Multiple sequence alignment - TraesCS5A01G117200

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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 TraesCS5A01G117200 chr5A 100.000 4004 0 0 1 4004 238850114 238846111 0 7395
1 TraesCS5A01G117200 chr5A 97.294 3733 89 9 1 3729 667749502 667745778 0 6324
2 TraesCS5A01G117200 chr5A 97.867 1313 25 3 162 1473 492858084 492859394 0 2266
3 TraesCS5A01G117200 chr7A 97.604 4007 89 6 1 4004 46419367 46423369 0 6861
4 TraesCS5A01G117200 chr7A 98.256 3096 44 4 912 4004 60262666 60265754 0 5409
5 TraesCS5A01G117200 chrUn 98.386 3098 38 5 912 4004 206782011 206785101 0 5433
6 TraesCS5A01G117200 chr4D 98.162 3102 41 7 912 4004 123318832 123321926 0 5398
7 TraesCS5A01G117200 chr1B 97.901 3096 48 8 912 4004 672570735 672567654 0 5341
8 TraesCS5A01G117200 chr1B 96.771 991 32 0 1 991 339012733 339013723 0 1653
9 TraesCS5A01G117200 chr2B 97.805 3098 55 8 912 4004 391093499 391090410 0 5332
10 TraesCS5A01G117200 chr2B 96.878 993 25 2 1 991 449203914 449202926 0 1657
11 TraesCS5A01G117200 chr2B 96.371 992 31 4 1 991 87959213 87960200 0 1628
12 TraesCS5A01G117200 chr3B 97.675 3097 64 6 912 4004 483384066 483387158 0 5313
13 TraesCS5A01G117200 chr3B 97.674 3096 67 5 912 4004 669797166 669794073 0 5313
14 TraesCS5A01G117200 chr3B 96.266 991 33 1 1 991 92227533 92226547 0 1622
15 TraesCS5A01G117200 chr6B 96.468 991 33 2 1 991 388026145 388027133 0 1635
16 TraesCS5A01G117200 chr6B 96.367 991 36 0 1 991 297425821 297426811 0 1631


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 TraesCS5A01G117200 chr5A 238846111 238850114 4003 True 7395 7395 100.000 1 4004 1 chr5A.!!$R1 4003
1 TraesCS5A01G117200 chr5A 667745778 667749502 3724 True 6324 6324 97.294 1 3729 1 chr5A.!!$R2 3728
2 TraesCS5A01G117200 chr5A 492858084 492859394 1310 False 2266 2266 97.867 162 1473 1 chr5A.!!$F1 1311
3 TraesCS5A01G117200 chr7A 46419367 46423369 4002 False 6861 6861 97.604 1 4004 1 chr7A.!!$F1 4003
4 TraesCS5A01G117200 chr7A 60262666 60265754 3088 False 5409 5409 98.256 912 4004 1 chr7A.!!$F2 3092
5 TraesCS5A01G117200 chrUn 206782011 206785101 3090 False 5433 5433 98.386 912 4004 1 chrUn.!!$F1 3092
6 TraesCS5A01G117200 chr4D 123318832 123321926 3094 False 5398 5398 98.162 912 4004 1 chr4D.!!$F1 3092
7 TraesCS5A01G117200 chr1B 672567654 672570735 3081 True 5341 5341 97.901 912 4004 1 chr1B.!!$R1 3092
8 TraesCS5A01G117200 chr1B 339012733 339013723 990 False 1653 1653 96.771 1 991 1 chr1B.!!$F1 990
9 TraesCS5A01G117200 chr2B 391090410 391093499 3089 True 5332 5332 97.805 912 4004 1 chr2B.!!$R1 3092
10 TraesCS5A01G117200 chr2B 449202926 449203914 988 True 1657 1657 96.878 1 991 1 chr2B.!!$R2 990
11 TraesCS5A01G117200 chr2B 87959213 87960200 987 False 1628 1628 96.371 1 991 1 chr2B.!!$F1 990
12 TraesCS5A01G117200 chr3B 483384066 483387158 3092 False 5313 5313 97.675 912 4004 1 chr3B.!!$F1 3092
13 TraesCS5A01G117200 chr3B 669794073 669797166 3093 True 5313 5313 97.674 912 4004 1 chr3B.!!$R2 3092
14 TraesCS5A01G117200 chr3B 92226547 92227533 986 True 1622 1622 96.266 1 991 1 chr3B.!!$R1 990
15 TraesCS5A01G117200 chr6B 388026145 388027133 988 False 1635 1635 96.468 1 991 1 chr6B.!!$F2 990
16 TraesCS5A01G117200 chr6B 297425821 297426811 990 False 1631 1631 96.367 1 991 1 chr6B.!!$F1 990

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
986 993 1.003580 TCGGGAGCAGAGCTGAAAAAT 59.996 47.619 0.85 0.0 39.88 1.82 F
1979 1994 0.768622 TGAACGGTGGGAGGTCAAAT 59.231 50.000 0.00 0.0 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 2321 0.178068 GGATGCTAGTCGGCTTTGGA 59.822 55.0 0.0 0.0 0.0 3.53 R
3306 3331 0.618458 TGACGGCTTGGCTTCCTATT 59.382 50.0 0.0 0.0 0.0 1.73 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
25 26 2.223829 CGCCTTGAGGATTCTATGACGT 60.224 50.000 0.06 0.00 37.39 4.34
516 519 3.259876 AGACACTACGCACCTCCAAATTA 59.740 43.478 0.00 0.00 0.00 1.40
810 817 7.884877 TCAGTTATCAATTGACAAAGATGACCT 59.115 33.333 11.07 0.00 30.07 3.85
853 860 7.982761 AACGACAATGGTATGGTACTTTTTA 57.017 32.000 0.00 0.00 0.00 1.52
986 993 1.003580 TCGGGAGCAGAGCTGAAAAAT 59.996 47.619 0.85 0.00 39.88 1.82
1213 1225 5.182190 TGGCATTTCAACGAGCAAACTAATA 59.818 36.000 0.00 0.00 0.00 0.98
1486 1498 1.226603 CCATTCCCGTCGTCGAGAC 60.227 63.158 2.98 0.00 46.16 3.36
1510 1522 6.884295 ACACTAAAAGAACTATAGCATGCCAA 59.116 34.615 15.66 2.91 0.00 4.52
1634 1646 1.411246 GGTGTGGTGGAGCGATATACA 59.589 52.381 0.00 0.00 0.00 2.29
1877 1892 2.174424 AGGTCCTACGGTAGGTAAGAGG 59.826 54.545 28.55 9.07 46.32 3.69
1979 1994 0.768622 TGAACGGTGGGAGGTCAAAT 59.231 50.000 0.00 0.00 0.00 2.32
2038 2058 6.487331 TGATCTAGATAGACTCCGTCCTTTTC 59.513 42.308 4.89 0.00 34.72 2.29
2219 2240 5.474578 TCACATGAGCATAGGGAATCTAC 57.525 43.478 0.00 0.00 0.00 2.59
2292 2314 4.968080 GAGATCTGATCTATTGGGGCCTAT 59.032 45.833 19.57 0.00 40.38 2.57
2299 2321 6.091555 TGATCTATTGGGGCCTATAACTTCT 58.908 40.000 0.84 0.00 0.00 2.85
3216 3240 3.427233 GCTTCGCTTCATCATCTTGCTTT 60.427 43.478 0.00 0.00 0.00 3.51
3259 3283 5.163784 GCACTATAACATAGGCATGCATGAG 60.164 44.000 30.64 15.82 35.39 2.90
3306 3331 1.399714 CCGACCACTACATAGGAGCA 58.600 55.000 0.00 0.00 0.00 4.26
3384 3409 4.020485 ACGGCCTACTTATAGCCCTATTTG 60.020 45.833 0.00 0.00 0.00 2.32
3422 3447 0.109723 TCAACGGGCCTTACAAGCTT 59.890 50.000 0.84 0.00 0.00 3.74
3555 3580 1.303643 GTACCAGCCAAGCCAGCTT 60.304 57.895 0.00 0.00 38.95 3.74
3887 3913 5.640147 TCCTTTTTGAGAAAGATGGGCTTA 58.360 37.500 0.00 0.00 35.24 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.680735 GCCACAACACCATTGAGTGAA 59.319 47.619 10.89 0.00 40.34 3.18
88 89 1.487976 CCTTCTGATGCAGCCTTCCTA 59.512 52.381 0.00 0.00 0.00 2.94
810 817 6.017275 TGTCGTTTTTAGGGCGAAAAAGAATA 60.017 34.615 8.43 1.56 38.59 1.75
853 860 3.245730 ACCCACACAATCTCCATTGGAAT 60.246 43.478 6.88 1.14 43.47 3.01
861 868 0.673644 CGGACACCCACACAATCTCC 60.674 60.000 0.00 0.00 0.00 3.71
929 936 0.109272 GACTGATCTTGACGTCGGCA 60.109 55.000 11.62 0.00 0.00 5.69
986 993 8.378115 ACAAAGAATCATTGGAATTTCCCATA 57.622 30.769 12.90 0.00 35.03 2.74
1486 1498 6.925610 TGGCATGCTATAGTTCTTTTAGTG 57.074 37.500 18.92 0.00 0.00 2.74
1510 1522 0.179001 CCACCTCAACTCCCCGTTTT 60.179 55.000 0.00 0.00 32.27 2.43
1799 1811 1.376037 GTTGTCCTCTCTTGGCCCG 60.376 63.158 0.00 0.00 0.00 6.13
1829 1841 0.811915 CGAAGCGAAGAAGGAGGAGA 59.188 55.000 0.00 0.00 0.00 3.71
1877 1892 1.279840 GGTCAAGTGCTTGTGCGTC 59.720 57.895 11.17 0.63 43.34 5.19
1951 1966 1.005512 CCACCGTTCACGACATCCA 60.006 57.895 0.00 0.00 43.02 3.41
1979 1994 8.816894 ACTGTATTCAGAGGTCAATTCTCTTTA 58.183 33.333 6.32 0.00 43.76 1.85
2038 2058 9.454859 AATTTCTTGAGTCACCCTTATCTAAAG 57.545 33.333 0.00 0.00 0.00 1.85
2219 2240 1.294659 GCCAAGTCGAAGGCTCAGTG 61.295 60.000 15.35 0.00 40.46 3.66
2292 2314 3.368116 GCTAGTCGGCTTTGGAGAAGTTA 60.368 47.826 0.00 0.00 0.00 2.24
2299 2321 0.178068 GGATGCTAGTCGGCTTTGGA 59.822 55.000 0.00 0.00 0.00 3.53
3234 3258 4.084011 TGCATGCCTATGTTATAGTGCA 57.916 40.909 16.68 11.59 38.83 4.57
3306 3331 0.618458 TGACGGCTTGGCTTCCTATT 59.382 50.000 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.