Multiple sequence alignment - TraesCS1B01G392100

Loading Multiple Alignment...

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 TraesCS1B01G392100 chr1B 100.000 2445 0 0 1 2445 624999728 625002172 0.000000e+00 4516
1 TraesCS1B01G392100 chr1B 97.988 1292 23 2 236 1525 36238622 36237332 0.000000e+00 2239
2 TraesCS1B01G392100 chr1B 97.614 922 19 1 1527 2445 129080718 129079797 0.000000e+00 1578
3 TraesCS1B01G392100 chr1B 97.614 922 19 1 1527 2445 563868042 563867121 0.000000e+00 1578
4 TraesCS1B01G392100 chr1B 97.614 922 19 1 1527 2445 626189106 626188185 0.000000e+00 1578
5 TraesCS1B01G392100 chrUn 98.302 1296 19 2 232 1525 370480816 370482110 0.000000e+00 2268
6 TraesCS1B01G392100 chrUn 97.988 1292 23 2 236 1525 42460718 42459428 0.000000e+00 2239
7 TraesCS1B01G392100 chrUn 97.841 1297 25 2 231 1525 281979669 281978374 0.000000e+00 2237
8 TraesCS1B01G392100 chr3B 98.220 1292 20 2 236 1525 825685389 825684099 0.000000e+00 2255
9 TraesCS1B01G392100 chr3B 97.840 1296 22 3 235 1525 784875364 784876658 0.000000e+00 2233
10 TraesCS1B01G392100 chr3B 97.627 927 17 3 1522 2445 205021414 205022338 0.000000e+00 1585
11 TraesCS1B01G392100 chr3B 90.196 255 3 2 1 234 670126835 670127088 1.830000e-81 313
12 TraesCS1B01G392100 chr2B 98.065 1292 22 2 236 1525 762951978 762950688 0.000000e+00 2244
13 TraesCS1B01G392100 chr2B 97.414 928 20 3 1521 2445 680454399 680455325 0.000000e+00 1578
14 TraesCS1B01G392100 chr5B 97.841 1297 25 2 231 1525 694337232 694335937 0.000000e+00 2237
15 TraesCS1B01G392100 chr5B 97.841 1297 25 2 231 1525 694352172 694350877 0.000000e+00 2237
16 TraesCS1B01G392100 chr5B 97.627 927 17 3 1521 2443 579106773 579107698 0.000000e+00 1585
17 TraesCS1B01G392100 chr5B 97.722 922 18 1 1527 2445 656209267 656208346 0.000000e+00 1583
18 TraesCS1B01G392100 chr5B 87.160 257 10 7 1 235 492774861 492774606 1.110000e-68 270
19 TraesCS1B01G392100 chr5B 85.992 257 13 7 1 235 492776574 492776319 1.120000e-63 254
20 TraesCS1B01G392100 chr6B 97.614 922 19 1 1527 2445 649904055 649903134 0.000000e+00 1578
21 TraesCS1B01G392100 chr3A 97.417 929 19 3 1521 2445 16219686 16220613 0.000000e+00 1578
22 TraesCS1B01G392100 chr4A 89.024 246 5 2 10 235 698359979 698360222 3.980000e-73 285
23 TraesCS1B01G392100 chr4A 86.770 257 12 1 1 235 507978334 507978078 1.440000e-67 267
24 TraesCS1B01G392100 chr5A 86.381 257 11 4 1 235 44348929 44348675 2.410000e-65 259


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 TraesCS1B01G392100 chr1B 624999728 625002172 2444 False 4516 4516 100.000 1 2445 1 chr1B.!!$F1 2444
1 TraesCS1B01G392100 chr1B 36237332 36238622 1290 True 2239 2239 97.988 236 1525 1 chr1B.!!$R1 1289
2 TraesCS1B01G392100 chr1B 129079797 129080718 921 True 1578 1578 97.614 1527 2445 1 chr1B.!!$R2 918
3 TraesCS1B01G392100 chr1B 563867121 563868042 921 True 1578 1578 97.614 1527 2445 1 chr1B.!!$R3 918
4 TraesCS1B01G392100 chr1B 626188185 626189106 921 True 1578 1578 97.614 1527 2445 1 chr1B.!!$R4 918
5 TraesCS1B01G392100 chrUn 370480816 370482110 1294 False 2268 2268 98.302 232 1525 1 chrUn.!!$F1 1293
6 TraesCS1B01G392100 chrUn 42459428 42460718 1290 True 2239 2239 97.988 236 1525 1 chrUn.!!$R1 1289
7 TraesCS1B01G392100 chrUn 281978374 281979669 1295 True 2237 2237 97.841 231 1525 1 chrUn.!!$R2 1294
8 TraesCS1B01G392100 chr3B 825684099 825685389 1290 True 2255 2255 98.220 236 1525 1 chr3B.!!$R1 1289
9 TraesCS1B01G392100 chr3B 784875364 784876658 1294 False 2233 2233 97.840 235 1525 1 chr3B.!!$F3 1290
10 TraesCS1B01G392100 chr3B 205021414 205022338 924 False 1585 1585 97.627 1522 2445 1 chr3B.!!$F1 923
11 TraesCS1B01G392100 chr2B 762950688 762951978 1290 True 2244 2244 98.065 236 1525 1 chr2B.!!$R1 1289
12 TraesCS1B01G392100 chr2B 680454399 680455325 926 False 1578 1578 97.414 1521 2445 1 chr2B.!!$F1 924
13 TraesCS1B01G392100 chr5B 694335937 694337232 1295 True 2237 2237 97.841 231 1525 1 chr5B.!!$R2 1294
14 TraesCS1B01G392100 chr5B 694350877 694352172 1295 True 2237 2237 97.841 231 1525 1 chr5B.!!$R3 1294
15 TraesCS1B01G392100 chr5B 579106773 579107698 925 False 1585 1585 97.627 1521 2443 1 chr5B.!!$F1 922
16 TraesCS1B01G392100 chr5B 656208346 656209267 921 True 1583 1583 97.722 1527 2445 1 chr5B.!!$R1 918
17 TraesCS1B01G392100 chr5B 492774606 492776574 1968 True 262 270 86.576 1 235 2 chr5B.!!$R4 234
18 TraesCS1B01G392100 chr6B 649903134 649904055 921 True 1578 1578 97.614 1527 2445 1 chr6B.!!$R1 918
19 TraesCS1B01G392100 chr3A 16219686 16220613 927 False 1578 1578 97.417 1521 2445 1 chr3A.!!$F1 924

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
121 123 0.178891 TCAACCCCTGGAGCTCTTCT 60.179 55.0 14.64 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 3086 0.614979 ACCGGCTCAGCTTCTTCCTA 60.615 55.0 0.0 0.0 0.0 2.94 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
19 20 0.807496 GCTTGAGATGGTGCTGGAAC 59.193 55.000 0.00 0.0 0.00 3.62
39 40 1.236616 TGTCAGCCGTCATTTGCCTG 61.237 55.000 0.00 0.0 0.00 4.85
47 48 1.073025 TCATTTGCCTGCGAGGTGT 59.927 52.632 4.45 0.0 37.80 4.16
119 121 0.622665 CATCAACCCCTGGAGCTCTT 59.377 55.000 14.64 0.0 0.00 2.85
121 123 0.178891 TCAACCCCTGGAGCTCTTCT 60.179 55.000 14.64 0.0 0.00 2.85
152 175 4.751767 TTGATTTTTGCTGGAACCTTGT 57.248 36.364 0.00 0.0 0.00 3.16
172 195 8.085909 ACCTTGTATTATTTTTGCTACAACCAC 58.914 33.333 0.00 0.0 32.35 4.16
174 197 9.128107 CTTGTATTATTTTTGCTACAACCACTG 57.872 33.333 0.00 0.0 32.35 3.66
175 198 7.598278 TGTATTATTTTTGCTACAACCACTGG 58.402 34.615 0.00 0.0 0.00 4.00
176 199 5.461032 TTATTTTTGCTACAACCACTGGG 57.539 39.130 0.00 0.0 41.29 4.45
177 200 1.698506 TTTTGCTACAACCACTGGGG 58.301 50.000 0.00 0.0 44.81 4.96
178 201 0.825840 TTTGCTACAACCACTGGGGC 60.826 55.000 0.00 0.0 42.05 5.80
179 202 1.715019 TTGCTACAACCACTGGGGCT 61.715 55.000 0.00 0.0 42.05 5.19
180 203 1.377333 GCTACAACCACTGGGGCTC 60.377 63.158 0.00 0.0 42.05 4.70
181 204 1.842381 GCTACAACCACTGGGGCTCT 61.842 60.000 0.00 0.0 42.05 4.09
182 205 0.693049 CTACAACCACTGGGGCTCTT 59.307 55.000 0.00 0.0 42.05 2.85
183 206 1.073923 CTACAACCACTGGGGCTCTTT 59.926 52.381 0.00 0.0 42.05 2.52
184 207 0.261696 ACAACCACTGGGGCTCTTTT 59.738 50.000 0.00 0.0 42.05 2.27
185 208 1.342975 ACAACCACTGGGGCTCTTTTT 60.343 47.619 0.00 0.0 42.05 1.94
217 240 1.039856 TTTTTGCTGGAACTGGAGCC 58.960 50.000 0.00 0.0 34.04 4.70
218 241 0.185901 TTTTGCTGGAACTGGAGCCT 59.814 50.000 0.00 0.0 34.04 4.58
219 242 0.185901 TTTGCTGGAACTGGAGCCTT 59.814 50.000 0.00 0.0 34.04 4.35
220 243 1.064003 TTGCTGGAACTGGAGCCTTA 58.936 50.000 0.00 0.0 34.04 2.69
221 244 1.289160 TGCTGGAACTGGAGCCTTAT 58.711 50.000 0.00 0.0 34.04 1.73
222 245 1.635487 TGCTGGAACTGGAGCCTTATT 59.365 47.619 0.00 0.0 34.04 1.40
223 246 2.041620 TGCTGGAACTGGAGCCTTATTT 59.958 45.455 0.00 0.0 34.04 1.40
224 247 2.424956 GCTGGAACTGGAGCCTTATTTG 59.575 50.000 0.00 0.0 0.00 2.32
225 248 2.424956 CTGGAACTGGAGCCTTATTTGC 59.575 50.000 0.00 0.0 0.00 3.68
226 249 2.041620 TGGAACTGGAGCCTTATTTGCT 59.958 45.455 0.00 0.0 43.03 3.91
227 250 2.424956 GGAACTGGAGCCTTATTTGCTG 59.575 50.000 0.00 0.0 39.69 4.41
228 251 2.134789 ACTGGAGCCTTATTTGCTGG 57.865 50.000 0.00 0.0 39.69 4.85
229 252 1.635487 ACTGGAGCCTTATTTGCTGGA 59.365 47.619 0.00 0.0 39.69 3.86
230 253 2.041620 ACTGGAGCCTTATTTGCTGGAA 59.958 45.455 0.00 0.0 39.69 3.53
325 348 2.107378 TCCATTAGTGCCAGTTCCAACA 59.893 45.455 0.00 0.0 0.00 3.33
507 530 5.221322 GGTCGTCCTATATAAACCCTTCGTT 60.221 44.000 0.00 0.0 35.70 3.85
559 582 1.748493 CTCCCTCTCCTCTGTTCTTCG 59.252 57.143 0.00 0.0 0.00 3.79
846 869 5.451520 CCTTCTAAATCTCCGTCGTAACCAT 60.452 44.000 0.00 0.0 0.00 3.55
1023 1051 2.635714 GTTTTGATATCCGTCCCCGTT 58.364 47.619 0.00 0.0 0.00 4.44
1026 1054 0.688418 TGATATCCGTCCCCGTTGGT 60.688 55.000 0.00 0.0 34.77 3.67
1047 1075 4.382685 GGTCCTCGTCCTTGTTATGATTCA 60.383 45.833 0.00 0.0 0.00 2.57
1315 2177 4.521146 AGATCAAGATGGAGAAAATGCGT 58.479 39.130 0.00 0.0 0.00 5.24
1525 2788 8.795842 ATTAATTTGGTCTATTCGGTGTTGTA 57.204 30.769 0.00 0.0 0.00 2.41
1818 3086 0.905357 AGAAGCTGAGCCGGTAATGT 59.095 50.000 1.90 0.0 0.00 2.71
1837 3105 0.614979 TAGGAAGAAGCTGAGCCGGT 60.615 55.000 1.90 0.0 0.00 5.28
1870 3138 1.209990 AGCTGAAGAAGAGGCATCAGG 59.790 52.381 0.00 0.0 39.69 3.86
2133 3401 1.134694 GACAACGAATTGCCCGAGC 59.865 57.895 0.00 0.0 39.66 5.03
2164 3432 1.032014 GCAAAGAAGGTTGTCTGCCA 58.968 50.000 0.00 0.0 0.00 4.92
2214 3482 2.670229 GCATGCCCTAATGATTGCATCG 60.670 50.000 6.36 0.0 42.22 3.84
2329 3597 2.509561 GCGCCCGAGGAAGAAGAC 60.510 66.667 0.00 0.0 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.957395 AGGCAAATGACGGCTGACAG 60.957 55.000 0.00 0.00 37.96 3.51
39 40 2.159296 AGTTCCAACAAAAACACCTCGC 60.159 45.455 0.00 0.00 0.00 5.03
104 106 0.118144 AGAGAAGAGCTCCAGGGGTT 59.882 55.000 10.93 0.00 45.10 4.11
119 121 7.448161 TCCAGCAAAAATCAAATTCAGTAGAGA 59.552 33.333 0.00 0.00 0.00 3.10
121 123 7.523293 TCCAGCAAAAATCAAATTCAGTAGA 57.477 32.000 0.00 0.00 0.00 2.59
152 175 6.153680 CCCCAGTGGTTGTAGCAAAAATAATA 59.846 38.462 8.74 0.00 0.00 0.98
198 221 1.039856 GGCTCCAGTTCCAGCAAAAA 58.960 50.000 0.00 0.00 37.38 1.94
199 222 0.185901 AGGCTCCAGTTCCAGCAAAA 59.814 50.000 0.00 0.00 37.38 2.44
200 223 0.185901 AAGGCTCCAGTTCCAGCAAA 59.814 50.000 0.00 0.00 37.38 3.68
201 224 1.064003 TAAGGCTCCAGTTCCAGCAA 58.936 50.000 0.00 0.00 37.38 3.91
202 225 1.289160 ATAAGGCTCCAGTTCCAGCA 58.711 50.000 0.00 0.00 37.38 4.41
203 226 2.424956 CAAATAAGGCTCCAGTTCCAGC 59.575 50.000 0.00 0.00 34.65 4.85
204 227 2.424956 GCAAATAAGGCTCCAGTTCCAG 59.575 50.000 0.00 0.00 0.00 3.86
205 228 2.041620 AGCAAATAAGGCTCCAGTTCCA 59.958 45.455 0.00 0.00 36.81 3.53
206 229 2.424956 CAGCAAATAAGGCTCCAGTTCC 59.575 50.000 0.00 0.00 40.23 3.62
207 230 2.424956 CCAGCAAATAAGGCTCCAGTTC 59.575 50.000 0.00 0.00 40.23 3.01
208 231 2.041620 TCCAGCAAATAAGGCTCCAGTT 59.958 45.455 0.00 0.00 40.23 3.16
209 232 1.635487 TCCAGCAAATAAGGCTCCAGT 59.365 47.619 0.00 0.00 40.23 4.00
210 233 2.424956 GTTCCAGCAAATAAGGCTCCAG 59.575 50.000 0.00 0.00 40.23 3.86
211 234 2.446435 GTTCCAGCAAATAAGGCTCCA 58.554 47.619 0.00 0.00 40.23 3.86
212 235 1.751351 GGTTCCAGCAAATAAGGCTCC 59.249 52.381 0.00 0.00 40.23 4.70
213 236 2.728007 AGGTTCCAGCAAATAAGGCTC 58.272 47.619 0.00 0.00 40.23 4.70
214 237 2.907458 AGGTTCCAGCAAATAAGGCT 57.093 45.000 0.00 0.00 43.77 4.58
215 238 3.128764 GTGTAGGTTCCAGCAAATAAGGC 59.871 47.826 0.00 0.00 0.00 4.35
216 239 4.589908 AGTGTAGGTTCCAGCAAATAAGG 58.410 43.478 0.00 0.00 0.00 2.69
217 240 6.407202 ACTAGTGTAGGTTCCAGCAAATAAG 58.593 40.000 0.00 0.00 0.00 1.73
218 241 6.368779 ACTAGTGTAGGTTCCAGCAAATAA 57.631 37.500 0.00 0.00 0.00 1.40
219 242 6.893554 TCTACTAGTGTAGGTTCCAGCAAATA 59.106 38.462 5.39 0.00 44.61 1.40
220 243 4.910458 ACTAGTGTAGGTTCCAGCAAAT 57.090 40.909 0.00 0.00 0.00 2.32
221 244 5.081728 TCTACTAGTGTAGGTTCCAGCAAA 58.918 41.667 5.39 0.00 44.61 3.68
222 245 4.669700 TCTACTAGTGTAGGTTCCAGCAA 58.330 43.478 5.39 0.00 44.61 3.91
223 246 4.311520 TCTACTAGTGTAGGTTCCAGCA 57.688 45.455 5.39 0.00 44.61 4.41
224 247 5.656213 TTTCTACTAGTGTAGGTTCCAGC 57.344 43.478 5.39 0.00 44.61 4.85
225 248 7.097834 CCTTTTTCTACTAGTGTAGGTTCCAG 58.902 42.308 5.39 0.00 44.61 3.86
226 249 6.013984 CCCTTTTTCTACTAGTGTAGGTTCCA 60.014 42.308 5.39 0.00 44.61 3.53
227 250 6.013898 ACCCTTTTTCTACTAGTGTAGGTTCC 60.014 42.308 5.39 0.00 44.61 3.62
228 251 7.002250 ACCCTTTTTCTACTAGTGTAGGTTC 57.998 40.000 5.39 0.00 44.61 3.62
229 252 6.556116 TGACCCTTTTTCTACTAGTGTAGGTT 59.444 38.462 5.39 0.00 44.61 3.50
230 253 6.080009 TGACCCTTTTTCTACTAGTGTAGGT 58.920 40.000 5.39 1.00 44.61 3.08
316 339 1.296715 CCGCCTAGCTGTTGGAACT 59.703 57.895 0.00 0.00 0.00 3.01
325 348 4.150454 AGCTCCTCCCGCCTAGCT 62.150 66.667 0.00 0.00 40.41 3.32
393 416 3.136809 TGCCACCACTTTCTTTAGTACCA 59.863 43.478 0.00 0.00 0.00 3.25
507 530 0.033504 GAAGAACAGAGTGCGGGTGA 59.966 55.000 0.00 0.00 0.00 4.02
559 582 3.119316 TGATGAACTCGAGAGGAAGAAGC 60.119 47.826 21.68 0.63 0.00 3.86
1023 1051 2.531771 TCATAACAAGGACGAGGACCA 58.468 47.619 0.00 0.00 0.00 4.02
1026 1054 4.709886 TCTGAATCATAACAAGGACGAGGA 59.290 41.667 0.00 0.00 0.00 3.71
1340 2356 1.001746 AGCCTCACTATCGATGGCATG 59.998 52.381 21.70 9.25 45.42 4.06
1525 2788 2.017049 GAAAAGTATGCACGCCCTCAT 58.983 47.619 0.00 0.00 0.00 2.90
1818 3086 0.614979 ACCGGCTCAGCTTCTTCCTA 60.615 55.000 0.00 0.00 0.00 2.94
1837 3105 2.236146 TCTTCAGCTTCTTCCCGCATTA 59.764 45.455 0.00 0.00 0.00 1.90
1870 3138 2.546795 CCTAGATCATCAACGGGCTCAC 60.547 54.545 0.00 0.00 0.00 3.51
2164 3432 3.689872 TCTGCACCTCTAACCCTAGAT 57.310 47.619 0.00 0.00 33.59 1.98
2214 3482 1.061570 CGTACTCACCGCGGTAGAC 59.938 63.158 33.70 23.24 0.00 2.59
2318 3586 1.270907 TGGCAGGAGTCTTCTTCCTC 58.729 55.000 0.00 0.00 0.00 3.71
2329 3597 0.679002 CCACATCACCTTGGCAGGAG 60.679 60.000 9.53 2.72 44.19 3.69


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

AutoCloner maintained by Alex Coulton.