Multiple sequence alignment - TraesCS3B01G088200

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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 TraesCS3B01G088200 chr3B 100.000 4967 0 0 1 4967 56132694 56127728 0.000000e+00 9173
1 TraesCS3B01G088200 chr3B 85.719 3102 397 28 934 4011 56071176 56068097 0.000000e+00 3232
2 TraesCS3B01G088200 chr3B 90.686 1750 163 0 928 2677 56080041 56078292 0.000000e+00 2329
3 TraesCS3B01G088200 chr3B 87.618 1591 161 25 2670 4244 56077957 56076387 0.000000e+00 1814
4 TraesCS3B01G088200 chr3D 97.549 4814 104 8 1 4808 33375729 33370924 0.000000e+00 8224
5 TraesCS3B01G088200 chr3D 89.823 3331 307 19 928 4244 33356983 33353671 0.000000e+00 4244
6 TraesCS3B01G088200 chr3D 85.842 3122 395 24 934 4026 33335655 33332552 0.000000e+00 3273
7 TraesCS3B01G088200 chr3A 96.663 4645 123 6 1 4635 46027287 46022665 0.000000e+00 7690
8 TraesCS3B01G088200 chr3A 90.449 3099 285 3 928 4019 46009587 46006493 0.000000e+00 4072
9 TraesCS3B01G088200 chr3A 79.201 976 167 18 3071 4026 45940609 45939650 0.000000e+00 645
10 TraesCS3B01G088200 chr3A 94.842 349 15 1 4619 4967 46013598 46013253 4.370000e-150 542
11 TraesCS3B01G088200 chr3A 87.220 446 57 0 1104 1549 45941055 45940610 4.440000e-140 508


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 TraesCS3B01G088200 chr3B 56127728 56132694 4966 True 9173.0 9173 100.0000 1 4967 1 chr3B.!!$R2 4966
1 TraesCS3B01G088200 chr3B 56068097 56071176 3079 True 3232.0 3232 85.7190 934 4011 1 chr3B.!!$R1 3077
2 TraesCS3B01G088200 chr3B 56076387 56080041 3654 True 2071.5 2329 89.1520 928 4244 2 chr3B.!!$R3 3316
3 TraesCS3B01G088200 chr3D 33370924 33375729 4805 True 8224.0 8224 97.5490 1 4808 1 chr3D.!!$R3 4807
4 TraesCS3B01G088200 chr3D 33353671 33356983 3312 True 4244.0 4244 89.8230 928 4244 1 chr3D.!!$R2 3316
5 TraesCS3B01G088200 chr3D 33332552 33335655 3103 True 3273.0 3273 85.8420 934 4026 1 chr3D.!!$R1 3092
6 TraesCS3B01G088200 chr3A 46022665 46027287 4622 True 7690.0 7690 96.6630 1 4635 1 chr3A.!!$R1 4634
7 TraesCS3B01G088200 chr3A 46006493 46013598 7105 True 2307.0 4072 92.6455 928 4967 2 chr3A.!!$R3 4039
8 TraesCS3B01G088200 chr3A 45939650 45941055 1405 True 576.5 645 83.2105 1104 4026 2 chr3A.!!$R2 2922

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
412 414 0.905357 AGTATGGTCAAAGCCGCTCT 59.095 50.000 0.0 0.0 0.00 4.09 F
1152 4237 1.299850 CGCTGTTCGTGAGGACACA 60.300 57.895 0.0 0.0 46.84 3.72 F
2796 6235 1.807814 AACTTCCAGAGTCCACAGGT 58.192 50.000 0.0 0.0 37.72 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2223 5312 1.676967 CTGCTTGAGTTGAGGGGGC 60.677 63.158 0.0 0.0 0.00 5.80 R
2817 6256 1.133823 TGGCAACCAAGCAAAGAGAGA 60.134 47.619 0.0 0.0 35.83 3.10 R
4145 7646 0.595095 GCACTTCCAGGCTTCACAAG 59.405 55.000 0.0 0.0 0.00 3.16 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
252 253 1.971357 CGGATAGGTCCTATGGCAAGT 59.029 52.381 16.53 0.00 42.73 3.16
267 268 3.259374 TGGCAAGTTTGACAAGAAACCAA 59.741 39.130 0.00 0.00 44.72 3.67
298 300 6.284459 GGTCTTCTACCTTCCATGTAATGAG 58.716 44.000 0.00 0.00 46.36 2.90
401 403 1.137872 CTGGAGCACAGGAGTATGGTC 59.862 57.143 0.82 0.00 43.70 4.02
412 414 0.905357 AGTATGGTCAAAGCCGCTCT 59.095 50.000 0.00 0.00 0.00 4.09
649 654 5.049405 CAGCCTTTAGTTTCGTGTCATTCTT 60.049 40.000 0.00 0.00 0.00 2.52
917 922 3.124578 TGCAGACAAGAGCATTGTGTA 57.875 42.857 11.56 0.00 35.51 2.90
1152 4237 1.299850 CGCTGTTCGTGAGGACACA 60.300 57.895 0.00 0.00 46.84 3.72
1296 4381 3.555956 CACCTAGATCGGTATGTTGCAAC 59.444 47.826 22.83 22.83 34.94 4.17
1355 4440 5.918608 TGATCATAAGGTGGCTAGAAGAAC 58.081 41.667 0.00 0.00 0.00 3.01
2279 5368 3.996363 GCTTTGTTGCCTCCTAATTTTGG 59.004 43.478 0.00 0.00 0.00 3.28
2604 5701 4.899352 AGAGCATAAGTGTTTGAGGAGT 57.101 40.909 0.00 0.00 0.00 3.85
2652 5749 8.463930 ACTTCAAGTTGATTCACAAGGAAATA 57.536 30.769 6.36 0.00 39.39 1.40
2722 6161 4.641989 GCATCCAAAACATACCAGAGTCAT 59.358 41.667 0.00 0.00 0.00 3.06
2745 6184 2.026262 GGGGAACTTGGTGCTATTGAGA 60.026 50.000 0.00 0.00 0.00 3.27
2796 6235 1.807814 AACTTCCAGAGTCCACAGGT 58.192 50.000 0.00 0.00 37.72 4.00
2817 6256 4.263243 GGTAGCCTCATCAGCCTTGAATAT 60.263 45.833 0.00 0.00 36.78 1.28
3052 6491 1.271982 TGTGGGTCGAGAAGCTAGAGT 60.272 52.381 0.00 0.00 0.00 3.24
3067 6506 1.681327 GAGTCAGCGGTACCAGGGA 60.681 63.158 13.54 2.31 0.00 4.20
3170 6615 3.306088 CGTTACCAGACTGATGAGGTTGT 60.306 47.826 3.32 0.00 35.62 3.32
3186 6631 4.210331 AGGTTGTGAGAATTCAGCAAGTT 58.790 39.130 8.44 0.00 32.98 2.66
3192 6637 7.137490 TGTGAGAATTCAGCAAGTTTATGAG 57.863 36.000 8.44 0.00 32.98 2.90
3285 6730 1.673920 CTACTCTCAGAACCGGAGCTC 59.326 57.143 9.46 4.71 32.38 4.09
3295 6740 0.107456 ACCGGAGCTCAATATGCCAG 59.893 55.000 17.19 0.00 0.00 4.85
3959 7416 2.961741 TCTTCCCGGATGAATCTCTCTG 59.038 50.000 0.73 0.00 0.00 3.35
3968 7425 7.255977 CCCGGATGAATCTCTCTGTAATTAGAA 60.256 40.741 0.73 0.00 0.00 2.10
4111 7612 5.068198 AGGCTTACAAGATCGGTTCGTATTA 59.932 40.000 0.00 0.00 0.00 0.98
4267 7768 2.715737 TTTACATGGCCGCTCAAAAC 57.284 45.000 0.00 0.00 0.00 2.43
4377 7879 3.104843 GCTATGGAGCTCTTCGATTGT 57.895 47.619 14.64 0.00 45.98 2.71
4389 7891 1.596603 TCGATTGTAGGCGGACGATA 58.403 50.000 0.00 0.00 0.00 2.92
4395 7897 1.602888 TAGGCGGACGATAGGAGGC 60.603 63.158 0.00 0.00 43.77 4.70
4419 7921 4.444306 CCCTGTTTGTTGAGTTCTGGAGTA 60.444 45.833 0.00 0.00 0.00 2.59
4442 7944 6.667007 AAAATGTTGTTGCTTTTTCTCTGG 57.333 33.333 0.00 0.00 0.00 3.86
4513 8015 0.179015 TGGGCTGCCTACAAAAACGA 60.179 50.000 19.68 0.00 0.00 3.85
4515 8017 0.948678 GGCTGCCTACAAAAACGACA 59.051 50.000 12.43 0.00 0.00 4.35
4701 8203 4.674101 GCGCCTTTGTTATGCTTGTCAATA 60.674 41.667 0.00 0.00 0.00 1.90
4733 8235 0.325577 TAGGCAGGCACTCATCTGGA 60.326 55.000 0.00 0.00 34.60 3.86
4757 8259 7.175990 GGAATATGTTTGGAGTTGTGGTTCTTA 59.824 37.037 0.00 0.00 0.00 2.10
4773 8275 6.264518 GTGGTTCTTATCTTGGGAGTGAAAAA 59.735 38.462 0.00 0.00 0.00 1.94
4803 8305 9.347240 AGGCGATCTAAACTACTAGTAATAACA 57.653 33.333 3.76 0.00 0.00 2.41
4804 8306 9.609950 GGCGATCTAAACTACTAGTAATAACAG 57.390 37.037 3.76 0.00 0.00 3.16
4822 8324 9.849166 TAATAACAGTATTTTTGGCTTTGTAGC 57.151 29.630 0.00 0.00 37.60 3.58
4823 8325 6.405278 AACAGTATTTTTGGCTTTGTAGCT 57.595 33.333 0.00 0.00 46.90 3.32
4824 8326 7.519032 AACAGTATTTTTGGCTTTGTAGCTA 57.481 32.000 0.00 0.00 46.90 3.32
4825 8327 7.703058 ACAGTATTTTTGGCTTTGTAGCTAT 57.297 32.000 0.00 0.00 46.90 2.97
4826 8328 8.122472 ACAGTATTTTTGGCTTTGTAGCTATT 57.878 30.769 0.00 0.00 46.90 1.73
4827 8329 8.585018 ACAGTATTTTTGGCTTTGTAGCTATTT 58.415 29.630 0.00 0.00 46.90 1.40
4832 8334 6.753107 TTTGGCTTTGTAGCTATTTAGACC 57.247 37.500 0.00 0.00 46.90 3.85
4833 8335 5.693769 TGGCTTTGTAGCTATTTAGACCT 57.306 39.130 0.00 0.00 46.90 3.85
4834 8336 5.671493 TGGCTTTGTAGCTATTTAGACCTC 58.329 41.667 0.00 0.00 46.90 3.85
4835 8337 5.425539 TGGCTTTGTAGCTATTTAGACCTCT 59.574 40.000 0.00 0.00 46.90 3.69
4836 8338 6.070194 TGGCTTTGTAGCTATTTAGACCTCTT 60.070 38.462 0.00 0.00 46.90 2.85
4837 8339 6.824196 GGCTTTGTAGCTATTTAGACCTCTTT 59.176 38.462 0.00 0.00 46.90 2.52
4838 8340 7.201652 GGCTTTGTAGCTATTTAGACCTCTTTG 60.202 40.741 0.00 0.00 46.90 2.77
4839 8341 7.549488 GCTTTGTAGCTATTTAGACCTCTTTGA 59.451 37.037 0.00 0.00 44.27 2.69
4840 8342 9.606631 CTTTGTAGCTATTTAGACCTCTTTGAT 57.393 33.333 0.00 0.00 0.00 2.57
4841 8343 9.959721 TTTGTAGCTATTTAGACCTCTTTGATT 57.040 29.630 0.00 0.00 0.00 2.57
4842 8344 9.601217 TTGTAGCTATTTAGACCTCTTTGATTC 57.399 33.333 0.00 0.00 0.00 2.52
4843 8345 8.758829 TGTAGCTATTTAGACCTCTTTGATTCA 58.241 33.333 0.00 0.00 0.00 2.57
4844 8346 9.601217 GTAGCTATTTAGACCTCTTTGATTCAA 57.399 33.333 0.00 0.00 0.00 2.69
4846 8348 9.520515 AGCTATTTAGACCTCTTTGATTCAAAA 57.479 29.630 12.62 4.19 32.75 2.44
4847 8349 9.780413 GCTATTTAGACCTCTTTGATTCAAAAG 57.220 33.333 12.62 11.84 38.31 2.27
4851 8353 6.734104 AGACCTCTTTGATTCAAAAGATCG 57.266 37.500 12.62 1.84 43.41 3.69
4852 8354 6.234177 AGACCTCTTTGATTCAAAAGATCGT 58.766 36.000 12.62 10.36 43.41 3.73
4853 8355 7.386851 AGACCTCTTTGATTCAAAAGATCGTA 58.613 34.615 12.62 0.00 43.41 3.43
4854 8356 8.043710 AGACCTCTTTGATTCAAAAGATCGTAT 58.956 33.333 12.62 6.72 43.41 3.06
4855 8357 9.314321 GACCTCTTTGATTCAAAAGATCGTATA 57.686 33.333 12.62 0.00 43.41 1.47
4856 8358 9.319143 ACCTCTTTGATTCAAAAGATCGTATAG 57.681 33.333 12.62 0.00 43.41 1.31
4857 8359 8.768955 CCTCTTTGATTCAAAAGATCGTATAGG 58.231 37.037 12.62 5.48 43.41 2.57
4858 8360 9.534565 CTCTTTGATTCAAAAGATCGTATAGGA 57.465 33.333 12.62 0.00 43.41 2.94
4859 8361 9.884636 TCTTTGATTCAAAAGATCGTATAGGAA 57.115 29.630 12.62 0.00 40.41 3.36
4890 8392 9.836864 AAGAAGAAGAAAATAAATTGCTTTGGT 57.163 25.926 0.00 0.00 0.00 3.67
4891 8393 9.836864 AGAAGAAGAAAATAAATTGCTTTGGTT 57.163 25.926 0.00 0.00 0.00 3.67
4892 8394 9.868389 GAAGAAGAAAATAAATTGCTTTGGTTG 57.132 29.630 0.00 0.00 0.00 3.77
4893 8395 8.962884 AGAAGAAAATAAATTGCTTTGGTTGT 57.037 26.923 0.00 0.00 0.00 3.32
4894 8396 9.394767 AGAAGAAAATAAATTGCTTTGGTTGTT 57.605 25.926 0.00 0.00 0.00 2.83
4896 8398 9.786105 AAGAAAATAAATTGCTTTGGTTGTTTG 57.214 25.926 0.00 0.00 0.00 2.93
4897 8399 9.171877 AGAAAATAAATTGCTTTGGTTGTTTGA 57.828 25.926 0.00 0.00 0.00 2.69
4898 8400 9.949174 GAAAATAAATTGCTTTGGTTGTTTGAT 57.051 25.926 0.00 0.00 0.00 2.57
4899 8401 9.949174 AAAATAAATTGCTTTGGTTGTTTGATC 57.051 25.926 0.00 0.00 0.00 2.92
4900 8402 8.907222 AATAAATTGCTTTGGTTGTTTGATCT 57.093 26.923 0.00 0.00 0.00 2.75
4901 8403 6.607735 AAATTGCTTTGGTTGTTTGATCTG 57.392 33.333 0.00 0.00 0.00 2.90
4902 8404 4.734398 TTGCTTTGGTTGTTTGATCTGT 57.266 36.364 0.00 0.00 0.00 3.41
4903 8405 4.734398 TGCTTTGGTTGTTTGATCTGTT 57.266 36.364 0.00 0.00 0.00 3.16
4904 8406 4.431809 TGCTTTGGTTGTTTGATCTGTTG 58.568 39.130 0.00 0.00 0.00 3.33
4905 8407 3.803778 GCTTTGGTTGTTTGATCTGTTGG 59.196 43.478 0.00 0.00 0.00 3.77
4906 8408 4.441356 GCTTTGGTTGTTTGATCTGTTGGA 60.441 41.667 0.00 0.00 0.00 3.53
4907 8409 5.659463 CTTTGGTTGTTTGATCTGTTGGAA 58.341 37.500 0.00 0.00 0.00 3.53
4908 8410 5.867903 TTGGTTGTTTGATCTGTTGGAAT 57.132 34.783 0.00 0.00 0.00 3.01
4909 8411 5.199024 TGGTTGTTTGATCTGTTGGAATG 57.801 39.130 0.00 0.00 0.00 2.67
4910 8412 4.892345 TGGTTGTTTGATCTGTTGGAATGA 59.108 37.500 0.00 0.00 0.00 2.57
4911 8413 5.362143 TGGTTGTTTGATCTGTTGGAATGAA 59.638 36.000 0.00 0.00 0.00 2.57
4912 8414 5.691754 GGTTGTTTGATCTGTTGGAATGAAC 59.308 40.000 0.00 0.00 0.00 3.18
4913 8415 5.452078 TGTTTGATCTGTTGGAATGAACC 57.548 39.130 0.00 0.00 0.00 3.62
4914 8416 5.139727 TGTTTGATCTGTTGGAATGAACCT 58.860 37.500 0.00 0.00 0.00 3.50
4915 8417 5.598005 TGTTTGATCTGTTGGAATGAACCTT 59.402 36.000 0.00 0.00 0.00 3.50
4916 8418 5.710513 TTGATCTGTTGGAATGAACCTTG 57.289 39.130 0.00 0.00 0.00 3.61
4917 8419 4.081406 TGATCTGTTGGAATGAACCTTGG 58.919 43.478 0.00 0.00 0.00 3.61
4918 8420 3.874383 TCTGTTGGAATGAACCTTGGA 57.126 42.857 0.00 0.00 0.00 3.53
4919 8421 4.177537 TCTGTTGGAATGAACCTTGGAA 57.822 40.909 0.00 0.00 0.00 3.53
4920 8422 4.541705 TCTGTTGGAATGAACCTTGGAAA 58.458 39.130 0.00 0.00 0.00 3.13
4921 8423 4.959210 TCTGTTGGAATGAACCTTGGAAAA 59.041 37.500 0.00 0.00 0.00 2.29
4922 8424 5.423610 TCTGTTGGAATGAACCTTGGAAAAA 59.576 36.000 0.00 0.00 0.00 1.94
4943 8445 6.759497 AAAAAGAGTCTCCGGATTTATTGG 57.241 37.500 3.57 0.00 0.00 3.16
4944 8446 3.477210 AGAGTCTCCGGATTTATTGGC 57.523 47.619 3.57 0.00 0.00 4.52
4945 8447 3.041946 AGAGTCTCCGGATTTATTGGCT 58.958 45.455 3.57 0.00 0.00 4.75
4946 8448 3.070302 AGAGTCTCCGGATTTATTGGCTC 59.930 47.826 3.57 8.79 0.00 4.70
4947 8449 3.041946 AGTCTCCGGATTTATTGGCTCT 58.958 45.455 3.57 0.00 0.00 4.09
4948 8450 4.223953 AGTCTCCGGATTTATTGGCTCTA 58.776 43.478 3.57 0.00 0.00 2.43
4949 8451 4.039366 AGTCTCCGGATTTATTGGCTCTAC 59.961 45.833 3.57 0.00 0.00 2.59
4950 8452 3.964688 TCTCCGGATTTATTGGCTCTACA 59.035 43.478 3.57 0.00 0.00 2.74
4951 8453 4.593206 TCTCCGGATTTATTGGCTCTACAT 59.407 41.667 3.57 0.00 0.00 2.29
4952 8454 5.071788 TCTCCGGATTTATTGGCTCTACATT 59.928 40.000 3.57 0.00 0.00 2.71
4953 8455 5.690865 TCCGGATTTATTGGCTCTACATTT 58.309 37.500 0.00 0.00 0.00 2.32
4954 8456 5.763204 TCCGGATTTATTGGCTCTACATTTC 59.237 40.000 0.00 0.00 0.00 2.17
4955 8457 5.530915 CCGGATTTATTGGCTCTACATTTCA 59.469 40.000 0.00 0.00 0.00 2.69
4956 8458 6.039270 CCGGATTTATTGGCTCTACATTTCAA 59.961 38.462 0.00 0.00 0.00 2.69
4957 8459 7.416213 CCGGATTTATTGGCTCTACATTTCAAA 60.416 37.037 0.00 0.00 0.00 2.69
4958 8460 7.973388 CGGATTTATTGGCTCTACATTTCAAAA 59.027 33.333 0.00 0.00 0.00 2.44
4959 8461 9.305925 GGATTTATTGGCTCTACATTTCAAAAG 57.694 33.333 0.00 0.00 0.00 2.27
4960 8462 9.860898 GATTTATTGGCTCTACATTTCAAAAGT 57.139 29.630 0.00 0.00 0.00 2.66
4963 8465 9.515226 TTATTGGCTCTACATTTCAAAAGTACT 57.485 29.630 0.00 0.00 0.00 2.73
4965 8467 9.686683 ATTGGCTCTACATTTCAAAAGTACTAT 57.313 29.630 0.00 0.00 0.00 2.12
4966 8468 9.515226 TTGGCTCTACATTTCAAAAGTACTATT 57.485 29.630 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 6.543831 CCTTCCTCATTGTAAATTCCCACTAG 59.456 42.308 0.00 0.00 0.00 2.57
252 253 4.202141 CCAGCTGATTGGTTTCTTGTCAAA 60.202 41.667 17.39 0.00 33.38 2.69
298 300 1.003118 TGCTCACACCTCATGGTTACC 59.997 52.381 0.00 0.00 46.05 2.85
401 403 3.553511 CACTGTATAGAAGAGCGGCTTTG 59.446 47.826 2.97 0.00 36.83 2.77
412 414 3.967326 AGCAGCCATACCACTGTATAGAA 59.033 43.478 0.00 0.00 35.89 2.10
649 654 1.605232 CACATGAGCTTGCAGTGACAA 59.395 47.619 0.00 0.00 32.14 3.18
766 771 3.366052 AATACCCTGGTCACATTCCAC 57.634 47.619 0.00 0.00 0.00 4.02
887 892 4.220602 TGCTCTTGTCTGCATAAGTGAGTA 59.779 41.667 10.07 3.47 33.94 2.59
917 922 2.223876 CCTTGTGCTGTGCAAATTGTCT 60.224 45.455 0.00 0.00 41.47 3.41
1152 4237 0.255318 CTTCCATGGCCAGAGCTTCT 59.745 55.000 13.05 0.00 39.73 2.85
1355 4440 9.512435 CATCAAGCTTTTCATTTATGTCCTTAG 57.488 33.333 0.00 0.00 0.00 2.18
2223 5312 1.676967 CTGCTTGAGTTGAGGGGGC 60.677 63.158 0.00 0.00 0.00 5.80
2636 5733 8.246180 GCTTTCTGAATATTTCCTTGTGAATCA 58.754 33.333 0.00 0.00 31.67 2.57
2652 5749 4.314121 GGATATGCTCGAGCTTTCTGAAT 58.686 43.478 35.27 21.55 42.66 2.57
2722 6161 2.109128 TCAATAGCACCAAGTTCCCCAA 59.891 45.455 0.00 0.00 0.00 4.12
2745 6184 7.174413 TCTCAGTATAGCTCAGATCTAGCAAT 58.826 38.462 19.65 8.23 42.62 3.56
2817 6256 1.133823 TGGCAACCAAGCAAAGAGAGA 60.134 47.619 0.00 0.00 35.83 3.10
3052 6491 1.982395 CAGTCCCTGGTACCGCTGA 60.982 63.158 7.57 0.00 0.00 4.26
3067 6506 4.811557 GCTGTTCTTCAGTACAAGTTCAGT 59.188 41.667 0.00 0.00 45.23 3.41
3090 6529 6.520272 CAGTCCCAGTTCTCTAAGATTATGG 58.480 44.000 0.00 0.00 0.00 2.74
3170 6615 7.414873 GCATCTCATAAACTTGCTGAATTCTCA 60.415 37.037 7.05 2.06 0.00 3.27
3186 6631 6.840527 TGGTGATGGAATAAGCATCTCATAA 58.159 36.000 0.00 0.00 27.96 1.90
3192 6637 3.005155 GGCTTGGTGATGGAATAAGCATC 59.995 47.826 0.00 0.00 44.03 3.91
3285 6730 4.724074 ATGACACAAACCTGGCATATTG 57.276 40.909 0.00 0.00 38.19 1.90
3295 6740 3.081061 TGAGGTGCATATGACACAAACC 58.919 45.455 22.92 13.05 39.87 3.27
3429 6874 1.002033 GCTGCACTTCTCACACCTTTG 60.002 52.381 0.00 0.00 0.00 2.77
3588 7036 0.405198 TGGGGCAATCAAGAAGCAGA 59.595 50.000 0.00 0.00 0.00 4.26
3959 7416 9.384764 AGCTATTTCACTCACCTTTCTAATTAC 57.615 33.333 0.00 0.00 0.00 1.89
3968 7425 8.568794 GTTTTTCTTAGCTATTTCACTCACCTT 58.431 33.333 0.00 0.00 0.00 3.50
4145 7646 0.595095 GCACTTCCAGGCTTCACAAG 59.405 55.000 0.00 0.00 0.00 3.16
4267 7768 5.413833 GGCCATATCTGTAACCAATCTGATG 59.586 44.000 0.00 0.00 0.00 3.07
4377 7879 1.602888 GCCTCCTATCGTCCGCCTA 60.603 63.158 0.00 0.00 0.00 3.93
4395 7897 1.956477 CCAGAACTCAACAAACAGGGG 59.044 52.381 0.00 0.00 0.00 4.79
4419 7921 6.405538 TCCAGAGAAAAAGCAACAACATTTT 58.594 32.000 0.00 0.00 0.00 1.82
4513 8015 6.716628 TCCAAAAACTAATGAGCTTCTGATGT 59.283 34.615 0.00 0.00 0.00 3.06
4515 8017 7.951347 ATCCAAAAACTAATGAGCTTCTGAT 57.049 32.000 0.00 0.00 0.00 2.90
4680 8182 6.254157 CACATATTGACAAGCATAACAAAGGC 59.746 38.462 0.00 0.00 34.24 4.35
4701 8203 2.101917 GCCTGCCTAATTTCATGCACAT 59.898 45.455 0.00 0.00 0.00 3.21
4733 8235 6.976934 AAGAACCACAACTCCAAACATATT 57.023 33.333 0.00 0.00 0.00 1.28
4757 8259 5.105756 CGCCTTAATTTTTCACTCCCAAGAT 60.106 40.000 0.00 0.00 0.00 2.40
4814 8316 9.606631 ATCAAAGAGGTCTAAATAGCTACAAAG 57.393 33.333 0.00 0.00 0.00 2.77
4815 8317 9.959721 AATCAAAGAGGTCTAAATAGCTACAAA 57.040 29.630 0.00 0.00 0.00 2.83
4816 8318 9.601217 GAATCAAAGAGGTCTAAATAGCTACAA 57.399 33.333 0.00 0.00 0.00 2.41
4817 8319 8.758829 TGAATCAAAGAGGTCTAAATAGCTACA 58.241 33.333 0.00 0.00 0.00 2.74
4818 8320 9.601217 TTGAATCAAAGAGGTCTAAATAGCTAC 57.399 33.333 0.00 0.00 0.00 3.58
4820 8322 9.520515 TTTTGAATCAAAGAGGTCTAAATAGCT 57.479 29.630 8.51 0.00 34.72 3.32
4821 8323 9.780413 CTTTTGAATCAAAGAGGTCTAAATAGC 57.220 33.333 8.51 0.00 34.72 2.97
4825 8327 8.721478 CGATCTTTTGAATCAAAGAGGTCTAAA 58.279 33.333 19.10 2.09 34.72 1.85
4826 8328 7.878127 ACGATCTTTTGAATCAAAGAGGTCTAA 59.122 33.333 19.10 2.62 34.72 2.10
4827 8329 7.386851 ACGATCTTTTGAATCAAAGAGGTCTA 58.613 34.615 19.10 3.15 34.72 2.59
4828 8330 6.234177 ACGATCTTTTGAATCAAAGAGGTCT 58.766 36.000 19.10 10.32 34.72 3.85
4829 8331 6.487689 ACGATCTTTTGAATCAAAGAGGTC 57.512 37.500 8.51 12.65 34.72 3.85
4830 8332 9.319143 CTATACGATCTTTTGAATCAAAGAGGT 57.681 33.333 8.51 11.72 34.72 3.85
4831 8333 8.768955 CCTATACGATCTTTTGAATCAAAGAGG 58.231 37.037 8.51 4.26 34.72 3.69
4832 8334 9.534565 TCCTATACGATCTTTTGAATCAAAGAG 57.465 33.333 8.51 9.33 34.72 2.85
4833 8335 9.884636 TTCCTATACGATCTTTTGAATCAAAGA 57.115 29.630 8.51 8.92 34.72 2.52
4864 8366 9.836864 ACCAAAGCAATTTATTTTCTTCTTCTT 57.163 25.926 0.00 0.00 0.00 2.52
4865 8367 9.836864 AACCAAAGCAATTTATTTTCTTCTTCT 57.163 25.926 0.00 0.00 0.00 2.85
4866 8368 9.868389 CAACCAAAGCAATTTATTTTCTTCTTC 57.132 29.630 0.00 0.00 0.00 2.87
4867 8369 9.394767 ACAACCAAAGCAATTTATTTTCTTCTT 57.605 25.926 0.00 0.00 0.00 2.52
4868 8370 8.962884 ACAACCAAAGCAATTTATTTTCTTCT 57.037 26.923 0.00 0.00 0.00 2.85
4870 8372 9.786105 CAAACAACCAAAGCAATTTATTTTCTT 57.214 25.926 0.00 0.00 0.00 2.52
4871 8373 9.171877 TCAAACAACCAAAGCAATTTATTTTCT 57.828 25.926 0.00 0.00 0.00 2.52
4872 8374 9.949174 ATCAAACAACCAAAGCAATTTATTTTC 57.051 25.926 0.00 0.00 0.00 2.29
4873 8375 9.949174 GATCAAACAACCAAAGCAATTTATTTT 57.051 25.926 0.00 0.00 0.00 1.82
4874 8376 9.341078 AGATCAAACAACCAAAGCAATTTATTT 57.659 25.926 0.00 0.00 0.00 1.40
4875 8377 8.776470 CAGATCAAACAACCAAAGCAATTTATT 58.224 29.630 0.00 0.00 0.00 1.40
4876 8378 7.933033 ACAGATCAAACAACCAAAGCAATTTAT 59.067 29.630 0.00 0.00 0.00 1.40
4877 8379 7.271511 ACAGATCAAACAACCAAAGCAATTTA 58.728 30.769 0.00 0.00 0.00 1.40
4878 8380 6.114767 ACAGATCAAACAACCAAAGCAATTT 58.885 32.000 0.00 0.00 0.00 1.82
4879 8381 5.673514 ACAGATCAAACAACCAAAGCAATT 58.326 33.333 0.00 0.00 0.00 2.32
4880 8382 5.280654 ACAGATCAAACAACCAAAGCAAT 57.719 34.783 0.00 0.00 0.00 3.56
4881 8383 4.734398 ACAGATCAAACAACCAAAGCAA 57.266 36.364 0.00 0.00 0.00 3.91
4882 8384 4.431809 CAACAGATCAAACAACCAAAGCA 58.568 39.130 0.00 0.00 0.00 3.91
4883 8385 3.803778 CCAACAGATCAAACAACCAAAGC 59.196 43.478 0.00 0.00 0.00 3.51
4884 8386 5.261209 TCCAACAGATCAAACAACCAAAG 57.739 39.130 0.00 0.00 0.00 2.77
4885 8387 5.667539 TTCCAACAGATCAAACAACCAAA 57.332 34.783 0.00 0.00 0.00 3.28
4886 8388 5.362143 TCATTCCAACAGATCAAACAACCAA 59.638 36.000 0.00 0.00 0.00 3.67
4887 8389 4.892345 TCATTCCAACAGATCAAACAACCA 59.108 37.500 0.00 0.00 0.00 3.67
4888 8390 5.452078 TCATTCCAACAGATCAAACAACC 57.548 39.130 0.00 0.00 0.00 3.77
4889 8391 5.691754 GGTTCATTCCAACAGATCAAACAAC 59.308 40.000 0.00 0.00 0.00 3.32
4890 8392 5.598005 AGGTTCATTCCAACAGATCAAACAA 59.402 36.000 0.00 0.00 0.00 2.83
4891 8393 5.139727 AGGTTCATTCCAACAGATCAAACA 58.860 37.500 0.00 0.00 0.00 2.83
4892 8394 5.712152 AGGTTCATTCCAACAGATCAAAC 57.288 39.130 0.00 0.00 0.00 2.93
4893 8395 5.010922 CCAAGGTTCATTCCAACAGATCAAA 59.989 40.000 0.00 0.00 0.00 2.69
4894 8396 4.523943 CCAAGGTTCATTCCAACAGATCAA 59.476 41.667 0.00 0.00 0.00 2.57
4895 8397 4.081406 CCAAGGTTCATTCCAACAGATCA 58.919 43.478 0.00 0.00 0.00 2.92
4896 8398 4.335416 TCCAAGGTTCATTCCAACAGATC 58.665 43.478 0.00 0.00 0.00 2.75
4897 8399 4.387026 TCCAAGGTTCATTCCAACAGAT 57.613 40.909 0.00 0.00 0.00 2.90
4898 8400 3.874383 TCCAAGGTTCATTCCAACAGA 57.126 42.857 0.00 0.00 0.00 3.41
4899 8401 4.935352 TTTCCAAGGTTCATTCCAACAG 57.065 40.909 0.00 0.00 0.00 3.16
4900 8402 5.683876 TTTTTCCAAGGTTCATTCCAACA 57.316 34.783 0.00 0.00 0.00 3.33
4920 8422 5.125578 GCCAATAAATCCGGAGACTCTTTTT 59.874 40.000 11.34 6.23 0.00 1.94
4921 8423 4.640647 GCCAATAAATCCGGAGACTCTTTT 59.359 41.667 11.34 7.01 0.00 2.27
4922 8424 4.080299 AGCCAATAAATCCGGAGACTCTTT 60.080 41.667 11.34 7.80 0.00 2.52
4923 8425 3.456277 AGCCAATAAATCCGGAGACTCTT 59.544 43.478 11.34 0.00 0.00 2.85
4924 8426 3.041946 AGCCAATAAATCCGGAGACTCT 58.958 45.455 11.34 0.00 0.00 3.24
4925 8427 3.070302 AGAGCCAATAAATCCGGAGACTC 59.930 47.826 11.34 2.01 0.00 3.36
4926 8428 3.041946 AGAGCCAATAAATCCGGAGACT 58.958 45.455 11.34 0.00 0.00 3.24
4927 8429 3.477210 AGAGCCAATAAATCCGGAGAC 57.523 47.619 11.34 0.00 0.00 3.36
4928 8430 3.964688 TGTAGAGCCAATAAATCCGGAGA 59.035 43.478 11.34 0.00 0.00 3.71
4929 8431 4.336889 TGTAGAGCCAATAAATCCGGAG 57.663 45.455 11.34 0.00 0.00 4.63
4930 8432 4.974645 ATGTAGAGCCAATAAATCCGGA 57.025 40.909 6.61 6.61 0.00 5.14
4931 8433 5.530915 TGAAATGTAGAGCCAATAAATCCGG 59.469 40.000 0.00 0.00 0.00 5.14
4932 8434 6.618287 TGAAATGTAGAGCCAATAAATCCG 57.382 37.500 0.00 0.00 0.00 4.18
4933 8435 9.305925 CTTTTGAAATGTAGAGCCAATAAATCC 57.694 33.333 0.00 0.00 0.00 3.01
4934 8436 9.860898 ACTTTTGAAATGTAGAGCCAATAAATC 57.139 29.630 0.00 0.00 0.00 2.17
4937 8439 9.515226 AGTACTTTTGAAATGTAGAGCCAATAA 57.485 29.630 4.18 0.00 0.00 1.40
4939 8441 9.686683 ATAGTACTTTTGAAATGTAGAGCCAAT 57.313 29.630 0.00 0.00 0.00 3.16
4940 8442 9.515226 AATAGTACTTTTGAAATGTAGAGCCAA 57.485 29.630 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.