Multiple sequence alignment - TraesCS4A01G279900

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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 TraesCS4A01G279900 chr4A 100.000 2246 0 0 1 2246 587723356 587725601 0.000000e+00 4148.0
1 TraesCS4A01G279900 chr4A 97.240 1377 35 3 258 1634 630614059 630612686 0.000000e+00 2329.0
2 TraesCS4A01G279900 chr4A 97.421 349 8 1 1624 1971 630612567 630612219 5.340000e-166 593.0
3 TraesCS4A01G279900 chr4A 98.305 236 4 0 1 236 457585172 457585407 4.460000e-112 414.0
4 TraesCS4A01G279900 chr7A 97.987 1341 25 2 258 1597 106589701 106588362 0.000000e+00 2326.0
5 TraesCS4A01G279900 chr7A 96.523 1064 34 2 258 1321 647417342 647416282 0.000000e+00 1757.0
6 TraesCS4A01G279900 chr7A 97.881 236 5 0 1 236 728277343 728277108 2.080000e-110 409.0
7 TraesCS4A01G279900 chr7A 98.283 233 3 1 1 232 717357112 717356880 7.470000e-110 407.0
8 TraesCS4A01G279900 chr2A 96.866 1340 41 1 258 1597 88835192 88836530 0.000000e+00 2241.0
9 TraesCS4A01G279900 chr2A 96.567 1340 45 1 258 1597 708688662 708690000 0.000000e+00 2218.0
10 TraesCS4A01G279900 chr2A 97.468 237 5 1 1 236 763602774 763602538 9.660000e-109 403.0
11 TraesCS4A01G279900 chr3A 96.791 1340 37 2 258 1597 41657295 41658628 0.000000e+00 2231.0
12 TraesCS4A01G279900 chr3A 96.343 1340 44 4 258 1597 743242683 743241349 0.000000e+00 2198.0
13 TraesCS4A01G279900 chr3A 96.711 1064 33 2 258 1321 122543176 122542115 0.000000e+00 1770.0
14 TraesCS4A01G279900 chr3A 99.153 236 2 0 1 236 634017 634252 2.060000e-115 425.0
15 TraesCS4A01G279900 chr3A 97.881 236 5 0 1 236 669129603 669129838 2.080000e-110 409.0
16 TraesCS4A01G279900 chr5A 96.125 1084 36 5 239 1321 388937527 388936449 0.000000e+00 1764.0
17 TraesCS4A01G279900 chr1A 98.553 622 8 1 1624 2244 537533710 537534331 0.000000e+00 1098.0
18 TraesCS4A01G279900 chr1A 97.890 237 4 1 1 236 420435333 420435097 2.080000e-110 409.0
19 TraesCS4A01G279900 chr1A 100.000 38 0 0 1597 1634 537533554 537533591 1.110000e-08 71.3
20 TraesCS4A01G279900 chr6B 97.849 279 6 0 1319 1597 673370236 673370514 1.210000e-132 483.0
21 TraesCS4A01G279900 chr4B 97.491 279 7 0 1319 1597 559905701 559905423 5.610000e-131 477.0
22 TraesCS4A01G279900 chr5B 98.729 236 3 0 1 236 73530357 73530122 9.590000e-114 420.0
23 TraesCS4A01G279900 chr6A 97.468 237 5 1 1 236 5161634 5161398 9.660000e-109 403.0
24 TraesCS4A01G279900 chr5D 94.012 167 9 1 2078 2244 26920561 26920726 3.700000e-63 252.0
25 TraesCS4A01G279900 chr1B 90.055 181 15 2 2029 2209 645038933 645039110 4.820000e-57 231.0
26 TraesCS4A01G279900 chr3D 91.018 167 15 0 2078 2244 112717143 112717309 2.240000e-55 226.0


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 TraesCS4A01G279900 chr4A 587723356 587725601 2245 False 4148.00 4148 100.0000 1 2246 1 chr4A.!!$F2 2245
1 TraesCS4A01G279900 chr4A 630612219 630614059 1840 True 1461.00 2329 97.3305 258 1971 2 chr4A.!!$R1 1713
2 TraesCS4A01G279900 chr7A 106588362 106589701 1339 True 2326.00 2326 97.9870 258 1597 1 chr7A.!!$R1 1339
3 TraesCS4A01G279900 chr7A 647416282 647417342 1060 True 1757.00 1757 96.5230 258 1321 1 chr7A.!!$R2 1063
4 TraesCS4A01G279900 chr2A 88835192 88836530 1338 False 2241.00 2241 96.8660 258 1597 1 chr2A.!!$F1 1339
5 TraesCS4A01G279900 chr2A 708688662 708690000 1338 False 2218.00 2218 96.5670 258 1597 1 chr2A.!!$F2 1339
6 TraesCS4A01G279900 chr3A 41657295 41658628 1333 False 2231.00 2231 96.7910 258 1597 1 chr3A.!!$F2 1339
7 TraesCS4A01G279900 chr3A 743241349 743242683 1334 True 2198.00 2198 96.3430 258 1597 1 chr3A.!!$R2 1339
8 TraesCS4A01G279900 chr3A 122542115 122543176 1061 True 1770.00 1770 96.7110 258 1321 1 chr3A.!!$R1 1063
9 TraesCS4A01G279900 chr5A 388936449 388937527 1078 True 1764.00 1764 96.1250 239 1321 1 chr5A.!!$R1 1082
10 TraesCS4A01G279900 chr1A 537533554 537534331 777 False 584.65 1098 99.2765 1597 2244 2 chr1A.!!$F1 647

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
81 82 0.32336 TCCATTTTTCTGGGCCTCGG 60.323 55.0 4.53 0.0 36.89 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 1428 0.110486 GGGCAAGGACAAGGACAAGA 59.89 55.0 0.0 0.0 0.0 3.02 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
21 22 4.632538 AATTTTCGCTAAGTACATGGGC 57.367 40.909 0.00 0.00 0.00 5.36
22 23 2.032680 TTTCGCTAAGTACATGGGCC 57.967 50.000 0.00 0.00 0.00 5.80
23 24 1.200519 TTCGCTAAGTACATGGGCCT 58.799 50.000 4.53 0.00 0.00 5.19
24 25 0.464036 TCGCTAAGTACATGGGCCTG 59.536 55.000 4.53 3.00 0.00 4.85
25 26 0.532862 CGCTAAGTACATGGGCCTGG 60.533 60.000 4.53 0.00 0.00 4.45
26 27 0.819666 GCTAAGTACATGGGCCTGGC 60.820 60.000 11.05 11.05 0.00 4.85
36 37 3.482383 GGCCTGGCCCAACAATTT 58.518 55.556 27.77 0.00 44.06 1.82
37 38 1.003476 GGCCTGGCCCAACAATTTG 60.003 57.895 27.77 0.00 44.06 2.32
65 66 5.913137 TTTTGTTTTCTGAGCTTCTTCCA 57.087 34.783 0.00 0.00 0.00 3.53
66 67 6.469782 TTTTGTTTTCTGAGCTTCTTCCAT 57.530 33.333 0.00 0.00 0.00 3.41
67 68 6.469782 TTTGTTTTCTGAGCTTCTTCCATT 57.530 33.333 0.00 0.00 0.00 3.16
68 69 6.469782 TTGTTTTCTGAGCTTCTTCCATTT 57.530 33.333 0.00 0.00 0.00 2.32
69 70 6.469782 TGTTTTCTGAGCTTCTTCCATTTT 57.530 33.333 0.00 0.00 0.00 1.82
70 71 6.877236 TGTTTTCTGAGCTTCTTCCATTTTT 58.123 32.000 0.00 0.00 0.00 1.94
71 72 6.980397 TGTTTTCTGAGCTTCTTCCATTTTTC 59.020 34.615 0.00 0.00 0.00 2.29
72 73 6.966534 TTTCTGAGCTTCTTCCATTTTTCT 57.033 33.333 0.00 0.00 0.00 2.52
73 74 5.954296 TCTGAGCTTCTTCCATTTTTCTG 57.046 39.130 0.00 0.00 0.00 3.02
74 75 4.763793 TCTGAGCTTCTTCCATTTTTCTGG 59.236 41.667 0.00 0.00 37.66 3.86
75 76 3.828451 TGAGCTTCTTCCATTTTTCTGGG 59.172 43.478 0.00 0.00 36.89 4.45
76 77 2.564504 AGCTTCTTCCATTTTTCTGGGC 59.435 45.455 0.00 0.00 36.89 5.36
77 78 2.354103 GCTTCTTCCATTTTTCTGGGCC 60.354 50.000 0.00 0.00 36.89 5.80
78 79 2.999185 TCTTCCATTTTTCTGGGCCT 57.001 45.000 4.53 0.00 36.89 5.19
79 80 2.807676 TCTTCCATTTTTCTGGGCCTC 58.192 47.619 4.53 0.00 36.89 4.70
80 81 1.474077 CTTCCATTTTTCTGGGCCTCG 59.526 52.381 4.53 0.00 36.89 4.63
81 82 0.323360 TCCATTTTTCTGGGCCTCGG 60.323 55.000 4.53 0.00 36.89 4.63
82 83 1.512694 CATTTTTCTGGGCCTCGGC 59.487 57.895 4.53 0.00 41.06 5.54
93 94 4.394712 CCTCGGCCTTTCTGCGGT 62.395 66.667 0.00 0.00 33.69 5.68
94 95 2.815647 CTCGGCCTTTCTGCGGTC 60.816 66.667 0.00 0.00 33.69 4.79
95 96 4.388499 TCGGCCTTTCTGCGGTCC 62.388 66.667 0.00 0.00 33.69 4.46
96 97 4.697756 CGGCCTTTCTGCGGTCCA 62.698 66.667 0.00 0.00 0.00 4.02
97 98 2.044946 GGCCTTTCTGCGGTCCAT 60.045 61.111 0.00 0.00 0.00 3.41
98 99 1.678970 GGCCTTTCTGCGGTCCATT 60.679 57.895 0.00 0.00 0.00 3.16
99 100 1.250840 GGCCTTTCTGCGGTCCATTT 61.251 55.000 0.00 0.00 0.00 2.32
100 101 1.459450 GCCTTTCTGCGGTCCATTTA 58.541 50.000 0.00 0.00 0.00 1.40
101 102 1.816224 GCCTTTCTGCGGTCCATTTAA 59.184 47.619 0.00 0.00 0.00 1.52
102 103 2.427095 GCCTTTCTGCGGTCCATTTAAT 59.573 45.455 0.00 0.00 0.00 1.40
103 104 3.119137 GCCTTTCTGCGGTCCATTTAATT 60.119 43.478 0.00 0.00 0.00 1.40
104 105 4.423732 CCTTTCTGCGGTCCATTTAATTG 58.576 43.478 0.00 0.00 0.00 2.32
105 106 4.082245 CCTTTCTGCGGTCCATTTAATTGT 60.082 41.667 0.00 0.00 0.00 2.71
106 107 5.461032 TTTCTGCGGTCCATTTAATTGTT 57.539 34.783 0.00 0.00 0.00 2.83
107 108 5.461032 TTCTGCGGTCCATTTAATTGTTT 57.539 34.783 0.00 0.00 0.00 2.83
108 109 6.576662 TTCTGCGGTCCATTTAATTGTTTA 57.423 33.333 0.00 0.00 0.00 2.01
109 110 6.576662 TCTGCGGTCCATTTAATTGTTTAA 57.423 33.333 0.00 0.00 0.00 1.52
110 111 6.982852 TCTGCGGTCCATTTAATTGTTTAAA 58.017 32.000 0.00 0.00 40.57 1.52
111 112 7.607250 TCTGCGGTCCATTTAATTGTTTAAAT 58.393 30.769 0.00 0.00 44.88 1.40
112 113 8.091449 TCTGCGGTCCATTTAATTGTTTAAATT 58.909 29.630 0.00 0.00 42.62 1.82
113 114 8.608844 TGCGGTCCATTTAATTGTTTAAATTT 57.391 26.923 0.00 0.00 42.62 1.82
114 115 9.057089 TGCGGTCCATTTAATTGTTTAAATTTT 57.943 25.926 0.00 0.00 42.62 1.82
115 116 9.885934 GCGGTCCATTTAATTGTTTAAATTTTT 57.114 25.926 0.00 0.00 42.62 1.94
164 165 5.262588 GTCCAATATTGTTTGGGCTAAGG 57.737 43.478 14.25 0.00 45.88 2.69
165 166 3.704061 TCCAATATTGTTTGGGCTAAGGC 59.296 43.478 14.25 0.00 45.21 4.35
181 182 2.532854 GGCCTCTTCTAGCCCATCA 58.467 57.895 0.00 0.00 43.76 3.07
182 183 0.839946 GGCCTCTTCTAGCCCATCAA 59.160 55.000 0.00 0.00 43.76 2.57
183 184 1.423161 GGCCTCTTCTAGCCCATCAAT 59.577 52.381 0.00 0.00 43.76 2.57
184 185 2.639839 GGCCTCTTCTAGCCCATCAATA 59.360 50.000 0.00 0.00 43.76 1.90
185 186 3.265479 GGCCTCTTCTAGCCCATCAATAT 59.735 47.826 0.00 0.00 43.76 1.28
186 187 4.263683 GGCCTCTTCTAGCCCATCAATATT 60.264 45.833 0.00 0.00 43.76 1.28
187 188 5.320277 GCCTCTTCTAGCCCATCAATATTT 58.680 41.667 0.00 0.00 0.00 1.40
188 189 5.772169 GCCTCTTCTAGCCCATCAATATTTT 59.228 40.000 0.00 0.00 0.00 1.82
189 190 6.072230 GCCTCTTCTAGCCCATCAATATTTTC 60.072 42.308 0.00 0.00 0.00 2.29
190 191 7.000472 CCTCTTCTAGCCCATCAATATTTTCA 59.000 38.462 0.00 0.00 0.00 2.69
191 192 7.174599 CCTCTTCTAGCCCATCAATATTTTCAG 59.825 40.741 0.00 0.00 0.00 3.02
192 193 6.488006 TCTTCTAGCCCATCAATATTTTCAGC 59.512 38.462 0.00 0.00 0.00 4.26
193 194 5.072741 TCTAGCCCATCAATATTTTCAGCC 58.927 41.667 0.00 0.00 0.00 4.85
194 195 2.967887 AGCCCATCAATATTTTCAGCCC 59.032 45.455 0.00 0.00 0.00 5.19
195 196 2.699846 GCCCATCAATATTTTCAGCCCA 59.300 45.455 0.00 0.00 0.00 5.36
196 197 3.493176 GCCCATCAATATTTTCAGCCCAC 60.493 47.826 0.00 0.00 0.00 4.61
197 198 3.962718 CCCATCAATATTTTCAGCCCACT 59.037 43.478 0.00 0.00 0.00 4.00
198 199 5.139727 CCCATCAATATTTTCAGCCCACTA 58.860 41.667 0.00 0.00 0.00 2.74
199 200 5.598005 CCCATCAATATTTTCAGCCCACTAA 59.402 40.000 0.00 0.00 0.00 2.24
200 201 6.268387 CCCATCAATATTTTCAGCCCACTAAT 59.732 38.462 0.00 0.00 0.00 1.73
201 202 7.202029 CCCATCAATATTTTCAGCCCACTAATT 60.202 37.037 0.00 0.00 0.00 1.40
202 203 7.869429 CCATCAATATTTTCAGCCCACTAATTC 59.131 37.037 0.00 0.00 0.00 2.17
203 204 7.953005 TCAATATTTTCAGCCCACTAATTCA 57.047 32.000 0.00 0.00 0.00 2.57
204 205 8.359875 TCAATATTTTCAGCCCACTAATTCAA 57.640 30.769 0.00 0.00 0.00 2.69
205 206 8.811017 TCAATATTTTCAGCCCACTAATTCAAA 58.189 29.630 0.00 0.00 0.00 2.69
206 207 9.090692 CAATATTTTCAGCCCACTAATTCAAAG 57.909 33.333 0.00 0.00 0.00 2.77
207 208 5.467035 TTTTCAGCCCACTAATTCAAAGG 57.533 39.130 0.00 0.00 0.00 3.11
208 209 4.380843 TTCAGCCCACTAATTCAAAGGA 57.619 40.909 0.00 0.00 0.00 3.36
209 210 3.686016 TCAGCCCACTAATTCAAAGGAC 58.314 45.455 0.00 0.00 0.00 3.85
210 211 3.330701 TCAGCCCACTAATTCAAAGGACT 59.669 43.478 0.00 0.00 0.00 3.85
211 212 3.441572 CAGCCCACTAATTCAAAGGACTG 59.558 47.826 0.00 0.00 0.00 3.51
212 213 2.755103 GCCCACTAATTCAAAGGACTGG 59.245 50.000 0.00 0.00 0.00 4.00
213 214 3.561313 GCCCACTAATTCAAAGGACTGGA 60.561 47.826 0.00 0.00 0.00 3.86
214 215 4.010349 CCCACTAATTCAAAGGACTGGAC 58.990 47.826 0.00 0.00 0.00 4.02
215 216 4.506625 CCCACTAATTCAAAGGACTGGACA 60.507 45.833 0.00 0.00 0.00 4.02
216 217 5.070001 CCACTAATTCAAAGGACTGGACAA 58.930 41.667 0.00 0.00 0.00 3.18
217 218 5.048713 CCACTAATTCAAAGGACTGGACAAC 60.049 44.000 0.00 0.00 0.00 3.32
218 219 5.530915 CACTAATTCAAAGGACTGGACAACA 59.469 40.000 0.00 0.00 0.00 3.33
233 234 6.713762 TGGACAACAGAGAAACAATTCAAT 57.286 33.333 0.00 0.00 38.06 2.57
234 235 7.111247 TGGACAACAGAGAAACAATTCAATT 57.889 32.000 0.00 0.00 38.06 2.32
235 236 7.555087 TGGACAACAGAGAAACAATTCAATTT 58.445 30.769 0.00 0.00 38.06 1.82
236 237 8.690884 TGGACAACAGAGAAACAATTCAATTTA 58.309 29.630 0.00 0.00 38.06 1.40
237 238 9.696917 GGACAACAGAGAAACAATTCAATTTAT 57.303 29.630 0.00 0.00 38.06 1.40
508 509 9.515226 AATCTAAAAGCACATTAACTTGTAGGA 57.485 29.630 0.00 0.00 35.34 2.94
541 542 9.190858 TGTGCATAAATAAAGTAAAACAAGCAG 57.809 29.630 0.00 0.00 0.00 4.24
903 904 5.098211 GGTAAGCTCATTGTGCATTTTCTC 58.902 41.667 12.76 0.00 0.00 2.87
954 955 7.923414 AGTAACCACCAAAATCTCTCAATAC 57.077 36.000 0.00 0.00 0.00 1.89
1024 1026 3.804873 GGCATCGAATAGAAGAGTTGGTC 59.195 47.826 0.00 0.00 0.00 4.02
1146 1148 2.415608 CGACCTCGCCCTTGAGCTA 61.416 63.158 0.00 0.00 34.56 3.32
1426 1428 2.946990 TGATGATGCGATGATGTTGCTT 59.053 40.909 0.00 0.00 38.13 3.91
1569 1572 1.355720 ACAGGAAACAAGGGGGATCAG 59.644 52.381 0.00 0.00 0.00 2.90
1574 1577 4.096681 GGAAACAAGGGGGATCAGAAAAT 58.903 43.478 0.00 0.00 0.00 1.82
1701 1834 1.694150 TCACCAACAGGTCCAGAAGAG 59.306 52.381 0.00 0.00 31.84 2.85
1884 2017 5.644644 CAGACATGCTTAATCCTTCCAAAC 58.355 41.667 0.00 0.00 0.00 2.93
2170 2303 3.572584 GCTGACAAGCTCATTTTTCAGG 58.427 45.455 2.39 0.00 46.60 3.86
2244 2377 7.605691 ACTTGAGAAGAGAACATTATTCACCAG 59.394 37.037 0.00 0.00 0.00 4.00
2245 2378 7.244886 TGAGAAGAGAACATTATTCACCAGA 57.755 36.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.380320 GGCCCATGTACTTAGCGAAAATT 59.620 43.478 0.00 0.00 0.00 1.82
1 2 2.949644 GGCCCATGTACTTAGCGAAAAT 59.050 45.455 0.00 0.00 0.00 1.82
2 3 2.026636 AGGCCCATGTACTTAGCGAAAA 60.027 45.455 0.00 0.00 0.00 2.29
3 4 1.557832 AGGCCCATGTACTTAGCGAAA 59.442 47.619 0.00 0.00 0.00 3.46
4 5 1.134521 CAGGCCCATGTACTTAGCGAA 60.135 52.381 0.00 0.00 0.00 4.70
5 6 0.464036 CAGGCCCATGTACTTAGCGA 59.536 55.000 0.00 0.00 0.00 4.93
6 7 0.532862 CCAGGCCCATGTACTTAGCG 60.533 60.000 0.00 0.00 0.00 4.26
7 8 0.819666 GCCAGGCCCATGTACTTAGC 60.820 60.000 0.00 0.00 0.00 3.09
8 9 0.179018 GGCCAGGCCCATGTACTTAG 60.179 60.000 21.62 0.00 44.06 2.18
9 10 1.919771 GGCCAGGCCCATGTACTTA 59.080 57.895 21.62 0.00 44.06 2.24
10 11 2.683475 GGCCAGGCCCATGTACTT 59.317 61.111 21.62 0.00 44.06 2.24
20 21 4.699626 CAAATTGTTGGGCCAGGC 57.300 55.556 6.23 1.26 0.00 4.85
42 43 6.279513 TGGAAGAAGCTCAGAAAACAAAAA 57.720 33.333 0.00 0.00 0.00 1.94
43 44 5.913137 TGGAAGAAGCTCAGAAAACAAAA 57.087 34.783 0.00 0.00 0.00 2.44
44 45 6.469782 AATGGAAGAAGCTCAGAAAACAAA 57.530 33.333 0.00 0.00 0.00 2.83
45 46 6.469782 AAATGGAAGAAGCTCAGAAAACAA 57.530 33.333 0.00 0.00 0.00 2.83
46 47 6.469782 AAAATGGAAGAAGCTCAGAAAACA 57.530 33.333 0.00 0.00 0.00 2.83
47 48 7.168804 CAGAAAAATGGAAGAAGCTCAGAAAAC 59.831 37.037 0.00 0.00 0.00 2.43
48 49 7.205297 CAGAAAAATGGAAGAAGCTCAGAAAA 58.795 34.615 0.00 0.00 0.00 2.29
49 50 6.239120 CCAGAAAAATGGAAGAAGCTCAGAAA 60.239 38.462 0.00 0.00 43.57 2.52
50 51 5.242393 CCAGAAAAATGGAAGAAGCTCAGAA 59.758 40.000 0.00 0.00 43.57 3.02
51 52 4.763793 CCAGAAAAATGGAAGAAGCTCAGA 59.236 41.667 0.00 0.00 43.57 3.27
52 53 4.082354 CCCAGAAAAATGGAAGAAGCTCAG 60.082 45.833 0.00 0.00 43.57 3.35
53 54 3.828451 CCCAGAAAAATGGAAGAAGCTCA 59.172 43.478 0.00 0.00 43.57 4.26
54 55 3.367806 GCCCAGAAAAATGGAAGAAGCTC 60.368 47.826 0.00 0.00 43.57 4.09
55 56 2.564504 GCCCAGAAAAATGGAAGAAGCT 59.435 45.455 0.00 0.00 43.57 3.74
56 57 2.354103 GGCCCAGAAAAATGGAAGAAGC 60.354 50.000 0.00 0.00 43.57 3.86
57 58 3.168292 AGGCCCAGAAAAATGGAAGAAG 58.832 45.455 0.00 0.00 43.57 2.85
58 59 3.165071 GAGGCCCAGAAAAATGGAAGAA 58.835 45.455 0.00 0.00 43.57 2.52
59 60 2.807676 GAGGCCCAGAAAAATGGAAGA 58.192 47.619 0.00 0.00 43.57 2.87
60 61 1.474077 CGAGGCCCAGAAAAATGGAAG 59.526 52.381 0.00 0.00 43.57 3.46
61 62 1.544724 CGAGGCCCAGAAAAATGGAA 58.455 50.000 0.00 0.00 43.57 3.53
62 63 0.323360 CCGAGGCCCAGAAAAATGGA 60.323 55.000 0.00 0.00 43.57 3.41
63 64 1.948721 GCCGAGGCCCAGAAAAATGG 61.949 60.000 0.00 0.00 40.29 3.16
64 65 1.512694 GCCGAGGCCCAGAAAAATG 59.487 57.895 0.00 0.00 34.56 2.32
65 66 4.018409 GCCGAGGCCCAGAAAAAT 57.982 55.556 0.00 0.00 34.56 1.82
76 77 4.394712 ACCGCAGAAAGGCCGAGG 62.395 66.667 0.00 0.00 0.00 4.63
77 78 2.815647 GACCGCAGAAAGGCCGAG 60.816 66.667 0.00 0.00 0.00 4.63
78 79 4.388499 GGACCGCAGAAAGGCCGA 62.388 66.667 0.00 0.00 0.00 5.54
79 80 3.976701 ATGGACCGCAGAAAGGCCG 62.977 63.158 0.00 0.00 0.00 6.13
80 81 1.250840 AAATGGACCGCAGAAAGGCC 61.251 55.000 0.00 0.00 0.00 5.19
81 82 1.459450 TAAATGGACCGCAGAAAGGC 58.541 50.000 0.00 0.00 0.00 4.35
82 83 4.082245 ACAATTAAATGGACCGCAGAAAGG 60.082 41.667 0.00 0.00 0.00 3.11
83 84 5.059404 ACAATTAAATGGACCGCAGAAAG 57.941 39.130 0.00 0.00 0.00 2.62
84 85 5.461032 AACAATTAAATGGACCGCAGAAA 57.539 34.783 0.00 0.00 0.00 2.52
85 86 5.461032 AAACAATTAAATGGACCGCAGAA 57.539 34.783 0.00 0.00 0.00 3.02
86 87 6.576662 TTAAACAATTAAATGGACCGCAGA 57.423 33.333 0.00 0.00 0.00 4.26
87 88 7.826260 ATTTAAACAATTAAATGGACCGCAG 57.174 32.000 5.92 0.00 45.51 5.18
88 89 8.608844 AAATTTAAACAATTAAATGGACCGCA 57.391 26.923 7.18 0.00 46.17 5.69
89 90 9.885934 AAAAATTTAAACAATTAAATGGACCGC 57.114 25.926 7.18 0.00 46.17 5.68
158 159 3.999821 GGCTAGAAGAGGCCTTAGC 57.000 57.895 21.34 21.34 45.09 3.09
165 166 7.000472 TGAAAATATTGATGGGCTAGAAGAGG 59.000 38.462 0.00 0.00 0.00 3.69
166 167 7.308469 GCTGAAAATATTGATGGGCTAGAAGAG 60.308 40.741 0.00 0.00 0.00 2.85
167 168 6.488006 GCTGAAAATATTGATGGGCTAGAAGA 59.512 38.462 0.00 0.00 0.00 2.87
168 169 6.294397 GGCTGAAAATATTGATGGGCTAGAAG 60.294 42.308 0.00 0.00 0.00 2.85
169 170 5.536161 GGCTGAAAATATTGATGGGCTAGAA 59.464 40.000 0.00 0.00 0.00 2.10
170 171 5.072741 GGCTGAAAATATTGATGGGCTAGA 58.927 41.667 0.00 0.00 0.00 2.43
171 172 4.219288 GGGCTGAAAATATTGATGGGCTAG 59.781 45.833 0.00 0.00 0.00 3.42
172 173 4.151883 GGGCTGAAAATATTGATGGGCTA 58.848 43.478 0.00 0.00 0.00 3.93
173 174 2.967887 GGGCTGAAAATATTGATGGGCT 59.032 45.455 0.00 0.00 0.00 5.19
174 175 2.699846 TGGGCTGAAAATATTGATGGGC 59.300 45.455 0.00 0.00 0.00 5.36
175 176 3.962718 AGTGGGCTGAAAATATTGATGGG 59.037 43.478 0.00 0.00 0.00 4.00
176 177 6.713762 TTAGTGGGCTGAAAATATTGATGG 57.286 37.500 0.00 0.00 0.00 3.51
177 178 8.415553 TGAATTAGTGGGCTGAAAATATTGATG 58.584 33.333 0.00 0.00 0.00 3.07
178 179 8.537728 TGAATTAGTGGGCTGAAAATATTGAT 57.462 30.769 0.00 0.00 0.00 2.57
179 180 7.953005 TGAATTAGTGGGCTGAAAATATTGA 57.047 32.000 0.00 0.00 0.00 2.57
180 181 9.090692 CTTTGAATTAGTGGGCTGAAAATATTG 57.909 33.333 0.00 0.00 0.00 1.90
181 182 8.260114 CCTTTGAATTAGTGGGCTGAAAATATT 58.740 33.333 0.00 0.00 0.00 1.28
182 183 7.619302 TCCTTTGAATTAGTGGGCTGAAAATAT 59.381 33.333 0.00 0.00 0.00 1.28
183 184 6.951198 TCCTTTGAATTAGTGGGCTGAAAATA 59.049 34.615 0.00 0.00 0.00 1.40
184 185 5.779771 TCCTTTGAATTAGTGGGCTGAAAAT 59.220 36.000 0.00 0.00 0.00 1.82
185 186 5.010617 GTCCTTTGAATTAGTGGGCTGAAAA 59.989 40.000 0.00 0.00 0.00 2.29
186 187 4.522789 GTCCTTTGAATTAGTGGGCTGAAA 59.477 41.667 0.00 0.00 0.00 2.69
187 188 4.079253 GTCCTTTGAATTAGTGGGCTGAA 58.921 43.478 0.00 0.00 0.00 3.02
188 189 3.330701 AGTCCTTTGAATTAGTGGGCTGA 59.669 43.478 0.00 0.00 30.84 4.26
189 190 3.441572 CAGTCCTTTGAATTAGTGGGCTG 59.558 47.826 0.00 0.00 42.84 4.85
190 191 3.562176 CCAGTCCTTTGAATTAGTGGGCT 60.562 47.826 0.00 0.00 32.35 5.19
191 192 2.755103 CCAGTCCTTTGAATTAGTGGGC 59.245 50.000 0.00 0.00 0.00 5.36
192 193 4.010349 GTCCAGTCCTTTGAATTAGTGGG 58.990 47.826 0.00 0.00 0.00 4.61
193 194 4.651778 TGTCCAGTCCTTTGAATTAGTGG 58.348 43.478 0.00 0.00 0.00 4.00
194 195 5.530915 TGTTGTCCAGTCCTTTGAATTAGTG 59.469 40.000 0.00 0.00 0.00 2.74
195 196 5.690865 TGTTGTCCAGTCCTTTGAATTAGT 58.309 37.500 0.00 0.00 0.00 2.24
196 197 5.997746 TCTGTTGTCCAGTCCTTTGAATTAG 59.002 40.000 0.00 0.00 42.19 1.73
197 198 5.935945 TCTGTTGTCCAGTCCTTTGAATTA 58.064 37.500 0.00 0.00 42.19 1.40
198 199 4.792068 TCTGTTGTCCAGTCCTTTGAATT 58.208 39.130 0.00 0.00 42.19 2.17
199 200 4.103153 TCTCTGTTGTCCAGTCCTTTGAAT 59.897 41.667 0.00 0.00 42.19 2.57
200 201 3.454447 TCTCTGTTGTCCAGTCCTTTGAA 59.546 43.478 0.00 0.00 42.19 2.69
201 202 3.038280 TCTCTGTTGTCCAGTCCTTTGA 58.962 45.455 0.00 0.00 42.19 2.69
202 203 3.475566 TCTCTGTTGTCCAGTCCTTTG 57.524 47.619 0.00 0.00 42.19 2.77
203 204 4.200092 GTTTCTCTGTTGTCCAGTCCTTT 58.800 43.478 0.00 0.00 42.19 3.11
204 205 3.199946 TGTTTCTCTGTTGTCCAGTCCTT 59.800 43.478 0.00 0.00 42.19 3.36
205 206 2.771943 TGTTTCTCTGTTGTCCAGTCCT 59.228 45.455 0.00 0.00 42.19 3.85
206 207 3.194005 TGTTTCTCTGTTGTCCAGTCC 57.806 47.619 0.00 0.00 42.19 3.85
207 208 5.296780 TGAATTGTTTCTCTGTTGTCCAGTC 59.703 40.000 0.00 0.00 42.19 3.51
208 209 5.192927 TGAATTGTTTCTCTGTTGTCCAGT 58.807 37.500 0.00 0.00 42.19 4.00
209 210 5.756195 TGAATTGTTTCTCTGTTGTCCAG 57.244 39.130 0.00 0.00 42.97 3.86
210 211 6.713762 ATTGAATTGTTTCTCTGTTGTCCA 57.286 33.333 0.00 0.00 32.78 4.02
211 212 9.696917 ATAAATTGAATTGTTTCTCTGTTGTCC 57.303 29.630 0.00 0.00 32.78 4.02
233 234 9.549078 TGTCGCAGGTGTATATTTGATTATAAA 57.451 29.630 0.00 0.00 0.00 1.40
234 235 9.549078 TTGTCGCAGGTGTATATTTGATTATAA 57.451 29.630 0.00 0.00 0.00 0.98
235 236 9.719355 ATTGTCGCAGGTGTATATTTGATTATA 57.281 29.630 0.00 0.00 0.00 0.98
236 237 8.621532 ATTGTCGCAGGTGTATATTTGATTAT 57.378 30.769 0.00 0.00 0.00 1.28
237 238 7.713073 TGATTGTCGCAGGTGTATATTTGATTA 59.287 33.333 0.00 0.00 0.00 1.75
246 247 3.407698 TGTTTGATTGTCGCAGGTGTAT 58.592 40.909 0.00 0.00 0.00 2.29
248 249 1.674359 TGTTTGATTGTCGCAGGTGT 58.326 45.000 0.00 0.00 0.00 4.16
249 250 2.995466 ATGTTTGATTGTCGCAGGTG 57.005 45.000 0.00 0.00 0.00 4.00
250 251 3.188460 GTGTATGTTTGATTGTCGCAGGT 59.812 43.478 0.00 0.00 0.00 4.00
251 252 3.426159 GGTGTATGTTTGATTGTCGCAGG 60.426 47.826 0.00 0.00 0.00 4.85
253 254 3.058570 GTGGTGTATGTTTGATTGTCGCA 60.059 43.478 0.00 0.00 0.00 5.10
254 255 3.488489 GTGGTGTATGTTTGATTGTCGC 58.512 45.455 0.00 0.00 0.00 5.19
255 256 3.185594 ACGTGGTGTATGTTTGATTGTCG 59.814 43.478 0.00 0.00 0.00 4.35
256 257 4.742438 ACGTGGTGTATGTTTGATTGTC 57.258 40.909 0.00 0.00 0.00 3.18
541 542 5.371526 TCCACTGATTTCTATGCCTCATTC 58.628 41.667 0.00 0.00 0.00 2.67
691 692 5.827666 ACGGTTAAATTCTGGTTCTTTGTG 58.172 37.500 0.00 0.00 0.00 3.33
813 814 6.086871 GGCTTCTGTGTGCTAATTAAACTTC 58.913 40.000 0.00 0.00 0.00 3.01
954 955 4.218852 GGGAGGTCTCTAGTTAATGATCGG 59.781 50.000 0.00 0.00 0.00 4.18
1146 1148 2.282391 TTGCCTTGCAGATGCGGT 60.282 55.556 0.00 0.00 45.83 5.68
1426 1428 0.110486 GGGCAAGGACAAGGACAAGA 59.890 55.000 0.00 0.00 0.00 3.02
1569 1572 3.282831 ACTTGCAGGCGTTACATTTTC 57.717 42.857 0.00 0.00 0.00 2.29
1574 1577 2.559668 AGTACTACTTGCAGGCGTTACA 59.440 45.455 0.00 0.00 0.00 2.41
1884 2017 4.313282 CATGTACATATGGAGCACCTCAG 58.687 47.826 8.32 0.00 37.04 3.35
2072 2205 3.985279 TCACGTTATGACTTGTGTGTAGC 59.015 43.478 0.00 0.00 34.08 3.58
2170 2303 0.961019 TTTGTGCAAGAGCCCATGAC 59.039 50.000 0.00 0.00 41.13 3.06


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

AutoCloner maintained by Alex Coulton.