Multiple sequence alignment - TraesCS6D01G009000

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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 TraesCS6D01G009000 chr6D 100.000 5041 0 0 1 5041 3492676 3487636 0.000000e+00 9310.0
1 TraesCS6D01G009000 chr6D 96.341 1995 57 7 3062 5041 3476628 3474635 0.000000e+00 3267.0
2 TraesCS6D01G009000 chr6D 91.691 349 24 5 1564 1908 3476967 3476620 3.530000e-131 479.0
3 TraesCS6D01G009000 chr6A 93.352 3520 176 18 885 4362 2277180 2273677 0.000000e+00 5151.0
4 TraesCS6D01G009000 chr6A 84.314 153 13 3 1446 1587 383964822 383964670 6.810000e-29 139.0
5 TraesCS6D01G009000 chr6A 97.500 80 2 0 774 853 2277256 2277177 2.450000e-28 137.0
6 TraesCS6D01G009000 chr6A 98.182 55 1 0 677 731 2277896 2277842 4.150000e-16 97.1
7 TraesCS6D01G009000 chr6A 89.189 74 8 0 3064 3137 58311686 58311759 5.370000e-15 93.5
8 TraesCS6D01G009000 chr6B 93.333 1500 63 9 3062 4554 6820933 6819464 0.000000e+00 2182.0
9 TraesCS6D01G009000 chr6B 91.359 1111 62 12 3062 4155 6834584 6833491 0.000000e+00 1489.0
10 TraesCS6D01G009000 chr6B 92.830 530 29 4 834 1358 6835711 6835186 0.000000e+00 760.0
11 TraesCS6D01G009000 chr6B 88.099 563 39 10 1374 1910 6835134 6834574 1.180000e-180 643.0
12 TraesCS6D01G009000 chr6B 89.024 492 33 7 4551 5041 6818944 6818473 1.560000e-164 590.0
13 TraesCS6D01G009000 chr6B 89.904 208 19 2 1564 1769 6826517 6826310 2.990000e-67 267.0
14 TraesCS6D01G009000 chr6B 95.139 144 5 2 1766 1908 6821067 6820925 5.080000e-55 226.0
15 TraesCS6D01G009000 chr6B 90.476 147 11 3 629 774 6835998 6835854 1.850000e-44 191.0
16 TraesCS6D01G009000 chr6B 83.660 153 14 3 1446 1587 422321313 422321161 3.170000e-27 134.0
17 TraesCS6D01G009000 chrUn 97.245 1234 27 6 3813 5041 316606536 316607767 0.000000e+00 2084.0
18 TraesCS6D01G009000 chr1D 88.790 1124 109 11 1917 3029 402303457 402302340 0.000000e+00 1362.0
19 TraesCS6D01G009000 chr1D 88.350 1133 119 13 1939 3062 481421962 481423090 0.000000e+00 1349.0
20 TraesCS6D01G009000 chr1D 87.295 1157 133 11 1917 3067 417913764 417912616 0.000000e+00 1310.0
21 TraesCS6D01G009000 chr1D 89.280 597 59 3 1 596 439140347 439140939 0.000000e+00 743.0
22 TraesCS6D01G009000 chr1D 88.167 600 62 6 3 594 93503427 93502829 0.000000e+00 706.0
23 TraesCS6D01G009000 chr3D 88.194 1135 121 10 1940 3065 567669801 567668671 0.000000e+00 1341.0
24 TraesCS6D01G009000 chr3D 89.916 595 49 5 1 594 21606548 21607132 0.000000e+00 756.0
25 TraesCS6D01G009000 chr3D 88.442 597 55 8 3 594 7961181 7961768 0.000000e+00 708.0
26 TraesCS6D01G009000 chr3D 88.350 103 12 0 1447 1549 128214007 128214109 1.910000e-24 124.0
27 TraesCS6D01G009000 chr3D 88.350 103 12 0 1447 1549 401476755 401476857 1.910000e-24 124.0
28 TraesCS6D01G009000 chr5A 87.359 1155 136 8 1934 3082 142746223 142745073 0.000000e+00 1315.0
29 TraesCS6D01G009000 chr5A 89.465 598 61 2 1 596 687662391 687662988 0.000000e+00 754.0
30 TraesCS6D01G009000 chr5A 89.465 598 61 2 1 596 687668791 687669388 0.000000e+00 754.0
31 TraesCS6D01G009000 chr5A 86.420 81 11 0 3057 3137 19105084 19105004 6.950000e-14 89.8
32 TraesCS6D01G009000 chr2D 87.687 1137 131 8 1929 3060 323521192 323520060 0.000000e+00 1315.0
33 TraesCS6D01G009000 chr2D 85.185 81 8 3 3053 3132 37398410 37398487 4.180000e-11 80.5
34 TraesCS6D01G009000 chr3A 87.733 1125 131 6 1929 3048 680983624 680984746 0.000000e+00 1306.0
35 TraesCS6D01G009000 chr4D 87.240 1152 131 14 1919 3062 508964278 508963135 0.000000e+00 1299.0
36 TraesCS6D01G009000 chr4A 87.605 597 71 3 1 596 624844577 624843983 0.000000e+00 689.0
37 TraesCS6D01G009000 chr4A 85.345 116 16 1 1447 1562 739303840 739303954 8.870000e-23 119.0
38 TraesCS6D01G009000 chr1A 87.605 597 71 3 1 596 569245684 569246278 0.000000e+00 689.0
39 TraesCS6D01G009000 chr3B 87.333 600 70 5 1 596 24063147 24063744 0.000000e+00 682.0
40 TraesCS6D01G009000 chr5B 88.571 105 12 0 1446 1550 194185147 194185043 1.470000e-25 128.0
41 TraesCS6D01G009000 chr5B 87.805 82 10 0 3057 3138 20822238 20822319 4.150000e-16 97.1
42 TraesCS6D01G009000 chr7B 76.718 262 39 17 1085 1336 680170341 680170590 5.300000e-25 126.0
43 TraesCS6D01G009000 chr7A 87.850 107 13 0 1449 1555 681095258 681095152 5.300000e-25 126.0
44 TraesCS6D01G009000 chr7A 78.472 144 22 7 1152 1289 692908352 692908492 8.990000e-13 86.1
45 TraesCS6D01G009000 chr4B 88.350 103 12 0 1447 1549 80678354 80678252 1.910000e-24 124.0
46 TraesCS6D01G009000 chr5D 85.185 81 12 0 3057 3137 28480041 28479961 3.230000e-12 84.2


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 TraesCS6D01G009000 chr6D 3487636 3492676 5040 True 9310.000000 9310 100.000000 1 5041 1 chr6D.!!$R1 5040
1 TraesCS6D01G009000 chr6D 3474635 3476967 2332 True 1873.000000 3267 94.016000 1564 5041 2 chr6D.!!$R2 3477
2 TraesCS6D01G009000 chr6A 2273677 2277896 4219 True 1795.033333 5151 96.344667 677 4362 3 chr6A.!!$R2 3685
3 TraesCS6D01G009000 chr6B 6818473 6821067 2594 True 999.333333 2182 92.498667 1766 5041 3 chr6B.!!$R3 3275
4 TraesCS6D01G009000 chr6B 6833491 6835998 2507 True 770.750000 1489 90.691000 629 4155 4 chr6B.!!$R4 3526
5 TraesCS6D01G009000 chrUn 316606536 316607767 1231 False 2084.000000 2084 97.245000 3813 5041 1 chrUn.!!$F1 1228
6 TraesCS6D01G009000 chr1D 402302340 402303457 1117 True 1362.000000 1362 88.790000 1917 3029 1 chr1D.!!$R2 1112
7 TraesCS6D01G009000 chr1D 481421962 481423090 1128 False 1349.000000 1349 88.350000 1939 3062 1 chr1D.!!$F2 1123
8 TraesCS6D01G009000 chr1D 417912616 417913764 1148 True 1310.000000 1310 87.295000 1917 3067 1 chr1D.!!$R3 1150
9 TraesCS6D01G009000 chr1D 439140347 439140939 592 False 743.000000 743 89.280000 1 596 1 chr1D.!!$F1 595
10 TraesCS6D01G009000 chr1D 93502829 93503427 598 True 706.000000 706 88.167000 3 594 1 chr1D.!!$R1 591
11 TraesCS6D01G009000 chr3D 567668671 567669801 1130 True 1341.000000 1341 88.194000 1940 3065 1 chr3D.!!$R1 1125
12 TraesCS6D01G009000 chr3D 21606548 21607132 584 False 756.000000 756 89.916000 1 594 1 chr3D.!!$F2 593
13 TraesCS6D01G009000 chr3D 7961181 7961768 587 False 708.000000 708 88.442000 3 594 1 chr3D.!!$F1 591
14 TraesCS6D01G009000 chr5A 142745073 142746223 1150 True 1315.000000 1315 87.359000 1934 3082 1 chr5A.!!$R2 1148
15 TraesCS6D01G009000 chr5A 687662391 687662988 597 False 754.000000 754 89.465000 1 596 1 chr5A.!!$F1 595
16 TraesCS6D01G009000 chr5A 687668791 687669388 597 False 754.000000 754 89.465000 1 596 1 chr5A.!!$F2 595
17 TraesCS6D01G009000 chr2D 323520060 323521192 1132 True 1315.000000 1315 87.687000 1929 3060 1 chr2D.!!$R1 1131
18 TraesCS6D01G009000 chr3A 680983624 680984746 1122 False 1306.000000 1306 87.733000 1929 3048 1 chr3A.!!$F1 1119
19 TraesCS6D01G009000 chr4D 508963135 508964278 1143 True 1299.000000 1299 87.240000 1919 3062 1 chr4D.!!$R1 1143
20 TraesCS6D01G009000 chr4A 624843983 624844577 594 True 689.000000 689 87.605000 1 596 1 chr4A.!!$R1 595
21 TraesCS6D01G009000 chr1A 569245684 569246278 594 False 689.000000 689 87.605000 1 596 1 chr1A.!!$F1 595
22 TraesCS6D01G009000 chr3B 24063147 24063744 597 False 682.000000 682 87.333000 1 596 1 chr3B.!!$F1 595

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
573 594 0.178533 AAACAGACGTCCGTTTGGGA 59.821 50.0 25.06 0.0 44.68 4.37 F
959 1596 0.249447 TGCTCGGCGTGGATTGATAG 60.249 55.0 6.85 0.0 0.00 2.08 F
2379 3122 1.112113 GAGGAGCCTACCATTGACGA 58.888 55.0 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 2370 0.327924 TGGAATTGGACAGTGGCGAT 59.672 50.000 0.00 0.00 0.00 4.58 R
2464 3207 1.076485 ACAGATGATGCCCCCAAGC 60.076 57.895 0.00 0.00 0.00 4.01 R
4132 4916 2.234908 AGTAGGAAGTCGCTTTCTGCAT 59.765 45.455 14.76 2.48 43.06 3.96 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
95 96 1.820906 GCCCTTGCGATCATGAGCA 60.821 57.895 12.15 8.69 42.15 4.26
109 110 1.896220 TGAGCATGGACTTGACCAAC 58.104 50.000 0.00 0.00 43.47 3.77
424 441 2.352323 GGCGTGGTATTTGGAAAGTTGG 60.352 50.000 0.00 0.00 0.00 3.77
439 460 6.054941 GGAAAGTTGGTGTTTGAAAATGGAT 58.945 36.000 0.00 0.00 0.00 3.41
440 461 7.147655 TGGAAAGTTGGTGTTTGAAAATGGATA 60.148 33.333 0.00 0.00 0.00 2.59
447 468 6.831353 TGGTGTTTGAAAATGGATACGGATAT 59.169 34.615 0.00 0.00 42.51 1.63
505 526 0.323725 GCCACCACATCCCAGAACAT 60.324 55.000 0.00 0.00 0.00 2.71
540 561 0.808755 CATTGCCCTACCCAAACGAC 59.191 55.000 0.00 0.00 0.00 4.34
558 579 1.069358 GACCAAAATCCGGGCAAAACA 59.931 47.619 0.00 0.00 0.00 2.83
573 594 0.178533 AAACAGACGTCCGTTTGGGA 59.821 50.000 25.06 0.00 44.68 4.37
596 617 1.452108 GCGCTGGAGTTGGCCTAAT 60.452 57.895 3.32 0.00 0.00 1.73
597 618 1.718757 GCGCTGGAGTTGGCCTAATG 61.719 60.000 3.32 0.00 0.00 1.90
598 619 1.718757 CGCTGGAGTTGGCCTAATGC 61.719 60.000 3.32 0.47 40.16 3.56
599 620 0.394899 GCTGGAGTTGGCCTAATGCT 60.395 55.000 3.32 0.00 40.92 3.79
600 621 1.957113 GCTGGAGTTGGCCTAATGCTT 60.957 52.381 3.32 0.00 40.92 3.91
601 622 2.450476 CTGGAGTTGGCCTAATGCTTT 58.550 47.619 3.32 0.00 40.92 3.51
602 623 2.827921 CTGGAGTTGGCCTAATGCTTTT 59.172 45.455 3.32 0.00 40.92 2.27
603 624 2.825532 TGGAGTTGGCCTAATGCTTTTC 59.174 45.455 3.32 0.00 40.92 2.29
604 625 2.825532 GGAGTTGGCCTAATGCTTTTCA 59.174 45.455 3.32 0.00 40.92 2.69
605 626 3.367395 GGAGTTGGCCTAATGCTTTTCAC 60.367 47.826 3.32 0.00 40.92 3.18
606 627 3.500343 AGTTGGCCTAATGCTTTTCACT 58.500 40.909 3.32 0.00 40.92 3.41
607 628 3.256631 AGTTGGCCTAATGCTTTTCACTG 59.743 43.478 3.32 0.00 40.92 3.66
608 629 1.545582 TGGCCTAATGCTTTTCACTGC 59.454 47.619 3.32 0.00 40.92 4.40
609 630 1.545582 GGCCTAATGCTTTTCACTGCA 59.454 47.619 0.00 0.00 43.67 4.41
610 631 2.416431 GGCCTAATGCTTTTCACTGCAG 60.416 50.000 13.48 13.48 42.74 4.41
611 632 2.872370 CCTAATGCTTTTCACTGCAGC 58.128 47.619 15.27 0.00 42.74 5.25
617 638 3.904571 TGCTTTTCACTGCAGCATAAAG 58.095 40.909 15.27 19.41 38.65 1.85
618 639 3.569277 TGCTTTTCACTGCAGCATAAAGA 59.431 39.130 26.38 15.18 38.65 2.52
619 640 4.037803 TGCTTTTCACTGCAGCATAAAGAA 59.962 37.500 26.38 18.98 38.65 2.52
620 641 4.984161 GCTTTTCACTGCAGCATAAAGAAA 59.016 37.500 26.38 18.30 33.45 2.52
621 642 5.107722 GCTTTTCACTGCAGCATAAAGAAAC 60.108 40.000 26.38 13.21 33.45 2.78
622 643 5.512753 TTTCACTGCAGCATAAAGAAACA 57.487 34.783 15.27 0.00 0.00 2.83
623 644 4.488126 TCACTGCAGCATAAAGAAACAC 57.512 40.909 15.27 0.00 0.00 3.32
624 645 3.882288 TCACTGCAGCATAAAGAAACACA 59.118 39.130 15.27 0.00 0.00 3.72
625 646 4.023792 TCACTGCAGCATAAAGAAACACAG 60.024 41.667 15.27 0.00 0.00 3.66
626 647 4.023792 CACTGCAGCATAAAGAAACACAGA 60.024 41.667 15.27 0.00 0.00 3.41
627 648 4.214971 ACTGCAGCATAAAGAAACACAGAG 59.785 41.667 15.27 0.00 0.00 3.35
642 663 0.386100 CAGAGACACTGTCGACACCG 60.386 60.000 15.76 11.01 41.30 4.94
651 672 2.971959 TCGACACCGGTTCGACGA 60.972 61.111 26.94 21.04 36.24 4.20
653 674 1.443194 CGACACCGGTTCGACGAAT 60.443 57.895 25.28 0.00 35.47 3.34
654 675 1.400990 CGACACCGGTTCGACGAATC 61.401 60.000 25.28 12.52 35.47 2.52
655 676 0.387622 GACACCGGTTCGACGAATCA 60.388 55.000 20.10 0.00 35.47 2.57
657 678 1.337447 ACACCGGTTCGACGAATCAAT 60.337 47.619 20.10 4.94 35.47 2.57
658 679 2.094597 ACACCGGTTCGACGAATCAATA 60.095 45.455 20.10 0.00 35.47 1.90
660 681 3.368539 CACCGGTTCGACGAATCAATAAA 59.631 43.478 20.10 0.00 35.47 1.40
665 686 5.286797 CGGTTCGACGAATCAATAAAGTGTA 59.713 40.000 20.10 0.00 35.47 2.90
803 1410 4.572571 TGTTTTCGCCCGCCTGGT 62.573 61.111 0.00 0.00 36.04 4.00
853 1487 3.365265 CTTGCCTTCACGGGGTGC 61.365 66.667 0.00 0.00 32.98 5.01
959 1596 0.249447 TGCTCGGCGTGGATTGATAG 60.249 55.000 6.85 0.00 0.00 2.08
1346 1983 5.284582 ACTTTCTCTCTCCATTACATCCCT 58.715 41.667 0.00 0.00 0.00 4.20
1412 2087 1.692519 ACGCCTGAACTGAAGTTACCT 59.307 47.619 0.00 0.00 38.56 3.08
1669 2370 4.918588 TGAGACTCATGTAGGTACACTCA 58.081 43.478 0.00 0.00 39.30 3.41
1672 2373 4.576873 AGACTCATGTAGGTACACTCATCG 59.423 45.833 0.00 0.00 39.30 3.84
1781 2499 7.633193 ATTTTGTTACACAGACCAAACACTA 57.367 32.000 0.00 0.00 31.92 2.74
1987 2722 2.833582 GCCGGATCTCGACTGGGA 60.834 66.667 5.05 0.00 42.43 4.37
2080 2815 4.838152 GATCTTGAGCGGGCGCCA 62.838 66.667 30.85 3.35 43.17 5.69
2107 2844 2.911509 GTGTGTGTGGCCATGGCA 60.912 61.111 36.56 20.63 44.11 4.92
2203 2943 2.032528 CTCGCAGTGGCTTCCCAA 59.967 61.111 0.00 0.00 44.33 4.12
2316 3058 1.153369 CGTTGGAGGCGATGGTGAT 60.153 57.895 0.00 0.00 0.00 3.06
2379 3122 1.112113 GAGGAGCCTACCATTGACGA 58.888 55.000 0.00 0.00 0.00 4.20
2464 3207 1.871772 ACGTCTTAGTCGTCACCCG 59.128 57.895 0.00 0.00 36.85 5.28
2466 3209 1.881602 GTCTTAGTCGTCACCCGCT 59.118 57.895 0.00 0.00 36.19 5.52
2663 3407 1.007336 GGACGACGATGTCTTGCGTT 61.007 55.000 0.00 0.00 41.34 4.84
2714 3459 2.847441 AGGTCGATGCGTCAGTATCTA 58.153 47.619 6.75 0.00 37.34 1.98
2774 3520 4.029186 CAGCGTGCGCATGTGGTT 62.029 61.111 29.00 11.21 44.88 3.67
2886 3632 6.220930 GTGCGATATCTGTTTGGTATTAGGA 58.779 40.000 0.34 0.00 0.00 2.94
2913 3659 2.438434 CGGCACCCCTTCATCACC 60.438 66.667 0.00 0.00 0.00 4.02
3048 3796 2.133520 AGAGGTCGAGGGTACATCCTA 58.866 52.381 0.00 0.00 37.25 2.94
3054 3802 4.586001 GGTCGAGGGTACATCCTACATTTA 59.414 45.833 0.00 0.00 37.25 1.40
3219 3980 3.876309 AGTTTACACCACAACTCCCAT 57.124 42.857 0.00 0.00 0.00 4.00
3306 4073 1.757118 GAGTGTGCCTACATAGGAGCA 59.243 52.381 9.25 3.79 46.63 4.26
3307 4074 2.168521 GAGTGTGCCTACATAGGAGCAA 59.831 50.000 9.25 0.00 46.63 3.91
3639 4419 7.180408 ACCTCCACAAGTACTATGAACATACTT 59.820 37.037 8.33 0.00 39.23 2.24
3884 4664 0.392461 CCGAAATGGAAGAGGCCGAA 60.392 55.000 0.00 0.00 42.00 4.30
4098 4882 9.967451 TCCAATGATAACCTGTTGTAAAATCTA 57.033 29.630 0.00 0.00 0.00 1.98
4132 4916 4.380761 GCAGTGTATGGCATCATTTTGTGA 60.381 41.667 1.65 0.00 42.06 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 2.440409 GCTCATGTTGGTCAAGTCCAT 58.560 47.619 0.00 0.00 37.33 3.41
109 110 0.735471 TCCTCGTCTTCTCGCTCATG 59.265 55.000 0.00 0.00 0.00 3.07
179 180 1.079127 CGGCCAATCAGACGACCTT 60.079 57.895 2.24 0.00 0.00 3.50
342 355 1.585006 CAGCGACCTACACGTCCTT 59.415 57.895 0.00 0.00 0.00 3.36
371 385 4.832608 CGGCCCTAGTTCACGCCC 62.833 72.222 0.00 0.00 38.19 6.13
424 441 7.925993 TCATATCCGTATCCATTTTCAAACAC 58.074 34.615 0.00 0.00 0.00 3.32
439 460 1.735926 TTGGCCCCATCATATCCGTA 58.264 50.000 0.00 0.00 0.00 4.02
440 461 0.850100 TTTGGCCCCATCATATCCGT 59.150 50.000 0.00 0.00 0.00 4.69
447 468 1.381599 GCATCCTTTGGCCCCATCA 60.382 57.895 0.00 0.00 0.00 3.07
483 504 2.753043 CTGGGATGTGGTGGCTGC 60.753 66.667 0.00 0.00 0.00 5.25
485 506 1.380302 GTTCTGGGATGTGGTGGCT 59.620 57.895 0.00 0.00 0.00 4.75
492 513 0.033796 CTGGGCATGTTCTGGGATGT 60.034 55.000 0.00 0.00 0.00 3.06
505 526 1.480212 AATGGAGTCGTGTCTGGGCA 61.480 55.000 0.00 0.00 0.00 5.36
540 561 1.342819 TCTGTTTTGCCCGGATTTTGG 59.657 47.619 0.73 0.00 0.00 3.28
558 579 1.214589 CGATCCCAAACGGACGTCT 59.785 57.895 16.46 0.00 46.09 4.18
573 594 2.434884 CCAACTCCAGCGCACGAT 60.435 61.111 11.47 0.00 0.00 3.73
597 618 4.164822 TCTTTATGCTGCAGTGAAAAGC 57.835 40.909 16.64 0.00 37.46 3.51
598 619 5.978919 TGTTTCTTTATGCTGCAGTGAAAAG 59.021 36.000 16.64 19.54 0.00 2.27
599 620 5.748152 GTGTTTCTTTATGCTGCAGTGAAAA 59.252 36.000 16.64 11.66 0.00 2.29
600 621 5.163571 TGTGTTTCTTTATGCTGCAGTGAAA 60.164 36.000 16.64 11.83 0.00 2.69
601 622 4.337836 TGTGTTTCTTTATGCTGCAGTGAA 59.662 37.500 16.64 4.27 0.00 3.18
602 623 3.882288 TGTGTTTCTTTATGCTGCAGTGA 59.118 39.130 16.64 2.45 0.00 3.41
603 624 4.023792 TCTGTGTTTCTTTATGCTGCAGTG 60.024 41.667 16.64 0.00 0.00 3.66
604 625 4.136796 TCTGTGTTTCTTTATGCTGCAGT 58.863 39.130 16.64 0.00 0.00 4.40
605 626 4.453478 TCTCTGTGTTTCTTTATGCTGCAG 59.547 41.667 10.11 10.11 0.00 4.41
606 627 4.214119 GTCTCTGTGTTTCTTTATGCTGCA 59.786 41.667 4.13 4.13 0.00 4.41
607 628 4.214119 TGTCTCTGTGTTTCTTTATGCTGC 59.786 41.667 0.00 0.00 0.00 5.25
608 629 5.468072 AGTGTCTCTGTGTTTCTTTATGCTG 59.532 40.000 0.00 0.00 0.00 4.41
609 630 5.468072 CAGTGTCTCTGTGTTTCTTTATGCT 59.532 40.000 0.00 0.00 39.17 3.79
610 631 5.683859 CAGTGTCTCTGTGTTTCTTTATGC 58.316 41.667 0.00 0.00 39.17 3.14
624 645 1.516365 CCGGTGTCGACAGTGTCTCT 61.516 60.000 20.73 0.00 39.00 3.10
625 646 1.081376 CCGGTGTCGACAGTGTCTC 60.081 63.158 20.73 13.60 39.00 3.36
626 647 1.389609 AACCGGTGTCGACAGTGTCT 61.390 55.000 20.73 0.60 39.00 3.41
627 648 0.938168 GAACCGGTGTCGACAGTGTC 60.938 60.000 20.73 13.56 39.00 3.67
635 656 1.400990 GATTCGTCGAACCGGTGTCG 61.401 60.000 24.21 24.21 0.00 4.35
638 659 1.355971 ATTGATTCGTCGAACCGGTG 58.644 50.000 8.52 0.00 0.00 4.94
642 663 5.526010 ACACTTTATTGATTCGTCGAACC 57.474 39.130 10.39 0.00 0.00 3.62
653 674 7.359765 GCGCTTTCTACTGTTACACTTTATTGA 60.360 37.037 0.00 0.00 0.00 2.57
654 675 6.736853 GCGCTTTCTACTGTTACACTTTATTG 59.263 38.462 0.00 0.00 0.00 1.90
655 676 6.649557 AGCGCTTTCTACTGTTACACTTTATT 59.350 34.615 2.64 0.00 0.00 1.40
657 678 5.535333 AGCGCTTTCTACTGTTACACTTTA 58.465 37.500 2.64 0.00 0.00 1.85
658 679 4.377897 AGCGCTTTCTACTGTTACACTTT 58.622 39.130 2.64 0.00 0.00 2.66
660 681 3.662247 AGCGCTTTCTACTGTTACACT 57.338 42.857 2.64 0.00 0.00 3.55
665 686 2.548480 GTCCAAAGCGCTTTCTACTGTT 59.452 45.455 31.63 6.66 0.00 3.16
675 696 2.670934 CAGCAGGTCCAAAGCGCT 60.671 61.111 2.64 2.64 34.63 5.92
891 1528 0.469917 ATACCAGACGAATGGCCAGG 59.530 55.000 13.05 7.59 44.80 4.45
959 1596 2.671396 ACAACGAGATGTCAAATACGGC 59.329 45.455 0.00 0.00 0.00 5.68
1039 1676 1.152525 GGGAGATGGTAGGGAGCGA 60.153 63.158 0.00 0.00 0.00 4.93
1346 1983 3.391296 GGAGGGATATTGCAGTAGGAACA 59.609 47.826 0.00 0.00 0.00 3.18
1412 2087 3.699538 TCTTCAGCGAGCTACTAATTCCA 59.300 43.478 0.00 0.00 0.00 3.53
1587 2285 8.049721 CCACCTTGATAACTCTATTCTTCCTTT 58.950 37.037 0.00 0.00 0.00 3.11
1592 2291 5.430089 AGGCCACCTTGATAACTCTATTCTT 59.570 40.000 5.01 0.00 0.00 2.52
1669 2370 0.327924 TGGAATTGGACAGTGGCGAT 59.672 50.000 0.00 0.00 0.00 4.58
1672 2373 2.450476 AGATTGGAATTGGACAGTGGC 58.550 47.619 0.00 0.00 0.00 5.01
1781 2499 7.830099 AAAGACAGAGAGAAAATCCAAATGT 57.170 32.000 0.00 0.00 0.00 2.71
2031 2766 4.680237 CGCCTCCAAGCCACGACA 62.680 66.667 0.00 0.00 0.00 4.35
2080 2815 1.298116 CACACACACGTCGTCTCGT 60.298 57.895 0.00 0.00 45.10 4.18
2107 2844 2.736995 CATCGTTGCGTGACCGGT 60.737 61.111 6.92 6.92 33.68 5.28
2176 2913 3.560251 ACTGCGAGGCAACACCCT 61.560 61.111 0.00 0.00 38.41 4.34
2203 2943 2.579201 CTCCACTTGATCCGCCGT 59.421 61.111 0.00 0.00 0.00 5.68
2275 3015 2.684192 AAAACGACACCCATGGGCGA 62.684 55.000 31.73 0.00 39.32 5.54
2464 3207 1.076485 ACAGATGATGCCCCCAAGC 60.076 57.895 0.00 0.00 0.00 4.01
2466 3209 1.213619 TCCACAGATGATGCCCCCAA 61.214 55.000 0.00 0.00 0.00 4.12
2567 3310 2.372264 CCAAGATCCACCACCATCAAG 58.628 52.381 0.00 0.00 0.00 3.02
2663 3407 2.220615 CTACCATCGACGCCACCACA 62.221 60.000 0.00 0.00 0.00 4.17
2714 3459 3.514539 TCCATCGATCCATCCTCAGATT 58.485 45.455 0.00 0.00 0.00 2.40
2886 3632 2.189521 GGGTGCCGAATGTCCGAT 59.810 61.111 0.00 0.00 0.00 4.18
2913 3659 1.607628 CCTGTCGTTACTCCTATCCCG 59.392 57.143 0.00 0.00 0.00 5.14
3123 3881 5.596361 TGGCCACACCATACCAAAATATAAG 59.404 40.000 0.00 0.00 46.36 1.73
3124 3882 5.519808 TGGCCACACCATACCAAAATATAA 58.480 37.500 0.00 0.00 46.36 0.98
3125 3883 5.130705 TGGCCACACCATACCAAAATATA 57.869 39.130 0.00 0.00 46.36 0.86
3126 3884 3.987745 TGGCCACACCATACCAAAATAT 58.012 40.909 0.00 0.00 46.36 1.28
3127 3885 3.458044 TGGCCACACCATACCAAAATA 57.542 42.857 0.00 0.00 46.36 1.40
3139 3897 0.972883 TAATTTTGGGCTGGCCACAC 59.027 50.000 23.90 0.00 37.98 3.82
3306 4073 6.566914 TGGGGGAAATATAGTGGTTTTCTTT 58.433 36.000 0.00 0.00 31.57 2.52
3307 4074 6.160483 TGGGGGAAATATAGTGGTTTTCTT 57.840 37.500 0.00 0.00 31.57 2.52
3884 4664 3.651904 CCCTCTTGATCATGATCTCCCTT 59.348 47.826 30.65 0.00 38.60 3.95
4098 4882 3.620488 CCATACACTGCTTACAACCCAT 58.380 45.455 0.00 0.00 0.00 4.00
4101 4885 2.432444 TGCCATACACTGCTTACAACC 58.568 47.619 0.00 0.00 0.00 3.77
4132 4916 2.234908 AGTAGGAAGTCGCTTTCTGCAT 59.765 45.455 14.76 2.48 43.06 3.96


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

AutoCloner maintained by Alex Coulton.