Multiple sequence alignment - TraesCS6B01G188400

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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 TraesCS6B01G188400 chr6B 100.000 3268 0 0 1 3268 216894761 216898028 0 6035
1 TraesCS6B01G188400 chr6B 92.230 592 42 2 1 589 639182010 639182600 0 835
2 TraesCS6B01G188400 chr2B 95.090 3218 155 3 1 3216 791334687 791331471 0 5064
3 TraesCS6B01G188400 chr2B 94.276 3267 183 4 1 3265 637162649 637165913 0 4994
4 TraesCS6B01G188400 chr2B 93.640 2893 177 7 376 3265 177237103 177239991 0 4316
5 TraesCS6B01G188400 chr2B 92.857 588 40 2 2 589 111719648 111720233 0 852
6 TraesCS6B01G188400 chr4B 94.523 3268 178 1 1 3268 637699207 637695941 0 5042
7 TraesCS6B01G188400 chr3B 94.368 3267 179 5 1 3265 729226730 729229993 0 5009
8 TraesCS6B01G188400 chr4A 93.301 3269 209 8 1 3265 655846298 655849560 0 4815
9 TraesCS6B01G188400 chr4A 93.240 3269 211 8 1 3265 655893449 655896711 0 4804
10 TraesCS6B01G188400 chr4A 94.087 2892 167 4 376 3265 656355765 656358654 0 4390
11 TraesCS6B01G188400 chr4A 94.018 2892 169 4 376 3265 656148467 656151356 0 4379
12 TraesCS6B01G188400 chr3D 92.347 588 42 2 2 589 39834121 39833537 0 833


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 TraesCS6B01G188400 chr6B 216894761 216898028 3267 False 6035 6035 100.000 1 3268 1 chr6B.!!$F1 3267
1 TraesCS6B01G188400 chr6B 639182010 639182600 590 False 835 835 92.230 1 589 1 chr6B.!!$F2 588
2 TraesCS6B01G188400 chr2B 791331471 791334687 3216 True 5064 5064 95.090 1 3216 1 chr2B.!!$R1 3215
3 TraesCS6B01G188400 chr2B 637162649 637165913 3264 False 4994 4994 94.276 1 3265 1 chr2B.!!$F3 3264
4 TraesCS6B01G188400 chr2B 177237103 177239991 2888 False 4316 4316 93.640 376 3265 1 chr2B.!!$F2 2889
5 TraesCS6B01G188400 chr2B 111719648 111720233 585 False 852 852 92.857 2 589 1 chr2B.!!$F1 587
6 TraesCS6B01G188400 chr4B 637695941 637699207 3266 True 5042 5042 94.523 1 3268 1 chr4B.!!$R1 3267
7 TraesCS6B01G188400 chr3B 729226730 729229993 3263 False 5009 5009 94.368 1 3265 1 chr3B.!!$F1 3264
8 TraesCS6B01G188400 chr4A 655846298 655849560 3262 False 4815 4815 93.301 1 3265 1 chr4A.!!$F1 3264
9 TraesCS6B01G188400 chr4A 655893449 655896711 3262 False 4804 4804 93.240 1 3265 1 chr4A.!!$F2 3264
10 TraesCS6B01G188400 chr4A 656355765 656358654 2889 False 4390 4390 94.087 376 3265 1 chr4A.!!$F4 2889
11 TraesCS6B01G188400 chr4A 656148467 656151356 2889 False 4379 4379 94.018 376 3265 1 chr4A.!!$F3 2889
12 TraesCS6B01G188400 chr3D 39833537 39834121 584 True 833 833 92.347 2 589 1 chr3D.!!$R1 587

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
848 853 0.968901 ATTACCACGACGAGGCCTCA 60.969 55.0 31.67 9.87 0.00 3.86 F
1141 1146 1.247567 CATCCACGGCAAGGAAAAGT 58.752 50.0 0.00 0.00 38.93 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 1840 0.046552 TTGGGCCTACAAGGGGGATA 59.953 55.0 4.53 0.0 35.37 2.59 R
2678 2686 0.324368 TCTGTGCCTCCGACACCTAT 60.324 55.0 0.00 0.0 37.22 2.57 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
32 33 4.028490 GGGTGTGGCACGATGGGA 62.028 66.667 13.77 0.00 34.83 4.37
36 37 4.028490 GTGGCACGATGGGACCCA 62.028 66.667 17.73 17.73 38.19 4.51
265 266 3.446161 TGGAACCGTCTGTTATCTTCGAT 59.554 43.478 0.00 0.00 37.29 3.59
400 405 6.763715 TGGAATTATAGAGGCACTGGTATT 57.236 37.500 0.00 0.00 41.55 1.89
494 499 5.009310 TGTGAAGTCTTTAGAGTTACGAGCA 59.991 40.000 0.00 0.00 37.79 4.26
525 530 1.374631 GGCACGTGAGAGTGATGCA 60.375 57.895 22.23 0.00 44.43 3.96
540 545 1.895131 GATGCATTGGGAAGTGTGGTT 59.105 47.619 0.00 0.00 0.00 3.67
566 571 1.419374 GCATCGGTGCGAATAGTAGG 58.581 55.000 4.15 0.00 42.28 3.18
720 725 7.772332 TGGTTTACGCAAAAACATTTGTTAT 57.228 28.000 11.68 0.00 39.89 1.89
758 763 2.045561 TGACAGTTGCTTTTTCCCGA 57.954 45.000 0.00 0.00 0.00 5.14
848 853 0.968901 ATTACCACGACGAGGCCTCA 60.969 55.000 31.67 9.87 0.00 3.86
1064 1069 2.046892 CCAGAGCACCGAGGTTGG 60.047 66.667 0.00 0.00 0.00 3.77
1071 1076 2.100631 CACCGAGGTTGGCGATGTC 61.101 63.158 0.00 0.00 0.00 3.06
1141 1146 1.247567 CATCCACGGCAAGGAAAAGT 58.752 50.000 0.00 0.00 38.93 2.66
1398 1403 9.643693 CTCCATGTTTCTGTTTAATTAGCATTT 57.356 29.630 0.00 0.00 0.00 2.32
1416 1421 6.168389 AGCATTTTCACCCTGAAATTTGATC 58.832 36.000 0.00 0.00 44.75 2.92
1600 1605 7.437267 GTGCACTTTCTGTTCTAGTGTAGTTTA 59.563 37.037 10.32 0.00 40.99 2.01
1833 1840 5.579047 TGATGGATCCACCTTAAATGTGTT 58.421 37.500 18.99 0.00 39.86 3.32
1899 1906 4.227300 AGGATATGTTCTACACCTTTGCCA 59.773 41.667 0.00 0.00 0.00 4.92
2230 2238 1.771255 ACTGGAGAGTGCAAAAGAGGT 59.229 47.619 0.00 0.00 0.00 3.85
2300 2308 7.011109 CGAAAATATAGAAAACTGGTCGTGGAT 59.989 37.037 0.00 0.00 0.00 3.41
2478 2486 8.889717 GGCTTGCTAAGTACTATGTTTATTCAA 58.110 33.333 0.00 0.00 0.00 2.69
2552 2560 7.488322 ACTAAATGCAAAGCAGTCTTTTTACA 58.512 30.769 0.00 0.00 43.65 2.41
2642 2650 0.679505 ACGCAGTTAGAGAGGCACAA 59.320 50.000 0.00 0.00 37.78 3.33
2678 2686 1.289694 CCACCGGCGTGTGTTACTA 59.710 57.895 21.25 0.00 38.41 1.82
2679 2687 0.108520 CCACCGGCGTGTGTTACTAT 60.109 55.000 21.25 0.00 38.41 2.12
2762 2770 1.765314 GAGGCACATGGATGGAGTAGT 59.235 52.381 0.00 0.00 0.00 2.73
2799 2807 5.220912 CGAATACATAGTTACAGGGTCACGA 60.221 44.000 0.00 0.00 0.00 4.35
2983 2991 4.228899 GTGGGGTGTGACACGTTT 57.771 55.556 9.90 0.00 34.83 3.60
3058 3066 4.998033 GGAAGTTGGGTTTTTGTTGTTTCA 59.002 37.500 0.00 0.00 0.00 2.69
3103 3111 5.010933 TGTTCAAAAGTGTGGTACCAGAAA 58.989 37.500 16.93 0.60 0.00 2.52
3151 3159 3.003480 GTCATGGTTGTCAAGCCTCTAC 58.997 50.000 12.07 2.37 0.00 2.59
3265 3274 1.279271 GTAGGAGAGGCACCATTGTGT 59.721 52.381 0.00 0.00 44.65 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.577328 GCCACACCCATGTCACTTCG 61.577 60.000 0.00 0.00 36.72 3.79
13 14 2.045045 CCATCGTGCCACACCCAT 60.045 61.111 0.00 0.00 0.00 4.00
32 33 1.825474 CTTGTCGTGACTCCTATGGGT 59.175 52.381 1.23 0.00 0.00 4.51
36 37 3.057456 GTGACACTTGTCGTGACTCCTAT 60.057 47.826 4.94 0.00 46.81 2.57
265 266 6.037500 CGAATCTTGATGCTAAAATCAGACCA 59.962 38.462 0.00 0.00 37.83 4.02
400 405 4.637091 CACATTTGTGCATCCATAGAGTCA 59.363 41.667 0.00 0.00 39.39 3.41
525 530 3.244911 CCTCTACAACCACACTTCCCAAT 60.245 47.826 0.00 0.00 0.00 3.16
566 571 1.975363 GCACGACCAATGCTCTCTGC 61.975 60.000 0.00 0.00 40.08 4.26
720 725 4.994217 TGTCAAATCGTCTGATTAAGCACA 59.006 37.500 0.00 0.00 44.02 4.57
811 816 1.206878 ATGAGGGCAGTAGACATGCA 58.793 50.000 0.00 0.00 45.68 3.96
848 853 2.285368 TGGAGGAGGCGGTTGGAT 60.285 61.111 0.00 0.00 0.00 3.41
1064 1069 2.187946 CAGGGACCTGGACATCGC 59.812 66.667 10.55 0.00 40.17 4.58
1141 1146 2.011548 GCTGGTGCATACGACATCCAA 61.012 52.381 0.00 0.00 39.41 3.53
1236 1241 3.383505 CCCTGGTATACTCGACATCAACA 59.616 47.826 2.25 0.00 0.00 3.33
1317 1322 0.387929 CCGCGGTGATGTGGTATACT 59.612 55.000 19.50 0.00 34.75 2.12
1398 1403 6.935771 CCAATTTGATCAAATTTCAGGGTGAA 59.064 34.615 33.67 6.85 45.67 3.18
1627 1633 7.594758 CCACGTTAACACATCAATTCAAGAAAT 59.405 33.333 6.39 0.00 0.00 2.17
1697 1703 6.255453 ACACAAGCACAACATGTCATTTTTAC 59.745 34.615 0.00 0.00 0.00 2.01
1833 1840 0.046552 TTGGGCCTACAAGGGGGATA 59.953 55.000 4.53 0.00 35.37 2.59
1880 1887 3.009033 AGCTGGCAAAGGTGTAGAACATA 59.991 43.478 0.00 0.00 34.56 2.29
2230 2238 9.575868 AGTAAGGATCGTCATAATTCTTCTCTA 57.424 33.333 0.00 0.00 0.00 2.43
2280 2288 5.353123 GCAAATCCACGACCAGTTTTCTATA 59.647 40.000 0.00 0.00 0.00 1.31
2300 2308 3.510719 GACAAGCAGAAACACAAGCAAA 58.489 40.909 0.00 0.00 0.00 3.68
2440 2448 5.772521 ACTTAGCAAGCCAAATAACTTGTG 58.227 37.500 4.83 0.00 44.12 3.33
2525 2533 9.458374 GTAAAAAGACTGCTTTGCATTTAGTTA 57.542 29.630 0.00 0.00 43.32 2.24
2534 2542 6.495706 ACTTAGTGTAAAAAGACTGCTTTGC 58.504 36.000 0.00 0.00 43.32 3.68
2552 2560 6.257193 GTGTGCACAACTAAACTGTACTTAGT 59.743 38.462 23.59 0.00 40.52 2.24
2642 2650 1.694150 TGGCTCTACAGACTGCAAACT 59.306 47.619 1.25 0.00 0.00 2.66
2678 2686 0.324368 TCTGTGCCTCCGACACCTAT 60.324 55.000 0.00 0.00 37.22 2.57
2679 2687 0.541063 TTCTGTGCCTCCGACACCTA 60.541 55.000 0.00 0.00 37.22 3.08
2695 2703 9.434420 CTTCATTTCTGTAGAGACTTCAATTCT 57.566 33.333 0.00 0.00 0.00 2.40
2754 2762 2.092321 GGAGCTCACCTCTACTACTCCA 60.092 54.545 17.19 0.00 41.50 3.86
2762 2770 3.292492 TGTATTCGGAGCTCACCTCTA 57.708 47.619 17.19 0.00 40.57 2.43
2799 2807 1.251251 GGCTCTGCACACTTCCAAAT 58.749 50.000 0.00 0.00 0.00 2.32
2904 2912 1.662517 AACGTCACAACAGTGCATCA 58.337 45.000 0.00 0.00 33.28 3.07
2967 2975 1.452289 CCAAACGTGTCACACCCCA 60.452 57.895 1.24 0.00 0.00 4.96
3058 3066 8.635765 AACATCCACAGTATTGATAGTTGTTT 57.364 30.769 0.00 0.00 0.00 2.83
3103 3111 1.290203 CTGCGTATTCGGAAGCATGT 58.710 50.000 3.96 0.00 39.02 3.21
3151 3159 1.564622 CCAGACACGCGTGACTTTG 59.435 57.895 42.94 29.35 33.60 2.77


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

AutoCloner maintained by Alex Coulton.