Multiple sequence alignment - TraesCS5B01G333400

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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 TraesCS5B01G333400 chr5B 100.000 2324 0 0 1 2324 517367644 517369967 0.000000e+00 4292
1 TraesCS5B01G333400 chr5A 89.428 1731 102 34 203 1888 543336434 543338128 0.000000e+00 2108
2 TraesCS5B01G333400 chr5A 89.261 1732 104 34 203 1888 543490475 543492170 0.000000e+00 2093
3 TraesCS5B01G333400 chr5A 95.408 392 5 9 1935 2324 543492172 543492552 1.530000e-171 612
4 TraesCS5B01G333400 chr5A 94.444 396 6 10 1935 2324 543338137 543338522 1.540000e-166 595
5 TraesCS5B01G333400 chr5A 88.889 207 11 6 1 205 543490250 543490446 6.410000e-61 244
6 TraesCS5B01G333400 chr5A 92.241 116 5 1 1 116 543336070 543336181 6.650000e-36 161
7 TraesCS5B01G333400 chr5D 87.566 756 63 13 203 941 428164246 428164987 0.000000e+00 846
8 TraesCS5B01G333400 chr5D 89.756 205 12 3 1 205 428164021 428164216 1.070000e-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 TraesCS5B01G333400 chr5B 517367644 517369967 2323 False 4292.000000 4292 100.000000 1 2324 1 chr5B.!!$F1 2323
1 TraesCS5B01G333400 chr5A 543490250 543492552 2302 False 983.000000 2093 91.186000 1 2324 3 chr5A.!!$F2 2323
2 TraesCS5B01G333400 chr5A 543336070 543338522 2452 False 954.666667 2108 92.037667 1 2324 3 chr5A.!!$F1 2323
3 TraesCS5B01G333400 chr5D 428164021 428164987 966 False 550.000000 846 88.661000 1 941 2 chr5D.!!$F1 940

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
636 835 0.040157 CAAACGATGTGGCAGGTGTG 60.04 55.0 0.0 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 2077 0.179018 GAGTCCCAAACCAGTGCAGT 60.179 55.0 0.0 0.0 0.0 4.4 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
57 58 4.141158 GGGACCAGAAAAGACCATCCATAT 60.141 45.833 0.00 0.00 0.00 1.78
58 59 5.073144 GGGACCAGAAAAGACCATCCATATA 59.927 44.000 0.00 0.00 0.00 0.86
59 60 6.240292 GGGACCAGAAAAGACCATCCATATAT 60.240 42.308 0.00 0.00 0.00 0.86
60 61 7.037586 GGGACCAGAAAAGACCATCCATATATA 60.038 40.741 0.00 0.00 0.00 0.86
103 104 1.003851 CGACGTGTGACACAAAACCT 58.996 50.000 16.74 0.00 33.40 3.50
119 122 4.741928 AAACCTTCAATGACCTTACCCT 57.258 40.909 0.00 0.00 0.00 4.34
125 128 3.459828 TCAATGACCTTACCCTCCATGA 58.540 45.455 0.00 0.00 0.00 3.07
141 144 3.044156 CCATGATCCCCCGAGATGATAT 58.956 50.000 0.00 0.00 0.00 1.63
142 145 3.457380 CCATGATCCCCCGAGATGATATT 59.543 47.826 0.00 0.00 0.00 1.28
143 146 4.080129 CCATGATCCCCCGAGATGATATTT 60.080 45.833 0.00 0.00 0.00 1.40
144 147 5.503927 CATGATCCCCCGAGATGATATTTT 58.496 41.667 0.00 0.00 0.00 1.82
181 319 4.953579 GGGTAGGAGGATGCAACATTTTTA 59.046 41.667 0.00 0.00 0.00 1.52
205 343 4.844349 TCTAAAAGGCTATGGTGCTCTT 57.156 40.909 0.00 0.00 0.00 2.85
207 345 3.439857 AAAAGGCTATGGTGCTCTTCA 57.560 42.857 0.00 0.00 0.00 3.02
209 347 3.439857 AAGGCTATGGTGCTCTTCAAA 57.560 42.857 0.00 0.00 0.00 2.69
210 348 2.716217 AGGCTATGGTGCTCTTCAAAC 58.284 47.619 0.00 0.00 0.00 2.93
211 349 2.040278 AGGCTATGGTGCTCTTCAAACA 59.960 45.455 0.00 0.00 0.00 2.83
212 350 2.162408 GGCTATGGTGCTCTTCAAACAC 59.838 50.000 0.00 0.00 0.00 3.32
213 351 3.077359 GCTATGGTGCTCTTCAAACACT 58.923 45.455 0.00 0.00 34.70 3.55
215 353 1.024271 TGGTGCTCTTCAAACACTGC 58.976 50.000 0.00 0.00 34.70 4.40
223 393 4.500375 GCTCTTCAAACACTGCATTCCTTT 60.500 41.667 0.00 0.00 0.00 3.11
227 397 5.843673 TCAAACACTGCATTCCTTTGTTA 57.156 34.783 0.00 0.00 30.28 2.41
232 402 4.019174 CACTGCATTCCTTTGTTAGGGAT 58.981 43.478 0.00 0.00 43.71 3.85
236 406 5.684704 TGCATTCCTTTGTTAGGGATAGAG 58.315 41.667 0.00 0.00 40.62 2.43
241 411 4.348168 TCCTTTGTTAGGGATAGAGATGGC 59.652 45.833 0.00 0.00 44.86 4.40
255 425 1.306141 ATGGCGAGGGAGAAGTCCA 60.306 57.895 0.00 0.00 46.07 4.02
270 441 2.796557 AGTCCAACGAGTCTGAGATGA 58.203 47.619 0.00 0.00 0.00 2.92
274 445 1.468914 CAACGAGTCTGAGATGACCGA 59.531 52.381 0.00 0.00 37.66 4.69
278 449 3.135225 CGAGTCTGAGATGACCGATAGT 58.865 50.000 0.00 0.00 37.66 2.12
294 468 6.927416 ACCGATAGTATTGTGTTGAGTTACA 58.073 36.000 0.00 0.00 0.00 2.41
315 489 5.410067 ACACCAATTACAATTAGCACATGC 58.590 37.500 0.00 0.00 42.49 4.06
342 518 8.432110 ACAACATGACATATTTAGCGATAACA 57.568 30.769 0.00 0.00 0.00 2.41
347 545 9.750882 CATGACATATTTAGCGATAACAATGAG 57.249 33.333 16.77 1.11 0.00 2.90
350 548 8.662781 ACATATTTAGCGATAACAATGAGTGT 57.337 30.769 16.77 4.81 44.64 3.55
351 549 8.551205 ACATATTTAGCGATAACAATGAGTGTG 58.449 33.333 16.77 0.00 40.60 3.82
352 550 8.764287 CATATTTAGCGATAACAATGAGTGTGA 58.236 33.333 7.95 0.00 40.60 3.58
353 551 6.403333 TTTAGCGATAACAATGAGTGTGAC 57.597 37.500 0.00 0.00 40.60 3.67
354 552 2.923655 AGCGATAACAATGAGTGTGACG 59.076 45.455 0.00 0.00 40.60 4.35
355 553 2.534939 GCGATAACAATGAGTGTGACGC 60.535 50.000 13.32 13.32 43.66 5.19
356 554 2.029244 CGATAACAATGAGTGTGACGCC 59.971 50.000 0.00 0.00 40.60 5.68
357 555 1.424403 TAACAATGAGTGTGACGCCG 58.576 50.000 0.00 0.00 40.60 6.46
358 556 0.531974 AACAATGAGTGTGACGCCGT 60.532 50.000 0.00 0.00 40.60 5.68
359 557 0.531974 ACAATGAGTGTGACGCCGTT 60.532 50.000 0.00 0.00 39.72 4.44
360 558 0.110688 CAATGAGTGTGACGCCGTTG 60.111 55.000 0.00 0.00 0.00 4.10
361 559 0.249699 AATGAGTGTGACGCCGTTGA 60.250 50.000 0.00 0.00 0.00 3.18
362 560 0.249699 ATGAGTGTGACGCCGTTGAA 60.250 50.000 0.00 0.00 0.00 2.69
363 561 0.249699 TGAGTGTGACGCCGTTGAAT 60.250 50.000 0.00 0.00 0.00 2.57
364 562 0.865769 GAGTGTGACGCCGTTGAATT 59.134 50.000 0.00 0.00 0.00 2.17
365 563 0.586319 AGTGTGACGCCGTTGAATTG 59.414 50.000 0.00 0.00 0.00 2.32
366 564 0.996727 GTGTGACGCCGTTGAATTGC 60.997 55.000 0.00 0.00 0.00 3.56
367 565 1.281353 GTGACGCCGTTGAATTGCA 59.719 52.632 0.00 0.00 0.00 4.08
368 566 0.317436 GTGACGCCGTTGAATTGCAA 60.317 50.000 0.00 0.00 0.00 4.08
381 579 4.548494 TGAATTGCAACTGCTGTATTGTG 58.452 39.130 0.00 0.00 42.66 3.33
387 585 2.744202 CAACTGCTGTATTGTGTCTCCC 59.256 50.000 0.00 0.00 0.00 4.30
398 596 1.379977 TGTCTCCCTAGCCGTCTGG 60.380 63.158 0.00 0.00 38.77 3.86
415 613 3.131577 GTCTGGATATGTAACGGTGACCA 59.868 47.826 1.11 0.00 0.00 4.02
425 623 3.604875 AACGGTGACCACGATAAGAAT 57.395 42.857 1.11 0.00 34.93 2.40
426 624 2.888594 ACGGTGACCACGATAAGAATG 58.111 47.619 1.11 0.00 34.93 2.67
441 639 7.491696 ACGATAAGAATGAGTGTTAAACTAGGC 59.508 37.037 0.00 0.00 40.07 3.93
442 640 7.042658 CGATAAGAATGAGTGTTAAACTAGGCC 60.043 40.741 0.00 0.00 40.07 5.19
447 645 4.312443 TGAGTGTTAAACTAGGCCGAAAG 58.688 43.478 0.00 0.00 40.07 2.62
538 737 1.852942 GAGTGACGACTTCAAGCACA 58.147 50.000 0.00 0.00 35.39 4.57
584 783 0.529773 GACACGCTGGACACAGTTGA 60.530 55.000 0.00 0.00 46.62 3.18
607 806 3.939592 CTGGATATGCTATGCACTGGATG 59.060 47.826 0.00 0.00 43.04 3.51
616 815 2.182842 GCACTGGATGGATGGACGC 61.183 63.158 0.00 0.00 0.00 5.19
618 817 1.995066 ACTGGATGGATGGACGCCA 60.995 57.895 1.01 1.01 40.24 5.69
619 818 1.224315 CTGGATGGATGGACGCCAA 59.776 57.895 2.68 0.00 39.21 4.52
633 832 4.079446 CCAAACGATGTGGCAGGT 57.921 55.556 0.00 0.00 0.00 4.00
634 833 1.580942 CCAAACGATGTGGCAGGTG 59.419 57.895 0.00 0.00 0.00 4.00
635 834 1.172180 CCAAACGATGTGGCAGGTGT 61.172 55.000 0.00 0.00 0.00 4.16
636 835 0.040157 CAAACGATGTGGCAGGTGTG 60.040 55.000 0.00 0.00 0.00 3.82
637 836 0.465460 AAACGATGTGGCAGGTGTGT 60.465 50.000 0.00 0.00 0.00 3.72
638 837 1.165907 AACGATGTGGCAGGTGTGTG 61.166 55.000 0.00 0.00 0.00 3.82
639 838 1.597854 CGATGTGGCAGGTGTGTGT 60.598 57.895 0.00 0.00 0.00 3.72
642 841 1.108727 ATGTGGCAGGTGTGTGTTGG 61.109 55.000 0.00 0.00 0.00 3.77
644 843 2.194597 GGCAGGTGTGTGTTGGGA 59.805 61.111 0.00 0.00 0.00 4.37
649 848 0.106719 AGGTGTGTGTTGGGAGTTGG 60.107 55.000 0.00 0.00 0.00 3.77
669 868 3.315796 CGCGAACGTTCACCTTGT 58.684 55.556 26.71 0.00 33.53 3.16
670 869 1.083657 CGCGAACGTTCACCTTGTG 60.084 57.895 26.71 13.20 32.42 3.33
671 870 1.278637 GCGAACGTTCACCTTGTGG 59.721 57.895 26.71 9.79 39.83 4.17
672 871 1.155424 GCGAACGTTCACCTTGTGGA 61.155 55.000 26.71 0.00 37.04 4.02
673 872 0.859232 CGAACGTTCACCTTGTGGAG 59.141 55.000 26.71 3.78 37.04 3.86
686 893 3.498397 CCTTGTGGAGTACATGTGTGAAC 59.502 47.826 9.11 0.00 39.48 3.18
709 920 1.114627 GGTCAGGCCAAATGGATTCC 58.885 55.000 5.01 0.00 37.39 3.01
712 923 0.395586 CAGGCCAAATGGATTCCGGA 60.396 55.000 5.01 0.00 37.39 5.14
717 928 2.629617 GCCAAATGGATTCCGGATCATT 59.370 45.455 4.15 13.20 36.43 2.57
773 984 6.759497 AATTAAAGCGTATCCAGAAAAGCT 57.241 33.333 0.00 0.00 36.40 3.74
851 1067 7.690256 AGAGAAATTAACTAGGAGCCAAAGAA 58.310 34.615 0.00 0.00 0.00 2.52
852 1068 8.164070 AGAGAAATTAACTAGGAGCCAAAGAAA 58.836 33.333 0.00 0.00 0.00 2.52
853 1069 8.341892 AGAAATTAACTAGGAGCCAAAGAAAG 57.658 34.615 0.00 0.00 0.00 2.62
854 1070 8.164070 AGAAATTAACTAGGAGCCAAAGAAAGA 58.836 33.333 0.00 0.00 0.00 2.52
872 1090 0.253610 GACCAGACGGGAGAGAGAGA 59.746 60.000 0.00 0.00 41.15 3.10
953 1171 2.124695 GAAAGCCCTACAGCCCGG 60.125 66.667 0.00 0.00 0.00 5.73
979 1197 2.109181 CGGCGAAGGGGAAGATCC 59.891 66.667 0.00 0.00 35.23 3.36
1009 1227 0.674581 CAAGACGAAGATGGCTGGCA 60.675 55.000 6.31 6.31 0.00 4.92
1056 1283 3.735029 ACGTCGCCTGAGGTCGAC 61.735 66.667 27.04 27.04 43.32 4.20
1101 1328 2.813901 GAGAGCAGCGCCTCATCT 59.186 61.111 14.84 8.79 34.26 2.90
1175 1402 1.471829 GGGGCCTTTGTTCTTGGTGG 61.472 60.000 0.84 0.00 0.00 4.61
1178 1405 1.484653 GGCCTTTGTTCTTGGTGGTTT 59.515 47.619 0.00 0.00 0.00 3.27
1204 1431 0.749649 CTGGGAGGAAGATGACGAGG 59.250 60.000 0.00 0.00 0.00 4.63
1206 1433 1.036707 GGGAGGAAGATGACGAGGAG 58.963 60.000 0.00 0.00 0.00 3.69
1286 1513 1.214589 CGACGGAGGAAATCGGTGT 59.785 57.895 0.00 0.00 41.20 4.16
1287 1514 0.389426 CGACGGAGGAAATCGGTGTT 60.389 55.000 0.00 0.00 41.20 3.32
1291 1518 0.168128 GGAGGAAATCGGTGTTTGCG 59.832 55.000 0.00 0.00 34.98 4.85
1326 1556 5.337652 CCGGAAGAACAAGAAGGAATAGACT 60.338 44.000 0.00 0.00 0.00 3.24
1342 1572 6.240176 GGAATAGACTAGGAGAGATGAGAGGT 60.240 46.154 0.00 0.00 0.00 3.85
1379 1610 7.717875 TCCTGTAATTAATGTAATTTCTCGGGG 59.282 37.037 0.00 0.00 39.06 5.73
1394 1625 1.732308 GGGGGTAGCTCGTAGTTCG 59.268 63.158 0.00 0.00 41.41 3.95
1420 1651 0.325110 CAGCCCTCTCCTTCCTCTCA 60.325 60.000 0.00 0.00 0.00 3.27
1421 1652 0.415429 AGCCCTCTCCTTCCTCTCAA 59.585 55.000 0.00 0.00 0.00 3.02
1438 1669 0.249073 CAACGGGAGGAGTCGCTATG 60.249 60.000 0.00 0.00 33.42 2.23
1453 1684 4.570772 GTCGCTATGGATCTTTGCTGTAAA 59.429 41.667 0.00 0.00 0.00 2.01
1488 1719 7.266922 TGTGTTAAGAATTTACTGGTTGGTC 57.733 36.000 0.00 0.00 0.00 4.02
1541 1780 4.853924 TTCTCTTCTGAATTGGTTTGGC 57.146 40.909 0.00 0.00 0.00 4.52
1542 1781 4.104383 TCTCTTCTGAATTGGTTTGGCT 57.896 40.909 0.00 0.00 0.00 4.75
1551 1790 3.806949 ATTGGTTTGGCTCCAGACTTA 57.193 42.857 9.11 0.00 36.28 2.24
1554 1793 4.487714 TGGTTTGGCTCCAGACTTATAG 57.512 45.455 9.11 0.00 32.48 1.31
1569 1808 1.037493 TATAGCCCCGTACTGTGCTG 58.963 55.000 4.58 0.00 35.34 4.41
1672 1911 3.122850 CCATGGATTCCGCTTGGC 58.877 61.111 5.56 0.00 0.00 4.52
1682 1921 3.558411 CGCTTGGCAGCTCGCTAC 61.558 66.667 7.85 0.00 44.85 3.58
1809 2049 7.812648 TCTATTCGTGAAATTTGGTGTTTAGG 58.187 34.615 0.00 0.00 0.00 2.69
1837 2077 0.462225 TTTGGAAACGACGAGGTGCA 60.462 50.000 0.00 0.00 0.00 4.57
1888 2128 4.022589 AGCAGAAATGTTTGATCTGTGTGG 60.023 41.667 4.19 0.00 42.00 4.17
1891 2131 2.291209 ATGTTTGATCTGTGTGGGCA 57.709 45.000 0.00 0.00 0.00 5.36
1892 2132 1.608055 TGTTTGATCTGTGTGGGCAG 58.392 50.000 0.00 0.00 37.81 4.85
1897 2137 2.745698 TCTGTGTGGGCAGAGCAG 59.254 61.111 0.00 0.00 40.23 4.24
1898 2138 1.838396 TCTGTGTGGGCAGAGCAGA 60.838 57.895 0.00 0.00 40.23 4.26
1899 2139 1.670406 CTGTGTGGGCAGAGCAGAC 60.670 63.158 0.00 0.00 38.70 3.51
1900 2140 2.109517 CTGTGTGGGCAGAGCAGACT 62.110 60.000 0.00 0.00 38.70 3.24
1901 2141 1.670406 GTGTGGGCAGAGCAGACTG 60.670 63.158 0.00 0.00 40.43 3.51
1914 2154 3.736530 GCAGACTGCACAGAAATGTAG 57.263 47.619 22.62 0.00 44.26 2.74
1915 2155 3.329386 GCAGACTGCACAGAAATGTAGA 58.671 45.455 22.62 0.00 44.26 2.59
1916 2156 3.937706 GCAGACTGCACAGAAATGTAGAT 59.062 43.478 22.62 0.00 44.26 1.98
1917 2157 4.033817 GCAGACTGCACAGAAATGTAGATC 59.966 45.833 22.62 0.00 44.26 2.75
1918 2158 5.173664 CAGACTGCACAGAAATGTAGATCA 58.826 41.667 4.31 0.00 35.98 2.92
1919 2159 5.291371 CAGACTGCACAGAAATGTAGATCAG 59.709 44.000 4.31 0.00 35.98 2.90
1920 2160 5.046735 AGACTGCACAGAAATGTAGATCAGT 60.047 40.000 4.31 0.00 35.98 3.41
1921 2161 6.153510 AGACTGCACAGAAATGTAGATCAGTA 59.846 38.462 4.31 0.00 35.98 2.74
1922 2162 6.336566 ACTGCACAGAAATGTAGATCAGTAG 58.663 40.000 4.31 0.00 35.98 2.57
1923 2163 6.153510 ACTGCACAGAAATGTAGATCAGTAGA 59.846 38.462 4.31 0.00 35.98 2.59
1924 2164 7.117285 TGCACAGAAATGTAGATCAGTAGAT 57.883 36.000 0.00 0.00 37.13 1.98
1925 2165 8.237811 TGCACAGAAATGTAGATCAGTAGATA 57.762 34.615 0.00 0.00 33.72 1.98
1926 2166 8.864087 TGCACAGAAATGTAGATCAGTAGATAT 58.136 33.333 0.00 0.00 33.72 1.63
1927 2167 9.138062 GCACAGAAATGTAGATCAGTAGATATG 57.862 37.037 0.00 0.00 33.72 1.78
1928 2168 9.636879 CACAGAAATGTAGATCAGTAGATATGG 57.363 37.037 0.00 0.00 33.72 2.74
1929 2169 9.373450 ACAGAAATGTAGATCAGTAGATATGGT 57.627 33.333 0.00 0.00 33.72 3.55
1930 2170 9.636879 CAGAAATGTAGATCAGTAGATATGGTG 57.363 37.037 0.00 0.00 33.72 4.17
1931 2171 8.811017 AGAAATGTAGATCAGTAGATATGGTGG 58.189 37.037 0.00 0.00 33.72 4.61
1932 2172 8.727100 AAATGTAGATCAGTAGATATGGTGGA 57.273 34.615 0.00 0.00 33.72 4.02
1933 2173 7.710676 ATGTAGATCAGTAGATATGGTGGAC 57.289 40.000 0.00 0.00 33.72 4.02
2187 2433 9.796120 GACTGATATGAGGCTACAGATAAATAC 57.204 37.037 0.00 0.00 33.53 1.89
2188 2434 9.540538 ACTGATATGAGGCTACAGATAAATACT 57.459 33.333 0.00 0.00 33.53 2.12
2190 2436 8.972127 TGATATGAGGCTACAGATAAATACTCC 58.028 37.037 0.00 0.00 0.00 3.85
2191 2437 9.196139 GATATGAGGCTACAGATAAATACTCCT 57.804 37.037 0.00 0.00 0.00 3.69
2284 2530 1.670949 GCAGCCAGAGAGATCGACCA 61.671 60.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.239400 GGTCTTTTCTGGTCCCAAAGG 58.761 52.381 5.77 0.00 0.00 3.11
30 31 2.944129 TGGTCTTTTCTGGTCCCAAAG 58.056 47.619 0.00 0.00 0.00 2.77
35 36 2.879103 TGGATGGTCTTTTCTGGTCC 57.121 50.000 0.00 0.00 0.00 4.46
103 104 3.849574 TCATGGAGGGTAAGGTCATTGAA 59.150 43.478 0.00 0.00 0.00 2.69
119 122 0.190815 TCATCTCGGGGGATCATGGA 59.809 55.000 0.00 0.00 0.00 3.41
154 292 1.134371 GTTGCATCCTCCTACCCAGTC 60.134 57.143 0.00 0.00 0.00 3.51
181 319 5.760131 AGAGCACCATAGCCTTTTAGAAAT 58.240 37.500 0.00 0.00 34.23 2.17
198 336 3.303406 GAATGCAGTGTTTGAAGAGCAC 58.697 45.455 0.00 0.00 39.52 4.40
205 343 4.734398 AACAAAGGAATGCAGTGTTTGA 57.266 36.364 19.86 0.00 33.31 2.69
223 393 3.157881 CTCGCCATCTCTATCCCTAACA 58.842 50.000 0.00 0.00 0.00 2.41
227 397 0.252012 CCCTCGCCATCTCTATCCCT 60.252 60.000 0.00 0.00 0.00 4.20
232 402 1.215673 ACTTCTCCCTCGCCATCTCTA 59.784 52.381 0.00 0.00 0.00 2.43
236 406 1.330655 TGGACTTCTCCCTCGCCATC 61.331 60.000 0.00 0.00 35.34 3.51
241 411 0.171455 CTCGTTGGACTTCTCCCTCG 59.829 60.000 0.00 0.00 35.34 4.63
255 425 1.822506 TCGGTCATCTCAGACTCGTT 58.177 50.000 0.00 0.00 38.57 3.85
270 441 6.927416 TGTAACTCAACACAATACTATCGGT 58.073 36.000 0.00 0.00 0.00 4.69
294 468 5.657826 TGCATGTGCTAATTGTAATTGGT 57.342 34.783 6.55 0.00 42.66 3.67
315 489 9.158364 GTTATCGCTAAATATGTCATGTTGTTG 57.842 33.333 0.00 0.00 0.00 3.33
342 518 0.249699 TCAACGGCGTCACACTCATT 60.250 50.000 15.17 0.00 0.00 2.57
347 545 0.996727 GCAATTCAACGGCGTCACAC 60.997 55.000 15.17 0.00 0.00 3.82
350 548 0.317436 GTTGCAATTCAACGGCGTCA 60.317 50.000 15.17 1.26 44.71 4.35
351 549 2.420097 GTTGCAATTCAACGGCGTC 58.580 52.632 15.17 0.00 44.71 5.19
352 550 4.626225 GTTGCAATTCAACGGCGT 57.374 50.000 6.77 6.77 44.71 5.68
358 556 4.983538 CACAATACAGCAGTTGCAATTCAA 59.016 37.500 0.59 0.00 45.16 2.69
359 557 4.037803 ACACAATACAGCAGTTGCAATTCA 59.962 37.500 0.59 0.00 45.16 2.57
360 558 4.549458 ACACAATACAGCAGTTGCAATTC 58.451 39.130 0.59 0.00 45.16 2.17
361 559 4.279169 AGACACAATACAGCAGTTGCAATT 59.721 37.500 0.59 0.00 45.16 2.32
362 560 3.822735 AGACACAATACAGCAGTTGCAAT 59.177 39.130 0.59 0.00 45.16 3.56
363 561 3.213506 AGACACAATACAGCAGTTGCAA 58.786 40.909 6.90 0.00 45.16 4.08
364 562 2.807967 GAGACACAATACAGCAGTTGCA 59.192 45.455 6.90 0.00 45.16 4.08
365 563 2.160417 GGAGACACAATACAGCAGTTGC 59.840 50.000 0.00 0.00 42.49 4.17
366 564 2.744202 GGGAGACACAATACAGCAGTTG 59.256 50.000 0.00 0.00 0.00 3.16
367 565 2.639839 AGGGAGACACAATACAGCAGTT 59.360 45.455 0.00 0.00 0.00 3.16
368 566 2.260822 AGGGAGACACAATACAGCAGT 58.739 47.619 0.00 0.00 0.00 4.40
369 567 3.739519 GCTAGGGAGACACAATACAGCAG 60.740 52.174 0.00 0.00 0.00 4.24
370 568 2.168521 GCTAGGGAGACACAATACAGCA 59.831 50.000 0.00 0.00 0.00 4.41
371 569 2.483889 GGCTAGGGAGACACAATACAGC 60.484 54.545 0.00 0.00 0.00 4.40
372 570 2.223829 CGGCTAGGGAGACACAATACAG 60.224 54.545 0.00 0.00 0.00 2.74
381 579 0.468400 ATCCAGACGGCTAGGGAGAC 60.468 60.000 3.42 0.00 31.96 3.36
387 585 3.366070 CCGTTACATATCCAGACGGCTAG 60.366 52.174 0.00 0.00 45.40 3.42
398 596 3.425577 TCGTGGTCACCGTTACATATC 57.574 47.619 0.00 0.00 0.00 1.63
415 613 7.491696 GCCTAGTTTAACACTCATTCTTATCGT 59.508 37.037 0.00 0.00 36.88 3.73
425 623 4.312443 CTTTCGGCCTAGTTTAACACTCA 58.688 43.478 0.00 0.00 36.88 3.41
426 624 3.124806 GCTTTCGGCCTAGTTTAACACTC 59.875 47.826 0.00 0.00 34.09 3.51
441 639 0.318869 TGCATGCAACTTGCTTTCGG 60.319 50.000 20.30 0.00 45.31 4.30
442 640 1.489574 TTGCATGCAACTTGCTTTCG 58.510 45.000 28.80 2.35 45.31 3.46
460 658 8.052748 ACCATTACTTGTGGTCATGTATATGTT 58.947 33.333 0.00 0.00 46.79 2.71
487 685 3.044986 CCGCTGCAAATATTTTCCGATG 58.955 45.455 0.00 0.00 0.00 3.84
518 717 0.778815 GTGCTTGAAGTCGTCACTCG 59.221 55.000 0.00 0.00 35.39 4.18
525 724 2.222289 CGATACGTTGTGCTTGAAGTCG 60.222 50.000 0.00 0.00 0.00 4.18
538 737 4.576873 AGATCAGACAGTCATCGATACGTT 59.423 41.667 2.66 0.00 0.00 3.99
584 783 2.974794 TCCAGTGCATAGCATATCCAGT 59.025 45.455 0.00 0.00 41.91 4.00
592 791 1.202842 CCATCCATCCAGTGCATAGCA 60.203 52.381 0.00 0.00 35.60 3.49
607 806 1.024579 ACATCGTTTGGCGTCCATCC 61.025 55.000 0.00 0.00 42.13 3.51
616 815 1.172180 ACACCTGCCACATCGTTTGG 61.172 55.000 0.00 0.00 37.17 3.28
618 817 0.465460 ACACACCTGCCACATCGTTT 60.465 50.000 0.00 0.00 0.00 3.60
619 818 1.148273 ACACACCTGCCACATCGTT 59.852 52.632 0.00 0.00 0.00 3.85
628 827 0.751643 AACTCCCAACACACACCTGC 60.752 55.000 0.00 0.00 0.00 4.85
629 828 1.024271 CAACTCCCAACACACACCTG 58.976 55.000 0.00 0.00 0.00 4.00
630 829 0.106719 CCAACTCCCAACACACACCT 60.107 55.000 0.00 0.00 0.00 4.00
632 831 0.106918 TCCCAACTCCCAACACACAC 60.107 55.000 0.00 0.00 0.00 3.82
633 832 0.106918 GTCCCAACTCCCAACACACA 60.107 55.000 0.00 0.00 0.00 3.72
634 833 1.164041 CGTCCCAACTCCCAACACAC 61.164 60.000 0.00 0.00 0.00 3.82
635 834 1.147376 CGTCCCAACTCCCAACACA 59.853 57.895 0.00 0.00 0.00 3.72
636 835 2.258726 GCGTCCCAACTCCCAACAC 61.259 63.158 0.00 0.00 0.00 3.32
637 836 2.112297 GCGTCCCAACTCCCAACA 59.888 61.111 0.00 0.00 0.00 3.33
638 837 2.999739 TTCGCGTCCCAACTCCCAAC 63.000 60.000 5.77 0.00 0.00 3.77
639 838 2.809307 TTCGCGTCCCAACTCCCAA 61.809 57.895 5.77 0.00 0.00 4.12
642 841 3.110178 CGTTCGCGTCCCAACTCC 61.110 66.667 5.77 0.00 35.57 3.85
666 865 3.135712 AGGTTCACACATGTACTCCACAA 59.864 43.478 0.00 0.00 41.55 3.33
667 866 2.703536 AGGTTCACACATGTACTCCACA 59.296 45.455 0.00 0.00 42.69 4.17
669 868 3.495983 CCAAGGTTCACACATGTACTCCA 60.496 47.826 0.00 0.00 0.00 3.86
670 869 3.074412 CCAAGGTTCACACATGTACTCC 58.926 50.000 0.00 0.00 0.00 3.85
671 870 3.740115 ACCAAGGTTCACACATGTACTC 58.260 45.455 0.00 0.00 0.00 2.59
672 871 3.135712 TGACCAAGGTTCACACATGTACT 59.864 43.478 0.00 0.00 0.00 2.73
673 872 3.472652 TGACCAAGGTTCACACATGTAC 58.527 45.455 0.00 0.00 0.00 2.90
717 928 6.552725 TGGGTGGCTTGCATTAATATCATTAA 59.447 34.615 0.00 0.00 0.00 1.40
798 1009 5.010012 CCTTTGCTTTTGAAGAGAAGGCTTA 59.990 40.000 0.00 0.00 36.21 3.09
851 1067 0.699399 TCTCTCTCCCGTCTGGTCTT 59.301 55.000 0.00 0.00 34.77 3.01
852 1068 0.254747 CTCTCTCTCCCGTCTGGTCT 59.745 60.000 0.00 0.00 34.77 3.85
853 1069 0.253610 TCTCTCTCTCCCGTCTGGTC 59.746 60.000 0.00 0.00 34.77 4.02
854 1070 0.254747 CTCTCTCTCTCCCGTCTGGT 59.745 60.000 0.00 0.00 34.77 4.00
872 1090 1.306997 TGATTTCGCCTCCTCCCCT 60.307 57.895 0.00 0.00 0.00 4.79
1096 1323 3.157252 GGAGGAGCCGCCAGATGA 61.157 66.667 4.27 0.00 40.02 2.92
1153 1380 1.228429 CAAGAACAAAGGCCCCCGA 60.228 57.895 0.00 0.00 0.00 5.14
1164 1391 1.065345 TCCACGAAACCACCAAGAACA 60.065 47.619 0.00 0.00 0.00 3.18
1175 1402 0.395312 TTCCTCCCAGTCCACGAAAC 59.605 55.000 0.00 0.00 0.00 2.78
1178 1405 0.041238 ATCTTCCTCCCAGTCCACGA 59.959 55.000 0.00 0.00 0.00 4.35
1226 1453 1.883084 CGGTAGCGATTCACCCTGC 60.883 63.158 9.07 0.00 0.00 4.85
1231 1458 0.249489 ATCAGGCGGTAGCGATTCAC 60.249 55.000 20.16 0.00 46.35 3.18
1236 1463 2.782222 GGTGATCAGGCGGTAGCGA 61.782 63.158 20.16 0.00 46.35 4.93
1326 1556 2.445145 CCCTCACCTCTCATCTCTCCTA 59.555 54.545 0.00 0.00 0.00 2.94
1342 1572 1.681229 ATTACAGGAAAGCCCCCTCA 58.319 50.000 0.00 0.00 34.66 3.86
1394 1625 4.219999 GGAGAGGGCTGCGAGCTC 62.220 72.222 2.73 2.73 43.65 4.09
1399 1630 3.080121 AGGAAGGAGAGGGCTGCG 61.080 66.667 0.00 0.00 37.57 5.18
1420 1651 1.392710 CCATAGCGACTCCTCCCGTT 61.393 60.000 0.00 0.00 0.00 4.44
1421 1652 1.828660 CCATAGCGACTCCTCCCGT 60.829 63.158 0.00 0.00 0.00 5.28
1438 1669 7.150783 AGATGAAGTTTTACAGCAAAGATCC 57.849 36.000 0.00 0.00 0.00 3.36
1477 1708 0.541063 TCAGCTCCGACCAACCAGTA 60.541 55.000 0.00 0.00 0.00 2.74
1541 1780 1.705873 ACGGGGCTATAAGTCTGGAG 58.294 55.000 0.00 0.00 0.00 3.86
1542 1781 2.176364 AGTACGGGGCTATAAGTCTGGA 59.824 50.000 0.00 0.00 0.00 3.86
1551 1790 1.823295 CAGCACAGTACGGGGCTAT 59.177 57.895 22.63 0.00 34.25 2.97
1569 1808 1.663173 GCCGAGATCCAGACTAGGC 59.337 63.158 0.00 0.00 45.40 3.93
1693 1932 2.406616 GGCATCGATTGTTGGCCGT 61.407 57.895 7.84 0.00 35.06 5.68
1695 1934 1.728490 GGAGGCATCGATTGTTGGCC 61.728 60.000 14.25 14.25 44.92 5.36
1724 1963 7.920682 CGCCTGGAAATGCTTAATTACTAAAAT 59.079 33.333 0.00 0.00 0.00 1.82
1809 2049 4.344448 TCGTCGTTTCCAAATCAAACAAC 58.656 39.130 0.00 0.00 33.99 3.32
1837 2077 0.179018 GAGTCCCAAACCAGTGCAGT 60.179 55.000 0.00 0.00 0.00 4.40
1891 2131 2.224475 ACATTTCTGTGCAGTCTGCTCT 60.224 45.455 24.76 3.28 45.31 4.09
1892 2132 2.149578 ACATTTCTGTGCAGTCTGCTC 58.850 47.619 24.76 21.25 45.31 4.26
1894 2134 3.329386 TCTACATTTCTGTGCAGTCTGC 58.671 45.455 18.32 18.32 45.29 4.26
1895 2135 5.173664 TGATCTACATTTCTGTGCAGTCTG 58.826 41.667 0.00 0.00 36.79 3.51
1896 2136 5.046735 ACTGATCTACATTTCTGTGCAGTCT 60.047 40.000 0.00 0.00 36.79 3.24
1897 2137 5.174395 ACTGATCTACATTTCTGTGCAGTC 58.826 41.667 0.00 0.00 36.79 3.51
1898 2138 5.157940 ACTGATCTACATTTCTGTGCAGT 57.842 39.130 0.00 0.00 36.79 4.40
1899 2139 6.567959 TCTACTGATCTACATTTCTGTGCAG 58.432 40.000 0.00 0.00 36.79 4.41
1900 2140 6.530019 TCTACTGATCTACATTTCTGTGCA 57.470 37.500 0.00 0.00 36.79 4.57
1901 2141 9.138062 CATATCTACTGATCTACATTTCTGTGC 57.862 37.037 0.00 0.00 34.23 4.57
1902 2142 9.636879 CCATATCTACTGATCTACATTTCTGTG 57.363 37.037 0.00 0.00 34.23 3.66
1903 2143 9.373450 ACCATATCTACTGATCTACATTTCTGT 57.627 33.333 0.00 0.00 35.49 3.41
1904 2144 9.636879 CACCATATCTACTGATCTACATTTCTG 57.363 37.037 0.00 0.00 34.32 3.02
1905 2145 8.811017 CCACCATATCTACTGATCTACATTTCT 58.189 37.037 0.00 0.00 34.32 2.52
1906 2146 8.807118 TCCACCATATCTACTGATCTACATTTC 58.193 37.037 0.00 0.00 34.32 2.17
1907 2147 8.589338 GTCCACCATATCTACTGATCTACATTT 58.411 37.037 0.00 0.00 34.32 2.32
1908 2148 7.094162 CGTCCACCATATCTACTGATCTACATT 60.094 40.741 0.00 0.00 34.32 2.71
1909 2149 6.375736 CGTCCACCATATCTACTGATCTACAT 59.624 42.308 0.00 0.00 34.32 2.29
1910 2150 5.705905 CGTCCACCATATCTACTGATCTACA 59.294 44.000 0.00 0.00 34.32 2.74
1911 2151 5.392165 GCGTCCACCATATCTACTGATCTAC 60.392 48.000 0.00 0.00 34.32 2.59
1912 2152 4.700692 GCGTCCACCATATCTACTGATCTA 59.299 45.833 0.00 0.00 34.32 1.98
1913 2153 3.508012 GCGTCCACCATATCTACTGATCT 59.492 47.826 0.00 0.00 34.32 2.75
1914 2154 3.367498 GGCGTCCACCATATCTACTGATC 60.367 52.174 0.00 0.00 34.32 2.92
1915 2155 2.563179 GGCGTCCACCATATCTACTGAT 59.437 50.000 0.00 0.00 36.74 2.90
1916 2156 1.961394 GGCGTCCACCATATCTACTGA 59.039 52.381 0.00 0.00 0.00 3.41
1917 2157 1.964223 AGGCGTCCACCATATCTACTG 59.036 52.381 0.00 0.00 0.00 2.74
1918 2158 2.383442 AGGCGTCCACCATATCTACT 57.617 50.000 0.00 0.00 0.00 2.57
1919 2159 4.495422 CATTAGGCGTCCACCATATCTAC 58.505 47.826 0.00 0.00 0.00 2.59
1920 2160 3.513912 CCATTAGGCGTCCACCATATCTA 59.486 47.826 0.00 0.00 0.00 1.98
1921 2161 2.303022 CCATTAGGCGTCCACCATATCT 59.697 50.000 0.00 0.00 0.00 1.98
1922 2162 2.699954 CCATTAGGCGTCCACCATATC 58.300 52.381 0.00 0.00 0.00 1.63
1923 2163 2.859165 CCATTAGGCGTCCACCATAT 57.141 50.000 0.00 0.00 0.00 1.78
2108 2348 2.853235 AGGAAAGGAAACCCACGTAG 57.147 50.000 0.00 0.00 0.00 3.51
2284 2530 5.010282 ACAAAGACCAGTTTCAAACAGTCT 58.990 37.500 16.42 16.42 44.26 3.24


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

AutoCloner maintained by Alex Coulton.