Multiple sequence alignment - TraesCS2A01G574800

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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 TraesCS2A01G574800 chr2A 100.000 5190 0 0 1 5190 769555608 769550419 0.000000e+00 9585.0
1 TraesCS2A01G574800 chr2D 97.048 4065 90 9 403 4458 644498035 644493992 0.000000e+00 6815.0
2 TraesCS2A01G574800 chr2D 94.107 577 17 5 4617 5190 644493995 644493433 0.000000e+00 861.0
3 TraesCS2A01G574800 chr2D 97.619 42 1 0 1 42 644498233 644498192 7.210000e-09 73.1
4 TraesCS2A01G574800 chr2B 96.671 3815 103 11 976 4788 791018976 791022768 0.000000e+00 6320.0
5 TraesCS2A01G574800 chr2B 91.310 725 39 15 273 978 791009588 791010307 0.000000e+00 968.0
6 TraesCS2A01G574800 chr2B 96.629 178 5 1 4449 4626 794234601 794234777 1.410000e-75 294.0
7 TraesCS2A01G574800 chr2B 92.053 151 5 5 1 148 791009445 791009591 6.810000e-49 206.0
8 TraesCS2A01G574800 chr2B 84.892 139 15 3 143 276 794028260 794028397 9.070000e-28 135.0
9 TraesCS2A01G574800 chr1B 74.361 1408 319 34 2233 3625 677528276 677529656 3.510000e-156 562.0
10 TraesCS2A01G574800 chr1B 86.923 130 12 3 146 271 461302698 461302826 1.950000e-29 141.0
11 TraesCS2A01G574800 chr1B 82.927 123 7 2 148 270 105688342 105688450 1.190000e-16 99.0
12 TraesCS2A01G574800 chr1B 85.000 100 6 2 147 237 154158168 154158267 5.530000e-15 93.5
13 TraesCS2A01G574800 chr3A 98.844 173 2 0 4457 4629 12673014 12673186 5.050000e-80 309.0
14 TraesCS2A01G574800 chr3A 98.844 173 2 0 4457 4629 12675198 12675370 5.050000e-80 309.0
15 TraesCS2A01G574800 chr3A 91.791 134 4 3 142 274 71804232 71804105 4.130000e-41 180.0
16 TraesCS2A01G574800 chr3A 80.315 127 10 6 156 273 38600254 38600134 1.200000e-11 82.4
17 TraesCS2A01G574800 chr6A 98.824 170 1 1 4454 4622 469845230 469845399 8.450000e-78 302.0
18 TraesCS2A01G574800 chr5A 98.817 169 2 0 4456 4624 327433244 327433412 8.450000e-78 302.0
19 TraesCS2A01G574800 chr5A 91.837 49 4 0 145 193 565680610 565680658 9.330000e-08 69.4
20 TraesCS2A01G574800 chr7B 98.246 171 3 0 4456 4626 730811973 730812143 3.040000e-77 300.0
21 TraesCS2A01G574800 chr7B 81.379 145 15 4 145 277 1251069 1251213 1.980000e-19 108.0
22 TraesCS2A01G574800 chr7A 97.701 174 3 1 4457 4630 50348438 50348610 1.090000e-76 298.0
23 TraesCS2A01G574800 chr7A 85.496 131 13 1 143 273 564275667 564275543 1.170000e-26 132.0
24 TraesCS2A01G574800 chr5B 93.467 199 8 5 4424 4621 615198097 615198291 1.830000e-74 291.0
25 TraesCS2A01G574800 chr3B 86.765 136 12 3 145 276 482345892 482345759 4.190000e-31 147.0
26 TraesCS2A01G574800 chr1D 87.129 101 4 2 146 237 343891899 343891999 7.110000e-19 106.0
27 TraesCS2A01G574800 chr1D 85.965 57 5 3 71 127 413064356 413064409 2.020000e-04 58.4


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 TraesCS2A01G574800 chr2A 769550419 769555608 5189 True 9585.000000 9585 100.0000 1 5190 1 chr2A.!!$R1 5189
1 TraesCS2A01G574800 chr2D 644493433 644498233 4800 True 2583.033333 6815 96.2580 1 5190 3 chr2D.!!$R1 5189
2 TraesCS2A01G574800 chr2B 791018976 791022768 3792 False 6320.000000 6320 96.6710 976 4788 1 chr2B.!!$F1 3812
3 TraesCS2A01G574800 chr2B 791009445 791010307 862 False 587.000000 968 91.6815 1 978 2 chr2B.!!$F4 977
4 TraesCS2A01G574800 chr1B 677528276 677529656 1380 False 562.000000 562 74.3610 2233 3625 1 chr1B.!!$F4 1392
5 TraesCS2A01G574800 chr3A 12673014 12675370 2356 False 309.000000 309 98.8440 4457 4629 2 chr3A.!!$F1 172

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
162 200 0.100861 CTAAGGGAGCGTTCGGAGTC 59.899 60.000 0.00 0.00 0.00 3.36 F
301 339 0.176910 GCCTGGAGAGCAGGTTCTAC 59.823 60.000 0.00 0.00 41.73 2.59 F
1181 1236 0.320771 ACAGGGTCATCTCGTTGCAC 60.321 55.000 0.00 0.00 0.00 4.57 F
2329 2384 1.021202 TGGCAATATACCAAGCACGC 58.979 50.000 0.00 0.00 33.12 5.34 F
3009 3064 1.145738 ACAACATCCAGACAAGGCCTT 59.854 47.619 13.78 13.78 0.00 4.35 F
4034 4090 2.738846 CTCAAAAGTGACCATCAGACCG 59.261 50.000 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 1216 0.320683 TGCAACGAGATGACCCTGTG 60.321 55.000 0.00 0.0 0.00 3.66 R
1311 1366 1.159285 TGAGCAATTGAAGTCTGCCG 58.841 50.000 10.34 0.0 36.73 5.69 R
3134 3189 3.380004 CACCTTCACTGCAACAAGGTTTA 59.620 43.478 17.21 0.0 46.48 2.01 R
3890 3946 1.555533 AGTGGGCCTCTTAGCAGTTAC 59.444 52.381 4.53 0.0 0.00 2.50 R
4120 4176 1.656652 CCCGTGTTGGCATTCTAGAG 58.343 55.000 0.00 0.0 35.87 2.43 R
5064 5123 2.159421 CCAAACATCAGTGCTCTGCATC 60.159 50.000 10.95 0.0 41.91 3.91 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
152 190 5.810080 ATAATCAGTACCACTAAGGGAGC 57.190 43.478 0.00 0.00 43.89 4.70
153 191 1.471119 TCAGTACCACTAAGGGAGCG 58.529 55.000 0.00 0.00 43.89 5.03
154 192 1.183549 CAGTACCACTAAGGGAGCGT 58.816 55.000 0.00 0.00 43.89 5.07
156 194 1.823610 AGTACCACTAAGGGAGCGTTC 59.176 52.381 0.00 0.00 43.89 3.95
157 195 0.813184 TACCACTAAGGGAGCGTTCG 59.187 55.000 0.00 0.00 43.89 3.95
158 196 1.153628 CCACTAAGGGAGCGTTCGG 60.154 63.158 0.00 0.00 0.00 4.30
162 200 0.100861 CTAAGGGAGCGTTCGGAGTC 59.899 60.000 0.00 0.00 0.00 3.36
163 201 1.318158 TAAGGGAGCGTTCGGAGTCC 61.318 60.000 0.00 0.00 0.00 3.85
166 204 2.490685 GAGCGTTCGGAGTCCCTC 59.509 66.667 2.80 0.00 0.00 4.30
167 205 3.066233 GAGCGTTCGGAGTCCCTCC 62.066 68.421 2.80 0.00 46.44 4.30
176 214 2.363147 AGTCCCTCCGCTCCAGAC 60.363 66.667 0.00 0.00 0.00 3.51
178 216 2.043852 TCCCTCCGCTCCAGACTC 60.044 66.667 0.00 0.00 0.00 3.36
179 217 2.363018 CCCTCCGCTCCAGACTCA 60.363 66.667 0.00 0.00 0.00 3.41
180 218 2.422231 CCCTCCGCTCCAGACTCAG 61.422 68.421 0.00 0.00 0.00 3.35
181 219 2.493973 CTCCGCTCCAGACTCAGC 59.506 66.667 0.00 0.00 0.00 4.26
183 221 2.003658 CTCCGCTCCAGACTCAGCTC 62.004 65.000 0.00 0.00 33.09 4.09
185 223 2.202730 GCTCCAGACTCAGCTCGC 60.203 66.667 0.00 0.00 32.48 5.03
186 224 2.101965 CTCCAGACTCAGCTCGCG 59.898 66.667 0.00 0.00 0.00 5.87
187 225 3.408501 CTCCAGACTCAGCTCGCGG 62.409 68.421 6.13 0.00 0.00 6.46
189 227 2.101965 CAGACTCAGCTCGCGGAG 59.898 66.667 15.76 15.76 42.51 4.63
209 247 3.543680 GCTGTAGGCTGAAATAGTGGA 57.456 47.619 0.00 0.00 38.06 4.02
210 248 3.462021 GCTGTAGGCTGAAATAGTGGAG 58.538 50.000 0.00 0.00 38.06 3.86
211 249 3.462021 CTGTAGGCTGAAATAGTGGAGC 58.538 50.000 0.00 0.00 0.00 4.70
213 251 2.706339 AGGCTGAAATAGTGGAGCTG 57.294 50.000 0.00 0.00 0.00 4.24
215 253 1.210478 GGCTGAAATAGTGGAGCTGGA 59.790 52.381 0.00 0.00 0.00 3.86
217 255 3.347216 GCTGAAATAGTGGAGCTGGAAA 58.653 45.455 0.00 0.00 0.00 3.13
219 257 4.400567 GCTGAAATAGTGGAGCTGGAAAAT 59.599 41.667 0.00 0.00 0.00 1.82
222 260 5.584649 TGAAATAGTGGAGCTGGAAAATACG 59.415 40.000 0.00 0.00 0.00 3.06
223 261 4.755266 ATAGTGGAGCTGGAAAATACGT 57.245 40.909 0.00 0.00 0.00 3.57
224 262 2.699954 AGTGGAGCTGGAAAATACGTG 58.300 47.619 0.00 0.00 0.00 4.49
225 263 1.130561 GTGGAGCTGGAAAATACGTGC 59.869 52.381 0.00 0.00 0.00 5.34
226 264 1.003118 TGGAGCTGGAAAATACGTGCT 59.997 47.619 0.00 0.00 0.00 4.40
227 265 1.666189 GGAGCTGGAAAATACGTGCTC 59.334 52.381 10.76 10.76 44.08 4.26
228 266 1.666189 GAGCTGGAAAATACGTGCTCC 59.334 52.381 8.60 4.91 40.44 4.70
229 267 1.003118 AGCTGGAAAATACGTGCTCCA 59.997 47.619 0.00 3.95 36.53 3.86
230 268 1.130561 GCTGGAAAATACGTGCTCCAC 59.869 52.381 0.00 0.00 34.28 4.02
231 269 2.422597 CTGGAAAATACGTGCTCCACA 58.577 47.619 0.00 0.00 34.28 4.17
232 270 2.416547 CTGGAAAATACGTGCTCCACAG 59.583 50.000 0.00 0.00 34.28 3.66
233 271 2.037902 TGGAAAATACGTGCTCCACAGA 59.962 45.455 0.00 0.00 32.97 3.41
234 272 3.270877 GGAAAATACGTGCTCCACAGAT 58.729 45.455 0.00 0.00 33.40 2.90
235 273 3.309954 GGAAAATACGTGCTCCACAGATC 59.690 47.826 0.00 0.00 33.40 2.75
236 274 2.604046 AATACGTGCTCCACAGATCC 57.396 50.000 0.00 0.00 33.40 3.36
237 275 0.385751 ATACGTGCTCCACAGATCCG 59.614 55.000 0.00 0.00 33.40 4.18
238 276 0.963856 TACGTGCTCCACAGATCCGT 60.964 55.000 0.00 0.00 33.40 4.69
239 277 1.807165 CGTGCTCCACAGATCCGTG 60.807 63.158 1.81 1.81 33.40 4.94
245 283 4.919653 CACAGATCCGTGGAGGTG 57.080 61.111 0.76 0.00 41.99 4.00
246 284 1.219124 CACAGATCCGTGGAGGTGG 59.781 63.158 0.76 0.00 41.99 4.61
247 285 1.078528 ACAGATCCGTGGAGGTGGA 59.921 57.895 0.00 0.00 41.99 4.02
248 286 0.972983 ACAGATCCGTGGAGGTGGAG 60.973 60.000 0.00 0.00 41.99 3.86
250 288 2.039624 ATCCGTGGAGGTGGAGCT 59.960 61.111 0.00 0.00 41.99 4.09
251 289 2.303549 GATCCGTGGAGGTGGAGCTG 62.304 65.000 0.00 0.00 37.68 4.24
252 290 4.087892 CCGTGGAGGTGGAGCTGG 62.088 72.222 0.00 0.00 34.51 4.85
253 291 4.767255 CGTGGAGGTGGAGCTGGC 62.767 72.222 0.00 0.00 0.00 4.85
254 292 4.767255 GTGGAGGTGGAGCTGGCG 62.767 72.222 0.00 0.00 0.00 5.69
257 295 3.706373 GAGGTGGAGCTGGCGGAA 61.706 66.667 0.00 0.00 0.00 4.30
258 296 3.249189 AGGTGGAGCTGGCGGAAA 61.249 61.111 0.00 0.00 0.00 3.13
259 297 2.747855 GGTGGAGCTGGCGGAAAG 60.748 66.667 0.00 0.00 0.00 2.62
282 320 3.437049 CCGAACAGGCCTTAAGAAAGAAG 59.563 47.826 0.00 0.00 34.37 2.85
301 339 0.176910 GCCTGGAGAGCAGGTTCTAC 59.823 60.000 0.00 0.00 41.73 2.59
327 365 2.094854 ACTAGACGCCCAAAGTCTAACG 60.095 50.000 0.00 0.82 46.64 3.18
346 384 1.775344 CTACGTCACTGCTGCAACG 59.225 57.895 20.10 20.10 40.77 4.10
416 459 1.344438 CAGTGACAGGTTGCTCCTACA 59.656 52.381 1.02 3.14 46.24 2.74
652 695 5.523188 TGTGTGTTTTTCCATCAGATTTTGC 59.477 36.000 0.00 0.00 0.00 3.68
858 905 1.865865 AGTGTAGTGTTGCCTGTTCG 58.134 50.000 0.00 0.00 0.00 3.95
909 956 1.500474 CTTGTATCCTGGCTGAGGGA 58.500 55.000 2.89 0.00 43.06 4.20
924 978 4.262808 GCTGAGGGACATGCTACATCTAAT 60.263 45.833 0.00 0.00 0.00 1.73
936 991 2.572290 ACATCTAATTAGCGCCCCAAC 58.428 47.619 2.29 0.00 0.00 3.77
1038 1093 2.488355 CAAGGAGCAGCAATGCCG 59.512 61.111 0.00 0.00 34.90 5.69
1181 1236 0.320771 ACAGGGTCATCTCGTTGCAC 60.321 55.000 0.00 0.00 0.00 4.57
1686 1741 3.848975 ACATTTCCTCTCTGATGGGTCTT 59.151 43.478 0.00 0.00 0.00 3.01
2329 2384 1.021202 TGGCAATATACCAAGCACGC 58.979 50.000 0.00 0.00 33.12 5.34
2787 2842 3.308323 GTGTTTTTGCAAATTCTTCGGCA 59.692 39.130 13.65 1.24 0.00 5.69
3009 3064 1.145738 ACAACATCCAGACAAGGCCTT 59.854 47.619 13.78 13.78 0.00 4.35
3134 3189 6.059787 AGATGACCAAGCTGAAGAAAGTAT 57.940 37.500 0.00 0.00 0.00 2.12
3363 3418 6.785191 ACATCCTTATACAAATGAGCAAACG 58.215 36.000 0.00 0.00 0.00 3.60
3778 3833 6.648502 CAATGCGGATTTACAATTATTTGCC 58.351 36.000 0.00 0.00 36.22 4.52
3890 3946 4.515191 TCGGAATTCTTGTCTTGGAAACTG 59.485 41.667 5.23 0.00 0.00 3.16
4034 4090 2.738846 CTCAAAAGTGACCATCAGACCG 59.261 50.000 0.00 0.00 0.00 4.79
4120 4176 1.487976 TGCTCTCAGGAATCACCATCC 59.512 52.381 0.00 0.00 42.04 3.51
4200 4256 5.065090 TGTCAACACAATGAAGACTGTGAAG 59.935 40.000 9.06 1.77 44.68 3.02
4384 4443 4.860907 GTGGAATACGACGTCTGTTATGTT 59.139 41.667 14.70 6.86 0.00 2.71
4452 4511 2.833794 TGACTTGCTGGTGTTGTAGTC 58.166 47.619 0.00 0.00 34.17 2.59
4645 4704 8.751242 AGAAGTTTAGTCCCTGATTTACTACTC 58.249 37.037 0.00 0.00 0.00 2.59
4646 4705 7.421087 AGTTTAGTCCCTGATTTACTACTCC 57.579 40.000 0.00 0.00 0.00 3.85
4647 4706 7.190501 AGTTTAGTCCCTGATTTACTACTCCT 58.809 38.462 0.00 0.00 0.00 3.69
4648 4707 8.342270 AGTTTAGTCCCTGATTTACTACTCCTA 58.658 37.037 0.00 0.00 0.00 2.94
4649 4708 8.412456 GTTTAGTCCCTGATTTACTACTCCTAC 58.588 40.741 0.00 0.00 0.00 3.18
4650 4709 6.344232 AGTCCCTGATTTACTACTCCTACT 57.656 41.667 0.00 0.00 0.00 2.57
4663 4722 4.792521 ACTCCTACTTGTCAGTGATCAC 57.207 45.455 18.47 18.47 34.06 3.06
4667 4726 5.080337 TCCTACTTGTCAGTGATCACTCTT 58.920 41.667 25.58 2.45 40.20 2.85
4768 4827 6.073331 CCTTTTGACAGACTGAGATCAACTTC 60.073 42.308 10.08 0.00 30.99 3.01
4781 4840 1.202879 TCAACTTCATTTCCTGCGGGT 60.203 47.619 12.43 0.00 0.00 5.28
4788 4847 0.178975 ATTTCCTGCGGGTGTCCAAA 60.179 50.000 12.43 4.54 0.00 3.28
4789 4848 0.395862 TTTCCTGCGGGTGTCCAAAA 60.396 50.000 12.43 0.08 0.00 2.44
4850 4909 5.220681 GCTTCGTCCCATTAAAGACTGAATC 60.221 44.000 0.00 0.00 30.78 2.52
4879 4938 4.757149 GGTTGAAACAGTTGTCTGCTAGAT 59.243 41.667 0.00 0.00 44.77 1.98
4883 4942 3.407424 ACAGTTGTCTGCTAGATTGCA 57.593 42.857 0.00 0.00 44.77 4.08
4967 5026 4.438200 CGAGCGCTGGTTAACCATTTATTT 60.438 41.667 27.24 11.31 46.46 1.40
4978 5037 8.708742 GGTTAACCATTTATTTTTCTTGTGAGC 58.291 33.333 20.12 0.00 35.64 4.26
5141 5203 9.774742 GGTAATATAGTTCAGCACAAGAAAAAG 57.225 33.333 0.00 0.00 0.00 2.27
5175 5237 2.409975 ACACCGTGTAATCTTTGTCCG 58.590 47.619 1.18 0.00 0.00 4.79
5177 5239 3.005684 ACACCGTGTAATCTTTGTCCGTA 59.994 43.478 1.18 0.00 0.00 4.02
5181 5243 4.478699 CGTGTAATCTTTGTCCGTAGTGA 58.521 43.478 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 85 8.277713 GCACACAACTATCTTCGTTAAAGTAAA 58.722 33.333 0.00 0.00 36.31 2.01
53 87 6.924612 TGCACACAACTATCTTCGTTAAAGTA 59.075 34.615 0.00 0.00 36.31 2.24
148 186 3.069318 AGGGACTCCGAACGCTCC 61.069 66.667 0.00 0.00 38.33 4.70
162 200 2.363018 TGAGTCTGGAGCGGAGGG 60.363 66.667 0.00 0.00 0.00 4.30
163 201 3.074999 GCTGAGTCTGGAGCGGAGG 62.075 68.421 0.00 0.00 0.00 4.30
166 204 2.493973 GAGCTGAGTCTGGAGCGG 59.506 66.667 0.00 0.00 40.34 5.52
167 205 2.101965 CGAGCTGAGTCTGGAGCG 59.898 66.667 0.00 0.00 40.34 5.03
168 206 2.202730 GCGAGCTGAGTCTGGAGC 60.203 66.667 0.00 0.00 35.28 4.70
170 208 3.443925 CCGCGAGCTGAGTCTGGA 61.444 66.667 8.23 0.00 0.00 3.86
171 209 3.408501 CTCCGCGAGCTGAGTCTGG 62.409 68.421 8.23 0.00 0.00 3.86
189 227 3.462021 CTCCACTATTTCAGCCTACAGC 58.538 50.000 0.00 0.00 44.25 4.40
191 229 3.107601 AGCTCCACTATTTCAGCCTACA 58.892 45.455 0.00 0.00 31.81 2.74
192 230 3.462021 CAGCTCCACTATTTCAGCCTAC 58.538 50.000 0.00 0.00 31.81 3.18
193 231 2.435805 CCAGCTCCACTATTTCAGCCTA 59.564 50.000 0.00 0.00 31.81 3.93
194 232 1.211457 CCAGCTCCACTATTTCAGCCT 59.789 52.381 0.00 0.00 31.81 4.58
196 234 2.698855 TCCAGCTCCACTATTTCAGC 57.301 50.000 0.00 0.00 0.00 4.26
198 236 5.584649 CGTATTTTCCAGCTCCACTATTTCA 59.415 40.000 0.00 0.00 0.00 2.69
199 237 5.585047 ACGTATTTTCCAGCTCCACTATTTC 59.415 40.000 0.00 0.00 0.00 2.17
200 238 5.354234 CACGTATTTTCCAGCTCCACTATTT 59.646 40.000 0.00 0.00 0.00 1.40
201 239 4.876107 CACGTATTTTCCAGCTCCACTATT 59.124 41.667 0.00 0.00 0.00 1.73
202 240 4.442706 CACGTATTTTCCAGCTCCACTAT 58.557 43.478 0.00 0.00 0.00 2.12
204 242 2.699954 CACGTATTTTCCAGCTCCACT 58.300 47.619 0.00 0.00 0.00 4.00
205 243 1.130561 GCACGTATTTTCCAGCTCCAC 59.869 52.381 0.00 0.00 0.00 4.02
206 244 1.003118 AGCACGTATTTTCCAGCTCCA 59.997 47.619 0.00 0.00 0.00 3.86
207 245 1.666189 GAGCACGTATTTTCCAGCTCC 59.334 52.381 8.60 0.00 41.83 4.70
208 246 1.666189 GGAGCACGTATTTTCCAGCTC 59.334 52.381 10.76 10.76 45.65 4.09
209 247 1.003118 TGGAGCACGTATTTTCCAGCT 59.997 47.619 5.66 0.00 34.90 4.24
210 248 1.130561 GTGGAGCACGTATTTTCCAGC 59.869 52.381 9.06 0.00 40.20 4.85
211 249 2.416547 CTGTGGAGCACGTATTTTCCAG 59.583 50.000 9.06 0.00 40.20 3.86
213 251 2.695359 TCTGTGGAGCACGTATTTTCC 58.305 47.619 0.00 0.00 37.14 3.13
215 253 3.270877 GGATCTGTGGAGCACGTATTTT 58.729 45.455 0.00 0.00 37.14 1.82
217 255 1.202417 CGGATCTGTGGAGCACGTATT 60.202 52.381 0.00 0.00 37.14 1.89
219 257 0.963856 ACGGATCTGTGGAGCACGTA 60.964 55.000 6.33 0.00 37.14 3.57
222 260 4.192000 CACGGATCTGTGGAGCAC 57.808 61.111 24.60 0.00 36.20 4.40
228 266 1.219124 CCACCTCCACGGATCTGTG 59.781 63.158 25.22 25.22 39.60 3.66
229 267 0.972983 CTCCACCTCCACGGATCTGT 60.973 60.000 0.00 0.00 36.31 3.41
230 268 1.819229 CTCCACCTCCACGGATCTG 59.181 63.158 0.00 0.00 36.31 2.90
231 269 2.060980 GCTCCACCTCCACGGATCT 61.061 63.158 0.00 0.00 36.31 2.75
232 270 2.060980 AGCTCCACCTCCACGGATC 61.061 63.158 0.00 0.00 36.31 3.36
233 271 2.039624 AGCTCCACCTCCACGGAT 59.960 61.111 0.00 0.00 36.31 4.18
234 272 2.997315 CAGCTCCACCTCCACGGA 60.997 66.667 0.00 0.00 36.31 4.69
235 273 4.087892 CCAGCTCCACCTCCACGG 62.088 72.222 0.00 0.00 39.35 4.94
236 274 4.767255 GCCAGCTCCACCTCCACG 62.767 72.222 0.00 0.00 0.00 4.94
237 275 4.767255 CGCCAGCTCCACCTCCAC 62.767 72.222 0.00 0.00 0.00 4.02
240 278 3.254024 TTTCCGCCAGCTCCACCTC 62.254 63.158 0.00 0.00 0.00 3.85
241 279 3.249189 TTTCCGCCAGCTCCACCT 61.249 61.111 0.00 0.00 0.00 4.00
242 280 2.747855 CTTTCCGCCAGCTCCACC 60.748 66.667 0.00 0.00 0.00 4.61
243 281 3.435186 GCTTTCCGCCAGCTCCAC 61.435 66.667 0.00 0.00 34.15 4.02
261 299 3.120165 GCTTCTTTCTTAAGGCCTGTTCG 60.120 47.826 5.69 0.00 32.02 3.95
262 300 3.191581 GGCTTCTTTCTTAAGGCCTGTTC 59.808 47.826 5.69 0.00 42.12 3.18
263 301 3.157881 GGCTTCTTTCTTAAGGCCTGTT 58.842 45.455 5.69 0.00 42.12 3.16
268 306 3.013219 CTCCAGGCTTCTTTCTTAAGGC 58.987 50.000 1.85 0.00 46.75 4.35
269 307 4.512484 CTCTCCAGGCTTCTTTCTTAAGG 58.488 47.826 1.85 0.00 32.02 2.69
270 308 3.938334 GCTCTCCAGGCTTCTTTCTTAAG 59.062 47.826 0.00 0.00 0.00 1.85
271 309 3.327757 TGCTCTCCAGGCTTCTTTCTTAA 59.672 43.478 0.00 0.00 0.00 1.85
272 310 2.906389 TGCTCTCCAGGCTTCTTTCTTA 59.094 45.455 0.00 0.00 0.00 2.10
273 311 1.701847 TGCTCTCCAGGCTTCTTTCTT 59.298 47.619 0.00 0.00 0.00 2.52
274 312 1.278699 CTGCTCTCCAGGCTTCTTTCT 59.721 52.381 0.00 0.00 37.93 2.52
301 339 3.119101 AGACTTTGGGCGTCTAGTGTATG 60.119 47.826 0.00 0.00 39.80 2.39
327 365 1.493311 GTTGCAGCAGTGACGTAGC 59.507 57.895 0.00 0.00 0.00 3.58
346 384 1.960689 TCTAGTTTTGTTTGCCCTGCC 59.039 47.619 0.00 0.00 0.00 4.85
352 390 5.220397 GCCTTTGTTGTCTAGTTTTGTTTGC 60.220 40.000 0.00 0.00 0.00 3.68
357 395 5.281727 GGAAGCCTTTGTTGTCTAGTTTTG 58.718 41.667 0.00 0.00 0.00 2.44
392 430 1.604278 GGAGCAACCTGTCACTGTTTC 59.396 52.381 0.00 0.00 35.41 2.78
416 459 9.524106 CATATGTTTTGCTTGTTGTGATGATAT 57.476 29.630 0.00 0.00 0.00 1.63
592 635 7.977853 GTCATCCGTAGAGGTCTGTAAATTTTA 59.022 37.037 0.00 0.00 41.99 1.52
705 748 7.803279 AGACCTACTTGAAAGTTACAAAAGG 57.197 36.000 0.21 3.76 40.37 3.11
886 933 1.139853 CTCAGCCAGGATACAAGGGAC 59.860 57.143 0.00 0.00 41.41 4.46
909 956 3.997021 GGCGCTAATTAGATGTAGCATGT 59.003 43.478 16.85 0.00 42.39 3.21
924 978 0.109723 AGAACAAGTTGGGGCGCTAA 59.890 50.000 7.64 0.00 0.00 3.09
936 991 0.038744 ACCCTGGCCATGAGAACAAG 59.961 55.000 5.51 0.00 0.00 3.16
1043 1098 3.404141 GAGGAGTGCGAGCTCGTCC 62.404 68.421 34.46 30.90 41.74 4.79
1161 1216 0.320683 TGCAACGAGATGACCCTGTG 60.321 55.000 0.00 0.00 0.00 3.66
1181 1236 2.295885 GACAGATTGAAGGAGCCCATG 58.704 52.381 0.00 0.00 0.00 3.66
1308 1363 1.160137 GCAATTGAAGTCTGCCGAGT 58.840 50.000 10.34 0.00 0.00 4.18
1309 1364 1.396301 GAGCAATTGAAGTCTGCCGAG 59.604 52.381 10.34 0.00 36.73 4.63
1310 1365 1.270785 TGAGCAATTGAAGTCTGCCGA 60.271 47.619 10.34 0.00 36.73 5.54
1311 1366 1.159285 TGAGCAATTGAAGTCTGCCG 58.841 50.000 10.34 0.00 36.73 5.69
1312 1367 2.555757 AGTTGAGCAATTGAAGTCTGCC 59.444 45.455 10.34 0.00 36.73 4.85
1313 1368 3.911661 AGTTGAGCAATTGAAGTCTGC 57.088 42.857 10.34 0.00 36.29 4.26
1314 1369 5.855395 GCTAAAGTTGAGCAATTGAAGTCTG 59.145 40.000 10.34 0.00 39.84 3.51
1460 1515 6.567687 TGGATAAAAACAAGAATTCGAGCA 57.432 33.333 0.00 0.00 0.00 4.26
1845 1900 2.621763 AGTGCCGCTGAAGAAGTTG 58.378 52.632 0.00 0.00 0.00 3.16
2329 2384 4.086706 ACAACTTGGTCAGGTTTCCTAG 57.913 45.455 0.00 0.00 33.95 3.02
2759 2814 5.233957 AGAATTTGCAAAAACACCAAAGC 57.766 34.783 17.19 0.00 32.65 3.51
2787 2842 7.499895 AGTTTGCCATTGTTTTCAATTGAGATT 59.500 29.630 8.41 0.00 46.94 2.40
2827 2882 3.828875 AGGAGGCAAATGTAGAGTAGC 57.171 47.619 0.00 0.00 0.00 3.58
3009 3064 6.095860 CCAACTGCAAATAAGAGATCATTGGA 59.904 38.462 0.00 0.00 34.87 3.53
3134 3189 3.380004 CACCTTCACTGCAACAAGGTTTA 59.620 43.478 17.21 0.00 46.48 2.01
3363 3418 7.612244 TGAAGTAGATCTAGGTACATATGCTCC 59.388 40.741 1.64 5.66 0.00 4.70
3752 3807 6.648502 CAAATAATTGTAAATCCGCATTGCC 58.351 36.000 2.41 0.00 0.00 4.52
3890 3946 1.555533 AGTGGGCCTCTTAGCAGTTAC 59.444 52.381 4.53 0.00 0.00 2.50
4060 4116 2.571212 ACTGAAACGAGGCAATCAACA 58.429 42.857 0.00 0.00 0.00 3.33
4120 4176 1.656652 CCCGTGTTGGCATTCTAGAG 58.343 55.000 0.00 0.00 35.87 2.43
4452 4511 2.732844 AGGAACGGAGGGAGTACTAG 57.267 55.000 0.00 0.00 0.00 2.57
4645 4704 5.047731 TCAAGAGTGATCACTGACAAGTAGG 60.048 44.000 32.50 11.05 42.66 3.18
4646 4705 6.018589 TCAAGAGTGATCACTGACAAGTAG 57.981 41.667 32.50 12.80 42.66 2.57
4647 4706 6.405278 TTCAAGAGTGATCACTGACAAGTA 57.595 37.500 32.50 6.92 42.66 2.24
4648 4707 4.944619 TCAAGAGTGATCACTGACAAGT 57.055 40.909 32.50 7.19 42.66 3.16
4649 4708 6.609237 TTTTCAAGAGTGATCACTGACAAG 57.391 37.500 32.50 16.49 42.66 3.16
4650 4709 6.599244 AGTTTTTCAAGAGTGATCACTGACAA 59.401 34.615 32.50 19.32 42.66 3.18
4663 4722 7.553881 TGACAAGGAGTTAGTTTTTCAAGAG 57.446 36.000 0.00 0.00 0.00 2.85
4667 4726 4.272504 CGCTGACAAGGAGTTAGTTTTTCA 59.727 41.667 0.00 0.00 36.30 2.69
4716 4775 7.516198 AAACATGTTTAACTCAGCTCTTGAT 57.484 32.000 22.10 0.00 34.68 2.57
4781 4840 5.124776 CCTTAATTAGCATCGGTTTTGGACA 59.875 40.000 0.00 0.00 0.00 4.02
4788 4847 5.353394 TCAGACCTTAATTAGCATCGGTT 57.647 39.130 0.00 0.00 0.00 4.44
4789 4848 5.104900 AGTTCAGACCTTAATTAGCATCGGT 60.105 40.000 0.00 0.00 0.00 4.69
4850 4909 3.885297 AGACAACTGTTTCAACCATGGAG 59.115 43.478 21.47 10.83 0.00 3.86
4879 4938 7.287696 TCCATCTGATCATAGTAGTAGTTGCAA 59.712 37.037 0.00 0.00 0.00 4.08
4967 5026 5.234329 CAGAAACGAGTTAGCTCACAAGAAA 59.766 40.000 7.41 0.00 41.71 2.52
4978 5037 5.404366 TCAACGGAAATCAGAAACGAGTTAG 59.596 40.000 0.00 0.00 0.00 2.34
5064 5123 2.159421 CCAAACATCAGTGCTCTGCATC 60.159 50.000 10.95 0.00 41.91 3.91
5141 5203 4.616953 ACACGGTGTTCCAATGATTTTTC 58.383 39.130 8.21 0.00 0.00 2.29
5142 5204 4.664150 ACACGGTGTTCCAATGATTTTT 57.336 36.364 8.21 0.00 0.00 1.94
5143 5205 5.776173 TTACACGGTGTTCCAATGATTTT 57.224 34.783 20.15 0.00 0.00 1.82
5144 5206 5.710099 AGATTACACGGTGTTCCAATGATTT 59.290 36.000 20.15 0.00 0.00 2.17
5145 5207 5.253330 AGATTACACGGTGTTCCAATGATT 58.747 37.500 20.15 0.00 0.00 2.57
5146 5208 4.843728 AGATTACACGGTGTTCCAATGAT 58.156 39.130 20.15 2.06 0.00 2.45


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

AutoCloner maintained by Alex Coulton.