Multiple sequence alignment - TraesCS1A01G225500

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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 TraesCS1A01G225500 chr1A 100.000 2144 0 0 1 2144 395491897 395489754 0 3960
1 TraesCS1A01G225500 chr1A 94.636 1305 42 2 1 1277 298619740 298618436 0 1997
2 TraesCS1A01G225500 chr2A 95.419 2161 71 2 1 2133 58556453 58554293 0 3417
3 TraesCS1A01G225500 chr7B 95.373 2161 72 2 1 2133 20886048 20888208 0 3411
4 TraesCS1A01G225500 chr3D 92.781 2161 110 16 4 2133 497963234 497965379 0 3085
5 TraesCS1A01G225500 chr3D 92.738 2162 113 17 4 2133 49542518 49544667 0 3083
6 TraesCS1A01G225500 chr5A 92.487 1717 94 12 4 1690 423037863 423036152 0 2423
7 TraesCS1A01G225500 chr5A 91.943 844 65 3 848 1690 662626625 662625784 0 1179
8 TraesCS1A01G225500 chr3A 92.137 1717 96 11 4 1690 142911330 142909623 0 2386
9 TraesCS1A01G225500 chr3B 95.676 1295 55 1 840 2133 703878045 703879339 0 2080
10 TraesCS1A01G225500 chr3B 94.050 1311 50 2 1 1283 754453303 754454613 0 1964
11 TraesCS1A01G225500 chr3B 96.508 859 30 0 1275 2133 754454793 754455651 0 1421
12 TraesCS1A01G225500 chr7D 95.221 837 36 2 4 840 4251174 4252006 0 1321
13 TraesCS1A01G225500 chr7D 94.293 806 43 2 1330 2133 4252449 4253253 0 1230
14 TraesCS1A01G225500 chr7D 91.733 883 72 1 1251 2133 22667932 22668813 0 1225
15 TraesCS1A01G225500 chr5D 92.072 883 70 0 1251 2133 396167581 396166699 0 1243


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 TraesCS1A01G225500 chr1A 395489754 395491897 2143 True 3960.0 3960 100.000 1 2144 1 chr1A.!!$R2 2143
1 TraesCS1A01G225500 chr1A 298618436 298619740 1304 True 1997.0 1997 94.636 1 1277 1 chr1A.!!$R1 1276
2 TraesCS1A01G225500 chr2A 58554293 58556453 2160 True 3417.0 3417 95.419 1 2133 1 chr2A.!!$R1 2132
3 TraesCS1A01G225500 chr7B 20886048 20888208 2160 False 3411.0 3411 95.373 1 2133 1 chr7B.!!$F1 2132
4 TraesCS1A01G225500 chr3D 497963234 497965379 2145 False 3085.0 3085 92.781 4 2133 1 chr3D.!!$F2 2129
5 TraesCS1A01G225500 chr3D 49542518 49544667 2149 False 3083.0 3083 92.738 4 2133 1 chr3D.!!$F1 2129
6 TraesCS1A01G225500 chr5A 423036152 423037863 1711 True 2423.0 2423 92.487 4 1690 1 chr5A.!!$R1 1686
7 TraesCS1A01G225500 chr5A 662625784 662626625 841 True 1179.0 1179 91.943 848 1690 1 chr5A.!!$R2 842
8 TraesCS1A01G225500 chr3A 142909623 142911330 1707 True 2386.0 2386 92.137 4 1690 1 chr3A.!!$R1 1686
9 TraesCS1A01G225500 chr3B 703878045 703879339 1294 False 2080.0 2080 95.676 840 2133 1 chr3B.!!$F1 1293
10 TraesCS1A01G225500 chr3B 754453303 754455651 2348 False 1692.5 1964 95.279 1 2133 2 chr3B.!!$F2 2132
11 TraesCS1A01G225500 chr7D 4251174 4253253 2079 False 1275.5 1321 94.757 4 2133 2 chr7D.!!$F2 2129
12 TraesCS1A01G225500 chr7D 22667932 22668813 881 False 1225.0 1225 91.733 1251 2133 1 chr7D.!!$F1 882
13 TraesCS1A01G225500 chr5D 396166699 396167581 882 True 1243.0 1243 92.072 1251 2133 1 chr5D.!!$R1 882

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
517 518 2.092429 TGTCCTTGGAGTATTCATGGGC 60.092 50.0 0.0 0.0 43.51 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2320 0.87439 TGCCTGCTCGTGACATTTTC 59.126 50.0 0.0 0.0 0.0 2.29 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
135 136 3.953542 AGGGAACTCAAGAACAAGGTT 57.046 42.857 0.00 0.00 32.90 3.50
151 152 6.969993 ACAAGGTTAGGAACAAAATGCTTA 57.030 33.333 0.00 0.00 0.00 3.09
256 257 5.554437 TGTGACACCCTATTTTGACAGTA 57.446 39.130 2.45 0.00 0.00 2.74
340 341 5.063944 ACAGAGCACAAAGTTTATGATAGCG 59.936 40.000 0.00 0.00 0.00 4.26
369 370 6.924111 TGAAATTCCTTTATTCTCTGTTGGC 58.076 36.000 0.00 0.00 0.00 4.52
462 463 7.587757 CACTTGTTATTTCCAAAAGACGAGAAG 59.412 37.037 0.00 0.00 0.00 2.85
474 475 4.957759 AGACGAGAAGAAGAGAGTAAGC 57.042 45.455 0.00 0.00 0.00 3.09
511 512 2.420687 CCTGGCTGTCCTTGGAGTATTC 60.421 54.545 0.00 0.00 0.00 1.75
517 518 2.092429 TGTCCTTGGAGTATTCATGGGC 60.092 50.000 0.00 0.00 43.51 5.36
558 559 7.789831 TCTGATTGGTTTCTAGTATGGAGGTAT 59.210 37.037 0.00 0.00 0.00 2.73
633 634 5.569059 CGGTGTCATTGCAAAGAAGTATTTC 59.431 40.000 5.85 0.00 0.00 2.17
810 811 6.353323 TCGGGTTTATGATTATCAGCTTGAA 58.647 36.000 0.29 0.00 0.00 2.69
1060 1088 4.452455 GCTATGATTCCTGGTATTGGTTCG 59.548 45.833 0.00 0.00 0.00 3.95
1064 1092 3.773418 TTCCTGGTATTGGTTCGTTGA 57.227 42.857 0.00 0.00 0.00 3.18
1093 1121 8.256611 TCTTCAAAAAGATCTCCAGATAAACG 57.743 34.615 0.00 0.00 36.59 3.60
1109 1137 6.094048 CAGATAAACGACAATGGTGAAGGATT 59.906 38.462 0.00 0.00 0.00 3.01
1234 1263 8.731275 TGTCGTTATGGATGTGAGATTATTTT 57.269 30.769 0.00 0.00 0.00 1.82
1365 1583 4.878397 AGAAAAGAACACAGAGACAAGGTG 59.122 41.667 0.00 0.00 38.47 4.00
1503 1721 0.671472 CAGAGCATTGGTGTCGAGCA 60.671 55.000 0.00 0.00 0.00 4.26
1511 1731 4.094294 GCATTGGTGTCGAGCATACTTTAA 59.906 41.667 0.00 0.00 0.00 1.52
1521 1741 4.212214 CGAGCATACTTTAAGATTGGCTCC 59.788 45.833 18.42 8.30 42.52 4.70
1582 1802 9.569167 CATTTAATAATGCCATCATGAGATCAC 57.431 33.333 0.09 0.00 35.15 3.06
1631 1851 9.484806 AATGGAAATCATTAGAAAGAAGGTCAT 57.515 29.630 0.00 0.00 43.71 3.06
1661 1881 4.799564 TCCAACAAAACAGAGCAAAGTT 57.200 36.364 0.00 0.00 0.00 2.66
1677 1897 2.664402 AGTTTCAGAAGTGGCATGGT 57.336 45.000 0.00 0.00 0.00 3.55
1848 2068 7.392953 TGTTCATGTAGATATTGGCAACTTTCA 59.607 33.333 0.00 0.00 37.61 2.69
1981 2201 3.245016 TGTTCTTCAGCCTGTGAATGGAT 60.245 43.478 6.29 0.00 44.44 3.41
2100 2320 1.413077 GAGAAACCTAGGGACCCATCG 59.587 57.143 14.60 0.82 0.00 3.84
2133 2353 1.002868 AGGCACTCAGGTCACATGC 60.003 57.895 0.00 0.00 35.51 4.06
2134 2354 1.302752 GGCACTCAGGTCACATGCA 60.303 57.895 0.00 0.00 38.05 3.96
2135 2355 1.303799 GGCACTCAGGTCACATGCAG 61.304 60.000 0.00 0.00 38.05 4.41
2136 2356 1.303799 GCACTCAGGTCACATGCAGG 61.304 60.000 0.00 0.00 36.30 4.85
2137 2357 0.675837 CACTCAGGTCACATGCAGGG 60.676 60.000 2.31 0.00 0.00 4.45
2138 2358 1.748122 CTCAGGTCACATGCAGGGC 60.748 63.158 2.31 0.00 0.00 5.19
2139 2359 2.753043 CAGGTCACATGCAGGGCC 60.753 66.667 2.31 0.00 0.00 5.80
2140 2360 4.415150 AGGTCACATGCAGGGCCG 62.415 66.667 2.31 0.00 0.00 6.13
2142 2362 4.722700 GTCACATGCAGGGCCGGT 62.723 66.667 1.90 0.00 0.00 5.28
2143 2363 4.408821 TCACATGCAGGGCCGGTC 62.409 66.667 1.90 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 136 7.038302 TCCTCTTCTCTAAGCATTTTGTTCCTA 60.038 37.037 0.00 0.00 32.36 2.94
151 152 4.095946 ACTGCTTTCTCATCCTCTTCTCT 58.904 43.478 0.00 0.00 0.00 3.10
200 201 4.492494 TCATCAAGCTTGCAATCCTCTA 57.508 40.909 21.99 1.08 0.00 2.43
256 257 9.788889 TGCTTCATCATAAGATAAATCATCTGT 57.211 29.630 0.00 0.00 43.56 3.41
340 341 8.049655 ACAGAGAATAAAGGAATTTCAGAAGC 57.950 34.615 0.00 0.00 0.00 3.86
456 457 2.159503 TGCGCTTACTCTCTTCTTCTCG 60.160 50.000 9.73 0.00 0.00 4.04
462 463 3.420828 GCATTTTGCGCTTACTCTCTTC 58.579 45.455 9.73 0.00 31.71 2.87
511 512 1.076118 TGCTGGTAATGGGCCCATG 60.076 57.895 38.06 24.86 36.68 3.66
587 588 0.546122 TGTGACCAGCTTGTTGTCCT 59.454 50.000 0.00 0.00 0.00 3.85
633 634 1.753073 GGATTGTCCCTGATTTGCCTG 59.247 52.381 0.00 0.00 0.00 4.85
954 982 1.523154 CGCAAAGCAACTGCCCCTTA 61.523 55.000 0.00 0.00 43.38 2.69
1060 1088 7.707104 TGGAGATCTTTTTGAAGAAACTCAAC 58.293 34.615 18.63 9.82 37.68 3.18
1064 1092 9.799106 TTATCTGGAGATCTTTTTGAAGAAACT 57.201 29.630 0.00 0.00 36.05 2.66
1093 1121 4.871933 AAACCAATCCTTCACCATTGTC 57.128 40.909 0.00 0.00 0.00 3.18
1109 1137 5.868454 TCTGTTGATCAGAGATGAAAACCA 58.132 37.500 0.00 0.00 46.77 3.67
1500 1718 5.379706 AGGAGCCAATCTTAAAGTATGCT 57.620 39.130 0.00 0.00 0.00 3.79
1503 1721 6.825721 CACAGAAGGAGCCAATCTTAAAGTAT 59.174 38.462 0.00 0.00 0.00 2.12
1511 1731 2.235898 GAGTCACAGAAGGAGCCAATCT 59.764 50.000 0.00 0.00 0.00 2.40
1582 1802 2.098117 CCGTTACTACAGGGTAGAACCG 59.902 54.545 10.17 7.94 39.83 4.44
1631 1851 4.531854 TCTGTTTTGTTGGATCCTCACAA 58.468 39.130 20.27 20.27 0.00 3.33
1661 1881 1.702401 TGGTACCATGCCACTTCTGAA 59.298 47.619 11.60 0.00 0.00 3.02
1716 1936 4.404394 TGACACCTAGCGGATCTTTCAATA 59.596 41.667 0.00 0.00 0.00 1.90
1887 2107 7.013220 TGTATAGGTCCAAATCTCTAGAGCAT 58.987 38.462 15.35 6.85 0.00 3.79
1954 2174 4.025040 TCACAGGCTGAAGAACATGATT 57.975 40.909 23.66 0.00 0.00 2.57
1981 2201 4.665451 TCAGAAATTGGCCAATCTTCTGA 58.335 39.130 40.33 40.33 43.09 3.27
2100 2320 0.874390 TGCCTGCTCGTGACATTTTC 59.126 50.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.