Multiple sequence alignment - TraesCS7D01G387800

Loading Multiple Alignment...

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 TraesCS7D01G387800 chr7D 100.000 2390 0 0 1 2390 501611033 501608644 0.000000e+00 4414
1 TraesCS7D01G387800 chr7D 87.620 727 54 20 641 1353 501778232 501777528 0.000000e+00 811
2 TraesCS7D01G387800 chr7D 88.584 692 33 28 676 1353 501599638 501600297 0.000000e+00 798
3 TraesCS7D01G387800 chr7D 83.704 675 51 23 1061 1707 501508940 501509583 1.230000e-162 582
4 TraesCS7D01G387800 chr7D 88.281 128 11 4 514 639 474659199 474659324 1.480000e-32 150
5 TraesCS7D01G387800 chr7D 87.879 132 10 4 514 640 481712008 481712138 1.480000e-32 150
6 TraesCS7D01G387800 chr7B 90.244 1107 62 23 640 1727 531222732 531221653 0.000000e+00 1404
7 TraesCS7D01G387800 chr7B 88.209 670 36 21 692 1353 531179841 531180475 0.000000e+00 760
8 TraesCS7D01G387800 chr7B 92.308 533 31 9 5 530 96400938 96400409 0.000000e+00 749
9 TraesCS7D01G387800 chr7B 92.678 519 32 6 1 518 9073399 9072886 0.000000e+00 743
10 TraesCS7D01G387800 chr7B 79.236 1074 119 47 704 1729 530869596 530870613 0.000000e+00 652
11 TraesCS7D01G387800 chr7B 89.697 495 32 14 1889 2375 531221503 531221020 4.370000e-172 614
12 TraesCS7D01G387800 chr7A 86.220 1045 64 32 640 1646 568696069 568695067 0.000000e+00 1059
13 TraesCS7D01G387800 chr7A 89.155 793 44 9 1629 2390 568695051 568694270 0.000000e+00 950
14 TraesCS7D01G387800 chr7A 85.809 754 41 27 640 1353 569112910 569112183 0.000000e+00 739
15 TraesCS7D01G387800 chr7A 92.514 521 30 7 1 519 720724536 720725049 0.000000e+00 737
16 TraesCS7D01G387800 chr7A 89.757 576 36 13 775 1337 568129599 568130164 0.000000e+00 715
17 TraesCS7D01G387800 chr7A 90.765 379 27 6 977 1353 568579793 568580165 1.280000e-137 499
18 TraesCS7D01G387800 chr7A 89.516 124 12 1 518 640 519767254 519767131 3.180000e-34 156
19 TraesCS7D01G387800 chr2B 93.204 515 29 6 6 518 707594590 707594080 0.000000e+00 752
20 TraesCS7D01G387800 chr4A 92.471 518 35 4 1 518 736715035 736714522 0.000000e+00 737
21 TraesCS7D01G387800 chr4A 89.781 137 12 2 514 649 615117061 615117196 8.780000e-40 174
22 TraesCS7D01G387800 chr1B 92.486 519 33 6 1 518 674073207 674072694 0.000000e+00 737
23 TraesCS7D01G387800 chr5D 92.352 523 30 7 1 520 550659613 550660128 0.000000e+00 736
24 TraesCS7D01G387800 chr5D 89.928 139 10 4 514 651 478455929 478456064 2.440000e-40 176
25 TraesCS7D01G387800 chr5D 89.231 130 12 2 514 642 315919046 315919174 6.840000e-36 161
26 TraesCS7D01G387800 chr5D 87.500 128 14 2 514 640 260691583 260691709 1.910000e-31 147
27 TraesCS7D01G387800 chr5B 92.308 520 34 6 1 516 19747865 19748382 0.000000e+00 734
28 TraesCS7D01G387800 chr6B 91.095 539 40 5 1 536 567937357 567936824 0.000000e+00 723
29 TraesCS7D01G387800 chr2D 89.313 131 11 3 514 643 375370904 375370776 6.840000e-36 161
30 TraesCS7D01G387800 chr6A 87.692 130 14 2 514 642 408979453 408979581 1.480000e-32 150


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 TraesCS7D01G387800 chr7D 501608644 501611033 2389 True 4414.0 4414 100.0000 1 2390 1 chr7D.!!$R1 2389
1 TraesCS7D01G387800 chr7D 501777528 501778232 704 True 811.0 811 87.6200 641 1353 1 chr7D.!!$R2 712
2 TraesCS7D01G387800 chr7D 501599638 501600297 659 False 798.0 798 88.5840 676 1353 1 chr7D.!!$F4 677
3 TraesCS7D01G387800 chr7D 501508940 501509583 643 False 582.0 582 83.7040 1061 1707 1 chr7D.!!$F3 646
4 TraesCS7D01G387800 chr7B 531221020 531222732 1712 True 1009.0 1404 89.9705 640 2375 2 chr7B.!!$R3 1735
5 TraesCS7D01G387800 chr7B 531179841 531180475 634 False 760.0 760 88.2090 692 1353 1 chr7B.!!$F2 661
6 TraesCS7D01G387800 chr7B 96400409 96400938 529 True 749.0 749 92.3080 5 530 1 chr7B.!!$R2 525
7 TraesCS7D01G387800 chr7B 9072886 9073399 513 True 743.0 743 92.6780 1 518 1 chr7B.!!$R1 517
8 TraesCS7D01G387800 chr7B 530869596 530870613 1017 False 652.0 652 79.2360 704 1729 1 chr7B.!!$F1 1025
9 TraesCS7D01G387800 chr7A 568694270 568696069 1799 True 1004.5 1059 87.6875 640 2390 2 chr7A.!!$R3 1750
10 TraesCS7D01G387800 chr7A 569112183 569112910 727 True 739.0 739 85.8090 640 1353 1 chr7A.!!$R2 713
11 TraesCS7D01G387800 chr7A 720724536 720725049 513 False 737.0 737 92.5140 1 519 1 chr7A.!!$F3 518
12 TraesCS7D01G387800 chr7A 568129599 568130164 565 False 715.0 715 89.7570 775 1337 1 chr7A.!!$F1 562
13 TraesCS7D01G387800 chr2B 707594080 707594590 510 True 752.0 752 93.2040 6 518 1 chr2B.!!$R1 512
14 TraesCS7D01G387800 chr4A 736714522 736715035 513 True 737.0 737 92.4710 1 518 1 chr4A.!!$R1 517
15 TraesCS7D01G387800 chr1B 674072694 674073207 513 True 737.0 737 92.4860 1 518 1 chr1B.!!$R1 517
16 TraesCS7D01G387800 chr5D 550659613 550660128 515 False 736.0 736 92.3520 1 520 1 chr5D.!!$F4 519
17 TraesCS7D01G387800 chr5B 19747865 19748382 517 False 734.0 734 92.3080 1 516 1 chr5B.!!$F1 515
18 TraesCS7D01G387800 chr6B 567936824 567937357 533 True 723.0 723 91.0950 1 536 1 chr6B.!!$R1 535

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
673 696 0.735632 CCGCAGCAACAGAGAGAGAC 60.736 60.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 2003 0.319986 GGGAGAGCGGCTAATACTGC 60.32 60.0 0.6 0.35 42.55 4.4 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
265 269 4.108570 ACAGGGACCAATACCTATGACAA 58.891 43.478 0.00 0.00 36.81 3.18
310 314 4.410400 GGGGCGCAAGTACCTGCT 62.410 66.667 14.30 0.00 40.33 4.24
519 542 2.094417 GCACGAGCCTTTTTGCTAGTAG 59.906 50.000 0.00 0.00 43.98 2.57
520 543 2.094417 CACGAGCCTTTTTGCTAGTAGC 59.906 50.000 15.56 15.56 43.98 3.58
522 545 2.678190 CGAGCCTTTTTGCTAGTAGCCT 60.678 50.000 19.41 7.09 42.95 4.58
541 564 9.799106 AGTAGCCTAATAAATGAAGTATTGCAT 57.201 29.630 0.00 0.00 0.00 3.96
542 565 9.831737 GTAGCCTAATAAATGAAGTATTGCATG 57.168 33.333 0.00 0.00 0.00 4.06
543 566 8.469309 AGCCTAATAAATGAAGTATTGCATGT 57.531 30.769 0.00 0.00 0.00 3.21
544 567 8.917088 AGCCTAATAAATGAAGTATTGCATGTT 58.083 29.630 0.00 0.00 0.00 2.71
549 572 9.520204 AATAAATGAAGTATTGCATGTTAGCAC 57.480 29.630 0.00 0.00 45.61 4.40
550 573 6.513806 AATGAAGTATTGCATGTTAGCACA 57.486 33.333 0.00 0.00 45.61 4.57
551 574 6.704289 ATGAAGTATTGCATGTTAGCACAT 57.296 33.333 0.00 0.00 45.61 3.21
552 575 7.806409 ATGAAGTATTGCATGTTAGCACATA 57.194 32.000 0.00 0.00 45.61 2.29
553 576 7.806409 TGAAGTATTGCATGTTAGCACATAT 57.194 32.000 0.00 0.00 45.61 1.78
554 577 8.900983 TGAAGTATTGCATGTTAGCACATATA 57.099 30.769 0.00 0.00 45.61 0.86
555 578 9.506018 TGAAGTATTGCATGTTAGCACATATAT 57.494 29.630 0.00 0.00 45.61 0.86
567 590 9.850628 TGTTAGCACATATATATTACTTCCGAC 57.149 33.333 0.00 0.00 0.00 4.79
568 591 9.007252 GTTAGCACATATATATTACTTCCGACG 57.993 37.037 0.00 0.00 0.00 5.12
569 592 7.387119 AGCACATATATATTACTTCCGACGA 57.613 36.000 0.00 0.00 0.00 4.20
570 593 7.997482 AGCACATATATATTACTTCCGACGAT 58.003 34.615 0.00 0.00 0.00 3.73
571 594 9.117183 AGCACATATATATTACTTCCGACGATA 57.883 33.333 0.00 0.00 0.00 2.92
572 595 9.383462 GCACATATATATTACTTCCGACGATAG 57.617 37.037 0.00 0.00 46.19 2.08
578 601 7.846644 ATATTACTTCCGACGATAGAGGTAG 57.153 40.000 0.00 0.00 39.28 3.18
579 602 3.557228 ACTTCCGACGATAGAGGTAGT 57.443 47.619 0.00 0.00 40.60 2.73
580 603 4.679373 ACTTCCGACGATAGAGGTAGTA 57.321 45.455 0.00 0.00 42.24 1.82
581 604 5.028549 ACTTCCGACGATAGAGGTAGTAA 57.971 43.478 0.00 0.00 42.24 2.24
582 605 4.813697 ACTTCCGACGATAGAGGTAGTAAC 59.186 45.833 0.00 0.00 42.24 2.50
583 606 4.406648 TCCGACGATAGAGGTAGTAACA 57.593 45.455 0.00 0.00 38.27 2.41
584 607 4.965814 TCCGACGATAGAGGTAGTAACAT 58.034 43.478 0.00 0.00 38.27 2.71
585 608 6.101650 TCCGACGATAGAGGTAGTAACATA 57.898 41.667 0.00 0.00 38.27 2.29
586 609 6.162079 TCCGACGATAGAGGTAGTAACATAG 58.838 44.000 0.00 0.00 38.27 2.23
587 610 5.350914 CCGACGATAGAGGTAGTAACATAGG 59.649 48.000 0.00 0.00 41.38 2.57
588 611 5.163874 CGACGATAGAGGTAGTAACATAGGC 60.164 48.000 0.00 0.00 41.38 3.93
589 612 5.878627 ACGATAGAGGTAGTAACATAGGCT 58.121 41.667 0.00 0.00 41.38 4.58
590 613 7.013823 ACGATAGAGGTAGTAACATAGGCTA 57.986 40.000 0.00 0.00 41.38 3.93
591 614 7.104939 ACGATAGAGGTAGTAACATAGGCTAG 58.895 42.308 0.00 0.00 41.38 3.42
592 615 7.104939 CGATAGAGGTAGTAACATAGGCTAGT 58.895 42.308 0.00 0.00 39.76 2.57
593 616 8.256605 CGATAGAGGTAGTAACATAGGCTAGTA 58.743 40.741 0.00 0.00 39.76 1.82
594 617 9.956640 GATAGAGGTAGTAACATAGGCTAGTAA 57.043 37.037 0.00 0.00 0.00 2.24
595 618 9.737844 ATAGAGGTAGTAACATAGGCTAGTAAC 57.262 37.037 0.00 0.00 0.00 2.50
596 619 7.580910 AGAGGTAGTAACATAGGCTAGTAACA 58.419 38.462 0.00 0.00 0.00 2.41
597 620 8.226112 AGAGGTAGTAACATAGGCTAGTAACAT 58.774 37.037 0.00 0.00 0.00 2.71
598 621 8.179509 AGGTAGTAACATAGGCTAGTAACATG 57.820 38.462 0.00 0.00 0.00 3.21
599 622 7.232941 AGGTAGTAACATAGGCTAGTAACATGG 59.767 40.741 0.00 0.00 0.00 3.66
600 623 7.232127 GGTAGTAACATAGGCTAGTAACATGGA 59.768 40.741 0.00 0.00 0.00 3.41
601 624 7.052142 AGTAACATAGGCTAGTAACATGGAC 57.948 40.000 0.00 0.00 0.00 4.02
602 625 5.950544 AACATAGGCTAGTAACATGGACA 57.049 39.130 0.00 0.00 0.00 4.02
603 626 6.500589 AACATAGGCTAGTAACATGGACAT 57.499 37.500 0.00 0.00 0.00 3.06
604 627 5.858381 ACATAGGCTAGTAACATGGACATG 58.142 41.667 10.57 10.57 44.15 3.21
620 643 8.809159 CATGGACATGTTCTAGTCTATGTTAG 57.191 38.462 5.55 0.00 44.07 2.34
621 644 7.956328 TGGACATGTTCTAGTCTATGTTAGT 57.044 36.000 5.55 0.00 34.18 2.24
622 645 9.642343 ATGGACATGTTCTAGTCTATGTTAGTA 57.358 33.333 5.55 0.00 35.10 1.82
623 646 8.900781 TGGACATGTTCTAGTCTATGTTAGTAC 58.099 37.037 5.55 0.00 34.18 2.73
624 647 8.351461 GGACATGTTCTAGTCTATGTTAGTACC 58.649 40.741 0.00 0.00 34.18 3.34
625 648 8.235359 ACATGTTCTAGTCTATGTTAGTACCC 57.765 38.462 0.00 0.00 30.05 3.69
626 649 7.837689 ACATGTTCTAGTCTATGTTAGTACCCA 59.162 37.037 0.00 0.00 30.05 4.51
627 650 8.861086 CATGTTCTAGTCTATGTTAGTACCCAT 58.139 37.037 0.00 0.00 0.00 4.00
628 651 8.834004 TGTTCTAGTCTATGTTAGTACCCATT 57.166 34.615 0.00 0.00 0.00 3.16
629 652 8.692710 TGTTCTAGTCTATGTTAGTACCCATTG 58.307 37.037 0.00 0.00 0.00 2.82
630 653 8.693625 GTTCTAGTCTATGTTAGTACCCATTGT 58.306 37.037 0.00 0.00 0.00 2.71
631 654 8.234136 TCTAGTCTATGTTAGTACCCATTGTG 57.766 38.462 0.00 0.00 0.00 3.33
632 655 6.235231 AGTCTATGTTAGTACCCATTGTGG 57.765 41.667 0.00 0.00 37.25 4.17
633 656 4.814771 GTCTATGTTAGTACCCATTGTGGC 59.185 45.833 0.00 0.00 35.79 5.01
634 657 4.719773 TCTATGTTAGTACCCATTGTGGCT 59.280 41.667 0.00 0.00 35.79 4.75
635 658 5.900699 TCTATGTTAGTACCCATTGTGGCTA 59.099 40.000 0.00 0.00 35.79 3.93
636 659 4.481368 TGTTAGTACCCATTGTGGCTAG 57.519 45.455 0.00 0.00 35.79 3.42
637 660 3.841845 TGTTAGTACCCATTGTGGCTAGT 59.158 43.478 0.00 0.00 35.79 2.57
638 661 4.081309 TGTTAGTACCCATTGTGGCTAGTC 60.081 45.833 0.00 0.00 35.79 2.59
642 665 4.781087 AGTACCCATTGTGGCTAGTCTTAA 59.219 41.667 0.00 0.00 35.79 1.85
667 690 4.099170 GCAGCCGCAGCAACAGAG 62.099 66.667 2.39 0.00 43.56 3.35
669 692 2.047465 AGCCGCAGCAACAGAGAG 60.047 61.111 0.00 0.00 43.56 3.20
670 693 2.047844 GCCGCAGCAACAGAGAGA 60.048 61.111 0.00 0.00 39.53 3.10
671 694 2.099431 GCCGCAGCAACAGAGAGAG 61.099 63.158 0.00 0.00 39.53 3.20
672 695 1.588597 CCGCAGCAACAGAGAGAGA 59.411 57.895 0.00 0.00 0.00 3.10
673 696 0.735632 CCGCAGCAACAGAGAGAGAC 60.736 60.000 0.00 0.00 0.00 3.36
688 721 3.299977 GACCGCCAAACCCAACCC 61.300 66.667 0.00 0.00 0.00 4.11
811 876 1.414181 CCGCTCTCTCTCTCTCTCTCT 59.586 57.143 0.00 0.00 0.00 3.10
813 878 2.101415 CGCTCTCTCTCTCTCTCTCTCA 59.899 54.545 0.00 0.00 0.00 3.27
814 879 3.462021 GCTCTCTCTCTCTCTCTCTCAC 58.538 54.545 0.00 0.00 0.00 3.51
815 880 3.118629 GCTCTCTCTCTCTCTCTCTCACA 60.119 52.174 0.00 0.00 0.00 3.58
913 992 2.032549 CAGAACAAGCGAGAAACCACTG 60.033 50.000 0.00 0.00 0.00 3.66
975 1105 2.042433 AGATAAGAGGGAGAGGGATCGG 59.958 54.545 0.00 0.00 0.00 4.18
1011 1141 2.608623 TCCTTCATCATGAGGCCGATA 58.391 47.619 1.57 0.00 0.00 2.92
1351 1493 3.276091 CTGTTGCCGTGAACGCCA 61.276 61.111 0.00 0.00 38.18 5.69
1357 1499 4.657824 CCGTGAACGCCACCGACT 62.658 66.667 0.00 0.00 42.76 4.18
1512 1701 7.067615 CAGAGAAGATAGAGCTGTAGTGGTTTA 59.932 40.741 0.00 0.00 0.00 2.01
1523 1712 3.560896 TGTAGTGGTTTACGTTTCTTGGC 59.439 43.478 0.00 0.00 0.00 4.52
1585 1774 3.521560 GGCGTATGTTGAGATCTGTGAA 58.478 45.455 0.00 0.00 0.00 3.18
1617 1806 2.766345 TGGAATTTTGGCTTGCATCC 57.234 45.000 0.00 0.00 0.00 3.51
1664 1886 1.152881 GGCTGCTCCCCAATTCGAT 60.153 57.895 0.00 0.00 0.00 3.59
1665 1887 0.753111 GGCTGCTCCCCAATTCGATT 60.753 55.000 0.00 0.00 0.00 3.34
1666 1888 1.106285 GCTGCTCCCCAATTCGATTT 58.894 50.000 0.00 0.00 0.00 2.17
1667 1889 1.202336 GCTGCTCCCCAATTCGATTTG 60.202 52.381 12.10 12.10 0.00 2.32
1668 1890 2.368439 CTGCTCCCCAATTCGATTTGA 58.632 47.619 19.02 1.59 0.00 2.69
1680 1902 6.529125 CCAATTCGATTTGATTTCCACTTGAG 59.471 38.462 19.02 0.00 0.00 3.02
1686 1908 7.174772 TCGATTTGATTTCCACTTGAGATTTCA 59.825 33.333 0.00 0.00 0.00 2.69
1756 2003 2.480419 GGAAGTTTCACCGTGAGTCATG 59.520 50.000 5.28 5.28 0.00 3.07
1760 2007 0.392706 TTCACCGTGAGTCATGCAGT 59.607 50.000 6.84 0.00 0.00 4.40
1765 2012 3.798878 CACCGTGAGTCATGCAGTATTAG 59.201 47.826 6.84 0.00 0.00 1.73
1832 2083 0.388134 GTGCGAAGTGACGGAGCTTA 60.388 55.000 0.00 0.00 33.91 3.09
1835 2093 1.897641 CGAAGTGACGGAGCTTACTC 58.102 55.000 0.00 0.00 42.66 2.59
1860 2118 1.041437 CCCCGGGCAAACTTTTAACA 58.959 50.000 17.73 0.00 0.00 2.41
1870 2128 6.705825 GGGCAAACTTTTAACATGATTGTTCT 59.294 34.615 0.00 0.00 42.43 3.01
1871 2129 7.870445 GGGCAAACTTTTAACATGATTGTTCTA 59.130 33.333 0.00 0.00 42.43 2.10
1872 2130 8.915654 GGCAAACTTTTAACATGATTGTTCTAG 58.084 33.333 0.00 0.00 42.43 2.43
1883 2141 6.591834 ACATGATTGTTCTAGTAGACTGCAAC 59.408 38.462 0.00 0.00 29.55 4.17
1887 2145 3.254892 GTTCTAGTAGACTGCAACTGCC 58.745 50.000 0.00 0.00 41.18 4.85
1966 2231 2.124903 CGTACACAGTGAAAACGAGCT 58.875 47.619 7.81 0.00 35.66 4.09
2006 2271 3.514309 ACGAGTATAGGATTACATGGGGC 59.486 47.826 0.00 0.00 0.00 5.80
2305 2576 4.995487 AGTGGAAGTACGAATTTTCTCACC 59.005 41.667 0.00 0.00 0.00 4.02
2337 2608 4.799715 TCCTGGTCTCCCTTTGTTTTTA 57.200 40.909 0.00 0.00 0.00 1.52
2348 2619 4.494484 CCTTTGTTTTTAGGGCATGCTAC 58.506 43.478 18.92 11.20 0.00 3.58
2376 2648 7.661437 TCTCATACACCTATAATTGTTGCATCC 59.339 37.037 0.00 0.00 0.00 3.51
2377 2649 7.517320 TCATACACCTATAATTGTTGCATCCT 58.483 34.615 0.00 0.00 0.00 3.24
2378 2650 7.998383 TCATACACCTATAATTGTTGCATCCTT 59.002 33.333 0.00 0.00 0.00 3.36
2385 2657 2.198827 TTGTTGCATCCTTGGTCGAT 57.801 45.000 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 12 8.523915 TTTCTAGTCATGCATGTCCATATTTT 57.476 30.769 25.43 5.80 0.00 1.82
16 18 7.067372 CCTTTTATTTCTAGTCATGCATGTCCA 59.933 37.037 25.43 9.16 0.00 4.02
265 269 8.523915 TTTCATCACTATTTCTTGCCATACAT 57.476 30.769 0.00 0.00 0.00 2.29
493 516 0.248458 CAAAAAGGCTCGTGCGTTGT 60.248 50.000 16.94 9.73 45.11 3.32
503 526 4.569719 TTAGGCTACTAGCAAAAAGGCT 57.430 40.909 10.27 9.53 44.75 4.58
541 564 9.850628 GTCGGAAGTAATATATATGTGCTAACA 57.149 33.333 0.00 0.00 41.58 2.41
542 565 9.007252 CGTCGGAAGTAATATATATGTGCTAAC 57.993 37.037 0.00 0.00 0.00 2.34
543 566 8.949177 TCGTCGGAAGTAATATATATGTGCTAA 58.051 33.333 0.00 0.00 0.00 3.09
544 567 8.496707 TCGTCGGAAGTAATATATATGTGCTA 57.503 34.615 0.00 0.00 0.00 3.49
545 568 7.387119 TCGTCGGAAGTAATATATATGTGCT 57.613 36.000 0.00 0.00 0.00 4.40
546 569 9.383462 CTATCGTCGGAAGTAATATATATGTGC 57.617 37.037 0.00 0.00 0.00 4.57
552 575 9.545105 CTACCTCTATCGTCGGAAGTAATATAT 57.455 37.037 0.00 0.00 0.00 0.86
553 576 8.535335 ACTACCTCTATCGTCGGAAGTAATATA 58.465 37.037 0.00 0.00 0.00 0.86
554 577 7.393216 ACTACCTCTATCGTCGGAAGTAATAT 58.607 38.462 0.00 0.00 0.00 1.28
555 578 6.763355 ACTACCTCTATCGTCGGAAGTAATA 58.237 40.000 0.00 0.00 0.00 0.98
556 579 5.619220 ACTACCTCTATCGTCGGAAGTAAT 58.381 41.667 0.00 0.00 0.00 1.89
557 580 5.028549 ACTACCTCTATCGTCGGAAGTAA 57.971 43.478 0.00 0.00 0.00 2.24
558 581 4.679373 ACTACCTCTATCGTCGGAAGTA 57.321 45.455 0.00 0.00 0.00 2.24
559 582 3.557228 ACTACCTCTATCGTCGGAAGT 57.443 47.619 0.00 0.00 0.00 3.01
560 583 4.813161 TGTTACTACCTCTATCGTCGGAAG 59.187 45.833 0.00 0.00 0.00 3.46
561 584 4.769688 TGTTACTACCTCTATCGTCGGAA 58.230 43.478 0.00 0.00 0.00 4.30
562 585 4.406648 TGTTACTACCTCTATCGTCGGA 57.593 45.455 0.00 0.00 0.00 4.55
563 586 5.350914 CCTATGTTACTACCTCTATCGTCGG 59.649 48.000 0.00 0.00 0.00 4.79
564 587 5.163874 GCCTATGTTACTACCTCTATCGTCG 60.164 48.000 0.00 0.00 0.00 5.12
565 588 5.939296 AGCCTATGTTACTACCTCTATCGTC 59.061 44.000 0.00 0.00 0.00 4.20
566 589 5.878627 AGCCTATGTTACTACCTCTATCGT 58.121 41.667 0.00 0.00 0.00 3.73
567 590 7.104939 ACTAGCCTATGTTACTACCTCTATCG 58.895 42.308 0.00 0.00 0.00 2.92
568 591 9.956640 TTACTAGCCTATGTTACTACCTCTATC 57.043 37.037 0.00 0.00 0.00 2.08
569 592 9.737844 GTTACTAGCCTATGTTACTACCTCTAT 57.262 37.037 0.00 0.00 0.00 1.98
570 593 8.717717 TGTTACTAGCCTATGTTACTACCTCTA 58.282 37.037 0.00 0.00 0.00 2.43
571 594 7.580910 TGTTACTAGCCTATGTTACTACCTCT 58.419 38.462 0.00 0.00 0.00 3.69
572 595 7.814264 TGTTACTAGCCTATGTTACTACCTC 57.186 40.000 0.00 0.00 0.00 3.85
573 596 7.232941 CCATGTTACTAGCCTATGTTACTACCT 59.767 40.741 0.00 0.00 0.00 3.08
574 597 7.232127 TCCATGTTACTAGCCTATGTTACTACC 59.768 40.741 0.00 0.00 0.00 3.18
575 598 8.081025 GTCCATGTTACTAGCCTATGTTACTAC 58.919 40.741 0.00 0.00 0.00 2.73
576 599 7.781219 TGTCCATGTTACTAGCCTATGTTACTA 59.219 37.037 0.00 0.00 0.00 1.82
577 600 6.610020 TGTCCATGTTACTAGCCTATGTTACT 59.390 38.462 0.00 0.00 0.00 2.24
578 601 6.812998 TGTCCATGTTACTAGCCTATGTTAC 58.187 40.000 0.00 0.00 0.00 2.50
579 602 7.441836 CATGTCCATGTTACTAGCCTATGTTA 58.558 38.462 0.00 0.00 34.23 2.41
580 603 5.950544 TGTCCATGTTACTAGCCTATGTT 57.049 39.130 0.00 0.00 0.00 2.71
581 604 5.858381 CATGTCCATGTTACTAGCCTATGT 58.142 41.667 0.00 0.00 34.23 2.29
595 618 8.417106 ACTAACATAGACTAGAACATGTCCATG 58.583 37.037 0.00 5.74 44.15 3.66
596 619 8.540507 ACTAACATAGACTAGAACATGTCCAT 57.459 34.615 0.00 0.00 34.02 3.41
597 620 7.956328 ACTAACATAGACTAGAACATGTCCA 57.044 36.000 0.00 0.00 34.02 4.02
598 621 8.351461 GGTACTAACATAGACTAGAACATGTCC 58.649 40.741 0.00 0.00 34.02 4.02
599 622 8.351461 GGGTACTAACATAGACTAGAACATGTC 58.649 40.741 0.00 0.00 31.40 3.06
600 623 7.837689 TGGGTACTAACATAGACTAGAACATGT 59.162 37.037 0.00 0.00 33.12 3.21
601 624 8.234136 TGGGTACTAACATAGACTAGAACATG 57.766 38.462 0.00 0.00 0.00 3.21
602 625 9.435570 AATGGGTACTAACATAGACTAGAACAT 57.564 33.333 0.00 0.00 0.00 2.71
603 626 8.692710 CAATGGGTACTAACATAGACTAGAACA 58.307 37.037 0.00 0.00 0.00 3.18
604 627 8.693625 ACAATGGGTACTAACATAGACTAGAAC 58.306 37.037 0.00 0.00 0.00 3.01
605 628 8.692710 CACAATGGGTACTAACATAGACTAGAA 58.307 37.037 0.00 0.00 0.00 2.10
606 629 7.287005 CCACAATGGGTACTAACATAGACTAGA 59.713 40.741 0.00 0.00 32.67 2.43
607 630 7.434492 CCACAATGGGTACTAACATAGACTAG 58.566 42.308 0.00 0.00 32.67 2.57
608 631 6.183360 GCCACAATGGGTACTAACATAGACTA 60.183 42.308 0.00 0.00 38.19 2.59
609 632 5.396436 GCCACAATGGGTACTAACATAGACT 60.396 44.000 0.00 0.00 38.19 3.24
610 633 4.814771 GCCACAATGGGTACTAACATAGAC 59.185 45.833 0.00 0.00 38.19 2.59
611 634 5.031066 GCCACAATGGGTACTAACATAGA 57.969 43.478 0.00 0.00 38.19 1.98
623 646 4.336433 CACATTAAGACTAGCCACAATGGG 59.664 45.833 10.62 4.82 38.19 4.00
624 647 4.201950 GCACATTAAGACTAGCCACAATGG 60.202 45.833 10.62 0.00 41.55 3.16
625 648 4.395854 TGCACATTAAGACTAGCCACAATG 59.604 41.667 0.00 0.00 0.00 2.82
626 649 4.588899 TGCACATTAAGACTAGCCACAAT 58.411 39.130 0.00 0.00 0.00 2.71
627 650 4.014569 TGCACATTAAGACTAGCCACAA 57.985 40.909 0.00 0.00 0.00 3.33
628 651 3.694043 TGCACATTAAGACTAGCCACA 57.306 42.857 0.00 0.00 0.00 4.17
629 652 3.242870 GCATGCACATTAAGACTAGCCAC 60.243 47.826 14.21 0.00 0.00 5.01
630 653 2.945008 GCATGCACATTAAGACTAGCCA 59.055 45.455 14.21 0.00 0.00 4.75
631 654 2.945008 TGCATGCACATTAAGACTAGCC 59.055 45.455 18.46 0.00 0.00 3.93
632 655 3.547613 GCTGCATGCACATTAAGACTAGC 60.548 47.826 18.46 10.39 42.31 3.42
633 656 3.003068 GGCTGCATGCACATTAAGACTAG 59.997 47.826 18.46 3.34 45.15 2.57
634 657 2.945008 GGCTGCATGCACATTAAGACTA 59.055 45.455 18.46 0.00 45.15 2.59
635 658 1.747355 GGCTGCATGCACATTAAGACT 59.253 47.619 18.46 0.00 45.15 3.24
636 659 1.532505 CGGCTGCATGCACATTAAGAC 60.533 52.381 18.46 7.27 45.15 3.01
637 660 0.734309 CGGCTGCATGCACATTAAGA 59.266 50.000 18.46 0.00 45.15 2.10
638 661 0.868602 GCGGCTGCATGCACATTAAG 60.869 55.000 18.46 7.18 45.15 1.85
667 690 1.072505 TTGGGTTTGGCGGTCTCTC 59.927 57.895 0.00 0.00 0.00 3.20
669 692 2.265904 GGTTGGGTTTGGCGGTCTC 61.266 63.158 0.00 0.00 0.00 3.36
670 693 2.203437 GGTTGGGTTTGGCGGTCT 60.203 61.111 0.00 0.00 0.00 3.85
671 694 3.299977 GGGTTGGGTTTGGCGGTC 61.300 66.667 0.00 0.00 0.00 4.79
672 695 3.680920 TTGGGTTGGGTTTGGCGGT 62.681 57.895 0.00 0.00 0.00 5.68
673 696 2.840102 TTGGGTTGGGTTTGGCGG 60.840 61.111 0.00 0.00 0.00 6.13
688 721 1.741525 CTGTTGCTGGGTTGGGTTG 59.258 57.895 0.00 0.00 0.00 3.77
770 827 3.573489 AAAAGAAACCGCGCGCTCG 62.573 57.895 30.48 21.00 39.07 5.03
771 828 1.792446 GAAAAGAAACCGCGCGCTC 60.792 57.895 30.48 19.71 0.00 5.03
772 829 2.251371 GAAAAGAAACCGCGCGCT 59.749 55.556 30.48 13.72 0.00 5.92
773 830 2.799502 GGAAAAGAAACCGCGCGC 60.800 61.111 27.36 23.91 0.00 6.86
913 992 2.125673 ATCTGTGGGCGTGCGTAC 60.126 61.111 0.00 0.00 0.00 3.67
975 1105 1.959042 AGGATGAATCACACGGATGC 58.041 50.000 0.00 0.00 36.02 3.91
1417 1566 1.211709 CAAAATTGGTCCCGCGGTC 59.788 57.895 26.12 16.49 0.00 4.79
1512 1701 0.600255 CTCACCTCGCCAAGAAACGT 60.600 55.000 0.00 0.00 0.00 3.99
1523 1712 4.803426 GCCGCTCACCTCACCTCG 62.803 72.222 0.00 0.00 0.00 4.63
1585 1774 3.508744 AAATTCCATTCGCTTTCGCAT 57.491 38.095 0.00 0.00 35.30 4.73
1664 1886 6.449698 GCTGAAATCTCAAGTGGAAATCAAA 58.550 36.000 0.00 0.00 0.00 2.69
1665 1887 5.335113 CGCTGAAATCTCAAGTGGAAATCAA 60.335 40.000 0.00 0.00 0.00 2.57
1666 1888 4.154737 CGCTGAAATCTCAAGTGGAAATCA 59.845 41.667 0.00 0.00 0.00 2.57
1667 1889 4.656041 CGCTGAAATCTCAAGTGGAAATC 58.344 43.478 0.00 0.00 0.00 2.17
1668 1890 3.119708 GCGCTGAAATCTCAAGTGGAAAT 60.120 43.478 0.00 0.00 0.00 2.17
1680 1902 2.405025 CCAAACGAAAAGCGCTGAAATC 59.595 45.455 12.58 6.29 46.04 2.17
1686 1908 1.358759 CACCCAAACGAAAAGCGCT 59.641 52.632 2.64 2.64 46.04 5.92
1756 2003 0.319986 GGGAGAGCGGCTAATACTGC 60.320 60.000 0.60 0.35 42.55 4.40
1760 2007 1.203187 AGGATGGGAGAGCGGCTAATA 60.203 52.381 0.60 0.00 0.00 0.98
1765 2012 2.447586 GATCAGGATGGGAGAGCGGC 62.448 65.000 0.00 0.00 36.16 6.53
1860 2118 6.815641 CAGTTGCAGTCTACTAGAACAATCAT 59.184 38.462 0.00 0.00 0.00 2.45
1870 2128 0.530744 CCGGCAGTTGCAGTCTACTA 59.469 55.000 6.43 0.00 44.36 1.82
1871 2129 1.293498 CCGGCAGTTGCAGTCTACT 59.707 57.895 6.43 0.00 44.36 2.57
1872 2130 0.602905 AACCGGCAGTTGCAGTCTAC 60.603 55.000 0.00 0.00 44.36 2.59
1883 2141 0.881118 AACATGCACTTAACCGGCAG 59.119 50.000 0.00 0.00 41.40 4.85
1887 2145 2.970609 CGTTTCAACATGCACTTAACCG 59.029 45.455 0.00 0.00 0.00 4.44
1929 2187 5.464057 TGTGTACGTTTCAACATAGACAAGG 59.536 40.000 0.00 0.00 29.75 3.61
1936 2194 6.905544 TTTCACTGTGTACGTTTCAACATA 57.094 33.333 7.79 0.00 0.00 2.29
1966 2231 8.876275 ATACTCGTTTTCACTGTGTACTTTTA 57.124 30.769 7.79 0.00 0.00 1.52
2185 2450 4.281688 TGTAAGAAAAGTACTACGTGCCCT 59.718 41.667 0.00 0.00 0.00 5.19
2279 2550 7.148623 GGTGAGAAAATTCGTACTTCCACTAAG 60.149 40.741 0.00 0.00 41.33 2.18
2282 2553 4.995487 GGTGAGAAAATTCGTACTTCCACT 59.005 41.667 0.00 0.00 0.00 4.00
2286 2557 8.073768 TGATTTTGGTGAGAAAATTCGTACTTC 58.926 33.333 0.00 0.00 36.00 3.01
2337 2608 3.041211 TGTATGAGAAGTAGCATGCCCT 58.959 45.455 15.66 7.97 0.00 5.19
2348 2619 8.437360 TGCAACAATTATAGGTGTATGAGAAG 57.563 34.615 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.