Multiple sequence alignment - TraesCS6D01G053000

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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 TraesCS6D01G053000 chr6D 100.000 3689 0 0 1 3689 25617657 25613969 0.000000e+00 6813
1 TraesCS6D01G053000 chr6D 77.778 846 123 45 18 827 2689861 2690677 9.330000e-126 460
2 TraesCS6D01G053000 chr6B 93.978 2491 117 15 895 3374 41437070 41434602 0.000000e+00 3738
3 TraesCS6D01G053000 chr6B 97.386 306 8 0 3380 3685 41434508 41434203 4.220000e-144 521
4 TraesCS6D01G053000 chr6B 77.461 843 140 38 18 827 679680199 679679374 3.360000e-125 459
5 TraesCS6D01G053000 chr6B 78.251 423 69 16 41 451 633520496 633520085 2.200000e-62 250
6 TraesCS6D01G053000 chr6A 94.466 2367 115 8 881 3238 23604081 23601722 0.000000e+00 3631
7 TraesCS6D01G053000 chr6A 87.154 506 54 7 1 502 14156573 14157071 6.920000e-157 564
8 TraesCS6D01G053000 chr6A 95.666 323 14 0 3367 3689 23595641 23595319 1.520000e-143 520
9 TraesCS6D01G053000 chr6A 83.805 389 42 4 2860 3240 23595859 23595484 2.110000e-92 350
10 TraesCS6D01G053000 chr6A 95.172 145 1 2 3236 3374 23595861 23595717 1.330000e-54 224
11 TraesCS6D01G053000 chr7B 82.458 838 105 23 9 834 426109602 426110409 0.000000e+00 695
12 TraesCS6D01G053000 chr5A 82.168 572 87 13 39 601 444854780 444854215 9.270000e-131 477
13 TraesCS6D01G053000 chr3A 77.527 841 141 36 18 827 111960800 111961623 2.600000e-126 462
14 TraesCS6D01G053000 chr3A 77.645 501 83 13 339 825 357517913 357518398 1.010000e-70 278
15 TraesCS6D01G053000 chr2A 77.527 841 142 35 18 827 47877746 47876922 2.600000e-126 462
16 TraesCS6D01G053000 chr5D 79.564 367 67 8 2813 3175 552408526 552408888 4.730000e-64 255
17 TraesCS6D01G053000 chr5D 79.245 371 54 17 2887 3240 551545002 551544638 1.710000e-58 237
18 TraesCS6D01G053000 chr5D 77.128 376 68 15 2812 3178 551469009 551468643 6.250000e-48 202
19 TraesCS6D01G053000 chr5D 77.982 327 65 4 2822 3145 551408924 551408602 8.080000e-47 198
20 TraesCS6D01G053000 chr5D 77.879 330 61 9 2816 3139 542410371 542410048 1.050000e-45 195
21 TraesCS6D01G053000 chr7D 90.476 189 16 2 647 834 112055888 112055701 7.910000e-62 248
22 TraesCS6D01G053000 chr5B 82.917 240 14 8 1229 1468 125799171 125798959 1.350000e-44 191
23 TraesCS6D01G053000 chr4A 76.613 372 69 17 2813 3175 616662906 616663268 4.860000e-44 189


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 TraesCS6D01G053000 chr6D 25613969 25617657 3688 True 6813.000000 6813 100.000000 1 3689 1 chr6D.!!$R1 3688
1 TraesCS6D01G053000 chr6D 2689861 2690677 816 False 460.000000 460 77.778000 18 827 1 chr6D.!!$F1 809
2 TraesCS6D01G053000 chr6B 41434203 41437070 2867 True 2129.500000 3738 95.682000 895 3685 2 chr6B.!!$R3 2790
3 TraesCS6D01G053000 chr6B 679679374 679680199 825 True 459.000000 459 77.461000 18 827 1 chr6B.!!$R2 809
4 TraesCS6D01G053000 chr6A 23601722 23604081 2359 True 3631.000000 3631 94.466000 881 3238 1 chr6A.!!$R1 2357
5 TraesCS6D01G053000 chr6A 23595319 23595861 542 True 364.666667 520 91.547667 2860 3689 3 chr6A.!!$R2 829
6 TraesCS6D01G053000 chr7B 426109602 426110409 807 False 695.000000 695 82.458000 9 834 1 chr7B.!!$F1 825
7 TraesCS6D01G053000 chr5A 444854215 444854780 565 True 477.000000 477 82.168000 39 601 1 chr5A.!!$R1 562
8 TraesCS6D01G053000 chr3A 111960800 111961623 823 False 462.000000 462 77.527000 18 827 1 chr3A.!!$F1 809
9 TraesCS6D01G053000 chr2A 47876922 47877746 824 True 462.000000 462 77.527000 18 827 1 chr2A.!!$R1 809

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
282 308 0.603065 AATGCCAAGCGGGTTTCTTC 59.397 50.000 0.00 0.00 39.65 2.87 F
697 760 0.660488 GGGCTTTTTGCAAAAACCCG 59.340 50.000 34.33 26.01 45.15 5.28 F
701 764 1.090052 TTTTTGCAAAAACCCGGGCG 61.090 50.000 28.85 5.11 33.29 6.13 F
827 891 1.262151 GCACGACGAAGCCAAGTTTTA 59.738 47.619 0.00 0.00 0.00 1.52 F
1677 1745 1.273327 GTGATTGCTTTGGAAGGTGGG 59.727 52.381 0.00 0.00 0.00 4.61 F
2345 2419 0.036765 TACACGAGGGGTCACAATGC 60.037 55.000 0.00 0.00 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1703 0.842635 GCTCCCACATCCCATCTCTT 59.157 55.000 0.00 0.0 0.00 2.85 R
1788 1859 1.067212 CCCCTTCCATCTCGTCTTACG 59.933 57.143 0.00 0.0 44.19 3.18 R
1812 1883 1.225855 TAGTGCTTGCAGTTTCACCG 58.774 50.000 8.30 0.0 0.00 4.94 R
1940 2014 1.271127 GGGAGGCTTCCTTCTGCTCT 61.271 60.000 15.38 0.0 43.49 4.09 R
2516 2590 2.479730 GCGTTCATCACAGGACGAGTAT 60.480 50.000 0.00 0.0 37.69 2.12 R
3346 3428 2.618241 TCTGCAGCAAGAAAAACACGAT 59.382 40.909 9.47 0.0 0.00 3.73 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
31 32 3.697045 ACACCCAGTGTCGAAAAATTCAA 59.303 39.130 0.00 0.00 43.92 2.69
35 36 6.582295 CACCCAGTGTCGAAAAATTCAATTAG 59.418 38.462 0.00 0.00 0.00 1.73
36 37 6.488683 ACCCAGTGTCGAAAAATTCAATTAGA 59.511 34.615 0.00 0.00 0.00 2.10
44 45 8.618952 GTCGAAAAATTCAATTAGAAACTGTCG 58.381 33.333 0.00 0.00 40.22 4.35
131 153 4.392921 TGTACCCACAACCAATGTTTTG 57.607 40.909 0.00 0.00 41.46 2.44
135 157 3.454082 ACCCACAACCAATGTTTTGACAT 59.546 39.130 0.00 0.00 41.46 3.06
144 166 5.051816 CCAATGTTTTGACATGAGCAAACT 58.948 37.500 14.79 4.47 35.20 2.66
165 187 9.979270 CAAACTTGTTCTAATAATCTAGTGCAG 57.021 33.333 0.00 0.00 0.00 4.41
217 243 3.845781 TCAGTTCAGAAAACAGAGCCT 57.154 42.857 0.00 0.00 0.00 4.58
226 252 7.164230 TCAGAAAACAGAGCCTTTTTAAACA 57.836 32.000 0.00 0.00 0.00 2.83
268 294 1.945394 CCAGCACTACAGATGAATGCC 59.055 52.381 0.00 0.00 36.96 4.40
272 298 2.223433 GCACTACAGATGAATGCCAAGC 60.223 50.000 0.00 0.00 0.00 4.01
282 308 0.603065 AATGCCAAGCGGGTTTCTTC 59.397 50.000 0.00 0.00 39.65 2.87
286 312 1.953311 GCCAAGCGGGTTTCTTCCATA 60.953 52.381 0.00 0.00 39.65 2.74
378 406 8.068892 ACTGACAAAAACCCTAACATAAACAA 57.931 30.769 0.00 0.00 0.00 2.83
392 420 4.082136 ACATAAACAAGGGAGAGAGACGTC 60.082 45.833 7.70 7.70 0.00 4.34
476 518 2.511600 GGGCTCCATCGTTGTCGG 60.512 66.667 0.00 0.00 37.69 4.79
479 524 2.126071 CTCCATCGTTGTCGGCGT 60.126 61.111 6.85 0.00 37.69 5.68
490 551 4.137872 TCGGCGTCGTCCCAATCC 62.138 66.667 10.18 0.00 37.69 3.01
492 553 2.189521 GGCGTCGTCCCAATCCAT 59.810 61.111 0.00 0.00 0.00 3.41
497 558 2.124736 CGTCCCAATCCATGCCGT 60.125 61.111 0.00 0.00 0.00 5.68
529 590 2.404923 ACGATCGAGAGGAGAGACAA 57.595 50.000 24.34 0.00 0.00 3.18
605 666 3.882131 GCCATATGCGGGGTCATAT 57.118 52.632 0.00 0.00 39.51 1.78
608 669 1.009078 CATATGCGGGGTCATATGCG 58.991 55.000 9.83 0.00 45.09 4.73
609 670 0.744414 ATATGCGGGGTCATATGCGC 60.744 55.000 15.71 15.71 38.01 6.09
618 679 3.684788 GGGGTCATATGCGCATAACTTAG 59.315 47.826 32.02 19.02 0.00 2.18
619 680 3.684788 GGGTCATATGCGCATAACTTAGG 59.315 47.826 32.02 14.47 0.00 2.69
641 702 2.363147 ACACCTCTCCCGCCTCTC 60.363 66.667 0.00 0.00 0.00 3.20
645 706 2.043450 CTCTCCCGCCTCTCCAGT 60.043 66.667 0.00 0.00 0.00 4.00
681 744 5.891551 TGAGAAGTAAATAAATTCCAGGGGC 59.108 40.000 0.00 0.00 0.00 5.80
697 760 0.660488 GGGCTTTTTGCAAAAACCCG 59.340 50.000 34.33 26.01 45.15 5.28
701 764 1.090052 TTTTTGCAAAAACCCGGGCG 61.090 50.000 28.85 5.11 33.29 6.13
704 767 4.693525 GCAAAAACCCGGGCGACG 62.694 66.667 24.08 6.80 43.80 5.12
751 814 4.457496 CAGTGAGTCCCGCGCCAT 62.457 66.667 0.00 0.00 0.00 4.40
799 863 5.926214 TCGTATCCAAACGTGATTTTGAA 57.074 34.783 0.00 0.00 43.31 2.69
800 864 6.301687 TCGTATCCAAACGTGATTTTGAAA 57.698 33.333 0.00 0.00 43.31 2.69
802 866 5.059221 CGTATCCAAACGTGATTTTGAAAGC 59.941 40.000 0.00 0.00 38.54 3.51
805 869 5.355596 TCCAAACGTGATTTTGAAAGCATT 58.644 33.333 0.00 0.00 38.54 3.56
827 891 1.262151 GCACGACGAAGCCAAGTTTTA 59.738 47.619 0.00 0.00 0.00 1.52
828 892 2.661979 GCACGACGAAGCCAAGTTTTAG 60.662 50.000 0.00 0.00 0.00 1.85
834 898 2.034053 CGAAGCCAAGTTTTAGCACCAA 59.966 45.455 0.00 0.00 0.00 3.67
835 899 3.381045 GAAGCCAAGTTTTAGCACCAAC 58.619 45.455 0.00 0.00 0.00 3.77
836 900 2.666317 AGCCAAGTTTTAGCACCAACT 58.334 42.857 0.00 0.00 34.58 3.16
837 901 2.362077 AGCCAAGTTTTAGCACCAACTG 59.638 45.455 0.00 0.00 33.38 3.16
838 902 2.360801 GCCAAGTTTTAGCACCAACTGA 59.639 45.455 0.00 0.00 33.38 3.41
839 903 3.181480 GCCAAGTTTTAGCACCAACTGAA 60.181 43.478 0.00 0.00 33.38 3.02
840 904 4.501400 GCCAAGTTTTAGCACCAACTGAAT 60.501 41.667 0.00 0.00 33.38 2.57
841 905 5.600696 CCAAGTTTTAGCACCAACTGAATT 58.399 37.500 0.00 0.00 33.38 2.17
842 906 6.048509 CCAAGTTTTAGCACCAACTGAATTT 58.951 36.000 0.00 0.00 33.38 1.82
843 907 6.538381 CCAAGTTTTAGCACCAACTGAATTTT 59.462 34.615 0.00 0.00 33.38 1.82
844 908 7.254421 CCAAGTTTTAGCACCAACTGAATTTTC 60.254 37.037 0.00 0.00 33.38 2.29
845 909 7.112452 AGTTTTAGCACCAACTGAATTTTCT 57.888 32.000 0.00 0.00 31.80 2.52
846 910 7.555965 AGTTTTAGCACCAACTGAATTTTCTT 58.444 30.769 0.00 0.00 31.80 2.52
847 911 7.492344 AGTTTTAGCACCAACTGAATTTTCTTG 59.508 33.333 0.00 0.00 31.80 3.02
848 912 6.463995 TTAGCACCAACTGAATTTTCTTGT 57.536 33.333 0.00 0.00 0.00 3.16
849 913 4.936891 AGCACCAACTGAATTTTCTTGTC 58.063 39.130 0.00 0.00 0.00 3.18
850 914 4.402155 AGCACCAACTGAATTTTCTTGTCA 59.598 37.500 0.00 0.00 0.00 3.58
851 915 5.105392 AGCACCAACTGAATTTTCTTGTCAA 60.105 36.000 0.00 0.00 0.00 3.18
852 916 5.754890 GCACCAACTGAATTTTCTTGTCAAT 59.245 36.000 0.00 0.00 0.00 2.57
853 917 6.258507 GCACCAACTGAATTTTCTTGTCAATT 59.741 34.615 0.00 0.00 0.00 2.32
854 918 7.201635 GCACCAACTGAATTTTCTTGTCAATTT 60.202 33.333 0.00 0.00 0.00 1.82
855 919 8.667463 CACCAACTGAATTTTCTTGTCAATTTT 58.333 29.630 0.00 0.00 0.00 1.82
856 920 9.883142 ACCAACTGAATTTTCTTGTCAATTTTA 57.117 25.926 0.00 0.00 0.00 1.52
866 930 8.854979 TTTCTTGTCAATTTTAGACACATGTG 57.145 30.769 24.25 24.25 44.95 3.21
867 931 7.800155 TCTTGTCAATTTTAGACACATGTGA 57.200 32.000 31.94 9.05 44.95 3.58
868 932 8.394971 TCTTGTCAATTTTAGACACATGTGAT 57.605 30.769 31.94 20.75 44.95 3.06
869 933 8.291740 TCTTGTCAATTTTAGACACATGTGATG 58.708 33.333 31.94 15.30 44.95 3.07
870 934 7.509141 TGTCAATTTTAGACACATGTGATGT 57.491 32.000 31.94 16.97 46.22 3.06
871 935 8.614469 TGTCAATTTTAGACACATGTGATGTA 57.386 30.769 31.94 16.00 42.70 2.29
872 936 9.061435 TGTCAATTTTAGACACATGTGATGTAA 57.939 29.630 31.94 20.29 42.70 2.41
1069 1134 3.984186 CTCGGCCTCCCCTTCCTCA 62.984 68.421 0.00 0.00 0.00 3.86
1073 1138 1.920835 GCCTCCCCTTCCTCACACT 60.921 63.158 0.00 0.00 0.00 3.55
1620 1688 2.047274 GGTTACAGCGAGCCTGCA 60.047 61.111 0.24 0.00 45.78 4.41
1626 1694 3.630013 AGCGAGCCTGCAGTCCAA 61.630 61.111 13.81 0.00 37.31 3.53
1677 1745 1.273327 GTGATTGCTTTGGAAGGTGGG 59.727 52.381 0.00 0.00 0.00 4.61
1695 1763 2.092968 TGGGGATGAAGACAATTCGAGG 60.093 50.000 0.00 0.00 0.00 4.63
1743 1814 7.964604 TGATGATGCTATTTCTGATTCAGAG 57.035 36.000 15.59 6.41 41.75 3.35
1744 1815 7.732996 TGATGATGCTATTTCTGATTCAGAGA 58.267 34.615 15.59 12.38 41.75 3.10
1745 1816 8.208903 TGATGATGCTATTTCTGATTCAGAGAA 58.791 33.333 15.59 13.05 41.75 2.87
1759 1830 2.678836 TCAGAGAACGACGAAGAGGATC 59.321 50.000 0.00 0.00 0.00 3.36
1788 1859 1.276145 GACACCAACGACGAGCAGTC 61.276 60.000 0.00 2.66 46.16 3.51
1807 1878 2.022195 TCGTAAGACGAGATGGAAGGG 58.978 52.381 0.00 0.00 46.73 3.95
1812 1883 2.034048 GACGAGATGGAAGGGGGAGC 62.034 65.000 0.00 0.00 0.00 4.70
1860 1931 2.129555 GAAGTGAGAGGGGCAGGCAA 62.130 60.000 0.00 0.00 0.00 4.52
1940 2014 4.667573 AGATGGTCAGACAGAAGTAGTGA 58.332 43.478 2.17 0.00 0.00 3.41
2138 2212 2.613133 AGTGGAAGCTCTCGTACGATAC 59.387 50.000 19.87 11.08 0.00 2.24
2187 2261 3.574614 CGTTGGTGGTGAATTTGATTCC 58.425 45.455 0.00 0.00 38.50 3.01
2198 2272 7.153985 GGTGAATTTGATTCCAATTCAGACAA 58.846 34.615 20.36 2.48 38.50 3.18
2208 2282 4.017222 TCCAATTCAGACAATGGAAGGGAT 60.017 41.667 0.00 0.00 38.95 3.85
2230 2304 4.026744 TGACAAACTGGAACCAAAATGGA 58.973 39.130 2.85 0.00 40.96 3.41
2345 2419 0.036765 TACACGAGGGGTCACAATGC 60.037 55.000 0.00 0.00 0.00 3.56
2357 2431 2.165030 GTCACAATGCTGATGAAAGGGG 59.835 50.000 0.00 0.00 0.00 4.79
2458 2532 0.038251 TGGCAGCAGAGAGTACAACG 60.038 55.000 0.00 0.00 0.00 4.10
2586 2660 1.179174 CGAGGGGCGATGGATACTCA 61.179 60.000 0.00 0.00 44.57 3.41
2628 2702 1.519455 CAGCTCGATGGACCGGAAC 60.519 63.158 9.46 0.00 0.00 3.62
2731 2805 5.869888 AGTAAAGCTAATGTAGTCTGTGTGC 59.130 40.000 0.00 0.00 0.00 4.57
2742 2816 2.035449 AGTCTGTGTGCGTGCTAACTAA 59.965 45.455 0.00 0.00 0.00 2.24
2976 3052 8.095169 CCCTACTAATTTTATCTGGCTATCGTT 58.905 37.037 0.00 0.00 0.00 3.85
3230 3309 6.638610 TGTTTCCAAAATATTCGGCATCAAT 58.361 32.000 0.00 0.00 0.00 2.57
3247 3326 6.151648 GGCATCAATAACATACCATACTGCAT 59.848 38.462 0.00 0.00 0.00 3.96
3252 3331 6.686484 ATAACATACCATACTGCATCTCCA 57.314 37.500 0.00 0.00 0.00 3.86
3289 3368 2.350102 GGTAAGTTAACTTGCACGCACC 60.350 50.000 29.69 22.96 39.81 5.01
3297 3376 0.241749 CTTGCACGCACCACATGAAT 59.758 50.000 0.00 0.00 0.00 2.57
3299 3378 0.672889 TGCACGCACCACATGAATTT 59.327 45.000 0.00 0.00 0.00 1.82
3300 3379 1.335780 TGCACGCACCACATGAATTTC 60.336 47.619 0.00 0.00 0.00 2.17
3334 3416 9.159254 TCTACACATCATATGTTCTTCCCTAAT 57.841 33.333 1.90 0.00 42.70 1.73
3346 3428 5.725551 TCTTCCCTAATTTTATCTGCCCA 57.274 39.130 0.00 0.00 0.00 5.36
3349 3431 4.651778 TCCCTAATTTTATCTGCCCATCG 58.348 43.478 0.00 0.00 0.00 3.84
3374 3459 3.648339 TTTCTTGCTGCAGATTTGGAC 57.352 42.857 20.43 0.00 0.00 4.02
3375 3460 1.538047 TCTTGCTGCAGATTTGGACC 58.462 50.000 20.43 0.00 0.00 4.46
3392 3565 3.141272 TGGACCCAGTTTACCCTTGAAAT 59.859 43.478 0.00 0.00 0.00 2.17
3526 3699 2.095853 CGACATCAACAACATACCAGGC 59.904 50.000 0.00 0.00 0.00 4.85
3552 3725 9.552114 CAGTTGATCTGATTTTTAATCACTCAC 57.448 33.333 0.00 2.16 46.27 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.000815 CACTGGGTGTGCGTAAAGT 57.999 52.632 0.00 0.00 40.06 2.66
13 14 8.690840 GTTTCTAATTGAATTTTTCGACACTGG 58.309 33.333 0.00 0.00 34.24 4.00
16 17 9.233232 ACAGTTTCTAATTGAATTTTTCGACAC 57.767 29.630 0.00 0.00 34.24 3.67
35 36 8.507470 AGCTAATTGAATTTTTCGACAGTTTC 57.493 30.769 0.00 0.00 0.00 2.78
36 37 9.394477 GTAGCTAATTGAATTTTTCGACAGTTT 57.606 29.630 0.00 0.00 0.00 2.66
44 45 9.607285 TTTCGACAGTAGCTAATTGAATTTTTC 57.393 29.630 12.17 0.09 0.00 2.29
54 55 7.907214 ACTGAATTTTTCGACAGTAGCTAAT 57.093 32.000 0.00 0.00 40.96 1.73
131 153 9.495754 GATTATTAGAACAAGTTTGCTCATGTC 57.504 33.333 0.00 0.00 0.00 3.06
135 157 9.944376 ACTAGATTATTAGAACAAGTTTGCTCA 57.056 29.630 0.00 0.00 0.00 4.26
144 166 5.753438 CCGCTGCACTAGATTATTAGAACAA 59.247 40.000 0.00 0.00 0.00 2.83
162 184 0.671796 AAAAACTAACCACCCGCTGC 59.328 50.000 0.00 0.00 0.00 5.25
165 187 2.223745 TCTCAAAAACTAACCACCCGC 58.776 47.619 0.00 0.00 0.00 6.13
195 219 4.526970 AGGCTCTGTTTTCTGAACTGAAA 58.473 39.130 0.00 3.45 34.55 2.69
198 222 4.907879 AAAGGCTCTGTTTTCTGAACTG 57.092 40.909 0.00 0.00 0.00 3.16
200 224 7.544217 TGTTTAAAAAGGCTCTGTTTTCTGAAC 59.456 33.333 0.00 4.93 0.00 3.18
201 225 7.607250 TGTTTAAAAAGGCTCTGTTTTCTGAA 58.393 30.769 0.00 0.00 0.00 3.02
203 227 7.042523 CCATGTTTAAAAAGGCTCTGTTTTCTG 60.043 37.037 0.00 0.00 0.00 3.02
204 228 6.986231 CCATGTTTAAAAAGGCTCTGTTTTCT 59.014 34.615 0.00 0.00 0.00 2.52
268 294 2.287915 CGATATGGAAGAAACCCGCTTG 59.712 50.000 0.00 0.00 0.00 4.01
272 298 1.226746 GCCGATATGGAAGAAACCCG 58.773 55.000 0.00 0.00 42.00 5.28
282 308 4.566545 TGCTTGTTAAATGCCGATATGG 57.433 40.909 0.00 0.00 42.50 2.74
286 312 3.023119 TGGATGCTTGTTAAATGCCGAT 58.977 40.909 0.00 0.00 0.00 4.18
378 406 2.820479 CGCGACGTCTCTCTCCCT 60.820 66.667 14.70 0.00 0.00 4.20
392 420 0.924090 CCTCGATTTTTCTCTCCGCG 59.076 55.000 0.00 0.00 0.00 6.46
471 513 3.636313 GATTGGGACGACGCCGACA 62.636 63.158 0.00 0.00 39.50 4.35
476 518 2.823829 GCATGGATTGGGACGACGC 61.824 63.158 0.00 0.00 0.00 5.19
479 524 2.189257 CGGCATGGATTGGGACGA 59.811 61.111 0.00 0.00 0.00 4.20
507 568 1.600485 GTCTCTCCTCTCGATCGTTCC 59.400 57.143 15.94 0.00 0.00 3.62
529 590 1.316706 CGCCTCGAGTTCTCCTCCTT 61.317 60.000 12.31 0.00 36.82 3.36
605 666 0.035915 TGGCACCTAAGTTATGCGCA 60.036 50.000 14.96 14.96 40.37 6.09
606 667 0.377203 GTGGCACCTAAGTTATGCGC 59.623 55.000 6.29 0.00 40.37 6.09
607 668 1.396996 GTGTGGCACCTAAGTTATGCG 59.603 52.381 16.26 0.00 40.37 4.73
654 715 7.396055 CCCCTGGAATTTATTTACTTCTCACAA 59.604 37.037 0.00 0.00 0.00 3.33
663 724 6.093495 GCAAAAAGCCCCTGGAATTTATTTAC 59.907 38.462 0.00 0.00 37.23 2.01
668 729 2.975489 TGCAAAAAGCCCCTGGAATTTA 59.025 40.909 0.00 0.00 44.83 1.40
681 744 0.660488 GCCCGGGTTTTTGCAAAAAG 59.340 50.000 32.09 22.15 38.44 2.27
715 778 4.624364 CAGTGGCTGGACCGTGCA 62.624 66.667 10.78 0.00 43.94 4.57
766 829 0.249120 TGGATACGAACTGGTGCTGG 59.751 55.000 0.00 0.00 42.51 4.85
799 863 0.385974 GCTTCGTCGTGCAAATGCTT 60.386 50.000 6.97 0.00 42.66 3.91
800 864 1.207593 GCTTCGTCGTGCAAATGCT 59.792 52.632 6.97 0.00 42.66 3.79
802 866 0.040514 TTGGCTTCGTCGTGCAAATG 60.041 50.000 13.03 0.00 0.00 2.32
805 869 1.092921 AACTTGGCTTCGTCGTGCAA 61.093 50.000 13.03 1.60 0.00 4.08
827 891 4.402155 TGACAAGAAAATTCAGTTGGTGCT 59.598 37.500 0.00 0.00 0.00 4.40
828 892 4.681744 TGACAAGAAAATTCAGTTGGTGC 58.318 39.130 0.00 0.00 0.00 5.01
840 904 9.299963 CACATGTGTCTAAAATTGACAAGAAAA 57.700 29.630 18.03 0.00 44.63 2.29
841 905 8.681806 TCACATGTGTCTAAAATTGACAAGAAA 58.318 29.630 24.63 0.00 44.63 2.52
842 906 8.219546 TCACATGTGTCTAAAATTGACAAGAA 57.780 30.769 24.63 0.00 44.63 2.52
843 907 7.800155 TCACATGTGTCTAAAATTGACAAGA 57.200 32.000 24.63 0.00 44.63 3.02
844 908 8.077991 ACATCACATGTGTCTAAAATTGACAAG 58.922 33.333 24.63 1.30 44.63 3.16
845 909 7.939782 ACATCACATGTGTCTAAAATTGACAA 58.060 30.769 24.63 1.15 44.63 3.18
846 910 7.509141 ACATCACATGTGTCTAAAATTGACA 57.491 32.000 24.63 1.60 43.01 3.58
854 918 9.447157 TGAATCAATTACATCACATGTGTCTAA 57.553 29.630 24.63 17.17 44.60 2.10
855 919 9.447157 TTGAATCAATTACATCACATGTGTCTA 57.553 29.630 24.63 6.96 44.60 2.59
856 920 7.926674 TGAATCAATTACATCACATGTGTCT 57.073 32.000 24.63 11.33 44.60 3.41
857 921 8.969121 TTTGAATCAATTACATCACATGTGTC 57.031 30.769 24.63 11.07 44.60 3.67
858 922 8.795513 TCTTTGAATCAATTACATCACATGTGT 58.204 29.630 24.63 9.13 44.60 3.72
859 923 9.628746 TTCTTTGAATCAATTACATCACATGTG 57.371 29.630 20.18 20.18 44.60 3.21
864 928 9.993881 CGTTTTTCTTTGAATCAATTACATCAC 57.006 29.630 0.00 0.00 0.00 3.06
865 929 9.743057 ACGTTTTTCTTTGAATCAATTACATCA 57.257 25.926 0.00 0.00 0.00 3.07
868 932 8.812329 CCAACGTTTTTCTTTGAATCAATTACA 58.188 29.630 0.00 0.00 0.00 2.41
869 933 9.026074 TCCAACGTTTTTCTTTGAATCAATTAC 57.974 29.630 0.00 0.00 0.00 1.89
870 934 9.587772 TTCCAACGTTTTTCTTTGAATCAATTA 57.412 25.926 0.00 0.00 0.00 1.40
871 935 8.485976 TTCCAACGTTTTTCTTTGAATCAATT 57.514 26.923 0.00 0.00 0.00 2.32
872 936 8.485976 TTTCCAACGTTTTTCTTTGAATCAAT 57.514 26.923 0.00 0.00 0.00 2.57
873 937 7.891183 TTTCCAACGTTTTTCTTTGAATCAA 57.109 28.000 0.00 0.00 0.00 2.57
874 938 7.412455 GCTTTTCCAACGTTTTTCTTTGAATCA 60.412 33.333 0.00 0.00 0.00 2.57
875 939 6.899771 GCTTTTCCAACGTTTTTCTTTGAATC 59.100 34.615 0.00 0.00 0.00 2.52
876 940 6.454981 CGCTTTTCCAACGTTTTTCTTTGAAT 60.455 34.615 0.00 0.00 0.00 2.57
877 941 5.164041 CGCTTTTCCAACGTTTTTCTTTGAA 60.164 36.000 0.00 0.00 0.00 2.69
878 942 4.324936 CGCTTTTCCAACGTTTTTCTTTGA 59.675 37.500 0.00 0.00 0.00 2.69
879 943 4.564281 CGCTTTTCCAACGTTTTTCTTTG 58.436 39.130 0.00 0.00 0.00 2.77
1576 1641 1.450312 CCTCCACAGCGTCATTCCC 60.450 63.158 0.00 0.00 0.00 3.97
1626 1694 3.784763 ACATCCCATCTCTTTCCATCAGT 59.215 43.478 0.00 0.00 0.00 3.41
1635 1703 0.842635 GCTCCCACATCCCATCTCTT 59.157 55.000 0.00 0.00 0.00 2.85
1638 1706 2.446848 CGGCTCCCACATCCCATCT 61.447 63.158 0.00 0.00 0.00 2.90
1677 1745 3.198872 GACCCTCGAATTGTCTTCATCC 58.801 50.000 0.00 0.00 0.00 3.51
1695 1763 3.634397 TCATGAATCCAACTCCTGACC 57.366 47.619 0.00 0.00 0.00 4.02
1743 1814 3.489180 TCAAGATCCTCTTCGTCGTTC 57.511 47.619 0.00 0.00 33.78 3.95
1744 1815 4.457834 AATCAAGATCCTCTTCGTCGTT 57.542 40.909 0.00 0.00 33.78 3.85
1745 1816 4.457834 AAATCAAGATCCTCTTCGTCGT 57.542 40.909 0.00 0.00 33.78 4.34
1759 1830 3.628017 GTCGTTGGTGTCCAAAATCAAG 58.372 45.455 2.65 0.00 45.73 3.02
1770 1841 1.299926 GACTGCTCGTCGTTGGTGT 60.300 57.895 0.00 0.00 32.04 4.16
1788 1859 1.067212 CCCCTTCCATCTCGTCTTACG 59.933 57.143 0.00 0.00 44.19 3.18
1807 1878 1.856265 CTTGCAGTTTCACCGCTCCC 61.856 60.000 0.00 0.00 0.00 4.30
1812 1883 1.225855 TAGTGCTTGCAGTTTCACCG 58.774 50.000 8.30 0.00 0.00 4.94
1860 1931 2.277008 AGGAACCATGACCTCTCCAT 57.723 50.000 0.00 0.00 0.00 3.41
1940 2014 1.271127 GGGAGGCTTCCTTCTGCTCT 61.271 60.000 15.38 0.00 43.49 4.09
2025 2099 3.420397 CGACTCGGAGAAAGAACCC 57.580 57.895 12.86 0.00 34.09 4.11
2138 2212 1.965935 TCGTATCACATTGCCATGGG 58.034 50.000 15.13 0.00 34.72 4.00
2187 2261 4.951715 TCATCCCTTCCATTGTCTGAATTG 59.048 41.667 0.00 0.00 0.00 2.32
2198 2272 2.649312 TCCAGTTTGTCATCCCTTCCAT 59.351 45.455 0.00 0.00 0.00 3.41
2208 2282 4.026744 TCCATTTTGGTTCCAGTTTGTCA 58.973 39.130 0.00 0.00 39.03 3.58
2230 2304 1.499870 ACTAGACCTATTCGGGGCTCT 59.500 52.381 0.00 0.00 41.78 4.09
2345 2419 3.834231 ACCAAATTGACCCCTTTCATCAG 59.166 43.478 0.00 0.00 0.00 2.90
2357 2431 2.729360 GCAAAGCCGTTACCAAATTGAC 59.271 45.455 0.00 0.00 0.00 3.18
2458 2532 8.207545 ACTCCTGAATCTACTTTTCATATCACC 58.792 37.037 0.00 0.00 32.94 4.02
2514 2588 4.732647 GCGTTCATCACAGGACGAGTATTA 60.733 45.833 0.00 0.00 37.69 0.98
2516 2590 2.479730 GCGTTCATCACAGGACGAGTAT 60.480 50.000 0.00 0.00 37.69 2.12
2574 2648 2.876550 TGGTCGTAGTGAGTATCCATCG 59.123 50.000 0.00 0.00 0.00 3.84
2586 2660 3.259064 CAATTCCGATGTTGGTCGTAGT 58.741 45.455 0.00 0.00 39.89 2.73
2628 2702 2.824041 CTGAATTGCCGTCCCCCG 60.824 66.667 0.00 0.00 0.00 5.73
2640 2714 5.144100 AGTGAATATCCGTCTCCTCTGAAT 58.856 41.667 0.00 0.00 0.00 2.57
2731 2805 5.459107 GTCTGGTCATACATTAGTTAGCACG 59.541 44.000 0.00 0.00 0.00 5.34
2903 2979 6.150641 GCAGAAGATATTCATGTGGTGCATAT 59.849 38.462 2.42 0.00 35.74 1.78
2976 3052 5.508489 CCAAATCTGCAGCAAGAAGAAGAAA 60.508 40.000 9.47 0.00 34.86 2.52
2979 3055 3.504906 TCCAAATCTGCAGCAAGAAGAAG 59.495 43.478 9.47 0.00 34.86 2.85
3181 3260 4.202202 GCCATACTAGAATGAGTCACAGCT 60.202 45.833 0.00 0.00 0.00 4.24
3230 3309 5.602561 ACTGGAGATGCAGTATGGTATGTTA 59.397 40.000 5.07 0.00 35.86 2.41
3247 3326 3.321682 CCATTTGGCAGAAAAACTGGAGA 59.678 43.478 0.00 0.00 45.82 3.71
3252 3331 5.869649 ACTTACCATTTGGCAGAAAAACT 57.130 34.783 0.00 0.00 39.32 2.66
3289 3368 6.965500 GTGTAGATGCAGAAGAAATTCATGTG 59.035 38.462 0.00 0.00 0.00 3.21
3297 3376 7.989170 ACATATGATGTGTAGATGCAGAAGAAA 59.011 33.333 10.38 0.00 43.01 2.52
3299 3378 7.059202 ACATATGATGTGTAGATGCAGAAGA 57.941 36.000 10.38 0.00 43.01 2.87
3300 3379 7.656542 AGAACATATGATGTGTAGATGCAGAAG 59.343 37.037 10.38 0.00 44.07 2.85
3334 3416 5.242838 AGAAAAACACGATGGGCAGATAAAA 59.757 36.000 0.00 0.00 0.00 1.52
3343 3425 2.664916 CAGCAAGAAAAACACGATGGG 58.335 47.619 0.00 0.00 0.00 4.00
3346 3428 2.618241 TCTGCAGCAAGAAAAACACGAT 59.382 40.909 9.47 0.00 0.00 3.73
3349 3431 4.025480 CCAAATCTGCAGCAAGAAAAACAC 60.025 41.667 9.47 0.00 0.00 3.32
3374 3459 3.323403 TGCAATTTCAAGGGTAAACTGGG 59.677 43.478 0.00 0.00 0.00 4.45
3375 3460 4.039124 AGTGCAATTTCAAGGGTAAACTGG 59.961 41.667 0.00 0.00 0.00 4.00
3392 3565 5.652014 CCAAAATTCTACAGGGATAGTGCAA 59.348 40.000 0.00 0.00 0.00 4.08
3450 3623 3.056250 TCACAGCCTCTGAGATTCTGAAC 60.056 47.826 20.30 0.00 35.18 3.18
3459 3632 4.734398 AGAATAAGTCACAGCCTCTGAG 57.266 45.455 0.00 0.00 35.18 3.35
3526 3699 9.552114 GTGAGTGATTAAAAATCAGATCAACTG 57.448 33.333 14.40 0.00 46.97 3.16


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

AutoCloner maintained by Alex Coulton.