Multiple sequence alignment - TraesCS5B01G418500

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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 TraesCS5B01G418500 chr5B 100.000 2267 0 0 1 2267 594760969 594758703 0.000000e+00 4187.0
1 TraesCS5B01G418500 chr5D 89.496 1409 70 28 203 1563 483659764 483658386 0.000000e+00 1711.0
2 TraesCS5B01G418500 chr5D 85.760 625 55 16 1612 2229 483658372 483657775 4.110000e-177 630.0
3 TraesCS5B01G418500 chr5A 90.064 1248 69 22 244 1451 605144753 605143521 0.000000e+00 1567.0
4 TraesCS5B01G418500 chr5A 83.812 661 60 18 1588 2229 605140933 605140301 3.240000e-163 584.0
5 TraesCS5B01G418500 chr5A 81.690 355 39 15 147 489 663403846 663403506 2.870000e-69 272.0
6 TraesCS5B01G418500 chr5A 96.000 100 3 1 1489 1588 605143516 605143418 6.480000e-36 161.0
7 TraesCS5B01G418500 chr4D 82.073 357 36 15 152 494 483461936 483461594 1.710000e-71 279.0
8 TraesCS5B01G418500 chr4D 81.408 355 39 15 147 489 483449779 483449440 4.800000e-67 265.0
9 TraesCS5B01G418500 chr4D 79.592 392 50 17 889 1271 483448576 483448206 1.040000e-63 254.0
10 TraesCS5B01G418500 chr4D 76.749 529 67 26 1662 2148 429558026 429558540 6.250000e-61 244.0
11 TraesCS5B01G418500 chr4B 82.336 351 34 15 147 483 613710613 613710949 1.710000e-71 279.0
12 TraesCS5B01G418500 chr4B 97.436 39 1 0 1389 1427 642195607 642195645 1.450000e-07 67.6
13 TraesCS5B01G418500 chr2B 83.505 194 17 12 2080 2263 776403665 776403853 1.390000e-37 167.0
14 TraesCS5B01G418500 chr2B 84.615 169 15 9 2099 2263 666728727 666728566 8.380000e-35 158.0
15 TraesCS5B01G418500 chr2B 97.436 39 1 0 1389 1427 206114779 206114817 1.450000e-07 67.6
16 TraesCS5B01G418500 chr2B 97.436 39 1 0 1389 1427 281874094 281874132 1.450000e-07 67.6
17 TraesCS5B01G418500 chr6D 84.659 176 16 9 2080 2247 398731869 398732041 5.010000e-37 165.0
18 TraesCS5B01G418500 chr6D 93.478 46 2 1 1389 1434 41640863 41640907 1.450000e-07 67.6
19 TraesCS5B01G418500 chr3A 82.069 145 13 10 2099 2236 39731329 39731191 6.620000e-21 111.0
20 TraesCS5B01G418500 chr1B 86.458 96 8 5 2122 2212 416773514 416773609 1.430000e-17 100.0
21 TraesCS5B01G418500 chr7B 80.000 150 13 14 2091 2229 488137208 488137351 6.670000e-16 95.3
22 TraesCS5B01G418500 chr7B 97.436 39 1 0 1389 1427 539218325 539218287 1.450000e-07 67.6
23 TraesCS5B01G418500 chr7B 97.436 39 1 0 1389 1427 685247203 685247165 1.450000e-07 67.6
24 TraesCS5B01G418500 chr3D 84.722 72 8 3 2065 2133 420054584 420054513 4.040000e-08 69.4
25 TraesCS5B01G418500 chr7A 97.436 39 1 0 1389 1427 581374291 581374253 1.450000e-07 67.6


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 TraesCS5B01G418500 chr5B 594758703 594760969 2266 True 4187.000000 4187 100.000000 1 2267 1 chr5B.!!$R1 2266
1 TraesCS5B01G418500 chr5D 483657775 483659764 1989 True 1170.500000 1711 87.628000 203 2229 2 chr5D.!!$R1 2026
2 TraesCS5B01G418500 chr5A 605140301 605144753 4452 True 770.666667 1567 89.958667 244 2229 3 chr5A.!!$R2 1985
3 TraesCS5B01G418500 chr4D 483448206 483449779 1573 True 259.500000 265 80.500000 147 1271 2 chr4D.!!$R2 1124
4 TraesCS5B01G418500 chr4D 429558026 429558540 514 False 244.000000 244 76.749000 1662 2148 1 chr4D.!!$F1 486

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
428 455 0.037975 TAGGTCCTGCGTCGGTTTTC 60.038 55.000 0.00 0.0 0.00 2.29 F
1195 1800 1.078918 CGGCCACAGCAAGAGATCA 60.079 57.895 2.24 0.0 42.56 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1239 1844 1.566298 GGTGCTGAGGGTTGGATCCT 61.566 60.0 14.23 0.0 37.33 3.24 R
2168 5313 6.279513 TCTTTTGTAAGGGTAATGCCAATG 57.720 37.5 0.00 0.0 39.65 2.82 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
26 27 9.321562 TGGATTCCTATACGAATTTGTAAAGAC 57.678 33.333 9.62 0.00 32.56 3.01
27 28 9.321562 GGATTCCTATACGAATTTGTAAAGACA 57.678 33.333 9.62 0.00 32.56 3.41
32 33 9.931210 CCTATACGAATTTGTAAAGACAATTCC 57.069 33.333 9.62 0.00 44.96 3.01
37 38 9.840427 ACGAATTTGTAAAGACAATTCCATAAG 57.160 29.630 0.00 0.00 44.96 1.73
38 39 8.798153 CGAATTTGTAAAGACAATTCCATAAGC 58.202 33.333 0.00 0.00 44.96 3.09
39 40 9.087424 GAATTTGTAAAGACAATTCCATAAGCC 57.913 33.333 0.00 0.00 44.96 4.35
40 41 7.531857 TTTGTAAAGACAATTCCATAAGCCA 57.468 32.000 0.00 0.00 44.96 4.75
41 42 7.531857 TTGTAAAGACAATTCCATAAGCCAA 57.468 32.000 0.00 0.00 40.72 4.52
42 43 7.531857 TGTAAAGACAATTCCATAAGCCAAA 57.468 32.000 0.00 0.00 30.68 3.28
43 44 7.601856 TGTAAAGACAATTCCATAAGCCAAAG 58.398 34.615 0.00 0.00 30.68 2.77
44 45 5.665916 AAGACAATTCCATAAGCCAAAGG 57.334 39.130 0.00 0.00 0.00 3.11
116 117 7.546778 TTAAAATTCTTTGTTCCAAACAGGC 57.453 32.000 0.00 0.00 43.27 4.85
117 118 3.751479 ATTCTTTGTTCCAAACAGGCC 57.249 42.857 0.00 0.00 43.27 5.19
118 119 2.452600 TCTTTGTTCCAAACAGGCCT 57.547 45.000 0.00 0.00 43.27 5.19
119 120 2.745968 TCTTTGTTCCAAACAGGCCTT 58.254 42.857 0.00 0.00 43.27 4.35
120 121 3.904717 TCTTTGTTCCAAACAGGCCTTA 58.095 40.909 0.00 0.00 43.27 2.69
121 122 4.479158 TCTTTGTTCCAAACAGGCCTTAT 58.521 39.130 0.00 0.00 43.27 1.73
122 123 5.636123 TCTTTGTTCCAAACAGGCCTTATA 58.364 37.500 0.00 0.00 43.27 0.98
123 124 6.252995 TCTTTGTTCCAAACAGGCCTTATAT 58.747 36.000 0.00 0.00 43.27 0.86
124 125 6.723977 TCTTTGTTCCAAACAGGCCTTATATT 59.276 34.615 0.00 0.00 43.27 1.28
125 126 7.891183 TCTTTGTTCCAAACAGGCCTTATATTA 59.109 33.333 0.00 0.00 43.27 0.98
126 127 7.639113 TTGTTCCAAACAGGCCTTATATTAG 57.361 36.000 0.00 0.00 43.27 1.73
127 128 6.727394 TGTTCCAAACAGGCCTTATATTAGT 58.273 36.000 0.00 0.00 36.25 2.24
128 129 6.601613 TGTTCCAAACAGGCCTTATATTAGTG 59.398 38.462 0.00 0.00 36.25 2.74
129 130 6.321821 TCCAAACAGGCCTTATATTAGTGT 57.678 37.500 0.00 0.00 37.29 3.55
130 131 6.354130 TCCAAACAGGCCTTATATTAGTGTC 58.646 40.000 0.00 0.00 37.29 3.67
131 132 6.157994 TCCAAACAGGCCTTATATTAGTGTCT 59.842 38.462 0.00 0.00 37.29 3.41
132 133 7.346175 TCCAAACAGGCCTTATATTAGTGTCTA 59.654 37.037 0.00 0.00 37.29 2.59
133 134 7.990886 CCAAACAGGCCTTATATTAGTGTCTAA 59.009 37.037 0.00 0.00 0.00 2.10
134 135 8.827677 CAAACAGGCCTTATATTAGTGTCTAAC 58.172 37.037 0.00 0.00 0.00 2.34
135 136 7.063934 ACAGGCCTTATATTAGTGTCTAACC 57.936 40.000 0.00 0.00 0.00 2.85
136 137 6.157211 CAGGCCTTATATTAGTGTCTAACCG 58.843 44.000 0.00 0.00 0.00 4.44
137 138 6.015688 CAGGCCTTATATTAGTGTCTAACCGA 60.016 42.308 0.00 0.00 0.00 4.69
138 139 6.552350 AGGCCTTATATTAGTGTCTAACCGAA 59.448 38.462 0.00 0.00 0.00 4.30
139 140 6.867293 GGCCTTATATTAGTGTCTAACCGAAG 59.133 42.308 0.00 0.00 0.00 3.79
140 141 6.365518 GCCTTATATTAGTGTCTAACCGAAGC 59.634 42.308 0.00 0.00 0.00 3.86
141 142 7.431249 CCTTATATTAGTGTCTAACCGAAGCA 58.569 38.462 0.00 0.00 0.00 3.91
142 143 8.088981 CCTTATATTAGTGTCTAACCGAAGCAT 58.911 37.037 0.00 0.00 0.00 3.79
143 144 9.477484 CTTATATTAGTGTCTAACCGAAGCATT 57.523 33.333 0.00 0.00 0.00 3.56
144 145 7.715265 ATATTAGTGTCTAACCGAAGCATTG 57.285 36.000 0.00 0.00 0.00 2.82
145 146 3.678056 AGTGTCTAACCGAAGCATTGA 57.322 42.857 0.00 0.00 0.00 2.57
159 160 1.881973 GCATTGAGAGTCCTTTGTGCA 59.118 47.619 0.00 0.00 0.00 4.57
160 161 2.294233 GCATTGAGAGTCCTTTGTGCAA 59.706 45.455 0.00 0.00 0.00 4.08
173 174 1.250328 TGTGCAAGCTCTTCCAATGG 58.750 50.000 0.00 0.00 0.00 3.16
176 177 2.494870 GTGCAAGCTCTTCCAATGGATT 59.505 45.455 1.39 0.00 0.00 3.01
183 184 3.429960 GCTCTTCCAATGGATTGAAAGCC 60.430 47.826 1.39 0.00 40.14 4.35
190 191 0.539438 TGGATTGAAAGCCTGCCGTT 60.539 50.000 0.00 0.00 34.95 4.44
191 192 0.109132 GGATTGAAAGCCTGCCGTTG 60.109 55.000 0.00 0.00 0.00 4.10
192 193 0.733909 GATTGAAAGCCTGCCGTTGC 60.734 55.000 0.00 0.00 38.26 4.17
193 194 2.158561 ATTGAAAGCCTGCCGTTGCC 62.159 55.000 0.00 0.00 36.33 4.52
194 195 3.294493 GAAAGCCTGCCGTTGCCA 61.294 61.111 0.00 0.00 36.33 4.92
195 196 2.837291 AAAGCCTGCCGTTGCCAA 60.837 55.556 0.00 0.00 36.33 4.52
196 197 2.753931 GAAAGCCTGCCGTTGCCAAG 62.754 60.000 0.00 0.00 36.33 3.61
197 198 4.586235 AGCCTGCCGTTGCCAAGT 62.586 61.111 0.00 0.00 36.33 3.16
200 201 4.347453 CTGCCGTTGCCAAGTGCC 62.347 66.667 0.00 0.00 40.16 5.01
202 203 3.910490 GCCGTTGCCAAGTGCCAA 61.910 61.111 0.00 0.00 40.16 4.52
400 412 5.494390 TGATCATCCATGACCCAAGATAG 57.506 43.478 0.00 0.00 40.03 2.08
403 426 4.297768 TCATCCATGACCCAAGATAGACA 58.702 43.478 0.00 0.00 0.00 3.41
410 433 4.422057 TGACCCAAGATAGACAACTGGTA 58.578 43.478 0.00 0.00 0.00 3.25
428 455 0.037975 TAGGTCCTGCGTCGGTTTTC 60.038 55.000 0.00 0.00 0.00 2.29
456 484 1.248486 TGTCTCACTCTTGACCCTCG 58.752 55.000 0.00 0.00 32.67 4.63
459 492 2.125912 CACTCTTGACCCTCGCGG 60.126 66.667 6.13 0.00 37.81 6.46
496 533 6.642917 TCGTTTTGATCGAACAAGTAAACTC 58.357 36.000 15.21 0.00 34.36 3.01
508 550 9.074443 CGAACAAGTAAACTCTAATCTAACCTC 57.926 37.037 0.00 0.00 0.00 3.85
518 560 7.584532 ACTCTAATCTAACCTCAGCCTAACTA 58.415 38.462 0.00 0.00 0.00 2.24
609 760 1.176527 ATTGCAAACCCCATCAGACG 58.823 50.000 1.71 0.00 0.00 4.18
789 1356 4.218417 TCAAGATGAAAAGGGTTTGCTAGC 59.782 41.667 8.10 8.10 0.00 3.42
790 1357 4.039603 AGATGAAAAGGGTTTGCTAGCT 57.960 40.909 17.23 0.00 0.00 3.32
791 1358 5.179452 AGATGAAAAGGGTTTGCTAGCTA 57.821 39.130 17.23 5.31 0.00 3.32
792 1359 5.189180 AGATGAAAAGGGTTTGCTAGCTAG 58.811 41.667 16.84 16.84 0.00 3.42
936 1531 7.678947 ATTAACCTGCAGATACATAAGCATC 57.321 36.000 17.39 0.00 36.28 3.91
959 1558 1.271163 GGCAGTTTAGGTGTAGCCACA 60.271 52.381 0.00 0.00 43.71 4.17
1032 1631 3.782244 CCGTGCTTCTGCGTCTGC 61.782 66.667 0.00 0.00 43.34 4.26
1035 1634 1.206072 GTGCTTCTGCGTCTGCTTG 59.794 57.895 0.00 0.00 43.34 4.01
1042 1641 3.470567 GCGTCTGCTTGGTCGTCG 61.471 66.667 0.00 0.00 38.39 5.12
1052 1651 2.745492 GGTCGTCGTCCTCCTCGT 60.745 66.667 0.91 0.00 0.00 4.18
1195 1800 1.078918 CGGCCACAGCAAGAGATCA 60.079 57.895 2.24 0.00 42.56 2.92
1239 1844 0.906756 CCAAGAGGCTCAGTCCTGGA 60.907 60.000 18.26 0.00 36.38 3.86
1314 1923 3.741344 GTGTCCATCGGCTTCATGTATAC 59.259 47.826 0.00 0.00 0.00 1.47
1315 1924 3.641436 TGTCCATCGGCTTCATGTATACT 59.359 43.478 4.17 0.00 0.00 2.12
1316 1925 4.100963 TGTCCATCGGCTTCATGTATACTT 59.899 41.667 4.17 0.00 0.00 2.24
1317 1926 4.686554 GTCCATCGGCTTCATGTATACTTC 59.313 45.833 4.17 0.00 0.00 3.01
1318 1927 4.343814 TCCATCGGCTTCATGTATACTTCA 59.656 41.667 4.17 0.00 0.00 3.02
1336 1945 4.452455 ACTTCATTCAGTTTGCGGTAAGAG 59.548 41.667 0.00 0.00 0.00 2.85
1341 1950 4.330944 TCAGTTTGCGGTAAGAGAAGAA 57.669 40.909 0.00 0.00 0.00 2.52
1564 2176 3.550678 CGGCCTTGTCTAATCTTCGTAAC 59.449 47.826 0.00 0.00 0.00 2.50
1569 2181 6.496571 CCTTGTCTAATCTTCGTAACGATCT 58.503 40.000 0.00 0.00 35.23 2.75
1574 2186 7.909121 TGTCTAATCTTCGTAACGATCTTTCTC 59.091 37.037 0.00 0.00 35.23 2.87
1610 4707 2.036346 GTCACATTTCAAGCAAGGCCTT 59.964 45.455 13.78 13.78 0.00 4.35
1717 4814 7.116736 AGGATTTGGGTCATTCGTTTACTAAT 58.883 34.615 0.00 0.00 0.00 1.73
1726 4823 7.009815 GGTCATTCGTTTACTAATCAATCGACA 59.990 37.037 0.00 0.00 29.54 4.35
1727 4824 8.377681 GTCATTCGTTTACTAATCAATCGACAA 58.622 33.333 0.00 0.00 29.54 3.18
1728 4825 9.093970 TCATTCGTTTACTAATCAATCGACAAT 57.906 29.630 0.00 0.00 29.54 2.71
1729 4826 9.358123 CATTCGTTTACTAATCAATCGACAATC 57.642 33.333 0.00 0.00 29.54 2.67
1730 4827 7.145187 TCGTTTACTAATCAATCGACAATCG 57.855 36.000 0.00 0.00 42.10 3.34
1772 4869 9.537848 GTTTAAGTCAATTTCAGTGTTATACCG 57.462 33.333 0.00 0.00 0.00 4.02
1784 4881 3.685756 GTGTTATACCGCAACTTAAGCCA 59.314 43.478 1.29 0.00 0.00 4.75
1846 4943 2.012673 GCCAATGCAAAACAACAACCA 58.987 42.857 0.00 0.00 37.47 3.67
1862 4959 8.954950 ACAACAACCAATTGATGAACAAATAA 57.045 26.923 7.12 0.00 40.18 1.40
1940 5058 7.642071 AATGCACACTATTCACACAAAAATC 57.358 32.000 0.00 0.00 0.00 2.17
1941 5059 6.141560 TGCACACTATTCACACAAAAATCA 57.858 33.333 0.00 0.00 0.00 2.57
1955 5073 8.377681 CACACAAAAATCATGCATTTCTATGAC 58.622 33.333 0.00 0.00 36.26 3.06
2174 5319 7.573968 AAAGTAATGGATTAGAGACATTGGC 57.426 36.000 0.00 0.00 36.36 4.52
2181 5326 4.762251 GGATTAGAGACATTGGCATTACCC 59.238 45.833 0.00 0.00 37.83 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.321562 GTCTTTACAAATTCGTATAGGAATCCA 57.678 33.333 18.36 4.64 35.65 3.41
1 2 9.321562 TGTCTTTACAAATTCGTATAGGAATCC 57.678 33.333 18.36 0.00 35.65 3.01
18 19 7.309744 CCTTTGGCTTATGGAATTGTCTTTACA 60.310 37.037 0.00 0.00 0.00 2.41
19 20 7.035612 CCTTTGGCTTATGGAATTGTCTTTAC 58.964 38.462 0.00 0.00 0.00 2.01
20 21 6.350949 GCCTTTGGCTTATGGAATTGTCTTTA 60.351 38.462 0.73 0.00 46.69 1.85
21 22 5.569428 GCCTTTGGCTTATGGAATTGTCTTT 60.569 40.000 0.73 0.00 46.69 2.52
22 23 4.081476 GCCTTTGGCTTATGGAATTGTCTT 60.081 41.667 0.73 0.00 46.69 3.01
23 24 3.448660 GCCTTTGGCTTATGGAATTGTCT 59.551 43.478 0.73 0.00 46.69 3.41
24 25 3.785486 GCCTTTGGCTTATGGAATTGTC 58.215 45.455 0.73 0.00 46.69 3.18
25 26 3.893326 GCCTTTGGCTTATGGAATTGT 57.107 42.857 0.73 0.00 46.69 2.71
103 104 6.601613 CACTAATATAAGGCCTGTTTGGAACA 59.398 38.462 5.69 0.00 39.52 3.18
104 105 6.602009 ACACTAATATAAGGCCTGTTTGGAAC 59.398 38.462 5.69 0.00 38.35 3.62
105 106 6.727394 ACACTAATATAAGGCCTGTTTGGAA 58.273 36.000 5.69 0.00 38.35 3.53
106 107 6.157994 AGACACTAATATAAGGCCTGTTTGGA 59.842 38.462 5.69 0.00 38.35 3.53
107 108 6.357367 AGACACTAATATAAGGCCTGTTTGG 58.643 40.000 5.69 2.42 39.35 3.28
108 109 8.827677 GTTAGACACTAATATAAGGCCTGTTTG 58.172 37.037 5.69 3.24 0.00 2.93
109 110 7.991460 GGTTAGACACTAATATAAGGCCTGTTT 59.009 37.037 5.69 0.00 0.00 2.83
110 111 7.506971 GGTTAGACACTAATATAAGGCCTGTT 58.493 38.462 5.69 0.00 0.00 3.16
111 112 6.239232 CGGTTAGACACTAATATAAGGCCTGT 60.239 42.308 5.69 0.00 0.00 4.00
112 113 6.015688 TCGGTTAGACACTAATATAAGGCCTG 60.016 42.308 5.69 0.00 0.00 4.85
113 114 6.073314 TCGGTTAGACACTAATATAAGGCCT 58.927 40.000 0.00 0.00 0.00 5.19
114 115 6.336842 TCGGTTAGACACTAATATAAGGCC 57.663 41.667 0.00 0.00 0.00 5.19
115 116 6.365518 GCTTCGGTTAGACACTAATATAAGGC 59.634 42.308 0.00 0.00 0.00 4.35
116 117 7.431249 TGCTTCGGTTAGACACTAATATAAGG 58.569 38.462 0.00 0.00 0.00 2.69
117 118 9.477484 AATGCTTCGGTTAGACACTAATATAAG 57.523 33.333 0.00 0.00 0.00 1.73
118 119 9.256477 CAATGCTTCGGTTAGACACTAATATAA 57.744 33.333 0.00 0.00 0.00 0.98
119 120 8.635328 TCAATGCTTCGGTTAGACACTAATATA 58.365 33.333 0.00 0.00 0.00 0.86
120 121 7.497595 TCAATGCTTCGGTTAGACACTAATAT 58.502 34.615 0.00 0.00 0.00 1.28
121 122 6.869695 TCAATGCTTCGGTTAGACACTAATA 58.130 36.000 0.00 0.00 0.00 0.98
122 123 5.730550 TCAATGCTTCGGTTAGACACTAAT 58.269 37.500 0.00 0.00 0.00 1.73
123 124 5.047590 TCTCAATGCTTCGGTTAGACACTAA 60.048 40.000 0.00 0.00 0.00 2.24
124 125 4.461431 TCTCAATGCTTCGGTTAGACACTA 59.539 41.667 0.00 0.00 0.00 2.74
125 126 3.258372 TCTCAATGCTTCGGTTAGACACT 59.742 43.478 0.00 0.00 0.00 3.55
126 127 3.585862 TCTCAATGCTTCGGTTAGACAC 58.414 45.455 0.00 0.00 0.00 3.67
127 128 3.258372 ACTCTCAATGCTTCGGTTAGACA 59.742 43.478 0.00 0.00 0.00 3.41
128 129 3.851098 ACTCTCAATGCTTCGGTTAGAC 58.149 45.455 0.00 0.00 0.00 2.59
129 130 3.119101 GGACTCTCAATGCTTCGGTTAGA 60.119 47.826 0.00 0.00 0.00 2.10
130 131 3.118956 AGGACTCTCAATGCTTCGGTTAG 60.119 47.826 0.00 0.00 0.00 2.34
131 132 2.832129 AGGACTCTCAATGCTTCGGTTA 59.168 45.455 0.00 0.00 0.00 2.85
132 133 1.625818 AGGACTCTCAATGCTTCGGTT 59.374 47.619 0.00 0.00 0.00 4.44
133 134 1.270907 AGGACTCTCAATGCTTCGGT 58.729 50.000 0.00 0.00 0.00 4.69
134 135 2.393271 AAGGACTCTCAATGCTTCGG 57.607 50.000 0.00 0.00 0.00 4.30
135 136 3.070018 ACAAAGGACTCTCAATGCTTCG 58.930 45.455 0.00 0.00 0.00 3.79
136 137 3.365767 GCACAAAGGACTCTCAATGCTTC 60.366 47.826 0.00 0.00 0.00 3.86
137 138 2.555757 GCACAAAGGACTCTCAATGCTT 59.444 45.455 0.00 0.00 0.00 3.91
138 139 2.157738 GCACAAAGGACTCTCAATGCT 58.842 47.619 0.00 0.00 0.00 3.79
139 140 1.881973 TGCACAAAGGACTCTCAATGC 59.118 47.619 0.00 0.00 0.00 3.56
140 141 3.611057 GCTTGCACAAAGGACTCTCAATG 60.611 47.826 0.00 0.00 36.30 2.82
141 142 2.555757 GCTTGCACAAAGGACTCTCAAT 59.444 45.455 0.00 0.00 36.30 2.57
142 143 1.949525 GCTTGCACAAAGGACTCTCAA 59.050 47.619 0.00 0.00 36.30 3.02
143 144 1.141657 AGCTTGCACAAAGGACTCTCA 59.858 47.619 0.00 0.00 36.30 3.27
144 145 1.803555 GAGCTTGCACAAAGGACTCTC 59.196 52.381 0.00 0.00 36.30 3.20
145 146 1.419387 AGAGCTTGCACAAAGGACTCT 59.581 47.619 0.00 0.00 36.30 3.24
173 174 0.733909 GCAACGGCAGGCTTTCAATC 60.734 55.000 0.00 0.00 40.72 2.67
176 177 3.294493 GGCAACGGCAGGCTTTCA 61.294 61.111 0.00 0.00 43.71 2.69
200 201 2.774799 GCCGGCCCTAATGCAGTTG 61.775 63.158 18.11 0.00 0.00 3.16
202 203 4.856801 CGCCGGCCCTAATGCAGT 62.857 66.667 23.46 0.00 0.00 4.40
221 222 2.858344 CGGGAATATTATAAGCTCGCCG 59.142 50.000 0.00 0.00 0.00 6.46
223 224 5.169295 AGAACGGGAATATTATAAGCTCGC 58.831 41.667 0.00 0.00 0.00 5.03
400 412 0.389948 CGCAGGACCTACCAGTTGTC 60.390 60.000 0.00 0.00 42.04 3.18
403 426 1.874345 CGACGCAGGACCTACCAGTT 61.874 60.000 0.00 0.00 42.04 3.16
410 433 1.301479 GAAAACCGACGCAGGACCT 60.301 57.895 3.59 0.00 34.73 3.85
428 455 1.107114 AGAGTGAGACATACCTGCCG 58.893 55.000 0.00 0.00 0.00 5.69
456 484 1.934463 CGATAGTGATGGCAACCGC 59.066 57.895 0.00 0.00 37.44 5.68
518 560 6.072286 GCTATATGCATTGAGCCTGTTGTATT 60.072 38.462 17.55 0.00 44.83 1.89
609 760 4.589908 ACAAGATGTCATTTCAGGTACCC 58.410 43.478 8.74 0.00 0.00 3.69
637 1074 3.678548 CCGTTTTCTTCGACTTTCTAGGG 59.321 47.826 0.00 0.00 0.00 3.53
789 1356 1.326852 CTGAAGCGCTCAATGCACTAG 59.673 52.381 12.06 0.00 43.06 2.57
790 1357 1.362768 CTGAAGCGCTCAATGCACTA 58.637 50.000 12.06 0.00 43.06 2.74
791 1358 1.303799 CCTGAAGCGCTCAATGCACT 61.304 55.000 12.06 0.00 43.06 4.40
792 1359 1.136147 CCTGAAGCGCTCAATGCAC 59.864 57.895 12.06 0.00 43.06 4.57
804 1375 2.697751 AGCTAGCTGGTATGACCTGAAG 59.302 50.000 18.57 4.43 39.29 3.02
866 1459 6.214399 AGGCTAAATATGAACACTACGCTAC 58.786 40.000 0.00 0.00 0.00 3.58
868 1461 5.277857 AGGCTAAATATGAACACTACGCT 57.722 39.130 0.00 0.00 0.00 5.07
869 1462 8.752766 TTATAGGCTAAATATGAACACTACGC 57.247 34.615 0.00 0.00 0.00 4.42
882 1475 6.014156 AGGAGACGAGCATTTATAGGCTAAAT 60.014 38.462 0.00 0.00 42.35 1.40
931 1526 0.324943 ACCTAAACTGCCGTGATGCT 59.675 50.000 0.00 0.00 0.00 3.79
936 1531 1.076332 GCTACACCTAAACTGCCGTG 58.924 55.000 0.00 0.00 0.00 4.94
1032 1631 1.507174 GAGGAGGACGACGACCAAG 59.493 63.158 18.31 0.00 0.00 3.61
1035 1634 2.745492 ACGAGGAGGACGACGACC 60.745 66.667 8.37 8.37 34.70 4.79
1042 1641 3.519930 GGAGCCGACGAGGAGGAC 61.520 72.222 0.00 0.00 45.00 3.85
1173 1775 4.560743 TCTTGCTGTGGCCGCACA 62.561 61.111 16.89 15.66 37.07 4.57
1184 1786 1.411977 CCAGATCGGTGATCTCTTGCT 59.588 52.381 6.35 0.00 45.03 3.91
1239 1844 1.566298 GGTGCTGAGGGTTGGATCCT 61.566 60.000 14.23 0.00 37.33 3.24
1314 1923 4.690748 TCTCTTACCGCAAACTGAATGAAG 59.309 41.667 0.00 0.00 0.00 3.02
1315 1924 4.637276 TCTCTTACCGCAAACTGAATGAA 58.363 39.130 0.00 0.00 0.00 2.57
1316 1925 4.265904 TCTCTTACCGCAAACTGAATGA 57.734 40.909 0.00 0.00 0.00 2.57
1317 1926 4.690748 TCTTCTCTTACCGCAAACTGAATG 59.309 41.667 0.00 0.00 0.00 2.67
1318 1927 4.894784 TCTTCTCTTACCGCAAACTGAAT 58.105 39.130 0.00 0.00 0.00 2.57
1564 2176 8.449397 ACATTCTTTTGATGAAGAGAAAGATCG 58.551 33.333 7.28 0.00 37.79 3.69
1569 2181 8.224389 TGTGACATTCTTTTGATGAAGAGAAA 57.776 30.769 2.13 0.00 37.01 2.52
1574 2186 8.806177 TGAAATGTGACATTCTTTTGATGAAG 57.194 30.769 11.70 0.00 0.00 3.02
1726 4823 8.918961 TTAAACATGTTTTTGTTCAGTCGATT 57.081 26.923 27.66 1.46 38.85 3.34
1727 4824 8.188139 ACTTAAACATGTTTTTGTTCAGTCGAT 58.812 29.630 27.66 2.12 38.85 3.59
1728 4825 7.531716 ACTTAAACATGTTTTTGTTCAGTCGA 58.468 30.769 27.66 3.63 38.85 4.20
1729 4826 7.483375 TGACTTAAACATGTTTTTGTTCAGTCG 59.517 33.333 27.66 7.87 43.96 4.18
1730 4827 8.682128 TGACTTAAACATGTTTTTGTTCAGTC 57.318 30.769 27.66 23.71 42.84 3.51
1731 4828 9.651913 ATTGACTTAAACATGTTTTTGTTCAGT 57.348 25.926 27.66 18.27 38.85 3.41
1770 4867 2.606108 GGAAAATGGCTTAAGTTGCGG 58.394 47.619 4.02 0.00 0.00 5.69
1772 4869 3.676291 TGGGAAAATGGCTTAAGTTGC 57.324 42.857 4.02 0.00 0.00 4.17
1784 4881 5.878406 TGTGTTGGTTTGTATGGGAAAAT 57.122 34.783 0.00 0.00 0.00 1.82
2016 5134 9.541884 AAAGGGTAATATCACTGTTACCAATTT 57.458 29.630 14.21 11.44 45.91 1.82
2168 5313 6.279513 TCTTTTGTAAGGGTAATGCCAATG 57.720 37.500 0.00 0.00 39.65 2.82
2171 5316 6.551601 TCTTTTCTTTTGTAAGGGTAATGCCA 59.448 34.615 0.00 0.00 39.65 4.92


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

AutoCloner maintained by Alex Coulton.