Multiple sequence alignment - TraesCS6D01G153600

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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 TraesCS6D01G153600 chr6D 100.000 6911 0 0 1 6911 127388986 127382076 0.000000e+00 12763.0
1 TraesCS6D01G153600 chr6A 96.537 6757 132 24 1 6733 150964068 150970746 0.000000e+00 11088.0
2 TraesCS6D01G153600 chr6A 93.421 152 10 0 6760 6911 150979444 150979595 6.970000e-55 226.0
3 TraesCS6D01G153600 chr6B 93.239 4304 192 43 477 4756 226405432 226401204 0.000000e+00 6244.0
4 TraesCS6D01G153600 chr6B 94.557 1139 42 10 4840 5976 226401209 226400089 0.000000e+00 1742.0
5 TraesCS6D01G153600 chr6B 81.761 477 33 17 7 439 226406226 226405760 3.970000e-92 350.0
6 TraesCS6D01G153600 chr6B 80.255 471 36 29 5990 6436 226400109 226399672 1.130000e-77 302.0
7 TraesCS6D01G153600 chr6B 90.411 73 5 1 2205 2277 75961421 75961351 2.050000e-15 95.3
8 TraesCS6D01G153600 chr6B 100.000 30 0 0 6882 6911 226399234 226399205 1.000000e-03 56.5
9 TraesCS6D01G153600 chr7B 86.232 138 17 2 2926 3061 4821782 4821919 1.550000e-31 148.0
10 TraesCS6D01G153600 chr7B 86.232 138 17 2 2926 3061 727193706 727193569 1.550000e-31 148.0
11 TraesCS6D01G153600 chr4B 86.232 138 17 2 2926 3061 646212953 646212816 1.550000e-31 148.0
12 TraesCS6D01G153600 chr3B 86.232 138 17 2 2926 3061 821822605 821822742 1.550000e-31 148.0
13 TraesCS6D01G153600 chr1B 86.232 138 17 2 2926 3061 626110242 626110105 1.550000e-31 148.0
14 TraesCS6D01G153600 chr5B 85.507 138 18 2 2926 3061 101329567 101329704 7.230000e-30 143.0
15 TraesCS6D01G153600 chr3A 85.507 138 18 2 2926 3061 514460079 514459942 7.230000e-30 143.0
16 TraesCS6D01G153600 chr3D 88.421 95 11 0 1887 1981 363802842 363802936 1.580000e-21 115.0
17 TraesCS6D01G153600 chr3D 81.481 135 16 7 1887 2017 363802420 363802549 1.230000e-17 102.0
18 TraesCS6D01G153600 chrUn 87.368 95 12 0 1887 1981 112535966 112535872 7.330000e-20 110.0
19 TraesCS6D01G153600 chr5A 95.122 41 2 0 1887 1927 311327010 311326970 1.610000e-06 65.8
20 TraesCS6D01G153600 chr5A 95.122 41 2 0 1887 1927 311327866 311327826 1.610000e-06 65.8
21 TraesCS6D01G153600 chr5A 95.122 41 2 0 1887 1927 311328721 311328681 1.610000e-06 65.8
22 TraesCS6D01G153600 chr5A 95.122 41 2 0 1887 1927 311329578 311329538 1.610000e-06 65.8
23 TraesCS6D01G153600 chr7D 100.000 28 0 0 6229 6256 167080919 167080946 1.300000e-02 52.8


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 TraesCS6D01G153600 chr6D 127382076 127388986 6910 True 12763.0 12763 100.0000 1 6911 1 chr6D.!!$R1 6910
1 TraesCS6D01G153600 chr6A 150964068 150970746 6678 False 11088.0 11088 96.5370 1 6733 1 chr6A.!!$F1 6732
2 TraesCS6D01G153600 chr6B 226399205 226406226 7021 True 1738.9 6244 89.9624 7 6911 5 chr6B.!!$R2 6904

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
571 906 0.038526 CTCTGGTACGCGGTTCTGTT 60.039 55.000 12.47 0.00 0.00 3.16 F
572 907 0.319211 TCTGGTACGCGGTTCTGTTG 60.319 55.000 12.47 0.00 0.00 3.33 F
689 1025 0.663153 AGACTTCAAACTTGCACGGC 59.337 50.000 0.00 0.00 0.00 5.68 F
1842 2199 1.340889 TGAACTGCCAAGGAACAATGC 59.659 47.619 0.00 0.00 0.00 3.56 F
2465 2823 3.055385 AGTTACAGTTGCATATGACCCGT 60.055 43.478 6.97 0.24 0.00 5.28 F
3141 3499 2.494059 ACATCAGACACGTTTGAAGGG 58.506 47.619 0.00 0.00 0.00 3.95 F
3925 4287 1.336424 GCCTAGACTCGGCTAGCATTC 60.336 57.143 18.24 6.53 44.17 2.67 F
5340 5719 1.296392 CAAGTCGGGATCAGCACCA 59.704 57.895 0.00 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1982 0.184211 GGTGGTACAAAGGTGTGGGT 59.816 55.000 0.00 0.00 44.16 4.51 R
2464 2822 2.961526 ATCGTGGACCAGTGACATAC 57.038 50.000 0.00 0.00 0.00 2.39 R
2465 2823 4.021229 AGTAATCGTGGACCAGTGACATA 58.979 43.478 0.00 0.00 0.00 2.29 R
3141 3499 7.352739 TCGAACTAGTTTCAAAAAGATCTTGC 58.647 34.615 9.17 0.00 33.24 4.01 R
3925 4287 2.417933 GCACATACAAGGTCTTCAGCTG 59.582 50.000 7.63 7.63 0.00 4.24 R
4473 4836 4.082245 ACACACAAGCTAGCACAAAAAGTT 60.082 37.500 18.83 0.00 0.00 2.66 R
5640 6019 2.341101 GGTCTTCCGCGAGAGGTCA 61.341 63.158 8.23 0.00 0.00 4.02 R
6533 6976 0.178973 AAAGGGGAACAACGAAGGGG 60.179 55.000 0.00 0.00 0.00 4.79 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
204 216 1.428448 CAGCAAATCCGAACGAGTCA 58.572 50.000 0.00 0.00 0.00 3.41
212 224 3.586100 TCCGAACGAGTCATCAAATCA 57.414 42.857 0.00 0.00 0.00 2.57
216 228 5.411361 TCCGAACGAGTCATCAAATCAAAAT 59.589 36.000 0.00 0.00 0.00 1.82
253 288 1.000019 ACTACAGGCGGCCAGAGTA 60.000 57.895 23.09 18.25 0.00 2.59
343 389 1.064458 GCGCCTCCGAGTCTTCTAC 59.936 63.158 0.00 0.00 36.29 2.59
344 390 1.378124 GCGCCTCCGAGTCTTCTACT 61.378 60.000 0.00 0.00 42.80 2.57
353 399 1.701422 AGTCTTCTACTCCCTCCCCT 58.299 55.000 0.00 0.00 30.33 4.79
358 404 2.021652 CTACTCCCTCCCCTCCCCT 61.022 68.421 0.00 0.00 0.00 4.79
359 405 2.019272 TACTCCCTCCCCTCCCCTC 61.019 68.421 0.00 0.00 0.00 4.30
360 406 4.179599 CTCCCTCCCCTCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
363 409 3.795924 CCTCCCCTCCCCTCCCAT 61.796 72.222 0.00 0.00 0.00 4.00
364 410 2.122189 CTCCCCTCCCCTCCCATC 60.122 72.222 0.00 0.00 0.00 3.51
365 411 3.791076 TCCCCTCCCCTCCCATCC 61.791 72.222 0.00 0.00 0.00 3.51
366 412 4.928520 CCCCTCCCCTCCCATCCC 62.929 77.778 0.00 0.00 0.00 3.85
367 413 4.122670 CCCTCCCCTCCCATCCCA 62.123 72.222 0.00 0.00 0.00 4.37
372 418 2.038438 CCCTCCCATCCCATCCCA 60.038 66.667 0.00 0.00 0.00 4.37
568 903 1.935327 GCTCTCTGGTACGCGGTTCT 61.935 60.000 12.47 0.00 0.00 3.01
569 904 0.179161 CTCTCTGGTACGCGGTTCTG 60.179 60.000 12.47 3.23 0.00 3.02
570 905 0.892358 TCTCTGGTACGCGGTTCTGT 60.892 55.000 12.47 0.00 0.00 3.41
571 906 0.038526 CTCTGGTACGCGGTTCTGTT 60.039 55.000 12.47 0.00 0.00 3.16
572 907 0.319211 TCTGGTACGCGGTTCTGTTG 60.319 55.000 12.47 0.00 0.00 3.33
689 1025 0.663153 AGACTTCAAACTTGCACGGC 59.337 50.000 0.00 0.00 0.00 5.68
710 1046 2.926838 CAGTTCGTTTGGTTTGGTTTGG 59.073 45.455 0.00 0.00 0.00 3.28
711 1047 2.563620 AGTTCGTTTGGTTTGGTTTGGT 59.436 40.909 0.00 0.00 0.00 3.67
712 1048 3.007074 AGTTCGTTTGGTTTGGTTTGGTT 59.993 39.130 0.00 0.00 0.00 3.67
713 1049 3.679824 TCGTTTGGTTTGGTTTGGTTT 57.320 38.095 0.00 0.00 0.00 3.27
714 1050 4.796038 TCGTTTGGTTTGGTTTGGTTTA 57.204 36.364 0.00 0.00 0.00 2.01
767 1113 4.223659 CGGGTAAAAACAAATCGTTGAGG 58.776 43.478 0.00 0.00 38.07 3.86
802 1148 3.236528 CGCAATTTAACACGCCGTTATTC 59.763 43.478 0.00 0.00 39.81 1.75
950 1296 9.634021 TCTGTCACATAGATAGAAGAACAGTAT 57.366 33.333 0.00 0.00 40.94 2.12
981 1327 5.421056 TCCATTAATAGGTTCTGACGAGTGT 59.579 40.000 0.00 0.00 0.00 3.55
1013 1359 3.604582 GGTTCTTGATGCTCTGCTACTT 58.395 45.455 0.00 0.00 0.00 2.24
1384 1731 7.361457 TCAATATGGAGGTCCTTAGTACTTG 57.639 40.000 0.00 0.00 36.82 3.16
1431 1779 6.666113 GTCATAAATGGGGTAAAAAGAGGGAA 59.334 38.462 0.00 0.00 0.00 3.97
1767 2124 7.530426 AATGAATTGCCAAGGAACTATATCC 57.470 36.000 0.00 0.00 38.49 2.59
1842 2199 1.340889 TGAACTGCCAAGGAACAATGC 59.659 47.619 0.00 0.00 0.00 3.56
2464 2822 3.309682 CAGTTACAGTTGCATATGACCCG 59.690 47.826 6.97 0.00 0.00 5.28
2465 2823 3.055385 AGTTACAGTTGCATATGACCCGT 60.055 43.478 6.97 0.24 0.00 5.28
3141 3499 2.494059 ACATCAGACACGTTTGAAGGG 58.506 47.619 0.00 0.00 0.00 3.95
3502 3860 3.866883 TTTTTGGATTCCGATTGCCTC 57.133 42.857 0.00 0.00 0.00 4.70
3865 4227 6.016024 ACAGTAGTAGTTTGTCGGTATCAACA 60.016 38.462 0.00 0.00 0.00 3.33
3925 4287 1.336424 GCCTAGACTCGGCTAGCATTC 60.336 57.143 18.24 6.53 44.17 2.67
4811 5190 6.150318 CAGACACCATATGATACGTTCCTAC 58.850 44.000 3.65 0.00 0.00 3.18
4970 5349 4.125703 ACACAAAGAAGCTCAGAGAACAG 58.874 43.478 0.00 0.00 0.00 3.16
5340 5719 1.296392 CAAGTCGGGATCAGCACCA 59.704 57.895 0.00 0.00 0.00 4.17
5640 6019 1.449601 GGACGTGATCACCGCCATT 60.450 57.895 20.03 0.00 0.00 3.16
5724 6103 4.923942 CTGGGCATGCCGATCGCT 62.924 66.667 29.90 0.00 38.78 4.93
5864 6243 3.112709 GTTGCACGTCGAGGAGGC 61.113 66.667 12.85 14.68 0.00 4.70
6144 6533 4.559153 CTTTTCCTTTTGTGCGGAATGAT 58.441 39.130 0.00 0.00 38.95 2.45
6279 6670 2.179764 CGGACCAATTTGCGGATGT 58.820 52.632 0.00 0.00 0.00 3.06
6280 6671 0.179166 CGGACCAATTTGCGGATGTG 60.179 55.000 0.00 0.00 0.00 3.21
6281 6672 0.173255 GGACCAATTTGCGGATGTGG 59.827 55.000 0.36 0.36 35.39 4.17
6282 6673 1.173043 GACCAATTTGCGGATGTGGA 58.827 50.000 7.84 0.00 33.39 4.02
6311 6702 2.291365 CTGATGTCGGCAATCCAATCA 58.709 47.619 0.00 0.00 0.00 2.57
6315 6706 2.571212 TGTCGGCAATCCAATCATACC 58.429 47.619 0.00 0.00 0.00 2.73
6367 6767 5.981088 ATTGGACTATGTTCATGCAAACA 57.019 34.783 6.43 6.43 42.92 2.83
6486 6929 0.182299 AGCCATGAGCCCTAGAAAGC 59.818 55.000 0.00 0.00 45.47 3.51
6489 6932 1.407437 CCATGAGCCCTAGAAAGCGTT 60.407 52.381 0.00 0.00 0.00 4.84
6490 6933 2.359900 CATGAGCCCTAGAAAGCGTTT 58.640 47.619 0.00 0.00 0.00 3.60
6523 6966 2.021457 CTTGTTGTTCCCCTTCGTGTT 58.979 47.619 0.00 0.00 0.00 3.32
6525 6968 1.065345 TGTTGTTCCCCTTCGTGTTCA 60.065 47.619 0.00 0.00 0.00 3.18
6526 6969 1.332686 GTTGTTCCCCTTCGTGTTCAC 59.667 52.381 0.00 0.00 0.00 3.18
6527 6970 0.542333 TGTTCCCCTTCGTGTTCACA 59.458 50.000 3.87 0.00 0.00 3.58
6528 6971 1.142060 TGTTCCCCTTCGTGTTCACAT 59.858 47.619 3.87 0.00 0.00 3.21
6529 6972 1.804748 GTTCCCCTTCGTGTTCACATC 59.195 52.381 3.87 0.00 0.00 3.06
6530 6973 0.323629 TCCCCTTCGTGTTCACATCC 59.676 55.000 3.87 0.00 0.00 3.51
6531 6974 1.019278 CCCCTTCGTGTTCACATCCG 61.019 60.000 3.87 0.00 0.00 4.18
6532 6975 0.037697 CCCTTCGTGTTCACATCCGA 60.038 55.000 3.87 0.00 0.00 4.55
6533 6976 1.068474 CCTTCGTGTTCACATCCGAC 58.932 55.000 3.87 0.00 0.00 4.79
6534 6977 1.068474 CTTCGTGTTCACATCCGACC 58.932 55.000 3.87 0.00 0.00 4.79
6535 6978 0.320073 TTCGTGTTCACATCCGACCC 60.320 55.000 3.87 0.00 0.00 4.46
6536 6979 1.740296 CGTGTTCACATCCGACCCC 60.740 63.158 3.87 0.00 0.00 4.95
6537 6980 1.677552 GTGTTCACATCCGACCCCT 59.322 57.895 0.00 0.00 0.00 4.79
6538 6981 0.036306 GTGTTCACATCCGACCCCTT 59.964 55.000 0.00 0.00 0.00 3.95
6539 6982 0.323629 TGTTCACATCCGACCCCTTC 59.676 55.000 0.00 0.00 0.00 3.46
6547 6990 3.961729 CGACCCCTTCGTTGTTCC 58.038 61.111 0.00 0.00 43.24 3.62
6552 6995 0.178973 CCCCTTCGTTGTTCCCCTTT 60.179 55.000 0.00 0.00 0.00 3.11
6569 7012 0.179142 TTTGTGTTCACGTCCGACGA 60.179 50.000 27.03 2.85 46.05 4.20
6571 7014 1.009222 GTGTTCACGTCCGACGACT 60.009 57.895 27.03 2.85 46.05 4.18
6671 7143 4.308458 CGACCTGGCCGTCACCAA 62.308 66.667 10.86 0.00 39.86 3.67
6734 7206 1.065928 CGCCAGCGGGACTAGTTAG 59.934 63.158 7.23 0.00 35.59 2.34
6735 7207 1.227292 GCCAGCGGGACTAGTTAGC 60.227 63.158 7.23 3.38 35.59 3.09
6736 7208 1.677637 GCCAGCGGGACTAGTTAGCT 61.678 60.000 7.23 12.84 38.90 3.32
6737 7209 0.386113 CCAGCGGGACTAGTTAGCTC 59.614 60.000 14.92 0.00 35.82 4.09
6739 7211 0.394080 AGCGGGACTAGTTAGCTCGT 60.394 55.000 12.84 0.00 31.94 4.18
6741 7213 0.381089 CGGGACTAGTTAGCTCGTGG 59.619 60.000 0.00 0.00 0.00 4.94
6759 7231 3.072486 GCGCCAGCGGGACTAGTTA 62.072 63.158 14.63 0.00 40.19 2.24
6760 7232 1.065928 CGCCAGCGGGACTAGTTAG 59.934 63.158 7.23 0.00 35.59 2.34
6761 7233 1.227292 GCCAGCGGGACTAGTTAGC 60.227 63.158 7.23 3.38 35.59 3.09
6785 7257 0.179032 TGAATGACACGTGGTTGCCT 60.179 50.000 21.57 0.00 0.00 4.75
6789 7261 4.849310 ACACGTGGTTGCCTGCGT 62.849 61.111 21.57 0.00 36.64 5.24
6790 7262 4.012895 CACGTGGTTGCCTGCGTC 62.013 66.667 7.95 0.00 34.88 5.19
6796 7268 4.120331 GTTGCCTGCGTCCATGGC 62.120 66.667 6.96 0.96 46.26 4.40
6864 7359 0.317479 CTCCTCACGAAGTTCGGGTT 59.683 55.000 25.77 4.16 44.95 4.11
6877 7372 2.969827 GGGTTTTCCGCCACCATG 59.030 61.111 0.00 0.00 41.82 3.66
6878 7373 2.645192 GGGTTTTCCGCCACCATGG 61.645 63.158 11.19 11.19 41.82 3.66
6879 7374 1.906333 GGTTTTCCGCCACCATGGT 60.906 57.895 13.00 13.00 40.46 3.55
6880 7375 1.468506 GGTTTTCCGCCACCATGGTT 61.469 55.000 16.84 0.00 40.46 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
334 380 1.571936 GAGGGGAGGGAGTAGAAGACT 59.428 57.143 0.00 0.00 42.90 3.24
343 389 4.179599 GGAGGGGAGGGGAGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
353 399 2.293934 GGATGGGATGGGAGGGGA 59.706 66.667 0.00 0.00 0.00 4.81
358 404 1.465986 GGGATGGGATGGGATGGGA 60.466 63.158 0.00 0.00 0.00 4.37
359 405 2.910737 CGGGATGGGATGGGATGGG 61.911 68.421 0.00 0.00 0.00 4.00
360 406 2.129555 GACGGGATGGGATGGGATGG 62.130 65.000 0.00 0.00 0.00 3.51
361 407 1.376466 GACGGGATGGGATGGGATG 59.624 63.158 0.00 0.00 0.00 3.51
362 408 1.847968 GGACGGGATGGGATGGGAT 60.848 63.158 0.00 0.00 0.00 3.85
363 409 2.447765 GGACGGGATGGGATGGGA 60.448 66.667 0.00 0.00 0.00 4.37
364 410 3.570212 GGGACGGGATGGGATGGG 61.570 72.222 0.00 0.00 0.00 4.00
365 411 2.689573 TAGGGGACGGGATGGGATGG 62.690 65.000 0.00 0.00 0.00 3.51
366 412 0.766674 TTAGGGGACGGGATGGGATG 60.767 60.000 0.00 0.00 0.00 3.51
367 413 0.196118 ATTAGGGGACGGGATGGGAT 59.804 55.000 0.00 0.00 0.00 3.85
372 418 0.178900 GAGGGATTAGGGGACGGGAT 60.179 60.000 0.00 0.00 0.00 3.85
508 843 3.524541 AGACAAACAGCCAAAAAGCTTG 58.475 40.909 0.00 0.00 42.61 4.01
509 844 3.734902 CGAGACAAACAGCCAAAAAGCTT 60.735 43.478 0.00 0.00 42.61 3.74
568 903 2.477176 GCGGCAACTCCACACAACA 61.477 57.895 0.00 0.00 34.01 3.33
569 904 2.331451 GCGGCAACTCCACACAAC 59.669 61.111 0.00 0.00 34.01 3.32
570 905 2.904866 GGCGGCAACTCCACACAA 60.905 61.111 3.07 0.00 42.67 3.33
571 906 4.947147 GGGCGGCAACTCCACACA 62.947 66.667 12.47 0.00 45.97 3.72
610 946 4.615912 CGAAGCACCAAATTTAACAGGGAG 60.616 45.833 0.00 0.00 0.00 4.30
655 991 2.240493 AGTCTCAGAAACAACCACCG 57.760 50.000 0.00 0.00 0.00 4.94
689 1025 2.926838 CCAAACCAAACCAAACGAACTG 59.073 45.455 0.00 0.00 0.00 3.16
710 1046 0.170339 ATTTTGCTCCGCGCCTAAAC 59.830 50.000 0.00 0.00 38.05 2.01
711 1047 0.450184 GATTTTGCTCCGCGCCTAAA 59.550 50.000 0.00 1.14 38.05 1.85
712 1048 0.392461 AGATTTTGCTCCGCGCCTAA 60.392 50.000 0.00 0.00 38.05 2.69
713 1049 1.089481 CAGATTTTGCTCCGCGCCTA 61.089 55.000 0.00 0.00 38.05 3.93
714 1050 2.045926 AGATTTTGCTCCGCGCCT 60.046 55.556 0.00 0.00 38.05 5.52
802 1148 0.323360 TTCCCCCAAATCTTCAGCCG 60.323 55.000 0.00 0.00 0.00 5.52
950 1296 6.374333 GTCAGAACCTATTAATGGAGTGCAAA 59.626 38.462 0.00 0.00 0.00 3.68
981 1327 1.124780 TCAAGAACCCACGTCCAAGA 58.875 50.000 0.00 0.00 0.00 3.02
1013 1359 3.786368 TGGTCAGAACAACATCATGGA 57.214 42.857 0.00 0.00 0.00 3.41
1128 1475 2.840102 CTCTCCTTCCGCGGGGAT 60.840 66.667 27.83 0.00 43.41 3.85
1384 1731 8.272545 TGACAATATGCAGATATTTCCATAGC 57.727 34.615 0.00 0.00 33.21 2.97
1431 1779 3.652057 AGCTACCACATGTATTTGGCT 57.348 42.857 0.00 1.61 36.20 4.75
1557 1913 5.767168 GCAGCTAAATGAGGATTTGTAGGAT 59.233 40.000 0.00 0.00 33.63 3.24
1626 1982 0.184211 GGTGGTACAAAGGTGTGGGT 59.816 55.000 0.00 0.00 44.16 4.51
1754 2111 5.063017 TCGTGGAGAGGATATAGTTCCTT 57.937 43.478 0.00 0.00 46.35 3.36
1842 2199 5.702670 TCACAGTATGAAGAAAGAAAGGCTG 59.297 40.000 0.00 0.00 39.69 4.85
2464 2822 2.961526 ATCGTGGACCAGTGACATAC 57.038 50.000 0.00 0.00 0.00 2.39
2465 2823 4.021229 AGTAATCGTGGACCAGTGACATA 58.979 43.478 0.00 0.00 0.00 2.29
3141 3499 7.352739 TCGAACTAGTTTCAAAAAGATCTTGC 58.647 34.615 9.17 0.00 33.24 4.01
3865 4227 7.068470 TGGTCATGTACATCACATTTGCATAAT 59.932 33.333 12.22 0.00 46.01 1.28
3925 4287 2.417933 GCACATACAAGGTCTTCAGCTG 59.582 50.000 7.63 7.63 0.00 4.24
4473 4836 4.082245 ACACACAAGCTAGCACAAAAAGTT 60.082 37.500 18.83 0.00 0.00 2.66
4970 5349 6.319911 TCATATGATCACTCGGAGATCCATAC 59.680 42.308 12.86 0.00 40.87 2.39
5340 5719 5.480642 ACTGGATCGATCTCAGCAAATAT 57.519 39.130 28.85 15.16 32.10 1.28
5583 5962 3.381983 ACGATGTCGGCAGCCTCA 61.382 61.111 10.54 9.25 44.95 3.86
5640 6019 2.341101 GGTCTTCCGCGAGAGGTCA 61.341 63.158 8.23 0.00 0.00 4.02
5724 6103 4.329545 GGGAACAGGACGCCAGCA 62.330 66.667 0.00 0.00 0.00 4.41
6270 6661 2.823593 CCGCATCCACATCCGCAA 60.824 61.111 0.00 0.00 0.00 4.85
6276 6667 0.543277 ATCAGTGTCCGCATCCACAT 59.457 50.000 0.00 0.00 33.99 3.21
6277 6668 0.391528 CATCAGTGTCCGCATCCACA 60.392 55.000 0.00 0.00 33.99 4.17
6278 6669 0.391661 ACATCAGTGTCCGCATCCAC 60.392 55.000 0.00 0.00 31.41 4.02
6279 6670 1.982430 ACATCAGTGTCCGCATCCA 59.018 52.632 0.00 0.00 31.41 3.41
6280 6671 4.941609 ACATCAGTGTCCGCATCC 57.058 55.556 0.00 0.00 31.41 3.51
6486 6929 1.873591 CAAGGACTTGGAGGTCAAACG 59.126 52.381 4.15 0.00 37.91 3.60
6489 6932 2.241176 ACAACAAGGACTTGGAGGTCAA 59.759 45.455 15.72 0.00 44.45 3.18
6490 6933 1.843851 ACAACAAGGACTTGGAGGTCA 59.156 47.619 15.72 0.00 44.45 4.02
6523 6966 3.294750 CGAAGGGGTCGGATGTGA 58.705 61.111 0.00 0.00 46.45 3.58
6531 6974 1.303074 GGGGAACAACGAAGGGGTC 60.303 63.158 0.00 0.00 0.00 4.46
6532 6975 1.358051 AAGGGGAACAACGAAGGGGT 61.358 55.000 0.00 0.00 0.00 4.95
6533 6976 0.178973 AAAGGGGAACAACGAAGGGG 60.179 55.000 0.00 0.00 0.00 4.79
6534 6977 0.958822 CAAAGGGGAACAACGAAGGG 59.041 55.000 0.00 0.00 0.00 3.95
6535 6978 1.336755 CACAAAGGGGAACAACGAAGG 59.663 52.381 0.00 0.00 0.00 3.46
6536 6979 2.021457 ACACAAAGGGGAACAACGAAG 58.979 47.619 0.00 0.00 0.00 3.79
6537 6980 2.131776 ACACAAAGGGGAACAACGAA 57.868 45.000 0.00 0.00 0.00 3.85
6538 6981 2.018515 GAACACAAAGGGGAACAACGA 58.981 47.619 0.00 0.00 0.00 3.85
6539 6982 1.746220 TGAACACAAAGGGGAACAACG 59.254 47.619 0.00 0.00 0.00 4.10
6540 6983 2.478879 CGTGAACACAAAGGGGAACAAC 60.479 50.000 5.80 0.00 0.00 3.32
6541 6984 1.746220 CGTGAACACAAAGGGGAACAA 59.254 47.619 5.80 0.00 0.00 2.83
6547 6990 0.531090 TCGGACGTGAACACAAAGGG 60.531 55.000 0.00 0.00 0.00 3.95
6552 6995 1.298563 GTCGTCGGACGTGAACACA 60.299 57.895 27.53 6.10 43.14 3.72
6591 7044 1.143481 CATGTCCCATGTCCTATGCCA 59.857 52.381 0.00 0.00 0.00 4.92
6621 7093 1.299468 GAGTAGGGCATGCGAGACG 60.299 63.158 12.44 0.00 0.00 4.18
6660 7132 2.438434 CCTCCATTGGTGACGGCC 60.438 66.667 6.33 0.00 0.00 6.13
6667 7139 0.405585 CCAACCTCACCTCCATTGGT 59.594 55.000 1.86 0.00 41.77 3.67
6671 7143 1.274703 ATCGCCAACCTCACCTCCAT 61.275 55.000 0.00 0.00 0.00 3.41
6741 7213 2.955751 CTAACTAGTCCCGCTGGCGC 62.956 65.000 9.63 0.00 38.24 6.53
6743 7215 1.227292 GCTAACTAGTCCCGCTGGC 60.227 63.158 0.00 0.00 0.00 4.85
6744 7216 1.065928 CGCTAACTAGTCCCGCTGG 59.934 63.158 0.00 0.00 0.00 4.85
6745 7217 1.065928 CCGCTAACTAGTCCCGCTG 59.934 63.158 0.00 0.00 0.00 5.18
6746 7218 2.783288 GCCGCTAACTAGTCCCGCT 61.783 63.158 0.00 0.00 0.00 5.52
6747 7219 2.279318 GCCGCTAACTAGTCCCGC 60.279 66.667 0.00 0.00 0.00 6.13
6748 7220 2.025727 CGCCGCTAACTAGTCCCG 59.974 66.667 0.00 0.00 0.00 5.14
6749 7221 1.226888 CACGCCGCTAACTAGTCCC 60.227 63.158 0.00 0.00 0.00 4.46
6753 7225 1.852895 GTCATTCACGCCGCTAACTAG 59.147 52.381 0.00 0.00 0.00 2.57
6777 7249 2.672651 CATGGACGCAGGCAACCA 60.673 61.111 8.43 8.43 36.83 3.67
6778 7250 3.443045 CCATGGACGCAGGCAACC 61.443 66.667 5.56 0.00 37.17 3.77
6839 7334 1.806461 AACTTCGTGAGGAGCAGCGA 61.806 55.000 0.00 0.00 41.85 4.93
6840 7335 1.347817 GAACTTCGTGAGGAGCAGCG 61.348 60.000 0.00 0.00 41.85 5.18
6844 7339 1.446272 CCCGAACTTCGTGAGGAGC 60.446 63.158 10.22 0.00 41.85 4.70
6864 7359 1.152652 ACAACCATGGTGGCGGAAA 60.153 52.632 20.60 0.00 42.67 3.13
6875 7370 0.257039 GAGGAGGCCATGACAACCAT 59.743 55.000 5.01 0.00 35.44 3.55
6876 7371 1.685224 GAGGAGGCCATGACAACCA 59.315 57.895 5.01 0.00 0.00 3.67
6877 7372 1.450312 CGAGGAGGCCATGACAACC 60.450 63.158 5.01 0.00 0.00 3.77
6878 7373 2.109126 GCGAGGAGGCCATGACAAC 61.109 63.158 5.01 0.00 0.00 3.32
6879 7374 2.244117 GAGCGAGGAGGCCATGACAA 62.244 60.000 5.01 0.00 0.00 3.18
6880 7375 2.685017 AGCGAGGAGGCCATGACA 60.685 61.111 5.01 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.