Multiple sequence alignment - TraesCS3A01G118700

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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 TraesCS3A01G118700 chr3A 100.000 8737 0 0 1 8737 90864829 90856093 0.000000e+00 16135.0
1 TraesCS3A01G118700 chr3D 96.149 8075 205 27 1 8056 76384764 76376777 0.000000e+00 13092.0
2 TraesCS3A01G118700 chr3D 95.335 686 29 1 8055 8737 76376694 76376009 0.000000e+00 1086.0
3 TraesCS3A01G118700 chr3B 95.128 6609 209 31 1 6580 123358626 123352102 0.000000e+00 10316.0
4 TraesCS3A01G118700 chr3B 95.415 1025 20 4 6661 7661 123351749 123350728 0.000000e+00 1607.0
5 TraesCS3A01G118700 chr3B 90.476 273 17 1 8474 8737 123350731 123350459 1.400000e-92 351.0
6 TraesCS3A01G118700 chr6A 80.134 448 72 14 6151 6594 573821992 573821558 1.420000e-82 318.0
7 TraesCS3A01G118700 chr1B 79.018 448 74 10 6151 6594 554655310 554655741 1.110000e-73 289.0
8 TraesCS3A01G118700 chr1B 95.918 49 2 0 1447 1495 249622188 249622236 7.270000e-11 80.5
9 TraesCS3A01G118700 chr6B 79.018 448 73 13 6151 6594 546034653 546034223 3.990000e-73 287.0
10 TraesCS3A01G118700 chr6B 82.988 241 36 5 6146 6384 645901996 645902233 6.870000e-51 213.0
11 TraesCS3A01G118700 chr6B 77.387 199 37 5 4006 4196 645810961 645810763 2.580000e-20 111.0
12 TraesCS3A01G118700 chr5B 81.871 342 55 4 6151 6489 461888647 461888984 1.860000e-71 281.0
13 TraesCS3A01G118700 chr5B 81.159 345 54 6 2901 3243 35550010 35549675 5.200000e-67 267.0
14 TraesCS3A01G118700 chr2B 81.818 341 55 6 6151 6488 501796787 501797123 6.680000e-71 279.0
15 TraesCS3A01G118700 chr2A 77.455 448 71 18 6151 6594 398489193 398488772 3.150000e-59 241.0
16 TraesCS3A01G118700 chr2A 77.143 455 72 20 6146 6594 398834130 398834558 1.470000e-57 235.0
17 TraesCS3A01G118700 chr2A 85.714 77 10 1 4120 4196 398489564 398489489 7.270000e-11 80.5
18 TraesCS3A01G118700 chr2A 85.714 77 10 1 4120 4196 398833766 398833841 7.270000e-11 80.5
19 TraesCS3A01G118700 chr1D 95.918 49 2 0 1447 1495 169068240 169068192 7.270000e-11 80.5
20 TraesCS3A01G118700 chr1A 95.745 47 2 0 1447 1493 225516976 225516930 9.410000e-10 76.8
21 TraesCS3A01G118700 chr1A 100.000 30 0 0 8041 8070 580738343 580738314 1.000000e-03 56.5
22 TraesCS3A01G118700 chr7D 86.364 66 8 1 8040 8105 26731086 26731150 4.380000e-08 71.3
23 TraesCS3A01G118700 chrUn 93.478 46 3 0 8414 8459 405467503 405467548 1.570000e-07 69.4
24 TraesCS3A01G118700 chr4B 77.320 97 22 0 8037 8133 633757639 633757735 3.410000e-04 58.4
25 TraesCS3A01G118700 chr7B 100.000 28 0 0 8041 8068 641143545 641143572 1.600000e-02 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 TraesCS3A01G118700 chr3A 90856093 90864829 8736 True 16135.000000 16135 100.000 1 8737 1 chr3A.!!$R1 8736
1 TraesCS3A01G118700 chr3D 76376009 76384764 8755 True 7089.000000 13092 95.742 1 8737 2 chr3D.!!$R1 8736
2 TraesCS3A01G118700 chr3B 123350459 123358626 8167 True 4091.333333 10316 93.673 1 8737 3 chr3B.!!$R1 8736

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
642 647 0.343018 TGGGGATGATGAGGAGGTCA 59.657 55.000 0.00 0.00 40.38 4.02 F
1408 1413 0.032678 CAAGATCGATCTGGGACCCG 59.967 60.000 27.93 7.66 37.19 5.28 F
1706 1721 0.036010 CAGAGCCAACAAGATCCGGT 60.036 55.000 0.00 0.00 0.00 5.28 F
2366 2381 0.320160 GGAAGCGTGACGGTAAAGGT 60.320 55.000 11.01 0.00 36.27 3.50 F
4295 4312 0.321671 GTAGTTCACCAGGCTGCTCA 59.678 55.000 9.56 0.00 0.00 4.26 F
4783 4800 1.072173 ACATGTCAACTGGCAGTGCTA 59.928 47.619 22.83 8.29 30.80 3.49 F
6467 6507 0.183731 GGCTTCAGGTATCCAAGGGG 59.816 60.000 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1721 1.000843 CTCCATGTGGTGTCACTCGAA 59.999 52.381 2.35 0.0 43.94 3.71 R
3326 3341 1.002366 CCTGATTGAAGCTTCCGACG 58.998 55.000 23.42 8.2 0.00 5.12 R
3379 3394 3.610619 CTGACCGAGGTGCATGGCA 62.611 63.158 0.00 0.0 35.60 4.92 R
4364 4381 0.841289 ACCCGTCTCCAAGGAACAAA 59.159 50.000 0.00 0.0 0.00 2.83 R
5322 5339 0.236187 GGCGCACAAACGATACAACA 59.764 50.000 10.83 0.0 34.06 3.33 R
6772 7084 0.109086 CTGTCCGAAGCATCAGACGT 60.109 55.000 1.24 0.0 0.00 4.34 R
7776 8112 0.109781 AACATGTCCAAACGCATCGC 60.110 50.000 0.00 0.0 0.00 4.58 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
78 79 3.632145 ACAAGTAGAAAACAGGGCACAAG 59.368 43.478 0.00 0.00 0.00 3.16
80 81 1.886542 GTAGAAAACAGGGCACAAGGG 59.113 52.381 0.00 0.00 0.00 3.95
117 119 0.447801 CAGCGCCAACACAGGTAATC 59.552 55.000 2.29 0.00 0.00 1.75
126 128 4.035558 CCAACACAGGTAATCGAATCCATG 59.964 45.833 0.00 0.00 0.00 3.66
297 302 7.153478 GTTGCAAACTTGTTGTAAGATCAAG 57.847 36.000 0.00 0.00 45.32 3.02
309 314 1.542492 AGATCAAGTTGCAAGCAGGG 58.458 50.000 0.00 0.00 0.00 4.45
314 319 1.068055 CAAGTTGCAAGCAGGGATGTC 60.068 52.381 0.00 0.00 0.00 3.06
316 321 2.334946 TTGCAAGCAGGGATGTCGC 61.335 57.895 0.00 0.00 0.00 5.19
317 322 2.747460 GCAAGCAGGGATGTCGCA 60.747 61.111 0.00 0.00 0.00 5.10
344 349 8.499162 GTCATCATACATTTACTTGCATACTCC 58.501 37.037 0.00 0.00 0.00 3.85
347 352 8.437360 TCATACATTTACTTGCATACTCCAAG 57.563 34.615 0.00 0.00 43.98 3.61
366 371 2.224606 AGCATATGATGTGAAAGCCGG 58.775 47.619 6.97 0.00 0.00 6.13
370 375 4.790878 CATATGATGTGAAAGCCGGATTG 58.209 43.478 5.31 0.00 0.00 2.67
388 393 7.087639 CCGGATTGATCTTCTCTAGACATAAC 58.912 42.308 0.00 0.00 35.19 1.89
469 474 8.322091 AGGCACTAACAAGAAGATTAATACAGT 58.678 33.333 0.00 0.00 36.02 3.55
470 475 8.947115 GGCACTAACAAGAAGATTAATACAGTT 58.053 33.333 0.00 0.00 0.00 3.16
493 498 9.656323 AGTTATACAGGGTCTAACAGATTCATA 57.344 33.333 7.20 0.00 30.78 2.15
523 528 2.213499 CAGAACTGGCCGGAATATGAC 58.787 52.381 21.41 1.15 0.00 3.06
539 544 1.302192 GACAGTACCTGCCGGCAAA 60.302 57.895 32.09 16.29 34.37 3.68
642 647 0.343018 TGGGGATGATGAGGAGGTCA 59.657 55.000 0.00 0.00 40.38 4.02
677 682 2.369015 TGGGGGCGTGGGGATTAT 60.369 61.111 0.00 0.00 0.00 1.28
810 815 4.493747 CCGACCGACGAAGGAGCC 62.494 72.222 7.84 0.00 45.77 4.70
853 858 0.638242 GCGCTTTTTATTTTCCGCCG 59.362 50.000 0.00 0.00 35.86 6.46
1021 1026 1.199615 CTTCTTCCTCCTCCACCTCC 58.800 60.000 0.00 0.00 0.00 4.30
1022 1027 0.491823 TTCTTCCTCCTCCACCTCCA 59.508 55.000 0.00 0.00 0.00 3.86
1023 1028 0.252284 TCTTCCTCCTCCACCTCCAC 60.252 60.000 0.00 0.00 0.00 4.02
1024 1029 1.229529 TTCCTCCTCCACCTCCACC 60.230 63.158 0.00 0.00 0.00 4.61
1025 1030 1.751143 TTCCTCCTCCACCTCCACCT 61.751 60.000 0.00 0.00 0.00 4.00
1026 1031 1.687493 CCTCCTCCACCTCCACCTC 60.687 68.421 0.00 0.00 0.00 3.85
1329 1334 3.933048 CTCCTGCCCTGTTGCCTGG 62.933 68.421 0.00 0.00 0.00 4.45
1399 1404 2.018866 CCGGCGAGCAAGATCGATC 61.019 63.158 17.91 17.91 45.56 3.69
1400 1405 1.007964 CGGCGAGCAAGATCGATCT 60.008 57.895 22.32 22.32 45.56 2.75
1401 1406 1.274126 CGGCGAGCAAGATCGATCTG 61.274 60.000 27.93 20.96 45.56 2.90
1402 1407 0.943359 GGCGAGCAAGATCGATCTGG 60.943 60.000 27.93 25.53 45.56 3.86
1403 1408 0.943359 GCGAGCAAGATCGATCTGGG 60.943 60.000 27.93 22.43 45.56 4.45
1404 1409 0.670706 CGAGCAAGATCGATCTGGGA 59.329 55.000 27.93 0.00 45.56 4.37
1405 1410 1.601663 CGAGCAAGATCGATCTGGGAC 60.602 57.143 27.93 16.79 45.56 4.46
1406 1411 0.755686 AGCAAGATCGATCTGGGACC 59.244 55.000 27.93 12.59 37.19 4.46
1407 1412 0.250081 GCAAGATCGATCTGGGACCC 60.250 60.000 27.93 8.89 37.19 4.46
1408 1413 0.032678 CAAGATCGATCTGGGACCCG 59.967 60.000 27.93 7.66 37.19 5.28
1629 1644 1.552337 CTTCAAGCACTCCCTCTGCTA 59.448 52.381 0.00 0.00 44.45 3.49
1706 1721 0.036010 CAGAGCCAACAAGATCCGGT 60.036 55.000 0.00 0.00 0.00 5.28
1926 1941 5.206905 ACCCAATGGTATTTCTAAGCCTT 57.793 39.130 0.00 0.00 45.45 4.35
1993 2008 0.951040 GAGAACAGAGTTGGTGGCGG 60.951 60.000 0.00 0.00 0.00 6.13
1997 2012 1.003355 CAGAGTTGGTGGCGGTGAT 60.003 57.895 0.00 0.00 0.00 3.06
2005 2020 1.221840 GTGGCGGTGATCCTGTCAT 59.778 57.895 1.41 0.00 39.48 3.06
2078 2093 5.639506 GTCTTGTTCGGAAAATGATCTCTCA 59.360 40.000 0.00 0.00 35.41 3.27
2289 2304 6.931840 GGAATCTAATCTTCACCGCTCTAATT 59.068 38.462 0.00 0.00 0.00 1.40
2366 2381 0.320160 GGAAGCGTGACGGTAAAGGT 60.320 55.000 11.01 0.00 36.27 3.50
2897 2912 1.318886 TACATGCAAATGGTGGCCCG 61.319 55.000 0.00 0.00 0.00 6.13
3120 3135 9.407380 TGAAATATGTCATATTGGTGTTAAGCT 57.593 29.630 17.00 0.00 35.71 3.74
3297 3312 4.513318 ACTTGCTTCTTGAGACTTGCTTAC 59.487 41.667 0.00 0.00 0.00 2.34
3326 3341 7.041780 TCAGCAGTATTTCTTTTCTGTTCACTC 60.042 37.037 0.00 0.00 0.00 3.51
3379 3394 7.758528 GCTGAATGCTTTTAATGAATCAGAAGT 59.241 33.333 0.00 0.00 36.11 3.01
3549 3564 5.606505 TGTCTAAAGTTGACTGCACATACA 58.393 37.500 0.00 0.00 35.63 2.29
3551 3566 4.994852 TCTAAAGTTGACTGCACATACACC 59.005 41.667 0.00 0.00 0.00 4.16
3631 3646 4.931661 TTTCGAAGGTACAGAACTCACT 57.068 40.909 0.00 0.00 0.00 3.41
3749 3766 2.747446 ACTATCCATGGTTTGCACGTTC 59.253 45.455 12.58 0.00 0.00 3.95
3803 3820 1.228245 TCAGCTGCACCCCAAGTTC 60.228 57.895 9.47 0.00 0.00 3.01
3808 3825 1.227823 TGCACCCCAAGTTCGACTG 60.228 57.895 0.00 0.00 0.00 3.51
3862 3879 2.037772 ACTGTGGAGTTACAAGCCAGAG 59.962 50.000 12.08 12.08 45.60 3.35
4115 4132 2.545946 GGCAGAGTTTATCTTCCGATGC 59.454 50.000 0.00 0.00 35.47 3.91
4197 4214 8.746922 TTTGTCTTGATAATCAAAGTGAATGC 57.253 30.769 0.00 0.00 35.73 3.56
4295 4312 0.321671 GTAGTTCACCAGGCTGCTCA 59.678 55.000 9.56 0.00 0.00 4.26
4317 4334 8.891720 GCTCATTCTGAAATTTCTGTAGAAGAT 58.108 33.333 18.64 3.98 33.93 2.40
4502 4519 8.437742 CAAACTTTGTTCTTCCAATCATAATGC 58.562 33.333 0.00 0.00 0.00 3.56
4650 4667 6.729690 AACTTGGTTCAGGAATTGAATGAA 57.270 33.333 0.00 0.00 46.85 2.57
4783 4800 1.072173 ACATGTCAACTGGCAGTGCTA 59.928 47.619 22.83 8.29 30.80 3.49
4905 4922 3.935203 CTCACAACATCGCCAAGACTAAT 59.065 43.478 0.00 0.00 0.00 1.73
4911 4928 3.270027 CATCGCCAAGACTAATGGTTCA 58.730 45.455 0.00 0.00 40.23 3.18
5030 5047 6.438741 TGGAGGGAATATGATACTCAGATCAC 59.561 42.308 0.00 0.00 38.64 3.06
5035 5052 9.160496 GGGAATATGATACTCAGATCACAATTC 57.840 37.037 0.00 11.39 38.64 2.17
5313 5330 1.197721 CGCTTGGTTGAAGGTCATGAC 59.802 52.381 17.91 17.91 31.56 3.06
5314 5331 2.229792 GCTTGGTTGAAGGTCATGACA 58.770 47.619 26.47 3.80 31.56 3.58
5322 5339 6.891361 TGGTTGAAGGTCATGACAATAATGAT 59.109 34.615 26.47 3.74 36.49 2.45
5367 5384 5.124457 CCAAGATTATCTTTGCCATATCGGG 59.876 44.000 4.51 0.00 33.78 5.14
5424 5441 8.193438 CGTGTGATATATGACATGGATAGTGAT 58.807 37.037 14.70 0.00 28.99 3.06
5481 5498 7.282450 TCTCAGCGAGATAAGAACAACACTATA 59.718 37.037 4.47 0.00 33.35 1.31
5584 5601 6.238593 GCTCACCATTGATCAGATTAAGGAAC 60.239 42.308 1.31 0.00 0.00 3.62
5751 5776 5.294552 GCCTTACTTTCCTGTACATGATCAC 59.705 44.000 0.00 0.00 0.00 3.06
5980 6017 5.555966 TGGAGCACTGTGTTAACATAATGA 58.444 37.500 16.58 0.00 35.22 2.57
6048 6085 6.420604 ACAACACCAATCGATTAAAGCAAAAG 59.579 34.615 10.97 0.00 0.00 2.27
6054 6091 8.306761 ACCAATCGATTAAAGCAAAAGATTCTT 58.693 29.630 10.97 0.00 29.35 2.52
6056 6093 9.132521 CAATCGATTAAAGCAAAAGATTCTTGT 57.867 29.630 10.97 0.00 29.35 3.16
6127 6166 9.007901 ACTTGATTTGGAGTTTCTCTTCTAATG 57.992 33.333 0.00 0.00 29.68 1.90
6177 6216 2.999185 TGCTTCCAGGGAAAGGATTT 57.001 45.000 1.90 0.00 43.98 2.17
6196 6236 8.552083 AGGATTTATTGTTGCATTTCTTTTCC 57.448 30.769 0.00 0.00 0.00 3.13
6210 6250 4.937201 TCTTTTCCGCTATCATGCTCTA 57.063 40.909 0.00 0.00 0.00 2.43
6259 6299 4.046462 CCAGCAAACAATGTTGAGACTTG 58.954 43.478 0.00 0.00 42.37 3.16
6402 6442 2.936032 AAGGAAAGAGGCCGCCCT 60.936 61.111 5.55 0.00 46.74 5.19
6467 6507 0.183731 GGCTTCAGGTATCCAAGGGG 59.816 60.000 0.00 0.00 0.00 4.79
6592 6632 0.238289 CAAATCAACGGCTCGTGCTT 59.762 50.000 9.61 0.00 39.99 3.91
6772 7084 0.537188 GAGAACAGATTCCCCTCGCA 59.463 55.000 0.00 0.00 35.18 5.10
6837 7149 6.374333 GGACTAACAGTATGAAAAGGAATGCA 59.626 38.462 0.00 0.00 39.69 3.96
7268 7601 6.405176 CGATAGGATCAATGCAGTAGATAGCA 60.405 42.308 0.00 0.00 45.92 3.49
7603 7936 1.202580 GGACATATGGCTCTGCGTCTT 60.203 52.381 8.85 0.00 0.00 3.01
7604 7937 2.035961 GGACATATGGCTCTGCGTCTTA 59.964 50.000 8.85 0.00 0.00 2.10
7616 7949 3.068448 TCTGCGTCTTACAAGTGTTGGTA 59.932 43.478 0.00 0.00 34.12 3.25
7647 7983 4.149747 CGCACTGTTTGTTTTTCTGTTTGT 59.850 37.500 0.00 0.00 0.00 2.83
7651 7987 6.423604 CACTGTTTGTTTTTCTGTTTGTCCTT 59.576 34.615 0.00 0.00 0.00 3.36
7675 8011 2.040464 ACATGGGCCGGGATCTCT 60.040 61.111 2.18 0.00 0.00 3.10
7695 8031 4.280019 GCGGTGGAGGTTGGGGTT 62.280 66.667 0.00 0.00 0.00 4.11
7746 8082 1.648467 GATTGGTTCAGCTCGGGCAC 61.648 60.000 11.40 0.00 41.70 5.01
7775 8111 1.412453 TTCCAAGGGTGTGTACGGCT 61.412 55.000 0.00 0.00 0.00 5.52
7776 8112 1.671054 CCAAGGGTGTGTACGGCTG 60.671 63.158 0.00 0.00 0.00 4.85
7777 8113 2.032071 AAGGGTGTGTACGGCTGC 59.968 61.111 0.00 0.00 0.00 5.25
7779 8115 4.367023 GGGTGTGTACGGCTGCGA 62.367 66.667 0.00 0.00 0.00 5.10
7780 8116 2.125673 GGTGTGTACGGCTGCGAT 60.126 61.111 0.00 0.00 0.00 4.58
7781 8117 2.452813 GGTGTGTACGGCTGCGATG 61.453 63.158 0.00 0.00 0.00 3.84
7782 8118 2.813474 TGTGTACGGCTGCGATGC 60.813 61.111 0.00 0.00 0.00 3.91
7811 8147 7.512130 TGGACATGTTGAGCATAGATTATCTT 58.488 34.615 0.00 0.00 35.74 2.40
7865 8201 7.599621 TGCTGATATGAGATTTTGTTTGTTTGG 59.400 33.333 0.00 0.00 0.00 3.28
7983 8319 3.088532 GGTCCACAGATTGGCATACAAA 58.911 45.455 0.00 0.00 46.47 2.83
7984 8320 3.701040 GGTCCACAGATTGGCATACAAAT 59.299 43.478 0.00 0.00 46.47 2.32
8086 8506 4.082895 AGACGTTTTCTCGCACTACACTAT 60.083 41.667 0.00 0.00 0.00 2.12
8121 8541 8.918202 AACATCTTACACTATGAAACAAAGGA 57.082 30.769 0.00 0.00 0.00 3.36
8199 8619 9.528018 TCTAATTCACACAACAAGAAATTTTCC 57.472 29.630 5.52 0.00 0.00 3.13
8210 8630 6.888105 ACAAGAAATTTTCCACACCATTTCT 58.112 32.000 5.52 0.00 44.32 2.52
8219 8639 2.095853 CCACACCATTTCTACGATGCAC 59.904 50.000 0.00 0.00 0.00 4.57
8240 8660 3.769844 ACTCCATCCAACGTGTATTCTCT 59.230 43.478 0.00 0.00 0.00 3.10
8241 8661 4.115516 CTCCATCCAACGTGTATTCTCTG 58.884 47.826 0.00 0.00 0.00 3.35
8247 8670 3.432252 CCAACGTGTATTCTCTGGTTCAC 59.568 47.826 0.00 0.00 0.00 3.18
8338 8761 4.641094 CGACAAATCCTCCTCACTAGTACT 59.359 45.833 0.00 0.00 0.00 2.73
8369 8792 2.169832 ACTGTTGAACATGGGAGTCG 57.830 50.000 0.00 0.00 0.00 4.18
8443 8866 1.561769 TAGGGTCACTGGCATGTGGG 61.562 60.000 14.28 0.00 38.40 4.61
8709 9141 7.333174 TGACAAGATAATCAAGTACGATTGCAA 59.667 33.333 0.00 0.00 36.31 4.08
8725 9157 5.049405 CGATTGCAAGAAGAACTACAAAGGT 60.049 40.000 4.94 0.00 31.69 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.073923 AGTAGTTTCCCTTGTGCCCTG 59.926 52.381 0.00 0.00 0.00 4.45
78 79 4.072839 CTGGTTCTTCCAAGTAGTTTCCC 58.927 47.826 0.00 0.00 46.59 3.97
80 81 3.186613 CGCTGGTTCTTCCAAGTAGTTTC 59.813 47.826 0.00 0.00 46.59 2.78
101 103 1.434555 TTCGATTACCTGTGTTGGCG 58.565 50.000 0.00 0.00 0.00 5.69
117 119 8.136800 TGACCAATTTCATAATTCATGGATTCG 58.863 33.333 1.37 0.00 35.16 3.34
152 157 4.034048 GCAGGTACAATCCGTTAATCACTG 59.966 45.833 0.00 0.00 0.00 3.66
234 239 7.166473 GCAAAGCTAGTATCCATGAATTTTTCG 59.834 37.037 0.00 0.00 0.00 3.46
289 294 1.891150 CCCTGCTTGCAACTTGATCTT 59.109 47.619 0.00 0.00 0.00 2.40
297 302 1.503542 CGACATCCCTGCTTGCAAC 59.496 57.895 0.00 0.00 0.00 4.17
301 306 1.364626 GACTGCGACATCCCTGCTTG 61.365 60.000 0.00 0.00 0.00 4.01
309 314 5.663795 AAATGTATGATGACTGCGACATC 57.336 39.130 11.62 11.62 42.81 3.06
314 319 5.200454 GCAAGTAAATGTATGATGACTGCG 58.800 41.667 0.00 0.00 0.00 5.18
316 321 9.049523 AGTATGCAAGTAAATGTATGATGACTG 57.950 33.333 0.00 0.00 0.00 3.51
317 322 9.265901 GAGTATGCAAGTAAATGTATGATGACT 57.734 33.333 0.00 0.00 0.00 3.41
344 349 3.549423 CCGGCTTTCACATCATATGCTTG 60.549 47.826 0.00 0.95 0.00 4.01
347 352 2.221169 TCCGGCTTTCACATCATATGC 58.779 47.619 0.00 0.00 0.00 3.14
388 393 4.754372 TGCAGTGTGAAGCTTCTATTTG 57.246 40.909 26.09 18.82 0.00 2.32
401 406 1.238439 CCTACCAGGTTTGCAGTGTG 58.762 55.000 0.00 0.00 0.00 3.82
469 474 9.429109 TGTATGAATCTGTTAGACCCTGTATAA 57.571 33.333 0.00 0.00 0.00 0.98
470 475 8.857098 GTGTATGAATCTGTTAGACCCTGTATA 58.143 37.037 0.00 0.00 0.00 1.47
471 476 7.470147 CGTGTATGAATCTGTTAGACCCTGTAT 60.470 40.741 0.00 0.00 0.00 2.29
472 477 6.183360 CGTGTATGAATCTGTTAGACCCTGTA 60.183 42.308 0.00 0.00 0.00 2.74
473 478 5.394224 CGTGTATGAATCTGTTAGACCCTGT 60.394 44.000 0.00 0.00 0.00 4.00
474 479 5.043903 CGTGTATGAATCTGTTAGACCCTG 58.956 45.833 0.00 0.00 0.00 4.45
475 480 4.954202 TCGTGTATGAATCTGTTAGACCCT 59.046 41.667 0.00 0.00 0.00 4.34
476 481 5.258456 TCGTGTATGAATCTGTTAGACCC 57.742 43.478 0.00 0.00 0.00 4.46
477 482 5.067413 TCCTCGTGTATGAATCTGTTAGACC 59.933 44.000 0.00 0.00 0.00 3.85
478 483 6.132791 TCCTCGTGTATGAATCTGTTAGAC 57.867 41.667 0.00 0.00 0.00 2.59
479 484 5.221067 GCTCCTCGTGTATGAATCTGTTAGA 60.221 44.000 0.00 0.00 0.00 2.10
480 485 4.979197 GCTCCTCGTGTATGAATCTGTTAG 59.021 45.833 0.00 0.00 0.00 2.34
481 486 4.401202 TGCTCCTCGTGTATGAATCTGTTA 59.599 41.667 0.00 0.00 0.00 2.41
493 498 1.668294 CCAGTTCTGCTCCTCGTGT 59.332 57.895 0.00 0.00 0.00 4.49
613 618 1.987807 ATCATCCCCACTTCAGGCCG 61.988 60.000 0.00 0.00 0.00 6.13
660 665 2.369015 ATAATCCCCACGCCCCCA 60.369 61.111 0.00 0.00 0.00 4.96
661 666 2.115266 CATAATCCCCACGCCCCC 59.885 66.667 0.00 0.00 0.00 5.40
663 668 1.597027 CGTCATAATCCCCACGCCC 60.597 63.158 0.00 0.00 0.00 6.13
664 669 0.600255 CTCGTCATAATCCCCACGCC 60.600 60.000 0.00 0.00 32.21 5.68
665 670 0.600255 CCTCGTCATAATCCCCACGC 60.600 60.000 0.00 0.00 32.21 5.34
666 671 0.600255 GCCTCGTCATAATCCCCACG 60.600 60.000 0.00 0.00 0.00 4.94
667 672 0.468226 TGCCTCGTCATAATCCCCAC 59.532 55.000 0.00 0.00 0.00 4.61
668 673 0.758734 CTGCCTCGTCATAATCCCCA 59.241 55.000 0.00 0.00 0.00 4.96
810 815 0.378962 TGCGGTGGTCTTTGTTTTCG 59.621 50.000 0.00 0.00 0.00 3.46
909 914 4.409218 CGTCGCCGGGTTTCTCGA 62.409 66.667 2.18 0.00 0.00 4.04
980 985 1.008327 GGACATTGGGGAAGGGGAAAT 59.992 52.381 0.00 0.00 0.00 2.17
1151 1156 2.491022 GGAGGAGGTCGATCCACGG 61.491 68.421 7.77 0.00 42.26 4.94
1329 1334 6.682863 CACGGATGAATCAGATTAACGAAAAC 59.317 38.462 12.47 0.00 0.00 2.43
1415 1430 4.749310 AGAAGCTGCTCCACGCCG 62.749 66.667 1.00 0.00 38.05 6.46
1629 1644 1.187087 CGCTTCCTCTTACTCCCTGT 58.813 55.000 0.00 0.00 0.00 4.00
1706 1721 1.000843 CTCCATGTGGTGTCACTCGAA 59.999 52.381 2.35 0.00 43.94 3.71
1913 1928 7.353525 TCATGAAATGGGAAGGCTTAGAAATA 58.646 34.615 0.00 0.00 46.73 1.40
1993 2008 7.115378 CAGTTTTTAAGCAAATGACAGGATCAC 59.885 37.037 0.00 0.00 41.24 3.06
1997 2012 6.545666 TCTCAGTTTTTAAGCAAATGACAGGA 59.454 34.615 0.00 0.00 0.00 3.86
2005 2020 5.752955 GTGCCATTCTCAGTTTTTAAGCAAA 59.247 36.000 0.00 0.00 0.00 3.68
2078 2093 2.054799 TCACCTGGTAGCTTTGGAACT 58.945 47.619 0.00 0.00 0.00 3.01
2146 2161 3.931907 AGCTAACATCAATGTGCCCTA 57.068 42.857 0.00 0.00 41.61 3.53
2289 2304 6.433716 TCATTCTTGTATGGATTGTTCAAGCA 59.566 34.615 3.35 0.00 36.47 3.91
2366 2381 1.447838 GCGACGCTTCCTGAATGGA 60.448 57.895 13.73 0.00 44.51 3.41
2897 2912 3.871594 CAGTCCCATCGTTATGAACTTCC 59.128 47.826 0.00 0.00 34.84 3.46
3120 3135 8.514330 AACTTGTAAACAGATTTAAGTGGACA 57.486 30.769 0.00 0.00 32.04 4.02
3252 3267 7.891498 AGTGTTTCAAACCTAAAGTACCATT 57.109 32.000 0.00 0.00 0.00 3.16
3297 3312 6.414408 ACAGAAAAGAAATACTGCTGATCG 57.586 37.500 0.00 0.00 34.25 3.69
3326 3341 1.002366 CCTGATTGAAGCTTCCGACG 58.998 55.000 23.42 8.20 0.00 5.12
3379 3394 3.610619 CTGACCGAGGTGCATGGCA 62.611 63.158 0.00 0.00 35.60 4.92
3549 3564 5.582269 CACTGATGAGTTGTTTGATATCGGT 59.418 40.000 0.00 0.00 35.24 4.69
3551 3566 5.812127 TCCACTGATGAGTTGTTTGATATCG 59.188 40.000 0.00 0.00 0.00 2.92
3749 3766 6.344500 AGCTATTAATCAGCATATTCTCCCG 58.656 40.000 15.00 0.00 41.66 5.14
3803 3820 1.808945 ACTAACCCTCACGTACAGTCG 59.191 52.381 0.00 0.00 0.00 4.18
3808 3825 3.922850 GCAACTAACTAACCCTCACGTAC 59.077 47.826 0.00 0.00 0.00 3.67
3862 3879 3.181464 GCCTAGGTTTCTCCCACAGATAC 60.181 52.174 11.31 0.00 36.75 2.24
3869 3886 0.914417 CTGGGCCTAGGTTTCTCCCA 60.914 60.000 19.71 19.71 44.16 4.37
4197 4214 2.092681 CACGTCCACATGATTTCGAGTG 59.907 50.000 0.00 0.00 0.00 3.51
4317 4334 9.317936 CTATGTTGTGAAATAGACTGCTGATTA 57.682 33.333 0.00 0.00 0.00 1.75
4364 4381 0.841289 ACCCGTCTCCAAGGAACAAA 59.159 50.000 0.00 0.00 0.00 2.83
4502 4519 9.145865 GTTTAGATTTCTCTGGAGAGTTTGTAG 57.854 37.037 3.61 0.00 42.60 2.74
4650 4667 2.151202 GTGACACGACCAATTGGATGT 58.849 47.619 31.22 27.03 38.94 3.06
4783 4800 5.729974 GTTCGTGTTTTCTTAGAACCACT 57.270 39.130 16.68 0.00 36.23 4.00
4905 4922 1.774254 TCAGGAAGCCTCTTTGAACCA 59.226 47.619 0.00 0.00 0.00 3.67
4911 4928 8.554490 TTCTAGTATTATCAGGAAGCCTCTTT 57.446 34.615 0.00 0.00 0.00 2.52
4953 4970 1.336240 GCAACACAAGCCAATGACTCC 60.336 52.381 0.00 0.00 0.00 3.85
5030 5047 0.452987 CTGCCCATCGGTGTGAATTG 59.547 55.000 0.00 0.00 0.00 2.32
5035 5052 1.742880 CACTCTGCCCATCGGTGTG 60.743 63.158 0.00 0.00 38.65 3.82
5313 5330 7.304792 CGCACAAACGATACAACATCATTATTG 60.305 37.037 0.00 0.00 34.06 1.90
5314 5331 6.686679 CGCACAAACGATACAACATCATTATT 59.313 34.615 0.00 0.00 34.06 1.40
5322 5339 0.236187 GGCGCACAAACGATACAACA 59.764 50.000 10.83 0.00 34.06 3.33
5424 5441 5.434408 CATCCTGAAATCCACTCTTCATCA 58.566 41.667 0.00 0.00 31.40 3.07
5481 5498 7.939039 TCAAACAAATCCTCTGTTAACTCAGAT 59.061 33.333 7.22 1.68 42.47 2.90
5584 5601 4.060900 AGCGGTGCATTATCAACATCTAG 58.939 43.478 0.00 0.00 0.00 2.43
5592 5609 0.251634 TGTCCAGCGGTGCATTATCA 59.748 50.000 9.63 0.00 0.00 2.15
5600 5617 0.320683 TTCAGTGATGTCCAGCGGTG 60.321 55.000 7.86 7.86 0.00 4.94
5897 5934 8.723942 AAACAGACCTACATAAGCATAAGAAG 57.276 34.615 0.00 0.00 0.00 2.85
6009 6046 2.622942 GGTGTTGTCAAAGATTGGAGCA 59.377 45.455 0.00 0.00 0.00 4.26
6026 6063 6.325919 TCTTTTGCTTTAATCGATTGGTGT 57.674 33.333 20.87 0.00 0.00 4.16
6054 6091 6.148150 CCGCCTAAACTATTTGAACTAACACA 59.852 38.462 0.00 0.00 0.00 3.72
6056 6093 6.232692 ACCGCCTAAACTATTTGAACTAACA 58.767 36.000 0.00 0.00 0.00 2.41
6104 6143 7.391554 CCACATTAGAAGAGAAACTCCAAATCA 59.608 37.037 0.00 0.00 0.00 2.57
6108 6147 6.187727 ACCACATTAGAAGAGAAACTCCAA 57.812 37.500 0.00 0.00 0.00 3.53
6127 6166 1.885887 TGCAGCCACTTAATGAACCAC 59.114 47.619 0.00 0.00 0.00 4.16
6139 6178 2.805845 CATGAGCTTATTTGCAGCCAC 58.194 47.619 0.00 0.00 38.09 5.01
6177 6216 5.132897 AGCGGAAAAGAAATGCAACAATA 57.867 34.783 0.00 0.00 0.00 1.90
6196 6236 5.714047 TGGTAAGATTAGAGCATGATAGCG 58.286 41.667 0.00 0.00 40.15 4.26
6227 6267 1.236616 TGTTTGCTGGACTGCGATGG 61.237 55.000 0.00 0.00 35.36 3.51
6467 6507 2.515926 TATGTGATCTCTGCTTCGGC 57.484 50.000 0.00 0.00 42.19 5.54
6638 6679 1.172180 CCGGCCTGAAGCTTTTGACA 61.172 55.000 0.00 0.00 43.05 3.58
6639 6680 0.889186 TCCGGCCTGAAGCTTTTGAC 60.889 55.000 0.00 0.00 43.05 3.18
6640 6681 0.606401 CTCCGGCCTGAAGCTTTTGA 60.606 55.000 0.00 0.00 43.05 2.69
6641 6682 0.606401 TCTCCGGCCTGAAGCTTTTG 60.606 55.000 0.00 0.00 43.05 2.44
6642 6683 0.110486 TTCTCCGGCCTGAAGCTTTT 59.890 50.000 0.00 0.00 43.05 2.27
6643 6684 0.110486 TTTCTCCGGCCTGAAGCTTT 59.890 50.000 0.00 0.00 43.05 3.51
6644 6685 0.606673 GTTTCTCCGGCCTGAAGCTT 60.607 55.000 0.00 0.00 43.05 3.74
6645 6686 1.003233 GTTTCTCCGGCCTGAAGCT 60.003 57.895 0.00 0.00 43.05 3.74
6646 6687 2.391389 CGTTTCTCCGGCCTGAAGC 61.391 63.158 0.00 4.09 42.60 3.86
6647 6688 1.741770 CCGTTTCTCCGGCCTGAAG 60.742 63.158 0.00 0.00 41.78 3.02
6648 6689 2.345991 CCGTTTCTCCGGCCTGAA 59.654 61.111 0.00 0.00 41.78 3.02
6772 7084 0.109086 CTGTCCGAAGCATCAGACGT 60.109 55.000 1.24 0.00 0.00 4.34
6837 7149 3.430042 TCCTCAGAGAATGCAAAGCTT 57.570 42.857 0.00 0.00 0.00 3.74
7268 7601 0.325602 TGGTTTTTCTACGGCCCGAT 59.674 50.000 11.71 0.00 0.00 4.18
7647 7983 1.300963 GCCCATGTCTGAGCAAGGA 59.699 57.895 0.00 0.00 29.40 3.36
7651 7987 4.100084 CCGGCCCATGTCTGAGCA 62.100 66.667 0.00 0.00 0.00 4.26
7675 8011 3.636231 CCCAACCTCCACCGCTGA 61.636 66.667 0.00 0.00 0.00 4.26
7695 8031 2.497675 GGAAGAGCCACATGAGACTACA 59.502 50.000 0.00 0.00 36.34 2.74
7775 8111 1.233950 ACATGTCCAAACGCATCGCA 61.234 50.000 0.00 0.00 0.00 5.10
7776 8112 0.109781 AACATGTCCAAACGCATCGC 60.110 50.000 0.00 0.00 0.00 4.58
7777 8113 1.196581 TCAACATGTCCAAACGCATCG 59.803 47.619 0.00 0.00 0.00 3.84
7779 8115 1.068333 GCTCAACATGTCCAAACGCAT 60.068 47.619 0.00 0.00 0.00 4.73
7780 8116 0.310543 GCTCAACATGTCCAAACGCA 59.689 50.000 0.00 0.00 0.00 5.24
7781 8117 0.310543 TGCTCAACATGTCCAAACGC 59.689 50.000 0.00 0.00 0.00 4.84
7782 8118 2.995466 ATGCTCAACATGTCCAAACG 57.005 45.000 0.00 0.00 37.70 3.60
7811 8147 4.266714 TCGACATATACAGACCACTGACA 58.733 43.478 0.00 0.00 46.03 3.58
7845 8181 8.687242 TGTGTACCAAACAAACAAAATCTCATA 58.313 29.630 0.00 0.00 40.63 2.15
7865 8201 9.751542 AGCATGTCTAACTTAGATATTGTGTAC 57.248 33.333 5.53 0.00 34.87 2.90
8072 8492 7.520119 TTTATTGACAATAGTGTAGTGCGAG 57.480 36.000 7.89 0.00 38.41 5.03
8074 8494 7.514805 TGTTTTATTGACAATAGTGTAGTGCG 58.485 34.615 7.89 0.00 38.41 5.34
8075 8495 9.490663 GATGTTTTATTGACAATAGTGTAGTGC 57.509 33.333 7.89 0.00 38.41 4.40
8105 8525 9.877178 AGATACTACTTCCTTTGTTTCATAGTG 57.123 33.333 0.00 0.00 0.00 2.74
8187 8607 7.114811 CGTAGAAATGGTGTGGAAAATTTCTTG 59.885 37.037 13.03 5.21 38.69 3.02
8199 8619 3.002791 AGTGCATCGTAGAAATGGTGTG 58.997 45.455 0.00 0.00 43.58 3.82
8210 8630 1.470805 CGTTGGATGGAGTGCATCGTA 60.471 52.381 17.26 7.24 36.83 3.43
8219 8639 4.115516 CAGAGAATACACGTTGGATGGAG 58.884 47.826 0.00 0.00 0.00 3.86
8241 8661 0.698818 AGGGAGTGAATGGGTGAACC 59.301 55.000 0.00 0.00 40.81 3.62
8247 8670 1.492176 AGTGCATAGGGAGTGAATGGG 59.508 52.381 0.00 0.00 0.00 4.00
8358 8781 2.082140 TATGCTACCGACTCCCATGT 57.918 50.000 0.00 0.00 0.00 3.21
8362 8785 0.608640 CCCATATGCTACCGACTCCC 59.391 60.000 0.00 0.00 0.00 4.30
8393 8816 1.069358 CTCTCTAAGTCGGCCAATCCC 59.931 57.143 2.24 0.00 0.00 3.85
8435 8858 4.740431 GTTTGCGGCCCCACATGC 62.740 66.667 0.00 0.00 0.00 4.06
8443 8866 1.728490 GGATCATCTGGTTTGCGGCC 61.728 60.000 0.00 0.00 0.00 6.13
8489 8912 2.437200 TAGGTTGGTTGACGTAACGG 57.563 50.000 0.00 0.00 40.28 4.44
8709 9141 4.040584 GGGAGTCACCTTTGTAGTTCTTCT 59.959 45.833 0.00 0.00 38.98 2.85


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

AutoCloner maintained by Alex Coulton.