Multiple sequence alignment - TraesCS6A01G386400

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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 TraesCS6A01G386400 chr6A 100.000 2741 0 0 1 2741 603271001 603273741 0.000000e+00 5062
1 TraesCS6A01G386400 chr6D 88.235 1666 132 30 392 2015 456545848 456547491 0.000000e+00 1932
2 TraesCS6A01G386400 chr6D 89.374 687 65 6 2055 2741 456547496 456548174 0.000000e+00 857
3 TraesCS6A01G386400 chr6B 88.507 1514 142 17 456 1951 694345486 694346985 0.000000e+00 1803
4 TraesCS6A01G386400 chr6B 88.393 448 40 3 1944 2380 694347165 694347611 1.870000e-146 529
5 TraesCS6A01G386400 chr6B 85.399 363 46 7 15 372 694344709 694345069 1.200000e-98 370
6 TraesCS6A01G386400 chr2B 83.028 436 58 12 1755 2186 23288494 23288917 5.540000e-102 381
7 TraesCS6A01G386400 chr4B 80.778 437 63 12 1755 2183 529354763 529355186 3.410000e-84 322
8 TraesCS6A01G386400 chr5D 78.070 456 62 18 1749 2199 74709429 74709851 1.260000e-63 254


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 TraesCS6A01G386400 chr6A 603271001 603273741 2740 False 5062.000000 5062 100.0000 1 2741 1 chr6A.!!$F1 2740
1 TraesCS6A01G386400 chr6D 456545848 456548174 2326 False 1394.500000 1932 88.8045 392 2741 2 chr6D.!!$F1 2349
2 TraesCS6A01G386400 chr6B 694344709 694347611 2902 False 900.666667 1803 87.4330 15 2380 3 chr6B.!!$F1 2365

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
166 169 0.036388 ACCATACTCACCAAGCCACG 60.036 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 2625 0.38852 GCTGGTGTTTTGGCGATTCC 60.389 55.0 0.0 0.0 0.0 3.01 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
19 20 2.624316 TGTCGACACGAGGTTATGTC 57.376 50.000 15.76 0.00 41.54 3.06
20 21 1.881324 TGTCGACACGAGGTTATGTCA 59.119 47.619 15.76 0.00 44.54 3.58
21 22 2.248487 GTCGACACGAGGTTATGTCAC 58.752 52.381 11.55 0.00 44.54 3.67
22 23 1.881324 TCGACACGAGGTTATGTCACA 59.119 47.619 5.33 0.00 44.54 3.58
23 24 1.983605 CGACACGAGGTTATGTCACAC 59.016 52.381 5.33 0.00 44.54 3.82
24 25 2.351447 CGACACGAGGTTATGTCACACT 60.351 50.000 5.33 0.00 44.54 3.55
25 26 3.120095 CGACACGAGGTTATGTCACACTA 60.120 47.826 5.33 0.00 44.54 2.74
26 27 4.438336 CGACACGAGGTTATGTCACACTAT 60.438 45.833 5.33 0.00 44.54 2.12
27 28 5.401531 ACACGAGGTTATGTCACACTATT 57.598 39.130 0.00 0.00 0.00 1.73
43 44 9.026074 GTCACACTATTTTGACTAGCTTAGATC 57.974 37.037 0.00 0.00 39.30 2.75
45 46 9.593134 CACACTATTTTGACTAGCTTAGATCTT 57.407 33.333 0.00 0.00 0.00 2.40
58 59 9.926158 CTAGCTTAGATCTTGATTGTGTGATAT 57.074 33.333 0.00 0.00 0.00 1.63
78 79 9.343103 GTGATATACATCATAACGAACGATCTT 57.657 33.333 0.14 0.00 43.03 2.40
81 82 4.042398 ACATCATAACGAACGATCTTCCG 58.958 43.478 0.14 0.00 0.00 4.30
96 97 4.057406 TCTTCCGTTCGGTGAAAACTAA 57.943 40.909 11.04 0.00 0.00 2.24
98 99 4.508861 TCTTCCGTTCGGTGAAAACTAAAG 59.491 41.667 11.04 4.55 0.00 1.85
103 104 5.453266 CCGTTCGGTGAAAACTAAAGAAAAC 59.547 40.000 2.82 0.00 0.00 2.43
104 105 5.453266 CGTTCGGTGAAAACTAAAGAAAACC 59.547 40.000 0.00 0.00 0.00 3.27
128 131 9.945904 ACCTGTTTAACAAAACTTTATTTCCAA 57.054 25.926 0.00 0.00 33.95 3.53
146 149 2.677836 CCAATACGATGGTGAGTTGGTG 59.322 50.000 11.00 0.00 35.65 4.17
166 169 0.036388 ACCATACTCACCAAGCCACG 60.036 55.000 0.00 0.00 0.00 4.94
168 171 1.645034 CATACTCACCAAGCCACGAG 58.355 55.000 0.00 0.00 0.00 4.18
169 172 1.204704 CATACTCACCAAGCCACGAGA 59.795 52.381 0.00 0.00 0.00 4.04
198 202 6.294473 CACATAAGCTAAGGTCATCTTGGAT 58.706 40.000 0.00 0.00 36.21 3.41
202 206 2.158696 GCTAAGGTCATCTTGGATGGCT 60.159 50.000 11.13 0.00 36.21 4.75
208 212 5.522641 AGGTCATCTTGGATGGCTAAATTT 58.477 37.500 11.13 0.00 0.00 1.82
209 213 5.595952 AGGTCATCTTGGATGGCTAAATTTC 59.404 40.000 11.13 0.00 0.00 2.17
217 221 7.603404 TCTTGGATGGCTAAATTTCAAAACATG 59.397 33.333 0.00 0.00 0.00 3.21
238 242 7.765307 ACATGAGAATATCCAAAACATGTGAC 58.235 34.615 0.00 0.00 42.90 3.67
241 245 6.375174 TGAGAATATCCAAAACATGTGACTGG 59.625 38.462 12.75 12.75 0.00 4.00
261 265 4.013728 TGGGCTTATGTGTGTGGATTAAC 58.986 43.478 0.00 0.00 0.00 2.01
262 266 3.064820 GGGCTTATGTGTGTGGATTAACG 59.935 47.826 0.00 0.00 0.00 3.18
263 267 3.687698 GGCTTATGTGTGTGGATTAACGT 59.312 43.478 0.00 0.00 0.00 3.99
271 275 6.228995 TGTGTGTGGATTAACGTATGGTTTA 58.771 36.000 0.00 0.00 40.09 2.01
276 280 9.628746 GTGTGGATTAACGTATGGTTTAAAAAT 57.371 29.630 0.00 0.00 40.09 1.82
278 282 9.628746 GTGGATTAACGTATGGTTTAAAAATGT 57.371 29.630 0.00 0.00 40.09 2.71
302 306 9.378551 TGTATGAATACTTCAAATGGTGTACTC 57.621 33.333 0.00 0.00 43.95 2.59
316 320 3.454375 GTGTACTCGAATGGTACCCATG 58.546 50.000 10.07 0.00 44.40 3.66
318 322 0.837272 ACTCGAATGGTACCCATGGG 59.163 55.000 30.23 30.23 44.40 4.00
351 355 8.397575 AGGAACTTTAGAGGAACAAAAAGATC 57.602 34.615 0.00 0.00 27.25 2.75
356 360 8.841300 ACTTTAGAGGAACAAAAAGATCTGAAC 58.159 33.333 0.00 0.00 33.98 3.18
357 361 5.931441 AGAGGAACAAAAAGATCTGAACG 57.069 39.130 0.00 0.00 0.00 3.95
358 362 5.368989 AGAGGAACAAAAAGATCTGAACGT 58.631 37.500 0.00 0.00 0.00 3.99
368 372 4.991153 AGATCTGAACGTGATAGAGCAA 57.009 40.909 12.65 0.00 29.71 3.91
372 376 6.478344 AGATCTGAACGTGATAGAGCAAAATC 59.522 38.462 12.65 1.81 29.71 2.17
373 377 4.870426 TCTGAACGTGATAGAGCAAAATCC 59.130 41.667 0.00 0.00 0.00 3.01
374 378 3.616821 TGAACGTGATAGAGCAAAATCCG 59.383 43.478 0.00 0.00 0.00 4.18
375 379 3.247006 ACGTGATAGAGCAAAATCCGT 57.753 42.857 0.00 0.00 0.00 4.69
376 380 3.187700 ACGTGATAGAGCAAAATCCGTC 58.812 45.455 0.00 0.00 29.19 4.79
378 382 3.000322 CGTGATAGAGCAAAATCCGTCAC 60.000 47.826 0.00 0.00 33.82 3.67
379 383 3.932710 GTGATAGAGCAAAATCCGTCACA 59.067 43.478 0.00 0.00 35.65 3.58
380 384 3.932710 TGATAGAGCAAAATCCGTCACAC 59.067 43.478 0.00 0.00 0.00 3.82
382 386 2.417719 AGAGCAAAATCCGTCACACTC 58.582 47.619 0.00 0.00 0.00 3.51
383 387 2.143122 GAGCAAAATCCGTCACACTCA 58.857 47.619 0.00 0.00 0.00 3.41
384 388 1.873591 AGCAAAATCCGTCACACTCAC 59.126 47.619 0.00 0.00 0.00 3.51
385 389 1.398451 GCAAAATCCGTCACACTCACG 60.398 52.381 0.00 0.00 36.99 4.35
386 390 2.131972 CAAAATCCGTCACACTCACGA 58.868 47.619 0.00 0.00 39.75 4.35
387 391 2.519377 AAATCCGTCACACTCACGAA 57.481 45.000 0.00 0.00 39.75 3.85
410 414 6.610075 AGTGAAAATATTGTTTGAGCCCAT 57.390 33.333 0.00 0.00 0.00 4.00
422 426 2.875296 TGAGCCCATGTATATTTGGCC 58.125 47.619 0.00 0.00 43.18 5.36
430 434 7.006509 GCCCATGTATATTTGGCCATCTATAT 58.993 38.462 6.09 12.85 36.07 0.86
442 446 8.408043 TTGGCCATCTATATAAATTCAACCTG 57.592 34.615 6.09 0.00 0.00 4.00
443 447 7.526041 TGGCCATCTATATAAATTCAACCTGT 58.474 34.615 0.00 0.00 0.00 4.00
445 449 7.308435 GCCATCTATATAAATTCAACCTGTGC 58.692 38.462 0.00 0.00 0.00 4.57
446 450 7.575720 GCCATCTATATAAATTCAACCTGTGCC 60.576 40.741 0.00 0.00 0.00 5.01
452 790 6.909550 ATAAATTCAACCTGTGCCTTGTAA 57.090 33.333 0.00 0.00 0.00 2.41
454 792 5.391312 AATTCAACCTGTGCCTTGTAATC 57.609 39.130 0.00 0.00 0.00 1.75
459 797 2.094675 CCTGTGCCTTGTAATCCCAAG 58.905 52.381 0.00 0.00 41.21 3.61
520 863 5.779241 AATCCTACAATCCAAAGGAGTCA 57.221 39.130 0.00 0.00 42.53 3.41
527 870 4.020218 ACAATCCAAAGGAGTCATCGAGAA 60.020 41.667 0.00 0.00 34.05 2.87
528 871 3.876274 TCCAAAGGAGTCATCGAGAAG 57.124 47.619 0.00 0.00 0.00 2.85
533 876 3.006112 AGGAGTCATCGAGAAGCTACA 57.994 47.619 0.00 0.00 0.00 2.74
622 983 9.476202 AACAACTAAAAGATTACCAAATCAAGC 57.524 29.630 1.35 0.00 43.44 4.01
645 1006 1.146041 GCCACTGGTGTGAGTGACA 59.854 57.895 0.00 0.00 45.39 3.58
655 1016 2.560542 GTGTGAGTGACATGTCTCCTCT 59.439 50.000 29.60 21.29 36.78 3.69
657 1018 3.256879 TGTGAGTGACATGTCTCCTCTTC 59.743 47.826 29.60 24.54 32.95 2.87
666 1027 3.181967 CTCCTCTTCGTTGGCGCG 61.182 66.667 0.00 0.00 38.14 6.86
683 1044 1.901650 GCGACGAGGAGCAACCAAAG 61.902 60.000 0.00 0.00 42.04 2.77
689 1050 1.832167 GGAGCAACCAAAGCCACCA 60.832 57.895 0.00 0.00 38.79 4.17
690 1051 1.187567 GGAGCAACCAAAGCCACCAT 61.188 55.000 0.00 0.00 38.79 3.55
693 1054 1.229975 GCAACCAAAGCCACCATTGC 61.230 55.000 0.00 0.00 36.07 3.56
697 1058 1.004679 CAAAGCCACCATTGCCCAC 60.005 57.895 0.00 0.00 0.00 4.61
698 1059 1.459158 AAAGCCACCATTGCCCACA 60.459 52.632 0.00 0.00 0.00 4.17
700 1061 1.757423 AAGCCACCATTGCCCACAAC 61.757 55.000 0.00 0.00 38.99 3.32
708 1069 2.613474 CCATTGCCCACAACATCCAAAG 60.613 50.000 0.00 0.00 38.99 2.77
723 1084 2.159114 TCCAAAGTGGCACAAAGAAAGC 60.159 45.455 21.41 0.00 44.16 3.51
725 1086 1.102978 AAGTGGCACAAAGAAAGCGT 58.897 45.000 21.41 0.00 44.16 5.07
726 1087 0.381801 AGTGGCACAAAGAAAGCGTG 59.618 50.000 21.41 0.00 44.16 5.34
728 1089 0.662619 TGGCACAAAGAAAGCGTGAG 59.337 50.000 0.00 0.00 31.92 3.51
730 1091 1.333619 GGCACAAAGAAAGCGTGAGAA 59.666 47.619 0.00 0.00 32.23 2.87
734 1095 4.147133 GCACAAAGAAAGCGTGAGAATTTC 59.853 41.667 0.00 0.00 38.10 2.17
737 1098 3.140325 AGAAAGCGTGAGAATTTCCCA 57.860 42.857 0.00 0.00 38.39 4.37
760 1121 6.591834 CCACAAAAAGTGTTGGTAACATGAAA 59.408 34.615 0.00 0.00 46.55 2.69
1608 1983 2.687425 TGTTCATGACTTTGTGGTGTGG 59.313 45.455 0.00 0.00 0.00 4.17
1648 2023 9.881649 GATTTTATAGAGTGATGGATGCTCATA 57.118 33.333 0.00 0.00 0.00 2.15
1656 2031 4.877823 GTGATGGATGCTCATAGTTCAACA 59.122 41.667 0.00 0.00 0.00 3.33
1688 2070 8.962884 TGTAGTATGCAACAAGATCATACAAT 57.037 30.769 12.34 0.00 42.85 2.71
1757 2139 6.741992 TTGTTTCATGATGCTAAGTACCTG 57.258 37.500 0.00 0.00 0.00 4.00
1828 2215 2.000447 CTTCCATCTTCCCGACGAAAC 59.000 52.381 0.00 0.00 0.00 2.78
1873 2260 2.704572 CAACAGAACTCCCAGATCCAC 58.295 52.381 0.00 0.00 0.00 4.02
1911 2298 3.527533 CTGGTAGCCGCTTAACATGTTA 58.472 45.455 14.35 14.35 0.00 2.41
1912 2299 3.936453 CTGGTAGCCGCTTAACATGTTAA 59.064 43.478 25.48 25.48 34.28 2.01
1913 2300 7.422576 GCTGGTAGCCGCTTAACATGTTAAG 62.423 48.000 37.46 37.46 43.36 1.85
1931 2318 6.627243 TGTTAAGCACTTAAGCTCGATTCTA 58.373 36.000 1.29 0.00 45.89 2.10
1986 2560 2.953466 TTCTTCCCTGGTACGAATCG 57.047 50.000 0.00 0.00 0.00 3.34
2015 2589 1.226717 CTTCGCGGTGGTAGCTCTC 60.227 63.158 6.13 0.00 0.00 3.20
2017 2591 3.449227 CGCGGTGGTAGCTCTCCA 61.449 66.667 0.00 6.48 0.00 3.86
2031 2605 8.439971 TGGTAGCTCTCCATAAATAATGTGAAT 58.560 33.333 6.48 0.00 33.34 2.57
2032 2606 9.289782 GGTAGCTCTCCATAAATAATGTGAATT 57.710 33.333 0.00 0.00 33.34 2.17
2036 2610 8.854117 GCTCTCCATAAATAATGTGAATTCCTT 58.146 33.333 2.27 0.00 33.34 3.36
2049 2623 7.048629 TGTGAATTCCTTATTTTGCAACTCA 57.951 32.000 0.00 0.00 0.00 3.41
2051 2625 7.599621 TGTGAATTCCTTATTTTGCAACTCATG 59.400 33.333 0.00 0.00 0.00 3.07
2053 2627 6.855763 ATTCCTTATTTTGCAACTCATGGA 57.144 33.333 0.00 1.90 0.00 3.41
2091 2665 4.584325 AGCTCCTCATTTTTGCACTACAAA 59.416 37.500 0.00 0.00 46.51 2.83
2107 2681 7.880713 TGCACTACAAACCATCTTAGATTTGTA 59.119 33.333 14.84 14.84 42.06 2.41
2130 2704 1.336887 GCTAACTTCACGGAGCTGACA 60.337 52.381 0.00 0.00 32.04 3.58
2173 2747 3.360867 CTGACTTAGAGAAGCCAGGAGA 58.639 50.000 0.00 0.00 38.98 3.71
2209 2783 7.122353 GCCGAATAGGTCCTAAGAGTATGATTA 59.878 40.741 1.78 0.00 43.70 1.75
2381 2966 5.221422 ACACCATCGTTCCAAAATGACAATT 60.221 36.000 0.00 0.00 33.31 2.32
2383 2968 6.527722 CACCATCGTTCCAAAATGACAATTAG 59.472 38.462 0.00 0.00 33.31 1.73
2390 2975 4.644685 TCCAAAATGACAATTAGCTAGCCC 59.355 41.667 12.13 0.00 0.00 5.19
2392 2977 5.069516 CCAAAATGACAATTAGCTAGCCCAT 59.930 40.000 12.13 0.00 0.00 4.00
2397 2982 4.068599 GACAATTAGCTAGCCCATCTTCC 58.931 47.826 12.13 0.00 0.00 3.46
2401 2986 2.115337 AGCTAGCCCATCTTCCATCT 57.885 50.000 12.13 0.00 0.00 2.90
2424 3009 5.927030 TCTTTGACAATGAGTAATCGCAAC 58.073 37.500 0.00 0.00 0.00 4.17
2426 3011 3.006940 TGACAATGAGTAATCGCAACCC 58.993 45.455 0.00 0.00 0.00 4.11
2441 3026 2.159324 GCAACCCTTCTAGCTCAAATGC 60.159 50.000 0.00 0.00 0.00 3.56
2444 3029 0.659957 CCTTCTAGCTCAAATGCCGC 59.340 55.000 0.00 0.00 0.00 6.53
2464 3049 5.285651 CCGCCTTCTTAACATGTTGAAAAA 58.714 37.500 21.42 6.35 0.00 1.94
2487 3072 2.489329 AGAAAACCATGACGCAATCCAG 59.511 45.455 0.00 0.00 0.00 3.86
2514 3099 4.038162 GGTCTTACATATCAAGAGCTCGGT 59.962 45.833 8.37 0.00 43.74 4.69
2530 3115 3.306780 GCTCGGTATGCCAACATATAGGT 60.307 47.826 0.00 0.00 40.79 3.08
2561 3146 6.657541 TGGTAGAACAATAACATTTCTCACCC 59.342 38.462 0.00 0.00 31.93 4.61
2574 3159 0.610687 CTCACCCTTCGAAGGCTCTT 59.389 55.000 34.54 17.35 45.10 2.85
2590 3175 1.543802 CTCTTCAGGCGAGTGAGAAGT 59.456 52.381 0.00 0.00 38.78 3.01
2593 3178 0.603569 TCAGGCGAGTGAGAAGTTCC 59.396 55.000 0.00 0.00 0.00 3.62
2630 3215 5.006941 TCACAACATGCATCATGAATAGTCG 59.993 40.000 13.11 0.00 43.81 4.18
2631 3216 4.216731 CAACATGCATCATGAATAGTCGC 58.783 43.478 13.11 0.00 43.81 5.19
2632 3217 3.469739 ACATGCATCATGAATAGTCGCA 58.530 40.909 13.11 2.69 43.81 5.10
2635 3220 4.541085 TGCATCATGAATAGTCGCAAAG 57.459 40.909 0.00 0.00 0.00 2.77
2636 3221 4.190772 TGCATCATGAATAGTCGCAAAGA 58.809 39.130 0.00 0.00 0.00 2.52
2637 3222 4.818005 TGCATCATGAATAGTCGCAAAGAT 59.182 37.500 0.00 0.00 0.00 2.40
2638 3223 5.145059 GCATCATGAATAGTCGCAAAGATG 58.855 41.667 0.00 0.00 35.51 2.90
2639 3224 5.049886 GCATCATGAATAGTCGCAAAGATGA 60.050 40.000 0.00 3.69 34.92 2.92
2640 3225 6.512253 GCATCATGAATAGTCGCAAAGATGAA 60.512 38.462 0.00 0.00 34.92 2.57
2649 3234 1.900237 GCAAAGATGAACATGCGTCC 58.100 50.000 0.00 0.00 0.00 4.79
2651 3236 2.677836 GCAAAGATGAACATGCGTCCTA 59.322 45.455 0.00 0.00 0.00 2.94
2652 3237 3.313526 GCAAAGATGAACATGCGTCCTAT 59.686 43.478 0.00 0.00 0.00 2.57
2677 3262 3.686726 CACACCTCTAAAAGCAGTCCATC 59.313 47.826 0.00 0.00 0.00 3.51
2678 3263 3.274288 CACCTCTAAAAGCAGTCCATCC 58.726 50.000 0.00 0.00 0.00 3.51
2680 3265 2.555199 CTCTAAAAGCAGTCCATCCGG 58.445 52.381 0.00 0.00 0.00 5.14
2684 3269 1.207791 AAAGCAGTCCATCCGGAGAT 58.792 50.000 11.34 0.00 43.99 2.75
2714 3299 4.253685 ACGACCTGTCCACATTTATCTTG 58.746 43.478 0.00 0.00 0.00 3.02
2718 3303 1.742831 TGTCCACATTTATCTTGGCGC 59.257 47.619 0.00 0.00 0.00 6.53
2719 3304 1.742831 GTCCACATTTATCTTGGCGCA 59.257 47.619 10.83 0.00 0.00 6.09
2722 3307 2.223340 CCACATTTATCTTGGCGCACTC 60.223 50.000 10.83 0.00 0.00 3.51
2723 3308 2.419673 CACATTTATCTTGGCGCACTCA 59.580 45.455 10.83 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.248487 GTGACATAACCTCGTGTCGAC 58.752 52.381 9.11 9.11 45.88 4.20
3 4 1.983605 GTGTGACATAACCTCGTGTCG 59.016 52.381 0.00 0.00 45.88 4.35
4 5 3.299340 AGTGTGACATAACCTCGTGTC 57.701 47.619 0.00 0.00 43.81 3.67
5 6 5.401531 AATAGTGTGACATAACCTCGTGT 57.598 39.130 0.00 0.00 0.00 4.49
6 7 6.367695 TCAAAATAGTGTGACATAACCTCGTG 59.632 38.462 0.00 0.00 0.00 4.35
7 8 6.367969 GTCAAAATAGTGTGACATAACCTCGT 59.632 38.462 8.61 0.00 43.02 4.18
8 9 6.590292 AGTCAAAATAGTGTGACATAACCTCG 59.410 38.462 15.47 0.00 45.40 4.63
9 10 7.907214 AGTCAAAATAGTGTGACATAACCTC 57.093 36.000 15.47 0.00 45.40 3.85
10 11 7.549488 GCTAGTCAAAATAGTGTGACATAACCT 59.451 37.037 15.47 0.00 45.40 3.50
11 12 7.549488 AGCTAGTCAAAATAGTGTGACATAACC 59.451 37.037 15.47 0.11 45.40 2.85
12 13 8.480643 AGCTAGTCAAAATAGTGTGACATAAC 57.519 34.615 15.47 2.64 45.40 1.89
14 15 9.803315 CTAAGCTAGTCAAAATAGTGTGACATA 57.197 33.333 15.47 4.81 45.40 2.29
15 16 8.531982 TCTAAGCTAGTCAAAATAGTGTGACAT 58.468 33.333 15.47 3.95 45.40 3.06
16 17 7.892609 TCTAAGCTAGTCAAAATAGTGTGACA 58.107 34.615 15.47 1.64 45.40 3.58
17 18 8.934507 ATCTAAGCTAGTCAAAATAGTGTGAC 57.065 34.615 5.32 5.32 43.70 3.67
18 19 8.972127 AGATCTAAGCTAGTCAAAATAGTGTGA 58.028 33.333 0.00 0.00 0.00 3.58
19 20 9.593134 AAGATCTAAGCTAGTCAAAATAGTGTG 57.407 33.333 0.00 0.00 0.00 3.82
20 21 9.593134 CAAGATCTAAGCTAGTCAAAATAGTGT 57.407 33.333 0.00 0.00 0.00 3.55
21 22 9.809096 TCAAGATCTAAGCTAGTCAAAATAGTG 57.191 33.333 0.00 0.00 0.00 2.74
25 26 9.678260 ACAATCAAGATCTAAGCTAGTCAAAAT 57.322 29.630 0.00 0.00 0.00 1.82
26 27 8.939929 CACAATCAAGATCTAAGCTAGTCAAAA 58.060 33.333 0.00 0.00 0.00 2.44
27 28 8.097038 ACACAATCAAGATCTAAGCTAGTCAAA 58.903 33.333 0.00 0.00 0.00 2.69
45 46 9.757227 TTCGTTATGATGTATATCACACAATCA 57.243 29.630 4.06 0.00 45.54 2.57
48 49 7.916450 TCGTTCGTTATGATGTATATCACACAA 59.084 33.333 4.06 0.00 45.54 3.33
58 59 5.209977 CGGAAGATCGTTCGTTATGATGTA 58.790 41.667 0.61 0.00 32.54 2.29
78 79 4.057406 TCTTTAGTTTTCACCGAACGGA 57.943 40.909 20.14 0.00 38.96 4.69
81 82 6.471198 CAGGTTTTCTTTAGTTTTCACCGAAC 59.529 38.462 0.00 0.00 0.00 3.95
83 84 5.648960 ACAGGTTTTCTTTAGTTTTCACCGA 59.351 36.000 0.00 0.00 0.00 4.69
84 85 5.886992 ACAGGTTTTCTTTAGTTTTCACCG 58.113 37.500 0.00 0.00 0.00 4.94
126 129 3.370978 GTCACCAACTCACCATCGTATTG 59.629 47.826 0.00 0.00 0.00 1.90
128 131 2.093658 GGTCACCAACTCACCATCGTAT 60.094 50.000 0.00 0.00 0.00 3.06
130 133 0.034896 GGTCACCAACTCACCATCGT 59.965 55.000 0.00 0.00 0.00 3.73
132 135 2.496899 ATGGTCACCAACTCACCATC 57.503 50.000 0.00 0.00 46.12 3.51
146 149 1.739067 GTGGCTTGGTGAGTATGGTC 58.261 55.000 0.00 0.00 0.00 4.02
166 169 4.954875 ACCTTAGCTTATGTGCATCTCTC 58.045 43.478 0.00 0.00 34.99 3.20
168 171 4.697514 TGACCTTAGCTTATGTGCATCTC 58.302 43.478 0.00 0.00 34.99 2.75
169 172 4.760530 TGACCTTAGCTTATGTGCATCT 57.239 40.909 0.00 0.00 34.99 2.90
208 212 9.642327 CATGTTTTGGATATTCTCATGTTTTGA 57.358 29.630 0.00 0.00 0.00 2.69
209 213 9.426837 ACATGTTTTGGATATTCTCATGTTTTG 57.573 29.630 0.00 0.00 40.52 2.44
217 221 6.183360 CCCAGTCACATGTTTTGGATATTCTC 60.183 42.308 17.48 0.00 0.00 2.87
227 231 4.022068 CACATAAGCCCAGTCACATGTTTT 60.022 41.667 0.00 0.00 0.00 2.43
232 236 2.040278 ACACACATAAGCCCAGTCACAT 59.960 45.455 0.00 0.00 0.00 3.21
238 242 2.425143 ATCCACACACATAAGCCCAG 57.575 50.000 0.00 0.00 0.00 4.45
241 245 3.687698 ACGTTAATCCACACACATAAGCC 59.312 43.478 0.00 0.00 0.00 4.35
285 289 4.695455 CCATTCGAGTACACCATTTGAAGT 59.305 41.667 0.00 0.00 0.00 3.01
316 320 9.339850 GTTCCTCTAAAGTTCCTTATTTATCCC 57.660 37.037 0.00 0.00 0.00 3.85
345 349 5.330455 TGCTCTATCACGTTCAGATCTTT 57.670 39.130 0.00 0.00 0.00 2.52
346 350 4.991153 TGCTCTATCACGTTCAGATCTT 57.009 40.909 0.00 0.00 0.00 2.40
351 355 4.259970 CGGATTTTGCTCTATCACGTTCAG 60.260 45.833 0.00 0.00 0.00 3.02
356 360 3.000322 GTGACGGATTTTGCTCTATCACG 60.000 47.826 0.00 0.00 0.00 4.35
357 361 3.932710 TGTGACGGATTTTGCTCTATCAC 59.067 43.478 0.00 0.00 36.58 3.06
358 362 3.932710 GTGTGACGGATTTTGCTCTATCA 59.067 43.478 0.00 0.00 0.00 2.15
368 372 2.223971 ACTTCGTGAGTGTGACGGATTT 60.224 45.455 0.00 0.00 37.17 2.17
379 383 7.925993 TCAAACAATATTTTCACTTCGTGAGT 58.074 30.769 0.00 0.00 43.69 3.41
380 384 7.059945 GCTCAAACAATATTTTCACTTCGTGAG 59.940 37.037 0.00 0.00 43.69 3.51
382 386 6.088085 GGCTCAAACAATATTTTCACTTCGTG 59.912 38.462 0.00 0.00 34.45 4.35
383 387 6.149633 GGCTCAAACAATATTTTCACTTCGT 58.850 36.000 0.00 0.00 0.00 3.85
384 388 5.572896 GGGCTCAAACAATATTTTCACTTCG 59.427 40.000 0.00 0.00 0.00 3.79
385 389 6.454795 TGGGCTCAAACAATATTTTCACTTC 58.545 36.000 0.00 0.00 0.00 3.01
386 390 6.418057 TGGGCTCAAACAATATTTTCACTT 57.582 33.333 0.00 0.00 0.00 3.16
387 391 6.014327 ACATGGGCTCAAACAATATTTTCACT 60.014 34.615 0.00 0.00 0.00 3.41
389 393 6.357579 ACATGGGCTCAAACAATATTTTCA 57.642 33.333 0.00 0.00 0.00 2.69
422 426 8.627208 AGGCACAGGTTGAATTTATATAGATG 57.373 34.615 0.00 0.00 0.00 2.90
430 434 6.071616 GGATTACAAGGCACAGGTTGAATTTA 60.072 38.462 0.00 0.00 0.00 1.40
499 842 5.453903 CGATGACTCCTTTGGATTGTAGGAT 60.454 44.000 0.00 0.00 37.44 3.24
500 843 4.141937 CGATGACTCCTTTGGATTGTAGGA 60.142 45.833 0.00 0.00 36.65 2.94
502 845 5.011090 TCGATGACTCCTTTGGATTGTAG 57.989 43.478 0.00 0.00 0.00 2.74
503 846 4.709886 TCTCGATGACTCCTTTGGATTGTA 59.290 41.667 0.00 0.00 0.00 2.41
504 847 3.515502 TCTCGATGACTCCTTTGGATTGT 59.484 43.478 0.00 0.00 0.00 2.71
505 848 4.128925 TCTCGATGACTCCTTTGGATTG 57.871 45.455 0.00 0.00 0.00 2.67
506 849 4.764172 CTTCTCGATGACTCCTTTGGATT 58.236 43.478 0.00 0.00 0.00 3.01
507 850 3.431486 GCTTCTCGATGACTCCTTTGGAT 60.431 47.826 0.00 0.00 0.00 3.41
508 851 2.093973 GCTTCTCGATGACTCCTTTGGA 60.094 50.000 0.00 0.00 0.00 3.53
509 852 2.093764 AGCTTCTCGATGACTCCTTTGG 60.094 50.000 0.00 0.00 0.00 3.28
511 854 3.764434 TGTAGCTTCTCGATGACTCCTTT 59.236 43.478 0.00 0.00 0.00 3.11
514 857 3.784701 TTGTAGCTTCTCGATGACTCC 57.215 47.619 0.00 0.00 0.00 3.85
598 957 7.273381 CGGCTTGATTTGGTAATCTTTTAGTTG 59.727 37.037 0.00 0.00 40.68 3.16
601 960 6.094881 TCCGGCTTGATTTGGTAATCTTTTAG 59.905 38.462 0.00 0.00 40.68 1.85
603 962 4.770010 TCCGGCTTGATTTGGTAATCTTTT 59.230 37.500 0.00 0.00 40.68 2.27
607 966 2.033424 GCTCCGGCTTGATTTGGTAATC 59.967 50.000 0.00 0.00 37.11 1.75
609 968 1.459450 GCTCCGGCTTGATTTGGTAA 58.541 50.000 0.00 0.00 35.22 2.85
610 969 0.393808 GGCTCCGGCTTGATTTGGTA 60.394 55.000 0.00 0.00 38.73 3.25
622 983 3.596066 CTCACACCAGTGGCTCCGG 62.596 68.421 9.78 0.00 45.91 5.14
645 1006 0.108615 CGCCAACGAAGAGGAGACAT 60.109 55.000 0.00 0.00 43.93 3.06
666 1027 1.578206 GGCTTTGGTTGCTCCTCGTC 61.578 60.000 0.80 0.00 37.07 4.20
689 1050 2.037511 CACTTTGGATGTTGTGGGCAAT 59.962 45.455 0.00 0.00 36.92 3.56
690 1051 1.411977 CACTTTGGATGTTGTGGGCAA 59.588 47.619 0.00 0.00 0.00 4.52
697 1058 2.886862 TTGTGCCACTTTGGATGTTG 57.113 45.000 0.00 0.00 40.96 3.33
698 1059 3.030291 TCTTTGTGCCACTTTGGATGTT 58.970 40.909 0.00 0.00 40.96 2.71
700 1061 3.731652 TTCTTTGTGCCACTTTGGATG 57.268 42.857 0.00 0.00 40.96 3.51
708 1069 0.380378 TCACGCTTTCTTTGTGCCAC 59.620 50.000 0.00 0.00 33.69 5.01
711 1072 2.755836 TTCTCACGCTTTCTTTGTGC 57.244 45.000 0.00 0.00 33.69 4.57
737 1098 7.607250 TCTTTCATGTTACCAACACTTTTTGT 58.393 30.769 0.00 0.00 45.50 2.83
798 1160 7.634522 TCCCGCTTGATTTGTTTTTATTTTTG 58.365 30.769 0.00 0.00 0.00 2.44
799 1161 7.519809 GCTCCCGCTTGATTTGTTTTTATTTTT 60.520 33.333 0.00 0.00 0.00 1.94
805 1167 2.547855 GGCTCCCGCTTGATTTGTTTTT 60.548 45.455 0.00 0.00 36.09 1.94
810 1172 0.962356 AGTGGCTCCCGCTTGATTTG 60.962 55.000 0.00 0.00 42.24 2.32
832 1198 0.110688 CATGTCACGCTCAAACCACG 60.111 55.000 0.00 0.00 0.00 4.94
838 1204 0.969149 AGGAGACATGTCACGCTCAA 59.031 50.000 27.02 0.00 0.00 3.02
873 1242 1.454295 ACCGGTGGTTTGGTTGTCC 60.454 57.895 6.12 0.00 33.81 4.02
875 1244 1.000646 ACACCGGTGGTTTGGTTGT 60.001 52.632 36.47 11.21 35.96 3.32
950 1319 1.893808 GAGTGGTGGTGTGTGGCAG 60.894 63.158 0.00 0.00 0.00 4.85
951 1320 2.191908 GAGTGGTGGTGTGTGGCA 59.808 61.111 0.00 0.00 0.00 4.92
1516 1891 0.948678 GCCAGCAAAAACACTACGGA 59.051 50.000 0.00 0.00 0.00 4.69
1648 2023 8.560355 TGCATACTACATAACATTGTTGAACT 57.440 30.769 12.30 0.00 0.00 3.01
1656 2031 9.394767 TGATCTTGTTGCATACTACATAACATT 57.605 29.630 0.00 0.00 31.55 2.71
1684 2066 5.469760 GCAAATTCCCTACAAAGCAAATTGT 59.530 36.000 7.54 7.54 45.14 2.71
1688 2070 3.648009 CGCAAATTCCCTACAAAGCAAA 58.352 40.909 0.00 0.00 0.00 3.68
1777 2159 3.631227 GGAGCTGGATTTGAGGATTTCTG 59.369 47.826 0.00 0.00 0.00 3.02
1838 2225 2.552315 TCTGTTGCCGAATGGTTCTTTC 59.448 45.455 0.00 0.00 37.67 2.62
1873 2260 0.596083 CAGCCCAAGACTAGCGATCG 60.596 60.000 11.69 11.69 0.00 3.69
1911 2298 4.116238 GCTAGAATCGAGCTTAAGTGCTT 58.884 43.478 8.12 0.00 44.17 3.91
1913 2300 3.448686 TGCTAGAATCGAGCTTAAGTGC 58.551 45.455 15.88 0.00 40.76 4.40
1914 2301 4.447054 CCATGCTAGAATCGAGCTTAAGTG 59.553 45.833 15.88 7.35 40.76 3.16
1915 2302 4.100189 ACCATGCTAGAATCGAGCTTAAGT 59.900 41.667 15.88 8.17 40.76 2.24
1916 2303 4.626042 ACCATGCTAGAATCGAGCTTAAG 58.374 43.478 15.88 0.00 40.76 1.85
1917 2304 4.672587 ACCATGCTAGAATCGAGCTTAA 57.327 40.909 15.88 0.00 40.76 1.85
1918 2305 4.218635 CCTACCATGCTAGAATCGAGCTTA 59.781 45.833 15.88 0.00 40.76 3.09
1919 2306 3.006323 CCTACCATGCTAGAATCGAGCTT 59.994 47.826 15.88 7.37 40.76 3.74
1931 2318 1.216990 CCTTTCCTCCCTACCATGCT 58.783 55.000 0.00 0.00 0.00 3.79
1986 2560 2.372350 CACCGCGAAGTGAAAGAAAAC 58.628 47.619 8.23 0.00 43.07 2.43
2031 2605 6.662865 TTCCATGAGTTGCAAAATAAGGAA 57.337 33.333 15.75 15.75 29.74 3.36
2032 2606 6.404623 CGATTCCATGAGTTGCAAAATAAGGA 60.405 38.462 0.00 3.77 0.00 3.36
2036 2610 4.439974 GGCGATTCCATGAGTTGCAAAATA 60.440 41.667 0.00 0.00 31.47 1.40
2046 2620 2.415893 GGTGTTTTGGCGATTCCATGAG 60.416 50.000 0.00 0.00 46.04 2.90
2049 2623 1.545582 CTGGTGTTTTGGCGATTCCAT 59.454 47.619 0.00 0.00 46.04 3.41
2051 2625 0.388520 GCTGGTGTTTTGGCGATTCC 60.389 55.000 0.00 0.00 0.00 3.01
2053 2627 0.598065 GAGCTGGTGTTTTGGCGATT 59.402 50.000 0.00 0.00 0.00 3.34
2066 2640 1.891150 AGTGCAAAAATGAGGAGCTGG 59.109 47.619 0.00 0.00 0.00 4.85
2091 2665 9.740710 AAGTTAGCTTTACAAATCTAAGATGGT 57.259 29.630 0.00 0.00 30.08 3.55
2107 2681 2.037251 TCAGCTCCGTGAAGTTAGCTTT 59.963 45.455 0.00 0.00 42.52 3.51
2130 2704 1.228552 ACGAAGCTGGGCCAAACAT 60.229 52.632 8.04 0.00 0.00 2.71
2193 2767 8.495260 TCAGAGTGTCTAATCATACTCTTAGGA 58.505 37.037 0.00 0.00 45.48 2.94
2330 2904 6.102897 ACCCAATGTAGCATCTACTATCAC 57.897 41.667 5.70 0.00 0.00 3.06
2336 2910 4.344102 TGTCCTACCCAATGTAGCATCTAC 59.656 45.833 0.00 0.00 44.77 2.59
2381 2966 3.169099 GAGATGGAAGATGGGCTAGCTA 58.831 50.000 15.72 4.59 0.00 3.32
2383 2968 1.977129 AGAGATGGAAGATGGGCTAGC 59.023 52.381 6.04 6.04 0.00 3.42
2390 2975 6.598457 ACTCATTGTCAAAGAGATGGAAGATG 59.402 38.462 21.47 0.00 33.69 2.90
2392 2977 6.119240 ACTCATTGTCAAAGAGATGGAAGA 57.881 37.500 21.47 0.00 33.69 2.87
2397 2982 6.036408 TGCGATTACTCATTGTCAAAGAGATG 59.964 38.462 21.47 9.01 33.69 2.90
2401 2986 5.106712 GGTTGCGATTACTCATTGTCAAAGA 60.107 40.000 0.00 0.00 0.00 2.52
2424 3009 1.303309 CGGCATTTGAGCTAGAAGGG 58.697 55.000 0.00 0.00 34.17 3.95
2426 3011 0.659957 GGCGGCATTTGAGCTAGAAG 59.340 55.000 3.07 0.00 34.17 2.85
2441 3026 4.497473 TTTCAACATGTTAAGAAGGCGG 57.503 40.909 11.53 0.00 0.00 6.13
2464 3049 3.320541 TGGATTGCGTCATGGTTTTCTTT 59.679 39.130 0.00 0.00 0.00 2.52
2468 3053 2.513753 TCTGGATTGCGTCATGGTTTT 58.486 42.857 0.00 0.00 0.00 2.43
2471 3056 2.086869 CTTTCTGGATTGCGTCATGGT 58.913 47.619 0.00 0.00 0.00 3.55
2487 3072 6.419413 CGAGCTCTTGATATGTAAGACCTTTC 59.581 42.308 12.85 0.00 31.35 2.62
2511 3096 4.265904 TCACCTATATGTTGGCATACCG 57.734 45.455 0.00 0.00 40.05 4.02
2514 3099 7.927788 ACCATTATCACCTATATGTTGGCATA 58.072 34.615 0.00 0.00 41.31 3.14
2548 3133 3.412386 CCTTCGAAGGGTGAGAAATGTT 58.588 45.455 32.76 0.00 42.66 2.71
2561 3146 1.080995 CGCCTGAAGAGCCTTCGAAG 61.081 60.000 18.51 18.51 0.00 3.79
2574 3159 0.603569 GGAACTTCTCACTCGCCTGA 59.396 55.000 0.00 0.00 0.00 3.86
2590 3175 3.490439 TGTGATGCAGAAGAAGTGGAA 57.510 42.857 0.00 0.00 0.00 3.53
2593 3178 4.473199 CATGTTGTGATGCAGAAGAAGTG 58.527 43.478 0.00 0.00 0.00 3.16
2620 3205 6.722301 CATGTTCATCTTTGCGACTATTCAT 58.278 36.000 0.00 0.00 0.00 2.57
2630 3215 1.470098 AGGACGCATGTTCATCTTTGC 59.530 47.619 0.00 0.00 0.00 3.68
2631 3216 4.024556 GGATAGGACGCATGTTCATCTTTG 60.025 45.833 0.00 0.00 0.00 2.77
2632 3217 4.130118 GGATAGGACGCATGTTCATCTTT 58.870 43.478 0.00 0.00 0.00 2.52
2635 3220 2.224281 TGGGATAGGACGCATGTTCATC 60.224 50.000 0.00 0.00 0.00 2.92
2636 3221 1.768275 TGGGATAGGACGCATGTTCAT 59.232 47.619 0.00 0.00 0.00 2.57
2637 3222 1.134521 GTGGGATAGGACGCATGTTCA 60.135 52.381 0.00 0.00 35.38 3.18
2638 3223 1.134521 TGTGGGATAGGACGCATGTTC 60.135 52.381 0.00 0.00 35.38 3.18
2639 3224 0.908910 TGTGGGATAGGACGCATGTT 59.091 50.000 0.00 0.00 35.38 2.71
2640 3225 0.178068 GTGTGGGATAGGACGCATGT 59.822 55.000 0.00 0.00 35.38 3.21
2649 3234 4.080863 ACTGCTTTTAGAGGTGTGGGATAG 60.081 45.833 0.00 0.00 0.00 2.08
2651 3236 2.644798 ACTGCTTTTAGAGGTGTGGGAT 59.355 45.455 0.00 0.00 0.00 3.85
2652 3237 2.038557 GACTGCTTTTAGAGGTGTGGGA 59.961 50.000 0.00 0.00 0.00 4.37
2677 3262 1.337387 GGTCGTTCCTTCTATCTCCGG 59.663 57.143 0.00 0.00 0.00 5.14
2678 3263 2.033550 CAGGTCGTTCCTTCTATCTCCG 59.966 54.545 0.00 0.00 45.67 4.63
2680 3265 3.067040 GGACAGGTCGTTCCTTCTATCTC 59.933 52.174 0.00 0.00 45.67 2.75
2684 3269 1.891150 GTGGACAGGTCGTTCCTTCTA 59.109 52.381 0.00 0.00 45.67 2.10
2698 3283 1.742831 GCGCCAAGATAAATGTGGACA 59.257 47.619 0.00 0.00 34.05 4.02
2699 3284 1.742831 TGCGCCAAGATAAATGTGGAC 59.257 47.619 4.18 0.00 34.05 4.02
2714 3299 1.298859 CTACCCAAACTGAGTGCGCC 61.299 60.000 4.18 0.00 0.00 6.53
2718 3303 2.104111 TGGACACTACCCAAACTGAGTG 59.896 50.000 0.00 0.00 43.97 3.51
2719 3304 2.404559 TGGACACTACCCAAACTGAGT 58.595 47.619 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.