Multiple sequence alignment - TraesCS3D01G492700

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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 TraesCS3D01G492700 chr3D 100.000 2342 0 0 1 2342 586404429 586406770 0.000000e+00 4325
1 TraesCS3D01G492700 chr3D 96.186 603 17 4 1360 1958 586575394 586574794 0.000000e+00 981
2 TraesCS3D01G492700 chr3D 92.402 487 37 0 114 600 591013310 591013796 0.000000e+00 695
3 TraesCS3D01G492700 chr3D 92.029 414 27 3 949 1362 586575842 586575435 5.610000e-161 577
4 TraesCS3D01G492700 chr3D 91.774 389 30 2 1956 2342 586573040 586572652 7.360000e-150 540
5 TraesCS3D01G492700 chr3D 92.511 227 11 4 725 946 586576345 586576120 1.040000e-83 320
6 TraesCS3D01G492700 chr3D 98.246 114 2 0 3 116 89924575 89924688 1.420000e-47 200
7 TraesCS3D01G492700 chr3D 97.414 116 2 1 1 116 467571061 467571175 1.840000e-46 196
8 TraesCS3D01G492700 chr3D 93.458 107 6 1 1956 2061 586574471 586574365 8.660000e-35 158
9 TraesCS3D01G492700 chr7D 93.496 492 31 1 114 604 46985517 46986008 0.000000e+00 730
10 TraesCS3D01G492700 chr7D 92.638 489 36 0 114 602 175659920 175659432 0.000000e+00 704
11 TraesCS3D01G492700 chr7D 92.623 488 36 0 114 601 149752018 149751531 0.000000e+00 702
12 TraesCS3D01G492700 chr7D 97.414 116 3 0 1 116 46985343 46985458 5.100000e-47 198
13 TraesCS3D01G492700 chr7D 97.414 116 2 1 1 116 603388720 603388834 1.840000e-46 196
14 TraesCS3D01G492700 chr7D 92.405 79 6 0 602 680 320861085 320861007 1.900000e-21 113
15 TraesCS3D01G492700 chr2B 93.469 490 31 1 114 602 713942559 713943048 0.000000e+00 726
16 TraesCS3D01G492700 chr2B 92.405 79 6 0 602 680 121813224 121813146 1.900000e-21 113
17 TraesCS3D01G492700 chr1A 93.061 490 34 0 114 603 425686727 425686238 0.000000e+00 717
18 TraesCS3D01G492700 chr2A 92.683 492 35 1 114 604 600420376 600419885 0.000000e+00 708
19 TraesCS3D01G492700 chr2A 92.137 496 38 1 114 608 676269708 676270203 0.000000e+00 699
20 TraesCS3D01G492700 chr2A 92.405 79 6 0 602 680 75933377 75933299 1.900000e-21 113
21 TraesCS3D01G492700 chr1D 92.121 495 38 1 114 608 66392183 66391690 0.000000e+00 697
22 TraesCS3D01G492700 chr1D 97.414 116 3 0 1 116 366024347 366024232 5.100000e-47 198
23 TraesCS3D01G492700 chr3B 86.491 570 42 8 794 1363 783146367 783146901 5.570000e-166 593
24 TraesCS3D01G492700 chr3B 89.105 257 21 4 1360 1610 783146941 783147196 1.750000e-81 313
25 TraesCS3D01G492700 chr3B 93.532 201 13 0 1757 1957 783148255 783148455 1.360000e-77 300
26 TraesCS3D01G492700 chr3B 89.565 115 9 2 1636 1750 783148088 783148199 2.430000e-30 143
27 TraesCS3D01G492700 chr6B 97.414 116 3 0 1 116 76352524 76352639 5.100000e-47 198
28 TraesCS3D01G492700 chr6B 91.139 79 7 0 602 680 451601913 451601991 8.850000e-20 108
29 TraesCS3D01G492700 chr5D 97.414 116 3 0 1 116 441789194 441789309 5.100000e-47 198
30 TraesCS3D01G492700 chrUn 96.552 116 4 0 1 116 33340977 33341092 2.380000e-45 193
31 TraesCS3D01G492700 chrUn 96.552 116 4 0 1 116 314871403 314871518 2.380000e-45 193
32 TraesCS3D01G492700 chrUn 88.235 85 7 3 602 685 95258038 95257956 5.330000e-17 99
33 TraesCS3D01G492700 chr7B 92.405 79 6 0 602 680 101140677 101140755 1.900000e-21 113
34 TraesCS3D01G492700 chr7B 94.286 70 4 0 600 669 412800410 412800479 8.850000e-20 108
35 TraesCS3D01G492700 chr3A 91.139 79 7 0 602 680 232198010 232198088 8.850000e-20 108
36 TraesCS3D01G492700 chr4B 94.203 69 4 0 602 670 376163548 376163480 3.180000e-19 106


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 TraesCS3D01G492700 chr3D 586404429 586406770 2341 False 4325.00 4325 100.00000 1 2342 1 chr3D.!!$F3 2341
1 TraesCS3D01G492700 chr3D 586572652 586576345 3693 True 515.20 981 93.19160 725 2342 5 chr3D.!!$R1 1617
2 TraesCS3D01G492700 chr7D 46985343 46986008 665 False 464.00 730 95.45500 1 604 2 chr7D.!!$F2 603
3 TraesCS3D01G492700 chr3B 783146367 783148455 2088 False 337.25 593 89.67325 794 1957 4 chr3B.!!$F1 1163

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
711 773 0.107214 AATGGTATGCTCCGGTGTGG 60.107 55.0 0.0 0.0 40.09 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 2919 0.253044 ACGCCTACACCATGCATTCT 59.747 50.0 0.0 0.0 0.0 2.4 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
26 27 2.092914 CCAACTCCACTCAATACCTCCC 60.093 54.545 0.00 0.00 0.00 4.30
138 200 3.774959 GATCTCGACGGCATGGCGT 62.775 63.158 42.54 42.54 0.00 5.68
190 252 3.893763 CTCGCGCAGGAGGACGAT 61.894 66.667 8.75 0.00 33.53 3.73
193 255 4.819761 GCGCAGGAGGACGATGCA 62.820 66.667 0.30 0.00 39.97 3.96
196 258 1.078848 GCAGGAGGACGATGCAGTT 60.079 57.895 0.00 0.00 39.75 3.16
243 305 0.824759 GAGACCTGGCACGGTAGATT 59.175 55.000 8.34 0.00 35.59 2.40
247 309 1.559682 ACCTGGCACGGTAGATTCAAT 59.440 47.619 6.82 0.00 33.88 2.57
271 333 4.713814 AGTACAGCTCTGAAGATGGATTGA 59.286 41.667 3.60 0.00 43.33 2.57
280 342 2.359981 AGATGGATTGATGGCAGGTG 57.640 50.000 0.00 0.00 0.00 4.00
300 362 2.758327 TGCGACGGCCTCATACCT 60.758 61.111 0.00 0.00 38.85 3.08
341 403 3.142838 GCGCCGGACTGGTAGGTA 61.143 66.667 5.05 0.00 41.21 3.08
357 419 2.446994 TACCCCATACCCGGCAGG 60.447 66.667 0.00 0.00 43.78 4.85
469 531 3.014304 ACTGGATAGGAGTAGCGACAA 57.986 47.619 0.00 0.00 0.00 3.18
486 548 3.420576 CGACAATTGTTGCTTAAACGGTG 59.579 43.478 13.36 0.00 42.10 4.94
557 619 2.106477 TAAAGTGGTCGCATGCATCA 57.894 45.000 19.57 8.71 0.00 3.07
558 620 1.466856 AAAGTGGTCGCATGCATCAT 58.533 45.000 19.57 0.00 0.00 2.45
559 621 1.466856 AAGTGGTCGCATGCATCATT 58.533 45.000 19.57 5.59 0.00 2.57
560 622 1.466856 AGTGGTCGCATGCATCATTT 58.533 45.000 19.57 2.15 0.00 2.32
583 645 4.426313 CAAAGGCCGGGGGTCCTC 62.426 72.222 2.18 0.00 30.95 3.71
597 659 3.332783 GGGGTCCTCCTCCTTTTCTAAAA 59.667 47.826 0.00 0.00 35.33 1.52
620 682 5.425196 AAAATACACCCGTATGTGGTAGT 57.575 39.130 0.00 0.00 38.37 2.73
621 683 4.660789 AATACACCCGTATGTGGTAGTC 57.339 45.455 0.00 0.00 38.37 2.59
622 684 1.188863 ACACCCGTATGTGGTAGTCC 58.811 55.000 0.00 0.00 40.62 3.85
623 685 1.187974 CACCCGTATGTGGTAGTCCA 58.812 55.000 0.00 0.00 42.05 4.02
624 686 1.760613 CACCCGTATGTGGTAGTCCAT 59.239 52.381 0.00 0.00 46.20 3.41
625 687 2.169769 CACCCGTATGTGGTAGTCCATT 59.830 50.000 0.00 0.00 46.20 3.16
626 688 2.841881 ACCCGTATGTGGTAGTCCATTT 59.158 45.455 0.00 0.00 46.20 2.32
627 689 3.202906 CCCGTATGTGGTAGTCCATTTG 58.797 50.000 0.00 0.00 46.20 2.32
628 690 3.118555 CCCGTATGTGGTAGTCCATTTGA 60.119 47.826 0.00 0.00 46.20 2.69
629 691 4.509616 CCGTATGTGGTAGTCCATTTGAA 58.490 43.478 0.00 0.00 46.20 2.69
630 692 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
631 693 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
632 694 6.458206 CCGTATGTGGTAGTCCATTTGAAATG 60.458 42.308 10.84 10.84 46.20 2.32
633 695 6.093495 CGTATGTGGTAGTCCATTTGAAATGT 59.907 38.462 15.93 1.43 46.20 2.71
634 696 5.957842 TGTGGTAGTCCATTTGAAATGTC 57.042 39.130 15.93 9.10 46.20 3.06
635 697 5.630121 TGTGGTAGTCCATTTGAAATGTCT 58.370 37.500 15.93 14.81 46.20 3.41
636 698 6.774673 TGTGGTAGTCCATTTGAAATGTCTA 58.225 36.000 15.93 13.97 46.20 2.59
637 699 6.878923 TGTGGTAGTCCATTTGAAATGTCTAG 59.121 38.462 15.93 1.90 46.20 2.43
638 700 7.103641 GTGGTAGTCCATTTGAAATGTCTAGA 58.896 38.462 15.93 4.16 46.20 2.43
639 701 7.606456 GTGGTAGTCCATTTGAAATGTCTAGAA 59.394 37.037 15.93 7.22 46.20 2.10
640 702 8.160765 TGGTAGTCCATTTGAAATGTCTAGAAA 58.839 33.333 15.93 0.00 39.03 2.52
641 703 8.669243 GGTAGTCCATTTGAAATGTCTAGAAAG 58.331 37.037 15.93 0.00 0.00 2.62
642 704 9.436957 GTAGTCCATTTGAAATGTCTAGAAAGA 57.563 33.333 15.93 1.84 0.00 2.52
659 721 9.823647 TCTAGAAAGACAAATATTTAGGAGCTG 57.176 33.333 0.00 0.00 0.00 4.24
660 722 9.823647 CTAGAAAGACAAATATTTAGGAGCTGA 57.176 33.333 0.00 0.00 0.00 4.26
661 723 8.729805 AGAAAGACAAATATTTAGGAGCTGAG 57.270 34.615 0.00 0.00 0.00 3.35
662 724 8.543774 AGAAAGACAAATATTTAGGAGCTGAGA 58.456 33.333 0.00 0.00 0.00 3.27
663 725 8.729805 AAAGACAAATATTTAGGAGCTGAGAG 57.270 34.615 0.00 0.00 0.00 3.20
664 726 7.667575 AGACAAATATTTAGGAGCTGAGAGA 57.332 36.000 0.00 0.00 0.00 3.10
665 727 7.725251 AGACAAATATTTAGGAGCTGAGAGAG 58.275 38.462 0.00 0.00 0.00 3.20
666 728 7.344352 AGACAAATATTTAGGAGCTGAGAGAGT 59.656 37.037 0.00 0.00 0.00 3.24
667 729 8.540507 ACAAATATTTAGGAGCTGAGAGAGTA 57.459 34.615 0.00 0.00 0.00 2.59
668 730 9.153479 ACAAATATTTAGGAGCTGAGAGAGTAT 57.847 33.333 0.00 0.00 0.00 2.12
671 733 6.811253 ATTTAGGAGCTGAGAGAGTATACG 57.189 41.667 0.00 0.00 0.00 3.06
672 734 3.134574 AGGAGCTGAGAGAGTATACGG 57.865 52.381 0.00 0.00 0.00 4.02
673 735 2.156098 GGAGCTGAGAGAGTATACGGG 58.844 57.143 0.00 0.00 0.00 5.28
674 736 2.224572 GGAGCTGAGAGAGTATACGGGA 60.225 54.545 0.00 0.00 0.00 5.14
675 737 3.478509 GAGCTGAGAGAGTATACGGGAA 58.521 50.000 0.00 0.00 0.00 3.97
676 738 4.076394 GAGCTGAGAGAGTATACGGGAAT 58.924 47.826 0.00 0.00 0.00 3.01
677 739 4.475345 AGCTGAGAGAGTATACGGGAATT 58.525 43.478 0.00 0.00 0.00 2.17
678 740 5.632118 AGCTGAGAGAGTATACGGGAATTA 58.368 41.667 0.00 0.00 0.00 1.40
679 741 6.249951 AGCTGAGAGAGTATACGGGAATTAT 58.750 40.000 0.00 0.00 0.00 1.28
680 742 6.376018 AGCTGAGAGAGTATACGGGAATTATC 59.624 42.308 0.00 0.00 0.00 1.75
681 743 6.376018 GCTGAGAGAGTATACGGGAATTATCT 59.624 42.308 0.00 0.00 0.00 1.98
682 744 7.094118 GCTGAGAGAGTATACGGGAATTATCTT 60.094 40.741 0.00 0.00 0.00 2.40
683 745 8.112016 TGAGAGAGTATACGGGAATTATCTTG 57.888 38.462 0.00 0.00 0.00 3.02
684 746 7.724506 TGAGAGAGTATACGGGAATTATCTTGT 59.275 37.037 0.00 0.00 0.00 3.16
685 747 7.887381 AGAGAGTATACGGGAATTATCTTGTG 58.113 38.462 0.00 0.00 0.00 3.33
686 748 6.456501 AGAGTATACGGGAATTATCTTGTGC 58.543 40.000 0.00 0.00 0.00 4.57
687 749 6.041637 AGAGTATACGGGAATTATCTTGTGCA 59.958 38.462 0.00 0.00 0.00 4.57
688 750 6.588204 AGTATACGGGAATTATCTTGTGCAA 58.412 36.000 0.00 0.00 0.00 4.08
689 751 7.051623 AGTATACGGGAATTATCTTGTGCAAA 58.948 34.615 0.00 0.00 0.00 3.68
690 752 6.767524 ATACGGGAATTATCTTGTGCAAAA 57.232 33.333 0.00 0.00 0.00 2.44
691 753 5.059404 ACGGGAATTATCTTGTGCAAAAG 57.941 39.130 10.64 10.64 0.00 2.27
692 754 4.764823 ACGGGAATTATCTTGTGCAAAAGA 59.235 37.500 21.47 21.47 40.36 2.52
693 755 5.242838 ACGGGAATTATCTTGTGCAAAAGAA 59.757 36.000 22.92 8.43 39.54 2.52
694 756 6.071391 ACGGGAATTATCTTGTGCAAAAGAAT 60.071 34.615 22.92 10.45 39.54 2.40
695 757 6.254157 CGGGAATTATCTTGTGCAAAAGAATG 59.746 38.462 22.92 3.91 39.54 2.67
696 758 6.536224 GGGAATTATCTTGTGCAAAAGAATGG 59.464 38.462 22.92 0.00 39.54 3.16
697 759 7.099120 GGAATTATCTTGTGCAAAAGAATGGT 58.901 34.615 22.92 9.37 39.54 3.55
698 760 8.250332 GGAATTATCTTGTGCAAAAGAATGGTA 58.750 33.333 22.92 8.37 39.54 3.25
699 761 9.807649 GAATTATCTTGTGCAAAAGAATGGTAT 57.192 29.630 22.92 8.29 39.54 2.73
700 762 9.590451 AATTATCTTGTGCAAAAGAATGGTATG 57.410 29.630 22.92 0.00 39.54 2.39
701 763 4.808558 TCTTGTGCAAAAGAATGGTATGC 58.191 39.130 17.22 0.00 33.25 3.14
702 764 4.523943 TCTTGTGCAAAAGAATGGTATGCT 59.476 37.500 17.22 0.00 37.86 3.79
703 765 4.439305 TGTGCAAAAGAATGGTATGCTC 57.561 40.909 0.00 0.00 37.86 4.26
704 766 3.193267 TGTGCAAAAGAATGGTATGCTCC 59.807 43.478 0.00 0.00 37.86 4.70
705 767 2.423185 TGCAAAAGAATGGTATGCTCCG 59.577 45.455 0.00 0.00 37.86 4.63
706 768 2.223572 GCAAAAGAATGGTATGCTCCGG 60.224 50.000 0.00 0.00 34.29 5.14
707 769 3.016736 CAAAAGAATGGTATGCTCCGGT 58.983 45.455 0.00 0.00 0.00 5.28
708 770 2.332063 AAGAATGGTATGCTCCGGTG 57.668 50.000 0.00 0.00 0.00 4.94
709 771 1.204146 AGAATGGTATGCTCCGGTGT 58.796 50.000 0.00 0.00 0.00 4.16
710 772 1.134401 AGAATGGTATGCTCCGGTGTG 60.134 52.381 0.00 0.00 0.00 3.82
711 773 0.107214 AATGGTATGCTCCGGTGTGG 60.107 55.000 0.00 0.00 40.09 4.17
721 783 2.649531 TCCGGTGTGGAATGAACTTT 57.350 45.000 0.00 0.00 46.38 2.66
722 784 2.938838 TCCGGTGTGGAATGAACTTTT 58.061 42.857 0.00 0.00 46.38 2.27
723 785 4.088056 TCCGGTGTGGAATGAACTTTTA 57.912 40.909 0.00 0.00 46.38 1.52
764 826 7.328404 ACCCATTATTGGAATGTTCCTTTTT 57.672 32.000 12.65 0.00 46.92 1.94
785 852 3.926821 TTTTAAATTGGTCGGGTGCTC 57.073 42.857 0.00 0.00 0.00 4.26
865 932 1.482593 AGAGACAAATAGACAGGGCCG 59.517 52.381 0.00 0.00 0.00 6.13
884 951 1.227674 CGAGAGCTGCCCAATACCC 60.228 63.158 0.00 0.00 0.00 3.69
898 965 4.097286 CCCAATACCCAACGTATTCAAAGG 59.903 45.833 0.00 0.00 44.30 3.11
926 993 5.946389 CGAACGTCGACTATTCAAAAGAATG 59.054 40.000 21.99 3.72 43.74 2.67
939 1006 2.572191 AAGAATGCCGAACGTCGATA 57.428 45.000 0.00 0.00 43.74 2.92
946 1288 4.087510 TGCCGAACGTCGATATATAAGG 57.912 45.455 0.00 0.00 43.74 2.69
961 1303 7.229707 CGATATATAAGGCAGTGCTCCTATACT 59.770 40.741 16.11 0.00 32.65 2.12
977 1319 7.092748 TCCTATACTAGCTAACACTCTCCAT 57.907 40.000 0.00 0.00 0.00 3.41
981 1323 1.207791 AGCTAACACTCTCCATGGGG 58.792 55.000 13.02 9.18 0.00 4.96
1047 1389 2.279502 TAATCCTCGCGCTCGTGCTT 62.280 55.000 5.56 0.00 36.97 3.91
1092 1434 3.989698 CTTCACCGGCATCGACGCT 62.990 63.158 2.49 0.00 39.00 5.07
1131 1473 1.922220 GTCGTCGTCATCGTCGTCG 60.922 63.158 0.00 0.00 45.27 5.12
1151 1493 1.401905 GTCTTCCCGCATAAAGCTTGG 59.598 52.381 0.00 0.00 42.61 3.61
1185 1527 0.248825 CTGAGCTCCTGGATTCGACG 60.249 60.000 12.15 0.00 0.00 5.12
1198 1540 3.359523 CGACGACGGTGGACCTGA 61.360 66.667 0.00 0.00 35.72 3.86
1252 1594 4.699522 GCGCGGGTTCCCTGAACT 62.700 66.667 8.83 0.00 41.70 3.01
1342 1684 1.274447 GAAGGTACCAGTGCCGTTAGT 59.726 52.381 15.94 0.00 40.50 2.24
1662 2919 2.503382 GCAAGCGGTGGGGGAAAAA 61.503 57.895 0.00 0.00 0.00 1.94
1663 2920 1.665442 CAAGCGGTGGGGGAAAAAG 59.335 57.895 0.00 0.00 0.00 2.27
1727 2984 2.739913 CGAAATCTAAGTGGGCAAACGA 59.260 45.455 0.00 0.00 0.00 3.85
1875 3181 0.382873 GTGGTCCGTTGAAAACCCAC 59.617 55.000 0.00 0.00 46.28 4.61
2052 5115 9.764363 CATGTAGCATAGTTTTTCATAGGTAGA 57.236 33.333 0.00 0.00 0.00 2.59
2074 5137 2.557924 GGTGTTGAGATTGGAACATGCA 59.442 45.455 0.00 0.00 39.30 3.96
2075 5138 3.194116 GGTGTTGAGATTGGAACATGCAT 59.806 43.478 0.00 0.00 39.30 3.96
2123 5187 7.880160 TGATATGAAATTGGAGTAAAGGTGG 57.120 36.000 0.00 0.00 0.00 4.61
2125 5189 3.161866 TGAAATTGGAGTAAAGGTGGGC 58.838 45.455 0.00 0.00 0.00 5.36
2132 5196 5.922960 TGGAGTAAAGGTGGGCAATATAT 57.077 39.130 0.00 0.00 0.00 0.86
2197 5261 8.399768 GCTTTGGCTTTAAATTCTCTCATAAC 57.600 34.615 0.00 0.00 35.22 1.89
2198 5262 7.218963 GCTTTGGCTTTAAATTCTCTCATAACG 59.781 37.037 0.00 0.00 35.22 3.18
2285 5349 9.970553 ATATAGAATGCACAAATCTGATGGTAT 57.029 29.630 0.00 0.00 0.00 2.73
2306 5370 9.491675 TGGTATCGTAGTTTTGTGAAATAAAGA 57.508 29.630 0.00 0.00 0.00 2.52
2324 5388 3.559238 AGACTTGGCTATTGTTTTGCG 57.441 42.857 0.00 0.00 0.00 4.85
2337 5401 3.779759 TGTTTTGCGAAGTTTGCTCAAT 58.220 36.364 16.08 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 1.756024 CCAAGGGGGTAACGACACA 59.244 57.895 0.00 0.00 37.60 3.72
127 189 4.386951 TGCACTACGCCATGCCGT 62.387 61.111 7.01 7.01 41.33 5.68
132 194 0.530650 CCGAATCTGCACTACGCCAT 60.531 55.000 0.00 0.00 41.33 4.40
138 200 2.089201 TCGAACTCCGAATCTGCACTA 58.911 47.619 0.00 0.00 45.43 2.74
190 252 1.528076 ACCATGACGCCAAACTGCA 60.528 52.632 0.00 0.00 0.00 4.41
193 255 2.268076 GCCACCATGACGCCAAACT 61.268 57.895 0.00 0.00 0.00 2.66
196 258 4.634703 ACGCCACCATGACGCCAA 62.635 61.111 0.00 0.00 0.00 4.52
204 266 4.094646 TGCCATCGACGCCACCAT 62.095 61.111 4.01 0.00 0.00 3.55
243 305 5.893824 TCCATCTTCAGAGCTGTACTATTGA 59.106 40.000 0.00 0.00 0.00 2.57
247 309 5.893824 TCAATCCATCTTCAGAGCTGTACTA 59.106 40.000 0.00 0.00 0.00 1.82
377 439 6.737346 GCAGCCAAACCTAAACATTTAAGACA 60.737 38.462 0.00 0.00 0.00 3.41
438 500 3.048600 TCCTATCCAGTTGATGAAGGGG 58.951 50.000 0.00 0.00 34.76 4.79
469 531 1.960689 AGCCACCGTTTAAGCAACAAT 59.039 42.857 0.00 0.00 34.68 2.71
480 542 3.070590 ACAGTAAGACTAAAGCCACCGTT 59.929 43.478 0.00 0.00 0.00 4.44
483 545 4.386711 ACAACAGTAAGACTAAAGCCACC 58.613 43.478 0.00 0.00 0.00 4.61
486 548 7.097834 AGTGATACAACAGTAAGACTAAAGCC 58.902 38.462 0.00 0.00 0.00 4.35
557 619 1.402787 CCCGGCCTTTGCATCTAAAT 58.597 50.000 0.00 0.00 40.13 1.40
558 620 0.682855 CCCCGGCCTTTGCATCTAAA 60.683 55.000 0.00 0.00 40.13 1.85
559 621 1.077068 CCCCGGCCTTTGCATCTAA 60.077 57.895 0.00 0.00 40.13 2.10
560 622 2.595095 CCCCGGCCTTTGCATCTA 59.405 61.111 0.00 0.00 40.13 1.98
573 635 1.911702 GAAAAGGAGGAGGACCCCCG 61.912 65.000 0.00 0.00 37.58 5.73
597 659 5.807909 ACTACCACATACGGGTGTATTTTT 58.192 37.500 0.00 0.00 39.28 1.94
600 662 3.385755 GGACTACCACATACGGGTGTATT 59.614 47.826 0.00 0.00 39.48 1.89
602 664 2.291475 TGGACTACCACATACGGGTGTA 60.291 50.000 0.00 0.00 41.77 2.90
603 665 1.188863 GGACTACCACATACGGGTGT 58.811 55.000 0.00 0.00 39.48 4.16
604 666 1.187974 TGGACTACCACATACGGGTG 58.812 55.000 0.00 0.00 41.77 4.61
605 667 3.695803 TGGACTACCACATACGGGT 57.304 52.632 0.00 0.00 41.77 5.28
615 677 8.561738 TTTCTAGACATTTCAAATGGACTACC 57.438 34.615 14.70 0.00 0.00 3.18
616 678 9.436957 TCTTTCTAGACATTTCAAATGGACTAC 57.563 33.333 14.70 1.26 0.00 2.73
633 695 9.823647 CAGCTCCTAAATATTTGTCTTTCTAGA 57.176 33.333 11.05 0.00 0.00 2.43
634 696 9.823647 TCAGCTCCTAAATATTTGTCTTTCTAG 57.176 33.333 11.05 0.00 0.00 2.43
635 697 9.823647 CTCAGCTCCTAAATATTTGTCTTTCTA 57.176 33.333 11.05 0.00 0.00 2.10
636 698 8.543774 TCTCAGCTCCTAAATATTTGTCTTTCT 58.456 33.333 11.05 0.00 0.00 2.52
637 699 8.723942 TCTCAGCTCCTAAATATTTGTCTTTC 57.276 34.615 11.05 0.00 0.00 2.62
638 700 8.543774 TCTCTCAGCTCCTAAATATTTGTCTTT 58.456 33.333 11.05 0.00 0.00 2.52
639 701 8.083828 TCTCTCAGCTCCTAAATATTTGTCTT 57.916 34.615 11.05 0.00 0.00 3.01
640 702 7.344352 ACTCTCTCAGCTCCTAAATATTTGTCT 59.656 37.037 11.05 0.00 0.00 3.41
641 703 7.496747 ACTCTCTCAGCTCCTAAATATTTGTC 58.503 38.462 11.05 0.00 0.00 3.18
642 704 7.430760 ACTCTCTCAGCTCCTAAATATTTGT 57.569 36.000 11.05 0.00 0.00 2.83
645 707 8.952278 CGTATACTCTCTCAGCTCCTAAATATT 58.048 37.037 0.56 0.00 0.00 1.28
646 708 7.554835 CCGTATACTCTCTCAGCTCCTAAATAT 59.445 40.741 0.56 0.00 0.00 1.28
647 709 6.879993 CCGTATACTCTCTCAGCTCCTAAATA 59.120 42.308 0.56 0.00 0.00 1.40
648 710 5.708230 CCGTATACTCTCTCAGCTCCTAAAT 59.292 44.000 0.56 0.00 0.00 1.40
649 711 5.064558 CCGTATACTCTCTCAGCTCCTAAA 58.935 45.833 0.56 0.00 0.00 1.85
650 712 4.505215 CCCGTATACTCTCTCAGCTCCTAA 60.505 50.000 0.56 0.00 0.00 2.69
651 713 3.008157 CCCGTATACTCTCTCAGCTCCTA 59.992 52.174 0.56 0.00 0.00 2.94
652 714 2.224670 CCCGTATACTCTCTCAGCTCCT 60.225 54.545 0.56 0.00 0.00 3.69
653 715 2.156098 CCCGTATACTCTCTCAGCTCC 58.844 57.143 0.56 0.00 0.00 4.70
654 716 3.128852 TCCCGTATACTCTCTCAGCTC 57.871 52.381 0.56 0.00 0.00 4.09
655 717 3.579534 TTCCCGTATACTCTCTCAGCT 57.420 47.619 0.56 0.00 0.00 4.24
656 718 4.857509 AATTCCCGTATACTCTCTCAGC 57.142 45.455 0.56 0.00 0.00 4.26
657 719 7.931578 AGATAATTCCCGTATACTCTCTCAG 57.068 40.000 0.56 0.00 0.00 3.35
658 720 7.724506 ACAAGATAATTCCCGTATACTCTCTCA 59.275 37.037 0.56 0.00 0.00 3.27
659 721 8.024285 CACAAGATAATTCCCGTATACTCTCTC 58.976 40.741 0.56 0.00 0.00 3.20
660 722 7.524038 GCACAAGATAATTCCCGTATACTCTCT 60.524 40.741 0.56 0.00 0.00 3.10
661 723 6.586844 GCACAAGATAATTCCCGTATACTCTC 59.413 42.308 0.56 0.00 0.00 3.20
662 724 6.041637 TGCACAAGATAATTCCCGTATACTCT 59.958 38.462 0.56 0.00 0.00 3.24
663 725 6.220930 TGCACAAGATAATTCCCGTATACTC 58.779 40.000 0.56 0.00 0.00 2.59
664 726 6.169557 TGCACAAGATAATTCCCGTATACT 57.830 37.500 0.56 0.00 0.00 2.12
665 727 6.854496 TTGCACAAGATAATTCCCGTATAC 57.146 37.500 0.00 0.00 0.00 1.47
666 728 7.771361 TCTTTTGCACAAGATAATTCCCGTATA 59.229 33.333 11.24 0.00 0.00 1.47
667 729 6.601613 TCTTTTGCACAAGATAATTCCCGTAT 59.398 34.615 11.24 0.00 0.00 3.06
668 730 5.941058 TCTTTTGCACAAGATAATTCCCGTA 59.059 36.000 11.24 0.00 0.00 4.02
669 731 4.764823 TCTTTTGCACAAGATAATTCCCGT 59.235 37.500 11.24 0.00 0.00 5.28
670 732 5.309323 TCTTTTGCACAAGATAATTCCCG 57.691 39.130 11.24 0.00 0.00 5.14
671 733 6.536224 CCATTCTTTTGCACAAGATAATTCCC 59.464 38.462 15.70 0.00 32.69 3.97
672 734 7.099120 ACCATTCTTTTGCACAAGATAATTCC 58.901 34.615 15.70 0.00 32.69 3.01
673 735 9.807649 ATACCATTCTTTTGCACAAGATAATTC 57.192 29.630 15.70 0.00 32.69 2.17
674 736 9.590451 CATACCATTCTTTTGCACAAGATAATT 57.410 29.630 15.70 4.73 32.69 1.40
675 737 7.707893 GCATACCATTCTTTTGCACAAGATAAT 59.292 33.333 15.70 5.18 32.69 1.28
676 738 7.035004 GCATACCATTCTTTTGCACAAGATAA 58.965 34.615 15.70 2.92 32.69 1.75
677 739 6.377996 AGCATACCATTCTTTTGCACAAGATA 59.622 34.615 15.70 6.18 35.79 1.98
678 740 5.186409 AGCATACCATTCTTTTGCACAAGAT 59.814 36.000 15.70 4.13 35.79 2.40
679 741 4.523943 AGCATACCATTCTTTTGCACAAGA 59.476 37.500 11.24 11.24 35.79 3.02
680 742 4.813027 AGCATACCATTCTTTTGCACAAG 58.187 39.130 6.25 6.25 35.79 3.16
681 743 4.321899 GGAGCATACCATTCTTTTGCACAA 60.322 41.667 0.00 0.00 35.79 3.33
682 744 3.193267 GGAGCATACCATTCTTTTGCACA 59.807 43.478 0.00 0.00 35.79 4.57
683 745 3.731867 CGGAGCATACCATTCTTTTGCAC 60.732 47.826 0.00 0.00 35.79 4.57
684 746 2.423185 CGGAGCATACCATTCTTTTGCA 59.577 45.455 0.00 0.00 35.79 4.08
685 747 2.223572 CCGGAGCATACCATTCTTTTGC 60.224 50.000 0.00 0.00 0.00 3.68
686 748 3.016736 ACCGGAGCATACCATTCTTTTG 58.983 45.455 9.46 0.00 0.00 2.44
687 749 3.016736 CACCGGAGCATACCATTCTTTT 58.983 45.455 9.46 0.00 0.00 2.27
688 750 2.026262 ACACCGGAGCATACCATTCTTT 60.026 45.455 9.46 0.00 0.00 2.52
689 751 1.559682 ACACCGGAGCATACCATTCTT 59.440 47.619 9.46 0.00 0.00 2.52
690 752 1.134401 CACACCGGAGCATACCATTCT 60.134 52.381 9.46 0.00 0.00 2.40
691 753 1.299541 CACACCGGAGCATACCATTC 58.700 55.000 9.46 0.00 0.00 2.67
692 754 0.107214 CCACACCGGAGCATACCATT 60.107 55.000 9.46 0.00 36.56 3.16
693 755 0.980754 TCCACACCGGAGCATACCAT 60.981 55.000 9.46 0.00 39.64 3.55
694 756 1.610967 TCCACACCGGAGCATACCA 60.611 57.895 9.46 0.00 39.64 3.25
695 757 3.305314 TCCACACCGGAGCATACC 58.695 61.111 9.46 0.00 39.64 2.73
702 764 2.649531 AAAGTTCATTCCACACCGGA 57.350 45.000 9.46 0.00 44.40 5.14
703 765 6.503589 TTATAAAAGTTCATTCCACACCGG 57.496 37.500 0.00 0.00 0.00 5.28
764 826 3.637229 TGAGCACCCGACCAATTTAAAAA 59.363 39.130 0.00 0.00 0.00 1.94
768 835 2.799126 ATGAGCACCCGACCAATTTA 57.201 45.000 0.00 0.00 0.00 1.40
777 844 3.370978 CGGCTAATAATAATGAGCACCCG 59.629 47.826 0.00 0.00 40.98 5.28
785 852 6.632834 GTGAACAACAGCGGCTAATAATAATG 59.367 38.462 0.26 0.00 0.00 1.90
865 932 1.889573 GGTATTGGGCAGCTCTCGC 60.890 63.158 0.00 0.00 0.00 5.03
884 951 4.433283 CGTTCGGTACCTTTGAATACGTTG 60.433 45.833 10.90 0.00 0.00 4.10
898 965 3.389687 TGAATAGTCGACGTTCGGTAC 57.610 47.619 22.74 8.13 40.88 3.34
926 993 2.850647 GCCTTATATATCGACGTTCGGC 59.149 50.000 7.39 0.00 40.88 5.54
939 1006 6.322712 GCTAGTATAGGAGCACTGCCTTATAT 59.677 42.308 0.00 0.00 39.70 0.86
946 1288 4.278669 TGTTAGCTAGTATAGGAGCACTGC 59.721 45.833 8.20 0.00 41.36 4.40
961 1303 2.292918 ACCCCATGGAGAGTGTTAGCTA 60.293 50.000 15.22 0.00 34.81 3.32
977 1319 1.789523 AGCTTAGCTAATCGACCCCA 58.210 50.000 4.30 0.00 36.99 4.96
1074 1416 3.554692 GCGTCGATGCCGGTGAAG 61.555 66.667 19.11 0.00 36.24 3.02
1075 1417 4.063967 AGCGTCGATGCCGGTGAA 62.064 61.111 25.54 0.00 34.34 3.18
1101 1443 2.436795 CGACGACGTTGGCATTACA 58.563 52.632 9.88 0.00 34.56 2.41
1120 1462 1.798735 GGGAAGACGACGACGATGA 59.201 57.895 15.32 0.00 42.66 2.92
1121 1463 1.582937 CGGGAAGACGACGACGATG 60.583 63.158 15.32 0.00 42.66 3.84
1122 1464 2.789917 CGGGAAGACGACGACGAT 59.210 61.111 15.32 0.00 42.66 3.73
1123 1465 4.093952 GCGGGAAGACGACGACGA 62.094 66.667 15.32 0.00 42.66 4.20
1124 1466 2.313717 TATGCGGGAAGACGACGACG 62.314 60.000 5.58 5.58 45.75 5.12
1165 1507 1.107114 GTCGAATCCAGGAGCTCAGA 58.893 55.000 17.19 9.42 0.00 3.27
1167 1509 0.679960 TCGTCGAATCCAGGAGCTCA 60.680 55.000 17.19 0.00 0.00 4.26
1185 1527 2.663196 CCCTTCAGGTCCACCGTC 59.337 66.667 0.00 0.00 42.08 4.79
1240 1582 3.075833 CCTTGTTGGAGTTCAGGGAACC 61.076 54.545 5.54 0.00 42.85 3.62
1252 1594 2.598394 GCAGGCTGCCTTGTTGGA 60.598 61.111 28.87 0.00 37.42 3.53
1342 1684 1.070786 GCTGTTCCGTTCACTCCCA 59.929 57.895 0.00 0.00 0.00 4.37
1423 1808 8.475331 AGTTATACGTACTTCAAGAAACATGG 57.525 34.615 0.00 0.00 0.00 3.66
1456 1846 7.064134 CACTCAACAGTTGTACAAACAAGACTA 59.936 37.037 10.51 0.00 46.06 2.59
1662 2919 0.253044 ACGCCTACACCATGCATTCT 59.747 50.000 0.00 0.00 0.00 2.40
1663 2920 1.867233 CTACGCCTACACCATGCATTC 59.133 52.381 0.00 0.00 0.00 2.67
1875 3181 6.486248 CATTCATCATAACGTTTGGTACAGG 58.514 40.000 5.91 0.00 42.39 4.00
2037 3669 7.159372 TCTCAACACCTCTACCTATGAAAAAC 58.841 38.462 0.00 0.00 0.00 2.43
2042 5105 5.363868 CCAATCTCAACACCTCTACCTATGA 59.636 44.000 0.00 0.00 0.00 2.15
2052 5115 2.821969 GCATGTTCCAATCTCAACACCT 59.178 45.455 0.00 0.00 35.37 4.00
2074 5137 9.071276 CATACTACTGGCATCCTATTTTTGAAT 57.929 33.333 0.00 0.00 0.00 2.57
2075 5138 8.271458 TCATACTACTGGCATCCTATTTTTGAA 58.729 33.333 0.00 0.00 0.00 2.69
2122 5186 7.289587 GTTGTGTTTTCAACATATATTGCCC 57.710 36.000 4.95 0.00 44.35 5.36
2152 5216 9.545105 CCAAAGCTCCAAATGCATATAAAATTA 57.455 29.630 0.00 0.00 0.00 1.40
2153 5217 7.012610 GCCAAAGCTCCAAATGCATATAAAATT 59.987 33.333 0.00 0.00 35.50 1.82
2273 5337 7.327975 TCACAAAACTACGATACCATCAGATT 58.672 34.615 0.00 0.00 0.00 2.40
2285 5349 8.339714 CCAAGTCTTTATTTCACAAAACTACGA 58.660 33.333 0.00 0.00 0.00 3.43
2306 5370 3.317993 ACTTCGCAAAACAATAGCCAAGT 59.682 39.130 0.00 0.00 35.41 3.16
2308 5372 4.314740 AACTTCGCAAAACAATAGCCAA 57.685 36.364 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.