Multiple sequence alignment - TraesCS3A01G171300

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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 TraesCS3A01G171300 chr3A 100.000 3198 0 0 1 3198 185172866 185176063 0.000000e+00 5906.0
1 TraesCS3A01G171300 chr3D 89.777 1702 65 49 952 2616 159615913 159617542 0.000000e+00 2078.0
2 TraesCS3A01G171300 chr3D 90.942 817 61 6 72 882 445086431 445087240 0.000000e+00 1086.0
3 TraesCS3A01G171300 chr3D 92.759 580 30 7 2623 3198 159617736 159618307 0.000000e+00 828.0
4 TraesCS3A01G171300 chr3B 90.566 1060 38 27 1005 2031 236353261 236354291 0.000000e+00 1347.0
5 TraesCS3A01G171300 chr3B 89.138 893 85 6 1 887 766018054 766018940 0.000000e+00 1101.0
6 TraesCS3A01G171300 chr3B 93.628 565 26 6 2623 3185 236355091 236355647 0.000000e+00 835.0
7 TraesCS3A01G171300 chr3B 86.918 558 32 20 2065 2616 236354375 236354897 3.550000e-164 588.0
8 TraesCS3A01G171300 chr6D 90.971 886 70 5 1 880 107937402 107936521 0.000000e+00 1184.0
9 TraesCS3A01G171300 chr7D 91.314 875 56 7 9 874 168498614 168497751 0.000000e+00 1177.0
10 TraesCS3A01G171300 chr7D 87.232 885 96 11 1 880 383312442 383311570 0.000000e+00 992.0
11 TraesCS3A01G171300 chr2B 88.475 885 84 9 1 878 228753738 228752865 0.000000e+00 1053.0
12 TraesCS3A01G171300 chr2B 92.029 138 8 2 2623 2759 772141404 772141539 1.170000e-44 191.0
13 TraesCS3A01G171300 chr6A 88.202 890 88 9 1 882 489840472 489839592 0.000000e+00 1046.0
14 TraesCS3A01G171300 chr5A 88.063 888 89 13 1 878 648613902 648613022 0.000000e+00 1037.0
15 TraesCS3A01G171300 chr4D 87.318 891 89 11 1 880 32245247 32246124 0.000000e+00 998.0
16 TraesCS3A01G171300 chr4D 97.222 36 1 0 2745 2780 190490947 190490912 9.580000e-06 62.1


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 TraesCS3A01G171300 chr3A 185172866 185176063 3197 False 5906.000000 5906 100.000000 1 3198 1 chr3A.!!$F1 3197
1 TraesCS3A01G171300 chr3D 159615913 159618307 2394 False 1453.000000 2078 91.268000 952 3198 2 chr3D.!!$F2 2246
2 TraesCS3A01G171300 chr3D 445086431 445087240 809 False 1086.000000 1086 90.942000 72 882 1 chr3D.!!$F1 810
3 TraesCS3A01G171300 chr3B 766018054 766018940 886 False 1101.000000 1101 89.138000 1 887 1 chr3B.!!$F1 886
4 TraesCS3A01G171300 chr3B 236353261 236355647 2386 False 923.333333 1347 90.370667 1005 3185 3 chr3B.!!$F2 2180
5 TraesCS3A01G171300 chr6D 107936521 107937402 881 True 1184.000000 1184 90.971000 1 880 1 chr6D.!!$R1 879
6 TraesCS3A01G171300 chr7D 168497751 168498614 863 True 1177.000000 1177 91.314000 9 874 1 chr7D.!!$R1 865
7 TraesCS3A01G171300 chr7D 383311570 383312442 872 True 992.000000 992 87.232000 1 880 1 chr7D.!!$R2 879
8 TraesCS3A01G171300 chr2B 228752865 228753738 873 True 1053.000000 1053 88.475000 1 878 1 chr2B.!!$R1 877
9 TraesCS3A01G171300 chr6A 489839592 489840472 880 True 1046.000000 1046 88.202000 1 882 1 chr6A.!!$R1 881
10 TraesCS3A01G171300 chr5A 648613022 648613902 880 True 1037.000000 1037 88.063000 1 878 1 chr5A.!!$R1 877
11 TraesCS3A01G171300 chr4D 32245247 32246124 877 False 998.000000 998 87.318000 1 880 1 chr4D.!!$F1 879

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
945 970 0.104487 TAACCAAACACGCCGACTGA 59.896 50.0 0.0 0.0 0.00 3.41 F
949 974 0.110688 CAAACACGCCGACTGATGTG 60.111 55.0 0.0 0.0 38.28 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2291 0.179119 CCTCCGTTTTATCGTCCGCT 60.179 55.0 0.0 0.0 0.0 5.52 R
2403 2531 0.532115 GCATTGGCTCCCGTCAAAAT 59.468 50.0 0.0 0.0 38.4 1.82 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
100 101 2.408022 CCGCTCTCTCGGTTACGG 59.592 66.667 0.00 0.00 44.18 4.02
140 141 1.644786 CGAAATGGAGCCACGGAACC 61.645 60.000 0.00 0.00 0.00 3.62
151 152 4.680237 CGGAACCACGGCTGCTGA 62.680 66.667 16.72 0.00 0.00 4.26
193 194 3.261580 CAACACGACAGCCAATATCTCA 58.738 45.455 0.00 0.00 0.00 3.27
270 272 1.938577 CTCATCGGCAGAGTCCATTTG 59.061 52.381 0.00 0.00 0.00 2.32
321 326 1.737008 GCGTCGAAGGAGACAACCC 60.737 63.158 0.00 0.00 40.98 4.11
361 367 1.186200 CACAGACCAGCTAGCTACCA 58.814 55.000 18.86 0.00 0.00 3.25
396 402 4.429212 CGTGCCGGTCGGATGTGA 62.429 66.667 14.15 0.00 37.50 3.58
397 403 2.509336 GTGCCGGTCGGATGTGAG 60.509 66.667 14.15 0.00 37.50 3.51
431 437 4.735132 CTTCTTGGTCGCGGGCGA 62.735 66.667 12.26 12.26 46.87 5.54
570 591 1.582610 GAGTCGCCGGCAAAAATGGA 61.583 55.000 28.98 10.87 0.00 3.41
773 798 3.795342 CGCCCGCGGACGAAAAAT 61.795 61.111 30.91 0.00 43.93 1.82
781 806 1.864176 GGACGAAAAATGGACGCGT 59.136 52.632 13.85 13.85 37.97 6.01
794 819 0.865769 GACGCGTGTCCATTTGAGTT 59.134 50.000 20.70 0.00 39.30 3.01
806 831 4.555709 TGAGTTGGCGCGTTGGGT 62.556 61.111 8.43 0.00 0.00 4.51
843 868 2.422591 GACCCAAACGGACGACCA 59.577 61.111 4.48 0.00 35.59 4.02
853 878 2.018324 GGACGACCACGGACGAAAC 61.018 63.158 14.64 5.70 44.46 2.78
854 879 1.299316 GACGACCACGGACGAAACA 60.299 57.895 14.64 0.00 44.46 2.83
874 899 1.276622 AGTCGCCCCATTAGAGTTGT 58.723 50.000 0.00 0.00 0.00 3.32
887 912 9.408648 CCCATTAGAGTTGTTCTTATTAACCAT 57.591 33.333 0.00 0.00 37.36 3.55
890 915 9.886132 ATTAGAGTTGTTCTTATTAACCATCGT 57.114 29.630 0.00 0.00 37.36 3.73
892 917 8.699283 AGAGTTGTTCTTATTAACCATCGTAC 57.301 34.615 0.00 0.00 29.61 3.67
893 918 7.487189 AGAGTTGTTCTTATTAACCATCGTACG 59.513 37.037 9.53 9.53 29.61 3.67
894 919 6.532657 AGTTGTTCTTATTAACCATCGTACGG 59.467 38.462 16.52 1.50 0.00 4.02
895 920 5.964758 TGTTCTTATTAACCATCGTACGGT 58.035 37.500 16.52 4.91 38.85 4.83
897 922 6.873076 TGTTCTTATTAACCATCGTACGGTTT 59.127 34.615 16.52 2.78 44.46 3.27
898 923 7.387397 TGTTCTTATTAACCATCGTACGGTTTT 59.613 33.333 16.52 6.40 44.46 2.43
899 924 7.903995 TCTTATTAACCATCGTACGGTTTTT 57.096 32.000 16.52 6.02 44.46 1.94
923 948 2.961522 GGTGTCAACCATTGTACGTG 57.038 50.000 0.00 0.00 46.75 4.49
924 949 1.069500 GGTGTCAACCATTGTACGTGC 60.069 52.381 0.00 0.00 46.75 5.34
925 950 1.069500 GTGTCAACCATTGTACGTGCC 60.069 52.381 0.00 0.00 0.00 5.01
926 951 1.202710 TGTCAACCATTGTACGTGCCT 60.203 47.619 0.00 0.00 0.00 4.75
927 952 2.037381 TGTCAACCATTGTACGTGCCTA 59.963 45.455 0.00 0.00 0.00 3.93
928 953 3.068560 GTCAACCATTGTACGTGCCTAA 58.931 45.455 0.00 0.00 0.00 2.69
929 954 3.068560 TCAACCATTGTACGTGCCTAAC 58.931 45.455 0.00 0.00 0.00 2.34
930 955 2.103537 ACCATTGTACGTGCCTAACC 57.896 50.000 0.00 0.00 0.00 2.85
931 956 1.348366 ACCATTGTACGTGCCTAACCA 59.652 47.619 0.00 0.00 0.00 3.67
932 957 2.224572 ACCATTGTACGTGCCTAACCAA 60.225 45.455 0.00 0.00 0.00 3.67
933 958 2.814919 CCATTGTACGTGCCTAACCAAA 59.185 45.455 0.00 0.00 0.00 3.28
934 959 3.365565 CCATTGTACGTGCCTAACCAAAC 60.366 47.826 0.00 0.00 0.00 2.93
935 960 2.616634 TGTACGTGCCTAACCAAACA 57.383 45.000 0.00 0.00 0.00 2.83
936 961 2.211806 TGTACGTGCCTAACCAAACAC 58.788 47.619 0.00 0.00 0.00 3.32
938 963 4.935630 GTGCCTAACCAAACACGC 57.064 55.556 0.00 0.00 0.00 5.34
939 964 1.284715 GTGCCTAACCAAACACGCC 59.715 57.895 0.00 0.00 0.00 5.68
940 965 2.255172 TGCCTAACCAAACACGCCG 61.255 57.895 0.00 0.00 0.00 6.46
941 966 1.962306 GCCTAACCAAACACGCCGA 60.962 57.895 0.00 0.00 0.00 5.54
942 967 1.864176 CCTAACCAAACACGCCGAC 59.136 57.895 0.00 0.00 0.00 4.79
943 968 0.601841 CCTAACCAAACACGCCGACT 60.602 55.000 0.00 0.00 0.00 4.18
944 969 0.511221 CTAACCAAACACGCCGACTG 59.489 55.000 0.00 0.00 0.00 3.51
945 970 0.104487 TAACCAAACACGCCGACTGA 59.896 50.000 0.00 0.00 0.00 3.41
946 971 0.534203 AACCAAACACGCCGACTGAT 60.534 50.000 0.00 0.00 0.00 2.90
947 972 1.227999 ACCAAACACGCCGACTGATG 61.228 55.000 0.00 0.00 0.00 3.07
948 973 1.227999 CCAAACACGCCGACTGATGT 61.228 55.000 0.00 0.00 0.00 3.06
949 974 0.110688 CAAACACGCCGACTGATGTG 60.111 55.000 0.00 0.00 38.28 3.21
950 975 1.227999 AAACACGCCGACTGATGTGG 61.228 55.000 0.00 0.00 36.67 4.17
951 976 3.490759 CACGCCGACTGATGTGGC 61.491 66.667 0.00 0.00 45.39 5.01
957 982 4.760047 GACTGATGTGGCGCCCGT 62.760 66.667 26.77 16.88 0.00 5.28
971 996 4.514577 CCGTGCCGGTGAGCCTAG 62.515 72.222 1.90 0.00 42.73 3.02
982 1007 3.776659 GAGCCTAGCGTCGCCCTTC 62.777 68.421 14.86 1.14 0.00 3.46
983 1008 3.839432 GCCTAGCGTCGCCCTTCT 61.839 66.667 14.86 0.00 0.00 2.85
984 1009 2.893398 CCTAGCGTCGCCCTTCTT 59.107 61.111 14.86 0.00 0.00 2.52
985 1010 1.227002 CCTAGCGTCGCCCTTCTTC 60.227 63.158 14.86 0.00 0.00 2.87
1007 1032 2.826674 TTTTGGCTTCCTATGAGGGG 57.173 50.000 0.00 0.00 35.59 4.79
1098 1123 3.842923 CTCCCCGTGCTCATCGCT 61.843 66.667 0.00 0.00 40.11 4.93
1581 1612 1.917955 CGACGTCGCTCATGTAAATGT 59.082 47.619 26.59 0.00 0.00 2.71
1622 1653 4.796231 GCGTCCATCGTCAGGCGT 62.796 66.667 0.00 0.00 42.13 5.68
1623 1654 2.579787 CGTCCATCGTCAGGCGTC 60.580 66.667 0.00 0.00 42.13 5.19
1624 1655 2.571757 GTCCATCGTCAGGCGTCA 59.428 61.111 0.00 0.00 42.13 4.35
1625 1656 1.517257 GTCCATCGTCAGGCGTCAG 60.517 63.158 0.00 0.00 42.13 3.51
1626 1657 2.887568 CCATCGTCAGGCGTCAGC 60.888 66.667 0.00 0.00 42.13 4.26
1627 1658 3.250323 CATCGTCAGGCGTCAGCG 61.250 66.667 0.00 0.00 46.35 5.18
1880 1916 0.830444 ACCGCCACTCCACTCTGTAA 60.830 55.000 0.00 0.00 0.00 2.41
1893 1929 5.894393 TCCACTCTGTAAAATTTTCACCCAA 59.106 36.000 6.72 0.00 0.00 4.12
1918 1954 4.520874 TCATTACTCGGCTCATCCTTCTAG 59.479 45.833 0.00 0.00 0.00 2.43
2026 2090 5.420725 AAGTAGCAACATCCACTGTCATA 57.579 39.130 0.00 0.00 36.98 2.15
2036 2163 7.563888 ACATCCACTGTCATATTTTCATCTG 57.436 36.000 0.00 0.00 29.94 2.90
2054 2181 4.731313 TCTGGCCTACTAGATCATCTGA 57.269 45.455 3.32 0.00 0.00 3.27
2055 2182 5.268131 TCTGGCCTACTAGATCATCTGAT 57.732 43.478 3.32 0.00 37.51 2.90
2056 2183 5.015515 TCTGGCCTACTAGATCATCTGATG 58.984 45.833 11.42 11.42 34.37 3.07
2164 2291 0.806102 GATTGCTCAAGTCGCGGCTA 60.806 55.000 16.40 0.00 0.00 3.93
2218 2345 2.594541 CGGCTCGCCTATGAGTTTC 58.405 57.895 6.35 0.00 38.28 2.78
2268 2395 0.947180 GTCAAACGGGTAGCGCAAGA 60.947 55.000 11.47 0.00 43.02 3.02
2307 2435 2.291741 GCCATTTGGGATCGATTCAGAC 59.708 50.000 5.94 0.00 40.01 3.51
2390 2518 1.598132 CGAGCTGATCTTGAGCCAATG 59.402 52.381 0.00 0.00 37.12 2.82
2391 2519 1.334243 GAGCTGATCTTGAGCCAATGC 59.666 52.381 0.00 0.00 37.12 3.56
2415 2543 9.796120 TGCTATTTTATTTTATTTTGACGGGAG 57.204 29.630 0.00 0.00 0.00 4.30
2416 2544 8.752254 GCTATTTTATTTTATTTTGACGGGAGC 58.248 33.333 0.00 0.00 0.00 4.70
2417 2545 9.244799 CTATTTTATTTTATTTTGACGGGAGCC 57.755 33.333 0.00 0.00 0.00 4.70
2418 2546 6.591750 TTTATTTTATTTTGACGGGAGCCA 57.408 33.333 0.00 0.00 0.00 4.75
2419 2547 6.591750 TTATTTTATTTTGACGGGAGCCAA 57.408 33.333 0.00 0.00 0.00 4.52
2420 2548 5.675684 ATTTTATTTTGACGGGAGCCAAT 57.324 34.783 0.00 0.00 30.62 3.16
2421 2549 4.448537 TTTATTTTGACGGGAGCCAATG 57.551 40.909 0.00 0.00 30.62 2.82
2493 2626 9.920946 AATGATCCTACTCCTTTAGCATTTTTA 57.079 29.630 0.00 0.00 0.00 1.52
2551 2685 0.383949 ACATTTTTGGAGCGCACGTT 59.616 45.000 11.47 0.00 0.00 3.99
2569 2703 2.094258 CGTTGTCAAGCGTTCTATGCAT 59.906 45.455 3.79 3.79 31.07 3.96
2574 2708 4.507756 TGTCAAGCGTTCTATGCATGTATC 59.492 41.667 10.16 0.00 31.42 2.24
2699 3026 5.248477 TGCTGTGTAGGTATTTTTCTCTCCT 59.752 40.000 0.00 0.00 0.00 3.69
2771 3098 4.699925 AGGCATTAATATGGTACGTGGT 57.300 40.909 0.00 0.00 32.15 4.16
2800 3127 6.524734 CCCTATGCTAACTATCATGTTGTCA 58.475 40.000 0.00 0.00 0.00 3.58
2856 3186 6.274157 TCTAGTTGAAAAGGTTTTGTGCAA 57.726 33.333 0.00 0.00 0.00 4.08
2925 3256 3.688694 ACACGTCTGGCCAAACTATAA 57.311 42.857 7.01 0.00 0.00 0.98
2954 3285 7.690224 CGAACACGTCTATATCATCATACAGAG 59.310 40.741 0.00 0.00 0.00 3.35
2982 3313 7.286313 TGGTGTATAAATCTCATAACATGCCA 58.714 34.615 0.00 0.00 0.00 4.92
3043 3374 9.507280 CTTGCTATTTGATGTAAACTTGGTATG 57.493 33.333 0.00 0.00 0.00 2.39
3054 3385 3.495434 ACTTGGTATGGACGTTGGAAA 57.505 42.857 0.00 0.00 0.00 3.13
3055 3386 3.143728 ACTTGGTATGGACGTTGGAAAC 58.856 45.455 0.00 0.00 45.31 2.78
3084 3415 2.819608 GGAGTCAATTTAGCTGTGCCAA 59.180 45.455 0.00 0.00 0.00 4.52
3114 3445 6.106673 GCTCAAATCTGTACAGGCTACTTAA 58.893 40.000 22.48 0.90 0.00 1.85
3126 3457 4.702131 CAGGCTACTTAACAGGCAAAATCT 59.298 41.667 8.18 0.00 40.87 2.40
3185 3518 6.985059 CCTACCCTAGAAAAAGATAGGTTTCG 59.015 42.308 0.00 0.00 38.50 3.46
3186 3519 5.183969 ACCCTAGAAAAAGATAGGTTTCGC 58.816 41.667 0.00 0.00 38.50 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 2.613506 CCACCTTCCGGCGTTGAAC 61.614 63.158 6.01 0.00 0.00 3.18
140 141 0.167470 CTCAACAATCAGCAGCCGTG 59.833 55.000 0.00 0.00 0.00 4.94
151 152 2.555227 GGTCCATCACCACCTCAACAAT 60.555 50.000 0.00 0.00 45.98 2.71
217 218 3.502211 ACAATTTCCTTTGCGACTTCGAT 59.498 39.130 2.02 0.00 43.02 3.59
247 248 0.976641 TGGACTCTGCCGATGAGTTT 59.023 50.000 6.43 0.00 43.88 2.66
253 254 1.091771 CGCAAATGGACTCTGCCGAT 61.092 55.000 0.00 0.00 32.27 4.18
259 260 2.615493 CCAAGGTACGCAAATGGACTCT 60.615 50.000 0.00 0.00 32.82 3.24
270 272 0.237498 GACAGTTTGCCAAGGTACGC 59.763 55.000 0.00 0.00 0.00 4.42
626 649 4.095400 GCCTCCCCTCCCCTCTCA 62.095 72.222 0.00 0.00 0.00 3.27
630 653 4.058505 ATTGGCCTCCCCTCCCCT 62.059 66.667 3.32 0.00 0.00 4.79
632 655 3.023735 ACATTGGCCTCCCCTCCC 61.024 66.667 3.32 0.00 0.00 4.30
741 766 4.162690 GCGACCCATTCTCGGCCT 62.163 66.667 0.00 0.00 0.00 5.19
781 806 1.851021 CGCGCCAACTCAAATGGACA 61.851 55.000 0.00 0.00 40.56 4.02
843 868 1.952635 GGCGACTTGTTTCGTCCGT 60.953 57.895 0.00 0.00 41.26 4.69
853 878 2.009774 CAACTCTAATGGGGCGACTTG 58.990 52.381 0.00 0.00 0.00 3.16
854 879 1.628846 ACAACTCTAATGGGGCGACTT 59.371 47.619 0.00 0.00 0.00 3.01
874 899 7.903995 AAAACCGTACGATGGTTAATAAGAA 57.096 32.000 18.76 0.00 46.25 2.52
897 922 2.840651 ACAATGGTTGACACCCCAAAAA 59.159 40.909 0.00 0.00 43.49 1.94
898 923 2.472029 ACAATGGTTGACACCCCAAAA 58.528 42.857 0.00 0.00 43.49 2.44
899 924 2.166907 ACAATGGTTGACACCCCAAA 57.833 45.000 0.00 0.00 43.49 3.28
900 925 2.588620 GTACAATGGTTGACACCCCAA 58.411 47.619 0.00 0.00 43.49 4.12
901 926 1.543650 CGTACAATGGTTGACACCCCA 60.544 52.381 0.00 0.00 43.49 4.96
902 927 1.161843 CGTACAATGGTTGACACCCC 58.838 55.000 0.00 0.00 43.49 4.95
903 928 1.533731 CACGTACAATGGTTGACACCC 59.466 52.381 0.00 0.00 43.49 4.61
904 929 1.069500 GCACGTACAATGGTTGACACC 60.069 52.381 0.00 0.00 44.56 4.16
905 930 1.069500 GGCACGTACAATGGTTGACAC 60.069 52.381 0.00 0.00 0.00 3.67
906 931 1.202710 AGGCACGTACAATGGTTGACA 60.203 47.619 0.00 0.00 0.00 3.58
907 932 1.519408 AGGCACGTACAATGGTTGAC 58.481 50.000 0.00 0.00 0.00 3.18
908 933 3.068560 GTTAGGCACGTACAATGGTTGA 58.931 45.455 0.00 0.00 0.00 3.18
909 934 2.160813 GGTTAGGCACGTACAATGGTTG 59.839 50.000 0.00 0.00 0.00 3.77
910 935 2.224572 TGGTTAGGCACGTACAATGGTT 60.225 45.455 0.00 0.00 0.00 3.67
911 936 1.348366 TGGTTAGGCACGTACAATGGT 59.652 47.619 0.00 0.00 0.00 3.55
912 937 2.102070 TGGTTAGGCACGTACAATGG 57.898 50.000 0.00 0.00 0.00 3.16
913 938 3.251245 TGTTTGGTTAGGCACGTACAATG 59.749 43.478 0.00 0.00 0.00 2.82
914 939 3.251487 GTGTTTGGTTAGGCACGTACAAT 59.749 43.478 0.00 0.00 0.00 2.71
915 940 2.613133 GTGTTTGGTTAGGCACGTACAA 59.387 45.455 0.00 0.00 0.00 2.41
916 941 2.211806 GTGTTTGGTTAGGCACGTACA 58.788 47.619 0.00 0.00 0.00 2.90
917 942 1.192980 CGTGTTTGGTTAGGCACGTAC 59.807 52.381 7.63 0.00 46.30 3.67
918 943 1.500108 CGTGTTTGGTTAGGCACGTA 58.500 50.000 7.63 0.00 46.30 3.57
919 944 2.313267 CGTGTTTGGTTAGGCACGT 58.687 52.632 7.63 0.00 46.30 4.49
921 946 1.284715 GGCGTGTTTGGTTAGGCAC 59.715 57.895 0.00 0.00 0.00 5.01
922 947 2.255172 CGGCGTGTTTGGTTAGGCA 61.255 57.895 0.00 0.00 0.00 4.75
923 948 1.962306 TCGGCGTGTTTGGTTAGGC 60.962 57.895 6.85 0.00 0.00 3.93
924 949 0.601841 AGTCGGCGTGTTTGGTTAGG 60.602 55.000 6.85 0.00 0.00 2.69
925 950 0.511221 CAGTCGGCGTGTTTGGTTAG 59.489 55.000 6.85 0.00 0.00 2.34
926 951 0.104487 TCAGTCGGCGTGTTTGGTTA 59.896 50.000 6.85 0.00 0.00 2.85
927 952 0.534203 ATCAGTCGGCGTGTTTGGTT 60.534 50.000 6.85 0.00 0.00 3.67
928 953 1.070786 ATCAGTCGGCGTGTTTGGT 59.929 52.632 6.85 0.00 0.00 3.67
929 954 1.227999 ACATCAGTCGGCGTGTTTGG 61.228 55.000 6.85 0.00 0.00 3.28
930 955 0.110688 CACATCAGTCGGCGTGTTTG 60.111 55.000 6.85 4.45 0.00 2.93
931 956 1.227999 CCACATCAGTCGGCGTGTTT 61.228 55.000 6.85 0.00 0.00 2.83
932 957 1.667830 CCACATCAGTCGGCGTGTT 60.668 57.895 6.85 0.00 0.00 3.32
933 958 2.048222 CCACATCAGTCGGCGTGT 60.048 61.111 6.85 0.00 0.00 4.49
934 959 3.490759 GCCACATCAGTCGGCGTG 61.491 66.667 6.85 0.00 34.10 5.34
940 965 4.760047 ACGGGCGCCACATCAGTC 62.760 66.667 30.85 6.91 0.00 3.51
958 983 4.874977 GACGCTAGGCTCACCGGC 62.875 72.222 0.00 0.00 42.76 6.13
959 984 4.554363 CGACGCTAGGCTCACCGG 62.554 72.222 0.00 0.00 42.76 5.28
961 986 4.874977 GGCGACGCTAGGCTCACC 62.875 72.222 20.77 0.00 0.00 4.02
962 987 4.874977 GGGCGACGCTAGGCTCAC 62.875 72.222 20.77 0.00 0.00 3.51
964 989 3.776659 GAAGGGCGACGCTAGGCTC 62.777 68.421 20.77 6.04 0.00 4.70
965 990 3.839432 GAAGGGCGACGCTAGGCT 61.839 66.667 20.77 0.00 0.00 4.58
971 996 0.591659 AAAAAGAAGAAGGGCGACGC 59.408 50.000 12.43 12.43 0.00 5.19
1003 1028 2.854076 CAAGCCCACCTTTCCCCT 59.146 61.111 0.00 0.00 0.00 4.79
1007 1032 1.856265 CGACTGCAAGCCCACCTTTC 61.856 60.000 0.00 0.00 37.60 2.62
1356 1381 0.390603 CGCCGTTTACCAGGATGTGA 60.391 55.000 0.00 0.00 0.00 3.58
1384 1413 4.754667 GGGAAGGGTCGACGCACC 62.755 72.222 31.03 29.08 35.42 5.01
1399 1430 1.756408 ATCAGATCAGCGCTGAGGGG 61.756 60.000 39.64 30.04 44.75 4.79
1526 1557 2.190578 CCGGTGGCCTTGGATCTC 59.809 66.667 3.32 0.00 0.00 2.75
1622 1653 4.639171 TCAGAACGCACGCGCTGA 62.639 61.111 12.02 13.77 44.19 4.26
1623 1654 4.415501 GTCAGAACGCACGCGCTG 62.416 66.667 12.02 11.63 44.19 5.18
1624 1655 4.647615 AGTCAGAACGCACGCGCT 62.648 61.111 12.02 0.00 44.19 5.92
1625 1656 3.615562 GAAGTCAGAACGCACGCGC 62.616 63.158 12.02 0.00 44.19 6.86
1626 1657 2.465920 GAAGTCAGAACGCACGCG 59.534 61.111 10.36 10.36 46.03 6.01
1627 1658 2.300787 ACGAAGTCAGAACGCACGC 61.301 57.895 0.00 0.00 29.74 5.34
1629 1660 1.853319 CCACGAAGTCAGAACGCAC 59.147 57.895 0.00 0.00 41.61 5.34
1630 1661 1.954146 GCCACGAAGTCAGAACGCA 60.954 57.895 0.00 0.00 41.61 5.24
1631 1662 1.664965 AGCCACGAAGTCAGAACGC 60.665 57.895 0.00 0.00 41.61 4.84
1633 1664 0.601311 AGCAGCCACGAAGTCAGAAC 60.601 55.000 0.00 0.00 41.61 3.01
1634 1665 0.601046 CAGCAGCCACGAAGTCAGAA 60.601 55.000 0.00 0.00 41.61 3.02
1635 1666 1.005748 CAGCAGCCACGAAGTCAGA 60.006 57.895 0.00 0.00 41.61 3.27
1636 1667 1.301244 ACAGCAGCCACGAAGTCAG 60.301 57.895 0.00 0.00 41.61 3.51
1637 1668 1.595109 CACAGCAGCCACGAAGTCA 60.595 57.895 0.00 0.00 41.61 3.41
1638 1669 2.320587 CCACAGCAGCCACGAAGTC 61.321 63.158 0.00 0.00 41.61 3.01
1640 1671 2.281070 ACCACAGCAGCCACGAAG 60.281 61.111 0.00 0.00 0.00 3.79
1641 1672 2.280797 GACCACAGCAGCCACGAA 60.281 61.111 0.00 0.00 0.00 3.85
1880 1916 7.096551 CCGAGTAATGATTTGGGTGAAAATTT 58.903 34.615 0.00 0.00 29.89 1.82
1893 1929 4.346418 AGAAGGATGAGCCGAGTAATGATT 59.654 41.667 0.00 0.00 43.43 2.57
1918 1954 1.859080 GCGATCGATGTTTGTAGGGAC 59.141 52.381 21.57 0.00 0.00 4.46
2026 2090 6.753913 TGATCTAGTAGGCCAGATGAAAAT 57.246 37.500 5.01 0.00 31.63 1.82
2036 2163 3.118811 GCCATCAGATGATCTAGTAGGCC 60.119 52.174 12.41 0.00 31.21 5.19
2054 2181 0.957395 CAACCAACAGCTCTCGCCAT 60.957 55.000 0.00 0.00 36.60 4.40
2055 2182 1.597854 CAACCAACAGCTCTCGCCA 60.598 57.895 0.00 0.00 36.60 5.69
2056 2183 0.674895 ATCAACCAACAGCTCTCGCC 60.675 55.000 0.00 0.00 36.60 5.54
2164 2291 0.179119 CCTCCGTTTTATCGTCCGCT 60.179 55.000 0.00 0.00 0.00 5.52
2176 2303 1.282157 CATTCTTCCTTCCCCTCCGTT 59.718 52.381 0.00 0.00 0.00 4.44
2307 2435 3.318275 TCGATCTTGATCCGACCCTAAAG 59.682 47.826 5.18 0.00 0.00 1.85
2361 2489 4.326826 TCAAGATCAGCTCGTTTTTGGAT 58.673 39.130 0.00 0.00 0.00 3.41
2362 2490 3.738982 TCAAGATCAGCTCGTTTTTGGA 58.261 40.909 0.00 0.00 0.00 3.53
2365 2493 2.485814 GGCTCAAGATCAGCTCGTTTTT 59.514 45.455 3.79 0.00 37.05 1.94
2390 2518 8.752254 GCTCCCGTCAAAATAAAATAAAATAGC 58.248 33.333 0.00 0.00 0.00 2.97
2391 2519 9.244799 GGCTCCCGTCAAAATAAAATAAAATAG 57.755 33.333 0.00 0.00 0.00 1.73
2392 2520 8.750298 TGGCTCCCGTCAAAATAAAATAAAATA 58.250 29.630 0.00 0.00 0.00 1.40
2393 2521 7.616313 TGGCTCCCGTCAAAATAAAATAAAAT 58.384 30.769 0.00 0.00 0.00 1.82
2394 2522 6.994221 TGGCTCCCGTCAAAATAAAATAAAA 58.006 32.000 0.00 0.00 0.00 1.52
2395 2523 6.591750 TGGCTCCCGTCAAAATAAAATAAA 57.408 33.333 0.00 0.00 0.00 1.40
2396 2524 6.591750 TTGGCTCCCGTCAAAATAAAATAA 57.408 33.333 0.00 0.00 30.50 1.40
2397 2525 6.568869 CATTGGCTCCCGTCAAAATAAAATA 58.431 36.000 0.00 0.00 38.40 1.40
2398 2526 5.418676 CATTGGCTCCCGTCAAAATAAAAT 58.581 37.500 0.00 0.00 38.40 1.82
2399 2527 4.815269 CATTGGCTCCCGTCAAAATAAAA 58.185 39.130 0.00 0.00 38.40 1.52
2400 2528 3.367910 GCATTGGCTCCCGTCAAAATAAA 60.368 43.478 0.00 0.00 38.40 1.40
2401 2529 2.165437 GCATTGGCTCCCGTCAAAATAA 59.835 45.455 0.00 0.00 38.40 1.40
2402 2530 1.748493 GCATTGGCTCCCGTCAAAATA 59.252 47.619 0.00 0.00 38.40 1.40
2403 2531 0.532115 GCATTGGCTCCCGTCAAAAT 59.468 50.000 0.00 0.00 38.40 1.82
2404 2532 1.963679 GCATTGGCTCCCGTCAAAA 59.036 52.632 0.00 0.00 38.40 2.44
2405 2533 3.680156 GCATTGGCTCCCGTCAAA 58.320 55.556 0.00 0.00 38.40 2.69
2415 2543 2.820197 GGGGCTAAAGTATAGCATTGGC 59.180 50.000 9.44 0.00 42.06 4.52
2416 2544 3.821033 GTGGGGCTAAAGTATAGCATTGG 59.179 47.826 9.44 0.00 42.06 3.16
2417 2545 4.516698 CAGTGGGGCTAAAGTATAGCATTG 59.483 45.833 9.44 0.00 42.06 2.82
2418 2546 4.718961 CAGTGGGGCTAAAGTATAGCATT 58.281 43.478 9.44 0.00 42.06 3.56
2419 2547 3.496870 GCAGTGGGGCTAAAGTATAGCAT 60.497 47.826 9.44 0.00 42.06 3.79
2420 2548 2.158813 GCAGTGGGGCTAAAGTATAGCA 60.159 50.000 9.44 0.00 42.06 3.49
2421 2549 2.104963 AGCAGTGGGGCTAAAGTATAGC 59.895 50.000 0.00 0.00 43.70 2.97
2427 2560 2.109126 GCGAGCAGTGGGGCTAAAG 61.109 63.158 0.00 0.00 45.99 1.85
2434 2567 2.590007 GCTATGGCGAGCAGTGGG 60.590 66.667 6.35 0.00 42.36 4.61
2519 2653 9.956797 CGCTCCAAAAATGTTTTAGAATTATTG 57.043 29.630 0.00 0.00 0.00 1.90
2529 2663 1.857837 CGTGCGCTCCAAAAATGTTTT 59.142 42.857 9.73 0.00 0.00 2.43
2541 2675 2.127609 GCTTGACAACGTGCGCTC 60.128 61.111 9.73 3.51 0.00 5.03
2551 2685 2.698803 ACATGCATAGAACGCTTGACA 58.301 42.857 0.00 0.00 37.80 3.58
2609 2745 9.642343 ACGGGCATCCATATATATATATATCGT 57.358 33.333 18.54 18.44 34.56 3.73
2614 2750 9.422681 GGTCTACGGGCATCCATATATATATAT 57.577 37.037 9.12 9.12 0.00 0.86
2615 2751 7.837689 GGGTCTACGGGCATCCATATATATATA 59.162 40.741 4.90 4.92 0.00 0.86
2616 2752 6.668283 GGGTCTACGGGCATCCATATATATAT 59.332 42.308 0.00 0.00 0.00 0.86
2617 2753 6.014647 GGGTCTACGGGCATCCATATATATA 58.985 44.000 0.00 0.00 0.00 0.86
2618 2754 4.838986 GGGTCTACGGGCATCCATATATAT 59.161 45.833 0.00 0.00 0.00 0.86
2619 2755 4.220724 GGGTCTACGGGCATCCATATATA 58.779 47.826 0.00 0.00 0.00 0.86
2620 2756 3.039011 GGGTCTACGGGCATCCATATAT 58.961 50.000 0.00 0.00 0.00 0.86
2621 2757 2.225420 TGGGTCTACGGGCATCCATATA 60.225 50.000 0.00 0.00 0.00 0.86
2673 3000 5.865085 AGAGAAAAATACCTACACAGCACA 58.135 37.500 0.00 0.00 0.00 4.57
2674 3001 5.351740 GGAGAGAAAAATACCTACACAGCAC 59.648 44.000 0.00 0.00 0.00 4.40
2771 3098 3.856900 TGATAGTTAGCATAGGGCCTGA 58.143 45.455 18.53 0.04 46.50 3.86
2856 3186 3.008485 TCAAGTTGCCAGGGTTTTGTTTT 59.992 39.130 0.00 0.00 0.00 2.43
2925 3256 5.183014 TGATGATATAGACGTGTTCGCTT 57.817 39.130 0.00 0.00 41.18 4.68
2954 3285 8.076178 GCATGTTATGAGATTTATACACCAACC 58.924 37.037 0.00 0.00 0.00 3.77
3035 3366 3.058501 GTGTTTCCAACGTCCATACCAAG 60.059 47.826 0.00 0.00 0.00 3.61
3043 3374 3.120041 CCAAAATGTGTTTCCAACGTCC 58.880 45.455 0.00 0.00 0.00 4.79
3054 3385 6.040842 ACAGCTAAATTGACTCCAAAATGTGT 59.959 34.615 0.00 0.00 35.67 3.72
3055 3386 6.364165 CACAGCTAAATTGACTCCAAAATGTG 59.636 38.462 0.00 0.00 35.67 3.21
3084 3415 3.935203 CCTGTACAGATTTGAGCGTCAAT 59.065 43.478 24.68 0.00 36.11 2.57


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

AutoCloner maintained by Alex Coulton.