Multiple sequence alignment - TraesCS2B01G629600

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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 TraesCS2B01G629600 chr2B 100.000 3099 0 0 1 3099 800704864 800701766 0.000000e+00 5723
1 TraesCS2B01G629600 chr2B 96.844 3105 68 11 1 3099 132067346 132070426 0.000000e+00 5164
2 TraesCS2B01G629600 chr2B 92.063 3112 203 34 1 3099 797501748 797504828 0.000000e+00 4338
3 TraesCS2B01G629600 chr5B 97.067 3103 81 8 1 3099 172609666 172612762 0.000000e+00 5217
4 TraesCS2B01G629600 chr5B 92.990 3110 178 26 1 3099 157580379 157583459 0.000000e+00 4499
5 TraesCS2B01G629600 chr5B 91.716 2885 198 26 1 2873 426076408 426079263 0.000000e+00 3965
6 TraesCS2B01G629600 chr5B 91.419 2890 200 28 1 2876 570094380 570091525 0.000000e+00 3919
7 TraesCS2B01G629600 chr5B 84.647 3133 357 74 1 3099 531751643 531754685 0.000000e+00 3007
8 TraesCS2B01G629600 chr5B 84.564 298 30 10 2805 3099 680699883 680699599 6.540000e-72 281
9 TraesCS2B01G629600 chr7B 91.788 2886 195 25 1 2873 379741884 379744740 0.000000e+00 3978
10 TraesCS2B01G629600 chr3B 91.719 2886 199 26 1 2876 170817767 170814912 0.000000e+00 3969
11 TraesCS2B01G629600 chr3B 91.649 2886 198 26 1 2873 772612517 772615372 0.000000e+00 3954
12 TraesCS2B01G629600 chr3B 83.710 1682 210 49 1427 3098 85419392 85421019 0.000000e+00 1530


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 TraesCS2B01G629600 chr2B 800701766 800704864 3098 True 5723 5723 100.000 1 3099 1 chr2B.!!$R1 3098
1 TraesCS2B01G629600 chr2B 132067346 132070426 3080 False 5164 5164 96.844 1 3099 1 chr2B.!!$F1 3098
2 TraesCS2B01G629600 chr2B 797501748 797504828 3080 False 4338 4338 92.063 1 3099 1 chr2B.!!$F2 3098
3 TraesCS2B01G629600 chr5B 172609666 172612762 3096 False 5217 5217 97.067 1 3099 1 chr5B.!!$F2 3098
4 TraesCS2B01G629600 chr5B 157580379 157583459 3080 False 4499 4499 92.990 1 3099 1 chr5B.!!$F1 3098
5 TraesCS2B01G629600 chr5B 426076408 426079263 2855 False 3965 3965 91.716 1 2873 1 chr5B.!!$F3 2872
6 TraesCS2B01G629600 chr5B 570091525 570094380 2855 True 3919 3919 91.419 1 2876 1 chr5B.!!$R1 2875
7 TraesCS2B01G629600 chr5B 531751643 531754685 3042 False 3007 3007 84.647 1 3099 1 chr5B.!!$F4 3098
8 TraesCS2B01G629600 chr7B 379741884 379744740 2856 False 3978 3978 91.788 1 2873 1 chr7B.!!$F1 2872
9 TraesCS2B01G629600 chr3B 170814912 170817767 2855 True 3969 3969 91.719 1 2876 1 chr3B.!!$R1 2875
10 TraesCS2B01G629600 chr3B 772612517 772615372 2855 False 3954 3954 91.649 1 2873 1 chr3B.!!$F2 2872
11 TraesCS2B01G629600 chr3B 85419392 85421019 1627 False 1530 1530 83.710 1427 3098 1 chr3B.!!$F1 1671

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
901 925 0.035152 TGAACGGCCGGAGTAGACTA 60.035 55.0 31.76 1.69 0.0 2.59 F
1629 1661 0.767998 TTGCCACACCATGTCACCTA 59.232 50.0 0.00 0.00 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2167 0.815734 GCGTGAACTACCCTCTGCTA 59.184 55.000 0.0 0.0 0.0 3.49 R
2561 2644 3.809279 CGCTGTAATGCATGATGACCTTA 59.191 43.478 0.0 0.0 0.0 2.69 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
128 143 8.647143 TTCAAACCTTTCTCATGTGATTTTTC 57.353 30.769 0.00 0.00 0.00 2.29
134 151 8.355913 ACCTTTCTCATGTGATTTTTCTTCTTC 58.644 33.333 0.00 0.00 0.00 2.87
355 373 2.104451 CAGGCTAGAACATCAGGCATCT 59.896 50.000 0.00 0.00 39.68 2.90
373 391 2.747177 TCTGTACATCGGGGAGTGATT 58.253 47.619 0.00 0.00 0.00 2.57
436 454 1.512230 GCAATGAAGGATGCCGCAA 59.488 52.632 0.00 0.00 36.56 4.85
674 695 2.653953 AAGGTTACTGTGGCGCGTGT 62.654 55.000 8.43 0.00 0.00 4.49
720 742 1.314730 CCCGTAAGCAACCAACAGTT 58.685 50.000 0.00 0.00 40.16 3.16
895 917 4.003788 CAGGTGAACGGCCGGAGT 62.004 66.667 31.76 14.69 0.00 3.85
901 925 0.035152 TGAACGGCCGGAGTAGACTA 60.035 55.000 31.76 1.69 0.00 2.59
1151 1175 0.830648 CCGGCCAGTAGGAATGAGAA 59.169 55.000 2.24 0.00 36.89 2.87
1389 1414 9.019764 ACATCTTTTGTAGTTTGAATTTTGTCG 57.980 29.630 0.00 0.00 36.57 4.35
1629 1661 0.767998 TTGCCACACCATGTCACCTA 59.232 50.000 0.00 0.00 0.00 3.08
1857 1916 5.211973 ACCTACATCTCACATCATACACCT 58.788 41.667 0.00 0.00 0.00 4.00
1862 1922 7.383102 ACATCTCACATCATACACCTTTTTC 57.617 36.000 0.00 0.00 0.00 2.29
1883 1943 8.657387 TTTTCCCTCACAATCCATATGTTTTA 57.343 30.769 1.24 0.00 0.00 1.52
2012 2083 2.037053 CAGAGGAGGACATCGCGAT 58.963 57.895 17.62 17.62 31.71 4.58
2058 2129 2.031012 TGCAGAGACGGCAACTGG 59.969 61.111 15.34 0.67 38.54 4.00
2096 2167 1.280457 GACCCCTGGTTCTGTGAGAT 58.720 55.000 0.00 0.00 35.25 2.75
2286 2358 8.037758 TCACTCATTTTGCTTTGTTCCTTTTTA 58.962 29.630 0.00 0.00 0.00 1.52
2483 2566 2.871216 ATCTCGCCGAGTCCGTGAGA 62.871 60.000 21.66 21.66 44.04 3.27
2561 2644 2.820059 ACATCGATATGTGTGCCGAT 57.180 45.000 0.00 0.00 44.79 4.18
2693 2776 7.210174 TGAAGAAATATGTGAGTAATCCTCCG 58.790 38.462 0.00 0.00 39.65 4.63
2995 3090 8.846943 TTTATGTGAACTCTGCTTCTCATTTA 57.153 30.769 6.37 0.00 36.35 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 143 3.131709 TCTTCACCCTGCAAGAAGAAG 57.868 47.619 14.47 12.60 43.28 2.85
134 151 2.557920 AGTCTTCTTCACCCTGCAAG 57.442 50.000 0.00 0.00 0.00 4.01
355 373 3.635373 GACTAATCACTCCCCGATGTACA 59.365 47.826 0.00 0.00 0.00 2.90
373 391 3.149981 CTGTCCTGGCAGATATCGACTA 58.850 50.000 17.94 4.78 38.70 2.59
436 454 3.286694 ATGGGGTTGCGTGGCTCAT 62.287 57.895 0.00 0.00 0.00 2.90
720 742 2.360600 GCCGGTGCATTGGGTACA 60.361 61.111 1.90 0.00 37.47 2.90
901 925 2.358247 CACTGCGGGTAAAGGCGT 60.358 61.111 0.00 0.00 0.00 5.68
1151 1175 1.194218 GGTAAATGCCATTGGGTGCT 58.806 50.000 4.53 0.00 36.17 4.40
1389 1414 4.097892 ACACCCCGAAAAGAATATGATTGC 59.902 41.667 0.00 0.00 0.00 3.56
1832 1891 7.013220 AGGTGTATGATGTGAGATGTAGGTAT 58.987 38.462 0.00 0.00 0.00 2.73
1857 1916 7.552050 AAACATATGGATTGTGAGGGAAAAA 57.448 32.000 7.80 0.00 0.00 1.94
1862 1922 7.503566 AGTCATAAAACATATGGATTGTGAGGG 59.496 37.037 16.83 0.00 0.00 4.30
1883 1943 7.181125 AGTGTGTTAGGATAAGGAGAAAGTCAT 59.819 37.037 0.00 0.00 0.00 3.06
1970 2041 1.074405 TGTTGCCTCCTCAATCTTGCT 59.926 47.619 0.00 0.00 0.00 3.91
2012 2083 0.968405 GAACTTGATTGCCCTTGCCA 59.032 50.000 0.00 0.00 36.33 4.92
2058 2129 0.946221 CGCGCTTCTGATGGTATCCC 60.946 60.000 5.56 0.00 0.00 3.85
2096 2167 0.815734 GCGTGAACTACCCTCTGCTA 59.184 55.000 0.00 0.00 0.00 3.49
2196 2267 2.283101 TGCTGGCCCTCGCATTTT 60.283 55.556 0.00 0.00 36.38 1.82
2286 2358 6.805713 ACGAGGAACAAGATGAAAAATGTTT 58.194 32.000 0.00 0.00 36.22 2.83
2302 2378 5.068636 TCATGTATAGGGAGTACGAGGAAC 58.931 45.833 0.00 0.00 0.00 3.62
2561 2644 3.809279 CGCTGTAATGCATGATGACCTTA 59.191 43.478 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.