Multiple sequence alignment - TraesCS2A01G141700

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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 TraesCS2A01G141700 chr2A 100.000 2636 0 0 1 2636 86989722 86987087 0.000000e+00 4868
1 TraesCS2A01G141700 chr2D 91.176 1904 84 27 1 1820 86718068 86716165 0.000000e+00 2508
2 TraesCS2A01G141700 chr2D 90.909 99 8 1 2538 2636 86715615 86715518 5.920000e-27 132
3 TraesCS2A01G141700 chr2B 92.483 1663 84 10 224 1854 139571327 139569674 0.000000e+00 2340
4 TraesCS2A01G141700 chr2B 89.405 840 59 18 1800 2636 139569697 139568885 0.000000e+00 1031


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 TraesCS2A01G141700 chr2A 86987087 86989722 2635 True 4868.0 4868 100.0000 1 2636 1 chr2A.!!$R1 2635
1 TraesCS2A01G141700 chr2D 86715518 86718068 2550 True 1320.0 2508 91.0425 1 2636 2 chr2D.!!$R1 2635
2 TraesCS2A01G141700 chr2B 139568885 139571327 2442 True 1685.5 2340 90.9440 224 2636 2 chr2B.!!$R1 2412

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
45 52 0.106318 AGCTTGATGCCCATCCTTCC 60.106 55.0 5.86 0.0 44.23 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1757 1.210545 ATATGTACGCCCGCGAAACG 61.211 55.0 17.16 11.07 42.83 3.6 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
45 52 0.106318 AGCTTGATGCCCATCCTTCC 60.106 55.000 5.86 0.00 44.23 3.46
94 108 3.149196 CACAGTTTACCAGCAACCTCAT 58.851 45.455 0.00 0.00 0.00 2.90
102 116 1.026182 CAGCAACCTCATAGCGGCAA 61.026 55.000 1.45 0.00 0.00 4.52
129 143 0.732571 TTCATTCATCGAAAGCCGGC 59.267 50.000 21.89 21.89 39.14 6.13
133 147 3.508840 CATCGAAAGCCGGCCACC 61.509 66.667 26.15 11.38 39.14 4.61
149 163 2.677902 GCCACCGAAGAGATCATTGTCA 60.678 50.000 0.00 0.00 0.00 3.58
151 165 3.368843 CCACCGAAGAGATCATTGTCACT 60.369 47.826 0.00 0.00 0.00 3.41
179 218 1.964223 GATGCTCCCGTCCTCATTAGA 59.036 52.381 0.00 0.00 0.00 2.10
187 226 2.493713 GTCCTCATTAGACGCGTCAT 57.506 50.000 37.85 25.11 0.00 3.06
191 230 0.529773 TCATTAGACGCGTCATGGCC 60.530 55.000 37.85 13.73 0.00 5.36
205 244 4.205587 GTCATGGCCTCTGAAATCTCATT 58.794 43.478 3.32 0.00 0.00 2.57
461 509 4.213694 CAGTAGGCTAGTACGTATCCACTG 59.786 50.000 0.60 10.10 0.00 3.66
530 589 2.784380 GTCACGATCGCATTGTAGTCTC 59.216 50.000 16.60 0.00 0.00 3.36
745 804 2.125912 GACGCATCGCTGTCAGGT 60.126 61.111 1.14 0.00 34.30 4.00
765 824 8.553696 GTCAGGTTCTTAGAAAAATTTCGTACA 58.446 33.333 0.00 0.00 41.92 2.90
801 860 5.355350 CGGCTGGAGGAATTTAATATCATCC 59.645 44.000 12.38 12.38 44.65 3.51
816 875 0.609151 CATCCTGCAAATGTGGGCAA 59.391 50.000 0.00 0.00 39.93 4.52
835 894 4.295051 GCAACATGTACGTCAATTTGGTT 58.705 39.130 0.00 0.00 0.00 3.67
882 941 6.212791 ACCAAGACAAGCTACCACTATTTCTA 59.787 38.462 0.00 0.00 0.00 2.10
885 944 5.007385 ACAAGCTACCACTATTTCTACCG 57.993 43.478 0.00 0.00 0.00 4.02
905 964 2.159142 CGGAGTAAGCAACCGGATTAGT 60.159 50.000 9.46 4.49 42.48 2.24
1242 1307 3.184683 GTGCTCTGCGCCTTCTCG 61.185 66.667 4.18 0.00 38.05 4.04
1373 1438 3.391382 CGGGGCGAGGGACTTCTT 61.391 66.667 0.00 0.00 41.55 2.52
1521 1586 2.821366 CAGGTGGTCATGGCGCTC 60.821 66.667 7.64 0.00 0.00 5.03
1692 1757 0.729140 GCCGTGTGCTATGTGTTTGC 60.729 55.000 0.00 0.00 36.87 3.68
1697 1762 2.719046 GTGTGCTATGTGTTTGCGTTTC 59.281 45.455 0.00 0.00 0.00 2.78
1739 1831 2.787601 AGTCGAGTTTTCTGTGCGTA 57.212 45.000 0.00 0.00 0.00 4.42
1868 2001 6.843752 TCAATTCTGTACCCTTTTCTTGGTA 58.156 36.000 0.00 0.00 36.04 3.25
1957 2090 5.830000 AAACAGTAACCAGGAAAGACAAC 57.170 39.130 0.00 0.00 0.00 3.32
1974 2113 5.120399 AGACAACAGGACACAAAACGATAA 58.880 37.500 0.00 0.00 0.00 1.75
1976 2115 4.219033 CAACAGGACACAAAACGATAAGC 58.781 43.478 0.00 0.00 0.00 3.09
2055 2201 2.134346 GCCGAAGCTTGAAAATTGCAA 58.866 42.857 2.10 0.00 35.50 4.08
2059 2205 4.090930 CCGAAGCTTGAAAATTGCAATGAG 59.909 41.667 13.82 7.54 0.00 2.90
2060 2206 4.433805 CGAAGCTTGAAAATTGCAATGAGC 60.434 41.667 13.82 16.08 45.96 4.26
2061 2207 3.332034 AGCTTGAAAATTGCAATGAGCC 58.668 40.909 13.82 3.73 44.83 4.70
2062 2208 2.093152 GCTTGAAAATTGCAATGAGCCG 59.907 45.455 13.82 1.86 44.83 5.52
2066 2216 1.255882 AAATTGCAATGAGCCGACCA 58.744 45.000 13.82 0.00 44.83 4.02
2092 2242 0.389025 AAAGCCCGCAAACTTCCTTG 59.611 50.000 0.00 0.00 0.00 3.61
2144 2294 6.484288 TGAAGAAAGAATCCCATTGCTAGAA 58.516 36.000 0.00 0.00 0.00 2.10
2191 2341 8.830201 TTACATGTCATTTCCTTTCAAAATGG 57.170 30.769 0.00 0.00 42.01 3.16
2506 2659 8.789881 TTTGACACACTAAATGTTTAAATCCG 57.210 30.769 0.00 0.00 40.64 4.18
2597 2785 0.737219 GTCATTGCTGCCACCATCTC 59.263 55.000 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.730064 GCTTTGAAGCCGTACATCGAA 59.270 47.619 4.38 0.00 46.20 3.71
30 31 2.192979 GCGGAAGGATGGGCATCA 59.807 61.111 0.00 0.00 39.54 3.07
32 33 3.419580 TGGCGGAAGGATGGGCAT 61.420 61.111 0.00 0.00 0.00 4.40
45 52 2.973899 ACTGGCTAGTGAGTGGCG 59.026 61.111 0.13 0.00 35.34 5.69
74 81 3.508845 ATGAGGTTGCTGGTAAACTGT 57.491 42.857 0.00 0.00 0.00 3.55
94 108 0.902984 TGAAGGGAGACTTGCCGCTA 60.903 55.000 0.00 0.00 40.21 4.26
102 116 4.764172 CTTTCGATGAATGAAGGGAGACT 58.236 43.478 0.00 0.00 0.00 3.24
129 143 2.932614 GTGACAATGATCTCTTCGGTGG 59.067 50.000 0.00 0.00 0.00 4.61
133 147 3.193263 CCCAGTGACAATGATCTCTTCG 58.807 50.000 4.07 0.00 0.00 3.79
179 218 2.449031 TTTCAGAGGCCATGACGCGT 62.449 55.000 13.85 13.85 0.00 6.01
182 221 2.208431 GAGATTTCAGAGGCCATGACG 58.792 52.381 5.01 0.00 0.00 4.35
187 226 3.009363 TGACAATGAGATTTCAGAGGCCA 59.991 43.478 5.01 0.00 36.61 5.36
191 230 7.546358 AGTAGAGTGACAATGAGATTTCAGAG 58.454 38.462 0.00 0.00 36.61 3.35
205 244 7.231519 CCCATGTATCAGATAAGTAGAGTGACA 59.768 40.741 0.00 0.00 0.00 3.58
461 509 5.915758 CGTAGGATGCAAGTGTATTCTACTC 59.084 44.000 19.52 2.35 43.09 2.59
518 577 3.601443 ACTGGTGAGAGACTACAATGC 57.399 47.619 0.00 0.00 0.00 3.56
530 589 2.544686 CCTATCGTCTCGTACTGGTGAG 59.455 54.545 0.00 0.00 0.00 3.51
765 824 1.069765 CCAGCCGCGAAGTCCATAT 59.930 57.895 8.23 0.00 0.00 1.78
801 860 1.270412 ACATGTTGCCCACATTTGCAG 60.270 47.619 0.00 0.00 44.40 4.41
816 875 7.820386 TGATAGTAACCAAATTGACGTACATGT 59.180 33.333 2.69 2.69 0.00 3.21
824 883 7.312154 TGCAATGTGATAGTAACCAAATTGAC 58.688 34.615 16.76 11.18 39.27 3.18
835 894 8.341892 TGGTTGTAAATTGCAATGTGATAGTA 57.658 30.769 13.82 0.00 0.00 1.82
885 944 3.538634 ACTAATCCGGTTGCTTACTCC 57.461 47.619 0.00 0.00 0.00 3.85
905 964 2.925966 AATCCATGGGAGCTTGGAAA 57.074 45.000 13.02 0.00 44.83 3.13
1119 1184 4.702081 GTCGACGTCGGCAGCAGT 62.702 66.667 35.32 0.00 44.43 4.40
1194 1259 2.597510 GTGACCACCCTGTTGGCC 60.598 66.667 0.00 0.00 40.77 5.36
1563 1628 4.033776 TGGCGCTTGGAGGGGAAG 62.034 66.667 7.64 0.00 0.00 3.46
1692 1757 1.210545 ATATGTACGCCCGCGAAACG 61.211 55.000 17.16 11.07 42.83 3.60
1731 1823 1.565156 AACGGCACATGTACGCACAG 61.565 55.000 18.56 8.41 38.30 3.66
1930 2063 6.126710 TGTCTTTCCTGGTTACTGTTTTCCTA 60.127 38.462 0.00 0.00 0.00 2.94
1957 2090 4.481930 TTGCTTATCGTTTTGTGTCCTG 57.518 40.909 0.00 0.00 0.00 3.86
2006 2152 9.887406 ACGACGTACAATCAAAAGAAAAATATT 57.113 25.926 0.00 0.00 0.00 1.28
2009 2155 7.528182 CGTACGACGTACAATCAAAAGAAAAAT 59.472 33.333 31.17 0.00 38.77 1.82
2012 2158 5.610124 GCGTACGACGTACAATCAAAAGAAA 60.610 40.000 31.17 0.00 44.73 2.52
2036 2182 3.989167 TCATTGCAATTTTCAAGCTTCGG 59.011 39.130 9.83 0.00 0.00 4.30
2041 2187 2.093152 CGGCTCATTGCAATTTTCAAGC 59.907 45.455 9.83 12.90 45.15 4.01
2055 2201 3.545703 CTTTTCCTTATGGTCGGCTCAT 58.454 45.455 0.00 0.00 34.23 2.90
2059 2205 0.738975 GGCTTTTCCTTATGGTCGGC 59.261 55.000 0.00 0.00 34.23 5.54
2060 2206 1.389555 GGGCTTTTCCTTATGGTCGG 58.610 55.000 0.00 0.00 34.39 4.79
2061 2207 1.014352 CGGGCTTTTCCTTATGGTCG 58.986 55.000 0.00 0.00 34.39 4.79
2062 2208 0.738975 GCGGGCTTTTCCTTATGGTC 59.261 55.000 0.00 0.00 34.39 4.02
2066 2216 2.525368 AGTTTGCGGGCTTTTCCTTAT 58.475 42.857 0.00 0.00 34.39 1.73
2092 2242 6.903883 TCGGTCTTCAAAGCTTAATATGTC 57.096 37.500 0.00 0.00 0.00 3.06
2168 2318 7.065120 TCCATTTTGAAAGGAAATGACATGT 57.935 32.000 0.00 0.00 43.71 3.21
2231 2381 9.915629 GAAGTAGAAGAGTTCTTTTCATCACTA 57.084 33.333 6.01 0.00 41.14 2.74
2356 2509 3.128068 TGCAAGATAGCAAGCATGAACTG 59.872 43.478 0.00 0.00 42.46 3.16
2376 2529 6.265649 TCTCCAACCTTCTATGATAGTACTGC 59.734 42.308 5.39 0.00 0.00 4.40
2473 2626 5.243730 ACATTTAGTGTGTCAAATCAAGGGG 59.756 40.000 0.00 0.00 40.28 4.79
2505 2658 8.499162 AGATGTCAGATTTGTTAGTTTTCTTCG 58.501 33.333 0.00 0.00 0.00 3.79
2517 2670 3.769844 ACGAGGGTAGATGTCAGATTTGT 59.230 43.478 0.00 0.00 0.00 2.83
2605 2793 0.601558 TTTCTCTAGCCGTCTTGCGT 59.398 50.000 0.00 0.00 39.32 5.24


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

AutoCloner maintained by Alex Coulton.