Multiple sequence alignment - TraesCS5A01G439300

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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 TraesCS5A01G439300 chr5A 100.000 3644 0 0 1 3644 620996801 620993158 0.000000e+00 6730.0
1 TraesCS5A01G439300 chr5B 91.543 2625 154 15 557 3137 615697495 615694895 0.000000e+00 3555.0
2 TraesCS5A01G439300 chr5B 93.385 514 30 4 4 515 615698006 615697495 0.000000e+00 758.0
3 TraesCS5A01G439300 chr5B 85.535 159 15 3 3444 3602 615694505 615694355 3.770000e-35 159.0
4 TraesCS5A01G439300 chr5B 95.833 72 3 0 3237 3308 615694604 615694533 2.300000e-22 117.0
5 TraesCS5A01G439300 chr5D 94.340 2191 96 6 605 2783 496910645 496908471 0.000000e+00 3334.0
6 TraesCS5A01G439300 chr5D 94.200 500 27 2 1 499 496911249 496910751 0.000000e+00 761.0
7 TraesCS5A01G439300 chr5D 84.211 323 21 8 3322 3634 496906812 496906510 1.660000e-73 287.0
8 TraesCS5A01G439300 chr5D 79.562 274 18 10 2876 3149 496907184 496906949 1.050000e-35 161.0
9 TraesCS5A01G439300 chr5D 92.647 68 5 0 2781 2848 496907246 496907179 8.330000e-17 99.0
10 TraesCS5A01G439300 chr2B 86.113 1433 161 21 1325 2727 182008508 182009932 0.000000e+00 1509.0
11 TraesCS5A01G439300 chr2A 84.542 1365 155 25 1455 2781 135199792 135198446 0.000000e+00 1301.0
12 TraesCS5A01G439300 chr2A 87.143 70 8 1 3376 3445 307448059 307447991 1.080000e-10 78.7
13 TraesCS5A01G439300 chr2D 84.069 929 105 19 1860 2781 128402145 128401253 0.000000e+00 856.0
14 TraesCS5A01G439300 chr4B 88.889 90 7 3 3358 3445 483511720 483511808 1.380000e-19 108.0
15 TraesCS5A01G439300 chr1A 85.714 98 12 2 3358 3454 363670981 363670885 6.440000e-18 102.0
16 TraesCS5A01G439300 chr1A 86.667 75 8 2 3360 3433 8320081 8320154 8.390000e-12 82.4
17 TraesCS5A01G439300 chr6A 91.781 73 5 1 3377 3449 545812659 545812588 2.320000e-17 100.0
18 TraesCS5A01G439300 chr6B 92.754 69 4 1 3377 3445 85703653 85703720 8.330000e-17 99.0
19 TraesCS5A01G439300 chr7A 91.304 69 5 1 3377 3445 520786204 520786271 3.870000e-15 93.5
20 TraesCS5A01G439300 chr3D 88.235 68 7 1 3361 3427 532868859 532868792 3.020000e-11 80.5
21 TraesCS5A01G439300 chr4A 82.222 90 14 2 3357 3445 698801889 698801977 3.900000e-10 76.8


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 TraesCS5A01G439300 chr5A 620993158 620996801 3643 True 6730.00 6730 100.000 1 3644 1 chr5A.!!$R1 3643
1 TraesCS5A01G439300 chr5B 615694355 615698006 3651 True 1147.25 3555 91.574 4 3602 4 chr5B.!!$R1 3598
2 TraesCS5A01G439300 chr5D 496906510 496911249 4739 True 928.40 3334 88.992 1 3634 5 chr5D.!!$R1 3633
3 TraesCS5A01G439300 chr2B 182008508 182009932 1424 False 1509.00 1509 86.113 1325 2727 1 chr2B.!!$F1 1402
4 TraesCS5A01G439300 chr2A 135198446 135199792 1346 True 1301.00 1301 84.542 1455 2781 1 chr2A.!!$R1 1326
5 TraesCS5A01G439300 chr2D 128401253 128402145 892 True 856.00 856 84.069 1860 2781 1 chr2D.!!$R1 921

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
499 500 1.308998 CGCAAGGTGACAGTTCCTTT 58.691 50.0 7.89 0.0 41.44 3.11 F
1426 1478 0.105453 TGAGGAGGAGGATAGCACCC 60.105 60.0 0.00 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2094 2175 0.529378 GGGTTCCAATGAGCTGCTTG 59.471 55.0 2.53 0.0 0.0 4.01 R
3019 4363 0.251033 TGCCTGAAGAGTTGCATGCT 60.251 50.0 20.33 0.0 0.0 3.79 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
55 56 3.884037 AGGTTCCAACTTCCAACAGAT 57.116 42.857 0.00 0.00 0.00 2.90
113 114 4.083324 GCAAAAGGAACGATGATCTTGACA 60.083 41.667 0.00 0.00 0.00 3.58
229 230 3.091545 CCTAAATTGGCAAGGAGAAGCA 58.908 45.455 5.96 0.00 31.64 3.91
368 369 4.324991 GGGGAACGCCGGTGAAGT 62.325 66.667 24.59 6.12 34.11 3.01
499 500 1.308998 CGCAAGGTGACAGTTCCTTT 58.691 50.000 7.89 0.00 41.44 3.11
524 525 6.555463 TTTTCCCTCCCTATTACAGTACTG 57.445 41.667 21.44 21.44 0.00 2.74
525 526 5.476950 TTCCCTCCCTATTACAGTACTGA 57.523 43.478 29.30 8.39 0.00 3.41
526 527 5.476950 TCCCTCCCTATTACAGTACTGAA 57.523 43.478 29.30 17.92 0.00 3.02
527 528 5.845734 TCCCTCCCTATTACAGTACTGAAA 58.154 41.667 29.30 13.67 0.00 2.69
528 529 6.449956 TCCCTCCCTATTACAGTACTGAAAT 58.550 40.000 29.30 9.77 0.00 2.17
529 530 6.906901 TCCCTCCCTATTACAGTACTGAAATT 59.093 38.462 29.30 14.27 0.00 1.82
530 531 7.404980 TCCCTCCCTATTACAGTACTGAAATTT 59.595 37.037 29.30 9.00 0.00 1.82
531 532 8.711170 CCCTCCCTATTACAGTACTGAAATTTA 58.289 37.037 29.30 7.94 0.00 1.40
532 533 9.765795 CCTCCCTATTACAGTACTGAAATTTAG 57.234 37.037 29.30 18.53 0.00 1.85
533 534 9.765795 CTCCCTATTACAGTACTGAAATTTAGG 57.234 37.037 29.30 24.34 0.00 2.69
534 535 8.208903 TCCCTATTACAGTACTGAAATTTAGGC 58.791 37.037 29.30 0.00 0.00 3.93
535 536 7.990886 CCCTATTACAGTACTGAAATTTAGGCA 59.009 37.037 29.30 0.92 0.00 4.75
536 537 9.046296 CCTATTACAGTACTGAAATTTAGGCAG 57.954 37.037 29.30 10.69 35.81 4.85
537 538 9.817809 CTATTACAGTACTGAAATTTAGGCAGA 57.182 33.333 29.30 0.00 33.94 4.26
538 539 7.900782 TTACAGTACTGAAATTTAGGCAGAC 57.099 36.000 29.30 6.26 33.94 3.51
539 540 6.115448 ACAGTACTGAAATTTAGGCAGACT 57.885 37.500 29.30 7.91 33.94 3.24
563 564 2.654896 AGGGCTTTTCTTTCTGGGGTAT 59.345 45.455 0.00 0.00 0.00 2.73
647 675 3.989787 GGTGGCGGGCTTGTTTGG 61.990 66.667 2.38 0.00 0.00 3.28
879 909 3.074412 TCCTGTTTTCTTCCAGCGATTC 58.926 45.455 0.00 0.00 0.00 2.52
942 973 2.218530 GGTTCAAAACTGCGCATTTGTC 59.781 45.455 26.95 21.58 37.68 3.18
1174 1205 1.082690 GAAGAAGAAGAAGGCGCTGG 58.917 55.000 7.64 0.00 0.00 4.85
1251 1282 1.090052 GCAACATCTACACCCCGCTC 61.090 60.000 0.00 0.00 0.00 5.03
1297 1340 1.048160 TCGTGGCCAGGATGATGCTA 61.048 55.000 23.92 0.00 39.69 3.49
1298 1341 0.179048 CGTGGCCAGGATGATGCTAA 60.179 55.000 20.97 0.00 39.69 3.09
1299 1342 1.602311 GTGGCCAGGATGATGCTAAG 58.398 55.000 5.11 0.00 39.69 2.18
1375 1418 1.451028 GGCAGTGAGGATGAGGTGC 60.451 63.158 0.00 0.00 0.00 5.01
1426 1478 0.105453 TGAGGAGGAGGATAGCACCC 60.105 60.000 0.00 0.00 0.00 4.61
1545 1597 2.281761 CACGCCAAGCTGAACCCT 60.282 61.111 0.00 0.00 0.00 4.34
1698 1760 0.529337 CTGGCATGCTGGACTACTCG 60.529 60.000 18.92 0.00 0.00 4.18
1719 1781 0.803380 GGCTTGTTGATGCGAATGCC 60.803 55.000 0.00 0.00 41.78 4.40
1824 1886 6.251471 ACATCTGAGGTTTTTCCAGATTGAT 58.749 36.000 0.00 0.00 42.97 2.57
1885 1955 3.149196 GACTGTCCAATTCAGAAGGCAA 58.851 45.455 0.00 0.00 36.81 4.52
1998 2071 2.429930 CCCTTGACTGGGCGTGAA 59.570 61.111 0.00 0.00 40.84 3.18
2094 2175 5.373812 TCCTCCTGATATCTTCCAAAACC 57.626 43.478 3.98 0.00 0.00 3.27
2424 2505 2.450476 GGCCAGATGAAGTTCAACCAT 58.550 47.619 10.14 0.00 0.00 3.55
2460 2541 0.034059 CGATAAGCTCGGGCAAGGAT 59.966 55.000 11.40 0.00 43.82 3.24
2466 2547 0.398318 GCTCGGGCAAGGATAGGAAT 59.602 55.000 0.00 0.00 38.54 3.01
2481 2562 1.048601 GGAATGGGATGAGGCTCGTA 58.951 55.000 9.68 0.00 0.00 3.43
2490 2571 2.282674 AGGCTCGTACACGTCCCA 60.283 61.111 13.09 0.00 40.80 4.37
2508 2589 1.002659 CCATCCTTCACCGTGTACCAA 59.997 52.381 0.00 0.00 0.00 3.67
2535 2616 4.660938 GGGCCACGGTTCAGCCTT 62.661 66.667 4.39 0.00 46.31 4.35
2565 2646 2.530151 TGCCTGGACTTCAGCCCT 60.530 61.111 0.00 0.00 42.05 5.19
2568 2649 2.673523 CTGGACTTCAGCCCTGGG 59.326 66.667 8.86 8.86 36.60 4.45
2589 2670 3.459063 GGGTTCCTCTCCGTCGGG 61.459 72.222 12.29 2.17 0.00 5.14
2613 2694 0.663269 CCGGCGGAAAAGTTTTGCTC 60.663 55.000 24.41 9.46 0.00 4.26
2651 2732 1.612442 AGAACGCTTAGGGCTCCCA 60.612 57.895 7.82 0.00 39.13 4.37
2697 2785 2.057922 TCTGCTTCCAGAGAAAACCCT 58.942 47.619 0.00 0.00 42.98 4.34
2749 2840 1.239968 CCTCTTGCCTTGTGAGTGCC 61.240 60.000 0.00 0.00 0.00 5.01
2773 2864 5.735892 CGTTGTCACAGATATTTTGATGCTG 59.264 40.000 0.00 0.00 0.00 4.41
2807 4151 2.335011 GGTGCCCGTTGTTTGAGC 59.665 61.111 0.00 0.00 0.00 4.26
2808 4152 2.485795 GGTGCCCGTTGTTTGAGCA 61.486 57.895 0.00 0.00 0.00 4.26
2851 4195 2.508526 AGAAGTTGATTGGTGTGGCTC 58.491 47.619 0.00 0.00 0.00 4.70
2852 4196 2.107204 AGAAGTTGATTGGTGTGGCTCT 59.893 45.455 0.00 0.00 0.00 4.09
2860 4204 3.857157 TTGGTGTGGCTCTAGAAAAGT 57.143 42.857 0.00 0.00 0.00 2.66
2861 4205 3.857157 TGGTGTGGCTCTAGAAAAGTT 57.143 42.857 0.00 0.00 0.00 2.66
2867 4211 2.003301 GGCTCTAGAAAAGTTGGAGCG 58.997 52.381 0.00 0.00 46.96 5.03
2910 4254 6.925165 CAGCTCTAAATGTTTGTTTCACCATT 59.075 34.615 0.00 0.00 0.00 3.16
2913 4257 8.611757 GCTCTAAATGTTTGTTTCACCATTTTT 58.388 29.630 0.00 0.00 38.23 1.94
3007 4351 4.870426 CGACATCAGCCAAGTAATGTAAGT 59.130 41.667 0.00 0.00 32.70 2.24
3011 4355 7.338710 ACATCAGCCAAGTAATGTAAGTATGT 58.661 34.615 0.00 0.00 30.84 2.29
3015 4359 9.899661 TCAGCCAAGTAATGTAAGTATGTAAAT 57.100 29.630 0.00 0.00 0.00 1.40
3016 4360 9.935682 CAGCCAAGTAATGTAAGTATGTAAATG 57.064 33.333 0.00 0.00 0.00 2.32
3017 4361 9.681062 AGCCAAGTAATGTAAGTATGTAAATGT 57.319 29.630 0.00 0.00 0.00 2.71
3025 4369 9.950680 AATGTAAGTATGTAAATGTAAGCATGC 57.049 29.630 10.51 10.51 35.15 4.06
3026 4370 8.499403 TGTAAGTATGTAAATGTAAGCATGCA 57.501 30.769 21.98 0.00 35.15 3.96
3027 4371 8.951243 TGTAAGTATGTAAATGTAAGCATGCAA 58.049 29.630 21.98 4.29 35.15 4.08
3028 4372 9.221775 GTAAGTATGTAAATGTAAGCATGCAAC 57.778 33.333 21.98 17.61 35.15 4.17
3029 4373 7.630242 AGTATGTAAATGTAAGCATGCAACT 57.370 32.000 21.98 6.32 35.15 3.16
3030 4374 7.697691 AGTATGTAAATGTAAGCATGCAACTC 58.302 34.615 21.98 7.79 35.15 3.01
3031 4375 6.764308 ATGTAAATGTAAGCATGCAACTCT 57.236 33.333 21.98 6.73 35.15 3.24
3032 4376 6.573664 TGTAAATGTAAGCATGCAACTCTT 57.426 33.333 21.98 15.37 35.15 2.85
3033 4377 6.611381 TGTAAATGTAAGCATGCAACTCTTC 58.389 36.000 21.98 9.01 35.15 2.87
3034 4378 5.710513 AAATGTAAGCATGCAACTCTTCA 57.289 34.783 21.98 9.05 35.15 3.02
3035 4379 4.959596 ATGTAAGCATGCAACTCTTCAG 57.040 40.909 21.98 0.00 33.37 3.02
3036 4380 3.076621 TGTAAGCATGCAACTCTTCAGG 58.923 45.455 21.98 0.00 0.00 3.86
3037 4381 0.886563 AAGCATGCAACTCTTCAGGC 59.113 50.000 21.98 0.00 39.93 4.85
3038 4382 0.251033 AGCATGCAACTCTTCAGGCA 60.251 50.000 21.98 0.00 41.81 4.75
3059 4403 5.051891 CAAAGGATGCTTTCTGTTGTAGG 57.948 43.478 9.53 0.00 0.00 3.18
3060 4404 4.640771 AAGGATGCTTTCTGTTGTAGGA 57.359 40.909 0.00 0.00 0.00 2.94
3061 4405 4.851639 AGGATGCTTTCTGTTGTAGGAT 57.148 40.909 0.00 0.00 0.00 3.24
3062 4406 5.184892 AGGATGCTTTCTGTTGTAGGATT 57.815 39.130 0.00 0.00 0.00 3.01
3063 4407 5.574188 AGGATGCTTTCTGTTGTAGGATTT 58.426 37.500 0.00 0.00 0.00 2.17
3064 4408 5.649831 AGGATGCTTTCTGTTGTAGGATTTC 59.350 40.000 0.00 0.00 0.00 2.17
3065 4409 5.415701 GGATGCTTTCTGTTGTAGGATTTCA 59.584 40.000 0.00 0.00 0.00 2.69
3066 4410 6.071952 GGATGCTTTCTGTTGTAGGATTTCAA 60.072 38.462 0.00 0.00 0.00 2.69
3067 4411 6.707440 TGCTTTCTGTTGTAGGATTTCAAA 57.293 33.333 0.00 0.00 0.00 2.69
3068 4412 6.738114 TGCTTTCTGTTGTAGGATTTCAAAG 58.262 36.000 0.00 0.00 0.00 2.77
3088 4447 7.581476 TCAAAGCGTAGAATTTCTTTTCGATT 58.419 30.769 3.86 9.43 29.65 3.34
3156 4552 7.443259 ACTTGGCGTTGTTAGTTATTTATGT 57.557 32.000 0.00 0.00 0.00 2.29
3158 4554 8.662141 ACTTGGCGTTGTTAGTTATTTATGTAG 58.338 33.333 0.00 0.00 0.00 2.74
3163 4559 7.634817 GCGTTGTTAGTTATTTATGTAGCAGTG 59.365 37.037 0.00 0.00 0.00 3.66
3188 4584 0.462581 TTCTTAGCATGCAGGAGCCG 60.463 55.000 21.98 0.70 41.13 5.52
3211 4607 3.893753 TGGTTCCTTTGATCCTTTCCA 57.106 42.857 0.00 0.00 32.45 3.53
3218 4614 3.703052 CCTTTGATCCTTTCCAATCCAGG 59.297 47.826 0.00 0.00 0.00 4.45
3264 4823 2.296190 ACTATTCCTGCGCGTGATCATA 59.704 45.455 8.43 0.00 0.00 2.15
3272 4831 3.913089 TGCGCGTGATCATATCTTATGT 58.087 40.909 8.43 0.00 0.00 2.29
3308 4867 7.840931 AGCTTTTATGACCAATAAGGAAAAGG 58.159 34.615 0.00 0.00 37.68 3.11
3309 4868 7.673926 AGCTTTTATGACCAATAAGGAAAAGGA 59.326 33.333 0.00 0.00 37.68 3.36
3310 4869 7.976175 GCTTTTATGACCAATAAGGAAAAGGAG 59.024 37.037 0.00 0.00 37.68 3.69
3311 4870 7.404671 TTTATGACCAATAAGGAAAAGGAGC 57.595 36.000 0.00 0.00 41.22 4.70
3313 4872 4.934356 TGACCAATAAGGAAAAGGAGCAT 58.066 39.130 0.00 0.00 41.22 3.79
3314 4873 4.706476 TGACCAATAAGGAAAAGGAGCATG 59.294 41.667 0.00 0.00 41.22 4.06
3315 4874 4.026052 ACCAATAAGGAAAAGGAGCATGG 58.974 43.478 0.00 0.00 41.22 3.66
3316 4875 4.264352 ACCAATAAGGAAAAGGAGCATGGA 60.264 41.667 0.00 0.00 41.22 3.41
3317 4876 4.340381 CCAATAAGGAAAAGGAGCATGGAG 59.660 45.833 0.00 0.00 41.22 3.86
3318 4877 4.870021 ATAAGGAAAAGGAGCATGGAGT 57.130 40.909 0.00 0.00 0.00 3.85
3321 4880 1.272147 GGAAAAGGAGCATGGAGTGGT 60.272 52.381 0.00 0.00 42.28 4.16
3325 4884 4.823276 GAGCATGGAGTGGTCGAG 57.177 61.111 0.00 0.00 44.51 4.04
3326 4885 1.142748 GAGCATGGAGTGGTCGAGG 59.857 63.158 0.00 0.00 44.51 4.63
3327 4886 1.608717 GAGCATGGAGTGGTCGAGGT 61.609 60.000 0.00 0.00 44.51 3.85
3328 4887 0.324368 AGCATGGAGTGGTCGAGGTA 60.324 55.000 0.00 0.00 31.66 3.08
3329 4888 0.753262 GCATGGAGTGGTCGAGGTAT 59.247 55.000 0.00 0.00 0.00 2.73
3330 4889 1.269831 GCATGGAGTGGTCGAGGTATC 60.270 57.143 0.00 0.00 0.00 2.24
3346 4905 9.005777 GTCGAGGTATCTTATGTAGAGAAGATT 57.994 37.037 14.17 0.00 40.07 2.40
3368 4927 9.796120 AGATTTGATATTAGCTTATACTCGCTC 57.204 33.333 0.00 0.00 37.68 5.03
3370 4929 7.462571 TTGATATTAGCTTATACTCGCTCCA 57.537 36.000 0.00 0.00 37.68 3.86
3372 4931 7.708051 TGATATTAGCTTATACTCGCTCCATC 58.292 38.462 0.00 0.00 37.68 3.51
3375 4934 4.881019 AGCTTATACTCGCTCCATCAAT 57.119 40.909 0.00 0.00 0.00 2.57
3490 5050 4.417506 GGTTTACATTTACCCAATCGTGC 58.582 43.478 0.00 0.00 0.00 5.34
3493 5053 2.006888 ACATTTACCCAATCGTGCTCG 58.993 47.619 0.81 0.81 38.55 5.03
3510 5070 2.548920 GCTCGGTTTATAGGATGCTGCT 60.549 50.000 0.00 0.00 0.00 4.24
3529 5089 1.679139 TGGAACAGAGTTGCCTTGTG 58.321 50.000 0.00 0.00 0.00 3.33
3530 5090 0.312102 GGAACAGAGTTGCCTTGTGC 59.688 55.000 0.00 0.00 41.77 4.57
3531 5091 0.040958 GAACAGAGTTGCCTTGTGCG 60.041 55.000 0.00 0.00 45.60 5.34
3532 5092 1.447317 AACAGAGTTGCCTTGTGCGG 61.447 55.000 0.00 0.00 45.60 5.69
3592 5159 4.532126 TCACCACCTATGTTCTCTTCATGT 59.468 41.667 0.00 0.00 0.00 3.21
3605 5172 2.777692 TCTTCATGTAGGCCCCTAAAGG 59.222 50.000 0.00 0.00 0.00 3.11
3630 5197 2.238646 ACCTTTCGAATGTCCATAGCCA 59.761 45.455 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 7.488150 TGTTGTTTCGTTGTTATGTGCAAATTA 59.512 29.630 0.00 0.00 0.00 1.40
113 114 8.681584 TCATCAAATTCCCCAGATAATAATCCT 58.318 33.333 0.00 0.00 31.98 3.24
219 220 3.015327 GCTTCACATCATGCTTCTCCTT 58.985 45.455 0.00 0.00 0.00 3.36
229 230 5.763698 CCTATCATCTGTTGCTTCACATCAT 59.236 40.000 0.00 0.00 0.00 2.45
307 308 2.908796 CCCTAGCCCTTCCCGAAC 59.091 66.667 0.00 0.00 0.00 3.95
474 475 2.049156 TGTCACCTTGCGCTCTCG 60.049 61.111 9.73 0.00 39.07 4.04
505 506 6.749036 ATTTCAGTACTGTAATAGGGAGGG 57.251 41.667 21.98 0.00 30.45 4.30
506 507 9.765795 CTAAATTTCAGTACTGTAATAGGGAGG 57.234 37.037 23.13 10.32 31.70 4.30
507 508 9.765795 CCTAAATTTCAGTACTGTAATAGGGAG 57.234 37.037 23.68 18.26 31.70 4.30
510 511 8.958119 TGCCTAAATTTCAGTACTGTAATAGG 57.042 34.615 25.47 25.47 33.17 2.57
513 514 8.322091 AGTCTGCCTAAATTTCAGTACTGTAAT 58.678 33.333 21.99 20.28 33.00 1.89
514 515 7.676947 AGTCTGCCTAAATTTCAGTACTGTAA 58.323 34.615 21.99 18.92 0.00 2.41
515 516 7.241042 AGTCTGCCTAAATTTCAGTACTGTA 57.759 36.000 21.99 10.57 0.00 2.74
517 518 6.650807 TGAAGTCTGCCTAAATTTCAGTACTG 59.349 38.462 17.17 17.17 0.00 2.74
518 519 6.769512 TGAAGTCTGCCTAAATTTCAGTACT 58.230 36.000 0.00 0.00 0.00 2.73
519 520 6.092807 CCTGAAGTCTGCCTAAATTTCAGTAC 59.907 42.308 0.00 0.00 39.70 2.73
520 521 6.173339 CCTGAAGTCTGCCTAAATTTCAGTA 58.827 40.000 0.00 0.00 39.70 2.74
521 522 5.006386 CCTGAAGTCTGCCTAAATTTCAGT 58.994 41.667 0.00 0.00 39.70 3.41
522 523 4.397417 CCCTGAAGTCTGCCTAAATTTCAG 59.603 45.833 0.00 0.00 40.53 3.02
523 524 4.335416 CCCTGAAGTCTGCCTAAATTTCA 58.665 43.478 0.00 0.00 0.00 2.69
524 525 3.129462 GCCCTGAAGTCTGCCTAAATTTC 59.871 47.826 0.00 0.00 0.00 2.17
525 526 3.092301 GCCCTGAAGTCTGCCTAAATTT 58.908 45.455 0.00 0.00 0.00 1.82
526 527 2.310052 AGCCCTGAAGTCTGCCTAAATT 59.690 45.455 0.00 0.00 0.00 1.82
527 528 1.918957 AGCCCTGAAGTCTGCCTAAAT 59.081 47.619 0.00 0.00 0.00 1.40
528 529 1.362224 AGCCCTGAAGTCTGCCTAAA 58.638 50.000 0.00 0.00 0.00 1.85
529 530 1.362224 AAGCCCTGAAGTCTGCCTAA 58.638 50.000 0.00 0.00 0.00 2.69
530 531 1.362224 AAAGCCCTGAAGTCTGCCTA 58.638 50.000 0.00 0.00 0.00 3.93
531 532 0.480252 AAAAGCCCTGAAGTCTGCCT 59.520 50.000 0.00 0.00 0.00 4.75
532 533 0.884514 GAAAAGCCCTGAAGTCTGCC 59.115 55.000 0.00 0.00 0.00 4.85
533 534 1.902938 AGAAAAGCCCTGAAGTCTGC 58.097 50.000 0.00 0.00 0.00 4.26
534 535 4.023365 CAGAAAGAAAAGCCCTGAAGTCTG 60.023 45.833 0.00 0.00 0.00 3.51
535 536 4.140536 CAGAAAGAAAAGCCCTGAAGTCT 58.859 43.478 0.00 0.00 0.00 3.24
536 537 3.254411 CCAGAAAGAAAAGCCCTGAAGTC 59.746 47.826 0.00 0.00 0.00 3.01
537 538 3.225940 CCAGAAAGAAAAGCCCTGAAGT 58.774 45.455 0.00 0.00 0.00 3.01
538 539 2.560105 CCCAGAAAGAAAAGCCCTGAAG 59.440 50.000 0.00 0.00 0.00 3.02
539 540 2.597455 CCCAGAAAGAAAAGCCCTGAA 58.403 47.619 0.00 0.00 0.00 3.02
1041 1072 1.446966 GCTGTCGTCCTTCTCCAGC 60.447 63.158 0.00 0.00 41.37 4.85
1157 1188 0.248843 CTCCAGCGCCTTCTTCTTCT 59.751 55.000 2.29 0.00 0.00 2.85
1325 1368 0.606604 ATAAACAGGCAGGTCGTCGT 59.393 50.000 0.00 0.00 0.00 4.34
1375 1418 1.143889 GGGCTTCCTCCCCTTATCAAG 59.856 57.143 0.00 0.00 40.51 3.02
1426 1478 0.987294 ACCTTGAGGATGTCCACCTG 59.013 55.000 3.59 0.00 37.93 4.00
1545 1597 1.558167 TATCCGCCCAGCCAGTGAAA 61.558 55.000 0.00 0.00 0.00 2.69
1698 1760 1.796617 GCATTCGCATCAACAAGCCTC 60.797 52.381 0.00 0.00 38.36 4.70
1719 1781 0.543749 GACCACTGGAAGGATCCTGG 59.456 60.000 17.02 14.46 46.13 4.45
1824 1886 0.850100 TCTTGGGGTTTCTCTTGCCA 59.150 50.000 0.00 0.00 0.00 4.92
1885 1955 2.503356 CAGAGCCATCAGGTAGAAAGGT 59.497 50.000 0.00 0.00 37.19 3.50
1998 2071 1.655372 AGCTCTCCAGGCTTTTCTCT 58.345 50.000 0.00 0.00 36.56 3.10
2073 2154 5.116084 TGGTTTTGGAAGATATCAGGAGG 57.884 43.478 5.32 0.00 0.00 4.30
2094 2175 0.529378 GGGTTCCAATGAGCTGCTTG 59.471 55.000 2.53 0.00 0.00 4.01
2236 2317 2.750637 GGAGCCCTCGTCGACAGA 60.751 66.667 17.16 12.55 0.00 3.41
2355 2436 3.403558 AGCGGCTTCCTCTTCCCC 61.404 66.667 0.00 0.00 0.00 4.81
2454 2535 3.560882 GCCTCATCCCATTCCTATCCTTG 60.561 52.174 0.00 0.00 0.00 3.61
2460 2541 1.342074 CGAGCCTCATCCCATTCCTA 58.658 55.000 0.00 0.00 0.00 2.94
2466 2547 1.663379 CGTGTACGAGCCTCATCCCA 61.663 60.000 0.00 0.00 43.02 4.37
2481 2562 1.677552 GGTGAAGGATGGGACGTGT 59.322 57.895 0.00 0.00 0.00 4.49
2490 2571 3.143728 GTTTTGGTACACGGTGAAGGAT 58.856 45.455 16.29 0.00 39.29 3.24
2523 2604 0.320697 GGTACTGAAGGCTGAACCGT 59.679 55.000 0.00 0.00 46.52 4.83
2535 2616 1.982395 CAGGCACCTCGGGTACTGA 60.982 63.158 15.61 0.00 44.24 3.41
2565 2646 2.683933 GAGAGGAACCCGCTCCCA 60.684 66.667 5.58 0.00 43.14 4.37
2613 2694 3.118992 TCTGATAGTGGTGCAGCTTGTAG 60.119 47.826 18.08 8.06 0.00 2.74
2697 2785 8.771920 AAGAATCACGTTACAGATAACATCAA 57.228 30.769 0.00 0.00 40.77 2.57
2749 2840 5.735892 CAGCATCAAAATATCTGTGACAACG 59.264 40.000 0.00 0.00 0.00 4.10
2839 4183 4.373156 ACTTTTCTAGAGCCACACCAAT 57.627 40.909 0.00 0.00 0.00 3.16
2840 4184 3.857157 ACTTTTCTAGAGCCACACCAA 57.143 42.857 0.00 0.00 0.00 3.67
2851 4195 6.128526 CCTTCTAAACGCTCCAACTTTTCTAG 60.129 42.308 0.00 0.00 0.00 2.43
2852 4196 5.699458 CCTTCTAAACGCTCCAACTTTTCTA 59.301 40.000 0.00 0.00 0.00 2.10
2860 4204 3.811083 TCAAACCTTCTAAACGCTCCAA 58.189 40.909 0.00 0.00 0.00 3.53
2861 4205 3.478857 TCAAACCTTCTAAACGCTCCA 57.521 42.857 0.00 0.00 0.00 3.86
2867 4211 5.048434 AGAGCTGCAATCAAACCTTCTAAAC 60.048 40.000 1.02 0.00 0.00 2.01
2910 4254 4.513692 CAGAATCACGGTCACCTGTTAAAA 59.486 41.667 0.00 0.00 0.00 1.52
2913 4257 2.631062 ACAGAATCACGGTCACCTGTTA 59.369 45.455 0.00 0.00 31.62 2.41
2916 4260 1.270305 ACACAGAATCACGGTCACCTG 60.270 52.381 0.00 0.00 0.00 4.00
2984 4328 4.870426 ACTTACATTACTTGGCTGATGTCG 59.130 41.667 0.00 0.00 34.76 4.35
3007 4351 7.864108 AGAGTTGCATGCTTACATTTACATA 57.136 32.000 20.33 0.00 32.87 2.29
3011 4355 6.127925 CCTGAAGAGTTGCATGCTTACATTTA 60.128 38.462 20.33 11.04 32.87 1.40
3015 4359 3.076621 CCTGAAGAGTTGCATGCTTACA 58.923 45.455 20.33 8.37 0.00 2.41
3016 4360 2.159462 GCCTGAAGAGTTGCATGCTTAC 60.159 50.000 20.33 16.37 0.00 2.34
3017 4361 2.086869 GCCTGAAGAGTTGCATGCTTA 58.913 47.619 20.33 3.93 0.00 3.09
3018 4362 0.886563 GCCTGAAGAGTTGCATGCTT 59.113 50.000 20.33 3.73 0.00 3.91
3019 4363 0.251033 TGCCTGAAGAGTTGCATGCT 60.251 50.000 20.33 0.00 0.00 3.79
3021 4365 2.352421 CCTTTGCCTGAAGAGTTGCATG 60.352 50.000 0.00 0.00 33.08 4.06
3022 4366 1.891150 CCTTTGCCTGAAGAGTTGCAT 59.109 47.619 0.00 0.00 33.08 3.96
3023 4367 1.133823 TCCTTTGCCTGAAGAGTTGCA 60.134 47.619 0.00 0.00 0.00 4.08
3024 4368 1.609208 TCCTTTGCCTGAAGAGTTGC 58.391 50.000 0.00 0.00 0.00 4.17
3025 4369 2.094854 GCATCCTTTGCCTGAAGAGTTG 60.095 50.000 0.00 0.00 46.15 3.16
3026 4370 2.165998 GCATCCTTTGCCTGAAGAGTT 58.834 47.619 0.00 0.00 46.15 3.01
3027 4371 1.831580 GCATCCTTTGCCTGAAGAGT 58.168 50.000 0.00 0.00 46.15 3.24
3037 4381 4.761739 TCCTACAACAGAAAGCATCCTTTG 59.238 41.667 0.00 0.00 41.22 2.77
3038 4382 4.985538 TCCTACAACAGAAAGCATCCTTT 58.014 39.130 0.00 0.00 43.73 3.11
3054 4398 7.606456 AGAAATTCTACGCTTTGAAATCCTACA 59.394 33.333 0.00 0.00 0.00 2.74
3055 4399 7.975750 AGAAATTCTACGCTTTGAAATCCTAC 58.024 34.615 0.00 0.00 0.00 3.18
3056 4400 8.561738 AAGAAATTCTACGCTTTGAAATCCTA 57.438 30.769 0.00 0.00 0.00 2.94
3057 4401 7.454260 AAGAAATTCTACGCTTTGAAATCCT 57.546 32.000 0.00 0.00 0.00 3.24
3058 4402 8.520835 AAAAGAAATTCTACGCTTTGAAATCC 57.479 30.769 0.00 0.00 31.53 3.01
3059 4403 8.358687 CGAAAAGAAATTCTACGCTTTGAAATC 58.641 33.333 0.00 0.00 31.53 2.17
3060 4404 8.073768 TCGAAAAGAAATTCTACGCTTTGAAAT 58.926 29.630 0.00 0.00 31.53 2.17
3061 4405 7.411274 TCGAAAAGAAATTCTACGCTTTGAAA 58.589 30.769 0.00 0.00 31.53 2.69
3062 4406 6.950545 TCGAAAAGAAATTCTACGCTTTGAA 58.049 32.000 0.00 0.00 31.53 2.69
3063 4407 6.533819 TCGAAAAGAAATTCTACGCTTTGA 57.466 33.333 0.00 0.00 31.53 2.69
3064 4408 7.781763 AATCGAAAAGAAATTCTACGCTTTG 57.218 32.000 0.00 0.00 31.53 2.77
3065 4409 8.797266 AAAATCGAAAAGAAATTCTACGCTTT 57.203 26.923 0.00 4.90 32.38 3.51
3088 4447 8.161425 AGTTAGCTCCCAAACTCTTTGTATAAA 58.839 33.333 0.00 0.00 38.98 1.40
3098 4457 2.185004 TGCAGTTAGCTCCCAAACTC 57.815 50.000 0.00 0.00 45.94 3.01
3156 4552 5.294306 GCATGCTAAGAACATAACACTGCTA 59.706 40.000 11.37 0.00 0.00 3.49
3158 4554 4.142622 TGCATGCTAAGAACATAACACTGC 60.143 41.667 20.33 0.00 0.00 4.40
3163 4559 4.260948 GCTCCTGCATGCTAAGAACATAAC 60.261 45.833 20.33 0.00 39.41 1.89
3172 4568 1.699054 ATCCGGCTCCTGCATGCTAA 61.699 55.000 20.33 3.11 41.91 3.09
3188 4584 3.701542 GGAAAGGATCAAAGGAACCATCC 59.298 47.826 0.00 0.00 46.98 3.51
3198 4594 4.673328 TCCTGGATTGGAAAGGATCAAA 57.327 40.909 0.00 0.00 35.14 2.69
3211 4607 8.721479 ACATATTATGCATAGCTATCCTGGATT 58.279 33.333 15.55 0.00 0.00 3.01
3249 4808 1.788258 AAGATATGATCACGCGCAGG 58.212 50.000 5.73 0.00 0.00 4.85
3272 4831 8.410673 TTGGTCATAAAAGCTATGGTTTGTTA 57.589 30.769 0.00 0.00 33.41 2.41
3308 4867 1.142748 CCTCGACCACTCCATGCTC 59.857 63.158 0.00 0.00 0.00 4.26
3309 4868 0.324368 TACCTCGACCACTCCATGCT 60.324 55.000 0.00 0.00 0.00 3.79
3310 4869 0.753262 ATACCTCGACCACTCCATGC 59.247 55.000 0.00 0.00 0.00 4.06
3311 4870 2.311463 AGATACCTCGACCACTCCATG 58.689 52.381 0.00 0.00 0.00 3.66
3313 4872 2.526888 AAGATACCTCGACCACTCCA 57.473 50.000 0.00 0.00 0.00 3.86
3314 4873 3.890147 ACATAAGATACCTCGACCACTCC 59.110 47.826 0.00 0.00 0.00 3.85
3315 4874 5.996513 TCTACATAAGATACCTCGACCACTC 59.003 44.000 0.00 0.00 0.00 3.51
3316 4875 5.938279 TCTACATAAGATACCTCGACCACT 58.062 41.667 0.00 0.00 0.00 4.00
3317 4876 5.996513 TCTCTACATAAGATACCTCGACCAC 59.003 44.000 0.00 0.00 32.41 4.16
3318 4877 6.183810 TCTCTACATAAGATACCTCGACCA 57.816 41.667 0.00 0.00 32.41 4.02
3321 4880 9.575868 AAATCTTCTCTACATAAGATACCTCGA 57.424 33.333 0.00 0.00 40.66 4.04
3322 4881 9.619316 CAAATCTTCTCTACATAAGATACCTCG 57.381 37.037 0.00 0.00 40.66 4.63
3346 4905 7.462571 TGGAGCGAGTATAAGCTAATATCAA 57.537 36.000 0.00 0.00 44.69 2.57
3365 4924 7.602517 AACGCTCTTATATTATTGATGGAGC 57.397 36.000 0.00 0.00 40.72 4.70
3403 4962 8.090831 AGAAATATAAGCGCATTCAGATCACTA 58.909 33.333 11.47 0.00 0.00 2.74
3404 4963 6.933521 AGAAATATAAGCGCATTCAGATCACT 59.066 34.615 11.47 0.00 0.00 3.41
3405 4964 7.126726 AGAAATATAAGCGCATTCAGATCAC 57.873 36.000 11.47 0.00 0.00 3.06
3406 4965 7.734924 AAGAAATATAAGCGCATTCAGATCA 57.265 32.000 11.47 0.00 0.00 2.92
3409 4968 9.271828 TGATAAAGAAATATAAGCGCATTCAGA 57.728 29.630 11.47 0.00 0.00 3.27
3410 4969 9.539139 CTGATAAAGAAATATAAGCGCATTCAG 57.461 33.333 11.47 0.00 0.00 3.02
3411 4970 9.271828 TCTGATAAAGAAATATAAGCGCATTCA 57.728 29.630 11.47 0.00 29.54 2.57
3412 4971 9.752274 CTCTGATAAAGAAATATAAGCGCATTC 57.248 33.333 11.47 4.12 33.37 2.67
3413 4972 8.725148 CCTCTGATAAAGAAATATAAGCGCATT 58.275 33.333 11.47 3.50 33.37 3.56
3414 4973 7.335422 CCCTCTGATAAAGAAATATAAGCGCAT 59.665 37.037 11.47 0.00 33.37 4.73
3415 4974 6.650807 CCCTCTGATAAAGAAATATAAGCGCA 59.349 38.462 11.47 0.00 33.37 6.09
3433 4992 2.312140 AGCTACCAACTACTCCCTCTGA 59.688 50.000 0.00 0.00 0.00 3.27
3490 5050 3.062763 CAGCAGCATCCTATAAACCGAG 58.937 50.000 0.00 0.00 0.00 4.63
3493 5053 3.492102 TCCAGCAGCATCCTATAAACC 57.508 47.619 0.00 0.00 0.00 3.27
3520 5080 2.804167 CACAACCGCACAAGGCAA 59.196 55.556 0.00 0.00 45.17 4.52
3525 5085 3.898509 GCAGGCACAACCGCACAA 61.899 61.111 0.00 0.00 46.52 3.33
3554 5114 3.321497 GTGGTGAAGTTACAGAGCAGAG 58.679 50.000 0.00 0.00 0.00 3.35
3555 5115 2.037251 GGTGGTGAAGTTACAGAGCAGA 59.963 50.000 0.00 0.00 0.00 4.26
3605 5172 1.234821 TGGACATTCGAAAGGTGCAC 58.765 50.000 18.84 8.80 0.00 4.57


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

AutoCloner maintained by Alex Coulton.