Multiple sequence alignment - TraesCS2B01G143500

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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 TraesCS2B01G143500 chr2B 100.000 2222 0 0 1 2222 110039453 110037232 0.000000e+00 4104
1 TraesCS2B01G143500 chr2D 96.050 1696 55 8 535 2222 72489740 72488049 0.000000e+00 2750
2 TraesCS2B01G143500 chr2D 94.164 1148 32 10 1082 2222 72730029 72728910 0.000000e+00 1716
3 TraesCS2B01G143500 chr2D 94.082 490 29 0 294 783 72764614 72764125 0.000000e+00 745
4 TraesCS2B01G143500 chr2D 95.652 253 6 2 852 1100 72764124 72763873 3.440000e-108 401
5 TraesCS2B01G143500 chr2D 93.103 87 5 1 5 91 575332874 575332789 2.320000e-25 126
6 TraesCS2B01G143500 chr2D 94.203 69 4 0 481 549 72572307 72572239 3.020000e-19 106
7 TraesCS2B01G143500 chr4A 94.253 87 5 0 5 91 673051118 673051032 1.380000e-27 134
8 TraesCS2B01G143500 chr5A 92.391 92 7 0 2 93 287619141 287619232 4.980000e-27 132
9 TraesCS2B01G143500 chr5B 93.103 87 6 0 6 92 325798891 325798805 6.440000e-26 128
10 TraesCS2B01G143500 chr3D 92.222 90 7 0 2 91 143158383 143158472 6.440000e-26 128
11 TraesCS2B01G143500 chr3D 91.111 90 8 0 5 94 80415656 80415567 3.000000e-24 122
12 TraesCS2B01G143500 chr1D 92.222 90 7 0 2 91 466101252 466101341 6.440000e-26 128
13 TraesCS2B01G143500 chr7A 93.023 86 6 0 5 90 109341047 109341132 2.320000e-25 126
14 TraesCS2B01G143500 chr6A 93.023 86 6 0 5 90 606096106 606096021 2.320000e-25 126


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 TraesCS2B01G143500 chr2B 110037232 110039453 2221 True 4104 4104 100.000 1 2222 1 chr2B.!!$R1 2221
1 TraesCS2B01G143500 chr2D 72488049 72489740 1691 True 2750 2750 96.050 535 2222 1 chr2D.!!$R1 1687
2 TraesCS2B01G143500 chr2D 72728910 72730029 1119 True 1716 1716 94.164 1082 2222 1 chr2D.!!$R3 1140
3 TraesCS2B01G143500 chr2D 72763873 72764614 741 True 573 745 94.867 294 1100 2 chr2D.!!$R5 806

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
297 298 0.035439 TTTCTCATCCCCTCCAACGC 60.035 55.0 0.0 0.0 0.0 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 1613 1.135024 CGCCTCCAATCCCATTTGTTG 60.135 52.381 0.0 0.0 0.0 3.33 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
30 31 5.365403 TTTAGTGGATGCCTTAACAAACG 57.635 39.130 0.00 0.00 0.00 3.60
31 32 3.134574 AGTGGATGCCTTAACAAACGA 57.865 42.857 0.00 0.00 0.00 3.85
32 33 3.686016 AGTGGATGCCTTAACAAACGAT 58.314 40.909 0.00 0.00 0.00 3.73
33 34 4.839121 AGTGGATGCCTTAACAAACGATA 58.161 39.130 0.00 0.00 0.00 2.92
34 35 5.437060 AGTGGATGCCTTAACAAACGATAT 58.563 37.500 0.00 0.00 0.00 1.63
35 36 6.588204 AGTGGATGCCTTAACAAACGATATA 58.412 36.000 0.00 0.00 0.00 0.86
36 37 7.224297 AGTGGATGCCTTAACAAACGATATAT 58.776 34.615 0.00 0.00 0.00 0.86
37 38 7.719633 AGTGGATGCCTTAACAAACGATATATT 59.280 33.333 0.00 0.00 0.00 1.28
38 39 8.349983 GTGGATGCCTTAACAAACGATATATTT 58.650 33.333 0.00 0.00 0.00 1.40
39 40 8.908903 TGGATGCCTTAACAAACGATATATTTT 58.091 29.630 0.00 0.00 0.00 1.82
40 41 9.744468 GGATGCCTTAACAAACGATATATTTTT 57.256 29.630 0.00 0.00 0.00 1.94
64 65 9.944663 TTTATTCTCACATGAAATATAAACCGC 57.055 29.630 0.00 0.00 0.00 5.68
65 66 6.371809 TTCTCACATGAAATATAAACCGCC 57.628 37.500 0.00 0.00 0.00 6.13
66 67 5.432645 TCTCACATGAAATATAAACCGCCA 58.567 37.500 0.00 0.00 0.00 5.69
67 68 6.061441 TCTCACATGAAATATAAACCGCCAT 58.939 36.000 0.00 0.00 0.00 4.40
68 69 6.017192 TCTCACATGAAATATAAACCGCCATG 60.017 38.462 0.00 0.00 36.81 3.66
69 70 5.825151 TCACATGAAATATAAACCGCCATGA 59.175 36.000 0.00 0.00 35.32 3.07
70 71 6.489700 TCACATGAAATATAAACCGCCATGAT 59.510 34.615 0.00 0.00 35.32 2.45
71 72 6.583427 CACATGAAATATAAACCGCCATGATG 59.417 38.462 0.00 0.00 35.32 3.07
72 73 5.703978 TGAAATATAAACCGCCATGATGG 57.296 39.130 7.21 7.21 41.55 3.51
86 87 5.356291 CCATGATGGCATTTCCCTTAAAA 57.644 39.130 0.00 0.00 30.68 1.52
87 88 5.743117 CCATGATGGCATTTCCCTTAAAAA 58.257 37.500 0.00 0.00 30.68 1.94
106 107 1.519408 AAAAGACCGATTCGTGGTGG 58.481 50.000 5.20 0.00 40.63 4.61
107 108 0.953960 AAAGACCGATTCGTGGTGGC 60.954 55.000 5.20 0.00 40.63 5.01
108 109 1.827399 AAGACCGATTCGTGGTGGCT 61.827 55.000 5.20 0.00 40.63 4.75
109 110 0.968901 AGACCGATTCGTGGTGGCTA 60.969 55.000 5.20 0.00 40.63 3.93
110 111 0.527817 GACCGATTCGTGGTGGCTAG 60.528 60.000 5.20 0.00 40.63 3.42
111 112 1.883084 CCGATTCGTGGTGGCTAGC 60.883 63.158 6.04 6.04 0.00 3.42
112 113 2.230940 CGATTCGTGGTGGCTAGCG 61.231 63.158 9.00 0.00 0.00 4.26
113 114 1.153628 GATTCGTGGTGGCTAGCGT 60.154 57.895 9.00 0.00 0.00 5.07
114 115 0.739813 GATTCGTGGTGGCTAGCGTT 60.740 55.000 9.00 0.00 0.00 4.84
115 116 0.739813 ATTCGTGGTGGCTAGCGTTC 60.740 55.000 9.00 1.23 0.00 3.95
116 117 1.812686 TTCGTGGTGGCTAGCGTTCT 61.813 55.000 9.00 0.00 0.00 3.01
117 118 0.961857 TCGTGGTGGCTAGCGTTCTA 60.962 55.000 9.00 0.00 0.00 2.10
118 119 0.525668 CGTGGTGGCTAGCGTTCTAG 60.526 60.000 9.00 0.00 44.03 2.43
176 177 4.109656 CCCCTCCTGCCTACCCCT 62.110 72.222 0.00 0.00 0.00 4.79
177 178 2.042930 CCCTCCTGCCTACCCCTT 59.957 66.667 0.00 0.00 0.00 3.95
178 179 2.073101 CCCTCCTGCCTACCCCTTC 61.073 68.421 0.00 0.00 0.00 3.46
179 180 2.073101 CCTCCTGCCTACCCCTTCC 61.073 68.421 0.00 0.00 0.00 3.46
180 181 2.042261 TCCTGCCTACCCCTTCCC 59.958 66.667 0.00 0.00 0.00 3.97
181 182 3.097162 CCTGCCTACCCCTTCCCC 61.097 72.222 0.00 0.00 0.00 4.81
182 183 2.286121 CTGCCTACCCCTTCCCCA 60.286 66.667 0.00 0.00 0.00 4.96
183 184 2.286121 TGCCTACCCCTTCCCCAG 60.286 66.667 0.00 0.00 0.00 4.45
184 185 3.810188 GCCTACCCCTTCCCCAGC 61.810 72.222 0.00 0.00 0.00 4.85
185 186 3.480133 CCTACCCCTTCCCCAGCG 61.480 72.222 0.00 0.00 0.00 5.18
186 187 4.176752 CTACCCCTTCCCCAGCGC 62.177 72.222 0.00 0.00 0.00 5.92
190 191 4.176752 CCCTTCCCCAGCGCCTAC 62.177 72.222 2.29 0.00 0.00 3.18
191 192 3.083997 CCTTCCCCAGCGCCTACT 61.084 66.667 2.29 0.00 0.00 2.57
192 193 2.501610 CTTCCCCAGCGCCTACTC 59.498 66.667 2.29 0.00 0.00 2.59
193 194 3.081409 TTCCCCAGCGCCTACTCC 61.081 66.667 2.29 0.00 0.00 3.85
202 203 3.902086 GCCTACTCCCGCCGTCTC 61.902 72.222 0.00 0.00 0.00 3.36
203 204 2.124236 CCTACTCCCGCCGTCTCT 60.124 66.667 0.00 0.00 0.00 3.10
204 205 2.482333 CCTACTCCCGCCGTCTCTG 61.482 68.421 0.00 0.00 0.00 3.35
205 206 3.127352 CTACTCCCGCCGTCTCTGC 62.127 68.421 0.00 0.00 0.00 4.26
211 212 3.764466 CGCCGTCTCTGCCCTCTT 61.764 66.667 0.00 0.00 0.00 2.85
212 213 2.185608 GCCGTCTCTGCCCTCTTC 59.814 66.667 0.00 0.00 0.00 2.87
213 214 2.896443 CCGTCTCTGCCCTCTTCC 59.104 66.667 0.00 0.00 0.00 3.46
214 215 2.726351 CCGTCTCTGCCCTCTTCCC 61.726 68.421 0.00 0.00 0.00 3.97
215 216 2.726351 CGTCTCTGCCCTCTTCCCC 61.726 68.421 0.00 0.00 0.00 4.81
216 217 2.364317 TCTCTGCCCTCTTCCCCG 60.364 66.667 0.00 0.00 0.00 5.73
217 218 4.168291 CTCTGCCCTCTTCCCCGC 62.168 72.222 0.00 0.00 0.00 6.13
257 258 4.154347 CCGAGCTCTGCCCTCCAC 62.154 72.222 12.85 0.00 0.00 4.02
258 259 4.154347 CGAGCTCTGCCCTCCACC 62.154 72.222 12.85 0.00 0.00 4.61
259 260 4.154347 GAGCTCTGCCCTCCACCG 62.154 72.222 6.43 0.00 0.00 4.94
268 269 4.154347 CCTCCACCGCAGCTCCTC 62.154 72.222 0.00 0.00 0.00 3.71
269 270 3.385384 CTCCACCGCAGCTCCTCA 61.385 66.667 0.00 0.00 0.00 3.86
270 271 2.685017 TCCACCGCAGCTCCTCAT 60.685 61.111 0.00 0.00 0.00 2.90
271 272 2.202987 CCACCGCAGCTCCTCATC 60.203 66.667 0.00 0.00 0.00 2.92
272 273 2.729479 CCACCGCAGCTCCTCATCT 61.729 63.158 0.00 0.00 0.00 2.90
273 274 1.521010 CACCGCAGCTCCTCATCTG 60.521 63.158 0.00 0.00 0.00 2.90
277 278 4.859400 CAGCTCCTCATCTGCAGG 57.141 61.111 15.13 0.00 0.00 4.85
278 279 1.906253 CAGCTCCTCATCTGCAGGT 59.094 57.895 15.13 2.68 32.20 4.00
279 280 0.252479 CAGCTCCTCATCTGCAGGTT 59.748 55.000 15.13 0.00 32.20 3.50
280 281 0.990374 AGCTCCTCATCTGCAGGTTT 59.010 50.000 15.13 0.00 32.20 3.27
281 282 1.065564 AGCTCCTCATCTGCAGGTTTC 60.066 52.381 15.13 0.00 32.20 2.78
282 283 1.065564 GCTCCTCATCTGCAGGTTTCT 60.066 52.381 15.13 0.00 32.20 2.52
283 284 2.903798 CTCCTCATCTGCAGGTTTCTC 58.096 52.381 15.13 0.00 32.20 2.87
284 285 2.235650 CTCCTCATCTGCAGGTTTCTCA 59.764 50.000 15.13 0.00 32.20 3.27
285 286 2.842496 TCCTCATCTGCAGGTTTCTCAT 59.158 45.455 15.13 0.00 32.20 2.90
286 287 3.118482 TCCTCATCTGCAGGTTTCTCATC 60.118 47.826 15.13 0.00 32.20 2.92
287 288 3.204526 CTCATCTGCAGGTTTCTCATCC 58.795 50.000 15.13 0.00 0.00 3.51
288 289 2.092753 TCATCTGCAGGTTTCTCATCCC 60.093 50.000 15.13 0.00 0.00 3.85
289 290 0.620556 TCTGCAGGTTTCTCATCCCC 59.379 55.000 15.13 0.00 0.00 4.81
290 291 0.622665 CTGCAGGTTTCTCATCCCCT 59.377 55.000 5.57 0.00 0.00 4.79
291 292 0.620556 TGCAGGTTTCTCATCCCCTC 59.379 55.000 0.00 0.00 0.00 4.30
292 293 0.106967 GCAGGTTTCTCATCCCCTCC 60.107 60.000 0.00 0.00 0.00 4.30
297 298 0.035439 TTTCTCATCCCCTCCAACGC 60.035 55.000 0.00 0.00 0.00 4.84
300 301 2.438434 CATCCCCTCCAACGCCAC 60.438 66.667 0.00 0.00 0.00 5.01
326 327 1.383803 GCCCCTCCATCACCTCTCT 60.384 63.158 0.00 0.00 0.00 3.10
331 332 2.586425 CCTCCATCACCTCTCTCTCTC 58.414 57.143 0.00 0.00 0.00 3.20
436 437 5.235305 TCTGCAACTTGTTTTCTGAAGAC 57.765 39.130 4.26 4.26 0.00 3.01
442 443 6.314784 CAACTTGTTTTCTGAAGACGACTTT 58.685 36.000 0.83 0.00 36.39 2.66
443 444 6.496338 ACTTGTTTTCTGAAGACGACTTTT 57.504 33.333 0.83 0.00 36.39 2.27
448 449 2.755650 TCTGAAGACGACTTTTCCTGC 58.244 47.619 0.83 0.00 36.39 4.85
454 455 2.891580 AGACGACTTTTCCTGCTAGTCA 59.108 45.455 0.00 0.00 38.52 3.41
455 456 3.057174 AGACGACTTTTCCTGCTAGTCAG 60.057 47.826 7.07 7.07 42.49 3.51
505 506 0.470341 GATTGGAGGTAGGTGGAGGC 59.530 60.000 0.00 0.00 0.00 4.70
511 512 1.614413 GAGGTAGGTGGAGGCTAATCG 59.386 57.143 0.00 0.00 0.00 3.34
532 533 6.510879 TCGCATAAGAGAAAACTACTCTGA 57.489 37.500 0.00 0.00 42.85 3.27
543 544 9.490379 GAGAAAACTACTCTGACAAAATTCCTA 57.510 33.333 0.00 0.00 0.00 2.94
546 547 8.608844 AAACTACTCTGACAAAATTCCTACAG 57.391 34.615 0.00 0.00 0.00 2.74
557 558 6.897413 ACAAAATTCCTACAGGCTATTTCCAT 59.103 34.615 7.97 0.00 32.10 3.41
713 714 7.592885 AGTACTTCTGTGACTTTTGGTACTA 57.407 36.000 0.00 0.00 37.45 1.82
743 744 3.122369 GGCCAGATATGCCTTGCTT 57.878 52.632 0.00 0.00 45.70 3.91
924 925 8.846943 AACATGTTCTGACTGTACATCATAAA 57.153 30.769 4.92 0.00 35.02 1.40
972 974 2.654863 TCTGATGATCCGCTAGTGACA 58.345 47.619 4.44 2.75 0.00 3.58
1065 1071 0.462759 GAGCTTTATCGGCAGCAGGT 60.463 55.000 0.00 0.00 38.61 4.00
1113 1119 3.149196 CAAGAATTATAGGGCCATGCGT 58.851 45.455 6.18 0.00 0.00 5.24
1144 1150 0.625316 AATATGTGCTGCCTGTGGGA 59.375 50.000 0.00 0.00 33.58 4.37
1167 1173 5.690464 AGGAAGTGAAGATTATGCTGTCT 57.310 39.130 0.00 0.00 0.00 3.41
1188 1194 6.369890 TGTCTGAAGAGCATATTGAAGAACAC 59.630 38.462 0.00 0.00 0.00 3.32
1198 1204 6.238484 GCATATTGAAGAACACAGGTATGGAC 60.238 42.308 0.00 0.00 0.00 4.02
1242 1248 9.836076 GTGTAAATGTCTTATGTTTTCTTACCC 57.164 33.333 0.00 0.00 0.00 3.69
1334 1340 3.338126 GATGCACTGCTGCTGTGGC 62.338 63.158 31.62 24.95 44.57 5.01
1604 1613 8.561738 TTTAGGTGAATAATTGAGGACAAGAC 57.438 34.615 0.00 0.00 39.46 3.01
1853 1863 5.994668 CCTAGTTCTTTTCTTCAGTTCTGCT 59.005 40.000 0.00 0.00 0.00 4.24
1899 1909 2.044551 CTTCCTCAGCCCCTTGCC 60.045 66.667 0.00 0.00 42.71 4.52
2215 2228 6.607689 CGCCACACTCTTATCACAAATTTTA 58.392 36.000 0.00 0.00 0.00 1.52
2217 2230 7.271223 CGCCACACTCTTATCACAAATTTTAAG 59.729 37.037 0.00 0.00 0.00 1.85
2219 2232 7.542130 CCACACTCTTATCACAAATTTTAAGGC 59.458 37.037 7.27 0.00 0.00 4.35
2220 2233 7.271223 CACACTCTTATCACAAATTTTAAGGCG 59.729 37.037 7.27 3.44 0.00 5.52
2221 2234 7.040686 ACACTCTTATCACAAATTTTAAGGCGT 60.041 33.333 7.27 3.88 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.039493 TCGTTTGTTAAGGCATCCACTAAAAA 59.961 34.615 0.00 0.00 0.00 1.94
7 8 5.531659 TCGTTTGTTAAGGCATCCACTAAAA 59.468 36.000 0.00 0.00 0.00 1.52
10 11 4.274602 TCGTTTGTTAAGGCATCCACTA 57.725 40.909 0.00 0.00 0.00 2.74
11 12 3.134574 TCGTTTGTTAAGGCATCCACT 57.865 42.857 0.00 0.00 0.00 4.00
12 13 5.751243 ATATCGTTTGTTAAGGCATCCAC 57.249 39.130 0.00 0.00 0.00 4.02
13 14 8.458573 AAATATATCGTTTGTTAAGGCATCCA 57.541 30.769 0.00 0.00 0.00 3.41
14 15 9.744468 AAAAATATATCGTTTGTTAAGGCATCC 57.256 29.630 0.00 0.00 0.00 3.51
38 39 9.944663 GCGGTTTATATTTCATGTGAGAATAAA 57.055 29.630 0.00 0.00 0.00 1.40
39 40 8.564574 GGCGGTTTATATTTCATGTGAGAATAA 58.435 33.333 0.00 0.00 0.00 1.40
40 41 7.717436 TGGCGGTTTATATTTCATGTGAGAATA 59.283 33.333 0.00 0.00 0.00 1.75
41 42 6.545666 TGGCGGTTTATATTTCATGTGAGAAT 59.454 34.615 0.00 0.00 0.00 2.40
42 43 5.883115 TGGCGGTTTATATTTCATGTGAGAA 59.117 36.000 0.00 0.00 0.00 2.87
43 44 5.432645 TGGCGGTTTATATTTCATGTGAGA 58.567 37.500 0.00 0.00 0.00 3.27
44 45 5.749596 TGGCGGTTTATATTTCATGTGAG 57.250 39.130 0.00 0.00 0.00 3.51
45 46 5.825151 TCATGGCGGTTTATATTTCATGTGA 59.175 36.000 0.00 0.00 34.11 3.58
46 47 6.070897 TCATGGCGGTTTATATTTCATGTG 57.929 37.500 0.00 0.00 34.11 3.21
47 48 6.294675 CCATCATGGCGGTTTATATTTCATGT 60.295 38.462 0.00 0.00 34.11 3.21
48 49 6.094719 CCATCATGGCGGTTTATATTTCATG 58.905 40.000 0.00 0.00 33.83 3.07
49 50 6.271488 CCATCATGGCGGTTTATATTTCAT 57.729 37.500 0.00 0.00 0.00 2.57
50 51 5.703978 CCATCATGGCGGTTTATATTTCA 57.296 39.130 0.00 0.00 0.00 2.69
64 65 5.356291 TTTTAAGGGAAATGCCATCATGG 57.644 39.130 0.00 0.00 41.55 3.66
86 87 1.877443 CCACCACGAATCGGTCTTTTT 59.123 47.619 7.80 0.00 33.25 1.94
87 88 1.519408 CCACCACGAATCGGTCTTTT 58.481 50.000 7.80 0.00 33.25 2.27
88 89 0.953960 GCCACCACGAATCGGTCTTT 60.954 55.000 7.80 0.00 33.25 2.52
89 90 1.375523 GCCACCACGAATCGGTCTT 60.376 57.895 7.80 0.00 33.25 3.01
90 91 0.968901 TAGCCACCACGAATCGGTCT 60.969 55.000 7.80 0.00 33.25 3.85
91 92 0.527817 CTAGCCACCACGAATCGGTC 60.528 60.000 7.80 0.00 33.25 4.79
92 93 1.515954 CTAGCCACCACGAATCGGT 59.484 57.895 7.80 0.00 37.16 4.69
93 94 1.883084 GCTAGCCACCACGAATCGG 60.883 63.158 7.80 0.00 0.00 4.18
94 95 2.230940 CGCTAGCCACCACGAATCG 61.231 63.158 9.66 0.00 0.00 3.34
95 96 0.739813 AACGCTAGCCACCACGAATC 60.740 55.000 9.66 0.00 0.00 2.52
96 97 0.739813 GAACGCTAGCCACCACGAAT 60.740 55.000 9.66 0.00 0.00 3.34
97 98 1.373748 GAACGCTAGCCACCACGAA 60.374 57.895 9.66 0.00 0.00 3.85
98 99 0.961857 TAGAACGCTAGCCACCACGA 60.962 55.000 9.66 0.00 0.00 4.35
99 100 0.525668 CTAGAACGCTAGCCACCACG 60.526 60.000 9.66 0.00 37.87 4.94
100 101 3.347411 CTAGAACGCTAGCCACCAC 57.653 57.895 9.66 0.00 37.87 4.16
159 160 3.660092 AAGGGGTAGGCAGGAGGGG 62.660 68.421 0.00 0.00 0.00 4.79
160 161 2.042930 AAGGGGTAGGCAGGAGGG 59.957 66.667 0.00 0.00 0.00 4.30
161 162 2.073101 GGAAGGGGTAGGCAGGAGG 61.073 68.421 0.00 0.00 0.00 4.30
162 163 2.073101 GGGAAGGGGTAGGCAGGAG 61.073 68.421 0.00 0.00 0.00 3.69
163 164 2.042261 GGGAAGGGGTAGGCAGGA 59.958 66.667 0.00 0.00 0.00 3.86
164 165 3.097162 GGGGAAGGGGTAGGCAGG 61.097 72.222 0.00 0.00 0.00 4.85
165 166 2.286121 TGGGGAAGGGGTAGGCAG 60.286 66.667 0.00 0.00 0.00 4.85
166 167 2.286121 CTGGGGAAGGGGTAGGCA 60.286 66.667 0.00 0.00 0.00 4.75
167 168 3.810188 GCTGGGGAAGGGGTAGGC 61.810 72.222 0.00 0.00 0.00 3.93
168 169 3.480133 CGCTGGGGAAGGGGTAGG 61.480 72.222 0.00 0.00 35.22 3.18
169 170 4.176752 GCGCTGGGGAAGGGGTAG 62.177 72.222 0.00 0.00 39.23 3.18
173 174 4.176752 GTAGGCGCTGGGGAAGGG 62.177 72.222 7.64 0.00 41.73 3.95
174 175 3.083997 AGTAGGCGCTGGGGAAGG 61.084 66.667 7.64 0.00 0.00 3.46
175 176 2.501610 GAGTAGGCGCTGGGGAAG 59.498 66.667 7.64 0.00 0.00 3.46
176 177 3.081409 GGAGTAGGCGCTGGGGAA 61.081 66.667 7.64 0.00 0.00 3.97
185 186 3.902086 GAGACGGCGGGAGTAGGC 61.902 72.222 13.24 0.00 0.00 3.93
186 187 2.124236 AGAGACGGCGGGAGTAGG 60.124 66.667 13.24 0.00 0.00 3.18
187 188 3.111939 CAGAGACGGCGGGAGTAG 58.888 66.667 13.24 0.00 0.00 2.57
188 189 3.138798 GCAGAGACGGCGGGAGTA 61.139 66.667 13.24 0.00 0.00 2.59
194 195 3.708220 GAAGAGGGCAGAGACGGCG 62.708 68.421 4.80 4.80 0.00 6.46
195 196 2.185608 GAAGAGGGCAGAGACGGC 59.814 66.667 0.00 0.00 0.00 5.68
196 197 2.726351 GGGAAGAGGGCAGAGACGG 61.726 68.421 0.00 0.00 0.00 4.79
197 198 2.726351 GGGGAAGAGGGCAGAGACG 61.726 68.421 0.00 0.00 0.00 4.18
198 199 2.726351 CGGGGAAGAGGGCAGAGAC 61.726 68.421 0.00 0.00 0.00 3.36
199 200 2.364317 CGGGGAAGAGGGCAGAGA 60.364 66.667 0.00 0.00 0.00 3.10
200 201 4.168291 GCGGGGAAGAGGGCAGAG 62.168 72.222 0.00 0.00 0.00 3.35
240 241 4.154347 GTGGAGGGCAGAGCTCGG 62.154 72.222 9.76 9.76 32.17 4.63
241 242 4.154347 GGTGGAGGGCAGAGCTCG 62.154 72.222 8.37 4.60 32.17 5.03
242 243 4.154347 CGGTGGAGGGCAGAGCTC 62.154 72.222 5.27 5.27 0.00 4.09
251 252 4.154347 GAGGAGCTGCGGTGGAGG 62.154 72.222 0.00 0.00 0.00 4.30
252 253 2.641439 GATGAGGAGCTGCGGTGGAG 62.641 65.000 0.00 0.00 0.00 3.86
253 254 2.685017 ATGAGGAGCTGCGGTGGA 60.685 61.111 0.00 0.00 0.00 4.02
254 255 2.202987 GATGAGGAGCTGCGGTGG 60.203 66.667 0.00 0.00 0.00 4.61
255 256 1.521010 CAGATGAGGAGCTGCGGTG 60.521 63.158 0.00 0.00 0.00 4.94
256 257 2.898738 CAGATGAGGAGCTGCGGT 59.101 61.111 0.00 0.00 0.00 5.68
260 261 0.252479 AACCTGCAGATGAGGAGCTG 59.748 55.000 17.39 0.00 38.73 4.24
261 262 0.990374 AAACCTGCAGATGAGGAGCT 59.010 50.000 17.39 0.00 34.37 4.09
262 263 1.065564 AGAAACCTGCAGATGAGGAGC 60.066 52.381 17.39 0.00 34.37 4.70
263 264 2.235650 TGAGAAACCTGCAGATGAGGAG 59.764 50.000 17.39 0.00 34.37 3.69
264 265 2.259917 TGAGAAACCTGCAGATGAGGA 58.740 47.619 17.39 0.00 34.37 3.71
265 266 2.775911 TGAGAAACCTGCAGATGAGG 57.224 50.000 17.39 0.19 36.57 3.86
266 267 3.204526 GGATGAGAAACCTGCAGATGAG 58.795 50.000 17.39 0.00 0.00 2.90
267 268 2.092753 GGGATGAGAAACCTGCAGATGA 60.093 50.000 17.39 0.00 0.00 2.92
268 269 2.295885 GGGATGAGAAACCTGCAGATG 58.704 52.381 17.39 1.02 0.00 2.90
269 270 1.213926 GGGGATGAGAAACCTGCAGAT 59.786 52.381 17.39 0.00 0.00 2.90
270 271 0.620556 GGGGATGAGAAACCTGCAGA 59.379 55.000 17.39 0.00 0.00 4.26
271 272 0.622665 AGGGGATGAGAAACCTGCAG 59.377 55.000 6.78 6.78 30.71 4.41
272 273 0.620556 GAGGGGATGAGAAACCTGCA 59.379 55.000 0.00 0.00 32.42 4.41
273 274 0.106967 GGAGGGGATGAGAAACCTGC 60.107 60.000 0.00 0.00 34.31 4.85
274 275 1.289160 TGGAGGGGATGAGAAACCTG 58.711 55.000 0.00 0.00 32.42 4.00
275 276 1.636003 GTTGGAGGGGATGAGAAACCT 59.364 52.381 0.00 0.00 35.67 3.50
276 277 1.679032 CGTTGGAGGGGATGAGAAACC 60.679 57.143 0.00 0.00 0.00 3.27
277 278 1.739067 CGTTGGAGGGGATGAGAAAC 58.261 55.000 0.00 0.00 0.00 2.78
278 279 0.035439 GCGTTGGAGGGGATGAGAAA 60.035 55.000 0.00 0.00 0.00 2.52
279 280 1.602237 GCGTTGGAGGGGATGAGAA 59.398 57.895 0.00 0.00 0.00 2.87
280 281 2.367202 GGCGTTGGAGGGGATGAGA 61.367 63.158 0.00 0.00 0.00 3.27
281 282 2.190578 GGCGTTGGAGGGGATGAG 59.809 66.667 0.00 0.00 0.00 2.90
282 283 2.609299 TGGCGTTGGAGGGGATGA 60.609 61.111 0.00 0.00 0.00 2.92
283 284 2.438434 GTGGCGTTGGAGGGGATG 60.438 66.667 0.00 0.00 0.00 3.51
284 285 2.610859 AGTGGCGTTGGAGGGGAT 60.611 61.111 0.00 0.00 0.00 3.85
285 286 3.636231 CAGTGGCGTTGGAGGGGA 61.636 66.667 0.00 0.00 0.00 4.81
288 289 4.335647 AGGCAGTGGCGTTGGAGG 62.336 66.667 11.51 0.00 42.47 4.30
289 290 2.743928 GAGGCAGTGGCGTTGGAG 60.744 66.667 11.51 0.00 42.47 3.86
290 291 4.329545 GGAGGCAGTGGCGTTGGA 62.330 66.667 11.51 0.00 42.47 3.53
448 449 5.299782 ACGGCTCTTATCCTAAACTGACTAG 59.700 44.000 0.00 0.00 0.00 2.57
454 455 6.338937 CAGTAAACGGCTCTTATCCTAAACT 58.661 40.000 0.00 0.00 0.00 2.66
455 456 5.006455 GCAGTAAACGGCTCTTATCCTAAAC 59.994 44.000 0.00 0.00 34.22 2.01
505 506 8.963130 CAGAGTAGTTTTCTCTTATGCGATTAG 58.037 37.037 0.00 0.00 39.84 1.73
511 512 7.891183 TTGTCAGAGTAGTTTTCTCTTATGC 57.109 36.000 0.00 0.00 39.84 3.14
532 533 6.252995 TGGAAATAGCCTGTAGGAATTTTGT 58.747 36.000 1.17 0.00 34.52 2.83
543 544 5.121380 ACTGATCAATGGAAATAGCCTGT 57.879 39.130 0.00 0.00 0.00 4.00
546 547 8.317679 AGTCTATACTGATCAATGGAAATAGCC 58.682 37.037 0.00 0.00 33.57 3.93
574 575 2.354199 GACCAAACAAACCGTACGGAAA 59.646 45.455 39.52 0.00 38.96 3.13
651 652 4.589908 ACAAGTGGTTGATGATAGAACCC 58.410 43.478 0.00 0.00 40.94 4.11
681 682 4.730966 AGTCACAGAAGTACTTCCTCTCA 58.269 43.478 28.05 9.37 40.33 3.27
713 714 5.513788 GGCATATCTGGCCCGATGATATTAT 60.514 44.000 19.08 1.23 45.87 1.28
761 762 2.413837 CAACTGTACAGGACCCTTTCG 58.586 52.381 26.12 0.00 0.00 3.46
808 809 9.364989 CAGAATCAAACTCTACTCCTAGAAAAG 57.635 37.037 0.00 0.00 0.00 2.27
879 880 9.988815 ACATGTTAATAGCTAGAGGTTCAATAG 57.011 33.333 0.00 0.00 0.00 1.73
924 925 6.150976 TGACGGAAATCATGAAACTGCTAAAT 59.849 34.615 0.00 0.00 0.00 1.40
972 974 5.302059 TCACTAGCAAAGTACACAGAGAACT 59.698 40.000 0.00 0.00 35.76 3.01
1113 1119 4.640201 GCAGCACATATTTTAACCTCCTCA 59.360 41.667 0.00 0.00 0.00 3.86
1144 1150 5.879223 CAGACAGCATAATCTTCACTTCCTT 59.121 40.000 0.00 0.00 0.00 3.36
1167 1173 5.645067 CCTGTGTTCTTCAATATGCTCTTCA 59.355 40.000 0.00 0.00 0.00 3.02
1242 1248 5.130477 ACTCTACATAGTGTTGGGTATTGGG 59.870 44.000 0.00 0.00 35.15 4.12
1334 1340 6.653989 CCCTTACCATATTATTCTAGCCCTG 58.346 44.000 0.00 0.00 0.00 4.45
1427 1434 4.330894 CAGTTTGCTGAGAATGCGAATAGA 59.669 41.667 0.00 0.00 45.28 1.98
1430 1437 3.076621 TCAGTTTGCTGAGAATGCGAAT 58.923 40.909 0.00 0.00 45.94 3.34
1431 1438 2.493035 TCAGTTTGCTGAGAATGCGAA 58.507 42.857 0.00 0.00 45.94 4.70
1458 1467 7.611855 AGAAGGAAATTTCACCAACTACTATGG 59.388 37.037 19.49 0.00 43.84 2.74
1604 1613 1.135024 CGCCTCCAATCCCATTTGTTG 60.135 52.381 0.00 0.00 0.00 3.33
2135 2146 1.588674 TGGCTAACACTTTGTGGACG 58.411 50.000 2.72 0.00 37.94 4.79
2136 2147 3.490249 GGTTTGGCTAACACTTTGTGGAC 60.490 47.826 13.54 0.00 38.55 4.02


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

AutoCloner maintained by Alex Coulton.