Multiple sequence alignment - TraesCS1A01G349700

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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 TraesCS1A01G349700 chr1A 100.000 2636 0 0 1 2636 534687348 534684713 0.000000e+00 4868
1 TraesCS1A01G349700 chr1A 96.683 1869 62 0 767 2635 16218898 16220766 0.000000e+00 3109
2 TraesCS1A01G349700 chr2A 97.458 2636 67 0 1 2636 5147566 5150201 0.000000e+00 4497
3 TraesCS1A01G349700 chr2A 97.248 763 20 1 1 763 303638000 303637239 0.000000e+00 1291
4 TraesCS1A01G349700 chr4A 97.307 2636 71 0 1 2636 238129045 238126410 0.000000e+00 4475
5 TraesCS1A01G349700 chr4A 97.003 2636 78 1 1 2636 500426 497792 0.000000e+00 4429
6 TraesCS1A01G349700 chr4A 97.016 2580 77 0 1 2580 535126 532547 0.000000e+00 4338
7 TraesCS1A01G349700 chr4A 95.179 560 26 1 207 766 551493634 551493076 0.000000e+00 883
8 TraesCS1A01G349700 chr4A 95.652 207 9 0 1 207 551494425 551494219 1.510000e-87 333
9 TraesCS1A01G349700 chr5A 97.003 2636 79 0 1 2636 511206245 511208880 0.000000e+00 4431
10 TraesCS1A01G349700 chr5A 97.540 1870 46 0 767 2636 687970178 687972047 0.000000e+00 3199
11 TraesCS1A01G349700 chr5A 97.273 1870 50 1 767 2636 562122493 562120625 0.000000e+00 3169
12 TraesCS1A01G349700 chr6A 97.059 1870 54 1 767 2636 553572041 553570173 0.000000e+00 3147
13 TraesCS1A01G349700 chr7A 96.579 760 26 0 1 760 49820288 49821047 0.000000e+00 1260
14 TraesCS1A01G349700 chr4D 95.437 526 19 1 238 763 295218927 295218407 0.000000e+00 833
15 TraesCS1A01G349700 chr4D 96.667 120 4 0 88 207 295252164 295252045 1.600000e-47 200
16 TraesCS1A01G349700 chr4D 93.913 115 7 0 1 115 295252282 295252168 9.700000e-40 174


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 TraesCS1A01G349700 chr1A 534684713 534687348 2635 True 4868 4868 100.0000 1 2636 1 chr1A.!!$R1 2635
1 TraesCS1A01G349700 chr1A 16218898 16220766 1868 False 3109 3109 96.6830 767 2635 1 chr1A.!!$F1 1868
2 TraesCS1A01G349700 chr2A 5147566 5150201 2635 False 4497 4497 97.4580 1 2636 1 chr2A.!!$F1 2635
3 TraesCS1A01G349700 chr2A 303637239 303638000 761 True 1291 1291 97.2480 1 763 1 chr2A.!!$R1 762
4 TraesCS1A01G349700 chr4A 238126410 238129045 2635 True 4475 4475 97.3070 1 2636 1 chr4A.!!$R3 2635
5 TraesCS1A01G349700 chr4A 497792 500426 2634 True 4429 4429 97.0030 1 2636 1 chr4A.!!$R1 2635
6 TraesCS1A01G349700 chr4A 532547 535126 2579 True 4338 4338 97.0160 1 2580 1 chr4A.!!$R2 2579
7 TraesCS1A01G349700 chr4A 551493076 551494425 1349 True 608 883 95.4155 1 766 2 chr4A.!!$R4 765
8 TraesCS1A01G349700 chr5A 511206245 511208880 2635 False 4431 4431 97.0030 1 2636 1 chr5A.!!$F1 2635
9 TraesCS1A01G349700 chr5A 687970178 687972047 1869 False 3199 3199 97.5400 767 2636 1 chr5A.!!$F2 1869
10 TraesCS1A01G349700 chr5A 562120625 562122493 1868 True 3169 3169 97.2730 767 2636 1 chr5A.!!$R1 1869
11 TraesCS1A01G349700 chr6A 553570173 553572041 1868 True 3147 3147 97.0590 767 2636 1 chr6A.!!$R1 1869
12 TraesCS1A01G349700 chr7A 49820288 49821047 759 False 1260 1260 96.5790 1 760 1 chr7A.!!$F1 759
13 TraesCS1A01G349700 chr4D 295218407 295218927 520 True 833 833 95.4370 238 763 1 chr4D.!!$R1 525

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
83 84 1.153647 CCTTGCATGCGTCTCCGTA 60.154 57.895 14.09 0.0 36.15 4.02 F
979 1565 4.910195 AGTTGTTCCATGCACTGAATCTA 58.090 39.130 3.32 0.0 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1035 1621 1.376424 CATGTTGAGGCCGAGCAGT 60.376 57.895 0.0 0.0 0.00 4.40 R
2225 2811 0.612174 ACAAGCTCCTGGACTCGCTA 60.612 55.000 9.1 0.0 31.48 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
50 51 4.455533 TCTTGTTTATCTCGTGCTGCATTT 59.544 37.500 5.27 0.00 0.00 2.32
83 84 1.153647 CCTTGCATGCGTCTCCGTA 60.154 57.895 14.09 0.00 36.15 4.02
363 949 6.604396 TGTATCCTATTACCTTGTTCGTCTCA 59.396 38.462 0.00 0.00 0.00 3.27
837 1423 6.878317 TCTATCATGCTTGTAACTAGTGCTT 58.122 36.000 0.00 0.00 0.00 3.91
979 1565 4.910195 AGTTGTTCCATGCACTGAATCTA 58.090 39.130 3.32 0.00 0.00 1.98
1035 1621 3.133464 GGCATGCTTGTGGCGCTA 61.133 61.111 18.92 0.00 45.43 4.26
1071 1657 1.656587 TGTCCTGGAGTGCCATTAGT 58.343 50.000 0.00 0.00 44.91 2.24
1220 1806 2.118679 ACTACCATGGTGCTGATGCTA 58.881 47.619 28.17 2.56 40.48 3.49
1299 1885 8.204836 ACTTCTAGCTTTTCTGACTCAAAGTTA 58.795 33.333 0.00 1.25 33.27 2.24
1352 1938 7.316640 ACTGCTAACACAGAGAGTATTTACTG 58.683 38.462 0.00 0.00 40.25 2.74
1538 2124 1.537202 CTTGTACTTGAAGCTGTGGGC 59.463 52.381 0.00 0.00 42.19 5.36
1550 2136 0.527565 CTGTGGGCTAATGTTGGTGC 59.472 55.000 0.00 0.00 0.00 5.01
1573 2159 5.574443 GCTTTTGTTCTACTTGGATGCATTC 59.426 40.000 0.00 0.00 0.00 2.67
1590 2176 1.107945 TTCGTACCCATCATCGAGCA 58.892 50.000 0.00 0.00 33.98 4.26
1751 2337 5.339200 CCCTTTATTCTCTCCTGCCTTTGTA 60.339 44.000 0.00 0.00 0.00 2.41
1812 2398 2.351726 GCCAGTTGAATGTATGGTCGTC 59.648 50.000 0.00 0.00 35.17 4.20
1912 2498 8.400186 TGCATATTCATATTGTGTCTCTGTTTG 58.600 33.333 0.00 0.00 0.00 2.93
2097 2683 2.089201 CAGATGAAGCCATGTTGCTGA 58.911 47.619 0.00 0.00 41.80 4.26
2127 2713 1.381191 TCAGCCCTGACTATCGCCA 60.381 57.895 0.00 0.00 34.14 5.69
2225 2811 8.248904 AGTTGCATAGAAATATGAGAGAGTCT 57.751 34.615 0.00 0.00 0.00 3.24
2369 2955 6.632834 GCTCTTGTTTAAGTATTGTGTGTGTG 59.367 38.462 0.00 0.00 35.38 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 4.274602 TGCAAGGTACATTTAACTCCGA 57.725 40.909 0.00 0.00 0.00 4.55
83 84 1.040646 TCAAGTCACGAGCAGTTCCT 58.959 50.000 0.00 0.00 0.00 3.36
188 189 4.202050 GGGCGCATCTGTTAAATGAAAGAT 60.202 41.667 10.83 0.00 0.00 2.40
363 949 4.097741 CACAGAGAGGAGACAAATCGATCT 59.902 45.833 0.00 0.00 0.00 2.75
653 1239 3.503748 GCCTACAATCAGACACAAGCTTT 59.496 43.478 0.00 0.00 0.00 3.51
701 1287 5.688176 GCTACTCTTGTTACTATAGTGCAGC 59.312 44.000 15.90 4.81 0.00 5.25
837 1423 4.350368 TCCTGTCTAACAACATGAGCAA 57.650 40.909 0.00 0.00 0.00 3.91
1035 1621 1.376424 CATGTTGAGGCCGAGCAGT 60.376 57.895 0.00 0.00 0.00 4.40
1071 1657 3.356639 GATGAGCGTGAGGGCGACA 62.357 63.158 0.00 0.00 38.18 4.35
1299 1885 7.435068 AAAACTCATGCAGTACGAAGTTAAT 57.565 32.000 0.00 0.00 45.11 1.40
1352 1938 4.708726 ACAAAATCTCTATGTTGGCAGC 57.291 40.909 0.00 0.00 34.99 5.25
1538 2124 6.970484 AGTAGAACAAAAGCACCAACATTAG 58.030 36.000 0.00 0.00 0.00 1.73
1550 2136 5.796935 CGAATGCATCCAAGTAGAACAAAAG 59.203 40.000 0.00 0.00 0.00 2.27
1573 2159 1.593006 GTTTGCTCGATGATGGGTACG 59.407 52.381 0.00 0.00 0.00 3.67
1590 2176 2.953821 CCGCTGTTGCATCCGTTT 59.046 55.556 0.00 0.00 39.64 3.60
1751 2337 3.370978 GTCAGCACACGCATACTAACATT 59.629 43.478 0.00 0.00 42.27 2.71
1931 2517 9.233232 CTTTTTGTTGTCGAGCTAGTTAAAATT 57.767 29.630 0.00 0.00 0.00 1.82
2097 2683 2.158475 TCAGGGCTGAGACCAAACAAAT 60.158 45.455 7.31 0.00 34.14 2.32
2127 2713 3.219928 ATGCCGGACTCGCTCGAT 61.220 61.111 5.05 0.00 34.56 3.59
2225 2811 0.612174 ACAAGCTCCTGGACTCGCTA 60.612 55.000 9.10 0.00 31.48 4.26
2314 2900 8.309656 CAGATCACATAATACAAGCTCTATCCA 58.690 37.037 0.00 0.00 0.00 3.41
2369 2955 7.467623 CAGTATTTAGATTGGCAGAGACAAAC 58.532 38.462 0.00 0.00 32.77 2.93
2566 3152 4.762289 TTTTTATTGTTGGGTTGTGGCT 57.238 36.364 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.