Multiple sequence alignment - TraesCS6B01G191200

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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 TraesCS6B01G191200 chr6B 100.000 3050 0 0 1 3050 225312941 225309892 0.000000e+00 5633.0
1 TraesCS6B01G191200 chr6D 94.655 2058 70 18 560 2591 126617514 126615471 0.000000e+00 3155.0
2 TraesCS6B01G191200 chr6D 95.455 330 14 1 2721 3050 13805900 13805572 2.690000e-145 525.0
3 TraesCS6B01G191200 chr6D 95.152 330 16 0 2721 3050 13775610 13775281 3.480000e-144 521.0
4 TraesCS6B01G191200 chr6D 95.152 330 16 0 2721 3050 13780150 13779821 3.480000e-144 521.0
5 TraesCS6B01G191200 chr6D 95.152 330 15 1 2721 3050 13785533 13785205 1.250000e-143 520.0
6 TraesCS6B01G191200 chr6D 95.152 330 15 1 2721 3050 13793707 13793379 1.250000e-143 520.0
7 TraesCS6B01G191200 chr6D 95.152 330 15 1 2721 3050 13800228 13799900 1.250000e-143 520.0
8 TraesCS6B01G191200 chr6D 91.791 134 9 2 2590 2723 13772390 13772259 5.190000e-43 185.0
9 TraesCS6B01G191200 chr6D 91.852 135 8 2 2589 2723 13780337 13780206 5.190000e-43 185.0
10 TraesCS6B01G191200 chr6D 91.791 134 9 2 2590 2723 13787989 13787858 5.190000e-43 185.0
11 TraesCS6B01G191200 chr6D 91.791 134 9 2 2590 2723 13797012 13796881 5.190000e-43 185.0
12 TraesCS6B01G191200 chr6A 94.286 805 42 1 565 1369 153520472 153521272 0.000000e+00 1229.0
13 TraesCS6B01G191200 chr6A 84.108 1183 68 44 1472 2592 153521468 153522592 0.000000e+00 1033.0
14 TraesCS6B01G191200 chr6A 86.486 444 29 14 1 441 153519977 153520392 2.770000e-125 459.0
15 TraesCS6B01G191200 chr6A 96.825 63 2 0 1395 1457 153521331 153521393 4.160000e-19 106.0
16 TraesCS6B01G191200 chr7B 96.061 330 13 0 2721 3050 284960766 284960437 3.460000e-149 538.0
17 TraesCS6B01G191200 chr7B 94.030 134 6 1 2590 2723 284960952 284960821 5.160000e-48 202.0
18 TraesCS6B01G191200 chr5D 95.468 331 14 1 2721 3050 423217931 423217601 7.490000e-146 527.0
19 TraesCS6B01G191200 chr3B 95.152 330 16 0 2721 3050 128678805 128679134 3.480000e-144 521.0
20 TraesCS6B01G191200 chr7D 95.455 132 4 2 2589 2720 4788397 4788526 3.080000e-50 209.0
21 TraesCS6B01G191200 chr5B 93.985 133 4 3 2590 2720 377695871 377696001 6.670000e-47 198.0
22 TraesCS6B01G191200 chr1B 93.182 132 9 0 2589 2720 32137721 32137590 8.630000e-46 195.0
23 TraesCS6B01G191200 chrUn 91.791 134 9 2 2590 2723 362647006 362646875 5.190000e-43 185.0
24 TraesCS6B01G191200 chr1A 100.000 50 0 0 444 493 22658595 22658644 3.240000e-15 93.5


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 TraesCS6B01G191200 chr6B 225309892 225312941 3049 True 5633.000000 5633 100.000000 1 3050 1 chr6B.!!$R1 3049
1 TraesCS6B01G191200 chr6D 126615471 126617514 2043 True 3155.000000 3155 94.655000 560 2591 1 chr6D.!!$R2 2031
2 TraesCS6B01G191200 chr6D 13793379 13800228 6849 True 408.333333 520 94.031667 2590 3050 3 chr6D.!!$R6 460
3 TraesCS6B01G191200 chr6D 13772259 13775610 3351 True 353.000000 521 93.471500 2590 3050 2 chr6D.!!$R3 460
4 TraesCS6B01G191200 chr6D 13779821 13780337 516 True 353.000000 521 93.502000 2589 3050 2 chr6D.!!$R4 461
5 TraesCS6B01G191200 chr6D 13785205 13787989 2784 True 352.500000 520 93.471500 2590 3050 2 chr6D.!!$R5 460
6 TraesCS6B01G191200 chr6A 153519977 153522592 2615 False 706.750000 1229 90.426250 1 2592 4 chr6A.!!$F1 2591
7 TraesCS6B01G191200 chr7B 284960437 284960952 515 True 370.000000 538 95.045500 2590 3050 2 chr7B.!!$R1 460

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
554 563 0.322648 TGTCCACCTGAGCTCACATG 59.677 55.0 13.74 13.54 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 2367 1.536662 ATCCAGCCGGGGTCTATCC 60.537 63.158 2.18 0.0 37.22 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
30 31 5.414765 GTGAGATTTAATTTCGGGGTTGTCT 59.585 40.000 0.00 0.00 0.00 3.41
33 34 5.583457 AGATTTAATTTCGGGGTTGTCTACG 59.417 40.000 0.00 0.00 0.00 3.51
41 42 1.514873 GGTTGTCTACGCGTACCGG 60.515 63.158 16.41 6.24 42.52 5.28
53 54 2.124903 GCGTACCGGTTGTATGAGATG 58.875 52.381 15.04 0.00 38.51 2.90
62 63 6.486657 ACCGGTTGTATGAGATGAATATTTGG 59.513 38.462 0.00 0.00 0.00 3.28
178 182 8.926715 TCTATGTGTGACGATATATATTTGCC 57.073 34.615 0.00 0.00 0.00 4.52
213 217 4.445385 TGGCGAGAGAAAAGTTTTACGTAC 59.555 41.667 0.00 0.00 0.00 3.67
241 245 7.224297 TCAGTAAATGTTGAGGAAAGTAAGCT 58.776 34.615 0.00 0.00 0.00 3.74
246 250 5.298989 TGTTGAGGAAAGTAAGCTGGTAA 57.701 39.130 0.00 0.00 0.00 2.85
297 301 1.203287 TCGATGACAGTTCAGAGCTGG 59.797 52.381 17.74 0.80 38.22 4.85
309 313 1.129998 CAGAGCTGGAGAAACAATGCG 59.870 52.381 0.00 0.00 0.00 4.73
339 343 3.665323 CGATCACCAAGCTTCGTCAAAAG 60.665 47.826 0.00 0.00 0.00 2.27
365 369 2.202797 CCTCCACGGACGCATCTG 60.203 66.667 0.00 0.00 37.24 2.90
379 383 0.598680 CATCTGTTCCGATCCCGAGC 60.599 60.000 0.00 0.00 38.22 5.03
404 408 0.454600 TGAGCTCGGATGAACGGTAC 59.545 55.000 9.64 0.00 0.00 3.34
413 417 5.662456 TCGGATGAACGGTACAATCAAATA 58.338 37.500 0.00 0.00 0.00 1.40
418 422 9.019764 GGATGAACGGTACAATCAAATAAAATG 57.980 33.333 0.00 0.00 0.00 2.32
419 423 9.781834 GATGAACGGTACAATCAAATAAAATGA 57.218 29.630 0.00 0.00 0.00 2.57
465 469 5.947228 TTTTTGTGCCAAACATTGACAAA 57.053 30.435 0.00 0.00 38.99 2.83
466 470 6.506500 TTTTTGTGCCAAACATTGACAAAT 57.493 29.167 9.48 0.00 37.28 2.32
482 486 4.874396 TGACAAATGTTTGATTGCTTGCAA 59.126 33.333 10.57 10.57 40.55 4.08
483 487 5.353400 TGACAAATGTTTGATTGCTTGCAAA 59.647 32.000 12.17 0.00 40.55 3.68
484 488 5.812652 ACAAATGTTTGATTGCTTGCAAAG 58.187 33.333 12.17 0.00 43.20 2.77
486 490 6.127952 ACAAATGTTTGATTGCTTGCAAAGTT 60.128 30.769 12.17 0.00 42.67 2.66
487 491 6.748198 CAAATGTTTGATTGCTTGCAAAGTTT 59.252 30.769 12.17 0.00 42.67 2.66
488 492 7.044576 CAAATGTTTGATTGCTTGCAAAGTTTC 60.045 33.333 12.17 6.00 42.67 2.78
503 507 2.233271 AGTTTCATCACCTGGCACAAG 58.767 47.619 0.00 0.00 38.70 3.16
509 513 3.507233 TCATCACCTGGCACAAGAAAATC 59.493 43.478 0.00 0.00 38.70 2.17
511 515 3.499338 TCACCTGGCACAAGAAAATCAT 58.501 40.909 0.00 0.00 38.70 2.45
513 517 5.263599 TCACCTGGCACAAGAAAATCATAT 58.736 37.500 0.00 0.00 38.70 1.78
551 560 1.257743 TACTGTCCACCTGAGCTCAC 58.742 55.000 13.74 2.16 0.00 3.51
552 561 0.760567 ACTGTCCACCTGAGCTCACA 60.761 55.000 13.74 7.31 0.00 3.58
553 562 0.612229 CTGTCCACCTGAGCTCACAT 59.388 55.000 13.74 0.00 0.00 3.21
554 563 0.322648 TGTCCACCTGAGCTCACATG 59.677 55.000 13.74 13.54 0.00 3.21
555 564 0.610174 GTCCACCTGAGCTCACATGA 59.390 55.000 13.74 4.36 0.00 3.07
556 565 0.900421 TCCACCTGAGCTCACATGAG 59.100 55.000 13.74 2.19 44.75 2.90
557 566 0.612229 CCACCTGAGCTCACATGAGT 59.388 55.000 13.74 2.56 43.85 3.41
558 567 1.002888 CCACCTGAGCTCACATGAGTT 59.997 52.381 13.74 4.31 43.85 3.01
560 569 1.002888 ACCTGAGCTCACATGAGTTGG 59.997 52.381 13.74 12.48 43.85 3.77
562 571 1.277273 CTGAGCTCACATGAGTTGGGA 59.723 52.381 13.74 0.00 43.85 4.37
563 572 1.699083 TGAGCTCACATGAGTTGGGAA 59.301 47.619 13.74 0.00 43.85 3.97
564 573 2.306805 TGAGCTCACATGAGTTGGGAAT 59.693 45.455 13.74 0.00 43.85 3.01
565 574 2.941720 GAGCTCACATGAGTTGGGAATC 59.058 50.000 9.40 0.00 43.85 2.52
566 575 2.306805 AGCTCACATGAGTTGGGAATCA 59.693 45.455 10.50 0.00 43.85 2.57
575 584 5.957842 TGAGTTGGGAATCATAACAACAC 57.042 39.130 8.79 3.56 44.10 3.32
579 588 7.069331 TGAGTTGGGAATCATAACAACACTTTT 59.931 33.333 8.79 0.00 44.10 2.27
713 722 7.834821 GCTAGTTAGCTTTACTACATACGTC 57.165 40.000 0.00 0.00 45.62 4.34
714 723 7.412853 GCTAGTTAGCTTTACTACATACGTCA 58.587 38.462 0.00 0.00 45.62 4.35
715 724 8.074972 GCTAGTTAGCTTTACTACATACGTCAT 58.925 37.037 0.00 0.00 45.62 3.06
718 727 8.684520 AGTTAGCTTTACTACATACGTCATTCT 58.315 33.333 0.00 0.00 0.00 2.40
866 875 3.462021 GGTTTCTCGATCTTCTCATGGG 58.538 50.000 0.00 0.00 0.00 4.00
929 943 7.154435 TGTAGTATCTTTATACCGAGCCATC 57.846 40.000 0.00 0.00 39.08 3.51
953 967 4.202253 ACACTGAAGCTAGACATCAACACA 60.202 41.667 0.00 0.00 0.00 3.72
976 990 8.451748 CACACATACATCTGCGTATACTATACT 58.548 37.037 0.56 0.00 30.83 2.12
977 991 9.662947 ACACATACATCTGCGTATACTATACTA 57.337 33.333 0.56 0.00 30.83 1.82
978 992 9.917872 CACATACATCTGCGTATACTATACTAC 57.082 37.037 0.56 0.00 30.83 2.73
979 993 9.662947 ACATACATCTGCGTATACTATACTACA 57.337 33.333 0.56 2.86 30.83 2.74
1030 1046 3.056821 TGACTCCTTGGTTACATCACGAG 60.057 47.826 0.00 0.00 0.00 4.18
1038 1054 4.847198 TGGTTACATCACGAGTAGTAGGA 58.153 43.478 0.00 0.00 0.00 2.94
1098 1114 3.097614 AGTGCTCTATGACGGTAGGTTT 58.902 45.455 0.00 0.00 0.00 3.27
1213 1229 7.040409 CCCTTGTAAGCCCATGATTTATTAGTC 60.040 40.741 0.00 0.00 0.00 2.59
1241 1257 3.127895 TGTTTACAGCACTGTGGTTTGTC 59.872 43.478 10.19 1.54 44.63 3.18
1365 1381 0.107945 GAGGCTGAGTGCAACCCTAG 60.108 60.000 0.00 0.00 45.15 3.02
1457 1506 3.994204 TGTATTGGTGCATGCATGATC 57.006 42.857 30.64 19.72 0.00 2.92
1460 1509 5.071370 TGTATTGGTGCATGCATGATCATA 58.929 37.500 30.64 14.03 0.00 2.15
1463 1512 6.844097 ATTGGTGCATGCATGATCATAATA 57.156 33.333 30.64 9.35 0.00 0.98
1468 1517 8.463607 TGGTGCATGCATGATCATAATAATAAG 58.536 33.333 30.64 0.00 0.00 1.73
1498 1607 2.471370 GGATCATGCACGTACGTACATG 59.529 50.000 38.33 38.33 46.03 3.21
1528 1637 2.591429 CTTGTGGCAGGCGTGTCA 60.591 61.111 10.09 10.09 35.32 3.58
1950 2083 2.358247 CGCCGCTACAACCTTGGT 60.358 61.111 0.00 0.00 0.00 3.67
2083 2216 4.339247 TCAAATACCCACGTACCTAGCTAC 59.661 45.833 0.00 0.00 0.00 3.58
2138 2271 2.972267 CATGGGCATGGCAACGTT 59.028 55.556 22.06 0.00 42.51 3.99
2158 2291 6.751157 ACGTTATCGATCACATGGGTATAAA 58.249 36.000 0.00 0.00 40.62 1.40
2162 2295 5.862678 TCGATCACATGGGTATAAAGACA 57.137 39.130 0.00 0.00 0.00 3.41
2174 2307 8.958119 TGGGTATAAAGACAAGCTACAAATAG 57.042 34.615 0.00 0.00 0.00 1.73
2234 2367 5.717654 AGAGTACTTAGTCTTCCCAAAGGAG 59.282 44.000 0.00 0.00 45.19 3.69
2264 2402 4.398319 CCCGGCTGGATGAATAAAAGTAT 58.602 43.478 15.09 0.00 37.49 2.12
2318 2456 9.646427 AAAGAGTACTCTACATAGCTTTTGAAG 57.354 33.333 25.42 0.00 39.39 3.02
2503 2687 1.926510 GCTGACAAAAGCAACACCAAC 59.073 47.619 0.00 0.00 43.01 3.77
2557 2741 2.771943 TCTCATAAACGGGATGGAGCTT 59.228 45.455 0.00 0.00 0.00 3.74
2591 2776 1.033746 CCATGCCGGAGATGCACTTT 61.034 55.000 5.05 0.00 42.38 2.66
2592 2777 0.813184 CATGCCGGAGATGCACTTTT 59.187 50.000 5.05 0.00 42.38 2.27
2593 2778 1.203052 CATGCCGGAGATGCACTTTTT 59.797 47.619 5.05 0.00 42.38 1.94
2660 2845 5.230323 TGCATACGGCCACCTTTATTATA 57.770 39.130 2.24 0.00 43.89 0.98
2696 2881 9.403583 AGTTTAACAAAGGTCATGAAGTCTTAA 57.596 29.630 0.00 0.00 0.00 1.85
2714 2899 7.146648 AGTCTTAAACAAACGAACCACAAAAA 58.853 30.769 0.00 0.00 0.00 1.94
2743 4122 4.157246 TGCCTATCCTATTACATGACCGT 58.843 43.478 0.00 0.00 0.00 4.83
2877 8506 2.693591 CAGTGGCTCGGAAGATAACCTA 59.306 50.000 0.00 0.00 40.84 3.08
2924 8553 8.017418 TCTGTTAAAAACCAAATCATTCCTGT 57.983 30.769 0.00 0.00 0.00 4.00
3036 9800 5.524971 AACGTGGTGATATTATTCGGAGA 57.475 39.130 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 7.275888 TGCCCAAATATTCATCTCATACAAC 57.724 36.000 0.00 0.00 0.00 3.32
213 217 9.884465 CTTACTTTCCTCAACATTTACTGAAAG 57.116 33.333 0.00 0.00 41.64 2.62
246 250 3.968265 ACAGGCTACACAAATATTGGCT 58.032 40.909 0.00 0.00 34.12 4.75
297 301 2.535732 CGCTAGCTTCGCATTGTTTCTC 60.536 50.000 13.93 0.00 0.00 2.87
309 313 0.933796 GCTTGGTGATCGCTAGCTTC 59.066 55.000 13.93 10.16 0.00 3.86
365 369 0.319125 GATGAGCTCGGGATCGGAAC 60.319 60.000 9.64 0.00 36.95 3.62
379 383 2.741612 GTTCATCCGAGCTCAGATGAG 58.258 52.381 31.33 14.50 47.00 2.90
459 463 4.439968 TGCAAGCAATCAAACATTTGTCA 58.560 34.783 4.36 0.00 39.18 3.58
460 464 5.406767 TTGCAAGCAATCAAACATTTGTC 57.593 34.783 2.89 0.00 39.18 3.18
461 465 5.354792 ACTTTGCAAGCAATCAAACATTTGT 59.645 32.000 8.46 0.00 39.18 2.83
462 466 5.812652 ACTTTGCAAGCAATCAAACATTTG 58.187 33.333 8.46 0.00 39.48 2.32
464 468 6.093771 TGAAACTTTGCAAGCAATCAAACATT 59.906 30.769 8.46 0.00 35.70 2.71
465 469 5.585445 TGAAACTTTGCAAGCAATCAAACAT 59.415 32.000 8.46 0.00 35.70 2.71
466 470 4.934001 TGAAACTTTGCAAGCAATCAAACA 59.066 33.333 8.46 4.70 35.70 2.83
467 471 5.467902 TGAAACTTTGCAAGCAATCAAAC 57.532 34.783 8.46 2.32 35.70 2.93
468 472 5.816258 TGATGAAACTTTGCAAGCAATCAAA 59.184 32.000 8.46 0.64 35.70 2.69
469 473 5.234757 GTGATGAAACTTTGCAAGCAATCAA 59.765 36.000 8.46 0.00 35.70 2.57
471 475 4.151157 GGTGATGAAACTTTGCAAGCAATC 59.849 41.667 8.46 3.92 35.70 2.67
472 476 4.060205 GGTGATGAAACTTTGCAAGCAAT 58.940 39.130 8.46 0.00 35.70 3.56
473 477 3.132646 AGGTGATGAAACTTTGCAAGCAA 59.867 39.130 2.89 2.89 0.00 3.91
474 478 2.694628 AGGTGATGAAACTTTGCAAGCA 59.305 40.909 0.00 0.00 0.00 3.91
475 479 3.054878 CAGGTGATGAAACTTTGCAAGC 58.945 45.455 0.00 0.00 0.00 4.01
476 480 3.645884 CCAGGTGATGAAACTTTGCAAG 58.354 45.455 0.00 0.00 0.00 4.01
478 482 1.340889 GCCAGGTGATGAAACTTTGCA 59.659 47.619 0.00 0.00 0.00 4.08
479 483 1.340889 TGCCAGGTGATGAAACTTTGC 59.659 47.619 0.00 0.00 0.00 3.68
482 486 2.363306 TGTGCCAGGTGATGAAACTT 57.637 45.000 0.00 0.00 0.00 2.66
483 487 2.158623 TCTTGTGCCAGGTGATGAAACT 60.159 45.455 0.00 0.00 0.00 2.66
484 488 2.229792 TCTTGTGCCAGGTGATGAAAC 58.770 47.619 0.00 0.00 0.00 2.78
486 490 2.655090 TTCTTGTGCCAGGTGATGAA 57.345 45.000 0.00 0.00 0.00 2.57
487 491 2.655090 TTTCTTGTGCCAGGTGATGA 57.345 45.000 0.00 0.00 0.00 2.92
488 492 3.256383 TGATTTTCTTGTGCCAGGTGATG 59.744 43.478 0.00 0.00 0.00 3.07
491 495 3.947910 ATGATTTTCTTGTGCCAGGTG 57.052 42.857 0.00 0.00 0.00 4.00
493 497 7.910441 AAAAATATGATTTTCTTGTGCCAGG 57.090 32.000 0.00 0.00 0.00 4.45
521 525 8.736244 GCTCAGGTGGACAGTAAAAATAAAATA 58.264 33.333 0.00 0.00 0.00 1.40
527 531 4.202461 TGAGCTCAGGTGGACAGTAAAAAT 60.202 41.667 13.74 0.00 0.00 1.82
528 532 3.135712 TGAGCTCAGGTGGACAGTAAAAA 59.864 43.478 13.74 0.00 0.00 1.94
538 547 0.612229 ACTCATGTGAGCTCAGGTGG 59.388 55.000 18.89 14.05 45.79 4.61
551 560 6.151648 AGTGTTGTTATGATTCCCAACTCATG 59.848 38.462 0.00 0.00 38.35 3.07
552 561 6.248433 AGTGTTGTTATGATTCCCAACTCAT 58.752 36.000 0.00 0.00 38.35 2.90
553 562 5.630121 AGTGTTGTTATGATTCCCAACTCA 58.370 37.500 0.00 0.00 38.35 3.41
554 563 6.575162 AAGTGTTGTTATGATTCCCAACTC 57.425 37.500 0.00 0.00 38.35 3.01
555 564 6.976934 AAAGTGTTGTTATGATTCCCAACT 57.023 33.333 0.00 0.00 38.35 3.16
556 565 6.423604 CCAAAAGTGTTGTTATGATTCCCAAC 59.576 38.462 0.00 0.00 38.10 3.77
557 566 6.098982 ACCAAAAGTGTTGTTATGATTCCCAA 59.901 34.615 0.00 0.00 0.00 4.12
558 567 5.600484 ACCAAAAGTGTTGTTATGATTCCCA 59.400 36.000 0.00 0.00 0.00 4.37
560 569 6.015434 AGGACCAAAAGTGTTGTTATGATTCC 60.015 38.462 0.00 0.00 0.00 3.01
562 571 6.015434 GGAGGACCAAAAGTGTTGTTATGATT 60.015 38.462 0.00 0.00 35.97 2.57
563 572 5.476945 GGAGGACCAAAAGTGTTGTTATGAT 59.523 40.000 0.00 0.00 35.97 2.45
564 573 4.825085 GGAGGACCAAAAGTGTTGTTATGA 59.175 41.667 0.00 0.00 35.97 2.15
565 574 4.582656 TGGAGGACCAAAAGTGTTGTTATG 59.417 41.667 0.00 0.00 43.91 1.90
566 575 4.798882 TGGAGGACCAAAAGTGTTGTTAT 58.201 39.130 0.00 0.00 43.91 1.89
579 588 1.068417 CGAAACACGTGGAGGACCA 59.932 57.895 21.57 0.00 44.76 4.02
718 727 4.038522 CAGGCATGTCTTTCTAGCTAGCTA 59.961 45.833 22.85 22.85 0.00 3.32
720 729 3.129871 CAGGCATGTCTTTCTAGCTAGC 58.870 50.000 16.35 6.62 0.00 3.42
866 875 9.719279 CTTAGGCGTCATATTTATAGTAGCTAC 57.281 37.037 16.43 16.43 0.00 3.58
929 943 4.151335 GTGTTGATGTCTAGCTTCAGTGTG 59.849 45.833 0.00 0.00 33.60 3.82
953 967 9.662947 TGTAGTATAGTATACGCAGATGTATGT 57.337 33.333 13.43 0.00 35.85 2.29
1008 1024 2.894765 TCGTGATGTAACCAAGGAGTCA 59.105 45.455 0.00 0.00 0.00 3.41
1030 1046 3.132467 GGGTCCAACACATCTCCTACTAC 59.868 52.174 0.00 0.00 0.00 2.73
1038 1054 0.698818 GGAAGGGGTCCAACACATCT 59.301 55.000 0.00 0.00 46.97 2.90
1098 1114 2.779755 ACTCCATGCCGTTAATGACA 57.220 45.000 0.00 0.00 0.00 3.58
1164 1180 2.037941 ATGTCACGCTGATATCGTCG 57.962 50.000 12.88 12.88 38.19 5.12
1213 1229 6.012658 ACCACAGTGCTGTAAACATAAATG 57.987 37.500 4.37 0.00 42.83 2.32
1224 1240 0.034574 TGGACAAACCACAGTGCTGT 60.035 50.000 0.00 0.00 44.64 4.40
1241 1257 7.490962 TTCACAGATTACACAGTTAACTTGG 57.509 36.000 5.07 3.52 0.00 3.61
1463 1512 6.592994 CGTGCATGATCCATGAGTATCTTATT 59.407 38.462 10.77 0.00 43.81 1.40
1468 1517 3.657634 ACGTGCATGATCCATGAGTATC 58.342 45.455 14.17 0.00 43.81 2.24
1787 1920 4.101448 CCACCTCCCGCCCTTCAG 62.101 72.222 0.00 0.00 0.00 3.02
1893 2026 4.673298 TTGTGGCGCATCGACGGT 62.673 61.111 10.83 0.00 37.93 4.83
2013 2146 2.364579 CTGGTGTAGGCCCCGGTA 60.365 66.667 0.00 0.00 0.00 4.02
2046 2179 5.104693 TGGGTATTTGAGCTCGAAGGATTAA 60.105 40.000 20.82 3.59 0.00 1.40
2083 2216 3.436704 CCCGTATGTGGCAGCTATTTATG 59.563 47.826 0.00 0.00 0.00 1.90
2138 2271 7.533289 TGTCTTTATACCCATGTGATCGATA 57.467 36.000 0.00 0.00 0.00 2.92
2211 2344 5.105269 CCTCCTTTGGGAAGACTAAGTACTC 60.105 48.000 0.00 0.00 41.69 2.59
2212 2345 4.778427 CCTCCTTTGGGAAGACTAAGTACT 59.222 45.833 0.00 0.00 41.69 2.73
2213 2346 4.776308 TCCTCCTTTGGGAAGACTAAGTAC 59.224 45.833 0.00 0.00 41.69 2.73
2214 2347 5.019657 TCCTCCTTTGGGAAGACTAAGTA 57.980 43.478 0.00 0.00 41.69 2.24
2215 2348 3.870559 TCCTCCTTTGGGAAGACTAAGT 58.129 45.455 0.00 0.00 41.69 2.24
2216 2349 5.900123 TCTATCCTCCTTTGGGAAGACTAAG 59.100 44.000 0.00 0.00 41.69 2.18
2218 2351 5.209659 GTCTATCCTCCTTTGGGAAGACTA 58.790 45.833 0.00 0.00 41.69 2.59
2219 2352 4.034410 GTCTATCCTCCTTTGGGAAGACT 58.966 47.826 0.00 0.00 41.69 3.24
2220 2353 3.134985 GGTCTATCCTCCTTTGGGAAGAC 59.865 52.174 0.00 0.00 41.69 3.01
2234 2367 1.536662 ATCCAGCCGGGGTCTATCC 60.537 63.158 2.18 0.00 37.22 2.59
2372 2523 5.010933 TCTTGAGAGTATATAGAAGGCGGG 58.989 45.833 0.00 0.00 0.00 6.13
2557 2741 4.623932 GGCATGGAGATACATGTCCTTA 57.376 45.455 0.00 0.00 45.31 2.69
2597 2782 4.196971 CGGAGTTATACCCCTTTTTCAGG 58.803 47.826 0.00 0.00 43.49 3.86
2598 2783 4.196971 CCGGAGTTATACCCCTTTTTCAG 58.803 47.826 0.00 0.00 0.00 3.02
2601 2786 2.357465 GGCCGGAGTTATACCCCTTTTT 60.357 50.000 5.05 0.00 0.00 1.94
2660 2845 9.830975 ATGACCTTTGTTAAACTTATTTGCTTT 57.169 25.926 0.00 0.00 0.00 3.51
2674 2859 8.740123 TGTTTAAGACTTCATGACCTTTGTTA 57.260 30.769 0.00 0.00 0.00 2.41
2696 2881 2.997303 GCCTTTTTGTGGTTCGTTTGTT 59.003 40.909 0.00 0.00 0.00 2.83
2743 4122 4.819630 GCTATATTCAACCGGTTTGGATGA 59.180 41.667 19.55 9.80 46.81 2.92
2797 4176 0.958876 CCAGGGAGCGTTTGGTTACC 60.959 60.000 0.00 0.00 0.00 2.85
2823 8452 0.171455 GTGGTCGCTACTCACTCAGG 59.829 60.000 3.71 0.00 0.00 3.86
2885 8514 8.739461 GGTTTTTAACAGAACAACAAATACTCG 58.261 33.333 0.00 0.00 0.00 4.18
2924 8553 2.054799 ACTTTGGGCAGTCTGGAACTA 58.945 47.619 1.14 0.00 36.07 2.24


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

AutoCloner maintained by Alex Coulton.