Multiple sequence alignment - TraesCS6A01G112900

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 TraesCS6A01G112900 chr6A 100.000 2553 0 0 1 2553 82987779 82985227 0 4715
1 TraesCS6A01G112900 chr3A 95.896 2583 71 15 1 2552 710758734 710756156 0 4150
2 TraesCS6A01G112900 chr3A 95.764 2573 79 8 1 2552 666692732 666695295 0 4120
3 TraesCS6A01G112900 chr3A 95.268 2578 93 9 1 2552 568428066 568430640 0 4058
4 TraesCS6A01G112900 chr3A 95.948 2443 75 6 1 2422 11148633 11151072 0 3941
5 TraesCS6A01G112900 chr5A 95.922 2575 78 9 1 2552 671939815 671937245 0 4148
6 TraesCS6A01G112900 chr5A 96.500 2457 76 7 1 2451 691697223 691694771 0 4052
7 TraesCS6A01G112900 chr5A 95.338 2574 78 8 1 2552 692009849 692012402 0 4050
8 TraesCS6A01G112900 chr5A 95.035 2578 82 13 1 2552 1849071 1851628 0 4010
9 TraesCS6A01G112900 chr2A 95.652 2576 79 12 1 2552 35547475 35550041 0 4106
10 TraesCS6A01G112900 chr4A 95.499 2577 89 12 1 2552 616137268 616134694 0 4091
11 TraesCS6A01G112900 chr7A 94.798 2576 82 10 1 2552 112679106 112676559 0 3967
12 TraesCS6A01G112900 chr1A 94.608 2578 85 18 1 2552 576105933 576108482 0 3941
13 TraesCS6A01G112900 chr5B 93.498 2507 129 7 1 2487 16244378 16241886 0 3696
14 TraesCS6A01G112900 chrUn 94.757 1068 26 9 1513 2552 48355806 48354741 0 1635


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 TraesCS6A01G112900 chr6A 82985227 82987779 2552 True 4715 4715 100.000 1 2553 1 chr6A.!!$R1 2552
1 TraesCS6A01G112900 chr3A 710756156 710758734 2578 True 4150 4150 95.896 1 2552 1 chr3A.!!$R1 2551
2 TraesCS6A01G112900 chr3A 666692732 666695295 2563 False 4120 4120 95.764 1 2552 1 chr3A.!!$F3 2551
3 TraesCS6A01G112900 chr3A 568428066 568430640 2574 False 4058 4058 95.268 1 2552 1 chr3A.!!$F2 2551
4 TraesCS6A01G112900 chr3A 11148633 11151072 2439 False 3941 3941 95.948 1 2422 1 chr3A.!!$F1 2421
5 TraesCS6A01G112900 chr5A 671937245 671939815 2570 True 4148 4148 95.922 1 2552 1 chr5A.!!$R1 2551
6 TraesCS6A01G112900 chr5A 691694771 691697223 2452 True 4052 4052 96.500 1 2451 1 chr5A.!!$R2 2450
7 TraesCS6A01G112900 chr5A 692009849 692012402 2553 False 4050 4050 95.338 1 2552 1 chr5A.!!$F2 2551
8 TraesCS6A01G112900 chr5A 1849071 1851628 2557 False 4010 4010 95.035 1 2552 1 chr5A.!!$F1 2551
9 TraesCS6A01G112900 chr2A 35547475 35550041 2566 False 4106 4106 95.652 1 2552 1 chr2A.!!$F1 2551
10 TraesCS6A01G112900 chr4A 616134694 616137268 2574 True 4091 4091 95.499 1 2552 1 chr4A.!!$R1 2551
11 TraesCS6A01G112900 chr7A 112676559 112679106 2547 True 3967 3967 94.798 1 2552 1 chr7A.!!$R1 2551
12 TraesCS6A01G112900 chr1A 576105933 576108482 2549 False 3941 3941 94.608 1 2552 1 chr1A.!!$F1 2551
13 TraesCS6A01G112900 chr5B 16241886 16244378 2492 True 3696 3696 93.498 1 2487 1 chr5B.!!$R1 2486
14 TraesCS6A01G112900 chrUn 48354741 48355806 1065 True 1635 1635 94.757 1513 2552 1 chrUn.!!$R1 1039

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
303 305 0.381801 CATGGTTGTTATGCGCCTCC 59.618 55.0 4.18 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 1943 2.021355 CAGATGTGCCTCTGGAGTTC 57.979 55.0 1.2 0.0 39.2 3.01 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
303 305 0.381801 CATGGTTGTTATGCGCCTCC 59.618 55.000 4.18 0.00 0.00 4.30
715 718 4.095211 GGGTGGTTAGGATAGGGTAGATC 58.905 52.174 0.00 0.00 0.00 2.75
767 770 8.770828 CCGTGATTGTAGGGTTAATTAGTTATG 58.229 37.037 0.00 0.00 0.00 1.90
784 787 6.978343 AGTTATGTTGAAGTAATGCGCTTA 57.022 33.333 9.73 1.78 0.00 3.09
793 796 3.535561 AGTAATGCGCTTAGATGCAAGT 58.464 40.909 9.73 0.00 45.45 3.16
943 950 0.787084 TCCCTTGCCCCACCAAATTA 59.213 50.000 0.00 0.00 0.00 1.40
1014 1021 1.537776 CGAGAGATGTCCATGTCCAGC 60.538 57.143 1.18 0.00 32.06 4.85
1115 1122 4.518970 ACTGAAGCGTTTGACAACCATATT 59.481 37.500 0.00 0.00 0.00 1.28
1137 1144 3.333381 TGGAGAAGAATGGAAACCATGGA 59.667 43.478 21.47 0.00 44.40 3.41
1140 1147 3.009033 AGAAGAATGGAAACCATGGACGA 59.991 43.478 21.47 7.11 44.40 4.20
1552 1562 0.817634 TGATGGCCGCGGGATTTTAG 60.818 55.000 29.38 0.00 0.00 1.85
1616 1626 8.547967 TCATCACTCATTAGAAGTTGTTAACC 57.452 34.615 2.48 0.00 0.00 2.85
1690 1700 5.055265 TGTATGACCAGACCAAGGAAAAA 57.945 39.130 0.00 0.00 0.00 1.94
1869 1899 9.840427 ATTTGTAAAGTAGCACATTACATCAAC 57.160 29.630 13.77 0.00 40.50 3.18
2491 2578 1.629749 CCCTGATAACCCTAACCCCCA 60.630 57.143 0.00 0.00 0.00 4.96
2495 2589 0.428520 ATAACCCTAACCCCCACCCT 59.571 55.000 0.00 0.00 0.00 4.34
2552 2657 1.799933 TTTTGCCCCACATGGAAACT 58.200 45.000 0.00 0.00 37.39 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
472 475 6.620877 TGAGTAGTTCTGGTGTAATTGGAT 57.379 37.500 0.00 0.00 0.00 3.41
528 531 3.762407 TCGACCAAGAAGTCATTTCCA 57.238 42.857 0.00 0.00 36.52 3.53
660 663 3.519107 TGTTTCTCCTCACATAGCCATCA 59.481 43.478 0.00 0.00 0.00 3.07
715 718 2.930826 ACCTTCCCATTATACCGCAG 57.069 50.000 0.00 0.00 0.00 5.18
767 770 4.201812 TGCATCTAAGCGCATTACTTCAAC 60.202 41.667 11.47 0.00 37.31 3.18
943 950 4.310769 CTTCATCGCCGGAGAAGAATAAT 58.689 43.478 23.05 0.00 40.85 1.28
984 991 2.360844 GACATCTCTCGTCTCTCACCA 58.639 52.381 0.00 0.00 0.00 4.17
1115 1122 3.333381 TCCATGGTTTCCATTCTTCTCCA 59.667 43.478 12.58 0.00 42.23 3.86
1137 1144 3.745975 TCTCGCATTTCACAAATTCTCGT 59.254 39.130 0.00 0.00 0.00 4.18
1140 1147 3.503363 TGCTCTCGCATTTCACAAATTCT 59.497 39.130 0.00 0.00 42.25 2.40
1411 1421 4.576330 GGCATAGCCCTTATTATCCACT 57.424 45.455 0.00 0.00 44.06 4.00
1552 1562 9.662545 CAAATCCCACAACAATTATTGAAAAAC 57.337 29.630 12.28 0.00 33.57 2.43
1581 1591 8.853077 TTCTAATGAGTGATGATCAACAAGTT 57.147 30.769 7.30 3.55 0.00 2.66
1690 1700 8.743714 GTCCTTTCCAATAGATTTCAAATGAGT 58.256 33.333 0.00 0.00 0.00 3.41
1912 1943 2.021355 CAGATGTGCCTCTGGAGTTC 57.979 55.000 1.20 0.00 39.20 3.01
2390 2463 2.590282 TCCATCCGGTACCATCGATA 57.410 50.000 13.54 0.00 0.00 2.92
2459 2546 4.264038 GGGTTATCAGGGTTTAGGGTTCAA 60.264 45.833 0.00 0.00 0.00 2.69
2491 2578 3.175710 GTGTGTGTGGGGGAGGGT 61.176 66.667 0.00 0.00 0.00 4.34
2495 2589 1.911702 TTTCGTGTGTGTGTGGGGGA 61.912 55.000 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.