Multiple sequence alignment - TraesCS7A01G089300

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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 TraesCS7A01G089300 chr7A 100.000 5637 0 0 1 5637 54669236 54663600 0.000000e+00 10410.0
1 TraesCS7A01G089300 chr7D 94.072 5078 235 46 587 5631 51740239 51735195 0.000000e+00 7649.0
2 TraesCS7A01G089300 chr7D 93.356 587 14 5 1 587 51741048 51740487 0.000000e+00 845.0
3 TraesCS7A01G089300 chr4A 96.311 4039 114 16 680 4690 666118352 666114321 0.000000e+00 6601.0
4 TraesCS7A01G089300 chr4A 86.681 931 90 21 4723 5630 666114324 666113405 0.000000e+00 1002.0
5 TraesCS7A01G089300 chr4A 90.000 570 28 7 1 556 666119188 666118634 0.000000e+00 710.0
6 TraesCS7A01G089300 chr4A 86.311 431 32 12 52 481 669175133 669175537 1.440000e-120 444.0
7 TraesCS7A01G089300 chr4A 90.400 125 12 0 709 833 715366994 715367118 1.260000e-36 165.0
8 TraesCS7A01G089300 chr4A 91.781 73 6 0 708 780 669176111 669176183 9.990000e-18 102.0
9 TraesCS7A01G089300 chr6B 88.129 497 42 13 35 529 130897637 130897156 4.900000e-160 575.0
10 TraesCS7A01G089300 chr6B 74.747 297 46 18 5141 5429 439409327 439409602 7.720000e-19 106.0
11 TraesCS7A01G089300 chr3A 88.426 432 30 12 52 481 719623439 719623026 2.340000e-138 503.0
12 TraesCS7A01G089300 chr3A 87.963 432 30 13 52 481 645616735 645616324 1.830000e-134 490.0
13 TraesCS7A01G089300 chr3A 88.971 136 13 2 708 841 645615753 645615618 3.490000e-37 167.0
14 TraesCS7A01G089300 chr3A 89.922 129 13 0 708 836 719622455 719622327 3.490000e-37 167.0
15 TraesCS7A01G089300 chr7B 87.842 329 26 11 52 375 570106254 570106573 1.920000e-99 374.0
16 TraesCS7A01G089300 chr3D 89.474 266 21 5 52 313 561008863 561008601 4.210000e-86 329.0
17 TraesCS7A01G089300 chr3D 95.455 88 4 0 394 481 561008604 561008517 2.120000e-29 141.0
18 TraesCS7A01G089300 chr5B 85.417 288 27 6 69 344 406929752 406930036 9.240000e-73 285.0
19 TraesCS7A01G089300 chr5B 74.275 276 56 9 5169 5430 107372273 107371999 9.990000e-18 102.0
20 TraesCS7A01G089300 chr2D 77.725 211 37 4 5187 5397 67578712 67578912 2.760000e-23 121.0
21 TraesCS7A01G089300 chr2D 79.618 157 22 5 5169 5323 598801201 598801053 2.780000e-18 104.0
22 TraesCS7A01G089300 chr1A 83.333 90 13 2 5144 5231 463356322 463356411 1.300000e-11 82.4
23 TraesCS7A01G089300 chr1A 82.796 93 13 3 5142 5231 59512215 59512307 4.680000e-11 80.5
24 TraesCS7A01G089300 chrUn 87.097 62 8 0 5198 5259 48395395 48395334 2.820000e-08 71.3
25 TraesCS7A01G089300 chrUn 78.571 126 13 11 5506 5630 349405798 349405910 2.820000e-08 71.3
26 TraesCS7A01G089300 chr5A 78.571 126 13 11 5506 5630 658923215 658923327 2.820000e-08 71.3
27 TraesCS7A01G089300 chr5A 78.571 126 13 11 5506 5630 658930699 658930811 2.820000e-08 71.3
28 TraesCS7A01G089300 chr1D 79.439 107 14 6 5156 5259 240119231 240119130 1.010000e-07 69.4
29 TraesCS7A01G089300 chr1B 84.375 64 8 2 5169 5230 616318833 616318896 1.700000e-05 62.1


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 TraesCS7A01G089300 chr7A 54663600 54669236 5636 True 10410.0 10410 100.000000 1 5637 1 chr7A.!!$R1 5636
1 TraesCS7A01G089300 chr7D 51735195 51741048 5853 True 4247.0 7649 93.714000 1 5631 2 chr7D.!!$R1 5630
2 TraesCS7A01G089300 chr4A 666113405 666119188 5783 True 2771.0 6601 90.997333 1 5630 3 chr4A.!!$R1 5629
3 TraesCS7A01G089300 chr4A 669175133 669176183 1050 False 273.0 444 89.046000 52 780 2 chr4A.!!$F2 728
4 TraesCS7A01G089300 chr3A 719622327 719623439 1112 True 335.0 503 89.174000 52 836 2 chr3A.!!$R2 784
5 TraesCS7A01G089300 chr3A 645615618 645616735 1117 True 328.5 490 88.467000 52 841 2 chr3A.!!$R1 789

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
674 963 0.178068 TCCTGGATTCAAGCGCTACC 59.822 55.0 12.05 10.32 0.0 3.18 F
1614 2061 0.251653 TCTCCGGTAACCAGCTCACT 60.252 55.0 0.00 0.00 0.0 3.41 F
2538 2985 0.036010 CAGATTTGAGGCTGTCGGGT 60.036 55.0 0.00 0.00 0.0 5.28 F
3681 4128 0.039035 AGAGTGCGGACCTCTTCTCT 59.961 55.0 2.38 0.00 35.8 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2349 1.480789 TGCTGCTCGGAATAGTACCA 58.519 50.0 0.00 0.0 0.00 3.25 R
3355 3802 1.874345 CGGAGTCCTGCTACCGTGTT 61.874 60.0 7.77 0.0 40.42 3.32 R
4239 4687 0.973496 TACCAGGTGCGATGTAGCCA 60.973 55.0 0.76 0.0 36.02 4.75 R
5445 5933 0.526524 CACTACTGGCTCGCTGTAGC 60.527 60.0 16.29 0.0 41.99 3.58 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
235 236 7.995289 ACACACACTGATCAACTAAATGAAAA 58.005 30.769 0.00 0.00 32.06 2.29
367 377 7.753132 TGAACAACAATGAAAAAGTACACTGAC 59.247 33.333 0.00 0.00 0.00 3.51
376 386 8.958119 TGAAAAAGTACACTGACTAATGAAGT 57.042 30.769 0.00 0.00 42.80 3.01
379 389 9.826574 AAAAAGTACACTGACTAATGAAGTACA 57.173 29.630 0.00 0.00 39.07 2.90
380 390 8.813643 AAAGTACACTGACTAATGAAGTACAC 57.186 34.615 0.00 0.00 39.07 2.90
381 391 7.762588 AGTACACTGACTAATGAAGTACACT 57.237 36.000 0.00 0.00 39.07 3.55
382 392 7.818642 AGTACACTGACTAATGAAGTACACTC 58.181 38.462 0.00 0.00 39.07 3.51
383 393 6.650427 ACACTGACTAATGAAGTACACTCA 57.350 37.500 0.00 0.00 39.07 3.41
384 394 7.233389 ACACTGACTAATGAAGTACACTCAT 57.767 36.000 4.98 4.98 39.07 2.90
385 395 8.349568 ACACTGACTAATGAAGTACACTCATA 57.650 34.615 10.02 1.25 39.07 2.15
386 396 8.803235 ACACTGACTAATGAAGTACACTCATAA 58.197 33.333 10.02 0.00 39.07 1.90
387 397 9.077674 CACTGACTAATGAAGTACACTCATAAC 57.922 37.037 10.02 4.74 39.07 1.89
388 398 9.026121 ACTGACTAATGAAGTACACTCATAACT 57.974 33.333 10.02 0.29 39.07 2.24
389 399 9.295214 CTGACTAATGAAGTACACTCATAACTG 57.705 37.037 10.02 5.13 39.07 3.16
548 587 4.720902 CGTGGATGGGTGCCTGCA 62.721 66.667 0.00 0.00 0.00 4.41
549 588 2.283101 GTGGATGGGTGCCTGCAA 60.283 61.111 0.00 0.00 0.00 4.08
550 589 1.907807 GTGGATGGGTGCCTGCAAA 60.908 57.895 0.00 0.00 0.00 3.68
551 590 1.152376 TGGATGGGTGCCTGCAAAA 60.152 52.632 0.00 0.00 0.00 2.44
552 591 0.762082 TGGATGGGTGCCTGCAAAAA 60.762 50.000 0.00 0.00 0.00 1.94
614 903 1.304952 CCGACCTCCTCTCCAGACT 59.695 63.158 0.00 0.00 0.00 3.24
652 941 1.303561 GCCATCCCTGTGAAGCACA 60.304 57.895 0.00 0.00 42.45 4.57
660 949 4.386413 GTGAAGCACACCTCCTGG 57.614 61.111 3.21 0.00 43.05 4.45
672 961 0.465705 CCTCCTGGATTCAAGCGCTA 59.534 55.000 12.05 0.00 34.57 4.26
674 963 0.178068 TCCTGGATTCAAGCGCTACC 59.822 55.000 12.05 10.32 0.00 3.18
676 965 1.576356 CTGGATTCAAGCGCTACCTC 58.424 55.000 12.05 5.44 0.00 3.85
677 966 1.137872 CTGGATTCAAGCGCTACCTCT 59.862 52.381 12.05 0.00 0.00 3.69
688 977 1.736032 CGCTACCTCTCACCCGAAAAG 60.736 57.143 0.00 0.00 0.00 2.27
785 1202 3.125316 GCGAATCCGACTGACAGAAAAAT 59.875 43.478 10.08 0.00 38.22 1.82
794 1211 3.181440 ACTGACAGAAAAATGGCCTGAGA 60.181 43.478 10.08 0.00 0.00 3.27
955 1375 7.398829 TGCTAACCCAAACTAGAATAATCACA 58.601 34.615 0.00 0.00 0.00 3.58
1137 1560 1.334384 GCCCTTCTCTCACCCCTCTC 61.334 65.000 0.00 0.00 0.00 3.20
1138 1561 0.338120 CCCTTCTCTCACCCCTCTCT 59.662 60.000 0.00 0.00 0.00 3.10
1182 1629 3.356290 ACTTGTTGAATCCATGGCTACC 58.644 45.455 6.96 0.00 0.00 3.18
1258 1705 1.522668 CATGTTCGGTGAGGCAAAGA 58.477 50.000 0.00 0.00 0.00 2.52
1333 1780 0.449388 GAAATCCAGCCTGACAAGCG 59.551 55.000 0.00 0.00 34.64 4.68
1518 1965 0.538057 CCTTGCTCACCAGCCTTGAA 60.538 55.000 0.00 0.00 46.26 2.69
1545 1992 1.059913 ACAACTTCCACCTCTCAGGG 58.940 55.000 0.00 0.00 40.58 4.45
1557 2004 2.609299 TCAGGGCGGATTCCACCA 60.609 61.111 11.81 0.00 0.00 4.17
1614 2061 0.251653 TCTCCGGTAACCAGCTCACT 60.252 55.000 0.00 0.00 0.00 3.41
1872 2319 0.519077 GGAAACTCGCTGCTTTGGAG 59.481 55.000 0.00 0.00 0.00 3.86
1899 2346 8.657387 AGCTAGATTTGGCTGATAACTATCTA 57.343 34.615 0.00 0.00 39.96 1.98
2014 2461 7.492669 ACGAGATGACACACCTTAATAATCTTG 59.507 37.037 0.00 0.00 32.75 3.02
2017 2464 5.565509 TGACACACCTTAATAATCTTGCCA 58.434 37.500 0.00 0.00 0.00 4.92
2062 2509 0.465705 CACGTCCACTATCCCTGCAT 59.534 55.000 0.00 0.00 0.00 3.96
2267 2714 2.093128 ACGAGAACAACTTGTCTGGGTT 60.093 45.455 0.00 0.00 38.77 4.11
2295 2742 4.445448 CCTTATGTGCTAGGGAATCTTGCT 60.445 45.833 0.00 0.00 43.12 3.91
2438 2885 2.627221 CAGCTGAGCTAGGCAATCTAGA 59.373 50.000 8.42 0.00 46.48 2.43
2538 2985 0.036010 CAGATTTGAGGCTGTCGGGT 60.036 55.000 0.00 0.00 0.00 5.28
2569 3016 0.465460 TGGACCTTTGCCTCACACAC 60.465 55.000 0.00 0.00 0.00 3.82
2589 3036 5.291614 CACACTTTCAAACCTCACCAATTTG 59.708 40.000 0.00 0.00 35.15 2.32
2716 3163 3.650070 CCTTTCCAGGAAGTTTCAAGC 57.350 47.619 1.07 0.00 44.19 4.01
2739 3186 3.201708 ACTGCAGCTCCTTAATCATCCTT 59.798 43.478 15.27 0.00 0.00 3.36
2763 3210 9.498176 CTTGACATCATGTATAATCAGATGGAA 57.502 33.333 0.00 0.00 40.17 3.53
3077 3524 2.414559 GCATTCCTCAACACATTGGTCG 60.415 50.000 0.00 0.00 36.39 4.79
3118 3565 3.005554 CTCGACCTGTCAAGCAATCAAT 58.994 45.455 0.00 0.00 0.00 2.57
3122 3569 4.201851 CGACCTGTCAAGCAATCAATTAGG 60.202 45.833 0.00 0.00 0.00 2.69
3155 3602 3.891366 CCAGAAGAAGTTGGGAAATGTGT 59.109 43.478 0.00 0.00 0.00 3.72
3396 3843 4.550831 CGAAGCATGTCCGTATTTGATGTC 60.551 45.833 0.00 0.00 0.00 3.06
3405 3852 6.127168 TGTCCGTATTTGATGTCTCCTACAAT 60.127 38.462 0.00 0.00 42.70 2.71
3460 3907 1.821216 TTCCTCGGCAGAATGGTTTC 58.179 50.000 0.00 0.00 35.86 2.78
3666 4113 5.625150 AGAGAAAGTGCCATTGTAAAGAGT 58.375 37.500 0.00 0.00 0.00 3.24
3681 4128 0.039035 AGAGTGCGGACCTCTTCTCT 59.961 55.000 2.38 0.00 35.80 3.10
3753 4200 7.739911 GCAACGGATAATTTTGATGAAAAACAC 59.260 33.333 0.00 0.00 40.51 3.32
3765 4212 4.998671 TGAAAAACACTGCATTGGAGAA 57.001 36.364 12.54 0.00 0.00 2.87
3768 4215 2.957402 AACACTGCATTGGAGAAGGA 57.043 45.000 12.54 0.00 0.00 3.36
3793 4241 6.012858 AGGATTTGGTAATGTCTACAAGGTGA 60.013 38.462 0.00 0.00 0.00 4.02
3837 4285 2.224597 TGCAGTGAAGAAGCTTCATCCA 60.225 45.455 27.57 17.99 0.00 3.41
4010 4458 1.093159 GCCTCAATCCTGAGCAACAG 58.907 55.000 4.31 4.31 46.76 3.16
4049 4497 3.648339 TGATTGGCAGAAAAGAGCAAC 57.352 42.857 0.00 0.00 0.00 4.17
4195 4643 0.451783 CTTTGGCACGGCAAGGATAC 59.548 55.000 9.49 0.00 0.00 2.24
4239 4687 2.111878 GCGCTGGCAGGGACATAT 59.888 61.111 32.71 0.00 39.62 1.78
4283 4731 2.271944 ACTACCCCAGTGAAAACTGC 57.728 50.000 0.22 0.00 35.62 4.40
4286 4734 0.550914 ACCCCAGTGAAAACTGCTGA 59.449 50.000 0.00 0.00 36.46 4.26
4342 4790 1.457346 ACTATGCTGCCTTGCTTGAC 58.543 50.000 0.00 0.00 0.00 3.18
4515 4963 1.605058 CTCGACCACCGTCTTCCCAT 61.605 60.000 0.00 0.00 39.75 4.00
4518 4966 2.819595 CCACCGTCTTCCCATGCG 60.820 66.667 0.00 0.00 0.00 4.73
4628 5076 0.672889 GCAGATCCATCGAGCTCTCA 59.327 55.000 12.85 0.00 30.45 3.27
4637 5085 3.549827 CCATCGAGCTCTCAGTGTATGAC 60.550 52.174 12.85 0.00 33.22 3.06
4721 5174 2.105128 CGGCCGAGCGAATCTTCT 59.895 61.111 24.07 0.00 0.00 2.85
4755 5218 8.462589 TGATTAATAAGCTGCAAATATGGTCA 57.537 30.769 1.02 1.60 0.00 4.02
4811 5274 6.017852 GTCGGAATCAAGAATGAATTCCCTAC 60.018 42.308 2.27 3.73 38.57 3.18
4827 5290 4.827789 TCCCTACCAAGCTCACCTTATAT 58.172 43.478 0.00 0.00 31.00 0.86
4851 5314 3.568578 GGGATCTTCGCCCAGGAT 58.431 61.111 0.00 0.00 45.31 3.24
4853 5316 0.536006 GGGATCTTCGCCCAGGATTG 60.536 60.000 0.00 0.00 45.31 2.67
4906 5370 1.666888 GCAATGGCTTGTCTTGGTTCG 60.667 52.381 0.00 0.00 36.96 3.95
5008 5473 2.446036 CGGGGGTAGGGAGAAGGG 60.446 72.222 0.00 0.00 0.00 3.95
5067 5532 4.706962 AGGACAGAAATACAAAGCCCATTC 59.293 41.667 0.00 0.00 0.00 2.67
5068 5533 4.438744 GGACAGAAATACAAAGCCCATTCG 60.439 45.833 0.00 0.00 0.00 3.34
5070 5535 4.522789 ACAGAAATACAAAGCCCATTCGTT 59.477 37.500 0.00 0.00 0.00 3.85
5071 5536 5.095490 CAGAAATACAAAGCCCATTCGTTC 58.905 41.667 0.00 0.00 0.00 3.95
5072 5537 4.764823 AGAAATACAAAGCCCATTCGTTCA 59.235 37.500 0.00 0.00 0.00 3.18
5073 5538 4.434713 AATACAAAGCCCATTCGTTCAC 57.565 40.909 0.00 0.00 0.00 3.18
5130 5605 1.657794 GGAGCGATTCGTAGCGACC 60.658 63.158 3.22 2.29 34.89 4.79
5131 5606 2.004489 GAGCGATTCGTAGCGACCG 61.004 63.158 3.22 7.71 34.89 4.79
5132 5607 2.023741 GCGATTCGTAGCGACCGA 59.976 61.111 3.22 0.00 34.89 4.69
5135 5610 1.653533 GATTCGTAGCGACCGACCG 60.654 63.158 0.00 0.00 34.89 4.79
5136 5611 2.040213 GATTCGTAGCGACCGACCGA 62.040 60.000 0.72 0.00 34.89 4.69
5137 5612 2.315038 ATTCGTAGCGACCGACCGAC 62.315 60.000 0.72 0.00 34.89 4.79
5138 5613 4.527157 CGTAGCGACCGACCGACC 62.527 72.222 0.72 0.00 0.00 4.79
5139 5614 4.185059 GTAGCGACCGACCGACCC 62.185 72.222 0.72 0.00 0.00 4.46
5140 5615 4.720902 TAGCGACCGACCGACCCA 62.721 66.667 0.72 0.00 0.00 4.51
5180 5655 2.895372 CCATACGGCCCGACTTGC 60.895 66.667 11.71 0.00 0.00 4.01
5181 5656 2.186903 CATACGGCCCGACTTGCT 59.813 61.111 11.71 0.00 0.00 3.91
5182 5657 1.440060 CATACGGCCCGACTTGCTA 59.560 57.895 11.71 0.00 0.00 3.49
5185 5660 2.023414 TACGGCCCGACTTGCTATGG 62.023 60.000 11.71 0.00 0.00 2.74
5186 5661 2.203209 GGCCCGACTTGCTATGGG 60.203 66.667 0.00 0.00 44.88 4.00
5188 5663 2.203209 CCCGACTTGCTATGGGCC 60.203 66.667 0.00 0.00 40.92 5.80
5273 5760 3.646162 TGCAGTTTAAGGAAGAGGTCTGA 59.354 43.478 0.00 0.00 0.00 3.27
5276 5763 3.583526 AGTTTAAGGAAGAGGTCTGACCC 59.416 47.826 22.81 14.19 39.75 4.46
5277 5764 1.848652 TAAGGAAGAGGTCTGACCCG 58.151 55.000 22.81 0.00 39.75 5.28
5278 5765 1.545706 AAGGAAGAGGTCTGACCCGC 61.546 60.000 22.81 15.20 39.75 6.13
5279 5766 2.182030 GAAGAGGTCTGACCCGCG 59.818 66.667 22.81 0.00 39.75 6.46
5280 5767 3.358076 GAAGAGGTCTGACCCGCGG 62.358 68.421 21.04 21.04 39.75 6.46
5281 5768 3.881019 AAGAGGTCTGACCCGCGGA 62.881 63.158 30.73 5.58 39.75 5.54
5282 5769 3.379445 GAGGTCTGACCCGCGGAA 61.379 66.667 30.73 11.15 39.75 4.30
5317 5805 2.167662 CTTTTTGACTAATGGGCCGGT 58.832 47.619 1.90 0.00 0.00 5.28
5323 5811 0.912487 ACTAATGGGCCGGTCTTGGA 60.912 55.000 5.77 0.00 0.00 3.53
5350 5838 2.170012 TTTAGGCCTGACGATAGGGT 57.830 50.000 17.99 0.00 43.77 4.34
5352 5840 0.554305 TAGGCCTGACGATAGGGTCA 59.446 55.000 17.99 0.00 44.25 4.02
5362 5850 4.733725 TAGGGTCAGGCCGGGCTT 62.734 66.667 30.73 16.62 38.44 4.35
5363 5851 2.615191 ATAGGGTCAGGCCGGGCTTA 62.615 60.000 30.73 19.47 38.44 3.09
5364 5852 4.176752 GGGTCAGGCCGGGCTTAG 62.177 72.222 30.73 18.87 38.44 2.18
5483 5971 0.109723 GGGCTGGTCCAGTAACAACA 59.890 55.000 20.24 0.00 36.21 3.33
5485 5973 2.084546 GGCTGGTCCAGTAACAACATC 58.915 52.381 20.24 0.00 33.43 3.06
5631 6119 9.008965 TGTAAATGCAGTGTATACAAATGTTCT 57.991 29.630 7.25 0.00 0.00 3.01
5632 6120 9.840427 GTAAATGCAGTGTATACAAATGTTCTT 57.160 29.630 7.25 7.02 0.00 2.52
5634 6122 9.762933 AAATGCAGTGTATACAAATGTTCTTTT 57.237 25.926 7.25 6.21 0.00 2.27
5635 6123 9.762933 AATGCAGTGTATACAAATGTTCTTTTT 57.237 25.926 7.25 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 7.382488 TCTTCAGTTCATTCTAGTGTTTCTTCG 59.618 37.037 0.00 0.00 0.00 3.79
97 98 9.703892 ATTAGTATCAGTCAATGTTCAGATAGC 57.296 33.333 0.00 0.00 0.00 2.97
246 247 3.509184 GCTTCCAAAATCTTTGGCTCTCT 59.491 43.478 12.42 0.00 39.38 3.10
590 629 2.519780 AGAGGAGGTCGGCGGATC 60.520 66.667 7.21 2.47 0.00 3.36
591 630 2.519780 GAGAGGAGGTCGGCGGAT 60.520 66.667 7.21 0.00 0.00 4.18
614 903 0.742505 CGCAGGTACGGGAGATGTTA 59.257 55.000 0.00 0.00 0.00 2.41
652 941 1.078143 GCGCTTGAATCCAGGAGGT 60.078 57.895 0.00 0.00 35.89 3.85
658 947 1.137086 GAGAGGTAGCGCTTGAATCCA 59.863 52.381 18.68 0.00 0.00 3.41
660 949 2.197577 GTGAGAGGTAGCGCTTGAATC 58.802 52.381 18.68 9.44 0.00 2.52
672 961 1.375326 GGCTTTTCGGGTGAGAGGT 59.625 57.895 0.00 0.00 0.00 3.85
674 963 0.250727 TTGGGCTTTTCGGGTGAGAG 60.251 55.000 0.00 0.00 0.00 3.20
676 965 0.821711 TGTTGGGCTTTTCGGGTGAG 60.822 55.000 0.00 0.00 0.00 3.51
677 966 0.395862 TTGTTGGGCTTTTCGGGTGA 60.396 50.000 0.00 0.00 0.00 4.02
706 1122 0.529378 GTACCGGGTCATCTTGTCGT 59.471 55.000 6.32 0.00 0.00 4.34
764 1180 4.436050 CCATTTTTCTGTCAGTCGGATTCG 60.436 45.833 0.00 0.00 37.82 3.34
774 1190 3.149196 GTCTCAGGCCATTTTTCTGTCA 58.851 45.455 5.01 0.00 0.00 3.58
785 1202 4.580995 TGTTTTTAAATTCGTCTCAGGCCA 59.419 37.500 5.01 0.00 0.00 5.36
794 1211 7.504924 TCCAGATGTCTGTTTTTAAATTCGT 57.495 32.000 9.03 0.00 42.27 3.85
937 1357 7.607991 AGTCTTGGTGTGATTATTCTAGTTTGG 59.392 37.037 0.00 0.00 0.00 3.28
1121 1544 2.024846 TGGTAGAGAGGGGTGAGAGAAG 60.025 54.545 0.00 0.00 0.00 2.85
1137 1560 3.018856 TGTCGGTGGTACTATGTGGTAG 58.981 50.000 0.00 0.00 36.44 3.18
1138 1561 3.018856 CTGTCGGTGGTACTATGTGGTA 58.981 50.000 0.00 0.00 0.00 3.25
1333 1780 3.426568 GGCTGAACCGCTGCTGAC 61.427 66.667 0.00 0.00 40.85 3.51
1518 1965 2.887152 GAGGTGGAAGTTGTTGCTGATT 59.113 45.455 0.00 0.00 0.00 2.57
1545 1992 2.359478 ACGGTTGGTGGAATCCGC 60.359 61.111 3.84 3.84 45.76 5.54
1557 2004 4.778143 GGGAGCATGCCGACGGTT 62.778 66.667 15.66 0.09 36.28 4.44
1872 2319 4.967036 AGTTATCAGCCAAATCTAGCTCC 58.033 43.478 0.00 0.00 37.18 4.70
1899 2346 2.159085 GCTGCTCGGAATAGTACCAGTT 60.159 50.000 0.00 0.00 0.00 3.16
1902 2349 1.480789 TGCTGCTCGGAATAGTACCA 58.519 50.000 0.00 0.00 0.00 3.25
2014 2461 3.143728 TGTGTGATATCATGAGCATGGC 58.856 45.455 9.02 0.00 39.24 4.40
2017 2464 7.761038 ATTGATTGTGTGATATCATGAGCAT 57.239 32.000 9.02 0.00 31.34 3.79
2267 2714 5.608437 AGATTCCCTAGCACATAAGGAATGA 59.392 40.000 10.72 0.00 42.46 2.57
2295 2742 2.766828 GAGGCTAAGCTCCTGAAGGTTA 59.233 50.000 0.00 0.00 43.78 2.85
2535 2982 3.644335 AGGTCCAGACAGTCTATTACCC 58.356 50.000 18.31 9.11 0.00 3.69
2538 2985 4.081087 GGCAAAGGTCCAGACAGTCTATTA 60.081 45.833 1.67 0.00 0.00 0.98
2589 3036 4.385825 TGTAACTCAACTCAATGTCCACC 58.614 43.478 0.00 0.00 0.00 4.61
2716 3163 2.877168 GGATGATTAAGGAGCTGCAGTG 59.123 50.000 16.64 0.00 0.00 3.66
2739 3186 8.098912 CCTTCCATCTGATTATACATGATGTCA 58.901 37.037 0.00 0.00 34.44 3.58
2763 3210 4.444022 CCAAGCTGTTGTGCTATATCTCCT 60.444 45.833 0.00 0.00 43.24 3.69
3067 3514 3.691118 AGAACATCCATTCGACCAATGTG 59.309 43.478 3.49 0.00 40.51 3.21
3077 3524 4.331168 CGAGAACCTCAAGAACATCCATTC 59.669 45.833 0.00 0.00 0.00 2.67
3118 3565 6.500751 ACTTCTTCTGGTATTCTTCCACCTAA 59.499 38.462 0.00 0.00 35.73 2.69
3122 3569 5.412904 CCAACTTCTTCTGGTATTCTTCCAC 59.587 44.000 0.00 0.00 0.00 4.02
3155 3602 4.832823 TCAGTTTCATGGACTGTAGTCTCA 59.167 41.667 21.59 8.39 43.80 3.27
3273 3720 2.104792 TCCTATTTCTGGAGGAATGGCG 59.895 50.000 0.00 0.00 38.96 5.69
3355 3802 1.874345 CGGAGTCCTGCTACCGTGTT 61.874 60.000 7.77 0.00 40.42 3.32
3396 3843 6.582636 TGTGCCTTGTAATCTATTGTAGGAG 58.417 40.000 0.00 0.00 0.00 3.69
3405 3852 3.369052 CCGGAACTGTGCCTTGTAATCTA 60.369 47.826 2.72 0.00 0.00 1.98
3460 3907 3.443037 CGCAGAGACCTCTATTGTGAAG 58.557 50.000 0.00 0.00 37.98 3.02
3666 4113 3.157881 CCATATAGAGAAGAGGTCCGCA 58.842 50.000 0.00 0.00 0.00 5.69
3681 4128 9.431887 GCTATTTTACCATCGAAGTTCCATATA 57.568 33.333 0.00 0.00 0.00 0.86
3753 4200 3.294038 AATCCTCCTTCTCCAATGCAG 57.706 47.619 0.00 0.00 0.00 4.41
3765 4212 6.353082 CCTTGTAGACATTACCAAATCCTCCT 60.353 42.308 0.00 0.00 0.00 3.69
3768 4215 6.012858 TCACCTTGTAGACATTACCAAATCCT 60.013 38.462 0.00 0.00 0.00 3.24
3837 4285 3.675348 TCATGCATCCCTTCCTCAATT 57.325 42.857 0.00 0.00 0.00 2.32
4010 4458 1.994779 CAAATTGGATTGCTTGGTCGC 59.005 47.619 0.00 0.00 0.00 5.19
4049 4497 3.340928 TGCACAACATCCTTGATGAGAG 58.659 45.455 10.84 3.57 42.09 3.20
4195 4643 3.309138 CAGTTCGATGAATCAGGCTTCAG 59.691 47.826 0.00 0.00 38.47 3.02
4203 4651 1.739035 GCGGTCCAGTTCGATGAATCA 60.739 52.381 0.00 0.00 0.00 2.57
4230 4678 1.276421 GCGATGTAGCCATATGTCCCT 59.724 52.381 1.24 0.00 0.00 4.20
4239 4687 0.973496 TACCAGGTGCGATGTAGCCA 60.973 55.000 0.76 0.00 36.02 4.75
4342 4790 1.136336 GGCGTGTAAGAAAGTTCTGCG 60.136 52.381 0.00 0.00 37.65 5.18
4515 4963 4.717629 CCTCGTCGGTCTTGCGCA 62.718 66.667 5.66 5.66 0.00 6.09
4628 5076 4.346418 GGAATCAGGATCCAGTCATACACT 59.654 45.833 15.82 0.00 36.92 3.55
4637 5085 2.406559 ACTCAGGGAATCAGGATCCAG 58.593 52.381 15.82 6.08 38.80 3.86
4721 5174 8.962884 TTGCAGCTTATTAATCATCAAGACTA 57.037 30.769 0.00 0.00 0.00 2.59
4811 5274 3.322254 AGGTCGATATAAGGTGAGCTTGG 59.678 47.826 7.22 0.00 35.83 3.61
4827 5290 2.423898 GGCGAAGATCCCAGGTCGA 61.424 63.158 0.65 0.00 35.54 4.20
4851 5314 2.347490 GTCCTGAGCTTCCGCCAA 59.653 61.111 0.00 0.00 36.60 4.52
4858 5321 2.586792 GGGATGCGTCCTGAGCTT 59.413 61.111 24.11 0.00 44.44 3.74
4903 5367 0.976641 AGGAGACAATCAGTGGCGAA 59.023 50.000 0.00 0.00 41.91 4.70
4906 5370 1.134551 GGAGAGGAGACAATCAGTGGC 60.135 57.143 0.00 0.00 34.17 5.01
4909 5373 1.479709 CCGGAGAGGAGACAATCAGT 58.520 55.000 0.00 0.00 45.00 3.41
4912 5376 1.443828 GGCCGGAGAGGAGACAATC 59.556 63.158 5.05 0.00 45.00 2.67
5067 5532 1.006832 CTTGGATAAGGGCGTGAACG 58.993 55.000 0.00 0.00 43.27 3.95
5131 5606 4.717313 GGCCAGGTTGGGTCGGTC 62.717 72.222 0.00 0.00 38.19 4.79
5135 5610 2.362889 CCATGGCCAGGTTGGGTC 60.363 66.667 17.55 0.00 38.19 4.46
5136 5611 3.996621 CCCATGGCCAGGTTGGGT 61.997 66.667 28.47 0.45 44.30 4.51
5166 5641 1.440060 CATAGCAAGTCGGGCCGTA 59.560 57.895 27.32 10.19 0.00 4.02
5232 5719 2.901051 AAATACGACAGGCCCGAGCG 62.901 60.000 6.90 5.74 41.24 5.03
5277 5764 3.508840 CATTGGGGCTCGTTCCGC 61.509 66.667 5.98 5.98 39.30 5.54
5278 5765 2.824041 CCATTGGGGCTCGTTCCG 60.824 66.667 0.00 0.00 0.00 4.30
5291 5778 3.055167 GCCCATTAGTCAAAAAGCCCATT 60.055 43.478 0.00 0.00 0.00 3.16
5293 5780 1.899142 GCCCATTAGTCAAAAAGCCCA 59.101 47.619 0.00 0.00 0.00 5.36
5307 5794 2.355115 GTCCAAGACCGGCCCATT 59.645 61.111 0.00 0.00 0.00 3.16
5317 5805 4.103153 CAGGCCTAAATATGAGGTCCAAGA 59.897 45.833 3.98 0.00 39.73 3.02
5323 5811 3.305720 TCGTCAGGCCTAAATATGAGGT 58.694 45.455 3.98 0.00 36.37 3.85
5327 5815 4.223032 ACCCTATCGTCAGGCCTAAATATG 59.777 45.833 3.98 0.00 34.02 1.78
5330 5818 2.633481 GACCCTATCGTCAGGCCTAAAT 59.367 50.000 3.98 0.00 34.02 1.40
5362 5850 3.132289 CCGACACAGAAAATCTAGGCCTA 59.868 47.826 13.09 13.09 0.00 3.93
5363 5851 2.093447 CCGACACAGAAAATCTAGGCCT 60.093 50.000 11.78 11.78 0.00 5.19
5364 5852 2.280628 CCGACACAGAAAATCTAGGCC 58.719 52.381 0.00 0.00 0.00 5.19
5371 5859 1.613437 CCAAAGCCCGACACAGAAAAT 59.387 47.619 0.00 0.00 0.00 1.82
5445 5933 0.526524 CACTACTGGCTCGCTGTAGC 60.527 60.000 16.29 0.00 41.99 3.58
5448 5936 2.650116 CCCACTACTGGCTCGCTGT 61.650 63.158 0.00 0.00 36.00 4.40
5483 5971 1.406898 AGACATGCGTGACGAGATGAT 59.593 47.619 19.77 8.49 0.00 2.45
5485 5973 1.633561 AAGACATGCGTGACGAGATG 58.366 50.000 14.17 12.37 0.00 2.90
5590 6078 8.454106 ACTGCATTTACATCTTCTAAATGTGTC 58.546 33.333 10.89 0.00 41.05 3.67


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

AutoCloner maintained by Alex Coulton.