Multiple sequence alignment - TraesCS7B01G164300

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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 TraesCS7B01G164300 chr7B 100.000 2366 0 0 1 2366 226897987 226900352 0.000000e+00 4370.0
1 TraesCS7B01G164300 chr7B 91.023 479 43 0 96 574 226677124 226677602 0.000000e+00 647.0
2 TraesCS7B01G164300 chr7D 93.276 1041 48 10 677 1713 249786846 249787868 0.000000e+00 1515.0
3 TraesCS7B01G164300 chr7D 94.225 658 23 7 1716 2366 249787977 249788626 0.000000e+00 990.0
4 TraesCS7B01G164300 chr7D 91.504 565 46 2 1 565 249786283 249786845 0.000000e+00 776.0
5 TraesCS7B01G164300 chr7D 86.231 581 72 7 3 581 217615846 217616420 7.180000e-175 623.0
6 TraesCS7B01G164300 chr7D 89.897 485 47 2 96 580 249736028 249736510 7.180000e-175 623.0
7 TraesCS7B01G164300 chr7A 89.968 937 42 13 777 1713 271381977 271381093 0.000000e+00 1162.0
8 TraesCS7B01G164300 chr7A 96.682 663 10 3 1716 2366 271381002 271380340 0.000000e+00 1092.0
9 TraesCS7B01G164300 chr7A 84.279 458 50 7 1907 2364 271624971 271624536 6.040000e-116 427.0
10 TraesCS7B01G164300 chr1D 87.024 578 74 1 3 580 200226048 200225472 0.000000e+00 651.0
11 TraesCS7B01G164300 chr6D 85.911 582 75 5 1 580 246555195 246554619 4.320000e-172 614.0
12 TraesCS7B01G164300 chr2A 84.138 580 90 2 1 580 285420493 285421070 5.710000e-156 560.0
13 TraesCS7B01G164300 chr2A 83.539 486 69 8 94 574 305010106 305010585 6.000000e-121 444.0
14 TraesCS7B01G164300 chr1B 85.020 494 63 4 99 583 457385913 457386404 2.110000e-135 492.0
15 TraesCS7B01G164300 chr3B 81.368 585 84 12 5 580 728064601 728064033 9.970000e-124 453.0
16 TraesCS7B01G164300 chr3B 80.000 345 56 8 29 363 607834341 607834000 2.350000e-60 243.0
17 TraesCS7B01G164300 chr3B 93.878 49 3 0 732 780 802898591 802898639 9.070000e-10 75.0
18 TraesCS7B01G164300 chr4A 92.857 42 1 2 66 106 301919173 301919133 2.540000e-05 60.2


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 TraesCS7B01G164300 chr7B 226897987 226900352 2365 False 4370.000000 4370 100.000000 1 2366 1 chr7B.!!$F2 2365
1 TraesCS7B01G164300 chr7D 249786283 249788626 2343 False 1093.666667 1515 93.001667 1 2366 3 chr7D.!!$F3 2365
2 TraesCS7B01G164300 chr7D 217615846 217616420 574 False 623.000000 623 86.231000 3 581 1 chr7D.!!$F1 578
3 TraesCS7B01G164300 chr7A 271380340 271381977 1637 True 1127.000000 1162 93.325000 777 2366 2 chr7A.!!$R2 1589
4 TraesCS7B01G164300 chr1D 200225472 200226048 576 True 651.000000 651 87.024000 3 580 1 chr1D.!!$R1 577
5 TraesCS7B01G164300 chr6D 246554619 246555195 576 True 614.000000 614 85.911000 1 580 1 chr6D.!!$R1 579
6 TraesCS7B01G164300 chr2A 285420493 285421070 577 False 560.000000 560 84.138000 1 580 1 chr2A.!!$F1 579
7 TraesCS7B01G164300 chr3B 728064033 728064601 568 True 453.000000 453 81.368000 5 580 1 chr3B.!!$R2 575

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
639 651 0.105964 CATCCAATTAGGTCGCCCGA 59.894 55.0 0.0 0.0 39.02 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1656 0.447801 CGTAGCCACATTCCTGTTGC 59.552 55.0 0.0 0.0 42.76 4.17 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
147 148 0.589223 CTGCCGGTCTATCTCTCGTC 59.411 60.000 1.90 0.00 0.00 4.20
170 171 0.389166 CGGACAGTTGAGCCACTCTC 60.389 60.000 0.00 0.00 42.23 3.20
191 200 0.748005 TTGGAAGGCCGAAGCTATGC 60.748 55.000 0.00 0.00 39.73 3.14
192 201 1.153168 GGAAGGCCGAAGCTATGCA 60.153 57.895 0.00 0.00 39.73 3.96
261 270 6.280855 TCCAAGTCAAGATAATGAAGACGA 57.719 37.500 0.00 0.00 34.56 4.20
277 286 2.170607 AGACGACATGTTTATCCCCTGG 59.829 50.000 0.00 0.00 0.00 4.45
382 391 4.755266 TCCTACTCATCTAGGGTTTTGC 57.245 45.455 0.00 0.00 34.91 3.68
398 407 4.728058 GCTCACCTGATCTCGAGC 57.272 61.111 7.81 9.41 43.60 5.03
412 421 3.210227 TCTCGAGCTAGATCAACTCTGG 58.790 50.000 7.81 0.00 35.28 3.86
424 433 6.531923 AGATCAACTCTGGAACCATCATATG 58.468 40.000 0.00 0.00 31.12 1.78
445 456 9.783256 CATATGCACACATCAATATAATCAAGG 57.217 33.333 0.00 0.00 37.74 3.61
469 480 6.063496 AGGACATAGGGTTTTACCTCTTTC 57.937 41.667 0.00 0.00 42.09 2.62
485 496 1.423794 TTTCAGAGGGCCCGAACCTT 61.424 55.000 18.44 0.00 38.79 3.50
551 563 1.661990 TACAGCTCGGGACCCCCTAT 61.662 60.000 4.46 0.00 42.67 2.57
561 573 0.114560 GACCCCCTATCCGAGATCCA 59.885 60.000 0.00 0.00 0.00 3.41
581 593 2.225491 CACCGATTTTGACACCGACAAT 59.775 45.455 0.00 0.00 0.00 2.71
582 594 2.225491 ACCGATTTTGACACCGACAATG 59.775 45.455 0.00 0.00 0.00 2.82
583 595 2.482336 CCGATTTTGACACCGACAATGA 59.518 45.455 0.00 0.00 0.00 2.57
584 596 3.479006 CGATTTTGACACCGACAATGAC 58.521 45.455 0.00 0.00 0.00 3.06
585 597 3.666902 CGATTTTGACACCGACAATGACC 60.667 47.826 0.00 0.00 0.00 4.02
586 598 1.600023 TTTGACACCGACAATGACCC 58.400 50.000 0.00 0.00 0.00 4.46
587 599 0.250553 TTGACACCGACAATGACCCC 60.251 55.000 0.00 0.00 0.00 4.95
588 600 1.740296 GACACCGACAATGACCCCG 60.740 63.158 0.00 0.00 0.00 5.73
589 601 2.435938 CACCGACAATGACCCCGG 60.436 66.667 0.00 0.00 46.65 5.73
590 602 2.605295 ACCGACAATGACCCCGGA 60.605 61.111 0.73 0.00 44.29 5.14
591 603 2.125269 CCGACAATGACCCCGGAC 60.125 66.667 0.73 0.00 44.29 4.79
592 604 2.508439 CGACAATGACCCCGGACG 60.508 66.667 0.73 0.00 0.00 4.79
593 605 2.818274 GACAATGACCCCGGACGC 60.818 66.667 0.73 0.00 0.00 5.19
594 606 3.599285 GACAATGACCCCGGACGCA 62.599 63.158 0.73 0.00 0.00 5.24
595 607 3.124921 CAATGACCCCGGACGCAC 61.125 66.667 0.73 0.00 0.00 5.34
596 608 3.632080 AATGACCCCGGACGCACA 61.632 61.111 0.73 0.00 0.00 4.57
597 609 3.894547 AATGACCCCGGACGCACAC 62.895 63.158 0.73 0.00 0.00 3.82
615 627 4.082523 CCGCGGTCCACCTGTCAT 62.083 66.667 19.50 0.00 0.00 3.06
616 628 2.815211 CGCGGTCCACCTGTCATG 60.815 66.667 0.00 0.00 0.00 3.07
617 629 2.662596 GCGGTCCACCTGTCATGA 59.337 61.111 0.00 0.00 0.00 3.07
618 630 1.003839 GCGGTCCACCTGTCATGAA 60.004 57.895 0.00 0.00 0.00 2.57
619 631 1.298859 GCGGTCCACCTGTCATGAAC 61.299 60.000 0.00 0.00 0.00 3.18
620 632 0.673644 CGGTCCACCTGTCATGAACC 60.674 60.000 0.00 0.00 0.00 3.62
621 633 0.400213 GGTCCACCTGTCATGAACCA 59.600 55.000 0.00 0.00 0.00 3.67
622 634 1.004745 GGTCCACCTGTCATGAACCAT 59.995 52.381 0.00 0.00 0.00 3.55
623 635 2.359900 GTCCACCTGTCATGAACCATC 58.640 52.381 0.00 0.00 0.00 3.51
624 636 1.281867 TCCACCTGTCATGAACCATCC 59.718 52.381 0.00 0.00 0.00 3.51
625 637 1.004628 CCACCTGTCATGAACCATCCA 59.995 52.381 0.00 0.00 0.00 3.41
626 638 2.555006 CCACCTGTCATGAACCATCCAA 60.555 50.000 0.00 0.00 0.00 3.53
627 639 3.359033 CACCTGTCATGAACCATCCAAT 58.641 45.455 0.00 0.00 0.00 3.16
628 640 3.765511 CACCTGTCATGAACCATCCAATT 59.234 43.478 0.00 0.00 0.00 2.32
629 641 4.949238 CACCTGTCATGAACCATCCAATTA 59.051 41.667 0.00 0.00 0.00 1.40
630 642 5.066893 CACCTGTCATGAACCATCCAATTAG 59.933 44.000 0.00 0.00 0.00 1.73
631 643 4.581824 CCTGTCATGAACCATCCAATTAGG 59.418 45.833 0.00 0.00 39.47 2.69
632 644 5.191727 TGTCATGAACCATCCAATTAGGT 57.808 39.130 0.00 0.00 39.02 3.08
633 645 5.192927 TGTCATGAACCATCCAATTAGGTC 58.807 41.667 0.00 0.00 39.02 3.85
634 646 4.273480 GTCATGAACCATCCAATTAGGTCG 59.727 45.833 0.00 0.00 39.02 4.79
635 647 2.639065 TGAACCATCCAATTAGGTCGC 58.361 47.619 0.00 0.00 39.02 5.19
636 648 1.947456 GAACCATCCAATTAGGTCGCC 59.053 52.381 0.00 0.00 39.02 5.54
637 649 0.182775 ACCATCCAATTAGGTCGCCC 59.817 55.000 0.00 0.00 39.02 6.13
638 650 0.884704 CCATCCAATTAGGTCGCCCG 60.885 60.000 0.00 0.00 39.02 6.13
639 651 0.105964 CATCCAATTAGGTCGCCCGA 59.894 55.000 0.00 0.00 39.02 5.14
640 652 0.393077 ATCCAATTAGGTCGCCCGAG 59.607 55.000 0.00 0.00 39.02 4.63
641 653 0.974010 TCCAATTAGGTCGCCCGAGT 60.974 55.000 0.00 0.00 39.02 4.18
642 654 0.107848 CCAATTAGGTCGCCCGAGTT 60.108 55.000 0.00 0.00 35.12 3.01
643 655 1.677820 CCAATTAGGTCGCCCGAGTTT 60.678 52.381 0.00 0.00 35.12 2.66
644 656 1.396996 CAATTAGGTCGCCCGAGTTTG 59.603 52.381 0.00 0.00 35.12 2.93
645 657 0.899720 ATTAGGTCGCCCGAGTTTGA 59.100 50.000 0.00 0.00 35.12 2.69
646 658 0.245539 TTAGGTCGCCCGAGTTTGAG 59.754 55.000 0.00 0.00 35.12 3.02
647 659 0.896940 TAGGTCGCCCGAGTTTGAGT 60.897 55.000 0.00 0.00 35.12 3.41
648 660 1.737008 GGTCGCCCGAGTTTGAGTC 60.737 63.158 0.00 0.00 0.00 3.36
649 661 2.087009 GTCGCCCGAGTTTGAGTCG 61.087 63.158 0.00 0.00 40.53 4.18
650 662 2.049433 CGCCCGAGTTTGAGTCGT 60.049 61.111 4.69 0.00 39.29 4.34
651 663 1.663702 CGCCCGAGTTTGAGTCGTT 60.664 57.895 4.69 0.00 39.29 3.85
652 664 1.615107 CGCCCGAGTTTGAGTCGTTC 61.615 60.000 4.69 0.00 39.29 3.95
653 665 0.599204 GCCCGAGTTTGAGTCGTTCA 60.599 55.000 4.69 0.00 39.29 3.18
654 666 1.419374 CCCGAGTTTGAGTCGTTCAG 58.581 55.000 4.69 0.00 39.29 3.02
655 667 1.419374 CCGAGTTTGAGTCGTTCAGG 58.581 55.000 4.69 0.00 39.29 3.86
656 668 0.784778 CGAGTTTGAGTCGTTCAGGC 59.215 55.000 0.00 0.00 36.37 4.85
657 669 1.865865 GAGTTTGAGTCGTTCAGGCA 58.134 50.000 0.00 0.00 37.07 4.75
658 670 1.795286 GAGTTTGAGTCGTTCAGGCAG 59.205 52.381 0.00 0.00 37.07 4.85
659 671 1.412710 AGTTTGAGTCGTTCAGGCAGA 59.587 47.619 0.00 0.00 37.07 4.26
660 672 2.037772 AGTTTGAGTCGTTCAGGCAGAT 59.962 45.455 0.00 0.00 37.07 2.90
661 673 2.370281 TTGAGTCGTTCAGGCAGATC 57.630 50.000 0.00 0.00 37.07 2.75
662 674 0.171231 TGAGTCGTTCAGGCAGATCG 59.829 55.000 4.22 4.22 40.05 3.69
663 675 0.526524 GAGTCGTTCAGGCAGATCGG 60.527 60.000 9.94 0.00 39.36 4.18
664 676 0.965866 AGTCGTTCAGGCAGATCGGA 60.966 55.000 9.94 0.00 39.36 4.55
665 677 0.802607 GTCGTTCAGGCAGATCGGAC 60.803 60.000 9.94 0.00 39.36 4.79
666 678 1.874019 CGTTCAGGCAGATCGGACG 60.874 63.158 0.00 0.00 36.15 4.79
667 679 1.519455 GTTCAGGCAGATCGGACGG 60.519 63.158 0.00 0.00 0.00 4.79
668 680 3.371097 TTCAGGCAGATCGGACGGC 62.371 63.158 0.00 0.00 0.00 5.68
669 681 3.842923 CAGGCAGATCGGACGGCT 61.843 66.667 0.00 0.00 35.68 5.52
670 682 3.532155 AGGCAGATCGGACGGCTC 61.532 66.667 0.00 0.00 0.00 4.70
671 683 4.933064 GGCAGATCGGACGGCTCG 62.933 72.222 0.00 0.00 0.00 5.03
672 684 4.933064 GCAGATCGGACGGCTCGG 62.933 72.222 0.00 0.00 0.00 4.63
673 685 3.209812 CAGATCGGACGGCTCGGA 61.210 66.667 0.00 0.00 0.00 4.55
674 686 2.902846 AGATCGGACGGCTCGGAG 60.903 66.667 0.00 0.00 0.00 4.63
675 687 2.900838 GATCGGACGGCTCGGAGA 60.901 66.667 9.69 0.00 0.00 3.71
687 699 2.190170 TCGGAGAGCTCGAGATGCC 61.190 63.158 18.75 12.79 32.51 4.40
757 770 1.114119 CCTAGGAAGGCGGGTACTCC 61.114 65.000 1.05 0.00 35.64 3.85
830 843 1.971695 CAGGGGAAACTTGGACGGC 60.972 63.158 0.00 0.00 0.00 5.68
877 890 0.169009 GTCAGATTTTGCTCGGCACC 59.831 55.000 0.00 0.00 38.71 5.01
903 916 5.243207 GGAACCCCGGATGTATATACAAAG 58.757 45.833 19.11 12.64 39.99 2.77
904 917 4.281898 ACCCCGGATGTATATACAAAGC 57.718 45.455 19.11 11.37 39.99 3.51
905 918 3.008704 ACCCCGGATGTATATACAAAGCC 59.991 47.826 19.11 17.71 39.99 4.35
977 991 0.324830 GTGTAGCTCTCCCCTGGTCT 60.325 60.000 0.00 0.00 0.00 3.85
993 1007 2.305635 TGGTCTAAGCAGAGGCATTTCA 59.694 45.455 0.00 0.00 44.61 2.69
1277 1291 1.092345 GCCGGTGAGAAGGAAGATGC 61.092 60.000 1.90 0.00 0.00 3.91
1381 1395 2.338984 GACGCCGTGAAGTCCACT 59.661 61.111 0.00 0.00 43.53 4.00
1384 1398 2.310233 CGCCGTGAAGTCCACTGTG 61.310 63.158 0.00 0.00 43.53 3.66
1385 1399 1.227556 GCCGTGAAGTCCACTGTGT 60.228 57.895 7.08 0.00 43.53 3.72
1408 1422 8.884726 GTGTCCTCTCTGTATTTTATTTCCTTC 58.115 37.037 0.00 0.00 0.00 3.46
1448 1462 8.872845 CATGGTTTTTGCTTGAGATTATTAACC 58.127 33.333 0.00 0.00 33.64 2.85
1449 1463 7.957002 TGGTTTTTGCTTGAGATTATTAACCA 58.043 30.769 0.00 0.00 39.01 3.67
1450 1464 8.424918 TGGTTTTTGCTTGAGATTATTAACCAA 58.575 29.630 0.00 0.00 38.55 3.67
1472 1488 6.128849 CCAATGCTACACTTTGCAATTACAAC 60.129 38.462 0.00 0.00 42.74 3.32
1509 1525 0.698238 TGGCCACTGCACCTTTAGAT 59.302 50.000 0.00 0.00 40.13 1.98
1542 1558 4.398988 TGCTTTGCTCGATGATTTATGGTT 59.601 37.500 0.00 0.00 0.00 3.67
1543 1559 4.972440 GCTTTGCTCGATGATTTATGGTTC 59.028 41.667 0.00 0.00 0.00 3.62
1544 1560 5.449041 GCTTTGCTCGATGATTTATGGTTCA 60.449 40.000 0.00 0.00 0.00 3.18
1545 1561 6.698008 TTTGCTCGATGATTTATGGTTCAT 57.302 33.333 0.00 0.00 35.33 2.57
1546 1562 5.678132 TGCTCGATGATTTATGGTTCATG 57.322 39.130 0.00 0.00 32.84 3.07
1547 1563 4.516321 TGCTCGATGATTTATGGTTCATGG 59.484 41.667 0.00 0.00 32.84 3.66
1577 1593 3.823873 TGTGTGCAATTCGATTTTACCCT 59.176 39.130 0.00 0.00 0.00 4.34
1626 1642 4.702131 GGTGATAGGTTCAAGCTGTCAAAT 59.298 41.667 16.62 0.00 43.55 2.32
1640 1656 4.381932 GCTGTCAAATCATTACAAAGGGGG 60.382 45.833 0.00 0.00 0.00 5.40
1641 1657 3.513515 TGTCAAATCATTACAAAGGGGGC 59.486 43.478 0.00 0.00 0.00 5.80
1642 1658 3.513515 GTCAAATCATTACAAAGGGGGCA 59.486 43.478 0.00 0.00 0.00 5.36
1643 1659 4.020662 GTCAAATCATTACAAAGGGGGCAA 60.021 41.667 0.00 0.00 0.00 4.52
1644 1660 4.020662 TCAAATCATTACAAAGGGGGCAAC 60.021 41.667 0.00 0.00 0.00 4.17
1645 1661 2.685106 TCATTACAAAGGGGGCAACA 57.315 45.000 0.00 0.00 39.74 3.33
1646 1662 2.524306 TCATTACAAAGGGGGCAACAG 58.476 47.619 0.00 0.00 39.74 3.16
1647 1663 1.550072 CATTACAAAGGGGGCAACAGG 59.450 52.381 0.00 0.00 39.74 4.00
1659 1681 0.447801 GCAACAGGAATGTGGCTACG 59.552 55.000 0.44 0.00 35.90 3.51
1661 1683 2.632377 CAACAGGAATGTGGCTACGAT 58.368 47.619 0.00 0.00 0.00 3.73
1722 1850 5.779241 TTTTTATGACCCTGACTGGAGAT 57.221 39.130 0.00 0.00 38.35 2.75
1797 1934 2.103143 CGCCTGTCTCGTGCCTAG 59.897 66.667 0.00 0.00 0.00 3.02
2083 2223 2.181954 AGAGAAACTGCAAGGAGCTG 57.818 50.000 0.00 0.00 45.94 4.24
2107 2247 6.151648 TGTGCTCTGATATCATCGATCATGTA 59.848 38.462 5.72 0.00 32.96 2.29
2187 2327 6.564152 AGGATGTCTAGATAAATTGTCCCCAT 59.436 38.462 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.338020 GCTTTGTGGACCAGTTCCTTG 59.662 52.381 0.00 0.00 46.10 3.61
126 127 1.448119 CGAGAGATAGACCGGCAGCA 61.448 60.000 0.00 0.00 0.00 4.41
170 171 1.605710 CATAGCTTCGGCCTTCCAATG 59.394 52.381 0.00 0.00 43.01 2.82
191 200 2.029020 TCTTCCTGAACACGGAGTCATG 60.029 50.000 0.00 0.00 41.61 3.07
192 201 2.248248 TCTTCCTGAACACGGAGTCAT 58.752 47.619 0.00 0.00 41.61 3.06
261 270 2.000048 ACCACCAGGGGATAAACATGT 59.000 47.619 0.00 0.00 42.91 3.21
291 300 0.914644 GGGGTCCCTAAGGTTACACC 59.085 60.000 8.15 0.00 38.99 4.16
382 391 2.844946 TCTAGCTCGAGATCAGGTGAG 58.155 52.381 18.75 2.67 0.00 3.51
398 407 5.604758 TGATGGTTCCAGAGTTGATCTAG 57.395 43.478 0.00 0.00 36.10 2.43
412 421 5.503662 TTGATGTGTGCATATGATGGTTC 57.496 39.130 6.97 0.00 35.07 3.62
424 433 6.712095 TCCTCCTTGATTATATTGATGTGTGC 59.288 38.462 0.00 0.00 0.00 4.57
445 456 5.695424 AAGAGGTAAAACCCTATGTCCTC 57.305 43.478 0.00 0.00 39.75 3.71
469 480 2.045926 CAAGGTTCGGGCCCTCTG 60.046 66.667 22.43 4.11 0.00 3.35
551 563 1.828595 TCAAAATCGGTGGATCTCGGA 59.171 47.619 0.00 0.00 30.81 4.55
561 573 1.956297 TTGTCGGTGTCAAAATCGGT 58.044 45.000 0.00 0.00 0.00 4.69
598 610 4.082523 ATGACAGGTGGACCGCGG 62.083 66.667 26.86 26.86 42.08 6.46
599 611 2.779951 TTCATGACAGGTGGACCGCG 62.780 60.000 0.00 0.00 42.08 6.46
600 612 1.003839 TTCATGACAGGTGGACCGC 60.004 57.895 0.00 0.00 42.08 5.68
601 613 0.673644 GGTTCATGACAGGTGGACCG 60.674 60.000 0.00 0.00 35.61 4.79
602 614 0.400213 TGGTTCATGACAGGTGGACC 59.600 55.000 0.00 0.00 44.18 4.46
603 615 2.359900 GATGGTTCATGACAGGTGGAC 58.640 52.381 0.00 0.00 0.00 4.02
604 616 1.281867 GGATGGTTCATGACAGGTGGA 59.718 52.381 0.00 0.00 0.00 4.02
605 617 1.004628 TGGATGGTTCATGACAGGTGG 59.995 52.381 0.00 0.00 0.00 4.61
606 618 2.495155 TGGATGGTTCATGACAGGTG 57.505 50.000 0.00 0.00 0.00 4.00
607 619 3.744940 ATTGGATGGTTCATGACAGGT 57.255 42.857 0.00 0.00 0.00 4.00
608 620 4.581824 CCTAATTGGATGGTTCATGACAGG 59.418 45.833 0.00 0.00 38.35 4.00
609 621 5.195940 ACCTAATTGGATGGTTCATGACAG 58.804 41.667 0.00 0.00 39.71 3.51
610 622 5.191727 ACCTAATTGGATGGTTCATGACA 57.808 39.130 0.00 0.00 39.71 3.58
611 623 4.273480 CGACCTAATTGGATGGTTCATGAC 59.727 45.833 0.00 0.00 39.71 3.06
612 624 4.450976 CGACCTAATTGGATGGTTCATGA 58.549 43.478 0.00 0.00 39.71 3.07
613 625 3.003689 GCGACCTAATTGGATGGTTCATG 59.996 47.826 0.00 0.00 39.71 3.07
614 626 3.214328 GCGACCTAATTGGATGGTTCAT 58.786 45.455 0.00 0.00 39.71 2.57
615 627 2.639065 GCGACCTAATTGGATGGTTCA 58.361 47.619 0.00 0.00 39.71 3.18
616 628 1.947456 GGCGACCTAATTGGATGGTTC 59.053 52.381 0.00 0.00 39.71 3.62
617 629 2.052782 GGCGACCTAATTGGATGGTT 57.947 50.000 0.00 0.00 39.71 3.67
618 630 3.800826 GGCGACCTAATTGGATGGT 57.199 52.632 0.00 0.00 39.71 3.55
631 643 2.087009 CGACTCAAACTCGGGCGAC 61.087 63.158 0.00 0.00 0.00 5.19
632 644 2.079020 AACGACTCAAACTCGGGCGA 62.079 55.000 0.00 0.00 35.37 5.54
633 645 1.615107 GAACGACTCAAACTCGGGCG 61.615 60.000 0.00 0.00 35.37 6.13
634 646 0.599204 TGAACGACTCAAACTCGGGC 60.599 55.000 0.00 0.00 35.37 6.13
635 647 1.419374 CTGAACGACTCAAACTCGGG 58.581 55.000 0.00 0.00 35.37 5.14
636 648 1.419374 CCTGAACGACTCAAACTCGG 58.581 55.000 0.00 0.00 35.37 4.63
637 649 0.784778 GCCTGAACGACTCAAACTCG 59.215 55.000 0.00 0.00 37.17 4.18
638 650 1.795286 CTGCCTGAACGACTCAAACTC 59.205 52.381 0.00 0.00 32.17 3.01
639 651 1.412710 TCTGCCTGAACGACTCAAACT 59.587 47.619 0.00 0.00 32.17 2.66
640 652 1.865865 TCTGCCTGAACGACTCAAAC 58.134 50.000 0.00 0.00 32.17 2.93
641 653 2.688507 GATCTGCCTGAACGACTCAAA 58.311 47.619 0.00 0.00 32.17 2.69
642 654 1.402852 CGATCTGCCTGAACGACTCAA 60.403 52.381 0.00 0.00 42.45 3.02
643 655 0.171231 CGATCTGCCTGAACGACTCA 59.829 55.000 0.00 0.00 42.45 3.41
644 656 0.526524 CCGATCTGCCTGAACGACTC 60.527 60.000 2.91 0.00 42.45 3.36
645 657 0.965866 TCCGATCTGCCTGAACGACT 60.966 55.000 2.91 0.00 42.45 4.18
646 658 0.802607 GTCCGATCTGCCTGAACGAC 60.803 60.000 2.91 0.00 42.45 4.34
647 659 1.511305 GTCCGATCTGCCTGAACGA 59.489 57.895 2.91 0.00 42.45 3.85
648 660 1.874019 CGTCCGATCTGCCTGAACG 60.874 63.158 0.00 0.00 40.07 3.95
649 661 1.519455 CCGTCCGATCTGCCTGAAC 60.519 63.158 0.00 0.00 0.00 3.18
650 662 2.892640 CCGTCCGATCTGCCTGAA 59.107 61.111 0.00 0.00 0.00 3.02
651 663 3.838271 GCCGTCCGATCTGCCTGA 61.838 66.667 0.00 0.00 0.00 3.86
652 664 3.781770 GAGCCGTCCGATCTGCCTG 62.782 68.421 0.00 0.00 0.00 4.85
653 665 3.532155 GAGCCGTCCGATCTGCCT 61.532 66.667 0.00 0.00 0.00 4.75
654 666 4.933064 CGAGCCGTCCGATCTGCC 62.933 72.222 0.00 0.00 0.00 4.85
655 667 4.933064 CCGAGCCGTCCGATCTGC 62.933 72.222 0.00 0.00 0.00 4.26
656 668 3.187699 CTCCGAGCCGTCCGATCTG 62.188 68.421 0.00 0.00 0.00 2.90
657 669 2.902846 CTCCGAGCCGTCCGATCT 60.903 66.667 0.00 0.00 0.00 2.75
658 670 2.899044 CTCTCCGAGCCGTCCGATC 61.899 68.421 0.00 0.00 0.00 3.69
659 671 2.902846 CTCTCCGAGCCGTCCGAT 60.903 66.667 0.00 0.00 0.00 4.18
669 681 2.190170 GGCATCTCGAGCTCTCCGA 61.190 63.158 12.85 3.81 34.61 4.55
670 682 2.334653 GGCATCTCGAGCTCTCCG 59.665 66.667 12.85 0.00 0.00 4.63
671 683 2.334653 CGGCATCTCGAGCTCTCC 59.665 66.667 12.85 5.23 0.00 3.71
672 684 2.354539 GCGGCATCTCGAGCTCTC 60.355 66.667 12.85 0.00 0.00 3.20
673 685 2.625973 CTTGCGGCATCTCGAGCTCT 62.626 60.000 12.85 0.00 0.00 4.09
674 686 2.202797 TTGCGGCATCTCGAGCTC 60.203 61.111 7.81 2.73 0.00 4.09
675 687 2.202851 CTTGCGGCATCTCGAGCT 60.203 61.111 7.81 0.00 0.00 4.09
676 688 3.934684 GCTTGCGGCATCTCGAGC 61.935 66.667 7.81 5.58 41.35 5.03
680 692 3.885521 GCTGGCTTGCGGCATCTC 61.886 66.667 2.28 0.00 45.40 2.75
687 699 3.880846 GATTCCGGCTGGCTTGCG 61.881 66.667 6.73 0.00 34.14 4.85
728 741 1.219124 CTTCCTAGGCTGCTCGCAA 59.781 57.895 2.96 0.00 41.67 4.85
749 762 5.801380 TCTACAAAGAATGTTGGAGTACCC 58.199 41.667 0.00 0.00 43.63 3.69
805 818 2.175931 TCCAAGTTTCCCCTGCACTAAA 59.824 45.455 0.00 0.00 0.00 1.85
830 843 5.008019 CCATCTTGGAACGTATGAAATCCTG 59.992 44.000 3.53 0.00 40.96 3.86
877 890 1.724545 TATACATCCGGGGTTCCCAG 58.275 55.000 10.25 5.63 45.83 4.45
903 916 0.178767 GGCTTTGGATTGGATTGGGC 59.821 55.000 0.00 0.00 0.00 5.36
904 917 1.207811 GTGGCTTTGGATTGGATTGGG 59.792 52.381 0.00 0.00 0.00 4.12
905 918 1.207811 GGTGGCTTTGGATTGGATTGG 59.792 52.381 0.00 0.00 0.00 3.16
977 991 3.052455 TCGTTGAAATGCCTCTGCTTA 57.948 42.857 0.00 0.00 38.71 3.09
1311 1325 2.915659 ACCTCGACCTCAACGGCA 60.916 61.111 0.00 0.00 35.61 5.69
1381 1395 7.918076 AGGAAATAAAATACAGAGAGGACACA 58.082 34.615 0.00 0.00 0.00 3.72
1384 1398 9.449719 TTGAAGGAAATAAAATACAGAGAGGAC 57.550 33.333 0.00 0.00 0.00 3.85
1385 1399 9.449719 GTTGAAGGAAATAAAATACAGAGAGGA 57.550 33.333 0.00 0.00 0.00 3.71
1408 1422 2.743752 CCATGCGTGCGGAGAGTTG 61.744 63.158 0.00 0.00 0.00 3.16
1448 1462 6.128849 GGTTGTAATTGCAAAGTGTAGCATTG 60.129 38.462 10.72 0.00 40.94 2.82
1449 1463 5.925969 GGTTGTAATTGCAAAGTGTAGCATT 59.074 36.000 10.72 0.00 40.94 3.56
1450 1464 5.469479 GGTTGTAATTGCAAAGTGTAGCAT 58.531 37.500 10.72 0.00 40.94 3.79
1509 1525 2.946329 TCGAGCAAAGCAACCACTAAAA 59.054 40.909 0.00 0.00 0.00 1.52
1577 1593 1.595929 GGCCGAACCGAGAAACACA 60.596 57.895 0.00 0.00 0.00 3.72
1626 1642 2.524306 CTGTTGCCCCCTTTGTAATGA 58.476 47.619 0.00 0.00 0.00 2.57
1640 1656 0.447801 CGTAGCCACATTCCTGTTGC 59.552 55.000 0.00 0.00 42.76 4.17
1641 1657 2.093306 TCGTAGCCACATTCCTGTTG 57.907 50.000 0.00 0.00 31.62 3.33
1642 1658 4.481368 TTATCGTAGCCACATTCCTGTT 57.519 40.909 0.00 0.00 31.62 3.16
1643 1659 4.481368 TTTATCGTAGCCACATTCCTGT 57.519 40.909 0.00 0.00 35.44 4.00
1644 1660 5.751680 CATTTTATCGTAGCCACATTCCTG 58.248 41.667 0.00 0.00 0.00 3.86
1645 1661 4.275936 GCATTTTATCGTAGCCACATTCCT 59.724 41.667 0.00 0.00 0.00 3.36
1646 1662 4.275936 AGCATTTTATCGTAGCCACATTCC 59.724 41.667 0.00 0.00 0.00 3.01
1647 1663 5.207768 CAGCATTTTATCGTAGCCACATTC 58.792 41.667 0.00 0.00 0.00 2.67
1659 1681 5.652452 AGAGTTTACCCACCAGCATTTTATC 59.348 40.000 0.00 0.00 0.00 1.75
1661 1683 4.993028 AGAGTTTACCCACCAGCATTTTA 58.007 39.130 0.00 0.00 0.00 1.52
1703 1725 4.895889 CAGTATCTCCAGTCAGGGTCATAA 59.104 45.833 0.00 0.00 38.24 1.90
1704 1726 4.474394 CAGTATCTCCAGTCAGGGTCATA 58.526 47.826 0.00 0.00 38.24 2.15
1713 1735 6.778559 ACTTCTTATACCCAGTATCTCCAGTC 59.221 42.308 0.00 0.00 30.79 3.51
1714 1736 6.684538 ACTTCTTATACCCAGTATCTCCAGT 58.315 40.000 0.00 0.00 30.79 4.00
1722 1850 9.038072 TCACAAATGTACTTCTTATACCCAGTA 57.962 33.333 0.00 0.00 0.00 2.74
1797 1934 1.820519 TGCTGGGAAGCAAATCATCAC 59.179 47.619 0.00 0.00 42.40 3.06
1895 2032 4.098960 ACCATGCTCATCCAAATCATGAAC 59.901 41.667 0.00 0.00 37.34 3.18
1936 2074 1.216427 AGGGCCTTCATTCTCCCAATC 59.784 52.381 0.00 0.00 41.22 2.67
2045 2185 2.369860 TCTTGTTGATGCCAGTCACTCT 59.630 45.455 0.00 0.00 0.00 3.24
2083 2223 5.409211 ACATGATCGATGATATCAGAGCAC 58.591 41.667 13.28 5.41 36.82 4.40
2107 2247 1.956170 CGACAAGGACAGCAAGCGT 60.956 57.895 0.00 0.00 0.00 5.07
2187 2327 3.975982 TGAATATGAAGGCCATCTGGAGA 59.024 43.478 9.78 0.00 36.71 3.71


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

AutoCloner maintained by Alex Coulton.