Multiple sequence alignment - TraesCS6B01G230800

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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 TraesCS6B01G230800 chr6B 100.000 6452 0 0 1 6452 375643790 375637339 0.000000e+00 11915.0
1 TraesCS6B01G230800 chr6B 97.832 4381 88 5 1 4379 710549430 710545055 0.000000e+00 7557.0
2 TraesCS6B01G230800 chr6B 97.852 3584 67 4 2867 6449 196484764 196488338 0.000000e+00 6183.0
3 TraesCS6B01G230800 chr6B 98.766 2837 34 1 1 2836 196481932 196484768 0.000000e+00 5044.0
4 TraesCS6B01G230800 chr6B 97.730 2599 35 2 162 2760 393070785 393073359 0.000000e+00 4451.0
5 TraesCS6B01G230800 chr6B 96.477 2384 79 5 4067 6449 55867762 55870141 0.000000e+00 3932.0
6 TraesCS6B01G230800 chr6B 97.889 1421 27 1 5032 6449 393090025 393091445 0.000000e+00 2455.0
7 TraesCS6B01G230800 chr6B 98.817 169 2 0 1 169 393069421 393069589 1.050000e-77 302.0
8 TraesCS6B01G230800 chr5B 97.719 6139 130 7 316 6452 446180555 446174425 0.000000e+00 10552.0
9 TraesCS6B01G230800 chr7B 97.004 4773 134 7 1682 6449 411605889 411610657 0.000000e+00 8013.0
10 TraesCS6B01G230800 chr7B 95.277 614 28 1 1075 1688 411605206 411605818 0.000000e+00 972.0
11 TraesCS6B01G230800 chr2B 97.746 4303 74 6 2167 6448 779303542 779307842 0.000000e+00 7387.0
12 TraesCS6B01G230800 chr7D 93.734 4181 231 12 2280 6449 625868598 625872758 0.000000e+00 6240.0
13 TraesCS6B01G230800 chr7D 92.857 910 48 8 695 1602 32521925 32521031 0.000000e+00 1304.0
14 TraesCS6B01G230800 chr2A 93.026 4187 252 15 2280 6452 743397707 743393547 0.000000e+00 6078.0
15 TraesCS6B01G230800 chr2A 93.013 916 60 4 687 1600 90615991 90615078 0.000000e+00 1334.0
16 TraesCS6B01G230800 chr2D 93.110 4180 225 28 2280 6449 97593096 97597222 0.000000e+00 6065.0
17 TraesCS6B01G230800 chr1B 97.477 3329 73 5 3125 6449 586566841 586570162 0.000000e+00 5672.0
18 TraesCS6B01G230800 chr1B 97.264 3070 76 4 3386 6452 12716879 12713815 0.000000e+00 5197.0
19 TraesCS6B01G230800 chr1B 97.394 2226 49 3 82 2307 586557560 586559776 0.000000e+00 3781.0
20 TraesCS6B01G230800 chr1B 97.701 87 2 0 1 87 586553267 586553353 4.030000e-32 150.0
21 TraesCS6B01G230800 chr6D 94.405 2985 140 8 2280 5254 62081459 62078492 0.000000e+00 4562.0
22 TraesCS6B01G230800 chr6D 92.198 910 55 7 695 1602 62083094 62082199 0.000000e+00 1273.0
23 TraesCS6B01G230800 chr6D 93.555 481 24 2 1810 2283 54816047 54816527 0.000000e+00 710.0
24 TraesCS6B01G230800 chr6D 93.555 481 24 2 1810 2283 156017551 156017071 0.000000e+00 710.0
25 TraesCS6B01G230800 chr6D 75.731 342 37 28 1706 2002 11769930 11770270 5.250000e-26 130.0
26 TraesCS6B01G230800 chr1A 87.167 1652 181 22 4816 6449 517804749 517806387 0.000000e+00 1847.0
27 TraesCS6B01G230800 chr1A 91.703 916 73 3 687 1600 379472351 379473265 0.000000e+00 1267.0
28 TraesCS6B01G230800 chr3A 91.060 481 36 4 1810 2283 500017623 500018103 1.520000e-180 643.0
29 TraesCS6B01G230800 chr3A 97.059 34 1 0 1682 1715 723997146 723997113 2.510000e-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 TraesCS6B01G230800 chr6B 375637339 375643790 6451 True 11915.0 11915 100.0000 1 6452 1 chr6B.!!$R1 6451
1 TraesCS6B01G230800 chr6B 710545055 710549430 4375 True 7557.0 7557 97.8320 1 4379 1 chr6B.!!$R2 4378
2 TraesCS6B01G230800 chr6B 196481932 196488338 6406 False 5613.5 6183 98.3090 1 6449 2 chr6B.!!$F3 6448
3 TraesCS6B01G230800 chr6B 55867762 55870141 2379 False 3932.0 3932 96.4770 4067 6449 1 chr6B.!!$F1 2382
4 TraesCS6B01G230800 chr6B 393090025 393091445 1420 False 2455.0 2455 97.8890 5032 6449 1 chr6B.!!$F2 1417
5 TraesCS6B01G230800 chr6B 393069421 393073359 3938 False 2376.5 4451 98.2735 1 2760 2 chr6B.!!$F4 2759
6 TraesCS6B01G230800 chr5B 446174425 446180555 6130 True 10552.0 10552 97.7190 316 6452 1 chr5B.!!$R1 6136
7 TraesCS6B01G230800 chr7B 411605206 411610657 5451 False 4492.5 8013 96.1405 1075 6449 2 chr7B.!!$F1 5374
8 TraesCS6B01G230800 chr2B 779303542 779307842 4300 False 7387.0 7387 97.7460 2167 6448 1 chr2B.!!$F1 4281
9 TraesCS6B01G230800 chr7D 625868598 625872758 4160 False 6240.0 6240 93.7340 2280 6449 1 chr7D.!!$F1 4169
10 TraesCS6B01G230800 chr7D 32521031 32521925 894 True 1304.0 1304 92.8570 695 1602 1 chr7D.!!$R1 907
11 TraesCS6B01G230800 chr2A 743393547 743397707 4160 True 6078.0 6078 93.0260 2280 6452 1 chr2A.!!$R2 4172
12 TraesCS6B01G230800 chr2A 90615078 90615991 913 True 1334.0 1334 93.0130 687 1600 1 chr2A.!!$R1 913
13 TraesCS6B01G230800 chr2D 97593096 97597222 4126 False 6065.0 6065 93.1100 2280 6449 1 chr2D.!!$F1 4169
14 TraesCS6B01G230800 chr1B 586566841 586570162 3321 False 5672.0 5672 97.4770 3125 6449 1 chr1B.!!$F3 3324
15 TraesCS6B01G230800 chr1B 12713815 12716879 3064 True 5197.0 5197 97.2640 3386 6452 1 chr1B.!!$R1 3066
16 TraesCS6B01G230800 chr1B 586557560 586559776 2216 False 3781.0 3781 97.3940 82 2307 1 chr1B.!!$F2 2225
17 TraesCS6B01G230800 chr6D 62078492 62083094 4602 True 2917.5 4562 93.3015 695 5254 2 chr6D.!!$R2 4559
18 TraesCS6B01G230800 chr1A 517804749 517806387 1638 False 1847.0 1847 87.1670 4816 6449 1 chr1A.!!$F2 1633
19 TraesCS6B01G230800 chr1A 379472351 379473265 914 False 1267.0 1267 91.7030 687 1600 1 chr1A.!!$F1 913

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
643 1847 2.011548 GCAGTATGTTCGTGCCATGGA 61.012 52.381 18.40 0.00 39.31 3.41 F
1585 2795 0.670854 GCTCTGTTTCCTCGTGGACC 60.671 60.000 5.53 0.58 43.06 4.46 F
1944 3321 3.331150 TGTAATATTATCCGGCTTGCCG 58.669 45.455 25.17 25.17 0.00 5.69 F
3319 4914 4.858850 TGGATGATTGAGTACTTTGGCAT 58.141 39.130 0.00 0.00 0.00 4.40 F
4011 5607 1.034356 CGTGGGTACGGATACATGGA 58.966 55.000 0.00 0.00 46.23 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 3089 1.355720 AGTTGGGGGATTGAACTCAGG 59.644 52.381 0.00 0.0 0.00 3.86 R
2979 4574 2.209064 AATGTCCGACCACGTCCTCG 62.209 60.000 4.70 4.7 43.34 4.63 R
3484 5079 7.492352 AACTAACTTGCGAGTAAGATTTTGT 57.508 32.000 7.13 0.0 34.21 2.83 R
4224 5823 5.128499 TCTTGCAACAATCTTTCCCTTTCAA 59.872 36.000 0.00 0.0 0.00 2.69 R
5939 7585 3.059188 CGTCGTAACAGGAAATTGCAACT 60.059 43.478 0.00 0.0 0.00 3.16 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
643 1847 2.011548 GCAGTATGTTCGTGCCATGGA 61.012 52.381 18.40 0.00 39.31 3.41
1255 2463 2.552743 GCTTGGCCGTAGAAAAGAAGTT 59.447 45.455 8.77 0.00 0.00 2.66
1585 2795 0.670854 GCTCTGTTTCCTCGTGGACC 60.671 60.000 5.53 0.58 43.06 4.46
1624 2920 5.473039 AGCATTAGATTGGTTTTTGAGCAC 58.527 37.500 0.00 0.00 35.04 4.40
1716 3089 6.613755 TTTTATTAGATAAGTGCCGGCTTC 57.386 37.500 29.70 20.25 0.00 3.86
1944 3321 3.331150 TGTAATATTATCCGGCTTGCCG 58.669 45.455 25.17 25.17 0.00 5.69
2439 4034 7.897575 TTGTTTTTGTGTGCAGTAAAGAAAT 57.102 28.000 0.00 0.00 0.00 2.17
3319 4914 4.858850 TGGATGATTGAGTACTTTGGCAT 58.141 39.130 0.00 0.00 0.00 4.40
3484 5079 8.786826 ACAGAAGACAAAACATATAATCGGAA 57.213 30.769 0.00 0.00 0.00 4.30
3791 5386 1.333308 TGCGATTATTCATGCGTTGGG 59.667 47.619 0.00 0.00 0.00 4.12
3792 5387 1.333619 GCGATTATTCATGCGTTGGGT 59.666 47.619 0.00 0.00 0.00 4.51
3840 5436 8.625786 TTATAGTGTCAATATTGATGCTGCAT 57.374 30.769 20.65 16.20 39.73 3.96
3970 5566 3.825014 AGACCGCTTACAAAGACACTCTA 59.175 43.478 0.00 0.00 0.00 2.43
4011 5607 1.034356 CGTGGGTACGGATACATGGA 58.966 55.000 0.00 0.00 46.23 3.41
4031 5627 5.502079 TGGACAAAACTTCAACTGGTTCTA 58.498 37.500 0.00 0.00 0.00 2.10
4224 5823 4.308265 GAGAGGTTAAAAGAAGAGCGTGT 58.692 43.478 0.00 0.00 0.00 4.49
4628 6234 8.523915 TCTTCATGTTCACCTGCATTTTATAT 57.476 30.769 0.00 0.00 0.00 0.86
4925 6531 5.538877 TCTCTTCCTGTTGATATAGGGGTT 58.461 41.667 0.00 0.00 33.67 4.11
5030 6637 7.136822 TGCTGTTATTGAGGATACCAAGTAT 57.863 36.000 0.00 0.00 31.68 2.12
5194 6825 3.885297 CTCTGTGTTTTGGGTGATTCAGT 59.115 43.478 0.00 0.00 0.00 3.41
5867 7513 3.930848 AGTATCGCCACGGAAAGTTTAAG 59.069 43.478 0.00 0.00 0.00 1.85
5939 7585 8.792633 CCTATTTGTCACCATCAAAAGAAGTAA 58.207 33.333 0.00 0.00 38.11 2.24
6101 7747 1.879737 GCAACATGCCTGATGCCACA 61.880 55.000 12.26 0.00 43.31 4.17
6306 7952 2.978010 GTGAGTGTTGCCACGGGG 60.978 66.667 0.00 0.00 46.56 5.73
6326 7972 1.686052 GAAACATGTGGCAAGTTCCCA 59.314 47.619 0.00 0.00 0.00 4.37
6367 8013 3.324556 ACACTTTATTGCCACAATTGCCT 59.675 39.130 5.05 0.00 0.00 4.75
6449 8096 5.864418 TTCGTGGCAATAGGTACTTATCT 57.136 39.130 0.00 0.00 41.75 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
633 1837 1.793258 TGCAAATTTTCCATGGCACG 58.207 45.000 6.96 0.0 0.00 5.34
951 2156 1.340889 GAGAGCTCAGATCCAATCGCT 59.659 52.381 17.77 0.0 0.00 4.93
1472 2682 2.435663 CCTGGCCACCATGTCACA 59.564 61.111 0.00 0.0 30.82 3.58
1716 3089 1.355720 AGTTGGGGGATTGAACTCAGG 59.644 52.381 0.00 0.0 0.00 3.86
2251 3653 7.599998 GTGAATGAACATGAAAGGCAAAGTATT 59.400 33.333 0.00 0.0 0.00 1.89
2375 3970 4.530710 ACAAAGCATTGATGTTCTGCAT 57.469 36.364 8.96 0.0 38.94 3.96
2439 4034 4.955811 TCCTTGTTAAGAGAACAGAGCA 57.044 40.909 0.00 0.0 0.00 4.26
2755 4350 8.592809 ACAGCCCAAATCATACAAGAAAAATTA 58.407 29.630 0.00 0.0 0.00 1.40
2979 4574 2.209064 AATGTCCGACCACGTCCTCG 62.209 60.000 4.70 4.7 43.34 4.63
3484 5079 7.492352 AACTAACTTGCGAGTAAGATTTTGT 57.508 32.000 7.13 0.0 34.21 2.83
3970 5566 0.731417 GCTGCGATGACTTGCATTCT 59.269 50.000 0.00 0.0 41.02 2.40
4011 5607 8.364894 ACTTTTTAGAACCAGTTGAAGTTTTGT 58.635 29.630 0.00 0.0 0.00 2.83
4224 5823 5.128499 TCTTGCAACAATCTTTCCCTTTCAA 59.872 36.000 0.00 0.0 0.00 2.69
4628 6234 7.442364 GCTAGCTAATTATGAAGACCAATGACA 59.558 37.037 7.70 0.0 0.00 3.58
5030 6637 8.918202 AATAAGAAAACCATAATATGAGCGGA 57.082 30.769 1.10 0.0 0.00 5.54
5194 6825 6.716934 TGCTTTTAACTTAATGGTGTTGGA 57.283 33.333 0.00 0.0 0.00 3.53
5867 7513 4.003519 AGCGAGAAATTATTGCGACAAC 57.996 40.909 0.00 0.0 31.98 3.32
5901 7547 6.773200 TGGTGACAAATAGGTATCACAACAAA 59.227 34.615 5.66 0.0 42.66 2.83
5939 7585 3.059188 CGTCGTAACAGGAAATTGCAACT 60.059 43.478 0.00 0.0 0.00 3.16
6306 7952 1.686052 TGGGAACTTGCCACATGTTTC 59.314 47.619 0.00 0.0 30.85 2.78


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

AutoCloner maintained by Alex Coulton.