Multiple sequence alignment - TraesCS4A01G410400

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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 TraesCS4A01G410400 chr4A 100.000 3329 0 0 1 3329 683497536 683494208 0.000000e+00 6148
1 TraesCS4A01G410400 chr4A 97.920 721 15 0 1 721 58351932 58351212 0.000000e+00 1249
2 TraesCS4A01G410400 chr4D 89.060 2669 173 48 722 3329 476314286 476311676 0.000000e+00 3201
3 TraesCS4A01G410400 chr4B 87.439 2683 196 64 722 3324 600669379 600666758 0.000000e+00 2957
4 TraesCS4A01G410400 chr4B 84.821 112 17 0 1590 1701 67880717 67880606 2.710000e-21 113
5 TraesCS4A01G410400 chr1A 97.781 721 16 0 1 721 334158955 334159675 0.000000e+00 1243
6 TraesCS4A01G410400 chr6D 97.087 721 21 0 1 721 450090146 450090866 0.000000e+00 1216
7 TraesCS4A01G410400 chr6B 94.875 722 36 1 1 721 348697893 348697172 0.000000e+00 1127
8 TraesCS4A01G410400 chr7B 94.591 721 32 2 1 721 99628269 99627556 0.000000e+00 1109
9 TraesCS4A01G410400 chr1B 88.421 95 11 0 1581 1675 105205110 105205016 7.550000e-22 115


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 TraesCS4A01G410400 chr4A 683494208 683497536 3328 True 6148 6148 100.000 1 3329 1 chr4A.!!$R2 3328
1 TraesCS4A01G410400 chr4A 58351212 58351932 720 True 1249 1249 97.920 1 721 1 chr4A.!!$R1 720
2 TraesCS4A01G410400 chr4D 476311676 476314286 2610 True 3201 3201 89.060 722 3329 1 chr4D.!!$R1 2607
3 TraesCS4A01G410400 chr4B 600666758 600669379 2621 True 2957 2957 87.439 722 3324 1 chr4B.!!$R2 2602
4 TraesCS4A01G410400 chr1A 334158955 334159675 720 False 1243 1243 97.781 1 721 1 chr1A.!!$F1 720
5 TraesCS4A01G410400 chr6D 450090146 450090866 720 False 1216 1216 97.087 1 721 1 chr6D.!!$F1 720
6 TraesCS4A01G410400 chr6B 348697172 348697893 721 True 1127 1127 94.875 1 721 1 chr6B.!!$R1 720
7 TraesCS4A01G410400 chr7B 99627556 99628269 713 True 1109 1109 94.591 1 721 1 chr7B.!!$R1 720

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
985 1014 0.249489 CCACTCCCATTCGACCGATC 60.249 60.0 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
2380 2418 0.462759 GCCTACAATCGAAGCTGCCT 60.463 55.0 0.0 0.0 0.0 4.75 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
48 49 2.364579 CAATGCACCCCCAGCCAT 60.365 61.111 0.00 0.00 0.00 4.40
55 56 1.230149 ACCCCCAGCCATCAGGTTA 60.230 57.895 0.00 0.00 37.19 2.85
175 177 2.106566 TGCATTGTATTCCCGCCATTT 58.893 42.857 0.00 0.00 0.00 2.32
317 319 3.287867 TCCTCGGGTATACGAAAGAGT 57.712 47.619 0.00 0.00 42.98 3.24
441 443 3.846405 AAGTGCCCTCCGTCCTCCA 62.846 63.158 0.00 0.00 0.00 3.86
512 514 1.646540 CACGTTTCGCAGCAAAGGA 59.353 52.632 13.47 0.00 0.00 3.36
687 689 2.529632 TCCTATATGCTGAGCGGACAT 58.470 47.619 0.00 0.00 0.00 3.06
746 748 6.502136 TGTTTTTGATATGGCGTGATACAA 57.498 33.333 0.00 0.00 0.00 2.41
747 749 6.914259 TGTTTTTGATATGGCGTGATACAAA 58.086 32.000 0.00 0.00 0.00 2.83
762 764 8.368126 GCGTGATACAAATCTTTCTCAAAATTG 58.632 33.333 0.00 0.00 32.93 2.32
830 845 5.021033 TCACGGCGTAGGGATTTTTATTA 57.979 39.130 14.22 0.00 0.00 0.98
836 851 7.148035 ACGGCGTAGGGATTTTTATTACAAAAT 60.148 33.333 12.58 0.00 38.75 1.82
850 865 0.429363 CAAAATCACGAAAACGCGCC 59.571 50.000 5.73 0.00 33.86 6.53
887 902 1.143401 GCTGGGGTCGGTAAGTAGC 59.857 63.158 0.00 0.00 0.00 3.58
906 921 2.125673 CTACTGGCACGAACCGGG 60.126 66.667 6.32 0.00 40.73 5.73
948 977 2.280524 CTGAACGCGAACCCACCA 60.281 61.111 15.93 0.00 0.00 4.17
980 1009 1.559065 TTCCCCCACTCCCATTCGAC 61.559 60.000 0.00 0.00 0.00 4.20
983 1012 2.355986 CCCACTCCCATTCGACCGA 61.356 63.158 0.00 0.00 0.00 4.69
984 1013 1.686325 CCCACTCCCATTCGACCGAT 61.686 60.000 0.00 0.00 0.00 4.18
985 1014 0.249489 CCACTCCCATTCGACCGATC 60.249 60.000 0.00 0.00 0.00 3.69
1362 1394 3.854669 CCTCCGGCGGCTTCTGAT 61.855 66.667 23.83 0.00 0.00 2.90
1382 1414 3.622826 CGTCCAGGAACCACCGGT 61.623 66.667 0.00 0.00 44.74 5.28
1710 1742 2.047844 CAGGTGACCGCACTCCTG 60.048 66.667 11.57 11.57 44.52 3.86
1781 1813 2.680352 GTGGAGGCTGGACCGAGA 60.680 66.667 0.00 0.00 46.52 4.04
1782 1814 2.680352 TGGAGGCTGGACCGAGAC 60.680 66.667 0.00 0.00 46.52 3.36
1784 1816 2.680352 GAGGCTGGACCGAGACCA 60.680 66.667 0.00 0.00 46.52 4.02
1872 1904 2.756283 AAGGGCGCGCTCTACTCT 60.756 61.111 37.08 16.97 0.00 3.24
1875 1907 3.827898 GGCGCGCTCTACTCTGGT 61.828 66.667 32.29 0.00 0.00 4.00
1879 1911 2.878429 CGCTCTACTCTGGTGCGT 59.122 61.111 0.00 0.00 40.32 5.24
2082 2117 4.379174 GTGCACTACACCCACAGG 57.621 61.111 10.32 0.00 44.02 4.00
2208 2243 1.566018 CGTCGTTCAAACCCAGAGGC 61.566 60.000 0.00 0.00 36.11 4.70
2342 2380 5.448654 TGCAGCCTGAATTATTCATTAGGT 58.551 37.500 8.17 3.79 39.30 3.08
2344 2382 5.766222 CAGCCTGAATTATTCATTAGGTGC 58.234 41.667 8.17 5.20 39.30 5.01
2345 2383 5.300034 CAGCCTGAATTATTCATTAGGTGCA 59.700 40.000 8.17 0.00 39.30 4.57
2346 2384 5.300286 AGCCTGAATTATTCATTAGGTGCAC 59.700 40.000 8.80 8.80 39.30 4.57
2350 2388 6.186957 TGAATTATTCATTAGGTGCACCACT 58.813 36.000 36.39 20.32 34.71 4.00
2363 2401 1.529244 ACCACTGGCCTCTGCAAAC 60.529 57.895 3.32 0.00 40.13 2.93
2365 2403 2.281761 ACTGGCCTCTGCAAACCG 60.282 61.111 3.32 0.00 40.13 4.44
2367 2405 2.281484 TGGCCTCTGCAAACCGAC 60.281 61.111 3.32 0.00 40.13 4.79
2369 2407 3.056328 GCCTCTGCAAACCGACCC 61.056 66.667 0.00 0.00 37.47 4.46
2426 2482 4.716784 TGAGCAATCAGTAGGATACCAGTT 59.283 41.667 0.00 0.00 44.47 3.16
2433 2489 5.977635 TCAGTAGGATACCAGTTCAATGTG 58.022 41.667 0.00 0.00 44.47 3.21
2459 2515 2.711542 ACCAGTGGCAATGCTTAGTAC 58.288 47.619 9.78 0.00 0.00 2.73
2460 2516 2.305927 ACCAGTGGCAATGCTTAGTACT 59.694 45.455 9.78 0.00 0.00 2.73
2461 2517 2.939103 CCAGTGGCAATGCTTAGTACTC 59.061 50.000 9.87 0.00 0.00 2.59
2462 2518 2.939103 CAGTGGCAATGCTTAGTACTCC 59.061 50.000 4.82 0.00 0.00 3.85
2463 2519 2.571653 AGTGGCAATGCTTAGTACTCCA 59.428 45.455 4.82 0.00 0.00 3.86
2527 2583 7.161404 ACTGCAATCACTTCATTCTTACTGTA 58.839 34.615 0.00 0.00 0.00 2.74
2528 2584 7.118390 ACTGCAATCACTTCATTCTTACTGTAC 59.882 37.037 0.00 0.00 0.00 2.90
2529 2585 7.161404 TGCAATCACTTCATTCTTACTGTACT 58.839 34.615 0.00 0.00 0.00 2.73
2530 2586 7.661437 TGCAATCACTTCATTCTTACTGTACTT 59.339 33.333 0.00 0.00 0.00 2.24
2531 2587 7.959651 GCAATCACTTCATTCTTACTGTACTTG 59.040 37.037 0.00 0.00 0.00 3.16
2532 2588 8.993121 CAATCACTTCATTCTTACTGTACTTGT 58.007 33.333 0.00 0.00 0.00 3.16
2533 2589 8.764524 ATCACTTCATTCTTACTGTACTTGTC 57.235 34.615 0.00 0.00 0.00 3.18
2534 2590 7.722363 TCACTTCATTCTTACTGTACTTGTCA 58.278 34.615 0.00 0.00 0.00 3.58
2535 2591 7.652105 TCACTTCATTCTTACTGTACTTGTCAC 59.348 37.037 0.00 0.00 0.00 3.67
2536 2592 7.438160 CACTTCATTCTTACTGTACTTGTCACA 59.562 37.037 0.00 0.00 0.00 3.58
2544 2600 5.499139 ACTGTACTTGTCACAAAACCATG 57.501 39.130 0.00 0.00 0.00 3.66
2561 2617 4.836825 ACCATGTCTCAGATGTTAACAGG 58.163 43.478 14.65 7.91 0.00 4.00
2564 2620 5.105187 CCATGTCTCAGATGTTAACAGGAGA 60.105 44.000 23.08 23.08 32.67 3.71
2567 2623 5.304357 TGTCTCAGATGTTAACAGGAGAACA 59.696 40.000 26.12 22.91 39.74 3.18
2570 2626 7.226720 GTCTCAGATGTTAACAGGAGAACAAAA 59.773 37.037 26.12 10.83 38.94 2.44
2571 2627 7.939039 TCTCAGATGTTAACAGGAGAACAAAAT 59.061 33.333 23.98 3.09 38.94 1.82
2572 2628 7.874940 TCAGATGTTAACAGGAGAACAAAATG 58.125 34.615 14.65 0.04 38.94 2.32
2573 2629 6.583806 CAGATGTTAACAGGAGAACAAAATGC 59.416 38.462 14.65 0.00 38.94 3.56
2574 2630 4.854399 TGTTAACAGGAGAACAAAATGCG 58.146 39.130 3.59 0.00 32.74 4.73
2576 2632 5.066634 TGTTAACAGGAGAACAAAATGCGAA 59.933 36.000 3.59 0.00 32.74 4.70
2578 2634 2.554032 ACAGGAGAACAAAATGCGAAGG 59.446 45.455 0.00 0.00 0.00 3.46
2579 2635 2.554032 CAGGAGAACAAAATGCGAAGGT 59.446 45.455 0.00 0.00 0.00 3.50
2587 2655 4.119136 ACAAAATGCGAAGGTTTTTCAGG 58.881 39.130 0.00 0.00 0.00 3.86
2591 2659 4.871933 ATGCGAAGGTTTTTCAGGATTT 57.128 36.364 0.00 0.00 0.00 2.17
2600 2668 6.701340 AGGTTTTTCAGGATTTTTATCTGCC 58.299 36.000 0.00 0.00 0.00 4.85
2603 2674 7.064966 GGTTTTTCAGGATTTTTATCTGCCATG 59.935 37.037 0.00 0.00 0.00 3.66
2618 2689 1.135199 GCCATGTCAAAGGAGCACATG 60.135 52.381 4.59 4.59 44.73 3.21
2642 2713 3.888934 GCAGAACGCATCAAGAAAAAGA 58.111 40.909 0.00 0.00 41.79 2.52
2659 2730 2.071778 AGACTGGCAAGGAAGCAAAA 57.928 45.000 0.00 0.00 35.83 2.44
2666 2737 2.360801 GGCAAGGAAGCAAAACTACACA 59.639 45.455 0.00 0.00 35.83 3.72
2667 2738 3.372060 GCAAGGAAGCAAAACTACACAC 58.628 45.455 0.00 0.00 0.00 3.82
2677 2748 5.065218 AGCAAAACTACACACTCTTGACAAG 59.935 40.000 9.03 9.03 0.00 3.16
2691 2762 5.123227 TCTTGACAAGTCCAGAAACGAATT 58.877 37.500 14.75 0.00 29.71 2.17
2693 2764 5.418310 TGACAAGTCCAGAAACGAATTTC 57.582 39.130 0.00 0.00 44.02 2.17
2701 2772 3.374058 CCAGAAACGAATTTCCATACGCT 59.626 43.478 0.00 0.00 44.66 5.07
2714 2785 2.431057 CCATACGCTAAGGAAGTCTGGT 59.569 50.000 0.00 0.00 30.47 4.00
2742 2813 9.528018 CTAAGGTTTTTACTGATCATCTCTCTC 57.472 37.037 0.00 0.00 0.00 3.20
2743 2814 7.732222 AGGTTTTTACTGATCATCTCTCTCT 57.268 36.000 0.00 0.00 0.00 3.10
2744 2815 7.781056 AGGTTTTTACTGATCATCTCTCTCTC 58.219 38.462 0.00 0.00 0.00 3.20
2745 2816 7.619302 AGGTTTTTACTGATCATCTCTCTCTCT 59.381 37.037 0.00 0.00 0.00 3.10
2746 2817 7.920682 GGTTTTTACTGATCATCTCTCTCTCTC 59.079 40.741 0.00 0.00 0.00 3.20
2747 2818 8.686334 GTTTTTACTGATCATCTCTCTCTCTCT 58.314 37.037 0.00 0.00 0.00 3.10
2748 2819 8.450578 TTTTACTGATCATCTCTCTCTCTCTC 57.549 38.462 0.00 0.00 0.00 3.20
2749 2820 5.901413 ACTGATCATCTCTCTCTCTCTCT 57.099 43.478 0.00 0.00 0.00 3.10
2750 2821 5.862845 ACTGATCATCTCTCTCTCTCTCTC 58.137 45.833 0.00 0.00 0.00 3.20
2751 2822 5.605908 ACTGATCATCTCTCTCTCTCTCTCT 59.394 44.000 0.00 0.00 0.00 3.10
2761 2832 3.202151 TCTCTCTCTCTCTTTCTCTCCCC 59.798 52.174 0.00 0.00 0.00 4.81
2790 2861 0.326264 CCTAGTGCTTGGGCTTCACT 59.674 55.000 0.00 0.00 42.89 3.41
2838 2909 0.179100 CTGATGCGTCGAGGATTGGT 60.179 55.000 9.75 0.00 0.00 3.67
2841 2912 1.899437 ATGCGTCGAGGATTGGTGGT 61.899 55.000 9.75 0.00 0.00 4.16
3049 3156 6.240894 TGAGAAATGATGTAACCAAAGCTCT 58.759 36.000 0.00 0.00 0.00 4.09
3050 3157 6.149973 TGAGAAATGATGTAACCAAAGCTCTG 59.850 38.462 0.00 0.00 0.00 3.35
3056 3163 7.418337 TGATGTAACCAAAGCTCTGATAGTA 57.582 36.000 0.00 0.00 0.00 1.82
3073 3180 8.129840 TCTGATAGTAAAGAGATAAACTGTCGC 58.870 37.037 0.00 0.00 34.07 5.19
3080 3188 5.189659 AGAGATAAACTGTCGCTGGTATC 57.810 43.478 0.00 0.00 0.00 2.24
3087 3195 8.677148 ATAAACTGTCGCTGGTATCAATAATT 57.323 30.769 0.00 0.00 0.00 1.40
3088 3196 7.391148 AAACTGTCGCTGGTATCAATAATTT 57.609 32.000 0.00 0.00 0.00 1.82
3108 3216 5.567138 TTTATTCTAAAGAGCAGCTTGGC 57.433 39.130 0.00 0.00 36.80 4.52
3112 3223 1.577328 TAAAGAGCAGCTTGGCGCAC 61.577 55.000 10.83 0.00 42.61 5.34
3113 3224 4.631247 AGAGCAGCTTGGCGCACA 62.631 61.111 10.83 1.22 42.61 4.57
3127 3238 1.552226 CGCACATGCACAAATGATCC 58.448 50.000 4.49 0.00 42.21 3.36
3185 3296 3.740631 TGTGCCAGCTATAGACTCATG 57.259 47.619 3.21 0.00 0.00 3.07
3220 3332 8.854614 ACACTTGAATATTACAGAGAAAAGCT 57.145 30.769 0.00 0.00 0.00 3.74
3230 3342 5.165961 ACAGAGAAAAGCTATGCAGGTAA 57.834 39.130 0.00 0.00 39.44 2.85
3313 3426 1.089920 CAATGTGTCCAGCTAGCCAC 58.910 55.000 12.13 12.74 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 0.253160 AGGGGCCTGTCATAACCTGA 60.253 55.000 0.84 0.00 0.00 3.86
55 56 1.002857 AGCTTTTAGGGGCCTGTCAT 58.997 50.000 0.84 0.00 0.00 3.06
175 177 5.773176 TCTTCAGTTACCAGACATGTCACTA 59.227 40.000 27.02 10.32 0.00 2.74
441 443 2.046892 GGTGTGCCATCGTCTGCT 60.047 61.111 0.00 0.00 34.09 4.24
687 689 5.550403 AGTTTGACAGGAAGGGGTTATTCTA 59.450 40.000 0.00 0.00 0.00 2.10
737 739 9.611284 TCAATTTTGAGAAAGATTTGTATCACG 57.389 29.630 0.00 0.00 31.39 4.35
799 801 4.070716 TCCCTACGCCGTGAAATTAAAAA 58.929 39.130 0.00 0.00 0.00 1.94
800 802 3.672808 TCCCTACGCCGTGAAATTAAAA 58.327 40.909 0.00 0.00 0.00 1.52
801 803 3.331478 TCCCTACGCCGTGAAATTAAA 57.669 42.857 0.00 0.00 0.00 1.52
874 889 2.098770 CCAGTAGTGCTACTTACCGACC 59.901 54.545 8.98 0.00 43.35 4.79
887 902 1.736645 CCGGTTCGTGCCAGTAGTG 60.737 63.158 0.00 0.00 0.00 2.74
911 926 2.428890 AGCTATATGTAGATCGGCAGCC 59.571 50.000 0.00 0.00 0.00 4.85
912 927 3.129462 TCAGCTATATGTAGATCGGCAGC 59.871 47.826 0.00 0.00 0.00 5.25
913 928 4.972514 TCAGCTATATGTAGATCGGCAG 57.027 45.455 0.00 0.00 0.00 4.85
914 929 4.379499 CGTTCAGCTATATGTAGATCGGCA 60.379 45.833 0.00 0.00 0.00 5.69
917 932 3.781323 CGCGTTCAGCTATATGTAGATCG 59.219 47.826 0.00 0.00 45.59 3.69
918 933 4.971008 TCGCGTTCAGCTATATGTAGATC 58.029 43.478 5.77 0.00 45.59 2.75
919 934 5.154932 GTTCGCGTTCAGCTATATGTAGAT 58.845 41.667 5.77 0.00 45.59 1.98
920 935 4.534168 GTTCGCGTTCAGCTATATGTAGA 58.466 43.478 5.77 0.00 45.59 2.59
921 936 3.669122 GGTTCGCGTTCAGCTATATGTAG 59.331 47.826 5.77 0.00 45.59 2.74
948 977 2.818274 GGGAATTCCGCGTTCGCT 60.818 61.111 18.30 0.00 36.11 4.93
1354 1386 1.880340 CCTGGACGCGATCAGAAGC 60.880 63.158 25.94 5.41 33.11 3.86
1359 1391 2.279810 TGGTTCCTGGACGCGATCA 61.280 57.895 15.93 9.70 0.00 2.92
1362 1394 3.998672 GGTGGTTCCTGGACGCGA 61.999 66.667 15.93 0.00 0.00 5.87
1698 1730 3.655810 CTCTGCCAGGAGTGCGGTC 62.656 68.421 0.00 0.00 36.47 4.79
1707 1739 3.057547 CTCGTCGTCCTCTGCCAGG 62.058 68.421 0.00 0.00 45.15 4.45
1710 1742 4.838486 CGCTCGTCGTCCTCTGCC 62.838 72.222 0.00 0.00 0.00 4.85
1782 1814 4.717629 TCGTCGAAGCGCTGGTGG 62.718 66.667 12.58 0.00 0.00 4.61
1784 1816 4.421479 CCTCGTCGAAGCGCTGGT 62.421 66.667 12.58 0.00 0.00 4.00
1980 2012 1.513622 GGACGAGGAGAGCAGGAAC 59.486 63.158 0.00 0.00 0.00 3.62
2055 2090 1.219393 GTAGTGCACCTCCAGCTCC 59.781 63.158 14.63 0.00 0.00 4.70
2199 2234 0.548682 AGTGAATCTGGCCTCTGGGT 60.549 55.000 3.32 0.00 34.45 4.51
2208 2243 1.503542 GCCGTTGCAGTGAATCTGG 59.496 57.895 0.00 0.00 43.78 3.86
2260 2295 1.890894 CGTCTCCGGTGAAGACCAT 59.109 57.895 13.31 0.00 43.33 3.55
2263 2298 2.504244 CGCGTCTCCGGTGAAGAC 60.504 66.667 21.25 16.08 33.68 3.01
2342 2380 4.648626 GCAGAGGCCAGTGGTGCA 62.649 66.667 15.64 0.00 34.18 4.57
2344 2382 1.529010 TTTGCAGAGGCCAGTGGTG 60.529 57.895 11.74 1.71 40.13 4.17
2345 2383 1.529244 GTTTGCAGAGGCCAGTGGT 60.529 57.895 11.74 0.00 40.13 4.16
2346 2384 2.270986 GGTTTGCAGAGGCCAGTGG 61.271 63.158 5.01 4.20 40.13 4.00
2350 2388 2.281484 GTCGGTTTGCAGAGGCCA 60.281 61.111 5.01 0.00 40.13 5.36
2365 2403 4.065281 CCTGTGGTCGACGGGGTC 62.065 72.222 9.92 0.00 46.49 4.46
2380 2418 0.462759 GCCTACAATCGAAGCTGCCT 60.463 55.000 0.00 0.00 0.00 4.75
2426 2482 3.008923 TGCCACTGGTATCTTCACATTGA 59.991 43.478 0.00 0.00 0.00 2.57
2433 2489 2.648059 AGCATTGCCACTGGTATCTTC 58.352 47.619 4.70 0.00 0.00 2.87
2504 2560 7.161404 AGTACAGTAAGAATGAAGTGATTGCA 58.839 34.615 0.00 0.00 0.00 4.08
2507 2563 9.209175 GACAAGTACAGTAAGAATGAAGTGATT 57.791 33.333 0.00 0.00 0.00 2.57
2527 2583 4.269183 TGAGACATGGTTTTGTGACAAGT 58.731 39.130 0.00 0.00 0.00 3.16
2528 2584 4.576053 TCTGAGACATGGTTTTGTGACAAG 59.424 41.667 0.00 0.00 0.00 3.16
2529 2585 4.522114 TCTGAGACATGGTTTTGTGACAA 58.478 39.130 0.00 0.00 0.00 3.18
2530 2586 4.149511 TCTGAGACATGGTTTTGTGACA 57.850 40.909 0.00 0.00 0.00 3.58
2531 2587 4.516698 ACATCTGAGACATGGTTTTGTGAC 59.483 41.667 0.00 0.00 0.00 3.67
2532 2588 4.717877 ACATCTGAGACATGGTTTTGTGA 58.282 39.130 0.00 0.00 0.00 3.58
2533 2589 5.443185 AACATCTGAGACATGGTTTTGTG 57.557 39.130 0.00 0.00 0.00 3.33
2534 2590 6.545666 TGTTAACATCTGAGACATGGTTTTGT 59.454 34.615 3.59 0.00 0.00 2.83
2535 2591 6.969366 TGTTAACATCTGAGACATGGTTTTG 58.031 36.000 3.59 0.00 0.00 2.44
2536 2592 6.207417 CCTGTTAACATCTGAGACATGGTTTT 59.793 38.462 9.13 0.00 0.00 2.43
2544 2600 5.784177 TGTTCTCCTGTTAACATCTGAGAC 58.216 41.667 22.30 18.57 30.88 3.36
2561 2617 5.518487 TGAAAAACCTTCGCATTTTGTTCTC 59.482 36.000 0.00 0.00 0.00 2.87
2564 2620 4.570369 CCTGAAAAACCTTCGCATTTTGTT 59.430 37.500 0.00 0.00 0.00 2.83
2567 2623 4.664150 TCCTGAAAAACCTTCGCATTTT 57.336 36.364 0.00 0.00 0.00 1.82
2570 2626 4.871933 AAATCCTGAAAAACCTTCGCAT 57.128 36.364 0.00 0.00 0.00 4.73
2571 2627 4.664150 AAAATCCTGAAAAACCTTCGCA 57.336 36.364 0.00 0.00 0.00 5.10
2572 2628 7.062255 CAGATAAAAATCCTGAAAAACCTTCGC 59.938 37.037 0.00 0.00 0.00 4.70
2573 2629 7.062255 GCAGATAAAAATCCTGAAAAACCTTCG 59.938 37.037 0.00 0.00 0.00 3.79
2574 2630 7.331934 GGCAGATAAAAATCCTGAAAAACCTTC 59.668 37.037 0.00 0.00 0.00 3.46
2576 2632 6.269769 TGGCAGATAAAAATCCTGAAAAACCT 59.730 34.615 0.00 0.00 0.00 3.50
2578 2634 7.603784 ACATGGCAGATAAAAATCCTGAAAAAC 59.396 33.333 0.00 0.00 0.00 2.43
2579 2635 7.678837 ACATGGCAGATAAAAATCCTGAAAAA 58.321 30.769 0.00 0.00 0.00 1.94
2587 2655 6.866480 TCCTTTGACATGGCAGATAAAAATC 58.134 36.000 0.00 0.00 0.00 2.17
2591 2659 3.696051 GCTCCTTTGACATGGCAGATAAA 59.304 43.478 0.00 0.00 0.00 1.40
2600 2668 2.273370 GCATGTGCTCCTTTGACATG 57.727 50.000 0.00 0.00 46.46 3.21
2623 2694 4.023707 CCAGTCTTTTTCTTGATGCGTTCT 60.024 41.667 0.00 0.00 0.00 3.01
2625 2696 3.550842 GCCAGTCTTTTTCTTGATGCGTT 60.551 43.478 0.00 0.00 0.00 4.84
2626 2697 2.030805 GCCAGTCTTTTTCTTGATGCGT 60.031 45.455 0.00 0.00 0.00 5.24
2627 2698 2.030893 TGCCAGTCTTTTTCTTGATGCG 60.031 45.455 0.00 0.00 0.00 4.73
2631 2702 3.897239 TCCTTGCCAGTCTTTTTCTTGA 58.103 40.909 0.00 0.00 0.00 3.02
2641 2712 1.683385 AGTTTTGCTTCCTTGCCAGTC 59.317 47.619 0.00 0.00 0.00 3.51
2642 2713 1.780503 AGTTTTGCTTCCTTGCCAGT 58.219 45.000 0.00 0.00 0.00 4.00
2659 2730 3.704566 TGGACTTGTCAAGAGTGTGTAGT 59.295 43.478 19.53 0.00 0.00 2.73
2666 2737 3.132289 TCGTTTCTGGACTTGTCAAGAGT 59.868 43.478 19.53 0.00 0.00 3.24
2667 2738 3.717707 TCGTTTCTGGACTTGTCAAGAG 58.282 45.455 19.53 6.52 0.00 2.85
2677 2748 4.726876 GCGTATGGAAATTCGTTTCTGGAC 60.727 45.833 1.50 0.00 0.00 4.02
2691 2762 3.132289 CCAGACTTCCTTAGCGTATGGAA 59.868 47.826 0.00 10.04 41.31 3.53
2693 2764 2.431057 ACCAGACTTCCTTAGCGTATGG 59.569 50.000 0.00 0.00 43.65 2.74
2701 2772 3.517612 ACCTTAGCACCAGACTTCCTTA 58.482 45.455 0.00 0.00 0.00 2.69
2714 2785 7.624549 AGAGATGATCAGTAAAAACCTTAGCA 58.375 34.615 0.09 0.00 0.00 3.49
2742 2813 3.380471 TGGGGAGAGAAAGAGAGAGAG 57.620 52.381 0.00 0.00 0.00 3.20
2743 2814 3.270696 TCATGGGGAGAGAAAGAGAGAGA 59.729 47.826 0.00 0.00 0.00 3.10
2744 2815 3.641046 TCATGGGGAGAGAAAGAGAGAG 58.359 50.000 0.00 0.00 0.00 3.20
2745 2816 3.765432 TCATGGGGAGAGAAAGAGAGA 57.235 47.619 0.00 0.00 0.00 3.10
2746 2817 3.710677 ACATCATGGGGAGAGAAAGAGAG 59.289 47.826 0.00 0.00 0.00 3.20
2747 2818 3.729108 ACATCATGGGGAGAGAAAGAGA 58.271 45.455 0.00 0.00 0.00 3.10
2748 2819 4.197750 CAACATCATGGGGAGAGAAAGAG 58.802 47.826 0.00 0.00 0.00 2.85
2749 2820 3.623203 GCAACATCATGGGGAGAGAAAGA 60.623 47.826 0.00 0.00 0.00 2.52
2750 2821 2.686915 GCAACATCATGGGGAGAGAAAG 59.313 50.000 0.00 0.00 0.00 2.62
2751 2822 2.621407 GGCAACATCATGGGGAGAGAAA 60.621 50.000 0.00 0.00 0.00 2.52
2790 2861 1.679944 GCTTCATGCTGCCAGACCTTA 60.680 52.381 0.00 0.00 38.95 2.69
2832 2903 1.737793 CCTTTCACGCTACCACCAATC 59.262 52.381 0.00 0.00 0.00 2.67
2838 2909 3.074281 CCCCCTTTCACGCTACCA 58.926 61.111 0.00 0.00 0.00 3.25
2872 2943 1.672356 CTCTGACCTTTGGGCACGG 60.672 63.158 0.00 0.00 35.63 4.94
2878 2949 0.875059 GGAAACGCTCTGACCTTTGG 59.125 55.000 0.00 0.00 0.00 3.28
2900 2971 3.803082 CAATGGCCCACACGCTCG 61.803 66.667 0.00 0.00 0.00 5.03
2984 3055 0.468226 AGGAACACCTCAAGCGTTGA 59.532 50.000 0.00 1.48 38.17 3.18
2988 3059 1.672356 CCCAGGAACACCTCAAGCG 60.672 63.158 0.00 0.00 30.75 4.68
3049 3156 7.915923 CAGCGACAGTTTATCTCTTTACTATCA 59.084 37.037 0.00 0.00 0.00 2.15
3050 3157 7.380065 CCAGCGACAGTTTATCTCTTTACTATC 59.620 40.741 0.00 0.00 0.00 2.08
3056 3163 4.273148 ACCAGCGACAGTTTATCTCTTT 57.727 40.909 0.00 0.00 0.00 2.52
3087 3195 3.623060 CGCCAAGCTGCTCTTTAGAATAA 59.377 43.478 1.00 0.00 31.27 1.40
3088 3196 3.198068 CGCCAAGCTGCTCTTTAGAATA 58.802 45.455 1.00 0.00 31.27 1.75
3108 3216 1.552226 GGATCATTTGTGCATGTGCG 58.448 50.000 0.00 0.00 45.83 5.34
3112 3223 1.826096 TGTGGGGATCATTTGTGCATG 59.174 47.619 0.00 0.00 0.00 4.06
3113 3224 2.234896 TGTGGGGATCATTTGTGCAT 57.765 45.000 0.00 0.00 0.00 3.96
3127 3238 6.054295 TGAAGATTGGATTTTTGTTTGTGGG 58.946 36.000 0.00 0.00 0.00 4.61
3185 3296 2.206576 ATTCAAGTGTCCAAGGAGGC 57.793 50.000 0.00 0.00 37.29 4.70
3220 3332 4.274705 CGGCACATATGTTTTACCTGCATA 59.725 41.667 5.37 0.00 0.00 3.14
3230 3342 2.096819 CGCTTTACCGGCACATATGTTT 59.903 45.455 5.37 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.