Multiple sequence alignment - TraesCS5D01G322500

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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 TraesCS5D01G322500 chr5D 100.000 3832 0 0 1 3832 414068122 414071953 0.000000e+00 7077.0
1 TraesCS5D01G322500 chr5B 96.274 3865 93 24 1 3832 499121774 499125620 0.000000e+00 6292.0
2 TraesCS5D01G322500 chr5A 92.370 3853 195 46 1 3829 526582775 526586552 0.000000e+00 5395.0
3 TraesCS5D01G322500 chr5A 92.857 56 2 1 3006 3061 547648776 547648829 3.170000e-11 80.5
4 TraesCS5D01G322500 chr6B 97.917 48 1 0 3012 3059 135867581 135867628 2.450000e-12 84.2
5 TraesCS5D01G322500 chr6B 94.444 54 3 0 3006 3059 555953984 555953931 2.450000e-12 84.2
6 TraesCS5D01G322500 chr6B 91.525 59 3 2 3011 3067 19132650 19132708 3.170000e-11 80.5
7 TraesCS5D01G322500 chr4B 96.078 51 2 0 3013 3063 49466852 49466802 2.450000e-12 84.2
8 TraesCS5D01G322500 chr4B 94.231 52 3 0 3008 3059 158268843 158268792 3.170000e-11 80.5
9 TraesCS5D01G322500 chr7D 95.918 49 2 0 3013 3061 3845014 3844966 3.170000e-11 80.5
10 TraesCS5D01G322500 chr4A 94.231 52 3 0 3013 3064 633055376 633055325 3.170000e-11 80.5


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 TraesCS5D01G322500 chr5D 414068122 414071953 3831 False 7077 7077 100.000 1 3832 1 chr5D.!!$F1 3831
1 TraesCS5D01G322500 chr5B 499121774 499125620 3846 False 6292 6292 96.274 1 3832 1 chr5B.!!$F1 3831
2 TraesCS5D01G322500 chr5A 526582775 526586552 3777 False 5395 5395 92.370 1 3829 1 chr5A.!!$F1 3828

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
356 360 0.035439 TTTCCAGGCCGTTGATCCTC 60.035 55.000 0.00 0.0 0.0 3.71 F
445 450 1.134098 CCGGATGCTGATAAACCTGGT 60.134 52.381 0.00 0.0 0.0 4.00 F
876 911 1.896694 CAGTGGGGCTCTCTGTCTC 59.103 63.158 8.27 0.0 33.6 3.36 F
1789 1830 4.205587 AGATGCAGGGAATGTGAGATTTC 58.794 43.478 0.00 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 1517 0.179179 GGTCCGTGCTACGTACTGAC 60.179 60.000 0.00 0.00 40.58 3.51 R
1478 1519 1.226211 CGGTCCGTGCTACGTACTG 60.226 63.158 2.08 4.05 40.58 2.74 R
2796 2842 2.169144 CAGGGAATGGGCTCAAAAATCC 59.831 50.000 0.00 0.00 0.00 3.01 R
3623 3675 1.138247 CAAGAGCAGAAATGCCCGC 59.862 57.895 0.00 0.00 34.90 6.13 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
76 77 5.763876 AGCAGACCTTTGACTTAGGTTAT 57.236 39.130 0.00 0.00 45.88 1.89
107 108 4.631377 TCAGAATCCAATACGCTTCAACTG 59.369 41.667 0.00 0.00 0.00 3.16
119 120 3.678806 CGCTTCAACTGTGCTCCCTAATA 60.679 47.826 0.00 0.00 0.00 0.98
156 157 9.490379 GGTCCGAGAATGTTCATATACTTATTT 57.510 33.333 0.00 0.00 0.00 1.40
243 246 3.799281 AATGCCCGTGGAACAATTATG 57.201 42.857 0.00 0.00 44.16 1.90
356 360 0.035439 TTTCCAGGCCGTTGATCCTC 60.035 55.000 0.00 0.00 0.00 3.71
362 366 1.450312 GCCGTTGATCCTCACCAGG 60.450 63.158 0.00 0.00 42.01 4.45
405 409 1.270274 TGCTGAATGTGAACCATGTGC 59.730 47.619 0.00 0.00 32.82 4.57
445 450 1.134098 CCGGATGCTGATAAACCTGGT 60.134 52.381 0.00 0.00 0.00 4.00
463 468 2.890945 TGGTCATCTTCTCAGTTGTCGA 59.109 45.455 0.00 0.00 0.00 4.20
475 480 3.498397 TCAGTTGTCGATCTTTCCTTTGC 59.502 43.478 0.00 0.00 0.00 3.68
545 551 8.441608 CAACAAACATCAGAGTATCAAAGAGAG 58.558 37.037 0.00 0.00 37.82 3.20
757 763 5.741040 GCAGTATCTACACTAACGTTGTACC 59.259 44.000 11.99 0.00 0.00 3.34
868 903 3.483869 CTAGGGGCAGTGGGGCTC 61.484 72.222 0.00 0.00 44.62 4.70
872 907 4.106925 GGGCAGTGGGGCTCTCTG 62.107 72.222 12.02 12.02 42.84 3.35
873 908 3.325753 GGCAGTGGGGCTCTCTGT 61.326 66.667 17.04 0.00 38.75 3.41
874 909 2.267324 GCAGTGGGGCTCTCTGTC 59.733 66.667 17.04 6.70 38.75 3.51
875 910 2.289532 GCAGTGGGGCTCTCTGTCT 61.290 63.158 17.04 0.00 38.75 3.41
876 911 1.896694 CAGTGGGGCTCTCTGTCTC 59.103 63.158 8.27 0.00 33.60 3.36
1789 1830 4.205587 AGATGCAGGGAATGTGAGATTTC 58.794 43.478 0.00 0.00 0.00 2.17
1980 2026 5.166398 GCTTCCATTTCTTCTTCCAACATG 58.834 41.667 0.00 0.00 0.00 3.21
1989 2035 8.833231 TTTCTTCTTCCAACATGAAGTACTAG 57.167 34.615 0.00 0.00 41.96 2.57
1990 2036 7.540474 TCTTCTTCCAACATGAAGTACTAGT 57.460 36.000 0.00 0.00 41.96 2.57
1991 2037 7.378966 TCTTCTTCCAACATGAAGTACTAGTG 58.621 38.462 5.39 0.00 41.96 2.74
2254 2300 5.944599 AGAGAAATGATTGATGAAGCACAGT 59.055 36.000 0.00 0.00 28.11 3.55
2796 2842 6.150976 TGCACTGGACTATTGTTTTAAGATGG 59.849 38.462 0.00 0.00 0.00 3.51
2892 2939 8.098220 TGGCTACTGCATTGTAATATGTAATG 57.902 34.615 0.00 0.00 41.91 1.90
3046 3095 7.505585 TCTGTCCCAAAATAAGTGTCTTTGATT 59.494 33.333 0.00 0.00 32.87 2.57
3332 3382 2.811902 TCAATCTTCATCTTTGCGCG 57.188 45.000 0.00 0.00 0.00 6.86
3623 3675 7.826744 TGCTACTGTAGATAGATGGATGTAGAG 59.173 40.741 18.64 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.743057 TGAACATGTATCCAGACCTCAG 57.257 45.455 0.00 0.00 0.00 3.35
51 52 3.244596 ACCTAAGTCAAAGGTCTGCTTCC 60.245 47.826 0.00 0.00 44.20 3.46
76 77 6.115446 AGCGTATTGGATTCTGATTTCTGAA 58.885 36.000 2.89 2.89 38.01 3.02
107 108 8.919777 ACCTAAATGTTATTATTAGGGAGCAC 57.080 34.615 13.63 0.00 46.49 4.40
119 120 7.827236 TGAACATTCTCGGACCTAAATGTTATT 59.173 33.333 20.00 7.05 46.68 1.40
156 157 2.297315 CACACTCAGTCCAAGTAGCTCA 59.703 50.000 0.00 0.00 0.00 4.26
356 360 1.372004 CATTTGCACGCACCTGGTG 60.372 57.895 22.46 22.46 38.42 4.17
362 366 2.282701 ATCAATCCATTTGCACGCAC 57.717 45.000 0.00 0.00 35.16 5.34
405 409 0.175989 GAAGACCTTCAGTAGCCCCG 59.824 60.000 4.98 0.00 39.31 5.73
445 450 5.651387 AAGATCGACAACTGAGAAGATGA 57.349 39.130 0.00 0.00 0.00 2.92
463 468 3.636764 ACAAGGAAACGCAAAGGAAAGAT 59.363 39.130 0.00 0.00 0.00 2.40
475 480 4.041723 CAGCAAGGTAAAACAAGGAAACG 58.958 43.478 0.00 0.00 0.00 3.60
528 534 4.100653 CCATGCCTCTCTTTGATACTCTGA 59.899 45.833 0.00 0.00 0.00 3.27
545 551 0.322456 TCCAGCTGTGTTACCATGCC 60.322 55.000 13.81 0.00 0.00 4.40
613 619 6.566753 GCATAAGAAACTTTGACAGGAGACAC 60.567 42.308 0.00 0.00 0.00 3.67
749 755 8.822855 TGAAAATACAGCAATATAGGTACAACG 58.177 33.333 0.00 0.00 0.00 4.10
814 835 8.758633 TGGAAGAACGTTTTATTTCAAAAACA 57.241 26.923 0.46 0.00 45.47 2.83
815 836 9.078753 TCTGGAAGAACGTTTTATTTCAAAAAC 57.921 29.630 0.46 2.82 42.31 2.43
860 895 0.980423 AAAGAGACAGAGAGCCCCAC 59.020 55.000 0.00 0.00 0.00 4.61
862 897 2.224646 ACAAAAAGAGACAGAGAGCCCC 60.225 50.000 0.00 0.00 0.00 5.80
863 898 2.810852 CACAAAAAGAGACAGAGAGCCC 59.189 50.000 0.00 0.00 0.00 5.19
865 900 3.249559 CCACACAAAAAGAGACAGAGAGC 59.750 47.826 0.00 0.00 0.00 4.09
868 903 3.545703 ACCCACACAAAAAGAGACAGAG 58.454 45.455 0.00 0.00 0.00 3.35
870 905 2.618709 GGACCCACACAAAAAGAGACAG 59.381 50.000 0.00 0.00 0.00 3.51
871 906 2.650322 GGACCCACACAAAAAGAGACA 58.350 47.619 0.00 0.00 0.00 3.41
872 907 1.954382 GGGACCCACACAAAAAGAGAC 59.046 52.381 5.33 0.00 0.00 3.36
873 908 1.566703 TGGGACCCACACAAAAAGAGA 59.433 47.619 9.95 0.00 0.00 3.10
874 909 2.065899 TGGGACCCACACAAAAAGAG 57.934 50.000 9.95 0.00 0.00 2.85
1015 1056 3.849951 GATGAGCGGGCGGAGGAA 61.850 66.667 0.00 0.00 0.00 3.36
1476 1517 0.179179 GGTCCGTGCTACGTACTGAC 60.179 60.000 0.00 0.00 40.58 3.51
1477 1518 1.638388 CGGTCCGTGCTACGTACTGA 61.638 60.000 2.08 0.00 38.83 3.41
1478 1519 1.226211 CGGTCCGTGCTACGTACTG 60.226 63.158 2.08 4.05 40.58 2.74
1479 1520 3.044059 GCGGTCCGTGCTACGTACT 62.044 63.158 13.94 0.00 40.58 2.73
1789 1830 6.145535 GTCTGTGAGCAAATAAAACTCAAGG 58.854 40.000 0.00 0.00 41.80 3.61
1980 2026 3.262420 CACATGCCACCACTAGTACTTC 58.738 50.000 0.00 0.00 0.00 3.01
2183 2229 7.798982 GTGACTCTGCAATCTTGTTTAAGTAAC 59.201 37.037 0.00 0.00 35.38 2.50
2254 2300 4.157246 TCAAGGCTAGAAGTCAAGGTACA 58.843 43.478 0.00 0.00 0.00 2.90
2796 2842 2.169144 CAGGGAATGGGCTCAAAAATCC 59.831 50.000 0.00 0.00 0.00 3.01
2892 2939 7.861372 CCATCATGAATCTAAGAAATCAGCAAC 59.139 37.037 0.00 0.00 0.00 4.17
3067 3116 7.933033 ACACATACAAAGGAAGCAAAATTCAAT 59.067 29.630 0.00 0.00 0.00 2.57
3376 3426 6.262944 TCACACAATGTTGCTTCTTCATTAGT 59.737 34.615 0.00 0.00 31.76 2.24
3623 3675 1.138247 CAAGAGCAGAAATGCCCGC 59.862 57.895 0.00 0.00 34.90 6.13


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

AutoCloner maintained by Alex Coulton.