Multiple sequence alignment - TraesCS1A01G067100

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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 TraesCS1A01G067100 chr1A 100.000 2195 0 0 1 2195 49248229 49246035 0 4054
1 TraesCS1A01G067100 chr1A 83.493 1666 256 16 541 2195 49357311 49355654 0 1535
2 TraesCS1A01G067100 chr1A 82.948 1642 268 11 554 2189 49295892 49294257 0 1471
3 TraesCS1A01G067100 chr1A 81.383 1837 304 30 357 2175 49349456 49347640 0 1463
4 TraesCS1A01G067100 chr1B 93.588 2199 99 12 1 2195 70172807 70170647 0 3241
5 TraesCS1A01G067100 chr1B 88.874 2202 212 12 1 2195 70188500 70186325 0 2678
6 TraesCS1A01G067100 chr1B 82.952 1660 260 17 541 2189 70696678 70695031 0 1476
7 TraesCS1A01G067100 chr1D 88.465 2202 220 18 1 2195 49620060 49617886 0 2628
8 TraesCS1A01G067100 chr1D 82.654 1839 298 17 358 2189 49975921 49974097 0 1609
9 TraesCS1A01G067100 chr1D 83.554 1660 254 16 541 2189 50111102 50109451 0 1535


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 TraesCS1A01G067100 chr1A 49246035 49248229 2194 True 4054 4054 100.000 1 2195 1 chr1A.!!$R1 2194
1 TraesCS1A01G067100 chr1A 49355654 49357311 1657 True 1535 1535 83.493 541 2195 1 chr1A.!!$R4 1654
2 TraesCS1A01G067100 chr1A 49294257 49295892 1635 True 1471 1471 82.948 554 2189 1 chr1A.!!$R2 1635
3 TraesCS1A01G067100 chr1A 49347640 49349456 1816 True 1463 1463 81.383 357 2175 1 chr1A.!!$R3 1818
4 TraesCS1A01G067100 chr1B 70170647 70172807 2160 True 3241 3241 93.588 1 2195 1 chr1B.!!$R1 2194
5 TraesCS1A01G067100 chr1B 70186325 70188500 2175 True 2678 2678 88.874 1 2195 1 chr1B.!!$R2 2194
6 TraesCS1A01G067100 chr1B 70695031 70696678 1647 True 1476 1476 82.952 541 2189 1 chr1B.!!$R3 1648
7 TraesCS1A01G067100 chr1D 49617886 49620060 2174 True 2628 2628 88.465 1 2195 1 chr1D.!!$R1 2194
8 TraesCS1A01G067100 chr1D 49974097 49975921 1824 True 1609 1609 82.654 358 2189 1 chr1D.!!$R2 1831
9 TraesCS1A01G067100 chr1D 50109451 50111102 1651 True 1535 1535 83.554 541 2189 1 chr1D.!!$R3 1648

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
393 414 0.034574 AAGCACCACACACCAGACAA 60.035 50.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2051 0.885879 TGCAAGCATGGAAGAAGCAG 59.114 50.0 0.0 0.0 0.0 4.24 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
81 83 0.809385 CTGTGAGCTGAGCCCAATTG 59.191 55.000 0.00 0.00 0.00 2.32
85 87 0.455005 GAGCTGAGCCCAATTGCTTC 59.545 55.000 0.00 0.00 42.95 3.86
95 97 3.255642 GCCCAATTGCTTCACTCTAACAA 59.744 43.478 0.00 0.00 0.00 2.83
100 102 6.072286 CCAATTGCTTCACTCTAACAAGTCAT 60.072 38.462 0.00 0.00 0.00 3.06
104 106 6.233434 TGCTTCACTCTAACAAGTCATGAAT 58.767 36.000 0.00 0.00 0.00 2.57
111 113 6.870965 ACTCTAACAAGTCATGAATCTGACAC 59.129 38.462 0.00 0.00 46.45 3.67
114 116 3.750130 ACAAGTCATGAATCTGACACAGC 59.250 43.478 0.00 0.00 46.45 4.40
124 126 2.929641 TCTGACACAGCCACATTCAAA 58.070 42.857 0.00 0.00 0.00 2.69
209 214 4.789481 GCACATCATACACCAATTTAGCCG 60.789 45.833 0.00 0.00 0.00 5.52
287 300 1.257743 GGTGCAGTGAGACCAGAGTA 58.742 55.000 6.84 0.00 31.97 2.59
293 306 2.828520 CAGTGAGACCAGAGTACACCAT 59.171 50.000 0.00 0.00 35.37 3.55
302 315 3.515502 CCAGAGTACACCATGAGGAAGAA 59.484 47.826 0.00 0.00 38.69 2.52
309 322 4.023980 ACACCATGAGGAAGAACTCGATA 58.976 43.478 0.00 0.00 40.39 2.92
341 354 4.978099 ACAAGATCCACCATCATATGACC 58.022 43.478 7.78 0.00 33.29 4.02
342 355 4.202503 ACAAGATCCACCATCATATGACCC 60.203 45.833 7.78 0.00 33.29 4.46
343 356 2.915604 AGATCCACCATCATATGACCCC 59.084 50.000 7.78 0.00 33.29 4.95
344 357 1.055849 TCCACCATCATATGACCCCG 58.944 55.000 7.78 0.00 0.00 5.73
345 358 1.055849 CCACCATCATATGACCCCGA 58.944 55.000 7.78 0.00 0.00 5.14
346 359 1.419762 CCACCATCATATGACCCCGAA 59.580 52.381 7.78 0.00 0.00 4.30
347 360 2.494059 CACCATCATATGACCCCGAAC 58.506 52.381 7.78 0.00 0.00 3.95
348 361 2.123589 ACCATCATATGACCCCGAACA 58.876 47.619 7.78 0.00 0.00 3.18
349 362 2.158813 ACCATCATATGACCCCGAACAC 60.159 50.000 7.78 0.00 0.00 3.32
350 363 2.494059 CATCATATGACCCCGAACACC 58.506 52.381 7.78 0.00 0.00 4.16
393 414 0.034574 AAGCACCACACACCAGACAA 60.035 50.000 0.00 0.00 0.00 3.18
417 438 0.397564 TGCACAAGGAGACAGCATGA 59.602 50.000 0.00 0.00 39.69 3.07
427 448 1.344438 AGACAGCATGAAGACGGAACA 59.656 47.619 0.00 0.00 39.69 3.18
428 449 2.143122 GACAGCATGAAGACGGAACAA 58.857 47.619 0.00 0.00 39.69 2.83
483 504 0.607217 CAGAGCAGAACACCATGGCA 60.607 55.000 13.04 0.00 0.00 4.92
503 524 1.299541 CACGGCATTATCACCCAGAC 58.700 55.000 0.00 0.00 0.00 3.51
506 527 0.535102 GGCATTATCACCCAGACCGG 60.535 60.000 0.00 0.00 0.00 5.28
699 720 2.676342 AGACAACAACAACGAAGTGGTC 59.324 45.455 0.00 0.00 44.39 4.02
753 774 8.955388 TCAACTTTAGACATATAATTTGCTGCA 58.045 29.630 0.00 0.00 0.00 4.41
777 798 3.265995 TGACTATCTCCCCCTTTTCCAAC 59.734 47.826 0.00 0.00 0.00 3.77
794 815 8.554835 TTTTCCAACAACGTTCTGATGATATA 57.445 30.769 0.00 0.00 0.00 0.86
924 945 4.320057 CCGTAAGTAGAGGCATTAGGTACG 60.320 50.000 0.00 0.00 33.45 3.67
1094 1119 6.375736 TCATCGGTGCAATTATTCCTACAAAA 59.624 34.615 0.00 0.00 0.00 2.44
1183 1208 4.330620 ACAACTTCTTTGCAGCAATTGTTG 59.669 37.500 25.05 25.05 39.01 3.33
1223 1248 6.418101 ACCCATCCAGTATGATGTTATATGC 58.582 40.000 0.00 0.00 40.43 3.14
1804 1835 6.200808 CGCATTTCAGTCAACATATGCATAA 58.799 36.000 11.13 0.00 38.55 1.90
2053 2084 3.650298 TTGCAGAGGGAGGCCATGC 62.650 63.158 5.01 5.81 37.40 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.370209 CCTGAAATGCTGTGAGATCTGGA 60.370 47.826 0.00 0.00 0.00 3.86
81 83 6.593382 AGATTCATGACTTGTTAGAGTGAAGC 59.407 38.462 0.00 0.00 32.13 3.86
85 87 7.288317 GTCAGATTCATGACTTGTTAGAGTG 57.712 40.000 0.00 0.00 45.03 3.51
100 102 2.865119 ATGTGGCTGTGTCAGATTCA 57.135 45.000 0.66 0.00 32.44 2.57
104 106 2.636647 TTGAATGTGGCTGTGTCAGA 57.363 45.000 0.66 0.00 32.44 3.27
111 113 2.827322 TCTTGGGATTTGAATGTGGCTG 59.173 45.455 0.00 0.00 0.00 4.85
114 116 4.870123 TTGTCTTGGGATTTGAATGTGG 57.130 40.909 0.00 0.00 0.00 4.17
124 126 6.494491 TGTTTCTCAATCATTTGTCTTGGGAT 59.506 34.615 0.00 0.00 29.94 3.85
171 176 2.719531 TGTGCAGTTCCAAGGTGTTA 57.280 45.000 0.00 0.00 0.00 2.41
209 214 0.740737 CCTGCGGATGGTTTCCATTC 59.259 55.000 0.00 0.00 45.26 2.67
229 241 2.597217 TTTGGAACCCAGCTGCGG 60.597 61.111 8.66 13.80 33.81 5.69
230 242 1.733402 TTGTTTGGAACCCAGCTGCG 61.733 55.000 8.66 1.40 33.81 5.18
231 243 0.681175 ATTGTTTGGAACCCAGCTGC 59.319 50.000 8.66 0.00 33.81 5.25
232 244 2.231235 GGTATTGTTTGGAACCCAGCTG 59.769 50.000 6.78 6.78 33.81 4.24
233 245 2.158385 TGGTATTGTTTGGAACCCAGCT 60.158 45.455 0.00 0.00 33.81 4.24
234 246 2.243810 TGGTATTGTTTGGAACCCAGC 58.756 47.619 0.00 0.00 33.81 4.85
287 300 2.248248 TCGAGTTCTTCCTCATGGTGT 58.752 47.619 0.00 0.00 34.23 4.16
293 306 5.105716 CCAGAGTTTATCGAGTTCTTCCTCA 60.106 44.000 0.00 0.00 0.00 3.86
302 315 4.087182 TCTTGTCCCAGAGTTTATCGAGT 58.913 43.478 0.00 0.00 0.00 4.18
334 347 0.544697 GTGGGTGTTCGGGGTCATAT 59.455 55.000 0.00 0.00 0.00 1.78
335 348 0.836830 TGTGGGTGTTCGGGGTCATA 60.837 55.000 0.00 0.00 0.00 2.15
336 349 1.710996 TTGTGGGTGTTCGGGGTCAT 61.711 55.000 0.00 0.00 0.00 3.06
337 350 1.710996 ATTGTGGGTGTTCGGGGTCA 61.711 55.000 0.00 0.00 0.00 4.02
338 351 0.325602 TATTGTGGGTGTTCGGGGTC 59.674 55.000 0.00 0.00 0.00 4.46
339 352 0.996583 ATATTGTGGGTGTTCGGGGT 59.003 50.000 0.00 0.00 0.00 4.95
340 353 2.137810 AATATTGTGGGTGTTCGGGG 57.862 50.000 0.00 0.00 0.00 5.73
341 354 4.529109 AAAAATATTGTGGGTGTTCGGG 57.471 40.909 0.00 0.00 0.00 5.14
342 355 5.047943 TGGTAAAAATATTGTGGGTGTTCGG 60.048 40.000 0.00 0.00 0.00 4.30
343 356 6.015027 TGGTAAAAATATTGTGGGTGTTCG 57.985 37.500 0.00 0.00 0.00 3.95
344 357 9.581099 CTAATGGTAAAAATATTGTGGGTGTTC 57.419 33.333 0.00 0.00 0.00 3.18
345 358 8.038351 GCTAATGGTAAAAATATTGTGGGTGTT 58.962 33.333 0.00 0.00 0.00 3.32
346 359 7.179338 TGCTAATGGTAAAAATATTGTGGGTGT 59.821 33.333 0.00 0.00 0.00 4.16
347 360 7.551585 TGCTAATGGTAAAAATATTGTGGGTG 58.448 34.615 0.00 0.00 0.00 4.61
348 361 7.726033 TGCTAATGGTAAAAATATTGTGGGT 57.274 32.000 0.00 0.00 0.00 4.51
349 362 9.442047 TTTTGCTAATGGTAAAAATATTGTGGG 57.558 29.630 0.00 0.00 36.77 4.61
412 433 3.914364 GTCATTTTGTTCCGTCTTCATGC 59.086 43.478 0.00 0.00 0.00 4.06
417 438 4.156008 GCTATGGTCATTTTGTTCCGTCTT 59.844 41.667 0.00 0.00 0.00 3.01
427 448 3.315191 GGCGTGTATGCTATGGTCATTTT 59.685 43.478 0.00 0.00 34.52 1.82
428 449 2.878406 GGCGTGTATGCTATGGTCATTT 59.122 45.455 0.00 0.00 34.52 2.32
483 504 0.908910 TCTGGGTGATAATGCCGTGT 59.091 50.000 0.00 0.00 0.00 4.49
503 524 3.019003 ATCCACTCGCCAAGACCGG 62.019 63.158 0.00 0.00 0.00 5.28
506 527 0.036388 TTCCATCCACTCGCCAAGAC 60.036 55.000 0.00 0.00 0.00 3.01
544 565 2.082231 GTTCGGAGCTCCCTTTTAACC 58.918 52.381 27.20 0.00 0.00 2.85
699 720 6.419980 AAGATCATCTCTTTTGAAGCTTCG 57.580 37.500 21.11 7.32 41.60 3.79
753 774 4.119155 TGGAAAAGGGGGAGATAGTCAAT 58.881 43.478 0.00 0.00 0.00 2.57
794 815 5.740513 GCTCCCAGCTCTCGTCTTATAAATT 60.741 44.000 0.00 0.00 38.45 1.82
1094 1119 6.042552 CACATACAGGATAGTTCTTGGAGGAT 59.957 42.308 0.00 0.00 33.43 3.24
1183 1208 0.752658 GGGTTATTTCATGCTGGGGC 59.247 55.000 0.00 0.00 39.26 5.80
1223 1248 5.360591 AGAGAGTTAAACCTGACACTGTTG 58.639 41.667 0.00 0.00 0.00 3.33
1804 1835 2.848694 AGTGTGGGATGATGGATGAAGT 59.151 45.455 0.00 0.00 0.00 3.01
2020 2051 0.885879 TGCAAGCATGGAAGAAGCAG 59.114 50.000 0.00 0.00 0.00 4.24
2053 2084 5.579904 CAGATACTGTCACTTGGAACTCATG 59.420 44.000 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.