Multiple sequence alignment - TraesCS7D01G286400

Loading Multiple Alignment...

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 TraesCS7D01G286400 chr7D 100.000 2747 0 0 1 2747 307161905 307164651 0 5073
1 TraesCS7D01G286400 chr7D 97.348 2753 66 5 1 2747 307033665 307030914 0 4673
2 TraesCS7D01G286400 chr7D 96.900 2161 54 8 1 2149 382088783 382090942 0 3607
3 TraesCS7D01G286400 chr7D 96.392 2162 61 10 1 2149 626712209 626710052 0 3544
4 TraesCS7D01G286400 chr1D 97.168 2754 68 5 1 2747 275787602 275784852 0 4645
5 TraesCS7D01G286400 chr3D 97.360 2235 54 4 517 2747 602860678 602858445 0 3795
6 TraesCS7D01G286400 chr4D 96.300 2162 64 10 1 2149 123400501 123402659 0 3535
7 TraesCS7D01G286400 chr4D 96.120 2165 66 10 1 2149 134961994 134964156 0 3517
8 TraesCS7D01G286400 chr1A 95.240 2164 85 9 1 2149 94579878 94582038 0 3410
9 TraesCS7D01G286400 chr7A 95.049 2161 93 5 1 2149 211365442 211363284 0 3386
10 TraesCS7D01G286400 chr7A 99.331 598 4 0 2150 2747 638503472 638504069 0 1083
11 TraesCS7D01G286400 chr3A 96.536 895 23 5 1860 2747 51883245 51882352 0 1474
12 TraesCS7D01G286400 chrUn 99.331 598 4 0 2150 2747 393029843 393029246 0 1083
13 TraesCS7D01G286400 chrUn 98.997 598 6 0 2150 2747 171012478 171011881 0 1072
14 TraesCS7D01G286400 chr6B 99.331 598 4 0 2150 2747 596597666 596598263 0 1083
15 TraesCS7D01G286400 chr4A 99.331 598 4 0 2150 2747 79640582 79641179 0 1083


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 TraesCS7D01G286400 chr7D 307161905 307164651 2746 False 5073 5073 100.000 1 2747 1 chr7D.!!$F1 2746
1 TraesCS7D01G286400 chr7D 307030914 307033665 2751 True 4673 4673 97.348 1 2747 1 chr7D.!!$R1 2746
2 TraesCS7D01G286400 chr7D 382088783 382090942 2159 False 3607 3607 96.900 1 2149 1 chr7D.!!$F2 2148
3 TraesCS7D01G286400 chr7D 626710052 626712209 2157 True 3544 3544 96.392 1 2149 1 chr7D.!!$R2 2148
4 TraesCS7D01G286400 chr1D 275784852 275787602 2750 True 4645 4645 97.168 1 2747 1 chr1D.!!$R1 2746
5 TraesCS7D01G286400 chr3D 602858445 602860678 2233 True 3795 3795 97.360 517 2747 1 chr3D.!!$R1 2230
6 TraesCS7D01G286400 chr4D 123400501 123402659 2158 False 3535 3535 96.300 1 2149 1 chr4D.!!$F1 2148
7 TraesCS7D01G286400 chr4D 134961994 134964156 2162 False 3517 3517 96.120 1 2149 1 chr4D.!!$F2 2148
8 TraesCS7D01G286400 chr1A 94579878 94582038 2160 False 3410 3410 95.240 1 2149 1 chr1A.!!$F1 2148
9 TraesCS7D01G286400 chr7A 211363284 211365442 2158 True 3386 3386 95.049 1 2149 1 chr7A.!!$R1 2148
10 TraesCS7D01G286400 chr7A 638503472 638504069 597 False 1083 1083 99.331 2150 2747 1 chr7A.!!$F1 597
11 TraesCS7D01G286400 chr3A 51882352 51883245 893 True 1474 1474 96.536 1860 2747 1 chr3A.!!$R1 887
12 TraesCS7D01G286400 chrUn 393029246 393029843 597 True 1083 1083 99.331 2150 2747 1 chrUn.!!$R2 597
13 TraesCS7D01G286400 chrUn 171011881 171012478 597 True 1072 1072 98.997 2150 2747 1 chrUn.!!$R1 597
14 TraesCS7D01G286400 chr6B 596597666 596598263 597 False 1083 1083 99.331 2150 2747 1 chr6B.!!$F1 597
15 TraesCS7D01G286400 chr4A 79640582 79641179 597 False 1083 1083 99.331 2150 2747 1 chr4A.!!$F1 597

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
53 54 0.871722 TGACATTCGTTGGGCTTTCG 59.128 50.000 0.0 0.0 0.0 3.46 F
950 965 1.416401 AGAAGAGTGTCGGCTTGGAAA 59.584 47.619 0.0 0.0 0.0 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 1695 1.983224 TCCGCTTTGGAGGAGAAGG 59.017 57.895 0.0 0.0 43.74 3.46 R
2280 2308 0.043334 AGTAGGCTGGTGACCCTGAT 59.957 55.000 0.0 0.0 32.65 2.90 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
53 54 0.871722 TGACATTCGTTGGGCTTTCG 59.128 50.000 0.00 0.00 0.00 3.46
60 61 3.353836 TTGGGCTTTCGTCTGCGC 61.354 61.111 0.00 0.00 41.57 6.09
121 122 2.694109 GGCCGAAGACTAGTGATAGGTT 59.306 50.000 0.00 0.00 0.00 3.50
177 178 2.293122 GTGTAAGCACAGCAATGAACCA 59.707 45.455 0.00 0.00 44.64 3.67
181 182 1.795170 GCACAGCAATGAACCACGGT 61.795 55.000 0.00 0.00 0.00 4.83
207 208 2.424246 CCTCAGACGACCCTTCTAAGAC 59.576 54.545 0.00 0.00 0.00 3.01
255 258 2.104792 CCCTTTGACTCTTCCACTGACA 59.895 50.000 0.00 0.00 0.00 3.58
480 486 3.178865 GGGGATAATCATTCCGGTCCTA 58.821 50.000 0.00 0.00 33.82 2.94
495 501 2.482333 CCTAGGAGAGGTGGCGACG 61.482 68.421 1.05 0.00 40.98 5.12
567 573 4.096003 GCGCACCCTAAGCCCAGA 62.096 66.667 0.30 0.00 0.00 3.86
577 583 2.311463 CTAAGCCCAGATTCTCGGAGA 58.689 52.381 2.97 2.97 0.00 3.71
619 625 8.143835 CGGCTTCCTTAATATCCAAATTTCAAT 58.856 33.333 0.00 0.00 0.00 2.57
778 793 6.331369 CTTCAACAGAAGCCCTTAAAATCA 57.669 37.500 0.00 0.00 33.07 2.57
837 852 2.759795 GTGGGGGAGAAGCAAGCT 59.240 61.111 0.00 0.00 0.00 3.74
922 937 8.364894 TCAGTAAGTAATTCAGTGAGTGCTTTA 58.635 33.333 12.33 1.22 0.00 1.85
950 965 1.416401 AGAAGAGTGTCGGCTTGGAAA 59.584 47.619 0.00 0.00 0.00 3.13
958 973 4.081917 AGTGTCGGCTTGGAAAAAGAAAAA 60.082 37.500 0.00 0.00 0.00 1.94
965 980 8.147704 TCGGCTTGGAAAAAGAAAAAGAAATAT 58.852 29.630 0.00 0.00 0.00 1.28
1076 1091 6.655003 ACCATGATACTTTCTGTTTTGTCGAT 59.345 34.615 0.00 0.00 0.00 3.59
1081 1096 4.461198 ACTTTCTGTTTTGTCGATCCCTT 58.539 39.130 0.00 0.00 0.00 3.95
1143 1158 4.162812 CGGTACATTCCATTTTGTTTCCG 58.837 43.478 0.00 0.00 36.56 4.30
1230 1245 5.011982 TCTCCCCAGTAGTTCATATAGGG 57.988 47.826 0.00 0.00 32.65 3.53
1960 1983 1.202604 GGAAGGTTGTGAAGACCGTCA 60.203 52.381 10.50 0.00 44.32 4.35
2111 2139 4.710324 CCTACTACTTGTTGGTTTGGTGA 58.290 43.478 0.00 0.00 36.91 4.02
2272 2300 1.757699 AGATTCCCGAGGCAGTCTTAC 59.242 52.381 0.00 0.00 0.00 2.34
2475 2503 7.173032 TCTCACAGTATAGGCCGATATCTTTA 58.827 38.462 8.95 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 4.735132 CGAAAGCTCCGCGGGACA 62.735 66.667 27.83 4.76 0.00 4.02
177 178 1.529948 TCGTCTGAGGGTTCACCGT 60.530 57.895 0.00 0.00 46.96 4.83
181 182 0.471211 AAGGGTCGTCTGAGGGTTCA 60.471 55.000 0.00 0.00 0.00 3.18
207 208 2.324541 CTACTGAGGATCTCCCCCTTG 58.675 57.143 0.00 0.00 36.42 3.61
255 258 8.297426 CCGTATGAGCATTCGGTACATATATAT 58.703 37.037 17.10 0.00 43.75 0.86
495 501 1.548357 TTCCCTCAGCTCAGACTGGC 61.548 60.000 1.81 5.25 38.26 4.85
567 573 2.297315 TCGCAATAGCATCTCCGAGAAT 59.703 45.455 1.27 0.00 42.27 2.40
577 583 2.494059 AGCCGTATTTCGCAATAGCAT 58.506 42.857 2.84 0.00 42.27 3.79
837 852 1.320344 CCGGGTCGATCAGAGGTTCA 61.320 60.000 0.00 0.00 0.00 3.18
922 937 6.316390 CCAAGCCGACACTCTTCTTATAAAAT 59.684 38.462 0.00 0.00 0.00 1.82
937 952 4.158764 TCTTTTTCTTTTTCCAAGCCGACA 59.841 37.500 0.00 0.00 0.00 4.35
950 965 7.096230 CGCGGTTGTTCATATTTCTTTTTCTTT 60.096 33.333 0.00 0.00 0.00 2.52
958 973 2.095853 CAGCGCGGTTGTTCATATTTCT 59.904 45.455 8.73 0.00 0.00 2.52
1076 1091 4.905456 TCAAACTAGAGACCAAAGAAGGGA 59.095 41.667 0.00 0.00 0.00 4.20
1081 1096 5.825593 ACCATCAAACTAGAGACCAAAGA 57.174 39.130 0.00 0.00 0.00 2.52
1143 1158 3.851098 AGTGTCGCAAAAGACTAGGATC 58.149 45.455 0.00 0.00 41.47 3.36
1276 1291 4.755411 TCTTCGTGAATCTCCGCTATTTT 58.245 39.130 0.00 0.00 0.00 1.82
1331 1346 2.445145 TCCCACCAAAAGATCAGTCCAA 59.555 45.455 0.00 0.00 0.00 3.53
1542 1558 7.042335 GCATAGTAAGTACTATAGCCCCAATG 58.958 42.308 10.03 0.72 45.16 2.82
1643 1659 4.380843 TGGCCAAAAGGAGAAATAGTCA 57.619 40.909 0.61 0.00 0.00 3.41
1679 1695 1.983224 TCCGCTTTGGAGGAGAAGG 59.017 57.895 0.00 0.00 43.74 3.46
1850 1867 4.864247 GGCAATTTAAACATGTTCGCATCT 59.136 37.500 12.39 0.00 35.23 2.90
1960 1983 3.330126 TCCTTTCCTCCGGAGTCATAT 57.670 47.619 29.25 0.00 31.21 1.78
2111 2139 3.379452 CTCATACCCACTCCTCTTTCCT 58.621 50.000 0.00 0.00 0.00 3.36
2272 2300 1.764723 TGGTGACCCTGATGATAGCAG 59.235 52.381 0.00 0.00 0.00 4.24
2280 2308 0.043334 AGTAGGCTGGTGACCCTGAT 59.957 55.000 0.00 0.00 32.65 2.90
2475 2503 5.981315 GCATAGCTTGTAAATGACATTGCAT 59.019 36.000 0.34 0.00 39.16 3.96


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

AutoCloner maintained by Alex Coulton.