Multiple sequence alignment - TraesCS2B01G083200

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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 TraesCS2B01G083200 chr2B 100.000 2288 0 0 1 2288 46495733 46493446 0.000000e+00 4226
1 TraesCS2B01G083200 chr2B 92.574 1414 103 2 311 1724 479889675 479888264 0.000000e+00 2028
2 TraesCS2B01G083200 chr2B 96.020 201 5 3 112 310 34805717 34805518 7.880000e-85 324
3 TraesCS2B01G083200 chr2B 86.614 254 33 1 1942 2195 46467599 46467347 1.730000e-71 279
4 TraesCS2B01G083200 chr5B 93.803 1420 79 4 311 1729 641300289 641298878 0.000000e+00 2126
5 TraesCS2B01G083200 chr5B 93.913 115 7 0 1 115 641300396 641300282 8.400000e-40 174
6 TraesCS2B01G083200 chr4B 93.455 1421 87 5 311 1728 551785023 551786440 0.000000e+00 2104
7 TraesCS2B01G083200 chr4B 92.822 1421 96 5 311 1728 551730415 551731832 0.000000e+00 2054
8 TraesCS2B01G083200 chr6B 93.507 1417 79 7 311 1722 189103869 189105277 0.000000e+00 2095
9 TraesCS2B01G083200 chr6B 92.585 1416 102 3 311 1725 452621264 452619851 0.000000e+00 2030
10 TraesCS2B01G083200 chr6D 93.286 1415 92 3 311 1724 450906267 450907679 0.000000e+00 2084
11 TraesCS2B01G083200 chr4D 93.329 1409 88 5 320 1724 102106595 102105189 0.000000e+00 2076
12 TraesCS2B01G083200 chr4D 93.043 115 8 0 1 115 473774028 473773914 3.910000e-38 169
13 TraesCS2B01G083200 chr7B 92.757 1422 93 8 305 1724 150842415 150843828 0.000000e+00 2047
14 TraesCS2B01G083200 chr2A 94.513 565 26 3 1724 2288 30754872 30754313 0.000000e+00 867
15 TraesCS2B01G083200 chr2A 90.863 197 16 2 115 310 575886959 575887154 1.740000e-66 263
16 TraesCS2B01G083200 chr2A 90.816 196 17 1 116 310 293898830 293898635 6.270000e-66 261
17 TraesCS2B01G083200 chr2D 92.060 403 26 3 1724 2125 28826061 28825664 1.530000e-156 562
18 TraesCS2B01G083200 chr2D 90.909 198 16 2 115 310 414964743 414964940 4.850000e-67 265
19 TraesCS2B01G083200 chr2D 90.863 197 17 1 115 310 207546743 207546547 1.740000e-66 263
20 TraesCS2B01G083200 chr2D 93.210 162 11 0 2121 2282 28789525 28789364 2.940000e-59 239
21 TraesCS2B01G083200 chr2D 93.913 115 7 0 1 115 591014180 591014294 8.400000e-40 174
22 TraesCS2B01G083200 chrUn 95.522 201 6 3 112 310 240836824 240836625 3.670000e-83 318
23 TraesCS2B01G083200 chr7D 91.878 197 14 2 115 310 537208963 537209158 8.050000e-70 274
24 TraesCS2B01G083200 chr7D 94.783 115 6 0 1 115 533933011 533933125 1.810000e-41 180
25 TraesCS2B01G083200 chr7A 91.371 197 16 1 115 310 71232387 71232583 3.750000e-68 268
26 TraesCS2B01G083200 chr5A 91.371 197 15 2 115 310 622452161 622452356 3.750000e-68 268
27 TraesCS2B01G083200 chr1B 91.803 122 10 0 1 122 602894009 602894130 1.090000e-38 171
28 TraesCS2B01G083200 chr4A 93.043 115 8 0 1 115 19185741 19185627 3.910000e-38 169
29 TraesCS2B01G083200 chr4A 93.043 115 8 0 1 115 60891792 60891906 3.910000e-38 169
30 TraesCS2B01G083200 chr3D 93.043 115 8 0 1 115 45633681 45633567 3.910000e-38 169
31 TraesCS2B01G083200 chr3D 93.043 115 8 0 1 115 124068481 124068367 3.910000e-38 169


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 TraesCS2B01G083200 chr2B 46493446 46495733 2287 True 4226 4226 100.000 1 2288 1 chr2B.!!$R3 2287
1 TraesCS2B01G083200 chr2B 479888264 479889675 1411 True 2028 2028 92.574 311 1724 1 chr2B.!!$R4 1413
2 TraesCS2B01G083200 chr5B 641298878 641300396 1518 True 1150 2126 93.858 1 1729 2 chr5B.!!$R1 1728
3 TraesCS2B01G083200 chr4B 551785023 551786440 1417 False 2104 2104 93.455 311 1728 1 chr4B.!!$F2 1417
4 TraesCS2B01G083200 chr4B 551730415 551731832 1417 False 2054 2054 92.822 311 1728 1 chr4B.!!$F1 1417
5 TraesCS2B01G083200 chr6B 189103869 189105277 1408 False 2095 2095 93.507 311 1722 1 chr6B.!!$F1 1411
6 TraesCS2B01G083200 chr6B 452619851 452621264 1413 True 2030 2030 92.585 311 1725 1 chr6B.!!$R1 1414
7 TraesCS2B01G083200 chr6D 450906267 450907679 1412 False 2084 2084 93.286 311 1724 1 chr6D.!!$F1 1413
8 TraesCS2B01G083200 chr4D 102105189 102106595 1406 True 2076 2076 93.329 320 1724 1 chr4D.!!$R1 1404
9 TraesCS2B01G083200 chr7B 150842415 150843828 1413 False 2047 2047 92.757 305 1724 1 chr7B.!!$F1 1419
10 TraesCS2B01G083200 chr2A 30754313 30754872 559 True 867 867 94.513 1724 2288 1 chr2A.!!$R1 564

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
87 88 0.03213 TTAGCGTCATCGGAGATGGC 59.968 55.0 9.77 7.3 45.12 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 1614 1.069427 GTTTGGTTGCCTGCATGCA 59.931 52.632 21.29 21.29 40.07 3.96 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
54 55 3.507411 AGTAGCTCTTGTACTTGGACCA 58.493 45.455 0.00 0.00 0.00 4.02
63 64 3.042682 TGTACTTGGACCACTTCTTCCA 58.957 45.455 0.00 0.00 40.30 3.53
66 67 2.104963 ACTTGGACCACTTCTTCCACTC 59.895 50.000 0.00 0.00 41.79 3.51
84 85 2.952978 ACTCTTTAGCGTCATCGGAGAT 59.047 45.455 0.00 0.00 45.12 2.75
87 88 0.032130 TTAGCGTCATCGGAGATGGC 59.968 55.000 9.77 7.30 45.12 4.40
107 108 1.660167 CTGATTCATGGCTCAGCGAA 58.340 50.000 11.03 0.00 33.12 4.70
108 109 2.219458 CTGATTCATGGCTCAGCGAAT 58.781 47.619 11.03 0.00 33.12 3.34
109 110 1.944709 TGATTCATGGCTCAGCGAATG 59.055 47.619 3.26 4.08 0.00 2.67
110 111 2.216046 GATTCATGGCTCAGCGAATGA 58.784 47.619 9.11 9.11 32.94 2.57
111 112 2.336945 TTCATGGCTCAGCGAATGAT 57.663 45.000 12.99 0.00 37.28 2.45
112 113 1.589803 TCATGGCTCAGCGAATGATG 58.410 50.000 9.11 0.00 37.28 3.07
113 114 1.134310 TCATGGCTCAGCGAATGATGT 60.134 47.619 9.11 0.00 37.28 3.06
114 115 1.263484 CATGGCTCAGCGAATGATGTC 59.737 52.381 5.22 0.00 37.28 3.06
115 116 0.462581 TGGCTCAGCGAATGATGTCC 60.463 55.000 0.00 0.00 37.28 4.02
116 117 0.462581 GGCTCAGCGAATGATGTCCA 60.463 55.000 0.00 0.00 37.28 4.02
117 118 0.935898 GCTCAGCGAATGATGTCCAG 59.064 55.000 0.00 0.00 37.28 3.86
118 119 1.741732 GCTCAGCGAATGATGTCCAGT 60.742 52.381 0.00 0.00 37.28 4.00
119 120 1.931841 CTCAGCGAATGATGTCCAGTG 59.068 52.381 0.00 0.00 37.28 3.66
120 121 1.012086 CAGCGAATGATGTCCAGTGG 58.988 55.000 1.40 1.40 0.00 4.00
121 122 0.745845 AGCGAATGATGTCCAGTGGC 60.746 55.000 3.51 0.00 43.37 5.01
122 123 2.009108 CGAATGATGTCCAGTGGCG 58.991 57.895 3.51 0.00 0.00 5.69
123 124 1.431488 CGAATGATGTCCAGTGGCGG 61.431 60.000 3.51 0.00 0.00 6.13
124 125 0.107703 GAATGATGTCCAGTGGCGGA 60.108 55.000 3.51 0.00 0.00 5.54
125 126 0.107508 AATGATGTCCAGTGGCGGAG 60.108 55.000 3.51 0.00 35.10 4.63
146 147 6.992715 CGGAGCCAGAAAATATATATTAGGGG 59.007 42.308 8.39 9.01 0.00 4.79
147 148 7.290813 GGAGCCAGAAAATATATATTAGGGGG 58.709 42.308 8.39 9.32 0.00 5.40
165 166 3.614092 GGGGGCCAAGTACTACTAAAAC 58.386 50.000 4.39 0.00 0.00 2.43
166 167 3.009363 GGGGGCCAAGTACTACTAAAACA 59.991 47.826 4.39 0.00 0.00 2.83
167 168 4.259356 GGGGCCAAGTACTACTAAAACAG 58.741 47.826 4.39 0.00 0.00 3.16
168 169 4.259356 GGGCCAAGTACTACTAAAACAGG 58.741 47.826 4.39 0.00 0.00 4.00
169 170 4.263199 GGGCCAAGTACTACTAAAACAGGT 60.263 45.833 4.39 0.00 0.00 4.00
170 171 5.311265 GGCCAAGTACTACTAAAACAGGTT 58.689 41.667 0.00 0.00 0.00 3.50
171 172 5.180680 GGCCAAGTACTACTAAAACAGGTTG 59.819 44.000 0.00 0.00 0.00 3.77
172 173 5.993441 GCCAAGTACTACTAAAACAGGTTGA 59.007 40.000 0.00 0.00 0.00 3.18
173 174 6.147328 GCCAAGTACTACTAAAACAGGTTGAG 59.853 42.308 0.00 0.00 0.00 3.02
174 175 6.649557 CCAAGTACTACTAAAACAGGTTGAGG 59.350 42.308 0.00 0.00 0.00 3.86
175 176 6.990908 AGTACTACTAAAACAGGTTGAGGT 57.009 37.500 0.00 0.00 0.00 3.85
176 177 6.756221 AGTACTACTAAAACAGGTTGAGGTG 58.244 40.000 0.00 0.00 0.00 4.00
177 178 4.969484 ACTACTAAAACAGGTTGAGGTGG 58.031 43.478 0.00 0.00 0.00 4.61
178 179 3.945640 ACTAAAACAGGTTGAGGTGGT 57.054 42.857 0.00 0.00 0.00 4.16
179 180 3.816994 ACTAAAACAGGTTGAGGTGGTC 58.183 45.455 0.00 0.00 0.00 4.02
180 181 2.067365 AAAACAGGTTGAGGTGGTCC 57.933 50.000 0.00 0.00 0.00 4.46
181 182 0.923358 AAACAGGTTGAGGTGGTCCA 59.077 50.000 0.00 0.00 35.89 4.02
182 183 0.923358 AACAGGTTGAGGTGGTCCAA 59.077 50.000 0.00 0.00 35.89 3.53
183 184 0.923358 ACAGGTTGAGGTGGTCCAAA 59.077 50.000 0.00 0.00 35.89 3.28
184 185 1.133792 ACAGGTTGAGGTGGTCCAAAG 60.134 52.381 0.00 0.00 35.89 2.77
185 186 1.133792 CAGGTTGAGGTGGTCCAAAGT 60.134 52.381 0.00 0.00 35.89 2.66
186 187 1.133792 AGGTTGAGGTGGTCCAAAGTG 60.134 52.381 0.00 0.00 35.89 3.16
187 188 1.409661 GGTTGAGGTGGTCCAAAGTGT 60.410 52.381 0.00 0.00 35.89 3.55
188 189 2.375146 GTTGAGGTGGTCCAAAGTGTT 58.625 47.619 0.00 0.00 35.89 3.32
189 190 2.051334 TGAGGTGGTCCAAAGTGTTG 57.949 50.000 0.00 0.00 35.89 3.33
190 191 1.562008 TGAGGTGGTCCAAAGTGTTGA 59.438 47.619 0.00 0.00 36.83 3.18
191 192 2.025793 TGAGGTGGTCCAAAGTGTTGAA 60.026 45.455 0.00 0.00 36.83 2.69
192 193 3.020984 GAGGTGGTCCAAAGTGTTGAAA 58.979 45.455 0.00 0.00 36.83 2.69
193 194 3.436243 AGGTGGTCCAAAGTGTTGAAAA 58.564 40.909 0.00 0.00 36.83 2.29
194 195 4.030216 AGGTGGTCCAAAGTGTTGAAAAT 58.970 39.130 0.00 0.00 36.83 1.82
195 196 4.469586 AGGTGGTCCAAAGTGTTGAAAATT 59.530 37.500 0.00 0.00 36.83 1.82
196 197 5.659079 AGGTGGTCCAAAGTGTTGAAAATTA 59.341 36.000 0.00 0.00 36.83 1.40
197 198 5.983118 GGTGGTCCAAAGTGTTGAAAATTAG 59.017 40.000 0.00 0.00 36.83 1.73
198 199 6.406512 GGTGGTCCAAAGTGTTGAAAATTAGT 60.407 38.462 0.00 0.00 36.83 2.24
199 200 7.039270 GTGGTCCAAAGTGTTGAAAATTAGTT 58.961 34.615 0.00 0.00 36.83 2.24
200 201 7.547722 GTGGTCCAAAGTGTTGAAAATTAGTTT 59.452 33.333 0.00 0.00 36.83 2.66
201 202 8.097662 TGGTCCAAAGTGTTGAAAATTAGTTTT 58.902 29.630 0.00 0.00 40.13 2.43
202 203 8.941977 GGTCCAAAGTGTTGAAAATTAGTTTTT 58.058 29.630 0.00 0.00 40.25 1.94
237 238 8.630054 ATTAGTACTAATTTTGCCACTGTTCA 57.370 30.769 20.27 0.00 32.21 3.18
238 239 8.630054 TTAGTACTAATTTTGCCACTGTTCAT 57.370 30.769 11.38 0.00 0.00 2.57
239 240 9.727859 TTAGTACTAATTTTGCCACTGTTCATA 57.272 29.630 11.38 0.00 0.00 2.15
240 241 8.268850 AGTACTAATTTTGCCACTGTTCATAG 57.731 34.615 0.00 0.00 0.00 2.23
241 242 5.954335 ACTAATTTTGCCACTGTTCATAGC 58.046 37.500 0.00 0.00 0.00 2.97
242 243 4.870123 AATTTTGCCACTGTTCATAGCA 57.130 36.364 0.00 0.00 0.00 3.49
243 244 4.870123 ATTTTGCCACTGTTCATAGCAA 57.130 36.364 0.00 0.00 41.39 3.91
245 246 4.870123 TTTGCCACTGTTCATAGCAAAT 57.130 36.364 4.48 0.00 45.59 2.32
246 247 4.870123 TTGCCACTGTTCATAGCAAATT 57.130 36.364 0.00 0.00 40.26 1.82
247 248 5.973899 TTGCCACTGTTCATAGCAAATTA 57.026 34.783 0.00 0.00 40.26 1.40
248 249 5.309323 TGCCACTGTTCATAGCAAATTAC 57.691 39.130 0.00 0.00 0.00 1.89
249 250 4.764308 TGCCACTGTTCATAGCAAATTACA 59.236 37.500 0.00 0.00 0.00 2.41
250 251 5.418524 TGCCACTGTTCATAGCAAATTACAT 59.581 36.000 0.00 0.00 0.00 2.29
251 252 5.745294 GCCACTGTTCATAGCAAATTACATG 59.255 40.000 0.00 0.00 0.00 3.21
252 253 6.625740 GCCACTGTTCATAGCAAATTACATGT 60.626 38.462 2.69 2.69 0.00 3.21
253 254 7.415095 GCCACTGTTCATAGCAAATTACATGTA 60.415 37.037 0.08 0.08 0.00 2.29
254 255 8.124823 CCACTGTTCATAGCAAATTACATGTAG 58.875 37.037 5.56 0.00 0.00 2.74
255 256 8.882736 CACTGTTCATAGCAAATTACATGTAGA 58.117 33.333 5.56 0.00 0.00 2.59
256 257 9.448438 ACTGTTCATAGCAAATTACATGTAGAA 57.552 29.630 5.56 0.41 0.00 2.10
259 260 9.884465 GTTCATAGCAAATTACATGTAGAATCC 57.116 33.333 5.56 0.00 0.00 3.01
260 261 9.851686 TTCATAGCAAATTACATGTAGAATCCT 57.148 29.630 5.56 4.52 0.00 3.24
261 262 9.276590 TCATAGCAAATTACATGTAGAATCCTG 57.723 33.333 5.56 3.08 0.00 3.86
262 263 6.949352 AGCAAATTACATGTAGAATCCTGG 57.051 37.500 5.56 0.00 0.00 4.45
263 264 6.426587 AGCAAATTACATGTAGAATCCTGGT 58.573 36.000 5.56 4.46 0.00 4.00
264 265 6.319658 AGCAAATTACATGTAGAATCCTGGTG 59.680 38.462 5.56 0.00 0.00 4.17
265 266 6.095440 GCAAATTACATGTAGAATCCTGGTGT 59.905 38.462 5.56 0.00 0.00 4.16
266 267 7.362920 GCAAATTACATGTAGAATCCTGGTGTT 60.363 37.037 5.56 0.00 0.00 3.32
267 268 9.173021 CAAATTACATGTAGAATCCTGGTGTTA 57.827 33.333 5.56 0.00 0.00 2.41
268 269 8.964476 AATTACATGTAGAATCCTGGTGTTAG 57.036 34.615 5.56 0.00 0.00 2.34
269 270 5.359194 ACATGTAGAATCCTGGTGTTAGG 57.641 43.478 0.00 0.00 39.29 2.69
270 271 4.164221 ACATGTAGAATCCTGGTGTTAGGG 59.836 45.833 0.00 0.00 38.42 3.53
271 272 3.112263 TGTAGAATCCTGGTGTTAGGGG 58.888 50.000 0.00 0.00 38.42 4.79
272 273 1.596496 AGAATCCTGGTGTTAGGGGG 58.404 55.000 0.00 0.00 38.42 5.40
314 315 2.202987 GCCTCCGCCACTGATGAG 60.203 66.667 0.00 0.00 0.00 2.90
387 388 0.036577 GTGCAGTGGCTCTCATGAGT 60.037 55.000 21.92 0.00 42.13 3.41
389 390 1.479730 TGCAGTGGCTCTCATGAGTAG 59.520 52.381 21.92 17.52 42.13 2.57
426 427 1.530283 CATCTCAGCCATGGAGCCA 59.470 57.895 18.40 0.00 32.38 4.75
467 469 0.586802 GTGTTCTCGAACTTGGTGCC 59.413 55.000 10.75 0.00 41.67 5.01
678 682 2.550606 TGACAGTCATGCCGTTTTAACC 59.449 45.455 0.00 0.00 0.00 2.85
685 689 0.039978 TGCCGTTTTAACCACATGCG 60.040 50.000 0.00 0.00 0.00 4.73
875 880 1.006102 CGAAGACGCCTGAGGTTGT 60.006 57.895 0.00 0.00 0.00 3.32
999 1007 1.372087 CGAAGCTTGAGTGCATCCCC 61.372 60.000 2.10 0.00 34.99 4.81
1017 1025 0.744414 CCATGCCCCTGTACTTCACG 60.744 60.000 0.00 0.00 0.00 4.35
1203 1212 1.913762 CCTCACTCCCGACACCCTT 60.914 63.158 0.00 0.00 0.00 3.95
1368 1378 7.744087 ATGCTTTGAACTGTTATGAAGTGTA 57.256 32.000 0.00 0.00 0.00 2.90
1506 1516 1.871039 CAAAGAGGTTACCACACACCG 59.129 52.381 3.51 0.00 38.21 4.94
1588 1598 0.185901 ACCAGGCAGTGTGGTTCAAT 59.814 50.000 0.00 0.00 46.73 2.57
1604 1614 1.005097 TCAATCCATGCAGGCAAGAGT 59.995 47.619 0.00 0.00 37.29 3.24
1678 1688 5.480422 TGTATAGTCAGGCTGAGTTGAGAAA 59.520 40.000 28.44 11.14 31.49 2.52
1684 1694 4.711846 TCAGGCTGAGTTGAGAAAGCTATA 59.288 41.667 14.43 0.00 35.93 1.31
1732 1742 0.041312 CAAACACGCCCTCAAAGACG 60.041 55.000 0.00 0.00 0.00 4.18
1733 1743 0.179067 AAACACGCCCTCAAAGACGA 60.179 50.000 0.00 0.00 0.00 4.20
1787 1797 8.654997 AGTAATCACTATACCTACGACTAGGAA 58.345 37.037 6.12 0.00 36.34 3.36
1867 1877 7.770897 ACATTTAGTCGGCAAATCTCTTATTCT 59.229 33.333 0.00 0.00 0.00 2.40
1978 1988 6.987992 TGTAATTATTATCGGAAGGTTTCGCT 59.012 34.615 0.00 0.00 0.00 4.93
2066 2076 1.586154 GGGATGTTCCGTGGCAGTTG 61.586 60.000 0.00 0.00 37.43 3.16
2120 2130 9.457436 TTTTCTCCCATTTGTTAGTTATAGACC 57.543 33.333 0.00 0.00 0.00 3.85
2145 2155 8.369424 CCTCTCATCTTGTTTCATCTCATATCT 58.631 37.037 0.00 0.00 0.00 1.98
2166 2176 1.486310 TGGAGCACTCTTGTCACTTGT 59.514 47.619 0.00 0.00 0.00 3.16
2173 2183 6.940739 AGCACTCTTGTCACTTGTATTATCT 58.059 36.000 0.00 0.00 0.00 1.98
2198 2208 4.100189 TGTTTCCCCCAATAGTTGTTGTTG 59.900 41.667 0.00 0.00 0.00 3.33
2236 2246 4.006780 TCTGCTGCAGTTTGTAGATTGA 57.993 40.909 27.24 2.70 31.36 2.57
2247 2257 2.959516 TGTAGATTGACAACCTGCTCG 58.040 47.619 0.00 0.00 0.00 5.03
2271 2281 0.178767 CTGCAGATTGATCCCCGTCA 59.821 55.000 8.42 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.041437 ACTAGGCTCCTAATGACCGC 58.959 55.000 0.00 0.00 0.00 5.68
54 55 3.321111 TGACGCTAAAGAGTGGAAGAAGT 59.679 43.478 0.00 0.00 37.52 3.01
63 64 2.366533 TCTCCGATGACGCTAAAGAGT 58.633 47.619 0.00 0.00 38.29 3.24
66 67 2.398498 CCATCTCCGATGACGCTAAAG 58.602 52.381 5.46 0.00 38.29 1.85
87 88 0.179065 TCGCTGAGCCATGAATCAGG 60.179 55.000 21.47 14.49 42.62 3.86
100 101 1.405933 CCACTGGACATCATTCGCTGA 60.406 52.381 0.00 0.00 38.53 4.26
107 108 1.524002 CTCCGCCACTGGACATCAT 59.476 57.895 0.00 0.00 33.48 2.45
108 109 2.981302 CTCCGCCACTGGACATCA 59.019 61.111 0.00 0.00 33.48 3.07
109 110 2.512515 GCTCCGCCACTGGACATC 60.513 66.667 0.00 0.00 33.48 3.06
120 121 6.483640 CCCTAATATATATTTTCTGGCTCCGC 59.516 42.308 13.09 0.00 0.00 5.54
121 122 6.992715 CCCCTAATATATATTTTCTGGCTCCG 59.007 42.308 13.09 0.67 0.00 4.63
122 123 7.290813 CCCCCTAATATATATTTTCTGGCTCC 58.709 42.308 13.09 0.00 0.00 4.70
144 145 3.009363 TGTTTTAGTAGTACTTGGCCCCC 59.991 47.826 8.40 0.00 0.00 5.40
145 146 4.259356 CTGTTTTAGTAGTACTTGGCCCC 58.741 47.826 8.40 0.00 0.00 5.80
146 147 4.259356 CCTGTTTTAGTAGTACTTGGCCC 58.741 47.826 8.40 0.00 0.00 5.80
147 148 4.903054 ACCTGTTTTAGTAGTACTTGGCC 58.097 43.478 8.40 0.00 0.00 5.36
148 149 5.993441 TCAACCTGTTTTAGTAGTACTTGGC 59.007 40.000 8.40 0.00 0.00 4.52
149 150 6.649557 CCTCAACCTGTTTTAGTAGTACTTGG 59.350 42.308 8.40 4.73 0.00 3.61
150 151 7.170998 CACCTCAACCTGTTTTAGTAGTACTTG 59.829 40.741 8.40 0.00 0.00 3.16
151 152 7.215085 CACCTCAACCTGTTTTAGTAGTACTT 58.785 38.462 8.40 0.00 0.00 2.24
152 153 6.239515 CCACCTCAACCTGTTTTAGTAGTACT 60.240 42.308 8.14 8.14 0.00 2.73
153 154 5.930569 CCACCTCAACCTGTTTTAGTAGTAC 59.069 44.000 0.00 0.00 0.00 2.73
154 155 5.603813 ACCACCTCAACCTGTTTTAGTAGTA 59.396 40.000 0.00 0.00 0.00 1.82
155 156 4.411212 ACCACCTCAACCTGTTTTAGTAGT 59.589 41.667 0.00 0.00 0.00 2.73
156 157 4.969484 ACCACCTCAACCTGTTTTAGTAG 58.031 43.478 0.00 0.00 0.00 2.57
157 158 4.202388 GGACCACCTCAACCTGTTTTAGTA 60.202 45.833 0.00 0.00 0.00 1.82
158 159 3.434596 GGACCACCTCAACCTGTTTTAGT 60.435 47.826 0.00 0.00 0.00 2.24
159 160 3.146847 GGACCACCTCAACCTGTTTTAG 58.853 50.000 0.00 0.00 0.00 1.85
160 161 2.510382 TGGACCACCTCAACCTGTTTTA 59.490 45.455 0.00 0.00 37.04 1.52
161 162 1.286553 TGGACCACCTCAACCTGTTTT 59.713 47.619 0.00 0.00 37.04 2.43
162 163 0.923358 TGGACCACCTCAACCTGTTT 59.077 50.000 0.00 0.00 37.04 2.83
163 164 0.923358 TTGGACCACCTCAACCTGTT 59.077 50.000 0.00 0.00 37.04 3.16
164 165 0.923358 TTTGGACCACCTCAACCTGT 59.077 50.000 0.00 0.00 37.04 4.00
165 166 1.133792 ACTTTGGACCACCTCAACCTG 60.134 52.381 0.00 0.00 37.04 4.00
166 167 1.133792 CACTTTGGACCACCTCAACCT 60.134 52.381 0.00 0.00 37.04 3.50
167 168 1.318576 CACTTTGGACCACCTCAACC 58.681 55.000 0.00 0.00 37.04 3.77
168 169 2.052782 ACACTTTGGACCACCTCAAC 57.947 50.000 0.00 0.00 37.04 3.18
169 170 2.025793 TCAACACTTTGGACCACCTCAA 60.026 45.455 0.00 0.00 37.04 3.02
170 171 1.562008 TCAACACTTTGGACCACCTCA 59.438 47.619 0.00 0.00 37.04 3.86
171 172 2.341846 TCAACACTTTGGACCACCTC 57.658 50.000 0.00 0.00 37.04 3.85
172 173 2.818751 TTCAACACTTTGGACCACCT 57.181 45.000 0.00 0.00 37.04 4.00
173 174 3.878160 TTTTCAACACTTTGGACCACC 57.122 42.857 0.00 0.00 33.06 4.61
174 175 6.569780 ACTAATTTTCAACACTTTGGACCAC 58.430 36.000 0.00 0.00 33.06 4.16
175 176 6.783708 ACTAATTTTCAACACTTTGGACCA 57.216 33.333 0.00 0.00 33.06 4.02
176 177 8.487313 AAAACTAATTTTCAACACTTTGGACC 57.513 30.769 0.00 0.00 32.29 4.46
211 212 9.073475 TGAACAGTGGCAAAATTAGTACTAATT 57.927 29.630 27.78 27.78 44.89 1.40
212 213 8.630054 TGAACAGTGGCAAAATTAGTACTAAT 57.370 30.769 20.27 20.27 37.36 1.73
213 214 8.630054 ATGAACAGTGGCAAAATTAGTACTAA 57.370 30.769 17.41 17.41 0.00 2.24
214 215 9.378551 CTATGAACAGTGGCAAAATTAGTACTA 57.621 33.333 0.00 0.00 0.00 1.82
215 216 7.148239 GCTATGAACAGTGGCAAAATTAGTACT 60.148 37.037 0.00 0.00 0.00 2.73
216 217 6.967199 GCTATGAACAGTGGCAAAATTAGTAC 59.033 38.462 0.00 0.00 0.00 2.73
217 218 6.657117 TGCTATGAACAGTGGCAAAATTAGTA 59.343 34.615 0.00 0.00 0.00 1.82
218 219 5.476599 TGCTATGAACAGTGGCAAAATTAGT 59.523 36.000 0.00 0.00 0.00 2.24
219 220 5.953183 TGCTATGAACAGTGGCAAAATTAG 58.047 37.500 0.00 0.00 0.00 1.73
220 221 5.973899 TGCTATGAACAGTGGCAAAATTA 57.026 34.783 0.00 0.00 0.00 1.40
221 222 4.870123 TGCTATGAACAGTGGCAAAATT 57.130 36.364 0.00 0.00 0.00 1.82
222 223 4.870123 TTGCTATGAACAGTGGCAAAAT 57.130 36.364 0.00 0.00 39.45 1.82
223 224 4.662468 TTTGCTATGAACAGTGGCAAAA 57.338 36.364 11.11 0.00 45.60 2.44
225 226 4.870123 AATTTGCTATGAACAGTGGCAA 57.130 36.364 0.00 0.00 40.43 4.52
226 227 4.764308 TGTAATTTGCTATGAACAGTGGCA 59.236 37.500 0.00 0.00 0.00 4.92
227 228 5.309323 TGTAATTTGCTATGAACAGTGGC 57.691 39.130 0.00 0.00 0.00 5.01
228 229 6.855836 ACATGTAATTTGCTATGAACAGTGG 58.144 36.000 0.00 0.00 0.00 4.00
229 230 8.882736 TCTACATGTAATTTGCTATGAACAGTG 58.117 33.333 7.06 0.00 0.00 3.66
230 231 9.448438 TTCTACATGTAATTTGCTATGAACAGT 57.552 29.630 7.06 0.00 0.00 3.55
233 234 9.884465 GGATTCTACATGTAATTTGCTATGAAC 57.116 33.333 7.06 0.27 0.00 3.18
234 235 9.851686 AGGATTCTACATGTAATTTGCTATGAA 57.148 29.630 7.06 4.19 0.00 2.57
235 236 9.276590 CAGGATTCTACATGTAATTTGCTATGA 57.723 33.333 7.06 0.00 0.00 2.15
236 237 8.509690 CCAGGATTCTACATGTAATTTGCTATG 58.490 37.037 7.06 0.31 0.00 2.23
237 238 8.220559 ACCAGGATTCTACATGTAATTTGCTAT 58.779 33.333 7.06 0.00 0.00 2.97
238 239 7.498900 CACCAGGATTCTACATGTAATTTGCTA 59.501 37.037 7.06 0.00 0.00 3.49
239 240 6.319658 CACCAGGATTCTACATGTAATTTGCT 59.680 38.462 7.06 2.34 0.00 3.91
240 241 6.095440 ACACCAGGATTCTACATGTAATTTGC 59.905 38.462 7.06 0.04 0.00 3.68
241 242 7.630242 ACACCAGGATTCTACATGTAATTTG 57.370 36.000 7.06 4.03 0.00 2.32
242 243 9.396022 CTAACACCAGGATTCTACATGTAATTT 57.604 33.333 7.06 0.00 0.00 1.82
243 244 7.993183 CCTAACACCAGGATTCTACATGTAATT 59.007 37.037 7.06 0.00 38.00 1.40
244 245 7.420214 CCCTAACACCAGGATTCTACATGTAAT 60.420 40.741 7.06 0.00 38.00 1.89
245 246 6.126883 CCCTAACACCAGGATTCTACATGTAA 60.127 42.308 7.06 0.00 38.00 2.41
246 247 5.365605 CCCTAACACCAGGATTCTACATGTA 59.634 44.000 5.25 5.25 38.00 2.29
247 248 4.164221 CCCTAACACCAGGATTCTACATGT 59.836 45.833 2.69 2.69 38.00 3.21
248 249 4.444876 CCCCTAACACCAGGATTCTACATG 60.445 50.000 0.00 0.00 38.00 3.21
249 250 3.716872 CCCCTAACACCAGGATTCTACAT 59.283 47.826 0.00 0.00 38.00 2.29
250 251 3.112263 CCCCTAACACCAGGATTCTACA 58.888 50.000 0.00 0.00 38.00 2.74
251 252 2.438392 CCCCCTAACACCAGGATTCTAC 59.562 54.545 0.00 0.00 38.00 2.59
252 253 2.771688 CCCCCTAACACCAGGATTCTA 58.228 52.381 0.00 0.00 38.00 2.10
253 254 1.596496 CCCCCTAACACCAGGATTCT 58.404 55.000 0.00 0.00 38.00 2.40
298 299 2.503061 CCTCATCAGTGGCGGAGG 59.497 66.667 10.05 10.05 40.82 4.30
299 300 1.142748 GACCTCATCAGTGGCGGAG 59.857 63.158 0.00 0.00 31.50 4.63
300 301 1.191489 TTGACCTCATCAGTGGCGGA 61.191 55.000 0.00 0.00 38.99 5.54
301 302 1.021390 GTTGACCTCATCAGTGGCGG 61.021 60.000 0.00 0.00 38.99 6.13
302 303 0.036952 AGTTGACCTCATCAGTGGCG 60.037 55.000 0.00 0.00 38.99 5.69
303 304 1.446907 CAGTTGACCTCATCAGTGGC 58.553 55.000 0.00 0.00 38.99 5.01
304 305 1.446907 GCAGTTGACCTCATCAGTGG 58.553 55.000 0.00 0.00 38.99 4.00
305 306 1.271001 TGGCAGTTGACCTCATCAGTG 60.271 52.381 0.00 0.00 38.99 3.66
306 307 1.059098 TGGCAGTTGACCTCATCAGT 58.941 50.000 0.00 0.00 38.99 3.41
307 308 2.286872 GATGGCAGTTGACCTCATCAG 58.713 52.381 0.00 0.00 38.99 2.90
308 309 1.405933 CGATGGCAGTTGACCTCATCA 60.406 52.381 0.00 0.00 35.32 3.07
309 310 1.293924 CGATGGCAGTTGACCTCATC 58.706 55.000 0.00 0.00 0.00 2.92
314 315 4.166011 GCGCGATGGCAGTTGACC 62.166 66.667 12.10 0.00 39.92 4.02
426 427 0.468226 TGGAGGTGTGCTCGAACTTT 59.532 50.000 0.00 0.00 0.00 2.66
559 561 2.834549 TGTCAATCTTCCTCCTCTCCAC 59.165 50.000 0.00 0.00 0.00 4.02
685 689 9.387405 AACACAGAGTTCATGGCTTATTGAAGC 62.387 40.741 0.94 0.94 46.68 3.86
875 880 4.829518 CCATGCGCTCGTCGTCGA 62.830 66.667 9.73 4.42 44.12 4.20
918 925 3.055094 CCTCATGGTAGTGGCTGTAGTTT 60.055 47.826 0.00 0.00 0.00 2.66
950 957 4.563580 GGATGACCTTGCAGAAGTGAGTTA 60.564 45.833 0.00 0.00 0.00 2.24
999 1007 0.249120 TCGTGAAGTACAGGGGCATG 59.751 55.000 0.00 0.00 35.42 4.06
1050 1058 1.227853 GCCGGTGTTGTTCCTGAGT 60.228 57.895 1.90 0.00 0.00 3.41
1401 1411 7.124901 AGAGCAGAGTATAAACAGAGGATCAAA 59.875 37.037 0.00 0.00 37.82 2.69
1532 1542 2.242708 TGTTAGTGGACAAACCCAAGGT 59.757 45.455 0.00 0.00 38.06 3.50
1588 1598 1.676635 GCACTCTTGCCTGCATGGA 60.677 57.895 6.40 0.00 43.66 3.41
1604 1614 1.069427 GTTTGGTTGCCTGCATGCA 59.931 52.632 21.29 21.29 40.07 3.96
1732 1742 4.929211 GCCAATTTTACCACCTGAAACATC 59.071 41.667 0.00 0.00 0.00 3.06
1733 1743 4.262851 GGCCAATTTTACCACCTGAAACAT 60.263 41.667 0.00 0.00 0.00 2.71
1784 1794 3.699038 TGCTCTCTAGAGAAGCTTCTTCC 59.301 47.826 29.02 17.58 44.74 3.46
1787 1797 4.342092 GGATTGCTCTCTAGAGAAGCTTCT 59.658 45.833 28.83 28.83 44.74 2.85
1950 1960 9.807386 CGAAACCTTCCGATAATAATTACATTC 57.193 33.333 0.00 0.00 0.00 2.67
1954 1964 7.417496 AGCGAAACCTTCCGATAATAATTAC 57.583 36.000 0.00 0.00 0.00 1.89
1993 2003 9.601971 TTATGTGCAAATTAGTCGACTTAAAAC 57.398 29.630 25.44 13.21 0.00 2.43
2043 2053 2.700773 GCCACGGAACATCCCAAGC 61.701 63.158 0.00 0.00 31.13 4.01
2044 2054 1.303236 TGCCACGGAACATCCCAAG 60.303 57.895 0.00 0.00 31.13 3.61
2066 2076 3.582780 ACGTCGTCAAAGGGTTCTATTC 58.417 45.455 0.00 0.00 0.00 1.75
2119 2129 8.369424 AGATATGAGATGAAACAAGATGAGAGG 58.631 37.037 0.00 0.00 0.00 3.69
2120 2130 9.767228 AAGATATGAGATGAAACAAGATGAGAG 57.233 33.333 0.00 0.00 0.00 3.20
2145 2155 2.092968 ACAAGTGACAAGAGTGCTCCAA 60.093 45.455 0.00 0.00 0.00 3.53
2166 2176 9.196139 CAACTATTGGGGGAAACAAAGATAATA 57.804 33.333 0.00 0.00 0.00 0.98
2173 2183 4.717280 ACAACAACTATTGGGGGAAACAAA 59.283 37.500 0.00 0.00 33.63 2.83
2198 2208 3.823304 AGCAGAAGTGTGGAAGGAAATTC 59.177 43.478 0.00 0.00 37.17 2.17
2236 2246 1.956170 CAGTTCGCGAGCAGGTTGT 60.956 57.895 24.99 0.00 0.00 3.32
2247 2257 0.659957 GGGATCAATCTGCAGTTCGC 59.340 55.000 14.67 8.73 42.89 4.70


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

AutoCloner maintained by Alex Coulton.