Multiple sequence alignment - TraesCS5D01G021800

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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 TraesCS5D01G021800 chr5D 100.000 3569 0 0 1 3569 14537273 14533705 0.000000e+00 6591
1 TraesCS5D01G021800 chr5A 93.935 1995 80 21 458 2431 11135756 11133782 0.000000e+00 2976
2 TraesCS5D01G021800 chr5A 95.719 654 25 3 2919 3569 216989042 216989695 0.000000e+00 1050
3 TraesCS5D01G021800 chr5A 92.857 420 26 4 9 428 11149299 11148884 1.100000e-169 606
4 TraesCS5D01G021800 chr5A 86.031 451 28 7 2498 2920 11133757 11133314 5.430000e-123 451
5 TraesCS5D01G021800 chr5B 92.085 1655 73 23 1 1605 13499466 13497820 0.000000e+00 2278
6 TraesCS5D01G021800 chr5B 92.912 776 47 2 1640 2415 13497723 13496956 0.000000e+00 1122
7 TraesCS5D01G021800 chr3B 95.566 654 25 4 2919 3569 93357359 93356707 0.000000e+00 1044
8 TraesCS5D01G021800 chr3B 95.107 654 28 4 2919 3569 93456935 93456283 0.000000e+00 1027
9 TraesCS5D01G021800 chr3B 94.954 654 29 4 2919 3569 93416816 93416164 0.000000e+00 1022
10 TraesCS5D01G021800 chr4B 94.351 655 33 3 2919 3569 134117478 134116824 0.000000e+00 1002
11 TraesCS5D01G021800 chr1B 93.558 652 39 3 2920 3569 529541814 529542464 0.000000e+00 968
12 TraesCS5D01G021800 chr1B 94.272 611 30 3 2964 3569 487943067 487943677 0.000000e+00 929
13 TraesCS5D01G021800 chr1B 85.057 783 105 6 1615 2396 21512543 21511772 0.000000e+00 787
14 TraesCS5D01G021800 chr1B 80.376 479 76 14 1143 1612 21513078 21512609 7.330000e-92 348
15 TraesCS5D01G021800 chr6B 93.435 655 38 5 2918 3569 551004204 551004856 0.000000e+00 966
16 TraesCS5D01G021800 chr6B 81.463 793 131 12 1625 2408 9170131 9170916 1.400000e-178 636
17 TraesCS5D01G021800 chr6B 83.475 472 58 14 1116 1574 32818878 32819342 4.260000e-114 422
18 TraesCS5D01G021800 chr7B 92.649 653 42 6 2921 3569 725972552 725973202 0.000000e+00 935
19 TraesCS5D01G021800 chr6D 81.550 813 132 16 1593 2398 4839195 4839996 0.000000e+00 654
20 TraesCS5D01G021800 chr6D 81.105 344 49 11 1251 1583 18884242 18884580 9.830000e-66 261
21 TraesCS5D01G021800 chr6D 84.411 263 39 2 2137 2398 18890402 18890663 1.270000e-64 257
22 TraesCS5D01G021800 chr6A 81.772 790 130 12 1614 2398 3913478 3914258 0.000000e+00 649
23 TraesCS5D01G021800 chr6A 84.100 478 62 7 1116 1583 18930882 18931355 1.950000e-122 449
24 TraesCS5D01G021800 chr6A 82.915 398 66 2 1934 2330 18931523 18931919 1.220000e-94 357


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 TraesCS5D01G021800 chr5D 14533705 14537273 3568 True 6591.0 6591 100.0000 1 3569 1 chr5D.!!$R1 3568
1 TraesCS5D01G021800 chr5A 11133314 11135756 2442 True 1713.5 2976 89.9830 458 2920 2 chr5A.!!$R2 2462
2 TraesCS5D01G021800 chr5A 216989042 216989695 653 False 1050.0 1050 95.7190 2919 3569 1 chr5A.!!$F1 650
3 TraesCS5D01G021800 chr5B 13496956 13499466 2510 True 1700.0 2278 92.4985 1 2415 2 chr5B.!!$R1 2414
4 TraesCS5D01G021800 chr3B 93356707 93357359 652 True 1044.0 1044 95.5660 2919 3569 1 chr3B.!!$R1 650
5 TraesCS5D01G021800 chr3B 93456283 93456935 652 True 1027.0 1027 95.1070 2919 3569 1 chr3B.!!$R3 650
6 TraesCS5D01G021800 chr3B 93416164 93416816 652 True 1022.0 1022 94.9540 2919 3569 1 chr3B.!!$R2 650
7 TraesCS5D01G021800 chr4B 134116824 134117478 654 True 1002.0 1002 94.3510 2919 3569 1 chr4B.!!$R1 650
8 TraesCS5D01G021800 chr1B 529541814 529542464 650 False 968.0 968 93.5580 2920 3569 1 chr1B.!!$F2 649
9 TraesCS5D01G021800 chr1B 487943067 487943677 610 False 929.0 929 94.2720 2964 3569 1 chr1B.!!$F1 605
10 TraesCS5D01G021800 chr1B 21511772 21513078 1306 True 567.5 787 82.7165 1143 2396 2 chr1B.!!$R1 1253
11 TraesCS5D01G021800 chr6B 551004204 551004856 652 False 966.0 966 93.4350 2918 3569 1 chr6B.!!$F3 651
12 TraesCS5D01G021800 chr6B 9170131 9170916 785 False 636.0 636 81.4630 1625 2408 1 chr6B.!!$F1 783
13 TraesCS5D01G021800 chr7B 725972552 725973202 650 False 935.0 935 92.6490 2921 3569 1 chr7B.!!$F1 648
14 TraesCS5D01G021800 chr6D 4839195 4839996 801 False 654.0 654 81.5500 1593 2398 1 chr6D.!!$F1 805
15 TraesCS5D01G021800 chr6A 3913478 3914258 780 False 649.0 649 81.7720 1614 2398 1 chr6A.!!$F1 784
16 TraesCS5D01G021800 chr6A 18930882 18931919 1037 False 403.0 449 83.5075 1116 2330 2 chr6A.!!$F2 1214

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
64 67 1.615392 GGTCATGCCTCAAAACAAGCT 59.385 47.619 0.0 0.0 0.0 3.74 F
468 491 2.288961 TTAAGCATCTCGTCCGTTCC 57.711 50.000 0.0 0.0 0.0 3.62 F
1877 2032 0.251916 CATTCTACCAAGGGCCGACA 59.748 55.000 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1078 1125 0.546122 TATGGCGAGGGATGCTTTGT 59.454 50.0 0.0 0.0 0.00 2.83 R
2449 2610 0.038159 GTGCAGTCACTACCGAAGCT 60.038 55.0 0.0 0.0 40.03 3.74 R
3500 3696 0.250553 TGGAGGCGTCGTTGGAAATT 60.251 50.0 0.0 0.0 0.00 1.82 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
19 20 2.717639 AGACACATGGCAGATAACCC 57.282 50.000 0.00 0.00 0.00 4.11
64 67 1.615392 GGTCATGCCTCAAAACAAGCT 59.385 47.619 0.00 0.00 0.00 3.74
76 79 7.257722 CCTCAAAACAAGCTTTTCTCTTTGTA 58.742 34.615 0.00 0.00 0.00 2.41
93 96 8.664798 TCTCTTTGTAAAATACATCATCGTTGG 58.335 33.333 0.00 0.00 38.68 3.77
126 129 8.845227 TCACTACTCATTCATTGCAAAACTTAA 58.155 29.630 1.71 0.00 0.00 1.85
157 160 8.822652 AATTTGATTCATTGAGACAAACCTTC 57.177 30.769 16.58 0.00 34.21 3.46
171 174 6.990349 AGACAAACCTTCGACAAAAGATTCTA 59.010 34.615 0.00 0.00 0.00 2.10
237 241 7.676893 TGGGTCACTACTTAGGAAGAATCTAAA 59.323 37.037 0.00 0.00 0.00 1.85
336 340 4.142038 ACAGCTTATTTTGAAACCGAGGT 58.858 39.130 0.00 0.00 0.00 3.85
337 341 5.310451 ACAGCTTATTTTGAAACCGAGGTA 58.690 37.500 0.00 0.00 0.00 3.08
345 349 2.823959 TGAAACCGAGGTAGTGGGTAT 58.176 47.619 0.00 0.00 35.90 2.73
468 491 2.288961 TTAAGCATCTCGTCCGTTCC 57.711 50.000 0.00 0.00 0.00 3.62
489 512 4.833380 TCCCGAATAAAGCTAGCTAGATGT 59.167 41.667 25.15 16.26 0.00 3.06
677 700 5.611796 TCAAATTCACTACAGATGTGTGC 57.388 39.130 5.61 0.00 37.52 4.57
758 785 6.647334 TTTTACCTCACAAATGAATGAGCA 57.353 33.333 0.00 0.00 40.92 4.26
831 859 9.239002 CTTTCAAATGTGATTTTTACGGTAACA 57.761 29.630 0.00 0.00 32.48 2.41
834 862 7.327275 TCAAATGTGATTTTTACGGTAACATGC 59.673 33.333 0.00 0.00 0.00 4.06
836 864 7.618502 ATGTGATTTTTACGGTAACATGCTA 57.381 32.000 0.00 0.00 0.00 3.49
857 886 6.770785 TGCTATGCCCGTATATTTTCTCTTTT 59.229 34.615 0.00 0.00 0.00 2.27
875 904 6.042638 TCTTTTCAGATGGTTGGTCTAGAG 57.957 41.667 0.00 0.00 0.00 2.43
1063 1110 7.944729 ATATCACACTCACCATAAAGCTTTT 57.055 32.000 18.47 2.49 0.00 2.27
1085 1132 4.974368 TTTCGAAAAGGAAGACAAAGCA 57.026 36.364 8.44 0.00 0.00 3.91
1353 1404 7.593825 ACTGATGTCCTTACAAGTTTAATTGC 58.406 34.615 0.00 0.00 39.58 3.56
1366 1418 6.925610 AGTTTAATTGCATCTCGATTGCTA 57.074 33.333 18.01 12.68 31.39 3.49
1370 1422 1.123077 TGCATCTCGATTGCTAGGGT 58.877 50.000 18.01 0.00 0.00 4.34
1456 1527 3.499338 TCATGGCCACTGATTTCTGTTT 58.501 40.909 8.16 0.00 0.00 2.83
1457 1528 4.661222 TCATGGCCACTGATTTCTGTTTA 58.339 39.130 8.16 0.00 0.00 2.01
1458 1529 4.701651 TCATGGCCACTGATTTCTGTTTAG 59.298 41.667 8.16 0.00 0.00 1.85
1483 1554 9.871238 AGAAGTTAGCTAATTTCTGTATTTCGA 57.129 29.630 31.86 0.00 39.69 3.71
1488 1559 9.832445 TTAGCTAATTTCTGTATTTCGATTCCT 57.168 29.630 0.86 0.00 0.00 3.36
1540 1611 3.062763 GCTGACCATGGAGATATTCGTG 58.937 50.000 21.47 2.75 0.00 4.35
1799 1954 3.484742 GATCGATGTCGCCAGCCGA 62.485 63.158 0.54 0.00 45.15 5.54
1877 2032 0.251916 CATTCTACCAAGGGCCGACA 59.748 55.000 0.00 0.00 0.00 4.35
1888 2043 3.717294 GCCGACACTGATGGGGGT 61.717 66.667 0.00 0.00 0.00 4.95
1890 2045 2.268920 CGACACTGATGGGGGTGG 59.731 66.667 0.00 0.00 37.72 4.61
1926 2087 3.788145 CCGCCGGTTCCACCCATA 61.788 66.667 1.90 0.00 33.75 2.74
1927 2088 2.203015 CGCCGGTTCCACCCATAG 60.203 66.667 1.90 0.00 33.75 2.23
1928 2089 2.727392 CGCCGGTTCCACCCATAGA 61.727 63.158 1.90 0.00 33.75 1.98
1929 2090 1.146263 GCCGGTTCCACCCATAGAG 59.854 63.158 1.90 0.00 33.75 2.43
2422 2583 1.071471 CCAAACTCCCTGCGTGACT 59.929 57.895 0.00 0.00 0.00 3.41
2431 2592 3.545574 TGCGTGACTGCACCCAGA 61.546 61.111 0.00 0.00 42.09 3.86
2432 2593 3.044305 GCGTGACTGCACCCAGAC 61.044 66.667 0.00 0.00 42.09 3.51
2433 2594 2.357517 CGTGACTGCACCCAGACC 60.358 66.667 0.00 0.00 42.09 3.85
2434 2595 2.872388 CGTGACTGCACCCAGACCT 61.872 63.158 0.00 0.00 42.09 3.85
2435 2596 1.302033 GTGACTGCACCCAGACCTG 60.302 63.158 0.00 0.00 41.77 4.00
2436 2597 2.359230 GACTGCACCCAGACCTGC 60.359 66.667 0.00 0.00 41.77 4.85
2439 2600 2.848679 TGCACCCAGACCTGCAGA 60.849 61.111 17.39 0.00 38.49 4.26
2440 2601 2.046507 GCACCCAGACCTGCAGAG 60.047 66.667 17.39 8.04 33.31 3.35
2442 2603 1.908340 GCACCCAGACCTGCAGAGAT 61.908 60.000 17.39 0.00 33.31 2.75
2446 2607 0.743701 CCAGACCTGCAGAGATGCAC 60.744 60.000 17.39 0.00 40.23 4.57
2448 2609 1.079543 GACCTGCAGAGATGCACGT 60.080 57.895 17.39 0.70 40.23 4.49
2449 2610 0.173481 GACCTGCAGAGATGCACGTA 59.827 55.000 17.39 0.00 40.23 3.57
2450 2611 0.174389 ACCTGCAGAGATGCACGTAG 59.826 55.000 17.39 0.00 40.23 3.51
2451 2612 1.150567 CCTGCAGAGATGCACGTAGC 61.151 60.000 17.39 0.00 40.23 3.58
2452 2613 0.179116 CTGCAGAGATGCACGTAGCT 60.179 55.000 8.42 0.00 45.94 3.32
2453 2614 0.247460 TGCAGAGATGCACGTAGCTT 59.753 50.000 10.54 5.14 45.94 3.74
2454 2615 0.926846 GCAGAGATGCACGTAGCTTC 59.073 55.000 13.95 13.95 45.94 3.86
2457 2618 4.496670 GATGCACGTAGCTTCGGT 57.503 55.556 17.35 0.09 45.94 4.69
2458 2619 3.635433 GATGCACGTAGCTTCGGTA 57.365 52.632 17.35 6.14 45.94 4.02
2459 2620 1.478137 GATGCACGTAGCTTCGGTAG 58.522 55.000 17.35 7.59 45.94 3.18
2460 2621 0.815734 ATGCACGTAGCTTCGGTAGT 59.184 50.000 17.35 0.00 45.94 2.73
2461 2622 0.109458 TGCACGTAGCTTCGGTAGTG 60.109 55.000 17.35 7.15 45.94 2.74
2462 2623 0.169672 GCACGTAGCTTCGGTAGTGA 59.830 55.000 17.35 0.00 41.15 3.41
2463 2624 1.892468 CACGTAGCTTCGGTAGTGAC 58.108 55.000 17.35 0.00 34.94 3.67
2464 2625 1.467734 CACGTAGCTTCGGTAGTGACT 59.532 52.381 17.35 0.00 34.94 3.41
2465 2626 1.467734 ACGTAGCTTCGGTAGTGACTG 59.532 52.381 17.35 0.00 34.94 3.51
2466 2627 1.794437 CGTAGCTTCGGTAGTGACTGC 60.794 57.143 4.63 0.00 0.00 4.40
2467 2628 1.201647 GTAGCTTCGGTAGTGACTGCA 59.798 52.381 2.55 0.00 0.00 4.41
2468 2629 0.038159 AGCTTCGGTAGTGACTGCAC 60.038 55.000 2.55 0.00 45.49 4.57
2469 2630 1.014564 GCTTCGGTAGTGACTGCACC 61.015 60.000 2.55 0.00 46.32 5.01
2470 2631 0.389948 CTTCGGTAGTGACTGCACCC 60.390 60.000 2.55 0.00 46.32 4.61
2471 2632 1.116536 TTCGGTAGTGACTGCACCCA 61.117 55.000 2.55 0.00 46.32 4.51
2472 2633 0.902984 TCGGTAGTGACTGCACCCAT 60.903 55.000 2.55 0.00 46.32 4.00
2473 2634 0.740868 CGGTAGTGACTGCACCCATG 60.741 60.000 2.55 0.00 46.32 3.66
2474 2635 0.392998 GGTAGTGACTGCACCCATGG 60.393 60.000 4.14 4.14 46.32 3.66
2475 2636 0.324943 GTAGTGACTGCACCCATGGT 59.675 55.000 11.73 0.00 46.32 3.55
2488 2649 3.571590 ACCCATGGTGTTTAAAAGCTGA 58.428 40.909 11.73 0.00 32.98 4.26
2489 2650 3.964031 ACCCATGGTGTTTAAAAGCTGAA 59.036 39.130 11.73 0.00 32.98 3.02
2490 2651 4.592778 ACCCATGGTGTTTAAAAGCTGAAT 59.407 37.500 11.73 0.00 32.98 2.57
2491 2652 5.170748 CCCATGGTGTTTAAAAGCTGAATC 58.829 41.667 11.73 0.00 0.00 2.52
2492 2653 5.279406 CCCATGGTGTTTAAAAGCTGAATCA 60.279 40.000 11.73 0.00 0.00 2.57
2493 2654 6.400568 CCATGGTGTTTAAAAGCTGAATCAT 58.599 36.000 2.57 0.00 0.00 2.45
2494 2655 6.875195 CCATGGTGTTTAAAAGCTGAATCATT 59.125 34.615 2.57 0.00 0.00 2.57
2495 2656 7.388500 CCATGGTGTTTAAAAGCTGAATCATTT 59.612 33.333 2.57 0.00 0.00 2.32
2496 2657 8.776470 CATGGTGTTTAAAAGCTGAATCATTTT 58.224 29.630 0.00 1.02 0.00 1.82
2514 2675 6.597562 TCATTTTTACTGGTGTTGGAGTAGT 58.402 36.000 0.00 0.00 0.00 2.73
2516 2677 7.876068 TCATTTTTACTGGTGTTGGAGTAGTAG 59.124 37.037 0.00 0.00 0.00 2.57
2517 2678 4.796038 TTACTGGTGTTGGAGTAGTAGC 57.204 45.455 0.00 0.00 0.00 3.58
2518 2679 2.890814 ACTGGTGTTGGAGTAGTAGCT 58.109 47.619 0.00 0.00 0.00 3.32
2519 2680 4.043608 ACTGGTGTTGGAGTAGTAGCTA 57.956 45.455 0.00 0.00 0.00 3.32
2521 2682 4.402793 ACTGGTGTTGGAGTAGTAGCTATG 59.597 45.833 0.00 0.00 0.00 2.23
2522 2683 4.350245 TGGTGTTGGAGTAGTAGCTATGT 58.650 43.478 0.00 0.00 0.00 2.29
2523 2684 5.512298 TGGTGTTGGAGTAGTAGCTATGTA 58.488 41.667 0.00 0.00 0.00 2.29
2524 2685 5.359009 TGGTGTTGGAGTAGTAGCTATGTAC 59.641 44.000 0.00 2.40 0.00 2.90
2525 2686 5.505324 GGTGTTGGAGTAGTAGCTATGTACG 60.505 48.000 0.00 0.00 0.00 3.67
2526 2687 4.577693 TGTTGGAGTAGTAGCTATGTACGG 59.422 45.833 0.00 0.00 0.00 4.02
2552 2713 1.665679 GCAATCATGACCGTGAATCGT 59.334 47.619 0.00 0.00 37.94 3.73
2587 2748 7.434897 GGCATTAATTAAACGATGAGCATTTCA 59.565 33.333 1.21 0.00 40.85 2.69
2696 2883 4.571176 CGCATAGCATACCGAGAGACTATA 59.429 45.833 0.00 0.00 0.00 1.31
2738 2925 8.454106 CGTATTCTTCCATCAATTCAGACTTTT 58.546 33.333 0.00 0.00 0.00 2.27
2753 2940 6.223120 TCAGACTTTTGAATGAGTTGATCGA 58.777 36.000 0.00 0.00 0.00 3.59
2763 2950 2.610833 TGAGTTGATCGATGCAAGCATC 59.389 45.455 21.87 21.87 46.71 3.91
2788 2975 6.317391 CCAGAGGGATTCTCATGAAACTTTAC 59.683 42.308 0.00 0.00 44.81 2.01
2794 2981 5.570262 TTCTCATGAAACTTTACGTGACG 57.430 39.130 2.24 2.24 0.00 4.35
2798 2985 4.804665 TCATGAAACTTTACGTGACGAACA 59.195 37.500 13.70 0.18 0.00 3.18
2838 3025 5.316167 TGATCTAATGTTGCACTGAACCTT 58.684 37.500 0.00 0.00 0.00 3.50
2842 3029 0.033601 TGTTGCACTGAACCTTGGGT 60.034 50.000 0.00 0.00 37.65 4.51
2858 3045 4.401925 CTTGGGTCACTCCTTTCAAGAAT 58.598 43.478 0.00 0.00 36.06 2.40
2862 3049 3.680458 GGTCACTCCTTTCAAGAATCGAC 59.320 47.826 0.00 0.00 0.00 4.20
2872 3059 1.195448 CAAGAATCGACACGCAAGCTT 59.805 47.619 0.00 0.00 45.62 3.74
2873 3060 1.512926 AGAATCGACACGCAAGCTTT 58.487 45.000 0.00 0.00 45.62 3.51
2876 3063 2.316119 ATCGACACGCAAGCTTTTTC 57.684 45.000 0.00 0.00 45.62 2.29
2882 3070 3.372060 ACACGCAAGCTTTTTCTTTAGC 58.628 40.909 0.00 0.00 45.62 3.09
2998 3186 2.525105 ACAACAAGGTGGTGAAGGTT 57.475 45.000 0.00 0.00 37.20 3.50
3108 3299 0.970937 TACTAGGCAGCGCAACTCCT 60.971 55.000 11.47 12.42 32.64 3.69
3147 3341 1.360393 AAGGAAACAGGCAGGGGTGA 61.360 55.000 0.00 0.00 0.00 4.02
3333 3529 3.195002 CGCCGTCATCGTTGCCAT 61.195 61.111 0.00 0.00 35.01 4.40
3342 3538 2.016318 CATCGTTGCCATAGAAGCCAA 58.984 47.619 0.00 0.00 0.00 4.52
3500 3696 0.895530 CGGGAGTAGAGGCTGTGAAA 59.104 55.000 0.00 0.00 0.00 2.69
3504 3700 4.336280 GGGAGTAGAGGCTGTGAAAATTT 58.664 43.478 0.00 0.00 0.00 1.82
3507 3703 4.985538 AGTAGAGGCTGTGAAAATTTCCA 58.014 39.130 3.00 0.61 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 79 5.253330 ACTCCACCAACGATGATGTATTTT 58.747 37.500 0.00 0.00 0.00 1.82
86 89 2.897969 AGTAGTGAACTCCACCAACGAT 59.102 45.455 0.00 0.00 46.87 3.73
148 151 6.540914 TGTAGAATCTTTTGTCGAAGGTTTGT 59.459 34.615 0.00 0.00 30.38 2.83
183 186 7.958567 GCTTGTGTTTTTGTAAAAAGTAAACCC 59.041 33.333 2.96 0.00 38.44 4.11
189 192 6.093357 CCCATGCTTGTGTTTTTGTAAAAAGT 59.907 34.615 2.96 0.00 38.44 2.66
336 340 5.636123 TCCAAGCAAAAGAAATACCCACTA 58.364 37.500 0.00 0.00 0.00 2.74
337 341 4.479158 TCCAAGCAAAAGAAATACCCACT 58.521 39.130 0.00 0.00 0.00 4.00
420 424 8.791327 TGAGTATCTGTCAAAGCAAATATTCA 57.209 30.769 0.00 0.00 34.92 2.57
468 491 6.678878 TGTACATCTAGCTAGCTTTATTCGG 58.321 40.000 24.88 8.98 0.00 4.30
489 512 7.040340 TCCCAAAAGTTAATCGAAGCATTTGTA 60.040 33.333 0.00 0.00 0.00 2.41
542 565 8.193953 ACTTGGTTTCCACATGATATTTTCTT 57.806 30.769 0.00 0.00 30.78 2.52
738 765 5.499313 TCATGCTCATTCATTTGTGAGGTA 58.501 37.500 4.74 0.00 41.62 3.08
758 785 7.572523 TGAACAAGTGAAATCTGAAGTTCAT 57.427 32.000 5.91 0.00 41.12 2.57
825 853 2.536761 TACGGGCATAGCATGTTACC 57.463 50.000 0.00 0.00 0.00 2.85
831 859 6.054860 AGAGAAAATATACGGGCATAGCAT 57.945 37.500 0.00 0.00 0.00 3.79
834 862 8.378172 TGAAAAGAGAAAATATACGGGCATAG 57.622 34.615 0.00 0.00 0.00 2.23
836 864 7.054124 TCTGAAAAGAGAAAATATACGGGCAT 58.946 34.615 0.00 0.00 0.00 4.40
857 886 4.678256 AGTTCTCTAGACCAACCATCTGA 58.322 43.478 6.29 0.00 0.00 3.27
1063 1110 5.317733 TGCTTTGTCTTCCTTTTCGAAAA 57.682 34.783 21.35 21.35 0.00 2.29
1078 1125 0.546122 TATGGCGAGGGATGCTTTGT 59.454 50.000 0.00 0.00 0.00 2.83
1085 1132 3.307059 GCAAGAACTATATGGCGAGGGAT 60.307 47.826 0.00 0.00 0.00 3.85
1353 1404 3.674528 ATGACCCTAGCAATCGAGATG 57.325 47.619 0.00 0.00 0.00 2.90
1366 1418 3.649502 TCATCAGTGATGCATATGACCCT 59.350 43.478 25.53 0.00 39.63 4.34
1370 1422 5.469084 GCTTCTTCATCAGTGATGCATATGA 59.531 40.000 25.53 14.32 39.63 2.15
1457 1528 9.871238 TCGAAATACAGAAATTAGCTAACTTCT 57.129 29.630 21.37 21.37 32.61 2.85
1498 1569 5.830991 CAGCTTAGGTCTACTCTTCCTACAT 59.169 44.000 0.00 0.00 34.15 2.29
1499 1570 5.045066 TCAGCTTAGGTCTACTCTTCCTACA 60.045 44.000 0.00 0.00 34.15 2.74
1540 1611 3.330267 CAAGGCACTGAAGAAGAGGTAC 58.670 50.000 0.00 0.00 40.86 3.34
1860 2015 0.834687 AGTGTCGGCCCTTGGTAGAA 60.835 55.000 0.00 0.00 0.00 2.10
1877 2032 3.717294 GACGCCACCCCCATCAGT 61.717 66.667 0.00 0.00 0.00 3.41
1917 2078 2.125326 CGCCGTCTCTATGGGTGGA 61.125 63.158 0.00 0.00 31.75 4.02
2051 2212 1.011968 GCACGAACATCCACGCTGTA 61.012 55.000 0.00 0.00 0.00 2.74
2296 2457 2.894387 GCTGCTCATGGAGGACGC 60.894 66.667 0.00 0.00 31.89 5.19
2352 2513 0.044855 AGGACCAAGTAGAGCCCCAT 59.955 55.000 0.00 0.00 0.00 4.00
2436 2597 1.195347 CGAAGCTACGTGCATCTCTG 58.805 55.000 0.00 0.00 45.94 3.35
2439 2600 1.065701 CTACCGAAGCTACGTGCATCT 59.934 52.381 0.00 0.00 45.94 2.90
2440 2601 1.202268 ACTACCGAAGCTACGTGCATC 60.202 52.381 0.00 1.64 45.94 3.91
2442 2603 0.109458 CACTACCGAAGCTACGTGCA 60.109 55.000 0.00 0.00 45.94 4.57
2446 2607 1.794437 GCAGTCACTACCGAAGCTACG 60.794 57.143 0.00 0.00 0.00 3.51
2448 2609 1.201647 GTGCAGTCACTACCGAAGCTA 59.798 52.381 0.00 0.00 40.03 3.32
2449 2610 0.038159 GTGCAGTCACTACCGAAGCT 60.038 55.000 0.00 0.00 40.03 3.74
2450 2611 1.014564 GGTGCAGTCACTACCGAAGC 61.015 60.000 0.00 0.00 42.72 3.86
2451 2612 0.389948 GGGTGCAGTCACTACCGAAG 60.390 60.000 0.00 0.00 42.72 3.79
2452 2613 1.116536 TGGGTGCAGTCACTACCGAA 61.117 55.000 0.00 0.00 42.72 4.30
2453 2614 0.902984 ATGGGTGCAGTCACTACCGA 60.903 55.000 0.00 0.00 42.72 4.69
2454 2615 0.740868 CATGGGTGCAGTCACTACCG 60.741 60.000 0.00 0.00 42.72 4.02
2455 2616 0.392998 CCATGGGTGCAGTCACTACC 60.393 60.000 2.85 0.00 42.72 3.18
2456 2617 0.324943 ACCATGGGTGCAGTCACTAC 59.675 55.000 18.09 0.00 42.72 2.73
2457 2618 2.772102 ACCATGGGTGCAGTCACTA 58.228 52.632 18.09 0.00 42.72 2.74
2458 2619 3.580084 ACCATGGGTGCAGTCACT 58.420 55.556 18.09 0.00 42.72 3.41
2467 2628 3.571590 TCAGCTTTTAAACACCATGGGT 58.428 40.909 18.09 8.43 35.62 4.51
2468 2629 4.599047 TTCAGCTTTTAAACACCATGGG 57.401 40.909 18.09 7.72 0.00 4.00
2469 2630 5.782047 TGATTCAGCTTTTAAACACCATGG 58.218 37.500 11.19 11.19 0.00 3.66
2470 2631 7.894376 AATGATTCAGCTTTTAAACACCATG 57.106 32.000 0.00 0.00 0.00 3.66
2471 2632 8.907222 AAAATGATTCAGCTTTTAAACACCAT 57.093 26.923 0.00 0.00 0.00 3.55
2472 2633 8.729805 AAAAATGATTCAGCTTTTAAACACCA 57.270 26.923 7.23 0.00 0.00 4.17
2478 2639 9.474920 CACCAGTAAAAATGATTCAGCTTTTAA 57.525 29.630 13.78 0.00 0.00 1.52
2479 2640 8.637986 ACACCAGTAAAAATGATTCAGCTTTTA 58.362 29.630 10.31 10.31 0.00 1.52
2480 2641 7.500141 ACACCAGTAAAAATGATTCAGCTTTT 58.500 30.769 11.72 11.72 0.00 2.27
2481 2642 7.054491 ACACCAGTAAAAATGATTCAGCTTT 57.946 32.000 0.00 0.00 0.00 3.51
2482 2643 6.655078 ACACCAGTAAAAATGATTCAGCTT 57.345 33.333 0.00 0.00 0.00 3.74
2483 2644 6.449698 CAACACCAGTAAAAATGATTCAGCT 58.550 36.000 0.00 0.00 0.00 4.24
2484 2645 5.634859 CCAACACCAGTAAAAATGATTCAGC 59.365 40.000 0.00 0.00 0.00 4.26
2485 2646 6.980593 TCCAACACCAGTAAAAATGATTCAG 58.019 36.000 0.00 0.00 0.00 3.02
2486 2647 6.549364 ACTCCAACACCAGTAAAAATGATTCA 59.451 34.615 0.00 0.00 0.00 2.57
2487 2648 6.981722 ACTCCAACACCAGTAAAAATGATTC 58.018 36.000 0.00 0.00 0.00 2.52
2488 2649 6.976934 ACTCCAACACCAGTAAAAATGATT 57.023 33.333 0.00 0.00 0.00 2.57
2489 2650 7.231467 ACTACTCCAACACCAGTAAAAATGAT 58.769 34.615 0.00 0.00 0.00 2.45
2490 2651 6.597562 ACTACTCCAACACCAGTAAAAATGA 58.402 36.000 0.00 0.00 0.00 2.57
2491 2652 6.877611 ACTACTCCAACACCAGTAAAAATG 57.122 37.500 0.00 0.00 0.00 2.32
2492 2653 6.653740 GCTACTACTCCAACACCAGTAAAAAT 59.346 38.462 0.00 0.00 0.00 1.82
2493 2654 5.993441 GCTACTACTCCAACACCAGTAAAAA 59.007 40.000 0.00 0.00 0.00 1.94
2494 2655 5.306160 AGCTACTACTCCAACACCAGTAAAA 59.694 40.000 0.00 0.00 0.00 1.52
2495 2656 4.836736 AGCTACTACTCCAACACCAGTAAA 59.163 41.667 0.00 0.00 0.00 2.01
2496 2657 4.413760 AGCTACTACTCCAACACCAGTAA 58.586 43.478 0.00 0.00 0.00 2.24
2514 2675 0.664761 GCGTGGTCCGTACATAGCTA 59.335 55.000 0.00 0.00 39.32 3.32
2516 2677 0.458889 TTGCGTGGTCCGTACATAGC 60.459 55.000 0.00 0.00 39.32 2.97
2517 2678 2.124903 GATTGCGTGGTCCGTACATAG 58.875 52.381 0.00 0.00 39.32 2.23
2518 2679 1.477295 TGATTGCGTGGTCCGTACATA 59.523 47.619 0.00 0.00 39.32 2.29
2519 2680 0.248012 TGATTGCGTGGTCCGTACAT 59.752 50.000 0.00 0.00 39.32 2.29
2521 2682 0.650512 CATGATTGCGTGGTCCGTAC 59.349 55.000 0.00 0.00 39.32 3.67
2522 2683 0.533032 TCATGATTGCGTGGTCCGTA 59.467 50.000 0.00 0.00 39.32 4.02
2523 2684 1.019278 GTCATGATTGCGTGGTCCGT 61.019 55.000 0.00 0.00 39.32 4.69
2524 2685 1.705337 GGTCATGATTGCGTGGTCCG 61.705 60.000 0.00 0.00 40.40 4.79
2525 2686 1.705337 CGGTCATGATTGCGTGGTCC 61.705 60.000 0.00 0.00 0.00 4.46
2526 2687 1.019278 ACGGTCATGATTGCGTGGTC 61.019 55.000 0.00 0.00 0.00 4.02
2552 2713 4.035792 CGTTTAATTAATGCCGTCCCATGA 59.964 41.667 0.00 0.00 0.00 3.07
2587 2748 5.005682 GCTGAAAAGCGAAAACACTTGAAAT 59.994 36.000 0.00 0.00 0.00 2.17
2659 2820 4.079970 TGCTATGCGATACCTAACTAGCT 58.920 43.478 0.00 0.00 33.13 3.32
2660 2821 4.436242 TGCTATGCGATACCTAACTAGC 57.564 45.455 0.00 0.00 0.00 3.42
2661 2822 6.496571 GGTATGCTATGCGATACCTAACTAG 58.503 44.000 16.42 0.00 38.45 2.57
2662 2823 5.065602 CGGTATGCTATGCGATACCTAACTA 59.934 44.000 18.94 0.00 38.86 2.24
2663 2824 4.142447 CGGTATGCTATGCGATACCTAACT 60.142 45.833 18.94 0.00 38.86 2.24
2664 2825 4.103357 CGGTATGCTATGCGATACCTAAC 58.897 47.826 18.94 0.00 38.86 2.34
2666 2827 3.613030 TCGGTATGCTATGCGATACCTA 58.387 45.455 18.94 11.67 38.86 3.08
2707 2894 6.654959 TGAATTGATGGAAGAATACGGGTAA 58.345 36.000 0.00 0.00 0.00 2.85
2709 2896 5.104527 TCTGAATTGATGGAAGAATACGGGT 60.105 40.000 0.00 0.00 0.00 5.28
2714 2901 9.519191 TCAAAAGTCTGAATTGATGGAAGAATA 57.481 29.630 0.00 0.00 0.00 1.75
2715 2902 8.413309 TCAAAAGTCTGAATTGATGGAAGAAT 57.587 30.769 0.00 0.00 0.00 2.40
2719 2906 8.180706 TCATTCAAAAGTCTGAATTGATGGAA 57.819 30.769 0.00 0.00 42.16 3.53
2738 2925 3.064408 GCTTGCATCGATCAACTCATTCA 59.936 43.478 0.00 0.00 0.00 2.57
2753 2940 2.314402 TCCCTCTGGATGCTTGCAT 58.686 52.632 7.91 7.91 35.03 3.96
2763 2950 4.500499 AGTTTCATGAGAATCCCTCTGG 57.500 45.455 0.00 0.00 42.44 3.86
2769 2956 6.534934 GTCACGTAAAGTTTCATGAGAATCC 58.465 40.000 0.00 0.00 32.89 3.01
2794 2981 3.063452 CAGCCGTACAATGGTATGTGTTC 59.937 47.826 0.00 0.00 35.19 3.18
2798 2985 3.388024 AGATCAGCCGTACAATGGTATGT 59.612 43.478 0.00 0.00 35.19 2.29
2838 3025 3.557054 CGATTCTTGAAAGGAGTGACCCA 60.557 47.826 0.00 0.00 40.05 4.51
2842 3029 4.307432 GTGTCGATTCTTGAAAGGAGTGA 58.693 43.478 0.00 0.00 0.00 3.41
2858 3045 1.295792 AGAAAAAGCTTGCGTGTCGA 58.704 45.000 0.00 0.00 0.00 4.20
2862 3049 2.401720 CGCTAAAGAAAAAGCTTGCGTG 59.598 45.455 13.49 0.00 36.29 5.34
2876 3063 3.642705 AGCCTTTTCTTTTGCGCTAAAG 58.357 40.909 30.32 30.32 36.64 1.85
2882 3070 6.710692 ATTAATGAAGCCTTTTCTTTTGCG 57.289 33.333 0.00 0.00 0.00 4.85
2893 3081 7.961326 AACTGTTCCATAATTAATGAAGCCT 57.039 32.000 0.00 0.00 37.86 4.58
2894 3082 9.435688 AAAAACTGTTCCATAATTAATGAAGCC 57.564 29.630 0.00 0.00 37.86 4.35
2998 3186 3.757270 GATCTTCGGATCTGGTCCTAGA 58.243 50.000 5.25 8.09 45.46 2.43
3065 3256 4.019771 TGGATTGTATGGAGTGTTGTGCTA 60.020 41.667 0.00 0.00 0.00 3.49
3108 3299 4.872691 CCTTAGTAGTTCTTCGTCGGAGTA 59.127 45.833 0.00 0.00 0.00 2.59
3147 3341 1.182667 TCGGTGATCTTCCATGACGT 58.817 50.000 0.00 0.00 0.00 4.34
3333 3529 3.945436 CGTGCACGTTGGCTTCTA 58.055 55.556 30.50 0.00 34.04 2.10
3444 3640 1.134280 TGAAAGCCTAGATCCTGCTGC 60.134 52.381 2.37 0.00 35.08 5.25
3500 3696 0.250553 TGGAGGCGTCGTTGGAAATT 60.251 50.000 0.00 0.00 0.00 1.82
3504 3700 2.342279 CTTGGAGGCGTCGTTGGA 59.658 61.111 0.00 0.00 0.00 3.53
3507 3703 2.657237 CTCCTTGGAGGCGTCGTT 59.343 61.111 8.74 0.00 34.61 3.85


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

AutoCloner maintained by Alex Coulton.