Multiple sequence alignment - TraesCS5D01G412100

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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 TraesCS5D01G412100 chr5D 100.000 4986 0 0 1 4986 475498786 475503771 0.000000e+00 9208.0
1 TraesCS5D01G412100 chr5B 91.326 2006 80 35 3016 4984 582834719 582836667 0.000000e+00 2654.0
2 TraesCS5D01G412100 chr5B 91.188 1725 67 28 846 2488 582832484 582834205 0.000000e+00 2265.0
3 TraesCS5D01G412100 chr5B 92.778 540 35 4 2482 3019 582834154 582834691 0.000000e+00 778.0
4 TraesCS5D01G412100 chr5A 91.065 1925 81 38 641 2483 594952785 594954700 0.000000e+00 2518.0
5 TraesCS5D01G412100 chr5A 88.533 1779 112 34 2576 4308 594954721 594956453 0.000000e+00 2071.0
6 TraesCS5D01G412100 chr5A 89.286 728 55 17 1 719 594952066 594952779 0.000000e+00 891.0
7 TraesCS5D01G412100 chr5A 89.588 461 33 9 4460 4912 594956731 594957184 5.600000e-159 571.0
8 TraesCS5D01G412100 chr5A 89.474 171 14 2 4297 4467 594956473 594956639 3.910000e-51 213.0
9 TraesCS5D01G412100 chr5A 84.564 149 15 5 2654 2799 594979436 594979579 1.870000e-29 141.0
10 TraesCS5D01G412100 chr5A 76.382 199 38 7 2138 2332 594978178 594978371 1.140000e-16 99.0
11 TraesCS5D01G412100 chr5A 88.158 76 9 0 4911 4986 594957290 594957365 1.910000e-14 91.6
12 TraesCS5D01G412100 chr1D 88.682 1184 96 23 3016 4171 409538005 409539178 0.000000e+00 1410.0
13 TraesCS5D01G412100 chr1D 80.278 1440 178 56 1635 3013 409536569 409537963 0.000000e+00 989.0
14 TraesCS5D01G412100 chr1D 88.401 569 47 10 972 1529 409535913 409536473 0.000000e+00 667.0
15 TraesCS5D01G412100 chr1B 87.638 1181 106 25 3017 4171 551723674 551724840 0.000000e+00 1336.0
16 TraesCS5D01G412100 chr1B 80.556 1440 174 64 1636 3015 551722248 551723641 0.000000e+00 1011.0
17 TraesCS5D01G412100 chr1B 86.092 568 58 5 972 1529 551721600 551722156 4.300000e-165 592.0
18 TraesCS5D01G412100 chr1A 91.162 792 50 9 3017 3788 505539797 505540588 0.000000e+00 1057.0
19 TraesCS5D01G412100 chr1A 82.008 1245 146 44 1809 3019 505538568 505539768 0.000000e+00 987.0
20 TraesCS5D01G412100 chr1A 87.698 569 51 5 972 1529 505537728 505538288 0.000000e+00 645.0
21 TraesCS5D01G412100 chr1A 88.197 305 33 2 3824 4127 505540881 505541183 1.320000e-95 361.0
22 TraesCS5D01G412100 chr7B 82.051 78 10 4 490 566 741399695 741399769 4.170000e-06 63.9
23 TraesCS5D01G412100 chr7B 100.000 30 0 0 469 498 21713664 21713693 6.970000e-04 56.5
24 TraesCS5D01G412100 chr2D 86.441 59 5 3 514 571 512138602 512138658 1.500000e-05 62.1
25 TraesCS5D01G412100 chr3D 85.965 57 6 2 512 566 76915130 76915186 5.390000e-05 60.2
26 TraesCS5D01G412100 chr2A 88.235 51 4 2 524 574 655421261 655421309 5.390000e-05 60.2
27 TraesCS5D01G412100 chr2A 100.000 28 0 0 538 565 144269507 144269480 9.000000e-03 52.8
28 TraesCS5D01G412100 chr6B 100.000 29 0 0 470 498 720527741 720527769 3.000000e-03 54.7


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 TraesCS5D01G412100 chr5D 475498786 475503771 4985 False 9208.000000 9208 100.000000 1 4986 1 chr5D.!!$F1 4985
1 TraesCS5D01G412100 chr5B 582832484 582836667 4183 False 1899.000000 2654 91.764000 846 4984 3 chr5B.!!$F1 4138
2 TraesCS5D01G412100 chr5A 594952066 594957365 5299 False 1059.266667 2518 89.350667 1 4986 6 chr5A.!!$F1 4985
3 TraesCS5D01G412100 chr1D 409535913 409539178 3265 False 1022.000000 1410 85.787000 972 4171 3 chr1D.!!$F1 3199
4 TraesCS5D01G412100 chr1B 551721600 551724840 3240 False 979.666667 1336 84.762000 972 4171 3 chr1B.!!$F1 3199
5 TraesCS5D01G412100 chr1A 505537728 505541183 3455 False 762.500000 1057 87.266250 972 4127 4 chr1A.!!$F1 3155

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
137 138 0.255033 CCTACTTAAGGTGCCACCCC 59.745 60.000 11.06 0.00 39.75 4.95 F
141 142 0.323451 CTTAAGGTGCCACCCCCTTC 60.323 60.000 11.06 0.00 41.30 3.46 F
897 995 0.394216 CGAGGCCCATTCCACATTCA 60.394 55.000 0.00 0.00 0.00 2.57 F
1106 1218 1.409427 CGAGAAGCAGGTAACCCTAGG 59.591 57.143 0.06 0.06 39.89 3.02 F
1619 1738 2.362717 CCCGTAGAAAAGCCCACAAAAA 59.637 45.455 0.00 0.00 0.00 1.94 F
2629 2876 0.387112 CCGCGAAATGCATGTTGTGT 60.387 50.000 8.23 0.00 46.97 3.72 F
3030 3329 1.078778 ATCGCAATGTACACGGGCA 60.079 52.632 13.58 3.96 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 1701 0.680280 TACGGGACAGTCAGAGCTCC 60.680 60.000 10.93 0.0 0.00 4.70 R
1973 2161 3.055891 GGATCTTTGGGTTGGATGGTTTG 60.056 47.826 0.00 0.0 0.00 2.93 R
2462 2668 0.040058 TCTGTGGGCAGGCATGATTT 59.960 50.000 0.62 0.0 42.78 2.17 R
2470 2676 0.256752 TGAATCCATCTGTGGGCAGG 59.743 55.000 0.00 0.0 46.06 4.85 R
3012 3271 0.463654 ATGCCCGTGTACATTGCGAT 60.464 50.000 0.00 0.0 0.00 4.58 R
3646 3970 0.400213 AGGAAGATCGGGCAAACACA 59.600 50.000 0.00 0.0 0.00 3.72 R
4918 5768 0.321387 AGCACACTGGAGATGCACTG 60.321 55.000 0.00 0.0 41.97 3.66 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
32 33 5.184479 CCCAACATAGAATATGATTGCCCTG 59.816 44.000 3.87 0.00 0.00 4.45
41 42 5.927281 ATATGATTGCCCTGAATAATGCC 57.073 39.130 0.00 0.00 0.00 4.40
50 51 4.039609 GCCCTGAATAATGCCAAATAAGCT 59.960 41.667 0.00 0.00 0.00 3.74
137 138 0.255033 CCTACTTAAGGTGCCACCCC 59.745 60.000 11.06 0.00 39.75 4.95
141 142 0.323451 CTTAAGGTGCCACCCCCTTC 60.323 60.000 11.06 0.00 41.30 3.46
142 143 0.774491 TTAAGGTGCCACCCCCTTCT 60.774 55.000 11.06 0.00 41.30 2.85
154 156 1.408822 CCCCCTTCTTACATGGAGTGC 60.409 57.143 0.00 0.00 0.00 4.40
174 176 1.037030 CACATCAACCCCATTCCCCG 61.037 60.000 0.00 0.00 0.00 5.73
175 177 1.306296 CATCAACCCCATTCCCCGT 59.694 57.895 0.00 0.00 0.00 5.28
202 204 2.691526 TCGAGGTATAGCGACCAAACAT 59.308 45.455 8.02 0.00 42.47 2.71
236 238 0.409484 AGTAGTGGGCCAGCCATTTT 59.591 50.000 6.40 0.00 37.98 1.82
273 275 5.397553 TTTTTCTCTACTTTCCCCCTGTT 57.602 39.130 0.00 0.00 0.00 3.16
321 324 9.739276 ATTTCTTTTGGTTTCCTTTTTCTTCTT 57.261 25.926 0.00 0.00 0.00 2.52
395 398 7.011016 GGAAACAATTTTCAAATTCGTCCACTT 59.989 33.333 10.57 1.16 42.72 3.16
541 546 4.381185 GGAACTTTTTGAAACCCACGAACT 60.381 41.667 0.00 0.00 0.00 3.01
585 590 9.860898 ACATTTTATGAAATCTGTAGCTTTTCC 57.139 29.630 0.00 0.00 33.25 3.13
606 611 4.690748 TCCTCAAAGTAGTGAGCATTTTCG 59.309 41.667 0.00 0.00 43.18 3.46
802 899 0.657840 GCTGCGGCACTAGTATTTGG 59.342 55.000 14.08 0.00 38.54 3.28
810 907 5.113383 CGGCACTAGTATTTGGTATTCACA 58.887 41.667 0.00 0.00 0.00 3.58
820 917 2.261729 TGGTATTCACAGTGGCTGGTA 58.738 47.619 0.00 0.00 35.51 3.25
836 933 4.757149 GGCTGGTATAAGTAGCTCCAAATG 59.243 45.833 0.00 0.00 37.58 2.32
872 970 1.076339 GGATGGGATCGGGCCAAAA 60.076 57.895 4.39 0.00 0.00 2.44
876 974 0.395586 TGGGATCGGGCCAAAATCAG 60.396 55.000 4.39 0.00 0.00 2.90
897 995 0.394216 CGAGGCCCATTCCACATTCA 60.394 55.000 0.00 0.00 0.00 2.57
917 1015 4.030913 TCACCCCATCGATTTCTTACTCT 58.969 43.478 0.00 0.00 0.00 3.24
1036 1138 2.504244 GCCTCACCGACTTCGACG 60.504 66.667 0.00 0.00 43.02 5.12
1106 1218 1.409427 CGAGAAGCAGGTAACCCTAGG 59.591 57.143 0.06 0.06 39.89 3.02
1338 1455 4.651008 TGGTTCCACGACGCCGAC 62.651 66.667 0.00 0.00 39.50 4.79
1501 1618 3.210358 CCGTGTGGCGTTTATTGATTT 57.790 42.857 0.00 0.00 39.32 2.17
1507 1624 4.035017 GTGGCGTTTATTGATTTGGATCG 58.965 43.478 0.00 0.00 34.91 3.69
1581 1698 5.511234 AATCTGCAATGAAGCTGGAATAC 57.489 39.130 0.00 0.00 34.63 1.89
1584 1701 2.938451 TGCAATGAAGCTGGAATACTCG 59.062 45.455 0.00 0.00 34.99 4.18
1601 1720 2.888863 GGAGCTCTGACTGTCCCG 59.111 66.667 14.64 0.00 0.00 5.14
1619 1738 2.362717 CCCGTAGAAAAGCCCACAAAAA 59.637 45.455 0.00 0.00 0.00 1.94
1647 1791 2.758423 GGGGGCATTTTACTTCGATTGT 59.242 45.455 0.00 0.00 0.00 2.71
1669 1813 3.444034 TGGTCGTGAGAGGTAGAAAGATG 59.556 47.826 0.00 0.00 43.49 2.90
1758 1908 8.282455 TGTGTTTAGTTATGTTGGTTTCTCAA 57.718 30.769 0.00 0.00 0.00 3.02
1847 2029 5.685520 AGATGAAGAACCTAAGAACTCCC 57.314 43.478 0.00 0.00 0.00 4.30
2299 2494 4.466370 TGATATCGAGGTTGGTTCTTCTGT 59.534 41.667 0.00 0.00 0.00 3.41
2334 2529 3.257393 CTCTCTGCCACTGTTATGTGTC 58.743 50.000 0.00 0.00 36.30 3.67
2406 2612 4.286297 AGCCAGTGAGTTAAATGCACTA 57.714 40.909 0.00 0.00 40.63 2.74
2447 2653 2.811431 TGTCAACAACATGGAATCCGAC 59.189 45.455 0.00 0.00 31.20 4.79
2448 2654 3.074412 GTCAACAACATGGAATCCGACT 58.926 45.455 0.00 0.00 0.00 4.18
2449 2655 4.250464 GTCAACAACATGGAATCCGACTA 58.750 43.478 0.00 0.00 0.00 2.59
2450 2656 4.092968 GTCAACAACATGGAATCCGACTAC 59.907 45.833 0.00 0.00 0.00 2.73
2451 2657 3.973206 ACAACATGGAATCCGACTACA 57.027 42.857 0.00 0.00 0.00 2.74
2452 2658 4.487714 ACAACATGGAATCCGACTACAT 57.512 40.909 0.00 0.00 0.00 2.29
2453 2659 4.442706 ACAACATGGAATCCGACTACATC 58.557 43.478 0.00 0.00 0.00 3.06
2454 2660 4.081142 ACAACATGGAATCCGACTACATCA 60.081 41.667 0.00 0.00 0.00 3.07
2455 2661 4.963318 ACATGGAATCCGACTACATCAT 57.037 40.909 0.00 0.00 0.00 2.45
2456 2662 5.296151 ACATGGAATCCGACTACATCATT 57.704 39.130 0.00 0.00 0.00 2.57
2457 2663 5.059161 ACATGGAATCCGACTACATCATTG 58.941 41.667 0.00 0.00 0.00 2.82
2458 2664 4.753516 TGGAATCCGACTACATCATTGT 57.246 40.909 0.00 0.00 39.98 2.71
2459 2665 5.097742 TGGAATCCGACTACATCATTGTT 57.902 39.130 0.00 0.00 37.28 2.83
2460 2666 4.875536 TGGAATCCGACTACATCATTGTTG 59.124 41.667 0.00 0.00 37.28 3.33
2461 2667 4.876107 GGAATCCGACTACATCATTGTTGT 59.124 41.667 5.73 5.73 43.14 3.32
2462 2668 6.046593 GGAATCCGACTACATCATTGTTGTA 58.953 40.000 7.24 7.24 41.03 2.41
2463 2669 6.537301 GGAATCCGACTACATCATTGTTGTAA 59.463 38.462 8.51 0.00 41.03 2.41
2464 2670 7.065324 GGAATCCGACTACATCATTGTTGTAAA 59.935 37.037 8.51 0.00 41.03 2.01
2465 2671 8.506168 AATCCGACTACATCATTGTTGTAAAT 57.494 30.769 8.51 1.58 41.03 1.40
2466 2672 7.534085 TCCGACTACATCATTGTTGTAAATC 57.466 36.000 8.51 8.15 41.03 2.17
2467 2673 7.100409 TCCGACTACATCATTGTTGTAAATCA 58.900 34.615 8.51 0.00 41.03 2.57
2468 2674 7.768582 TCCGACTACATCATTGTTGTAAATCAT 59.231 33.333 8.51 0.00 41.03 2.45
2469 2675 7.852454 CCGACTACATCATTGTTGTAAATCATG 59.148 37.037 8.51 0.00 41.03 3.07
2470 2676 7.374228 CGACTACATCATTGTTGTAAATCATGC 59.626 37.037 8.51 0.00 41.03 4.06
2471 2677 7.483307 ACTACATCATTGTTGTAAATCATGCC 58.517 34.615 8.51 0.00 39.53 4.40
2472 2678 6.534475 ACATCATTGTTGTAAATCATGCCT 57.466 33.333 0.00 0.00 29.55 4.75
2473 2679 6.334989 ACATCATTGTTGTAAATCATGCCTG 58.665 36.000 0.00 0.00 29.55 4.85
2474 2680 4.746729 TCATTGTTGTAAATCATGCCTGC 58.253 39.130 0.00 0.00 0.00 4.85
2475 2681 3.591196 TTGTTGTAAATCATGCCTGCC 57.409 42.857 0.00 0.00 0.00 4.85
2476 2682 1.824230 TGTTGTAAATCATGCCTGCCC 59.176 47.619 0.00 0.00 0.00 5.36
2477 2683 1.824230 GTTGTAAATCATGCCTGCCCA 59.176 47.619 0.00 0.00 0.00 5.36
2478 2684 1.473258 TGTAAATCATGCCTGCCCAC 58.527 50.000 0.00 0.00 0.00 4.61
2479 2685 1.272369 TGTAAATCATGCCTGCCCACA 60.272 47.619 0.00 0.00 0.00 4.17
2480 2686 1.406539 GTAAATCATGCCTGCCCACAG 59.593 52.381 0.00 0.00 44.05 3.66
2552 2790 9.646522 ATTGATTAAACAATAGCTGGACCTATT 57.353 29.630 9.03 0.00 38.49 1.73
2574 2812 4.980590 TCATTGCTGCGGTAATTTTAGTG 58.019 39.130 6.07 0.00 0.00 2.74
2584 2822 6.094061 GCGGTAATTTTAGTGGCATTTTGTA 58.906 36.000 0.00 0.00 0.00 2.41
2613 2851 9.708222 CTAATGAAGCAATATATATGTTTCCGC 57.292 33.333 15.17 0.00 37.25 5.54
2629 2876 0.387112 CCGCGAAATGCATGTTGTGT 60.387 50.000 8.23 0.00 46.97 3.72
2645 2892 4.938226 TGTTGTGTGTTGTGATCAGTTACA 59.062 37.500 0.00 0.00 0.00 2.41
2764 3014 8.099537 AGCATAAACTATCCAGATATCCTTGTG 58.900 37.037 0.00 0.00 0.00 3.33
2810 3060 5.902613 TGTGGAAAATTTCAGGAGCTATG 57.097 39.130 8.09 0.00 0.00 2.23
2828 3079 5.047847 GCTATGCATTGTGAATTGAAGCAT 58.952 37.500 3.54 0.00 42.98 3.79
3025 3324 7.969387 ATAAATTTGACATCGCAATGTACAC 57.031 32.000 0.00 0.00 46.20 2.90
3030 3329 1.078778 ATCGCAATGTACACGGGCA 60.079 52.632 13.58 3.96 0.00 5.36
3483 3807 5.661312 ACTCTGTGGCACAATAGATTACCTA 59.339 40.000 27.25 1.67 44.16 3.08
3504 3828 3.030291 AGCACCAGAGATGGTAGAGAAG 58.970 50.000 0.00 0.00 40.85 2.85
3788 4118 7.652909 TCTCATTTGCAAGGTAACATTTGAAAG 59.347 33.333 0.00 0.00 41.41 2.62
3790 4120 7.437862 TCATTTGCAAGGTAACATTTGAAAGTC 59.562 33.333 0.00 0.00 41.41 3.01
3820 4406 9.586435 GTTATATCTTTTCTTTGGACAAATGGG 57.414 33.333 0.00 0.00 0.00 4.00
3821 4407 4.335400 TCTTTTCTTTGGACAAATGGGC 57.665 40.909 0.00 0.00 0.00 5.36
3822 4408 3.070878 TCTTTTCTTTGGACAAATGGGCC 59.929 43.478 0.00 0.00 0.00 5.80
3923 4514 5.981915 TCTCTTGACGATATTCTGAAGCATG 59.018 40.000 0.00 0.00 0.00 4.06
4085 4680 4.023707 GTCCAACATATAATCCTGCACTGC 60.024 45.833 0.00 0.00 0.00 4.40
4181 4778 8.528643 TGGATCGATTTCTAGACAGTTTTTCTA 58.471 33.333 0.00 0.00 0.00 2.10
4220 4817 8.635765 AATTTTGGTAGCGTGGAATATATCAT 57.364 30.769 0.00 0.00 0.00 2.45
4372 5000 6.710744 GGGTAGTGGGTAGAATATGTCATTTG 59.289 42.308 0.00 0.00 0.00 2.32
4519 5248 0.245539 GGTTGTGGAGGATCGAACGA 59.754 55.000 0.00 0.00 34.37 3.85
4556 5285 9.273137 TCTCTAATCTTTCCCAACTAATCTCTT 57.727 33.333 0.00 0.00 0.00 2.85
4561 5290 9.674068 AATCTTTCCCAACTAATCTCTTAGAAC 57.326 33.333 0.00 0.00 38.19 3.01
4569 5298 8.307483 CCAACTAATCTCTTAGAACTGAACTCA 58.693 37.037 0.00 0.00 38.19 3.41
4588 5317 4.637534 ACTCACAGATGCAATGTATGAACC 59.362 41.667 7.53 0.00 0.00 3.62
4593 5322 5.889853 ACAGATGCAATGTATGAACCTGAAT 59.110 36.000 6.16 0.00 0.00 2.57
4600 5329 6.204359 CAATGTATGAACCTGAATGCTTAGC 58.796 40.000 0.00 0.00 0.00 3.09
4704 5433 3.635734 CTTCTTGCCGTTGCGAGCG 62.636 63.158 0.00 0.00 46.88 5.03
4929 5779 6.228995 TGAAATATGATCTCAGTGCATCTCC 58.771 40.000 0.00 0.00 0.00 3.71
4931 5781 3.755112 ATGATCTCAGTGCATCTCCAG 57.245 47.619 0.00 0.00 0.00 3.86
4937 5787 0.321387 CAGTGCATCTCCAGTGTGCT 60.321 55.000 5.21 0.00 39.52 4.40
4938 5788 0.321387 AGTGCATCTCCAGTGTGCTG 60.321 55.000 5.21 0.00 42.22 4.41
4976 5832 2.545952 CGCTACCACTGTTCTGAACTGT 60.546 50.000 22.39 22.39 43.20 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.340232 GGCATTATTCAGGGCAATCATATTCTA 59.660 37.037 0.00 0.00 0.00 2.10
22 23 3.029483 TGGCATTATTCAGGGCAATCA 57.971 42.857 0.00 0.00 33.89 2.57
32 33 7.755582 AAAACGAGCTTATTTGGCATTATTC 57.244 32.000 0.00 0.00 0.00 1.75
39 40 8.182227 AGACTAAATAAAACGAGCTTATTTGGC 58.818 33.333 16.74 11.88 39.19 4.52
50 51 8.223177 TGGACCAAAAAGACTAAATAAAACGA 57.777 30.769 0.00 0.00 0.00 3.85
137 138 2.290260 TGTGGCACTCCATGTAAGAAGG 60.290 50.000 19.83 0.00 45.62 3.46
141 142 2.989909 TGATGTGGCACTCCATGTAAG 58.010 47.619 19.83 0.00 45.62 2.34
142 143 3.081061 GTTGATGTGGCACTCCATGTAA 58.919 45.455 19.83 0.00 45.62 2.41
154 156 0.687427 GGGGAATGGGGTTGATGTGG 60.687 60.000 0.00 0.00 0.00 4.17
174 176 1.007618 GCTATACCTCGACCCGCAC 60.008 63.158 0.00 0.00 0.00 5.34
175 177 2.549198 CGCTATACCTCGACCCGCA 61.549 63.158 0.00 0.00 0.00 5.69
215 217 4.033776 TGGCTGGCCCACTACTGC 62.034 66.667 9.28 0.00 39.18 4.40
255 257 3.323775 ACAAACAGGGGGAAAGTAGAGA 58.676 45.455 0.00 0.00 0.00 3.10
256 258 3.790089 ACAAACAGGGGGAAAGTAGAG 57.210 47.619 0.00 0.00 0.00 2.43
257 259 4.466827 GAAACAAACAGGGGGAAAGTAGA 58.533 43.478 0.00 0.00 0.00 2.59
258 260 3.572682 GGAAACAAACAGGGGGAAAGTAG 59.427 47.826 0.00 0.00 0.00 2.57
259 261 3.205733 AGGAAACAAACAGGGGGAAAGTA 59.794 43.478 0.00 0.00 0.00 2.24
260 262 2.023404 AGGAAACAAACAGGGGGAAAGT 60.023 45.455 0.00 0.00 0.00 2.66
261 263 2.677914 AGGAAACAAACAGGGGGAAAG 58.322 47.619 0.00 0.00 0.00 2.62
262 264 2.858787 AGGAAACAAACAGGGGGAAA 57.141 45.000 0.00 0.00 0.00 3.13
265 267 4.591072 TCAATTAAGGAAACAAACAGGGGG 59.409 41.667 0.00 0.00 0.00 5.40
300 303 7.685481 AGGAAAGAAGAAAAAGGAAACCAAAA 58.315 30.769 0.00 0.00 0.00 2.44
368 371 5.460419 TGGACGAATTTGAAAATTGTTTCCG 59.540 36.000 5.76 5.61 42.20 4.30
387 390 6.060028 TCTCATTTTTCAGAAAAGTGGACG 57.940 37.500 23.70 15.44 38.28 4.79
463 466 9.474920 ACAATATTCATGAATTTGAAAACACGT 57.525 25.926 29.59 14.93 38.98 4.49
475 479 9.740239 CTCGGATTTCAAACAATATTCATGAAT 57.260 29.630 23.75 23.75 30.81 2.57
517 522 2.427812 TCGTGGGTTTCAAAAAGTTCCC 59.572 45.455 0.00 0.00 35.85 3.97
518 523 3.786516 TCGTGGGTTTCAAAAAGTTCC 57.213 42.857 0.00 0.00 0.00 3.62
584 589 4.690748 TCGAAAATGCTCACTACTTTGAGG 59.309 41.667 2.48 0.00 42.95 3.86
585 590 5.845985 TCGAAAATGCTCACTACTTTGAG 57.154 39.130 0.00 0.00 45.15 3.02
709 806 5.656480 GTGGCGGTGGTGAATTTAAAATAT 58.344 37.500 0.00 0.00 0.00 1.28
716 813 1.527380 ACGTGGCGGTGGTGAATTT 60.527 52.632 0.00 0.00 0.00 1.82
802 899 5.671493 ACTTATACCAGCCACTGTGAATAC 58.329 41.667 9.86 0.00 0.00 1.89
810 907 2.966516 GGAGCTACTTATACCAGCCACT 59.033 50.000 0.00 0.00 35.88 4.00
820 917 2.158460 GGGCCCATTTGGAGCTACTTAT 60.158 50.000 19.95 0.00 37.39 1.73
872 970 2.512896 GAATGGGCCTCGGCTGAT 59.487 61.111 4.53 0.00 41.60 2.90
876 974 3.721370 ATGTGGAATGGGCCTCGGC 62.721 63.158 4.53 0.00 41.06 5.54
878 976 0.394216 TGAATGTGGAATGGGCCTCG 60.394 55.000 4.53 0.00 0.00 4.63
897 995 4.030913 TCAGAGTAAGAAATCGATGGGGT 58.969 43.478 0.00 0.00 0.00 4.95
1036 1138 2.785258 GCCGATGAACTTGCCGAC 59.215 61.111 0.00 0.00 0.00 4.79
1106 1218 1.587043 GAAGCTCGAAGGTTTGGGGC 61.587 60.000 0.00 0.00 35.86 5.80
1501 1618 0.916086 ATAACAACTGGGCCGATCCA 59.084 50.000 0.00 0.00 36.21 3.41
1507 1624 2.032680 TAGCGAATAACAACTGGGCC 57.967 50.000 0.00 0.00 0.00 5.80
1581 1698 1.662438 GGGACAGTCAGAGCTCCGAG 61.662 65.000 10.93 0.56 0.00 4.63
1584 1701 0.680280 TACGGGACAGTCAGAGCTCC 60.680 60.000 10.93 0.00 0.00 4.70
1601 1720 5.116069 TCGATTTTTGTGGGCTTTTCTAC 57.884 39.130 0.00 0.00 0.00 2.59
1619 1738 4.652822 GAAGTAAAATGCCCCCTATCGAT 58.347 43.478 2.16 2.16 0.00 3.59
1647 1791 3.150458 TCTTTCTACCTCTCACGACCA 57.850 47.619 0.00 0.00 0.00 4.02
1777 1927 8.842280 ACCAAAATTCTTAACGATCAAACAGTA 58.158 29.630 0.00 0.00 0.00 2.74
1783 1933 9.391006 AGCTATACCAAAATTCTTAACGATCAA 57.609 29.630 0.00 0.00 0.00 2.57
1806 1956 4.137116 TCTTGCGGTGAAATACATAGCT 57.863 40.909 0.00 0.00 35.76 3.32
1807 1957 4.511454 TCATCTTGCGGTGAAATACATAGC 59.489 41.667 0.00 0.00 35.48 2.97
1847 2029 6.539649 TCCTTGTGTTTCTAAAGATGTTCG 57.460 37.500 0.00 0.00 0.00 3.95
1973 2161 3.055891 GGATCTTTGGGTTGGATGGTTTG 60.056 47.826 0.00 0.00 0.00 2.93
2247 2442 0.958382 TTTTCCGGCTTGATGTCCCG 60.958 55.000 0.00 0.00 41.60 5.14
2334 2529 8.394877 TCTTAAAATACGCAGTTTGGTATGATG 58.605 33.333 0.00 0.00 37.78 3.07
2421 2627 4.744631 GGATTCCATGTTGTTGACAAACAC 59.255 41.667 0.00 0.00 45.91 3.32
2447 2653 7.646526 CAGGCATGATTTACAACAATGATGTAG 59.353 37.037 0.00 0.00 39.40 2.74
2448 2654 7.482474 CAGGCATGATTTACAACAATGATGTA 58.518 34.615 0.00 0.00 39.40 2.29
2449 2655 6.334989 CAGGCATGATTTACAACAATGATGT 58.665 36.000 0.00 1.07 43.14 3.06
2450 2656 5.233476 GCAGGCATGATTTACAACAATGATG 59.767 40.000 0.62 0.00 32.56 3.07
2451 2657 5.353938 GCAGGCATGATTTACAACAATGAT 58.646 37.500 0.62 0.00 0.00 2.45
2452 2658 4.381825 GGCAGGCATGATTTACAACAATGA 60.382 41.667 0.62 0.00 0.00 2.57
2453 2659 3.866910 GGCAGGCATGATTTACAACAATG 59.133 43.478 0.62 0.00 0.00 2.82
2454 2660 3.118665 GGGCAGGCATGATTTACAACAAT 60.119 43.478 0.62 0.00 0.00 2.71
2455 2661 2.233431 GGGCAGGCATGATTTACAACAA 59.767 45.455 0.62 0.00 0.00 2.83
2456 2662 1.824230 GGGCAGGCATGATTTACAACA 59.176 47.619 0.62 0.00 0.00 3.33
2457 2663 1.824230 TGGGCAGGCATGATTTACAAC 59.176 47.619 0.62 0.00 0.00 3.32
2458 2664 1.824230 GTGGGCAGGCATGATTTACAA 59.176 47.619 0.62 0.00 0.00 2.41
2459 2665 1.272369 TGTGGGCAGGCATGATTTACA 60.272 47.619 0.62 0.00 0.00 2.41
2460 2666 1.406539 CTGTGGGCAGGCATGATTTAC 59.593 52.381 0.62 0.00 39.01 2.01
2461 2667 1.284491 TCTGTGGGCAGGCATGATTTA 59.716 47.619 0.62 0.00 42.78 1.40
2462 2668 0.040058 TCTGTGGGCAGGCATGATTT 59.960 50.000 0.62 0.00 42.78 2.17
2463 2669 0.260816 ATCTGTGGGCAGGCATGATT 59.739 50.000 0.62 0.00 42.78 2.57
2464 2670 0.467474 CATCTGTGGGCAGGCATGAT 60.467 55.000 0.62 0.00 42.78 2.45
2465 2671 1.077285 CATCTGTGGGCAGGCATGA 60.077 57.895 0.62 0.00 42.78 3.07
2466 2672 2.125326 CCATCTGTGGGCAGGCATG 61.125 63.158 0.00 0.00 42.11 4.06
2467 2673 1.652187 ATCCATCTGTGGGCAGGCAT 61.652 55.000 0.00 0.00 46.06 4.40
2468 2674 1.866483 AATCCATCTGTGGGCAGGCA 61.866 55.000 0.00 0.00 46.06 4.75
2469 2675 1.076485 AATCCATCTGTGGGCAGGC 60.076 57.895 0.00 0.00 46.06 4.85
2470 2676 0.256752 TGAATCCATCTGTGGGCAGG 59.743 55.000 0.00 0.00 46.06 4.85
2471 2677 1.211212 TCTGAATCCATCTGTGGGCAG 59.789 52.381 0.00 0.00 46.06 4.85
2472 2678 1.065199 GTCTGAATCCATCTGTGGGCA 60.065 52.381 0.00 0.00 46.06 5.36
2473 2679 1.211457 AGTCTGAATCCATCTGTGGGC 59.789 52.381 0.00 0.00 46.06 5.36
2474 2680 3.452264 TGTAGTCTGAATCCATCTGTGGG 59.548 47.826 0.00 0.00 46.06 4.61
2476 2682 5.910614 TGATGTAGTCTGAATCCATCTGTG 58.089 41.667 11.10 0.00 34.44 3.66
2477 2683 6.744175 ATGATGTAGTCTGAATCCATCTGT 57.256 37.500 11.10 0.00 34.44 3.41
2478 2684 6.990939 ACAATGATGTAGTCTGAATCCATCTG 59.009 38.462 11.10 5.62 38.24 2.90
2479 2685 7.134362 ACAATGATGTAGTCTGAATCCATCT 57.866 36.000 11.10 0.00 38.24 2.90
2480 2686 7.281774 ACAACAATGATGTAGTCTGAATCCATC 59.718 37.037 4.05 4.05 39.40 3.51
2481 2687 7.114754 ACAACAATGATGTAGTCTGAATCCAT 58.885 34.615 0.00 0.00 39.40 3.41
2482 2688 6.475504 ACAACAATGATGTAGTCTGAATCCA 58.524 36.000 0.00 0.00 39.40 3.41
2483 2689 6.992063 ACAACAATGATGTAGTCTGAATCC 57.008 37.500 0.00 0.00 39.40 3.01
2490 2696 9.450807 GGCATAATTTACAACAATGATGTAGTC 57.549 33.333 3.68 0.00 39.40 2.59
2491 2697 9.189156 AGGCATAATTTACAACAATGATGTAGT 57.811 29.630 3.68 0.00 39.40 2.73
2528 2766 8.271458 TGAATAGGTCCAGCTATTGTTTAATCA 58.729 33.333 14.31 3.64 0.00 2.57
2552 2790 4.142491 CCACTAAAATTACCGCAGCAATGA 60.142 41.667 0.00 0.00 0.00 2.57
2574 2812 6.194796 TGCTTCATTAGAGTACAAAATGCC 57.805 37.500 0.00 0.00 31.98 4.40
2613 2851 3.061073 CACAACACACAACATGCATTTCG 60.061 43.478 0.00 0.00 0.00 3.46
2667 2914 8.964476 ATCTCAAGTATTTTTCACATATCGGT 57.036 30.769 0.00 0.00 0.00 4.69
2810 3060 5.292345 TGCATAATGCTTCAATTCACAATGC 59.708 36.000 0.00 0.00 45.31 3.56
2828 3079 7.062322 AGTTCCCAACAATATGAGATGCATAA 58.938 34.615 0.00 0.00 42.45 1.90
2841 3092 5.243730 CCAACAGTCATAAGTTCCCAACAAT 59.756 40.000 0.00 0.00 0.00 2.71
2842 3093 4.582656 CCAACAGTCATAAGTTCCCAACAA 59.417 41.667 0.00 0.00 0.00 2.83
2906 3164 9.447157 AAAGCCAATTTTAAAATGCAAGCTATA 57.553 25.926 19.60 0.00 0.00 1.31
2921 3179 8.561738 TTTCGTCTCTCTATAAAGCCAATTTT 57.438 30.769 0.00 0.00 32.01 1.82
3006 3265 2.158645 CCGTGTACATTGCGATGTCAAA 59.841 45.455 23.02 7.44 42.83 2.69
3009 3268 0.650512 CCCGTGTACATTGCGATGTC 59.349 55.000 23.02 14.56 42.83 3.06
3011 3270 1.351707 GCCCGTGTACATTGCGATG 59.648 57.895 12.66 12.66 39.25 3.84
3012 3271 0.463654 ATGCCCGTGTACATTGCGAT 60.464 50.000 0.00 0.00 0.00 4.58
3013 3272 1.078778 ATGCCCGTGTACATTGCGA 60.079 52.632 0.00 0.00 0.00 5.10
3198 3500 7.531716 ACAGTATTTGATAGTCTCTATAGCGC 58.468 38.462 0.00 0.00 0.00 5.92
3383 3707 2.163613 CGGCCCTGTAAAATGGAAGTTC 59.836 50.000 0.00 0.00 0.00 3.01
3504 3828 0.924090 CAGCGTAATCGTGAGCCTTC 59.076 55.000 0.00 0.00 39.49 3.46
3603 3927 2.114616 AGCTCTTACCTCATCAGGGTG 58.885 52.381 0.00 0.00 45.53 4.61
3644 3968 1.611491 GGAAGATCGGGCAAACACAAA 59.389 47.619 0.00 0.00 0.00 2.83
3646 3970 0.400213 AGGAAGATCGGGCAAACACA 59.600 50.000 0.00 0.00 0.00 3.72
3647 3971 1.534729 AAGGAAGATCGGGCAAACAC 58.465 50.000 0.00 0.00 0.00 3.32
3649 3973 2.159382 TCAAAGGAAGATCGGGCAAAC 58.841 47.619 0.00 0.00 0.00 2.93
3806 4137 3.070015 GGATATGGCCCATTTGTCCAAAG 59.930 47.826 0.00 0.00 33.32 2.77
3810 4141 2.683211 AGGATATGGCCCATTTGTCC 57.317 50.000 0.00 7.92 0.00 4.02
3813 4144 4.901250 ACCTTAAAGGATATGGCCCATTTG 59.099 41.667 0.00 0.00 37.67 2.32
3814 4145 4.901250 CACCTTAAAGGATATGGCCCATTT 59.099 41.667 0.00 0.00 37.67 2.32
3820 4406 6.064717 ACTTCATCACCTTAAAGGATATGGC 58.935 40.000 0.00 0.00 37.67 4.40
3821 4407 7.775093 TCAACTTCATCACCTTAAAGGATATGG 59.225 37.037 0.00 0.00 37.67 2.74
3822 4408 8.737168 TCAACTTCATCACCTTAAAGGATATG 57.263 34.615 0.00 0.00 37.67 1.78
3923 4514 3.126858 TCTGCATTCTTTACAATCCACGC 59.873 43.478 0.00 0.00 0.00 5.34
4057 4652 6.095440 GTGCAGGATTATATGTTGGACAGTTT 59.905 38.462 0.00 0.00 31.50 2.66
4058 4653 5.590259 GTGCAGGATTATATGTTGGACAGTT 59.410 40.000 0.00 0.00 31.50 3.16
4085 4680 6.166279 TGTAAGGTGCTAAGATTTCTGAGTG 58.834 40.000 0.00 0.00 0.00 3.51
4181 4778 8.612619 CGCTACCAAAATTCAGAATAATACAGT 58.387 33.333 0.00 0.00 0.00 3.55
4192 4789 4.701956 ATTCCACGCTACCAAAATTCAG 57.298 40.909 0.00 0.00 0.00 3.02
4202 4799 6.208988 TCCAGATGATATATTCCACGCTAC 57.791 41.667 0.00 0.00 0.00 3.58
4220 4817 6.038161 CGTAATCCATAGTTTGCATTTCCAGA 59.962 38.462 0.00 0.00 0.00 3.86
4305 4933 4.574828 CCATTCGTTATCAGGAAATCCGTT 59.425 41.667 0.00 0.00 42.08 4.44
4372 5000 7.816995 TGCAAAATATCACAAAGTAATTCCACC 59.183 33.333 0.00 0.00 0.00 4.61
4552 5281 5.576384 GCATCTGTGAGTTCAGTTCTAAGAG 59.424 44.000 0.00 0.00 36.85 2.85
4556 5285 4.871933 TGCATCTGTGAGTTCAGTTCTA 57.128 40.909 0.00 0.00 36.85 2.10
4561 5290 5.583457 TCATACATTGCATCTGTGAGTTCAG 59.417 40.000 11.57 0.00 36.85 3.02
4569 5298 4.847198 TCAGGTTCATACATTGCATCTGT 58.153 39.130 7.49 7.49 0.00 3.41
4600 5329 3.989167 CACCAAACCATTTGTAGCACATG 59.011 43.478 0.00 0.00 38.98 3.21
4610 5339 2.802719 ACGGATAGCACCAAACCATTT 58.197 42.857 0.00 0.00 0.00 2.32
4868 5605 5.900123 ACCACCAAGAGAGCATTAGTAGTAT 59.100 40.000 0.00 0.00 0.00 2.12
4912 5762 2.167900 CACTGGAGATGCACTGAGATCA 59.832 50.000 0.00 0.00 0.00 2.92
4916 5766 1.723220 CACACTGGAGATGCACTGAG 58.277 55.000 0.00 0.00 0.00 3.35
4918 5768 0.321387 AGCACACTGGAGATGCACTG 60.321 55.000 0.00 0.00 41.97 3.66
4931 5781 0.604780 AGATGCACTGGACAGCACAC 60.605 55.000 0.00 0.00 44.49 3.82


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

AutoCloner maintained by Alex Coulton.