Multiple sequence alignment - TraesCS3B01G248600

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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 TraesCS3B01G248600 chr3B 100.000 7773 0 0 1 7773 396269473 396277245 0.000000e+00 14355.0
1 TraesCS3B01G248600 chr3B 100.000 65 0 0 7481 7545 396276888 396276952 3.810000e-23 121.0
2 TraesCS3B01G248600 chr3B 100.000 65 0 0 7416 7480 396276953 396277017 3.810000e-23 121.0
3 TraesCS3B01G248600 chr3B 89.011 91 5 3 7107 7194 603571700 603571788 2.970000e-19 108.0
4 TraesCS3B01G248600 chr3B 87.059 85 8 1 7108 7189 113517657 113517573 8.300000e-15 93.5
5 TraesCS3B01G248600 chr3D 97.863 6457 105 16 715 7148 322433600 322440046 0.000000e+00 11129.0
6 TraesCS3B01G248600 chr3D 81.774 620 71 18 15 624 322432919 322433506 1.520000e-131 481.0
7 TraesCS3B01G248600 chr3D 95.618 251 5 3 7215 7465 322440037 322440281 1.570000e-106 398.0
8 TraesCS3B01G248600 chr3D 92.251 271 8 3 7481 7743 322440233 322440498 9.530000e-99 372.0
9 TraesCS3B01G248600 chr3D 97.917 48 1 0 673 720 322433524 322433571 5.000000e-12 84.2
10 TraesCS3B01G248600 chr3D 92.857 42 3 0 7731 7772 322441529 322441570 2.340000e-05 62.1
11 TraesCS3B01G248600 chr3A 94.277 4735 179 28 1870 6563 401027275 401022592 0.000000e+00 7158.0
12 TraesCS3B01G248600 chr3A 93.263 1900 98 17 1 1878 401029695 401027804 0.000000e+00 2772.0
13 TraesCS3B01G248600 chr3A 91.971 548 28 11 6927 7465 401019947 401019407 0.000000e+00 754.0
14 TraesCS3B01G248600 chr3A 95.415 349 12 2 6571 6916 401020345 401019998 3.170000e-153 553.0
15 TraesCS3B01G248600 chr3A 89.873 158 14 2 7530 7687 401018309 401018154 1.320000e-47 202.0
16 TraesCS3B01G248600 chr3A 96.226 106 4 0 7668 7773 401018034 401017929 2.880000e-39 174.0
17 TraesCS3B01G248600 chr3A 92.941 85 2 4 7108 7189 599793103 599793020 3.810000e-23 121.0
18 TraesCS3B01G248600 chr3A 87.059 85 7 2 7108 7189 401019679 401019762 8.300000e-15 93.5
19 TraesCS3B01G248600 chr3A 84.615 91 9 3 7107 7194 599793019 599793107 1.390000e-12 86.1
20 TraesCS3B01G248600 chr2D 94.545 165 9 0 2403 2567 79056163 79056327 1.000000e-63 255.0
21 TraesCS3B01G248600 chr2A 93.939 165 10 0 2403 2567 79316001 79316165 4.660000e-62 250.0
22 TraesCS3B01G248600 chr2A 87.059 85 8 1 7107 7188 102688040 102688124 8.300000e-15 93.5
23 TraesCS3B01G248600 chr4D 93.939 165 7 3 2404 2566 74079348 74079511 6.020000e-61 246.0
24 TraesCS3B01G248600 chr7B 92.814 167 12 0 2407 2573 505937314 505937480 7.790000e-60 243.0
25 TraesCS3B01G248600 chr6D 93.789 161 9 1 2400 2559 392273066 392273226 2.800000e-59 241.0
26 TraesCS3B01G248600 chr6D 93.789 161 9 1 2402 2561 410398437 410398277 2.800000e-59 241.0
27 TraesCS3B01G248600 chr5A 92.308 169 10 2 2397 2565 321920791 321920626 3.630000e-58 237.0
28 TraesCS3B01G248600 chr1B 84.158 101 12 2 7092 7189 658497414 658497513 2.310000e-15 95.3
29 TraesCS3B01G248600 chr6A 82.979 94 13 3 7099 7189 595581118 595581211 1.800000e-11 82.4


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 TraesCS3B01G248600 chr3B 396269473 396277245 7772 False 4865.666667 14355 100.000000 1 7773 3 chr3B.!!$F2 7772
1 TraesCS3B01G248600 chr3D 322432919 322441570 8651 False 2087.716667 11129 93.046667 15 7772 6 chr3D.!!$F1 7757
2 TraesCS3B01G248600 chr3A 401017929 401029695 11766 True 1935.500000 7158 93.504167 1 7773 6 chr3A.!!$R2 7772

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
948 996 1.154093 GGTGACTCGTCGAATGCGA 60.154 57.895 0.00 0.00 45.71 5.10 F
1070 1118 0.038892 CACTACAACGTACGTGCCCT 60.039 55.000 23.57 2.48 0.00 5.19 F
1368 1417 1.826054 CGGCCAACCTCAACCACAA 60.826 57.895 2.24 0.00 0.00 3.33 F
1893 2487 2.398588 TGGAGTCCTGAACTGTGAAGT 58.601 47.619 11.33 0.00 38.74 3.01 F
3016 3633 3.766591 TGTTTGTCTTTGTGTGGTGGAAT 59.233 39.130 0.00 0.00 0.00 3.01 F
4022 4645 1.762957 TGCTCTTGGCTATCTACCACC 59.237 52.381 0.00 0.00 42.39 4.61 F
4398 5040 5.273674 TCATGCAGTTGAATTTGTTTGGA 57.726 34.783 0.00 0.00 0.00 3.53 F
5345 5987 2.125952 CGTCTGCTGATGCACGGA 60.126 61.111 0.00 0.00 45.31 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 2487 2.158769 AGCACATCAACTGGAACTGTCA 60.159 45.455 0.00 0.0 40.38 3.58 R
2212 2806 2.237143 CCACCAGCTGATCTCTAAACCA 59.763 50.000 17.39 0.0 0.00 3.67 R
3251 3869 2.071778 AGCAGAAGCACCCAAAAGAA 57.928 45.000 0.00 0.0 45.49 2.52 R
3569 4191 1.327303 TTGGCTTGTTGTGGATGGAC 58.673 50.000 0.00 0.0 0.00 4.02 R
4252 4891 0.106519 GGGCTCTGGGCAACATACAT 60.107 55.000 0.21 0.0 44.01 2.29 R
4906 5548 1.270826 TCTTCAGAGGAGCTGTCAACG 59.729 52.381 0.00 0.0 45.14 4.10 R
5927 6569 2.741228 GCACAACTTGCCCAAATGTTCA 60.741 45.455 0.00 0.0 46.63 3.18 R
6836 9723 2.291605 TGAGGCTTCTGCTAGGTAGTCA 60.292 50.000 0.00 0.0 39.59 3.41 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
55 56 1.832167 GAGAGGAGGAGCGAGGCAT 60.832 63.158 0.00 0.00 0.00 4.40
107 117 2.809174 CAACCGATGTCGCGCTGA 60.809 61.111 5.56 1.08 38.18 4.26
143 153 2.597217 CCAAAGCCAAGGCACCGA 60.597 61.111 14.40 0.00 44.88 4.69
164 174 2.190578 CCTTCTCCATGGACGGGC 59.809 66.667 11.44 0.00 0.00 6.13
187 197 3.703127 GGAAAGACCGCGGGGAGT 61.703 66.667 31.76 12.14 36.97 3.85
277 287 2.360483 GACTCGAGCAGATGGATCTCAA 59.640 50.000 13.61 0.00 34.22 3.02
280 290 2.762887 TCGAGCAGATGGATCTCAAAGT 59.237 45.455 0.00 0.00 34.22 2.66
285 295 3.607741 CAGATGGATCTCAAAGTGCAGT 58.392 45.455 0.00 0.00 34.22 4.40
486 500 4.433194 GGGCTAGGGAGGGTGGGT 62.433 72.222 0.00 0.00 0.00 4.51
614 628 2.212900 GATGGACGGGCAAAAGCACC 62.213 60.000 0.00 0.00 0.00 5.01
630 644 7.282916 CAAAAGCACCGATGACTTTATTTTTG 58.717 34.615 0.49 0.00 33.69 2.44
633 647 7.209471 AGCACCGATGACTTTATTTTTGTTA 57.791 32.000 0.00 0.00 0.00 2.41
634 648 7.826690 AGCACCGATGACTTTATTTTTGTTAT 58.173 30.769 0.00 0.00 0.00 1.89
635 649 8.952278 AGCACCGATGACTTTATTTTTGTTATA 58.048 29.630 0.00 0.00 0.00 0.98
636 650 9.006215 GCACCGATGACTTTATTTTTGTTATAC 57.994 33.333 0.00 0.00 0.00 1.47
948 996 1.154093 GGTGACTCGTCGAATGCGA 60.154 57.895 0.00 0.00 45.71 5.10
1008 1056 1.862602 GACCAAAAGGGATGCGCGTT 61.863 55.000 8.43 0.00 41.15 4.84
1070 1118 0.038892 CACTACAACGTACGTGCCCT 60.039 55.000 23.57 2.48 0.00 5.19
1114 1162 2.661176 TCCCTGACATCTAAACCCCT 57.339 50.000 0.00 0.00 0.00 4.79
1117 1166 3.265995 TCCCTGACATCTAAACCCCTTTC 59.734 47.826 0.00 0.00 0.00 2.62
1126 1175 2.677542 AAACCCCTTTCACCCTTCTC 57.322 50.000 0.00 0.00 0.00 2.87
1368 1417 1.826054 CGGCCAACCTCAACCACAA 60.826 57.895 2.24 0.00 0.00 3.33
1633 1688 2.593468 GAAGCTGCCACCTCGCCATA 62.593 60.000 0.00 0.00 0.00 2.74
1693 1748 4.382457 CAGCAATGTGTTGTAAAACCATCG 59.618 41.667 0.00 0.00 37.65 3.84
1893 2487 2.398588 TGGAGTCCTGAACTGTGAAGT 58.601 47.619 11.33 0.00 38.74 3.01
2038 2632 8.078060 TGTGTGTGAGATCCTCATTATTCTTA 57.922 34.615 0.00 0.00 42.73 2.10
2113 2707 4.238514 CAGAGAGGTTTAAGGTTCTGTCG 58.761 47.826 0.00 0.00 0.00 4.35
2212 2806 4.163458 TGGAACTGGCGTAAGAATAGGATT 59.837 41.667 0.00 0.00 43.02 3.01
2339 2933 4.154918 GCAAACTCAAGTCATGGTAAGGAG 59.845 45.833 0.00 0.00 0.00 3.69
2794 3410 6.438259 TTTCATTTACAGTGTTCACGGAAA 57.562 33.333 0.00 3.63 0.00 3.13
2819 3435 7.686438 TGACTGAAATATGTGTAGCATTTGT 57.314 32.000 0.00 0.00 38.94 2.83
2828 3444 5.981088 TGTGTAGCATTTGTGGAATTGAT 57.019 34.783 0.00 0.00 0.00 2.57
2832 3448 7.714377 TGTGTAGCATTTGTGGAATTGATTTTT 59.286 29.630 0.00 0.00 0.00 1.94
3016 3633 3.766591 TGTTTGTCTTTGTGTGGTGGAAT 59.233 39.130 0.00 0.00 0.00 3.01
3031 3648 8.827677 GTGTGGTGGAATATTTTATCTACTGTC 58.172 37.037 0.00 0.00 0.00 3.51
3035 3652 8.548721 GGTGGAATATTTTATCTACTGTCGTTG 58.451 37.037 0.00 0.00 0.00 4.10
3040 3657 8.873215 ATATTTTATCTACTGTCGTTGTCCAG 57.127 34.615 0.00 0.00 34.82 3.86
3235 3853 9.639563 TGAGTTTGAATTATGGGCAATTAGATA 57.360 29.630 0.00 0.00 0.00 1.98
3251 3869 9.154847 GCAATTAGATAAACATTTGAGCCTTTT 57.845 29.630 0.00 0.00 0.00 2.27
3569 4191 4.614946 CTTCTTTTTGTCTCAAAGCCCTG 58.385 43.478 0.00 0.00 32.17 4.45
3706 4328 7.890515 TGTGTCTTAATTTCATGTATTTGCCA 58.109 30.769 0.00 0.00 0.00 4.92
4022 4645 1.762957 TGCTCTTGGCTATCTACCACC 59.237 52.381 0.00 0.00 42.39 4.61
4312 4951 7.346751 TCAGAGCAAAAGGTAGAACAAATTT 57.653 32.000 0.00 0.00 0.00 1.82
4362 5004 7.558161 TGTTATATCATGGAGCTGAAACTTG 57.442 36.000 0.00 0.00 0.00 3.16
4398 5040 5.273674 TCATGCAGTTGAATTTGTTTGGA 57.726 34.783 0.00 0.00 0.00 3.53
4906 5548 3.041940 CGTGAAGACGGTGTGGCC 61.042 66.667 0.00 0.00 42.18 5.36
4961 5603 9.702494 GAGGAATCAAAGTTGAATCAAAAGAAT 57.298 29.630 10.46 0.00 41.13 2.40
5080 5722 3.827008 TCTGATGAACTATCTGGGTGC 57.173 47.619 0.00 0.00 36.71 5.01
5130 5772 7.451566 AGGTGTTAGCAGTAAGGATTCAAATTT 59.548 33.333 0.00 0.00 0.00 1.82
5134 5776 6.916360 AGCAGTAAGGATTCAAATTTCCAA 57.084 33.333 0.00 0.00 34.27 3.53
5240 5882 7.726291 TGAATGTATCAAAAGAAAACCCTGGTA 59.274 33.333 0.00 0.00 34.30 3.25
5328 5970 4.836825 TCCCATTTCAGTGATTCTCTGAC 58.163 43.478 15.99 0.00 40.90 3.51
5345 5987 2.125952 CGTCTGCTGATGCACGGA 60.126 61.111 0.00 0.00 45.31 4.69
5548 6190 3.405831 TCATGCTTGTTCTGTTGAGGAG 58.594 45.455 0.00 0.00 0.00 3.69
5683 6325 8.334632 CCAAAAATTTCAAATGGTTCACTACAC 58.665 33.333 0.00 0.00 0.00 2.90
6256 6901 6.606796 TGCCAATGACAACCTTGTAATATGAT 59.393 34.615 0.00 0.00 42.43 2.45
6563 7208 7.948447 TCTTACCATACAGGCATACACTATACT 59.052 37.037 0.00 0.00 43.14 2.12
6692 9579 7.710907 TGCTGTATCCTCATGACATTTTACTAC 59.289 37.037 0.00 0.00 0.00 2.73
6836 9723 0.108585 ACCCGCATGACAAGACAACT 59.891 50.000 0.00 0.00 0.00 3.16
6849 9736 4.021894 ACAAGACAACTGACTACCTAGCAG 60.022 45.833 0.00 0.00 35.24 4.24
6884 9771 8.299570 GGCGAAATAATCATATCCAGAACAATT 58.700 33.333 0.00 0.00 0.00 2.32
6987 9918 3.987547 TCGCCAGCATTTTCATTTTTCA 58.012 36.364 0.00 0.00 0.00 2.69
7034 9965 5.540337 AGACATAGGTCAAGTTTCTCAGTGA 59.460 40.000 10.58 0.00 46.80 3.41
7116 10047 7.021196 GCTTAGCTTAAGATGATACTCTCTCG 58.979 42.308 6.67 0.00 38.02 4.04
7198 10131 6.014327 TGTTACGGAGGGAGTAAGTTACAATT 60.014 38.462 15.28 0.00 35.09 2.32
7321 10254 6.036577 TGACTGACACTGCATTATGAAGTA 57.963 37.500 5.39 0.00 32.81 2.24
7322 10255 5.869344 TGACTGACACTGCATTATGAAGTAC 59.131 40.000 5.39 4.41 32.81 2.73
7323 10256 6.042638 ACTGACACTGCATTATGAAGTACT 57.957 37.500 5.39 0.00 32.81 2.73
7440 10373 5.989168 TGATGCTACATACACCCTTTATTCG 59.011 40.000 0.00 0.00 0.00 3.34
7446 10379 7.172703 GCTACATACACCCTTTATTCGCTAATT 59.827 37.037 0.00 0.00 0.00 1.40
7465 10398 7.201496 CGCTAATTGTACTATCAAAACGTCCTT 60.201 37.037 0.00 0.00 0.00 3.36
7466 10399 9.090692 GCTAATTGTACTATCAAAACGTCCTTA 57.909 33.333 0.00 0.00 0.00 2.69
7469 10402 7.878477 TTGTACTATCAAAACGTCCTTAGTG 57.122 36.000 0.00 0.00 0.00 2.74
7471 10404 7.660112 TGTACTATCAAAACGTCCTTAGTGAA 58.340 34.615 0.00 0.00 0.00 3.18
7472 10405 7.596248 TGTACTATCAAAACGTCCTTAGTGAAC 59.404 37.037 0.00 0.00 0.00 3.18
7475 10408 5.728351 TCAAAACGTCCTTAGTGAACAAG 57.272 39.130 0.00 0.00 0.00 3.16
7476 10409 4.573201 TCAAAACGTCCTTAGTGAACAAGG 59.427 41.667 0.00 0.00 43.40 3.61
7477 10410 3.832615 AACGTCCTTAGTGAACAAGGT 57.167 42.857 0.00 0.00 42.73 3.50
7478 10411 4.942761 AACGTCCTTAGTGAACAAGGTA 57.057 40.909 0.00 0.00 42.73 3.08
7482 10415 4.566987 GTCCTTAGTGAACAAGGTACCTG 58.433 47.826 17.14 12.24 42.73 4.00
7483 10416 4.282703 GTCCTTAGTGAACAAGGTACCTGA 59.717 45.833 17.14 0.11 42.73 3.86
7484 10417 5.046520 GTCCTTAGTGAACAAGGTACCTGAT 60.047 44.000 17.14 3.39 42.73 2.90
7485 10418 5.046591 TCCTTAGTGAACAAGGTACCTGATG 60.047 44.000 17.14 13.80 42.73 3.07
7486 10419 3.059352 AGTGAACAAGGTACCTGATGC 57.941 47.619 17.14 5.91 0.00 3.91
7487 10420 2.639839 AGTGAACAAGGTACCTGATGCT 59.360 45.455 17.14 1.59 0.00 3.79
7489 10422 3.933332 GTGAACAAGGTACCTGATGCTAC 59.067 47.826 17.14 7.40 0.00 3.58
7490 10423 3.580895 TGAACAAGGTACCTGATGCTACA 59.419 43.478 17.14 9.13 0.00 2.74
7491 10424 4.225042 TGAACAAGGTACCTGATGCTACAT 59.775 41.667 17.14 0.00 0.00 2.29
7492 10425 5.423931 TGAACAAGGTACCTGATGCTACATA 59.576 40.000 17.14 0.00 0.00 2.29
7493 10426 5.277857 ACAAGGTACCTGATGCTACATAC 57.722 43.478 17.14 0.00 0.00 2.39
7495 10428 4.939052 AGGTACCTGATGCTACATACAC 57.061 45.455 15.42 0.00 0.00 2.90
7496 10429 3.641906 AGGTACCTGATGCTACATACACC 59.358 47.826 15.42 0.00 0.00 4.16
7497 10430 3.244112 GGTACCTGATGCTACATACACCC 60.244 52.174 4.06 0.00 0.00 4.61
7498 10431 2.764269 ACCTGATGCTACATACACCCT 58.236 47.619 0.00 0.00 0.00 4.34
7499 10432 3.115390 ACCTGATGCTACATACACCCTT 58.885 45.455 0.00 0.00 0.00 3.95
7500 10433 3.523564 ACCTGATGCTACATACACCCTTT 59.476 43.478 0.00 0.00 0.00 3.11
7501 10434 4.719773 ACCTGATGCTACATACACCCTTTA 59.280 41.667 0.00 0.00 0.00 1.85
7502 10435 5.369699 ACCTGATGCTACATACACCCTTTAT 59.630 40.000 0.00 0.00 0.00 1.40
7503 10436 6.126478 ACCTGATGCTACATACACCCTTTATT 60.126 38.462 0.00 0.00 0.00 1.40
7505 10438 5.989168 TGATGCTACATACACCCTTTATTCG 59.011 40.000 0.00 0.00 0.00 3.34
7506 10439 4.124238 TGCTACATACACCCTTTATTCGC 58.876 43.478 0.00 0.00 0.00 4.70
7507 10440 4.141801 TGCTACATACACCCTTTATTCGCT 60.142 41.667 0.00 0.00 0.00 4.93
7509 10442 5.987347 GCTACATACACCCTTTATTCGCTAA 59.013 40.000 0.00 0.00 0.00 3.09
7511 10444 7.172703 GCTACATACACCCTTTATTCGCTAATT 59.827 37.037 0.00 0.00 0.00 1.40
7512 10445 7.259290 ACATACACCCTTTATTCGCTAATTG 57.741 36.000 0.00 0.00 0.00 2.32
7513 10446 6.826741 ACATACACCCTTTATTCGCTAATTGT 59.173 34.615 0.00 0.00 0.00 2.71
7514 10447 7.988599 ACATACACCCTTTATTCGCTAATTGTA 59.011 33.333 0.00 0.00 0.00 2.41
7516 10449 6.412214 ACACCCTTTATTCGCTAATTGTACT 58.588 36.000 0.00 0.00 0.00 2.73
7518 10451 8.208903 ACACCCTTTATTCGCTAATTGTACTAT 58.791 33.333 0.00 0.00 0.00 2.12
7519 10452 8.709646 CACCCTTTATTCGCTAATTGTACTATC 58.290 37.037 0.00 0.00 0.00 2.08
7526 10459 7.585286 TTCGCTAATTGTACTATCAAAACGT 57.415 32.000 0.00 0.00 0.00 3.99
7527 10460 7.213252 TCGCTAATTGTACTATCAAAACGTC 57.787 36.000 0.00 0.00 0.00 4.34
7528 10461 6.254157 TCGCTAATTGTACTATCAAAACGTCC 59.746 38.462 0.00 0.00 0.00 4.79
7554 11520 2.295349 TGAACAAGGTACTCACTCCGAC 59.705 50.000 0.00 0.00 38.49 4.79
7617 11583 1.959226 GGACGGTCACAACGCACAT 60.959 57.895 10.76 0.00 34.00 3.21
7637 11603 6.366877 GCACATTTGCTTCATTCAACAATACT 59.633 34.615 0.00 0.00 46.17 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.686112 CCTCGCTCCTCCTCTCCTTT 60.686 60.000 0.00 0.00 0.00 3.11
143 153 2.370445 CGTCCATGGAGAAGGCCCT 61.370 63.158 16.81 0.00 0.00 5.19
148 158 2.202932 CGCCCGTCCATGGAGAAG 60.203 66.667 16.81 9.75 0.00 2.85
164 174 4.814294 CGCGGTCTTTCCTCCCCG 62.814 72.222 0.00 0.00 43.22 5.73
356 370 2.423898 CCGTCCTACCACGAGGCAT 61.424 63.158 0.00 0.00 42.69 4.40
357 371 3.066190 CCGTCCTACCACGAGGCA 61.066 66.667 0.00 0.00 42.69 4.75
383 397 2.758327 CCTCGGTCGGGTCCATCA 60.758 66.667 0.00 0.00 0.00 3.07
455 469 2.252072 TAGCCCGGGCATGAACTGTC 62.252 60.000 45.13 14.03 44.88 3.51
456 470 2.257409 CTAGCCCGGGCATGAACTGT 62.257 60.000 45.13 25.57 44.88 3.55
633 647 9.477484 GTCATTAATCCTCTTCACGTAATGTAT 57.523 33.333 0.00 0.00 33.00 2.29
634 648 8.692710 AGTCATTAATCCTCTTCACGTAATGTA 58.307 33.333 0.00 0.00 33.00 2.29
635 649 7.556844 AGTCATTAATCCTCTTCACGTAATGT 58.443 34.615 0.00 0.00 33.00 2.71
636 650 8.425577 AAGTCATTAATCCTCTTCACGTAATG 57.574 34.615 0.00 0.00 32.64 1.90
665 679 5.452255 CCACCAATCTGTACCTACCTACTA 58.548 45.833 0.00 0.00 0.00 1.82
666 680 4.287552 CCACCAATCTGTACCTACCTACT 58.712 47.826 0.00 0.00 0.00 2.57
667 681 3.181468 GCCACCAATCTGTACCTACCTAC 60.181 52.174 0.00 0.00 0.00 3.18
1008 1056 0.693049 GGAGAAAAGCTGAGGGGACA 59.307 55.000 0.00 0.00 0.00 4.02
1070 1118 0.776080 AGGGAGGAGGAAGCCCAAAA 60.776 55.000 0.00 0.00 44.55 2.44
1114 1162 2.957474 CAAAAGGGGAGAAGGGTGAAA 58.043 47.619 0.00 0.00 0.00 2.69
1117 1166 0.178964 TGCAAAAGGGGAGAAGGGTG 60.179 55.000 0.00 0.00 0.00 4.61
1155 1204 2.027751 GAGTATCCGCGGTGAGGC 59.972 66.667 27.15 12.04 0.00 4.70
1693 1748 4.402793 TGGACTTGAGAGTAATGCTCCTAC 59.597 45.833 0.00 0.00 45.21 3.18
1861 1918 3.782523 TCAGGACTCCAAAGGCATCTATT 59.217 43.478 0.00 0.00 28.86 1.73
1893 2487 2.158769 AGCACATCAACTGGAACTGTCA 60.159 45.455 0.00 0.00 40.38 3.58
2013 2607 6.550938 AGAATAATGAGGATCTCACACACA 57.449 37.500 0.00 0.00 43.63 3.72
2038 2632 9.289782 ACAAGAGCAAGAACTGTATTCTTTTAT 57.710 29.630 0.00 0.00 36.69 1.40
2113 2707 6.323266 CAGATAGTCCGCCAGTATATTGTAC 58.677 44.000 0.00 0.00 0.00 2.90
2212 2806 2.237143 CCACCAGCTGATCTCTAAACCA 59.763 50.000 17.39 0.00 0.00 3.67
2339 2933 8.257306 TGGAGTTAGGAAATTGGCATATTTTTC 58.743 33.333 8.38 6.63 0.00 2.29
2747 3363 2.476619 GCCTACAATATAGCACAGCGTG 59.523 50.000 4.61 4.61 36.51 5.34
2794 3410 8.186163 CACAAATGCTACACATATTTCAGTCAT 58.814 33.333 0.00 0.00 38.34 3.06
3016 3633 8.058667 TCTGGACAACGACAGTAGATAAAATA 57.941 34.615 0.00 0.00 36.17 1.40
3235 3853 6.095300 CCCAAAAGAAAAAGGCTCAAATGTTT 59.905 34.615 0.00 0.00 0.00 2.83
3240 3858 4.512484 CACCCAAAAGAAAAAGGCTCAAA 58.488 39.130 0.00 0.00 0.00 2.69
3251 3869 2.071778 AGCAGAAGCACCCAAAAGAA 57.928 45.000 0.00 0.00 45.49 2.52
3387 4006 3.941483 AGTCTGCTGGGTATTTCAAATCG 59.059 43.478 0.00 0.00 0.00 3.34
3569 4191 1.327303 TTGGCTTGTTGTGGATGGAC 58.673 50.000 0.00 0.00 0.00 4.02
3706 4328 3.127548 CAGGAGCAAACGAGCATTGTATT 59.872 43.478 0.00 0.00 36.85 1.89
3864 4487 7.148639 GCAGAACTCAACAAAGTTACATCGATA 60.149 37.037 0.00 0.00 39.55 2.92
4190 4829 5.699097 ATAGCGAAGTAGAATGGACTCTC 57.301 43.478 0.00 0.00 0.00 3.20
4252 4891 0.106519 GGGCTCTGGGCAACATACAT 60.107 55.000 0.21 0.00 44.01 2.29
4906 5548 1.270826 TCTTCAGAGGAGCTGTCAACG 59.729 52.381 0.00 0.00 45.14 4.10
4961 5603 1.331399 TGGACACCACCAACGTCAGA 61.331 55.000 0.00 0.00 36.96 3.27
5134 5776 2.304180 CACATTCCCAGACAAGTCTCCT 59.696 50.000 0.00 0.00 37.98 3.69
5174 5816 8.073467 TGAAAACTATTTCCTTCAAAACCACT 57.927 30.769 0.00 0.00 43.54 4.00
5240 5882 9.211485 CATAGATTCATTGCACTTTTCCTTTTT 57.789 29.630 0.00 0.00 0.00 1.94
5548 6190 7.062605 CACAAATTTTCATTAGCTGTGACATCC 59.937 37.037 0.00 0.00 33.24 3.51
5683 6325 3.655481 GGAACCACCTTGTGAGCG 58.345 61.111 0.00 0.00 35.23 5.03
5842 6484 8.620116 AAAATGCAGCCAAGTAAATTAACAAT 57.380 26.923 0.00 0.00 0.00 2.71
5927 6569 2.741228 GCACAACTTGCCCAAATGTTCA 60.741 45.455 0.00 0.00 46.63 3.18
6256 6901 5.965033 AGATCTTCAGAAGCCCTTCATTA 57.035 39.130 5.15 0.00 41.84 1.90
6495 7140 5.163364 ACAATGGCACTTGATTTTTGGTACA 60.163 36.000 13.95 0.00 0.00 2.90
6692 9579 6.038161 TGTCAACCAACAGAAATAGACACAAG 59.962 38.462 0.00 0.00 30.64 3.16
6836 9723 2.291605 TGAGGCTTCTGCTAGGTAGTCA 60.292 50.000 0.00 0.00 39.59 3.41
6884 9771 2.542020 TGACGGAGAAATGTTCAGCA 57.458 45.000 0.00 0.00 0.00 4.41
6933 9820 6.976934 TTGACCTAAGAAAGCAGGAATTTT 57.023 33.333 0.00 0.00 35.76 1.82
6987 9918 6.375174 TCTCATGTACAATTACAAAGCATGCT 59.625 34.615 16.30 16.30 41.64 3.79
7178 10111 5.484715 TCAAATTGTAACTTACTCCCTCCG 58.515 41.667 0.71 0.00 0.00 4.63
7198 10131 6.928492 GCATGGTTTCTTTTTAGTCCAATCAA 59.072 34.615 0.00 0.00 0.00 2.57
7321 10254 6.417044 CGTTGCGAGCATAGTAAAACTATAGT 59.583 38.462 0.00 0.00 39.26 2.12
7322 10255 6.129168 CCGTTGCGAGCATAGTAAAACTATAG 60.129 42.308 0.00 0.00 39.26 1.31
7323 10256 5.688621 CCGTTGCGAGCATAGTAAAACTATA 59.311 40.000 0.00 0.00 39.26 1.31
7440 10373 7.535489 AGGACGTTTTGATAGTACAATTAGC 57.465 36.000 0.00 0.00 0.00 3.09
7446 10379 7.218228 TCACTAAGGACGTTTTGATAGTACA 57.782 36.000 0.00 0.00 0.00 2.90
7465 10398 3.838317 AGCATCAGGTACCTTGTTCACTA 59.162 43.478 13.15 0.00 0.00 2.74
7466 10399 2.639839 AGCATCAGGTACCTTGTTCACT 59.360 45.455 13.15 2.29 0.00 3.41
7467 10400 3.059352 AGCATCAGGTACCTTGTTCAC 57.941 47.619 13.15 0.00 0.00 3.18
7469 10402 4.202245 TGTAGCATCAGGTACCTTGTTC 57.798 45.455 13.15 2.16 45.73 3.18
7471 10404 4.714802 TGTATGTAGCATCAGGTACCTTGT 59.285 41.667 13.15 0.00 45.73 3.16
7472 10405 5.050490 GTGTATGTAGCATCAGGTACCTTG 58.950 45.833 13.15 10.70 45.73 3.61
7475 10408 3.244112 GGGTGTATGTAGCATCAGGTACC 60.244 52.174 2.73 2.73 45.73 3.34
7476 10409 3.641906 AGGGTGTATGTAGCATCAGGTAC 59.358 47.826 0.00 0.00 46.33 3.34
7477 10410 3.923648 AGGGTGTATGTAGCATCAGGTA 58.076 45.455 0.00 0.00 0.00 3.08
7478 10411 2.764269 AGGGTGTATGTAGCATCAGGT 58.236 47.619 0.00 0.00 0.00 4.00
7482 10415 5.107065 GCGAATAAAGGGTGTATGTAGCATC 60.107 44.000 0.00 0.00 0.00 3.91
7483 10416 4.755123 GCGAATAAAGGGTGTATGTAGCAT 59.245 41.667 0.00 0.00 0.00 3.79
7484 10417 4.124238 GCGAATAAAGGGTGTATGTAGCA 58.876 43.478 0.00 0.00 0.00 3.49
7485 10418 4.377897 AGCGAATAAAGGGTGTATGTAGC 58.622 43.478 0.00 0.00 0.00 3.58
7486 10419 8.495949 CAATTAGCGAATAAAGGGTGTATGTAG 58.504 37.037 0.00 0.00 0.00 2.74
7487 10420 7.988599 ACAATTAGCGAATAAAGGGTGTATGTA 59.011 33.333 0.00 0.00 0.00 2.29
7489 10422 7.259290 ACAATTAGCGAATAAAGGGTGTATG 57.741 36.000 0.00 0.00 0.00 2.39
7490 10423 8.208903 AGTACAATTAGCGAATAAAGGGTGTAT 58.791 33.333 0.00 0.00 0.00 2.29
7491 10424 7.558604 AGTACAATTAGCGAATAAAGGGTGTA 58.441 34.615 0.00 0.00 0.00 2.90
7492 10425 6.412214 AGTACAATTAGCGAATAAAGGGTGT 58.588 36.000 0.00 0.00 0.00 4.16
7493 10426 6.920569 AGTACAATTAGCGAATAAAGGGTG 57.079 37.500 0.00 0.00 0.00 4.61
7495 10428 8.827177 TGATAGTACAATTAGCGAATAAAGGG 57.173 34.615 0.00 0.00 0.00 3.95
7500 10433 9.304731 ACGTTTTGATAGTACAATTAGCGAATA 57.695 29.630 0.00 0.00 0.00 1.75
7501 10434 8.193250 ACGTTTTGATAGTACAATTAGCGAAT 57.807 30.769 0.00 0.00 0.00 3.34
7502 10435 7.201461 GGACGTTTTGATAGTACAATTAGCGAA 60.201 37.037 0.00 0.00 0.00 4.70
7503 10436 6.254157 GGACGTTTTGATAGTACAATTAGCGA 59.746 38.462 0.00 0.00 0.00 4.93
7505 10438 7.535489 AGGACGTTTTGATAGTACAATTAGC 57.465 36.000 0.00 0.00 0.00 3.09
7509 10442 8.308931 TCACTAAGGACGTTTTGATAGTACAAT 58.691 33.333 0.00 0.00 0.00 2.71
7511 10444 7.218228 TCACTAAGGACGTTTTGATAGTACA 57.782 36.000 0.00 0.00 0.00 2.90
7512 10445 7.596248 TGTTCACTAAGGACGTTTTGATAGTAC 59.404 37.037 0.00 0.00 0.00 2.73
7513 10446 7.660112 TGTTCACTAAGGACGTTTTGATAGTA 58.340 34.615 0.00 0.00 0.00 1.82
7514 10447 6.518493 TGTTCACTAAGGACGTTTTGATAGT 58.482 36.000 0.00 0.00 0.00 2.12
7516 10449 6.425721 CCTTGTTCACTAAGGACGTTTTGATA 59.574 38.462 0.00 0.00 46.08 2.15
7518 10451 4.573201 CCTTGTTCACTAAGGACGTTTTGA 59.427 41.667 0.00 0.00 46.08 2.69
7519 10452 4.334481 ACCTTGTTCACTAAGGACGTTTTG 59.666 41.667 10.50 0.00 46.08 2.44
7523 10456 3.893813 AGTACCTTGTTCACTAAGGACGT 59.106 43.478 10.50 0.00 46.08 4.34
7524 10457 4.022589 TGAGTACCTTGTTCACTAAGGACG 60.023 45.833 10.50 0.00 46.08 4.79
7525 10458 5.228665 GTGAGTACCTTGTTCACTAAGGAC 58.771 45.833 10.50 4.97 46.08 3.85
7526 10459 5.464030 GTGAGTACCTTGTTCACTAAGGA 57.536 43.478 10.50 0.00 46.08 3.36
7593 11559 0.601576 CGTTGTGACCGTCCAATCCA 60.602 55.000 0.00 0.00 0.00 3.41
7637 11603 8.885494 ACAAGCTTCTTTTGCAATTATACAAA 57.115 26.923 0.00 0.00 34.11 2.83


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

AutoCloner maintained by Alex Coulton.