Multiple sequence alignment - TraesCS6A01G306200

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 TraesCS6A01G306200 chr6A 100.000 1755 0 0 1 1755 539864676 539866430 0.000000e+00 3241
1 TraesCS6A01G306200 chr6A 100.000 377 0 0 2048 2424 539866723 539867099 0.000000e+00 697
2 TraesCS6A01G306200 chr6D 93.968 1774 55 18 1 1755 393298434 393300174 0.000000e+00 2636
3 TraesCS6A01G306200 chr6D 91.349 393 8 8 2048 2424 393300249 393300631 4.620000e-142 514
4 TraesCS6A01G306200 chr6B 92.745 1778 70 22 1 1755 587797871 587799612 0.000000e+00 2514
5 TraesCS6A01G306200 chr6B 91.129 372 7 12 2053 2424 587799622 587799967 4.690000e-132 481
6 TraesCS6A01G306200 chr7D 89.172 157 17 0 1263 1419 139829120 139829276 1.900000e-46 196
7 TraesCS6A01G306200 chr7B 89.172 157 17 0 1263 1419 104757901 104758057 1.900000e-46 196


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 TraesCS6A01G306200 chr6A 539864676 539867099 2423 False 1969.0 3241 100.0000 1 2424 2 chr6A.!!$F1 2423
1 TraesCS6A01G306200 chr6D 393298434 393300631 2197 False 1575.0 2636 92.6585 1 2424 2 chr6D.!!$F1 2423
2 TraesCS6A01G306200 chr6B 587797871 587799967 2096 False 1497.5 2514 91.9370 1 2424 2 chr6B.!!$F1 2423

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
405 413 0.169009 GATTTCCTGGACGTTGCTGC 59.831 55.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 1601 0.610687 AGGGAGCAGAAAAGAGACGG 59.389 55.0 0.0 0.0 0.0 4.79 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 3.305398 GTTCTCACGACAAGGACAGAT 57.695 47.619 0.00 0.00 0.00 2.90
99 100 0.608130 CGACAAGGACAGATGGGTGA 59.392 55.000 0.00 0.00 0.00 4.02
100 101 1.001974 CGACAAGGACAGATGGGTGAA 59.998 52.381 0.00 0.00 0.00 3.18
101 102 2.704572 GACAAGGACAGATGGGTGAAG 58.295 52.381 0.00 0.00 0.00 3.02
102 103 1.352352 ACAAGGACAGATGGGTGAAGG 59.648 52.381 0.00 0.00 0.00 3.46
103 104 0.329596 AAGGACAGATGGGTGAAGGC 59.670 55.000 0.00 0.00 0.00 4.35
104 105 0.548682 AGGACAGATGGGTGAAGGCT 60.549 55.000 0.00 0.00 0.00 4.58
105 106 0.393537 GGACAGATGGGTGAAGGCTG 60.394 60.000 0.00 0.00 0.00 4.85
106 107 0.615331 GACAGATGGGTGAAGGCTGA 59.385 55.000 0.00 0.00 0.00 4.26
121 122 2.500910 AGGCTGAAGAGAAGAGGTCATG 59.499 50.000 0.00 0.00 0.00 3.07
140 141 4.535781 CATGGATCCATGTCCCTGTTTAA 58.464 43.478 36.88 3.88 46.20 1.52
141 142 4.879295 TGGATCCATGTCCCTGTTTAAT 57.121 40.909 11.44 0.00 37.48 1.40
143 144 6.334378 TGGATCCATGTCCCTGTTTAATTA 57.666 37.500 11.44 0.00 37.48 1.40
144 145 6.364701 TGGATCCATGTCCCTGTTTAATTAG 58.635 40.000 11.44 0.00 37.48 1.73
145 146 5.241728 GGATCCATGTCCCTGTTTAATTAGC 59.758 44.000 6.95 0.00 31.82 3.09
146 147 5.450818 TCCATGTCCCTGTTTAATTAGCT 57.549 39.130 0.00 0.00 0.00 3.32
147 148 5.826643 TCCATGTCCCTGTTTAATTAGCTT 58.173 37.500 0.00 0.00 0.00 3.74
148 149 6.252995 TCCATGTCCCTGTTTAATTAGCTTT 58.747 36.000 0.00 0.00 0.00 3.51
150 151 7.338449 TCCATGTCCCTGTTTAATTAGCTTTAC 59.662 37.037 0.00 0.00 0.00 2.01
175 179 1.070776 GTGCGTGTTCTTTCTCCGAAC 60.071 52.381 0.00 0.00 40.79 3.95
193 197 4.508124 CCGAACAGCTTATTACTCCATGAC 59.492 45.833 0.00 0.00 0.00 3.06
215 219 6.076981 ACCAAAACTCTCAATTTGCACTAG 57.923 37.500 0.00 0.00 35.66 2.57
216 220 4.919754 CCAAAACTCTCAATTTGCACTAGC 59.080 41.667 0.00 0.00 42.57 3.42
253 257 1.668419 CCGATGATTGACAGGGGTTC 58.332 55.000 0.00 0.00 0.00 3.62
299 307 6.936407 GTGGTACATACACGTACGCTTAACG 61.936 48.000 16.72 2.31 46.33 3.18
405 413 0.169009 GATTTCCTGGACGTTGCTGC 59.831 55.000 0.00 0.00 0.00 5.25
413 421 3.071459 GACGTTGCTGCATCGGTCG 62.071 63.158 29.59 18.81 31.83 4.79
517 526 0.609131 CCAGTGGTGGGTGGTCATTC 60.609 60.000 0.00 0.00 40.67 2.67
522 531 1.247567 GGTGGGTGGTCATTCAAGTG 58.752 55.000 0.00 0.00 0.00 3.16
545 554 2.507992 CAACGAGCTGCCTCTCCG 60.508 66.667 0.00 0.00 35.90 4.63
578 587 4.457496 CGCCGATGACAGTGGGCT 62.457 66.667 11.14 0.00 40.43 5.19
732 751 0.743345 GTTCCCCAATCCGTTCTCCG 60.743 60.000 0.00 0.00 0.00 4.63
823 842 1.007964 CCAGCGAGTATCCTGAGCG 60.008 63.158 0.00 0.00 36.06 5.03
894 913 2.210116 CCTTTTGAGCGTACACACTGT 58.790 47.619 0.00 0.00 0.00 3.55
907 926 3.338818 CACACTGTGTGGCTTTGTTAG 57.661 47.619 28.71 3.37 44.27 2.34
1089 1108 0.907230 AGTCTCTGCTCCCCAACTCC 60.907 60.000 0.00 0.00 0.00 3.85
1150 1169 2.933492 GCTTACCACCACAACAGCGATA 60.933 50.000 0.00 0.00 0.00 2.92
1157 1176 1.136690 CACAACAGCGATACACACGT 58.863 50.000 0.00 0.00 0.00 4.49
1175 1194 1.274596 GTACGCACATTACTCCACCG 58.725 55.000 0.00 0.00 0.00 4.94
1178 1197 1.019278 CGCACATTACTCCACCGCTT 61.019 55.000 0.00 0.00 0.00 4.68
1190 1209 3.200593 CCGCTTGCCAGCTAGCTG 61.201 66.667 33.58 33.58 44.85 4.24
1236 1255 2.180131 GACTTGCACGAAGCCAGCAG 62.180 60.000 0.00 0.00 44.83 4.24
1248 1267 2.004808 GCCAGCAGGAAATAACGGGC 62.005 60.000 0.00 0.00 36.89 6.13
2164 2191 6.608002 ACCACTACTACGGTACTACTACTACT 59.392 42.308 0.00 0.00 32.31 2.57
2165 2192 7.778853 ACCACTACTACGGTACTACTACTACTA 59.221 40.741 0.00 0.00 32.31 1.82
2166 2193 8.077386 CCACTACTACGGTACTACTACTACTAC 58.923 44.444 0.00 0.00 0.00 2.73
2167 2194 8.077386 CACTACTACGGTACTACTACTACTACC 58.923 44.444 0.00 0.00 0.00 3.18
2168 2195 8.000127 ACTACTACGGTACTACTACTACTACCT 59.000 40.741 0.00 0.00 0.00 3.08
2169 2196 7.045126 ACTACGGTACTACTACTACTACCTG 57.955 44.000 0.00 0.00 0.00 4.00
2230 2257 6.915843 CAGCTTTAACTTTTGTTGGAATACGT 59.084 34.615 0.00 0.00 43.41 3.57
2231 2258 8.071368 CAGCTTTAACTTTTGTTGGAATACGTA 58.929 33.333 0.00 0.00 43.41 3.57
2232 2259 8.071967 AGCTTTAACTTTTGTTGGAATACGTAC 58.928 33.333 0.00 0.00 43.41 3.67
2275 2317 4.726583 ACTAGACTGGAGTGTACTGTTCA 58.273 43.478 0.00 0.00 0.00 3.18
2286 2328 8.995220 TGGAGTGTACTGTTCATTTTTATGTAC 58.005 33.333 0.00 0.00 0.00 2.90
2363 2409 1.681327 GCCCTCGATCGGCCCTATA 60.681 63.158 16.41 0.00 40.78 1.31
2364 2410 1.043673 GCCCTCGATCGGCCCTATAT 61.044 60.000 16.41 0.00 40.78 0.86
2365 2411 1.753141 GCCCTCGATCGGCCCTATATA 60.753 57.143 16.41 0.00 40.78 0.86
2366 2412 2.877866 CCCTCGATCGGCCCTATATAT 58.122 52.381 16.41 0.00 0.00 0.86
2374 2420 1.002033 CGGCCCTATATATCCGTACGC 60.002 57.143 10.49 0.00 37.33 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 0.393537 CAGCCTTCACCCATCTGTCC 60.394 60.000 0.00 0.00 0.00 4.02
90 91 1.558756 CTCTTCAGCCTTCACCCATCT 59.441 52.381 0.00 0.00 0.00 2.90
93 94 1.349026 CTTCTCTTCAGCCTTCACCCA 59.651 52.381 0.00 0.00 0.00 4.51
99 100 2.614259 TGACCTCTTCTCTTCAGCCTT 58.386 47.619 0.00 0.00 0.00 4.35
100 101 2.317371 TGACCTCTTCTCTTCAGCCT 57.683 50.000 0.00 0.00 0.00 4.58
101 102 2.419851 CCATGACCTCTTCTCTTCAGCC 60.420 54.545 0.00 0.00 0.00 4.85
102 103 2.499289 TCCATGACCTCTTCTCTTCAGC 59.501 50.000 0.00 0.00 0.00 4.26
103 104 4.202243 GGATCCATGACCTCTTCTCTTCAG 60.202 50.000 6.95 0.00 0.00 3.02
104 105 3.708631 GGATCCATGACCTCTTCTCTTCA 59.291 47.826 6.95 0.00 0.00 3.02
105 106 3.708631 TGGATCCATGACCTCTTCTCTTC 59.291 47.826 11.44 0.00 0.00 2.87
106 107 3.729108 TGGATCCATGACCTCTTCTCTT 58.271 45.455 11.44 0.00 0.00 2.85
121 122 5.241728 GCTAATTAAACAGGGACATGGATCC 59.758 44.000 4.20 4.20 38.13 3.36
140 141 3.818773 ACACGCACCTTTGTAAAGCTAAT 59.181 39.130 0.00 0.00 34.69 1.73
141 142 3.207778 ACACGCACCTTTGTAAAGCTAA 58.792 40.909 0.00 0.00 34.69 3.09
143 144 1.675552 ACACGCACCTTTGTAAAGCT 58.324 45.000 0.00 0.00 34.69 3.74
144 145 2.032924 AGAACACGCACCTTTGTAAAGC 59.967 45.455 0.00 0.00 34.69 3.51
145 146 3.963383 AGAACACGCACCTTTGTAAAG 57.037 42.857 0.00 0.00 35.79 1.85
146 147 4.396790 AGAAAGAACACGCACCTTTGTAAA 59.603 37.500 0.00 0.00 31.06 2.01
147 148 3.942748 AGAAAGAACACGCACCTTTGTAA 59.057 39.130 0.00 0.00 31.06 2.41
148 149 3.537580 AGAAAGAACACGCACCTTTGTA 58.462 40.909 0.00 0.00 31.06 2.41
150 151 2.287009 GGAGAAAGAACACGCACCTTTG 60.287 50.000 0.00 0.00 31.06 2.77
175 179 6.375455 AGTTTTGGTCATGGAGTAATAAGCTG 59.625 38.462 0.00 0.00 0.00 4.24
193 197 4.919754 GCTAGTGCAAATTGAGAGTTTTGG 59.080 41.667 0.00 0.00 39.41 3.28
215 219 1.266989 GGCATTGCCTAATTAGTCGGC 59.733 52.381 20.66 9.21 46.69 5.54
253 257 1.996292 ACTGATGTGTGGACGAATCG 58.004 50.000 0.00 0.00 0.00 3.34
299 307 1.077357 TCTCCTGGCTCCGAGTCTC 60.077 63.158 0.90 0.00 0.00 3.36
302 310 2.363147 GGTCTCCTGGCTCCGAGT 60.363 66.667 0.00 0.00 0.00 4.18
405 413 4.889856 TCGCCATGCCGACCGATG 62.890 66.667 0.00 0.00 31.36 3.84
517 526 2.672996 CTCGTTGGGCCCCACTTG 60.673 66.667 22.91 11.81 30.78 3.16
555 564 4.794439 CTGTCATCGGCGCGTGGA 62.794 66.667 8.43 5.75 0.00 4.02
577 586 3.637432 GTCTAATCACTGATGAGCCGAG 58.363 50.000 0.00 0.00 38.57 4.63
578 587 2.033424 CGTCTAATCACTGATGAGCCGA 59.967 50.000 1.11 0.00 38.57 5.54
623 642 0.459063 GTAGGAACGCTAACGGGGTG 60.459 60.000 0.00 0.00 46.04 4.61
732 751 2.369203 GGAGAGGGTGTCTTTATAGGGC 59.631 54.545 0.00 0.00 34.71 5.19
865 884 2.597217 CTCAAAAGGTGCCGGGCA 60.597 61.111 19.77 19.77 35.60 5.36
908 927 3.905678 CAGACTCCCGCCGGCTAG 61.906 72.222 26.68 20.54 0.00 3.42
998 1017 0.863538 CGACCTTCTGCTCGACATCG 60.864 60.000 0.00 0.00 41.45 3.84
1038 1057 1.107114 TGAGCTCGTTGATCTCCTCC 58.893 55.000 9.64 0.00 31.32 4.30
1045 1064 2.625737 CTTGGACATGAGCTCGTTGAT 58.374 47.619 19.90 3.95 0.00 2.57
1123 1142 2.882137 TGTTGTGGTGGTAAGCTTAAGC 59.118 45.455 20.09 20.09 42.49 3.09
1124 1143 3.058224 GCTGTTGTGGTGGTAAGCTTAAG 60.058 47.826 7.99 0.00 0.00 1.85
1125 1144 2.882137 GCTGTTGTGGTGGTAAGCTTAA 59.118 45.455 7.99 0.00 0.00 1.85
1126 1145 2.500229 GCTGTTGTGGTGGTAAGCTTA 58.500 47.619 0.86 0.86 0.00 3.09
1127 1146 1.318576 GCTGTTGTGGTGGTAAGCTT 58.681 50.000 3.48 3.48 0.00 3.74
1150 1169 2.322161 GAGTAATGTGCGTACGTGTGT 58.678 47.619 17.90 1.65 0.00 3.72
1157 1176 0.458889 GCGGTGGAGTAATGTGCGTA 60.459 55.000 0.00 0.00 0.00 4.42
1190 1209 1.901464 ACGGACAATGCAACCACCC 60.901 57.895 0.00 0.00 0.00 4.61
1236 1255 1.729284 TTCACTCGCCCGTTATTTCC 58.271 50.000 0.00 0.00 0.00 3.13
1248 1267 2.919229 GCCTGCATTTTCATTTCACTCG 59.081 45.455 0.00 0.00 0.00 4.18
1409 1428 1.158484 TACGATCACGAGCGGAGGAG 61.158 60.000 9.70 0.00 45.50 3.69
1492 1511 3.083997 GGCCGGAGAGACCCATGT 61.084 66.667 5.05 0.00 34.64 3.21
1579 1601 0.610687 AGGGAGCAGAAAAGAGACGG 59.389 55.000 0.00 0.00 0.00 4.79
1580 1602 2.464157 AAGGGAGCAGAAAAGAGACG 57.536 50.000 0.00 0.00 0.00 4.18
1621 1648 7.541437 AGCTTAGAGACACGTAGTACATTTTTC 59.459 37.037 0.38 0.00 41.61 2.29
2051 2078 5.799213 AGTAGATCAAGAAAGGGACAACAG 58.201 41.667 0.00 0.00 0.00 3.16
2164 2191 7.450074 ACGATGATATTAATTTGCTCCAGGTA 58.550 34.615 0.00 0.00 0.00 3.08
2165 2192 6.299141 ACGATGATATTAATTTGCTCCAGGT 58.701 36.000 0.00 0.00 0.00 4.00
2166 2193 6.427853 TGACGATGATATTAATTTGCTCCAGG 59.572 38.462 0.00 0.00 0.00 4.45
2167 2194 7.425577 TGACGATGATATTAATTTGCTCCAG 57.574 36.000 0.00 0.00 0.00 3.86
2168 2195 7.445096 ACATGACGATGATATTAATTTGCTCCA 59.555 33.333 0.00 0.00 33.36 3.86
2169 2196 7.810658 ACATGACGATGATATTAATTTGCTCC 58.189 34.615 0.00 0.00 33.36 4.70
2317 2362 2.877168 GCATAGAGGAAGCAACCATGAG 59.123 50.000 0.00 0.00 0.00 2.90
2374 2420 2.423517 CGTTGCTTCACGTGCGTG 60.424 61.111 17.44 17.44 46.64 5.34


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

AutoCloner maintained by Alex Coulton.