Multiple sequence alignment - TraesCS6D01G037100

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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 TraesCS6D01G037100 chr6D 100.000 3155 0 0 1 3155 15359317 15356163 0.000000e+00 5827
1 TraesCS6D01G037100 chr6D 78.053 1171 236 19 1075 2235 7994185 7993026 0.000000e+00 719
2 TraesCS6D01G037100 chr6B 96.553 2292 56 9 885 3155 27077090 27074801 0.000000e+00 3773
3 TraesCS6D01G037100 chr6B 82.619 1283 190 27 973 2231 26389182 26390455 0.000000e+00 1103
4 TraesCS6D01G037100 chr6B 77.747 1429 287 26 983 2396 26500510 26501922 0.000000e+00 848
5 TraesCS6D01G037100 chr6B 93.462 520 29 3 1 518 27077693 27077177 0.000000e+00 767
6 TraesCS6D01G037100 chr6B 78.023 1224 248 20 959 2172 16433107 16434319 0.000000e+00 750
7 TraesCS6D01G037100 chr6A 97.378 2174 51 4 985 3155 15940118 15937948 0.000000e+00 3694
8 TraesCS6D01G037100 chr6A 78.628 1268 236 28 984 2235 15914156 15912908 0.000000e+00 808
9 TraesCS6D01G037100 chr6A 91.051 447 35 4 4 449 15941180 15940738 1.620000e-167 599
10 TraesCS6D01G037100 chr2B 78.247 1278 259 18 966 2235 709426202 709424936 0.000000e+00 802
11 TraesCS6D01G037100 chr2B 90.857 175 16 0 1968 2142 166698374 166698548 5.260000e-58 235
12 TraesCS6D01G037100 chr2B 90.857 175 16 0 1968 2142 295240595 295240421 5.260000e-58 235
13 TraesCS6D01G037100 chr1A 78.385 1263 247 23 963 2217 589248527 589247283 0.000000e+00 797
14 TraesCS6D01G037100 chr3A 80.260 385 51 14 2255 2634 748565127 748565491 1.870000e-67 267


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 TraesCS6D01G037100 chr6D 15356163 15359317 3154 True 5827.0 5827 100.0000 1 3155 1 chr6D.!!$R2 3154
1 TraesCS6D01G037100 chr6D 7993026 7994185 1159 True 719.0 719 78.0530 1075 2235 1 chr6D.!!$R1 1160
2 TraesCS6D01G037100 chr6B 27074801 27077693 2892 True 2270.0 3773 95.0075 1 3155 2 chr6B.!!$R1 3154
3 TraesCS6D01G037100 chr6B 26389182 26390455 1273 False 1103.0 1103 82.6190 973 2231 1 chr6B.!!$F2 1258
4 TraesCS6D01G037100 chr6B 26500510 26501922 1412 False 848.0 848 77.7470 983 2396 1 chr6B.!!$F3 1413
5 TraesCS6D01G037100 chr6B 16433107 16434319 1212 False 750.0 750 78.0230 959 2172 1 chr6B.!!$F1 1213
6 TraesCS6D01G037100 chr6A 15937948 15941180 3232 True 2146.5 3694 94.2145 4 3155 2 chr6A.!!$R2 3151
7 TraesCS6D01G037100 chr6A 15912908 15914156 1248 True 808.0 808 78.6280 984 2235 1 chr6A.!!$R1 1251
8 TraesCS6D01G037100 chr2B 709424936 709426202 1266 True 802.0 802 78.2470 966 2235 1 chr2B.!!$R2 1269
9 TraesCS6D01G037100 chr1A 589247283 589248527 1244 True 797.0 797 78.3850 963 2217 1 chr1A.!!$R1 1254

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
576 580 0.038892 CACAAACCAGATGCTGCCAC 60.039 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2471 2894 0.392998 CTGGGTCCTGGTTTGATCCG 60.393 60.0 0.0 0.0 35.66 4.18 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
256 258 6.826741 ACTGACCACTAACTATTGTTTGTTGT 59.173 34.615 9.91 9.91 39.40 3.32
257 259 7.338449 ACTGACCACTAACTATTGTTTGTTGTT 59.662 33.333 10.98 0.00 39.40 2.83
258 260 7.476667 TGACCACTAACTATTGTTTGTTGTTG 58.523 34.615 10.98 0.12 39.40 3.33
259 261 6.270064 ACCACTAACTATTGTTTGTTGTTGC 58.730 36.000 4.60 0.00 39.40 4.17
260 262 6.127591 ACCACTAACTATTGTTTGTTGTTGCA 60.128 34.615 4.60 0.00 39.40 4.08
314 316 2.038426 TGGTGTGTTCTCCTGTATGTGG 59.962 50.000 0.00 0.00 0.00 4.17
323 325 3.323115 TCTCCTGTATGTGGATGAGCATC 59.677 47.826 1.86 1.86 37.11 3.91
344 346 4.795469 TCATACCTGCATGATGAAATGGT 58.205 39.130 0.00 0.66 29.93 3.55
353 355 5.657745 TGCATGATGAAATGGTCCTTAACAT 59.342 36.000 0.00 0.00 0.00 2.71
357 359 7.337480 TGATGAAATGGTCCTTAACATCATG 57.663 36.000 15.99 0.00 38.02 3.07
369 371 9.463443 GTCCTTAACATCATGCAAAAATATACC 57.537 33.333 0.00 0.00 0.00 2.73
482 486 7.797121 AAGTGGAATGTAGATGGGAAATTTT 57.203 32.000 0.00 0.00 0.00 1.82
507 511 4.454678 ACAGAGACATGCTTGTTCTTTCA 58.545 39.130 6.70 0.00 35.79 2.69
524 528 6.988622 TCTTTCAAAAGAAGAACACGGTTA 57.011 33.333 2.74 0.00 41.75 2.85
525 529 7.380431 TCTTTCAAAAGAAGAACACGGTTAA 57.620 32.000 2.74 0.00 41.75 2.01
526 530 7.818642 TCTTTCAAAAGAAGAACACGGTTAAA 58.181 30.769 2.74 0.00 41.75 1.52
528 532 8.989653 TTTCAAAAGAAGAACACGGTTAAATT 57.010 26.923 0.00 0.00 0.00 1.82
529 533 8.989653 TTCAAAAGAAGAACACGGTTAAATTT 57.010 26.923 0.00 0.00 0.00 1.82
558 562 9.725019 TTTCTCTAAATTGAGTTCTAGAATGCA 57.275 29.630 8.75 7.25 35.68 3.96
559 563 8.709386 TCTCTAAATTGAGTTCTAGAATGCAC 57.291 34.615 8.75 0.00 35.68 4.57
560 564 8.314021 TCTCTAAATTGAGTTCTAGAATGCACA 58.686 33.333 8.75 4.39 35.68 4.57
561 565 8.846943 TCTAAATTGAGTTCTAGAATGCACAA 57.153 30.769 8.75 12.29 0.00 3.33
562 566 9.283768 TCTAAATTGAGTTCTAGAATGCACAAA 57.716 29.630 8.75 0.00 0.00 2.83
563 567 9.334693 CTAAATTGAGTTCTAGAATGCACAAAC 57.665 33.333 8.75 0.00 0.00 2.93
564 568 5.689383 TTGAGTTCTAGAATGCACAAACC 57.311 39.130 8.75 0.00 0.00 3.27
565 569 4.713553 TGAGTTCTAGAATGCACAAACCA 58.286 39.130 8.75 0.00 0.00 3.67
566 570 4.756642 TGAGTTCTAGAATGCACAAACCAG 59.243 41.667 8.75 0.00 0.00 4.00
567 571 4.973168 AGTTCTAGAATGCACAAACCAGA 58.027 39.130 8.75 0.00 0.00 3.86
568 572 5.564550 AGTTCTAGAATGCACAAACCAGAT 58.435 37.500 8.75 0.00 0.00 2.90
569 573 5.413833 AGTTCTAGAATGCACAAACCAGATG 59.586 40.000 8.75 0.00 0.00 2.90
570 574 3.691118 TCTAGAATGCACAAACCAGATGC 59.309 43.478 0.00 0.00 39.88 3.91
571 575 2.522185 AGAATGCACAAACCAGATGCT 58.478 42.857 0.00 0.00 40.13 3.79
572 576 2.230508 AGAATGCACAAACCAGATGCTG 59.769 45.455 0.00 0.00 40.13 4.41
573 577 0.245539 ATGCACAAACCAGATGCTGC 59.754 50.000 0.00 0.00 40.13 5.25
574 578 1.080298 GCACAAACCAGATGCTGCC 60.080 57.895 0.00 0.00 36.40 4.85
575 579 1.808531 GCACAAACCAGATGCTGCCA 61.809 55.000 0.00 0.00 36.40 4.92
576 580 0.038892 CACAAACCAGATGCTGCCAC 60.039 55.000 0.00 0.00 0.00 5.01
577 581 0.178981 ACAAACCAGATGCTGCCACT 60.179 50.000 0.00 0.00 0.00 4.00
578 582 0.963962 CAAACCAGATGCTGCCACTT 59.036 50.000 0.00 0.00 0.00 3.16
579 583 2.161855 CAAACCAGATGCTGCCACTTA 58.838 47.619 0.00 0.00 0.00 2.24
580 584 1.826385 AACCAGATGCTGCCACTTAC 58.174 50.000 0.00 0.00 0.00 2.34
581 585 0.987294 ACCAGATGCTGCCACTTACT 59.013 50.000 0.00 0.00 0.00 2.24
582 586 1.352352 ACCAGATGCTGCCACTTACTT 59.648 47.619 0.00 0.00 0.00 2.24
583 587 2.571653 ACCAGATGCTGCCACTTACTTA 59.428 45.455 0.00 0.00 0.00 2.24
584 588 3.009033 ACCAGATGCTGCCACTTACTTAA 59.991 43.478 0.00 0.00 0.00 1.85
585 589 4.202441 CCAGATGCTGCCACTTACTTAAT 58.798 43.478 0.00 0.00 0.00 1.40
586 590 4.641989 CCAGATGCTGCCACTTACTTAATT 59.358 41.667 0.00 0.00 0.00 1.40
587 591 5.822519 CCAGATGCTGCCACTTACTTAATTA 59.177 40.000 0.00 0.00 0.00 1.40
588 592 6.318648 CCAGATGCTGCCACTTACTTAATTAA 59.681 38.462 0.00 0.00 0.00 1.40
589 593 7.412853 CAGATGCTGCCACTTACTTAATTAAG 58.587 38.462 21.21 21.21 39.18 1.85
590 594 6.543831 AGATGCTGCCACTTACTTAATTAAGG 59.456 38.462 25.25 12.70 37.62 2.69
591 595 4.947388 TGCTGCCACTTACTTAATTAAGGG 59.053 41.667 25.25 17.83 37.62 3.95
592 596 5.190677 GCTGCCACTTACTTAATTAAGGGA 58.809 41.667 25.25 12.67 34.81 4.20
593 597 5.297029 GCTGCCACTTACTTAATTAAGGGAG 59.703 44.000 25.25 22.30 34.81 4.30
594 598 5.190677 TGCCACTTACTTAATTAAGGGAGC 58.809 41.667 25.25 18.54 34.81 4.70
595 599 5.190677 GCCACTTACTTAATTAAGGGAGCA 58.809 41.667 25.25 6.93 34.81 4.26
596 600 5.066117 GCCACTTACTTAATTAAGGGAGCAC 59.934 44.000 25.25 12.88 34.81 4.40
597 601 6.177610 CCACTTACTTAATTAAGGGAGCACA 58.822 40.000 25.25 4.32 34.81 4.57
598 602 6.657541 CCACTTACTTAATTAAGGGAGCACAA 59.342 38.462 25.25 9.26 34.81 3.33
599 603 7.339466 CCACTTACTTAATTAAGGGAGCACAAT 59.661 37.037 25.25 7.17 34.81 2.71
600 604 8.739972 CACTTACTTAATTAAGGGAGCACAATT 58.260 33.333 25.25 6.54 34.81 2.32
601 605 9.309224 ACTTACTTAATTAAGGGAGCACAATTT 57.691 29.630 25.25 6.10 37.62 1.82
647 651 8.981724 ATTGATCTGAAATGAAGACATGTTTG 57.018 30.769 0.00 0.00 36.79 2.93
648 652 7.514784 TGATCTGAAATGAAGACATGTTTGT 57.485 32.000 0.00 0.00 39.32 2.83
649 653 7.944061 TGATCTGAAATGAAGACATGTTTGTT 58.056 30.769 0.00 0.00 35.79 2.83
650 654 8.077991 TGATCTGAAATGAAGACATGTTTGTTC 58.922 33.333 0.00 4.76 35.79 3.18
651 655 7.572523 TCTGAAATGAAGACATGTTTGTTCT 57.427 32.000 0.00 0.00 35.79 3.01
652 656 7.999679 TCTGAAATGAAGACATGTTTGTTCTT 58.000 30.769 0.00 0.00 35.79 2.52
653 657 8.469200 TCTGAAATGAAGACATGTTTGTTCTTT 58.531 29.630 0.00 5.93 35.79 2.52
654 658 8.633075 TGAAATGAAGACATGTTTGTTCTTTC 57.367 30.769 0.00 13.78 35.79 2.62
655 659 8.469200 TGAAATGAAGACATGTTTGTTCTTTCT 58.531 29.630 21.87 13.38 35.79 2.52
656 660 9.950680 GAAATGAAGACATGTTTGTTCTTTCTA 57.049 29.630 0.00 0.00 35.79 2.10
659 663 9.956720 ATGAAGACATGTTTGTTCTTTCTAAAG 57.043 29.630 0.00 0.00 35.79 1.85
660 664 8.956426 TGAAGACATGTTTGTTCTTTCTAAAGT 58.044 29.630 0.00 0.00 35.79 2.66
661 665 9.788960 GAAGACATGTTTGTTCTTTCTAAAGTT 57.211 29.630 0.00 0.00 35.79 2.66
663 667 9.573133 AGACATGTTTGTTCTTTCTAAAGTTTG 57.427 29.630 0.00 0.00 35.79 2.93
664 668 8.185003 ACATGTTTGTTCTTTCTAAAGTTTGC 57.815 30.769 0.00 0.00 37.31 3.68
665 669 8.034804 ACATGTTTGTTCTTTCTAAAGTTTGCT 58.965 29.630 0.00 0.00 37.31 3.91
666 670 8.534778 CATGTTTGTTCTTTCTAAAGTTTGCTC 58.465 33.333 0.00 0.00 37.31 4.26
667 671 7.598278 TGTTTGTTCTTTCTAAAGTTTGCTCA 58.402 30.769 0.00 0.00 37.31 4.26
668 672 8.085296 TGTTTGTTCTTTCTAAAGTTTGCTCAA 58.915 29.630 0.00 0.00 37.31 3.02
669 673 8.921670 GTTTGTTCTTTCTAAAGTTTGCTCAAA 58.078 29.630 0.00 0.00 37.31 2.69
670 674 9.482627 TTTGTTCTTTCTAAAGTTTGCTCAAAA 57.517 25.926 0.00 0.00 37.31 2.44
671 675 9.651913 TTGTTCTTTCTAAAGTTTGCTCAAAAT 57.348 25.926 0.00 0.00 37.31 1.82
711 715 9.832445 ATAAATAATCAACATGAACTACGGACT 57.168 29.630 0.00 0.00 0.00 3.85
713 717 9.832445 AAATAATCAACATGAACTACGGACTAT 57.168 29.630 0.00 0.00 0.00 2.12
717 721 9.832445 AATCAACATGAACTACGGACTATATTT 57.168 29.630 0.00 0.00 0.00 1.40
718 722 8.867112 TCAACATGAACTACGGACTATATTTC 57.133 34.615 0.00 0.00 0.00 2.17
719 723 8.471609 TCAACATGAACTACGGACTATATTTCA 58.528 33.333 0.00 0.00 0.00 2.69
720 724 9.261180 CAACATGAACTACGGACTATATTTCAT 57.739 33.333 0.00 0.00 34.19 2.57
721 725 9.832445 AACATGAACTACGGACTATATTTCATT 57.168 29.630 0.00 0.00 32.57 2.57
722 726 9.832445 ACATGAACTACGGACTATATTTCATTT 57.168 29.630 0.00 0.00 32.57 2.32
725 729 9.878667 TGAACTACGGACTATATTTCATTTTGA 57.121 29.630 0.00 0.00 0.00 2.69
762 766 8.622948 TTTTTGGGTTTTGTTTTGATAACACT 57.377 26.923 0.00 0.00 0.00 3.55
763 767 8.622948 TTTTGGGTTTTGTTTTGATAACACTT 57.377 26.923 0.00 0.00 0.00 3.16
764 768 7.835634 TTGGGTTTTGTTTTGATAACACTTC 57.164 32.000 0.00 0.00 0.00 3.01
765 769 6.342111 TGGGTTTTGTTTTGATAACACTTCC 58.658 36.000 0.00 0.00 0.00 3.46
766 770 6.070767 TGGGTTTTGTTTTGATAACACTTCCA 60.071 34.615 0.00 0.00 0.00 3.53
767 771 6.819146 GGGTTTTGTTTTGATAACACTTCCAA 59.181 34.615 0.00 0.00 0.00 3.53
768 772 7.497579 GGGTTTTGTTTTGATAACACTTCCAAT 59.502 33.333 0.00 0.00 0.00 3.16
769 773 8.888716 GGTTTTGTTTTGATAACACTTCCAATT 58.111 29.630 0.00 0.00 0.00 2.32
772 776 9.883142 TTTGTTTTGATAACACTTCCAATTTCT 57.117 25.926 0.00 0.00 0.00 2.52
773 777 8.870160 TGTTTTGATAACACTTCCAATTTCTG 57.130 30.769 0.00 0.00 0.00 3.02
774 778 8.690884 TGTTTTGATAACACTTCCAATTTCTGA 58.309 29.630 0.00 0.00 0.00 3.27
775 779 9.185192 GTTTTGATAACACTTCCAATTTCTGAG 57.815 33.333 0.00 0.00 0.00 3.35
776 780 8.463930 TTTGATAACACTTCCAATTTCTGAGT 57.536 30.769 0.00 0.00 0.00 3.41
777 781 7.439157 TGATAACACTTCCAATTTCTGAGTG 57.561 36.000 0.00 0.00 42.48 3.51
778 782 6.430925 TGATAACACTTCCAATTTCTGAGTGG 59.569 38.462 6.73 0.00 44.86 4.00
785 789 4.589216 CCAATTTCTGAGTGGAAGCAAA 57.411 40.909 0.00 0.00 46.42 3.68
786 790 4.553323 CCAATTTCTGAGTGGAAGCAAAG 58.447 43.478 0.00 0.00 46.42 2.77
787 791 3.930634 ATTTCTGAGTGGAAGCAAAGC 57.069 42.857 0.00 0.00 0.00 3.51
788 792 1.609208 TTCTGAGTGGAAGCAAAGCC 58.391 50.000 0.00 0.00 0.00 4.35
789 793 0.250901 TCTGAGTGGAAGCAAAGCCC 60.251 55.000 0.00 0.00 0.00 5.19
790 794 0.251077 CTGAGTGGAAGCAAAGCCCT 60.251 55.000 0.00 0.00 0.00 5.19
791 795 0.185901 TGAGTGGAAGCAAAGCCCTT 59.814 50.000 0.00 0.00 0.00 3.95
792 796 1.423541 TGAGTGGAAGCAAAGCCCTTA 59.576 47.619 0.00 0.00 0.00 2.69
793 797 2.158534 TGAGTGGAAGCAAAGCCCTTAA 60.159 45.455 0.00 0.00 0.00 1.85
794 798 2.229062 GAGTGGAAGCAAAGCCCTTAAC 59.771 50.000 0.00 0.00 0.00 2.01
795 799 1.960689 GTGGAAGCAAAGCCCTTAACA 59.039 47.619 0.00 0.00 0.00 2.41
796 800 2.364002 GTGGAAGCAAAGCCCTTAACAA 59.636 45.455 0.00 0.00 0.00 2.83
797 801 2.364002 TGGAAGCAAAGCCCTTAACAAC 59.636 45.455 0.00 0.00 0.00 3.32
798 802 2.364002 GGAAGCAAAGCCCTTAACAACA 59.636 45.455 0.00 0.00 0.00 3.33
799 803 3.006859 GGAAGCAAAGCCCTTAACAACAT 59.993 43.478 0.00 0.00 0.00 2.71
800 804 3.665745 AGCAAAGCCCTTAACAACATG 57.334 42.857 0.00 0.00 0.00 3.21
801 805 3.230134 AGCAAAGCCCTTAACAACATGA 58.770 40.909 0.00 0.00 0.00 3.07
802 806 3.640967 AGCAAAGCCCTTAACAACATGAA 59.359 39.130 0.00 0.00 0.00 2.57
803 807 4.100808 AGCAAAGCCCTTAACAACATGAAA 59.899 37.500 0.00 0.00 0.00 2.69
804 808 4.996758 GCAAAGCCCTTAACAACATGAAAT 59.003 37.500 0.00 0.00 0.00 2.17
820 824 1.401905 GAAATGGCCCACTCAACGATC 59.598 52.381 0.00 0.00 0.00 3.69
847 851 2.734755 CCCAAGATGGCATAGTCCAA 57.265 50.000 0.00 0.00 39.96 3.53
858 862 2.030457 GCATAGTCCAAACGACGGATTG 59.970 50.000 0.00 4.24 46.92 2.67
883 887 1.084370 AGCAGAAACGCGAGCCATAC 61.084 55.000 15.93 0.00 36.85 2.39
1732 2152 0.944386 GGCTGTCTCGTTCAAAAGCA 59.056 50.000 0.00 0.00 32.28 3.91
2175 2595 5.144100 TGAACCAAGAAAAGGCTATGGAAA 58.856 37.500 9.32 0.00 35.16 3.13
2246 2666 4.022242 TGCTGGTAACTCTTGTCTCAGTAC 60.022 45.833 0.00 0.00 37.61 2.73
2354 2777 2.489938 TTTGATTCCTGAACCCCGAG 57.510 50.000 0.00 0.00 0.00 4.63
2376 2799 7.710907 CCGAGATGATGTTCTTGTTATTCCTTA 59.289 37.037 0.00 0.00 0.00 2.69
2471 2894 0.028902 GTGTGCGTGGACCAACTTTC 59.971 55.000 0.00 0.00 0.00 2.62
2986 3413 5.127519 TGCCATGAATAACAAGGAAATCCAG 59.872 40.000 1.67 0.00 39.44 3.86
3059 3486 4.705337 ACAAAGTTTTTCCGCTACAACA 57.295 36.364 0.00 0.00 0.00 3.33
3138 3565 3.123790 TGCATATGTAACACCGTTGTTCG 59.876 43.478 0.01 0.00 42.67 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
299 301 3.118629 TGCTCATCCACATACAGGAGAAC 60.119 47.826 0.00 0.00 38.83 3.01
314 316 3.671716 TCATGCAGGTATGATGCTCATC 58.328 45.455 0.00 3.03 44.17 2.92
323 325 4.022589 GGACCATTTCATCATGCAGGTATG 60.023 45.833 0.00 1.43 0.00 2.39
344 346 9.194972 TGGTATATTTTTGCATGATGTTAAGGA 57.805 29.630 0.00 0.00 0.00 3.36
353 355 9.585099 GAAAAGTCATGGTATATTTTTGCATGA 57.415 29.630 0.00 0.00 0.00 3.07
357 359 8.250332 TGAGGAAAAGTCATGGTATATTTTTGC 58.750 33.333 0.00 0.00 0.00 3.68
482 486 6.542005 TGAAAGAACAAGCATGTCTCTGTTTA 59.458 34.615 0.00 0.00 39.40 2.01
532 536 9.725019 TGCATTCTAGAACTCAATTTAGAGAAA 57.275 29.630 7.48 0.00 38.98 2.52
533 537 9.155975 GTGCATTCTAGAACTCAATTTAGAGAA 57.844 33.333 7.48 0.00 38.98 2.87
534 538 8.314021 TGTGCATTCTAGAACTCAATTTAGAGA 58.686 33.333 7.48 0.00 38.98 3.10
535 539 8.484641 TGTGCATTCTAGAACTCAATTTAGAG 57.515 34.615 7.48 0.00 41.44 2.43
536 540 8.846943 TTGTGCATTCTAGAACTCAATTTAGA 57.153 30.769 7.48 0.00 0.00 2.10
537 541 9.334693 GTTTGTGCATTCTAGAACTCAATTTAG 57.665 33.333 7.48 0.00 0.00 1.85
538 542 8.296713 GGTTTGTGCATTCTAGAACTCAATTTA 58.703 33.333 7.48 0.00 0.00 1.40
540 544 6.265196 TGGTTTGTGCATTCTAGAACTCAATT 59.735 34.615 7.48 0.00 0.00 2.32
543 547 4.713553 TGGTTTGTGCATTCTAGAACTCA 58.286 39.130 7.48 5.88 0.00 3.41
545 549 4.973168 TCTGGTTTGTGCATTCTAGAACT 58.027 39.130 7.48 0.00 0.00 3.01
546 550 5.634896 CATCTGGTTTGTGCATTCTAGAAC 58.365 41.667 7.48 0.00 0.00 3.01
547 551 4.156556 GCATCTGGTTTGTGCATTCTAGAA 59.843 41.667 7.82 7.82 38.68 2.10
548 552 3.691118 GCATCTGGTTTGTGCATTCTAGA 59.309 43.478 0.00 0.00 38.68 2.43
552 556 2.602878 CAGCATCTGGTTTGTGCATTC 58.397 47.619 0.00 0.00 41.19 2.67
553 557 1.337447 GCAGCATCTGGTTTGTGCATT 60.337 47.619 0.00 0.00 41.19 3.56
554 558 0.245539 GCAGCATCTGGTTTGTGCAT 59.754 50.000 0.00 0.00 41.19 3.96
555 559 1.661480 GCAGCATCTGGTTTGTGCA 59.339 52.632 0.00 0.00 41.19 4.57
556 560 1.080298 GGCAGCATCTGGTTTGTGC 60.080 57.895 0.00 0.00 39.10 4.57
557 561 0.038892 GTGGCAGCATCTGGTTTGTG 60.039 55.000 0.00 0.00 31.21 3.33
558 562 0.178981 AGTGGCAGCATCTGGTTTGT 60.179 50.000 0.00 0.00 31.21 2.83
559 563 0.963962 AAGTGGCAGCATCTGGTTTG 59.036 50.000 0.00 0.00 31.21 2.93
560 564 2.162681 GTAAGTGGCAGCATCTGGTTT 58.837 47.619 0.00 0.00 31.21 3.27
561 565 1.352352 AGTAAGTGGCAGCATCTGGTT 59.648 47.619 0.00 0.00 31.21 3.67
562 566 0.987294 AGTAAGTGGCAGCATCTGGT 59.013 50.000 0.00 0.00 31.21 4.00
563 567 2.119801 AAGTAAGTGGCAGCATCTGG 57.880 50.000 0.00 0.00 31.21 3.86
564 568 5.824904 AATTAAGTAAGTGGCAGCATCTG 57.175 39.130 0.00 0.00 34.12 2.90
565 569 6.543831 CCTTAATTAAGTAAGTGGCAGCATCT 59.456 38.462 20.99 0.00 30.39 2.90
566 570 6.238759 CCCTTAATTAAGTAAGTGGCAGCATC 60.239 42.308 20.99 0.00 30.39 3.91
567 571 5.594317 CCCTTAATTAAGTAAGTGGCAGCAT 59.406 40.000 20.99 0.00 30.39 3.79
568 572 4.947388 CCCTTAATTAAGTAAGTGGCAGCA 59.053 41.667 20.99 0.00 30.39 4.41
569 573 5.190677 TCCCTTAATTAAGTAAGTGGCAGC 58.809 41.667 20.99 0.00 30.39 5.25
570 574 5.297029 GCTCCCTTAATTAAGTAAGTGGCAG 59.703 44.000 20.99 16.54 30.39 4.85
571 575 5.190677 GCTCCCTTAATTAAGTAAGTGGCA 58.809 41.667 20.99 10.04 30.39 4.92
572 576 5.066117 GTGCTCCCTTAATTAAGTAAGTGGC 59.934 44.000 20.99 17.64 30.39 5.01
573 577 6.177610 TGTGCTCCCTTAATTAAGTAAGTGG 58.822 40.000 20.99 17.80 30.39 4.00
574 578 7.681939 TTGTGCTCCCTTAATTAAGTAAGTG 57.318 36.000 20.99 9.77 30.39 3.16
575 579 8.879427 AATTGTGCTCCCTTAATTAAGTAAGT 57.121 30.769 20.99 4.51 30.39 2.24
622 626 8.582437 ACAAACATGTCTTCATTTCAGATCAAT 58.418 29.630 0.00 0.00 31.15 2.57
623 627 7.944061 ACAAACATGTCTTCATTTCAGATCAA 58.056 30.769 0.00 0.00 31.15 2.57
624 628 7.514784 ACAAACATGTCTTCATTTCAGATCA 57.485 32.000 0.00 0.00 31.15 2.92
625 629 8.295288 AGAACAAACATGTCTTCATTTCAGATC 58.705 33.333 0.00 0.00 31.15 2.75
626 630 8.174733 AGAACAAACATGTCTTCATTTCAGAT 57.825 30.769 0.00 0.00 31.15 2.90
627 631 7.572523 AGAACAAACATGTCTTCATTTCAGA 57.427 32.000 0.00 0.00 31.15 3.27
628 632 8.638685 AAAGAACAAACATGTCTTCATTTCAG 57.361 30.769 0.00 0.00 31.15 3.02
629 633 8.469200 AGAAAGAACAAACATGTCTTCATTTCA 58.531 29.630 20.33 0.00 31.15 2.69
630 634 8.862550 AGAAAGAACAAACATGTCTTCATTTC 57.137 30.769 0.00 11.27 31.15 2.17
633 637 9.956720 CTTTAGAAAGAACAAACATGTCTTCAT 57.043 29.630 0.00 0.00 38.28 2.57
634 638 8.956426 ACTTTAGAAAGAACAAACATGTCTTCA 58.044 29.630 8.97 0.00 39.31 3.02
635 639 9.788960 AACTTTAGAAAGAACAAACATGTCTTC 57.211 29.630 8.97 0.72 39.31 2.87
637 641 9.573133 CAAACTTTAGAAAGAACAAACATGTCT 57.427 29.630 8.97 0.00 39.31 3.41
638 642 8.321005 GCAAACTTTAGAAAGAACAAACATGTC 58.679 33.333 8.97 0.00 39.31 3.06
639 643 8.034804 AGCAAACTTTAGAAAGAACAAACATGT 58.965 29.630 8.97 0.00 39.31 3.21
640 644 8.411318 AGCAAACTTTAGAAAGAACAAACATG 57.589 30.769 8.97 0.00 39.31 3.21
641 645 8.250332 TGAGCAAACTTTAGAAAGAACAAACAT 58.750 29.630 8.97 0.00 39.31 2.71
642 646 7.598278 TGAGCAAACTTTAGAAAGAACAAACA 58.402 30.769 8.97 0.82 39.31 2.83
643 647 8.460831 TTGAGCAAACTTTAGAAAGAACAAAC 57.539 30.769 8.97 0.00 39.31 2.93
644 648 9.482627 TTTTGAGCAAACTTTAGAAAGAACAAA 57.517 25.926 8.97 8.22 39.31 2.83
645 649 9.651913 ATTTTGAGCAAACTTTAGAAAGAACAA 57.348 25.926 8.97 3.69 39.31 2.83
685 689 9.832445 AGTCCGTAGTTCATGTTGATTATTTAT 57.168 29.630 0.00 0.00 0.00 1.40
687 691 9.832445 ATAGTCCGTAGTTCATGTTGATTATTT 57.168 29.630 0.00 0.00 0.00 1.40
691 695 9.832445 AAATATAGTCCGTAGTTCATGTTGATT 57.168 29.630 0.00 0.00 0.00 2.57
692 696 9.477484 GAAATATAGTCCGTAGTTCATGTTGAT 57.523 33.333 0.00 0.00 0.00 2.57
693 697 8.471609 TGAAATATAGTCCGTAGTTCATGTTGA 58.528 33.333 0.00 0.00 32.99 3.18
694 698 8.642908 TGAAATATAGTCCGTAGTTCATGTTG 57.357 34.615 0.00 0.00 32.99 3.33
695 699 9.832445 AATGAAATATAGTCCGTAGTTCATGTT 57.168 29.630 8.87 0.00 42.56 2.71
696 700 9.832445 AAATGAAATATAGTCCGTAGTTCATGT 57.168 29.630 8.87 2.51 42.56 3.21
699 703 9.878667 TCAAAATGAAATATAGTCCGTAGTTCA 57.121 29.630 0.00 0.00 39.50 3.18
737 741 8.622948 AGTGTTATCAAAACAAAACCCAAAAA 57.377 26.923 0.00 0.00 31.20 1.94
738 742 8.622948 AAGTGTTATCAAAACAAAACCCAAAA 57.377 26.923 0.00 0.00 31.20 2.44
739 743 7.334671 GGAAGTGTTATCAAAACAAAACCCAAA 59.665 33.333 0.00 0.00 31.20 3.28
740 744 6.819146 GGAAGTGTTATCAAAACAAAACCCAA 59.181 34.615 0.00 0.00 31.20 4.12
741 745 6.070767 TGGAAGTGTTATCAAAACAAAACCCA 60.071 34.615 0.00 0.00 31.20 4.51
742 746 6.342111 TGGAAGTGTTATCAAAACAAAACCC 58.658 36.000 0.00 0.00 31.20 4.11
743 747 7.835634 TTGGAAGTGTTATCAAAACAAAACC 57.164 32.000 0.00 0.00 31.20 3.27
746 750 9.883142 AGAAATTGGAAGTGTTATCAAAACAAA 57.117 25.926 0.00 0.00 31.20 2.83
747 751 9.311916 CAGAAATTGGAAGTGTTATCAAAACAA 57.688 29.630 0.00 0.00 31.20 2.83
748 752 8.690884 TCAGAAATTGGAAGTGTTATCAAAACA 58.309 29.630 0.00 0.00 0.00 2.83
749 753 9.185192 CTCAGAAATTGGAAGTGTTATCAAAAC 57.815 33.333 0.00 0.00 0.00 2.43
750 754 8.912988 ACTCAGAAATTGGAAGTGTTATCAAAA 58.087 29.630 0.00 0.00 0.00 2.44
751 755 8.352201 CACTCAGAAATTGGAAGTGTTATCAAA 58.648 33.333 0.00 0.00 0.00 2.69
752 756 7.040478 CCACTCAGAAATTGGAAGTGTTATCAA 60.040 37.037 0.00 0.00 31.39 2.57
753 757 6.430925 CCACTCAGAAATTGGAAGTGTTATCA 59.569 38.462 0.00 0.00 31.39 2.15
754 758 6.655003 TCCACTCAGAAATTGGAAGTGTTATC 59.345 38.462 0.00 0.00 36.45 1.75
755 759 6.542821 TCCACTCAGAAATTGGAAGTGTTAT 58.457 36.000 0.00 0.00 36.45 1.89
756 760 5.935945 TCCACTCAGAAATTGGAAGTGTTA 58.064 37.500 0.00 0.00 36.45 2.41
757 761 4.792068 TCCACTCAGAAATTGGAAGTGTT 58.208 39.130 0.00 0.00 36.45 3.32
758 762 4.437682 TCCACTCAGAAATTGGAAGTGT 57.562 40.909 0.00 0.00 36.45 3.55
762 766 3.831323 TGCTTCCACTCAGAAATTGGAA 58.169 40.909 2.47 2.47 45.27 3.53
763 767 3.507162 TGCTTCCACTCAGAAATTGGA 57.493 42.857 0.00 0.00 37.66 3.53
764 768 4.553323 CTTTGCTTCCACTCAGAAATTGG 58.447 43.478 0.00 0.00 0.00 3.16
765 769 3.985925 GCTTTGCTTCCACTCAGAAATTG 59.014 43.478 0.00 0.00 0.00 2.32
766 770 3.006217 GGCTTTGCTTCCACTCAGAAATT 59.994 43.478 0.00 0.00 0.00 1.82
767 771 2.560105 GGCTTTGCTTCCACTCAGAAAT 59.440 45.455 0.00 0.00 0.00 2.17
768 772 1.956477 GGCTTTGCTTCCACTCAGAAA 59.044 47.619 0.00 0.00 0.00 2.52
769 773 1.609208 GGCTTTGCTTCCACTCAGAA 58.391 50.000 0.00 0.00 0.00 3.02
770 774 0.250901 GGGCTTTGCTTCCACTCAGA 60.251 55.000 0.00 0.00 0.00 3.27
771 775 0.251077 AGGGCTTTGCTTCCACTCAG 60.251 55.000 0.00 0.00 0.00 3.35
772 776 0.185901 AAGGGCTTTGCTTCCACTCA 59.814 50.000 0.00 0.00 0.00 3.41
773 777 2.200373 TAAGGGCTTTGCTTCCACTC 57.800 50.000 0.00 0.00 0.00 3.51
774 778 2.239400 GTTAAGGGCTTTGCTTCCACT 58.761 47.619 0.00 0.00 0.00 4.00
775 779 1.960689 TGTTAAGGGCTTTGCTTCCAC 59.039 47.619 0.00 0.00 0.00 4.02
776 780 2.364002 GTTGTTAAGGGCTTTGCTTCCA 59.636 45.455 0.00 0.00 0.00 3.53
777 781 2.364002 TGTTGTTAAGGGCTTTGCTTCC 59.636 45.455 0.00 0.00 0.00 3.46
778 782 3.726291 TGTTGTTAAGGGCTTTGCTTC 57.274 42.857 0.00 0.00 0.00 3.86
779 783 3.640967 TCATGTTGTTAAGGGCTTTGCTT 59.359 39.130 0.00 0.00 0.00 3.91
780 784 3.230134 TCATGTTGTTAAGGGCTTTGCT 58.770 40.909 0.00 0.00 0.00 3.91
781 785 3.658757 TCATGTTGTTAAGGGCTTTGC 57.341 42.857 0.00 0.00 0.00 3.68
782 786 5.409214 CCATTTCATGTTGTTAAGGGCTTTG 59.591 40.000 0.00 0.00 0.00 2.77
783 787 5.550290 CCATTTCATGTTGTTAAGGGCTTT 58.450 37.500 0.00 0.00 0.00 3.51
784 788 4.563374 GCCATTTCATGTTGTTAAGGGCTT 60.563 41.667 0.00 0.00 42.43 4.35
785 789 3.055891 GCCATTTCATGTTGTTAAGGGCT 60.056 43.478 0.00 0.00 42.43 5.19
786 790 3.261580 GCCATTTCATGTTGTTAAGGGC 58.738 45.455 0.00 0.00 39.78 5.19
787 791 3.369366 GGGCCATTTCATGTTGTTAAGGG 60.369 47.826 4.39 0.00 0.00 3.95
788 792 3.260380 TGGGCCATTTCATGTTGTTAAGG 59.740 43.478 0.00 0.00 0.00 2.69
789 793 4.021192 AGTGGGCCATTTCATGTTGTTAAG 60.021 41.667 10.70 0.00 0.00 1.85
790 794 3.900601 AGTGGGCCATTTCATGTTGTTAA 59.099 39.130 10.70 0.00 0.00 2.01
791 795 3.505386 AGTGGGCCATTTCATGTTGTTA 58.495 40.909 10.70 0.00 0.00 2.41
792 796 2.299867 GAGTGGGCCATTTCATGTTGTT 59.700 45.455 10.70 0.00 0.00 2.83
793 797 1.895131 GAGTGGGCCATTTCATGTTGT 59.105 47.619 10.70 0.00 0.00 3.32
794 798 1.894466 TGAGTGGGCCATTTCATGTTG 59.106 47.619 10.70 0.00 0.00 3.33
795 799 2.299867 GTTGAGTGGGCCATTTCATGTT 59.700 45.455 20.09 0.00 0.00 2.71
796 800 1.895131 GTTGAGTGGGCCATTTCATGT 59.105 47.619 20.09 0.00 0.00 3.21
797 801 1.135315 CGTTGAGTGGGCCATTTCATG 60.135 52.381 20.09 13.75 0.00 3.07
798 802 1.176527 CGTTGAGTGGGCCATTTCAT 58.823 50.000 20.09 1.81 0.00 2.57
799 803 0.109532 TCGTTGAGTGGGCCATTTCA 59.890 50.000 10.70 14.62 0.00 2.69
800 804 1.401905 GATCGTTGAGTGGGCCATTTC 59.598 52.381 10.70 11.89 0.00 2.17
801 805 1.463674 GATCGTTGAGTGGGCCATTT 58.536 50.000 10.70 0.06 0.00 2.32
802 806 0.744414 CGATCGTTGAGTGGGCCATT 60.744 55.000 10.70 4.87 0.00 3.16
803 807 1.153369 CGATCGTTGAGTGGGCCAT 60.153 57.895 10.70 0.00 0.00 4.40
804 808 2.264480 CGATCGTTGAGTGGGCCA 59.736 61.111 0.00 0.00 0.00 5.36
805 809 3.195698 GCGATCGTTGAGTGGGCC 61.196 66.667 17.81 0.00 0.00 5.80
820 824 3.428797 CCATCTTGGGCTCATGCG 58.571 61.111 0.00 0.00 40.82 4.73
841 845 0.321298 CCCAATCCGTCGTTTGGACT 60.321 55.000 20.14 0.00 44.23 3.85
847 851 3.622060 CTGGGCCCAATCCGTCGTT 62.622 63.158 28.29 0.00 0.00 3.85
883 887 0.918619 CCCGTACAGTTATGTTCGCG 59.081 55.000 0.00 0.00 45.56 5.87
886 890 1.657094 CGTGCCCGTACAGTTATGTTC 59.343 52.381 0.00 0.00 41.01 3.18
1059 1460 3.691342 CGGTGGGGCGAAGAGACA 61.691 66.667 0.00 0.00 0.00 3.41
1732 2152 1.899437 TTGGCGGCGATCTTCTCCTT 61.899 55.000 12.98 0.00 0.00 3.36
1757 2177 6.481644 CCACCTGAATATCTTCTTCAAGTAGC 59.518 42.308 0.00 0.00 32.53 3.58
2175 2595 4.420168 GCGCCATACACATGTTACAAATT 58.580 39.130 0.00 0.00 0.00 1.82
2246 2666 4.676196 GCCAACATCAAGTTAGGCAATGAG 60.676 45.833 12.99 0.00 45.58 2.90
2471 2894 0.392998 CTGGGTCCTGGTTTGATCCG 60.393 60.000 0.00 0.00 35.66 4.18
2579 3002 9.492973 AGAAAATACAATGAAATCAAAACAGGG 57.507 29.630 0.00 0.00 0.00 4.45
2866 3293 3.392285 AGTCCCACCTAGGTTACGTTTTT 59.608 43.478 13.15 0.00 34.66 1.94
3059 3486 0.256752 TGGCTCCATGCAAGCTGTAT 59.743 50.000 15.38 0.00 45.15 2.29


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

AutoCloner maintained by Alex Coulton.