Multiple sequence alignment - TraesCS5A01G545700

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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 TraesCS5A01G545700 chr5A 100.000 2747 0 0 1 2747 700441749 700444495 0.000000e+00 5073.0
1 TraesCS5A01G545700 chr5A 100.000 28 0 0 707 734 3808993 3808966 5.000000e-03 52.8
2 TraesCS5A01G545700 chrUn 87.570 2502 160 57 335 2742 110519432 110521876 0.000000e+00 2758.0
3 TraesCS5A01G545700 chrUn 80.836 287 43 8 1 285 110519150 110519426 5.960000e-52 215.0
4 TraesCS5A01G545700 chr4B 86.670 2108 138 59 708 2736 660588091 660590134 0.000000e+00 2204.0
5 TraesCS5A01G545700 chr4B 82.555 407 42 13 9 415 660586745 660587122 5.670000e-87 331.0
6 TraesCS5A01G545700 chr4B 100.000 28 0 0 707 734 135811645 135811672 5.000000e-03 52.8
7 TraesCS5A01G545700 chr4D 87.162 148 16 2 547 694 466669249 466669393 6.090000e-37 165.0
8 TraesCS5A01G545700 chr3D 86.452 155 15 4 544 698 431291625 431291773 6.090000e-37 165.0
9 TraesCS5A01G545700 chr3D 85.135 148 19 2 547 694 83491889 83492033 6.130000e-32 148.0
10 TraesCS5A01G545700 chr6B 85.811 148 17 3 547 694 70877372 70877515 1.320000e-33 154.0
11 TraesCS5A01G545700 chr1A 85.526 152 17 3 546 694 575386985 575387134 1.320000e-33 154.0
12 TraesCS5A01G545700 chr7D 83.951 162 20 5 548 708 16787565 16787721 1.700000e-32 150.0
13 TraesCS5A01G545700 chr6D 85.135 148 15 2 547 694 1486632 1486492 7.930000e-31 145.0
14 TraesCS5A01G545700 chr2A 84.459 148 19 3 547 694 656999302 656999445 2.850000e-30 143.0
15 TraesCS5A01G545700 chr2A 100.000 28 0 0 707 734 719478071 719478098 5.000000e-03 52.8
16 TraesCS5A01G545700 chr3A 83.784 148 20 3 547 694 738953722 738953865 1.330000e-28 137.0
17 TraesCS5A01G545700 chr4A 100.000 28 0 0 707 734 659211429 659211456 5.000000e-03 52.8
18 TraesCS5A01G545700 chr2B 100.000 28 0 0 707 734 748695267 748695240 5.000000e-03 52.8
19 TraesCS5A01G545700 chr1B 100.000 28 0 0 707 734 657182913 657182886 5.000000e-03 52.8


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 TraesCS5A01G545700 chr5A 700441749 700444495 2746 False 5073.0 5073 100.0000 1 2747 1 chr5A.!!$F1 2746
1 TraesCS5A01G545700 chrUn 110519150 110521876 2726 False 1486.5 2758 84.2030 1 2742 2 chrUn.!!$F1 2741
2 TraesCS5A01G545700 chr4B 660586745 660590134 3389 False 1267.5 2204 84.6125 9 2736 2 chr4B.!!$F2 2727

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
243 265 0.247894 TGTCGCGTTGTTTGACTTGC 60.248 50.0 5.77 0.00 33.81 4.01 F
571 1474 0.464036 TTGCCAAGTGTCAGTCGACT 59.536 50.0 13.58 13.58 43.06 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1316 2285 0.036022 GACCACCTTGAAGAGCAGCT 59.964 55.0 0.00 0.0 0.00 4.24 R
2562 3580 0.587285 GACGATGACGACGGCTCTAT 59.413 55.0 0.65 0.0 42.66 1.98 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
48 49 3.817647 GTGACCATTGAAGCAAAGAGAGT 59.182 43.478 0.00 0.00 0.00 3.24
61 62 4.376819 GCAAAGAGAGTGACAATCAAGACG 60.377 45.833 5.59 0.00 0.00 4.18
62 63 4.855715 AAGAGAGTGACAATCAAGACGA 57.144 40.909 5.59 0.00 0.00 4.20
107 108 2.739943 TCAAGGAGTCGAGGATCATGT 58.260 47.619 0.00 0.00 33.17 3.21
111 112 1.202580 GGAGTCGAGGATCATGTTGGG 60.203 57.143 0.00 0.00 33.17 4.12
132 133 2.892374 CAACACTAGCATCATGGACGA 58.108 47.619 0.00 0.00 0.00 4.20
178 200 4.914312 AATGCAAAAAGACATCAATGCG 57.086 36.364 0.00 0.00 36.62 4.73
181 203 2.159934 GCAAAAAGACATCAATGCGCAC 60.160 45.455 14.90 0.00 0.00 5.34
183 205 1.246649 AAAGACATCAATGCGCACCA 58.753 45.000 14.90 0.00 0.00 4.17
186 208 0.734309 GACATCAATGCGCACCATGA 59.266 50.000 24.45 22.49 33.49 3.07
229 251 2.704725 ACCATGTGTTGAATTGTCGC 57.295 45.000 0.00 0.00 0.00 5.19
243 265 0.247894 TGTCGCGTTGTTTGACTTGC 60.248 50.000 5.77 0.00 33.81 4.01
247 269 1.530852 CGCGTTGTTTGACTTGCTGAA 60.531 47.619 0.00 0.00 0.00 3.02
286 310 8.851960 TTACGTTGATATTCCATATCTATCGC 57.148 34.615 0.00 0.00 41.69 4.58
303 327 3.678915 TCGCTGAATGTGTGCAATATG 57.321 42.857 0.00 0.00 0.00 1.78
309 333 6.358822 CGCTGAATGTGTGCAATATGATAAAG 59.641 38.462 0.00 0.00 0.00 1.85
310 334 7.420002 GCTGAATGTGTGCAATATGATAAAGA 58.580 34.615 0.00 0.00 0.00 2.52
330 354 2.096220 TAGTGAAAAATACGCCGCCA 57.904 45.000 0.00 0.00 0.00 5.69
333 357 1.068816 GTGAAAAATACGCCGCCAAGT 60.069 47.619 0.00 0.00 0.00 3.16
349 373 2.506444 CAAGTACCCGGGTTTTAGCAA 58.494 47.619 35.42 9.14 0.00 3.91
368 392 3.855524 GCAAACAAACCCGTGTTATCCAG 60.856 47.826 0.00 0.00 40.86 3.86
375 399 3.760693 CGTGTTATCCAGGGACAGG 57.239 57.895 0.00 0.00 35.77 4.00
377 401 0.912486 GTGTTATCCAGGGACAGGCT 59.088 55.000 0.00 0.00 33.77 4.58
456 1273 7.506114 AGAATTAGAATTATACTCACCCGCAA 58.494 34.615 0.00 0.00 0.00 4.85
487 1313 1.977056 TATATCACTCGCACCGTCCT 58.023 50.000 0.00 0.00 0.00 3.85
490 1316 1.323271 ATCACTCGCACCGTCCTGAT 61.323 55.000 0.00 0.00 0.00 2.90
558 1461 7.446769 TCTAGATACAGTTACAGTTTTGCCAA 58.553 34.615 0.00 0.00 0.00 4.52
559 1462 6.560253 AGATACAGTTACAGTTTTGCCAAG 57.440 37.500 0.00 0.00 0.00 3.61
561 1464 4.370364 ACAGTTACAGTTTTGCCAAGTG 57.630 40.909 0.10 0.10 32.92 3.16
563 1466 4.142469 ACAGTTACAGTTTTGCCAAGTGTC 60.142 41.667 9.00 0.00 33.97 3.67
571 1474 0.464036 TTGCCAAGTGTCAGTCGACT 59.536 50.000 13.58 13.58 43.06 4.18
587 1490 3.000322 GTCGACTGAGACTTTGTTGTGTG 60.000 47.826 8.70 0.00 38.09 3.82
589 1492 3.000322 CGACTGAGACTTTGTTGTGTGTC 60.000 47.826 0.00 0.00 0.00 3.67
590 1493 4.184629 GACTGAGACTTTGTTGTGTGTCT 58.815 43.478 0.00 0.00 41.76 3.41
596 1499 5.730550 AGACTTTGTTGTGTGTCTTAGTCA 58.269 37.500 0.00 0.00 36.50 3.41
602 1505 9.256477 CTTTGTTGTGTGTCTTAGTCAATACTA 57.744 33.333 0.00 0.00 37.15 1.82
604 1507 9.772973 TTGTTGTGTGTCTTAGTCAATACTATT 57.227 29.630 0.00 0.00 38.02 1.73
703 1632 3.904339 ACTTGACTGAGACCTAACCACAT 59.096 43.478 0.00 0.00 0.00 3.21
709 1638 4.406003 ACTGAGACCTAACCACATCCATAC 59.594 45.833 0.00 0.00 0.00 2.39
715 1644 8.045720 AGACCTAACCACATCCATACATTTAT 57.954 34.615 0.00 0.00 0.00 1.40
716 1645 8.502738 AGACCTAACCACATCCATACATTTATT 58.497 33.333 0.00 0.00 0.00 1.40
717 1646 9.131791 GACCTAACCACATCCATACATTTATTT 57.868 33.333 0.00 0.00 0.00 1.40
718 1647 9.487442 ACCTAACCACATCCATACATTTATTTT 57.513 29.630 0.00 0.00 0.00 1.82
722 1651 9.434420 AACCACATCCATACATTTATTTTTGTG 57.566 29.630 0.00 0.00 0.00 3.33
723 1652 8.811017 ACCACATCCATACATTTATTTTTGTGA 58.189 29.630 0.00 0.00 34.22 3.58
724 1653 9.086336 CCACATCCATACATTTATTTTTGTGAC 57.914 33.333 0.00 0.00 34.22 3.67
725 1654 9.636879 CACATCCATACATTTATTTTTGTGACA 57.363 29.630 0.00 0.00 34.22 3.58
736 1665 8.804688 TTTATTTTTGTGACAAGTAATTCGGG 57.195 30.769 11.28 0.00 0.00 5.14
739 1668 1.001068 TGTGACAAGTAATTCGGGCGA 59.999 47.619 0.00 0.00 0.00 5.54
740 1669 1.659098 GTGACAAGTAATTCGGGCGAG 59.341 52.381 0.00 0.00 0.00 5.03
741 1670 1.274167 TGACAAGTAATTCGGGCGAGT 59.726 47.619 0.00 0.00 0.00 4.18
752 1681 1.726265 GGGCGAGTGGAGTAGTACG 59.274 63.158 0.00 0.00 0.00 3.67
761 1690 3.825014 AGTGGAGTAGTACGCAAAAGAGA 59.175 43.478 6.37 0.00 0.00 3.10
762 1691 4.082679 AGTGGAGTAGTACGCAAAAGAGAG 60.083 45.833 6.37 0.00 0.00 3.20
765 1694 4.439016 GGAGTAGTACGCAAAAGAGAGGAG 60.439 50.000 6.37 0.00 0.00 3.69
766 1695 4.333690 AGTAGTACGCAAAAGAGAGGAGA 58.666 43.478 0.00 0.00 0.00 3.71
767 1696 3.579335 AGTACGCAAAAGAGAGGAGAC 57.421 47.619 0.00 0.00 0.00 3.36
768 1697 2.095161 AGTACGCAAAAGAGAGGAGACG 60.095 50.000 0.00 0.00 0.00 4.18
769 1698 0.959553 ACGCAAAAGAGAGGAGACGA 59.040 50.000 0.00 0.00 0.00 4.20
770 1699 1.546476 ACGCAAAAGAGAGGAGACGAT 59.454 47.619 0.00 0.00 0.00 3.73
777 1706 2.096248 AGAGAGGAGACGATGAACACC 58.904 52.381 0.00 0.00 0.00 4.16
778 1707 1.819288 GAGAGGAGACGATGAACACCA 59.181 52.381 0.00 0.00 0.00 4.17
783 1712 2.996621 GGAGACGATGAACACCAGAAAG 59.003 50.000 0.00 0.00 0.00 2.62
963 1908 0.607217 GCGCATCATCCATCCATCCA 60.607 55.000 0.30 0.00 0.00 3.41
967 1912 2.640184 CATCATCCATCCATCCATCCG 58.360 52.381 0.00 0.00 0.00 4.18
968 1913 1.733385 TCATCCATCCATCCATCCGT 58.267 50.000 0.00 0.00 0.00 4.69
969 1914 2.057140 TCATCCATCCATCCATCCGTT 58.943 47.619 0.00 0.00 0.00 4.44
970 1915 2.038952 TCATCCATCCATCCATCCGTTC 59.961 50.000 0.00 0.00 0.00 3.95
971 1916 0.764890 TCCATCCATCCATCCGTTCC 59.235 55.000 0.00 0.00 0.00 3.62
972 1917 0.767375 CCATCCATCCATCCGTTCCT 59.233 55.000 0.00 0.00 0.00 3.36
973 1918 1.271054 CCATCCATCCATCCGTTCCTC 60.271 57.143 0.00 0.00 0.00 3.71
974 1919 1.696336 CATCCATCCATCCGTTCCTCT 59.304 52.381 0.00 0.00 0.00 3.69
975 1920 1.414158 TCCATCCATCCGTTCCTCTC 58.586 55.000 0.00 0.00 0.00 3.20
976 1921 1.062886 TCCATCCATCCGTTCCTCTCT 60.063 52.381 0.00 0.00 0.00 3.10
977 1922 1.342819 CCATCCATCCGTTCCTCTCTC 59.657 57.143 0.00 0.00 0.00 3.20
978 1923 1.342819 CATCCATCCGTTCCTCTCTCC 59.657 57.143 0.00 0.00 0.00 3.71
979 1924 0.631753 TCCATCCGTTCCTCTCTCCT 59.368 55.000 0.00 0.00 0.00 3.69
980 1925 1.007238 TCCATCCGTTCCTCTCTCCTT 59.993 52.381 0.00 0.00 0.00 3.36
981 1926 1.410882 CCATCCGTTCCTCTCTCCTTC 59.589 57.143 0.00 0.00 0.00 3.46
982 1927 1.410882 CATCCGTTCCTCTCTCCTTCC 59.589 57.143 0.00 0.00 0.00 3.46
983 1928 0.705253 TCCGTTCCTCTCTCCTTCCT 59.295 55.000 0.00 0.00 0.00 3.36
984 1929 1.077334 TCCGTTCCTCTCTCCTTCCTT 59.923 52.381 0.00 0.00 0.00 3.36
985 1930 1.478916 CCGTTCCTCTCTCCTTCCTTC 59.521 57.143 0.00 0.00 0.00 3.46
986 1931 1.478916 CGTTCCTCTCTCCTTCCTTCC 59.521 57.143 0.00 0.00 0.00 3.46
987 1932 2.827755 GTTCCTCTCTCCTTCCTTCCT 58.172 52.381 0.00 0.00 0.00 3.36
988 1933 2.499693 GTTCCTCTCTCCTTCCTTCCTG 59.500 54.545 0.00 0.00 0.00 3.86
989 1934 1.719378 TCCTCTCTCCTTCCTTCCTGT 59.281 52.381 0.00 0.00 0.00 4.00
990 1935 2.107366 CCTCTCTCCTTCCTTCCTGTC 58.893 57.143 0.00 0.00 0.00 3.51
991 1936 2.107366 CTCTCTCCTTCCTTCCTGTCC 58.893 57.143 0.00 0.00 0.00 4.02
992 1937 1.433199 TCTCTCCTTCCTTCCTGTCCA 59.567 52.381 0.00 0.00 0.00 4.02
993 1938 1.552792 CTCTCCTTCCTTCCTGTCCAC 59.447 57.143 0.00 0.00 0.00 4.02
994 1939 1.150135 TCTCCTTCCTTCCTGTCCACT 59.850 52.381 0.00 0.00 0.00 4.00
995 1940 2.382305 TCTCCTTCCTTCCTGTCCACTA 59.618 50.000 0.00 0.00 0.00 2.74
1088 2045 1.831652 AACCTCCTCTTCGGCACCAG 61.832 60.000 0.00 0.00 0.00 4.00
1094 2051 2.979676 CTTCGGCACCAGCAGCAA 60.980 61.111 0.00 0.00 44.61 3.91
1095 2052 2.974489 CTTCGGCACCAGCAGCAAG 61.974 63.158 0.00 0.00 44.61 4.01
1098 2055 4.666253 GGCACCAGCAGCAAGGGA 62.666 66.667 8.61 0.00 44.61 4.20
1100 2057 2.633509 GCACCAGCAGCAAGGGAAG 61.634 63.158 8.61 0.26 41.58 3.46
1101 2058 1.073722 CACCAGCAGCAAGGGAAGA 59.926 57.895 8.61 0.00 0.00 2.87
1106 2063 1.968540 GCAGCAAGGGAAGAAGCGT 60.969 57.895 0.00 0.00 0.00 5.07
1149 2118 3.470888 ATCCTGGGCGACTTCGGG 61.471 66.667 0.02 0.00 40.23 5.14
1236 2205 2.117156 GCTGCACCGCATCCTCATT 61.117 57.895 0.00 0.00 38.13 2.57
1450 2419 1.554617 TCATCGCCAGGATCAACAAGA 59.445 47.619 0.00 0.00 31.28 3.02
1452 2421 0.036388 TCGCCAGGATCAACAAGACC 60.036 55.000 0.00 0.00 0.00 3.85
1565 2535 7.776030 TCAGTTATAGTACCCTCTTCTCTCTTG 59.224 40.741 0.00 0.00 0.00 3.02
1572 2542 1.898472 CCTCTTCTCTCTTGTGCTCCA 59.102 52.381 0.00 0.00 0.00 3.86
1573 2543 2.301296 CCTCTTCTCTCTTGTGCTCCAA 59.699 50.000 0.00 0.00 0.00 3.53
1636 2614 3.961480 TCATCGGTGAACTGAACTGAT 57.039 42.857 0.00 0.00 43.01 2.90
1683 2677 0.652592 CCAACGACTTCATCATCGCC 59.347 55.000 0.00 0.00 42.12 5.54
1756 2750 2.633657 CATGCTAATGGCGACCGC 59.366 61.111 5.75 5.75 45.43 5.68
1791 2786 4.039488 TGTTCCTCTTTCTTTGCATTGCAT 59.961 37.500 12.95 0.00 38.76 3.96
1817 2812 7.725251 ACATACACAGTTTTGTTTCATGGAAT 58.275 30.769 0.00 0.00 34.62 3.01
1818 2813 7.652909 ACATACACAGTTTTGTTTCATGGAATG 59.347 33.333 0.00 0.00 39.99 2.67
1819 2814 5.358922 ACACAGTTTTGTTTCATGGAATGG 58.641 37.500 0.00 0.00 39.38 3.16
1820 2815 5.128499 ACACAGTTTTGTTTCATGGAATGGA 59.872 36.000 0.00 0.00 39.38 3.41
1827 2822 3.006752 TGTTTCATGGAATGGAAGCCAAC 59.993 43.478 0.00 0.00 43.94 3.77
1828 2823 1.851304 TCATGGAATGGAAGCCAACC 58.149 50.000 0.00 0.00 46.73 3.77
1829 2824 1.358787 TCATGGAATGGAAGCCAACCT 59.641 47.619 12.00 0.00 46.73 3.50
1835 2830 2.736670 ATGGAAGCCAACCTATCCAC 57.263 50.000 0.00 0.00 44.25 4.02
1836 2831 0.623723 TGGAAGCCAACCTATCCACC 59.376 55.000 0.00 0.00 37.05 4.61
1837 2832 0.623723 GGAAGCCAACCTATCCACCA 59.376 55.000 0.00 0.00 32.08 4.17
1847 2842 2.706190 ACCTATCCACCATTGTAGCTCC 59.294 50.000 0.00 0.00 0.00 4.70
1850 2845 0.618458 TCCACCATTGTAGCTCCACC 59.382 55.000 0.00 0.00 0.00 4.61
1851 2846 0.394352 CCACCATTGTAGCTCCACCC 60.394 60.000 0.00 0.00 0.00 4.61
1861 2856 2.337359 AGCTCCACCCCTAGTGTTTA 57.663 50.000 0.00 0.00 45.74 2.01
1866 2861 4.514401 CTCCACCCCTAGTGTTTAATGAC 58.486 47.826 0.00 0.00 45.74 3.06
1874 2869 6.280643 CCCTAGTGTTTAATGACGATGATGA 58.719 40.000 0.00 0.00 0.00 2.92
1875 2870 6.931281 CCCTAGTGTTTAATGACGATGATGAT 59.069 38.462 0.00 0.00 0.00 2.45
1876 2871 7.095481 CCCTAGTGTTTAATGACGATGATGATG 60.095 40.741 0.00 0.00 0.00 3.07
1877 2872 7.653311 CCTAGTGTTTAATGACGATGATGATGA 59.347 37.037 0.00 0.00 0.00 2.92
1878 2873 9.201127 CTAGTGTTTAATGACGATGATGATGAT 57.799 33.333 0.00 0.00 0.00 2.45
1881 2876 5.868043 TTAATGACGATGATGATGATGCC 57.132 39.130 0.00 0.00 0.00 4.40
1964 2960 3.003275 AGGCACGATTACAACAACACTTG 59.997 43.478 0.00 0.00 0.00 3.16
1968 2964 6.128499 GGCACGATTACAACAACACTTGTATA 60.128 38.462 0.00 0.00 44.59 1.47
1970 2966 7.960738 GCACGATTACAACAACACTTGTATAAT 59.039 33.333 0.00 5.07 44.59 1.28
2033 3050 5.477510 ACTGATCTGTACTTGCTGAAGAAG 58.522 41.667 3.02 0.00 32.98 2.85
2237 3255 3.567478 TTGATCTGGTCGTGCGCGT 62.567 57.895 20.50 0.00 39.49 6.01
2238 3256 2.809601 GATCTGGTCGTGCGCGTT 60.810 61.111 20.50 0.00 39.49 4.84
2239 3257 3.071459 GATCTGGTCGTGCGCGTTG 62.071 63.158 20.50 8.39 39.49 4.10
2273 3291 0.732880 CACGTCCTTGTAGAGCGTGG 60.733 60.000 7.39 0.00 45.96 4.94
2602 3623 2.667969 CGTCGCTGTCTTCATTGATTCA 59.332 45.455 0.00 0.00 0.00 2.57
2603 3624 3.241900 CGTCGCTGTCTTCATTGATTCAG 60.242 47.826 8.11 8.11 0.00 3.02
2657 3684 4.743057 AAATTATGAGGGAAGCAAAGCC 57.257 40.909 0.00 0.00 0.00 4.35
2691 3718 4.166888 GGCATGGCAGAGCGGAGA 62.167 66.667 15.47 0.00 0.00 3.71
2692 3719 2.124983 GCATGGCAGAGCGGAGAA 60.125 61.111 0.00 0.00 0.00 2.87
2708 3735 2.630580 GGAGAAGAGCCATTATCGGAGT 59.369 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.891373 TCTCTCTCAAGTTCCAGCCG 59.109 55.000 0.00 0.00 0.00 5.52
7 8 3.829601 TCACCTTCTCTCTCTCAAGTTCC 59.170 47.826 0.00 0.00 0.00 3.62
14 15 3.766591 TCAATGGTCACCTTCTCTCTCTC 59.233 47.826 0.00 0.00 0.00 3.20
15 16 3.784178 TCAATGGTCACCTTCTCTCTCT 58.216 45.455 0.00 0.00 0.00 3.10
48 49 3.466836 ACTTGCTTCGTCTTGATTGTCA 58.533 40.909 0.00 0.00 0.00 3.58
78 79 3.549827 CCTCGACTCCTTGATGATCTTCG 60.550 52.174 4.32 0.00 0.00 3.79
107 108 2.093890 CATGATGCTAGTGTTGCCCAA 58.906 47.619 0.00 0.00 0.00 4.12
111 112 1.328680 CGTCCATGATGCTAGTGTTGC 59.671 52.381 0.00 0.00 0.00 4.17
116 117 3.118629 ACATTGTCGTCCATGATGCTAGT 60.119 43.478 0.00 0.00 0.00 2.57
132 133 3.480470 CAGAACCACTCCTTGACATTGT 58.520 45.455 0.00 0.00 0.00 2.71
229 251 4.104776 ACAATTCAGCAAGTCAAACAACG 58.895 39.130 0.00 0.00 0.00 4.10
270 294 7.761249 CACACATTCAGCGATAGATATGGAATA 59.239 37.037 0.00 0.00 39.76 1.75
280 304 3.957671 ATTGCACACATTCAGCGATAG 57.042 42.857 0.00 0.00 30.84 2.08
285 309 7.420002 TCTTTATCATATTGCACACATTCAGC 58.580 34.615 0.00 0.00 0.00 4.26
303 327 6.790825 GCGGCGTATTTTTCACTATCTTTATC 59.209 38.462 9.37 0.00 0.00 1.75
309 333 2.610374 TGGCGGCGTATTTTTCACTATC 59.390 45.455 9.37 0.00 0.00 2.08
310 334 2.634600 TGGCGGCGTATTTTTCACTAT 58.365 42.857 9.37 0.00 0.00 2.12
320 344 2.502577 GGGTACTTGGCGGCGTAT 59.497 61.111 9.37 0.00 0.00 3.06
330 354 2.886523 GTTTGCTAAAACCCGGGTACTT 59.113 45.455 30.52 24.82 39.90 2.24
333 357 2.653234 TGTTTGCTAAAACCCGGGTA 57.347 45.000 30.52 11.17 44.29 3.69
349 373 2.510613 CCTGGATAACACGGGTTTGTT 58.489 47.619 9.10 0.56 42.46 2.83
368 392 2.043248 TCGTCCCTAGCCTGTCCC 60.043 66.667 0.00 0.00 0.00 4.46
375 399 1.066430 TCACCAAATGTCGTCCCTAGC 60.066 52.381 0.00 0.00 0.00 3.42
377 401 3.605634 CATTCACCAAATGTCGTCCCTA 58.394 45.455 0.00 0.00 40.00 3.53
400 424 3.070446 ACGTTAACAGGTCATCTCCAACA 59.930 43.478 6.39 0.00 0.00 3.33
467 1284 2.229062 CAGGACGGTGCGAGTGATATAT 59.771 50.000 0.00 0.00 0.00 0.86
472 1298 1.532604 AATCAGGACGGTGCGAGTGA 61.533 55.000 0.00 0.00 0.00 3.41
532 1435 7.620880 TGGCAAAACTGTAACTGTATCTAGAT 58.379 34.615 10.73 10.73 0.00 1.98
543 1446 4.142469 ACTGACACTTGGCAAAACTGTAAC 60.142 41.667 0.00 0.00 29.15 2.50
563 1466 3.243877 CACAACAAAGTCTCAGTCGACTG 59.756 47.826 34.76 34.76 43.14 3.51
571 1474 5.730550 ACTAAGACACACAACAAAGTCTCA 58.269 37.500 0.00 0.00 40.22 3.27
573 1476 5.730550 TGACTAAGACACACAACAAAGTCT 58.269 37.500 0.00 0.00 42.72 3.24
577 1480 9.772973 ATAGTATTGACTAAGACACACAACAAA 57.227 29.630 0.00 0.00 41.53 2.83
579 1482 9.772973 AAATAGTATTGACTAAGACACACAACA 57.227 29.630 0.00 0.00 41.53 3.33
683 1586 3.260884 GGATGTGGTTAGGTCTCAGTCAA 59.739 47.826 0.00 0.00 0.00 3.18
697 1626 8.811017 TCACAAAAATAAATGTATGGATGTGGT 58.189 29.630 12.03 0.00 32.89 4.16
715 1644 4.612943 GCCCGAATTACTTGTCACAAAAA 58.387 39.130 0.00 0.00 0.00 1.94
716 1645 3.304123 CGCCCGAATTACTTGTCACAAAA 60.304 43.478 0.00 0.00 0.00 2.44
717 1646 2.224549 CGCCCGAATTACTTGTCACAAA 59.775 45.455 0.00 0.00 0.00 2.83
718 1647 1.801771 CGCCCGAATTACTTGTCACAA 59.198 47.619 0.00 0.00 0.00 3.33
719 1648 1.001068 TCGCCCGAATTACTTGTCACA 59.999 47.619 0.00 0.00 0.00 3.58
720 1649 1.659098 CTCGCCCGAATTACTTGTCAC 59.341 52.381 0.00 0.00 0.00 3.67
721 1650 1.274167 ACTCGCCCGAATTACTTGTCA 59.726 47.619 0.00 0.00 0.00 3.58
722 1651 1.659098 CACTCGCCCGAATTACTTGTC 59.341 52.381 0.00 0.00 0.00 3.18
723 1652 1.674817 CCACTCGCCCGAATTACTTGT 60.675 52.381 0.00 0.00 0.00 3.16
724 1653 1.006832 CCACTCGCCCGAATTACTTG 58.993 55.000 0.00 0.00 0.00 3.16
725 1654 0.899720 TCCACTCGCCCGAATTACTT 59.100 50.000 0.00 0.00 0.00 2.24
726 1655 0.460311 CTCCACTCGCCCGAATTACT 59.540 55.000 0.00 0.00 0.00 2.24
736 1665 0.169672 TTGCGTACTACTCCACTCGC 59.830 55.000 0.00 0.00 43.14 5.03
739 1668 3.825014 TCTCTTTTGCGTACTACTCCACT 59.175 43.478 0.00 0.00 0.00 4.00
740 1669 4.167268 CTCTCTTTTGCGTACTACTCCAC 58.833 47.826 0.00 0.00 0.00 4.02
741 1670 3.192844 CCTCTCTTTTGCGTACTACTCCA 59.807 47.826 0.00 0.00 0.00 3.86
752 1681 3.238108 TCATCGTCTCCTCTCTTTTGC 57.762 47.619 0.00 0.00 0.00 3.68
761 1690 1.924731 TCTGGTGTTCATCGTCTCCT 58.075 50.000 0.00 0.00 0.00 3.69
762 1691 2.743636 TTCTGGTGTTCATCGTCTCC 57.256 50.000 0.00 0.00 0.00 3.71
765 1694 2.143122 TGCTTTCTGGTGTTCATCGTC 58.857 47.619 0.00 0.00 0.00 4.20
766 1695 2.254546 TGCTTTCTGGTGTTCATCGT 57.745 45.000 0.00 0.00 0.00 3.73
767 1696 3.837213 AATGCTTTCTGGTGTTCATCG 57.163 42.857 0.00 0.00 0.00 3.84
768 1697 6.012658 TGTAAATGCTTTCTGGTGTTCATC 57.987 37.500 0.00 0.00 0.00 2.92
769 1698 6.594788 ATGTAAATGCTTTCTGGTGTTCAT 57.405 33.333 0.00 0.00 0.00 2.57
770 1699 6.403866 AATGTAAATGCTTTCTGGTGTTCA 57.596 33.333 0.00 0.00 0.00 3.18
777 1706 7.486647 AGCAAGGATAATGTAAATGCTTTCTG 58.513 34.615 0.00 0.00 39.44 3.02
778 1707 7.201857 GGAGCAAGGATAATGTAAATGCTTTCT 60.202 37.037 0.00 0.00 42.24 2.52
783 1712 4.320494 CCGGAGCAAGGATAATGTAAATGC 60.320 45.833 0.00 0.00 0.00 3.56
895 1836 0.178068 TGCTTCTTATCTGGCCGTCC 59.822 55.000 0.00 0.00 0.00 4.79
963 1908 1.289530 AGGAAGGAGAGAGGAACGGAT 59.710 52.381 0.00 0.00 0.00 4.18
967 1912 2.499693 CAGGAAGGAAGGAGAGAGGAAC 59.500 54.545 0.00 0.00 0.00 3.62
968 1913 2.112691 ACAGGAAGGAAGGAGAGAGGAA 59.887 50.000 0.00 0.00 0.00 3.36
969 1914 1.719378 ACAGGAAGGAAGGAGAGAGGA 59.281 52.381 0.00 0.00 0.00 3.71
970 1915 2.107366 GACAGGAAGGAAGGAGAGAGG 58.893 57.143 0.00 0.00 0.00 3.69
971 1916 2.107366 GGACAGGAAGGAAGGAGAGAG 58.893 57.143 0.00 0.00 0.00 3.20
972 1917 1.433199 TGGACAGGAAGGAAGGAGAGA 59.567 52.381 0.00 0.00 0.00 3.10
973 1918 1.552792 GTGGACAGGAAGGAAGGAGAG 59.447 57.143 0.00 0.00 0.00 3.20
974 1919 1.150135 AGTGGACAGGAAGGAAGGAGA 59.850 52.381 0.00 0.00 0.00 3.71
975 1920 1.650528 AGTGGACAGGAAGGAAGGAG 58.349 55.000 0.00 0.00 0.00 3.69
976 1921 2.158219 TGTAGTGGACAGGAAGGAAGGA 60.158 50.000 0.00 0.00 32.86 3.36
977 1922 2.028020 GTGTAGTGGACAGGAAGGAAGG 60.028 54.545 0.00 0.00 39.29 3.46
978 1923 2.028020 GGTGTAGTGGACAGGAAGGAAG 60.028 54.545 0.00 0.00 39.29 3.46
979 1924 1.975680 GGTGTAGTGGACAGGAAGGAA 59.024 52.381 0.00 0.00 39.29 3.36
980 1925 1.132977 TGGTGTAGTGGACAGGAAGGA 60.133 52.381 0.00 0.00 39.29 3.36
981 1926 1.348064 TGGTGTAGTGGACAGGAAGG 58.652 55.000 0.00 0.00 39.29 3.46
982 1927 2.355108 CCATGGTGTAGTGGACAGGAAG 60.355 54.545 2.57 0.00 39.29 3.46
983 1928 1.628340 CCATGGTGTAGTGGACAGGAA 59.372 52.381 2.57 0.00 39.29 3.36
984 1929 1.275666 CCATGGTGTAGTGGACAGGA 58.724 55.000 2.57 0.00 39.29 3.86
985 1930 0.392998 GCCATGGTGTAGTGGACAGG 60.393 60.000 14.67 0.00 39.29 4.00
986 1931 0.740868 CGCCATGGTGTAGTGGACAG 60.741 60.000 17.59 0.00 39.29 3.51
987 1932 1.295101 CGCCATGGTGTAGTGGACA 59.705 57.895 17.59 0.00 37.72 4.02
988 1933 2.106683 GCGCCATGGTGTAGTGGAC 61.107 63.158 25.68 4.16 37.72 4.02
989 1934 2.238847 GAGCGCCATGGTGTAGTGGA 62.239 60.000 25.68 0.00 37.72 4.02
990 1935 1.815421 GAGCGCCATGGTGTAGTGG 60.815 63.158 25.68 2.51 38.55 4.00
991 1936 0.462581 ATGAGCGCCATGGTGTAGTG 60.463 55.000 25.68 1.03 33.39 2.74
992 1937 0.462581 CATGAGCGCCATGGTGTAGT 60.463 55.000 25.68 11.53 46.85 2.73
993 1938 2.314256 CATGAGCGCCATGGTGTAG 58.686 57.895 25.68 10.28 46.85 2.74
994 1939 4.538233 CATGAGCGCCATGGTGTA 57.462 55.556 25.68 13.39 46.85 2.90
1088 2045 1.518903 AACGCTTCTTCCCTTGCTGC 61.519 55.000 0.00 0.00 0.00 5.25
1094 2051 0.951040 CTTGCGAACGCTTCTTCCCT 60.951 55.000 19.32 0.00 42.51 4.20
1095 2052 1.497722 CTTGCGAACGCTTCTTCCC 59.502 57.895 19.32 0.00 42.51 3.97
1096 2053 1.228657 ACCTTGCGAACGCTTCTTCC 61.229 55.000 19.32 0.00 42.51 3.46
1097 2054 0.110644 CACCTTGCGAACGCTTCTTC 60.111 55.000 19.32 0.00 42.51 2.87
1098 2055 1.507141 CCACCTTGCGAACGCTTCTT 61.507 55.000 19.32 0.14 42.51 2.52
1100 2057 2.251642 ACCACCTTGCGAACGCTTC 61.252 57.895 19.32 0.00 42.51 3.86
1101 2058 2.203153 ACCACCTTGCGAACGCTT 60.203 55.556 19.32 0.00 42.51 4.68
1316 2285 0.036022 GACCACCTTGAAGAGCAGCT 59.964 55.000 0.00 0.00 0.00 4.24
1487 2456 4.699522 GGTTGGGCGCCTCGAACT 62.700 66.667 28.56 0.00 0.00 3.01
1546 2515 4.017808 GCACAAGAGAGAAGAGGGTACTA 58.982 47.826 0.00 0.00 0.00 1.82
1551 2521 1.206849 GGAGCACAAGAGAGAAGAGGG 59.793 57.143 0.00 0.00 0.00 4.30
1636 2614 1.962807 CCCACCTGCACAAATTTCAGA 59.037 47.619 6.88 0.00 0.00 3.27
1683 2677 1.081774 GATCTGGTCGATCCTCGCG 60.082 63.158 0.00 0.00 42.24 5.87
1751 2745 2.124151 AAGATGGCATGGGCGGTC 60.124 61.111 3.81 0.00 42.47 4.79
1752 2746 2.440796 CAAGATGGCATGGGCGGT 60.441 61.111 3.81 0.00 42.47 5.68
1754 2748 1.434696 GAACAAGATGGCATGGGCG 59.565 57.895 3.81 0.00 42.47 6.13
1756 2750 1.064166 AGAGGAACAAGATGGCATGGG 60.064 52.381 3.81 0.00 0.00 4.00
1764 2758 6.453092 CAATGCAAAGAAAGAGGAACAAGAT 58.547 36.000 0.00 0.00 0.00 2.40
1791 2786 7.809546 TCCATGAAACAAAACTGTGTATGTA 57.190 32.000 0.00 0.00 0.00 2.29
1817 2812 0.623723 GGTGGATAGGTTGGCTTCCA 59.376 55.000 0.00 0.00 35.93 3.53
1818 2813 0.623723 TGGTGGATAGGTTGGCTTCC 59.376 55.000 0.00 0.00 0.00 3.46
1819 2814 2.689983 CAATGGTGGATAGGTTGGCTTC 59.310 50.000 0.00 0.00 0.00 3.86
1820 2815 2.042979 ACAATGGTGGATAGGTTGGCTT 59.957 45.455 0.00 0.00 0.00 4.35
1827 2822 2.705658 TGGAGCTACAATGGTGGATAGG 59.294 50.000 0.00 0.00 0.00 2.57
1828 2823 3.495100 GGTGGAGCTACAATGGTGGATAG 60.495 52.174 0.00 0.00 0.00 2.08
1829 2824 2.438021 GGTGGAGCTACAATGGTGGATA 59.562 50.000 0.00 0.00 0.00 2.59
1835 2830 1.417890 CTAGGGGTGGAGCTACAATGG 59.582 57.143 0.00 0.00 0.00 3.16
1836 2831 2.119495 ACTAGGGGTGGAGCTACAATG 58.881 52.381 0.00 0.00 0.00 2.82
1837 2832 2.119495 CACTAGGGGTGGAGCTACAAT 58.881 52.381 0.00 0.00 41.90 2.71
1850 2845 6.280643 TCATCATCGTCATTAAACACTAGGG 58.719 40.000 0.00 0.00 0.00 3.53
1851 2846 7.653311 TCATCATCATCGTCATTAAACACTAGG 59.347 37.037 0.00 0.00 0.00 3.02
1861 2856 3.746940 TGGCATCATCATCATCGTCATT 58.253 40.909 0.00 0.00 0.00 2.57
1878 2873 2.578128 GGCAAAATGGCGATGGCA 59.422 55.556 1.01 0.00 43.52 4.92
1881 2876 2.296831 TGATTGGCAAAATGGCGATG 57.703 45.000 3.01 0.00 45.76 3.84
2004 3016 5.105187 TCAGCAAGTACAGATCAGTAGCATT 60.105 40.000 9.60 0.00 0.00 3.56
2014 3026 6.763355 TCTTTCTTCTTCAGCAAGTACAGAT 58.237 36.000 0.00 0.00 0.00 2.90
2015 3027 6.040955 TCTCTTTCTTCTTCAGCAAGTACAGA 59.959 38.462 0.00 0.00 0.00 3.41
2023 3040 5.480642 AGTGATCTCTTTCTTCTTCAGCA 57.519 39.130 0.00 0.00 0.00 4.41
2033 3050 5.353678 CCAACCTCATCAAGTGATCTCTTTC 59.646 44.000 7.30 0.00 35.97 2.62
2239 3257 4.120331 GTGGGCATGTGCTTCGCC 62.120 66.667 4.84 0.00 45.47 5.54
2440 3458 1.668793 CGTGGAGCTGTGCATGTCA 60.669 57.895 0.00 0.00 0.00 3.58
2529 3547 4.161295 CGGCGGCCTTGATCCTGA 62.161 66.667 18.34 0.00 0.00 3.86
2562 3580 0.587285 GACGATGACGACGGCTCTAT 59.413 55.000 0.65 0.00 42.66 1.98
2563 3581 2.012237 GACGATGACGACGGCTCTA 58.988 57.895 0.65 0.00 42.66 2.43
2602 3623 5.659440 TTTTGGCAAACAAGAAGACTTCT 57.341 34.783 13.10 12.12 40.82 2.85
2603 3624 6.908870 ATTTTTGGCAAACAAGAAGACTTC 57.091 33.333 13.10 7.14 40.82 3.01
2657 3684 2.658285 TGCCAGCCTCATCCTTATTTG 58.342 47.619 0.00 0.00 0.00 2.32
2691 3718 3.964031 AGAAGACTCCGATAATGGCTCTT 59.036 43.478 0.00 0.00 31.86 2.85
2692 3719 3.320541 CAGAAGACTCCGATAATGGCTCT 59.679 47.826 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.