Multiple sequence alignment - TraesCS3A01G411100

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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 TraesCS3A01G411100 chr3A 100.000 4517 0 0 1 4517 655204152 655208668 0.000000e+00 8342
1 TraesCS3A01G411100 chr3A 98.037 815 16 0 3703 4517 655219407 655220221 0.000000e+00 1417
2 TraesCS3A01G411100 chr3A 97.674 817 19 0 3701 4517 474351861 474351045 0.000000e+00 1404
3 TraesCS3A01G411100 chr3A 97.555 818 17 2 3702 4517 154309154 154308338 0.000000e+00 1397
4 TraesCS3A01G411100 chr3A 97.546 815 20 0 3703 4517 538328011 538327197 0.000000e+00 1395
5 TraesCS3A01G411100 chr7D 94.309 3233 169 12 55 3277 572647290 572644063 0.000000e+00 4937
6 TraesCS3A01G411100 chr7D 78.910 1394 270 22 767 2149 609935520 609934140 0.000000e+00 924
7 TraesCS3A01G411100 chr7D 77.942 1487 291 34 715 2183 589312672 589311205 0.000000e+00 894
8 TraesCS3A01G411100 chr7D 94.919 433 19 3 3269 3700 572636539 572636109 0.000000e+00 675
9 TraesCS3A01G411100 chr3B 87.475 2499 263 35 55 2527 42974183 42971709 0.000000e+00 2835
10 TraesCS3A01G411100 chr3B 88.235 1088 117 9 2609 3693 42971538 42970459 0.000000e+00 1290
11 TraesCS3A01G411100 chr3B 77.984 1458 290 27 707 2150 571309207 571310647 0.000000e+00 885
12 TraesCS3A01G411100 chr3B 91.026 78 4 3 1 77 274088512 274088437 7.990000e-18 102
13 TraesCS3A01G411100 chr2D 88.607 2089 213 16 451 2527 537434445 537432370 0.000000e+00 2516
14 TraesCS3A01G411100 chr2D 87.854 1095 119 11 2609 3693 537432110 537431020 0.000000e+00 1273
15 TraesCS3A01G411100 chr2D 94.444 72 2 2 1 72 615794543 615794612 4.780000e-20 110
16 TraesCS3A01G411100 chr1D 88.309 2087 219 16 451 2524 454414125 454416199 0.000000e+00 2479
17 TraesCS3A01G411100 chr1D 87.883 2088 225 22 451 2525 478703239 478705311 0.000000e+00 2429
18 TraesCS3A01G411100 chr1D 87.688 1129 122 14 2576 3693 454416335 454417457 0.000000e+00 1299
19 TraesCS3A01G411100 chr1D 87.147 1097 126 11 2606 3693 478705296 478706386 0.000000e+00 1230
20 TraesCS3A01G411100 chr1D 92.105 76 4 2 1 75 77619997 77620071 6.180000e-19 106
21 TraesCS3A01G411100 chr5A 87.990 2090 225 18 451 2527 702830800 702828724 0.000000e+00 2446
22 TraesCS3A01G411100 chr5A 97.552 817 20 0 3701 4517 194834792 194835608 0.000000e+00 1399
23 TraesCS3A01G411100 chr5A 89.281 793 74 9 2613 3398 702828501 702827713 0.000000e+00 983
24 TraesCS3A01G411100 chr4A 97.791 815 18 0 3703 4517 443228493 443227679 0.000000e+00 1406
25 TraesCS3A01G411100 chr4A 97.433 818 20 1 3700 4517 555828292 555827476 0.000000e+00 1393
26 TraesCS3A01G411100 chr4A 93.151 73 3 2 1 73 95217398 95217468 6.180000e-19 106
27 TraesCS3A01G411100 chr7A 97.546 815 20 0 3703 4517 80331885 80331071 0.000000e+00 1395
28 TraesCS3A01G411100 chr1A 97.549 816 19 1 3703 4517 497453356 497452541 0.000000e+00 1395
29 TraesCS3A01G411100 chr1A 75.963 649 150 5 2840 3486 253365217 253365861 3.370000e-86 329
30 TraesCS3A01G411100 chr6B 98.462 65 0 1 1 64 244498260 244498324 3.690000e-21 113
31 TraesCS3A01G411100 chr6D 93.243 74 4 1 1 73 12757278 12757351 1.720000e-19 108
32 TraesCS3A01G411100 chr6D 94.366 71 2 2 1 69 244666397 244666327 1.720000e-19 108
33 TraesCS3A01G411100 chr5D 94.366 71 2 2 1 70 539840855 539840786 1.720000e-19 108
34 TraesCS3A01G411100 chr2B 94.366 71 2 2 1 69 587908407 587908477 1.720000e-19 108
35 TraesCS3A01G411100 chr4D 77.099 131 28 2 2865 2994 52081827 52081698 1.740000e-09 75


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 TraesCS3A01G411100 chr3A 655204152 655208668 4516 False 8342.0 8342 100.0000 1 4517 1 chr3A.!!$F1 4516
1 TraesCS3A01G411100 chr3A 655219407 655220221 814 False 1417.0 1417 98.0370 3703 4517 1 chr3A.!!$F2 814
2 TraesCS3A01G411100 chr3A 474351045 474351861 816 True 1404.0 1404 97.6740 3701 4517 1 chr3A.!!$R2 816
3 TraesCS3A01G411100 chr3A 154308338 154309154 816 True 1397.0 1397 97.5550 3702 4517 1 chr3A.!!$R1 815
4 TraesCS3A01G411100 chr3A 538327197 538328011 814 True 1395.0 1395 97.5460 3703 4517 1 chr3A.!!$R3 814
5 TraesCS3A01G411100 chr7D 572644063 572647290 3227 True 4937.0 4937 94.3090 55 3277 1 chr7D.!!$R2 3222
6 TraesCS3A01G411100 chr7D 609934140 609935520 1380 True 924.0 924 78.9100 767 2149 1 chr7D.!!$R4 1382
7 TraesCS3A01G411100 chr7D 589311205 589312672 1467 True 894.0 894 77.9420 715 2183 1 chr7D.!!$R3 1468
8 TraesCS3A01G411100 chr3B 42970459 42974183 3724 True 2062.5 2835 87.8550 55 3693 2 chr3B.!!$R2 3638
9 TraesCS3A01G411100 chr3B 571309207 571310647 1440 False 885.0 885 77.9840 707 2150 1 chr3B.!!$F1 1443
10 TraesCS3A01G411100 chr2D 537431020 537434445 3425 True 1894.5 2516 88.2305 451 3693 2 chr2D.!!$R1 3242
11 TraesCS3A01G411100 chr1D 454414125 454417457 3332 False 1889.0 2479 87.9985 451 3693 2 chr1D.!!$F2 3242
12 TraesCS3A01G411100 chr1D 478703239 478706386 3147 False 1829.5 2429 87.5150 451 3693 2 chr1D.!!$F3 3242
13 TraesCS3A01G411100 chr5A 702827713 702830800 3087 True 1714.5 2446 88.6355 451 3398 2 chr5A.!!$R1 2947
14 TraesCS3A01G411100 chr5A 194834792 194835608 816 False 1399.0 1399 97.5520 3701 4517 1 chr5A.!!$F1 816
15 TraesCS3A01G411100 chr4A 443227679 443228493 814 True 1406.0 1406 97.7910 3703 4517 1 chr4A.!!$R1 814
16 TraesCS3A01G411100 chr4A 555827476 555828292 816 True 1393.0 1393 97.4330 3700 4517 1 chr4A.!!$R2 817
17 TraesCS3A01G411100 chr7A 80331071 80331885 814 True 1395.0 1395 97.5460 3703 4517 1 chr7A.!!$R1 814
18 TraesCS3A01G411100 chr1A 497452541 497453356 815 True 1395.0 1395 97.5490 3703 4517 1 chr1A.!!$R1 814
19 TraesCS3A01G411100 chr1A 253365217 253365861 644 False 329.0 329 75.9630 2840 3486 1 chr1A.!!$F1 646

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
727 742 0.108424 GCAGCTTGAGGACGAGATGT 60.108 55.000 0.0 0.0 43.47 3.06 F
1667 1685 0.179084 GATTTCGGGATGCGTGGAGA 60.179 55.000 0.0 0.0 0.00 3.71 F
3036 3302 1.002544 GTGAAGAAGGTGCCAGCTAGT 59.997 52.381 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2562 2709 0.110056 CGCTCACATGGCAAGTTCAC 60.110 55.0 0.00 0.0 0.00 3.18 R
3045 3311 0.392193 CATTCCAAGTCCAGCGCTCT 60.392 55.0 7.13 0.0 0.00 4.09 R
4288 4558 1.014044 TCGCGTTCAGAGCATCCAAC 61.014 55.0 5.77 0.0 33.66 3.77 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
75 76 9.878599 GTATCACAACCACATGTATATAAAAGC 57.121 33.333 0.00 0.00 30.84 3.51
76 77 7.328277 TCACAACCACATGTATATAAAAGCC 57.672 36.000 0.00 0.00 30.84 4.35
85 86 8.243426 CACATGTATATAAAAGCCGCCATTAAT 58.757 33.333 0.00 0.00 0.00 1.40
131 132 3.895704 ATGGGGTTTTAGTGAGGTTGT 57.104 42.857 0.00 0.00 0.00 3.32
137 138 4.546570 GGTTTTAGTGAGGTTGTTGCATC 58.453 43.478 0.00 0.00 0.00 3.91
236 238 2.050144 TCTGTGGAGAGAAACTTGCCT 58.950 47.619 0.00 0.00 0.00 4.75
406 417 1.203052 TGGACCGACTACCATTTCGTC 59.797 52.381 0.00 0.00 33.23 4.20
428 439 1.796459 GTACTACAAGTTGCCACGTGG 59.204 52.381 30.66 30.66 36.76 4.94
537 551 4.316205 TGACTACTTCACATTCACACGT 57.684 40.909 0.00 0.00 0.00 4.49
542 556 6.220930 ACTACTTCACATTCACACGTACAAT 58.779 36.000 0.00 0.00 0.00 2.71
558 572 7.068348 ACACGTACAATAGACCTATCAGTCAAT 59.932 37.037 0.00 0.00 39.34 2.57
578 593 2.563702 TCAAACAGGACCGGTTGTTAC 58.436 47.619 21.81 3.40 36.56 2.50
627 642 4.108336 CTGGATATGACACTGTTGAGACG 58.892 47.826 0.00 0.00 0.00 4.18
727 742 0.108424 GCAGCTTGAGGACGAGATGT 60.108 55.000 0.00 0.00 43.47 3.06
756 771 4.697756 GCGCCACCAGTAGCACCA 62.698 66.667 0.00 0.00 0.00 4.17
990 1008 5.707298 AGATGTTATGGTGAGAACAAACTGG 59.293 40.000 0.00 0.00 36.88 4.00
995 1013 1.680338 GTGAGAACAAACTGGCCTGT 58.320 50.000 9.88 9.88 0.00 4.00
1108 1126 1.069204 TGAAGTTTCTGAGCGCTCACT 59.931 47.619 35.30 26.56 35.46 3.41
1143 1161 2.032808 GCAAGAGGAACAGTTCGTGAAC 60.033 50.000 13.23 4.58 41.45 3.18
1237 1255 2.332063 GCTAAGAAGCCTGCCATACA 57.668 50.000 0.00 0.00 43.40 2.29
1246 1264 1.027357 CCTGCCATACATGCCTTCAC 58.973 55.000 0.00 0.00 0.00 3.18
1303 1321 5.745312 AAGTCAACTATCAGACATGGACA 57.255 39.130 0.00 0.00 37.23 4.02
1307 1325 5.700832 GTCAACTATCAGACATGGACAACAA 59.299 40.000 0.00 0.00 34.93 2.83
1358 1376 3.288964 ACGATCCCGACTTCTTCTACAT 58.711 45.455 0.00 0.00 39.50 2.29
1400 1418 3.537580 ACCACGTTGTGAACATGTACTT 58.462 40.909 0.00 0.00 35.23 2.24
1532 1550 1.091537 AACAACCACAACCAGTCACG 58.908 50.000 0.00 0.00 0.00 4.35
1603 1621 4.998671 TGGCTGTTCAAAACATTTCTGA 57.001 36.364 0.00 0.00 41.26 3.27
1637 1655 1.621107 CTTGCGCCAATGAACATGAC 58.379 50.000 4.18 0.00 0.00 3.06
1641 1659 1.605500 CGCCAATGAACATGACAACG 58.394 50.000 0.00 0.00 0.00 4.10
1667 1685 0.179084 GATTTCGGGATGCGTGGAGA 60.179 55.000 0.00 0.00 0.00 3.71
1684 1702 3.648067 TGGAGACATTGAGGAAGTGTTCT 59.352 43.478 0.00 0.00 33.40 3.01
1760 1781 2.200373 TTAGGCCCTTCTTTGCTGAC 57.800 50.000 0.00 0.00 0.00 3.51
1886 1907 9.167311 GTCCAAGACAATGATAGACTACAAAAT 57.833 33.333 0.00 0.00 32.09 1.82
1903 1924 9.981460 ACTACAAAATCTTTGGAATAGGAGAAT 57.019 29.630 4.30 0.00 0.00 2.40
1915 1936 5.013599 GGAATAGGAGAATATTCTGGGTGCT 59.986 44.000 22.61 11.51 40.51 4.40
1990 2011 5.064325 GTGAGGGGTTTAACGCTGTTATAAG 59.936 44.000 11.75 0.00 33.39 1.73
2031 2052 7.463961 AGCAATTCAATTCTCAGATTTGTCT 57.536 32.000 8.75 0.00 31.34 3.41
2080 2101 2.667470 TCTAGGAGCCGAGCTACAATT 58.333 47.619 10.26 0.00 42.99 2.32
2222 2244 6.436261 CGTACGTGAAATCACTGATATAGGT 58.564 40.000 7.22 2.65 44.34 3.08
2290 2319 1.137282 TGGCATGCATGTGCTAAATGG 59.863 47.619 26.79 0.00 44.45 3.16
2389 2420 6.642131 ACGAATTTTGCCATGCATATGATAAC 59.358 34.615 6.97 0.00 38.76 1.89
2392 2423 4.486574 TTGCCATGCATATGATAACGTG 57.513 40.909 6.97 0.15 38.76 4.49
2397 2428 3.192541 TGCATATGATAACGTGGCTGT 57.807 42.857 6.97 0.00 0.00 4.40
2412 2443 3.506312 CTGTCGTGCACGTGCCAAC 62.506 63.158 35.72 28.20 41.18 3.77
2462 2494 1.362768 TGTCGCAAGCTGCTAATCTG 58.637 50.000 0.90 0.00 42.25 2.90
2524 2557 1.881324 TGTGACACTGATGTTGCCATG 59.119 47.619 7.20 0.00 39.95 3.66
2557 2704 2.494870 GGAAAAGATGGCTTGCATGAGT 59.505 45.455 3.33 0.00 33.79 3.41
2558 2705 3.056322 GGAAAAGATGGCTTGCATGAGTT 60.056 43.478 3.33 0.00 33.79 3.01
2562 2709 3.806380 AGATGGCTTGCATGAGTTAGAG 58.194 45.455 3.33 0.00 0.00 2.43
2584 2777 1.246056 AACTTGCCATGTGAGCGCAT 61.246 50.000 11.47 0.00 31.44 4.73
2592 2804 2.352030 CCATGTGAGCGCATTGAAGTTT 60.352 45.455 11.47 0.00 0.00 2.66
2627 2839 1.838112 TGAACTTGCCAGGCATAAGG 58.162 50.000 17.09 8.72 38.76 2.69
2703 2964 1.371512 TGCCGTGCATTTGCGAAAG 60.372 52.632 0.00 0.00 45.83 2.62
2945 3211 9.197306 AGACATATCAAATGGTGTGTACTACTA 57.803 33.333 0.00 0.00 0.00 1.82
2972 3238 3.687212 TGTTGCAAGTTTGAAAGAGACGA 59.313 39.130 0.00 0.00 0.00 4.20
3036 3302 1.002544 GTGAAGAAGGTGCCAGCTAGT 59.997 52.381 0.00 0.00 0.00 2.57
3045 3311 4.543689 AGGTGCCAGCTAGTTACATACTA 58.456 43.478 0.00 0.00 38.33 1.82
3103 3369 3.329889 ATGGCGCCCAGGAAGTGA 61.330 61.111 26.77 0.73 36.75 3.41
3228 3494 0.037590 AAATGTGCAGGGCCGTAGAA 59.962 50.000 0.00 0.00 0.00 2.10
3351 3617 0.606401 CATCAACAGGGCCGTCAACT 60.606 55.000 0.00 0.00 0.00 3.16
3359 3625 1.628846 AGGGCCGTCAACTGATAACTT 59.371 47.619 0.00 0.00 0.00 2.66
3366 3632 4.152402 CCGTCAACTGATAACTTTGAGGTG 59.848 45.833 0.00 0.00 34.70 4.00
3386 3652 1.660560 GGCTCTGGCGCATCAAACAT 61.661 55.000 10.83 0.00 39.81 2.71
3388 3654 0.806868 CTCTGGCGCATCAAACATGT 59.193 50.000 10.83 0.00 0.00 3.21
3409 3675 1.202806 ACACACACATCCAGAACCCTG 60.203 52.381 0.00 0.00 40.09 4.45
3413 3679 0.251297 CACATCCAGAACCCTGCCAA 60.251 55.000 0.00 0.00 39.07 4.52
3418 3684 0.890996 CCAGAACCCTGCCAAGACAC 60.891 60.000 0.00 0.00 39.07 3.67
3448 3715 1.739371 GCGACCGAAGCAGATTAGGTT 60.739 52.381 4.55 0.00 45.87 3.50
3453 3720 2.939103 CCGAAGCAGATTAGGTTCAAGG 59.061 50.000 6.68 0.00 44.08 3.61
3458 3725 1.667724 CAGATTAGGTTCAAGGCAGCG 59.332 52.381 0.00 0.00 0.00 5.18
3486 3753 0.316204 CCAAGGCAAGCACAAGAAGG 59.684 55.000 0.00 0.00 0.00 3.46
3489 3756 0.771127 AGGCAAGCACAAGAAGGGTA 59.229 50.000 0.00 0.00 0.00 3.69
3513 3780 7.611213 ACGAAGTAATCATTTTCGGAAAGAT 57.389 32.000 8.66 1.77 45.71 2.40
3523 3790 5.759506 TTTTCGGAAAGATTAGTGTGCAA 57.240 34.783 3.09 0.00 0.00 4.08
3558 3825 4.082300 CGAAACAATGTGAATCATGGGGAA 60.082 41.667 0.00 0.00 36.81 3.97
3581 3848 2.009051 TGAATGATGGTGCGCACTAAG 58.991 47.619 36.84 0.00 0.00 2.18
3589 3858 2.677836 TGGTGCGCACTAAGATGAATTC 59.322 45.455 36.84 17.79 0.00 2.17
3605 3874 7.344134 AGATGAATTCTGTGATGGAGAAATGA 58.656 34.615 7.05 0.00 33.22 2.57
3620 3889 5.014808 AGAAATGATAAACTTGCCATGCC 57.985 39.130 0.00 0.00 0.00 4.40
3622 3891 5.893255 AGAAATGATAAACTTGCCATGCCTA 59.107 36.000 0.00 0.00 0.00 3.93
3651 3920 6.359804 ACTGAATATTGCCAGTATGTGACAT 58.640 36.000 2.65 2.65 41.38 3.06
3660 3929 5.584649 TGCCAGTATGTGACATAAAACTAGC 59.415 40.000 6.89 8.44 0.00 3.42
3689 3958 1.081840 GCAAGCGGCAGAGTGTTTC 60.082 57.895 1.45 0.00 43.97 2.78
3692 3961 1.334869 CAAGCGGCAGAGTGTTTCTTT 59.665 47.619 1.45 0.00 32.41 2.52
3693 3962 1.680338 AGCGGCAGAGTGTTTCTTTT 58.320 45.000 1.45 0.00 32.41 2.27
3694 3963 2.024414 AGCGGCAGAGTGTTTCTTTTT 58.976 42.857 1.45 0.00 32.41 1.94
3695 3964 2.119457 GCGGCAGAGTGTTTCTTTTTG 58.881 47.619 0.00 0.00 32.41 2.44
3696 3965 2.479560 GCGGCAGAGTGTTTCTTTTTGT 60.480 45.455 0.00 0.00 32.41 2.83
3697 3966 3.242936 GCGGCAGAGTGTTTCTTTTTGTA 60.243 43.478 0.00 0.00 32.41 2.41
3698 3967 4.556699 GCGGCAGAGTGTTTCTTTTTGTAT 60.557 41.667 0.00 0.00 32.41 2.29
4264 4534 2.507886 TCCCAAACCTTCACAGACTTCA 59.492 45.455 0.00 0.00 0.00 3.02
4288 4558 2.094906 CACTGGCAATCCACAATGTCTG 60.095 50.000 0.00 0.00 37.47 3.51
4360 4630 8.816894 TCCTCAAGTGTAATAAGTCTTCAGATT 58.183 33.333 0.00 0.00 0.00 2.40
4400 4670 7.630082 ACTTAAGTGATGCCCAATTTACTCTA 58.370 34.615 7.48 0.00 34.59 2.43
4468 4740 1.376037 CTTCGAGGTGGGTTGCTCC 60.376 63.158 0.00 0.00 0.00 4.70
4484 4756 1.412343 GCTCCCAAAAGACAAAAGCCA 59.588 47.619 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 9.836076 CGTCTCCAACGTATCTATAATTTATGA 57.164 33.333 0.00 0.00 46.42 2.15
40 41 2.735134 GTGGTTGTGATACGTCTCCAAC 59.265 50.000 18.46 18.46 36.77 3.77
41 42 2.365941 TGTGGTTGTGATACGTCTCCAA 59.634 45.455 0.00 0.00 0.00 3.53
42 43 1.964933 TGTGGTTGTGATACGTCTCCA 59.035 47.619 0.00 0.00 0.00 3.86
43 44 2.736144 TGTGGTTGTGATACGTCTCC 57.264 50.000 0.00 0.00 0.00 3.71
44 45 3.585862 ACATGTGGTTGTGATACGTCTC 58.414 45.455 0.00 0.00 0.00 3.36
45 46 3.678056 ACATGTGGTTGTGATACGTCT 57.322 42.857 0.00 0.00 0.00 4.18
46 47 8.806177 TTATATACATGTGGTTGTGATACGTC 57.194 34.615 9.11 0.00 0.00 4.34
47 48 9.602568 TTTTATATACATGTGGTTGTGATACGT 57.397 29.630 9.11 0.00 0.00 3.57
49 50 9.878599 GCTTTTATATACATGTGGTTGTGATAC 57.121 33.333 9.11 0.00 0.00 2.24
50 51 9.062524 GGCTTTTATATACATGTGGTTGTGATA 57.937 33.333 9.11 0.00 0.00 2.15
51 52 7.255104 CGGCTTTTATATACATGTGGTTGTGAT 60.255 37.037 9.11 0.00 0.00 3.06
52 53 6.037720 CGGCTTTTATATACATGTGGTTGTGA 59.962 38.462 9.11 0.00 0.00 3.58
53 54 6.198687 CGGCTTTTATATACATGTGGTTGTG 58.801 40.000 9.11 0.00 0.00 3.33
75 76 5.766150 TTATTGACCTTCATTAATGGCGG 57.234 39.130 15.36 16.46 0.00 6.13
120 121 2.683968 GACGATGCAACAACCTCACTA 58.316 47.619 0.00 0.00 0.00 2.74
131 132 2.292103 TCATGTGATCGACGATGCAA 57.708 45.000 16.49 0.01 0.00 4.08
137 138 2.097396 GCGGTTATTCATGTGATCGACG 60.097 50.000 0.00 0.00 0.00 5.12
186 187 0.103937 ACGCACACCCCATTTTTGTG 59.896 50.000 0.00 0.00 42.96 3.33
236 238 4.202161 ACAACCTTTGTTTCACACACACAA 60.202 37.500 0.00 0.00 42.22 3.33
254 256 1.658994 TTGACACGGTTCTGACAACC 58.341 50.000 0.00 0.00 36.96 3.77
321 325 9.865321 TTTTCAATTTCATTTGGCAATTTCAAA 57.135 22.222 0.00 6.28 38.30 2.69
406 417 2.475111 CACGTGGCAACTTGTAGTACTG 59.525 50.000 7.95 0.00 37.61 2.74
537 551 9.817809 GTTTGATTGACTGATAGGTCTATTGTA 57.182 33.333 0.00 0.00 37.16 2.41
542 556 6.667848 TCCTGTTTGATTGACTGATAGGTCTA 59.332 38.462 0.00 0.00 37.16 2.59
558 572 2.563702 GTAACAACCGGTCCTGTTTGA 58.436 47.619 25.40 9.68 37.05 2.69
578 593 1.815421 GACGTGCCTACCATGCTGG 60.815 63.158 0.00 1.16 45.02 4.85
601 616 2.586258 ACAGTGTCATATCCAGTCGC 57.414 50.000 0.00 0.00 0.00 5.19
627 642 3.691609 CAGATCCTTGGTTGCTTACTTCC 59.308 47.826 0.00 0.00 0.00 3.46
641 656 4.444022 CCGAGTTTCCATCATCAGATCCTT 60.444 45.833 0.00 0.00 30.20 3.36
749 764 0.313987 CATCCGCTCGTATGGTGCTA 59.686 55.000 0.00 0.00 33.03 3.49
756 771 3.206150 AGCAAATTTCATCCGCTCGTAT 58.794 40.909 0.00 0.00 0.00 3.06
842 857 6.373186 TCTTAAGCGTTCTTCGATGATCTA 57.627 37.500 1.37 0.00 42.86 1.98
857 872 5.227908 TGTACTCTCCAGTTTTCTTAAGCG 58.772 41.667 0.00 0.00 33.62 4.68
933 951 1.490574 GGACTGCTAGACCATCACCT 58.509 55.000 0.00 0.00 30.29 4.00
944 962 2.992689 TGCGTTCCGGGACTGCTA 60.993 61.111 23.86 12.12 0.00 3.49
990 1008 2.024176 TTAGCTTCATTCGGACAGGC 57.976 50.000 0.00 0.00 0.00 4.85
995 1013 2.028839 TCCACGTTTAGCTTCATTCGGA 60.029 45.455 0.00 0.00 0.00 4.55
1121 1139 0.868406 CACGAACTGTTCCTCTTGCC 59.132 55.000 14.48 0.00 0.00 4.52
1237 1255 2.825532 GGTTTACCACATGTGAAGGCAT 59.174 45.455 27.46 7.53 35.64 4.40
1246 1264 3.066291 TGCTACCAGGTTTACCACATG 57.934 47.619 0.00 0.00 38.89 3.21
1358 1376 7.279981 CGTGGTCTTCATCATCCAGTTTTATTA 59.720 37.037 0.00 0.00 0.00 0.98
1400 1418 0.811219 GCGTGCTGCACCATCTATCA 60.811 55.000 25.61 0.00 45.45 2.15
1532 1550 1.862602 AAAACCGCATCCGAACTGCC 61.863 55.000 0.00 0.00 36.24 4.85
1603 1621 2.684655 AAGGCCGCCCATGCATTT 60.685 55.556 5.55 0.00 37.32 2.32
1637 1655 1.024579 CCCGAAATCCTGGTCCGTTG 61.025 60.000 0.00 0.00 0.00 4.10
1641 1659 0.819666 GCATCCCGAAATCCTGGTCC 60.820 60.000 0.00 0.00 0.00 4.46
1667 1685 4.780815 TGTTGAGAACACTTCCTCAATGT 58.219 39.130 7.88 0.00 46.89 2.71
1684 1702 4.415881 AGTGTCTGTGTATGGTTGTTGA 57.584 40.909 0.00 0.00 0.00 3.18
1760 1781 1.512926 CTTTGTGGAGTTCCGGTCTG 58.487 55.000 0.00 0.00 39.43 3.51
1796 1817 2.124411 TCTGGGGTTAAGCTATGGTCC 58.876 52.381 4.41 0.00 0.00 4.46
1834 1855 6.721318 TGGTACTTTTCTATCATTGCCTTCT 58.279 36.000 0.00 0.00 0.00 2.85
1886 1907 7.350921 ACCCAGAATATTCTCCTATTCCAAAGA 59.649 37.037 15.24 0.00 38.38 2.52
1897 1918 3.326297 AGCTAGCACCCAGAATATTCTCC 59.674 47.826 18.83 2.44 34.74 3.71
1903 1924 7.174946 GCATAAAATAAGCTAGCACCCAGAATA 59.825 37.037 18.83 0.77 0.00 1.75
1915 1936 8.889717 GGTAGAAACACTGCATAAAATAAGCTA 58.110 33.333 0.00 0.00 32.90 3.32
1990 2011 3.906720 TGCTAGGGTTCACATACCTTC 57.093 47.619 0.00 0.00 38.30 3.46
2031 2052 5.313520 TGTTGTATTGCGCTGTACTACTA 57.686 39.130 24.47 15.19 31.07 1.82
2069 2090 5.347635 TGTGTTAGCTAACAATTGTAGCTCG 59.652 40.000 34.72 13.56 46.54 5.03
2080 2101 6.036735 GTCTTTGAGTGTTGTGTTAGCTAACA 59.963 38.462 30.81 30.81 43.32 2.41
2131 2152 4.836825 TGTTCTCATCATTTGTCTCTCCC 58.163 43.478 0.00 0.00 0.00 4.30
2242 2264 8.147058 TGTTAATTTTCTGTTTGTATGCATGGT 58.853 29.630 10.16 0.00 0.00 3.55
2290 2319 4.192429 AGTACAAATTGAATGGCAAGGC 57.808 40.909 0.00 0.00 40.42 4.35
2397 2428 2.590291 ATGTTGGCACGTGCACGA 60.590 55.556 42.94 25.08 44.36 4.35
2462 2494 7.761409 TCTACATTTGCATTACATTTCTCCAC 58.239 34.615 0.00 0.00 0.00 4.02
2524 2557 6.226052 AGCCATCTTTTCCAACTCATTTTTC 58.774 36.000 0.00 0.00 0.00 2.29
2557 2704 4.318332 CTCACATGGCAAGTTCACTCTAA 58.682 43.478 0.00 0.00 0.00 2.10
2558 2705 3.866066 GCTCACATGGCAAGTTCACTCTA 60.866 47.826 0.00 0.00 0.00 2.43
2562 2709 0.110056 CGCTCACATGGCAAGTTCAC 60.110 55.000 0.00 0.00 0.00 3.18
2584 2777 1.336440 CCACGTGCATGGAAACTTCAA 59.664 47.619 10.91 0.00 43.02 2.69
2627 2839 7.492020 TGATTTATGCATGGCAAGTTCATTTAC 59.508 33.333 10.16 0.00 43.62 2.01
2687 2948 1.981254 ATTCTTTCGCAAATGCACGG 58.019 45.000 6.18 0.00 42.21 4.94
2728 2990 6.176896 TGCTACTACATGGCAATTTTCAGTA 58.823 36.000 0.00 0.00 42.70 2.74
2797 3061 0.611200 ATAGTGTACCCGCTGCACAA 59.389 50.000 0.00 0.00 37.93 3.33
2841 3105 3.059800 GGTCTCACAGCGTACAAACTTTC 60.060 47.826 0.00 0.00 0.00 2.62
2850 3114 1.583495 CGGACAGGTCTCACAGCGTA 61.583 60.000 0.00 0.00 0.00 4.42
2917 3183 6.711277 AGTACACACCATTTGATATGTCTGT 58.289 36.000 0.00 0.00 0.00 3.41
2945 3211 6.698766 GTCTCTTTCAAACTTGCAACATTGAT 59.301 34.615 18.05 0.00 32.35 2.57
3036 3302 3.552875 AGTCCAGCGCTCTAGTATGTAA 58.447 45.455 7.13 0.00 0.00 2.41
3045 3311 0.392193 CATTCCAAGTCCAGCGCTCT 60.392 55.000 7.13 0.00 0.00 4.09
3051 3317 2.995283 TCATCAGCATTCCAAGTCCAG 58.005 47.619 0.00 0.00 0.00 3.86
3103 3369 1.162181 CCATCTTCATGCACCGCGAT 61.162 55.000 8.23 0.00 0.00 4.58
3207 3473 0.392998 CTACGGCCCTGCACATTTCT 60.393 55.000 0.00 0.00 0.00 2.52
3214 3480 2.668632 CCTTTCTACGGCCCTGCA 59.331 61.111 0.00 0.00 0.00 4.41
3228 3494 4.144297 TCTCTAATGCTTTTGTGTGCCTT 58.856 39.130 0.00 0.00 0.00 4.35
3351 3617 2.912956 AGAGCCCACCTCAAAGTTATCA 59.087 45.455 0.00 0.00 43.31 2.15
3359 3625 4.020617 CGCCAGAGCCCACCTCAA 62.021 66.667 0.00 0.00 43.31 3.02
3366 3632 2.751436 TTTGATGCGCCAGAGCCC 60.751 61.111 4.18 0.00 36.02 5.19
3386 3652 2.224426 GGGTTCTGGATGTGTGTGTACA 60.224 50.000 0.00 0.00 34.63 2.90
3388 3654 2.038426 CAGGGTTCTGGATGTGTGTGTA 59.962 50.000 0.00 0.00 37.36 2.90
3409 3675 1.269257 GCCTTTTGTGAGTGTCTTGGC 60.269 52.381 0.00 0.00 0.00 4.52
3413 3679 1.583054 GTCGCCTTTTGTGAGTGTCT 58.417 50.000 0.00 0.00 33.18 3.41
3418 3684 0.512952 CTTCGGTCGCCTTTTGTGAG 59.487 55.000 0.00 0.00 33.18 3.51
3448 3715 0.742281 GATCTCAAGCGCTGCCTTGA 60.742 55.000 23.03 23.03 46.48 3.02
3453 3720 1.720301 CTTGGATCTCAAGCGCTGC 59.280 57.895 12.58 0.00 45.24 5.25
3472 3739 0.517316 CGTACCCTTCTTGTGCTTGC 59.483 55.000 0.00 0.00 0.00 4.01
3486 3753 6.651755 TTCCGAAAATGATTACTTCGTACC 57.348 37.500 10.09 0.00 40.17 3.34
3489 3756 7.611213 ATCTTTCCGAAAATGATTACTTCGT 57.389 32.000 10.09 0.00 40.17 3.85
3495 3762 8.181573 GCACACTAATCTTTCCGAAAATGATTA 58.818 33.333 11.92 11.92 31.11 1.75
3501 3768 5.278266 CCTTGCACACTAATCTTTCCGAAAA 60.278 40.000 0.00 0.00 0.00 2.29
3504 3771 3.007506 TCCTTGCACACTAATCTTTCCGA 59.992 43.478 0.00 0.00 0.00 4.55
3506 3773 4.702131 ACATCCTTGCACACTAATCTTTCC 59.298 41.667 0.00 0.00 0.00 3.13
3508 3775 4.082571 GCACATCCTTGCACACTAATCTTT 60.083 41.667 0.00 0.00 42.49 2.52
3523 3790 1.246649 TTGTTTCGCATGCACATCCT 58.753 45.000 19.57 0.00 0.00 3.24
3535 3802 3.443329 TCCCCATGATTCACATTGTTTCG 59.557 43.478 0.00 0.00 37.07 3.46
3558 3825 1.820519 AGTGCGCACCATCATTCAAAT 59.179 42.857 35.51 10.89 0.00 2.32
3581 3848 7.563888 TCATTTCTCCATCACAGAATTCATC 57.436 36.000 8.44 0.00 29.89 2.92
3589 3858 6.971184 GCAAGTTTATCATTTCTCCATCACAG 59.029 38.462 0.00 0.00 0.00 3.66
3605 3874 7.341769 TCAGTTTTATAGGCATGGCAAGTTTAT 59.658 33.333 22.64 12.04 0.00 1.40
3622 3891 9.407380 TCACATACTGGCAATATTCAGTTTTAT 57.593 29.630 13.31 1.67 43.19 1.40
3660 3929 2.127496 CGCTTGCGTGCTGTCAAG 60.127 61.111 6.86 7.66 41.79 3.02
3670 3939 2.770587 GAAACACTCTGCCGCTTGCG 62.771 60.000 8.14 8.14 45.60 4.85
3681 3950 9.226345 CTTTCAGTCATACAAAAAGAAACACTC 57.774 33.333 0.00 0.00 29.08 3.51
3684 3953 7.487829 GCACTTTCAGTCATACAAAAAGAAACA 59.512 33.333 9.67 0.00 30.97 2.83
3689 3958 5.510671 ACGCACTTTCAGTCATACAAAAAG 58.489 37.500 0.00 0.00 32.00 2.27
3692 3961 6.795098 ATAACGCACTTTCAGTCATACAAA 57.205 33.333 0.00 0.00 0.00 2.83
3693 3962 7.043656 CGATATAACGCACTTTCAGTCATACAA 60.044 37.037 0.00 0.00 0.00 2.41
3694 3963 6.416750 CGATATAACGCACTTTCAGTCATACA 59.583 38.462 0.00 0.00 0.00 2.29
3695 3964 6.635641 TCGATATAACGCACTTTCAGTCATAC 59.364 38.462 0.00 0.00 0.00 2.39
3696 3965 6.635641 GTCGATATAACGCACTTTCAGTCATA 59.364 38.462 0.00 0.00 0.00 2.15
3697 3966 5.459107 GTCGATATAACGCACTTTCAGTCAT 59.541 40.000 0.00 0.00 0.00 3.06
3698 3967 4.796830 GTCGATATAACGCACTTTCAGTCA 59.203 41.667 0.00 0.00 0.00 3.41
4171 4441 3.034635 AGCTCAAGGAGAATACGGTGAT 58.965 45.455 0.00 0.00 0.00 3.06
4288 4558 1.014044 TCGCGTTCAGAGCATCCAAC 61.014 55.000 5.77 0.00 33.66 3.77
4360 4630 7.342769 TCACTTAAGTCTTCTTGTCTGTGTA 57.657 36.000 4.77 0.00 35.36 2.90
4400 4670 2.301738 GCCCTAACCACCCAGAGCT 61.302 63.158 0.00 0.00 0.00 4.09
4468 4740 2.545106 GTGCATGGCTTTTGTCTTTTGG 59.455 45.455 0.00 0.00 0.00 3.28
4473 4745 1.985473 TCAGTGCATGGCTTTTGTCT 58.015 45.000 0.00 0.00 0.00 3.41
4484 4756 1.743958 GCTGCTCAGATTTCAGTGCAT 59.256 47.619 0.29 0.00 32.87 3.96


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

AutoCloner maintained by Alex Coulton.