Multiple sequence alignment - TraesCS6B01G078900

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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 TraesCS6B01G078900 chr6B 100.000 2598 0 0 1 2598 55435447 55438044 0.000000e+00 4798.0
1 TraesCS6B01G078900 chr6B 86.221 958 85 24 828 1745 55651519 55650569 0.000000e+00 994.0
2 TraesCS6B01G078900 chr6B 88.953 697 49 13 797 1479 55695567 55694885 0.000000e+00 835.0
3 TraesCS6B01G078900 chr6B 88.376 585 44 17 844 1420 54877223 54876655 0.000000e+00 682.0
4 TraesCS6B01G078900 chr6B 90.964 166 11 2 1479 1641 67121019 67121183 1.210000e-53 220.0
5 TraesCS6B01G078900 chr6B 86.076 158 13 2 1765 1921 67121282 67121431 7.440000e-36 161.0
6 TraesCS6B01G078900 chrUn 83.618 1874 138 63 833 2594 103670325 103672141 0.000000e+00 1604.0
7 TraesCS6B01G078900 chrUn 87.528 890 69 25 846 1700 103772377 103771495 0.000000e+00 990.0
8 TraesCS6B01G078900 chrUn 79.614 363 47 17 179 518 103516812 103516454 4.320000e-58 235.0
9 TraesCS6B01G078900 chr6A 84.035 1472 116 54 828 2243 28666787 28665379 0.000000e+00 1306.0
10 TraesCS6B01G078900 chr6A 86.199 884 63 26 845 1700 31264721 31263869 0.000000e+00 902.0
11 TraesCS6B01G078900 chr6A 87.840 773 65 17 869 1613 28640806 28641577 0.000000e+00 880.0
12 TraesCS6B01G078900 chr6A 89.322 590 47 15 841 1420 29081704 29082287 0.000000e+00 726.0
13 TraesCS6B01G078900 chr6A 87.214 524 37 18 845 1345 28773806 28773290 1.040000e-158 569.0
14 TraesCS6B01G078900 chr6A 84.416 539 58 13 4 526 28667633 28667105 8.300000e-140 507.0
15 TraesCS6B01G078900 chr6A 83.142 522 66 11 1 509 28639961 28640473 8.470000e-125 457.0
16 TraesCS6B01G078900 chr6A 86.550 342 19 10 2281 2598 28665178 28664840 4.110000e-93 351.0
17 TraesCS6B01G078900 chr1B 82.872 759 80 28 882 1593 398836461 398837216 1.010000e-178 636.0
18 TraesCS6B01G078900 chr7B 84.044 633 63 18 882 1480 589740772 589740144 2.240000e-160 575.0
19 TraesCS6B01G078900 chr2D 88.718 390 27 8 1858 2246 133477613 133477240 6.550000e-126 460.0
20 TraesCS6B01G078900 chr2D 91.304 46 4 0 2513 2558 9560400 9560355 2.160000e-06 63.9
21 TraesCS6B01G078900 chr2D 100.000 28 0 0 2513 2540 259255820 259255793 5.000000e-03 52.8
22 TraesCS6B01G078900 chr5A 89.231 325 21 8 2281 2594 559870170 559870491 6.740000e-106 394.0
23 TraesCS6B01G078900 chr7A 88.000 325 25 9 2281 2594 89339101 89338780 3.160000e-99 372.0
24 TraesCS6B01G078900 chr3A 86.930 329 25 10 2281 2594 324368604 324368929 1.140000e-93 353.0
25 TraesCS6B01G078900 chr5B 87.500 48 6 0 2511 2558 50347241 50347194 3.610000e-04 56.5


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 TraesCS6B01G078900 chr6B 55435447 55438044 2597 False 4798.000000 4798 100.000000 1 2598 1 chr6B.!!$F1 2597
1 TraesCS6B01G078900 chr6B 55650569 55651519 950 True 994.000000 994 86.221000 828 1745 1 chr6B.!!$R2 917
2 TraesCS6B01G078900 chr6B 55694885 55695567 682 True 835.000000 835 88.953000 797 1479 1 chr6B.!!$R3 682
3 TraesCS6B01G078900 chr6B 54876655 54877223 568 True 682.000000 682 88.376000 844 1420 1 chr6B.!!$R1 576
4 TraesCS6B01G078900 chrUn 103670325 103672141 1816 False 1604.000000 1604 83.618000 833 2594 1 chrUn.!!$F1 1761
5 TraesCS6B01G078900 chrUn 103771495 103772377 882 True 990.000000 990 87.528000 846 1700 1 chrUn.!!$R2 854
6 TraesCS6B01G078900 chr6A 31263869 31264721 852 True 902.000000 902 86.199000 845 1700 1 chr6A.!!$R2 855
7 TraesCS6B01G078900 chr6A 29081704 29082287 583 False 726.000000 726 89.322000 841 1420 1 chr6A.!!$F1 579
8 TraesCS6B01G078900 chr6A 28664840 28667633 2793 True 721.333333 1306 85.000333 4 2598 3 chr6A.!!$R3 2594
9 TraesCS6B01G078900 chr6A 28639961 28641577 1616 False 668.500000 880 85.491000 1 1613 2 chr6A.!!$F2 1612
10 TraesCS6B01G078900 chr6A 28773290 28773806 516 True 569.000000 569 87.214000 845 1345 1 chr6A.!!$R1 500
11 TraesCS6B01G078900 chr1B 398836461 398837216 755 False 636.000000 636 82.872000 882 1593 1 chr1B.!!$F1 711
12 TraesCS6B01G078900 chr7B 589740144 589740772 628 True 575.000000 575 84.044000 882 1480 1 chr7B.!!$R1 598

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
993 1072 0.179 CCATCTCCTCCCCTGAAACG 59.821 60.0 0.0 0.0 0.0 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2136 2356 0.250513 GAGCTCCACTCCGGTTCATT 59.749 55.0 0.87 0.0 39.75 2.57 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
69 70 4.818546 CACAGGGCATTTCGATATTTCTCT 59.181 41.667 0.00 0.00 0.00 3.10
70 71 5.297776 CACAGGGCATTTCGATATTTCTCTT 59.702 40.000 0.00 0.00 0.00 2.85
81 82 8.425577 TTCGATATTTCTCTTGCCTTTCTAAG 57.574 34.615 0.00 0.00 0.00 2.18
171 174 4.156455 ACCAATCAGTATCCTCGCAAAT 57.844 40.909 0.00 0.00 0.00 2.32
185 188 5.417266 TCCTCGCAAATGAACATATTTGGAA 59.583 36.000 11.73 0.00 44.37 3.53
186 189 5.745294 CCTCGCAAATGAACATATTTGGAAG 59.255 40.000 11.73 1.05 44.37 3.46
196 199 7.461749 TGAACATATTTGGAAGACCTTTCTCT 58.538 34.615 0.00 0.00 37.04 3.10
198 201 8.712228 AACATATTTGGAAGACCTTTCTCTTT 57.288 30.769 0.00 0.00 37.04 2.52
229 232 2.300152 TCTAACAGAGCAACCAGAGTGG 59.700 50.000 0.00 0.00 45.02 4.00
236 239 1.980765 AGCAACCAGAGTGGAAGATGA 59.019 47.619 0.00 0.00 40.96 2.92
237 240 2.079925 GCAACCAGAGTGGAAGATGAC 58.920 52.381 0.00 0.00 40.96 3.06
250 253 1.389555 AGATGACGCATGGTACGAGA 58.610 50.000 0.00 0.00 0.00 4.04
252 255 0.249073 ATGACGCATGGTACGAGAGC 60.249 55.000 0.00 0.00 0.00 4.09
290 294 2.975799 GCCCAAACCGCTCGTTCA 60.976 61.111 0.00 0.00 31.78 3.18
319 323 0.944386 TTTTGTGCTCGTTCCTCTGC 59.056 50.000 0.00 0.00 0.00 4.26
320 324 1.221466 TTTGTGCTCGTTCCTCTGCG 61.221 55.000 0.00 0.00 0.00 5.18
321 325 3.482783 GTGCTCGTTCCTCTGCGC 61.483 66.667 0.00 0.00 0.00 6.09
322 326 3.684990 TGCTCGTTCCTCTGCGCT 61.685 61.111 9.73 0.00 0.00 5.92
326 330 0.459237 CTCGTTCCTCTGCGCTTCAT 60.459 55.000 9.73 0.00 0.00 2.57
368 372 2.738013 ACTTAGTGGCCTACAACGTC 57.262 50.000 3.32 0.00 0.00 4.34
379 384 4.388165 GGCCTACAACGTCTTCTAAAAGTC 59.612 45.833 0.00 0.00 33.95 3.01
389 403 6.975772 ACGTCTTCTAAAAGTCAGCAGATATC 59.024 38.462 0.00 0.00 33.95 1.63
415 429 9.592720 CAGTTTTTGTGTTAGTTTTTGGAAAAG 57.407 29.630 0.00 0.00 0.00 2.27
479 494 8.615878 TCATAAATTCGAAAAGTTCTCTGGAA 57.384 30.769 0.00 0.00 0.00 3.53
512 527 5.704217 TCCACACGTTTTAAAATGTTTGC 57.296 34.783 24.51 4.47 36.05 3.68
514 529 5.812642 TCCACACGTTTTAAAATGTTTGCAT 59.187 32.000 24.51 8.56 36.05 3.96
515 530 6.313905 TCCACACGTTTTAAAATGTTTGCATT 59.686 30.769 24.51 3.48 46.38 3.56
588 618 7.916077 TTAGAAAATGTTTAGAAACCCCCAA 57.084 32.000 2.80 0.00 38.11 4.12
589 619 6.816616 AGAAAATGTTTAGAAACCCCCAAA 57.183 33.333 2.80 0.00 38.11 3.28
590 620 7.201702 AGAAAATGTTTAGAAACCCCCAAAA 57.798 32.000 2.80 0.00 38.11 2.44
591 621 7.051623 AGAAAATGTTTAGAAACCCCCAAAAC 58.948 34.615 2.80 0.00 38.11 2.43
592 622 4.967084 ATGTTTAGAAACCCCCAAAACC 57.033 40.909 2.80 0.00 38.11 3.27
593 623 3.721021 TGTTTAGAAACCCCCAAAACCA 58.279 40.909 2.80 0.00 38.11 3.67
594 624 3.707102 TGTTTAGAAACCCCCAAAACCAG 59.293 43.478 2.80 0.00 38.11 4.00
597 627 2.394632 AGAAACCCCCAAAACCAGAAC 58.605 47.619 0.00 0.00 0.00 3.01
598 628 1.067974 GAAACCCCCAAAACCAGAACG 59.932 52.381 0.00 0.00 0.00 3.95
599 629 1.396607 AACCCCCAAAACCAGAACGC 61.397 55.000 0.00 0.00 0.00 4.84
600 630 2.642700 CCCCAAAACCAGAACGCG 59.357 61.111 3.53 3.53 0.00 6.01
602 632 1.574428 CCCAAAACCAGAACGCGAG 59.426 57.895 15.93 0.00 0.00 5.03
606 647 1.155424 AAAACCAGAACGCGAGCGAA 61.155 50.000 24.72 0.00 42.83 4.70
609 650 1.154654 CCAGAACGCGAGCGAAAAC 60.155 57.895 24.72 11.23 42.83 2.43
611 652 2.202008 GAACGCGAGCGAAAACCG 60.202 61.111 24.72 2.68 42.83 4.44
627 668 5.966503 CGAAAACCGAATAAACAAACACAGA 59.033 36.000 0.00 0.00 41.76 3.41
656 697 8.907222 AAAAATGTCCATAAGCTTCACAAAAT 57.093 26.923 0.00 0.00 0.00 1.82
658 699 7.472334 AATGTCCATAAGCTTCACAAAATCT 57.528 32.000 0.00 0.00 0.00 2.40
661 702 6.072508 TGTCCATAAGCTTCACAAAATCTGTC 60.073 38.462 0.00 0.00 35.47 3.51
662 703 6.003326 TCCATAAGCTTCACAAAATCTGTCA 58.997 36.000 0.00 0.00 35.47 3.58
755 797 3.676291 TTAAATGTTTCCAAGCTGCCC 57.324 42.857 0.00 0.00 0.00 5.36
987 1066 2.288643 GCTCCCATCTCCTCCCCT 59.711 66.667 0.00 0.00 0.00 4.79
993 1072 0.179000 CCATCTCCTCCCCTGAAACG 59.821 60.000 0.00 0.00 0.00 3.60
998 1077 2.434359 CTCCCCTGAAACGTCGCC 60.434 66.667 0.00 0.00 0.00 5.54
1045 1135 4.326766 CGCCGCAACAACCACCAG 62.327 66.667 0.00 0.00 0.00 4.00
1047 1137 3.215568 CCGCAACAACCACCAGCA 61.216 61.111 0.00 0.00 0.00 4.41
1048 1138 2.332514 CGCAACAACCACCAGCAG 59.667 61.111 0.00 0.00 0.00 4.24
1049 1139 2.480610 CGCAACAACCACCAGCAGT 61.481 57.895 0.00 0.00 0.00 4.40
1050 1140 1.163420 CGCAACAACCACCAGCAGTA 61.163 55.000 0.00 0.00 0.00 2.74
1051 1141 1.028905 GCAACAACCACCAGCAGTAA 58.971 50.000 0.00 0.00 0.00 2.24
1052 1142 1.407258 GCAACAACCACCAGCAGTAAA 59.593 47.619 0.00 0.00 0.00 2.01
1053 1143 2.159170 GCAACAACCACCAGCAGTAAAA 60.159 45.455 0.00 0.00 0.00 1.52
1054 1144 3.677424 GCAACAACCACCAGCAGTAAAAA 60.677 43.478 0.00 0.00 0.00 1.94
1055 1145 3.793797 ACAACCACCAGCAGTAAAAAC 57.206 42.857 0.00 0.00 0.00 2.43
1064 1193 3.128589 CCAGCAGTAAAAACACACACACT 59.871 43.478 0.00 0.00 0.00 3.55
1268 1400 0.545171 TCATCTACGAGGAGACCCGT 59.455 55.000 0.00 0.00 42.15 5.28
1458 1603 3.028590 GCGCCGCCATACTCGTAC 61.029 66.667 0.00 0.00 0.00 3.67
1459 1604 2.719979 CGCCGCCATACTCGTACT 59.280 61.111 0.00 0.00 0.00 2.73
1460 1605 1.944035 CGCCGCCATACTCGTACTA 59.056 57.895 0.00 0.00 0.00 1.82
1526 1686 0.658536 GCTGCTGTCTGTTGTTTCGC 60.659 55.000 0.00 0.00 0.00 4.70
1531 1694 2.480419 GCTGTCTGTTGTTTCGCTGTAT 59.520 45.455 0.00 0.00 0.00 2.29
1540 1717 5.119588 TGTTGTTTCGCTGTATTACTAGCAC 59.880 40.000 14.41 8.46 39.87 4.40
1614 1792 6.238484 GCTCTGTTGTTAAATCTTGTCAGTGT 60.238 38.462 0.00 0.00 0.00 3.55
1641 1819 7.378728 GCTTTGTTAAATCTTAGCAGTTCGTTT 59.621 33.333 0.00 0.00 0.00 3.60
1647 1825 3.596214 TCTTAGCAGTTCGTTTCCCATC 58.404 45.455 0.00 0.00 0.00 3.51
1651 1829 1.339151 GCAGTTCGTTTCCCATCTCCT 60.339 52.381 0.00 0.00 0.00 3.69
1652 1830 2.350522 CAGTTCGTTTCCCATCTCCTG 58.649 52.381 0.00 0.00 0.00 3.86
1665 1843 0.315251 TCTCCTGTTGTCTGTCGCTG 59.685 55.000 0.00 0.00 0.00 5.18
1666 1844 0.668706 CTCCTGTTGTCTGTCGCTGG 60.669 60.000 0.00 0.00 0.00 4.85
1667 1845 1.112916 TCCTGTTGTCTGTCGCTGGA 61.113 55.000 0.00 0.00 0.00 3.86
1690 1868 0.108662 CTTTTCTGCCCCCAAATCGC 60.109 55.000 0.00 0.00 0.00 4.58
1703 1881 1.795872 CAAATCGCTCGTGTTGGTGTA 59.204 47.619 0.00 0.00 0.00 2.90
1705 1883 0.885879 ATCGCTCGTGTTGGTGTAGA 59.114 50.000 0.00 0.00 0.00 2.59
1710 1888 2.866460 GCTCGTGTTGGTGTAGATGTGT 60.866 50.000 0.00 0.00 0.00 3.72
1719 1897 6.768381 TGTTGGTGTAGATGTGTTGTTGATTA 59.232 34.615 0.00 0.00 0.00 1.75
1726 1904 7.717436 TGTAGATGTGTTGTTGATTAGAACCAA 59.283 33.333 0.00 0.00 0.00 3.67
1732 1910 5.654650 TGTTGTTGATTAGAACCAAACCTGT 59.345 36.000 0.00 0.00 0.00 4.00
1756 1941 4.607293 TTCTGTGTCAGCTGTGAAGTAT 57.393 40.909 14.67 0.00 33.27 2.12
1794 1996 0.324552 TCCCCAATTCCATGGCTGTG 60.325 55.000 6.96 4.10 39.26 3.66
1795 1997 1.332144 CCCCAATTCCATGGCTGTGG 61.332 60.000 6.96 13.16 39.26 4.17
1796 1998 0.615544 CCCAATTCCATGGCTGTGGT 60.616 55.000 19.92 0.00 40.27 4.16
1797 1999 0.533491 CCAATTCCATGGCTGTGGTG 59.467 55.000 6.96 0.00 40.27 4.17
1798 2000 0.108520 CAATTCCATGGCTGTGGTGC 60.109 55.000 6.96 0.00 40.27 5.01
1822 2027 5.587443 CCATTATCACTTCATCTTGTGCTCA 59.413 40.000 0.00 0.00 34.49 4.26
2033 2252 7.613022 TGTGATAAGAGGCATCTGATTTCTTTT 59.387 33.333 0.00 6.57 35.37 2.27
2034 2253 8.127954 GTGATAAGAGGCATCTGATTTCTTTTC 58.872 37.037 0.00 12.77 35.37 2.29
2035 2254 8.051535 TGATAAGAGGCATCTGATTTCTTTTCT 58.948 33.333 0.00 0.00 35.37 2.52
2036 2255 8.820153 ATAAGAGGCATCTGATTTCTTTTCTT 57.180 30.769 0.00 7.50 35.37 2.52
2037 2256 7.536159 AAGAGGCATCTGATTTCTTTTCTTT 57.464 32.000 0.00 0.00 35.37 2.52
2040 2259 5.541484 AGGCATCTGATTTCTTTTCTTTGGT 59.459 36.000 0.00 0.00 0.00 3.67
2075 2294 3.760684 TCTAACTACCTGACCCGAGTTTC 59.239 47.826 0.00 0.00 34.15 2.78
2116 2336 3.811497 TGATTCTTTGGCTGCAGATATCG 59.189 43.478 20.43 1.92 0.00 2.92
2135 2355 1.679680 CGCCTGATTGCAGATGGAAAT 59.320 47.619 0.00 0.00 45.17 2.17
2136 2356 2.880268 CGCCTGATTGCAGATGGAAATA 59.120 45.455 0.00 0.00 45.17 1.40
2169 2389 1.367659 GAGCTCAAGGTGCAGACATC 58.632 55.000 9.40 0.00 0.00 3.06
2265 2508 4.507756 CGAAATGATCAAAGGAGCACGATA 59.492 41.667 0.00 0.00 43.13 2.92
2273 2516 8.147704 TGATCAAAGGAGCACGATAATGTATAA 58.852 33.333 0.00 0.00 33.81 0.98
2274 2517 8.902540 ATCAAAGGAGCACGATAATGTATAAA 57.097 30.769 0.00 0.00 0.00 1.40
2276 2519 7.766738 TCAAAGGAGCACGATAATGTATAAACA 59.233 33.333 0.00 0.00 40.69 2.83
2277 2520 7.715265 AAGGAGCACGATAATGTATAAACAG 57.285 36.000 0.00 0.00 39.49 3.16
2279 2522 5.696724 GGAGCACGATAATGTATAAACAGCT 59.303 40.000 0.00 0.00 39.49 4.24
2280 2523 6.866770 GGAGCACGATAATGTATAAACAGCTA 59.133 38.462 0.00 0.00 39.49 3.32
2281 2524 7.148787 GGAGCACGATAATGTATAAACAGCTAC 60.149 40.741 0.00 0.00 39.49 3.58
2282 2525 7.434492 AGCACGATAATGTATAAACAGCTACT 58.566 34.615 0.00 0.00 39.49 2.57
2296 2687 3.007290 ACAGCTACTGTGCATCTGAAGAA 59.993 43.478 0.00 0.00 43.63 2.52
2298 2689 3.007290 AGCTACTGTGCATCTGAAGAACA 59.993 43.478 0.00 0.00 34.99 3.18
2326 2718 6.817184 TGGAAACTGTATGAGATTAGGCTAC 58.183 40.000 0.00 0.00 0.00 3.58
2329 2721 8.639761 GGAAACTGTATGAGATTAGGCTACTTA 58.360 37.037 0.00 0.00 0.00 2.24
2498 2901 3.243068 CCAACCGAGTTTCCAAAACTGAG 60.243 47.826 9.65 3.93 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.771267 TCTTATATAAGTCTTGCTCGTCCTCA 59.229 38.462 19.58 0.00 34.93 3.86
53 54 7.701445 AGAAAGGCAAGAGAAATATCGAAATG 58.299 34.615 0.00 0.00 0.00 2.32
54 55 7.872113 AGAAAGGCAAGAGAAATATCGAAAT 57.128 32.000 0.00 0.00 0.00 2.17
107 108 8.484641 TTTTGCACATCAACAGTAAAATCAAA 57.515 26.923 0.00 0.00 33.73 2.69
158 161 6.857964 CCAAATATGTTCATTTGCGAGGATAC 59.142 38.462 3.57 0.00 42.19 2.24
165 168 5.516339 GGTCTTCCAAATATGTTCATTTGCG 59.484 40.000 3.57 0.00 42.19 4.85
171 174 7.461749 AGAGAAAGGTCTTCCAAATATGTTCA 58.538 34.615 0.00 0.00 32.80 3.18
185 188 2.930826 TCGCCAAAAGAGAAAGGTCT 57.069 45.000 0.00 0.00 36.55 3.85
186 189 3.982576 TTTCGCCAAAAGAGAAAGGTC 57.017 42.857 0.00 0.00 39.07 3.85
196 199 4.277174 TGCTCTGTTAGATTTTCGCCAAAA 59.723 37.500 0.00 0.00 35.92 2.44
198 201 3.407698 TGCTCTGTTAGATTTTCGCCAA 58.592 40.909 0.00 0.00 0.00 4.52
229 232 2.120232 CTCGTACCATGCGTCATCTTC 58.880 52.381 0.00 0.00 0.00 2.87
236 239 1.433879 GAGCTCTCGTACCATGCGT 59.566 57.895 6.43 0.00 0.00 5.24
237 240 1.299468 GGAGCTCTCGTACCATGCG 60.299 63.158 14.64 0.00 0.00 4.73
252 255 2.279517 GCATGGTACGAGCGGGAG 60.280 66.667 0.00 0.00 0.00 4.30
316 320 2.995466 TTTTTCCTCATGAAGCGCAG 57.005 45.000 11.47 0.00 33.63 5.18
357 361 4.986659 TGACTTTTAGAAGACGTTGTAGGC 59.013 41.667 0.00 0.00 36.69 3.93
362 366 4.745125 TCTGCTGACTTTTAGAAGACGTTG 59.255 41.667 0.00 0.00 36.69 4.10
368 372 8.715191 AACTGATATCTGCTGACTTTTAGAAG 57.285 34.615 9.35 0.00 38.87 2.85
379 384 7.810658 ACTAACACAAAAACTGATATCTGCTG 58.189 34.615 9.35 5.18 0.00 4.41
389 403 9.592720 CTTTTCCAAAAACTAACACAAAAACTG 57.407 29.630 0.00 0.00 0.00 3.16
454 468 8.615878 TTCCAGAGAACTTTTCGAATTTATGA 57.384 30.769 0.00 0.00 34.02 2.15
488 503 6.147164 TGCAAACATTTTAAAACGTGTGGAAA 59.853 30.769 16.71 0.00 0.00 3.13
489 504 5.637810 TGCAAACATTTTAAAACGTGTGGAA 59.362 32.000 16.71 2.55 0.00 3.53
561 576 8.769359 TGGGGGTTTCTAAACATTTTCTAAAAA 58.231 29.630 7.80 0.00 40.63 1.94
562 577 8.320338 TGGGGGTTTCTAAACATTTTCTAAAA 57.680 30.769 7.80 0.00 40.63 1.52
563 578 7.916077 TGGGGGTTTCTAAACATTTTCTAAA 57.084 32.000 7.80 0.00 40.63 1.85
567 597 6.261381 GGTTTTGGGGGTTTCTAAACATTTTC 59.739 38.462 7.80 0.00 40.63 2.29
568 598 6.123651 GGTTTTGGGGGTTTCTAAACATTTT 58.876 36.000 7.80 0.00 40.63 1.82
583 613 1.852067 CTCGCGTTCTGGTTTTGGGG 61.852 60.000 5.77 0.00 0.00 4.96
584 614 1.574428 CTCGCGTTCTGGTTTTGGG 59.426 57.895 5.77 0.00 0.00 4.12
585 615 1.082104 GCTCGCGTTCTGGTTTTGG 60.082 57.895 5.77 0.00 0.00 3.28
586 616 1.438710 CGCTCGCGTTCTGGTTTTG 60.439 57.895 5.77 0.00 34.35 2.44
588 618 1.155424 TTTCGCTCGCGTTCTGGTTT 61.155 50.000 5.77 0.00 40.74 3.27
589 619 1.155424 TTTTCGCTCGCGTTCTGGTT 61.155 50.000 5.77 0.00 40.74 3.67
590 620 1.593209 TTTTCGCTCGCGTTCTGGT 60.593 52.632 5.77 0.00 40.74 4.00
591 621 1.154654 GTTTTCGCTCGCGTTCTGG 60.155 57.895 5.77 0.00 40.74 3.86
592 622 1.154654 GGTTTTCGCTCGCGTTCTG 60.155 57.895 5.77 0.00 40.74 3.02
593 623 2.654912 CGGTTTTCGCTCGCGTTCT 61.655 57.895 5.77 0.00 40.74 3.01
594 624 2.149606 TTCGGTTTTCGCTCGCGTTC 62.150 55.000 5.77 0.00 40.74 3.95
597 627 0.367548 TTATTCGGTTTTCGCTCGCG 59.632 50.000 0.00 0.00 39.05 5.87
598 628 2.163638 GTTTATTCGGTTTTCGCTCGC 58.836 47.619 0.00 0.00 39.05 5.03
599 629 3.443054 TGTTTATTCGGTTTTCGCTCG 57.557 42.857 0.00 0.00 39.05 5.03
600 630 4.971220 TGTTTGTTTATTCGGTTTTCGCTC 59.029 37.500 0.00 0.00 39.05 5.03
602 632 4.499758 TGTGTTTGTTTATTCGGTTTTCGC 59.500 37.500 0.00 0.00 39.05 4.70
606 647 8.535690 TTTTTCTGTGTTTGTTTATTCGGTTT 57.464 26.923 0.00 0.00 0.00 3.27
633 674 7.816031 CAGATTTTGTGAAGCTTATGGACATTT 59.184 33.333 0.00 0.00 0.00 2.32
636 677 5.769662 ACAGATTTTGTGAAGCTTATGGACA 59.230 36.000 0.00 0.00 38.99 4.02
637 678 6.072508 TGACAGATTTTGTGAAGCTTATGGAC 60.073 38.462 0.00 0.00 41.05 4.02
727 769 8.028938 GCAGCTTGGAAACATTTAAAGATTCTA 58.971 33.333 0.00 0.00 42.32 2.10
728 770 6.870439 GCAGCTTGGAAACATTTAAAGATTCT 59.130 34.615 0.00 0.00 42.32 2.40
730 772 5.934043 GGCAGCTTGGAAACATTTAAAGATT 59.066 36.000 0.00 0.00 42.32 2.40
731 773 5.482006 GGCAGCTTGGAAACATTTAAAGAT 58.518 37.500 0.00 0.00 42.32 2.40
732 774 4.262420 GGGCAGCTTGGAAACATTTAAAGA 60.262 41.667 0.00 0.00 42.32 2.52
733 775 3.996363 GGGCAGCTTGGAAACATTTAAAG 59.004 43.478 0.00 0.00 42.32 1.85
734 776 3.645687 AGGGCAGCTTGGAAACATTTAAA 59.354 39.130 0.00 0.00 42.32 1.52
735 777 3.238597 AGGGCAGCTTGGAAACATTTAA 58.761 40.909 0.00 0.00 42.32 1.52
736 778 2.888212 AGGGCAGCTTGGAAACATTTA 58.112 42.857 0.00 0.00 42.32 1.40
739 781 1.720781 AAAGGGCAGCTTGGAAACAT 58.279 45.000 0.00 0.00 42.32 2.71
787 837 8.050930 CCTAGGTAGCTTGGAAATAAACCTAAA 58.949 37.037 16.25 0.00 34.64 1.85
788 838 7.571025 CCTAGGTAGCTTGGAAATAAACCTAA 58.429 38.462 16.25 0.00 34.64 2.69
789 839 6.408891 GCCTAGGTAGCTTGGAAATAAACCTA 60.409 42.308 23.96 0.00 34.16 3.08
790 840 5.631717 GCCTAGGTAGCTTGGAAATAAACCT 60.632 44.000 23.96 4.54 35.71 3.50
791 841 4.579340 GCCTAGGTAGCTTGGAAATAAACC 59.421 45.833 23.96 2.21 0.00 3.27
792 842 4.579340 GGCCTAGGTAGCTTGGAAATAAAC 59.421 45.833 23.96 6.09 0.00 2.01
793 843 4.228666 TGGCCTAGGTAGCTTGGAAATAAA 59.771 41.667 23.96 1.79 0.00 1.40
794 844 3.783642 TGGCCTAGGTAGCTTGGAAATAA 59.216 43.478 23.96 3.36 0.00 1.40
795 845 3.389866 TGGCCTAGGTAGCTTGGAAATA 58.610 45.455 23.96 5.63 0.00 1.40
993 1072 0.672711 GGGGGATTTATAGCGGCGAC 60.673 60.000 12.98 1.23 0.00 5.19
998 1077 1.508632 CGTGTGGGGGATTTATAGCG 58.491 55.000 0.00 0.00 0.00 4.26
1032 1121 1.028905 TTACTGCTGGTGGTTGTTGC 58.971 50.000 0.00 0.00 0.00 4.17
1034 1123 3.511934 TGTTTTTACTGCTGGTGGTTGTT 59.488 39.130 0.00 0.00 0.00 2.83
1037 1126 3.093057 TGTGTTTTTACTGCTGGTGGTT 58.907 40.909 0.00 0.00 0.00 3.67
1045 1135 4.094294 TCTGAGTGTGTGTGTTTTTACTGC 59.906 41.667 0.00 0.00 0.00 4.40
1047 1137 5.163754 GCTTCTGAGTGTGTGTGTTTTTACT 60.164 40.000 0.00 0.00 0.00 2.24
1048 1138 5.028375 GCTTCTGAGTGTGTGTGTTTTTAC 58.972 41.667 0.00 0.00 0.00 2.01
1049 1139 4.095782 GGCTTCTGAGTGTGTGTGTTTTTA 59.904 41.667 0.00 0.00 0.00 1.52
1050 1140 3.119495 GGCTTCTGAGTGTGTGTGTTTTT 60.119 43.478 0.00 0.00 0.00 1.94
1051 1141 2.423538 GGCTTCTGAGTGTGTGTGTTTT 59.576 45.455 0.00 0.00 0.00 2.43
1052 1142 2.017049 GGCTTCTGAGTGTGTGTGTTT 58.983 47.619 0.00 0.00 0.00 2.83
1053 1143 1.065491 TGGCTTCTGAGTGTGTGTGTT 60.065 47.619 0.00 0.00 0.00 3.32
1054 1144 0.541392 TGGCTTCTGAGTGTGTGTGT 59.459 50.000 0.00 0.00 0.00 3.72
1055 1145 1.667236 TTGGCTTCTGAGTGTGTGTG 58.333 50.000 0.00 0.00 0.00 3.82
1064 1193 1.153568 CGGCGAGATTGGCTTCTGA 60.154 57.895 0.00 0.00 0.00 3.27
1268 1400 0.391661 GGAAGATCTTGAGCACGCCA 60.392 55.000 14.00 0.00 0.00 5.69
1450 1582 4.944619 TGGCTAGCTAGTAGTACGAGTA 57.055 45.455 21.62 3.44 0.00 2.59
1458 1603 3.639094 AGACAACCATGGCTAGCTAGTAG 59.361 47.826 21.62 9.26 45.56 2.57
1459 1604 3.643237 AGACAACCATGGCTAGCTAGTA 58.357 45.455 21.62 11.84 45.56 1.82
1460 1605 2.472029 AGACAACCATGGCTAGCTAGT 58.528 47.619 21.62 1.73 45.56 2.57
1526 1686 5.196341 TCCATTCCGTGCTAGTAATACAG 57.804 43.478 0.00 0.00 0.00 2.74
1531 1694 5.105106 TGAGATTTCCATTCCGTGCTAGTAA 60.105 40.000 0.00 0.00 0.00 2.24
1540 1717 4.644103 AAATGCTGAGATTTCCATTCCG 57.356 40.909 0.00 0.00 0.00 4.30
1614 1792 6.017440 ACGAACTGCTAAGATTTAACAAAGCA 60.017 34.615 0.00 0.00 37.62 3.91
1641 1819 1.902508 GACAGACAACAGGAGATGGGA 59.097 52.381 0.00 0.00 0.00 4.37
1647 1825 0.668706 CCAGCGACAGACAACAGGAG 60.669 60.000 0.00 0.00 0.00 3.69
1651 1829 1.000607 GTACTCCAGCGACAGACAACA 60.001 52.381 0.00 0.00 0.00 3.33
1652 1830 1.269998 AGTACTCCAGCGACAGACAAC 59.730 52.381 0.00 0.00 0.00 3.32
1665 1843 0.696501 TGGGGGCAGAAAAGTACTCC 59.303 55.000 0.00 0.00 0.00 3.85
1666 1844 2.579410 TTGGGGGCAGAAAAGTACTC 57.421 50.000 0.00 0.00 0.00 2.59
1667 1845 3.431415 GATTTGGGGGCAGAAAAGTACT 58.569 45.455 0.00 0.00 0.00 2.73
1690 1868 3.026630 ACACATCTACACCAACACGAG 57.973 47.619 0.00 0.00 0.00 4.18
1703 1881 7.425606 GTTTGGTTCTAATCAACAACACATCT 58.574 34.615 0.00 0.00 0.00 2.90
1705 1883 6.323739 AGGTTTGGTTCTAATCAACAACACAT 59.676 34.615 0.00 0.00 0.00 3.21
1710 1888 8.472007 AATACAGGTTTGGTTCTAATCAACAA 57.528 30.769 0.00 0.00 0.00 2.83
1719 1897 5.445964 ACACAGAAATACAGGTTTGGTTCT 58.554 37.500 0.00 0.00 0.00 3.01
1726 1904 4.067896 CAGCTGACACAGAAATACAGGTT 58.932 43.478 8.42 0.00 37.24 3.50
1732 1910 4.960938 ACTTCACAGCTGACACAGAAATA 58.039 39.130 23.35 0.00 32.44 1.40
1756 1941 3.535561 GGAAAGCTCCATCTGAATCGAA 58.464 45.455 0.00 0.00 41.96 3.71
1759 1944 2.092212 TGGGGAAAGCTCCATCTGAATC 60.092 50.000 0.00 0.00 40.67 2.52
1760 1945 1.925255 TGGGGAAAGCTCCATCTGAAT 59.075 47.619 0.00 0.00 40.67 2.57
1761 1946 1.371467 TGGGGAAAGCTCCATCTGAA 58.629 50.000 0.00 0.00 40.67 3.02
1771 1973 0.178767 GCCATGGAATTGGGGAAAGC 59.821 55.000 18.40 0.00 37.24 3.51
1794 1996 4.641989 ACAAGATGAAGTGATAATGGCACC 59.358 41.667 0.00 0.00 36.95 5.01
1795 1997 5.575957 CACAAGATGAAGTGATAATGGCAC 58.424 41.667 0.00 0.00 37.97 5.01
1796 1998 4.096833 GCACAAGATGAAGTGATAATGGCA 59.903 41.667 0.00 0.00 37.97 4.92
1797 1999 4.337555 AGCACAAGATGAAGTGATAATGGC 59.662 41.667 0.00 0.00 37.97 4.40
1798 2000 5.587443 TGAGCACAAGATGAAGTGATAATGG 59.413 40.000 0.00 0.00 37.97 3.16
1799 2001 6.673154 TGAGCACAAGATGAAGTGATAATG 57.327 37.500 0.00 0.00 37.97 1.90
1800 2002 5.296283 GCTGAGCACAAGATGAAGTGATAAT 59.704 40.000 0.00 0.00 37.97 1.28
1801 2003 4.633126 GCTGAGCACAAGATGAAGTGATAA 59.367 41.667 0.00 0.00 37.97 1.75
1822 2027 4.751767 TTCAAACTTGGTTCAATTGGCT 57.248 36.364 5.42 0.00 0.00 4.75
1899 2109 3.570975 TGTTCAATTGCAGAGCACTCAAT 59.429 39.130 0.00 0.00 38.71 2.57
1948 2160 7.063780 GCATCTATGTGCAAAAACTAGCAAAAT 59.936 33.333 0.00 0.00 44.43 1.82
1975 2187 2.092592 TGCATCAGATGGTCTGCATTCT 60.093 45.455 12.54 0.00 43.95 2.40
1976 2188 2.294979 TGCATCAGATGGTCTGCATTC 58.705 47.619 12.54 0.00 43.95 2.67
1977 2189 2.430248 TGCATCAGATGGTCTGCATT 57.570 45.000 12.54 0.00 43.95 3.56
1980 2192 3.795623 AAAATGCATCAGATGGTCTGC 57.204 42.857 12.54 0.00 43.95 4.26
2003 2215 8.985315 AAATCAGATGCCTCTTATCACAATTA 57.015 30.769 0.00 0.00 0.00 1.40
2005 2217 7.288560 AGAAATCAGATGCCTCTTATCACAAT 58.711 34.615 0.00 0.00 0.00 2.71
2056 2275 2.299297 CAGAAACTCGGGTCAGGTAGTT 59.701 50.000 0.00 0.00 33.72 2.24
2116 2336 4.924305 TTATTTCCATCTGCAATCAGGC 57.076 40.909 0.00 0.00 40.69 4.85
2135 2355 1.480954 GAGCTCCACTCCGGTTCATTA 59.519 52.381 0.87 0.00 39.75 1.90
2136 2356 0.250513 GAGCTCCACTCCGGTTCATT 59.749 55.000 0.87 0.00 39.75 2.57
2169 2389 1.089920 GCACACTAACCATGAGCCTG 58.910 55.000 0.00 0.00 0.00 4.85
2265 2508 7.011763 CAGATGCACAGTAGCTGTTTATACATT 59.988 37.037 0.00 0.00 42.59 2.71
2273 2516 3.007290 TCTTCAGATGCACAGTAGCTGTT 59.993 43.478 0.00 0.00 42.59 3.16
2274 2517 2.564504 TCTTCAGATGCACAGTAGCTGT 59.435 45.455 0.00 0.00 46.51 4.40
2276 2519 3.007290 TGTTCTTCAGATGCACAGTAGCT 59.993 43.478 0.00 0.00 34.99 3.32
2277 2520 3.329386 TGTTCTTCAGATGCACAGTAGC 58.671 45.455 0.00 0.00 0.00 3.58
2279 2522 4.281941 AGACTGTTCTTCAGATGCACAGTA 59.718 41.667 17.82 0.00 46.27 2.74
2280 2523 3.070734 AGACTGTTCTTCAGATGCACAGT 59.929 43.478 17.83 17.83 46.27 3.55
2281 2524 3.432592 CAGACTGTTCTTCAGATGCACAG 59.567 47.826 12.64 12.64 46.27 3.66
2282 2525 3.396560 CAGACTGTTCTTCAGATGCACA 58.603 45.455 0.00 0.00 46.27 4.57
2298 2689 6.407525 GCCTAATCTCATACAGTTTCCAGACT 60.408 42.308 0.00 0.00 0.00 3.24
2326 2718 6.358030 GCTACTGTGCATCGCAAAATATTAAG 59.642 38.462 0.00 0.00 41.47 1.85
2329 2721 4.096231 TGCTACTGTGCATCGCAAAATATT 59.904 37.500 0.00 0.00 41.47 1.28
2330 2722 3.627123 TGCTACTGTGCATCGCAAAATAT 59.373 39.130 0.00 0.00 41.47 1.28
2358 2751 3.913763 CCATGAGTTGCAAAATGTACACG 59.086 43.478 0.00 0.00 0.00 4.49
2416 2809 7.415592 TTTGAAATGGTGCCAATATGATACA 57.584 32.000 0.00 0.00 0.00 2.29
2461 2864 5.238650 ACTCGGTTGGTTTGAAACTTATCAG 59.761 40.000 8.09 0.92 0.00 2.90
2542 2970 2.892852 TCCAAAATTGAAGTGGAGGCTG 59.107 45.455 0.00 0.00 36.51 4.85


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

AutoCloner maintained by Alex Coulton.