Multiple sequence alignment - TraesCS7D01G536700

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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 TraesCS7D01G536700 chr7D 100.000 2942 0 0 1 2942 628399062 628402003 0.000000e+00 5433
1 TraesCS7D01G536700 chr7A 92.426 2601 122 28 4 2585 724737435 724734891 0.000000e+00 3642
2 TraesCS7D01G536700 chr7A 84.570 337 44 6 2591 2926 724728654 724728325 7.860000e-86 327
3 TraesCS7D01G536700 chr7B 90.994 2576 147 32 390 2942 730555485 730552972 0.000000e+00 3393
4 TraesCS7D01G536700 chr7B 91.805 2294 116 22 538 2808 730672755 730670511 0.000000e+00 3129
5 TraesCS7D01G536700 chr7B 91.805 2294 114 22 538 2808 730698949 730696707 0.000000e+00 3127
6 TraesCS7D01G536700 chr7B 93.269 2080 111 14 739 2808 730649028 730646968 0.000000e+00 3038
7 TraesCS7D01G536700 chr7B 92.379 1929 124 14 1021 2942 730618236 730616324 0.000000e+00 2726
8 TraesCS7D01G536700 chr7B 91.566 83 3 1 299 377 730558036 730557954 8.620000e-21 111
9 TraesCS7D01G536700 chr7B 91.566 83 3 1 299 377 730674638 730674556 8.620000e-21 111
10 TraesCS7D01G536700 chr7B 91.566 83 3 1 299 377 730701050 730700968 8.620000e-21 111
11 TraesCS7D01G536700 chrUn 91.864 885 40 7 516 1383 456475259 456476128 0.000000e+00 1206
12 TraesCS7D01G536700 chrUn 93.243 74 5 0 393 466 456475167 456475240 3.100000e-20 110
13 TraesCS7D01G536700 chr6D 80.387 826 123 18 730 1555 441291137 441291923 2.530000e-165 592
14 TraesCS7D01G536700 chr6D 79.717 848 131 21 730 1576 441397487 441398294 2.540000e-160 575


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 TraesCS7D01G536700 chr7D 628399062 628402003 2941 False 5433 5433 100.0000 1 2942 1 chr7D.!!$F1 2941
1 TraesCS7D01G536700 chr7A 724734891 724737435 2544 True 3642 3642 92.4260 4 2585 1 chr7A.!!$R2 2581
2 TraesCS7D01G536700 chr7B 730646968 730649028 2060 True 3038 3038 93.2690 739 2808 1 chr7B.!!$R2 2069
3 TraesCS7D01G536700 chr7B 730616324 730618236 1912 True 2726 2726 92.3790 1021 2942 1 chr7B.!!$R1 1921
4 TraesCS7D01G536700 chr7B 730552972 730558036 5064 True 1752 3393 91.2800 299 2942 2 chr7B.!!$R3 2643
5 TraesCS7D01G536700 chr7B 730670511 730674638 4127 True 1620 3129 91.6855 299 2808 2 chr7B.!!$R4 2509
6 TraesCS7D01G536700 chr7B 730696707 730701050 4343 True 1619 3127 91.6855 299 2808 2 chr7B.!!$R5 2509
7 TraesCS7D01G536700 chrUn 456475167 456476128 961 False 658 1206 92.5535 393 1383 2 chrUn.!!$F1 990
8 TraesCS7D01G536700 chr6D 441291137 441291923 786 False 592 592 80.3870 730 1555 1 chr6D.!!$F1 825
9 TraesCS7D01G536700 chr6D 441397487 441398294 807 False 575 575 79.7170 730 1576 1 chr6D.!!$F2 846

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
487 2955 0.030773 TGCTGCACGGAGATCGATAC 59.969 55.0 0.0 0.00 42.43 2.24 F
488 2956 0.664767 GCTGCACGGAGATCGATACC 60.665 60.0 0.0 4.38 42.43 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 4022 0.376152 CGTCCATGATCTGTTGCAGC 59.624 55.0 0.0 0.0 0.0 5.25 R
2239 4910 0.927537 CTGCGACGAACTGAACAACA 59.072 50.0 0.0 0.0 0.0 3.33 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
40 41 1.228737 ATCGGGGTTTTGTGTGGGG 60.229 57.895 0.00 0.00 0.00 4.96
60 61 3.933332 GGGACTAGAACAGGTTTGATTCG 59.067 47.826 0.00 0.00 0.00 3.34
61 62 4.562963 GGGACTAGAACAGGTTTGATTCGT 60.563 45.833 0.00 0.00 0.00 3.85
113 114 2.879002 ATTGTCTCATGACGATCGCT 57.121 45.000 16.60 2.00 42.09 4.93
116 117 1.203928 GTCTCATGACGATCGCTTGG 58.796 55.000 16.60 2.89 33.15 3.61
128 129 2.753966 CGCTTGGTGAGGAATGCCG 61.754 63.158 0.00 0.00 39.96 5.69
164 165 2.281276 GTCGGACCCCACCAACAC 60.281 66.667 0.00 0.00 0.00 3.32
218 219 4.333649 ACTTTGCCATGTCTCACATAATCG 59.666 41.667 0.00 0.00 36.53 3.34
233 234 0.729478 AATCGACACAGCTGACGACG 60.729 55.000 23.35 21.05 45.16 5.12
241 242 1.472878 ACAGCTGACGACGACATGTAT 59.527 47.619 23.35 0.00 0.00 2.29
246 247 2.356695 CTGACGACGACATGTATGGGTA 59.643 50.000 0.00 0.00 0.00 3.69
304 305 3.314553 CAACGGCCGGTATACAATAGAG 58.685 50.000 31.76 2.06 0.00 2.43
311 312 5.184479 GGCCGGTATACAATAGAGACATGTA 59.816 44.000 1.90 0.00 34.35 2.29
385 390 2.820059 TAGAAGCATATGACCCTGCG 57.180 50.000 6.97 0.00 43.17 5.18
386 391 0.107456 AGAAGCATATGACCCTGCGG 59.893 55.000 6.97 0.00 43.17 5.69
387 392 1.510480 GAAGCATATGACCCTGCGGC 61.510 60.000 6.97 0.00 43.17 6.53
388 393 3.349006 GCATATGACCCTGCGGCG 61.349 66.667 6.97 0.51 0.00 6.46
442 2910 2.951745 GTGCATCGAGCCGACGAG 60.952 66.667 0.00 0.00 45.22 4.18
453 2921 1.179814 GCCGACGAGGATATGACCCT 61.180 60.000 0.00 0.00 45.00 4.34
481 2949 4.291047 CAACTGCTGCACGGAGAT 57.709 55.556 0.00 0.00 34.75 2.75
482 2950 2.084844 CAACTGCTGCACGGAGATC 58.915 57.895 0.00 0.00 34.75 2.75
483 2951 1.446792 AACTGCTGCACGGAGATCG 60.447 57.895 0.00 0.00 45.88 3.69
484 2952 1.877576 AACTGCTGCACGGAGATCGA 61.878 55.000 0.00 0.00 42.43 3.59
485 2953 1.067084 CTGCTGCACGGAGATCGAT 59.933 57.895 0.00 0.00 42.43 3.59
486 2954 0.312102 CTGCTGCACGGAGATCGATA 59.688 55.000 0.00 0.00 42.43 2.92
487 2955 0.030773 TGCTGCACGGAGATCGATAC 59.969 55.000 0.00 0.00 42.43 2.24
488 2956 0.664767 GCTGCACGGAGATCGATACC 60.665 60.000 0.00 4.38 42.43 2.73
489 2957 0.668535 CTGCACGGAGATCGATACCA 59.331 55.000 17.44 1.90 42.43 3.25
520 2988 1.281287 AGGCAAGCATGTCTGATGTCT 59.719 47.619 0.00 0.00 40.84 3.41
526 2994 1.209019 GCATGTCTGATGTCTCCCACT 59.791 52.381 0.00 0.00 0.00 4.00
563 3205 1.478510 GGAGATGTGAGACGTGGTGAT 59.521 52.381 0.00 0.00 0.00 3.06
565 3207 3.589988 GAGATGTGAGACGTGGTGATTT 58.410 45.455 0.00 0.00 0.00 2.17
567 3209 1.877637 TGTGAGACGTGGTGATTTGG 58.122 50.000 0.00 0.00 0.00 3.28
568 3210 1.140052 TGTGAGACGTGGTGATTTGGT 59.860 47.619 0.00 0.00 0.00 3.67
606 3262 8.358148 ACGAGAGAATTATGTACGTGGAAATAT 58.642 33.333 0.00 0.00 0.00 1.28
610 3266 9.188588 GAGAATTATGTACGTGGAAATATCGAA 57.811 33.333 0.00 0.00 0.00 3.71
611 3267 9.537192 AGAATTATGTACGTGGAAATATCGAAA 57.463 29.630 0.00 0.00 0.00 3.46
953 3622 4.092968 CCTAGCTAAACCAACAACGACATC 59.907 45.833 0.00 0.00 0.00 3.06
974 3643 4.510571 TCCCATTCCTTCGCTAGTTTTAC 58.489 43.478 0.00 0.00 0.00 2.01
979 3648 7.041984 CCCATTCCTTCGCTAGTTTTACTAATC 60.042 40.741 0.00 0.00 29.00 1.75
980 3649 7.041984 CCATTCCTTCGCTAGTTTTACTAATCC 60.042 40.741 0.00 0.00 29.00 3.01
981 3650 5.910614 TCCTTCGCTAGTTTTACTAATCCC 58.089 41.667 0.00 0.00 29.00 3.85
983 3652 6.155737 TCCTTCGCTAGTTTTACTAATCCCTT 59.844 38.462 0.00 0.00 29.00 3.95
984 3653 6.258068 CCTTCGCTAGTTTTACTAATCCCTTG 59.742 42.308 0.00 0.00 29.00 3.61
985 3654 5.667466 TCGCTAGTTTTACTAATCCCTTGG 58.333 41.667 0.00 0.00 29.00 3.61
986 3655 4.272748 CGCTAGTTTTACTAATCCCTTGGC 59.727 45.833 0.00 0.00 29.00 4.52
987 3656 4.579340 GCTAGTTTTACTAATCCCTTGGCC 59.421 45.833 0.00 0.00 29.00 5.36
1087 3756 2.520536 AAGCAGCGTCTGAAGGGGT 61.521 57.895 10.46 0.00 32.44 4.95
1107 3776 1.227674 GATGAAGAAGGCGGGCGAT 60.228 57.895 0.00 0.00 0.00 4.58
1131 3800 4.338539 ACCCTGTGCGACGTCGAC 62.339 66.667 39.74 30.58 43.02 4.20
1157 3826 3.376078 GGTGGTGTACGGCGAGGA 61.376 66.667 16.62 0.00 0.00 3.71
1186 3855 1.492993 GCCTGAGGTGTTCCCTTCCT 61.493 60.000 0.00 0.00 46.51 3.36
1203 3872 4.329545 TCTGACAAGGCGGTGGGC 62.330 66.667 0.00 0.00 42.51 5.36
1353 4022 2.490217 CGCGAGACCAGGTACCTG 59.510 66.667 31.71 31.71 43.26 4.00
1451 4120 3.037549 AGGTGGAGGAGATGATCAAGAC 58.962 50.000 0.00 0.00 0.00 3.01
1458 4127 2.707791 GGAGATGATCAAGACCATGGGA 59.292 50.000 18.09 3.49 0.00 4.37
1578 4247 2.113774 CAACAGCAGGAGGGCACA 59.886 61.111 0.00 0.00 35.83 4.57
1925 4595 1.472878 TCTGGAGTTCGATTGGAGTCG 59.527 52.381 0.00 0.00 42.74 4.18
2012 4682 6.237149 CGTCTCGTCTCGTTTTATTAGTTTCC 60.237 42.308 0.00 0.00 0.00 3.13
2023 4693 7.217447 CGTTTTATTAGTTTCCGCATGGTTAAG 59.783 37.037 0.00 0.00 36.30 1.85
2031 4701 4.481368 TCCGCATGGTTAAGTTCTACAT 57.519 40.909 0.00 0.00 36.30 2.29
2040 4710 7.136822 TGGTTAAGTTCTACATATGGCATCT 57.863 36.000 1.65 0.00 0.00 2.90
2056 4726 3.808726 GGCATCTGTGAAGATGAGACATC 59.191 47.826 17.68 3.87 46.25 3.06
2057 4727 3.490155 GCATCTGTGAAGATGAGACATCG 59.510 47.826 17.68 0.00 46.25 3.84
2060 4730 4.013050 TCTGTGAAGATGAGACATCGAGT 58.987 43.478 0.00 0.00 0.00 4.18
2062 4732 5.648092 TCTGTGAAGATGAGACATCGAGTTA 59.352 40.000 0.00 0.00 0.00 2.24
2218 4888 2.761767 GGGGTCTCTAAGTCTCTTCCAC 59.238 54.545 0.00 0.00 0.00 4.02
2239 4910 1.625818 AGGCCTTCGTTGATCTCTGTT 59.374 47.619 0.00 0.00 0.00 3.16
2280 4954 6.015504 CAGATCGTAAGTTGCATGTGTTTAC 58.984 40.000 0.00 0.00 39.48 2.01
2295 4969 4.214119 TGTGTTTACAGAAATCAGCAGCTC 59.786 41.667 0.00 0.00 31.91 4.09
2362 5036 3.136626 GGTAGTTCCCTGATTGCTACCAT 59.863 47.826 12.53 0.00 46.49 3.55
2402 5076 1.068474 GTCGTGTTTCGGGAGATGTG 58.932 55.000 0.00 0.00 39.57 3.21
2429 5104 5.535333 CAGGGCCTTTAATTTCATGCTATG 58.465 41.667 1.32 0.00 0.00 2.23
2431 5106 5.302823 AGGGCCTTTAATTTCATGCTATGTC 59.697 40.000 0.00 0.00 0.00 3.06
2444 5119 5.874810 TCATGCTATGTCTGGTGTCTAAAAC 59.125 40.000 0.00 0.00 0.00 2.43
2448 5123 6.014070 TGCTATGTCTGGTGTCTAAAACCTTA 60.014 38.462 0.00 0.00 38.60 2.69
2484 5159 3.620374 AGAAACGTGCTGAAGATATGCTG 59.380 43.478 0.00 0.00 0.00 4.41
2493 5168 2.103771 TGAAGATATGCTGTCCTGGAGC 59.896 50.000 0.00 0.00 36.95 4.70
2519 5194 9.590451 CAATGTAAATGTGCTGGAGAATTAATT 57.410 29.630 0.00 0.00 0.00 1.40
2580 5255 1.336125 GCTCATGCTTGCCTGGATAAC 59.664 52.381 0.00 0.00 36.03 1.89
2609 5284 4.032445 GCGACTTTATTACATTGCGACAGA 59.968 41.667 0.00 0.00 0.00 3.41
2614 5289 3.698029 ATTACATTGCGACAGAATGGC 57.302 42.857 0.00 0.00 44.64 4.40
2633 5308 1.067142 GCACACAGTAGTCCCGATTGA 60.067 52.381 0.00 0.00 0.00 2.57
2648 5323 5.588648 TCCCGATTGACCAATATTTCTGAAC 59.411 40.000 0.00 0.00 0.00 3.18
2651 5326 6.458751 CCGATTGACCAATATTTCTGAACCTG 60.459 42.308 0.00 0.00 0.00 4.00
2652 5327 6.094048 CGATTGACCAATATTTCTGAACCTGT 59.906 38.462 0.00 0.00 0.00 4.00
2653 5328 7.279981 CGATTGACCAATATTTCTGAACCTGTA 59.720 37.037 0.00 0.00 0.00 2.74
2654 5329 8.877864 ATTGACCAATATTTCTGAACCTGTAA 57.122 30.769 0.00 0.00 0.00 2.41
2655 5330 8.877864 TTGACCAATATTTCTGAACCTGTAAT 57.122 30.769 0.00 0.00 0.00 1.89
2698 5373 9.273016 TGAAGAACCAAGTAAGAATAAGAACTG 57.727 33.333 0.00 0.00 0.00 3.16
2700 5375 8.608844 AGAACCAAGTAAGAATAAGAACTGTG 57.391 34.615 0.00 0.00 0.00 3.66
2705 5380 8.660373 CCAAGTAAGAATAAGAACTGTGATCAC 58.340 37.037 19.27 19.27 0.00 3.06
2719 5394 3.006003 TGTGATCACTTGCAATGCACATT 59.994 39.130 25.55 0.00 38.71 2.71
2758 5434 2.184322 GTCGATGCTCGCCTCCAA 59.816 61.111 0.00 0.00 40.21 3.53
2762 5438 3.329542 GATGCTCGCCTCCAACCCA 62.330 63.158 0.00 0.00 0.00 4.51
2768 5444 0.539986 TCGCCTCCAACCCATAGTTC 59.460 55.000 0.00 0.00 36.18 3.01
2791 5467 1.790481 GCTAGGTGATTTTTGCGCGTC 60.790 52.381 8.43 0.00 0.00 5.19
2793 5469 0.517316 AGGTGATTTTTGCGCGTCTC 59.483 50.000 8.43 0.00 0.00 3.36
2805 5481 2.393768 GCGTCTCCTGTGCATGGTG 61.394 63.158 8.29 6.53 0.00 4.17
2809 5485 1.550524 GTCTCCTGTGCATGGTGACTA 59.449 52.381 24.22 3.12 41.90 2.59
2819 5495 2.870435 GCATGGTGACTACGTCTGGTTT 60.870 50.000 0.00 0.00 33.15 3.27
2834 5510 3.073798 TCTGGTTTCAGGTGATTAAGCCA 59.926 43.478 0.00 0.00 41.23 4.75
2836 5512 4.219115 TGGTTTCAGGTGATTAAGCCAAA 58.781 39.130 0.00 0.00 31.55 3.28
2839 5515 5.010617 GGTTTCAGGTGATTAAGCCAAAGAA 59.989 40.000 0.00 0.00 0.00 2.52
2846 5522 3.751175 TGATTAAGCCAAAGAAGACCACG 59.249 43.478 0.00 0.00 0.00 4.94
2859 5535 3.485463 AGACCACGTTTTCTTCATCCA 57.515 42.857 0.00 0.00 0.00 3.41
2864 5540 2.157668 CACGTTTTCTTCATCCACTCCG 59.842 50.000 0.00 0.00 0.00 4.63
2871 5547 3.024547 TCTTCATCCACTCCGTCCTTAG 58.975 50.000 0.00 0.00 0.00 2.18
2876 5552 3.657398 TCCACTCCGTCCTTAGTCATA 57.343 47.619 0.00 0.00 0.00 2.15
2878 5554 5.314718 TCCACTCCGTCCTTAGTCATATA 57.685 43.478 0.00 0.00 0.00 0.86
2879 5555 5.888901 TCCACTCCGTCCTTAGTCATATAT 58.111 41.667 0.00 0.00 0.00 0.86
2884 5560 6.434652 ACTCCGTCCTTAGTCATATATCTTGG 59.565 42.308 0.00 0.00 0.00 3.61
2892 5568 5.791336 AGTCATATATCTTGGCAAGACGA 57.209 39.130 30.71 21.70 41.01 4.20
2894 5570 4.383052 GTCATATATCTTGGCAAGACGACG 59.617 45.833 30.71 18.00 41.01 5.12
2895 5571 2.961526 ATATCTTGGCAAGACGACGT 57.038 45.000 30.71 17.55 41.01 4.34
2896 5572 2.273370 TATCTTGGCAAGACGACGTC 57.727 50.000 30.71 20.25 41.01 4.34
2897 5573 0.317160 ATCTTGGCAAGACGACGTCA 59.683 50.000 30.71 7.77 41.01 4.35
2898 5574 0.317160 TCTTGGCAAGACGACGTCAT 59.683 50.000 28.31 15.47 34.60 3.06
2899 5575 1.542472 TCTTGGCAAGACGACGTCATA 59.458 47.619 28.31 7.98 34.60 2.15
2905 5581 2.793933 CAAGACGACGTCATAACCGAT 58.206 47.619 28.31 3.52 34.60 4.18
2913 5589 3.966154 ACGTCATAACCGATGATCAGAC 58.034 45.455 0.09 0.00 46.34 3.51
2915 5591 2.726760 GTCATAACCGATGATCAGACGC 59.273 50.000 16.25 0.00 46.34 5.19
2917 5593 1.018910 TAACCGATGATCAGACGCGA 58.981 50.000 15.93 0.00 0.00 5.87
2927 5603 1.137825 CAGACGCGAGAAGGAGACC 59.862 63.158 15.93 0.00 0.00 3.85
2939 5615 2.665603 GAGACCCTGTGGCCTCAC 59.334 66.667 3.32 0.00 43.87 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.550551 CCGATGTGGCTTCTAATCAACATATAT 59.449 37.037 0.00 0.00 0.00 0.86
1 2 6.873605 CCGATGTGGCTTCTAATCAACATATA 59.126 38.462 0.00 0.00 0.00 0.86
2 3 5.702670 CCGATGTGGCTTCTAATCAACATAT 59.297 40.000 0.00 0.00 0.00 1.78
40 41 5.694910 TCAACGAATCAAACCTGTTCTAGTC 59.305 40.000 0.00 0.00 0.00 2.59
60 61 0.729690 GCTTCATCGAGGGCTTCAAC 59.270 55.000 0.00 0.00 0.00 3.18
61 62 0.740868 CGCTTCATCGAGGGCTTCAA 60.741 55.000 0.00 0.00 0.00 2.69
113 114 1.375396 CGTCGGCATTCCTCACCAA 60.375 57.895 0.00 0.00 0.00 3.67
116 117 2.167861 GCTCGTCGGCATTCCTCAC 61.168 63.158 0.00 0.00 0.00 3.51
128 129 1.006805 ATGGATGCTAGCGCTCGTC 60.007 57.895 16.34 11.86 36.97 4.20
143 144 2.901281 TTGGTGGGGTCCGACATGG 61.901 63.158 0.00 0.00 40.09 3.66
164 165 2.027625 GAACCCGACTTGTGAGCCG 61.028 63.158 0.00 0.00 0.00 5.52
209 210 2.279921 CGTCAGCTGTGTCGATTATGTG 59.720 50.000 14.67 0.00 37.40 3.21
210 211 2.163613 TCGTCAGCTGTGTCGATTATGT 59.836 45.455 14.67 0.00 38.96 2.29
211 212 2.531912 GTCGTCAGCTGTGTCGATTATG 59.468 50.000 24.21 7.43 44.23 1.90
218 219 0.387367 ATGTCGTCGTCAGCTGTGTC 60.387 55.000 14.67 4.87 0.00 3.67
233 234 4.481368 TGAAGGTGTACCCATACATGTC 57.519 45.455 0.00 0.00 43.21 3.06
241 242 1.553248 CGGAAGATGAAGGTGTACCCA 59.447 52.381 0.00 0.00 36.42 4.51
246 247 0.246635 CGACCGGAAGATGAAGGTGT 59.753 55.000 9.46 0.00 37.07 4.16
304 305 6.521133 CGATGCTTCTTTGTTTCTTACATGTC 59.479 38.462 0.00 0.00 36.44 3.06
311 312 4.610945 CCAACGATGCTTCTTTGTTTCTT 58.389 39.130 14.96 0.00 31.07 2.52
381 386 1.207593 CTTCTTTTGTCCGCCGCAG 59.792 57.895 0.00 0.00 0.00 5.18
382 387 0.816018 TTCTTCTTTTGTCCGCCGCA 60.816 50.000 0.00 0.00 0.00 5.69
385 390 2.159382 TCCATTCTTCTTTTGTCCGCC 58.841 47.619 0.00 0.00 0.00 6.13
386 391 3.440173 TCATCCATTCTTCTTTTGTCCGC 59.560 43.478 0.00 0.00 0.00 5.54
387 392 5.824904 ATCATCCATTCTTCTTTTGTCCG 57.175 39.130 0.00 0.00 0.00 4.79
388 393 7.872113 ACTATCATCCATTCTTCTTTTGTCC 57.128 36.000 0.00 0.00 0.00 4.02
470 2938 0.668535 TGGTATCGATCTCCGTGCAG 59.331 55.000 0.00 0.00 39.75 4.41
471 2939 0.384309 GTGGTATCGATCTCCGTGCA 59.616 55.000 0.00 0.00 39.75 4.57
472 2940 0.318784 GGTGGTATCGATCTCCGTGC 60.319 60.000 0.00 1.29 39.75 5.34
473 2941 1.319541 AGGTGGTATCGATCTCCGTG 58.680 55.000 0.00 0.00 39.75 4.94
474 2942 2.158711 TGTAGGTGGTATCGATCTCCGT 60.159 50.000 0.00 0.00 39.75 4.69
475 2943 2.225963 GTGTAGGTGGTATCGATCTCCG 59.774 54.545 0.00 0.00 40.25 4.63
476 2944 2.225963 CGTGTAGGTGGTATCGATCTCC 59.774 54.545 0.00 6.90 0.00 3.71
477 2945 2.225963 CCGTGTAGGTGGTATCGATCTC 59.774 54.545 0.00 0.00 34.51 2.75
478 2946 2.158711 TCCGTGTAGGTGGTATCGATCT 60.159 50.000 0.00 0.00 41.99 2.75
479 2947 2.224606 TCCGTGTAGGTGGTATCGATC 58.775 52.381 0.00 0.00 41.99 3.69
480 2948 2.353357 TCCGTGTAGGTGGTATCGAT 57.647 50.000 2.16 2.16 41.99 3.59
481 2949 2.019249 CTTCCGTGTAGGTGGTATCGA 58.981 52.381 0.00 0.00 41.99 3.59
482 2950 1.066605 CCTTCCGTGTAGGTGGTATCG 59.933 57.143 0.00 0.00 41.99 2.92
483 2951 1.202498 GCCTTCCGTGTAGGTGGTATC 60.202 57.143 0.00 0.00 41.99 2.24
484 2952 0.828677 GCCTTCCGTGTAGGTGGTAT 59.171 55.000 0.00 0.00 41.99 2.73
485 2953 0.542467 TGCCTTCCGTGTAGGTGGTA 60.542 55.000 0.00 0.00 41.99 3.25
486 2954 1.412453 TTGCCTTCCGTGTAGGTGGT 61.412 55.000 0.00 0.00 41.99 4.16
487 2955 0.673644 CTTGCCTTCCGTGTAGGTGG 60.674 60.000 0.00 0.00 41.99 4.61
488 2956 1.298859 GCTTGCCTTCCGTGTAGGTG 61.299 60.000 0.00 0.00 41.99 4.00
489 2957 1.003718 GCTTGCCTTCCGTGTAGGT 60.004 57.895 0.00 0.00 41.99 3.08
520 2988 5.071788 CCCATAATAAGCAGAGTAAGTGGGA 59.928 44.000 0.00 0.00 44.10 4.37
526 2994 7.290014 TCACATCTCCCATAATAAGCAGAGTAA 59.710 37.037 0.00 0.00 0.00 2.24
613 3269 1.954382 GCCTCTCGTCCCAAACTTTTT 59.046 47.619 0.00 0.00 0.00 1.94
614 3270 1.605753 GCCTCTCGTCCCAAACTTTT 58.394 50.000 0.00 0.00 0.00 2.27
615 3271 0.250770 GGCCTCTCGTCCCAAACTTT 60.251 55.000 0.00 0.00 0.00 2.66
616 3272 1.375326 GGCCTCTCGTCCCAAACTT 59.625 57.895 0.00 0.00 0.00 2.66
688 3352 4.808364 CGTCCTCTGATTCTTTCCAATCTC 59.192 45.833 0.00 0.00 34.35 2.75
779 3443 5.848833 TTTTGGCGTCCTTTTAAACCTTA 57.151 34.783 0.00 0.00 0.00 2.69
953 3622 4.514401 AGTAAAACTAGCGAAGGAATGGG 58.486 43.478 0.00 0.00 0.00 4.00
974 3643 2.203351 GGCCGGCCAAGGGATTAG 60.203 66.667 40.73 0.00 35.81 1.73
1062 3731 0.038251 TCAGACGCTGCTTGTACCTG 60.038 55.000 0.00 0.00 0.00 4.00
1087 3756 1.745115 CGCCCGCCTTCTTCATCAA 60.745 57.895 0.00 0.00 0.00 2.57
1186 3855 4.329545 GCCCACCGCCTTGTCAGA 62.330 66.667 0.00 0.00 0.00 3.27
1353 4022 0.376152 CGTCCATGATCTGTTGCAGC 59.624 55.000 0.00 0.00 0.00 5.25
1388 4057 4.988598 CCACGCTGAGGCCAACGT 62.989 66.667 5.01 5.97 44.81 3.99
1458 4127 1.202879 TGAGTTTTCCCCATGCGTTCT 60.203 47.619 0.00 0.00 0.00 3.01
1546 4215 2.437180 TTGCTCTGGCGCCTGATG 60.437 61.111 32.72 25.71 42.25 3.07
1871 4541 1.953686 TCTGCATCATCGTATCACCGA 59.046 47.619 0.00 0.00 41.73 4.69
1925 4595 4.662349 CCAGCTTACATGGGAGGGAACC 62.662 59.091 0.00 0.00 41.24 3.62
2012 4682 5.334105 GCCATATGTAGAACTTAACCATGCG 60.334 44.000 1.24 0.00 0.00 4.73
2023 4693 6.283694 TCTTCACAGATGCCATATGTAGAAC 58.716 40.000 4.38 0.00 32.07 3.01
2040 4710 4.790765 AACTCGATGTCTCATCTTCACA 57.209 40.909 7.89 0.00 0.00 3.58
2056 4726 6.677913 ACAACAATTCCAGGAAATTAACTCG 58.322 36.000 5.81 0.00 0.00 4.18
2057 4727 9.788960 GATACAACAATTCCAGGAAATTAACTC 57.211 33.333 5.81 0.00 0.00 3.01
2062 4732 8.193953 ACAAGATACAACAATTCCAGGAAATT 57.806 30.769 5.81 0.00 0.00 1.82
2218 4888 1.066573 ACAGAGATCAACGAAGGCCTG 60.067 52.381 5.69 0.00 0.00 4.85
2239 4910 0.927537 CTGCGACGAACTGAACAACA 59.072 50.000 0.00 0.00 0.00 3.33
2280 4954 1.802960 ACAACGAGCTGCTGATTTCTG 59.197 47.619 7.01 0.00 0.00 3.02
2295 4969 2.063266 AGTGCCGTAATACACACAACG 58.937 47.619 13.67 0.00 39.30 4.10
2362 5036 7.860373 CACGACCATGTTTCTTTCTTTTAATCA 59.140 33.333 0.00 0.00 0.00 2.57
2419 5094 5.675684 TTAGACACCAGACATAGCATGAA 57.324 39.130 0.00 0.00 0.00 2.57
2429 5104 4.625028 ACGTAAGGTTTTAGACACCAGAC 58.375 43.478 0.00 0.00 46.39 3.51
2444 5119 3.967332 TCTACCCTCCAAAACGTAAGG 57.033 47.619 0.00 0.00 46.39 2.69
2448 5123 2.486918 CGTTTCTACCCTCCAAAACGT 58.513 47.619 10.17 0.00 45.26 3.99
2457 5132 1.968493 TCTTCAGCACGTTTCTACCCT 59.032 47.619 0.00 0.00 0.00 4.34
2484 5159 3.428045 GCACATTTACATTGCTCCAGGAC 60.428 47.826 0.00 0.00 33.26 3.85
2493 5168 9.590451 AATTAATTCTCCAGCACATTTACATTG 57.410 29.630 0.00 0.00 0.00 2.82
2519 5194 5.574891 ACCATGCAATTAAGTCGCAAATA 57.425 34.783 0.00 0.00 39.48 1.40
2552 5227 0.675837 GCAAGCATGAGCAGTCCAGA 60.676 55.000 0.00 0.00 45.49 3.86
2558 5233 0.752009 ATCCAGGCAAGCATGAGCAG 60.752 55.000 8.43 0.00 45.49 4.24
2561 5236 1.600957 CGTTATCCAGGCAAGCATGAG 59.399 52.381 8.43 0.00 0.00 2.90
2580 5255 5.109150 CGCAATGTAATAAAGTCGCAAATCG 60.109 40.000 0.00 0.00 40.15 3.34
2609 5284 0.036388 CGGGACTACTGTGTGCCATT 60.036 55.000 16.45 0.00 46.85 3.16
2614 5289 2.607187 GTCAATCGGGACTACTGTGTG 58.393 52.381 0.00 0.00 34.92 3.82
2615 5290 1.549170 GGTCAATCGGGACTACTGTGT 59.451 52.381 0.00 0.00 37.91 3.72
2622 5297 5.104527 TCAGAAATATTGGTCAATCGGGACT 60.105 40.000 0.00 0.00 37.91 3.85
2623 5298 5.123227 TCAGAAATATTGGTCAATCGGGAC 58.877 41.667 0.00 0.00 37.06 4.46
2624 5299 5.366482 TCAGAAATATTGGTCAATCGGGA 57.634 39.130 0.00 0.00 32.50 5.14
2654 5329 9.750125 GGTTCTTCACTTGTTCTGAATTTTAAT 57.250 29.630 0.00 0.00 0.00 1.40
2655 5330 8.744652 TGGTTCTTCACTTGTTCTGAATTTTAA 58.255 29.630 0.00 0.00 0.00 1.52
2662 5337 4.843728 ACTTGGTTCTTCACTTGTTCTGA 58.156 39.130 0.00 0.00 0.00 3.27
2676 5351 8.603242 TCACAGTTCTTATTCTTACTTGGTTC 57.397 34.615 0.00 0.00 0.00 3.62
2698 5373 2.710220 TGTGCATTGCAAGTGATCAC 57.290 45.000 18.47 18.47 41.47 3.06
2700 5375 3.611113 GTCAATGTGCATTGCAAGTGATC 59.389 43.478 13.94 9.41 45.77 2.92
2705 5380 4.083164 TCAGTAGTCAATGTGCATTGCAAG 60.083 41.667 13.94 4.22 45.77 4.01
2719 5394 1.000607 GCACGGTGAACTCAGTAGTCA 60.001 52.381 13.29 0.00 33.75 3.41
2758 5434 2.032620 CACCTAGCTCGAACTATGGGT 58.967 52.381 12.80 8.07 0.00 4.51
2762 5438 5.294552 GCAAAAATCACCTAGCTCGAACTAT 59.705 40.000 0.00 0.00 0.00 2.12
2768 5444 1.529826 GCGCAAAAATCACCTAGCTCG 60.530 52.381 0.30 0.00 0.00 5.03
2791 5467 1.737029 CGTAGTCACCATGCACAGGAG 60.737 57.143 13.62 6.11 0.00 3.69
2793 5469 0.037326 ACGTAGTCACCATGCACAGG 60.037 55.000 5.50 5.50 29.74 4.00
2809 5485 2.930826 AATCACCTGAAACCAGACGT 57.069 45.000 0.00 0.00 33.56 4.34
2819 5495 5.003804 GTCTTCTTTGGCTTAATCACCTGA 58.996 41.667 0.00 0.00 0.00 3.86
2834 5510 5.008712 GGATGAAGAAAACGTGGTCTTCTTT 59.991 40.000 28.17 20.48 46.57 2.52
2836 5512 4.065789 GGATGAAGAAAACGTGGTCTTCT 58.934 43.478 28.17 19.31 46.57 2.85
2839 5515 3.139077 GTGGATGAAGAAAACGTGGTCT 58.861 45.455 0.00 0.00 0.00 3.85
2864 5540 7.600752 GTCTTGCCAAGATATATGACTAAGGAC 59.399 40.741 10.87 0.00 40.18 3.85
2871 5547 4.383052 CGTCGTCTTGCCAAGATATATGAC 59.617 45.833 10.87 12.00 40.18 3.06
2876 5552 2.165641 TGACGTCGTCTTGCCAAGATAT 59.834 45.455 24.75 0.00 40.18 1.63
2878 5554 0.317160 TGACGTCGTCTTGCCAAGAT 59.683 50.000 24.75 0.00 40.18 2.40
2879 5555 0.317160 ATGACGTCGTCTTGCCAAGA 59.683 50.000 24.75 2.24 33.15 3.02
2884 5560 0.638746 CGGTTATGACGTCGTCTTGC 59.361 55.000 24.75 15.23 33.15 4.01
2896 5572 1.716050 CGCGTCTGATCATCGGTTATG 59.284 52.381 17.68 0.00 36.88 1.90
2897 5573 1.607148 TCGCGTCTGATCATCGGTTAT 59.393 47.619 5.77 0.00 0.00 1.89
2898 5574 1.002792 CTCGCGTCTGATCATCGGTTA 60.003 52.381 5.77 0.00 0.00 2.85
2899 5575 0.248661 CTCGCGTCTGATCATCGGTT 60.249 55.000 5.77 0.00 0.00 4.44
2905 5581 0.735471 CTCCTTCTCGCGTCTGATCA 59.265 55.000 5.77 0.00 0.00 2.92
2913 5589 2.344203 ACAGGGTCTCCTTCTCGCG 61.344 63.158 0.00 0.00 42.67 5.87
2915 5591 1.893786 CCACAGGGTCTCCTTCTCG 59.106 63.158 0.00 0.00 42.67 4.04
2917 5593 1.920835 GGCCACAGGGTCTCCTTCT 60.921 63.158 0.00 0.00 42.67 2.85


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

AutoCloner maintained by Alex Coulton.