Multiple sequence alignment - TraesCS2B01G330600

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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 TraesCS2B01G330600 chr2B 100.000 2111 0 0 1 2111 474900078 474902188 0.000000e+00 3899.0
1 TraesCS2B01G330600 chr1A 98.354 2066 19 11 60 2111 554458262 554460326 0.000000e+00 3613.0
2 TraesCS2B01G330600 chr1A 100.000 36 0 0 1 36 197665120 197665155 1.350000e-07 67.6
3 TraesCS2B01G330600 chr1A 100.000 36 0 0 1 36 446249126 446249161 1.350000e-07 67.6
4 TraesCS2B01G330600 chr1A 100.000 36 0 0 1 36 554455721 554455686 1.350000e-07 67.6
5 TraesCS2B01G330600 chr1D 97.573 2060 36 10 60 2110 254416860 254418914 0.000000e+00 3515.0
6 TraesCS2B01G330600 chr1D 96.573 2072 44 14 60 2111 51878278 51876214 0.000000e+00 3408.0
7 TraesCS2B01G330600 chr1D 100.000 36 0 0 1 36 51878555 51878590 1.350000e-07 67.6
8 TraesCS2B01G330600 chr1D 100.000 36 0 0 1 36 254416581 254416546 1.350000e-07 67.6
9 TraesCS2B01G330600 chr5D 96.875 2080 33 16 60 2111 503287095 503289170 0.000000e+00 3452.0
10 TraesCS2B01G330600 chr5D 96.523 2071 38 17 60 2109 6181151 6179094 0.000000e+00 3395.0
11 TraesCS2B01G330600 chr5D 100.000 36 0 0 1 36 120799388 120799353 1.350000e-07 67.6
12 TraesCS2B01G330600 chr5D 100.000 36 0 0 1 36 503286817 503286782 1.350000e-07 67.6
13 TraesCS2B01G330600 chr6D 96.962 2074 30 18 60 2111 45511776 45509714 0.000000e+00 3450.0
14 TraesCS2B01G330600 chr5A 96.744 2058 51 12 60 2111 607200295 607198248 0.000000e+00 3415.0
15 TraesCS2B01G330600 chr7B 95.720 2056 70 15 60 2109 105256800 105254757 0.000000e+00 3293.0
16 TraesCS2B01G330600 chr4B 95.238 1533 53 12 587 2111 308683448 308681928 0.000000e+00 2409.0
17 TraesCS2B01G330600 chr2A 96.493 998 17 7 60 1045 335830832 335829841 0.000000e+00 1633.0
18 TraesCS2B01G330600 chr7D 100.000 36 0 0 1 36 616271932 616271967 1.350000e-07 67.6
19 TraesCS2B01G330600 chr4D 100.000 36 0 0 1 36 504873771 504873806 1.350000e-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 TraesCS2B01G330600 chr2B 474900078 474902188 2110 False 3899 3899 100.000 1 2111 1 chr2B.!!$F1 2110
1 TraesCS2B01G330600 chr1A 554458262 554460326 2064 False 3613 3613 98.354 60 2111 1 chr1A.!!$F3 2051
2 TraesCS2B01G330600 chr1D 254416860 254418914 2054 False 3515 3515 97.573 60 2110 1 chr1D.!!$F2 2050
3 TraesCS2B01G330600 chr1D 51876214 51878278 2064 True 3408 3408 96.573 60 2111 1 chr1D.!!$R1 2051
4 TraesCS2B01G330600 chr5D 503287095 503289170 2075 False 3452 3452 96.875 60 2111 1 chr5D.!!$F1 2051
5 TraesCS2B01G330600 chr5D 6179094 6181151 2057 True 3395 3395 96.523 60 2109 1 chr5D.!!$R1 2049
6 TraesCS2B01G330600 chr6D 45509714 45511776 2062 True 3450 3450 96.962 60 2111 1 chr6D.!!$R1 2051
7 TraesCS2B01G330600 chr5A 607198248 607200295 2047 True 3415 3415 96.744 60 2111 1 chr5A.!!$R1 2051
8 TraesCS2B01G330600 chr7B 105254757 105256800 2043 True 3293 3293 95.720 60 2109 1 chr7B.!!$R1 2049
9 TraesCS2B01G330600 chr4B 308681928 308683448 1520 True 2409 2409 95.238 587 2111 1 chr4B.!!$R1 1524
10 TraesCS2B01G330600 chr2A 335829841 335830832 991 True 1633 1633 96.493 60 1045 1 chr2A.!!$R1 985

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
55 56 5.304686 ACTGAGGTTGATTGGTGTTAAGA 57.695 39.13 0.0 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1278 1308 3.840666 AGAGATGGCTGAGTGGACTAAAA 59.159 43.478 0.0 0.0 0.0 1.52 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
23 24 6.777827 GTATTCGAGTTGAAGAAGTACGAG 57.222 41.667 0.00 0.00 40.65 4.18
24 25 5.624344 ATTCGAGTTGAAGAAGTACGAGA 57.376 39.130 0.00 0.00 40.65 4.04
25 26 5.428496 TTCGAGTTGAAGAAGTACGAGAA 57.572 39.130 0.00 0.00 31.44 2.87
26 27 5.624344 TCGAGTTGAAGAAGTACGAGAAT 57.376 39.130 0.00 0.00 0.00 2.40
27 28 6.010294 TCGAGTTGAAGAAGTACGAGAATT 57.990 37.500 0.00 0.00 0.00 2.17
28 29 6.084925 TCGAGTTGAAGAAGTACGAGAATTC 58.915 40.000 0.00 0.00 0.00 2.17
29 30 6.072618 TCGAGTTGAAGAAGTACGAGAATTCT 60.073 38.462 7.95 7.95 34.81 2.40
30 31 7.118825 TCGAGTTGAAGAAGTACGAGAATTCTA 59.881 37.037 8.25 0.00 33.05 2.10
31 32 7.911205 CGAGTTGAAGAAGTACGAGAATTCTAT 59.089 37.037 8.25 2.32 33.05 1.98
39 40 8.842280 AGAAGTACGAGAATTCTATAACTGAGG 58.158 37.037 8.25 0.00 31.63 3.86
40 41 8.522542 AAGTACGAGAATTCTATAACTGAGGT 57.477 34.615 8.25 0.00 0.00 3.85
41 42 8.522542 AGTACGAGAATTCTATAACTGAGGTT 57.477 34.615 8.25 0.00 39.26 3.50
42 43 8.407064 AGTACGAGAATTCTATAACTGAGGTTG 58.593 37.037 8.25 0.00 36.92 3.77
43 44 7.406031 ACGAGAATTCTATAACTGAGGTTGA 57.594 36.000 8.25 0.00 36.92 3.18
44 45 8.012957 ACGAGAATTCTATAACTGAGGTTGAT 57.987 34.615 8.25 0.00 36.92 2.57
45 46 8.478877 ACGAGAATTCTATAACTGAGGTTGATT 58.521 33.333 8.25 0.00 36.92 2.57
46 47 8.759641 CGAGAATTCTATAACTGAGGTTGATTG 58.240 37.037 8.25 0.00 36.92 2.67
47 48 8.970859 AGAATTCTATAACTGAGGTTGATTGG 57.029 34.615 6.06 0.00 36.92 3.16
48 49 8.552296 AGAATTCTATAACTGAGGTTGATTGGT 58.448 33.333 6.06 0.00 36.92 3.67
49 50 8.511604 AATTCTATAACTGAGGTTGATTGGTG 57.488 34.615 0.00 0.00 36.92 4.17
50 51 6.620877 TCTATAACTGAGGTTGATTGGTGT 57.379 37.500 0.00 0.00 36.92 4.16
51 52 7.016153 TCTATAACTGAGGTTGATTGGTGTT 57.984 36.000 0.00 0.00 36.92 3.32
52 53 8.141298 TCTATAACTGAGGTTGATTGGTGTTA 57.859 34.615 0.00 0.00 36.92 2.41
53 54 8.598916 TCTATAACTGAGGTTGATTGGTGTTAA 58.401 33.333 0.00 0.00 36.92 2.01
54 55 7.687941 ATAACTGAGGTTGATTGGTGTTAAG 57.312 36.000 0.00 0.00 36.92 1.85
55 56 5.304686 ACTGAGGTTGATTGGTGTTAAGA 57.695 39.130 0.00 0.00 0.00 2.10
56 57 5.690865 ACTGAGGTTGATTGGTGTTAAGAA 58.309 37.500 0.00 0.00 0.00 2.52
57 58 6.126409 ACTGAGGTTGATTGGTGTTAAGAAA 58.874 36.000 0.00 0.00 0.00 2.52
58 59 6.605594 ACTGAGGTTGATTGGTGTTAAGAAAA 59.394 34.615 0.00 0.00 0.00 2.29
62 63 6.382859 AGGTTGATTGGTGTTAAGAAAAACCT 59.617 34.615 0.00 0.00 42.77 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.541086 TCTCGTACTTCTTCAACTCGAATAC 58.459 40.000 0.00 0.00 31.69 1.89
1 2 6.732531 TCTCGTACTTCTTCAACTCGAATA 57.267 37.500 0.00 0.00 31.69 1.75
2 3 5.624344 TCTCGTACTTCTTCAACTCGAAT 57.376 39.130 0.00 0.00 31.69 3.34
3 4 5.428496 TTCTCGTACTTCTTCAACTCGAA 57.572 39.130 0.00 0.00 0.00 3.71
4 5 5.624344 ATTCTCGTACTTCTTCAACTCGA 57.376 39.130 0.00 0.00 0.00 4.04
5 6 6.087522 AGAATTCTCGTACTTCTTCAACTCG 58.912 40.000 0.88 0.00 0.00 4.18
13 14 8.842280 CCTCAGTTATAGAATTCTCGTACTTCT 58.158 37.037 12.24 0.48 33.91 2.85
14 15 8.623030 ACCTCAGTTATAGAATTCTCGTACTTC 58.377 37.037 12.24 0.00 0.00 3.01
15 16 8.522542 ACCTCAGTTATAGAATTCTCGTACTT 57.477 34.615 12.24 0.00 0.00 2.24
16 17 8.407064 CAACCTCAGTTATAGAATTCTCGTACT 58.593 37.037 12.24 10.40 33.27 2.73
17 18 8.404000 TCAACCTCAGTTATAGAATTCTCGTAC 58.596 37.037 12.24 8.28 33.27 3.67
18 19 8.515695 TCAACCTCAGTTATAGAATTCTCGTA 57.484 34.615 12.24 3.85 33.27 3.43
19 20 7.406031 TCAACCTCAGTTATAGAATTCTCGT 57.594 36.000 12.24 4.88 33.27 4.18
20 21 8.759641 CAATCAACCTCAGTTATAGAATTCTCG 58.240 37.037 12.24 0.00 33.27 4.04
21 22 9.050601 CCAATCAACCTCAGTTATAGAATTCTC 57.949 37.037 12.24 0.00 33.27 2.87
22 23 8.552296 ACCAATCAACCTCAGTTATAGAATTCT 58.448 33.333 13.56 13.56 33.27 2.40
23 24 8.616076 CACCAATCAACCTCAGTTATAGAATTC 58.384 37.037 0.00 0.00 33.27 2.17
24 25 8.109634 ACACCAATCAACCTCAGTTATAGAATT 58.890 33.333 0.00 0.00 33.27 2.17
25 26 7.633789 ACACCAATCAACCTCAGTTATAGAAT 58.366 34.615 0.00 0.00 33.27 2.40
26 27 7.016153 ACACCAATCAACCTCAGTTATAGAA 57.984 36.000 0.00 0.00 33.27 2.10
27 28 6.620877 ACACCAATCAACCTCAGTTATAGA 57.379 37.500 0.00 0.00 33.27 1.98
28 29 8.786826 TTAACACCAATCAACCTCAGTTATAG 57.213 34.615 0.00 0.00 33.27 1.31
29 30 8.598916 TCTTAACACCAATCAACCTCAGTTATA 58.401 33.333 0.00 0.00 33.27 0.98
30 31 7.458397 TCTTAACACCAATCAACCTCAGTTAT 58.542 34.615 0.00 0.00 33.27 1.89
31 32 6.833041 TCTTAACACCAATCAACCTCAGTTA 58.167 36.000 0.00 0.00 33.27 2.24
32 33 5.690865 TCTTAACACCAATCAACCTCAGTT 58.309 37.500 0.00 0.00 36.33 3.16
33 34 5.304686 TCTTAACACCAATCAACCTCAGT 57.695 39.130 0.00 0.00 0.00 3.41
34 35 6.633500 TTTCTTAACACCAATCAACCTCAG 57.367 37.500 0.00 0.00 0.00 3.35
35 36 7.262048 GTTTTTCTTAACACCAATCAACCTCA 58.738 34.615 0.00 0.00 0.00 3.86
36 37 6.700081 GGTTTTTCTTAACACCAATCAACCTC 59.300 38.462 0.00 0.00 34.79 3.85
37 38 6.382859 AGGTTTTTCTTAACACCAATCAACCT 59.617 34.615 0.00 0.00 36.70 3.50
38 39 6.578944 AGGTTTTTCTTAACACCAATCAACC 58.421 36.000 0.00 0.00 36.70 3.77
39 40 7.489160 AGAGGTTTTTCTTAACACCAATCAAC 58.511 34.615 0.00 0.00 36.70 3.18
40 41 7.654022 AGAGGTTTTTCTTAACACCAATCAA 57.346 32.000 0.00 0.00 36.70 2.57
41 42 7.417342 CCAAGAGGTTTTTCTTAACACCAATCA 60.417 37.037 0.00 0.00 36.70 2.57
42 43 6.923508 CCAAGAGGTTTTTCTTAACACCAATC 59.076 38.462 0.00 0.00 36.70 2.67
43 44 6.685368 GCCAAGAGGTTTTTCTTAACACCAAT 60.685 38.462 0.00 0.00 36.70 3.16
44 45 5.394773 GCCAAGAGGTTTTTCTTAACACCAA 60.395 40.000 0.00 0.00 36.70 3.67
45 46 4.098807 GCCAAGAGGTTTTTCTTAACACCA 59.901 41.667 0.00 0.00 36.70 4.17
46 47 4.500887 GGCCAAGAGGTTTTTCTTAACACC 60.501 45.833 0.00 0.00 35.70 4.16
47 48 4.098807 TGGCCAAGAGGTTTTTCTTAACAC 59.901 41.667 0.61 0.00 35.70 3.32
48 49 4.098807 GTGGCCAAGAGGTTTTTCTTAACA 59.901 41.667 7.24 0.00 35.70 2.41
49 50 4.617959 GTGGCCAAGAGGTTTTTCTTAAC 58.382 43.478 7.24 0.00 35.70 2.01
50 51 3.316868 CGTGGCCAAGAGGTTTTTCTTAA 59.683 43.478 14.14 0.00 35.70 1.85
51 52 2.882137 CGTGGCCAAGAGGTTTTTCTTA 59.118 45.455 14.14 0.00 35.70 2.10
52 53 1.681264 CGTGGCCAAGAGGTTTTTCTT 59.319 47.619 14.14 0.00 37.90 2.52
53 54 1.318576 CGTGGCCAAGAGGTTTTTCT 58.681 50.000 14.14 0.00 37.19 2.52
54 55 0.318699 GCGTGGCCAAGAGGTTTTTC 60.319 55.000 23.82 0.00 37.19 2.29
55 56 1.739667 GCGTGGCCAAGAGGTTTTT 59.260 52.632 23.82 0.00 37.19 1.94
56 57 3.443588 GCGTGGCCAAGAGGTTTT 58.556 55.556 23.82 0.00 37.19 2.43
1278 1308 3.840666 AGAGATGGCTGAGTGGACTAAAA 59.159 43.478 0.00 0.00 0.00 1.52
1759 1797 7.064253 GCGCAGTCTAAGTCTAAGGAAATAAAA 59.936 37.037 0.30 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.