Multiple sequence alignment - TraesCS1A01G108900

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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 TraesCS1A01G108900 chr1A 100.000 4772 0 0 1 4772 108081104 108076333 0.000000e+00 8813
1 TraesCS1A01G108900 chr1A 90.323 124 12 0 4430 4553 459323392 459323515 3.820000e-36 163
2 TraesCS1A01G108900 chr1D 97.514 3218 53 12 1158 4369 76800132 76796936 0.000000e+00 5474
3 TraesCS1A01G108900 chr1D 97.359 1174 15 2 1 1163 76801327 76800159 0.000000e+00 1982
4 TraesCS1A01G108900 chr1D 90.123 162 10 3 4617 4772 76796940 76796779 6.260000e-49 206
5 TraesCS1A01G108900 chr1B 96.254 2296 56 6 2085 4369 120407203 120404927 0.000000e+00 3736
6 TraesCS1A01G108900 chr1B 93.367 1191 38 12 4 1163 120409613 120408433 0.000000e+00 1724
7 TraesCS1A01G108900 chr1B 96.281 941 24 6 1158 2087 120408406 120407466 0.000000e+00 1533
8 TraesCS1A01G108900 chr1B 91.129 124 10 1 4430 4553 45761625 45761503 2.950000e-37 167
9 TraesCS1A01G108900 chr1B 78.819 288 27 22 4365 4618 625937806 625938093 3.820000e-36 163
10 TraesCS1A01G108900 chr1B 90.323 124 12 0 4430 4553 669931761 669931638 3.820000e-36 163
11 TraesCS1A01G108900 chr1B 81.731 208 16 10 4430 4618 509106123 509106327 2.300000e-33 154
12 TraesCS1A01G108900 chr3B 81.533 287 19 12 4365 4618 377115405 377115120 6.260000e-49 206
13 TraesCS1A01G108900 chr3B 91.935 124 10 0 4430 4553 45513314 45513191 1.770000e-39 174
14 TraesCS1A01G108900 chr3B 91.339 127 8 3 4430 4553 795260643 795260769 2.280000e-38 171
15 TraesCS1A01G108900 chr2A 85.437 206 11 7 4430 4617 9334498 9334702 3.770000e-46 196
16 TraesCS1A01G108900 chr3D 80.546 293 23 15 4356 4615 15022476 15022767 1.360000e-45 195
17 TraesCS1A01G108900 chr3D 79.263 217 20 8 4430 4626 552786235 552786446 1.390000e-25 128
18 TraesCS1A01G108900 chr6A 84.951 206 13 4 4430 4618 404354616 404354820 4.870000e-45 193
19 TraesCS1A01G108900 chr7A 84.058 207 16 13 4430 4620 125104372 125104577 2.930000e-42 183
20 TraesCS1A01G108900 chr5D 83.254 209 19 12 4430 4624 307517806 307518012 1.360000e-40 178
21 TraesCS1A01G108900 chr5D 79.167 288 26 5 4364 4618 452550159 452549873 8.210000e-38 169
22 TraesCS1A01G108900 chr2D 83.495 206 16 4 4430 4618 261242841 261243045 4.910000e-40 176
23 TraesCS1A01G108900 chr5A 91.406 128 10 1 4427 4553 631584116 631583989 1.770000e-39 174
24 TraesCS1A01G108900 chr4D 79.181 293 25 21 4363 4620 313032102 313032393 2.280000e-38 171


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 TraesCS1A01G108900 chr1A 108076333 108081104 4771 True 8813 8813 100.000000 1 4772 1 chr1A.!!$R1 4771
1 TraesCS1A01G108900 chr1D 76796779 76801327 4548 True 2554 5474 94.998667 1 4772 3 chr1D.!!$R1 4771
2 TraesCS1A01G108900 chr1B 120404927 120409613 4686 True 2331 3736 95.300667 4 4369 3 chr1B.!!$R3 4365

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
290 295 1.557443 GGTCAAAGTCGACTGCACGG 61.557 60.0 20.85 7.31 36.12 4.94 F
1823 1894 1.358830 ATTGGCCCTATGAGCTGGCT 61.359 55.0 11.44 0.00 44.71 4.75 F
2554 2895 0.106868 TCCATCTCCAGGCTTGCATG 60.107 55.0 0.00 0.00 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2245 2586 2.094026 GCCTTTTCCAATAACTGCCAGG 60.094 50.0 0.0 0.0 0.00 4.45 R
2905 3246 0.466963 ATGGTCGCATCAGCATCTGA 59.533 50.0 0.0 0.0 44.99 3.27 R
4549 4902 0.042131 ACCACCCCTTCGTCCAGATA 59.958 55.0 0.0 0.0 0.00 1.98 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
104 109 7.758820 TTTATTAATCCCTCTGTCCCTACAA 57.241 36.000 0.00 0.00 34.49 2.41
290 295 1.557443 GGTCAAAGTCGACTGCACGG 61.557 60.000 20.85 7.31 36.12 4.94
316 322 9.358872 GCAAAAGGATTTCTATTTTAAGACTGG 57.641 33.333 0.00 0.00 37.28 4.00
667 697 6.705863 AGTTATGCATCAAAGATTCTTCCC 57.294 37.500 0.19 0.00 0.00 3.97
893 924 2.026542 GGGGGTTCGATAAGGTTCTTGT 60.027 50.000 0.00 0.00 0.00 3.16
894 925 3.268330 GGGGTTCGATAAGGTTCTTGTC 58.732 50.000 0.00 0.00 0.00 3.18
895 926 3.055312 GGGGTTCGATAAGGTTCTTGTCT 60.055 47.826 0.00 0.00 0.00 3.41
896 927 4.565028 GGGGTTCGATAAGGTTCTTGTCTT 60.565 45.833 0.00 0.00 0.00 3.01
897 928 4.392138 GGGTTCGATAAGGTTCTTGTCTTG 59.608 45.833 0.00 0.00 0.00 3.02
941 972 4.816925 AGAGTTGTTGCCTTTGAAGACTAC 59.183 41.667 0.00 0.00 0.00 2.73
1823 1894 1.358830 ATTGGCCCTATGAGCTGGCT 61.359 55.000 11.44 0.00 44.71 4.75
1862 1933 5.416952 ACATCCTTTTACTCCAGAAGCAATG 59.583 40.000 0.00 0.00 0.00 2.82
2245 2586 4.691860 AAGTTGACATGAATGCTACTGC 57.308 40.909 0.00 0.00 40.20 4.40
2554 2895 0.106868 TCCATCTCCAGGCTTGCATG 60.107 55.000 0.00 0.00 0.00 4.06
2696 3037 1.803555 TGCGTGCAGATTCAAATTCGA 59.196 42.857 0.00 0.00 0.00 3.71
3390 3731 1.699656 CGGCTGCTGTTGAATCTCGG 61.700 60.000 0.00 0.00 0.00 4.63
3498 3839 4.984146 ACTTCTGAAAAGGCCTAGAGTT 57.016 40.909 5.16 0.00 0.00 3.01
3808 4149 9.472361 GTTCGCTAACTCATTGGTATTCTATAA 57.528 33.333 0.00 0.00 32.54 0.98
3846 4187 2.095567 CAGTGAATTCCGGTTGCTTCTG 60.096 50.000 0.00 1.76 0.00 3.02
3854 4195 1.896660 GGTTGCTTCTGTCGCCCAA 60.897 57.895 0.00 0.00 0.00 4.12
3900 4241 6.358118 TCATAAACTTGATAATCACCGCAC 57.642 37.500 0.00 0.00 0.00 5.34
3968 4309 4.096382 AGAACGTGCACAATTTTCTTGAGT 59.904 37.500 18.64 0.00 0.00 3.41
4031 4381 3.429543 CGGAACATGCACAATTTTCTTGG 59.570 43.478 0.00 0.00 0.00 3.61
4225 4578 0.032515 TATTCTGTCCGAGCCCTGGA 60.033 55.000 0.00 0.00 0.00 3.86
4268 4621 1.477553 ATGGCTTACATGTGCTTGGG 58.522 50.000 9.11 0.00 38.70 4.12
4346 4699 6.518208 TTGGCTGGTATAAATGTTTGGTAC 57.482 37.500 0.00 0.00 0.00 3.34
4382 4735 6.224420 AGTTTACTAGAACAATGTTCGTGC 57.776 37.500 18.99 7.77 31.94 5.34
4383 4736 4.896562 TTACTAGAACAATGTTCGTGCG 57.103 40.909 18.99 11.55 0.00 5.34
4384 4737 2.750948 ACTAGAACAATGTTCGTGCGT 58.249 42.857 18.99 12.09 0.00 5.24
4385 4738 2.475111 ACTAGAACAATGTTCGTGCGTG 59.525 45.455 18.99 9.91 0.00 5.34
4386 4739 0.586319 AGAACAATGTTCGTGCGTGG 59.414 50.000 18.99 0.00 0.00 4.94
4387 4740 0.996727 GAACAATGTTCGTGCGTGGC 60.997 55.000 10.58 0.00 0.00 5.01
4388 4741 1.719725 AACAATGTTCGTGCGTGGCA 61.720 50.000 0.00 0.00 35.60 4.92
4389 4742 1.009108 CAATGTTCGTGCGTGGCAA 60.009 52.632 0.00 0.00 41.47 4.52
4390 4743 1.008995 AATGTTCGTGCGTGGCAAC 60.009 52.632 0.00 0.00 41.47 4.17
4406 4759 7.129109 CGTGGCAACGGAATATAAATATTCT 57.871 36.000 17.82 2.05 46.25 2.40
4407 4760 8.246908 CGTGGCAACGGAATATAAATATTCTA 57.753 34.615 17.82 0.00 46.25 2.10
4408 4761 8.380644 CGTGGCAACGGAATATAAATATTCTAG 58.619 37.037 17.82 14.98 46.25 2.43
4409 4762 9.216117 GTGGCAACGGAATATAAATATTCTAGT 57.784 33.333 17.82 15.43 44.96 2.57
4471 4824 8.812513 TCATCAAATTCTGACCATGAATTACT 57.187 30.769 0.00 0.00 41.54 2.24
4472 4825 9.246670 TCATCAAATTCTGACCATGAATTACTT 57.753 29.630 0.00 0.00 41.54 2.24
4473 4826 9.865321 CATCAAATTCTGACCATGAATTACTTT 57.135 29.630 0.00 0.00 41.54 2.66
4474 4827 9.865321 ATCAAATTCTGACCATGAATTACTTTG 57.135 29.630 0.00 0.00 41.54 2.77
4475 4828 8.859090 TCAAATTCTGACCATGAATTACTTTGT 58.141 29.630 0.00 0.00 41.54 2.83
4518 4871 9.369672 TGGTAAGTAAAGTAAAATGGAATTGGT 57.630 29.630 0.00 0.00 36.10 3.67
4527 4880 9.435688 AAGTAAAATGGAATTGGTTTAGAATGC 57.564 29.630 0.00 0.00 36.10 3.56
4528 4881 8.592809 AGTAAAATGGAATTGGTTTAGAATGCA 58.407 29.630 0.00 0.00 36.10 3.96
4529 4882 9.213799 GTAAAATGGAATTGGTTTAGAATGCAA 57.786 29.630 0.00 0.00 36.10 4.08
4530 4883 7.910441 AAATGGAATTGGTTTAGAATGCAAG 57.090 32.000 0.00 0.00 36.10 4.01
4531 4884 6.610075 ATGGAATTGGTTTAGAATGCAAGT 57.390 33.333 0.00 0.00 0.00 3.16
4532 4885 7.716799 ATGGAATTGGTTTAGAATGCAAGTA 57.283 32.000 0.00 0.00 0.00 2.24
4533 4886 7.531857 TGGAATTGGTTTAGAATGCAAGTAA 57.468 32.000 0.00 0.00 0.00 2.24
4534 4887 7.957002 TGGAATTGGTTTAGAATGCAAGTAAA 58.043 30.769 0.00 0.00 0.00 2.01
4535 4888 8.592809 TGGAATTGGTTTAGAATGCAAGTAAAT 58.407 29.630 0.00 0.00 0.00 1.40
4536 4889 9.435688 GGAATTGGTTTAGAATGCAAGTAAATT 57.564 29.630 0.00 0.00 0.00 1.82
4540 4893 9.921637 TTGGTTTAGAATGCAAGTAAATTAAGG 57.078 29.630 0.00 0.00 0.00 2.69
4541 4894 9.084533 TGGTTTAGAATGCAAGTAAATTAAGGT 57.915 29.630 0.00 0.00 0.00 3.50
4542 4895 9.353999 GGTTTAGAATGCAAGTAAATTAAGGTG 57.646 33.333 0.00 0.00 0.00 4.00
4547 4900 9.023962 AGAATGCAAGTAAATTAAGGTGATTGA 57.976 29.630 0.00 0.00 0.00 2.57
4548 4901 9.807649 GAATGCAAGTAAATTAAGGTGATTGAT 57.192 29.630 0.00 0.00 0.00 2.57
4558 4911 7.969536 ATTAAGGTGATTGATTATCTGGACG 57.030 36.000 0.00 0.00 34.17 4.79
4559 4912 5.614324 AAGGTGATTGATTATCTGGACGA 57.386 39.130 0.00 0.00 34.17 4.20
4560 4913 5.614324 AGGTGATTGATTATCTGGACGAA 57.386 39.130 0.00 0.00 34.17 3.85
4561 4914 5.605534 AGGTGATTGATTATCTGGACGAAG 58.394 41.667 0.00 0.00 34.17 3.79
4562 4915 4.752101 GGTGATTGATTATCTGGACGAAGG 59.248 45.833 0.00 0.00 34.17 3.46
4563 4916 4.752101 GTGATTGATTATCTGGACGAAGGG 59.248 45.833 0.00 0.00 34.17 3.95
4564 4917 3.838244 TTGATTATCTGGACGAAGGGG 57.162 47.619 0.00 0.00 0.00 4.79
4565 4918 2.759355 TGATTATCTGGACGAAGGGGT 58.241 47.619 0.00 0.00 0.00 4.95
4566 4919 2.434336 TGATTATCTGGACGAAGGGGTG 59.566 50.000 0.00 0.00 0.00 4.61
4567 4920 1.200519 TTATCTGGACGAAGGGGTGG 58.799 55.000 0.00 0.00 0.00 4.61
4568 4921 0.042131 TATCTGGACGAAGGGGTGGT 59.958 55.000 0.00 0.00 0.00 4.16
4569 4922 1.553690 ATCTGGACGAAGGGGTGGTG 61.554 60.000 0.00 0.00 0.00 4.17
4570 4923 3.246112 TGGACGAAGGGGTGGTGG 61.246 66.667 0.00 0.00 0.00 4.61
4571 4924 4.029809 GGACGAAGGGGTGGTGGG 62.030 72.222 0.00 0.00 0.00 4.61
4572 4925 2.926242 GACGAAGGGGTGGTGGGA 60.926 66.667 0.00 0.00 0.00 4.37
4573 4926 2.448931 ACGAAGGGGTGGTGGGAA 60.449 61.111 0.00 0.00 0.00 3.97
4574 4927 2.351276 CGAAGGGGTGGTGGGAAG 59.649 66.667 0.00 0.00 0.00 3.46
4575 4928 2.221299 CGAAGGGGTGGTGGGAAGA 61.221 63.158 0.00 0.00 0.00 2.87
4576 4929 1.774894 CGAAGGGGTGGTGGGAAGAA 61.775 60.000 0.00 0.00 0.00 2.52
4577 4930 0.481128 GAAGGGGTGGTGGGAAGAAA 59.519 55.000 0.00 0.00 0.00 2.52
4578 4931 0.482887 AAGGGGTGGTGGGAAGAAAG 59.517 55.000 0.00 0.00 0.00 2.62
4579 4932 1.076727 GGGGTGGTGGGAAGAAAGG 59.923 63.158 0.00 0.00 0.00 3.11
4580 4933 1.726192 GGGGTGGTGGGAAGAAAGGT 61.726 60.000 0.00 0.00 0.00 3.50
4581 4934 0.539669 GGGTGGTGGGAAGAAAGGTG 60.540 60.000 0.00 0.00 0.00 4.00
4582 4935 0.476771 GGTGGTGGGAAGAAAGGTGA 59.523 55.000 0.00 0.00 0.00 4.02
4583 4936 1.133606 GGTGGTGGGAAGAAAGGTGAA 60.134 52.381 0.00 0.00 0.00 3.18
4584 4937 2.490902 GGTGGTGGGAAGAAAGGTGAAT 60.491 50.000 0.00 0.00 0.00 2.57
4585 4938 2.558359 GTGGTGGGAAGAAAGGTGAATG 59.442 50.000 0.00 0.00 0.00 2.67
4586 4939 2.445145 TGGTGGGAAGAAAGGTGAATGA 59.555 45.455 0.00 0.00 0.00 2.57
4587 4940 3.117322 TGGTGGGAAGAAAGGTGAATGAA 60.117 43.478 0.00 0.00 0.00 2.57
4588 4941 3.895041 GGTGGGAAGAAAGGTGAATGAAA 59.105 43.478 0.00 0.00 0.00 2.69
4589 4942 4.262036 GGTGGGAAGAAAGGTGAATGAAAC 60.262 45.833 0.00 0.00 0.00 2.78
4590 4943 3.895041 TGGGAAGAAAGGTGAATGAAACC 59.105 43.478 0.00 0.00 38.03 3.27
4599 4952 4.969484 AGGTGAATGAAACCTTACGTTCT 58.031 39.130 0.00 0.00 46.14 3.01
4600 4953 5.374071 AGGTGAATGAAACCTTACGTTCTT 58.626 37.500 0.00 0.00 46.14 2.52
4601 4954 5.826208 AGGTGAATGAAACCTTACGTTCTTT 59.174 36.000 0.00 0.00 46.14 2.52
4602 4955 6.320418 AGGTGAATGAAACCTTACGTTCTTTT 59.680 34.615 0.00 0.00 46.14 2.27
4603 4956 6.976349 GGTGAATGAAACCTTACGTTCTTTTT 59.024 34.615 0.00 0.00 34.66 1.94
4604 4957 7.166970 GGTGAATGAAACCTTACGTTCTTTTTC 59.833 37.037 0.00 0.00 34.66 2.29
4605 4958 7.698970 GTGAATGAAACCTTACGTTCTTTTTCA 59.301 33.333 13.89 13.89 37.37 2.69
4606 4959 8.244802 TGAATGAAACCTTACGTTCTTTTTCAA 58.755 29.630 14.92 2.20 36.75 2.69
4607 4960 8.628882 AATGAAACCTTACGTTCTTTTTCAAG 57.371 30.769 14.92 2.35 36.75 3.02
4608 4961 7.148355 TGAAACCTTACGTTCTTTTTCAAGT 57.852 32.000 0.00 0.00 31.71 3.16
4609 4962 8.266392 TGAAACCTTACGTTCTTTTTCAAGTA 57.734 30.769 0.00 0.00 31.71 2.24
4610 4963 8.392612 TGAAACCTTACGTTCTTTTTCAAGTAG 58.607 33.333 0.00 0.00 31.71 2.57
4611 4964 7.854557 AACCTTACGTTCTTTTTCAAGTAGT 57.145 32.000 0.00 0.00 0.00 2.73
4612 4965 8.947055 AACCTTACGTTCTTTTTCAAGTAGTA 57.053 30.769 0.00 0.00 0.00 1.82
4613 4966 8.585189 ACCTTACGTTCTTTTTCAAGTAGTAG 57.415 34.615 0.00 0.00 0.00 2.57
4614 4967 8.416329 ACCTTACGTTCTTTTTCAAGTAGTAGA 58.584 33.333 0.00 0.00 0.00 2.59
4615 4968 8.913656 CCTTACGTTCTTTTTCAAGTAGTAGAG 58.086 37.037 0.00 0.00 0.00 2.43
4625 4978 3.562973 TCAAGTAGTAGAGATTACGCCCG 59.437 47.826 0.00 0.00 0.00 6.13
4643 4996 1.001048 CCGCGTGTATCCCTAAATCGA 60.001 52.381 4.92 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 6.829849 TCATCTATCATGTGGCAGATAACAA 58.170 36.000 0.00 0.00 0.00 2.83
104 109 3.642141 TGAGAAGGCCAAAAAGACCTTT 58.358 40.909 5.01 0.00 43.82 3.11
280 285 1.577328 ATCCTTTTGCCGTGCAGTCG 61.577 55.000 0.00 0.00 40.61 4.18
290 295 9.358872 CCAGTCTTAAAATAGAAATCCTTTTGC 57.641 33.333 0.00 0.00 0.00 3.68
316 322 6.040278 GGTAGTAGATACAACCCACTAGTTCC 59.960 46.154 0.00 0.00 35.96 3.62
893 924 2.768527 CCCTCACTGGATAGCTTCAAGA 59.231 50.000 0.00 0.00 38.35 3.02
894 925 2.503356 ACCCTCACTGGATAGCTTCAAG 59.497 50.000 0.00 0.00 38.35 3.02
895 926 2.551270 ACCCTCACTGGATAGCTTCAA 58.449 47.619 0.00 0.00 38.35 2.69
896 927 2.254152 ACCCTCACTGGATAGCTTCA 57.746 50.000 0.00 0.00 38.35 3.02
897 928 3.636153 AAACCCTCACTGGATAGCTTC 57.364 47.619 0.00 0.00 38.35 3.86
903 934 3.910627 ACAACTCTAAACCCTCACTGGAT 59.089 43.478 0.00 0.00 38.35 3.41
941 972 7.099266 TCAATTTATTCACTAGCATGGGTTG 57.901 36.000 0.00 0.00 0.00 3.77
1434 1498 5.594725 AGCAAATGAGAAGCATGATGAAGAT 59.405 36.000 0.00 0.00 37.28 2.40
1628 1692 7.023171 TGTATGGGTTAACAATAAGACCTGT 57.977 36.000 8.10 0.00 32.73 4.00
1862 1933 9.444600 TTTTATCATTTGTACTAACAGGAGACC 57.555 33.333 0.00 0.00 36.83 3.85
2130 2469 5.786311 AGCTGCAAATTGATGCTAAGAAAA 58.214 33.333 10.44 0.00 46.54 2.29
2245 2586 2.094026 GCCTTTTCCAATAACTGCCAGG 60.094 50.000 0.00 0.00 0.00 4.45
2696 3037 7.125792 ACAAGGGAAGACGATGTAATATCTT 57.874 36.000 0.00 0.00 35.27 2.40
2752 3093 2.483014 TAACCTTTGATGGTGTCCGG 57.517 50.000 0.00 0.00 40.73 5.14
2817 3158 8.463930 TTTCATCTCTTGACAAAATAACAGGT 57.536 30.769 0.00 0.00 32.84 4.00
2905 3246 0.466963 ATGGTCGCATCAGCATCTGA 59.533 50.000 0.00 0.00 44.99 3.27
3309 3650 5.221244 ACCACTGTCATTTGACCTAAAAAGC 60.221 40.000 8.16 0.00 44.15 3.51
3315 3656 2.552155 GCCACCACTGTCATTTGACCTA 60.552 50.000 8.16 0.00 44.15 3.08
3318 3659 1.537202 GAGCCACCACTGTCATTTGAC 59.463 52.381 3.72 3.72 44.97 3.18
3498 3839 5.103898 ACAGTACTCATAGTCCTCATCCAGA 60.104 44.000 0.00 0.00 0.00 3.86
3808 4149 2.493278 CACTGCCCTTGATCGGAAAAAT 59.507 45.455 0.00 0.00 0.00 1.82
3846 4187 2.098117 CCTCATTCTCATTTTGGGCGAC 59.902 50.000 0.00 0.00 0.00 5.19
3854 4195 3.858638 ACCTAACCCCCTCATTCTCATTT 59.141 43.478 0.00 0.00 0.00 2.32
3895 4236 3.792053 GATAGCTGGGTCGGTGCGG 62.792 68.421 0.00 0.00 0.00 5.69
3900 4241 4.543590 AATAATCTGATAGCTGGGTCGG 57.456 45.455 0.00 0.00 0.00 4.79
3968 4309 4.837972 TGGTAATGGTCGAAATGATGACA 58.162 39.130 0.00 0.00 36.83 3.58
4031 4381 0.173708 AGGCTCGAAATGACGACTCC 59.826 55.000 0.00 0.00 37.37 3.85
4115 4465 5.906113 TGCAATCTATTTTCCGCCTAAAA 57.094 34.783 0.00 0.00 33.15 1.52
4260 4613 2.294512 CTGAAAAAGAGGTCCCAAGCAC 59.705 50.000 0.00 0.00 0.00 4.40
4268 4621 7.872113 AATCATCCATACTGAAAAAGAGGTC 57.128 36.000 0.00 0.00 0.00 3.85
4303 4656 6.012157 AGCCAAATATATCCTAGCCAACATCT 60.012 38.462 0.00 0.00 0.00 2.90
4359 4712 5.107607 CGCACGAACATTGTTCTAGTAAACT 60.108 40.000 23.29 0.00 0.00 2.66
4365 4718 2.159841 CCACGCACGAACATTGTTCTAG 60.160 50.000 23.29 17.02 0.00 2.43
4369 4722 1.008995 GCCACGCACGAACATTGTT 60.009 52.632 0.63 0.63 0.00 2.83
4370 4723 1.719725 TTGCCACGCACGAACATTGT 61.720 50.000 0.00 0.00 38.71 2.71
4371 4724 1.009108 TTGCCACGCACGAACATTG 60.009 52.632 0.00 0.00 38.71 2.82
4372 4725 1.008995 GTTGCCACGCACGAACATT 60.009 52.632 0.00 0.00 38.71 2.71
4373 4726 2.637025 GTTGCCACGCACGAACAT 59.363 55.556 0.00 0.00 38.71 2.71
4374 4727 3.931130 CGTTGCCACGCACGAACA 61.931 61.111 0.00 0.00 40.18 3.18
4375 4728 4.659874 CCGTTGCCACGCACGAAC 62.660 66.667 4.52 0.00 45.72 3.95
4376 4729 4.893601 TCCGTTGCCACGCACGAA 62.894 61.111 4.52 0.00 45.72 3.85
4377 4730 2.766875 TATTCCGTTGCCACGCACGA 62.767 55.000 4.52 0.00 45.72 4.35
4378 4731 1.701545 ATATTCCGTTGCCACGCACG 61.702 55.000 4.52 0.00 45.72 5.34
4379 4732 1.292061 TATATTCCGTTGCCACGCAC 58.708 50.000 4.52 0.00 45.72 5.34
4380 4733 2.025589 TTATATTCCGTTGCCACGCA 57.974 45.000 4.52 0.00 45.72 5.24
4381 4734 3.619233 ATTTATATTCCGTTGCCACGC 57.381 42.857 4.52 0.00 45.72 5.34
4382 4735 7.129109 AGAATATTTATATTCCGTTGCCACG 57.871 36.000 15.47 2.82 46.13 4.94
4383 4736 9.216117 ACTAGAATATTTATATTCCGTTGCCAC 57.784 33.333 15.47 0.00 46.13 5.01
4445 4798 9.246670 AGTAATTCATGGTCAGAATTTGATGAA 57.753 29.630 6.48 0.00 41.54 2.57
4446 4799 8.812513 AGTAATTCATGGTCAGAATTTGATGA 57.187 30.769 6.48 0.00 41.54 2.92
4447 4800 9.865321 AAAGTAATTCATGGTCAGAATTTGATG 57.135 29.630 6.48 0.00 41.54 3.07
4448 4801 9.865321 CAAAGTAATTCATGGTCAGAATTTGAT 57.135 29.630 6.48 0.00 41.54 2.57
4449 4802 8.859090 ACAAAGTAATTCATGGTCAGAATTTGA 58.141 29.630 6.48 0.00 41.54 2.69
4492 4845 9.369672 ACCAATTCCATTTTACTTTACTTACCA 57.630 29.630 0.00 0.00 0.00 3.25
4501 4854 9.435688 GCATTCTAAACCAATTCCATTTTACTT 57.564 29.630 0.00 0.00 0.00 2.24
4502 4855 8.592809 TGCATTCTAAACCAATTCCATTTTACT 58.407 29.630 0.00 0.00 0.00 2.24
4503 4856 8.770438 TGCATTCTAAACCAATTCCATTTTAC 57.230 30.769 0.00 0.00 0.00 2.01
4504 4857 9.434420 CTTGCATTCTAAACCAATTCCATTTTA 57.566 29.630 0.00 0.00 0.00 1.52
4505 4858 7.938490 ACTTGCATTCTAAACCAATTCCATTTT 59.062 29.630 0.00 0.00 0.00 1.82
4506 4859 7.452562 ACTTGCATTCTAAACCAATTCCATTT 58.547 30.769 0.00 0.00 0.00 2.32
4507 4860 7.008021 ACTTGCATTCTAAACCAATTCCATT 57.992 32.000 0.00 0.00 0.00 3.16
4508 4861 6.610075 ACTTGCATTCTAAACCAATTCCAT 57.390 33.333 0.00 0.00 0.00 3.41
4509 4862 7.531857 TTACTTGCATTCTAAACCAATTCCA 57.468 32.000 0.00 0.00 0.00 3.53
4510 4863 9.435688 AATTTACTTGCATTCTAAACCAATTCC 57.564 29.630 0.00 0.00 0.00 3.01
4514 4867 9.921637 CCTTAATTTACTTGCATTCTAAACCAA 57.078 29.630 0.00 0.00 0.00 3.67
4515 4868 9.084533 ACCTTAATTTACTTGCATTCTAAACCA 57.915 29.630 0.00 0.00 0.00 3.67
4516 4869 9.353999 CACCTTAATTTACTTGCATTCTAAACC 57.646 33.333 0.00 0.00 0.00 3.27
4521 4874 9.023962 TCAATCACCTTAATTTACTTGCATTCT 57.976 29.630 0.00 0.00 0.00 2.40
4522 4875 9.807649 ATCAATCACCTTAATTTACTTGCATTC 57.192 29.630 0.00 0.00 0.00 2.67
4532 4885 8.840321 CGTCCAGATAATCAATCACCTTAATTT 58.160 33.333 0.00 0.00 37.03 1.82
4533 4886 8.210946 TCGTCCAGATAATCAATCACCTTAATT 58.789 33.333 0.00 0.00 37.03 1.40
4534 4887 7.735917 TCGTCCAGATAATCAATCACCTTAAT 58.264 34.615 0.00 0.00 37.03 1.40
4535 4888 7.119709 TCGTCCAGATAATCAATCACCTTAA 57.880 36.000 0.00 0.00 37.03 1.85
4536 4889 6.724893 TCGTCCAGATAATCAATCACCTTA 57.275 37.500 0.00 0.00 37.03 2.69
4537 4890 5.614324 TCGTCCAGATAATCAATCACCTT 57.386 39.130 0.00 0.00 37.03 3.50
4538 4891 5.453903 CCTTCGTCCAGATAATCAATCACCT 60.454 44.000 0.00 0.00 37.03 4.00
4539 4892 4.752101 CCTTCGTCCAGATAATCAATCACC 59.248 45.833 0.00 0.00 37.03 4.02
4540 4893 4.752101 CCCTTCGTCCAGATAATCAATCAC 59.248 45.833 0.00 0.00 37.03 3.06
4541 4894 4.202357 CCCCTTCGTCCAGATAATCAATCA 60.202 45.833 0.00 0.00 37.03 2.57
4542 4895 4.202367 ACCCCTTCGTCCAGATAATCAATC 60.202 45.833 0.00 0.00 34.52 2.67
4543 4896 3.716872 ACCCCTTCGTCCAGATAATCAAT 59.283 43.478 0.00 0.00 0.00 2.57
4544 4897 3.112263 ACCCCTTCGTCCAGATAATCAA 58.888 45.455 0.00 0.00 0.00 2.57
4545 4898 2.434336 CACCCCTTCGTCCAGATAATCA 59.566 50.000 0.00 0.00 0.00 2.57
4546 4899 2.224305 CCACCCCTTCGTCCAGATAATC 60.224 54.545 0.00 0.00 0.00 1.75
4547 4900 1.768870 CCACCCCTTCGTCCAGATAAT 59.231 52.381 0.00 0.00 0.00 1.28
4548 4901 1.200519 CCACCCCTTCGTCCAGATAA 58.799 55.000 0.00 0.00 0.00 1.75
4549 4902 0.042131 ACCACCCCTTCGTCCAGATA 59.958 55.000 0.00 0.00 0.00 1.98
4550 4903 1.229529 ACCACCCCTTCGTCCAGAT 60.230 57.895 0.00 0.00 0.00 2.90
4551 4904 2.203182 ACCACCCCTTCGTCCAGA 59.797 61.111 0.00 0.00 0.00 3.86
4552 4905 2.347490 CACCACCCCTTCGTCCAG 59.653 66.667 0.00 0.00 0.00 3.86
4553 4906 3.246112 CCACCACCCCTTCGTCCA 61.246 66.667 0.00 0.00 0.00 4.02
4554 4907 4.029809 CCCACCACCCCTTCGTCC 62.030 72.222 0.00 0.00 0.00 4.79
4555 4908 2.465055 CTTCCCACCACCCCTTCGTC 62.465 65.000 0.00 0.00 0.00 4.20
4556 4909 2.448931 TTCCCACCACCCCTTCGT 60.449 61.111 0.00 0.00 0.00 3.85
4557 4910 1.774894 TTCTTCCCACCACCCCTTCG 61.775 60.000 0.00 0.00 0.00 3.79
4558 4911 0.481128 TTTCTTCCCACCACCCCTTC 59.519 55.000 0.00 0.00 0.00 3.46
4559 4912 0.482887 CTTTCTTCCCACCACCCCTT 59.517 55.000 0.00 0.00 0.00 3.95
4560 4913 1.435346 CCTTTCTTCCCACCACCCCT 61.435 60.000 0.00 0.00 0.00 4.79
4561 4914 1.076727 CCTTTCTTCCCACCACCCC 59.923 63.158 0.00 0.00 0.00 4.95
4562 4915 0.539669 CACCTTTCTTCCCACCACCC 60.540 60.000 0.00 0.00 0.00 4.61
4563 4916 0.476771 TCACCTTTCTTCCCACCACC 59.523 55.000 0.00 0.00 0.00 4.61
4564 4917 2.358322 TTCACCTTTCTTCCCACCAC 57.642 50.000 0.00 0.00 0.00 4.16
4565 4918 2.445145 TCATTCACCTTTCTTCCCACCA 59.555 45.455 0.00 0.00 0.00 4.17
4566 4919 3.154827 TCATTCACCTTTCTTCCCACC 57.845 47.619 0.00 0.00 0.00 4.61
4567 4920 4.262036 GGTTTCATTCACCTTTCTTCCCAC 60.262 45.833 0.00 0.00 0.00 4.61
4568 4921 3.895041 GGTTTCATTCACCTTTCTTCCCA 59.105 43.478 0.00 0.00 0.00 4.37
4569 4922 4.152647 AGGTTTCATTCACCTTTCTTCCC 58.847 43.478 0.00 0.00 42.45 3.97
4578 4931 5.684550 AAGAACGTAAGGTTTCATTCACC 57.315 39.130 0.00 0.00 37.50 4.02
4579 4932 7.698970 TGAAAAAGAACGTAAGGTTTCATTCAC 59.301 33.333 11.26 0.00 37.50 3.18
4580 4933 7.763356 TGAAAAAGAACGTAAGGTTTCATTCA 58.237 30.769 11.26 4.74 37.50 2.57
4581 4934 8.623310 TTGAAAAAGAACGTAAGGTTTCATTC 57.377 30.769 14.38 4.55 37.50 2.67
4582 4935 8.248253 ACTTGAAAAAGAACGTAAGGTTTCATT 58.752 29.630 14.38 6.13 37.50 2.57
4583 4936 7.768240 ACTTGAAAAAGAACGTAAGGTTTCAT 58.232 30.769 14.38 3.16 37.50 2.57
4584 4937 7.148355 ACTTGAAAAAGAACGTAAGGTTTCA 57.852 32.000 11.26 11.26 37.50 2.69
4585 4938 8.393366 ACTACTTGAAAAAGAACGTAAGGTTTC 58.607 33.333 0.00 0.00 37.50 2.78
4586 4939 8.272545 ACTACTTGAAAAAGAACGTAAGGTTT 57.727 30.769 0.00 0.00 37.50 3.27
4587 4940 7.854557 ACTACTTGAAAAAGAACGTAAGGTT 57.145 32.000 0.00 0.00 37.50 3.50
4589 4942 8.807667 TCTACTACTTGAAAAAGAACGTAAGG 57.192 34.615 0.00 0.00 46.39 2.69
4596 4949 9.136952 GCGTAATCTCTACTACTTGAAAAAGAA 57.863 33.333 0.00 0.00 0.00 2.52
4597 4950 7.758528 GGCGTAATCTCTACTACTTGAAAAAGA 59.241 37.037 0.00 0.00 0.00 2.52
4598 4951 7.010275 GGGCGTAATCTCTACTACTTGAAAAAG 59.990 40.741 0.00 0.00 0.00 2.27
4599 4952 6.815142 GGGCGTAATCTCTACTACTTGAAAAA 59.185 38.462 0.00 0.00 0.00 1.94
4600 4953 6.335777 GGGCGTAATCTCTACTACTTGAAAA 58.664 40.000 0.00 0.00 0.00 2.29
4601 4954 5.449588 CGGGCGTAATCTCTACTACTTGAAA 60.450 44.000 0.00 0.00 0.00 2.69
4602 4955 4.036027 CGGGCGTAATCTCTACTACTTGAA 59.964 45.833 0.00 0.00 0.00 2.69
4603 4956 3.562973 CGGGCGTAATCTCTACTACTTGA 59.437 47.826 0.00 0.00 0.00 3.02
4604 4957 3.852572 GCGGGCGTAATCTCTACTACTTG 60.853 52.174 0.00 0.00 0.00 3.16
4605 4958 2.292845 GCGGGCGTAATCTCTACTACTT 59.707 50.000 0.00 0.00 0.00 2.24
4606 4959 1.878734 GCGGGCGTAATCTCTACTACT 59.121 52.381 0.00 0.00 0.00 2.57
4607 4960 1.399471 CGCGGGCGTAATCTCTACTAC 60.399 57.143 4.64 0.00 34.35 2.73
4608 4961 0.870393 CGCGGGCGTAATCTCTACTA 59.130 55.000 4.64 0.00 34.35 1.82
4609 4962 1.653115 CGCGGGCGTAATCTCTACT 59.347 57.895 4.64 0.00 34.35 2.57
4610 4963 4.223514 CGCGGGCGTAATCTCTAC 57.776 61.111 4.64 0.00 34.35 2.59
4620 4973 2.632136 TTTAGGGATACACGCGGGCG 62.632 60.000 9.12 12.04 46.03 6.13
4625 4978 6.963049 AATTATCGATTTAGGGATACACGC 57.037 37.500 1.71 0.00 39.74 5.34
4697 5052 9.593134 GTCATACAGAAAGTAGAACATCTGAAT 57.407 33.333 15.45 2.52 41.38 2.57
4706 5061 9.778741 ATCACAAAAGTCATACAGAAAGTAGAA 57.221 29.630 0.00 0.00 35.85 2.10
4711 5066 8.993121 AGTGTATCACAAAAGTCATACAGAAAG 58.007 33.333 2.80 0.00 36.74 2.62


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

AutoCloner maintained by Alex Coulton.