Multiple sequence alignment - TraesCS5A01G238900

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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 TraesCS5A01G238900 chr5A 100.000 2552 0 0 1 2552 455088178 455090729 0.000000e+00 4713.0
1 TraesCS5A01G238900 chr5B 93.899 2098 104 15 27 2115 418471021 418473103 0.000000e+00 3144.0
2 TraesCS5A01G238900 chr5B 89.840 374 28 6 582 955 709933557 709933920 2.970000e-129 472.0
3 TraesCS5A01G238900 chr5B 81.315 289 31 11 2278 2548 418506606 418506889 1.990000e-51 213.0
4 TraesCS5A01G238900 chr5D 94.882 1739 64 13 27 1757 354258643 354260364 0.000000e+00 2695.0
5 TraesCS5A01G238900 chr5D 89.037 374 34 4 582 955 412722501 412722135 8.320000e-125 457.0
6 TraesCS5A01G238900 chr5D 87.607 234 19 4 2228 2454 354260609 354260839 1.950000e-66 263.0
7 TraesCS5A01G238900 chr5D 95.395 152 7 0 2094 2245 354260432 354260583 2.540000e-60 243.0
8 TraesCS5A01G238900 chr5D 100.000 30 0 0 2044 2073 354260401 354260430 3.550000e-04 56.5
9 TraesCS5A01G238900 chr3B 89.362 47 4 1 2500 2546 15984097 15984142 9.860000e-05 58.4


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 TraesCS5A01G238900 chr5A 455088178 455090729 2551 False 4713.000 4713 100.000 1 2552 1 chr5A.!!$F1 2551
1 TraesCS5A01G238900 chr5B 418471021 418473103 2082 False 3144.000 3144 93.899 27 2115 1 chr5B.!!$F1 2088
2 TraesCS5A01G238900 chr5D 354258643 354260839 2196 False 814.375 2695 94.471 27 2454 4 chr5D.!!$F1 2427

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
975 980 1.672881 GCCTTCTCCATCATTTGTCGG 59.327 52.381 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2460 2521 0.322546 GGACCATCCAACTTCGGCTT 60.323 55.0 0.0 0.0 36.28 4.35 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
22 23 4.833478 ACTGCAACTATTCTGACCTGAT 57.167 40.909 0.00 0.00 0.00 2.90
23 24 5.939764 ACTGCAACTATTCTGACCTGATA 57.060 39.130 0.00 0.00 0.00 2.15
24 25 5.911752 ACTGCAACTATTCTGACCTGATAG 58.088 41.667 0.00 0.00 0.00 2.08
25 26 5.163364 ACTGCAACTATTCTGACCTGATAGG 60.163 44.000 0.00 0.00 42.49 2.57
45 46 5.041191 AGGCTGATACATGGAAGGTTAAG 57.959 43.478 0.00 0.00 28.09 1.85
48 49 4.274459 GCTGATACATGGAAGGTTAAGCTG 59.726 45.833 8.16 0.00 30.09 4.24
189 190 6.048732 TGTCATGGAACTGTAAATAGCTCA 57.951 37.500 0.00 0.00 0.00 4.26
260 261 7.616935 ACATCTTGTTCATACCATGATCCTTTT 59.383 33.333 0.00 0.00 39.39 2.27
300 301 6.372659 GCATTCAGTACATTCCTTCTGAAAGA 59.627 38.462 9.82 0.00 45.58 2.52
476 478 4.500205 GGGGCGGTAATTTTATTAACTGGC 60.500 45.833 1.53 1.53 41.62 4.85
478 480 4.201940 GGCGGTAATTTTATTAACTGGCGT 60.202 41.667 0.00 0.00 34.62 5.68
528 530 9.173939 GTGATTCTTTTCACTACACAATTTCTG 57.826 33.333 0.00 0.00 42.22 3.02
610 614 5.646793 TCTGTCTAGTTATTGTACACGCTCT 59.353 40.000 0.00 0.00 0.00 4.09
620 624 6.648725 ATTGTACACGCTCTTATTCTTCAC 57.351 37.500 0.00 0.00 0.00 3.18
696 701 1.882623 GCTTTGGACCAGTTCTCAAGG 59.117 52.381 0.00 0.00 0.00 3.61
819 824 4.588951 TCCTTTCAGTGCAAGTTCTAGAGA 59.411 41.667 1.81 0.00 0.00 3.10
820 825 4.928615 CCTTTCAGTGCAAGTTCTAGAGAG 59.071 45.833 1.81 0.00 0.00 3.20
866 871 4.209538 TGCAGCTATCAGGCATTTGTATT 58.790 39.130 0.00 0.00 31.58 1.89
868 873 4.320788 GCAGCTATCAGGCATTTGTATTCC 60.321 45.833 0.00 0.00 34.17 3.01
969 974 5.370880 ACCAGTTATAGCCTTCTCCATCATT 59.629 40.000 0.00 0.00 0.00 2.57
973 978 6.995091 AGTTATAGCCTTCTCCATCATTTGTC 59.005 38.462 0.00 0.00 0.00 3.18
975 980 1.672881 GCCTTCTCCATCATTTGTCGG 59.327 52.381 0.00 0.00 0.00 4.79
976 981 2.292267 CCTTCTCCATCATTTGTCGGG 58.708 52.381 0.00 0.00 0.00 5.14
989 994 2.042831 GTCGGGAGCTGCAGCAAAT 61.043 57.895 38.24 20.29 45.16 2.32
1035 1040 5.513233 AGCATCCTGACCTTCAAATACAAT 58.487 37.500 0.00 0.00 0.00 2.71
1446 1451 4.357279 GGGGACAGCTGCAGCCTT 62.357 66.667 34.39 22.02 43.38 4.35
1460 1465 2.581354 CCTTGAGGACTGCCGGAG 59.419 66.667 5.05 1.84 39.96 4.63
1491 1496 2.482142 GGAGATCGACAGGAACCATGAC 60.482 54.545 0.00 0.00 0.00 3.06
1552 1557 1.485066 GCCCGAGGAAGAGGATGTAAA 59.515 52.381 0.00 0.00 0.00 2.01
1562 1567 5.105756 GGAAGAGGATGTAAACATTTGTGGG 60.106 44.000 0.00 0.00 36.57 4.61
1563 1568 4.998051 AGAGGATGTAAACATTTGTGGGT 58.002 39.130 0.00 0.00 36.57 4.51
1564 1569 5.010282 AGAGGATGTAAACATTTGTGGGTC 58.990 41.667 0.00 0.00 36.57 4.46
1566 1571 5.144100 AGGATGTAAACATTTGTGGGTCAA 58.856 37.500 0.00 0.00 36.57 3.18
1567 1572 5.243730 AGGATGTAAACATTTGTGGGTCAAG 59.756 40.000 0.00 0.00 36.57 3.02
1568 1573 4.314740 TGTAAACATTTGTGGGTCAAGC 57.685 40.909 0.00 0.00 37.35 4.01
1569 1574 3.701542 TGTAAACATTTGTGGGTCAAGCA 59.298 39.130 0.00 0.00 37.35 3.91
1570 1575 3.902881 AAACATTTGTGGGTCAAGCAA 57.097 38.095 0.00 0.00 37.35 3.91
1581 1586 1.197036 GGTCAAGCAAAAGCCTACGTC 59.803 52.381 0.00 0.00 0.00 4.34
1583 1588 2.096218 GTCAAGCAAAAGCCTACGTCTG 60.096 50.000 0.00 0.00 0.00 3.51
1586 1591 0.517316 GCAAAAGCCTACGTCTGGTG 59.483 55.000 0.00 0.00 0.00 4.17
1706 1715 2.665649 TAACCAGCACATACGACAGG 57.334 50.000 0.00 0.00 0.00 4.00
1764 1773 2.967459 TATGTTCAAAGTGCAGCGTG 57.033 45.000 0.00 0.00 0.00 5.34
1781 1790 2.061773 CGTGAAGCTCATGTTCGAAGT 58.938 47.619 0.00 0.00 0.00 3.01
1785 1794 5.273944 GTGAAGCTCATGTTCGAAGTTTTT 58.726 37.500 0.00 0.00 0.00 1.94
1804 1813 7.378181 AGTTTTTGACCAATTATTGCACCTAG 58.622 34.615 0.00 0.00 0.00 3.02
1821 1830 5.106673 GCACCTAGAAATACTGTGGTTTGAC 60.107 44.000 0.00 0.00 35.68 3.18
1855 1864 2.930826 AAGTTTCGACCATGTGGAGT 57.069 45.000 5.96 0.00 38.94 3.85
1856 1865 2.457366 AGTTTCGACCATGTGGAGTC 57.543 50.000 5.96 0.00 38.94 3.36
1864 1873 3.695060 CGACCATGTGGAGTCTAGTTACT 59.305 47.826 5.96 0.00 38.94 2.24
1878 1887 6.208994 AGTCTAGTTACTGTCTGACGGAAATT 59.791 38.462 22.76 3.29 0.00 1.82
1895 1904 6.429692 ACGGAAATTACTGTGTTTGATCATGA 59.570 34.615 0.00 0.00 0.00 3.07
1899 1908 9.462174 GAAATTACTGTGTTTGATCATGAAACA 57.538 29.630 7.25 7.25 40.23 2.83
1948 1960 4.722203 AATGCGAATCATTAGCTTCTCG 57.278 40.909 3.99 0.00 43.24 4.04
1961 1973 2.066262 GCTTCTCGTTCACATTTCCGA 58.934 47.619 0.00 0.00 0.00 4.55
1962 1974 2.159827 GCTTCTCGTTCACATTTCCGAC 60.160 50.000 0.00 0.00 0.00 4.79
2091 2103 5.508200 TTTGCGTCAAAGATTTGTTAGGT 57.492 34.783 5.29 0.00 39.18 3.08
2092 2104 5.508200 TTGCGTCAAAGATTTGTTAGGTT 57.492 34.783 5.29 0.00 39.18 3.50
2126 2138 9.482627 GTCTTCCTCTGAACCATAATATTACTG 57.517 37.037 0.00 0.00 0.00 2.74
2162 2174 2.016318 CGCAGGGTATTGATGCTTTGA 58.984 47.619 0.00 0.00 37.81 2.69
2188 2200 8.700973 AGATTTACTAGAAGATTCCCAAGACTC 58.299 37.037 0.00 0.00 0.00 3.36
2198 2210 0.389166 CCCAAGACTCGAGACACTGC 60.389 60.000 21.68 0.93 0.00 4.40
2249 2304 6.761242 AGCTATATTCGCAAGTATGTTGACAA 59.239 34.615 0.00 0.00 39.48 3.18
2256 2311 5.238432 TCGCAAGTATGTTGACAAGTGAAAT 59.762 36.000 0.00 0.00 39.48 2.17
2270 2325 8.819015 TGACAAGTGAAATGTGAAATCATTTTG 58.181 29.630 6.20 4.01 44.62 2.44
2289 2344 6.790232 TTTTGTTTTCAAGGAGGATGAACT 57.210 33.333 0.00 0.00 41.09 3.01
2305 2360 2.292267 GAACTCCCATGCATCGAACAT 58.708 47.619 0.00 0.00 0.00 2.71
2351 2406 3.458044 ACTCGAGGCCATCCATATAGA 57.542 47.619 18.41 0.00 33.74 1.98
2358 2413 5.939883 CGAGGCCATCCATATAGAAAAATCA 59.060 40.000 5.01 0.00 33.74 2.57
2362 2417 8.175431 AGGCCATCCATATAGAAAAATCATCTT 58.825 33.333 5.01 0.00 33.74 2.40
2413 2468 4.225042 ACCAATGGGCGATATAGCAATAGA 59.775 41.667 10.13 0.00 39.27 1.98
2435 2496 3.883180 GGGCGCAACACACAACGT 61.883 61.111 10.83 0.00 0.00 3.99
2439 2500 0.923911 GCGCAACACACAACGTCTTC 60.924 55.000 0.30 0.00 0.00 2.87
2440 2501 0.371989 CGCAACACACAACGTCTTCA 59.628 50.000 0.00 0.00 0.00 3.02
2454 2515 4.310769 ACGTCTTCAAGAAGGAATCACTG 58.689 43.478 9.73 1.28 38.88 3.66
2455 2516 3.124297 CGTCTTCAAGAAGGAATCACTGC 59.876 47.826 9.73 0.00 38.88 4.40
2456 2517 4.322567 GTCTTCAAGAAGGAATCACTGCT 58.677 43.478 9.73 0.00 38.88 4.24
2457 2518 4.391523 GTCTTCAAGAAGGAATCACTGCTC 59.608 45.833 9.73 0.00 38.88 4.26
2458 2519 2.964740 TCAAGAAGGAATCACTGCTCG 58.035 47.619 0.00 0.00 0.00 5.03
2459 2520 1.396301 CAAGAAGGAATCACTGCTCGC 59.604 52.381 0.00 0.00 0.00 5.03
2460 2521 0.610174 AGAAGGAATCACTGCTCGCA 59.390 50.000 0.00 0.00 0.00 5.10
2461 2522 1.002430 AGAAGGAATCACTGCTCGCAA 59.998 47.619 0.00 0.00 0.00 4.85
2462 2523 1.396301 GAAGGAATCACTGCTCGCAAG 59.604 52.381 0.00 0.00 0.00 4.01
2471 2532 2.174349 GCTCGCAAGCCGAAGTTG 59.826 61.111 0.00 0.00 46.81 3.16
2472 2533 2.863153 CTCGCAAGCCGAAGTTGG 59.137 61.111 0.00 0.00 46.81 3.77
2473 2534 1.667830 CTCGCAAGCCGAAGTTGGA 60.668 57.895 0.00 0.00 46.81 3.53
2474 2535 1.003839 TCGCAAGCCGAAGTTGGAT 60.004 52.632 0.00 0.00 44.21 3.41
2475 2536 1.135315 CGCAAGCCGAAGTTGGATG 59.865 57.895 0.00 0.00 40.02 3.51
2476 2537 1.508088 GCAAGCCGAAGTTGGATGG 59.492 57.895 0.00 0.00 0.00 3.51
2477 2538 1.244019 GCAAGCCGAAGTTGGATGGT 61.244 55.000 0.00 0.00 0.00 3.55
2478 2539 0.804989 CAAGCCGAAGTTGGATGGTC 59.195 55.000 0.00 0.00 0.00 4.02
2479 2540 0.322546 AAGCCGAAGTTGGATGGTCC 60.323 55.000 0.00 0.00 36.96 4.46
2480 2541 1.002624 GCCGAAGTTGGATGGTCCA 60.003 57.895 0.00 0.00 46.61 4.02
2490 2551 3.695830 TGGATGGTCCAACTAGTTGTC 57.304 47.619 29.05 20.43 45.00 3.18
2491 2552 2.976185 TGGATGGTCCAACTAGTTGTCA 59.024 45.455 29.05 23.47 45.00 3.58
2492 2553 3.007940 TGGATGGTCCAACTAGTTGTCAG 59.992 47.826 29.05 16.94 45.00 3.51
2493 2554 3.260884 GGATGGTCCAACTAGTTGTCAGA 59.739 47.826 29.05 18.72 38.85 3.27
2494 2555 4.499183 GATGGTCCAACTAGTTGTCAGAG 58.501 47.826 29.05 16.30 38.85 3.35
2495 2556 2.037251 TGGTCCAACTAGTTGTCAGAGC 59.963 50.000 29.05 26.21 38.85 4.09
2496 2557 2.037251 GGTCCAACTAGTTGTCAGAGCA 59.963 50.000 29.05 5.95 38.85 4.26
2497 2558 3.494398 GGTCCAACTAGTTGTCAGAGCAA 60.494 47.826 29.05 6.12 38.85 3.91
2498 2559 3.743396 GTCCAACTAGTTGTCAGAGCAAG 59.257 47.826 29.05 13.79 38.85 4.01
2499 2560 3.070018 CCAACTAGTTGTCAGAGCAAGG 58.930 50.000 29.05 10.26 38.85 3.61
2500 2561 3.070018 CAACTAGTTGTCAGAGCAAGGG 58.930 50.000 24.70 0.00 35.92 3.95
2501 2562 1.002544 ACTAGTTGTCAGAGCAAGGGC 59.997 52.381 0.00 0.00 41.61 5.19
2502 2563 6.844484 CAACTAGTTGTCAGAGCAAGGGCT 62.844 50.000 24.70 0.00 43.58 5.19
2503 2564 7.531955 CAACTAGTTGTCAGAGCAAGGGCTA 62.532 48.000 24.70 0.00 42.17 3.93
2504 2565 8.747034 CAACTAGTTGTCAGAGCAAGGGCTAT 62.747 46.154 24.70 0.00 42.17 2.97
2516 2577 3.641017 GGGCTATCATCCCTGAAGC 57.359 57.895 0.00 0.00 40.66 3.86
2517 2578 0.767375 GGGCTATCATCCCTGAAGCA 59.233 55.000 0.00 0.00 40.66 3.91
2518 2579 1.271271 GGGCTATCATCCCTGAAGCAG 60.271 57.143 0.00 0.00 40.66 4.24
2519 2580 1.696336 GGCTATCATCCCTGAAGCAGA 59.304 52.381 0.00 0.00 37.31 4.26
2520 2581 2.305343 GGCTATCATCCCTGAAGCAGAT 59.695 50.000 0.00 0.00 37.31 2.90
2521 2582 3.598299 GCTATCATCCCTGAAGCAGATC 58.402 50.000 0.00 0.00 36.44 2.75
2522 2583 3.261390 GCTATCATCCCTGAAGCAGATCT 59.739 47.826 0.00 0.00 36.44 2.75
2523 2584 4.262981 GCTATCATCCCTGAAGCAGATCTT 60.263 45.833 0.00 0.00 36.44 2.40
2532 2593 3.731274 GAAGCAGATCTTCGAACCAAC 57.269 47.619 0.00 0.00 41.48 3.77
2533 2594 2.839486 AGCAGATCTTCGAACCAACA 57.161 45.000 0.00 0.00 0.00 3.33
2534 2595 2.417719 AGCAGATCTTCGAACCAACAC 58.582 47.619 0.00 0.00 0.00 3.32
2535 2596 1.464997 GCAGATCTTCGAACCAACACC 59.535 52.381 0.00 0.00 0.00 4.16
2536 2597 2.872038 GCAGATCTTCGAACCAACACCT 60.872 50.000 0.00 0.00 0.00 4.00
2537 2598 3.403038 CAGATCTTCGAACCAACACCTT 58.597 45.455 0.00 0.00 0.00 3.50
2538 2599 3.433615 CAGATCTTCGAACCAACACCTTC 59.566 47.826 0.00 0.00 0.00 3.46
2539 2600 2.992124 TCTTCGAACCAACACCTTCA 57.008 45.000 0.00 0.00 0.00 3.02
2540 2601 3.269538 TCTTCGAACCAACACCTTCAA 57.730 42.857 0.00 0.00 0.00 2.69
2541 2602 2.940410 TCTTCGAACCAACACCTTCAAC 59.060 45.455 0.00 0.00 0.00 3.18
2542 2603 2.404923 TCGAACCAACACCTTCAACA 57.595 45.000 0.00 0.00 0.00 3.33
2543 2604 2.712709 TCGAACCAACACCTTCAACAA 58.287 42.857 0.00 0.00 0.00 2.83
2544 2605 2.680841 TCGAACCAACACCTTCAACAAG 59.319 45.455 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.939764 ATCAGGTCAGAATAGTTGCAGTA 57.060 39.130 0.00 0.00 0.00 2.74
1 2 4.833478 ATCAGGTCAGAATAGTTGCAGT 57.167 40.909 0.00 0.00 0.00 4.40
2 3 5.295950 CCTATCAGGTCAGAATAGTTGCAG 58.704 45.833 0.00 0.00 0.00 4.41
3 4 4.443457 GCCTATCAGGTCAGAATAGTTGCA 60.443 45.833 0.00 0.00 37.80 4.08
4 5 4.061596 GCCTATCAGGTCAGAATAGTTGC 58.938 47.826 0.00 0.00 37.80 4.17
5 6 5.069648 TCAGCCTATCAGGTCAGAATAGTTG 59.930 44.000 0.00 0.00 37.80 3.16
6 7 5.211973 TCAGCCTATCAGGTCAGAATAGTT 58.788 41.667 0.00 0.00 37.80 2.24
7 8 4.809193 TCAGCCTATCAGGTCAGAATAGT 58.191 43.478 0.00 0.00 37.80 2.12
8 9 5.999205 ATCAGCCTATCAGGTCAGAATAG 57.001 43.478 0.00 0.00 37.80 1.73
9 10 6.314917 TGTATCAGCCTATCAGGTCAGAATA 58.685 40.000 0.00 0.00 37.80 1.75
10 11 5.150715 TGTATCAGCCTATCAGGTCAGAAT 58.849 41.667 0.00 0.00 37.80 2.40
11 12 4.546674 TGTATCAGCCTATCAGGTCAGAA 58.453 43.478 0.00 0.00 37.80 3.02
12 13 4.184649 TGTATCAGCCTATCAGGTCAGA 57.815 45.455 0.00 0.00 37.80 3.27
13 14 4.322574 CCATGTATCAGCCTATCAGGTCAG 60.323 50.000 0.00 0.00 37.80 3.51
14 15 3.580022 CCATGTATCAGCCTATCAGGTCA 59.420 47.826 0.00 0.00 37.80 4.02
15 16 3.834813 TCCATGTATCAGCCTATCAGGTC 59.165 47.826 0.00 0.00 37.80 3.85
16 17 3.861846 TCCATGTATCAGCCTATCAGGT 58.138 45.455 0.00 0.00 37.80 4.00
17 18 4.323333 CCTTCCATGTATCAGCCTATCAGG 60.323 50.000 0.00 0.00 38.80 3.86
18 19 4.285517 ACCTTCCATGTATCAGCCTATCAG 59.714 45.833 0.00 0.00 0.00 2.90
19 20 4.234550 ACCTTCCATGTATCAGCCTATCA 58.765 43.478 0.00 0.00 0.00 2.15
20 21 4.899352 ACCTTCCATGTATCAGCCTATC 57.101 45.455 0.00 0.00 0.00 2.08
21 22 6.745474 GCTTAACCTTCCATGTATCAGCCTAT 60.745 42.308 0.00 0.00 0.00 2.57
22 23 5.454755 GCTTAACCTTCCATGTATCAGCCTA 60.455 44.000 0.00 0.00 0.00 3.93
23 24 4.687219 GCTTAACCTTCCATGTATCAGCCT 60.687 45.833 0.00 0.00 0.00 4.58
24 25 3.565902 GCTTAACCTTCCATGTATCAGCC 59.434 47.826 0.00 0.00 0.00 4.85
25 26 4.274459 CAGCTTAACCTTCCATGTATCAGC 59.726 45.833 0.00 0.00 0.00 4.26
45 46 3.381370 TGCAGATCTCATCAGCAGC 57.619 52.632 0.77 0.00 45.16 5.25
48 49 2.544686 GTCATGTGCAGATCTCATCAGC 59.455 50.000 0.00 0.00 41.56 4.26
103 104 0.394352 CAACTACCCATCCACTGGCC 60.394 60.000 0.00 0.00 44.46 5.36
189 190 5.778542 TCTACTGGAAGGTCTTATTAGCCT 58.221 41.667 0.00 0.00 39.30 4.58
300 301 5.753721 AAAAGAAGTCAGCACCTAGATCT 57.246 39.130 0.00 0.00 0.00 2.75
437 438 2.260869 CCCCAAACAGACAGCACCG 61.261 63.158 0.00 0.00 0.00 4.94
476 478 9.689075 CATGTAGTAAACACAATCTATTCAACG 57.311 33.333 0.00 0.00 42.09 4.10
528 530 0.034337 TCCTGTACCGTGCCTGAAAC 59.966 55.000 0.00 0.00 0.00 2.78
584 588 6.684686 AGCGTGTACAATAACTAGACAGAAA 58.315 36.000 0.00 0.00 0.00 2.52
667 671 4.015872 ACTGGTCCAAAGCGATTTCTTA 57.984 40.909 0.00 0.00 0.00 2.10
672 676 2.224523 TGAGAACTGGTCCAAAGCGATT 60.225 45.455 0.00 0.00 0.00 3.34
718 723 2.110967 CATCCAAGCTGCTCGGTGG 61.111 63.158 6.51 9.47 0.00 4.61
719 724 1.078918 TCATCCAAGCTGCTCGGTG 60.079 57.895 6.51 5.13 0.00 4.94
720 725 1.220206 CTCATCCAAGCTGCTCGGT 59.780 57.895 6.51 0.00 0.00 4.69
819 824 2.108952 AGTTGCAGAAGTTGGGATTCCT 59.891 45.455 2.01 0.00 0.00 3.36
820 825 2.519013 AGTTGCAGAAGTTGGGATTCC 58.481 47.619 0.00 0.00 0.00 3.01
866 871 2.038975 AGAGCTAAGGTGGCCGGA 59.961 61.111 5.05 0.00 0.00 5.14
868 873 0.741221 GAACAGAGCTAAGGTGGCCG 60.741 60.000 0.00 0.00 0.00 6.13
941 946 3.707102 GGAGAAGGCTATAACTGGTCTGT 59.293 47.826 0.00 0.00 0.00 3.41
969 974 2.956799 TTTGCTGCAGCTCCCGACAA 62.957 55.000 36.61 19.58 42.66 3.18
973 978 1.381928 ATGATTTGCTGCAGCTCCCG 61.382 55.000 36.61 1.54 42.66 5.14
975 980 1.065701 CAGATGATTTGCTGCAGCTCC 59.934 52.381 36.61 22.61 42.66 4.70
976 981 2.476873 CAGATGATTTGCTGCAGCTC 57.523 50.000 36.61 26.48 42.66 4.09
989 994 3.230115 TGCGACATGTTGCAGATGA 57.770 47.368 32.48 13.26 44.49 2.92
1035 1040 0.963856 TGAACCGGAGCTTCGCTAGA 60.964 55.000 9.56 0.00 39.88 2.43
1107 1112 2.171448 AGGCTTGTACATCATCAGGTCC 59.829 50.000 0.00 0.00 0.00 4.46
1206 1211 1.153667 CTCGAACCTCTGCAGGAGC 60.154 63.158 15.13 0.00 43.65 4.70
1446 1451 2.060383 CATCCTCCGGCAGTCCTCA 61.060 63.158 0.00 0.00 0.00 3.86
1460 1465 1.757118 TGTCGATCTCCTTCACCATCC 59.243 52.381 0.00 0.00 0.00 3.51
1491 1496 1.089481 CATCCATGTCCACGAACCCG 61.089 60.000 0.00 0.00 42.50 5.28
1552 1557 3.795877 CTTTTGCTTGACCCACAAATGT 58.204 40.909 0.00 0.00 38.08 2.71
1562 1567 2.096218 CAGACGTAGGCTTTTGCTTGAC 60.096 50.000 0.00 0.00 46.54 3.18
1563 1568 2.143122 CAGACGTAGGCTTTTGCTTGA 58.857 47.619 0.00 0.00 46.54 3.02
1564 1569 1.197721 CCAGACGTAGGCTTTTGCTTG 59.802 52.381 0.00 0.00 46.54 4.01
1566 1571 0.396811 ACCAGACGTAGGCTTTTGCT 59.603 50.000 6.44 0.00 46.54 3.91
1567 1572 0.517316 CACCAGACGTAGGCTTTTGC 59.483 55.000 6.44 0.00 46.64 3.68
1568 1573 0.517316 GCACCAGACGTAGGCTTTTG 59.483 55.000 6.44 0.00 0.00 2.44
1569 1574 0.605589 GGCACCAGACGTAGGCTTTT 60.606 55.000 6.44 0.00 0.00 2.27
1570 1575 1.003718 GGCACCAGACGTAGGCTTT 60.004 57.895 6.44 0.00 0.00 3.51
1700 1709 4.701956 ATTTCCAACAAATAGCCTGTCG 57.298 40.909 0.00 0.00 0.00 4.35
1706 1715 5.337578 TGGCCTTATTTCCAACAAATAGC 57.662 39.130 3.32 0.00 0.00 2.97
1764 1773 5.396654 GTCAAAAACTTCGAACATGAGCTTC 59.603 40.000 0.00 0.00 0.00 3.86
1773 1782 7.043059 TGCAATAATTGGTCAAAAACTTCGAAC 60.043 33.333 0.00 0.00 0.00 3.95
1777 1786 6.705825 AGGTGCAATAATTGGTCAAAAACTTC 59.294 34.615 0.00 0.00 0.00 3.01
1781 1790 7.531857 TCTAGGTGCAATAATTGGTCAAAAA 57.468 32.000 0.00 0.00 0.00 1.94
1785 1794 8.052748 AGTATTTCTAGGTGCAATAATTGGTCA 58.947 33.333 0.00 0.00 0.00 4.02
1821 1830 6.310711 GGTCGAAACTTTTCTACTCTACATGG 59.689 42.308 0.00 0.00 34.43 3.66
1827 1836 5.696724 CACATGGTCGAAACTTTTCTACTCT 59.303 40.000 0.00 0.00 34.43 3.24
1855 1864 6.585695 AATTTCCGTCAGACAGTAACTAGA 57.414 37.500 0.00 0.00 0.00 2.43
1856 1865 7.485277 CAGTAATTTCCGTCAGACAGTAACTAG 59.515 40.741 0.41 0.00 0.00 2.57
1864 1873 4.330944 ACACAGTAATTTCCGTCAGACA 57.669 40.909 0.41 0.00 0.00 3.41
1899 1908 8.508883 TTGTATAACCACTTACACAACAAAGT 57.491 30.769 0.00 0.00 36.38 2.66
1917 1926 9.056005 AGCTAATGATTCGCATTTCTTGTATAA 57.944 29.630 4.47 0.00 44.68 0.98
1948 1960 6.603237 TGATATCATGTCGGAAATGTGAAC 57.397 37.500 7.99 1.06 0.00 3.18
1984 1996 9.449719 CCTTTGACAACAGGAGTAAAAGTATAT 57.550 33.333 9.54 0.00 0.00 0.86
2042 2054 2.636893 GTGTCCTATCCATGCATCCTCT 59.363 50.000 0.00 0.00 0.00 3.69
2044 2056 2.411583 TGTGTCCTATCCATGCATCCT 58.588 47.619 0.00 0.00 0.00 3.24
2091 2103 7.311092 TGGTTCAGAGGAAGACTGTATAAAA 57.689 36.000 0.00 0.00 36.81 1.52
2092 2104 6.928348 TGGTTCAGAGGAAGACTGTATAAA 57.072 37.500 0.00 0.00 36.81 1.40
2126 2138 6.250344 ACCCTGCGAAATTAGTTTTCTTAC 57.750 37.500 0.00 0.00 41.37 2.34
2131 2143 6.827586 TCAATACCCTGCGAAATTAGTTTT 57.172 33.333 0.00 0.00 0.00 2.43
2162 2174 8.616799 AGTCTTGGGAATCTTCTAGTAAATCT 57.383 34.615 0.00 0.00 0.00 2.40
2188 2200 2.165380 CCACATTGGCAGTGTCTCG 58.835 57.895 13.15 2.40 35.24 4.04
2256 2311 7.495279 CCTCCTTGAAAACAAAATGATTTCACA 59.505 33.333 13.21 6.56 44.84 3.58
2289 2344 1.102809 GGCATGTTCGATGCATGGGA 61.103 55.000 23.18 0.00 46.21 4.37
2292 2347 1.009335 CCGGCATGTTCGATGCATG 60.009 57.895 19.84 19.84 46.21 4.06
2293 2348 2.837883 GCCGGCATGTTCGATGCAT 61.838 57.895 24.80 0.00 46.21 3.96
2305 2360 5.961396 TTAGTTTATTTTGTAAGCCGGCA 57.039 34.783 31.54 5.56 0.00 5.69
2334 2389 5.939883 TGATTTTTCTATATGGATGGCCTCG 59.060 40.000 3.32 0.00 34.31 4.63
2335 2390 7.833183 AGATGATTTTTCTATATGGATGGCCTC 59.167 37.037 3.32 0.00 34.31 4.70
2382 2437 2.799126 TCGCCCATTGGTTTGATAGT 57.201 45.000 1.20 0.00 0.00 2.12
2383 2438 5.065218 GCTATATCGCCCATTGGTTTGATAG 59.935 44.000 1.20 3.82 30.93 2.08
2391 2446 4.572389 GTCTATTGCTATATCGCCCATTGG 59.428 45.833 0.00 0.00 0.00 3.16
2392 2447 5.178061 TGTCTATTGCTATATCGCCCATTG 58.822 41.667 0.00 0.00 0.00 2.82
2393 2448 5.187772 TCTGTCTATTGCTATATCGCCCATT 59.812 40.000 0.00 0.00 0.00 3.16
2395 2450 4.086457 TCTGTCTATTGCTATATCGCCCA 58.914 43.478 0.00 0.00 0.00 5.36
2396 2451 4.440802 CCTCTGTCTATTGCTATATCGCCC 60.441 50.000 0.00 0.00 0.00 6.13
2413 2468 2.591715 GTGTGTTGCGCCCTCTGT 60.592 61.111 4.18 0.00 0.00 3.41
2435 2496 4.573900 GAGCAGTGATTCCTTCTTGAAGA 58.426 43.478 11.53 0.00 0.00 2.87
2439 2500 1.396301 GCGAGCAGTGATTCCTTCTTG 59.604 52.381 0.00 0.00 0.00 3.02
2440 2501 1.002430 TGCGAGCAGTGATTCCTTCTT 59.998 47.619 0.00 0.00 0.00 2.52
2455 2516 1.021390 ATCCAACTTCGGCTTGCGAG 61.021 55.000 0.00 0.00 0.00 5.03
2456 2517 1.003839 ATCCAACTTCGGCTTGCGA 60.004 52.632 0.00 0.00 0.00 5.10
2457 2518 1.135315 CATCCAACTTCGGCTTGCG 59.865 57.895 0.00 0.00 0.00 4.85
2458 2519 1.244019 ACCATCCAACTTCGGCTTGC 61.244 55.000 0.00 0.00 0.00 4.01
2459 2520 0.804989 GACCATCCAACTTCGGCTTG 59.195 55.000 0.00 0.00 0.00 4.01
2460 2521 0.322546 GGACCATCCAACTTCGGCTT 60.323 55.000 0.00 0.00 36.28 4.35
2461 2522 1.299976 GGACCATCCAACTTCGGCT 59.700 57.895 0.00 0.00 36.28 5.52
2462 2523 1.002624 TGGACCATCCAACTTCGGC 60.003 57.895 0.00 0.00 45.00 5.54
2470 2531 2.976185 TGACAACTAGTTGGACCATCCA 59.024 45.455 33.11 17.97 46.61 3.41
2471 2532 3.260884 TCTGACAACTAGTTGGACCATCC 59.739 47.826 33.11 16.11 44.45 3.51
2472 2533 4.499183 CTCTGACAACTAGTTGGACCATC 58.501 47.826 33.11 22.92 44.45 3.51
2473 2534 3.307059 GCTCTGACAACTAGTTGGACCAT 60.307 47.826 33.11 16.43 44.45 3.55
2474 2535 2.037251 GCTCTGACAACTAGTTGGACCA 59.963 50.000 33.11 25.46 44.45 4.02
2475 2536 2.037251 TGCTCTGACAACTAGTTGGACC 59.963 50.000 33.11 22.95 44.45 4.46
2476 2537 3.386768 TGCTCTGACAACTAGTTGGAC 57.613 47.619 33.11 26.22 44.45 4.02
2477 2538 3.244215 CCTTGCTCTGACAACTAGTTGGA 60.244 47.826 33.11 21.74 44.45 3.53
2478 2539 3.070018 CCTTGCTCTGACAACTAGTTGG 58.930 50.000 33.11 19.13 44.45 3.77
2479 2540 3.070018 CCCTTGCTCTGACAACTAGTTG 58.930 50.000 29.76 29.76 45.58 3.16
2480 2541 2.551071 GCCCTTGCTCTGACAACTAGTT 60.551 50.000 1.12 1.12 33.53 2.24
2481 2542 1.002544 GCCCTTGCTCTGACAACTAGT 59.997 52.381 0.00 0.00 33.53 2.57
2482 2543 1.731720 GCCCTTGCTCTGACAACTAG 58.268 55.000 0.00 0.00 33.53 2.57
2483 2544 3.935993 GCCCTTGCTCTGACAACTA 57.064 52.632 0.00 0.00 33.53 2.24
2484 2545 4.809070 GCCCTTGCTCTGACAACT 57.191 55.556 0.00 0.00 33.53 3.16
2498 2559 0.767375 TGCTTCAGGGATGATAGCCC 59.233 55.000 0.00 0.00 46.40 5.19
2499 2560 1.696336 TCTGCTTCAGGGATGATAGCC 59.304 52.381 0.00 0.00 31.51 3.93
2500 2561 3.261390 AGATCTGCTTCAGGGATGATAGC 59.739 47.826 0.00 0.00 31.51 2.97
2501 2562 5.486735 AAGATCTGCTTCAGGGATGATAG 57.513 43.478 0.00 0.00 28.17 2.08
2513 2574 2.808543 GTGTTGGTTCGAAGATCTGCTT 59.191 45.455 0.00 0.00 40.25 3.91
2514 2575 2.417719 GTGTTGGTTCGAAGATCTGCT 58.582 47.619 0.00 0.00 35.04 4.24
2515 2576 1.464997 GGTGTTGGTTCGAAGATCTGC 59.535 52.381 0.00 0.00 35.04 4.26
2516 2577 3.045601 AGGTGTTGGTTCGAAGATCTG 57.954 47.619 0.00 0.00 35.04 2.90
2517 2578 3.071023 TGAAGGTGTTGGTTCGAAGATCT 59.929 43.478 0.00 0.00 35.04 2.75
2518 2579 3.399330 TGAAGGTGTTGGTTCGAAGATC 58.601 45.455 0.00 0.00 35.04 2.75
2519 2580 3.485463 TGAAGGTGTTGGTTCGAAGAT 57.515 42.857 0.00 0.00 35.04 2.40
2520 2581 2.940410 GTTGAAGGTGTTGGTTCGAAGA 59.060 45.455 0.00 0.00 0.00 2.87
2521 2582 2.680841 TGTTGAAGGTGTTGGTTCGAAG 59.319 45.455 0.00 0.00 0.00 3.79
2522 2583 2.712709 TGTTGAAGGTGTTGGTTCGAA 58.287 42.857 0.00 0.00 0.00 3.71
2523 2584 2.404923 TGTTGAAGGTGTTGGTTCGA 57.595 45.000 0.00 0.00 0.00 3.71
2524 2585 2.223479 CCTTGTTGAAGGTGTTGGTTCG 60.223 50.000 0.00 0.00 43.63 3.95
2525 2586 3.436700 CCTTGTTGAAGGTGTTGGTTC 57.563 47.619 0.00 0.00 43.63 3.62


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

AutoCloner maintained by Alex Coulton.