Multiple sequence alignment - TraesCS7D01G139900

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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 TraesCS7D01G139900 chr7D 100.000 3047 0 0 1 3047 89485437 89488483 0.000000e+00 5627.0
1 TraesCS7D01G139900 chr7D 89.262 1788 138 28 983 2747 89522285 89524041 0.000000e+00 2189.0
2 TraesCS7D01G139900 chr7D 89.386 1319 100 23 834 2148 89731869 89730587 0.000000e+00 1624.0
3 TraesCS7D01G139900 chr7D 92.493 1079 76 5 983 2058 89791428 89790352 0.000000e+00 1539.0
4 TraesCS7D01G139900 chr7D 88.211 721 53 17 67 780 89520167 89520862 0.000000e+00 832.0
5 TraesCS7D01G139900 chr7D 93.770 305 18 1 2743 3047 89523879 89524182 9.960000e-125 457.0
6 TraesCS7D01G139900 chr7D 92.982 57 3 1 35 91 89519224 89519279 7.000000e-12 82.4
7 TraesCS7D01G139900 chr7A 95.669 2078 69 10 983 3047 90586487 90588556 0.000000e+00 3319.0
8 TraesCS7D01G139900 chr7A 94.141 1024 54 4 1037 2060 90664985 90663968 0.000000e+00 1554.0
9 TraesCS7D01G139900 chr7A 88.494 704 59 11 67 762 90612948 90613637 0.000000e+00 832.0
10 TraesCS7D01G139900 chr7B 87.795 2589 209 53 139 2703 40345932 40348437 0.000000e+00 2931.0
11 TraesCS7D01G139900 chr7B 95.176 1078 52 0 983 2060 40443752 40442675 0.000000e+00 1703.0
12 TraesCS7D01G139900 chr7B 87.838 1184 109 20 893 2058 40576546 40575380 0.000000e+00 1356.0
13 TraesCS7D01G139900 chr7B 86.447 273 25 4 2743 3015 40348313 40348573 3.840000e-74 289.0
14 TraesCS7D01G139900 chr7B 85.405 185 17 6 372 550 584258853 584258673 1.870000e-42 183.0
15 TraesCS7D01G139900 chr7B 93.333 105 7 0 39 143 40344314 40344418 4.070000e-34 156.0
16 TraesCS7D01G139900 chr7B 89.286 56 4 2 1 54 578434513 578434568 5.450000e-08 69.4
17 TraesCS7D01G139900 chrUn 88.629 1196 114 16 876 2058 91490340 91491526 0.000000e+00 1435.0
18 TraesCS7D01G139900 chr1B 100.000 38 0 0 1 38 41782586 41782549 1.520000e-08 71.3
19 TraesCS7D01G139900 chr1B 91.489 47 2 2 1 47 433435288 433435332 2.540000e-06 63.9
20 TraesCS7D01G139900 chr4B 91.837 49 3 1 3 50 626735625 626735577 1.960000e-07 67.6
21 TraesCS7D01G139900 chr4B 89.796 49 3 2 1 48 491469247 491469200 9.120000e-06 62.1
22 TraesCS7D01G139900 chr1D 90.000 50 5 0 1 50 440954807 440954758 7.050000e-07 65.8
23 TraesCS7D01G139900 chr6B 90.196 51 1 4 1 51 46752227 46752273 2.540000e-06 63.9
24 TraesCS7D01G139900 chr2B 91.489 47 3 1 1 47 719962810 719962855 2.540000e-06 63.9
25 TraesCS7D01G139900 chr2A 91.489 47 3 1 1 46 561271108 561271154 2.540000e-06 63.9


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 TraesCS7D01G139900 chr7D 89485437 89488483 3046 False 5627.000000 5627 100.000000 1 3047 1 chr7D.!!$F1 3046
1 TraesCS7D01G139900 chr7D 89730587 89731869 1282 True 1624.000000 1624 89.386000 834 2148 1 chr7D.!!$R1 1314
2 TraesCS7D01G139900 chr7D 89790352 89791428 1076 True 1539.000000 1539 92.493000 983 2058 1 chr7D.!!$R2 1075
3 TraesCS7D01G139900 chr7D 89519224 89524182 4958 False 890.100000 2189 91.056250 35 3047 4 chr7D.!!$F2 3012
4 TraesCS7D01G139900 chr7A 90586487 90588556 2069 False 3319.000000 3319 95.669000 983 3047 1 chr7A.!!$F1 2064
5 TraesCS7D01G139900 chr7A 90663968 90664985 1017 True 1554.000000 1554 94.141000 1037 2060 1 chr7A.!!$R1 1023
6 TraesCS7D01G139900 chr7A 90612948 90613637 689 False 832.000000 832 88.494000 67 762 1 chr7A.!!$F2 695
7 TraesCS7D01G139900 chr7B 40442675 40443752 1077 True 1703.000000 1703 95.176000 983 2060 1 chr7B.!!$R1 1077
8 TraesCS7D01G139900 chr7B 40575380 40576546 1166 True 1356.000000 1356 87.838000 893 2058 1 chr7B.!!$R2 1165
9 TraesCS7D01G139900 chr7B 40344314 40348573 4259 False 1125.333333 2931 89.191667 39 3015 3 chr7B.!!$F2 2976
10 TraesCS7D01G139900 chrUn 91490340 91491526 1186 False 1435.000000 1435 88.629000 876 2058 1 chrUn.!!$F1 1182

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
25 26 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
32 33 0.107017 CCGGACGGAGGGAGTACTTA 60.107 60.0 4.40 0.00 37.50 2.24 F
763 3209 0.179045 CGTGGCCCAATTAGGAGAGG 60.179 60.0 0.00 0.00 41.22 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 5330 0.175760 CTGTCCGTGGGTCATACCTG 59.824 60.0 0.00 0.0 38.64 4.00 R
1657 5376 0.331616 AGGCCATTGGGGTAAGTGAC 59.668 55.0 5.01 0.0 39.65 3.67 R
2685 6577 0.030101 GCTGCACTTAAACACCGCAA 59.970 50.0 0.00 0.0 31.10 4.85 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
20 21 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
21 22 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
22 23 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
23 24 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
24 25 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
25 26 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
26 27 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
27 28 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
28 29 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
29 30 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
30 31 1.856539 TTCCGGACGGAGGGAGTACT 61.857 60.000 13.64 0.00 46.06 2.73
31 32 1.379576 CCGGACGGAGGGAGTACTT 60.380 63.158 4.40 0.00 37.50 2.24
32 33 0.107017 CCGGACGGAGGGAGTACTTA 60.107 60.000 4.40 0.00 37.50 2.24
33 34 1.020437 CGGACGGAGGGAGTACTTAC 58.980 60.000 0.00 0.00 0.00 2.34
37 38 4.468713 GGACGGAGGGAGTACTTACTTAT 58.531 47.826 0.00 0.00 36.50 1.73
42 43 6.438425 ACGGAGGGAGTACTTACTTATTTTCA 59.562 38.462 0.00 0.00 36.50 2.69
114 1027 1.349357 AGCAAGGAAGGAACCAGTCTC 59.651 52.381 0.00 0.00 0.00 3.36
155 2586 6.892456 AGAAACCCTCTTTCTTTCTTTCTTGT 59.108 34.615 0.00 0.00 35.39 3.16
236 2670 9.006215 GTGTATGTCTGTTTTAACAACTCAAAC 57.994 33.333 0.00 0.00 38.66 2.93
308 2742 8.331742 GTTCTATCTTATCTTTTCTTTCCGCTG 58.668 37.037 0.00 0.00 0.00 5.18
309 2743 7.556844 TCTATCTTATCTTTTCTTTCCGCTGT 58.443 34.615 0.00 0.00 0.00 4.40
316 2750 1.508632 TTCTTTCCGCTGTTTCCTCG 58.491 50.000 0.00 0.00 0.00 4.63
328 2762 1.134907 GTTTCCTCGGGCGATCAAGTA 60.135 52.381 0.00 0.00 0.00 2.24
351 2785 0.614812 TCAGTGCCATTAGCTGCTGA 59.385 50.000 13.43 4.03 45.26 4.26
361 2795 5.461078 GCCATTAGCTGCTGAATTAAACATG 59.539 40.000 13.43 0.00 38.99 3.21
370 2804 3.505386 TGAATTAAACATGTGGGCCTGT 58.495 40.909 4.53 0.00 0.00 4.00
560 3002 4.154015 TGTGTAGATCGGTGAAAATTGCTG 59.846 41.667 0.00 0.00 0.00 4.41
744 3190 1.403687 ATCTCGGCCCAAGTAGGAGC 61.404 60.000 0.00 0.00 41.22 4.70
754 3200 1.562672 AAGTAGGAGCGTGGCCCAAT 61.563 55.000 0.00 0.00 0.00 3.16
759 3205 1.223487 GAGCGTGGCCCAATTAGGA 59.777 57.895 0.00 0.00 41.22 2.94
760 3206 0.815615 GAGCGTGGCCCAATTAGGAG 60.816 60.000 0.00 0.00 41.22 3.69
761 3207 1.223487 GCGTGGCCCAATTAGGAGA 59.777 57.895 0.00 0.00 41.22 3.71
762 3208 0.815615 GCGTGGCCCAATTAGGAGAG 60.816 60.000 0.00 0.00 41.22 3.20
763 3209 0.179045 CGTGGCCCAATTAGGAGAGG 60.179 60.000 0.00 0.00 41.22 3.69
776 3222 0.616111 GGAGAGGAGAAGTGGCAGGA 60.616 60.000 0.00 0.00 0.00 3.86
790 3256 1.334869 GGCAGGACAGACAAACAGTTG 59.665 52.381 0.00 0.00 40.84 3.16
803 3269 2.665185 AGTTGCTCCCGCGTTCAC 60.665 61.111 4.92 0.00 39.65 3.18
832 3299 4.702131 AGAAACCATGAAAAGGAATCGGAG 59.298 41.667 0.00 0.00 0.00 4.63
1551 5270 0.904865 TCACGGACAGCTCCAGGAAT 60.905 55.000 0.00 0.00 36.12 3.01
1831 5551 0.036306 GAGGCCCGACAAGAAAGGAA 59.964 55.000 0.00 0.00 0.00 3.36
2088 5809 9.482627 GAGATGTATGAGTTAGGATAGGTTTTG 57.517 37.037 0.00 0.00 0.00 2.44
2362 6093 7.545965 AGGTTAATTCTCACATAAACGAGACTG 59.454 37.037 0.00 0.00 37.99 3.51
2587 6479 5.606348 TGGCCTAAAACATTTGAGTTGTT 57.394 34.783 3.32 0.00 38.91 2.83
2588 6480 6.716934 TGGCCTAAAACATTTGAGTTGTTA 57.283 33.333 3.32 0.00 36.32 2.41
2589 6481 6.508777 TGGCCTAAAACATTTGAGTTGTTAC 58.491 36.000 3.32 0.00 36.32 2.50
2590 6482 6.322712 TGGCCTAAAACATTTGAGTTGTTACT 59.677 34.615 3.32 0.00 36.32 2.24
2591 6483 6.640907 GGCCTAAAACATTTGAGTTGTTACTG 59.359 38.462 0.00 0.00 36.32 2.74
2592 6484 7.422399 GCCTAAAACATTTGAGTTGTTACTGA 58.578 34.615 0.00 0.00 36.32 3.41
2593 6485 7.918562 GCCTAAAACATTTGAGTTGTTACTGAA 59.081 33.333 0.00 0.00 36.32 3.02
2594 6486 9.796120 CCTAAAACATTTGAGTTGTTACTGAAA 57.204 29.630 0.00 0.00 40.84 2.69
2626 6518 8.567285 AAGATACAGGGTTCACTAAAGAATTG 57.433 34.615 0.00 0.00 0.00 2.32
2627 6519 7.918076 AGATACAGGGTTCACTAAAGAATTGA 58.082 34.615 0.00 0.00 0.00 2.57
2628 6520 8.383175 AGATACAGGGTTCACTAAAGAATTGAA 58.617 33.333 0.00 0.00 0.00 2.69
2629 6521 6.884280 ACAGGGTTCACTAAAGAATTGAAG 57.116 37.500 0.00 0.00 29.97 3.02
2630 6522 5.241728 ACAGGGTTCACTAAAGAATTGAAGC 59.758 40.000 4.55 4.55 43.73 3.86
2631 6523 5.474876 CAGGGTTCACTAAAGAATTGAAGCT 59.525 40.000 11.30 0.00 43.86 3.74
2632 6524 5.474876 AGGGTTCACTAAAGAATTGAAGCTG 59.525 40.000 11.30 0.00 43.86 4.24
2633 6525 5.157067 GGTTCACTAAAGAATTGAAGCTGC 58.843 41.667 5.69 0.00 42.07 5.25
2634 6526 5.278463 GGTTCACTAAAGAATTGAAGCTGCA 60.278 40.000 1.02 0.00 42.07 4.41
2635 6527 5.362556 TCACTAAAGAATTGAAGCTGCAC 57.637 39.130 0.00 0.00 0.00 4.57
2636 6528 4.821260 TCACTAAAGAATTGAAGCTGCACA 59.179 37.500 0.00 0.00 0.00 4.57
2637 6529 5.049198 TCACTAAAGAATTGAAGCTGCACAG 60.049 40.000 0.00 0.00 0.00 3.66
2638 6530 4.823989 ACTAAAGAATTGAAGCTGCACAGT 59.176 37.500 0.00 0.00 0.00 3.55
2639 6531 3.911661 AAGAATTGAAGCTGCACAGTC 57.088 42.857 0.00 0.00 0.00 3.51
2640 6532 2.854963 AGAATTGAAGCTGCACAGTCA 58.145 42.857 0.00 0.00 0.00 3.41
2641 6533 2.812591 AGAATTGAAGCTGCACAGTCAG 59.187 45.455 0.00 0.00 37.15 3.51
2642 6534 2.556144 ATTGAAGCTGCACAGTCAGA 57.444 45.000 0.00 0.00 36.19 3.27
2643 6535 2.330440 TTGAAGCTGCACAGTCAGAA 57.670 45.000 0.00 0.00 36.19 3.02
2644 6536 1.586422 TGAAGCTGCACAGTCAGAAC 58.414 50.000 1.02 0.00 36.19 3.01
2645 6537 1.139654 TGAAGCTGCACAGTCAGAACT 59.860 47.619 1.02 0.00 36.19 3.01
2646 6538 2.216898 GAAGCTGCACAGTCAGAACTT 58.783 47.619 1.02 0.00 36.19 2.66
2647 6539 2.338577 AGCTGCACAGTCAGAACTTT 57.661 45.000 1.02 0.00 36.19 2.66
2648 6540 2.216898 AGCTGCACAGTCAGAACTTTC 58.783 47.619 1.02 0.00 36.19 2.62
2649 6541 1.265365 GCTGCACAGTCAGAACTTTCC 59.735 52.381 0.00 0.00 36.19 3.13
2650 6542 1.876156 CTGCACAGTCAGAACTTTCCC 59.124 52.381 0.00 0.00 36.19 3.97
2651 6543 1.239347 GCACAGTCAGAACTTTCCCC 58.761 55.000 0.00 0.00 31.71 4.81
2652 6544 1.202818 GCACAGTCAGAACTTTCCCCT 60.203 52.381 0.00 0.00 31.71 4.79
2653 6545 2.749800 GCACAGTCAGAACTTTCCCCTT 60.750 50.000 0.00 0.00 31.71 3.95
2654 6546 3.555966 CACAGTCAGAACTTTCCCCTTT 58.444 45.455 0.00 0.00 31.71 3.11
2655 6547 3.954258 CACAGTCAGAACTTTCCCCTTTT 59.046 43.478 0.00 0.00 31.71 2.27
2656 6548 4.402474 CACAGTCAGAACTTTCCCCTTTTT 59.598 41.667 0.00 0.00 31.71 1.94
2657 6549 4.645136 ACAGTCAGAACTTTCCCCTTTTTC 59.355 41.667 0.00 0.00 31.71 2.29
2658 6550 4.644685 CAGTCAGAACTTTCCCCTTTTTCA 59.355 41.667 0.00 0.00 31.71 2.69
2659 6551 5.127031 CAGTCAGAACTTTCCCCTTTTTCAA 59.873 40.000 0.00 0.00 31.71 2.69
2660 6552 5.899547 AGTCAGAACTTTCCCCTTTTTCAAT 59.100 36.000 0.00 0.00 28.74 2.57
2661 6553 6.384015 AGTCAGAACTTTCCCCTTTTTCAATT 59.616 34.615 0.00 0.00 28.74 2.32
2662 6554 7.047891 GTCAGAACTTTCCCCTTTTTCAATTT 58.952 34.615 0.00 0.00 0.00 1.82
2663 6555 8.201464 GTCAGAACTTTCCCCTTTTTCAATTTA 58.799 33.333 0.00 0.00 0.00 1.40
2664 6556 8.933653 TCAGAACTTTCCCCTTTTTCAATTTAT 58.066 29.630 0.00 0.00 0.00 1.40
2665 6557 9.208022 CAGAACTTTCCCCTTTTTCAATTTATC 57.792 33.333 0.00 0.00 0.00 1.75
2666 6558 9.159254 AGAACTTTCCCCTTTTTCAATTTATCT 57.841 29.630 0.00 0.00 0.00 1.98
2691 6583 9.862371 CTATCTCTTCTAATACATAATTGCGGT 57.138 33.333 0.00 0.00 0.00 5.68
2692 6584 7.946655 TCTCTTCTAATACATAATTGCGGTG 57.053 36.000 0.00 0.00 0.00 4.94
2693 6585 7.497595 TCTCTTCTAATACATAATTGCGGTGT 58.502 34.615 0.00 0.00 0.00 4.16
2694 6586 7.985184 TCTCTTCTAATACATAATTGCGGTGTT 59.015 33.333 0.00 0.00 0.00 3.32
2695 6587 8.500753 TCTTCTAATACATAATTGCGGTGTTT 57.499 30.769 0.00 0.00 0.00 2.83
2696 6588 9.602568 TCTTCTAATACATAATTGCGGTGTTTA 57.397 29.630 0.00 0.00 0.00 2.01
2699 6591 9.386010 TCTAATACATAATTGCGGTGTTTAAGT 57.614 29.630 0.00 0.00 0.00 2.24
2700 6592 9.433317 CTAATACATAATTGCGGTGTTTAAGTG 57.567 33.333 0.00 0.00 0.00 3.16
2701 6593 4.481463 ACATAATTGCGGTGTTTAAGTGC 58.519 39.130 0.00 0.00 0.00 4.40
2702 6594 4.022762 ACATAATTGCGGTGTTTAAGTGCA 60.023 37.500 0.00 0.00 0.00 4.57
2703 6595 2.704725 ATTGCGGTGTTTAAGTGCAG 57.295 45.000 0.00 0.00 36.83 4.41
2704 6596 0.030101 TTGCGGTGTTTAAGTGCAGC 59.970 50.000 0.00 0.00 36.83 5.25
2706 6598 1.440353 CGGTGTTTAAGTGCAGCGC 60.440 57.895 0.00 0.00 46.64 5.92
2707 6599 1.652012 GGTGTTTAAGTGCAGCGCA 59.348 52.632 11.47 0.00 35.60 6.09
2716 6608 2.715005 TGCAGCGCACAAACACTC 59.285 55.556 11.47 0.00 31.71 3.51
2717 6609 2.050985 GCAGCGCACAAACACTCC 60.051 61.111 11.47 0.00 0.00 3.85
2718 6610 2.833533 GCAGCGCACAAACACTCCA 61.834 57.895 11.47 0.00 0.00 3.86
2719 6611 1.726865 CAGCGCACAAACACTCCAA 59.273 52.632 11.47 0.00 0.00 3.53
2720 6612 0.311790 CAGCGCACAAACACTCCAAT 59.688 50.000 11.47 0.00 0.00 3.16
2721 6613 1.535028 CAGCGCACAAACACTCCAATA 59.465 47.619 11.47 0.00 0.00 1.90
2722 6614 2.162208 CAGCGCACAAACACTCCAATAT 59.838 45.455 11.47 0.00 0.00 1.28
2723 6615 2.819608 AGCGCACAAACACTCCAATATT 59.180 40.909 11.47 0.00 0.00 1.28
2724 6616 3.255642 AGCGCACAAACACTCCAATATTT 59.744 39.130 11.47 0.00 0.00 1.40
2725 6617 3.608073 GCGCACAAACACTCCAATATTTC 59.392 43.478 0.30 0.00 0.00 2.17
2726 6618 4.793071 CGCACAAACACTCCAATATTTCA 58.207 39.130 0.00 0.00 0.00 2.69
2727 6619 4.616802 CGCACAAACACTCCAATATTTCAC 59.383 41.667 0.00 0.00 0.00 3.18
2728 6620 5.562696 CGCACAAACACTCCAATATTTCACT 60.563 40.000 0.00 0.00 0.00 3.41
2729 6621 6.215845 GCACAAACACTCCAATATTTCACTT 58.784 36.000 0.00 0.00 0.00 3.16
2730 6622 7.367285 GCACAAACACTCCAATATTTCACTTA 58.633 34.615 0.00 0.00 0.00 2.24
2731 6623 7.865385 GCACAAACACTCCAATATTTCACTTAA 59.135 33.333 0.00 0.00 0.00 1.85
2732 6624 9.912634 CACAAACACTCCAATATTTCACTTAAT 57.087 29.630 0.00 0.00 0.00 1.40
2979 6871 4.953579 ACCTTGTAGTTGGACAATGTTGTT 59.046 37.500 0.00 0.00 42.43 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2 3 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3 4 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
6 7 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
7 8 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
10 11 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
11 12 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
12 13 1.856539 AAGTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
13 14 0.107017 TAAGTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
14 15 1.020437 GTAAGTACTCCCTCCGTCCG 58.980 60.000 0.00 0.00 0.00 4.79
15 16 2.433662 AGTAAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
16 17 6.462552 AAATAAGTAAGTACTCCCTCCGTC 57.537 41.667 0.00 0.00 34.99 4.79
17 18 6.438425 TGAAAATAAGTAAGTACTCCCTCCGT 59.562 38.462 0.00 0.00 34.99 4.69
18 19 6.870769 TGAAAATAAGTAAGTACTCCCTCCG 58.129 40.000 0.00 0.00 34.99 4.63
19 20 8.265764 ACATGAAAATAAGTAAGTACTCCCTCC 58.734 37.037 0.00 0.00 34.99 4.30
20 21 9.668497 AACATGAAAATAAGTAAGTACTCCCTC 57.332 33.333 0.00 0.00 34.99 4.30
42 43 8.218488 AGACCCAAAGAGTAGTTTTTCTAACAT 58.782 33.333 0.00 0.00 0.00 2.71
48 49 6.694877 AACAGACCCAAAGAGTAGTTTTTC 57.305 37.500 0.00 0.00 0.00 2.29
188 2622 8.344446 ACACACATAGTAGTCTACATACACAA 57.656 34.615 12.54 0.00 0.00 3.33
195 2629 7.827729 ACAGACATACACACATAGTAGTCTACA 59.172 37.037 12.54 0.00 33.14 2.74
198 2632 7.704578 AACAGACATACACACATAGTAGTCT 57.295 36.000 0.00 0.00 33.90 3.24
236 2670 2.050350 CAGACCCAGCCAGCAATGG 61.050 63.158 0.00 0.00 36.27 3.16
247 2681 2.025793 TGAGTTGACCAAAACAGACCCA 60.026 45.455 0.00 0.00 32.21 4.51
292 2726 4.145052 AGGAAACAGCGGAAAGAAAAGAT 58.855 39.130 0.00 0.00 0.00 2.40
305 2739 2.125106 ATCGCCCGAGGAAACAGC 60.125 61.111 0.00 0.00 0.00 4.40
308 2742 0.391263 ACTTGATCGCCCGAGGAAAC 60.391 55.000 0.00 0.00 0.00 2.78
309 2743 1.187974 TACTTGATCGCCCGAGGAAA 58.812 50.000 0.00 0.00 0.00 3.13
316 2750 3.487544 GCACTGATTTTACTTGATCGCCC 60.488 47.826 0.00 0.00 0.00 6.13
320 2754 6.914757 GCTAATGGCACTGATTTTACTTGATC 59.085 38.462 0.00 0.00 41.35 2.92
328 2762 3.094572 AGCAGCTAATGGCACTGATTTT 58.905 40.909 6.99 0.00 44.79 1.82
351 2785 3.645687 ACAACAGGCCCACATGTTTAATT 59.354 39.130 5.40 0.00 37.54 1.40
361 2795 0.666374 GTAACACACAACAGGCCCAC 59.334 55.000 0.00 0.00 0.00 4.61
420 2854 7.513505 CGCAACTGACATGAACACTTTTTAAAG 60.514 37.037 0.00 0.80 41.73 1.85
522 2964 6.346120 CGATCTACACATAGTACAATGCTTGC 60.346 42.308 0.00 0.00 0.00 4.01
597 3039 8.106247 TGTAGTGTCTTTTGGGTTTCATAATC 57.894 34.615 0.00 0.00 0.00 1.75
694 3140 8.489990 GGTGTTCTTAGACCCTATTTTCTAAC 57.510 38.462 0.00 0.00 32.19 2.34
722 3168 2.900546 CTCCTACTTGGGCCGAGATTAT 59.099 50.000 27.80 7.34 36.20 1.28
744 3190 0.179045 CCTCTCCTAATTGGGCCACG 60.179 60.000 5.23 0.00 36.20 4.94
754 3200 2.461695 CTGCCACTTCTCCTCTCCTAA 58.538 52.381 0.00 0.00 0.00 2.69
759 3205 0.178921 TGTCCTGCCACTTCTCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
760 3206 0.248843 CTGTCCTGCCACTTCTCCTC 59.751 60.000 0.00 0.00 0.00 3.71
761 3207 0.178921 TCTGTCCTGCCACTTCTCCT 60.179 55.000 0.00 0.00 0.00 3.69
762 3208 0.036858 GTCTGTCCTGCCACTTCTCC 60.037 60.000 0.00 0.00 0.00 3.71
763 3209 0.681733 TGTCTGTCCTGCCACTTCTC 59.318 55.000 0.00 0.00 0.00 2.87
776 3222 1.680338 GGGAGCAACTGTTTGTCTGT 58.320 50.000 0.00 0.00 34.90 3.41
1503 5222 1.727511 CGCCGGTTACCTGGTCGATA 61.728 60.000 0.63 0.00 0.00 2.92
1551 5270 5.079689 TCTCATGTTGCGACCTATTGTAA 57.920 39.130 0.45 0.00 0.00 2.41
1611 5330 0.175760 CTGTCCGTGGGTCATACCTG 59.824 60.000 0.00 0.00 38.64 4.00
1657 5376 0.331616 AGGCCATTGGGGTAAGTGAC 59.668 55.000 5.01 0.00 39.65 3.67
1831 5551 1.831736 GTGTAGTGCCACCCAGTATCT 59.168 52.381 0.00 0.00 32.25 1.98
2362 6093 4.207019 CGTTCTGTTTTTCCAAGATTGCAC 59.793 41.667 0.00 0.00 0.00 4.57
2452 6185 1.140407 CCTAAGCAGCGTGACGTAGC 61.140 60.000 14.11 14.11 0.00 3.58
2600 6492 9.667107 CAATTCTTTAGTGAACCCTGTATCTTA 57.333 33.333 0.00 0.00 0.00 2.10
2601 6493 8.383175 TCAATTCTTTAGTGAACCCTGTATCTT 58.617 33.333 0.00 0.00 0.00 2.40
2602 6494 7.918076 TCAATTCTTTAGTGAACCCTGTATCT 58.082 34.615 0.00 0.00 0.00 1.98
2603 6495 8.561738 TTCAATTCTTTAGTGAACCCTGTATC 57.438 34.615 0.00 0.00 36.04 2.24
2604 6496 7.121315 GCTTCAATTCTTTAGTGAACCCTGTAT 59.879 37.037 0.00 0.00 36.04 2.29
2605 6497 6.430000 GCTTCAATTCTTTAGTGAACCCTGTA 59.570 38.462 0.00 0.00 36.04 2.74
2606 6498 5.241728 GCTTCAATTCTTTAGTGAACCCTGT 59.758 40.000 0.00 0.00 36.04 4.00
2607 6499 5.474876 AGCTTCAATTCTTTAGTGAACCCTG 59.525 40.000 0.00 0.00 36.04 4.45
2608 6500 5.474876 CAGCTTCAATTCTTTAGTGAACCCT 59.525 40.000 0.00 0.00 36.04 4.34
2609 6501 5.703876 CAGCTTCAATTCTTTAGTGAACCC 58.296 41.667 0.00 0.00 36.04 4.11
2610 6502 5.157067 GCAGCTTCAATTCTTTAGTGAACC 58.843 41.667 0.00 0.00 36.04 3.62
2611 6503 5.626955 GTGCAGCTTCAATTCTTTAGTGAAC 59.373 40.000 0.00 0.00 36.04 3.18
2612 6504 5.299028 TGTGCAGCTTCAATTCTTTAGTGAA 59.701 36.000 0.00 0.00 38.42 3.18
2613 6505 4.821260 TGTGCAGCTTCAATTCTTTAGTGA 59.179 37.500 0.00 0.00 0.00 3.41
2614 6506 5.112220 TGTGCAGCTTCAATTCTTTAGTG 57.888 39.130 0.00 0.00 0.00 2.74
2615 6507 4.823989 ACTGTGCAGCTTCAATTCTTTAGT 59.176 37.500 0.00 0.00 0.00 2.24
2616 6508 5.049198 TGACTGTGCAGCTTCAATTCTTTAG 60.049 40.000 0.00 0.00 0.00 1.85
2617 6509 4.821260 TGACTGTGCAGCTTCAATTCTTTA 59.179 37.500 0.00 0.00 0.00 1.85
2618 6510 3.633525 TGACTGTGCAGCTTCAATTCTTT 59.366 39.130 0.00 0.00 0.00 2.52
2619 6511 3.216800 TGACTGTGCAGCTTCAATTCTT 58.783 40.909 0.00 0.00 0.00 2.52
2620 6512 2.812591 CTGACTGTGCAGCTTCAATTCT 59.187 45.455 0.00 0.00 0.00 2.40
2621 6513 2.810274 TCTGACTGTGCAGCTTCAATTC 59.190 45.455 0.00 0.00 35.86 2.17
2622 6514 2.854963 TCTGACTGTGCAGCTTCAATT 58.145 42.857 0.00 0.00 35.86 2.32
2623 6515 2.551459 GTTCTGACTGTGCAGCTTCAAT 59.449 45.455 0.00 0.00 35.86 2.57
2624 6516 1.942657 GTTCTGACTGTGCAGCTTCAA 59.057 47.619 0.00 0.00 35.86 2.69
2625 6517 1.139654 AGTTCTGACTGTGCAGCTTCA 59.860 47.619 0.00 0.00 35.86 3.02
2626 6518 1.876322 AGTTCTGACTGTGCAGCTTC 58.124 50.000 0.00 0.00 35.86 3.86
2627 6519 2.338577 AAGTTCTGACTGTGCAGCTT 57.661 45.000 0.00 0.00 35.91 3.74
2628 6520 2.216898 GAAAGTTCTGACTGTGCAGCT 58.783 47.619 0.00 0.00 35.91 4.24
2629 6521 1.265365 GGAAAGTTCTGACTGTGCAGC 59.735 52.381 0.00 0.00 35.91 5.25
2630 6522 1.876156 GGGAAAGTTCTGACTGTGCAG 59.124 52.381 0.00 0.00 33.38 4.41
2631 6523 1.476833 GGGGAAAGTTCTGACTGTGCA 60.477 52.381 0.00 0.00 33.38 4.57
2632 6524 1.202818 AGGGGAAAGTTCTGACTGTGC 60.203 52.381 0.00 0.00 35.91 4.57
2633 6525 2.938956 AGGGGAAAGTTCTGACTGTG 57.061 50.000 0.00 0.00 35.91 3.66
2634 6526 3.953542 AAAGGGGAAAGTTCTGACTGT 57.046 42.857 0.00 0.00 35.91 3.55
2635 6527 4.644685 TGAAAAAGGGGAAAGTTCTGACTG 59.355 41.667 0.00 0.00 35.91 3.51
2636 6528 4.867086 TGAAAAAGGGGAAAGTTCTGACT 58.133 39.130 0.00 0.00 37.87 3.41
2637 6529 5.592104 TTGAAAAAGGGGAAAGTTCTGAC 57.408 39.130 0.00 0.00 0.00 3.51
2638 6530 6.806668 AATTGAAAAAGGGGAAAGTTCTGA 57.193 33.333 0.00 0.00 0.00 3.27
2639 6531 9.208022 GATAAATTGAAAAAGGGGAAAGTTCTG 57.792 33.333 0.00 0.00 0.00 3.02
2640 6532 9.159254 AGATAAATTGAAAAAGGGGAAAGTTCT 57.841 29.630 0.00 0.00 0.00 3.01
2665 6557 9.862371 ACCGCAATTATGTATTAGAAGAGATAG 57.138 33.333 0.00 0.00 0.00 2.08
2666 6558 9.639601 CACCGCAATTATGTATTAGAAGAGATA 57.360 33.333 0.00 0.00 0.00 1.98
2667 6559 8.150945 ACACCGCAATTATGTATTAGAAGAGAT 58.849 33.333 0.00 0.00 0.00 2.75
2668 6560 7.497595 ACACCGCAATTATGTATTAGAAGAGA 58.502 34.615 0.00 0.00 0.00 3.10
2669 6561 7.715265 ACACCGCAATTATGTATTAGAAGAG 57.285 36.000 0.00 0.00 0.00 2.85
2670 6562 8.500753 AAACACCGCAATTATGTATTAGAAGA 57.499 30.769 0.00 0.00 0.00 2.87
2673 6565 9.386010 ACTTAAACACCGCAATTATGTATTAGA 57.614 29.630 0.00 0.00 0.00 2.10
2674 6566 9.433317 CACTTAAACACCGCAATTATGTATTAG 57.567 33.333 0.00 0.00 0.00 1.73
2675 6567 7.911205 GCACTTAAACACCGCAATTATGTATTA 59.089 33.333 0.00 0.00 0.00 0.98
2676 6568 6.750039 GCACTTAAACACCGCAATTATGTATT 59.250 34.615 0.00 0.00 0.00 1.89
2677 6569 6.127869 TGCACTTAAACACCGCAATTATGTAT 60.128 34.615 0.00 0.00 0.00 2.29
2678 6570 5.181433 TGCACTTAAACACCGCAATTATGTA 59.819 36.000 0.00 0.00 0.00 2.29
2679 6571 4.022762 TGCACTTAAACACCGCAATTATGT 60.023 37.500 0.00 0.00 0.00 2.29
2680 6572 4.480541 TGCACTTAAACACCGCAATTATG 58.519 39.130 0.00 0.00 0.00 1.90
2681 6573 4.732784 CTGCACTTAAACACCGCAATTAT 58.267 39.130 0.00 0.00 31.10 1.28
2682 6574 3.610585 GCTGCACTTAAACACCGCAATTA 60.611 43.478 0.00 0.00 31.10 1.40
2683 6575 2.862140 GCTGCACTTAAACACCGCAATT 60.862 45.455 0.00 0.00 31.10 2.32
2684 6576 1.335872 GCTGCACTTAAACACCGCAAT 60.336 47.619 0.00 0.00 31.10 3.56
2685 6577 0.030101 GCTGCACTTAAACACCGCAA 59.970 50.000 0.00 0.00 31.10 4.85
2686 6578 1.652012 GCTGCACTTAAACACCGCA 59.348 52.632 0.00 0.00 0.00 5.69
2687 6579 1.440353 CGCTGCACTTAAACACCGC 60.440 57.895 0.00 0.00 0.00 5.68
2688 6580 1.440353 GCGCTGCACTTAAACACCG 60.440 57.895 0.00 0.00 0.00 4.94
2689 6581 1.652012 TGCGCTGCACTTAAACACC 59.348 52.632 9.73 0.00 31.71 4.16
2699 6591 2.715005 GAGTGTTTGTGCGCTGCA 59.285 55.556 9.73 4.86 35.60 4.41
2700 6592 2.050985 GGAGTGTTTGTGCGCTGC 60.051 61.111 9.73 1.68 0.00 5.25
2701 6593 0.311790 ATTGGAGTGTTTGTGCGCTG 59.688 50.000 9.73 0.00 0.00 5.18
2702 6594 1.890876 TATTGGAGTGTTTGTGCGCT 58.109 45.000 9.73 0.00 0.00 5.92
2703 6595 2.919666 ATATTGGAGTGTTTGTGCGC 57.080 45.000 0.00 0.00 0.00 6.09
2704 6596 4.616802 GTGAAATATTGGAGTGTTTGTGCG 59.383 41.667 0.00 0.00 0.00 5.34
2705 6597 5.772521 AGTGAAATATTGGAGTGTTTGTGC 58.227 37.500 0.00 0.00 0.00 4.57
2706 6598 9.912634 ATTAAGTGAAATATTGGAGTGTTTGTG 57.087 29.630 0.00 0.00 0.00 3.33
2721 6613 9.699410 TGGTAAGGATCATGAATTAAGTGAAAT 57.301 29.630 0.00 0.00 0.00 2.17
2722 6614 9.527157 TTGGTAAGGATCATGAATTAAGTGAAA 57.473 29.630 0.00 0.00 0.00 2.69
2723 6615 9.527157 TTTGGTAAGGATCATGAATTAAGTGAA 57.473 29.630 0.00 0.00 0.00 3.18
2724 6616 9.527157 TTTTGGTAAGGATCATGAATTAAGTGA 57.473 29.630 0.00 0.00 0.00 3.41
2979 6871 5.439721 CTGGGATCCAAATATGACTCACAA 58.560 41.667 15.23 0.00 30.80 3.33


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

AutoCloner maintained by Alex Coulton.