 0.00 0.00 0.00 2.29
1256 1264 3.295973 CCAAACAAGGGGAAGACAGAAA 58.704 45.455 0.00 0.00 0.00 2.52
1258 1266 1.850345 ACCAAACAAGGGGAAGACAGA 59.150 47.619 0.00 0.00 0.00 3.41
1261 1269 2.358322 TGACCAAACAAGGGGAAGAC 57.642 50.000 0.00 0.00 0.00 3.01
1295 1303 3.488310 CGCAATGAAATAAGGCATGCTTC 59.512 43.478 18.92 13.28 0.00 3.86
1317 1325 6.851222 AGGTATGATTCGTCATGTGAATTC 57.149 37.500 14.25 0.00 36.24 2.17
1339 1347 7.225538 GTCCATGAATCCTGATAACTTGTGTAG 59.774 40.741 0.00 0.00 0.00 2.74
1356 1364 2.442236 AATCAAGGGCGTCCATGAAT 57.558 45.000 19.00 7.11 43.04 2.57
1365 1373 5.649557 TGTGAAATTTGATAATCAAGGGCG 58.350 37.500 0.00 0.00 37.70 6.13
1441 1453 6.591448 AGCAGGCAAAACTTTAAATAATCTGC 59.409 34.615 0.00 0.00 41.81 4.26
1552 1565 5.126707 ACGGAGGGAGTACTTACTAAACATG 59.873 44.000 0.00 0.00 36.50 3.21
1560 1573 2.732763 AGGAACGGAGGGAGTACTTAC 58.267 52.381 0.00 0.00 0.00 2.34
1586 1599 9.667107 CCATAATGAAACCTCTACAAAGACTTA 57.333 33.333 0.00 0.00 0.00 2.24
1587 1600 8.383175 TCCATAATGAAACCTCTACAAAGACTT 58.617 33.333 0.00 0.00 0.00 3.01
1588 1601 7.824779 GTCCATAATGAAACCTCTACAAAGACT 59.175 37.037 0.00 0.00 0.00 3.24
1592 1605 8.598916 TGTAGTCCATAATGAAACCTCTACAAA 58.401 33.333 0.00 0.00 34.46 2.83
1594 1607 7.727578 TGTAGTCCATAATGAAACCTCTACA 57.272 36.000 0.00 0.00 34.82 2.74
1595 1608 9.694137 GTATGTAGTCCATAATGAAACCTCTAC 57.306 37.037 0.00 0.00 37.77 2.59
1596 1609 8.573885 CGTATGTAGTCCATAATGAAACCTCTA 58.426 37.037 0.00 0.00 37.77 2.43
1598 1611 6.645415 CCGTATGTAGTCCATAATGAAACCTC 59.355 42.308 0.00 0.00 37.77 3.85
1599 1612 6.325545 TCCGTATGTAGTCCATAATGAAACCT 59.674 38.462 0.00 0.00 37.77 3.50
1601 1614 6.145696 GCTCCGTATGTAGTCCATAATGAAAC 59.854 42.308 0.00 0.00 37.77 2.78
1602 1615 6.183360 TGCTCCGTATGTAGTCCATAATGAAA 60.183 38.462 0.00 0.00 37.77 2.69
1604 1617 4.830600 TGCTCCGTATGTAGTCCATAATGA 59.169 41.667 0.00 0.00 37.77 2.57
1605 1618 5.134202 TGCTCCGTATGTAGTCCATAATG 57.866 43.478 0.00 0.00 37.77 1.90
1607 1620 5.601583 TTTGCTCCGTATGTAGTCCATAA 57.398 39.130 0.00 0.00 37.77 1.90
1608 1621 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
1609 1622 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
1610 1623 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
1612 1625 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
1613 1626 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
1614 1627 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
1615 1628 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
1616 1629 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
1617 1630 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
1618 1631 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
1619 1632 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
1620 1633 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
1621 1634 4.872691 AGTAGATTCACTCATTTTGCTCCG 59.127 41.667 0.00 0.00 0.00 4.63
1622 1635 6.597280 AGAAGTAGATTCACTCATTTTGCTCC 59.403 38.462 0.00 0.00 40.67 4.70
1623 1636 7.608308 AGAAGTAGATTCACTCATTTTGCTC 57.392 36.000 0.00 0.00 40.67 4.26
1624 1637 9.507329 TTTAGAAGTAGATTCACTCATTTTGCT 57.493 29.630 0.00 0.00 40.67 3.91
1629 1642 9.453572 TGCATTTTAGAAGTAGATTCACTCATT 57.546 29.630 0.00 0.00 40.67 2.57
1630 1643 9.624373 ATGCATTTTAGAAGTAGATTCACTCAT 57.376 29.630 0.00 0.00 40.67 2.90
1631 1644 9.102757 GATGCATTTTAGAAGTAGATTCACTCA 57.897 33.333 0.00 0.00 40.67 3.41
1632 1645 9.323985 AGATGCATTTTAGAAGTAGATTCACTC 57.676 33.333 0.00 0.00 40.67 3.51
1649 1662 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
1650 1663 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
1651 1664 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
1653 1666 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
1654 1667 8.466798 TGAACCACATACGGATGTATATAGATG 58.533 37.037 14.23 0.00 44.82 2.90
1655 1668 8.589701 TGAACCACATACGGATGTATATAGAT 57.410 34.615 14.23 0.00 44.82 1.98
1657 1670 9.952188 CTATGAACCACATACGGATGTATATAG 57.048 37.037 14.23 12.28 44.82 1.31
1660 1673 7.449086 TCACTATGAACCACATACGGATGTATA 59.551 37.037 14.23 6.48 44.82 1.47
1669 1682 9.250624 GTAGAGATTTCACTATGAACCACATAC 57.749 37.037 0.00 0.00 35.89 2.39
1671 1684 7.851228 TGTAGAGATTTCACTATGAACCACAT 58.149 34.615 0.00 0.00 35.89 3.21
1673 1686 8.547967 TTTGTAGAGATTTCACTATGAACCAC 57.452 34.615 0.00 0.00 35.89 4.16
1676 1689 9.646427 AGTCTTTGTAGAGATTTCACTATGAAC 57.354 33.333 0.00 0.00 35.89 3.18
1695 1708 8.827677 CCCTCCGTTTCTAAATATAAGTCTTTG 58.172 37.037 0.00 0.00 0.00 2.77
1696 1709 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
1697 1710 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
1698 1711 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
1699 1712 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
1700 1713 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
1701 1714 8.858094 ACTACTCCCTCCGTTTCTAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
1702 1715 8.773033 ACTACTCCCTCCGTTTCTAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
1703 1716 9.289782 GTACTACTCCCTCCGTTTCTAAATATA 57.710 37.037 0.00 0.00 0.00 0.86
1704 1717 7.781693 TGTACTACTCCCTCCGTTTCTAAATAT 59.218 37.037 0.00 0.00 0.00 1.28
1705 1718 7.118723 TGTACTACTCCCTCCGTTTCTAAATA 58.881 38.462 0.00 0.00 0.00 1.40
1706 1719 5.954150 TGTACTACTCCCTCCGTTTCTAAAT 59.046 40.000 0.00 0.00 0.00 1.40
1707 1720 5.324409 TGTACTACTCCCTCCGTTTCTAAA 58.676 41.667 0.00 0.00 0.00 1.85
1708 1721 4.922206 TGTACTACTCCCTCCGTTTCTAA 58.078 43.478 0.00 0.00 0.00 2.10
1709 1722 4.225942 TCTGTACTACTCCCTCCGTTTCTA 59.774 45.833 0.00 0.00 0.00 2.10
1710 1723 3.009916 TCTGTACTACTCCCTCCGTTTCT 59.990 47.826 0.00 0.00 0.00 2.52
1711 1724 3.350833 TCTGTACTACTCCCTCCGTTTC 58.649 50.000 0.00 0.00 0.00 2.78
1712 1725 3.446442 TCTGTACTACTCCCTCCGTTT 57.554 47.619 0.00 0.00 0.00 3.60
1713 1726 3.202595 AGATCTGTACTACTCCCTCCGTT 59.797 47.826 0.00 0.00 0.00 4.44
1798 1811 3.383505 AGGAAACGGGAAAAAGGTGAAAG 59.616 43.478 0.00 0.00 0.00 2.62
1813 1826 1.536462 CGCCAACGCAAAAGGAAACG 61.536 55.000 0.00 0.00 34.03 3.60
1866 1879 6.545504 TGAACAAGCACTTTGAACTCTATC 57.454 37.500 0.00 0.00 39.21 2.08
1890 1903 4.116238 GACTGAGTTCCTTATACTGCTGC 58.884 47.826 0.00 0.00 0.00 5.25
1920 1933 3.189495 GCAGAAAGCCAAAGAGGACTAAC 59.811 47.826 0.00 0.00 41.22 2.34
2140 2155 2.681706 CGAAGAACATGAGCTGTGTCT 58.318 47.619 0.00 0.00 38.39 3.41
2181 2196 1.522569 GCAGACTAATGGGACGGCT 59.477 57.895 0.00 0.00 0.00 5.52
2233 2254 0.944386 TGCTTCCAAGAACTGCGAAC 59.056 50.000 0.00 0.00 0.00 3.95
2308 2347 5.813672 ACAGCCGTTTAACGATATGTACATT 59.186 36.000 19.61 1.88 46.05 2.71
2337 2376 7.225538 AGACACTAATCATTTAGATTGCTTCGG 59.774 37.037 0.85 0.00 46.24 4.30
2346 2385 6.374333 GGCAAACCAGACACTAATCATTTAGA 59.626 38.462 0.03 0.00 36.08 2.10
2418 2458 3.593247 GCTAGACGCAAGCAACATG 57.407 52.632 0.00 0.00 45.62 3.21
2534 2577 2.208132 ATACCCAACGAACATGCCAA 57.792 45.000 0.00 0.00 0.00 4.52
2539 2582 3.275999 GCAAGGTATACCCAACGAACAT 58.724 45.455 18.65 0.00 36.42 2.71
2736 2804 1.426621 CGCATGTCTGAAGCGCAAT 59.573 52.632 11.47 0.00 45.14 3.56
2897 2965 7.231519 TGACATAGGTTGACATAGATCTACTGG 59.768 40.741 4.10 0.51 0.00 4.00
2924 2992 3.260632 TGCAATCGCCTGCTATTATCCTA 59.739 43.478 9.52 0.00 43.07 2.94
3017 3169 2.105993 ACCCCACTTCAACAAGGTAGAC 59.894 50.000 0.00 0.00 33.37 2.59
3052 3204 4.126437 CACGATATGGTGGAATAAGCACA 58.874 43.478 9.83 0.00 34.27 4.57
3084 3236 7.792736 TCCCTTTAGTATACTTATCCATGTGGT 59.207 37.037 11.40 0.00 36.34 4.16
3094 3246 9.496710 TGAGGATTGTTCCCTTTAGTATACTTA 57.503 33.333 11.40 0.00 43.76 2.24
3157 3309 1.981495 CCCTTTCAACTGGTCTCCTCT 59.019 52.381 0.00 0.00 0.00 3.69



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

AutoCloner maintained by Alex Coulton.