Multiple sequence alignment - TraesCS3B01G254800

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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 TraesCS3B01G254800 chr3B 100.000 6642 0 0 1 6642 411268252 411274893 0.000000e+00 12266
1 TraesCS3B01G254800 chr3A 94.798 6152 197 33 1 6091 422326916 422333005 0.000000e+00 9474
2 TraesCS3B01G254800 chr3A 87.810 525 31 18 6134 6642 422335805 422336312 9.600000e-163 584
3 TraesCS3B01G254800 chr3D 94.990 5928 185 35 1 5899 310004555 309998711 0.000000e+00 9199
4 TraesCS3B01G254800 chr3D 88.830 376 24 9 6272 6640 309997851 309997487 4.730000e-121 446
5 TraesCS3B01G254800 chr3D 87.543 289 31 2 192 475 310107605 310107317 4.970000e-86 329
6 TraesCS3B01G254800 chr3D 94.388 196 11 0 1 196 310117324 310117129 1.080000e-77 302
7 TraesCS3B01G254800 chr3D 95.122 123 6 0 5972 6094 309998590 309998468 1.890000e-45 195
8 TraesCS3B01G254800 chr5B 100.000 59 0 0 4970 5028 63274798 63274740 7.040000e-20 110


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 TraesCS3B01G254800 chr3B 411268252 411274893 6641 False 12266 12266 100.000000 1 6642 1 chr3B.!!$F1 6641
1 TraesCS3B01G254800 chr3A 422326916 422336312 9396 False 5029 9474 91.304000 1 6642 2 chr3A.!!$F1 6641
2 TraesCS3B01G254800 chr3D 309997487 310004555 7068 True 3280 9199 92.980667 1 6640 3 chr3D.!!$R3 6639

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
742 762 0.171231 GCAAAGAAATCCAGCCGTCC 59.829 55.000 0.00 0.0 0.00 4.79 F
1514 1538 0.403655 TCAACTTGCCCAGCCACATA 59.596 50.000 0.00 0.0 0.00 2.29 F
2262 2299 0.962356 AGGAGGATTTGTTGCGCCTG 60.962 55.000 4.18 0.0 44.26 4.85 F
2838 2875 0.248377 GCTGCGTTTCTCCATGCATC 60.248 55.000 0.00 0.0 38.04 3.91 F
4186 4251 2.093553 TGATGACATCGGAGCATTGACA 60.094 45.455 10.79 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 2279 0.618458 AGGCGCAACAAATCCTCCTA 59.382 50.000 10.83 0.00 0.00 2.94 R
2337 2374 3.902881 AGGCAGACTCTGTTAAGGATG 57.097 47.619 7.89 0.00 33.43 3.51 R
4228 4293 1.398692 TGAAAAGTTCAGGCCGCTTT 58.601 45.000 0.00 4.47 34.08 3.51 R
4264 4329 2.208872 AGTAGAATCCCCTTGCATGGT 58.791 47.619 16.81 0.00 0.00 3.55 R
6054 6194 0.109086 ATCTCAGCGACAACTCACGG 60.109 55.000 0.00 0.00 0.00 4.94 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
37 38 8.170730 AGGGAGTAAAGAAGGAAAATACACATT 58.829 33.333 0.00 0.00 0.00 2.71
44 45 6.681777 AGAAGGAAAATACACATTTCAGTGC 58.318 36.000 0.00 0.00 43.23 4.40
136 137 5.009210 GTCCCTTGTTGTATAGTTTGTTGCA 59.991 40.000 0.00 0.00 0.00 4.08
159 160 0.461548 GCACTCATCCTCGTCCATCA 59.538 55.000 0.00 0.00 0.00 3.07
178 179 1.080025 GCTCCCACTCCACGTGTAC 60.080 63.158 15.65 0.00 42.20 2.90
223 224 7.986085 ATCAAGTGTAGTTGCTCTTGTTAAT 57.014 32.000 10.36 0.00 39.54 1.40
224 225 7.189693 TCAAGTGTAGTTGCTCTTGTTAATG 57.810 36.000 10.36 0.00 39.54 1.90
226 227 5.621193 AGTGTAGTTGCTCTTGTTAATGGT 58.379 37.500 0.00 0.00 0.00 3.55
279 280 5.546621 ACAATATACGACATGCCCTACTT 57.453 39.130 0.00 0.00 0.00 2.24
289 290 3.824443 ACATGCCCTACTTTTAACGCTTT 59.176 39.130 0.00 0.00 0.00 3.51
309 311 7.639461 ACGCTTTGTTGCATTTCTTTTATTTTG 59.361 29.630 0.00 0.00 0.00 2.44
332 334 4.816385 GCGATGGACTCTTATTCAATTGGA 59.184 41.667 5.42 0.00 0.00 3.53
362 368 4.619973 CACACCATATGCACAAAAGTGTT 58.380 39.130 8.40 0.00 35.07 3.32
377 383 8.356657 CACAAAAGTGTTTAATAATCCAGGTCA 58.643 33.333 0.00 0.00 35.07 4.02
379 385 7.703058 AAAGTGTTTAATAATCCAGGTCAGG 57.297 36.000 0.00 0.00 0.00 3.86
380 386 6.636454 AGTGTTTAATAATCCAGGTCAGGA 57.364 37.500 0.00 0.00 43.01 3.86
382 388 7.643123 AGTGTTTAATAATCCAGGTCAGGAAT 58.357 34.615 0.00 0.00 41.92 3.01
384 390 8.406297 GTGTTTAATAATCCAGGTCAGGAATTC 58.594 37.037 0.00 0.00 41.92 2.17
385 391 8.336235 TGTTTAATAATCCAGGTCAGGAATTCT 58.664 33.333 5.23 0.00 41.92 2.40
386 392 9.847224 GTTTAATAATCCAGGTCAGGAATTCTA 57.153 33.333 5.23 0.00 41.92 2.10
397 404 6.708054 AGGTCAGGAATTCTAATTATCAAGCG 59.292 38.462 5.23 0.00 0.00 4.68
424 431 7.859325 TTTAGCGAAACTCTAAATATTGCCT 57.141 32.000 0.00 0.00 32.78 4.75
432 439 7.730364 AACTCTAAATATTGCCTTATGTCCG 57.270 36.000 0.00 0.00 0.00 4.79
435 442 4.568152 AAATATTGCCTTATGTCCGTGC 57.432 40.909 0.00 0.00 0.00 5.34
438 452 1.305219 TTGCCTTATGTCCGTGCTGC 61.305 55.000 0.00 0.00 0.00 5.25
450 464 2.164827 TCCGTGCTGCGAGAAACTATTA 59.835 45.455 2.97 0.00 44.77 0.98
476 490 8.954350 ACACTAGAAAAGAACGCTAATACTAGA 58.046 33.333 0.00 0.00 32.20 2.43
518 532 0.744874 CCGAGTACACCCATCGATGT 59.255 55.000 23.27 9.56 38.72 3.06
519 533 1.951602 CCGAGTACACCCATCGATGTA 59.048 52.381 23.27 8.51 38.72 2.29
529 543 0.984829 CATCGATGTATGCTACGCGG 59.015 55.000 17.50 0.00 32.39 6.46
605 623 2.642154 TAAAGTGGGGCGAGAAAACA 57.358 45.000 0.00 0.00 0.00 2.83
613 631 2.483106 GGGGCGAGAAAACAAGAGTAAC 59.517 50.000 0.00 0.00 0.00 2.50
645 663 3.194116 TCGGCTGTTAACTCTCCGTTAAT 59.806 43.478 22.96 0.00 46.49 1.40
688 708 5.207768 GTGCAATATTCCTCTGCATAAACG 58.792 41.667 2.53 0.00 46.90 3.60
742 762 0.171231 GCAAAGAAATCCAGCCGTCC 59.829 55.000 0.00 0.00 0.00 4.79
1313 1337 3.120889 CGATTAGTATACGACTTCGCGGA 60.121 47.826 6.13 0.00 44.43 5.54
1455 1479 1.524008 TTGCAGCGAGGAGACGAAGA 61.524 55.000 0.00 0.00 35.09 2.87
1496 1520 2.810439 ACGCCTATCTGAGCAAGATC 57.190 50.000 5.28 0.00 42.27 2.75
1514 1538 0.403655 TCAACTTGCCCAGCCACATA 59.596 50.000 0.00 0.00 0.00 2.29
1559 1583 3.866582 ATACTGCTCTGCGGCCCC 61.867 66.667 0.00 0.00 38.71 5.80
1870 1898 1.328279 GCAGTGCCCTGGTTAGTTTT 58.672 50.000 2.85 0.00 39.22 2.43
1889 1917 2.773993 TTTAATCCCGTCCTGTGTCC 57.226 50.000 0.00 0.00 0.00 4.02
1890 1918 1.946984 TTAATCCCGTCCTGTGTCCT 58.053 50.000 0.00 0.00 0.00 3.85
1909 1937 6.375455 GTGTCCTGTGATTGATAGGTTTCATT 59.625 38.462 0.00 0.00 34.50 2.57
1931 1959 8.358895 TCATTTTTCTGTGCTACATTTGATTGA 58.641 29.630 0.00 0.00 0.00 2.57
2045 2074 2.616842 GGTTGTGTGGACCTACTGTTTG 59.383 50.000 0.00 0.00 34.27 2.93
2047 2076 3.637911 TGTGTGGACCTACTGTTTGTT 57.362 42.857 0.00 0.00 0.00 2.83
2049 2078 5.100344 TGTGTGGACCTACTGTTTGTTTA 57.900 39.130 0.00 0.00 0.00 2.01
2050 2079 5.120399 TGTGTGGACCTACTGTTTGTTTAG 58.880 41.667 0.00 0.00 0.00 1.85
2054 2083 7.443272 GTGTGGACCTACTGTTTGTTTAGTTAT 59.557 37.037 0.00 0.00 0.00 1.89
2055 2084 8.649591 TGTGGACCTACTGTTTGTTTAGTTATA 58.350 33.333 0.00 0.00 0.00 0.98
2153 2190 2.817844 GCAAGTTAAAAGGGTCGACCAT 59.182 45.455 34.40 27.09 43.89 3.55
2259 2296 1.268743 GCATAGGAGGATTTGTTGCGC 60.269 52.381 0.00 0.00 0.00 6.09
2262 2299 0.962356 AGGAGGATTTGTTGCGCCTG 60.962 55.000 4.18 0.00 44.26 4.85
2281 2318 4.261614 GCCTGCTAGCTTGTAAAAACTTGT 60.262 41.667 17.23 0.00 0.00 3.16
2558 2595 9.667107 TCTTCCTATCAACTCGTTTTCATTATT 57.333 29.630 0.00 0.00 0.00 1.40
2709 2746 7.414098 CGAGGTAAAAACACATCTAATTGAGGG 60.414 40.741 0.00 0.00 0.00 4.30
2838 2875 0.248377 GCTGCGTTTCTCCATGCATC 60.248 55.000 0.00 0.00 38.04 3.91
2903 2940 3.678056 TTTCTCGTCACTTATGCCACT 57.322 42.857 0.00 0.00 0.00 4.00
2910 2947 4.081917 TCGTCACTTATGCCACTGTTCATA 60.082 41.667 0.00 0.00 0.00 2.15
2911 2948 4.629634 CGTCACTTATGCCACTGTTCATAA 59.370 41.667 10.16 10.16 34.90 1.90
2948 2985 2.724977 TTCGACGAGCTTCAGACAAT 57.275 45.000 0.00 0.00 0.00 2.71
3089 3152 4.154015 TGTGCCTTCTTGTGAATACGATTG 59.846 41.667 0.00 0.00 0.00 2.67
3236 3299 2.883574 CACCATCCACAACATTGCATC 58.116 47.619 0.00 0.00 0.00 3.91
3318 3381 6.268566 GTTTCTGAATGCAATCCAGTTATCC 58.731 40.000 0.00 0.00 0.00 2.59
3398 3461 6.531240 TGTTCAAGAAAATGTTGAGCAAACTC 59.469 34.615 4.69 0.00 40.75 3.01
3644 3707 6.056236 CAGTCTGATCTGTGATGATTTGGAT 58.944 40.000 0.00 0.00 0.00 3.41
3809 3874 9.586732 TTAGCTAATTTATTATCAGGCCATTGT 57.413 29.630 5.01 0.00 0.00 2.71
4003 4068 6.531021 AGGTAGGTATCCCATATTTTCAACG 58.469 40.000 0.00 0.00 0.00 4.10
4186 4251 2.093553 TGATGACATCGGAGCATTGACA 60.094 45.455 10.79 0.00 0.00 3.58
4228 4293 2.355108 GGAGCTTGTCATGCTTCCACTA 60.355 50.000 13.94 0.00 41.30 2.74
4264 4329 3.874383 TTCAATGGTGGTCTCCTGAAA 57.126 42.857 0.00 0.00 0.00 2.69
4723 4788 6.552725 TGATAACCTCTAGATGAGTTGCTGAT 59.447 38.462 11.31 0.53 41.11 2.90
4771 4837 2.108970 GTCGGTCTCCCTACTTTGGAT 58.891 52.381 0.00 0.00 0.00 3.41
4814 4880 4.469227 AGAAGCTGCTATCCAAAGAGAAGA 59.531 41.667 0.90 0.00 0.00 2.87
4916 4982 5.875224 TGAATCATTGGTGAAGTAGGAACA 58.125 37.500 0.00 0.00 38.01 3.18
4928 4994 7.224949 GGTGAAGTAGGAACAGTATATTCAAGC 59.775 40.741 0.00 0.00 0.00 4.01
5131 5197 6.582636 TCATATATCAAGTGTGTCTCCCAAC 58.417 40.000 0.00 0.00 0.00 3.77
5661 5729 1.110442 TGCAAGGTTGGGAGTTTGTG 58.890 50.000 0.00 0.00 0.00 3.33
5669 5737 5.887754 AGGTTGGGAGTTTGTGTATACATT 58.112 37.500 9.18 0.00 36.53 2.71
5730 5800 0.107945 ATGAAGCGGAGGAAGTGCTC 60.108 55.000 0.00 0.00 38.17 4.26
5736 5806 2.701780 GGAGGAAGTGCTCGCGAGA 61.702 63.158 38.74 20.88 39.12 4.04
5752 5822 3.117046 GCGAGAGATGTTTAGCTGTACC 58.883 50.000 0.00 0.00 0.00 3.34
5753 5823 3.707793 CGAGAGATGTTTAGCTGTACCC 58.292 50.000 0.00 0.00 0.00 3.69
5754 5824 3.130516 CGAGAGATGTTTAGCTGTACCCA 59.869 47.826 0.00 0.00 0.00 4.51
5755 5825 4.202161 CGAGAGATGTTTAGCTGTACCCAT 60.202 45.833 0.00 0.00 0.00 4.00
5756 5826 5.675538 GAGAGATGTTTAGCTGTACCCATT 58.324 41.667 0.00 0.00 0.00 3.16
5757 5827 5.431765 AGAGATGTTTAGCTGTACCCATTG 58.568 41.667 0.00 0.00 0.00 2.82
5797 5867 7.894376 TGTTTAAATAGACCGGTCTTTGTAG 57.106 36.000 40.23 0.00 40.93 2.74
5859 5929 2.930950 TGTTGAACCTTGTTCTGGGAG 58.069 47.619 8.30 0.00 0.00 4.30
5862 5932 1.142870 TGAACCTTGTTCTGGGAGTGG 59.857 52.381 8.30 0.00 0.00 4.00
5875 5945 4.099573 TCTGGGAGTGGATCGATTAACTTC 59.900 45.833 13.32 11.65 0.00 3.01
5929 6069 3.485463 TGGTGAGAAGGTTTCGATTGT 57.515 42.857 0.00 0.00 34.02 2.71
6062 6202 2.083835 CTGACCGTCACCCGTGAGTT 62.084 60.000 0.00 0.00 40.75 3.01
6086 6226 1.862008 GCTGAGATGTTCCGTAGCTCG 60.862 57.143 0.00 0.00 33.46 5.03
6095 6235 3.111939 CGTAGCTCGGGAGTCAGG 58.888 66.667 0.00 0.00 35.71 3.86
6097 6237 1.440938 CGTAGCTCGGGAGTCAGGAG 61.441 65.000 0.00 5.54 35.71 3.69
6098 6238 0.394625 GTAGCTCGGGAGTCAGGAGT 60.395 60.000 10.33 2.50 0.00 3.85
6099 6239 1.134159 GTAGCTCGGGAGTCAGGAGTA 60.134 57.143 10.33 1.78 0.00 2.59
6101 6241 1.183549 GCTCGGGAGTCAGGAGTAAA 58.816 55.000 10.33 0.00 0.00 2.01
6102 6242 1.757699 GCTCGGGAGTCAGGAGTAAAT 59.242 52.381 10.33 0.00 0.00 1.40
6104 6244 3.004944 GCTCGGGAGTCAGGAGTAAATAG 59.995 52.174 10.33 0.00 0.00 1.73
6105 6245 2.957006 TCGGGAGTCAGGAGTAAATAGC 59.043 50.000 0.00 0.00 0.00 2.97
6106 6246 2.036089 CGGGAGTCAGGAGTAAATAGCC 59.964 54.545 0.00 0.00 0.00 3.93
6107 6247 3.039011 GGGAGTCAGGAGTAAATAGCCA 58.961 50.000 0.00 0.00 0.00 4.75
6108 6248 3.070302 GGGAGTCAGGAGTAAATAGCCAG 59.930 52.174 0.00 0.00 0.00 4.85
6109 6249 3.493524 GGAGTCAGGAGTAAATAGCCAGC 60.494 52.174 0.00 0.00 0.00 4.85
6110 6250 3.107601 AGTCAGGAGTAAATAGCCAGCA 58.892 45.455 0.00 0.00 0.00 4.41
6111 6251 3.519510 AGTCAGGAGTAAATAGCCAGCAA 59.480 43.478 0.00 0.00 0.00 3.91
6112 6252 3.623510 GTCAGGAGTAAATAGCCAGCAAC 59.376 47.826 0.00 0.00 0.00 4.17
6114 6254 3.624861 CAGGAGTAAATAGCCAGCAACTG 59.375 47.826 0.00 0.00 0.00 3.16
6115 6255 2.356069 GGAGTAAATAGCCAGCAACTGC 59.644 50.000 0.00 0.00 42.49 4.40
6116 6256 2.356069 GAGTAAATAGCCAGCAACTGCC 59.644 50.000 0.00 0.00 43.38 4.85
6117 6257 2.091541 GTAAATAGCCAGCAACTGCCA 58.908 47.619 0.00 0.00 43.38 4.92
6118 6258 1.856629 AAATAGCCAGCAACTGCCAT 58.143 45.000 0.00 0.00 43.38 4.40
6121 6261 1.631405 TAGCCAGCAACTGCCATTTT 58.369 45.000 0.00 0.00 43.38 1.82
6122 6262 0.760572 AGCCAGCAACTGCCATTTTT 59.239 45.000 0.00 0.00 43.38 1.94
6162 9061 2.325082 CCCCAGCGAACGTTTCTGG 61.325 63.158 29.06 29.06 45.24 3.86
6254 9155 9.950496 ACTTCAAAAATATCACACAGAGATAGT 57.050 29.630 0.00 0.00 32.00 2.12
6266 9167 3.119101 ACAGAGATAGTAAACGCACCCTG 60.119 47.826 0.00 0.00 0.00 4.45
6325 9237 8.037758 ACACACACAGAAAAACCATAAAAATGA 58.962 29.630 0.00 0.00 0.00 2.57
6326 9238 9.044150 CACACACAGAAAAACCATAAAAATGAT 57.956 29.630 0.00 0.00 0.00 2.45
6400 9312 2.715046 AGAAATGCCGATCAGAAGCAA 58.285 42.857 0.00 0.00 40.46 3.91
6433 9345 4.391523 CCGCGAAAAATGAAAAATCCCATT 59.608 37.500 8.23 0.00 34.75 3.16
6560 9482 6.795144 ATGCCATGATCCAATTAAAACTGA 57.205 33.333 0.00 0.00 0.00 3.41
6563 9485 5.807011 GCCATGATCCAATTAAAACTGACAC 59.193 40.000 0.00 0.00 0.00 3.67
6565 9487 6.128035 CCATGATCCAATTAAAACTGACACGA 60.128 38.462 0.00 0.00 0.00 4.35
6566 9488 6.236017 TGATCCAATTAAAACTGACACGAC 57.764 37.500 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.705441 AGATATTGAAACGGAAAGCACTGAA 59.295 36.000 0.00 0.00 0.00 3.02
44 45 7.116233 CCCACAAAAAGATATTGAAACGGAAAG 59.884 37.037 0.00 0.00 0.00 2.62
136 137 0.176680 GGACGAGGATGAGTGCACAT 59.823 55.000 21.04 4.26 0.00 3.21
200 201 6.204688 CCATTAACAAGAGCAACTACACTTGA 59.795 38.462 0.00 0.00 39.67 3.02
249 250 7.500892 AGGGCATGTCGTATATTGTTGAAAATA 59.499 33.333 0.00 0.00 0.00 1.40
272 273 3.978855 GCAACAAAGCGTTAAAAGTAGGG 59.021 43.478 0.00 0.00 35.52 3.53
279 280 6.654793 AAAGAAATGCAACAAAGCGTTAAA 57.345 29.167 0.00 0.00 42.56 1.52
289 290 6.834959 TCGCAAAATAAAAGAAATGCAACA 57.165 29.167 0.00 0.00 33.55 3.33
309 311 4.816385 TCCAATTGAATAAGAGTCCATCGC 59.184 41.667 7.12 0.00 0.00 4.58
358 364 7.881775 ATTCCTGACCTGGATTATTAAACAC 57.118 36.000 0.00 0.00 35.83 3.32
380 386 9.599322 CGCTAAATTCGCTTGATAATTAGAATT 57.401 29.630 3.50 3.50 39.19 2.17
382 388 8.360325 TCGCTAAATTCGCTTGATAATTAGAA 57.640 30.769 0.00 0.00 0.00 2.10
384 390 8.883168 GTTTCGCTAAATTCGCTTGATAATTAG 58.117 33.333 0.00 0.00 0.00 1.73
385 391 8.609176 AGTTTCGCTAAATTCGCTTGATAATTA 58.391 29.630 0.00 0.00 0.00 1.40
386 392 7.472543 AGTTTCGCTAAATTCGCTTGATAATT 58.527 30.769 0.00 0.00 0.00 1.40
397 404 9.170584 GGCAATATTTAGAGTTTCGCTAAATTC 57.829 33.333 18.04 0.00 41.25 2.17
424 431 0.245266 TTCTCGCAGCACGGACATAA 59.755 50.000 0.00 0.00 43.89 1.90
432 439 3.927142 AGTGTAATAGTTTCTCGCAGCAC 59.073 43.478 0.00 0.00 0.00 4.40
435 442 8.462143 TTTTCTAGTGTAATAGTTTCTCGCAG 57.538 34.615 0.00 0.00 0.00 5.18
450 464 8.954350 TCTAGTATTAGCGTTCTTTTCTAGTGT 58.046 33.333 0.00 0.00 0.00 3.55
476 490 1.956477 GACTGCACAAGGACCACATTT 59.044 47.619 0.00 0.00 0.00 2.32
529 543 1.577328 CGCACCTGACAATCCACACC 61.577 60.000 0.00 0.00 0.00 4.16
605 623 5.347907 CAGCCGAATAGAAAACGTTACTCTT 59.652 40.000 15.66 10.58 0.00 2.85
613 631 5.347907 AGAGTTAACAGCCGAATAGAAAACG 59.652 40.000 8.61 0.00 0.00 3.60
623 641 0.963962 AACGGAGAGTTAACAGCCGA 59.036 50.000 28.59 0.00 44.43 5.54
645 663 3.079578 ACGTTCATCTACTGACGGAAGA 58.920 45.455 0.00 0.00 34.67 2.87
688 708 3.083600 CTCGGCATCGCAAACCGTC 62.084 63.158 0.00 0.00 46.92 4.79
1496 1520 0.527565 GTATGTGGCTGGGCAAGTTG 59.472 55.000 0.00 0.00 0.00 3.16
1870 1898 2.027561 CAGGACACAGGACGGGATTAAA 60.028 50.000 0.00 0.00 0.00 1.52
1884 1912 5.245531 TGAAACCTATCAATCACAGGACAC 58.754 41.667 0.00 0.00 33.44 3.67
1885 1913 5.497464 TGAAACCTATCAATCACAGGACA 57.503 39.130 0.00 0.00 33.44 4.02
1886 1914 7.396540 AAATGAAACCTATCAATCACAGGAC 57.603 36.000 0.00 0.00 33.44 3.85
1887 1915 8.421249 AAAAATGAAACCTATCAATCACAGGA 57.579 30.769 0.00 0.00 33.44 3.86
1888 1916 8.526147 AGAAAAATGAAACCTATCAATCACAGG 58.474 33.333 0.00 0.00 32.06 4.00
1889 1917 9.350357 CAGAAAAATGAAACCTATCAATCACAG 57.650 33.333 0.00 0.00 32.06 3.66
1890 1918 8.859090 ACAGAAAAATGAAACCTATCAATCACA 58.141 29.630 0.00 0.00 32.06 3.58
1931 1959 5.896073 ATTCTCTCCGTCCCTCAAAATAT 57.104 39.130 0.00 0.00 0.00 1.28
2045 2074 9.445878 GGGGCCTCAATACTATTATAACTAAAC 57.554 37.037 0.84 0.00 0.00 2.01
2047 2076 8.822805 CAGGGGCCTCAATACTATTATAACTAA 58.177 37.037 4.79 0.00 0.00 2.24
2049 2078 6.296489 GCAGGGGCCTCAATACTATTATAACT 60.296 42.308 4.79 0.00 0.00 2.24
2050 2079 5.880887 GCAGGGGCCTCAATACTATTATAAC 59.119 44.000 4.79 0.00 0.00 1.89
2055 2084 2.959465 GCAGGGGCCTCAATACTATT 57.041 50.000 4.79 0.00 0.00 1.73
2242 2279 0.618458 AGGCGCAACAAATCCTCCTA 59.382 50.000 10.83 0.00 0.00 2.94
2259 2296 5.438761 ACAAGTTTTTACAAGCTAGCAGG 57.561 39.130 18.83 10.84 0.00 4.85
2281 2318 6.666113 TCGGTAAGATGGTAGCCATATGAATA 59.334 38.462 3.65 0.00 45.26 1.75
2337 2374 3.902881 AGGCAGACTCTGTTAAGGATG 57.097 47.619 7.89 0.00 33.43 3.51
2910 2947 6.963242 CGTCGAATCATTTGATCAATCAACTT 59.037 34.615 9.40 0.08 45.63 2.66
2911 2948 6.313658 TCGTCGAATCATTTGATCAATCAACT 59.686 34.615 9.40 0.00 45.63 3.16
2948 2985 6.015918 ACCATAAATCAATGAGGGTGTTTGA 58.984 36.000 0.00 0.00 34.18 2.69
3236 3299 4.987285 AGCTCATCAGTCATAACATAAGCG 59.013 41.667 0.00 0.00 0.00 4.68
3644 3707 8.421002 TGTAAATCGTCATCTGGATCTAATGAA 58.579 33.333 6.74 0.00 31.61 2.57
3809 3874 4.220821 CGCCCTAGATAGCTGGAGATAAAA 59.779 45.833 0.00 0.00 0.00 1.52
4186 4251 7.344352 AGCTCCTGAAGTGACTCTTTTATATCT 59.656 37.037 0.00 0.00 36.40 1.98
4228 4293 1.398692 TGAAAAGTTCAGGCCGCTTT 58.601 45.000 0.00 4.47 34.08 3.51
4264 4329 2.208872 AGTAGAATCCCCTTGCATGGT 58.791 47.619 16.81 0.00 0.00 3.55
4453 4518 5.357032 GTCCACCTCATCCACGAAAATAATT 59.643 40.000 0.00 0.00 0.00 1.40
4696 4761 6.700960 CAGCAACTCATCTAGAGGTTATCAAG 59.299 42.308 4.02 0.00 43.38 3.02
4702 4767 4.469227 ACATCAGCAACTCATCTAGAGGTT 59.531 41.667 4.02 3.79 43.38 3.50
4723 4788 9.814899 ATTATTCTGTTTGAAAAACATGACACA 57.185 25.926 0.00 0.00 38.29 3.72
4771 4837 8.589338 AGCTTCTTCAAAATCAACTCTCTACTA 58.411 33.333 0.00 0.00 0.00 1.82
4814 4880 9.454859 CTCCTTAAAGTCAATACCTTCTTCAAT 57.545 33.333 0.00 0.00 0.00 2.57
4916 4982 7.890515 TCAGAGAATGATCGCTTGAATATACT 58.109 34.615 0.00 0.00 32.96 2.12
4928 4994 7.379262 CAGTTCTAGTCATTCAGAGAATGATCG 59.621 40.741 21.19 13.99 38.71 3.69
5102 5168 9.125026 GGGAGACACACTTGATATATGAAAAAT 57.875 33.333 0.00 0.00 0.00 1.82
5131 5197 1.933500 GCATGTGTTTGCAGGCTTCAG 60.934 52.381 0.00 0.00 42.14 3.02
5462 5529 4.008330 GGGTGAAAAGGTTTAGACTAGCC 58.992 47.826 0.00 0.00 0.00 3.93
5661 5729 6.352682 TCAACCGCACATACAAATGTATAC 57.647 37.500 5.78 0.00 44.70 1.47
5669 5737 3.142174 TCACATTCAACCGCACATACAA 58.858 40.909 0.00 0.00 0.00 2.41
5730 5800 1.914634 ACAGCTAAACATCTCTCGCG 58.085 50.000 0.00 0.00 0.00 5.87
5736 5806 3.947834 GCAATGGGTACAGCTAAACATCT 59.052 43.478 0.00 0.00 0.00 2.90
5797 5867 8.655970 GGGATTTTCACAACAACTATTATTTGC 58.344 33.333 0.00 0.00 0.00 3.68
5875 5945 6.531948 CCACTCTAGGAATTCTAACAAGTTCG 59.468 42.308 5.23 0.00 0.00 3.95
6054 6194 0.109086 ATCTCAGCGACAACTCACGG 60.109 55.000 0.00 0.00 0.00 4.94
6062 6202 1.132453 CTACGGAACATCTCAGCGACA 59.868 52.381 0.00 0.00 0.00 4.35
6086 6226 3.039011 TGGCTATTTACTCCTGACTCCC 58.961 50.000 0.00 0.00 0.00 4.30
6091 6231 3.519510 AGTTGCTGGCTATTTACTCCTGA 59.480 43.478 0.00 0.00 0.00 3.86
6094 6234 2.356069 GCAGTTGCTGGCTATTTACTCC 59.644 50.000 0.00 0.00 38.21 3.85
6095 6235 3.682372 GCAGTTGCTGGCTATTTACTC 57.318 47.619 0.00 0.00 38.21 2.59
6125 6265 2.558800 GGGGTGGGCTAATCCTCAAAAA 60.559 50.000 0.00 0.00 34.39 1.94
6126 6266 1.006639 GGGGTGGGCTAATCCTCAAAA 59.993 52.381 0.00 0.00 34.39 2.44
6127 6267 0.629058 GGGGTGGGCTAATCCTCAAA 59.371 55.000 0.00 0.00 34.39 2.69
6128 6268 1.286305 GGGGGTGGGCTAATCCTCAA 61.286 60.000 0.00 0.00 34.39 3.02
6129 6269 1.696314 GGGGGTGGGCTAATCCTCA 60.696 63.158 0.00 0.00 34.39 3.86
6131 6271 1.697754 CTGGGGGTGGGCTAATCCT 60.698 63.158 0.00 0.00 34.39 3.24
6132 6272 2.927056 CTGGGGGTGGGCTAATCC 59.073 66.667 0.00 0.00 0.00 3.01
6133 6273 2.195956 GCTGGGGGTGGGCTAATC 59.804 66.667 0.00 0.00 0.00 1.75
6140 6280 4.636435 AACGTTCGCTGGGGGTGG 62.636 66.667 0.00 0.00 0.00 4.61
6141 6281 2.593436 AAACGTTCGCTGGGGGTG 60.593 61.111 0.00 0.00 0.00 4.61
6142 6282 2.281276 GAAACGTTCGCTGGGGGT 60.281 61.111 0.00 0.00 0.00 4.95
6143 6283 2.032071 AGAAACGTTCGCTGGGGG 59.968 61.111 0.00 0.00 34.02 5.40
6144 6284 2.325082 CCAGAAACGTTCGCTGGGG 61.325 63.158 29.03 14.21 44.24 4.96
6162 9061 2.118294 AGGAAAAGGCCTGGGTGC 59.882 61.111 5.69 0.00 36.76 5.01
6245 9146 3.130516 TCAGGGTGCGTTTACTATCTCTG 59.869 47.826 0.00 0.00 0.00 3.35
6246 9147 3.362706 TCAGGGTGCGTTTACTATCTCT 58.637 45.455 0.00 0.00 0.00 3.10
6247 9148 3.795623 TCAGGGTGCGTTTACTATCTC 57.204 47.619 0.00 0.00 0.00 2.75
6254 9155 0.037590 ATGGCTTCAGGGTGCGTTTA 59.962 50.000 0.00 0.00 0.00 2.01
6257 9158 0.827507 AAAATGGCTTCAGGGTGCGT 60.828 50.000 0.00 0.00 0.00 5.24
6258 9159 0.388907 CAAAATGGCTTCAGGGTGCG 60.389 55.000 0.00 0.00 0.00 5.34
6366 9278 5.233476 TCGGCATTTCTATCGTTGTGTTATC 59.767 40.000 0.00 0.00 0.00 1.75
6367 9279 5.113383 TCGGCATTTCTATCGTTGTGTTAT 58.887 37.500 0.00 0.00 0.00 1.89
6368 9280 4.496360 TCGGCATTTCTATCGTTGTGTTA 58.504 39.130 0.00 0.00 0.00 2.41
6375 9287 4.302455 CTTCTGATCGGCATTTCTATCGT 58.698 43.478 0.00 0.00 0.00 3.73
6376 9288 3.122613 GCTTCTGATCGGCATTTCTATCG 59.877 47.826 0.00 0.00 0.00 2.92
6406 9318 2.058913 TTTTCATTTTTCGCGGGCTC 57.941 45.000 6.13 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.