Multiple sequence alignment - TraesCS6A01G105300

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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 TraesCS6A01G105300 chr6A 100.000 2258 0 0 1 2258 73699504 73697247 0 4170
1 TraesCS6A01G105300 chr5A 94.292 2260 125 4 1 2258 564820887 564818630 0 3456
2 TraesCS6A01G105300 chr1A 93.935 2259 133 3 1 2258 490920593 490918338 0 3410
3 TraesCS6A01G105300 chr2A 91.449 2257 189 4 1 2256 113381048 113378795 0 3096
4 TraesCS6A01G105300 chr7A 91.191 2259 195 4 1 2258 485519589 485517334 0 3066
5 TraesCS6A01G105300 chr1D 88.668 2259 253 3 1 2258 477195749 477193493 0 2750
6 TraesCS6A01G105300 chr6B 87.356 2262 276 9 1 2258 429156175 429158430 0 2584
7 TraesCS6A01G105300 chr6B 86.510 2261 298 7 1 2258 209890582 209892838 0 2479
8 TraesCS6A01G105300 chr7D 87.338 2243 280 4 1 2241 465917862 465915622 0 2566
9 TraesCS6A01G105300 chr4A 87.074 2259 290 2 1 2258 365587604 365589861 0 2553


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 TraesCS6A01G105300 chr6A 73697247 73699504 2257 True 4170 4170 100.000 1 2258 1 chr6A.!!$R1 2257
1 TraesCS6A01G105300 chr5A 564818630 564820887 2257 True 3456 3456 94.292 1 2258 1 chr5A.!!$R1 2257
2 TraesCS6A01G105300 chr1A 490918338 490920593 2255 True 3410 3410 93.935 1 2258 1 chr1A.!!$R1 2257
3 TraesCS6A01G105300 chr2A 113378795 113381048 2253 True 3096 3096 91.449 1 2256 1 chr2A.!!$R1 2255
4 TraesCS6A01G105300 chr7A 485517334 485519589 2255 True 3066 3066 91.191 1 2258 1 chr7A.!!$R1 2257
5 TraesCS6A01G105300 chr1D 477193493 477195749 2256 True 2750 2750 88.668 1 2258 1 chr1D.!!$R1 2257
6 TraesCS6A01G105300 chr6B 429156175 429158430 2255 False 2584 2584 87.356 1 2258 1 chr6B.!!$F2 2257
7 TraesCS6A01G105300 chr6B 209890582 209892838 2256 False 2479 2479 86.510 1 2258 1 chr6B.!!$F1 2257
8 TraesCS6A01G105300 chr7D 465915622 465917862 2240 True 2566 2566 87.338 1 2241 1 chr7D.!!$R1 2240
9 TraesCS6A01G105300 chr4A 365587604 365589861 2257 False 2553 2553 87.074 1 2258 1 chr4A.!!$F1 2257

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
783 788 0.238553 GCTTCGTGAGGAACTTTGGC 59.761 55.0 0.0 0.0 41.55 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 1595 0.110238 GCACATACTGTTGCACGTGG 60.11 55.0 18.88 2.06 0.0 4.94 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
93 94 4.769688 ACCATAAAGATGAGATTGACGCA 58.230 39.130 0.00 0.00 34.73 5.24
99 100 1.662629 GATGAGATTGACGCACAGGTG 59.337 52.381 0.00 0.00 0.00 4.00
134 135 5.647658 TGCGTCAAGGAATCATACAGAAAAT 59.352 36.000 0.00 0.00 0.00 1.82
144 145 3.117888 TCATACAGAAAATCTCCAGCCCC 60.118 47.826 0.00 0.00 0.00 5.80
156 157 1.078143 CAGCCCCTTTTCCTCTCCG 60.078 63.158 0.00 0.00 0.00 4.63
159 160 1.602771 CCCCTTTTCCTCTCCGGTC 59.397 63.158 0.00 0.00 0.00 4.79
247 248 4.042311 TCACCATAGTGGCTAAGTTTCCAA 59.958 41.667 0.00 0.00 42.67 3.53
285 287 2.631062 ACTGTTGGATGAGTTACACGGA 59.369 45.455 0.00 0.00 0.00 4.69
378 381 2.203437 ACGGCCTTCCAAACCCAC 60.203 61.111 0.00 0.00 0.00 4.61
414 417 1.814429 TCAAGGTGGTCTCCTTTGGA 58.186 50.000 1.95 0.00 44.36 3.53
639 644 2.765689 AGCAGCTGTCCTATCTAGGT 57.234 50.000 16.64 0.00 44.02 3.08
640 645 3.039252 AGCAGCTGTCCTATCTAGGTT 57.961 47.619 16.64 0.00 44.02 3.50
783 788 0.238553 GCTTCGTGAGGAACTTTGGC 59.761 55.000 0.00 0.00 41.55 4.52
789 794 2.159707 CGTGAGGAACTTTGGCGTAATG 60.160 50.000 0.00 0.00 41.55 1.90
839 844 0.615850 GGAGTCCCCTTTGTCTGGAG 59.384 60.000 0.00 0.00 0.00 3.86
891 896 2.745821 CAAGCAACAGCTAATCTCAGCA 59.254 45.455 0.00 0.00 44.35 4.41
894 899 2.703416 CAACAGCTAATCTCAGCACCA 58.297 47.619 0.00 0.00 44.35 4.17
898 903 3.244700 ACAGCTAATCTCAGCACCAGTTT 60.245 43.478 0.00 0.00 44.35 2.66
930 935 1.871080 ACTTTCAGGAGCAGTTCGTG 58.129 50.000 0.73 0.73 41.85 4.35
1065 1070 5.859205 ATGAAAAAGAGTTCTTGGCAGTT 57.141 34.783 0.00 0.00 36.12 3.16
1071 1076 7.817418 AAAAGAGTTCTTGGCAGTTATTGTA 57.183 32.000 0.00 0.00 36.12 2.41
1255 1260 1.961277 CTCAGAAAACACGGCCGCT 60.961 57.895 28.58 10.43 0.00 5.52
1270 1275 2.229589 CGCTGATGCTCTGTCTCGC 61.230 63.158 0.00 0.00 36.97 5.03
1277 1282 2.259818 CTCTGTCTCGCGCCAACT 59.740 61.111 0.00 0.00 0.00 3.16
1547 1555 2.631062 CGGGCTACCCAGTTACATATCA 59.369 50.000 3.08 0.00 45.83 2.15
1552 1560 5.057149 GCTACCCAGTTACATATCACAAGG 58.943 45.833 0.00 0.00 0.00 3.61
1584 1592 2.437200 TCGCTTGGCCAAAAATGAAG 57.563 45.000 20.91 6.82 0.00 3.02
1587 1595 2.416747 GCTTGGCCAAAAATGAAGACC 58.583 47.619 20.91 0.00 0.00 3.85
1655 1663 1.594194 CCAGACAGAGCAGCGTCTCT 61.594 60.000 5.15 5.15 43.78 3.10
1774 1783 4.026744 TCTTTGGGTCATTGTGGACAAAA 58.973 39.130 0.00 0.00 39.55 2.44
1801 1810 4.396522 GAGATATGCTCATTTCTTGCCCT 58.603 43.478 4.72 0.00 43.38 5.19
1821 1830 4.428209 CCTTAGCTCATCCATATACAGCG 58.572 47.826 0.00 0.00 35.14 5.18
1851 1860 1.202510 GCCCAGCTCTACATGACTCAG 60.203 57.143 0.00 0.00 0.00 3.35
2019 2029 2.094539 CGCGTGAATCAGTGCGTG 59.905 61.111 18.06 6.32 45.12 5.34
2051 2061 1.283793 GCTGCTTCACACATGCGTT 59.716 52.632 0.00 0.00 0.00 4.84
2200 2210 1.067283 CGTCCACTTCATGCTCAGTCT 60.067 52.381 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 0.178861 AGAGGAAAAGGGGCTGGAGA 60.179 55.000 0.00 0.00 0.00 3.71
144 145 3.191371 CCAAAATGACCGGAGAGGAAAAG 59.809 47.826 9.46 0.00 45.00 2.27
228 229 4.202050 GGCATTGGAAACTTAGCCACTATG 60.202 45.833 0.00 0.00 39.60 2.23
247 248 3.686016 ACAGTTCTTCAATTACGGGCAT 58.314 40.909 0.00 0.00 0.00 4.40
378 381 5.583854 CACCTTGAATTCATAGTGACCTGAG 59.416 44.000 24.02 9.94 33.58 3.35
432 435 0.611714 GGAGGCCTCCGTTGAAAGTA 59.388 55.000 35.77 0.00 40.36 2.24
474 478 1.078759 AGAGTAGCACACATTCGCGC 61.079 55.000 0.00 0.00 0.00 6.86
480 484 3.670895 CGTCGAAGAAGAGTAGCACACAT 60.671 47.826 0.00 0.00 38.59 3.21
513 517 7.494625 ACGTGATCTTCAAGAGTTTTACTGAAA 59.505 33.333 0.00 0.00 30.40 2.69
639 644 4.759693 ACGCCTTTTTCACTGATGACATAA 59.240 37.500 0.00 0.00 33.38 1.90
640 645 4.154015 CACGCCTTTTTCACTGATGACATA 59.846 41.667 0.00 0.00 33.38 2.29
783 788 1.813753 CAGGGGTCGTGCCATTACG 60.814 63.158 0.00 0.00 44.98 3.18
789 794 2.112297 TTGAACAGGGGTCGTGCC 59.888 61.111 0.00 0.00 0.00 5.01
839 844 0.308993 GGCTGTGTCAGTGTTGCTTC 59.691 55.000 0.00 0.00 33.43 3.86
891 896 0.558712 TGGGTAAGGCCAAAACTGGT 59.441 50.000 5.01 0.00 39.65 4.00
894 899 2.767644 AGTTGGGTAAGGCCAAAACT 57.232 45.000 5.01 2.13 39.44 2.66
898 903 2.593026 CTGAAAGTTGGGTAAGGCCAA 58.407 47.619 5.01 0.00 39.65 4.52
930 935 1.066430 TCACTAGCATCGGTTTCCACC 60.066 52.381 0.00 0.00 40.16 4.61
976 981 1.912220 CGATGGGGTGCCCTTTCTA 59.088 57.895 7.26 0.00 45.70 2.10
1065 1070 4.030216 TCCACTGATCCACTGCTACAATA 58.970 43.478 0.00 0.00 0.00 1.90
1071 1076 0.901124 GTCTCCACTGATCCACTGCT 59.099 55.000 0.00 0.00 0.00 4.24
1155 1160 2.158519 CCAAGGGGTGGTAAGTCTTTGT 60.159 50.000 0.00 0.00 43.20 2.83
1234 1239 1.600916 GGCCGTGTTTTCTGAGCCT 60.601 57.895 0.00 0.00 37.42 4.58
1240 1245 1.302511 ATCAGCGGCCGTGTTTTCT 60.303 52.632 28.70 11.31 0.00 2.52
1255 1260 2.202663 GCGCGAGACAGAGCATCA 60.203 61.111 12.10 0.00 37.82 3.07
1270 1275 3.791973 AGTATCTCAGAAGAGTTGGCG 57.208 47.619 0.00 0.00 42.66 5.69
1277 1282 6.262049 GTCACTGCAGATAGTATCTCAGAAGA 59.738 42.308 28.06 23.52 37.58 2.87
1390 1395 3.646715 CCCTTTGGGTCTGGCCGA 61.647 66.667 0.00 0.00 38.25 5.54
1547 1555 4.848685 ACAAGCGTCGAACCTTGT 57.151 50.000 20.24 20.24 44.86 3.16
1552 1560 0.718220 CAAGCGAACAAGCGTCGAAC 60.718 55.000 0.00 0.00 43.00 3.95
1584 1592 0.796312 CATACTGTTGCACGTGGGTC 59.204 55.000 18.88 0.59 0.00 4.46
1587 1595 0.110238 GCACATACTGTTGCACGTGG 60.110 55.000 18.88 2.06 0.00 4.94
1655 1663 2.839486 CAGAGGTTGCAACAGACCTA 57.161 50.000 29.55 0.00 46.01 3.08
1801 1810 4.082190 GGACGCTGTATATGGATGAGCTAA 60.082 45.833 0.00 0.00 0.00 3.09
1851 1860 6.370994 CAGGCAATCCATGTATCTTGTAGATC 59.629 42.308 0.00 0.00 33.74 2.75
1881 1891 0.175989 GGTCCCTGTCCGAGACAATC 59.824 60.000 7.90 0.92 42.26 2.67
2019 2029 1.809684 AGCAGCGTAAGAAGGTTTCC 58.190 50.000 0.00 0.00 43.02 3.13
2051 2061 1.327690 ATAACTCCAGCGCCTCGGAA 61.328 55.000 2.29 0.00 0.00 4.30
2088 2098 8.181904 AGTGATGTGAAGAATTGTACCAAAAT 57.818 30.769 0.00 0.00 0.00 1.82
2173 2183 1.078759 CATGAAGTGGACGCCGAGAC 61.079 60.000 0.00 0.00 0.00 3.36
2187 2197 0.532573 GGGACGAGACTGAGCATGAA 59.467 55.000 0.00 0.00 0.00 2.57
2200 2210 1.407656 AACCAAGCAGACAGGGACGA 61.408 55.000 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.