Multiple sequence alignment - TraesCS2D01G512900

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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 TraesCS2D01G512900 chr2D 100.000 6565 0 0 1 6565 604286559 604293123 0.000000e+00 12124.0
1 TraesCS2D01G512900 chr2D 92.151 2064 141 15 2805 4856 604052920 604050866 0.000000e+00 2894.0
2 TraesCS2D01G512900 chr2D 92.134 1462 90 11 635 2092 604056719 604055279 0.000000e+00 2039.0
3 TraesCS2D01G512900 chr2D 89.086 1237 116 13 5103 6330 604025623 604024397 0.000000e+00 1519.0
4 TraesCS2D01G512900 chr2D 79.315 730 123 22 5521 6237 322137660 322138374 2.750000e-133 486.0
5 TraesCS2D01G512900 chr2D 78.552 732 128 22 5521 6242 322174889 322175601 7.760000e-124 455.0
6 TraesCS2D01G512900 chr2D 87.688 398 29 14 2326 2712 604055283 604054895 4.670000e-121 446.0
7 TraesCS2D01G512900 chr2D 90.948 232 18 3 4870 5099 604026222 604025992 6.390000e-80 309.0
8 TraesCS2D01G512900 chr2D 71.762 772 174 39 3036 3784 585687814 585687064 1.880000e-40 178.0
9 TraesCS2D01G512900 chr2D 87.288 118 14 1 4988 5104 604025994 604025877 4.130000e-27 134.0
10 TraesCS2D01G512900 chr2D 81.203 133 22 3 3650 3780 585750029 585749898 3.240000e-18 104.0
11 TraesCS2D01G512900 chr2B 94.365 4525 197 28 861 5372 734916362 734920841 0.000000e+00 6890.0
12 TraesCS2D01G512900 chr2B 94.554 3360 146 23 852 4198 734943695 734947030 0.000000e+00 5156.0
13 TraesCS2D01G512900 chr2B 95.204 2377 101 13 4196 6565 734951008 734953378 0.000000e+00 3746.0
14 TraesCS2D01G512900 chr2B 95.129 1047 48 3 5521 6565 734920838 734921883 0.000000e+00 1648.0
15 TraesCS2D01G512900 chr2B 79.548 753 133 15 3892 4635 759347236 759347976 9.760000e-143 518.0
16 TraesCS2D01G512900 chr2B 79.092 727 129 18 5521 6236 390392935 390393649 4.600000e-131 479.0
17 TraesCS2D01G512900 chr2B 94.301 193 9 1 460 650 734915970 734916162 1.790000e-75 294.0
18 TraesCS2D01G512900 chr2B 93.264 193 10 2 460 650 734940787 734940978 1.390000e-71 281.0
19 TraesCS2D01G512900 chr2B 91.758 182 12 1 635 813 734916188 734916369 3.930000e-62 250.0
20 TraesCS2D01G512900 chr2B 95.862 145 6 0 6330 6474 647738967 647739111 1.100000e-57 235.0
21 TraesCS2D01G512900 chr2B 96.154 104 3 1 713 815 734942308 734942411 1.130000e-37 169.0
22 TraesCS2D01G512900 chr2B 85.271 129 19 0 1632 1760 737792232 737792104 4.130000e-27 134.0
23 TraesCS2D01G512900 chr2B 82.432 148 24 2 6329 6475 59754568 59754422 1.920000e-25 128.0
24 TraesCS2D01G512900 chr2B 93.182 88 4 1 635 722 734940996 734941081 1.920000e-25 128.0
25 TraesCS2D01G512900 chr2A 97.582 3557 80 6 3011 6565 736036962 736040514 0.000000e+00 6087.0
26 TraesCS2D01G512900 chr2A 92.523 2354 107 24 636 2977 736034665 736036961 0.000000e+00 3308.0
27 TraesCS2D01G512900 chr2A 75.847 1652 327 58 3040 4663 751233178 751234785 0.000000e+00 774.0
28 TraesCS2D01G512900 chr2A 74.923 1631 332 62 3043 4646 751208989 751210569 0.000000e+00 675.0
29 TraesCS2D01G512900 chr2A 72.370 789 171 42 3036 3800 719730479 719729714 8.630000e-49 206.0
30 TraesCS2D01G512900 chr2A 80.247 243 26 13 218 439 736027262 736027503 5.270000e-36 163.0
31 TraesCS2D01G512900 chr2A 89.024 82 7 1 644 725 736034776 736034855 4.190000e-17 100.0
32 TraesCS2D01G512900 chr2A 96.000 50 2 0 740 789 736034673 736034722 1.520000e-11 82.4
33 TraesCS2D01G512900 chr3B 80.443 542 100 6 5553 6090 429529953 429529414 6.130000e-110 409.0
34 TraesCS2D01G512900 chr5B 93.671 237 15 0 6328 6564 617619174 617619410 8.100000e-94 355.0
35 TraesCS2D01G512900 chr6A 75.039 649 138 22 5521 6157 534037097 534037733 5.010000e-71 279.0
36 TraesCS2D01G512900 chr6A 85.926 135 13 3 2596 2728 100182529 100182399 8.880000e-29 139.0
37 TraesCS2D01G512900 chr6D 87.407 135 9 3 2596 2728 83104826 83104698 1.470000e-31 148.0
38 TraesCS2D01G512900 chr6D 87.826 115 10 3 2596 2706 84028570 84028684 1.490000e-26 132.0
39 TraesCS2D01G512900 chr6B 85.926 135 13 3 2596 2728 158147212 158147082 8.880000e-29 139.0
40 TraesCS2D01G512900 chr4B 82.432 148 24 2 6329 6475 513115132 513115278 1.920000e-25 128.0
41 TraesCS2D01G512900 chr4B 82.432 148 24 2 6329 6475 618689252 618689398 1.920000e-25 128.0
42 TraesCS2D01G512900 chr7D 81.944 144 21 3 6329 6469 574802585 574802444 4.160000e-22 117.0


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 TraesCS2D01G512900 chr2D 604286559 604293123 6564 False 12124.00 12124 100.000000 1 6565 1 chr2D.!!$F3 6564
1 TraesCS2D01G512900 chr2D 604050866 604056719 5853 True 1793.00 2894 90.657667 635 4856 3 chr2D.!!$R4 4221
2 TraesCS2D01G512900 chr2D 604024397 604026222 1825 True 654.00 1519 89.107333 4870 6330 3 chr2D.!!$R3 1460
3 TraesCS2D01G512900 chr2D 322137660 322138374 714 False 486.00 486 79.315000 5521 6237 1 chr2D.!!$F1 716
4 TraesCS2D01G512900 chr2D 322174889 322175601 712 False 455.00 455 78.552000 5521 6242 1 chr2D.!!$F2 721
5 TraesCS2D01G512900 chr2B 734915970 734921883 5913 False 2270.50 6890 93.888250 460 6565 4 chr2B.!!$F4 6105
6 TraesCS2D01G512900 chr2B 734940787 734953378 12591 False 1896.00 5156 94.471600 460 6565 5 chr2B.!!$F5 6105
7 TraesCS2D01G512900 chr2B 759347236 759347976 740 False 518.00 518 79.548000 3892 4635 1 chr2B.!!$F3 743
8 TraesCS2D01G512900 chr2B 390392935 390393649 714 False 479.00 479 79.092000 5521 6236 1 chr2B.!!$F1 715
9 TraesCS2D01G512900 chr2A 736034665 736040514 5849 False 2394.35 6087 93.782250 636 6565 4 chr2A.!!$F4 5929
10 TraesCS2D01G512900 chr2A 751233178 751234785 1607 False 774.00 774 75.847000 3040 4663 1 chr2A.!!$F3 1623
11 TraesCS2D01G512900 chr2A 751208989 751210569 1580 False 675.00 675 74.923000 3043 4646 1 chr2A.!!$F2 1603
12 TraesCS2D01G512900 chr2A 719729714 719730479 765 True 206.00 206 72.370000 3036 3800 1 chr2A.!!$R1 764
13 TraesCS2D01G512900 chr3B 429529414 429529953 539 True 409.00 409 80.443000 5553 6090 1 chr3B.!!$R1 537
14 TraesCS2D01G512900 chr6A 534037097 534037733 636 False 279.00 279 75.039000 5521 6157 1 chr6A.!!$F1 636

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
603 606 0.107410 TGTACTAAATGGGCTGGCCG 60.107 55.000 16.08 3.10 36.85 6.13 F
1445 4019 1.338105 CCTCATCGACTGCCTCAACAA 60.338 52.381 0.00 0.00 0.00 2.83 F
2061 4643 0.895530 ATTGTCGACGACTGGATGGT 59.104 50.000 26.86 4.42 33.15 3.55 F
2563 5163 1.493772 TCGTTTCCTGCGTAACAGTG 58.506 50.000 0.00 0.00 45.68 3.66 F
2572 5172 1.901650 GCGTAACAGTGCCAGCTCAC 61.902 60.000 0.00 0.00 37.24 3.51 F
4345 12841 1.045407 TGACTCACCAAGCCTTACGT 58.955 50.000 0.00 0.00 0.00 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 4318 1.596752 TTGCGACGACCAATGCAGT 60.597 52.632 0.00 0.0 38.75 4.40 R
2563 5163 2.231215 ACAAGATATCGTGAGCTGGC 57.769 50.000 23.09 0.0 0.00 4.85 R
3609 8113 1.442769 TTGAACTCATCAGCCGCTTC 58.557 50.000 0.00 0.0 39.77 3.86 R
4209 12705 1.656652 CTTCCATTGCGTACTCAGGG 58.343 55.000 0.00 0.0 0.00 4.45 R
4375 12874 9.643693 AGTTATTATGATGCTTTGAGTTTTTGG 57.356 29.630 0.00 0.0 0.00 3.28 R
5634 14512 0.972134 ATGAGATCGGATGGCGATGT 59.028 50.000 0.00 0.0 0.00 3.06 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
48 49 9.506018 AAAAAGTATGGCAATTTTGAAATAGCT 57.494 25.926 8.57 0.00 0.00 3.32
49 50 8.707938 AAAGTATGGCAATTTTGAAATAGCTC 57.292 30.769 0.00 0.00 0.00 4.09
50 51 7.408756 AGTATGGCAATTTTGAAATAGCTCA 57.591 32.000 0.00 0.00 0.00 4.26
51 52 8.015185 AGTATGGCAATTTTGAAATAGCTCAT 57.985 30.769 0.00 0.00 0.00 2.90
52 53 8.480501 AGTATGGCAATTTTGAAATAGCTCATT 58.519 29.630 0.00 0.00 0.00 2.57
53 54 7.781548 ATGGCAATTTTGAAATAGCTCATTC 57.218 32.000 0.00 0.00 0.00 2.67
54 55 6.699366 TGGCAATTTTGAAATAGCTCATTCA 58.301 32.000 9.40 9.40 33.93 2.57
55 56 7.160049 TGGCAATTTTGAAATAGCTCATTCAA 58.840 30.769 18.04 18.04 42.17 2.69
56 57 7.825270 TGGCAATTTTGAAATAGCTCATTCAAT 59.175 29.630 20.97 9.73 43.04 2.57
57 58 8.671028 GGCAATTTTGAAATAGCTCATTCAATT 58.329 29.630 20.97 13.72 43.04 2.32
215 216 9.587772 TTACAAATTTGAAGAAAAATTCACCGA 57.412 25.926 24.64 0.00 38.49 4.69
216 217 8.661352 ACAAATTTGAAGAAAAATTCACCGAT 57.339 26.923 24.64 0.00 38.49 4.18
217 218 9.757227 ACAAATTTGAAGAAAAATTCACCGATA 57.243 25.926 24.64 0.00 38.49 2.92
249 250 9.825109 AAAAATTCATCGGTTTAGAAGGAAAAA 57.175 25.926 0.00 0.00 0.00 1.94
276 277 8.110860 TCAGGAATTCATAAAAGAAGTTCACC 57.889 34.615 7.93 0.00 0.00 4.02
277 278 7.023575 CAGGAATTCATAAAAGAAGTTCACCG 58.976 38.462 7.93 0.00 0.00 4.94
278 279 6.940298 AGGAATTCATAAAAGAAGTTCACCGA 59.060 34.615 7.93 0.00 0.00 4.69
279 280 7.611855 AGGAATTCATAAAAGAAGTTCACCGAT 59.388 33.333 7.93 0.00 0.00 4.18
280 281 8.244113 GGAATTCATAAAAGAAGTTCACCGATT 58.756 33.333 7.93 0.00 0.00 3.34
281 282 9.626045 GAATTCATAAAAGAAGTTCACCGATTT 57.374 29.630 5.50 1.59 0.00 2.17
282 283 9.981114 AATTCATAAAAGAAGTTCACCGATTTT 57.019 25.926 5.50 5.47 0.00 1.82
283 284 8.795786 TTCATAAAAGAAGTTCACCGATTTTG 57.204 30.769 5.50 0.00 0.00 2.44
284 285 8.160521 TCATAAAAGAAGTTCACCGATTTTGA 57.839 30.769 5.50 1.59 0.00 2.69
285 286 8.625651 TCATAAAAGAAGTTCACCGATTTTGAA 58.374 29.630 5.50 0.00 0.00 2.69
286 287 9.410556 CATAAAAGAAGTTCACCGATTTTGAAT 57.589 29.630 5.50 0.00 35.47 2.57
288 289 8.797266 AAAAGAAGTTCACCGATTTTGAATAC 57.203 30.769 5.50 0.00 35.47 1.89
289 290 7.504924 AAGAAGTTCACCGATTTTGAATACA 57.495 32.000 5.50 0.00 35.47 2.29
290 291 7.504924 AGAAGTTCACCGATTTTGAATACAA 57.495 32.000 5.50 0.00 35.47 2.41
291 292 7.936584 AGAAGTTCACCGATTTTGAATACAAA 58.063 30.769 5.50 0.00 43.10 2.83
331 332 9.502145 GAAAAGTTTGCAAATTTAAGGAAAAGG 57.498 29.630 18.82 0.00 0.00 3.11
332 333 8.800370 AAAGTTTGCAAATTTAAGGAAAAGGA 57.200 26.923 18.82 0.00 0.00 3.36
333 334 8.978874 AAGTTTGCAAATTTAAGGAAAAGGAT 57.021 26.923 17.29 0.00 0.00 3.24
385 386 9.996554 AAAAAGGAGAGAAAAAGAACAAGAAAA 57.003 25.926 0.00 0.00 0.00 2.29
386 387 9.996554 AAAAGGAGAGAAAAAGAACAAGAAAAA 57.003 25.926 0.00 0.00 0.00 1.94
387 388 9.645059 AAAGGAGAGAAAAAGAACAAGAAAAAG 57.355 29.630 0.00 0.00 0.00 2.27
388 389 7.776107 AGGAGAGAAAAAGAACAAGAAAAAGG 58.224 34.615 0.00 0.00 0.00 3.11
389 390 7.615757 AGGAGAGAAAAAGAACAAGAAAAAGGA 59.384 33.333 0.00 0.00 0.00 3.36
390 391 8.251026 GGAGAGAAAAAGAACAAGAAAAAGGAA 58.749 33.333 0.00 0.00 0.00 3.36
391 392 9.639601 GAGAGAAAAAGAACAAGAAAAAGGAAA 57.360 29.630 0.00 0.00 0.00 3.13
392 393 9.996554 AGAGAAAAAGAACAAGAAAAAGGAAAA 57.003 25.926 0.00 0.00 0.00 2.29
415 416 7.533289 AAAAGAAAACCCGAATTAAGATCCA 57.467 32.000 0.00 0.00 0.00 3.41
416 417 6.510879 AAGAAAACCCGAATTAAGATCCAC 57.489 37.500 0.00 0.00 0.00 4.02
417 418 4.634443 AGAAAACCCGAATTAAGATCCACG 59.366 41.667 0.00 0.00 0.00 4.94
418 419 1.949465 ACCCGAATTAAGATCCACGC 58.051 50.000 0.00 0.00 0.00 5.34
419 420 0.859232 CCCGAATTAAGATCCACGCG 59.141 55.000 3.53 3.53 0.00 6.01
420 421 0.859232 CCGAATTAAGATCCACGCGG 59.141 55.000 12.47 0.00 0.00 6.46
429 430 2.029964 TCCACGCGGAAACTGTCC 59.970 61.111 12.47 0.00 43.90 4.02
437 438 2.244946 GGAAACTGTCCAGCGAACC 58.755 57.895 0.00 0.00 46.97 3.62
438 439 1.566018 GGAAACTGTCCAGCGAACCG 61.566 60.000 0.00 0.00 46.97 4.44
439 440 1.566018 GAAACTGTCCAGCGAACCGG 61.566 60.000 0.00 0.00 0.00 5.28
440 441 3.530910 AACTGTCCAGCGAACCGGG 62.531 63.158 6.32 0.00 0.00 5.73
441 442 3.691342 CTGTCCAGCGAACCGGGA 61.691 66.667 6.32 0.00 35.29 5.14
442 443 3.234630 CTGTCCAGCGAACCGGGAA 62.235 63.158 6.32 0.00 39.60 3.97
443 444 2.031465 GTCCAGCGAACCGGGAAA 59.969 61.111 6.32 0.00 39.60 3.13
444 445 1.598685 GTCCAGCGAACCGGGAAAA 60.599 57.895 6.32 0.00 39.60 2.29
445 446 0.958876 GTCCAGCGAACCGGGAAAAT 60.959 55.000 6.32 0.00 39.60 1.82
446 447 0.675522 TCCAGCGAACCGGGAAAATC 60.676 55.000 6.32 0.00 34.70 2.17
447 448 1.654023 CCAGCGAACCGGGAAAATCC 61.654 60.000 6.32 0.00 35.23 3.01
454 455 4.218722 CGGGAAAATCCGGTCTGG 57.781 61.111 0.00 0.00 45.78 3.86
455 456 1.451387 CGGGAAAATCCGGTCTGGG 60.451 63.158 0.00 0.00 45.78 4.45
456 457 1.906105 CGGGAAAATCCGGTCTGGGA 61.906 60.000 0.00 0.00 45.78 4.37
457 458 0.330267 GGGAAAATCCGGTCTGGGAA 59.670 55.000 0.00 0.00 40.09 3.97
458 459 1.272258 GGGAAAATCCGGTCTGGGAAA 60.272 52.381 0.00 0.00 40.09 3.13
563 566 4.097286 CCTAGGTTACTGCTGTCTTCTCTC 59.903 50.000 0.00 0.00 0.00 3.20
603 606 0.107410 TGTACTAAATGGGCTGGCCG 60.107 55.000 16.08 3.10 36.85 6.13
1117 3691 1.407618 CATTCTGGATCGACACGGGTA 59.592 52.381 0.00 0.00 0.00 3.69
1445 4019 1.338105 CCTCATCGACTGCCTCAACAA 60.338 52.381 0.00 0.00 0.00 2.83
1744 4318 1.879380 GTGTGACAAATGCTAGTGCCA 59.121 47.619 0.00 0.00 38.71 4.92
1762 4336 1.596752 ACTGCATTGGTCGTCGCAA 60.597 52.632 0.00 0.00 33.21 4.85
1911 4485 2.726850 GAACTTGGCGCAAACGGTCC 62.727 60.000 10.83 0.00 40.57 4.46
1979 4560 1.733360 GGCTTTGGCGTGTAAATACGA 59.267 47.619 3.30 0.00 46.46 3.43
2061 4643 0.895530 ATTGTCGACGACTGGATGGT 59.104 50.000 26.86 4.42 33.15 3.55
2194 4779 6.077322 CACATATAACCCCTGAATCCCAATT 58.923 40.000 0.00 0.00 0.00 2.32
2530 5129 5.885230 TTTTCCTGCTACTTGATGTCATG 57.115 39.130 0.00 0.00 0.00 3.07
2563 5163 1.493772 TCGTTTCCTGCGTAACAGTG 58.506 50.000 0.00 0.00 45.68 3.66
2572 5172 1.901650 GCGTAACAGTGCCAGCTCAC 61.902 60.000 0.00 0.00 37.24 3.51
4209 12705 2.147958 TCAAACAGCGGTTACATGTCC 58.852 47.619 0.00 0.00 35.82 4.02
4345 12841 1.045407 TGACTCACCAAGCCTTACGT 58.955 50.000 0.00 0.00 0.00 3.57
4664 13163 1.673767 ACCATGGAACAGGAGACCAT 58.326 50.000 21.47 0.00 46.40 3.55
4882 13385 4.160642 TCGGTAGTAGTTCCTGCATCTA 57.839 45.455 0.00 0.00 0.00 1.98
5032 13537 6.215495 TGGTATTTTTGTATAAAGGCTGGC 57.785 37.500 0.00 0.00 0.00 4.85
5338 14212 5.277250 TGAAGATGATAGGTCCCAACACTA 58.723 41.667 0.00 0.00 0.00 2.74
5368 14242 0.033504 TGCCGACTTCAGTCTCCAAC 59.966 55.000 5.44 0.00 42.66 3.77
5472 14348 4.797693 TTTGAATTTTGTGCAGTGCATG 57.202 36.364 22.87 0.00 41.91 4.06
5496 14372 7.345691 TGTGTTGATTTACCTGATACCATCAT 58.654 34.615 0.00 0.00 38.85 2.45
5579 14456 3.536956 AAGTGACCTCAAACGAAGACA 57.463 42.857 0.00 0.00 0.00 3.41
5634 14512 6.064060 ACATGAACATCTTTGAAGTCTTGGA 58.936 36.000 0.00 0.00 0.00 3.53
5912 14797 5.221601 CCATATGAGTGTCTGATGGTTAGCT 60.222 44.000 3.65 0.00 33.72 3.32
6207 15097 6.014070 TCCAGCCGCCTTTTATATACATAAGA 60.014 38.462 0.00 0.00 0.00 2.10
6221 15111 4.491234 ACATAAGAGATGACGACCGATC 57.509 45.455 0.00 0.00 0.00 3.69
6255 15145 6.364165 AGCACAAAATCGAACAAATCAATCTG 59.636 34.615 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.506018 AGCTATTTCAAAATTGCCATACTTTTT 57.494 25.926 15.15 0.00 44.49 1.94
23 24 9.154847 GAGCTATTTCAAAATTGCCATACTTTT 57.845 29.630 15.15 0.00 44.49 2.27
24 25 8.313292 TGAGCTATTTCAAAATTGCCATACTTT 58.687 29.630 15.15 0.00 44.49 2.66
25 26 7.839907 TGAGCTATTTCAAAATTGCCATACTT 58.160 30.769 15.15 0.36 44.49 2.24
26 27 7.408756 TGAGCTATTTCAAAATTGCCATACT 57.591 32.000 15.15 0.93 44.49 2.12
27 28 8.652810 AATGAGCTATTTCAAAATTGCCATAC 57.347 30.769 15.15 7.94 44.49 2.39
28 29 8.476447 TGAATGAGCTATTTCAAAATTGCCATA 58.524 29.630 15.15 5.86 44.49 2.74
29 30 7.332557 TGAATGAGCTATTTCAAAATTGCCAT 58.667 30.769 15.15 14.48 44.49 4.40
30 31 6.699366 TGAATGAGCTATTTCAAAATTGCCA 58.301 32.000 15.15 13.31 44.49 4.92
31 32 7.599630 TTGAATGAGCTATTTCAAAATTGCC 57.400 32.000 16.97 9.45 44.49 4.52
189 190 9.587772 TCGGTGAATTTTTCTTCAAATTTGTAA 57.412 25.926 17.47 9.76 36.64 2.41
190 191 9.757227 ATCGGTGAATTTTTCTTCAAATTTGTA 57.243 25.926 17.47 7.68 36.64 2.41
191 192 8.661352 ATCGGTGAATTTTTCTTCAAATTTGT 57.339 26.923 17.47 0.00 36.64 2.83
223 224 9.825109 TTTTTCCTTCTAAACCGATGAATTTTT 57.175 25.926 0.00 0.00 0.00 1.94
250 251 8.743714 GGTGAACTTCTTTTATGAATTCCTGAT 58.256 33.333 2.27 0.00 0.00 2.90
251 252 7.094805 CGGTGAACTTCTTTTATGAATTCCTGA 60.095 37.037 2.27 0.00 0.00 3.86
252 253 7.023575 CGGTGAACTTCTTTTATGAATTCCTG 58.976 38.462 2.27 0.00 0.00 3.86
253 254 6.940298 TCGGTGAACTTCTTTTATGAATTCCT 59.060 34.615 2.27 0.00 0.00 3.36
254 255 7.141100 TCGGTGAACTTCTTTTATGAATTCC 57.859 36.000 2.27 0.00 0.00 3.01
255 256 9.626045 AAATCGGTGAACTTCTTTTATGAATTC 57.374 29.630 0.00 0.00 0.00 2.17
256 257 9.981114 AAAATCGGTGAACTTCTTTTATGAATT 57.019 25.926 0.00 0.00 0.00 2.17
257 258 9.410556 CAAAATCGGTGAACTTCTTTTATGAAT 57.589 29.630 0.00 0.00 0.00 2.57
258 259 8.625651 TCAAAATCGGTGAACTTCTTTTATGAA 58.374 29.630 0.00 0.00 0.00 2.57
259 260 8.160521 TCAAAATCGGTGAACTTCTTTTATGA 57.839 30.769 0.00 0.00 0.00 2.15
260 261 8.795786 TTCAAAATCGGTGAACTTCTTTTATG 57.204 30.769 0.00 0.00 30.08 1.90
262 263 9.887406 GTATTCAAAATCGGTGAACTTCTTTTA 57.113 29.630 0.00 0.00 37.80 1.52
263 264 8.410141 TGTATTCAAAATCGGTGAACTTCTTTT 58.590 29.630 0.00 0.00 37.80 2.27
264 265 7.936584 TGTATTCAAAATCGGTGAACTTCTTT 58.063 30.769 0.00 0.00 37.80 2.52
265 266 7.504924 TGTATTCAAAATCGGTGAACTTCTT 57.495 32.000 0.00 0.00 37.80 2.52
266 267 7.504924 TTGTATTCAAAATCGGTGAACTTCT 57.495 32.000 0.00 0.00 37.80 2.85
267 268 8.568732 TTTTGTATTCAAAATCGGTGAACTTC 57.431 30.769 6.17 0.00 45.03 3.01
305 306 9.502145 CCTTTTCCTTAAATTTGCAAACTTTTC 57.498 29.630 15.41 0.00 0.00 2.29
306 307 9.237187 TCCTTTTCCTTAAATTTGCAAACTTTT 57.763 25.926 15.41 14.32 0.00 2.27
307 308 8.800370 TCCTTTTCCTTAAATTTGCAAACTTT 57.200 26.923 15.41 16.87 0.00 2.66
308 309 8.978874 ATCCTTTTCCTTAAATTTGCAAACTT 57.021 26.923 15.41 13.02 0.00 2.66
359 360 9.996554 TTTTCTTGTTCTTTTTCTCTCCTTTTT 57.003 25.926 0.00 0.00 0.00 1.94
360 361 9.996554 TTTTTCTTGTTCTTTTTCTCTCCTTTT 57.003 25.926 0.00 0.00 0.00 2.27
361 362 9.645059 CTTTTTCTTGTTCTTTTTCTCTCCTTT 57.355 29.630 0.00 0.00 0.00 3.11
362 363 8.253810 CCTTTTTCTTGTTCTTTTTCTCTCCTT 58.746 33.333 0.00 0.00 0.00 3.36
363 364 7.615757 TCCTTTTTCTTGTTCTTTTTCTCTCCT 59.384 33.333 0.00 0.00 0.00 3.69
364 365 7.772166 TCCTTTTTCTTGTTCTTTTTCTCTCC 58.228 34.615 0.00 0.00 0.00 3.71
365 366 9.639601 TTTCCTTTTTCTTGTTCTTTTTCTCTC 57.360 29.630 0.00 0.00 0.00 3.20
366 367 9.996554 TTTTCCTTTTTCTTGTTCTTTTTCTCT 57.003 25.926 0.00 0.00 0.00 3.10
390 391 7.870954 GTGGATCTTAATTCGGGTTTTCTTTTT 59.129 33.333 0.00 0.00 0.00 1.94
391 392 7.375834 GTGGATCTTAATTCGGGTTTTCTTTT 58.624 34.615 0.00 0.00 0.00 2.27
392 393 6.349033 CGTGGATCTTAATTCGGGTTTTCTTT 60.349 38.462 0.00 0.00 0.00 2.52
393 394 5.123344 CGTGGATCTTAATTCGGGTTTTCTT 59.877 40.000 0.00 0.00 0.00 2.52
394 395 4.634443 CGTGGATCTTAATTCGGGTTTTCT 59.366 41.667 0.00 0.00 0.00 2.52
395 396 4.729746 GCGTGGATCTTAATTCGGGTTTTC 60.730 45.833 0.00 0.00 0.00 2.29
396 397 3.128068 GCGTGGATCTTAATTCGGGTTTT 59.872 43.478 0.00 0.00 0.00 2.43
397 398 2.681344 GCGTGGATCTTAATTCGGGTTT 59.319 45.455 0.00 0.00 0.00 3.27
398 399 2.285977 GCGTGGATCTTAATTCGGGTT 58.714 47.619 0.00 0.00 0.00 4.11
399 400 1.805120 CGCGTGGATCTTAATTCGGGT 60.805 52.381 0.00 0.00 0.00 5.28
400 401 0.859232 CGCGTGGATCTTAATTCGGG 59.141 55.000 0.00 0.00 0.00 5.14
401 402 0.859232 CCGCGTGGATCTTAATTCGG 59.141 55.000 10.20 0.00 37.49 4.30
402 403 1.847818 TCCGCGTGGATCTTAATTCG 58.152 50.000 15.21 0.00 40.17 3.34
403 404 3.621715 AGTTTCCGCGTGGATCTTAATTC 59.378 43.478 20.33 0.00 45.91 2.17
404 405 3.374058 CAGTTTCCGCGTGGATCTTAATT 59.626 43.478 20.33 3.83 45.91 1.40
405 406 2.936498 CAGTTTCCGCGTGGATCTTAAT 59.064 45.455 20.33 1.30 45.91 1.40
406 407 2.289195 ACAGTTTCCGCGTGGATCTTAA 60.289 45.455 20.33 7.19 45.91 1.85
407 408 1.274167 ACAGTTTCCGCGTGGATCTTA 59.726 47.619 20.33 0.00 45.91 2.10
408 409 0.034896 ACAGTTTCCGCGTGGATCTT 59.965 50.000 20.33 4.11 45.91 2.40
409 410 0.389948 GACAGTTTCCGCGTGGATCT 60.390 55.000 20.33 16.93 45.91 2.75
410 411 1.359459 GGACAGTTTCCGCGTGGATC 61.359 60.000 20.33 12.75 45.91 3.36
411 412 1.375523 GGACAGTTTCCGCGTGGAT 60.376 57.895 20.33 2.48 45.91 3.41
412 413 2.029964 GGACAGTTTCCGCGTGGA 59.970 61.111 15.21 15.21 44.61 4.02
419 420 1.566018 CGGTTCGCTGGACAGTTTCC 61.566 60.000 0.82 0.00 46.13 3.13
420 421 1.566018 CCGGTTCGCTGGACAGTTTC 61.566 60.000 0.00 0.00 46.74 2.78
421 422 1.597027 CCGGTTCGCTGGACAGTTT 60.597 57.895 0.00 0.00 46.74 2.66
422 423 2.030562 CCGGTTCGCTGGACAGTT 59.969 61.111 0.00 0.00 46.74 3.16
423 424 4.003788 CCCGGTTCGCTGGACAGT 62.004 66.667 0.00 0.00 46.74 3.55
424 425 2.725203 TTTCCCGGTTCGCTGGACAG 62.725 60.000 0.00 0.00 46.74 3.51
425 426 2.326773 TTTTCCCGGTTCGCTGGACA 62.327 55.000 0.00 0.00 46.74 4.02
426 427 0.958876 ATTTTCCCGGTTCGCTGGAC 60.959 55.000 0.00 0.00 46.74 4.02
427 428 0.675522 GATTTTCCCGGTTCGCTGGA 60.676 55.000 0.00 0.00 46.74 3.86
428 429 1.654023 GGATTTTCCCGGTTCGCTGG 61.654 60.000 0.00 0.00 43.38 4.85
429 430 1.800681 GGATTTTCCCGGTTCGCTG 59.199 57.895 0.00 0.00 0.00 5.18
430 431 1.743995 CGGATTTTCCCGGTTCGCT 60.744 57.895 0.00 0.00 45.43 4.93
431 432 2.789249 CGGATTTTCCCGGTTCGC 59.211 61.111 0.00 0.00 45.43 4.70
438 439 0.330267 TTCCCAGACCGGATTTTCCC 59.670 55.000 9.46 0.00 36.56 3.97
439 440 1.816835 GTTTCCCAGACCGGATTTTCC 59.183 52.381 9.46 0.00 36.56 3.13
440 441 2.791655 AGTTTCCCAGACCGGATTTTC 58.208 47.619 9.46 0.00 36.56 2.29
441 442 2.971901 AGTTTCCCAGACCGGATTTT 57.028 45.000 9.46 0.00 36.56 1.82
442 443 2.971901 AAGTTTCCCAGACCGGATTT 57.028 45.000 9.46 0.00 36.56 2.17
443 444 2.971901 AAAGTTTCCCAGACCGGATT 57.028 45.000 9.46 0.00 36.56 3.01
444 445 2.971901 AAAAGTTTCCCAGACCGGAT 57.028 45.000 9.46 0.00 36.56 4.18
445 446 2.740506 AAAAAGTTTCCCAGACCGGA 57.259 45.000 9.46 0.00 36.56 5.14
446 447 4.922471 TTTAAAAAGTTTCCCAGACCGG 57.078 40.909 0.00 0.00 0.00 5.28
447 448 5.045215 GGTTTTAAAAAGTTTCCCAGACCG 58.955 41.667 1.31 0.00 0.00 4.79
448 449 5.979993 TGGTTTTAAAAAGTTTCCCAGACC 58.020 37.500 1.31 0.00 0.00 3.85
449 450 6.537301 CCTTGGTTTTAAAAAGTTTCCCAGAC 59.463 38.462 1.31 0.00 0.00 3.51
450 451 6.352308 CCCTTGGTTTTAAAAAGTTTCCCAGA 60.352 38.462 1.31 0.00 0.00 3.86
451 452 5.820423 CCCTTGGTTTTAAAAAGTTTCCCAG 59.180 40.000 1.31 1.04 0.00 4.45
452 453 5.746284 CCCTTGGTTTTAAAAAGTTTCCCA 58.254 37.500 1.31 2.00 0.00 4.37
453 454 4.577283 GCCCTTGGTTTTAAAAAGTTTCCC 59.423 41.667 1.31 0.00 0.00 3.97
454 455 5.433526 AGCCCTTGGTTTTAAAAAGTTTCC 58.566 37.500 1.31 0.00 0.00 3.13
455 456 6.995511 AAGCCCTTGGTTTTAAAAAGTTTC 57.004 33.333 1.31 0.00 0.00 2.78
456 457 6.376018 GGAAAGCCCTTGGTTTTAAAAAGTTT 59.624 34.615 1.31 0.00 41.99 2.66
457 458 5.883673 GGAAAGCCCTTGGTTTTAAAAAGTT 59.116 36.000 1.31 0.00 41.99 2.66
458 459 5.433526 GGAAAGCCCTTGGTTTTAAAAAGT 58.566 37.500 1.31 0.00 41.99 2.66
525 526 1.940613 CCTAGGCCATGTTAACGCTTC 59.059 52.381 5.01 0.00 0.00 3.86
603 606 2.433318 GCACCACACTCCTCGCTC 60.433 66.667 0.00 0.00 0.00 5.03
607 610 0.034337 TAAACGGCACCACACTCCTC 59.966 55.000 0.00 0.00 0.00 3.71
612 615 1.958417 CGAATTAAACGGCACCACAC 58.042 50.000 0.00 0.00 0.00 3.82
1260 3834 1.602605 TGAGAAGACGCCGAGGTCA 60.603 57.895 0.00 0.00 39.42 4.02
1445 4019 1.664965 GTGCTCTTGCGTTCCTCGT 60.665 57.895 0.00 0.00 43.34 4.18
1476 4050 4.124351 TACGGGAGCAAGTCGCCG 62.124 66.667 0.00 0.00 44.04 6.46
1744 4318 1.596752 TTGCGACGACCAATGCAGT 60.597 52.632 0.00 0.00 38.75 4.40
1762 4336 2.165030 CGTACGTACCTGGAGATTTGGT 59.835 50.000 19.67 0.00 37.83 3.67
1911 4485 2.032030 CCACAAGTTCTAGCACCAAACG 60.032 50.000 0.00 0.00 0.00 3.60
1979 4560 3.375922 CAGTGTACGGCCGGAATTTTTAT 59.624 43.478 31.76 7.29 0.00 1.40
2061 4643 3.333219 CAGCAGGGCCCCTCTTGA 61.333 66.667 21.43 0.00 0.00 3.02
2169 4752 4.051478 TGGGATTCAGGGGTTATATGTGT 58.949 43.478 0.00 0.00 0.00 3.72
2170 4753 4.722526 TGGGATTCAGGGGTTATATGTG 57.277 45.455 0.00 0.00 0.00 3.21
2194 4779 2.231721 TCGAATCCGGTCATACACACAA 59.768 45.455 0.00 0.00 36.24 3.33
2312 4897 5.390991 GCAGGTTAACTAAATGCTCTGTCAC 60.391 44.000 5.42 0.00 34.10 3.67
2530 5129 5.347635 GCAGGAAACGATATTTCAAAAACCC 59.652 40.000 0.00 0.00 0.00 4.11
2563 5163 2.231215 ACAAGATATCGTGAGCTGGC 57.769 50.000 23.09 0.00 0.00 4.85
2923 7408 9.150348 GACTTTACCATCCAAAAATACCAAATG 57.850 33.333 0.00 0.00 0.00 2.32
3609 8113 1.442769 TTGAACTCATCAGCCGCTTC 58.557 50.000 0.00 0.00 39.77 3.86
3750 8254 7.295340 AGTTAGAACATACCAAAAAGGAAGGT 58.705 34.615 0.00 0.00 41.22 3.50
3803 8308 7.872483 AGTTTTGCAAGAAGTCTTCAAAAGAAA 59.128 29.630 14.97 7.21 39.94 2.52
4209 12705 1.656652 CTTCCATTGCGTACTCAGGG 58.343 55.000 0.00 0.00 0.00 4.45
4375 12874 9.643693 AGTTATTATGATGCTTTGAGTTTTTGG 57.356 29.630 0.00 0.00 0.00 3.28
4664 13163 2.158623 GGACATGCCCACATTATCTCCA 60.159 50.000 0.00 0.00 32.87 3.86
4873 13376 4.946157 AGACAAGGTGAAAATAGATGCAGG 59.054 41.667 0.00 0.00 0.00 4.85
4882 13385 6.187727 TCTTCCACTAGACAAGGTGAAAAT 57.812 37.500 0.00 0.00 35.69 1.82
4980 13485 6.020599 CAGAACTTCATACCGAATGACTAACG 60.021 42.308 0.49 0.00 44.42 3.18
5032 13537 9.748708 TCCAACTCTGAAAAATATGAACTTTTG 57.251 29.630 0.00 0.00 0.00 2.44
5338 14212 2.224670 TGAAGTCGGCACCCAATTAAGT 60.225 45.455 0.00 0.00 0.00 2.24
5472 14348 7.807977 ATGATGGTATCAGGTAAATCAACAC 57.192 36.000 0.00 0.00 43.53 3.32
5579 14456 8.798859 ATACAAAACTTCTTCATGTAGAGCAT 57.201 30.769 2.09 0.00 38.60 3.79
5634 14512 0.972134 ATGAGATCGGATGGCGATGT 59.028 50.000 0.00 0.00 0.00 3.06
5912 14797 3.637432 CGCAAAACAGGCAATAACTCAA 58.363 40.909 0.00 0.00 0.00 3.02
6221 15111 5.623264 TGTTCGATTTTGTGCTGTTATTTCG 59.377 36.000 0.00 0.00 0.00 3.46
6255 15145 8.635877 AGATAGATGAACACGAAAAGTATGAC 57.364 34.615 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.