Multiple sequence alignment - TraesCS6A01G292600

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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 TraesCS6A01G292600 chr6A 100.000 2174 0 0 1 2174 524334137 524331964 0.000000e+00 4015.0
1 TraesCS6A01G292600 chr6B 85.469 757 74 24 1434 2174 572091585 572090849 0.000000e+00 756.0
2 TraesCS6A01G292600 chr6B 90.608 543 32 10 906 1441 572092154 572091624 0.000000e+00 702.0
3 TraesCS6A01G292600 chr6B 82.516 469 35 23 363 824 572092712 572092284 3.410000e-98 368.0
4 TraesCS6A01G292600 chr6B 90.842 273 20 4 41 311 572093379 572093110 5.700000e-96 361.0
5 TraesCS6A01G292600 chr6B 91.892 148 9 2 1 147 572093525 572093380 1.020000e-48 204.0
6 TraesCS6A01G292600 chr6D 85.337 757 75 22 1434 2174 382551592 382550856 0.000000e+00 750.0
7 TraesCS6A01G292600 chr6D 89.234 548 37 13 904 1441 382552169 382551634 0.000000e+00 665.0
8 TraesCS6A01G292600 chr6D 91.304 276 18 2 648 918 382552492 382552218 2.640000e-99 372.0
9 TraesCS6A01G292600 chr6D 93.304 224 13 2 362 585 382552719 382552498 1.610000e-86 329.0
10 TraesCS6A01G292600 chr6D 91.772 158 10 2 4 160 382553012 382552857 1.310000e-52 217.0
11 TraesCS6A01G292600 chr5D 81.674 442 42 21 909 1324 10038158 10038586 4.470000e-87 331.0
12 TraesCS6A01G292600 chr5D 87.712 236 19 3 123 348 10037162 10037397 1.280000e-67 267.0
13 TraesCS6A01G292600 chr5A 81.321 439 53 19 907 1324 8059037 8059467 1.610000e-86 329.0
14 TraesCS6A01G292600 chr5A 87.766 188 16 7 362 548 8058578 8058759 1.690000e-51 213.0
15 TraesCS6A01G292600 chr5B 81.567 434 35 13 127 548 42158977 42158577 1.250000e-82 316.0
16 TraesCS6A01G292600 chr5B 82.020 406 39 20 941 1322 42158244 42157849 4.500000e-82 315.0
17 TraesCS6A01G292600 chr5B 92.727 55 3 1 1271 1324 10267361 10267307 6.430000e-11 78.7
18 TraesCS6A01G292600 chr4B 100.000 28 0 0 2005 2032 134047225 134047198 4.000000e-03 52.8
19 TraesCS6A01G292600 chr4A 100.000 28 0 0 2005 2032 485708788 485708815 4.000000e-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 TraesCS6A01G292600 chr6A 524331964 524334137 2173 True 4015.0 4015 100.0000 1 2174 1 chr6A.!!$R1 2173
1 TraesCS6A01G292600 chr6B 572090849 572093525 2676 True 478.2 756 88.2654 1 2174 5 chr6B.!!$R1 2173
2 TraesCS6A01G292600 chr6D 382550856 382553012 2156 True 466.6 750 90.1902 4 2174 5 chr6D.!!$R1 2170
3 TraesCS6A01G292600 chr5D 10037162 10038586 1424 False 299.0 331 84.6930 123 1324 2 chr5D.!!$F1 1201
4 TraesCS6A01G292600 chr5A 8058578 8059467 889 False 271.0 329 84.5435 362 1324 2 chr5A.!!$F1 962
5 TraesCS6A01G292600 chr5B 42157849 42158977 1128 True 315.5 316 81.7935 127 1322 2 chr5B.!!$R2 1195

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
247 363 0.525761 CATGAATTCGGTTTGGGCGT 59.474 50.0 0.04 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1474 2455 0.461961 ACTGGATGGACTAGCGCTTC 59.538 55.0 18.68 8.16 0.0 3.86 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
80 81 8.362639 GTTTTCCCATGATTGTGATGCTATAAT 58.637 33.333 0.00 0.00 0.00 1.28
84 85 6.095021 CCCATGATTGTGATGCTATAATCAGG 59.905 42.308 0.00 0.00 40.12 3.86
134 240 5.053145 CCAGAATGATGTAGGTGCTCTAAC 58.947 45.833 0.00 0.00 39.69 2.34
147 253 3.994392 GTGCTCTAACCTTGACGAATGAA 59.006 43.478 0.00 0.00 0.00 2.57
180 286 5.947228 TTCATGAGCTTTCGTCAGATTTT 57.053 34.783 0.00 0.00 0.00 1.82
242 357 4.398988 TCCTTGGATCATGAATTCGGTTTG 59.601 41.667 0.00 0.00 0.00 2.93
247 363 0.525761 CATGAATTCGGTTTGGGCGT 59.474 50.000 0.04 0.00 0.00 5.68
277 393 4.809193 AGATGGAGGTTACTAGCAGATCA 58.191 43.478 0.00 0.00 0.00 2.92
331 821 4.614967 AGATTTGGAATCTCATTGGGGT 57.385 40.909 0.00 0.00 0.00 4.95
332 822 4.540715 AGATTTGGAATCTCATTGGGGTC 58.459 43.478 0.00 0.00 0.00 4.46
333 823 3.824001 TTTGGAATCTCATTGGGGTCA 57.176 42.857 0.00 0.00 0.00 4.02
334 824 3.370840 TTGGAATCTCATTGGGGTCAG 57.629 47.619 0.00 0.00 0.00 3.51
335 825 2.278245 TGGAATCTCATTGGGGTCAGT 58.722 47.619 0.00 0.00 0.00 3.41
336 826 3.459828 TGGAATCTCATTGGGGTCAGTA 58.540 45.455 0.00 0.00 0.00 2.74
337 827 3.849574 TGGAATCTCATTGGGGTCAGTAA 59.150 43.478 0.00 0.00 0.00 2.24
338 828 4.478317 TGGAATCTCATTGGGGTCAGTAAT 59.522 41.667 0.00 0.00 0.00 1.89
339 829 5.669904 TGGAATCTCATTGGGGTCAGTAATA 59.330 40.000 0.00 0.00 0.00 0.98
340 830 6.332635 TGGAATCTCATTGGGGTCAGTAATAT 59.667 38.462 0.00 0.00 0.00 1.28
341 831 6.881602 GGAATCTCATTGGGGTCAGTAATATC 59.118 42.308 0.00 0.00 0.00 1.63
342 832 7.392766 AATCTCATTGGGGTCAGTAATATCA 57.607 36.000 0.00 0.00 0.00 2.15
343 833 6.425210 TCTCATTGGGGTCAGTAATATCAG 57.575 41.667 0.00 0.00 0.00 2.90
344 834 6.143206 TCTCATTGGGGTCAGTAATATCAGA 58.857 40.000 0.00 0.00 0.00 3.27
345 835 6.268617 TCTCATTGGGGTCAGTAATATCAGAG 59.731 42.308 0.00 0.00 0.00 3.35
346 836 5.307976 TCATTGGGGTCAGTAATATCAGAGG 59.692 44.000 0.00 0.00 0.00 3.69
347 837 4.280789 TGGGGTCAGTAATATCAGAGGT 57.719 45.455 0.00 0.00 0.00 3.85
348 838 4.631234 TGGGGTCAGTAATATCAGAGGTT 58.369 43.478 0.00 0.00 0.00 3.50
349 839 4.408921 TGGGGTCAGTAATATCAGAGGTTG 59.591 45.833 0.00 0.00 0.00 3.77
350 840 4.381411 GGGTCAGTAATATCAGAGGTTGC 58.619 47.826 0.00 0.00 0.00 4.17
351 841 4.381411 GGTCAGTAATATCAGAGGTTGCC 58.619 47.826 0.00 0.00 0.00 4.52
352 842 4.101741 GGTCAGTAATATCAGAGGTTGCCT 59.898 45.833 0.00 0.00 36.03 4.75
353 843 5.053145 GTCAGTAATATCAGAGGTTGCCTG 58.947 45.833 0.00 0.00 31.76 4.85
354 844 4.716784 TCAGTAATATCAGAGGTTGCCTGT 59.283 41.667 0.00 0.00 31.76 4.00
355 845 5.053145 CAGTAATATCAGAGGTTGCCTGTC 58.947 45.833 0.00 0.00 31.76 3.51
356 846 4.716784 AGTAATATCAGAGGTTGCCTGTCA 59.283 41.667 0.00 0.00 31.76 3.58
357 847 3.834489 ATATCAGAGGTTGCCTGTCAG 57.166 47.619 0.00 0.00 31.76 3.51
358 848 1.649321 ATCAGAGGTTGCCTGTCAGA 58.351 50.000 0.00 0.00 31.76 3.27
359 849 1.423584 TCAGAGGTTGCCTGTCAGAA 58.576 50.000 0.00 0.00 31.76 3.02
360 850 1.768275 TCAGAGGTTGCCTGTCAGAAA 59.232 47.619 0.00 0.00 31.76 2.52
391 882 0.763986 AGGTGGTGCTGGCCAAAAAT 60.764 50.000 7.01 0.00 40.68 1.82
459 951 1.672881 GTGGTCATGGTTGCTAGCATC 59.327 52.381 20.13 17.82 40.37 3.91
473 965 7.119262 GGTTGCTAGCATCGTATATTGGTATTT 59.881 37.037 20.13 0.00 0.00 1.40
491 983 6.214412 TGGTATTTTTGGAAGGTGGCATATTT 59.786 34.615 0.00 0.00 0.00 1.40
493 985 8.428852 GGTATTTTTGGAAGGTGGCATATTTAT 58.571 33.333 0.00 0.00 0.00 1.40
496 988 7.595819 TTTTGGAAGGTGGCATATTTATAGG 57.404 36.000 0.00 0.00 0.00 2.57
531 1023 2.197465 GGGAAGTGTTAGGACAGGGAT 58.803 52.381 0.00 0.00 36.20 3.85
577 1074 5.189659 ACAGAGCTAGGCTTAAATACTCG 57.810 43.478 0.00 0.00 39.88 4.18
590 1087 4.850347 AAATACTCGGATTAGGGACTCG 57.150 45.455 0.00 0.00 41.75 4.18
592 1089 1.108132 ACTCGGATTAGGGACTCGGC 61.108 60.000 0.00 0.00 41.75 5.54
593 1090 0.824182 CTCGGATTAGGGACTCGGCT 60.824 60.000 0.00 0.00 41.75 5.52
594 1091 0.822532 TCGGATTAGGGACTCGGCTC 60.823 60.000 0.00 0.00 41.75 4.70
606 1109 3.854669 CGGCTCACTGGGCTAGGG 61.855 72.222 2.02 0.00 0.00 3.53
610 1113 2.759973 TCACTGGGCTAGGGCTCG 60.760 66.667 2.02 0.00 43.00 5.03
628 1131 4.039366 GGCTCGGAAGACTATTGGATTAGT 59.961 45.833 0.00 0.00 35.13 2.24
642 1388 9.469807 CTATTGGATTAGTACTCATTCAGTCAC 57.530 37.037 0.00 0.00 36.43 3.67
644 1390 8.589701 TTGGATTAGTACTCATTCAGTCACTA 57.410 34.615 0.00 0.00 36.43 2.74
671 1417 9.209175 GTCATTGTATCACTTCTAAACTGACTT 57.791 33.333 0.00 0.00 0.00 3.01
726 1479 1.338579 CCTCTCCTGGCAGTGTCTTTC 60.339 57.143 14.43 0.00 0.00 2.62
742 1495 3.071479 TCTTTCATTCTTGCCGTGGTAC 58.929 45.455 0.00 0.00 0.00 3.34
781 1536 3.570975 ACAATCAATGAAGCAACTGAGCA 59.429 39.130 0.00 0.00 36.85 4.26
800 1555 2.507484 CAGCAACATCCTGACTTTGGA 58.493 47.619 0.00 0.00 38.06 3.53
897 1679 7.549615 AAACGTAGCTTCTGTTACTTTCTTT 57.450 32.000 0.00 0.00 0.00 2.52
903 1687 4.671068 GCTTCTGTTACTTTCTTTTGCGAC 59.329 41.667 0.00 0.00 0.00 5.19
963 1830 3.057969 TCCTCTGTCGAAATGCATGTT 57.942 42.857 0.00 0.00 0.00 2.71
981 1853 9.743581 ATGCATGTTCATAACCTTATATCATCA 57.256 29.630 0.00 0.00 0.00 3.07
1011 1883 1.337118 TTCTCGCAATGGGGCTTTTT 58.663 45.000 0.00 0.00 0.00 1.94
1021 1893 2.425592 GGCTTTTTGGTGGTGGCC 59.574 61.111 0.00 0.00 0.00 5.36
1164 2042 1.784525 AGCCGAAGAAAGACGACAAG 58.215 50.000 0.00 0.00 0.00 3.16
1189 2070 2.358737 GATTATCGCGCCCCTGGG 60.359 66.667 5.50 5.50 38.57 4.45
1201 2088 0.471780 CCCCTGGGCCAAAAGAAGTT 60.472 55.000 8.04 0.00 0.00 2.66
1203 2090 1.070601 CCCTGGGCCAAAAGAAGTTTG 59.929 52.381 8.04 0.00 45.36 2.93
1204 2091 1.762370 CCTGGGCCAAAAGAAGTTTGT 59.238 47.619 8.04 0.00 44.46 2.83
1218 2105 4.274459 AGAAGTTTGTTCTGACATGACAGC 59.726 41.667 18.71 7.86 37.75 4.40
1221 2108 4.581824 AGTTTGTTCTGACATGACAGCAAT 59.418 37.500 18.71 3.82 37.75 3.56
1243 2166 6.981762 ATGTGATCTTCAAGTGCTTAGAAG 57.018 37.500 13.13 13.13 39.98 2.85
1266 2189 0.822164 GACGGTGCATAGTGGGTACT 59.178 55.000 1.64 0.00 40.99 2.73
1267 2190 2.026641 GACGGTGCATAGTGGGTACTA 58.973 52.381 1.64 0.00 43.19 1.82
1268 2191 1.753073 ACGGTGCATAGTGGGTACTAC 59.247 52.381 0.00 0.00 41.92 2.73
1284 2207 7.277319 GTGGGTACTACTAGCTGTGAAATTTAC 59.723 40.741 0.00 0.00 36.67 2.01
1325 2250 9.832445 TGGATCTTTATGATGAAACCTTAGTAC 57.168 33.333 0.00 0.00 35.14 2.73
1326 2251 8.979574 GGATCTTTATGATGAAACCTTAGTACG 58.020 37.037 0.00 0.00 35.14 3.67
1327 2252 9.530633 GATCTTTATGATGAAACCTTAGTACGT 57.469 33.333 0.00 0.00 35.14 3.57
1374 2299 6.834959 ATGCAAACATCCGATCGATATATC 57.165 37.500 18.66 2.34 0.00 1.63
1382 2307 3.068165 TCCGATCGATATATCATGGCACC 59.932 47.826 18.66 0.00 0.00 5.01
1577 2558 2.093973 CCTAGAACAAGAGTGCACGGAT 60.094 50.000 12.01 0.00 0.00 4.18
1579 2560 3.678056 AGAACAAGAGTGCACGGATAA 57.322 42.857 12.01 0.00 0.00 1.75
1580 2561 4.002906 AGAACAAGAGTGCACGGATAAA 57.997 40.909 12.01 0.00 0.00 1.40
1598 2579 6.621613 GGATAAAAACTGGGAAGCAAACTAG 58.378 40.000 0.00 0.00 0.00 2.57
1608 2589 3.304726 GGAAGCAAACTAGCAGTTGGTTC 60.305 47.826 24.29 24.29 38.66 3.62
1640 2621 4.213482 AGCAAACTAAAAAGCTGTAGTCGG 59.787 41.667 5.68 3.52 35.72 4.79
1655 2636 1.000145 GTCGGAAGCTTTGGATCGAC 59.000 55.000 17.36 17.36 39.73 4.20
1672 2653 2.234661 TCGACCTGATCTGAATGCAGTT 59.765 45.455 0.00 0.00 42.84 3.16
1673 2654 2.350804 CGACCTGATCTGAATGCAGTTG 59.649 50.000 0.00 0.00 42.84 3.16
1674 2655 3.603532 GACCTGATCTGAATGCAGTTGA 58.396 45.455 0.00 0.00 42.84 3.18
1675 2656 3.341823 ACCTGATCTGAATGCAGTTGAC 58.658 45.455 0.00 0.00 42.84 3.18
1682 2663 4.923893 TCTGAATGCAGTTGACAAAACAG 58.076 39.130 0.00 0.00 42.84 3.16
1690 2671 4.455877 GCAGTTGACAAAACAGGTAGCTAT 59.544 41.667 0.00 0.00 0.00 2.97
1691 2672 5.642063 GCAGTTGACAAAACAGGTAGCTATA 59.358 40.000 0.00 0.00 0.00 1.31
1692 2673 6.148811 GCAGTTGACAAAACAGGTAGCTATAA 59.851 38.462 0.00 0.00 0.00 0.98
1695 2676 7.717875 AGTTGACAAAACAGGTAGCTATAAACA 59.282 33.333 0.00 0.00 0.00 2.83
1901 2892 1.798813 CCCGTTGTACTTGAACTCTGC 59.201 52.381 0.00 0.00 0.00 4.26
1902 2893 2.479837 CCGTTGTACTTGAACTCTGCA 58.520 47.619 0.00 0.00 0.00 4.41
1903 2894 2.221055 CCGTTGTACTTGAACTCTGCAC 59.779 50.000 0.00 0.00 0.00 4.57
1904 2895 2.863740 CGTTGTACTTGAACTCTGCACA 59.136 45.455 0.00 0.00 0.00 4.57
1905 2896 3.302480 CGTTGTACTTGAACTCTGCACAC 60.302 47.826 0.00 0.00 0.00 3.82
1906 2897 3.535280 TGTACTTGAACTCTGCACACA 57.465 42.857 0.00 0.00 0.00 3.72
1907 2898 3.194861 TGTACTTGAACTCTGCACACAC 58.805 45.455 0.00 0.00 0.00 3.82
1908 2899 2.401583 ACTTGAACTCTGCACACACA 57.598 45.000 0.00 0.00 0.00 3.72
1909 2900 2.009774 ACTTGAACTCTGCACACACAC 58.990 47.619 0.00 0.00 0.00 3.82
1910 2901 2.009051 CTTGAACTCTGCACACACACA 58.991 47.619 0.00 0.00 0.00 3.72
1911 2902 1.368641 TGAACTCTGCACACACACAC 58.631 50.000 0.00 0.00 0.00 3.82
1912 2903 1.338579 TGAACTCTGCACACACACACA 60.339 47.619 0.00 0.00 0.00 3.72
1913 2904 1.062587 GAACTCTGCACACACACACAC 59.937 52.381 0.00 0.00 0.00 3.82
1914 2905 0.036483 ACTCTGCACACACACACACA 60.036 50.000 0.00 0.00 0.00 3.72
1915 2906 0.374758 CTCTGCACACACACACACAC 59.625 55.000 0.00 0.00 0.00 3.82
1916 2907 0.321122 TCTGCACACACACACACACA 60.321 50.000 0.00 0.00 0.00 3.72
1917 2908 0.179192 CTGCACACACACACACACAC 60.179 55.000 0.00 0.00 0.00 3.82
1918 2909 0.886490 TGCACACACACACACACACA 60.886 50.000 0.00 0.00 0.00 3.72
1919 2910 0.454285 GCACACACACACACACACAC 60.454 55.000 0.00 0.00 0.00 3.82
1920 2911 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1921 2912 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1922 2913 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1923 2914 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1924 2915 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1925 2916 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1926 2917 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1927 2918 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1928 2919 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1938 2929 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1948 2939 2.351097 CACACACACACAAGCGCG 60.351 61.111 0.00 0.00 0.00 6.86
1976 2976 3.183574 TCACGAACAAACGCATACAGAAG 59.816 43.478 0.00 0.00 36.70 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.029380 AGTCAAGGTTTAAAATGCCGCC 60.029 45.455 0.00 0.00 0.00 6.13
92 198 4.344679 TCTGGAGAAAATGCAACAACCAAT 59.655 37.500 0.00 0.00 0.00 3.16
94 200 3.295093 TCTGGAGAAAATGCAACAACCA 58.705 40.909 0.00 0.00 0.00 3.67
96 202 5.531634 TCATTCTGGAGAAAATGCAACAAC 58.468 37.500 0.00 0.00 37.61 3.32
110 216 3.378512 AGAGCACCTACATCATTCTGGA 58.621 45.455 0.00 0.00 0.00 3.86
134 240 3.431856 CATGCATGTTCATTCGTCAAGG 58.568 45.455 18.91 0.00 0.00 3.61
141 247 5.412640 TCATGAAACCATGCATGTTCATTC 58.587 37.500 29.22 23.18 41.88 2.67
147 253 2.453521 AGCTCATGAAACCATGCATGT 58.546 42.857 24.58 10.59 41.88 3.21
242 357 2.409870 CCATCTTGCAAGGACGCCC 61.410 63.158 25.73 0.00 0.00 6.13
247 363 2.912956 AGTAACCTCCATCTTGCAAGGA 59.087 45.455 25.73 15.41 32.99 3.36
300 416 5.671735 TGAGATTCCAAATCTAGGATTGGGA 59.328 40.000 20.50 15.63 44.99 4.37
331 821 4.716784 ACAGGCAACCTCTGATATTACTGA 59.283 41.667 0.00 0.00 36.22 3.41
332 822 5.028549 ACAGGCAACCTCTGATATTACTG 57.971 43.478 0.00 0.00 36.22 2.74
333 823 4.716784 TGACAGGCAACCTCTGATATTACT 59.283 41.667 0.00 0.00 36.22 2.24
334 824 5.023533 TGACAGGCAACCTCTGATATTAC 57.976 43.478 0.00 0.00 36.22 1.89
335 825 4.962362 TCTGACAGGCAACCTCTGATATTA 59.038 41.667 1.81 0.00 36.22 0.98
336 826 3.776969 TCTGACAGGCAACCTCTGATATT 59.223 43.478 1.81 0.00 36.22 1.28
337 827 3.378512 TCTGACAGGCAACCTCTGATAT 58.621 45.455 1.81 0.00 36.22 1.63
338 828 2.820178 TCTGACAGGCAACCTCTGATA 58.180 47.619 1.81 0.00 36.22 2.15
339 829 1.649321 TCTGACAGGCAACCTCTGAT 58.351 50.000 1.81 0.00 36.22 2.90
340 830 1.423584 TTCTGACAGGCAACCTCTGA 58.576 50.000 1.81 0.00 36.22 3.27
341 831 2.260844 TTTCTGACAGGCAACCTCTG 57.739 50.000 1.81 0.00 38.16 3.35
342 832 2.173569 ACTTTTCTGACAGGCAACCTCT 59.826 45.455 1.81 0.00 37.17 3.69
343 833 2.576615 ACTTTTCTGACAGGCAACCTC 58.423 47.619 1.81 0.00 37.17 3.85
344 834 2.736670 ACTTTTCTGACAGGCAACCT 57.263 45.000 1.81 0.00 37.17 3.50
345 835 6.374333 TGATATTACTTTTCTGACAGGCAACC 59.626 38.462 1.81 0.00 37.17 3.77
346 836 7.334421 TCTGATATTACTTTTCTGACAGGCAAC 59.666 37.037 1.81 0.00 0.00 4.17
347 837 7.394016 TCTGATATTACTTTTCTGACAGGCAA 58.606 34.615 1.81 0.00 0.00 4.52
348 838 6.946340 TCTGATATTACTTTTCTGACAGGCA 58.054 36.000 1.81 0.00 0.00 4.75
349 839 6.481644 CCTCTGATATTACTTTTCTGACAGGC 59.518 42.308 1.81 0.00 0.00 4.85
350 840 7.493971 CACCTCTGATATTACTTTTCTGACAGG 59.506 40.741 1.81 0.00 0.00 4.00
351 841 7.493971 CCACCTCTGATATTACTTTTCTGACAG 59.506 40.741 0.00 0.00 0.00 3.51
352 842 7.038302 ACCACCTCTGATATTACTTTTCTGACA 60.038 37.037 0.00 0.00 0.00 3.58
353 843 7.278868 CACCACCTCTGATATTACTTTTCTGAC 59.721 40.741 0.00 0.00 0.00 3.51
354 844 7.331026 CACCACCTCTGATATTACTTTTCTGA 58.669 38.462 0.00 0.00 0.00 3.27
355 845 6.037610 GCACCACCTCTGATATTACTTTTCTG 59.962 42.308 0.00 0.00 0.00 3.02
356 846 6.069963 AGCACCACCTCTGATATTACTTTTCT 60.070 38.462 0.00 0.00 0.00 2.52
357 847 6.037610 CAGCACCACCTCTGATATTACTTTTC 59.962 42.308 0.00 0.00 32.26 2.29
358 848 5.882557 CAGCACCACCTCTGATATTACTTTT 59.117 40.000 0.00 0.00 32.26 2.27
359 849 5.431765 CAGCACCACCTCTGATATTACTTT 58.568 41.667 0.00 0.00 32.26 2.66
360 850 4.141620 CCAGCACCACCTCTGATATTACTT 60.142 45.833 0.00 0.00 32.26 2.24
391 882 0.339859 AGCTACCACTCCATCCCTGA 59.660 55.000 0.00 0.00 0.00 3.86
459 951 7.422399 CCACCTTCCAAAAATACCAATATACG 58.578 38.462 0.00 0.00 0.00 3.06
473 965 6.916909 TCCTATAAATATGCCACCTTCCAAA 58.083 36.000 0.00 0.00 0.00 3.28
491 983 5.293643 TCCCTCAACCCTTCAAATCCTATA 58.706 41.667 0.00 0.00 0.00 1.31
493 985 3.537337 TCCCTCAACCCTTCAAATCCTA 58.463 45.455 0.00 0.00 0.00 2.94
496 988 3.507622 CACTTCCCTCAACCCTTCAAATC 59.492 47.826 0.00 0.00 0.00 2.17
577 1074 0.389757 GTGAGCCGAGTCCCTAATCC 59.610 60.000 0.00 0.00 0.00 3.01
590 1087 4.182433 GCCCTAGCCCAGTGAGCC 62.182 72.222 0.00 0.00 0.00 4.70
592 1089 2.790791 CGAGCCCTAGCCCAGTGAG 61.791 68.421 0.00 0.00 41.25 3.51
593 1090 2.759973 CGAGCCCTAGCCCAGTGA 60.760 66.667 0.00 0.00 41.25 3.41
594 1091 3.854669 CCGAGCCCTAGCCCAGTG 61.855 72.222 0.00 0.00 41.25 3.66
606 1109 5.203060 ACTAATCCAATAGTCTTCCGAGC 57.797 43.478 0.00 0.00 30.26 5.03
610 1113 9.699703 GAATGAGTACTAATCCAATAGTCTTCC 57.300 37.037 0.00 0.00 37.34 3.46
628 1131 7.468141 ACAATGACTAGTGACTGAATGAGTA 57.532 36.000 0.00 0.00 33.83 2.59
644 1390 8.589338 AGTCAGTTTAGAAGTGATACAATGACT 58.411 33.333 0.00 0.00 42.40 3.41
671 1417 8.083828 AGATAGATTAAGCAGAGGAAAAGTCA 57.916 34.615 0.00 0.00 0.00 3.41
726 1479 0.672401 ACGGTACCACGGCAAGAATG 60.672 55.000 13.54 0.00 38.39 2.67
757 1510 4.320714 GCTCAGTTGCTTCATTGATTGTGA 60.321 41.667 0.00 0.00 0.00 3.58
781 1536 2.957402 TCCAAAGTCAGGATGTTGCT 57.043 45.000 0.00 0.00 37.40 3.91
862 1625 1.616865 AGCTACGTTTACTGGCACTGA 59.383 47.619 0.00 0.00 0.00 3.41
963 1830 8.985922 CCTGGAGATGATGATATAAGGTTATGA 58.014 37.037 0.00 0.00 0.00 2.15
981 1853 2.859165 TTGCGAGAAAACCTGGAGAT 57.141 45.000 0.00 0.00 0.00 2.75
1011 1883 0.032615 AAAACTTGAGGCCACCACCA 60.033 50.000 5.01 0.00 0.00 4.17
1021 1893 2.362077 CCACTCCCACCAAAAACTTGAG 59.638 50.000 0.00 0.00 0.00 3.02
1164 2042 1.276145 GGCGCGATAATCACTCGTCC 61.276 60.000 12.10 0.00 38.37 4.79
1191 2072 7.219535 CTGTCATGTCAGAACAAACTTCTTTTG 59.780 37.037 13.92 0.00 42.45 2.44
1201 2088 3.884693 ACATTGCTGTCATGTCAGAACAA 59.115 39.130 21.91 16.67 39.30 2.83
1203 2090 3.499537 TCACATTGCTGTCATGTCAGAAC 59.500 43.478 21.91 7.27 37.61 3.01
1204 2091 3.742385 TCACATTGCTGTCATGTCAGAA 58.258 40.909 21.91 10.28 37.61 3.02
1218 2105 6.732531 TCTAAGCACTTGAAGATCACATTG 57.267 37.500 0.00 0.00 0.00 2.82
1221 2108 5.858381 ACTTCTAAGCACTTGAAGATCACA 58.142 37.500 19.94 0.00 39.42 3.58
1243 2166 0.526954 CCCACTATGCACCGTCGTAC 60.527 60.000 0.00 0.00 0.00 3.67
1266 2189 5.588648 GCCATGGTAAATTTCACAGCTAGTA 59.411 40.000 14.67 0.00 0.00 1.82
1267 2190 4.399303 GCCATGGTAAATTTCACAGCTAGT 59.601 41.667 14.67 0.00 0.00 2.57
1268 2191 4.398988 TGCCATGGTAAATTTCACAGCTAG 59.601 41.667 14.67 0.00 0.00 3.42
1269 2192 4.339748 TGCCATGGTAAATTTCACAGCTA 58.660 39.130 14.67 0.00 0.00 3.32
1270 2193 3.164268 TGCCATGGTAAATTTCACAGCT 58.836 40.909 14.67 0.00 0.00 4.24
1271 2194 3.591196 TGCCATGGTAAATTTCACAGC 57.409 42.857 14.67 0.00 0.00 4.40
1284 2207 1.205417 GATCCACAAACCTTGCCATGG 59.795 52.381 7.63 7.63 0.00 3.66
1347 2272 1.531149 CGATCGGATGTTTGCATACCC 59.469 52.381 7.38 0.00 35.07 3.69
1374 2299 2.884012 TGAAACTTGTACTGGTGCCATG 59.116 45.455 0.00 0.00 0.00 3.66
1474 2455 0.461961 ACTGGATGGACTAGCGCTTC 59.538 55.000 18.68 8.16 0.00 3.86
1501 2482 5.708736 TTGAATATGGGTCTGAAGGCTTA 57.291 39.130 0.00 0.00 0.00 3.09
1504 2485 5.859205 AATTTGAATATGGGTCTGAAGGC 57.141 39.130 0.00 0.00 0.00 4.35
1556 2537 1.272490 TCCGTGCACTCTTGTTCTAGG 59.728 52.381 16.19 4.48 0.00 3.02
1577 2558 4.890581 TGCTAGTTTGCTTCCCAGTTTTTA 59.109 37.500 0.00 0.00 0.00 1.52
1579 2560 3.295973 TGCTAGTTTGCTTCCCAGTTTT 58.704 40.909 0.00 0.00 0.00 2.43
1580 2561 2.887152 CTGCTAGTTTGCTTCCCAGTTT 59.113 45.455 0.00 0.00 0.00 2.66
1598 2579 2.989166 GCTTAATGCTTGAACCAACTGC 59.011 45.455 0.00 0.00 38.95 4.40
1608 2589 7.042523 ACAGCTTTTTAGTTTGCTTAATGCTTG 60.043 33.333 0.00 0.00 43.37 4.01
1633 2614 2.159282 TCGATCCAAAGCTTCCGACTAC 60.159 50.000 0.00 0.00 0.00 2.73
1640 2621 2.386661 TCAGGTCGATCCAAAGCTTC 57.613 50.000 0.00 0.00 39.02 3.86
1655 2636 3.340928 TGTCAACTGCATTCAGATCAGG 58.659 45.455 0.00 0.00 42.95 3.86
1668 2649 7.667043 TTATAGCTACCTGTTTTGTCAACTG 57.333 36.000 0.00 0.00 0.00 3.16
1669 2650 7.717875 TGTTTATAGCTACCTGTTTTGTCAACT 59.282 33.333 0.00 0.00 0.00 3.16
1672 2653 7.221450 AGTGTTTATAGCTACCTGTTTTGTCA 58.779 34.615 0.00 0.00 0.00 3.58
1673 2654 7.603024 AGAGTGTTTATAGCTACCTGTTTTGTC 59.397 37.037 0.00 0.00 0.00 3.18
1674 2655 7.450903 AGAGTGTTTATAGCTACCTGTTTTGT 58.549 34.615 0.00 0.00 0.00 2.83
1675 2656 7.907214 AGAGTGTTTATAGCTACCTGTTTTG 57.093 36.000 0.00 0.00 0.00 2.44
1682 2663 7.309316 GGGTCATCTAGAGTGTTTATAGCTACC 60.309 44.444 0.00 0.00 0.00 3.18
1690 2671 4.398358 CGTCAGGGTCATCTAGAGTGTTTA 59.602 45.833 0.00 0.00 0.00 2.01
1691 2672 3.193691 CGTCAGGGTCATCTAGAGTGTTT 59.806 47.826 0.00 0.00 0.00 2.83
1692 2673 2.755655 CGTCAGGGTCATCTAGAGTGTT 59.244 50.000 0.00 0.00 0.00 3.32
1695 2676 2.024825 GCCGTCAGGGTCATCTAGAGT 61.025 57.143 0.00 0.00 38.44 3.24
1808 2799 4.033776 CCAAGGGCAAGAGGGCGA 62.034 66.667 0.00 0.00 44.56 5.54
1901 2892 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1902 2893 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1903 2894 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1904 2895 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1905 2896 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1906 2897 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1907 2898 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1908 2899 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1909 2900 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1910 2901 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1911 2902 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1912 2903 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1913 2904 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1914 2905 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1915 2906 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1916 2907 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1917 2908 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1918 2909 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1919 2910 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1920 2911 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1921 2912 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1922 2913 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1923 2914 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1924 2915 1.535028 CTTGTGTGTGTGTGTGTGTGT 59.465 47.619 0.00 0.00 0.00 3.72
1925 2916 1.728825 GCTTGTGTGTGTGTGTGTGTG 60.729 52.381 0.00 0.00 0.00 3.82
1926 2917 0.521291 GCTTGTGTGTGTGTGTGTGT 59.479 50.000 0.00 0.00 0.00 3.72
1927 2918 0.521034 CGCTTGTGTGTGTGTGTGTG 60.521 55.000 0.00 0.00 0.00 3.82
1928 2919 1.793581 CGCTTGTGTGTGTGTGTGT 59.206 52.632 0.00 0.00 0.00 3.72
1986 2986 1.028905 GTGAGCTGATCTCCGCTACT 58.971 55.000 0.00 0.00 41.18 2.57
1988 2988 2.420138 GGTGAGCTGATCTCCGCTA 58.580 57.895 0.00 0.00 41.18 4.26
1989 2989 3.215245 GGTGAGCTGATCTCCGCT 58.785 61.111 0.00 4.75 41.18 5.52
2082 3094 3.419759 GCGGCCAAGTACACGGTG 61.420 66.667 6.58 6.58 0.00 4.94


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

AutoCloner maintained by Alex Coulton.