Multiple sequence alignment - TraesCS6B01G265100

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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 TraesCS6B01G265100 chr6B 100.000 3097 0 0 1 3097 476716733 476713637 0.000000e+00 5720.0
1 TraesCS6B01G265100 chr6B 94.147 598 33 2 1 597 479151554 479150958 0.000000e+00 909.0
2 TraesCS6B01G265100 chr6B 100.000 34 0 0 2731 2764 476713970 476713937 2.580000e-06 63.9
3 TraesCS6B01G265100 chr6B 100.000 34 0 0 2764 2797 476714003 476713970 2.580000e-06 63.9
4 TraesCS6B01G265100 chr6A 89.883 1028 61 13 1760 2764 445778339 445777332 0.000000e+00 1282.0
5 TraesCS6B01G265100 chr6A 90.987 821 36 8 623 1407 445779510 445778692 0.000000e+00 1072.0
6 TraesCS6B01G265100 chr6A 94.340 318 13 3 1426 1742 445778701 445778388 1.670000e-132 483.0
7 TraesCS6B01G265100 chr6A 92.029 138 11 0 2960 3097 445773646 445773509 8.760000e-46 195.0
8 TraesCS6B01G265100 chr6D 92.465 783 22 11 1760 2519 309041531 309040763 0.000000e+00 1085.0
9 TraesCS6B01G265100 chr6D 91.727 689 20 8 753 1407 309042572 309041887 0.000000e+00 922.0
10 TraesCS6B01G265100 chr6D 93.913 345 14 3 1421 1765 309041901 309041564 5.920000e-142 514.0
11 TraesCS6B01G265100 chr6D 91.611 298 19 4 2805 3097 309040770 309040474 1.030000e-109 407.0
12 TraesCS6B01G265100 chr6D 88.235 153 13 3 604 753 309042756 309042606 8.830000e-41 178.0
13 TraesCS6B01G265100 chr7B 95.645 597 24 2 1 596 667383517 667384112 0.000000e+00 957.0
14 TraesCS6B01G265100 chr1B 95.151 598 27 2 1 597 683374724 683374128 0.000000e+00 942.0
15 TraesCS6B01G265100 chr2B 95.142 597 27 2 1 596 775455883 775455288 0.000000e+00 941.0
16 TraesCS6B01G265100 chr2B 94.816 598 29 2 1 597 785795967 785795371 0.000000e+00 931.0
17 TraesCS6B01G265100 chr2B 94.649 598 30 2 1 597 785790490 785789894 0.000000e+00 926.0
18 TraesCS6B01G265100 chr2B 90.780 141 13 0 1000 1140 551258672 551258812 4.080000e-44 189.0
19 TraesCS6B01G265100 chr5B 94.975 597 28 2 1 596 434449462 434450057 0.000000e+00 935.0
20 TraesCS6B01G265100 chr3A 94.649 598 30 2 1 597 748203902 748203306 0.000000e+00 926.0
21 TraesCS6B01G265100 chr7D 94.305 597 31 3 1 596 592541884 592542478 0.000000e+00 911.0
22 TraesCS6B01G265100 chr2D 90.071 141 14 0 1000 1140 472070134 472070274 1.900000e-42 183.0
23 TraesCS6B01G265100 chr2A 90.071 141 14 0 1000 1140 613439935 613440075 1.900000e-42 183.0
24 TraesCS6B01G265100 chr1D 78.082 146 21 9 2805 2940 199060844 199060700 7.120000e-12 82.4


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 TraesCS6B01G265100 chr6B 476713637 476716733 3096 True 1949.266667 5720 100.00000 1 3097 3 chr6B.!!$R2 3096
1 TraesCS6B01G265100 chr6B 479150958 479151554 596 True 909.000000 909 94.14700 1 597 1 chr6B.!!$R1 596
2 TraesCS6B01G265100 chr6A 445773509 445779510 6001 True 758.000000 1282 91.80975 623 3097 4 chr6A.!!$R1 2474
3 TraesCS6B01G265100 chr6D 309040474 309042756 2282 True 621.200000 1085 91.59020 604 3097 5 chr6D.!!$R1 2493
4 TraesCS6B01G265100 chr7B 667383517 667384112 595 False 957.000000 957 95.64500 1 596 1 chr7B.!!$F1 595
5 TraesCS6B01G265100 chr1B 683374128 683374724 596 True 942.000000 942 95.15100 1 597 1 chr1B.!!$R1 596
6 TraesCS6B01G265100 chr2B 775455288 775455883 595 True 941.000000 941 95.14200 1 596 1 chr2B.!!$R1 595
7 TraesCS6B01G265100 chr2B 785795371 785795967 596 True 931.000000 931 94.81600 1 597 1 chr2B.!!$R3 596
8 TraesCS6B01G265100 chr2B 785789894 785790490 596 True 926.000000 926 94.64900 1 597 1 chr2B.!!$R2 596
9 TraesCS6B01G265100 chr5B 434449462 434450057 595 False 935.000000 935 94.97500 1 596 1 chr5B.!!$F1 595
10 TraesCS6B01G265100 chr3A 748203306 748203902 596 True 926.000000 926 94.64900 1 597 1 chr3A.!!$R1 596
11 TraesCS6B01G265100 chr7D 592541884 592542478 594 False 911.000000 911 94.30500 1 596 1 chr7D.!!$F1 595

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
371 372 0.395173 TCATCCTCGACGACATGGGA 60.395 55.0 6.08 6.08 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2223 2359 0.247736 AGCTTTGAGAGGCCGTACAG 59.752 55.0 0.0 0.0 0.0 2.74 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
37 38 4.830826 ACTGTTTCCGATTCTTTTGGAC 57.169 40.909 0.00 0.00 37.65 4.02
194 195 3.536287 AGTCTTCTCCATCCCTCCTTTT 58.464 45.455 0.00 0.00 0.00 2.27
250 251 3.917760 CCCGCCTCTCGTGATCCC 61.918 72.222 0.00 0.00 36.19 3.85
256 257 0.812811 CCTCTCGTGATCCCGTACGA 60.813 60.000 18.76 5.95 45.87 3.43
261 262 0.582482 CGTGATCCCGTACGAGAGAG 59.418 60.000 18.76 0.00 42.54 3.20
280 281 0.898326 GGGGGCGATCAGGTTTTTGT 60.898 55.000 0.00 0.00 0.00 2.83
287 288 1.880027 GATCAGGTTTTTGTGGAGCGT 59.120 47.619 0.00 0.00 0.00 5.07
332 333 2.114825 GACTTCACGAACGACGACTTT 58.885 47.619 0.00 0.00 45.77 2.66
339 340 1.870993 CGAACGACGACTTTTTCCCCT 60.871 52.381 0.00 0.00 45.77 4.79
371 372 0.395173 TCATCCTCGACGACATGGGA 60.395 55.000 6.08 6.08 0.00 4.37
599 600 9.630098 AGTAATTTGCTCATATTTCAACAACTG 57.370 29.630 0.00 0.00 0.00 3.16
600 601 6.956299 ATTTGCTCATATTTCAACAACTGC 57.044 33.333 0.00 0.00 0.00 4.40
601 602 4.439305 TGCTCATATTTCAACAACTGCC 57.561 40.909 0.00 0.00 0.00 4.85
602 603 3.193267 TGCTCATATTTCAACAACTGCCC 59.807 43.478 0.00 0.00 0.00 5.36
607 608 0.459489 TTTCAACAACTGCCCAGCAC 59.541 50.000 0.00 0.00 33.79 4.40
627 628 4.380867 GCACGATTGTTTGGATGGAAGAAT 60.381 41.667 0.00 0.00 0.00 2.40
679 682 1.077501 CACGGCCTGGAATGGACAT 60.078 57.895 0.00 0.00 33.86 3.06
807 844 1.374758 GTTCTGTGCGGTCTGGAGG 60.375 63.158 0.00 0.00 0.00 4.30
1205 1264 3.131240 ACGGCAAATATGTTTCGCTTC 57.869 42.857 8.43 0.00 0.00 3.86
1219 1278 4.537135 TTCGCTTCTGTGTCCTCTTATT 57.463 40.909 0.00 0.00 0.00 1.40
1220 1279 5.654603 TTCGCTTCTGTGTCCTCTTATTA 57.345 39.130 0.00 0.00 0.00 0.98
1253 1316 2.627699 ACGTCTGTGCAAAATGGGAATT 59.372 40.909 0.00 0.00 0.00 2.17
1358 1433 1.448717 GCTCTTCAAGGAGACGGGC 60.449 63.158 0.00 0.00 34.60 6.13
1397 1472 3.825812 GCCAGGTAATGCGAAATCG 57.174 52.632 0.00 0.00 43.27 3.34
1413 1488 5.599715 CGAAATCGCAATCCTAGTTTATCG 58.400 41.667 0.00 0.00 0.00 2.92
1414 1489 5.401376 CGAAATCGCAATCCTAGTTTATCGA 59.599 40.000 0.00 0.00 0.00 3.59
1415 1490 6.074516 CGAAATCGCAATCCTAGTTTATCGAA 60.075 38.462 0.00 0.00 0.00 3.71
1416 1491 7.516155 CGAAATCGCAATCCTAGTTTATCGAAA 60.516 37.037 0.00 0.00 0.00 3.46
1417 1492 7.548196 AATCGCAATCCTAGTTTATCGAAAA 57.452 32.000 0.00 0.00 0.00 2.29
1418 1493 6.971527 TCGCAATCCTAGTTTATCGAAAAA 57.028 33.333 0.00 0.00 0.00 1.94
1475 1550 7.308782 AGATATTCTGACATTTTGTTCCGTC 57.691 36.000 0.00 0.00 0.00 4.79
1476 1551 3.870723 TTCTGACATTTTGTTCCGTCG 57.129 42.857 0.00 0.00 0.00 5.12
1477 1552 2.828877 TCTGACATTTTGTTCCGTCGT 58.171 42.857 0.00 0.00 0.00 4.34
1529 1604 1.070758 AGGTACAGTTCCAGTGTGCAG 59.929 52.381 0.00 0.00 36.11 4.41
1542 1617 0.599991 TGTGCAGACGTCGCATCTTT 60.600 50.000 28.33 2.18 42.32 2.52
1565 1640 2.423926 TCTCAGAGATTATTCGCCGC 57.576 50.000 0.00 0.00 0.00 6.53
1598 1674 9.303116 TCACATGTGTTATGGGTAAACTATTTT 57.697 29.630 24.63 0.00 0.00 1.82
1631 1707 2.964464 TCAAAATCTCCTGCAGGCAAAA 59.036 40.909 28.91 9.99 34.44 2.44
1728 1804 3.914426 TGGAGAAGGTAAGAGGAATGC 57.086 47.619 0.00 0.00 0.00 3.56
1744 1820 9.686683 AAGAGGAATGCTGTAATGTTACTTATT 57.313 29.630 4.71 3.20 34.77 1.40
1769 1883 3.646534 TGGATAGTGGAGCAAGATCTCA 58.353 45.455 0.00 0.00 34.84 3.27
1782 1896 8.037166 GGAGCAAGATCTCAAAAATAATTTGGT 58.963 33.333 0.00 0.00 34.84 3.67
1826 1943 3.460103 TCTTTACGTTTCGGTTCAGCTT 58.540 40.909 0.00 0.00 0.00 3.74
1830 1947 2.401351 ACGTTTCGGTTCAGCTTACTC 58.599 47.619 0.00 0.00 0.00 2.59
2098 2233 1.869767 CCCGCAAGATGAAGCATAGAC 59.130 52.381 0.00 0.00 43.02 2.59
2108 2243 9.064706 CAAGATGAAGCATAGACCAAAGATTAT 57.935 33.333 0.00 0.00 0.00 1.28
2109 2244 9.638176 AAGATGAAGCATAGACCAAAGATTATT 57.362 29.630 0.00 0.00 0.00 1.40
2123 2259 7.039082 ACCAAAGATTATTAGGAGCAAAGCAAA 60.039 33.333 0.00 0.00 0.00 3.68
2128 2264 8.806146 AGATTATTAGGAGCAAAGCAAAGAAAA 58.194 29.630 0.00 0.00 0.00 2.29
2187 2323 1.739067 AGCCTCCGCAATTTACAGAC 58.261 50.000 0.00 0.00 37.52 3.51
2223 2359 2.514458 TCCTTCCCTGCTTCCATTTC 57.486 50.000 0.00 0.00 0.00 2.17
2425 2561 9.709495 TCTTTGATTCAAATGATTTGTAAAGGG 57.291 29.630 16.62 4.95 41.36 3.95
2487 2623 7.066525 GCCATTCCAAAAATTCATGAACATGAT 59.933 33.333 11.07 2.31 46.12 2.45
2488 2624 8.394877 CCATTCCAAAAATTCATGAACATGATG 58.605 33.333 11.07 11.68 46.12 3.07
2502 2638 4.487714 ACATGATGTCCCTTTCGTGTAT 57.512 40.909 0.00 0.00 39.64 2.29
2571 2708 7.995289 TGCATTTCGGTATTTCTTTATGACAT 58.005 30.769 0.00 0.00 0.00 3.06
2597 2734 3.821421 ATGTATCTCTGGACGAAACCC 57.179 47.619 0.00 0.00 0.00 4.11
2605 2742 1.880027 CTGGACGAAACCCTTCTTTGG 59.120 52.381 0.00 0.00 0.00 3.28
2613 2750 2.068831 ACCCTTCTTTGGATACCCCA 57.931 50.000 0.00 0.00 44.93 4.96
2649 2786 1.955778 TGCATCATTTTATGGCCTCCG 59.044 47.619 3.32 0.00 0.00 4.63
2666 2805 3.987868 CCTCCGTTCATATACATGGAACG 59.012 47.826 20.47 20.47 40.89 3.95
2676 2815 8.818141 TCATATACATGGAACGAGAAGATTTC 57.182 34.615 0.00 0.00 32.61 2.17
2685 2824 6.072508 TGGAACGAGAAGATTTCTTGGATTTG 60.073 38.462 10.06 0.00 44.03 2.32
2696 2835 3.631250 TCTTGGATTTGTAGCCCAATCC 58.369 45.455 4.27 4.27 39.03 3.01
2697 2836 2.452600 TGGATTTGTAGCCCAATCCC 57.547 50.000 8.18 5.24 33.40 3.85
2698 2837 1.929494 TGGATTTGTAGCCCAATCCCT 59.071 47.619 8.18 0.00 33.40 4.20
2699 2838 2.314549 TGGATTTGTAGCCCAATCCCTT 59.685 45.455 8.18 0.00 33.40 3.95
2700 2839 2.959030 GGATTTGTAGCCCAATCCCTTC 59.041 50.000 0.11 0.00 31.81 3.46
2701 2840 2.525105 TTTGTAGCCCAATCCCTTCC 57.475 50.000 0.00 0.00 31.81 3.46
2704 2843 0.474614 GTAGCCCAATCCCTTCCCTC 59.525 60.000 0.00 0.00 0.00 4.30
2710 2849 2.624293 CCCAATCCCTTCCCTCTTTTCC 60.624 54.545 0.00 0.00 0.00 3.13
2720 2859 5.009710 CCTTCCCTCTTTTCCACAGTTAAAC 59.990 44.000 0.00 0.00 0.00 2.01
2740 2879 2.829094 TCGGGGCGAGATTCCATTA 58.171 52.632 0.00 0.00 0.00 1.90
2741 2880 0.679505 TCGGGGCGAGATTCCATTAG 59.320 55.000 0.00 0.00 0.00 1.73
2742 2881 0.679505 CGGGGCGAGATTCCATTAGA 59.320 55.000 0.00 0.00 0.00 2.10
2743 2882 1.337260 CGGGGCGAGATTCCATTAGAG 60.337 57.143 0.00 0.00 0.00 2.43
2744 2883 1.002544 GGGGCGAGATTCCATTAGAGG 59.997 57.143 0.00 0.00 0.00 3.69
2745 2884 1.002544 GGGCGAGATTCCATTAGAGGG 59.997 57.143 0.00 0.00 0.00 4.30
2746 2885 1.002544 GGCGAGATTCCATTAGAGGGG 59.997 57.143 0.00 0.00 0.00 4.79
2747 2886 1.002544 GCGAGATTCCATTAGAGGGGG 59.997 57.143 0.00 0.00 0.00 5.40
2748 2887 2.330216 CGAGATTCCATTAGAGGGGGT 58.670 52.381 0.00 0.00 0.00 4.95
2749 2888 2.300437 CGAGATTCCATTAGAGGGGGTC 59.700 54.545 0.00 0.00 0.00 4.46
2750 2889 2.300437 GAGATTCCATTAGAGGGGGTCG 59.700 54.545 0.00 0.00 0.00 4.79
2751 2890 2.090719 AGATTCCATTAGAGGGGGTCGA 60.091 50.000 0.00 0.00 0.00 4.20
2752 2891 2.489528 TTCCATTAGAGGGGGTCGAT 57.510 50.000 0.00 0.00 0.00 3.59
2753 2892 2.489528 TCCATTAGAGGGGGTCGATT 57.510 50.000 0.00 0.00 0.00 3.34
2754 2893 2.047061 TCCATTAGAGGGGGTCGATTG 58.953 52.381 0.00 0.00 0.00 2.67
2755 2894 1.768870 CCATTAGAGGGGGTCGATTGT 59.231 52.381 0.00 0.00 0.00 2.71
2756 2895 2.969950 CCATTAGAGGGGGTCGATTGTA 59.030 50.000 0.00 0.00 0.00 2.41
2757 2896 3.389983 CCATTAGAGGGGGTCGATTGTAA 59.610 47.826 0.00 0.00 0.00 2.41
2758 2897 4.041691 CCATTAGAGGGGGTCGATTGTAAT 59.958 45.833 0.00 0.00 0.00 1.89
2759 2898 5.247564 CCATTAGAGGGGGTCGATTGTAATA 59.752 44.000 0.00 0.00 0.00 0.98
2760 2899 6.398918 CATTAGAGGGGGTCGATTGTAATAG 58.601 44.000 0.00 0.00 0.00 1.73
2761 2900 2.633481 AGAGGGGGTCGATTGTAATAGC 59.367 50.000 0.00 0.00 0.00 2.97
2762 2901 1.697982 AGGGGGTCGATTGTAATAGCC 59.302 52.381 0.00 0.00 0.00 3.93
2763 2902 1.418637 GGGGGTCGATTGTAATAGCCA 59.581 52.381 0.00 0.00 0.00 4.75
2764 2903 2.550208 GGGGGTCGATTGTAATAGCCAG 60.550 54.545 0.00 0.00 0.00 4.85
2765 2904 2.367567 GGGGTCGATTGTAATAGCCAGA 59.632 50.000 0.00 0.00 0.00 3.86
2766 2905 3.008049 GGGGTCGATTGTAATAGCCAGAT 59.992 47.826 0.00 0.00 0.00 2.90
2767 2906 4.505039 GGGGTCGATTGTAATAGCCAGATT 60.505 45.833 0.00 0.00 0.00 2.40
2768 2907 4.691216 GGGTCGATTGTAATAGCCAGATTC 59.309 45.833 0.00 0.00 0.00 2.52
2769 2908 4.691216 GGTCGATTGTAATAGCCAGATTCC 59.309 45.833 0.00 0.00 0.00 3.01
2770 2909 5.297547 GTCGATTGTAATAGCCAGATTCCA 58.702 41.667 0.00 0.00 0.00 3.53
2771 2910 5.934625 GTCGATTGTAATAGCCAGATTCCAT 59.065 40.000 0.00 0.00 0.00 3.41
2772 2911 6.428159 GTCGATTGTAATAGCCAGATTCCATT 59.572 38.462 0.00 0.00 0.00 3.16
2773 2912 7.602644 GTCGATTGTAATAGCCAGATTCCATTA 59.397 37.037 0.00 0.00 0.00 1.90
2791 2930 4.041691 CCATTAGAGGGGGTCGATTGTAAT 59.958 45.833 0.00 0.00 0.00 1.89
2811 2950 8.972458 TGTAATAGCCAAAGAGCAACATATTA 57.028 30.769 0.00 0.00 34.23 0.98
2812 2951 9.573166 TGTAATAGCCAAAGAGCAACATATTAT 57.427 29.630 0.00 0.00 34.23 1.28
2816 2955 6.974965 AGCCAAAGAGCAACATATTATTAGC 58.025 36.000 0.00 0.00 34.23 3.09
2817 2956 6.547141 AGCCAAAGAGCAACATATTATTAGCA 59.453 34.615 0.00 0.00 34.23 3.49
2820 2959 9.585099 CCAAAGAGCAACATATTATTAGCAAAA 57.415 29.630 0.00 0.00 0.00 2.44
2852 2992 6.510317 GCATCATGATCATCTCATAAGCATCG 60.510 42.308 4.86 0.00 42.91 3.84
2958 4275 6.156519 GTCCAACATACCCTTTCAAACAATC 58.843 40.000 0.00 0.00 0.00 2.67
2994 6656 1.000233 TTCATCATGTGGGCCCACC 60.000 57.895 44.65 29.67 45.63 4.61
3007 6669 2.027561 GGGCCCACCAAAATTTAAGGAC 60.028 50.000 19.95 3.53 39.85 3.85
3010 6672 4.159693 GGCCCACCAAAATTTAAGGACTAG 59.840 45.833 14.59 0.00 35.26 2.57
3011 6673 4.159693 GCCCACCAAAATTTAAGGACTAGG 59.840 45.833 14.59 10.26 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.720193 ACGTCCGAGTCGTCACGG 61.720 66.667 27.78 11.83 46.29 4.94
250 251 3.584052 CGCCCCCTCTCTCGTACG 61.584 72.222 9.53 9.53 0.00 3.67
256 257 2.123077 CCTGATCGCCCCCTCTCT 60.123 66.667 0.00 0.00 0.00 3.10
261 262 0.898326 ACAAAAACCTGATCGCCCCC 60.898 55.000 0.00 0.00 0.00 5.40
287 288 1.153901 GCCAGCAGTCGCGTAAGTA 60.154 57.895 5.77 0.00 45.49 2.24
332 333 1.681076 GTTGCCGAGGTAGGGGAAA 59.319 57.895 0.00 0.00 36.60 3.13
339 340 0.325296 AGGATGAGGTTGCCGAGGTA 60.325 55.000 0.00 0.00 0.00 3.08
371 372 2.660552 CCGGCGTTGACGTTGTCT 60.661 61.111 6.01 0.00 42.22 3.41
409 410 6.114187 ACAGAAAGGACAGAATCACATACA 57.886 37.500 0.00 0.00 0.00 2.29
428 429 5.661056 ATTCTACCACGATCTCAAACAGA 57.339 39.130 0.00 0.00 34.78 3.41
592 593 0.823356 AATCGTGCTGGGCAGTTGTT 60.823 50.000 0.00 0.00 40.08 2.83
594 595 1.210931 CAATCGTGCTGGGCAGTTG 59.789 57.895 0.00 0.00 40.08 3.16
595 596 0.823356 AACAATCGTGCTGGGCAGTT 60.823 50.000 0.00 0.00 40.08 3.16
597 598 0.387622 CAAACAATCGTGCTGGGCAG 60.388 55.000 0.00 0.00 40.08 4.85
598 599 1.659233 CAAACAATCGTGCTGGGCA 59.341 52.632 0.00 0.00 35.60 5.36
599 600 1.080569 CCAAACAATCGTGCTGGGC 60.081 57.895 0.00 0.00 30.55 5.36
600 601 1.135315 CATCCAAACAATCGTGCTGGG 60.135 52.381 0.00 0.00 33.61 4.45
601 602 1.135315 CCATCCAAACAATCGTGCTGG 60.135 52.381 0.00 0.00 33.94 4.85
602 603 1.811965 TCCATCCAAACAATCGTGCTG 59.188 47.619 0.00 0.00 0.00 4.41
607 608 4.107622 GCATTCTTCCATCCAAACAATCG 58.892 43.478 0.00 0.00 0.00 3.34
627 628 2.448453 TGACATGCTGAAATGGATGCA 58.552 42.857 0.00 0.00 39.00 3.96
679 682 2.036604 TGTCGTGTCTGGATTAAGTGCA 59.963 45.455 0.00 0.00 0.00 4.57
807 844 2.228343 GCAAAGATAGGAGATGCATGGC 59.772 50.000 2.46 0.00 37.00 4.40
841 891 1.135916 CGATGGGCGACGCTTTAAAAA 60.136 47.619 20.77 0.00 44.57 1.94
1253 1316 3.170791 TGCAGAAAATGAAACGCCAAA 57.829 38.095 0.00 0.00 0.00 3.28
1358 1433 6.205784 TGGCGTAAAATTCTTTGAGAAGTTG 58.794 36.000 4.41 0.00 41.04 3.16
1418 1493 4.641989 CAGTATGCTAGGACTGCCATTTTT 59.358 41.667 0.00 0.00 36.91 1.94
1419 1494 4.202441 CAGTATGCTAGGACTGCCATTTT 58.798 43.478 0.00 0.00 36.91 1.82
1420 1495 3.813443 CAGTATGCTAGGACTGCCATTT 58.187 45.455 0.00 0.00 36.91 2.32
1421 1496 3.482156 CAGTATGCTAGGACTGCCATT 57.518 47.619 0.00 0.00 36.91 3.16
1475 1550 1.737793 GGATTTGCCACCTGAGTAACG 59.262 52.381 0.00 0.00 36.34 3.18
1476 1551 1.737793 CGGATTTGCCACCTGAGTAAC 59.262 52.381 0.00 0.00 35.94 2.50
1477 1552 1.948611 GCGGATTTGCCACCTGAGTAA 60.949 52.381 0.00 0.00 35.94 2.24
1529 1604 1.921230 GAGAAGGAAAGATGCGACGTC 59.079 52.381 5.18 5.18 0.00 4.34
1542 1617 3.004839 CGGCGAATAATCTCTGAGAAGGA 59.995 47.826 12.00 0.29 0.00 3.36
1565 1640 2.677836 CCATAACACATGTGACGGGAAG 59.322 50.000 31.94 13.55 0.00 3.46
1598 1674 7.066887 TGCAGGAGATTTTGAATTCGCTATTTA 59.933 33.333 0.04 0.00 0.00 1.40
1599 1675 6.127647 TGCAGGAGATTTTGAATTCGCTATTT 60.128 34.615 0.04 0.00 0.00 1.40
1600 1676 5.357878 TGCAGGAGATTTTGAATTCGCTATT 59.642 36.000 0.04 0.00 0.00 1.73
1631 1707 2.239150 AGATGACATCTTGCTTGGAGCT 59.761 45.455 12.37 0.00 35.52 4.09
1743 1819 5.663106 AGATCTTGCTCCACTATCCAAGTAA 59.337 40.000 0.00 0.00 35.76 2.24
1744 1820 5.211973 AGATCTTGCTCCACTATCCAAGTA 58.788 41.667 0.00 0.00 35.76 2.24
1745 1821 4.036518 AGATCTTGCTCCACTATCCAAGT 58.963 43.478 0.00 0.00 39.81 3.16
1746 1822 4.100653 TGAGATCTTGCTCCACTATCCAAG 59.899 45.833 0.00 0.00 36.81 3.61
1749 1825 4.679373 TTGAGATCTTGCTCCACTATCC 57.321 45.455 0.00 0.00 33.95 2.59
1790 1907 5.596845 ACGTAAAGATTTGCAATGTGGTTT 58.403 33.333 0.00 0.00 0.00 3.27
1826 1943 0.687757 AGCATTCGCCCTCCAGAGTA 60.688 55.000 0.00 0.00 39.83 2.59
1830 1947 1.227674 GGTAGCATTCGCCCTCCAG 60.228 63.158 0.00 0.00 39.83 3.86
1910 2027 2.815478 CAGTAGAGGATTCCGTTGAGC 58.185 52.381 0.00 0.00 0.00 4.26
2076 2211 0.819259 TATGCTTCATCTTGCGGGGC 60.819 55.000 0.00 0.00 0.00 5.80
2098 2233 6.455360 TGCTTTGCTCCTAATAATCTTTGG 57.545 37.500 0.00 0.00 0.00 3.28
2170 2306 2.699954 ACTGTCTGTAAATTGCGGAGG 58.300 47.619 0.00 0.00 0.00 4.30
2187 2323 6.378280 AGGGAAGGAAGTATTGCAAATTACTG 59.622 38.462 12.35 0.00 39.77 2.74
2223 2359 0.247736 AGCTTTGAGAGGCCGTACAG 59.752 55.000 0.00 0.00 0.00 2.74
2487 2623 5.765677 TCAAAAATCATACACGAAAGGGACA 59.234 36.000 0.00 0.00 38.45 4.02
2488 2624 6.084277 GTCAAAAATCATACACGAAAGGGAC 58.916 40.000 0.00 0.00 38.45 4.46
2534 2671 7.672983 ATACCGAAATGCAATATACAGAAGG 57.327 36.000 0.00 0.00 0.00 3.46
2537 2674 8.902540 AGAAATACCGAAATGCAATATACAGA 57.097 30.769 0.00 0.00 0.00 3.41
2571 2708 7.039923 GGGTTTCGTCCAGAGATACATATTAGA 60.040 40.741 0.00 0.00 0.00 2.10
2574 2711 5.602978 AGGGTTTCGTCCAGAGATACATATT 59.397 40.000 0.00 0.00 0.00 1.28
2586 2723 1.491332 TCCAAAGAAGGGTTTCGTCCA 59.509 47.619 0.00 0.00 38.38 4.02
2605 2742 6.368516 CACAACATTGAACAAATTGGGGTATC 59.631 38.462 14.67 0.00 0.00 2.24
2613 2750 7.499321 AATGATGCACAACATTGAACAAATT 57.501 28.000 12.61 0.00 39.84 1.82
2649 2786 8.594881 AATCTTCTCGTTCCATGTATATGAAC 57.405 34.615 0.25 3.50 36.36 3.18
2666 2805 6.183360 GGGCTACAAATCCAAGAAATCTTCTC 60.183 42.308 0.00 0.00 39.61 2.87
2676 2815 2.695147 GGGATTGGGCTACAAATCCAAG 59.305 50.000 14.12 0.00 43.46 3.61
2685 2824 0.474614 GAGGGAAGGGATTGGGCTAC 59.525 60.000 0.00 0.00 0.00 3.58
2696 2835 2.959465 ACTGTGGAAAAGAGGGAAGG 57.041 50.000 0.00 0.00 0.00 3.46
2697 2836 5.009710 GGTTTAACTGTGGAAAAGAGGGAAG 59.990 44.000 0.00 0.00 0.00 3.46
2698 2837 4.891168 GGTTTAACTGTGGAAAAGAGGGAA 59.109 41.667 0.00 0.00 0.00 3.97
2699 2838 4.167307 AGGTTTAACTGTGGAAAAGAGGGA 59.833 41.667 0.00 0.00 0.00 4.20
2700 2839 4.470602 AGGTTTAACTGTGGAAAAGAGGG 58.529 43.478 0.00 0.00 0.00 4.30
2701 2840 4.213482 CGAGGTTTAACTGTGGAAAAGAGG 59.787 45.833 0.00 0.00 0.00 3.69
2704 2843 3.252458 CCCGAGGTTTAACTGTGGAAAAG 59.748 47.826 0.00 0.00 0.00 2.27
2710 2849 1.296056 CGCCCCGAGGTTTAACTGTG 61.296 60.000 0.00 0.00 34.57 3.66
2736 2875 4.682778 TTACAATCGACCCCCTCTAATG 57.317 45.455 0.00 0.00 0.00 1.90
2740 2879 2.633481 GCTATTACAATCGACCCCCTCT 59.367 50.000 0.00 0.00 0.00 3.69
2741 2880 2.289506 GGCTATTACAATCGACCCCCTC 60.290 54.545 0.00 0.00 0.00 4.30
2742 2881 1.697982 GGCTATTACAATCGACCCCCT 59.302 52.381 0.00 0.00 0.00 4.79
2743 2882 1.418637 TGGCTATTACAATCGACCCCC 59.581 52.381 0.00 0.00 0.00 5.40
2744 2883 2.367567 TCTGGCTATTACAATCGACCCC 59.632 50.000 0.00 0.00 0.00 4.95
2745 2884 3.746045 TCTGGCTATTACAATCGACCC 57.254 47.619 0.00 0.00 0.00 4.46
2746 2885 4.691216 GGAATCTGGCTATTACAATCGACC 59.309 45.833 0.00 0.00 0.00 4.79
2747 2886 5.297547 TGGAATCTGGCTATTACAATCGAC 58.702 41.667 0.00 0.00 26.39 4.20
2748 2887 5.545063 TGGAATCTGGCTATTACAATCGA 57.455 39.130 0.00 0.00 26.39 3.59
2749 2888 6.808008 AATGGAATCTGGCTATTACAATCG 57.192 37.500 2.80 0.00 33.44 3.34
2750 2889 9.160496 CTCTAATGGAATCTGGCTATTACAATC 57.840 37.037 2.80 0.00 33.44 2.67
2751 2890 8.105829 CCTCTAATGGAATCTGGCTATTACAAT 58.894 37.037 2.80 0.00 33.44 2.71
2752 2891 7.453393 CCTCTAATGGAATCTGGCTATTACAA 58.547 38.462 2.80 0.00 33.44 2.41
2753 2892 6.013379 CCCTCTAATGGAATCTGGCTATTACA 60.013 42.308 1.36 1.36 34.22 2.41
2754 2893 6.410540 CCCTCTAATGGAATCTGGCTATTAC 58.589 44.000 0.00 0.00 0.00 1.89
2755 2894 5.488919 CCCCTCTAATGGAATCTGGCTATTA 59.511 44.000 0.00 0.00 0.00 0.98
2756 2895 4.290722 CCCCTCTAATGGAATCTGGCTATT 59.709 45.833 0.00 0.00 0.00 1.73
2757 2896 3.848975 CCCCTCTAATGGAATCTGGCTAT 59.151 47.826 0.00 0.00 0.00 2.97
2758 2897 3.251484 CCCCTCTAATGGAATCTGGCTA 58.749 50.000 0.00 0.00 0.00 3.93
2759 2898 2.061061 CCCCTCTAATGGAATCTGGCT 58.939 52.381 0.00 0.00 0.00 4.75
2760 2899 1.074566 CCCCCTCTAATGGAATCTGGC 59.925 57.143 0.00 0.00 0.00 4.85
2761 2900 2.373502 GACCCCCTCTAATGGAATCTGG 59.626 54.545 0.00 0.00 0.00 3.86
2762 2901 2.037772 CGACCCCCTCTAATGGAATCTG 59.962 54.545 0.00 0.00 0.00 2.90
2763 2902 2.090719 TCGACCCCCTCTAATGGAATCT 60.091 50.000 0.00 0.00 0.00 2.40
2764 2903 2.326428 TCGACCCCCTCTAATGGAATC 58.674 52.381 0.00 0.00 0.00 2.52
2765 2904 2.489528 TCGACCCCCTCTAATGGAAT 57.510 50.000 0.00 0.00 0.00 3.01
2766 2905 2.438021 CAATCGACCCCCTCTAATGGAA 59.562 50.000 0.00 0.00 0.00 3.53
2767 2906 2.047061 CAATCGACCCCCTCTAATGGA 58.953 52.381 0.00 0.00 0.00 3.41
2768 2907 1.768870 ACAATCGACCCCCTCTAATGG 59.231 52.381 0.00 0.00 0.00 3.16
2769 2908 4.682778 TTACAATCGACCCCCTCTAATG 57.317 45.455 0.00 0.00 0.00 1.90
2770 2909 5.046520 GCTATTACAATCGACCCCCTCTAAT 60.047 44.000 0.00 0.00 0.00 1.73
2771 2910 4.282703 GCTATTACAATCGACCCCCTCTAA 59.717 45.833 0.00 0.00 0.00 2.10
2772 2911 3.830755 GCTATTACAATCGACCCCCTCTA 59.169 47.826 0.00 0.00 0.00 2.43
2773 2912 2.633481 GCTATTACAATCGACCCCCTCT 59.367 50.000 0.00 0.00 0.00 3.69
2791 2930 7.719193 TGCTAATAATATGTTGCTCTTTGGCTA 59.281 33.333 0.00 0.00 0.00 3.93
2811 2950 9.419297 GATCATGATGCACAATATTTTGCTAAT 57.581 29.630 23.23 12.21 39.62 1.73
2812 2951 8.414778 TGATCATGATGCACAATATTTTGCTAA 58.585 29.630 23.23 11.79 39.62 3.09
2814 2953 6.811954 TGATCATGATGCACAATATTTTGCT 58.188 32.000 23.23 11.69 39.62 3.91
2815 2954 7.598869 AGATGATCATGATGCACAATATTTTGC 59.401 33.333 14.30 17.76 36.22 3.68
2816 2955 9.129209 GAGATGATCATGATGCACAATATTTTG 57.871 33.333 14.30 0.00 38.86 2.44
2817 2956 8.856103 TGAGATGATCATGATGCACAATATTTT 58.144 29.630 14.30 0.00 31.12 1.82
2886 4203 9.925545 AGACCTTTAAGAAAAAGTTTAGGGTTA 57.074 29.630 0.00 0.00 0.00 2.85
2893 4210 8.480501 GGGGTTTAGACCTTTAAGAAAAAGTTT 58.519 33.333 1.94 0.00 45.75 2.66
2895 4212 7.359849 AGGGGTTTAGACCTTTAAGAAAAAGT 58.640 34.615 1.94 0.00 45.75 2.66
2958 4275 1.815003 GAACTTGAGGCCATGACAAGG 59.185 52.381 24.52 13.55 43.28 3.61
2963 6625 3.284617 CATGATGAACTTGAGGCCATGA 58.715 45.455 5.01 0.00 33.72 3.07


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

AutoCloner maintained by Alex Coulton.