Multiple sequence alignment - TraesCS7A01G216800

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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 TraesCS7A01G216800 chr7A 100.000 2704 0 0 1 2704 183486721 183484018 0.000000e+00 4994.0
1 TraesCS7A01G216800 chr7A 83.916 572 69 13 1454 2017 182860103 182859547 2.380000e-145 525.0
2 TraesCS7A01G216800 chr7A 84.860 535 38 15 2110 2639 183310076 183309580 1.450000e-137 499.0
3 TraesCS7A01G216800 chr7A 85.556 450 43 11 1577 2017 183310991 183310555 4.110000e-123 451.0
4 TraesCS7A01G216800 chr7A 84.101 434 47 11 1588 2017 183657919 183657504 1.510000e-107 399.0
5 TraesCS7A01G216800 chr7A 85.757 337 39 8 2006 2338 182858652 182858321 5.540000e-92 348.0
6 TraesCS7A01G216800 chr7A 81.796 412 49 11 1456 1860 182722153 182721761 3.360000e-84 322.0
7 TraesCS7A01G216800 chr7A 84.146 328 45 5 2006 2331 183657232 183656910 7.270000e-81 311.0
8 TraesCS7A01G216800 chr7A 83.495 206 19 9 2400 2603 183656885 183656693 7.690000e-41 178.0
9 TraesCS7A01G216800 chr7A 79.459 185 25 8 918 1093 183648760 183648580 4.730000e-23 119.0
10 TraesCS7A01G216800 chr7D 96.659 1257 31 4 1457 2704 178942691 178941437 0.000000e+00 2078.0
11 TraesCS7A01G216800 chr7D 89.567 901 43 10 599 1459 178943612 178942723 0.000000e+00 1096.0
12 TraesCS7A01G216800 chr7D 89.844 512 36 9 1 504 161463640 161463137 0.000000e+00 643.0
13 TraesCS7A01G216800 chr7D 86.693 511 55 11 1 504 69534289 69533785 3.040000e-154 555.0
14 TraesCS7A01G216800 chr7D 83.255 639 57 21 2006 2639 178863101 178862508 2.370000e-150 542.0
15 TraesCS7A01G216800 chr7D 87.192 406 46 4 1462 1862 178703332 178702928 8.820000e-125 457.0
16 TraesCS7A01G216800 chr7D 82.685 514 69 11 1464 1968 179125701 179125199 3.200000e-119 438.0
17 TraesCS7A01G216800 chr7D 84.530 362 38 7 1620 1975 178863945 178863596 2.580000e-90 342.0
18 TraesCS7A01G216800 chr7D 83.912 317 38 9 2020 2331 179124752 179124444 9.470000e-75 291.0
19 TraesCS7A01G216800 chr7D 76.596 470 67 32 662 1114 178994884 178994441 4.530000e-53 219.0
20 TraesCS7A01G216800 chr7D 90.291 103 6 4 2400 2500 179124419 179124319 6.070000e-27 132.0
21 TraesCS7A01G216800 chr7B 95.687 1252 42 9 1459 2702 144815379 144814132 0.000000e+00 2002.0
22 TraesCS7A01G216800 chr7B 92.692 821 34 8 661 1459 144816233 144815417 0.000000e+00 1160.0
23 TraesCS7A01G216800 chr7B 80.757 977 104 50 906 1860 144709016 144708102 0.000000e+00 686.0
24 TraesCS7A01G216800 chr7B 84.752 564 62 16 1464 2017 145057585 145057036 6.580000e-151 544.0
25 TraesCS7A01G216800 chr7B 85.714 511 62 9 1 504 90800788 90800282 1.840000e-146 529.0
26 TraesCS7A01G216800 chr7B 84.439 437 50 8 1544 1975 144738627 144738204 5.390000e-112 414.0
27 TraesCS7A01G216800 chr7B 79.779 633 72 26 2013 2639 144737852 144737270 2.510000e-110 409.0
28 TraesCS7A01G216800 chr7B 84.228 298 39 6 2037 2331 145056426 145056134 1.580000e-72 283.0
29 TraesCS7A01G216800 chr7B 81.148 244 28 10 2400 2641 145056109 145055882 2.140000e-41 180.0
30 TraesCS7A01G216800 chr7B 81.172 239 27 13 1445 1666 145032617 145032380 2.770000e-40 176.0
31 TraesCS7A01G216800 chr7B 80.508 118 15 6 980 1093 145033214 145033101 1.730000e-12 84.2
32 TraesCS7A01G216800 chr1B 90.020 491 41 7 1 487 16854698 16855184 1.770000e-176 628.0
33 TraesCS7A01G216800 chr1B 88.350 515 46 11 1 507 642729892 642729384 8.280000e-170 606.0
34 TraesCS7A01G216800 chr1B 92.727 55 3 1 2648 2702 70183123 70183070 8.030000e-11 78.7
35 TraesCS7A01G216800 chr3D 87.695 512 48 10 1 504 559032456 559032960 1.400000e-162 582.0
36 TraesCS7A01G216800 chr4B 87.500 512 48 12 1 504 97383158 97382655 6.490000e-161 577.0
37 TraesCS7A01G216800 chr5B 87.354 514 49 12 1 504 41954494 41953987 2.330000e-160 575.0
38 TraesCS7A01G216800 chr4A 86.863 510 53 7 1 504 400735546 400735045 2.350000e-155 558.0


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 TraesCS7A01G216800 chr7A 183484018 183486721 2703 True 4994.000000 4994 100.000000 1 2704 1 chr7A.!!$R2 2703
1 TraesCS7A01G216800 chr7A 183309580 183310991 1411 True 475.000000 499 85.208000 1577 2639 2 chr7A.!!$R5 1062
2 TraesCS7A01G216800 chr7A 182858321 182860103 1782 True 436.500000 525 84.836500 1454 2338 2 chr7A.!!$R4 884
3 TraesCS7A01G216800 chr7A 183656693 183657919 1226 True 296.000000 399 83.914000 1588 2603 3 chr7A.!!$R6 1015
4 TraesCS7A01G216800 chr7D 178941437 178943612 2175 True 1587.000000 2078 93.113000 599 2704 2 chr7D.!!$R6 2105
5 TraesCS7A01G216800 chr7D 161463137 161463640 503 True 643.000000 643 89.844000 1 504 1 chr7D.!!$R2 503
6 TraesCS7A01G216800 chr7D 69533785 69534289 504 True 555.000000 555 86.693000 1 504 1 chr7D.!!$R1 503
7 TraesCS7A01G216800 chr7D 178862508 178863945 1437 True 442.000000 542 83.892500 1620 2639 2 chr7D.!!$R5 1019
8 TraesCS7A01G216800 chr7D 179124319 179125701 1382 True 287.000000 438 85.629333 1464 2500 3 chr7D.!!$R7 1036
9 TraesCS7A01G216800 chr7B 144814132 144816233 2101 True 1581.000000 2002 94.189500 661 2702 2 chr7B.!!$R4 2041
10 TraesCS7A01G216800 chr7B 144708102 144709016 914 True 686.000000 686 80.757000 906 1860 1 chr7B.!!$R2 954
11 TraesCS7A01G216800 chr7B 90800282 90800788 506 True 529.000000 529 85.714000 1 504 1 chr7B.!!$R1 503
12 TraesCS7A01G216800 chr7B 144737270 144738627 1357 True 411.500000 414 82.109000 1544 2639 2 chr7B.!!$R3 1095
13 TraesCS7A01G216800 chr7B 145055882 145057585 1703 True 335.666667 544 83.376000 1464 2641 3 chr7B.!!$R6 1177
14 TraesCS7A01G216800 chr1B 642729384 642729892 508 True 606.000000 606 88.350000 1 507 1 chr1B.!!$R2 506
15 TraesCS7A01G216800 chr3D 559032456 559032960 504 False 582.000000 582 87.695000 1 504 1 chr3D.!!$F1 503
16 TraesCS7A01G216800 chr4B 97382655 97383158 503 True 577.000000 577 87.500000 1 504 1 chr4B.!!$R1 503
17 TraesCS7A01G216800 chr5B 41953987 41954494 507 True 575.000000 575 87.354000 1 504 1 chr5B.!!$R1 503
18 TraesCS7A01G216800 chr4A 400735045 400735546 501 True 558.000000 558 86.863000 1 504 1 chr4A.!!$R1 503

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
554 566 0.179171 CAGGAGCGCATGAAAAGCTG 60.179 55.0 11.47 0.0 41.84 4.24 F
556 568 0.242017 GGAGCGCATGAAAAGCTGTT 59.758 50.0 11.47 0.0 41.84 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1823 0.037605 AAGCTTTGCAATGCTCAGCC 60.038 50.000 32.46 9.94 38.31 4.85 R
1739 1865 1.404851 CGAGCCCAGGAAGAGAAAGTC 60.405 57.143 0.00 0.00 0.00 3.01 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
88 90 6.219473 AGATGAATACTACAATCAGAAGGCG 58.781 40.000 0.00 0.00 0.00 5.52
97 99 0.246635 ATCAGAAGGCGCAGTTACGT 59.753 50.000 10.83 0.00 34.88 3.57
169 171 6.419791 TCCAATACTATGGTTTAACCCTGTG 58.580 40.000 12.02 2.71 41.46 3.66
337 341 6.774170 AGACATATCCTGCAATGCAATAAAGA 59.226 34.615 9.92 1.83 38.41 2.52
340 344 5.927281 ATCCTGCAATGCAATAAAGAGTT 57.073 34.783 9.92 0.00 38.41 3.01
363 367 8.490311 AGTTTTCTCAACCCAAATTTATGGAAA 58.510 29.630 11.77 8.11 43.54 3.13
365 369 7.610580 TTCTCAACCCAAATTTATGGAAACT 57.389 32.000 11.77 0.00 43.54 2.66
389 393 1.963515 ACACAGAAGGCCCATGAAAAC 59.036 47.619 0.00 0.00 0.00 2.43
390 394 1.962807 CACAGAAGGCCCATGAAAACA 59.037 47.619 0.00 0.00 0.00 2.83
391 395 2.364970 CACAGAAGGCCCATGAAAACAA 59.635 45.455 0.00 0.00 0.00 2.83
392 396 2.365293 ACAGAAGGCCCATGAAAACAAC 59.635 45.455 0.00 0.00 0.00 3.32
404 409 4.608948 TGAAAACAACAACAACAACCCT 57.391 36.364 0.00 0.00 0.00 4.34
504 516 1.840061 CGCGCGTATGCTTCTAGTG 59.160 57.895 24.19 0.00 39.65 2.74
507 519 1.759994 CGCGTATGCTTCTAGTGGAG 58.240 55.000 5.20 0.00 39.65 3.86
508 520 1.333931 CGCGTATGCTTCTAGTGGAGA 59.666 52.381 5.20 0.00 39.65 3.71
509 521 2.603412 CGCGTATGCTTCTAGTGGAGAG 60.603 54.545 5.20 0.00 39.65 3.20
510 522 2.359531 GCGTATGCTTCTAGTGGAGAGT 59.640 50.000 0.00 0.00 38.39 3.24
511 523 3.181485 GCGTATGCTTCTAGTGGAGAGTT 60.181 47.826 0.00 0.00 38.39 3.01
512 524 4.355437 CGTATGCTTCTAGTGGAGAGTTG 58.645 47.826 0.00 0.00 34.93 3.16
513 525 4.096532 CGTATGCTTCTAGTGGAGAGTTGA 59.903 45.833 0.00 0.00 34.93 3.18
514 526 5.393135 CGTATGCTTCTAGTGGAGAGTTGAA 60.393 44.000 0.00 0.00 34.93 2.69
515 527 4.955811 TGCTTCTAGTGGAGAGTTGAAA 57.044 40.909 0.00 0.00 34.93 2.69
516 528 4.632153 TGCTTCTAGTGGAGAGTTGAAAC 58.368 43.478 0.00 0.00 34.93 2.78
517 529 4.345257 TGCTTCTAGTGGAGAGTTGAAACT 59.655 41.667 0.00 0.00 43.16 2.66
518 530 5.163301 TGCTTCTAGTGGAGAGTTGAAACTT 60.163 40.000 0.00 0.00 39.88 2.66
519 531 5.178438 GCTTCTAGTGGAGAGTTGAAACTTG 59.822 44.000 0.00 0.00 39.88 3.16
520 532 5.215252 TCTAGTGGAGAGTTGAAACTTGG 57.785 43.478 0.00 0.00 39.88 3.61
521 533 3.933861 AGTGGAGAGTTGAAACTTGGT 57.066 42.857 0.00 0.00 39.88 3.67
522 534 3.545703 AGTGGAGAGTTGAAACTTGGTG 58.454 45.455 0.00 0.00 39.88 4.17
523 535 2.618709 GTGGAGAGTTGAAACTTGGTGG 59.381 50.000 0.00 0.00 39.88 4.61
524 536 2.507886 TGGAGAGTTGAAACTTGGTGGA 59.492 45.455 0.00 0.00 39.88 4.02
525 537 3.138283 TGGAGAGTTGAAACTTGGTGGAT 59.862 43.478 0.00 0.00 39.88 3.41
526 538 3.503748 GGAGAGTTGAAACTTGGTGGATG 59.496 47.826 0.00 0.00 39.88 3.51
527 539 2.887152 AGAGTTGAAACTTGGTGGATGC 59.113 45.455 0.00 0.00 39.88 3.91
528 540 2.622942 GAGTTGAAACTTGGTGGATGCA 59.377 45.455 0.00 0.00 39.88 3.96
529 541 2.624838 AGTTGAAACTTGGTGGATGCAG 59.375 45.455 0.00 0.00 35.21 4.41
530 542 2.362077 GTTGAAACTTGGTGGATGCAGT 59.638 45.455 0.00 0.00 0.00 4.40
531 543 2.229792 TGAAACTTGGTGGATGCAGTC 58.770 47.619 0.00 0.00 0.00 3.51
532 544 2.229792 GAAACTTGGTGGATGCAGTCA 58.770 47.619 0.00 0.00 0.00 3.41
533 545 2.592102 AACTTGGTGGATGCAGTCAT 57.408 45.000 0.00 0.00 35.17 3.06
534 546 1.830279 ACTTGGTGGATGCAGTCATG 58.170 50.000 0.00 0.00 31.96 3.07
550 562 4.077844 TGCAGGAGCGCATGAAAA 57.922 50.000 11.47 0.00 46.23 2.29
551 563 1.878070 TGCAGGAGCGCATGAAAAG 59.122 52.632 11.47 0.00 46.23 2.27
552 564 1.515736 GCAGGAGCGCATGAAAAGC 60.516 57.895 11.47 0.00 0.00 3.51
553 565 1.930908 GCAGGAGCGCATGAAAAGCT 61.931 55.000 11.47 0.37 44.80 3.74
554 566 0.179171 CAGGAGCGCATGAAAAGCTG 60.179 55.000 11.47 0.00 41.84 4.24
555 567 0.607489 AGGAGCGCATGAAAAGCTGT 60.607 50.000 11.47 0.00 41.84 4.40
556 568 0.242017 GGAGCGCATGAAAAGCTGTT 59.758 50.000 11.47 0.00 41.84 3.16
557 569 1.336240 GGAGCGCATGAAAAGCTGTTT 60.336 47.619 11.47 0.00 41.84 2.83
558 570 2.095263 GGAGCGCATGAAAAGCTGTTTA 60.095 45.455 11.47 0.00 41.84 2.01
559 571 2.911102 GAGCGCATGAAAAGCTGTTTAC 59.089 45.455 11.47 0.00 41.84 2.01
560 572 2.293122 AGCGCATGAAAAGCTGTTTACA 59.707 40.909 11.47 0.00 40.07 2.41
561 573 3.057315 AGCGCATGAAAAGCTGTTTACAT 60.057 39.130 11.47 0.00 40.07 2.29
562 574 3.059834 GCGCATGAAAAGCTGTTTACATG 59.940 43.478 12.07 12.07 37.06 3.21
563 575 4.475028 CGCATGAAAAGCTGTTTACATGA 58.525 39.130 18.15 0.00 36.59 3.07
564 576 4.321745 CGCATGAAAAGCTGTTTACATGAC 59.678 41.667 18.15 10.56 36.59 3.06
565 577 4.321745 GCATGAAAAGCTGTTTACATGACG 59.678 41.667 18.15 0.00 36.59 4.35
566 578 5.451908 CATGAAAAGCTGTTTACATGACGT 58.548 37.500 11.27 0.00 36.59 4.34
567 579 5.090652 TGAAAAGCTGTTTACATGACGTC 57.909 39.130 9.11 9.11 0.00 4.34
568 580 4.572795 TGAAAAGCTGTTTACATGACGTCA 59.427 37.500 22.48 22.48 0.00 4.35
569 581 5.238432 TGAAAAGCTGTTTACATGACGTCAT 59.762 36.000 25.18 25.18 36.96 3.06
570 582 5.689383 AAAGCTGTTTACATGACGTCATT 57.311 34.783 28.04 20.10 33.61 2.57
571 583 4.928661 AGCTGTTTACATGACGTCATTC 57.071 40.909 28.04 15.50 33.61 2.67
572 584 3.684788 AGCTGTTTACATGACGTCATTCC 59.315 43.478 28.04 13.96 33.61 3.01
573 585 3.181510 GCTGTTTACATGACGTCATTCCC 60.182 47.826 28.04 14.29 33.61 3.97
574 586 4.253685 CTGTTTACATGACGTCATTCCCT 58.746 43.478 28.04 13.07 33.61 4.20
575 587 5.408880 TGTTTACATGACGTCATTCCCTA 57.591 39.130 28.04 12.13 33.61 3.53
576 588 5.984725 TGTTTACATGACGTCATTCCCTAT 58.015 37.500 28.04 11.82 33.61 2.57
577 589 6.411376 TGTTTACATGACGTCATTCCCTATT 58.589 36.000 28.04 2.95 33.61 1.73
578 590 6.882140 TGTTTACATGACGTCATTCCCTATTT 59.118 34.615 28.04 2.14 33.61 1.40
579 591 7.392113 TGTTTACATGACGTCATTCCCTATTTT 59.608 33.333 28.04 1.32 33.61 1.82
580 592 7.931578 TTACATGACGTCATTCCCTATTTTT 57.068 32.000 28.04 0.74 33.61 1.94
581 593 6.436843 ACATGACGTCATTCCCTATTTTTC 57.563 37.500 28.04 0.00 33.61 2.29
582 594 6.180472 ACATGACGTCATTCCCTATTTTTCT 58.820 36.000 28.04 0.02 33.61 2.52
583 595 6.659242 ACATGACGTCATTCCCTATTTTTCTT 59.341 34.615 28.04 0.00 33.61 2.52
584 596 6.494893 TGACGTCATTCCCTATTTTTCTTG 57.505 37.500 15.76 0.00 0.00 3.02
585 597 6.001460 TGACGTCATTCCCTATTTTTCTTGT 58.999 36.000 15.76 0.00 0.00 3.16
586 598 6.072728 TGACGTCATTCCCTATTTTTCTTGTG 60.073 38.462 15.76 0.00 0.00 3.33
587 599 6.001460 ACGTCATTCCCTATTTTTCTTGTGA 58.999 36.000 0.00 0.00 0.00 3.58
588 600 6.659242 ACGTCATTCCCTATTTTTCTTGTGAT 59.341 34.615 0.00 0.00 0.00 3.06
589 601 6.968904 CGTCATTCCCTATTTTTCTTGTGATG 59.031 38.462 0.00 0.00 0.00 3.07
590 602 7.362056 CGTCATTCCCTATTTTTCTTGTGATGT 60.362 37.037 0.00 0.00 0.00 3.06
591 603 7.970614 GTCATTCCCTATTTTTCTTGTGATGTC 59.029 37.037 0.00 0.00 0.00 3.06
592 604 7.669304 TCATTCCCTATTTTTCTTGTGATGTCA 59.331 33.333 0.00 0.00 0.00 3.58
593 605 8.472413 CATTCCCTATTTTTCTTGTGATGTCAT 58.528 33.333 0.00 0.00 0.00 3.06
594 606 7.395190 TCCCTATTTTTCTTGTGATGTCATG 57.605 36.000 0.00 0.00 0.00 3.07
595 607 6.947733 TCCCTATTTTTCTTGTGATGTCATGT 59.052 34.615 0.00 0.00 0.00 3.21
596 608 8.106462 TCCCTATTTTTCTTGTGATGTCATGTA 58.894 33.333 0.00 0.00 0.00 2.29
597 609 8.184192 CCCTATTTTTCTTGTGATGTCATGTAC 58.816 37.037 0.00 0.00 0.00 2.90
637 649 1.161603 GGGAGGGGATTGGATTGGAT 58.838 55.000 0.00 0.00 0.00 3.41
676 706 2.513666 TCGGGATCAATGCACGCC 60.514 61.111 0.00 0.00 0.00 5.68
733 771 3.674906 CCGATCGAGGCTCTAGGG 58.325 66.667 18.66 3.83 0.00 3.53
734 772 2.631580 CCGATCGAGGCTCTAGGGC 61.632 68.421 18.66 5.86 41.20 5.19
805 843 3.120546 CGTCAGATGTTCGAACAAATGCT 60.121 43.478 32.69 22.95 43.03 3.79
1367 1443 2.573462 TCTGGTGCATTAGGCTCTCTTT 59.427 45.455 0.00 0.00 45.15 2.52
1428 1506 9.739276 CATACATTATTCCCCTTGCTTAATCTA 57.261 33.333 0.00 0.00 0.00 1.98
1598 1723 2.295349 ACTCAGCCATTTTGAAGCACAG 59.705 45.455 0.00 0.00 0.00 3.66
1666 1791 2.670934 CAAAGCCGCAGCCTCAGT 60.671 61.111 0.00 0.00 41.25 3.41
1698 1823 2.434884 AGCCATTCCGTGTGAGCG 60.435 61.111 0.00 0.00 0.00 5.03
1739 1865 4.137116 TCCCATTTCAGGTACGATTCTG 57.863 45.455 0.00 0.00 0.00 3.02
1860 1988 3.616956 TGATCTGGGTACAAGCTCAAG 57.383 47.619 0.00 0.00 0.00 3.02
1871 1999 0.608582 AAGCTCAAGCCTGCTTCCTG 60.609 55.000 0.42 0.00 45.09 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 88 6.686130 AAACTATGATATACGTAACTGCGC 57.314 37.500 0.00 0.00 34.88 6.09
142 144 7.060421 CAGGGTTAAACCATAGTATTGGATGT 58.940 38.462 13.24 0.00 41.02 3.06
169 171 2.438434 CAAGCATGTCCCGGACCC 60.438 66.667 15.24 3.71 0.00 4.46
270 274 8.393259 TCATCATTTGCTTGGGTAGGATATTAT 58.607 33.333 0.00 0.00 0.00 1.28
281 285 1.541147 ACACGTCATCATTTGCTTGGG 59.459 47.619 0.00 0.00 0.00 4.12
287 291 4.926860 TGCTAAGACACGTCATCATTTG 57.073 40.909 0.00 0.00 0.00 2.32
337 341 7.610580 TCCATAAATTTGGGTTGAGAAAACT 57.389 32.000 0.00 0.00 37.37 2.66
340 344 8.028652 AGTTTCCATAAATTTGGGTTGAGAAA 57.971 30.769 0.00 3.88 37.37 2.52
354 358 7.430441 GCCTTCTGTGTTTTAGTTTCCATAAA 58.570 34.615 0.00 0.00 0.00 1.40
363 367 3.157087 CATGGGCCTTCTGTGTTTTAGT 58.843 45.455 4.53 0.00 0.00 2.24
365 369 3.517296 TCATGGGCCTTCTGTGTTTTA 57.483 42.857 4.53 0.00 0.00 1.52
389 393 1.064952 GGTCGAGGGTTGTTGTTGTTG 59.935 52.381 0.00 0.00 0.00 3.33
390 394 1.064979 AGGTCGAGGGTTGTTGTTGTT 60.065 47.619 0.00 0.00 0.00 2.83
391 395 0.544697 AGGTCGAGGGTTGTTGTTGT 59.455 50.000 0.00 0.00 0.00 3.32
392 396 0.944386 CAGGTCGAGGGTTGTTGTTG 59.056 55.000 0.00 0.00 0.00 3.33
462 469 2.265683 CGCCGTTCTACTTTTCTACCC 58.734 52.381 0.00 0.00 0.00 3.69
504 516 3.208747 TCCACCAAGTTTCAACTCTCC 57.791 47.619 0.00 0.00 38.57 3.71
507 519 2.622942 TGCATCCACCAAGTTTCAACTC 59.377 45.455 0.00 0.00 38.57 3.01
508 520 2.624838 CTGCATCCACCAAGTTTCAACT 59.375 45.455 0.00 0.00 42.04 3.16
509 521 2.362077 ACTGCATCCACCAAGTTTCAAC 59.638 45.455 0.00 0.00 0.00 3.18
510 522 2.622942 GACTGCATCCACCAAGTTTCAA 59.377 45.455 0.00 0.00 0.00 2.69
511 523 2.229792 GACTGCATCCACCAAGTTTCA 58.770 47.619 0.00 0.00 0.00 2.69
512 524 2.229792 TGACTGCATCCACCAAGTTTC 58.770 47.619 0.00 0.00 0.00 2.78
513 525 2.363306 TGACTGCATCCACCAAGTTT 57.637 45.000 0.00 0.00 0.00 2.66
514 526 2.165167 CATGACTGCATCCACCAAGTT 58.835 47.619 0.00 0.00 30.68 2.66
515 527 1.830279 CATGACTGCATCCACCAAGT 58.170 50.000 0.00 0.00 30.68 3.16
527 539 2.435410 TGCGCTCCTGCATGACTG 60.435 61.111 9.73 0.00 40.62 3.51
534 546 1.515736 GCTTTTCATGCGCTCCTGC 60.516 57.895 9.73 0.00 0.00 4.85
535 547 0.179171 CAGCTTTTCATGCGCTCCTG 60.179 55.000 9.73 3.71 35.28 3.86
536 548 0.607489 ACAGCTTTTCATGCGCTCCT 60.607 50.000 9.73 0.00 35.28 3.69
537 549 0.242017 AACAGCTTTTCATGCGCTCC 59.758 50.000 9.73 0.00 35.28 4.70
538 550 2.056094 AAACAGCTTTTCATGCGCTC 57.944 45.000 9.73 0.00 35.28 5.03
539 551 2.293122 TGTAAACAGCTTTTCATGCGCT 59.707 40.909 9.73 0.00 35.28 5.92
540 552 2.660490 TGTAAACAGCTTTTCATGCGC 58.340 42.857 0.00 0.00 35.28 6.09
541 553 4.321745 GTCATGTAAACAGCTTTTCATGCG 59.678 41.667 11.06 0.00 41.50 4.73
542 554 4.321745 CGTCATGTAAACAGCTTTTCATGC 59.678 41.667 11.06 7.17 41.50 4.06
543 555 5.451908 ACGTCATGTAAACAGCTTTTCATG 58.548 37.500 10.08 10.08 42.37 3.07
544 556 5.238432 TGACGTCATGTAAACAGCTTTTCAT 59.762 36.000 15.76 0.00 29.87 2.57
545 557 4.572795 TGACGTCATGTAAACAGCTTTTCA 59.427 37.500 15.76 0.00 0.00 2.69
546 558 5.090652 TGACGTCATGTAAACAGCTTTTC 57.909 39.130 15.76 0.00 0.00 2.29
547 559 5.689383 ATGACGTCATGTAAACAGCTTTT 57.311 34.783 29.49 1.13 34.83 2.27
548 560 5.334879 GGAATGACGTCATGTAAACAGCTTT 60.335 40.000 30.57 11.83 36.56 3.51
549 561 4.154195 GGAATGACGTCATGTAAACAGCTT 59.846 41.667 30.57 12.36 36.56 3.74
550 562 3.684788 GGAATGACGTCATGTAAACAGCT 59.315 43.478 30.57 12.36 36.56 4.24
551 563 3.181510 GGGAATGACGTCATGTAAACAGC 60.182 47.826 30.57 12.49 36.56 4.40
552 564 4.253685 AGGGAATGACGTCATGTAAACAG 58.746 43.478 30.57 0.00 36.56 3.16
553 565 4.280436 AGGGAATGACGTCATGTAAACA 57.720 40.909 30.57 1.26 36.56 2.83
554 566 6.920569 AATAGGGAATGACGTCATGTAAAC 57.079 37.500 30.57 18.41 36.56 2.01
555 567 7.931578 AAAATAGGGAATGACGTCATGTAAA 57.068 32.000 30.57 15.86 36.56 2.01
556 568 7.827236 AGAAAAATAGGGAATGACGTCATGTAA 59.173 33.333 30.57 15.19 36.56 2.41
557 569 7.335627 AGAAAAATAGGGAATGACGTCATGTA 58.664 34.615 30.57 19.05 36.56 2.29
558 570 6.180472 AGAAAAATAGGGAATGACGTCATGT 58.820 36.000 30.57 19.91 36.56 3.21
559 571 6.683974 AGAAAAATAGGGAATGACGTCATG 57.316 37.500 30.57 0.00 36.56 3.07
560 572 6.659242 ACAAGAAAAATAGGGAATGACGTCAT 59.341 34.615 25.18 25.18 38.41 3.06
561 573 6.001460 ACAAGAAAAATAGGGAATGACGTCA 58.999 36.000 22.48 22.48 0.00 4.35
562 574 6.148811 TCACAAGAAAAATAGGGAATGACGTC 59.851 38.462 9.11 9.11 0.00 4.34
563 575 6.001460 TCACAAGAAAAATAGGGAATGACGT 58.999 36.000 0.00 0.00 0.00 4.34
564 576 6.494893 TCACAAGAAAAATAGGGAATGACG 57.505 37.500 0.00 0.00 0.00 4.35
565 577 7.830739 ACATCACAAGAAAAATAGGGAATGAC 58.169 34.615 0.00 0.00 0.00 3.06
566 578 7.669304 TGACATCACAAGAAAAATAGGGAATGA 59.331 33.333 0.00 0.00 0.00 2.57
567 579 7.829725 TGACATCACAAGAAAAATAGGGAATG 58.170 34.615 0.00 0.00 0.00 2.67
568 580 8.472413 CATGACATCACAAGAAAAATAGGGAAT 58.528 33.333 0.00 0.00 0.00 3.01
569 581 7.451255 ACATGACATCACAAGAAAAATAGGGAA 59.549 33.333 0.00 0.00 0.00 3.97
570 582 6.947733 ACATGACATCACAAGAAAAATAGGGA 59.052 34.615 0.00 0.00 0.00 4.20
571 583 7.161773 ACATGACATCACAAGAAAAATAGGG 57.838 36.000 0.00 0.00 0.00 3.53
572 584 8.950210 AGTACATGACATCACAAGAAAAATAGG 58.050 33.333 0.00 0.00 0.00 2.57
573 585 9.979270 GAGTACATGACATCACAAGAAAAATAG 57.021 33.333 0.00 0.00 0.00 1.73
574 586 8.946085 GGAGTACATGACATCACAAGAAAAATA 58.054 33.333 0.00 0.00 0.00 1.40
575 587 7.448161 TGGAGTACATGACATCACAAGAAAAAT 59.552 33.333 0.00 0.00 0.00 1.82
576 588 6.770303 TGGAGTACATGACATCACAAGAAAAA 59.230 34.615 0.00 0.00 0.00 1.94
577 589 6.295249 TGGAGTACATGACATCACAAGAAAA 58.705 36.000 0.00 0.00 0.00 2.29
578 590 5.863965 TGGAGTACATGACATCACAAGAAA 58.136 37.500 0.00 0.00 0.00 2.52
579 591 5.482006 CTGGAGTACATGACATCACAAGAA 58.518 41.667 0.00 0.00 0.00 2.52
580 592 4.081476 CCTGGAGTACATGACATCACAAGA 60.081 45.833 0.00 0.00 0.00 3.02
581 593 4.186926 CCTGGAGTACATGACATCACAAG 58.813 47.826 0.00 0.00 0.00 3.16
582 594 3.055167 CCCTGGAGTACATGACATCACAA 60.055 47.826 0.00 0.00 0.00 3.33
583 595 2.501316 CCCTGGAGTACATGACATCACA 59.499 50.000 0.00 0.00 0.00 3.58
584 596 2.158900 CCCCTGGAGTACATGACATCAC 60.159 54.545 0.00 0.00 0.00 3.06
585 597 2.118679 CCCCTGGAGTACATGACATCA 58.881 52.381 0.00 0.00 0.00 3.07
586 598 1.417890 CCCCCTGGAGTACATGACATC 59.582 57.143 0.00 0.00 0.00 3.06
587 599 1.511613 CCCCCTGGAGTACATGACAT 58.488 55.000 0.00 0.00 0.00 3.06
588 600 3.006061 CCCCCTGGAGTACATGACA 57.994 57.895 0.00 0.00 0.00 3.58
611 623 3.178611 AATCCCCTCCCCGCCATC 61.179 66.667 0.00 0.00 0.00 3.51
656 668 1.449423 CGTGCATTGATCCCGACCA 60.449 57.895 0.00 0.00 0.00 4.02
659 671 2.513666 GGCGTGCATTGATCCCGA 60.514 61.111 0.00 0.00 0.00 5.14
699 729 2.733593 GCGCCATATCCGACCGAC 60.734 66.667 0.00 0.00 0.00 4.79
733 771 2.820973 CCAGCCAGAGCCTAGAGC 59.179 66.667 0.00 0.00 41.25 4.09
734 772 2.806009 GGCCAGCCAGAGCCTAGAG 61.806 68.421 3.12 0.00 46.14 2.43
735 773 2.765807 GGCCAGCCAGAGCCTAGA 60.766 66.667 3.12 0.00 46.14 2.43
768 806 4.715130 ACGGGCACTGCTAGGGGA 62.715 66.667 0.00 0.00 39.14 4.81
915 953 2.062070 GGCTCTTCTCCGGCCATAT 58.938 57.895 2.24 0.00 44.69 1.78
916 954 3.550974 GGCTCTTCTCCGGCCATA 58.449 61.111 2.24 0.00 44.69 2.74
978 1023 0.239879 TTTGACATTTTCGCTCCGCC 59.760 50.000 0.00 0.00 0.00 6.13
1022 1069 1.066573 CGAAGTCATCCACTTGCCTCT 60.067 52.381 0.00 0.00 46.10 3.69
1311 1382 5.034554 ACACGCATCTCAACTGTTAAATG 57.965 39.130 0.00 0.00 0.00 2.32
1367 1443 5.399991 TCCTCAGGACCACTTTAGACTTAA 58.600 41.667 0.00 0.00 0.00 1.85
1428 1506 6.538021 GTCATATCAAGAAACAGTCAGCATCT 59.462 38.462 0.00 0.00 0.00 2.90
1666 1791 1.068948 TGGCTGCCCTGTTAACCTAA 58.931 50.000 17.53 0.00 0.00 2.69
1698 1823 0.037605 AAGCTTTGCAATGCTCAGCC 60.038 50.000 32.46 9.94 38.31 4.85
1739 1865 1.404851 CGAGCCCAGGAAGAGAAAGTC 60.405 57.143 0.00 0.00 0.00 3.01
1871 1999 2.553247 GGCCATAATCAACCCCTAGCTC 60.553 54.545 0.00 0.00 0.00 4.09
2090 3495 9.419297 TCGAAGAATTATGTAACATACTATGCC 57.581 33.333 0.00 0.00 0.00 4.40
2230 3640 2.018542 TATACGGTTGCAAGTGAGCC 57.981 50.000 0.00 0.00 0.00 4.70
2332 3742 2.292828 AGCCTAACAGCCAAACACAT 57.707 45.000 0.00 0.00 0.00 3.21
2646 4058 1.563924 TTTTTCCGATCGGAGGGAGA 58.436 50.000 33.67 18.53 46.06 3.71


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

AutoCloner maintained by Alex Coulton.