Multiple sequence alignment - TraesCS3B01G362600

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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 TraesCS3B01G362600 chr3B 100.000 3264 0 0 1 3264 574265488 574268751 0.000000e+00 6028
1 TraesCS3B01G362600 chr3D 89.514 1440 88 26 1 1391 438469879 438471304 0.000000e+00 1764
2 TraesCS3B01G362600 chr3D 90.891 1010 50 14 1388 2378 438471334 438472320 0.000000e+00 1317
3 TraesCS3B01G362600 chr3D 90.000 890 81 7 2379 3264 497381982 497382867 0.000000e+00 1144
4 TraesCS3B01G362600 chr3A 93.193 999 51 13 1388 2378 577066547 577067536 0.000000e+00 1452
5 TraesCS3B01G362600 chr3A 88.934 985 77 11 432 1391 577065540 577066517 0.000000e+00 1186
6 TraesCS3B01G362600 chr3A 93.009 329 17 2 1 329 577065222 577065544 2.950000e-130 475
7 TraesCS3B01G362600 chr2A 91.134 891 66 9 2379 3264 765659175 765658293 0.000000e+00 1195
8 TraesCS3B01G362600 chr6B 90.899 890 73 4 2379 3261 9195845 9196733 0.000000e+00 1188
9 TraesCS3B01G362600 chr6B 90.247 892 80 7 2375 3264 133170896 133171782 0.000000e+00 1158
10 TraesCS3B01G362600 chr5D 90.991 888 69 10 2379 3264 550650523 550651401 0.000000e+00 1186
11 TraesCS3B01G362600 chr7D 89.597 894 81 9 2379 3264 31420500 31419611 0.000000e+00 1125
12 TraesCS3B01G362600 chr1D 89.485 894 81 7 2379 3264 4202710 4203598 0.000000e+00 1118
13 TraesCS3B01G362600 chr1D 89.539 889 83 7 2379 3264 303230169 303229288 0.000000e+00 1118
14 TraesCS3B01G362600 chr4D 89.397 896 81 11 2377 3264 467208736 467207847 0.000000e+00 1116


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 TraesCS3B01G362600 chr3B 574265488 574268751 3263 False 6028.000000 6028 100.0000 1 3264 1 chr3B.!!$F1 3263
1 TraesCS3B01G362600 chr3D 438469879 438472320 2441 False 1540.500000 1764 90.2025 1 2378 2 chr3D.!!$F2 2377
2 TraesCS3B01G362600 chr3D 497381982 497382867 885 False 1144.000000 1144 90.0000 2379 3264 1 chr3D.!!$F1 885
3 TraesCS3B01G362600 chr3A 577065222 577067536 2314 False 1037.666667 1452 91.7120 1 2378 3 chr3A.!!$F1 2377
4 TraesCS3B01G362600 chr2A 765658293 765659175 882 True 1195.000000 1195 91.1340 2379 3264 1 chr2A.!!$R1 885
5 TraesCS3B01G362600 chr6B 9195845 9196733 888 False 1188.000000 1188 90.8990 2379 3261 1 chr6B.!!$F1 882
6 TraesCS3B01G362600 chr6B 133170896 133171782 886 False 1158.000000 1158 90.2470 2375 3264 1 chr6B.!!$F2 889
7 TraesCS3B01G362600 chr5D 550650523 550651401 878 False 1186.000000 1186 90.9910 2379 3264 1 chr5D.!!$F1 885
8 TraesCS3B01G362600 chr7D 31419611 31420500 889 True 1125.000000 1125 89.5970 2379 3264 1 chr7D.!!$R1 885
9 TraesCS3B01G362600 chr1D 4202710 4203598 888 False 1118.000000 1118 89.4850 2379 3264 1 chr1D.!!$F1 885
10 TraesCS3B01G362600 chr1D 303229288 303230169 881 True 1118.000000 1118 89.5390 2379 3264 1 chr1D.!!$R1 885
11 TraesCS3B01G362600 chr4D 467207847 467208736 889 True 1116.000000 1116 89.3970 2377 3264 1 chr4D.!!$R1 887

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
370 496 0.178068 GAATCGCCTGGTTAGCTCCA 59.822 55.0 0.0 0.0 36.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2295 2507 0.599728 CTAGAGATGCTCCAAGCGGC 60.6 60.0 0.0 0.0 46.26 6.53 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
154 155 2.554032 GGTTTGTGATCAGGTTCAGGTG 59.446 50.000 0.00 0.00 0.00 4.00
165 171 2.943033 AGGTTCAGGTGAAAAACAGACG 59.057 45.455 0.00 0.00 35.58 4.18
168 174 1.210967 TCAGGTGAAAAACAGACGGGT 59.789 47.619 0.00 0.00 0.00 5.28
169 175 2.021457 CAGGTGAAAAACAGACGGGTT 58.979 47.619 0.00 0.00 0.00 4.11
170 176 2.032924 CAGGTGAAAAACAGACGGGTTC 59.967 50.000 0.00 0.00 0.00 3.62
193 199 5.649395 TCTTCTTCTTCATCGATGGCAAATT 59.351 36.000 24.61 0.00 0.00 1.82
197 203 4.516323 TCTTCATCGATGGCAAATTGAGA 58.484 39.130 24.61 11.85 0.00 3.27
207 213 2.040544 AAATTGAGACGCTGCCGGG 61.041 57.895 2.18 0.00 39.22 5.73
213 219 4.700365 GACGCTGCCGGGTTTTGC 62.700 66.667 2.18 0.00 39.22 3.68
215 221 3.053291 CGCTGCCGGGTTTTGCTA 61.053 61.111 2.18 0.00 0.00 3.49
329 455 0.531200 GAGTACCCGAACTCCACCTG 59.469 60.000 0.00 0.00 40.06 4.00
330 456 1.079336 GTACCCGAACTCCACCTGC 60.079 63.158 0.00 0.00 0.00 4.85
331 457 2.642254 TACCCGAACTCCACCTGCG 61.642 63.158 0.00 0.00 0.00 5.18
332 458 4.760047 CCCGAACTCCACCTGCGG 62.760 72.222 0.00 0.00 41.53 5.69
333 459 3.691342 CCGAACTCCACCTGCGGA 61.691 66.667 0.00 0.00 44.43 5.54
334 460 2.342279 CGAACTCCACCTGCGGAA 59.658 61.111 0.00 0.00 33.65 4.30
335 461 1.301401 CGAACTCCACCTGCGGAAA 60.301 57.895 0.00 0.00 33.65 3.13
336 462 1.566018 CGAACTCCACCTGCGGAAAC 61.566 60.000 0.00 0.00 33.65 2.78
367 493 4.835927 CGAATCGCCTGGTTAGCT 57.164 55.556 0.00 0.00 0.00 3.32
368 494 2.594541 CGAATCGCCTGGTTAGCTC 58.405 57.895 0.00 0.00 0.00 4.09
369 495 0.876342 CGAATCGCCTGGTTAGCTCC 60.876 60.000 0.00 0.00 0.00 4.70
370 496 0.178068 GAATCGCCTGGTTAGCTCCA 59.822 55.000 0.00 0.00 36.00 3.86
375 501 4.192000 CTGGTTAGCTCCAGCGTG 57.808 61.111 8.43 0.00 46.53 5.34
376 502 1.293498 CTGGTTAGCTCCAGCGTGT 59.707 57.895 8.43 0.00 46.53 4.49
377 503 0.737715 CTGGTTAGCTCCAGCGTGTC 60.738 60.000 8.43 0.00 46.53 3.67
382 508 4.357947 GCTCCAGCGTGTCGTGGA 62.358 66.667 10.84 10.84 40.72 4.02
383 509 2.338620 CTCCAGCGTGTCGTGGAA 59.661 61.111 11.84 1.86 42.41 3.53
384 510 1.734477 CTCCAGCGTGTCGTGGAAG 60.734 63.158 11.84 5.89 42.41 3.46
385 511 2.738521 CCAGCGTGTCGTGGAAGG 60.739 66.667 5.37 0.00 35.67 3.46
386 512 3.414700 CAGCGTGTCGTGGAAGGC 61.415 66.667 0.00 0.00 0.00 4.35
387 513 4.681978 AGCGTGTCGTGGAAGGCC 62.682 66.667 0.00 0.00 0.00 5.19
389 515 4.351938 CGTGTCGTGGAAGGCCGA 62.352 66.667 0.00 0.00 36.79 5.54
390 516 2.029964 GTGTCGTGGAAGGCCGAA 59.970 61.111 0.00 0.00 36.79 4.30
391 517 2.029964 TGTCGTGGAAGGCCGAAC 59.970 61.111 0.00 0.00 36.79 3.95
392 518 3.110178 GTCGTGGAAGGCCGAACG 61.110 66.667 13.97 13.97 35.54 3.95
393 519 3.296836 TCGTGGAAGGCCGAACGA 61.297 61.111 17.40 17.40 39.43 3.85
394 520 2.809601 CGTGGAAGGCCGAACGAG 60.810 66.667 14.72 0.00 36.09 4.18
395 521 2.342648 GTGGAAGGCCGAACGAGT 59.657 61.111 0.00 0.00 36.79 4.18
396 522 1.737008 GTGGAAGGCCGAACGAGTC 60.737 63.158 0.00 0.00 36.79 3.36
404 530 3.796443 CGAACGAGTCGCCGAGGA 61.796 66.667 19.11 0.00 44.14 3.71
405 531 2.799371 GAACGAGTCGCCGAGGAT 59.201 61.111 13.59 0.00 0.00 3.24
406 532 1.139095 GAACGAGTCGCCGAGGATT 59.861 57.895 13.59 0.00 0.00 3.01
407 533 0.458025 GAACGAGTCGCCGAGGATTT 60.458 55.000 13.59 0.00 0.00 2.17
408 534 0.458025 AACGAGTCGCCGAGGATTTC 60.458 55.000 13.59 0.00 0.00 2.17
526 652 3.918220 CAGCAGCGCGTTCGATCC 61.918 66.667 8.43 0.00 38.10 3.36
540 666 1.751927 GATCCCAGCACAGCTTGGG 60.752 63.158 14.24 14.24 41.17 4.12
551 677 2.592308 GCTTGGGCTTCCGGAGAT 59.408 61.111 3.34 0.00 35.22 2.75
610 736 1.063616 CTGGATTCGTGCAGCTCATTG 59.936 52.381 0.00 0.00 0.00 2.82
638 769 1.992170 GCATGGAGCAGAAGCAAAAG 58.008 50.000 0.00 0.00 45.49 2.27
654 785 1.838073 AAAGTACCAGAGTGGCCGGG 61.838 60.000 2.18 0.00 42.67 5.73
745 879 2.490685 GGAGAGACGCGAAGGACC 59.509 66.667 15.93 6.89 0.00 4.46
856 994 1.674441 CACCTTATCCTCGACGTGCTA 59.326 52.381 0.00 0.00 0.00 3.49
991 1145 1.480954 TGGATAAGAGTGGCCGTTCTC 59.519 52.381 9.06 10.95 0.00 2.87
1000 1154 4.754667 GCCGTTCTCCCGACCCAC 62.755 72.222 0.00 0.00 0.00 4.61
1211 1372 4.270153 AGGGAGCTGGTGGTGGGA 62.270 66.667 0.00 0.00 0.00 4.37
1214 1375 2.829384 GGAGCTGGTGGTGGGAACA 61.829 63.158 0.00 0.00 38.70 3.18
1245 1406 1.660575 CTGTTCTCGGCGACAACGT 60.661 57.895 20.25 0.00 41.98 3.99
1420 1614 1.180029 GCAATCTGATGCACCCTGTT 58.820 50.000 0.00 0.00 45.70 3.16
1425 1619 2.715046 TCTGATGCACCCTGTTGATTC 58.285 47.619 0.00 0.00 0.00 2.52
1426 1620 2.040145 TCTGATGCACCCTGTTGATTCA 59.960 45.455 0.00 0.00 0.00 2.57
1437 1631 3.622163 CCTGTTGATTCATCAGCTGAGTC 59.378 47.826 22.96 16.38 40.17 3.36
1438 1632 3.603532 TGTTGATTCATCAGCTGAGTCC 58.396 45.455 22.96 9.59 39.28 3.85
1446 1640 1.597742 TCAGCTGAGTCCAGTTTTGC 58.402 50.000 13.74 0.00 42.35 3.68
1467 1661 4.705991 TGCTCATGAAATTCAGGCAATGTA 59.294 37.500 14.93 0.00 31.30 2.29
1473 1667 5.324409 TGAAATTCAGGCAATGTAGAACCT 58.676 37.500 0.00 0.00 0.00 3.50
1488 1682 6.182627 TGTAGAACCTTACGAGTTCATCCTA 58.817 40.000 6.44 0.00 44.91 2.94
1527 1721 0.673333 TGCGAGTGGCCAACATACTG 60.673 55.000 7.24 0.00 42.61 2.74
1811 2015 3.058224 GTCAACTTACTGATGGTGTTGCC 60.058 47.826 0.00 0.00 38.19 4.52
1898 2103 3.941188 CCACTGGCACTGACGGGT 61.941 66.667 0.00 0.00 0.00 5.28
1901 2106 2.358737 CTGGCACTGACGGGTTCC 60.359 66.667 0.00 0.00 0.00 3.62
1994 2199 0.095417 GGCAGTCGTCGCAAAAGATC 59.905 55.000 0.00 0.00 0.00 2.75
2040 2245 4.116961 CCAAATATGATTGCAGCAAGTGG 58.883 43.478 14.47 7.99 0.00 4.00
2041 2246 4.116961 CAAATATGATTGCAGCAAGTGGG 58.883 43.478 14.47 0.00 0.00 4.61
2080 2285 4.757354 CGCGCGGATTTGCTTGCA 62.757 61.111 24.84 0.00 0.00 4.08
2140 2347 4.378874 GCTTGGAACACTTGTAATGAGCTC 60.379 45.833 6.82 6.82 39.29 4.09
2176 2385 5.967088 AGGTGACTATAAGCTTGTACACTG 58.033 41.667 9.86 0.00 40.61 3.66
2215 2427 7.283127 GGTTATTCCAATGTACACACTGATCAT 59.717 37.037 0.00 0.00 35.97 2.45
2216 2428 6.688637 ATTCCAATGTACACACTGATCATG 57.311 37.500 0.00 0.00 0.00 3.07
2218 2430 5.803552 TCCAATGTACACACTGATCATGAA 58.196 37.500 0.00 0.00 0.00 2.57
2224 2436 7.509141 TGTACACACTGATCATGAACAATTT 57.491 32.000 7.13 0.00 0.00 1.82
2291 2503 1.678728 CCATGCACGTGAGGTACCATT 60.679 52.381 22.23 0.00 0.00 3.16
2292 2504 1.398041 CATGCACGTGAGGTACCATTG 59.602 52.381 22.23 3.22 0.00 2.82
2293 2505 0.953471 TGCACGTGAGGTACCATTGC 60.953 55.000 22.23 14.34 0.00 3.56
2294 2506 0.953471 GCACGTGAGGTACCATTGCA 60.953 55.000 22.23 3.63 31.86 4.08
2295 2507 1.078709 CACGTGAGGTACCATTGCAG 58.921 55.000 15.94 2.68 0.00 4.41
2296 2508 0.673644 ACGTGAGGTACCATTGCAGC 60.674 55.000 15.94 0.00 0.00 5.25
2329 2541 6.014669 AGCATCTCTAGCCGATCTCTTAAAAT 60.015 38.462 0.00 0.00 0.00 1.82
2339 2551 8.145122 AGCCGATCTCTTAAAATACTTTAGAGG 58.855 37.037 0.00 0.00 30.84 3.69
2342 2554 9.187455 CGATCTCTTAAAATACTTTAGAGGAGC 57.813 37.037 0.00 0.00 30.84 4.70
2382 2594 4.068599 GCCTAAATGGGATCTAGCTGTTC 58.931 47.826 0.00 0.00 36.00 3.18
2615 2844 2.436646 CGGCGCCATGACCTCTTT 60.437 61.111 28.98 0.00 0.00 2.52
2622 2851 1.945819 GCCATGACCTCTTTCGCTTCA 60.946 52.381 0.00 0.00 0.00 3.02
2655 2884 4.444838 CGGTCAATCCCCGCGTCA 62.445 66.667 4.92 0.00 38.85 4.35
2749 2980 2.898738 CTCCATGTCCTCAGCGCT 59.101 61.111 2.64 2.64 0.00 5.92
2794 3031 4.731612 CTCAGCACCAGTCGCGCT 62.732 66.667 5.56 0.00 36.10 5.92
2830 3068 2.037304 GCCCCCTCTGGATCCTCCTA 62.037 65.000 14.23 0.00 37.46 2.94
2846 3084 1.134310 TCCTAGACACTCGCCGTCATA 60.134 52.381 0.00 0.00 35.77 2.15
3244 3487 1.000993 ACCAGGCGATCCTCTCTGT 59.999 57.895 0.00 0.00 41.93 3.41
3253 3496 2.676748 GATCCTCTCTGTCATCCAGGT 58.323 52.381 0.00 0.00 41.83 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 3.222603 GAACCTGATCACAAACCCTGTT 58.777 45.455 0.00 0.00 35.47 3.16
130 131 2.816087 CTGAACCTGATCACAAACCCTG 59.184 50.000 0.00 0.00 0.00 4.45
154 155 4.575236 AGAAGAAGAACCCGTCTGTTTTTC 59.425 41.667 0.00 0.00 38.78 2.29
165 171 3.873952 CCATCGATGAAGAAGAAGAACCC 59.126 47.826 26.86 0.00 0.00 4.11
168 174 4.206477 TGCCATCGATGAAGAAGAAGAA 57.794 40.909 26.86 0.00 0.00 2.52
169 175 3.893326 TGCCATCGATGAAGAAGAAGA 57.107 42.857 26.86 0.00 0.00 2.87
170 176 4.952262 TTTGCCATCGATGAAGAAGAAG 57.048 40.909 26.86 8.24 0.00 2.85
193 199 3.469863 AAAACCCGGCAGCGTCTCA 62.470 57.895 0.00 0.00 0.00 3.27
197 203 3.835790 TAGCAAAACCCGGCAGCGT 62.836 57.895 0.00 0.00 0.00 5.07
207 213 7.819900 TCCTCTTCATTTCTCTAGTAGCAAAAC 59.180 37.037 0.00 0.00 0.00 2.43
213 219 6.831353 TGACCTCCTCTTCATTTCTCTAGTAG 59.169 42.308 0.00 0.00 0.00 2.57
214 220 6.603997 GTGACCTCCTCTTCATTTCTCTAGTA 59.396 42.308 0.00 0.00 0.00 1.82
215 221 5.420739 GTGACCTCCTCTTCATTTCTCTAGT 59.579 44.000 0.00 0.00 0.00 2.57
267 274 4.436998 GTCGGCGTCACCCTCCTG 62.437 72.222 6.85 0.00 33.26 3.86
350 476 0.876342 GGAGCTAACCAGGCGATTCG 60.876 60.000 0.62 0.62 34.52 3.34
351 477 0.178068 TGGAGCTAACCAGGCGATTC 59.822 55.000 0.00 0.00 34.77 2.52
352 478 2.296920 TGGAGCTAACCAGGCGATT 58.703 52.632 0.00 0.00 34.77 3.34
353 479 4.050313 TGGAGCTAACCAGGCGAT 57.950 55.556 0.00 0.00 34.77 4.58
359 485 1.292223 GACACGCTGGAGCTAACCA 59.708 57.895 0.00 0.00 39.32 3.67
360 486 1.805945 CGACACGCTGGAGCTAACC 60.806 63.158 0.00 0.00 39.32 2.85
361 487 1.080705 ACGACACGCTGGAGCTAAC 60.081 57.895 0.00 0.00 39.32 2.34
362 488 1.080772 CACGACACGCTGGAGCTAA 60.081 57.895 0.00 0.00 39.32 3.09
363 489 2.566529 CACGACACGCTGGAGCTA 59.433 61.111 0.00 0.00 39.32 3.32
364 490 4.363990 CCACGACACGCTGGAGCT 62.364 66.667 0.00 0.00 39.32 4.09
365 491 3.858868 TTCCACGACACGCTGGAGC 62.859 63.158 12.23 0.00 37.92 4.70
366 492 1.734477 CTTCCACGACACGCTGGAG 60.734 63.158 12.23 6.66 37.92 3.86
367 493 2.338620 CTTCCACGACACGCTGGA 59.661 61.111 0.00 0.00 36.12 3.86
368 494 2.738521 CCTTCCACGACACGCTGG 60.739 66.667 0.00 0.00 32.42 4.85
369 495 3.414700 GCCTTCCACGACACGCTG 61.415 66.667 0.00 0.00 0.00 5.18
370 496 4.681978 GGCCTTCCACGACACGCT 62.682 66.667 0.00 0.00 0.00 5.07
372 498 3.851845 TTCGGCCTTCCACGACACG 62.852 63.158 0.00 0.00 39.04 4.49
373 499 2.029964 TTCGGCCTTCCACGACAC 59.970 61.111 0.00 0.00 39.04 3.67
374 500 2.029964 GTTCGGCCTTCCACGACA 59.970 61.111 0.00 0.00 39.04 4.35
375 501 3.110178 CGTTCGGCCTTCCACGAC 61.110 66.667 0.00 0.00 39.04 4.34
376 502 3.277211 CTCGTTCGGCCTTCCACGA 62.277 63.158 12.99 12.99 38.12 4.35
377 503 2.809601 CTCGTTCGGCCTTCCACG 60.810 66.667 0.00 3.73 34.26 4.94
378 504 1.737008 GACTCGTTCGGCCTTCCAC 60.737 63.158 0.00 0.00 0.00 4.02
379 505 2.654877 GACTCGTTCGGCCTTCCA 59.345 61.111 0.00 0.00 0.00 3.53
380 506 2.506438 CGACTCGTTCGGCCTTCC 60.506 66.667 0.00 0.00 44.60 3.46
388 514 0.458025 AAATCCTCGGCGACTCGTTC 60.458 55.000 4.99 0.00 0.00 3.95
389 515 0.458025 GAAATCCTCGGCGACTCGTT 60.458 55.000 4.99 0.00 0.00 3.85
390 516 1.139095 GAAATCCTCGGCGACTCGT 59.861 57.895 4.99 0.00 0.00 4.18
391 517 1.939785 CGAAATCCTCGGCGACTCG 60.940 63.158 4.99 5.87 44.20 4.18
392 518 3.999051 CGAAATCCTCGGCGACTC 58.001 61.111 4.99 0.00 44.20 3.36
400 526 2.174319 GCTGCGTCCCGAAATCCTC 61.174 63.158 0.00 0.00 0.00 3.71
401 527 2.125106 GCTGCGTCCCGAAATCCT 60.125 61.111 0.00 0.00 0.00 3.24
402 528 3.564027 CGCTGCGTCCCGAAATCC 61.564 66.667 14.93 0.00 0.00 3.01
403 529 4.223964 GCGCTGCGTCCCGAAATC 62.224 66.667 24.04 0.00 0.00 2.17
420 546 0.520404 GACAAGGTGAGCACAGCATG 59.480 55.000 15.65 15.47 45.57 4.06
421 547 0.109153 TGACAAGGTGAGCACAGCAT 59.891 50.000 15.65 0.18 45.57 3.79
422 548 0.109153 ATGACAAGGTGAGCACAGCA 59.891 50.000 15.65 0.00 45.57 4.41
423 549 0.801251 GATGACAAGGTGAGCACAGC 59.199 55.000 5.09 5.09 43.79 4.40
424 550 1.446907 GGATGACAAGGTGAGCACAG 58.553 55.000 2.75 0.00 0.00 3.66
425 551 0.320683 CGGATGACAAGGTGAGCACA 60.321 55.000 2.75 0.00 0.00 4.57
426 552 0.320771 ACGGATGACAAGGTGAGCAC 60.321 55.000 0.00 0.00 0.00 4.40
427 553 0.320683 CACGGATGACAAGGTGAGCA 60.321 55.000 0.00 0.00 32.23 4.26
428 554 1.021390 CCACGGATGACAAGGTGAGC 61.021 60.000 5.70 0.00 32.23 4.26
429 555 1.021390 GCCACGGATGACAAGGTGAG 61.021 60.000 5.70 0.00 32.23 3.51
430 556 1.003839 GCCACGGATGACAAGGTGA 60.004 57.895 5.70 0.00 32.23 4.02
431 557 0.606401 AAGCCACGGATGACAAGGTG 60.606 55.000 0.00 0.00 0.00 4.00
432 558 0.110486 AAAGCCACGGATGACAAGGT 59.890 50.000 0.00 0.00 0.00 3.50
433 559 0.523072 CAAAGCCACGGATGACAAGG 59.477 55.000 0.00 0.00 0.00 3.61
434 560 0.523072 CCAAAGCCACGGATGACAAG 59.477 55.000 0.00 0.00 0.00 3.16
435 561 0.109532 TCCAAAGCCACGGATGACAA 59.890 50.000 0.00 0.00 0.00 3.18
516 642 2.434185 TGTGCTGGGATCGAACGC 60.434 61.111 2.59 2.59 0.00 4.84
518 644 0.674895 AAGCTGTGCTGGGATCGAAC 60.675 55.000 0.00 0.00 39.62 3.95
540 666 4.060038 TCTTGTTATGATCTCCGGAAGC 57.940 45.455 5.23 0.00 0.00 3.86
544 670 5.207110 ACTGATCTTGTTATGATCTCCGG 57.793 43.478 0.00 0.00 40.51 5.14
545 671 6.536582 ACAAACTGATCTTGTTATGATCTCCG 59.463 38.462 5.38 0.00 40.51 4.63
610 736 1.085091 CTGCTCCATGCTCTTGTGAC 58.915 55.000 0.00 0.00 43.37 3.67
638 769 3.782443 CCCCGGCCACTCTGGTAC 61.782 72.222 2.24 0.00 40.46 3.34
856 994 4.021925 GCGCCCCCTCAGTCAGTT 62.022 66.667 0.00 0.00 0.00 3.16
949 1103 4.800993 CAGACGAGTGTGATATTTGGTCTC 59.199 45.833 0.00 0.00 31.64 3.36
952 1106 3.513912 TCCAGACGAGTGTGATATTTGGT 59.486 43.478 1.70 0.00 0.00 3.67
1097 1258 3.177249 GAGCGCGTGGTTACCGAC 61.177 66.667 8.43 0.00 0.00 4.79
1103 1264 3.165160 AACAGAGGAGCGCGTGGTT 62.165 57.895 8.43 0.00 0.00 3.67
1172 1333 2.355837 TGACTGACAACCGCGAGC 60.356 61.111 8.23 0.00 0.00 5.03
1420 1614 2.836372 ACTGGACTCAGCTGATGAATCA 59.164 45.455 18.63 10.45 44.59 2.57
1425 1619 2.095364 GCAAAACTGGACTCAGCTGATG 60.095 50.000 18.63 13.72 44.59 3.07
1426 1620 2.157738 GCAAAACTGGACTCAGCTGAT 58.842 47.619 18.63 7.64 44.59 2.90
1437 1631 4.927425 CCTGAATTTCATGAGCAAAACTGG 59.073 41.667 0.00 0.00 0.00 4.00
1438 1632 4.387862 GCCTGAATTTCATGAGCAAAACTG 59.612 41.667 5.93 0.00 0.00 3.16
1446 1640 6.688637 TCTACATTGCCTGAATTTCATGAG 57.311 37.500 5.93 0.00 0.00 2.90
1467 1661 4.401837 GGTAGGATGAACTCGTAAGGTTCT 59.598 45.833 7.85 0.00 43.43 3.01
1473 1667 1.406539 GGCGGTAGGATGAACTCGTAA 59.593 52.381 0.00 0.00 0.00 3.18
1811 2015 2.749076 TGCATCAGGAATTCAGGTTTCG 59.251 45.455 7.93 0.00 0.00 3.46
1986 2191 4.530875 ACCATAGCCTTCAGGATCTTTTG 58.469 43.478 0.00 0.00 37.39 2.44
1994 2199 4.963318 TGAATCTACCATAGCCTTCAGG 57.037 45.455 0.00 0.00 38.53 3.86
2070 2275 3.505680 TCGTGGAAGTAATGCAAGCAAAT 59.494 39.130 0.00 0.00 0.00 2.32
2080 2285 4.283722 ACCAGTTTCTCTCGTGGAAGTAAT 59.716 41.667 0.00 0.00 33.95 1.89
2140 2347 5.776173 ATAGTCACCTTAGTCGATCAAGG 57.224 43.478 20.60 20.60 45.73 3.61
2176 2385 9.740710 ACATTGGAATAACCTCTATAATAAGCC 57.259 33.333 0.00 0.00 39.86 4.35
2215 2427 7.093988 TGTTTGGAAGAAGAGACAAATTGTTCA 60.094 33.333 0.00 0.00 35.56 3.18
2216 2428 7.257722 TGTTTGGAAGAAGAGACAAATTGTTC 58.742 34.615 0.00 0.48 35.56 3.18
2218 2430 6.681368 GCTGTTTGGAAGAAGAGACAAATTGT 60.681 38.462 0.00 0.00 35.56 2.71
2224 2436 3.558931 TGCTGTTTGGAAGAAGAGACA 57.441 42.857 0.00 0.00 0.00 3.41
2250 2462 7.625185 GCATGGTAGAAAATTCAGACTCAAGAC 60.625 40.741 0.00 0.00 0.00 3.01
2291 2503 4.728110 ATGCTCCAAGCGGCTGCA 62.728 61.111 21.93 14.02 46.26 4.41
2292 2504 3.885521 GATGCTCCAAGCGGCTGC 61.886 66.667 10.33 10.33 46.26 5.25
2293 2505 2.124819 AGATGCTCCAAGCGGCTG 60.125 61.111 1.81 0.00 46.26 4.85
2294 2506 1.045350 TAGAGATGCTCCAAGCGGCT 61.045 55.000 0.00 0.00 46.26 5.52
2295 2507 0.599728 CTAGAGATGCTCCAAGCGGC 60.600 60.000 0.00 0.00 46.26 6.53
2296 2508 0.599728 GCTAGAGATGCTCCAAGCGG 60.600 60.000 0.00 0.00 46.26 5.52
2367 2579 2.145397 AGTCGAACAGCTAGATCCCA 57.855 50.000 0.00 0.00 0.00 4.37
2368 2580 2.541999 CGAAGTCGAACAGCTAGATCCC 60.542 54.545 0.00 0.00 43.02 3.85
2382 2594 5.747197 ACAATAAGGCTACAATACGAAGTCG 59.253 40.000 0.00 0.00 43.93 4.18
2457 2671 1.077716 GGGGTGGCCTATCACACAC 60.078 63.158 3.32 0.00 42.50 3.82
2458 2672 0.918799 ATGGGGTGGCCTATCACACA 60.919 55.000 3.32 0.00 42.50 3.72
2459 2673 1.072331 CTATGGGGTGGCCTATCACAC 59.928 57.143 3.32 0.00 40.15 3.82
2655 2884 1.456287 GTTGAGGAGGGTGGCAAGT 59.544 57.895 0.00 0.00 0.00 3.16
2706 2937 4.713946 GGTGATGCCGAAGAACCA 57.286 55.556 0.00 0.00 0.00 3.67
2830 3068 1.807886 GGTATGACGGCGAGTGTCT 59.192 57.895 16.62 0.00 37.26 3.41
2888 3126 4.385405 GGTGCTGTGAGCGAGGCT 62.385 66.667 0.00 0.00 46.26 4.58
2997 3240 3.873883 GATGACGCCAGCAGCAGC 61.874 66.667 0.00 0.00 44.04 5.25


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

AutoCloner maintained by Alex Coulton.