Multiple sequence alignment - TraesCS2B01G407800

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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 TraesCS2B01G407800 chr2B 100.000 2606 0 0 1 2606 579523807 579526412 0.000000e+00 4813.0
1 TraesCS2B01G407800 chr2D 92.396 2538 113 30 81 2555 492899515 492902035 0.000000e+00 3544.0
2 TraesCS2B01G407800 chr2A 91.355 1897 89 30 78 1935 640863652 640861792 0.000000e+00 2525.0
3 TraesCS2B01G407800 chr2A 89.167 600 31 8 1961 2553 640861638 640861066 0.000000e+00 717.0
4 TraesCS2B01G407800 chr1B 86.869 99 13 0 2015 2113 57435393 57435491 7.620000e-21 111.0
5 TraesCS2B01G407800 chr6B 94.340 53 3 0 2554 2606 42679172 42679224 5.980000e-12 82.4
6 TraesCS2B01G407800 chr4A 92.157 51 4 0 2556 2606 633747523 633747473 3.600000e-09 73.1


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 TraesCS2B01G407800 chr2B 579523807 579526412 2605 False 4813 4813 100.000 1 2606 1 chr2B.!!$F1 2605
1 TraesCS2B01G407800 chr2D 492899515 492902035 2520 False 3544 3544 92.396 81 2555 1 chr2D.!!$F1 2474
2 TraesCS2B01G407800 chr2A 640861066 640863652 2586 True 1621 2525 90.261 78 2553 2 chr2A.!!$R1 2475

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
19 20 0.887247 CACATTGACATCCGGCCAAA 59.113 50.0 2.24 0.0 0.00 3.28 F
23 24 0.953471 TTGACATCCGGCCAAAGTCG 60.953 55.0 2.24 0.0 42.04 4.18 F
33 34 1.006832 GCCAAAGTCGCACATCGTAT 58.993 50.0 0.00 0.0 39.67 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1506 0.168348 CCATGAGTTCGTCGTCGTCT 59.832 55.000 1.33 2.43 38.33 4.18 R
1449 1509 1.674611 GCACCATGAGTTCGTCGTCG 61.675 60.000 0.00 0.00 38.55 5.12 R
1774 1844 2.416547 CCGTGATCAGCATTCTTTTCGT 59.583 45.455 0.00 0.00 0.00 3.85 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
17 18 4.317359 CACATTGACATCCGGCCA 57.683 55.556 2.24 0.00 0.00 5.36
18 19 2.565647 CACATTGACATCCGGCCAA 58.434 52.632 2.24 0.00 0.00 4.52
19 20 0.887247 CACATTGACATCCGGCCAAA 59.113 50.000 2.24 0.00 0.00 3.28
20 21 1.135315 CACATTGACATCCGGCCAAAG 60.135 52.381 2.24 0.00 0.00 2.77
21 22 1.176527 CATTGACATCCGGCCAAAGT 58.823 50.000 2.24 0.00 0.00 2.66
22 23 1.133025 CATTGACATCCGGCCAAAGTC 59.867 52.381 2.24 5.58 0.00 3.01
23 24 0.953471 TTGACATCCGGCCAAAGTCG 60.953 55.000 2.24 0.00 42.04 4.18
24 25 2.746277 ACATCCGGCCAAAGTCGC 60.746 61.111 2.24 0.00 40.68 5.19
25 26 2.745884 CATCCGGCCAAAGTCGCA 60.746 61.111 2.24 0.00 40.68 5.10
26 27 2.746277 ATCCGGCCAAAGTCGCAC 60.746 61.111 2.24 0.00 40.68 5.34
27 28 3.545124 ATCCGGCCAAAGTCGCACA 62.545 57.895 2.24 0.00 40.68 4.57
28 29 2.819984 ATCCGGCCAAAGTCGCACAT 62.820 55.000 2.24 0.00 40.68 3.21
29 30 2.480555 CGGCCAAAGTCGCACATC 59.519 61.111 2.24 0.00 32.22 3.06
30 31 2.480555 GGCCAAAGTCGCACATCG 59.519 61.111 0.00 0.00 40.15 3.84
31 32 2.325082 GGCCAAAGTCGCACATCGT 61.325 57.895 0.00 0.00 39.67 3.73
32 33 1.017177 GGCCAAAGTCGCACATCGTA 61.017 55.000 0.00 0.00 39.67 3.43
33 34 1.006832 GCCAAAGTCGCACATCGTAT 58.993 50.000 0.00 0.00 39.67 3.06
34 35 1.396996 GCCAAAGTCGCACATCGTATT 59.603 47.619 0.00 0.00 39.67 1.89
35 36 2.159572 GCCAAAGTCGCACATCGTATTT 60.160 45.455 0.00 0.00 39.67 1.40
36 37 3.669557 GCCAAAGTCGCACATCGTATTTT 60.670 43.478 0.00 0.00 39.67 1.82
37 38 4.472286 CCAAAGTCGCACATCGTATTTTT 58.528 39.130 0.00 0.00 39.67 1.94
68 69 7.676731 GGAACGTCAGTAACTTATTAGTAGC 57.323 40.000 0.00 0.00 33.17 3.58
69 70 6.694844 GGAACGTCAGTAACTTATTAGTAGCC 59.305 42.308 0.00 0.00 33.17 3.93
70 71 6.141560 ACGTCAGTAACTTATTAGTAGCCC 57.858 41.667 0.00 0.00 33.17 5.19
71 72 5.890419 ACGTCAGTAACTTATTAGTAGCCCT 59.110 40.000 0.00 0.00 33.17 5.19
72 73 6.039159 ACGTCAGTAACTTATTAGTAGCCCTC 59.961 42.308 0.00 0.00 33.17 4.30
73 74 6.262720 CGTCAGTAACTTATTAGTAGCCCTCT 59.737 42.308 0.00 0.00 33.17 3.69
74 75 7.201803 CGTCAGTAACTTATTAGTAGCCCTCTT 60.202 40.741 0.00 0.00 33.17 2.85
75 76 9.129532 GTCAGTAACTTATTAGTAGCCCTCTTA 57.870 37.037 0.00 0.00 33.17 2.10
76 77 9.129532 TCAGTAACTTATTAGTAGCCCTCTTAC 57.870 37.037 0.00 0.00 33.17 2.34
77 78 8.910944 CAGTAACTTATTAGTAGCCCTCTTACA 58.089 37.037 0.00 0.00 33.17 2.41
78 79 8.911965 AGTAACTTATTAGTAGCCCTCTTACAC 58.088 37.037 0.00 0.00 33.17 2.90
79 80 6.728089 ACTTATTAGTAGCCCTCTTACACC 57.272 41.667 0.00 0.00 31.21 4.16
105 109 2.995258 TCACCGCAACGTTTAATAGGAC 59.005 45.455 0.00 0.00 0.00 3.85
106 110 2.997986 CACCGCAACGTTTAATAGGACT 59.002 45.455 0.00 0.00 0.00 3.85
107 111 4.082300 TCACCGCAACGTTTAATAGGACTA 60.082 41.667 0.00 0.00 0.00 2.59
116 120 9.961265 CAACGTTTAATAGGACTATATCTGACA 57.039 33.333 0.00 0.00 0.00 3.58
122 126 7.603180 AATAGGACTATATCTGACAGCACAA 57.397 36.000 0.00 0.00 0.00 3.33
228 237 1.070105 CGACAGGGAAACGGAACCA 59.930 57.895 0.00 0.00 0.00 3.67
279 301 1.164041 TGTGAGAGCGTGACGTCTCA 61.164 55.000 25.13 25.13 45.54 3.27
318 341 3.381136 GCCTTGCCCGCAATGGAA 61.381 61.111 16.96 0.00 42.00 3.53
321 344 1.039233 CCTTGCCCGCAATGGAAGAT 61.039 55.000 1.98 0.00 42.00 2.40
329 352 2.487086 CCGCAATGGAAGATGGGTGATA 60.487 50.000 0.00 0.00 42.00 2.15
371 394 2.338015 CCTGTCAATTGCTGCCGCT 61.338 57.895 0.00 0.00 36.97 5.52
407 430 3.286329 TGTAGACATGGACGTAGCCTA 57.714 47.619 0.00 0.00 0.00 3.93
409 432 2.730934 AGACATGGACGTAGCCTAGA 57.269 50.000 0.00 0.00 0.00 2.43
452 475 1.530323 GGAGTGTACACGGCCAAAAT 58.470 50.000 26.25 7.74 36.20 1.82
467 491 3.019564 CCAAAATCCGAGCCAAGAGATT 58.980 45.455 0.00 0.00 0.00 2.40
483 507 4.883083 AGAGATTCAGTTGTTTACTCGCA 58.117 39.130 0.00 0.00 33.85 5.10
498 522 2.626780 CGCAGCCCGATCCTCGATA 61.627 63.158 0.00 0.00 43.74 2.92
531 558 1.252215 TATGGCCGAGGACGTGTTGA 61.252 55.000 0.00 0.00 37.88 3.18
532 559 2.432628 GGCCGAGGACGTGTTGAG 60.433 66.667 0.00 0.00 37.88 3.02
533 560 3.112709 GCCGAGGACGTGTTGAGC 61.113 66.667 0.00 0.00 37.88 4.26
534 561 2.432628 CCGAGGACGTGTTGAGCC 60.433 66.667 0.00 0.00 37.88 4.70
545 572 2.292267 GTGTTGAGCCCTGTATGGATG 58.708 52.381 0.00 0.00 38.35 3.51
547 574 3.111484 TGTTGAGCCCTGTATGGATGTA 58.889 45.455 0.00 0.00 38.35 2.29
550 577 5.221641 TGTTGAGCCCTGTATGGATGTATAC 60.222 44.000 0.00 0.00 38.35 1.47
559 588 6.602009 CCTGTATGGATGTATACGTAGATGGA 59.398 42.308 0.08 0.00 36.54 3.41
563 592 9.136952 GTATGGATGTATACGTAGATGGAAAAC 57.863 37.037 0.08 0.00 0.00 2.43
673 702 3.682292 ATCTCCGGTTTCAGGCGCC 62.682 63.158 21.89 21.89 0.00 6.53
701 730 3.406361 CGCACGAGCACCACAGAC 61.406 66.667 5.50 0.00 42.27 3.51
702 731 3.044305 GCACGAGCACCACAGACC 61.044 66.667 0.00 0.00 41.58 3.85
703 732 2.734723 CACGAGCACCACAGACCG 60.735 66.667 0.00 0.00 0.00 4.79
704 733 4.664677 ACGAGCACCACAGACCGC 62.665 66.667 0.00 0.00 0.00 5.68
705 734 4.662961 CGAGCACCACAGACCGCA 62.663 66.667 0.00 0.00 0.00 5.69
706 735 2.740055 GAGCACCACAGACCGCAG 60.740 66.667 0.00 0.00 0.00 5.18
707 736 4.996434 AGCACCACAGACCGCAGC 62.996 66.667 0.00 0.00 0.00 5.25
972 1032 2.434185 GCACCCACGCTTCGATCA 60.434 61.111 0.00 0.00 0.00 2.92
1446 1506 2.687805 CGCTGACGAGGAGGACGAA 61.688 63.158 0.00 0.00 43.93 3.85
1449 1509 0.448593 CTGACGAGGAGGACGAAGAC 59.551 60.000 0.00 0.00 34.70 3.01
1707 1770 3.746492 GGATCTTCTGTTGCTACGTTTGT 59.254 43.478 0.00 0.00 0.00 2.83
1771 1841 7.891498 AACAAGTGGTTATGTTTTTCCTACT 57.109 32.000 0.00 0.00 38.15 2.57
1773 1843 8.617290 ACAAGTGGTTATGTTTTTCCTACTAG 57.383 34.615 0.00 0.00 0.00 2.57
1774 1844 8.434392 ACAAGTGGTTATGTTTTTCCTACTAGA 58.566 33.333 0.00 0.00 0.00 2.43
1775 1845 8.718734 CAAGTGGTTATGTTTTTCCTACTAGAC 58.281 37.037 0.00 0.00 0.00 2.59
1841 1911 4.044426 GCTGGTTTGAACTTGCAACTAAG 58.956 43.478 0.00 0.00 0.00 2.18
1850 1920 5.762711 TGAACTTGCAACTAAGCACAATAGA 59.237 36.000 0.00 0.00 45.61 1.98
2006 2204 7.972527 ACAAACACGTACAATTGTAACTGTTA 58.027 30.769 26.96 6.70 34.45 2.41
2011 2209 9.480053 ACACGTACAATTGTAACTGTTATACTT 57.520 29.630 19.63 0.00 31.52 2.24
2013 2211 9.695526 ACGTACAATTGTAACTGTTATACTTCA 57.304 29.630 19.63 0.00 31.52 3.02
2059 2257 2.158623 AGACAATTCAGACAGCCCACAA 60.159 45.455 0.00 0.00 0.00 3.33
2086 2284 6.906157 AGTTCAATGTCATCTGTCCAAAAT 57.094 33.333 0.00 0.00 0.00 1.82
2099 2297 9.294030 CATCTGTCCAAAATGTCTTATAAAAGC 57.706 33.333 0.00 0.00 32.36 3.51
2100 2298 8.402798 TCTGTCCAAAATGTCTTATAAAAGCA 57.597 30.769 0.00 0.00 32.36 3.91
2117 2315 0.108281 GCAAACGGAGGGAGTAGTCC 60.108 60.000 8.22 8.22 43.05 3.85
2176 2374 4.378910 CAGTCGTACGTGTATATGTGCATC 59.621 45.833 16.05 0.00 0.00 3.91
2181 2379 4.972286 ACGTGTATATGTGCATCGATTG 57.028 40.909 0.00 0.00 0.00 2.67
2184 2382 4.457810 GTGTATATGTGCATCGATTGTGC 58.542 43.478 0.00 0.00 42.81 4.57
2294 2494 0.249868 TTCTCGTTGGCACACTCCTG 60.250 55.000 0.00 0.00 39.29 3.86
2450 2650 4.886247 TGGAACCGAAGTTAAACTGTTG 57.114 40.909 0.00 0.00 35.94 3.33
2491 2692 6.533730 TCTGATGGTTGTGAGATAACTGTTT 58.466 36.000 0.00 0.00 0.00 2.83
2541 2749 0.179070 GGCTCTCCCTCCGATTTCAC 60.179 60.000 0.00 0.00 0.00 3.18
2555 2763 7.063544 CCTCCGATTTCACTTAGTAGAAACAAG 59.936 40.741 10.46 6.73 36.65 3.16
2556 2764 7.663827 TCCGATTTCACTTAGTAGAAACAAGA 58.336 34.615 10.46 6.54 36.65 3.02
2557 2765 7.813148 TCCGATTTCACTTAGTAGAAACAAGAG 59.187 37.037 10.46 3.97 36.65 2.85
2558 2766 7.599245 CCGATTTCACTTAGTAGAAACAAGAGT 59.401 37.037 10.46 0.00 36.65 3.24
2559 2767 8.640291 CGATTTCACTTAGTAGAAACAAGAGTC 58.360 37.037 10.46 5.08 36.65 3.36
2560 2768 9.477484 GATTTCACTTAGTAGAAACAAGAGTCA 57.523 33.333 10.46 0.00 36.65 3.41
2561 2769 9.832445 ATTTCACTTAGTAGAAACAAGAGTCAA 57.168 29.630 10.46 0.00 36.65 3.18
2562 2770 9.832445 TTTCACTTAGTAGAAACAAGAGTCAAT 57.168 29.630 0.00 0.00 0.00 2.57
2563 2771 9.832445 TTCACTTAGTAGAAACAAGAGTCAATT 57.168 29.630 0.00 0.00 0.00 2.32
2564 2772 9.832445 TCACTTAGTAGAAACAAGAGTCAATTT 57.168 29.630 0.00 0.00 0.00 1.82
2566 2774 9.832445 ACTTAGTAGAAACAAGAGTCAATTTCA 57.168 29.630 13.21 1.72 34.22 2.69
2568 2776 7.497925 AGTAGAAACAAGAGTCAATTTCACC 57.502 36.000 13.21 5.95 34.22 4.02
2569 2777 7.054124 AGTAGAAACAAGAGTCAATTTCACCA 58.946 34.615 13.21 0.58 34.22 4.17
2570 2778 6.136541 AGAAACAAGAGTCAATTTCACCAC 57.863 37.500 13.21 0.00 34.22 4.16
2571 2779 4.918810 AACAAGAGTCAATTTCACCACC 57.081 40.909 0.00 0.00 0.00 4.61
2572 2780 2.878406 ACAAGAGTCAATTTCACCACCG 59.122 45.455 0.00 0.00 0.00 4.94
2573 2781 2.185004 AGAGTCAATTTCACCACCGG 57.815 50.000 0.00 0.00 0.00 5.28
2574 2782 1.420138 AGAGTCAATTTCACCACCGGT 59.580 47.619 0.00 0.00 35.62 5.28
2584 2792 3.813080 ACCACCGGTGCTTAAACTT 57.187 47.368 29.75 1.90 32.98 2.66
2585 2793 1.314730 ACCACCGGTGCTTAAACTTG 58.685 50.000 29.75 14.24 32.98 3.16
2586 2794 0.596082 CCACCGGTGCTTAAACTTGG 59.404 55.000 29.75 7.60 0.00 3.61
2587 2795 0.039527 CACCGGTGCTTAAACTTGGC 60.040 55.000 24.02 0.00 0.00 4.52
2588 2796 0.466555 ACCGGTGCTTAAACTTGGCA 60.467 50.000 6.12 0.00 0.00 4.92
2589 2797 0.671251 CCGGTGCTTAAACTTGGCAA 59.329 50.000 0.00 0.00 37.73 4.52
2590 2798 1.335872 CCGGTGCTTAAACTTGGCAAG 60.336 52.381 25.06 25.06 37.73 4.01
2591 2799 1.606668 CGGTGCTTAAACTTGGCAAGA 59.393 47.619 32.50 8.70 37.73 3.02
2592 2800 2.034053 CGGTGCTTAAACTTGGCAAGAA 59.966 45.455 32.50 15.88 37.73 2.52
2593 2801 3.305335 CGGTGCTTAAACTTGGCAAGAAT 60.305 43.478 32.50 21.35 37.73 2.40
2594 2802 4.083003 CGGTGCTTAAACTTGGCAAGAATA 60.083 41.667 32.50 20.38 37.73 1.75
2595 2803 5.161358 GGTGCTTAAACTTGGCAAGAATAC 58.839 41.667 32.50 18.48 37.73 1.89
2596 2804 5.048013 GGTGCTTAAACTTGGCAAGAATACT 60.048 40.000 32.50 7.90 37.73 2.12
2597 2805 6.447162 GTGCTTAAACTTGGCAAGAATACTT 58.553 36.000 32.50 13.77 37.73 2.24
2598 2806 7.308951 GGTGCTTAAACTTGGCAAGAATACTTA 60.309 37.037 32.50 16.91 37.73 2.24
2599 2807 8.244113 GTGCTTAAACTTGGCAAGAATACTTAT 58.756 33.333 32.50 5.55 37.73 1.73
2600 2808 8.802267 TGCTTAAACTTGGCAAGAATACTTATT 58.198 29.630 32.50 11.58 34.70 1.40
2601 2809 9.639601 GCTTAAACTTGGCAAGAATACTTATTT 57.360 29.630 32.50 20.34 34.70 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.887247 TTTGGCCGGATGTCAATGTG 59.113 50.000 5.05 0.00 0.00 3.21
1 2 1.176527 CTTTGGCCGGATGTCAATGT 58.823 50.000 5.05 0.00 0.00 2.71
3 4 1.463674 GACTTTGGCCGGATGTCAAT 58.536 50.000 5.05 0.00 0.00 2.57
6 7 2.750888 GCGACTTTGGCCGGATGTC 61.751 63.158 5.05 12.36 0.00 3.06
7 8 2.746277 GCGACTTTGGCCGGATGT 60.746 61.111 5.05 0.00 0.00 3.06
8 9 2.745884 TGCGACTTTGGCCGGATG 60.746 61.111 5.05 0.00 0.00 3.51
9 10 2.746277 GTGCGACTTTGGCCGGAT 60.746 61.111 5.05 0.00 0.00 4.18
10 11 3.545124 ATGTGCGACTTTGGCCGGA 62.545 57.895 5.05 0.00 0.00 5.14
11 12 3.039202 GATGTGCGACTTTGGCCGG 62.039 63.158 0.00 0.00 0.00 6.13
12 13 2.480555 GATGTGCGACTTTGGCCG 59.519 61.111 0.00 0.00 0.00 6.13
13 14 1.017177 TACGATGTGCGACTTTGGCC 61.017 55.000 0.00 0.00 44.57 5.36
14 15 1.006832 ATACGATGTGCGACTTTGGC 58.993 50.000 0.00 0.00 44.57 4.52
15 16 3.740044 AAATACGATGTGCGACTTTGG 57.260 42.857 0.00 0.00 44.57 3.28
37 38 3.795877 AGTTACTGACGTTCCGGAAAAA 58.204 40.909 20.79 3.79 0.00 1.94
38 39 3.457610 AGTTACTGACGTTCCGGAAAA 57.542 42.857 20.79 4.61 0.00 2.29
39 40 3.457610 AAGTTACTGACGTTCCGGAAA 57.542 42.857 20.79 1.60 0.00 3.13
40 41 4.789012 ATAAGTTACTGACGTTCCGGAA 57.211 40.909 14.35 14.35 0.00 4.30
41 42 4.789012 AATAAGTTACTGACGTTCCGGA 57.211 40.909 0.00 0.00 0.00 5.14
42 43 5.644644 ACTAATAAGTTACTGACGTTCCGG 58.355 41.667 0.00 0.00 29.00 5.14
43 44 6.413235 GCTACTAATAAGTTACTGACGTTCCG 59.587 42.308 0.00 0.00 37.15 4.30
44 45 6.694844 GGCTACTAATAAGTTACTGACGTTCC 59.305 42.308 0.00 0.00 37.15 3.62
45 46 6.694844 GGGCTACTAATAAGTTACTGACGTTC 59.305 42.308 0.00 0.00 37.15 3.95
46 47 6.379417 AGGGCTACTAATAAGTTACTGACGTT 59.621 38.462 0.00 0.00 37.15 3.99
47 48 5.890419 AGGGCTACTAATAAGTTACTGACGT 59.110 40.000 0.00 0.00 37.15 4.34
48 49 6.262720 AGAGGGCTACTAATAAGTTACTGACG 59.737 42.308 0.00 0.00 37.15 4.35
49 50 7.585579 AGAGGGCTACTAATAAGTTACTGAC 57.414 40.000 0.00 0.00 37.15 3.51
50 51 9.129532 GTAAGAGGGCTACTAATAAGTTACTGA 57.870 37.037 0.00 0.00 37.15 3.41
51 52 8.910944 TGTAAGAGGGCTACTAATAAGTTACTG 58.089 37.037 0.00 0.00 37.15 2.74
52 53 8.911965 GTGTAAGAGGGCTACTAATAAGTTACT 58.088 37.037 0.00 0.00 37.15 2.24
53 54 8.140628 GGTGTAAGAGGGCTACTAATAAGTTAC 58.859 40.741 0.00 0.00 37.15 2.50
54 55 8.063770 AGGTGTAAGAGGGCTACTAATAAGTTA 58.936 37.037 0.00 0.00 37.15 2.24
55 56 6.901857 AGGTGTAAGAGGGCTACTAATAAGTT 59.098 38.462 0.00 0.00 37.15 2.66
56 57 6.442091 AGGTGTAAGAGGGCTACTAATAAGT 58.558 40.000 0.00 0.00 39.91 2.24
57 58 6.980416 AGGTGTAAGAGGGCTACTAATAAG 57.020 41.667 0.00 0.00 0.00 1.73
58 59 6.899075 TGAAGGTGTAAGAGGGCTACTAATAA 59.101 38.462 0.00 0.00 0.00 1.40
59 60 6.437755 TGAAGGTGTAAGAGGGCTACTAATA 58.562 40.000 0.00 0.00 0.00 0.98
60 61 5.278061 TGAAGGTGTAAGAGGGCTACTAAT 58.722 41.667 0.00 0.00 0.00 1.73
61 62 4.680407 TGAAGGTGTAAGAGGGCTACTAA 58.320 43.478 0.00 0.00 0.00 2.24
62 63 4.326600 TGAAGGTGTAAGAGGGCTACTA 57.673 45.455 0.00 0.00 0.00 1.82
63 64 3.185880 TGAAGGTGTAAGAGGGCTACT 57.814 47.619 0.00 0.00 0.00 2.57
64 65 3.451178 TGATGAAGGTGTAAGAGGGCTAC 59.549 47.826 0.00 0.00 0.00 3.58
65 66 3.451178 GTGATGAAGGTGTAAGAGGGCTA 59.549 47.826 0.00 0.00 0.00 3.93
66 67 2.237392 GTGATGAAGGTGTAAGAGGGCT 59.763 50.000 0.00 0.00 0.00 5.19
67 68 2.633488 GTGATGAAGGTGTAAGAGGGC 58.367 52.381 0.00 0.00 0.00 5.19
68 69 2.418746 CGGTGATGAAGGTGTAAGAGGG 60.419 54.545 0.00 0.00 0.00 4.30
69 70 2.893637 CGGTGATGAAGGTGTAAGAGG 58.106 52.381 0.00 0.00 0.00 3.69
70 71 2.271800 GCGGTGATGAAGGTGTAAGAG 58.728 52.381 0.00 0.00 0.00 2.85
71 72 1.621317 TGCGGTGATGAAGGTGTAAGA 59.379 47.619 0.00 0.00 0.00 2.10
72 73 2.093306 TGCGGTGATGAAGGTGTAAG 57.907 50.000 0.00 0.00 0.00 2.34
73 74 2.147958 GTTGCGGTGATGAAGGTGTAA 58.852 47.619 0.00 0.00 0.00 2.41
74 75 1.803334 GTTGCGGTGATGAAGGTGTA 58.197 50.000 0.00 0.00 0.00 2.90
75 76 1.227999 CGTTGCGGTGATGAAGGTGT 61.228 55.000 0.00 0.00 0.00 4.16
76 77 1.227999 ACGTTGCGGTGATGAAGGTG 61.228 55.000 0.00 0.00 0.00 4.00
77 78 0.534203 AACGTTGCGGTGATGAAGGT 60.534 50.000 0.00 0.00 0.00 3.50
78 79 0.591170 AAACGTTGCGGTGATGAAGG 59.409 50.000 0.00 0.00 0.00 3.46
79 80 3.529634 TTAAACGTTGCGGTGATGAAG 57.470 42.857 0.00 0.00 0.00 3.02
105 109 5.687730 CCTAACGTTGTGCTGTCAGATATAG 59.312 44.000 11.99 0.00 0.00 1.31
106 110 5.358725 TCCTAACGTTGTGCTGTCAGATATA 59.641 40.000 11.99 0.00 0.00 0.86
107 111 4.159693 TCCTAACGTTGTGCTGTCAGATAT 59.840 41.667 11.99 0.00 0.00 1.63
116 120 3.011119 TGTTTTGTCCTAACGTTGTGCT 58.989 40.909 11.99 0.00 0.00 4.40
122 126 4.097286 ACAATGCTTGTTTTGTCCTAACGT 59.903 37.500 0.00 0.00 42.22 3.99
175 184 2.489971 ACGGAATTGTGTGTAGGTGTG 58.510 47.619 0.00 0.00 0.00 3.82
182 191 2.290008 TGGAGCATACGGAATTGTGTGT 60.290 45.455 0.00 0.00 33.94 3.72
228 237 3.869493 AAAAATGGTCTGGGCCAGT 57.131 47.368 31.60 11.18 42.47 4.00
254 276 0.453615 GTCACGCTCTCACAGTCTCG 60.454 60.000 0.00 0.00 0.00 4.04
279 301 4.578105 GCGAGATGGATGAGAAGGAAAAAT 59.422 41.667 0.00 0.00 0.00 1.82
318 341 0.979665 CATCCCGCTATCACCCATCT 59.020 55.000 0.00 0.00 0.00 2.90
321 344 2.818169 GCCATCCCGCTATCACCCA 61.818 63.158 0.00 0.00 0.00 4.51
371 394 7.048178 CATGTCTACATACGTACGCACGAATA 61.048 42.308 16.41 0.00 41.91 1.75
385 408 3.828921 AGGCTACGTCCATGTCTACATA 58.171 45.455 0.00 0.00 34.26 2.29
407 430 8.770828 CGGTTTATTTGTTGTATATCCGATTCT 58.229 33.333 0.00 0.00 36.97 2.40
409 432 7.716123 TCCGGTTTATTTGTTGTATATCCGATT 59.284 33.333 0.00 0.00 36.97 3.34
452 475 1.561643 ACTGAATCTCTTGGCTCGGA 58.438 50.000 0.00 0.00 0.00 4.55
467 491 1.508632 GGCTGCGAGTAAACAACTGA 58.491 50.000 0.00 0.00 39.07 3.41
498 522 5.105917 CCTCGGCCATACAGTTAACAAAATT 60.106 40.000 8.61 0.00 0.00 1.82
531 558 3.507411 ACGTATACATCCATACAGGGCT 58.493 45.455 3.32 0.00 38.24 5.19
532 559 3.955650 ACGTATACATCCATACAGGGC 57.044 47.619 3.32 0.00 38.24 5.19
533 560 6.183360 CCATCTACGTATACATCCATACAGGG 60.183 46.154 3.32 0.00 38.24 4.45
534 561 6.602009 TCCATCTACGTATACATCCATACAGG 59.398 42.308 3.32 0.00 39.47 4.00
550 577 3.727723 GGATACGACGTTTTCCATCTACG 59.272 47.826 19.28 0.00 40.85 3.51
559 588 2.523015 CGCTACAGGATACGACGTTTT 58.477 47.619 5.50 0.00 46.39 2.43
563 592 0.041488 GACCGCTACAGGATACGACG 60.041 60.000 0.00 0.00 46.39 5.12
589 618 1.532505 CGCTGCCGATCAAAAAGATGG 60.533 52.381 0.00 0.00 37.00 3.51
591 620 1.398390 GTCGCTGCCGATCAAAAAGAT 59.602 47.619 0.00 0.00 46.38 2.40
617 646 4.273318 CCAGAAATCCGGAATCCTTTCTT 58.727 43.478 22.41 9.89 36.16 2.52
650 679 1.613255 GCCTGAAACCGGAGATTTGGA 60.613 52.381 9.46 0.00 0.00 3.53
784 830 0.037882 ATGATGATGGCTACGAGCGG 60.038 55.000 0.00 0.00 43.62 5.52
785 831 1.458445 CAATGATGATGGCTACGAGCG 59.542 52.381 0.00 0.00 43.62 5.03
786 832 1.196354 GCAATGATGATGGCTACGAGC 59.804 52.381 0.00 0.00 41.46 5.03
787 833 1.802960 GGCAATGATGATGGCTACGAG 59.197 52.381 0.00 0.00 39.99 4.18
788 834 1.543208 GGGCAATGATGATGGCTACGA 60.543 52.381 0.00 0.00 42.51 3.43
789 835 0.877071 GGGCAATGATGATGGCTACG 59.123 55.000 0.00 0.00 42.51 3.51
1446 1506 0.168348 CCATGAGTTCGTCGTCGTCT 59.832 55.000 1.33 2.43 38.33 4.18
1449 1509 1.674611 GCACCATGAGTTCGTCGTCG 61.675 60.000 0.00 0.00 38.55 5.12
1670 1733 6.537566 CAGAAGATCCACATTTTCTGTAACG 58.462 40.000 10.49 0.00 42.48 3.18
1707 1770 8.450578 ACATCAAAATATTTCGCCTAGAATCA 57.549 30.769 0.10 0.00 38.86 2.57
1770 1840 5.276114 CGTGATCAGCATTCTTTTCGTCTAG 60.276 44.000 0.00 0.00 0.00 2.43
1771 1841 4.562789 CGTGATCAGCATTCTTTTCGTCTA 59.437 41.667 0.00 0.00 0.00 2.59
1773 1843 3.484229 CCGTGATCAGCATTCTTTTCGTC 60.484 47.826 0.00 0.00 0.00 4.20
1774 1844 2.416547 CCGTGATCAGCATTCTTTTCGT 59.583 45.455 0.00 0.00 0.00 3.85
1775 1845 2.672874 TCCGTGATCAGCATTCTTTTCG 59.327 45.455 0.00 0.00 0.00 3.46
1841 1911 4.137116 TGTATCCCAGTGTCTATTGTGC 57.863 45.455 0.00 0.00 0.00 4.57
1850 1920 6.186957 TCATAAAGCAATTGTATCCCAGTGT 58.813 36.000 7.40 0.00 0.00 3.55
1905 1975 2.649531 TCACATTTTGGGACGAAGGT 57.350 45.000 0.00 0.00 0.00 3.50
1956 2132 4.262377 CCATGCAACACATTTTACTTCCCA 60.262 41.667 0.00 0.00 36.64 4.37
1995 2193 9.990360 TGAACAGATGAAGTATAACAGTTACAA 57.010 29.630 0.00 0.00 0.00 2.41
2011 2209 8.304596 AGACGTCTTATAAAAGTGAACAGATGA 58.695 33.333 13.58 0.00 34.13 2.92
2013 2211 9.790389 CTAGACGTCTTATAAAAGTGAACAGAT 57.210 33.333 25.44 0.00 34.13 2.90
2059 2257 8.408043 TTTGGACAGATGACATTGAACTATTT 57.592 30.769 0.00 0.00 0.00 1.40
2086 2284 4.698304 CCCTCCGTTTGCTTTTATAAGACA 59.302 41.667 0.00 0.00 32.92 3.41
2099 2297 1.263356 TGGACTACTCCCTCCGTTTG 58.737 55.000 0.00 0.00 35.34 2.93
2100 2298 2.249309 ATGGACTACTCCCTCCGTTT 57.751 50.000 0.00 0.00 35.34 3.60
2176 2374 0.455464 CACAGTGGCATGCACAATCG 60.455 55.000 21.36 11.02 0.00 3.34
2181 2379 1.202222 GCTAATCACAGTGGCATGCAC 60.202 52.381 21.36 15.34 0.00 4.57
2184 2382 2.612672 CTCTGCTAATCACAGTGGCATG 59.387 50.000 0.00 0.00 36.50 4.06
2425 2625 6.105397 ACAGTTTAACTTCGGTTCCATCTA 57.895 37.500 0.00 0.00 39.17 1.98
2450 2650 4.185467 TCAGAGATGCTCTCAACAAGAC 57.815 45.455 13.42 0.00 45.73 3.01
2518 2726 0.399091 AATCGGAGGGAGAGCCATCA 60.399 55.000 0.00 0.00 46.64 3.07
2555 2763 1.892209 ACCGGTGGTGAAATTGACTC 58.108 50.000 6.12 0.00 32.98 3.36
2566 2774 1.314730 CAAGTTTAAGCACCGGTGGT 58.685 50.000 32.82 32.82 44.00 4.16
2567 2775 0.596082 CCAAGTTTAAGCACCGGTGG 59.404 55.000 34.58 17.30 0.00 4.61
2568 2776 0.039527 GCCAAGTTTAAGCACCGGTG 60.040 55.000 30.66 30.66 0.00 4.94
2569 2777 0.466555 TGCCAAGTTTAAGCACCGGT 60.467 50.000 0.00 0.00 0.00 5.28
2570 2778 0.671251 TTGCCAAGTTTAAGCACCGG 59.329 50.000 0.00 0.00 35.96 5.28
2571 2779 1.606668 TCTTGCCAAGTTTAAGCACCG 59.393 47.619 4.04 0.00 35.96 4.94
2572 2780 3.726291 TTCTTGCCAAGTTTAAGCACC 57.274 42.857 4.04 0.00 35.96 5.01
2573 2781 6.013842 AGTATTCTTGCCAAGTTTAAGCAC 57.986 37.500 4.04 0.00 35.96 4.40
2574 2782 6.648879 AAGTATTCTTGCCAAGTTTAAGCA 57.351 33.333 4.04 0.00 32.09 3.91
2575 2783 9.639601 AAATAAGTATTCTTGCCAAGTTTAAGC 57.360 29.630 4.04 0.00 35.36 3.09


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

AutoCloner maintained by Alex Coulton.