Multiple sequence alignment - TraesCS3D01G210200

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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 TraesCS3D01G210200 chr3D 100.000 3284 0 0 1 3284 278451282 278447999 0.000000e+00 6065.0
1 TraesCS3D01G210200 chr3A 95.685 2480 83 9 808 3284 360825054 360827512 0.000000e+00 3965.0
2 TraesCS3D01G210200 chr3A 97.022 806 22 2 1 805 360823856 360824660 0.000000e+00 1354.0
3 TraesCS3D01G210200 chr3B 95.400 2500 77 16 804 3284 372240346 372242826 0.000000e+00 3945.0
4 TraesCS3D01G210200 chr3B 96.639 714 19 1 1 709 372238907 372239620 0.000000e+00 1181.0
5 TraesCS3D01G210200 chr3B 97.391 115 3 0 691 805 372239635 372239749 2.590000e-46 196.0
6 TraesCS3D01G210200 chr6B 91.358 81 3 3 800 879 256326228 256326151 1.250000e-19 108.0
7 TraesCS3D01G210200 chr2A 90.123 81 4 2 797 877 419206887 419206963 5.800000e-18 102.0
8 TraesCS3D01G210200 chr2A 88.095 84 6 2 800 883 608038664 608038743 2.700000e-16 97.1
9 TraesCS3D01G210200 chr2B 90.909 77 4 1 804 880 560893468 560893395 2.090000e-17 100.0
10 TraesCS3D01G210200 chr7A 88.235 85 6 2 796 880 91646236 91646316 7.500000e-17 99.0
11 TraesCS3D01G210200 chr4D 88.095 84 6 2 800 883 469889076 469888997 2.700000e-16 97.1
12 TraesCS3D01G210200 chr4A 87.059 85 7 2 797 880 614112408 614112327 3.490000e-15 93.5


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 TraesCS3D01G210200 chr3D 278447999 278451282 3283 True 6065.0 6065 100.000000 1 3284 1 chr3D.!!$R1 3283
1 TraesCS3D01G210200 chr3A 360823856 360827512 3656 False 2659.5 3965 96.353500 1 3284 2 chr3A.!!$F1 3283
2 TraesCS3D01G210200 chr3B 372238907 372242826 3919 False 1774.0 3945 96.476667 1 3284 3 chr3B.!!$F1 3283

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
121 122 0.107312 ACTGCAGCATGATGGTCTCC 60.107 55.0 15.27 0.00 39.69 3.71 F
194 195 0.248377 CGTCGAGGTAGCTTTACGGG 60.248 60.0 17.37 2.16 0.00 5.28 F
534 541 0.531200 ACGAGCTGTACAAGGTAGCC 59.469 55.0 0.00 0.00 36.52 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 2061 1.065854 CCCAGCTCGTCATCTTCCTTT 60.066 52.381 0.0 0.0 0.00 3.11 R
2064 2727 1.278937 CGTAGTCGCCGTCATCGAT 59.721 57.895 0.0 0.0 38.29 3.59 R
2290 2953 3.758554 GGCCTTGTGAGAAGCTAAAATGA 59.241 43.478 0.0 0.0 0.00 2.57 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
27 28 3.053619 GTGATGGGGAGGTAAAGTGGAAT 60.054 47.826 0.00 0.00 0.00 3.01
96 97 0.169009 GTTTCACTGATCCTTGCGGC 59.831 55.000 0.00 0.00 0.00 6.53
121 122 0.107312 ACTGCAGCATGATGGTCTCC 60.107 55.000 15.27 0.00 39.69 3.71
194 195 0.248377 CGTCGAGGTAGCTTTACGGG 60.248 60.000 17.37 2.16 0.00 5.28
228 234 9.851686 ATAATAACCTGCAATATGTCAAGAGAA 57.148 29.630 0.00 0.00 0.00 2.87
391 397 3.406764 AGGTAAGCAGAGCACTGAAAAG 58.593 45.455 15.88 0.00 46.03 2.27
534 541 0.531200 ACGAGCTGTACAAGGTAGCC 59.469 55.000 0.00 0.00 36.52 3.93
592 599 2.359107 TTGAGGCGCTCAAGGCTG 60.359 61.111 7.64 0.00 44.27 4.85
595 602 2.431683 AGGCGCTCAAGGCTGAAA 59.568 55.556 7.64 0.00 45.75 2.69
1014 1671 2.095461 CAGAGAATGAGGGTGACGAGA 58.905 52.381 0.00 0.00 0.00 4.04
1398 2061 2.048222 CGCAGCAACTCCGAGGAA 60.048 61.111 0.00 0.00 0.00 3.36
1431 2094 2.123425 CTGGGGGCGCCTCTACTA 60.123 66.667 28.78 11.32 0.00 1.82
1491 2154 3.134127 GGGCTCGCCATGAACCAC 61.134 66.667 10.51 0.00 34.28 4.16
1538 2201 2.514824 GTTCCTCCGCTCATGGGC 60.515 66.667 7.77 7.77 0.00 5.36
2040 2703 4.538233 TCGGCCATCGACTACGTA 57.462 55.556 2.24 0.00 43.74 3.57
2079 2742 2.413351 CCATCGATGACGGCGACT 59.587 61.111 26.86 0.00 40.94 4.18
2290 2953 6.126863 TGGTGGATTTGATCTGAAACTAGT 57.873 37.500 0.00 0.00 0.00 2.57
2348 3021 4.581824 GTGTGTATGCATGGGATCTCAATT 59.418 41.667 10.16 0.00 0.00 2.32
2392 3068 8.255394 AGCAAAATATTATTGGCAACTTTCAC 57.745 30.769 0.00 0.00 37.61 3.18
2403 3079 2.030701 GCAACTTTCACGACCAAACGTA 59.969 45.455 0.00 0.00 44.76 3.57
2410 3086 4.979943 TCACGACCAAACGTATATACCA 57.020 40.909 7.30 0.00 44.76 3.25
2691 3368 6.259167 TGAATTAATATACACAACGCAGACCC 59.741 38.462 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 8.542926 CCATACATAGGATCCACATAAATGAGA 58.457 37.037 15.82 2.78 0.00 3.27
96 97 1.466866 CCATCATGCTGCAGTGTTTCG 60.467 52.381 16.64 0.44 0.00 3.46
121 122 1.280421 AGGAGTAGCCCTTCTGCAAAG 59.720 52.381 0.00 0.00 37.37 2.77
228 234 4.832266 TGCACCCTGTGTTAGATGAAAAAT 59.168 37.500 0.00 0.00 35.75 1.82
242 248 3.161450 ACGACCAGTGCACCCTGT 61.161 61.111 14.63 8.31 0.00 4.00
534 541 3.880846 GCGAGGCCCAGCGATTTG 61.881 66.667 13.66 0.00 0.00 2.32
591 598 1.642037 GCTGCGAGCTCTGCATTTCA 61.642 55.000 25.80 9.49 42.32 2.69
592 599 1.062206 GCTGCGAGCTCTGCATTTC 59.938 57.895 25.80 16.98 42.32 2.17
595 602 1.953231 TAGTGCTGCGAGCTCTGCAT 61.953 55.000 25.80 16.93 43.91 3.96
762 802 0.185416 TACCGTTTCCCCCTTTGCAA 59.815 50.000 0.00 0.00 0.00 4.08
777 817 8.339714 ACAAACATACCAAAAATATCGATACCG 58.660 33.333 7.41 0.00 37.07 4.02
805 845 3.608073 GCAAAATGAATGAACCTACACGC 59.392 43.478 0.00 0.00 0.00 5.34
806 846 5.046910 AGCAAAATGAATGAACCTACACG 57.953 39.130 0.00 0.00 0.00 4.49
1361 2018 2.429236 CGACGAACACGAGCTGCT 60.429 61.111 0.00 0.00 0.00 4.24
1398 2061 1.065854 CCCAGCTCGTCATCTTCCTTT 60.066 52.381 0.00 0.00 0.00 3.11
1554 2217 4.423209 GGGGAGGAGAGGGGCACT 62.423 72.222 0.00 0.00 0.00 4.40
2006 2669 2.785105 GAACGGATGAACGCGTCGG 61.785 63.158 14.44 6.97 37.37 4.79
2064 2727 1.278937 CGTAGTCGCCGTCATCGAT 59.721 57.895 0.00 0.00 38.29 3.59
2290 2953 3.758554 GGCCTTGTGAGAAGCTAAAATGA 59.241 43.478 0.00 0.00 0.00 2.57
2392 3068 7.697352 TTTGTATGGTATATACGTTTGGTCG 57.303 36.000 6.79 0.00 0.00 4.79
2410 3086 8.952278 TCGTTAAAATCTGCCTTGTATTTGTAT 58.048 29.630 0.00 0.00 0.00 2.29
2475 3152 5.176590 GCTAGTGTTTGAGTTGAGTTCTCTG 59.823 44.000 1.53 0.00 33.59 3.35
2683 3360 0.179048 TTAGCATCCATGGGTCTGCG 60.179 55.000 21.38 3.01 37.46 5.18
2691 3368 2.847327 ATCGGGTCTTAGCATCCATG 57.153 50.000 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.