Multiple sequence alignment - TraesCS5D01G239400

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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 TraesCS5D01G239400 chr5D 100.000 5228 0 0 1 5228 347438544 347433317 0.000000e+00 9655.0
1 TraesCS5D01G239400 chr5D 82.192 292 51 1 4483 4773 453858834 453858543 3.130000e-62 250.0
2 TraesCS5D01G239400 chr5A 96.682 2441 69 5 1699 4129 444540376 444542814 0.000000e+00 4048.0
3 TraesCS5D01G239400 chr5A 93.995 1682 69 19 1 1668 444538730 444540393 0.000000e+00 2518.0
4 TraesCS5D01G239400 chr5A 91.011 712 43 7 4158 4854 444542811 444543516 0.000000e+00 941.0
5 TraesCS5D01G239400 chr5A 91.254 343 26 2 4886 5228 444543519 444543857 1.030000e-126 464.0
6 TraesCS5D01G239400 chr5B 93.539 1656 69 10 3150 4783 403717918 403719557 0.000000e+00 2431.0
7 TraesCS5D01G239400 chr5B 95.464 1455 51 8 1699 3148 403716294 403717738 0.000000e+00 2307.0
8 TraesCS5D01G239400 chr5B 93.540 1130 46 11 555 1668 403715193 403716311 0.000000e+00 1657.0
9 TraesCS5D01G239400 chr5B 94.236 399 21 2 1 398 403714002 403714399 4.480000e-170 608.0
10 TraesCS5D01G239400 chr5B 87.336 229 24 3 4884 5110 403722032 403722257 1.870000e-64 257.0
11 TraesCS5D01G239400 chr6B 82.667 300 51 1 4479 4777 460511265 460511564 1.120000e-66 265.0
12 TraesCS5D01G239400 chr6D 80.456 307 58 1 4483 4787 296673587 296673281 3.150000e-57 233.0
13 TraesCS5D01G239400 chr6D 94.915 59 2 1 4125 4183 124534982 124535039 2.000000e-14 91.6
14 TraesCS5D01G239400 chrUn 94.915 59 2 1 4125 4183 189409946 189410003 2.000000e-14 91.6
15 TraesCS5D01G239400 chrUn 94.915 59 2 1 4125 4183 225927116 225927173 2.000000e-14 91.6
16 TraesCS5D01G239400 chrUn 93.548 62 3 1 4125 4186 251406650 251406590 2.000000e-14 91.6
17 TraesCS5D01G239400 chrUn 93.548 62 3 1 4125 4186 426137475 426137415 2.000000e-14 91.6
18 TraesCS5D01G239400 chrUn 93.548 62 3 1 4125 4186 453903843 453903783 2.000000e-14 91.6
19 TraesCS5D01G239400 chr4D 94.915 59 2 1 4125 4183 123715292 123715349 2.000000e-14 91.6
20 TraesCS5D01G239400 chr1D 93.548 62 3 1 4125 4186 141314272 141314212 2.000000e-14 91.6


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 TraesCS5D01G239400 chr5D 347433317 347438544 5227 True 9655.00 9655 100.0000 1 5228 1 chr5D.!!$R1 5227
1 TraesCS5D01G239400 chr5A 444538730 444543857 5127 False 1992.75 4048 93.2355 1 5228 4 chr5A.!!$F1 5227
2 TraesCS5D01G239400 chr5B 403714002 403722257 8255 False 1452.00 2431 92.8230 1 5110 5 chr5B.!!$F1 5109

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
334 338 0.242017 GATTGTCAGCAGGGCAACAC 59.758 55.000 0.0 0.0 39.74 3.32 F
1051 1729 1.489230 ACACACCCGTTCTTTTCTCCT 59.511 47.619 0.0 0.0 0.00 3.69 F
1813 2496 0.799534 GTGCATGTTCGCTGGCAATC 60.800 55.000 0.0 0.0 38.10 2.67 F
3056 3739 0.824109 TCCCTTGTGGCTCATACTCG 59.176 55.000 0.0 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1301 1980 1.129998 GCGATATGGATCATGTGCTGC 59.870 52.381 0.0 0.0 31.78 5.25 R
2378 3061 2.125552 TGAATGAGGTCCTGCGCG 60.126 61.111 0.0 0.0 0.00 6.86 R
3240 4101 0.106819 ATGGGCTGATTCTGAGCACC 60.107 55.000 0.0 0.0 39.28 5.01 R
4546 5429 0.037326 CGGCTCACCTTTGTGCTAGA 60.037 55.000 0.0 0.0 42.46 2.43 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
159 163 8.228464 CAGCATGCATATACAAAGATACTTCTG 58.772 37.037 21.98 0.00 30.72 3.02
160 164 7.020010 GCATGCATATACAAAGATACTTCTGC 58.980 38.462 14.21 0.00 30.72 4.26
265 269 1.595382 CATCCCATCGGCGAAGGAC 60.595 63.158 30.69 0.00 0.00 3.85
334 338 0.242017 GATTGTCAGCAGGGCAACAC 59.758 55.000 0.00 0.00 39.74 3.32
424 428 5.988287 TGCACATAGATTGATAGTTCACCA 58.012 37.500 0.00 0.00 0.00 4.17
430 434 5.824904 AGATTGATAGTTCACCAATGCAC 57.175 39.130 0.00 0.00 31.40 4.57
491 1126 6.531240 TCAAATTTCAACACAAGTTCTTCTGC 59.469 34.615 0.00 0.00 35.28 4.26
754 1417 1.989508 CTTGGGGTGGGAAATGGCC 60.990 63.158 0.00 0.00 0.00 5.36
1008 1686 8.445493 CCCTTTCGTTTATTTGTCGTATAACTT 58.555 33.333 0.00 0.00 0.00 2.66
1018 1696 3.327172 TGTCGTATAACTTGGGGTCCAAA 59.673 43.478 0.84 0.00 43.44 3.28
1032 1710 3.123050 GGTCCAAATTGCAAAGTGACAC 58.877 45.455 1.71 0.00 0.00 3.67
1035 1713 3.194329 TCCAAATTGCAAAGTGACACACA 59.806 39.130 1.71 0.00 36.74 3.72
1047 1725 2.011222 TGACACACACCCGTTCTTTTC 58.989 47.619 0.00 0.00 0.00 2.29
1048 1726 2.285977 GACACACACCCGTTCTTTTCT 58.714 47.619 0.00 0.00 0.00 2.52
1049 1727 2.285977 ACACACACCCGTTCTTTTCTC 58.714 47.619 0.00 0.00 0.00 2.87
1050 1728 1.602377 CACACACCCGTTCTTTTCTCC 59.398 52.381 0.00 0.00 0.00 3.71
1051 1729 1.489230 ACACACCCGTTCTTTTCTCCT 59.511 47.619 0.00 0.00 0.00 3.69
1052 1730 2.701951 ACACACCCGTTCTTTTCTCCTA 59.298 45.455 0.00 0.00 0.00 2.94
1053 1731 3.244112 ACACACCCGTTCTTTTCTCCTAG 60.244 47.826 0.00 0.00 0.00 3.02
1054 1732 2.302157 ACACCCGTTCTTTTCTCCTAGG 59.698 50.000 0.82 0.82 0.00 3.02
1055 1733 2.565834 CACCCGTTCTTTTCTCCTAGGA 59.434 50.000 11.98 11.98 0.00 2.94
1056 1734 2.832733 ACCCGTTCTTTTCTCCTAGGAG 59.167 50.000 30.15 30.15 43.21 3.69
1057 1735 2.418884 CCCGTTCTTTTCTCCTAGGAGC 60.419 54.545 30.99 15.59 41.71 4.70
1058 1736 2.233922 CCGTTCTTTTCTCCTAGGAGCA 59.766 50.000 30.99 20.33 41.71 4.26
1059 1737 3.306780 CCGTTCTTTTCTCCTAGGAGCAA 60.307 47.826 30.99 24.88 41.71 3.91
1062 1740 4.810191 TCTTTTCTCCTAGGAGCAAGAC 57.190 45.455 31.00 0.00 41.71 3.01
1286 1965 4.082523 CACACGCCCCTCCGTCAT 62.083 66.667 0.00 0.00 39.83 3.06
1459 2138 4.965119 AAATTTGGCTGACGTTAGGATC 57.035 40.909 9.62 0.00 0.00 3.36
1502 2181 6.541641 ACCTTCAGAGCTTGATGATAATTGTC 59.458 38.462 11.01 0.00 35.27 3.18
1630 2309 2.018542 TGTTAGACTTGTATGCGGCC 57.981 50.000 0.00 0.00 0.00 6.13
1652 2331 3.820467 CAGTGGAGAACATGGTGCTTAAA 59.180 43.478 0.00 0.00 0.00 1.52
1653 2332 4.074970 AGTGGAGAACATGGTGCTTAAAG 58.925 43.478 0.00 0.00 0.00 1.85
1654 2333 4.072131 GTGGAGAACATGGTGCTTAAAGA 58.928 43.478 0.00 0.00 0.00 2.52
1655 2334 4.518970 GTGGAGAACATGGTGCTTAAAGAA 59.481 41.667 0.00 0.00 0.00 2.52
1656 2335 5.183904 GTGGAGAACATGGTGCTTAAAGAAT 59.816 40.000 0.00 0.00 0.00 2.40
1657 2336 5.415701 TGGAGAACATGGTGCTTAAAGAATC 59.584 40.000 0.00 0.00 0.00 2.52
1658 2337 5.415701 GGAGAACATGGTGCTTAAAGAATCA 59.584 40.000 0.00 0.00 0.00 2.57
1659 2338 6.096001 GGAGAACATGGTGCTTAAAGAATCAT 59.904 38.462 0.00 0.00 0.00 2.45
1660 2339 7.283127 GGAGAACATGGTGCTTAAAGAATCATA 59.717 37.037 0.00 0.00 0.00 2.15
1661 2340 8.757982 AGAACATGGTGCTTAAAGAATCATAT 57.242 30.769 0.00 0.00 0.00 1.78
1662 2341 8.844244 AGAACATGGTGCTTAAAGAATCATATC 58.156 33.333 0.00 0.00 0.00 1.63
1663 2342 8.523915 AACATGGTGCTTAAAGAATCATATCA 57.476 30.769 0.00 0.00 0.00 2.15
1664 2343 8.701908 ACATGGTGCTTAAAGAATCATATCAT 57.298 30.769 0.00 0.00 0.00 2.45
1665 2344 8.790718 ACATGGTGCTTAAAGAATCATATCATC 58.209 33.333 0.00 0.00 0.00 2.92
1666 2345 8.789762 CATGGTGCTTAAAGAATCATATCATCA 58.210 33.333 0.00 0.00 0.00 3.07
1667 2346 8.929260 TGGTGCTTAAAGAATCATATCATCAT 57.071 30.769 0.00 0.00 0.00 2.45
1668 2347 9.358406 TGGTGCTTAAAGAATCATATCATCATT 57.642 29.630 0.00 0.00 0.00 2.57
1669 2348 9.837525 GGTGCTTAAAGAATCATATCATCATTC 57.162 33.333 0.00 0.00 0.00 2.67
1740 2419 8.429237 TGAATCCCATTTTGTAACCTAATGTT 57.571 30.769 0.00 0.00 41.11 2.71
1813 2496 0.799534 GTGCATGTTCGCTGGCAATC 60.800 55.000 0.00 0.00 38.10 2.67
1902 2585 3.056607 TCTTGCTGATCTGATCGACACAA 60.057 43.478 12.65 11.90 0.00 3.33
1973 2656 3.222173 TGACTATTGGTTTGGCAGTGT 57.778 42.857 0.00 0.00 0.00 3.55
2051 2734 4.342951 ACATTCAGCCCAAATACCATCATG 59.657 41.667 0.00 0.00 0.00 3.07
2054 2737 4.146564 TCAGCCCAAATACCATCATGATG 58.853 43.478 25.97 25.97 38.51 3.07
2069 2752 6.183360 CCATCATGATGAAACTAATGTGTGCT 60.183 38.462 32.71 0.00 41.20 4.40
2119 2802 4.322650 GCATTAACCTTTCTCAATTGGGCA 60.323 41.667 5.42 0.00 0.00 5.36
2294 2977 5.710513 ATATTATGCACACGCCATGAATT 57.289 34.783 0.00 0.00 37.32 2.17
2378 3061 3.950395 AGAATATTGTTGGAGCAGAAGCC 59.050 43.478 0.00 0.00 43.56 4.35
2519 3202 4.190772 CAACTGCCCAAACAAAGAAACAT 58.809 39.130 0.00 0.00 0.00 2.71
2593 3276 1.153208 CAGATGCTGCTGAGACCCC 60.153 63.158 0.00 0.00 38.14 4.95
2942 3625 7.679638 GCGGCAAGAACTAAAGTTTATGATGAT 60.680 37.037 11.00 0.00 38.56 2.45
3056 3739 0.824109 TCCCTTGTGGCTCATACTCG 59.176 55.000 0.00 0.00 0.00 4.18
3465 4335 5.655488 TCTCTATTTTTCTCGCTTCAGGAG 58.345 41.667 0.00 0.00 0.00 3.69
3682 4553 6.211184 TGCAGGTAATTTTGAACAAGGATGAT 59.789 34.615 0.00 0.00 0.00 2.45
3732 4603 5.304101 GGATCATGAGACCACTAGAACAGAT 59.696 44.000 14.40 0.00 0.00 2.90
4015 4886 3.446516 GCTCCCTTGATTTTGATTGAGCT 59.553 43.478 0.00 0.00 40.51 4.09
4130 5001 4.336713 CAGCTAGAGGTATTTTGGAAAGGC 59.663 45.833 0.00 0.00 0.00 4.35
4145 5016 0.393537 AAGGCTTGCTTCGGGATCAG 60.394 55.000 0.00 0.00 0.00 2.90
4173 5044 1.053424 ACTAAAGTTGTCAGGCCGGA 58.947 50.000 5.05 0.00 0.00 5.14
4214 5085 8.653191 TCTTGAACCTATAAAGTACAAGGTCAA 58.347 33.333 0.00 6.06 41.51 3.18
4215 5086 8.842358 TTGAACCTATAAAGTACAAGGTCAAG 57.158 34.615 0.00 0.00 41.51 3.02
4226 5097 0.036022 AAGGTCAAGAGCACTGAGGC 59.964 55.000 1.84 0.00 0.00 4.70
4227 5098 1.123861 AGGTCAAGAGCACTGAGGCA 61.124 55.000 1.84 0.00 35.83 4.75
4299 5170 2.176045 TCTGGCCGAAGTATGTTCTGA 58.824 47.619 0.00 0.00 0.00 3.27
4362 5233 6.540551 ACTTTAAAACGGCATTTGGAAAACAT 59.459 30.769 0.00 0.00 0.00 2.71
4399 5270 8.099364 TGTCTTTCTTGAATTTCACTGGATAC 57.901 34.615 0.00 0.00 0.00 2.24
4449 5320 3.831911 CCCTTTATTTTGAGAACTGCCCA 59.168 43.478 0.00 0.00 0.00 5.36
4451 5322 5.394553 CCCTTTATTTTGAGAACTGCCCATC 60.395 44.000 0.00 0.00 0.00 3.51
4517 5400 6.732896 ACTCAGGGATTACATCGAAAGTAT 57.267 37.500 0.00 0.00 0.00 2.12
4545 5428 9.667107 CTGATTAACATGTAAGGAAAAGGAGTA 57.333 33.333 0.00 0.00 0.00 2.59
4616 5503 5.069119 ACAAGTTTGAATCCCTGAAAACTCC 59.931 40.000 0.00 0.00 40.91 3.85
4628 5515 5.280215 CCCTGAAAACTCCAGACATAAGACT 60.280 44.000 0.00 0.00 33.65 3.24
4712 5599 6.204359 CAAAGGTTTTGACAATCAGACTCAG 58.796 40.000 0.00 0.00 0.00 3.35
4765 5652 3.438297 AGTCACATAGCATCACGGTAC 57.562 47.619 0.00 0.00 0.00 3.34
4786 8082 6.759827 GGTACGCCAATAACTCTGAGATAAAA 59.240 38.462 12.44 0.00 34.09 1.52
4827 8123 0.756294 TGGTTGTGTCTGTCACCGAT 59.244 50.000 2.72 0.00 45.61 4.18
4828 8124 1.148310 GGTTGTGTCTGTCACCGATG 58.852 55.000 2.72 0.00 45.61 3.84
4829 8125 1.540363 GGTTGTGTCTGTCACCGATGT 60.540 52.381 2.72 0.00 45.61 3.06
4836 8132 4.451096 GTGTCTGTCACCGATGTGTATTTT 59.549 41.667 0.00 0.00 43.26 1.82
4856 8152 9.556030 GTATTTTGAAGGTTCTAAAAAGATCCG 57.444 33.333 3.93 0.00 36.00 4.18
4857 8153 6.569179 TTTGAAGGTTCTAAAAAGATCCGG 57.431 37.500 0.00 0.00 33.94 5.14
4858 8154 5.237236 TGAAGGTTCTAAAAAGATCCGGT 57.763 39.130 0.00 0.00 33.94 5.28
4859 8155 5.627135 TGAAGGTTCTAAAAAGATCCGGTT 58.373 37.500 0.00 0.00 33.94 4.44
4860 8156 6.066032 TGAAGGTTCTAAAAAGATCCGGTTT 58.934 36.000 0.00 0.00 33.94 3.27
4861 8157 7.225725 TGAAGGTTCTAAAAAGATCCGGTTTA 58.774 34.615 0.00 0.00 33.94 2.01
4862 8158 7.886446 TGAAGGTTCTAAAAAGATCCGGTTTAT 59.114 33.333 0.00 0.00 33.94 1.40
4863 8159 7.625828 AGGTTCTAAAAAGATCCGGTTTATG 57.374 36.000 0.00 0.00 33.94 1.90
4864 8160 7.399634 AGGTTCTAAAAAGATCCGGTTTATGA 58.600 34.615 0.00 0.00 33.94 2.15
4865 8161 8.053355 AGGTTCTAAAAAGATCCGGTTTATGAT 58.947 33.333 0.00 0.00 33.94 2.45
4866 8162 8.129211 GGTTCTAAAAAGATCCGGTTTATGATG 58.871 37.037 0.00 0.00 0.00 3.07
4867 8163 7.801716 TCTAAAAAGATCCGGTTTATGATGG 57.198 36.000 0.00 0.00 0.00 3.51
4868 8164 5.852282 AAAAAGATCCGGTTTATGATGGG 57.148 39.130 0.00 0.00 0.00 4.00
4869 8165 4.519906 AAAGATCCGGTTTATGATGGGT 57.480 40.909 0.00 0.00 0.00 4.51
4870 8166 5.640158 AAAGATCCGGTTTATGATGGGTA 57.360 39.130 0.00 0.00 0.00 3.69
4871 8167 5.640158 AAGATCCGGTTTATGATGGGTAA 57.360 39.130 0.00 0.00 0.00 2.85
4872 8168 5.228945 AGATCCGGTTTATGATGGGTAAG 57.771 43.478 0.00 0.00 0.00 2.34
4873 8169 4.905456 AGATCCGGTTTATGATGGGTAAGA 59.095 41.667 0.00 0.00 0.00 2.10
4874 8170 4.682778 TCCGGTTTATGATGGGTAAGAG 57.317 45.455 0.00 0.00 0.00 2.85
4875 8171 4.035112 TCCGGTTTATGATGGGTAAGAGT 58.965 43.478 0.00 0.00 0.00 3.24
4876 8172 4.127171 CCGGTTTATGATGGGTAAGAGTG 58.873 47.826 0.00 0.00 0.00 3.51
4877 8173 4.141801 CCGGTTTATGATGGGTAAGAGTGA 60.142 45.833 0.00 0.00 0.00 3.41
4878 8174 4.809426 CGGTTTATGATGGGTAAGAGTGAC 59.191 45.833 0.00 0.00 0.00 3.67
4879 8175 4.809426 GGTTTATGATGGGTAAGAGTGACG 59.191 45.833 0.00 0.00 0.00 4.35
4880 8176 4.665833 TTATGATGGGTAAGAGTGACGG 57.334 45.455 0.00 0.00 0.00 4.79
4881 8177 1.191535 TGATGGGTAAGAGTGACGGG 58.808 55.000 0.00 0.00 0.00 5.28
4882 8178 0.179081 GATGGGTAAGAGTGACGGGC 60.179 60.000 0.00 0.00 0.00 6.13
4895 8191 3.333189 CGGGCGTGCGATCATGAG 61.333 66.667 0.09 0.00 0.00 2.90
4906 8202 1.134580 CGATCATGAGGCAGAACTGGT 60.135 52.381 0.09 0.00 0.00 4.00
4907 8203 2.286872 GATCATGAGGCAGAACTGGTG 58.713 52.381 0.09 0.00 0.00 4.17
4924 8220 2.093394 TGGTGAAAAGTTGTCGAGGACA 60.093 45.455 0.00 0.00 41.09 4.02
4940 8238 4.583871 GAGGACACCATGATGAAAGAAGT 58.416 43.478 0.00 0.00 0.00 3.01
4946 8244 7.294017 ACACCATGATGAAAGAAGTTGAAAT 57.706 32.000 0.00 0.00 0.00 2.17
4948 8246 6.588756 CACCATGATGAAAGAAGTTGAAATGG 59.411 38.462 0.00 0.00 37.46 3.16
4963 8261 2.363306 AATGGCTGTGTTCAGGTTCA 57.637 45.000 0.00 0.00 41.57 3.18
4964 8262 2.363306 ATGGCTGTGTTCAGGTTCAA 57.637 45.000 0.00 0.00 41.57 2.69
4966 8264 3.500448 TGGCTGTGTTCAGGTTCAATA 57.500 42.857 0.00 0.00 41.57 1.90
4993 8291 3.507162 ACATGACCAGTGGTTTGATGA 57.493 42.857 25.44 7.06 35.25 2.92
5048 8346 9.045745 TGAATGGCAGATTAGGATATGTATGTA 57.954 33.333 0.00 0.00 0.00 2.29
5049 8347 9.539825 GAATGGCAGATTAGGATATGTATGTAG 57.460 37.037 0.00 0.00 0.00 2.74
5050 8348 8.615360 ATGGCAGATTAGGATATGTATGTAGT 57.385 34.615 0.00 0.00 0.00 2.73
5074 8372 9.388506 AGTAGTATACAGTACGAACTTATGTGT 57.611 33.333 5.50 0.00 46.26 3.72
5094 8393 5.122554 TGTGTTTAATGGTAGGTGTTATGCG 59.877 40.000 0.00 0.00 0.00 4.73
5133 8432 6.238648 AGTATCAACTTTTGGGTCTAACTGG 58.761 40.000 0.00 0.00 29.00 4.00
5154 8453 6.119240 TGGATATGAAGATCATCCACCTTC 57.881 41.667 7.46 0.00 42.55 3.46
5216 8515 4.404715 GTGGCTTCTAGTGTAACCATCCTA 59.595 45.833 0.00 0.00 37.80 2.94
5221 8520 6.546772 GCTTCTAGTGTAACCATCCTACTACT 59.453 42.308 0.00 0.00 37.80 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 3.057876 TGCAGTTTTAGGCATGGTTAACG 60.058 43.478 0.00 0.00 34.58 3.18
221 225 0.668535 GGGAGTGGCAAACTGTTGTC 59.331 55.000 0.00 0.00 40.07 3.18
265 269 2.125673 ATTCGAACGAGTGGCCCG 60.126 61.111 0.00 0.00 0.00 6.13
334 338 6.176183 ACTGTGAATATTCCTGTCTTTCTGG 58.824 40.000 12.90 0.00 36.63 3.86
417 421 2.258286 GCCGGTGCATTGGTGAAC 59.742 61.111 1.90 0.00 37.47 3.18
424 428 0.396060 AAAAATGTGGCCGGTGCATT 59.604 45.000 1.90 8.80 40.13 3.56
430 434 4.362279 CATCAATAGAAAAATGTGGCCGG 58.638 43.478 0.00 0.00 0.00 6.13
491 1126 7.080724 GTGCAGAATTTAGGTTCTTGAAAGAG 58.919 38.462 0.00 0.00 36.33 2.85
603 1266 1.277579 TATCCTACAACAACCCGCCA 58.722 50.000 0.00 0.00 0.00 5.69
758 1421 1.515020 CTCCTCCTCTCCAAGCACG 59.485 63.158 0.00 0.00 0.00 5.34
864 1527 1.375853 GCGAGCAGAGAGAGCAGAGA 61.376 60.000 0.00 0.00 0.00 3.10
1008 1686 1.415659 CACTTTGCAATTTGGACCCCA 59.584 47.619 0.00 0.00 0.00 4.96
1018 1696 1.408702 GGGTGTGTGTCACTTTGCAAT 59.591 47.619 0.00 0.00 45.50 3.56
1032 1710 2.256117 AGGAGAAAAGAACGGGTGTG 57.744 50.000 0.00 0.00 0.00 3.82
1035 1713 2.832733 CTCCTAGGAGAAAAGAACGGGT 59.167 50.000 31.97 0.00 44.53 5.28
1047 1725 1.040339 AGGCGTCTTGCTCCTAGGAG 61.040 60.000 31.35 31.35 45.43 3.69
1048 1726 1.000486 AGGCGTCTTGCTCCTAGGA 60.000 57.895 11.98 11.98 45.43 2.94
1049 1727 1.439644 GAGGCGTCTTGCTCCTAGG 59.560 63.158 0.82 0.82 45.43 3.02
1050 1728 1.439644 GGAGGCGTCTTGCTCCTAG 59.560 63.158 6.34 0.00 45.43 3.02
1051 1729 2.415608 CGGAGGCGTCTTGCTCCTA 61.416 63.158 6.34 0.00 45.43 2.94
1052 1730 3.764466 CGGAGGCGTCTTGCTCCT 61.764 66.667 6.34 0.00 45.43 3.69
1286 1965 3.345737 CTGCAAGCTATCGTTCCGA 57.654 52.632 0.00 0.00 41.13 4.55
1301 1980 1.129998 GCGATATGGATCATGTGCTGC 59.870 52.381 0.00 0.00 31.78 5.25
1330 2009 1.131883 CAAGCTCAAATCAGAAGGCCG 59.868 52.381 0.00 0.00 0.00 6.13
1459 2138 1.459592 GGTTGATCTGACGTGAAACCG 59.540 52.381 0.00 0.00 0.00 4.44
1502 2181 6.680874 ACCAGACTATCGAAACTACTAGTG 57.319 41.667 5.39 0.00 0.00 2.74
1630 2309 1.901591 AAGCACCATGTTCTCCACTG 58.098 50.000 0.00 0.00 0.00 3.66
1697 2376 9.596308 TGGGATTCATGATGATATGATTCTTTT 57.404 29.630 0.00 0.00 37.49 2.27
1698 2377 9.769677 ATGGGATTCATGATGATATGATTCTTT 57.230 29.630 0.00 0.00 37.49 2.52
1699 2378 9.769677 AATGGGATTCATGATGATATGATTCTT 57.230 29.630 0.00 0.00 37.49 2.52
1740 2419 6.882610 AGATGCTCAAAACATACTGACAAA 57.117 33.333 0.00 0.00 0.00 2.83
1902 2585 8.352137 TCATTTTCATCACAATCCACAATACT 57.648 30.769 0.00 0.00 0.00 2.12
1912 2595 8.842358 AGAAAGCAAATCATTTTCATCACAAT 57.158 26.923 0.00 0.00 34.18 2.71
1913 2596 8.552865 CAAGAAAGCAAATCATTTTCATCACAA 58.447 29.630 0.00 0.00 34.18 3.33
1915 2598 8.007716 CACAAGAAAGCAAATCATTTTCATCAC 58.992 33.333 0.00 0.00 34.18 3.06
1973 2656 4.119862 GCTCCGCAAAAGATATGTAGACA 58.880 43.478 0.00 0.00 0.00 3.41
2029 2712 4.585581 TCATGATGGTATTTGGGCTGAATG 59.414 41.667 0.00 0.00 0.00 2.67
2051 2734 6.073058 TGTCAAGAGCACACATTAGTTTCATC 60.073 38.462 0.00 0.00 0.00 2.92
2054 2737 5.673337 TGTCAAGAGCACACATTAGTTTC 57.327 39.130 0.00 0.00 0.00 2.78
2093 2776 6.229733 CCCAATTGAGAAAGGTTAATGCAAA 58.770 36.000 7.12 0.00 0.00 3.68
2119 2802 4.546829 ATTTGAGAAAGCCATGCACAAT 57.453 36.364 0.00 0.00 0.00 2.71
2270 2953 5.861222 TTCATGGCGTGTGCATAATATAG 57.139 39.130 6.60 0.00 45.35 1.31
2294 2977 6.324512 TCACCTAAGTAACAGTAGTTTCCACA 59.675 38.462 0.00 0.00 39.15 4.17
2335 3018 8.743085 ATTCTGCAGAATTGTACACATAGAAT 57.257 30.769 31.78 8.96 41.64 2.40
2346 3029 6.626623 GCTCCAACAATATTCTGCAGAATTGT 60.627 38.462 39.03 33.96 41.64 2.71
2378 3061 2.125552 TGAATGAGGTCCTGCGCG 60.126 61.111 0.00 0.00 0.00 6.86
2519 3202 4.449743 GCTGGATCTTTTTGTGTACGTGTA 59.550 41.667 0.00 0.00 0.00 2.90
2593 3276 4.937193 CTCTCTTGGAGGCAGCAG 57.063 61.111 0.00 0.00 38.35 4.24
2942 3625 8.359642 CCTTCCATTTCAAAATAGTCACTTTGA 58.640 33.333 0.00 0.00 39.24 2.69
3056 3739 9.877178 AAAGAATCGGAATGAGTGGATATATAC 57.123 33.333 0.00 0.00 0.00 1.47
3130 3813 8.625786 TCGGTTAATAGCTAAAAGTTTTTCCT 57.374 30.769 6.10 6.00 0.00 3.36
3131 3814 9.681692 TTTCGGTTAATAGCTAAAAGTTTTTCC 57.318 29.630 6.10 0.00 0.00 3.13
3136 3819 9.135843 GCAAATTTCGGTTAATAGCTAAAAGTT 57.864 29.630 0.00 0.00 0.00 2.66
3138 3821 8.682128 TGCAAATTTCGGTTAATAGCTAAAAG 57.318 30.769 0.00 0.00 0.00 2.27
3240 4101 0.106819 ATGGGCTGATTCTGAGCACC 60.107 55.000 0.00 0.00 39.28 5.01
3394 4264 5.643379 TCATCCAATTAGAACAACTTGCC 57.357 39.130 0.00 0.00 0.00 4.52
3630 4501 6.831769 AGATACTTGCAAAATTATATCGGCG 58.168 36.000 0.00 0.00 0.00 6.46
3732 4603 1.737236 GTATGCGTTGAACCTGATGCA 59.263 47.619 0.00 0.00 41.53 3.96
4015 4886 3.170505 CGCATCAAAATTCGCAGCTAAA 58.829 40.909 0.00 0.00 0.00 1.85
4130 5001 2.609427 TGATCTGATCCCGAAGCAAG 57.391 50.000 14.71 0.00 0.00 4.01
4173 5044 1.992557 TCAAGACCCCACAAAGCCTAT 59.007 47.619 0.00 0.00 0.00 2.57
4200 5071 4.130118 CAGTGCTCTTGACCTTGTACTTT 58.870 43.478 0.00 0.00 0.00 2.66
4206 5077 1.805869 CCTCAGTGCTCTTGACCTTG 58.194 55.000 0.00 0.00 0.00 3.61
4286 5157 5.578727 AGTTCGCTGATTCAGAACATACTTC 59.421 40.000 17.87 0.00 44.67 3.01
4299 5170 2.232452 AGCACTACAGAGTTCGCTGATT 59.768 45.455 10.22 0.00 34.52 2.57
4362 5233 3.678056 AGAAAGACATGGCGTAGTTGA 57.322 42.857 0.00 0.00 0.00 3.18
4426 5297 3.368427 GGGCAGTTCTCAAAATAAAGGGC 60.368 47.826 0.00 0.00 0.00 5.19
4449 5320 5.450965 CGCTTGAAGGAATAAAATGCCTGAT 60.451 40.000 0.00 0.00 31.06 2.90
4451 5322 4.107622 CGCTTGAAGGAATAAAATGCCTG 58.892 43.478 0.00 0.00 31.06 4.85
4465 5336 3.396560 TGAGCATATGATCCGCTTGAAG 58.603 45.455 17.90 0.00 35.75 3.02
4517 5400 9.667107 CTCCTTTTCCTTACATGTTAATCAGTA 57.333 33.333 2.30 0.00 0.00 2.74
4545 5428 1.406069 CGGCTCACCTTTGTGCTAGAT 60.406 52.381 0.00 0.00 42.46 1.98
4546 5429 0.037326 CGGCTCACCTTTGTGCTAGA 60.037 55.000 0.00 0.00 42.46 2.43
4547 5430 1.639298 GCGGCTCACCTTTGTGCTAG 61.639 60.000 0.00 0.00 42.46 3.42
4578 5463 9.099454 GATTCAAACTTGTCTACACTTATAGGG 57.901 37.037 0.00 0.00 0.00 3.53
4616 5503 7.800155 TCAGAGAGATGTAGTCTTATGTCTG 57.200 40.000 0.00 0.00 37.29 3.51
4628 5515 5.227569 TGGCAAGTTTTCAGAGAGATGTA 57.772 39.130 0.00 0.00 0.00 2.29
4730 5617 8.046708 TGCTATGTGACTAACTATGGACAAATT 58.953 33.333 0.00 0.00 0.00 1.82
4765 5652 6.538742 TCCTTTTTATCTCAGAGTTATTGGCG 59.461 38.462 0.00 0.00 0.00 5.69
4786 8082 7.224297 ACCATGCGTTTATACAGATAATCCTT 58.776 34.615 0.00 0.00 0.00 3.36
4836 8132 5.237236 ACCGGATCTTTTTAGAACCTTCA 57.763 39.130 9.46 0.00 0.00 3.02
4854 8150 4.127171 CACTCTTACCCATCATAAACCGG 58.873 47.826 0.00 0.00 0.00 5.28
4855 8151 4.809426 GTCACTCTTACCCATCATAAACCG 59.191 45.833 0.00 0.00 0.00 4.44
4856 8152 4.809426 CGTCACTCTTACCCATCATAAACC 59.191 45.833 0.00 0.00 0.00 3.27
4857 8153 4.809426 CCGTCACTCTTACCCATCATAAAC 59.191 45.833 0.00 0.00 0.00 2.01
4858 8154 4.141801 CCCGTCACTCTTACCCATCATAAA 60.142 45.833 0.00 0.00 0.00 1.40
4859 8155 3.386726 CCCGTCACTCTTACCCATCATAA 59.613 47.826 0.00 0.00 0.00 1.90
4860 8156 2.963101 CCCGTCACTCTTACCCATCATA 59.037 50.000 0.00 0.00 0.00 2.15
4861 8157 1.762957 CCCGTCACTCTTACCCATCAT 59.237 52.381 0.00 0.00 0.00 2.45
4862 8158 1.191535 CCCGTCACTCTTACCCATCA 58.808 55.000 0.00 0.00 0.00 3.07
4863 8159 0.179081 GCCCGTCACTCTTACCCATC 60.179 60.000 0.00 0.00 0.00 3.51
4864 8160 1.905512 GCCCGTCACTCTTACCCAT 59.094 57.895 0.00 0.00 0.00 4.00
4865 8161 2.642254 CGCCCGTCACTCTTACCCA 61.642 63.158 0.00 0.00 0.00 4.51
4866 8162 2.183555 CGCCCGTCACTCTTACCC 59.816 66.667 0.00 0.00 0.00 3.69
4867 8163 1.445582 CACGCCCGTCACTCTTACC 60.446 63.158 0.00 0.00 0.00 2.85
4868 8164 2.092882 GCACGCCCGTCACTCTTAC 61.093 63.158 0.00 0.00 0.00 2.34
4869 8165 2.260434 GCACGCCCGTCACTCTTA 59.740 61.111 0.00 0.00 0.00 2.10
4872 8168 4.796231 ATCGCACGCCCGTCACTC 62.796 66.667 0.00 0.00 0.00 3.51
4873 8169 4.796231 GATCGCACGCCCGTCACT 62.796 66.667 0.00 0.00 0.00 3.41
4875 8171 4.141965 ATGATCGCACGCCCGTCA 62.142 61.111 0.00 0.00 0.00 4.35
4876 8172 3.630148 CATGATCGCACGCCCGTC 61.630 66.667 0.00 0.00 0.00 4.79
4877 8173 4.141965 TCATGATCGCACGCCCGT 62.142 61.111 0.00 0.00 0.00 5.28
4878 8174 3.333189 CTCATGATCGCACGCCCG 61.333 66.667 0.00 0.00 0.00 6.13
4879 8175 2.969238 CCTCATGATCGCACGCCC 60.969 66.667 0.00 0.00 0.00 6.13
4880 8176 3.643978 GCCTCATGATCGCACGCC 61.644 66.667 9.45 0.00 0.00 5.68
4881 8177 2.879070 CTGCCTCATGATCGCACGC 61.879 63.158 12.32 1.89 0.00 5.34
4882 8178 0.807275 TTCTGCCTCATGATCGCACG 60.807 55.000 12.32 9.52 0.00 5.34
4895 8191 2.427095 ACAACTTTTCACCAGTTCTGCC 59.573 45.455 0.00 0.00 31.83 4.85
4906 8202 2.557317 GGTGTCCTCGACAACTTTTCA 58.443 47.619 2.56 0.00 45.70 2.69
4924 8220 6.694447 CCATTTCAACTTCTTTCATCATGGT 58.306 36.000 0.00 0.00 0.00 3.55
4940 8238 2.665165 ACCTGAACACAGCCATTTCAA 58.335 42.857 0.00 0.00 0.00 2.69
4946 8244 2.363306 ATTGAACCTGAACACAGCCA 57.637 45.000 0.00 0.00 0.00 4.75
4948 8246 3.821033 ACCTTATTGAACCTGAACACAGC 59.179 43.478 0.00 0.00 0.00 4.40
4987 8285 3.133183 CACATGGGCCAATGAATCATCAA 59.867 43.478 27.65 0.00 39.49 2.57
4993 8291 4.101430 GGTTTATCACATGGGCCAATGAAT 59.899 41.667 27.65 19.83 0.00 2.57
5048 8346 9.388506 ACACATAAGTTCGTACTGTATACTACT 57.611 33.333 4.17 0.00 34.01 2.57
5049 8347 9.994432 AACACATAAGTTCGTACTGTATACTAC 57.006 33.333 4.17 0.00 34.01 2.73
5056 8354 7.658575 ACCATTAAACACATAAGTTCGTACTGT 59.341 33.333 0.00 0.00 34.01 3.55
5062 8360 7.118680 ACACCTACCATTAAACACATAAGTTCG 59.881 37.037 0.00 0.00 0.00 3.95
5074 8372 4.846040 ACCGCATAACACCTACCATTAAA 58.154 39.130 0.00 0.00 0.00 1.52
5079 8377 3.451540 TCATTACCGCATAACACCTACCA 59.548 43.478 0.00 0.00 0.00 3.25
5094 8393 8.788325 AAGTTGATACTACCAAGTTCATTACC 57.212 34.615 0.00 0.00 37.15 2.85
5133 8432 9.956640 AAATAGAAGGTGGATGATCTTCATATC 57.043 33.333 10.48 0.00 43.51 1.63
5154 8453 5.415701 ACATGCCAAGTAGGTCACAAAATAG 59.584 40.000 0.00 0.00 40.61 1.73
5198 8497 7.870027 AGAGTAGTAGGATGGTTACACTAGAA 58.130 38.462 0.00 0.00 0.00 2.10
5200 8499 6.711645 GGAGAGTAGTAGGATGGTTACACTAG 59.288 46.154 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.