Multiple sequence alignment - TraesCS5A01G144100

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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 TraesCS5A01G144100 chr5A 100.000 2867 0 0 1 2867 320214566 320211700 0.000000e+00 5295.0
1 TraesCS5A01G144100 chr5B 93.997 2249 100 16 322 2553 270438815 270436585 0.000000e+00 3373.0
2 TraesCS5A01G144100 chr5B 91.575 273 12 5 2569 2831 270436599 270436328 1.620000e-97 366.0
3 TraesCS5A01G144100 chr5B 88.757 169 6 4 2 163 270438976 270438814 8.110000e-46 195.0
4 TraesCS5A01G144100 chr5B 100.000 37 0 0 2831 2867 270436310 270436274 5.130000e-08 69.4
5 TraesCS5A01G144100 chr5B 100.000 32 0 0 2423 2454 696593809 696593778 3.080000e-05 60.2
6 TraesCS5A01G144100 chr5D 92.601 2230 113 19 322 2532 234145205 234147401 0.000000e+00 3157.0
7 TraesCS5A01G144100 chr5D 90.809 272 14 5 2569 2831 234149174 234149443 1.260000e-93 353.0
8 TraesCS5A01G144100 chr5D 87.097 217 21 1 2249 2458 4029928 4030144 3.690000e-59 239.0
9 TraesCS5A01G144100 chr5D 93.827 162 4 2 2 163 234145051 234145206 3.690000e-59 239.0
10 TraesCS5A01G144100 chr7B 85.324 695 63 14 805 1465 531654994 531655683 0.000000e+00 682.0
11 TraesCS5A01G144100 chr7B 83.858 731 96 14 1508 2233 531655917 531656630 0.000000e+00 676.0
12 TraesCS5A01G144100 chr7B 87.500 216 19 2 2249 2456 384201090 384201305 2.850000e-60 243.0
13 TraesCS5A01G144100 chr7B 84.507 142 20 2 420 559 531654002 531654143 3.850000e-29 139.0
14 TraesCS5A01G144100 chr7B 85.156 128 14 2 325 451 531650594 531650717 3.000000e-25 126.0
15 TraesCS5A01G144100 chr7D 85.057 696 64 14 805 1465 502873659 502874349 0.000000e+00 673.0
16 TraesCS5A01G144100 chr7D 83.817 723 101 11 1517 2233 502874618 502875330 0.000000e+00 673.0
17 TraesCS5A01G144100 chr7D 97.006 167 5 0 158 324 397555081 397554915 6.050000e-72 281.0
18 TraesCS5A01G144100 chr7D 86.636 217 17 5 2249 2456 388997442 388997655 2.220000e-56 230.0
19 TraesCS5A01G144100 chr7D 85.315 143 15 5 420 559 502872661 502872800 2.980000e-30 143.0
20 TraesCS5A01G144100 chr7A 85.643 599 60 12 888 1465 570113205 570113798 8.790000e-170 606.0
21 TraesCS5A01G144100 chr7A 83.463 514 67 10 1508 2019 570114178 570114675 2.010000e-126 462.0
22 TraesCS5A01G144100 chr7A 84.024 169 20 4 325 491 570111919 570112082 3.820000e-34 156.0
23 TraesCS5A01G144100 chr7A 85.000 120 16 2 442 559 570112188 570112307 1.400000e-23 121.0
24 TraesCS5A01G144100 chr3D 96.491 171 5 1 158 327 87926166 87925996 6.050000e-72 281.0
25 TraesCS5A01G144100 chr3A 94.536 183 8 2 143 324 600923060 600923241 6.050000e-72 281.0
26 TraesCS5A01G144100 chr3A 86.341 205 18 5 2258 2455 479138421 479138220 6.220000e-52 215.0
27 TraesCS5A01G144100 chr2A 95.954 173 6 1 162 333 184561154 184561326 2.180000e-71 279.0
28 TraesCS5A01G144100 chr2A 95.758 165 6 1 162 326 367649161 367649324 6.090000e-67 265.0
29 TraesCS5A01G144100 chr3B 95.402 174 6 2 159 331 654649708 654649880 2.810000e-70 276.0
30 TraesCS5A01G144100 chr3B 81.776 214 31 3 2251 2457 4460924 4461136 3.800000e-39 172.0
31 TraesCS5A01G144100 chr2D 96.970 165 4 1 162 326 296364049 296364212 2.810000e-70 276.0
32 TraesCS5A01G144100 chr2D 83.190 232 27 7 2249 2470 428709939 428710168 4.840000e-48 202.0
33 TraesCS5A01G144100 chr2B 93.194 191 8 4 162 350 366017679 366017492 2.810000e-70 276.0
34 TraesCS5A01G144100 chr4B 95.402 174 5 2 158 331 532435166 532434996 1.010000e-69 274.0
35 TraesCS5A01G144100 chr4B 86.636 217 21 3 2250 2458 183525198 183524982 1.720000e-57 233.0
36 TraesCS5A01G144100 chr6B 87.215 219 17 4 2249 2458 650790932 650791148 3.690000e-59 239.0
37 TraesCS5A01G144100 chr6B 74.107 224 35 17 2252 2458 633050788 633051005 1.430000e-08 71.3
38 TraesCS5A01G144100 chr1D 84.507 213 27 1 2249 2455 147883291 147883503 3.740000e-49 206.0
39 TraesCS5A01G144100 chrUn 100.000 32 0 0 2423 2454 363221596 363221627 3.080000e-05 60.2


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 TraesCS5A01G144100 chr5A 320211700 320214566 2866 True 5295.000000 5295 100.000000 1 2867 1 chr5A.!!$R1 2866
1 TraesCS5A01G144100 chr5B 270436274 270438976 2702 True 1000.850000 3373 93.582250 2 2867 4 chr5B.!!$R2 2865
2 TraesCS5A01G144100 chr5D 234145051 234149443 4392 False 1249.666667 3157 92.412333 2 2831 3 chr5D.!!$F2 2829
3 TraesCS5A01G144100 chr7B 531650594 531656630 6036 False 405.750000 682 84.711250 325 2233 4 chr7B.!!$F2 1908
4 TraesCS5A01G144100 chr7D 502872661 502875330 2669 False 496.333333 673 84.729667 420 2233 3 chr7D.!!$F2 1813
5 TraesCS5A01G144100 chr7A 570111919 570114675 2756 False 336.250000 606 84.532500 325 2019 4 chr7A.!!$F1 1694

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
515 3957 0.60864 TTGAACTCTTCTCCGAGGGC 59.391 55.0 0.0 0.0 35.33 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 6683 0.321387 ATGCATAGCTCGCCTGATGG 60.321 55.0 0.0 0.0 0.0 3.51 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
103 111 9.777575 AAGCAAAAGAAACTTGAATTGAATTTG 57.222 25.926 0.00 0.00 0.00 2.32
104 112 9.165035 AGCAAAAGAAACTTGAATTGAATTTGA 57.835 25.926 4.12 0.00 0.00 2.69
105 113 9.771915 GCAAAAGAAACTTGAATTGAATTTGAA 57.228 25.926 4.12 0.00 0.00 2.69
155 163 7.042523 CCAAATTTTGTAGCTGGAAGAACTTTG 60.043 37.037 8.26 2.02 34.07 2.77
161 169 6.303839 TGTAGCTGGAAGAACTTTGGTTTAT 58.696 36.000 0.00 0.00 35.58 1.40
162 170 7.455058 TGTAGCTGGAAGAACTTTGGTTTATA 58.545 34.615 0.00 0.00 35.58 0.98
163 171 6.819397 AGCTGGAAGAACTTTGGTTTATAC 57.181 37.500 0.00 0.00 35.58 1.47
164 172 6.543735 AGCTGGAAGAACTTTGGTTTATACT 58.456 36.000 0.00 0.00 35.58 2.12
165 173 6.655425 AGCTGGAAGAACTTTGGTTTATACTC 59.345 38.462 0.00 0.00 35.58 2.59
166 174 6.127980 GCTGGAAGAACTTTGGTTTATACTCC 60.128 42.308 0.00 0.00 35.58 3.85
167 175 6.243148 TGGAAGAACTTTGGTTTATACTCCC 58.757 40.000 0.00 0.00 35.58 4.30
168 176 6.045106 TGGAAGAACTTTGGTTTATACTCCCT 59.955 38.462 0.00 0.00 35.58 4.20
169 177 6.946583 GGAAGAACTTTGGTTTATACTCCCTT 59.053 38.462 0.00 0.00 35.58 3.95
170 178 7.120873 GGAAGAACTTTGGTTTATACTCCCTTC 59.879 40.741 0.00 0.00 35.58 3.46
171 179 6.171213 AGAACTTTGGTTTATACTCCCTTCG 58.829 40.000 0.00 0.00 35.58 3.79
172 180 5.494390 ACTTTGGTTTATACTCCCTTCGT 57.506 39.130 0.00 0.00 0.00 3.85
173 181 5.872963 ACTTTGGTTTATACTCCCTTCGTT 58.127 37.500 0.00 0.00 0.00 3.85
174 182 5.936372 ACTTTGGTTTATACTCCCTTCGTTC 59.064 40.000 0.00 0.00 0.00 3.95
175 183 4.476628 TGGTTTATACTCCCTTCGTTCC 57.523 45.455 0.00 0.00 0.00 3.62
176 184 4.098894 TGGTTTATACTCCCTTCGTTCCT 58.901 43.478 0.00 0.00 0.00 3.36
177 185 5.271598 TGGTTTATACTCCCTTCGTTCCTA 58.728 41.667 0.00 0.00 0.00 2.94
178 186 5.721000 TGGTTTATACTCCCTTCGTTCCTAA 59.279 40.000 0.00 0.00 0.00 2.69
179 187 6.213195 TGGTTTATACTCCCTTCGTTCCTAAA 59.787 38.462 0.00 0.00 0.00 1.85
180 188 7.092757 TGGTTTATACTCCCTTCGTTCCTAAAT 60.093 37.037 0.00 0.00 0.00 1.40
181 189 8.424133 GGTTTATACTCCCTTCGTTCCTAAATA 58.576 37.037 0.00 0.00 0.00 1.40
182 190 9.993454 GTTTATACTCCCTTCGTTCCTAAATAT 57.007 33.333 0.00 0.00 0.00 1.28
186 194 7.672122 ACTCCCTTCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
187 195 7.724287 ACTCCCTTCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
188 196 7.564292 ACTCCCTTCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
189 197 8.315220 TCCCTTCGTTCCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
190 198 8.765517 TCCCTTCGTTCCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
191 199 9.392259 CCCTTCGTTCCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
219 227 8.307483 AGAGATTTCAATATGGACTACATACGG 58.693 37.037 0.00 0.00 44.41 4.02
220 228 8.190326 AGATTTCAATATGGACTACATACGGA 57.810 34.615 0.00 0.00 44.41 4.69
221 229 8.816894 AGATTTCAATATGGACTACATACGGAT 58.183 33.333 0.00 0.00 44.41 4.18
222 230 8.777865 ATTTCAATATGGACTACATACGGATG 57.222 34.615 5.94 5.94 44.41 3.51
224 232 8.411991 TTCAATATGGACTACATACGGATGTA 57.588 34.615 19.32 19.32 44.77 2.29
225 233 8.589701 TCAATATGGACTACATACGGATGTAT 57.410 34.615 20.64 9.39 45.42 2.29
226 234 9.689501 TCAATATGGACTACATACGGATGTATA 57.310 33.333 20.64 11.30 45.42 1.47
231 239 8.728337 TGGACTACATACGGATGTATATAGAC 57.272 38.462 20.64 10.95 45.42 2.59
232 240 8.323567 TGGACTACATACGGATGTATATAGACA 58.676 37.037 20.64 12.12 45.42 3.41
233 241 9.339850 GGACTACATACGGATGTATATAGACAT 57.660 37.037 20.64 12.70 45.42 3.06
264 272 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
265 273 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
266 274 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
267 275 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
268 276 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
269 277 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
270 278 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
271 279 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
272 280 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
273 281 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
274 282 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
275 283 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
276 284 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
277 285 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
278 286 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
279 287 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
280 288 5.801531 TTTGCTCCGTATGTAGTCCATAT 57.198 39.130 0.00 0.00 38.29 1.78
281 289 5.801531 TTGCTCCGTATGTAGTCCATATT 57.198 39.130 0.00 0.00 38.29 1.28
282 290 5.134202 TGCTCCGTATGTAGTCCATATTG 57.866 43.478 0.00 0.00 38.29 1.90
283 291 4.021456 TGCTCCGTATGTAGTCCATATTGG 60.021 45.833 0.00 0.00 38.29 3.16
284 292 4.219944 GCTCCGTATGTAGTCCATATTGGA 59.780 45.833 0.00 0.00 45.98 3.53
317 325 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
318 326 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
319 327 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
320 328 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
369 377 8.908786 TCTGTTCTTCTTCTACATGTTCATTT 57.091 30.769 2.30 0.00 0.00 2.32
391 399 2.690173 TTGGTTCCAAATTACACGCG 57.310 45.000 3.53 3.53 0.00 6.01
476 3917 6.086222 TGAAGAAAAATCTTGATAAGCGTGC 58.914 36.000 0.00 0.00 0.00 5.34
515 3957 0.608640 TTGAACTCTTCTCCGAGGGC 59.391 55.000 0.00 0.00 35.33 5.19
635 4079 7.448748 TGAAAACCTCCTTTGATTAGTAAGC 57.551 36.000 0.00 0.00 0.00 3.09
636 4080 7.231467 TGAAAACCTCCTTTGATTAGTAAGCT 58.769 34.615 0.00 0.00 0.00 3.74
793 5033 6.455360 ACATGTCATTGTCTTGACTGTTTT 57.545 33.333 0.00 0.00 45.07 2.43
797 5037 8.773645 CATGTCATTGTCTTGACTGTTTTAGTA 58.226 33.333 6.20 0.00 45.07 1.82
801 5041 9.391006 TCATTGTCTTGACTGTTTTAGTACTTT 57.609 29.630 0.00 0.00 40.53 2.66
854 5094 2.422127 GTCCTCAGTTTCTCTCCGAGAG 59.578 54.545 18.07 18.07 43.64 3.20
1176 5430 4.157105 AGCTCTCTTCTCTTCCTTTCGTAC 59.843 45.833 0.00 0.00 0.00 3.67
1239 5493 2.736670 ATGGTCTATTGTTCCTGGGC 57.263 50.000 0.00 0.00 0.00 5.36
1343 5604 9.883142 CTTCCAGTATGAATATTATCTTCCTCC 57.117 37.037 0.00 0.00 39.69 4.30
1533 6174 8.458573 AAAAACAATGTCCACTTGTATCACTA 57.541 30.769 0.00 0.00 35.84 2.74
1552 6193 6.718294 TCACTAGAGTATGTGAGACAAGGTA 58.282 40.000 0.00 0.00 38.15 3.08
1555 6196 6.946583 ACTAGAGTATGTGAGACAAGGTACAA 59.053 38.462 0.00 0.00 0.00 2.41
1601 6243 5.920107 GCTATAGGCTCTTCCATTTTGGACA 60.920 44.000 1.04 0.00 41.44 4.02
1619 6261 2.597995 AAAACAGGCCCGTTTTGGT 58.402 47.368 25.51 5.31 45.09 3.67
1667 6309 7.335422 ACATAACTTTTCCTACTCTTCTGCATG 59.665 37.037 0.00 0.00 0.00 4.06
1673 6315 3.055819 TCCTACTCTTCTGCATGTCAACC 60.056 47.826 0.00 0.00 0.00 3.77
2047 6692 2.471255 GGAGTTGTTCCATCAGGCG 58.529 57.895 0.00 0.00 46.01 5.52
2053 6698 1.123077 TGTTCCATCAGGCGAGCTAT 58.877 50.000 0.00 0.00 33.74 2.97
2100 6747 1.591158 CTTGTGCTTTGCTTGCTTGTG 59.409 47.619 0.00 0.00 0.00 3.33
2270 6929 4.742012 TCCCCTTAGTATTTTGTGCCAAA 58.258 39.130 0.00 0.00 0.00 3.28
2275 6934 7.446931 CCCCTTAGTATTTTGTGCCAAATTTTT 59.553 33.333 1.89 0.00 0.00 1.94
2295 6954 6.548441 TTTTACCGTAGATTTGACCAACAG 57.452 37.500 0.00 0.00 0.00 3.16
2297 6956 3.926616 ACCGTAGATTTGACCAACAGAG 58.073 45.455 0.00 0.00 0.00 3.35
2462 7121 5.008811 CAGGACGGAGGTAGTACTTTATCTG 59.991 48.000 0.00 4.53 28.49 2.90
2487 7146 4.823442 AGTTTCTGTCAGTTGCATCAATCA 59.177 37.500 0.00 0.00 0.00 2.57
2545 8970 6.554982 ACTGTATCTAAGTATGCCAATCCTCA 59.445 38.462 0.00 0.00 0.00 3.86
2546 8971 6.759272 TGTATCTAAGTATGCCAATCCTCAC 58.241 40.000 0.00 0.00 0.00 3.51
2547 8972 4.689612 TCTAAGTATGCCAATCCTCACC 57.310 45.455 0.00 0.00 0.00 4.02
2548 8973 4.037222 TCTAAGTATGCCAATCCTCACCA 58.963 43.478 0.00 0.00 0.00 4.17
2549 8974 3.737559 AAGTATGCCAATCCTCACCAA 57.262 42.857 0.00 0.00 0.00 3.67
2550 8975 3.287867 AGTATGCCAATCCTCACCAAG 57.712 47.619 0.00 0.00 0.00 3.61
2551 8976 2.846206 AGTATGCCAATCCTCACCAAGA 59.154 45.455 0.00 0.00 0.00 3.02
2552 8977 3.461085 AGTATGCCAATCCTCACCAAGAT 59.539 43.478 0.00 0.00 0.00 2.40
2553 8978 4.660303 AGTATGCCAATCCTCACCAAGATA 59.340 41.667 0.00 0.00 0.00 1.98
2554 8979 4.524802 ATGCCAATCCTCACCAAGATAA 57.475 40.909 0.00 0.00 0.00 1.75
2555 8980 4.524802 TGCCAATCCTCACCAAGATAAT 57.475 40.909 0.00 0.00 0.00 1.28
2556 8981 4.870636 TGCCAATCCTCACCAAGATAATT 58.129 39.130 0.00 0.00 0.00 1.40
2557 8982 5.271598 TGCCAATCCTCACCAAGATAATTT 58.728 37.500 0.00 0.00 0.00 1.82
2558 8983 5.360714 TGCCAATCCTCACCAAGATAATTTC 59.639 40.000 0.00 0.00 0.00 2.17
2559 8984 5.360714 GCCAATCCTCACCAAGATAATTTCA 59.639 40.000 0.00 0.00 0.00 2.69
2560 8985 6.041296 GCCAATCCTCACCAAGATAATTTCAT 59.959 38.462 0.00 0.00 0.00 2.57
2561 8986 7.231317 GCCAATCCTCACCAAGATAATTTCATA 59.769 37.037 0.00 0.00 0.00 2.15
2562 8987 9.135189 CCAATCCTCACCAAGATAATTTCATAA 57.865 33.333 0.00 0.00 0.00 1.90
2652 9077 6.239487 CCGATACAATAGAATTCCCTGGTACA 60.239 42.308 0.65 0.00 0.00 2.90
2672 9097 9.617523 TGGTACATAATATGATTGATATGCCTG 57.382 33.333 7.33 0.00 30.61 4.85
2693 9118 6.202954 GCCTGTATATGTCATGTGAAAGGTAC 59.797 42.308 0.00 0.00 0.00 3.34
2694 9119 7.272244 CCTGTATATGTCATGTGAAAGGTACA 58.728 38.462 0.00 0.00 0.00 2.90
2695 9120 7.933577 CCTGTATATGTCATGTGAAAGGTACAT 59.066 37.037 0.00 0.00 39.23 2.29
2698 9123 5.801350 ATGTCATGTGAAAGGTACATTCG 57.199 39.130 0.00 0.00 39.09 3.34
2753 9188 5.133941 TGCAACACCTAGTTTATCAACCAA 58.866 37.500 0.00 0.00 38.74 3.67
2812 9247 5.727791 GCGATTATGTCACACATCAGTTTCC 60.728 44.000 0.00 0.00 39.88 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.854614 AGTGCTTCTTACATTTCAAAGTCTAT 57.145 30.769 0.00 0.00 0.00 1.98
102 110 9.897744 GATTCTCATAACAACTTTGAACATTCA 57.102 29.630 0.00 0.00 34.92 2.57
103 111 9.346725 GGATTCTCATAACAACTTTGAACATTC 57.653 33.333 0.00 0.00 0.00 2.67
104 112 8.306761 GGGATTCTCATAACAACTTTGAACATT 58.693 33.333 0.00 0.00 0.00 2.71
105 113 7.451255 TGGGATTCTCATAACAACTTTGAACAT 59.549 33.333 0.00 0.00 0.00 2.71
106 114 6.775142 TGGGATTCTCATAACAACTTTGAACA 59.225 34.615 0.00 0.00 0.00 3.18
155 163 4.750021 AGGAACGAAGGGAGTATAAACC 57.250 45.455 0.00 0.00 0.00 3.27
161 169 8.773033 ACTTATATTTAGGAACGAAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
162 170 7.564292 AGACTTATATTTAGGAACGAAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
163 171 7.953752 AGACTTATATTTAGGAACGAAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
164 172 7.909485 AGACTTATATTTAGGAACGAAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
165 173 8.959705 AAAGACTTATATTTAGGAACGAAGGG 57.040 34.615 0.00 0.00 0.00 3.95
193 201 8.307483 CCGTATGTAGTCCATATTGAAATCTCT 58.693 37.037 0.00 0.00 38.29 3.10
194 202 8.304596 TCCGTATGTAGTCCATATTGAAATCTC 58.695 37.037 0.00 0.00 38.29 2.75
195 203 8.190326 TCCGTATGTAGTCCATATTGAAATCT 57.810 34.615 0.00 0.00 38.29 2.40
196 204 8.873830 CATCCGTATGTAGTCCATATTGAAATC 58.126 37.037 0.00 0.00 38.29 2.17
197 205 8.375506 ACATCCGTATGTAGTCCATATTGAAAT 58.624 33.333 0.00 0.00 44.66 2.17
198 206 7.732025 ACATCCGTATGTAGTCCATATTGAAA 58.268 34.615 0.00 0.00 44.66 2.69
199 207 7.297936 ACATCCGTATGTAGTCCATATTGAA 57.702 36.000 0.00 0.00 44.66 2.69
200 208 6.911250 ACATCCGTATGTAGTCCATATTGA 57.089 37.500 0.00 0.00 44.66 2.57
242 250 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
243 251 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
244 252 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
245 253 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
246 254 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
247 255 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
248 256 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
249 257 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
250 258 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
251 259 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
252 260 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
253 261 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
254 262 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
255 263 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
256 264 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
257 265 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
258 266 5.801531 ATATGGACTACATACGGAGCAAA 57.198 39.130 0.00 0.00 44.41 3.68
259 267 5.510690 CCAATATGGACTACATACGGAGCAA 60.511 44.000 0.00 0.00 44.41 3.91
260 268 4.021456 CCAATATGGACTACATACGGAGCA 60.021 45.833 0.00 0.00 44.41 4.26
261 269 4.219944 TCCAATATGGACTACATACGGAGC 59.780 45.833 0.00 0.00 42.67 4.70
262 270 5.977489 TCCAATATGGACTACATACGGAG 57.023 43.478 0.00 0.00 42.67 4.63
291 299 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
292 300 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
293 301 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
294 302 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
295 303 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
296 304 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
297 305 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
298 306 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
299 307 7.731688 ACATACTCCCTCCGTTCCTAAATATAA 59.268 37.037 0.00 0.00 0.00 0.98
300 308 7.243824 ACATACTCCCTCCGTTCCTAAATATA 58.756 38.462 0.00 0.00 0.00 0.86
301 309 6.082707 ACATACTCCCTCCGTTCCTAAATAT 58.917 40.000 0.00 0.00 0.00 1.28
302 310 5.461327 ACATACTCCCTCCGTTCCTAAATA 58.539 41.667 0.00 0.00 0.00 1.40
303 311 4.296056 ACATACTCCCTCCGTTCCTAAAT 58.704 43.478 0.00 0.00 0.00 1.40
304 312 3.716431 ACATACTCCCTCCGTTCCTAAA 58.284 45.455 0.00 0.00 0.00 1.85
305 313 3.393426 ACATACTCCCTCCGTTCCTAA 57.607 47.619 0.00 0.00 0.00 2.69
306 314 4.736611 ATACATACTCCCTCCGTTCCTA 57.263 45.455 0.00 0.00 0.00 2.94
307 315 3.614568 ATACATACTCCCTCCGTTCCT 57.385 47.619 0.00 0.00 0.00 3.36
308 316 5.245526 ACATAATACATACTCCCTCCGTTCC 59.754 44.000 0.00 0.00 0.00 3.62
309 317 6.015688 TGACATAATACATACTCCCTCCGTTC 60.016 42.308 0.00 0.00 0.00 3.95
310 318 5.836898 TGACATAATACATACTCCCTCCGTT 59.163 40.000 0.00 0.00 0.00 4.44
311 319 5.391256 TGACATAATACATACTCCCTCCGT 58.609 41.667 0.00 0.00 0.00 4.69
312 320 5.977489 TGACATAATACATACTCCCTCCG 57.023 43.478 0.00 0.00 0.00 4.63
313 321 7.680730 ACATTGACATAATACATACTCCCTCC 58.319 38.462 0.00 0.00 0.00 4.30
314 322 9.561069 AAACATTGACATAATACATACTCCCTC 57.439 33.333 0.00 0.00 0.00 4.30
315 323 9.342308 CAAACATTGACATAATACATACTCCCT 57.658 33.333 0.00 0.00 0.00 4.20
316 324 9.120538 ACAAACATTGACATAATACATACTCCC 57.879 33.333 0.00 0.00 0.00 4.30
369 377 4.379603 CCGCGTGTAATTTGGAACCAATTA 60.380 41.667 4.92 5.93 35.70 1.40
371 379 2.094957 CCGCGTGTAATTTGGAACCAAT 60.095 45.455 4.92 0.00 35.70 3.16
391 399 1.134250 GCTCATCAGGAGTTCCTTCCC 60.134 57.143 0.00 0.00 46.09 3.97
471 3912 2.225491 TGTTAAATGACCAAGAGCACGC 59.775 45.455 0.00 0.00 0.00 5.34
476 3917 9.533253 AGTTCAAATTTGTTAAATGACCAAGAG 57.467 29.630 17.47 0.00 0.00 2.85
515 3957 4.944962 TTAGACATTTCCTGTGCAATCG 57.055 40.909 0.00 0.00 38.54 3.34
525 3967 6.678900 GCTTGATGTGGACATTAGACATTTCC 60.679 42.308 0.00 0.00 36.57 3.13
651 4095 7.629157 TGTGGTCATTAGTCTATGAATCCAAA 58.371 34.615 0.00 0.00 34.41 3.28
854 5094 8.758715 CAAATGAAAGAAACAGAGAAATTCCAC 58.241 33.333 0.00 0.00 0.00 4.02
1176 5430 5.928976 TCCATGTGACCTGTGGATATAAAG 58.071 41.667 0.00 0.00 37.12 1.85
1239 5493 2.097825 CCAGGAAGAAAGGCAAGGATG 58.902 52.381 0.00 0.00 0.00 3.51
1305 5566 8.641498 ATTCATACTGGAAGATGAAACAGTTT 57.359 30.769 0.00 0.00 41.03 2.66
1407 5683 1.518774 CCAGTGATGCAAATGGCCC 59.481 57.895 0.00 0.00 43.89 5.80
1533 6174 6.211584 ACATTGTACCTTGTCTCACATACTCT 59.788 38.462 0.00 0.00 0.00 3.24
1555 6196 9.730705 ATAGCAGCTAATGTTACATATCAACAT 57.269 29.630 6.13 6.44 46.05 2.71
1644 6286 6.769512 ACATGCAGAAGAGTAGGAAAAGTTA 58.230 36.000 0.00 0.00 0.00 2.24
1667 6309 2.031857 TGTTTTCCGCGTAATGGTTGAC 60.032 45.455 4.92 0.00 0.00 3.18
1673 6315 9.445786 AAGATAATATTTGTTTTCCGCGTAATG 57.554 29.630 4.92 0.00 0.00 1.90
1714 6356 7.617225 TGAAAAGTGGATCGGTTCTCTAAATA 58.383 34.615 0.00 0.00 0.00 1.40
1717 6359 5.477607 TGAAAAGTGGATCGGTTCTCTAA 57.522 39.130 0.00 0.00 0.00 2.10
1720 6362 4.610680 CGTTTGAAAAGTGGATCGGTTCTC 60.611 45.833 0.00 0.00 0.00 2.87
2038 6683 0.321387 ATGCATAGCTCGCCTGATGG 60.321 55.000 0.00 0.00 0.00 3.51
2100 6747 7.130917 CAGAAGTTCAATCTACATAGCAATGC 58.869 38.462 5.50 0.00 36.50 3.56
2197 6846 6.795098 TGTAGTATCTTCAACACGCAAAAT 57.205 33.333 0.00 0.00 0.00 1.82
2270 6929 7.446013 TCTGTTGGTCAAATCTACGGTAAAAAT 59.554 33.333 0.00 0.00 0.00 1.82
2275 6934 4.525487 ACTCTGTTGGTCAAATCTACGGTA 59.475 41.667 0.00 0.00 0.00 4.02
2462 7121 5.673337 TTGATGCAACTGACAGAAACTAC 57.327 39.130 10.08 0.00 0.00 2.73
2504 7163 6.212235 AGATACAGTTCAAGTATCAGCATCG 58.788 40.000 13.79 0.00 46.46 3.84
2565 8990 7.099120 GCATAACAATCTTGGTGAGGATTTTT 58.901 34.615 0.00 0.00 30.81 1.94
2566 8991 6.625740 CGCATAACAATCTTGGTGAGGATTTT 60.626 38.462 0.00 0.00 30.81 1.82
2567 8992 5.163622 CGCATAACAATCTTGGTGAGGATTT 60.164 40.000 0.00 0.00 30.81 2.17
2568 8993 4.336433 CGCATAACAATCTTGGTGAGGATT 59.664 41.667 0.00 0.00 33.09 3.01
2569 8994 3.879295 CGCATAACAATCTTGGTGAGGAT 59.121 43.478 0.00 0.00 0.00 3.24
2570 8995 3.055458 TCGCATAACAATCTTGGTGAGGA 60.055 43.478 0.00 0.00 0.00 3.71
2571 8996 3.270027 TCGCATAACAATCTTGGTGAGG 58.730 45.455 0.00 0.00 0.00 3.86
2572 8997 4.813161 AGATCGCATAACAATCTTGGTGAG 59.187 41.667 0.00 0.00 0.00 3.51
2573 8998 4.769688 AGATCGCATAACAATCTTGGTGA 58.230 39.130 0.00 0.00 0.00 4.02
2574 8999 5.490139 AAGATCGCATAACAATCTTGGTG 57.510 39.130 0.00 0.00 38.11 4.17
2672 9097 8.487970 CGAATGTACCTTTCACATGACATATAC 58.512 37.037 0.00 0.00 36.74 1.47
2693 9118 5.287513 AGAACGAAAACAAACAAACCGAATG 59.712 36.000 0.00 0.00 0.00 2.67
2694 9119 5.404096 AGAACGAAAACAAACAAACCGAAT 58.596 33.333 0.00 0.00 0.00 3.34
2695 9120 4.796369 AGAACGAAAACAAACAAACCGAA 58.204 34.783 0.00 0.00 0.00 4.30
2698 9123 6.976349 AGGATAAGAACGAAAACAAACAAACC 59.024 34.615 0.00 0.00 0.00 3.27
2753 9188 3.439857 TTCAGAATGGCAAACCTAGCT 57.560 42.857 0.00 0.00 36.16 3.32
2812 9247 1.067516 CAGAGTGCAAACAAACCCCTG 59.932 52.381 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.