Multiple sequence alignment - TraesCS7B01G208400

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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 TraesCS7B01G208400 chr7B 100.000 3441 0 0 1 3441 381026459 381023019 0 6355
1 TraesCS7B01G208400 chr7B 96.226 3445 122 7 1 3441 406726487 406729927 0 5635
2 TraesCS7B01G208400 chr2B 96.950 3443 91 11 4 3441 506424434 506421001 0 5764
3 TraesCS7B01G208400 chr2B 96.634 3446 104 9 4 3441 300243649 300240208 0 5710
4 TraesCS7B01G208400 chr2B 96.082 3446 122 12 4 3441 259485623 259482183 0 5603
5 TraesCS7B01G208400 chr2B 95.763 3446 135 10 4 3441 209875997 209872555 0 5544
6 TraesCS7B01G208400 chr2B 95.512 3454 138 14 1 3441 379155442 379158891 0 5504
7 TraesCS7B01G208400 chr1B 95.917 3453 125 13 1 3441 330756294 330759742 0 5581
8 TraesCS7B01G208400 chr5B 95.902 3441 134 6 1 3438 197387104 197390540 0 5566
9 TraesCS7B01G208400 chr5B 95.819 3444 126 12 4 3441 299228719 299225288 0 5546


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 TraesCS7B01G208400 chr7B 381023019 381026459 3440 True 6355 6355 100.000 1 3441 1 chr7B.!!$R1 3440
1 TraesCS7B01G208400 chr7B 406726487 406729927 3440 False 5635 5635 96.226 1 3441 1 chr7B.!!$F1 3440
2 TraesCS7B01G208400 chr2B 506421001 506424434 3433 True 5764 5764 96.950 4 3441 1 chr2B.!!$R4 3437
3 TraesCS7B01G208400 chr2B 300240208 300243649 3441 True 5710 5710 96.634 4 3441 1 chr2B.!!$R3 3437
4 TraesCS7B01G208400 chr2B 259482183 259485623 3440 True 5603 5603 96.082 4 3441 1 chr2B.!!$R2 3437
5 TraesCS7B01G208400 chr2B 209872555 209875997 3442 True 5544 5544 95.763 4 3441 1 chr2B.!!$R1 3437
6 TraesCS7B01G208400 chr2B 379155442 379158891 3449 False 5504 5504 95.512 1 3441 1 chr2B.!!$F1 3440
7 TraesCS7B01G208400 chr1B 330756294 330759742 3448 False 5581 5581 95.917 1 3441 1 chr1B.!!$F1 3440
8 TraesCS7B01G208400 chr5B 197387104 197390540 3436 False 5566 5566 95.902 1 3438 1 chr5B.!!$F1 3437
9 TraesCS7B01G208400 chr5B 299225288 299228719 3431 True 5546 5546 95.819 4 3441 1 chr5B.!!$R1 3437

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
477 494 1.134367 GCACCGCACATAGTCTCACTA 59.866 52.381 0.00 0.0 34.82 2.74 F
1177 1198 0.605319 CAGCGTACCAGAAAAGGCCA 60.605 55.000 5.01 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1310 0.927537 TTCTTCGACACACAACTGCG 59.072 50.0 0.0 0.0 0.00 5.18 R
3162 3197 0.178921 TCTCTCTTGACCTGTGGGCT 60.179 55.0 0.0 0.0 35.63 5.19 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
36 37 6.630443 CGCTGAAGCAGTGACATTATTATTTC 59.370 38.462 2.79 0.00 43.78 2.17
477 494 1.134367 GCACCGCACATAGTCTCACTA 59.866 52.381 0.00 0.00 34.82 2.74
679 696 2.024414 GTGGGATTTGGCAGGTCATAC 58.976 52.381 4.04 0.00 0.00 2.39
1155 1176 3.201494 ACGCTGGAGATCGTCTGG 58.799 61.111 0.00 0.00 33.09 3.86
1177 1198 0.605319 CAGCGTACCAGAAAAGGCCA 60.605 55.000 5.01 0.00 0.00 5.36
1230 1251 0.743345 GCGGCAGGTTTCGTAGGATT 60.743 55.000 0.00 0.00 0.00 3.01
1236 1257 1.897802 AGGTTTCGTAGGATTGTCGGT 59.102 47.619 0.00 0.00 0.00 4.69
1289 1310 2.124403 CCAGATGGCAGCAGTCCC 60.124 66.667 5.19 0.00 0.00 4.46
1299 1320 2.591715 GCAGTCCCGCAGTTGTGT 60.592 61.111 0.00 0.00 0.00 3.72
1305 1326 1.885388 CCCGCAGTTGTGTGTCGAA 60.885 57.895 0.00 0.00 31.71 3.71
1527 1550 7.894376 AAATGTATTTTTGAACCTGATGCAG 57.106 32.000 0.00 0.00 0.00 4.41
1604 1627 9.909644 GACTAGTGTAGTTTCTGAAGTTGATAA 57.090 33.333 0.00 0.00 39.59 1.75
1750 1775 3.750371 CACTGGTTCTGTGTTATCCCAA 58.250 45.455 0.00 0.00 0.00 4.12
1759 1784 5.009631 TCTGTGTTATCCCAATTCAACCAG 58.990 41.667 0.00 0.00 0.00 4.00
1805 1830 5.049474 TGCAGAACATACAACATTGACTGAC 60.049 40.000 0.00 0.00 0.00 3.51
2160 2188 1.373497 AGCGCAAGTGGAGAGTTCG 60.373 57.895 11.47 0.00 41.68 3.95
2370 2398 3.267483 TGATCGACTACATCACAGACGA 58.733 45.455 0.00 0.00 42.54 4.20
2388 2416 2.878406 ACGATTGGGAATATGCGAAAGG 59.122 45.455 0.00 0.00 0.00 3.11
2425 2453 0.396139 TCTACGACCGCCCCTATTGT 60.396 55.000 0.00 0.00 0.00 2.71
2453 2483 6.918067 TTACGGGATGAAGATACATCAGAT 57.082 37.500 0.00 0.00 45.68 2.90
2781 2812 6.071560 ACTCAGTACAATTGATCGGACAGTAA 60.072 38.462 13.59 0.00 0.00 2.24
3076 3110 2.852075 ACCGCCCAAGGTCAGGAA 60.852 61.111 0.00 0.00 41.46 3.36
3102 3136 3.812053 GCCCTGACAATGCTAGATACTTG 59.188 47.826 0.00 0.00 0.00 3.16
3360 3396 0.393808 GCTATCTGGGCCGGAAAACA 60.394 55.000 21.02 4.19 0.00 2.83
3427 3463 1.483415 GGTATACAAACCAGAGGGCGA 59.517 52.381 5.01 0.00 39.50 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.074230 CTGCTTCAGCGGGCACAAAA 62.074 55.000 0.00 0.00 45.83 2.44
36 37 8.392612 GCATTCAAAAGGATTATCAAATGGTTG 58.607 33.333 0.00 0.00 35.95 3.77
462 479 6.574350 ACCAAATACTAGTGAGACTATGTGC 58.426 40.000 5.39 0.00 29.08 4.57
477 494 8.611654 AAGTGTAATTGAACGTACCAAATACT 57.388 30.769 20.14 11.48 33.40 2.12
568 585 1.065199 TCAGCTGCTTATCCCACTTGG 60.065 52.381 9.47 0.00 0.00 3.61
679 696 4.159857 GACTAGTCTTGTCAAGCTGTACG 58.840 47.826 15.91 3.10 34.80 3.67
1119 1140 4.373116 TCGTTGCCGTGGAGCTCC 62.373 66.667 26.78 26.78 35.01 4.70
1155 1176 1.439679 CCTTTTCTGGTACGCTGGTC 58.560 55.000 0.00 0.00 0.00 4.02
1177 1198 0.616111 AGCCTGGAGATCACCTCGTT 60.616 55.000 10.73 0.00 42.89 3.85
1230 1251 2.109739 GTGCACACCAACACCGACA 61.110 57.895 13.17 0.00 0.00 4.35
1289 1310 0.927537 TTCTTCGACACACAACTGCG 59.072 50.000 0.00 0.00 0.00 5.18
1299 1320 1.412710 ACCAAGCAGAGTTCTTCGACA 59.587 47.619 0.00 0.00 0.00 4.35
1305 1326 2.047061 TGGTACACCAAGCAGAGTTCT 58.953 47.619 0.00 0.00 44.35 3.01
1527 1550 7.432252 CGCAAGATTTTCCAAATAGTAATCCAC 59.568 37.037 0.00 0.00 43.02 4.02
1604 1627 9.781633 ACATCGAGTACATAGACTACTCTATTT 57.218 33.333 0.00 0.00 37.59 1.40
1636 1660 9.956720 CTACATCAAGTTCAGAAACATCTTTTT 57.043 29.630 0.00 0.00 37.88 1.94
1704 1728 7.940137 TGCTTCACCAAGTCCTTAGTTTATTTA 59.060 33.333 0.00 0.00 31.45 1.40
1759 1784 9.250624 CTGCATTGGTACTAGTTTAGTCTATTC 57.749 37.037 0.00 0.00 40.14 1.75
1980 2008 7.577303 AGGGCAGAGACATTTTGAATATTAGA 58.423 34.615 0.00 0.00 0.00 2.10
2160 2188 4.101235 GTCGTACTCTTTTCCGGTGTATC 58.899 47.826 0.00 0.00 0.00 2.24
2370 2398 2.878406 CGACCTTTCGCATATTCCCAAT 59.122 45.455 0.00 0.00 38.71 3.16
2388 2416 1.157585 GAAGTTTTCAGCCTCCCGAC 58.842 55.000 0.00 0.00 0.00 4.79
2453 2483 2.774687 GGAAGTAAAACGAAGGCAGGA 58.225 47.619 0.00 0.00 0.00 3.86
2537 2567 4.252878 TGACAAGCACGACATAATCACAT 58.747 39.130 0.00 0.00 0.00 3.21
3075 3109 0.698238 TAGCATTGTCAGGGCCTGTT 59.302 50.000 31.60 13.44 32.61 3.16
3076 3110 0.254178 CTAGCATTGTCAGGGCCTGT 59.746 55.000 31.60 14.23 32.61 4.00
3102 3136 4.452733 CCCACGGGCTCGAGTTCC 62.453 72.222 15.95 14.69 40.11 3.62
3162 3197 0.178921 TCTCTCTTGACCTGTGGGCT 60.179 55.000 0.00 0.00 35.63 5.19
3299 3335 1.805539 GTCATGCACGTGCGCTCTA 60.806 57.895 33.22 17.73 45.83 2.43
3335 3371 2.196925 CGGCCCAGATAGCTCGTCT 61.197 63.158 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.