Multiple sequence alignment - TraesCS2B01G157500

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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 TraesCS2B01G157500 chr2B 100.000 3267 0 0 1 3267 131311313 131308047 0.000000e+00 6034.0
1 TraesCS2B01G157500 chr2D 88.969 2511 187 44 1 2474 79943526 79941069 0.000000e+00 3020.0
2 TraesCS2B01G157500 chr2D 95.489 798 30 2 2470 3267 79928532 79927741 0.000000e+00 1269.0
3 TraesCS2B01G157500 chr2D 86.913 703 74 8 2580 3267 79916244 79915545 0.000000e+00 773.0
4 TraesCS2B01G157500 chr2A 87.217 1588 119 37 706 2281 80538061 80536546 0.000000e+00 1731.0
5 TraesCS2B01G157500 chr2A 87.737 685 64 7 2590 3267 80533342 80532671 0.000000e+00 782.0
6 TraesCS2B01G157500 chr2A 84.185 411 43 7 296 703 80542722 80542331 2.380000e-101 379.0
7 TraesCS2B01G157500 chr2A 86.792 318 25 8 1 303 80543064 80542749 4.040000e-89 339.0
8 TraesCS2B01G157500 chr1B 88.235 51 4 2 3199 3248 635153528 635153479 3.520000e-05 60.2
9 TraesCS2B01G157500 chr1A 88.235 51 4 2 3199 3248 553477573 553477524 3.520000e-05 60.2


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 TraesCS2B01G157500 chr2B 131308047 131311313 3266 True 6034.0 6034 100.0000 1 3267 1 chr2B.!!$R1 3266
1 TraesCS2B01G157500 chr2D 79941069 79943526 2457 True 3020.0 3020 88.9690 1 2474 1 chr2D.!!$R3 2473
2 TraesCS2B01G157500 chr2D 79927741 79928532 791 True 1269.0 1269 95.4890 2470 3267 1 chr2D.!!$R2 797
3 TraesCS2B01G157500 chr2D 79915545 79916244 699 True 773.0 773 86.9130 2580 3267 1 chr2D.!!$R1 687
4 TraesCS2B01G157500 chr2A 80532671 80538061 5390 True 1256.5 1731 87.4770 706 3267 2 chr2A.!!$R1 2561
5 TraesCS2B01G157500 chr2A 80542331 80543064 733 True 359.0 379 85.4885 1 703 2 chr2A.!!$R2 702

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
501 547 0.033306 TGGCAGGCCAAGATATTGCA 60.033 50.0 11.25 0.0 44.12 4.08 F
889 945 0.038159 GGTTCACTCCACTCCACTCG 60.038 60.0 0.00 0.0 0.00 4.18 F
1696 1772 0.108520 TCGTCGAGGCCATTGGTAAC 60.109 55.0 5.01 0.0 0.00 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 1433 0.317352 TCGAAGATGATCTGCGCGAG 60.317 55.0 17.87 4.52 45.03 5.03 R
1831 1914 0.824109 TGATGAACAGCCCGTAGAGG 59.176 55.0 0.00 0.00 40.63 3.69 R
2568 2673 0.962356 CCTGGCCTAGTTGCACTTGG 60.962 60.0 3.32 10.71 42.76 3.61 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
25 26 1.068474 GGTCAACGTTCATCCACTCG 58.932 55.000 0.00 0.00 0.00 4.18
29 30 2.555325 TCAACGTTCATCCACTCGTACT 59.445 45.455 0.00 0.00 35.49 2.73
44 45 6.090898 CCACTCGTACTATTTCCAACAAAGAG 59.909 42.308 0.00 0.00 0.00 2.85
53 54 4.630644 TTCCAACAAAGAGAGAGAGCAT 57.369 40.909 0.00 0.00 0.00 3.79
55 56 3.580022 TCCAACAAAGAGAGAGAGCATGA 59.420 43.478 0.00 0.00 0.00 3.07
56 57 4.224594 TCCAACAAAGAGAGAGAGCATGAT 59.775 41.667 0.00 0.00 0.00 2.45
62 63 4.305989 AGAGAGAGAGCATGATCGAAAC 57.694 45.455 5.12 0.00 0.00 2.78
74 75 2.094234 TGATCGAAACGCAGATCCAAGA 60.094 45.455 0.00 0.00 41.76 3.02
77 78 1.126846 CGAAACGCAGATCCAAGACAC 59.873 52.381 0.00 0.00 0.00 3.67
78 79 1.464997 GAAACGCAGATCCAAGACACC 59.535 52.381 0.00 0.00 0.00 4.16
121 134 1.588082 GCAGACAGTTGCCCAATGG 59.412 57.895 0.00 0.00 38.13 3.16
149 162 0.183014 CATGCCCTCCAGAAGCATCT 59.817 55.000 2.65 0.00 45.16 2.90
173 187 8.642432 TCTGATTAGATGTCCATAAGAAATCGT 58.358 33.333 0.00 0.00 43.24 3.73
175 189 6.844696 TTAGATGTCCATAAGAAATCGTGC 57.155 37.500 0.00 0.00 43.24 5.34
231 245 1.072489 CAGCCTGAGCATGGAGATGAT 59.928 52.381 0.00 0.00 43.56 2.45
370 416 4.551388 CAGAGAGAACGAGTTAACAAGCT 58.449 43.478 8.61 0.00 0.00 3.74
409 455 4.292977 GGAAGCAAATCCTTATTCCACG 57.707 45.455 0.00 0.00 39.39 4.94
426 472 3.793144 GGCTGCAACCTCGAAGCG 61.793 66.667 0.50 0.00 36.50 4.68
500 546 2.811307 TGGCAGGCCAAGATATTGC 58.189 52.632 11.25 3.44 44.12 3.56
501 547 0.033306 TGGCAGGCCAAGATATTGCA 60.033 50.000 11.25 0.00 44.12 4.08
524 572 2.083774 GAACTGCATCACCGGAATTGA 58.916 47.619 9.46 0.75 0.00 2.57
544 592 9.521503 GAATTGAAAATTTTCATAGTAGAGCCC 57.478 33.333 29.13 9.88 45.65 5.19
566 614 3.243367 CGCAGGTCAATCTGGTTTTTGAA 60.243 43.478 0.00 0.00 33.90 2.69
591 639 9.893634 AATTATCCGGTTTTAAAAATTAAGGGG 57.106 29.630 0.00 0.00 0.00 4.79
633 685 9.673454 GAGTTGAACGACCATTTTTATACTTTT 57.327 29.630 0.00 0.00 0.00 2.27
693 748 3.057174 ACCTACTCTTCGAGTTGAGCAAG 60.057 47.826 1.45 8.90 40.28 4.01
738 793 1.592669 GATGTCGGCCCGTGAGATG 60.593 63.158 1.63 0.00 0.00 2.90
889 945 0.038159 GGTTCACTCCACTCCACTCG 60.038 60.000 0.00 0.00 0.00 4.18
924 980 2.047844 CAGCCACACAGTCCCGAG 60.048 66.667 0.00 0.00 0.00 4.63
1008 1064 2.267642 GCGTGGGTCATGGCACTA 59.732 61.111 0.00 0.00 0.00 2.74
1082 1138 3.999297 GAGGGGAGACGACGAGCCT 62.999 68.421 0.00 0.00 0.00 4.58
1084 1140 3.827898 GGGAGACGACGAGCCTGG 61.828 72.222 0.00 0.00 0.00 4.45
1263 1319 4.681978 GTTGTCTCCGGCACCGCT 62.682 66.667 2.83 0.00 38.24 5.52
1304 1360 1.139095 CCGTCGAGAGGGTAAGCAC 59.861 63.158 3.82 0.00 0.00 4.40
1308 1364 2.202756 GAGAGGGTAAGCACGCGG 60.203 66.667 12.47 0.00 42.24 6.46
1364 1433 1.751927 CCTGGGCTGATGCTGTTCC 60.752 63.158 0.00 0.00 39.59 3.62
1366 1435 0.747283 CTGGGCTGATGCTGTTCCTC 60.747 60.000 0.00 0.00 39.59 3.71
1367 1436 1.817099 GGGCTGATGCTGTTCCTCG 60.817 63.158 0.00 0.00 39.59 4.63
1479 1548 3.018856 CTCTCAGTCTCATCTCTGCAGT 58.981 50.000 14.67 0.00 0.00 4.40
1523 1592 9.787435 ACCAGACATAATTACAGTACTTTTTGA 57.213 29.630 0.00 0.00 0.00 2.69
1594 1670 1.760613 GTATCGGTTGGTGATCAGGGA 59.239 52.381 0.00 0.00 0.00 4.20
1651 1727 1.671054 GAGCTGCGCCAAAGGTGTA 60.671 57.895 4.18 0.00 35.34 2.90
1694 1770 1.514087 GTCGTCGAGGCCATTGGTA 59.486 57.895 5.01 0.00 0.00 3.25
1696 1772 0.108520 TCGTCGAGGCCATTGGTAAC 60.109 55.000 5.01 0.00 0.00 2.50
1700 1776 1.626321 TCGAGGCCATTGGTAACTGAA 59.374 47.619 5.01 0.00 37.61 3.02
1707 1783 6.435164 AGGCCATTGGTAACTGAAATATTCT 58.565 36.000 5.01 0.00 37.61 2.40
1716 1793 8.258007 TGGTAACTGAAATATTCTCTGTCGAAT 58.742 33.333 0.00 0.00 36.01 3.34
1720 1797 8.954950 ACTGAAATATTCTCTGTCGAATTGAT 57.045 30.769 0.00 0.00 35.40 2.57
1723 1800 9.816354 TGAAATATTCTCTGTCGAATTGATACA 57.184 29.630 0.00 0.00 35.40 2.29
1725 1802 9.599866 AAATATTCTCTGTCGAATTGATACACA 57.400 29.630 0.00 0.00 35.40 3.72
1726 1803 9.770097 AATATTCTCTGTCGAATTGATACACAT 57.230 29.630 0.00 0.00 35.40 3.21
1727 1804 6.892310 TTCTCTGTCGAATTGATACACATG 57.108 37.500 0.00 0.00 0.00 3.21
1728 1805 6.207691 TCTCTGTCGAATTGATACACATGA 57.792 37.500 0.00 0.00 0.00 3.07
1729 1806 6.809869 TCTCTGTCGAATTGATACACATGAT 58.190 36.000 0.00 0.00 0.00 2.45
1730 1807 6.698766 TCTCTGTCGAATTGATACACATGATG 59.301 38.462 0.00 0.00 0.00 3.07
1731 1808 6.572519 TCTGTCGAATTGATACACATGATGA 58.427 36.000 0.00 0.00 0.00 2.92
1732 1809 6.476706 TCTGTCGAATTGATACACATGATGAC 59.523 38.462 0.00 0.00 0.00 3.06
1733 1810 6.340522 TGTCGAATTGATACACATGATGACT 58.659 36.000 0.00 0.00 0.00 3.41
1756 1839 4.041075 TGGATTTACACCAACTGCTACTGA 59.959 41.667 0.00 0.00 34.25 3.41
1757 1840 4.392138 GGATTTACACCAACTGCTACTGAC 59.608 45.833 0.00 0.00 0.00 3.51
1758 1841 4.409718 TTTACACCAACTGCTACTGACA 57.590 40.909 0.00 0.00 0.00 3.58
1759 1842 2.240493 ACACCAACTGCTACTGACAC 57.760 50.000 0.00 0.00 0.00 3.67
1760 1843 1.762957 ACACCAACTGCTACTGACACT 59.237 47.619 0.00 0.00 0.00 3.55
1761 1844 2.138320 CACCAACTGCTACTGACACTG 58.862 52.381 0.00 0.00 0.00 3.66
1762 1845 1.762957 ACCAACTGCTACTGACACTGT 59.237 47.619 0.00 0.00 0.00 3.55
1763 1846 2.963101 ACCAACTGCTACTGACACTGTA 59.037 45.455 0.00 0.00 0.00 2.74
1764 1847 3.386726 ACCAACTGCTACTGACACTGTAA 59.613 43.478 0.00 0.00 0.00 2.41
1765 1848 4.141801 ACCAACTGCTACTGACACTGTAAA 60.142 41.667 0.00 0.00 0.00 2.01
1766 1849 4.997395 CCAACTGCTACTGACACTGTAAAT 59.003 41.667 0.00 0.00 0.00 1.40
1767 1850 5.470098 CCAACTGCTACTGACACTGTAAATT 59.530 40.000 0.00 0.00 0.00 1.82
1768 1851 6.017109 CCAACTGCTACTGACACTGTAAATTT 60.017 38.462 0.00 0.00 0.00 1.82
1769 1852 7.417612 CAACTGCTACTGACACTGTAAATTTT 58.582 34.615 0.00 0.00 0.00 1.82
1770 1853 7.568199 ACTGCTACTGACACTGTAAATTTTT 57.432 32.000 0.00 0.00 0.00 1.94
1804 1887 2.236893 TGCAGATGTGTATCTTGCTGGA 59.763 45.455 0.00 0.00 41.71 3.86
1831 1914 1.599240 GCTGATCTTCGGGATGGGC 60.599 63.158 0.00 0.00 34.33 5.36
1868 1951 1.959226 AGCAACGCGTCCAACGATT 60.959 52.632 14.44 0.00 46.05 3.34
1870 1953 0.164217 GCAACGCGTCCAACGATTTA 59.836 50.000 14.44 0.00 46.05 1.40
1927 2010 1.734465 CTGTTTGGGATGTTCGCTCTC 59.266 52.381 0.00 0.00 0.00 3.20
1946 2029 2.036475 CTCAAGGTGATACCGATCCCAG 59.964 54.545 0.00 0.00 44.90 4.45
2023 2116 3.458579 CGTCTCGTGCCGTCGTTG 61.459 66.667 0.00 0.00 0.00 4.10
2337 2430 7.593825 TGTACATGTAGGTTGATATCTGATCG 58.406 38.462 5.62 0.00 0.00 3.69
2341 2434 6.183309 TGTAGGTTGATATCTGATCGATCG 57.817 41.667 20.03 9.36 33.48 3.69
2368 2461 0.458025 GACCCCGACGTGCTAAGAAG 60.458 60.000 0.00 0.00 0.00 2.85
2371 2464 0.809385 CCCGACGTGCTAAGAAGAGA 59.191 55.000 0.00 0.00 0.00 3.10
2373 2466 2.251893 CCGACGTGCTAAGAAGAGAAC 58.748 52.381 0.00 0.00 0.00 3.01
2374 2467 1.905687 CGACGTGCTAAGAAGAGAACG 59.094 52.381 0.00 2.41 37.09 3.95
2375 2468 2.412455 CGACGTGCTAAGAAGAGAACGA 60.412 50.000 10.80 0.00 35.18 3.85
2377 2470 4.167268 GACGTGCTAAGAAGAGAACGAAT 58.833 43.478 10.80 0.00 35.18 3.34
2378 2471 4.167268 ACGTGCTAAGAAGAGAACGAATC 58.833 43.478 10.80 0.00 35.18 2.52
2379 2472 3.238570 CGTGCTAAGAAGAGAACGAATCG 59.761 47.826 0.00 0.00 33.03 3.34
2380 2473 4.413087 GTGCTAAGAAGAGAACGAATCGA 58.587 43.478 10.55 0.00 0.00 3.59
2381 2474 5.038033 GTGCTAAGAAGAGAACGAATCGAT 58.962 41.667 10.55 0.00 0.00 3.59
2382 2475 5.517054 GTGCTAAGAAGAGAACGAATCGATT 59.483 40.000 11.20 11.20 0.00 3.34
2383 2476 5.744345 TGCTAAGAAGAGAACGAATCGATTC 59.256 40.000 25.18 25.18 0.00 2.52
2392 2485 1.641677 GAATCGATTCGCGGTTGGG 59.358 57.895 21.57 0.00 44.78 4.12
2393 2486 1.772063 GAATCGATTCGCGGTTGGGG 61.772 60.000 21.57 0.00 44.78 4.96
2394 2487 2.246761 AATCGATTCGCGGTTGGGGA 62.247 55.000 6.13 0.00 42.78 4.81
2397 2490 2.203015 ATTCGCGGTTGGGGATCG 60.203 61.111 6.13 0.00 37.45 3.69
2398 2491 3.750373 ATTCGCGGTTGGGGATCGG 62.750 63.158 6.13 0.00 37.45 4.18
2419 2520 4.889427 TCGAGCACGAGGAACATG 57.111 55.556 0.88 0.00 43.81 3.21
2452 2557 4.654262 ACAGTGTAGGAAGGAAGAACTTGA 59.346 41.667 0.00 0.00 0.00 3.02
2493 2598 5.470845 AAACACGAAGTCTCTGAAGTTTG 57.529 39.130 0.00 0.00 41.61 2.93
2522 2627 1.987770 GCCGAATTGCTGACATTTGTG 59.012 47.619 0.00 0.00 0.00 3.33
2531 2636 2.293122 GCTGACATTTGTGTGCCAGTTA 59.707 45.455 0.00 0.00 0.00 2.24
2532 2637 3.057315 GCTGACATTTGTGTGCCAGTTAT 60.057 43.478 0.00 0.00 0.00 1.89
2533 2638 4.559300 GCTGACATTTGTGTGCCAGTTATT 60.559 41.667 0.00 0.00 0.00 1.40
2534 2639 5.335583 GCTGACATTTGTGTGCCAGTTATTA 60.336 40.000 0.00 0.00 0.00 0.98
2535 2640 6.252967 TGACATTTGTGTGCCAGTTATTAG 57.747 37.500 0.00 0.00 0.00 1.73
2536 2641 5.767665 TGACATTTGTGTGCCAGTTATTAGT 59.232 36.000 0.00 0.00 0.00 2.24
2537 2642 6.937465 TGACATTTGTGTGCCAGTTATTAGTA 59.063 34.615 0.00 0.00 0.00 1.82
2569 2674 4.418013 AAACAACAAAGTTTTTGCTGCC 57.582 36.364 0.00 0.00 38.49 4.85
2632 5740 3.330198 AGGGATTATGATCAGCCTTGGA 58.670 45.455 0.09 0.00 33.77 3.53
2729 5837 0.822532 ACGACAAGACTGGTCCGAGT 60.823 55.000 4.32 0.00 31.55 4.18
2884 5998 3.059386 GAAAACATCGGCCCGCCA 61.059 61.111 6.52 0.00 35.37 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.779569 ACGAGTGGATGAACGTTGAC 58.220 50.000 5.00 0.00 35.47 3.18
12 13 4.738740 GGAAATAGTACGAGTGGATGAACG 59.261 45.833 0.00 0.00 0.00 3.95
25 26 7.276878 GCTCTCTCTCTTTGTTGGAAATAGTAC 59.723 40.741 0.00 0.00 0.00 2.73
29 30 6.114187 TGCTCTCTCTCTTTGTTGGAAATA 57.886 37.500 0.00 0.00 0.00 1.40
44 45 1.520590 GCGTTTCGATCATGCTCTCTC 59.479 52.381 0.00 0.00 0.00 3.20
53 54 2.094234 TCTTGGATCTGCGTTTCGATCA 60.094 45.455 0.00 0.00 38.18 2.92
55 56 2.271800 GTCTTGGATCTGCGTTTCGAT 58.728 47.619 0.00 0.00 0.00 3.59
56 57 1.000394 TGTCTTGGATCTGCGTTTCGA 60.000 47.619 0.00 0.00 0.00 3.71
62 63 0.803768 CTCGGTGTCTTGGATCTGCG 60.804 60.000 0.00 0.00 0.00 5.18
107 120 2.555227 CCTTAGTCCATTGGGCAACTGT 60.555 50.000 10.50 0.00 0.00 3.55
147 160 8.642432 ACGATTTCTTATGGACATCTAATCAGA 58.358 33.333 0.00 0.00 31.07 3.27
149 162 7.171508 GCACGATTTCTTATGGACATCTAATCA 59.828 37.037 0.00 0.00 31.07 2.57
151 164 6.428159 GGCACGATTTCTTATGGACATCTAAT 59.572 38.462 0.00 0.00 31.07 1.73
158 172 5.585047 AGTTAAGGCACGATTTCTTATGGAC 59.415 40.000 0.00 0.00 0.00 4.02
170 184 1.338973 AGTCGACAAGTTAAGGCACGA 59.661 47.619 19.50 0.00 0.00 4.35
171 185 1.779569 AGTCGACAAGTTAAGGCACG 58.220 50.000 19.50 0.00 0.00 5.34
231 245 2.428890 CCTAAACAAACCACCAGCAACA 59.571 45.455 0.00 0.00 0.00 3.33
317 363 4.352893 TCATACCTCATCTCAAGGTGTCA 58.647 43.478 5.08 0.00 46.63 3.58
325 371 4.774726 GCTATTCCCTCATACCTCATCTCA 59.225 45.833 0.00 0.00 0.00 3.27
370 416 1.446099 CTAGCAACGCTCGCCTTCA 60.446 57.895 0.00 0.00 40.44 3.02
400 446 0.037590 AGGTTGCAGCCGTGGAATAA 59.962 50.000 14.49 0.00 36.28 1.40
409 455 3.793144 CGCTTCGAGGTTGCAGCC 61.793 66.667 12.39 12.39 0.00 4.85
426 472 2.854805 GCAACGAACCTTTGACAAGCTC 60.855 50.000 0.00 0.00 0.00 4.09
428 474 1.202245 TGCAACGAACCTTTGACAAGC 60.202 47.619 0.00 0.00 0.00 4.01
475 521 3.305177 CTTGGCCTGCCATTGCACC 62.305 63.158 12.40 0.00 46.64 5.01
487 533 1.683385 GTTCCCTGCAATATCTTGGCC 59.317 52.381 0.00 0.00 32.72 5.36
500 546 1.746615 CCGGTGATGCAGTTCCCTG 60.747 63.158 0.00 0.00 41.91 4.45
501 547 1.488705 TTCCGGTGATGCAGTTCCCT 61.489 55.000 0.00 0.00 0.00 4.20
524 572 4.947388 TGCGGGCTCTACTATGAAAATTTT 59.053 37.500 2.28 2.28 0.00 1.82
544 592 2.293122 TCAAAAACCAGATTGACCTGCG 59.707 45.455 0.00 0.00 30.94 5.18
566 614 7.988599 GCCCCTTAATTTTTAAAACCGGATAAT 59.011 33.333 9.46 0.00 0.00 1.28
633 685 5.556915 ACTTATCGTCCCATGACTTTTTCA 58.443 37.500 0.00 0.00 39.47 2.69
644 696 5.128171 ACATAGTGCTAAACTTATCGTCCCA 59.872 40.000 0.00 0.00 40.56 4.37
661 713 5.562506 TCGAAGAGTAGGTCAACATAGTG 57.437 43.478 0.00 0.00 0.00 2.74
693 748 2.450609 TCGAGGGTACAAAACTGAGC 57.549 50.000 0.00 0.00 0.00 4.26
738 793 2.899339 GCTTCTCGGGCCAGCATC 60.899 66.667 4.39 0.00 33.45 3.91
889 945 2.729491 GCTGGCGCGGTTGTTTTC 60.729 61.111 8.83 0.00 0.00 2.29
1064 1120 3.519930 GGCTCGTCGTCTCCCCTC 61.520 72.222 0.00 0.00 0.00 4.30
1067 1123 3.827898 CCAGGCTCGTCGTCTCCC 61.828 72.222 0.00 0.00 0.00 4.30
1084 1140 2.887086 CGGCCGGCGGTAACTAAC 60.887 66.667 28.82 8.47 0.00 2.34
1220 1276 4.720902 TGGTCCCGCCGTAGTCGA 62.721 66.667 0.00 0.00 41.21 4.20
1247 1303 2.992689 TAGCGGTGCCGGAGACAA 60.993 61.111 5.05 0.00 40.19 3.18
1251 1307 4.208686 GACCTAGCGGTGCCGGAG 62.209 72.222 5.05 0.00 45.73 4.63
1315 1371 3.494626 CACGCAAACGATAGGCATAAGAT 59.505 43.478 0.00 0.00 43.93 2.40
1364 1433 0.317352 TCGAAGATGATCTGCGCGAG 60.317 55.000 17.87 4.52 45.03 5.03
1366 1435 1.135046 AATCGAAGATGATCTGCGCG 58.865 50.000 17.87 11.39 45.03 6.86
1367 1436 2.096516 GGAAATCGAAGATGATCTGCGC 60.097 50.000 17.87 0.00 45.03 6.09
1479 1548 4.709886 TCTGGTTATCTGAATCGTGAGGAA 59.290 41.667 0.00 0.00 0.00 3.36
1521 1590 9.135843 CGATGTTACTCACTAATAACAAAGTCA 57.864 33.333 1.33 0.00 42.81 3.41
1522 1591 9.136952 ACGATGTTACTCACTAATAACAAAGTC 57.863 33.333 1.33 0.00 42.81 3.01
1523 1592 9.485206 AACGATGTTACTCACTAATAACAAAGT 57.515 29.630 1.33 2.62 42.81 2.66
1524 1593 9.953825 GAACGATGTTACTCACTAATAACAAAG 57.046 33.333 1.33 2.11 42.81 2.77
1525 1594 9.478768 TGAACGATGTTACTCACTAATAACAAA 57.521 29.630 1.33 0.00 42.81 2.83
1526 1595 9.135843 CTGAACGATGTTACTCACTAATAACAA 57.864 33.333 1.33 0.00 42.81 2.83
1527 1596 8.517056 TCTGAACGATGTTACTCACTAATAACA 58.483 33.333 0.00 0.00 43.49 2.41
1540 1616 9.825109 TTAATTACATCCATCTGAACGATGTTA 57.175 29.630 20.97 15.41 46.56 2.41
1559 1635 9.106070 ACCAACCGATACAAGATTCTTAATTAC 57.894 33.333 0.00 0.00 0.00 1.89
1568 1644 5.097742 TGATCACCAACCGATACAAGATT 57.902 39.130 0.00 0.00 0.00 2.40
1579 1655 1.004745 ACACATCCCTGATCACCAACC 59.995 52.381 0.00 0.00 0.00 3.77
1651 1727 0.839946 GGACCATCTGCCCTGTATGT 59.160 55.000 0.00 0.00 0.00 2.29
1694 1770 8.777865 TCAATTCGACAGAGAATATTTCAGTT 57.222 30.769 0.00 0.00 39.69 3.16
1700 1776 9.770097 ATGTGTATCAATTCGACAGAGAATATT 57.230 29.630 0.00 0.00 39.69 1.28
1707 1783 6.476706 GTCATCATGTGTATCAATTCGACAGA 59.523 38.462 0.00 0.00 0.00 3.41
1716 1793 8.046107 TGTAAATCCAGTCATCATGTGTATCAA 58.954 33.333 0.00 0.00 0.00 2.57
1720 1797 6.112734 GGTGTAAATCCAGTCATCATGTGTA 58.887 40.000 0.00 0.00 0.00 2.90
1721 1798 4.943705 GGTGTAAATCCAGTCATCATGTGT 59.056 41.667 0.00 0.00 0.00 3.72
1722 1799 4.943093 TGGTGTAAATCCAGTCATCATGTG 59.057 41.667 0.00 0.00 0.00 3.21
1723 1800 5.178096 TGGTGTAAATCCAGTCATCATGT 57.822 39.130 0.00 0.00 0.00 3.21
1724 1801 5.649395 AGTTGGTGTAAATCCAGTCATCATG 59.351 40.000 0.00 0.00 36.28 3.07
1725 1802 5.649395 CAGTTGGTGTAAATCCAGTCATCAT 59.351 40.000 0.00 0.00 36.28 2.45
1726 1803 5.003160 CAGTTGGTGTAAATCCAGTCATCA 58.997 41.667 0.00 0.00 36.28 3.07
1727 1804 4.142600 GCAGTTGGTGTAAATCCAGTCATC 60.143 45.833 0.00 0.00 36.28 2.92
1728 1805 3.758554 GCAGTTGGTGTAAATCCAGTCAT 59.241 43.478 0.00 0.00 36.28 3.06
1729 1806 3.146066 GCAGTTGGTGTAAATCCAGTCA 58.854 45.455 0.00 0.00 36.28 3.41
1730 1807 3.412386 AGCAGTTGGTGTAAATCCAGTC 58.588 45.455 0.00 0.00 36.28 3.51
1731 1808 3.508845 AGCAGTTGGTGTAAATCCAGT 57.491 42.857 0.00 0.00 36.28 4.00
1732 1809 4.393062 CAGTAGCAGTTGGTGTAAATCCAG 59.607 45.833 0.00 0.00 36.28 3.86
1733 1810 4.041075 TCAGTAGCAGTTGGTGTAAATCCA 59.959 41.667 0.00 0.00 0.00 3.41
1767 1850 4.185467 TCTGCAACAGCAAAGTGAAAAA 57.815 36.364 0.00 0.00 37.91 1.94
1768 1851 3.865011 TCTGCAACAGCAAAGTGAAAA 57.135 38.095 0.00 0.00 37.91 2.29
1769 1852 3.130869 ACATCTGCAACAGCAAAGTGAAA 59.869 39.130 0.00 0.00 37.91 2.69
1770 1853 2.689471 ACATCTGCAACAGCAAAGTGAA 59.311 40.909 0.00 0.00 37.91 3.18
1771 1854 2.033675 CACATCTGCAACAGCAAAGTGA 59.966 45.455 9.52 0.00 37.91 3.41
1772 1855 2.223641 ACACATCTGCAACAGCAAAGTG 60.224 45.455 12.11 12.11 37.91 3.16
1773 1856 2.026641 ACACATCTGCAACAGCAAAGT 58.973 42.857 0.00 0.00 37.91 2.66
1774 1857 2.787601 ACACATCTGCAACAGCAAAG 57.212 45.000 0.00 0.00 37.91 2.77
1775 1858 4.074259 AGATACACATCTGCAACAGCAAA 58.926 39.130 0.00 0.00 40.15 3.68
1776 1859 3.678289 AGATACACATCTGCAACAGCAA 58.322 40.909 0.00 0.00 40.15 3.91
1777 1860 3.339253 AGATACACATCTGCAACAGCA 57.661 42.857 0.00 0.00 40.15 4.41
1778 1861 3.730061 GCAAGATACACATCTGCAACAGC 60.730 47.826 0.00 0.00 40.81 4.40
1779 1862 3.688185 AGCAAGATACACATCTGCAACAG 59.312 43.478 0.00 0.00 40.81 3.16
1780 1863 3.437741 CAGCAAGATACACATCTGCAACA 59.562 43.478 0.00 0.00 40.81 3.33
1781 1864 3.181503 CCAGCAAGATACACATCTGCAAC 60.182 47.826 0.00 0.00 40.81 4.17
1831 1914 0.824109 TGATGAACAGCCCGTAGAGG 59.176 55.000 0.00 0.00 40.63 3.69
1927 2010 1.762957 ACTGGGATCGGTATCACCTTG 59.237 52.381 0.00 0.00 34.31 3.61
1946 2029 6.407475 ACAAAACTTGTTGAATGCTTTGAC 57.593 33.333 0.00 0.00 42.22 3.18
1970 2056 9.219603 CAGGTTTCTGAATCTGAATTTGTACTA 57.780 33.333 12.87 0.00 45.08 1.82
1971 2057 8.103948 CAGGTTTCTGAATCTGAATTTGTACT 57.896 34.615 12.87 0.00 45.08 2.73
2023 2116 1.743252 CTTCGGCCTCTCCTGCAAC 60.743 63.158 0.00 0.00 0.00 4.17
2296 2389 2.159156 TGTACATGTACATCACGAGGCC 60.159 50.000 30.31 0.00 40.77 5.19
2357 2450 3.238570 CGATTCGTTCTCTTCTTAGCACG 59.761 47.826 0.00 0.00 0.00 5.34
2374 2467 1.641677 CCCAACCGCGAATCGATTC 59.358 57.895 25.18 25.18 41.67 2.52
2375 2468 1.817941 CCCCAACCGCGAATCGATT 60.818 57.895 11.20 11.20 41.67 3.34
2377 2470 2.638330 GATCCCCAACCGCGAATCGA 62.638 60.000 8.23 0.00 41.67 3.59
2378 2471 2.203015 ATCCCCAACCGCGAATCG 60.203 61.111 8.23 0.00 38.08 3.34
2379 2472 2.244651 CGATCCCCAACCGCGAATC 61.245 63.158 8.23 0.00 0.00 2.52
2380 2473 2.203015 CGATCCCCAACCGCGAAT 60.203 61.111 8.23 0.00 0.00 3.34
2381 2474 4.460683 CCGATCCCCAACCGCGAA 62.461 66.667 8.23 0.00 0.00 4.70
2412 2513 5.054477 ACACTGTTACAGTACACATGTTCC 58.946 41.667 18.19 0.00 43.43 3.62
2419 2520 5.242393 TCCTTCCTACACTGTTACAGTACAC 59.758 44.000 18.19 0.00 43.43 2.90
2480 2585 5.030936 GCACAAACTTCAAACTTCAGAGAC 58.969 41.667 0.00 0.00 0.00 3.36
2493 2598 2.053627 CAGCAATTCGGCACAAACTTC 58.946 47.619 0.00 0.00 35.83 3.01
2522 2627 6.394025 AGAGTAGCTACTAATAACTGGCAC 57.606 41.667 26.11 9.27 36.50 5.01
2534 2639 8.959705 ACTTTGTTGTTTTTAGAGTAGCTACT 57.040 30.769 26.35 26.35 39.71 2.57
2535 2640 9.999009 AAACTTTGTTGTTTTTAGAGTAGCTAC 57.001 29.630 16.43 16.43 36.86 3.58
2568 2673 0.962356 CCTGGCCTAGTTGCACTTGG 60.962 60.000 3.32 10.71 42.76 3.61
2569 2674 1.589716 GCCTGGCCTAGTTGCACTTG 61.590 60.000 7.66 0.00 0.00 3.16
2801 5915 2.061773 GATTCCGCGATCGTGATCAAT 58.938 47.619 29.21 21.33 37.69 2.57
2812 5926 1.725665 CTGACCTACGATTCCGCGA 59.274 57.895 8.23 0.00 39.95 5.87
2884 5998 4.749310 CGCTGCTGTCCGGCTTCT 62.749 66.667 0.00 0.00 43.91 2.85


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

AutoCloner maintained by Alex Coulton.