Multiple sequence alignment - TraesCS6A01G317500

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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 TraesCS6A01G317500 chr6A 100.000 3201 0 0 1 3201 553767887 553764687 0.000000e+00 5912.0
1 TraesCS6A01G317500 chr6A 94.308 1757 77 11 797 2550 553913409 553911673 0.000000e+00 2669.0
2 TraesCS6A01G317500 chr6A 92.972 996 66 2 1517 2512 563485400 563486391 0.000000e+00 1448.0
3 TraesCS6A01G317500 chr6A 91.877 554 37 3 903 1454 563484752 563485299 0.000000e+00 767.0
4 TraesCS6A01G317500 chr6A 81.771 192 19 8 609 787 553913758 553913570 2.570000e-31 147.0
5 TraesCS6A01G317500 chr6A 89.381 113 12 0 1 113 131120955 131121067 3.330000e-30 143.0
6 TraesCS6A01G317500 chr6A 89.474 114 11 1 1 114 571036551 571036439 3.330000e-30 143.0
7 TraesCS6A01G317500 chr6A 78.462 195 24 8 606 788 563484360 563484548 9.390000e-21 111.0
8 TraesCS6A01G317500 chr6B 92.177 1764 96 14 788 2550 612271563 612269841 0.000000e+00 2455.0
9 TraesCS6A01G317500 chr6B 90.904 1759 113 21 788 2537 612745277 612743557 0.000000e+00 2318.0
10 TraesCS6A01G317500 chr6B 89.632 1630 126 25 910 2507 633730671 633732289 0.000000e+00 2034.0
11 TraesCS6A01G317500 chr6B 90.024 421 28 7 112 526 612272350 612271938 1.690000e-147 532.0
12 TraesCS6A01G317500 chr6B 81.183 186 17 12 609 787 612745611 612745437 2.000000e-27 134.0
13 TraesCS6A01G317500 chr6B 93.976 83 5 0 607 689 612271897 612271815 3.350000e-25 126.0
14 TraesCS6A01G317500 chr6B 76.549 226 18 15 568 787 633730271 633730467 1.220000e-14 91.6
15 TraesCS6A01G317500 chr6B 100.000 30 0 0 583 612 612271936 612271907 4.460000e-04 56.5
16 TraesCS6A01G317500 chr6D 91.732 1790 105 20 788 2550 408157214 408155441 0.000000e+00 2446.0
17 TraesCS6A01G317500 chr6D 92.214 1721 111 14 838 2550 59089163 59087458 0.000000e+00 2414.0
18 TraesCS6A01G317500 chr6D 89.566 1658 134 25 910 2537 420559256 420560904 0.000000e+00 2067.0
19 TraesCS6A01G317500 chr6D 89.002 1673 132 27 903 2537 420569167 420567509 0.000000e+00 2023.0
20 TraesCS6A01G317500 chr6D 78.516 256 22 10 543 787 408157612 408157379 1.550000e-28 137.0
21 TraesCS6A01G317500 chr6D 81.548 168 18 7 609 767 59089536 59089373 3.350000e-25 126.0
22 TraesCS6A01G317500 chr6D 85.714 77 6 2 698 774 420558956 420559027 3.420000e-10 76.8
23 TraesCS6A01G317500 chr6D 92.157 51 3 1 724 774 420569416 420569367 1.590000e-08 71.3
24 TraesCS6A01G317500 chr4A 98.624 654 6 1 2551 3201 682992472 682993125 0.000000e+00 1155.0
25 TraesCS6A01G317500 chr4A 92.035 113 9 0 1 113 513328112 513328000 3.310000e-35 159.0
26 TraesCS6A01G317500 chr3A 90.812 653 46 7 2551 3200 437990607 437989966 0.000000e+00 861.0
27 TraesCS6A01G317500 chr3A 92.789 527 9 2 2549 3072 572542458 572542958 0.000000e+00 736.0
28 TraesCS6A01G317500 chr3A 97.727 132 3 0 3070 3201 572548723 572548854 8.930000e-56 228.0
29 TraesCS6A01G317500 chr3A 89.381 113 12 0 1 113 114774826 114774714 3.330000e-30 143.0
30 TraesCS6A01G317500 chr1A 90.491 652 51 4 2551 3200 441837176 441837818 0.000000e+00 850.0
31 TraesCS6A01G317500 chr1A 90.265 113 11 0 1 113 255900370 255900258 7.150000e-32 148.0
32 TraesCS6A01G317500 chr7D 93.967 547 32 1 2655 3201 599196463 599195918 0.000000e+00 826.0
33 TraesCS6A01G317500 chr5D 90.909 594 34 7 2551 3142 370957069 370956494 0.000000e+00 780.0
34 TraesCS6A01G317500 chr5D 91.429 70 5 1 3094 3163 370956489 370956421 9.450000e-16 95.3
35 TraesCS6A01G317500 chr1D 84.816 652 67 16 2551 3182 474732842 474732203 7.540000e-176 627.0
36 TraesCS6A01G317500 chr2A 83.333 612 72 17 2590 3182 640273976 640273376 3.630000e-149 538.0
37 TraesCS6A01G317500 chr3D 80.994 342 54 10 2798 3129 18294739 18294399 8.810000e-66 261.0
38 TraesCS6A01G317500 chr7A 92.857 112 8 0 1 112 127262642 127262753 2.560000e-36 163.0
39 TraesCS6A01G317500 chr7A 89.474 114 12 0 1 114 30904391 30904504 9.250000e-31 145.0
40 TraesCS6A01G317500 chr7A 90.654 107 10 0 1 107 700665418 700665524 3.330000e-30 143.0
41 TraesCS6A01G317500 chr5A 90.265 113 11 0 1 113 463604640 463604528 7.150000e-32 148.0


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 TraesCS6A01G317500 chr6A 553764687 553767887 3200 True 5912.000000 5912 100.000000 1 3201 1 chr6A.!!$R1 3200
1 TraesCS6A01G317500 chr6A 553911673 553913758 2085 True 1408.000000 2669 88.039500 609 2550 2 chr6A.!!$R3 1941
2 TraesCS6A01G317500 chr6A 563484360 563486391 2031 False 775.333333 1448 87.770333 606 2512 3 chr6A.!!$F2 1906
3 TraesCS6A01G317500 chr6B 612743557 612745611 2054 True 1226.000000 2318 86.043500 609 2537 2 chr6B.!!$R2 1928
4 TraesCS6A01G317500 chr6B 633730271 633732289 2018 False 1062.800000 2034 83.090500 568 2507 2 chr6B.!!$F1 1939
5 TraesCS6A01G317500 chr6B 612269841 612272350 2509 True 792.375000 2455 94.044250 112 2550 4 chr6B.!!$R1 2438
6 TraesCS6A01G317500 chr6D 408155441 408157612 2171 True 1291.500000 2446 85.124000 543 2550 2 chr6D.!!$R2 2007
7 TraesCS6A01G317500 chr6D 59087458 59089536 2078 True 1270.000000 2414 86.881000 609 2550 2 chr6D.!!$R1 1941
8 TraesCS6A01G317500 chr6D 420558956 420560904 1948 False 1071.900000 2067 87.640000 698 2537 2 chr6D.!!$F1 1839
9 TraesCS6A01G317500 chr6D 420567509 420569416 1907 True 1047.150000 2023 90.579500 724 2537 2 chr6D.!!$R3 1813
10 TraesCS6A01G317500 chr4A 682992472 682993125 653 False 1155.000000 1155 98.624000 2551 3201 1 chr4A.!!$F1 650
11 TraesCS6A01G317500 chr3A 437989966 437990607 641 True 861.000000 861 90.812000 2551 3200 1 chr3A.!!$R2 649
12 TraesCS6A01G317500 chr3A 572542458 572542958 500 False 736.000000 736 92.789000 2549 3072 1 chr3A.!!$F1 523
13 TraesCS6A01G317500 chr1A 441837176 441837818 642 False 850.000000 850 90.491000 2551 3200 1 chr1A.!!$F1 649
14 TraesCS6A01G317500 chr7D 599195918 599196463 545 True 826.000000 826 93.967000 2655 3201 1 chr7D.!!$R1 546
15 TraesCS6A01G317500 chr5D 370956421 370957069 648 True 437.650000 780 91.169000 2551 3163 2 chr5D.!!$R1 612
16 TraesCS6A01G317500 chr1D 474732203 474732842 639 True 627.000000 627 84.816000 2551 3182 1 chr1D.!!$R1 631
17 TraesCS6A01G317500 chr2A 640273376 640273976 600 True 538.000000 538 83.333000 2590 3182 1 chr2A.!!$R1 592

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
526 529 0.037326 GGATCGCCTGACAGTTGACA 60.037 55.0 0.93 0.0 0.00 3.58 F
896 1240 0.458543 AAGCGCACATACGGAGAGTG 60.459 55.0 11.47 0.0 36.39 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 2394 1.671054 CCACGCGAACTCCACCATT 60.671 57.895 15.93 0.0 0.00 3.16 R
2538 2943 1.095600 CCGCTCTCACAGTAGTAGCA 58.904 55.000 0.00 0.0 32.69 3.49 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
26 27 9.838339 AAATGACATCTCGTTTTCTATTCCTAT 57.162 29.630 0.00 0.00 32.55 2.57
27 28 9.838339 AATGACATCTCGTTTTCTATTCCTATT 57.162 29.630 0.00 0.00 0.00 1.73
28 29 9.838339 ATGACATCTCGTTTTCTATTCCTATTT 57.162 29.630 0.00 0.00 0.00 1.40
61 62 9.904198 TTTAAGATACATGTCATCTCATTTCCA 57.096 29.630 0.00 0.00 31.45 3.53
62 63 9.904198 TTAAGATACATGTCATCTCATTTCCAA 57.096 29.630 0.00 0.00 31.45 3.53
63 64 7.798596 AGATACATGTCATCTCATTTCCAAC 57.201 36.000 0.00 0.00 0.00 3.77
64 65 7.341030 AGATACATGTCATCTCATTTCCAACA 58.659 34.615 0.00 0.00 0.00 3.33
65 66 7.830697 AGATACATGTCATCTCATTTCCAACAA 59.169 33.333 0.00 0.00 0.00 2.83
66 67 6.653526 ACATGTCATCTCATTTCCAACAAA 57.346 33.333 0.00 0.00 0.00 2.83
67 68 7.053316 ACATGTCATCTCATTTCCAACAAAA 57.947 32.000 0.00 0.00 0.00 2.44
68 69 7.673180 ACATGTCATCTCATTTCCAACAAAAT 58.327 30.769 0.00 0.00 0.00 1.82
69 70 8.152246 ACATGTCATCTCATTTCCAACAAAATT 58.848 29.630 0.00 0.00 0.00 1.82
70 71 8.995220 CATGTCATCTCATTTCCAACAAAATTT 58.005 29.630 0.00 0.00 0.00 1.82
71 72 8.592105 TGTCATCTCATTTCCAACAAAATTTC 57.408 30.769 0.00 0.00 0.00 2.17
72 73 8.423349 TGTCATCTCATTTCCAACAAAATTTCT 58.577 29.630 0.00 0.00 0.00 2.52
73 74 9.912634 GTCATCTCATTTCCAACAAAATTTCTA 57.087 29.630 0.00 0.00 0.00 2.10
77 78 9.927668 TCTCATTTCCAACAAAATTTCTATTCC 57.072 29.630 0.00 0.00 0.00 3.01
78 79 9.933723 CTCATTTCCAACAAAATTTCTATTCCT 57.066 29.630 0.00 0.00 0.00 3.36
111 112 7.865706 TCTATTCTATGAACCAAAAGAAGCC 57.134 36.000 0.00 0.00 31.90 4.35
112 113 7.633789 TCTATTCTATGAACCAAAAGAAGCCT 58.366 34.615 0.00 0.00 31.90 4.58
113 114 8.109634 TCTATTCTATGAACCAAAAGAAGCCTT 58.890 33.333 0.00 0.00 31.90 4.35
114 115 5.964958 TCTATGAACCAAAAGAAGCCTTG 57.035 39.130 0.00 0.00 31.91 3.61
115 116 5.630121 TCTATGAACCAAAAGAAGCCTTGA 58.370 37.500 0.00 0.00 31.91 3.02
116 117 4.590850 ATGAACCAAAAGAAGCCTTGAC 57.409 40.909 0.00 0.00 31.91 3.18
117 118 2.693074 TGAACCAAAAGAAGCCTTGACC 59.307 45.455 0.00 0.00 31.91 4.02
131 132 0.317160 TTGACCTGAACGATCGCACT 59.683 50.000 16.60 0.00 0.00 4.40
183 184 1.016627 TCTTGTCTGTTGCACAGCAC 58.983 50.000 10.36 9.91 45.54 4.40
199 200 0.809385 GCACATGCAGCAGTTCATCT 59.191 50.000 0.00 0.00 41.59 2.90
200 201 1.467543 GCACATGCAGCAGTTCATCTG 60.468 52.381 0.00 0.00 42.84 2.90
224 225 7.026562 TGAAGAAAACGTATTGCATTATGGTG 58.973 34.615 11.47 0.00 0.00 4.17
230 231 5.670485 ACGTATTGCATTATGGTGAGAGAA 58.330 37.500 11.47 0.00 0.00 2.87
237 238 5.945191 TGCATTATGGTGAGAGAATTGTTGA 59.055 36.000 0.00 0.00 0.00 3.18
241 242 7.672983 TTATGGTGAGAGAATTGTTGACTTC 57.327 36.000 0.00 0.00 0.00 3.01
249 250 5.994668 AGAGAATTGTTGACTTCCTGTCTTC 59.005 40.000 0.00 0.00 45.54 2.87
281 282 2.667418 CCAGGAGAGGCCACACTG 59.333 66.667 5.01 11.62 40.02 3.66
304 305 3.064324 AACCGCATGCCAAGAGCC 61.064 61.111 13.15 0.00 42.71 4.70
310 311 1.941999 GCATGCCAAGAGCCCAAGAC 61.942 60.000 6.36 0.00 42.71 3.01
322 325 3.944476 CCAAGACTGGGTCAAGGAG 57.056 57.895 0.52 0.00 39.30 3.69
332 335 4.003648 CTGGGTCAAGGAGATGTACAAAC 58.996 47.826 0.00 0.00 0.00 2.93
362 365 5.790593 ACCATCGACTAAGCTTAGTTTCAA 58.209 37.500 33.78 21.43 43.64 2.69
370 373 3.127425 AGCTTAGTTTCAAAGGAGCGT 57.873 42.857 0.00 0.00 35.41 5.07
398 401 2.935238 GCACGTAACCACTGTGGATGAT 60.935 50.000 32.30 16.84 40.96 2.45
406 409 2.821378 CCACTGTGGATGATTGAAGCAA 59.179 45.455 22.33 0.00 40.96 3.91
407 410 3.446161 CCACTGTGGATGATTGAAGCAAT 59.554 43.478 22.33 0.00 40.96 3.56
421 424 4.081406 TGAAGCAATGTCAAAGCCATACT 58.919 39.130 0.00 0.00 0.00 2.12
424 427 3.828451 AGCAATGTCAAAGCCATACTTGT 59.172 39.130 0.00 0.00 39.09 3.16
429 432 4.323417 TGTCAAAGCCATACTTGTAGGTG 58.677 43.478 0.00 0.00 39.09 4.00
430 433 4.202419 TGTCAAAGCCATACTTGTAGGTGT 60.202 41.667 0.00 0.00 39.09 4.16
431 434 5.012251 TGTCAAAGCCATACTTGTAGGTGTA 59.988 40.000 0.00 0.00 39.09 2.90
432 435 5.581085 GTCAAAGCCATACTTGTAGGTGTAG 59.419 44.000 0.00 0.00 39.09 2.74
433 436 4.755266 AAGCCATACTTGTAGGTGTAGG 57.245 45.455 0.00 0.00 37.17 3.18
434 437 3.721021 AGCCATACTTGTAGGTGTAGGT 58.279 45.455 0.00 0.00 0.00 3.08
435 438 4.101856 AGCCATACTTGTAGGTGTAGGTT 58.898 43.478 0.00 0.00 0.00 3.50
436 439 4.161754 AGCCATACTTGTAGGTGTAGGTTC 59.838 45.833 0.00 0.00 0.00 3.62
437 440 4.161754 GCCATACTTGTAGGTGTAGGTTCT 59.838 45.833 0.00 0.00 0.00 3.01
438 441 5.681695 GCCATACTTGTAGGTGTAGGTTCTC 60.682 48.000 0.00 0.00 0.00 2.87
481 484 4.234530 ACGTGTAGTAAGGAGTGTGTTC 57.765 45.455 0.00 0.00 0.00 3.18
490 493 7.787725 AGTAAGGAGTGTGTTCTTTAACTTG 57.212 36.000 0.00 0.00 36.51 3.16
498 501 5.513849 GTGTGTTCTTTAACTTGGTTTTCGG 59.486 40.000 0.00 0.00 36.51 4.30
514 517 3.861263 GGAACGCAACGGATCGCC 61.861 66.667 0.00 0.00 0.00 5.54
526 529 0.037326 GGATCGCCTGACAGTTGACA 60.037 55.000 0.93 0.00 0.00 3.58
527 530 1.071605 GATCGCCTGACAGTTGACAC 58.928 55.000 0.93 0.00 0.00 3.67
528 531 0.681733 ATCGCCTGACAGTTGACACT 59.318 50.000 0.93 0.00 0.00 3.55
536 539 2.522060 CAGTTGACACTGCCGAGAC 58.478 57.895 0.00 0.00 44.16 3.36
537 540 1.007271 AGTTGACACTGCCGAGACG 60.007 57.895 0.00 0.00 0.00 4.18
565 568 2.020559 CTGACGATTTCAGCGCGC 59.979 61.111 26.66 26.66 45.51 6.86
566 569 2.729675 CTGACGATTTCAGCGCGCA 61.730 57.895 35.10 13.52 45.51 6.09
661 707 1.404583 CGACCTCATGCTGATCACACA 60.405 52.381 0.00 0.00 0.00 3.72
686 733 2.668212 CGGCTGCTTTCCGTGGAA 60.668 61.111 0.00 0.00 41.85 3.53
689 736 1.301677 GGCTGCTTTCCGTGGAAGAG 61.302 60.000 0.00 4.39 35.38 2.85
718 786 2.103941 GACCATCAAGTCTCCATCCTCC 59.896 54.545 0.00 0.00 33.79 4.30
722 790 2.191400 TCAAGTCTCCATCCTCCAAGG 58.809 52.381 0.00 0.00 36.46 3.61
847 1187 1.453379 CAGCCAGGAGGAAGCCATG 60.453 63.158 0.00 0.00 36.89 3.66
896 1240 0.458543 AAGCGCACATACGGAGAGTG 60.459 55.000 11.47 0.00 36.39 3.51
973 1323 2.354729 GTGTGCCTGCCATACCCA 59.645 61.111 0.00 0.00 30.10 4.51
1212 1562 1.968540 GCTCTGCAAGTCCACCACC 60.969 63.158 0.00 0.00 33.76 4.61
1288 1638 4.765449 GTAACCCGCCCGTCACCC 62.765 72.222 0.00 0.00 0.00 4.61
1548 1945 7.411696 GCTGATCGAAGCACTTATCTGAATATG 60.412 40.741 4.21 0.00 43.01 1.78
1554 1953 8.642885 CGAAGCACTTATCTGAATATGTATGTC 58.357 37.037 0.00 0.00 0.00 3.06
1856 2257 4.254709 TGCTGGCGCACAAGGAGT 62.255 61.111 10.83 0.00 42.25 3.85
1993 2394 2.942879 GTCATGACCAACGCGCAA 59.057 55.556 15.31 0.00 0.00 4.85
2200 2601 2.029518 CTGACGCACAGTGGCTGA 59.970 61.111 1.84 0.00 41.30 4.26
2515 2920 3.118629 TGCCCAAGAACTAGCTCTACATG 60.119 47.826 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.838339 ATAGGAATAGAAAACGAGATGTCATTT 57.162 29.630 0.00 0.00 0.00 2.32
1 2 9.838339 AATAGGAATAGAAAACGAGATGTCATT 57.162 29.630 0.00 0.00 0.00 2.57
2 3 9.838339 AAATAGGAATAGAAAACGAGATGTCAT 57.162 29.630 0.00 0.00 0.00 3.06
35 36 9.904198 TGGAAATGAGATGACATGTATCTTAAA 57.096 29.630 14.85 8.06 35.14 1.52
36 37 9.904198 TTGGAAATGAGATGACATGTATCTTAA 57.096 29.630 14.85 9.70 35.14 1.85
37 38 9.330063 GTTGGAAATGAGATGACATGTATCTTA 57.670 33.333 14.85 12.48 35.14 2.10
38 39 7.830697 TGTTGGAAATGAGATGACATGTATCTT 59.169 33.333 14.85 4.26 35.14 2.40
39 40 7.341030 TGTTGGAAATGAGATGACATGTATCT 58.659 34.615 14.05 14.05 37.59 1.98
40 41 7.558161 TGTTGGAAATGAGATGACATGTATC 57.442 36.000 0.00 2.87 0.00 2.24
41 42 7.943079 TTGTTGGAAATGAGATGACATGTAT 57.057 32.000 0.00 0.00 0.00 2.29
42 43 7.757941 TTTGTTGGAAATGAGATGACATGTA 57.242 32.000 0.00 0.00 0.00 2.29
43 44 6.653526 TTTGTTGGAAATGAGATGACATGT 57.346 33.333 0.00 0.00 0.00 3.21
44 45 8.542497 AATTTTGTTGGAAATGAGATGACATG 57.458 30.769 0.00 0.00 30.06 3.21
45 46 9.211485 GAAATTTTGTTGGAAATGAGATGACAT 57.789 29.630 0.00 0.00 30.06 3.06
46 47 8.423349 AGAAATTTTGTTGGAAATGAGATGACA 58.577 29.630 0.00 0.00 30.06 3.58
47 48 8.822652 AGAAATTTTGTTGGAAATGAGATGAC 57.177 30.769 0.00 0.00 30.06 3.06
51 52 9.927668 GGAATAGAAATTTTGTTGGAAATGAGA 57.072 29.630 0.00 0.00 30.06 3.27
52 53 9.933723 AGGAATAGAAATTTTGTTGGAAATGAG 57.066 29.630 0.00 0.00 30.06 2.90
85 86 8.907885 GGCTTCTTTTGGTTCATAGAATAGAAT 58.092 33.333 0.00 0.00 0.00 2.40
86 87 8.109634 AGGCTTCTTTTGGTTCATAGAATAGAA 58.890 33.333 0.00 0.00 0.00 2.10
87 88 7.633789 AGGCTTCTTTTGGTTCATAGAATAGA 58.366 34.615 0.00 0.00 0.00 1.98
88 89 7.872113 AGGCTTCTTTTGGTTCATAGAATAG 57.128 36.000 0.00 0.00 0.00 1.73
89 90 7.888021 TCAAGGCTTCTTTTGGTTCATAGAATA 59.112 33.333 0.00 0.00 0.00 1.75
90 91 6.721208 TCAAGGCTTCTTTTGGTTCATAGAAT 59.279 34.615 0.00 0.00 0.00 2.40
91 92 6.016276 GTCAAGGCTTCTTTTGGTTCATAGAA 60.016 38.462 0.00 0.00 0.00 2.10
92 93 5.473504 GTCAAGGCTTCTTTTGGTTCATAGA 59.526 40.000 0.00 0.00 0.00 1.98
93 94 5.335976 GGTCAAGGCTTCTTTTGGTTCATAG 60.336 44.000 0.00 0.00 0.00 2.23
94 95 4.522789 GGTCAAGGCTTCTTTTGGTTCATA 59.477 41.667 0.00 0.00 0.00 2.15
95 96 3.321968 GGTCAAGGCTTCTTTTGGTTCAT 59.678 43.478 0.00 0.00 0.00 2.57
96 97 2.693074 GGTCAAGGCTTCTTTTGGTTCA 59.307 45.455 0.00 0.00 0.00 3.18
97 98 2.959030 AGGTCAAGGCTTCTTTTGGTTC 59.041 45.455 0.00 0.00 0.00 3.62
98 99 2.695147 CAGGTCAAGGCTTCTTTTGGTT 59.305 45.455 0.00 0.00 0.00 3.67
99 100 2.091885 TCAGGTCAAGGCTTCTTTTGGT 60.092 45.455 0.00 0.00 0.00 3.67
100 101 2.586425 TCAGGTCAAGGCTTCTTTTGG 58.414 47.619 0.00 0.00 0.00 3.28
101 102 3.548818 CGTTCAGGTCAAGGCTTCTTTTG 60.549 47.826 0.00 0.00 0.00 2.44
102 103 2.618709 CGTTCAGGTCAAGGCTTCTTTT 59.381 45.455 0.00 0.00 0.00 2.27
103 104 2.158813 TCGTTCAGGTCAAGGCTTCTTT 60.159 45.455 0.00 0.00 0.00 2.52
104 105 1.416401 TCGTTCAGGTCAAGGCTTCTT 59.584 47.619 0.00 0.00 0.00 2.52
105 106 1.048601 TCGTTCAGGTCAAGGCTTCT 58.951 50.000 0.00 0.00 0.00 2.85
106 107 2.003301 GATCGTTCAGGTCAAGGCTTC 58.997 52.381 0.00 0.00 0.00 3.86
107 108 1.673033 CGATCGTTCAGGTCAAGGCTT 60.673 52.381 7.03 0.00 0.00 4.35
108 109 0.108615 CGATCGTTCAGGTCAAGGCT 60.109 55.000 7.03 0.00 0.00 4.58
109 110 1.696832 GCGATCGTTCAGGTCAAGGC 61.697 60.000 17.81 0.00 0.00 4.35
110 111 0.389817 TGCGATCGTTCAGGTCAAGG 60.390 55.000 17.81 0.00 0.00 3.61
111 112 0.716108 GTGCGATCGTTCAGGTCAAG 59.284 55.000 17.81 0.00 0.00 3.02
112 113 0.317160 AGTGCGATCGTTCAGGTCAA 59.683 50.000 17.81 0.00 0.00 3.18
113 114 0.388520 CAGTGCGATCGTTCAGGTCA 60.389 55.000 17.81 0.72 0.00 4.02
114 115 0.388649 ACAGTGCGATCGTTCAGGTC 60.389 55.000 17.81 0.00 0.00 3.85
115 116 0.667487 CACAGTGCGATCGTTCAGGT 60.667 55.000 17.81 6.38 0.00 4.00
116 117 1.959899 GCACAGTGCGATCGTTCAGG 61.960 60.000 17.81 5.74 31.71 3.86
117 118 1.417592 GCACAGTGCGATCGTTCAG 59.582 57.895 17.81 9.39 31.71 3.02
183 184 3.007635 TCTTCAGATGAACTGCTGCATG 58.992 45.455 1.31 0.00 45.38 4.06
189 190 4.474226 ACGTTTTCTTCAGATGAACTGC 57.526 40.909 0.00 0.00 45.38 4.40
199 200 7.026562 CACCATAATGCAATACGTTTTCTTCA 58.973 34.615 0.00 0.00 0.00 3.02
200 201 7.247728 TCACCATAATGCAATACGTTTTCTTC 58.752 34.615 0.00 0.00 0.00 2.87
224 225 5.854431 GACAGGAAGTCAACAATTCTCTC 57.146 43.478 0.00 0.00 46.77 3.20
237 238 2.486727 GGGAAAACGGAAGACAGGAAGT 60.487 50.000 0.00 0.00 0.00 3.01
241 242 2.200373 ATGGGAAAACGGAAGACAGG 57.800 50.000 0.00 0.00 0.00 4.00
249 250 0.395173 CCTGGGGTATGGGAAAACGG 60.395 60.000 0.00 0.00 0.00 4.44
290 291 3.060020 CTTGGGCTCTTGGCATGCG 62.060 63.158 12.44 0.00 44.01 4.73
304 305 1.352083 TCTCCTTGACCCAGTCTTGG 58.648 55.000 0.00 0.00 44.60 3.61
310 311 3.981071 TTGTACATCTCCTTGACCCAG 57.019 47.619 0.00 0.00 0.00 4.45
322 325 5.350365 TCGATGGTTAGCAAGTTTGTACATC 59.650 40.000 0.00 0.00 0.00 3.06
332 335 3.786635 AGCTTAGTCGATGGTTAGCAAG 58.213 45.455 0.00 0.00 0.00 4.01
362 365 2.280797 TGCTTGCGAACGCTCCTT 60.281 55.556 19.32 0.00 42.51 3.36
370 373 0.531090 AGTGGTTACGTGCTTGCGAA 60.531 50.000 0.00 0.00 35.59 4.70
382 385 4.009675 GCTTCAATCATCCACAGTGGTTA 58.990 43.478 19.65 6.61 39.03 2.85
384 387 2.224843 TGCTTCAATCATCCACAGTGGT 60.225 45.455 19.65 4.19 39.03 4.16
398 401 4.523943 AGTATGGCTTTGACATTGCTTCAA 59.476 37.500 0.00 0.00 31.56 2.69
406 409 4.943705 CACCTACAAGTATGGCTTTGACAT 59.056 41.667 0.00 0.00 34.69 3.06
407 410 4.202419 ACACCTACAAGTATGGCTTTGACA 60.202 41.667 0.00 0.00 34.69 3.58
421 424 6.488769 TCTTTTGAGAACCTACACCTACAA 57.511 37.500 0.00 0.00 0.00 2.41
424 427 7.798071 TCTTTTCTTTTGAGAACCTACACCTA 58.202 34.615 0.00 0.00 0.00 3.08
481 484 3.727227 GCGTTCCGAAAACCAAGTTAAAG 59.273 43.478 0.00 0.00 0.00 1.85
490 493 1.369568 CCGTTGCGTTCCGAAAACC 60.370 57.895 0.00 0.00 0.00 3.27
498 501 2.813908 AGGCGATCCGTTGCGTTC 60.814 61.111 0.00 0.00 35.44 3.95
505 508 1.079819 CAACTGTCAGGCGATCCGT 60.080 57.895 4.53 0.00 37.47 4.69
531 534 1.671328 TCAGTAATGCTCTCCGTCTCG 59.329 52.381 0.00 0.00 0.00 4.04
532 535 2.539953 CGTCAGTAATGCTCTCCGTCTC 60.540 54.545 0.00 0.00 0.00 3.36
533 536 1.402259 CGTCAGTAATGCTCTCCGTCT 59.598 52.381 0.00 0.00 0.00 4.18
534 537 1.400846 TCGTCAGTAATGCTCTCCGTC 59.599 52.381 0.00 0.00 0.00 4.79
535 538 1.460504 TCGTCAGTAATGCTCTCCGT 58.539 50.000 0.00 0.00 0.00 4.69
536 539 2.783828 ATCGTCAGTAATGCTCTCCG 57.216 50.000 0.00 0.00 0.00 4.63
537 540 4.433615 TGAAATCGTCAGTAATGCTCTCC 58.566 43.478 0.00 0.00 0.00 3.71
648 681 1.078214 CCGGGTGTGTGATCAGCAT 60.078 57.895 0.00 0.00 37.53 3.79
686 733 2.316372 ACTTGATGGTCCTACTCCCTCT 59.684 50.000 0.00 0.00 0.00 3.69
689 736 2.696187 GAGACTTGATGGTCCTACTCCC 59.304 54.545 0.00 0.00 36.95 4.30
847 1187 0.462047 AAGATCGGTCGATGGCAACC 60.462 55.000 10.77 0.00 34.60 3.77
886 1230 0.612229 ACGACTCCTCACTCTCCGTA 59.388 55.000 0.00 0.00 0.00 4.02
896 1240 2.766400 CCTCCGCAGACGACTCCTC 61.766 68.421 0.00 0.00 43.93 3.71
983 1333 1.299648 ATCGGGGTGATGTGGTGTG 59.700 57.895 0.00 0.00 35.45 3.82
984 1334 3.820425 ATCGGGGTGATGTGGTGT 58.180 55.556 0.00 0.00 35.45 4.16
1182 1532 3.842923 CAGAGCGCGGGGATGTCT 61.843 66.667 8.83 0.00 0.00 3.41
1490 1856 2.486966 GCACCGAGCAGAAATGGC 59.513 61.111 0.00 0.00 44.79 4.40
1548 1945 3.291585 GCATGCATGCGTAAAGACATAC 58.708 45.455 33.99 6.15 44.67 2.39
1561 1960 3.164390 CTCGGCGTCTGCATGCATG 62.164 63.158 22.97 22.70 45.35 4.06
1993 2394 1.671054 CCACGCGAACTCCACCATT 60.671 57.895 15.93 0.00 0.00 3.16
2121 2522 3.005539 ACCAGGACGCCATGAGCT 61.006 61.111 0.00 0.00 40.39 4.09
2200 2601 2.262915 CTCTCCAGCGCCGAGTTT 59.737 61.111 18.59 0.00 0.00 2.66
2537 2942 1.202200 CCGCTCTCACAGTAGTAGCAC 60.202 57.143 0.00 0.00 32.69 4.40
2538 2943 1.095600 CCGCTCTCACAGTAGTAGCA 58.904 55.000 0.00 0.00 32.69 3.49
3038 3449 1.003580 TCATGTCTTGCTTCACTCCCC 59.996 52.381 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.