Multiple sequence alignment - TraesCS6A01G198600

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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 TraesCS6A01G198600 chr6A 100.000 3184 0 0 1 3184 306766978 306763795 0.000000e+00 5880.0
1 TraesCS6A01G198600 chr6D 95.340 2897 103 15 1 2871 232742744 232745634 0.000000e+00 4573.0
2 TraesCS6A01G198600 chr6D 94.937 316 11 3 2869 3184 232748381 232748691 1.030000e-134 490.0
3 TraesCS6A01G198600 chr6D 90.455 220 18 3 2570 2788 131604155 131603938 1.450000e-73 287.0
4 TraesCS6A01G198600 chr6D 78.138 247 28 17 2944 3184 131603889 131603663 1.990000e-27 134.0
5 TraesCS6A01G198600 chr6B 97.480 1746 32 8 839 2575 369527804 369526062 0.000000e+00 2970.0
6 TraesCS6A01G198600 chr6B 85.678 789 88 17 1 774 369531197 369530419 0.000000e+00 808.0
7 TraesCS6A01G198600 chr7B 80.000 115 20 3 30 141 191905206 191905320 7.320000e-12 82.4
8 TraesCS6A01G198600 chr5B 96.970 33 1 0 67 99 331881726 331881758 4.440000e-04 56.5


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 TraesCS6A01G198600 chr6A 306763795 306766978 3183 True 5880.0 5880 100.0000 1 3184 1 chr6A.!!$R1 3183
1 TraesCS6A01G198600 chr6D 232742744 232748691 5947 False 2531.5 4573 95.1385 1 3184 2 chr6D.!!$F1 3183
2 TraesCS6A01G198600 chr6B 369526062 369531197 5135 True 1889.0 2970 91.5790 1 2575 2 chr6B.!!$R1 2574

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
655 679 0.319405 GCTCTGCCTTGCACCATTTT 59.681 50.0 0.0 0.0 33.79 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 4816 0.179113 CTGGCTCTCTTCCTCTTCGC 60.179 60.0 0.0 0.0 0.0 4.7 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
78 80 1.200948 GCCTCTCGCAGAAGCAAATTT 59.799 47.619 2.95 0.00 42.27 1.82
148 150 7.133891 ACATATGTGTTCTTTTCCTTCTTCG 57.866 36.000 7.78 0.00 34.01 3.79
174 176 1.446099 GTGATTGTGCCTCTCGCGA 60.446 57.895 9.26 9.26 42.08 5.87
202 208 4.937201 ATATCACGAGAAGTATGTGCCA 57.063 40.909 0.00 0.00 33.69 4.92
205 211 2.094700 TCACGAGAAGTATGTGCCACTC 60.095 50.000 0.00 0.00 33.69 3.51
254 263 0.888619 TCGAGAGGCACGATTGTTCT 59.111 50.000 0.00 0.00 34.85 3.01
260 269 3.499918 AGAGGCACGATTGTTCTTTTCAG 59.500 43.478 0.00 0.00 0.00 3.02
267 276 3.667960 CGATTGTTCTTTTCAGGGAAGCG 60.668 47.826 0.00 0.00 0.00 4.68
294 303 3.676324 CGTGCCTCCTCGAGAAGTAAATT 60.676 47.826 15.71 0.00 0.00 1.82
295 304 4.254492 GTGCCTCCTCGAGAAGTAAATTT 58.746 43.478 15.71 0.00 0.00 1.82
304 313 6.595716 CCTCGAGAAGTAAATTTGTCCTTCAT 59.404 38.462 15.71 11.04 36.60 2.57
363 385 4.654915 TGACTCTCATGAAAGCAAATCCA 58.345 39.130 0.00 0.00 0.00 3.41
384 406 9.768662 AATCCATGCCTACATTTAAATGAAATC 57.231 29.630 30.18 17.41 39.67 2.17
386 408 9.639563 TCCATGCCTACATTTAAATGAAATCTA 57.360 29.630 30.18 13.45 39.67 1.98
402 424 8.618702 ATGAAATCTATGCCTATCACAAGAAG 57.381 34.615 0.00 0.00 0.00 2.85
553 577 2.586648 ACAAAATTCGAAGGGAGCCT 57.413 45.000 3.35 0.00 33.87 4.58
567 591 2.054140 GAGCCTCTAGAGCACGACCG 62.054 65.000 14.73 0.00 0.00 4.79
594 618 1.609580 CCGCACAGCCTACCAAAAGTA 60.610 52.381 0.00 0.00 0.00 2.24
624 648 0.321996 GGGCTCGTGAAGGAGAACTT 59.678 55.000 4.26 0.00 43.65 2.66
626 650 1.000955 GGCTCGTGAAGGAGAACTTGA 59.999 52.381 4.26 0.00 40.21 3.02
630 654 4.560128 CTCGTGAAGGAGAACTTGATGAA 58.440 43.478 0.00 0.00 37.77 2.57
655 679 0.319405 GCTCTGCCTTGCACCATTTT 59.681 50.000 0.00 0.00 33.79 1.82
835 1174 7.239763 TGGATAAGTCACTCAAGAATGTACA 57.760 36.000 0.00 0.00 0.00 2.90
836 1175 7.676004 TGGATAAGTCACTCAAGAATGTACAA 58.324 34.615 0.00 0.00 0.00 2.41
1493 4081 2.649129 GCGGGGCAGCAGGAAATTT 61.649 57.895 0.00 0.00 37.05 1.82
1582 4170 4.388499 GCACGGCCTTTCCCTCGA 62.388 66.667 0.00 0.00 0.00 4.04
1583 4171 2.584608 CACGGCCTTTCCCTCGAT 59.415 61.111 0.00 0.00 0.00 3.59
1897 4485 2.746362 GTGCAGTTCTTCCTCAAGATGG 59.254 50.000 0.00 0.00 38.50 3.51
1995 4583 1.484240 GCCTCTACAGCAGAAGATGGT 59.516 52.381 0.00 0.00 41.36 3.55
2228 4816 2.383855 AGACGAGGAAGAGATGGAAGG 58.616 52.381 0.00 0.00 0.00 3.46
2504 5093 9.685276 TTTGATGTGATTCTGTGATATTAAGGT 57.315 29.630 0.00 0.00 0.00 3.50
2645 5234 6.539464 TGTTTGAGTAACATACGTCCTGTTTT 59.461 34.615 18.17 9.77 41.73 2.43
2702 5291 6.769341 TGAATTGTAATGGAGATCATCAGGTG 59.231 38.462 0.00 0.00 34.44 4.00
2754 5343 9.160496 ACTCTCTTCAATAAGTGTGATTCATTC 57.840 33.333 0.00 0.00 34.13 2.67
2807 5396 1.512926 ACTTTACTGTGAGCAAGGCG 58.487 50.000 0.00 0.00 0.00 5.52
2880 8222 4.036144 GGAATGCATCACTCTAAGGCTTTC 59.964 45.833 4.45 0.00 37.69 2.62
2888 8230 0.249398 TCTAAGGCTTTCGGTCTGCC 59.751 55.000 4.45 0.00 46.42 4.85
2978 8320 7.105588 AGCATAGGAAAATTCAAAATTGACCC 58.894 34.615 0.00 0.00 36.83 4.46
2989 8331 0.779997 AATTGACCCTGGCTCCAGTT 59.220 50.000 14.27 1.48 42.15 3.16
3092 8434 8.958506 AGAAAGAGATGTACTTGTAGACGTTAT 58.041 33.333 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 37 0.914417 ATCCTGCCTCCCGGAAAAGA 60.914 55.000 0.73 0.00 32.12 2.52
78 80 4.404394 TGATTTACTTCTCGTGGAGGCATA 59.596 41.667 0.00 0.00 0.00 3.14
135 137 2.866762 CGCCTATCCGAAGAAGGAAAAG 59.133 50.000 0.00 0.00 44.50 2.27
148 150 2.321213 GGCACAATCACGCCTATCC 58.679 57.895 0.00 0.00 45.29 2.59
174 176 6.199154 CACATACTTCTCGTGATATTCGCTTT 59.801 38.462 0.00 0.00 32.23 3.51
179 181 5.175856 GTGGCACATACTTCTCGTGATATTC 59.824 44.000 13.86 0.00 44.52 1.75
184 186 1.893137 AGTGGCACATACTTCTCGTGA 59.107 47.619 21.41 0.00 44.52 4.35
254 263 1.271163 ACGGATTCGCTTCCCTGAAAA 60.271 47.619 0.00 0.00 40.63 2.29
260 269 3.202706 GGCACGGATTCGCTTCCC 61.203 66.667 0.00 0.00 40.63 3.97
267 276 1.066587 CTCGAGGAGGCACGGATTC 59.933 63.158 3.91 0.00 0.00 2.52
378 400 7.795047 TCTTCTTGTGATAGGCATAGATTTCA 58.205 34.615 0.00 0.00 0.00 2.69
457 481 6.597832 TTCTCAACTTTTCAGGGTTTTTCA 57.402 33.333 0.00 0.00 0.00 2.69
459 483 6.764379 TGTTTCTCAACTTTTCAGGGTTTTT 58.236 32.000 0.00 0.00 33.58 1.94
553 577 2.044555 CCACCGGTCGTGCTCTAGA 61.045 63.158 2.59 0.00 41.53 2.43
594 618 2.685380 CGAGCCCTCCCAAGGTCT 60.685 66.667 0.00 0.00 41.59 3.85
624 648 3.920231 AGGCAGAGCAACTATTCATCA 57.080 42.857 0.00 0.00 0.00 3.07
626 650 2.686915 GCAAGGCAGAGCAACTATTCAT 59.313 45.455 0.00 0.00 0.00 2.57
630 654 1.457346 GTGCAAGGCAGAGCAACTAT 58.543 50.000 0.00 0.00 43.20 2.12
655 679 1.206132 ACACTGGTGTCACGACAAAGA 59.794 47.619 14.75 0.00 43.77 2.52
811 1150 7.239763 TGTACATTCTTGAGTGACTTATCCA 57.760 36.000 0.00 0.00 0.00 3.41
817 1156 4.752101 GCTGTTGTACATTCTTGAGTGACT 59.248 41.667 0.00 0.00 0.00 3.41
1582 4170 1.620819 CAGCCTCCGCTTCATACCTAT 59.379 52.381 0.00 0.00 45.55 2.57
1583 4171 1.040646 CAGCCTCCGCTTCATACCTA 58.959 55.000 0.00 0.00 45.55 3.08
1799 4387 1.075601 ATGCTCCCCTTTTGAGGACA 58.924 50.000 0.00 0.00 32.77 4.02
1995 4583 2.573869 GCAGTAGCTGGCGAGTCA 59.426 61.111 0.00 0.00 37.91 3.41
2049 4637 2.124403 CTGCTGGCCCTGACATCC 60.124 66.667 0.00 0.00 0.00 3.51
2057 4645 3.455469 GGTGATTGCTGCTGGCCC 61.455 66.667 0.00 0.00 40.92 5.80
2120 4708 0.532196 GTACTGGTAAGATGGGCGCC 60.532 60.000 21.18 21.18 0.00 6.53
2199 4787 4.404640 TCTCTTCCTCGTCTTCCTTGTTA 58.595 43.478 0.00 0.00 0.00 2.41
2228 4816 0.179113 CTGGCTCTCTTCCTCTTCGC 60.179 60.000 0.00 0.00 0.00 4.70
2504 5093 4.608514 TGGGCCTGGGAGGGACAA 62.609 66.667 4.53 0.00 35.71 3.18
2645 5234 4.160439 CCATAGGCTACTGTTGAGAACTCA 59.840 45.833 0.00 0.00 37.91 3.41
2702 5291 6.260936 ACATATAACATAAGCAGCACAGTTCC 59.739 38.462 0.00 0.00 0.00 3.62
2754 5343 2.636830 CCACAATAACCTCTCCTGCTG 58.363 52.381 0.00 0.00 0.00 4.41
2888 8230 1.855978 TGTACACAACTGAAAGACGCG 59.144 47.619 3.53 3.53 37.43 6.01
2889 8231 2.605818 TGTGTACACAACTGAAAGACGC 59.394 45.455 26.07 0.00 38.56 5.19
3065 8407 6.844254 ACGTCTACAAGTACATCTCTTTCTC 58.156 40.000 0.00 0.00 0.00 2.87
3066 8408 6.821031 ACGTCTACAAGTACATCTCTTTCT 57.179 37.500 0.00 0.00 0.00 2.52
3067 8409 9.224058 GATAACGTCTACAAGTACATCTCTTTC 57.776 37.037 0.00 0.00 0.00 2.62
3068 8410 8.958506 AGATAACGTCTACAAGTACATCTCTTT 58.041 33.333 0.00 0.00 34.69 2.52
3069 8411 8.399425 CAGATAACGTCTACAAGTACATCTCTT 58.601 37.037 0.00 0.00 34.69 2.85
3075 8417 5.632244 TGCAGATAACGTCTACAAGTACA 57.368 39.130 0.00 0.00 34.69 2.90
3121 8463 8.004215 ACCATATTGTCTAGCCCATAAATGAAA 58.996 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.