Multiple sequence alignment - TraesCS7A01G180200

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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 TraesCS7A01G180200 chr7A 100.000 3258 0 0 1 3258 134548450 134551707 0.000000e+00 6017.0
1 TraesCS7A01G180200 chr3A 98.223 2476 35 7 791 3258 712620832 712623306 0.000000e+00 4320.0
2 TraesCS7A01G180200 chr3A 83.042 973 104 29 1881 2802 108025714 108026676 0.000000e+00 826.0
3 TraesCS7A01G180200 chr3A 84.322 472 52 16 2803 3258 108029255 108029720 2.980000e-120 442.0
4 TraesCS7A01G180200 chr7B 83.737 1445 153 44 1881 3258 51622570 51621141 0.000000e+00 1291.0
5 TraesCS7A01G180200 chr7B 91.456 515 25 10 43 550 97365718 97366220 0.000000e+00 689.0
6 TraesCS7A01G180200 chr6B 83.657 1444 155 43 1882 3258 659638284 659636855 0.000000e+00 1284.0
7 TraesCS7A01G180200 chr5B 83.460 1445 157 42 1882 3258 505692851 505691421 0.000000e+00 1269.0
8 TraesCS7A01G180200 chr5B 91.304 69 4 2 557 624 434730145 434730078 3.460000e-15 93.5
9 TraesCS7A01G180200 chr4B 83.358 1358 148 42 1882 3176 395822607 395823949 0.000000e+00 1184.0
10 TraesCS7A01G180200 chr4B 91.803 61 5 0 558 618 656891521 656891461 5.790000e-13 86.1
11 TraesCS7A01G180200 chr1A 90.273 843 56 9 791 1607 485565888 485565046 0.000000e+00 1079.0
12 TraesCS7A01G180200 chr1A 82.631 973 107 29 1881 2802 537066264 537065303 0.000000e+00 804.0
13 TraesCS7A01G180200 chr1A 84.746 472 51 13 2803 3258 537062633 537062167 1.380000e-123 453.0
14 TraesCS7A01G180200 chr1B 89.881 840 61 8 791 1607 518266341 518265503 0.000000e+00 1059.0
15 TraesCS7A01G180200 chr1D 89.750 839 64 8 791 1607 386127355 386126517 0.000000e+00 1053.0
16 TraesCS7A01G180200 chr5D 82.582 1131 114 42 1881 2959 505889097 505890196 0.000000e+00 920.0
17 TraesCS7A01G180200 chr7D 91.727 556 33 5 1 550 135434648 135435196 0.000000e+00 760.0
18 TraesCS7A01G180200 chr7D 96.970 66 2 0 619 684 135435490 135435555 9.560000e-21 111.0
19 TraesCS7A01G180200 chr6D 86.283 226 17 10 817 1028 161148525 161148750 1.950000e-57 233.0
20 TraesCS7A01G180200 chr4A 89.189 185 17 3 819 1000 94762738 94762922 9.090000e-56 228.0
21 TraesCS7A01G180200 chr4A 100.000 30 0 0 997 1026 94762937 94762966 4.540000e-04 56.5
22 TraesCS7A01G180200 chr6A 88.136 177 15 6 819 992 77889686 77889859 4.260000e-49 206.0
23 TraesCS7A01G180200 chr6A 87.730 163 18 2 819 980 78019204 78019365 4.290000e-44 189.0
24 TraesCS7A01G180200 chr6A 100.000 32 0 0 997 1028 77889884 77889915 3.510000e-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 TraesCS7A01G180200 chr7A 134548450 134551707 3257 False 6017.0 6017 100.0000 1 3258 1 chr7A.!!$F1 3257
1 TraesCS7A01G180200 chr3A 712620832 712623306 2474 False 4320.0 4320 98.2230 791 3258 1 chr3A.!!$F1 2467
2 TraesCS7A01G180200 chr3A 108025714 108029720 4006 False 634.0 826 83.6820 1881 3258 2 chr3A.!!$F2 1377
3 TraesCS7A01G180200 chr7B 51621141 51622570 1429 True 1291.0 1291 83.7370 1881 3258 1 chr7B.!!$R1 1377
4 TraesCS7A01G180200 chr7B 97365718 97366220 502 False 689.0 689 91.4560 43 550 1 chr7B.!!$F1 507
5 TraesCS7A01G180200 chr6B 659636855 659638284 1429 True 1284.0 1284 83.6570 1882 3258 1 chr6B.!!$R1 1376
6 TraesCS7A01G180200 chr5B 505691421 505692851 1430 True 1269.0 1269 83.4600 1882 3258 1 chr5B.!!$R2 1376
7 TraesCS7A01G180200 chr4B 395822607 395823949 1342 False 1184.0 1184 83.3580 1882 3176 1 chr4B.!!$F1 1294
8 TraesCS7A01G180200 chr1A 485565046 485565888 842 True 1079.0 1079 90.2730 791 1607 1 chr1A.!!$R1 816
9 TraesCS7A01G180200 chr1A 537062167 537066264 4097 True 628.5 804 83.6885 1881 3258 2 chr1A.!!$R2 1377
10 TraesCS7A01G180200 chr1B 518265503 518266341 838 True 1059.0 1059 89.8810 791 1607 1 chr1B.!!$R1 816
11 TraesCS7A01G180200 chr1D 386126517 386127355 838 True 1053.0 1053 89.7500 791 1607 1 chr1D.!!$R1 816
12 TraesCS7A01G180200 chr5D 505889097 505890196 1099 False 920.0 920 82.5820 1881 2959 1 chr5D.!!$F1 1078
13 TraesCS7A01G180200 chr7D 135434648 135435555 907 False 435.5 760 94.3485 1 684 2 chr7D.!!$F1 683

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
177 184 0.179065 CCTCAGGCAATCGCTGATCA 60.179 55.0 0.0 0.0 38.60 2.92 F
431 443 0.815213 TCATGCTCGGTAATGGCAGC 60.815 55.0 0.0 0.0 39.38 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 1799 1.198637 GCGATCTTTGCAGATATGGGC 59.801 52.381 0.00 0.0 40.14 5.36 R
2282 2376 1.979155 TCCTCGACCTGGTGCTCTG 60.979 63.158 2.82 0.0 0.00 3.35 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
43 47 8.766151 CAATCAATGATCATTCTCACTGAGTAG 58.234 37.037 18.16 3.11 35.15 2.57
44 48 7.651027 TCAATGATCATTCTCACTGAGTAGA 57.349 36.000 18.16 5.41 28.91 2.59
145 152 4.124851 AGGCCGTAGTAGTGAGAAAATG 57.875 45.455 0.00 0.00 0.00 2.32
157 164 4.702131 AGTGAGAAAATGTATCCCTGCAAC 59.298 41.667 0.00 0.00 0.00 4.17
177 184 0.179065 CCTCAGGCAATCGCTGATCA 60.179 55.000 0.00 0.00 38.60 2.92
211 218 2.874648 TATGAGCGCCTGCAGGTTGG 62.875 60.000 32.81 22.53 46.23 3.77
215 222 3.136123 CGCCTGCAGGTTGGGATG 61.136 66.667 32.81 11.14 37.57 3.51
240 247 6.844696 TGATGATATAAGAAACAGAACCGC 57.155 37.500 0.00 0.00 0.00 5.68
257 264 1.268437 CCGCAGCCTAACGTAGAGTAC 60.268 57.143 0.00 0.00 0.00 2.73
300 312 6.763135 GGAGAGTCATATTGTGCAGATTTGTA 59.237 38.462 0.00 0.00 0.00 2.41
301 313 7.042187 GGAGAGTCATATTGTGCAGATTTGTAG 60.042 40.741 0.00 0.00 0.00 2.74
302 314 7.559486 AGAGTCATATTGTGCAGATTTGTAGA 58.441 34.615 0.00 0.00 0.00 2.59
303 315 8.043113 AGAGTCATATTGTGCAGATTTGTAGAA 58.957 33.333 0.00 0.00 0.00 2.10
309 321 5.839262 TGTGCAGATTTGTAGAAAGTACG 57.161 39.130 0.00 0.00 0.00 3.67
422 434 2.948979 TGTTGTTCTTTTCATGCTCGGT 59.051 40.909 0.00 0.00 0.00 4.69
426 438 5.295431 TGTTCTTTTCATGCTCGGTAATG 57.705 39.130 0.00 0.00 0.00 1.90
431 443 0.815213 TCATGCTCGGTAATGGCAGC 60.815 55.000 0.00 0.00 39.38 5.25
524 537 6.131389 GCAGATTTGTTTTTGATGAGTTTGC 58.869 36.000 0.00 0.00 0.00 3.68
574 587 6.791867 AAGATGAGTAATGCTACACCTACA 57.208 37.500 0.00 0.00 0.00 2.74
575 588 6.985653 AGATGAGTAATGCTACACCTACAT 57.014 37.500 0.00 0.00 0.00 2.29
576 589 8.478775 AAGATGAGTAATGCTACACCTACATA 57.521 34.615 0.00 0.00 0.00 2.29
577 590 8.116651 AGATGAGTAATGCTACACCTACATAG 57.883 38.462 0.00 0.00 0.00 2.23
594 607 8.217131 CCTACATAGGTTAACATGGGTTTTAC 57.783 38.462 8.10 0.00 38.69 2.01
595 608 7.830201 CCTACATAGGTTAACATGGGTTTTACA 59.170 37.037 8.10 0.00 38.69 2.41
596 609 9.233649 CTACATAGGTTAACATGGGTTTTACAA 57.766 33.333 8.10 0.00 38.45 2.41
597 610 8.480133 ACATAGGTTAACATGGGTTTTACAAA 57.520 30.769 8.10 0.00 38.45 2.83
598 611 8.361889 ACATAGGTTAACATGGGTTTTACAAAC 58.638 33.333 8.10 0.00 38.45 2.93
599 612 6.793505 AGGTTAACATGGGTTTTACAAACA 57.206 33.333 8.10 0.00 38.45 2.83
600 613 6.811954 AGGTTAACATGGGTTTTACAAACAG 58.188 36.000 8.10 0.00 38.45 3.16
601 614 6.608002 AGGTTAACATGGGTTTTACAAACAGA 59.392 34.615 8.10 0.00 38.45 3.41
602 615 7.289084 AGGTTAACATGGGTTTTACAAACAGAT 59.711 33.333 8.10 0.00 38.45 2.90
603 616 7.383843 GGTTAACATGGGTTTTACAAACAGATG 59.616 37.037 8.10 5.38 38.45 2.90
604 617 5.467035 ACATGGGTTTTACAAACAGATGG 57.533 39.130 0.00 0.00 0.00 3.51
605 618 4.283212 ACATGGGTTTTACAAACAGATGGG 59.717 41.667 0.00 0.00 0.00 4.00
606 619 3.917300 TGGGTTTTACAAACAGATGGGT 58.083 40.909 2.00 0.00 0.00 4.51
607 620 4.290942 TGGGTTTTACAAACAGATGGGTT 58.709 39.130 2.00 0.00 0.00 4.11
608 621 4.100189 TGGGTTTTACAAACAGATGGGTTG 59.900 41.667 2.00 0.00 0.00 3.77
609 622 4.100344 GGGTTTTACAAACAGATGGGTTGT 59.900 41.667 3.06 3.06 0.00 3.32
610 623 5.047188 GGTTTTACAAACAGATGGGTTGTG 58.953 41.667 7.93 0.00 0.00 3.33
611 624 5.163499 GGTTTTACAAACAGATGGGTTGTGA 60.163 40.000 7.93 0.00 0.00 3.58
612 625 6.462347 GGTTTTACAAACAGATGGGTTGTGAT 60.462 38.462 7.93 0.00 0.00 3.06
613 626 5.957842 TTACAAACAGATGGGTTGTGATC 57.042 39.130 7.93 0.00 0.00 2.92
614 627 2.813754 ACAAACAGATGGGTTGTGATCG 59.186 45.455 0.00 0.00 0.00 3.69
615 628 2.113860 AACAGATGGGTTGTGATCGG 57.886 50.000 0.00 0.00 0.00 4.18
616 629 1.275666 ACAGATGGGTTGTGATCGGA 58.724 50.000 0.00 0.00 0.00 4.55
617 630 1.208052 ACAGATGGGTTGTGATCGGAG 59.792 52.381 0.00 0.00 0.00 4.63
618 631 1.482182 CAGATGGGTTGTGATCGGAGA 59.518 52.381 0.00 0.00 45.75 3.71
619 632 1.759445 AGATGGGTTGTGATCGGAGAG 59.241 52.381 0.00 0.00 43.63 3.20
620 633 1.757118 GATGGGTTGTGATCGGAGAGA 59.243 52.381 0.00 0.00 43.63 3.10
621 634 1.639722 TGGGTTGTGATCGGAGAGAA 58.360 50.000 0.00 0.00 43.63 2.87
622 635 1.974957 TGGGTTGTGATCGGAGAGAAA 59.025 47.619 0.00 0.00 43.63 2.52
623 636 2.028112 TGGGTTGTGATCGGAGAGAAAG 60.028 50.000 0.00 0.00 43.63 2.62
624 637 2.233922 GGGTTGTGATCGGAGAGAAAGA 59.766 50.000 0.00 0.00 43.63 2.52
625 638 3.516615 GGTTGTGATCGGAGAGAAAGAG 58.483 50.000 0.00 0.00 43.63 2.85
626 639 3.193691 GGTTGTGATCGGAGAGAAAGAGA 59.806 47.826 0.00 0.00 43.63 3.10
627 640 4.420168 GTTGTGATCGGAGAGAAAGAGAG 58.580 47.826 0.00 0.00 43.63 3.20
628 641 3.956744 TGTGATCGGAGAGAAAGAGAGA 58.043 45.455 0.00 0.00 43.63 3.10
629 642 3.692101 TGTGATCGGAGAGAAAGAGAGAC 59.308 47.826 0.00 0.00 43.63 3.36
630 643 3.066203 GTGATCGGAGAGAAAGAGAGACC 59.934 52.174 0.00 0.00 43.63 3.85
631 644 3.053991 TGATCGGAGAGAAAGAGAGACCT 60.054 47.826 0.00 0.00 43.63 3.85
632 645 3.443145 TCGGAGAGAAAGAGAGACCTT 57.557 47.619 0.00 0.00 0.00 3.50
633 646 3.768878 TCGGAGAGAAAGAGAGACCTTT 58.231 45.455 0.00 0.00 38.92 3.11
634 647 3.508012 TCGGAGAGAAAGAGAGACCTTTG 59.492 47.826 0.00 0.00 36.58 2.77
635 648 3.257127 CGGAGAGAAAGAGAGACCTTTGT 59.743 47.826 0.00 0.00 36.58 2.83
636 649 4.565022 GGAGAGAAAGAGAGACCTTTGTG 58.435 47.826 0.00 0.00 36.58 3.33
637 650 4.039852 GGAGAGAAAGAGAGACCTTTGTGT 59.960 45.833 0.00 0.00 36.58 3.72
638 651 5.454045 GGAGAGAAAGAGAGACCTTTGTGTT 60.454 44.000 0.00 0.00 36.58 3.32
639 652 5.363939 AGAGAAAGAGAGACCTTTGTGTTG 58.636 41.667 0.00 0.00 36.58 3.33
640 653 3.879892 AGAAAGAGAGACCTTTGTGTTGC 59.120 43.478 0.00 0.00 36.58 4.17
641 654 2.262423 AGAGAGACCTTTGTGTTGCC 57.738 50.000 0.00 0.00 0.00 4.52
642 655 0.868406 GAGAGACCTTTGTGTTGCCG 59.132 55.000 0.00 0.00 0.00 5.69
643 656 1.166531 AGAGACCTTTGTGTTGCCGC 61.167 55.000 0.00 0.00 0.00 6.53
644 657 2.051345 GACCTTTGTGTTGCCGCG 60.051 61.111 0.00 0.00 0.00 6.46
645 658 3.536498 GACCTTTGTGTTGCCGCGG 62.536 63.158 24.05 24.05 0.00 6.46
646 659 4.341502 CCTTTGTGTTGCCGCGGG 62.342 66.667 29.38 8.95 0.00 6.13
647 660 3.283684 CTTTGTGTTGCCGCGGGA 61.284 61.111 29.38 24.35 0.00 5.14
648 661 3.254014 CTTTGTGTTGCCGCGGGAG 62.254 63.158 29.38 6.31 0.00 4.30
660 673 4.148825 CGGGAGGCGGTGGAGAAG 62.149 72.222 0.00 0.00 0.00 2.85
661 674 3.787001 GGGAGGCGGTGGAGAAGG 61.787 72.222 0.00 0.00 0.00 3.46
662 675 3.787001 GGAGGCGGTGGAGAAGGG 61.787 72.222 0.00 0.00 0.00 3.95
663 676 2.683933 GAGGCGGTGGAGAAGGGA 60.684 66.667 0.00 0.00 0.00 4.20
664 677 2.685380 AGGCGGTGGAGAAGGGAG 60.685 66.667 0.00 0.00 0.00 4.30
665 678 2.683933 GGCGGTGGAGAAGGGAGA 60.684 66.667 0.00 0.00 0.00 3.71
666 679 2.579738 GCGGTGGAGAAGGGAGAC 59.420 66.667 0.00 0.00 0.00 3.36
667 680 2.885861 CGGTGGAGAAGGGAGACG 59.114 66.667 0.00 0.00 0.00 4.18
668 681 2.579738 GGTGGAGAAGGGAGACGC 59.420 66.667 0.00 0.00 0.00 5.19
669 682 2.182030 GTGGAGAAGGGAGACGCG 59.818 66.667 3.53 3.53 0.00 6.01
670 683 3.760035 TGGAGAAGGGAGACGCGC 61.760 66.667 5.73 0.00 0.00 6.86
671 684 4.856607 GGAGAAGGGAGACGCGCG 62.857 72.222 30.96 30.96 34.07 6.86
672 685 3.812019 GAGAAGGGAGACGCGCGA 61.812 66.667 39.36 0.00 34.07 5.87
673 686 3.743091 GAGAAGGGAGACGCGCGAG 62.743 68.421 39.36 10.29 34.07 5.03
674 687 4.856607 GAAGGGAGACGCGCGAGG 62.857 72.222 39.36 8.30 34.07 4.63
687 700 3.119193 CGAGGAGCAGAGAGAGGC 58.881 66.667 0.00 0.00 0.00 4.70
688 701 2.833533 CGAGGAGCAGAGAGAGGCG 61.834 68.421 0.00 0.00 34.54 5.52
689 702 1.752694 GAGGAGCAGAGAGAGGCGT 60.753 63.158 0.00 0.00 34.54 5.68
690 703 2.003658 GAGGAGCAGAGAGAGGCGTG 62.004 65.000 0.00 0.00 34.54 5.34
691 704 2.202730 GAGCAGAGAGAGGCGTGC 60.203 66.667 0.00 0.00 36.10 5.34
692 705 3.714871 GAGCAGAGAGAGGCGTGCC 62.715 68.421 1.67 1.67 36.54 5.01
722 735 4.452733 CCTCCGCCGTTGGTCCTC 62.453 72.222 0.00 0.00 0.00 3.71
723 736 4.452733 CTCCGCCGTTGGTCCTCC 62.453 72.222 0.00 0.00 0.00 4.30
725 738 4.452733 CCGCCGTTGGTCCTCCTC 62.453 72.222 0.00 0.00 34.23 3.71
726 739 4.796231 CGCCGTTGGTCCTCCTCG 62.796 72.222 0.00 0.00 34.23 4.63
727 740 3.379445 GCCGTTGGTCCTCCTCGA 61.379 66.667 0.00 0.00 35.33 4.04
728 741 2.572284 CCGTTGGTCCTCCTCGAC 59.428 66.667 0.00 0.00 35.33 4.20
729 742 2.273179 CCGTTGGTCCTCCTCGACA 61.273 63.158 0.00 0.00 35.33 4.35
730 743 1.213013 CGTTGGTCCTCCTCGACAG 59.787 63.158 0.00 0.00 35.33 3.51
731 744 1.079750 GTTGGTCCTCCTCGACAGC 60.080 63.158 0.00 0.00 34.24 4.40
732 745 2.283529 TTGGTCCTCCTCGACAGCC 61.284 63.158 0.00 0.00 34.24 4.85
733 746 3.827898 GGTCCTCCTCGACAGCCG 61.828 72.222 0.00 0.00 40.25 5.52
734 747 4.500116 GTCCTCCTCGACAGCCGC 62.500 72.222 0.00 0.00 38.37 6.53
786 799 4.077184 CTCCTGGCGGCGTACCAA 62.077 66.667 9.37 0.00 36.56 3.67
787 800 3.599285 CTCCTGGCGGCGTACCAAA 62.599 63.158 9.37 0.00 36.56 3.28
788 801 3.124921 CCTGGCGGCGTACCAAAG 61.125 66.667 9.37 0.00 36.56 2.77
789 802 3.799755 CTGGCGGCGTACCAAAGC 61.800 66.667 9.37 0.00 36.56 3.51
923 938 1.652930 GCTCTACGAAGCGCTCTCG 60.653 63.158 28.17 28.17 39.07 4.04
1499 1539 2.815589 GCTCCCAGTTTGTGATGGACTT 60.816 50.000 0.00 0.00 39.02 3.01
1708 1748 1.762370 TGTCAAGGTGAGCTTCTGTCA 59.238 47.619 0.00 0.00 0.00 3.58
1753 1793 1.774110 TCTGCATCACTCTCTCTCCC 58.226 55.000 0.00 0.00 0.00 4.30
1759 1799 4.100653 TGCATCACTCTCTCTCCCTTTATG 59.899 45.833 0.00 0.00 0.00 1.90
1837 1877 7.201702 TCCCACTATTGTTACCATGTTGATA 57.798 36.000 0.00 0.00 0.00 2.15
1981 2021 4.002256 TCTGTATATTGGTCACTCCCCA 57.998 45.455 0.00 0.00 34.77 4.96
2087 2128 5.514274 TGCTGTACATATCGAGTTCATCA 57.486 39.130 0.00 0.00 0.00 3.07
2098 2139 2.715046 GAGTTCATCATCCAAGCACCA 58.285 47.619 0.00 0.00 0.00 4.17
2099 2140 2.421424 GAGTTCATCATCCAAGCACCAC 59.579 50.000 0.00 0.00 0.00 4.16
2114 2155 2.485479 GCACCACTTGTGGAAAGAGAGA 60.485 50.000 24.67 0.00 45.55 3.10
2282 2376 2.624316 TCGTCACGATACTTCACCAC 57.376 50.000 0.00 0.00 0.00 4.16
2304 2398 1.979693 GCACCAGGTCGAGGACTCT 60.980 63.158 0.00 0.00 32.47 3.24
2724 2852 5.049405 GCACCTATACTAATTGGCATCACAC 60.049 44.000 0.00 0.00 31.80 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.107643 TGATTGTTCTGTGCCACCGA 59.892 50.000 0.00 0.00 0.00 4.69
9 10 6.561614 AGAATGATCATTGATTGTTCTGTGC 58.438 36.000 25.37 6.28 30.62 4.57
43 47 3.864003 GGACCTAGCGTGATGTTACTTTC 59.136 47.826 0.00 0.00 0.00 2.62
44 48 3.369157 GGGACCTAGCGTGATGTTACTTT 60.369 47.826 0.00 0.00 0.00 2.66
145 152 3.788672 CTGAGGGTTGCAGGGATAC 57.211 57.895 0.00 0.00 0.00 2.24
157 164 0.883814 GATCAGCGATTGCCTGAGGG 60.884 60.000 0.00 0.00 44.31 4.30
177 184 3.736252 CGCTCATATCGACGAGGAAAAAT 59.264 43.478 3.01 0.00 0.00 1.82
213 220 9.212641 CGGTTCTGTTTCTTATATCATCATCAT 57.787 33.333 0.00 0.00 0.00 2.45
214 221 7.171508 GCGGTTCTGTTTCTTATATCATCATCA 59.828 37.037 0.00 0.00 0.00 3.07
215 222 7.171508 TGCGGTTCTGTTTCTTATATCATCATC 59.828 37.037 0.00 0.00 0.00 2.92
240 247 4.430137 TGTTGTACTCTACGTTAGGCTG 57.570 45.455 0.00 0.00 0.00 4.85
257 264 5.358160 ACTCTCCTTCTCCTTTTGTTTGTTG 59.642 40.000 0.00 0.00 0.00 3.33
300 312 1.068055 CCACGCTGGTACGTACTTTCT 60.068 52.381 24.07 2.14 46.34 2.52
301 313 1.068333 TCCACGCTGGTACGTACTTTC 60.068 52.381 24.07 9.36 46.34 2.62
302 314 0.961019 TCCACGCTGGTACGTACTTT 59.039 50.000 24.07 2.90 46.34 2.66
303 315 1.133790 GATCCACGCTGGTACGTACTT 59.866 52.381 24.07 2.57 46.34 2.24
309 321 0.389426 ACAACGATCCACGCTGGTAC 60.389 55.000 0.00 0.00 46.94 3.34
431 443 3.791973 AGATGAAAGAGGAGCTGTACG 57.208 47.619 0.00 0.00 0.00 3.67
493 505 0.387239 AAAACAAATCTGCGAGCGCC 60.387 50.000 12.70 0.00 41.09 6.53
550 563 7.891498 TGTAGGTGTAGCATTACTCATCTTA 57.109 36.000 0.00 0.00 0.00 2.10
551 564 6.791867 TGTAGGTGTAGCATTACTCATCTT 57.208 37.500 0.00 0.00 0.00 2.40
552 565 6.985653 ATGTAGGTGTAGCATTACTCATCT 57.014 37.500 0.00 0.00 0.00 2.90
553 566 7.316640 CCTATGTAGGTGTAGCATTACTCATC 58.683 42.308 0.00 0.00 38.69 2.92
554 567 7.233389 CCTATGTAGGTGTAGCATTACTCAT 57.767 40.000 0.00 0.00 38.69 2.90
555 568 6.650427 CCTATGTAGGTGTAGCATTACTCA 57.350 41.667 0.00 0.00 38.69 3.41
565 578 7.037442 AAACCCATGTTAACCTATGTAGGTGTA 60.037 37.037 12.27 5.14 44.38 2.90
566 579 6.240351 AAACCCATGTTAACCTATGTAGGTGT 60.240 38.462 12.27 5.97 44.38 4.16
567 580 6.184789 AAACCCATGTTAACCTATGTAGGTG 58.815 40.000 12.27 0.77 44.38 4.00
568 581 6.397217 AAACCCATGTTAACCTATGTAGGT 57.603 37.500 5.90 5.90 45.92 3.08
569 582 7.830201 TGTAAAACCCATGTTAACCTATGTAGG 59.170 37.037 2.48 4.53 40.72 3.18
570 583 8.795842 TGTAAAACCCATGTTAACCTATGTAG 57.204 34.615 2.48 0.00 33.30 2.74
571 584 9.584008 TTTGTAAAACCCATGTTAACCTATGTA 57.416 29.630 2.48 0.00 33.30 2.29
572 585 8.361889 GTTTGTAAAACCCATGTTAACCTATGT 58.638 33.333 2.48 0.00 33.30 2.29
573 586 8.361139 TGTTTGTAAAACCCATGTTAACCTATG 58.639 33.333 2.48 1.07 33.30 2.23
574 587 8.480133 TGTTTGTAAAACCCATGTTAACCTAT 57.520 30.769 2.48 0.00 33.30 2.57
575 588 7.778853 TCTGTTTGTAAAACCCATGTTAACCTA 59.221 33.333 2.48 0.00 33.30 3.08
576 589 6.608002 TCTGTTTGTAAAACCCATGTTAACCT 59.392 34.615 2.48 0.00 33.30 3.50
577 590 6.807789 TCTGTTTGTAAAACCCATGTTAACC 58.192 36.000 2.48 0.00 33.30 2.85
578 591 7.383843 CCATCTGTTTGTAAAACCCATGTTAAC 59.616 37.037 0.00 0.00 33.30 2.01
579 592 7.437748 CCATCTGTTTGTAAAACCCATGTTAA 58.562 34.615 0.71 0.00 33.30 2.01
580 593 6.015010 CCCATCTGTTTGTAAAACCCATGTTA 60.015 38.462 0.71 0.00 33.30 2.41
581 594 5.221621 CCCATCTGTTTGTAAAACCCATGTT 60.222 40.000 0.71 0.00 35.82 2.71
582 595 4.283212 CCCATCTGTTTGTAAAACCCATGT 59.717 41.667 0.71 0.00 0.00 3.21
583 596 4.283212 ACCCATCTGTTTGTAAAACCCATG 59.717 41.667 0.71 3.27 0.00 3.66
584 597 4.488770 ACCCATCTGTTTGTAAAACCCAT 58.511 39.130 0.71 0.00 0.00 4.00
585 598 3.917300 ACCCATCTGTTTGTAAAACCCA 58.083 40.909 0.71 0.00 0.00 4.51
586 599 4.100344 ACAACCCATCTGTTTGTAAAACCC 59.900 41.667 0.71 0.00 0.00 4.11
587 600 5.047188 CACAACCCATCTGTTTGTAAAACC 58.953 41.667 0.71 0.00 0.00 3.27
588 601 5.897050 TCACAACCCATCTGTTTGTAAAAC 58.103 37.500 0.00 0.00 0.00 2.43
589 602 6.514212 CGATCACAACCCATCTGTTTGTAAAA 60.514 38.462 0.00 0.00 0.00 1.52
590 603 5.049060 CGATCACAACCCATCTGTTTGTAAA 60.049 40.000 0.00 0.00 0.00 2.01
591 604 4.454161 CGATCACAACCCATCTGTTTGTAA 59.546 41.667 0.00 0.00 0.00 2.41
592 605 4.000325 CGATCACAACCCATCTGTTTGTA 59.000 43.478 0.00 0.00 0.00 2.41
593 606 2.813754 CGATCACAACCCATCTGTTTGT 59.186 45.455 0.00 0.00 0.00 2.83
594 607 2.162208 CCGATCACAACCCATCTGTTTG 59.838 50.000 0.00 0.00 0.00 2.93
595 608 2.039746 TCCGATCACAACCCATCTGTTT 59.960 45.455 0.00 0.00 0.00 2.83
596 609 1.628340 TCCGATCACAACCCATCTGTT 59.372 47.619 0.00 0.00 0.00 3.16
597 610 1.208052 CTCCGATCACAACCCATCTGT 59.792 52.381 0.00 0.00 0.00 3.41
598 611 1.482182 TCTCCGATCACAACCCATCTG 59.518 52.381 0.00 0.00 0.00 2.90
599 612 1.759445 CTCTCCGATCACAACCCATCT 59.241 52.381 0.00 0.00 0.00 2.90
600 613 1.757118 TCTCTCCGATCACAACCCATC 59.243 52.381 0.00 0.00 0.00 3.51
601 614 1.866015 TCTCTCCGATCACAACCCAT 58.134 50.000 0.00 0.00 0.00 4.00
602 615 1.639722 TTCTCTCCGATCACAACCCA 58.360 50.000 0.00 0.00 0.00 4.51
603 616 2.233922 TCTTTCTCTCCGATCACAACCC 59.766 50.000 0.00 0.00 0.00 4.11
604 617 3.193691 TCTCTTTCTCTCCGATCACAACC 59.806 47.826 0.00 0.00 0.00 3.77
605 618 4.156922 TCTCTCTTTCTCTCCGATCACAAC 59.843 45.833 0.00 0.00 0.00 3.32
606 619 4.156922 GTCTCTCTTTCTCTCCGATCACAA 59.843 45.833 0.00 0.00 0.00 3.33
607 620 3.692101 GTCTCTCTTTCTCTCCGATCACA 59.308 47.826 0.00 0.00 0.00 3.58
608 621 3.066203 GGTCTCTCTTTCTCTCCGATCAC 59.934 52.174 0.00 0.00 0.00 3.06
609 622 3.053991 AGGTCTCTCTTTCTCTCCGATCA 60.054 47.826 0.00 0.00 0.00 2.92
610 623 3.551846 AGGTCTCTCTTTCTCTCCGATC 58.448 50.000 0.00 0.00 0.00 3.69
611 624 3.662759 AGGTCTCTCTTTCTCTCCGAT 57.337 47.619 0.00 0.00 0.00 4.18
612 625 3.443145 AAGGTCTCTCTTTCTCTCCGA 57.557 47.619 0.00 0.00 0.00 4.55
613 626 3.257127 ACAAAGGTCTCTCTTTCTCTCCG 59.743 47.826 0.00 0.00 35.04 4.63
614 627 4.039852 ACACAAAGGTCTCTCTTTCTCTCC 59.960 45.833 0.00 0.00 35.04 3.71
615 628 5.208463 ACACAAAGGTCTCTCTTTCTCTC 57.792 43.478 0.00 0.00 35.04 3.20
616 629 5.363939 CAACACAAAGGTCTCTCTTTCTCT 58.636 41.667 0.00 0.00 35.04 3.10
617 630 4.024472 GCAACACAAAGGTCTCTCTTTCTC 60.024 45.833 0.00 0.00 35.04 2.87
618 631 3.879892 GCAACACAAAGGTCTCTCTTTCT 59.120 43.478 0.00 0.00 35.04 2.52
619 632 3.003793 GGCAACACAAAGGTCTCTCTTTC 59.996 47.826 0.00 0.00 35.04 2.62
620 633 2.952310 GGCAACACAAAGGTCTCTCTTT 59.048 45.455 0.00 0.00 37.44 2.52
621 634 2.576615 GGCAACACAAAGGTCTCTCTT 58.423 47.619 0.00 0.00 0.00 2.85
622 635 1.541233 CGGCAACACAAAGGTCTCTCT 60.541 52.381 0.00 0.00 0.00 3.10
623 636 0.868406 CGGCAACACAAAGGTCTCTC 59.132 55.000 0.00 0.00 0.00 3.20
624 637 1.166531 GCGGCAACACAAAGGTCTCT 61.167 55.000 0.00 0.00 0.00 3.10
625 638 1.282875 GCGGCAACACAAAGGTCTC 59.717 57.895 0.00 0.00 0.00 3.36
626 639 2.542907 CGCGGCAACACAAAGGTCT 61.543 57.895 0.00 0.00 0.00 3.85
627 640 2.051345 CGCGGCAACACAAAGGTC 60.051 61.111 0.00 0.00 0.00 3.85
628 641 3.591835 CCGCGGCAACACAAAGGT 61.592 61.111 14.67 0.00 0.00 3.50
629 642 4.341502 CCCGCGGCAACACAAAGG 62.342 66.667 22.85 0.00 0.00 3.11
630 643 3.254014 CTCCCGCGGCAACACAAAG 62.254 63.158 22.85 2.11 0.00 2.77
631 644 3.283684 CTCCCGCGGCAACACAAA 61.284 61.111 22.85 0.00 0.00 2.83
643 656 4.148825 CTTCTCCACCGCCTCCCG 62.149 72.222 0.00 0.00 0.00 5.14
644 657 3.787001 CCTTCTCCACCGCCTCCC 61.787 72.222 0.00 0.00 0.00 4.30
645 658 3.787001 CCCTTCTCCACCGCCTCC 61.787 72.222 0.00 0.00 0.00 4.30
646 659 2.683933 TCCCTTCTCCACCGCCTC 60.684 66.667 0.00 0.00 0.00 4.70
647 660 2.685380 CTCCCTTCTCCACCGCCT 60.685 66.667 0.00 0.00 0.00 5.52
648 661 2.683933 TCTCCCTTCTCCACCGCC 60.684 66.667 0.00 0.00 0.00 6.13
649 662 2.579738 GTCTCCCTTCTCCACCGC 59.420 66.667 0.00 0.00 0.00 5.68
650 663 2.885861 CGTCTCCCTTCTCCACCG 59.114 66.667 0.00 0.00 0.00 4.94
651 664 2.579738 GCGTCTCCCTTCTCCACC 59.420 66.667 0.00 0.00 0.00 4.61
652 665 2.182030 CGCGTCTCCCTTCTCCAC 59.818 66.667 0.00 0.00 0.00 4.02
653 666 3.760035 GCGCGTCTCCCTTCTCCA 61.760 66.667 8.43 0.00 0.00 3.86
654 667 4.856607 CGCGCGTCTCCCTTCTCC 62.857 72.222 24.19 0.00 0.00 3.71
655 668 3.743091 CTCGCGCGTCTCCCTTCTC 62.743 68.421 30.98 0.00 0.00 2.87
656 669 3.816524 CTCGCGCGTCTCCCTTCT 61.817 66.667 30.98 0.00 0.00 2.85
657 670 4.856607 CCTCGCGCGTCTCCCTTC 62.857 72.222 30.98 0.00 0.00 3.46
666 679 4.903355 CTCTCTGCTCCTCGCGCG 62.903 72.222 26.76 26.76 43.27 6.86
667 680 3.468266 CTCTCTCTGCTCCTCGCGC 62.468 68.421 0.00 0.00 43.27 6.86
668 681 2.715005 CTCTCTCTGCTCCTCGCG 59.285 66.667 0.00 0.00 43.27 5.87
669 682 3.119193 CCTCTCTCTGCTCCTCGC 58.881 66.667 0.00 0.00 39.77 5.03
670 683 2.833533 CGCCTCTCTCTGCTCCTCG 61.834 68.421 0.00 0.00 0.00 4.63
671 684 1.752694 ACGCCTCTCTCTGCTCCTC 60.753 63.158 0.00 0.00 0.00 3.71
672 685 2.051518 CACGCCTCTCTCTGCTCCT 61.052 63.158 0.00 0.00 0.00 3.69
673 686 2.493973 CACGCCTCTCTCTGCTCC 59.506 66.667 0.00 0.00 0.00 4.70
674 687 2.202730 GCACGCCTCTCTCTGCTC 60.203 66.667 0.00 0.00 0.00 4.26
675 688 3.768922 GGCACGCCTCTCTCTGCT 61.769 66.667 0.00 0.00 0.00 4.24
705 718 4.452733 GAGGACCAACGGCGGAGG 62.453 72.222 13.24 15.31 0.00 4.30
706 719 4.452733 GGAGGACCAACGGCGGAG 62.453 72.222 13.24 2.29 35.97 4.63
708 721 4.452733 GAGGAGGACCAACGGCGG 62.453 72.222 13.24 0.00 38.94 6.13
709 722 4.796231 CGAGGAGGACCAACGGCG 62.796 72.222 4.80 4.80 38.94 6.46
710 723 3.379445 TCGAGGAGGACCAACGGC 61.379 66.667 0.00 0.00 38.18 5.68
711 724 2.214181 CTGTCGAGGAGGACCAACGG 62.214 65.000 0.00 0.00 38.18 4.44
712 725 1.213013 CTGTCGAGGAGGACCAACG 59.787 63.158 0.00 0.00 38.94 4.10
713 726 1.079750 GCTGTCGAGGAGGACCAAC 60.080 63.158 0.00 0.00 38.94 3.77
714 727 2.283529 GGCTGTCGAGGAGGACCAA 61.284 63.158 0.00 0.00 38.94 3.67
715 728 2.680352 GGCTGTCGAGGAGGACCA 60.680 66.667 0.00 0.00 38.94 4.02
716 729 3.827898 CGGCTGTCGAGGAGGACC 61.828 72.222 0.00 0.00 42.43 4.46
717 730 4.500116 GCGGCTGTCGAGGAGGAC 62.500 72.222 5.55 0.00 42.43 3.85
769 782 3.599285 TTTGGTACGCCGCCAGGAG 62.599 63.158 0.00 0.00 43.46 3.69
770 783 3.599285 CTTTGGTACGCCGCCAGGA 62.599 63.158 0.00 0.00 41.02 3.86
771 784 3.124921 CTTTGGTACGCCGCCAGG 61.125 66.667 0.00 0.00 37.31 4.45
772 785 3.799755 GCTTTGGTACGCCGCCAG 61.800 66.667 0.00 0.00 37.31 4.85
775 788 4.143363 GACGCTTTGGTACGCCGC 62.143 66.667 0.00 0.00 37.67 6.53
776 789 3.834373 CGACGCTTTGGTACGCCG 61.834 66.667 0.00 0.00 37.67 6.46
777 790 2.723719 GACGACGCTTTGGTACGCC 61.724 63.158 0.00 0.00 0.00 5.68
778 791 2.767697 GACGACGCTTTGGTACGC 59.232 61.111 0.00 0.00 0.00 4.42
779 792 1.727022 ACGACGACGCTTTGGTACG 60.727 57.895 7.30 0.00 43.96 3.67
780 793 0.936297 ACACGACGACGCTTTGGTAC 60.936 55.000 7.30 0.00 43.96 3.34
781 794 0.935831 CACACGACGACGCTTTGGTA 60.936 55.000 7.30 0.00 43.96 3.25
782 795 2.105528 ACACGACGACGCTTTGGT 59.894 55.556 7.30 0.00 43.96 3.67
783 796 1.876453 CTCACACGACGACGCTTTGG 61.876 60.000 7.30 0.00 43.96 3.28
784 797 1.206745 ACTCACACGACGACGCTTTG 61.207 55.000 7.30 0.80 43.96 2.77
785 798 0.933509 GACTCACACGACGACGCTTT 60.934 55.000 7.30 0.00 43.96 3.51
786 799 1.370172 GACTCACACGACGACGCTT 60.370 57.895 7.30 0.00 43.96 4.68
787 800 2.251667 GACTCACACGACGACGCT 59.748 61.111 7.30 0.00 43.96 5.07
788 801 3.157523 CGACTCACACGACGACGC 61.158 66.667 7.30 0.00 43.96 5.19
789 802 2.236803 ATCCGACTCACACGACGACG 62.237 60.000 5.58 5.58 45.75 5.12
923 938 3.112709 GCGTCCTCCGTGCAGAAC 61.113 66.667 0.00 0.00 39.32 3.01
1365 1405 3.837355 AGATTCTTGGCACCAAAAGACT 58.163 40.909 3.29 0.00 35.33 3.24
1366 1406 4.762251 AGTAGATTCTTGGCACCAAAAGAC 59.238 41.667 3.29 0.00 35.33 3.01
1499 1539 2.308570 AGATTACACAGCATTGGGACCA 59.691 45.455 0.00 0.00 0.00 4.02
1725 1765 7.059788 AGAGAGAGTGATGCAGATTAGAAGTA 58.940 38.462 0.00 0.00 0.00 2.24
1753 1793 6.585695 ATCTTTGCAGATATGGGCATAAAG 57.414 37.500 0.00 2.25 38.06 1.85
1759 1799 1.198637 GCGATCTTTGCAGATATGGGC 59.801 52.381 0.00 0.00 40.14 5.36
1981 2021 5.300034 TGACAGAAAACAATCAGCAATGACT 59.700 36.000 0.00 0.00 0.00 3.41
2282 2376 1.979155 TCCTCGACCTGGTGCTCTG 60.979 63.158 2.82 0.00 0.00 3.35
2304 2398 6.515365 GCGTGAGGTAAAGGTATTTTTCCAAA 60.515 38.462 0.00 0.00 38.35 3.28
2724 2852 8.503458 AGATCACATAAGAACTTGAAGGATTG 57.497 34.615 0.00 0.00 0.00 2.67
2844 5664 7.878127 AGTAATCTAGAGAGCTAGTCATCTGAC 59.122 40.741 0.00 2.01 43.72 3.51
2845 5665 7.973402 AGTAATCTAGAGAGCTAGTCATCTGA 58.027 38.462 0.00 0.00 43.72 3.27
2846 5666 8.621532 AAGTAATCTAGAGAGCTAGTCATCTG 57.378 38.462 0.00 0.00 43.72 2.90


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

AutoCloner maintained by Alex Coulton.