Multiple sequence alignment - TraesCS1A01G212100

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 TraesCS1A01G212100 chr1A 100.000 2267 0 0 1 2267 374952915 374955181 0 4187
1 TraesCS1A01G212100 chr6D 95.461 1498 60 3 775 2267 345776277 345777771 0 2383
2 TraesCS1A01G212100 chr6D 91.793 792 54 8 3 783 345767208 345767999 0 1092
3 TraesCS1A01G212100 chr3D 83.647 2287 341 22 4 2267 303136111 303138387 0 2121
4 TraesCS1A01G212100 chr6A 83.137 2289 354 21 3 2267 431238788 431236508 0 2060
5 TraesCS1A01G212100 chr5B 94.843 1144 51 4 1124 2267 507649382 507648247 0 1779
6 TraesCS1A01G212100 chr3B 84.089 1433 207 14 849 2267 422135753 422137178 0 1363
7 TraesCS1A01G212100 chr4B 93.741 735 43 3 1533 2267 402968862 402969593 0 1099
8 TraesCS1A01G212100 chr7B 93.579 732 45 2 1533 2264 113064511 113065240 0 1090
9 TraesCS1A01G212100 chr7A 85.339 914 128 5 1355 2267 116595157 116596065 0 941
10 TraesCS1A01G212100 chr1B 94.010 601 34 2 1667 2267 196625642 196626240 0 909


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 TraesCS1A01G212100 chr1A 374952915 374955181 2266 False 4187 4187 100.000 1 2267 1 chr1A.!!$F1 2266
1 TraesCS1A01G212100 chr6D 345776277 345777771 1494 False 2383 2383 95.461 775 2267 1 chr6D.!!$F2 1492
2 TraesCS1A01G212100 chr6D 345767208 345767999 791 False 1092 1092 91.793 3 783 1 chr6D.!!$F1 780
3 TraesCS1A01G212100 chr3D 303136111 303138387 2276 False 2121 2121 83.647 4 2267 1 chr3D.!!$F1 2263
4 TraesCS1A01G212100 chr6A 431236508 431238788 2280 True 2060 2060 83.137 3 2267 1 chr6A.!!$R1 2264
5 TraesCS1A01G212100 chr5B 507648247 507649382 1135 True 1779 1779 94.843 1124 2267 1 chr5B.!!$R1 1143
6 TraesCS1A01G212100 chr3B 422135753 422137178 1425 False 1363 1363 84.089 849 2267 1 chr3B.!!$F1 1418
7 TraesCS1A01G212100 chr4B 402968862 402969593 731 False 1099 1099 93.741 1533 2267 1 chr4B.!!$F1 734
8 TraesCS1A01G212100 chr7B 113064511 113065240 729 False 1090 1090 93.579 1533 2264 1 chr7B.!!$F1 731
9 TraesCS1A01G212100 chr7A 116595157 116596065 908 False 941 941 85.339 1355 2267 1 chr7A.!!$F1 912
10 TraesCS1A01G212100 chr1B 196625642 196626240 598 False 909 909 94.010 1667 2267 1 chr1B.!!$F1 600

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
315 325 0.174389 CGCAGCTCTTCTTCTAGGCA 59.826 55.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 1520 0.462225 TTGCTCGACGGTTTGGACAA 60.462 50.0 0.0 0.0 0.0 3.18 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
40 41 3.973516 CTACCGCGGCGCATCCTA 61.974 66.667 32.61 13.02 0.00 2.94
46 47 2.028190 CGGCGCATCCTAGTCCAG 59.972 66.667 10.83 0.00 0.00 3.86
49 50 1.464376 GGCGCATCCTAGTCCAGCTA 61.464 60.000 10.83 0.00 0.00 3.32
84 85 3.822192 CACTCCCGATGCCGACGA 61.822 66.667 0.00 0.00 38.22 4.20
86 87 4.907034 CTCCCGATGCCGACGACG 62.907 72.222 0.00 0.00 38.22 5.12
121 122 2.689034 CGCTCCCTCCCTCCCTTT 60.689 66.667 0.00 0.00 0.00 3.11
213 214 4.016629 CGACGACCGTGACCGACA 62.017 66.667 0.00 0.00 35.63 4.35
247 248 2.558359 TGACAGAGACGATGAGCAAGAA 59.442 45.455 0.00 0.00 0.00 2.52
308 318 2.433318 GCGACCGCAGCTCTTCTT 60.433 61.111 9.73 0.00 41.49 2.52
315 325 0.174389 CGCAGCTCTTCTTCTAGGCA 59.826 55.000 0.00 0.00 0.00 4.75
352 363 4.338539 GCTCACACGACGACCGGT 62.339 66.667 6.92 6.92 43.93 5.28
570 582 1.597027 CACTGAAGAAACCCGCGGT 60.597 57.895 26.12 9.63 37.65 5.68
592 604 0.622738 ATCACCTCCTGCATCACCCT 60.623 55.000 0.00 0.00 0.00 4.34
643 655 4.475444 CCTCCCCCACGCTCCCTA 62.475 72.222 0.00 0.00 0.00 3.53
719 731 1.229336 CAGGGTGGTCCTCTCCAGT 60.229 63.158 0.00 0.00 46.12 4.00
759 771 2.758207 TTCGTTGCCCCCAAGTCCA 61.758 57.895 0.00 0.00 0.00 4.02
778 790 2.571212 CAAGCACACCCTTGTTCACTA 58.429 47.619 0.00 0.00 37.89 2.74
855 867 2.158219 TCAAGTGGTTGGGACTCCTCTA 60.158 50.000 0.00 0.00 34.09 2.43
965 977 1.348064 ACCGGTCTGAACCTGATTCA 58.652 50.000 0.00 0.00 45.39 2.57
969 981 3.133003 CCGGTCTGAACCTGATTCATAGT 59.867 47.826 0.00 0.00 46.37 2.12
981 993 5.074746 TGATTCATAGTAGCCCCAGACTA 57.925 43.478 0.00 0.00 32.86 2.59
1025 1037 2.791383 ATCGTGATGCTAGCTGAGAC 57.209 50.000 17.23 6.49 0.00 3.36
1038 1050 0.662619 CTGAGACGTTGCTTTGCCAA 59.337 50.000 0.00 0.00 0.00 4.52
1095 1107 3.868077 CAGAAGCAGCCATAGACAAGTAC 59.132 47.826 0.00 0.00 0.00 2.73
1253 1274 0.329596 GGCCAAGGTGGAGAAGATGT 59.670 55.000 0.00 0.00 40.96 3.06
1257 1278 2.616510 CCAAGGTGGAGAAGATGTGACC 60.617 54.545 0.00 0.00 40.96 4.02
1289 1319 2.226674 GCTTCTGCCCTGTTTAGTTGAC 59.773 50.000 0.00 0.00 0.00 3.18
1319 1349 5.411493 TCCCAGTTCCTATGATTAGCCATA 58.589 41.667 0.00 0.00 0.00 2.74
1345 1375 5.410132 TCATGTTATTGTACTGTTCGTTGGG 59.590 40.000 0.00 0.00 0.00 4.12
1392 1422 5.385198 ACTACCTTGTGATGTTGATTTGGT 58.615 37.500 0.00 0.00 0.00 3.67
1411 1441 7.667043 TTTGGTAAGACTTATGTTAGTGCTG 57.333 36.000 0.00 0.00 0.00 4.41
1490 1520 6.423776 AATTGGAATGTTTGTGGTCTCAAT 57.576 33.333 0.00 0.00 0.00 2.57
1557 1587 3.997021 CTCTTGCAACCTCGTTTGTCTAT 59.003 43.478 0.00 0.00 0.00 1.98
1695 1730 8.055790 TCCTCTAGAATGAAGACTACATGAAGA 58.944 37.037 0.00 0.00 0.00 2.87
1898 1933 5.365619 AGACTTCAACCAAGTTTATCGTGT 58.634 37.500 0.00 0.00 46.10 4.49
1921 1956 3.674753 CCGAGACAAAAACCATGCAAATC 59.325 43.478 0.00 0.00 0.00 2.17
1985 2020 4.253685 TCCTGTGAGCTAAAAGAAATCCG 58.746 43.478 0.00 0.00 0.00 4.18
2020 2055 1.139058 AGTTCACTTGGAGCAACGAGT 59.861 47.619 0.00 0.00 35.47 4.18
2087 2122 3.711190 TGAGGATTGGGATCTCGATTTCA 59.289 43.478 0.00 2.18 32.66 2.69
2138 2173 1.299648 CTCTCGGACCATTGCCCAA 59.700 57.895 0.00 0.00 0.00 4.12
2183 2218 5.478332 GGACCAAAATGACCAAGATCTTTCT 59.522 40.000 4.86 0.00 0.00 2.52
2256 2291 1.460255 CCTGGGCTGAGGAAACCAA 59.540 57.895 0.00 0.00 34.69 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.500448 TCGATCAGATCTAGCTGGACT 57.500 47.619 0.13 0.00 36.55 3.85
46 47 5.468746 AGTGTAGTCTTCGATCAGATCTAGC 59.531 44.000 8.82 3.34 0.00 3.42
49 50 4.819630 GGAGTGTAGTCTTCGATCAGATCT 59.180 45.833 8.82 0.00 0.00 2.75
52 53 3.280295 GGGAGTGTAGTCTTCGATCAGA 58.720 50.000 0.00 0.00 0.00 3.27
168 169 4.388499 GTGCGTCCCCATCACGGT 62.388 66.667 0.00 0.00 37.74 4.83
226 227 2.162681 TCTTGCTCATCGTCTCTGTCA 58.837 47.619 0.00 0.00 0.00 3.58
293 294 1.202359 CCTAGAAGAAGAGCTGCGGTC 60.202 57.143 0.00 0.00 0.00 4.79
294 295 0.820871 CCTAGAAGAAGAGCTGCGGT 59.179 55.000 0.00 0.00 0.00 5.68
295 296 0.529555 GCCTAGAAGAAGAGCTGCGG 60.530 60.000 0.00 0.00 0.00 5.69
296 297 0.174389 TGCCTAGAAGAAGAGCTGCG 59.826 55.000 0.00 0.00 0.00 5.18
297 298 1.650825 GTGCCTAGAAGAAGAGCTGC 58.349 55.000 0.00 0.00 0.00 5.25
299 300 1.840737 TCGTGCCTAGAAGAAGAGCT 58.159 50.000 0.00 0.00 0.00 4.09
301 302 4.297510 CATCATCGTGCCTAGAAGAAGAG 58.702 47.826 0.00 0.00 0.00 2.85
302 303 3.491619 GCATCATCGTGCCTAGAAGAAGA 60.492 47.826 0.00 0.00 39.18 2.87
303 304 2.799412 GCATCATCGTGCCTAGAAGAAG 59.201 50.000 0.00 0.00 39.18 2.85
304 305 2.826428 GCATCATCGTGCCTAGAAGAA 58.174 47.619 0.00 0.00 39.18 2.52
315 325 4.221422 CCGTCCCGGCATCATCGT 62.221 66.667 0.00 0.00 41.17 3.73
339 350 4.274700 CACCACCGGTCGTCGTGT 62.275 66.667 2.59 0.00 37.11 4.49
352 363 4.357947 GTCACGCTCCTCGCACCA 62.358 66.667 0.00 0.00 43.23 4.17
376 387 0.249784 CTGCCGTCATCATAGCAGCT 60.250 55.000 0.00 0.00 45.44 4.24
379 390 1.227645 GCCTGCCGTCATCATAGCA 60.228 57.895 0.00 0.00 0.00 3.49
410 421 5.498393 AGTTGTCGATCTTCCTGTAGTCTA 58.502 41.667 0.00 0.00 0.00 2.59
411 422 4.337145 AGTTGTCGATCTTCCTGTAGTCT 58.663 43.478 0.00 0.00 0.00 3.24
570 582 2.042464 GGTGATGCAGGAGGTGATCTA 58.958 52.381 0.00 0.00 0.00 1.98
643 655 2.124320 AGCACAACGCAACCAGGT 60.124 55.556 0.00 0.00 46.13 4.00
719 731 2.029288 GCACGCTGCTGCAGTCTAA 61.029 57.895 28.50 0.00 40.96 2.10
759 771 2.172717 AGTAGTGAACAAGGGTGTGCTT 59.827 45.455 0.00 0.00 38.27 3.91
778 790 4.164258 GGCAACCACTTCAGCAGT 57.836 55.556 0.00 0.00 35.35 4.40
855 867 1.079127 CGGAGGACAAGGCACGAAT 60.079 57.895 0.00 0.00 0.00 3.34
965 977 2.966516 GCTTGTAGTCTGGGGCTACTAT 59.033 50.000 10.07 0.00 39.47 2.12
969 981 0.252513 TGGCTTGTAGTCTGGGGCTA 60.253 55.000 0.00 0.00 0.00 3.93
981 993 3.491447 GCATGTCTTTGTTCTTGGCTTGT 60.491 43.478 0.00 0.00 0.00 3.16
1101 1113 3.710722 AGCTGGCCGTGGAAGAGG 61.711 66.667 0.00 0.00 0.00 3.69
1289 1319 5.667539 ATCATAGGAACTGGGATACATCG 57.332 43.478 0.00 0.00 41.52 3.84
1319 1349 7.361713 CCCAACGAACAGTACAATAACATGAAT 60.362 37.037 0.00 0.00 0.00 2.57
1345 1375 1.601430 GAGCAAACATGCCTAGCTAGC 59.399 52.381 15.74 6.62 35.36 3.42
1392 1422 6.852420 AGGACAGCACTAACATAAGTCTTA 57.148 37.500 0.00 0.00 0.00 2.10
1411 1441 3.378427 GGGCTACATCATCAACAAAGGAC 59.622 47.826 0.00 0.00 0.00 3.85
1479 1509 2.955660 GGTTTGGACAATTGAGACCACA 59.044 45.455 13.59 8.80 31.87 4.17
1490 1520 0.462225 TTGCTCGACGGTTTGGACAA 60.462 50.000 0.00 0.00 0.00 3.18
1557 1587 3.620427 TGCGGCTAATTTTGTCTCCTA 57.380 42.857 0.00 0.00 0.00 2.94
1675 1710 7.093156 TGTCCATCTTCATGTAGTCTTCATTCT 60.093 37.037 0.00 0.00 0.00 2.40
1898 1933 1.974265 TGCATGGTTTTTGTCTCGGA 58.026 45.000 0.00 0.00 0.00 4.55
1921 1956 1.857217 CACCAAGCGAGATCGATCAAG 59.143 52.381 26.47 19.46 43.02 3.02
2020 2055 2.097825 GCTCAAGGTCGGGTTAGTCTA 58.902 52.381 0.00 0.00 0.00 2.59
2087 2122 1.171308 GCATGGAGAATGTGTGTGCT 58.829 50.000 0.00 0.00 38.65 4.40
2138 2173 2.503356 CCTTGTCACTAGCCAAGAGGAT 59.497 50.000 15.34 0.00 40.36 3.24
2183 2218 5.477607 TTAATCCAGAAGTTCTCGAACCA 57.522 39.130 1.26 0.00 42.06 3.67


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

AutoCloner maintained by Alex Coulton.