Multiple sequence alignment - TraesCS3D01G151400

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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 TraesCS3D01G151400 chr3D 100.000 5782 0 0 1 5782 116035657 116041438 0.000000e+00 10678.0
1 TraesCS3D01G151400 chr3B 95.196 4913 108 53 373 5213 169622245 169627101 0.000000e+00 7648.0
2 TraesCS3D01G151400 chr3B 89.796 147 14 1 1 147 169621963 169622108 2.750000e-43 187.0
3 TraesCS3D01G151400 chr3B 91.379 116 10 0 5330 5445 169627151 169627266 6.000000e-35 159.0
4 TraesCS3D01G151400 chr3A 91.680 5072 280 71 373 5365 112950847 112955855 0.000000e+00 6898.0
5 TraesCS3D01G151400 chr3A 89.769 303 19 4 5469 5762 112956109 112956408 1.520000e-100 377.0
6 TraesCS3D01G151400 chr3A 93.798 129 4 2 1 126 112950560 112950687 2.130000e-44 191.0
7 TraesCS3D01G151400 chr3A 100.000 47 0 0 5399 5445 112955990 112956036 2.870000e-13 87.9
8 TraesCS3D01G151400 chr1A 85.047 107 11 4 144 250 115501438 115501539 2.850000e-18 104.0
9 TraesCS3D01G151400 chr4D 91.379 58 3 1 189 246 17079325 17079270 1.730000e-10 78.7


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 TraesCS3D01G151400 chr3D 116035657 116041438 5781 False 10678.000000 10678 100.000000 1 5782 1 chr3D.!!$F1 5781
1 TraesCS3D01G151400 chr3B 169621963 169627266 5303 False 2664.666667 7648 92.123667 1 5445 3 chr3B.!!$F1 5444
2 TraesCS3D01G151400 chr3A 112950560 112956408 5848 False 1888.475000 6898 93.811750 1 5762 4 chr3A.!!$F1 5761

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
843 897 2.123425 CCCCACCGGAGCTAGCTA 60.123 66.667 19.38 0.0 0.00 3.32 F
1183 1241 0.611618 TCATGGGTGTGGTGCAATCC 60.612 55.000 0.00 0.0 0.00 3.01 F
1809 1878 1.129251 CATGTCGCACTTACAGCCTTG 59.871 52.381 0.00 0.0 0.00 3.61 F
2651 2725 1.838112 TTGGGCATTGTCAGGATGTC 58.162 50.000 0.00 0.0 37.40 3.06 F
4166 4272 1.261619 CTGAAACACGGAGTTCAGTGC 59.738 52.381 11.48 0.0 44.12 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2351 2425 3.260884 AGACGCCTTCTTGGAACTGATTA 59.739 43.478 0.00 0.00 38.35 1.75 R
3252 3337 2.086094 TGTTGTCAGGCTATGCATGTG 58.914 47.619 10.16 3.16 41.32 3.21 R
3338 3423 2.490903 GAGCTGATCATGTGCCAGTTTT 59.509 45.455 0.00 0.00 0.00 2.43 R
4267 4373 2.097038 CCTTTGCTCTGTCCGCGAG 61.097 63.158 8.23 0.00 0.00 5.03 R
5758 6121 0.040067 GTTGGCTGAAACTTGAGGCG 60.040 55.000 0.00 0.00 39.75 5.52 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
50 54 5.661759 TCTCTAAATTTCTGGTACTCCCTCC 59.338 44.000 0.00 0.00 0.00 4.30
56 60 4.635699 TTCTGGTACTCCCTCCTTTTTC 57.364 45.455 0.00 0.00 0.00 2.29
150 154 8.565896 ACATGAAGCTTTACAATATCAAGTGA 57.434 30.769 0.00 0.00 0.00 3.41
151 155 9.182214 ACATGAAGCTTTACAATATCAAGTGAT 57.818 29.630 0.00 0.00 38.51 3.06
211 215 5.697473 TTTTTGCACGAATCTCCATGTAA 57.303 34.783 0.00 0.00 0.00 2.41
212 216 5.697473 TTTTGCACGAATCTCCATGTAAA 57.303 34.783 0.00 0.00 0.00 2.01
213 217 5.697473 TTTGCACGAATCTCCATGTAAAA 57.303 34.783 0.00 0.00 0.00 1.52
214 218 5.895636 TTGCACGAATCTCCATGTAAAAT 57.104 34.783 0.00 0.00 0.00 1.82
215 219 5.484173 TGCACGAATCTCCATGTAAAATC 57.516 39.130 0.00 0.00 0.00 2.17
216 220 4.940654 TGCACGAATCTCCATGTAAAATCA 59.059 37.500 0.00 0.00 0.00 2.57
217 221 5.414144 TGCACGAATCTCCATGTAAAATCAA 59.586 36.000 0.00 0.00 0.00 2.57
218 222 6.072230 TGCACGAATCTCCATGTAAAATCAAA 60.072 34.615 0.00 0.00 0.00 2.69
219 223 6.470235 GCACGAATCTCCATGTAAAATCAAAG 59.530 38.462 0.00 0.00 0.00 2.77
220 224 7.626240 GCACGAATCTCCATGTAAAATCAAAGA 60.626 37.037 0.00 0.00 0.00 2.52
221 225 8.236586 CACGAATCTCCATGTAAAATCAAAGAA 58.763 33.333 0.00 0.00 0.00 2.52
222 226 8.792633 ACGAATCTCCATGTAAAATCAAAGAAA 58.207 29.630 0.00 0.00 0.00 2.52
223 227 9.282247 CGAATCTCCATGTAAAATCAAAGAAAG 57.718 33.333 0.00 0.00 0.00 2.62
240 244 9.958234 TCAAAGAAAGATAGTATCGAATCTGAG 57.042 33.333 12.94 10.01 32.79 3.35
241 245 9.958234 CAAAGAAAGATAGTATCGAATCTGAGA 57.042 33.333 12.94 0.00 32.79 3.27
242 246 9.959749 AAAGAAAGATAGTATCGAATCTGAGAC 57.040 33.333 12.94 0.00 32.79 3.36
243 247 8.918202 AGAAAGATAGTATCGAATCTGAGACT 57.082 34.615 11.97 7.32 42.63 3.24
244 248 9.349713 AGAAAGATAGTATCGAATCTGAGACTT 57.650 33.333 11.97 0.00 40.62 3.01
247 251 8.263940 AGATAGTATCGAATCTGAGACTTAGC 57.736 38.462 4.48 0.00 40.62 3.09
248 252 7.880713 AGATAGTATCGAATCTGAGACTTAGCA 59.119 37.037 4.48 0.00 40.62 3.49
249 253 6.701145 AGTATCGAATCTGAGACTTAGCAA 57.299 37.500 0.00 0.00 37.11 3.91
250 254 7.101652 AGTATCGAATCTGAGACTTAGCAAA 57.898 36.000 0.00 0.00 37.11 3.68
251 255 7.548097 AGTATCGAATCTGAGACTTAGCAAAA 58.452 34.615 0.00 0.00 37.11 2.44
252 256 8.200792 AGTATCGAATCTGAGACTTAGCAAAAT 58.799 33.333 0.00 0.00 37.11 1.82
253 257 7.856145 ATCGAATCTGAGACTTAGCAAAATT 57.144 32.000 0.00 0.00 0.00 1.82
254 258 7.065216 TCGAATCTGAGACTTAGCAAAATTG 57.935 36.000 0.00 0.00 0.00 2.32
255 259 6.873605 TCGAATCTGAGACTTAGCAAAATTGA 59.126 34.615 0.00 0.00 0.00 2.57
256 260 7.387673 TCGAATCTGAGACTTAGCAAAATTGAA 59.612 33.333 0.00 0.00 0.00 2.69
257 261 8.017373 CGAATCTGAGACTTAGCAAAATTGAAA 58.983 33.333 0.00 0.00 0.00 2.69
258 262 9.683069 GAATCTGAGACTTAGCAAAATTGAAAA 57.317 29.630 0.00 0.00 0.00 2.29
390 434 5.959618 AATTCTAAAAAGACACGGAAGGG 57.040 39.130 0.00 0.00 43.28 3.95
843 897 2.123425 CCCCACCGGAGCTAGCTA 60.123 66.667 19.38 0.00 0.00 3.32
844 898 2.203771 CCCCACCGGAGCTAGCTAG 61.204 68.421 19.38 16.84 0.00 3.42
883 937 2.260743 GTTCGTCCACCGGTCTCC 59.739 66.667 2.59 0.00 37.11 3.71
902 956 4.391216 TCTCCGTCTTAGTTACTCGTCTTG 59.609 45.833 0.00 0.00 0.00 3.02
931 988 3.057547 CTCTGAGAGACCGCGGGTG 62.058 68.421 31.76 10.72 35.25 4.61
932 989 3.374402 CTGAGAGACCGCGGGTGT 61.374 66.667 31.76 15.24 35.25 4.16
933 990 3.343788 CTGAGAGACCGCGGGTGTC 62.344 68.421 31.76 23.29 44.96 3.67
934 991 4.131088 GAGAGACCGCGGGTGTCC 62.131 72.222 31.76 13.37 45.64 4.02
1136 1193 1.280142 CGAGAGACCGATGGTAGCG 59.720 63.158 0.00 0.00 35.25 4.26
1183 1241 0.611618 TCATGGGTGTGGTGCAATCC 60.612 55.000 0.00 0.00 0.00 3.01
1191 1249 2.162208 GTGTGGTGCAATCCTGTACATG 59.838 50.000 0.00 0.00 39.72 3.21
1206 1264 2.338577 ACATGTGCTAGGATTGGCTC 57.661 50.000 0.00 0.00 0.00 4.70
1372 1438 7.124750 CCCCTCTATTTTCTTCCAAATGTTGAT 59.875 37.037 0.00 0.00 0.00 2.57
1403 1469 2.289274 CCACGCGATTATTTATGTGCCA 59.711 45.455 15.93 0.00 0.00 4.92
1464 1531 5.532406 TGCCAGATTTATGTCAGGAAATAGC 59.468 40.000 0.00 2.33 0.00 2.97
1533 1602 8.021973 CCAATACGATTAGCTAAGGTAGTGTAG 58.978 40.741 27.73 18.41 29.74 2.74
1809 1878 1.129251 CATGTCGCACTTACAGCCTTG 59.871 52.381 0.00 0.00 0.00 3.61
2351 2425 6.698008 TTGTGTTTCAGATCACTTCACAAT 57.302 33.333 14.58 0.00 38.69 2.71
2651 2725 1.838112 TTGGGCATTGTCAGGATGTC 58.162 50.000 0.00 0.00 37.40 3.06
3481 3567 5.106475 ACAGCTAAACAGACTAGAACTCGAG 60.106 44.000 11.84 11.84 0.00 4.04
3794 3898 6.223852 TCTCCTCGGATATTGCATAGAAAAC 58.776 40.000 0.00 0.00 0.00 2.43
4106 4210 5.541953 TTATGACAGATGACTATGCTGCT 57.458 39.130 0.00 0.00 33.03 4.24
4132 4236 6.735556 AGGTATCCATTTGAAGGAAATCAGT 58.264 36.000 0.00 0.00 38.93 3.41
4133 4237 7.184862 AGGTATCCATTTGAAGGAAATCAGTT 58.815 34.615 0.00 0.00 38.93 3.16
4166 4272 1.261619 CTGAAACACGGAGTTCAGTGC 59.738 52.381 11.48 0.00 44.12 4.40
4267 4373 3.578688 GATGTTGGCATGTGGAAAGAAC 58.421 45.455 0.00 0.00 35.07 3.01
4479 4589 6.321690 TCCAAACTCCAAACTTAATTTCCGAA 59.678 34.615 0.00 0.00 0.00 4.30
4502 4613 4.404507 ACATTGCATCGTTACAACTGTC 57.595 40.909 0.00 0.00 0.00 3.51
4954 5093 4.127907 CAGATGTGATGCAGCTACTGATT 58.872 43.478 2.53 0.00 42.70 2.57
5004 5151 1.145531 TGAGGGAATACCATGGGCATG 59.854 52.381 18.09 0.00 43.89 4.06
5005 5152 1.145738 GAGGGAATACCATGGGCATGT 59.854 52.381 18.09 0.00 43.89 3.21
5006 5153 2.375174 GAGGGAATACCATGGGCATGTA 59.625 50.000 18.09 0.00 43.89 2.29
5007 5154 2.108250 AGGGAATACCATGGGCATGTAC 59.892 50.000 18.09 0.40 43.89 2.90
5008 5155 2.158534 GGGAATACCATGGGCATGTACA 60.159 50.000 18.09 0.00 39.85 2.90
5072 5231 0.537371 AACAAGTGCCTGGTGCTACC 60.537 55.000 0.00 0.00 42.00 3.18
5127 5287 5.591472 TCTGAATATGCCACCTGATTCAAAG 59.409 40.000 0.00 0.00 37.73 2.77
5128 5288 4.098349 TGAATATGCCACCTGATTCAAAGC 59.902 41.667 0.00 0.00 35.82 3.51
5129 5289 2.226962 ATGCCACCTGATTCAAAGCT 57.773 45.000 0.00 0.00 0.00 3.74
5130 5290 1.538047 TGCCACCTGATTCAAAGCTC 58.462 50.000 0.00 0.00 0.00 4.09
5132 5292 1.471684 GCCACCTGATTCAAAGCTCTG 59.528 52.381 0.00 0.00 0.00 3.35
5133 5293 2.877300 GCCACCTGATTCAAAGCTCTGA 60.877 50.000 0.00 0.00 0.00 3.27
5134 5294 3.618351 CCACCTGATTCAAAGCTCTGAT 58.382 45.455 0.00 0.00 0.00 2.90
5135 5295 3.377485 CCACCTGATTCAAAGCTCTGATG 59.623 47.826 0.00 0.00 0.00 3.07
5136 5296 4.259356 CACCTGATTCAAAGCTCTGATGA 58.741 43.478 0.00 0.00 0.00 2.92
5137 5297 4.882427 CACCTGATTCAAAGCTCTGATGAT 59.118 41.667 0.00 0.00 0.00 2.45
5138 5298 6.053650 CACCTGATTCAAAGCTCTGATGATA 58.946 40.000 0.00 0.00 0.00 2.15
5181 5345 7.901029 TGCATGGTTTAAGTTTTCCATATGAA 58.099 30.769 3.65 0.00 38.43 2.57
5198 5362 9.820725 TCCATATGAAAATTCATCCATTTCAAC 57.179 29.630 11.69 0.00 44.17 3.18
5199 5363 9.826574 CCATATGAAAATTCATCCATTTCAACT 57.173 29.630 11.69 0.00 44.17 3.16
5214 5414 8.859090 TCCATTTCAACTATGTTCATTTCTTGT 58.141 29.630 0.00 0.00 0.00 3.16
5225 5425 7.290110 TGTTCATTTCTTGTCTGTCTCTCTA 57.710 36.000 0.00 0.00 0.00 2.43
5234 5434 2.685897 GTCTGTCTCTCTATTGCTCGGT 59.314 50.000 0.00 0.00 0.00 4.69
5292 5493 9.754382 CACCCAATCAATAATCAATCCTTTTAG 57.246 33.333 0.00 0.00 0.00 1.85
5294 5495 8.370182 CCCAATCAATAATCAATCCTTTTAGGG 58.630 37.037 0.00 0.00 35.59 3.53
5296 5497 9.971922 CAATCAATAATCAATCCTTTTAGGGTC 57.028 33.333 0.00 0.00 35.59 4.46
5298 5499 8.752005 TCAATAATCAATCCTTTTAGGGTCTG 57.248 34.615 0.00 0.00 35.59 3.51
5300 5501 8.971073 CAATAATCAATCCTTTTAGGGTCTGTT 58.029 33.333 0.00 0.00 35.59 3.16
5318 5519 1.929836 GTTCTATCGACAAGCAGCCAG 59.070 52.381 0.00 0.00 0.00 4.85
5326 5527 5.722021 TCGACAAGCAGCCAGATATTATA 57.278 39.130 0.00 0.00 0.00 0.98
5445 5751 2.527497 TGGACATTCATGTGTGGCAAT 58.473 42.857 0.00 0.00 41.95 3.56
5446 5752 2.898612 TGGACATTCATGTGTGGCAATT 59.101 40.909 0.00 0.00 41.95 2.32
5447 5753 3.324268 TGGACATTCATGTGTGGCAATTT 59.676 39.130 0.00 0.00 41.95 1.82
5448 5754 4.202336 TGGACATTCATGTGTGGCAATTTT 60.202 37.500 0.00 0.00 41.95 1.82
5449 5755 4.756135 GGACATTCATGTGTGGCAATTTTT 59.244 37.500 0.00 0.00 41.95 1.94
5485 5840 6.550938 ATCAGTATGGTGAGAGAAATGTCA 57.449 37.500 0.00 0.00 36.16 3.58
5549 5912 2.434359 GTCGGGGAAGGAACAGCG 60.434 66.667 0.00 0.00 0.00 5.18
5556 5919 0.102481 GGAAGGAACAGCGCGATCTA 59.898 55.000 12.10 0.00 0.00 1.98
5562 5925 2.602694 GGAACAGCGCGATCTAGTCTAC 60.603 54.545 12.10 0.00 0.00 2.59
5582 5945 1.098050 GGCTGAAACATGCCGATTCT 58.902 50.000 0.00 0.00 39.71 2.40
5585 5948 2.476854 GCTGAAACATGCCGATTCTGTC 60.477 50.000 0.00 0.00 30.86 3.51
5617 5980 1.202099 TACCGCAGAAACCCATGGGA 61.202 55.000 38.07 7.69 38.96 4.37
5637 6000 2.281484 GAACTGGCCACGCAAGGA 60.281 61.111 0.00 0.00 46.39 3.36
5641 6004 2.672651 TGGCCACGCAAGGACATG 60.673 61.111 0.00 0.00 43.33 3.21
5685 6048 7.770433 TGGGTTACTGATTAATCAACATCTGAG 59.230 37.037 18.47 7.43 37.52 3.35
5693 6056 6.785488 TTAATCAACATCTGAGTGTGACAC 57.215 37.500 7.83 7.83 37.52 3.67
5707 6070 4.876107 AGTGTGACACGAGTTTCAAGAAAT 59.124 37.500 10.41 0.00 39.64 2.17
5729 6092 9.455847 GAAATAAATAGATTGGATGTGACAAGC 57.544 33.333 0.00 0.00 34.65 4.01
5730 6093 5.841957 AAATAGATTGGATGTGACAAGCC 57.158 39.130 0.00 0.00 34.97 4.35
5751 6114 2.793790 CGAGTGCTGCATTCTCTGTATC 59.206 50.000 20.58 0.00 0.00 2.24
5752 6115 3.736126 CGAGTGCTGCATTCTCTGTATCA 60.736 47.826 20.58 0.00 0.00 2.15
5753 6116 4.186926 GAGTGCTGCATTCTCTGTATCAA 58.813 43.478 16.75 0.00 0.00 2.57
5754 6117 4.190001 AGTGCTGCATTCTCTGTATCAAG 58.810 43.478 5.27 0.00 0.00 3.02
5755 6118 3.937706 GTGCTGCATTCTCTGTATCAAGT 59.062 43.478 5.27 0.00 0.00 3.16
5756 6119 4.394300 GTGCTGCATTCTCTGTATCAAGTT 59.606 41.667 5.27 0.00 0.00 2.66
5757 6120 5.005740 TGCTGCATTCTCTGTATCAAGTTT 58.994 37.500 0.00 0.00 0.00 2.66
5758 6121 5.122869 TGCTGCATTCTCTGTATCAAGTTTC 59.877 40.000 0.00 0.00 0.00 2.78
5759 6122 5.726138 GCTGCATTCTCTGTATCAAGTTTCG 60.726 44.000 0.00 0.00 0.00 3.46
5760 6123 4.093408 TGCATTCTCTGTATCAAGTTTCGC 59.907 41.667 0.00 0.00 0.00 4.70
5761 6124 4.494855 GCATTCTCTGTATCAAGTTTCGCC 60.495 45.833 0.00 0.00 0.00 5.54
5762 6125 4.537135 TTCTCTGTATCAAGTTTCGCCT 57.463 40.909 0.00 0.00 0.00 5.52
5763 6126 4.111375 TCTCTGTATCAAGTTTCGCCTC 57.889 45.455 0.00 0.00 0.00 4.70
5775 6138 0.179032 TTCGCCTCAAGTTTCAGCCA 60.179 50.000 0.00 0.00 0.00 4.75
5776 6139 0.179032 TCGCCTCAAGTTTCAGCCAA 60.179 50.000 0.00 0.00 0.00 4.52
5777 6140 0.040067 CGCCTCAAGTTTCAGCCAAC 60.040 55.000 0.00 0.00 0.00 3.77
5778 6141 0.315251 GCCTCAAGTTTCAGCCAACC 59.685 55.000 0.00 0.00 0.00 3.77
5779 6142 1.691196 CCTCAAGTTTCAGCCAACCA 58.309 50.000 0.00 0.00 0.00 3.67
5780 6143 2.031120 CCTCAAGTTTCAGCCAACCAA 58.969 47.619 0.00 0.00 0.00 3.67
5781 6144 2.430332 CCTCAAGTTTCAGCCAACCAAA 59.570 45.455 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 54 8.485976 AGCTACTATGCAGAGTTAAGAAAAAG 57.514 34.615 20.67 9.18 34.99 2.27
56 60 7.038659 AGACAAAGCTACTATGCAGAGTTAAG 58.961 38.462 20.67 12.94 34.99 1.85
189 193 5.697473 TTACATGGAGATTCGTGCAAAAA 57.303 34.783 0.00 0.00 0.00 1.94
190 194 5.697473 TTTACATGGAGATTCGTGCAAAA 57.303 34.783 0.00 0.00 0.00 2.44
191 195 5.697473 TTTTACATGGAGATTCGTGCAAA 57.303 34.783 0.00 0.00 0.00 3.68
192 196 5.414144 TGATTTTACATGGAGATTCGTGCAA 59.586 36.000 0.00 0.00 0.00 4.08
193 197 4.940654 TGATTTTACATGGAGATTCGTGCA 59.059 37.500 0.00 0.00 0.00 4.57
194 198 5.484173 TGATTTTACATGGAGATTCGTGC 57.516 39.130 0.00 0.00 0.00 5.34
195 199 7.751732 TCTTTGATTTTACATGGAGATTCGTG 58.248 34.615 0.00 0.00 0.00 4.35
196 200 7.921786 TCTTTGATTTTACATGGAGATTCGT 57.078 32.000 0.00 0.00 0.00 3.85
197 201 9.282247 CTTTCTTTGATTTTACATGGAGATTCG 57.718 33.333 0.00 0.00 0.00 3.34
214 218 9.958234 CTCAGATTCGATACTATCTTTCTTTGA 57.042 33.333 0.00 0.00 0.00 2.69
215 219 9.958234 TCTCAGATTCGATACTATCTTTCTTTG 57.042 33.333 0.00 0.00 0.00 2.77
216 220 9.959749 GTCTCAGATTCGATACTATCTTTCTTT 57.040 33.333 0.00 0.00 0.00 2.52
217 221 9.349713 AGTCTCAGATTCGATACTATCTTTCTT 57.650 33.333 0.00 0.00 0.00 2.52
218 222 8.918202 AGTCTCAGATTCGATACTATCTTTCT 57.082 34.615 0.00 0.00 0.00 2.52
221 225 8.726988 GCTAAGTCTCAGATTCGATACTATCTT 58.273 37.037 0.00 0.00 0.00 2.40
222 226 7.880713 TGCTAAGTCTCAGATTCGATACTATCT 59.119 37.037 0.00 0.00 0.00 1.98
223 227 8.035165 TGCTAAGTCTCAGATTCGATACTATC 57.965 38.462 0.00 0.00 0.00 2.08
224 228 7.987750 TGCTAAGTCTCAGATTCGATACTAT 57.012 36.000 0.00 0.00 0.00 2.12
225 229 7.803279 TTGCTAAGTCTCAGATTCGATACTA 57.197 36.000 0.00 0.00 0.00 1.82
226 230 6.701145 TTGCTAAGTCTCAGATTCGATACT 57.299 37.500 0.00 0.00 0.00 2.12
227 231 7.757097 TTTTGCTAAGTCTCAGATTCGATAC 57.243 36.000 0.00 0.00 0.00 2.24
228 232 8.820933 CAATTTTGCTAAGTCTCAGATTCGATA 58.179 33.333 0.00 0.00 0.00 2.92
229 233 7.550551 TCAATTTTGCTAAGTCTCAGATTCGAT 59.449 33.333 0.00 0.00 0.00 3.59
230 234 6.873605 TCAATTTTGCTAAGTCTCAGATTCGA 59.126 34.615 0.00 0.00 0.00 3.71
231 235 7.065216 TCAATTTTGCTAAGTCTCAGATTCG 57.935 36.000 0.00 0.00 0.00 3.34
232 236 9.683069 TTTTCAATTTTGCTAAGTCTCAGATTC 57.317 29.630 0.00 0.00 0.00 2.52
387 431 6.731467 TGCTTCAAAAGAATTCTATACCCCT 58.269 36.000 8.75 0.00 0.00 4.79
390 434 9.780413 CTCTTTGCTTCAAAAGAATTCTATACC 57.220 33.333 8.75 0.00 43.67 2.73
514 558 2.355986 TGGTCAGATTCGGACGGGG 61.356 63.158 10.24 0.00 36.12 5.73
748 801 3.972328 AAGAGGGGGAGGAAGGCCC 62.972 68.421 0.00 0.00 45.25 5.80
749 802 2.286502 AAGAGGGGGAGGAAGGCC 60.287 66.667 0.00 0.00 0.00 5.19
750 803 1.307430 AGAAGAGGGGGAGGAAGGC 60.307 63.158 0.00 0.00 0.00 4.35
751 804 1.631071 GCAGAAGAGGGGGAGGAAGG 61.631 65.000 0.00 0.00 0.00 3.46
752 805 0.620121 AGCAGAAGAGGGGGAGGAAG 60.620 60.000 0.00 0.00 0.00 3.46
753 806 0.618968 GAGCAGAAGAGGGGGAGGAA 60.619 60.000 0.00 0.00 0.00 3.36
754 807 1.002274 GAGCAGAAGAGGGGGAGGA 59.998 63.158 0.00 0.00 0.00 3.71
755 808 1.002792 AGAGCAGAAGAGGGGGAGG 59.997 63.158 0.00 0.00 0.00 4.30
756 809 1.048160 GGAGAGCAGAAGAGGGGGAG 61.048 65.000 0.00 0.00 0.00 4.30
757 810 1.002274 GGAGAGCAGAAGAGGGGGA 59.998 63.158 0.00 0.00 0.00 4.81
758 811 2.069430 GGGAGAGCAGAAGAGGGGG 61.069 68.421 0.00 0.00 0.00 5.40
759 812 2.430610 CGGGAGAGCAGAAGAGGGG 61.431 68.421 0.00 0.00 0.00 4.79
760 813 2.430610 CCGGGAGAGCAGAAGAGGG 61.431 68.421 0.00 0.00 0.00 4.30
829 883 2.333225 CGCTAGCTAGCTCCGGTG 59.667 66.667 36.02 20.05 46.85 4.94
883 937 5.564504 CAGAACAAGACGAGTAACTAAGACG 59.435 44.000 0.00 0.00 0.00 4.18
902 956 2.125350 CTCAGAGCGGGGCAGAAC 60.125 66.667 0.00 0.00 0.00 3.01
1033 1090 2.202362 CAGCACGACGAGGACGAG 60.202 66.667 0.00 0.00 42.66 4.18
1136 1193 0.387239 GGCACAACCACAAATCGAGC 60.387 55.000 0.00 0.00 38.86 5.03
1183 1241 2.874701 GCCAATCCTAGCACATGTACAG 59.125 50.000 0.00 0.00 0.00 2.74
1191 1249 0.179936 AGCAGAGCCAATCCTAGCAC 59.820 55.000 0.00 0.00 0.00 4.40
1206 1264 4.834453 CGCCCTCAGCTCCAGCAG 62.834 72.222 0.48 0.00 45.16 4.24
1372 1438 3.974835 ATCGCGTGGAGGCATTGCA 62.975 57.895 11.39 0.00 0.00 4.08
1403 1469 9.553064 TGAACAATGTAGGCAATTACAAAATTT 57.447 25.926 0.00 0.00 37.13 1.82
1474 1542 9.545105 TGATTTGCAAACATCTTAATTTCAACT 57.455 25.926 15.41 0.00 0.00 3.16
1695 1764 8.538409 AAGCATCAAACAATGGAATTCTAAAC 57.462 30.769 5.23 0.00 31.22 2.01
1809 1878 3.316283 TGCATGATTTTTCGAAACCAGC 58.684 40.909 10.79 13.25 0.00 4.85
1853 1922 8.553459 AAGTTTATAGGTGCACATGATATAGC 57.447 34.615 20.43 10.93 0.00 2.97
2351 2425 3.260884 AGACGCCTTCTTGGAACTGATTA 59.739 43.478 0.00 0.00 38.35 1.75
3252 3337 2.086094 TGTTGTCAGGCTATGCATGTG 58.914 47.619 10.16 3.16 41.32 3.21
3335 3420 4.523943 AGCTGATCATGTGCCAGTTTTAAA 59.476 37.500 0.00 0.00 0.00 1.52
3338 3423 2.490903 GAGCTGATCATGTGCCAGTTTT 59.509 45.455 0.00 0.00 0.00 2.43
3481 3567 3.113386 GAAATCCTCGCAAGCGGCC 62.113 63.158 14.98 0.00 43.51 6.13
3794 3898 3.635373 CCATCATCCTCATGAAGGGTTTG 59.365 47.826 0.00 0.00 46.23 2.93
4106 4210 8.336235 ACTGATTTCCTTCAAATGGATACCTTA 58.664 33.333 0.00 0.00 34.60 2.69
4166 4272 5.779529 AGCTTATTAATGAACCATGCCTG 57.220 39.130 0.00 0.00 0.00 4.85
4267 4373 2.097038 CCTTTGCTCTGTCCGCGAG 61.097 63.158 8.23 0.00 0.00 5.03
4479 4589 5.181690 ACAGTTGTAACGATGCAATGTTT 57.818 34.783 11.55 0.00 33.60 2.83
4803 4933 3.118920 GCCCACCCAAACAAATGGTATAC 60.119 47.826 0.00 0.00 38.91 1.47
4839 4969 4.971282 AGGATCAAGAGGGATGATGTTACA 59.029 41.667 0.00 0.00 37.64 2.41
4954 5093 8.791675 TGAGTAAAGATCAACATGTGCATTTAA 58.208 29.630 0.00 0.00 0.00 1.52
5046 5194 2.096248 ACCAGGCACTTGTTCGAAAAA 58.904 42.857 0.00 0.00 34.60 1.94
5049 5197 1.444119 GCACCAGGCACTTGTTCGAA 61.444 55.000 0.00 0.00 43.97 3.71
5072 5231 4.836825 ACTGAAGATTCACATGGTAGGTG 58.163 43.478 0.00 0.00 37.60 4.00
5113 5273 3.063510 TCAGAGCTTTGAATCAGGTGG 57.936 47.619 4.11 0.00 0.00 4.61
5127 5287 7.654116 GGTTAGACCTAGTTTTATCATCAGAGC 59.346 40.741 0.00 0.00 34.73 4.09
5128 5288 8.696374 TGGTTAGACCTAGTTTTATCATCAGAG 58.304 37.037 0.00 0.00 39.58 3.35
5129 5289 8.603898 TGGTTAGACCTAGTTTTATCATCAGA 57.396 34.615 0.00 0.00 39.58 3.27
5130 5290 9.838339 ATTGGTTAGACCTAGTTTTATCATCAG 57.162 33.333 0.00 0.00 39.58 2.90
5132 5292 8.560374 GCATTGGTTAGACCTAGTTTTATCATC 58.440 37.037 0.00 0.00 39.58 2.92
5133 5293 8.052748 TGCATTGGTTAGACCTAGTTTTATCAT 58.947 33.333 0.00 0.00 39.58 2.45
5134 5294 7.398829 TGCATTGGTTAGACCTAGTTTTATCA 58.601 34.615 0.00 0.00 39.58 2.15
5135 5295 7.859325 TGCATTGGTTAGACCTAGTTTTATC 57.141 36.000 0.00 0.00 39.58 1.75
5136 5296 7.285401 CCATGCATTGGTTAGACCTAGTTTTAT 59.715 37.037 0.00 0.00 40.99 1.40
5137 5297 6.601613 CCATGCATTGGTTAGACCTAGTTTTA 59.398 38.462 0.00 0.00 40.99 1.52
5138 5298 5.418840 CCATGCATTGGTTAGACCTAGTTTT 59.581 40.000 0.00 0.00 40.99 2.43
5198 5362 8.034215 AGAGAGACAGACAAGAAATGAACATAG 58.966 37.037 0.00 0.00 0.00 2.23
5199 5363 7.901029 AGAGAGACAGACAAGAAATGAACATA 58.099 34.615 0.00 0.00 0.00 2.29
5206 5406 6.945218 AGCAATAGAGAGACAGACAAGAAAT 58.055 36.000 0.00 0.00 0.00 2.17
5214 5414 2.685388 CACCGAGCAATAGAGAGACAGA 59.315 50.000 0.00 0.00 0.00 3.41
5225 5425 0.447801 GCACGATTTCACCGAGCAAT 59.552 50.000 0.00 0.00 41.83 3.56
5234 5434 4.068599 TGAATACTTGGTGCACGATTTCA 58.931 39.130 11.45 10.95 0.00 2.69
5326 5527 9.533831 AACACCTGAATTCCATAATTTCTACTT 57.466 29.630 2.27 0.00 35.41 2.24
5377 5582 1.020861 GCCATGTGTCGAGTGCATGA 61.021 55.000 19.27 0.00 41.62 3.07
5449 5755 8.690203 TCACCATACTGATTTTTCAGAAGAAA 57.310 30.769 9.82 0.00 41.78 2.52
5451 5757 7.679783 TCTCACCATACTGATTTTTCAGAAGA 58.320 34.615 9.82 0.00 39.99 2.87
5452 5758 7.821359 TCTCTCACCATACTGATTTTTCAGAAG 59.179 37.037 9.82 0.01 39.99 2.85
5453 5759 7.679783 TCTCTCACCATACTGATTTTTCAGAA 58.320 34.615 9.82 0.00 39.99 3.02
5454 5760 7.244886 TCTCTCACCATACTGATTTTTCAGA 57.755 36.000 9.82 0.00 39.99 3.27
5456 5762 8.733458 CATTTCTCTCACCATACTGATTTTTCA 58.267 33.333 0.00 0.00 0.00 2.69
5457 5763 8.734386 ACATTTCTCTCACCATACTGATTTTTC 58.266 33.333 0.00 0.00 0.00 2.29
5461 5767 6.950842 TGACATTTCTCTCACCATACTGATT 58.049 36.000 0.00 0.00 0.00 2.57
5462 5768 6.550938 TGACATTTCTCTCACCATACTGAT 57.449 37.500 0.00 0.00 0.00 2.90
5463 5769 6.343703 CATGACATTTCTCTCACCATACTGA 58.656 40.000 0.00 0.00 0.00 3.41
5464 5770 5.007430 GCATGACATTTCTCTCACCATACTG 59.993 44.000 0.00 0.00 0.00 2.74
5465 5771 5.121811 GCATGACATTTCTCTCACCATACT 58.878 41.667 0.00 0.00 0.00 2.12
5468 5774 2.941064 CGCATGACATTTCTCTCACCAT 59.059 45.455 0.00 0.00 0.00 3.55
5469 5775 2.028203 TCGCATGACATTTCTCTCACCA 60.028 45.455 0.00 0.00 0.00 4.17
5470 5776 2.621338 TCGCATGACATTTCTCTCACC 58.379 47.619 0.00 0.00 0.00 4.02
5471 5777 4.330894 TCAATCGCATGACATTTCTCTCAC 59.669 41.667 0.00 0.00 0.00 3.51
5485 5840 1.737838 AATCCACGTGTCAATCGCAT 58.262 45.000 15.65 0.00 0.00 4.73
5497 5852 2.309528 TGTAGCCTGCTAAATCCACG 57.690 50.000 0.00 0.00 0.00 4.94
5525 5888 1.847798 TTCCTTCCCCGACCATGTGG 61.848 60.000 0.00 0.00 42.17 4.17
5549 5912 1.227639 TCAGCCGTAGACTAGATCGC 58.772 55.000 0.00 0.00 0.00 4.58
5556 5919 1.676014 GGCATGTTTCAGCCGTAGACT 60.676 52.381 0.00 0.00 41.70 3.24
5594 5957 3.486383 CCATGGGTTTCTGCGGTATATT 58.514 45.455 2.85 0.00 0.00 1.28
5595 5958 2.224769 CCCATGGGTTTCTGCGGTATAT 60.225 50.000 23.93 0.00 0.00 0.86
5617 5980 1.455383 CCTTGCGTGGCCAGTTCTTT 61.455 55.000 5.11 0.00 0.00 2.52
5637 6000 1.212375 TCCAATCCATCCCGTCATGT 58.788 50.000 0.00 0.00 0.00 3.21
5640 6003 1.134128 CACATCCAATCCATCCCGTCA 60.134 52.381 0.00 0.00 0.00 4.35
5641 6004 1.597742 CACATCCAATCCATCCCGTC 58.402 55.000 0.00 0.00 0.00 4.79
5685 6048 4.593597 TTTCTTGAAACTCGTGTCACAC 57.406 40.909 0.00 0.00 0.00 3.82
5707 6070 5.527214 CGGCTTGTCACATCCAATCTATTTA 59.473 40.000 0.00 0.00 0.00 1.40
5729 6092 0.390866 ACAGAGAATGCAGCACTCGG 60.391 55.000 0.00 4.33 36.03 4.63
5730 6093 2.284263 TACAGAGAATGCAGCACTCG 57.716 50.000 0.00 0.64 36.03 4.18
5751 6114 3.621794 CTGAAACTTGAGGCGAAACTTG 58.378 45.455 0.00 0.00 0.00 3.16
5752 6115 2.033424 GCTGAAACTTGAGGCGAAACTT 59.967 45.455 0.00 0.00 0.00 2.66
5753 6116 1.604278 GCTGAAACTTGAGGCGAAACT 59.396 47.619 0.00 0.00 0.00 2.66
5754 6117 1.335051 GGCTGAAACTTGAGGCGAAAC 60.335 52.381 0.00 0.00 0.00 2.78
5755 6118 0.951558 GGCTGAAACTTGAGGCGAAA 59.048 50.000 0.00 0.00 0.00 3.46
5756 6119 0.179032 TGGCTGAAACTTGAGGCGAA 60.179 50.000 0.00 0.00 39.75 4.70
5757 6120 0.179032 TTGGCTGAAACTTGAGGCGA 60.179 50.000 0.00 0.00 39.75 5.54
5758 6121 0.040067 GTTGGCTGAAACTTGAGGCG 60.040 55.000 0.00 0.00 39.75 5.52
5759 6122 0.315251 GGTTGGCTGAAACTTGAGGC 59.685 55.000 0.00 0.00 37.48 4.70
5760 6123 1.691196 TGGTTGGCTGAAACTTGAGG 58.309 50.000 0.00 0.00 0.00 3.86
5761 6124 3.799281 TTTGGTTGGCTGAAACTTGAG 57.201 42.857 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.