Multiple sequence alignment - TraesCS2D01G279800

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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 TraesCS2D01G279800 chr2D 100.000 3098 0 0 1 3098 351383350 351386447 0.000000e+00 5722
1 TraesCS2D01G279800 chr7A 97.463 1616 40 1 1484 3098 649824953 649826568 0.000000e+00 2756
2 TraesCS2D01G279800 chr1A 96.101 1616 62 1 1484 3098 120005827 120004212 0.000000e+00 2634
3 TraesCS2D01G279800 chr1A 93.390 817 45 7 671 1483 120009133 120008322 0.000000e+00 1201
4 TraesCS2D01G279800 chr2A 96.042 1617 60 4 1484 3098 82979919 82981533 0.000000e+00 2628
5 TraesCS2D01G279800 chr2A 93.880 817 41 5 671 1483 82976599 82977410 0.000000e+00 1223
6 TraesCS2D01G279800 chr3A 95.173 1616 77 1 1484 3098 708857047 708858662 0.000000e+00 2551
7 TraesCS2D01G279800 chr3A 93.988 815 36 8 671 1483 708847784 708848587 0.000000e+00 1221
8 TraesCS2D01G279800 chrUn 94.988 1616 80 1 1484 3098 92277472 92275857 0.000000e+00 2534
9 TraesCS2D01G279800 chr3B 92.773 1619 114 3 1481 3098 763654155 763655771 0.000000e+00 2338
10 TraesCS2D01G279800 chr3B 92.620 813 44 6 671 1483 763650854 763651650 0.000000e+00 1155
11 TraesCS2D01G279800 chr3B 91.443 818 61 6 671 1483 789351043 789351856 0.000000e+00 1114
12 TraesCS2D01G279800 chr3B 91.198 818 63 6 671 1483 789386080 789386893 0.000000e+00 1103
13 TraesCS2D01G279800 chr2B 91.878 1613 130 1 1487 3098 387100699 387102311 0.000000e+00 2252
14 TraesCS2D01G279800 chr2B 85.071 422 44 12 1 407 417775167 417775584 2.220000e-111 412
15 TraesCS2D01G279800 chr2B 89.286 112 6 2 532 643 417775889 417775994 5.390000e-28 135
16 TraesCS2D01G279800 chr7B 91.754 1613 130 3 1487 3098 621786976 621785366 0.000000e+00 2239
17 TraesCS2D01G279800 chr4A 91.135 1613 141 2 1487 3098 736453426 736455037 0.000000e+00 2185
18 TraesCS2D01G279800 chr5B 94.479 815 39 5 671 1483 661327772 661328582 0.000000e+00 1251
19 TraesCS2D01G279800 chr4D 93.293 820 40 10 671 1483 214968401 214967590 0.000000e+00 1195
20 TraesCS2D01G279800 chr3D 91.829 820 53 10 671 1483 578169398 578170210 0.000000e+00 1131


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 TraesCS2D01G279800 chr2D 351383350 351386447 3097 False 5722.0 5722 100.0000 1 3098 1 chr2D.!!$F1 3097
1 TraesCS2D01G279800 chr7A 649824953 649826568 1615 False 2756.0 2756 97.4630 1484 3098 1 chr7A.!!$F1 1614
2 TraesCS2D01G279800 chr1A 120004212 120009133 4921 True 1917.5 2634 94.7455 671 3098 2 chr1A.!!$R1 2427
3 TraesCS2D01G279800 chr2A 82976599 82981533 4934 False 1925.5 2628 94.9610 671 3098 2 chr2A.!!$F1 2427
4 TraesCS2D01G279800 chr3A 708857047 708858662 1615 False 2551.0 2551 95.1730 1484 3098 1 chr3A.!!$F2 1614
5 TraesCS2D01G279800 chr3A 708847784 708848587 803 False 1221.0 1221 93.9880 671 1483 1 chr3A.!!$F1 812
6 TraesCS2D01G279800 chrUn 92275857 92277472 1615 True 2534.0 2534 94.9880 1484 3098 1 chrUn.!!$R1 1614
7 TraesCS2D01G279800 chr3B 763650854 763655771 4917 False 1746.5 2338 92.6965 671 3098 2 chr3B.!!$F3 2427
8 TraesCS2D01G279800 chr3B 789351043 789351856 813 False 1114.0 1114 91.4430 671 1483 1 chr3B.!!$F1 812
9 TraesCS2D01G279800 chr3B 789386080 789386893 813 False 1103.0 1103 91.1980 671 1483 1 chr3B.!!$F2 812
10 TraesCS2D01G279800 chr2B 387100699 387102311 1612 False 2252.0 2252 91.8780 1487 3098 1 chr2B.!!$F1 1611
11 TraesCS2D01G279800 chr2B 417775167 417775994 827 False 273.5 412 87.1785 1 643 2 chr2B.!!$F2 642
12 TraesCS2D01G279800 chr7B 621785366 621786976 1610 True 2239.0 2239 91.7540 1487 3098 1 chr7B.!!$R1 1611
13 TraesCS2D01G279800 chr4A 736453426 736455037 1611 False 2185.0 2185 91.1350 1487 3098 1 chr4A.!!$F1 1611
14 TraesCS2D01G279800 chr5B 661327772 661328582 810 False 1251.0 1251 94.4790 671 1483 1 chr5B.!!$F1 812
15 TraesCS2D01G279800 chr4D 214967590 214968401 811 True 1195.0 1195 93.2930 671 1483 1 chr4D.!!$R1 812
16 TraesCS2D01G279800 chr3D 578169398 578170210 812 False 1131.0 1131 91.8290 671 1483 1 chr3D.!!$F1 812

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
456 472 0.255890 ACCCAATCCCTGACCGAATG 59.744 55.0 0.00 0.0 0.00 2.67 F
525 735 0.458543 AGATACAGGTTGCTCGTGCG 60.459 55.0 4.84 0.0 43.34 5.34 F
922 1140 0.963962 ACCGAGGCTAAGACGTTTCA 59.036 50.0 0.00 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 4223 1.001764 CCATGGCAGAAGCTGGTGA 60.002 57.895 0.00 0.0 41.70 4.02 R
1497 4225 1.578215 ATCCCATGGCAGAAGCTGGT 61.578 55.000 6.09 0.0 41.70 4.00 R
2736 5466 1.421268 TCTGTCATCAAGGCAACCTGT 59.579 47.619 0.00 0.0 32.13 4.00 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
25 26 5.360999 ACAAAAGGAAACTGAAGGAAAGAGG 59.639 40.000 0.00 0.00 42.68 3.69
26 27 3.147553 AGGAAACTGAAGGAAAGAGGC 57.852 47.619 0.00 0.00 41.13 4.70
35 36 6.825610 ACTGAAGGAAAGAGGCTGATTATAG 58.174 40.000 0.00 0.00 0.00 1.31
41 42 5.012148 GGAAAGAGGCTGATTATAGCACCTA 59.988 44.000 0.00 0.00 45.46 3.08
93 95 9.249053 TGTTCATAGAAAATAAAAGGCATGGTA 57.751 29.630 0.00 0.00 0.00 3.25
130 134 2.886523 TCCTTTTGTGGCAGTCATGAAG 59.113 45.455 0.00 0.00 0.00 3.02
133 137 1.511850 TTGTGGCAGTCATGAAGTCG 58.488 50.000 0.00 0.00 0.00 4.18
144 148 2.076863 CATGAAGTCGTCCTGGTTTCC 58.923 52.381 0.00 0.00 0.00 3.13
248 259 9.965748 ACAAACGATAAATCAAAACAAAAAGTG 57.034 25.926 0.00 0.00 0.00 3.16
249 260 9.419737 CAAACGATAAATCAAAACAAAAAGTGG 57.580 29.630 0.00 0.00 0.00 4.00
356 371 7.153985 CACATACTTCAATTTGTGGTGGAAAT 58.846 34.615 0.00 0.00 36.64 2.17
407 423 5.367060 GGAGAGAACCTGGTATTGTATTCCT 59.633 44.000 0.00 0.00 0.00 3.36
408 424 6.553852 GGAGAGAACCTGGTATTGTATTCCTA 59.446 42.308 0.00 0.00 0.00 2.94
409 425 7.256012 GGAGAGAACCTGGTATTGTATTCCTAG 60.256 44.444 0.00 0.00 0.00 3.02
410 426 7.133483 AGAGAACCTGGTATTGTATTCCTAGT 58.867 38.462 0.00 0.00 0.00 2.57
415 431 8.937207 ACCTGGTATTGTATTCCTAGTAGTAG 57.063 38.462 0.00 0.00 0.00 2.57
423 439 8.674263 TTGTATTCCTAGTAGTAGTAGACTGC 57.326 38.462 12.83 0.00 39.39 4.40
431 447 5.594724 GTAGTAGTAGACTGCTATGGTCG 57.405 47.826 10.19 0.00 41.85 4.79
433 449 4.975631 AGTAGTAGACTGCTATGGTCGAT 58.024 43.478 3.44 0.00 37.15 3.59
434 450 6.111669 AGTAGTAGACTGCTATGGTCGATA 57.888 41.667 3.44 0.00 37.15 2.92
435 451 6.167685 AGTAGTAGACTGCTATGGTCGATAG 58.832 44.000 3.44 0.00 37.15 2.08
436 452 4.328536 AGTAGACTGCTATGGTCGATAGG 58.671 47.826 4.28 0.00 38.58 2.57
437 453 3.510531 AGACTGCTATGGTCGATAGGA 57.489 47.619 4.28 0.51 38.58 2.94
438 454 3.150767 AGACTGCTATGGTCGATAGGAC 58.849 50.000 4.28 0.00 45.31 3.85
452 468 2.590092 GGACCCAATCCCTGACCG 59.410 66.667 0.00 0.00 42.46 4.79
453 469 1.993391 GGACCCAATCCCTGACCGA 60.993 63.158 0.00 0.00 42.46 4.69
455 471 0.546598 GACCCAATCCCTGACCGAAT 59.453 55.000 0.00 0.00 0.00 3.34
456 472 0.255890 ACCCAATCCCTGACCGAATG 59.744 55.000 0.00 0.00 0.00 2.67
458 474 1.340991 CCCAATCCCTGACCGAATGTT 60.341 52.381 0.00 0.00 0.00 2.71
459 475 2.446435 CCAATCCCTGACCGAATGTTT 58.554 47.619 0.00 0.00 0.00 2.83
460 476 2.825532 CCAATCCCTGACCGAATGTTTT 59.174 45.455 0.00 0.00 0.00 2.43
462 478 2.194201 TCCCTGACCGAATGTTTTCC 57.806 50.000 0.00 0.00 0.00 3.13
464 480 1.539827 CCCTGACCGAATGTTTTCCAC 59.460 52.381 0.00 0.00 0.00 4.02
466 482 2.226437 CCTGACCGAATGTTTTCCACTG 59.774 50.000 0.00 0.00 0.00 3.66
467 483 2.226330 TGACCGAATGTTTTCCACTGG 58.774 47.619 0.00 0.00 0.00 4.00
474 490 2.727123 TGTTTTCCACTGGAGAGCAA 57.273 45.000 2.96 0.00 31.21 3.91
475 491 3.011566 TGTTTTCCACTGGAGAGCAAA 57.988 42.857 2.96 0.00 31.21 3.68
476 492 3.565307 TGTTTTCCACTGGAGAGCAAAT 58.435 40.909 2.96 0.00 31.21 2.32
478 494 4.405358 TGTTTTCCACTGGAGAGCAAATTT 59.595 37.500 2.96 0.00 31.21 1.82
479 495 4.589216 TTTCCACTGGAGAGCAAATTTG 57.411 40.909 14.03 14.03 31.21 2.32
480 496 3.228188 TCCACTGGAGAGCAAATTTGT 57.772 42.857 19.03 6.52 0.00 2.83
481 497 3.565307 TCCACTGGAGAGCAAATTTGTT 58.435 40.909 19.03 13.67 0.00 2.83
482 498 3.960102 TCCACTGGAGAGCAAATTTGTTT 59.040 39.130 19.03 8.37 0.00 2.83
483 499 4.053295 CCACTGGAGAGCAAATTTGTTTG 58.947 43.478 19.03 7.46 35.15 2.93
484 500 4.441913 CCACTGGAGAGCAAATTTGTTTGT 60.442 41.667 19.03 7.06 34.56 2.83
485 501 5.111293 CACTGGAGAGCAAATTTGTTTGTT 58.889 37.500 19.03 4.04 34.56 2.83
487 503 6.418819 CACTGGAGAGCAAATTTGTTTGTTAG 59.581 38.462 19.03 13.01 34.56 2.34
488 504 5.288804 TGGAGAGCAAATTTGTTTGTTAGC 58.711 37.500 19.03 2.58 34.56 3.09
489 505 5.163468 TGGAGAGCAAATTTGTTTGTTAGCA 60.163 36.000 19.03 0.00 34.56 3.49
492 508 6.572519 AGAGCAAATTTGTTTGTTAGCAGAA 58.427 32.000 19.03 0.00 34.56 3.02
493 509 7.041107 AGAGCAAATTTGTTTGTTAGCAGAAA 58.959 30.769 19.03 0.00 34.56 2.52
504 714 7.386848 TGTTTGTTAGCAGAAACATAGTACTCC 59.613 37.037 0.00 0.00 39.04 3.85
506 716 7.949690 TGTTAGCAGAAACATAGTACTCCTA 57.050 36.000 0.00 0.00 34.50 2.94
507 717 7.997482 TGTTAGCAGAAACATAGTACTCCTAG 58.003 38.462 0.00 0.00 34.50 3.02
508 718 7.832685 TGTTAGCAGAAACATAGTACTCCTAGA 59.167 37.037 0.00 0.00 34.50 2.43
511 721 8.398878 AGCAGAAACATAGTACTCCTAGATAC 57.601 38.462 0.00 0.00 0.00 2.24
513 723 8.293867 GCAGAAACATAGTACTCCTAGATACAG 58.706 40.741 0.00 0.00 0.00 2.74
514 724 8.788806 CAGAAACATAGTACTCCTAGATACAGG 58.211 40.741 0.00 0.00 37.00 4.00
515 725 8.504409 AGAAACATAGTACTCCTAGATACAGGT 58.496 37.037 0.00 0.00 36.99 4.00
516 726 9.134055 GAAACATAGTACTCCTAGATACAGGTT 57.866 37.037 0.00 0.00 36.99 3.50
517 727 8.466617 AACATAGTACTCCTAGATACAGGTTG 57.533 38.462 0.00 0.00 36.99 3.77
518 728 6.490721 ACATAGTACTCCTAGATACAGGTTGC 59.509 42.308 0.00 0.00 36.99 4.17
519 729 5.132043 AGTACTCCTAGATACAGGTTGCT 57.868 43.478 0.00 0.00 36.99 3.91
520 730 5.134661 AGTACTCCTAGATACAGGTTGCTC 58.865 45.833 0.00 0.00 36.99 4.26
521 731 2.952978 ACTCCTAGATACAGGTTGCTCG 59.047 50.000 0.00 0.00 36.99 5.03
522 732 2.952978 CTCCTAGATACAGGTTGCTCGT 59.047 50.000 0.00 0.00 36.99 4.18
523 733 2.688446 TCCTAGATACAGGTTGCTCGTG 59.312 50.000 0.00 0.00 36.99 4.35
524 734 2.464865 CTAGATACAGGTTGCTCGTGC 58.535 52.381 1.71 1.71 35.61 5.34
525 735 0.458543 AGATACAGGTTGCTCGTGCG 60.459 55.000 4.84 0.00 43.34 5.34
526 736 2.025359 GATACAGGTTGCTCGTGCGC 62.025 60.000 0.00 0.00 43.34 6.09
527 737 2.779951 ATACAGGTTGCTCGTGCGCA 62.780 55.000 5.66 5.66 43.34 6.09
528 738 2.980213 TACAGGTTGCTCGTGCGCAA 62.980 55.000 14.00 0.00 46.73 4.85
548 758 6.399564 GCGCAACAAATTTATCTGGTGTAAAC 60.400 38.462 0.30 0.00 32.60 2.01
552 762 6.674066 ACAAATTTATCTGGTGTAAACCACG 58.326 36.000 0.00 0.00 45.52 4.94
553 763 6.263617 ACAAATTTATCTGGTGTAAACCACGT 59.736 34.615 0.00 0.00 45.52 4.49
554 764 7.444792 ACAAATTTATCTGGTGTAAACCACGTA 59.555 33.333 0.00 0.00 45.52 3.57
555 765 8.455682 CAAATTTATCTGGTGTAAACCACGTAT 58.544 33.333 0.00 0.00 45.52 3.06
556 766 6.971527 TTTATCTGGTGTAAACCACGTATG 57.028 37.500 0.00 0.00 45.52 2.39
562 772 5.979993 TGGTGTAAACCACGTATGATGTAT 58.020 37.500 0.00 0.00 45.52 2.29
571 781 4.233005 CACGTATGATGTATGAGCCTCAG 58.767 47.826 0.00 0.00 0.00 3.35
599 809 7.453393 TCAAACTTAGTCATGTTGAGAGGAAT 58.547 34.615 0.00 0.00 0.00 3.01
648 858 5.136250 CGATCATCGTCTCCAAAGAAAAG 57.864 43.478 0.00 0.00 34.72 2.27
649 859 4.864806 CGATCATCGTCTCCAAAGAAAAGA 59.135 41.667 0.00 0.00 34.72 2.52
650 860 5.348724 CGATCATCGTCTCCAAAGAAAAGAA 59.651 40.000 0.00 0.00 34.72 2.52
651 861 6.128553 CGATCATCGTCTCCAAAGAAAAGAAA 60.129 38.462 0.00 0.00 34.72 2.52
652 862 7.413438 CGATCATCGTCTCCAAAGAAAAGAAAT 60.413 37.037 0.00 0.00 34.72 2.17
653 863 6.902341 TCATCGTCTCCAAAGAAAAGAAATG 58.098 36.000 0.00 0.00 31.93 2.32
654 864 5.689383 TCGTCTCCAAAGAAAAGAAATGG 57.311 39.130 0.00 0.00 31.93 3.16
655 865 5.130350 TCGTCTCCAAAGAAAAGAAATGGT 58.870 37.500 0.00 0.00 31.93 3.55
656 866 5.592688 TCGTCTCCAAAGAAAAGAAATGGTT 59.407 36.000 0.00 0.00 31.93 3.67
657 867 6.768861 TCGTCTCCAAAGAAAAGAAATGGTTA 59.231 34.615 0.00 0.00 31.93 2.85
658 868 7.447238 TCGTCTCCAAAGAAAAGAAATGGTTAT 59.553 33.333 0.00 0.00 31.93 1.89
659 869 7.538678 CGTCTCCAAAGAAAAGAAATGGTTATG 59.461 37.037 0.00 0.00 31.93 1.90
660 870 8.576442 GTCTCCAAAGAAAAGAAATGGTTATGA 58.424 33.333 0.00 0.00 31.93 2.15
661 871 9.142014 TCTCCAAAGAAAAGAAATGGTTATGAA 57.858 29.630 0.00 0.00 32.90 2.57
662 872 9.196552 CTCCAAAGAAAAGAAATGGTTATGAAC 57.803 33.333 0.00 0.00 32.90 3.18
663 873 8.700051 TCCAAAGAAAAGAAATGGTTATGAACA 58.300 29.630 0.00 0.00 32.90 3.18
664 874 8.981647 CCAAAGAAAAGAAATGGTTATGAACAG 58.018 33.333 0.00 0.00 0.00 3.16
665 875 9.533253 CAAAGAAAAGAAATGGTTATGAACAGT 57.467 29.630 0.00 0.00 0.00 3.55
666 876 9.533253 AAAGAAAAGAAATGGTTATGAACAGTG 57.467 29.630 0.00 0.00 0.00 3.66
667 877 8.463930 AGAAAAGAAATGGTTATGAACAGTGA 57.536 30.769 0.00 0.00 0.00 3.41
668 878 8.571336 AGAAAAGAAATGGTTATGAACAGTGAG 58.429 33.333 0.00 0.00 0.00 3.51
669 879 8.463930 AAAAGAAATGGTTATGAACAGTGAGA 57.536 30.769 0.00 0.00 0.00 3.27
820 1035 7.986553 ATCTTCTTATCTCTTCTCCTCCAAA 57.013 36.000 0.00 0.00 0.00 3.28
922 1140 0.963962 ACCGAGGCTAAGACGTTTCA 59.036 50.000 0.00 0.00 0.00 2.69
1464 1684 2.026879 GGTCTCGCGGATGAGCTC 59.973 66.667 6.82 6.82 35.90 4.09
1553 4281 1.672030 CAGGCACAACATCTCCGCA 60.672 57.895 0.00 0.00 0.00 5.69
1815 4544 9.672673 TTTAGAATTAAGAGAAAGTCAGATGGG 57.327 33.333 0.00 0.00 0.00 4.00
1952 4681 4.447138 TGTCTATTGTTGTTTCCAGGGT 57.553 40.909 0.00 0.00 0.00 4.34
1992 4721 3.650139 AGATGTACAGAACGCGTTTCTT 58.350 40.909 27.32 14.94 42.37 2.52
2005 4734 2.548057 GCGTTTCTTCATGGTGTTCTGA 59.452 45.455 0.00 0.00 0.00 3.27
2181 4911 4.678256 TCCTTCTAAGTCTGACACCTCAT 58.322 43.478 10.88 0.00 0.00 2.90
2285 5015 1.805869 CTGTCACAGGGCTCTTGAAG 58.194 55.000 0.00 0.00 0.00 3.02
2340 5070 5.357257 TCGGAGACTTGCATTATTTCCTAC 58.643 41.667 0.00 0.00 0.00 3.18
2346 5076 6.828785 AGACTTGCATTATTTCCTACGGATTT 59.171 34.615 0.00 0.00 0.00 2.17
2456 5186 2.599677 CCCTCACCTACTCCTATGTCC 58.400 57.143 0.00 0.00 0.00 4.02
2461 5191 5.131142 CCTCACCTACTCCTATGTCCAATTT 59.869 44.000 0.00 0.00 0.00 1.82
2736 5466 3.134623 TGCTTTTTCAGACTCTGACTGGA 59.865 43.478 8.35 0.00 40.46 3.86
2867 5597 3.891977 CAGAGGCAGAGTATAAGGCACTA 59.108 47.826 0.00 0.00 38.49 2.74
2924 5654 6.783708 TCCATGTTAAAAGAACTTGGTGTT 57.216 33.333 17.16 0.00 42.63 3.32
2930 5661 6.038936 TGTTAAAAGAACTTGGTGTTAGGAGC 59.961 38.462 0.00 0.00 39.30 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.816672 CAGCCTCTTTCCTTCAGTTTCC 59.183 50.000 0.00 0.00 0.00 3.13
9 10 3.864789 TCAGCCTCTTTCCTTCAGTTT 57.135 42.857 0.00 0.00 0.00 2.66
15 16 5.372373 GTGCTATAATCAGCCTCTTTCCTT 58.628 41.667 0.00 0.00 41.04 3.36
22 23 5.799213 ACATTAGGTGCTATAATCAGCCTC 58.201 41.667 0.00 0.00 41.04 4.70
25 26 7.819415 TGTATGACATTAGGTGCTATAATCAGC 59.181 37.037 0.00 0.00 42.15 4.26
26 27 9.881649 ATGTATGACATTAGGTGCTATAATCAG 57.118 33.333 0.00 0.00 34.67 2.90
35 36 7.786178 TTACTTGATGTATGACATTAGGTGC 57.214 36.000 8.72 0.00 39.27 5.01
71 72 7.653311 GGCTTACCATGCCTTTTATTTTCTATG 59.347 37.037 0.00 0.00 46.38 2.23
93 95 0.693049 AGGATCTGACGTTTGGGCTT 59.307 50.000 0.00 0.00 0.00 4.35
97 99 3.304659 CCACAAAAGGATCTGACGTTTGG 60.305 47.826 11.37 5.50 40.17 3.28
98 100 3.853307 GCCACAAAAGGATCTGACGTTTG 60.853 47.826 0.00 7.10 41.13 2.93
102 104 1.466167 CTGCCACAAAAGGATCTGACG 59.534 52.381 0.00 0.00 0.00 4.35
105 107 2.507484 TGACTGCCACAAAAGGATCTG 58.493 47.619 0.00 0.00 0.00 2.90
130 134 1.161563 TTTGCGGAAACCAGGACGAC 61.162 55.000 0.00 0.00 0.00 4.34
166 170 6.979817 TCATGAATTTGAATTTTATCAGCCGG 59.020 34.615 0.00 0.00 0.00 6.13
167 171 7.990541 TCATGAATTTGAATTTTATCAGCCG 57.009 32.000 0.00 0.00 0.00 5.52
225 236 8.934507 TCCACTTTTTGTTTTGATTTATCGTT 57.065 26.923 0.00 0.00 0.00 3.85
235 246 9.623350 ATCAAACAATTTCCACTTTTTGTTTTG 57.377 25.926 9.25 6.57 45.18 2.44
336 351 5.128499 TGACATTTCCACCACAAATTGAAGT 59.872 36.000 0.00 0.00 0.00 3.01
356 371 3.181426 TGGGGTTGAGTAGTAGAGTGACA 60.181 47.826 0.00 0.00 0.00 3.58
384 400 6.487299 AGGAATACAATACCAGGTTCTCTC 57.513 41.667 0.00 0.00 0.00 3.20
390 406 8.509441 ACTACTACTAGGAATACAATACCAGGT 58.491 37.037 0.00 0.00 0.00 4.00
398 414 8.492782 AGCAGTCTACTACTACTAGGAATACAA 58.507 37.037 0.00 0.00 35.76 2.41
407 423 6.266330 TCGACCATAGCAGTCTACTACTACTA 59.734 42.308 0.00 0.00 38.24 1.82
408 424 5.070180 TCGACCATAGCAGTCTACTACTACT 59.930 44.000 0.00 0.00 35.76 2.57
409 425 5.295950 TCGACCATAGCAGTCTACTACTAC 58.704 45.833 0.00 0.00 35.76 2.73
410 426 5.541953 TCGACCATAGCAGTCTACTACTA 57.458 43.478 0.00 0.00 35.76 1.82
415 431 4.154556 GTCCTATCGACCATAGCAGTCTAC 59.845 50.000 0.00 0.00 35.23 2.59
417 433 3.150767 GTCCTATCGACCATAGCAGTCT 58.849 50.000 0.00 0.00 35.23 3.24
418 434 3.562567 GTCCTATCGACCATAGCAGTC 57.437 52.381 0.00 0.00 35.23 3.51
428 444 1.344763 CAGGGATTGGGTCCTATCGAC 59.655 57.143 0.00 2.41 46.91 4.20
429 445 1.219469 TCAGGGATTGGGTCCTATCGA 59.781 52.381 5.60 0.00 46.91 3.59
430 446 1.344763 GTCAGGGATTGGGTCCTATCG 59.655 57.143 5.60 0.00 46.91 2.92
431 447 1.700186 GGTCAGGGATTGGGTCCTATC 59.300 57.143 3.39 3.39 46.91 2.08
433 449 0.689745 CGGTCAGGGATTGGGTCCTA 60.690 60.000 0.00 0.00 46.91 2.94
434 450 1.995626 CGGTCAGGGATTGGGTCCT 60.996 63.158 0.00 0.00 46.91 3.85
436 452 0.546598 ATTCGGTCAGGGATTGGGTC 59.453 55.000 0.00 0.00 0.00 4.46
437 453 0.255890 CATTCGGTCAGGGATTGGGT 59.744 55.000 0.00 0.00 0.00 4.51
438 454 0.255890 ACATTCGGTCAGGGATTGGG 59.744 55.000 0.00 0.00 0.00 4.12
439 455 2.128771 AACATTCGGTCAGGGATTGG 57.871 50.000 0.00 0.00 0.00 3.16
440 456 3.119495 GGAAAACATTCGGTCAGGGATTG 60.119 47.826 0.00 0.00 0.00 2.67
441 457 3.089284 GGAAAACATTCGGTCAGGGATT 58.911 45.455 0.00 0.00 0.00 3.01
442 458 2.041081 TGGAAAACATTCGGTCAGGGAT 59.959 45.455 0.00 0.00 0.00 3.85
443 459 1.422024 TGGAAAACATTCGGTCAGGGA 59.578 47.619 0.00 0.00 0.00 4.20
445 461 2.226437 CAGTGGAAAACATTCGGTCAGG 59.774 50.000 0.00 0.00 0.00 3.86
446 462 2.226437 CCAGTGGAAAACATTCGGTCAG 59.774 50.000 1.68 0.00 0.00 3.51
448 464 2.484264 CTCCAGTGGAAAACATTCGGTC 59.516 50.000 14.17 0.00 0.00 4.79
449 465 2.105821 TCTCCAGTGGAAAACATTCGGT 59.894 45.455 14.17 0.00 0.00 4.69
451 467 2.160417 GCTCTCCAGTGGAAAACATTCG 59.840 50.000 14.17 0.00 0.00 3.34
452 468 3.149196 TGCTCTCCAGTGGAAAACATTC 58.851 45.455 14.17 0.00 0.00 2.67
453 469 3.228188 TGCTCTCCAGTGGAAAACATT 57.772 42.857 14.17 0.00 0.00 2.71
455 471 2.727123 TTGCTCTCCAGTGGAAAACA 57.273 45.000 14.17 8.38 0.00 2.83
456 472 4.590850 AATTTGCTCTCCAGTGGAAAAC 57.409 40.909 14.17 5.70 33.81 2.43
458 474 3.960102 ACAAATTTGCTCTCCAGTGGAAA 59.040 39.130 18.12 4.39 34.40 3.13
459 475 3.565307 ACAAATTTGCTCTCCAGTGGAA 58.435 40.909 18.12 3.70 0.00 3.53
460 476 3.228188 ACAAATTTGCTCTCCAGTGGA 57.772 42.857 18.12 12.40 0.00 4.02
475 491 9.893305 GTACTATGTTTCTGCTAACAAACAAAT 57.107 29.630 1.64 0.00 43.79 2.32
476 492 9.116067 AGTACTATGTTTCTGCTAACAAACAAA 57.884 29.630 0.00 0.00 43.79 2.83
478 494 7.386848 GGAGTACTATGTTTCTGCTAACAAACA 59.613 37.037 0.00 0.05 44.48 2.83
479 495 7.603024 AGGAGTACTATGTTTCTGCTAACAAAC 59.397 37.037 0.00 0.00 41.02 2.93
480 496 7.676947 AGGAGTACTATGTTTCTGCTAACAAA 58.323 34.615 0.00 0.00 41.02 2.83
481 497 7.241042 AGGAGTACTATGTTTCTGCTAACAA 57.759 36.000 0.00 0.00 41.02 2.83
482 498 6.852420 AGGAGTACTATGTTTCTGCTAACA 57.148 37.500 0.00 0.00 41.81 2.41
483 499 8.223177 TCTAGGAGTACTATGTTTCTGCTAAC 57.777 38.462 0.00 0.00 32.35 2.34
484 500 8.998277 ATCTAGGAGTACTATGTTTCTGCTAA 57.002 34.615 0.00 0.00 32.35 3.09
485 501 9.504708 GTATCTAGGAGTACTATGTTTCTGCTA 57.495 37.037 0.00 0.00 31.62 3.49
487 503 8.167605 TGTATCTAGGAGTACTATGTTTCTGC 57.832 38.462 0.00 0.00 0.00 4.26
488 504 8.788806 CCTGTATCTAGGAGTACTATGTTTCTG 58.211 40.741 0.00 0.00 40.42 3.02
489 505 8.504409 ACCTGTATCTAGGAGTACTATGTTTCT 58.496 37.037 0.00 0.00 40.42 2.52
492 508 7.014422 GCAACCTGTATCTAGGAGTACTATGTT 59.986 40.741 0.00 0.00 40.42 2.71
493 509 6.490721 GCAACCTGTATCTAGGAGTACTATGT 59.509 42.308 0.00 0.00 40.42 2.29
504 714 2.464865 GCACGAGCAACCTGTATCTAG 58.535 52.381 0.00 0.00 41.58 2.43
506 716 0.458543 CGCACGAGCAACCTGTATCT 60.459 55.000 5.50 0.00 42.27 1.98
507 717 1.999051 CGCACGAGCAACCTGTATC 59.001 57.895 5.50 0.00 42.27 2.24
508 718 2.100631 GCGCACGAGCAACCTGTAT 61.101 57.895 0.30 0.00 42.27 2.29
510 720 4.908687 TGCGCACGAGCAACCTGT 62.909 61.111 5.66 0.00 45.06 4.00
516 726 0.248825 AAATTTGTTGCGCACGAGCA 60.249 45.000 11.12 4.06 46.54 4.26
517 727 1.680668 TAAATTTGTTGCGCACGAGC 58.319 45.000 11.12 0.90 37.71 5.03
518 728 3.539563 CAGATAAATTTGTTGCGCACGAG 59.460 43.478 11.12 0.00 0.00 4.18
519 729 3.487536 CAGATAAATTTGTTGCGCACGA 58.512 40.909 11.12 2.18 0.00 4.35
520 730 2.593775 CCAGATAAATTTGTTGCGCACG 59.406 45.455 11.12 0.00 0.00 5.34
521 731 3.364621 CACCAGATAAATTTGTTGCGCAC 59.635 43.478 11.12 6.28 0.00 5.34
522 732 3.005261 ACACCAGATAAATTTGTTGCGCA 59.995 39.130 5.66 5.66 0.00 6.09
523 733 3.574614 ACACCAGATAAATTTGTTGCGC 58.425 40.909 0.00 0.00 0.00 6.09
524 734 6.088883 GGTTTACACCAGATAAATTTGTTGCG 59.911 38.462 0.00 0.00 43.61 4.85
525 735 7.346208 GGTTTACACCAGATAAATTTGTTGC 57.654 36.000 0.00 0.00 43.61 4.17
548 758 3.005791 TGAGGCTCATACATCATACGTGG 59.994 47.826 14.43 0.00 0.00 4.94
552 762 6.695429 TGATTCTGAGGCTCATACATCATAC 58.305 40.000 19.11 4.01 0.00 2.39
553 763 6.923199 TGATTCTGAGGCTCATACATCATA 57.077 37.500 19.11 2.73 0.00 2.15
554 764 5.820404 TGATTCTGAGGCTCATACATCAT 57.180 39.130 19.11 0.90 0.00 2.45
555 765 5.619132 TTGATTCTGAGGCTCATACATCA 57.381 39.130 19.11 20.26 0.00 3.07
556 766 6.054295 AGTTTGATTCTGAGGCTCATACATC 58.946 40.000 19.11 18.12 0.00 3.06
562 772 5.012046 TGACTAAGTTTGATTCTGAGGCTCA 59.988 40.000 17.68 17.68 0.00 4.26
571 781 7.604164 TCCTCTCAACATGACTAAGTTTGATTC 59.396 37.037 0.00 0.00 0.00 2.52
629 839 6.072508 CCATTTCTTTTCTTTGGAGACGATGA 60.073 38.462 0.00 0.00 0.00 2.92
634 844 8.576442 TCATAACCATTTCTTTTCTTTGGAGAC 58.424 33.333 0.00 0.00 0.00 3.36
639 849 9.533253 ACTGTTCATAACCATTTCTTTTCTTTG 57.467 29.630 0.00 0.00 0.00 2.77
642 852 8.463930 TCACTGTTCATAACCATTTCTTTTCT 57.536 30.769 0.00 0.00 0.00 2.52
643 853 8.567948 TCTCACTGTTCATAACCATTTCTTTTC 58.432 33.333 0.00 0.00 0.00 2.29
644 854 8.463930 TCTCACTGTTCATAACCATTTCTTTT 57.536 30.769 0.00 0.00 0.00 2.27
645 855 8.517878 CATCTCACTGTTCATAACCATTTCTTT 58.482 33.333 0.00 0.00 0.00 2.52
646 856 7.667219 ACATCTCACTGTTCATAACCATTTCTT 59.333 33.333 0.00 0.00 0.00 2.52
647 857 7.170965 ACATCTCACTGTTCATAACCATTTCT 58.829 34.615 0.00 0.00 0.00 2.52
648 858 7.383102 ACATCTCACTGTTCATAACCATTTC 57.617 36.000 0.00 0.00 0.00 2.17
649 859 7.765695 AACATCTCACTGTTCATAACCATTT 57.234 32.000 0.00 0.00 34.26 2.32
650 860 8.862325 TTAACATCTCACTGTTCATAACCATT 57.138 30.769 0.00 0.00 39.88 3.16
651 861 8.730680 GTTTAACATCTCACTGTTCATAACCAT 58.269 33.333 0.00 0.00 39.88 3.55
652 862 7.717436 TGTTTAACATCTCACTGTTCATAACCA 59.283 33.333 0.00 0.00 39.88 3.67
653 863 8.015658 GTGTTTAACATCTCACTGTTCATAACC 58.984 37.037 0.00 0.00 39.88 2.85
654 864 8.556194 TGTGTTTAACATCTCACTGTTCATAAC 58.444 33.333 0.00 0.00 39.88 1.89
655 865 8.669946 TGTGTTTAACATCTCACTGTTCATAA 57.330 30.769 0.00 0.00 39.88 1.90
685 895 2.601266 GGTGCACAATGTAACGTGACAC 60.601 50.000 20.43 0.00 38.39 3.67
725 940 0.609406 TCTCTAGACGCAGCTGGTGT 60.609 55.000 17.12 12.48 44.56 4.16
733 948 8.973182 TCTAATCTATCTCTATCTCTAGACGCA 58.027 37.037 0.00 0.00 30.70 5.24
820 1035 8.373981 CAAGATGGTTGAGATATTACAGGAGAT 58.626 37.037 0.00 0.00 0.00 2.75
922 1140 2.158914 TGATTACCATGTGCGAGATGCT 60.159 45.455 0.00 0.00 46.63 3.79
1495 4223 1.001764 CCATGGCAGAAGCTGGTGA 60.002 57.895 0.00 0.00 41.70 4.02
1497 4225 1.578215 ATCCCATGGCAGAAGCTGGT 61.578 55.000 6.09 0.00 41.70 4.00
1815 4544 3.270877 AGCTTTGTACCGATCAATGGTC 58.729 45.455 0.00 0.00 40.96 4.02
1952 4681 2.041755 TCTAGTTGCCTGAGACTCCAGA 59.958 50.000 0.00 0.00 36.29 3.86
1992 4721 4.103153 ACCTCTTCTTTCAGAACACCATGA 59.897 41.667 0.00 0.00 29.89 3.07
2005 4734 4.973168 TGCTTCATGTACACCTCTTCTTT 58.027 39.130 0.00 0.00 0.00 2.52
2181 4911 7.598869 TGTGTTGTGCTTGTTGTAAATAAACAA 59.401 29.630 2.16 2.16 43.39 2.83
2285 5015 2.278854 GCAAACTCTGAGCTGAGATCC 58.721 52.381 2.45 0.00 37.50 3.36
2340 5070 4.191544 TCATGCTTCTTCACCTAAATCCG 58.808 43.478 0.00 0.00 0.00 4.18
2346 5076 3.135348 CCATCCTCATGCTTCTTCACCTA 59.865 47.826 0.00 0.00 0.00 3.08
2736 5466 1.421268 TCTGTCATCAAGGCAACCTGT 59.579 47.619 0.00 0.00 32.13 4.00
2867 5597 1.677966 CTCAGCTGTGGCATTGGCT 60.678 57.895 14.67 6.10 41.70 4.75
2870 5600 1.746470 TGATCTCAGCTGTGGCATTG 58.254 50.000 14.67 0.00 41.70 2.82


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

AutoCloner maintained by Alex Coulton.