Multiple sequence alignment - TraesCS3A01G215000

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 TraesCS3A01G215000 chr3A 100.000 3552 0 0 1 3552 391493206 391489655 0.000000e+00 6560.0
1 TraesCS3A01G215000 chr3D 96.447 3349 97 11 160 3503 297463233 297466564 0.000000e+00 5505.0
2 TraesCS3A01G215000 chr3D 94.783 115 4 1 14 128 297463125 297463237 1.010000e-40 178.0
3 TraesCS3A01G215000 chr3B 96.990 3090 77 10 466 3552 391870907 391873983 0.000000e+00 5177.0
4 TraesCS3A01G215000 chr3B 92.469 478 24 4 1 469 391870118 391870592 0.000000e+00 673.0
5 TraesCS3A01G215000 chr1D 88.954 1023 67 18 2341 3348 44640966 44641957 0.000000e+00 1221.0
6 TraesCS3A01G215000 chr1D 86.864 236 25 2 2544 2778 44640700 44640930 3.520000e-65 259.0
7 TraesCS3A01G215000 chr1B 89.409 897 62 26 2403 3289 63958594 63959467 0.000000e+00 1099.0
8 TraesCS3A01G215000 chr1A 90.212 848 64 12 2504 3348 44406250 44407081 0.000000e+00 1088.0
9 TraesCS3A01G215000 chr1A 88.199 161 12 4 2341 2495 44406027 44406186 6.060000e-43 185.0
10 TraesCS3A01G215000 chr1A 97.436 39 1 0 2504 2542 44406179 44406217 2.290000e-07 67.6


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 TraesCS3A01G215000 chr3A 391489655 391493206 3551 True 6560.000000 6560 100.0000 1 3552 1 chr3A.!!$R1 3551
1 TraesCS3A01G215000 chr3D 297463125 297466564 3439 False 2841.500000 5505 95.6150 14 3503 2 chr3D.!!$F1 3489
2 TraesCS3A01G215000 chr3B 391870118 391873983 3865 False 2925.000000 5177 94.7295 1 3552 2 chr3B.!!$F1 3551
3 TraesCS3A01G215000 chr1D 44640700 44641957 1257 False 740.000000 1221 87.9090 2341 3348 2 chr1D.!!$F1 1007
4 TraesCS3A01G215000 chr1B 63958594 63959467 873 False 1099.000000 1099 89.4090 2403 3289 1 chr1B.!!$F1 886
5 TraesCS3A01G215000 chr1A 44406027 44407081 1054 False 446.866667 1088 91.9490 2341 3348 3 chr1A.!!$F1 1007

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
281 291 0.033796 AACCATCCCATCTGTGCCTG 60.034 55.0 0.00 0.00 0.0 4.85 F
983 1315 0.322008 CAGAGGAGTGACTTTGCCCC 60.322 60.0 0.00 0.00 0.0 5.80 F
1731 2063 1.021390 ACAAGAAGATCGGCAAGGCG 61.021 55.0 9.95 9.95 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1167 1499 0.035152 TGATGATGGTGTGCTGGGAC 60.035 55.000 0.00 0.0 0.00 4.46 R
2014 2346 1.542492 ACTCAGCAATGCAAGGGAAG 58.458 50.000 8.35 0.0 0.00 3.46 R
3455 3875 3.866703 TGTCACACTGGTGGGAATAAA 57.133 42.857 7.28 0.0 45.71 1.40 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
61 62 5.861727 AGACCAAAAGGAAACACGTAGTAT 58.138 37.500 0.00 0.00 41.61 2.12
86 87 1.949525 GGTTGTGAGAGCTGCAGAAAA 59.050 47.619 20.43 0.00 0.00 2.29
104 105 4.640647 AGAAAATTCCTATGGAAACTCGCC 59.359 41.667 2.98 0.00 45.41 5.54
139 140 3.868077 CAGCTACAAGTGGCAGACTATTC 59.132 47.826 11.14 0.00 39.73 1.75
278 288 1.811860 GCAACCATCCCATCTGTGC 59.188 57.895 0.00 0.00 0.00 4.57
281 291 0.033796 AACCATCCCATCTGTGCCTG 60.034 55.000 0.00 0.00 0.00 4.85
349 359 6.699063 CAACTTCAACAAATTTGAACAGAGC 58.301 36.000 24.64 0.00 34.96 4.09
355 365 0.883833 AATTTGAACAGAGCGCCCAG 59.116 50.000 2.29 0.00 0.00 4.45
371 381 5.126384 AGCGCCCAGTAATAAAAAGCAAATA 59.874 36.000 2.29 0.00 0.00 1.40
400 411 4.217550 AGGAAATTCACCCGTTTGTGTATG 59.782 41.667 0.00 0.00 37.51 2.39
456 468 1.156736 GCATGTGCTTTCACTACCGT 58.843 50.000 0.00 0.00 43.49 4.83
462 474 1.376812 CTTTCACTACCGTGGGCCC 60.377 63.158 17.59 17.59 41.53 5.80
513 843 6.441093 AGCACATACTACATCATTGGTTTG 57.559 37.500 0.00 0.00 0.00 2.93
528 858 1.263217 GGTTTGTCGACAACGCATTCT 59.737 47.619 29.74 0.00 39.58 2.40
602 932 2.996621 GAGACAACCATCTCCTCAAACG 59.003 50.000 0.00 0.00 39.46 3.60
783 1115 1.066858 CGCACCACTCAGACCAATACT 60.067 52.381 0.00 0.00 0.00 2.12
784 1116 2.165641 CGCACCACTCAGACCAATACTA 59.834 50.000 0.00 0.00 0.00 1.82
785 1117 3.522553 GCACCACTCAGACCAATACTAC 58.477 50.000 0.00 0.00 0.00 2.73
810 1142 8.531982 ACAGTATTATTTAGCTTGACTGACTCA 58.468 33.333 6.16 0.00 37.01 3.41
818 1150 1.273606 CTTGACTGACTCACCCGTCAT 59.726 52.381 1.57 0.00 42.51 3.06
830 1162 0.676782 CCCGTCATCCAACCACTTCC 60.677 60.000 0.00 0.00 0.00 3.46
983 1315 0.322008 CAGAGGAGTGACTTTGCCCC 60.322 60.000 0.00 0.00 0.00 5.80
1167 1499 2.691522 CTTCGCTCGCACATGTCG 59.308 61.111 0.00 3.20 0.00 4.35
1731 2063 1.021390 ACAAGAAGATCGGCAAGGCG 61.021 55.000 9.95 9.95 0.00 5.52
2000 2332 6.183360 CCTTCAGAGGACAAGGTTAGATAGAC 60.183 46.154 0.00 0.00 46.74 2.59
2014 2346 8.643324 AGGTTAGATAGACACTTGGAATGATAC 58.357 37.037 0.00 0.00 0.00 2.24
2030 2362 3.018856 TGATACTTCCCTTGCATTGCTG 58.981 45.455 10.49 2.91 0.00 4.41
2038 2370 2.618816 CCCTTGCATTGCTGAGTTCCTA 60.619 50.000 10.49 0.00 0.00 2.94
2445 2781 1.462731 AAAGATGGCGCTGGCAAACA 61.463 50.000 7.64 0.00 42.43 2.83
2467 2803 2.554344 GGAAAATGTGGACCAGGTAGCA 60.554 50.000 0.00 0.00 0.00 3.49
2573 2979 5.856455 TGATGTGTATACAGTGCGAATATCG 59.144 40.000 5.62 0.00 40.79 2.92
2597 3003 2.403252 ATTAGTGCCAGGAACTTCGG 57.597 50.000 4.99 0.00 34.60 4.30
2677 3083 8.732746 AATCTGGTATTGTGAACAGTTATACC 57.267 34.615 13.18 13.18 37.57 2.73
2765 3174 8.531982 ACTGTTCAATATAAGCAGTCTACAAGA 58.468 33.333 2.78 0.00 35.78 3.02
2803 3212 7.873719 TTTTGTCAAGACTCAAACCTAATGA 57.126 32.000 1.53 0.00 34.05 2.57
2941 3351 6.751514 TTGTCAACAAACTTGTGATACACT 57.248 33.333 0.00 0.00 41.31 3.55
3196 3614 2.181426 TCAAACGTTTTGTCCTTGCG 57.819 45.000 11.66 0.00 0.00 4.85
3289 3707 6.088217 CCTGCGATATCACATAAGAAACGTAG 59.912 42.308 3.12 0.00 0.00 3.51
3455 3875 7.872993 TCGAGAACAAGAGTTATTTCTGTTCAT 59.127 33.333 13.84 1.93 38.30 2.57
3487 3907 3.426159 CCAGTGTGACAACAAGTGTGTTC 60.426 47.826 0.00 0.00 45.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.114997 CACGTTTCCATGCCCGGC 62.115 66.667 1.04 1.04 0.00 6.13
11 12 2.867472 GTCACGTTTCCATGCCCG 59.133 61.111 0.00 0.00 0.00 6.13
61 62 0.243907 GCAGCTCTCACAACCGTCTA 59.756 55.000 0.00 0.00 0.00 2.59
86 87 1.810412 GCGGCGAGTTTCCATAGGAAT 60.810 52.381 12.98 0.00 41.71 3.01
139 140 1.442520 CGGCCAAGTTTGCGTGATG 60.443 57.895 2.24 0.00 0.00 3.07
256 266 2.519302 GATGGGATGGTTGCGGGG 60.519 66.667 0.00 0.00 0.00 5.73
281 291 2.009774 ACGATTAACATGCTGCCTGAC 58.990 47.619 11.93 0.00 0.00 3.51
349 359 5.454232 CGTATTTGCTTTTTATTACTGGGCG 59.546 40.000 0.00 0.00 0.00 6.13
355 365 9.615295 TTCCTGTTCGTATTTGCTTTTTATTAC 57.385 29.630 0.00 0.00 0.00 1.89
371 381 1.202722 ACGGGTGAATTTCCTGTTCGT 60.203 47.619 8.64 4.04 41.20 3.85
400 411 1.468520 TCAGGCGCTGTAAAAGAATGC 59.531 47.619 7.64 0.00 32.61 3.56
456 468 2.465813 CATATTTGTTTCCAGGGCCCA 58.534 47.619 27.56 0.00 0.00 5.36
462 474 7.713750 AGAATCATGAGCATATTTGTTTCCAG 58.286 34.615 0.09 0.00 0.00 3.86
513 843 4.348656 TGATACTAGAATGCGTTGTCGAC 58.651 43.478 9.11 9.11 39.71 4.20
602 932 2.991540 GCTGGACCCCCACTTTGC 60.992 66.667 0.00 0.00 37.58 3.68
784 1116 8.531982 TGAGTCAGTCAAGCTAAATAATACTGT 58.468 33.333 0.00 0.00 35.51 3.55
785 1117 8.812329 GTGAGTCAGTCAAGCTAAATAATACTG 58.188 37.037 0.00 0.00 36.74 2.74
810 1142 0.036306 GAAGTGGTTGGATGACGGGT 59.964 55.000 0.00 0.00 0.00 5.28
818 1150 0.394488 TTTGCGTGGAAGTGGTTGGA 60.394 50.000 0.00 0.00 0.00 3.53
830 1162 1.514678 TAGCTGGCTTGGTTTGCGTG 61.515 55.000 0.00 0.00 0.00 5.34
1167 1499 0.035152 TGATGATGGTGTGCTGGGAC 60.035 55.000 0.00 0.00 0.00 4.46
1245 1577 3.109547 GTGTTGATCCGCGTCGCA 61.110 61.111 18.75 0.00 0.00 5.10
1731 2063 0.672711 GCAGGTACCCTCGTTTCCAC 60.673 60.000 8.74 0.00 0.00 4.02
2014 2346 1.542492 ACTCAGCAATGCAAGGGAAG 58.458 50.000 8.35 0.00 0.00 3.46
2038 2370 8.743714 GGACATCAGAATGGAAAGAAAACTAAT 58.256 33.333 0.00 0.00 37.19 1.73
2167 2499 4.253685 CAGGATCGAGCCTTTCTTTGTAA 58.746 43.478 22.09 0.00 35.66 2.41
2445 2781 2.290960 GCTACCTGGTCCACATTTTCCT 60.291 50.000 0.63 0.00 0.00 3.36
2467 2803 6.100424 TCTCTTTCTCTTGTTCTTCCTCCTTT 59.900 38.462 0.00 0.00 0.00 3.11
2573 2979 4.092968 CGAAGTTCCTGGCACTAATTGTAC 59.907 45.833 0.00 0.00 0.00 2.90
2597 3003 8.870160 TTATAGCAAAATGATACATTGTTGCC 57.130 30.769 23.22 14.60 41.72 4.52
2677 3083 9.985730 ATAACTGGGTTAATATGCATTCAAATG 57.014 29.630 3.54 0.00 34.28 2.32
2684 3090 9.365906 TCATTTCATAACTGGGTTAATATGCAT 57.634 29.630 3.79 3.79 31.56 3.96
2692 3098 8.333235 ACCAATACTCATTTCATAACTGGGTTA 58.667 33.333 0.00 0.00 32.36 2.85
2803 3212 8.306761 CCAGACATGCTAAGTTTCCTTTAAAAT 58.693 33.333 0.00 0.00 31.89 1.82
3269 3687 8.644318 ACAACCTACGTTTCTTATGTGATATC 57.356 34.615 0.00 0.00 0.00 1.63
3289 3707 9.608617 GTTGACTAGAATAGCTTTAAAACAACC 57.391 33.333 0.00 0.00 44.39 3.77
3455 3875 3.866703 TGTCACACTGGTGGGAATAAA 57.133 42.857 7.28 0.00 45.71 1.40


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

AutoCloner maintained by Alex Coulton.