Multiple sequence alignment - TraesCS3A01G255900

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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 TraesCS3A01G255900 chr3A 100.000 8821 0 0 1 8821 477599838 477591018 0.000000e+00 16290.0
1 TraesCS3A01G255900 chr3A 74.373 558 104 24 3712 4249 733999065 733999603 1.500000e-47 202.0
2 TraesCS3A01G255900 chr3A 94.737 38 2 0 887 924 477598844 477598881 9.560000e-05 60.2
3 TraesCS3A01G255900 chr3A 97.143 35 1 0 958 992 477598915 477598949 9.560000e-05 60.2
4 TraesCS3A01G255900 chr3B 99.445 8826 44 5 1 8821 463122683 463113858 0.000000e+00 16022.0
5 TraesCS3A01G255900 chr3B 94.737 38 2 0 887 924 463121689 463121726 9.560000e-05 60.2
6 TraesCS3A01G255900 chr3B 97.143 35 1 0 958 992 463121760 463121794 9.560000e-05 60.2
7 TraesCS3A01G255900 chr3D 97.725 967 9 2 1 955 355417225 355418190 0.000000e+00 1652.0
8 TraesCS3A01G255900 chr3D 98.253 916 16 0 1006 1921 355419733 355420648 0.000000e+00 1604.0
9 TraesCS3A01G255900 chr3D 81.741 471 86 0 16 486 604354546 604355016 2.310000e-105 394.0
10 TraesCS3A01G255900 chr3D 94.737 38 2 0 958 995 355418159 355418122 9.560000e-05 60.2
11 TraesCS3A01G255900 chr1B 84.958 472 67 4 17 486 15174110 15173641 8.010000e-130 475.0
12 TraesCS3A01G255900 chr1B 83.801 463 52 16 5021 5466 15168553 15168097 1.370000e-112 418.0
13 TraesCS3A01G255900 chr1B 81.481 405 60 10 3694 4086 15169729 15169328 1.430000e-82 318.0
14 TraesCS3A01G255900 chr1B 93.103 87 6 0 4168 4254 15169221 15169135 2.580000e-25 128.0
15 TraesCS3A01G255900 chr1D 84.664 476 68 5 17 490 10265801 10265329 3.730000e-128 470.0
16 TraesCS3A01G255900 chr1D 83.117 462 57 13 5021 5466 10259967 10259511 1.380000e-107 401.0
17 TraesCS3A01G255900 chr1D 79.487 585 89 24 3694 4249 10261126 10260544 3.860000e-103 387.0
18 TraesCS3A01G255900 chr1A 84.091 484 71 6 7 486 11942874 11942393 6.240000e-126 462.0
19 TraesCS3A01G255900 chr1A 83.077 455 59 16 5021 5466 11936563 11936118 1.780000e-106 398.0
20 TraesCS3A01G255900 chr1A 79.549 577 94 15 3694 4249 11938181 11937608 2.990000e-104 390.0
21 TraesCS3A01G255900 chr1A 92.929 99 7 0 2821 2919 11938476 11938378 2.570000e-30 145.0
22 TraesCS3A01G255900 chrUn 81.741 471 86 0 16 486 42199642 42199172 2.310000e-105 394.0
23 TraesCS3A01G255900 chrUn 74.373 558 100 30 3712 4249 42195469 42194935 1.940000e-46 198.0
24 TraesCS3A01G255900 chr5D 87.879 99 12 0 2821 2919 369026928 369027026 5.600000e-22 117.0


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 TraesCS3A01G255900 chr3A 477591018 477599838 8820 True 16290.00 16290 100.00000 1 8821 1 chr3A.!!$R1 8820
1 TraesCS3A01G255900 chr3A 733999065 733999603 538 False 202.00 202 74.37300 3712 4249 1 chr3A.!!$F1 537
2 TraesCS3A01G255900 chr3B 463113858 463122683 8825 True 16022.00 16022 99.44500 1 8821 1 chr3B.!!$R1 8820
3 TraesCS3A01G255900 chr3D 355417225 355420648 3423 False 1628.00 1652 97.98900 1 1921 2 chr3D.!!$F2 1920
4 TraesCS3A01G255900 chr1B 15168097 15174110 6013 True 334.75 475 85.83575 17 5466 4 chr1B.!!$R1 5449
5 TraesCS3A01G255900 chr1D 10259511 10261126 1615 True 394.00 401 81.30200 3694 5466 2 chr1D.!!$R2 1772
6 TraesCS3A01G255900 chr1A 11936118 11942874 6756 True 348.75 462 84.91150 7 5466 4 chr1A.!!$R1 5459
7 TraesCS3A01G255900 chrUn 42194935 42199642 4707 True 296.00 394 78.05700 16 4249 2 chrUn.!!$R1 4233

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
122 123 4.593206 ACAACAACTGGAAGGAGACTATCA 59.407 41.667 0.00 0.00 42.68 2.15 F
1094 3637 4.777896 TGACCTGGAATACTTGCTAGAACT 59.222 41.667 0.00 0.00 0.00 3.01 F
1824 4404 6.581712 TGCAATGCTCAACATACTAGTATGA 58.418 36.000 37.75 22.19 44.22 2.15 F
2398 5292 2.941720 GCAAATTCTTTTGTGGCACCAA 59.058 40.909 16.26 7.74 43.43 3.67 F
3190 6177 2.746359 GGTGTGCCTCACAGAGCT 59.254 61.111 10.47 0.00 45.43 4.09 F
4568 7671 2.335316 TGCTTTCCGTACCTTGTTGT 57.665 45.000 0.00 0.00 0.00 3.32 F
4715 7818 5.527582 CCCAGACAGTGTGGCTTATTTATAC 59.472 44.000 11.47 0.00 29.42 1.47 F
5836 9480 2.969821 TATGGTTGAACTTGCCACCT 57.030 45.000 0.00 0.00 34.84 4.00 F
6742 10386 2.025037 TGCTTAGAGATTTGTGGCCCAT 60.025 45.455 0.00 0.00 0.00 4.00 F
7210 10854 0.895559 GGGACAACAGAAGCTTGGGG 60.896 60.000 2.10 0.00 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 4404 2.108952 AGAAAGGCACCAAGGAGAACAT 59.891 45.455 0.00 0.0 0.0 2.71 R
2398 5292 8.265764 GGAGTTAACCAATGATTACCTAAGAGT 58.734 37.037 0.88 0.0 0.0 3.24 R
3190 6177 7.064016 GCCCATAATTAAAATTTCAAACAGCGA 59.936 33.333 0.00 0.0 0.0 4.93 R
4215 7250 2.711009 TCTCTCTTGAACCACCACCAAT 59.289 45.455 0.00 0.0 0.0 3.16 R
5175 8809 3.006967 GTCAAAGCTCTGTCTCCCTTGTA 59.993 47.826 0.00 0.0 0.0 2.41 R
5836 9480 1.689813 TCACGTGCCAAACTCTTAGGA 59.310 47.619 11.67 0.0 0.0 2.94 R
6603 10247 4.081697 TGAAGATCGCATACCAGTCAGAAA 60.082 41.667 0.00 0.0 0.0 2.52 R
7193 10837 0.954452 CACCCCAAGCTTCTGTTGTC 59.046 55.000 0.00 0.0 0.0 3.18 R
7796 11442 1.217585 CGCTCAGGTATGGCATCACG 61.218 60.000 1.65 0.0 0.0 4.35 R
8084 11730 2.369860 ACATGTCTCTTCTGCTGTCCAA 59.630 45.455 0.00 0.0 0.0 3.53 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
122 123 4.593206 ACAACAACTGGAAGGAGACTATCA 59.407 41.667 0.00 0.00 42.68 2.15
800 904 7.938490 ACATTTTTCCAAGCCAAAGACATTATT 59.062 29.630 0.00 0.00 0.00 1.40
1094 3637 4.777896 TGACCTGGAATACTTGCTAGAACT 59.222 41.667 0.00 0.00 0.00 3.01
1824 4404 6.581712 TGCAATGCTCAACATACTAGTATGA 58.418 36.000 37.75 22.19 44.22 2.15
2398 5292 2.941720 GCAAATTCTTTTGTGGCACCAA 59.058 40.909 16.26 7.74 43.43 3.67
2938 5923 6.491403 AGGTATCTTCTCAAGCAAAAACACAT 59.509 34.615 0.00 0.00 0.00 3.21
3190 6177 2.746359 GGTGTGCCTCACAGAGCT 59.254 61.111 10.47 0.00 45.43 4.09
3358 6352 4.338118 AGTTGTGCCTTCTCGAAAATTCAA 59.662 37.500 0.00 0.00 0.00 2.69
4215 7250 6.457355 ACACATGCTGAATCAATTGCTTTTA 58.543 32.000 0.00 0.00 0.00 1.52
4370 7472 8.437360 TGTGAAGTGCAATGATAGGTAAATAG 57.563 34.615 0.00 0.00 0.00 1.73
4568 7671 2.335316 TGCTTTCCGTACCTTGTTGT 57.665 45.000 0.00 0.00 0.00 3.32
4715 7818 5.527582 CCCAGACAGTGTGGCTTATTTATAC 59.472 44.000 11.47 0.00 29.42 1.47
5836 9480 2.969821 TATGGTTGAACTTGCCACCT 57.030 45.000 0.00 0.00 34.84 4.00
6602 10246 6.177610 CAATGTAGTACAAGGGAAAAGCCTA 58.822 40.000 7.16 0.00 36.66 3.93
6603 10247 6.576778 ATGTAGTACAAGGGAAAAGCCTAT 57.423 37.500 7.16 0.00 36.66 2.57
6640 10284 7.251704 TGCGATCTTCATTATTTTCTTCTCC 57.748 36.000 0.00 0.00 0.00 3.71
6742 10386 2.025037 TGCTTAGAGATTTGTGGCCCAT 60.025 45.455 0.00 0.00 0.00 4.00
7193 10837 2.472029 AGATGTTCTGTCACTAGGGGG 58.528 52.381 0.00 0.00 0.00 5.40
7210 10854 0.895559 GGGACAACAGAAGCTTGGGG 60.896 60.000 2.10 0.00 0.00 4.96
7247 10891 3.135530 TGGCAAGCCACCTTTATTTGTTT 59.864 39.130 10.24 0.00 41.89 2.83
7281 10925 6.917477 TGTATGTTGTTGAGTTCATTGAAAGC 59.083 34.615 0.00 0.00 0.00 3.51
7393 11037 5.050363 TCACGATTTTCTTTTGACTTCTCCG 60.050 40.000 0.00 0.00 0.00 4.63
7395 11039 5.701290 ACGATTTTCTTTTGACTTCTCCGAT 59.299 36.000 0.00 0.00 0.00 4.18
7396 11040 6.204882 ACGATTTTCTTTTGACTTCTCCGATT 59.795 34.615 0.00 0.00 0.00 3.34
7397 11041 7.078228 CGATTTTCTTTTGACTTCTCCGATTT 58.922 34.615 0.00 0.00 0.00 2.17
7398 11042 7.591426 CGATTTTCTTTTGACTTCTCCGATTTT 59.409 33.333 0.00 0.00 0.00 1.82
7399 11043 9.249457 GATTTTCTTTTGACTTCTCCGATTTTT 57.751 29.630 0.00 0.00 0.00 1.94
7796 11442 0.529773 TATGTTCGATCCGCCAGTGC 60.530 55.000 0.00 0.00 0.00 4.40
8010 11656 3.922171 AGCTTACATCAAGGAGAAGGG 57.078 47.619 0.00 0.00 34.56 3.95
8084 11730 2.480845 GTGTTTCCGAGTTGCAGTAGT 58.519 47.619 0.00 0.00 0.00 2.73
8203 11849 9.185192 GCTATCACAGGCAAATCAATAAATAAC 57.815 33.333 0.00 0.00 0.00 1.89
8576 12222 5.746721 GCTCAAATTTTGGTACGACAAGTTT 59.253 36.000 9.18 0.00 0.00 2.66
8674 12320 2.629617 CCCAACAGCTCCAGTTCAAAAT 59.370 45.455 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 8.656849 GTGTTCTTAATCGTGAATGTAGTTGAT 58.343 33.333 0.00 0.00 0.00 2.57
800 904 4.260990 CGTCCAAGCACTACACAAAATGAA 60.261 41.667 0.00 0.00 0.00 2.57
1094 3637 9.716556 AGTTAACTTCCTTATCAAGAGGATAGA 57.283 33.333 1.12 0.00 42.63 1.98
1824 4404 2.108952 AGAAAGGCACCAAGGAGAACAT 59.891 45.455 0.00 0.00 0.00 2.71
2398 5292 8.265764 GGAGTTAACCAATGATTACCTAAGAGT 58.734 37.037 0.88 0.00 0.00 3.24
3190 6177 7.064016 GCCCATAATTAAAATTTCAAACAGCGA 59.936 33.333 0.00 0.00 0.00 4.93
4215 7250 2.711009 TCTCTCTTGAACCACCACCAAT 59.289 45.455 0.00 0.00 0.00 3.16
4370 7472 4.498682 GCCAGCTATCATTCAACAATCCAC 60.499 45.833 0.00 0.00 0.00 4.02
5175 8809 3.006967 GTCAAAGCTCTGTCTCCCTTGTA 59.993 47.826 0.00 0.00 0.00 2.41
5836 9480 1.689813 TCACGTGCCAAACTCTTAGGA 59.310 47.619 11.67 0.00 0.00 2.94
6535 10179 4.558226 AGCTTCTGTGATGGTGTTATGA 57.442 40.909 0.00 0.00 0.00 2.15
6602 10246 4.679373 AGATCGCATACCAGTCAGAAAT 57.321 40.909 0.00 0.00 0.00 2.17
6603 10247 4.081697 TGAAGATCGCATACCAGTCAGAAA 60.082 41.667 0.00 0.00 0.00 2.52
6640 10284 8.964476 AATCCTGTTAATATAAGGTCACTGTG 57.036 34.615 0.17 0.17 32.59 3.66
6742 10386 4.404073 GCTTGATAACTCTCCCAGAGAAGA 59.596 45.833 7.55 0.00 45.07 2.87
7193 10837 0.954452 CACCCCAAGCTTCTGTTGTC 59.046 55.000 0.00 0.00 0.00 3.18
7247 10891 9.645059 TGAACTCAACAACATACAAAATGAAAA 57.355 25.926 0.00 0.00 0.00 2.29
7281 10925 5.580297 GCCTAGAACAAAGATGAGAGAGTTG 59.420 44.000 0.00 0.00 0.00 3.16
7428 11073 7.095229 GCAATCAAGGAAAATTTTAGGAACCAC 60.095 37.037 2.75 0.00 0.00 4.16
7536 11181 4.508124 CACAGGGATTATCGAAGCACTTAC 59.492 45.833 0.00 0.00 30.31 2.34
7796 11442 1.217585 CGCTCAGGTATGGCATCACG 61.218 60.000 1.65 0.00 0.00 4.35
8010 11656 2.093890 TGGATCACAATCATGCACCAC 58.906 47.619 0.00 0.00 33.21 4.16
8084 11730 2.369860 ACATGTCTCTTCTGCTGTCCAA 59.630 45.455 0.00 0.00 0.00 3.53
8576 12222 4.022416 GCACATCTGTTTTATGGGTGTCAA 60.022 41.667 0.00 0.00 30.08 3.18


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

AutoCloner maintained by Alex Coulton.