Multiple sequence alignment - TraesCS1B01G393100

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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 TraesCS1B01G393100 chr1B 100.000 3291 0 0 1 3291 626096677 626099967 0 6078
1 TraesCS1B01G393100 chr1A 92.149 1694 79 19 1 1678 549300510 549302165 0 2342
2 TraesCS1B01G393100 chr1A 89.507 1601 101 37 1721 3275 549302163 549303742 0 1964
3 TraesCS1B01G393100 chr1D 91.903 1655 86 17 1 1644 455758912 455760529 0 2270
4 TraesCS1B01G393100 chr1D 91.608 846 49 7 2445 3275 455761496 455762334 0 1149
5 TraesCS1B01G393100 chr1D 91.754 667 33 7 1721 2374 455760555 455761212 0 907


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 TraesCS1B01G393100 chr1B 626096677 626099967 3290 False 6078 6078 100.000 1 3291 1 chr1B.!!$F1 3290
1 TraesCS1B01G393100 chr1A 549300510 549303742 3232 False 2153 2342 90.828 1 3275 2 chr1A.!!$F1 3274
2 TraesCS1B01G393100 chr1D 455758912 455762334 3422 False 1442 2270 91.755 1 3275 3 chr1D.!!$F1 3274

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
580 584 0.447801 AAAGCTTCCTAATGCGTGCG 59.552 50.0 0.0 0.0 0.0 5.34 F
1525 1554 0.390472 CAGGGAGTTGACGAGGAAGC 60.390 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1712 0.040204 ATAGGGCAAGGCAAGCAAGT 59.960 50.0 3.65 0.0 0.00 3.16 R
3223 3504 1.043116 CCCTGGAGCATGACTACGGA 61.043 60.0 9.13 0.0 37.92 4.69 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
85 86 4.475345 GTGGAGTATCTAGACCACCTCAT 58.525 47.826 16.04 0.00 44.59 2.90
129 130 6.543465 TCAGATTTTGACATATGGACATCACC 59.457 38.462 7.80 0.00 0.00 4.02
294 298 5.596836 TCCAAGCAATCTTTTGACAAAGT 57.403 34.783 0.10 0.00 40.47 2.66
414 418 2.312390 TGGAAGGGCAAAACTGGTAAC 58.688 47.619 0.00 0.00 0.00 2.50
456 460 8.915654 CAAAGTGTTTTAGATTTCTATTGCACC 58.084 33.333 0.00 0.00 30.79 5.01
489 493 9.911138 AAAAATTATTTGGTTTTCAATCATGCC 57.089 25.926 0.00 0.00 34.98 4.40
490 494 8.866970 AAATTATTTGGTTTTCAATCATGCCT 57.133 26.923 0.00 0.00 34.98 4.75
491 495 8.866970 AATTATTTGGTTTTCAATCATGCCTT 57.133 26.923 0.00 0.00 34.98 4.35
492 496 7.903995 TTATTTGGTTTTCAATCATGCCTTC 57.096 32.000 0.00 0.00 34.98 3.46
493 497 5.549742 TTTGGTTTTCAATCATGCCTTCT 57.450 34.783 0.00 0.00 34.98 2.85
494 498 5.549742 TTGGTTTTCAATCATGCCTTCTT 57.450 34.783 0.00 0.00 0.00 2.52
495 499 5.549742 TGGTTTTCAATCATGCCTTCTTT 57.450 34.783 0.00 0.00 0.00 2.52
496 500 5.927819 TGGTTTTCAATCATGCCTTCTTTT 58.072 33.333 0.00 0.00 0.00 2.27
497 501 6.355747 TGGTTTTCAATCATGCCTTCTTTTT 58.644 32.000 0.00 0.00 0.00 1.94
558 562 5.802956 TGTTGCCTTAAGAAAAGAAAACGTG 59.197 36.000 3.36 0.00 0.00 4.49
562 566 7.536855 TGCCTTAAGAAAAGAAAACGTGTTAA 58.463 30.769 3.36 0.00 0.00 2.01
575 579 4.680171 ACGTGTTAAAGCTTCCTAATGC 57.320 40.909 0.00 0.00 0.00 3.56
579 583 3.119990 TGTTAAAGCTTCCTAATGCGTGC 60.120 43.478 0.00 0.00 0.00 5.34
580 584 0.447801 AAAGCTTCCTAATGCGTGCG 59.552 50.000 0.00 0.00 0.00 5.34
581 585 0.673644 AAGCTTCCTAATGCGTGCGT 60.674 50.000 0.00 0.00 0.00 5.24
609 621 8.229253 AGAAATGCAAATGTCATAATAGCTCA 57.771 30.769 0.00 0.00 0.00 4.26
630 642 6.490241 TCATAATCATGCTCCTCTGAGAAA 57.510 37.500 6.17 0.00 41.42 2.52
705 719 8.998814 TGAAATATGAATCTCCAGTTAACCCTA 58.001 33.333 0.88 0.00 0.00 3.53
713 727 7.947782 ATCTCCAGTTAACCCTATCCATAAA 57.052 36.000 0.88 0.00 0.00 1.40
718 732 8.488668 TCCAGTTAACCCTATCCATAAAAGTAC 58.511 37.037 0.88 0.00 0.00 2.73
1049 1065 1.073722 CAGCTCCAGTGAAGGCCAA 59.926 57.895 5.01 0.00 0.00 4.52
1050 1066 1.073897 AGCTCCAGTGAAGGCCAAC 59.926 57.895 5.01 0.00 0.00 3.77
1051 1067 1.228245 GCTCCAGTGAAGGCCAACA 60.228 57.895 5.01 0.65 0.00 3.33
1062 1078 2.343387 GCCAACAACACCATGCCC 59.657 61.111 0.00 0.00 0.00 5.36
1121 1137 0.597072 GCGCTAGGGCTACGAGTAAT 59.403 55.000 23.47 0.00 36.09 1.89
1188 1207 1.063567 ACTGCGGAGGGAGAAGATAGT 60.064 52.381 9.36 0.00 35.29 2.12
1203 1222 0.530650 ATAGTGACGAAGCATGCCGG 60.531 55.000 15.66 6.37 0.00 6.13
1228 1247 1.078567 CCTGTCAGAGCAAGCCCTC 60.079 63.158 0.00 0.00 0.00 4.30
1257 1276 1.266989 GCCTCTGCACAAACAGGTAAC 59.733 52.381 0.00 0.00 38.26 2.50
1309 1335 0.995803 TTGATCGGTTCCCATCCCAA 59.004 50.000 0.00 0.00 0.00 4.12
1409 1438 4.160635 GCGGGTGCGAATTCACGG 62.161 66.667 6.22 0.00 37.83 4.94
1428 1457 0.521735 GGGGTTTGATGTGAACGCTC 59.478 55.000 4.46 0.00 39.20 5.03
1444 1473 1.899437 GCTCCTGTTCCGGTGGATGA 61.899 60.000 0.00 0.00 0.00 2.92
1451 1480 2.202797 CCGGTGGATGACAGAGCG 60.203 66.667 0.00 0.00 0.00 5.03
1453 1482 1.079819 CGGTGGATGACAGAGCGTT 60.080 57.895 0.00 0.00 0.00 4.84
1466 1495 0.595310 GAGCGTTGATAGCGAGGTCC 60.595 60.000 0.00 0.00 40.04 4.46
1517 1546 0.886490 CTGTGGCACAGGGAGTTGAC 60.886 60.000 34.59 0.00 42.35 3.18
1525 1554 0.390472 CAGGGAGTTGACGAGGAAGC 60.390 60.000 0.00 0.00 0.00 3.86
1535 1564 1.546476 GACGAGGAAGCTTCAGAGGAA 59.454 52.381 27.02 0.00 0.00 3.36
1671 1700 5.072741 TCTGCCTGCATATTTTCCTAATCC 58.927 41.667 0.00 0.00 0.00 3.01
1678 1707 8.591072 CCTGCATATTTTCCTAATCCATCAAAT 58.409 33.333 0.00 0.00 0.00 2.32
1679 1708 9.419297 CTGCATATTTTCCTAATCCATCAAATG 57.581 33.333 0.00 0.00 0.00 2.32
1692 1721 4.657075 CATCAAATGGAAACTTGCTTGC 57.343 40.909 0.00 0.00 0.00 4.01
1693 1722 3.110447 TCAAATGGAAACTTGCTTGCC 57.890 42.857 0.00 0.00 0.00 4.52
1694 1723 2.699846 TCAAATGGAAACTTGCTTGCCT 59.300 40.909 0.00 0.00 0.00 4.75
1695 1724 3.134442 TCAAATGGAAACTTGCTTGCCTT 59.866 39.130 0.00 0.00 0.00 4.35
1696 1725 2.825861 ATGGAAACTTGCTTGCCTTG 57.174 45.000 0.00 0.00 0.00 3.61
1697 1726 0.104671 TGGAAACTTGCTTGCCTTGC 59.895 50.000 0.00 0.00 0.00 4.01
1698 1727 0.601046 GGAAACTTGCTTGCCTTGCC 60.601 55.000 0.00 0.00 0.00 4.52
1699 1728 0.601046 GAAACTTGCTTGCCTTGCCC 60.601 55.000 0.00 0.00 0.00 5.36
1700 1729 1.050421 AAACTTGCTTGCCTTGCCCT 61.050 50.000 0.00 0.00 0.00 5.19
1701 1730 0.178964 AACTTGCTTGCCTTGCCCTA 60.179 50.000 0.00 0.00 0.00 3.53
1702 1731 0.040204 ACTTGCTTGCCTTGCCCTAT 59.960 50.000 0.00 0.00 0.00 2.57
1703 1732 0.743097 CTTGCTTGCCTTGCCCTATC 59.257 55.000 0.00 0.00 0.00 2.08
1704 1733 0.332632 TTGCTTGCCTTGCCCTATCT 59.667 50.000 0.00 0.00 0.00 1.98
1705 1734 0.332632 TGCTTGCCTTGCCCTATCTT 59.667 50.000 0.00 0.00 0.00 2.40
1706 1735 0.743097 GCTTGCCTTGCCCTATCTTG 59.257 55.000 0.00 0.00 0.00 3.02
1707 1736 1.957113 GCTTGCCTTGCCCTATCTTGT 60.957 52.381 0.00 0.00 0.00 3.16
1708 1737 2.450476 CTTGCCTTGCCCTATCTTGTT 58.550 47.619 0.00 0.00 0.00 2.83
1709 1738 2.128771 TGCCTTGCCCTATCTTGTTC 57.871 50.000 0.00 0.00 0.00 3.18
1710 1739 1.635487 TGCCTTGCCCTATCTTGTTCT 59.365 47.619 0.00 0.00 0.00 3.01
1711 1740 2.843730 TGCCTTGCCCTATCTTGTTCTA 59.156 45.455 0.00 0.00 0.00 2.10
1712 1741 3.118261 TGCCTTGCCCTATCTTGTTCTAG 60.118 47.826 0.00 0.00 0.00 2.43
1713 1742 3.118223 GCCTTGCCCTATCTTGTTCTAGT 60.118 47.826 0.00 0.00 0.00 2.57
1714 1743 4.446371 CCTTGCCCTATCTTGTTCTAGTG 58.554 47.826 0.00 0.00 0.00 2.74
1715 1744 3.543680 TGCCCTATCTTGTTCTAGTGC 57.456 47.619 0.00 0.00 0.00 4.40
1716 1745 2.837591 TGCCCTATCTTGTTCTAGTGCA 59.162 45.455 0.00 0.00 0.00 4.57
1717 1746 3.198872 GCCCTATCTTGTTCTAGTGCAC 58.801 50.000 9.40 9.40 0.00 4.57
1718 1747 3.798202 CCCTATCTTGTTCTAGTGCACC 58.202 50.000 14.63 0.00 0.00 5.01
1719 1748 3.452627 CCCTATCTTGTTCTAGTGCACCT 59.547 47.826 14.63 3.48 0.00 4.00
1720 1749 4.649674 CCCTATCTTGTTCTAGTGCACCTA 59.350 45.833 14.63 4.57 0.00 3.08
1721 1750 5.128827 CCCTATCTTGTTCTAGTGCACCTAA 59.871 44.000 14.63 2.33 0.00 2.69
1722 1751 6.351881 CCCTATCTTGTTCTAGTGCACCTAAA 60.352 42.308 14.63 1.96 0.00 1.85
1723 1752 7.103641 CCTATCTTGTTCTAGTGCACCTAAAA 58.896 38.462 14.63 0.00 0.00 1.52
1724 1753 7.770897 CCTATCTTGTTCTAGTGCACCTAAAAT 59.229 37.037 14.63 0.00 0.00 1.82
1725 1754 9.817809 CTATCTTGTTCTAGTGCACCTAAAATA 57.182 33.333 14.63 0.00 0.00 1.40
1727 1756 8.547967 TCTTGTTCTAGTGCACCTAAAATAAG 57.452 34.615 14.63 15.40 0.00 1.73
1728 1757 8.154856 TCTTGTTCTAGTGCACCTAAAATAAGT 58.845 33.333 14.63 0.00 0.00 2.24
1729 1758 9.431887 CTTGTTCTAGTGCACCTAAAATAAGTA 57.568 33.333 14.63 0.00 0.00 2.24
1730 1759 9.953565 TTGTTCTAGTGCACCTAAAATAAGTAT 57.046 29.630 14.63 0.00 0.00 2.12
1769 1802 6.703607 GGATTCATTCGGCATATATACAGGAG 59.296 42.308 0.00 0.00 0.00 3.69
1779 1812 5.123027 GCATATATACAGGAGCAAAAGAGCC 59.877 44.000 0.00 0.00 34.23 4.70
1792 1825 0.109723 AAGAGCCGTTTAGCCAACCA 59.890 50.000 0.00 0.00 30.65 3.67
1814 1847 4.379243 AGCCTTCGACCACGCCAG 62.379 66.667 0.00 0.00 39.58 4.85
1915 1956 4.202253 ACCATTTTCCAAAACAGAAGAGCC 60.202 41.667 0.00 0.00 0.00 4.70
1919 1960 1.494721 TCCAAAACAGAAGAGCCAGGT 59.505 47.619 0.00 0.00 0.00 4.00
1920 1961 2.708861 TCCAAAACAGAAGAGCCAGGTA 59.291 45.455 0.00 0.00 0.00 3.08
1921 1962 3.137544 TCCAAAACAGAAGAGCCAGGTAA 59.862 43.478 0.00 0.00 0.00 2.85
1922 1963 3.253432 CCAAAACAGAAGAGCCAGGTAAC 59.747 47.826 0.00 0.00 0.00 2.50
1939 1980 7.679638 GCCAGGTAACAAATCTAACATCATGTC 60.680 40.741 0.00 0.00 41.41 3.06
1940 1981 7.401860 CAGGTAACAAATCTAACATCATGTCG 58.598 38.462 0.00 0.00 41.41 4.35
1941 1982 7.064609 CAGGTAACAAATCTAACATCATGTCGT 59.935 37.037 0.00 0.00 41.41 4.34
2164 2205 2.203596 ACCCGTTCCACCGTCTCT 60.204 61.111 0.00 0.00 0.00 3.10
2165 2206 1.835712 ACCCGTTCCACCGTCTCTT 60.836 57.895 0.00 0.00 0.00 2.85
2170 2211 0.666577 GTTCCACCGTCTCTTCCGTG 60.667 60.000 0.00 0.00 0.00 4.94
2171 2212 1.111116 TTCCACCGTCTCTTCCGTGT 61.111 55.000 0.00 0.00 0.00 4.49
2172 2213 1.080705 CCACCGTCTCTTCCGTGTC 60.081 63.158 0.00 0.00 0.00 3.67
2481 2739 3.670625 TGCTATTACGTGGCTGACTTTT 58.329 40.909 0.00 0.00 34.98 2.27
2482 2740 4.823157 TGCTATTACGTGGCTGACTTTTA 58.177 39.130 0.00 0.00 34.98 1.52
2483 2741 4.868171 TGCTATTACGTGGCTGACTTTTAG 59.132 41.667 0.00 0.00 34.98 1.85
2500 2758 7.739498 ACTTTTAGAAGTCGATTTGGCTTTA 57.261 32.000 0.00 0.00 42.35 1.85
2511 2769 9.950680 AGTCGATTTGGCTTTATGTAAAATATG 57.049 29.630 0.00 0.00 0.00 1.78
2598 2859 4.739587 TTGTGTACCAGTCACAGTGTAA 57.260 40.909 0.00 0.00 44.71 2.41
2611 2872 4.340666 TCACAGTGTAACACATGCCATTTT 59.659 37.500 0.00 0.00 41.43 1.82
2612 2873 4.445052 CACAGTGTAACACATGCCATTTTG 59.555 41.667 0.00 0.00 41.43 2.44
2687 2956 1.537202 GTGATGTGGACCTCTGCAAAC 59.463 52.381 0.00 0.00 0.00 2.93
2716 2985 3.599730 TTGAGGCTGTATCACTGTCAG 57.400 47.619 0.00 0.00 0.00 3.51
2736 3006 4.517832 TCAGTAGTATGCGTATGTGTAGGG 59.482 45.833 0.00 0.00 0.00 3.53
2747 3017 2.685106 TGTGTAGGGGAATTTGCCAA 57.315 45.000 9.33 0.00 0.00 4.52
2817 3091 0.673644 AGGGAGCATGCAACGTGTAC 60.674 55.000 21.98 0.00 0.00 2.90
2843 3117 3.928375 CACTGGCCAAATAATCAAACTGC 59.072 43.478 7.01 0.00 0.00 4.40
2864 3138 3.206150 CTGTATGGAATTCTGGGTTCCG 58.794 50.000 5.23 0.00 46.49 4.30
2866 3140 1.295020 ATGGAATTCTGGGTTCCGGA 58.705 50.000 0.00 0.00 46.49 5.14
2892 3166 1.522668 CCGTCAGCATCAAGTTGGAA 58.477 50.000 2.34 0.00 0.00 3.53
2921 3195 2.910688 ACACCTGTCACCTAAGTGTG 57.089 50.000 0.00 0.00 44.83 3.82
2928 3202 2.963101 TGTCACCTAAGTGTGCACTACT 59.037 45.455 19.41 16.18 44.83 2.57
2929 3203 4.146564 TGTCACCTAAGTGTGCACTACTA 58.853 43.478 19.41 5.37 44.83 1.82
2930 3204 4.022589 TGTCACCTAAGTGTGCACTACTAC 60.023 45.833 19.41 7.71 44.83 2.73
2941 3215 8.011067 AGTGTGCACTACTACGTTAAAATTAC 57.989 34.615 19.41 1.03 40.43 1.89
2984 3265 7.004086 GGATATGGTTTGGACTTGGAATATGA 58.996 38.462 0.00 0.00 0.00 2.15
3030 3311 9.087424 TCGAACATATGAAACTCAGAACTATTG 57.913 33.333 10.38 0.00 0.00 1.90
3068 3349 3.367395 GCATGGCCAAAAGAGACTAAACC 60.367 47.826 10.96 0.00 0.00 3.27
3159 3440 0.458669 CATGGGGCTTTGAGATGTGC 59.541 55.000 0.00 0.00 0.00 4.57
3161 3442 2.409870 GGGGCTTTGAGATGTGCCG 61.410 63.158 0.00 0.00 45.75 5.69
3214 3495 7.659799 TCCGTATTATGTGATTTAGTTCATGGG 59.340 37.037 0.00 0.00 0.00 4.00
3223 3504 4.591321 TTTAGTTCATGGGAAGGAGCAT 57.409 40.909 0.00 0.00 32.62 3.79
3285 3570 9.720769 ATATTTGGTTAACATATACTTCCTCCG 57.279 33.333 8.10 0.00 0.00 4.63
3286 3571 6.549433 TTGGTTAACATATACTTCCTCCGT 57.451 37.500 8.10 0.00 0.00 4.69
3287 3572 6.152932 TGGTTAACATATACTTCCTCCGTC 57.847 41.667 8.10 0.00 0.00 4.79
3288 3573 5.069516 TGGTTAACATATACTTCCTCCGTCC 59.930 44.000 8.10 0.00 0.00 4.79
3289 3574 5.510349 GGTTAACATATACTTCCTCCGTCCC 60.510 48.000 8.10 0.00 0.00 4.46
3290 3575 3.323774 ACATATACTTCCTCCGTCCCA 57.676 47.619 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 2.167075 TGAGCTGCGATCATCTTCAAGA 59.833 45.455 0.00 0.00 0.00 3.02
129 130 8.314751 CCTATGGAAATAGGAGTAGTTGGTATG 58.685 40.741 5.97 0.00 45.08 2.39
360 364 8.337532 GCATGGTTGAAAGCCAAATAATTTATC 58.662 33.333 0.00 0.00 39.72 1.75
456 460 9.565213 TTGAAAACCAAATAATTTTTGCAACTG 57.435 25.926 0.00 0.00 0.00 3.16
464 468 9.299465 AGGCATGATTGAAAACCAAATAATTTT 57.701 25.926 0.00 0.00 38.43 1.82
502 506 5.927819 TGTCATTCCAAGAAAAGGCATTTT 58.072 33.333 9.13 9.13 41.34 1.82
503 507 5.549742 TGTCATTCCAAGAAAAGGCATTT 57.450 34.783 0.00 0.00 0.00 2.32
504 508 5.305128 TCTTGTCATTCCAAGAAAAGGCATT 59.695 36.000 1.35 0.00 45.82 3.56
558 562 3.426323 GCACGCATTAGGAAGCTTTAAC 58.574 45.455 0.00 0.00 0.00 2.01
562 566 0.673644 ACGCACGCATTAGGAAGCTT 60.674 50.000 0.00 0.00 0.00 3.74
575 579 0.040514 TTTGCATTTCTCCACGCACG 60.041 50.000 0.00 0.00 33.29 5.34
579 583 3.557577 TGACATTTGCATTTCTCCACG 57.442 42.857 0.00 0.00 0.00 4.94
580 584 7.380602 GCTATTATGACATTTGCATTTCTCCAC 59.619 37.037 0.00 0.00 0.00 4.02
581 585 7.286087 AGCTATTATGACATTTGCATTTCTCCA 59.714 33.333 0.00 0.00 0.00 3.86
609 621 6.464180 GGAGTTTCTCAGAGGAGCATGATTAT 60.464 42.308 0.00 0.00 41.13 1.28
614 626 2.500910 AGGAGTTTCTCAGAGGAGCATG 59.499 50.000 0.00 0.00 41.13 4.06
643 655 9.467258 CACAAAACTATCACTTTGACATTCATT 57.533 29.630 1.80 0.00 36.30 2.57
644 656 8.084073 CCACAAAACTATCACTTTGACATTCAT 58.916 33.333 1.80 0.00 36.30 2.57
645 657 7.284261 TCCACAAAACTATCACTTTGACATTCA 59.716 33.333 1.80 0.00 36.30 2.57
646 658 7.591426 GTCCACAAAACTATCACTTTGACATTC 59.409 37.037 1.80 0.00 36.30 2.67
718 732 8.482429 GTGTGCAATCTATTTGAACTTTGAAAG 58.518 33.333 2.89 2.89 43.44 2.62
773 788 7.572523 TGTCTCCTGCTATTCCAATAATTTG 57.427 36.000 0.00 0.00 0.00 2.32
1071 1087 1.425066 TGGTCTTCTCCTTGGCATGTT 59.575 47.619 0.00 0.00 0.00 2.71
1121 1137 0.246635 GTCAGCTCTTTCGGTAGCCA 59.753 55.000 0.00 0.00 39.64 4.75
1188 1207 3.247056 TTCCCGGCATGCTTCGTCA 62.247 57.895 18.92 0.00 0.00 4.35
1203 1222 0.250467 TTGCTCTGACAGGCAGTTCC 60.250 55.000 15.28 0.00 45.14 3.62
1228 1247 2.359107 TGCAGAGGCTTGGCGAAG 60.359 61.111 3.77 3.77 41.91 3.79
1257 1276 2.805099 GTTCTGCAGGACTGTCTTCAAG 59.195 50.000 18.48 0.31 0.00 3.02
1265 1284 0.873054 CAGCTTGTTCTGCAGGACTG 59.127 55.000 25.44 18.23 0.00 3.51
1267 1286 1.002033 CAACAGCTTGTTCTGCAGGAC 60.002 52.381 18.94 18.94 38.77 3.85
1309 1335 6.216251 ACATAGCAACATATGGATGGACCTAT 59.784 38.462 7.80 5.84 37.45 2.57
1395 1424 3.131478 CCCCCGTGAATTCGCACC 61.131 66.667 18.57 0.00 35.37 5.01
1409 1438 0.521735 GAGCGTTCACATCAAACCCC 59.478 55.000 0.00 0.00 0.00 4.95
1428 1457 0.391661 CTGTCATCCACCGGAACAGG 60.392 60.000 9.46 4.34 37.08 4.00
1444 1473 0.101399 CCTCGCTATCAACGCTCTGT 59.899 55.000 0.00 0.00 0.00 3.41
1451 1480 2.094182 TGACAAGGACCTCGCTATCAAC 60.094 50.000 0.00 0.00 0.00 3.18
1453 1482 1.476891 GTGACAAGGACCTCGCTATCA 59.523 52.381 0.00 0.00 0.00 2.15
1466 1495 2.047274 ATGGACGGCGGTGACAAG 60.047 61.111 13.24 0.00 0.00 3.16
1517 1546 1.821753 TCTTCCTCTGAAGCTTCCTCG 59.178 52.381 23.42 11.90 46.28 4.63
1535 1564 3.777522 CCCTTCCACCTCTATTGTCTTCT 59.222 47.826 0.00 0.00 0.00 2.85
1545 1574 0.193574 TTCCTCACCCTTCCACCTCT 59.806 55.000 0.00 0.00 0.00 3.69
1671 1700 3.434299 GGCAAGCAAGTTTCCATTTGATG 59.566 43.478 0.00 0.00 0.00 3.07
1678 1707 0.104671 GCAAGGCAAGCAAGTTTCCA 59.895 50.000 0.00 0.00 0.00 3.53
1679 1708 0.601046 GGCAAGGCAAGCAAGTTTCC 60.601 55.000 3.65 0.00 0.00 3.13
1680 1709 0.601046 GGGCAAGGCAAGCAAGTTTC 60.601 55.000 3.65 0.00 0.00 2.78
1682 1711 0.178964 TAGGGCAAGGCAAGCAAGTT 60.179 50.000 3.65 0.00 0.00 2.66
1683 1712 0.040204 ATAGGGCAAGGCAAGCAAGT 59.960 50.000 3.65 0.00 0.00 3.16
1684 1713 0.743097 GATAGGGCAAGGCAAGCAAG 59.257 55.000 3.65 0.00 0.00 4.01
1685 1714 0.332632 AGATAGGGCAAGGCAAGCAA 59.667 50.000 3.65 0.00 0.00 3.91
1686 1715 0.332632 AAGATAGGGCAAGGCAAGCA 59.667 50.000 3.65 0.00 0.00 3.91
1687 1716 0.743097 CAAGATAGGGCAAGGCAAGC 59.257 55.000 0.00 0.00 0.00 4.01
1688 1717 2.134789 ACAAGATAGGGCAAGGCAAG 57.865 50.000 0.00 0.00 0.00 4.01
1689 1718 2.041620 AGAACAAGATAGGGCAAGGCAA 59.958 45.455 0.00 0.00 0.00 4.52
1690 1719 1.635487 AGAACAAGATAGGGCAAGGCA 59.365 47.619 0.00 0.00 0.00 4.75
1691 1720 2.426842 AGAACAAGATAGGGCAAGGC 57.573 50.000 0.00 0.00 0.00 4.35
1692 1721 4.446371 CACTAGAACAAGATAGGGCAAGG 58.554 47.826 0.00 0.00 0.00 3.61
1693 1722 3.873952 GCACTAGAACAAGATAGGGCAAG 59.126 47.826 0.00 0.00 45.79 4.01
1694 1723 3.873910 GCACTAGAACAAGATAGGGCAA 58.126 45.455 0.00 0.00 45.79 4.52
1695 1724 3.543680 GCACTAGAACAAGATAGGGCA 57.456 47.619 0.00 0.00 45.79 5.36
1696 1725 3.198872 GTGCACTAGAACAAGATAGGGC 58.801 50.000 10.32 0.00 46.51 5.19
1697 1726 3.452627 AGGTGCACTAGAACAAGATAGGG 59.547 47.826 17.98 0.00 0.00 3.53
1698 1727 4.744795 AGGTGCACTAGAACAAGATAGG 57.255 45.455 17.98 0.00 0.00 2.57
1699 1728 8.723942 ATTTTAGGTGCACTAGAACAAGATAG 57.276 34.615 17.98 0.00 29.60 2.08
1701 1730 9.167311 CTTATTTTAGGTGCACTAGAACAAGAT 57.833 33.333 17.98 5.59 34.09 2.40
1702 1731 8.154856 ACTTATTTTAGGTGCACTAGAACAAGA 58.845 33.333 17.98 0.00 34.09 3.02
1703 1732 8.324163 ACTTATTTTAGGTGCACTAGAACAAG 57.676 34.615 17.98 14.09 36.73 3.16
1704 1733 9.953565 ATACTTATTTTAGGTGCACTAGAACAA 57.046 29.630 17.98 3.93 29.60 2.83
1730 1759 8.363390 GCCGAATGAATCCATCTATATCATCTA 58.637 37.037 0.00 0.00 30.76 1.98
1731 1760 7.147602 TGCCGAATGAATCCATCTATATCATCT 60.148 37.037 0.00 0.00 30.76 2.90
1742 1771 6.994496 CCTGTATATATGCCGAATGAATCCAT 59.006 38.462 0.00 0.00 33.66 3.41
1769 1802 0.596082 TGGCTAAACGGCTCTTTTGC 59.404 50.000 0.00 5.11 39.32 3.68
1779 1812 0.798776 CTCAGCTGGTTGGCTAAACG 59.201 55.000 15.13 0.00 41.00 3.60
1792 1825 2.659610 GTGGTCGAAGGCTCAGCT 59.340 61.111 0.00 0.00 0.00 4.24
1814 1847 2.358322 TTTGGAACCAGACCTCAACC 57.642 50.000 0.00 0.00 0.00 3.77
1915 1956 7.064609 ACGACATGATGTTAGATTTGTTACCTG 59.935 37.037 0.00 0.00 0.00 4.00
1919 1960 8.440059 GTGAACGACATGATGTTAGATTTGTTA 58.560 33.333 0.00 0.00 0.00 2.41
1920 1961 7.041440 TGTGAACGACATGATGTTAGATTTGTT 60.041 33.333 0.00 0.00 0.00 2.83
1921 1962 6.426633 TGTGAACGACATGATGTTAGATTTGT 59.573 34.615 0.00 0.00 0.00 2.83
1922 1963 6.830736 TGTGAACGACATGATGTTAGATTTG 58.169 36.000 0.00 0.00 0.00 2.32
1939 1980 0.318699 TCAGCTTCGTCCTGTGAACG 60.319 55.000 0.00 0.00 41.39 3.95
1940 1981 1.795286 CTTCAGCTTCGTCCTGTGAAC 59.205 52.381 0.00 0.00 0.00 3.18
1941 1982 1.873903 GCTTCAGCTTCGTCCTGTGAA 60.874 52.381 0.00 0.00 38.21 3.18
2164 2205 1.504900 CGGAGATGACGACACGGAA 59.495 57.895 0.00 0.00 0.00 4.30
2165 2206 2.404186 CCGGAGATGACGACACGGA 61.404 63.158 8.54 0.00 43.69 4.69
2170 2211 2.806237 GGTCCCGGAGATGACGAC 59.194 66.667 0.73 0.00 31.47 4.34
2171 2212 2.827190 CGGTCCCGGAGATGACGA 60.827 66.667 0.73 0.00 35.56 4.20
2172 2213 3.122250 GACGGTCCCGGAGATGACG 62.122 68.421 0.73 7.91 44.69 4.35
2307 2348 4.652131 AACATGAACGGGCCGGCA 62.652 61.111 31.78 26.70 0.00 5.69
2414 2486 7.358066 CGAGCTCATCTACCGTTATAAAACTA 58.642 38.462 15.40 0.00 33.15 2.24
2481 2739 8.780846 TTTACATAAAGCCAAATCGACTTCTA 57.219 30.769 0.00 0.00 0.00 2.10
2482 2740 7.681939 TTTACATAAAGCCAAATCGACTTCT 57.318 32.000 0.00 0.00 0.00 2.85
2483 2741 8.911247 ATTTTACATAAAGCCAAATCGACTTC 57.089 30.769 0.00 0.00 0.00 3.01
2500 2758 9.591792 ACATCATCGATCGATCATATTTTACAT 57.408 29.630 27.20 0.00 31.62 2.29
2511 2769 3.363378 GCAAACCACATCATCGATCGATC 60.363 47.826 27.20 15.68 31.62 3.69
2563 2824 6.659242 ACTGGTACACAAATGGAAATTAGAGG 59.341 38.462 0.00 0.00 0.00 3.69
2611 2872 5.299782 GGGTCACAGTTAATGTTTAACCACA 59.700 40.000 9.77 0.00 41.41 4.17
2612 2873 5.299782 TGGGTCACAGTTAATGTTTAACCAC 59.700 40.000 9.77 2.69 41.41 4.16
2673 2942 3.072330 TGATTGTAGTTTGCAGAGGTCCA 59.928 43.478 0.00 0.00 0.00 4.02
2687 2956 6.202379 CAGTGATACAGCCTCAATGATTGTAG 59.798 42.308 4.93 1.91 40.23 2.74
2716 2985 3.822735 TCCCCTACACATACGCATACTAC 59.177 47.826 0.00 0.00 0.00 2.73
2736 3006 8.037166 AGAGAAGTTTCATAATTGGCAAATTCC 58.963 33.333 3.01 0.00 37.23 3.01
2747 3017 6.294731 GCAACCACCAAGAGAAGTTTCATAAT 60.295 38.462 0.00 0.00 0.00 1.28
2843 3117 3.206150 CGGAACCCAGAATTCCATACAG 58.794 50.000 0.65 0.00 45.15 2.74
2941 3215 9.451002 ACCATATCCCTATATAGATAATCGACG 57.549 37.037 11.53 0.00 0.00 5.12
2965 3239 5.358160 CCTCTTCATATTCCAAGTCCAAACC 59.642 44.000 0.00 0.00 0.00 3.27
2984 3265 3.260128 CGACCTAAACACCTAACCCTCTT 59.740 47.826 0.00 0.00 0.00 2.85
3089 3370 1.977854 CGGACCATCCCCTTCATGATA 59.022 52.381 0.00 0.00 31.13 2.15
3114 3395 2.515901 GGACACCCTTGGCACAGT 59.484 61.111 0.00 0.00 42.39 3.55
3148 3429 3.173540 CCATCCGGCACATCTCAAA 57.826 52.632 0.00 0.00 0.00 2.69
3159 3440 4.873810 TTCGCCATGGCCATCCGG 62.874 66.667 30.79 21.91 37.98 5.14
3161 3442 1.754234 AAGTTCGCCATGGCCATCC 60.754 57.895 30.79 15.77 37.98 3.51
3174 3455 6.641314 ACATAATACGGATCGATGACAAGTTC 59.359 38.462 0.54 0.00 0.00 3.01
3214 3495 2.748605 CATGACTACGGATGCTCCTTC 58.251 52.381 0.00 0.00 33.30 3.46
3223 3504 1.043116 CCCTGGAGCATGACTACGGA 61.043 60.000 9.13 0.00 37.92 4.69
3226 3507 1.789523 TACCCCTGGAGCATGACTAC 58.210 55.000 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.