Multiple sequence alignment - TraesCS1D01G208000

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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 TraesCS1D01G208000 chr1D 100.000 3092 0 0 1 3092 294130591 294133682 0.000000e+00 5710.0
1 TraesCS1D01G208000 chr1B 96.206 1766 41 12 624 2373 395751969 395753724 0.000000e+00 2867.0
2 TraesCS1D01G208000 chr1B 91.054 626 55 1 4 629 395730863 395731487 0.000000e+00 845.0
3 TraesCS1D01G208000 chr1B 92.120 368 17 11 2376 2734 395753772 395754136 2.750000e-140 508.0
4 TraesCS1D01G208000 chr1B 88.611 360 35 5 2736 3092 395754095 395754451 1.700000e-117 433.0
5 TraesCS1D01G208000 chr1A 96.548 1738 24 9 786 2500 366543056 366544780 0.000000e+00 2844.0
6 TraesCS1D01G208000 chr1A 90.135 517 50 1 1 516 366542441 366542957 0.000000e+00 671.0
7 TraesCS1D01G208000 chr1A 97.826 92 2 0 2509 2600 366544840 366544931 3.190000e-35 159.0
8 TraesCS1D01G208000 chr4D 88.647 1101 112 13 1001 2093 487631864 487632959 0.000000e+00 1328.0
9 TraesCS1D01G208000 chr4B 88.374 1101 115 13 1001 2093 623163618 623164713 0.000000e+00 1312.0
10 TraesCS1D01G208000 chr5A 87.942 1103 119 13 1001 2093 669564673 669565771 0.000000e+00 1288.0
11 TraesCS1D01G208000 chr2D 75.502 249 55 5 497 742 608437156 608437401 1.950000e-22 117.0
12 TraesCS1D01G208000 chr2D 88.136 59 6 1 639 697 516857171 516857114 5.530000e-08 69.4
13 TraesCS1D01G208000 chr5B 90.141 71 7 0 39 109 575599732 575599662 3.280000e-15 93.5


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 TraesCS1D01G208000 chr1D 294130591 294133682 3091 False 5710.000000 5710 100.000000 1 3092 1 chr1D.!!$F1 3091
1 TraesCS1D01G208000 chr1B 395751969 395754451 2482 False 1269.333333 2867 92.312333 624 3092 3 chr1B.!!$F2 2468
2 TraesCS1D01G208000 chr1B 395730863 395731487 624 False 845.000000 845 91.054000 4 629 1 chr1B.!!$F1 625
3 TraesCS1D01G208000 chr1A 366542441 366544931 2490 False 1224.666667 2844 94.836333 1 2600 3 chr1A.!!$F1 2599
4 TraesCS1D01G208000 chr4D 487631864 487632959 1095 False 1328.000000 1328 88.647000 1001 2093 1 chr4D.!!$F1 1092
5 TraesCS1D01G208000 chr4B 623163618 623164713 1095 False 1312.000000 1312 88.374000 1001 2093 1 chr4B.!!$F1 1092
6 TraesCS1D01G208000 chr5A 669564673 669565771 1098 False 1288.000000 1288 87.942000 1001 2093 1 chr5A.!!$F1 1092

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
339 340 0.169009 GTTGATGCCTTTCGAGGTGC 59.831 55.0 0.0 0.0 0.0 5.01 F
657 659 0.247736 AGTGAGGAGTGGCGTGATTC 59.752 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2031 2057 0.971959 GCATTGGGGTGAAGATGCCA 60.972 55.000 0.0 0.0 39.08 4.92 R
2175 2201 3.151912 AGATCAAAACCAAGAGCTGCT 57.848 42.857 0.0 0.0 0.00 4.24 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
111 112 5.221009 GGAATGAAGCTAGAGATGGCAAAAG 60.221 44.000 0.00 0.00 0.00 2.27
117 118 4.886489 AGCTAGAGATGGCAAAAGAATTCC 59.114 41.667 0.65 0.00 0.00 3.01
207 208 4.439253 AAGCTAGAACAAAGGTGAAGGT 57.561 40.909 0.00 0.00 0.00 3.50
211 212 3.214696 AGAACAAAGGTGAAGGTCCAG 57.785 47.619 0.00 0.00 0.00 3.86
267 268 0.916086 TTGGCCAATACGGATGGAGT 59.084 50.000 16.05 0.00 40.56 3.85
324 325 0.179094 GTCCTGTGTGACCACGTTGA 60.179 55.000 0.00 0.00 44.92 3.18
339 340 0.169009 GTTGATGCCTTTCGAGGTGC 59.831 55.000 0.00 0.00 0.00 5.01
449 450 3.376234 CGAAGTACAGAGGATCCACGTTA 59.624 47.826 15.82 1.60 33.66 3.18
457 458 3.444388 AGAGGATCCACGTTAAGACAGAC 59.556 47.826 15.82 0.00 33.66 3.51
467 468 5.008811 CACGTTAAGACAGACTATAGGGAGG 59.991 48.000 4.43 0.00 0.00 4.30
469 470 3.983533 AAGACAGACTATAGGGAGGCT 57.016 47.619 4.43 0.00 33.93 4.58
486 487 1.717194 GCTGTTGCCATGTTCAATGG 58.283 50.000 0.00 0.00 41.99 3.16
491 492 1.314534 TGCCATGTTCAATGGGAGCG 61.315 55.000 6.50 0.00 39.53 5.03
517 519 1.073722 CCTTTCTGCAGCTGGACCA 59.926 57.895 17.12 3.94 0.00 4.02
555 557 2.263741 GGCTAATGCAGGGATGGCG 61.264 63.158 0.00 0.00 41.91 5.69
604 606 2.512896 GCCAATCGAGCCTCCCAT 59.487 61.111 0.00 0.00 0.00 4.00
605 607 1.754745 GCCAATCGAGCCTCCCATA 59.245 57.895 0.00 0.00 0.00 2.74
606 608 0.326264 GCCAATCGAGCCTCCCATAT 59.674 55.000 0.00 0.00 0.00 1.78
607 609 1.677217 GCCAATCGAGCCTCCCATATC 60.677 57.143 0.00 0.00 0.00 1.63
608 610 1.905215 CCAATCGAGCCTCCCATATCT 59.095 52.381 0.00 0.00 0.00 1.98
609 611 2.304180 CCAATCGAGCCTCCCATATCTT 59.696 50.000 0.00 0.00 0.00 2.40
610 612 3.515502 CCAATCGAGCCTCCCATATCTTA 59.484 47.826 0.00 0.00 0.00 2.10
611 613 4.382470 CCAATCGAGCCTCCCATATCTTAG 60.382 50.000 0.00 0.00 0.00 2.18
612 614 2.171840 TCGAGCCTCCCATATCTTAGC 58.828 52.381 0.00 0.00 0.00 3.09
613 615 2.175202 CGAGCCTCCCATATCTTAGCT 58.825 52.381 0.00 0.00 0.00 3.32
614 616 3.010250 TCGAGCCTCCCATATCTTAGCTA 59.990 47.826 0.00 0.00 0.00 3.32
615 617 3.380004 CGAGCCTCCCATATCTTAGCTAG 59.620 52.174 0.00 0.00 0.00 3.42
616 618 4.605183 GAGCCTCCCATATCTTAGCTAGA 58.395 47.826 0.00 0.00 37.28 2.43
617 619 4.349365 AGCCTCCCATATCTTAGCTAGAC 58.651 47.826 0.00 0.00 35.19 2.59
618 620 4.045334 AGCCTCCCATATCTTAGCTAGACT 59.955 45.833 0.00 0.00 35.19 3.24
619 621 4.401202 GCCTCCCATATCTTAGCTAGACTC 59.599 50.000 0.00 0.00 35.19 3.36
620 622 4.638421 CCTCCCATATCTTAGCTAGACTCG 59.362 50.000 0.00 0.00 35.19 4.18
621 623 4.011023 TCCCATATCTTAGCTAGACTCGC 58.989 47.826 0.00 0.00 35.19 5.03
622 624 3.181505 CCCATATCTTAGCTAGACTCGCG 60.182 52.174 0.00 0.00 35.19 5.87
627 629 1.532007 CTTAGCTAGACTCGCGGTAGG 59.468 57.143 6.13 0.00 0.00 3.18
631 633 1.666054 CTAGACTCGCGGTAGGTTCT 58.334 55.000 6.13 0.00 0.00 3.01
655 657 1.593787 CAGTGAGGAGTGGCGTGAT 59.406 57.895 0.00 0.00 0.00 3.06
657 659 0.247736 AGTGAGGAGTGGCGTGATTC 59.752 55.000 0.00 0.00 0.00 2.52
667 669 4.094684 CGTGATTCGCCTCCAGAC 57.905 61.111 0.00 0.00 0.00 3.51
676 678 1.751351 TCGCCTCCAGACTGTATCTTG 59.249 52.381 0.93 0.00 34.41 3.02
715 718 6.979238 ACGAGATCCGAAACTTTATTAAGGAG 59.021 38.462 10.05 0.00 41.76 3.69
772 777 2.268076 GGTCCAAGCCGTGTGCAAT 61.268 57.895 0.00 0.00 44.83 3.56
781 786 1.655484 CCGTGTGCAATAGCTGATGA 58.345 50.000 0.00 0.00 42.74 2.92
782 787 1.596260 CCGTGTGCAATAGCTGATGAG 59.404 52.381 0.00 0.00 42.74 2.90
856 870 2.583593 GCATCCTCTGCCGTCGTC 60.584 66.667 0.00 0.00 45.66 4.20
857 871 2.105128 CATCCTCTGCCGTCGTCC 59.895 66.667 0.00 0.00 0.00 4.79
858 872 3.518998 ATCCTCTGCCGTCGTCCG 61.519 66.667 0.00 0.00 0.00 4.79
903 917 3.375699 TCTCTCTCCCATTTACCACCTC 58.624 50.000 0.00 0.00 0.00 3.85
904 918 3.107601 CTCTCTCCCATTTACCACCTCA 58.892 50.000 0.00 0.00 0.00 3.86
905 919 3.107601 TCTCTCCCATTTACCACCTCAG 58.892 50.000 0.00 0.00 0.00 3.35
906 920 3.107601 CTCTCCCATTTACCACCTCAGA 58.892 50.000 0.00 0.00 0.00 3.27
907 921 2.838202 TCTCCCATTTACCACCTCAGAC 59.162 50.000 0.00 0.00 0.00 3.51
988 1011 2.640332 AGTCAAACCTTTCTCTCCTCCC 59.360 50.000 0.00 0.00 0.00 4.30
1808 1834 4.194720 GCAGGACGAGATCGCCGT 62.195 66.667 14.38 14.38 44.43 5.68
1833 1859 1.033574 CTAAGGAGGTCGGCTTCGAT 58.966 55.000 0.00 0.00 45.21 3.59
1935 1961 1.079819 CAACTCGCTGGTGATCCGT 60.080 57.895 0.00 0.00 34.70 4.69
2175 2201 1.275291 AGCGGAATCAGACGAGGAAAA 59.725 47.619 0.00 0.00 0.00 2.29
2253 2280 5.713792 TCTTGTTCTTAGACTGAGACTGG 57.286 43.478 0.00 0.00 0.00 4.00
2629 2761 3.173151 TCTACTCAGCAGATCCAAACCA 58.827 45.455 0.00 0.00 0.00 3.67
2713 2845 6.540551 TGTACACTTTCAAAGCATCTACAACA 59.459 34.615 0.00 0.00 0.00 3.33
2720 2852 8.795786 TTTCAAAGCATCTACAACAACAATAC 57.204 30.769 0.00 0.00 0.00 1.89
2734 2866 5.385198 ACAACAATACACAAATCTGGACCT 58.615 37.500 0.00 0.00 0.00 3.85
2735 2867 5.473504 ACAACAATACACAAATCTGGACCTC 59.526 40.000 0.00 0.00 0.00 3.85
2736 2868 5.241403 ACAATACACAAATCTGGACCTCA 57.759 39.130 0.00 0.00 0.00 3.86
2737 2869 5.003804 ACAATACACAAATCTGGACCTCAC 58.996 41.667 0.00 0.00 0.00 3.51
2738 2870 5.221925 ACAATACACAAATCTGGACCTCACT 60.222 40.000 0.00 0.00 0.00 3.41
2739 2871 3.864789 ACACAAATCTGGACCTCACTT 57.135 42.857 0.00 0.00 0.00 3.16
2740 2872 4.170468 ACACAAATCTGGACCTCACTTT 57.830 40.909 0.00 0.00 0.00 2.66
2741 2873 4.137543 ACACAAATCTGGACCTCACTTTC 58.862 43.478 0.00 0.00 0.00 2.62
2742 2874 4.136796 CACAAATCTGGACCTCACTTTCA 58.863 43.478 0.00 0.00 0.00 2.69
2743 2875 4.580167 CACAAATCTGGACCTCACTTTCAA 59.420 41.667 0.00 0.00 0.00 2.69
2744 2876 5.067674 CACAAATCTGGACCTCACTTTCAAA 59.932 40.000 0.00 0.00 0.00 2.69
2745 2877 5.300286 ACAAATCTGGACCTCACTTTCAAAG 59.700 40.000 0.00 0.00 0.00 2.77
2746 2878 2.851195 TCTGGACCTCACTTTCAAAGC 58.149 47.619 0.00 0.00 0.00 3.51
2747 2879 2.172505 TCTGGACCTCACTTTCAAAGCA 59.827 45.455 0.00 0.00 0.00 3.91
2748 2880 3.152341 CTGGACCTCACTTTCAAAGCAT 58.848 45.455 0.00 0.00 0.00 3.79
2749 2881 3.149196 TGGACCTCACTTTCAAAGCATC 58.851 45.455 0.00 0.00 0.00 3.91
2750 2882 3.181440 TGGACCTCACTTTCAAAGCATCT 60.181 43.478 0.00 0.00 0.00 2.90
2751 2883 3.823304 GGACCTCACTTTCAAAGCATCTT 59.177 43.478 0.00 0.00 0.00 2.40
2752 2884 5.003804 GGACCTCACTTTCAAAGCATCTTA 58.996 41.667 0.00 0.00 0.00 2.10
2753 2885 5.106515 GGACCTCACTTTCAAAGCATCTTAC 60.107 44.000 0.00 0.00 0.00 2.34
2754 2886 5.376625 ACCTCACTTTCAAAGCATCTTACA 58.623 37.500 0.00 0.00 0.00 2.41
2755 2887 5.827797 ACCTCACTTTCAAAGCATCTTACAA 59.172 36.000 0.00 0.00 0.00 2.41
2756 2888 6.145535 CCTCACTTTCAAAGCATCTTACAAC 58.854 40.000 0.00 0.00 0.00 3.32
2757 2889 6.072112 TCACTTTCAAAGCATCTTACAACC 57.928 37.500 0.00 0.00 0.00 3.77
2758 2890 5.592282 TCACTTTCAAAGCATCTTACAACCA 59.408 36.000 0.00 0.00 0.00 3.67
2759 2891 5.687285 CACTTTCAAAGCATCTTACAACCAC 59.313 40.000 0.00 0.00 0.00 4.16
2760 2892 5.359576 ACTTTCAAAGCATCTTACAACCACA 59.640 36.000 0.00 0.00 0.00 4.17
2761 2893 5.843673 TTCAAAGCATCTTACAACCACAA 57.156 34.783 0.00 0.00 0.00 3.33
2762 2894 6.403866 TTCAAAGCATCTTACAACCACAAT 57.596 33.333 0.00 0.00 0.00 2.71
2763 2895 7.517614 TTCAAAGCATCTTACAACCACAATA 57.482 32.000 0.00 0.00 0.00 1.90
2764 2896 6.908825 TCAAAGCATCTTACAACCACAATAC 58.091 36.000 0.00 0.00 0.00 1.89
2765 2897 6.488344 TCAAAGCATCTTACAACCACAATACA 59.512 34.615 0.00 0.00 0.00 2.29
2766 2898 5.880054 AGCATCTTACAACCACAATACAC 57.120 39.130 0.00 0.00 0.00 2.90
2767 2899 5.312895 AGCATCTTACAACCACAATACACA 58.687 37.500 0.00 0.00 0.00 3.72
2768 2900 5.767665 AGCATCTTACAACCACAATACACAA 59.232 36.000 0.00 0.00 0.00 3.33
2769 2901 6.264292 AGCATCTTACAACCACAATACACAAA 59.736 34.615 0.00 0.00 0.00 2.83
2770 2902 7.039784 AGCATCTTACAACCACAATACACAAAT 60.040 33.333 0.00 0.00 0.00 2.32
2771 2903 7.273381 GCATCTTACAACCACAATACACAAATC 59.727 37.037 0.00 0.00 0.00 2.17
2772 2904 8.514594 CATCTTACAACCACAATACACAAATCT 58.485 33.333 0.00 0.00 0.00 2.40
2773 2905 7.870826 TCTTACAACCACAATACACAAATCTG 58.129 34.615 0.00 0.00 0.00 2.90
2774 2906 5.452078 ACAACCACAATACACAAATCTGG 57.548 39.130 0.00 0.00 0.00 3.86
2775 2907 5.136828 ACAACCACAATACACAAATCTGGA 58.863 37.500 0.00 0.00 0.00 3.86
2776 2908 5.009610 ACAACCACAATACACAAATCTGGAC 59.990 40.000 0.00 0.00 0.00 4.02
2777 2909 4.079253 ACCACAATACACAAATCTGGACC 58.921 43.478 0.00 0.00 0.00 4.46
2778 2910 3.443681 CCACAATACACAAATCTGGACCC 59.556 47.826 0.00 0.00 0.00 4.46
2779 2911 3.443681 CACAATACACAAATCTGGACCCC 59.556 47.826 0.00 0.00 0.00 4.95
2780 2912 3.023832 CAATACACAAATCTGGACCCCC 58.976 50.000 0.00 0.00 0.00 5.40
2781 2913 0.616371 TACACAAATCTGGACCCCCG 59.384 55.000 0.00 0.00 34.29 5.73
2782 2914 1.131303 ACACAAATCTGGACCCCCGA 61.131 55.000 0.00 0.00 34.29 5.14
2783 2915 0.037590 CACAAATCTGGACCCCCGAA 59.962 55.000 0.00 0.00 34.29 4.30
2784 2916 0.774908 ACAAATCTGGACCCCCGAAA 59.225 50.000 0.00 0.00 34.29 3.46
2785 2917 1.173913 CAAATCTGGACCCCCGAAAC 58.826 55.000 0.00 0.00 34.29 2.78
2786 2918 0.322187 AAATCTGGACCCCCGAAACG 60.322 55.000 0.00 0.00 34.29 3.60
2787 2919 1.486145 AATCTGGACCCCCGAAACGT 61.486 55.000 0.00 0.00 34.29 3.99
2788 2920 1.486145 ATCTGGACCCCCGAAACGTT 61.486 55.000 0.00 0.00 34.29 3.99
2789 2921 1.228033 CTGGACCCCCGAAACGTTT 60.228 57.895 14.57 14.57 34.29 3.60
2798 2930 1.277440 CGAAACGTTTGTGGACCCG 59.723 57.895 20.10 9.91 0.00 5.28
2811 2943 4.001248 ACCCGTTCGGTCGTATCA 57.999 55.556 10.36 0.00 43.58 2.15
2829 2961 5.643777 CGTATCACTTTGATCCCTCACTTTT 59.356 40.000 0.00 0.00 38.26 2.27
2830 2962 6.183360 CGTATCACTTTGATCCCTCACTTTTC 60.183 42.308 0.00 0.00 38.26 2.29
2831 2963 5.310409 TCACTTTGATCCCTCACTTTTCT 57.690 39.130 0.00 0.00 0.00 2.52
2832 2964 5.065914 TCACTTTGATCCCTCACTTTTCTG 58.934 41.667 0.00 0.00 0.00 3.02
2840 2972 4.398319 TCCCTCACTTTTCTGGACAAATC 58.602 43.478 0.00 0.00 0.00 2.17
2842 2974 4.457257 CCCTCACTTTTCTGGACAAATCTC 59.543 45.833 0.00 0.00 0.00 2.75
2860 2992 2.133281 TCGACCCTCGAATGTTCCTA 57.867 50.000 0.00 0.00 46.90 2.94
2864 2996 3.268330 GACCCTCGAATGTTCCTAAACC 58.732 50.000 0.00 0.00 34.28 3.27
2900 3032 6.877611 TCACTTTGATACCTCACTTTTTCC 57.122 37.500 0.00 0.00 0.00 3.13
2910 3042 0.318614 CACTTTTTCCCGCGCACAAT 60.319 50.000 8.75 0.00 0.00 2.71
2915 3047 0.952280 TTTCCCGCGCACAATTACAA 59.048 45.000 8.75 0.00 0.00 2.41
2921 3053 1.665679 CGCGCACAATTACAATCCTCT 59.334 47.619 8.75 0.00 0.00 3.69
2922 3054 2.537529 CGCGCACAATTACAATCCTCTG 60.538 50.000 8.75 0.00 0.00 3.35
2924 3056 3.485877 GCGCACAATTACAATCCTCTGTC 60.486 47.826 0.30 0.00 0.00 3.51
2926 3058 4.033358 CGCACAATTACAATCCTCTGTCTC 59.967 45.833 0.00 0.00 0.00 3.36
2927 3059 5.181748 GCACAATTACAATCCTCTGTCTCT 58.818 41.667 0.00 0.00 0.00 3.10
2928 3060 5.293079 GCACAATTACAATCCTCTGTCTCTC 59.707 44.000 0.00 0.00 0.00 3.20
2943 3078 5.966935 TCTGTCTCTCCCATTTATCCTTTCT 59.033 40.000 0.00 0.00 0.00 2.52
2970 3105 9.797556 ATGTCAGATATTTCATCAAACACATTG 57.202 29.630 0.00 0.00 40.58 2.82
2987 3122 2.073117 TTGTGTGCATCATACGACGT 57.927 45.000 5.52 5.52 0.00 4.34
3006 3141 3.140814 GCCCCGCAACCCAATCTC 61.141 66.667 0.00 0.00 0.00 2.75
3009 3144 2.398554 CCCGCAACCCAATCTCGTG 61.399 63.158 0.00 0.00 0.00 4.35
3083 3218 2.325484 GGGTTGGGTGAAAATTGGACT 58.675 47.619 0.00 0.00 0.00 3.85
3087 3222 4.559153 GTTGGGTGAAAATTGGACTGATG 58.441 43.478 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.912763 GCCATTGCAAGAACCCCCA 60.913 57.895 4.94 0.00 37.47 4.96
5 6 1.593265 CCAGCCATTGCAAGAACCC 59.407 57.895 4.94 0.00 41.13 4.11
31 32 6.465607 GCATCATTTCTTTCTCCTCCTATCCT 60.466 42.308 0.00 0.00 0.00 3.24
35 36 5.678583 CAGCATCATTTCTTTCTCCTCCTA 58.321 41.667 0.00 0.00 0.00 2.94
111 112 7.709947 TGATATTTCATGTGCTTCTGGAATTC 58.290 34.615 0.00 0.00 0.00 2.17
170 171 0.321996 GCTTTCCTCTGGACGGTCTT 59.678 55.000 8.23 0.00 0.00 3.01
207 208 0.907486 CTTCCACCTCTCATGCTGGA 59.093 55.000 5.65 0.00 0.00 3.86
211 212 1.300963 TGGCTTCCACCTCTCATGC 59.699 57.895 0.00 0.00 0.00 4.06
267 268 4.312443 CTTTACCTCGTCTTTTGCCACTA 58.688 43.478 0.00 0.00 0.00 2.74
339 340 1.301677 GGGAAAGAAGTGAGCCGCAG 61.302 60.000 0.00 0.00 0.00 5.18
429 430 5.014858 TCTTAACGTGGATCCTCTGTACTT 58.985 41.667 14.23 1.99 0.00 2.24
449 450 3.052490 ACAGCCTCCCTATAGTCTGTCTT 60.052 47.826 0.00 0.00 29.81 3.01
479 480 0.321210 TTCTTCGCGCTCCCATTGAA 60.321 50.000 5.56 0.00 0.00 2.69
486 487 0.670854 AGAAAGGTTCTTCGCGCTCC 60.671 55.000 5.56 0.00 36.36 4.70
491 492 0.110010 GCTGCAGAAAGGTTCTTCGC 60.110 55.000 20.43 0.00 38.11 4.70
517 519 3.434309 CCCTTTGATGTCCTCCACAATT 58.566 45.455 0.00 0.00 38.97 2.32
525 527 2.025037 TGCATTAGCCCTTTGATGTCCT 60.025 45.455 0.00 0.00 41.13 3.85
555 557 0.035056 CCATGAGACTCAACACCCCC 60.035 60.000 9.70 0.00 0.00 5.40
561 563 2.626840 GCCTCTTCCATGAGACTCAAC 58.373 52.381 9.70 0.00 36.23 3.18
563 565 0.820226 CGCCTCTTCCATGAGACTCA 59.180 55.000 7.80 7.80 36.23 3.41
593 595 2.175202 AGCTAAGATATGGGAGGCTCG 58.825 52.381 8.69 0.00 0.00 5.03
594 596 4.401202 GTCTAGCTAAGATATGGGAGGCTC 59.599 50.000 5.78 5.78 36.36 4.70
595 597 4.045334 AGTCTAGCTAAGATATGGGAGGCT 59.955 45.833 0.00 0.00 36.36 4.58
596 598 4.349365 AGTCTAGCTAAGATATGGGAGGC 58.651 47.826 0.00 0.00 36.36 4.70
597 599 4.638421 CGAGTCTAGCTAAGATATGGGAGG 59.362 50.000 0.00 0.00 36.36 4.30
598 600 4.095782 GCGAGTCTAGCTAAGATATGGGAG 59.904 50.000 0.00 0.00 36.36 4.30
599 601 4.011023 GCGAGTCTAGCTAAGATATGGGA 58.989 47.826 0.00 0.00 36.36 4.37
601 603 3.181505 CCGCGAGTCTAGCTAAGATATGG 60.182 52.174 8.23 0.00 36.36 2.74
604 606 3.123157 ACCGCGAGTCTAGCTAAGATA 57.877 47.619 8.23 0.00 36.36 1.98
605 607 1.970092 ACCGCGAGTCTAGCTAAGAT 58.030 50.000 8.23 0.00 36.36 2.40
606 608 2.481854 CTACCGCGAGTCTAGCTAAGA 58.518 52.381 8.23 0.00 0.00 2.10
607 609 1.532007 CCTACCGCGAGTCTAGCTAAG 59.468 57.143 8.23 0.00 0.00 2.18
608 610 1.134280 ACCTACCGCGAGTCTAGCTAA 60.134 52.381 8.23 0.00 0.00 3.09
609 611 0.467384 ACCTACCGCGAGTCTAGCTA 59.533 55.000 8.23 0.00 0.00 3.32
610 612 0.394080 AACCTACCGCGAGTCTAGCT 60.394 55.000 8.23 0.00 0.00 3.32
611 613 0.029167 GAACCTACCGCGAGTCTAGC 59.971 60.000 8.23 0.00 0.00 3.42
612 614 1.331138 CAGAACCTACCGCGAGTCTAG 59.669 57.143 8.23 0.12 0.00 2.43
613 615 1.065926 TCAGAACCTACCGCGAGTCTA 60.066 52.381 8.23 0.00 0.00 2.59
614 616 0.322277 TCAGAACCTACCGCGAGTCT 60.322 55.000 8.23 0.00 0.00 3.24
615 617 0.099082 CTCAGAACCTACCGCGAGTC 59.901 60.000 8.23 0.00 0.00 3.36
616 618 0.322277 TCTCAGAACCTACCGCGAGT 60.322 55.000 8.23 6.57 0.00 4.18
617 619 0.099082 GTCTCAGAACCTACCGCGAG 59.901 60.000 8.23 0.00 0.00 5.03
618 620 1.310933 GGTCTCAGAACCTACCGCGA 61.311 60.000 8.23 0.00 36.32 5.87
619 621 1.139095 GGTCTCAGAACCTACCGCG 59.861 63.158 0.00 0.00 36.32 6.46
620 622 0.173708 CTGGTCTCAGAACCTACCGC 59.826 60.000 0.00 0.00 43.49 5.68
621 623 1.202582 CACTGGTCTCAGAACCTACCG 59.797 57.143 0.00 0.00 43.49 4.02
622 624 2.494073 CTCACTGGTCTCAGAACCTACC 59.506 54.545 0.00 0.00 43.49 3.18
627 629 2.029470 CACTCCTCACTGGTCTCAGAAC 60.029 54.545 0.00 0.00 43.49 3.01
631 633 1.188219 GCCACTCCTCACTGGTCTCA 61.188 60.000 0.00 0.00 37.07 3.27
655 657 2.145397 AGATACAGTCTGGAGGCGAA 57.855 50.000 4.53 0.00 35.31 4.70
657 659 1.804372 GCAAGATACAGTCTGGAGGCG 60.804 57.143 4.53 0.00 37.23 5.52
663 665 6.128982 CGCTATTACATGCAAGATACAGTCTG 60.129 42.308 0.00 0.00 37.23 3.51
667 669 5.119279 GTCCGCTATTACATGCAAGATACAG 59.881 44.000 0.00 0.00 0.00 2.74
676 678 2.417339 TCTCGTCCGCTATTACATGC 57.583 50.000 0.00 0.00 0.00 4.06
739 742 0.178961 GGACCTGGGCTGGAAGTTTT 60.179 55.000 0.00 0.00 35.30 2.43
742 745 1.774217 TTGGACCTGGGCTGGAAGT 60.774 57.895 0.00 0.00 35.30 3.01
772 777 3.329386 GTGTTTGCACTCTCATCAGCTA 58.671 45.455 0.00 0.00 42.13 3.32
781 786 2.594592 GGCCCGTGTTTGCACTCT 60.595 61.111 0.00 0.00 43.16 3.24
782 787 4.025401 CGGCCCGTGTTTGCACTC 62.025 66.667 0.00 0.00 43.16 3.51
802 807 2.282147 CTGGACTCTGCTCAGCTCCG 62.282 65.000 0.00 0.00 31.36 4.63
803 808 0.969917 TCTGGACTCTGCTCAGCTCC 60.970 60.000 0.00 0.00 0.00 4.70
852 866 0.734942 GCTGGATTCGAAACGGACGA 60.735 55.000 14.18 0.00 37.99 4.20
853 867 0.736325 AGCTGGATTCGAAACGGACG 60.736 55.000 14.18 0.00 0.00 4.79
854 868 0.721718 CAGCTGGATTCGAAACGGAC 59.278 55.000 5.57 7.10 0.00 4.79
855 869 0.391130 CCAGCTGGATTCGAAACGGA 60.391 55.000 29.88 0.00 37.39 4.69
856 870 1.369091 CCCAGCTGGATTCGAAACGG 61.369 60.000 34.91 9.20 37.39 4.44
857 871 1.982073 GCCCAGCTGGATTCGAAACG 61.982 60.000 34.91 14.69 37.39 3.60
858 872 0.960364 TGCCCAGCTGGATTCGAAAC 60.960 55.000 34.91 12.30 37.39 2.78
903 917 1.142748 GCGATCTGGGTCTGGTCTG 59.857 63.158 0.00 0.00 0.00 3.51
904 918 0.904865 TTGCGATCTGGGTCTGGTCT 60.905 55.000 0.00 0.00 0.00 3.85
905 919 0.179000 ATTGCGATCTGGGTCTGGTC 59.821 55.000 0.00 0.00 0.00 4.02
906 920 0.179000 GATTGCGATCTGGGTCTGGT 59.821 55.000 6.70 0.00 0.00 4.00
907 921 0.467384 AGATTGCGATCTGGGTCTGG 59.533 55.000 16.02 0.00 41.09 3.86
988 1011 1.670590 GCTCCATCTCCCCGATCTG 59.329 63.158 0.00 0.00 0.00 2.90
1808 1834 2.110967 CCGACCTCCTTAGCGACGA 61.111 63.158 0.00 0.00 0.00 4.20
1833 1859 1.666011 GTCCAGCTCCTTGACGACA 59.334 57.895 0.00 0.00 0.00 4.35
2031 2057 0.971959 GCATTGGGGTGAAGATGCCA 60.972 55.000 0.00 0.00 39.08 4.92
2175 2201 3.151912 AGATCAAAACCAAGAGCTGCT 57.848 42.857 0.00 0.00 0.00 4.24
2253 2280 3.464907 GAGCTCCCCGGAACTAATTAAC 58.535 50.000 0.73 0.00 0.00 2.01
2288 2315 5.516044 ACAGGGAAAATATAAAGTGGGGAC 58.484 41.667 0.00 0.00 0.00 4.46
2713 2845 5.473504 GTGAGGTCCAGATTTGTGTATTGTT 59.526 40.000 0.00 0.00 0.00 2.83
2720 2852 4.136796 TGAAAGTGAGGTCCAGATTTGTG 58.863 43.478 0.00 0.00 0.00 3.33
2734 2866 5.592282 TGGTTGTAAGATGCTTTGAAAGTGA 59.408 36.000 6.81 0.00 0.00 3.41
2735 2867 5.687285 GTGGTTGTAAGATGCTTTGAAAGTG 59.313 40.000 6.81 0.00 0.00 3.16
2736 2868 5.359576 TGTGGTTGTAAGATGCTTTGAAAGT 59.640 36.000 6.81 0.00 0.00 2.66
2737 2869 5.830912 TGTGGTTGTAAGATGCTTTGAAAG 58.169 37.500 0.00 0.00 0.00 2.62
2738 2870 5.843673 TGTGGTTGTAAGATGCTTTGAAA 57.156 34.783 0.00 0.00 0.00 2.69
2739 2871 5.843673 TTGTGGTTGTAAGATGCTTTGAA 57.156 34.783 0.00 0.00 0.00 2.69
2740 2872 6.488344 TGTATTGTGGTTGTAAGATGCTTTGA 59.512 34.615 0.00 0.00 0.00 2.69
2741 2873 6.582295 GTGTATTGTGGTTGTAAGATGCTTTG 59.418 38.462 0.00 0.00 0.00 2.77
2742 2874 6.264292 TGTGTATTGTGGTTGTAAGATGCTTT 59.736 34.615 0.00 0.00 0.00 3.51
2743 2875 5.767665 TGTGTATTGTGGTTGTAAGATGCTT 59.232 36.000 0.00 0.00 0.00 3.91
2744 2876 5.312895 TGTGTATTGTGGTTGTAAGATGCT 58.687 37.500 0.00 0.00 0.00 3.79
2745 2877 5.621197 TGTGTATTGTGGTTGTAAGATGC 57.379 39.130 0.00 0.00 0.00 3.91
2746 2878 8.514594 AGATTTGTGTATTGTGGTTGTAAGATG 58.485 33.333 0.00 0.00 0.00 2.90
2747 2879 8.514594 CAGATTTGTGTATTGTGGTTGTAAGAT 58.485 33.333 0.00 0.00 0.00 2.40
2748 2880 7.040755 CCAGATTTGTGTATTGTGGTTGTAAGA 60.041 37.037 0.00 0.00 0.00 2.10
2749 2881 7.040755 TCCAGATTTGTGTATTGTGGTTGTAAG 60.041 37.037 0.00 0.00 0.00 2.34
2750 2882 6.773200 TCCAGATTTGTGTATTGTGGTTGTAA 59.227 34.615 0.00 0.00 0.00 2.41
2751 2883 6.205853 GTCCAGATTTGTGTATTGTGGTTGTA 59.794 38.462 0.00 0.00 0.00 2.41
2752 2884 5.009610 GTCCAGATTTGTGTATTGTGGTTGT 59.990 40.000 0.00 0.00 0.00 3.32
2753 2885 5.460646 GTCCAGATTTGTGTATTGTGGTTG 58.539 41.667 0.00 0.00 0.00 3.77
2754 2886 4.522789 GGTCCAGATTTGTGTATTGTGGTT 59.477 41.667 0.00 0.00 0.00 3.67
2755 2887 4.079253 GGTCCAGATTTGTGTATTGTGGT 58.921 43.478 0.00 0.00 0.00 4.16
2756 2888 3.443681 GGGTCCAGATTTGTGTATTGTGG 59.556 47.826 0.00 0.00 0.00 4.17
2757 2889 3.443681 GGGGTCCAGATTTGTGTATTGTG 59.556 47.826 0.00 0.00 0.00 3.33
2758 2890 3.563479 GGGGGTCCAGATTTGTGTATTGT 60.563 47.826 0.00 0.00 0.00 2.71
2759 2891 3.023832 GGGGGTCCAGATTTGTGTATTG 58.976 50.000 0.00 0.00 0.00 1.90
2760 2892 2.356741 CGGGGGTCCAGATTTGTGTATT 60.357 50.000 0.00 0.00 0.00 1.89
2761 2893 1.211949 CGGGGGTCCAGATTTGTGTAT 59.788 52.381 0.00 0.00 0.00 2.29
2762 2894 0.616371 CGGGGGTCCAGATTTGTGTA 59.384 55.000 0.00 0.00 0.00 2.90
2763 2895 1.131303 TCGGGGGTCCAGATTTGTGT 61.131 55.000 0.00 0.00 0.00 3.72
2764 2896 0.037590 TTCGGGGGTCCAGATTTGTG 59.962 55.000 0.00 0.00 0.00 3.33
2765 2897 0.774908 TTTCGGGGGTCCAGATTTGT 59.225 50.000 0.00 0.00 0.00 2.83
2766 2898 1.173913 GTTTCGGGGGTCCAGATTTG 58.826 55.000 0.00 0.00 0.00 2.32
2767 2899 0.322187 CGTTTCGGGGGTCCAGATTT 60.322 55.000 0.00 0.00 0.00 2.17
2768 2900 1.298667 CGTTTCGGGGGTCCAGATT 59.701 57.895 0.00 0.00 0.00 2.40
2769 2901 1.486145 AACGTTTCGGGGGTCCAGAT 61.486 55.000 0.00 0.00 0.00 2.90
2770 2902 1.698067 AAACGTTTCGGGGGTCCAGA 61.698 55.000 7.96 0.00 0.00 3.86
2771 2903 1.228033 AAACGTTTCGGGGGTCCAG 60.228 57.895 7.96 0.00 0.00 3.86
2772 2904 1.526455 CAAACGTTTCGGGGGTCCA 60.526 57.895 11.37 0.00 0.00 4.02
2773 2905 1.526686 ACAAACGTTTCGGGGGTCC 60.527 57.895 11.37 0.00 0.00 4.46
2774 2906 1.650363 CACAAACGTTTCGGGGGTC 59.350 57.895 11.37 0.00 0.00 4.46
2775 2907 1.824760 CCACAAACGTTTCGGGGGT 60.825 57.895 11.37 2.61 0.00 4.95
2776 2908 1.526455 TCCACAAACGTTTCGGGGG 60.526 57.895 22.99 18.40 0.00 5.40
2777 2909 1.650363 GTCCACAAACGTTTCGGGG 59.350 57.895 21.26 20.42 0.00 5.73
2778 2910 1.650363 GGTCCACAAACGTTTCGGG 59.350 57.895 20.56 19.04 0.00 5.14
2779 2911 1.650363 GGGTCCACAAACGTTTCGG 59.350 57.895 11.37 14.57 0.00 4.30
2780 2912 1.277440 CGGGTCCACAAACGTTTCG 59.723 57.895 11.37 9.51 0.00 3.46
2781 2913 0.734309 AACGGGTCCACAAACGTTTC 59.266 50.000 11.37 0.00 45.97 2.78
2782 2914 2.871021 AACGGGTCCACAAACGTTT 58.129 47.368 7.96 7.96 45.97 3.60
2783 2915 4.641784 AACGGGTCCACAAACGTT 57.358 50.000 0.00 0.00 43.74 3.99
2784 2916 1.884004 CGAACGGGTCCACAAACGT 60.884 57.895 0.00 0.00 41.88 3.99
2785 2917 2.600475 CCGAACGGGTCCACAAACG 61.600 63.158 5.25 0.00 0.00 3.60
2786 2918 3.336566 CCGAACGGGTCCACAAAC 58.663 61.111 5.25 0.00 0.00 2.93
2798 2930 3.550678 GGATCAAAGTGATACGACCGAAC 59.449 47.826 0.00 0.00 37.20 3.95
2811 2943 4.104738 TCCAGAAAAGTGAGGGATCAAAGT 59.895 41.667 0.00 0.00 0.00 2.66
2829 2961 1.825474 GAGGGTCGAGATTTGTCCAGA 59.175 52.381 0.00 0.00 0.00 3.86
2830 2962 1.469940 CGAGGGTCGAGATTTGTCCAG 60.470 57.143 0.00 0.00 43.74 3.86
2831 2963 0.530744 CGAGGGTCGAGATTTGTCCA 59.469 55.000 0.00 0.00 43.74 4.02
2832 2964 0.815734 TCGAGGGTCGAGATTTGTCC 59.184 55.000 0.00 0.00 44.82 4.02
2840 2972 5.203760 GTTTAGGAACATTCGAGGGTCGAG 61.204 50.000 0.00 0.00 41.57 4.04
2842 2974 2.928116 GTTTAGGAACATTCGAGGGTCG 59.072 50.000 0.00 0.00 37.17 4.79
2860 2992 8.288022 ATCAAAGTGATATGACCGAATGGGTTT 61.288 37.037 0.00 0.00 41.97 3.27
2864 2996 6.147821 GGTATCAAAGTGATATGACCGAATGG 59.852 42.308 1.51 0.00 40.97 3.16
2872 3004 9.739276 AAAAAGTGAGGTATCAAAGTGATATGA 57.261 29.630 1.51 0.00 40.97 2.15
2874 3006 9.178758 GGAAAAAGTGAGGTATCAAAGTGATAT 57.821 33.333 1.51 0.00 40.97 1.63
2879 3011 4.760204 CGGGAAAAAGTGAGGTATCAAAGT 59.240 41.667 0.00 0.00 37.14 2.66
2900 3032 0.732571 AGGATTGTAATTGTGCGCGG 59.267 50.000 8.83 0.00 0.00 6.46
2910 3042 4.061131 TGGGAGAGACAGAGGATTGTAA 57.939 45.455 0.00 0.00 0.00 2.41
2915 3047 4.843516 GGATAAATGGGAGAGACAGAGGAT 59.156 45.833 0.00 0.00 0.00 3.24
2921 3053 7.348274 ACATAGAAAGGATAAATGGGAGAGACA 59.652 37.037 0.00 0.00 0.00 3.41
2922 3054 7.740805 ACATAGAAAGGATAAATGGGAGAGAC 58.259 38.462 0.00 0.00 0.00 3.36
2924 3056 7.739825 TGACATAGAAAGGATAAATGGGAGAG 58.260 38.462 0.00 0.00 0.00 3.20
2926 3058 7.739825 TCTGACATAGAAAGGATAAATGGGAG 58.260 38.462 0.00 0.00 30.84 4.30
2927 3059 7.690454 TCTGACATAGAAAGGATAAATGGGA 57.310 36.000 0.00 0.00 30.84 4.37
2968 3103 1.724082 CACGTCGTATGATGCACACAA 59.276 47.619 0.00 0.00 34.28 3.33
2970 3105 0.645355 CCACGTCGTATGATGCACAC 59.355 55.000 0.00 0.00 34.28 3.82
3006 3141 1.943116 CTCTCCACTCTGCTCCCACG 61.943 65.000 0.00 0.00 0.00 4.94
3009 3144 0.033601 TCTCTCTCCACTCTGCTCCC 60.034 60.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.