Multiple sequence alignment - TraesCS3B01G192200

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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 TraesCS3B01G192200 chr3B 100.000 3286 0 0 1 3286 205778902 205782187 0.000000e+00 6069
1 TraesCS3B01G192200 chr3B 95.041 121 6 0 453 573 368604055 368604175 1.200000e-44 191
2 TraesCS3B01G192200 chr3B 91.954 87 7 0 259 345 239915502 239915416 4.450000e-24 122
3 TraesCS3B01G192200 chr3D 95.113 1412 66 3 570 1978 148696219 148694808 0.000000e+00 2222
4 TraesCS3B01G192200 chr3D 97.168 459 12 1 1 458 148696674 148696216 0.000000e+00 774
5 TraesCS3B01G192200 chr3D 91.954 87 7 0 259 345 163130235 163130149 4.450000e-24 122
6 TraesCS3B01G192200 chr6D 95.569 1309 55 3 1980 3286 430937603 430936296 0.000000e+00 2093
7 TraesCS3B01G192200 chr5D 95.493 1309 56 3 1980 3286 419457297 419455990 0.000000e+00 2087
8 TraesCS3B01G192200 chr1B 95.420 1310 60 0 1977 3286 483384457 483385766 0.000000e+00 2087
9 TraesCS3B01G192200 chr1B 95.420 1310 59 1 1977 3286 362883765 362885073 0.000000e+00 2085
10 TraesCS3B01G192200 chr1B 94.262 122 6 1 452 573 541470952 541471072 5.600000e-43 185
11 TraesCS3B01G192200 chr1D 95.351 1312 58 3 1977 3286 215071823 215073133 0.000000e+00 2082
12 TraesCS3B01G192200 chr7D 95.340 1309 58 3 1980 3286 187778593 187777286 0.000000e+00 2076
13 TraesCS3B01G192200 chr7D 89.855 138 14 0 444 581 182605337 182605474 9.370000e-41 178
14 TraesCS3B01G192200 chr6B 95.333 1307 61 0 1980 3286 609470027 609468721 0.000000e+00 2076
15 TraesCS3B01G192200 chr2B 95.333 1307 61 0 1980 3286 95621069 95619763 0.000000e+00 2076
16 TraesCS3B01G192200 chr7B 95.267 1310 61 1 1977 3286 302268969 302270277 0.000000e+00 2074
17 TraesCS3B01G192200 chr7B 94.309 123 7 0 454 576 252178053 252178175 4.330000e-44 189
18 TraesCS3B01G192200 chr4B 96.581 117 4 0 457 573 649268495 649268379 9.300000e-46 195
19 TraesCS3B01G192200 chr4B 93.548 124 7 1 450 573 457415573 457415451 2.010000e-42 183
20 TraesCS3B01G192200 chr4A 95.041 121 6 0 456 576 720134445 720134565 1.200000e-44 191
21 TraesCS3B01G192200 chr4A 90.909 132 12 0 450 581 702148916 702148785 9.370000e-41 178
22 TraesCS3B01G192200 chr4D 93.651 126 7 1 453 578 428946375 428946499 1.560000e-43 187
23 TraesCS3B01G192200 chr3A 90.805 87 7 1 259 344 195464266 195464180 7.450000e-22 115


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 TraesCS3B01G192200 chr3B 205778902 205782187 3285 False 6069 6069 100.0000 1 3286 1 chr3B.!!$F1 3285
1 TraesCS3B01G192200 chr3D 148694808 148696674 1866 True 1498 2222 96.1405 1 1978 2 chr3D.!!$R2 1977
2 TraesCS3B01G192200 chr6D 430936296 430937603 1307 True 2093 2093 95.5690 1980 3286 1 chr6D.!!$R1 1306
3 TraesCS3B01G192200 chr5D 419455990 419457297 1307 True 2087 2087 95.4930 1980 3286 1 chr5D.!!$R1 1306
4 TraesCS3B01G192200 chr1B 483384457 483385766 1309 False 2087 2087 95.4200 1977 3286 1 chr1B.!!$F2 1309
5 TraesCS3B01G192200 chr1B 362883765 362885073 1308 False 2085 2085 95.4200 1977 3286 1 chr1B.!!$F1 1309
6 TraesCS3B01G192200 chr1D 215071823 215073133 1310 False 2082 2082 95.3510 1977 3286 1 chr1D.!!$F1 1309
7 TraesCS3B01G192200 chr7D 187777286 187778593 1307 True 2076 2076 95.3400 1980 3286 1 chr7D.!!$R1 1306
8 TraesCS3B01G192200 chr6B 609468721 609470027 1306 True 2076 2076 95.3330 1980 3286 1 chr6B.!!$R1 1306
9 TraesCS3B01G192200 chr2B 95619763 95621069 1306 True 2076 2076 95.3330 1980 3286 1 chr2B.!!$R1 1306
10 TraesCS3B01G192200 chr7B 302268969 302270277 1308 False 2074 2074 95.2670 1977 3286 1 chr7B.!!$F2 1309

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
471 473 0.038744 AAAGTACTCCCTCCGTCCGA 59.961 55.0 0.0 0.0 0.0 4.55 F
1196 1199 0.598065 ATTTCAAAGGCCGCAGTGTC 59.402 50.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2022 0.610785 AACATTCGTCGGGCCCATTT 60.611 50.000 24.92 0.0 0.0 2.32 R
2609 2615 1.281287 AGGTGACGAGGCTACTACAGA 59.719 52.381 0.00 0.0 0.0 3.41 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
165 167 0.883833 AACACTGTATGCCAGCTTGC 59.116 50.000 2.09 2.09 45.68 4.01
204 206 5.237344 AGTTTGTATTGAGCTGTCTGTGTTC 59.763 40.000 0.00 0.00 0.00 3.18
255 257 6.889301 ACTAGATGGGCATGAATTAACATG 57.111 37.500 0.00 0.00 46.96 3.21
334 336 3.465990 ACATGATTGTGGCTCCTCG 57.534 52.632 0.00 0.00 33.85 4.63
340 342 0.976641 ATTGTGGCTCCTCGAACTCA 59.023 50.000 0.00 0.00 0.00 3.41
360 362 2.994186 AAAAATGGAGATGGGCATGC 57.006 45.000 9.90 9.90 0.00 4.06
372 374 1.297689 GGCATGCAGTGGAGTCTGA 59.702 57.895 21.36 0.00 37.61 3.27
431 433 5.488262 AAATGTAAGCCATCAAAAAGCCT 57.512 34.783 0.00 0.00 31.75 4.58
454 456 7.202011 GCCTGATTAACCCAGTAGAGATCTAAA 60.202 40.741 0.00 0.00 0.00 1.85
455 457 8.364142 CCTGATTAACCCAGTAGAGATCTAAAG 58.636 40.741 0.00 0.00 0.00 1.85
456 458 8.840200 TGATTAACCCAGTAGAGATCTAAAGT 57.160 34.615 0.00 0.00 0.00 2.66
457 459 9.931698 TGATTAACCCAGTAGAGATCTAAAGTA 57.068 33.333 0.00 0.00 0.00 2.24
459 461 9.939424 ATTAACCCAGTAGAGATCTAAAGTACT 57.061 33.333 0.00 0.00 0.00 2.73
460 462 7.885009 AACCCAGTAGAGATCTAAAGTACTC 57.115 40.000 0.00 0.00 0.00 2.59
461 463 6.367161 ACCCAGTAGAGATCTAAAGTACTCC 58.633 44.000 0.00 0.00 0.00 3.85
462 464 5.771165 CCCAGTAGAGATCTAAAGTACTCCC 59.229 48.000 0.00 0.00 0.00 4.30
463 465 6.411086 CCCAGTAGAGATCTAAAGTACTCCCT 60.411 46.154 0.00 0.00 0.00 4.20
464 466 6.713450 CCAGTAGAGATCTAAAGTACTCCCTC 59.287 46.154 0.00 0.00 0.00 4.30
465 467 6.713450 CAGTAGAGATCTAAAGTACTCCCTCC 59.287 46.154 0.00 0.00 0.00 4.30
466 468 4.721132 AGAGATCTAAAGTACTCCCTCCG 58.279 47.826 0.00 0.00 0.00 4.63
467 469 4.166531 AGAGATCTAAAGTACTCCCTCCGT 59.833 45.833 0.00 0.00 0.00 4.69
468 470 4.463070 AGATCTAAAGTACTCCCTCCGTC 58.537 47.826 0.00 0.00 0.00 4.79
469 471 3.010200 TCTAAAGTACTCCCTCCGTCC 57.990 52.381 0.00 0.00 0.00 4.79
470 472 1.674962 CTAAAGTACTCCCTCCGTCCG 59.325 57.143 0.00 0.00 0.00 4.79
471 473 0.038744 AAAGTACTCCCTCCGTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
472 474 0.038744 AAGTACTCCCTCCGTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
473 475 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
474 476 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
475 477 1.273327 GTACTCCCTCCGTCCGAAAAA 59.727 52.381 0.00 0.00 0.00 1.94
497 499 8.641499 AAAAACTTGTCGAAGAAATGCATAAA 57.359 26.923 0.00 0.00 39.69 1.40
498 500 8.641499 AAAACTTGTCGAAGAAATGCATAAAA 57.359 26.923 0.00 0.00 39.69 1.52
499 501 8.641499 AAACTTGTCGAAGAAATGCATAAAAA 57.359 26.923 0.00 0.00 39.69 1.94
500 502 8.816640 AACTTGTCGAAGAAATGCATAAAAAT 57.183 26.923 0.00 0.00 39.69 1.82
501 503 8.231304 ACTTGTCGAAGAAATGCATAAAAATG 57.769 30.769 0.00 0.00 39.69 2.32
502 504 7.329226 ACTTGTCGAAGAAATGCATAAAAATGG 59.671 33.333 0.00 0.00 39.69 3.16
503 505 6.918626 TGTCGAAGAAATGCATAAAAATGGA 58.081 32.000 0.00 0.00 39.69 3.41
504 506 7.546358 TGTCGAAGAAATGCATAAAAATGGAT 58.454 30.769 0.00 0.00 39.69 3.41
505 507 7.488792 TGTCGAAGAAATGCATAAAAATGGATG 59.511 33.333 0.00 0.00 39.69 3.51
506 508 7.489113 GTCGAAGAAATGCATAAAAATGGATGT 59.511 33.333 0.00 0.00 39.69 3.06
507 509 8.681806 TCGAAGAAATGCATAAAAATGGATGTA 58.318 29.630 0.00 0.00 32.82 2.29
508 510 9.467258 CGAAGAAATGCATAAAAATGGATGTAT 57.533 29.630 0.00 0.00 32.82 2.29
516 518 9.851686 TGCATAAAAATGGATGTATCTAGAACT 57.148 29.630 0.00 0.00 0.00 3.01
549 551 9.367160 TGTCTATATACATCCATTTCTCTGACA 57.633 33.333 0.00 0.00 0.00 3.58
556 558 9.911788 ATACATCCATTTCTCTGACAAGTATTT 57.088 29.630 0.00 0.00 0.00 1.40
557 559 8.273780 ACATCCATTTCTCTGACAAGTATTTC 57.726 34.615 0.00 0.00 0.00 2.17
558 560 7.337942 ACATCCATTTCTCTGACAAGTATTTCC 59.662 37.037 0.00 0.00 0.00 3.13
559 561 5.874810 TCCATTTCTCTGACAAGTATTTCCG 59.125 40.000 0.00 0.00 0.00 4.30
560 562 5.065218 CCATTTCTCTGACAAGTATTTCCGG 59.935 44.000 0.00 0.00 0.00 5.14
561 563 5.477607 TTTCTCTGACAAGTATTTCCGGA 57.522 39.130 0.00 0.00 0.00 5.14
562 564 4.451629 TCTCTGACAAGTATTTCCGGAC 57.548 45.455 1.83 0.00 0.00 4.79
563 565 3.119602 TCTCTGACAAGTATTTCCGGACG 60.120 47.826 1.83 0.00 0.00 4.79
564 566 2.094390 TCTGACAAGTATTTCCGGACGG 60.094 50.000 1.83 3.96 0.00 4.79
565 567 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
566 568 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
567 569 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
568 570 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
702 704 3.256558 CTCGAAGCTCATGATGAACACA 58.743 45.455 0.00 0.00 0.00 3.72
770 773 3.359695 TGGCTGAAAGTTATACACCCC 57.640 47.619 0.00 0.00 35.30 4.95
964 967 8.798859 AGTATCAATTCACTTAAACTGCAGAT 57.201 30.769 23.35 5.41 0.00 2.90
975 978 8.015087 CACTTAAACTGCAGATCATTTACGAAA 58.985 33.333 23.35 0.93 0.00 3.46
984 987 6.513230 GCAGATCATTTACGAAATATGTGGCA 60.513 38.462 0.00 0.00 0.00 4.92
990 993 5.539582 TTACGAAATATGTGGCAGACAAC 57.460 39.130 0.00 0.00 38.36 3.32
1055 1058 2.770164 TCCTTGGAGTTAGCAAGAGC 57.230 50.000 0.00 0.00 42.56 4.09
1130 1133 1.130561 GCGCAAGTCTTGGAATGGTAC 59.869 52.381 14.40 0.00 41.68 3.34
1154 1157 7.605449 ACAATAAACTGGGATGAACATTTCAG 58.395 34.615 12.80 12.80 43.98 3.02
1168 1171 7.397221 TGAACATTTCAGAGTAGTCAATGGAT 58.603 34.615 11.66 3.26 34.08 3.41
1189 1192 0.732538 GGTGCGAATTTCAAAGGCCG 60.733 55.000 0.00 0.00 0.00 6.13
1196 1199 0.598065 ATTTCAAAGGCCGCAGTGTC 59.402 50.000 0.00 0.00 0.00 3.67
1233 1236 3.090210 TCCATGCAACTGGATGTGAAT 57.910 42.857 4.87 0.00 40.43 2.57
1239 1242 2.097142 GCAACTGGATGTGAATGAGCTC 59.903 50.000 6.82 6.82 0.00 4.09
1271 1274 7.403312 TCATTCAGAAGAACTTTTCCAACAA 57.597 32.000 0.00 0.00 36.39 2.83
1287 1290 3.058639 CCAACAAGACTGCTAAGCTTGTC 60.059 47.826 9.86 7.90 43.64 3.18
1312 1315 7.626084 TCTCAATTTACCCTCCCTACTTTGATA 59.374 37.037 0.00 0.00 0.00 2.15
1414 1417 3.685139 TGATGGAGTCCTTTGACAGAC 57.315 47.619 11.33 0.00 44.33 3.51
1458 1461 4.310769 AGAGAAAACATGACGGACTTCTG 58.689 43.478 0.00 0.00 0.00 3.02
1462 1465 0.898320 ACATGACGGACTTCTGGGAG 59.102 55.000 0.00 0.00 0.00 4.30
1473 1476 5.444176 GGACTTCTGGGAGATGAATTGAAT 58.556 41.667 0.00 0.00 0.00 2.57
1475 1478 7.056635 GGACTTCTGGGAGATGAATTGAATAA 58.943 38.462 0.00 0.00 0.00 1.40
1505 1508 2.894763 TGCATAAATCAGGCAATGGC 57.105 45.000 0.00 0.00 41.89 4.40
1620 1623 6.206634 AGACCAAATTTTCTGCATTTCGTCTA 59.793 34.615 7.84 0.00 39.12 2.59
1625 1628 9.430838 CAAATTTTCTGCATTTCGTCTATCTAG 57.569 33.333 0.00 0.00 0.00 2.43
1650 1653 8.007742 AGAGATTATCCAGTACATGTCCTTAGT 58.992 37.037 0.00 0.00 0.00 2.24
1653 1656 5.599999 ATCCAGTACATGTCCTTAGTCAC 57.400 43.478 0.00 0.00 0.00 3.67
1668 1671 5.050567 CCTTAGTCACAAGAACGTTACAACC 60.051 44.000 0.00 0.00 0.00 3.77
1689 1692 4.062991 CCGTAAGTTAGCCTGTTCTGTTT 58.937 43.478 0.00 0.00 0.00 2.83
1697 1700 3.891049 AGCCTGTTCTGTTTCTTTGAGT 58.109 40.909 0.00 0.00 0.00 3.41
1700 1703 5.885912 AGCCTGTTCTGTTTCTTTGAGTTTA 59.114 36.000 0.00 0.00 0.00 2.01
1702 1705 7.068716 AGCCTGTTCTGTTTCTTTGAGTTTAAT 59.931 33.333 0.00 0.00 0.00 1.40
1704 1707 8.405531 CCTGTTCTGTTTCTTTGAGTTTAATGA 58.594 33.333 0.00 0.00 0.00 2.57
1705 1708 9.443283 CTGTTCTGTTTCTTTGAGTTTAATGAG 57.557 33.333 0.00 0.00 0.00 2.90
1706 1709 7.915397 TGTTCTGTTTCTTTGAGTTTAATGAGC 59.085 33.333 0.00 0.00 0.00 4.26
1707 1710 7.807977 TCTGTTTCTTTGAGTTTAATGAGCT 57.192 32.000 0.00 0.00 0.00 4.09
1709 1712 9.337396 TCTGTTTCTTTGAGTTTAATGAGCTTA 57.663 29.630 0.00 0.00 0.00 3.09
1783 1788 9.814899 TTGCAGAAAGAAAATTCAATTTCTACA 57.185 25.926 0.00 8.67 46.25 2.74
1795 1800 5.507077 TCAATTTCTACAACTGTTGAACGC 58.493 37.500 26.00 0.00 38.94 4.84
1799 1804 6.665474 TTTCTACAACTGTTGAACGCTTTA 57.335 33.333 26.00 6.13 38.94 1.85
1810 1815 3.450578 TGAACGCTTTAAAGACGACAGT 58.549 40.909 27.17 15.04 32.56 3.55
1814 1819 2.096909 CGCTTTAAAGACGACAGTGGTG 60.097 50.000 19.48 0.00 0.00 4.17
1846 1851 2.260434 GCAGCCAACATGCCACAG 59.740 61.111 0.00 0.00 37.73 3.66
1881 1886 5.581085 CCTTACACCAGTCACTTATAGTTGC 59.419 44.000 0.00 0.00 0.00 4.17
1923 1928 6.667414 AGAGAGTATGTCCTGAAACATCTCTT 59.333 38.462 14.42 7.29 38.84 2.85
1927 1932 7.227156 AGTATGTCCTGAAACATCTCTTTTGT 58.773 34.615 0.00 0.00 40.32 2.83
2017 2022 5.392165 CCGTAATCGTTTTTAGCCCAATTGA 60.392 40.000 7.12 0.00 35.01 2.57
2062 2067 2.293170 GTTGGGCTCCTATGAAGCTTC 58.707 52.381 19.89 19.89 0.00 3.86
2063 2068 0.465705 TGGGCTCCTATGAAGCTTCG 59.534 55.000 21.11 7.32 0.00 3.79
2073 2078 5.540337 TCCTATGAAGCTTCGGTCTGAATAT 59.460 40.000 21.11 8.43 35.63 1.28
2211 2216 6.981722 CCTGTTGGCATAAAGTTTAAAGTCT 58.018 36.000 0.00 0.00 0.00 3.24
2215 2220 8.691797 TGTTGGCATAAAGTTTAAAGTCTTTCT 58.308 29.630 0.00 0.00 35.79 2.52
2233 2238 9.896645 AGTCTTTCTAGATAAAAGCATCATCAA 57.103 29.630 0.00 0.00 34.43 2.57
2282 2287 3.754965 TGAGTGCTAATGTTTCAGGCTT 58.245 40.909 0.00 0.00 0.00 4.35
2309 2314 0.538584 TGATGGAGCAGCACGATCTT 59.461 50.000 14.29 0.00 0.00 2.40
2388 2394 8.466086 GTTTCAAAACCATTCATATCTTGACC 57.534 34.615 0.00 0.00 31.34 4.02
2449 2455 4.044065 TCCATTAGGGATTGGACTTGTGTT 59.956 41.667 0.00 0.00 42.15 3.32
2552 2558 3.197116 CCCAGAATTACGTAGGAAGGTGT 59.803 47.826 0.00 0.00 0.00 4.16
2609 2615 2.224606 CAGCAAGAGGTGACATTGTGT 58.775 47.619 0.00 0.00 45.95 3.72
2664 2670 4.100653 TGGCTGTTCAATCATTTGTTCCAA 59.899 37.500 0.00 0.00 34.32 3.53
2670 2676 6.822676 TGTTCAATCATTTGTTCCAAAGCTTT 59.177 30.769 5.69 5.69 34.32 3.51
2717 2724 5.721232 AGTGTACCAGTGAGTTACTAATGC 58.279 41.667 0.00 0.00 37.60 3.56
2746 2753 7.815398 AAAACAAACAAAGTAGGTTAAACGG 57.185 32.000 0.00 0.00 0.00 4.44
2845 2852 6.315144 CACTTTCGGAACATATGTCCATGTAA 59.685 38.462 9.23 0.00 38.19 2.41
3088 3095 8.561738 AAGGTGAAATGATACGTTAAGACAAT 57.438 30.769 0.00 0.00 0.00 2.71
3130 3137 6.176183 AGAGTAACTGACATTAGCTGCAAAT 58.824 36.000 1.02 0.00 0.00 2.32
3137 3144 6.430925 ACTGACATTAGCTGCAAATCAAGTAA 59.569 34.615 1.02 0.00 0.00 2.24
3199 3206 5.605488 AGGAGGAGTAAGGACTTACAACAAA 59.395 40.000 20.65 0.00 45.79 2.83
3254 3261 1.962807 CTGGTGTGGCAATCCTTGAAA 59.037 47.619 9.93 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 7.015226 TGAGTTGCCGTGAATTAATTGATAG 57.985 36.000 5.17 0.00 0.00 2.08
138 140 3.420839 GGCATACAGTGTTAATGGCAC 57.579 47.619 21.55 2.01 43.53 5.01
204 206 6.957984 AGATATACGCATGCAGTTCAATAG 57.042 37.500 19.57 0.00 0.00 1.73
219 221 7.392494 TGCCCATCTAGTTCTTAGATATACG 57.608 40.000 0.00 0.00 45.35 3.06
255 257 6.791303 TCATAAGGAACAACACAACAGAAAC 58.209 36.000 0.00 0.00 0.00 2.78
360 362 2.093764 GTCCCTGAATCAGACTCCACTG 60.094 54.545 12.53 0.00 39.02 3.66
421 423 4.479158 ACTGGGTTAATCAGGCTTTTTGA 58.521 39.130 11.69 0.00 36.62 2.69
431 433 8.840200 ACTTTAGATCTCTACTGGGTTAATCA 57.160 34.615 0.00 0.00 0.00 2.57
454 456 0.038744 TTTCGGACGGAGGGAGTACT 59.961 55.000 0.00 0.00 0.00 2.73
455 457 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
456 458 1.631405 TTTTTCGGACGGAGGGAGTA 58.369 50.000 0.00 0.00 0.00 2.59
457 459 2.444281 TTTTTCGGACGGAGGGAGT 58.556 52.632 0.00 0.00 0.00 3.85
472 474 8.641499 TTTATGCATTTCTTCGACAAGTTTTT 57.359 26.923 3.54 0.00 0.00 1.94
473 475 8.641499 TTTTATGCATTTCTTCGACAAGTTTT 57.359 26.923 3.54 0.00 0.00 2.43
474 476 8.641499 TTTTTATGCATTTCTTCGACAAGTTT 57.359 26.923 3.54 0.00 0.00 2.66
475 477 8.702438 CATTTTTATGCATTTCTTCGACAAGTT 58.298 29.630 3.54 0.00 0.00 2.66
476 478 7.329226 CCATTTTTATGCATTTCTTCGACAAGT 59.671 33.333 3.54 0.00 0.00 3.16
477 479 7.541783 TCCATTTTTATGCATTTCTTCGACAAG 59.458 33.333 3.54 0.00 0.00 3.16
478 480 7.374272 TCCATTTTTATGCATTTCTTCGACAA 58.626 30.769 3.54 0.00 0.00 3.18
479 481 6.918626 TCCATTTTTATGCATTTCTTCGACA 58.081 32.000 3.54 0.00 0.00 4.35
480 482 7.489113 ACATCCATTTTTATGCATTTCTTCGAC 59.511 33.333 3.54 0.00 0.00 4.20
481 483 7.546358 ACATCCATTTTTATGCATTTCTTCGA 58.454 30.769 3.54 0.00 0.00 3.71
482 484 7.760131 ACATCCATTTTTATGCATTTCTTCG 57.240 32.000 3.54 0.00 0.00 3.79
490 492 9.851686 AGTTCTAGATACATCCATTTTTATGCA 57.148 29.630 0.00 0.00 0.00 3.96
523 525 9.367160 TGTCAGAGAAATGGATGTATATAGACA 57.633 33.333 2.07 2.07 0.00 3.41
530 532 9.911788 AAATACTTGTCAGAGAAATGGATGTAT 57.088 29.630 0.00 0.00 0.00 2.29
531 533 9.383519 GAAATACTTGTCAGAGAAATGGATGTA 57.616 33.333 0.00 0.00 0.00 2.29
532 534 7.337942 GGAAATACTTGTCAGAGAAATGGATGT 59.662 37.037 0.00 0.00 0.00 3.06
533 535 7.466455 CGGAAATACTTGTCAGAGAAATGGATG 60.466 40.741 0.00 0.00 0.00 3.51
534 536 6.540189 CGGAAATACTTGTCAGAGAAATGGAT 59.460 38.462 0.00 0.00 0.00 3.41
535 537 5.874810 CGGAAATACTTGTCAGAGAAATGGA 59.125 40.000 0.00 0.00 0.00 3.41
536 538 5.065218 CCGGAAATACTTGTCAGAGAAATGG 59.935 44.000 0.00 0.00 0.00 3.16
537 539 5.874810 TCCGGAAATACTTGTCAGAGAAATG 59.125 40.000 0.00 0.00 0.00 2.32
538 540 5.875359 GTCCGGAAATACTTGTCAGAGAAAT 59.125 40.000 5.23 0.00 0.00 2.17
539 541 5.235516 GTCCGGAAATACTTGTCAGAGAAA 58.764 41.667 5.23 0.00 0.00 2.52
540 542 4.617530 CGTCCGGAAATACTTGTCAGAGAA 60.618 45.833 5.23 0.00 0.00 2.87
541 543 3.119602 CGTCCGGAAATACTTGTCAGAGA 60.120 47.826 5.23 0.00 0.00 3.10
542 544 3.179830 CGTCCGGAAATACTTGTCAGAG 58.820 50.000 5.23 0.00 0.00 3.35
543 545 2.094390 CCGTCCGGAAATACTTGTCAGA 60.094 50.000 5.23 0.00 37.50 3.27
544 546 2.094390 TCCGTCCGGAAATACTTGTCAG 60.094 50.000 5.23 0.00 42.05 3.51
545 547 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
546 548 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
547 549 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
548 550 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
549 551 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
550 552 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
551 553 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
552 554 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
553 555 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
554 556 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
555 557 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
556 558 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
557 559 1.041447 AACATACTCCCTCCGTCCGG 61.041 60.000 0.00 0.00 0.00 5.14
558 560 0.822164 AAACATACTCCCTCCGTCCG 59.178 55.000 0.00 0.00 0.00 4.79
559 561 3.345508 AAAAACATACTCCCTCCGTCC 57.654 47.619 0.00 0.00 0.00 4.79
599 601 4.506654 GCAGGATGTCATCATGATTTTTGC 59.493 41.667 27.21 9.34 43.29 3.68
702 704 9.503399 AAATAATTCCTTGTTCTAGTTCGAAGT 57.497 29.630 10.90 10.90 0.00 3.01
738 740 6.759497 AACTTTCAGCCATACCAGAAATAC 57.241 37.500 0.00 0.00 30.51 1.89
742 744 6.821665 GTGTATAACTTTCAGCCATACCAGAA 59.178 38.462 0.00 0.00 0.00 3.02
770 773 6.805760 CACCATAAGATCTCAGTGTATGATCG 59.194 42.308 11.38 0.88 40.84 3.69
871 874 8.885722 AGCAATGCCAAAATGATAAACTAAATG 58.114 29.630 0.00 0.00 0.00 2.32
882 885 4.039004 AGTGTAACAGCAATGCCAAAATGA 59.961 37.500 0.00 0.00 41.43 2.57
943 946 7.692460 ATGATCTGCAGTTTAAGTGAATTGA 57.308 32.000 14.67 0.00 0.00 2.57
964 967 5.877564 TGTCTGCCACATATTTCGTAAATGA 59.122 36.000 0.00 0.00 32.38 2.57
975 978 8.121305 TCTTATTTTTGTTGTCTGCCACATAT 57.879 30.769 0.00 0.00 33.90 1.78
984 987 8.641541 ACAACCATCATCTTATTTTTGTTGTCT 58.358 29.630 0.00 0.00 39.44 3.41
990 993 7.377398 TCACCACAACCATCATCTTATTTTTG 58.623 34.615 0.00 0.00 0.00 2.44
1055 1058 6.436843 AAGATCTAATAAACAAGCAACCCG 57.563 37.500 0.00 0.00 0.00 5.28
1123 1126 6.951198 TGTTCATCCCAGTTTATTGTACCATT 59.049 34.615 0.00 0.00 0.00 3.16
1130 1133 7.829725 TCTGAAATGTTCATCCCAGTTTATTG 58.170 34.615 11.26 0.00 39.30 1.90
1154 1157 2.609459 CGCACCAATCCATTGACTACTC 59.391 50.000 0.56 0.00 40.14 2.59
1168 1171 1.270041 GGCCTTTGAAATTCGCACCAA 60.270 47.619 0.00 0.00 0.00 3.67
1189 1192 3.440522 GGACCTTCCAAATTAGACACTGC 59.559 47.826 0.00 0.00 36.28 4.40
1233 1236 5.672421 TCTGAATGAAGAGAATGAGCTCA 57.328 39.130 20.79 20.79 37.37 4.26
1251 1254 6.094048 CAGTCTTGTTGGAAAAGTTCTTCTGA 59.906 38.462 0.00 0.00 0.00 3.27
1252 1255 6.261118 CAGTCTTGTTGGAAAAGTTCTTCTG 58.739 40.000 0.00 0.00 0.00 3.02
1260 1263 4.276926 AGCTTAGCAGTCTTGTTGGAAAAG 59.723 41.667 7.07 0.00 0.00 2.27
1271 1274 4.550076 ATTGAGACAAGCTTAGCAGTCT 57.450 40.909 24.79 24.79 44.40 3.24
1287 1290 6.062258 TCAAAGTAGGGAGGGTAAATTGAG 57.938 41.667 0.00 0.00 0.00 3.02
1449 1452 3.118629 TCAATTCATCTCCCAGAAGTCCG 60.119 47.826 0.00 0.00 0.00 4.79
1458 1461 6.603201 TGTTCCACTTATTCAATTCATCTCCC 59.397 38.462 0.00 0.00 0.00 4.30
1462 1465 7.221452 GCATGTGTTCCACTTATTCAATTCATC 59.779 37.037 0.00 0.00 35.11 2.92
1473 1476 6.095300 CCTGATTTATGCATGTGTTCCACTTA 59.905 38.462 10.16 0.00 35.11 2.24
1475 1478 4.400251 CCTGATTTATGCATGTGTTCCACT 59.600 41.667 10.16 0.00 35.11 4.00
1505 1508 4.971939 ACTTGTTTCAAATTCATTGGGGG 58.028 39.130 0.00 0.00 39.62 5.40
1511 1514 9.492973 CCTTATCCAAACTTGTTTCAAATTCAT 57.507 29.630 0.00 0.00 0.00 2.57
1620 1623 8.397957 AGGACATGTACTGGATAATCTCTAGAT 58.602 37.037 10.64 0.00 36.06 1.98
1625 1628 8.184304 ACTAAGGACATGTACTGGATAATCTC 57.816 38.462 12.48 0.00 0.00 2.75
1650 1653 2.891112 ACGGTTGTAACGTTCTTGTGA 58.109 42.857 2.82 0.00 42.70 3.58
1653 1656 5.393902 AACTTACGGTTGTAACGTTCTTG 57.606 39.130 2.82 0.00 42.70 3.02
1668 1671 4.989168 AGAAACAGAACAGGCTAACTTACG 59.011 41.667 0.00 0.00 0.00 3.18
1775 1780 5.751243 AAGCGTTCAACAGTTGTAGAAAT 57.249 34.783 13.14 0.00 0.00 2.17
1780 1785 6.480285 GTCTTTAAAGCGTTCAACAGTTGTA 58.520 36.000 13.14 0.35 0.00 2.41
1783 1788 4.330620 TCGTCTTTAAAGCGTTCAACAGTT 59.669 37.500 22.41 0.00 0.00 3.16
1786 1791 3.617706 TGTCGTCTTTAAAGCGTTCAACA 59.382 39.130 22.41 18.15 0.00 3.33
1795 1800 3.247648 CCACACCACTGTCGTCTTTAAAG 59.752 47.826 9.04 9.04 0.00 1.85
1799 1804 0.828022 TCCACACCACTGTCGTCTTT 59.172 50.000 0.00 0.00 0.00 2.52
1835 1840 3.077484 AGCAAGATACTGTGGCATGTT 57.923 42.857 0.00 0.00 0.00 2.71
1846 1851 5.105473 TGACTGGTGTAAGGTAGCAAGATAC 60.105 44.000 0.00 0.00 0.00 2.24
1881 1886 8.616942 CATACTCTCTATAGATATCAACACCCG 58.383 40.741 2.11 0.00 0.00 5.28
2017 2022 0.610785 AACATTCGTCGGGCCCATTT 60.611 50.000 24.92 0.00 0.00 2.32
2110 2115 3.815401 GCCACAGGCTACAGTAATTATGG 59.185 47.826 0.00 0.00 46.69 2.74
2206 2211 9.896645 TGATGATGCTTTTATCTAGAAAGACTT 57.103 29.630 6.81 0.00 36.45 3.01
2241 2246 7.330208 GCACTCAAGTCAAATGATTTATGCTTT 59.670 33.333 11.26 0.00 30.69 3.51
2249 2254 7.458409 ACATTAGCACTCAAGTCAAATGATT 57.542 32.000 12.24 0.00 0.00 2.57
2260 2265 3.754965 AGCCTGAAACATTAGCACTCAA 58.245 40.909 0.00 0.00 0.00 3.02
2282 2287 3.739209 CGTGCTGCTCCATCAGATTCTAA 60.739 47.826 0.00 0.00 36.19 2.10
2388 2394 5.106555 ACAAGAATAGTGGTTGAGAAATGCG 60.107 40.000 0.00 0.00 0.00 4.73
2449 2455 6.094193 CAGAGTGATATATCTGTGCTCCAA 57.906 41.667 13.79 0.00 38.49 3.53
2609 2615 1.281287 AGGTGACGAGGCTACTACAGA 59.719 52.381 0.00 0.00 0.00 3.41
2664 2670 6.691508 ACAAGTTCAAACTTTCAGAAAGCTT 58.308 32.000 21.00 13.45 46.52 3.74
2670 2676 9.832445 ACTAATCTACAAGTTCAAACTTTCAGA 57.168 29.630 13.96 13.96 46.52 3.27
2717 2724 6.937886 AACCTACTTTGTTTGTTTTTGTCG 57.062 33.333 0.00 0.00 0.00 4.35
2845 2852 6.992715 GGAAATAGACAATACAGTAGGCATGT 59.007 38.462 0.00 0.00 34.62 3.21
2969 2976 4.741676 GCACACAATGATAAAATAGCCTGC 59.258 41.667 0.00 0.00 0.00 4.85
3088 3095 9.826574 AGTTACTCTGTTCACTTTTATACACAA 57.173 29.630 0.00 0.00 0.00 3.33
3121 3128 9.143631 GTTCATTTAATTACTTGATTTGCAGCT 57.856 29.630 0.00 0.00 0.00 4.24
3137 3144 7.994425 TGGTACTGTGATGTGTTCATTTAAT 57.006 32.000 0.00 0.00 36.54 1.40
3199 3206 0.536006 GAGCACACCAGTTCAAGCCT 60.536 55.000 0.00 0.00 0.00 4.58
3254 3261 2.035704 TGAACCGAATGCAGTGCAAATT 59.964 40.909 23.90 13.21 43.62 1.82


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

AutoCloner maintained by Alex Coulton.