Multiple sequence alignment - TraesCS3B01G537400

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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 TraesCS3B01G537400 chr3B 100.000 4587 0 0 1 4587 777577683 777582269 0.000000e+00 8471.0
1 TraesCS3B01G537400 chr3B 97.297 37 1 0 1109 1145 544109566 544109602 3.830000e-06 63.9
2 TraesCS3B01G537400 chr3D 94.601 4445 113 42 197 4587 581116955 581112584 0.000000e+00 6761.0
3 TraesCS3B01G537400 chr3D 87.831 189 14 7 4 192 581117488 581117309 3.590000e-51 213.0
4 TraesCS3B01G537400 chr3D 97.297 37 1 0 1109 1145 417738712 417738748 3.830000e-06 63.9
5 TraesCS3B01G537400 chr3A 93.810 4443 173 52 197 4587 716755855 716760247 0.000000e+00 6588.0
6 TraesCS3B01G537400 chr3A 87.368 190 15 7 1 190 716755336 716755516 4.650000e-50 209.0
7 TraesCS3B01G537400 chr5D 78.828 751 129 28 2590 3328 222739328 222740060 3.210000e-131 479.0
8 TraesCS3B01G537400 chr5D 89.937 159 16 0 1004 1162 222737951 222738109 6.020000e-49 206.0
9 TraesCS3B01G537400 chr5A 78.429 751 132 28 2590 3328 304539225 304538493 3.230000e-126 462.0
10 TraesCS3B01G537400 chr5A 92.000 150 12 0 1013 1162 304540594 304540445 1.290000e-50 211.0
11 TraesCS3B01G537400 chr5B 78.162 751 134 28 2590 3328 250234455 250233723 7.000000e-123 451.0
12 TraesCS3B01G537400 chr5B 91.333 150 13 0 1013 1162 250235826 250235677 6.020000e-49 206.0
13 TraesCS3B01G537400 chr6B 100.000 29 0 0 4140 4168 51137555 51137527 2.000000e-03 54.7
14 TraesCS3B01G537400 chr2A 100.000 28 0 0 4142 4169 115139976 115139949 8.000000e-03 52.8


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 TraesCS3B01G537400 chr3B 777577683 777582269 4586 False 8471.0 8471 100.0000 1 4587 1 chr3B.!!$F2 4586
1 TraesCS3B01G537400 chr3D 581112584 581117488 4904 True 3487.0 6761 91.2160 4 4587 2 chr3D.!!$R1 4583
2 TraesCS3B01G537400 chr3A 716755336 716760247 4911 False 3398.5 6588 90.5890 1 4587 2 chr3A.!!$F1 4586
3 TraesCS3B01G537400 chr5D 222737951 222740060 2109 False 342.5 479 84.3825 1004 3328 2 chr5D.!!$F1 2324
4 TraesCS3B01G537400 chr5A 304538493 304540594 2101 True 336.5 462 85.2145 1013 3328 2 chr5A.!!$R1 2315
5 TraesCS3B01G537400 chr5B 250233723 250235826 2103 True 328.5 451 84.7475 1013 3328 2 chr5B.!!$R1 2315

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
221 576 1.696832 GGAAGCCATGCGTCGTCTTC 61.697 60.0 0.00 0.0 37.89 2.87 F
1556 2028 0.757935 GCCGTCCTCACCCAGGTATA 60.758 60.0 0.00 0.0 43.95 1.47 F
2198 2884 0.170116 AAAAGGCACACACACACACG 59.830 50.0 0.00 0.0 0.00 4.49 F
2506 3378 0.036010 GCCATACCTGTGAGCTGTGT 60.036 55.0 0.00 0.0 0.00 3.72 F
3034 3924 1.030488 TCGAGAACTGTAGCCGGGAG 61.030 60.0 2.18 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 2874 0.098728 GCAAGAAAGCGTGTGTGTGT 59.901 50.000 0.00 0.0 0.00 3.72 R
2486 3350 0.251354 CACAGCTCACAGGTATGGCT 59.749 55.000 0.00 0.0 0.00 4.75 R
3481 4371 0.463833 GGTTCATCACGTCCATCCCC 60.464 60.000 0.00 0.0 0.00 4.81 R
3583 4473 2.404995 GCTGCCAGCCATGTCTCAC 61.405 63.158 5.06 0.0 34.48 3.51 R
3904 4806 3.252400 CAACACACATGCACAAAACAGT 58.748 40.909 0.00 0.0 0.00 3.55 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
45 46 7.858052 ATATGTCTTTCTGAAAAACTTTGCG 57.142 32.000 7.98 0.00 0.00 4.85
46 47 3.857093 TGTCTTTCTGAAAAACTTTGCGC 59.143 39.130 0.00 0.00 0.00 6.09
47 48 3.061863 GTCTTTCTGAAAAACTTTGCGCG 60.062 43.478 0.00 0.00 0.00 6.86
180 181 2.030823 CACAGCGTTGTAGCCATACATG 59.969 50.000 4.02 0.00 41.49 3.21
192 193 8.972458 TGTAGCCATACATGCTTCTTTTAATA 57.028 30.769 0.00 0.00 40.23 0.98
193 194 9.402320 TGTAGCCATACATGCTTCTTTTAATAA 57.598 29.630 0.00 0.00 40.23 1.40
213 568 9.906660 TTAATAATTTATAAAGGAAGCCATGCG 57.093 29.630 3.94 0.00 0.00 4.73
221 576 1.696832 GGAAGCCATGCGTCGTCTTC 61.697 60.000 0.00 0.00 37.89 2.87
227 582 2.095213 GCCATGCGTCGTCTTCAATTTA 59.905 45.455 0.00 0.00 0.00 1.40
266 621 2.294233 GGCAAGCAGACACTTCAATCAA 59.706 45.455 0.00 0.00 0.00 2.57
389 744 2.358737 GCCCCTGAAGTGTGGACG 60.359 66.667 0.00 0.00 0.00 4.79
463 822 8.776470 CATTTTAATCCCACCAATTATTCATGC 58.224 33.333 0.00 0.00 0.00 4.06
464 823 4.589216 AATCCCACCAATTATTCATGCG 57.411 40.909 0.00 0.00 0.00 4.73
465 824 3.011566 TCCCACCAATTATTCATGCGT 57.988 42.857 0.00 0.00 0.00 5.24
466 825 2.687425 TCCCACCAATTATTCATGCGTG 59.313 45.455 0.00 0.00 0.00 5.34
568 927 9.581289 CCATATAACCTTTAGAGAGAGAGAGAA 57.419 37.037 0.00 0.00 0.00 2.87
572 931 7.462571 AACCTTTAGAGAGAGAGAGAAAGAC 57.537 40.000 0.00 0.00 0.00 3.01
575 934 6.095440 CCTTTAGAGAGAGAGAGAAAGACAGG 59.905 46.154 0.00 0.00 0.00 4.00
576 935 4.927267 AGAGAGAGAGAGAAAGACAGGA 57.073 45.455 0.00 0.00 0.00 3.86
587 964 4.344104 AGAAAGACAGGAAGAGAGAGAGG 58.656 47.826 0.00 0.00 0.00 3.69
899 1292 3.577667 CAGCTCTCGATCTGATTCATCC 58.422 50.000 4.11 0.00 32.26 3.51
928 1321 1.939082 TTCCTCCTCTCCCTCTCCGG 61.939 65.000 0.00 0.00 0.00 5.14
944 1337 2.560542 CTCCGGATTGACTGATAGAGGG 59.439 54.545 3.57 0.00 0.00 4.30
963 1356 4.851214 GAGGAGGAGGAGGCGGCT 62.851 72.222 13.09 13.09 0.00 5.52
1023 1416 4.580835 GACACCCTCAAGTCGCTC 57.419 61.111 0.00 0.00 0.00 5.03
1555 2027 2.064581 GCCGTCCTCACCCAGGTAT 61.065 63.158 0.00 0.00 43.95 2.73
1556 2028 0.757935 GCCGTCCTCACCCAGGTATA 60.758 60.000 0.00 0.00 43.95 1.47
1564 2036 6.289064 GTCCTCACCCAGGTATAATTACTTG 58.711 44.000 0.00 0.00 43.95 3.16
1574 2046 7.202047 CCAGGTATAATTACTTGCTCTTCCTCT 60.202 40.741 0.00 0.00 34.86 3.69
1576 2048 6.864165 GGTATAATTACTTGCTCTTCCTCTCG 59.136 42.308 0.00 0.00 0.00 4.04
1598 2074 5.902431 TCGAATTAATCCCCAATTCCCAATT 59.098 36.000 0.00 0.00 38.58 2.32
1766 2245 4.335874 AGCAGCATTGATTTGATCTCTGTC 59.664 41.667 0.00 0.00 0.00 3.51
1767 2246 4.497674 GCAGCATTGATTTGATCTCTGTCC 60.498 45.833 0.00 0.00 0.00 4.02
1768 2247 3.875727 AGCATTGATTTGATCTCTGTCCG 59.124 43.478 0.00 0.00 0.00 4.79
1769 2248 3.873361 GCATTGATTTGATCTCTGTCCGA 59.127 43.478 0.00 0.00 0.00 4.55
1770 2249 4.025061 GCATTGATTTGATCTCTGTCCGAG 60.025 45.833 0.00 0.00 41.30 4.63
1771 2250 4.808414 TTGATTTGATCTCTGTCCGAGT 57.192 40.909 0.00 0.00 40.75 4.18
1772 2251 4.115401 TGATTTGATCTCTGTCCGAGTG 57.885 45.455 0.00 0.00 40.75 3.51
1773 2252 3.511540 TGATTTGATCTCTGTCCGAGTGT 59.488 43.478 0.00 0.00 40.75 3.55
1814 2293 0.809385 TACTCGAGTGTGGTAGCAGC 59.191 55.000 28.12 0.00 0.00 5.25
1815 2294 1.179174 ACTCGAGTGTGGTAGCAGCA 61.179 55.000 19.30 0.00 0.00 4.41
2148 2834 4.629115 GCACACCACGGCTGCAAC 62.629 66.667 0.50 0.00 0.00 4.17
2150 2836 2.124320 ACACCACGGCTGCAACTT 60.124 55.556 0.50 0.00 0.00 2.66
2173 2859 4.812476 CGATTCGGCGGCACTCCA 62.812 66.667 10.53 0.00 28.55 3.86
2174 2860 2.892425 GATTCGGCGGCACTCCAG 60.892 66.667 10.53 0.00 28.55 3.86
2175 2861 4.473520 ATTCGGCGGCACTCCAGG 62.474 66.667 10.53 0.00 28.55 4.45
2179 2865 3.706373 GGCGGCACTCCAGGAAGA 61.706 66.667 3.07 0.00 30.60 2.87
2180 2866 2.347490 GCGGCACTCCAGGAAGAA 59.653 61.111 0.00 0.00 0.00 2.52
2181 2867 1.302511 GCGGCACTCCAGGAAGAAA 60.303 57.895 0.00 0.00 0.00 2.52
2182 2868 0.889186 GCGGCACTCCAGGAAGAAAA 60.889 55.000 0.00 0.00 0.00 2.29
2183 2869 1.160137 CGGCACTCCAGGAAGAAAAG 58.840 55.000 0.00 0.00 0.00 2.27
2184 2870 1.539157 GGCACTCCAGGAAGAAAAGG 58.461 55.000 0.00 0.00 0.00 3.11
2186 2872 1.819305 GCACTCCAGGAAGAAAAGGCA 60.819 52.381 0.00 0.00 0.00 4.75
2187 2873 1.882623 CACTCCAGGAAGAAAAGGCAC 59.117 52.381 0.00 0.00 0.00 5.01
2188 2874 1.494721 ACTCCAGGAAGAAAAGGCACA 59.505 47.619 0.00 0.00 0.00 4.57
2189 2875 1.882623 CTCCAGGAAGAAAAGGCACAC 59.117 52.381 0.00 0.00 0.00 3.82
2190 2876 1.214175 TCCAGGAAGAAAAGGCACACA 59.786 47.619 0.00 0.00 0.00 3.72
2191 2877 1.338020 CCAGGAAGAAAAGGCACACAC 59.662 52.381 0.00 0.00 0.00 3.82
2192 2878 2.023673 CAGGAAGAAAAGGCACACACA 58.976 47.619 0.00 0.00 0.00 3.72
2198 2884 0.170116 AAAAGGCACACACACACACG 59.830 50.000 0.00 0.00 0.00 4.49
2275 3135 3.508402 TGAGCCGGTTAATTTCCCTTTTC 59.492 43.478 1.90 0.00 0.00 2.29
2341 3201 2.350804 CGCCATGATGCTGCTATACATC 59.649 50.000 0.00 0.00 42.46 3.06
2372 3232 0.547954 ACCCTTCTGTTCCTCCTCCC 60.548 60.000 0.00 0.00 0.00 4.30
2405 3265 1.134401 ACAGGGACAATCCACTATGCG 60.134 52.381 0.00 0.00 38.64 4.73
2429 3293 6.567511 CGCATCTCATATATGGGTAGAGATCG 60.568 46.154 12.38 12.68 42.43 3.69
2437 3301 4.674281 ATGGGTAGAGATCGTTTCCTTC 57.326 45.455 0.00 0.00 0.00 3.46
2475 3339 4.344102 TGCTTATATTACCACCGCTCTCTT 59.656 41.667 0.00 0.00 0.00 2.85
2484 3348 0.968393 ACCGCTCTCTTGGTCTCTCC 60.968 60.000 0.00 0.00 31.16 3.71
2485 3349 0.967887 CCGCTCTCTTGGTCTCTCCA 60.968 60.000 0.00 0.00 45.60 3.86
2506 3378 0.036010 GCCATACCTGTGAGCTGTGT 60.036 55.000 0.00 0.00 0.00 3.72
2580 3452 1.851021 TTTTGCGACGGTGATGGCTG 61.851 55.000 0.00 0.00 0.00 4.85
2755 3627 2.677875 GCCAAGCACCTTCCCCTG 60.678 66.667 0.00 0.00 0.00 4.45
3034 3924 1.030488 TCGAGAACTGTAGCCGGGAG 61.030 60.000 2.18 0.00 0.00 4.30
3187 4077 3.276846 GACCCAAACGTGCGCACT 61.277 61.111 35.27 20.93 0.00 4.40
3190 4080 2.407210 CCAAACGTGCGCACTGTT 59.593 55.556 35.27 32.73 32.51 3.16
3205 4095 4.612412 GTTGACGGGGTCACGCCA 62.612 66.667 12.14 0.00 42.60 5.69
3208 4098 4.309950 GACGGGGTCACGCCACTT 62.310 66.667 12.14 0.00 38.96 3.16
3220 4110 2.109126 GCCACTTGACATCCTCCGC 61.109 63.158 0.00 0.00 0.00 5.54
3481 4371 1.909302 AGGATGGTGTACCTCAACCTG 59.091 52.381 11.67 0.00 36.82 4.00
3583 4473 3.089874 TCCCCTCATGGCTTCCCG 61.090 66.667 0.00 0.00 0.00 5.14
3599 4489 2.046988 CGTGAGACATGGCTGGCA 60.047 61.111 5.31 6.31 30.17 4.92
3827 4728 7.185318 TCGTTAGGGTCTACATTAATTTCCA 57.815 36.000 0.00 0.00 0.00 3.53
3828 4729 7.622713 TCGTTAGGGTCTACATTAATTTCCAA 58.377 34.615 0.00 0.00 0.00 3.53
3829 4730 8.102047 TCGTTAGGGTCTACATTAATTTCCAAA 58.898 33.333 0.00 0.00 0.00 3.28
3830 4731 8.732531 CGTTAGGGTCTACATTAATTTCCAAAA 58.267 33.333 0.00 0.00 0.00 2.44
3894 4796 9.883142 TGAGAGGTGATGTTTTAAAAACAATTT 57.117 25.926 1.31 0.00 33.42 1.82
3982 4884 2.151202 TGGACAAGAAAGGTCGATTGC 58.849 47.619 0.00 0.00 36.12 3.56
4036 4938 7.951530 TTTTTCTGCTCAAATGATCCTTTTC 57.048 32.000 0.00 0.00 0.00 2.29
4105 5012 0.536687 ATGCGCTAGTACTCCCGCTA 60.537 55.000 28.65 19.88 45.97 4.26
4130 5037 5.336744 ACACAAATGTAAGACGTTTTGGTG 58.663 37.500 11.59 10.73 35.31 4.17
4180 5087 6.093771 CAGAGGGAGTATTACTTATCGCGTAT 59.906 42.308 5.77 0.65 0.00 3.06
4181 5088 6.093771 AGAGGGAGTATTACTTATCGCGTATG 59.906 42.308 5.77 3.22 0.00 2.39
4186 5093 9.219497 GGAGTATTACTTATCGCGTATGTAATC 57.781 37.037 25.12 20.10 40.23 1.75
4233 5140 0.869880 GCCGTGCCAACACTTGTTTC 60.870 55.000 0.00 0.00 45.10 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.737172 GGGATGTGCGCGCAAAGT 61.737 61.111 38.24 24.29 0.00 2.66
39 40 1.643868 TAAGGGATGTGCGCGCAAAG 61.644 55.000 38.24 0.00 34.07 2.77
40 41 1.237954 TTAAGGGATGTGCGCGCAAA 61.238 50.000 38.24 33.48 34.07 3.68
42 43 2.046796 TTAAGGGATGTGCGCGCA 60.047 55.556 33.09 33.09 34.07 6.09
43 44 1.644786 AAGTTAAGGGATGTGCGCGC 61.645 55.000 27.26 27.26 34.07 6.86
44 45 0.802494 AAAGTTAAGGGATGTGCGCG 59.198 50.000 0.00 0.00 34.07 6.86
45 46 3.297830 AAAAAGTTAAGGGATGTGCGC 57.702 42.857 0.00 0.00 0.00 6.09
71 72 4.019174 CCATGGCAACTTCCATTTCTACT 58.981 43.478 0.00 0.00 44.04 2.57
130 131 9.154632 ACACCATCACATGTCCTAGTAATAATA 57.845 33.333 0.00 0.00 0.00 0.98
131 132 8.034313 ACACCATCACATGTCCTAGTAATAAT 57.966 34.615 0.00 0.00 0.00 1.28
132 133 7.432148 ACACCATCACATGTCCTAGTAATAA 57.568 36.000 0.00 0.00 0.00 1.40
134 135 5.957771 ACACCATCACATGTCCTAGTAAT 57.042 39.130 0.00 0.00 0.00 1.89
136 137 5.717654 TGTTACACCATCACATGTCCTAGTA 59.282 40.000 0.00 0.00 0.00 1.82
138 139 4.870426 GTGTTACACCATCACATGTCCTAG 59.130 45.833 3.79 0.00 33.04 3.02
139 140 4.284746 TGTGTTACACCATCACATGTCCTA 59.715 41.667 13.29 0.00 37.20 2.94
140 141 3.072330 TGTGTTACACCATCACATGTCCT 59.928 43.478 13.29 0.00 37.20 3.85
141 142 3.407698 TGTGTTACACCATCACATGTCC 58.592 45.455 13.29 0.00 37.20 4.02
142 143 3.120199 GCTGTGTTACACCATCACATGTC 60.120 47.826 13.29 0.00 40.49 3.06
143 144 2.813754 GCTGTGTTACACCATCACATGT 59.186 45.455 13.29 0.00 40.49 3.21
144 145 2.159667 CGCTGTGTTACACCATCACATG 60.160 50.000 13.29 0.00 40.49 3.21
145 146 2.076100 CGCTGTGTTACACCATCACAT 58.924 47.619 13.29 0.00 40.49 3.21
146 147 1.202592 ACGCTGTGTTACACCATCACA 60.203 47.619 13.29 0.00 39.31 3.58
147 148 1.508632 ACGCTGTGTTACACCATCAC 58.491 50.000 13.29 0.00 32.73 3.06
148 149 1.870402 CAACGCTGTGTTACACCATCA 59.130 47.619 13.29 0.00 39.29 3.07
165 166 5.567138 AAAGAAGCATGTATGGCTACAAC 57.433 39.130 0.00 0.00 41.66 3.32
192 193 5.505654 CGACGCATGGCTTCCTTTATAAATT 60.506 40.000 0.00 0.00 0.00 1.82
193 194 4.024048 CGACGCATGGCTTCCTTTATAAAT 60.024 41.667 0.00 0.00 0.00 1.40
194 195 3.311322 CGACGCATGGCTTCCTTTATAAA 59.689 43.478 0.00 0.00 0.00 1.40
213 568 3.929610 AGCAGAGCTAAATTGAAGACGAC 59.070 43.478 0.00 0.00 36.99 4.34
221 576 5.016051 TGTAGGAGAGCAGAGCTAAATTG 57.984 43.478 0.00 0.00 39.88 2.32
227 582 1.484038 CCTTGTAGGAGAGCAGAGCT 58.516 55.000 0.00 0.00 38.80 4.09
266 621 5.819379 ACTGATGCGAGTCATAAATCATGTT 59.181 36.000 0.00 0.00 35.05 2.71
314 669 4.330960 AATTGGGGTGGGGTGGGC 62.331 66.667 0.00 0.00 0.00 5.36
334 689 4.423209 AGAGGGTGAGGCCTCCCC 62.423 72.222 35.34 35.34 45.15 4.81
341 696 0.040351 TGGACAGAGAGAGGGTGAGG 59.960 60.000 0.00 0.00 0.00 3.86
568 927 2.292192 CCCCTCTCTCTCTTCCTGTCTT 60.292 54.545 0.00 0.00 0.00 3.01
570 929 1.775385 CCCCTCTCTCTCTTCCTGTC 58.225 60.000 0.00 0.00 0.00 3.51
572 931 0.325110 TGCCCCTCTCTCTCTTCCTG 60.325 60.000 0.00 0.00 0.00 3.86
575 934 0.616111 TGGTGCCCCTCTCTCTCTTC 60.616 60.000 0.00 0.00 0.00 2.87
576 935 0.617249 CTGGTGCCCCTCTCTCTCTT 60.617 60.000 0.00 0.00 0.00 2.85
807 1200 0.109689 GCTGCTTTGCTCTTCTGCTG 60.110 55.000 0.00 0.00 0.00 4.41
899 1292 2.168313 GGAGAGGAGGAAGAAGAAGCTG 59.832 54.545 0.00 0.00 0.00 4.24
928 1321 2.903135 CCTCCCCCTCTATCAGTCAATC 59.097 54.545 0.00 0.00 0.00 2.67
963 1356 2.086869 GCACCTGCTTCTTGCTAATCA 58.913 47.619 0.00 0.00 43.37 2.57
1023 1416 2.169352 CAGGTTGAGGTAGTCCATGGAG 59.831 54.545 16.81 0.00 35.89 3.86
1284 1677 4.828925 GCTGAGCCTGAGCCGGAC 62.829 72.222 5.05 0.00 41.25 4.79
1347 1819 0.889306 GGAACACCTCGTAGCTCACT 59.111 55.000 0.00 0.00 0.00 3.41
1555 2027 6.525578 TTCGAGAGGAAGAGCAAGTAATTA 57.474 37.500 0.00 0.00 0.00 1.40
1556 2028 5.407407 TTCGAGAGGAAGAGCAAGTAATT 57.593 39.130 0.00 0.00 0.00 1.40
1564 2036 4.311606 GGGATTAATTCGAGAGGAAGAGC 58.688 47.826 0.00 0.00 38.24 4.09
1574 2046 4.528076 TGGGAATTGGGGATTAATTCGA 57.472 40.909 0.00 0.00 42.59 3.71
1576 2048 7.379059 AGAATTGGGAATTGGGGATTAATTC 57.621 36.000 0.00 0.00 41.53 2.17
1766 2245 2.159327 AAAAAGGTACGGACACTCGG 57.841 50.000 0.00 0.00 0.00 4.63
1767 2246 5.406175 TCATTTAAAAAGGTACGGACACTCG 59.594 40.000 0.00 0.00 0.00 4.18
1768 2247 6.790285 TCATTTAAAAAGGTACGGACACTC 57.210 37.500 0.00 0.00 0.00 3.51
1769 2248 6.769341 ACTTCATTTAAAAAGGTACGGACACT 59.231 34.615 0.00 0.00 0.00 3.55
1770 2249 6.962686 ACTTCATTTAAAAAGGTACGGACAC 58.037 36.000 0.00 0.00 0.00 3.67
1771 2250 7.571080 AACTTCATTTAAAAAGGTACGGACA 57.429 32.000 0.00 0.00 0.00 4.02
1772 2251 8.777413 AGTAACTTCATTTAAAAAGGTACGGAC 58.223 33.333 16.63 0.00 45.89 4.79
1773 2252 8.907222 AGTAACTTCATTTAAAAAGGTACGGA 57.093 30.769 16.63 0.00 45.89 4.69
1814 2293 3.110196 GACGACGTCGACGATACTG 57.890 57.895 41.52 25.88 43.02 2.74
2173 2859 2.024414 GTGTGTGTGCCTTTTCTTCCT 58.976 47.619 0.00 0.00 0.00 3.36
2174 2860 1.748493 TGTGTGTGTGCCTTTTCTTCC 59.252 47.619 0.00 0.00 0.00 3.46
2175 2861 2.163412 TGTGTGTGTGTGCCTTTTCTTC 59.837 45.455 0.00 0.00 0.00 2.87
2177 2863 1.472480 GTGTGTGTGTGTGCCTTTTCT 59.528 47.619 0.00 0.00 0.00 2.52
2179 2865 0.170116 CGTGTGTGTGTGTGCCTTTT 59.830 50.000 0.00 0.00 0.00 2.27
2180 2866 1.800032 CGTGTGTGTGTGTGCCTTT 59.200 52.632 0.00 0.00 0.00 3.11
2181 2867 2.760159 GCGTGTGTGTGTGTGCCTT 61.760 57.895 0.00 0.00 0.00 4.35
2182 2868 3.202001 GCGTGTGTGTGTGTGCCT 61.202 61.111 0.00 0.00 0.00 4.75
2183 2869 2.265073 AAAGCGTGTGTGTGTGTGCC 62.265 55.000 0.00 0.00 0.00 5.01
2184 2870 0.861450 GAAAGCGTGTGTGTGTGTGC 60.861 55.000 0.00 0.00 0.00 4.57
2186 2872 1.130373 CAAGAAAGCGTGTGTGTGTGT 59.870 47.619 0.00 0.00 0.00 3.72
2187 2873 1.813896 CAAGAAAGCGTGTGTGTGTG 58.186 50.000 0.00 0.00 0.00 3.82
2188 2874 0.098728 GCAAGAAAGCGTGTGTGTGT 59.901 50.000 0.00 0.00 0.00 3.72
2189 2875 0.378257 AGCAAGAAAGCGTGTGTGTG 59.622 50.000 0.00 0.00 40.15 3.82
2190 2876 1.094785 AAGCAAGAAAGCGTGTGTGT 58.905 45.000 0.00 0.00 40.15 3.72
2191 2877 1.847999 CAAAGCAAGAAAGCGTGTGTG 59.152 47.619 0.00 0.00 40.15 3.82
2192 2878 1.472480 ACAAAGCAAGAAAGCGTGTGT 59.528 42.857 0.00 0.00 36.65 3.72
2198 2884 3.001634 GGAGCAAAACAAAGCAAGAAAGC 59.998 43.478 0.00 0.00 0.00 3.51
2341 3201 2.086869 CAGAAGGGTGCAACAGTATGG 58.913 52.381 3.06 0.00 43.62 2.74
2372 3232 7.448161 TGGATTGTCCCTGTGCATAAAATATAG 59.552 37.037 0.00 0.00 35.03 1.31
2405 3265 6.264292 ACGATCTCTACCCATATATGAGATGC 59.736 42.308 14.54 7.25 42.40 3.91
2429 3293 5.523438 AGAGGAGACGATATGAAGGAAAC 57.477 43.478 0.00 0.00 0.00 2.78
2437 3301 9.509855 GTAATATAAGCAAGAGGAGACGATATG 57.490 37.037 0.00 0.00 0.00 1.78
2484 3348 1.339438 ACAGCTCACAGGTATGGCTTG 60.339 52.381 0.00 0.00 0.00 4.01
2485 3349 0.987294 ACAGCTCACAGGTATGGCTT 59.013 50.000 0.00 0.00 0.00 4.35
2486 3350 0.251354 CACAGCTCACAGGTATGGCT 59.749 55.000 0.00 0.00 0.00 4.75
2506 3378 3.252400 CACTCACAAAGTTGCAAAAGCA 58.748 40.909 0.00 0.00 35.45 3.91
2518 3390 7.280652 CACATCCATCATATGTACACTCACAAA 59.719 37.037 0.00 0.00 35.82 2.83
2755 3627 1.872679 GATCTTGGCGACGACGTCC 60.873 63.158 21.63 14.00 43.97 4.79
3175 4065 1.061887 GTCAACAGTGCGCACGTTT 59.938 52.632 32.70 27.02 36.20 3.60
3187 4077 4.612412 GGCGTGACCCCGTCAACA 62.612 66.667 0.00 0.00 44.49 3.33
3205 4095 1.079819 CGTGCGGAGGATGTCAAGT 60.080 57.895 0.00 0.00 0.00 3.16
3208 4098 3.356639 GAGCGTGCGGAGGATGTCA 62.357 63.158 0.00 0.00 37.14 3.58
3220 4110 1.444553 GAAGTCGGAGGTGAGCGTG 60.445 63.158 0.00 0.00 0.00 5.34
3481 4371 0.463833 GGTTCATCACGTCCATCCCC 60.464 60.000 0.00 0.00 0.00 4.81
3583 4473 2.404995 GCTGCCAGCCATGTCTCAC 61.405 63.158 5.06 0.00 34.48 3.51
3830 4731 5.525199 ACACGTCGCCAATTAAGAATTTTT 58.475 33.333 0.00 0.00 0.00 1.94
3831 4732 5.116069 ACACGTCGCCAATTAAGAATTTT 57.884 34.783 0.00 0.00 0.00 1.82
3832 4733 4.759516 ACACGTCGCCAATTAAGAATTT 57.240 36.364 0.00 0.00 0.00 1.82
3833 4734 4.454504 AGAACACGTCGCCAATTAAGAATT 59.545 37.500 0.00 0.00 0.00 2.17
3834 4735 4.000988 AGAACACGTCGCCAATTAAGAAT 58.999 39.130 0.00 0.00 0.00 2.40
3846 4747 5.963004 TCAAAATTCTCAAAAGAACACGTCG 59.037 36.000 0.00 0.00 44.13 5.12
3894 4796 8.598924 CACATGCACAAAACAGTAACATTTTTA 58.401 29.630 0.00 0.00 0.00 1.52
3904 4806 3.252400 CAACACACATGCACAAAACAGT 58.748 40.909 0.00 0.00 0.00 3.55
4036 4938 3.366273 CCCAATCGACCTTGTGTGATTTG 60.366 47.826 0.00 0.00 0.00 2.32
4105 5012 7.012515 TCACCAAAACGTCTTACATTTGTGTAT 59.987 33.333 7.22 0.00 32.29 2.29
4130 5037 9.462174 TGTTCACAAATGTAAGATTGACAATTC 57.538 29.630 1.39 0.00 0.00 2.17
4180 5087 7.116736 TGGAGTACATACACTGAGAGATTACA 58.883 38.462 0.00 0.00 0.00 2.41
4181 5088 7.569639 TGGAGTACATACACTGAGAGATTAC 57.430 40.000 0.00 0.00 0.00 1.89
4190 5097 6.089551 GCGCTAAATATGGAGTACATACACTG 59.910 42.308 0.00 0.00 44.41 3.66
4241 5148 5.815233 TTGGCCAAACAATTCCAATAAGA 57.185 34.783 17.98 0.00 34.01 2.10
4246 5153 5.195940 TGAATTTTGGCCAAACAATTCCAA 58.804 33.333 33.11 22.21 36.86 3.53
4412 5320 8.576442 CCAAAGAGAAAAATTACCACTACATGT 58.424 33.333 2.69 2.69 0.00 3.21
4426 5334 7.471399 GCCTCAAATAACTCCCAAAGAGAAAAA 60.471 37.037 0.00 0.00 46.50 1.94


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

AutoCloner maintained by Alex Coulton.