Multiple sequence alignment - TraesCS5B01G026300

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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 TraesCS5B01G026300 chr5B 100.000 2242 0 0 1 2242 25060684 25062925 0.000000e+00 4141.0
1 TraesCS5B01G026300 chr5B 100.000 529 0 0 2550 3078 25063233 25063761 0.000000e+00 977.0
2 TraesCS5B01G026300 chr5B 84.706 170 14 4 2550 2719 25265217 25265374 3.180000e-35 159.0
3 TraesCS5B01G026300 chr5D 93.204 1339 48 14 922 2242 34045353 34044040 0.000000e+00 1929.0
4 TraesCS5B01G026300 chr5D 91.876 517 35 5 1 515 34048052 34047541 0.000000e+00 715.0
5 TraesCS5B01G026300 chr5D 86.801 447 34 9 2550 2985 34043514 34043082 2.780000e-130 475.0
6 TraesCS5B01G026300 chr5D 96.610 59 2 0 3020 3078 34041545 34041487 7.020000e-17 99.0
7 TraesCS5B01G026300 chr5A 88.526 1377 62 40 936 2242 22486343 22484993 0.000000e+00 1580.0
8 TraesCS5B01G026300 chr6A 85.567 194 21 5 2650 2843 452642042 452642228 2.420000e-46 196.0
9 TraesCS5B01G026300 chr6B 88.199 161 14 4 2688 2843 511697423 511697263 1.460000e-43 187.0
10 TraesCS5B01G026300 chr2D 85.526 152 20 2 2563 2713 57257047 57257197 1.140000e-34 158.0
11 TraesCS5B01G026300 chr2D 83.240 179 16 4 2550 2714 73139400 73139222 5.320000e-33 152.0
12 TraesCS5B01G026300 chr2D 84.868 152 17 5 2564 2714 442288773 442288919 6.880000e-32 148.0
13 TraesCS5B01G026300 chr2D 90.476 105 10 0 1386 1490 378525639 378525743 4.140000e-29 139.0
14 TraesCS5B01G026300 chr2D 90.361 83 7 1 2757 2838 22162562 22162480 1.170000e-19 108.0
15 TraesCS5B01G026300 chrUn 76.316 304 47 20 2550 2833 87224730 87225028 4.140000e-29 139.0
16 TraesCS5B01G026300 chr3D 85.385 130 19 0 2709 2838 56310406 56310277 5.350000e-28 135.0
17 TraesCS5B01G026300 chr2B 89.524 105 11 0 1386 1490 449670161 449670265 1.930000e-27 134.0
18 TraesCS5B01G026300 chr2A 89.524 105 11 0 1386 1490 513286712 513286816 1.930000e-27 134.0
19 TraesCS5B01G026300 chr6D 82.119 151 19 6 2567 2714 271823522 271823667 4.170000e-24 122.0
20 TraesCS5B01G026300 chr6D 90.323 62 5 1 2564 2624 408180821 408180882 2.540000e-11 80.5
21 TraesCS5B01G026300 chr4B 91.228 57 4 1 2566 2622 90889863 90889808 3.290000e-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 TraesCS5B01G026300 chr5B 25060684 25063761 3077 False 2559.0 4141 100.00000 1 3078 2 chr5B.!!$F2 3077
1 TraesCS5B01G026300 chr5D 34041487 34048052 6565 True 804.5 1929 92.12275 1 3078 4 chr5D.!!$R1 3077
2 TraesCS5B01G026300 chr5A 22484993 22486343 1350 True 1580.0 1580 88.52600 936 2242 1 chr5A.!!$R1 1306

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
602 2096 0.028637 GCCGAGCATTCTAAAGCTGC 59.971 55.0 0.0 0.0 42.04 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2177 4054 1.415659 CAAACATGGTTGGCTCCCAAA 59.584 47.619 16.07 0.0 45.73 3.28 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
27 28 3.134804 GGCCATCCAATGTAGTACTCACT 59.865 47.826 0.00 0.00 38.91 3.41
55 56 3.341823 GAGATCATCACAACTTGCTGGT 58.658 45.455 0.00 0.00 0.00 4.00
135 136 0.928505 TTGATGCCACATGGGAGGAT 59.071 50.000 0.00 0.00 39.50 3.24
137 138 1.421268 TGATGCCACATGGGAGGATAC 59.579 52.381 0.00 0.00 39.50 2.24
146 147 0.906775 TGGGAGGATACCGTTCAACC 59.093 55.000 0.00 0.00 37.17 3.77
147 148 0.179092 GGGAGGATACCGTTCAACCG 60.179 60.000 0.00 0.00 37.17 4.44
189 190 2.679996 GCTTGGGGGCAATCCGTT 60.680 61.111 0.00 0.00 36.01 4.44
229 230 3.944250 AACCCAAGCCCGCCATCAG 62.944 63.158 0.00 0.00 0.00 2.90
235 236 2.809861 AAGCCCGCCATCAGTGACAG 62.810 60.000 0.00 0.00 0.00 3.51
247 248 2.351418 TCAGTGACAGTCAACAAAAGCG 59.649 45.455 4.32 0.00 0.00 4.68
248 249 1.064060 AGTGACAGTCAACAAAAGCGC 59.936 47.619 4.32 0.00 0.00 5.92
305 307 1.953559 AAGCTGACGCAGACAAAAGA 58.046 45.000 10.46 0.00 39.10 2.52
332 334 0.033208 ATGACAACCAATCCGGCCAT 60.033 50.000 2.24 0.00 39.03 4.40
355 357 2.576648 GGGACAAATCAGGGGTAAGAGT 59.423 50.000 0.00 0.00 0.00 3.24
376 378 1.020861 TGTCATCACGCAGCCACATC 61.021 55.000 0.00 0.00 0.00 3.06
378 380 3.197790 ATCACGCAGCCACATCGC 61.198 61.111 0.00 0.00 0.00 4.58
386 388 3.498834 GCCACATCGCATCGTGCA 61.499 61.111 9.95 0.00 45.36 4.57
462 464 2.350522 CTCACAAGGGAAAGACATCCG 58.649 52.381 0.00 0.00 40.62 4.18
463 465 0.804989 CACAAGGGAAAGACATCCGC 59.195 55.000 0.00 0.00 40.62 5.54
469 471 2.025887 AGGGAAAGACATCCGCTGAATT 60.026 45.455 0.00 0.00 40.62 2.17
473 475 4.876107 GGAAAGACATCCGCTGAATTAGAA 59.124 41.667 0.00 0.00 0.00 2.10
475 477 6.038714 GGAAAGACATCCGCTGAATTAGAAAT 59.961 38.462 0.00 0.00 0.00 2.17
476 478 5.998454 AGACATCCGCTGAATTAGAAATG 57.002 39.130 0.00 0.00 0.00 2.32
477 479 5.674525 AGACATCCGCTGAATTAGAAATGA 58.325 37.500 0.00 0.00 0.00 2.57
478 480 5.525378 AGACATCCGCTGAATTAGAAATGAC 59.475 40.000 0.00 0.00 0.00 3.06
483 485 4.142902 CCGCTGAATTAGAAATGACACGTT 60.143 41.667 0.00 0.00 0.00 3.99
485 487 6.178507 CGCTGAATTAGAAATGACACGTTAG 58.821 40.000 0.00 0.00 0.00 2.34
491 493 2.729882 AGAAATGACACGTTAGCGACAC 59.270 45.455 5.81 0.00 42.00 3.67
496 498 3.044986 TGACACGTTAGCGACACTTTAC 58.955 45.455 5.81 0.00 42.00 2.01
500 502 3.492011 CACGTTAGCGACACTTTACCTTT 59.508 43.478 5.81 0.00 42.00 3.11
503 505 4.376717 CGTTAGCGACACTTTACCTTTTCC 60.377 45.833 0.00 0.00 41.33 3.13
510 512 5.252969 ACACTTTACCTTTTCCGTTTTCC 57.747 39.130 0.00 0.00 0.00 3.13
511 513 4.951715 ACACTTTACCTTTTCCGTTTTCCT 59.048 37.500 0.00 0.00 0.00 3.36
512 514 5.066893 ACACTTTACCTTTTCCGTTTTCCTC 59.933 40.000 0.00 0.00 0.00 3.71
514 516 5.889853 ACTTTACCTTTTCCGTTTTCCTCTT 59.110 36.000 0.00 0.00 0.00 2.85
515 517 7.012610 CACTTTACCTTTTCCGTTTTCCTCTTA 59.987 37.037 0.00 0.00 0.00 2.10
523 2017 4.647611 TCCGTTTTCCTCTTATGCAAGAA 58.352 39.130 0.00 0.00 40.28 2.52
529 2023 8.450964 CGTTTTCCTCTTATGCAAGAAAGATTA 58.549 33.333 9.22 0.72 40.28 1.75
534 2028 8.708378 TCCTCTTATGCAAGAAAGATTATCTCA 58.292 33.333 9.22 0.00 40.28 3.27
537 2031 9.842775 TCTTATGCAAGAAAGATTATCTCATGT 57.157 29.630 0.00 0.00 37.85 3.21
554 2048 4.560128 TCATGTAAGCGAATCCTATGAGC 58.440 43.478 0.00 0.00 0.00 4.26
559 2053 2.681706 AGCGAATCCTATGAGCGAATG 58.318 47.619 0.00 0.00 0.00 2.67
561 2055 3.255888 AGCGAATCCTATGAGCGAATGTA 59.744 43.478 0.00 0.00 0.00 2.29
569 2063 7.227049 TCCTATGAGCGAATGTAATATGTGA 57.773 36.000 0.00 0.00 0.00 3.58
584 2078 8.253810 TGTAATATGTGATGAGCTAATCTAGGC 58.746 37.037 12.50 1.45 0.00 3.93
602 2096 0.028637 GCCGAGCATTCTAAAGCTGC 59.971 55.000 0.00 0.00 42.04 5.25
612 2106 3.234630 TAAAGCTGCGACTGGCCGT 62.235 57.895 0.00 0.00 42.61 5.68
619 2113 4.778415 CGACTGGCCGTGGACTCG 62.778 72.222 4.94 0.00 0.00 4.18
621 2115 3.628280 GACTGGCCGTGGACTCGTC 62.628 68.421 4.94 0.00 0.00 4.20
626 2120 4.778415 CCGTGGACTCGTCTGCGG 62.778 72.222 14.41 14.41 39.10 5.69
660 2155 1.869767 ACGCTACGGTATAAGACGAGG 59.130 52.381 0.00 0.00 0.00 4.63
669 2164 2.076622 ATAAGACGAGGCGCGCATCT 62.077 55.000 37.97 27.21 46.04 2.90
685 2181 3.721035 GCATCTCCAAAAAGTTGCAACT 58.279 40.909 26.36 26.36 40.26 3.16
690 2186 1.406614 CCAAAAAGTTGCAACTGGCCA 60.407 47.619 31.73 4.71 43.89 5.36
694 2190 3.898509 GTTGCAACTGGCCACGCA 61.899 61.111 22.36 14.25 43.89 5.24
710 2206 3.296516 GCACTTTGCTGCGACATAC 57.703 52.632 0.00 0.00 40.96 2.39
719 2215 0.864377 CTGCGACATACGGTGGTACG 60.864 60.000 0.00 0.00 42.83 3.67
720 2216 1.587088 GCGACATACGGTGGTACGG 60.587 63.158 0.00 0.00 42.83 4.02
723 2219 1.268032 CGACATACGGTGGTACGGTAC 60.268 57.143 9.82 9.82 36.86 3.34
755 2251 1.293498 GTGTCACCGGTGATGCTCT 59.707 57.895 38.11 0.00 42.18 4.09
760 2256 1.986757 ACCGGTGATGCTCTGAGCT 60.987 57.895 28.04 15.01 42.97 4.09
769 2265 4.172512 CTCTGAGCTGCGGGGCAT 62.173 66.667 0.00 0.00 38.13 4.40
776 2272 3.384532 CTGCGGGGCATTTTGGCT 61.385 61.111 0.94 0.00 43.20 4.75
782 2278 1.379309 GGGCATTTTGGCTACCCGA 60.379 57.895 0.94 0.00 43.20 5.14
820 2316 1.686052 AGAGAATGAGATGAGGGACGC 59.314 52.381 0.00 0.00 0.00 5.19
821 2317 0.755686 AGAATGAGATGAGGGACGCC 59.244 55.000 0.00 0.00 0.00 5.68
822 2318 0.250081 GAATGAGATGAGGGACGCCC 60.250 60.000 6.80 6.80 45.90 6.13
862 2358 2.476051 GTGCTGCAATGGTCGACG 59.524 61.111 9.92 0.00 0.00 5.12
864 2360 1.079197 TGCTGCAATGGTCGACGAT 60.079 52.632 9.92 8.58 0.00 3.73
865 2361 1.349627 GCTGCAATGGTCGACGATG 59.650 57.895 14.14 11.14 0.00 3.84
866 2362 1.349627 CTGCAATGGTCGACGATGC 59.650 57.895 23.68 23.68 0.00 3.91
867 2363 2.321060 GCAATGGTCGACGATGCG 59.679 61.111 14.14 9.50 0.00 4.73
868 2364 3.005898 CAATGGTCGACGATGCGG 58.994 61.111 14.14 3.55 0.00 5.69
869 2365 2.890474 AATGGTCGACGATGCGGC 60.890 61.111 14.14 0.00 34.63 6.53
885 2381 4.101790 GCGACGGTGCCACAATGG 62.102 66.667 0.00 0.00 41.55 3.16
886 2382 2.668212 CGACGGTGCCACAATGGT 60.668 61.111 0.00 0.00 40.46 3.55
887 2383 2.677003 CGACGGTGCCACAATGGTC 61.677 63.158 0.00 0.00 40.46 4.02
888 2384 2.668212 ACGGTGCCACAATGGTCG 60.668 61.111 0.00 1.96 40.46 4.79
889 2385 4.101790 CGGTGCCACAATGGTCGC 62.102 66.667 0.00 0.00 40.46 5.19
890 2386 3.747976 GGTGCCACAATGGTCGCC 61.748 66.667 0.00 6.25 40.46 5.54
891 2387 4.101790 GTGCCACAATGGTCGCCG 62.102 66.667 0.00 0.00 40.46 6.46
961 2773 1.001597 GTAGGTGGTGATCGATCGGTC 60.002 57.143 21.50 21.50 0.00 4.79
1063 2875 1.594293 AACAAGACACACCTCGCCG 60.594 57.895 0.00 0.00 0.00 6.46
1141 2957 2.614057 CCAAAGCACACTCGTCTTCTTT 59.386 45.455 0.00 0.00 0.00 2.52
1162 2978 2.768527 TCTTCCCCATTCTGTCAGCTAG 59.231 50.000 0.00 0.00 0.00 3.42
1163 2979 0.833287 TCCCCATTCTGTCAGCTAGC 59.167 55.000 6.62 6.62 0.00 3.42
1182 2998 1.903955 GCCTTCTTCCTCCTCCTCCTT 60.904 57.143 0.00 0.00 0.00 3.36
1183 2999 2.556766 CCTTCTTCCTCCTCCTCCTTT 58.443 52.381 0.00 0.00 0.00 3.11
1184 3000 2.503765 CCTTCTTCCTCCTCCTCCTTTC 59.496 54.545 0.00 0.00 0.00 2.62
1185 3001 3.177228 CTTCTTCCTCCTCCTCCTTTCA 58.823 50.000 0.00 0.00 0.00 2.69
1304 3120 0.397941 CAGCAAGGACTCCCACAAGA 59.602 55.000 0.00 0.00 33.88 3.02
1898 3744 2.281070 CCTCGCCGGGGATGATTG 60.281 66.667 22.85 9.69 0.00 2.67
1911 3757 3.691609 GGGATGATTGTGAGGTTCTTCAC 59.308 47.826 7.89 7.89 46.02 3.18
1940 3786 4.581868 TCCGGACCTGTAAATTAACCTTG 58.418 43.478 0.00 0.00 0.00 3.61
1943 3789 5.106436 CCGGACCTGTAAATTAACCTTGTTC 60.106 44.000 0.00 0.00 0.00 3.18
2010 3859 0.330604 AGGACCAGCGAGTAGGTGTA 59.669 55.000 1.73 0.00 46.29 2.90
2011 3860 0.455005 GGACCAGCGAGTAGGTGTAC 59.545 60.000 1.73 0.00 46.29 2.90
2012 3861 1.171308 GACCAGCGAGTAGGTGTACA 58.829 55.000 0.00 0.00 46.29 2.90
2088 3942 8.443953 ACTCCTGATTGAGTATTAAATTGAGC 57.556 34.615 0.00 0.00 43.65 4.26
2114 3972 3.700538 AGGCATTGCTCCTGTTAATTGA 58.299 40.909 8.82 0.00 31.53 2.57
2155 4026 5.995565 TGAGTAGTGTAGGTTGTGCTAAT 57.004 39.130 0.00 0.00 0.00 1.73
2226 4107 8.314021 GGGTGGTTCTTTCAATTAATTCTGATT 58.686 33.333 0.00 0.00 0.00 2.57
2575 4674 1.372582 CGTCATCACCCCAATGTCTG 58.627 55.000 0.00 0.00 0.00 3.51
2586 4685 3.245264 CCCCAATGTCTGTCTTAGGGTTT 60.245 47.826 0.00 0.00 32.90 3.27
2595 4694 1.562942 GTCTTAGGGTTTAGGGTGGGG 59.437 57.143 0.00 0.00 0.00 4.96
2596 4695 0.257905 CTTAGGGTTTAGGGTGGGGC 59.742 60.000 0.00 0.00 0.00 5.80
2597 4696 1.564483 TTAGGGTTTAGGGTGGGGCG 61.564 60.000 0.00 0.00 0.00 6.13
2598 4697 4.435970 GGGTTTAGGGTGGGGCGG 62.436 72.222 0.00 0.00 0.00 6.13
2599 4698 3.654143 GGTTTAGGGTGGGGCGGT 61.654 66.667 0.00 0.00 0.00 5.68
2600 4699 2.360726 GTTTAGGGTGGGGCGGTG 60.361 66.667 0.00 0.00 0.00 4.94
2601 4700 3.653078 TTTAGGGTGGGGCGGTGG 61.653 66.667 0.00 0.00 0.00 4.61
2602 4701 4.986774 TTAGGGTGGGGCGGTGGT 62.987 66.667 0.00 0.00 0.00 4.16
2634 4733 1.198094 TGTGGGGATTCGCAGGAGAA 61.198 55.000 2.94 0.00 36.48 2.87
2647 4746 2.554032 GCAGGAGAAAAAGCTTAGTGCA 59.446 45.455 0.00 0.00 45.94 4.57
2652 4751 2.108250 AGAAAAAGCTTAGTGCAGGGGA 59.892 45.455 0.00 0.00 45.94 4.81
2693 4792 3.480133 GGAGGACCGATGGTGGGG 61.480 72.222 0.00 0.00 35.25 4.96
2754 4864 3.512516 GATGGCTGGCGGCTCAAC 61.513 66.667 19.30 9.53 41.46 3.18
2759 4869 2.048222 CTGGCGGCTCAACGAAGA 60.048 61.111 11.43 0.00 35.47 2.87
2786 4896 3.736759 GTGTCGAGAGGTTGAAGAAAGAC 59.263 47.826 0.00 0.00 0.00 3.01
2817 4927 4.927978 TTGATTTCACATCCAACGGTTT 57.072 36.364 0.00 0.00 0.00 3.27
2824 4934 6.642707 TTCACATCCAACGGTTTAAGAATT 57.357 33.333 0.00 0.00 0.00 2.17
2838 4948 7.468084 CGGTTTAAGAATTGACTGACCTCAAAA 60.468 37.037 0.00 0.00 33.85 2.44
2887 4997 1.343465 ACATTCCCGTTTCGAGTCAGT 59.657 47.619 0.00 0.00 0.00 3.41
2891 5001 3.226346 TCCCGTTTCGAGTCAGTTATG 57.774 47.619 0.00 0.00 0.00 1.90
2955 5065 8.849168 CAAGTCCAAGCCATACATATATTGAAA 58.151 33.333 0.00 0.00 0.00 2.69
2970 5080 8.853126 CATATATTGAAAGAGGAGCCAAATTCA 58.147 33.333 0.00 0.00 0.00 2.57
2974 5084 4.834496 TGAAAGAGGAGCCAAATTCAATGT 59.166 37.500 0.00 0.00 0.00 2.71
2975 5085 5.305128 TGAAAGAGGAGCCAAATTCAATGTT 59.695 36.000 0.00 0.00 0.00 2.71
3008 5150 1.779569 CACCGCTCGACTACTTTTGT 58.220 50.000 0.00 0.00 0.00 2.83
3010 5152 1.068127 ACCGCTCGACTACTTTTGTGT 59.932 47.619 0.00 0.00 0.00 3.72
3011 5153 1.455786 CCGCTCGACTACTTTTGTGTG 59.544 52.381 0.00 0.00 0.00 3.82
3012 5154 1.136611 CGCTCGACTACTTTTGTGTGC 60.137 52.381 0.00 0.00 0.00 4.57
3013 5155 2.135933 GCTCGACTACTTTTGTGTGCT 58.864 47.619 0.00 0.00 0.00 4.40
3016 5158 4.762809 CTCGACTACTTTTGTGTGCTTTC 58.237 43.478 0.00 0.00 0.00 2.62
3017 5159 3.558418 TCGACTACTTTTGTGTGCTTTCC 59.442 43.478 0.00 0.00 0.00 3.13
3018 5160 3.560068 CGACTACTTTTGTGTGCTTTCCT 59.440 43.478 0.00 0.00 0.00 3.36
3030 6642 2.160417 GTGCTTTCCTCCATTTGAGTCG 59.840 50.000 0.00 0.00 39.65 4.18
3046 6658 4.385825 TGAGTCGCCAAATTAGACAAACT 58.614 39.130 0.00 0.00 37.36 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.176411 AGTTGTGATGATCTCCACTGGA 58.824 45.455 15.50 0.00 34.57 3.86
55 56 1.685224 GACCAGATGGGGTTCTGCA 59.315 57.895 3.48 0.00 42.53 4.41
135 136 2.690786 CATTCCTTCGGTTGAACGGTA 58.309 47.619 2.80 0.00 0.00 4.02
137 138 0.168128 GCATTCCTTCGGTTGAACGG 59.832 55.000 0.00 0.00 0.00 4.44
189 190 2.499289 GCTGACATCCTCTCCTTGAGAA 59.501 50.000 0.00 0.00 45.39 2.87
225 226 3.002656 CGCTTTTGTTGACTGTCACTGAT 59.997 43.478 10.56 0.00 0.00 2.90
229 230 1.064060 AGCGCTTTTGTTGACTGTCAC 59.936 47.619 10.56 6.70 0.00 3.67
235 236 2.046313 CATGACAGCGCTTTTGTTGAC 58.954 47.619 7.50 0.00 0.00 3.18
247 248 1.354506 GATTCGCAGGCATGACAGC 59.645 57.895 5.73 5.73 0.00 4.40
248 249 1.640069 CGATTCGCAGGCATGACAG 59.360 57.895 0.62 0.00 0.00 3.51
305 307 0.895100 ATTGGTTGTCATGGCAGCGT 60.895 50.000 8.12 0.00 0.00 5.07
332 334 1.638589 CTTACCCCTGATTTGTCCCCA 59.361 52.381 0.00 0.00 0.00 4.96
355 357 1.960763 GTGGCTGCGTGATGACACA 60.961 57.895 0.00 0.00 46.20 3.72
367 369 2.705220 CACGATGCGATGTGGCTG 59.295 61.111 0.00 0.00 32.47 4.85
378 380 1.295357 TGCGGTTAGGTTGCACGATG 61.295 55.000 0.00 0.00 32.86 3.84
402 404 2.858476 ATCCACACCAGGCCCACA 60.858 61.111 0.00 0.00 0.00 4.17
410 412 2.727123 AGTTGTGTTGATCCACACCA 57.273 45.000 23.19 12.67 45.67 4.17
452 454 6.599244 TCATTTCTAATTCAGCGGATGTCTTT 59.401 34.615 0.00 0.00 0.00 2.52
456 458 5.065218 GTGTCATTTCTAATTCAGCGGATGT 59.935 40.000 0.00 0.00 0.00 3.06
462 464 5.960105 GCTAACGTGTCATTTCTAATTCAGC 59.040 40.000 0.00 0.00 0.00 4.26
463 465 6.034577 TCGCTAACGTGTCATTTCTAATTCAG 59.965 38.462 0.00 0.00 41.18 3.02
469 471 3.916172 GTGTCGCTAACGTGTCATTTCTA 59.084 43.478 0.00 0.00 41.18 2.10
473 475 2.433868 AGTGTCGCTAACGTGTCATT 57.566 45.000 0.00 0.00 41.18 2.57
475 477 2.212869 AAAGTGTCGCTAACGTGTCA 57.787 45.000 0.00 0.00 41.18 3.58
476 478 2.406357 GGTAAAGTGTCGCTAACGTGTC 59.594 50.000 0.00 0.00 41.18 3.67
477 479 2.035066 AGGTAAAGTGTCGCTAACGTGT 59.965 45.455 0.00 0.00 41.18 4.49
478 480 2.669364 AGGTAAAGTGTCGCTAACGTG 58.331 47.619 0.00 0.00 41.18 4.49
483 485 3.243839 ACGGAAAAGGTAAAGTGTCGCTA 60.244 43.478 0.00 0.00 0.00 4.26
485 487 1.869132 ACGGAAAAGGTAAAGTGTCGC 59.131 47.619 0.00 0.00 0.00 5.19
491 493 6.387041 AAGAGGAAAACGGAAAAGGTAAAG 57.613 37.500 0.00 0.00 0.00 1.85
496 498 4.217550 TGCATAAGAGGAAAACGGAAAAGG 59.782 41.667 0.00 0.00 0.00 3.11
500 502 4.647611 TCTTGCATAAGAGGAAAACGGAA 58.352 39.130 0.00 0.00 37.99 4.30
503 505 6.241207 TCTTTCTTGCATAAGAGGAAAACG 57.759 37.500 0.00 0.00 43.41 3.60
511 513 9.842775 ACATGAGATAATCTTTCTTGCATAAGA 57.157 29.630 0.00 8.35 41.06 2.10
515 517 8.566260 GCTTACATGAGATAATCTTTCTTGCAT 58.434 33.333 0.00 0.00 0.00 3.96
523 2017 7.675062 AGGATTCGCTTACATGAGATAATCTT 58.325 34.615 0.00 0.00 0.00 2.40
529 2023 6.596309 TCATAGGATTCGCTTACATGAGAT 57.404 37.500 0.00 0.00 0.00 2.75
534 2028 3.255888 TCGCTCATAGGATTCGCTTACAT 59.744 43.478 0.00 0.00 0.00 2.29
537 2031 4.237724 CATTCGCTCATAGGATTCGCTTA 58.762 43.478 0.00 0.00 0.00 3.09
554 2048 9.363763 AGATTAGCTCATCACATATTACATTCG 57.636 33.333 10.44 0.00 0.00 3.34
559 2053 7.708752 GGCCTAGATTAGCTCATCACATATTAC 59.291 40.741 10.44 0.00 0.00 1.89
561 2055 6.629068 CGGCCTAGATTAGCTCATCACATATT 60.629 42.308 10.44 0.00 0.00 1.28
569 2063 1.548269 GCTCGGCCTAGATTAGCTCAT 59.452 52.381 8.81 0.00 0.00 2.90
584 2078 0.302890 CGCAGCTTTAGAATGCTCGG 59.697 55.000 0.00 0.00 37.31 4.63
602 2096 4.778415 CGAGTCCACGGCCAGTCG 62.778 72.222 2.24 3.24 0.00 4.18
612 2106 4.056125 CTGCCGCAGACGAGTCCA 62.056 66.667 15.74 0.00 43.93 4.02
613 2107 3.749064 TCTGCCGCAGACGAGTCC 61.749 66.667 19.36 0.00 43.93 3.85
636 2130 0.233074 TCTTATACCGTAGCGTCGCG 59.767 55.000 12.30 0.00 0.00 5.87
637 2131 1.668043 GTCTTATACCGTAGCGTCGC 58.332 55.000 9.80 9.80 0.00 5.19
638 2132 1.522676 TCGTCTTATACCGTAGCGTCG 59.477 52.381 0.00 0.00 0.00 5.12
639 2133 2.096516 CCTCGTCTTATACCGTAGCGTC 60.097 54.545 0.00 0.00 0.00 5.19
642 2136 1.399471 CGCCTCGTCTTATACCGTAGC 60.399 57.143 0.00 0.00 0.00 3.58
660 2155 0.387239 AACTTTTTGGAGATGCGCGC 60.387 50.000 27.26 27.26 0.00 6.86
669 2164 1.134551 GGCCAGTTGCAACTTTTTGGA 60.135 47.619 29.81 0.00 43.89 3.53
694 2190 0.320421 ACCGTATGTCGCAGCAAAGT 60.320 50.000 0.00 0.00 38.35 2.66
703 2199 1.013596 TACCGTACCACCGTATGTCG 58.986 55.000 0.00 0.00 39.52 4.35
707 2203 1.134521 TCTCGTACCGTACCACCGTAT 60.135 52.381 3.04 0.00 0.00 3.06
709 2205 1.003839 TCTCGTACCGTACCACCGT 60.004 57.895 3.04 0.00 0.00 4.83
710 2206 1.298157 TGTCTCGTACCGTACCACCG 61.298 60.000 3.04 0.00 0.00 4.94
719 2215 1.585521 CGCGTCCATGTCTCGTACC 60.586 63.158 0.00 0.00 0.00 3.34
720 2216 1.132199 CACGCGTCCATGTCTCGTAC 61.132 60.000 9.86 0.00 0.00 3.67
723 2219 2.126463 ACACGCGTCCATGTCTCG 60.126 61.111 9.86 0.00 0.00 4.04
734 2230 3.478394 CATCACCGGTGACACGCG 61.478 66.667 38.46 20.19 43.11 6.01
747 2243 2.186125 CCGCAGCTCAGAGCATCA 59.814 61.111 24.64 0.00 45.56 3.07
755 2251 2.283101 AAAATGCCCCGCAGCTCA 60.283 55.556 0.00 0.00 43.65 4.26
760 2256 2.036414 TAGCCAAAATGCCCCGCA 59.964 55.556 0.00 0.00 44.86 5.69
769 2265 1.302993 GCACCTCGGGTAGCCAAAA 60.303 57.895 12.31 0.00 32.11 2.44
796 2292 2.437281 TCCCTCATCTCATTCTCTTGCC 59.563 50.000 0.00 0.00 0.00 4.52
839 2335 4.170062 CCATTGCAGCACCGCTCG 62.170 66.667 0.00 0.00 36.40 5.03
843 2339 2.741985 TCGACCATTGCAGCACCG 60.742 61.111 0.00 0.00 0.00 4.94
844 2340 2.870372 GTCGACCATTGCAGCACC 59.130 61.111 3.51 0.00 0.00 5.01
868 2364 4.101790 CCATTGTGGCACCGTCGC 62.102 66.667 16.26 0.00 0.00 5.19
869 2365 2.668212 ACCATTGTGGCACCGTCG 60.668 61.111 16.26 2.73 42.67 5.12
870 2366 2.677003 CGACCATTGTGGCACCGTC 61.677 63.158 16.26 13.52 42.67 4.79
871 2367 2.668212 CGACCATTGTGGCACCGT 60.668 61.111 16.26 5.81 42.67 4.83
872 2368 4.101790 GCGACCATTGTGGCACCG 62.102 66.667 16.26 11.15 44.68 4.94
873 2369 3.747976 GGCGACCATTGTGGCACC 61.748 66.667 16.26 0.00 46.84 5.01
874 2370 4.101790 CGGCGACCATTGTGGCAC 62.102 66.667 11.55 11.55 46.84 5.01
916 2412 0.179092 GGCTAACCGATGGTAGCGTT 60.179 55.000 3.75 0.00 33.12 4.84
917 2413 1.440476 GGCTAACCGATGGTAGCGT 59.560 57.895 3.75 0.00 33.12 5.07
918 2414 4.338327 GGCTAACCGATGGTAGCG 57.662 61.111 3.75 0.00 33.12 4.26
1063 2875 4.400961 AGCAGGAGGAAGCCACGC 62.401 66.667 0.00 0.00 0.00 5.34
1141 2957 1.661463 AGCTGACAGAATGGGGAAGA 58.339 50.000 6.65 0.00 43.62 2.87
1162 2978 0.326143 AGGAGGAGGAGGAAGAAGGC 60.326 60.000 0.00 0.00 0.00 4.35
1163 2979 2.262266 AAGGAGGAGGAGGAAGAAGG 57.738 55.000 0.00 0.00 0.00 3.46
1182 2998 0.807275 CATGGATCGCTCGCAGTGAA 60.807 55.000 0.00 0.00 38.36 3.18
1183 2999 1.227060 CATGGATCGCTCGCAGTGA 60.227 57.895 0.00 2.61 39.30 3.41
1184 3000 2.242572 CCATGGATCGCTCGCAGTG 61.243 63.158 5.56 0.00 0.00 3.66
1185 3001 2.107750 CCATGGATCGCTCGCAGT 59.892 61.111 5.56 0.00 0.00 4.40
1304 3120 4.162690 GACGGGCGGCTTCCTGAT 62.163 66.667 9.56 0.00 36.35 2.90
1969 3815 1.515487 GCAGCCATTTAAACCCGGG 59.485 57.895 22.25 22.25 0.00 5.73
2010 3859 2.030717 CACAGACGAAGCTCACTAGTGT 60.031 50.000 21.99 2.89 0.00 3.55
2011 3860 2.590073 CACAGACGAAGCTCACTAGTG 58.410 52.381 17.17 17.17 0.00 2.74
2012 3861 1.542030 CCACAGACGAAGCTCACTAGT 59.458 52.381 0.00 0.00 0.00 2.57
2088 3942 2.634815 ACAGGAGCAATGCCTATCTG 57.365 50.000 0.00 7.34 33.51 2.90
2095 3949 5.517770 GTCAATCAATTAACAGGAGCAATGC 59.482 40.000 0.00 0.00 0.00 3.56
2155 4026 9.748708 CCAAAAGTCAATAATCTTGAAACAAGA 57.251 29.630 14.94 14.94 0.00 3.02
2177 4054 1.415659 CAAACATGGTTGGCTCCCAAA 59.584 47.619 16.07 0.00 45.73 3.28
2557 4656 2.026822 AGACAGACATTGGGGTGATGAC 60.027 50.000 0.00 0.00 0.00 3.06
2575 4674 1.562942 CCCCACCCTAAACCCTAAGAC 59.437 57.143 0.00 0.00 0.00 3.01
2610 4709 2.750237 GCGAATCCCCACACCACC 60.750 66.667 0.00 0.00 0.00 4.61
2634 4733 1.547901 GGTCCCCTGCACTAAGCTTTT 60.548 52.381 3.20 0.00 45.94 2.27
2647 4746 1.019650 ACCATCACTCTAGGTCCCCT 58.980 55.000 0.00 0.00 37.71 4.79
2652 4751 0.397254 CCCCGACCATCACTCTAGGT 60.397 60.000 0.00 0.00 38.63 3.08
2685 4784 2.602676 CGGAACCACTCCCCACCAT 61.603 63.158 0.00 0.00 41.87 3.55
2686 4785 3.246112 CGGAACCACTCCCCACCA 61.246 66.667 0.00 0.00 41.87 4.17
2693 4792 3.400054 CCCTCCCCGGAACCACTC 61.400 72.222 0.73 0.00 33.16 3.51
2733 4832 4.923942 AGCCGCCAGCCATCATCG 62.924 66.667 0.00 0.00 45.47 3.84
2734 4833 2.976903 GAGCCGCCAGCCATCATC 60.977 66.667 0.00 0.00 45.47 2.92
2735 4834 3.348554 TTGAGCCGCCAGCCATCAT 62.349 57.895 0.00 0.00 45.47 2.45
2736 4835 4.032452 TTGAGCCGCCAGCCATCA 62.032 61.111 0.00 0.00 45.47 3.07
2737 4836 3.512516 GTTGAGCCGCCAGCCATC 61.513 66.667 0.00 0.00 45.47 3.51
2754 4864 2.162608 ACCTCTCGACACATCTTCTTCG 59.837 50.000 0.00 0.00 0.00 3.79
2759 4869 3.574396 TCTTCAACCTCTCGACACATCTT 59.426 43.478 0.00 0.00 0.00 2.40
2786 4896 0.173255 GTGAAATCAATGGCCCACGG 59.827 55.000 0.00 0.00 0.00 4.94
2853 4963 3.522553 GGGAATGTCTAGAAACCAGTCG 58.477 50.000 0.00 0.00 0.00 4.18
2855 4965 2.904434 ACGGGAATGTCTAGAAACCAGT 59.096 45.455 0.00 0.17 0.00 4.00
2859 4969 4.240096 TCGAAACGGGAATGTCTAGAAAC 58.760 43.478 0.00 0.00 0.00 2.78
2867 4977 1.343465 ACTGACTCGAAACGGGAATGT 59.657 47.619 0.00 0.00 0.00 2.71
2887 4997 5.519927 CAGACTTCACATGTCATACGCATAA 59.480 40.000 0.00 0.00 36.94 1.90
2891 5001 3.511699 TCAGACTTCACATGTCATACGC 58.488 45.455 0.00 0.00 36.94 4.42
2955 5065 4.021719 CACAACATTGAATTTGGCTCCTCT 60.022 41.667 0.00 0.00 0.00 3.69
2970 5080 4.391830 CGGTGCTATACAAGTCACAACATT 59.608 41.667 0.00 0.00 35.31 2.71
2974 5084 2.028476 AGCGGTGCTATACAAGTCACAA 60.028 45.455 0.00 0.00 36.99 3.33
2975 5085 1.548719 AGCGGTGCTATACAAGTCACA 59.451 47.619 0.00 0.00 36.99 3.58
3018 5160 4.394920 GTCTAATTTGGCGACTCAAATGGA 59.605 41.667 10.87 9.84 43.93 3.41
3030 6642 7.622048 GCAATTAAGCAGTTTGTCTAATTTGGC 60.622 37.037 0.00 0.00 0.00 4.52
3046 6658 1.715993 TACGCACGAGCAATTAAGCA 58.284 45.000 5.50 0.00 42.27 3.91


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

AutoCloner maintained by Alex Coulton.