Multiple sequence alignment - TraesCS3A01G191400

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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 TraesCS3A01G191400 chr3A 100.000 3177 0 0 1 3177 243869608 243872784 0.000000e+00 5867
1 TraesCS3A01G191400 chr3D 93.168 2898 130 19 331 3177 185067358 185070238 0.000000e+00 4193
2 TraesCS3A01G191400 chr3B 89.907 2913 136 38 331 3177 263787242 263790062 0.000000e+00 3605
3 TraesCS3A01G191400 chr5A 95.821 335 12 2 2 334 40802910 40802576 1.000000e-149 540
4 TraesCS3A01G191400 chr5A 96.061 330 9 4 7 334 622759982 622759655 4.660000e-148 534
5 TraesCS3A01G191400 chr7A 96.037 328 11 2 7 333 95817110 95817436 1.680000e-147 532
6 TraesCS3A01G191400 chr7A 95.468 331 11 3 7 333 528301775 528301445 2.810000e-145 525
7 TraesCS3A01G191400 chr7A 94.864 331 15 2 3 331 40928306 40928636 1.690000e-142 516
8 TraesCS3A01G191400 chr2A 95.441 329 14 1 7 334 709695856 709696184 1.010000e-144 523
9 TraesCS3A01G191400 chr1A 94.940 336 14 2 7 339 568121322 568121657 1.010000e-144 523
10 TraesCS3A01G191400 chr4A 94.880 332 15 2 5 334 609572126 609572457 4.700000e-143 518
11 TraesCS3A01G191400 chr6B 94.595 333 16 2 3 334 526200643 526200312 6.080000e-142 514


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 TraesCS3A01G191400 chr3A 243869608 243872784 3176 False 5867 5867 100.000 1 3177 1 chr3A.!!$F1 3176
1 TraesCS3A01G191400 chr3D 185067358 185070238 2880 False 4193 4193 93.168 331 3177 1 chr3D.!!$F1 2846
2 TraesCS3A01G191400 chr3B 263787242 263790062 2820 False 3605 3605 89.907 331 3177 1 chr3B.!!$F1 2846

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
192 193 0.023103 CGTGTTTGCGTTGTGTTTGC 59.977 50.000 0.00 0.00 0.0 3.68 F
203 204 0.382158 TGTGTTTGCGCCGAATTTGA 59.618 45.000 4.18 0.00 0.0 2.69 F
1222 1258 0.672401 GGTGATCCCTTGTCGCGAAA 60.672 55.000 12.06 0.54 0.0 3.46 F
1282 1318 1.059549 CGTAATTTTAGTCGCGGCGTT 59.940 47.619 22.90 14.13 0.0 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1253 1289 0.027063 CTAAAATTACGCACGCCCGG 59.973 55.000 0.00 0.00 0.00 5.73 R
1998 2052 0.103026 CATGTCCTCGATCGAAGCCA 59.897 55.000 19.92 9.81 0.00 4.75 R
2037 2091 0.686224 CCTCTGCTCCAGGATCATCC 59.314 60.000 0.00 0.00 36.58 3.51 R
2868 2951 1.064654 GGAACTTGATGCATCGGAAGC 59.935 52.381 21.34 10.55 0.00 3.86 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
40 41 4.712425 GCGGTGACTACACGCGGT 62.712 66.667 12.47 8.38 46.77 5.68
41 42 2.049802 CGGTGACTACACGCGGTT 60.050 61.111 12.47 0.00 46.77 4.44
42 43 2.084681 CGGTGACTACACGCGGTTC 61.085 63.158 12.47 1.85 46.77 3.62
43 44 1.288127 GGTGACTACACGCGGTTCT 59.712 57.895 12.47 0.00 46.77 3.01
44 45 0.523072 GGTGACTACACGCGGTTCTA 59.477 55.000 12.47 0.00 46.77 2.10
45 46 1.611043 GTGACTACACGCGGTTCTAC 58.389 55.000 12.47 0.00 37.28 2.59
46 47 1.069022 GTGACTACACGCGGTTCTACA 60.069 52.381 12.47 0.68 37.28 2.74
47 48 1.198408 TGACTACACGCGGTTCTACAG 59.802 52.381 12.47 2.13 0.00 2.74
48 49 0.109412 ACTACACGCGGTTCTACAGC 60.109 55.000 12.47 0.00 35.94 4.40
49 50 0.801067 CTACACGCGGTTCTACAGCC 60.801 60.000 12.47 0.00 35.89 4.85
50 51 2.216750 TACACGCGGTTCTACAGCCC 62.217 60.000 12.47 0.00 35.89 5.19
51 52 4.078516 ACGCGGTTCTACAGCCCC 62.079 66.667 12.47 0.00 35.89 5.80
52 53 4.832608 CGCGGTTCTACAGCCCCC 62.833 72.222 0.00 0.00 35.89 5.40
53 54 3.400054 GCGGTTCTACAGCCCCCT 61.400 66.667 0.00 0.00 33.12 4.79
54 55 2.901042 CGGTTCTACAGCCCCCTC 59.099 66.667 0.00 0.00 0.00 4.30
55 56 2.901042 GGTTCTACAGCCCCCTCG 59.099 66.667 0.00 0.00 0.00 4.63
56 57 2.732619 GGTTCTACAGCCCCCTCGG 61.733 68.421 0.00 0.00 0.00 4.63
65 66 3.642078 CCCCCTCGGCATGTAGAA 58.358 61.111 0.00 0.00 0.00 2.10
66 67 1.146263 CCCCCTCGGCATGTAGAAC 59.854 63.158 0.00 0.00 0.00 3.01
67 68 1.146263 CCCCTCGGCATGTAGAACC 59.854 63.158 0.00 0.00 0.00 3.62
69 70 1.883084 CCTCGGCATGTAGAACCGC 60.883 63.158 4.05 0.00 46.49 5.68
70 71 2.202690 TCGGCATGTAGAACCGCG 60.203 61.111 0.00 0.00 46.49 6.46
71 72 2.508439 CGGCATGTAGAACCGCGT 60.508 61.111 4.92 0.00 40.55 6.01
72 73 2.798501 CGGCATGTAGAACCGCGTG 61.799 63.158 4.92 0.00 40.55 5.34
73 74 2.461110 GGCATGTAGAACCGCGTGG 61.461 63.158 14.93 14.93 42.84 4.94
74 75 2.461110 GCATGTAGAACCGCGTGGG 61.461 63.158 21.14 6.53 40.75 4.61
75 76 2.125269 ATGTAGAACCGCGTGGGC 60.125 61.111 21.14 11.05 40.62 5.36
126 127 3.464494 GGGTAGCCCGCGGTAGTT 61.464 66.667 26.12 10.37 32.13 2.24
127 128 2.580815 GGTAGCCCGCGGTAGTTT 59.419 61.111 26.12 6.86 0.00 2.66
128 129 1.078918 GGTAGCCCGCGGTAGTTTT 60.079 57.895 26.12 4.98 0.00 2.43
129 130 0.674581 GGTAGCCCGCGGTAGTTTTT 60.675 55.000 26.12 3.49 0.00 1.94
171 172 6.669485 ATGTTTAAATTTGAACGAACTCGC 57.331 33.333 17.83 0.00 44.43 5.03
172 173 4.971220 TGTTTAAATTTGAACGAACTCGCC 59.029 37.500 17.83 0.00 44.43 5.54
173 174 2.699251 AAATTTGAACGAACTCGCCC 57.301 45.000 0.00 0.00 44.43 6.13
174 175 0.515564 AATTTGAACGAACTCGCCCG 59.484 50.000 0.00 0.00 44.43 6.13
175 176 0.601841 ATTTGAACGAACTCGCCCGT 60.602 50.000 0.00 0.00 44.43 5.28
176 177 1.492319 TTTGAACGAACTCGCCCGTG 61.492 55.000 0.00 0.00 44.43 4.94
177 178 2.355481 GAACGAACTCGCCCGTGT 60.355 61.111 0.00 0.00 44.43 4.49
178 179 1.952635 GAACGAACTCGCCCGTGTT 60.953 57.895 7.71 7.71 44.43 3.32
179 180 1.493134 GAACGAACTCGCCCGTGTTT 61.493 55.000 9.12 0.00 44.43 2.83
180 181 1.768112 AACGAACTCGCCCGTGTTTG 61.768 55.000 16.75 16.75 44.43 2.93
181 182 2.251371 GAACTCGCCCGTGTTTGC 59.749 61.111 9.12 0.00 32.85 3.68
186 187 4.244802 CGCCCGTGTTTGCGTTGT 62.245 61.111 0.00 0.00 45.43 3.32
187 188 2.653766 GCCCGTGTTTGCGTTGTG 60.654 61.111 0.00 0.00 0.00 3.33
188 189 2.795297 CCCGTGTTTGCGTTGTGT 59.205 55.556 0.00 0.00 0.00 3.72
189 190 1.137825 CCCGTGTTTGCGTTGTGTT 59.862 52.632 0.00 0.00 0.00 3.32
190 191 0.456995 CCCGTGTTTGCGTTGTGTTT 60.457 50.000 0.00 0.00 0.00 2.83
191 192 0.637738 CCGTGTTTGCGTTGTGTTTG 59.362 50.000 0.00 0.00 0.00 2.93
192 193 0.023103 CGTGTTTGCGTTGTGTTTGC 59.977 50.000 0.00 0.00 0.00 3.68
193 194 0.023103 GTGTTTGCGTTGTGTTTGCG 59.977 50.000 0.00 0.00 0.00 4.85
197 198 4.599434 GCGTTGTGTTTGCGCCGA 62.599 61.111 4.18 0.00 44.67 5.54
198 199 2.023461 CGTTGTGTTTGCGCCGAA 59.977 55.556 4.18 0.00 0.00 4.30
199 200 1.369930 CGTTGTGTTTGCGCCGAAT 60.370 52.632 4.18 0.00 0.00 3.34
200 201 0.932585 CGTTGTGTTTGCGCCGAATT 60.933 50.000 4.18 0.00 0.00 2.17
201 202 1.204792 GTTGTGTTTGCGCCGAATTT 58.795 45.000 4.18 0.00 0.00 1.82
202 203 1.071568 GTTGTGTTTGCGCCGAATTTG 60.072 47.619 4.18 0.00 0.00 2.32
203 204 0.382158 TGTGTTTGCGCCGAATTTGA 59.618 45.000 4.18 0.00 0.00 2.69
204 205 1.202302 TGTGTTTGCGCCGAATTTGAA 60.202 42.857 4.18 0.00 0.00 2.69
205 206 1.189227 GTGTTTGCGCCGAATTTGAAC 59.811 47.619 4.18 0.00 0.00 3.18
206 207 1.202302 TGTTTGCGCCGAATTTGAACA 60.202 42.857 4.18 0.49 0.00 3.18
207 208 2.058057 GTTTGCGCCGAATTTGAACAT 58.942 42.857 4.18 0.00 0.00 2.71
208 209 2.430546 TTGCGCCGAATTTGAACATT 57.569 40.000 4.18 0.00 0.00 2.71
209 210 2.430546 TGCGCCGAATTTGAACATTT 57.569 40.000 4.18 0.00 0.00 2.32
210 211 2.748605 TGCGCCGAATTTGAACATTTT 58.251 38.095 4.18 0.00 0.00 1.82
211 212 3.902150 TGCGCCGAATTTGAACATTTTA 58.098 36.364 4.18 0.00 0.00 1.52
212 213 4.299155 TGCGCCGAATTTGAACATTTTAA 58.701 34.783 4.18 0.00 0.00 1.52
213 214 4.745125 TGCGCCGAATTTGAACATTTTAAA 59.255 33.333 4.18 0.00 0.00 1.52
214 215 5.234329 TGCGCCGAATTTGAACATTTTAAAA 59.766 32.000 4.18 2.51 0.00 1.52
215 216 6.130058 GCGCCGAATTTGAACATTTTAAAAA 58.870 32.000 4.44 0.00 0.00 1.94
216 217 6.084421 GCGCCGAATTTGAACATTTTAAAAAC 59.916 34.615 4.44 0.00 0.00 2.43
217 218 6.571887 CGCCGAATTTGAACATTTTAAAAACC 59.428 34.615 4.44 0.00 0.00 3.27
218 219 6.853872 GCCGAATTTGAACATTTTAAAAACCC 59.146 34.615 4.44 0.00 0.00 4.11
219 220 7.066505 CCGAATTTGAACATTTTAAAAACCCG 58.933 34.615 4.44 0.00 0.00 5.28
220 221 7.254488 CCGAATTTGAACATTTTAAAAACCCGT 60.254 33.333 4.44 0.00 0.00 5.28
221 222 7.790216 CGAATTTGAACATTTTAAAAACCCGTC 59.210 33.333 4.44 0.06 0.00 4.79
222 223 6.570690 TTTGAACATTTTAAAAACCCGTCG 57.429 33.333 4.44 0.00 0.00 5.12
223 224 4.608951 TGAACATTTTAAAAACCCGTCGG 58.391 39.130 3.60 3.60 0.00 4.79
245 246 4.147449 CGCGACTGGGGAGCATCA 62.147 66.667 0.00 0.00 36.25 3.07
246 247 2.512515 GCGACTGGGGAGCATCAC 60.513 66.667 0.00 0.00 38.30 3.06
247 248 2.202797 CGACTGGGGAGCATCACG 60.203 66.667 0.00 0.00 41.82 4.35
248 249 2.982130 GACTGGGGAGCATCACGT 59.018 61.111 0.00 0.00 41.82 4.49
249 250 1.153549 GACTGGGGAGCATCACGTC 60.154 63.158 0.00 0.00 41.82 4.34
250 251 2.187946 CTGGGGAGCATCACGTCC 59.812 66.667 0.00 0.00 41.82 4.79
253 254 3.399181 GGGAGCATCACGTCCCCA 61.399 66.667 0.00 0.00 46.23 4.96
254 255 2.668632 GGAGCATCACGTCCCCAA 59.331 61.111 0.00 0.00 36.25 4.12
255 256 1.224592 GGAGCATCACGTCCCCAAT 59.775 57.895 0.00 0.00 36.25 3.16
256 257 1.097547 GGAGCATCACGTCCCCAATG 61.098 60.000 0.00 0.00 36.25 2.82
257 258 1.718757 GAGCATCACGTCCCCAATGC 61.719 60.000 7.80 7.80 43.75 3.56
258 259 3.101209 CATCACGTCCCCAATGCG 58.899 61.111 0.00 0.00 0.00 4.73
259 260 2.824041 ATCACGTCCCCAATGCGC 60.824 61.111 0.00 0.00 0.00 6.09
264 265 3.370231 GTCCCCAATGCGCGGTTT 61.370 61.111 8.83 0.00 0.00 3.27
265 266 2.041686 GTCCCCAATGCGCGGTTTA 61.042 57.895 8.83 0.00 0.00 2.01
266 267 1.747367 TCCCCAATGCGCGGTTTAG 60.747 57.895 8.83 0.00 0.00 1.85
267 268 2.102161 CCCAATGCGCGGTTTAGC 59.898 61.111 8.83 0.00 0.00 3.09
292 293 4.751820 CGTCCCCGGGGGCAATTT 62.752 66.667 42.08 0.00 43.94 1.82
293 294 2.284331 GTCCCCGGGGGCAATTTT 60.284 61.111 39.93 0.00 43.94 1.82
294 295 1.916273 GTCCCCGGGGGCAATTTTT 60.916 57.895 39.93 0.00 43.94 1.94
425 426 1.134670 GCAGCGAAGTATGGGAAGTCT 60.135 52.381 0.00 0.00 0.00 3.24
433 434 4.246712 AGTATGGGAAGTCTAGGAACGA 57.753 45.455 0.00 0.00 0.00 3.85
442 443 3.887352 AGTCTAGGAACGACTCATAGCA 58.113 45.455 0.00 0.00 38.15 3.49
469 470 1.152756 AGCAGGGGTGACACCAAAC 60.153 57.895 25.75 14.88 41.02 2.93
523 531 5.755409 ATGTCTGTGGTACCAATACTTGA 57.245 39.130 18.31 5.96 0.00 3.02
538 546 1.642762 ACTTGAATGGATGGAGGGCTT 59.357 47.619 0.00 0.00 0.00 4.35
548 556 3.008049 GGATGGAGGGCTTGTTATATCGT 59.992 47.826 0.00 0.00 0.00 3.73
561 569 4.340097 TGTTATATCGTCTCGTCCAACCAT 59.660 41.667 0.00 0.00 0.00 3.55
583 591 3.117926 TCAAATATGAAGGCTAGCTGGCA 60.118 43.478 24.41 10.29 44.55 4.92
618 626 3.180613 GTTAGAGTTGCTCTTAGCGGTC 58.819 50.000 3.87 0.00 46.26 4.79
625 633 1.343142 TGCTCTTAGCGGTCAGAAACA 59.657 47.619 0.00 0.00 46.26 2.83
641 649 6.583806 GTCAGAAACATTTTGGTATGCTCTTG 59.416 38.462 0.00 0.00 0.00 3.02
717 727 5.357032 CGAGAAACCCTAAAACAATAGCCAT 59.643 40.000 0.00 0.00 0.00 4.40
1091 1107 4.767255 CTCCAGCTCCACCGCCAC 62.767 72.222 0.00 0.00 0.00 5.01
1190 1212 1.135402 GTTCGTTGATGTTCCATGGCC 60.135 52.381 6.96 0.00 0.00 5.36
1222 1258 0.672401 GGTGATCCCTTGTCGCGAAA 60.672 55.000 12.06 0.54 0.00 3.46
1224 1260 2.546778 GTGATCCCTTGTCGCGAAATA 58.453 47.619 12.06 0.00 0.00 1.40
1225 1261 3.131396 GTGATCCCTTGTCGCGAAATAT 58.869 45.455 12.06 0.00 0.00 1.28
1229 1265 4.594123 TCCCTTGTCGCGAAATATGATA 57.406 40.909 12.06 0.00 0.00 2.15
1253 1289 3.802685 CGAAATCGGTGGAGGAATTAGTC 59.197 47.826 0.00 0.00 35.37 2.59
1282 1318 1.059549 CGTAATTTTAGTCGCGGCGTT 59.940 47.619 22.90 14.13 0.00 4.84
1285 1321 1.149987 ATTTTAGTCGCGGCGTTTCA 58.850 45.000 22.90 0.00 0.00 2.69
1311 1347 1.958205 CTCGATGGGAATGGCTCGC 60.958 63.158 0.00 0.00 37.51 5.03
1347 1389 2.175878 ACAATCTGTCTGCACCAGTC 57.824 50.000 8.16 0.00 32.61 3.51
1515 1562 4.326766 GCAGCTCGCGGTTTGCAA 62.327 61.111 19.54 0.00 46.97 4.08
1532 1579 1.721926 GCAAGTTGCTACAGACGAGTC 59.278 52.381 20.71 0.00 40.96 3.36
1560 1607 8.121305 TGAGTTTACATGCCATATGTTTTCTT 57.879 30.769 1.24 0.00 33.76 2.52
1563 1610 9.855021 AGTTTACATGCCATATGTTTTCTTTAC 57.145 29.630 1.24 0.00 33.76 2.01
1858 1912 4.335315 TGTCGTTTGTCATTGCTCTTCTTT 59.665 37.500 0.00 0.00 0.00 2.52
1885 1939 1.957177 TCGAGACTTCAGTGCAAGACT 59.043 47.619 8.67 7.74 32.07 3.24
1921 1975 3.613432 GCCATGTTTCTCTTGCCAAGAAG 60.613 47.826 8.74 3.40 37.02 2.85
1930 1984 1.243342 TTGCCAAGAAGATGCCCGTG 61.243 55.000 0.00 0.00 0.00 4.94
1958 2012 1.744741 GCTTCTGCAGAGGCTGGTC 60.745 63.158 35.85 13.17 42.93 4.02
1969 2023 2.401766 GGCTGGTCCAACTGATGCG 61.402 63.158 0.00 0.00 34.01 4.73
1972 2026 2.359850 GGTCCAACTGATGCGGCA 60.360 61.111 4.58 4.58 0.00 5.69
1998 2052 1.215423 ACCAGAGAAGCCAAAACCAGT 59.785 47.619 0.00 0.00 0.00 4.00
2021 2075 1.663379 TTCGATCGAGGACATGCCGT 61.663 55.000 18.54 0.00 43.43 5.68
2037 2091 2.720758 CGTTCGAGTCCAAGCAGCG 61.721 63.158 0.00 0.00 0.00 5.18
2170 2224 4.999950 TCCAAGATGAAGAAGCTCAAGAAC 59.000 41.667 0.00 0.00 0.00 3.01
2173 2227 3.993081 AGATGAAGAAGCTCAAGAACGTG 59.007 43.478 0.00 0.00 0.00 4.49
2262 2316 5.634859 CCTCTAATGCATTGGTGTTTGTTTC 59.365 40.000 22.27 0.00 0.00 2.78
2292 2346 6.869421 ACAATTTTTCTGTTCTGAAACACG 57.131 33.333 0.00 0.00 40.45 4.49
2293 2347 5.288472 ACAATTTTTCTGTTCTGAAACACGC 59.712 36.000 0.00 0.00 40.45 5.34
2315 2369 7.325821 CACGCAATCGGTTATAATGCAATTAAT 59.674 33.333 8.33 0.00 40.34 1.40
2559 2624 3.053831 TGAAAGGAACATCGGTCCTTC 57.946 47.619 13.54 8.17 42.47 3.46
2564 2629 1.641577 GAACATCGGTCCTTCTTCGG 58.358 55.000 0.00 0.00 0.00 4.30
2765 2839 5.422012 AGGAAGGAACAACAAGAACAACAAT 59.578 36.000 0.00 0.00 0.00 2.71
2766 2840 5.519927 GGAAGGAACAACAAGAACAACAATG 59.480 40.000 0.00 0.00 0.00 2.82
2767 2841 5.659440 AGGAACAACAAGAACAACAATGT 57.341 34.783 0.00 0.00 43.14 2.71
2768 2842 6.767524 AGGAACAACAAGAACAACAATGTA 57.232 33.333 0.00 0.00 39.40 2.29
2769 2843 6.560711 AGGAACAACAAGAACAACAATGTAC 58.439 36.000 0.00 0.00 39.40 2.90
2770 2844 5.454232 GGAACAACAAGAACAACAATGTACG 59.546 40.000 0.00 0.00 39.40 3.67
2868 2951 4.713824 TTATAACACTCACCGTCTGGAG 57.286 45.455 0.00 0.00 39.21 3.86
2873 2956 1.216710 CTCACCGTCTGGAGCTTCC 59.783 63.158 0.00 0.00 39.21 3.46
2898 2981 3.256383 TGCATCAAGTTCCCACTGAAATG 59.744 43.478 0.00 0.00 33.94 2.32
3127 3232 3.507233 TCCAGTGGCAATGAATTTCTGAC 59.493 43.478 17.68 0.00 0.00 3.51
3130 3235 4.022589 CAGTGGCAATGAATTTCTGACTGT 60.023 41.667 9.76 0.00 0.00 3.55
3156 3261 1.075970 TCTCGGATCTCCACCCCAG 60.076 63.158 0.00 0.00 35.14 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.712425 ACCGCGTGTAGTCACCGC 62.712 66.667 4.92 0.00 41.09 5.68
24 25 2.049802 AACCGCGTGTAGTCACCG 60.050 61.111 4.92 0.00 41.09 4.94
25 26 0.523072 TAGAACCGCGTGTAGTCACC 59.477 55.000 4.92 0.00 41.09 4.02
26 27 1.069022 TGTAGAACCGCGTGTAGTCAC 60.069 52.381 4.92 0.88 40.79 3.67
27 28 1.198408 CTGTAGAACCGCGTGTAGTCA 59.802 52.381 4.92 0.00 0.00 3.41
28 29 1.892468 CTGTAGAACCGCGTGTAGTC 58.108 55.000 4.92 0.00 0.00 2.59
29 30 0.109412 GCTGTAGAACCGCGTGTAGT 60.109 55.000 4.92 0.00 0.00 2.73
30 31 0.801067 GGCTGTAGAACCGCGTGTAG 60.801 60.000 4.92 0.00 0.00 2.74
31 32 1.213537 GGCTGTAGAACCGCGTGTA 59.786 57.895 4.92 0.00 0.00 2.90
32 33 2.048503 GGCTGTAGAACCGCGTGT 60.049 61.111 4.92 0.00 0.00 4.49
33 34 2.813908 GGGCTGTAGAACCGCGTG 60.814 66.667 4.92 0.00 0.00 5.34
34 35 4.078516 GGGGCTGTAGAACCGCGT 62.079 66.667 4.92 0.00 0.00 6.01
35 36 4.832608 GGGGGCTGTAGAACCGCG 62.833 72.222 0.00 0.00 39.68 6.46
36 37 3.387225 GAGGGGGCTGTAGAACCGC 62.387 68.421 0.00 0.00 38.13 5.68
37 38 2.901042 GAGGGGGCTGTAGAACCG 59.099 66.667 0.00 0.00 0.00 4.44
38 39 2.732619 CCGAGGGGGCTGTAGAACC 61.733 68.421 0.00 0.00 0.00 3.62
39 40 2.901042 CCGAGGGGGCTGTAGAAC 59.099 66.667 0.00 0.00 0.00 3.01
48 49 1.146263 GTTCTACATGCCGAGGGGG 59.854 63.158 0.00 0.00 39.58 5.40
49 50 1.146263 GGTTCTACATGCCGAGGGG 59.854 63.158 0.00 0.00 0.00 4.79
50 51 4.857251 GGTTCTACATGCCGAGGG 57.143 61.111 0.00 0.00 0.00 4.30
55 56 2.461110 CCACGCGGTTCTACATGCC 61.461 63.158 12.47 0.00 0.00 4.40
56 57 2.461110 CCCACGCGGTTCTACATGC 61.461 63.158 12.47 0.00 0.00 4.06
57 58 2.461110 GCCCACGCGGTTCTACATG 61.461 63.158 12.47 0.00 0.00 3.21
58 59 2.125269 GCCCACGCGGTTCTACAT 60.125 61.111 12.47 0.00 0.00 2.29
109 110 2.526450 AAAACTACCGCGGGCTACCC 62.526 60.000 31.76 0.00 41.09 3.69
110 111 0.674581 AAAAACTACCGCGGGCTACC 60.675 55.000 31.76 0.00 0.00 3.18
111 112 2.845019 AAAAACTACCGCGGGCTAC 58.155 52.632 31.76 0.00 0.00 3.58
145 146 8.846607 GCGAGTTCGTTCAAATTTAAACATATT 58.153 29.630 5.09 0.00 42.22 1.28
146 147 7.483691 GGCGAGTTCGTTCAAATTTAAACATAT 59.516 33.333 5.09 0.00 42.22 1.78
147 148 6.797995 GGCGAGTTCGTTCAAATTTAAACATA 59.202 34.615 5.09 0.00 42.22 2.29
148 149 5.627780 GGCGAGTTCGTTCAAATTTAAACAT 59.372 36.000 5.09 0.00 42.22 2.71
149 150 4.971220 GGCGAGTTCGTTCAAATTTAAACA 59.029 37.500 5.09 0.00 42.22 2.83
150 151 4.380678 GGGCGAGTTCGTTCAAATTTAAAC 59.619 41.667 3.27 0.00 42.22 2.01
151 152 4.538917 GGGCGAGTTCGTTCAAATTTAAA 58.461 39.130 3.27 0.00 42.22 1.52
152 153 3.364167 CGGGCGAGTTCGTTCAAATTTAA 60.364 43.478 3.27 0.00 42.22 1.52
153 154 2.158058 CGGGCGAGTTCGTTCAAATTTA 59.842 45.455 3.27 0.00 42.22 1.40
154 155 1.069500 CGGGCGAGTTCGTTCAAATTT 60.069 47.619 3.27 0.00 42.22 1.82
155 156 0.515564 CGGGCGAGTTCGTTCAAATT 59.484 50.000 3.27 0.00 42.22 1.82
156 157 0.601841 ACGGGCGAGTTCGTTCAAAT 60.602 50.000 3.27 0.00 42.22 2.32
157 158 1.227321 ACGGGCGAGTTCGTTCAAA 60.227 52.632 3.27 0.00 42.22 2.69
158 159 1.952133 CACGGGCGAGTTCGTTCAA 60.952 57.895 3.27 0.00 42.22 2.69
159 160 2.355363 CACGGGCGAGTTCGTTCA 60.355 61.111 3.27 0.00 42.22 3.18
160 161 1.493134 AAACACGGGCGAGTTCGTTC 61.493 55.000 3.27 0.00 42.22 3.95
161 162 1.522130 AAACACGGGCGAGTTCGTT 60.522 52.632 3.27 0.00 42.22 3.85
162 163 2.107546 AAACACGGGCGAGTTCGT 59.892 55.556 3.27 0.00 42.22 3.85
163 164 2.549282 CAAACACGGGCGAGTTCG 59.451 61.111 0.00 0.00 43.27 3.95
164 165 2.251371 GCAAACACGGGCGAGTTC 59.749 61.111 0.00 0.00 0.00 3.01
170 171 2.653766 CACAACGCAAACACGGGC 60.654 61.111 0.00 0.00 37.37 6.13
171 172 0.456995 AAACACAACGCAAACACGGG 60.457 50.000 0.00 0.00 37.37 5.28
172 173 0.637738 CAAACACAACGCAAACACGG 59.362 50.000 0.00 0.00 37.37 4.94
173 174 0.023103 GCAAACACAACGCAAACACG 59.977 50.000 0.00 0.00 39.50 4.49
174 175 0.023103 CGCAAACACAACGCAAACAC 59.977 50.000 0.00 0.00 0.00 3.32
175 176 2.353807 CGCAAACACAACGCAAACA 58.646 47.368 0.00 0.00 0.00 2.83
181 182 0.932585 AATTCGGCGCAAACACAACG 60.933 50.000 10.83 0.00 0.00 4.10
182 183 1.071568 CAAATTCGGCGCAAACACAAC 60.072 47.619 10.83 0.00 0.00 3.32
183 184 1.202302 TCAAATTCGGCGCAAACACAA 60.202 42.857 10.83 0.00 0.00 3.33
184 185 0.382158 TCAAATTCGGCGCAAACACA 59.618 45.000 10.83 0.00 0.00 3.72
185 186 1.189227 GTTCAAATTCGGCGCAAACAC 59.811 47.619 10.83 0.00 0.00 3.32
186 187 1.202302 TGTTCAAATTCGGCGCAAACA 60.202 42.857 10.83 0.00 0.00 2.83
187 188 1.482278 TGTTCAAATTCGGCGCAAAC 58.518 45.000 10.83 0.00 0.00 2.93
188 189 2.430546 ATGTTCAAATTCGGCGCAAA 57.569 40.000 10.83 2.72 0.00 3.68
189 190 2.430546 AATGTTCAAATTCGGCGCAA 57.569 40.000 10.83 0.00 0.00 4.85
190 191 2.430546 AAATGTTCAAATTCGGCGCA 57.569 40.000 10.83 0.00 0.00 6.09
191 192 4.894798 TTAAAATGTTCAAATTCGGCGC 57.105 36.364 0.00 0.00 0.00 6.53
192 193 6.571887 GGTTTTTAAAATGTTCAAATTCGGCG 59.428 34.615 0.00 0.00 0.00 6.46
193 194 6.853872 GGGTTTTTAAAATGTTCAAATTCGGC 59.146 34.615 0.55 0.00 0.00 5.54
194 195 7.066505 CGGGTTTTTAAAATGTTCAAATTCGG 58.933 34.615 0.55 0.00 0.00 4.30
195 196 7.622880 ACGGGTTTTTAAAATGTTCAAATTCG 58.377 30.769 0.55 0.00 0.00 3.34
196 197 7.790216 CGACGGGTTTTTAAAATGTTCAAATTC 59.210 33.333 0.55 0.00 0.00 2.17
197 198 7.254488 CCGACGGGTTTTTAAAATGTTCAAATT 60.254 33.333 5.81 0.00 0.00 1.82
198 199 6.201234 CCGACGGGTTTTTAAAATGTTCAAAT 59.799 34.615 5.81 0.00 0.00 2.32
199 200 5.519206 CCGACGGGTTTTTAAAATGTTCAAA 59.481 36.000 5.81 0.00 0.00 2.69
200 201 5.041940 CCGACGGGTTTTTAAAATGTTCAA 58.958 37.500 5.81 0.00 0.00 2.69
201 202 4.499357 CCCGACGGGTTTTTAAAATGTTCA 60.499 41.667 25.54 0.00 38.25 3.18
202 203 3.982701 CCCGACGGGTTTTTAAAATGTTC 59.017 43.478 25.54 0.00 38.25 3.18
203 204 3.243805 CCCCGACGGGTTTTTAAAATGTT 60.244 43.478 30.60 0.00 45.50 2.71
204 205 2.296752 CCCCGACGGGTTTTTAAAATGT 59.703 45.455 30.60 0.00 45.50 2.71
205 206 2.949142 CCCCGACGGGTTTTTAAAATG 58.051 47.619 30.60 8.11 45.50 2.32
227 228 4.899239 GATGCTCCCCAGTCGCGG 62.899 72.222 6.13 0.00 0.00 6.46
228 229 4.147449 TGATGCTCCCCAGTCGCG 62.147 66.667 0.00 0.00 0.00 5.87
229 230 2.512515 GTGATGCTCCCCAGTCGC 60.513 66.667 0.00 0.00 0.00 5.19
230 231 2.202797 CGTGATGCTCCCCAGTCG 60.203 66.667 0.00 0.00 0.00 4.18
231 232 1.153549 GACGTGATGCTCCCCAGTC 60.154 63.158 0.00 0.00 0.00 3.51
232 233 2.660064 GGACGTGATGCTCCCCAGT 61.660 63.158 0.00 0.00 0.00 4.00
233 234 2.187946 GGACGTGATGCTCCCCAG 59.812 66.667 0.00 0.00 0.00 4.45
234 235 3.399181 GGGACGTGATGCTCCCCA 61.399 66.667 0.00 0.00 40.53 4.96
236 237 2.270874 ATTGGGGACGTGATGCTCCC 62.271 60.000 0.00 0.00 45.17 4.30
237 238 1.097547 CATTGGGGACGTGATGCTCC 61.098 60.000 0.00 0.00 0.00 4.70
238 239 1.718757 GCATTGGGGACGTGATGCTC 61.719 60.000 0.00 0.00 39.31 4.26
239 240 1.750399 GCATTGGGGACGTGATGCT 60.750 57.895 0.00 0.00 39.31 3.79
240 241 2.800736 GCATTGGGGACGTGATGC 59.199 61.111 0.00 0.00 36.86 3.91
241 242 3.101209 CGCATTGGGGACGTGATG 58.899 61.111 0.00 0.00 0.00 3.07
242 243 2.824041 GCGCATTGGGGACGTGAT 60.824 61.111 0.30 0.00 0.00 3.06
250 251 2.102161 GCTAAACCGCGCATTGGG 59.898 61.111 8.75 2.12 0.00 4.12
317 318 0.249657 CGACTTAGGGCATCTCCAGC 60.250 60.000 0.00 0.00 36.21 4.85
318 319 1.067821 GACGACTTAGGGCATCTCCAG 59.932 57.143 0.00 0.00 36.21 3.86
319 320 1.112113 GACGACTTAGGGCATCTCCA 58.888 55.000 0.00 0.00 36.21 3.86
320 321 0.030908 CGACGACTTAGGGCATCTCC 59.969 60.000 0.00 0.00 0.00 3.71
321 322 1.022735 TCGACGACTTAGGGCATCTC 58.977 55.000 0.00 0.00 0.00 2.75
322 323 1.134560 GTTCGACGACTTAGGGCATCT 59.865 52.381 0.00 0.00 0.00 2.90
323 324 1.135199 TGTTCGACGACTTAGGGCATC 60.135 52.381 0.00 0.00 0.00 3.91
324 325 0.892755 TGTTCGACGACTTAGGGCAT 59.107 50.000 0.00 0.00 0.00 4.40
325 326 0.038892 GTGTTCGACGACTTAGGGCA 60.039 55.000 0.00 0.00 0.00 5.36
326 327 0.735287 GGTGTTCGACGACTTAGGGC 60.735 60.000 0.00 0.00 0.00 5.19
327 328 0.886563 AGGTGTTCGACGACTTAGGG 59.113 55.000 0.00 0.00 0.00 3.53
328 329 2.030540 TCAAGGTGTTCGACGACTTAGG 60.031 50.000 0.00 0.00 0.00 2.69
329 330 3.058432 TCTCAAGGTGTTCGACGACTTAG 60.058 47.826 0.00 0.00 0.00 2.18
425 426 2.950309 GGACTGCTATGAGTCGTTCCTA 59.050 50.000 0.00 0.00 42.97 2.94
433 434 1.680522 CTGGCCGGACTGCTATGAGT 61.681 60.000 9.82 0.00 0.00 3.41
469 470 3.095898 CTTTCTTTAGCCGCCGCCG 62.096 63.158 0.00 0.00 34.57 6.46
523 531 3.979501 ATAACAAGCCCTCCATCCATT 57.020 42.857 0.00 0.00 0.00 3.16
538 546 3.695556 TGGTTGGACGAGACGATATAACA 59.304 43.478 0.00 0.00 0.00 2.41
548 556 5.351948 TCATATTTGATGGTTGGACGAGA 57.648 39.130 0.00 0.00 0.00 4.04
561 569 3.117926 TGCCAGCTAGCCTTCATATTTGA 60.118 43.478 12.13 0.00 0.00 2.69
583 591 6.784969 AGCAACTCTAACATAGACCCATATCT 59.215 38.462 0.00 0.00 0.00 1.98
618 626 5.346822 GCAAGAGCATACCAAAATGTTTCTG 59.653 40.000 0.00 0.00 41.58 3.02
641 649 8.971321 CCACTTGATATGCATTTTAAATAGTGC 58.029 33.333 3.54 11.59 38.05 4.40
752 762 7.739498 ACAGTGGACGTATTATTTTTCAACT 57.261 32.000 0.00 0.00 0.00 3.16
833 844 7.015877 GCTCCTCACGTAAGAAAACAATAAAG 58.984 38.462 0.00 0.00 43.62 1.85
837 848 4.385825 TGCTCCTCACGTAAGAAAACAAT 58.614 39.130 0.00 0.00 43.62 2.71
981 997 0.541764 TGGCTGTGGATTTGGGTTCC 60.542 55.000 0.00 0.00 0.00 3.62
1095 1111 2.480610 ATTATTGCTGGCGGCGGTG 61.481 57.895 20.06 5.87 45.43 4.94
1096 1112 2.124320 ATTATTGCTGGCGGCGGT 60.124 55.556 20.06 7.16 45.43 5.68
1216 1252 5.007039 CCGATTTCGTTATCATATTTCGCG 58.993 41.667 0.00 0.00 37.74 5.87
1222 1258 5.245301 TCCTCCACCGATTTCGTTATCATAT 59.755 40.000 0.00 0.00 37.74 1.78
1224 1260 3.386726 TCCTCCACCGATTTCGTTATCAT 59.613 43.478 0.00 0.00 37.74 2.45
1225 1261 2.761767 TCCTCCACCGATTTCGTTATCA 59.238 45.455 0.00 0.00 37.74 2.15
1229 1265 2.781681 ATTCCTCCACCGATTTCGTT 57.218 45.000 0.00 0.00 37.74 3.85
1253 1289 0.027063 CTAAAATTACGCACGCCCGG 59.973 55.000 0.00 0.00 0.00 5.73
1282 1318 0.250234 CCCATCGAGGACAAGCTGAA 59.750 55.000 0.00 0.00 41.22 3.02
1285 1321 1.134280 CATTCCCATCGAGGACAAGCT 60.134 52.381 0.00 0.00 41.22 3.74
1311 1347 6.042143 CAGATTGTTTGAATAAATTCCCGGG 58.958 40.000 16.85 16.85 35.97 5.73
1347 1389 8.574737 AGAGAAAAATGAACATTCTTCCAAGAG 58.425 33.333 9.16 0.00 36.22 2.85
1468 1515 6.037172 GTGTGCTTACGGATTTCATAAGACAT 59.963 38.462 0.00 0.00 0.00 3.06
1469 1516 5.350365 GTGTGCTTACGGATTTCATAAGACA 59.650 40.000 0.00 0.00 0.00 3.41
1470 1517 5.220605 GGTGTGCTTACGGATTTCATAAGAC 60.221 44.000 0.00 0.00 0.00 3.01
1471 1518 4.873827 GGTGTGCTTACGGATTTCATAAGA 59.126 41.667 0.00 0.00 0.00 2.10
1472 1519 4.260212 CGGTGTGCTTACGGATTTCATAAG 60.260 45.833 0.00 0.00 0.00 1.73
1473 1520 3.619483 CGGTGTGCTTACGGATTTCATAA 59.381 43.478 0.00 0.00 0.00 1.90
1474 1521 3.191669 CGGTGTGCTTACGGATTTCATA 58.808 45.455 0.00 0.00 0.00 2.15
1515 1562 3.255888 TCAATGACTCGTCTGTAGCAACT 59.744 43.478 0.00 0.00 0.00 3.16
1532 1579 8.706492 AAAACATATGGCATGTAAACTCAATG 57.294 30.769 10.98 4.93 0.00 2.82
1652 1700 6.761242 GCTTACCTGATGTACACATTGACATA 59.239 38.462 0.00 0.00 36.42 2.29
1785 1834 7.752239 CGATGTAAACATTGAAATTCTGAGCTT 59.248 33.333 4.57 0.00 39.56 3.74
1821 1875 6.015688 TGACAAACGACACTTAGTAGGATCTT 60.016 38.462 0.00 0.00 0.00 2.40
1858 1912 1.813178 CACTGAAGTCTCGAGGCTACA 59.187 52.381 21.92 10.98 0.00 2.74
1921 1975 2.033448 TGGACAACCACGGGCATC 59.967 61.111 0.00 0.00 41.77 3.91
1930 1984 1.845809 CTGCAGAAGCGTGGACAACC 61.846 60.000 8.42 0.00 46.23 3.77
1942 1996 1.418097 TTGGACCAGCCTCTGCAGAA 61.418 55.000 18.85 1.63 41.13 3.02
1958 2012 2.758089 GCTCTGCCGCATCAGTTGG 61.758 63.158 0.00 0.00 35.63 3.77
1969 2023 1.304509 GCTTCTCTGGTTGCTCTGCC 61.305 60.000 0.00 0.00 0.00 4.85
1972 2026 0.767375 TTGGCTTCTCTGGTTGCTCT 59.233 50.000 0.00 0.00 0.00 4.09
1998 2052 0.103026 CATGTCCTCGATCGAAGCCA 59.897 55.000 19.92 9.81 0.00 4.75
2021 2075 1.888436 ATCCGCTGCTTGGACTCGAA 61.888 55.000 0.00 0.00 38.60 3.71
2037 2091 0.686224 CCTCTGCTCCAGGATCATCC 59.314 60.000 0.00 0.00 36.58 3.51
2173 2227 1.695893 CGACATCATGTGCCGGTCAC 61.696 60.000 18.49 18.49 45.82 3.67
2216 2270 2.848562 CGCAACACGTAGGTTTACAG 57.151 50.000 0.00 0.00 36.87 2.74
2262 2316 7.962934 TCAGAACAGAAAAATTGTACAAACG 57.037 32.000 13.23 0.00 0.00 3.60
2590 2655 1.065551 ACTTTCAGCAAGCACGAAACC 59.934 47.619 0.00 0.00 35.65 3.27
2593 2658 1.599071 CAGACTTTCAGCAAGCACGAA 59.401 47.619 0.00 0.00 35.65 3.85
2615 2680 3.377172 CCAGTGGAAACTCGTTTGAAAGT 59.623 43.478 1.68 0.00 32.11 2.66
2622 2687 1.676006 CAAAGCCAGTGGAAACTCGTT 59.324 47.619 15.20 0.00 0.00 3.85
2855 2938 1.216710 GGAAGCTCCAGACGGTGAG 59.783 63.158 0.00 0.00 36.28 3.51
2859 2942 1.227089 CATCGGAAGCTCCAGACGG 60.227 63.158 0.00 0.00 35.91 4.79
2868 2951 1.064654 GGAACTTGATGCATCGGAAGC 59.935 52.381 21.34 10.55 0.00 3.86
2873 2956 1.399440 CAGTGGGAACTTGATGCATCG 59.601 52.381 21.34 10.83 0.00 3.84
2898 2981 5.305585 TGGTGTTCCTGTTCTTCAGTTATC 58.694 41.667 0.00 0.00 42.19 1.75
2923 3006 4.154918 GCAGACCCAGAATCAACTTAAGTG 59.845 45.833 9.34 3.91 0.00 3.16
2991 3081 1.789464 GCATCCAGTTCTCGCTATTCG 59.211 52.381 0.00 0.00 40.15 3.34


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

AutoCloner maintained by Alex Coulton.