Multiple sequence alignment - TraesCS4A01G341400

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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 TraesCS4A01G341400 chr4A 100.000 3674 0 0 1 3674 621797876 621801549 0.000000e+00 6785.0
1 TraesCS4A01G341400 chr2A 98.340 3614 57 2 64 3674 507377777 507381390 0.000000e+00 6338.0
2 TraesCS4A01G341400 chr2A 97.851 3629 61 4 63 3674 581569056 581572684 0.000000e+00 6253.0
3 TraesCS4A01G341400 chr1A 98.093 3618 60 5 64 3674 319325432 319329047 0.000000e+00 6290.0
4 TraesCS4A01G341400 chr1A 93.690 2726 155 12 954 3674 556700812 556698099 0.000000e+00 4065.0
5 TraesCS4A01G341400 chr3A 98.067 3622 57 3 64 3674 171633011 171629392 0.000000e+00 6288.0
6 TraesCS4A01G341400 chr7B 94.772 3615 139 21 63 3674 600477503 600473936 0.000000e+00 5583.0
7 TraesCS4A01G341400 chr6B 94.405 3628 125 19 64 3674 646740643 646737077 0.000000e+00 5504.0
8 TraesCS4A01G341400 chr6B 94.888 3228 115 22 453 3674 245608001 245611184 0.000000e+00 5001.0
9 TraesCS4A01G341400 chr6B 91.126 2096 156 18 916 2993 515035533 515037616 0.000000e+00 2813.0
10 TraesCS4A01G341400 chr2B 95.142 3376 106 24 304 3674 451516817 451513495 0.000000e+00 5273.0
11 TraesCS4A01G341400 chr2B 91.745 2774 174 24 916 3674 17506221 17508954 0.000000e+00 3803.0
12 TraesCS4A01G341400 chr2B 94.661 1180 58 5 64 1240 36414871 36416048 0.000000e+00 1825.0
13 TraesCS4A01G341400 chr7A 93.724 2629 103 11 376 2997 299422680 299420107 0.000000e+00 3884.0
14 TraesCS4A01G341400 chr7A 94.773 880 44 2 2795 3674 546541945 546541068 0.000000e+00 1369.0
15 TraesCS4A01G341400 chr1D 91.951 2721 164 21 962 3674 56893569 56890896 0.000000e+00 3760.0
16 TraesCS4A01G341400 chr4B 91.714 2100 139 17 916 2993 648696554 648698640 0.000000e+00 2881.0
17 TraesCS4A01G341400 chrUn 95.238 42 2 0 17 58 306905782 306905823 2.370000e-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 TraesCS4A01G341400 chr4A 621797876 621801549 3673 False 6785 6785 100.000 1 3674 1 chr4A.!!$F1 3673
1 TraesCS4A01G341400 chr2A 507377777 507381390 3613 False 6338 6338 98.340 64 3674 1 chr2A.!!$F1 3610
2 TraesCS4A01G341400 chr2A 581569056 581572684 3628 False 6253 6253 97.851 63 3674 1 chr2A.!!$F2 3611
3 TraesCS4A01G341400 chr1A 319325432 319329047 3615 False 6290 6290 98.093 64 3674 1 chr1A.!!$F1 3610
4 TraesCS4A01G341400 chr1A 556698099 556700812 2713 True 4065 4065 93.690 954 3674 1 chr1A.!!$R1 2720
5 TraesCS4A01G341400 chr3A 171629392 171633011 3619 True 6288 6288 98.067 64 3674 1 chr3A.!!$R1 3610
6 TraesCS4A01G341400 chr7B 600473936 600477503 3567 True 5583 5583 94.772 63 3674 1 chr7B.!!$R1 3611
7 TraesCS4A01G341400 chr6B 646737077 646740643 3566 True 5504 5504 94.405 64 3674 1 chr6B.!!$R1 3610
8 TraesCS4A01G341400 chr6B 245608001 245611184 3183 False 5001 5001 94.888 453 3674 1 chr6B.!!$F1 3221
9 TraesCS4A01G341400 chr6B 515035533 515037616 2083 False 2813 2813 91.126 916 2993 1 chr6B.!!$F2 2077
10 TraesCS4A01G341400 chr2B 451513495 451516817 3322 True 5273 5273 95.142 304 3674 1 chr2B.!!$R1 3370
11 TraesCS4A01G341400 chr2B 17506221 17508954 2733 False 3803 3803 91.745 916 3674 1 chr2B.!!$F1 2758
12 TraesCS4A01G341400 chr2B 36414871 36416048 1177 False 1825 1825 94.661 64 1240 1 chr2B.!!$F2 1176
13 TraesCS4A01G341400 chr7A 299420107 299422680 2573 True 3884 3884 93.724 376 2997 1 chr7A.!!$R1 2621
14 TraesCS4A01G341400 chr7A 546541068 546541945 877 True 1369 1369 94.773 2795 3674 1 chr7A.!!$R2 879
15 TraesCS4A01G341400 chr1D 56890896 56893569 2673 True 3760 3760 91.951 962 3674 1 chr1D.!!$R1 2712
16 TraesCS4A01G341400 chr4B 648696554 648698640 2086 False 2881 2881 91.714 916 2993 1 chr4B.!!$F1 2077

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
37 38 1.805945 GAACCTGTCGCTGGCGTAG 60.806 63.158 14.55 13.19 40.74 3.51 F
39 40 2.202623 CCTGTCGCTGGCGTAGAC 60.203 66.667 14.55 6.61 40.74 2.59 F
40 41 2.577112 CTGTCGCTGGCGTAGACG 60.577 66.667 14.55 0.00 41.59 4.18 F
1205 1239 2.344093 TTAGGAGAGAAAGGGCTGGT 57.656 50.000 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1129 1163 4.020662 TGCATTAAATCCTTGGGTTTCCAC 60.021 41.667 0.61 0.0 43.94 4.02 R
1205 1239 4.350368 TCTGCATGACTGTCTACCAAAA 57.650 40.909 9.51 0.0 0.00 2.44 R
1576 1623 5.186409 CACTTCCAATTTGACCATCCTCATT 59.814 40.000 0.00 0.0 0.00 2.57 R
2797 2867 0.536006 ACAAGGAGTTGAGCACCTGC 60.536 55.000 0.00 0.0 38.23 4.85 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
22 23 3.065015 CTCTCGTTGAGCGCGAAC 58.935 61.111 12.10 13.52 41.07 3.95
23 24 2.430244 TCTCGTTGAGCGCGAACC 60.430 61.111 12.10 0.00 41.07 3.62
24 25 2.430921 CTCGTTGAGCGCGAACCT 60.431 61.111 12.10 0.00 41.07 3.50
25 26 2.720758 CTCGTTGAGCGCGAACCTG 61.721 63.158 12.10 8.20 41.07 4.00
26 27 3.036084 CGTTGAGCGCGAACCTGT 61.036 61.111 12.10 0.00 0.00 4.00
27 28 2.853914 GTTGAGCGCGAACCTGTC 59.146 61.111 12.10 0.00 0.00 3.51
36 37 2.260434 GAACCTGTCGCTGGCGTA 59.740 61.111 14.55 4.94 40.74 4.42
37 38 1.805945 GAACCTGTCGCTGGCGTAG 60.806 63.158 14.55 13.19 40.74 3.51
38 39 2.209064 GAACCTGTCGCTGGCGTAGA 62.209 60.000 14.55 0.37 40.74 2.59
39 40 2.202623 CCTGTCGCTGGCGTAGAC 60.203 66.667 14.55 6.61 40.74 2.59
40 41 2.577112 CTGTCGCTGGCGTAGACG 60.577 66.667 14.55 0.00 41.59 4.18
50 51 3.238241 CGTAGACGCTGCCGAACG 61.238 66.667 0.00 0.00 38.29 3.95
51 52 3.542742 GTAGACGCTGCCGAACGC 61.543 66.667 0.00 0.00 38.29 4.84
52 53 4.789075 TAGACGCTGCCGAACGCC 62.789 66.667 0.00 0.00 38.29 5.68
84 85 5.864474 CGAGAGTTAATTGCACAGAAGTACT 59.136 40.000 0.00 0.00 0.00 2.73
1129 1163 3.947910 ATCTGAATTTGGTTGCAGTGG 57.052 42.857 0.00 0.00 0.00 4.00
1205 1239 2.344093 TTAGGAGAGAAAGGGCTGGT 57.656 50.000 0.00 0.00 0.00 4.00
1576 1623 2.532250 TGAGGACAGTGATGCCTCTA 57.468 50.000 22.52 12.41 46.56 2.43
2153 2209 4.016444 GCCAGGAATTTCAGGTATCACAA 58.984 43.478 0.00 0.00 0.00 3.33
2556 2613 6.238538 GGAGCAGAGTAATAGTCACTACTGTC 60.239 46.154 0.00 0.00 36.36 3.51
2948 3020 1.303643 GGGGAGAAGTGGGCAAGTG 60.304 63.158 0.00 0.00 0.00 3.16
3527 3611 2.233431 GTGGCACATGAAGAGAGAGAGT 59.767 50.000 13.86 0.00 44.52 3.24
3656 3740 1.604604 GCAAGTTACAAGTGGGCAGA 58.395 50.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.853914 GACAGGTTCGCGCTCAAC 59.146 61.111 5.56 8.25 0.00 3.18
11 12 2.733218 CGACAGGTTCGCGCTCAA 60.733 61.111 5.56 0.00 41.87 3.02
19 20 1.805945 CTACGCCAGCGACAGGTTC 60.806 63.158 20.32 0.00 42.83 3.62
20 21 2.261671 CTACGCCAGCGACAGGTT 59.738 61.111 20.32 0.00 42.83 3.50
21 22 2.675423 TCTACGCCAGCGACAGGT 60.675 61.111 20.32 0.00 42.83 4.00
22 23 2.202623 GTCTACGCCAGCGACAGG 60.203 66.667 20.32 5.61 42.83 4.00
23 24 2.577112 CGTCTACGCCAGCGACAG 60.577 66.667 20.32 14.55 42.83 3.51
33 34 3.238241 CGTTCGGCAGCGTCTACG 61.238 66.667 0.00 0.00 43.27 3.51
34 35 3.542742 GCGTTCGGCAGCGTCTAC 61.543 66.667 0.00 0.00 42.87 2.59
35 36 4.789075 GGCGTTCGGCAGCGTCTA 62.789 66.667 13.49 0.00 46.16 2.59
41 42 4.728102 TACGGTGGCGTTCGGCAG 62.728 66.667 20.64 12.94 46.16 4.85
56 57 4.491676 TCTGTGCAATTAACTCTCGGTAC 58.508 43.478 0.00 0.00 0.00 3.34
57 58 4.794278 TCTGTGCAATTAACTCTCGGTA 57.206 40.909 0.00 0.00 0.00 4.02
58 59 3.678056 TCTGTGCAATTAACTCTCGGT 57.322 42.857 0.00 0.00 0.00 4.69
59 60 3.997021 ACTTCTGTGCAATTAACTCTCGG 59.003 43.478 0.00 0.00 0.00 4.63
60 61 5.864474 AGTACTTCTGTGCAATTAACTCTCG 59.136 40.000 0.00 0.00 0.00 4.04
61 62 7.813148 TGTAGTACTTCTGTGCAATTAACTCTC 59.187 37.037 0.00 0.00 0.00 3.20
294 315 1.609501 CCGGACCAGGTTGGAGAGA 60.610 63.158 0.00 0.00 40.96 3.10
333 354 3.407967 GGGAGGGGAATGGTGCGA 61.408 66.667 0.00 0.00 0.00 5.10
1129 1163 4.020662 TGCATTAAATCCTTGGGTTTCCAC 60.021 41.667 0.61 0.00 43.94 4.02
1205 1239 4.350368 TCTGCATGACTGTCTACCAAAA 57.650 40.909 9.51 0.00 0.00 2.44
1576 1623 5.186409 CACTTCCAATTTGACCATCCTCATT 59.814 40.000 0.00 0.00 0.00 2.57
1804 1858 5.561725 GCTTCTGCTTCTTCTTTACAGGTTG 60.562 44.000 0.00 0.00 36.03 3.77
2153 2209 9.339850 CAACAATTATCCTCTGATCTGAATTCT 57.660 33.333 7.05 0.00 32.18 2.40
2394 2451 4.206375 TGGGCACATCTACACCATATTTG 58.794 43.478 0.00 0.00 0.00 2.32
2556 2613 1.066002 CTTGCAGTTGGTGTTGGAGTG 59.934 52.381 0.00 0.00 0.00 3.51
2797 2867 0.536006 ACAAGGAGTTGAGCACCTGC 60.536 55.000 0.00 0.00 38.23 4.85
3527 3611 3.073798 TCCCATCTTGCTTCCTTAACACA 59.926 43.478 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.