Multiple sequence alignment - TraesCS5A01G232000

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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 TraesCS5A01G232000 chr5A 100.000 2378 0 0 1 2378 447371012 447368635 0.000000e+00 4392
1 TraesCS5A01G232000 chr5A 98.718 78 0 1 564 640 638032904 638032981 1.150000e-28 137
2 TraesCS5A01G232000 chr5A 97.368 76 2 0 564 639 447370374 447370449 1.920000e-26 130
3 TraesCS5A01G232000 chr5A 97.403 77 1 1 564 639 638032980 638032904 1.920000e-26 130
4 TraesCS5A01G232000 chr5D 95.225 1487 48 7 893 2378 344691796 344693260 0.000000e+00 2331
5 TraesCS5A01G232000 chr5D 96.654 538 18 0 1 538 572707 573244 0.000000e+00 894
6 TraesCS5A01G232000 chr5D 94.118 255 8 2 638 891 344689889 344690137 4.800000e-102 381
7 TraesCS5A01G232000 chr5D 91.011 89 5 2 567 655 332506328 332506243 1.490000e-22 117
8 TraesCS5A01G232000 chr5B 90.704 1732 67 20 693 2378 407128455 407126772 0.000000e+00 2220
9 TraesCS5A01G232000 chr5B 94.521 73 3 1 638 709 407130990 407130918 6.950000e-21 111
10 TraesCS5A01G232000 chr7D 97.212 538 14 1 1 538 291509508 291508972 0.000000e+00 909
11 TraesCS5A01G232000 chr7D 96.654 538 18 0 1 538 198336986 198336449 0.000000e+00 894
12 TraesCS5A01G232000 chr3B 97.015 536 16 0 3 538 275341680 275341145 0.000000e+00 902
13 TraesCS5A01G232000 chr4D 96.654 538 18 0 1 538 323563534 323564071 0.000000e+00 894
14 TraesCS5A01G232000 chr4D 96.468 538 19 0 1 538 242938548 242938011 0.000000e+00 889
15 TraesCS5A01G232000 chr4D 96.468 538 19 0 1 538 295020153 295020690 0.000000e+00 889
16 TraesCS5A01G232000 chr1D 96.468 538 19 0 1 538 223524156 223523619 0.000000e+00 889
17 TraesCS5A01G232000 chr1D 96.468 538 19 0 1 538 288470790 288471327 0.000000e+00 889
18 TraesCS5A01G232000 chr1D 83.394 548 66 9 1368 1895 457876188 457876730 3.550000e-133 484
19 TraesCS5A01G232000 chr1A 81.555 553 65 17 1368 1895 550338940 550339480 2.830000e-114 422
20 TraesCS5A01G232000 chr1B 81.818 242 22 12 1368 1592 627943967 627944203 1.450000e-42 183
21 TraesCS5A01G232000 chr2D 95.294 85 3 1 564 648 642198791 642198708 1.480000e-27 134
22 TraesCS5A01G232000 chr2B 97.436 78 2 0 564 641 514348603 514348526 1.480000e-27 134
23 TraesCS5A01G232000 chr3D 96.203 79 2 1 563 640 458620848 458620770 6.900000e-26 128
24 TraesCS5A01G232000 chr2A 95.181 83 0 1 563 641 667018452 667018370 6.900000e-26 128
25 TraesCS5A01G232000 chr7B 92.941 85 5 1 556 640 372036644 372036727 3.210000e-24 122


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 TraesCS5A01G232000 chr5A 447368635 447371012 2377 True 4392.0 4392 100.0000 1 2378 1 chr5A.!!$R1 2377
1 TraesCS5A01G232000 chr5D 344689889 344693260 3371 False 1356.0 2331 94.6715 638 2378 2 chr5D.!!$F2 1740
2 TraesCS5A01G232000 chr5D 572707 573244 537 False 894.0 894 96.6540 1 538 1 chr5D.!!$F1 537
3 TraesCS5A01G232000 chr5B 407126772 407130990 4218 True 1165.5 2220 92.6125 638 2378 2 chr5B.!!$R1 1740
4 TraesCS5A01G232000 chr7D 291508972 291509508 536 True 909.0 909 97.2120 1 538 1 chr7D.!!$R2 537
5 TraesCS5A01G232000 chr7D 198336449 198336986 537 True 894.0 894 96.6540 1 538 1 chr7D.!!$R1 537
6 TraesCS5A01G232000 chr3B 275341145 275341680 535 True 902.0 902 97.0150 3 538 1 chr3B.!!$R1 535
7 TraesCS5A01G232000 chr4D 323563534 323564071 537 False 894.0 894 96.6540 1 538 1 chr4D.!!$F2 537
8 TraesCS5A01G232000 chr4D 242938011 242938548 537 True 889.0 889 96.4680 1 538 1 chr4D.!!$R1 537
9 TraesCS5A01G232000 chr4D 295020153 295020690 537 False 889.0 889 96.4680 1 538 1 chr4D.!!$F1 537
10 TraesCS5A01G232000 chr1D 223523619 223524156 537 True 889.0 889 96.4680 1 538 1 chr1D.!!$R1 537
11 TraesCS5A01G232000 chr1D 288470790 288471327 537 False 889.0 889 96.4680 1 538 1 chr1D.!!$F1 537
12 TraesCS5A01G232000 chr1D 457876188 457876730 542 False 484.0 484 83.3940 1368 1895 1 chr1D.!!$F2 527
13 TraesCS5A01G232000 chr1A 550338940 550339480 540 False 422.0 422 81.5550 1368 1895 1 chr1A.!!$F1 527

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
211 212 0.103715 ATACCCCCATCCTCCTGCAT 60.104 55.0 0.0 0.0 0.00 3.96 F
544 545 0.250234 TGCAGTCCTATCTGTGCCAC 59.750 55.0 0.0 0.0 37.70 5.01 F
1314 5460 0.173481 ACAGGGTGATGATGTCGTCG 59.827 55.0 0.0 0.0 34.69 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1169 5315 0.978385 CTTCGACTTCGTCTTGAGCG 59.022 55.000 0.00 0.00 40.80 5.03 R
1354 5500 1.669115 GCTTCTTCGGTGCAGCAGA 60.669 57.895 17.33 9.29 32.17 4.26 R
2147 6357 8.958119 ACAGCGAAGGAATAAATAAGAATGTA 57.042 30.769 0.00 0.00 0.00 2.29 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
34 35 3.187637 TGTTGTACATGTCGCCTTTTAGC 59.812 43.478 0.00 0.00 0.00 3.09
74 75 0.534203 ACAACATTGCGGGTCGAACT 60.534 50.000 0.00 0.00 0.00 3.01
123 124 2.936919 TTGTGGCACTCTCTTGTCAT 57.063 45.000 19.83 0.00 32.63 3.06
211 212 0.103715 ATACCCCCATCCTCCTGCAT 60.104 55.000 0.00 0.00 0.00 3.96
326 327 3.724716 CGCACATCATGTACTCGGTTTTG 60.725 47.826 0.00 0.00 0.00 2.44
335 336 4.624015 TGTACTCGGTTTTGGTTCTACTG 58.376 43.478 0.00 0.00 0.00 2.74
538 539 1.347050 CCCCTGATGCAGTCCTATCTG 59.653 57.143 0.00 0.00 38.35 2.90
539 540 2.045524 CCCTGATGCAGTCCTATCTGT 58.954 52.381 0.00 0.00 37.70 3.41
540 541 2.224233 CCCTGATGCAGTCCTATCTGTG 60.224 54.545 0.00 0.00 37.70 3.66
541 542 2.481854 CTGATGCAGTCCTATCTGTGC 58.518 52.381 0.00 0.00 37.70 4.57
542 543 1.139654 TGATGCAGTCCTATCTGTGCC 59.860 52.381 0.00 0.00 37.70 5.01
543 544 1.139654 GATGCAGTCCTATCTGTGCCA 59.860 52.381 0.00 0.00 37.70 4.92
544 545 0.250234 TGCAGTCCTATCTGTGCCAC 59.750 55.000 0.00 0.00 37.70 5.01
545 546 0.539051 GCAGTCCTATCTGTGCCACT 59.461 55.000 0.00 0.00 37.70 4.00
546 547 1.065854 GCAGTCCTATCTGTGCCACTT 60.066 52.381 0.00 0.00 37.70 3.16
547 548 2.625737 CAGTCCTATCTGTGCCACTTG 58.374 52.381 0.00 0.00 0.00 3.16
548 549 2.027745 CAGTCCTATCTGTGCCACTTGT 60.028 50.000 0.00 0.00 0.00 3.16
549 550 2.027745 AGTCCTATCTGTGCCACTTGTG 60.028 50.000 0.00 0.00 0.00 3.33
550 551 1.089920 CCTATCTGTGCCACTTGTGC 58.910 55.000 0.00 0.00 0.00 4.57
551 552 1.339438 CCTATCTGTGCCACTTGTGCT 60.339 52.381 0.00 0.00 0.00 4.40
552 553 2.430465 CTATCTGTGCCACTTGTGCTT 58.570 47.619 0.00 0.00 0.00 3.91
553 554 2.566833 ATCTGTGCCACTTGTGCTTA 57.433 45.000 0.00 0.00 0.00 3.09
554 555 1.882912 TCTGTGCCACTTGTGCTTAG 58.117 50.000 0.00 0.00 0.00 2.18
555 556 1.140852 TCTGTGCCACTTGTGCTTAGT 59.859 47.619 0.00 0.00 0.00 2.24
556 557 2.367241 TCTGTGCCACTTGTGCTTAGTA 59.633 45.455 0.00 0.00 0.00 1.82
557 558 3.138304 CTGTGCCACTTGTGCTTAGTAA 58.862 45.455 0.00 0.00 0.00 2.24
558 559 3.750371 TGTGCCACTTGTGCTTAGTAAT 58.250 40.909 0.00 0.00 0.00 1.89
559 560 4.141287 TGTGCCACTTGTGCTTAGTAATT 58.859 39.130 0.00 0.00 0.00 1.40
560 561 5.309638 TGTGCCACTTGTGCTTAGTAATTA 58.690 37.500 0.00 0.00 0.00 1.40
561 562 5.180492 TGTGCCACTTGTGCTTAGTAATTAC 59.820 40.000 7.57 7.57 0.00 1.89
562 563 4.698304 TGCCACTTGTGCTTAGTAATTACC 59.302 41.667 12.05 0.00 0.00 2.85
563 564 4.941873 GCCACTTGTGCTTAGTAATTACCT 59.058 41.667 12.05 2.84 0.00 3.08
564 565 6.110707 GCCACTTGTGCTTAGTAATTACCTA 58.889 40.000 12.05 1.93 0.00 3.08
565 566 6.036844 GCCACTTGTGCTTAGTAATTACCTAC 59.963 42.308 12.05 5.43 0.00 3.18
566 567 7.328737 CCACTTGTGCTTAGTAATTACCTACT 58.671 38.462 12.05 0.00 36.16 2.57
567 568 7.491696 CCACTTGTGCTTAGTAATTACCTACTC 59.508 40.741 12.05 2.21 34.03 2.59
568 569 7.491696 CACTTGTGCTTAGTAATTACCTACTCC 59.508 40.741 12.05 0.00 34.03 3.85
569 570 6.475596 TGTGCTTAGTAATTACCTACTCCC 57.524 41.667 12.05 0.00 34.03 4.30
570 571 6.200114 TGTGCTTAGTAATTACCTACTCCCT 58.800 40.000 12.05 0.00 34.03 4.20
571 572 6.323225 TGTGCTTAGTAATTACCTACTCCCTC 59.677 42.308 12.05 0.00 34.03 4.30
572 573 5.837438 TGCTTAGTAATTACCTACTCCCTCC 59.163 44.000 12.05 0.00 34.03 4.30
573 574 5.048154 GCTTAGTAATTACCTACTCCCTCCG 60.048 48.000 12.05 0.00 34.03 4.63
574 575 4.533001 AGTAATTACCTACTCCCTCCGT 57.467 45.455 12.05 0.00 0.00 4.69
575 576 4.468713 AGTAATTACCTACTCCCTCCGTC 58.531 47.826 12.05 0.00 0.00 4.79
576 577 2.378378 ATTACCTACTCCCTCCGTCC 57.622 55.000 0.00 0.00 0.00 4.79
577 578 0.259938 TTACCTACTCCCTCCGTCCC 59.740 60.000 0.00 0.00 0.00 4.46
578 579 0.920763 TACCTACTCCCTCCGTCCCA 60.921 60.000 0.00 0.00 0.00 4.37
579 580 1.001248 CCTACTCCCTCCGTCCCAA 59.999 63.158 0.00 0.00 0.00 4.12
580 581 0.616679 CCTACTCCCTCCGTCCCAAA 60.617 60.000 0.00 0.00 0.00 3.28
581 582 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
582 583 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
583 584 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
584 585 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
585 586 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
586 587 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
587 588 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
588 589 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
589 590 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
590 591 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
591 592 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
592 593 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
593 594 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
594 595 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
595 596 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
596 597 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
597 598 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
598 599 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
599 600 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
600 601 6.697019 CCCAAAATAAGTGACTCAACTTTGTG 59.303 38.462 0.00 0.00 40.77 3.33
601 602 7.257722 CCAAAATAAGTGACTCAACTTTGTGT 58.742 34.615 0.00 0.00 40.77 3.72
602 603 8.402472 CCAAAATAAGTGACTCAACTTTGTGTA 58.598 33.333 0.00 0.00 40.77 2.90
603 604 9.221775 CAAAATAAGTGACTCAACTTTGTGTAC 57.778 33.333 0.00 0.00 40.77 2.90
604 605 8.500753 AAATAAGTGACTCAACTTTGTGTACA 57.499 30.769 0.00 0.00 40.77 2.90
605 606 8.500753 AATAAGTGACTCAACTTTGTGTACAA 57.499 30.769 0.00 0.00 40.77 2.41
606 607 6.811253 AAGTGACTCAACTTTGTGTACAAA 57.189 33.333 9.56 9.56 42.90 2.83
618 619 6.811253 TTTGTGTACAAAGTTGAGTCACTT 57.189 33.333 6.11 0.00 40.55 3.16
619 620 7.908827 TTTGTGTACAAAGTTGAGTCACTTA 57.091 32.000 6.11 0.00 40.55 2.24
620 621 8.500753 TTTGTGTACAAAGTTGAGTCACTTAT 57.499 30.769 6.11 0.00 40.55 1.73
621 622 8.500753 TTGTGTACAAAGTTGAGTCACTTATT 57.499 30.769 0.00 0.00 35.87 1.40
622 623 8.500753 TGTGTACAAAGTTGAGTCACTTATTT 57.499 30.769 0.00 0.00 35.87 1.40
623 624 8.952278 TGTGTACAAAGTTGAGTCACTTATTTT 58.048 29.630 0.00 0.00 35.87 1.82
624 625 9.221775 GTGTACAAAGTTGAGTCACTTATTTTG 57.778 33.333 0.00 8.80 35.87 2.44
625 626 8.402472 TGTACAAAGTTGAGTCACTTATTTTGG 58.598 33.333 12.94 0.78 35.87 3.28
626 627 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
627 628 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
628 629 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
629 630 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
630 631 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
631 632 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
632 633 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
633 634 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
634 635 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
635 636 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
636 637 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
643 644 1.341383 TGGGACGGAGGGAGTACTAAC 60.341 57.143 0.00 0.00 0.00 2.34
651 652 5.131784 CGGAGGGAGTACTAACTAGTGAAT 58.868 45.833 0.00 0.00 35.56 2.57
779 3260 1.697432 ACTTGTGCTTAGCCACACCTA 59.303 47.619 0.29 0.00 44.72 3.08
798 3279 6.127026 ACACCTACTCCTTCCAAATCTGATAC 60.127 42.308 0.00 0.00 0.00 2.24
830 3311 0.252467 AGGGCTTGTCCAGTAGCTCT 60.252 55.000 0.00 0.00 43.26 4.09
831 3312 1.007238 AGGGCTTGTCCAGTAGCTCTA 59.993 52.381 0.00 0.00 46.09 2.43
832 3313 1.410882 GGGCTTGTCCAGTAGCTCTAG 59.589 57.143 0.00 0.00 34.98 2.43
833 3314 1.202475 GGCTTGTCCAGTAGCTCTAGC 60.202 57.143 0.00 0.00 37.54 3.42
834 3315 3.536166 GGCTTGTCCAGTAGCTCTAGCT 61.536 54.545 9.80 9.80 44.20 3.32
835 3316 5.350001 GGCTTGTCCAGTAGCTCTAGCTC 62.350 56.522 7.96 0.81 42.25 4.09
847 3328 2.546789 GCTCTAGCTCGTCCTCTTCTAC 59.453 54.545 0.00 0.00 38.21 2.59
891 3379 4.249661 CAGCAAGGAAGGTTAGAAGAGTC 58.750 47.826 0.00 0.00 0.00 3.36
919 5064 6.829985 TTCCTTCTGATCCATATTCCTTCA 57.170 37.500 0.00 0.00 0.00 3.02
1017 5163 1.092345 GCATGGAGCCCGAAGAGAAC 61.092 60.000 0.00 0.00 37.23 3.01
1026 5172 1.370064 CGAAGAGAACCCCAACCGT 59.630 57.895 0.00 0.00 0.00 4.83
1038 5184 3.687102 AACCGTCCGCCATCACGA 61.687 61.111 0.00 0.00 38.32 4.35
1083 5229 1.757118 GCACTATGGTCCTGCTACTCA 59.243 52.381 0.00 0.00 0.00 3.41
1169 5315 2.445453 GATCTCGTCGACTGTCTCAC 57.555 55.000 14.70 1.78 0.00 3.51
1266 5412 3.733960 CGGACTGTCGACGAGGCA 61.734 66.667 18.50 0.00 0.00 4.75
1314 5460 0.173481 ACAGGGTGATGATGTCGTCG 59.827 55.000 0.00 0.00 34.69 5.12
1334 5480 1.455383 CCGCCAAAGACTGCAGGTTT 61.455 55.000 19.93 14.15 0.00 3.27
1336 5482 1.600413 CGCCAAAGACTGCAGGTTTTC 60.600 52.381 19.93 6.29 0.00 2.29
1354 5500 2.273449 CTGCGCCTCCTCCCAAAT 59.727 61.111 4.18 0.00 0.00 2.32
1404 5550 0.958091 TTTGGTGCGCTGTGCTTATT 59.042 45.000 14.92 0.00 46.63 1.40
1566 5725 5.049818 GCTATGATGTTAGCTTTGTGCCTAG 60.050 44.000 0.00 0.00 44.23 3.02
1569 5728 4.455533 TGATGTTAGCTTTGTGCCTAGTTG 59.544 41.667 0.00 0.00 44.23 3.16
1600 5759 6.166984 TCAGGCATAAATGTTTTGGTTTGA 57.833 33.333 0.00 0.00 0.00 2.69
1767 5940 2.359230 GGCTGCAGACACCTGGAC 60.359 66.667 20.43 0.00 40.72 4.02
1886 6068 0.178981 ACACCTGGTTCTGCAAGCAT 60.179 50.000 0.00 0.00 39.29 3.79
1889 6071 2.041701 ACCTGGTTCTGCAAGCATTTT 58.958 42.857 0.00 0.00 39.29 1.82
2083 6293 9.262358 ACTTTAATTGAAGTAATCGCCTAGATC 57.738 33.333 13.51 0.00 38.06 2.75
2143 6353 5.473796 TTTCCGATCGTAATAAACAAGCC 57.526 39.130 15.09 0.00 0.00 4.35
2147 6357 6.460781 TCCGATCGTAATAAACAAGCCATAT 58.539 36.000 15.09 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.319911 GCTAAAAGGCGACATGTACAACAA 60.320 41.667 0.00 0.00 0.00 2.83
34 35 3.357079 GTGCTGAGTGTTGGCCGG 61.357 66.667 0.00 0.00 0.00 6.13
74 75 0.320421 GCAAGTTCTACAGGACGGCA 60.320 55.000 0.00 0.00 0.00 5.69
123 124 3.272574 CCAAGCTTCTGGCATTCTCTA 57.727 47.619 0.00 0.00 44.79 2.43
187 188 3.531059 CAGGAGGATGGGGGTATTGATA 58.469 50.000 0.00 0.00 0.00 2.15
211 212 4.887071 CCTTTCGATATTTGGGGTCAATGA 59.113 41.667 0.00 0.00 32.28 2.57
326 327 2.838813 AGGGTTTAGGCTCAGTAGAACC 59.161 50.000 0.00 0.00 36.64 3.62
335 336 2.943690 GGAATCGAAAGGGTTTAGGCTC 59.056 50.000 0.00 0.00 0.00 4.70
538 539 4.766404 AATTACTAAGCACAAGTGGCAC 57.234 40.909 10.29 10.29 0.00 5.01
539 540 4.698304 GGTAATTACTAAGCACAAGTGGCA 59.302 41.667 15.05 0.00 0.00 4.92
540 541 4.941873 AGGTAATTACTAAGCACAAGTGGC 59.058 41.667 15.05 0.00 0.00 5.01
541 542 7.328737 AGTAGGTAATTACTAAGCACAAGTGG 58.671 38.462 15.05 0.00 32.25 4.00
542 543 7.491696 GGAGTAGGTAATTACTAAGCACAAGTG 59.508 40.741 15.05 0.00 34.13 3.16
543 544 7.364497 GGGAGTAGGTAATTACTAAGCACAAGT 60.364 40.741 15.05 0.00 34.13 3.16
544 545 6.985059 GGGAGTAGGTAATTACTAAGCACAAG 59.015 42.308 15.05 0.00 34.13 3.16
545 546 6.670902 AGGGAGTAGGTAATTACTAAGCACAA 59.329 38.462 15.05 0.00 34.13 3.33
546 547 6.200114 AGGGAGTAGGTAATTACTAAGCACA 58.800 40.000 15.05 0.00 34.13 4.57
547 548 6.239261 GGAGGGAGTAGGTAATTACTAAGCAC 60.239 46.154 15.05 6.54 34.13 4.40
548 549 5.837438 GGAGGGAGTAGGTAATTACTAAGCA 59.163 44.000 15.05 0.00 34.13 3.91
549 550 5.048154 CGGAGGGAGTAGGTAATTACTAAGC 60.048 48.000 15.05 4.23 34.13 3.09
550 551 6.067350 ACGGAGGGAGTAGGTAATTACTAAG 58.933 44.000 15.05 0.00 34.13 2.18
551 552 6.018433 ACGGAGGGAGTAGGTAATTACTAA 57.982 41.667 15.05 1.37 34.13 2.24
552 553 5.456763 GGACGGAGGGAGTAGGTAATTACTA 60.457 48.000 15.05 3.61 34.13 1.82
553 554 4.468713 GACGGAGGGAGTAGGTAATTACT 58.531 47.826 15.05 4.51 36.61 2.24
554 555 3.571828 GGACGGAGGGAGTAGGTAATTAC 59.428 52.174 7.09 7.09 0.00 1.89
555 556 3.437052 GGGACGGAGGGAGTAGGTAATTA 60.437 52.174 0.00 0.00 0.00 1.40
556 557 2.675583 GGACGGAGGGAGTAGGTAATT 58.324 52.381 0.00 0.00 0.00 1.40
557 558 1.133231 GGGACGGAGGGAGTAGGTAAT 60.133 57.143 0.00 0.00 0.00 1.89
558 559 0.259938 GGGACGGAGGGAGTAGGTAA 59.740 60.000 0.00 0.00 0.00 2.85
559 560 0.920763 TGGGACGGAGGGAGTAGGTA 60.921 60.000 0.00 0.00 0.00 3.08
560 561 1.807771 TTGGGACGGAGGGAGTAGGT 61.808 60.000 0.00 0.00 0.00 3.08
561 562 0.616679 TTTGGGACGGAGGGAGTAGG 60.617 60.000 0.00 0.00 0.00 3.18
562 563 1.272807 TTTTGGGACGGAGGGAGTAG 58.727 55.000 0.00 0.00 0.00 2.57
563 564 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
564 565 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
565 566 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
566 567 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
567 568 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
568 569 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
569 570 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
570 571 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
571 572 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
572 573 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
573 574 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
574 575 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
575 576 6.697019 CACAAAGTTGAGTCACTTATTTTGGG 59.303 38.462 12.94 7.38 35.87 4.12
576 577 7.257722 ACACAAAGTTGAGTCACTTATTTTGG 58.742 34.615 12.94 6.99 35.87 3.28
577 578 9.221775 GTACACAAAGTTGAGTCACTTATTTTG 57.778 33.333 8.80 8.80 35.87 2.44
578 579 8.952278 TGTACACAAAGTTGAGTCACTTATTTT 58.048 29.630 0.00 0.00 35.87 1.82
579 580 8.500753 TGTACACAAAGTTGAGTCACTTATTT 57.499 30.769 0.00 0.00 35.87 1.40
580 581 8.500753 TTGTACACAAAGTTGAGTCACTTATT 57.499 30.769 0.00 0.00 35.87 1.40
581 582 8.500753 TTTGTACACAAAGTTGAGTCACTTAT 57.499 30.769 3.44 0.00 40.55 1.73
582 583 7.908827 TTTGTACACAAAGTTGAGTCACTTA 57.091 32.000 3.44 0.00 40.55 2.24
583 584 6.811253 TTTGTACACAAAGTTGAGTCACTT 57.189 33.333 3.44 0.00 40.55 3.16
595 596 6.811253 AAGTGACTCAACTTTGTACACAAA 57.189 33.333 7.28 7.28 42.90 2.83
596 597 8.500753 AATAAGTGACTCAACTTTGTACACAA 57.499 30.769 0.00 0.00 40.77 3.33
597 598 8.500753 AAATAAGTGACTCAACTTTGTACACA 57.499 30.769 0.00 0.00 40.77 3.72
598 599 9.221775 CAAAATAAGTGACTCAACTTTGTACAC 57.778 33.333 0.00 0.00 40.77 2.90
599 600 8.402472 CCAAAATAAGTGACTCAACTTTGTACA 58.598 33.333 0.00 0.00 40.77 2.90
600 601 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
601 602 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
602 603 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
603 604 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
604 605 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
605 606 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
606 607 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
607 608 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
608 609 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
609 610 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
610 611 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
611 612 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
612 613 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
613 614 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
614 615 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
615 616 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
616 617 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
617 618 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
618 619 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
619 620 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
620 621 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
621 622 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
622 623 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
623 624 1.002069 TTAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
624 625 1.064091 AGTTAGTACTCCCTCCGTCCC 60.064 57.143 0.00 0.00 0.00 4.46
625 626 2.433662 AGTTAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
626 627 3.876320 CACTAGTTAGTACTCCCTCCGTC 59.124 52.174 0.00 0.00 35.78 4.79
627 628 3.521126 TCACTAGTTAGTACTCCCTCCGT 59.479 47.826 0.00 0.00 35.78 4.69
628 629 4.148128 TCACTAGTTAGTACTCCCTCCG 57.852 50.000 0.00 0.00 35.78 4.63
629 630 6.367161 AGATTCACTAGTTAGTACTCCCTCC 58.633 44.000 0.00 0.00 35.78 4.30
630 631 7.339976 ACAAGATTCACTAGTTAGTACTCCCTC 59.660 40.741 0.00 0.00 35.78 4.30
631 632 7.122948 CACAAGATTCACTAGTTAGTACTCCCT 59.877 40.741 0.00 0.00 35.78 4.20
632 633 7.122353 TCACAAGATTCACTAGTTAGTACTCCC 59.878 40.741 0.00 0.00 35.78 4.30
633 634 8.053026 TCACAAGATTCACTAGTTAGTACTCC 57.947 38.462 0.00 0.00 35.78 3.85
634 635 8.948145 TCTCACAAGATTCACTAGTTAGTACTC 58.052 37.037 0.00 0.00 35.78 2.59
635 636 8.865420 TCTCACAAGATTCACTAGTTAGTACT 57.135 34.615 0.00 0.00 38.44 2.73
643 644 7.710044 AGCACATATTCTCACAAGATTCACTAG 59.290 37.037 0.00 0.00 0.00 2.57
651 652 7.559486 ACTATGAAGCACATATTCTCACAAGA 58.441 34.615 4.54 0.00 40.18 3.02
779 3260 5.130145 CAGAGGTATCAGATTTGGAAGGAGT 59.870 44.000 0.00 0.00 0.00 3.85
798 3279 3.690460 ACAAGCCCTATTTCAACAGAGG 58.310 45.455 0.00 0.00 0.00 3.69
830 3311 1.133853 GGGGTAGAAGAGGACGAGCTA 60.134 57.143 0.00 0.00 0.00 3.32
831 3312 0.396001 GGGGTAGAAGAGGACGAGCT 60.396 60.000 0.00 0.00 0.00 4.09
832 3313 0.683504 TGGGGTAGAAGAGGACGAGC 60.684 60.000 0.00 0.00 0.00 5.03
833 3314 1.751924 CTTGGGGTAGAAGAGGACGAG 59.248 57.143 0.00 0.00 0.00 4.18
834 3315 1.848652 CTTGGGGTAGAAGAGGACGA 58.151 55.000 0.00 0.00 0.00 4.20
835 3316 0.175989 GCTTGGGGTAGAAGAGGACG 59.824 60.000 0.00 0.00 0.00 4.79
847 3328 3.970410 TGGCACAGAGGCTTGGGG 61.970 66.667 0.00 0.00 44.55 4.96
891 3379 7.403671 AGGAATATGGATCAGAAGGAATGATG 58.596 38.462 0.00 0.00 37.52 3.07
919 5064 8.293699 AGAACCACAAGAAAAACAGAAATACT 57.706 30.769 0.00 0.00 0.00 2.12
1026 5172 2.678580 TCCAGTCGTGATGGCGGA 60.679 61.111 0.00 0.00 37.76 5.54
1038 5184 5.483685 TGAAGTACTTTATGCAGTCCAGT 57.516 39.130 10.02 0.00 0.00 4.00
1083 5229 0.994247 TCTGCATCTGGTGGAATGGT 59.006 50.000 0.00 0.00 0.00 3.55
1169 5315 0.978385 CTTCGACTTCGTCTTGAGCG 59.022 55.000 0.00 0.00 40.80 5.03
1187 5333 1.757405 GCATCTCCTCTACCTCTGCCT 60.757 57.143 0.00 0.00 0.00 4.75
1191 5337 3.499338 CATGAGCATCTCCTCTACCTCT 58.501 50.000 0.00 0.00 34.92 3.69
1314 5460 3.741476 CCTGCAGTCTTTGGCGGC 61.741 66.667 13.81 0.00 35.06 6.53
1336 5482 3.350031 ATTTGGGAGGAGGCGCAGG 62.350 63.158 10.83 0.00 32.08 4.85
1354 5500 1.669115 GCTTCTTCGGTGCAGCAGA 60.669 57.895 17.33 9.29 32.17 4.26
1404 5550 2.944349 GTTTGAACAAAGACCGGTGGTA 59.056 45.455 14.63 0.00 35.25 3.25
1559 5718 4.214332 GCCTGATAATAAGCAACTAGGCAC 59.786 45.833 0.00 0.00 46.53 5.01
1566 5725 9.533253 AAACATTTATGCCTGATAATAAGCAAC 57.467 29.630 0.00 0.00 38.99 4.17
1569 5728 8.981647 CCAAAACATTTATGCCTGATAATAAGC 58.018 33.333 0.00 0.00 0.00 3.09
1600 5759 2.645838 AATGAGAACACACCACAGCT 57.354 45.000 0.00 0.00 0.00 4.24
1767 5940 3.196469 TCTGTTGCCTCCATCAGTTCTAG 59.804 47.826 0.00 0.00 39.01 2.43
1889 6071 7.639113 ATTTTTCCTTGACAGTACACAGAAA 57.361 32.000 0.00 0.00 0.00 2.52
2020 6230 2.216940 CACTTGCATGTGAAAAACGCAG 59.783 45.455 24.41 0.00 42.42 5.18
2083 6293 4.294416 CTCTACTGGAGTGGATTGTACG 57.706 50.000 0.00 0.00 35.00 3.67
2147 6357 8.958119 ACAGCGAAGGAATAAATAAGAATGTA 57.042 30.769 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.