Multiple sequence alignment - TraesCS2B01G230100

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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 TraesCS2B01G230100 chr2B 100.000 2312 0 0 1 2312 225690698 225693009 0.000000e+00 4270.0
1 TraesCS2B01G230100 chr2B 85.015 654 57 16 869 1493 628156983 628157624 5.420000e-176 627.0
2 TraesCS2B01G230100 chr2B 86.078 510 49 11 892 1396 625009131 625008639 1.570000e-146 529.0
3 TraesCS2B01G230100 chr2B 85.294 510 73 2 1 510 396641878 396642385 2.030000e-145 525.0
4 TraesCS2B01G230100 chr2B 90.515 369 30 2 951 1314 585890228 585890596 1.240000e-132 483.0
5 TraesCS2B01G230100 chr2B 78.528 163 16 9 2150 2312 91425036 91425179 3.160000e-14 89.8
6 TraesCS2B01G230100 chr2A 93.391 1498 59 14 833 2312 178170880 178172355 0.000000e+00 2182.0
7 TraesCS2B01G230100 chr2A 88.491 530 45 10 892 1411 673452027 673452550 5.420000e-176 627.0
8 TraesCS2B01G230100 chr2A 82.061 524 60 19 869 1385 672645222 672644726 1.280000e-112 416.0
9 TraesCS2B01G230100 chr2A 93.137 102 4 3 713 813 178170790 178170889 1.850000e-31 147.0
10 TraesCS2B01G230100 chr2D 96.163 808 25 2 835 1637 171445001 171444195 0.000000e+00 1315.0
11 TraesCS2B01G230100 chr2D 93.348 451 22 3 1863 2312 171443023 171442580 0.000000e+00 660.0
12 TraesCS2B01G230100 chr2D 87.430 533 41 14 892 1411 528998778 528999297 7.110000e-165 590.0
13 TraesCS2B01G230100 chr2D 87.109 512 63 3 1 510 264284791 264284281 5.540000e-161 577.0
14 TraesCS2B01G230100 chr2D 87.778 450 40 10 951 1398 527648195 527647759 1.580000e-141 512.0
15 TraesCS2B01G230100 chr2D 84.830 501 74 2 10 510 163722885 163722387 9.530000e-139 503.0
16 TraesCS2B01G230100 chr2D 83.789 512 80 3 1 510 439619230 439618720 1.240000e-132 483.0
17 TraesCS2B01G230100 chr7D 91.449 421 32 4 994 1411 134467046 134466627 1.990000e-160 575.0
18 TraesCS2B01G230100 chr7A 90.909 418 34 3 994 1408 133627440 133627024 2.010000e-155 558.0
19 TraesCS2B01G230100 chr3A 84.778 519 73 5 1 515 426142298 426141782 1.220000e-142 516.0
20 TraesCS2B01G230100 chr7B 85.149 505 72 2 9 513 519517048 519517549 4.400000e-142 514.0
21 TraesCS2B01G230100 chr7B 84.344 511 76 4 1 510 369498067 369498574 4.440000e-137 497.0
22 TraesCS2B01G230100 chr4B 83.858 508 81 1 1 507 641324073 641324580 1.240000e-132 483.0
23 TraesCS2B01G230100 chr3D 83.725 510 83 0 1 510 308019956 308019447 1.240000e-132 483.0


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 TraesCS2B01G230100 chr2B 225690698 225693009 2311 False 4270.0 4270 100.0000 1 2312 1 chr2B.!!$F2 2311
1 TraesCS2B01G230100 chr2B 628156983 628157624 641 False 627.0 627 85.0150 869 1493 1 chr2B.!!$F5 624
2 TraesCS2B01G230100 chr2B 396641878 396642385 507 False 525.0 525 85.2940 1 510 1 chr2B.!!$F3 509
3 TraesCS2B01G230100 chr2A 178170790 178172355 1565 False 1164.5 2182 93.2640 713 2312 2 chr2A.!!$F2 1599
4 TraesCS2B01G230100 chr2A 673452027 673452550 523 False 627.0 627 88.4910 892 1411 1 chr2A.!!$F1 519
5 TraesCS2B01G230100 chr2D 171442580 171445001 2421 True 987.5 1315 94.7555 835 2312 2 chr2D.!!$R5 1477
6 TraesCS2B01G230100 chr2D 528998778 528999297 519 False 590.0 590 87.4300 892 1411 1 chr2D.!!$F1 519
7 TraesCS2B01G230100 chr2D 264284281 264284791 510 True 577.0 577 87.1090 1 510 1 chr2D.!!$R2 509
8 TraesCS2B01G230100 chr2D 439618720 439619230 510 True 483.0 483 83.7890 1 510 1 chr2D.!!$R3 509
9 TraesCS2B01G230100 chr3A 426141782 426142298 516 True 516.0 516 84.7780 1 515 1 chr3A.!!$R1 514
10 TraesCS2B01G230100 chr7B 519517048 519517549 501 False 514.0 514 85.1490 9 513 1 chr7B.!!$F2 504
11 TraesCS2B01G230100 chr7B 369498067 369498574 507 False 497.0 497 84.3440 1 510 1 chr7B.!!$F1 509
12 TraesCS2B01G230100 chr4B 641324073 641324580 507 False 483.0 483 83.8580 1 507 1 chr4B.!!$F1 506
13 TraesCS2B01G230100 chr3D 308019447 308019956 509 True 483.0 483 83.7250 1 510 1 chr3D.!!$R1 509

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
686 691 0.107017 ATCACATGGGCTGCTACCAC 60.107 55.0 0.0 0.0 41.58 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1738 0.170561 CGACCAGAAGGACCACGTAG 59.829 60.0 0.0 0.0 38.69 3.51 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
60 61 8.418597 AGGATTTGCAATGCTCATAATAGATT 57.581 30.769 6.82 0.00 0.00 2.40
74 76 9.638300 CTCATAATAGATTTGTTCGTAAGCAAC 57.362 33.333 0.00 0.00 37.18 4.17
106 108 6.791303 TGTTCTTCTTCGCAGTTTTTATGTT 58.209 32.000 0.00 0.00 0.00 2.71
163 165 6.717997 ACACTATTACCGGTGGAAATTTCTTT 59.282 34.615 19.93 0.00 37.72 2.52
174 176 6.014584 GGTGGAAATTTCTTTATGTGTCCCTT 60.015 38.462 17.42 0.00 0.00 3.95
192 194 6.042552 TGTCCCTTTTTGGATGCTTTTAATGA 59.957 34.615 0.00 0.00 36.63 2.57
194 196 7.064966 GTCCCTTTTTGGATGCTTTTAATGATG 59.935 37.037 0.00 0.00 36.63 3.07
244 246 9.716507 CCTATCATTATTAACGAAACAACCTTG 57.283 33.333 0.00 0.00 0.00 3.61
260 262 1.998315 CCTTGACTCTCGAGCATGTTG 59.002 52.381 7.81 0.00 0.00 3.33
286 288 7.761249 GTGCAAAGGTTAGATGCTATTGAAAAT 59.239 33.333 0.00 0.00 40.66 1.82
364 367 3.933861 AATCGAATAGGGTCAAAGGCT 57.066 42.857 0.00 0.00 0.00 4.58
366 369 1.017387 CGAATAGGGTCAAAGGCTGC 58.983 55.000 0.00 0.00 0.00 5.25
404 408 9.831682 AGTTATTAAAAGAAAAGGGACCCATAA 57.168 29.630 14.60 0.94 0.00 1.90
413 417 8.306313 AGAAAAGGGACCCATAATTAATGAAC 57.694 34.615 14.60 0.00 37.86 3.18
453 457 1.673920 TCAAACCGACAAGTTGGAAGC 59.326 47.619 13.37 0.00 37.57 3.86
464 469 6.475402 CGACAAGTTGGAAGCAATTTTTAGTT 59.525 34.615 7.96 0.00 0.00 2.24
526 531 7.778470 AAAAACTCAAAAACAGTCAACAACA 57.222 28.000 0.00 0.00 0.00 3.33
527 532 7.778470 AAAACTCAAAAACAGTCAACAACAA 57.222 28.000 0.00 0.00 0.00 2.83
528 533 6.763303 AACTCAAAAACAGTCAACAACAAC 57.237 33.333 0.00 0.00 0.00 3.32
529 534 5.837437 ACTCAAAAACAGTCAACAACAACA 58.163 33.333 0.00 0.00 0.00 3.33
530 535 6.276847 ACTCAAAAACAGTCAACAACAACAA 58.723 32.000 0.00 0.00 0.00 2.83
531 536 6.758886 ACTCAAAAACAGTCAACAACAACAAA 59.241 30.769 0.00 0.00 0.00 2.83
532 537 7.278868 ACTCAAAAACAGTCAACAACAACAAAA 59.721 29.630 0.00 0.00 0.00 2.44
533 538 7.974675 TCAAAAACAGTCAACAACAACAAAAA 58.025 26.923 0.00 0.00 0.00 1.94
534 539 8.616076 TCAAAAACAGTCAACAACAACAAAAAT 58.384 25.926 0.00 0.00 0.00 1.82
535 540 9.869844 CAAAAACAGTCAACAACAACAAAAATA 57.130 25.926 0.00 0.00 0.00 1.40
538 543 7.826260 ACAGTCAACAACAACAAAAATAAGG 57.174 32.000 0.00 0.00 0.00 2.69
539 544 7.607250 ACAGTCAACAACAACAAAAATAAGGA 58.393 30.769 0.00 0.00 0.00 3.36
540 545 8.091449 ACAGTCAACAACAACAAAAATAAGGAA 58.909 29.630 0.00 0.00 0.00 3.36
541 546 8.594687 CAGTCAACAACAACAAAAATAAGGAAG 58.405 33.333 0.00 0.00 0.00 3.46
542 547 7.763985 AGTCAACAACAACAAAAATAAGGAAGG 59.236 33.333 0.00 0.00 0.00 3.46
543 548 7.762159 GTCAACAACAACAAAAATAAGGAAGGA 59.238 33.333 0.00 0.00 0.00 3.36
544 549 8.314751 TCAACAACAACAAAAATAAGGAAGGAA 58.685 29.630 0.00 0.00 0.00 3.36
545 550 8.940952 CAACAACAACAAAAATAAGGAAGGAAA 58.059 29.630 0.00 0.00 0.00 3.13
546 551 9.508642 AACAACAACAAAAATAAGGAAGGAAAA 57.491 25.926 0.00 0.00 0.00 2.29
547 552 9.508642 ACAACAACAAAAATAAGGAAGGAAAAA 57.491 25.926 0.00 0.00 0.00 1.94
562 567 9.500701 AGGAAGGAAAAATATATTTTTAGGCCA 57.499 29.630 27.90 0.00 46.55 5.36
577 582 9.715119 ATTTTTAGGCCAAATAAGGAAGTAGAT 57.285 29.630 5.01 0.00 0.00 1.98
578 583 9.541884 TTTTTAGGCCAAATAAGGAAGTAGATT 57.458 29.630 5.01 0.00 0.00 2.40
579 584 9.541884 TTTTAGGCCAAATAAGGAAGTAGATTT 57.458 29.630 5.01 0.00 0.00 2.17
580 585 9.541884 TTTAGGCCAAATAAGGAAGTAGATTTT 57.458 29.630 5.01 0.00 0.00 1.82
583 588 9.715119 AGGCCAAATAAGGAAGTAGATTTTATT 57.285 29.630 5.01 0.00 0.00 1.40
634 639 8.940397 TGAAAAGGTCAAATAAGGAATTCTCT 57.060 30.769 5.23 0.00 31.51 3.10
662 667 3.150335 CAGGCTCGGCTGGCTCTA 61.150 66.667 12.20 0.00 41.04 2.43
663 668 2.837291 AGGCTCGGCTGGCTCTAG 60.837 66.667 0.00 0.00 38.54 2.43
664 669 3.151022 GGCTCGGCTGGCTCTAGT 61.151 66.667 0.00 0.00 0.00 2.57
665 670 2.726351 GGCTCGGCTGGCTCTAGTT 61.726 63.158 0.00 0.00 0.00 2.24
666 671 1.520342 GCTCGGCTGGCTCTAGTTG 60.520 63.158 0.00 0.00 0.00 3.16
667 672 1.949847 GCTCGGCTGGCTCTAGTTGA 61.950 60.000 0.00 0.00 0.00 3.18
668 673 0.749649 CTCGGCTGGCTCTAGTTGAT 59.250 55.000 0.00 0.00 0.00 2.57
669 674 0.747255 TCGGCTGGCTCTAGTTGATC 59.253 55.000 0.00 0.00 0.00 2.92
670 675 0.461548 CGGCTGGCTCTAGTTGATCA 59.538 55.000 0.00 0.00 0.00 2.92
671 676 1.804372 CGGCTGGCTCTAGTTGATCAC 60.804 57.143 0.00 0.00 0.00 3.06
672 677 1.208052 GGCTGGCTCTAGTTGATCACA 59.792 52.381 0.00 0.00 0.00 3.58
673 678 2.158842 GGCTGGCTCTAGTTGATCACAT 60.159 50.000 0.00 0.00 0.00 3.21
674 679 2.871022 GCTGGCTCTAGTTGATCACATG 59.129 50.000 0.00 0.00 0.00 3.21
675 680 3.464907 CTGGCTCTAGTTGATCACATGG 58.535 50.000 0.00 0.00 0.00 3.66
676 681 2.171237 TGGCTCTAGTTGATCACATGGG 59.829 50.000 0.00 0.00 0.00 4.00
677 682 2.216898 GCTCTAGTTGATCACATGGGC 58.783 52.381 0.00 0.00 0.00 5.36
678 683 2.158842 GCTCTAGTTGATCACATGGGCT 60.159 50.000 0.00 0.00 0.00 5.19
679 684 3.464907 CTCTAGTTGATCACATGGGCTG 58.535 50.000 0.00 0.00 0.00 4.85
680 685 1.945394 CTAGTTGATCACATGGGCTGC 59.055 52.381 0.00 0.00 0.00 5.25
681 686 0.330604 AGTTGATCACATGGGCTGCT 59.669 50.000 0.00 0.00 0.00 4.24
682 687 1.561076 AGTTGATCACATGGGCTGCTA 59.439 47.619 0.00 0.00 0.00 3.49
683 688 1.672881 GTTGATCACATGGGCTGCTAC 59.327 52.381 0.00 0.00 0.00 3.58
684 689 0.181114 TGATCACATGGGCTGCTACC 59.819 55.000 0.00 0.00 0.00 3.18
685 690 0.181114 GATCACATGGGCTGCTACCA 59.819 55.000 0.00 0.00 43.22 3.25
686 691 0.107017 ATCACATGGGCTGCTACCAC 60.107 55.000 0.00 0.00 41.58 4.16
687 692 1.200760 TCACATGGGCTGCTACCACT 61.201 55.000 0.00 0.00 41.58 4.00
688 693 0.541392 CACATGGGCTGCTACCACTA 59.459 55.000 0.00 0.00 41.58 2.74
689 694 1.065491 CACATGGGCTGCTACCACTAA 60.065 52.381 0.00 0.00 41.58 2.24
690 695 1.633432 ACATGGGCTGCTACCACTAAA 59.367 47.619 0.00 0.00 41.58 1.85
691 696 2.041081 ACATGGGCTGCTACCACTAAAA 59.959 45.455 0.00 0.00 41.58 1.52
692 697 2.961531 TGGGCTGCTACCACTAAAAA 57.038 45.000 0.00 0.00 31.83 1.94
693 698 2.790433 TGGGCTGCTACCACTAAAAAG 58.210 47.619 0.00 0.00 31.83 2.27
694 699 1.472878 GGGCTGCTACCACTAAAAAGC 59.527 52.381 0.00 0.00 35.51 3.51
695 700 1.472878 GGCTGCTACCACTAAAAAGCC 59.527 52.381 0.00 0.00 41.70 4.35
696 701 2.437413 GCTGCTACCACTAAAAAGCCT 58.563 47.619 0.00 0.00 33.99 4.58
697 702 2.162408 GCTGCTACCACTAAAAAGCCTG 59.838 50.000 0.00 0.00 33.99 4.85
698 703 2.749621 CTGCTACCACTAAAAAGCCTGG 59.250 50.000 0.00 0.00 33.99 4.45
699 704 2.373836 TGCTACCACTAAAAAGCCTGGA 59.626 45.455 0.00 0.00 33.99 3.86
700 705 3.010138 TGCTACCACTAAAAAGCCTGGAT 59.990 43.478 0.00 0.00 33.99 3.41
701 706 3.628032 GCTACCACTAAAAAGCCTGGATC 59.372 47.826 0.00 0.00 0.00 3.36
702 707 2.711542 ACCACTAAAAAGCCTGGATCG 58.288 47.619 0.00 0.00 0.00 3.69
703 708 2.017049 CCACTAAAAAGCCTGGATCGG 58.983 52.381 0.00 0.00 0.00 4.18
710 715 4.593864 GCCTGGATCGGCCGTCTC 62.594 72.222 27.15 21.87 44.41 3.36
711 716 3.917760 CCTGGATCGGCCGTCTCC 61.918 72.222 30.37 30.37 40.66 3.71
728 733 3.132289 GTCTCCAAACGATCAGATGGGTA 59.868 47.826 7.56 0.00 33.37 3.69
731 736 2.419990 CCAAACGATCAGATGGGTAGCA 60.420 50.000 0.00 0.00 0.00 3.49
788 794 2.288152 GGTTGCCTGATTCGCTGAAAAA 60.288 45.455 0.00 0.00 0.00 1.94
791 797 1.729149 GCCTGATTCGCTGAAAAACCG 60.729 52.381 0.00 0.00 0.00 4.44
794 800 1.193650 TGATTCGCTGAAAAACCGACG 59.806 47.619 0.00 0.00 0.00 5.12
802 808 3.364565 GCTGAAAAACCGACGAGCATTTA 60.365 43.478 0.00 0.00 0.00 1.40
803 809 4.671766 GCTGAAAAACCGACGAGCATTTAT 60.672 41.667 0.00 0.00 0.00 1.40
804 810 5.365403 TGAAAAACCGACGAGCATTTATT 57.635 34.783 0.00 0.00 0.00 1.40
805 811 5.764131 TGAAAAACCGACGAGCATTTATTT 58.236 33.333 0.00 0.00 0.00 1.40
806 812 6.210078 TGAAAAACCGACGAGCATTTATTTT 58.790 32.000 0.00 0.00 0.00 1.82
807 813 6.697892 TGAAAAACCGACGAGCATTTATTTTT 59.302 30.769 0.00 0.00 32.32 1.94
940 950 1.580942 CAACCCCATCACAAGCGTG 59.419 57.895 0.00 0.00 45.08 5.34
1083 1106 1.811266 CCTCCGCGACAACATCCAG 60.811 63.158 8.23 0.00 0.00 3.86
1335 1370 2.592574 GCTGTGCTGTGCTGGTGA 60.593 61.111 0.00 0.00 0.00 4.02
1467 1521 2.031682 ACGAAATGCTTCAGTGCTGAAC 60.032 45.455 10.26 8.46 43.90 3.18
1493 1547 6.145048 CGTGTTACCGTTTTTCTAAGACTGAT 59.855 38.462 0.00 0.00 0.00 2.90
1495 1549 8.981647 GTGTTACCGTTTTTCTAAGACTGATTA 58.018 33.333 0.00 0.00 0.00 1.75
1496 1550 9.715121 TGTTACCGTTTTTCTAAGACTGATTAT 57.285 29.630 0.00 0.00 0.00 1.28
1674 1738 4.759516 TTTTTCCCGCAGTTATTCTGAC 57.240 40.909 0.00 0.00 46.27 3.51
1679 1743 2.159282 CCCGCAGTTATTCTGACTACGT 60.159 50.000 0.00 0.00 46.27 3.57
1680 1744 2.852413 CCGCAGTTATTCTGACTACGTG 59.148 50.000 0.00 0.00 46.27 4.49
1681 1745 2.852413 CGCAGTTATTCTGACTACGTGG 59.148 50.000 0.00 0.00 46.27 4.94
1686 1750 4.771054 AGTTATTCTGACTACGTGGTCCTT 59.229 41.667 26.64 12.53 35.54 3.36
1748 1812 5.913137 TTTTGTCACTCAACACAAGGATT 57.087 34.783 0.00 0.00 35.61 3.01
1779 1843 2.363038 ACATGCTTTGATGTTGTGCTGT 59.637 40.909 0.00 0.00 32.38 4.40
1854 2478 2.828877 CGTGGGTTTGTGTTCAGTAGA 58.171 47.619 0.00 0.00 0.00 2.59
1869 2876 9.298774 GTGTTCAGTAGACTGTAATACCATTAC 57.701 37.037 9.43 2.73 44.12 1.89
1881 2889 5.652744 AATACCATTACGCTTCGATGAAC 57.347 39.130 1.89 0.00 0.00 3.18
1910 2918 3.390967 TGATCCTGAATCCTGGCGAAATA 59.609 43.478 0.00 0.00 33.01 1.40
1934 2942 3.865446 TCATTGATGTGTAGCTGTCTGG 58.135 45.455 0.00 0.00 0.00 3.86
1969 2977 5.989168 TCAGTTTGATGTACTGACGAAATGT 59.011 36.000 0.00 0.00 45.15 2.71
1973 2981 7.226720 AGTTTGATGTACTGACGAAATGTTTCT 59.773 33.333 4.20 0.00 35.07 2.52
2117 3125 0.602060 TTTGCCGCTCATTGCAATCA 59.398 45.000 9.53 0.00 45.96 2.57
2198 3206 3.969976 CCCATCCTTCTCAAGTCCATCTA 59.030 47.826 0.00 0.00 0.00 1.98
2263 3271 3.735746 GGAAACTTGAACGCTTGGAATTG 59.264 43.478 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.779183 AGCATCTTTCAGATTCTCTCCCA 59.221 43.478 0.00 0.00 31.32 4.37
19 20 6.039717 TGCAAATCCTATACCAAGCATCTTTC 59.960 38.462 0.00 0.00 0.00 2.62
60 61 1.310904 GGTGGGTTGCTTACGAACAA 58.689 50.000 0.00 0.00 0.00 2.83
74 76 1.200020 GCGAAGAAGAACAATGGTGGG 59.800 52.381 0.00 0.00 0.00 4.61
163 165 4.046286 AGCATCCAAAAAGGGACACATA 57.954 40.909 0.00 0.00 40.44 2.29
174 176 8.359875 TCCTACATCATTAAAAGCATCCAAAA 57.640 30.769 0.00 0.00 0.00 2.44
192 194 3.780294 TGCACCCACTAAATCTCCTACAT 59.220 43.478 0.00 0.00 0.00 2.29
194 196 3.532542 GTGCACCCACTAAATCTCCTAC 58.467 50.000 5.22 0.00 38.93 3.18
260 262 5.818136 TCAATAGCATCTAACCTTTGCAC 57.182 39.130 0.00 0.00 38.84 4.57
347 350 1.017387 GCAGCCTTTGACCCTATTCG 58.983 55.000 0.00 0.00 0.00 3.34
404 408 6.459923 GGCTCTCTTCTATCCGTTCATTAAT 58.540 40.000 0.00 0.00 0.00 1.40
413 417 0.676736 GTGGGGCTCTCTTCTATCCG 59.323 60.000 0.00 0.00 0.00 4.18
438 442 3.369546 AAATTGCTTCCAACTTGTCGG 57.630 42.857 0.00 0.00 32.95 4.79
439 443 5.977129 ACTAAAAATTGCTTCCAACTTGTCG 59.023 36.000 0.00 0.00 32.95 4.35
453 457 5.795441 GCCGAGCTCAAGTAACTAAAAATTG 59.205 40.000 15.40 0.00 0.00 2.32
464 469 3.402628 AGAAAAAGCCGAGCTCAAGTA 57.597 42.857 15.40 0.00 38.25 2.24
515 520 8.472683 TTCCTTATTTTTGTTGTTGTTGACTG 57.527 30.769 0.00 0.00 0.00 3.51
517 522 7.762159 TCCTTCCTTATTTTTGTTGTTGTTGAC 59.238 33.333 0.00 0.00 0.00 3.18
518 523 7.841956 TCCTTCCTTATTTTTGTTGTTGTTGA 58.158 30.769 0.00 0.00 0.00 3.18
519 524 8.485976 TTCCTTCCTTATTTTTGTTGTTGTTG 57.514 30.769 0.00 0.00 0.00 3.33
520 525 9.508642 TTTTCCTTCCTTATTTTTGTTGTTGTT 57.491 25.926 0.00 0.00 0.00 2.83
521 526 9.508642 TTTTTCCTTCCTTATTTTTGTTGTTGT 57.491 25.926 0.00 0.00 0.00 3.32
536 541 9.500701 TGGCCTAAAAATATATTTTTCCTTCCT 57.499 29.630 30.22 14.19 44.17 3.36
551 556 9.715119 ATCTACTTCCTTATTTGGCCTAAAAAT 57.285 29.630 3.32 4.39 0.00 1.82
552 557 9.541884 AATCTACTTCCTTATTTGGCCTAAAAA 57.458 29.630 3.32 0.00 0.00 1.94
553 558 9.541884 AAATCTACTTCCTTATTTGGCCTAAAA 57.458 29.630 3.32 0.00 0.00 1.52
554 559 9.541884 AAAATCTACTTCCTTATTTGGCCTAAA 57.458 29.630 3.32 3.33 0.00 1.85
557 562 9.715119 AATAAAATCTACTTCCTTATTTGGCCT 57.285 29.630 3.32 0.00 0.00 5.19
608 613 9.539194 AGAGAATTCCTTATTTGACCTTTTCAT 57.461 29.630 0.65 0.00 32.84 2.57
609 614 8.940397 AGAGAATTCCTTATTTGACCTTTTCA 57.060 30.769 0.65 0.00 0.00 2.69
645 650 3.149338 CTAGAGCCAGCCGAGCCTG 62.149 68.421 0.00 0.00 0.00 4.85
646 651 2.837291 CTAGAGCCAGCCGAGCCT 60.837 66.667 0.00 0.00 0.00 4.58
647 652 2.726351 AACTAGAGCCAGCCGAGCC 61.726 63.158 0.00 0.00 0.00 4.70
648 653 1.520342 CAACTAGAGCCAGCCGAGC 60.520 63.158 0.00 0.00 0.00 5.03
649 654 0.749649 ATCAACTAGAGCCAGCCGAG 59.250 55.000 0.00 0.00 0.00 4.63
650 655 0.747255 GATCAACTAGAGCCAGCCGA 59.253 55.000 0.00 0.00 0.00 5.54
651 656 0.461548 TGATCAACTAGAGCCAGCCG 59.538 55.000 0.00 0.00 0.00 5.52
652 657 1.208052 TGTGATCAACTAGAGCCAGCC 59.792 52.381 0.00 0.00 0.00 4.85
653 658 2.680312 TGTGATCAACTAGAGCCAGC 57.320 50.000 0.00 0.00 0.00 4.85
654 659 3.464907 CCATGTGATCAACTAGAGCCAG 58.535 50.000 0.00 0.00 0.00 4.85
655 660 2.171237 CCCATGTGATCAACTAGAGCCA 59.829 50.000 0.00 0.00 0.00 4.75
656 661 2.843701 CCCATGTGATCAACTAGAGCC 58.156 52.381 0.00 0.00 0.00 4.70
657 662 2.158842 AGCCCATGTGATCAACTAGAGC 60.159 50.000 0.00 0.00 0.00 4.09
658 663 3.464907 CAGCCCATGTGATCAACTAGAG 58.535 50.000 0.00 0.00 0.00 2.43
659 664 2.420547 GCAGCCCATGTGATCAACTAGA 60.421 50.000 0.00 0.00 0.00 2.43
660 665 1.945394 GCAGCCCATGTGATCAACTAG 59.055 52.381 0.00 0.00 0.00 2.57
661 666 1.561076 AGCAGCCCATGTGATCAACTA 59.439 47.619 0.00 0.00 0.00 2.24
662 667 0.330604 AGCAGCCCATGTGATCAACT 59.669 50.000 0.00 0.00 0.00 3.16
663 668 1.672881 GTAGCAGCCCATGTGATCAAC 59.327 52.381 0.00 0.00 0.00 3.18
664 669 1.408683 GGTAGCAGCCCATGTGATCAA 60.409 52.381 0.00 0.00 0.00 2.57
665 670 0.181114 GGTAGCAGCCCATGTGATCA 59.819 55.000 0.00 0.00 0.00 2.92
666 671 0.181114 TGGTAGCAGCCCATGTGATC 59.819 55.000 0.00 0.00 0.00 2.92
667 672 0.107017 GTGGTAGCAGCCCATGTGAT 60.107 55.000 0.00 0.00 33.76 3.06
668 673 1.200760 AGTGGTAGCAGCCCATGTGA 61.201 55.000 0.00 0.00 33.76 3.58
669 674 0.541392 TAGTGGTAGCAGCCCATGTG 59.459 55.000 0.00 0.00 33.76 3.21
670 675 1.285280 TTAGTGGTAGCAGCCCATGT 58.715 50.000 0.00 0.00 33.76 3.21
671 676 2.418368 TTTAGTGGTAGCAGCCCATG 57.582 50.000 0.00 0.00 33.76 3.66
672 677 3.356290 CTTTTTAGTGGTAGCAGCCCAT 58.644 45.455 0.00 0.00 33.76 4.00
673 678 2.790433 CTTTTTAGTGGTAGCAGCCCA 58.210 47.619 0.00 0.00 0.00 5.36
674 679 1.472878 GCTTTTTAGTGGTAGCAGCCC 59.527 52.381 0.00 0.00 33.88 5.19
675 680 1.472878 GGCTTTTTAGTGGTAGCAGCC 59.527 52.381 0.00 0.00 38.72 4.85
676 681 2.162408 CAGGCTTTTTAGTGGTAGCAGC 59.838 50.000 0.00 0.00 35.36 5.25
677 682 2.749621 CCAGGCTTTTTAGTGGTAGCAG 59.250 50.000 0.00 0.00 35.36 4.24
678 683 2.373836 TCCAGGCTTTTTAGTGGTAGCA 59.626 45.455 0.00 0.00 35.36 3.49
679 684 3.067684 TCCAGGCTTTTTAGTGGTAGC 57.932 47.619 0.00 0.00 0.00 3.58
680 685 3.871594 CGATCCAGGCTTTTTAGTGGTAG 59.128 47.826 0.00 0.00 0.00 3.18
681 686 3.370103 CCGATCCAGGCTTTTTAGTGGTA 60.370 47.826 0.00 0.00 0.00 3.25
682 687 2.618045 CCGATCCAGGCTTTTTAGTGGT 60.618 50.000 0.00 0.00 0.00 4.16
683 688 2.017049 CCGATCCAGGCTTTTTAGTGG 58.983 52.381 0.00 0.00 0.00 4.00
694 699 3.917760 GGAGACGGCCGATCCAGG 61.918 72.222 34.26 9.30 33.08 4.45
695 700 2.238847 TTTGGAGACGGCCGATCCAG 62.239 60.000 36.96 13.07 43.71 3.86
696 701 2.287274 TTTGGAGACGGCCGATCCA 61.287 57.895 36.51 36.51 41.33 3.41
697 702 1.814169 GTTTGGAGACGGCCGATCC 60.814 63.158 33.31 33.31 0.00 3.36
698 703 2.165301 CGTTTGGAGACGGCCGATC 61.165 63.158 35.90 27.35 39.27 3.69
699 704 1.956629 ATCGTTTGGAGACGGCCGAT 61.957 55.000 35.90 20.71 42.98 4.18
700 705 2.552585 GATCGTTTGGAGACGGCCGA 62.553 60.000 35.90 5.52 42.98 5.54
701 706 2.125673 ATCGTTTGGAGACGGCCG 60.126 61.111 26.86 26.86 42.98 6.13
702 707 1.079405 TGATCGTTTGGAGACGGCC 60.079 57.895 0.00 0.00 42.98 6.13
703 708 0.108804 TCTGATCGTTTGGAGACGGC 60.109 55.000 0.00 0.00 42.98 5.68
704 709 2.196749 CATCTGATCGTTTGGAGACGG 58.803 52.381 0.00 0.00 42.98 4.79
705 710 2.196749 CCATCTGATCGTTTGGAGACG 58.803 52.381 2.31 0.00 44.06 4.18
706 711 2.093447 ACCCATCTGATCGTTTGGAGAC 60.093 50.000 8.71 0.00 0.00 3.36
707 712 2.187958 ACCCATCTGATCGTTTGGAGA 58.812 47.619 8.71 0.00 0.00 3.71
708 713 2.698855 ACCCATCTGATCGTTTGGAG 57.301 50.000 8.71 3.16 0.00 3.86
709 714 2.158957 GCTACCCATCTGATCGTTTGGA 60.159 50.000 8.71 0.00 0.00 3.53
710 715 2.213499 GCTACCCATCTGATCGTTTGG 58.787 52.381 1.62 1.62 0.00 3.28
711 716 2.905075 TGCTACCCATCTGATCGTTTG 58.095 47.619 0.00 0.00 0.00 2.93
731 736 4.547367 GCGGCCCATCTAGCGGTT 62.547 66.667 0.00 0.00 33.47 4.44
876 882 7.730332 AGTTTATATGGGAATGGGAAGGATTTC 59.270 37.037 0.00 0.00 0.00 2.17
940 950 0.402121 AGGAACTGCTTTGGAGGGTC 59.598 55.000 0.00 0.00 37.18 4.46
1281 1305 3.072468 CCGTAGAGGGTTCGGCCA 61.072 66.667 2.24 0.00 39.65 5.36
1335 1370 1.134907 ACACAAGAGAAACACGACCGT 60.135 47.619 0.00 0.00 0.00 4.83
1467 1521 4.746611 AGTCTTAGAAAAACGGTAACACGG 59.253 41.667 0.00 0.00 38.39 4.94
1493 1547 4.561500 TGATTGGAACGGACCAGAATAA 57.438 40.909 3.32 0.00 41.19 1.40
1495 1549 3.054434 TGATGATTGGAACGGACCAGAAT 60.054 43.478 3.32 0.00 41.19 2.40
1496 1550 2.304470 TGATGATTGGAACGGACCAGAA 59.696 45.455 3.32 0.00 41.19 3.02
1582 1643 4.346709 TCTCCCACAGTTTGTATTGAGTGA 59.653 41.667 0.00 0.00 0.00 3.41
1674 1738 0.170561 CGACCAGAAGGACCACGTAG 59.829 60.000 0.00 0.00 38.69 3.51
1679 1743 0.834612 AACAACGACCAGAAGGACCA 59.165 50.000 0.00 0.00 38.69 4.02
1680 1744 2.036862 ACTAACAACGACCAGAAGGACC 59.963 50.000 0.00 0.00 38.69 4.46
1681 1745 3.057734 CACTAACAACGACCAGAAGGAC 58.942 50.000 0.00 0.00 38.69 3.85
1686 1750 1.000506 GGAGCACTAACAACGACCAGA 59.999 52.381 0.00 0.00 0.00 3.86
1748 1812 7.611467 ACAACATCAAAGCATGTTTAGATCCTA 59.389 33.333 0.00 0.00 39.47 2.94
1789 2040 2.877097 TGGCACATATCACACCAACT 57.123 45.000 0.00 0.00 0.00 3.16
1854 2478 5.252969 TCGAAGCGTAATGGTATTACAGT 57.747 39.130 11.07 0.00 0.00 3.55
1869 2876 1.391485 CAGAGTTGGTTCATCGAAGCG 59.609 52.381 0.00 0.00 42.15 4.68
1881 2889 3.433314 CCAGGATTCAGGATCAGAGTTGG 60.433 52.174 0.00 0.00 36.43 3.77
1910 2918 5.356190 CCAGACAGCTACACATCAATGAAAT 59.644 40.000 0.00 0.00 0.00 2.17
1934 2942 8.598924 CAGTACATCAAACTGAACAGATCATAC 58.401 37.037 8.87 2.75 45.89 2.39
2016 3024 8.810041 AGGTGAGAAAATGAGCAGATTAAAATT 58.190 29.630 0.00 0.00 0.00 1.82
2017 3025 8.248945 CAGGTGAGAAAATGAGCAGATTAAAAT 58.751 33.333 0.00 0.00 0.00 1.82
2018 3026 7.309377 CCAGGTGAGAAAATGAGCAGATTAAAA 60.309 37.037 0.00 0.00 0.00 1.52
2019 3027 6.151648 CCAGGTGAGAAAATGAGCAGATTAAA 59.848 38.462 0.00 0.00 0.00 1.52
2020 3028 5.649395 CCAGGTGAGAAAATGAGCAGATTAA 59.351 40.000 0.00 0.00 0.00 1.40
2021 3029 5.045651 TCCAGGTGAGAAAATGAGCAGATTA 60.046 40.000 0.00 0.00 0.00 1.75
2022 3030 4.015084 CCAGGTGAGAAAATGAGCAGATT 58.985 43.478 0.00 0.00 0.00 2.40
2117 3125 5.536161 TGAAAGATGGCAAAGCTCTTTTACT 59.464 36.000 13.38 0.00 38.87 2.24
2230 3238 6.475402 AGCGTTCAAGTTTCCTTAAATGTTTG 59.525 34.615 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.