Multiple sequence alignment - TraesCS4A01G161300

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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 TraesCS4A01G161300 chr4A 100.000 2243 0 0 1 2243 350172240 350174482 0 4143
1 TraesCS4A01G161300 chr6A 96.389 2243 81 0 1 2243 155857299 155859541 0 3694
2 TraesCS4A01G161300 chr6A 95.854 2243 92 1 1 2243 375860759 375858518 0 3626
3 TraesCS4A01G161300 chr3B 96.386 2241 79 2 1 2240 483333212 483335451 0 3688
4 TraesCS4A01G161300 chr3B 95.857 2245 90 3 1 2243 575839742 575837499 0 3627
5 TraesCS4A01G161300 chr2A 96.346 2244 81 1 1 2243 750453591 750451348 0 3688
6 TraesCS4A01G161300 chr4B 96.207 2241 83 2 1 2240 209242557 209244796 0 3666
7 TraesCS4A01G161300 chr3A 95.641 2019 76 5 235 2243 230228527 230226511 0 3230
8 TraesCS4A01G161300 chr7B 96.412 1310 47 0 1 1310 742948738 742947429 0 2159
9 TraesCS4A01G161300 chr4D 96.136 1320 49 2 1 1319 123350121 123351439 0 2154
10 TraesCS4A01G161300 chr5B 97.989 1044 20 1 1201 2243 439641088 439642131 0 1810
11 TraesCS4A01G161300 chrUn 97.985 1042 19 2 1201 2240 171017238 171018279 0 1807
12 TraesCS4A01G161300 chr6B 92.828 725 49 3 1056 1779 401858417 401859139 0 1048


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 TraesCS4A01G161300 chr4A 350172240 350174482 2242 False 4143 4143 100.000 1 2243 1 chr4A.!!$F1 2242
1 TraesCS4A01G161300 chr6A 155857299 155859541 2242 False 3694 3694 96.389 1 2243 1 chr6A.!!$F1 2242
2 TraesCS4A01G161300 chr6A 375858518 375860759 2241 True 3626 3626 95.854 1 2243 1 chr6A.!!$R1 2242
3 TraesCS4A01G161300 chr3B 483333212 483335451 2239 False 3688 3688 96.386 1 2240 1 chr3B.!!$F1 2239
4 TraesCS4A01G161300 chr3B 575837499 575839742 2243 True 3627 3627 95.857 1 2243 1 chr3B.!!$R1 2242
5 TraesCS4A01G161300 chr2A 750451348 750453591 2243 True 3688 3688 96.346 1 2243 1 chr2A.!!$R1 2242
6 TraesCS4A01G161300 chr4B 209242557 209244796 2239 False 3666 3666 96.207 1 2240 1 chr4B.!!$F1 2239
7 TraesCS4A01G161300 chr3A 230226511 230228527 2016 True 3230 3230 95.641 235 2243 1 chr3A.!!$R1 2008
8 TraesCS4A01G161300 chr7B 742947429 742948738 1309 True 2159 2159 96.412 1 1310 1 chr7B.!!$R1 1309
9 TraesCS4A01G161300 chr4D 123350121 123351439 1318 False 2154 2154 96.136 1 1319 1 chr4D.!!$F1 1318
10 TraesCS4A01G161300 chr5B 439641088 439642131 1043 False 1810 1810 97.989 1201 2243 1 chr5B.!!$F1 1042
11 TraesCS4A01G161300 chrUn 171017238 171018279 1041 False 1807 1807 97.985 1201 2240 1 chrUn.!!$F1 1039
12 TraesCS4A01G161300 chr6B 401858417 401859139 722 False 1048 1048 92.828 1056 1779 1 chr6B.!!$F1 723

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
917 921 0.184451 ATTATGGAGGTGCAGGCCAG 59.816 55.0 5.01 0.0 34.74 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 1918 2.541907 AACTGGACTGCAGCCCCAT 61.542 57.895 23.61 11.22 0.0 4.0 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
39 41 0.768622 CGGCCTATATCCCCACCAAA 59.231 55.000 0.00 0.00 0.00 3.28
66 68 7.284034 GTGATCTCCATTACAGATGGACAAATT 59.716 37.037 3.70 0.00 42.81 1.82
100 102 5.352569 ACAGAGCTCTTTTATCACGGAATTG 59.647 40.000 15.27 0.00 0.00 2.32
128 130 3.363673 GCTATTAACGTTGGCTTATCCGC 60.364 47.826 11.99 0.00 37.80 5.54
260 262 1.067283 AGACCTTGATGCTGTGACTCG 60.067 52.381 0.00 0.00 0.00 4.18
287 289 1.065126 ACTCAATAGAGGTGCAAGGCC 60.065 52.381 0.00 0.00 46.44 5.19
379 381 2.146342 CTGTCAACGGCTTCTGTGATT 58.854 47.619 0.00 0.00 0.00 2.57
497 499 5.840940 ACTAACGAAAGAAAGATGGAACG 57.159 39.130 0.00 0.00 0.00 3.95
521 523 6.857964 CGAGATGCTTCTTTAAAAGAAAGCAA 59.142 34.615 24.41 14.56 46.13 3.91
885 889 3.007074 TCAAACTAGTGGTCCGCATAACA 59.993 43.478 4.97 0.00 0.00 2.41
916 920 0.630673 AATTATGGAGGTGCAGGCCA 59.369 50.000 5.01 4.75 35.91 5.36
917 921 0.184451 ATTATGGAGGTGCAGGCCAG 59.816 55.000 5.01 0.00 34.74 4.85
1047 1052 1.026182 CCGGAGCTGCTACAATTGCA 61.026 55.000 13.19 0.00 38.81 4.08
1054 1059 2.099592 GCTGCTACAATTGCATTAGCCA 59.900 45.455 18.65 9.66 39.86 4.75
1091 1096 3.107642 TGGAAACGTCCTCAGTTCTTC 57.892 47.619 0.00 0.00 45.22 2.87
1206 1211 1.411501 GCCCCAATGATGGCCTTTCTA 60.412 52.381 3.32 0.00 46.09 2.10
1213 1218 5.009410 CCAATGATGGCCTTTCTAATCTCAC 59.991 44.000 3.32 0.00 40.58 3.51
1427 1435 1.160137 GCGATTCAAGCCAAGAGTGT 58.840 50.000 0.00 0.00 0.00 3.55
1527 1535 4.938226 CCACCTTCCAATCTTCTTAGTCAC 59.062 45.833 0.00 0.00 0.00 3.67
1658 1666 7.417456 GGGACAGAAAGTTTTGTAAAATGGAGT 60.417 37.037 0.00 0.00 0.00 3.85
1910 1918 4.864247 GCTTTTCTGAACTGCTTGTTTTCA 59.136 37.500 6.57 0.00 39.30 2.69
1911 1919 5.521372 GCTTTTCTGAACTGCTTGTTTTCAT 59.479 36.000 6.57 0.00 39.30 2.57
2218 2235 6.921486 AATGATAGGAAATATGCCATGCAA 57.079 33.333 0.00 0.00 43.62 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.444022 GGATATAGGCCGATACGTCTCCTA 60.444 50.000 7.83 0.00 34.18 2.94
9 10 3.543665 GATATAGGCCGATACGTCTCCT 58.456 50.000 7.83 0.00 0.00 3.69
100 102 1.669265 GCCAACGTTAATAGCTGGTCC 59.331 52.381 0.00 0.00 0.00 4.46
128 130 2.258591 CAGACCCGACGTGACTGG 59.741 66.667 0.00 0.00 0.00 4.00
209 211 1.300697 GTGAAGGCGGTCACTTCGT 60.301 57.895 14.70 0.00 45.59 3.85
217 219 1.247567 CCAAATTGAGTGAAGGCGGT 58.752 50.000 0.00 0.00 0.00 5.68
260 262 3.142174 GCACCTCTATTGAGTAATGCCC 58.858 50.000 11.60 0.00 38.61 5.36
287 289 2.293399 GGTTGTTTGGGCACTTCTGTAG 59.707 50.000 0.00 0.00 0.00 2.74
379 381 5.809001 AGAAATTCTGTCTAGTGGCATTCA 58.191 37.500 0.00 0.00 0.00 2.57
646 649 4.803613 GGTTTATGCATGGAACGAAAATCC 59.196 41.667 10.16 0.00 37.48 3.01
656 660 1.477700 GCAGCTTGGTTTATGCATGGA 59.522 47.619 10.16 0.00 38.54 3.41
868 872 2.665649 TGTGTTATGCGGACCACTAG 57.334 50.000 5.15 0.00 0.00 2.57
885 889 8.538701 TGCACCTCCATAATTTTCAAATATTGT 58.461 29.630 0.00 0.00 0.00 2.71
916 920 8.908786 TTCTTGTTGATGATTCAAAGTACTCT 57.091 30.769 0.00 0.00 43.29 3.24
1054 1059 2.598565 TCCAATACCGATAGCAGCTCT 58.401 47.619 0.00 0.00 0.00 4.09
1108 1113 5.596836 TGTTTAGCCAATGATGGATTTCC 57.403 39.130 0.00 0.00 44.90 3.13
1427 1435 1.774894 AACCGCTCTTAAGGTGCCCA 61.775 55.000 1.85 0.00 41.21 5.36
1527 1535 3.432252 CGCCTAGTGGAAAAGTACACAAG 59.568 47.826 0.00 0.00 39.99 3.16
1648 1656 4.339814 AGTGAAAACGGCAACTCCATTTTA 59.660 37.500 0.00 0.00 34.01 1.52
1658 1666 3.018149 ACCAAAGTAGTGAAAACGGCAA 58.982 40.909 0.00 0.00 0.00 4.52
1910 1918 2.541907 AACTGGACTGCAGCCCCAT 61.542 57.895 23.61 11.22 0.00 4.00
1911 1919 3.177884 AACTGGACTGCAGCCCCA 61.178 61.111 22.44 22.44 0.00 4.96


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

AutoCloner maintained by Alex Coulton.