Multiple sequence alignment - TraesCS6B01G181600

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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 TraesCS6B01G181600 chr6B 100.000 2264 0 0 1 2264 203692213 203689950 0.000000e+00 4181.0
1 TraesCS6B01G181600 chr6D 92.522 1511 62 20 773 2264 114173319 114171841 0.000000e+00 2117.0
2 TraesCS6B01G181600 chr6A 85.873 1444 127 28 74 1463 141863536 141862116 0.000000e+00 1465.0
3 TraesCS6B01G181600 chr6A 93.204 618 34 3 1651 2264 141861934 141861321 0.000000e+00 902.0
4 TraesCS6B01G181600 chr6A 91.346 104 9 0 1528 1631 141862115 141862012 2.340000e-30 143.0
5 TraesCS6B01G181600 chr5A 97.059 34 1 0 173 206 573832980 573833013 8.730000e-05 58.4
6 TraesCS6B01G181600 chr3D 100.000 31 0 0 176 206 419930124 419930094 8.730000e-05 58.4
7 TraesCS6B01G181600 chr3A 97.059 34 1 0 173 206 530940974 530941007 8.730000e-05 58.4
8 TraesCS6B01G181600 chr1B 100.000 31 0 0 176 206 453746371 453746401 8.730000e-05 58.4
9 TraesCS6B01G181600 chr5B 94.118 34 2 0 173 206 380799476 380799509 4.000000e-03 52.8
10 TraesCS6B01G181600 chr5B 94.286 35 1 1 172 206 526550486 526550519 4.000000e-03 52.8
11 TraesCS6B01G181600 chr2D 94.118 34 2 0 173 206 470067925 470067958 4.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G181600 chr6B 203689950 203692213 2263 True 4181.000000 4181 100.000 1 2264 1 chr6B.!!$R1 2263
1 TraesCS6B01G181600 chr6D 114171841 114173319 1478 True 2117.000000 2117 92.522 773 2264 1 chr6D.!!$R1 1491
2 TraesCS6B01G181600 chr6A 141861321 141863536 2215 True 836.666667 1465 90.141 74 2264 3 chr6A.!!$R1 2190

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
61 62 0.032267 CCTAGAGGCCGTTCGGAATC 59.968 60.0 15.69 11.03 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1355 1403 0.181587 TCAAGCAGACGGGGTTCAAA 59.818 50.0 0.0 0.0 0.0 2.69 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
49 50 8.517062 AAATGAAAATGAATGAGACCTAGAGG 57.483 34.615 0.00 0.00 42.17 3.69
50 51 5.431765 TGAAAATGAATGAGACCTAGAGGC 58.568 41.667 0.00 0.00 39.32 4.70
51 52 4.429854 AAATGAATGAGACCTAGAGGCC 57.570 45.455 0.00 0.00 39.32 5.19
52 53 1.403814 TGAATGAGACCTAGAGGCCG 58.596 55.000 0.00 0.00 39.32 6.13
53 54 1.342076 TGAATGAGACCTAGAGGCCGT 60.342 52.381 0.00 0.00 39.32 5.68
54 55 1.757699 GAATGAGACCTAGAGGCCGTT 59.242 52.381 0.00 0.00 39.32 4.44
55 56 1.404843 ATGAGACCTAGAGGCCGTTC 58.595 55.000 0.00 0.00 39.32 3.95
56 57 1.030488 TGAGACCTAGAGGCCGTTCG 61.030 60.000 0.00 0.00 39.32 3.95
57 58 1.726533 GAGACCTAGAGGCCGTTCGG 61.727 65.000 6.90 6.90 39.32 4.30
58 59 1.751927 GACCTAGAGGCCGTTCGGA 60.752 63.158 15.69 0.00 39.32 4.55
59 60 1.304713 ACCTAGAGGCCGTTCGGAA 60.305 57.895 15.69 0.00 39.32 4.30
60 61 0.686769 ACCTAGAGGCCGTTCGGAAT 60.687 55.000 15.69 1.87 39.32 3.01
61 62 0.032267 CCTAGAGGCCGTTCGGAATC 59.968 60.000 15.69 11.03 0.00 2.52
62 63 0.744874 CTAGAGGCCGTTCGGAATCA 59.255 55.000 15.69 2.87 0.00 2.57
63 64 0.458669 TAGAGGCCGTTCGGAATCAC 59.541 55.000 15.69 2.87 0.00 3.06
64 65 1.218316 GAGGCCGTTCGGAATCACT 59.782 57.895 15.69 4.31 0.00 3.41
65 66 0.806492 GAGGCCGTTCGGAATCACTC 60.806 60.000 15.69 9.31 0.00 3.51
66 67 1.814169 GGCCGTTCGGAATCACTCC 60.814 63.158 15.69 0.94 41.40 3.85
67 68 1.079405 GCCGTTCGGAATCACTCCA 60.079 57.895 15.69 0.00 45.74 3.86
68 69 1.359459 GCCGTTCGGAATCACTCCAC 61.359 60.000 15.69 0.00 45.74 4.02
69 70 1.076533 CCGTTCGGAATCACTCCACG 61.077 60.000 5.19 0.00 45.74 4.94
70 71 1.683790 CGTTCGGAATCACTCCACGC 61.684 60.000 0.00 0.00 45.74 5.34
71 72 0.389948 GTTCGGAATCACTCCACGCT 60.390 55.000 0.00 0.00 45.74 5.07
72 73 1.135199 GTTCGGAATCACTCCACGCTA 60.135 52.381 0.00 0.00 45.74 4.26
89 90 2.545526 CGCTATGCCACTTCAATACTGG 59.454 50.000 0.00 0.00 0.00 4.00
92 93 2.113860 TGCCACTTCAATACTGGAGC 57.886 50.000 0.00 0.00 30.14 4.70
93 94 1.630369 TGCCACTTCAATACTGGAGCT 59.370 47.619 0.00 0.00 30.14 4.09
98 99 0.255890 TTCAATACTGGAGCTGGCCC 59.744 55.000 0.00 0.00 0.00 5.80
101 102 1.056700 AATACTGGAGCTGGCCCGAT 61.057 55.000 0.00 0.00 0.00 4.18
102 103 1.476007 ATACTGGAGCTGGCCCGATC 61.476 60.000 3.48 3.48 0.00 3.69
105 106 2.203126 GGAGCTGGCCCGATCTTG 60.203 66.667 12.38 0.00 0.00 3.02
132 133 3.118261 TGATGGGTAGGAAGTCTTCATGC 60.118 47.826 14.49 10.58 0.00 4.06
137 138 0.036010 AGGAAGTCTTCATGCCCACG 60.036 55.000 14.49 0.00 0.00 4.94
171 172 1.682684 CCCTGGTGCCGTAGAGTCT 60.683 63.158 0.00 0.00 0.00 3.24
177 178 1.470098 GGTGCCGTAGAGTCTTCGTTA 59.530 52.381 16.61 3.93 0.00 3.18
190 191 8.472683 AGAGTCTTCGTTAAATCAATCTGAAG 57.527 34.615 0.00 0.00 34.23 3.02
193 194 8.713271 AGTCTTCGTTAAATCAATCTGAAGAAC 58.287 33.333 3.60 0.28 41.16 3.01
206 207 4.792068 TCTGAAGAACCTGACACCAAATT 58.208 39.130 0.00 0.00 0.00 1.82
207 208 5.935945 TCTGAAGAACCTGACACCAAATTA 58.064 37.500 0.00 0.00 0.00 1.40
208 209 6.361433 TCTGAAGAACCTGACACCAAATTAA 58.639 36.000 0.00 0.00 0.00 1.40
223 245 5.708697 ACCAAATTAAGAAACCCTAACTCGG 59.291 40.000 0.00 0.00 0.00 4.63
229 251 2.176314 AAACCCTAACTCGGCGACCC 62.176 60.000 4.99 0.00 0.00 4.46
247 269 0.103937 CCGAGGAGCTGTCAGGAATC 59.896 60.000 1.14 0.00 0.00 2.52
252 274 3.640967 GAGGAGCTGTCAGGAATCTACAT 59.359 47.826 1.14 0.00 0.00 2.29
258 280 5.046014 AGCTGTCAGGAATCTACATTGAAGT 60.046 40.000 1.14 0.00 0.00 3.01
261 283 7.625185 GCTGTCAGGAATCTACATTGAAGTTTC 60.625 40.741 1.14 0.00 0.00 2.78
274 296 1.931841 GAAGTTTCGTCTAATCCGCCC 59.068 52.381 0.00 0.00 0.00 6.13
278 300 2.008268 TTCGTCTAATCCGCCCCGAC 62.008 60.000 0.00 0.00 0.00 4.79
291 313 2.809601 CCGACGGGCGAGTTTGAG 60.810 66.667 3.94 0.00 44.57 3.02
304 326 0.721718 GTTTGAGGAGAATCGGTGCG 59.278 55.000 0.00 0.00 34.37 5.34
305 327 1.019278 TTTGAGGAGAATCGGTGCGC 61.019 55.000 0.00 0.00 34.37 6.09
306 328 2.166130 TTGAGGAGAATCGGTGCGCA 62.166 55.000 5.66 5.66 34.37 6.09
307 329 1.447838 GAGGAGAATCGGTGCGCAA 60.448 57.895 14.00 0.00 34.37 4.85
310 332 0.451783 GGAGAATCGGTGCGCAAAAT 59.548 50.000 14.00 2.59 34.37 1.82
340 362 1.029408 ACAATAAGCGCCGCCATTCA 61.029 50.000 4.98 0.00 0.00 2.57
350 372 0.179166 CCGCCATTCATCCAAACGTG 60.179 55.000 0.00 0.00 0.00 4.49
351 373 0.798009 CGCCATTCATCCAAACGTGC 60.798 55.000 0.00 0.00 0.00 5.34
353 375 0.179166 CCATTCATCCAAACGTGCCG 60.179 55.000 0.00 0.00 0.00 5.69
354 376 0.798009 CATTCATCCAAACGTGCCGC 60.798 55.000 0.00 0.00 0.00 6.53
355 377 1.240641 ATTCATCCAAACGTGCCGCA 61.241 50.000 0.00 0.00 0.00 5.69
368 390 2.801699 CGTGCCGCATATGAGGACTAAA 60.802 50.000 27.60 5.57 37.14 1.85
380 402 9.101325 CATATGAGGACTAAAATCCCTAACCTA 57.899 37.037 0.00 0.00 39.91 3.08
399 421 4.599041 CCTATCTACTAGGCAGAGCTGAT 58.401 47.826 0.85 0.00 40.75 2.90
404 426 9.573166 CTATCTACTAGGCAGAGCTGATATATT 57.427 37.037 0.85 0.00 0.00 1.28
414 436 8.046107 GGCAGAGCTGATATATTAGGATTCTTT 58.954 37.037 6.64 0.00 0.00 2.52
416 438 9.598517 CAGAGCTGATATATTAGGATTCTTTCC 57.401 37.037 6.64 0.00 45.85 3.13
419 441 7.057264 GCTGATATATTAGGATTCTTTCCCCC 58.943 42.308 6.64 0.00 46.81 5.40
420 442 7.311929 GCTGATATATTAGGATTCTTTCCCCCA 60.312 40.741 6.64 0.00 46.81 4.96
422 444 7.744068 TGATATATTAGGATTCTTTCCCCCACT 59.256 37.037 0.00 0.00 46.81 4.00
424 446 5.913946 ATTAGGATTCTTTCCCCCACTAG 57.086 43.478 0.00 0.00 46.81 2.57
429 451 1.077429 CTTTCCCCCACTAGCAGCC 60.077 63.158 0.00 0.00 0.00 4.85
430 452 2.876368 CTTTCCCCCACTAGCAGCCG 62.876 65.000 0.00 0.00 0.00 5.52
439 461 4.819761 TAGCAGCCGCCGAAGCAG 62.820 66.667 0.00 0.00 39.83 4.24
443 465 3.068691 AGCCGCCGAAGCAGTAGA 61.069 61.111 0.00 0.00 39.83 2.59
458 480 2.237143 CAGTAGACAGAGGGGATGCAAA 59.763 50.000 0.00 0.00 0.00 3.68
499 523 8.668510 ATGAACGTAATGCTTTCTAGATGATT 57.331 30.769 0.00 0.00 0.00 2.57
503 527 9.774742 AACGTAATGCTTTCTAGATGATTTTTC 57.225 29.630 0.00 0.00 0.00 2.29
504 528 8.946085 ACGTAATGCTTTCTAGATGATTTTTCA 58.054 29.630 0.00 0.00 0.00 2.69
544 568 5.244851 AGCTCATAGAGGTATGGTATGTGTG 59.755 44.000 0.00 0.00 38.70 3.82
552 576 3.493129 GGTATGGTATGTGTGTATGCGTG 59.507 47.826 0.00 0.00 0.00 5.34
553 577 2.753055 TGGTATGTGTGTATGCGTGT 57.247 45.000 0.00 0.00 0.00 4.49
554 578 3.046968 TGGTATGTGTGTATGCGTGTT 57.953 42.857 0.00 0.00 0.00 3.32
555 579 3.403968 TGGTATGTGTGTATGCGTGTTT 58.596 40.909 0.00 0.00 0.00 2.83
559 583 6.987404 TGGTATGTGTGTATGCGTGTTTATAT 59.013 34.615 0.00 0.00 0.00 0.86
562 586 4.572795 TGTGTGTATGCGTGTTTATATGGG 59.427 41.667 0.00 0.00 0.00 4.00
565 589 4.573201 GTGTATGCGTGTTTATATGGGTGT 59.427 41.667 0.00 0.00 0.00 4.16
572 596 5.754406 GCGTGTTTATATGGGTGTGTGTATA 59.246 40.000 0.00 0.00 0.00 1.47
573 597 6.425721 GCGTGTTTATATGGGTGTGTGTATAT 59.574 38.462 0.00 0.00 0.00 0.86
606 633 6.631016 ACAATCGTCTATGTCTGTATTGTGT 58.369 36.000 0.00 0.00 35.42 3.72
607 634 7.097192 ACAATCGTCTATGTCTGTATTGTGTT 58.903 34.615 0.00 0.00 35.42 3.32
662 689 7.816945 ATTATTATTTTGTGTGACAAGCTGC 57.183 32.000 0.00 0.00 39.53 5.25
683 710 6.678900 GCTGCTTTTTGAGAAGTGAAAAGAGA 60.679 38.462 10.88 0.00 40.87 3.10
694 721 5.028549 AGTGAAAAGAGATGCGGTGATAT 57.971 39.130 0.00 0.00 0.00 1.63
695 722 6.161855 AGTGAAAAGAGATGCGGTGATATA 57.838 37.500 0.00 0.00 0.00 0.86
696 723 6.763355 AGTGAAAAGAGATGCGGTGATATAT 58.237 36.000 0.00 0.00 0.00 0.86
697 724 6.870965 AGTGAAAAGAGATGCGGTGATATATC 59.129 38.462 5.73 5.73 0.00 1.63
698 725 6.646653 GTGAAAAGAGATGCGGTGATATATCA 59.353 38.462 11.49 11.49 0.00 2.15
705 732 8.725148 AGAGATGCGGTGATATATCAAATTTTC 58.275 33.333 16.97 11.30 38.75 2.29
706 733 7.820648 AGATGCGGTGATATATCAAATTTTCC 58.179 34.615 16.97 11.52 38.75 3.13
707 734 6.951062 TGCGGTGATATATCAAATTTTCCA 57.049 33.333 16.97 5.45 38.75 3.53
709 736 7.592938 TGCGGTGATATATCAAATTTTCCATC 58.407 34.615 16.97 8.08 38.75 3.51
761 794 6.422776 TTTTTCAGATCTATTCGTCTTGGC 57.577 37.500 0.00 0.00 0.00 4.52
765 798 0.384309 ATCTATTCGTCTTGGCGCGA 59.616 50.000 12.10 0.00 35.17 5.87
853 886 0.116143 ATTTAAGCCCAGCCCAACCA 59.884 50.000 0.00 0.00 0.00 3.67
891 939 0.472925 ACCCAAACAAATCCCCCACC 60.473 55.000 0.00 0.00 0.00 4.61
892 940 0.178906 CCCAAACAAATCCCCCACCT 60.179 55.000 0.00 0.00 0.00 4.00
956 1004 1.171308 CGAACGAACCCTAGACTCCA 58.829 55.000 0.00 0.00 0.00 3.86
997 1045 1.824329 GAGATCTCCCAGGTCGCGA 60.824 63.158 12.00 3.71 0.00 5.87
1277 1325 1.606889 ACTAGATCCGGATCCGCCC 60.607 63.158 35.53 18.08 38.58 6.13
1344 1392 2.528743 CGGTGGTGCGATGAGATGC 61.529 63.158 0.00 0.00 0.00 3.91
1350 1398 1.267732 GGTGCGATGAGATGCTTTTCG 60.268 52.381 0.00 0.00 0.00 3.46
1355 1403 0.625849 ATGAGATGCTTTTCGGGGGT 59.374 50.000 0.00 0.00 0.00 4.95
1412 1464 6.094464 GGTTTAATTTAGGTAAGGTCGCATGT 59.906 38.462 0.00 0.00 0.00 3.21
1474 1526 2.357952 GGGTCTGTGAACTTGTTTGGTC 59.642 50.000 0.00 0.00 0.00 4.02
1476 1528 3.632145 GGTCTGTGAACTTGTTTGGTCAT 59.368 43.478 0.00 0.00 0.00 3.06
1481 1533 4.464244 TGTGAACTTGTTTGGTCATTTGGA 59.536 37.500 0.00 0.00 0.00 3.53
1482 1534 4.803613 GTGAACTTGTTTGGTCATTTGGAC 59.196 41.667 0.00 0.00 46.20 4.02
1504 1556 5.313712 ACGAGGTTTTGTATGAATTCTGGT 58.686 37.500 7.05 0.00 0.00 4.00
1530 1582 2.397597 GGAACAATATTGTGGGGGCAT 58.602 47.619 21.46 4.14 41.31 4.40
1635 1695 4.349663 TCTTGGTGTTTTCTGTTTCACG 57.650 40.909 0.00 0.00 0.00 4.35
1636 1696 2.553079 TGGTGTTTTCTGTTTCACGC 57.447 45.000 0.00 0.00 0.00 5.34
1663 1773 2.892215 TCATTCTGCCAGTGATGCAAAA 59.108 40.909 0.00 0.00 38.46 2.44
1703 1817 7.309920 TGAGTTTTACAAAGTTTGACCACTTC 58.690 34.615 22.23 12.13 35.87 3.01
1770 1884 7.064490 GGAAACTGTTGAATGACACATTTGTTT 59.936 33.333 0.00 0.00 35.47 2.83
1794 1908 8.995027 TTGGGTATCATTTGTGATTATAGCTT 57.005 30.769 0.00 0.00 0.00 3.74
1804 1918 5.729510 TGTGATTATAGCTTGCACTGTGTA 58.270 37.500 9.86 1.30 0.00 2.90
1834 1948 2.291741 GCTATGCATAGTTTGGGACTGC 59.708 50.000 29.62 12.43 39.48 4.40
1941 2055 6.173339 CCATATGATACTTCCAAATAGCGGT 58.827 40.000 3.65 0.00 0.00 5.68
1951 2065 4.693283 TCCAAATAGCGGTGTAAGATCTG 58.307 43.478 0.00 0.00 0.00 2.90
1958 2072 3.952323 AGCGGTGTAAGATCTGTTAGCTA 59.048 43.478 0.00 0.00 0.00 3.32
2005 2119 7.072961 AGGTTAGGTCAATGGTTATCAGATGAT 59.927 37.037 0.31 0.31 38.51 2.45
2022 2136 8.217131 TCAGATGATATGTCAGAAAAATGGTG 57.783 34.615 0.00 0.00 37.87 4.17
2031 2145 5.359576 TGTCAGAAAAATGGTGTAGCAAACT 59.640 36.000 0.00 0.00 0.00 2.66
2067 2181 7.660112 TCTGTTGAACTTCAAATGTGCATATT 58.340 30.769 5.76 2.38 38.22 1.28
2068 2182 8.791675 TCTGTTGAACTTCAAATGTGCATATTA 58.208 29.630 9.27 0.00 38.22 0.98
2069 2183 9.577110 CTGTTGAACTTCAAATGTGCATATTAT 57.423 29.630 9.27 0.00 38.22 1.28
2227 2341 9.052759 TGATAGTTTTGACAGAACCTTTCTTAC 57.947 33.333 5.29 0.00 38.11 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 8.964772 CCTCTAGGTCTCATTCATTTTCATTTT 58.035 33.333 0.00 0.00 0.00 1.82
24 25 7.067981 GCCTCTAGGTCTCATTCATTTTCATTT 59.932 37.037 0.00 0.00 37.57 2.32
25 26 6.545298 GCCTCTAGGTCTCATTCATTTTCATT 59.455 38.462 0.00 0.00 37.57 2.57
26 27 6.060788 GCCTCTAGGTCTCATTCATTTTCAT 58.939 40.000 0.00 0.00 37.57 2.57
27 28 5.431765 GCCTCTAGGTCTCATTCATTTTCA 58.568 41.667 0.00 0.00 37.57 2.69
28 29 4.819088 GGCCTCTAGGTCTCATTCATTTTC 59.181 45.833 0.00 0.00 36.72 2.29
29 30 4.684485 CGGCCTCTAGGTCTCATTCATTTT 60.684 45.833 0.00 0.00 37.76 1.82
30 31 3.181461 CGGCCTCTAGGTCTCATTCATTT 60.181 47.826 0.00 0.00 37.76 2.32
31 32 2.366916 CGGCCTCTAGGTCTCATTCATT 59.633 50.000 0.00 0.00 37.76 2.57
32 33 1.967066 CGGCCTCTAGGTCTCATTCAT 59.033 52.381 0.00 0.00 37.76 2.57
33 34 1.342076 ACGGCCTCTAGGTCTCATTCA 60.342 52.381 0.00 0.00 37.76 2.57
34 35 1.404843 ACGGCCTCTAGGTCTCATTC 58.595 55.000 0.00 0.00 37.76 2.67
35 36 1.757699 GAACGGCCTCTAGGTCTCATT 59.242 52.381 0.00 0.00 37.76 2.57
36 37 1.404843 GAACGGCCTCTAGGTCTCAT 58.595 55.000 0.00 0.00 37.76 2.90
37 38 1.030488 CGAACGGCCTCTAGGTCTCA 61.030 60.000 0.00 0.00 37.76 3.27
38 39 1.726533 CCGAACGGCCTCTAGGTCTC 61.727 65.000 0.00 0.00 37.76 3.36
39 40 1.753463 CCGAACGGCCTCTAGGTCT 60.753 63.158 0.00 0.00 37.76 3.85
40 41 1.318158 TTCCGAACGGCCTCTAGGTC 61.318 60.000 8.48 0.00 37.57 3.85
41 42 0.686769 ATTCCGAACGGCCTCTAGGT 60.687 55.000 8.48 0.00 37.57 3.08
42 43 0.032267 GATTCCGAACGGCCTCTAGG 59.968 60.000 8.48 0.00 38.53 3.02
43 44 0.744874 TGATTCCGAACGGCCTCTAG 59.255 55.000 8.48 0.00 34.68 2.43
44 45 0.458669 GTGATTCCGAACGGCCTCTA 59.541 55.000 8.48 0.00 34.68 2.43
45 46 1.218316 GTGATTCCGAACGGCCTCT 59.782 57.895 8.48 0.00 34.68 3.69
46 47 0.806492 GAGTGATTCCGAACGGCCTC 60.806 60.000 8.48 7.92 34.68 4.70
47 48 1.218316 GAGTGATTCCGAACGGCCT 59.782 57.895 8.48 0.00 34.68 5.19
48 49 1.814169 GGAGTGATTCCGAACGGCC 60.814 63.158 8.48 0.00 35.91 6.13
49 50 3.795638 GGAGTGATTCCGAACGGC 58.204 61.111 8.48 0.00 35.91 5.68
56 57 1.221414 GCATAGCGTGGAGTGATTCC 58.779 55.000 0.00 0.00 46.98 3.01
57 58 1.221414 GGCATAGCGTGGAGTGATTC 58.779 55.000 0.00 0.00 0.00 2.52
58 59 0.541392 TGGCATAGCGTGGAGTGATT 59.459 50.000 0.00 0.00 0.00 2.57
59 60 0.179073 GTGGCATAGCGTGGAGTGAT 60.179 55.000 0.00 0.00 0.00 3.06
60 61 1.218047 GTGGCATAGCGTGGAGTGA 59.782 57.895 0.00 0.00 0.00 3.41
61 62 0.391661 AAGTGGCATAGCGTGGAGTG 60.392 55.000 0.00 0.00 0.00 3.51
62 63 0.108138 GAAGTGGCATAGCGTGGAGT 60.108 55.000 0.00 0.00 0.00 3.85
63 64 0.108186 TGAAGTGGCATAGCGTGGAG 60.108 55.000 0.00 0.00 0.00 3.86
64 65 0.323302 TTGAAGTGGCATAGCGTGGA 59.677 50.000 0.00 0.00 0.00 4.02
65 66 1.382522 ATTGAAGTGGCATAGCGTGG 58.617 50.000 0.00 0.00 0.00 4.94
66 67 3.001634 CAGTATTGAAGTGGCATAGCGTG 59.998 47.826 0.00 0.00 0.00 5.34
67 68 3.198068 CAGTATTGAAGTGGCATAGCGT 58.802 45.455 0.00 0.00 0.00 5.07
68 69 2.545526 CCAGTATTGAAGTGGCATAGCG 59.454 50.000 0.00 0.00 41.84 4.26
69 70 3.808728 TCCAGTATTGAAGTGGCATAGC 58.191 45.455 0.00 0.00 46.94 2.97
70 71 3.812053 GCTCCAGTATTGAAGTGGCATAG 59.188 47.826 0.00 0.00 46.94 2.23
71 72 3.455910 AGCTCCAGTATTGAAGTGGCATA 59.544 43.478 0.00 0.00 46.94 3.14
72 73 2.240667 AGCTCCAGTATTGAAGTGGCAT 59.759 45.455 0.00 0.00 46.94 4.40
89 90 1.522580 GACAAGATCGGGCCAGCTC 60.523 63.158 4.39 0.57 0.00 4.09
101 102 3.026707 TCCTACCCATCATCGACAAGA 57.973 47.619 0.00 0.00 0.00 3.02
102 103 3.133003 ACTTCCTACCCATCATCGACAAG 59.867 47.826 0.00 0.00 0.00 3.16
105 106 2.959707 AGACTTCCTACCCATCATCGAC 59.040 50.000 0.00 0.00 0.00 4.20
113 114 1.559682 GGCATGAAGACTTCCTACCCA 59.440 52.381 12.66 0.00 0.00 4.51
114 115 1.134068 GGGCATGAAGACTTCCTACCC 60.134 57.143 16.46 16.46 0.00 3.69
116 117 2.633488 GTGGGCATGAAGACTTCCTAC 58.367 52.381 12.66 2.38 0.00 3.18
118 119 0.036010 CGTGGGCATGAAGACTTCCT 60.036 55.000 12.66 0.00 0.00 3.36
132 133 2.033448 TGGCCTTACAAGCGTGGG 59.967 61.111 3.32 0.00 0.00 4.61
152 153 3.372554 GACTCTACGGCACCAGGGC 62.373 68.421 0.00 0.00 39.06 5.19
161 162 6.973474 AGATTGATTTAACGAAGACTCTACGG 59.027 38.462 0.00 0.00 0.00 4.02
171 172 7.659799 TCAGGTTCTTCAGATTGATTTAACGAA 59.340 33.333 0.00 0.00 0.00 3.85
177 178 5.474876 GGTGTCAGGTTCTTCAGATTGATTT 59.525 40.000 0.00 0.00 0.00 2.17
190 191 6.213677 GGTTTCTTAATTTGGTGTCAGGTTC 58.786 40.000 0.00 0.00 0.00 3.62
193 194 4.832823 AGGGTTTCTTAATTTGGTGTCAGG 59.167 41.667 0.00 0.00 0.00 3.86
206 207 2.094545 GTCGCCGAGTTAGGGTTTCTTA 60.095 50.000 0.00 0.00 0.00 2.10
207 208 0.971386 TCGCCGAGTTAGGGTTTCTT 59.029 50.000 0.00 0.00 0.00 2.52
208 209 0.245813 GTCGCCGAGTTAGGGTTTCT 59.754 55.000 0.00 0.00 0.00 2.52
223 245 4.500116 GACAGCTCCTCGGGTCGC 62.500 72.222 0.00 0.00 0.00 5.19
229 251 1.110442 AGATTCCTGACAGCTCCTCG 58.890 55.000 0.00 0.00 0.00 4.63
237 259 6.368791 CGAAACTTCAATGTAGATTCCTGACA 59.631 38.462 4.78 0.00 0.00 3.58
247 269 6.508088 GCGGATTAGACGAAACTTCAATGTAG 60.508 42.308 0.00 0.00 0.00 2.74
252 274 2.997986 GGCGGATTAGACGAAACTTCAA 59.002 45.455 0.00 0.00 0.00 2.69
258 280 1.142314 CGGGGCGGATTAGACGAAA 59.858 57.895 0.00 0.00 0.00 3.46
261 283 2.027169 GTCGGGGCGGATTAGACG 59.973 66.667 0.00 0.00 0.00 4.18
274 296 2.809601 CTCAAACTCGCCCGTCGG 60.810 66.667 3.60 3.60 39.05 4.79
278 300 0.108138 ATTCTCCTCAAACTCGCCCG 60.108 55.000 0.00 0.00 0.00 6.13
282 304 2.263077 CACCGATTCTCCTCAAACTCG 58.737 52.381 0.00 0.00 0.00 4.18
291 313 0.451783 ATTTTGCGCACCGATTCTCC 59.548 50.000 11.12 0.00 0.00 3.71
304 326 6.466097 GCTTATTGTTCGAGTCAGTATTTTGC 59.534 38.462 0.00 0.00 0.00 3.68
305 327 6.678663 CGCTTATTGTTCGAGTCAGTATTTTG 59.321 38.462 0.00 0.00 0.00 2.44
306 328 6.672357 GCGCTTATTGTTCGAGTCAGTATTTT 60.672 38.462 0.00 0.00 0.00 1.82
307 329 5.220416 GCGCTTATTGTTCGAGTCAGTATTT 60.220 40.000 0.00 0.00 0.00 1.40
310 332 3.176708 GCGCTTATTGTTCGAGTCAGTA 58.823 45.455 0.00 0.00 0.00 2.74
350 372 3.437049 GGATTTTAGTCCTCATATGCGGC 59.563 47.826 6.87 2.81 35.32 6.53
351 373 4.003648 GGGATTTTAGTCCTCATATGCGG 58.996 47.826 5.30 5.30 38.38 5.69
353 375 6.655425 GGTTAGGGATTTTAGTCCTCATATGC 59.345 42.308 0.00 0.00 38.38 3.14
354 376 7.978925 AGGTTAGGGATTTTAGTCCTCATATG 58.021 38.462 0.00 0.00 38.38 1.78
355 377 9.860393 ATAGGTTAGGGATTTTAGTCCTCATAT 57.140 33.333 0.00 0.00 38.38 1.78
380 402 9.573166 CTAATATATCAGCTCTGCCTAGTAGAT 57.427 37.037 0.00 0.00 0.00 1.98
389 411 9.097257 GAAAGAATCCTAATATATCAGCTCTGC 57.903 37.037 0.00 0.00 0.00 4.26
419 441 2.887568 CTTCGGCGGCTGCTAGTG 60.888 66.667 18.85 5.39 42.25 2.74
420 442 4.821589 GCTTCGGCGGCTGCTAGT 62.822 66.667 18.85 0.00 42.25 2.57
422 444 4.819761 CTGCTTCGGCGGCTGCTA 62.820 66.667 18.85 2.89 45.37 3.49
429 451 0.524392 CTCTGTCTACTGCTTCGGCG 60.524 60.000 0.00 0.00 45.37 6.46
430 452 0.179124 CCTCTGTCTACTGCTTCGGC 60.179 60.000 0.00 0.00 42.19 5.54
439 461 3.350219 TTTTGCATCCCCTCTGTCTAC 57.650 47.619 0.00 0.00 0.00 2.59
458 480 6.084326 ACGTTCATAGGTTGCAATCTTTTT 57.916 33.333 19.17 0.32 0.00 1.94
463 485 4.970003 GCATTACGTTCATAGGTTGCAATC 59.030 41.667 0.59 0.23 30.26 2.67
465 487 4.006989 AGCATTACGTTCATAGGTTGCAA 58.993 39.130 0.00 0.00 31.55 4.08
474 497 8.668510 AATCATCTAGAAAGCATTACGTTCAT 57.331 30.769 0.00 0.00 39.01 2.57
507 531 7.856415 ACCTCTATGAGCTCTGTTTATTTTCT 58.144 34.615 16.19 0.00 0.00 2.52
508 532 9.771534 ATACCTCTATGAGCTCTGTTTATTTTC 57.228 33.333 16.19 0.00 0.00 2.29
509 533 9.553064 CATACCTCTATGAGCTCTGTTTATTTT 57.447 33.333 16.19 0.00 32.66 1.82
510 534 8.153550 CCATACCTCTATGAGCTCTGTTTATTT 58.846 37.037 16.19 0.00 32.66 1.40
511 535 7.291182 ACCATACCTCTATGAGCTCTGTTTATT 59.709 37.037 16.19 0.00 32.66 1.40
512 536 6.784969 ACCATACCTCTATGAGCTCTGTTTAT 59.215 38.462 16.19 1.74 32.66 1.40
519 543 5.478679 ACACATACCATACCTCTATGAGCTC 59.521 44.000 6.82 6.82 32.66 4.09
529 553 3.386726 ACGCATACACACATACCATACCT 59.613 43.478 0.00 0.00 0.00 3.08
544 568 4.573201 ACACACCCATATAAACACGCATAC 59.427 41.667 0.00 0.00 0.00 2.39
580 604 8.414003 ACACAATACAGACATAGACGATTGTAT 58.586 33.333 0.00 0.00 35.02 2.29
583 607 7.525688 AACACAATACAGACATAGACGATTG 57.474 36.000 0.00 0.00 0.00 2.67
584 608 9.647797 TTTAACACAATACAGACATAGACGATT 57.352 29.630 0.00 0.00 0.00 3.34
586 610 9.478768 TTTTTAACACAATACAGACATAGACGA 57.521 29.630 0.00 0.00 0.00 4.20
635 662 9.630098 CAGCTTGTCACACAAAATAATAATTCT 57.370 29.630 0.00 0.00 37.69 2.40
636 663 8.375465 GCAGCTTGTCACACAAAATAATAATTC 58.625 33.333 0.00 0.00 37.69 2.17
637 664 8.090214 AGCAGCTTGTCACACAAAATAATAATT 58.910 29.630 0.00 0.00 37.69 1.40
638 665 7.605449 AGCAGCTTGTCACACAAAATAATAAT 58.395 30.769 0.00 0.00 37.69 1.28
642 669 4.916983 AGCAGCTTGTCACACAAAATAA 57.083 36.364 0.00 0.00 37.69 1.40
643 670 4.916983 AAGCAGCTTGTCACACAAAATA 57.083 36.364 6.93 0.00 37.69 1.40
644 671 3.806625 AAGCAGCTTGTCACACAAAAT 57.193 38.095 6.93 0.00 37.69 1.82
649 676 3.111098 CTCAAAAAGCAGCTTGTCACAC 58.889 45.455 8.88 0.00 0.00 3.82
651 678 3.698029 TCTCAAAAAGCAGCTTGTCAC 57.302 42.857 8.88 0.00 0.00 3.67
662 689 6.359087 CGCATCTCTTTTCACTTCTCAAAAAG 59.641 38.462 0.00 0.00 39.97 2.27
683 710 7.523293 TGGAAAATTTGATATATCACCGCAT 57.477 32.000 15.10 2.43 36.36 4.73
743 776 1.789464 GCGCCAAGACGAATAGATCTG 59.211 52.381 5.18 0.00 34.06 2.90
744 777 1.600663 CGCGCCAAGACGAATAGATCT 60.601 52.381 0.00 0.00 34.06 2.75
745 778 0.778815 CGCGCCAAGACGAATAGATC 59.221 55.000 0.00 0.00 34.06 2.75
746 779 0.384309 TCGCGCCAAGACGAATAGAT 59.616 50.000 0.00 0.00 34.93 1.98
747 780 0.384309 ATCGCGCCAAGACGAATAGA 59.616 50.000 0.00 0.00 42.31 1.98
748 781 2.046283 TATCGCGCCAAGACGAATAG 57.954 50.000 0.00 0.00 42.31 1.73
749 782 2.717580 ATATCGCGCCAAGACGAATA 57.282 45.000 0.00 0.00 42.31 1.75
750 783 2.717580 TATATCGCGCCAAGACGAAT 57.282 45.000 0.00 0.00 42.31 3.34
751 784 2.030628 TGATATATCGCGCCAAGACGAA 60.031 45.455 0.00 0.00 42.31 3.85
752 785 1.538075 TGATATATCGCGCCAAGACGA 59.462 47.619 0.00 0.00 43.33 4.20
761 794 4.025396 GGCCATCTCATTTGATATATCGCG 60.025 45.833 0.00 0.00 0.00 5.87
765 798 5.198965 GCTGGGCCATCTCATTTGATATAT 58.801 41.667 6.72 0.00 0.00 0.86
853 886 3.433173 GGGTGGTAATCAGCGGAGTATTT 60.433 47.826 0.00 0.00 44.29 1.40
956 1004 1.653094 CTCTCTCTCCTCGTGCGCTT 61.653 60.000 9.73 0.00 0.00 4.68
1084 1132 1.540363 GGTGCTCTTCTTCACGTTGGA 60.540 52.381 0.00 0.00 34.20 3.53
1086 1134 0.508641 CGGTGCTCTTCTTCACGTTG 59.491 55.000 0.00 0.00 34.20 4.10
1355 1403 0.181587 TCAAGCAGACGGGGTTCAAA 59.818 50.000 0.00 0.00 0.00 2.69
1398 1448 1.274596 CACGTACATGCGACCTTACC 58.725 55.000 0.00 0.00 35.59 2.85
1399 1449 1.274596 CCACGTACATGCGACCTTAC 58.725 55.000 0.00 0.00 35.59 2.34
1412 1464 1.585267 ATCGTACCGCACACCACGTA 61.585 55.000 0.00 0.00 35.91 3.57
1474 1526 5.621197 TCATACAAAACCTCGTCCAAATG 57.379 39.130 0.00 0.00 0.00 2.32
1476 1528 6.488683 AGAATTCATACAAAACCTCGTCCAAA 59.511 34.615 8.44 0.00 0.00 3.28
1481 1533 5.313712 ACCAGAATTCATACAAAACCTCGT 58.686 37.500 8.44 0.00 0.00 4.18
1482 1534 5.880054 ACCAGAATTCATACAAAACCTCG 57.120 39.130 8.44 0.00 0.00 4.63
1485 1537 5.856455 CGACAACCAGAATTCATACAAAACC 59.144 40.000 8.44 0.00 0.00 3.27
1486 1538 5.856455 CCGACAACCAGAATTCATACAAAAC 59.144 40.000 8.44 0.00 0.00 2.43
1487 1539 5.048364 CCCGACAACCAGAATTCATACAAAA 60.048 40.000 8.44 0.00 0.00 2.44
1530 1582 3.490155 CGCAAGTGATTCAAATGCACAAA 59.510 39.130 19.18 0.00 36.84 2.83
1624 1676 2.302260 TGAAATGGGCGTGAAACAGAA 58.698 42.857 0.00 0.00 35.74 3.02
1635 1695 1.134907 CACTGGCAGAATGAAATGGGC 60.135 52.381 23.66 0.00 39.69 5.36
1636 1696 2.449464 TCACTGGCAGAATGAAATGGG 58.551 47.619 23.66 0.00 39.69 4.00
1682 1796 8.410141 CCATAGAAGTGGTCAAACTTTGTAAAA 58.590 33.333 1.44 0.00 40.48 1.52
1703 1817 4.510038 AACAGAAAAGTGCAAGCCATAG 57.490 40.909 0.00 0.00 0.00 2.23
1770 1884 7.040478 GCAAGCTATAATCACAAATGATACCCA 60.040 37.037 0.00 0.00 45.26 4.51
1794 1908 0.590682 CCAACGCAATACACAGTGCA 59.409 50.000 0.00 0.00 45.96 4.57
1804 1918 2.575532 ACTATGCATAGCCAACGCAAT 58.424 42.857 29.60 7.65 39.48 3.56
1834 1948 3.040147 AGGTTGATACAACTGTCACCG 57.960 47.619 13.05 0.00 0.00 4.94
1843 1957 6.058833 TGCAGTAACTTGAAGGTTGATACAA 58.941 36.000 0.00 0.00 0.00 2.41
1941 2055 9.368416 AGGTGAATATAGCTAACAGATCTTACA 57.632 33.333 0.00 0.00 0.00 2.41
2005 2119 7.230510 AGTTTGCTACACCATTTTTCTGACATA 59.769 33.333 0.00 0.00 0.00 2.29
2022 2136 6.735130 ACAGAACATTAAACCAGTTTGCTAC 58.265 36.000 6.03 0.00 34.23 3.58
2031 2145 7.397892 TGAAGTTCAACAGAACATTAAACCA 57.602 32.000 2.20 0.00 43.18 3.67
2067 2181 6.350949 GGCCTTCAAAAGCACTTAAATCCATA 60.351 38.462 0.00 0.00 0.00 2.74
2068 2182 5.482006 GCCTTCAAAAGCACTTAAATCCAT 58.518 37.500 0.00 0.00 0.00 3.41
2069 2183 4.262420 GGCCTTCAAAAGCACTTAAATCCA 60.262 41.667 0.00 0.00 0.00 3.41
2080 2194 1.869132 CTGCAAAAGGCCTTCAAAAGC 59.131 47.619 20.79 17.83 43.89 3.51
2200 2314 7.497925 AGAAAGGTTCTGTCAAAACTATCAC 57.502 36.000 0.00 0.00 38.91 3.06
2227 2341 9.019764 CACTTTTGTTCCTACACAATTTAGTTG 57.980 33.333 0.00 0.00 43.64 3.16


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

AutoCloner maintained by Alex Coulton.