Multiple sequence alignment - TraesCS6D01G130300

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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 TraesCS6D01G130300 chr6D 100.000 3600 0 0 522 4121 96719894 96716295 0.000000e+00 6649.0
1 TraesCS6D01G130300 chr6D 100.000 101 0 0 1 101 96720415 96720315 1.960000e-43 187.0
2 TraesCS6D01G130300 chr6D 80.087 231 31 9 3461 3686 431147754 431147974 1.530000e-34 158.0
3 TraesCS6D01G130300 chr6B 97.652 3492 74 6 636 4121 179755128 179751639 0.000000e+00 5987.0
4 TraesCS6D01G130300 chr6A 96.222 3441 87 14 699 4121 115464872 115461457 0.000000e+00 5594.0
5 TraesCS6D01G130300 chr5D 79.565 230 32 9 3461 3686 558943887 558944105 2.570000e-32 150.0
6 TraesCS6D01G130300 chr5A 94.286 35 2 0 599 633 674633317 674633351 2.000000e-03 54.7


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 TraesCS6D01G130300 chr6D 96716295 96720415 4120 True 3418 6649 100.000 1 4121 2 chr6D.!!$R1 4120
1 TraesCS6D01G130300 chr6B 179751639 179755128 3489 True 5987 5987 97.652 636 4121 1 chr6B.!!$R1 3485
2 TraesCS6D01G130300 chr6A 115461457 115464872 3415 True 5594 5594 96.222 699 4121 1 chr6A.!!$R1 3422

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
546 547 0.035458 GATGAATAGGAGGGCACGGG 59.965 60.0 0.0 0.0 0.00 5.28 F
560 561 0.396811 CACGGGAGGTTGAAGAAGGT 59.603 55.0 0.0 0.0 0.00 3.50 F
561 562 0.396811 ACGGGAGGTTGAAGAAGGTG 59.603 55.0 0.0 0.0 0.00 4.00 F
566 567 0.396811 AGGTTGAAGAAGGTGACCCG 59.603 55.0 0.0 0.0 35.12 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1609 0.464036 AGTCGAACACCTTGACAGCA 59.536 50.000 0.00 0.00 35.09 4.41 R
1773 1774 0.818938 TCGCCTTAATACAGGACGCA 59.181 50.000 0.00 0.00 35.71 5.24 R
1860 1861 1.953686 TGGCAGTAACCAGACAAAAGC 59.046 47.619 0.00 0.00 33.75 3.51 R
3134 3135 3.195610 AGATTCACCAGTGCGTCTGATAA 59.804 43.478 9.78 2.83 46.27 1.75 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
27 28 2.660802 GGTGGACCGACGGTTGAT 59.339 61.111 22.69 0.00 35.25 2.57
28 29 1.447314 GGTGGACCGACGGTTGATC 60.447 63.158 22.69 8.02 35.25 2.92
29 30 1.447314 GTGGACCGACGGTTGATCC 60.447 63.158 22.69 17.77 35.25 3.36
30 31 1.608336 TGGACCGACGGTTGATCCT 60.608 57.895 22.69 0.00 35.25 3.24
31 32 0.323633 TGGACCGACGGTTGATCCTA 60.324 55.000 22.69 2.45 35.25 2.94
32 33 0.384669 GGACCGACGGTTGATCCTAG 59.615 60.000 22.69 0.00 35.25 3.02
33 34 0.248949 GACCGACGGTTGATCCTAGC 60.249 60.000 22.69 0.34 35.25 3.42
34 35 1.299165 CCGACGGTTGATCCTAGCG 60.299 63.158 5.48 13.02 41.83 4.26
35 36 1.721664 CCGACGGTTGATCCTAGCGA 61.722 60.000 19.25 0.00 39.58 4.93
36 37 0.311165 CGACGGTTGATCCTAGCGAT 59.689 55.000 19.25 7.20 39.58 4.58
37 38 1.772182 GACGGTTGATCCTAGCGATG 58.228 55.000 19.25 0.00 39.58 3.84
38 39 1.337071 GACGGTTGATCCTAGCGATGA 59.663 52.381 19.25 0.00 39.58 2.92
39 40 1.964223 ACGGTTGATCCTAGCGATGAT 59.036 47.619 19.25 0.00 39.58 2.45
40 41 2.288457 ACGGTTGATCCTAGCGATGATG 60.288 50.000 19.25 0.00 39.58 3.07
41 42 2.029918 CGGTTGATCCTAGCGATGATGA 60.030 50.000 10.02 0.00 38.68 2.92
42 43 3.367806 CGGTTGATCCTAGCGATGATGAT 60.368 47.826 10.02 0.00 38.68 2.45
43 44 3.931468 GGTTGATCCTAGCGATGATGATG 59.069 47.826 0.00 0.00 0.00 3.07
44 45 4.562347 GGTTGATCCTAGCGATGATGATGT 60.562 45.833 0.00 0.00 0.00 3.06
45 46 5.336770 GGTTGATCCTAGCGATGATGATGTA 60.337 44.000 0.00 0.00 0.00 2.29
46 47 5.573337 TGATCCTAGCGATGATGATGTAG 57.427 43.478 0.00 0.00 0.00 2.74
47 48 4.400567 TGATCCTAGCGATGATGATGTAGG 59.599 45.833 0.00 0.00 0.00 3.18
48 49 3.092301 TCCTAGCGATGATGATGTAGGG 58.908 50.000 0.00 0.00 0.00 3.53
49 50 3.092301 CCTAGCGATGATGATGTAGGGA 58.908 50.000 0.00 0.00 0.00 4.20
50 51 3.130164 CCTAGCGATGATGATGTAGGGAG 59.870 52.174 0.00 0.00 0.00 4.30
51 52 1.898472 AGCGATGATGATGTAGGGAGG 59.102 52.381 0.00 0.00 0.00 4.30
52 53 1.674221 GCGATGATGATGTAGGGAGGC 60.674 57.143 0.00 0.00 0.00 4.70
53 54 1.066573 CGATGATGATGTAGGGAGGCC 60.067 57.143 0.00 0.00 0.00 5.19
54 55 0.979665 ATGATGATGTAGGGAGGCCG 59.020 55.000 0.00 0.00 0.00 6.13
55 56 1.121407 TGATGATGTAGGGAGGCCGG 61.121 60.000 0.00 0.00 0.00 6.13
56 57 1.074471 ATGATGTAGGGAGGCCGGT 60.074 57.895 1.90 0.00 0.00 5.28
57 58 1.410850 ATGATGTAGGGAGGCCGGTG 61.411 60.000 1.90 0.00 0.00 4.94
58 59 2.768344 ATGTAGGGAGGCCGGTGG 60.768 66.667 1.90 0.00 0.00 4.61
60 61 4.791069 GTAGGGAGGCCGGTGGGA 62.791 72.222 1.90 0.00 34.06 4.37
61 62 4.014075 TAGGGAGGCCGGTGGGAA 62.014 66.667 1.90 0.00 34.06 3.97
62 63 3.995809 TAGGGAGGCCGGTGGGAAG 62.996 68.421 1.90 0.00 34.06 3.46
65 66 3.327404 GAGGCCGGTGGGAAGGAA 61.327 66.667 1.90 0.00 34.06 3.36
66 67 3.330720 AGGCCGGTGGGAAGGAAG 61.331 66.667 1.90 0.00 34.06 3.46
67 68 4.426313 GGCCGGTGGGAAGGAAGG 62.426 72.222 1.90 0.00 34.06 3.46
68 69 3.327404 GCCGGTGGGAAGGAAGGA 61.327 66.667 1.90 0.00 34.06 3.36
69 70 2.990479 CCGGTGGGAAGGAAGGAG 59.010 66.667 0.00 0.00 34.06 3.69
70 71 2.269241 CGGTGGGAAGGAAGGAGC 59.731 66.667 0.00 0.00 0.00 4.70
71 72 2.294078 CGGTGGGAAGGAAGGAGCT 61.294 63.158 0.00 0.00 0.00 4.09
72 73 1.604915 GGTGGGAAGGAAGGAGCTC 59.395 63.158 4.71 4.71 0.00 4.09
73 74 1.219393 GTGGGAAGGAAGGAGCTCG 59.781 63.158 7.83 0.00 0.00 5.03
74 75 1.229209 TGGGAAGGAAGGAGCTCGT 60.229 57.895 7.83 5.12 0.00 4.18
75 76 1.258445 TGGGAAGGAAGGAGCTCGTC 61.258 60.000 9.78 8.40 0.00 4.20
76 77 1.139947 GGAAGGAAGGAGCTCGTCG 59.860 63.158 9.78 0.00 0.00 5.12
77 78 1.139947 GAAGGAAGGAGCTCGTCGG 59.860 63.158 9.78 0.00 0.00 4.79
78 79 1.304217 AAGGAAGGAGCTCGTCGGA 60.304 57.895 9.78 0.00 0.00 4.55
79 80 1.316706 AAGGAAGGAGCTCGTCGGAG 61.317 60.000 9.78 0.00 43.46 4.63
80 81 2.776913 GGAAGGAGCTCGTCGGAGG 61.777 68.421 9.78 0.00 40.80 4.30
81 82 2.756283 AAGGAGCTCGTCGGAGGG 60.756 66.667 9.78 0.00 40.80 4.30
84 85 4.200283 GAGCTCGTCGGAGGGCTG 62.200 72.222 10.04 1.68 40.80 4.85
98 99 3.336122 GGCTGCCCCATCATCTTAG 57.664 57.895 7.66 0.00 0.00 2.18
99 100 0.767375 GGCTGCCCCATCATCTTAGA 59.233 55.000 7.66 0.00 0.00 2.10
100 101 1.271271 GGCTGCCCCATCATCTTAGAG 60.271 57.143 7.66 0.00 0.00 2.43
542 543 4.428294 CAAGAAGATGAATAGGAGGGCA 57.572 45.455 0.00 0.00 0.00 5.36
543 544 4.133078 CAAGAAGATGAATAGGAGGGCAC 58.867 47.826 0.00 0.00 0.00 5.01
544 545 2.366916 AGAAGATGAATAGGAGGGCACG 59.633 50.000 0.00 0.00 0.00 5.34
545 546 1.051812 AGATGAATAGGAGGGCACGG 58.948 55.000 0.00 0.00 0.00 4.94
546 547 0.035458 GATGAATAGGAGGGCACGGG 59.965 60.000 0.00 0.00 0.00 5.28
547 548 0.399949 ATGAATAGGAGGGCACGGGA 60.400 55.000 0.00 0.00 0.00 5.14
548 549 1.048724 TGAATAGGAGGGCACGGGAG 61.049 60.000 0.00 0.00 0.00 4.30
549 550 1.759459 GAATAGGAGGGCACGGGAGG 61.759 65.000 0.00 0.00 0.00 4.30
550 551 2.547123 AATAGGAGGGCACGGGAGGT 62.547 60.000 0.00 0.00 0.00 3.85
551 552 2.547123 ATAGGAGGGCACGGGAGGTT 62.547 60.000 0.00 0.00 0.00 3.50
552 553 4.410400 GGAGGGCACGGGAGGTTG 62.410 72.222 0.00 0.00 0.00 3.77
553 554 3.319198 GAGGGCACGGGAGGTTGA 61.319 66.667 0.00 0.00 0.00 3.18
554 555 2.852075 AGGGCACGGGAGGTTGAA 60.852 61.111 0.00 0.00 0.00 2.69
555 556 2.359975 GGGCACGGGAGGTTGAAG 60.360 66.667 0.00 0.00 0.00 3.02
556 557 2.747686 GGCACGGGAGGTTGAAGA 59.252 61.111 0.00 0.00 0.00 2.87
557 558 1.072505 GGCACGGGAGGTTGAAGAA 59.927 57.895 0.00 0.00 0.00 2.52
558 559 0.955919 GGCACGGGAGGTTGAAGAAG 60.956 60.000 0.00 0.00 0.00 2.85
559 560 0.955919 GCACGGGAGGTTGAAGAAGG 60.956 60.000 0.00 0.00 0.00 3.46
560 561 0.396811 CACGGGAGGTTGAAGAAGGT 59.603 55.000 0.00 0.00 0.00 3.50
561 562 0.396811 ACGGGAGGTTGAAGAAGGTG 59.603 55.000 0.00 0.00 0.00 4.00
562 563 0.685097 CGGGAGGTTGAAGAAGGTGA 59.315 55.000 0.00 0.00 0.00 4.02
563 564 1.608283 CGGGAGGTTGAAGAAGGTGAC 60.608 57.143 0.00 0.00 0.00 3.67
564 565 1.271434 GGGAGGTTGAAGAAGGTGACC 60.271 57.143 0.00 0.00 0.00 4.02
565 566 1.271434 GGAGGTTGAAGAAGGTGACCC 60.271 57.143 0.00 0.00 0.00 4.46
566 567 0.396811 AGGTTGAAGAAGGTGACCCG 59.603 55.000 0.00 0.00 35.12 5.28
567 568 0.605589 GGTTGAAGAAGGTGACCCGG 60.606 60.000 0.00 0.00 35.12 5.73
568 569 1.072505 TTGAAGAAGGTGACCCGGC 59.927 57.895 0.00 0.00 35.12 6.13
569 570 1.415672 TTGAAGAAGGTGACCCGGCT 61.416 55.000 0.00 0.00 35.12 5.52
570 571 1.376037 GAAGAAGGTGACCCGGCTG 60.376 63.158 0.00 0.00 35.12 4.85
571 572 2.113243 GAAGAAGGTGACCCGGCTGT 62.113 60.000 0.00 0.00 35.12 4.40
572 573 1.705997 AAGAAGGTGACCCGGCTGTT 61.706 55.000 0.00 0.00 35.12 3.16
573 574 1.671379 GAAGGTGACCCGGCTGTTC 60.671 63.158 0.00 0.00 35.12 3.18
574 575 2.391724 GAAGGTGACCCGGCTGTTCA 62.392 60.000 0.00 0.00 35.12 3.18
575 576 1.779061 AAGGTGACCCGGCTGTTCAT 61.779 55.000 0.00 0.00 35.12 2.57
576 577 1.303317 GGTGACCCGGCTGTTCATT 60.303 57.895 0.00 0.00 0.00 2.57
577 578 0.893727 GGTGACCCGGCTGTTCATTT 60.894 55.000 0.00 0.00 0.00 2.32
578 579 0.521735 GTGACCCGGCTGTTCATTTC 59.478 55.000 0.00 0.00 0.00 2.17
579 580 0.953471 TGACCCGGCTGTTCATTTCG 60.953 55.000 0.00 0.00 0.00 3.46
580 581 2.253414 GACCCGGCTGTTCATTTCGC 62.253 60.000 0.00 0.00 0.00 4.70
581 582 2.098298 CCGGCTGTTCATTTCGCG 59.902 61.111 0.00 0.00 0.00 5.87
582 583 2.677003 CCGGCTGTTCATTTCGCGT 61.677 57.895 5.77 0.00 0.00 6.01
583 584 1.225745 CGGCTGTTCATTTCGCGTC 60.226 57.895 5.77 0.00 0.00 5.19
584 585 1.134694 GGCTGTTCATTTCGCGTCC 59.865 57.895 5.77 0.00 0.00 4.79
585 586 1.225745 GCTGTTCATTTCGCGTCCG 60.226 57.895 5.77 0.00 0.00 4.79
586 587 1.623081 GCTGTTCATTTCGCGTCCGA 61.623 55.000 5.77 0.00 42.66 4.55
615 616 6.505044 GGTAACAATCGACTAACCCAAATT 57.495 37.500 0.00 0.00 0.00 1.82
616 617 6.549061 GGTAACAATCGACTAACCCAAATTC 58.451 40.000 0.00 0.00 0.00 2.17
617 618 6.149807 GGTAACAATCGACTAACCCAAATTCA 59.850 38.462 0.00 0.00 0.00 2.57
618 619 6.642707 AACAATCGACTAACCCAAATTCAA 57.357 33.333 0.00 0.00 0.00 2.69
619 620 6.642707 ACAATCGACTAACCCAAATTCAAA 57.357 33.333 0.00 0.00 0.00 2.69
620 621 7.045126 ACAATCGACTAACCCAAATTCAAAA 57.955 32.000 0.00 0.00 0.00 2.44
621 622 7.493367 ACAATCGACTAACCCAAATTCAAAAA 58.507 30.769 0.00 0.00 0.00 1.94
622 623 8.147704 ACAATCGACTAACCCAAATTCAAAAAT 58.852 29.630 0.00 0.00 0.00 1.82
623 624 8.647226 CAATCGACTAACCCAAATTCAAAAATC 58.353 33.333 0.00 0.00 0.00 2.17
624 625 7.278461 TCGACTAACCCAAATTCAAAAATCA 57.722 32.000 0.00 0.00 0.00 2.57
625 626 7.367285 TCGACTAACCCAAATTCAAAAATCAG 58.633 34.615 0.00 0.00 0.00 2.90
626 627 6.089417 CGACTAACCCAAATTCAAAAATCAGC 59.911 38.462 0.00 0.00 0.00 4.26
627 628 6.825610 ACTAACCCAAATTCAAAAATCAGCA 58.174 32.000 0.00 0.00 0.00 4.41
628 629 7.278875 ACTAACCCAAATTCAAAAATCAGCAA 58.721 30.769 0.00 0.00 0.00 3.91
629 630 7.772757 ACTAACCCAAATTCAAAAATCAGCAAA 59.227 29.630 0.00 0.00 0.00 3.68
630 631 6.375945 ACCCAAATTCAAAAATCAGCAAAC 57.624 33.333 0.00 0.00 0.00 2.93
631 632 6.121590 ACCCAAATTCAAAAATCAGCAAACT 58.878 32.000 0.00 0.00 0.00 2.66
632 633 6.602803 ACCCAAATTCAAAAATCAGCAAACTT 59.397 30.769 0.00 0.00 0.00 2.66
633 634 7.772757 ACCCAAATTCAAAAATCAGCAAACTTA 59.227 29.630 0.00 0.00 0.00 2.24
634 635 8.785946 CCCAAATTCAAAAATCAGCAAACTTAT 58.214 29.630 0.00 0.00 0.00 1.73
695 696 2.872858 CCTTCTACTTGCCGCTAAATCC 59.127 50.000 0.00 0.00 0.00 3.01
1098 1099 0.530870 GGCTGTACGAAGGGATGCTC 60.531 60.000 0.00 0.00 0.00 4.26
1257 1258 2.525248 CGCGCTCGTTGGCATGTAT 61.525 57.895 5.56 0.00 0.00 2.29
1350 1351 2.031768 GCGATGATGGGAGGGCTC 59.968 66.667 0.00 0.00 0.00 4.70
1353 1354 3.873026 GATGATGGGAGGGCTCGCG 62.873 68.421 0.00 0.00 44.39 5.87
1407 1408 2.827642 GCCAGGATGTGCAGGAGC 60.828 66.667 0.00 0.00 42.57 4.70
1415 1416 3.702048 GTGCAGGAGCGGGGTACA 61.702 66.667 0.00 0.00 46.23 2.90
1492 1493 1.129326 CGAGTTCAACGTTCTTCGCT 58.871 50.000 0.00 0.00 44.19 4.93
1528 1529 0.804364 GTGCATTCACGCCTTGATCA 59.196 50.000 0.00 0.00 32.84 2.92
1608 1609 1.466856 AGTGCATGCAAATGGACGAT 58.533 45.000 24.58 0.00 45.75 3.73
1677 1678 7.993183 TCTTGGAACATCCTTATAACTGGATTC 59.007 37.037 3.97 2.42 40.76 2.52
1773 1774 5.221641 TGAGGTCACTTACAGTAACATGCTT 60.222 40.000 0.00 0.00 0.00 3.91
2173 2174 5.359009 GTGTGTTGGAATTCCATGATCTCAT 59.641 40.000 27.53 0.00 46.97 2.90
3134 3135 3.807553 CTGGTTGATTTGGGCTTTTTGT 58.192 40.909 0.00 0.00 0.00 2.83
3354 3357 6.545504 AATTATATGCTCGGTTCATGTCAC 57.454 37.500 0.00 0.00 0.00 3.67
3386 3391 2.102757 AGAGCTTCATCGATGAGCATGT 59.897 45.455 32.32 21.33 38.19 3.21
3406 3411 4.173256 TGTACTACGATGAGTTGTGCATG 58.827 43.478 0.00 0.00 43.24 4.06
3946 3966 3.878778 GCCTATAGCCATTGACCATAGG 58.121 50.000 1.04 1.04 40.74 2.57
3971 3991 8.548721 GGACAATAGGTATTTCTGTTTCGTATG 58.451 37.037 0.00 0.00 0.00 2.39
3972 3992 9.309516 GACAATAGGTATTTCTGTTTCGTATGA 57.690 33.333 0.00 0.00 0.00 2.15
4050 4070 4.155462 GTGCTGAAAATCTGAGCTGAATGA 59.845 41.667 0.00 0.00 33.66 2.57
4098 4118 8.801299 TCATAGCTTCACAATGGTTGATTTAAA 58.199 29.630 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.447314 GATCAACCGTCGGTCCACC 60.447 63.158 19.16 4.26 33.12 4.61
11 12 1.447314 GGATCAACCGTCGGTCCAC 60.447 63.158 19.16 9.55 33.12 4.02
12 13 0.323633 TAGGATCAACCGTCGGTCCA 60.324 55.000 19.16 7.60 44.74 4.02
13 14 0.384669 CTAGGATCAACCGTCGGTCC 59.615 60.000 19.16 14.54 44.74 4.46
14 15 0.248949 GCTAGGATCAACCGTCGGTC 60.249 60.000 19.16 4.68 44.74 4.79
15 16 1.814527 GCTAGGATCAACCGTCGGT 59.185 57.895 12.23 12.23 44.74 4.69
16 17 1.299165 CGCTAGGATCAACCGTCGG 60.299 63.158 10.48 10.48 44.74 4.79
17 18 0.311165 ATCGCTAGGATCAACCGTCG 59.689 55.000 0.00 0.00 44.74 5.12
18 19 1.337071 TCATCGCTAGGATCAACCGTC 59.663 52.381 0.00 0.00 44.74 4.79
19 20 1.399714 TCATCGCTAGGATCAACCGT 58.600 50.000 0.00 0.00 44.74 4.83
20 21 2.029918 TCATCATCGCTAGGATCAACCG 60.030 50.000 0.00 0.00 44.74 4.44
21 22 3.667497 TCATCATCGCTAGGATCAACC 57.333 47.619 0.00 0.00 39.35 3.77
22 23 4.564041 ACATCATCATCGCTAGGATCAAC 58.436 43.478 0.00 0.00 31.28 3.18
23 24 4.879197 ACATCATCATCGCTAGGATCAA 57.121 40.909 0.00 0.00 31.28 2.57
24 25 4.400567 CCTACATCATCATCGCTAGGATCA 59.599 45.833 0.00 0.00 31.28 2.92
25 26 4.202101 CCCTACATCATCATCGCTAGGATC 60.202 50.000 0.00 0.00 31.28 3.36
26 27 3.703556 CCCTACATCATCATCGCTAGGAT 59.296 47.826 0.00 0.00 35.09 3.24
27 28 3.092301 CCCTACATCATCATCGCTAGGA 58.908 50.000 0.00 0.00 0.00 2.94
28 29 3.092301 TCCCTACATCATCATCGCTAGG 58.908 50.000 0.00 0.00 0.00 3.02
29 30 3.130164 CCTCCCTACATCATCATCGCTAG 59.870 52.174 0.00 0.00 0.00 3.42
30 31 3.092301 CCTCCCTACATCATCATCGCTA 58.908 50.000 0.00 0.00 0.00 4.26
31 32 1.898472 CCTCCCTACATCATCATCGCT 59.102 52.381 0.00 0.00 0.00 4.93
32 33 1.674221 GCCTCCCTACATCATCATCGC 60.674 57.143 0.00 0.00 0.00 4.58
33 34 1.066573 GGCCTCCCTACATCATCATCG 60.067 57.143 0.00 0.00 0.00 3.84
34 35 1.066573 CGGCCTCCCTACATCATCATC 60.067 57.143 0.00 0.00 0.00 2.92
35 36 0.979665 CGGCCTCCCTACATCATCAT 59.020 55.000 0.00 0.00 0.00 2.45
36 37 1.121407 CCGGCCTCCCTACATCATCA 61.121 60.000 0.00 0.00 0.00 3.07
37 38 1.122019 ACCGGCCTCCCTACATCATC 61.122 60.000 0.00 0.00 0.00 2.92
38 39 1.074471 ACCGGCCTCCCTACATCAT 60.074 57.895 0.00 0.00 0.00 2.45
39 40 2.063979 CACCGGCCTCCCTACATCA 61.064 63.158 0.00 0.00 0.00 3.07
40 41 2.808206 CCACCGGCCTCCCTACATC 61.808 68.421 0.00 0.00 0.00 3.06
41 42 2.768344 CCACCGGCCTCCCTACAT 60.768 66.667 0.00 0.00 0.00 2.29
43 44 4.791069 TCCCACCGGCCTCCCTAC 62.791 72.222 0.00 0.00 0.00 3.18
44 45 3.995809 CTTCCCACCGGCCTCCCTA 62.996 68.421 0.00 0.00 0.00 3.53
48 49 3.327404 TTCCTTCCCACCGGCCTC 61.327 66.667 0.00 0.00 0.00 4.70
49 50 3.330720 CTTCCTTCCCACCGGCCT 61.331 66.667 0.00 0.00 0.00 5.19
50 51 4.426313 CCTTCCTTCCCACCGGCC 62.426 72.222 0.00 0.00 0.00 6.13
51 52 3.327404 TCCTTCCTTCCCACCGGC 61.327 66.667 0.00 0.00 0.00 6.13
52 53 2.990479 CTCCTTCCTTCCCACCGG 59.010 66.667 0.00 0.00 0.00 5.28
53 54 2.245438 GAGCTCCTTCCTTCCCACCG 62.245 65.000 0.87 0.00 0.00 4.94
54 55 1.604915 GAGCTCCTTCCTTCCCACC 59.395 63.158 0.87 0.00 0.00 4.61
55 56 1.219393 CGAGCTCCTTCCTTCCCAC 59.781 63.158 8.47 0.00 0.00 4.61
56 57 1.229209 ACGAGCTCCTTCCTTCCCA 60.229 57.895 8.47 0.00 0.00 4.37
57 58 1.518302 GACGAGCTCCTTCCTTCCC 59.482 63.158 8.47 0.00 0.00 3.97
58 59 1.139947 CGACGAGCTCCTTCCTTCC 59.860 63.158 8.47 0.00 0.00 3.46
59 60 1.139947 CCGACGAGCTCCTTCCTTC 59.860 63.158 8.47 0.00 0.00 3.46
60 61 1.304217 TCCGACGAGCTCCTTCCTT 60.304 57.895 8.47 0.00 0.00 3.36
61 62 1.751162 CTCCGACGAGCTCCTTCCT 60.751 63.158 8.47 0.00 0.00 3.36
62 63 2.776913 CCTCCGACGAGCTCCTTCC 61.777 68.421 8.47 0.00 34.49 3.46
63 64 2.776913 CCCTCCGACGAGCTCCTTC 61.777 68.421 8.47 3.95 34.49 3.46
64 65 2.756283 CCCTCCGACGAGCTCCTT 60.756 66.667 8.47 0.00 34.49 3.36
67 68 4.200283 CAGCCCTCCGACGAGCTC 62.200 72.222 2.73 2.73 34.49 4.09
76 77 3.504204 GATGATGGGGCAGCCCTCC 62.504 68.421 30.52 18.65 44.66 4.30
77 78 2.004408 AAGATGATGGGGCAGCCCTC 62.004 60.000 30.52 20.82 44.66 4.30
78 79 0.698886 TAAGATGATGGGGCAGCCCT 60.699 55.000 30.52 11.82 44.66 5.19
79 80 0.251077 CTAAGATGATGGGGCAGCCC 60.251 60.000 24.23 24.23 44.51 5.19
80 81 0.767375 TCTAAGATGATGGGGCAGCC 59.233 55.000 1.26 1.26 0.00 4.85
81 82 2.181954 CTCTAAGATGATGGGGCAGC 57.818 55.000 0.00 0.00 0.00 5.25
521 522 4.133078 GTGCCCTCCTATTCATCTTCTTG 58.867 47.826 0.00 0.00 0.00 3.02
522 523 3.181461 CGTGCCCTCCTATTCATCTTCTT 60.181 47.826 0.00 0.00 0.00 2.52
523 524 2.366916 CGTGCCCTCCTATTCATCTTCT 59.633 50.000 0.00 0.00 0.00 2.85
524 525 2.548920 CCGTGCCCTCCTATTCATCTTC 60.549 54.545 0.00 0.00 0.00 2.87
525 526 1.417890 CCGTGCCCTCCTATTCATCTT 59.582 52.381 0.00 0.00 0.00 2.40
526 527 1.051812 CCGTGCCCTCCTATTCATCT 58.948 55.000 0.00 0.00 0.00 2.90
527 528 0.035458 CCCGTGCCCTCCTATTCATC 59.965 60.000 0.00 0.00 0.00 2.92
528 529 0.399949 TCCCGTGCCCTCCTATTCAT 60.400 55.000 0.00 0.00 0.00 2.57
529 530 1.002403 TCCCGTGCCCTCCTATTCA 59.998 57.895 0.00 0.00 0.00 2.57
530 531 1.749033 CTCCCGTGCCCTCCTATTC 59.251 63.158 0.00 0.00 0.00 1.75
531 532 1.766461 CCTCCCGTGCCCTCCTATT 60.766 63.158 0.00 0.00 0.00 1.73
532 533 2.122813 CCTCCCGTGCCCTCCTAT 60.123 66.667 0.00 0.00 0.00 2.57
533 534 3.248248 AACCTCCCGTGCCCTCCTA 62.248 63.158 0.00 0.00 0.00 2.94
534 535 4.658786 AACCTCCCGTGCCCTCCT 62.659 66.667 0.00 0.00 0.00 3.69
535 536 4.410400 CAACCTCCCGTGCCCTCC 62.410 72.222 0.00 0.00 0.00 4.30
536 537 2.804828 CTTCAACCTCCCGTGCCCTC 62.805 65.000 0.00 0.00 0.00 4.30
537 538 2.852075 TTCAACCTCCCGTGCCCT 60.852 61.111 0.00 0.00 0.00 5.19
538 539 2.359975 CTTCAACCTCCCGTGCCC 60.360 66.667 0.00 0.00 0.00 5.36
539 540 0.955919 CTTCTTCAACCTCCCGTGCC 60.956 60.000 0.00 0.00 0.00 5.01
540 541 0.955919 CCTTCTTCAACCTCCCGTGC 60.956 60.000 0.00 0.00 0.00 5.34
541 542 0.396811 ACCTTCTTCAACCTCCCGTG 59.603 55.000 0.00 0.00 0.00 4.94
542 543 0.396811 CACCTTCTTCAACCTCCCGT 59.603 55.000 0.00 0.00 0.00 5.28
543 544 0.685097 TCACCTTCTTCAACCTCCCG 59.315 55.000 0.00 0.00 0.00 5.14
544 545 1.271434 GGTCACCTTCTTCAACCTCCC 60.271 57.143 0.00 0.00 0.00 4.30
545 546 1.271434 GGGTCACCTTCTTCAACCTCC 60.271 57.143 0.00 0.00 0.00 4.30
546 547 1.608283 CGGGTCACCTTCTTCAACCTC 60.608 57.143 0.00 0.00 33.28 3.85
547 548 0.396811 CGGGTCACCTTCTTCAACCT 59.603 55.000 0.00 0.00 33.28 3.50
548 549 0.605589 CCGGGTCACCTTCTTCAACC 60.606 60.000 0.00 0.00 33.28 3.77
549 550 1.235281 GCCGGGTCACCTTCTTCAAC 61.235 60.000 2.18 0.00 33.28 3.18
550 551 1.072505 GCCGGGTCACCTTCTTCAA 59.927 57.895 2.18 0.00 33.28 2.69
551 552 1.841556 AGCCGGGTCACCTTCTTCA 60.842 57.895 0.00 0.00 33.28 3.02
552 553 1.376037 CAGCCGGGTCACCTTCTTC 60.376 63.158 1.27 0.00 33.28 2.87
553 554 1.705997 AACAGCCGGGTCACCTTCTT 61.706 55.000 1.27 0.00 33.28 2.52
554 555 2.113243 GAACAGCCGGGTCACCTTCT 62.113 60.000 1.27 0.00 33.28 2.85
555 556 1.671379 GAACAGCCGGGTCACCTTC 60.671 63.158 1.27 0.00 33.28 3.46
556 557 1.779061 ATGAACAGCCGGGTCACCTT 61.779 55.000 1.27 0.00 33.28 3.50
557 558 1.779061 AATGAACAGCCGGGTCACCT 61.779 55.000 1.27 0.00 33.28 4.00
558 559 0.893727 AAATGAACAGCCGGGTCACC 60.894 55.000 1.27 0.00 0.00 4.02
559 560 0.521735 GAAATGAACAGCCGGGTCAC 59.478 55.000 1.27 0.00 0.00 3.67
560 561 0.953471 CGAAATGAACAGCCGGGTCA 60.953 55.000 1.27 0.00 0.00 4.02
561 562 1.794222 CGAAATGAACAGCCGGGTC 59.206 57.895 1.27 0.00 0.00 4.46
562 563 2.332654 GCGAAATGAACAGCCGGGT 61.333 57.895 0.00 0.00 0.00 5.28
563 564 2.485122 GCGAAATGAACAGCCGGG 59.515 61.111 2.18 0.00 0.00 5.73
564 565 2.098298 CGCGAAATGAACAGCCGG 59.902 61.111 0.00 0.00 0.00 6.13
565 566 1.225745 GACGCGAAATGAACAGCCG 60.226 57.895 15.93 0.00 0.00 5.52
566 567 1.134694 GGACGCGAAATGAACAGCC 59.865 57.895 15.93 0.00 0.00 4.85
567 568 1.225745 CGGACGCGAAATGAACAGC 60.226 57.895 15.93 0.00 0.00 4.40
568 569 0.787787 TTCGGACGCGAAATGAACAG 59.212 50.000 15.93 0.00 0.00 3.16
569 570 0.787787 CTTCGGACGCGAAATGAACA 59.212 50.000 15.93 0.00 0.00 3.18
570 571 0.094730 CCTTCGGACGCGAAATGAAC 59.905 55.000 15.93 0.00 0.00 3.18
571 572 0.320073 ACCTTCGGACGCGAAATGAA 60.320 50.000 15.93 10.27 0.00 2.57
572 573 0.320073 AACCTTCGGACGCGAAATGA 60.320 50.000 15.93 1.43 0.00 2.57
573 574 0.179225 CAACCTTCGGACGCGAAATG 60.179 55.000 15.93 0.00 0.00 2.32
574 575 1.296056 CCAACCTTCGGACGCGAAAT 61.296 55.000 15.93 0.00 0.00 2.17
575 576 1.957186 CCAACCTTCGGACGCGAAA 60.957 57.895 15.93 0.00 0.00 3.46
576 577 1.804396 TACCAACCTTCGGACGCGAA 61.804 55.000 15.93 0.00 0.00 4.70
577 578 1.804396 TTACCAACCTTCGGACGCGA 61.804 55.000 15.93 0.00 0.00 5.87
578 579 1.373246 TTACCAACCTTCGGACGCG 60.373 57.895 3.53 3.53 0.00 6.01
579 580 0.600782 TGTTACCAACCTTCGGACGC 60.601 55.000 0.00 0.00 0.00 5.19
580 581 1.868469 TTGTTACCAACCTTCGGACG 58.132 50.000 0.00 0.00 0.00 4.79
581 582 2.414138 CGATTGTTACCAACCTTCGGAC 59.586 50.000 0.00 0.00 33.69 4.79
582 583 2.299582 TCGATTGTTACCAACCTTCGGA 59.700 45.455 9.41 0.00 36.23 4.55
583 584 2.414138 GTCGATTGTTACCAACCTTCGG 59.586 50.000 0.00 0.00 36.23 4.30
584 585 3.323243 AGTCGATTGTTACCAACCTTCG 58.677 45.455 0.00 5.05 36.62 3.79
585 586 5.121298 GGTTAGTCGATTGTTACCAACCTTC 59.879 44.000 0.00 0.00 33.10 3.46
586 587 4.999311 GGTTAGTCGATTGTTACCAACCTT 59.001 41.667 0.00 0.00 33.10 3.50
587 588 4.564199 GGGTTAGTCGATTGTTACCAACCT 60.564 45.833 7.65 0.00 35.58 3.50
588 589 3.686241 GGGTTAGTCGATTGTTACCAACC 59.314 47.826 9.67 5.59 32.26 3.77
589 590 4.317488 TGGGTTAGTCGATTGTTACCAAC 58.683 43.478 9.67 0.00 32.26 3.77
590 591 4.620589 TGGGTTAGTCGATTGTTACCAA 57.379 40.909 9.67 0.00 34.45 3.67
591 592 4.620589 TTGGGTTAGTCGATTGTTACCA 57.379 40.909 9.67 3.27 0.00 3.25
592 593 6.149807 TGAATTTGGGTTAGTCGATTGTTACC 59.850 38.462 0.00 0.00 0.00 2.85
593 594 7.136289 TGAATTTGGGTTAGTCGATTGTTAC 57.864 36.000 0.00 0.00 0.00 2.50
594 595 7.747155 TTGAATTTGGGTTAGTCGATTGTTA 57.253 32.000 0.00 0.00 0.00 2.41
595 596 6.642707 TTGAATTTGGGTTAGTCGATTGTT 57.357 33.333 0.00 0.00 0.00 2.83
596 597 6.642707 TTTGAATTTGGGTTAGTCGATTGT 57.357 33.333 0.00 0.00 0.00 2.71
597 598 7.938563 TTTTTGAATTTGGGTTAGTCGATTG 57.061 32.000 0.00 0.00 0.00 2.67
598 599 8.364142 TGATTTTTGAATTTGGGTTAGTCGATT 58.636 29.630 0.00 0.00 0.00 3.34
599 600 7.891561 TGATTTTTGAATTTGGGTTAGTCGAT 58.108 30.769 0.00 0.00 0.00 3.59
600 601 7.278461 TGATTTTTGAATTTGGGTTAGTCGA 57.722 32.000 0.00 0.00 0.00 4.20
601 602 6.089417 GCTGATTTTTGAATTTGGGTTAGTCG 59.911 38.462 0.00 0.00 0.00 4.18
602 603 6.928492 TGCTGATTTTTGAATTTGGGTTAGTC 59.072 34.615 0.00 0.00 0.00 2.59
603 604 6.825610 TGCTGATTTTTGAATTTGGGTTAGT 58.174 32.000 0.00 0.00 0.00 2.24
604 605 7.727331 TTGCTGATTTTTGAATTTGGGTTAG 57.273 32.000 0.00 0.00 0.00 2.34
605 606 7.772757 AGTTTGCTGATTTTTGAATTTGGGTTA 59.227 29.630 0.00 0.00 0.00 2.85
606 607 6.602803 AGTTTGCTGATTTTTGAATTTGGGTT 59.397 30.769 0.00 0.00 0.00 4.11
607 608 6.121590 AGTTTGCTGATTTTTGAATTTGGGT 58.878 32.000 0.00 0.00 0.00 4.51
608 609 6.622833 AGTTTGCTGATTTTTGAATTTGGG 57.377 33.333 0.00 0.00 0.00 4.12
615 616 9.357652 GCTTGATATAAGTTTGCTGATTTTTGA 57.642 29.630 0.00 0.00 0.00 2.69
616 617 8.598075 GGCTTGATATAAGTTTGCTGATTTTTG 58.402 33.333 0.00 0.00 0.00 2.44
617 618 8.313292 TGGCTTGATATAAGTTTGCTGATTTTT 58.687 29.630 0.00 0.00 0.00 1.94
618 619 7.839907 TGGCTTGATATAAGTTTGCTGATTTT 58.160 30.769 0.00 0.00 0.00 1.82
619 620 7.408756 TGGCTTGATATAAGTTTGCTGATTT 57.591 32.000 0.00 0.00 0.00 2.17
620 621 7.592885 ATGGCTTGATATAAGTTTGCTGATT 57.407 32.000 0.00 0.00 0.00 2.57
621 622 7.255730 GGAATGGCTTGATATAAGTTTGCTGAT 60.256 37.037 0.00 0.00 0.00 2.90
622 623 6.039717 GGAATGGCTTGATATAAGTTTGCTGA 59.960 38.462 0.00 0.00 0.00 4.26
623 624 6.211515 GGAATGGCTTGATATAAGTTTGCTG 58.788 40.000 0.00 0.00 0.00 4.41
624 625 5.302823 GGGAATGGCTTGATATAAGTTTGCT 59.697 40.000 0.00 0.00 0.00 3.91
625 626 5.068987 TGGGAATGGCTTGATATAAGTTTGC 59.931 40.000 0.00 0.00 0.00 3.68
626 627 6.713762 TGGGAATGGCTTGATATAAGTTTG 57.286 37.500 0.00 0.00 0.00 2.93
627 628 8.227507 AGTATGGGAATGGCTTGATATAAGTTT 58.772 33.333 0.00 0.00 0.00 2.66
628 629 7.759607 AGTATGGGAATGGCTTGATATAAGTT 58.240 34.615 0.00 0.00 0.00 2.66
629 630 7.335127 AGTATGGGAATGGCTTGATATAAGT 57.665 36.000 0.00 0.00 0.00 2.24
630 631 8.641498 AAAGTATGGGAATGGCTTGATATAAG 57.359 34.615 0.00 0.00 0.00 1.73
631 632 8.859090 CAAAAGTATGGGAATGGCTTGATATAA 58.141 33.333 0.00 0.00 0.00 0.98
632 633 8.004215 ACAAAAGTATGGGAATGGCTTGATATA 58.996 33.333 0.00 0.00 0.00 0.86
633 634 6.840705 ACAAAAGTATGGGAATGGCTTGATAT 59.159 34.615 0.00 0.00 0.00 1.63
634 635 6.194235 ACAAAAGTATGGGAATGGCTTGATA 58.806 36.000 0.00 0.00 0.00 2.15
638 639 4.677182 AGACAAAAGTATGGGAATGGCTT 58.323 39.130 0.00 0.00 0.00 4.35
744 745 0.611618 TTGGGTTCCGCTTGATGCAT 60.612 50.000 0.00 0.00 43.06 3.96
1080 1081 2.979130 GAGCATCCCTTCGTACAGC 58.021 57.895 0.00 0.00 0.00 4.40
1111 1112 2.126071 CGTGAAGTGCGTCGGGAT 60.126 61.111 0.00 0.00 0.00 3.85
1257 1258 4.308458 ACGCTGCCGCACTTGGTA 62.308 61.111 0.00 0.00 38.22 3.25
1368 1369 4.862092 AGCCTGAGCGCATCGTCG 62.862 66.667 11.47 0.00 46.67 5.12
1407 1408 3.396951 GGGATCAACATGTACCCCG 57.603 57.895 15.17 0.00 35.00 5.73
1415 1416 2.124736 CGGCCACGGGATCAACAT 60.125 61.111 2.24 0.00 36.18 2.71
1492 1493 2.032528 CTGCCCAAGCTGGAACGA 59.967 61.111 4.00 0.00 40.96 3.85
1528 1529 1.269958 GCCCCAAAGCCTTTTCTGAT 58.730 50.000 0.00 0.00 0.00 2.90
1608 1609 0.464036 AGTCGAACACCTTGACAGCA 59.536 50.000 0.00 0.00 35.09 4.41
1692 1693 7.050377 TCAATACTTCCAAAGCCTTCTCATAG 58.950 38.462 0.00 0.00 0.00 2.23
1773 1774 0.818938 TCGCCTTAATACAGGACGCA 59.181 50.000 0.00 0.00 35.71 5.24
1860 1861 1.953686 TGGCAGTAACCAGACAAAAGC 59.046 47.619 0.00 0.00 33.75 3.51
3134 3135 3.195610 AGATTCACCAGTGCGTCTGATAA 59.804 43.478 9.78 2.83 46.27 1.75
3354 3357 0.038251 TGAAGCTCTGCACCACGTAG 60.038 55.000 0.00 0.00 0.00 3.51
3386 3391 4.082463 TCACATGCACAACTCATCGTAGTA 60.082 41.667 0.00 0.00 0.00 1.82
3486 3491 5.924825 ACACTTACGGATACTGACTGAAAAC 59.075 40.000 0.00 0.00 0.00 2.43
3946 3966 9.309516 TCATACGAAACAGAAATACCTATTGTC 57.690 33.333 0.00 0.00 0.00 3.18
3971 3991 5.001232 TGCACCTAAGTCAATACAAAGGTC 58.999 41.667 0.00 0.00 39.63 3.85
3972 3992 4.980573 TGCACCTAAGTCAATACAAAGGT 58.019 39.130 0.00 0.00 41.30 3.50
4083 4103 5.409214 CCACTGGCTTTTAAATCAACCATTG 59.591 40.000 0.00 0.18 0.00 2.82


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

AutoCloner maintained by Alex Coulton.