Multiple sequence alignment - TraesCS5B01G411900

Loading Multiple Alignment...

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 TraesCS5B01G411900 chr5B 100.000 3314 0 0 1 3314 586867226 586863913 0.000000e+00 6120
1 TraesCS5B01G411900 chr5B 91.958 659 35 6 1792 2443 625120718 625120071 0.000000e+00 907
2 TraesCS5B01G411900 chr5B 91.958 659 35 6 1792 2443 628700267 628699620 0.000000e+00 907
3 TraesCS5B01G411900 chr5B 91.571 261 22 0 1 261 541950046 541949786 8.740000e-96 361
4 TraesCS5B01G411900 chr5B 86.503 163 10 3 2950 3100 625119958 625119796 5.690000e-38 169
5 TraesCS5B01G411900 chr5B 86.503 163 10 3 2950 3100 628699507 628699345 5.690000e-38 169
6 TraesCS5B01G411900 chr5D 88.197 2762 170 76 590 3290 479127400 479124734 0.000000e+00 3151
7 TraesCS5B01G411900 chr5A 91.755 1880 65 38 868 2704 597841813 597839981 0.000000e+00 2531
8 TraesCS5B01G411900 chr5A 91.489 423 28 7 180 597 33021025 33020606 2.870000e-160 575
9 TraesCS5B01G411900 chr5A 79.007 443 24 28 2881 3290 597839783 597839377 4.270000e-59 239
10 TraesCS5B01G411900 chr5A 84.181 177 8 9 590 766 597842361 597842205 1.590000e-33 154
11 TraesCS5B01G411900 chr2D 91.183 862 36 20 1792 2629 81516751 81515906 0.000000e+00 1134
12 TraesCS5B01G411900 chr2D 92.476 412 28 3 180 589 166313913 166314323 1.330000e-163 586
13 TraesCS5B01G411900 chr2D 78.321 655 111 19 1001 1641 309576862 309577499 8.620000e-106 394
14 TraesCS5B01G411900 chr2D 77.910 670 111 26 1673 2314 309577673 309578333 1.870000e-102 383
15 TraesCS5B01G411900 chr2D 79.402 301 24 15 2826 3100 81515739 81515451 9.450000e-41 178
16 TraesCS5B01G411900 chr6D 87.288 944 84 12 917 1857 5800685 5799775 0.000000e+00 1046
17 TraesCS5B01G411900 chr4A 97.627 590 13 1 1 589 680564487 680565076 0.000000e+00 1011
18 TraesCS5B01G411900 chr2A 96.785 591 17 1 1 589 164707593 164707003 0.000000e+00 985
19 TraesCS5B01G411900 chr2A 91.748 412 31 3 180 589 758110358 758109948 1.330000e-158 569
20 TraesCS5B01G411900 chr2A 77.812 658 115 20 1001 1644 429718844 429718204 8.680000e-101 377
21 TraesCS5B01G411900 chr6B 88.092 865 44 20 1792 2629 507371888 507372720 0.000000e+00 972
22 TraesCS5B01G411900 chr6B 93.119 654 32 5 1792 2443 615609089 615608447 0.000000e+00 946
23 TraesCS5B01G411900 chr6B 80.000 285 22 12 2826 3086 507372887 507373160 9.450000e-41 178
24 TraesCS5B01G411900 chr6B 87.162 148 8 2 2950 3086 615607987 615607840 1.230000e-34 158
25 TraesCS5B01G411900 chr6B 96.721 61 2 0 2440 2500 615608427 615608367 5.850000e-18 102
26 TraesCS5B01G411900 chr7A 92.261 659 33 6 1792 2443 487477319 487477966 0.000000e+00 918
27 TraesCS5B01G411900 chr7A 91.257 183 16 0 1 183 23108367 23108185 1.970000e-62 250
28 TraesCS5B01G411900 chr7A 88.435 147 7 1 2950 3086 487478079 487478225 5.690000e-38 169
29 TraesCS5B01G411900 chr4B 93.603 594 33 5 1 589 605846461 605847054 0.000000e+00 881
30 TraesCS5B01G411900 chr4B 91.400 593 47 3 1 589 90266638 90266046 0.000000e+00 809
31 TraesCS5B01G411900 chr4B 96.552 348 8 3 1 347 605788499 605788155 1.030000e-159 573
32 TraesCS5B01G411900 chr3A 91.768 413 31 3 180 590 146192144 146192555 3.710000e-159 571
33 TraesCS5B01G411900 chr7D 91.546 414 31 3 180 590 602173183 602173595 4.800000e-158 568
34 TraesCS5B01G411900 chr7D 93.443 183 12 0 1 183 22650620 22650438 4.210000e-69 272
35 TraesCS5B01G411900 chr7B 92.279 272 21 0 1 272 169124515 169124244 1.440000e-103 387
36 TraesCS5B01G411900 chr2B 77.964 658 114 20 1001 1644 362694158 362693518 1.870000e-102 383
37 TraesCS5B01G411900 chr3D 77.901 181 40 0 2103 2283 384491535 384491355 2.700000e-21 113


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G411900 chr5B 586863913 586867226 3313 True 6120.000000 6120 100.0000 1 3314 1 chr5B.!!$R2 3313
1 TraesCS5B01G411900 chr5B 625119796 625120718 922 True 538.000000 907 89.2305 1792 3100 2 chr5B.!!$R3 1308
2 TraesCS5B01G411900 chr5B 628699345 628700267 922 True 538.000000 907 89.2305 1792 3100 2 chr5B.!!$R4 1308
3 TraesCS5B01G411900 chr5D 479124734 479127400 2666 True 3151.000000 3151 88.1970 590 3290 1 chr5D.!!$R1 2700
4 TraesCS5B01G411900 chr5A 597839377 597842361 2984 True 974.666667 2531 84.9810 590 3290 3 chr5A.!!$R2 2700
5 TraesCS5B01G411900 chr2D 81515451 81516751 1300 True 656.000000 1134 85.2925 1792 3100 2 chr2D.!!$R1 1308
6 TraesCS5B01G411900 chr2D 309576862 309578333 1471 False 388.500000 394 78.1155 1001 2314 2 chr2D.!!$F2 1313
7 TraesCS5B01G411900 chr6D 5799775 5800685 910 True 1046.000000 1046 87.2880 917 1857 1 chr6D.!!$R1 940
8 TraesCS5B01G411900 chr4A 680564487 680565076 589 False 1011.000000 1011 97.6270 1 589 1 chr4A.!!$F1 588
9 TraesCS5B01G411900 chr2A 164707003 164707593 590 True 985.000000 985 96.7850 1 589 1 chr2A.!!$R1 588
10 TraesCS5B01G411900 chr2A 429718204 429718844 640 True 377.000000 377 77.8120 1001 1644 1 chr2A.!!$R2 643
11 TraesCS5B01G411900 chr6B 507371888 507373160 1272 False 575.000000 972 84.0460 1792 3086 2 chr6B.!!$F1 1294
12 TraesCS5B01G411900 chr6B 615607840 615609089 1249 True 402.000000 946 92.3340 1792 3086 3 chr6B.!!$R1 1294
13 TraesCS5B01G411900 chr7A 487477319 487478225 906 False 543.500000 918 90.3480 1792 3086 2 chr7A.!!$F1 1294
14 TraesCS5B01G411900 chr4B 605846461 605847054 593 False 881.000000 881 93.6030 1 589 1 chr4B.!!$F1 588
15 TraesCS5B01G411900 chr4B 90266046 90266638 592 True 809.000000 809 91.4000 1 589 1 chr4B.!!$R1 588
16 TraesCS5B01G411900 chr2B 362693518 362694158 640 True 383.000000 383 77.9640 1001 1644 1 chr2B.!!$R1 643

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
890 1199 1.002274 ACCCGCCAATCTCTCTCCT 59.998 57.895 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2724 3335 0.235665 GGTCGCATGGCAATGATACG 59.764 55.0 4.87 0.0 35.67 3.06 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
205 207 1.480545 GGAAGAGAAGGAGAGAGGCAC 59.519 57.143 0.00 0.00 0.00 5.01
537 546 9.743057 CTGACATGTAAAAATTACCAAACTTGA 57.257 29.630 0.00 0.00 0.00 3.02
558 567 6.252599 TGATACCAATCTACTTCCAATGCT 57.747 37.500 0.00 0.00 32.93 3.79
567 576 9.288576 CAATCTACTTCCAATGCTCCAATTATA 57.711 33.333 0.00 0.00 0.00 0.98
619 628 3.777522 AGGGAATGAAACCAAACCAAACA 59.222 39.130 0.00 0.00 0.00 2.83
677 691 1.301009 GGATCCATCCGTCGAAGGC 60.301 63.158 13.06 0.00 37.19 4.35
732 746 4.562425 CACACACACCACCCCGCT 62.562 66.667 0.00 0.00 0.00 5.52
766 780 1.745890 CGAACCCTCACTGACACCA 59.254 57.895 0.00 0.00 0.00 4.17
769 783 1.046472 AACCCTCACTGACACCACGA 61.046 55.000 0.00 0.00 0.00 4.35
781 804 4.767255 CCACGACCCCAGCAGAGC 62.767 72.222 0.00 0.00 0.00 4.09
782 805 4.767255 CACGACCCCAGCAGAGCC 62.767 72.222 0.00 0.00 0.00 4.70
799 833 2.343758 CGGGTCTGACTGGTGTGG 59.656 66.667 7.85 0.00 0.00 4.17
800 834 2.507854 CGGGTCTGACTGGTGTGGT 61.508 63.158 7.85 0.00 0.00 4.16
801 835 1.071471 GGGTCTGACTGGTGTGGTG 59.929 63.158 7.85 0.00 0.00 4.17
802 836 1.696097 GGGTCTGACTGGTGTGGTGT 61.696 60.000 7.85 0.00 0.00 4.16
890 1199 1.002274 ACCCGCCAATCTCTCTCCT 59.998 57.895 0.00 0.00 0.00 3.69
911 1220 1.122019 CCCTCCCACCTTATCTCCCG 61.122 65.000 0.00 0.00 0.00 5.14
995 1313 4.530857 CCCCACCTGACCGATCGC 62.531 72.222 10.32 0.00 0.00 4.58
1116 1434 1.074167 CTCCACCTCCCCCTGCTAT 60.074 63.158 0.00 0.00 0.00 2.97
1824 2309 2.976903 GCATGGCTCATCCTCCGC 60.977 66.667 0.00 0.00 35.26 5.54
2367 2887 1.271379 TCCGACGAGCAAACTGTACAT 59.729 47.619 0.00 0.00 0.00 2.29
2382 2904 5.378332 ACTGTACATAGTAGCCGAGAATCT 58.622 41.667 0.00 0.00 0.00 2.40
2383 2905 6.531923 ACTGTACATAGTAGCCGAGAATCTA 58.468 40.000 0.00 0.00 0.00 1.98
2384 2906 6.427547 ACTGTACATAGTAGCCGAGAATCTAC 59.572 42.308 0.00 0.00 36.35 2.59
2385 2907 6.531923 TGTACATAGTAGCCGAGAATCTACT 58.468 40.000 7.05 7.05 45.21 2.57
2396 2918 5.744819 GCCGAGAATCTACTTAGAAGACAAC 59.255 44.000 0.00 0.00 35.69 3.32
2515 3084 7.412853 TTTTTAGTTGGCTACTCCACTTTTT 57.587 32.000 4.51 0.00 46.55 1.94
2576 3161 3.777106 AACTGAGAGCCTTTGTGATCA 57.223 42.857 0.00 0.00 0.00 2.92
2577 3162 3.996921 ACTGAGAGCCTTTGTGATCAT 57.003 42.857 0.00 0.00 0.00 2.45
2582 3167 4.713814 TGAGAGCCTTTGTGATCATCTACT 59.286 41.667 0.00 0.00 0.00 2.57
2583 3168 5.893824 TGAGAGCCTTTGTGATCATCTACTA 59.106 40.000 0.00 0.00 0.00 1.82
2584 3169 6.155475 AGAGCCTTTGTGATCATCTACTAC 57.845 41.667 0.00 0.00 0.00 2.73
2585 3170 5.896678 AGAGCCTTTGTGATCATCTACTACT 59.103 40.000 0.00 0.00 0.00 2.57
2586 3171 7.063593 AGAGCCTTTGTGATCATCTACTACTA 58.936 38.462 0.00 0.00 0.00 1.82
2589 3174 7.999545 AGCCTTTGTGATCATCTACTACTACTA 59.000 37.037 0.00 0.00 0.00 1.82
2657 3243 4.214437 GCAAGACGTGAAAAGATGAACTG 58.786 43.478 0.00 0.00 0.00 3.16
2658 3244 4.776743 CAAGACGTGAAAAGATGAACTGG 58.223 43.478 0.00 0.00 0.00 4.00
2659 3245 2.808543 AGACGTGAAAAGATGAACTGGC 59.191 45.455 0.00 0.00 0.00 4.85
2678 3264 2.603560 GGCAGTAGTACTCATTTGCGAC 59.396 50.000 0.00 0.00 32.59 5.19
2704 3294 0.037447 TGGCATGAACCCGTGATTCA 59.963 50.000 0.00 0.00 40.25 2.57
2706 3296 1.543802 GGCATGAACCCGTGATTCAAA 59.456 47.619 0.00 0.00 39.43 2.69
2707 3297 2.415893 GGCATGAACCCGTGATTCAAAG 60.416 50.000 0.00 0.00 39.43 2.77
2708 3298 2.867429 CATGAACCCGTGATTCAAAGC 58.133 47.619 0.00 0.00 39.43 3.51
2710 3300 2.513753 TGAACCCGTGATTCAAAGCAT 58.486 42.857 0.00 0.00 33.16 3.79
2767 3381 3.611530 GCTTTTGCAAATACTCGGAGCAA 60.612 43.478 19.72 0.22 46.58 3.91
2769 3383 3.829886 TTGCAAATACTCGGAGCAAAG 57.170 42.857 4.58 0.00 41.65 2.77
2771 3385 3.002791 TGCAAATACTCGGAGCAAAGAG 58.997 45.455 4.58 0.00 40.16 2.85
2772 3386 2.223135 GCAAATACTCGGAGCAAAGAGC 60.223 50.000 4.58 0.00 46.19 4.09
2783 3397 0.440371 GCAAAGAGCGCTGTCTACAC 59.560 55.000 18.48 0.00 0.00 2.90
2796 3410 4.515191 GCTGTCTACACCTGTGATTTTCAA 59.485 41.667 3.94 0.00 0.00 2.69
2798 3412 6.459573 GCTGTCTACACCTGTGATTTTCAAAA 60.460 38.462 3.94 0.00 0.00 2.44
2799 3413 7.581213 TGTCTACACCTGTGATTTTCAAAAT 57.419 32.000 3.94 0.00 0.00 1.82
2800 3414 7.648142 TGTCTACACCTGTGATTTTCAAAATC 58.352 34.615 14.98 14.98 0.00 2.17
2801 3415 7.084486 GTCTACACCTGTGATTTTCAAAATCC 58.916 38.462 18.35 11.11 0.00 3.01
2802 3416 5.867903 ACACCTGTGATTTTCAAAATCCA 57.132 34.783 18.35 14.40 0.00 3.41
2805 3419 6.762661 ACACCTGTGATTTTCAAAATCCAAAG 59.237 34.615 18.35 12.81 0.00 2.77
2806 3420 5.759763 ACCTGTGATTTTCAAAATCCAAAGC 59.240 36.000 18.35 6.12 0.00 3.51
2807 3421 5.759273 CCTGTGATTTTCAAAATCCAAAGCA 59.241 36.000 18.35 9.55 0.00 3.91
2808 3422 6.260493 CCTGTGATTTTCAAAATCCAAAGCAA 59.740 34.615 18.35 0.00 28.26 3.91
2809 3423 7.040961 CCTGTGATTTTCAAAATCCAAAGCAAT 60.041 33.333 18.35 0.00 28.26 3.56
2810 3424 8.223177 TGTGATTTTCAAAATCCAAAGCAATT 57.777 26.923 18.35 0.00 28.26 2.32
2811 3425 8.684520 TGTGATTTTCAAAATCCAAAGCAATTT 58.315 25.926 18.35 0.00 28.26 1.82
2812 3426 9.518906 GTGATTTTCAAAATCCAAAGCAATTTT 57.481 25.926 18.35 0.00 35.91 1.82
2813 3427 9.517609 TGATTTTCAAAATCCAAAGCAATTTTG 57.482 25.926 18.35 12.18 46.72 2.44
2848 3462 1.574526 CCTGGCCCTTGGATCCTTGA 61.575 60.000 14.23 0.00 0.00 3.02
2866 3480 4.503991 CCTTGAAGGAGCAACTAGTCAAGT 60.504 45.833 4.95 0.00 40.08 3.16
2867 3481 5.974725 CCTTGAAGGAGCAACTAGTCAAGTT 60.975 44.000 4.95 0.00 43.23 2.66
2868 3482 5.036117 TGAAGGAGCAACTAGTCAAGTTT 57.964 39.130 0.00 0.00 46.61 2.66
2869 3483 4.816385 TGAAGGAGCAACTAGTCAAGTTTG 59.184 41.667 0.00 0.00 46.61 2.93
2872 3486 2.878406 GAGCAACTAGTCAAGTTTGCCA 59.122 45.455 10.59 0.00 46.61 4.92
2873 3487 3.287222 AGCAACTAGTCAAGTTTGCCAA 58.713 40.909 10.59 0.00 46.61 4.52
2874 3488 3.891366 AGCAACTAGTCAAGTTTGCCAAT 59.109 39.130 10.59 0.00 46.61 3.16
2875 3489 4.342092 AGCAACTAGTCAAGTTTGCCAATT 59.658 37.500 10.59 0.00 46.61 2.32
2909 3541 1.978580 GGAGAAGGACTTGTGAAGGGA 59.021 52.381 0.00 0.00 0.00 4.20
2919 3551 0.843309 TGTGAAGGGAAGCAACAGGA 59.157 50.000 0.00 0.00 0.00 3.86
2931 3563 2.115911 AACAGGAAACGCACGGCAA 61.116 52.632 0.00 0.00 0.00 4.52
2932 3564 2.058829 AACAGGAAACGCACGGCAAG 62.059 55.000 0.00 0.00 0.00 4.01
2933 3565 2.110213 AGGAAACGCACGGCAAGA 59.890 55.556 0.00 0.00 0.00 3.02
2934 3566 1.961277 AGGAAACGCACGGCAAGAG 60.961 57.895 0.00 0.00 0.00 2.85
2941 3573 2.266055 CACGGCAAGAGGGAGGAC 59.734 66.667 0.00 0.00 0.00 3.85
2977 3624 1.531365 CAATGGCAGGTGTGGTGGT 60.531 57.895 0.00 0.00 0.00 4.16
3088 3756 2.203998 AGTGTGGGGCTGGCTACT 60.204 61.111 0.00 0.00 0.00 2.57
3123 3791 3.192103 AAGCGTTGGAGGGGGTGTC 62.192 63.158 0.00 0.00 0.00 3.67
3151 3819 2.125512 CCCAGCGACTTCCTTCCG 60.126 66.667 0.00 0.00 0.00 4.30
3302 3974 5.600908 TCTTTCGAAAGGTAATCGTTTGG 57.399 39.130 31.82 8.11 40.99 3.28
3303 3975 4.453136 TCTTTCGAAAGGTAATCGTTTGGG 59.547 41.667 31.82 7.71 40.99 4.12
3304 3976 3.681593 TCGAAAGGTAATCGTTTGGGA 57.318 42.857 0.00 0.00 40.99 4.37
3305 3977 4.005487 TCGAAAGGTAATCGTTTGGGAA 57.995 40.909 0.00 0.00 40.99 3.97
3306 3978 3.747529 TCGAAAGGTAATCGTTTGGGAAC 59.252 43.478 0.00 0.00 40.99 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 107 4.099170 CTTCGTCGTCCTCGCCGT 62.099 66.667 0.00 0.00 39.43 5.68
537 546 5.132648 TGGAGCATTGGAAGTAGATTGGTAT 59.867 40.000 0.00 0.00 0.00 2.73
547 556 9.646522 AAATACTATAATTGGAGCATTGGAAGT 57.353 29.630 0.00 0.00 0.00 3.01
567 576 8.621532 TTCTGAGTAAATTGCACAGAAATACT 57.378 30.769 17.81 3.19 42.12 2.12
619 628 3.022287 CGCTGTGCCAGACGTTTT 58.978 55.556 6.40 0.00 32.44 2.43
749 763 0.600255 CGTGGTGTCAGTGAGGGTTC 60.600 60.000 0.00 0.00 0.00 3.62
750 764 1.046472 TCGTGGTGTCAGTGAGGGTT 61.046 55.000 0.00 0.00 0.00 4.11
781 804 2.343758 CACACCAGTCAGACCCGG 59.656 66.667 0.00 0.00 0.00 5.73
782 805 2.343758 CCACACCAGTCAGACCCG 59.656 66.667 0.00 0.00 0.00 5.28
783 806 1.071471 CACCACACCAGTCAGACCC 59.929 63.158 0.00 0.00 0.00 4.46
785 808 0.178068 ACACACCACACCAGTCAGAC 59.822 55.000 0.00 0.00 0.00 3.51
788 811 1.134640 GTACACACACCACACCAGTCA 60.135 52.381 0.00 0.00 0.00 3.41
799 833 1.142474 GGCTGTAACCGTACACACAC 58.858 55.000 0.00 0.00 35.23 3.82
800 834 0.751452 TGGCTGTAACCGTACACACA 59.249 50.000 0.00 0.00 35.23 3.72
801 835 1.730064 CATGGCTGTAACCGTACACAC 59.270 52.381 0.00 0.00 35.23 3.82
802 836 1.338294 CCATGGCTGTAACCGTACACA 60.338 52.381 0.00 0.00 35.23 3.72
824 858 2.516460 CAGGCTGGATCCTGCTGC 60.516 66.667 34.20 22.63 46.11 5.25
857 891 3.245694 TGGCGGGTGTATACTATATGGGA 60.246 47.826 4.17 0.00 0.00 4.37
862 1171 5.577100 AGAGATTGGCGGGTGTATACTATA 58.423 41.667 4.17 0.00 0.00 1.31
863 1172 4.417437 AGAGATTGGCGGGTGTATACTAT 58.583 43.478 4.17 0.00 0.00 2.12
864 1173 3.825014 GAGAGATTGGCGGGTGTATACTA 59.175 47.826 4.17 0.00 0.00 1.82
865 1174 2.628657 GAGAGATTGGCGGGTGTATACT 59.371 50.000 4.17 0.00 0.00 2.12
866 1175 2.628657 AGAGAGATTGGCGGGTGTATAC 59.371 50.000 0.00 0.00 0.00 1.47
890 1199 1.345112 GGGAGATAAGGTGGGAGGGAA 60.345 57.143 0.00 0.00 0.00 3.97
911 1220 4.475135 GCTCGGCTTGGAGACCCC 62.475 72.222 4.52 0.00 36.08 4.95
977 1295 3.075005 CGATCGGTCAGGTGGGGT 61.075 66.667 7.38 0.00 0.00 4.95
978 1296 4.530857 GCGATCGGTCAGGTGGGG 62.531 72.222 18.30 0.00 0.00 4.96
979 1297 4.530857 GGCGATCGGTCAGGTGGG 62.531 72.222 18.30 0.00 0.00 4.61
980 1298 4.873129 CGGCGATCGGTCAGGTGG 62.873 72.222 18.30 0.00 34.75 4.61
1518 1860 3.884581 CTCGAACACGAACCGCGGA 62.885 63.158 35.90 3.40 46.49 5.54
1983 2482 3.670377 GCGAACTTGCCGCCCTTT 61.670 61.111 0.00 0.00 46.22 3.11
2327 2842 4.114997 GACATGTTTGCCGCCCGG 62.115 66.667 0.00 1.59 38.57 5.73
2328 2843 2.211619 AATGACATGTTTGCCGCCCG 62.212 55.000 0.00 0.00 0.00 6.13
2329 2844 0.458370 GAATGACATGTTTGCCGCCC 60.458 55.000 0.00 0.00 0.00 6.13
2330 2845 0.458370 GGAATGACATGTTTGCCGCC 60.458 55.000 0.00 0.00 0.00 6.13
2331 2846 0.798009 CGGAATGACATGTTTGCCGC 60.798 55.000 14.22 0.00 0.00 6.53
2342 2857 1.126846 CAGTTTGCTCGTCGGAATGAC 59.873 52.381 0.00 0.00 44.53 3.06
2367 2887 7.656948 GTCTTCTAAGTAGATTCTCGGCTACTA 59.343 40.741 0.00 0.00 44.74 1.82
2382 2904 6.912951 ACCAGCTAAGTTGTCTTCTAAGTA 57.087 37.500 0.00 0.00 35.36 2.24
2383 2905 5.810080 ACCAGCTAAGTTGTCTTCTAAGT 57.190 39.130 0.00 0.00 35.36 2.24
2384 2906 6.459923 AGAACCAGCTAAGTTGTCTTCTAAG 58.540 40.000 6.06 0.00 35.36 2.18
2385 2907 6.420913 AGAACCAGCTAAGTTGTCTTCTAA 57.579 37.500 6.06 0.00 35.36 2.10
2396 2918 5.562890 GCAACCAACTAAAGAACCAGCTAAG 60.563 44.000 0.00 0.00 0.00 2.18
2515 3084 1.573108 ACAGCTAGCAAAGGAGGCTA 58.427 50.000 18.83 0.00 42.62 3.93
2576 3161 9.275398 CTCGAAATGGAGTTAGTAGTAGTAGAT 57.725 37.037 0.00 0.00 0.00 1.98
2577 3162 8.263640 ACTCGAAATGGAGTTAGTAGTAGTAGA 58.736 37.037 0.00 0.00 44.65 2.59
2641 3227 2.549754 ACTGCCAGTTCATCTTTTCACG 59.450 45.455 0.00 0.00 0.00 4.35
2657 3243 2.603560 GTCGCAAATGAGTACTACTGCC 59.396 50.000 0.00 0.00 0.00 4.85
2658 3244 3.304559 CAGTCGCAAATGAGTACTACTGC 59.695 47.826 0.00 1.65 0.00 4.40
2659 3245 4.733850 TCAGTCGCAAATGAGTACTACTG 58.266 43.478 10.58 10.58 35.54 2.74
2678 3264 0.742281 CGGGTTCATGCCAGTCTCAG 60.742 60.000 0.00 0.00 0.00 3.35
2718 3329 3.617669 GCATGGCAATGATACGTTACAC 58.382 45.455 4.87 0.00 35.67 2.90
2724 3335 0.235665 GGTCGCATGGCAATGATACG 59.764 55.000 4.87 0.00 35.67 3.06
2758 3369 2.125753 AGCGCTCTTTGCTCCGAG 60.126 61.111 2.64 0.00 38.62 4.63
2759 3370 2.433145 CAGCGCTCTTTGCTCCGA 60.433 61.111 7.13 0.00 41.72 4.55
2760 3371 2.734673 GACAGCGCTCTTTGCTCCG 61.735 63.158 7.13 0.00 41.72 4.63
2762 3373 0.995728 GTAGACAGCGCTCTTTGCTC 59.004 55.000 7.13 0.00 41.72 4.26
2773 3387 4.065088 TGAAAATCACAGGTGTAGACAGC 58.935 43.478 3.65 3.65 44.12 4.40
2783 3397 5.759273 TGCTTTGGATTTTGAAAATCACAGG 59.241 36.000 26.36 15.77 0.00 4.00
2806 3420 4.268405 GCCAAATGATACCTCGCAAAATTG 59.732 41.667 0.00 0.00 0.00 2.32
2807 3421 4.432712 GCCAAATGATACCTCGCAAAATT 58.567 39.130 0.00 0.00 0.00 1.82
2808 3422 3.181476 GGCCAAATGATACCTCGCAAAAT 60.181 43.478 0.00 0.00 0.00 1.82
2809 3423 2.165437 GGCCAAATGATACCTCGCAAAA 59.835 45.455 0.00 0.00 0.00 2.44
2810 3424 1.748493 GGCCAAATGATACCTCGCAAA 59.252 47.619 0.00 0.00 0.00 3.68
2811 3425 1.064758 AGGCCAAATGATACCTCGCAA 60.065 47.619 5.01 0.00 0.00 4.85
2812 3426 0.546122 AGGCCAAATGATACCTCGCA 59.454 50.000 5.01 0.00 0.00 5.10
2813 3427 0.947244 CAGGCCAAATGATACCTCGC 59.053 55.000 5.01 0.00 0.00 5.03
2814 3428 1.597742 CCAGGCCAAATGATACCTCG 58.402 55.000 5.01 0.00 0.00 4.63
2815 3429 1.322442 GCCAGGCCAAATGATACCTC 58.678 55.000 5.01 0.00 0.00 3.85
2816 3430 3.520623 GCCAGGCCAAATGATACCT 57.479 52.632 5.01 0.00 0.00 3.08
2848 3462 3.565902 GCAAACTTGACTAGTTGCTCCTT 59.434 43.478 7.56 0.00 46.34 3.36
2892 3524 2.155279 GCTTCCCTTCACAAGTCCTTC 58.845 52.381 0.00 0.00 0.00 3.46
2909 3541 1.355210 CGTGCGTTTCCTGTTGCTT 59.645 52.632 0.00 0.00 0.00 3.91
2919 3551 2.978010 CCCTCTTGCCGTGCGTTT 60.978 61.111 0.00 0.00 0.00 3.60
2931 3563 2.947785 ACCCCTCGTCCTCCCTCT 60.948 66.667 0.00 0.00 0.00 3.69
2932 3564 2.760385 CACCCCTCGTCCTCCCTC 60.760 72.222 0.00 0.00 0.00 4.30
2933 3565 4.400251 CCACCCCTCGTCCTCCCT 62.400 72.222 0.00 0.00 0.00 4.20
2977 3624 2.753043 GAGACCGGCCGTACTCCA 60.753 66.667 27.32 0.00 0.00 3.86
3105 3773 3.175710 ACACCCCCTCCAACGCTT 61.176 61.111 0.00 0.00 0.00 4.68
3151 3819 2.179517 CAGACGACAGCCGAGGAC 59.820 66.667 0.00 0.00 41.76 3.85


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

AutoCloner maintained by Alex Coulton.