Multiple sequence alignment - TraesCS6A01G328400

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 TraesCS6A01G328400 chr6A 100.000 2596 0 0 1 2596 561652013 561649418 0.000000e+00 4795
1 TraesCS6A01G328400 chr6A 99.158 831 6 1 1 830 561425944 561426774 0.000000e+00 1495
2 TraesCS6A01G328400 chr4B 95.086 2605 103 12 1 2596 22465474 22462886 0.000000e+00 4078
3 TraesCS6A01G328400 chr2B 94.998 2599 100 13 1 2596 601695283 601697854 0.000000e+00 4052
4 TraesCS6A01G328400 chr2B 92.331 1995 110 16 45 2022 663367625 663365657 0.000000e+00 2796
5 TraesCS6A01G328400 chr2B 93.310 583 39 0 2014 2596 663362354 663361772 0.000000e+00 861
6 TraesCS6A01G328400 chr3D 95.330 2441 85 10 164 2596 482857972 482855553 0.000000e+00 3849
7 TraesCS6A01G328400 chr4A 93.908 2446 105 22 164 2596 30742179 30744593 0.000000e+00 3651
8 TraesCS6A01G328400 chr2D 94.433 1940 67 20 1 1928 564584029 564585939 0.000000e+00 2946
9 TraesCS6A01G328400 chr2D 95.856 1641 62 5 960 2596 564448144 564449782 0.000000e+00 2649
10 TraesCS6A01G328400 chr2D 93.474 1471 85 8 1132 2596 556200845 556202310 0.000000e+00 2174
11 TraesCS6A01G328400 chr2D 92.479 1077 47 9 1 1071 556199799 556200847 0.000000e+00 1509
12 TraesCS6A01G328400 chr2A 92.648 2081 95 22 1 2067 695775792 695777828 0.000000e+00 2942
13 TraesCS6A01G328400 chr2A 92.610 2084 91 18 1 2067 695951508 695953545 0.000000e+00 2937
14 TraesCS6A01G328400 chr2A 97.452 157 4 0 2440 2596 695956773 695956929 4.260000e-68 268
15 TraesCS6A01G328400 chr2A 95.541 157 7 0 2440 2596 695781102 695781258 4.290000e-63 252
16 TraesCS6A01G328400 chr3A 81.055 417 68 8 1898 2310 679498678 679498269 3.220000e-84 322
17 TraesCS6A01G328400 chr6D 90.795 239 8 5 1 239 428238206 428238430 9.020000e-80 307


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 TraesCS6A01G328400 chr6A 561649418 561652013 2595 True 4795.0 4795 100.0000 1 2596 1 chr6A.!!$R1 2595
1 TraesCS6A01G328400 chr6A 561425944 561426774 830 False 1495.0 1495 99.1580 1 830 1 chr6A.!!$F1 829
2 TraesCS6A01G328400 chr4B 22462886 22465474 2588 True 4078.0 4078 95.0860 1 2596 1 chr4B.!!$R1 2595
3 TraesCS6A01G328400 chr2B 601695283 601697854 2571 False 4052.0 4052 94.9980 1 2596 1 chr2B.!!$F1 2595
4 TraesCS6A01G328400 chr2B 663361772 663367625 5853 True 1828.5 2796 92.8205 45 2596 2 chr2B.!!$R1 2551
5 TraesCS6A01G328400 chr3D 482855553 482857972 2419 True 3849.0 3849 95.3300 164 2596 1 chr3D.!!$R1 2432
6 TraesCS6A01G328400 chr4A 30742179 30744593 2414 False 3651.0 3651 93.9080 164 2596 1 chr4A.!!$F1 2432
7 TraesCS6A01G328400 chr2D 564584029 564585939 1910 False 2946.0 2946 94.4330 1 1928 1 chr2D.!!$F2 1927
8 TraesCS6A01G328400 chr2D 564448144 564449782 1638 False 2649.0 2649 95.8560 960 2596 1 chr2D.!!$F1 1636
9 TraesCS6A01G328400 chr2D 556199799 556202310 2511 False 1841.5 2174 92.9765 1 2596 2 chr2D.!!$F3 2595
10 TraesCS6A01G328400 chr2A 695951508 695956929 5421 False 1602.5 2937 95.0310 1 2596 2 chr2A.!!$F2 2595
11 TraesCS6A01G328400 chr2A 695775792 695781258 5466 False 1597.0 2942 94.0945 1 2596 2 chr2A.!!$F1 2595


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
937 971 0.4546 CTTGCTATTGTGGCAGGCAG 59.545 55.0 0.0 0.0 40.9 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2350 5748 0.243636 GCAATGCTGTTACCCACCAC 59.756 55.0 0.0 0.0 0.0 4.16 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 79 5.021033 TGGAAAAAGCAAATCAGCAAGAA 57.979 34.783 0.00 0.00 36.85 2.52
874 906 7.824779 GTGAACAGAGGGAGTATTTCTTTATGT 59.175 37.037 0.00 0.00 0.00 2.29
875 907 9.042450 TGAACAGAGGGAGTATTTCTTTATGTA 57.958 33.333 0.00 0.00 0.00 2.29
876 908 9.886132 GAACAGAGGGAGTATTTCTTTATGTAA 57.114 33.333 0.00 0.00 0.00 2.41
937 971 0.454600 CTTGCTATTGTGGCAGGCAG 59.545 55.000 0.00 0.00 40.90 4.85
952 986 2.429610 CAGGCAGCAAAATGGAGCTATT 59.570 45.455 0.00 0.00 39.50 1.73
1087 1121 2.017782 TGCAAAGTAAGGTGCGAACAA 58.982 42.857 0.00 0.00 43.93 2.83
1143 1187 6.464222 AGCACTATGTAAGCTCAACAACTTA 58.536 36.000 6.00 0.00 32.05 2.24
1171 1215 7.560368 TCCAGTACAAAACACAAATTTGGATT 58.440 30.769 21.74 12.35 41.08 3.01
1262 1306 3.418684 AATTTCTCTAGCGTTGTGGGT 57.581 42.857 0.00 0.00 0.00 4.51
1357 1402 2.964464 CACCTCTAGATCAGCTCACCAT 59.036 50.000 0.00 0.00 0.00 3.55
1373 1418 3.137544 TCACCATCCAACCAGTTACACTT 59.862 43.478 0.00 0.00 0.00 3.16
1467 1513 9.691362 GCTTCAAAGGTAATGATTCTGTTTTAA 57.309 29.630 0.00 0.00 0.00 1.52
1492 1538 4.488770 ACCACCCTAAATTTGTCCACAAT 58.511 39.130 0.00 0.00 35.55 2.71
1792 1843 9.969001 AAACCTACCTATAGCATTTCTAAAACA 57.031 29.630 0.00 0.00 0.00 2.83
1876 1935 8.989980 ACGCCTTAGTAGATTCTAAAAATATGC 58.010 33.333 0.00 0.00 30.88 3.14
2135 5516 7.341256 CCTCATTCCCCTAATACGCTAGTAATA 59.659 40.741 0.00 0.00 36.29 0.98
2163 5544 7.715249 TCTCATTTTCCATATTTCCCTTAGTCG 59.285 37.037 0.00 0.00 0.00 4.18
2201 5598 1.133976 CGATCCAAGGAAGGGAATGCT 60.134 52.381 0.00 0.00 38.09 3.79
2228 5626 1.534476 TGGCGACAGTGTCCCCTTA 60.534 57.895 24.04 5.81 32.27 2.69
2334 5732 1.233950 TGCGACGACAATGCCACAAT 61.234 50.000 0.00 0.00 0.00 2.71
2347 5745 1.004277 GCCACAATGGAGGGTAGAACA 59.996 52.381 0.00 0.00 40.96 3.18
2350 5748 1.916181 ACAATGGAGGGTAGAACAGGG 59.084 52.381 0.00 0.00 0.00 4.45
2359 5757 1.648116 GTAGAACAGGGTGGTGGGTA 58.352 55.000 0.00 0.00 0.00 3.69
2371 5769 0.958382 GGTGGGTAACAGCATTGCGA 60.958 55.000 2.38 0.00 46.64 5.10
2385 5783 2.125106 GCGAAAGGAGGTGCCGAT 60.125 61.111 0.00 0.00 43.43 4.18
2407 5805 1.355720 ACTCATTTGACCCAGGGAAGG 59.644 52.381 14.54 0.00 0.00 3.46
2446 8670 5.696822 TGTTTTAGTCTCGTACTGCTACTG 58.303 41.667 3.85 0.00 39.39 2.74
2537 8761 3.908103 GAGCATGTTTAGGGGGAGGTATA 59.092 47.826 0.00 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 9.803507 TGGCATTCATCTAATGAGAAATAGAAT 57.196 29.630 2.01 0.00 46.81 2.40
141 142 7.801716 ACACATTGTTGTACTATTTCACAGT 57.198 32.000 0.00 0.00 33.76 3.55
874 906 4.172505 CAACAGCGCTTGCCAATTAATTA 58.827 39.130 7.50 0.00 40.41 1.40
875 907 2.995258 CAACAGCGCTTGCCAATTAATT 59.005 40.909 7.50 0.00 40.41 1.40
876 908 2.609350 CAACAGCGCTTGCCAATTAAT 58.391 42.857 7.50 0.00 40.41 1.40
877 909 1.336702 CCAACAGCGCTTGCCAATTAA 60.337 47.619 7.50 0.00 40.41 1.40
937 971 5.329035 TGGAAAGAATAGCTCCATTTTGC 57.671 39.130 0.00 0.00 34.26 3.68
952 986 7.000472 CCTTCTGGAATATGCTAATGGAAAGA 59.000 38.462 0.00 0.00 34.57 2.52
1023 1057 2.644418 GTGCAAACTGATGCCGCA 59.356 55.556 0.00 0.00 45.83 5.69
1087 1121 2.231478 CTCCTAACATACGGCGATGGAT 59.769 50.000 16.62 9.10 0.00 3.41
1143 1187 6.816140 CCAAATTTGTGTTTTGTACTGGAAGT 59.184 34.615 16.73 0.00 39.75 3.01
1171 1215 2.948979 CAGGTTGCACTGAACAAACCTA 59.051 45.455 5.67 0.00 40.97 3.08
1236 1280 5.277779 CCACAACGCTAGAGAAATTTTCACA 60.278 40.000 11.53 0.00 0.00 3.58
1262 1306 0.960286 TAAATGCAACAGCAGCAGCA 59.040 45.000 3.17 0.00 46.36 4.41
1467 1513 4.717280 TGTGGACAAATTTAGGGTGGTTTT 59.283 37.500 0.00 0.00 0.00 2.43
1468 1514 4.290942 TGTGGACAAATTTAGGGTGGTTT 58.709 39.130 0.00 0.00 0.00 3.27
1492 1538 9.607988 AATAGATAACCATGTCGTAAACATCAA 57.392 29.630 0.00 0.00 45.78 2.57
1743 1794 2.860009 CTAGATGTCTAGGCCCGTGTA 58.140 52.381 0.00 0.00 41.65 2.90
1988 2058 6.263392 CGGGTGGGATATAGTCATACTCTATG 59.737 46.154 0.00 0.00 37.52 2.23
2135 5516 8.560903 ACTAAGGGAAATATGGAAAATGAGACT 58.439 33.333 0.00 0.00 0.00 3.24
2163 5544 0.798776 CGTGAAGTGATTGGGAGTGC 59.201 55.000 0.00 0.00 0.00 4.40
2201 5598 2.187685 CTGTCGCCATGGCTGCTA 59.812 61.111 33.07 16.00 39.32 3.49
2311 5709 1.154413 GGCATTGTCGTCGCAACAG 60.154 57.895 4.59 3.06 0.00 3.16
2334 5732 0.546747 CCACCCTGTTCTACCCTCCA 60.547 60.000 0.00 0.00 0.00 3.86
2347 5745 1.140134 ATGCTGTTACCCACCACCCT 61.140 55.000 0.00 0.00 0.00 4.34
2350 5748 0.243636 GCAATGCTGTTACCCACCAC 59.756 55.000 0.00 0.00 0.00 4.16
2359 5757 0.883833 CCTCCTTTCGCAATGCTGTT 59.116 50.000 2.94 0.00 0.00 3.16
2385 5783 1.741028 TCCCTGGGTCAAATGAGTGA 58.259 50.000 13.56 0.00 0.00 3.41
2433 5831 6.062749 AGATCCTTATTCAGTAGCAGTACGA 58.937 40.000 0.00 0.00 33.97 3.43



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

AutoCloner maintained by Alex Coulton.