Multiple sequence alignment - TraesCS7A01G377800

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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 TraesCS7A01G377800 chr7A 100.000 5433 0 0 1 5433 553234976 553229544 0.000000e+00 10033.0
1 TraesCS7A01G377800 chr7B 92.009 5506 278 72 1 5433 512359129 512353713 0.000000e+00 7581.0
2 TraesCS7A01G377800 chr7D 92.297 4959 241 58 1 4913 484929581 484924718 0.000000e+00 6911.0
3 TraesCS7A01G377800 chr7D 82.028 562 46 22 4905 5433 484924355 484923816 1.400000e-115 427.0
4 TraesCS7A01G377800 chr6B 83.333 78 11 2 2657 2733 278674128 278674052 2.710000e-08 71.3
5 TraesCS7A01G377800 chr1D 100.000 31 0 0 5388 5418 279234534 279234564 2.110000e-04 58.4
6 TraesCS7A01G377800 chr1A 100.000 31 0 0 5388 5418 351475459 351475489 2.110000e-04 58.4


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 TraesCS7A01G377800 chr7A 553229544 553234976 5432 True 10033 10033 100.0000 1 5433 1 chr7A.!!$R1 5432
1 TraesCS7A01G377800 chr7B 512353713 512359129 5416 True 7581 7581 92.0090 1 5433 1 chr7B.!!$R1 5432
2 TraesCS7A01G377800 chr7D 484923816 484929581 5765 True 3669 6911 87.1625 1 5433 2 chr7D.!!$R1 5432

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
619 646 0.615261 ACCCCGAGAGAAGGAGGTTC 60.615 60.000 0.00 0.0 31.26 3.62 F
806 834 0.774908 TGAACCCAATCCCGTTTCCT 59.225 50.000 0.00 0.0 0.00 3.36 F
1441 1470 0.535102 CTTTGTCCACGAAGGCACCT 60.535 55.000 0.00 0.0 37.29 4.00 F
2736 2788 0.603065 AGGCAAAATCAAAGGTCCGC 59.397 50.000 0.00 0.0 0.00 5.54 F
3334 3387 1.600916 ACAAAAGACAGCCGGGAGC 60.601 57.895 2.18 0.0 44.25 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1424 1453 0.981183 ATAGGTGCCTTCGTGGACAA 59.019 50.000 0.00 0.0 38.35 3.18 R
1979 2016 2.562298 TGAATGCAATCCTTTTCGGCTT 59.438 40.909 0.00 0.0 0.00 4.35 R
3314 3367 1.228124 TCCCGGCTGTCTTTTGTGG 60.228 57.895 0.00 0.0 0.00 4.17 R
4147 4223 0.108396 TTACTGCTGTGCCTGCTGAA 59.892 50.000 6.48 0.0 33.23 3.02 R
5321 5824 0.166814 GGCATGCGTGACAGTTTCTC 59.833 55.000 12.44 0.0 31.88 2.87 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
59 66 3.706594 AGGAGATCGGATGCAACTTTCTA 59.293 43.478 0.00 0.00 0.00 2.10
74 81 3.617263 ACTTTCTATGCGGCGTTTCTTAG 59.383 43.478 9.37 4.30 0.00 2.18
178 188 7.287950 CGATGATGTTCGTTAAGTGAGAAAAA 58.712 34.615 0.00 0.00 34.46 1.94
205 215 4.682787 TCATGTCGATTATGAGACGCTTT 58.317 39.130 10.24 0.00 40.05 3.51
208 218 4.490743 TGTCGATTATGAGACGCTTTTGA 58.509 39.130 0.00 0.00 40.05 2.69
212 222 5.985530 TCGATTATGAGACGCTTTTGATGAT 59.014 36.000 0.00 0.00 0.00 2.45
213 223 6.479990 TCGATTATGAGACGCTTTTGATGATT 59.520 34.615 0.00 0.00 0.00 2.57
216 226 9.294030 GATTATGAGACGCTTTTGATGATTTTT 57.706 29.630 0.00 0.00 0.00 1.94
223 233 7.109006 ACGCTTTTGATGATTTTTGTCAATC 57.891 32.000 0.00 0.00 32.48 2.67
235 245 9.195411 TGATTTTTGTCAATCTTAAGATGTTGC 57.805 29.630 18.61 11.07 34.66 4.17
236 246 9.415544 GATTTTTGTCAATCTTAAGATGTTGCT 57.584 29.630 18.61 0.00 34.49 3.91
238 248 7.750229 TTTGTCAATCTTAAGATGTTGCTCT 57.250 32.000 18.61 0.00 34.49 4.09
245 255 1.818642 AAGATGTTGCTCTGGCTCAC 58.181 50.000 0.00 0.00 39.59 3.51
258 271 1.544691 TGGCTCACTAACTCGAAGGTC 59.455 52.381 0.00 0.00 0.00 3.85
281 294 5.361571 TCTTCGTAAAGATAGGGTGTGCATA 59.638 40.000 0.00 0.00 36.59 3.14
287 300 7.275779 CGTAAAGATAGGGTGTGCATATATGTC 59.724 40.741 14.14 7.28 0.00 3.06
552 579 3.379445 GTCTCCCCTCGTCGCCAA 61.379 66.667 0.00 0.00 0.00 4.52
584 611 4.038080 CCGCAGTTGCCGAAACCC 62.038 66.667 0.00 0.00 39.85 4.11
585 612 4.383602 CGCAGTTGCCGAAACCCG 62.384 66.667 0.00 0.00 39.85 5.28
586 613 4.700365 GCAGTTGCCGAAACCCGC 62.700 66.667 0.00 0.00 39.85 6.13
587 614 4.038080 CAGTTGCCGAAACCCGCC 62.038 66.667 0.00 0.00 39.85 6.13
618 645 0.905337 CACCCCGAGAGAAGGAGGTT 60.905 60.000 0.00 0.00 32.45 3.50
619 646 0.615261 ACCCCGAGAGAAGGAGGTTC 60.615 60.000 0.00 0.00 31.26 3.62
653 680 4.816984 TCCGTCCTCTCCTCCGCC 62.817 72.222 0.00 0.00 0.00 6.13
806 834 0.774908 TGAACCCAATCCCGTTTCCT 59.225 50.000 0.00 0.00 0.00 3.36
820 849 2.163613 CGTTTCCTCCCAGTAATTTGGC 59.836 50.000 0.00 0.00 36.88 4.52
893 922 4.025401 CTTGCCGCGGCGAGTTTT 62.025 61.111 45.56 0.00 45.14 2.43
1023 1052 3.414700 GCAGTGTCCGAGGTTGCG 61.415 66.667 0.00 0.00 0.00 4.85
1194 1223 1.483004 TCGCCATCGGAGGACATAAAA 59.517 47.619 0.00 0.00 36.13 1.52
1239 1268 1.002011 GGTTCCCAAGGTGAGAGCC 60.002 63.158 0.00 0.00 0.00 4.70
1250 1279 1.001764 TGAGAGCCTGCCATGTTGG 60.002 57.895 0.00 0.00 41.55 3.77
1275 1304 3.325293 TTGTCCTTGCTGAGATCTCAC 57.675 47.619 21.67 17.48 35.46 3.51
1336 1365 2.237143 TCATGTGTTCTAGGGAAGCCAG 59.763 50.000 0.00 0.00 31.46 4.85
1424 1453 5.236695 GCTAAGAAAAACACTCCGAGTTCTT 59.763 40.000 14.10 14.10 38.50 2.52
1425 1454 6.238402 GCTAAGAAAAACACTCCGAGTTCTTT 60.238 38.462 14.64 7.84 36.82 2.52
1432 1461 1.269621 ACTCCGAGTTCTTTGTCCACG 60.270 52.381 0.00 0.00 0.00 4.94
1441 1470 0.535102 CTTTGTCCACGAAGGCACCT 60.535 55.000 0.00 0.00 37.29 4.00
1560 1589 6.431234 CCCCTATTACTTCTTGGATATTGCAC 59.569 42.308 0.00 0.00 0.00 4.57
1600 1629 5.063817 GCTGAAATGCAAAACTCTTTGTTGT 59.936 36.000 0.00 0.00 43.34 3.32
1618 1647 4.641541 TGTTGTCCAATATGAGGATGCAAG 59.358 41.667 0.00 0.00 37.52 4.01
1739 1768 2.930682 GTCGCTGGAGGATTCAAAGTAC 59.069 50.000 0.00 0.00 0.00 2.73
1765 1797 7.482113 CGTTGTTTGTTTGTTCTTGTGTGTATA 59.518 33.333 0.00 0.00 0.00 1.47
1766 1798 9.296400 GTTGTTTGTTTGTTCTTGTGTGTATAT 57.704 29.630 0.00 0.00 0.00 0.86
1768 1800 9.295214 TGTTTGTTTGTTCTTGTGTGTATATTG 57.705 29.630 0.00 0.00 0.00 1.90
1769 1801 9.296400 GTTTGTTTGTTCTTGTGTGTATATTGT 57.704 29.630 0.00 0.00 0.00 2.71
1770 1802 9.509855 TTTGTTTGTTCTTGTGTGTATATTGTC 57.490 29.630 0.00 0.00 0.00 3.18
1833 1865 1.956477 CTGTGCCCAATTATGGTAGGC 59.044 52.381 0.00 0.00 46.01 3.93
1913 1947 4.699925 TGGGACAGCTAGTTTTTGTAGT 57.300 40.909 0.00 0.00 0.00 2.73
1914 1948 5.811796 TGGGACAGCTAGTTTTTGTAGTA 57.188 39.130 0.00 0.00 0.00 1.82
1915 1949 5.790593 TGGGACAGCTAGTTTTTGTAGTAG 58.209 41.667 0.00 0.00 0.00 2.57
1916 1950 4.630505 GGGACAGCTAGTTTTTGTAGTAGC 59.369 45.833 0.00 0.00 44.04 3.58
1917 1951 5.235516 GGACAGCTAGTTTTTGTAGTAGCA 58.764 41.667 11.71 0.00 45.42 3.49
1918 1952 5.120363 GGACAGCTAGTTTTTGTAGTAGCAC 59.880 44.000 11.71 4.45 45.42 4.40
1964 2001 6.508030 TTGCATACCATAAAGGGTCTGATA 57.492 37.500 3.66 0.00 43.89 2.15
1967 2004 6.785466 TGCATACCATAAAGGGTCTGATACTA 59.215 38.462 3.66 0.00 43.89 1.82
1978 2015 5.597182 AGGGTCTGATACTAAAACTATGCGA 59.403 40.000 0.00 0.00 0.00 5.10
1979 2016 6.097839 AGGGTCTGATACTAAAACTATGCGAA 59.902 38.462 0.00 0.00 0.00 4.70
2002 2039 3.953612 AGCCGAAAAGGATTGCATTCATA 59.046 39.130 10.55 0.00 45.00 2.15
2015 2052 6.985188 TTGCATTCATACTTAGTGTCCTTC 57.015 37.500 0.00 0.00 0.00 3.46
2045 2082 4.736126 AGGTTACTTTTTGTTTGCTGCT 57.264 36.364 0.00 0.00 0.00 4.24
2056 2093 1.066908 GTTTGCTGCTGTGCTACCAAA 59.933 47.619 0.00 0.00 0.00 3.28
2238 2275 6.599638 GGATATAACCACCCTCTAAATGCATC 59.400 42.308 0.00 0.00 0.00 3.91
2261 2298 4.566488 CCTCCATCTGTGAAGCCTTAAACT 60.566 45.833 0.00 0.00 0.00 2.66
2321 2359 6.594159 GTGCACAAGTCTAGCTAATTCCTTTA 59.406 38.462 13.17 0.00 0.00 1.85
2540 2592 2.157640 CCCCTTCATATGGGTTTGCA 57.842 50.000 2.13 0.00 43.09 4.08
2736 2788 0.603065 AGGCAAAATCAAAGGTCCGC 59.397 50.000 0.00 0.00 0.00 5.54
2855 2908 2.847327 TGGAAGAAGCTGAACTCAGG 57.153 50.000 8.74 0.00 43.94 3.86
2928 2981 1.761174 GAACCACCAGCTCCCAAGA 59.239 57.895 0.00 0.00 0.00 3.02
2996 3049 3.251484 TCCTCCTTCCATTCTGTCAAGT 58.749 45.455 0.00 0.00 0.00 3.16
3104 3157 5.976458 TCCTGAATGCAAACTTTTCTTTGT 58.024 33.333 0.00 0.00 34.19 2.83
3314 3367 7.728847 TGTATACATGTCATGATGGTAAAGC 57.271 36.000 19.77 1.10 0.00 3.51
3334 3387 1.600916 ACAAAAGACAGCCGGGAGC 60.601 57.895 2.18 0.00 44.25 4.70
3451 3512 2.095372 GCCCTAACAACCGAATCGAAAG 59.905 50.000 3.36 0.00 0.00 2.62
3823 3884 4.018490 TGAAAATCTCCATCACCACATGG 58.982 43.478 0.00 0.00 44.45 3.66
3924 3991 8.796475 CAAGTTGACCATCCCTAATTATTATGG 58.204 37.037 14.70 14.70 42.32 2.74
4147 4223 1.940613 GGTCGCTCAAAGAACACAACT 59.059 47.619 0.00 0.00 0.00 3.16
4321 4400 3.607422 TCTGTTGACATTGCAACTTCG 57.393 42.857 0.00 0.00 46.31 3.79
4442 4521 3.433615 GCTCAACGCATAGAAAACAGTCT 59.566 43.478 0.00 0.00 38.92 3.24
4443 4522 4.083802 GCTCAACGCATAGAAAACAGTCTT 60.084 41.667 0.00 0.00 38.92 3.01
4483 4562 0.179078 CTGAGAGTCATGCCTCAGCC 60.179 60.000 19.34 5.62 46.48 4.85
4504 4583 3.367703 CCTCCCATGTCTGCATTTTTGTC 60.368 47.826 0.00 0.00 31.99 3.18
4689 4768 7.342581 TGCATATGACTACCTTGTATTTCCAA 58.657 34.615 6.97 0.00 0.00 3.53
4691 4770 7.520614 GCATATGACTACCTTGTATTTCCAAGC 60.521 40.741 6.97 0.00 40.40 4.01
4707 4786 1.264288 CAAGCCGCGAGACTTCTTTTT 59.736 47.619 8.23 0.00 0.00 1.94
4710 4789 1.797025 CCGCGAGACTTCTTTTTCCT 58.203 50.000 8.23 0.00 0.00 3.36
4716 4795 3.748048 CGAGACTTCTTTTTCCTGCATGA 59.252 43.478 0.00 0.00 0.00 3.07
4727 4806 3.243359 TCCTGCATGAGTTTTCCCTTT 57.757 42.857 0.00 0.00 0.00 3.11
4733 4812 4.895297 TGCATGAGTTTTCCCTTTTCTTCT 59.105 37.500 0.00 0.00 0.00 2.85
4739 4818 8.589701 TGAGTTTTCCCTTTTCTTCTTTTACT 57.410 30.769 0.00 0.00 0.00 2.24
4793 4872 5.288015 TGGTGCATTCAGTGTAATTTTGTG 58.712 37.500 0.00 0.00 0.00 3.33
4887 4966 6.651643 TGTAATTCACAAGTGGTACATACACC 59.348 38.462 0.00 0.00 35.33 4.16
4925 5375 9.035607 GTTATCAGGAACATTCTACATGTACAG 57.964 37.037 0.08 0.00 0.00 2.74
5037 5533 5.470777 CCGGACTTGGTTTATTCAGTTTACA 59.529 40.000 0.00 0.00 0.00 2.41
5048 5547 1.597027 AGTTTACAAGCTGCCGCGT 60.597 52.632 4.92 0.00 42.32 6.01
5132 5635 1.980765 TCCTTGCAGAGTTCCAGATGT 59.019 47.619 0.00 0.00 0.00 3.06
5158 5661 7.506114 AGTTTGTTTACTGGTAGTGAGATTGA 58.494 34.615 0.00 0.00 0.00 2.57
5249 5752 3.112709 GCTGCCCGTCGTTGAGAC 61.113 66.667 0.00 0.00 46.16 3.36
5321 5824 1.496393 CTGCAAGAGAAGCACAGCG 59.504 57.895 0.00 0.00 37.02 5.18
5327 5830 1.789506 AGAGAAGCACAGCGAGAAAC 58.210 50.000 0.00 0.00 0.00 2.78
5348 5852 2.126228 CACGCATGCCAAGCAAGG 60.126 61.111 13.15 0.00 43.62 3.61
5354 5858 0.108804 CATGCCAAGCAAGGAAGCAG 60.109 55.000 0.00 0.00 43.62 4.24
5374 5878 3.300667 GAAGTGGCGCGCTGAGTTG 62.301 63.158 32.29 0.00 0.00 3.16
5375 5879 4.609018 AGTGGCGCGCTGAGTTGT 62.609 61.111 32.29 5.92 0.00 3.32
5376 5880 3.649986 GTGGCGCGCTGAGTTGTT 61.650 61.111 32.29 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 66 2.112815 GCCCTAAGAAACGCCGCAT 61.113 57.895 0.00 0.00 0.00 4.73
106 114 1.244019 GCAAGCATCGGGGACAAGTT 61.244 55.000 0.00 0.00 0.00 2.66
112 120 1.265236 AAAAATGCAAGCATCGGGGA 58.735 45.000 8.14 0.00 35.31 4.81
175 185 7.904977 CGTCTCATAATCGACATGAACATTTTT 59.095 33.333 11.51 0.00 32.20 1.94
178 188 5.050769 GCGTCTCATAATCGACATGAACATT 60.051 40.000 11.51 0.00 32.20 2.71
192 202 8.081633 ACAAAAATCATCAAAAGCGTCTCATAA 58.918 29.630 0.00 0.00 0.00 1.90
195 205 5.830912 ACAAAAATCATCAAAAGCGTCTCA 58.169 33.333 0.00 0.00 0.00 3.27
212 222 8.632679 AGAGCAACATCTTAAGATTGACAAAAA 58.367 29.630 15.49 0.00 31.21 1.94
213 223 8.077991 CAGAGCAACATCTTAAGATTGACAAAA 58.922 33.333 15.49 0.00 31.21 2.44
216 226 5.645067 CCAGAGCAACATCTTAAGATTGACA 59.355 40.000 15.49 0.00 31.21 3.58
223 233 3.373439 GTGAGCCAGAGCAACATCTTAAG 59.627 47.826 0.00 0.00 43.56 1.85
235 245 2.159310 CCTTCGAGTTAGTGAGCCAGAG 60.159 54.545 0.00 0.00 0.00 3.35
236 246 1.819288 CCTTCGAGTTAGTGAGCCAGA 59.181 52.381 0.00 0.00 0.00 3.86
238 248 1.544691 GACCTTCGAGTTAGTGAGCCA 59.455 52.381 0.00 0.00 0.00 4.75
258 271 3.857052 TGCACACCCTATCTTTACGAAG 58.143 45.455 0.00 0.00 0.00 3.79
268 281 6.726299 ACTACAGACATATATGCACACCCTAT 59.274 38.462 12.79 0.00 0.00 2.57
281 294 6.607600 ACATACACTCACCACTACAGACATAT 59.392 38.462 0.00 0.00 0.00 1.78
287 300 3.254060 GCACATACACTCACCACTACAG 58.746 50.000 0.00 0.00 0.00 2.74
346 361 0.670162 CCACACTGGTTGCAAAGAGG 59.330 55.000 0.00 0.00 31.35 3.69
470 485 1.281867 GGGTGAATCTGGGATGTGACA 59.718 52.381 0.00 0.00 0.00 3.58
594 621 4.689549 TTCTCTCGGGGTGGCGGA 62.690 66.667 0.00 0.00 0.00 5.54
597 624 2.683933 TCCTTCTCTCGGGGTGGC 60.684 66.667 0.00 0.00 0.00 5.01
618 645 0.757188 GAGGGGCGATGAAGGAGAGA 60.757 60.000 0.00 0.00 0.00 3.10
619 646 1.745264 GAGGGGCGATGAAGGAGAG 59.255 63.158 0.00 0.00 0.00 3.20
626 653 4.458829 AGGACGGAGGGGCGATGA 62.459 66.667 0.00 0.00 0.00 2.92
628 655 4.144727 AGAGGACGGAGGGGCGAT 62.145 66.667 0.00 0.00 0.00 4.58
631 658 4.467107 AGGAGAGGACGGAGGGGC 62.467 72.222 0.00 0.00 0.00 5.80
685 712 1.192146 TTACCAGCAAGAGGAGCCGT 61.192 55.000 0.00 0.00 0.00 5.68
806 834 0.693622 TCCACGCCAAATTACTGGGA 59.306 50.000 0.00 0.00 36.92 4.37
820 849 3.560068 GCTATAAGTTGGGTCAATCCACG 59.440 47.826 0.00 0.00 36.38 4.94
893 922 4.293494 ACCTTCTTAGCTCATCATCCTCA 58.707 43.478 0.00 0.00 0.00 3.86
937 966 5.219633 CGGTTTATCAGAAACAACAAAGGG 58.780 41.667 0.00 0.00 32.04 3.95
1122 1151 0.611896 TGATCACCTCACTCTCGCCA 60.612 55.000 0.00 0.00 0.00 5.69
1194 1223 0.104304 GTATGTCCTCCGGTTGCGAT 59.896 55.000 0.00 0.00 0.00 4.58
1221 1250 1.492993 AGGCTCTCACCTTGGGAACC 61.493 60.000 0.00 0.00 40.81 3.62
1239 1268 2.164219 GGACAATGTACCAACATGGCAG 59.836 50.000 0.00 0.00 45.79 4.85
1250 1279 4.764172 AGATCTCAGCAAGGACAATGTAC 58.236 43.478 0.00 0.00 0.00 2.90
1275 1304 9.304731 CACAAAATTATCACCAAACCATCTATG 57.695 33.333 0.00 0.00 0.00 2.23
1336 1365 1.134580 GTAACCTTAGGGGAACGGCTC 60.135 57.143 2.32 0.00 38.76 4.70
1378 1407 2.731348 CTCTTATCGCCGCTCCGC 60.731 66.667 0.00 0.00 0.00 5.54
1424 1453 0.981183 ATAGGTGCCTTCGTGGACAA 59.019 50.000 0.00 0.00 38.35 3.18
1425 1454 0.981183 AATAGGTGCCTTCGTGGACA 59.019 50.000 0.00 0.00 38.35 4.02
1441 1470 4.081697 TCTGGATCAGAAACTCGTGCAATA 60.082 41.667 0.00 0.00 37.57 1.90
1453 1482 8.027524 AGCTATCAACTAAATCTGGATCAGAA 57.972 34.615 1.53 0.00 44.04 3.02
1525 1554 7.067494 CCAAGAAGTAATAGGGGAATTGAACTG 59.933 40.741 0.00 0.00 0.00 3.16
1531 1560 9.813826 CAATATCCAAGAAGTAATAGGGGAATT 57.186 33.333 0.00 0.00 0.00 2.17
1560 1589 7.328982 TGCATTTCAGCACTATAAAAATGTGTG 59.671 33.333 7.66 0.00 40.11 3.82
1600 1629 2.785269 ACCCTTGCATCCTCATATTGGA 59.215 45.455 0.00 0.00 38.06 3.53
1618 1647 7.516198 AGATCAAAATGCATTAGACATACCC 57.484 36.000 13.39 0.00 0.00 3.69
1724 1753 5.008316 ACAAACAACGTACTTTGAATCCTCC 59.992 40.000 18.05 0.00 32.63 4.30
1739 1768 4.442733 ACACACAAGAACAAACAAACAACG 59.557 37.500 0.00 0.00 0.00 4.10
1768 1800 9.099454 CCATAAAACAGATACAACTAAGGAGAC 57.901 37.037 0.00 0.00 0.00 3.36
1769 1801 9.042450 TCCATAAAACAGATACAACTAAGGAGA 57.958 33.333 0.00 0.00 0.00 3.71
1770 1802 9.838339 ATCCATAAAACAGATACAACTAAGGAG 57.162 33.333 0.00 0.00 0.00 3.69
1909 1943 6.428385 TTCCTTACTAACTCGTGCTACTAC 57.572 41.667 0.00 0.00 0.00 2.73
1910 1944 7.452880 TTTTCCTTACTAACTCGTGCTACTA 57.547 36.000 0.00 0.00 0.00 1.82
1911 1945 5.972107 TTTCCTTACTAACTCGTGCTACT 57.028 39.130 0.00 0.00 0.00 2.57
1912 1946 6.035758 CCATTTTCCTTACTAACTCGTGCTAC 59.964 42.308 0.00 0.00 0.00 3.58
1913 1947 6.103997 CCATTTTCCTTACTAACTCGTGCTA 58.896 40.000 0.00 0.00 0.00 3.49
1914 1948 4.935808 CCATTTTCCTTACTAACTCGTGCT 59.064 41.667 0.00 0.00 0.00 4.40
1915 1949 4.694037 ACCATTTTCCTTACTAACTCGTGC 59.306 41.667 0.00 0.00 0.00 5.34
1916 1950 6.796705 AACCATTTTCCTTACTAACTCGTG 57.203 37.500 0.00 0.00 0.00 4.35
1917 1951 7.812690 AAAACCATTTTCCTTACTAACTCGT 57.187 32.000 0.00 0.00 0.00 4.18
1918 1952 7.114388 GCAAAAACCATTTTCCTTACTAACTCG 59.886 37.037 0.00 0.00 36.62 4.18
1964 2001 3.592059 TCGGCTTTCGCATAGTTTTAGT 58.408 40.909 0.00 0.00 39.05 2.24
1967 2004 3.907894 TTTCGGCTTTCGCATAGTTTT 57.092 38.095 0.00 0.00 39.05 2.43
1978 2015 3.006752 TGAATGCAATCCTTTTCGGCTTT 59.993 39.130 0.00 0.00 0.00 3.51
1979 2016 2.562298 TGAATGCAATCCTTTTCGGCTT 59.438 40.909 0.00 0.00 0.00 4.35
2002 2039 8.203681 ACCTAACAAATAGAAGGACACTAAGT 57.796 34.615 0.00 0.00 33.04 2.24
2026 2063 4.492409 GCACAGCAGCAAACAAAAAGTAAC 60.492 41.667 0.00 0.00 0.00 2.50
2196 2233 7.445945 GTTATATCCAAGTGCATTAGGAGAGT 58.554 38.462 9.39 2.27 32.91 3.24
2238 2275 3.634397 TTAAGGCTTCACAGATGGAGG 57.366 47.619 1.30 0.00 31.11 4.30
2261 2298 8.617809 GTTGACAATACAGAAAGGAGTTTAACA 58.382 33.333 0.00 0.00 0.00 2.41
2471 2523 9.730705 ACTCTTTCACAATTAGATTCTTCATCA 57.269 29.630 0.00 0.00 33.75 3.07
2540 2592 4.948004 TCAGCTCTCTCATTGCATTTGAAT 59.052 37.500 0.00 0.00 0.00 2.57
2855 2908 3.619233 TTCAAACTTTTCCGTAGCTGC 57.381 42.857 0.00 0.00 0.00 5.25
2928 2981 4.969484 ACGGTTACCTTCTTCAACTCAAT 58.031 39.130 0.00 0.00 0.00 2.57
2996 3049 4.328983 GCGACCGATTCAGTTCTTAATTCA 59.671 41.667 0.00 0.00 0.00 2.57
3104 3157 6.404293 GCAAGACTTAAGTTTCCACAAGACAA 60.404 38.462 10.02 0.00 0.00 3.18
3201 3254 6.336566 TCTTACTAGAAGAATGCAGAAGCTG 58.663 40.000 0.00 0.00 42.74 4.24
3203 3256 7.209475 AGATCTTACTAGAAGAATGCAGAAGC 58.791 38.462 0.00 0.00 36.05 3.86
3231 3284 9.485206 CACAATTTAGGTGTAGTAAGTGTAGTT 57.515 33.333 0.00 0.00 0.00 2.24
3314 3367 1.228124 TCCCGGCTGTCTTTTGTGG 60.228 57.895 0.00 0.00 0.00 4.17
3334 3387 2.897207 CCATGCAACCCAGCCATG 59.103 61.111 0.00 0.00 0.00 3.66
3669 3730 3.438781 AGAAAATAATGCTTTCGGCGTGA 59.561 39.130 6.85 0.00 45.43 4.35
3681 3742 7.545362 ACTGCACTAGCTACAGAAAATAATG 57.455 36.000 14.84 0.00 42.74 1.90
3683 3744 6.934645 ACAACTGCACTAGCTACAGAAAATAA 59.065 34.615 14.84 0.00 42.74 1.40
3823 3884 3.550437 ATAGTGGCAAGAGACATGGAC 57.450 47.619 0.00 0.00 33.47 4.02
3869 3930 9.918630 CAAACTCATCAAAGAGGTAAATCAAAT 57.081 29.630 0.00 0.00 39.97 2.32
3870 3931 8.912988 ACAAACTCATCAAAGAGGTAAATCAAA 58.087 29.630 0.00 0.00 39.97 2.69
3894 3961 0.478072 AGGGATGGTCAACTTGCACA 59.522 50.000 0.00 0.00 0.00 4.57
4013 4081 6.620678 AGCATTACATGTTGCGAGTTAAAAT 58.379 32.000 15.08 0.00 43.61 1.82
4075 4151 3.553096 GGACCTACGATGAATAGCAGTGG 60.553 52.174 0.00 0.00 0.00 4.00
4076 4152 3.553096 GGGACCTACGATGAATAGCAGTG 60.553 52.174 0.00 0.00 0.00 3.66
4147 4223 0.108396 TTACTGCTGTGCCTGCTGAA 59.892 50.000 6.48 0.00 33.23 3.02
4442 4521 3.728845 CTTTCCGAAAGACTGGACTCAA 58.271 45.455 14.72 0.00 41.02 3.02
4443 4522 2.548067 GCTTTCCGAAAGACTGGACTCA 60.548 50.000 22.55 0.00 41.02 3.41
4483 4562 3.256383 TGACAAAAATGCAGACATGGGAG 59.744 43.478 0.00 0.00 36.36 4.30
4504 4583 4.522789 AGCCACAAGTTTACTACCCAAATG 59.477 41.667 0.00 0.00 0.00 2.32
4689 4768 1.149148 GAAAAAGAAGTCTCGCGGCT 58.851 50.000 6.13 0.00 0.00 5.52
4691 4770 1.461127 CAGGAAAAAGAAGTCTCGCGG 59.539 52.381 6.13 0.00 0.00 6.46
4707 4786 2.978156 AAGGGAAAACTCATGCAGGA 57.022 45.000 0.00 0.00 0.00 3.86
4710 4789 4.895297 AGAAGAAAAGGGAAAACTCATGCA 59.105 37.500 0.00 0.00 0.00 3.96
4716 4795 7.093509 TGCAGTAAAAGAAGAAAAGGGAAAACT 60.094 33.333 0.00 0.00 0.00 2.66
4727 4806 7.201600 GGCACAAATTTTGCAGTAAAAGAAGAA 60.202 33.333 19.78 0.00 41.26 2.52
4750 4829 4.567971 CCAAGTTCATAGCAAAATTGGCA 58.432 39.130 0.00 0.00 42.68 4.92
4761 4840 4.456911 ACACTGAATGCACCAAGTTCATAG 59.543 41.667 0.39 0.23 32.05 2.23
4762 4841 4.397420 ACACTGAATGCACCAAGTTCATA 58.603 39.130 0.39 0.00 32.05 2.15
4887 4966 4.118093 TCCTGATAACATGGTGTACGTG 57.882 45.455 0.00 0.00 41.98 4.49
4890 4969 6.823689 AGAATGTTCCTGATAACATGGTGTAC 59.176 38.462 0.00 0.00 46.72 2.90
4925 5375 3.676049 GCCTAATAAGGTTTTGCTGTGCC 60.676 47.826 0.00 0.00 45.64 5.01
5075 5574 4.704103 ACAGCGGCCTCTGAGGGA 62.704 66.667 29.09 0.00 35.37 4.20
5078 5577 1.227205 GATCACAGCGGCCTCTGAG 60.227 63.158 29.09 21.09 37.51 3.35
5079 5578 2.895680 GATCACAGCGGCCTCTGA 59.104 61.111 29.09 8.51 37.51 3.27
5081 5580 3.071206 ACGATCACAGCGGCCTCT 61.071 61.111 0.00 0.00 0.00 3.69
5083 5582 4.457496 CCACGATCACAGCGGCCT 62.457 66.667 0.00 0.00 0.00 5.19
5086 5585 2.512286 ATGCCACGATCACAGCGG 60.512 61.111 0.00 0.00 0.00 5.52
5087 5586 2.028766 GACATGCCACGATCACAGCG 62.029 60.000 0.00 0.00 0.00 5.18
5089 5588 2.001357 CGACATGCCACGATCACAG 58.999 57.895 0.00 0.00 0.00 3.66
5090 5589 2.100031 GCGACATGCCACGATCACA 61.100 57.895 10.79 0.00 37.76 3.58
5132 5635 8.644216 TCAATCTCACTACCAGTAAACAAACTA 58.356 33.333 0.00 0.00 0.00 2.24
5173 5676 1.459158 ATCCTCCATCAGAGCGGCT 60.459 57.895 0.00 0.00 41.74 5.52
5249 5752 4.194720 CGCCGAGGAGGAAGACGG 62.195 72.222 0.00 0.00 45.00 4.79
5321 5824 0.166814 GGCATGCGTGACAGTTTCTC 59.833 55.000 12.44 0.00 31.88 2.87
5327 5830 2.132517 TTGCTTGGCATGCGTGACAG 62.133 55.000 15.46 10.42 46.01 3.51
5372 5876 1.064758 ACTGGTCAGTCAGCCAAACAA 60.065 47.619 0.00 0.00 36.92 2.83
5374 5878 3.403936 ACTGGTCAGTCAGCCAAAC 57.596 52.632 0.00 0.00 36.92 2.93


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

AutoCloner maintained by Alex Coulton.