Multiple sequence alignment - TraesCS6B01G284700

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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 TraesCS6B01G284700 chr6B 100.000 3531 0 0 1 3531 513261101 513264631 0 6521
1 TraesCS6B01G284700 chr6D 93.655 3562 177 19 1 3531 30039259 30035716 0 5280
2 TraesCS6B01G284700 chr6D 89.864 3078 226 46 1 3054 192177815 192174800 0 3877
3 TraesCS6B01G284700 chr6D 89.530 659 63 5 2878 3531 192174880 192174223 0 830
4 TraesCS6B01G284700 chr4A 95.283 3074 133 9 1 3065 109513234 109516304 0 4863
5 TraesCS6B01G284700 chr4A 95.156 3076 136 10 1 3065 610968810 610971883 0 4843
6 TraesCS6B01G284700 chr4A 90.204 3083 257 30 1 3054 327033387 327030321 0 3978
7 TraesCS6B01G284700 chr6A 95.150 3072 138 9 1 3065 254270695 254273762 0 4837
8 TraesCS6B01G284700 chr2A 94.723 3070 143 7 1 3065 396601278 396598223 0 4754
9 TraesCS6B01G284700 chr2A 95.081 1667 79 3 1 1667 58204982 58203319 0 2621
10 TraesCS6B01G284700 chrUn 90.765 3086 255 16 1 3065 284016008 284019084 0 4093
11 TraesCS6B01G284700 chrUn 93.471 582 24 10 2960 3531 284019022 284019599 0 852
12 TraesCS6B01G284700 chr3B 97.838 2128 36 7 1409 3531 734460191 734462313 0 3666
13 TraesCS6B01G284700 chr7B 94.823 1835 93 2 1 1835 258337227 258335395 0 2861
14 TraesCS6B01G284700 chr3A 94.028 1708 92 3 1 1699 550670137 550668431 0 2580
15 TraesCS6B01G284700 chr1B 95.633 664 21 5 2873 3531 681432834 681433494 0 1059
16 TraesCS6B01G284700 chr1B 95.303 660 23 4 2877 3531 681419960 681420616 0 1040
17 TraesCS6B01G284700 chr4B 95.289 658 26 4 2877 3531 359844377 359843722 0 1038
18 TraesCS6B01G284700 chr7A 89.697 660 58 8 2877 3531 247701216 247700562 0 833
19 TraesCS6B01G284700 chr5A 87.977 682 68 11 2861 3531 67813371 67814049 0 793


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 TraesCS6B01G284700 chr6B 513261101 513264631 3530 False 6521.0 6521 100.000 1 3531 1 chr6B.!!$F1 3530
1 TraesCS6B01G284700 chr6D 30035716 30039259 3543 True 5280.0 5280 93.655 1 3531 1 chr6D.!!$R1 3530
2 TraesCS6B01G284700 chr6D 192174223 192177815 3592 True 2353.5 3877 89.697 1 3531 2 chr6D.!!$R2 3530
3 TraesCS6B01G284700 chr4A 109513234 109516304 3070 False 4863.0 4863 95.283 1 3065 1 chr4A.!!$F1 3064
4 TraesCS6B01G284700 chr4A 610968810 610971883 3073 False 4843.0 4843 95.156 1 3065 1 chr4A.!!$F2 3064
5 TraesCS6B01G284700 chr4A 327030321 327033387 3066 True 3978.0 3978 90.204 1 3054 1 chr4A.!!$R1 3053
6 TraesCS6B01G284700 chr6A 254270695 254273762 3067 False 4837.0 4837 95.150 1 3065 1 chr6A.!!$F1 3064
7 TraesCS6B01G284700 chr2A 396598223 396601278 3055 True 4754.0 4754 94.723 1 3065 1 chr2A.!!$R2 3064
8 TraesCS6B01G284700 chr2A 58203319 58204982 1663 True 2621.0 2621 95.081 1 1667 1 chr2A.!!$R1 1666
9 TraesCS6B01G284700 chrUn 284016008 284019599 3591 False 2472.5 4093 92.118 1 3531 2 chrUn.!!$F1 3530
10 TraesCS6B01G284700 chr3B 734460191 734462313 2122 False 3666.0 3666 97.838 1409 3531 1 chr3B.!!$F1 2122
11 TraesCS6B01G284700 chr7B 258335395 258337227 1832 True 2861.0 2861 94.823 1 1835 1 chr7B.!!$R1 1834
12 TraesCS6B01G284700 chr3A 550668431 550670137 1706 True 2580.0 2580 94.028 1 1699 1 chr3A.!!$R1 1698
13 TraesCS6B01G284700 chr1B 681432834 681433494 660 False 1059.0 1059 95.633 2873 3531 1 chr1B.!!$F2 658
14 TraesCS6B01G284700 chr1B 681419960 681420616 656 False 1040.0 1040 95.303 2877 3531 1 chr1B.!!$F1 654
15 TraesCS6B01G284700 chr4B 359843722 359844377 655 True 1038.0 1038 95.289 2877 3531 1 chr4B.!!$R1 654
16 TraesCS6B01G284700 chr7A 247700562 247701216 654 True 833.0 833 89.697 2877 3531 1 chr7A.!!$R1 654
17 TraesCS6B01G284700 chr5A 67813371 67814049 678 False 793.0 793 87.977 2861 3531 1 chr5A.!!$F1 670

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
323 325 0.471191 TCTCCCTAGGACGACGCATA 59.529 55.0 11.48 0.0 0.00 3.14 F
353 355 0.676151 CACCTGCTCTTTGCTCCCTC 60.676 60.0 0.00 0.0 43.37 4.30 F
762 764 0.977627 TCACCCAGATCGAGTGGCAT 60.978 55.0 10.54 0.0 33.24 4.40 F
2238 2273 0.251787 GGCCATGAGGTTTCCAAGGT 60.252 55.0 0.00 0.0 37.19 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1216 1220 1.412710 AGACTTCACCGTTTGAGCAGA 59.587 47.619 0.0 0.0 34.94 4.26 R
1225 1229 3.228453 TCACCTCTTTAGACTTCACCGT 58.772 45.455 0.0 0.0 0.00 4.83 R
2355 2390 2.867429 CTTGTCGGCATTGTTCCATTC 58.133 47.619 0.0 0.0 0.00 2.67 R
3361 3573 1.000394 TCGGTGAACTCGAAATGCTCA 60.000 47.619 0.0 0.0 33.42 4.26 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
323 325 0.471191 TCTCCCTAGGACGACGCATA 59.529 55.000 11.48 0.00 0.00 3.14
353 355 0.676151 CACCTGCTCTTTGCTCCCTC 60.676 60.000 0.00 0.00 43.37 4.30
659 661 1.067060 GGTGTGTTCAAACCCAAGAGC 59.933 52.381 0.90 0.00 0.00 4.09
762 764 0.977627 TCACCCAGATCGAGTGGCAT 60.978 55.000 10.54 0.00 33.24 4.40
825 827 2.099263 GCGAGCCTGTATACTCAAGACA 59.901 50.000 4.17 0.00 32.98 3.41
1031 1035 3.041946 AGACCCCTCATGATGTAAGGAC 58.958 50.000 0.00 0.00 31.44 3.85
1171 1175 4.965532 AGAAGGCAGAGACACCTATTACAT 59.034 41.667 0.00 0.00 34.31 2.29
1225 1229 8.939201 TTTAAATGATGTTGTTTCTGCTCAAA 57.061 26.923 0.00 0.00 0.00 2.69
1250 1254 4.463186 GGTGAAGTCTAAAGAGGTGAGCTA 59.537 45.833 0.00 0.00 0.00 3.32
1303 1307 8.284945 TGTCTCACGTACTATTTGGTACTAAT 57.715 34.615 0.00 0.00 39.67 1.73
1309 1313 9.577110 CACGTACTATTTGGTACTAATTTGAGA 57.423 33.333 0.00 0.00 39.67 3.27
1390 1420 0.387878 CTCCGCTCATCCGCTATCAC 60.388 60.000 0.00 0.00 0.00 3.06
1554 1584 2.303163 TAACATTGGATGGTCCGTCG 57.697 50.000 4.96 0.00 40.17 5.12
2209 2244 5.526111 TGTTGTTGCTGAAGTAGGACTTAAC 59.474 40.000 0.00 0.00 38.80 2.01
2238 2273 0.251787 GGCCATGAGGTTTCCAAGGT 60.252 55.000 0.00 0.00 37.19 3.50
2355 2390 1.327303 TTGCACAGGCTTAAGTTGGG 58.673 50.000 4.02 5.74 41.91 4.12
2645 2680 6.691754 TCAGTTTCACTTCAAATGTAGCAA 57.308 33.333 0.00 0.00 0.00 3.91
2953 3098 2.369983 TATACTCGTAGGGGTGTGGG 57.630 55.000 0.00 0.00 0.00 4.61
3484 3696 6.070824 GGAAAAATTGCCTCTCCTCCAAATAA 60.071 38.462 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 182 2.626840 CTGGTCTTCTAAGCTCTTGGC 58.373 52.381 0.00 0.00 42.19 4.52
323 325 2.037847 GCAGGTGGGCCCAAAGAT 59.962 61.111 30.64 10.09 34.66 2.40
353 355 5.291128 ACAAATTCGCCGAAGTGAGTAATAG 59.709 40.000 17.21 0.00 33.10 1.73
559 561 3.904717 TGTGCCTCTTTGGGAGTAAAAA 58.095 40.909 0.00 0.00 40.30 1.94
659 661 6.919188 TCGACGAATAGAAATTAAGAAAGCG 58.081 36.000 0.00 0.00 0.00 4.68
702 704 0.680601 TCGGCGGTGATAGTACCACA 60.681 55.000 7.21 0.00 40.89 4.17
762 764 2.971660 TGGTCAAGACGAAACTGTCA 57.028 45.000 0.00 0.00 41.41 3.58
825 827 5.945144 AAGCATAGGCAATTCCAATTTCT 57.055 34.783 0.67 0.00 44.61 2.52
966 970 2.891941 GATGGCCCAGAATGTCGGCA 62.892 60.000 0.00 0.00 44.08 5.69
1041 1045 2.252976 TGTTGTGCTGTAGTGCATGA 57.747 45.000 0.00 0.00 45.23 3.07
1043 1047 2.745821 CTGATGTTGTGCTGTAGTGCAT 59.254 45.455 0.00 0.00 45.23 3.96
1171 1175 4.271807 AGAGGACCAGTCTCCATTGATA 57.728 45.455 0.00 0.00 31.94 2.15
1216 1220 1.412710 AGACTTCACCGTTTGAGCAGA 59.587 47.619 0.00 0.00 34.94 4.26
1225 1229 3.228453 TCACCTCTTTAGACTTCACCGT 58.772 45.455 0.00 0.00 0.00 4.83
1390 1420 6.328714 CAGTGTCTGAGATATCATTATCCGG 58.671 44.000 5.32 0.00 35.74 5.14
1554 1584 8.827677 ACAAAGTTACTGAGTTCAACATCTAAC 58.172 33.333 0.00 0.00 0.00 2.34
2209 2244 3.287867 ACCTCATGGCCAGACTTAATG 57.712 47.619 13.05 2.09 36.63 1.90
2238 2273 5.070446 ACGGCAGATAAGTCCTCAATTATGA 59.930 40.000 0.00 0.00 0.00 2.15
2355 2390 2.867429 CTTGTCGGCATTGTTCCATTC 58.133 47.619 0.00 0.00 0.00 2.67
2645 2680 7.238710 AGTTCCCACCTGAATAAACAAAGTAT 58.761 34.615 0.00 0.00 0.00 2.12
3361 3573 1.000394 TCGGTGAACTCGAAATGCTCA 60.000 47.619 0.00 0.00 33.42 4.26
3461 3673 6.725834 TCTTATTTGGAGGAGAGGCAATTTTT 59.274 34.615 0.00 0.00 0.00 1.94
3466 3678 4.494091 CTCTTATTTGGAGGAGAGGCAA 57.506 45.455 0.00 0.00 33.63 4.52
3484 3696 3.041946 GGAATGACACCATACTCCCTCT 58.958 50.000 0.00 0.00 31.59 3.69


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

AutoCloner maintained by Alex Coulton.