Multiple sequence alignment - TraesCS3D01G180900

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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 TraesCS3D01G180900 chr3D 100.000 2285 0 0 1 2285 163116052 163113768 0.000000e+00 4220.0
1 TraesCS3D01G180900 chr3D 86.267 1085 77 36 553 1603 162876479 162875433 0.000000e+00 1112.0
2 TraesCS3D01G180900 chr3D 87.612 557 54 9 1733 2285 495800735 495801280 1.150000e-177 632.0
3 TraesCS3D01G180900 chr3B 88.283 1246 64 36 438 1652 239896081 239894887 0.000000e+00 1417.0
4 TraesCS3D01G180900 chr3B 94.026 385 16 3 1 378 239897576 239897192 5.470000e-161 577.0
5 TraesCS3D01G180900 chr3B 95.238 42 2 0 370 411 239896122 239896081 1.460000e-07 67.6
6 TraesCS3D01G180900 chr3A 84.539 1216 86 39 499 1658 195190154 195188985 0.000000e+00 1110.0
7 TraesCS3D01G180900 chr3A 94.444 216 8 2 83 294 195445475 195445260 1.690000e-86 329.0
8 TraesCS3D01G180900 chr3A 94.891 137 7 0 284 420 195445245 195445109 4.940000e-52 215.0
9 TraesCS3D01G180900 chr2D 87.762 572 53 9 1719 2285 187620060 187619501 0.000000e+00 652.0
10 TraesCS3D01G180900 chr4D 86.723 595 57 9 1700 2285 431675309 431674728 1.910000e-180 641.0
11 TraesCS3D01G180900 chr4D 86.387 595 58 12 1700 2285 431734847 431734267 1.490000e-176 628.0
12 TraesCS3D01G180900 chr4D 86.218 595 60 10 1700 2285 431621947 431621366 1.930000e-175 625.0
13 TraesCS3D01G180900 chr4D 86.050 595 61 9 1700 2285 431556182 431555601 8.970000e-174 619.0
14 TraesCS3D01G180900 chr1D 86.610 590 60 6 1704 2285 343277103 343276525 3.200000e-178 634.0
15 TraesCS3D01G180900 chr1D 86.486 592 56 11 1704 2285 18805805 18806382 1.490000e-176 628.0
16 TraesCS3D01G180900 chr6D 86.341 593 54 16 1705 2285 351929267 351928690 2.490000e-174 621.0


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 TraesCS3D01G180900 chr3D 163113768 163116052 2284 True 4220.0 4220 100.000000 1 2285 1 chr3D.!!$R2 2284
1 TraesCS3D01G180900 chr3D 162875433 162876479 1046 True 1112.0 1112 86.267000 553 1603 1 chr3D.!!$R1 1050
2 TraesCS3D01G180900 chr3D 495800735 495801280 545 False 632.0 632 87.612000 1733 2285 1 chr3D.!!$F1 552
3 TraesCS3D01G180900 chr3B 239894887 239897576 2689 True 687.2 1417 92.515667 1 1652 3 chr3B.!!$R1 1651
4 TraesCS3D01G180900 chr3A 195188985 195190154 1169 True 1110.0 1110 84.539000 499 1658 1 chr3A.!!$R1 1159
5 TraesCS3D01G180900 chr2D 187619501 187620060 559 True 652.0 652 87.762000 1719 2285 1 chr2D.!!$R1 566
6 TraesCS3D01G180900 chr4D 431674728 431675309 581 True 641.0 641 86.723000 1700 2285 1 chr4D.!!$R3 585
7 TraesCS3D01G180900 chr4D 431734267 431734847 580 True 628.0 628 86.387000 1700 2285 1 chr4D.!!$R4 585
8 TraesCS3D01G180900 chr4D 431621366 431621947 581 True 625.0 625 86.218000 1700 2285 1 chr4D.!!$R2 585
9 TraesCS3D01G180900 chr4D 431555601 431556182 581 True 619.0 619 86.050000 1700 2285 1 chr4D.!!$R1 585
10 TraesCS3D01G180900 chr1D 343276525 343277103 578 True 634.0 634 86.610000 1704 2285 1 chr1D.!!$R1 581
11 TraesCS3D01G180900 chr1D 18805805 18806382 577 False 628.0 628 86.486000 1704 2285 1 chr1D.!!$F1 581
12 TraesCS3D01G180900 chr6D 351928690 351929267 577 True 621.0 621 86.341000 1705 2285 1 chr6D.!!$R1 580

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
574 1663 0.038892 GAAGCAACCACGACTACGGA 60.039 55.0 0.0 0.0 44.46 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 3254 0.325272 TTGCCATGTACCCGCAACTA 59.675 50.0 7.12 0.0 37.58 2.24 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
43 44 2.882876 CCGACGACCAACCGAGAT 59.117 61.111 0.00 0.00 0.00 2.75
122 123 4.826404 TCGGCCCGGTAGCTGCTA 62.826 66.667 1.90 5.02 39.10 3.49
124 125 2.031163 GGCCCGGTAGCTGCTATG 59.969 66.667 13.20 8.60 0.00 2.23
183 184 1.078848 GTCCAGATGCGGCTCACTT 60.079 57.895 0.00 0.00 0.00 3.16
323 330 2.488820 GAGGCGACACGTAGACCC 59.511 66.667 0.00 0.00 0.00 4.46
340 348 2.362889 CCTTCCATGTGCCCCCAC 60.363 66.667 0.00 0.00 42.40 4.61
367 375 3.334583 ACTCAAAGCGAGGCAAGATAA 57.665 42.857 0.00 0.00 46.98 1.75
397 1483 3.684103 TTTGTTTTCGCATCGTGTTCT 57.316 38.095 0.00 0.00 0.00 3.01
405 1491 1.133598 CGCATCGTGTTCTACTACCCA 59.866 52.381 0.00 0.00 0.00 4.51
411 1497 5.824904 TCGTGTTCTACTACCCAGAATAC 57.175 43.478 2.88 2.88 39.44 1.89
413 1499 5.573337 GTGTTCTACTACCCAGAATACGT 57.427 43.478 0.00 0.00 35.39 3.57
414 1500 5.338365 GTGTTCTACTACCCAGAATACGTG 58.662 45.833 0.00 0.00 35.39 4.49
415 1501 4.400251 TGTTCTACTACCCAGAATACGTGG 59.600 45.833 0.00 0.00 34.67 4.94
416 1502 4.508551 TCTACTACCCAGAATACGTGGA 57.491 45.455 0.00 0.00 37.23 4.02
417 1503 5.057843 TCTACTACCCAGAATACGTGGAT 57.942 43.478 0.00 0.00 37.23 3.41
418 1504 6.191657 TCTACTACCCAGAATACGTGGATA 57.808 41.667 0.00 0.00 37.23 2.59
419 1505 6.604171 TCTACTACCCAGAATACGTGGATAA 58.396 40.000 0.00 0.00 37.23 1.75
420 1506 7.062322 TCTACTACCCAGAATACGTGGATAAA 58.938 38.462 0.00 0.00 37.23 1.40
421 1507 5.910614 ACTACCCAGAATACGTGGATAAAC 58.089 41.667 0.00 0.00 37.23 2.01
422 1508 5.659971 ACTACCCAGAATACGTGGATAAACT 59.340 40.000 0.00 0.00 37.23 2.66
423 1509 6.835488 ACTACCCAGAATACGTGGATAAACTA 59.165 38.462 0.00 0.00 37.23 2.24
424 1510 5.910614 ACCCAGAATACGTGGATAAACTAC 58.089 41.667 0.00 0.00 37.23 2.73
425 1511 5.163374 ACCCAGAATACGTGGATAAACTACC 60.163 44.000 0.00 0.00 37.23 3.18
426 1512 5.295152 CCAGAATACGTGGATAAACTACCC 58.705 45.833 0.00 0.00 37.23 3.69
427 1513 5.070047 CCAGAATACGTGGATAAACTACCCT 59.930 44.000 0.00 0.00 37.23 4.34
428 1514 6.266103 CCAGAATACGTGGATAAACTACCCTA 59.734 42.308 0.00 0.00 37.23 3.53
429 1515 7.201938 CCAGAATACGTGGATAAACTACCCTAA 60.202 40.741 0.00 0.00 37.23 2.69
430 1516 8.199449 CAGAATACGTGGATAAACTACCCTAAA 58.801 37.037 0.00 0.00 0.00 1.85
431 1517 8.761689 AGAATACGTGGATAAACTACCCTAAAA 58.238 33.333 0.00 0.00 0.00 1.52
432 1518 9.382275 GAATACGTGGATAAACTACCCTAAAAA 57.618 33.333 0.00 0.00 0.00 1.94
458 1544 9.813446 AAAGAATACGTGGATAAACCTTACTAG 57.187 33.333 0.00 0.00 39.86 2.57
515 1603 5.004345 CCCTGAAAATTATTTTTACTGCGCG 59.996 40.000 0.00 0.00 35.20 6.86
570 1659 1.202440 ACAACGAAGCAACCACGACTA 60.202 47.619 0.00 0.00 0.00 2.59
571 1660 1.191647 CAACGAAGCAACCACGACTAC 59.808 52.381 0.00 0.00 0.00 2.73
573 1662 1.342082 CGAAGCAACCACGACTACGG 61.342 60.000 0.00 0.00 44.46 4.02
574 1663 0.038892 GAAGCAACCACGACTACGGA 60.039 55.000 0.00 0.00 44.46 4.69
579 1669 2.533266 CAACCACGACTACGGATTACC 58.467 52.381 0.00 0.00 44.46 2.85
834 1957 4.693525 CAAAACCCCGCGCCGTTC 62.694 66.667 0.00 0.00 0.00 3.95
848 1971 0.607217 CCGTTCCGCCCTTTTTACCT 60.607 55.000 0.00 0.00 0.00 3.08
882 2005 2.094338 CCCGTCCCTCTTTATATACGGC 60.094 54.545 6.20 0.00 46.42 5.68
885 2008 2.094338 GTCCCTCTTTATATACGGCCCG 60.094 54.545 0.00 0.00 0.00 6.13
907 2038 4.920112 CGTTCGCCCACACCACCA 62.920 66.667 0.00 0.00 0.00 4.17
908 2039 2.517402 GTTCGCCCACACCACCAA 60.517 61.111 0.00 0.00 0.00 3.67
909 2040 1.901464 GTTCGCCCACACCACCAAT 60.901 57.895 0.00 0.00 0.00 3.16
949 2080 3.052082 CCCACGTTGGAGCAGCAG 61.052 66.667 0.00 0.00 40.96 4.24
950 2081 3.730761 CCACGTTGGAGCAGCAGC 61.731 66.667 0.00 0.00 40.96 5.25
955 2086 2.981909 TTGGAGCAGCAGCAGCAC 60.982 61.111 12.92 5.55 45.49 4.40
989 2120 3.151710 CCCACCAGCCGTCCGATA 61.152 66.667 0.00 0.00 0.00 2.92
990 2121 2.727392 CCCACCAGCCGTCCGATAA 61.727 63.158 0.00 0.00 0.00 1.75
1005 2146 2.289072 CCGATAAACAGATCCGATGGCT 60.289 50.000 0.00 0.00 0.00 4.75
1287 2431 2.047655 TACGCACGGGCTTGAAGG 60.048 61.111 8.62 0.00 38.10 3.46
1345 2493 5.484715 AGGAAAACTGCTATGCTACGTAAA 58.515 37.500 0.00 0.00 0.00 2.01
1346 2494 5.935789 AGGAAAACTGCTATGCTACGTAAAA 59.064 36.000 0.00 0.00 0.00 1.52
1347 2504 6.092259 AGGAAAACTGCTATGCTACGTAAAAG 59.908 38.462 0.00 0.00 0.00 2.27
1354 2511 2.103537 TGCTACGTAAAAGGGGAAGC 57.896 50.000 0.00 0.00 0.00 3.86
1436 2595 1.788886 ACGACGCATCAATCATCATCG 59.211 47.619 0.00 0.00 0.00 3.84
1454 2613 3.942130 TCGTCGATCCTATACTACGGA 57.058 47.619 0.00 0.00 0.00 4.69
1494 2653 1.039068 TGGCTGTTTCCCATTGTGTG 58.961 50.000 0.00 0.00 0.00 3.82
1501 2660 0.743688 TTCCCATTGTGTGTGTGTGC 59.256 50.000 0.00 0.00 0.00 4.57
1546 2713 2.104792 TGGATGCCCTGCTATAGTGTTC 59.895 50.000 0.84 0.00 0.00 3.18
1547 2714 2.104792 GGATGCCCTGCTATAGTGTTCA 59.895 50.000 0.84 0.00 0.00 3.18
1606 2773 6.147581 GGCTTGTACCTTTTACTTTTACAGC 58.852 40.000 0.00 0.00 0.00 4.40
1643 2815 6.956047 ACGAAAGAATCTAGCGTTTTCTTTT 58.044 32.000 15.75 4.50 45.10 2.27
1644 2816 7.070183 ACGAAAGAATCTAGCGTTTTCTTTTC 58.930 34.615 15.75 10.69 45.10 2.29
1645 2817 6.520104 CGAAAGAATCTAGCGTTTTCTTTTCC 59.480 38.462 15.75 7.76 45.10 3.13
1646 2818 7.511959 AAAGAATCTAGCGTTTTCTTTTCCT 57.488 32.000 11.43 0.00 43.55 3.36
1647 2819 8.617290 AAAGAATCTAGCGTTTTCTTTTCCTA 57.383 30.769 11.43 0.00 43.55 2.94
1650 2822 8.504815 AGAATCTAGCGTTTTCTTTTCCTAAAC 58.495 33.333 0.00 0.00 0.00 2.01
1651 2823 7.739498 ATCTAGCGTTTTCTTTTCCTAAACA 57.261 32.000 0.00 0.00 32.67 2.83
1652 2824 6.951643 TCTAGCGTTTTCTTTTCCTAAACAC 58.048 36.000 0.00 0.00 32.67 3.32
1653 2825 5.570234 AGCGTTTTCTTTTCCTAAACACA 57.430 34.783 0.00 0.00 32.67 3.72
1654 2826 6.144078 AGCGTTTTCTTTTCCTAAACACAT 57.856 33.333 0.00 0.00 32.67 3.21
1655 2827 5.977129 AGCGTTTTCTTTTCCTAAACACATG 59.023 36.000 0.00 0.00 32.67 3.21
1656 2828 5.746721 GCGTTTTCTTTTCCTAAACACATGT 59.253 36.000 0.00 0.00 32.67 3.21
1657 2829 6.254804 GCGTTTTCTTTTCCTAAACACATGTT 59.745 34.615 0.00 0.00 40.50 2.71
1658 2830 7.432838 GCGTTTTCTTTTCCTAAACACATGTTA 59.567 33.333 0.00 0.00 37.25 2.41
1659 2831 9.291664 CGTTTTCTTTTCCTAAACACATGTTAA 57.708 29.630 0.00 0.00 37.25 2.01
1672 2844 8.970691 AAACACATGTTAAGTATTGAATCTGC 57.029 30.769 0.00 0.00 37.25 4.26
1673 2845 7.686438 ACACATGTTAAGTATTGAATCTGCA 57.314 32.000 0.00 0.00 0.00 4.41
1674 2846 8.109705 ACACATGTTAAGTATTGAATCTGCAA 57.890 30.769 0.00 0.00 0.00 4.08
1675 2847 8.575589 ACACATGTTAAGTATTGAATCTGCAAA 58.424 29.630 0.00 0.00 0.00 3.68
1676 2848 8.853345 CACATGTTAAGTATTGAATCTGCAAAC 58.147 33.333 0.00 0.00 0.00 2.93
1677 2849 7.750458 ACATGTTAAGTATTGAATCTGCAAACG 59.250 33.333 0.00 0.00 0.00 3.60
1678 2850 7.428282 TGTTAAGTATTGAATCTGCAAACGA 57.572 32.000 0.00 0.00 0.00 3.85
1679 2851 7.866729 TGTTAAGTATTGAATCTGCAAACGAA 58.133 30.769 0.00 0.00 0.00 3.85
1680 2852 8.015087 TGTTAAGTATTGAATCTGCAAACGAAG 58.985 33.333 0.00 0.00 0.00 3.79
1681 2853 4.974591 AGTATTGAATCTGCAAACGAAGC 58.025 39.130 0.00 0.00 0.00 3.86
1682 2854 4.697352 AGTATTGAATCTGCAAACGAAGCT 59.303 37.500 0.00 0.00 0.00 3.74
1683 2855 3.542712 TTGAATCTGCAAACGAAGCTC 57.457 42.857 0.00 0.00 0.00 4.09
1684 2856 1.806542 TGAATCTGCAAACGAAGCTCC 59.193 47.619 0.00 0.00 0.00 4.70
1685 2857 2.079925 GAATCTGCAAACGAAGCTCCT 58.920 47.619 0.00 0.00 0.00 3.69
1686 2858 2.191128 ATCTGCAAACGAAGCTCCTT 57.809 45.000 0.00 0.00 0.00 3.36
1687 2859 1.512926 TCTGCAAACGAAGCTCCTTC 58.487 50.000 0.00 0.00 37.16 3.46
1688 2860 1.070758 TCTGCAAACGAAGCTCCTTCT 59.929 47.619 0.00 0.00 38.24 2.85
1689 2861 1.876156 CTGCAAACGAAGCTCCTTCTT 59.124 47.619 0.00 0.00 38.24 2.52
1690 2862 1.603802 TGCAAACGAAGCTCCTTCTTG 59.396 47.619 0.00 3.79 38.24 3.02
1691 2863 1.873591 GCAAACGAAGCTCCTTCTTGA 59.126 47.619 9.69 0.00 38.24 3.02
1692 2864 2.349912 GCAAACGAAGCTCCTTCTTGAC 60.350 50.000 9.69 1.32 38.24 3.18
1693 2865 3.134458 CAAACGAAGCTCCTTCTTGACT 58.866 45.455 0.00 0.00 38.24 3.41
1694 2866 4.307432 CAAACGAAGCTCCTTCTTGACTA 58.693 43.478 0.00 0.00 38.24 2.59
1695 2867 4.602340 AACGAAGCTCCTTCTTGACTAA 57.398 40.909 0.00 0.00 38.24 2.24
1696 2868 4.602340 ACGAAGCTCCTTCTTGACTAAA 57.398 40.909 0.00 0.00 38.24 1.85
1697 2869 5.153950 ACGAAGCTCCTTCTTGACTAAAT 57.846 39.130 0.00 0.00 38.24 1.40
1698 2870 5.552178 ACGAAGCTCCTTCTTGACTAAATT 58.448 37.500 0.00 0.00 38.24 1.82
1702 2874 7.117812 CGAAGCTCCTTCTTGACTAAATTTACA 59.882 37.037 0.00 0.00 38.24 2.41
1766 2943 0.647410 CGTGGATCATCGTTCAGTGC 59.353 55.000 0.00 0.00 0.00 4.40
1795 2973 4.331168 GCATAATCTTGACACACTGAGGTC 59.669 45.833 0.00 0.00 34.63 3.85
1796 2974 5.482006 CATAATCTTGACACACTGAGGTCA 58.518 41.667 0.00 0.00 41.93 4.02
1828 3006 3.782443 GTAGGACGGGGCTGGTGG 61.782 72.222 0.00 0.00 0.00 4.61
1829 3007 4.000620 TAGGACGGGGCTGGTGGA 62.001 66.667 0.00 0.00 0.00 4.02
1835 3013 3.661648 GGGGCTGGTGGATGTGGT 61.662 66.667 0.00 0.00 0.00 4.16
1849 3027 1.116308 TGTGGTCGTTGGAGAGTTCA 58.884 50.000 0.00 0.00 0.00 3.18
1850 3028 1.483004 TGTGGTCGTTGGAGAGTTCAA 59.517 47.619 0.00 0.00 0.00 2.69
1852 3030 1.760613 TGGTCGTTGGAGAGTTCAACT 59.239 47.619 0.00 0.00 41.47 3.16
1853 3031 2.223971 TGGTCGTTGGAGAGTTCAACTC 60.224 50.000 9.78 9.78 45.38 3.01
1996 3179 0.675633 GTTGGATGGCAACTGCAGTT 59.324 50.000 26.36 26.36 44.36 3.16
1997 3180 1.885887 GTTGGATGGCAACTGCAGTTA 59.114 47.619 30.67 16.98 44.36 2.24
1998 3181 1.533625 TGGATGGCAACTGCAGTTAC 58.466 50.000 30.67 25.03 44.36 2.50
1999 3182 0.447801 GGATGGCAACTGCAGTTACG 59.552 55.000 30.67 20.47 44.36 3.18
2000 3183 0.179189 GATGGCAACTGCAGTTACGC 60.179 55.000 30.67 27.96 44.36 4.42
2001 3184 1.911293 ATGGCAACTGCAGTTACGCG 61.911 55.000 30.67 19.41 44.36 6.01
2002 3185 2.604174 GGCAACTGCAGTTACGCGT 61.604 57.895 30.67 19.17 44.36 6.01
2023 3208 1.443194 CGCGTACGTGGCAACTAGT 60.443 57.895 20.84 0.00 37.61 2.57
2061 3246 0.036388 ATGATTCGTTGCTGGACGGT 60.036 50.000 7.73 0.00 42.98 4.83
2067 3252 0.599204 CGTTGCTGGACGGTAACTGT 60.599 55.000 9.78 0.00 39.27 3.55
2068 3253 1.336148 CGTTGCTGGACGGTAACTGTA 60.336 52.381 9.78 0.00 39.27 2.74
2069 3254 2.673043 CGTTGCTGGACGGTAACTGTAT 60.673 50.000 9.78 0.00 39.27 2.29
2077 3262 3.111098 GACGGTAACTGTATAGTTGCGG 58.889 50.000 20.14 20.14 46.55 5.69
2082 3267 4.142182 GGTAACTGTATAGTTGCGGGTACA 60.142 45.833 14.53 0.00 46.55 2.90
2092 3277 1.974343 GCGGGTACATGGCAACCAA 60.974 57.895 8.96 0.00 36.95 3.67
2110 3295 5.125100 ACCAAATAAGCACACATGACAAG 57.875 39.130 0.00 0.00 0.00 3.16
2202 3387 8.449686 AACTACTGTTTGACCATATGTGGCAAT 61.450 37.037 8.66 2.41 40.35 3.56
2241 3426 3.184986 GCAACTACGGTTTGATTACACGT 59.815 43.478 0.00 0.00 41.10 4.49
2247 3432 2.095466 CGGTTTGATTACACGTGGCAAT 60.095 45.455 21.57 17.85 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.849953 GTTGGTCGTCGGCGCATC 61.850 66.667 10.83 0.00 38.14 3.91
35 36 4.814294 GCGGTCGGCATCTCGGTT 62.814 66.667 0.00 0.00 42.87 4.44
122 123 4.271816 CCGTCGCTCGCTAGGCAT 62.272 66.667 0.00 0.00 38.35 4.40
323 330 2.362889 GTGGGGGCACATGGAAGG 60.363 66.667 0.00 0.00 0.00 3.46
340 348 1.401905 GCCTCGCTTTGAGTATTTGGG 59.598 52.381 0.00 0.00 43.64 4.12
367 375 7.791590 CACGATGCGAAAACAAAAACATTATTT 59.208 29.630 0.00 0.00 0.00 1.40
397 1483 6.835488 AGTTTATCCACGTATTCTGGGTAGTA 59.165 38.462 0.00 0.00 0.00 1.82
405 1491 7.902920 TTAGGGTAGTTTATCCACGTATTCT 57.097 36.000 0.00 0.00 0.00 2.40
430 1516 9.511272 AGTAAGGTTTATCCACGTATTCTTTTT 57.489 29.630 0.00 0.00 39.02 1.94
432 1518 9.813446 CTAGTAAGGTTTATCCACGTATTCTTT 57.187 33.333 0.00 0.00 39.02 2.52
433 1519 8.975295 ACTAGTAAGGTTTATCCACGTATTCTT 58.025 33.333 0.00 0.00 39.02 2.52
434 1520 8.411683 CACTAGTAAGGTTTATCCACGTATTCT 58.588 37.037 0.00 0.00 39.02 2.40
435 1521 7.168804 GCACTAGTAAGGTTTATCCACGTATTC 59.831 40.741 0.00 0.00 39.02 1.75
436 1522 6.982724 GCACTAGTAAGGTTTATCCACGTATT 59.017 38.462 0.00 0.00 39.02 1.89
437 1523 6.097270 TGCACTAGTAAGGTTTATCCACGTAT 59.903 38.462 0.00 0.00 39.02 3.06
449 1535 4.301628 GTTACACGTTGCACTAGTAAGGT 58.698 43.478 0.00 0.00 38.65 3.50
450 1536 3.362831 CGTTACACGTTGCACTAGTAAGG 59.637 47.826 0.00 0.00 36.74 2.69
451 1537 4.541778 CGTTACACGTTGCACTAGTAAG 57.458 45.455 0.00 0.00 36.74 2.34
472 1558 3.967734 TACGTCGTTGGCGTACTAC 57.032 52.632 1.78 0.00 42.85 2.73
491 1577 5.004345 CGCGCAGTAAAAATAATTTTCAGGG 59.996 40.000 8.75 0.00 39.42 4.45
515 1603 0.519077 CTTGCTCTTCTCGGTTTGGC 59.481 55.000 0.00 0.00 0.00 4.52
562 1651 0.386838 GGGGTAATCCGTAGTCGTGG 59.613 60.000 0.00 0.00 36.01 4.94
570 1659 2.910977 ACTTTTGAGAGGGGTAATCCGT 59.089 45.455 0.00 0.00 36.01 4.69
571 1660 3.532542 GACTTTTGAGAGGGGTAATCCG 58.467 50.000 0.00 0.00 36.01 4.18
573 1662 4.569719 TGGACTTTTGAGAGGGGTAATC 57.430 45.455 0.00 0.00 0.00 1.75
574 1663 5.333566 TTTGGACTTTTGAGAGGGGTAAT 57.666 39.130 0.00 0.00 0.00 1.89
579 1669 4.584325 TGACAATTTGGACTTTTGAGAGGG 59.416 41.667 0.78 0.00 0.00 4.30
635 1732 2.819595 CGGGTCGACATGGGCTTG 60.820 66.667 18.91 0.00 0.00 4.01
636 1733 4.096003 CCGGGTCGACATGGGCTT 62.096 66.667 18.91 0.00 0.00 4.35
640 1737 2.124736 ATTGCCGGGTCGACATGG 60.125 61.111 18.91 18.49 0.00 3.66
807 1930 2.544903 CGCGGGGTTTTGTCAAAGATTT 60.545 45.455 0.00 0.00 0.00 2.17
834 1957 2.404186 GGCGAGGTAAAAAGGGCGG 61.404 63.158 0.00 0.00 0.00 6.13
835 1958 1.376812 AGGCGAGGTAAAAAGGGCG 60.377 57.895 0.00 0.00 0.00 6.13
867 1990 1.405121 GGCGGGCCGTATATAAAGAGG 60.405 57.143 28.82 0.00 0.00 3.69
869 1992 0.609662 GGGCGGGCCGTATATAAAGA 59.390 55.000 28.82 0.00 36.85 2.52
895 2026 0.246360 GCTTTATTGGTGGTGTGGGC 59.754 55.000 0.00 0.00 0.00 5.36
907 2038 1.077005 TGAGGCTTGGTGGGCTTTATT 59.923 47.619 0.00 0.00 42.23 1.40
908 2039 0.704076 TGAGGCTTGGTGGGCTTTAT 59.296 50.000 0.00 0.00 42.23 1.40
909 2040 0.480690 TTGAGGCTTGGTGGGCTTTA 59.519 50.000 0.00 0.00 42.23 1.85
947 2078 4.994471 TCGGTGCTGGTGCTGCTG 62.994 66.667 0.00 0.00 40.48 4.41
948 2079 4.694233 CTCGGTGCTGGTGCTGCT 62.694 66.667 0.00 0.00 40.48 4.24
1005 2146 2.515057 GAGCCGGAGAGAGCGAGA 60.515 66.667 5.05 0.00 0.00 4.04
1290 2434 4.719106 AGGAGGGTCGTCGAGCGT 62.719 66.667 18.49 18.49 42.13 5.07
1403 2562 3.849953 GTCGTTAAGCCGCGCCAG 61.850 66.667 0.00 0.00 0.00 4.85
1436 2595 4.081752 TCTCCTCCGTAGTATAGGATCGAC 60.082 50.000 0.00 0.00 35.75 4.20
1454 2613 2.447379 ATCCAGGCCGCATCTCCT 60.447 61.111 0.00 0.00 0.00 3.69
1546 2713 6.706716 AGAAATACATCTGATCTGAGCACATG 59.293 38.462 9.19 9.19 0.00 3.21
1547 2714 6.828788 AGAAATACATCTGATCTGAGCACAT 58.171 36.000 8.37 0.00 0.00 3.21
1613 2785 9.962759 GAAAACGCTAGATTCTTTCGTTATTAA 57.037 29.630 19.06 0.00 41.67 1.40
1630 2802 6.680874 TGTGTTTAGGAAAAGAAAACGCTA 57.319 33.333 10.81 0.00 41.73 4.26
1647 2819 8.575589 TGCAGATTCAATACTTAACATGTGTTT 58.424 29.630 0.00 0.00 39.31 2.83
1650 2822 8.853345 GTTTGCAGATTCAATACTTAACATGTG 58.147 33.333 0.00 0.00 0.00 3.21
1651 2823 7.750458 CGTTTGCAGATTCAATACTTAACATGT 59.250 33.333 0.00 0.00 0.00 3.21
1652 2824 7.962373 TCGTTTGCAGATTCAATACTTAACATG 59.038 33.333 0.00 0.00 0.00 3.21
1653 2825 8.039603 TCGTTTGCAGATTCAATACTTAACAT 57.960 30.769 0.00 0.00 0.00 2.71
1654 2826 7.428282 TCGTTTGCAGATTCAATACTTAACA 57.572 32.000 0.00 0.00 0.00 2.41
1655 2827 7.007456 GCTTCGTTTGCAGATTCAATACTTAAC 59.993 37.037 0.00 0.00 0.00 2.01
1656 2828 7.021196 GCTTCGTTTGCAGATTCAATACTTAA 58.979 34.615 0.00 0.00 0.00 1.85
1657 2829 6.371548 AGCTTCGTTTGCAGATTCAATACTTA 59.628 34.615 0.00 0.00 0.00 2.24
1658 2830 5.182001 AGCTTCGTTTGCAGATTCAATACTT 59.818 36.000 0.00 0.00 0.00 2.24
1659 2831 4.697352 AGCTTCGTTTGCAGATTCAATACT 59.303 37.500 0.00 0.00 0.00 2.12
1660 2832 4.974591 AGCTTCGTTTGCAGATTCAATAC 58.025 39.130 0.00 0.00 0.00 1.89
1661 2833 4.094887 GGAGCTTCGTTTGCAGATTCAATA 59.905 41.667 0.00 0.00 0.00 1.90
1662 2834 3.119708 GGAGCTTCGTTTGCAGATTCAAT 60.120 43.478 0.00 0.00 0.00 2.57
1663 2835 2.226437 GGAGCTTCGTTTGCAGATTCAA 59.774 45.455 0.00 0.00 0.00 2.69
1664 2836 1.806542 GGAGCTTCGTTTGCAGATTCA 59.193 47.619 0.00 0.00 0.00 2.57
1665 2837 2.079925 AGGAGCTTCGTTTGCAGATTC 58.920 47.619 0.00 0.00 0.00 2.52
1666 2838 2.191128 AGGAGCTTCGTTTGCAGATT 57.809 45.000 0.00 0.00 0.00 2.40
1667 2839 2.079925 GAAGGAGCTTCGTTTGCAGAT 58.920 47.619 0.00 0.00 30.62 2.90
1668 2840 1.070758 AGAAGGAGCTTCGTTTGCAGA 59.929 47.619 0.00 0.00 44.34 4.26
1669 2841 1.517242 AGAAGGAGCTTCGTTTGCAG 58.483 50.000 0.00 0.00 44.34 4.41
1670 2842 1.603802 CAAGAAGGAGCTTCGTTTGCA 59.396 47.619 0.00 0.00 44.34 4.08
1671 2843 1.873591 TCAAGAAGGAGCTTCGTTTGC 59.126 47.619 0.00 0.00 44.34 3.68
1672 2844 3.134458 AGTCAAGAAGGAGCTTCGTTTG 58.866 45.455 0.00 0.00 44.34 2.93
1673 2845 3.477210 AGTCAAGAAGGAGCTTCGTTT 57.523 42.857 0.00 0.00 44.34 3.60
1674 2846 4.602340 TTAGTCAAGAAGGAGCTTCGTT 57.398 40.909 0.00 0.00 44.34 3.85
1675 2847 4.602340 TTTAGTCAAGAAGGAGCTTCGT 57.398 40.909 0.00 0.00 44.34 3.85
1676 2848 6.487689 AAATTTAGTCAAGAAGGAGCTTCG 57.512 37.500 0.00 0.00 44.34 3.79
1677 2849 8.324163 TGTAAATTTAGTCAAGAAGGAGCTTC 57.676 34.615 0.00 0.00 40.45 3.86
1678 2850 8.691661 TTGTAAATTTAGTCAAGAAGGAGCTT 57.308 30.769 0.00 0.00 0.00 3.74
1679 2851 8.691661 TTTGTAAATTTAGTCAAGAAGGAGCT 57.308 30.769 0.00 0.00 0.00 4.09
1680 2852 9.744468 TTTTTGTAAATTTAGTCAAGAAGGAGC 57.256 29.630 0.00 0.00 0.00 4.70
1689 2861 8.907685 GCGTTAGCATTTTTGTAAATTTAGTCA 58.092 29.630 0.00 0.00 44.35 3.41
1766 2943 5.854866 CAGTGTGTCAAGATTATGCAAACTG 59.145 40.000 0.00 0.00 36.87 3.16
1775 2952 5.545063 TTGACCTCAGTGTGTCAAGATTA 57.455 39.130 19.87 5.36 44.24 1.75
1828 3006 2.288825 TGAACTCTCCAACGACCACATC 60.289 50.000 0.00 0.00 0.00 3.06
1829 3007 1.691976 TGAACTCTCCAACGACCACAT 59.308 47.619 0.00 0.00 0.00 3.21
1849 3027 2.651361 CGTGGTGCGGAGAGAGTT 59.349 61.111 0.00 0.00 36.85 3.01
1850 3028 4.057428 GCGTGGTGCGGAGAGAGT 62.057 66.667 0.00 0.00 41.69 3.24
1893 3075 3.214328 CTGTGTGGGCAGAAACTAGTTT 58.786 45.455 20.67 20.67 38.70 2.66
2023 3208 6.832520 ATCATAGTTGCCATGTGTGTTTAA 57.167 33.333 0.00 0.00 0.00 1.52
2055 3240 3.111098 CGCAACTATACAGTTACCGTCC 58.889 50.000 0.00 0.00 43.30 4.79
2061 3246 5.452216 CCATGTACCCGCAACTATACAGTTA 60.452 44.000 0.00 0.00 43.30 2.24
2067 3252 1.763545 TGCCATGTACCCGCAACTATA 59.236 47.619 0.00 0.00 0.00 1.31
2068 3253 0.544223 TGCCATGTACCCGCAACTAT 59.456 50.000 0.00 0.00 0.00 2.12
2069 3254 0.325272 TTGCCATGTACCCGCAACTA 59.675 50.000 7.12 0.00 37.58 2.24
2077 3262 3.194542 TGCTTATTTGGTTGCCATGTACC 59.805 43.478 0.00 0.00 31.53 3.34
2082 3267 2.632028 TGTGTGCTTATTTGGTTGCCAT 59.368 40.909 0.00 0.00 31.53 4.40
2202 3387 4.382291 AGTTGCCGTGTGTGATTAACTAA 58.618 39.130 0.00 0.00 0.00 2.24
2241 3426 7.471260 GCCATGTCTAATTTATGGTAATTGCCA 60.471 37.037 18.16 18.16 42.60 4.92
2247 3432 9.860650 ATAGTTGCCATGTCTAATTTATGGTAA 57.139 29.630 0.00 0.00 41.95 2.85


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

AutoCloner maintained by Alex Coulton.