Multiple sequence alignment - TraesCS4A01G200900

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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 TraesCS4A01G200900 chr4A 100.000 2366 0 0 1 2366 489433254 489435619 0.000000e+00 4370.0
1 TraesCS4A01G200900 chr4A 76.744 430 66 20 960 1381 16247786 16247383 2.380000e-50 209.0
2 TraesCS4A01G200900 chr4A 87.117 163 20 1 544 705 568900520 568900358 1.440000e-42 183.0
3 TraesCS4A01G200900 chr4D 93.496 1599 52 23 780 2366 93070116 93068558 0.000000e+00 2329.0
4 TraesCS4A01G200900 chr4D 93.128 553 17 13 1 543 93070697 93070156 0.000000e+00 791.0
5 TraesCS4A01G200900 chr4D 77.209 430 64 23 960 1381 450331681 450332084 1.100000e-53 220.0
6 TraesCS4A01G200900 chr4D 90.566 53 1 2 707 755 93070154 93070102 1.520000e-07 67.6
7 TraesCS4A01G200900 chr4B 92.941 1445 46 23 945 2366 130625260 130623849 0.000000e+00 2052.0
8 TraesCS4A01G200900 chr4B 92.196 551 15 11 1 543 130625930 130625400 0.000000e+00 754.0
9 TraesCS4A01G200900 chr4B 77.030 431 63 25 960 1381 563628017 563628420 5.120000e-52 215.0
10 TraesCS4A01G200900 chr4B 93.878 49 3 0 707 755 130625398 130625350 9.070000e-10 75.0
11 TraesCS4A01G200900 chr5D 86.391 169 21 2 542 709 374607605 374607438 1.440000e-42 183.0
12 TraesCS4A01G200900 chr7D 86.667 165 20 2 542 705 543097219 543097056 5.190000e-42 182.0
13 TraesCS4A01G200900 chr7D 98.361 61 1 0 27 87 477932212 477932152 8.940000e-20 108.0
14 TraesCS4A01G200900 chr7D 85.263 95 14 0 958 1052 8479898 8479804 5.380000e-17 99.0
15 TraesCS4A01G200900 chr5B 86.747 166 18 4 542 705 611866522 611866685 5.190000e-42 182.0
16 TraesCS4A01G200900 chr5B 85.549 173 20 5 542 711 457987114 457986944 2.420000e-40 176.0
17 TraesCS4A01G200900 chr5B 94.495 109 6 0 1139 1247 625119396 625119504 4.040000e-38 169.0
18 TraesCS4A01G200900 chr5B 92.661 109 8 0 1139 1247 628698945 628699053 8.750000e-35 158.0
19 TraesCS4A01G200900 chr3B 86.747 166 18 4 542 705 673289285 673289448 5.190000e-42 182.0
20 TraesCS4A01G200900 chr3B 96.774 62 2 0 26 87 624317534 624317595 1.160000e-18 104.0
21 TraesCS4A01G200900 chr2D 96.364 110 4 0 1139 1248 81515039 81515148 5.190000e-42 182.0
22 TraesCS4A01G200900 chr6B 96.262 107 4 0 1142 1248 507373577 507373471 2.420000e-40 176.0
23 TraesCS4A01G200900 chr6B 92.661 109 8 0 1139 1247 615607424 615607532 8.750000e-35 158.0
24 TraesCS4A01G200900 chr2A 85.714 168 23 1 542 708 598639725 598639892 2.420000e-40 176.0
25 TraesCS4A01G200900 chr2A 96.774 62 2 0 26 87 138533284 138533223 1.160000e-18 104.0
26 TraesCS4A01G200900 chr1B 86.145 166 19 4 542 705 643105899 643105736 2.420000e-40 176.0
27 TraesCS4A01G200900 chr1B 90.361 83 8 0 5 87 342973180 342973262 2.490000e-20 110.0
28 TraesCS4A01G200900 chr2B 84.181 177 22 6 533 705 556659024 556659198 1.450000e-37 167.0
29 TraesCS4A01G200900 chr7A 94.340 106 6 0 1142 1247 487478638 487478533 1.880000e-36 163.0
30 TraesCS4A01G200900 chr7A 83.158 95 16 0 958 1052 8916271 8916177 1.160000e-13 87.9
31 TraesCS4A01G200900 chr1D 92.771 83 6 0 5 87 269726405 269726487 1.150000e-23 121.0
32 TraesCS4A01G200900 chr1A 92.771 83 6 0 5 87 333135589 333135671 1.150000e-23 121.0
33 TraesCS4A01G200900 chr3A 96.774 62 2 0 26 87 612524213 612524274 1.160000e-18 104.0


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 TraesCS4A01G200900 chr4A 489433254 489435619 2365 False 4370.000000 4370 100.000000 1 2366 1 chr4A.!!$F1 2365
1 TraesCS4A01G200900 chr4D 93068558 93070697 2139 True 1062.533333 2329 92.396667 1 2366 3 chr4D.!!$R1 2365
2 TraesCS4A01G200900 chr4B 130623849 130625930 2081 True 960.333333 2052 93.005000 1 2366 3 chr4B.!!$R1 2365

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
437 440 0.599558 ATGAGCATTGTGTGTGTGCC 59.4 50.0 0.0 0.0 39.62 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1831 1872 1.202405 GGTGTTGTTTGTTGAGGCCAG 60.202 52.381 5.01 0.0 0.0 4.85 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
86 87 2.069273 GATGAACCAGTTCGACACCTG 58.931 52.381 6.08 0.00 42.28 4.00
92 93 3.861840 ACCAGTTCGACACCTGATAATG 58.138 45.455 7.35 0.00 0.00 1.90
98 100 5.181245 AGTTCGACACCTGATAATGGTTTTG 59.819 40.000 0.00 0.00 35.28 2.44
124 126 3.485463 ACTCTCACGGATCAAACCAAA 57.515 42.857 0.00 0.00 0.00 3.28
301 304 1.436983 GGGCGATCCGATCAACCAAC 61.437 60.000 15.84 0.87 0.00 3.77
436 439 1.267533 TCATGAGCATTGTGTGTGTGC 59.732 47.619 0.00 0.00 39.10 4.57
437 440 0.599558 ATGAGCATTGTGTGTGTGCC 59.400 50.000 0.00 0.00 39.62 5.01
438 441 1.081906 GAGCATTGTGTGTGTGCCG 60.082 57.895 0.00 0.00 39.62 5.69
439 442 1.785041 GAGCATTGTGTGTGTGCCGT 61.785 55.000 0.00 0.00 39.62 5.68
534 554 4.936411 CAGTGACAGAGAGAGAAATGCATT 59.064 41.667 5.99 5.99 0.00 3.56
535 555 5.411977 CAGTGACAGAGAGAGAAATGCATTT 59.588 40.000 24.33 24.33 0.00 2.32
541 561 9.852091 GACAGAGAGAGAAATGCATTTTTAATT 57.148 29.630 24.81 11.69 0.00 1.40
551 571 9.226345 GAAATGCATTTTTAATTACTCTCTCCG 57.774 33.333 24.81 0.00 0.00 4.63
552 572 7.865706 ATGCATTTTTAATTACTCTCTCCGT 57.134 32.000 0.00 0.00 0.00 4.69
553 573 7.681939 TGCATTTTTAATTACTCTCTCCGTT 57.318 32.000 0.00 0.00 0.00 4.44
554 574 8.106247 TGCATTTTTAATTACTCTCTCCGTTT 57.894 30.769 0.00 0.00 0.00 3.60
555 575 8.234546 TGCATTTTTAATTACTCTCTCCGTTTC 58.765 33.333 0.00 0.00 0.00 2.78
556 576 7.696872 GCATTTTTAATTACTCTCTCCGTTTCC 59.303 37.037 0.00 0.00 0.00 3.13
557 577 8.726988 CATTTTTAATTACTCTCTCCGTTTCCA 58.273 33.333 0.00 0.00 0.00 3.53
558 578 8.680039 TTTTTAATTACTCTCTCCGTTTCCAA 57.320 30.769 0.00 0.00 0.00 3.53
559 579 8.680039 TTTTAATTACTCTCTCCGTTTCCAAA 57.320 30.769 0.00 0.00 0.00 3.28
560 580 8.857694 TTTAATTACTCTCTCCGTTTCCAAAT 57.142 30.769 0.00 0.00 0.00 2.32
561 581 9.947433 TTTAATTACTCTCTCCGTTTCCAAATA 57.053 29.630 0.00 0.00 0.00 1.40
562 582 7.845066 AATTACTCTCTCCGTTTCCAAATAC 57.155 36.000 0.00 0.00 0.00 1.89
563 583 6.600882 TTACTCTCTCCGTTTCCAAATACT 57.399 37.500 0.00 0.00 0.00 2.12
564 584 5.485209 ACTCTCTCCGTTTCCAAATACTT 57.515 39.130 0.00 0.00 0.00 2.24
565 585 5.238583 ACTCTCTCCGTTTCCAAATACTTG 58.761 41.667 0.00 0.00 0.00 3.16
566 586 5.221661 ACTCTCTCCGTTTCCAAATACTTGT 60.222 40.000 0.00 0.00 0.00 3.16
567 587 5.235516 TCTCTCCGTTTCCAAATACTTGTC 58.764 41.667 0.00 0.00 0.00 3.18
568 588 5.011738 TCTCTCCGTTTCCAAATACTTGTCT 59.988 40.000 0.00 0.00 0.00 3.41
569 589 5.617252 TCTCCGTTTCCAAATACTTGTCTT 58.383 37.500 0.00 0.00 0.00 3.01
570 590 6.059484 TCTCCGTTTCCAAATACTTGTCTTT 58.941 36.000 0.00 0.00 0.00 2.52
571 591 6.204108 TCTCCGTTTCCAAATACTTGTCTTTC 59.796 38.462 0.00 0.00 0.00 2.62
572 592 6.059484 TCCGTTTCCAAATACTTGTCTTTCT 58.941 36.000 0.00 0.00 0.00 2.52
573 593 7.218614 TCCGTTTCCAAATACTTGTCTTTCTA 58.781 34.615 0.00 0.00 0.00 2.10
574 594 7.386848 TCCGTTTCCAAATACTTGTCTTTCTAG 59.613 37.037 0.00 0.00 0.00 2.43
575 595 7.172703 CCGTTTCCAAATACTTGTCTTTCTAGT 59.827 37.037 0.00 0.00 36.28 2.57
576 596 8.221766 CGTTTCCAAATACTTGTCTTTCTAGTC 58.778 37.037 0.00 0.00 34.37 2.59
577 597 9.052759 GTTTCCAAATACTTGTCTTTCTAGTCA 57.947 33.333 0.00 0.00 34.37 3.41
578 598 9.793259 TTTCCAAATACTTGTCTTTCTAGTCAT 57.207 29.630 0.00 0.00 34.37 3.06
579 599 9.793259 TTCCAAATACTTGTCTTTCTAGTCATT 57.207 29.630 0.00 0.00 34.37 2.57
580 600 9.793259 TCCAAATACTTGTCTTTCTAGTCATTT 57.207 29.630 0.00 0.00 34.37 2.32
587 607 9.342308 ACTTGTCTTTCTAGTCATTTCAAATGA 57.658 29.630 8.85 8.85 0.00 2.57
599 619 9.773328 AGTCATTTCAAATGATTACAACATACG 57.227 29.630 15.91 0.00 0.00 3.06
600 620 9.009327 GTCATTTCAAATGATTACAACATACGG 57.991 33.333 15.91 0.00 0.00 4.02
601 621 8.951243 TCATTTCAAATGATTACAACATACGGA 58.049 29.630 8.85 0.00 0.00 4.69
602 622 9.734620 CATTTCAAATGATTACAACATACGGAT 57.265 29.630 3.82 0.00 0.00 4.18
635 655 9.594936 AGTCATATTTTAGAGTATAGGCTCACT 57.405 33.333 0.00 0.00 37.94 3.41
636 656 9.849166 GTCATATTTTAGAGTATAGGCTCACTC 57.151 37.037 17.25 17.25 41.25 3.51
637 657 9.588096 TCATATTTTAGAGTATAGGCTCACTCA 57.412 33.333 23.51 11.89 42.99 3.41
644 664 7.906199 AGAGTATAGGCTCACTCATTTTACT 57.094 36.000 23.51 5.80 42.99 2.24
645 665 8.312669 AGAGTATAGGCTCACTCATTTTACTT 57.687 34.615 23.51 5.24 42.99 2.24
646 666 8.417884 AGAGTATAGGCTCACTCATTTTACTTC 58.582 37.037 23.51 2.36 42.99 3.01
647 667 7.203910 AGTATAGGCTCACTCATTTTACTTCG 58.796 38.462 0.00 0.00 0.00 3.79
648 668 4.273148 AGGCTCACTCATTTTACTTCGT 57.727 40.909 0.00 0.00 0.00 3.85
649 669 5.401531 AGGCTCACTCATTTTACTTCGTA 57.598 39.130 0.00 0.00 0.00 3.43
650 670 5.978814 AGGCTCACTCATTTTACTTCGTAT 58.021 37.500 0.00 0.00 0.00 3.06
651 671 5.812642 AGGCTCACTCATTTTACTTCGTATG 59.187 40.000 0.00 0.00 0.00 2.39
652 672 5.581085 GGCTCACTCATTTTACTTCGTATGT 59.419 40.000 0.00 0.00 0.00 2.29
653 673 6.755141 GGCTCACTCATTTTACTTCGTATGTA 59.245 38.462 0.00 0.00 0.00 2.29
654 674 7.043325 GGCTCACTCATTTTACTTCGTATGTAG 60.043 40.741 0.00 0.00 0.00 2.74
655 675 7.488471 GCTCACTCATTTTACTTCGTATGTAGT 59.512 37.037 0.00 0.00 0.00 2.73
656 676 9.355215 CTCACTCATTTTACTTCGTATGTAGTT 57.645 33.333 0.00 0.00 0.00 2.24
699 719 9.264719 AGAAAAACAAATATTTGAAAGCAGAGG 57.735 29.630 30.18 4.51 40.55 3.69
700 720 7.967890 AAAACAAATATTTGAAAGCAGAGGG 57.032 32.000 30.18 4.03 40.55 4.30
701 721 6.916360 AACAAATATTTGAAAGCAGAGGGA 57.084 33.333 30.18 0.00 40.55 4.20
702 722 6.521151 ACAAATATTTGAAAGCAGAGGGAG 57.479 37.500 30.18 3.44 40.55 4.30
705 725 7.121315 ACAAATATTTGAAAGCAGAGGGAGTAC 59.879 37.037 30.18 0.00 40.55 2.73
718 738 5.944599 CAGAGGGAGTACTACTGTAGTTCAA 59.055 44.000 24.09 5.36 40.14 2.69
755 779 4.401519 TCACCTGTACAATACACCTAGCTC 59.598 45.833 0.00 0.00 34.46 4.09
756 780 3.705072 ACCTGTACAATACACCTAGCTCC 59.295 47.826 0.00 0.00 34.46 4.70
757 781 3.069729 CCTGTACAATACACCTAGCTCCC 59.930 52.174 0.00 0.00 34.46 4.30
758 782 3.036091 TGTACAATACACCTAGCTCCCC 58.964 50.000 0.00 0.00 32.89 4.81
759 783 2.263895 ACAATACACCTAGCTCCCCA 57.736 50.000 0.00 0.00 0.00 4.96
760 784 1.838077 ACAATACACCTAGCTCCCCAC 59.162 52.381 0.00 0.00 0.00 4.61
761 785 1.837439 CAATACACCTAGCTCCCCACA 59.163 52.381 0.00 0.00 0.00 4.17
762 786 2.238646 CAATACACCTAGCTCCCCACAA 59.761 50.000 0.00 0.00 0.00 3.33
763 787 2.032965 TACACCTAGCTCCCCACAAA 57.967 50.000 0.00 0.00 0.00 2.83
764 788 1.145571 ACACCTAGCTCCCCACAAAA 58.854 50.000 0.00 0.00 0.00 2.44
765 789 1.497286 ACACCTAGCTCCCCACAAAAA 59.503 47.619 0.00 0.00 0.00 1.94
859 883 7.432252 CCTTATAATCCGAAACAATTCAAGCAC 59.568 37.037 0.00 0.00 35.15 4.40
864 888 2.468777 CGAAACAATTCAAGCACTGCAC 59.531 45.455 3.30 0.00 35.15 4.57
865 889 3.446799 GAAACAATTCAAGCACTGCACA 58.553 40.909 3.30 0.00 35.54 4.57
866 890 2.787601 ACAATTCAAGCACTGCACAG 57.212 45.000 3.30 0.00 0.00 3.66
867 891 1.269413 ACAATTCAAGCACTGCACAGC 60.269 47.619 3.30 0.00 0.00 4.40
911 935 3.405170 AAAATGGCGCTAAAGTCATCG 57.595 42.857 7.64 0.00 0.00 3.84
947 975 3.069079 ACGTAGTACAAGAGGAGAGCA 57.931 47.619 0.38 0.00 41.94 4.26
948 976 3.622630 ACGTAGTACAAGAGGAGAGCAT 58.377 45.455 0.38 0.00 41.94 3.79
1059 1087 2.820619 CGCGCTGCTCTGCATCATT 61.821 57.895 5.56 0.00 38.13 2.57
1471 1499 1.971357 CCACCACAACCACTCTCTAGT 59.029 52.381 0.00 0.00 35.91 2.57
1472 1500 3.162666 CCACCACAACCACTCTCTAGTA 58.837 50.000 0.00 0.00 33.48 1.82
1473 1501 3.056749 CCACCACAACCACTCTCTAGTAC 60.057 52.174 0.00 0.00 33.48 2.73
1474 1502 3.572682 CACCACAACCACTCTCTAGTACA 59.427 47.826 0.00 0.00 33.48 2.90
1475 1503 3.827302 ACCACAACCACTCTCTAGTACAG 59.173 47.826 0.00 0.00 33.48 2.74
1476 1504 3.827302 CCACAACCACTCTCTAGTACAGT 59.173 47.826 0.00 0.00 33.48 3.55
1477 1505 5.008331 CCACAACCACTCTCTAGTACAGTA 58.992 45.833 0.00 0.00 33.48 2.74
1478 1506 5.106237 CCACAACCACTCTCTAGTACAGTAC 60.106 48.000 2.05 2.05 33.48 2.73
1549 1578 8.547173 AGACTGAGAGAATCAAGTGGATTTTAT 58.453 33.333 0.00 0.00 46.17 1.40
1562 1591 7.408756 AGTGGATTTTATCAAAAGCATGCTA 57.591 32.000 23.00 5.30 38.46 3.49
1619 1652 8.924303 ACAAACTAAAGCTCCCTAAAAAGAATT 58.076 29.630 0.00 0.00 0.00 2.17
1744 1777 8.341892 TCTACCTTCTGTACTGATAGCATATG 57.658 38.462 3.03 0.00 0.00 1.78
1745 1778 6.985653 ACCTTCTGTACTGATAGCATATGT 57.014 37.500 4.29 0.00 0.00 2.29
1828 1869 4.035909 ACAAAGTTAAAGGTGGCTTGTACG 59.964 41.667 0.00 0.00 0.00 3.67
1829 1870 3.480505 AGTTAAAGGTGGCTTGTACGT 57.519 42.857 0.00 0.00 0.00 3.57
1830 1871 4.605640 AGTTAAAGGTGGCTTGTACGTA 57.394 40.909 0.00 0.00 0.00 3.57
1831 1872 4.309933 AGTTAAAGGTGGCTTGTACGTAC 58.690 43.478 18.90 18.90 0.00 3.67
2159 2208 8.043710 ACTGTAGCTGTAATTCTGCTTTCTAAT 58.956 33.333 0.00 0.00 46.51 1.73
2160 2209 8.792830 TGTAGCTGTAATTCTGCTTTCTAATT 57.207 30.769 0.00 0.00 46.51 1.40
2161 2210 9.884636 TGTAGCTGTAATTCTGCTTTCTAATTA 57.115 29.630 0.00 0.00 46.51 1.40
2187 2236 5.416947 AGACAATACTGGACGGTGTTTATC 58.583 41.667 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 7.358352 CGTGAGAGTTTTTGCAAAACCATTATC 60.358 37.037 23.79 13.83 0.00 1.75
92 93 2.857748 CCGTGAGAGTTTTTGCAAAACC 59.142 45.455 23.79 17.43 0.00 3.27
98 100 3.896648 TTGATCCGTGAGAGTTTTTGC 57.103 42.857 0.00 0.00 0.00 3.68
124 126 1.881591 TTTTTACTGTTACCGCGGCT 58.118 45.000 28.58 15.49 0.00 5.52
301 304 4.778415 CCTCGTGTCGCACTCCCG 62.778 72.222 8.07 0.00 31.34 5.14
363 366 1.186030 CTCCATTCGTACGTGCGTAC 58.814 55.000 24.94 20.84 45.29 3.67
436 439 2.290916 AGACATAGCACGAGATACACGG 59.709 50.000 0.00 0.00 34.93 4.94
437 440 3.610786 AGACATAGCACGAGATACACG 57.389 47.619 0.00 0.00 0.00 4.49
438 441 6.003234 ACATAGACATAGCACGAGATACAC 57.997 41.667 0.00 0.00 0.00 2.90
439 442 5.998363 AGACATAGACATAGCACGAGATACA 59.002 40.000 0.00 0.00 0.00 2.29
534 554 8.680039 TTTGGAAACGGAGAGAGTAATTAAAA 57.320 30.769 0.00 0.00 0.00 1.52
535 555 8.857694 ATTTGGAAACGGAGAGAGTAATTAAA 57.142 30.769 0.00 0.00 0.00 1.52
541 561 6.014840 ACAAGTATTTGGAAACGGAGAGAGTA 60.015 38.462 2.81 0.00 38.66 2.59
542 562 5.221661 ACAAGTATTTGGAAACGGAGAGAGT 60.222 40.000 2.81 0.00 38.66 3.24
543 563 5.238583 ACAAGTATTTGGAAACGGAGAGAG 58.761 41.667 2.81 0.00 38.66 3.20
544 564 5.011738 AGACAAGTATTTGGAAACGGAGAGA 59.988 40.000 2.81 0.00 38.66 3.10
545 565 5.238583 AGACAAGTATTTGGAAACGGAGAG 58.761 41.667 2.81 0.00 38.66 3.20
546 566 5.223449 AGACAAGTATTTGGAAACGGAGA 57.777 39.130 2.81 0.00 38.66 3.71
547 567 5.941948 AAGACAAGTATTTGGAAACGGAG 57.058 39.130 2.81 0.00 38.66 4.63
548 568 6.059484 AGAAAGACAAGTATTTGGAAACGGA 58.941 36.000 2.81 0.00 38.66 4.69
549 569 6.313744 AGAAAGACAAGTATTTGGAAACGG 57.686 37.500 2.81 0.00 38.66 4.44
550 570 8.084590 ACTAGAAAGACAAGTATTTGGAAACG 57.915 34.615 0.00 0.00 38.66 3.60
551 571 9.052759 TGACTAGAAAGACAAGTATTTGGAAAC 57.947 33.333 0.00 0.00 38.66 2.78
552 572 9.793259 ATGACTAGAAAGACAAGTATTTGGAAA 57.207 29.630 0.00 0.00 38.66 3.13
553 573 9.793259 AATGACTAGAAAGACAAGTATTTGGAA 57.207 29.630 0.00 0.00 38.66 3.53
554 574 9.793259 AAATGACTAGAAAGACAAGTATTTGGA 57.207 29.630 0.00 0.00 38.66 3.53
561 581 9.342308 TCATTTGAAATGACTAGAAAGACAAGT 57.658 29.630 16.04 0.00 31.23 3.16
573 593 9.773328 CGTATGTTGTAATCATTTGAAATGACT 57.227 29.630 21.54 14.37 0.00 3.41
574 594 9.009327 CCGTATGTTGTAATCATTTGAAATGAC 57.991 33.333 21.54 11.23 0.00 3.06
575 595 8.951243 TCCGTATGTTGTAATCATTTGAAATGA 58.049 29.630 21.39 21.39 0.00 2.57
576 596 9.734620 ATCCGTATGTTGTAATCATTTGAAATG 57.265 29.630 11.54 11.54 0.00 2.32
609 629 9.594936 AGTGAGCCTATACTCTAAAATATGACT 57.405 33.333 0.00 0.00 37.58 3.41
610 630 9.849166 GAGTGAGCCTATACTCTAAAATATGAC 57.151 37.037 0.00 0.00 40.06 3.06
611 631 9.588096 TGAGTGAGCCTATACTCTAAAATATGA 57.412 33.333 9.27 0.00 42.86 2.15
618 638 9.422681 AGTAAAATGAGTGAGCCTATACTCTAA 57.577 33.333 9.27 0.00 42.86 2.10
619 639 8.998277 AGTAAAATGAGTGAGCCTATACTCTA 57.002 34.615 9.27 0.00 42.86 2.43
620 640 7.906199 AGTAAAATGAGTGAGCCTATACTCT 57.094 36.000 9.27 0.00 42.86 3.24
621 641 7.380065 CGAAGTAAAATGAGTGAGCCTATACTC 59.620 40.741 0.00 0.00 42.77 2.59
622 642 7.147880 ACGAAGTAAAATGAGTGAGCCTATACT 60.148 37.037 0.00 0.00 41.94 2.12
623 643 6.979238 ACGAAGTAAAATGAGTGAGCCTATAC 59.021 38.462 0.00 0.00 41.94 1.47
624 644 7.108841 ACGAAGTAAAATGAGTGAGCCTATA 57.891 36.000 0.00 0.00 41.94 1.31
625 645 5.978814 ACGAAGTAAAATGAGTGAGCCTAT 58.021 37.500 0.00 0.00 41.94 2.57
626 646 5.401531 ACGAAGTAAAATGAGTGAGCCTA 57.598 39.130 0.00 0.00 41.94 3.93
627 647 4.273148 ACGAAGTAAAATGAGTGAGCCT 57.727 40.909 0.00 0.00 41.94 4.58
673 693 9.264719 CCTCTGCTTTCAAATATTTGTTTTTCT 57.735 29.630 23.95 0.00 39.18 2.52
674 694 8.498358 CCCTCTGCTTTCAAATATTTGTTTTTC 58.502 33.333 23.95 13.01 39.18 2.29
675 695 8.210265 TCCCTCTGCTTTCAAATATTTGTTTTT 58.790 29.630 23.95 0.00 39.18 1.94
676 696 7.734942 TCCCTCTGCTTTCAAATATTTGTTTT 58.265 30.769 23.95 0.00 39.18 2.43
677 697 7.015584 ACTCCCTCTGCTTTCAAATATTTGTTT 59.984 33.333 23.95 0.00 39.18 2.83
678 698 6.494835 ACTCCCTCTGCTTTCAAATATTTGTT 59.505 34.615 23.95 0.00 39.18 2.83
679 699 6.012745 ACTCCCTCTGCTTTCAAATATTTGT 58.987 36.000 23.95 1.02 39.18 2.83
680 700 6.521151 ACTCCCTCTGCTTTCAAATATTTG 57.479 37.500 20.13 20.13 39.48 2.32
681 701 7.406104 AGTACTCCCTCTGCTTTCAAATATTT 58.594 34.615 0.00 0.00 0.00 1.40
682 702 6.963322 AGTACTCCCTCTGCTTTCAAATATT 58.037 36.000 0.00 0.00 0.00 1.28
683 703 6.567602 AGTACTCCCTCTGCTTTCAAATAT 57.432 37.500 0.00 0.00 0.00 1.28
684 704 6.668283 AGTAGTACTCCCTCTGCTTTCAAATA 59.332 38.462 0.00 0.00 0.00 1.40
685 705 4.917906 AGTACTCCCTCTGCTTTCAAAT 57.082 40.909 0.00 0.00 0.00 2.32
686 706 4.838986 AGTAGTACTCCCTCTGCTTTCAAA 59.161 41.667 0.00 0.00 0.00 2.69
687 707 4.220821 CAGTAGTACTCCCTCTGCTTTCAA 59.779 45.833 0.00 0.00 0.00 2.69
688 708 3.764434 CAGTAGTACTCCCTCTGCTTTCA 59.236 47.826 0.00 0.00 0.00 2.69
689 709 3.764972 ACAGTAGTACTCCCTCTGCTTTC 59.235 47.826 0.00 0.00 0.00 2.62
690 710 3.780626 ACAGTAGTACTCCCTCTGCTTT 58.219 45.455 0.00 0.00 0.00 3.51
691 711 3.459710 ACAGTAGTACTCCCTCTGCTT 57.540 47.619 0.00 0.00 0.00 3.91
692 712 3.524380 ACTACAGTAGTACTCCCTCTGCT 59.476 47.826 11.84 0.00 37.23 4.24
693 713 3.888583 ACTACAGTAGTACTCCCTCTGC 58.111 50.000 11.84 0.00 37.23 4.26
694 714 5.498393 TGAACTACAGTAGTACTCCCTCTG 58.502 45.833 13.87 7.15 38.26 3.35
695 715 5.775813 TGAACTACAGTAGTACTCCCTCT 57.224 43.478 13.87 0.00 38.26 3.69
696 716 7.407393 AATTGAACTACAGTAGTACTCCCTC 57.593 40.000 13.87 7.21 38.26 4.30
697 717 9.134055 GATAATTGAACTACAGTAGTACTCCCT 57.866 37.037 13.87 0.00 38.26 4.20
698 718 8.074972 CGATAATTGAACTACAGTAGTACTCCC 58.925 40.741 13.87 2.63 38.26 4.30
699 719 8.834465 TCGATAATTGAACTACAGTAGTACTCC 58.166 37.037 13.87 4.86 38.26 3.85
702 722 9.395707 CCATCGATAATTGAACTACAGTAGTAC 57.604 37.037 13.87 0.00 38.26 2.73
705 725 8.353684 ACTCCATCGATAATTGAACTACAGTAG 58.646 37.037 6.00 6.00 0.00 2.57
718 738 5.362717 TGTACAGGTGAACTCCATCGATAAT 59.637 40.000 0.00 0.00 0.00 1.28
788 812 1.131883 ACGTACGTGCAACCTAGCTAG 59.868 52.381 22.14 14.20 34.99 3.42
789 813 1.167851 ACGTACGTGCAACCTAGCTA 58.832 50.000 22.14 0.00 34.99 3.32
790 814 0.316204 AACGTACGTGCAACCTAGCT 59.684 50.000 23.57 0.00 34.99 3.32
791 815 0.712222 GAACGTACGTGCAACCTAGC 59.288 55.000 23.57 0.00 0.00 3.42
792 816 2.054687 TGAACGTACGTGCAACCTAG 57.945 50.000 26.66 0.00 29.25 3.02
793 817 2.728690 ATGAACGTACGTGCAACCTA 57.271 45.000 31.62 9.56 37.20 3.08
894 918 2.205074 CTTCGATGACTTTAGCGCCAT 58.795 47.619 2.29 0.00 0.00 4.40
900 924 8.386606 ACTACTTACGTACTTCGATGACTTTAG 58.613 37.037 5.16 0.00 42.86 1.85
936 964 2.614987 GCTTCACACATGCTCTCCTCTT 60.615 50.000 0.00 0.00 0.00 2.85
1422 1450 9.886132 AACACTAGTAATCAACCCACTAATTAG 57.114 33.333 11.05 11.05 0.00 1.73
1472 1500 9.216117 GATAAACACAATCCAAAGTAGTACTGT 57.784 33.333 5.39 0.00 0.00 3.55
1473 1501 9.214957 TGATAAACACAATCCAAAGTAGTACTG 57.785 33.333 5.39 0.00 0.00 2.74
1474 1502 9.959721 ATGATAAACACAATCCAAAGTAGTACT 57.040 29.630 0.00 0.00 0.00 2.73
1526 1554 8.728337 TGATAAAATCCACTTGATTCTCTCAG 57.272 34.615 0.00 0.00 42.97 3.35
1549 1578 2.228925 TGCAGTGTAGCATGCTTTTGA 58.771 42.857 28.02 4.26 42.98 2.69
1562 1591 9.851686 TCTCCATATAAATAAGAAATGCAGTGT 57.148 29.630 0.00 0.00 0.00 3.55
1619 1652 8.450578 TCATGCTTTGAGTTTTTCTTCTTCTA 57.549 30.769 0.00 0.00 0.00 2.10
1828 1869 2.685897 TGTTGTTTGTTGAGGCCAGTAC 59.314 45.455 5.01 0.00 0.00 2.73
1829 1870 2.685897 GTGTTGTTTGTTGAGGCCAGTA 59.314 45.455 5.01 0.00 0.00 2.74
1830 1871 1.476488 GTGTTGTTTGTTGAGGCCAGT 59.524 47.619 5.01 0.00 0.00 4.00
1831 1872 1.202405 GGTGTTGTTTGTTGAGGCCAG 60.202 52.381 5.01 0.00 0.00 4.85
2023 2064 8.950208 AGATTATAAAAGTGACAAGTCTAGCC 57.050 34.615 1.53 0.00 0.00 3.93
2119 2168 4.034048 CAGCTACAGTTAATTAACGGGCAG 59.966 45.833 25.60 21.99 40.96 4.85
2122 2171 7.781548 ATTACAGCTACAGTTAATTAACGGG 57.218 36.000 25.60 20.97 40.96 5.28
2125 2174 9.704098 GCAGAATTACAGCTACAGTTAATTAAC 57.296 33.333 18.77 18.77 36.46 2.01
2159 2208 5.613329 ACACCGTCCAGTATTGTCTTTTAA 58.387 37.500 0.00 0.00 0.00 1.52
2160 2209 5.217978 ACACCGTCCAGTATTGTCTTTTA 57.782 39.130 0.00 0.00 0.00 1.52
2161 2210 4.081322 ACACCGTCCAGTATTGTCTTTT 57.919 40.909 0.00 0.00 0.00 2.27
2162 2211 3.764237 ACACCGTCCAGTATTGTCTTT 57.236 42.857 0.00 0.00 0.00 2.52
2196 2250 6.266786 TGCACCAACTATATATTCTCTTCGGA 59.733 38.462 0.00 0.00 0.00 4.55
2197 2251 6.455647 TGCACCAACTATATATTCTCTTCGG 58.544 40.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.