Multiple sequence alignment - TraesCS6A01G172300

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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 TraesCS6A01G172300 chr6A 100.000 2349 0 0 1 2349 183314318 183311970 0.000000e+00 4338
1 TraesCS6A01G172300 chr6A 95.165 2358 102 8 1 2349 183929676 183932030 0.000000e+00 3712
2 TraesCS6A01G172300 chr6A 96.626 652 20 2 1698 2349 557605060 557604411 0.000000e+00 1081
3 TraesCS6A01G172300 chr6A 96.472 652 22 1 1698 2349 180406563 180407213 0.000000e+00 1075
4 TraesCS6A01G172300 chr6D 95.085 1709 75 5 1 1701 367879799 367878092 0.000000e+00 2682
5 TraesCS6A01G172300 chr5D 95.085 1709 73 7 1 1700 564670358 564672064 0.000000e+00 2680
6 TraesCS6A01G172300 chr7A 93.437 1676 100 6 34 1701 721643425 721641752 0.000000e+00 2477
7 TraesCS6A01G172300 chr7A 89.238 1719 161 16 1 1700 717769119 717767406 0.000000e+00 2128
8 TraesCS6A01G172300 chr5A 89.714 1711 159 13 1 1700 31278699 31280403 0.000000e+00 2169
9 TraesCS6A01G172300 chr1B 89.575 1717 156 16 1 1700 145446345 145444635 0.000000e+00 2158
10 TraesCS6A01G172300 chr6B 82.380 1731 256 30 3 1703 715763269 715761558 0.000000e+00 1461
11 TraesCS6A01G172300 chr2B 83.282 1621 237 25 97 1700 748211381 748212984 0.000000e+00 1461
12 TraesCS6A01G172300 chr2B 81.736 553 85 13 1152 1700 748363422 748363962 4.600000e-122 448
13 TraesCS6A01G172300 chr3A 96.626 652 21 1 1698 2349 455731758 455731108 0.000000e+00 1081
14 TraesCS6A01G172300 chr3D 96.472 652 22 1 1698 2349 286159556 286160206 0.000000e+00 1075
15 TraesCS6A01G172300 chr3D 87.166 187 18 6 1517 1700 397922117 397922300 8.510000e-50 207
16 TraesCS6A01G172300 chr2A 96.472 652 22 1 1698 2349 692095167 692095817 0.000000e+00 1075
17 TraesCS6A01G172300 chr2A 96.319 652 23 1 1698 2349 386122898 386122248 0.000000e+00 1070
18 TraesCS6A01G172300 chr4A 96.319 652 23 1 1698 2349 115181198 115181848 0.000000e+00 1070
19 TraesCS6A01G172300 chr1A 96.319 652 22 2 1698 2349 398031081 398030432 0.000000e+00 1070


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 TraesCS6A01G172300 chr6A 183311970 183314318 2348 True 4338 4338 100.000 1 2349 1 chr6A.!!$R1 2348
1 TraesCS6A01G172300 chr6A 183929676 183932030 2354 False 3712 3712 95.165 1 2349 1 chr6A.!!$F2 2348
2 TraesCS6A01G172300 chr6A 557604411 557605060 649 True 1081 1081 96.626 1698 2349 1 chr6A.!!$R2 651
3 TraesCS6A01G172300 chr6A 180406563 180407213 650 False 1075 1075 96.472 1698 2349 1 chr6A.!!$F1 651
4 TraesCS6A01G172300 chr6D 367878092 367879799 1707 True 2682 2682 95.085 1 1701 1 chr6D.!!$R1 1700
5 TraesCS6A01G172300 chr5D 564670358 564672064 1706 False 2680 2680 95.085 1 1700 1 chr5D.!!$F1 1699
6 TraesCS6A01G172300 chr7A 721641752 721643425 1673 True 2477 2477 93.437 34 1701 1 chr7A.!!$R2 1667
7 TraesCS6A01G172300 chr7A 717767406 717769119 1713 True 2128 2128 89.238 1 1700 1 chr7A.!!$R1 1699
8 TraesCS6A01G172300 chr5A 31278699 31280403 1704 False 2169 2169 89.714 1 1700 1 chr5A.!!$F1 1699
9 TraesCS6A01G172300 chr1B 145444635 145446345 1710 True 2158 2158 89.575 1 1700 1 chr1B.!!$R1 1699
10 TraesCS6A01G172300 chr6B 715761558 715763269 1711 True 1461 1461 82.380 3 1703 1 chr6B.!!$R1 1700
11 TraesCS6A01G172300 chr2B 748211381 748212984 1603 False 1461 1461 83.282 97 1700 1 chr2B.!!$F1 1603
12 TraesCS6A01G172300 chr2B 748363422 748363962 540 False 448 448 81.736 1152 1700 1 chr2B.!!$F2 548
13 TraesCS6A01G172300 chr3A 455731108 455731758 650 True 1081 1081 96.626 1698 2349 1 chr3A.!!$R1 651
14 TraesCS6A01G172300 chr3D 286159556 286160206 650 False 1075 1075 96.472 1698 2349 1 chr3D.!!$F1 651
15 TraesCS6A01G172300 chr2A 692095167 692095817 650 False 1075 1075 96.472 1698 2349 1 chr2A.!!$F1 651
16 TraesCS6A01G172300 chr2A 386122248 386122898 650 True 1070 1070 96.319 1698 2349 1 chr2A.!!$R1 651
17 TraesCS6A01G172300 chr4A 115181198 115181848 650 False 1070 1070 96.319 1698 2349 1 chr4A.!!$F1 651
18 TraesCS6A01G172300 chr1A 398030432 398031081 649 True 1070 1070 96.319 1698 2349 1 chr1A.!!$R1 651

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
564 581 0.243636 CCTTGCGTGTCCAATTTCCC 59.756 55.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 1669 0.25361 ACAGTTCAACGACCACCCAA 59.746 50.0 0.0 0.0 0.0 4.12 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
117 128 7.391148 TTCTCCTTAATGCATCTTTAACCAC 57.609 36.000 0.00 0.0 0.00 4.16
186 197 5.951148 TGATTGGGAAACTTGATAAGCATCA 59.049 36.000 0.00 0.0 39.47 3.07
370 385 2.102578 GGCTGTGGCAGGACATTATTT 58.897 47.619 0.00 0.0 40.87 1.40
496 512 6.128445 GGCGGGTAGAAAAGTAGTTCTTAAAC 60.128 42.308 0.00 0.0 38.75 2.01
564 581 0.243636 CCTTGCGTGTCCAATTTCCC 59.756 55.000 0.00 0.0 0.00 3.97
670 687 1.692042 CATCCCCCTCTGCTGGAGT 60.692 63.158 0.00 0.0 40.30 3.85
732 749 3.868077 CCTCTGACGAACCTGATCAAATC 59.132 47.826 0.00 0.0 0.00 2.17
793 816 8.244802 CCAAGTCTATATACGAATACCTGGAAG 58.755 40.741 0.00 0.0 0.00 3.46
951 978 6.551227 GGAATCCCTCCTGCTTTTGTAATAAT 59.449 38.462 0.00 0.0 41.61 1.28
1027 1054 1.403249 GGACTGTTGGATGCATGTTGC 60.403 52.381 2.46 0.0 45.29 4.17
1062 1089 6.707440 TGTCCGAATAACATTTGGCAATAT 57.293 33.333 0.00 0.0 0.00 1.28
1088 1115 1.555075 CCTGGTGCTACAGCTTCCTTA 59.445 52.381 13.83 0.0 42.66 2.69
1110 1137 9.137459 CCTTACAGATGGAGAGAAGTTCTATAA 57.863 37.037 5.09 0.0 35.87 0.98
1117 1144 9.838339 GATGGAGAGAAGTTCTATAATTTTGGA 57.162 33.333 5.09 0.0 35.87 3.53
1149 1176 2.530460 TGCTGGGCTATGTGGAATTT 57.470 45.000 0.00 0.0 0.00 1.82
1260 1287 1.362584 TCTGATGAGGGGAGAAGACCA 59.637 52.381 0.00 0.0 0.00 4.02
1293 1320 1.565305 CGTGGAGCTAAGATGCTGAC 58.435 55.000 0.00 0.0 44.17 3.51
1317 1344 1.402613 CAATGCCTCGAACATGATGCA 59.597 47.619 0.00 0.0 42.38 3.96
1513 1553 2.287308 GCCTGTTGATTTTGTGTGCGTA 60.287 45.455 0.00 0.0 0.00 4.42
1628 1669 3.324846 GCATTCCCCTTTCTTTGGTTTCT 59.675 43.478 0.00 0.0 0.00 2.52
1661 1703 7.894753 GTCGTTGAACTGTTATATTTCCGTTAC 59.105 37.037 0.00 0.0 0.00 2.50
1662 1704 7.598118 TCGTTGAACTGTTATATTTCCGTTACA 59.402 33.333 0.00 0.0 0.00 2.41
1686 1728 2.574824 AGTAATGGAAAGGGGTTACGCT 59.425 45.455 0.00 0.0 42.34 5.07
1727 1770 2.084546 GCCACCCTGTTCACTAATGAC 58.915 52.381 0.00 0.0 33.38 3.06
1882 1925 7.445402 TGCTAAATATTTCCCTGCTCATAAGAC 59.555 37.037 3.39 0.0 0.00 3.01
1947 1991 1.555967 AGAGAGTCTCCCACAAGCTC 58.444 55.000 16.74 0.0 0.00 4.09
1948 1992 1.203112 AGAGAGTCTCCCACAAGCTCA 60.203 52.381 16.74 0.0 0.00 4.26
2103 2147 4.141274 TCAGGGAAAGAACACCAGATGAAA 60.141 41.667 0.00 0.0 0.00 2.69
2218 2262 7.042658 CGAAGAAAAGGGGTATTCTATTTCTCG 60.043 40.741 0.00 0.0 36.43 4.04
2219 2263 7.433537 AGAAAAGGGGTATTCTATTTCTCGA 57.566 36.000 0.00 0.0 33.18 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 60 2.115337 AGAGGCTGCATTCCCTATCT 57.885 50.000 0.50 0.00 0.00 1.98
186 197 5.889853 TCATGCTCTTGCCAGAAGAATTTAT 59.110 36.000 0.00 0.00 38.71 1.40
496 512 2.567615 ACACTCTAGCCAAGTTACCAGG 59.432 50.000 0.00 0.00 0.00 4.45
640 657 3.797353 GGGATGGAGGCGCCTTCA 61.797 66.667 38.86 38.86 41.44 3.02
670 687 7.719424 ACCATATTACTCATATCCCTCCACTA 58.281 38.462 0.00 0.00 0.00 2.74
732 749 1.764571 TTCTCCCCAAGGACCACACG 61.765 60.000 0.00 0.00 37.19 4.49
793 816 0.111639 TTACACCCAGCCAAGTTCCC 59.888 55.000 0.00 0.00 0.00 3.97
868 892 8.365647 AGTCCGAATAGAGTCTTGAAAAAGTTA 58.634 33.333 0.00 0.00 0.00 2.24
1062 1089 1.699634 AGCTGTAGCACCAGGAGAAAA 59.300 47.619 6.65 0.00 45.16 2.29
1110 1137 4.248058 GCAAAGTGCAGCTAATCCAAAAT 58.752 39.130 0.00 0.00 44.26 1.82
1149 1176 4.139859 TCAAAGGTGGTTCTGTTACGAA 57.860 40.909 0.00 0.00 0.00 3.85
1260 1287 0.035152 TCCACGCTCCATTGCTTCAT 60.035 50.000 0.00 0.00 0.00 2.57
1293 1320 2.204237 TCATGTTCGAGGCATTGATCG 58.796 47.619 5.61 5.61 40.26 3.69
1513 1553 6.351881 CCCAGTGACACCAACATAACTACTAT 60.352 42.308 0.84 0.00 0.00 2.12
1628 1669 0.253610 ACAGTTCAACGACCACCCAA 59.746 50.000 0.00 0.00 0.00 4.12
1661 1703 5.705902 CGTAACCCCTTTCCATTACTTTTG 58.294 41.667 0.00 0.00 0.00 2.44
1662 1704 4.219070 GCGTAACCCCTTTCCATTACTTTT 59.781 41.667 0.00 0.00 0.00 2.27
1705 1748 2.086869 CATTAGTGAACAGGGTGGCTG 58.913 52.381 0.00 0.00 0.00 4.85
1765 1808 8.548877 TCTTAGCATCACCCTTTAATAAGAACT 58.451 33.333 0.00 0.00 32.92 3.01
1771 1814 8.890472 ACCATATCTTAGCATCACCCTTTAATA 58.110 33.333 0.00 0.00 0.00 0.98
1882 1925 4.525912 ATTTCCCTTAAAGCAGCTTGTG 57.474 40.909 8.88 1.92 0.00 3.33
2218 2262 4.002316 GCCTCTTGCATATCTTCAGGATC 58.998 47.826 0.00 0.00 40.77 3.36
2219 2263 4.018484 GCCTCTTGCATATCTTCAGGAT 57.982 45.455 0.00 0.00 40.77 3.24


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

AutoCloner maintained by Alex Coulton.