Multiple sequence alignment - TraesCS4D01G213900

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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 TraesCS4D01G213900 chr4D 100.000 2366 0 0 1 2366 366693177 366690812 0 4370
1 TraesCS4D01G213900 chr4B 88.795 1660 90 37 724 2325 451491161 451489540 0 1947
2 TraesCS4D01G213900 chr4B 89.109 808 53 15 1 775 451491984 451491179 0 972
3 TraesCS4D01G213900 chr4A 90.662 846 35 20 1542 2363 98559377 98560202 0 1085
4 TraesCS4D01G213900 chr4A 90.679 751 41 10 1 728 98557783 98558527 0 972
5 TraesCS4D01G213900 chr4A 87.912 637 40 21 826 1434 98558577 98559204 0 715


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 TraesCS4D01G213900 chr4D 366690812 366693177 2365 True 4370.0 4370 100.000 1 2366 1 chr4D.!!$R1 2365
1 TraesCS4D01G213900 chr4B 451489540 451491984 2444 True 1459.5 1947 88.952 1 2325 2 chr4B.!!$R1 2324
2 TraesCS4D01G213900 chr4A 98557783 98560202 2419 False 924.0 1085 89.751 1 2363 3 chr4A.!!$F1 2362

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
628 660 0.030638 CAACAGGCACCCGTTCTTTG 59.969 55.0 0.0 0.0 0.0 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 2150 0.32336 GGGCAATGGTCTACAGCCAA 60.323 55.0 0.0 0.0 41.06 4.52 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
29 30 0.999712 GACCAGGAAGGGATGGGAAA 59.000 55.000 0.00 0.00 43.89 3.13
73 74 2.034685 TGTATGTGAGCTCGTGATAGCC 59.965 50.000 9.64 0.00 43.86 3.93
125 133 2.353610 GGTGGAGCAAATGGGCCTG 61.354 63.158 4.53 0.00 0.00 4.85
138 146 1.425428 GGCCTGAGAATGAAACGCG 59.575 57.895 3.53 3.53 0.00 6.01
155 163 2.004017 CGCGGGTTAGTTTTGATGCTA 58.996 47.619 0.00 0.00 0.00 3.49
165 173 4.265073 AGTTTTGATGCTATCCTGTGGAC 58.735 43.478 0.00 0.00 32.98 4.02
177 185 1.359848 CTGTGGACGCAAGGACATAC 58.640 55.000 0.00 0.00 46.39 2.39
187 195 1.633432 CAAGGACATACCCAACCCTCA 59.367 52.381 0.00 0.00 40.05 3.86
188 196 1.584724 AGGACATACCCAACCCTCAG 58.415 55.000 0.00 0.00 40.05 3.35
189 197 1.203440 AGGACATACCCAACCCTCAGT 60.203 52.381 0.00 0.00 40.05 3.41
196 221 2.111043 CAACCCTCAGTGTGCGGT 59.889 61.111 0.00 0.00 0.00 5.68
214 239 3.009723 CGGTGATATTGTTGCTGGTCTT 58.990 45.455 0.00 0.00 0.00 3.01
361 386 1.673923 GGAAGGTTTCCGTTACTCCCG 60.674 57.143 0.00 0.00 40.59 5.14
375 400 0.320771 CTCCCGGTGTCCAGTTCTTG 60.321 60.000 0.00 0.00 0.00 3.02
499 530 7.891183 TCTTTTGGTATTGTGTATGGTATGGTT 59.109 33.333 0.00 0.00 0.00 3.67
512 543 4.527944 TGGTATGGTTTGAACTGTGTGAA 58.472 39.130 0.00 0.00 0.00 3.18
628 660 0.030638 CAACAGGCACCCGTTCTTTG 59.969 55.000 0.00 0.00 0.00 2.77
662 702 3.317608 CGCATTCCATGTGTTCTGC 57.682 52.632 0.00 0.00 36.09 4.26
664 704 2.009051 CGCATTCCATGTGTTCTGCTA 58.991 47.619 0.00 0.00 36.09 3.49
721 764 1.134075 CTCACGTCTGCAGCAATGC 59.866 57.895 9.47 0.00 0.00 3.56
739 782 4.435436 TGAGGTACCAGCGCGCAG 62.435 66.667 35.10 26.46 0.00 5.18
756 870 2.013563 GCAGGAGATCGCCATGTTTGA 61.014 52.381 18.44 0.00 0.00 2.69
830 963 1.070843 CCGTCTAAACTGTGTTGTGCG 60.071 52.381 0.00 0.00 0.00 5.34
839 972 2.279851 TGTTGTGCGTCAGACCGG 60.280 61.111 0.00 0.00 0.00 5.28
920 1053 2.946762 GCAAGTCAGTTGGTCGCC 59.053 61.111 0.00 0.00 36.56 5.54
937 1070 4.044439 CAGCCAGCCAGCCTCCTT 62.044 66.667 0.00 0.00 0.00 3.36
938 1071 2.285668 AGCCAGCCAGCCTCCTTA 60.286 61.111 0.00 0.00 0.00 2.69
939 1072 1.695597 AGCCAGCCAGCCTCCTTAT 60.696 57.895 0.00 0.00 0.00 1.73
940 1073 1.228094 GCCAGCCAGCCTCCTTATC 60.228 63.158 0.00 0.00 0.00 1.75
966 1103 1.275573 GAACCCCGCAGAGAAAGTAGT 59.724 52.381 0.00 0.00 0.00 2.73
978 1162 0.390735 AAAGTAGTAACCGCAGCCCG 60.391 55.000 0.00 0.00 0.00 6.13
979 1163 2.847435 AAGTAGTAACCGCAGCCCGC 62.847 60.000 0.00 0.00 35.03 6.13
980 1164 4.151582 TAGTAACCGCAGCCCGCC 62.152 66.667 0.00 0.00 37.30 6.13
989 1173 3.384532 CAGCCCGCCCAAGCAAAT 61.385 61.111 0.00 0.00 39.83 2.32
991 1175 1.754234 AGCCCGCCCAAGCAAATAG 60.754 57.895 0.00 0.00 39.83 1.73
992 1176 2.052104 GCCCGCCCAAGCAAATAGT 61.052 57.895 0.00 0.00 39.83 2.12
993 1177 0.750182 GCCCGCCCAAGCAAATAGTA 60.750 55.000 0.00 0.00 39.83 1.82
994 1178 1.308998 CCCGCCCAAGCAAATAGTAG 58.691 55.000 0.00 0.00 39.83 2.57
995 1179 1.134220 CCCGCCCAAGCAAATAGTAGA 60.134 52.381 0.00 0.00 39.83 2.59
996 1180 2.213499 CCGCCCAAGCAAATAGTAGAG 58.787 52.381 0.00 0.00 39.83 2.43
997 1181 2.213499 CGCCCAAGCAAATAGTAGAGG 58.787 52.381 0.00 0.00 39.83 3.69
998 1182 1.950216 GCCCAAGCAAATAGTAGAGGC 59.050 52.381 0.00 0.00 39.53 4.70
999 1183 2.213499 CCCAAGCAAATAGTAGAGGCG 58.787 52.381 0.00 0.00 0.00 5.52
1000 1184 2.158957 CCCAAGCAAATAGTAGAGGCGA 60.159 50.000 0.00 0.00 0.00 5.54
1001 1185 3.495100 CCCAAGCAAATAGTAGAGGCGAT 60.495 47.826 0.00 0.00 0.00 4.58
1002 1186 3.496130 CCAAGCAAATAGTAGAGGCGATG 59.504 47.826 0.00 0.00 0.00 3.84
1003 1187 3.393089 AGCAAATAGTAGAGGCGATGG 57.607 47.619 0.00 0.00 0.00 3.51
1004 1188 2.037772 AGCAAATAGTAGAGGCGATGGG 59.962 50.000 0.00 0.00 0.00 4.00
1005 1189 2.037251 GCAAATAGTAGAGGCGATGGGA 59.963 50.000 0.00 0.00 0.00 4.37
1006 1190 3.862642 GCAAATAGTAGAGGCGATGGGAG 60.863 52.174 0.00 0.00 0.00 4.30
1007 1191 2.223803 ATAGTAGAGGCGATGGGAGG 57.776 55.000 0.00 0.00 0.00 4.30
1008 1192 1.146452 TAGTAGAGGCGATGGGAGGA 58.854 55.000 0.00 0.00 0.00 3.71
1009 1193 0.178975 AGTAGAGGCGATGGGAGGAG 60.179 60.000 0.00 0.00 0.00 3.69
1010 1194 1.153989 TAGAGGCGATGGGAGGAGG 59.846 63.158 0.00 0.00 0.00 4.30
1011 1195 1.361176 TAGAGGCGATGGGAGGAGGA 61.361 60.000 0.00 0.00 0.00 3.71
1012 1196 2.123077 AGGCGATGGGAGGAGGAG 60.123 66.667 0.00 0.00 0.00 3.69
1013 1197 3.237741 GGCGATGGGAGGAGGAGG 61.238 72.222 0.00 0.00 0.00 4.30
1269 1453 2.347490 CACCCCGTCTGGTCCTTG 59.653 66.667 0.00 0.00 36.12 3.61
1372 1565 2.415608 GCCTCCGACTGACCGATCA 61.416 63.158 0.00 0.00 0.00 2.92
1394 1592 2.257676 GTCTCTTCGCCGTCCGTT 59.742 61.111 0.00 0.00 38.35 4.44
1419 1617 4.501559 CGTGCCAACATCAATCAATCAATC 59.498 41.667 0.00 0.00 0.00 2.67
1420 1618 5.412640 GTGCCAACATCAATCAATCAATCA 58.587 37.500 0.00 0.00 0.00 2.57
1421 1619 5.518847 GTGCCAACATCAATCAATCAATCAG 59.481 40.000 0.00 0.00 0.00 2.90
1422 1620 5.186215 TGCCAACATCAATCAATCAATCAGT 59.814 36.000 0.00 0.00 0.00 3.41
1434 1632 6.918626 TCAATCAATCAGTAAAAATTCCGCA 58.081 32.000 0.00 0.00 0.00 5.69
1435 1633 7.028962 TCAATCAATCAGTAAAAATTCCGCAG 58.971 34.615 0.00 0.00 0.00 5.18
1448 1646 4.208632 CGCAGGTGTGGATTCCTC 57.791 61.111 3.95 0.59 30.91 3.71
1449 1647 1.811266 CGCAGGTGTGGATTCCTCG 60.811 63.158 3.95 0.00 30.91 4.63
1450 1648 1.450312 GCAGGTGTGGATTCCTCGG 60.450 63.158 3.95 0.00 30.91 4.63
1451 1649 1.221840 CAGGTGTGGATTCCTCGGG 59.778 63.158 3.95 0.00 30.91 5.14
1452 1650 1.995626 AGGTGTGGATTCCTCGGGG 60.996 63.158 0.00 0.00 0.00 5.73
1453 1651 1.993391 GGTGTGGATTCCTCGGGGA 60.993 63.158 0.00 0.00 40.36 4.81
1479 1677 4.910458 ACACTTGCAGGAGTATTTACCT 57.090 40.909 1.40 0.00 36.92 3.08
1515 1726 2.224402 TGGTGTATGTGTACTTGCTGCA 60.224 45.455 0.00 0.00 0.00 4.41
1516 1727 3.009723 GGTGTATGTGTACTTGCTGCAT 58.990 45.455 1.84 0.00 0.00 3.96
1519 1735 5.050091 GGTGTATGTGTACTTGCTGCATATC 60.050 44.000 1.84 0.00 0.00 1.63
1540 1756 9.249457 CATATCTCTCTACGCACAGAAAAATAA 57.751 33.333 0.00 0.00 0.00 1.40
1554 1854 9.559958 CACAGAAAAATAATACCATGTGTCTTC 57.440 33.333 0.00 0.00 33.78 2.87
1569 1869 1.656095 GTCTTCGCCTCTCGTGAATTG 59.344 52.381 0.00 0.00 40.16 2.32
1585 1890 4.397417 GTGAATTGTGATTGCTCTAAGGCT 59.603 41.667 0.00 0.00 0.00 4.58
1586 1891 5.586243 GTGAATTGTGATTGCTCTAAGGCTA 59.414 40.000 0.00 0.00 0.00 3.93
1587 1892 6.094048 GTGAATTGTGATTGCTCTAAGGCTAA 59.906 38.462 0.00 0.00 0.00 3.09
1588 1893 6.830324 TGAATTGTGATTGCTCTAAGGCTAAT 59.170 34.615 0.00 0.00 0.00 1.73
1589 1894 6.874288 ATTGTGATTGCTCTAAGGCTAATC 57.126 37.500 0.00 0.00 34.07 1.75
1590 1895 4.708177 TGTGATTGCTCTAAGGCTAATCC 58.292 43.478 3.65 0.00 33.33 3.01
1592 1897 5.602561 TGTGATTGCTCTAAGGCTAATCCTA 59.397 40.000 3.65 0.00 46.94 2.94
1593 1898 6.270927 TGTGATTGCTCTAAGGCTAATCCTAT 59.729 38.462 3.65 0.00 46.94 2.57
1594 1899 6.816140 GTGATTGCTCTAAGGCTAATCCTATC 59.184 42.308 3.65 0.00 46.94 2.08
1595 1900 5.746990 TTGCTCTAAGGCTAATCCTATCC 57.253 43.478 0.00 0.00 46.94 2.59
1596 1901 5.017093 TGCTCTAAGGCTAATCCTATCCT 57.983 43.478 0.00 0.00 46.94 3.24
1597 1902 6.153942 TGCTCTAAGGCTAATCCTATCCTA 57.846 41.667 0.00 0.00 46.94 2.94
1598 1903 6.746894 TGCTCTAAGGCTAATCCTATCCTAT 58.253 40.000 0.00 0.00 46.94 2.57
1599 1904 6.609212 TGCTCTAAGGCTAATCCTATCCTATG 59.391 42.308 0.00 0.00 46.94 2.23
1600 1905 6.041523 GCTCTAAGGCTAATCCTATCCTATGG 59.958 46.154 0.00 0.00 46.94 2.74
1611 1916 6.985653 TCCTATCCTATGGTTTCTCTTCTG 57.014 41.667 0.00 0.00 0.00 3.02
1670 1976 9.614792 ACATACTTCTGATTTATTTCCTGTACC 57.385 33.333 0.00 0.00 0.00 3.34
1693 1999 2.799126 TTCAGTTCCACAACACAGGT 57.201 45.000 0.00 0.00 34.60 4.00
1702 2008 2.433970 CCACAACACAGGTTCCCAAAAT 59.566 45.455 0.00 0.00 34.21 1.82
1822 2143 2.493675 AGTCACACGCATCTGATGTAGT 59.506 45.455 18.19 15.15 0.00 2.73
1826 2147 4.338118 TCACACGCATCTGATGTAGTATGA 59.662 41.667 18.19 18.26 29.27 2.15
1828 2149 5.118203 CACACGCATCTGATGTAGTATGATG 59.882 44.000 18.19 10.98 37.96 3.07
1829 2150 5.221322 ACACGCATCTGATGTAGTATGATGT 60.221 40.000 18.19 9.87 37.44 3.06
1830 2151 5.693555 CACGCATCTGATGTAGTATGATGTT 59.306 40.000 18.19 0.00 37.44 2.71
1831 2152 5.693555 ACGCATCTGATGTAGTATGATGTTG 59.306 40.000 18.19 0.00 37.44 3.33
1832 2153 5.119743 CGCATCTGATGTAGTATGATGTTGG 59.880 44.000 18.19 0.00 37.44 3.77
1954 2288 3.922171 ACTGCAGAAATAGAAGAGGGG 57.078 47.619 23.35 0.00 0.00 4.79
2202 2540 1.075601 ACAATGCAGGGGAAGAAGGA 58.924 50.000 0.00 0.00 0.00 3.36
2205 2543 1.376649 ATGCAGGGGAAGAAGGAAGT 58.623 50.000 0.00 0.00 0.00 3.01
2325 2663 0.730265 GACAAGAAACCACACGCACA 59.270 50.000 0.00 0.00 0.00 4.57
2363 2701 2.029828 CGCTCCGGCTTGTAGATTCTAT 60.030 50.000 0.00 0.00 36.09 1.98
2364 2702 3.321497 GCTCCGGCTTGTAGATTCTATG 58.679 50.000 0.00 0.00 35.22 2.23
2365 2703 3.243907 GCTCCGGCTTGTAGATTCTATGT 60.244 47.826 0.00 0.00 35.22 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.542375 AGGGACCAGACCTGCCATT 60.542 57.895 0.00 0.00 36.85 3.16
73 74 6.533012 CAGAGTAGTATGTCACAAGGTTCATG 59.467 42.308 0.00 0.00 0.00 3.07
125 133 2.344025 ACTAACCCGCGTTTCATTCTC 58.656 47.619 4.92 0.00 33.17 2.87
138 146 5.066505 CACAGGATAGCATCAAAACTAACCC 59.933 44.000 0.00 0.00 33.09 4.11
155 163 1.296715 GTCCTTGCGTCCACAGGAT 59.703 57.895 0.00 0.00 32.73 3.24
165 173 1.029947 GGGTTGGGTATGTCCTTGCG 61.030 60.000 0.00 0.00 36.25 4.85
177 185 2.669569 CGCACACTGAGGGTTGGG 60.670 66.667 0.00 0.00 0.00 4.12
187 195 1.468520 GCAACAATATCACCGCACACT 59.531 47.619 0.00 0.00 0.00 3.55
188 196 1.468520 AGCAACAATATCACCGCACAC 59.531 47.619 0.00 0.00 0.00 3.82
189 197 1.468127 CAGCAACAATATCACCGCACA 59.532 47.619 0.00 0.00 0.00 4.57
196 221 4.826733 ACACAAAGACCAGCAACAATATCA 59.173 37.500 0.00 0.00 0.00 2.15
214 239 3.859443 AGCAAACAAAATCAGCACACAA 58.141 36.364 0.00 0.00 0.00 3.33
261 286 6.833346 TCCTATCCACCCATGTAAACAATA 57.167 37.500 0.00 0.00 0.00 1.90
361 386 0.798776 CGATGCAAGAACTGGACACC 59.201 55.000 0.00 0.00 0.00 4.16
375 400 0.664761 ATGTATTGCACAGCCGATGC 59.335 50.000 0.00 0.00 41.51 3.91
499 530 4.702831 TGCTACTGATTCACACAGTTCAA 58.297 39.130 0.00 0.00 44.69 2.69
651 691 7.326789 CCAACAAATAACTTAGCAGAACACATG 59.673 37.037 0.00 0.00 0.00 3.21
662 702 9.139174 CCAAACTATTGCCAACAAATAACTTAG 57.861 33.333 0.00 0.00 39.77 2.18
664 704 6.426633 GCCAAACTATTGCCAACAAATAACTT 59.573 34.615 0.00 0.00 39.77 2.66
721 764 4.435436 TGCGCGCTGGTACCTCAG 62.435 66.667 33.29 3.98 37.79 3.35
735 778 1.091771 AAACATGGCGATCTCCTGCG 61.092 55.000 2.88 0.00 0.00 5.18
739 782 5.335191 GGATTAATCAAACATGGCGATCTCC 60.335 44.000 17.07 0.00 0.00 3.71
746 860 5.581126 TGAGTGGATTAATCAAACATGGC 57.419 39.130 17.07 6.73 29.08 4.40
756 870 6.970640 AGAGGGATATGGATGAGTGGATTAAT 59.029 38.462 0.00 0.00 0.00 1.40
813 935 2.863740 CTGACGCACAACACAGTTTAGA 59.136 45.455 0.00 0.00 0.00 2.10
819 941 1.821241 CGGTCTGACGCACAACACAG 61.821 60.000 1.07 0.00 0.00 3.66
830 963 0.099436 GATGCATTTGCCGGTCTGAC 59.901 55.000 1.90 0.00 41.18 3.51
839 972 2.456989 CGGTGAATCTGATGCATTTGC 58.543 47.619 0.00 0.00 42.50 3.68
929 1062 3.137360 GGGTTCAAGATGATAAGGAGGCT 59.863 47.826 0.00 0.00 0.00 4.58
930 1063 3.481453 GGGTTCAAGATGATAAGGAGGC 58.519 50.000 0.00 0.00 0.00 4.70
932 1065 3.733337 CGGGGTTCAAGATGATAAGGAG 58.267 50.000 0.00 0.00 0.00 3.69
934 1067 2.222027 GCGGGGTTCAAGATGATAAGG 58.778 52.381 0.00 0.00 0.00 2.69
935 1068 2.874701 CTGCGGGGTTCAAGATGATAAG 59.125 50.000 0.00 0.00 0.00 1.73
936 1069 2.503765 TCTGCGGGGTTCAAGATGATAA 59.496 45.455 0.00 0.00 0.00 1.75
937 1070 2.103094 CTCTGCGGGGTTCAAGATGATA 59.897 50.000 0.00 0.00 0.00 2.15
938 1071 0.911769 TCTGCGGGGTTCAAGATGAT 59.088 50.000 0.00 0.00 0.00 2.45
939 1072 0.250234 CTCTGCGGGGTTCAAGATGA 59.750 55.000 0.00 0.00 0.00 2.92
940 1073 0.250234 TCTCTGCGGGGTTCAAGATG 59.750 55.000 0.00 0.00 0.00 2.90
978 1162 1.950216 GCCTCTACTATTTGCTTGGGC 59.050 52.381 0.00 0.00 39.26 5.36
979 1163 2.158957 TCGCCTCTACTATTTGCTTGGG 60.159 50.000 0.00 0.00 0.00 4.12
980 1164 3.179443 TCGCCTCTACTATTTGCTTGG 57.821 47.619 0.00 0.00 0.00 3.61
981 1165 3.496130 CCATCGCCTCTACTATTTGCTTG 59.504 47.826 0.00 0.00 0.00 4.01
982 1166 3.495100 CCCATCGCCTCTACTATTTGCTT 60.495 47.826 0.00 0.00 0.00 3.91
984 1168 2.037251 TCCCATCGCCTCTACTATTTGC 59.963 50.000 0.00 0.00 0.00 3.68
985 1169 3.306364 CCTCCCATCGCCTCTACTATTTG 60.306 52.174 0.00 0.00 0.00 2.32
986 1170 2.900546 CCTCCCATCGCCTCTACTATTT 59.099 50.000 0.00 0.00 0.00 1.40
987 1171 2.110188 TCCTCCCATCGCCTCTACTATT 59.890 50.000 0.00 0.00 0.00 1.73
988 1172 1.711375 TCCTCCCATCGCCTCTACTAT 59.289 52.381 0.00 0.00 0.00 2.12
989 1173 1.074084 CTCCTCCCATCGCCTCTACTA 59.926 57.143 0.00 0.00 0.00 1.82
991 1175 1.182385 CCTCCTCCCATCGCCTCTAC 61.182 65.000 0.00 0.00 0.00 2.59
992 1176 1.153989 CCTCCTCCCATCGCCTCTA 59.846 63.158 0.00 0.00 0.00 2.43
993 1177 2.123077 CCTCCTCCCATCGCCTCT 60.123 66.667 0.00 0.00 0.00 3.69
994 1178 2.123251 TCCTCCTCCCATCGCCTC 60.123 66.667 0.00 0.00 0.00 4.70
995 1179 2.123077 CTCCTCCTCCCATCGCCT 60.123 66.667 0.00 0.00 0.00 5.52
996 1180 3.237741 CCTCCTCCTCCCATCGCC 61.238 72.222 0.00 0.00 0.00 5.54
997 1181 3.237741 CCCTCCTCCTCCCATCGC 61.238 72.222 0.00 0.00 0.00 4.58
998 1182 2.525381 CCCCTCCTCCTCCCATCG 60.525 72.222 0.00 0.00 0.00 3.84
999 1183 2.851588 GCCCCTCCTCCTCCCATC 60.852 72.222 0.00 0.00 0.00 3.51
1000 1184 4.888325 CGCCCCTCCTCCTCCCAT 62.888 72.222 0.00 0.00 0.00 4.00
1019 1203 2.285144 TCCCGAACTCCTTCCCCC 60.285 66.667 0.00 0.00 0.00 5.40
1394 1592 1.902938 TTGATTGATGTTGGCACGGA 58.097 45.000 0.00 0.00 0.00 4.69
1419 1617 3.564511 CACACCTGCGGAATTTTTACTG 58.435 45.455 0.00 0.00 0.00 2.74
1420 1618 2.556622 CCACACCTGCGGAATTTTTACT 59.443 45.455 0.00 0.00 0.00 2.24
1421 1619 2.554893 TCCACACCTGCGGAATTTTTAC 59.445 45.455 0.00 0.00 0.00 2.01
1422 1620 2.865079 TCCACACCTGCGGAATTTTTA 58.135 42.857 0.00 0.00 0.00 1.52
1434 1632 1.995626 CCCCGAGGAATCCACACCT 60.996 63.158 0.61 0.00 39.41 4.00
1435 1633 1.993391 TCCCCGAGGAATCCACACC 60.993 63.158 0.61 0.00 40.08 4.16
1436 1634 3.721868 TCCCCGAGGAATCCACAC 58.278 61.111 0.61 0.00 40.08 3.82
1454 1652 6.549736 AGGTAAATACTCCTGCAAGTGTTTTT 59.450 34.615 15.62 12.52 40.01 1.94
1455 1653 6.068670 AGGTAAATACTCCTGCAAGTGTTTT 58.931 36.000 15.62 10.71 40.01 2.43
1456 1654 5.631119 AGGTAAATACTCCTGCAAGTGTTT 58.369 37.500 15.00 15.00 41.57 2.83
1457 1655 5.242795 AGGTAAATACTCCTGCAAGTGTT 57.757 39.130 1.14 0.00 32.67 3.32
1458 1656 4.910458 AGGTAAATACTCCTGCAAGTGT 57.090 40.909 1.14 0.00 32.29 3.55
1469 1667 7.285858 CAGGAAGCTCAGTAGTAGGTAAATACT 59.714 40.741 0.00 0.00 39.35 2.12
1472 1670 5.364157 CCAGGAAGCTCAGTAGTAGGTAAAT 59.636 44.000 0.00 0.00 0.00 1.40
1474 1672 4.264262 ACCAGGAAGCTCAGTAGTAGGTAA 60.264 45.833 0.00 0.00 0.00 2.85
1475 1673 3.268856 ACCAGGAAGCTCAGTAGTAGGTA 59.731 47.826 0.00 0.00 0.00 3.08
1476 1674 2.043252 ACCAGGAAGCTCAGTAGTAGGT 59.957 50.000 0.00 0.00 0.00 3.08
1477 1675 2.428890 CACCAGGAAGCTCAGTAGTAGG 59.571 54.545 0.00 0.00 0.00 3.18
1479 1677 3.170991 ACACCAGGAAGCTCAGTAGTA 57.829 47.619 0.00 0.00 0.00 1.82
1489 1700 3.684788 GCAAGTACACATACACCAGGAAG 59.315 47.826 0.00 0.00 33.30 3.46
1515 1726 9.988815 ATTATTTTTCTGTGCGTAGAGAGATAT 57.011 29.630 0.00 0.54 0.00 1.63
1519 1735 7.491372 TGGTATTATTTTTCTGTGCGTAGAGAG 59.509 37.037 0.00 0.00 0.00 3.20
1540 1756 2.101582 GAGAGGCGAAGACACATGGTAT 59.898 50.000 0.00 0.00 39.87 2.73
1585 1890 9.094578 CAGAAGAGAAACCATAGGATAGGATTA 57.905 37.037 0.00 0.00 0.00 1.75
1586 1891 7.474079 GCAGAAGAGAAACCATAGGATAGGATT 60.474 40.741 0.00 0.00 0.00 3.01
1587 1892 6.013812 GCAGAAGAGAAACCATAGGATAGGAT 60.014 42.308 0.00 0.00 0.00 3.24
1588 1893 5.305644 GCAGAAGAGAAACCATAGGATAGGA 59.694 44.000 0.00 0.00 0.00 2.94
1589 1894 5.306678 AGCAGAAGAGAAACCATAGGATAGG 59.693 44.000 0.00 0.00 0.00 2.57
1590 1895 6.418057 AGCAGAAGAGAAACCATAGGATAG 57.582 41.667 0.00 0.00 0.00 2.08
1591 1896 6.408548 CCAAGCAGAAGAGAAACCATAGGATA 60.409 42.308 0.00 0.00 0.00 2.59
1592 1897 5.435291 CAAGCAGAAGAGAAACCATAGGAT 58.565 41.667 0.00 0.00 0.00 3.24
1593 1898 4.323792 CCAAGCAGAAGAGAAACCATAGGA 60.324 45.833 0.00 0.00 0.00 2.94
1594 1899 3.944015 CCAAGCAGAAGAGAAACCATAGG 59.056 47.826 0.00 0.00 0.00 2.57
1595 1900 4.583871 ACCAAGCAGAAGAGAAACCATAG 58.416 43.478 0.00 0.00 0.00 2.23
1596 1901 4.640771 ACCAAGCAGAAGAGAAACCATA 57.359 40.909 0.00 0.00 0.00 2.74
1597 1902 3.515602 ACCAAGCAGAAGAGAAACCAT 57.484 42.857 0.00 0.00 0.00 3.55
1598 1903 4.326826 CATACCAAGCAGAAGAGAAACCA 58.673 43.478 0.00 0.00 0.00 3.67
1599 1904 3.691609 CCATACCAAGCAGAAGAGAAACC 59.308 47.826 0.00 0.00 0.00 3.27
1600 1905 3.691609 CCCATACCAAGCAGAAGAGAAAC 59.308 47.826 0.00 0.00 0.00 2.78
1611 1916 1.000359 AACTGCCCCCATACCAAGC 60.000 57.895 0.00 0.00 0.00 4.01
1670 1976 3.251729 CCTGTGTTGTGGAACTGAATGAG 59.748 47.826 0.00 0.00 38.04 2.90
1693 1999 1.144093 ACTCGTGGGTCATTTTGGGAA 59.856 47.619 0.00 0.00 0.00 3.97
1702 2008 1.208535 ACTTGTCAAACTCGTGGGTCA 59.791 47.619 0.00 0.00 0.00 4.02
1793 2114 0.534203 ATGCGTGTGACTTCCGGTTT 60.534 50.000 0.00 0.00 0.00 3.27
1822 2143 5.125356 CAATGGTCTACAGCCAACATCATA 58.875 41.667 0.00 0.00 39.72 2.15
1826 2147 2.094675 GCAATGGTCTACAGCCAACAT 58.905 47.619 0.00 0.00 39.72 2.71
1828 2149 0.811281 GGCAATGGTCTACAGCCAAC 59.189 55.000 0.00 0.00 39.54 3.77
1829 2150 0.323360 GGGCAATGGTCTACAGCCAA 60.323 55.000 0.00 0.00 41.06 4.52
1830 2151 1.302949 GGGCAATGGTCTACAGCCA 59.697 57.895 0.00 0.00 41.06 4.75
1831 2152 1.819632 CGGGCAATGGTCTACAGCC 60.820 63.158 0.00 0.00 39.15 4.85
1832 2153 1.819632 CCGGGCAATGGTCTACAGC 60.820 63.158 0.00 0.00 0.00 4.40
1954 2288 1.044611 GACAGATACTGCCCCTCTCC 58.955 60.000 0.00 0.00 34.37 3.71
2086 2421 1.746615 CATCAAGGTGGACAGGCCG 60.747 63.158 0.00 0.00 40.66 6.13
2192 2530 0.685660 ACGGTCACTTCCTTCTTCCC 59.314 55.000 0.00 0.00 0.00 3.97
2202 2540 1.230635 GCAGCATCACACGGTCACTT 61.231 55.000 0.00 0.00 0.00 3.16
2205 2543 1.071299 AAGCAGCATCACACGGTCA 59.929 52.632 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.