Multiple sequence alignment - TraesCS1D01G425700

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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 TraesCS1D01G425700 chr1D 100.000 2621 0 0 1 2621 479227581 479230201 0.000000e+00 4841
1 TraesCS1D01G425700 chr1A 94.595 1739 61 15 470 2203 575594531 575596241 0.000000e+00 2660
2 TraesCS1D01G425700 chr1A 88.276 435 29 11 2199 2618 575596336 575596763 3.890000e-138 501
3 TraesCS1D01G425700 chr1A 97.468 158 2 2 1 157 575594106 575594262 4.300000e-68 268
4 TraesCS1D01G425700 chr1A 85.135 222 9 9 244 464 575594269 575594467 3.420000e-49 206
5 TraesCS1D01G425700 chr1A 93.069 101 7 0 147 247 133417554 133417454 5.840000e-32 148
6 TraesCS1D01G425700 chr1B 94.573 866 37 6 1341 2203 667491883 667492741 0.000000e+00 1330
7 TraesCS1D01G425700 chr1B 91.837 833 50 9 476 1308 667491078 667491892 0.000000e+00 1146
8 TraesCS1D01G425700 chr1B 91.818 440 24 4 2194 2621 667492815 667493254 1.040000e-168 603
9 TraesCS1D01G425700 chr1B 90.435 115 8 2 128 242 47517453 47517342 5.840000e-32 148
10 TraesCS1D01G425700 chr4D 96.774 93 2 1 154 246 508008871 508008780 1.260000e-33 154
11 TraesCS1D01G425700 chr6D 91.589 107 7 2 150 256 443958608 443958504 2.100000e-31 147
12 TraesCS1D01G425700 chr2B 92.308 104 6 2 150 253 201234261 201234362 2.100000e-31 147
13 TraesCS1D01G425700 chr2B 92.308 104 6 2 144 246 440212155 440212053 2.100000e-31 147
14 TraesCS1D01G425700 chrUn 90.179 112 8 2 128 238 335557758 335557649 2.720000e-30 143
15 TraesCS1D01G425700 chr4A 90.826 109 7 2 128 235 632934348 632934454 2.720000e-30 143
16 TraesCS1D01G425700 chr3B 90.179 112 8 2 128 238 752216582 752216473 2.720000e-30 143


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 TraesCS1D01G425700 chr1D 479227581 479230201 2620 False 4841.000000 4841 100.000000 1 2621 1 chr1D.!!$F1 2620
1 TraesCS1D01G425700 chr1A 575594106 575596763 2657 False 908.750000 2660 91.368500 1 2618 4 chr1A.!!$F1 2617
2 TraesCS1D01G425700 chr1B 667491078 667493254 2176 False 1026.333333 1330 92.742667 476 2621 3 chr1B.!!$F1 2145

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
506 566 0.251742 CCAGGCACAAGAATTCCCCA 60.252 55.0 0.65 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2293 2462 1.570803 CCATCTCATTTTTGGGGCCA 58.429 50.0 4.39 0.0 0.0 5.36 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
109 110 5.339008 TGACTACTCAGTTGTGAACTTGT 57.661 39.130 0.00 0.00 40.46 3.16
122 123 3.250040 GTGAACTTGTGATGGTACCACAC 59.750 47.826 27.21 27.21 43.37 3.82
123 124 3.135712 TGAACTTGTGATGGTACCACACT 59.864 43.478 30.52 19.54 43.37 3.55
124 125 3.126001 ACTTGTGATGGTACCACACTG 57.874 47.619 30.52 26.25 43.37 3.66
160 161 9.990868 AAATCACCAATAAAATTACTACTCCCT 57.009 29.630 0.00 0.00 0.00 4.20
161 162 9.628500 AATCACCAATAAAATTACTACTCCCTC 57.372 33.333 0.00 0.00 0.00 4.30
162 163 8.388656 TCACCAATAAAATTACTACTCCCTCT 57.611 34.615 0.00 0.00 0.00 3.69
180 181 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
181 182 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
182 183 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
183 184 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
184 185 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
201 202 9.570488 AAGAGCGTTTAGATAACTAAAGTAGTG 57.430 33.333 5.51 0.00 45.42 2.74
202 203 8.954350 AGAGCGTTTAGATAACTAAAGTAGTGA 58.046 33.333 5.51 0.00 45.42 3.41
203 204 9.733219 GAGCGTTTAGATAACTAAAGTAGTGAT 57.267 33.333 5.51 0.00 45.42 3.06
204 205 9.733219 AGCGTTTAGATAACTAAAGTAGTGATC 57.267 33.333 5.51 5.03 45.42 2.92
215 216 9.978044 AACTAAAGTAGTGATCTAAACGTTCTT 57.022 29.630 0.00 0.00 39.39 2.52
232 233 8.862550 AACGTTCTTATATTAGTTTACGGAGG 57.137 34.615 0.00 0.00 32.54 4.30
233 234 7.428826 ACGTTCTTATATTAGTTTACGGAGGG 58.571 38.462 13.71 0.00 32.54 4.30
234 235 7.285401 ACGTTCTTATATTAGTTTACGGAGGGA 59.715 37.037 13.71 0.00 32.54 4.20
235 236 8.137437 CGTTCTTATATTAGTTTACGGAGGGAA 58.863 37.037 0.00 0.00 0.00 3.97
236 237 9.993454 GTTCTTATATTAGTTTACGGAGGGAAT 57.007 33.333 0.00 0.00 0.00 3.01
244 245 6.803366 AGTTTACGGAGGGAATACTTATGT 57.197 37.500 0.00 0.00 0.00 2.29
245 246 7.902920 AGTTTACGGAGGGAATACTTATGTA 57.097 36.000 0.00 0.00 0.00 2.29
246 247 8.310122 AGTTTACGGAGGGAATACTTATGTAA 57.690 34.615 0.00 0.00 31.80 2.41
247 248 8.931568 AGTTTACGGAGGGAATACTTATGTAAT 58.068 33.333 0.00 0.00 31.80 1.89
248 249 9.551734 GTTTACGGAGGGAATACTTATGTAATT 57.448 33.333 0.00 0.00 31.80 1.40
249 250 9.550406 TTTACGGAGGGAATACTTATGTAATTG 57.450 33.333 0.00 0.00 31.80 2.32
289 290 4.390264 ACCAACTTGTCTAAAGAAGCCTC 58.610 43.478 0.00 0.00 28.90 4.70
304 305 4.704540 AGAAGCCTCGGAGACATATAGATG 59.295 45.833 6.58 0.00 39.16 2.90
307 308 3.119316 GCCTCGGAGACATATAGATGTGG 60.119 52.174 7.92 2.90 46.64 4.17
311 312 4.588951 TCGGAGACATATAGATGTGGCTTT 59.411 41.667 7.92 0.00 46.64 3.51
362 364 6.648310 CCTGGCCTTTGCATATATAGATATCG 59.352 42.308 3.32 0.00 40.13 2.92
363 365 5.991606 TGGCCTTTGCATATATAGATATCGC 59.008 40.000 3.32 5.40 40.13 4.58
364 366 6.183361 TGGCCTTTGCATATATAGATATCGCT 60.183 38.462 3.32 0.00 40.13 4.93
365 367 6.146837 GGCCTTTGCATATATAGATATCGCTG 59.853 42.308 0.00 0.00 40.13 5.18
366 368 6.347240 GCCTTTGCATATATAGATATCGCTGC 60.347 42.308 0.00 2.81 37.47 5.25
367 369 6.703165 CCTTTGCATATATAGATATCGCTGCA 59.297 38.462 0.00 10.61 34.17 4.41
368 370 7.387122 CCTTTGCATATATAGATATCGCTGCAT 59.613 37.037 13.55 0.00 35.08 3.96
369 371 8.667076 TTTGCATATATAGATATCGCTGCATT 57.333 30.769 13.55 0.00 35.08 3.56
370 372 9.762933 TTTGCATATATAGATATCGCTGCATTA 57.237 29.630 13.55 0.00 35.08 1.90
371 373 9.933723 TTGCATATATAGATATCGCTGCATTAT 57.066 29.630 13.55 0.00 35.08 1.28
372 374 9.578439 TGCATATATAGATATCGCTGCATTATC 57.422 33.333 0.00 5.66 32.60 1.75
373 375 9.578439 GCATATATAGATATCGCTGCATTATCA 57.422 33.333 16.48 7.19 0.00 2.15
378 380 6.468333 AGATATCGCTGCATTATCAGATCT 57.532 37.500 16.48 0.00 36.19 2.75
379 381 6.274579 AGATATCGCTGCATTATCAGATCTG 58.725 40.000 17.07 17.07 36.19 2.90
380 382 4.532314 ATCGCTGCATTATCAGATCTGA 57.468 40.909 27.03 27.03 44.59 3.27
464 466 7.605309 CCTACACATGCATCATACATCACTATT 59.395 37.037 0.00 0.00 0.00 1.73
465 467 7.812690 ACACATGCATCATACATCACTATTT 57.187 32.000 0.00 0.00 0.00 1.40
499 559 2.363306 ATTCACACCAGGCACAAGAA 57.637 45.000 0.00 0.00 0.00 2.52
506 566 0.251742 CCAGGCACAAGAATTCCCCA 60.252 55.000 0.65 0.00 0.00 4.96
841 901 3.994392 ACGATGTTTTGTCGCAGTAGAAT 59.006 39.130 0.00 0.00 42.56 2.40
856 916 6.648310 CGCAGTAGAATTGGTCTATCATGATT 59.352 38.462 14.65 0.00 41.00 2.57
859 919 7.935755 CAGTAGAATTGGTCTATCATGATTGGT 59.064 37.037 14.65 0.00 41.00 3.67
960 1020 7.436376 CCTAGTGTGATTGGATATATGTATGCG 59.564 40.741 0.00 0.00 31.84 4.73
963 1023 8.311109 AGTGTGATTGGATATATGTATGCGTAA 58.689 33.333 0.00 0.00 31.84 3.18
991 1051 1.068402 TGCTGGATGAATTGTGTTGCG 60.068 47.619 0.00 0.00 0.00 4.85
997 1057 1.234821 TGAATTGTGTTGCGGTCTCC 58.765 50.000 0.00 0.00 0.00 3.71
1273 1333 5.245751 ACAGATTATCCCACTGCTCTCTATG 59.754 44.000 0.00 0.00 35.38 2.23
1380 1440 3.236816 CATCAAGTTTTGTGACATCGCC 58.763 45.455 0.00 0.00 0.00 5.54
1921 1985 2.356135 CACCATTCTTTACCCTGACCG 58.644 52.381 0.00 0.00 0.00 4.79
1990 2054 0.597568 CGAGCCATTGAAGCAAACCA 59.402 50.000 0.00 0.00 0.00 3.67
1999 2063 0.827507 GAAGCAAACCAGAGCCCCAA 60.828 55.000 0.00 0.00 0.00 4.12
2054 2118 6.211184 TCCATCCAGCTACAAAATGAAAACAT 59.789 34.615 0.00 0.00 0.00 2.71
2134 2200 3.523157 TGGAATGTAGCCAAGGAATCTGA 59.477 43.478 0.00 0.00 31.13 3.27
2160 2228 4.202295 TGGGCATATTGTAGAGCTTCAGAG 60.202 45.833 0.00 0.00 0.00 3.35
2161 2229 4.039730 GGGCATATTGTAGAGCTTCAGAGA 59.960 45.833 0.00 0.00 0.00 3.10
2171 2239 4.630111 AGAGCTTCAGAGAGTTTCAGTTG 58.370 43.478 0.00 0.00 0.00 3.16
2194 2262 6.825610 TGCAACCTCCAAACAGAATATTTTT 58.174 32.000 0.00 0.00 0.00 1.94
2214 2381 8.926715 ATTTTTGTTGAGTTCCTTCAAGTAAC 57.073 30.769 0.00 0.00 37.72 2.50
2219 2386 3.893200 TGAGTTCCTTCAAGTAACGGAGA 59.107 43.478 0.00 0.00 0.00 3.71
2247 2416 8.574251 TTGTTTCTGGTGTATATATGCTTTGT 57.426 30.769 2.37 0.00 0.00 2.83
2293 2462 7.341769 TGGAATATAATGTTAGGCTTGCAGTTT 59.658 33.333 0.00 0.00 0.00 2.66
2300 2469 3.233231 GCTTGCAGTTTGGCCCCA 61.233 61.111 0.00 0.00 0.00 4.96
2311 2480 3.008266 AGTTTGGCCCCAAAAATGAGATG 59.992 43.478 13.65 0.00 45.86 2.90
2356 2525 1.412387 GTGGTACAAGAACCGTCGAC 58.588 55.000 5.18 5.18 44.16 4.20
2379 2548 3.282157 CACCTTGCACGCTGCTGT 61.282 61.111 10.54 0.00 45.31 4.40
2544 2730 5.351465 ACTCCATAGCATTGTTTACTGAACG 59.649 40.000 0.00 0.00 41.29 3.95
2567 2753 3.392882 TGCTATGCTATTGTGATCGGTG 58.607 45.455 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 5.235850 ACAATTACAGTGTGGTACCATCA 57.764 39.130 19.72 14.89 0.00 3.07
157 158 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
158 159 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
175 176 9.570488 CACTACTTTAGTTATCTAAACGCTCTT 57.430 33.333 2.47 0.00 40.05 2.85
176 177 8.954350 TCACTACTTTAGTTATCTAAACGCTCT 58.046 33.333 2.47 0.00 40.05 4.09
177 178 9.733219 ATCACTACTTTAGTTATCTAAACGCTC 57.267 33.333 2.47 0.00 40.05 5.03
178 179 9.733219 GATCACTACTTTAGTTATCTAAACGCT 57.267 33.333 2.47 0.00 40.05 5.07
179 180 9.733219 AGATCACTACTTTAGTTATCTAAACGC 57.267 33.333 7.85 0.00 43.99 4.84
189 190 9.978044 AAGAACGTTTAGATCACTACTTTAGTT 57.022 29.630 0.46 0.00 36.76 2.24
206 207 9.305925 CCTCCGTAAACTAATATAAGAACGTTT 57.694 33.333 0.46 0.00 0.00 3.60
207 208 7.922811 CCCTCCGTAAACTAATATAAGAACGTT 59.077 37.037 0.00 0.00 0.00 3.99
208 209 7.285401 TCCCTCCGTAAACTAATATAAGAACGT 59.715 37.037 0.00 0.00 0.00 3.99
209 210 7.651808 TCCCTCCGTAAACTAATATAAGAACG 58.348 38.462 0.00 0.00 0.00 3.95
210 211 9.993454 ATTCCCTCCGTAAACTAATATAAGAAC 57.007 33.333 0.00 0.00 0.00 3.01
218 219 8.931568 ACATAAGTATTCCCTCCGTAAACTAAT 58.068 33.333 0.00 0.00 0.00 1.73
219 220 8.310122 ACATAAGTATTCCCTCCGTAAACTAA 57.690 34.615 0.00 0.00 0.00 2.24
220 221 7.902920 ACATAAGTATTCCCTCCGTAAACTA 57.097 36.000 0.00 0.00 0.00 2.24
221 222 6.803366 ACATAAGTATTCCCTCCGTAAACT 57.197 37.500 0.00 0.00 0.00 2.66
222 223 9.551734 AATTACATAAGTATTCCCTCCGTAAAC 57.448 33.333 0.00 0.00 0.00 2.01
223 224 9.550406 CAATTACATAAGTATTCCCTCCGTAAA 57.450 33.333 0.00 0.00 0.00 2.01
224 225 8.707449 ACAATTACATAAGTATTCCCTCCGTAA 58.293 33.333 0.00 0.00 0.00 3.18
225 226 8.145767 CACAATTACATAAGTATTCCCTCCGTA 58.854 37.037 0.00 0.00 0.00 4.02
226 227 6.990349 CACAATTACATAAGTATTCCCTCCGT 59.010 38.462 0.00 0.00 0.00 4.69
227 228 6.990349 ACACAATTACATAAGTATTCCCTCCG 59.010 38.462 0.00 0.00 0.00 4.63
228 229 9.490379 CTACACAATTACATAAGTATTCCCTCC 57.510 37.037 0.00 0.00 0.00 4.30
230 231 9.832445 CACTACACAATTACATAAGTATTCCCT 57.168 33.333 0.00 0.00 0.00 4.20
231 232 9.609346 ACACTACACAATTACATAAGTATTCCC 57.391 33.333 0.00 0.00 0.00 3.97
289 290 4.527509 AAGCCACATCTATATGTCTCCG 57.472 45.455 0.00 0.00 44.70 4.63
311 312 5.352846 GCACTGCCACCTTTTAAAAGAAAAA 59.647 36.000 26.11 9.11 38.28 1.94
411 413 4.130118 AGCTGAAACACGAGAAGAAACAT 58.870 39.130 0.00 0.00 0.00 2.71
499 559 0.767375 CCATGGACGATCTGGGGAAT 59.233 55.000 5.56 0.00 0.00 3.01
506 566 2.419297 GCTGAAACTCCATGGACGATCT 60.419 50.000 11.44 0.00 0.00 2.75
841 901 5.189539 TCAGACACCAATCATGATAGACCAA 59.810 40.000 9.04 0.00 0.00 3.67
856 916 1.788229 TGTCAGAGGTTCAGACACCA 58.212 50.000 0.86 0.00 37.87 4.17
859 919 2.700371 ACACATGTCAGAGGTTCAGACA 59.300 45.455 0.00 6.74 44.90 3.41
886 946 3.013648 TGGTCCAGGGTATAAGGTTCTCT 59.986 47.826 0.00 0.00 0.00 3.10
898 958 4.270153 TCAGGGCTGGTCCAGGGT 62.270 66.667 20.72 0.00 36.21 4.34
985 1045 0.981183 ACCATAAGGAGACCGCAACA 59.019 50.000 0.00 0.00 38.69 3.33
991 1051 2.158798 GGCAGGTAACCATAAGGAGACC 60.159 54.545 0.00 0.00 40.98 3.85
997 1057 4.222124 AGACTTGGCAGGTAACCATAAG 57.778 45.455 0.82 0.00 36.96 1.73
1260 1320 7.459795 TCCAGATATAACATAGAGAGCAGTG 57.540 40.000 0.00 0.00 0.00 3.66
1340 1400 5.484715 TGATGCAAGTAGTTAGGTGTTACC 58.515 41.667 0.00 0.00 38.99 2.85
1359 1419 3.236816 GGCGATGTCACAAAACTTGATG 58.763 45.455 0.00 0.00 0.00 3.07
1824 1885 7.321153 TGACCATCTAACAGCTTACTTACTTC 58.679 38.462 0.00 0.00 0.00 3.01
1832 1893 2.170607 GGCCTGACCATCTAACAGCTTA 59.829 50.000 0.00 0.00 38.86 3.09
1921 1985 3.146066 TCAAGGCAGTGGTGTCATAAAC 58.854 45.455 0.00 0.00 0.00 2.01
2054 2118 3.636300 AGCAGTGCTGGTTTTAAATGTCA 59.364 39.130 18.98 0.00 38.24 3.58
2134 2200 5.448654 TGAAGCTCTACAATATGCCCAATT 58.551 37.500 0.00 0.00 0.00 2.32
2160 2228 2.297701 TGGAGGTTGCAACTGAAACTC 58.702 47.619 27.64 22.67 34.00 3.01
2161 2229 2.435372 TGGAGGTTGCAACTGAAACT 57.565 45.000 27.64 16.32 34.00 2.66
2171 2239 6.705825 ACAAAAATATTCTGTTTGGAGGTTGC 59.294 34.615 13.16 0.00 36.72 4.17
2194 2262 4.124238 CCGTTACTTGAAGGAACTCAACA 58.876 43.478 17.46 0.00 38.49 3.33
2214 2381 2.561569 ACACCAGAAACAAGTTCTCCG 58.438 47.619 0.00 0.00 45.25 4.63
2219 2386 8.807948 AAGCATATATACACCAGAAACAAGTT 57.192 30.769 0.00 0.00 0.00 2.66
2224 2391 8.208718 TCACAAAGCATATATACACCAGAAAC 57.791 34.615 0.00 0.00 0.00 2.78
2247 2416 7.743116 TTCCAGGTAACATTACTCCTAATCA 57.257 36.000 2.00 0.00 41.41 2.57
2293 2462 1.570803 CCATCTCATTTTTGGGGCCA 58.429 50.000 4.39 0.00 0.00 5.36
2300 2469 2.618794 TGTTGGCCCCATCTCATTTTT 58.381 42.857 0.00 0.00 0.00 1.94
2311 2480 2.613506 CGAGTTCGTTGTTGGCCCC 61.614 63.158 0.00 0.00 34.11 5.80
2544 2730 2.414481 CCGATCACAATAGCATAGCAGC 59.586 50.000 0.00 0.00 0.00 5.25
2567 2753 5.186198 AGAAGTTATGTCTTGTACCCATGC 58.814 41.667 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.