Multiple sequence alignment - TraesCS2D01G417600

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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 TraesCS2D01G417600 chr2D 100.000 2609 0 0 1 2609 531894283 531896891 0.000000e+00 4819.0
1 TraesCS2D01G417600 chr2D 82.846 513 70 14 1 504 177453460 177452957 6.630000e-121 444.0
2 TraesCS2D01G417600 chr2D 82.595 316 21 19 998 1285 531711685 531711994 5.580000e-62 248.0
3 TraesCS2D01G417600 chr2A 85.592 1749 127 42 1 1692 676377758 676379438 0.000000e+00 1718.0
4 TraesCS2D01G417600 chr2A 92.668 491 31 3 2122 2609 676380550 676381038 0.000000e+00 702.0
5 TraesCS2D01G417600 chr2A 92.250 400 26 4 1739 2138 676380137 676380531 1.750000e-156 562.0
6 TraesCS2D01G417600 chr2A 83.333 324 27 13 978 1285 676371270 676371582 9.200000e-70 274.0
7 TraesCS2D01G417600 chr2B 91.555 971 41 20 549 1503 631700030 631700975 0.000000e+00 1301.0
8 TraesCS2D01G417600 chr2B 87.464 1053 73 16 1587 2609 631701044 631702067 0.000000e+00 1158.0
9 TraesCS2D01G417600 chr2B 83.056 301 25 17 998 1285 631601685 631601972 1.550000e-62 250.0
10 TraesCS2D01G417600 chr2B 87.342 79 8 2 2421 2498 423908136 423908213 3.580000e-14 89.8
11 TraesCS2D01G417600 chr2B 96.078 51 1 1 1491 1540 631700997 631701047 5.980000e-12 82.4
12 TraesCS2D01G417600 chr2B 90.698 43 3 1 1597 1639 765572042 765572083 3.630000e-04 56.5
13 TraesCS2D01G417600 chr1A 83.694 509 72 9 1 504 309396137 309395635 1.090000e-128 470.0
14 TraesCS2D01G417600 chr4B 83.004 506 77 8 3 504 643668943 643668443 1.420000e-122 449.0
15 TraesCS2D01G417600 chr3D 83.008 512 69 14 2 504 42767607 42768109 5.120000e-122 448.0
16 TraesCS2D01G417600 chr1D 82.087 508 79 10 4 504 447448811 447448309 8.630000e-115 424.0
17 TraesCS2D01G417600 chr1D 83.854 192 30 1 2419 2609 423673587 423673396 5.740000e-42 182.0
18 TraesCS2D01G417600 chr6D 81.128 514 75 17 1 504 146943248 146943749 2.430000e-105 392.0
19 TraesCS2D01G417600 chr1B 81.992 472 71 12 1 467 542426898 542427360 3.150000e-104 388.0
20 TraesCS2D01G417600 chr5A 80.392 510 88 9 1 504 681067049 681066546 6.820000e-101 377.0
21 TraesCS2D01G417600 chr5A 80.392 510 88 9 1 504 681138541 681138038 6.820000e-101 377.0
22 TraesCS2D01G417600 chr5A 90.164 61 6 0 2424 2484 567578772 567578712 2.150000e-11 80.5
23 TraesCS2D01G417600 chr6A 76.667 180 38 4 2432 2609 507589543 507589720 2.140000e-16 97.1
24 TraesCS2D01G417600 chr5B 76.842 190 32 11 2426 2609 211149450 211149633 2.140000e-16 97.1
25 TraesCS2D01G417600 chr3A 83.505 97 13 3 2421 2516 485992351 485992445 1.290000e-13 87.9
26 TraesCS2D01G417600 chr6B 80.208 96 16 3 2436 2530 676529006 676528913 4.660000e-08 69.4


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 TraesCS2D01G417600 chr2D 531894283 531896891 2608 False 4819.000000 4819 100.000 1 2609 1 chr2D.!!$F2 2608
1 TraesCS2D01G417600 chr2D 177452957 177453460 503 True 444.000000 444 82.846 1 504 1 chr2D.!!$R1 503
2 TraesCS2D01G417600 chr2A 676377758 676381038 3280 False 994.000000 1718 90.170 1 2609 3 chr2A.!!$F2 2608
3 TraesCS2D01G417600 chr2B 631700030 631702067 2037 False 847.133333 1301 91.699 549 2609 3 chr2B.!!$F4 2060
4 TraesCS2D01G417600 chr1A 309395635 309396137 502 True 470.000000 470 83.694 1 504 1 chr1A.!!$R1 503
5 TraesCS2D01G417600 chr4B 643668443 643668943 500 True 449.000000 449 83.004 3 504 1 chr4B.!!$R1 501
6 TraesCS2D01G417600 chr3D 42767607 42768109 502 False 448.000000 448 83.008 2 504 1 chr3D.!!$F1 502
7 TraesCS2D01G417600 chr1D 447448309 447448811 502 True 424.000000 424 82.087 4 504 1 chr1D.!!$R2 500
8 TraesCS2D01G417600 chr6D 146943248 146943749 501 False 392.000000 392 81.128 1 504 1 chr6D.!!$F1 503
9 TraesCS2D01G417600 chr5A 681066546 681067049 503 True 377.000000 377 80.392 1 504 1 chr5A.!!$R2 503
10 TraesCS2D01G417600 chr5A 681138038 681138541 503 True 377.000000 377 80.392 1 504 1 chr5A.!!$R3 503

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
319 338 0.169672 CTGGCATGAACTTTGAGCGG 59.83 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 2517 0.753111 GATTGCCGCCTGGAATCCTT 60.753 55.0 0.0 0.0 37.49 3.36 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
46 47 0.528901 CTGAACACCGTGTCACCGAA 60.529 55.000 4.23 0.00 0.00 4.30
59 64 0.250234 CACCGAAGAAGAGGCCATGA 59.750 55.000 5.01 0.00 0.00 3.07
110 115 1.730501 TCGACGACGAGTGACCTATT 58.269 50.000 5.75 0.00 43.81 1.73
111 116 1.662629 TCGACGACGAGTGACCTATTC 59.337 52.381 5.75 0.00 43.81 1.75
153 162 1.273886 TGTATGCCGACAAGTGTGCTA 59.726 47.619 0.00 0.00 0.00 3.49
154 163 2.093711 TGTATGCCGACAAGTGTGCTAT 60.094 45.455 0.00 0.00 0.00 2.97
166 175 0.901827 TGTGCTATCATGACCACGGT 59.098 50.000 0.00 0.00 0.00 4.83
193 204 3.192922 GTGGTCGAATTCCCGCCG 61.193 66.667 0.00 0.00 0.00 6.46
210 223 1.145162 CCGTTTTTGTGTGCTGGCAC 61.145 55.000 17.55 17.55 46.33 5.01
255 269 4.452114 GCGCCAATATGAACTATGTGATGA 59.548 41.667 0.00 0.00 0.00 2.92
319 338 0.169672 CTGGCATGAACTTTGAGCGG 59.830 55.000 0.00 0.00 0.00 5.52
352 371 6.294508 GCCACTAAAATATGATTTATGGCCGT 60.295 38.462 16.56 1.35 39.82 5.68
373 397 5.336849 CCGTGGGCCTTTTAAATTTATGTGA 60.337 40.000 4.53 0.00 0.00 3.58
399 423 1.503818 AATGGGTCACGCGTGTTGAC 61.504 55.000 35.74 26.59 0.00 3.18
402 426 2.958016 GTCACGCGTGTTGACCGT 60.958 61.111 35.74 0.00 35.29 4.83
412 436 2.985282 TTGACCGTACGGCCGACT 60.985 61.111 35.90 14.58 39.32 4.18
427 452 3.680458 GGCCGACTCAAAACAAAAACAAA 59.320 39.130 0.00 0.00 0.00 2.83
482 507 1.917782 AAAAGCGGATAAAGCGCGCA 61.918 50.000 35.10 13.97 40.04 6.09
490 516 1.259507 GATAAAGCGCGCATCCGTTTA 59.740 47.619 35.10 26.38 36.67 2.01
504 530 2.023223 GTTTAGGTCGGCGCGTTGA 61.023 57.895 8.43 2.59 0.00 3.18
505 531 1.079681 TTTAGGTCGGCGCGTTGAT 60.080 52.632 8.43 0.00 0.00 2.57
506 532 1.079875 TTTAGGTCGGCGCGTTGATC 61.080 55.000 8.43 6.41 0.00 2.92
507 533 2.894240 TTAGGTCGGCGCGTTGATCC 62.894 60.000 8.43 10.02 0.00 3.36
508 534 4.814294 GGTCGGCGCGTTGATCCT 62.814 66.667 8.43 0.00 0.00 3.24
509 535 2.813908 GTCGGCGCGTTGATCCTT 60.814 61.111 8.43 0.00 0.00 3.36
510 536 2.813474 TCGGCGCGTTGATCCTTG 60.813 61.111 8.43 0.00 0.00 3.61
524 550 3.840666 TGATCCTTGGAGTTGCTCTTAGT 59.159 43.478 0.00 0.00 0.00 2.24
525 551 5.023452 TGATCCTTGGAGTTGCTCTTAGTA 58.977 41.667 0.00 0.00 0.00 1.82
526 552 5.483937 TGATCCTTGGAGTTGCTCTTAGTAA 59.516 40.000 0.00 0.00 0.00 2.24
527 553 5.818678 TCCTTGGAGTTGCTCTTAGTAAA 57.181 39.130 0.00 0.00 0.00 2.01
528 554 5.548406 TCCTTGGAGTTGCTCTTAGTAAAC 58.452 41.667 0.00 0.00 0.00 2.01
529 555 4.695928 CCTTGGAGTTGCTCTTAGTAAACC 59.304 45.833 0.00 0.00 0.00 3.27
530 556 4.281898 TGGAGTTGCTCTTAGTAAACCC 57.718 45.455 0.00 0.00 0.00 4.11
531 557 3.649023 TGGAGTTGCTCTTAGTAAACCCA 59.351 43.478 0.00 0.00 0.00 4.51
532 558 4.254492 GGAGTTGCTCTTAGTAAACCCAG 58.746 47.826 0.00 0.00 0.00 4.45
533 559 4.020485 GGAGTTGCTCTTAGTAAACCCAGA 60.020 45.833 0.00 0.00 0.00 3.86
534 560 5.338463 GGAGTTGCTCTTAGTAAACCCAGAT 60.338 44.000 0.00 0.00 0.00 2.90
535 561 5.491982 AGTTGCTCTTAGTAAACCCAGATG 58.508 41.667 0.00 0.00 0.00 2.90
536 562 4.487714 TGCTCTTAGTAAACCCAGATGG 57.512 45.455 0.00 0.00 41.37 3.51
537 563 4.101114 TGCTCTTAGTAAACCCAGATGGA 58.899 43.478 0.00 0.00 37.39 3.41
538 564 4.081087 TGCTCTTAGTAAACCCAGATGGAC 60.081 45.833 0.00 0.00 37.39 4.02
539 565 4.081087 GCTCTTAGTAAACCCAGATGGACA 60.081 45.833 0.00 0.00 37.39 4.02
651 678 1.198408 GAACCCGATTCGTTTGGAACC 59.802 52.381 5.20 0.00 37.50 3.62
657 684 2.000447 GATTCGTTTGGAACCTCTCGG 59.000 52.381 0.00 0.00 37.50 4.63
752 779 9.849279 CCAAATGGGAATCAGCTATAGCTAGCA 62.849 44.444 26.45 13.91 45.79 3.49
855 882 1.850441 CGCGTTACCGGAGTAAATGAG 59.150 52.381 9.46 0.29 40.12 2.90
898 925 1.258982 GAATCGATGCATCCGTGTGAC 59.741 52.381 20.87 3.09 0.00 3.67
973 1000 2.519377 TACGCGGCTAAGCAATGTAT 57.481 45.000 12.47 0.00 36.85 2.29
974 1001 2.519377 ACGCGGCTAAGCAATGTATA 57.481 45.000 12.47 0.00 36.85 1.47
976 1003 1.459592 CGCGGCTAAGCAATGTATACC 59.540 52.381 0.00 0.00 36.85 2.73
977 1004 1.804748 GCGGCTAAGCAATGTATACCC 59.195 52.381 0.00 0.00 37.05 3.69
978 1005 2.423577 CGGCTAAGCAATGTATACCCC 58.576 52.381 0.00 0.00 0.00 4.95
979 1006 2.038557 CGGCTAAGCAATGTATACCCCT 59.961 50.000 0.00 0.00 0.00 4.79
980 1007 3.676093 GGCTAAGCAATGTATACCCCTC 58.324 50.000 0.00 0.00 0.00 4.30
981 1008 3.326747 GCTAAGCAATGTATACCCCTCG 58.673 50.000 0.00 0.00 0.00 4.63
982 1009 3.244112 GCTAAGCAATGTATACCCCTCGT 60.244 47.826 0.00 0.00 0.00 4.18
983 1010 2.910688 AGCAATGTATACCCCTCGTG 57.089 50.000 0.00 0.00 0.00 4.35
1098 1145 2.159099 ACTGTCTTGCGTTTCTCTGTGA 60.159 45.455 0.00 0.00 0.00 3.58
1099 1146 3.062763 CTGTCTTGCGTTTCTCTGTGAT 58.937 45.455 0.00 0.00 0.00 3.06
1100 1147 3.466836 TGTCTTGCGTTTCTCTGTGATT 58.533 40.909 0.00 0.00 0.00 2.57
1423 1472 1.867233 ACGTGTTGCTGATCACAAGAC 59.133 47.619 19.28 19.28 37.79 3.01
1455 1504 0.249398 ACACCAGGCAATCCTACGAC 59.751 55.000 0.00 0.00 41.93 4.34
1474 1534 1.001924 ACGATCTACATCAGCTGCTCG 60.002 52.381 9.47 10.36 0.00 5.03
1485 1545 6.153067 ACATCAGCTGCTCGTATATAGTTTC 58.847 40.000 9.47 0.00 0.00 2.78
1541 1644 4.042398 CGAGATTTGTATGACGGTGTAGG 58.958 47.826 0.00 0.00 0.00 3.18
1547 1650 3.954200 TGTATGACGGTGTAGGTCACTA 58.046 45.455 0.00 0.00 46.22 2.74
1569 1672 7.856398 CACTACATCGAGTTGTACTATTACCTG 59.144 40.741 0.00 0.00 34.40 4.00
1570 1673 5.589192 ACATCGAGTTGTACTATTACCTGC 58.411 41.667 0.00 0.00 0.00 4.85
1571 1674 4.644103 TCGAGTTGTACTATTACCTGCC 57.356 45.455 0.00 0.00 0.00 4.85
1572 1675 3.382546 TCGAGTTGTACTATTACCTGCCC 59.617 47.826 0.00 0.00 0.00 5.36
1573 1676 3.492137 CGAGTTGTACTATTACCTGCCCC 60.492 52.174 0.00 0.00 0.00 5.80
1574 1677 2.433239 AGTTGTACTATTACCTGCCCCG 59.567 50.000 0.00 0.00 0.00 5.73
1575 1678 0.754472 TGTACTATTACCTGCCCCGC 59.246 55.000 0.00 0.00 0.00 6.13
1576 1679 0.754472 GTACTATTACCTGCCCCGCA 59.246 55.000 0.00 0.00 36.92 5.69
1577 1680 1.139455 GTACTATTACCTGCCCCGCAA 59.861 52.381 0.00 0.00 38.41 4.85
1578 1681 0.621609 ACTATTACCTGCCCCGCAAA 59.378 50.000 0.00 0.00 38.41 3.68
1579 1682 1.004979 ACTATTACCTGCCCCGCAAAA 59.995 47.619 0.00 0.00 38.41 2.44
1580 1683 2.096248 CTATTACCTGCCCCGCAAAAA 58.904 47.619 0.00 0.00 38.41 1.94
1606 1709 4.517285 ACTGTACTATTACCTCCGTTCGA 58.483 43.478 0.00 0.00 0.00 3.71
1619 1722 4.092383 CCTCCGTTCGAAAATAAATGACGT 59.908 41.667 0.00 0.00 0.00 4.34
1698 1815 8.251026 TGTATCATGATATTGTTATCGGGAGTC 58.749 37.037 18.18 1.02 37.61 3.36
1699 1816 6.037786 TCATGATATTGTTATCGGGAGTCC 57.962 41.667 0.00 0.00 37.61 3.85
1711 1856 1.190643 GGGAGTCCTGGTCTCTTCAG 58.809 60.000 18.21 0.00 33.06 3.02
1721 1866 1.540363 GGTCTCTTCAGTTCGTTGGCA 60.540 52.381 0.00 0.00 0.00 4.92
1748 2517 8.252417 ACGAATTACACATAACACCAGTATACA 58.748 33.333 5.50 0.00 0.00 2.29
1762 2531 2.368875 AGTATACAAGGATTCCAGGCGG 59.631 50.000 5.29 0.00 0.00 6.13
1765 2534 1.678635 CAAGGATTCCAGGCGGCAA 60.679 57.895 13.08 0.00 0.00 4.52
1769 2538 0.825010 GGATTCCAGGCGGCAATCAT 60.825 55.000 13.08 0.00 0.00 2.45
1843 2612 8.890951 GTTTTGTGTTGTTATTTAATTGCATGC 58.109 29.630 11.82 11.82 0.00 4.06
1844 2613 7.719778 TTGTGTTGTTATTTAATTGCATGCA 57.280 28.000 18.46 18.46 0.00 3.96
1932 2709 9.418045 GTTAATTTTTGTTGGCACATACAGTAT 57.582 29.630 0.00 0.00 39.30 2.12
1933 2710 9.988815 TTAATTTTTGTTGGCACATACAGTATT 57.011 25.926 0.00 0.00 39.30 1.89
2014 2812 3.843027 TGCATGGGGTTTTTATGTTGGAT 59.157 39.130 0.00 0.00 0.00 3.41
2015 2813 4.190772 GCATGGGGTTTTTATGTTGGATG 58.809 43.478 0.00 0.00 0.00 3.51
2016 2814 4.768583 CATGGGGTTTTTATGTTGGATGG 58.231 43.478 0.00 0.00 0.00 3.51
2017 2815 4.133526 TGGGGTTTTTATGTTGGATGGA 57.866 40.909 0.00 0.00 0.00 3.41
2018 2816 4.693420 TGGGGTTTTTATGTTGGATGGAT 58.307 39.130 0.00 0.00 0.00 3.41
2019 2817 4.469227 TGGGGTTTTTATGTTGGATGGATG 59.531 41.667 0.00 0.00 0.00 3.51
2020 2818 4.141733 GGGGTTTTTATGTTGGATGGATGG 60.142 45.833 0.00 0.00 0.00 3.51
2021 2819 4.469586 GGGTTTTTATGTTGGATGGATGGT 59.530 41.667 0.00 0.00 0.00 3.55
2022 2820 5.045942 GGGTTTTTATGTTGGATGGATGGTT 60.046 40.000 0.00 0.00 0.00 3.67
2023 2821 6.472016 GGTTTTTATGTTGGATGGATGGTTT 58.528 36.000 0.00 0.00 0.00 3.27
2024 2822 6.939730 GGTTTTTATGTTGGATGGATGGTTTT 59.060 34.615 0.00 0.00 0.00 2.43
2025 2823 7.119116 GGTTTTTATGTTGGATGGATGGTTTTC 59.881 37.037 0.00 0.00 0.00 2.29
2026 2824 6.924913 TTTATGTTGGATGGATGGTTTTCA 57.075 33.333 0.00 0.00 0.00 2.69
2027 2825 6.528537 TTATGTTGGATGGATGGTTTTCAG 57.471 37.500 0.00 0.00 0.00 3.02
2028 2826 4.111255 TGTTGGATGGATGGTTTTCAGA 57.889 40.909 0.00 0.00 0.00 3.27
2029 2827 4.676109 TGTTGGATGGATGGTTTTCAGAT 58.324 39.130 0.00 0.00 0.00 2.90
2030 2828 5.085920 TGTTGGATGGATGGTTTTCAGATT 58.914 37.500 0.00 0.00 0.00 2.40
2031 2829 5.047164 TGTTGGATGGATGGTTTTCAGATTG 60.047 40.000 0.00 0.00 0.00 2.67
2032 2830 4.676109 TGGATGGATGGTTTTCAGATTGT 58.324 39.130 0.00 0.00 0.00 2.71
2033 2831 4.463539 TGGATGGATGGTTTTCAGATTGTG 59.536 41.667 0.00 0.00 0.00 3.33
2034 2832 4.706476 GGATGGATGGTTTTCAGATTGTGA 59.294 41.667 0.00 0.00 0.00 3.58
2070 2868 3.541713 CTAGGGAGCTGGCCGGTC 61.542 72.222 14.55 15.12 39.41 4.79
2079 2877 0.818040 GCTGGCCGGTCGGATAAAAT 60.818 55.000 21.88 0.00 37.50 1.82
2119 2917 7.760794 TGGCTTAAGATAAGTGATTGCAAATTG 59.239 33.333 6.67 0.00 0.00 2.32
2120 2918 7.761249 GGCTTAAGATAAGTGATTGCAAATTGT 59.239 33.333 6.67 0.00 0.00 2.71
2153 2984 1.603455 CGGGCCATGGTGAGTGTTT 60.603 57.895 14.67 0.00 0.00 2.83
2154 2985 1.178534 CGGGCCATGGTGAGTGTTTT 61.179 55.000 14.67 0.00 0.00 2.43
2155 2986 1.047801 GGGCCATGGTGAGTGTTTTT 58.952 50.000 14.67 0.00 0.00 1.94
2244 3084 5.747197 GCAAGAATTATTGTCCTCATGCAAG 59.253 40.000 13.94 0.00 32.56 4.01
2324 3165 1.780309 TGACCTGTTTCATTGGGAGGT 59.220 47.619 0.00 0.00 39.83 3.85
2355 3196 7.364522 TCTGATAATTGTCTTAACACAGCAC 57.635 36.000 3.72 0.00 34.35 4.40
2360 3201 3.040147 TGTCTTAACACAGCACCTAGC 57.960 47.619 0.00 0.00 46.19 3.42
2369 3210 2.510238 GCACCTAGCAGTGGAGCG 60.510 66.667 4.07 0.00 44.79 5.03
2422 3263 3.902150 TGCGCTATAGCTAAGCAAGTAG 58.098 45.455 21.98 9.53 40.08 2.57
2541 3382 9.436957 AGTTATATGGTTGGATTCATATTCGAC 57.563 33.333 0.00 0.00 37.62 4.20
2545 3386 6.228616 TGGTTGGATTCATATTCGACAGTA 57.771 37.500 0.00 0.00 0.00 2.74
2547 3388 6.127168 TGGTTGGATTCATATTCGACAGTAGT 60.127 38.462 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 2.392662 TCTCGAATCATGGCCTCTTCT 58.607 47.619 3.32 0.00 0.00 2.85
59 64 1.483827 TCAGCCTGCATCTTCTCGAAT 59.516 47.619 0.00 0.00 0.00 3.34
166 175 0.249120 ATTCGACCACGCCATCTTGA 59.751 50.000 0.00 0.00 39.58 3.02
168 177 1.369625 GAATTCGACCACGCCATCTT 58.630 50.000 0.00 0.00 39.58 2.40
193 204 0.457681 ACGTGCCAGCACACAAAAAC 60.458 50.000 21.67 0.00 46.47 2.43
295 313 2.490509 CTCAAAGTTCATGCCAGCATCA 59.509 45.455 1.19 0.00 33.90 3.07
297 315 1.203994 GCTCAAAGTTCATGCCAGCAT 59.796 47.619 0.00 0.00 37.08 3.79
330 349 6.208599 CCCACGGCCATAAATCATATTTTAGT 59.791 38.462 2.24 0.00 0.00 2.24
333 352 4.262420 GCCCACGGCCATAAATCATATTTT 60.262 41.667 2.24 0.00 44.06 1.82
335 354 2.825532 GCCCACGGCCATAAATCATATT 59.174 45.455 2.24 0.00 44.06 1.28
336 355 2.446435 GCCCACGGCCATAAATCATAT 58.554 47.619 2.24 0.00 44.06 1.78
337 356 1.904287 GCCCACGGCCATAAATCATA 58.096 50.000 2.24 0.00 44.06 2.15
352 371 7.067496 TGTTCACATAAATTTAAAAGGCCCA 57.933 32.000 0.00 0.00 0.00 5.36
373 397 0.521291 CGCGTGACCCATTTCATGTT 59.479 50.000 0.00 0.00 35.29 2.71
388 412 2.726912 CGTACGGTCAACACGCGT 60.727 61.111 5.58 5.58 34.85 6.01
399 423 1.373246 TTTTGAGTCGGCCGTACGG 60.373 57.895 30.06 30.06 38.57 4.02
402 426 1.950828 TTTGTTTTGAGTCGGCCGTA 58.049 45.000 27.15 9.34 0.00 4.02
412 436 3.365220 CGTCCGCTTTGTTTTTGTTTTGA 59.635 39.130 0.00 0.00 0.00 2.69
490 516 4.814294 GGATCAACGCGCCGACCT 62.814 66.667 5.73 0.00 0.00 3.85
504 530 6.174049 GTTTACTAAGAGCAACTCCAAGGAT 58.826 40.000 0.00 0.00 0.00 3.24
505 531 5.512576 GGTTTACTAAGAGCAACTCCAAGGA 60.513 44.000 0.00 0.00 0.00 3.36
506 532 4.695928 GGTTTACTAAGAGCAACTCCAAGG 59.304 45.833 0.00 0.00 0.00 3.61
507 533 4.695928 GGGTTTACTAAGAGCAACTCCAAG 59.304 45.833 0.00 0.00 0.00 3.61
508 534 4.103469 TGGGTTTACTAAGAGCAACTCCAA 59.897 41.667 0.00 0.00 0.00 3.53
509 535 3.649023 TGGGTTTACTAAGAGCAACTCCA 59.351 43.478 0.00 0.00 0.00 3.86
510 536 4.020485 TCTGGGTTTACTAAGAGCAACTCC 60.020 45.833 0.00 0.00 0.00 3.85
524 550 6.001460 CACTACTTTTGTCCATCTGGGTTTA 58.999 40.000 0.00 0.00 38.11 2.01
525 551 4.827284 CACTACTTTTGTCCATCTGGGTTT 59.173 41.667 0.00 0.00 38.11 3.27
526 552 4.141251 ACACTACTTTTGTCCATCTGGGTT 60.141 41.667 0.00 0.00 38.11 4.11
527 553 3.394606 ACACTACTTTTGTCCATCTGGGT 59.605 43.478 0.00 0.00 38.11 4.51
528 554 4.021102 ACACTACTTTTGTCCATCTGGG 57.979 45.455 0.00 0.00 35.41 4.45
529 555 4.631813 GCTACACTACTTTTGTCCATCTGG 59.368 45.833 0.00 0.00 0.00 3.86
530 556 5.482908 AGCTACACTACTTTTGTCCATCTG 58.517 41.667 0.00 0.00 0.00 2.90
531 557 5.246203 TGAGCTACACTACTTTTGTCCATCT 59.754 40.000 0.00 0.00 0.00 2.90
532 558 5.348997 GTGAGCTACACTACTTTTGTCCATC 59.651 44.000 8.50 0.00 45.13 3.51
533 559 5.238583 GTGAGCTACACTACTTTTGTCCAT 58.761 41.667 8.50 0.00 45.13 3.41
534 560 4.628074 GTGAGCTACACTACTTTTGTCCA 58.372 43.478 8.50 0.00 45.13 4.02
535 561 3.673809 CGTGAGCTACACTACTTTTGTCC 59.326 47.826 12.45 0.00 46.24 4.02
536 562 4.887763 CGTGAGCTACACTACTTTTGTC 57.112 45.455 12.45 0.00 46.24 3.18
559 585 9.042450 TCTCTGAAATTTCATACTACCTTGGTA 57.958 33.333 20.76 0.00 36.46 3.25
651 678 2.125912 CCACCGTTGAGCCGAGAG 60.126 66.667 0.00 0.00 0.00 3.20
657 684 1.227853 AACTGGTCCACCGTTGAGC 60.228 57.895 5.52 0.00 39.43 4.26
744 771 0.450583 CACCGAACGTCTGCTAGCTA 59.549 55.000 17.23 0.72 0.00 3.32
745 772 1.213013 CACCGAACGTCTGCTAGCT 59.787 57.895 17.23 0.00 0.00 3.32
752 779 4.052229 CGCCTCCACCGAACGTCT 62.052 66.667 0.00 0.00 0.00 4.18
911 938 7.093771 ACACATATCCAAATTTCAAAGGGTCTC 60.094 37.037 0.00 0.00 0.00 3.36
912 939 6.725834 ACACATATCCAAATTTCAAAGGGTCT 59.274 34.615 0.00 0.00 0.00 3.85
973 1000 3.066190 CCACGAGCACGAGGGGTA 61.066 66.667 11.40 0.00 44.22 3.69
978 1005 0.667487 ATTGACACCACGAGCACGAG 60.667 55.000 11.40 1.50 42.66 4.18
979 1006 0.666274 GATTGACACCACGAGCACGA 60.666 55.000 11.40 0.00 42.66 4.35
980 1007 0.943835 TGATTGACACCACGAGCACG 60.944 55.000 0.76 0.76 45.75 5.34
981 1008 0.512952 GTGATTGACACCACGAGCAC 59.487 55.000 0.00 0.00 43.05 4.40
982 1009 2.912986 GTGATTGACACCACGAGCA 58.087 52.632 0.00 0.00 43.05 4.26
1205 1254 1.594833 CTGGTAGTAGTTGGCGGCA 59.405 57.895 7.97 7.97 0.00 5.69
1408 1457 3.111853 ACGAAGTCTTGTGATCAGCAA 57.888 42.857 0.00 3.14 29.74 3.91
1455 1504 1.001924 ACGAGCAGCTGATGTAGATCG 60.002 52.381 20.43 12.60 35.21 3.69
1485 1545 8.959058 CAGCACAAATACTACTACGATAGAAAG 58.041 37.037 0.00 0.00 41.38 2.62
1541 1644 7.854916 GGTAATAGTACAACTCGATGTAGTGAC 59.145 40.741 14.17 10.03 39.26 3.67
1547 1650 5.451520 GGCAGGTAATAGTACAACTCGATGT 60.452 44.000 2.37 0.00 37.32 3.06
1554 1657 2.830104 CGGGGCAGGTAATAGTACAAC 58.170 52.381 2.37 0.00 31.21 3.32
1580 1683 6.587608 CGAACGGAGGTAATAGTACAGTTTTT 59.412 38.462 2.37 0.00 31.21 1.94
1581 1684 6.071952 TCGAACGGAGGTAATAGTACAGTTTT 60.072 38.462 2.37 0.00 31.21 2.43
1582 1685 5.415701 TCGAACGGAGGTAATAGTACAGTTT 59.584 40.000 2.37 0.00 31.21 2.66
1583 1686 4.943705 TCGAACGGAGGTAATAGTACAGTT 59.056 41.667 2.37 3.12 31.21 3.16
1584 1687 4.517285 TCGAACGGAGGTAATAGTACAGT 58.483 43.478 2.37 0.00 31.21 3.55
1585 1688 5.490139 TTCGAACGGAGGTAATAGTACAG 57.510 43.478 2.37 0.00 31.21 2.74
1586 1689 5.895636 TTTCGAACGGAGGTAATAGTACA 57.104 39.130 0.00 0.00 31.21 2.90
1587 1690 8.856490 TTATTTTCGAACGGAGGTAATAGTAC 57.144 34.615 0.00 0.00 0.00 2.73
1593 1696 6.183360 CGTCATTTATTTTCGAACGGAGGTAA 60.183 38.462 0.00 0.00 0.00 2.85
1694 1811 2.094957 CGAACTGAAGAGACCAGGACTC 60.095 54.545 10.73 10.73 36.03 3.36
1698 1815 2.408050 CAACGAACTGAAGAGACCAGG 58.592 52.381 0.00 0.00 36.03 4.45
1699 1816 2.408050 CCAACGAACTGAAGAGACCAG 58.592 52.381 0.00 0.00 37.64 4.00
1721 1866 9.090692 GTATACTGGTGTTATGTGTAATTCGTT 57.909 33.333 0.00 0.00 0.00 3.85
1733 1878 7.420214 CCTGGAATCCTTGTATACTGGTGTTAT 60.420 40.741 4.17 0.00 0.00 1.89
1748 2517 0.753111 GATTGCCGCCTGGAATCCTT 60.753 55.000 0.00 0.00 37.49 3.36
1765 2534 6.927936 CGAACAGACAATCAGAATCCTATGAT 59.072 38.462 0.00 0.00 37.77 2.45
1769 2538 5.914898 TCGAACAGACAATCAGAATCCTA 57.085 39.130 0.00 0.00 0.00 2.94
1843 2612 5.883661 ACAAGCAAATCATCGGAAGTAATG 58.116 37.500 0.00 0.00 0.00 1.90
1844 2613 6.324819 CAACAAGCAAATCATCGGAAGTAAT 58.675 36.000 0.00 0.00 0.00 1.89
2014 2812 6.267242 TCAATTCACAATCTGAAAACCATCCA 59.733 34.615 0.00 0.00 42.37 3.41
2015 2813 6.690530 TCAATTCACAATCTGAAAACCATCC 58.309 36.000 0.00 0.00 42.37 3.51
2016 2814 7.373493 ACTCAATTCACAATCTGAAAACCATC 58.627 34.615 0.00 0.00 42.37 3.51
2017 2815 7.294017 ACTCAATTCACAATCTGAAAACCAT 57.706 32.000 0.00 0.00 42.37 3.55
2018 2816 6.513230 CGACTCAATTCACAATCTGAAAACCA 60.513 38.462 0.00 0.00 42.37 3.67
2019 2817 5.853282 CGACTCAATTCACAATCTGAAAACC 59.147 40.000 0.00 0.00 42.37 3.27
2020 2818 6.575201 GTCGACTCAATTCACAATCTGAAAAC 59.425 38.462 8.70 0.00 42.37 2.43
2021 2819 6.563939 CGTCGACTCAATTCACAATCTGAAAA 60.564 38.462 14.70 0.00 42.37 2.29
2022 2820 5.107491 CGTCGACTCAATTCACAATCTGAAA 60.107 40.000 14.70 0.00 42.37 2.69
2023 2821 4.385748 CGTCGACTCAATTCACAATCTGAA 59.614 41.667 14.70 0.00 43.28 3.02
2024 2822 3.920412 CGTCGACTCAATTCACAATCTGA 59.080 43.478 14.70 0.00 0.00 3.27
2025 2823 3.061295 CCGTCGACTCAATTCACAATCTG 59.939 47.826 14.70 0.00 0.00 2.90
2026 2824 3.056821 TCCGTCGACTCAATTCACAATCT 60.057 43.478 14.70 0.00 0.00 2.40
2027 2825 3.250744 TCCGTCGACTCAATTCACAATC 58.749 45.455 14.70 0.00 0.00 2.67
2028 2826 3.313012 TCCGTCGACTCAATTCACAAT 57.687 42.857 14.70 0.00 0.00 2.71
2029 2827 2.804697 TCCGTCGACTCAATTCACAA 57.195 45.000 14.70 0.00 0.00 3.33
2030 2828 2.804697 TTCCGTCGACTCAATTCACA 57.195 45.000 14.70 0.00 0.00 3.58
2031 2829 2.412089 CCTTTCCGTCGACTCAATTCAC 59.588 50.000 14.70 0.00 0.00 3.18
2032 2830 2.683968 CCTTTCCGTCGACTCAATTCA 58.316 47.619 14.70 0.00 0.00 2.57
2033 2831 1.393883 GCCTTTCCGTCGACTCAATTC 59.606 52.381 14.70 0.00 0.00 2.17
2034 2832 1.002087 AGCCTTTCCGTCGACTCAATT 59.998 47.619 14.70 0.00 0.00 2.32
2070 2868 4.481930 TGCTTGGCGATAATTTTATCCG 57.518 40.909 5.05 0.00 36.95 4.18
2119 2917 3.165498 CGCCACGGAGCAAGTTAC 58.835 61.111 0.00 0.00 0.00 2.50
2157 2988 4.955925 ATTTGACGATCCACGCATAAAA 57.044 36.364 0.00 0.00 46.94 1.52
2159 2990 4.393371 TCAAATTTGACGATCCACGCATAA 59.607 37.500 16.91 0.00 46.94 1.90
2244 3084 1.594331 GCGGGGTCCAATATGTTCTC 58.406 55.000 0.00 0.00 0.00 2.87
2352 3193 2.510238 CGCTCCACTGCTAGGTGC 60.510 66.667 0.00 0.00 41.09 5.01
2355 3196 1.021390 CAAACCGCTCCACTGCTAGG 61.021 60.000 0.00 0.00 0.00 3.02
2422 3263 3.900966 AATAAACCCAGACGGAGGTAC 57.099 47.619 0.00 0.00 34.45 3.34


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

AutoCloner maintained by Alex Coulton.