Multiple sequence alignment - TraesCS6D01G200500

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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 TraesCS6D01G200500 chr6D 100.000 2408 0 0 1 2408 283157221 283154814 0.000000e+00 4447
1 TraesCS6D01G200500 chrUn 98.551 2140 28 3 1 2138 45100793 45098655 0.000000e+00 3777
2 TraesCS6D01G200500 chrUn 98.366 2142 31 4 1 2138 261513063 261515204 0.000000e+00 3759
3 TraesCS6D01G200500 chrUn 98.113 265 4 1 2144 2408 325546957 325546694 6.070000e-126 460
4 TraesCS6D01G200500 chrUn 98.113 265 4 1 2144 2408 325550053 325549790 6.070000e-126 460
5 TraesCS6D01G200500 chrUn 98.113 265 4 1 2144 2408 329020447 329020710 6.070000e-126 460
6 TraesCS6D01G200500 chr5B 98.459 2141 29 4 1 2138 130614902 130612763 0.000000e+00 3768
7 TraesCS6D01G200500 chr5B 98.272 2141 32 5 1 2138 130609878 130607740 0.000000e+00 3744
8 TraesCS6D01G200500 chr5B 97.994 2144 37 4 1 2138 130568754 130570897 0.000000e+00 3716
9 TraesCS6D01G200500 chr5B 97.358 265 6 1 2144 2408 34229157 34228894 1.310000e-122 449
10 TraesCS6D01G200500 chr2D 98.414 2144 28 4 1 2138 644703265 644701122 0.000000e+00 3766
11 TraesCS6D01G200500 chr3A 98.364 2140 33 2 1 2138 66030312 66032451 0.000000e+00 3757
12 TraesCS6D01G200500 chr7B 98.132 2141 37 3 1 2138 743033699 743035839 0.000000e+00 3729
13 TraesCS6D01G200500 chr2B 97.991 2140 40 3 1 2138 112869114 112866976 0.000000e+00 3711
14 TraesCS6D01G200500 chr7D 98.113 265 4 1 2144 2408 382093537 382093800 6.070000e-126 460
15 TraesCS6D01G200500 chr7D 98.837 258 3 0 2151 2408 606924929 606925186 6.070000e-126 460
16 TraesCS6D01G200500 chr7D 97.358 265 6 1 2144 2408 509190839 509191102 1.310000e-122 449
17 TraesCS6D01G200500 chr7D 97.358 265 6 1 2144 2408 626707457 626707194 1.310000e-122 449
18 TraesCS6D01G200500 chr4D 97.736 265 5 1 2144 2408 123405254 123405517 2.820000e-124 455


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 TraesCS6D01G200500 chr6D 283154814 283157221 2407 True 4447 4447 100.0000 1 2408 1 chr6D.!!$R1 2407
1 TraesCS6D01G200500 chrUn 45098655 45100793 2138 True 3777 3777 98.5510 1 2138 1 chrUn.!!$R1 2137
2 TraesCS6D01G200500 chrUn 261513063 261515204 2141 False 3759 3759 98.3660 1 2138 1 chrUn.!!$F1 2137
3 TraesCS6D01G200500 chrUn 325546694 325550053 3359 True 460 460 98.1130 2144 2408 2 chrUn.!!$R2 264
4 TraesCS6D01G200500 chr5B 130607740 130614902 7162 True 3756 3768 98.3655 1 2138 2 chr5B.!!$R2 2137
5 TraesCS6D01G200500 chr5B 130568754 130570897 2143 False 3716 3716 97.9940 1 2138 1 chr5B.!!$F1 2137
6 TraesCS6D01G200500 chr2D 644701122 644703265 2143 True 3766 3766 98.4140 1 2138 1 chr2D.!!$R1 2137
7 TraesCS6D01G200500 chr3A 66030312 66032451 2139 False 3757 3757 98.3640 1 2138 1 chr3A.!!$F1 2137
8 TraesCS6D01G200500 chr7B 743033699 743035839 2140 False 3729 3729 98.1320 1 2138 1 chr7B.!!$F1 2137
9 TraesCS6D01G200500 chr2B 112866976 112869114 2138 True 3711 3711 97.9910 1 2138 1 chr2B.!!$R1 2137

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
486 488 2.482796 TAGTAGTCCGGTCGCACCCA 62.483 60.0 0.0 0.0 33.75 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 6523 0.325933 CAGGAAGGCACATGAGTCCA 59.674 55.0 0.0 0.0 0.0 4.02 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
449 451 8.862085 AGGGTCTCTACAAGTCTATAAATAAGC 58.138 37.037 0.00 0.00 0.00 3.09
486 488 2.482796 TAGTAGTCCGGTCGCACCCA 62.483 60.000 0.00 0.00 33.75 4.51
837 839 6.490040 TCCAGAATAAATGGGCAATAGTTAGC 59.510 38.462 0.00 0.00 38.44 3.09
1066 1068 3.866582 CCCGGATCCAGCCAGGTC 61.867 72.222 13.41 0.00 39.02 3.85
1084 1086 2.711009 GGTCCTATTGATCATGTCCCCA 59.289 50.000 0.00 0.00 0.00 4.96
1364 6389 3.808656 GCGAAAGAGCTGCCTGGC 61.809 66.667 12.87 12.87 0.00 4.85
1389 6414 2.486636 CTAGGTTGCAGCACGTCCGA 62.487 60.000 2.05 0.00 0.00 4.55
1392 6417 2.027073 GTTGCAGCACGTCCGATCA 61.027 57.895 0.00 0.00 0.00 2.92
1408 6433 3.253677 CCGATCATTAACTCCTCGCTAGT 59.746 47.826 0.00 0.00 0.00 2.57
1497 6523 4.260620 GGTCGCACATTCATAATAGCGTTT 60.261 41.667 14.26 0.00 41.97 3.60
1520 6546 1.701847 ACTCATGTGCCTTCCTGAACT 59.298 47.619 0.00 0.00 0.00 3.01
1565 6591 0.179092 GTACGATTAGCCGGCCTTGT 60.179 55.000 26.15 19.83 0.00 3.16
1641 6667 2.127708 CATTAGGTTAGGGAGCTGGGT 58.872 52.381 0.00 0.00 37.30 4.51
1697 6723 1.693083 CCTAGGCGCGCAACACTAAC 61.693 60.000 34.42 12.85 0.00 2.34
1729 6755 5.005094 GCCAACCCACATTACTAACTAACA 58.995 41.667 0.00 0.00 0.00 2.41
1907 6935 5.500931 CGTCTTCCAAATCGCAGAGTTAATC 60.501 44.000 0.00 0.00 45.61 1.75
1940 6968 3.002791 GTGTTATTACTGAGCTGCTGCA 58.997 45.455 18.42 0.88 42.74 4.41
2138 7166 3.367395 CCATTTCCAGATAGCGAGCGATA 60.367 47.826 0.00 0.00 0.00 2.92
2139 7167 4.428209 CATTTCCAGATAGCGAGCGATAT 58.572 43.478 0.00 0.00 0.00 1.63
2140 7168 5.450550 CCATTTCCAGATAGCGAGCGATATA 60.451 44.000 0.25 0.00 0.00 0.86
2141 7169 4.884458 TTCCAGATAGCGAGCGATATAG 57.116 45.455 0.25 0.00 0.00 1.31
2142 7170 4.138487 TCCAGATAGCGAGCGATATAGA 57.862 45.455 0.25 0.00 0.00 1.98
2143 7171 4.709250 TCCAGATAGCGAGCGATATAGAT 58.291 43.478 0.25 0.00 0.00 1.98
2144 7172 5.126779 TCCAGATAGCGAGCGATATAGATT 58.873 41.667 0.25 0.00 0.00 2.40
2145 7173 6.289064 TCCAGATAGCGAGCGATATAGATTA 58.711 40.000 0.25 0.00 0.00 1.75
2146 7174 6.425417 TCCAGATAGCGAGCGATATAGATTAG 59.575 42.308 0.25 0.00 0.00 1.73
2147 7175 6.203915 CCAGATAGCGAGCGATATAGATTAGT 59.796 42.308 0.25 0.00 0.00 2.24
2148 7176 7.068955 CAGATAGCGAGCGATATAGATTAGTG 58.931 42.308 0.25 0.00 0.00 2.74
2149 7177 6.764085 AGATAGCGAGCGATATAGATTAGTGT 59.236 38.462 0.25 0.00 0.00 3.55
2244 7272 3.502595 TCACCTAGTTCAGAGAACACTCG 59.497 47.826 11.92 0.20 35.98 4.18
2358 7386 3.702792 TGAAAACAAAGGGAGTGGACAA 58.297 40.909 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1084 1086 5.505181 AGACAAGATACAACTGTTGGGAT 57.495 39.130 23.15 15.79 34.12 3.85
1364 6389 0.811616 GTGCTGCAACCTAGGGATCG 60.812 60.000 14.81 0.00 0.00 3.69
1389 6414 4.372656 GCAACTAGCGAGGAGTTAATGAT 58.627 43.478 0.00 0.00 35.36 2.45
1408 6433 1.375013 GTCCTAGAAACGGCGGCAA 60.375 57.895 13.24 0.00 0.00 4.52
1497 6523 0.325933 CAGGAAGGCACATGAGTCCA 59.674 55.000 0.00 0.00 0.00 4.02
1565 6591 0.329931 TCCTAATCCTTTTGCCGCCA 59.670 50.000 0.00 0.00 0.00 5.69
1641 6667 2.497675 GGATGCGGAGGAGCTATTATCA 59.502 50.000 0.00 0.00 32.33 2.15
1697 6723 2.214376 TGTGGGTTGGCTTGGATTAG 57.786 50.000 0.00 0.00 0.00 1.73
1729 6755 8.560124 ACCTCTAAGAAAGATGATTATCCACT 57.440 34.615 0.00 0.00 33.64 4.00
1907 6935 6.177610 TCAGTAATAACACCTAGGCTTTTGG 58.822 40.000 9.30 0.00 0.00 3.28
2138 7166 4.519730 GCCTCCTCGTGTACACTAATCTAT 59.480 45.833 23.01 0.00 0.00 1.98
2139 7167 3.881688 GCCTCCTCGTGTACACTAATCTA 59.118 47.826 23.01 3.86 0.00 1.98
2140 7168 2.688958 GCCTCCTCGTGTACACTAATCT 59.311 50.000 23.01 0.00 0.00 2.40
2141 7169 2.688958 AGCCTCCTCGTGTACACTAATC 59.311 50.000 23.01 6.42 0.00 1.75
2142 7170 2.736347 AGCCTCCTCGTGTACACTAAT 58.264 47.619 23.01 0.00 0.00 1.73
2143 7171 2.211250 AGCCTCCTCGTGTACACTAA 57.789 50.000 23.01 10.61 0.00 2.24
2144 7172 3.354948 TTAGCCTCCTCGTGTACACTA 57.645 47.619 23.01 12.11 0.00 2.74
2145 7173 2.211250 TTAGCCTCCTCGTGTACACT 57.789 50.000 23.01 4.99 0.00 3.55
2146 7174 2.165845 ACATTAGCCTCCTCGTGTACAC 59.834 50.000 16.32 16.32 0.00 2.90
2147 7175 2.453521 ACATTAGCCTCCTCGTGTACA 58.546 47.619 0.00 0.00 0.00 2.90
2148 7176 3.631227 ACTACATTAGCCTCCTCGTGTAC 59.369 47.826 0.00 0.00 0.00 2.90
2149 7177 3.630769 CACTACATTAGCCTCCTCGTGTA 59.369 47.826 0.00 0.00 0.00 2.90
2277 7305 6.061022 TCATTCTTGAATGCTAACACCCTA 57.939 37.500 16.09 0.00 0.00 3.53
2358 7386 7.363007 GGTTCTTGTTCCTTTCTCTTCTTTGTT 60.363 37.037 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.