Multiple sequence alignment - TraesCS4B01G219400

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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 TraesCS4B01G219400 chr4B 100.000 3134 0 0 1 3134 462210619 462213752 0.000000e+00 5788
1 TraesCS4B01G219400 chr4D 92.670 2524 126 28 653 3134 375118679 375121185 0.000000e+00 3581
2 TraesCS4B01G219400 chr4A 90.417 1847 132 28 651 2461 89449518 89447681 0.000000e+00 2388
3 TraesCS4B01G219400 chr4A 87.193 570 27 17 2505 3043 89447585 89447031 9.610000e-170 606
4 TraesCS4B01G219400 chr6A 92.743 565 34 5 1 561 535628618 535628057 0.000000e+00 809
5 TraesCS4B01G219400 chr6A 94.444 90 5 0 560 649 535627974 535627885 4.210000e-29 139
6 TraesCS4B01G219400 chr1A 82.456 570 55 20 1 561 542444806 542444273 1.020000e-124 457
7 TraesCS4B01G219400 chr1A 91.304 92 8 0 560 651 519285499 519285408 3.280000e-25 126
8 TraesCS4B01G219400 chr1A 90.323 93 9 0 559 651 354354292 354354384 4.240000e-24 122
9 TraesCS4B01G219400 chr3D 79.007 443 61 17 141 561 144059633 144059201 1.110000e-69 274
10 TraesCS4B01G219400 chr7A 85.153 229 23 5 163 382 547356546 547356320 1.130000e-54 224
11 TraesCS4B01G219400 chr7A 93.902 82 5 0 569 650 547356103 547356022 1.180000e-24 124
12 TraesCS4B01G219400 chr5D 81.443 291 39 6 2854 3134 69100013 69099728 1.130000e-54 224
13 TraesCS4B01G219400 chr5A 80.756 291 41 5 2854 3134 59704508 59704223 2.450000e-51 213
14 TraesCS4B01G219400 chr2B 84.659 176 21 4 350 522 443071318 443071490 1.490000e-38 171
15 TraesCS4B01G219400 chr2B 94.565 92 5 0 562 653 536930718 536930809 3.260000e-30 143
16 TraesCS4B01G219400 chr2B 92.308 91 7 0 560 650 443071571 443071661 2.540000e-26 130
17 TraesCS4B01G219400 chr7D 90.323 93 9 0 560 652 32171270 32171362 4.240000e-24 122
18 TraesCS4B01G219400 chr5B 90.323 93 9 0 559 651 39773932 39774024 4.240000e-24 122
19 TraesCS4B01G219400 chr6D 87.379 103 8 5 561 661 132853554 132853455 2.550000e-21 113


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 TraesCS4B01G219400 chr4B 462210619 462213752 3133 False 5788 5788 100.0000 1 3134 1 chr4B.!!$F1 3133
1 TraesCS4B01G219400 chr4D 375118679 375121185 2506 False 3581 3581 92.6700 653 3134 1 chr4D.!!$F1 2481
2 TraesCS4B01G219400 chr4A 89447031 89449518 2487 True 1497 2388 88.8050 651 3043 2 chr4A.!!$R1 2392
3 TraesCS4B01G219400 chr6A 535627885 535628618 733 True 474 809 93.5935 1 649 2 chr6A.!!$R1 648
4 TraesCS4B01G219400 chr1A 542444273 542444806 533 True 457 457 82.4560 1 561 1 chr1A.!!$R2 560

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
873 972 0.390472 CTCCTCTCCACGCAAAGGAC 60.39 60.0 0.0 0.0 34.29 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2652 2886 0.242017 GATCTTTGCAGCGCACCTTT 59.758 50.0 11.47 0.0 38.71 3.11 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
103 106 3.799137 TTGTATCGTTTGTTCCGAAGC 57.201 42.857 0.00 0.00 37.93 3.86
135 138 1.203364 ACAACATGACTCCCCTCCTCT 60.203 52.381 0.00 0.00 0.00 3.69
160 163 4.658901 CCCCTGTGGTTGTCTTATATAGGT 59.341 45.833 0.00 0.00 0.00 3.08
211 218 2.292569 GCGAGGTGGTACTATCGATCAA 59.707 50.000 0.00 0.00 37.35 2.57
283 290 1.344438 GGCCCAAGTGCTTTTAGCTTT 59.656 47.619 0.00 0.00 42.97 3.51
284 291 2.407090 GCCCAAGTGCTTTTAGCTTTG 58.593 47.619 0.00 5.21 42.97 2.77
285 292 2.407090 CCCAAGTGCTTTTAGCTTTGC 58.593 47.619 0.00 0.00 42.97 3.68
286 293 2.053627 CCAAGTGCTTTTAGCTTTGCG 58.946 47.619 0.00 0.00 42.97 4.85
307 314 4.758251 GCAAAACCATGGGCCGGC 62.758 66.667 21.18 21.18 0.00 6.13
308 315 4.081185 CAAAACCATGGGCCGGCC 62.081 66.667 38.57 38.57 0.00 6.13
322 329 0.456653 CCGGCCGCTTCTCATTTTTG 60.457 55.000 22.85 0.00 0.00 2.44
368 378 2.743538 TGCATGAGCCTCACGCAC 60.744 61.111 11.99 0.00 40.91 5.34
369 379 3.503363 GCATGAGCCTCACGCACC 61.503 66.667 8.06 0.00 35.40 5.01
383 396 4.495422 TCACGCACCTATTCTTCTTCTTC 58.505 43.478 0.00 0.00 0.00 2.87
493 506 7.849804 TTTTCTATGTTTCTCTATGTGCCTC 57.150 36.000 0.00 0.00 0.00 4.70
597 694 2.910360 AGACCCATACCCTACCCATT 57.090 50.000 0.00 0.00 0.00 3.16
599 696 2.021441 AGACCCATACCCTACCCATTCA 60.021 50.000 0.00 0.00 0.00 2.57
643 740 2.480610 CCCATGGGTCGAATTGCCG 61.481 63.158 23.93 0.00 0.00 5.69
649 746 1.673009 GGTCGAATTGCCGGGTTGA 60.673 57.895 2.18 0.00 0.00 3.18
650 747 1.500396 GTCGAATTGCCGGGTTGAC 59.500 57.895 2.18 0.00 0.00 3.18
651 748 0.953960 GTCGAATTGCCGGGTTGACT 60.954 55.000 2.18 0.00 0.00 3.41
847 944 4.201657 CACAAGCAACCCATCTGATCATA 58.798 43.478 0.00 0.00 0.00 2.15
873 972 0.390472 CTCCTCTCCACGCAAAGGAC 60.390 60.000 0.00 0.00 34.29 3.85
1017 1121 1.619432 GCCATGGGATTCCTCCACAAA 60.619 52.381 15.13 0.00 44.08 2.83
1053 1157 0.108424 CGAAGCTCAAGTCCCTCCTG 60.108 60.000 0.00 0.00 0.00 3.86
1155 1259 3.382832 CTCGTCCTCGGCCACCTT 61.383 66.667 2.24 0.00 37.69 3.50
1209 1313 1.174078 TGAAGCGAGACGTGGTGGTA 61.174 55.000 0.00 0.00 0.00 3.25
1215 1319 0.245813 GAGACGTGGTGGTACCCTTC 59.754 60.000 10.07 0.00 37.50 3.46
1223 1327 1.090052 GTGGTACCCTTCGATGCAGC 61.090 60.000 10.07 0.00 0.00 5.25
1354 1458 1.354040 CTGAGCAGTTAGACAAGCCG 58.646 55.000 0.00 0.00 0.00 5.52
1355 1459 0.037326 TGAGCAGTTAGACAAGCCGG 60.037 55.000 0.00 0.00 0.00 6.13
1407 1514 7.099764 TGTTCTCATCTTTGGTTCTCTATGTC 58.900 38.462 0.00 0.00 0.00 3.06
1442 1549 2.497273 ACATTGCTATTCTGTTTGGGCC 59.503 45.455 0.00 0.00 0.00 5.80
1606 1713 4.891727 GGCACCGGCATCGTCGAT 62.892 66.667 0.00 0.75 43.71 3.59
1662 1770 4.487714 TTTCTAGCGGGTCTCATTGATT 57.512 40.909 0.00 0.00 0.00 2.57
1664 1772 3.031013 TCTAGCGGGTCTCATTGATTCA 58.969 45.455 0.00 0.00 0.00 2.57
1670 1778 3.012518 GGGTCTCATTGATTCACAGTGG 58.987 50.000 0.00 0.00 36.95 4.00
1675 1783 6.239008 GGTCTCATTGATTCACAGTGGAAAAA 60.239 38.462 0.00 0.00 36.95 1.94
1679 1787 6.323482 TCATTGATTCACAGTGGAAAAAGGAA 59.677 34.615 0.00 0.00 36.95 3.36
1696 1804 3.901797 AAAGAGGAACTGCGGGCGG 62.902 63.158 0.00 0.00 41.55 6.13
1707 1815 4.096003 CGGGCGGGGAGTTCACAT 62.096 66.667 0.00 0.00 0.00 3.21
1759 1867 1.305201 GAAGCTGTCCGGAAACACAA 58.695 50.000 5.23 0.00 0.00 3.33
1761 1869 1.157870 AGCTGTCCGGAAACACAACG 61.158 55.000 5.23 0.00 0.00 4.10
1762 1870 1.155424 GCTGTCCGGAAACACAACGA 61.155 55.000 5.23 0.00 0.00 3.85
1770 1878 1.606668 GGAAACACAACGAGCATGGAA 59.393 47.619 0.00 0.00 0.00 3.53
1783 1891 4.394300 CGAGCATGGAACTGAAGAAGAAAT 59.606 41.667 0.00 0.00 0.00 2.17
1788 1896 6.515531 GCATGGAACTGAAGAAGAAATTGACA 60.516 38.462 0.00 0.00 0.00 3.58
1803 1911 1.019278 TGACAAAAGAGATCGCCGCC 61.019 55.000 0.00 0.00 0.00 6.13
1830 1938 3.392616 ACAACATCTTGGTGGACTTCTCT 59.607 43.478 0.00 0.00 39.97 3.10
1836 1944 1.722034 TGGTGGACTTCTCTGAGCTT 58.278 50.000 0.00 0.00 0.00 3.74
1839 1947 1.620819 GTGGACTTCTCTGAGCTTCCA 59.379 52.381 14.21 14.21 0.00 3.53
1859 1967 1.372087 GAAGCAACGGAGGATGGCAG 61.372 60.000 0.00 0.00 0.00 4.85
1860 1968 2.045926 GCAACGGAGGATGGCAGT 60.046 61.111 0.00 0.00 0.00 4.40
1866 1974 1.620819 ACGGAGGATGGCAGTGATATC 59.379 52.381 0.00 0.00 0.00 1.63
1870 1978 3.072184 GGAGGATGGCAGTGATATCTTGT 59.928 47.826 3.98 0.00 0.00 3.16
1875 1983 4.508551 TGGCAGTGATATCTTGTTGGAT 57.491 40.909 3.98 0.00 0.00 3.41
1880 1988 6.459298 GGCAGTGATATCTTGTTGGATTTCTG 60.459 42.308 3.98 0.00 0.00 3.02
1882 1990 7.678218 GCAGTGATATCTTGTTGGATTTCTGTC 60.678 40.741 3.98 0.00 0.00 3.51
1883 1991 6.536582 AGTGATATCTTGTTGGATTTCTGTCG 59.463 38.462 3.98 0.00 0.00 4.35
1899 2007 0.603975 GTCGGCTCCAAGAAGCAACT 60.604 55.000 0.00 0.00 44.35 3.16
1902 2010 0.877743 GGCTCCAAGAAGCAACTGAC 59.122 55.000 0.00 0.00 44.35 3.51
1945 2053 3.844090 GTCAGGAGCTCCTCGGCC 61.844 72.222 33.06 16.03 46.65 6.13
1951 2059 1.078143 GAGCTCCTCGGCCAAATGT 60.078 57.895 2.24 0.00 0.00 2.71
1995 2103 2.632996 AGGTTCAGAGTCGGACAATGAA 59.367 45.455 18.40 18.40 0.00 2.57
2010 2118 2.015736 ATGAACATCCTCGCTCACAC 57.984 50.000 0.00 0.00 0.00 3.82
2019 2127 0.232303 CTCGCTCACACGGAACAAAC 59.768 55.000 0.00 0.00 0.00 2.93
2064 2172 4.009675 AGAATGTGCACATCGTTACCAAT 58.990 39.130 31.45 13.47 35.10 3.16
2070 2178 3.435327 TGCACATCGTTACCAATTCTGAC 59.565 43.478 0.00 0.00 0.00 3.51
2145 2256 0.935898 GCGCATGAGAACTGAGATGG 59.064 55.000 0.30 0.00 0.00 3.51
2146 2257 1.741732 GCGCATGAGAACTGAGATGGT 60.742 52.381 0.30 0.00 0.00 3.55
2165 2280 0.975556 TGACCTCTGCATCCGGCTAA 60.976 55.000 0.00 0.00 45.15 3.09
2186 2301 5.514274 AAAAATGTAACGATATGGGCAGG 57.486 39.130 0.00 0.00 0.00 4.85
2188 2303 2.902705 TGTAACGATATGGGCAGGAC 57.097 50.000 0.00 0.00 0.00 3.85
2189 2304 2.112190 TGTAACGATATGGGCAGGACA 58.888 47.619 0.00 0.00 0.00 4.02
2247 2364 7.280652 TGTGAATAGACATGAATACACACATGG 59.719 37.037 0.00 0.00 45.31 3.66
2255 2372 6.719370 ACATGAATACACACATGGGTACTTTT 59.281 34.615 0.00 0.00 45.31 2.27
2264 2381 8.161425 ACACACATGGGTACTTTTAAACTATCT 58.839 33.333 0.00 0.00 0.00 1.98
2265 2382 8.450964 CACACATGGGTACTTTTAAACTATCTG 58.549 37.037 0.00 0.00 0.00 2.90
2279 2417 6.552445 AAACTATCTGCTAGTCCAGTCAAT 57.448 37.500 0.00 0.00 39.87 2.57
2282 2420 4.833478 ATCTGCTAGTCCAGTCAATTGT 57.167 40.909 5.13 0.00 34.47 2.71
2284 2422 5.073311 TCTGCTAGTCCAGTCAATTGTAC 57.927 43.478 5.13 2.82 34.47 2.90
2297 2435 9.146984 CCAGTCAATTGTACTATCGTCTAAAAA 57.853 33.333 5.13 0.00 0.00 1.94
2395 2535 2.377136 ACCTCATGGTCACCTGTCC 58.623 57.895 0.00 0.00 44.78 4.02
2397 2537 1.544825 CCTCATGGTCACCTGTCCGT 61.545 60.000 0.00 0.00 0.00 4.69
2408 2548 0.606401 CCTGTCCGTTGCTTGGTCAT 60.606 55.000 0.00 0.00 0.00 3.06
2464 2605 6.314648 GCTTTAAGTAACCACCATACCACTAC 59.685 42.308 0.00 0.00 0.00 2.73
2480 2621 4.343239 ACCACTACGTTATCCAACCTATCC 59.657 45.833 0.00 0.00 0.00 2.59
2488 2629 7.571025 ACGTTATCCAACCTATCCTTAATGTT 58.429 34.615 0.00 0.00 0.00 2.71
2565 2772 6.858993 GCAAACCAACAAATATTTACTCGACA 59.141 34.615 0.00 0.00 0.00 4.35
2581 2788 6.771188 ACTCGACAAGATCAGTACAAAAAG 57.229 37.500 0.00 0.00 0.00 2.27
2597 2831 4.875536 ACAAAAAGCAAAGATGGTCAAACC 59.124 37.500 0.00 0.00 35.91 3.27
2626 2860 0.755686 AAAAATGCACAGGGGCGAAA 59.244 45.000 0.00 0.00 36.28 3.46
2651 2885 3.194620 TGGAAGGGGAAATAAGCCAGTA 58.805 45.455 0.00 0.00 0.00 2.74
2652 2886 3.594232 TGGAAGGGGAAATAAGCCAGTAA 59.406 43.478 0.00 0.00 0.00 2.24
2728 2962 4.996758 GGATTTTCTTGTGGGTGATTTTGG 59.003 41.667 0.00 0.00 0.00 3.28
2741 2975 5.869344 GGGTGATTTTGGATTTTCTTGCTAC 59.131 40.000 0.00 0.00 0.00 3.58
2838 3073 6.450545 TCAAAATCAAATTTGTCGGCATACA 58.549 32.000 17.47 0.00 40.40 2.29
2942 3190 7.224297 AGAACCTGTAAAGAGCAAACTATTCA 58.776 34.615 0.00 0.00 0.00 2.57
3051 3299 6.780031 TCAAGTCAAATCCCTTTTTGTATCCA 59.220 34.615 0.00 0.00 37.73 3.41
3052 3300 7.288852 TCAAGTCAAATCCCTTTTTGTATCCAA 59.711 33.333 0.00 0.00 37.73 3.53
3115 3363 4.651994 CACTCCTTTGATGCAAATACGAC 58.348 43.478 0.00 0.00 32.70 4.34
3119 3367 5.938322 TCCTTTGATGCAAATACGACTTTC 58.062 37.500 0.00 0.00 32.70 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 3.342377 TTATTGCACTCACCCGATGAA 57.658 42.857 0.00 0.00 36.69 2.57
53 55 3.342377 TTTATTGCACTCACCCGATGA 57.658 42.857 0.00 0.00 35.45 2.92
89 92 0.660300 GGCTTGCTTCGGAACAAACG 60.660 55.000 7.02 0.00 0.00 3.60
103 106 0.386352 CATGTTGTCTGCGTGGCTTG 60.386 55.000 0.00 0.00 0.00 4.01
135 138 5.368523 CCTATATAAGACAACCACAGGGGAA 59.631 44.000 0.00 0.00 41.15 3.97
160 163 2.721425 AGAAAACGAAGGGTTGGACA 57.279 45.000 0.00 0.00 39.30 4.02
283 290 4.354939 CATGGTTTTGCCCGCGCA 62.355 61.111 8.75 0.00 45.49 6.09
285 292 4.433877 CCCATGGTTTTGCCCGCG 62.434 66.667 11.73 0.00 36.04 6.46
286 293 4.758251 GCCCATGGTTTTGCCCGC 62.758 66.667 11.73 0.00 36.04 6.13
307 314 2.436417 TCCCTCAAAAATGAGAAGCGG 58.564 47.619 7.39 0.76 38.13 5.52
308 315 3.181493 CCATCCCTCAAAAATGAGAAGCG 60.181 47.826 7.39 0.00 38.13 4.68
322 329 3.493303 GGACCTGGCCCATCCCTC 61.493 72.222 0.00 0.00 0.00 4.30
368 378 5.582665 CCAACCGAAGAAGAAGAAGAATAGG 59.417 44.000 0.00 0.00 0.00 2.57
369 379 5.064071 GCCAACCGAAGAAGAAGAAGAATAG 59.936 44.000 0.00 0.00 0.00 1.73
383 396 5.286082 CGAGAAAAATAATTGCCAACCGAAG 59.714 40.000 0.00 0.00 0.00 3.79
472 485 4.645136 ACGAGGCACATAGAGAAACATAGA 59.355 41.667 0.00 0.00 0.00 1.98
475 488 3.525537 CACGAGGCACATAGAGAAACAT 58.474 45.455 0.00 0.00 0.00 2.71
640 737 1.221021 CCTTAGGAGTCAACCCGGC 59.779 63.158 0.00 0.00 0.00 6.13
643 740 2.238144 GGTTACCCTTAGGAGTCAACCC 59.762 54.545 0.00 0.00 36.73 4.11
649 746 2.830321 CTCGTTGGTTACCCTTAGGAGT 59.170 50.000 0.00 0.00 36.73 3.85
650 747 2.167900 CCTCGTTGGTTACCCTTAGGAG 59.832 54.545 0.00 5.16 36.73 3.69
651 748 2.181975 CCTCGTTGGTTACCCTTAGGA 58.818 52.381 0.00 0.00 36.73 2.94
672 769 9.585099 TTTTAAAATATTGCGAGCAAATGAGAT 57.415 25.926 14.76 0.00 39.55 2.75
766 863 6.259550 AGAATTTGTAGGCTCATGTGTTTC 57.740 37.500 0.00 0.00 0.00 2.78
820 917 1.533753 ATGGGTTGCTTGTGGGTGG 60.534 57.895 0.00 0.00 0.00 4.61
821 918 0.540365 AGATGGGTTGCTTGTGGGTG 60.540 55.000 0.00 0.00 0.00 4.61
822 919 0.540365 CAGATGGGTTGCTTGTGGGT 60.540 55.000 0.00 0.00 0.00 4.51
823 920 0.251297 TCAGATGGGTTGCTTGTGGG 60.251 55.000 0.00 0.00 0.00 4.61
847 944 1.231641 CGTGGAGAGGAGGAGGGAT 59.768 63.158 0.00 0.00 0.00 3.85
873 972 1.546923 TGATCTTGGTTGCATTGCTGG 59.453 47.619 10.49 0.00 0.00 4.85
922 1021 9.772973 TTCTGTTATATTCGGTTGTATTGCTAT 57.227 29.630 0.00 0.00 0.00 2.97
1017 1121 1.302033 CGCTGTCTGCTTGGAGGTT 60.302 57.895 0.00 0.00 40.11 3.50
1209 1313 0.179045 GTATGGCTGCATCGAAGGGT 60.179 55.000 0.50 0.00 0.00 4.34
1215 1319 0.516001 GCATCAGTATGGCTGCATCG 59.484 55.000 0.50 0.00 44.66 3.84
1223 1327 3.376234 CAGAAACACCAGCATCAGTATGG 59.624 47.826 0.00 0.00 40.10 2.74
1354 1458 0.105778 GAGGCAGGCAGACATACTCC 59.894 60.000 0.00 0.00 0.00 3.85
1355 1459 0.826715 TGAGGCAGGCAGACATACTC 59.173 55.000 0.00 0.00 0.00 2.59
1407 1514 8.199449 AGAATAGCAATGTTTATTGTCCAATGG 58.801 33.333 2.80 0.00 44.41 3.16
1442 1549 4.554363 CTCGCCGCACTCCCTACG 62.554 72.222 0.00 0.00 0.00 3.51
1606 1713 5.950023 ACTATAGGAGTTCTTACGATGGGA 58.050 41.667 4.43 0.00 33.13 4.37
1626 1733 6.929049 CCCGCTAGAAATGATCAAATGTACTA 59.071 38.462 0.00 0.00 0.00 1.82
1627 1734 5.760253 CCCGCTAGAAATGATCAAATGTACT 59.240 40.000 0.00 0.00 0.00 2.73
1662 1770 4.080015 TCCTCTTTCCTTTTTCCACTGTGA 60.080 41.667 9.86 0.00 0.00 3.58
1664 1772 4.519906 TCCTCTTTCCTTTTTCCACTGT 57.480 40.909 0.00 0.00 0.00 3.55
1670 1778 3.304726 CCGCAGTTCCTCTTTCCTTTTTC 60.305 47.826 0.00 0.00 0.00 2.29
1675 1783 1.679898 CCCGCAGTTCCTCTTTCCT 59.320 57.895 0.00 0.00 0.00 3.36
1679 1787 4.394712 CCGCCCGCAGTTCCTCTT 62.395 66.667 0.00 0.00 0.00 2.85
1696 1804 0.951558 AACAACGCATGTGAACTCCC 59.048 50.000 14.43 0.00 42.99 4.30
1707 1815 1.586541 TGGCAACACAAACAACGCA 59.413 47.368 0.00 0.00 46.17 5.24
1737 1845 0.250295 TGTTTCCGGACAGCTTCCAG 60.250 55.000 1.83 4.43 46.29 3.86
1754 1862 1.202639 TCAGTTCCATGCTCGTTGTGT 60.203 47.619 0.00 0.00 0.00 3.72
1759 1867 2.300152 TCTTCTTCAGTTCCATGCTCGT 59.700 45.455 0.00 0.00 0.00 4.18
1761 1869 5.893897 ATTTCTTCTTCAGTTCCATGCTC 57.106 39.130 0.00 0.00 0.00 4.26
1762 1870 5.771666 TCAATTTCTTCTTCAGTTCCATGCT 59.228 36.000 0.00 0.00 0.00 3.79
1770 1878 8.511604 TCTCTTTTGTCAATTTCTTCTTCAGT 57.488 30.769 0.00 0.00 0.00 3.41
1783 1891 0.796312 GCGGCGATCTCTTTTGTCAA 59.204 50.000 12.98 0.00 0.00 3.18
1788 1896 1.519455 CTCGGCGGCGATCTCTTTT 60.519 57.895 34.71 0.00 0.00 2.27
1803 1911 2.480419 GTCCACCAAGATGTTGTTCTCG 59.520 50.000 1.49 0.00 30.95 4.04
1836 1944 0.250234 CATCCTCCGTTGCTTCTGGA 59.750 55.000 0.00 0.00 0.00 3.86
1839 1947 1.078143 GCCATCCTCCGTTGCTTCT 60.078 57.895 0.00 0.00 0.00 2.85
1859 1967 6.238211 CCGACAGAAATCCAACAAGATATCAC 60.238 42.308 5.32 0.00 0.00 3.06
1860 1968 5.817296 CCGACAGAAATCCAACAAGATATCA 59.183 40.000 5.32 0.00 0.00 2.15
1866 1974 2.154462 AGCCGACAGAAATCCAACAAG 58.846 47.619 0.00 0.00 0.00 3.16
1870 1978 0.690192 TGGAGCCGACAGAAATCCAA 59.310 50.000 0.00 0.00 37.12 3.53
1875 1983 1.878102 GCTTCTTGGAGCCGACAGAAA 60.878 52.381 0.00 0.00 36.66 2.52
1880 1988 0.603975 AGTTGCTTCTTGGAGCCGAC 60.604 55.000 0.00 0.00 42.01 4.79
1882 1990 0.603707 TCAGTTGCTTCTTGGAGCCG 60.604 55.000 0.00 0.00 42.01 5.52
1883 1991 0.877743 GTCAGTTGCTTCTTGGAGCC 59.122 55.000 0.00 0.00 42.01 4.70
1899 2007 2.020720 ACATTGTTGTTGCCTTCGTCA 58.979 42.857 0.00 0.00 29.55 4.35
1902 2010 2.393764 GGAACATTGTTGTTGCCTTCG 58.606 47.619 6.80 0.00 46.01 3.79
1945 2053 1.131126 GTCGTCCTGGCATGACATTTG 59.869 52.381 20.43 6.49 33.16 2.32
1951 2059 1.221566 CCATGTCGTCCTGGCATGA 59.778 57.895 10.80 0.00 41.62 3.07
1975 2083 2.737252 GTTCATTGTCCGACTCTGAACC 59.263 50.000 22.90 12.94 39.68 3.62
1995 2103 1.532604 TTCCGTGTGAGCGAGGATGT 61.533 55.000 0.00 0.00 32.19 3.06
2010 2118 2.548295 CCCGGGTGTGTTTGTTCCG 61.548 63.158 14.18 0.00 40.32 4.30
2019 2127 4.087892 CTCTCCAGCCCGGGTGTG 62.088 72.222 24.63 19.67 34.36 3.82
2070 2178 4.554292 CTGTAACCTCATCATCTGATCCG 58.446 47.826 0.00 0.00 32.10 4.18
2127 2238 1.931841 CACCATCTCAGTTCTCATGCG 59.068 52.381 0.00 0.00 0.00 4.73
2145 2256 1.676678 TAGCCGGATGCAGAGGTCAC 61.677 60.000 5.05 0.00 44.83 3.67
2146 2257 0.975556 TTAGCCGGATGCAGAGGTCA 60.976 55.000 5.05 0.00 44.83 4.02
2165 2280 4.578928 GTCCTGCCCATATCGTTACATTTT 59.421 41.667 0.00 0.00 0.00 1.82
2189 2304 2.038689 TGCACATGGACAAATGGCATTT 59.961 40.909 19.39 19.39 32.41 2.32
2202 2319 0.686224 AATTTGGTGGGTGCACATGG 59.314 50.000 20.43 0.00 0.00 3.66
2247 2364 8.255905 TGGACTAGCAGATAGTTTAAAAGTACC 58.744 37.037 0.00 0.00 45.06 3.34
2255 2372 7.661536 ATTGACTGGACTAGCAGATAGTTTA 57.338 36.000 0.00 0.00 45.06 2.01
2264 2381 6.459710 CGATAGTACAATTGACTGGACTAGCA 60.460 42.308 13.59 0.00 45.56 3.49
2265 2382 5.915758 CGATAGTACAATTGACTGGACTAGC 59.084 44.000 13.59 11.89 44.22 3.42
2297 2435 9.053840 CATGAGATACAGCTGATTTACATTTCT 57.946 33.333 23.35 5.81 0.00 2.52
2307 2446 1.001746 CGGCCATGAGATACAGCTGAT 59.998 52.381 23.35 9.62 30.65 2.90
2319 2458 2.063979 CCACTAGGGTCGGCCATGA 61.064 63.158 9.07 0.00 36.17 3.07
2352 2492 5.509501 CCATGACTGTTAAGCAATGTGGTTT 60.510 40.000 0.00 0.00 39.08 3.27
2392 2532 1.787847 CGATGACCAAGCAACGGAC 59.212 57.895 0.00 0.00 31.51 4.79
2395 2535 2.480555 GGCGATGACCAAGCAACG 59.519 61.111 0.00 0.00 37.16 4.10
2397 2537 1.573829 GAACGGCGATGACCAAGCAA 61.574 55.000 16.62 0.00 0.00 3.91
2408 2548 0.249120 ATCAAGGTGATGAACGGCGA 59.751 50.000 16.62 0.00 35.43 5.54
2464 2605 9.720769 ATAACATTAAGGATAGGTTGGATAACG 57.279 33.333 0.00 0.00 37.69 3.18
2480 2621 8.915871 AAATACTTGCACAGCATAACATTAAG 57.084 30.769 0.00 0.00 38.76 1.85
2488 2629 8.138074 TGTTTACAAAAATACTTGCACAGCATA 58.862 29.630 0.00 0.00 38.76 3.14
2565 2772 7.014615 ACCATCTTTGCTTTTTGTACTGATCTT 59.985 33.333 0.00 0.00 0.00 2.40
2581 2788 1.337167 GCCAGGTTTGACCATCTTTGC 60.337 52.381 0.00 0.00 41.95 3.68
2597 2831 1.228533 GTGCATTTTTGTTGGGCCAG 58.771 50.000 6.23 0.00 0.00 4.85
2626 2860 5.103086 ACTGGCTTATTTCCCCTTCCATATT 60.103 40.000 0.00 0.00 0.00 1.28
2651 2885 0.675633 ATCTTTGCAGCGCACCTTTT 59.324 45.000 11.47 0.00 38.71 2.27
2652 2886 0.242017 GATCTTTGCAGCGCACCTTT 59.758 50.000 11.47 0.00 38.71 3.11
2728 2962 5.860716 CAGCTCTTTTGGTAGCAAGAAAATC 59.139 40.000 7.51 0.00 41.32 2.17
2741 2975 4.326826 TGGTAACTGATCAGCTCTTTTGG 58.673 43.478 22.83 0.00 37.61 3.28
2908 3143 8.357290 TGCTCTTTACAGGTTCTATACTTGTA 57.643 34.615 0.00 0.00 44.37 2.41
2940 3188 4.920999 TCTCCACAAATGTCATTCCATGA 58.079 39.130 0.00 0.00 36.84 3.07
2942 3190 5.047802 GTGTTCTCCACAAATGTCATTCCAT 60.048 40.000 0.00 0.00 43.92 3.41
2961 3209 3.181524 CGGTTATCGTCACCATTGTGTTC 60.182 47.826 0.00 0.00 43.26 3.18
2987 3235 8.734386 CAGTGAGAGCTTGGAAATATTAGTTTT 58.266 33.333 0.00 0.00 0.00 2.43
3094 3342 4.579869 AGTCGTATTTGCATCAAAGGAGT 58.420 39.130 0.00 0.00 36.76 3.85


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

AutoCloner maintained by Alex Coulton.