Multiple sequence alignment - TraesCS6B01G323100

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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 TraesCS6B01G323100 chr6B 100.000 2851 0 0 1 2851 572112878 572110028 0 5265
1 TraesCS6B01G323100 chr6B 91.247 834 66 7 2019 2846 649810135 649809303 0 1129
2 TraesCS6B01G323100 chr6D 87.678 2110 109 80 1 2017 382563235 382561184 0 2316
3 TraesCS6B01G323100 chr6A 86.443 2117 130 81 1 2018 524363940 524361882 0 2174
4 TraesCS6B01G323100 chr1B 92.900 831 56 3 2019 2846 520874587 520873757 0 1205
5 TraesCS6B01G323100 chr7B 92.762 829 56 3 2019 2843 633759768 633760596 0 1195
6 TraesCS6B01G323100 chr2D 91.737 835 60 8 2019 2846 195229486 195228654 0 1151
7 TraesCS6B01G323100 chr3D 91.497 835 60 6 2019 2843 300145902 300146735 0 1138
8 TraesCS6B01G323100 chr3D 91.388 836 62 9 2019 2846 19830528 19831361 0 1136
9 TraesCS6B01G323100 chr3D 91.525 826 64 6 2027 2846 113579754 113580579 0 1133
10 TraesCS6B01G323100 chr2B 91.257 835 65 8 2019 2846 199744310 199743477 0 1131
11 TraesCS6B01G323100 chr2A 91.268 836 63 10 2018 2846 17392798 17391966 0 1131


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 TraesCS6B01G323100 chr6B 572110028 572112878 2850 True 5265 5265 100.000 1 2851 1 chr6B.!!$R1 2850
1 TraesCS6B01G323100 chr6B 649809303 649810135 832 True 1129 1129 91.247 2019 2846 1 chr6B.!!$R2 827
2 TraesCS6B01G323100 chr6D 382561184 382563235 2051 True 2316 2316 87.678 1 2017 1 chr6D.!!$R1 2016
3 TraesCS6B01G323100 chr6A 524361882 524363940 2058 True 2174 2174 86.443 1 2018 1 chr6A.!!$R1 2017
4 TraesCS6B01G323100 chr1B 520873757 520874587 830 True 1205 1205 92.900 2019 2846 1 chr1B.!!$R1 827
5 TraesCS6B01G323100 chr7B 633759768 633760596 828 False 1195 1195 92.762 2019 2843 1 chr7B.!!$F1 824
6 TraesCS6B01G323100 chr2D 195228654 195229486 832 True 1151 1151 91.737 2019 2846 1 chr2D.!!$R1 827
7 TraesCS6B01G323100 chr3D 300145902 300146735 833 False 1138 1138 91.497 2019 2843 1 chr3D.!!$F3 824
8 TraesCS6B01G323100 chr3D 19830528 19831361 833 False 1136 1136 91.388 2019 2846 1 chr3D.!!$F1 827
9 TraesCS6B01G323100 chr3D 113579754 113580579 825 False 1133 1133 91.525 2027 2846 1 chr3D.!!$F2 819
10 TraesCS6B01G323100 chr2B 199743477 199744310 833 True 1131 1131 91.257 2019 2846 1 chr2B.!!$R1 827
11 TraesCS6B01G323100 chr2A 17391966 17392798 832 True 1131 1131 91.268 2018 2846 1 chr2A.!!$R1 828

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
68 69 0.029567 CAGCTCGCCGTTCTACCTAG 59.97 60.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 1997 0.033504 ACAGTTGCTGGTACTCGGTG 59.966 55.0 1.08 0.0 35.51 4.94 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
36 37 1.481819 AACAACACGTACGCACCGTC 61.482 55.000 16.72 0.00 41.54 4.79
47 48 3.114616 CACCGTCGCTCAAGCTGG 61.115 66.667 0.00 2.28 39.32 4.85
65 66 1.516603 GTCAGCTCGCCGTTCTACC 60.517 63.158 0.00 0.00 0.00 3.18
68 69 0.029567 CAGCTCGCCGTTCTACCTAG 59.970 60.000 0.00 0.00 0.00 3.02
69 70 1.299240 GCTCGCCGTTCTACCTAGC 60.299 63.158 0.00 0.00 0.00 3.42
70 71 1.726533 GCTCGCCGTTCTACCTAGCT 61.727 60.000 0.00 0.00 0.00 3.32
71 72 0.739561 CTCGCCGTTCTACCTAGCTT 59.260 55.000 0.00 0.00 0.00 3.74
72 73 1.945394 CTCGCCGTTCTACCTAGCTTA 59.055 52.381 0.00 0.00 0.00 3.09
74 75 1.268948 CGCCGTTCTACCTAGCTTACC 60.269 57.143 0.00 0.00 0.00 2.85
77 78 3.368739 GCCGTTCTACCTAGCTTACCAAA 60.369 47.826 0.00 0.00 0.00 3.28
78 79 4.430908 CCGTTCTACCTAGCTTACCAAAG 58.569 47.826 0.00 0.00 35.68 2.77
79 80 4.430908 CGTTCTACCTAGCTTACCAAAGG 58.569 47.826 0.00 0.00 32.98 3.11
80 81 4.081807 CGTTCTACCTAGCTTACCAAAGGT 60.082 45.833 8.61 8.61 45.22 3.50
94 99 3.626924 AGGTCGCGCCTCCTGTTT 61.627 61.111 15.73 0.00 46.96 2.83
95 100 3.119096 GGTCGCGCCTCCTGTTTC 61.119 66.667 0.00 0.00 0.00 2.78
163 168 1.142748 CAGAGGTGTCATCGGAGGC 59.857 63.158 0.00 0.00 0.00 4.70
289 299 0.659417 CAGTATAGGTACCGTGCGCG 60.659 60.000 13.88 13.88 37.95 6.86
439 458 1.740043 GCAAGCTCTTCTCTGGCTCTC 60.740 57.143 0.00 0.00 35.06 3.20
457 476 1.811266 CGCCTATGCTGACACGCTT 60.811 57.895 0.00 0.00 34.43 4.68
490 510 0.178861 TCCCTGGGCCTCTCTTTCTT 60.179 55.000 8.22 0.00 0.00 2.52
501 521 3.071602 CCTCTCTTTCTTCTTGTGTCCCA 59.928 47.826 0.00 0.00 0.00 4.37
503 523 3.967326 TCTCTTTCTTCTTGTGTCCCAGA 59.033 43.478 0.00 0.00 0.00 3.86
505 525 3.711704 TCTTTCTTCTTGTGTCCCAGACT 59.288 43.478 0.00 0.00 33.15 3.24
506 526 3.753294 TTCTTCTTGTGTCCCAGACTC 57.247 47.619 0.00 0.00 33.15 3.36
507 527 2.964209 TCTTCTTGTGTCCCAGACTCT 58.036 47.619 0.00 0.00 33.15 3.24
508 528 4.114015 TCTTCTTGTGTCCCAGACTCTA 57.886 45.455 0.00 0.00 33.15 2.43
509 529 4.480115 TCTTCTTGTGTCCCAGACTCTAA 58.520 43.478 0.00 0.00 33.15 2.10
510 530 5.087323 TCTTCTTGTGTCCCAGACTCTAAT 58.913 41.667 0.00 0.00 33.15 1.73
511 531 5.186021 TCTTCTTGTGTCCCAGACTCTAATC 59.814 44.000 0.00 0.00 33.15 1.75
574 594 1.578215 ATGGTGGGCTCTGATTGGCT 61.578 55.000 0.00 0.00 0.00 4.75
603 623 4.754114 CCTATCTTAGAAATCTGTGGCTGC 59.246 45.833 0.00 0.00 0.00 5.25
608 628 2.786512 GAAATCTGTGGCTGCCCCCA 62.787 60.000 17.53 11.92 0.00 4.96
653 674 0.541530 AGAGGTCTCAGCTCACAGCA 60.542 55.000 5.57 0.00 45.56 4.41
656 677 1.368950 GTCTCAGCTCACAGCACCA 59.631 57.895 0.00 0.00 45.56 4.17
746 797 3.071602 AGCTGGCCCATGTTACTATGTAG 59.928 47.826 0.00 0.00 0.00 2.74
747 798 3.181454 GCTGGCCCATGTTACTATGTAGT 60.181 47.826 0.00 0.00 40.24 2.73
748 799 4.039973 GCTGGCCCATGTTACTATGTAGTA 59.960 45.833 0.00 0.00 37.73 1.82
749 800 5.539048 CTGGCCCATGTTACTATGTAGTAC 58.461 45.833 0.00 0.00 38.43 2.73
750 801 4.345837 TGGCCCATGTTACTATGTAGTACC 59.654 45.833 0.00 0.00 38.43 3.34
771 823 1.666553 CCTTTGCGTGCAGACGGTA 60.667 57.895 0.00 0.00 46.20 4.02
773 825 1.218875 CTTTGCGTGCAGACGGTACA 61.219 55.000 0.00 0.00 46.20 2.90
778 830 2.048597 TGCAGACGGTACAAGCGG 60.049 61.111 3.43 0.00 44.33 5.52
779 831 2.260434 GCAGACGGTACAAGCGGA 59.740 61.111 3.43 0.00 44.33 5.54
780 832 2.092882 GCAGACGGTACAAGCGGAC 61.093 63.158 3.43 0.00 44.33 4.79
920 985 1.204704 CATAGCGACCAGAGTCACCAA 59.795 52.381 0.00 0.00 43.73 3.67
929 994 3.256631 ACCAGAGTCACCAAATCAATTGC 59.743 43.478 0.00 0.00 37.73 3.56
1137 1209 3.944526 GACGCACCGCCGTACGTTA 62.945 63.158 15.21 0.00 42.02 3.18
1138 1210 3.535491 CGCACCGCCGTACGTTAC 61.535 66.667 15.21 2.25 41.42 2.50
1160 1232 3.756069 GTAGTACTACGTCTTGCAGTGG 58.244 50.000 16.96 0.00 0.00 4.00
1161 1233 2.236766 AGTACTACGTCTTGCAGTGGT 58.763 47.619 0.00 0.00 36.13 4.16
1162 1234 2.228343 AGTACTACGTCTTGCAGTGGTC 59.772 50.000 0.00 0.00 34.05 4.02
1230 1310 1.273267 TGGTGTGCAGATCTAGGAGGT 60.273 52.381 0.00 0.00 0.00 3.85
1411 1491 1.898154 GCCTTCGGGTTCTGCTCTA 59.102 57.895 0.00 0.00 37.45 2.43
1412 1492 0.460459 GCCTTCGGGTTCTGCTCTAC 60.460 60.000 0.00 0.00 37.45 2.59
1413 1493 0.895530 CCTTCGGGTTCTGCTCTACA 59.104 55.000 0.00 0.00 0.00 2.74
1414 1494 1.404315 CCTTCGGGTTCTGCTCTACAC 60.404 57.143 0.00 0.00 0.00 2.90
1415 1495 1.546476 CTTCGGGTTCTGCTCTACACT 59.454 52.381 0.00 0.00 0.00 3.55
1416 1496 1.174783 TCGGGTTCTGCTCTACACTC 58.825 55.000 0.00 0.00 0.00 3.51
1431 1511 4.363990 CTCACACTCGCACCGCCT 62.364 66.667 0.00 0.00 0.00 5.52
1438 1524 2.203084 TCGCACCGCCTGTTTCAA 60.203 55.556 0.00 0.00 0.00 2.69
1439 1525 1.781025 CTCGCACCGCCTGTTTCAAA 61.781 55.000 0.00 0.00 0.00 2.69
1440 1526 1.064946 CGCACCGCCTGTTTCAAAA 59.935 52.632 0.00 0.00 0.00 2.44
1441 1527 0.526524 CGCACCGCCTGTTTCAAAAA 60.527 50.000 0.00 0.00 0.00 1.94
1442 1528 1.864565 GCACCGCCTGTTTCAAAAAT 58.135 45.000 0.00 0.00 0.00 1.82
1443 1529 1.526464 GCACCGCCTGTTTCAAAAATG 59.474 47.619 0.00 0.00 0.00 2.32
1444 1530 2.820330 CACCGCCTGTTTCAAAAATGT 58.180 42.857 0.00 0.00 0.00 2.71
1445 1531 3.797184 GCACCGCCTGTTTCAAAAATGTA 60.797 43.478 0.00 0.00 0.00 2.29
1446 1532 4.363999 CACCGCCTGTTTCAAAAATGTAA 58.636 39.130 0.00 0.00 0.00 2.41
1447 1533 4.987912 CACCGCCTGTTTCAAAAATGTAAT 59.012 37.500 0.00 0.00 0.00 1.89
1448 1534 5.118510 CACCGCCTGTTTCAAAAATGTAATC 59.881 40.000 0.00 0.00 0.00 1.75
1449 1535 4.625311 CCGCCTGTTTCAAAAATGTAATCC 59.375 41.667 0.00 0.00 0.00 3.01
1453 1539 6.295292 GCCTGTTTCAAAAATGTAATCCCTCT 60.295 38.462 0.00 0.00 0.00 3.69
1455 1541 7.177392 CCTGTTTCAAAAATGTAATCCCTCTCT 59.823 37.037 0.00 0.00 0.00 3.10
1464 1550 7.475137 AATGTAATCCCTCTCTATCTGCTAC 57.525 40.000 0.00 0.00 0.00 3.58
1466 1552 6.242396 TGTAATCCCTCTCTATCTGCTACTC 58.758 44.000 0.00 0.00 0.00 2.59
1501 1588 1.068055 CAGTGCTGTGCCATCTTTTCC 60.068 52.381 0.00 0.00 0.00 3.13
1539 1626 1.004185 GCGTGCAAGCATATCACTCTG 60.004 52.381 20.14 0.00 37.05 3.35
1574 1661 1.783031 CGCCTGGTACGTCGCTATCT 61.783 60.000 0.00 0.00 0.00 1.98
1576 1663 0.317938 CCTGGTACGTCGCTATCTGC 60.318 60.000 0.00 0.00 38.57 4.26
1577 1664 0.663688 CTGGTACGTCGCTATCTGCT 59.336 55.000 0.00 0.00 40.11 4.24
1579 1666 1.871676 TGGTACGTCGCTATCTGCTAG 59.128 52.381 0.00 0.00 40.11 3.42
1603 1721 3.825328 ACTCATCACACTGCTTTTCCTT 58.175 40.909 0.00 0.00 0.00 3.36
1607 1725 2.912771 TCACACTGCTTTTCCTTTCGA 58.087 42.857 0.00 0.00 0.00 3.71
1614 1732 4.761739 ACTGCTTTTCCTTTCGATGATTCA 59.238 37.500 0.00 0.00 0.00 2.57
1642 1760 5.281693 TGAATTATGTGTTCGTCTTGCTG 57.718 39.130 0.00 0.00 0.00 4.41
1876 1997 4.499037 AACTACCGGAAACTTGAATTGC 57.501 40.909 9.46 0.00 0.00 3.56
1879 2000 1.339929 ACCGGAAACTTGAATTGCACC 59.660 47.619 9.46 0.00 0.00 5.01
1884 2005 3.500680 GGAAACTTGAATTGCACCGAGTA 59.499 43.478 0.00 0.00 0.00 2.59
1888 2009 2.093306 TGAATTGCACCGAGTACCAG 57.907 50.000 0.00 0.00 0.00 4.00
1956 2078 2.401766 CCAAGCGCAGGATGACACC 61.402 63.158 11.47 0.00 39.69 4.16
2095 2230 7.849389 TGCATGTATATATAATACAGGGAGGGT 59.151 37.037 10.66 0.00 37.84 4.34
2117 2252 6.778559 GGGTCTCTACCTCAACTATACAAGAT 59.221 42.308 0.00 0.00 45.95 2.40
2154 2289 4.391830 ACAACTCCAATACACGTGCAATAG 59.608 41.667 17.22 8.46 0.00 1.73
2203 2346 1.606350 GAAGCGTCGTTGGAGACACG 61.606 60.000 0.00 0.00 42.67 4.49
2214 2357 0.609681 GGAGACACGGAGACTGGACT 60.610 60.000 0.00 0.00 0.00 3.85
2267 2411 6.662755 TCCCTTAGTCATAACATCAGCAAAT 58.337 36.000 0.00 0.00 0.00 2.32
2398 2542 3.902086 GGAGAGGTAGACCGCGCC 61.902 72.222 9.29 9.29 46.60 6.53
2501 2645 0.673333 CCACGACATTAGCCACAGCA 60.673 55.000 0.00 0.00 43.56 4.41
2620 2765 4.351938 CGTCGAGTGTCGGGGCAA 62.352 66.667 0.00 0.00 40.88 4.52
2843 2990 2.180769 CACCGACGATGGAGCGAA 59.819 61.111 0.00 0.00 34.83 4.70
2846 2993 0.108329 ACCGACGATGGAGCGAAAAT 60.108 50.000 0.00 0.00 34.83 1.82
2847 2994 0.301687 CCGACGATGGAGCGAAAATG 59.698 55.000 0.00 0.00 34.83 2.32
2848 2995 0.999406 CGACGATGGAGCGAAAATGT 59.001 50.000 0.00 0.00 34.83 2.71
2849 2996 1.393539 CGACGATGGAGCGAAAATGTT 59.606 47.619 0.00 0.00 34.83 2.71
2850 2997 2.774007 GACGATGGAGCGAAAATGTTG 58.226 47.619 0.00 0.00 34.83 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.974875 TAGAACGGCGAGCTGACCA 60.975 57.895 16.62 0.00 0.00 4.02
47 48 1.516603 GGTAGAACGGCGAGCTGAC 60.517 63.158 16.62 4.47 0.00 3.51
65 66 1.278238 CGCGACCTTTGGTAAGCTAG 58.722 55.000 0.00 0.00 37.31 3.42
68 69 2.479198 GCGCGACCTTTGGTAAGC 59.521 61.111 12.10 6.61 35.25 3.09
69 70 3.174788 GGCGCGACCTTTGGTAAG 58.825 61.111 12.10 0.00 35.25 2.34
78 79 3.119096 GAAACAGGAGGCGCGACC 61.119 66.667 9.25 10.36 39.61 4.79
79 80 3.479269 CGAAACAGGAGGCGCGAC 61.479 66.667 12.10 7.34 0.00 5.19
80 81 3.626680 CTCGAAACAGGAGGCGCGA 62.627 63.158 12.10 0.00 0.00 5.87
94 99 2.231478 CTGAAAGCCAAGGTACTCTCGA 59.769 50.000 0.00 0.00 38.49 4.04
95 100 2.611518 CTGAAAGCCAAGGTACTCTCG 58.388 52.381 0.00 0.00 38.49 4.04
174 179 4.219999 GCGGCTCTCTCTGCTCCC 62.220 72.222 0.00 0.00 35.53 4.30
227 233 3.068165 CGATGCCCAGATAAGTAGACACA 59.932 47.826 0.00 0.00 0.00 3.72
229 235 2.035961 GCGATGCCCAGATAAGTAGACA 59.964 50.000 0.00 0.00 0.00 3.41
266 276 1.603802 GCACGGTACCTATACTGCGTA 59.396 52.381 10.90 0.00 40.86 4.42
457 476 0.965866 CAGGGACGCACAGGACTAGA 60.966 60.000 0.00 0.00 0.00 2.43
490 510 4.416516 TGATTAGAGTCTGGGACACAAGA 58.583 43.478 1.86 0.00 34.60 3.02
501 521 8.749026 AGCATCAAATCAAATGATTAGAGTCT 57.251 30.769 8.94 0.00 43.41 3.24
505 525 8.875803 GCAAAAGCATCAAATCAAATGATTAGA 58.124 29.630 8.94 0.00 43.41 2.10
506 526 7.844169 CGCAAAAGCATCAAATCAAATGATTAG 59.156 33.333 8.94 2.35 43.41 1.73
507 527 7.674472 GCGCAAAAGCATCAAATCAAATGATTA 60.674 33.333 0.30 0.00 39.19 1.75
508 528 6.539324 CGCAAAAGCATCAAATCAAATGATT 58.461 32.000 2.83 2.83 45.91 2.57
509 529 5.446741 GCGCAAAAGCATCAAATCAAATGAT 60.447 36.000 0.30 0.00 38.02 2.45
510 530 4.143073 GCGCAAAAGCATCAAATCAAATGA 60.143 37.500 0.30 0.00 37.05 2.57
511 531 4.085884 GCGCAAAAGCATCAAATCAAATG 58.914 39.130 0.30 0.00 37.05 2.32
574 594 4.410228 ACAGATTTCTAAGATAGGCAGCCA 59.590 41.667 15.80 0.00 0.00 4.75
608 628 1.056700 AGGACAGCCAACCAGACAGT 61.057 55.000 0.00 0.00 36.29 3.55
609 629 0.976641 TAGGACAGCCAACCAGACAG 59.023 55.000 0.00 0.00 36.29 3.51
610 630 0.976641 CTAGGACAGCCAACCAGACA 59.023 55.000 0.00 0.00 36.29 3.41
611 631 0.250513 CCTAGGACAGCCAACCAGAC 59.749 60.000 1.05 0.00 36.29 3.51
612 632 0.116342 TCCTAGGACAGCCAACCAGA 59.884 55.000 7.62 0.00 36.29 3.86
613 633 0.984230 TTCCTAGGACAGCCAACCAG 59.016 55.000 12.22 0.00 36.29 4.00
653 674 3.039011 GTGGTCTGGTATGGAGTATGGT 58.961 50.000 0.00 0.00 0.00 3.55
656 677 4.721776 ACAATGTGGTCTGGTATGGAGTAT 59.278 41.667 0.00 0.00 0.00 2.12
746 797 2.258013 TGCACGCAAAGGCAGGTAC 61.258 57.895 0.00 0.00 41.24 3.34
747 798 2.112087 TGCACGCAAAGGCAGGTA 59.888 55.556 0.00 0.00 41.24 3.08
765 817 2.125793 GGGTCCGCTTGTACCGTC 60.126 66.667 0.00 0.00 36.57 4.79
780 832 2.840102 CTAGCCTGGAGGACGGGG 60.840 72.222 0.00 0.00 46.45 5.73
920 985 2.086869 CTCGAGTGTGGGCAATTGATT 58.913 47.619 10.34 0.00 33.28 2.57
929 994 2.262915 GCAGGTCTCGAGTGTGGG 59.737 66.667 13.13 1.12 0.00 4.61
1145 1217 0.039437 ACGACCACTGCAAGACGTAG 60.039 55.000 6.74 0.00 37.43 3.51
1146 1218 1.069022 GTACGACCACTGCAAGACGTA 60.069 52.381 10.19 10.19 37.43 3.57
1147 1219 0.318445 GTACGACCACTGCAAGACGT 60.318 55.000 11.74 11.74 37.43 4.34
1148 1220 1.334992 CGTACGACCACTGCAAGACG 61.335 60.000 10.44 0.00 37.43 4.18
1149 1221 0.318445 ACGTACGACCACTGCAAGAC 60.318 55.000 24.41 0.00 37.43 3.01
1150 1222 0.039798 GACGTACGACCACTGCAAGA 60.040 55.000 24.41 0.00 37.43 3.02
1151 1223 1.007336 GGACGTACGACCACTGCAAG 61.007 60.000 27.90 0.00 42.29 4.01
1152 1224 1.007038 GGACGTACGACCACTGCAA 60.007 57.895 27.90 0.00 0.00 4.08
1153 1225 1.457823 AAGGACGTACGACCACTGCA 61.458 55.000 32.49 0.00 32.53 4.41
1154 1226 1.007336 CAAGGACGTACGACCACTGC 61.007 60.000 32.49 12.30 32.53 4.40
1155 1227 1.007336 GCAAGGACGTACGACCACTG 61.007 60.000 32.49 27.86 32.53 3.66
1156 1228 1.288127 GCAAGGACGTACGACCACT 59.712 57.895 32.49 19.43 32.53 4.00
1157 1229 2.084681 CGCAAGGACGTACGACCAC 61.085 63.158 32.49 21.73 32.53 4.16
1158 1230 2.256158 CGCAAGGACGTACGACCA 59.744 61.111 32.49 0.00 32.53 4.02
1159 1231 2.084681 CACGCAAGGACGTACGACC 61.085 63.158 26.08 26.08 46.34 4.79
1160 1232 2.713894 GCACGCAAGGACGTACGAC 61.714 63.158 24.41 16.49 46.34 4.34
1161 1233 2.429571 GCACGCAAGGACGTACGA 60.430 61.111 24.41 0.00 46.34 3.43
1162 1234 3.823421 CGCACGCAAGGACGTACG 61.823 66.667 15.01 15.01 46.34 3.67
1210 1290 1.273267 ACCTCCTAGATCTGCACACCA 60.273 52.381 5.18 0.00 0.00 4.17
1230 1310 2.003658 GATACCCCGTCGCCGTGTTA 62.004 60.000 0.00 0.00 0.00 2.41
1248 1328 0.955919 TGAGCGAGAAGACGAGCAGA 60.956 55.000 0.00 0.00 35.09 4.26
1411 1491 2.027605 CGGTGCGAGTGTGAGTGT 59.972 61.111 0.00 0.00 0.00 3.55
1412 1492 3.406361 GCGGTGCGAGTGTGAGTG 61.406 66.667 0.00 0.00 0.00 3.51
1413 1493 4.664677 GGCGGTGCGAGTGTGAGT 62.665 66.667 0.00 0.00 0.00 3.41
1414 1494 4.363990 AGGCGGTGCGAGTGTGAG 62.364 66.667 0.00 0.00 0.00 3.51
1415 1495 4.662961 CAGGCGGTGCGAGTGTGA 62.663 66.667 0.00 0.00 0.00 3.58
1416 1496 4.969196 ACAGGCGGTGCGAGTGTG 62.969 66.667 0.00 0.00 0.00 3.82
1431 1511 9.753674 ATAGAGAGGGATTACATTTTTGAAACA 57.246 29.630 0.00 0.00 0.00 2.83
1438 1524 7.385894 AGCAGATAGAGAGGGATTACATTTT 57.614 36.000 0.00 0.00 0.00 1.82
1439 1525 7.732593 AGTAGCAGATAGAGAGGGATTACATTT 59.267 37.037 0.00 0.00 0.00 2.32
1440 1526 7.245292 AGTAGCAGATAGAGAGGGATTACATT 58.755 38.462 0.00 0.00 0.00 2.71
1441 1527 6.799827 AGTAGCAGATAGAGAGGGATTACAT 58.200 40.000 0.00 0.00 0.00 2.29
1442 1528 6.207509 AGTAGCAGATAGAGAGGGATTACA 57.792 41.667 0.00 0.00 0.00 2.41
1443 1529 5.650703 GGAGTAGCAGATAGAGAGGGATTAC 59.349 48.000 0.00 0.00 0.00 1.89
1444 1530 5.313506 TGGAGTAGCAGATAGAGAGGGATTA 59.686 44.000 0.00 0.00 0.00 1.75
1445 1531 4.107149 TGGAGTAGCAGATAGAGAGGGATT 59.893 45.833 0.00 0.00 0.00 3.01
1446 1532 3.660177 TGGAGTAGCAGATAGAGAGGGAT 59.340 47.826 0.00 0.00 0.00 3.85
1447 1533 3.056832 TGGAGTAGCAGATAGAGAGGGA 58.943 50.000 0.00 0.00 0.00 4.20
1448 1534 3.181434 ACTGGAGTAGCAGATAGAGAGGG 60.181 52.174 0.00 0.00 0.00 4.30
1449 1535 4.098914 ACTGGAGTAGCAGATAGAGAGG 57.901 50.000 0.00 0.00 0.00 3.69
1453 1539 4.418973 ACGTACTGGAGTAGCAGATAGA 57.581 45.455 0.00 0.00 0.00 1.98
1455 1541 5.678583 AGTTACGTACTGGAGTAGCAGATA 58.321 41.667 0.00 0.00 35.19 1.98
1464 1550 3.822996 CACTGTGAGTTACGTACTGGAG 58.177 50.000 0.32 0.00 37.17 3.86
1466 1552 2.030185 AGCACTGTGAGTTACGTACTGG 60.030 50.000 12.86 0.00 37.17 4.00
1501 1588 1.703438 GCGAGGCTGCAGATGTTCAG 61.703 60.000 20.43 2.22 34.15 3.02
1530 1617 1.688311 CCTCGGTTCCCCAGAGTGATA 60.688 57.143 0.00 0.00 32.73 2.15
1539 1626 4.468689 CGCCTTCCTCGGTTCCCC 62.469 72.222 0.00 0.00 0.00 4.81
1569 1656 4.744137 GTGTGATGAGTTGCTAGCAGATAG 59.256 45.833 18.45 0.00 34.31 2.08
1570 1657 4.403752 AGTGTGATGAGTTGCTAGCAGATA 59.596 41.667 18.45 6.51 0.00 1.98
1574 1661 2.691927 CAGTGTGATGAGTTGCTAGCA 58.308 47.619 14.93 14.93 0.00 3.49
1576 1663 2.969990 AGCAGTGTGATGAGTTGCTAG 58.030 47.619 0.00 0.00 42.81 3.42
1577 1664 3.407424 AAGCAGTGTGATGAGTTGCTA 57.593 42.857 0.00 0.00 43.74 3.49
1579 1666 3.303406 GAAAAGCAGTGTGATGAGTTGC 58.697 45.455 0.00 0.00 35.09 4.17
1580 1667 3.567164 AGGAAAAGCAGTGTGATGAGTTG 59.433 43.478 0.00 0.00 0.00 3.16
1581 1668 3.825328 AGGAAAAGCAGTGTGATGAGTT 58.175 40.909 0.00 0.00 0.00 3.01
1582 1669 3.498774 AGGAAAAGCAGTGTGATGAGT 57.501 42.857 0.00 0.00 0.00 3.41
1583 1670 4.612259 CGAAAGGAAAAGCAGTGTGATGAG 60.612 45.833 0.00 0.00 0.00 2.90
1584 1671 3.250762 CGAAAGGAAAAGCAGTGTGATGA 59.749 43.478 0.00 0.00 0.00 2.92
1585 1672 3.250762 TCGAAAGGAAAAGCAGTGTGATG 59.749 43.478 0.00 0.00 0.00 3.07
1586 1673 3.476552 TCGAAAGGAAAAGCAGTGTGAT 58.523 40.909 0.00 0.00 0.00 3.06
1589 1676 3.476552 TCATCGAAAGGAAAAGCAGTGT 58.523 40.909 0.00 0.00 0.00 3.55
1590 1677 4.691860 ATCATCGAAAGGAAAAGCAGTG 57.308 40.909 0.00 0.00 0.00 3.66
1614 1732 7.962918 GCAAGACGAACACATAATTCATAAGTT 59.037 33.333 0.00 0.00 0.00 2.66
1642 1760 2.266055 CCTCCAACGTCCTCTGCC 59.734 66.667 0.00 0.00 0.00 4.85
1691 1809 1.276421 TGGAGCAGAAGCAGGTAGAAC 59.724 52.381 0.00 0.00 45.49 3.01
1735 1853 2.203788 AGGCCTGTCCAACTCCGA 60.204 61.111 3.11 0.00 37.29 4.55
1736 1854 2.046892 CAGGCCTGTCCAACTCCG 60.047 66.667 25.53 0.00 37.29 4.63
1770 1888 2.510238 GATCTCGCGGCAGCAAGT 60.510 61.111 10.08 0.00 45.49 3.16
1772 1890 4.838152 GGGATCTCGCGGCAGCAA 62.838 66.667 10.08 0.00 45.49 3.91
1876 1997 0.033504 ACAGTTGCTGGTACTCGGTG 59.966 55.000 1.08 0.00 35.51 4.94
1879 2000 2.096980 TCGATACAGTTGCTGGTACTCG 59.903 50.000 1.08 4.06 35.51 4.18
1884 2005 1.673033 GCACTCGATACAGTTGCTGGT 60.673 52.381 1.08 0.00 35.51 4.00
1888 2009 1.714794 ACTGCACTCGATACAGTTGC 58.285 50.000 8.77 1.97 41.78 4.17
1956 2078 1.135527 TGCCTACGGAAATACACGAGG 59.864 52.381 0.00 0.00 33.54 4.63
2095 2230 9.575868 CCTAATCTTGTATAGTTGAGGTAGAGA 57.424 37.037 0.00 0.00 0.00 3.10
2117 2252 0.770557 AGTTGTGGCCCACCTCCTAA 60.771 55.000 12.25 0.00 36.63 2.69
2154 2289 5.830000 GGGGGTGTTGAGTATGTATTTTC 57.170 43.478 0.00 0.00 0.00 2.29
2194 2337 0.894184 GTCCAGTCTCCGTGTCTCCA 60.894 60.000 0.00 0.00 0.00 3.86
2203 2346 2.232696 GAGGAGTTTCAGTCCAGTCTCC 59.767 54.545 0.00 0.00 40.24 3.71
2214 2357 2.037251 CTCCCGTCTTTGAGGAGTTTCA 59.963 50.000 0.00 0.00 41.96 2.69
2267 2411 3.632107 GTGCCGACGACGCAACAA 61.632 61.111 0.64 0.00 38.29 2.83
2330 2474 6.237516 CGAAGCATATTGAGCTCGATATTCAG 60.238 42.308 27.39 19.40 42.53 3.02
2478 2622 2.895372 GGCTAATGTCGTGGCCGG 60.895 66.667 0.00 0.00 35.08 6.13
2501 2645 2.835705 CGCCGAGGCAGAGTATCGT 61.836 63.158 15.03 0.00 42.06 3.73
2540 2684 1.298157 CTTGGTCATCGAAGCGGCAA 61.298 55.000 1.45 0.00 0.00 4.52
2620 2765 2.660064 GGATGTCGACTGGGCTGGT 61.660 63.158 17.92 0.00 0.00 4.00
2633 2778 1.379443 TCGTGGCCTACTCGGATGT 60.379 57.895 3.32 0.00 36.76 3.06
2720 2867 0.179020 CACTGGACCTTGGTGAAGCA 60.179 55.000 0.00 0.00 33.32 3.91


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

AutoCloner maintained by Alex Coulton.