Multiple sequence alignment - TraesCS5A01G361200

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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 TraesCS5A01G361200 chr5A 100.000 2483 0 0 1 2483 562486250 562488732 0.000000e+00 4586.0
1 TraesCS5A01G361200 chr5A 85.714 56 7 1 2276 2330 704100872 704100817 9.590000e-05 58.4
2 TraesCS5A01G361200 chr5A 85.714 56 7 1 2276 2330 704130779 704130724 9.590000e-05 58.4
3 TraesCS5A01G361200 chr5A 85.714 56 7 1 2276 2330 704218191 704218136 9.590000e-05 58.4
4 TraesCS5A01G361200 chr5A 85.714 56 7 1 2276 2330 704221364 704221309 9.590000e-05 58.4
5 TraesCS5A01G361200 chr5A 85.714 56 7 1 2276 2330 704261666 704261611 9.590000e-05 58.4
6 TraesCS5A01G361200 chr4A 96.535 1847 35 9 637 2483 398506554 398504737 0.000000e+00 3029.0
7 TraesCS5A01G361200 chr1A 96.535 1847 33 5 637 2483 513745671 513743856 0.000000e+00 3027.0
8 TraesCS5A01G361200 chr2D 89.294 906 82 11 1429 2330 117816476 117815582 0.000000e+00 1122.0
9 TraesCS5A01G361200 chr2D 92.857 42 2 1 91 132 601795740 601795700 2.670000e-05 60.2
10 TraesCS5A01G361200 chr3B 86.870 655 79 6 1679 2331 806377100 806376451 0.000000e+00 726.0
11 TraesCS5A01G361200 chr3B 79.078 282 47 10 1625 1902 73030368 73030641 1.520000e-42 183.0
12 TraesCS5A01G361200 chr3B 82.692 208 22 11 1020 1217 615632661 615632458 3.280000e-39 172.0
13 TraesCS5A01G361200 chr3B 96.429 84 2 1 1106 1189 615632598 615632516 1.200000e-28 137.0
14 TraesCS5A01G361200 chr5D 83.029 548 22 28 1 505 445190005 445190524 4.910000e-117 431.0
15 TraesCS5A01G361200 chr5D 100.000 42 0 0 544 585 445190538 445190579 7.360000e-11 78.7
16 TraesCS5A01G361200 chr1D 82.306 503 66 11 1840 2330 473383695 473383204 4.940000e-112 414.0
17 TraesCS5A01G361200 chr3D 81.710 503 69 11 1840 2330 36981471 36980980 4.980000e-107 398.0
18 TraesCS5A01G361200 chr3D 93.605 172 11 0 651 822 94656006 94656177 8.810000e-65 257.0
19 TraesCS5A01G361200 chr3D 91.279 172 15 0 1225 1396 462838613 462838442 4.130000e-58 235.0
20 TraesCS5A01G361200 chr3D 88.079 151 18 0 1246 1396 308763771 308763921 1.960000e-41 180.0
21 TraesCS5A01G361200 chr3D 82.524 206 26 9 1020 1217 462838853 462838650 3.280000e-39 172.0
22 TraesCS5A01G361200 chr3D 96.429 84 2 1 1106 1189 462838790 462838708 1.200000e-28 137.0
23 TraesCS5A01G361200 chr3D 90.291 103 7 3 823 922 94656212 94656314 5.570000e-27 132.0
24 TraesCS5A01G361200 chr7D 81.855 496 67 11 1847 2330 526737434 526737918 1.790000e-106 396.0
25 TraesCS5A01G361200 chr7D 91.860 172 14 0 651 822 112965393 112965222 8.870000e-60 241.0
26 TraesCS5A01G361200 chr7D 90.566 106 7 3 823 925 112965187 112965082 1.200000e-28 137.0
27 TraesCS5A01G361200 chr5B 83.149 451 58 8 1888 2330 345517006 345516566 1.790000e-106 396.0
28 TraesCS5A01G361200 chr5B 88.710 186 21 0 638 823 370077413 370077598 6.910000e-56 228.0
29 TraesCS5A01G361200 chr5B 82.456 285 25 14 99 361 542759109 542759390 2.480000e-55 226.0
30 TraesCS5A01G361200 chr3A 86.316 380 26 2 638 991 70824499 70824878 8.330000e-105 390.0
31 TraesCS5A01G361200 chr3A 79.528 381 46 21 637 991 631705104 631705478 2.470000e-60 243.0
32 TraesCS5A01G361200 chr3A 82.464 211 23 12 1020 1217 605981514 605981305 3.280000e-39 172.0
33 TraesCS5A01G361200 chr3A 95.238 84 3 1 1106 1189 605981451 605981369 5.570000e-27 132.0
34 TraesCS5A01G361200 chr6D 81.349 504 71 11 1840 2331 378260724 378261216 2.990000e-104 388.0
35 TraesCS5A01G361200 chr7B 85.366 287 32 9 638 920 735120564 735120284 3.120000e-74 289.0
36 TraesCS5A01G361200 chr7B 77.895 380 54 18 637 991 526855124 526855498 2.500000e-50 209.0
37 TraesCS5A01G361200 chr2B 94.054 185 11 0 638 822 801049098 801049282 5.230000e-72 281.0
38 TraesCS5A01G361200 chr2B 96.296 81 3 0 823 903 801049317 801049397 1.550000e-27 134.0
39 TraesCS5A01G361200 chr2B 91.566 83 7 0 1105 1187 654734315 654734397 5.610000e-22 115.0
40 TraesCS5A01G361200 chr2B 90.476 84 7 1 1105 1187 654683554 654683637 2.610000e-20 110.0
41 TraesCS5A01G361200 chr2B 90.244 82 8 0 1106 1187 654705390 654705471 9.390000e-20 108.0
42 TraesCS5A01G361200 chr6B 89.362 188 19 1 636 822 452159037 452158850 4.130000e-58 235.0
43 TraesCS5A01G361200 chrUn 91.667 84 6 1 1105 1187 248128717 248128800 5.610000e-22 115.0


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 TraesCS5A01G361200 chr5A 562486250 562488732 2482 False 4586.00 4586 100.0000 1 2483 1 chr5A.!!$F1 2482
1 TraesCS5A01G361200 chr4A 398504737 398506554 1817 True 3029.00 3029 96.5350 637 2483 1 chr4A.!!$R1 1846
2 TraesCS5A01G361200 chr1A 513743856 513745671 1815 True 3027.00 3027 96.5350 637 2483 1 chr1A.!!$R1 1846
3 TraesCS5A01G361200 chr2D 117815582 117816476 894 True 1122.00 1122 89.2940 1429 2330 1 chr2D.!!$R1 901
4 TraesCS5A01G361200 chr3B 806376451 806377100 649 True 726.00 726 86.8700 1679 2331 1 chr3B.!!$R1 652
5 TraesCS5A01G361200 chr5D 445190005 445190579 574 False 254.85 431 91.5145 1 585 2 chr5D.!!$F1 584

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
429 473 0.105039 CGAGGCATTCCCACCTACTC 59.895 60.0 0.0 0.0 36.05 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 2308 0.546598 CCTAACCCCTAAGGCCACAG 59.453 60.0 5.01 0.0 40.58 3.66 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
28 29 3.227276 CGAGTCCCTCATCCCCGG 61.227 72.222 0.00 0.00 0.00 5.73
160 165 2.202209 CGCGTGCGTGTACGAGTA 60.202 61.111 14.57 0.00 46.46 2.59
191 196 3.190535 GGATGTAGGCGATTTGTGTTTGT 59.809 43.478 0.00 0.00 0.00 2.83
214 219 3.650369 CGTCAAAACGGGTGGAGG 58.350 61.111 0.00 0.00 45.21 4.30
220 225 3.380954 GTCAAAACGGGTGGAGGTTTTAA 59.619 43.478 2.05 0.00 42.62 1.52
228 233 0.326927 TGGAGGTTTTAAGCCCGGAG 59.673 55.000 0.73 0.00 0.00 4.63
239 244 4.162690 CCCGGAGAAGGAAGGGCG 62.163 72.222 0.73 0.00 37.07 6.13
240 245 4.162690 CCGGAGAAGGAAGGGCGG 62.163 72.222 0.00 0.00 0.00 6.13
243 248 3.009714 GAGAAGGAAGGGCGGGGT 61.010 66.667 0.00 0.00 0.00 4.95
244 249 2.531942 AGAAGGAAGGGCGGGGTT 60.532 61.111 0.00 0.00 0.00 4.11
245 250 2.361230 GAAGGAAGGGCGGGGTTG 60.361 66.667 0.00 0.00 0.00 3.77
246 251 3.938637 GAAGGAAGGGCGGGGTTGG 62.939 68.421 0.00 0.00 0.00 3.77
349 384 3.431725 CCGGGCGCTGGAAACTTC 61.432 66.667 7.64 0.00 29.82 3.01
360 395 1.369403 GGAAACTTCCCCACCTACCT 58.631 55.000 0.00 0.00 41.62 3.08
416 455 0.252761 TTGATGATGAAGGCGAGGCA 59.747 50.000 0.00 0.00 0.00 4.75
417 456 0.471191 TGATGATGAAGGCGAGGCAT 59.529 50.000 0.00 0.00 0.00 4.40
428 472 1.972660 GCGAGGCATTCCCACCTACT 61.973 60.000 0.00 0.00 36.05 2.57
429 473 0.105039 CGAGGCATTCCCACCTACTC 59.895 60.000 0.00 0.00 36.05 2.59
430 474 1.501582 GAGGCATTCCCACCTACTCT 58.498 55.000 0.00 0.00 36.05 3.24
491 535 2.048127 GGTTCAGCGTCGCCTTCT 60.048 61.111 14.86 0.00 0.00 2.85
505 549 1.610624 GCCTTCTTGACCGTGGAATGA 60.611 52.381 0.00 0.00 0.00 2.57
506 550 2.350522 CCTTCTTGACCGTGGAATGAG 58.649 52.381 0.00 0.00 0.00 2.90
507 551 2.289694 CCTTCTTGACCGTGGAATGAGT 60.290 50.000 0.00 0.00 0.00 3.41
509 553 2.766313 TCTTGACCGTGGAATGAGTTG 58.234 47.619 0.00 0.00 0.00 3.16
511 555 2.163818 TGACCGTGGAATGAGTTGTC 57.836 50.000 0.00 0.00 0.00 3.18
513 557 2.069273 GACCGTGGAATGAGTTGTCTG 58.931 52.381 0.00 0.00 0.00 3.51
514 558 0.798776 CCGTGGAATGAGTTGTCTGC 59.201 55.000 0.00 0.00 0.00 4.26
515 559 0.798776 CGTGGAATGAGTTGTCTGCC 59.201 55.000 0.00 0.00 0.00 4.85
517 561 2.353704 CGTGGAATGAGTTGTCTGCCTA 60.354 50.000 0.00 0.00 0.00 3.93
518 562 3.679917 CGTGGAATGAGTTGTCTGCCTAT 60.680 47.826 0.00 0.00 0.00 2.57
519 563 4.441495 CGTGGAATGAGTTGTCTGCCTATA 60.441 45.833 0.00 0.00 0.00 1.31
520 564 4.811557 GTGGAATGAGTTGTCTGCCTATAC 59.188 45.833 0.00 0.00 0.00 1.47
521 565 4.469586 TGGAATGAGTTGTCTGCCTATACA 59.530 41.667 0.00 0.00 0.00 2.29
522 566 5.130975 TGGAATGAGTTGTCTGCCTATACAT 59.869 40.000 0.00 0.00 0.00 2.29
523 567 6.058183 GGAATGAGTTGTCTGCCTATACATT 58.942 40.000 0.00 0.00 0.00 2.71
524 568 6.017605 GGAATGAGTTGTCTGCCTATACATTG 60.018 42.308 0.00 0.00 0.00 2.82
525 569 5.675684 TGAGTTGTCTGCCTATACATTGA 57.324 39.130 0.00 0.00 0.00 2.57
526 570 5.419542 TGAGTTGTCTGCCTATACATTGAC 58.580 41.667 0.00 0.00 0.00 3.18
527 571 5.046663 TGAGTTGTCTGCCTATACATTGACA 60.047 40.000 0.00 0.00 33.41 3.58
528 572 5.178797 AGTTGTCTGCCTATACATTGACAC 58.821 41.667 0.00 0.00 34.73 3.67
529 573 3.780902 TGTCTGCCTATACATTGACACG 58.219 45.455 0.00 0.00 30.78 4.49
530 574 2.540101 GTCTGCCTATACATTGACACGC 59.460 50.000 0.00 0.00 0.00 5.34
531 575 2.430694 TCTGCCTATACATTGACACGCT 59.569 45.455 0.00 0.00 0.00 5.07
532 576 2.797156 CTGCCTATACATTGACACGCTC 59.203 50.000 0.00 0.00 0.00 5.03
533 577 2.430694 TGCCTATACATTGACACGCTCT 59.569 45.455 0.00 0.00 0.00 4.09
534 578 3.118775 TGCCTATACATTGACACGCTCTT 60.119 43.478 0.00 0.00 0.00 2.85
535 579 3.871594 GCCTATACATTGACACGCTCTTT 59.128 43.478 0.00 0.00 0.00 2.52
536 580 4.332819 GCCTATACATTGACACGCTCTTTT 59.667 41.667 0.00 0.00 0.00 2.27
537 581 5.502544 GCCTATACATTGACACGCTCTTTTC 60.503 44.000 0.00 0.00 0.00 2.29
538 582 4.946784 ATACATTGACACGCTCTTTTCC 57.053 40.909 0.00 0.00 0.00 3.13
539 583 2.851195 ACATTGACACGCTCTTTTCCT 58.149 42.857 0.00 0.00 0.00 3.36
540 584 2.808543 ACATTGACACGCTCTTTTCCTC 59.191 45.455 0.00 0.00 0.00 3.71
541 585 2.910688 TTGACACGCTCTTTTCCTCT 57.089 45.000 0.00 0.00 0.00 3.69
542 586 2.154854 TGACACGCTCTTTTCCTCTG 57.845 50.000 0.00 0.00 0.00 3.35
585 629 5.553123 TCATACCAAAGTACACCGTCAAAT 58.447 37.500 0.00 0.00 0.00 2.32
586 630 5.410132 TCATACCAAAGTACACCGTCAAATG 59.590 40.000 0.00 0.00 0.00 2.32
587 631 2.882137 ACCAAAGTACACCGTCAAATGG 59.118 45.455 0.00 0.00 0.00 3.16
588 632 2.882137 CCAAAGTACACCGTCAAATGGT 59.118 45.455 0.00 0.00 38.21 3.55
589 633 4.066490 CCAAAGTACACCGTCAAATGGTA 58.934 43.478 0.00 0.00 34.66 3.25
590 634 4.083696 CCAAAGTACACCGTCAAATGGTAC 60.084 45.833 0.00 0.00 34.66 3.34
591 635 4.612264 AAGTACACCGTCAAATGGTACT 57.388 40.909 0.00 0.00 44.64 2.73
592 636 5.726980 AAGTACACCGTCAAATGGTACTA 57.273 39.130 0.00 0.00 42.63 1.82
593 637 5.064441 AGTACACCGTCAAATGGTACTAC 57.936 43.478 0.00 0.00 41.90 2.73
594 638 4.523943 AGTACACCGTCAAATGGTACTACA 59.476 41.667 0.00 0.00 41.90 2.74
595 639 4.546829 ACACCGTCAAATGGTACTACAT 57.453 40.909 0.00 0.00 34.66 2.29
596 640 4.501071 ACACCGTCAAATGGTACTACATC 58.499 43.478 0.00 0.00 34.66 3.06
597 641 4.222145 ACACCGTCAAATGGTACTACATCT 59.778 41.667 0.00 0.00 34.66 2.90
598 642 5.419788 ACACCGTCAAATGGTACTACATCTA 59.580 40.000 0.00 0.00 34.66 1.98
599 643 5.747197 CACCGTCAAATGGTACTACATCTAC 59.253 44.000 0.00 0.00 34.66 2.59
600 644 5.419788 ACCGTCAAATGGTACTACATCTACA 59.580 40.000 0.00 0.00 35.27 2.74
601 645 6.097839 ACCGTCAAATGGTACTACATCTACAT 59.902 38.462 0.00 0.00 35.27 2.29
602 646 6.984474 CCGTCAAATGGTACTACATCTACATT 59.016 38.462 0.00 0.00 0.00 2.71
603 647 8.139350 CCGTCAAATGGTACTACATCTACATTA 58.861 37.037 0.00 0.00 0.00 1.90
604 648 8.965172 CGTCAAATGGTACTACATCTACATTAC 58.035 37.037 0.00 0.00 0.00 1.89
605 649 9.257651 GTCAAATGGTACTACATCTACATTACC 57.742 37.037 0.00 0.00 0.00 2.85
606 650 8.139350 TCAAATGGTACTACATCTACATTACCG 58.861 37.037 0.00 0.00 33.07 4.02
607 651 7.828508 AATGGTACTACATCTACATTACCGA 57.171 36.000 0.00 0.00 33.07 4.69
608 652 7.828508 ATGGTACTACATCTACATTACCGAA 57.171 36.000 0.00 0.00 33.07 4.30
609 653 7.643569 TGGTACTACATCTACATTACCGAAA 57.356 36.000 0.00 0.00 33.07 3.46
610 654 7.709947 TGGTACTACATCTACATTACCGAAAG 58.290 38.462 0.00 0.00 33.07 2.62
611 655 7.557358 TGGTACTACATCTACATTACCGAAAGA 59.443 37.037 0.00 0.00 33.07 2.52
612 656 8.574737 GGTACTACATCTACATTACCGAAAGAT 58.425 37.037 0.00 0.00 0.00 2.40
621 665 9.158233 TCTACATTACCGAAAGATAAAAACAGG 57.842 33.333 0.00 0.00 0.00 4.00
622 666 7.153217 ACATTACCGAAAGATAAAAACAGGG 57.847 36.000 0.00 0.00 0.00 4.45
623 667 6.152154 ACATTACCGAAAGATAAAAACAGGGG 59.848 38.462 0.00 0.00 0.00 4.79
624 668 2.823747 ACCGAAAGATAAAAACAGGGGC 59.176 45.455 0.00 0.00 0.00 5.80
625 669 2.823154 CCGAAAGATAAAAACAGGGGCA 59.177 45.455 0.00 0.00 0.00 5.36
626 670 3.366985 CCGAAAGATAAAAACAGGGGCAC 60.367 47.826 0.00 0.00 0.00 5.01
627 671 3.506067 CGAAAGATAAAAACAGGGGCACT 59.494 43.478 0.00 0.00 0.00 4.40
628 672 4.698304 CGAAAGATAAAAACAGGGGCACTA 59.302 41.667 0.00 0.00 0.00 2.74
629 673 5.391629 CGAAAGATAAAAACAGGGGCACTAC 60.392 44.000 0.00 0.00 0.00 2.73
630 674 4.650972 AGATAAAAACAGGGGCACTACA 57.349 40.909 0.00 0.00 0.00 2.74
631 675 4.332828 AGATAAAAACAGGGGCACTACAC 58.667 43.478 0.00 0.00 0.00 2.90
632 676 2.445682 AAAAACAGGGGCACTACACA 57.554 45.000 0.00 0.00 0.00 3.72
633 677 1.687563 AAAACAGGGGCACTACACAC 58.312 50.000 0.00 0.00 0.00 3.82
634 678 0.179001 AAACAGGGGCACTACACACC 60.179 55.000 0.00 0.00 0.00 4.16
635 679 2.047274 CAGGGGCACTACACACCG 60.047 66.667 0.00 0.00 0.00 4.94
644 688 3.488721 GGCACTACACACCGTATCTACTG 60.489 52.174 0.00 0.00 0.00 2.74
693 737 5.605534 AGAACCGAGTCATCTTATCCATTG 58.394 41.667 0.00 0.00 0.00 2.82
705 749 9.749340 TCATCTTATCCATTGAAGCATATGATT 57.251 29.630 5.77 5.77 0.00 2.57
729 773 6.065976 TGATGGTCTAAATCACTCCAACAT 57.934 37.500 0.00 0.00 0.00 2.71
732 776 8.274322 TGATGGTCTAAATCACTCCAACATATT 58.726 33.333 0.00 0.00 0.00 1.28
1048 1092 4.856801 CGGGCATCCAGGGGAACG 62.857 72.222 0.00 0.00 34.34 3.95
1115 1159 4.452733 CCACCGCTCCTTCCCGTC 62.453 72.222 0.00 0.00 0.00 4.79
1116 1160 4.796231 CACCGCTCCTTCCCGTCG 62.796 72.222 0.00 0.00 0.00 5.12
1119 1163 4.856607 CGCTCCTTCCCGTCGCTC 62.857 72.222 0.00 0.00 0.00 5.03
1120 1164 3.453679 GCTCCTTCCCGTCGCTCT 61.454 66.667 0.00 0.00 0.00 4.09
1121 1165 2.802106 CTCCTTCCCGTCGCTCTC 59.198 66.667 0.00 0.00 0.00 3.20
1122 1166 2.754658 TCCTTCCCGTCGCTCTCC 60.755 66.667 0.00 0.00 0.00 3.71
1123 1167 3.839432 CCTTCCCGTCGCTCTCCC 61.839 72.222 0.00 0.00 0.00 4.30
1124 1168 3.068691 CTTCCCGTCGCTCTCCCA 61.069 66.667 0.00 0.00 0.00 4.37
1125 1169 3.358076 CTTCCCGTCGCTCTCCCAC 62.358 68.421 0.00 0.00 0.00 4.61
1130 1174 4.500116 GTCGCTCTCCCACCGCTC 62.500 72.222 0.00 0.00 0.00 5.03
1133 1177 3.394836 GCTCTCCCACCGCTCCTT 61.395 66.667 0.00 0.00 0.00 3.36
1134 1178 2.896443 CTCTCCCACCGCTCCTTC 59.104 66.667 0.00 0.00 0.00 3.46
1135 1179 2.683933 TCTCCCACCGCTCCTTCC 60.684 66.667 0.00 0.00 0.00 3.46
1136 1180 3.787001 CTCCCACCGCTCCTTCCC 61.787 72.222 0.00 0.00 0.00 3.97
1621 1667 6.426633 TGTGATTAATCGCTTCTCAACTCAAA 59.573 34.615 25.19 2.38 38.12 2.69
1622 1668 7.041440 TGTGATTAATCGCTTCTCAACTCAAAA 60.041 33.333 25.19 1.99 38.12 2.44
1625 1671 9.346725 GATTAATCGCTTCTCAACTCAAAAATT 57.653 29.630 0.00 0.00 0.00 1.82
1948 1995 7.177216 TGAGAATGAAAACTGGCATATGACTTT 59.823 33.333 10.60 1.77 0.00 2.66
2170 2219 5.473504 ACTGTGAATGTTTATGAACCCACTC 59.526 40.000 14.18 2.23 34.80 3.51
2405 2455 1.902508 CCCAAGAGCTCTAAGGTGTGA 59.097 52.381 25.36 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 148 2.202209 TACTCGTACACGCACGCG 60.202 61.111 10.36 10.36 41.67 6.01
144 149 0.095245 TAGTACTCGTACACGCACGC 59.905 55.000 0.00 0.00 41.67 5.34
145 150 1.391485 ACTAGTACTCGTACACGCACG 59.609 52.381 0.00 0.00 43.28 5.34
160 165 1.112113 CGCCTACATCCACCACTAGT 58.888 55.000 0.00 0.00 0.00 2.57
191 196 1.814586 ACCCGTTTTGACGCGACAA 60.815 52.632 19.59 19.59 0.00 3.18
214 219 2.484742 TCCTTCTCCGGGCTTAAAAC 57.515 50.000 0.00 0.00 0.00 2.43
220 225 2.689034 CCCTTCCTTCTCCGGGCT 60.689 66.667 0.00 0.00 0.00 5.19
228 233 2.361230 CAACCCCGCCCTTCCTTC 60.361 66.667 0.00 0.00 0.00 3.46
264 293 1.512926 CAAACCAGACCGGAGTTGAG 58.487 55.000 9.46 0.00 36.18 3.02
268 297 2.030562 CGCAAACCAGACCGGAGT 59.969 61.111 9.46 0.00 38.63 3.85
349 384 1.478288 CGTAGAGGTAGGTAGGTGGGG 60.478 61.905 0.00 0.00 0.00 4.96
350 385 1.478288 CCGTAGAGGTAGGTAGGTGGG 60.478 61.905 0.00 0.00 34.51 4.61
389 428 3.181503 CGCCTTCATCATCAAGTCAAAGG 60.182 47.826 0.00 0.00 35.88 3.11
391 430 3.673902 TCGCCTTCATCATCAAGTCAAA 58.326 40.909 0.00 0.00 0.00 2.69
416 455 1.392710 CCGCGAGAGTAGGTGGGAAT 61.393 60.000 8.23 0.00 0.00 3.01
417 456 2.050350 CCGCGAGAGTAGGTGGGAA 61.050 63.158 8.23 0.00 0.00 3.97
459 503 2.524300 AACCGTTCGTTCATCCGTG 58.476 52.632 0.00 0.00 0.00 4.94
491 535 2.104111 AGACAACTCATTCCACGGTCAA 59.896 45.455 0.00 0.00 0.00 3.18
505 549 5.178797 GTGTCAATGTATAGGCAGACAACT 58.821 41.667 0.00 0.00 37.69 3.16
506 550 4.032900 CGTGTCAATGTATAGGCAGACAAC 59.967 45.833 0.00 0.00 37.69 3.32
507 551 4.180817 CGTGTCAATGTATAGGCAGACAA 58.819 43.478 0.00 0.00 37.69 3.18
509 553 2.540101 GCGTGTCAATGTATAGGCAGAC 59.460 50.000 0.00 0.00 0.00 3.51
511 555 2.797156 GAGCGTGTCAATGTATAGGCAG 59.203 50.000 0.00 0.00 0.00 4.85
513 557 3.099267 AGAGCGTGTCAATGTATAGGC 57.901 47.619 0.00 0.00 0.00 3.93
514 558 5.006746 GGAAAAGAGCGTGTCAATGTATAGG 59.993 44.000 0.00 0.00 0.00 2.57
515 559 5.812642 AGGAAAAGAGCGTGTCAATGTATAG 59.187 40.000 0.00 0.00 0.00 1.31
517 561 4.579869 AGGAAAAGAGCGTGTCAATGTAT 58.420 39.130 0.00 0.00 0.00 2.29
518 562 3.994392 GAGGAAAAGAGCGTGTCAATGTA 59.006 43.478 0.00 0.00 0.00 2.29
519 563 2.808543 GAGGAAAAGAGCGTGTCAATGT 59.191 45.455 0.00 0.00 0.00 2.71
520 564 3.070018 AGAGGAAAAGAGCGTGTCAATG 58.930 45.455 0.00 0.00 0.00 2.82
521 565 3.070018 CAGAGGAAAAGAGCGTGTCAAT 58.930 45.455 0.00 0.00 0.00 2.57
522 566 2.483876 CAGAGGAAAAGAGCGTGTCAA 58.516 47.619 0.00 0.00 0.00 3.18
523 567 1.270305 CCAGAGGAAAAGAGCGTGTCA 60.270 52.381 0.00 0.00 0.00 3.58
524 568 1.270358 ACCAGAGGAAAAGAGCGTGTC 60.270 52.381 0.00 0.00 0.00 3.67
525 569 0.759346 ACCAGAGGAAAAGAGCGTGT 59.241 50.000 0.00 0.00 0.00 4.49
526 570 1.270305 TGACCAGAGGAAAAGAGCGTG 60.270 52.381 0.00 0.00 0.00 5.34
527 571 1.048601 TGACCAGAGGAAAAGAGCGT 58.951 50.000 0.00 0.00 0.00 5.07
528 572 1.433534 GTGACCAGAGGAAAAGAGCG 58.566 55.000 0.00 0.00 0.00 5.03
529 573 1.433534 CGTGACCAGAGGAAAAGAGC 58.566 55.000 0.00 0.00 0.00 4.09
530 574 1.618837 TCCGTGACCAGAGGAAAAGAG 59.381 52.381 0.00 0.00 0.00 2.85
531 575 1.343465 GTCCGTGACCAGAGGAAAAGA 59.657 52.381 0.00 0.00 35.60 2.52
532 576 1.797025 GTCCGTGACCAGAGGAAAAG 58.203 55.000 0.00 0.00 35.60 2.27
533 577 0.032952 CGTCCGTGACCAGAGGAAAA 59.967 55.000 0.00 0.00 35.60 2.29
534 578 1.663739 CGTCCGTGACCAGAGGAAA 59.336 57.895 0.00 0.00 35.60 3.13
535 579 2.927580 GCGTCCGTGACCAGAGGAA 61.928 63.158 0.00 0.00 35.60 3.36
536 580 3.371063 GCGTCCGTGACCAGAGGA 61.371 66.667 0.00 0.00 0.00 3.71
537 581 3.343788 GAGCGTCCGTGACCAGAGG 62.344 68.421 0.00 0.00 0.00 3.69
538 582 2.179517 GAGCGTCCGTGACCAGAG 59.820 66.667 0.00 0.00 0.00 3.35
539 583 3.733960 CGAGCGTCCGTGACCAGA 61.734 66.667 0.00 0.00 0.00 3.86
540 584 4.778415 CCGAGCGTCCGTGACCAG 62.778 72.222 0.00 0.00 0.00 4.00
585 629 7.557358 TCTTTCGGTAATGTAGATGTAGTACCA 59.443 37.037 0.00 0.00 32.23 3.25
586 630 7.934457 TCTTTCGGTAATGTAGATGTAGTACC 58.066 38.462 0.00 0.00 0.00 3.34
595 639 9.158233 CCTGTTTTTATCTTTCGGTAATGTAGA 57.842 33.333 0.00 0.00 0.00 2.59
596 640 8.395633 CCCTGTTTTTATCTTTCGGTAATGTAG 58.604 37.037 0.00 0.00 0.00 2.74
597 641 7.337436 CCCCTGTTTTTATCTTTCGGTAATGTA 59.663 37.037 0.00 0.00 0.00 2.29
598 642 6.152154 CCCCTGTTTTTATCTTTCGGTAATGT 59.848 38.462 0.00 0.00 0.00 2.71
599 643 6.560711 CCCCTGTTTTTATCTTTCGGTAATG 58.439 40.000 0.00 0.00 0.00 1.90
600 644 5.126545 GCCCCTGTTTTTATCTTTCGGTAAT 59.873 40.000 0.00 0.00 0.00 1.89
601 645 4.460034 GCCCCTGTTTTTATCTTTCGGTAA 59.540 41.667 0.00 0.00 0.00 2.85
602 646 4.011698 GCCCCTGTTTTTATCTTTCGGTA 58.988 43.478 0.00 0.00 0.00 4.02
603 647 2.823747 GCCCCTGTTTTTATCTTTCGGT 59.176 45.455 0.00 0.00 0.00 4.69
604 648 2.823154 TGCCCCTGTTTTTATCTTTCGG 59.177 45.455 0.00 0.00 0.00 4.30
605 649 3.506067 AGTGCCCCTGTTTTTATCTTTCG 59.494 43.478 0.00 0.00 0.00 3.46
606 650 5.475564 TGTAGTGCCCCTGTTTTTATCTTTC 59.524 40.000 0.00 0.00 0.00 2.62
607 651 5.243060 GTGTAGTGCCCCTGTTTTTATCTTT 59.757 40.000 0.00 0.00 0.00 2.52
608 652 4.765339 GTGTAGTGCCCCTGTTTTTATCTT 59.235 41.667 0.00 0.00 0.00 2.40
609 653 4.202524 TGTGTAGTGCCCCTGTTTTTATCT 60.203 41.667 0.00 0.00 0.00 1.98
610 654 4.076394 TGTGTAGTGCCCCTGTTTTTATC 58.924 43.478 0.00 0.00 0.00 1.75
611 655 3.824443 GTGTGTAGTGCCCCTGTTTTTAT 59.176 43.478 0.00 0.00 0.00 1.40
612 656 3.215975 GTGTGTAGTGCCCCTGTTTTTA 58.784 45.455 0.00 0.00 0.00 1.52
613 657 2.028876 GTGTGTAGTGCCCCTGTTTTT 58.971 47.619 0.00 0.00 0.00 1.94
614 658 1.687563 GTGTGTAGTGCCCCTGTTTT 58.312 50.000 0.00 0.00 0.00 2.43
615 659 0.179001 GGTGTGTAGTGCCCCTGTTT 60.179 55.000 0.00 0.00 0.00 2.83
616 660 1.454539 GGTGTGTAGTGCCCCTGTT 59.545 57.895 0.00 0.00 0.00 3.16
617 661 2.879233 CGGTGTGTAGTGCCCCTGT 61.879 63.158 0.00 0.00 0.00 4.00
618 662 1.537814 TACGGTGTGTAGTGCCCCTG 61.538 60.000 0.00 0.00 0.00 4.45
619 663 0.616679 ATACGGTGTGTAGTGCCCCT 60.617 55.000 0.00 0.00 36.25 4.79
620 664 0.179092 GATACGGTGTGTAGTGCCCC 60.179 60.000 0.00 0.00 36.25 5.80
621 665 0.822164 AGATACGGTGTGTAGTGCCC 59.178 55.000 0.00 0.00 36.25 5.36
622 666 2.686915 AGTAGATACGGTGTGTAGTGCC 59.313 50.000 0.00 0.00 36.25 5.01
623 667 3.692576 CAGTAGATACGGTGTGTAGTGC 58.307 50.000 4.40 0.00 36.25 4.40
624 668 3.488721 GGCAGTAGATACGGTGTGTAGTG 60.489 52.174 11.08 11.08 36.25 2.74
625 669 2.686915 GGCAGTAGATACGGTGTGTAGT 59.313 50.000 0.00 0.00 36.25 2.73
626 670 2.686405 TGGCAGTAGATACGGTGTGTAG 59.314 50.000 0.00 0.00 36.25 2.74
627 671 2.424601 GTGGCAGTAGATACGGTGTGTA 59.575 50.000 0.00 0.00 37.49 2.90
628 672 1.203994 GTGGCAGTAGATACGGTGTGT 59.796 52.381 0.00 0.00 0.00 3.72
629 673 1.476891 AGTGGCAGTAGATACGGTGTG 59.523 52.381 0.00 0.00 0.00 3.82
630 674 1.848652 AGTGGCAGTAGATACGGTGT 58.151 50.000 0.00 0.00 0.00 4.16
631 675 5.700722 TTATAGTGGCAGTAGATACGGTG 57.299 43.478 8.22 0.00 0.00 4.94
632 676 6.239232 CCTTTTATAGTGGCAGTAGATACGGT 60.239 42.308 8.22 0.00 0.00 4.83
633 677 6.015688 TCCTTTTATAGTGGCAGTAGATACGG 60.016 42.308 8.22 6.00 0.00 4.02
634 678 6.862090 GTCCTTTTATAGTGGCAGTAGATACG 59.138 42.308 8.22 0.00 0.00 3.06
635 679 6.862090 CGTCCTTTTATAGTGGCAGTAGATAC 59.138 42.308 8.22 0.00 0.00 2.24
644 688 3.492829 CCCTCTCGTCCTTTTATAGTGGC 60.493 52.174 0.00 0.00 0.00 5.01
685 729 8.745590 CCATCAAATCATATGCTTCAATGGATA 58.254 33.333 18.93 0.00 33.38 2.59
693 737 9.837525 GATTTAGACCATCAAATCATATGCTTC 57.162 33.333 0.00 0.00 39.74 3.86
705 749 5.875224 TGTTGGAGTGATTTAGACCATCAA 58.125 37.500 0.00 0.00 32.37 2.57
1048 1092 4.767255 CAGGACCTCACTGCCGGC 62.767 72.222 22.73 22.73 0.00 6.13
1075 1119 2.184579 CGACGGGAGGAAGAAGCC 59.815 66.667 0.00 0.00 0.00 4.35
1116 1160 3.378399 GAAGGAGCGGTGGGAGAGC 62.378 68.421 0.00 0.00 0.00 4.09
1117 1161 2.726351 GGAAGGAGCGGTGGGAGAG 61.726 68.421 0.00 0.00 0.00 3.20
1118 1162 2.683933 GGAAGGAGCGGTGGGAGA 60.684 66.667 0.00 0.00 0.00 3.71
1119 1163 3.787001 GGGAAGGAGCGGTGGGAG 61.787 72.222 0.00 0.00 0.00 4.30
1288 1332 1.671379 GGAGAGGCCCACGTTGAAC 60.671 63.158 0.00 0.00 0.00 3.18
1514 1559 4.775058 AGACGTCCTCATACATATCTGC 57.225 45.455 13.01 0.00 0.00 4.26
1621 1667 8.380742 TCACAAGACTATAGAAGAGGGAATTT 57.619 34.615 6.78 0.00 0.00 1.82
1622 1668 7.841729 TCTCACAAGACTATAGAAGAGGGAATT 59.158 37.037 6.78 0.00 0.00 2.17
1625 1671 6.328782 TCTCACAAGACTATAGAAGAGGGA 57.671 41.667 6.78 0.00 0.00 4.20
1948 1995 1.475403 CTCCTTTCGAGGCCTCAGTA 58.525 55.000 31.67 14.17 34.67 2.74
2170 2219 9.770097 TGCCTTATCATCTTAGTTATTCAGAAG 57.230 33.333 0.00 0.00 0.00 2.85
2258 2308 0.546598 CCTAACCCCTAAGGCCACAG 59.453 60.000 5.01 0.00 40.58 3.66


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

AutoCloner maintained by Alex Coulton.