Multiple sequence alignment - TraesCS6D01G380300

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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 TraesCS6D01G380300 chr6D 100.000 7121 0 0 1 7121 461448512 461455632 0.000000e+00 13151.0
1 TraesCS6D01G380300 chr6A 94.430 6302 162 66 934 7121 608113063 608119289 0.000000e+00 9518.0
2 TraesCS6D01G380300 chr6A 91.109 866 38 20 1 835 608112002 608112859 0.000000e+00 1136.0
3 TraesCS6D01G380300 chr6B 94.074 6176 193 68 1048 7121 703283423 703289527 0.000000e+00 9217.0
4 TraesCS6D01G380300 chr6B 89.084 797 43 23 1 765 703281810 703282594 0.000000e+00 950.0
5 TraesCS6D01G380300 chr6B 91.803 61 5 0 831 891 703283135 703283195 1.270000e-12 86.1
6 TraesCS6D01G380300 chrUn 84.848 297 45 0 5333 5629 93449296 93449000 4.180000e-77 300.0
7 TraesCS6D01G380300 chrUn 81.206 282 50 2 4523 4804 93450459 93450181 2.590000e-54 224.0
8 TraesCS6D01G380300 chrUn 84.507 213 30 3 1981 2190 93453549 93453337 2.600000e-49 207.0
9 TraesCS6D01G380300 chr7B 84.512 297 46 0 5333 5629 743145591 743145887 1.940000e-75 294.0
10 TraesCS6D01G380300 chr7B 83.099 213 33 2 1981 2190 743142071 743142283 2.620000e-44 191.0


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 TraesCS6D01G380300 chr6D 461448512 461455632 7120 False 13151.000000 13151 100.000000 1 7121 1 chr6D.!!$F1 7120
1 TraesCS6D01G380300 chr6A 608112002 608119289 7287 False 5327.000000 9518 92.769500 1 7121 2 chr6A.!!$F1 7120
2 TraesCS6D01G380300 chr6B 703281810 703289527 7717 False 3417.700000 9217 91.653667 1 7121 3 chr6B.!!$F1 7120
3 TraesCS6D01G380300 chrUn 93449000 93453549 4549 True 243.666667 300 83.520333 1981 5629 3 chrUn.!!$R1 3648
4 TraesCS6D01G380300 chr7B 743142071 743145887 3816 False 242.500000 294 83.805500 1981 5629 2 chr7B.!!$F1 3648

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
844 921 0.183731 CACCCTTGGCTCTTATCCCC 59.816 60.000 0.00 0.00 0.00 4.81 F
845 922 0.253630 ACCCTTGGCTCTTATCCCCA 60.254 55.000 0.00 0.00 0.00 4.96 F
846 923 0.183731 CCCTTGGCTCTTATCCCCAC 59.816 60.000 0.00 0.00 0.00 4.61 F
1870 2522 0.665298 GATGCCGCCTTTCAAGATCC 59.335 55.000 0.00 0.00 0.00 3.36 F
3507 4979 1.332195 CGGACATGATGAGCTCCCTA 58.668 55.000 12.15 0.00 0.00 3.53 F
3741 5213 0.736325 AAGTCGGTTCGAGAATGCCG 60.736 55.000 8.12 8.12 44.95 5.69 F
3765 5237 2.027625 GGTCGCGTTCAAGGACCTG 61.028 63.158 5.77 0.00 45.34 4.00 F
5556 7475 2.941453 ACTATGTCGTCATCGTTGCT 57.059 45.000 0.00 0.00 38.33 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2839 3614 0.031178 CCTGCAAAAGCACACCTGAC 59.969 55.000 0.00 0.0 0.00 3.51 R
2876 3758 1.774639 TACTGGTTTGCGAAGTCGAC 58.225 50.000 7.70 7.7 43.02 4.20 R
2931 3813 1.112113 GAAGACTGCGGAGGGTATGA 58.888 55.000 9.36 0.0 0.00 2.15 R
3741 5213 0.721718 CCTTGAACGCGACCTCAATC 59.278 55.000 15.93 0.0 31.40 2.67 R
5049 6573 2.461695 ACACCGAGATGAAGTGGAGAT 58.538 47.619 0.00 0.0 35.79 2.75 R
5681 7600 2.224402 ACAAGGGAGTGTCAAGAGCTTC 60.224 50.000 0.00 0.0 0.00 3.86 R
5858 7778 1.298157 GGCATACGCACTTGTGAGCA 61.298 55.000 4.79 0.0 41.24 4.26 R
6941 8909 1.604308 CAACCTGCACCTGATGGCA 60.604 57.895 0.00 0.0 38.52 4.92 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
96 97 4.646945 TGAGCTAAACCATTGTTCAACCAA 59.353 37.500 0.00 0.00 32.15 3.67
97 98 4.944048 AGCTAAACCATTGTTCAACCAAC 58.056 39.130 0.00 0.00 32.15 3.77
98 99 4.649218 AGCTAAACCATTGTTCAACCAACT 59.351 37.500 0.00 0.00 35.79 3.16
110 111 5.888724 TGTTCAACCAACTATTTGTCTTCCA 59.111 36.000 0.00 0.00 35.79 3.53
137 138 4.064388 CCGCAAAGAAAAACCCATCAATT 58.936 39.130 0.00 0.00 0.00 2.32
538 588 9.308318 GTACCATTTAACAAAAATGTTCACAGT 57.692 29.630 9.03 2.80 36.24 3.55
836 913 1.079612 GCATTTGCACCCTTGGCTC 60.080 57.895 0.00 0.00 41.59 4.70
837 914 1.538687 GCATTTGCACCCTTGGCTCT 61.539 55.000 0.00 0.00 41.59 4.09
838 915 0.971386 CATTTGCACCCTTGGCTCTT 59.029 50.000 0.00 0.00 0.00 2.85
841 918 2.128771 TTGCACCCTTGGCTCTTATC 57.871 50.000 0.00 0.00 0.00 1.75
842 919 0.255890 TGCACCCTTGGCTCTTATCC 59.744 55.000 0.00 0.00 0.00 2.59
844 921 0.183731 CACCCTTGGCTCTTATCCCC 59.816 60.000 0.00 0.00 0.00 4.81
845 922 0.253630 ACCCTTGGCTCTTATCCCCA 60.254 55.000 0.00 0.00 0.00 4.96
846 923 0.183731 CCCTTGGCTCTTATCCCCAC 59.816 60.000 0.00 0.00 0.00 4.61
847 924 0.918983 CCTTGGCTCTTATCCCCACA 59.081 55.000 0.00 0.00 0.00 4.17
848 925 1.408822 CCTTGGCTCTTATCCCCACAC 60.409 57.143 0.00 0.00 0.00 3.82
849 926 1.281867 CTTGGCTCTTATCCCCACACA 59.718 52.381 0.00 0.00 0.00 3.72
850 927 1.367346 TGGCTCTTATCCCCACACAA 58.633 50.000 0.00 0.00 0.00 3.33
852 929 2.311542 TGGCTCTTATCCCCACACAAAT 59.688 45.455 0.00 0.00 0.00 2.32
853 930 3.525609 TGGCTCTTATCCCCACACAAATA 59.474 43.478 0.00 0.00 0.00 1.40
854 931 4.017958 TGGCTCTTATCCCCACACAAATAA 60.018 41.667 0.00 0.00 0.00 1.40
855 932 4.580580 GGCTCTTATCCCCACACAAATAAG 59.419 45.833 0.00 0.00 34.47 1.73
856 933 4.036852 GCTCTTATCCCCACACAAATAAGC 59.963 45.833 0.00 0.00 33.62 3.09
857 934 4.196193 TCTTATCCCCACACAAATAAGCG 58.804 43.478 0.00 0.00 33.62 4.68
858 935 2.799126 ATCCCCACACAAATAAGCGA 57.201 45.000 0.00 0.00 0.00 4.93
859 936 1.816074 TCCCCACACAAATAAGCGAC 58.184 50.000 0.00 0.00 0.00 5.19
860 937 1.072489 TCCCCACACAAATAAGCGACA 59.928 47.619 0.00 0.00 0.00 4.35
861 938 1.883275 CCCCACACAAATAAGCGACAA 59.117 47.619 0.00 0.00 0.00 3.18
862 939 2.351350 CCCCACACAAATAAGCGACAAC 60.351 50.000 0.00 0.00 0.00 3.32
863 940 2.552315 CCCACACAAATAAGCGACAACT 59.448 45.455 0.00 0.00 0.00 3.16
864 941 3.749088 CCCACACAAATAAGCGACAACTA 59.251 43.478 0.00 0.00 0.00 2.24
865 942 4.142902 CCCACACAAATAAGCGACAACTAG 60.143 45.833 0.00 0.00 0.00 2.57
866 943 4.394795 CACACAAATAAGCGACAACTAGC 58.605 43.478 0.00 0.00 0.00 3.42
867 944 3.435671 ACACAAATAAGCGACAACTAGCC 59.564 43.478 0.00 0.00 0.00 3.93
868 945 3.435327 CACAAATAAGCGACAACTAGCCA 59.565 43.478 0.00 0.00 0.00 4.75
869 946 4.094887 CACAAATAAGCGACAACTAGCCAT 59.905 41.667 0.00 0.00 0.00 4.40
870 947 4.094887 ACAAATAAGCGACAACTAGCCATG 59.905 41.667 0.00 0.00 0.00 3.66
872 949 1.026718 AAGCGACAACTAGCCATGGC 61.027 55.000 30.12 30.12 42.33 4.40
895 972 4.772886 AAGCCAACTATTTATCTCCCGT 57.227 40.909 0.00 0.00 0.00 5.28
896 973 5.881923 AAGCCAACTATTTATCTCCCGTA 57.118 39.130 0.00 0.00 0.00 4.02
899 976 5.129815 AGCCAACTATTTATCTCCCGTAACA 59.870 40.000 0.00 0.00 0.00 2.41
900 977 5.465724 GCCAACTATTTATCTCCCGTAACAG 59.534 44.000 0.00 0.00 0.00 3.16
902 979 6.281405 CAACTATTTATCTCCCGTAACAGCT 58.719 40.000 0.00 0.00 0.00 4.24
904 981 6.885922 ACTATTTATCTCCCGTAACAGCTTT 58.114 36.000 0.00 0.00 0.00 3.51
905 982 7.336396 ACTATTTATCTCCCGTAACAGCTTTT 58.664 34.615 0.00 0.00 0.00 2.27
906 983 7.827729 ACTATTTATCTCCCGTAACAGCTTTTT 59.172 33.333 0.00 0.00 0.00 1.94
929 1006 2.990066 AGGGGTCTCATAAAAGCTCG 57.010 50.000 0.00 0.00 0.00 5.03
930 1007 2.467880 AGGGGTCTCATAAAAGCTCGA 58.532 47.619 0.00 0.00 0.00 4.04
931 1008 2.838202 AGGGGTCTCATAAAAGCTCGAA 59.162 45.455 0.00 0.00 0.00 3.71
949 1132 3.930229 TCGAATTCTCAAACATACACCCG 59.070 43.478 3.52 0.00 0.00 5.28
955 1138 4.000325 TCTCAAACATACACCCGTTGATG 59.000 43.478 0.00 0.00 0.00 3.07
985 1523 2.361737 GGGCCACTGGAAGGAAGC 60.362 66.667 4.39 0.00 39.30 3.86
1037 1581 4.741239 ATGGTCCGTCTGCCCCCT 62.741 66.667 0.00 0.00 0.00 4.79
1038 1582 4.974438 TGGTCCGTCTGCCCCCTT 62.974 66.667 0.00 0.00 0.00 3.95
1039 1583 4.097361 GGTCCGTCTGCCCCCTTC 62.097 72.222 0.00 0.00 0.00 3.46
1041 1585 4.332543 TCCGTCTGCCCCCTTCCT 62.333 66.667 0.00 0.00 0.00 3.36
1042 1586 4.101448 CCGTCTGCCCCCTTCCTG 62.101 72.222 0.00 0.00 0.00 3.86
1594 2239 2.941720 GTGCATGTCCATTCTCCTTCTC 59.058 50.000 0.00 0.00 0.00 2.87
1610 2255 3.496160 CCTTCTCCTTCTCCGTTTTTCCA 60.496 47.826 0.00 0.00 0.00 3.53
1781 2430 2.947652 CAGCCACATCCACATTCTTAGG 59.052 50.000 0.00 0.00 0.00 2.69
1814 2466 4.880759 TGGTAGCATTTTGAACCATTGTG 58.119 39.130 0.00 0.00 37.09 3.33
1870 2522 0.665298 GATGCCGCCTTTCAAGATCC 59.335 55.000 0.00 0.00 0.00 3.36
1879 2531 3.004524 GCCTTTCAAGATCCAGATCATGC 59.995 47.826 10.17 0.00 40.22 4.06
2223 2881 5.649557 CCAACATCACTGACAAAAAGAACA 58.350 37.500 0.00 0.00 0.00 3.18
2225 2883 5.248870 ACATCACTGACAAAAAGAACACC 57.751 39.130 0.00 0.00 0.00 4.16
2226 2884 4.704540 ACATCACTGACAAAAAGAACACCA 59.295 37.500 0.00 0.00 0.00 4.17
2230 2888 4.079253 ACTGACAAAAAGAACACCACTGT 58.921 39.130 0.00 0.00 0.00 3.55
2232 2890 5.010617 ACTGACAAAAAGAACACCACTGTTT 59.989 36.000 0.00 0.00 40.93 2.83
2234 2892 5.923684 TGACAAAAAGAACACCACTGTTTTC 59.076 36.000 0.00 0.00 40.93 2.29
2235 2893 5.234752 ACAAAAAGAACACCACTGTTTTCC 58.765 37.500 0.00 0.00 40.93 3.13
2238 2896 2.024414 AGAACACCACTGTTTTCCAGC 58.976 47.619 0.00 0.00 45.68 4.85
2242 2900 2.094234 ACACCACTGTTTTCCAGCAAAC 60.094 45.455 0.00 0.00 45.68 2.93
2243 2901 2.166254 CACCACTGTTTTCCAGCAAACT 59.834 45.455 0.00 0.00 45.68 2.66
2244 2902 2.831526 ACCACTGTTTTCCAGCAAACTT 59.168 40.909 0.00 0.00 45.68 2.66
2276 2934 3.755378 TCTCATTTGCTCAGAAAGAAGCC 59.245 43.478 0.00 0.00 0.00 4.35
2282 2940 4.247267 TGCTCAGAAAGAAGCCAAATTG 57.753 40.909 0.00 0.00 0.00 2.32
2283 2941 3.890756 TGCTCAGAAAGAAGCCAAATTGA 59.109 39.130 0.00 0.00 0.00 2.57
2285 2943 5.011329 TGCTCAGAAAGAAGCCAAATTGAAT 59.989 36.000 0.00 0.00 0.00 2.57
2340 3003 6.056884 TCAAATGCAAGCAGAAAGGAAATTT 58.943 32.000 0.00 0.00 0.00 1.82
2341 3004 5.934935 AATGCAAGCAGAAAGGAAATTTG 57.065 34.783 0.00 0.00 0.00 2.32
2743 3514 2.341846 AGTTCCATCACAACCGTTGT 57.658 45.000 11.24 11.24 46.75 3.32
2763 3534 4.552355 TGTTCGTAATCATATACCCTGCG 58.448 43.478 0.00 0.00 0.00 5.18
2766 3537 2.268298 GTAATCATATACCCTGCGCCG 58.732 52.381 4.18 0.00 0.00 6.46
2781 3552 2.158928 TGCGCCGGTGGTATATTTAGTT 60.159 45.455 18.41 0.00 0.00 2.24
2838 3613 6.071165 TGTTTATCTGTTCAGATGCTGAGAGA 60.071 38.462 21.15 9.36 41.75 3.10
2839 3614 4.659111 ATCTGTTCAGATGCTGAGAGAG 57.341 45.455 13.57 6.17 41.75 3.20
2876 3758 2.127708 AGGTATTACTGCAGGAAGGGG 58.872 52.381 18.11 0.00 0.00 4.79
2931 3813 4.015084 CTCATTGCAGAGGAGTTGGAATT 58.985 43.478 0.00 0.00 34.87 2.17
2962 3844 1.363744 CAGTCTTCTTGATCCGTGCC 58.636 55.000 0.00 0.00 0.00 5.01
3113 4527 2.924290 GCCACTAAGCGAATCGATATCC 59.076 50.000 6.91 0.00 0.00 2.59
3336 4778 3.580904 TCGTGAGAGGTGGAAAACG 57.419 52.632 0.00 0.00 34.84 3.60
3507 4979 1.332195 CGGACATGATGAGCTCCCTA 58.668 55.000 12.15 0.00 0.00 3.53
3559 5031 5.509498 TCCAAATGGAAATAGGAGACAAGG 58.491 41.667 0.00 0.00 42.18 3.61
3741 5213 0.736325 AAGTCGGTTCGAGAATGCCG 60.736 55.000 8.12 8.12 44.95 5.69
3765 5237 2.027625 GGTCGCGTTCAAGGACCTG 61.028 63.158 5.77 0.00 45.34 4.00
5049 6573 4.479796 AGATCTCATTTCCTGGGGAATTCA 59.520 41.667 7.93 0.00 41.71 2.57
5556 7475 2.941453 ACTATGTCGTCATCGTTGCT 57.059 45.000 0.00 0.00 38.33 3.91
5738 7658 5.900865 TTGCTCATGATACATGCTTTTGA 57.099 34.783 0.00 0.00 0.00 2.69
5858 7778 3.089784 GCGTTCGTGATCGCCAAT 58.910 55.556 12.92 0.00 45.54 3.16
6349 8282 4.757149 GGCGTTATCCATTTCAGATTAGCT 59.243 41.667 0.00 0.00 0.00 3.32
6350 8283 5.334414 GGCGTTATCCATTTCAGATTAGCTG 60.334 44.000 0.00 0.00 46.31 4.24
6377 8310 4.408270 ATGATAGCACATGTCAGAGGAACT 59.592 41.667 0.00 0.00 33.39 3.01
6378 8311 4.223700 TGATAGCACATGTCAGAGGAACTT 59.776 41.667 0.00 0.00 41.55 2.66
6379 8312 2.775890 AGCACATGTCAGAGGAACTTG 58.224 47.619 0.00 0.00 41.55 3.16
6402 8344 5.758296 TGTCCTTCAGTCAGTGTAACATTTC 59.242 40.000 0.00 0.00 41.43 2.17
6404 8346 6.260050 GTCCTTCAGTCAGTGTAACATTTCAA 59.740 38.462 0.00 0.00 41.43 2.69
6568 8511 8.762645 AGGTCACATCTCAATATCTTTGTTCTA 58.237 33.333 0.00 0.00 0.00 2.10
6584 8530 3.193903 TGTTCTATCGACCGGAAACATGA 59.806 43.478 9.46 0.00 0.00 3.07
6589 8535 0.732571 CGACCGGAAACATGATTGGG 59.267 55.000 9.46 0.00 0.00 4.12
6662 8608 4.708726 AATTCACTTCACTATTGCAGCC 57.291 40.909 0.00 0.00 0.00 4.85
6663 8609 2.857186 TCACTTCACTATTGCAGCCA 57.143 45.000 0.00 0.00 0.00 4.75
6664 8610 2.426522 TCACTTCACTATTGCAGCCAC 58.573 47.619 0.00 0.00 0.00 5.01
6665 8611 2.038952 TCACTTCACTATTGCAGCCACT 59.961 45.455 0.00 0.00 0.00 4.00
6666 8612 2.816087 CACTTCACTATTGCAGCCACTT 59.184 45.455 0.00 0.00 0.00 3.16
6667 8613 2.816087 ACTTCACTATTGCAGCCACTTG 59.184 45.455 0.00 0.00 0.00 3.16
6668 8614 2.857186 TCACTATTGCAGCCACTTGA 57.143 45.000 0.00 0.00 0.00 3.02
6669 8615 2.703416 TCACTATTGCAGCCACTTGAG 58.297 47.619 0.00 0.00 0.00 3.02
6671 8617 3.076621 CACTATTGCAGCCACTTGAGAA 58.923 45.455 0.00 0.00 0.00 2.87
6672 8618 3.126514 CACTATTGCAGCCACTTGAGAAG 59.873 47.826 0.00 0.00 0.00 2.85
6685 8650 1.356124 TGAGAAGCCTTGAGAAGCCT 58.644 50.000 0.00 0.00 0.00 4.58
6703 8668 4.265073 AGCCTTGAAACTGAGCGAATAAT 58.735 39.130 0.00 0.00 0.00 1.28
6781 8749 4.757149 GCCAAGATATTACAGCAGTAAGGG 59.243 45.833 7.79 3.85 43.02 3.95
6941 8909 2.520536 AAACCAGCCGAGCCTGTCT 61.521 57.895 0.00 0.00 0.00 3.41
7061 9029 2.744202 GACCTTGCACGTGAAGATCATT 59.256 45.455 22.23 3.35 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 3.886123 CGGGGAATGGAAGACAAATAGT 58.114 45.455 0.00 0.00 0.00 2.12
97 98 2.618709 GCGGGGAATGGAAGACAAATAG 59.381 50.000 0.00 0.00 0.00 1.73
98 99 2.025793 TGCGGGGAATGGAAGACAAATA 60.026 45.455 0.00 0.00 0.00 1.40
110 111 1.346395 GGGTTTTTCTTTGCGGGGAAT 59.654 47.619 0.00 0.00 0.00 3.01
137 138 6.262720 TGTGTGAGAATGTGATGTCATGAAAA 59.737 34.615 0.00 0.00 0.00 2.29
304 313 6.054941 TCTATCGATGCACACAACCATAATT 58.945 36.000 8.54 0.00 0.00 1.40
418 429 5.933187 TTTAGAAGCTGCGTGAACAATTA 57.067 34.783 0.00 0.00 0.00 1.40
698 748 8.964420 AAACGTTCAAACAATTATATGACCTG 57.036 30.769 0.00 0.00 0.00 4.00
836 913 4.035208 GTCGCTTATTTGTGTGGGGATAAG 59.965 45.833 0.00 0.00 35.95 1.73
837 914 3.942748 GTCGCTTATTTGTGTGGGGATAA 59.057 43.478 0.00 0.00 0.00 1.75
838 915 3.055021 TGTCGCTTATTTGTGTGGGGATA 60.055 43.478 0.00 0.00 0.00 2.59
841 918 1.529226 TGTCGCTTATTTGTGTGGGG 58.471 50.000 0.00 0.00 0.00 4.96
842 919 2.552315 AGTTGTCGCTTATTTGTGTGGG 59.448 45.455 0.00 0.00 0.00 4.61
844 921 4.394795 GCTAGTTGTCGCTTATTTGTGTG 58.605 43.478 0.00 0.00 0.00 3.82
845 922 3.435671 GGCTAGTTGTCGCTTATTTGTGT 59.564 43.478 0.00 0.00 0.00 3.72
846 923 3.435327 TGGCTAGTTGTCGCTTATTTGTG 59.565 43.478 0.00 0.00 0.00 3.33
847 924 3.670625 TGGCTAGTTGTCGCTTATTTGT 58.329 40.909 0.00 0.00 0.00 2.83
848 925 4.496341 CCATGGCTAGTTGTCGCTTATTTG 60.496 45.833 0.00 0.00 0.00 2.32
849 926 3.627577 CCATGGCTAGTTGTCGCTTATTT 59.372 43.478 0.00 0.00 0.00 1.40
850 927 3.206150 CCATGGCTAGTTGTCGCTTATT 58.794 45.455 0.00 0.00 0.00 1.40
852 929 1.742411 GCCATGGCTAGTTGTCGCTTA 60.742 52.381 29.98 0.00 38.26 3.09
853 930 1.026718 GCCATGGCTAGTTGTCGCTT 61.027 55.000 29.98 0.00 38.26 4.68
854 931 1.450312 GCCATGGCTAGTTGTCGCT 60.450 57.895 29.98 0.00 38.26 4.93
855 932 3.102097 GCCATGGCTAGTTGTCGC 58.898 61.111 29.98 0.00 38.26 5.19
872 949 5.855045 ACGGGAGATAAATAGTTGGCTTAG 58.145 41.667 0.00 0.00 0.00 2.18
873 950 5.881923 ACGGGAGATAAATAGTTGGCTTA 57.118 39.130 0.00 0.00 0.00 3.09
874 951 4.772886 ACGGGAGATAAATAGTTGGCTT 57.227 40.909 0.00 0.00 0.00 4.35
875 952 5.129815 TGTTACGGGAGATAAATAGTTGGCT 59.870 40.000 0.00 0.00 0.00 4.75
876 953 5.362263 TGTTACGGGAGATAAATAGTTGGC 58.638 41.667 0.00 0.00 0.00 4.52
878 955 6.281405 AGCTGTTACGGGAGATAAATAGTTG 58.719 40.000 0.00 0.00 0.00 3.16
879 956 6.481434 AGCTGTTACGGGAGATAAATAGTT 57.519 37.500 0.00 0.00 0.00 2.24
880 957 6.481434 AAGCTGTTACGGGAGATAAATAGT 57.519 37.500 0.00 0.00 0.00 2.12
881 958 7.787725 AAAAGCTGTTACGGGAGATAAATAG 57.212 36.000 0.00 0.00 0.00 1.73
905 982 5.646360 CGAGCTTTTATGAGACCCCTAAAAA 59.354 40.000 0.00 0.00 0.00 1.94
906 983 5.046159 TCGAGCTTTTATGAGACCCCTAAAA 60.046 40.000 0.00 0.00 0.00 1.52
907 984 4.468510 TCGAGCTTTTATGAGACCCCTAAA 59.531 41.667 0.00 0.00 0.00 1.85
908 985 4.028131 TCGAGCTTTTATGAGACCCCTAA 58.972 43.478 0.00 0.00 0.00 2.69
909 986 3.638860 TCGAGCTTTTATGAGACCCCTA 58.361 45.455 0.00 0.00 0.00 3.53
910 987 2.467880 TCGAGCTTTTATGAGACCCCT 58.532 47.619 0.00 0.00 0.00 4.79
911 988 2.981859 TCGAGCTTTTATGAGACCCC 57.018 50.000 0.00 0.00 0.00 4.95
912 989 5.119694 AGAATTCGAGCTTTTATGAGACCC 58.880 41.667 0.00 0.00 0.00 4.46
914 991 6.893958 TGAGAATTCGAGCTTTTATGAGAC 57.106 37.500 0.00 0.00 0.00 3.36
916 993 7.521529 TGTTTGAGAATTCGAGCTTTTATGAG 58.478 34.615 0.00 0.00 0.00 2.90
917 994 7.433708 TGTTTGAGAATTCGAGCTTTTATGA 57.566 32.000 0.00 0.00 0.00 2.15
918 995 9.214953 GTATGTTTGAGAATTCGAGCTTTTATG 57.785 33.333 0.00 0.00 0.00 1.90
920 997 8.227791 GTGTATGTTTGAGAATTCGAGCTTTTA 58.772 33.333 0.00 0.00 0.00 1.52
921 998 7.078228 GTGTATGTTTGAGAATTCGAGCTTTT 58.922 34.615 0.00 0.00 0.00 2.27
922 999 6.348540 GGTGTATGTTTGAGAATTCGAGCTTT 60.349 38.462 0.00 0.00 0.00 3.51
924 1001 4.631813 GGTGTATGTTTGAGAATTCGAGCT 59.368 41.667 0.00 0.00 0.00 4.09
925 1002 4.201822 GGGTGTATGTTTGAGAATTCGAGC 60.202 45.833 0.00 0.00 0.00 5.03
926 1003 4.032900 CGGGTGTATGTTTGAGAATTCGAG 59.967 45.833 0.00 0.00 0.00 4.04
927 1004 3.930229 CGGGTGTATGTTTGAGAATTCGA 59.070 43.478 0.00 0.00 0.00 3.71
928 1005 3.682858 ACGGGTGTATGTTTGAGAATTCG 59.317 43.478 0.00 0.00 0.00 3.34
929 1006 5.180492 TCAACGGGTGTATGTTTGAGAATTC 59.820 40.000 0.00 0.00 0.00 2.17
930 1007 5.067273 TCAACGGGTGTATGTTTGAGAATT 58.933 37.500 0.00 0.00 0.00 2.17
931 1008 4.647611 TCAACGGGTGTATGTTTGAGAAT 58.352 39.130 0.00 0.00 0.00 2.40
949 1132 2.352715 CCCTTTCGGCCTTTTCATCAAC 60.353 50.000 0.00 0.00 0.00 3.18
985 1523 2.355513 CCTTCATCTCAACTGGACCTGG 60.356 54.545 3.15 0.00 0.00 4.45
1024 1568 4.332543 AGGAAGGGGGCAGACGGA 62.333 66.667 0.00 0.00 0.00 4.69
1037 1581 2.578021 AGAAATAGGAGCAAGCCAGGAA 59.422 45.455 0.00 0.00 0.00 3.36
1038 1582 2.092753 CAGAAATAGGAGCAAGCCAGGA 60.093 50.000 0.00 0.00 0.00 3.86
1039 1583 2.295885 CAGAAATAGGAGCAAGCCAGG 58.704 52.381 0.00 0.00 0.00 4.45
1041 1585 1.283029 AGCAGAAATAGGAGCAAGCCA 59.717 47.619 0.00 0.00 0.00 4.75
1042 1586 1.946081 GAGCAGAAATAGGAGCAAGCC 59.054 52.381 0.00 0.00 0.00 4.35
1044 1588 3.118482 TGGAGAGCAGAAATAGGAGCAAG 60.118 47.826 0.00 0.00 0.00 4.01
1046 1590 2.169352 GTGGAGAGCAGAAATAGGAGCA 59.831 50.000 0.00 0.00 0.00 4.26
1121 1729 4.064768 TGGCTGGCATTGGGAGGG 62.065 66.667 0.00 0.00 0.00 4.30
1339 1947 4.821589 GGCGTGCTCCTCGAAGGG 62.822 72.222 0.00 0.00 35.59 3.95
1594 2239 1.880027 CCACTGGAAAAACGGAGAAGG 59.120 52.381 0.00 0.00 0.00 3.46
1627 2272 2.363680 AGATCACCACACGAGATGGATC 59.636 50.000 10.60 0.00 39.87 3.36
1631 2276 1.534805 CGGAGATCACCACACGAGATG 60.535 57.143 9.99 0.00 0.00 2.90
1632 2277 0.741326 CGGAGATCACCACACGAGAT 59.259 55.000 9.99 0.00 0.00 2.75
1759 2404 1.180029 AAGAATGTGGATGTGGCTGC 58.820 50.000 0.00 0.00 0.00 5.25
1760 2405 2.947652 CCTAAGAATGTGGATGTGGCTG 59.052 50.000 0.00 0.00 0.00 4.85
1781 2430 4.644103 AAATGCTACCATGCAGAATGTC 57.356 40.909 0.00 0.00 46.71 3.06
1870 2522 1.941294 GCCACAGAGAAGCATGATCTG 59.059 52.381 13.09 13.09 44.81 2.90
1879 2531 0.321122 GGTCACCTGCCACAGAGAAG 60.321 60.000 0.00 0.00 32.44 2.85
2195 2850 0.883153 TGTCAGTGATGTTGGCATGC 59.117 50.000 9.90 9.90 35.07 4.06
2244 2902 7.053316 TCTGAGCAAATGAGAAATGGAAAAA 57.947 32.000 0.00 0.00 0.00 1.94
2257 2915 3.928727 TGGCTTCTTTCTGAGCAAATG 57.071 42.857 0.00 0.00 0.00 2.32
2259 2917 4.942761 ATTTGGCTTCTTTCTGAGCAAA 57.057 36.364 0.00 0.00 0.00 3.68
2263 2921 8.248945 ACATATTCAATTTGGCTTCTTTCTGAG 58.751 33.333 0.00 0.00 0.00 3.35
2305 2968 5.643664 TGCTTGCATTTGAGTTAGCATAAG 58.356 37.500 1.41 0.00 36.80 1.73
2743 3514 3.581755 GCGCAGGGTATATGATTACGAA 58.418 45.455 0.30 0.00 0.00 3.85
2763 3534 2.551032 GCCAACTAAATATACCACCGGC 59.449 50.000 0.00 0.00 0.00 6.13
2766 3537 4.827284 AGCATGCCAACTAAATATACCACC 59.173 41.667 15.66 0.00 0.00 4.61
2838 3613 1.027357 CTGCAAAAGCACACCTGACT 58.973 50.000 0.00 0.00 0.00 3.41
2839 3614 0.031178 CCTGCAAAAGCACACCTGAC 59.969 55.000 0.00 0.00 0.00 3.51
2876 3758 1.774639 TACTGGTTTGCGAAGTCGAC 58.225 50.000 7.70 7.70 43.02 4.20
2931 3813 1.112113 GAAGACTGCGGAGGGTATGA 58.888 55.000 9.36 0.00 0.00 2.15
2962 3844 1.002134 AAGGCCACATTCAGGACGG 60.002 57.895 5.01 0.00 39.93 4.79
3113 4527 5.221048 CGGCTTCCAAAAGGATAATAACCAG 60.221 44.000 0.00 0.00 32.79 4.00
3300 4742 3.793144 GCCTGCGCCGTCTCTTTG 61.793 66.667 4.18 0.00 0.00 2.77
3489 4961 2.603021 TCTAGGGAGCTCATCATGTCC 58.397 52.381 17.19 5.39 0.00 4.02
3586 5058 2.894387 GCTCCGGCTGTGCATCTC 60.894 66.667 0.00 0.00 33.65 2.75
3741 5213 0.721718 CCTTGAACGCGACCTCAATC 59.278 55.000 15.93 0.00 31.40 2.67
3765 5237 2.179517 CCCGTCAGCGTCAGAGTC 59.820 66.667 0.00 0.00 36.15 3.36
4061 5548 1.982226 TGGCTAACTCTACTTGGGCAA 59.018 47.619 0.00 0.00 34.77 4.52
5049 6573 2.461695 ACACCGAGATGAAGTGGAGAT 58.538 47.619 0.00 0.00 35.79 2.75
5681 7600 2.224402 ACAAGGGAGTGTCAAGAGCTTC 60.224 50.000 0.00 0.00 0.00 3.86
5858 7778 1.298157 GGCATACGCACTTGTGAGCA 61.298 55.000 4.79 0.00 41.24 4.26
6248 8180 4.756642 TGCTCTTTACATCTCCACAACAAG 59.243 41.667 0.00 0.00 0.00 3.16
6349 8282 5.510861 CCTCTGACATGTGCTATCATCATCA 60.511 44.000 1.15 0.00 0.00 3.07
6350 8283 4.930405 CCTCTGACATGTGCTATCATCATC 59.070 45.833 1.15 0.00 0.00 2.92
6351 8284 4.591924 TCCTCTGACATGTGCTATCATCAT 59.408 41.667 1.15 0.00 0.00 2.45
6377 8310 4.746535 TGTTACACTGACTGAAGGACAA 57.253 40.909 0.00 0.00 0.00 3.18
6378 8311 4.955811 ATGTTACACTGACTGAAGGACA 57.044 40.909 0.00 0.00 0.00 4.02
6379 8312 5.758296 TGAAATGTTACACTGACTGAAGGAC 59.242 40.000 0.00 0.00 0.00 3.85
6402 8344 9.079833 CCAGAAATAATTAGACATTTGCACTTG 57.920 33.333 0.00 0.00 0.00 3.16
6404 8346 7.123247 AGCCAGAAATAATTAGACATTTGCACT 59.877 33.333 0.00 0.00 0.00 4.40
6421 8363 5.995565 TGTAGTACAGTACAGCCAGAAAT 57.004 39.130 13.37 0.00 0.00 2.17
6568 8511 2.288666 CCAATCATGTTTCCGGTCGAT 58.711 47.619 0.00 0.00 0.00 3.59
6584 8530 4.081476 GTGCTTTATCCTTTCTTGCCCAAT 60.081 41.667 0.00 0.00 0.00 3.16
6589 8535 7.814587 AGTATTTTGTGCTTTATCCTTTCTTGC 59.185 33.333 0.00 0.00 0.00 4.01
6639 8585 5.098211 GGCTGCAATAGTGAAGTGAATTTC 58.902 41.667 0.50 0.00 32.15 2.17
6662 8608 2.483491 GCTTCTCAAGGCTTCTCAAGTG 59.517 50.000 0.00 0.00 0.00 3.16
6663 8609 2.777094 GCTTCTCAAGGCTTCTCAAGT 58.223 47.619 0.00 0.00 0.00 3.16
6703 8668 3.249080 CCTCCTTAACGAAACTTTGCGAA 59.751 43.478 0.00 0.00 0.00 4.70
6717 8682 7.103641 CAGCTATAAAACTGTCACCTCCTTAA 58.896 38.462 0.00 0.00 0.00 1.85
6752 8720 5.366768 ACTGCTGTAATATCTTGGCCTTCTA 59.633 40.000 3.32 0.00 0.00 2.10
6941 8909 1.604308 CAACCTGCACCTGATGGCA 60.604 57.895 0.00 0.00 38.52 4.92
7092 9060 1.913451 AAGGTCAGAGACGCGTCGAG 61.913 60.000 31.56 24.19 32.65 4.04


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

AutoCloner maintained by Alex Coulton.