Multiple sequence alignment - TraesCS5B01G428600

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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 TraesCS5B01G428600 chr5B 100.000 6453 0 0 1 6453 604143891 604150343 0.000000e+00 11917
1 TraesCS5B01G428600 chr5D 93.925 4741 194 41 1763 6453 490008399 490013095 0.000000e+00 7073
2 TraesCS5B01G428600 chr5D 89.159 1808 93 43 1 1767 490006600 490008345 0.000000e+00 2158
3 TraesCS5B01G428600 chr5A 93.514 4749 210 41 1759 6453 611634423 611639127 0.000000e+00 6974
4 TraesCS5B01G428600 chr5A 87.141 1812 108 40 1 1767 611632642 611634373 0.000000e+00 1940
5 TraesCS5B01G428600 chr5A 84.255 470 55 13 2899 3359 589355645 589355186 2.140000e-119 440
6 TraesCS5B01G428600 chr1A 83.966 474 54 14 2899 3359 7280337 7280801 9.940000e-118 435
7 TraesCS5B01G428600 chr2B 80.172 464 60 20 2829 3277 37296850 37297296 1.040000e-82 318
8 TraesCS5B01G428600 chr2B 97.000 100 3 0 1 100 356316306 356316207 1.110000e-37 169
9 TraesCS5B01G428600 chr2A 99.000 100 1 0 1 100 372737181 372737280 5.140000e-41 180
10 TraesCS5B01G428600 chr2D 98.000 100 2 0 1 100 298942553 298942652 2.390000e-39 174
11 TraesCS5B01G428600 chr3D 92.453 106 8 0 1 106 7969732 7969837 1.120000e-32 152
12 TraesCS5B01G428600 chr3A 90.291 103 10 0 4 106 12562618 12562516 1.130000e-27 135
13 TraesCS5B01G428600 chr3B 94.118 85 5 0 1 85 10171957 10172041 5.250000e-26 130
14 TraesCS5B01G428600 chr1D 88.636 88 8 2 36 122 108361892 108361806 8.850000e-19 106


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 TraesCS5B01G428600 chr5B 604143891 604150343 6452 False 11917.0 11917 100.0000 1 6453 1 chr5B.!!$F1 6452
1 TraesCS5B01G428600 chr5D 490006600 490013095 6495 False 4615.5 7073 91.5420 1 6453 2 chr5D.!!$F1 6452
2 TraesCS5B01G428600 chr5A 611632642 611639127 6485 False 4457.0 6974 90.3275 1 6453 2 chr5A.!!$F1 6452

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
465 490 0.238553 GGTGGTGCGAGCTTTTCTTC 59.761 55.000 0.00 0.00 0.00 2.87 F
1281 1349 0.392461 TTTCAGGGAGCGATTTCGGG 60.392 55.000 1.75 0.00 40.23 5.14 F
1289 1357 0.611714 AGCGATTTCGGGGTTACTGT 59.388 50.000 1.75 0.00 40.23 3.55 F
2146 2281 1.153168 CCCTTACCCGGTGCTGATG 60.153 63.158 0.00 0.00 0.00 3.07 F
2336 2474 2.292828 AATCCACAAACTCCACCAGG 57.707 50.000 0.00 0.00 0.00 4.45 F
3337 3487 2.426522 TGCCTCTTTGTGCTGATGTAC 58.573 47.619 0.00 0.00 0.00 2.90 F
4034 4184 2.103373 TCCCTGAGATTCGAAGACAGG 58.897 52.381 26.78 26.78 45.09 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1357 0.896923 GCCACCCAGCATGATCAAAA 59.103 50.000 0.00 0.0 39.69 2.44 R
3223 3372 3.021269 TGTGGTGTAGCACTAGAAACG 57.979 47.619 14.40 0.0 34.40 3.60 R
3240 3389 6.612247 AATGCATTGCAATATTTGGATGTG 57.388 33.333 16.46 0.0 43.62 3.21 R
3692 3842 1.652947 TCACCAGTCCTAACCTTCCC 58.347 55.000 0.00 0.0 0.00 3.97 R
3778 3928 4.058817 GCCATGGGAGACTAAGAATAACG 58.941 47.826 15.13 0.0 0.00 3.18 R
4544 4694 0.179158 GACCGGAGCTCGAGTTTCTC 60.179 60.000 9.46 11.8 42.43 2.87 R
5923 6101 0.029300 CACTGCGCCAAAATATCGGG 59.971 55.000 4.18 0.0 0.00 5.14 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
215 219 4.828925 GCCGTCTCAGCAGCTCCC 62.829 72.222 0.00 0.00 0.00 4.30
366 390 1.798813 CGGATTTCTTGGATTTGCGGC 60.799 52.381 0.00 0.00 0.00 6.53
453 478 2.297701 CTATATGGTGTTGGGTGGTGC 58.702 52.381 0.00 0.00 0.00 5.01
465 490 0.238553 GGTGGTGCGAGCTTTTCTTC 59.761 55.000 0.00 0.00 0.00 2.87
487 512 4.100279 CCCCCTCTTTTGTTTAGTGTCT 57.900 45.455 0.00 0.00 0.00 3.41
492 528 6.014499 CCCCTCTTTTGTTTAGTGTCTAGAGA 60.014 42.308 0.00 0.00 31.76 3.10
498 538 8.693120 TTTTGTTTAGTGTCTAGAGAGAGAGA 57.307 34.615 0.00 0.00 30.20 3.10
566 606 2.038387 ACCGAAGAGAGAGAGAGAGC 57.962 55.000 0.00 0.00 0.00 4.09
567 607 1.280710 ACCGAAGAGAGAGAGAGAGCA 59.719 52.381 0.00 0.00 0.00 4.26
568 608 2.092429 ACCGAAGAGAGAGAGAGAGCAT 60.092 50.000 0.00 0.00 0.00 3.79
569 609 3.135712 ACCGAAGAGAGAGAGAGAGCATA 59.864 47.826 0.00 0.00 0.00 3.14
570 610 3.748048 CCGAAGAGAGAGAGAGAGCATAG 59.252 52.174 0.00 0.00 0.00 2.23
571 611 3.748048 CGAAGAGAGAGAGAGAGCATAGG 59.252 52.174 0.00 0.00 0.00 2.57
572 612 4.503123 CGAAGAGAGAGAGAGAGCATAGGA 60.503 50.000 0.00 0.00 0.00 2.94
573 613 4.630644 AGAGAGAGAGAGAGCATAGGAG 57.369 50.000 0.00 0.00 0.00 3.69
795 848 5.446143 TTTTTCATGGACGTATGCAACTT 57.554 34.783 0.00 0.00 0.00 2.66
796 849 5.446143 TTTTCATGGACGTATGCAACTTT 57.554 34.783 0.00 0.00 0.00 2.66
797 850 5.446143 TTTCATGGACGTATGCAACTTTT 57.554 34.783 0.00 0.00 0.00 2.27
798 851 5.446143 TTCATGGACGTATGCAACTTTTT 57.554 34.783 0.00 0.00 0.00 1.94
799 852 4.793071 TCATGGACGTATGCAACTTTTTG 58.207 39.130 0.00 0.00 35.62 2.44
800 853 3.634568 TGGACGTATGCAACTTTTTGG 57.365 42.857 0.00 0.00 32.81 3.28
801 854 2.287909 TGGACGTATGCAACTTTTTGGC 60.288 45.455 0.00 0.00 32.81 4.52
802 855 2.324860 GACGTATGCAACTTTTTGGCC 58.675 47.619 0.00 0.00 32.81 5.36
863 916 3.009115 CCTCCTTTCCGCCTCCCA 61.009 66.667 0.00 0.00 0.00 4.37
940 993 1.586154 AAAAACTCCAGCCATCCGCG 61.586 55.000 0.00 0.00 44.76 6.46
966 1023 1.178276 GTCCTCCGCAAGAGAGAGAA 58.822 55.000 2.33 0.00 46.50 2.87
968 1025 1.821753 TCCTCCGCAAGAGAGAGAAAG 59.178 52.381 2.33 0.00 46.50 2.62
972 1029 3.919216 TCCGCAAGAGAGAGAAAGAAAG 58.081 45.455 0.00 0.00 43.02 2.62
1113 1173 1.227002 GGTCCTGAAGATCCGTCGC 60.227 63.158 0.00 0.00 0.00 5.19
1162 1222 2.613977 CCTTCTTGTTCTGCTCCGATGT 60.614 50.000 0.00 0.00 0.00 3.06
1163 1223 2.839486 TCTTGTTCTGCTCCGATGTT 57.161 45.000 0.00 0.00 0.00 2.71
1166 1226 2.839486 TGTTCTGCTCCGATGTTTCT 57.161 45.000 0.00 0.00 0.00 2.52
1172 1232 3.997021 TCTGCTCCGATGTTTCTTTTCTC 59.003 43.478 0.00 0.00 0.00 2.87
1197 1257 6.822442 TCCTTCCTCGTAATAATGCATTGTA 58.178 36.000 22.27 10.94 0.00 2.41
1205 1265 8.655651 TCGTAATAATGCATTGTAGATGTTCA 57.344 30.769 22.27 0.00 0.00 3.18
1261 1329 0.804989 GATTCTGTGGTTTCTGCGGG 59.195 55.000 0.00 0.00 0.00 6.13
1272 1340 2.747855 CTGCGGGTTTCAGGGAGC 60.748 66.667 0.00 0.00 0.00 4.70
1274 1342 4.388499 GCGGGTTTCAGGGAGCGA 62.388 66.667 0.00 0.00 0.00 4.93
1281 1349 0.392461 TTTCAGGGAGCGATTTCGGG 60.392 55.000 1.75 0.00 40.23 5.14
1289 1357 0.611714 AGCGATTTCGGGGTTACTGT 59.388 50.000 1.75 0.00 40.23 3.55
1371 1440 1.959042 ATTGATTGAGGCAGTAGGCG 58.041 50.000 0.00 0.00 46.16 5.52
1390 1459 3.429085 GCGGCTGATTTGATAACAACAG 58.571 45.455 0.00 0.00 35.63 3.16
1414 1486 4.887748 AGTTCAGTGTGGTTGTATCTGAG 58.112 43.478 0.00 0.00 36.68 3.35
1622 1698 7.090173 GGTTGTCATTGTGTTACTATGCAAAT 58.910 34.615 0.00 0.00 33.50 2.32
1623 1699 8.240682 GGTTGTCATTGTGTTACTATGCAAATA 58.759 33.333 0.00 0.00 33.50 1.40
1720 1796 4.765339 GGGAATAAAGTTGGTAAGTGCTGT 59.235 41.667 0.00 0.00 0.00 4.40
1751 1827 7.243604 TGCTTGTAATTTCAATTGGAGGATT 57.756 32.000 5.42 0.00 0.00 3.01
1754 1830 9.087424 GCTTGTAATTTCAATTGGAGGATTTAC 57.913 33.333 5.42 5.12 0.00 2.01
1776 1910 4.178540 CAAATTGAAATGCTCGGCTCAAT 58.821 39.130 0.00 6.22 39.58 2.57
1812 1946 7.606349 TCCATCGATCTGATTTGTATTAGGAG 58.394 38.462 0.00 0.00 34.13 3.69
1924 2058 7.943413 TGTTTCATTTACCAATCATGTGTTG 57.057 32.000 0.00 0.00 0.00 3.33
1926 2060 8.200120 TGTTTCATTTACCAATCATGTGTTGAA 58.800 29.630 12.91 3.26 38.03 2.69
2130 2265 6.051179 AGTAAGTTTGTTCCTCTACATCCC 57.949 41.667 0.00 0.00 0.00 3.85
2146 2281 1.153168 CCCTTACCCGGTGCTGATG 60.153 63.158 0.00 0.00 0.00 3.07
2193 2328 4.102035 TGATTGAGTCTGATCACAGTCG 57.898 45.455 0.00 0.00 43.81 4.18
2336 2474 2.292828 AATCCACAAACTCCACCAGG 57.707 50.000 0.00 0.00 0.00 4.45
2744 2887 4.023193 ACAACTGCCCAAGTTCTTTATTCG 60.023 41.667 0.00 0.00 46.60 3.34
2990 3133 7.094205 CCCAGAATATATCAGAAAATTTCCCCG 60.094 40.741 1.57 0.00 0.00 5.73
3078 3222 6.149474 ACCATTGTAACAAATCTACAGAGTGC 59.851 38.462 0.00 0.00 31.17 4.40
3240 3389 4.053295 TCAAACGTTTCTAGTGCTACACC 58.947 43.478 11.37 0.00 34.49 4.16
3261 3411 4.081031 ACCACATCCAAATATTGCAATGCA 60.081 37.500 22.27 2.72 36.47 3.96
3331 3481 2.816087 AGTTGTATGCCTCTTTGTGCTG 59.184 45.455 0.00 0.00 0.00 4.41
3337 3487 2.426522 TGCCTCTTTGTGCTGATGTAC 58.573 47.619 0.00 0.00 0.00 2.90
4034 4184 2.103373 TCCCTGAGATTCGAAGACAGG 58.897 52.381 26.78 26.78 45.09 4.00
4061 4211 8.930760 CCAGATTACTCTTACTTGAAGAAACTG 58.069 37.037 0.00 0.00 43.75 3.16
4159 4309 9.920946 ATTTATCCACTGGAAGCTTTCTATAAA 57.079 29.630 6.25 8.66 37.60 1.40
4161 4311 5.497474 TCCACTGGAAGCTTTCTATAAACC 58.503 41.667 6.25 0.00 37.60 3.27
4165 4315 6.316390 CACTGGAAGCTTTCTATAAACCGATT 59.684 38.462 6.25 0.00 37.60 3.34
4267 4417 8.783660 AGTATCCTCATATGAGTTCCAGTAAA 57.216 34.615 27.03 5.54 40.48 2.01
4268 4418 8.643324 AGTATCCTCATATGAGTTCCAGTAAAC 58.357 37.037 27.03 13.37 40.48 2.01
4299 4449 9.961265 TGTTCGAGTATGTATTATCTTACCTTG 57.039 33.333 0.00 0.00 0.00 3.61
4321 4471 9.503427 CCTTGTCGATTGGTATTATTTTCTTTC 57.497 33.333 0.00 0.00 0.00 2.62
4433 4583 2.294512 CCTTCAGGTTTGCCTTCTTGTC 59.705 50.000 0.00 0.00 44.18 3.18
4441 4591 4.023536 GGTTTGCCTTCTTGTCGTTTATCA 60.024 41.667 0.00 0.00 0.00 2.15
4755 4911 0.251354 TCTGCTTGAGATCTGGTGGC 59.749 55.000 0.00 0.00 0.00 5.01
4863 5019 0.532417 AGCTCATCGAAGATGGCTGC 60.532 55.000 18.28 15.11 45.12 5.25
4960 5116 1.299165 CCCATCATCGTCGACCGTC 60.299 63.158 10.58 0.00 37.94 4.79
5009 5165 2.100603 CGGAGAACGGCTCGTCTC 59.899 66.667 0.69 8.82 44.91 3.36
5020 5182 2.362503 TCGTCTCCACCCATCGCT 60.363 61.111 0.00 0.00 0.00 4.93
5122 5284 0.173708 GAAGGAAGTGATCGACGGCT 59.826 55.000 0.00 0.00 0.00 5.52
5158 5320 4.592778 ACAATTGCCAAGGATTTAACACCT 59.407 37.500 5.05 0.00 38.23 4.00
5205 5367 4.392047 TCAGCAGACATGAACAATGACTT 58.608 39.130 0.00 0.00 38.94 3.01
5206 5368 4.214758 TCAGCAGACATGAACAATGACTTG 59.785 41.667 0.00 0.00 38.94 3.16
5207 5369 4.214758 CAGCAGACATGAACAATGACTTGA 59.785 41.667 0.00 0.00 38.94 3.02
5242 5407 1.101331 CAGAATGGCCAGGAAAGAGC 58.899 55.000 13.05 0.00 0.00 4.09
5477 5643 7.099764 TCATAAGAATCTTGGTGTTCTCTCAC 58.900 38.462 5.64 0.00 33.76 3.51
5494 5660 5.763204 TCTCTCACATTTTAGTTGTTCCACC 59.237 40.000 0.00 0.00 0.00 4.61
5609 5776 1.554160 ACCCAAGCAGAGAGATGTCTG 59.446 52.381 0.00 2.74 45.91 3.51
5643 5810 4.819630 TGAACTTGTGCTAGGTTTACCTTG 59.180 41.667 6.76 6.38 46.09 3.61
5669 5836 5.520376 ACCCAAACTCTGATTTTGTTCAG 57.480 39.130 16.21 7.30 43.70 3.02
5681 5848 4.993029 TTTTGTTCAGTTACCACCCAAG 57.007 40.909 0.00 0.00 0.00 3.61
5682 5849 1.975660 TGTTCAGTTACCACCCAAGC 58.024 50.000 0.00 0.00 0.00 4.01
5684 5851 2.706723 TGTTCAGTTACCACCCAAGCTA 59.293 45.455 0.00 0.00 0.00 3.32
5689 5856 4.825085 TCAGTTACCACCCAAGCTAAAAAG 59.175 41.667 0.00 0.00 0.00 2.27
5696 5866 2.628178 ACCCAAGCTAAAAAGAACTGGC 59.372 45.455 0.00 0.00 0.00 4.85
5741 5911 7.493367 TCAATTAACCGGTTTTGATCTGTTTT 58.507 30.769 27.64 0.00 0.00 2.43
5749 5919 6.381801 CGGTTTTGATCTGTTTTAGCTGAAT 58.618 36.000 0.00 0.00 0.00 2.57
5752 5923 8.703336 GGTTTTGATCTGTTTTAGCTGAATTTC 58.297 33.333 0.00 0.00 0.00 2.17
5793 5965 9.675464 TGGATTATTTACGACTTACTGGAAAAT 57.325 29.630 0.00 0.00 0.00 1.82
5855 6031 2.297597 AGTCGGACTTGACCTCTCAAAG 59.702 50.000 4.45 0.00 39.77 2.77
5923 6101 7.581476 TGAGAATTGATAAACTGGAACGTTTC 58.419 34.615 0.46 0.00 36.71 2.78
5937 6116 1.399089 ACGTTTCCCGATATTTTGGCG 59.601 47.619 0.00 0.00 40.70 5.69
5939 6118 1.133407 GTTTCCCGATATTTTGGCGCA 59.867 47.619 10.83 0.00 0.00 6.09
5972 6151 0.250510 TGTGCTTGGCATTACGGTGA 60.251 50.000 0.00 0.00 41.91 4.02
5985 6164 7.882791 TGGCATTACGGTGAATTATGATAATCT 59.117 33.333 0.00 0.00 0.00 2.40
6023 6202 8.043710 CCAGTTTTTGCCCATTTTGGTATATTA 58.956 33.333 0.00 0.00 35.17 0.98
6064 6243 6.038714 CACTTAGTTCCATGGCTATTTTCCTC 59.961 42.308 6.96 0.00 0.00 3.71
6245 6434 7.049754 AGTTTTGCAGGATTCTCAATGTTTTT 58.950 30.769 0.00 0.00 0.00 1.94
6267 6456 3.640967 TGTTTCAAGTTGAATGGAAGGGG 59.359 43.478 18.69 0.00 36.11 4.79
6303 6492 0.921896 ATGGAAGGGAGGTGGTGATG 59.078 55.000 0.00 0.00 0.00 3.07
6307 6496 0.987294 AAGGGAGGTGGTGATGTGAG 59.013 55.000 0.00 0.00 0.00 3.51
6326 6515 0.743097 GCCAGATCAGAATTGGTGGC 59.257 55.000 2.95 2.95 38.23 5.01
6328 6517 1.747355 CCAGATCAGAATTGGTGGCAC 59.253 52.381 9.70 9.70 0.00 5.01
6330 6519 2.681848 CAGATCAGAATTGGTGGCACTC 59.318 50.000 18.45 7.05 0.00 3.51
6383 6572 1.639298 GATGAGGTGGTCAAGTGCGC 61.639 60.000 0.00 0.00 39.19 6.09
6422 6629 0.541863 ACCAGAACCGGATCCATCAC 59.458 55.000 9.46 0.13 0.00 3.06
6427 6634 2.368875 AGAACCGGATCCATCACCATAC 59.631 50.000 9.46 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
337 355 2.180204 AAGAAATCCGCCGCATCCG 61.180 57.895 0.00 0.00 0.00 4.18
341 359 0.679640 AATCCAAGAAATCCGCCGCA 60.680 50.000 0.00 0.00 0.00 5.69
379 403 3.264947 CTGGAGCAGCAACAGCAG 58.735 61.111 0.00 0.00 0.00 4.24
485 510 3.889538 CCGTCTCTCTCTCTCTCTCTAGA 59.110 52.174 0.00 0.00 0.00 2.43
486 511 3.553096 GCCGTCTCTCTCTCTCTCTCTAG 60.553 56.522 0.00 0.00 0.00 2.43
487 512 2.364324 GCCGTCTCTCTCTCTCTCTCTA 59.636 54.545 0.00 0.00 0.00 2.43
492 528 1.153249 CGGCCGTCTCTCTCTCTCT 60.153 63.158 19.50 0.00 0.00 3.10
566 606 1.077005 CCTCCTCCTCCTCCTCCTATG 59.923 61.905 0.00 0.00 0.00 2.23
567 607 1.059364 TCCTCCTCCTCCTCCTCCTAT 60.059 57.143 0.00 0.00 0.00 2.57
568 608 0.350904 TCCTCCTCCTCCTCCTCCTA 59.649 60.000 0.00 0.00 0.00 2.94
569 609 0.556380 TTCCTCCTCCTCCTCCTCCT 60.556 60.000 0.00 0.00 0.00 3.69
570 610 0.105709 CTTCCTCCTCCTCCTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
571 611 0.930726 TCTTCCTCCTCCTCCTCCTC 59.069 60.000 0.00 0.00 0.00 3.71
572 612 0.634465 GTCTTCCTCCTCCTCCTCCT 59.366 60.000 0.00 0.00 0.00 3.69
573 613 0.753848 CGTCTTCCTCCTCCTCCTCC 60.754 65.000 0.00 0.00 0.00 4.30
774 827 5.446143 AAAGTTGCATACGTCCATGAAAA 57.554 34.783 2.44 0.00 0.00 2.29
779 832 3.613910 GCCAAAAAGTTGCATACGTCCAT 60.614 43.478 0.00 0.00 33.01 3.41
780 833 2.287909 GCCAAAAAGTTGCATACGTCCA 60.288 45.455 0.00 0.00 33.01 4.02
781 834 2.324860 GCCAAAAAGTTGCATACGTCC 58.675 47.619 0.00 0.00 33.01 4.79
782 835 2.030274 AGGCCAAAAAGTTGCATACGTC 60.030 45.455 5.01 0.00 33.01 4.34
783 836 1.960689 AGGCCAAAAAGTTGCATACGT 59.039 42.857 5.01 0.00 33.01 3.57
784 837 2.030363 TCAGGCCAAAAAGTTGCATACG 60.030 45.455 5.01 0.00 33.01 3.06
785 838 3.578688 CTCAGGCCAAAAAGTTGCATAC 58.421 45.455 5.01 0.00 33.01 2.39
786 839 2.562298 CCTCAGGCCAAAAAGTTGCATA 59.438 45.455 5.01 0.00 33.01 3.14
787 840 1.345415 CCTCAGGCCAAAAAGTTGCAT 59.655 47.619 5.01 0.00 33.01 3.96
788 841 0.752054 CCTCAGGCCAAAAAGTTGCA 59.248 50.000 5.01 0.00 33.01 4.08
789 842 0.752658 ACCTCAGGCCAAAAAGTTGC 59.247 50.000 5.01 0.00 33.01 4.17
790 843 2.294512 GAGACCTCAGGCCAAAAAGTTG 59.705 50.000 5.01 0.00 34.25 3.16
791 844 2.587522 GAGACCTCAGGCCAAAAAGTT 58.412 47.619 5.01 0.00 0.00 2.66
792 845 1.202940 GGAGACCTCAGGCCAAAAAGT 60.203 52.381 5.01 0.00 0.00 2.66
793 846 1.539157 GGAGACCTCAGGCCAAAAAG 58.461 55.000 5.01 0.00 0.00 2.27
794 847 3.745723 GGAGACCTCAGGCCAAAAA 57.254 52.632 5.01 0.00 0.00 1.94
845 898 2.687566 GGGAGGCGGAAAGGAGGA 60.688 66.667 0.00 0.00 0.00 3.71
947 1004 1.178276 TTCTCTCTCTTGCGGAGGAC 58.822 55.000 6.66 0.00 42.10 3.85
1113 1173 1.079612 GAACCAACGGTACCCTCGG 60.080 63.158 6.25 6.45 33.12 4.63
1126 1186 1.064825 GAAGGTGGAGGAAGGAACCA 58.935 55.000 0.00 0.00 35.01 3.67
1129 1189 2.418669 ACAAGAAGGTGGAGGAAGGAA 58.581 47.619 0.00 0.00 0.00 3.36
1162 1222 4.957684 ACGAGGAAGGAGAGAAAAGAAA 57.042 40.909 0.00 0.00 0.00 2.52
1163 1223 6.607004 ATTACGAGGAAGGAGAGAAAAGAA 57.393 37.500 0.00 0.00 0.00 2.52
1166 1226 6.761714 GCATTATTACGAGGAAGGAGAGAAAA 59.238 38.462 0.00 0.00 0.00 2.29
1172 1232 5.760253 ACAATGCATTATTACGAGGAAGGAG 59.240 40.000 12.53 0.00 0.00 3.69
1197 1257 3.285484 CCATTGCTAAGGCTGAACATCT 58.715 45.455 0.00 0.00 39.59 2.90
1234 1302 1.366319 AACCACAGAATCAGAGGCCT 58.634 50.000 3.86 3.86 0.00 5.19
1261 1329 0.727398 CCGAAATCGCTCCCTGAAAC 59.273 55.000 0.00 0.00 38.18 2.78
1272 1340 3.499157 TCAAAACAGTAACCCCGAAATCG 59.501 43.478 0.00 0.00 39.44 3.34
1274 1342 5.074115 TGATCAAAACAGTAACCCCGAAAT 58.926 37.500 0.00 0.00 0.00 2.17
1281 1349 4.380867 CCCAGCATGATCAAAACAGTAACC 60.381 45.833 0.00 0.00 39.69 2.85
1289 1357 0.896923 GCCACCCAGCATGATCAAAA 59.103 50.000 0.00 0.00 39.69 2.44
1371 1440 6.743575 ACTACTGTTGTTATCAAATCAGCC 57.256 37.500 4.77 0.00 33.66 4.85
1390 1459 5.779922 TCAGATACAACCACACTGAACTAC 58.220 41.667 0.00 0.00 35.20 2.73
1414 1486 3.093057 AGGGAAAAATGCTCCTCTTCC 57.907 47.619 0.00 0.00 35.76 3.46
1470 1543 1.130561 GGCCACTCAATACGTTTGCTC 59.869 52.381 0.00 0.00 0.00 4.26
1476 1549 0.908910 TCCATGGCCACTCAATACGT 59.091 50.000 8.16 0.00 0.00 3.57
1478 1551 1.312815 GCTCCATGGCCACTCAATAC 58.687 55.000 8.16 0.00 0.00 1.89
1481 1554 0.918258 TATGCTCCATGGCCACTCAA 59.082 50.000 8.16 0.00 0.00 3.02
1482 1555 1.142936 ATATGCTCCATGGCCACTCA 58.857 50.000 8.16 1.61 0.00 3.41
1547 1620 2.509964 ACCAAGGTATAGCTCCCCAAAG 59.490 50.000 4.63 0.00 0.00 2.77
1677 1753 2.094649 CCACTTCCTCTCCGTTCTGTAC 60.095 54.545 0.00 0.00 0.00 2.90
1685 1761 3.197983 ACTTTATTCCCACTTCCTCTCCG 59.802 47.826 0.00 0.00 0.00 4.63
1720 1796 7.984050 TCCAATTGAAATTACAAGCAAGTTTGA 59.016 29.630 7.12 0.00 33.22 2.69
1751 1827 4.217334 TGAGCCGAGCATTTCAATTTGTAA 59.783 37.500 0.00 0.00 0.00 2.41
1754 1830 3.220507 TGAGCCGAGCATTTCAATTTG 57.779 42.857 0.00 0.00 0.00 2.32
1757 1833 2.756760 ACATTGAGCCGAGCATTTCAAT 59.243 40.909 0.00 6.22 40.00 2.57
1776 1910 4.160252 TCAGATCGATGGAAATGTGAGACA 59.840 41.667 0.54 0.00 0.00 3.41
1812 1946 1.696832 GATGCTTCGACTTCACGGGC 61.697 60.000 0.00 0.00 34.96 6.13
2130 2265 3.813596 GCATCAGCACCGGGTAAG 58.186 61.111 6.32 0.00 41.58 2.34
2146 2281 5.221880 TGCACTTGTTTCATAACTTCATGC 58.778 37.500 0.00 0.00 35.24 4.06
2336 2474 5.479124 TGAGACCCAGTAAAAGTTAGTCC 57.521 43.478 0.00 0.00 0.00 3.85
2448 2586 9.294030 CACAATTCAAATAATCTCAACTAAGCC 57.706 33.333 0.00 0.00 0.00 4.35
2727 2870 6.848451 TGATTTACGAATAAAGAACTTGGGC 58.152 36.000 0.00 0.00 33.78 5.36
2977 3120 5.607939 AGAAAAACACGGGGAAATTTTCT 57.392 34.783 13.51 13.51 42.43 2.52
3025 3169 7.106239 ACCACTAGGAAGTATCACATCAAAAG 58.894 38.462 0.00 0.00 38.69 2.27
3030 3174 7.450634 TGGTATACCACTAGGAAGTATCACATC 59.549 40.741 21.05 0.00 42.01 3.06
3223 3372 3.021269 TGTGGTGTAGCACTAGAAACG 57.979 47.619 14.40 0.00 34.40 3.60
3240 3389 6.612247 AATGCATTGCAATATTTGGATGTG 57.388 33.333 16.46 0.00 43.62 3.21
3261 3411 9.396022 CCTAACATATACACTGTCCAAGAAAAT 57.604 33.333 0.00 0.00 0.00 1.82
3372 3522 7.739498 TTTTATTCTCCCTGTACAGACAAAC 57.261 36.000 24.68 0.00 34.35 2.93
3428 3578 6.995091 GCTCACCTATTCCAAGATGAGTATTT 59.005 38.462 0.00 0.00 36.71 1.40
3692 3842 1.652947 TCACCAGTCCTAACCTTCCC 58.347 55.000 0.00 0.00 0.00 3.97
3778 3928 4.058817 GCCATGGGAGACTAAGAATAACG 58.941 47.826 15.13 0.00 0.00 3.18
4034 4184 7.604545 AGTTTCTTCAAGTAAGAGTAATCTGGC 59.395 37.037 0.00 0.00 44.95 4.85
4061 4211 4.152759 TCACGAACAAATACATCCCGAAAC 59.847 41.667 0.00 0.00 0.00 2.78
4159 4309 4.461198 AGACCACTTTTCTCAAAATCGGT 58.539 39.130 3.17 3.17 37.45 4.69
4165 4315 7.093945 GCCCATAATTAGACCACTTTTCTCAAA 60.094 37.037 0.00 0.00 0.00 2.69
4267 4417 7.717568 AGATAATACATACTCGAACAAGCTGT 58.282 34.615 0.00 0.00 0.00 4.40
4268 4418 8.581057 AAGATAATACATACTCGAACAAGCTG 57.419 34.615 0.00 0.00 0.00 4.24
4433 4583 9.034544 TGATCTCAGTGTTTCATATGATAAACG 57.965 33.333 6.17 4.51 38.21 3.60
4441 4591 7.805163 TGGGTATTGATCTCAGTGTTTCATAT 58.195 34.615 0.00 0.00 0.00 1.78
4487 4637 2.656002 CGGATCTCTTGTCCTACTGGA 58.344 52.381 0.00 0.00 40.69 3.86
4544 4694 0.179158 GACCGGAGCTCGAGTTTCTC 60.179 60.000 9.46 11.80 42.43 2.87
4663 4819 5.389935 CGAAGAGCTTCAACACTTGGTTATC 60.390 44.000 10.51 0.00 37.72 1.75
4960 5116 1.315257 CGGATTGGTGGAGCCTTTGG 61.315 60.000 0.00 0.00 38.35 3.28
5009 5165 2.511600 GTTCCGAGCGATGGGTGG 60.512 66.667 0.45 0.00 0.00 4.61
5029 5191 2.203126 CGGCTTGATCTCCCTGGC 60.203 66.667 0.00 0.00 0.00 4.85
5122 5284 2.013563 GCAATTGTCATCGCCTCCAGA 61.014 52.381 7.40 0.00 0.00 3.86
5158 5320 3.496898 GTGAGTGCACAGATCGACA 57.503 52.632 21.04 4.48 44.51 4.35
5205 5367 4.200838 TCTGCTTAACCATTCGTCATCA 57.799 40.909 0.00 0.00 0.00 3.07
5206 5368 5.504665 CCATTCTGCTTAACCATTCGTCATC 60.505 44.000 0.00 0.00 0.00 2.92
5207 5369 4.336433 CCATTCTGCTTAACCATTCGTCAT 59.664 41.667 0.00 0.00 0.00 3.06
5242 5407 2.034066 ATGGCAACCAGGACACCG 59.966 61.111 0.00 0.00 36.75 4.94
5494 5660 0.729116 GTCTCGGTCATGCACAATGG 59.271 55.000 0.00 0.00 36.86 3.16
5545 5712 6.892658 TGAATGTGGTAGTATTGCAAAACT 57.107 33.333 1.71 0.00 0.00 2.66
5560 5727 5.594926 AGCTTGAAAAACTCTTGAATGTGG 58.405 37.500 0.00 0.00 0.00 4.17
5597 5764 2.760092 GGAGAACAGCAGACATCTCTCT 59.240 50.000 0.00 0.00 38.64 3.10
5598 5765 2.495270 TGGAGAACAGCAGACATCTCTC 59.505 50.000 0.00 0.00 38.64 3.20
5614 5781 2.906389 ACCTAGCACAAGTTCATGGAGA 59.094 45.455 0.00 0.00 0.00 3.71
5643 5810 4.441792 ACAAAATCAGAGTTTGGGTTTGC 58.558 39.130 23.55 0.00 39.74 3.68
5669 5836 5.301045 AGTTCTTTTTAGCTTGGGTGGTAAC 59.699 40.000 0.00 0.00 30.87 2.50
5681 5848 8.912658 GTTGTATTTTAGCCAGTTCTTTTTAGC 58.087 33.333 0.00 0.00 0.00 3.09
5684 5851 8.691797 TGAGTTGTATTTTAGCCAGTTCTTTTT 58.308 29.630 0.00 0.00 0.00 1.94
5689 5856 7.617041 AGATGAGTTGTATTTTAGCCAGTTC 57.383 36.000 0.00 0.00 0.00 3.01
5741 5911 6.818644 GTGACCAATCTAGTGAAATTCAGCTA 59.181 38.462 0.00 1.05 0.00 3.32
5749 5919 5.762179 ATCCAGTGACCAATCTAGTGAAA 57.238 39.130 0.00 0.00 0.00 2.69
5752 5923 9.046296 GTAAATAATCCAGTGACCAATCTAGTG 57.954 37.037 0.00 0.00 0.00 2.74
5855 6031 8.330302 GTGAAATTTCAACTTATTGGCATATGC 58.670 33.333 22.07 19.79 39.21 3.14
5923 6101 0.029300 CACTGCGCCAAAATATCGGG 59.971 55.000 4.18 0.00 0.00 5.14
5929 6107 0.749649 TGGTTTCACTGCGCCAAAAT 59.250 45.000 4.18 0.00 0.00 1.82
5937 6116 1.802508 GCACAACCTTGGTTTCACTGC 60.803 52.381 1.76 4.34 0.00 4.40
5939 6118 2.143876 AGCACAACCTTGGTTTCACT 57.856 45.000 1.76 0.00 0.00 3.41
5985 6164 5.279256 GGGCAAAAACTGGTTGAATAAGCTA 60.279 40.000 0.00 0.00 35.38 3.32
6023 6202 0.700564 AGTGGCATGAGTGGGTCAAT 59.299 50.000 0.00 0.00 39.19 2.57
6218 6403 6.899393 ACATTGAGAATCCTGCAAAACTTA 57.101 33.333 0.00 0.00 0.00 2.24
6226 6415 6.479660 TGAAACAAAAACATTGAGAATCCTGC 59.520 34.615 0.00 0.00 0.00 4.85
6232 6421 8.824159 TCAACTTGAAACAAAAACATTGAGAA 57.176 26.923 0.00 0.00 0.00 2.87
6233 6422 8.824159 TTCAACTTGAAACAAAAACATTGAGA 57.176 26.923 1.47 0.00 32.71 3.27
6245 6434 3.640967 CCCCTTCCATTCAACTTGAAACA 59.359 43.478 8.28 0.00 40.12 2.83
6267 6456 6.460781 CCTTCCATTTAACCAGTTTTAACCC 58.539 40.000 0.00 0.00 0.00 4.11
6303 6492 2.681848 CACCAATTCTGATCTGGCTCAC 59.318 50.000 5.66 0.00 33.19 3.51
6307 6496 0.743097 GCCACCAATTCTGATCTGGC 59.257 55.000 2.95 2.95 37.62 4.85
6326 6515 2.941415 GCAATAACCTGGACCTGGAGTG 60.941 54.545 23.36 12.34 0.00 3.51
6328 6517 1.408822 GGCAATAACCTGGACCTGGAG 60.409 57.143 23.36 8.76 0.00 3.86
6330 6519 0.748005 CGGCAATAACCTGGACCTGG 60.748 60.000 15.59 15.59 0.00 4.45
6332 6521 0.988832 TTCGGCAATAACCTGGACCT 59.011 50.000 0.00 0.00 0.00 3.85
6333 6522 1.743394 CTTTCGGCAATAACCTGGACC 59.257 52.381 0.00 0.00 0.00 4.46
6334 6523 1.743394 CCTTTCGGCAATAACCTGGAC 59.257 52.381 0.00 0.00 0.00 4.02
6364 6553 1.639298 GCGCACTTGACCACCTCATC 61.639 60.000 0.30 0.00 0.00 2.92
6400 6604 2.124695 GGATCCGGTTCTGGTGGC 60.125 66.667 12.19 0.00 0.00 5.01
6422 6629 3.622166 AGGTGGGTCGTTTAAGTATGG 57.378 47.619 0.00 0.00 0.00 2.74
6427 6634 2.681344 GGCATTAGGTGGGTCGTTTAAG 59.319 50.000 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.