Multiple sequence alignment - TraesCS4A01G073800

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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 TraesCS4A01G073800 chr4A 100.000 3834 0 0 1 3834 72926183 72922350 0 7081
1 TraesCS4A01G073800 chr4B 90.695 3858 223 65 28 3834 480926644 480922872 0 5011
2 TraesCS4A01G073800 chr4D 93.845 2177 109 15 1670 3834 391038888 391036725 0 3254
3 TraesCS4A01G073800 chr4D 89.254 1675 94 34 13 1667 391040678 391039070 0 2017


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 TraesCS4A01G073800 chr4A 72922350 72926183 3833 True 7081.0 7081 100.0000 1 3834 1 chr4A.!!$R1 3833
1 TraesCS4A01G073800 chr4B 480922872 480926644 3772 True 5011.0 5011 90.6950 28 3834 1 chr4B.!!$R1 3806
2 TraesCS4A01G073800 chr4D 391036725 391040678 3953 True 2635.5 3254 91.5495 13 3834 2 chr4D.!!$R1 3821

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
595 608 0.108615 AGCGCCACAAGTAGTAGCAG 60.109 55.0 2.29 0.0 34.26 4.24 F
1205 1227 0.032130 GTGCGCGATGATCCTTCCTA 59.968 55.0 12.10 0.0 0.00 2.94 F
1490 1515 0.526211 GGGGATTCTTCGTTGTTGGC 59.474 55.0 0.00 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1579 0.174845 CGGTGAGGCCATTCTCGTAA 59.825 55.000 5.01 0.0 36.61 3.18 R
2781 3001 1.134175 AGTGGTTTGTTTTGTGCGAGG 59.866 47.619 0.00 0.0 0.00 4.63 R
3394 3633 0.833287 GGGCCTCTGCAATCTGAGTA 59.167 55.000 0.84 0.0 40.13 2.59 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
22 23 0.678366 ACACCACACGGCAACTTCAA 60.678 50.000 0.00 0.00 34.57 2.69
36 37 6.134061 GGCAACTTCAACTTTTAACTCGTAG 58.866 40.000 0.00 0.00 0.00 3.51
37 38 6.018507 GGCAACTTCAACTTTTAACTCGTAGA 60.019 38.462 0.00 0.00 0.00 2.59
39 40 7.583040 GCAACTTCAACTTTTAACTCGTAGAAG 59.417 37.037 0.00 0.00 34.09 2.85
42 43 9.374838 ACTTCAACTTTTAACTCGTAGAAGAAA 57.625 29.630 0.00 0.00 34.09 2.52
43 44 9.634300 CTTCAACTTTTAACTCGTAGAAGAAAC 57.366 33.333 0.00 0.00 34.09 2.78
44 45 7.834529 TCAACTTTTAACTCGTAGAAGAAACG 58.165 34.615 0.00 0.00 41.64 3.60
45 46 7.489113 TCAACTTTTAACTCGTAGAAGAAACGT 59.511 33.333 0.00 0.00 41.08 3.99
46 47 8.745837 CAACTTTTAACTCGTAGAAGAAACGTA 58.254 33.333 0.00 0.00 41.08 3.57
110 112 0.690762 TGGCCAGTTCTTACCTGACC 59.309 55.000 0.00 0.00 33.48 4.02
130 132 3.842923 GCTGCGAGCTCTGGCCTA 61.843 66.667 12.85 0.00 38.45 3.93
150 152 1.511887 CCAAGAAAACGCCGCGATG 60.512 57.895 21.79 0.73 0.00 3.84
274 279 3.059352 AGCTTGGCGTCAGTAAGAAAT 57.941 42.857 0.00 0.00 0.00 2.17
279 284 3.585862 TGGCGTCAGTAAGAAATGAGTC 58.414 45.455 0.00 0.00 0.00 3.36
287 292 7.063074 CGTCAGTAAGAAATGAGTCCGTAAAAT 59.937 37.037 0.00 0.00 0.00 1.82
293 298 4.434713 AATGAGTCCGTAAAATTGCACC 57.565 40.909 0.00 0.00 0.00 5.01
294 299 1.801771 TGAGTCCGTAAAATTGCACCG 59.198 47.619 0.00 0.00 0.00 4.94
295 300 1.129811 GAGTCCGTAAAATTGCACCGG 59.870 52.381 0.00 0.00 39.98 5.28
296 301 1.158434 GTCCGTAAAATTGCACCGGA 58.842 50.000 9.46 0.00 44.74 5.14
297 302 1.444836 TCCGTAAAATTGCACCGGAG 58.555 50.000 9.46 0.00 42.33 4.63
298 303 1.002201 TCCGTAAAATTGCACCGGAGA 59.998 47.619 9.46 0.00 42.33 3.71
299 304 1.396996 CCGTAAAATTGCACCGGAGAG 59.603 52.381 9.46 0.00 41.08 3.20
319 324 0.108992 CGGAGATCCACGAAACGGAA 60.109 55.000 0.69 0.00 35.77 4.30
342 347 2.615869 GCCCGTACGTAACATGGTTTA 58.384 47.619 15.21 0.00 0.00 2.01
343 348 2.348362 GCCCGTACGTAACATGGTTTAC 59.652 50.000 15.21 0.00 0.00 2.01
350 355 4.056452 CGTAACATGGTTTACGTGAACC 57.944 45.455 29.81 29.81 46.00 3.62
351 356 3.120580 CGTAACATGGTTTACGTGAACCC 60.121 47.826 32.15 18.22 46.85 4.11
352 357 2.943036 ACATGGTTTACGTGAACCCT 57.057 45.000 32.15 23.21 46.85 4.34
353 358 4.354893 AACATGGTTTACGTGAACCCTA 57.645 40.909 32.15 19.38 46.85 3.53
355 360 5.680594 ACATGGTTTACGTGAACCCTATA 57.319 39.130 32.15 18.41 46.85 1.31
357 362 7.364149 ACATGGTTTACGTGAACCCTATATA 57.636 36.000 32.15 17.44 46.85 0.86
358 363 7.212274 ACATGGTTTACGTGAACCCTATATAC 58.788 38.462 32.15 11.24 46.85 1.47
359 364 7.070322 ACATGGTTTACGTGAACCCTATATACT 59.930 37.037 32.15 10.42 46.85 2.12
360 365 6.808829 TGGTTTACGTGAACCCTATATACTG 58.191 40.000 32.15 0.00 46.85 2.74
361 366 6.380846 TGGTTTACGTGAACCCTATATACTGT 59.619 38.462 32.15 0.00 46.85 3.55
362 367 7.559533 TGGTTTACGTGAACCCTATATACTGTA 59.440 37.037 32.15 11.95 46.85 2.74
363 368 7.862873 GGTTTACGTGAACCCTATATACTGTAC 59.137 40.741 27.23 1.45 42.63 2.90
364 369 8.624776 GTTTACGTGAACCCTATATACTGTACT 58.375 37.037 11.90 0.00 0.00 2.73
366 371 7.736447 ACGTGAACCCTATATACTGTACTAC 57.264 40.000 0.00 0.00 0.00 2.73
404 413 1.070643 GGTTTACGTGACGGGAAAACG 60.071 52.381 10.66 0.00 42.82 3.60
421 430 0.745845 ACGCATCCAAGTCATGAGCC 60.746 55.000 0.00 0.00 0.00 4.70
422 431 0.745486 CGCATCCAAGTCATGAGCCA 60.745 55.000 0.00 0.00 0.00 4.75
423 432 1.688772 GCATCCAAGTCATGAGCCAT 58.311 50.000 0.00 0.00 0.00 4.40
424 433 1.607628 GCATCCAAGTCATGAGCCATC 59.392 52.381 0.00 0.00 0.00 3.51
425 434 1.871676 CATCCAAGTCATGAGCCATCG 59.128 52.381 0.00 0.00 0.00 3.84
426 435 1.194218 TCCAAGTCATGAGCCATCGA 58.806 50.000 0.00 0.00 0.00 3.59
439 448 1.691127 CCATCGAATCGGATCAGTCG 58.309 55.000 1.76 4.58 34.85 4.18
459 468 1.116536 TCACCACCCGTGCAACTAGA 61.117 55.000 0.00 0.00 42.69 2.43
460 469 0.949105 CACCACCCGTGCAACTAGAC 60.949 60.000 0.00 0.00 35.18 2.59
472 481 0.248539 AACTAGACGCGCGAATCTCC 60.249 55.000 39.36 16.72 0.00 3.71
501 510 3.443045 GCGTGCCACATGGAAGGG 61.443 66.667 0.87 0.00 37.39 3.95
534 543 2.664971 CGTTATCCCGTCGCTGTAGATC 60.665 54.545 0.00 0.00 0.00 2.75
548 557 3.820467 CTGTAGATCAACAGCAACCCAAA 59.180 43.478 0.00 0.00 40.40 3.28
549 558 3.820467 TGTAGATCAACAGCAACCCAAAG 59.180 43.478 0.00 0.00 0.00 2.77
586 599 2.671177 CCGTCTCAAGCGCCACAAG 61.671 63.158 2.29 0.00 0.00 3.16
587 600 1.956170 CGTCTCAAGCGCCACAAGT 60.956 57.895 2.29 0.00 0.00 3.16
588 601 0.666274 CGTCTCAAGCGCCACAAGTA 60.666 55.000 2.29 0.00 0.00 2.24
589 602 1.071605 GTCTCAAGCGCCACAAGTAG 58.928 55.000 2.29 0.00 0.00 2.57
590 603 0.679505 TCTCAAGCGCCACAAGTAGT 59.320 50.000 2.29 0.00 0.00 2.73
591 604 1.890489 TCTCAAGCGCCACAAGTAGTA 59.110 47.619 2.29 0.00 0.00 1.82
592 605 2.094700 TCTCAAGCGCCACAAGTAGTAG 60.095 50.000 2.29 0.00 0.00 2.57
593 606 0.721718 CAAGCGCCACAAGTAGTAGC 59.278 55.000 2.29 0.00 0.00 3.58
594 607 0.320374 AAGCGCCACAAGTAGTAGCA 59.680 50.000 2.29 0.00 34.26 3.49
595 608 0.108615 AGCGCCACAAGTAGTAGCAG 60.109 55.000 2.29 0.00 34.26 4.24
675 688 3.612251 CCAATTGGGCAGGCAGAG 58.388 61.111 17.36 0.00 0.00 3.35
676 689 2.718073 CCAATTGGGCAGGCAGAGC 61.718 63.158 17.36 0.00 0.00 4.09
693 706 0.109153 AGCCAGACAGTGACATGCAA 59.891 50.000 0.00 0.00 0.00 4.08
694 707 1.171308 GCCAGACAGTGACATGCAAT 58.829 50.000 0.00 0.00 0.00 3.56
755 774 2.820037 CCCGCCTCCTCTTTTCGC 60.820 66.667 0.00 0.00 0.00 4.70
782 801 1.595093 ATTACGCTTGCAAGGCACCC 61.595 55.000 27.10 9.58 38.71 4.61
919 941 1.354155 CCGCTATATATCCGCGCGA 59.646 57.895 34.63 18.26 45.99 5.87
1205 1227 0.032130 GTGCGCGATGATCCTTCCTA 59.968 55.000 12.10 0.00 0.00 2.94
1253 1275 1.534595 GCCAGTAGGATCGTACTACGG 59.465 57.143 23.77 21.69 44.20 4.02
1298 1320 2.046314 AGGGTCGTTGCGATTGGG 60.046 61.111 0.00 0.00 38.42 4.12
1308 1330 2.195683 CGATTGGGTGGATGGGGG 59.804 66.667 0.00 0.00 0.00 5.40
1309 1331 2.382770 CGATTGGGTGGATGGGGGA 61.383 63.158 0.00 0.00 0.00 4.81
1310 1332 1.538666 GATTGGGTGGATGGGGGAG 59.461 63.158 0.00 0.00 0.00 4.30
1311 1333 2.011617 GATTGGGTGGATGGGGGAGG 62.012 65.000 0.00 0.00 0.00 4.30
1312 1334 2.522453 ATTGGGTGGATGGGGGAGGA 62.522 60.000 0.00 0.00 0.00 3.71
1313 1335 2.774351 GGGTGGATGGGGGAGGAG 60.774 72.222 0.00 0.00 0.00 3.69
1314 1336 2.042930 GGTGGATGGGGGAGGAGT 59.957 66.667 0.00 0.00 0.00 3.85
1315 1337 2.378634 GGTGGATGGGGGAGGAGTG 61.379 68.421 0.00 0.00 0.00 3.51
1316 1338 2.042762 TGGATGGGGGAGGAGTGG 59.957 66.667 0.00 0.00 0.00 4.00
1317 1339 2.372688 GGATGGGGGAGGAGTGGA 59.627 66.667 0.00 0.00 0.00 4.02
1318 1340 1.768077 GGATGGGGGAGGAGTGGAG 60.768 68.421 0.00 0.00 0.00 3.86
1319 1341 1.768077 GATGGGGGAGGAGTGGAGG 60.768 68.421 0.00 0.00 0.00 4.30
1320 1342 2.257541 GATGGGGGAGGAGTGGAGGA 62.258 65.000 0.00 0.00 0.00 3.71
1321 1343 2.365768 GGGGGAGGAGTGGAGGAC 60.366 72.222 0.00 0.00 0.00 3.85
1322 1344 2.781406 GGGGAGGAGTGGAGGACT 59.219 66.667 0.00 0.00 37.76 3.85
1323 1345 1.687493 GGGGAGGAGTGGAGGACTG 60.687 68.421 0.00 0.00 33.83 3.51
1324 1346 1.687493 GGGAGGAGTGGAGGACTGG 60.687 68.421 0.00 0.00 33.83 4.00
1325 1347 1.687493 GGAGGAGTGGAGGACTGGG 60.687 68.421 0.00 0.00 33.83 4.45
1326 1348 1.687493 GAGGAGTGGAGGACTGGGG 60.687 68.421 0.00 0.00 33.83 4.96
1338 1360 1.173913 GACTGGGGAATGAAAACCGG 58.826 55.000 0.00 0.00 35.48 5.28
1440 1462 2.717809 GCGTGCGTCTCCGAGTTTC 61.718 63.158 0.00 0.00 35.63 2.78
1482 1507 2.831333 CTGACTCATGGGGATTCTTCG 58.169 52.381 0.00 0.00 0.00 3.79
1490 1515 0.526211 GGGGATTCTTCGTTGTTGGC 59.474 55.000 0.00 0.00 0.00 4.52
1554 1579 1.597027 CTCCACCGGCGACAACTTT 60.597 57.895 9.30 0.00 0.00 2.66
1563 1588 2.410730 CGGCGACAACTTTTACGAGAAT 59.589 45.455 0.00 0.00 0.00 2.40
1572 1597 2.396590 TTTACGAGAATGGCCTCACC 57.603 50.000 3.32 0.00 39.84 4.02
1709 1915 4.728772 TCAGAGAAATGGGAAGCTTTTCA 58.271 39.130 0.00 2.51 32.94 2.69
1765 1976 5.637809 ACGTTTTTGTTCCTTTCAGTTCTC 58.362 37.500 0.00 0.00 0.00 2.87
1856 2067 6.493116 AGATTCGTTTGCATGAGATCATTTC 58.507 36.000 0.00 0.00 33.61 2.17
1875 2086 5.627499 TTTCTTGTCAATGCAGGTACATC 57.373 39.130 0.00 0.00 0.00 3.06
1892 2103 7.904977 CAGGTACATCGTCATATTTTGTTTGAG 59.095 37.037 0.00 0.00 0.00 3.02
1894 2105 6.252967 ACATCGTCATATTTTGTTTGAGCA 57.747 33.333 0.00 0.00 0.00 4.26
1895 2106 6.676950 ACATCGTCATATTTTGTTTGAGCAA 58.323 32.000 0.00 0.00 0.00 3.91
1983 2198 7.925483 AGAACAGCATAAGACTTGACTATCATC 59.075 37.037 0.00 0.00 0.00 2.92
2062 2277 1.550976 CTCAAGTACTGGACTCACCCC 59.449 57.143 0.00 0.00 37.44 4.95
2102 2317 3.760035 GAGGAGTGGCGCCTCGAA 61.760 66.667 29.70 3.37 40.30 3.71
2104 2319 2.815647 GGAGTGGCGCCTCGAAAG 60.816 66.667 29.70 0.00 31.98 2.62
2105 2320 2.815647 GAGTGGCGCCTCGAAAGG 60.816 66.667 29.70 0.00 46.44 3.11
2205 2420 6.658188 TTCACATCCCTTTTCCGTAAATTT 57.342 33.333 0.00 0.00 0.00 1.82
2397 2617 9.408731 GTTTTAAAAAGCACAGAAAAAGAATCG 57.591 29.630 1.31 0.00 0.00 3.34
2430 2650 3.756082 TTCATGCCCTTCCAGGTTAAT 57.244 42.857 0.00 0.00 31.93 1.40
2500 2720 2.072298 GCAGCAGAGACAGGTTAACAG 58.928 52.381 8.10 1.77 0.00 3.16
2524 2744 8.963130 CAGCGTTTGATAAACATTGTTCTTTTA 58.037 29.630 1.83 0.00 41.44 1.52
2543 2763 2.086054 AAGAACAGAGCAGTAAGGCG 57.914 50.000 0.00 0.00 39.27 5.52
2572 2792 6.662414 TTCACACTTGTTGAAGTTGTCTAG 57.338 37.500 0.00 0.00 40.68 2.43
2583 2803 3.611766 AGTTGTCTAGCCTTAACGCAT 57.388 42.857 0.00 0.00 0.00 4.73
2585 2805 3.000727 GTTGTCTAGCCTTAACGCATGT 58.999 45.455 0.00 0.00 0.00 3.21
2675 2895 6.100279 AGTCTACCAGCCAAATGATGATAAGA 59.900 38.462 0.00 0.00 0.00 2.10
2774 2994 4.124238 TGTTTCTGGGAAAGTCTTGTACG 58.876 43.478 0.00 0.00 0.00 3.67
2778 2998 3.640029 TCTGGGAAAGTCTTGTACGAGTT 59.360 43.478 10.00 0.00 0.00 3.01
2779 2999 4.100498 TCTGGGAAAGTCTTGTACGAGTTT 59.900 41.667 10.00 6.64 38.80 2.66
2781 3001 5.291971 TGGGAAAGTCTTGTACGAGTTTAC 58.708 41.667 10.00 7.26 36.85 2.01
2798 3018 3.423996 TTACCTCGCACAAAACAAACC 57.576 42.857 0.00 0.00 0.00 3.27
2873 3093 4.261801 GCAGGAGAATTAGTTTGGTAGCA 58.738 43.478 0.00 0.00 0.00 3.49
3049 3277 5.068198 GTCCATTGGTTCTGATGCATACATT 59.932 40.000 0.00 0.00 36.35 2.71
3229 3461 7.581213 TTCTTCAGCTTTCACAAATAAAGGA 57.419 32.000 0.00 0.00 35.04 3.36
3241 3473 7.607250 TCACAAATAAAGGACACTTGTTTGTT 58.393 30.769 15.46 5.50 44.79 2.83
3394 3633 3.511146 CAGGTCATGCATTAAGTTTGGGT 59.489 43.478 0.00 0.00 0.00 4.51
3507 3746 8.967664 TTACAAGTACCAGAATAACTTTGTGT 57.032 30.769 0.00 0.00 31.21 3.72
3516 3755 7.759433 ACCAGAATAACTTTGTGTCAAAAACTG 59.241 33.333 0.00 0.00 0.00 3.16
3518 3757 7.973388 CAGAATAACTTTGTGTCAAAAACTGGA 59.027 33.333 0.00 0.00 0.00 3.86
3532 3771 2.888834 ACTGGACAAATGTTGCCAAC 57.111 45.000 0.00 0.00 36.75 3.77
3546 3785 5.537188 TGTTGCCAACAAAATATCACTTCC 58.463 37.500 8.02 0.00 38.72 3.46
3591 3831 5.179368 CAGAATAACTCTGGCAAAAACTCGA 59.821 40.000 0.00 0.00 46.89 4.04
3607 3847 2.293399 ACTCGACAACCAAGAAAATGGC 59.707 45.455 0.00 0.00 44.75 4.40
3736 3976 7.614192 AGGAACGGTCTTCCATAATGTTTTAAT 59.386 33.333 0.00 0.00 41.00 1.40
3742 3982 8.135529 GGTCTTCCATAATGTTTTAATACCAGC 58.864 37.037 0.00 0.00 0.00 4.85
3757 3999 5.808366 ATACCAGCGAATCCATCTTAGAA 57.192 39.130 0.00 0.00 0.00 2.10
3803 4045 1.515521 CCAAAACTCTCCACGGCCAC 61.516 60.000 2.24 0.00 0.00 5.01
3804 4046 0.817634 CAAAACTCTCCACGGCCACA 60.818 55.000 2.24 0.00 0.00 4.17
3826 4068 4.282950 TCAGACGTAATGCTACCTAACG 57.717 45.455 0.00 0.00 39.37 3.18
3827 4069 2.787680 CAGACGTAATGCTACCTAACGC 59.212 50.000 0.00 0.00 37.07 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.196808 GAAGTTGCCGTGTGGTGTATG 59.803 52.381 0.00 0.00 37.67 2.39
2 3 0.178301 TGAAGTTGCCGTGTGGTGTA 59.822 50.000 0.00 0.00 37.67 2.90
3 4 0.678366 TTGAAGTTGCCGTGTGGTGT 60.678 50.000 0.00 0.00 37.67 4.16
4 5 0.248458 GTTGAAGTTGCCGTGTGGTG 60.248 55.000 0.00 0.00 37.67 4.17
5 6 0.393808 AGTTGAAGTTGCCGTGTGGT 60.394 50.000 0.00 0.00 37.67 4.16
6 7 0.738389 AAGTTGAAGTTGCCGTGTGG 59.262 50.000 0.00 0.00 38.77 4.17
7 8 2.559998 AAAGTTGAAGTTGCCGTGTG 57.440 45.000 0.00 0.00 0.00 3.82
8 9 4.157105 AGTTAAAAGTTGAAGTTGCCGTGT 59.843 37.500 0.00 0.00 0.00 4.49
9 10 4.668289 AGTTAAAAGTTGAAGTTGCCGTG 58.332 39.130 0.00 0.00 0.00 4.94
10 11 4.495184 CGAGTTAAAAGTTGAAGTTGCCGT 60.495 41.667 0.00 0.00 0.00 5.68
11 12 3.966218 CGAGTTAAAAGTTGAAGTTGCCG 59.034 43.478 0.00 0.00 0.00 5.69
43 44 0.316772 CCTCAGCGTCCACGTATACG 60.317 60.000 23.24 23.24 46.33 3.06
44 45 0.030369 CCCTCAGCGTCCACGTATAC 59.970 60.000 0.36 0.00 42.22 1.47
45 46 0.394762 ACCCTCAGCGTCCACGTATA 60.395 55.000 0.36 0.00 42.22 1.47
46 47 1.681327 ACCCTCAGCGTCCACGTAT 60.681 57.895 0.36 0.00 42.22 3.06
56 58 0.246086 CTGTCTCACTCACCCTCAGC 59.754 60.000 0.00 0.00 0.00 4.26
60 62 1.967066 CTGAACTGTCTCACTCACCCT 59.033 52.381 0.00 0.00 0.00 4.34
130 132 1.024579 ATCGCGGCGTTTTCTTGGAT 61.025 50.000 22.90 1.69 0.00 3.41
150 152 1.268352 CTGAGGCTCGCTAGTACATCC 59.732 57.143 10.42 0.00 0.00 3.51
274 279 1.801771 CGGTGCAATTTTACGGACTCA 59.198 47.619 0.00 0.00 0.00 3.41
279 284 1.396996 CTCTCCGGTGCAATTTTACGG 59.603 52.381 0.00 0.00 45.52 4.02
293 298 2.725008 GTGGATCTCCGCTCTCCG 59.275 66.667 2.48 0.00 43.02 4.63
294 299 1.384989 TTCGTGGATCTCCGCTCTCC 61.385 60.000 8.09 0.00 44.11 3.71
295 300 0.456221 TTTCGTGGATCTCCGCTCTC 59.544 55.000 8.09 0.00 44.11 3.20
296 301 0.173708 GTTTCGTGGATCTCCGCTCT 59.826 55.000 8.09 0.00 44.11 4.09
297 302 1.140407 CGTTTCGTGGATCTCCGCTC 61.140 60.000 8.09 0.00 44.11 5.03
298 303 1.153823 CGTTTCGTGGATCTCCGCT 60.154 57.895 8.09 0.00 44.11 5.52
299 304 2.165301 CCGTTTCGTGGATCTCCGC 61.165 63.158 0.00 0.00 42.91 5.54
319 324 0.179067 CCATGTTACGTACGGGCCAT 60.179 55.000 21.06 14.16 0.00 4.40
342 347 7.512992 AGTAGTACAGTATATAGGGTTCACGT 58.487 38.462 2.52 0.00 0.00 4.49
343 348 7.976135 AGTAGTACAGTATATAGGGTTCACG 57.024 40.000 2.52 0.00 0.00 4.35
357 362 8.149647 ACGATGAGCTTATAGTAGTAGTACAGT 58.850 37.037 10.33 1.00 0.00 3.55
358 363 8.436970 CACGATGAGCTTATAGTAGTAGTACAG 58.563 40.741 10.33 0.11 0.00 2.74
359 364 7.387122 CCACGATGAGCTTATAGTAGTAGTACA 59.613 40.741 10.33 0.00 0.00 2.90
360 365 7.387397 ACCACGATGAGCTTATAGTAGTAGTAC 59.613 40.741 3.95 0.00 0.00 2.73
361 366 7.448420 ACCACGATGAGCTTATAGTAGTAGTA 58.552 38.462 3.95 0.00 0.00 1.82
362 367 6.297582 ACCACGATGAGCTTATAGTAGTAGT 58.702 40.000 3.95 0.00 0.00 2.73
363 368 6.804770 ACCACGATGAGCTTATAGTAGTAG 57.195 41.667 3.95 0.00 0.00 2.57
364 369 7.578310 AAACCACGATGAGCTTATAGTAGTA 57.422 36.000 3.95 0.00 0.00 1.82
366 371 7.854934 GTAAACCACGATGAGCTTATAGTAG 57.145 40.000 3.95 0.14 0.00 2.57
404 413 1.607628 GATGGCTCATGACTTGGATGC 59.392 52.381 0.00 0.00 0.00 3.91
421 430 2.287009 TGACGACTGATCCGATTCGATG 60.287 50.000 7.83 0.00 35.45 3.84
422 431 1.947456 TGACGACTGATCCGATTCGAT 59.053 47.619 7.83 0.00 35.45 3.59
423 432 1.063616 GTGACGACTGATCCGATTCGA 59.936 52.381 7.83 0.00 35.45 3.71
424 433 1.467875 GTGACGACTGATCCGATTCG 58.532 55.000 0.00 0.00 37.50 3.34
425 434 1.134367 TGGTGACGACTGATCCGATTC 59.866 52.381 0.00 0.00 0.00 2.52
426 435 1.135083 GTGGTGACGACTGATCCGATT 60.135 52.381 0.00 0.00 0.00 3.34
459 468 2.023414 TATTGGGGAGATTCGCGCGT 62.023 55.000 30.98 12.05 0.00 6.01
460 469 0.878523 TTATTGGGGAGATTCGCGCG 60.879 55.000 26.76 26.76 0.00 6.86
472 481 0.529833 TGGCACGCATTGTTATTGGG 59.470 50.000 0.00 0.00 0.00 4.12
534 543 3.594134 TGTTTTCTTTGGGTTGCTGTTG 58.406 40.909 0.00 0.00 0.00 3.33
548 557 2.749621 GGCCACGATCATCTTGTTTTCT 59.250 45.455 0.00 0.00 0.00 2.52
549 558 2.476185 CGGCCACGATCATCTTGTTTTC 60.476 50.000 2.24 0.00 44.60 2.29
586 599 3.695060 TCTTCTGTGCTACCTGCTACTAC 59.305 47.826 0.00 0.00 43.37 2.73
587 600 3.964411 TCTTCTGTGCTACCTGCTACTA 58.036 45.455 0.00 0.00 43.37 1.82
588 601 2.808919 TCTTCTGTGCTACCTGCTACT 58.191 47.619 0.00 0.00 43.37 2.57
589 602 3.594603 TTCTTCTGTGCTACCTGCTAC 57.405 47.619 0.00 0.00 43.37 3.58
590 603 3.617531 GCTTTCTTCTGTGCTACCTGCTA 60.618 47.826 0.00 0.00 43.37 3.49
591 604 2.873649 GCTTTCTTCTGTGCTACCTGCT 60.874 50.000 0.00 0.00 43.37 4.24
592 605 1.466558 GCTTTCTTCTGTGCTACCTGC 59.533 52.381 0.00 0.00 43.25 4.85
593 606 2.740981 CTGCTTTCTTCTGTGCTACCTG 59.259 50.000 0.00 0.00 0.00 4.00
594 607 2.634940 TCTGCTTTCTTCTGTGCTACCT 59.365 45.455 0.00 0.00 0.00 3.08
595 608 3.045601 TCTGCTTTCTTCTGTGCTACC 57.954 47.619 0.00 0.00 0.00 3.18
604 617 1.620822 TGGGGCTTTCTGCTTTCTTC 58.379 50.000 0.00 0.00 42.39 2.87
608 621 0.833409 CCCTTGGGGCTTTCTGCTTT 60.833 55.000 0.00 0.00 42.39 3.51
625 638 1.116536 TTTCTTTTCCGGTTGGGCCC 61.117 55.000 17.59 17.59 35.24 5.80
633 646 1.586541 GCCAGCCTTTCTTTTCCGG 59.413 57.895 0.00 0.00 0.00 5.14
675 688 1.135489 CATTGCATGTCACTGTCTGGC 60.135 52.381 0.00 0.00 0.00 4.85
676 689 1.135489 GCATTGCATGTCACTGTCTGG 60.135 52.381 3.15 0.00 0.00 3.86
677 690 1.538075 TGCATTGCATGTCACTGTCTG 59.462 47.619 7.38 0.00 31.71 3.51
678 691 1.900245 TGCATTGCATGTCACTGTCT 58.100 45.000 7.38 0.00 31.71 3.41
679 692 2.710220 TTGCATTGCATGTCACTGTC 57.290 45.000 12.95 0.00 38.76 3.51
680 693 2.823747 AGATTGCATTGCATGTCACTGT 59.176 40.909 12.95 0.00 38.76 3.55
693 706 2.224450 TGCGAGATCATGGAGATTGCAT 60.224 45.455 0.00 0.00 37.00 3.96
694 707 1.139455 TGCGAGATCATGGAGATTGCA 59.861 47.619 0.00 0.00 37.00 4.08
695 708 1.875009 TGCGAGATCATGGAGATTGC 58.125 50.000 0.00 0.00 37.00 3.56
696 709 3.001414 GGATGCGAGATCATGGAGATTG 58.999 50.000 0.00 0.00 37.00 2.67
697 710 2.905085 AGGATGCGAGATCATGGAGATT 59.095 45.455 0.00 0.00 37.00 2.40
699 712 2.006805 AGGATGCGAGATCATGGAGA 57.993 50.000 0.00 0.00 0.00 3.71
701 714 1.345741 GGAAGGATGCGAGATCATGGA 59.654 52.381 0.00 0.00 0.00 3.41
702 715 1.347050 AGGAAGGATGCGAGATCATGG 59.653 52.381 0.00 0.00 0.00 3.66
704 717 2.038295 GGAAGGAAGGATGCGAGATCAT 59.962 50.000 0.00 0.00 0.00 2.45
741 760 2.744768 CGCAGCGAAAAGAGGAGGC 61.745 63.158 9.98 0.00 0.00 4.70
782 801 3.410516 TGTGCACGACGCCGATTG 61.411 61.111 13.13 0.00 41.33 2.67
805 824 1.664151 GATGGTTAAGAAAGCGACGGG 59.336 52.381 0.00 0.00 35.82 5.28
808 827 2.678336 CTGGGATGGTTAAGAAAGCGAC 59.322 50.000 0.00 0.00 35.82 5.19
919 941 2.034687 AAAGCGATGGCCAGTGCT 59.965 55.556 24.65 24.65 41.24 4.40
1188 1210 3.114558 CTAGGAAGGATCATCGCGC 57.885 57.895 0.00 0.00 0.00 6.86
1205 1227 1.458588 GGAAGAGGAGATCGGGCCT 60.459 63.158 0.84 4.75 37.18 5.19
1253 1275 2.789203 CGCGGTTACGAGCTCAAGC 61.789 63.158 15.40 10.05 44.60 4.01
1280 1302 2.398554 CCCAATCGCAACGACCCTG 61.399 63.158 0.00 0.00 39.18 4.45
1298 1320 2.378634 CCACTCCTCCCCCATCCAC 61.379 68.421 0.00 0.00 0.00 4.02
1308 1330 1.687493 CCCCAGTCCTCCACTCCTC 60.687 68.421 0.00 0.00 30.26 3.71
1309 1331 1.751143 TTCCCCAGTCCTCCACTCCT 61.751 60.000 0.00 0.00 30.26 3.69
1310 1332 0.621862 ATTCCCCAGTCCTCCACTCC 60.622 60.000 0.00 0.00 30.26 3.85
1311 1333 0.543749 CATTCCCCAGTCCTCCACTC 59.456 60.000 0.00 0.00 30.26 3.51
1312 1334 0.119155 TCATTCCCCAGTCCTCCACT 59.881 55.000 0.00 0.00 34.67 4.00
1313 1335 0.991920 TTCATTCCCCAGTCCTCCAC 59.008 55.000 0.00 0.00 0.00 4.02
1314 1336 1.753903 TTTCATTCCCCAGTCCTCCA 58.246 50.000 0.00 0.00 0.00 3.86
1315 1337 2.447443 GTTTTCATTCCCCAGTCCTCC 58.553 52.381 0.00 0.00 0.00 4.30
1316 1338 2.447443 GGTTTTCATTCCCCAGTCCTC 58.553 52.381 0.00 0.00 0.00 3.71
1317 1339 1.271926 CGGTTTTCATTCCCCAGTCCT 60.272 52.381 0.00 0.00 0.00 3.85
1318 1340 1.173913 CGGTTTTCATTCCCCAGTCC 58.826 55.000 0.00 0.00 0.00 3.85
1319 1341 1.173913 CCGGTTTTCATTCCCCAGTC 58.826 55.000 0.00 0.00 0.00 3.51
1320 1342 0.898326 GCCGGTTTTCATTCCCCAGT 60.898 55.000 1.90 0.00 0.00 4.00
1321 1343 0.611896 AGCCGGTTTTCATTCCCCAG 60.612 55.000 1.90 0.00 0.00 4.45
1322 1344 0.897863 CAGCCGGTTTTCATTCCCCA 60.898 55.000 1.90 0.00 0.00 4.96
1323 1345 1.604147 CCAGCCGGTTTTCATTCCCC 61.604 60.000 1.90 0.00 0.00 4.81
1324 1346 0.898326 ACCAGCCGGTTTTCATTCCC 60.898 55.000 1.90 0.00 46.31 3.97
1325 1347 0.243636 CACCAGCCGGTTTTCATTCC 59.756 55.000 1.90 0.00 46.31 3.01
1326 1348 0.243636 CCACCAGCCGGTTTTCATTC 59.756 55.000 1.90 0.00 46.31 2.67
1459 1481 2.133520 AGAATCCCCATGAGTCAGCAT 58.866 47.619 0.00 0.00 40.53 3.79
1460 1482 1.588239 AGAATCCCCATGAGTCAGCA 58.412 50.000 0.00 0.00 40.53 4.41
1462 1484 2.169352 ACGAAGAATCCCCATGAGTCAG 59.831 50.000 0.00 0.00 40.53 3.51
1463 1485 2.187958 ACGAAGAATCCCCATGAGTCA 58.812 47.619 0.00 0.00 40.53 3.41
1464 1486 2.939103 CAACGAAGAATCCCCATGAGTC 59.061 50.000 0.00 0.00 38.36 3.36
1465 1487 2.305927 ACAACGAAGAATCCCCATGAGT 59.694 45.455 0.00 0.00 0.00 3.41
1482 1507 2.568090 CCCATCTGCGCCAACAAC 59.432 61.111 4.18 0.00 0.00 3.32
1490 1515 2.202932 CGACCTTCCCCATCTGCG 60.203 66.667 0.00 0.00 0.00 5.18
1554 1579 0.174845 CGGTGAGGCCATTCTCGTAA 59.825 55.000 5.01 0.00 36.61 3.18
1572 1597 4.758251 TGCTGGTCATGGACGCCG 62.758 66.667 0.00 0.00 32.65 6.46
1709 1915 0.868406 GCAGCACGTTAGAAAGCACT 59.132 50.000 0.00 0.00 0.00 4.40
1719 1925 2.328099 GCCTTAGCAGCAGCACGTT 61.328 57.895 3.17 0.00 45.49 3.99
1765 1976 0.461339 CCCGGTAGTCATGGTTTCCG 60.461 60.000 0.00 11.30 38.05 4.30
1795 2006 4.988598 ACCGGGTCAAGCTGTGCG 62.989 66.667 6.32 0.00 0.00 5.34
1832 2043 6.318144 AGAAATGATCTCATGCAAACGAATCT 59.682 34.615 0.00 0.00 36.56 2.40
1856 2067 3.002791 ACGATGTACCTGCATTGACAAG 58.997 45.455 0.00 0.00 34.98 3.16
1875 2086 7.621832 TTCTTTGCTCAAACAAAATATGACG 57.378 32.000 0.00 0.00 38.96 4.35
1958 2172 7.170658 GGATGATAGTCAAGTCTTATGCTGTTC 59.829 40.741 0.00 0.00 0.00 3.18
1983 2198 2.744760 TCTCTGAGAGAACAGGGATGG 58.255 52.381 10.22 0.00 41.69 3.51
2102 2317 5.835819 TCAGCAGATTAGCTATGTAGTCCTT 59.164 40.000 0.00 0.00 44.54 3.36
2104 2319 5.713792 TCAGCAGATTAGCTATGTAGTCC 57.286 43.478 0.00 0.00 44.54 3.85
2105 2320 6.155827 CCTTCAGCAGATTAGCTATGTAGTC 58.844 44.000 0.00 0.00 44.54 2.59
2188 2403 8.411991 AGATTGTAAAATTTACGGAAAAGGGA 57.588 30.769 10.81 0.00 0.00 4.20
2189 2404 9.783256 CTAGATTGTAAAATTTACGGAAAAGGG 57.217 33.333 10.81 0.00 0.00 3.95
2205 2420 6.126507 TGCCTCATCCAAATCCTAGATTGTAA 60.127 38.462 0.00 0.00 0.00 2.41
2383 2603 8.621286 AGTGTCATAAAACGATTCTTTTTCTGT 58.379 29.630 4.34 0.00 0.00 3.41
2397 2617 5.391312 AGGGCATGAAAGTGTCATAAAAC 57.609 39.130 0.00 0.00 45.69 2.43
2430 2650 3.885724 TTGATGTAGAAGTCGATGCCA 57.114 42.857 0.00 0.00 0.00 4.92
2469 2689 2.346847 GTCTCTGCTGCTAATGTGTTCG 59.653 50.000 0.00 0.00 0.00 3.95
2500 2720 9.777843 CTTAAAAGAACAATGTTTATCAAACGC 57.222 29.630 0.00 0.00 44.28 4.84
2524 2744 1.344763 ACGCCTTACTGCTCTGTTCTT 59.655 47.619 0.00 0.00 0.00 2.52
2543 2763 8.460831 ACAACTTCAACAAGTGTGAATTTAAC 57.539 30.769 0.00 0.00 42.45 2.01
2583 2803 2.484770 GGACTGGTACAACAGAAGCACA 60.485 50.000 0.24 0.00 40.97 4.57
2585 2805 1.765904 TGGACTGGTACAACAGAAGCA 59.234 47.619 0.24 0.00 40.97 3.91
2675 2895 4.870636 TGCCCATCATAAAAGAACTGGAT 58.129 39.130 0.00 0.00 0.00 3.41
2774 2994 3.955771 TGTTTTGTGCGAGGTAAACTC 57.044 42.857 0.00 0.00 43.02 3.01
2778 2998 2.753452 TGGTTTGTTTTGTGCGAGGTAA 59.247 40.909 0.00 0.00 0.00 2.85
2779 2999 2.097791 GTGGTTTGTTTTGTGCGAGGTA 59.902 45.455 0.00 0.00 0.00 3.08
2781 3001 1.134175 AGTGGTTTGTTTTGTGCGAGG 59.866 47.619 0.00 0.00 0.00 4.63
2787 3007 2.093711 GGCTGGAAGTGGTTTGTTTTGT 60.094 45.455 0.00 0.00 35.30 2.83
2798 3018 1.500474 TAGATGGAGGGCTGGAAGTG 58.500 55.000 0.00 0.00 35.30 3.16
2887 3107 3.134442 ACCACAGTGGCACATTCAATTTT 59.866 39.130 20.48 0.00 42.67 1.82
2939 3159 1.808411 CTGAACCACGCACCATACTT 58.192 50.000 0.00 0.00 0.00 2.24
2949 3169 1.221466 TTCTTCAGCGCTGAACCACG 61.221 55.000 41.19 31.90 43.90 4.94
2974 3194 7.944729 ATTGTAGATAATTCACAGCCAGTTT 57.055 32.000 0.00 0.00 0.00 2.66
2990 3210 6.229733 GCATCTCTGCTCCTTTATTGTAGAT 58.770 40.000 0.00 0.00 45.32 1.98
3049 3277 4.021981 CGCATCAATAGATCCCTGTGACTA 60.022 45.833 0.00 0.00 30.20 2.59
3153 3381 3.168035 ACCAATATGCAAAGGTCACCA 57.832 42.857 0.00 0.00 0.00 4.17
3229 3461 4.764823 TCTCTTCCACAAACAAACAAGTGT 59.235 37.500 0.00 0.00 0.00 3.55
3241 3473 3.349927 CCATGCATTCTCTCTTCCACAA 58.650 45.455 0.00 0.00 0.00 3.33
3394 3633 0.833287 GGGCCTCTGCAATCTGAGTA 59.167 55.000 0.84 0.00 40.13 2.59
3447 3686 8.956426 CCTGAAGTAATATTTTCTTGGCAACTA 58.044 33.333 0.00 0.00 37.61 2.24
3507 3746 4.187694 GGCAACATTTGTCCAGTTTTTGA 58.812 39.130 0.00 0.00 0.00 2.69
3532 3771 6.198650 TGCATGTCTGGAAGTGATATTTTG 57.801 37.500 0.00 0.00 33.76 2.44
3546 3785 5.700832 TCTGGTACTTTAGTTTGCATGTCTG 59.299 40.000 0.00 0.00 0.00 3.51
3591 3831 2.503356 TGGTTGCCATTTTCTTGGTTGT 59.497 40.909 0.00 0.00 39.11 3.32
3607 3847 3.070018 CTGTTACCTCTCAAGCTGGTTG 58.930 50.000 13.13 13.13 37.52 3.77
3673 3913 3.126514 CAGACAGCTTTCATGTGGCTTAG 59.873 47.826 2.12 1.90 33.74 2.18
3736 3976 5.607939 TTTCTAAGATGGATTCGCTGGTA 57.392 39.130 0.00 0.00 0.00 3.25
3742 3982 6.296026 TGGGGTAATTTCTAAGATGGATTCG 58.704 40.000 0.00 0.00 0.00 3.34
3757 3999 3.778265 ACTGTTGCTCATTGGGGTAATT 58.222 40.909 0.00 0.00 0.00 1.40
3803 4045 4.675565 CGTTAGGTAGCATTACGTCTGATG 59.324 45.833 0.00 0.00 0.00 3.07
3804 4046 4.792057 GCGTTAGGTAGCATTACGTCTGAT 60.792 45.833 0.00 0.00 34.89 2.90


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

AutoCloner maintained by Alex Coulton.