Multiple sequence alignment - TraesCS3A01G172400

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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 TraesCS3A01G172400 chr3A 100.000 3219 0 0 1 3219 187252817 187249599 0 5945
1 TraesCS3A01G172400 chr3D 96.530 2738 41 8 1 2697 160703640 160700916 0 4481
2 TraesCS3A01G172400 chr3D 93.690 523 27 3 2695 3216 160700801 160700284 0 778
3 TraesCS3A01G172400 chr3B 89.609 2791 166 56 1 2697 237337342 237334582 0 3434
4 TraesCS3A01G172400 chr3B 91.028 535 32 8 2695 3219 237334453 237333925 0 708


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 TraesCS3A01G172400 chr3A 187249599 187252817 3218 True 5945.0 5945 100.0000 1 3219 1 chr3A.!!$R1 3218
1 TraesCS3A01G172400 chr3D 160700284 160703640 3356 True 2629.5 4481 95.1100 1 3216 2 chr3D.!!$R1 3215
2 TraesCS3A01G172400 chr3B 237333925 237337342 3417 True 2071.0 3434 90.3185 1 3219 2 chr3B.!!$R1 3218

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
603 677 1.072806 TCTGATGTGCATATGGCCCTC 59.927 52.381 0.0 0.0 43.89 4.30 F
615 689 2.031465 GCCCTCGTCGGAAACCAA 59.969 61.111 0.0 0.0 33.16 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1509 1640 1.593196 CGGTTCAGGAACAAAGCTCA 58.407 50.0 13.62 0.0 42.85 4.26 R
2479 2618 2.887152 GGGTCCAAATCCATGTGATAGC 59.113 50.0 0.00 0.0 31.83 2.97 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
348 386 1.530293 CGCAGCTTGCTTGGATAGATC 59.470 52.381 6.58 0.00 42.25 2.75
349 387 1.878734 GCAGCTTGCTTGGATAGATCC 59.121 52.381 1.24 1.24 43.01 3.36
350 388 3.694566 GCAGCTTGCTTGGATAGATCCG 61.695 54.545 4.12 0.00 44.43 4.18
351 389 5.912184 GCAGCTTGCTTGGATAGATCCGA 62.912 52.174 4.12 1.29 44.43 4.55
519 563 9.056005 GCATGACCTTGTTAATACATCTATCAA 57.944 33.333 0.00 0.00 33.44 2.57
551 625 9.952188 CGATATGATTGAGTTACTTCTACAGAA 57.048 33.333 0.00 0.00 0.00 3.02
603 677 1.072806 TCTGATGTGCATATGGCCCTC 59.927 52.381 0.00 0.00 43.89 4.30
615 689 2.031465 GCCCTCGTCGGAAACCAA 59.969 61.111 0.00 0.00 33.16 3.67
806 936 6.252995 TCCCTAAAAGTTTTATGTGGCTGAT 58.747 36.000 8.48 0.00 0.00 2.90
1049 1179 4.219507 TGTCAATGGAGAGACTCTGAAGAC 59.780 45.833 10.44 10.63 35.81 3.01
1654 1786 5.011329 CCAGGTGACTACTTGTGTTTACCTA 59.989 44.000 0.00 0.00 40.21 3.08
1717 1850 3.889520 ACCAAAACCGTAAAGCCAAAA 57.110 38.095 0.00 0.00 0.00 2.44
2240 2379 5.498393 AGAATTCAGCATCACACAGAAGAT 58.502 37.500 8.44 0.00 0.00 2.40
2369 2508 2.223112 GCGCACTTATCAGGACATGTTG 60.223 50.000 0.30 0.00 0.00 3.33
2479 2618 7.224557 AGCAAAGTAAACCAAAGCTTTATGTTG 59.775 33.333 20.67 12.43 30.98 3.33
2547 2686 1.138859 GATGGTGTGTGATGATCCCGA 59.861 52.381 0.00 0.00 0.00 5.14
2577 2716 7.068348 CACCTTGATGATTTCTGATGAATCCTT 59.932 37.037 0.88 0.00 31.56 3.36
2578 2717 7.284944 ACCTTGATGATTTCTGATGAATCCTTC 59.715 37.037 0.88 0.02 31.56 3.46
2579 2718 7.284716 CCTTGATGATTTCTGATGAATCCTTCA 59.715 37.037 0.88 0.00 45.01 3.02
2603 2742 9.290988 TCATAGAATCATAGTCCAGACTACTTC 57.709 37.037 9.63 12.09 45.61 3.01
2728 2999 1.160137 GTGGTGAATTCAAGCGAGCT 58.840 50.000 10.35 0.00 0.00 4.09
2769 3040 7.340232 TGGATTATCAGTTGAAATTTCCTCCAG 59.660 37.037 15.48 2.61 0.00 3.86
2823 3099 9.958180 TGATCTAATCAAGTGGTGATCTAAAAA 57.042 29.630 0.00 0.00 46.80 1.94
2877 3157 2.083774 CTTTCCCTGCAATTCGTAGCA 58.916 47.619 0.00 0.00 39.25 3.49
2968 3248 4.222114 CCAAGAAAATGAACTTGCGACTC 58.778 43.478 0.00 0.00 41.15 3.36
2982 3262 5.122082 ACTTGCGACTCACTAACTAGACTAC 59.878 44.000 0.00 0.00 0.00 2.73
3005 3285 6.684686 ACATGTGAATCATTCCTTTGAACTG 58.315 36.000 0.00 0.00 34.09 3.16
3103 3385 0.691078 TGATGCCACTCTCCTACCCC 60.691 60.000 0.00 0.00 0.00 4.95
3111 3393 4.781934 CCACTCTCCTACCCCAATAAAAG 58.218 47.826 0.00 0.00 0.00 2.27
3115 3397 4.180723 TCTCCTACCCCAATAAAAGGTGT 58.819 43.478 0.00 0.00 35.02 4.16
3120 3402 5.045432 CCTACCCCAATAAAAGGTGTACTGA 60.045 44.000 0.00 0.00 35.02 3.41
3131 3413 4.657814 AGGTGTACTGAAACCATGGATT 57.342 40.909 21.47 14.05 39.05 3.01
3191 3473 6.874288 AAATCAAAGAGACAGAACAGAAGG 57.126 37.500 0.00 0.00 0.00 3.46
3199 3481 4.855340 AGACAGAACAGAAGGAAAAACCA 58.145 39.130 0.00 0.00 42.04 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 131 0.193574 ACTGGGAGGTTTGGGAGAGA 59.806 55.000 0.00 0.00 0.00 3.10
350 388 0.389948 AAACTGGATGCGACTCGGTC 60.390 55.000 0.00 0.00 0.00 4.79
351 389 0.892755 TAAACTGGATGCGACTCGGT 59.107 50.000 0.00 0.00 0.00 4.69
551 625 0.248661 CGTGGATCGATCTCGCACTT 60.249 55.000 23.96 0.00 42.86 3.16
554 628 0.816421 TACCGTGGATCGATCTCGCA 60.816 55.000 23.96 11.62 42.86 5.10
603 677 2.250188 GCATTTCATTGGTTTCCGACG 58.750 47.619 0.00 0.00 0.00 5.12
615 689 3.634504 TGTTCATAGCCCTGCATTTCAT 58.365 40.909 0.00 0.00 0.00 2.57
806 936 6.791867 AAGATGTAACCATGCTACAGAGTA 57.208 37.500 10.52 0.00 32.96 2.59
1049 1179 1.663702 ACTCGTCGCCCAAGAAACG 60.664 57.895 0.00 0.00 36.50 3.60
1509 1640 1.593196 CGGTTCAGGAACAAAGCTCA 58.407 50.000 13.62 0.00 42.85 4.26
1592 1724 8.420189 GCTCTCAAACAAAATTAGATTTGAACG 58.580 33.333 6.76 6.97 41.73 3.95
1654 1786 8.577296 GGGAAACAGCTTCTAAACTTAGAATTT 58.423 33.333 11.38 9.31 45.67 1.82
1663 1795 8.112016 AGAATAAAGGGAAACAGCTTCTAAAC 57.888 34.615 0.00 0.00 34.17 2.01
1717 1850 4.721776 TCCTGCCCAATAGATTAAGTCAGT 59.278 41.667 0.00 0.00 0.00 3.41
2057 2196 6.830838 AGATGTTGACTCAAGAAAAAGAAGGT 59.169 34.615 0.00 0.00 0.00 3.50
2187 2326 5.603596 ACAGGTAATTGTACTTGTCGTTCA 58.396 37.500 0.00 0.00 44.76 3.18
2191 2330 5.120208 CAGGAACAGGTAATTGTACTTGTCG 59.880 44.000 2.60 0.00 46.60 4.35
2240 2379 4.309099 GAGCATGCTTGATTTTCCAAACA 58.691 39.130 23.61 0.00 0.00 2.83
2369 2508 9.451002 TCATACAGCTACTACATAGATTAGGTC 57.549 37.037 0.00 0.00 31.83 3.85
2479 2618 2.887152 GGGTCCAAATCCATGTGATAGC 59.113 50.000 0.00 0.00 31.83 2.97
2547 2686 5.655090 TCATCAGAAATCATCAAGGTGCATT 59.345 36.000 0.00 0.00 0.00 3.56
2577 2716 9.290988 GAAGTAGTCTGGACTATGATTCTATGA 57.709 37.037 12.72 0.00 44.73 2.15
2578 2717 8.519526 GGAAGTAGTCTGGACTATGATTCTATG 58.480 40.741 12.72 0.00 44.73 2.23
2579 2718 8.228206 TGGAAGTAGTCTGGACTATGATTCTAT 58.772 37.037 12.72 0.00 44.73 1.98
2580 2719 7.583625 TGGAAGTAGTCTGGACTATGATTCTA 58.416 38.462 12.72 11.91 44.73 2.10
2581 2720 6.436027 TGGAAGTAGTCTGGACTATGATTCT 58.564 40.000 12.72 3.60 44.73 2.40
2582 2721 6.716934 TGGAAGTAGTCTGGACTATGATTC 57.283 41.667 12.72 14.92 44.73 2.52
2583 2722 6.407525 GCTTGGAAGTAGTCTGGACTATGATT 60.408 42.308 12.72 8.84 44.73 2.57
2584 2723 5.069781 GCTTGGAAGTAGTCTGGACTATGAT 59.930 44.000 12.72 3.91 44.73 2.45
2620 2759 8.620416 TGTTTGATCAACGGATATATTTTCCAG 58.380 33.333 7.89 1.90 38.36 3.86
2769 3040 2.143925 GGTCTTGTGCTACACTGAACC 58.856 52.381 0.00 0.72 35.11 3.62
2823 3099 6.721318 TCCCTCTGCAAACAAATATAAGACT 58.279 36.000 0.00 0.00 0.00 3.24
2839 3115 4.384940 GAAAGGATTGATACTCCCTCTGC 58.615 47.826 0.00 0.00 32.89 4.26
2877 3157 5.469084 GGAACGGTGAAAAGTACTCAAGAAT 59.531 40.000 0.00 0.00 0.00 2.40
2968 3248 9.809096 AATGATTCACATGTAGTCTAGTTAGTG 57.191 33.333 0.00 0.00 39.39 2.74
2982 3262 6.916440 TCAGTTCAAAGGAATGATTCACATG 58.084 36.000 7.56 2.69 39.39 3.21
3005 3285 6.328714 GGGCTTCTTGATCAATTTTTCTCTC 58.671 40.000 8.96 0.00 0.00 3.20
3103 3385 7.040062 TCCATGGTTTCAGTACACCTTTTATTG 60.040 37.037 12.58 0.00 33.76 1.90
3111 3393 4.331968 TGAATCCATGGTTTCAGTACACC 58.668 43.478 27.25 6.84 32.24 4.16
3115 3397 5.825532 TCCATTGAATCCATGGTTTCAGTA 58.174 37.500 28.50 19.93 35.89 2.74
3120 3402 5.900699 TCATGATCCATTGAATCCATGGTTT 59.099 36.000 12.58 10.04 36.83 3.27
3131 3413 5.067954 CCTAGTGCAATCATGATCCATTGA 58.932 41.667 9.06 3.65 32.56 2.57
3191 3473 4.112634 GTTCCACAAAGAGCTGGTTTTTC 58.887 43.478 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.