Multiple sequence alignment - TraesCS6D01G298200

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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 TraesCS6D01G298200 chr6D 100.000 3204 0 0 1 3204 409286914 409290117 0.000000e+00 5917
1 TraesCS6D01G298200 chr6D 92.131 826 51 4 1393 2216 408945910 408946723 0.000000e+00 1153
2 TraesCS6D01G298200 chr6D 86.983 822 66 23 338 1150 408944873 408945662 0.000000e+00 887
3 TraesCS6D01G298200 chr6D 89.583 240 15 8 1183 1414 408945663 408945900 2.420000e-76 296
4 TraesCS6D01G298200 chr6D 83.796 216 20 12 1 206 408944654 408944864 1.170000e-44 191
5 TraesCS6D01G298200 chr6B 94.705 1832 70 10 1393 3204 614127840 614129664 0.000000e+00 2820
6 TraesCS6D01G298200 chr6B 93.015 1088 43 17 340 1410 614126755 614127826 0.000000e+00 1557
7 TraesCS6D01G298200 chr6B 90.979 1042 58 11 1183 2216 613610324 613611337 0.000000e+00 1371
8 TraesCS6D01G298200 chr6B 86.094 827 69 29 340 1150 613609527 613610323 0.000000e+00 848
9 TraesCS6D01G298200 chr6B 95.872 218 6 3 1 216 614126541 614126757 1.830000e-92 350
10 TraesCS6D01G298200 chr6B 84.651 215 19 11 1 206 613609308 613609517 5.420000e-48 202
11 TraesCS6D01G298200 chr6A 89.085 1814 117 39 436 2216 554715417 554717182 0.000000e+00 2178
12 TraesCS6D01G298200 chr6A 95.694 1138 44 2 1393 2528 554787703 554788837 0.000000e+00 1825
13 TraesCS6D01G298200 chr6A 93.406 1107 48 18 340 1427 554786607 554787707 0.000000e+00 1616
14 TraesCS6D01G298200 chr6A 93.578 654 26 12 2557 3204 554788829 554789472 0.000000e+00 961
15 TraesCS6D01G298200 chr6A 95.413 218 7 3 1 216 554786393 554786609 8.510000e-91 344
16 TraesCS6D01G298200 chr6A 86.321 212 19 7 3 207 554715071 554715279 4.160000e-54 222
17 TraesCS6D01G298200 chr7B 77.398 615 96 28 1243 1848 97192384 97192964 3.080000e-85 326
18 TraesCS6D01G298200 chr7D 78.866 388 69 11 1467 1848 135357778 135358158 1.910000e-62 250
19 TraesCS6D01G298200 chr7A 78.608 388 70 10 1467 1848 134491662 134492042 8.880000e-61 244
20 TraesCS6D01G298200 chr7A 94.400 125 7 0 213 337 65974367 65974491 3.260000e-45 193
21 TraesCS6D01G298200 chr7A 92.537 134 10 0 204 337 504961201 504961068 3.260000e-45 193
22 TraesCS6D01G298200 chr1A 95.200 125 4 2 216 339 518716656 518716779 2.520000e-46 196
23 TraesCS6D01G298200 chr1B 91.971 137 10 1 209 344 572202432 572202568 1.170000e-44 191
24 TraesCS6D01G298200 chr1B 91.852 135 10 1 211 344 601258974 601258840 1.520000e-43 187
25 TraesCS6D01G298200 chr5B 92.537 134 7 3 213 344 467497004 467496872 4.220000e-44 189
26 TraesCS6D01G298200 chr3B 91.241 137 11 1 202 337 173856861 173856997 5.460000e-43 185
27 TraesCS6D01G298200 chr5A 87.261 157 16 4 195 347 275955377 275955533 3.280000e-40 176
28 TraesCS6D01G298200 chr4B 86.061 165 14 8 203 365 640988861 640988704 5.500000e-38 169
29 TraesCS6D01G298200 chr2D 86.885 122 14 2 1254 1374 627974070 627974190 5.580000e-28 135
30 TraesCS6D01G298200 chr2B 84.426 122 17 2 1254 1374 771043285 771043405 5.610000e-23 119


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 TraesCS6D01G298200 chr6D 409286914 409290117 3203 False 5917.000000 5917 100.000000 1 3204 1 chr6D.!!$F1 3203
1 TraesCS6D01G298200 chr6D 408944654 408946723 2069 False 631.750000 1153 88.123250 1 2216 4 chr6D.!!$F2 2215
2 TraesCS6D01G298200 chr6B 614126541 614129664 3123 False 1575.666667 2820 94.530667 1 3204 3 chr6B.!!$F2 3203
3 TraesCS6D01G298200 chr6B 613609308 613611337 2029 False 807.000000 1371 87.241333 1 2216 3 chr6B.!!$F1 2215
4 TraesCS6D01G298200 chr6A 554715071 554717182 2111 False 1200.000000 2178 87.703000 3 2216 2 chr6A.!!$F1 2213
5 TraesCS6D01G298200 chr6A 554786393 554789472 3079 False 1186.500000 1825 94.522750 1 3204 4 chr6A.!!$F2 3203
6 TraesCS6D01G298200 chr7B 97192384 97192964 580 False 326.000000 326 77.398000 1243 1848 1 chr7B.!!$F1 605

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
940 1044 0.267356 AAGCTAGGGAGGAGAGGCAT 59.733 55.0 0.0 0.0 0.0 4.40 F
1357 1481 0.030297 AGACCATCCTCCAGCTCCAT 60.030 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 2276 1.187974 TCGCCGAGGTTGGAAATAGA 58.812 50.000 0.0 0.0 0.00 1.98 R
2889 3099 1.328680 CTTGCACTGCCAATAGTAGCG 59.671 52.381 0.0 0.0 31.67 4.26 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
207 239 6.272318 TCGAATTGAAGTTGTTGAAATTGCT 58.728 32.000 0.00 0.00 0.00 3.91
214 246 7.542890 TGAAGTTGTTGAAATTGCTTCAGTTA 58.457 30.769 0.00 0.00 44.84 2.24
215 247 8.196771 TGAAGTTGTTGAAATTGCTTCAGTTAT 58.803 29.630 0.00 0.00 44.84 1.89
216 248 9.677567 GAAGTTGTTGAAATTGCTTCAGTTATA 57.322 29.630 0.00 0.00 44.84 0.98
217 249 9.463443 AAGTTGTTGAAATTGCTTCAGTTATAC 57.537 29.630 0.00 0.00 44.84 1.47
218 250 8.850156 AGTTGTTGAAATTGCTTCAGTTATACT 58.150 29.630 0.00 0.00 44.84 2.12
219 251 9.118236 GTTGTTGAAATTGCTTCAGTTATACTC 57.882 33.333 0.00 0.00 44.84 2.59
220 252 7.816640 TGTTGAAATTGCTTCAGTTATACTCC 58.183 34.615 0.00 0.00 44.84 3.85
221 253 7.094377 TGTTGAAATTGCTTCAGTTATACTCCC 60.094 37.037 0.00 0.00 44.84 4.30
222 254 6.721318 TGAAATTGCTTCAGTTATACTCCCT 58.279 36.000 0.00 0.00 39.20 4.20
223 255 6.823689 TGAAATTGCTTCAGTTATACTCCCTC 59.176 38.462 0.00 0.00 39.20 4.30
224 256 4.755266 TTGCTTCAGTTATACTCCCTCC 57.245 45.455 0.00 0.00 0.00 4.30
225 257 2.693591 TGCTTCAGTTATACTCCCTCCG 59.306 50.000 0.00 0.00 0.00 4.63
226 258 2.694109 GCTTCAGTTATACTCCCTCCGT 59.306 50.000 0.00 0.00 0.00 4.69
227 259 3.243468 GCTTCAGTTATACTCCCTCCGTC 60.243 52.174 0.00 0.00 0.00 4.79
228 260 2.941480 TCAGTTATACTCCCTCCGTCC 58.059 52.381 0.00 0.00 0.00 4.79
229 261 1.607628 CAGTTATACTCCCTCCGTCCG 59.392 57.143 0.00 0.00 0.00 4.79
230 262 1.492176 AGTTATACTCCCTCCGTCCGA 59.508 52.381 0.00 0.00 0.00 4.55
231 263 2.092212 AGTTATACTCCCTCCGTCCGAA 60.092 50.000 0.00 0.00 0.00 4.30
232 264 2.689983 GTTATACTCCCTCCGTCCGAAA 59.310 50.000 0.00 0.00 0.00 3.46
233 265 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
234 266 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
235 267 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
236 268 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
237 269 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
238 270 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
239 271 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
240 272 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
241 273 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
242 274 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
243 275 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
244 276 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
245 277 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
246 278 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
247 279 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
248 280 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
249 281 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
250 282 8.172484 CGTCCGAAAATACTTGTCATCAAAATA 58.828 33.333 0.00 0.00 32.87 1.40
251 283 9.490663 GTCCGAAAATACTTGTCATCAAAATAG 57.509 33.333 0.00 0.00 32.87 1.73
252 284 9.443323 TCCGAAAATACTTGTCATCAAAATAGA 57.557 29.630 0.00 0.00 32.87 1.98
304 336 9.832445 AATACGTCTAGATACATTCCATTTTGT 57.168 29.630 0.00 0.00 0.00 2.83
305 337 9.832445 ATACGTCTAGATACATTCCATTTTGTT 57.168 29.630 0.00 0.00 0.00 2.83
306 338 8.197988 ACGTCTAGATACATTCCATTTTGTTC 57.802 34.615 0.00 0.00 0.00 3.18
307 339 7.822334 ACGTCTAGATACATTCCATTTTGTTCA 59.178 33.333 0.00 0.00 0.00 3.18
308 340 8.830580 CGTCTAGATACATTCCATTTTGTTCAT 58.169 33.333 0.00 0.00 0.00 2.57
317 349 9.590451 ACATTCCATTTTGTTCATATTGATGAC 57.410 29.630 0.00 0.00 41.92 3.06
318 350 9.589111 CATTCCATTTTGTTCATATTGATGACA 57.411 29.630 0.00 0.00 41.92 3.58
320 352 9.642327 TTCCATTTTGTTCATATTGATGACAAG 57.358 29.630 0.00 0.00 41.92 3.16
321 353 8.805175 TCCATTTTGTTCATATTGATGACAAGT 58.195 29.630 0.00 0.00 41.92 3.16
328 360 8.611757 TGTTCATATTGATGACAAGTATTTCCG 58.388 33.333 0.00 0.00 41.92 4.30
329 361 7.728847 TCATATTGATGACAAGTATTTCCGG 57.271 36.000 0.00 0.00 37.15 5.14
330 362 7.505258 TCATATTGATGACAAGTATTTCCGGA 58.495 34.615 0.00 0.00 37.15 5.14
331 363 7.441157 TCATATTGATGACAAGTATTTCCGGAC 59.559 37.037 1.83 0.00 37.15 4.79
332 364 4.545208 TGATGACAAGTATTTCCGGACA 57.455 40.909 1.83 0.00 0.00 4.02
333 365 4.503910 TGATGACAAGTATTTCCGGACAG 58.496 43.478 1.83 0.00 0.00 3.51
334 366 4.221924 TGATGACAAGTATTTCCGGACAGA 59.778 41.667 1.83 0.00 0.00 3.41
335 367 4.188247 TGACAAGTATTTCCGGACAGAG 57.812 45.455 1.83 0.00 0.00 3.35
336 368 3.056107 TGACAAGTATTTCCGGACAGAGG 60.056 47.826 1.83 0.00 0.00 3.69
377 409 0.608640 CAGTACGCTTCCAGGAACCT 59.391 55.000 0.00 0.00 0.00 3.50
445 515 6.942005 CCCCAGCAAGTAATCACAATATATGA 59.058 38.462 0.00 0.00 0.00 2.15
539 615 1.488390 AACACCCAATGCATCATCCC 58.512 50.000 0.00 0.00 0.00 3.85
633 722 7.898014 AAAAGGATTAAGGAAAACAGAGTGT 57.102 32.000 0.00 0.00 0.00 3.55
634 723 8.990163 AAAAGGATTAAGGAAAACAGAGTGTA 57.010 30.769 0.00 0.00 0.00 2.90
635 724 9.588096 AAAAGGATTAAGGAAAACAGAGTGTAT 57.412 29.630 0.00 0.00 0.00 2.29
653 749 6.409704 AGTGTATAATGTGACTGCTGAATGT 58.590 36.000 0.00 0.00 0.00 2.71
670 769 1.164411 TGTTGATTGCCCAAGTAGCG 58.836 50.000 0.00 0.00 0.00 4.26
676 775 1.550130 TTGCCCAAGTAGCGGCTAGT 61.550 55.000 10.54 11.08 45.90 2.57
717 816 4.103153 TGGATCAACAGCCCTTATCTTAGG 59.897 45.833 0.00 0.00 34.92 2.69
813 913 3.368531 GCAGATTAGTCCTTTCCACTCGT 60.369 47.826 0.00 0.00 0.00 4.18
838 938 4.779993 ATCTAATCCTGACCTGGGTTTC 57.220 45.455 0.00 0.00 31.96 2.78
928 1029 1.208165 ACCCCAAGGACCAAGCTAGG 61.208 60.000 0.00 0.00 36.73 3.02
929 1030 1.609783 CCCAAGGACCAAGCTAGGG 59.390 63.158 2.88 2.88 0.00 3.53
930 1031 0.914417 CCCAAGGACCAAGCTAGGGA 60.914 60.000 11.10 0.00 36.96 4.20
940 1044 0.267356 AAGCTAGGGAGGAGAGGCAT 59.733 55.000 0.00 0.00 0.00 4.40
1023 1136 1.519719 GAGGTCTCCTTGCTGCGAT 59.480 57.895 0.00 0.00 31.76 4.58
1235 1359 1.800805 CGTCTGGTTCTTCTGTGCAT 58.199 50.000 0.00 0.00 0.00 3.96
1236 1360 1.728971 CGTCTGGTTCTTCTGTGCATC 59.271 52.381 0.00 0.00 0.00 3.91
1357 1481 0.030297 AGACCATCCTCCAGCTCCAT 60.030 55.000 0.00 0.00 0.00 3.41
1393 1537 3.055385 ACAAGTACGGCACACCTATCAAT 60.055 43.478 0.00 0.00 0.00 2.57
1446 1631 3.741344 GTGGTACTCTTGCTAACACACAG 59.259 47.826 0.00 0.00 0.00 3.66
1686 1875 3.050089 GGGATGACCAAAGTGCCAA 57.950 52.632 0.00 0.00 39.85 4.52
1757 1946 2.110835 TGCTTCAGTCGGCAGCAA 59.889 55.556 0.00 0.00 40.61 3.91
1822 2014 0.036010 CTGACCTGGAGCAAATCGGT 60.036 55.000 0.00 0.00 0.00 4.69
2027 2219 3.231736 GCGGCGAGGGGGAGAATA 61.232 66.667 12.98 0.00 0.00 1.75
2084 2276 2.357517 CGCCACTTGCCGACTTCT 60.358 61.111 0.00 0.00 36.24 2.85
2240 2432 0.317160 GTGCTACCCTTTGGTTTGCC 59.683 55.000 0.00 0.00 44.75 4.52
2318 2510 0.321671 TGCTGTAGCTCCAGTTGGAC 59.678 55.000 8.23 0.00 42.66 4.02
2366 2558 0.396974 TTGGCAACCCATATGCTCCC 60.397 55.000 0.00 0.00 41.78 4.30
2444 2636 7.628769 AAATTTTCCAGCTTGAATTTTGTGT 57.371 28.000 0.37 0.00 29.97 3.72
2450 2642 5.592282 TCCAGCTTGAATTTTGTGTGACTTA 59.408 36.000 0.00 0.00 0.00 2.24
2451 2643 6.096141 TCCAGCTTGAATTTTGTGTGACTTAA 59.904 34.615 0.00 0.00 0.00 1.85
2491 2693 5.013704 TCCTAGTTTAAGTGCTTCATGGGAA 59.986 40.000 0.00 0.00 0.00 3.97
2563 2769 6.554982 AGAATGACAGGCCTGTGAATAGTATA 59.445 38.462 42.40 16.18 45.05 1.47
3052 3262 8.031864 ACATATGCTGCTGTCACTACTAATATC 58.968 37.037 1.58 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
207 239 3.294214 GGACGGAGGGAGTATAACTGAA 58.706 50.000 0.00 0.00 0.00 3.02
214 246 1.856629 TTTTCGGACGGAGGGAGTAT 58.143 50.000 0.00 0.00 0.00 2.12
215 247 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
216 248 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
217 249 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
218 250 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
219 251 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
220 252 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
221 253 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
222 254 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
223 255 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
224 256 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
225 257 9.490663 CTATTTTGATGACAAGTATTTTCGGAC 57.509 33.333 0.00 0.00 37.32 4.79
226 258 9.443323 TCTATTTTGATGACAAGTATTTTCGGA 57.557 29.630 0.00 0.00 37.32 4.55
278 310 9.832445 ACAAAATGGAATGTATCTAGACGTATT 57.168 29.630 0.00 0.00 0.00 1.89
279 311 9.832445 AACAAAATGGAATGTATCTAGACGTAT 57.168 29.630 0.00 0.00 0.00 3.06
280 312 9.309516 GAACAAAATGGAATGTATCTAGACGTA 57.690 33.333 0.00 0.00 0.00 3.57
281 313 7.822334 TGAACAAAATGGAATGTATCTAGACGT 59.178 33.333 0.00 0.00 0.00 4.34
282 314 8.196802 TGAACAAAATGGAATGTATCTAGACG 57.803 34.615 0.00 0.00 0.00 4.18
291 323 9.590451 GTCATCAATATGAACAAAATGGAATGT 57.410 29.630 0.00 0.00 43.69 2.71
292 324 9.589111 TGTCATCAATATGAACAAAATGGAATG 57.411 29.630 0.00 0.00 43.69 2.67
294 326 9.642327 CTTGTCATCAATATGAACAAAATGGAA 57.358 29.630 0.00 0.00 43.69 3.53
295 327 8.805175 ACTTGTCATCAATATGAACAAAATGGA 58.195 29.630 0.00 0.00 43.69 3.41
296 328 8.991243 ACTTGTCATCAATATGAACAAAATGG 57.009 30.769 0.00 0.00 43.69 3.16
302 334 8.611757 CGGAAATACTTGTCATCAATATGAACA 58.388 33.333 0.00 0.00 43.69 3.18
303 335 8.070171 CCGGAAATACTTGTCATCAATATGAAC 58.930 37.037 0.00 0.00 43.69 3.18
304 336 7.990314 TCCGGAAATACTTGTCATCAATATGAA 59.010 33.333 0.00 0.00 43.69 2.57
305 337 7.441157 GTCCGGAAATACTTGTCATCAATATGA 59.559 37.037 5.23 0.00 39.87 2.15
306 338 7.226523 TGTCCGGAAATACTTGTCATCAATATG 59.773 37.037 5.23 0.00 32.82 1.78
307 339 7.279615 TGTCCGGAAATACTTGTCATCAATAT 58.720 34.615 5.23 0.00 32.82 1.28
308 340 6.645306 TGTCCGGAAATACTTGTCATCAATA 58.355 36.000 5.23 0.00 32.82 1.90
309 341 5.496556 TGTCCGGAAATACTTGTCATCAAT 58.503 37.500 5.23 0.00 32.82 2.57
310 342 4.900684 TGTCCGGAAATACTTGTCATCAA 58.099 39.130 5.23 0.00 0.00 2.57
311 343 4.221924 TCTGTCCGGAAATACTTGTCATCA 59.778 41.667 5.23 0.00 0.00 3.07
312 344 4.755411 TCTGTCCGGAAATACTTGTCATC 58.245 43.478 5.23 0.00 0.00 2.92
313 345 4.383118 CCTCTGTCCGGAAATACTTGTCAT 60.383 45.833 5.23 0.00 0.00 3.06
314 346 3.056107 CCTCTGTCCGGAAATACTTGTCA 60.056 47.826 5.23 0.00 0.00 3.58
315 347 3.194968 TCCTCTGTCCGGAAATACTTGTC 59.805 47.826 5.23 0.00 0.00 3.18
316 348 3.170717 TCCTCTGTCCGGAAATACTTGT 58.829 45.455 5.23 0.00 0.00 3.16
317 349 3.887621 TCCTCTGTCCGGAAATACTTG 57.112 47.619 5.23 0.00 0.00 3.16
318 350 6.099845 ACATATTCCTCTGTCCGGAAATACTT 59.900 38.462 5.23 0.00 43.26 2.24
319 351 5.602978 ACATATTCCTCTGTCCGGAAATACT 59.397 40.000 5.23 0.00 43.26 2.12
320 352 5.855045 ACATATTCCTCTGTCCGGAAATAC 58.145 41.667 5.23 0.00 43.26 1.89
321 353 5.839063 AGACATATTCCTCTGTCCGGAAATA 59.161 40.000 5.23 6.06 43.26 1.40
322 354 4.656112 AGACATATTCCTCTGTCCGGAAAT 59.344 41.667 5.23 3.53 43.26 2.17
323 355 4.030913 AGACATATTCCTCTGTCCGGAAA 58.969 43.478 5.23 0.00 43.26 3.13
324 356 3.643237 AGACATATTCCTCTGTCCGGAA 58.357 45.455 5.23 0.00 42.18 4.30
325 357 3.314307 AGACATATTCCTCTGTCCGGA 57.686 47.619 0.00 0.00 42.18 5.14
326 358 4.122776 CAAAGACATATTCCTCTGTCCGG 58.877 47.826 0.00 0.00 42.18 5.14
327 359 4.122776 CCAAAGACATATTCCTCTGTCCG 58.877 47.826 0.00 0.00 42.18 4.79
328 360 5.359194 TCCAAAGACATATTCCTCTGTCC 57.641 43.478 0.00 0.00 42.18 4.02
329 361 7.554118 TCAATTCCAAAGACATATTCCTCTGTC 59.446 37.037 0.00 0.00 41.65 3.51
330 362 7.405292 TCAATTCCAAAGACATATTCCTCTGT 58.595 34.615 0.00 0.00 0.00 3.41
331 363 7.870509 TCAATTCCAAAGACATATTCCTCTG 57.129 36.000 0.00 0.00 0.00 3.35
332 364 9.566432 GTATCAATTCCAAAGACATATTCCTCT 57.434 33.333 0.00 0.00 0.00 3.69
333 365 9.342308 TGTATCAATTCCAAAGACATATTCCTC 57.658 33.333 0.00 0.00 0.00 3.71
334 366 9.347240 CTGTATCAATTCCAAAGACATATTCCT 57.653 33.333 0.00 0.00 0.00 3.36
335 367 9.125026 ACTGTATCAATTCCAAAGACATATTCC 57.875 33.333 0.00 0.00 0.00 3.01
445 515 4.839550 AGCTCATCATGTGACATCTCCTAT 59.160 41.667 0.00 0.00 32.22 2.57
488 563 5.814764 AGAAAGCACAATCAGATCATCAC 57.185 39.130 0.00 0.00 0.00 3.06
489 564 7.926674 TTAAGAAAGCACAATCAGATCATCA 57.073 32.000 0.00 0.00 0.00 3.07
632 721 7.307493 TCAACATTCAGCAGTCACATTATAC 57.693 36.000 0.00 0.00 0.00 1.47
633 722 8.400186 CAATCAACATTCAGCAGTCACATTATA 58.600 33.333 0.00 0.00 0.00 0.98
634 723 7.255569 CAATCAACATTCAGCAGTCACATTAT 58.744 34.615 0.00 0.00 0.00 1.28
635 724 6.614160 CAATCAACATTCAGCAGTCACATTA 58.386 36.000 0.00 0.00 0.00 1.90
653 749 2.866872 CCGCTACTTGGGCAATCAA 58.133 52.632 0.00 0.00 0.00 2.57
670 769 3.053831 TGTTGACTTAAGCCACTAGCC 57.946 47.619 1.29 0.00 45.47 3.93
676 775 3.826524 TCCATGTTGTTGACTTAAGCCA 58.173 40.909 1.29 0.00 0.00 4.75
813 913 7.256190 CGAAACCCAGGTCAGGATTAGATTATA 60.256 40.741 0.00 0.00 0.00 0.98
838 938 1.714899 GGCCATGAAATCCGGTGTCG 61.715 60.000 0.00 0.00 0.00 4.35
928 1029 3.326297 ACAAAGCTATATGCCTCTCCTCC 59.674 47.826 0.00 0.00 44.23 4.30
929 1030 4.283212 AGACAAAGCTATATGCCTCTCCTC 59.717 45.833 0.00 0.00 44.23 3.71
930 1031 4.230455 AGACAAAGCTATATGCCTCTCCT 58.770 43.478 0.00 0.00 44.23 3.69
940 1044 3.967987 GGAAGGAGGGAGACAAAGCTATA 59.032 47.826 0.00 0.00 0.00 1.31
1023 1136 1.283029 CCCTTCTTGAGGCCATTCTCA 59.717 52.381 5.01 0.00 44.85 3.27
1157 1271 3.006430 TCTGTGCCTTGTATCGAGACAAA 59.994 43.478 24.30 9.17 38.80 2.83
1158 1272 2.560981 TCTGTGCCTTGTATCGAGACAA 59.439 45.455 23.03 23.03 36.98 3.18
1186 1304 2.290323 ACATTTCGGACCAAAGCTAGCT 60.290 45.455 12.68 12.68 0.00 3.32
1235 1359 0.394192 CTGTTGAGCCCTGTGTGAGA 59.606 55.000 0.00 0.00 0.00 3.27
1236 1360 0.604780 CCTGTTGAGCCCTGTGTGAG 60.605 60.000 0.00 0.00 0.00 3.51
1246 1370 0.819259 TCTTGCCACACCTGTTGAGC 60.819 55.000 0.00 0.00 0.00 4.26
1357 1481 2.714259 CTTGTTGCCAAGGACGGAA 58.286 52.632 0.00 0.00 43.62 4.30
1416 1598 9.408069 GTGTTAGCAAGAGTACCACATATATAC 57.592 37.037 0.00 0.00 0.00 1.47
1429 1614 4.572389 CAGTTTCTGTGTGTTAGCAAGAGT 59.428 41.667 0.00 0.00 0.00 3.24
1446 1631 4.044426 GGTTTGATCAGCACAACAGTTTC 58.956 43.478 9.57 0.00 0.00 2.78
1486 1675 2.750350 CGTCCAGGGAGGTGCTTT 59.250 61.111 0.00 0.00 39.02 3.51
1822 2014 2.283894 TGCGAAGGGCTCAGGAGA 60.284 61.111 0.00 0.00 44.05 3.71
2027 2219 2.281761 CAGCGGTTTCTGGGTGCT 60.282 61.111 0.00 0.00 36.05 4.40
2084 2276 1.187974 TCGCCGAGGTTGGAAATAGA 58.812 50.000 0.00 0.00 0.00 1.98
2126 2318 3.730761 GCTGTTGCCCTCAGCGTG 61.731 66.667 8.62 0.00 46.39 5.34
2149 2341 2.108970 GAGTCGGACCAAATAGGGAGT 58.891 52.381 4.14 0.00 43.89 3.85
2228 2420 5.833406 AAATTGAAAAGGCAAACCAAAGG 57.167 34.783 0.00 0.00 39.06 3.11
2491 2693 3.584848 AGTTAGTGAGCAAGATCCCAGTT 59.415 43.478 0.00 0.00 0.00 3.16
2889 3099 1.328680 CTTGCACTGCCAATAGTAGCG 59.671 52.381 0.00 0.00 31.67 4.26
3077 3287 3.141398 CAGTGCTTAGGAAAAGCTGACA 58.859 45.455 10.74 0.00 43.38 3.58


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

AutoCloner maintained by Alex Coulton.