Multiple sequence alignment - TraesCS1A01G201600

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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 TraesCS1A01G201600 chr1A 100.000 5461 0 0 1 5461 362861370 362866830 0.000000e+00 10085.0
1 TraesCS1A01G201600 chr1B 94.952 5210 157 36 44 5214 391571447 391576589 0.000000e+00 8067.0
2 TraesCS1A01G201600 chr1B 93.985 133 6 2 5304 5436 391576635 391576765 3.340000e-47 200.0
3 TraesCS1A01G201600 chr1D 95.510 3586 100 23 1 3551 290442486 290446045 0.000000e+00 5674.0
4 TraesCS1A01G201600 chr1D 94.108 1799 52 12 3664 5457 290446591 290448340 0.000000e+00 2686.0
5 TraesCS1A01G201600 chr1D 96.639 119 4 0 3548 3666 290446350 290446468 1.200000e-46 198.0
6 TraesCS1A01G201600 chrUn 89.121 239 12 4 5216 5440 246700384 246700622 8.950000e-73 285.0
7 TraesCS1A01G201600 chrUn 89.121 239 12 4 5216 5440 275332987 275332749 8.950000e-73 285.0
8 TraesCS1A01G201600 chrUn 89.121 239 12 4 5216 5440 413342578 413342340 8.950000e-73 285.0
9 TraesCS1A01G201600 chrUn 78.862 246 48 3 4932 5175 332190527 332190770 4.380000e-36 163.0
10 TraesCS1A01G201600 chr6D 89.121 239 12 4 5216 5440 430471614 430471852 8.950000e-73 285.0
11 TraesCS1A01G201600 chr6D 72.251 764 176 24 2355 3097 178005427 178004679 2.580000e-48 204.0
12 TraesCS1A01G201600 chr6D 80.392 102 18 2 2133 2233 178005646 178005546 5.870000e-10 76.8
13 TraesCS1A01G201600 chr3D 89.121 239 12 4 5216 5440 202627611 202627849 8.950000e-73 285.0
14 TraesCS1A01G201600 chr4D 88.703 239 13 4 5216 5440 135046112 135045874 4.170000e-71 279.0
15 TraesCS1A01G201600 chr2D 88.703 239 12 5 5216 5440 18017080 18017317 1.500000e-70 278.0
16 TraesCS1A01G201600 chr6A 71.990 764 178 24 2355 3097 230707825 230707077 5.580000e-45 193.0
17 TraesCS1A01G201600 chr6A 79.412 102 19 2 2133 2233 230708044 230707944 2.730000e-08 71.3
18 TraesCS1A01G201600 chr7A 80.162 247 44 4 4932 5176 352278040 352277797 4.350000e-41 180.0
19 TraesCS1A01G201600 chr6B 71.597 764 181 23 2355 3097 295767263 295768011 5.620000e-40 176.0
20 TraesCS1A01G201600 chr6B 82.979 188 23 6 4976 5161 210610867 210611047 1.570000e-35 161.0
21 TraesCS1A01G201600 chr6B 80.392 102 18 2 2133 2233 295767044 295767144 5.870000e-10 76.8
22 TraesCS1A01G201600 chr7B 78.947 247 48 3 4932 5176 725640175 725639931 1.220000e-36 165.0
23 TraesCS1A01G201600 chr7B 78.862 246 48 3 4932 5175 725604580 725604337 4.380000e-36 163.0
24 TraesCS1A01G201600 chr5B 80.909 220 32 8 4961 5176 610695087 610694874 1.220000e-36 165.0
25 TraesCS1A01G201600 chr4A 78.138 247 40 8 4932 5176 650324295 650324529 1.590000e-30 145.0
26 TraesCS1A01G201600 chr5D 88.000 50 4 2 4932 4980 331263094 331263046 2.120000e-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 TraesCS1A01G201600 chr1A 362861370 362866830 5460 False 10085.000000 10085 100.0000 1 5461 1 chr1A.!!$F1 5460
1 TraesCS1A01G201600 chr1B 391571447 391576765 5318 False 4133.500000 8067 94.4685 44 5436 2 chr1B.!!$F1 5392
2 TraesCS1A01G201600 chr1D 290442486 290448340 5854 False 2852.666667 5674 95.4190 1 5457 3 chr1D.!!$F1 5456

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
137 147 0.324552 TGGAACCCCCATCATGCAAG 60.325 55.0 0.0 0.0 40.82 4.01 F
1328 1394 0.097150 GCAGCCGAAACGAAATCCTC 59.903 55.0 0.0 0.0 0.00 3.71 F
2236 2302 0.251354 ATGAGCTTGCTGATGACGGT 59.749 50.0 0.0 0.0 0.00 4.83 F
2938 3004 0.107945 CTCTAGTGAGCCAACCTGCC 60.108 60.0 0.0 0.0 33.12 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1435 1501 0.035317 AGCGTGAAGTCAAGGCATCA 59.965 50.000 7.95 0.00 32.13 3.07 R
2317 2383 0.685785 TTCCAAGTGCACTTTGGCCA 60.686 50.000 29.23 18.36 33.11 5.36 R
3716 4220 0.099791 ACCCGCAAACTGAACAAACG 59.900 50.000 0.00 0.00 0.00 3.60 R
4743 5247 1.007387 CCAACCGAGCAAGGCAAAC 60.007 57.895 0.00 0.00 33.69 2.93 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
30 31 6.896307 TGGAACCCAGGTAAAAACTTTCTTTA 59.104 34.615 0.00 0.00 0.00 1.85
31 32 7.399478 TGGAACCCAGGTAAAAACTTTCTTTAA 59.601 33.333 0.00 0.00 0.00 1.52
32 33 8.259411 GGAACCCAGGTAAAAACTTTCTTTAAA 58.741 33.333 0.00 0.00 0.00 1.52
80 82 4.079730 GGAACCTCCTTATTCACCTTGGAT 60.080 45.833 0.00 0.00 32.53 3.41
86 88 5.285401 TCCTTATTCACCTTGGATCCTACA 58.715 41.667 14.23 0.00 0.00 2.74
87 89 5.366768 TCCTTATTCACCTTGGATCCTACAG 59.633 44.000 14.23 6.26 0.00 2.74
88 90 5.366768 CCTTATTCACCTTGGATCCTACAGA 59.633 44.000 14.23 1.92 0.00 3.41
90 92 5.983333 ATTCACCTTGGATCCTACAGATT 57.017 39.130 14.23 0.00 34.42 2.40
92 94 4.624913 TCACCTTGGATCCTACAGATTCT 58.375 43.478 14.23 0.00 34.42 2.40
93 95 5.032846 TCACCTTGGATCCTACAGATTCTT 58.967 41.667 14.23 0.00 34.42 2.52
137 147 0.324552 TGGAACCCCCATCATGCAAG 60.325 55.000 0.00 0.00 40.82 4.01
159 169 2.811104 CGAGACACGATTCAAAACACG 58.189 47.619 0.00 0.00 45.77 4.49
169 179 1.323412 TCAAAACACGGAACATGGGG 58.677 50.000 0.00 0.00 0.00 4.96
192 202 6.264970 GGGAGTCTGAAATTCCGTATAGTACT 59.735 42.308 0.00 0.00 31.59 2.73
196 206 6.637658 GTCTGAAATTCCGTATAGTACTCTGC 59.362 42.308 0.00 0.00 0.00 4.26
215 225 0.534877 CTGCAAGCTGGTACACCACA 60.535 55.000 0.00 0.00 42.01 4.17
216 226 0.817634 TGCAAGCTGGTACACCACAC 60.818 55.000 0.00 0.00 42.01 3.82
217 227 0.535102 GCAAGCTGGTACACCACACT 60.535 55.000 0.00 0.00 42.01 3.55
218 228 1.270625 GCAAGCTGGTACACCACACTA 60.271 52.381 0.00 0.00 42.01 2.74
219 229 2.413837 CAAGCTGGTACACCACACTAC 58.586 52.381 0.00 0.00 42.01 2.73
220 230 1.712056 AGCTGGTACACCACACTACA 58.288 50.000 0.00 0.00 42.01 2.74
221 231 1.343465 AGCTGGTACACCACACTACAC 59.657 52.381 0.00 0.00 42.01 2.90
222 232 1.607251 GCTGGTACACCACACTACACC 60.607 57.143 0.00 0.00 42.01 4.16
262 272 0.613012 AGGGCCATCAGTTTTGGAGC 60.613 55.000 6.18 0.00 36.26 4.70
303 313 3.627577 CACGGATCCTCCCTAAACAAATG 59.372 47.826 10.75 0.00 31.13 2.32
338 348 1.263217 GTACAAAGTGGCTGGTTGTCG 59.737 52.381 4.02 0.00 36.83 4.35
339 349 1.008538 CAAAGTGGCTGGTTGTCGC 60.009 57.895 0.00 0.00 0.00 5.19
363 377 1.153249 AGACGAGCGGGAGAGAGAG 60.153 63.158 0.00 0.00 0.00 3.20
654 671 1.373497 CACTCACGCACACTCCTCC 60.373 63.158 0.00 0.00 0.00 4.30
655 672 1.531840 ACTCACGCACACTCCTCCT 60.532 57.895 0.00 0.00 0.00 3.69
656 673 1.214062 CTCACGCACACTCCTCCTC 59.786 63.158 0.00 0.00 0.00 3.71
699 716 1.675641 CCACAGCGGGAGGGAAAAG 60.676 63.158 0.00 0.00 0.00 2.27
819 847 2.176546 CGTCGTCGGGTAAGCGAA 59.823 61.111 0.00 0.00 36.37 4.70
820 848 1.866496 CGTCGTCGGGTAAGCGAAG 60.866 63.158 0.00 0.00 36.37 3.79
838 867 2.338785 GCTCTGCCCCTGCTTGTTC 61.339 63.158 0.00 0.00 38.71 3.18
839 868 1.676967 CTCTGCCCCTGCTTGTTCC 60.677 63.158 0.00 0.00 38.71 3.62
886 921 2.185350 CCGGCTGCTTCTGTCGAT 59.815 61.111 0.00 0.00 32.46 3.59
915 975 4.608948 TGTTCTTGGGTGTTGTTGTTTT 57.391 36.364 0.00 0.00 0.00 2.43
1098 1158 1.201845 GGTAATTCGTTCGTTCGTGCC 60.202 52.381 0.00 0.00 0.00 5.01
1099 1159 0.709467 TAATTCGTTCGTTCGTGCCG 59.291 50.000 0.00 0.00 0.00 5.69
1108 1168 3.350612 TTCGTGCCGCCGGAAAAG 61.351 61.111 7.68 0.00 0.00 2.27
1219 1279 2.650813 ATCTTGCCGGCTCCGATCAC 62.651 60.000 29.70 0.00 42.83 3.06
1314 1380 3.569250 TTTAAAACCGATCAAGCAGCC 57.431 42.857 0.00 0.00 0.00 4.85
1328 1394 0.097150 GCAGCCGAAACGAAATCCTC 59.903 55.000 0.00 0.00 0.00 3.71
1404 1470 5.819379 TCTGAACCATGATAATTCAGTCTGC 59.181 40.000 19.51 0.00 46.20 4.26
1435 1501 5.876612 GTTCTGAATTCTGAACTGATGCT 57.123 39.130 33.69 0.00 45.44 3.79
1441 1507 2.034104 TCTGAACTGATGCTGATGCC 57.966 50.000 0.00 0.00 38.71 4.40
1484 1550 2.001159 GACTTGCTGCTGTGATCTCTG 58.999 52.381 0.00 0.00 0.00 3.35
1597 1663 1.067354 ACGGTTATCACCACGTTCTCC 60.067 52.381 0.00 0.00 44.53 3.71
1621 1687 1.604593 GGTGGCTGATGCTGTTGGT 60.605 57.895 0.00 0.00 39.59 3.67
2066 2132 2.910688 TGTCTCAGGTTTGTCTGTCC 57.089 50.000 0.00 0.00 36.25 4.02
2236 2302 0.251354 ATGAGCTTGCTGATGACGGT 59.749 50.000 0.00 0.00 0.00 4.83
2575 2641 5.640783 TGATGAAGATTATGCATCGGATCAC 59.359 40.000 0.19 5.44 40.89 3.06
2695 2761 1.603739 GGGTGGTGTGGGAAGAAGC 60.604 63.158 0.00 0.00 0.00 3.86
2803 2869 1.928868 CAGATGGGCAAAAGGAAGGT 58.071 50.000 0.00 0.00 0.00 3.50
2842 2908 3.023949 GCATGAGGAGGGCGTGTCT 62.024 63.158 0.00 0.00 0.00 3.41
2938 3004 0.107945 CTCTAGTGAGCCAACCTGCC 60.108 60.000 0.00 0.00 33.12 4.85
3178 3247 5.337219 TGACAACTAATTTAGCACACACG 57.663 39.130 3.28 0.00 0.00 4.49
3262 3333 3.680642 ATAACATCATGCTGTTGCGTC 57.319 42.857 22.02 0.00 43.34 5.19
3542 3613 5.352016 GTGGTGCGGTAGAAACACATAATAA 59.648 40.000 0.00 0.00 36.00 1.40
3662 4166 5.556915 TCTTCTTCCACGGTTCATGTTTAT 58.443 37.500 0.00 0.00 0.00 1.40
3715 4219 5.106436 TGTTCATGTGCTGATGATCAACTTC 60.106 40.000 0.00 0.00 31.87 3.01
3716 4220 3.943381 TCATGTGCTGATGATCAACTTCC 59.057 43.478 0.00 0.00 0.00 3.46
3825 4329 3.840666 ACATTGGACTAAGCTCTTCCTCA 59.159 43.478 9.08 0.00 0.00 3.86
4006 4510 9.581289 TGAAAGAGTAACCATTCTTCCATTTTA 57.419 29.630 0.00 0.00 32.71 1.52
4034 4538 4.350816 TCATCCAGGTTTCTTCTCCTTTCA 59.649 41.667 0.00 0.00 30.91 2.69
4058 4562 4.202161 ACAATCCCTGTCTTGATAGTAGCG 60.202 45.833 0.00 0.00 29.87 4.26
4076 4580 2.073816 GCGCTAGCTGTCTTGGTTTTA 58.926 47.619 13.93 0.00 41.01 1.52
4112 4616 2.672996 GGAACCATGGTGCACGCT 60.673 61.111 24.87 4.48 0.00 5.07
4298 4802 0.467384 CTCTCCCCGTGATGCTCAAT 59.533 55.000 0.00 0.00 0.00 2.57
4304 4808 0.742505 CCGTGATGCTCAATGCCATT 59.257 50.000 0.00 0.00 42.00 3.16
4412 4916 1.997874 GCCCCTGGAGGTCATCACT 60.998 63.158 0.00 0.00 0.00 3.41
4601 5105 4.579869 ACTTTACATCGTGAGGCTGAATT 58.420 39.130 0.00 0.00 0.00 2.17
4606 5110 2.254546 TCGTGAGGCTGAATTGTGTT 57.745 45.000 0.00 0.00 0.00 3.32
4653 5157 9.184523 AGTAGGATATGTACTTAGATCATCTGC 57.815 37.037 0.00 0.00 0.00 4.26
4736 5240 6.593770 AGTGCTGTTATCACAATTTATGTCGA 59.406 34.615 0.00 0.00 41.46 4.20
4759 5263 1.034838 TGTGTTTGCCTTGCTCGGTT 61.035 50.000 0.00 0.00 0.00 4.44
4786 5290 4.761739 TCAGTTTATCCTCTTTGTTGCCAG 59.238 41.667 0.00 0.00 0.00 4.85
4787 5291 4.520492 CAGTTTATCCTCTTTGTTGCCAGT 59.480 41.667 0.00 0.00 0.00 4.00
4788 5292 5.010012 CAGTTTATCCTCTTTGTTGCCAGTT 59.990 40.000 0.00 0.00 0.00 3.16
4789 5293 5.598417 AGTTTATCCTCTTTGTTGCCAGTTT 59.402 36.000 0.00 0.00 0.00 2.66
4790 5294 5.452078 TTATCCTCTTTGTTGCCAGTTTG 57.548 39.130 0.00 0.00 0.00 2.93
4791 5295 1.408702 TCCTCTTTGTTGCCAGTTTGC 59.591 47.619 0.00 0.00 0.00 3.68
4792 5296 1.538849 CCTCTTTGTTGCCAGTTTGCC 60.539 52.381 0.00 0.00 0.00 4.52
4793 5297 1.136695 CTCTTTGTTGCCAGTTTGCCA 59.863 47.619 0.00 0.00 0.00 4.92
4809 5313 1.694150 TGCCACTAGTTCTCAGTTGCT 59.306 47.619 0.00 0.00 36.07 3.91
4834 5338 3.312421 TCACTTCAGCAGTTTAGTTGTGC 59.688 43.478 0.00 0.00 37.48 4.57
4836 5340 4.511454 CACTTCAGCAGTTTAGTTGTGCTA 59.489 41.667 0.00 0.00 45.82 3.49
4837 5341 5.180117 CACTTCAGCAGTTTAGTTGTGCTAT 59.820 40.000 0.00 0.00 45.82 2.97
4838 5342 5.765182 ACTTCAGCAGTTTAGTTGTGCTATT 59.235 36.000 0.00 0.00 45.82 1.73
4839 5343 6.934645 ACTTCAGCAGTTTAGTTGTGCTATTA 59.065 34.615 0.00 0.00 45.82 0.98
4840 5344 6.968131 TCAGCAGTTTAGTTGTGCTATTAG 57.032 37.500 0.00 0.00 45.82 1.73
4841 5345 6.464222 TCAGCAGTTTAGTTGTGCTATTAGT 58.536 36.000 0.00 0.00 45.82 2.24
4842 5346 7.608153 TCAGCAGTTTAGTTGTGCTATTAGTA 58.392 34.615 0.00 0.00 45.82 1.82
4843 5347 7.544566 TCAGCAGTTTAGTTGTGCTATTAGTAC 59.455 37.037 5.09 5.09 45.82 2.73
4844 5348 7.545965 CAGCAGTTTAGTTGTGCTATTAGTACT 59.454 37.037 12.31 0.00 45.82 2.73
4845 5349 8.095169 AGCAGTTTAGTTGTGCTATTAGTACTT 58.905 33.333 12.31 0.00 45.72 2.24
4846 5350 8.718734 GCAGTTTAGTTGTGCTATTAGTACTTT 58.281 33.333 12.31 0.00 31.77 2.66
5214 5719 7.775093 TGGGTGAACCTCTTCATTAATATTGAG 59.225 37.037 0.00 0.00 38.69 3.02
5215 5720 7.993183 GGGTGAACCTCTTCATTAATATTGAGA 59.007 37.037 0.00 0.00 38.69 3.27
5216 5721 9.396022 GGTGAACCTCTTCATTAATATTGAGAA 57.604 33.333 0.00 0.00 38.69 2.87
5236 5741 5.615289 AGAATATTGATACTCACTGCACCC 58.385 41.667 0.00 0.00 0.00 4.61
5275 5783 3.135712 TCCAACCTCTGCACTTCACTAAA 59.864 43.478 0.00 0.00 0.00 1.85
5283 5791 4.578928 TCTGCACTTCACTAAAGAAAACCC 59.421 41.667 0.00 0.00 38.44 4.11
5284 5792 4.274147 TGCACTTCACTAAAGAAAACCCA 58.726 39.130 0.00 0.00 38.44 4.51
5285 5793 4.892934 TGCACTTCACTAAAGAAAACCCAT 59.107 37.500 0.00 0.00 38.44 4.00
5292 5800 7.996098 TCACTAAAGAAAACCCATCTTAAGG 57.004 36.000 1.85 0.00 36.14 2.69
5298 5806 6.665992 AGAAAACCCATCTTAAGGAAAACC 57.334 37.500 1.85 0.00 0.00 3.27
5302 5810 6.713731 AACCCATCTTAAGGAAAACCTCTA 57.286 37.500 1.85 0.00 0.00 2.43
5408 5916 3.246301 CCTCATGGATAGTGACCATCCT 58.754 50.000 11.24 0.00 45.00 3.24
5425 5933 8.421784 TGACCATCCTATCTAAAATATATCCGC 58.578 37.037 0.00 0.00 0.00 5.54
5440 5948 7.701539 ATATATCCGCTTTTCATAAATGCCA 57.298 32.000 5.11 0.00 38.04 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 95 9.653287 CACTGGTTGTAGAATATCTTTTGTAGA 57.347 33.333 0.00 0.00 37.28 2.59
137 147 1.529438 TGTTTTGAATCGTGTCTCGCC 59.471 47.619 0.00 0.00 39.67 5.54
159 169 2.879103 TTTCAGACTCCCCATGTTCC 57.121 50.000 0.00 0.00 0.00 3.62
169 179 8.071368 CAGAGTACTATACGGAATTTCAGACTC 58.929 40.741 0.00 5.00 0.00 3.36
192 202 0.603707 GTGTACCAGCTTGCAGCAGA 60.604 55.000 10.16 0.00 45.56 4.26
196 206 4.798433 TGGTGTACCAGCTTGCAG 57.202 55.556 0.00 0.00 42.01 4.41
212 222 1.072505 GGGGGTGTGGTGTAGTGTG 59.927 63.158 0.00 0.00 0.00 3.82
215 225 1.423794 CCAAGGGGGTGTGGTGTAGT 61.424 60.000 0.00 0.00 0.00 2.73
216 226 1.131303 TCCAAGGGGGTGTGGTGTAG 61.131 60.000 0.00 0.00 38.11 2.74
217 227 0.698198 TTCCAAGGGGGTGTGGTGTA 60.698 55.000 0.00 0.00 38.11 2.90
218 228 1.368268 ATTCCAAGGGGGTGTGGTGT 61.368 55.000 0.00 0.00 38.11 4.16
219 229 0.611896 GATTCCAAGGGGGTGTGGTG 60.612 60.000 0.00 0.00 38.11 4.17
220 230 0.776080 AGATTCCAAGGGGGTGTGGT 60.776 55.000 0.00 0.00 38.11 4.16
221 231 1.212935 CTAGATTCCAAGGGGGTGTGG 59.787 57.143 0.00 0.00 38.11 4.17
222 232 1.408822 GCTAGATTCCAAGGGGGTGTG 60.409 57.143 0.00 0.00 38.11 3.82
262 272 3.113979 TGCGCTGTCACATGCTCG 61.114 61.111 9.73 0.00 0.00 5.03
303 313 7.484959 GCCACTTTGTACTTGTGCTATTAATTC 59.515 37.037 0.00 0.00 0.00 2.17
325 335 2.899838 TGTGCGACAACCAGCCAC 60.900 61.111 0.00 0.00 0.00 5.01
339 349 3.669036 CTCCCGCTCGTCTCGTGTG 62.669 68.421 0.00 0.00 0.00 3.82
348 358 2.904866 CCCTCTCTCTCCCGCTCG 60.905 72.222 0.00 0.00 0.00 5.03
349 359 1.380650 AACCCTCTCTCTCCCGCTC 60.381 63.158 0.00 0.00 0.00 5.03
350 360 1.684049 CAACCCTCTCTCTCCCGCT 60.684 63.158 0.00 0.00 0.00 5.52
351 361 2.726351 CCAACCCTCTCTCTCCCGC 61.726 68.421 0.00 0.00 0.00 6.13
363 377 4.547367 CGAGCCCGGATCCAACCC 62.547 72.222 13.41 0.00 0.00 4.11
384 398 5.627503 GCATATGGGAATTATTGAATGGGGC 60.628 44.000 4.56 0.00 0.00 5.80
556 570 1.130749 CTCTACGATATTCCTCCGCGG 59.869 57.143 22.12 22.12 0.00 6.46
595 612 3.235200 ACTACTATCATCTGGTGGCCTC 58.765 50.000 3.32 0.00 0.00 4.70
817 845 2.045131 CAAGCAGGGGCAGAGCTTC 61.045 63.158 6.57 0.00 46.01 3.86
819 847 2.761304 GAACAAGCAGGGGCAGAGCT 62.761 60.000 0.00 0.00 44.61 4.09
820 848 2.282745 AACAAGCAGGGGCAGAGC 60.283 61.111 0.00 0.00 44.61 4.09
821 849 1.676967 GGAACAAGCAGGGGCAGAG 60.677 63.158 0.00 0.00 44.61 3.35
839 868 3.705638 CTGCTCCACGCACACACG 61.706 66.667 0.00 0.00 45.47 4.49
886 921 4.709397 ACAACACCCAAGAACAAATCAGAA 59.291 37.500 0.00 0.00 0.00 3.02
924 984 2.027073 CAGCACGGCAAAGCTCGTA 61.027 57.895 0.00 0.00 39.50 3.43
1098 1158 4.766088 GCAGCTGCTTTTCCGGCG 62.766 66.667 31.33 0.00 41.94 6.46
1108 1168 2.774774 CGTCGAAAGAGCAGCTGC 59.225 61.111 31.53 31.53 43.49 5.25
1219 1279 1.079127 AGCTCCACCAAATCCGTCG 60.079 57.895 0.00 0.00 0.00 5.12
1286 1346 6.084277 GCTTGATCGGTTTTAAAAGATCGTT 58.916 36.000 18.18 11.08 41.57 3.85
1289 1355 5.513141 GCTGCTTGATCGGTTTTAAAAGATC 59.487 40.000 17.26 17.26 39.74 2.75
1296 1362 1.083489 CGGCTGCTTGATCGGTTTTA 58.917 50.000 0.00 0.00 0.00 1.52
1328 1394 2.346847 CAGAGAAGTCGGAAATCTTGCG 59.653 50.000 0.00 0.00 46.40 4.85
1404 1470 3.920412 TCAGAATTCAGAACATGTCGACG 59.080 43.478 11.62 0.00 0.00 5.12
1429 1495 2.290450 TGAAGTCAAGGCATCAGCATCA 60.290 45.455 0.00 0.00 44.61 3.07
1435 1501 0.035317 AGCGTGAAGTCAAGGCATCA 59.965 50.000 7.95 0.00 32.13 3.07
1441 1507 1.462283 CATGGTCAGCGTGAAGTCAAG 59.538 52.381 0.00 0.00 0.00 3.02
2317 2383 0.685785 TTCCAAGTGCACTTTGGCCA 60.686 50.000 29.23 18.36 33.11 5.36
2575 2641 1.012086 CCTCAATGTCATCAGCACCG 58.988 55.000 0.00 0.00 0.00 4.94
2695 2761 2.829003 CCTCCCTGCATGCTGCTG 60.829 66.667 20.33 12.02 45.31 4.41
2842 2908 1.944896 TAGAGCCCCTCCGATCACCA 61.945 60.000 0.00 0.00 0.00 4.17
2938 3004 6.406692 TCTATCAGGTCCTTCGAATAAAGG 57.593 41.667 0.00 0.00 46.11 3.11
3542 3613 8.177119 ACAACCATACACAACAATAAGAATGT 57.823 30.769 0.00 0.00 0.00 2.71
3715 4219 0.593773 CCCGCAAACTGAACAAACGG 60.594 55.000 0.00 0.00 38.88 4.44
3716 4220 0.099791 ACCCGCAAACTGAACAAACG 59.900 50.000 0.00 0.00 0.00 3.60
3825 4329 7.659390 GTCAAGGCACTAATAAGAATAGATGCT 59.341 37.037 0.00 0.00 38.49 3.79
3968 4472 6.998074 TGGTTACTCTTTCATTCACATTCAGT 59.002 34.615 0.00 0.00 0.00 3.41
4006 4510 5.252630 AGGAGAAGAAACCTGGATGAGAAAT 59.747 40.000 0.00 0.00 34.99 2.17
4034 4538 5.675538 GCTACTATCAAGACAGGGATTGTT 58.324 41.667 0.00 0.00 41.05 2.83
4058 4562 4.315803 TCACTAAAACCAAGACAGCTAGC 58.684 43.478 6.62 6.62 0.00 3.42
4076 4580 2.567169 TCCGACATCCAGAACATTCACT 59.433 45.455 0.00 0.00 0.00 3.41
4112 4616 1.807165 GCTGATCGTTGAGAGCGCA 60.807 57.895 11.47 0.00 38.28 6.09
4298 4802 2.046023 CCAGCGAGACCAATGGCA 60.046 61.111 0.00 0.00 0.00 4.92
4304 4808 1.587043 CGAAGACTCCAGCGAGACCA 61.587 60.000 0.00 0.00 38.52 4.02
4343 4847 5.909621 AGACGAATACAAAGGCTAGTACA 57.090 39.130 0.00 0.00 0.00 2.90
4344 4848 6.789262 TGTAGACGAATACAAAGGCTAGTAC 58.211 40.000 2.30 0.00 32.80 2.73
4653 5157 5.175090 AGAAAGTTCCAAAGCGAAAAGAG 57.825 39.130 0.00 0.00 0.00 2.85
4736 5240 2.164219 CCGAGCAAGGCAAACACATAAT 59.836 45.455 0.00 0.00 0.00 1.28
4743 5247 1.007387 CCAACCGAGCAAGGCAAAC 60.007 57.895 0.00 0.00 33.69 2.93
4759 5263 5.009610 GCAACAAAGAGGATAAACTGAACCA 59.990 40.000 0.00 0.00 0.00 3.67
4786 5290 3.304057 GCAACTGAGAACTAGTGGCAAAC 60.304 47.826 0.00 0.00 43.18 2.93
4787 5291 2.878406 GCAACTGAGAACTAGTGGCAAA 59.122 45.455 0.00 0.00 43.18 3.68
4788 5292 2.104792 AGCAACTGAGAACTAGTGGCAA 59.895 45.455 7.21 0.00 45.52 4.52
4789 5293 1.694150 AGCAACTGAGAACTAGTGGCA 59.306 47.619 7.21 0.00 45.52 4.92
4790 5294 2.464157 AGCAACTGAGAACTAGTGGC 57.536 50.000 0.00 0.00 43.85 5.01
4791 5295 4.218635 TGACTAGCAACTGAGAACTAGTGG 59.781 45.833 14.89 0.00 44.02 4.00
4792 5296 5.048364 AGTGACTAGCAACTGAGAACTAGTG 60.048 44.000 14.89 0.00 44.02 2.74
4793 5297 5.074115 AGTGACTAGCAACTGAGAACTAGT 58.926 41.667 11.51 11.51 46.04 2.57
4809 5313 5.753438 CACAACTAAACTGCTGAAGTGACTA 59.247 40.000 0.00 0.00 39.81 2.59
5221 5726 1.413077 GTAGGGGGTGCAGTGAGTATC 59.587 57.143 0.00 0.00 0.00 2.24
5222 5727 1.497161 GTAGGGGGTGCAGTGAGTAT 58.503 55.000 0.00 0.00 0.00 2.12
5236 5741 4.461431 GGTTGGATTAAACAAGTGGTAGGG 59.539 45.833 0.00 0.00 0.00 3.53
5275 5783 6.665992 GGTTTTCCTTAAGATGGGTTTTCT 57.334 37.500 3.36 0.00 36.94 2.52
5292 5800 8.809468 ATTGGGATTTTCTACTAGAGGTTTTC 57.191 34.615 0.00 0.00 0.00 2.29
5298 5806 6.768381 GGGTGAATTGGGATTTTCTACTAGAG 59.232 42.308 0.00 0.00 0.00 2.43
5302 5810 5.536497 AGGGTGAATTGGGATTTTCTACT 57.464 39.130 0.00 0.00 0.00 2.57
5333 5841 3.244805 GGGGGTCACACTAAAGCTAAACT 60.245 47.826 0.00 0.00 0.00 2.66
5334 5842 3.079578 GGGGGTCACACTAAAGCTAAAC 58.920 50.000 0.00 0.00 0.00 2.01
5339 5847 0.984995 AGAGGGGGTCACACTAAAGC 59.015 55.000 0.00 0.00 0.00 3.51
5425 5933 9.982291 CATCTTTCATTTGGCATTTATGAAAAG 57.018 29.630 22.20 18.06 43.64 2.27


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

AutoCloner maintained by Alex Coulton.