Multiple sequence alignment - TraesCS6A01G080000

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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 TraesCS6A01G080000 chr6A 100.000 2834 0 0 1 2834 49100978 49098145 0.000000e+00 5234.0
1 TraesCS6A01G080000 chr7A 94.395 2837 126 6 11 2834 500181496 500184312 0.000000e+00 4327.0
2 TraesCS6A01G080000 chr7A 81.782 505 92 0 1333 1837 35448443 35447939 9.390000e-115 424.0
3 TraesCS6A01G080000 chr7A 97.902 143 3 0 2692 2834 68345042 68345184 6.060000e-62 248.0
4 TraesCS6A01G080000 chr7A 82.500 80 9 5 2602 2678 145401386 145401309 6.550000e-07 65.8
5 TraesCS6A01G080000 chr4A 97.554 1390 33 1 1445 2834 490611674 490610286 0.000000e+00 2377.0
6 TraesCS6A01G080000 chr4A 85.000 60 7 2 2586 2644 620276338 620276396 3.050000e-05 60.2
7 TraesCS6A01G080000 chr3A 82.779 1835 306 9 11 1837 601341448 601339616 0.000000e+00 1629.0
8 TraesCS6A01G080000 chr3A 96.601 353 12 0 2482 2834 194816152 194815800 1.130000e-163 586.0
9 TraesCS6A01G080000 chr3A 93.316 374 22 1 2461 2834 235438455 235438825 1.480000e-152 549.0
10 TraesCS6A01G080000 chr5B 82.334 1834 315 6 11 1837 392101122 392102953 0.000000e+00 1583.0
11 TraesCS6A01G080000 chr5B 82.334 1251 213 5 11 1254 392057282 392058531 0.000000e+00 1079.0
12 TraesCS6A01G080000 chr5B 82.954 1185 194 5 11 1188 392042261 392043444 0.000000e+00 1062.0
13 TraesCS6A01G080000 chr5B 82.576 528 92 0 1297 1824 392058902 392059429 1.540000e-127 466.0
14 TraesCS6A01G080000 chr5B 82.081 519 93 0 1319 1837 392043696 392044214 7.200000e-121 444.0
15 TraesCS6A01G080000 chr2A 81.318 1836 331 10 11 1837 207350145 207348313 0.000000e+00 1480.0
16 TraesCS6A01G080000 chr2A 83.128 1215 190 13 62 1264 678124782 678125993 0.000000e+00 1094.0
17 TraesCS6A01G080000 chr2A 81.086 534 101 0 1304 1837 678126321 678126854 7.260000e-116 427.0
18 TraesCS6A01G080000 chrUn 85.926 675 93 2 11 684 426444107 426444780 0.000000e+00 719.0
19 TraesCS6A01G080000 chrUn 85.757 674 96 0 11 684 426445408 426446081 0.000000e+00 713.0
20 TraesCS6A01G080000 chr5D 84.615 65 8 2 2584 2647 106714018 106713955 2.360000e-06 63.9
21 TraesCS6A01G080000 chr4D 89.362 47 4 1 2602 2647 195663865 195663819 1.100000e-04 58.4


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 TraesCS6A01G080000 chr6A 49098145 49100978 2833 True 5234.0 5234 100.0000 1 2834 1 chr6A.!!$R1 2833
1 TraesCS6A01G080000 chr7A 500181496 500184312 2816 False 4327.0 4327 94.3950 11 2834 1 chr7A.!!$F2 2823
2 TraesCS6A01G080000 chr7A 35447939 35448443 504 True 424.0 424 81.7820 1333 1837 1 chr7A.!!$R1 504
3 TraesCS6A01G080000 chr4A 490610286 490611674 1388 True 2377.0 2377 97.5540 1445 2834 1 chr4A.!!$R1 1389
4 TraesCS6A01G080000 chr3A 601339616 601341448 1832 True 1629.0 1629 82.7790 11 1837 1 chr3A.!!$R2 1826
5 TraesCS6A01G080000 chr5B 392101122 392102953 1831 False 1583.0 1583 82.3340 11 1837 1 chr5B.!!$F1 1826
6 TraesCS6A01G080000 chr5B 392057282 392059429 2147 False 772.5 1079 82.4550 11 1824 2 chr5B.!!$F3 1813
7 TraesCS6A01G080000 chr5B 392042261 392044214 1953 False 753.0 1062 82.5175 11 1837 2 chr5B.!!$F2 1826
8 TraesCS6A01G080000 chr2A 207348313 207350145 1832 True 1480.0 1480 81.3180 11 1837 1 chr2A.!!$R1 1826
9 TraesCS6A01G080000 chr2A 678124782 678126854 2072 False 760.5 1094 82.1070 62 1837 2 chr2A.!!$F1 1775
10 TraesCS6A01G080000 chrUn 426444107 426446081 1974 False 716.0 719 85.8415 11 684 2 chrUn.!!$F1 673

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
969 1086 0.749649 ACTAGATCTTGCTGGGCTCG 59.25 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 3374 0.784778 CGTCGAGTTTTGTCTCCTGC 59.215 55.0 0.0 0.0 0.0 4.85 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
174 175 4.947147 GTGGTGCGGCACTTCCCA 62.947 66.667 29.92 18.32 34.40 4.37
210 212 4.069304 TCAGGTTTATGTACCAGCACAAC 58.931 43.478 0.00 0.00 40.82 3.32
342 344 1.528824 CCTGTGCATCGAGGGGATT 59.471 57.895 0.00 0.00 31.28 3.01
378 380 2.098298 GAGTACGTCGCCGCGTTA 59.902 61.111 13.39 0.12 43.04 3.18
576 578 1.453155 GCGTGTTGATCCACCTTGAT 58.547 50.000 0.00 0.00 31.47 2.57
582 584 3.285484 GTTGATCCACCTTGATCTGCAT 58.715 45.455 0.00 0.00 41.42 3.96
602 604 1.152030 AGGACCACTCCAAGGCTCA 60.152 57.895 0.00 0.00 39.39 4.26
918 1032 2.424302 CGTCGTGGGGTTGGACTT 59.576 61.111 0.00 0.00 0.00 3.01
919 1033 1.959226 CGTCGTGGGGTTGGACTTG 60.959 63.158 0.00 0.00 0.00 3.16
920 1034 1.599797 GTCGTGGGGTTGGACTTGG 60.600 63.158 0.00 0.00 0.00 3.61
921 1035 2.282180 CGTGGGGTTGGACTTGGG 60.282 66.667 0.00 0.00 0.00 4.12
922 1036 2.824880 CGTGGGGTTGGACTTGGGA 61.825 63.158 0.00 0.00 0.00 4.37
923 1037 1.539665 GTGGGGTTGGACTTGGGAA 59.460 57.895 0.00 0.00 0.00 3.97
924 1038 0.826256 GTGGGGTTGGACTTGGGAAC 60.826 60.000 0.00 0.00 0.00 3.62
925 1039 1.602605 GGGGTTGGACTTGGGAACG 60.603 63.158 0.00 0.00 0.00 3.95
926 1040 2.265904 GGGTTGGACTTGGGAACGC 61.266 63.158 0.00 0.00 0.00 4.84
958 1075 3.437867 CGCCTCCGCACTAGATCT 58.562 61.111 0.00 0.00 34.03 2.75
969 1086 0.749649 ACTAGATCTTGCTGGGCTCG 59.250 55.000 0.00 0.00 0.00 5.03
987 1104 2.491022 GGGCTCCGCTAGTGACGAT 61.491 63.158 4.44 0.00 0.00 3.73
994 1111 2.731571 GCTAGTGACGATGGGGGCA 61.732 63.158 0.00 0.00 0.00 5.36
1177 2041 4.043100 GGGCTACGGCAACCCCTT 62.043 66.667 0.00 0.00 40.87 3.95
1381 2573 2.113986 GTGTTGGCCTGGCTCTGT 59.886 61.111 19.68 0.00 0.00 3.41
1513 2705 2.583520 GGCTCTCCCTGCACAGAG 59.416 66.667 0.00 7.85 39.44 3.35
1633 2825 2.248248 AGGACGGAGAAGACATCACAA 58.752 47.619 0.00 0.00 0.00 3.33
1649 2841 3.706373 AACCGCGGCTCTGGATGT 61.706 61.111 28.58 0.00 0.00 3.06
1887 3079 4.442332 CCATGTTATCACAAAGCCATGCAT 60.442 41.667 0.00 0.00 36.16 3.96
2092 3296 8.131100 CCTATCAATGTAATGTGTTGGAATGTC 58.869 37.037 0.00 0.00 0.00 3.06
2170 3374 6.973229 TCATCTTGTCATATTGTGTGTCTG 57.027 37.500 0.00 0.00 0.00 3.51
2255 3459 1.332375 GTAATTATGCGCAAAGGCCGA 59.668 47.619 17.11 0.00 36.38 5.54
2506 3710 6.142498 TGCAGGGGATTTCAACCAAATATAT 58.858 36.000 0.00 0.00 34.60 0.86
2508 3712 6.267471 GCAGGGGATTTCAACCAAATATATCA 59.733 38.462 0.00 0.00 34.60 2.15
2738 3942 1.683319 CCCTCTCGTCATCTCTGTCCA 60.683 57.143 0.00 0.00 0.00 4.02
2774 3978 1.043116 TCTCGCCGATGACAAGGGAT 61.043 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.390048 GGCGTGGCCTCTTTGTTA 57.610 55.556 3.32 0.00 46.69 2.41
66 67 3.702048 CGGGCTCCCTCGAACCAA 61.702 66.667 3.11 0.00 0.00 3.67
174 175 2.428544 ACCTGACGAGATACTGCTCT 57.571 50.000 0.00 0.00 32.71 4.09
237 239 1.218316 GGAGTTGCCGACGAGGAAT 59.782 57.895 0.00 0.00 45.00 3.01
378 380 4.082523 CACCCACGGCCGATGACT 62.083 66.667 35.90 5.52 0.00 3.41
551 553 1.019278 GTGGATCAACACGCGGTGAT 61.019 55.000 18.38 18.38 36.96 3.06
558 560 2.674852 CAGATCAAGGTGGATCAACACG 59.325 50.000 1.86 0.00 44.89 4.49
562 564 3.054213 TCATGCAGATCAAGGTGGATCAA 60.054 43.478 6.01 0.00 44.89 2.57
576 578 0.545071 TGGAGTGGTCCTCATGCAGA 60.545 55.000 0.00 0.00 44.30 4.26
582 584 1.152030 AGCCTTGGAGTGGTCCTCA 60.152 57.895 0.00 0.00 44.30 3.86
602 604 4.064491 GGTCGTCGTCGTCGTCGT 62.064 66.667 18.44 0.00 45.27 4.34
738 740 4.986587 CCGCGGTCGTTGTCGTCA 62.987 66.667 19.50 0.00 38.33 4.35
909 1011 2.613506 CGCGTTCCCAAGTCCAACC 61.614 63.158 0.00 0.00 0.00 3.77
952 1066 1.402896 CCCGAGCCCAGCAAGATCTA 61.403 60.000 0.00 0.00 0.00 1.98
994 1111 2.827423 CTGGAGCTCCATGGCGAT 59.173 61.111 35.11 0.00 46.46 4.58
1198 2062 1.817099 GCGAGCACAGCCTAAGCAT 60.817 57.895 0.00 0.00 43.56 3.79
1381 2573 2.494059 CTCCTGCCTTTCTTCGAACAA 58.506 47.619 0.00 0.00 0.00 2.83
1512 2704 0.389948 CTTTTAGTCTCGCACCGGCT 60.390 55.000 0.00 0.00 38.10 5.52
1513 2705 1.967597 GCTTTTAGTCTCGCACCGGC 61.968 60.000 0.00 0.00 0.00 6.13
1633 2825 1.686325 AATACATCCAGAGCCGCGGT 61.686 55.000 28.70 13.92 0.00 5.68
1649 2841 3.407698 TCCTTGAAACGCTCTGCAAATA 58.592 40.909 0.00 0.00 0.00 1.40
1887 3079 1.714787 ACTAGTACCACCTCCCAGACA 59.285 52.381 0.00 0.00 0.00 3.41
1980 3172 2.018515 ACTGTAAAAACACACCCACCG 58.981 47.619 0.00 0.00 0.00 4.94
1991 3195 5.878116 ACACACAACTCTGCTACTGTAAAAA 59.122 36.000 0.00 0.00 0.00 1.94
2031 3235 1.745087 CAACATGGGGTACACATCAGC 59.255 52.381 0.00 0.00 0.00 4.26
2092 3296 4.410400 GGGCAGTTGAGACCCCGG 62.410 72.222 0.00 0.00 37.70 5.73
2170 3374 0.784778 CGTCGAGTTTTGTCTCCTGC 59.215 55.000 0.00 0.00 0.00 4.85
2506 3710 6.349611 GCCTTTTATTCTTGTCTCTTGCATGA 60.350 38.462 0.00 1.92 0.00 3.07
2508 3712 5.477984 TGCCTTTTATTCTTGTCTCTTGCAT 59.522 36.000 0.00 0.00 0.00 3.96
2738 3942 3.866651 CGAGAAGGAGTGGACAATGATT 58.133 45.455 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.