Multiple sequence alignment - TraesCS6A01G075500

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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 TraesCS6A01G075500 chr6A 100.000 4954 0 0 1 4954 45651841 45656794 0.000000e+00 9149.0
1 TraesCS6A01G075500 chr6A 88.446 2034 180 30 2068 4093 33020586 33022572 0.000000e+00 2403.0
2 TraesCS6A01G075500 chr6A 91.563 1446 88 15 2894 4333 46489691 46488274 0.000000e+00 1964.0
3 TraesCS6A01G075500 chr6A 82.460 1813 221 47 160 1944 33018760 33020503 0.000000e+00 1496.0
4 TraesCS6A01G075500 chr6A 82.692 1196 190 7 2776 3955 13807758 13806564 0.000000e+00 1046.0
5 TraesCS6A01G075500 chr6A 86.408 103 10 2 4546 4648 33023609 33023707 5.240000e-20 110.0
6 TraesCS6A01G075500 chr6B 96.931 3878 108 8 464 4334 78452574 78456447 0.000000e+00 6492.0
7 TraesCS6A01G075500 chr6B 93.092 2345 142 14 99 2436 79720902 79718571 0.000000e+00 3415.0
8 TraesCS6A01G075500 chr6B 94.552 1909 82 9 2431 4334 79717635 79715744 0.000000e+00 2929.0
9 TraesCS6A01G075500 chr6B 87.075 1501 130 35 1947 3433 59872734 59874184 0.000000e+00 1639.0
10 TraesCS6A01G075500 chr6B 84.009 1357 168 25 524 1868 59870808 59872127 0.000000e+00 1258.0
11 TraesCS6A01G075500 chr6B 89.691 291 23 3 4335 4621 78456517 78456804 1.010000e-96 364.0
12 TraesCS6A01G075500 chr6B 82.166 471 38 14 4330 4785 79715682 79715243 3.650000e-96 363.0
13 TraesCS6A01G075500 chr6B 92.994 157 9 2 301 456 78388894 78389049 1.390000e-55 228.0
14 TraesCS6A01G075500 chr6B 90.099 101 7 3 4 101 79721046 79720946 1.450000e-25 128.0
15 TraesCS6A01G075500 chr6B 86.000 100 10 2 4549 4648 59930642 59930737 2.440000e-18 104.0
16 TraesCS6A01G075500 chr6D 83.451 3402 382 102 204 3540 29377452 29374167 0.000000e+00 2996.0
17 TraesCS6A01G075500 chr6D 82.832 565 64 12 3529 4093 29371007 29370476 4.490000e-130 475.0
18 TraesCS6A01G075500 chrUn 92.599 1851 121 9 771 2612 27714333 27716176 0.000000e+00 2645.0
19 TraesCS6A01G075500 chrUn 94.121 1752 74 11 2598 4334 27716266 27718003 0.000000e+00 2638.0
20 TraesCS6A01G075500 chrUn 87.849 609 53 15 99 695 27713569 27714168 0.000000e+00 695.0
21 TraesCS6A01G075500 chrUn 86.405 331 24 4 4334 4648 27718071 27718396 4.750000e-90 342.0
22 TraesCS6A01G075500 chrUn 88.889 171 9 4 4784 4953 27718833 27718994 8.410000e-48 202.0
23 TraesCS6A01G075500 chrUn 90.000 100 7 2 5 101 27713389 27713488 5.210000e-25 126.0
24 TraesCS6A01G075500 chr2A 90.909 66 5 1 4584 4648 746741873 746741808 2.460000e-13 87.9


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 TraesCS6A01G075500 chr6A 45651841 45656794 4953 False 9149.000000 9149 100.000000 1 4954 1 chr6A.!!$F1 4953
1 TraesCS6A01G075500 chr6A 46488274 46489691 1417 True 1964.000000 1964 91.563000 2894 4333 1 chr6A.!!$R2 1439
2 TraesCS6A01G075500 chr6A 33018760 33023707 4947 False 1336.333333 2403 85.771333 160 4648 3 chr6A.!!$F2 4488
3 TraesCS6A01G075500 chr6A 13806564 13807758 1194 True 1046.000000 1046 82.692000 2776 3955 1 chr6A.!!$R1 1179
4 TraesCS6A01G075500 chr6B 78452574 78456804 4230 False 3428.000000 6492 93.311000 464 4621 2 chr6B.!!$F4 4157
5 TraesCS6A01G075500 chr6B 79715243 79721046 5803 True 1708.750000 3415 89.977250 4 4785 4 chr6B.!!$R1 4781
6 TraesCS6A01G075500 chr6B 59870808 59874184 3376 False 1448.500000 1639 85.542000 524 3433 2 chr6B.!!$F3 2909
7 TraesCS6A01G075500 chr6D 29370476 29377452 6976 True 1735.500000 2996 83.141500 204 4093 2 chr6D.!!$R1 3889
8 TraesCS6A01G075500 chrUn 27713389 27718994 5605 False 1108.000000 2645 89.977167 5 4953 6 chrUn.!!$F1 4948

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
192 281 0.533531 CAGTTGCAGTCACCAGCTCA 60.534 55.000 0.00 0.0 0.00 4.26 F
194 283 1.227943 TTGCAGTCACCAGCTCACC 60.228 57.895 0.00 0.0 0.00 4.02 F
1026 1242 0.321671 TCCTGCCACTGCTAGTTGTC 59.678 55.000 0.00 0.0 38.71 3.18 F
2524 4294 0.967380 GCCCAGGCAAGCACATAGTT 60.967 55.000 3.12 0.0 41.49 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1026 1242 0.723414 CTAGGTGCAACATGACTGCG 59.277 55.0 3.64 2.47 42.97 5.18 R
1427 1649 2.004583 TGCTGTCGTATACCTTGCAC 57.995 50.0 0.00 0.00 0.00 4.57 R
2547 4317 2.094182 TCCTCGGATAGACTTGTTGCAC 60.094 50.0 0.00 0.00 0.00 4.57 R
4510 10139 1.095228 CAAGCGAGGGTGTGTGTGTT 61.095 55.0 0.00 0.00 0.00 3.32 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
31 35 0.625849 AAAGAGCATCCCCGTCCAAT 59.374 50.000 0.00 0.00 33.66 3.16
35 39 0.552848 AGCATCCCCGTCCAATCAAT 59.447 50.000 0.00 0.00 0.00 2.57
101 105 2.672996 TGCGGCAGGAAAAGAGCC 60.673 61.111 0.00 0.00 44.89 4.70
102 106 3.443925 GCGGCAGGAAAAGAGCCC 61.444 66.667 0.00 0.00 45.56 5.19
103 107 2.034066 CGGCAGGAAAAGAGCCCA 59.966 61.111 0.00 0.00 45.56 5.36
104 108 1.603455 CGGCAGGAAAAGAGCCCAA 60.603 57.895 0.00 0.00 45.56 4.12
105 109 1.866853 CGGCAGGAAAAGAGCCCAAC 61.867 60.000 0.00 0.00 45.56 3.77
188 277 1.151668 GTAGCAGTTGCAGTCACCAG 58.848 55.000 6.90 0.00 45.16 4.00
190 279 1.895707 GCAGTTGCAGTCACCAGCT 60.896 57.895 0.00 0.00 41.59 4.24
191 280 1.849976 GCAGTTGCAGTCACCAGCTC 61.850 60.000 0.00 0.00 41.59 4.09
192 281 0.533531 CAGTTGCAGTCACCAGCTCA 60.534 55.000 0.00 0.00 0.00 4.26
194 283 1.227943 TTGCAGTCACCAGCTCACC 60.228 57.895 0.00 0.00 0.00 4.02
195 284 2.740055 GCAGTCACCAGCTCACCG 60.740 66.667 0.00 0.00 0.00 4.94
196 285 2.737180 CAGTCACCAGCTCACCGT 59.263 61.111 0.00 0.00 0.00 4.83
197 286 1.373497 CAGTCACCAGCTCACCGTC 60.373 63.158 0.00 0.00 0.00 4.79
198 287 2.048127 GTCACCAGCTCACCGTCC 60.048 66.667 0.00 0.00 0.00 4.79
199 288 2.523168 TCACCAGCTCACCGTCCA 60.523 61.111 0.00 0.00 0.00 4.02
200 289 2.047844 CACCAGCTCACCGTCCAG 60.048 66.667 0.00 0.00 0.00 3.86
201 290 2.524394 ACCAGCTCACCGTCCAGT 60.524 61.111 0.00 0.00 0.00 4.00
202 291 2.140792 ACCAGCTCACCGTCCAGTT 61.141 57.895 0.00 0.00 0.00 3.16
230 320 3.260380 CAGTCTTCCAGTCCTGTTGAGAT 59.740 47.826 0.00 0.00 0.00 2.75
233 323 3.648067 TCTTCCAGTCCTGTTGAGATGTT 59.352 43.478 0.00 0.00 0.00 2.71
241 331 4.997395 GTCCTGTTGAGATGTTGCTCTTTA 59.003 41.667 0.00 0.00 35.91 1.85
299 399 1.815840 GGCTGTAGCTCGGCTTTCC 60.816 63.158 14.12 0.00 46.74 3.13
334 434 1.355718 ACCCAGATACCCATGGCCAG 61.356 60.000 13.05 0.00 35.10 4.85
368 469 4.343231 TCCACCAAAATCACACAGCATAT 58.657 39.130 0.00 0.00 0.00 1.78
404 505 7.255836 CGATACCATCACAGGAAGTAGGATAAA 60.256 40.741 0.00 0.00 0.00 1.40
419 520 5.505181 AGGATAAACCACACTCTTCACAT 57.495 39.130 0.00 0.00 42.04 3.21
420 521 5.491982 AGGATAAACCACACTCTTCACATC 58.508 41.667 0.00 0.00 42.04 3.06
430 533 5.570973 CACACTCTTCACATCTTAGTTCTCG 59.429 44.000 0.00 0.00 0.00 4.04
557 661 4.386049 TGTGCAAACAACCAAAAACTTACG 59.614 37.500 0.00 0.00 0.00 3.18
581 686 3.777478 TCGGAAACACGGTCTTCATATC 58.223 45.455 0.00 0.00 0.00 1.63
631 746 2.421424 CCAGAAATCCAAAGGCGAGAAG 59.579 50.000 0.00 0.00 0.00 2.85
803 1011 3.426525 GCAGCTTGACATTTACAAAGCAC 59.573 43.478 8.75 0.00 0.00 4.40
819 1028 9.862371 TTACAAAGCACTGTTAAAATTCTTCAA 57.138 25.926 0.00 0.00 0.00 2.69
824 1033 8.177119 AGCACTGTTAAAATTCTTCAACCATA 57.823 30.769 0.00 0.00 0.00 2.74
935 1147 7.177568 TGGCCATTAGTTTGCTCACTATTTTTA 59.822 33.333 0.00 0.00 0.00 1.52
956 1172 3.963428 TCCTCTTTTCCTGTAGTGCTC 57.037 47.619 0.00 0.00 0.00 4.26
995 1211 2.157738 GCAACTCCAGCTTCAGACAAT 58.842 47.619 0.00 0.00 0.00 2.71
1026 1242 0.321671 TCCTGCCACTGCTAGTTGTC 59.678 55.000 0.00 0.00 38.71 3.18
1132 1354 5.432680 TCCGTTTGGTATTGGTATTGGTA 57.567 39.130 0.00 0.00 36.30 3.25
1133 1355 5.184711 TCCGTTTGGTATTGGTATTGGTAC 58.815 41.667 0.00 0.00 36.30 3.34
1134 1356 5.045724 TCCGTTTGGTATTGGTATTGGTACT 60.046 40.000 0.00 0.00 36.30 2.73
1135 1357 5.065474 CCGTTTGGTATTGGTATTGGTACTG 59.935 44.000 0.00 0.00 0.00 2.74
1136 1358 5.065474 CGTTTGGTATTGGTATTGGTACTGG 59.935 44.000 0.00 0.00 0.00 4.00
1137 1359 4.159244 TGGTATTGGTATTGGTACTGGC 57.841 45.455 0.00 0.00 0.00 4.85
1427 1649 2.624838 ACATCAACAACTTGGGAAGCAG 59.375 45.455 0.00 0.00 0.00 4.24
1532 1754 5.068987 GCTGCCAAAATGATATACCAAAGGA 59.931 40.000 0.00 0.00 0.00 3.36
1554 1776 5.248477 GGATCTAAGGGGCTATATGTTCACA 59.752 44.000 0.00 0.00 0.00 3.58
1926 2652 6.872628 TCATCTTTAGATCATGTGCAATCC 57.127 37.500 0.00 0.00 31.21 3.01
1977 2736 4.833478 ATCATTACTTGCTGTCTGTCCT 57.167 40.909 0.00 0.00 0.00 3.85
2303 3101 2.627221 TGCAACATGCCACAACACTATT 59.373 40.909 0.00 0.00 44.23 1.73
2347 3145 4.134563 TCTCCAGGCAGAAAGTTTGTAAC 58.865 43.478 0.00 0.00 0.00 2.50
2357 3155 6.237463 GCAGAAAGTTTGTAACGGAAACAAAG 60.237 38.462 11.09 2.74 44.94 2.77
2524 4294 0.967380 GCCCAGGCAAGCACATAGTT 60.967 55.000 3.12 0.00 41.49 2.24
2547 4317 1.227823 TGTCTCCTTGTGTTGGGCG 60.228 57.895 0.00 0.00 0.00 6.13
2621 4496 9.328721 GGAAAATTGACAAAAACTCAAAAAGTG 57.671 29.630 0.00 0.00 38.58 3.16
2697 4572 6.594788 TCACTACCGTTTAGTCCACTTTAT 57.405 37.500 0.00 0.00 0.00 1.40
2813 4690 3.485877 GCATTGGCGTTGTCATTCTAGTC 60.486 47.826 0.00 0.00 0.00 2.59
3188 5071 1.457346 GATGTTGCCTTGAGGTGGAG 58.543 55.000 0.00 0.00 37.57 3.86
3536 5419 2.024176 GCTTGACAGACAAAAGCGAC 57.976 50.000 0.00 0.00 37.21 5.19
3609 8663 3.711704 ACTGAAACTTGAAGGTCCTGAGA 59.288 43.478 0.00 0.00 0.00 3.27
3659 8713 2.648059 CTGGCTATGAAGGGGAACAAG 58.352 52.381 0.00 0.00 0.00 3.16
3850 8907 3.565902 TGGATACAGCGTGATACTGAGAG 59.434 47.826 0.00 0.00 46.17 3.20
4011 9083 6.494893 TCATTGTTCATTTAACCTTCTCCG 57.505 37.500 0.00 0.00 37.27 4.63
4019 9091 2.000429 TAACCTTCTCCGCGTTTAGC 58.000 50.000 4.92 0.00 43.95 3.09
4274 9623 8.533569 AGTGATTTACTTTTCCTTTTTCAGGA 57.466 30.769 0.00 0.00 43.37 3.86
4383 9803 9.077885 ACTTGCTAGATTCTTTTATTTTCACCA 57.922 29.630 1.04 0.00 0.00 4.17
4413 10041 5.386958 TCAGGACACGATGTATTATAGGC 57.613 43.478 0.00 0.00 0.00 3.93
4432 10060 2.027427 GCCCCTAACCTACATTTGGCC 61.027 57.143 0.00 0.00 0.00 5.36
4435 10063 2.509964 CCCTAACCTACATTTGGCCTCT 59.490 50.000 3.32 0.00 0.00 3.69
4436 10064 3.714798 CCCTAACCTACATTTGGCCTCTA 59.285 47.826 3.32 0.00 0.00 2.43
4510 10139 5.483685 ACTTCAGTTGTGCCATAAGTCTA 57.516 39.130 0.00 0.00 0.00 2.59
4533 10178 0.738389 CACACACCCTCGCTTGTTTT 59.262 50.000 0.00 0.00 0.00 2.43
4562 10221 1.578206 GGAGCTTCTTTGCGTCACCC 61.578 60.000 0.00 0.00 38.13 4.61
4647 10310 0.621280 TCCCTGCATGGATGTCCTGA 60.621 55.000 6.63 0.00 38.35 3.86
4648 10311 0.256752 CCCTGCATGGATGTCCTGAA 59.743 55.000 0.97 0.00 38.35 3.02
4649 10312 1.386533 CCTGCATGGATGTCCTGAAC 58.613 55.000 0.09 0.00 38.35 3.18
4650 10313 1.012086 CTGCATGGATGTCCTGAACG 58.988 55.000 0.09 0.00 36.82 3.95
4651 10314 0.392863 TGCATGGATGTCCTGAACGG 60.393 55.000 0.09 0.00 36.82 4.44
4652 10315 1.097547 GCATGGATGTCCTGAACGGG 61.098 60.000 0.09 0.00 36.82 5.28
4653 10316 0.541392 CATGGATGTCCTGAACGGGA 59.459 55.000 0.09 0.00 36.82 5.14
4654 10317 1.141657 CATGGATGTCCTGAACGGGAT 59.858 52.381 5.63 0.00 37.73 3.85
4655 10318 0.830648 TGGATGTCCTGAACGGGATC 59.169 55.000 5.63 0.77 37.73 3.36
4656 10319 0.106894 GGATGTCCTGAACGGGATCC 59.893 60.000 1.92 1.92 37.73 3.36
4657 10320 0.106894 GATGTCCTGAACGGGATCCC 59.893 60.000 22.12 22.12 37.73 3.85
4667 10330 4.051932 GGGATCCCGTCCTGAACT 57.948 61.111 17.02 0.00 46.91 3.01
4668 10331 1.823976 GGGATCCCGTCCTGAACTC 59.176 63.158 17.02 0.00 46.91 3.01
4669 10332 1.687297 GGGATCCCGTCCTGAACTCC 61.687 65.000 17.02 0.00 46.91 3.85
4670 10333 0.688087 GGATCCCGTCCTGAACTCCT 60.688 60.000 0.00 0.00 44.16 3.69
4671 10334 0.461961 GATCCCGTCCTGAACTCCTG 59.538 60.000 0.00 0.00 0.00 3.86
4702 10365 4.725790 AGAAAATTGTTAGGATGCTGGC 57.274 40.909 0.00 0.00 0.00 4.85
4718 10389 2.699954 CTGGCTGAAGAACCATTACGT 58.300 47.619 0.00 0.00 34.82 3.57
4789 10796 4.318332 TCAGCAACCTGAGTATGAACTTG 58.682 43.478 0.00 0.00 42.98 3.16
4805 10812 3.971032 ACTTGGAGCTGTTCTTTTTCG 57.029 42.857 0.00 0.00 0.00 3.46
4851 10858 5.579511 CACGGTGGAAAATAGAAGAATACGT 59.420 40.000 0.00 0.00 0.00 3.57
4866 10873 8.919145 AGAAGAATACGTTGAGAGGAATCTTAT 58.081 33.333 0.00 0.00 0.00 1.73
4873 10880 6.266558 ACGTTGAGAGGAATCTTATAGCTGAT 59.733 38.462 0.00 0.00 0.00 2.90
4912 10919 9.639601 AGAAACAAAAGTTAGACAAAGAAAAGG 57.360 29.630 0.00 0.00 0.00 3.11
4913 10920 9.634163 GAAACAAAAGTTAGACAAAGAAAAGGA 57.366 29.630 0.00 0.00 0.00 3.36
4914 10921 9.990360 AAACAAAAGTTAGACAAAGAAAAGGAA 57.010 25.926 0.00 0.00 0.00 3.36
4915 10922 8.981724 ACAAAAGTTAGACAAAGAAAAGGAAC 57.018 30.769 0.00 0.00 0.00 3.62
4916 10923 8.581578 ACAAAAGTTAGACAAAGAAAAGGAACA 58.418 29.630 0.00 0.00 0.00 3.18
4917 10924 9.076596 CAAAAGTTAGACAAAGAAAAGGAACAG 57.923 33.333 0.00 0.00 0.00 3.16
4918 10925 8.575649 AAAGTTAGACAAAGAAAAGGAACAGA 57.424 30.769 0.00 0.00 0.00 3.41
4929 10936 2.278332 AGGAACAGAAAAGGTGGCTC 57.722 50.000 0.00 0.00 0.00 4.70
4947 10954 8.317679 AGGTGGCTCAATCATAAGTCTATAATC 58.682 37.037 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.982852 TGATTGGACGGGGATGCTCT 60.983 55.000 0.00 0.00 0.00 4.09
25 29 9.918379 ATTCTCAGGAAGGACCATTGATTGGAC 62.918 44.444 0.00 0.00 40.36 4.02
31 35 3.054139 CCATTCTCAGGAAGGACCATTGA 60.054 47.826 0.00 0.00 42.04 2.57
35 39 0.620556 GCCATTCTCAGGAAGGACCA 59.379 55.000 0.00 0.00 42.04 4.02
101 105 0.670546 ATGTTCAGTCGAGCCGTTGG 60.671 55.000 0.00 0.00 0.00 3.77
102 106 0.716108 GATGTTCAGTCGAGCCGTTG 59.284 55.000 0.00 0.00 0.00 4.10
103 107 0.603569 AGATGTTCAGTCGAGCCGTT 59.396 50.000 0.00 0.00 0.00 4.44
104 108 0.603569 AAGATGTTCAGTCGAGCCGT 59.396 50.000 0.00 0.00 0.00 5.68
105 109 1.391485 CAAAGATGTTCAGTCGAGCCG 59.609 52.381 0.00 0.00 0.00 5.52
188 277 1.014564 GTGCTAACTGGACGGTGAGC 61.015 60.000 12.79 12.79 42.48 4.26
190 279 1.116536 TGGTGCTAACTGGACGGTGA 61.117 55.000 0.00 0.00 37.93 4.02
191 280 0.670546 CTGGTGCTAACTGGACGGTG 60.671 60.000 0.00 0.00 37.93 4.94
192 281 1.119574 ACTGGTGCTAACTGGACGGT 61.120 55.000 0.00 0.00 37.93 4.83
194 283 0.603569 AGACTGGTGCTAACTGGACG 59.396 55.000 0.00 0.00 37.93 4.79
195 284 2.613223 GGAAGACTGGTGCTAACTGGAC 60.613 54.545 0.00 0.00 36.19 4.02
196 285 1.623811 GGAAGACTGGTGCTAACTGGA 59.376 52.381 0.00 0.00 0.00 3.86
197 286 1.347707 TGGAAGACTGGTGCTAACTGG 59.652 52.381 0.00 0.00 0.00 4.00
198 287 2.037772 ACTGGAAGACTGGTGCTAACTG 59.962 50.000 0.00 0.00 37.43 3.16
199 288 2.300437 GACTGGAAGACTGGTGCTAACT 59.700 50.000 0.00 0.00 37.43 2.24
200 289 2.613223 GGACTGGAAGACTGGTGCTAAC 60.613 54.545 0.00 0.00 37.43 2.34
201 290 1.623811 GGACTGGAAGACTGGTGCTAA 59.376 52.381 0.00 0.00 37.43 3.09
202 291 1.203187 AGGACTGGAAGACTGGTGCTA 60.203 52.381 0.00 0.00 37.43 3.49
230 320 2.076100 CTCGCCATGTAAAGAGCAACA 58.924 47.619 0.00 0.00 0.00 3.33
233 323 2.299993 CTCTCGCCATGTAAAGAGCA 57.700 50.000 0.00 0.00 0.00 4.26
299 399 0.958876 GGGTTTGCCTGTAGGGTTCG 60.959 60.000 0.00 0.00 37.43 3.95
334 434 1.604604 TTGGTGGAGTGCAAGCTTAC 58.395 50.000 0.00 0.00 0.00 2.34
368 469 6.493458 TCCTGTGATGGTATCGATTTATCTCA 59.507 38.462 1.71 10.98 0.00 3.27
404 505 5.305644 AGAACTAAGATGTGAAGAGTGTGGT 59.694 40.000 0.00 0.00 0.00 4.16
419 520 1.757118 CATCCAGGCCGAGAACTAAGA 59.243 52.381 0.00 0.00 0.00 2.10
420 521 1.808133 GCATCCAGGCCGAGAACTAAG 60.808 57.143 0.00 0.00 0.00 2.18
430 533 0.971959 TTTGGTGATGCATCCAGGCC 60.972 55.000 23.67 18.81 35.05 5.19
520 623 1.588674 TGCACAGTTAAACAGTCCGG 58.411 50.000 0.00 0.00 0.00 5.14
522 625 4.364415 TGTTTGCACAGTTAAACAGTCC 57.636 40.909 8.24 0.00 40.65 3.85
557 661 1.269413 TGAAGACCGTGTTTCCGAGTC 60.269 52.381 0.00 0.00 0.00 3.36
601 716 4.706476 CCTTTGGATTTCTGGCACTGAATA 59.294 41.667 0.00 0.00 45.27 1.75
824 1033 9.715121 TGTCGAAATATACCTGAAAGTTTTAGT 57.285 29.630 6.64 0.06 0.00 2.24
935 1147 4.081198 CAGAGCACTACAGGAAAAGAGGAT 60.081 45.833 0.00 0.00 0.00 3.24
985 1201 6.071728 AGGAAAGCCATGTTAATTGTCTGAAG 60.072 38.462 0.00 0.00 36.29 3.02
1026 1242 0.723414 CTAGGTGCAACATGACTGCG 59.277 55.000 3.64 2.47 42.97 5.18
1132 1354 3.370104 AGTCTCTAATAGCACAGCCAGT 58.630 45.455 0.00 0.00 0.00 4.00
1133 1355 4.399004 AAGTCTCTAATAGCACAGCCAG 57.601 45.455 0.00 0.00 0.00 4.85
1134 1356 4.222810 TCAAAGTCTCTAATAGCACAGCCA 59.777 41.667 0.00 0.00 0.00 4.75
1135 1357 4.759782 TCAAAGTCTCTAATAGCACAGCC 58.240 43.478 0.00 0.00 0.00 4.85
1136 1358 5.655488 TCTCAAAGTCTCTAATAGCACAGC 58.345 41.667 0.00 0.00 0.00 4.40
1137 1359 7.487484 TGATCTCAAAGTCTCTAATAGCACAG 58.513 38.462 0.00 0.00 0.00 3.66
1427 1649 2.004583 TGCTGTCGTATACCTTGCAC 57.995 50.000 0.00 0.00 0.00 4.57
1532 1754 6.959606 ATGTGAACATATAGCCCCTTAGAT 57.040 37.500 0.00 0.00 34.26 1.98
1977 2736 6.436847 TCAAGTATTTCCAGGCATCAAAATCA 59.563 34.615 0.00 0.00 0.00 2.57
2303 3101 6.969043 AGAACATGAACAATAATACCCTCCA 58.031 36.000 0.00 0.00 0.00 3.86
2347 3145 3.628487 TGGGTTACAAGACTTTGTTTCCG 59.372 43.478 0.00 0.00 45.01 4.30
2357 3155 3.335579 GGTGATGTCTGGGTTACAAGAC 58.664 50.000 9.57 9.57 0.00 3.01
2524 4294 2.487086 CCCAACACAAGGAGACACATCA 60.487 50.000 0.00 0.00 0.00 3.07
2547 4317 2.094182 TCCTCGGATAGACTTGTTGCAC 60.094 50.000 0.00 0.00 0.00 4.57
2621 4496 2.749621 ACGGATGCTTGTTTCTGGATTC 59.250 45.455 0.00 0.00 0.00 2.52
2678 4553 6.343716 TGTGATAAAGTGGACTAAACGGTA 57.656 37.500 0.00 0.00 0.00 4.02
2813 4690 6.775939 ACACGTATGCAGAAGATGATAATG 57.224 37.500 0.07 0.00 0.00 1.90
2995 4872 2.240667 CCTCCATGTCCAAGAATCTGGT 59.759 50.000 0.00 0.00 37.74 4.00
3137 5020 7.175467 AGCTTGACAATGTTCTTGTGATTGATA 59.825 33.333 0.00 0.00 32.47 2.15
3188 5071 8.946523 ATGAACTCATATACTAGCATGGGGACC 61.947 44.444 0.00 0.00 42.05 4.46
3442 5325 1.305201 GACGAACTGGGCTTTGTCAA 58.695 50.000 0.00 0.00 35.39 3.18
3536 5419 4.387862 AGAACAACACCGAAGCTATAAACG 59.612 41.667 0.00 0.00 0.00 3.60
3609 8663 2.088674 GACGACAGGCTCCGGCATAT 62.089 60.000 6.78 0.00 40.87 1.78
3659 8713 6.471976 TGATTGTCGAGCATATTATCAAGC 57.528 37.500 0.00 0.00 0.00 4.01
3850 8907 4.846779 ATCAGACCGAGAAAGCTATCTC 57.153 45.455 0.00 0.00 41.99 2.75
4011 9083 2.892373 TGCAACATACAGCTAAACGC 57.108 45.000 0.00 0.00 39.57 4.84
4019 9091 8.721478 AGTCTTACACTAAAATGCAACATACAG 58.279 33.333 0.00 0.00 31.37 2.74
4274 9623 4.684703 CGACCGAGTAAATCAGTGAACTTT 59.315 41.667 0.00 0.00 0.00 2.66
4391 9811 4.219944 GGCCTATAATACATCGTGTCCTGA 59.780 45.833 0.00 0.00 0.00 3.86
4408 10036 3.397955 CCAAATGTAGGTTAGGGGCCTAT 59.602 47.826 0.84 0.00 40.33 2.57
4413 10041 1.569072 AGGCCAAATGTAGGTTAGGGG 59.431 52.381 5.01 0.00 0.00 4.79
4462 10091 7.558161 TGTCTCTGCATTTTGTTATCCTATG 57.442 36.000 0.00 0.00 0.00 2.23
4467 10096 8.668353 TGAAGTATGTCTCTGCATTTTGTTATC 58.332 33.333 0.00 0.00 0.00 1.75
4510 10139 1.095228 CAAGCGAGGGTGTGTGTGTT 61.095 55.000 0.00 0.00 0.00 3.32
4533 10178 0.546267 AAGAAGCTCCCTGCCTCAGA 60.546 55.000 0.00 0.00 44.23 3.27
4589 10252 6.488006 ACATGGCATCATCCTTATTACAAGAC 59.512 38.462 0.00 0.00 0.00 3.01
4652 10315 0.461961 CAGGAGTTCAGGACGGGATC 59.538 60.000 0.00 0.00 0.00 3.36
4653 10316 0.041238 TCAGGAGTTCAGGACGGGAT 59.959 55.000 0.00 0.00 0.00 3.85
4654 10317 0.041238 ATCAGGAGTTCAGGACGGGA 59.959 55.000 0.00 0.00 0.00 5.14
4655 10318 0.176680 CATCAGGAGTTCAGGACGGG 59.823 60.000 0.00 0.00 0.00 5.28
4656 10319 1.186200 TCATCAGGAGTTCAGGACGG 58.814 55.000 0.00 0.00 0.00 4.79
4657 10320 2.029020 TGTTCATCAGGAGTTCAGGACG 60.029 50.000 0.00 0.00 0.00 4.79
4658 10321 3.685139 TGTTCATCAGGAGTTCAGGAC 57.315 47.619 0.00 0.00 0.00 3.85
4659 10322 4.705110 TTTGTTCATCAGGAGTTCAGGA 57.295 40.909 0.00 0.00 0.00 3.86
4660 10323 5.065914 TCTTTTGTTCATCAGGAGTTCAGG 58.934 41.667 0.00 0.00 0.00 3.86
4661 10324 6.624352 TTCTTTTGTTCATCAGGAGTTCAG 57.376 37.500 0.00 0.00 0.00 3.02
4662 10325 7.403312 TTTTCTTTTGTTCATCAGGAGTTCA 57.597 32.000 0.00 0.00 0.00 3.18
4663 10326 8.758715 CAATTTTCTTTTGTTCATCAGGAGTTC 58.241 33.333 0.00 0.00 0.00 3.01
4664 10327 8.260114 ACAATTTTCTTTTGTTCATCAGGAGTT 58.740 29.630 0.00 0.00 33.64 3.01
4665 10328 7.785033 ACAATTTTCTTTTGTTCATCAGGAGT 58.215 30.769 0.00 0.00 33.64 3.85
4666 10329 8.652810 AACAATTTTCTTTTGTTCATCAGGAG 57.347 30.769 0.00 0.00 42.11 3.69
4667 10330 9.748708 CTAACAATTTTCTTTTGTTCATCAGGA 57.251 29.630 5.17 0.00 44.05 3.86
4668 10331 8.981647 CCTAACAATTTTCTTTTGTTCATCAGG 58.018 33.333 5.17 3.92 44.05 3.86
4669 10332 9.748708 TCCTAACAATTTTCTTTTGTTCATCAG 57.251 29.630 5.17 0.00 44.05 2.90
4785 10457 3.541632 TCGAAAAAGAACAGCTCCAAGT 58.458 40.909 0.00 0.00 0.00 3.16
4789 10796 3.300857 GCTTTCGAAAAAGAACAGCTCC 58.699 45.455 12.41 0.00 43.90 4.70
4805 10812 1.001393 TGGGGATCCAACGGCTTTC 60.001 57.895 15.23 0.00 40.73 2.62
4851 10858 7.846101 TCATCAGCTATAAGATTCCTCTCAA 57.154 36.000 0.00 0.00 0.00 3.02
4887 10894 9.634163 TCCTTTTCTTTGTCTAACTTTTGTTTC 57.366 29.630 0.00 0.00 43.32 2.78
4888 10895 9.990360 TTCCTTTTCTTTGTCTAACTTTTGTTT 57.010 25.926 0.00 0.00 43.32 2.83
4892 10899 9.020731 TCTGTTCCTTTTCTTTGTCTAACTTTT 57.979 29.630 0.00 0.00 0.00 2.27
4905 10912 3.384789 GCCACCTTTTCTGTTCCTTTTCT 59.615 43.478 0.00 0.00 0.00 2.52
4912 10919 3.569701 TGATTGAGCCACCTTTTCTGTTC 59.430 43.478 0.00 0.00 0.00 3.18
4913 10920 3.565307 TGATTGAGCCACCTTTTCTGTT 58.435 40.909 0.00 0.00 0.00 3.16
4914 10921 3.228188 TGATTGAGCCACCTTTTCTGT 57.772 42.857 0.00 0.00 0.00 3.41
4915 10922 5.416952 ACTTATGATTGAGCCACCTTTTCTG 59.583 40.000 0.00 0.00 0.00 3.02
4916 10923 5.574188 ACTTATGATTGAGCCACCTTTTCT 58.426 37.500 0.00 0.00 0.00 2.52
4917 10924 5.649831 AGACTTATGATTGAGCCACCTTTTC 59.350 40.000 0.00 0.00 0.00 2.29
4918 10925 5.574188 AGACTTATGATTGAGCCACCTTTT 58.426 37.500 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.