Multiple sequence alignment - TraesCS6D01G138500

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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 TraesCS6D01G138500 chr6D 100.000 3014 0 0 1 3014 107385644 107388657 0.000000e+00 5566
1 TraesCS6D01G138500 chr6D 84.860 1354 182 14 639 1980 106704626 106703284 0.000000e+00 1343
2 TraesCS6D01G138500 chr6B 95.116 3051 97 14 1 3014 194859721 194862756 0.000000e+00 4761
3 TraesCS6D01G138500 chr6B 85.022 1342 172 20 650 1976 194425500 194424173 0.000000e+00 1338
4 TraesCS6D01G138500 chr6B 87.805 246 30 0 195 440 194425990 194425745 3.800000e-74 289
5 TraesCS6D01G138500 chr6A 94.334 2965 101 19 1 2929 131228629 131231562 0.000000e+00 4482
6 TraesCS6D01G138500 chr6A 82.247 1825 257 30 196 1976 129940059 129938258 0.000000e+00 1513
7 TraesCS6D01G138500 chr7D 77.944 1206 220 35 793 1979 600449182 600450360 0.000000e+00 712
8 TraesCS6D01G138500 chr7D 77.427 1205 225 35 793 1979 599809598 599808423 0.000000e+00 675
9 TraesCS6D01G138500 chr7D 81.313 594 103 8 2258 2847 599722559 599721970 2.720000e-130 475
10 TraesCS6D01G138500 chr7B 77.140 1203 228 35 793 1977 679672633 679671460 0.000000e+00 654
11 TraesCS6D01G138500 chr7B 78.697 568 102 15 1421 1976 679793153 679793713 7.940000e-96 361
12 TraesCS6D01G138500 chr7A 77.264 497 98 13 793 1282 692049123 692048635 8.230000e-71 278


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 TraesCS6D01G138500 chr6D 107385644 107388657 3013 False 5566.0 5566 100.0000 1 3014 1 chr6D.!!$F1 3013
1 TraesCS6D01G138500 chr6D 106703284 106704626 1342 True 1343.0 1343 84.8600 639 1980 1 chr6D.!!$R1 1341
2 TraesCS6D01G138500 chr6B 194859721 194862756 3035 False 4761.0 4761 95.1160 1 3014 1 chr6B.!!$F1 3013
3 TraesCS6D01G138500 chr6B 194424173 194425990 1817 True 813.5 1338 86.4135 195 1976 2 chr6B.!!$R1 1781
4 TraesCS6D01G138500 chr6A 131228629 131231562 2933 False 4482.0 4482 94.3340 1 2929 1 chr6A.!!$F1 2928
5 TraesCS6D01G138500 chr6A 129938258 129940059 1801 True 1513.0 1513 82.2470 196 1976 1 chr6A.!!$R1 1780
6 TraesCS6D01G138500 chr7D 600449182 600450360 1178 False 712.0 712 77.9440 793 1979 1 chr7D.!!$F1 1186
7 TraesCS6D01G138500 chr7D 599808423 599809598 1175 True 675.0 675 77.4270 793 1979 1 chr7D.!!$R2 1186
8 TraesCS6D01G138500 chr7D 599721970 599722559 589 True 475.0 475 81.3130 2258 2847 1 chr7D.!!$R1 589
9 TraesCS6D01G138500 chr7B 679671460 679672633 1173 True 654.0 654 77.1400 793 1977 1 chr7B.!!$R1 1184
10 TraesCS6D01G138500 chr7B 679793153 679793713 560 False 361.0 361 78.6970 1421 1976 1 chr7B.!!$F1 555

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
22 23 0.546122 ATATTTCCGAGCCTGCACCA 59.454 50.000 0.00 0.0 0.00 4.17 F
536 566 1.484444 AAGCAGAAAGGAGGACGGCT 61.484 55.000 0.00 0.0 36.74 5.52 F
1381 1430 2.195567 GGCAAGCTCACCAACTGCA 61.196 57.895 6.63 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1204 1253 0.675083 TTGACGTCGGCAAGGTAAGA 59.325 50.000 10.09 0.0 0.00 2.10 R
1734 1783 1.618837 CTTCCGAGAACTTCCTCACCA 59.381 52.381 0.00 0.0 32.86 4.17 R
2880 2934 2.671619 GTTTGCGTGCAGGGCCTA 60.672 61.111 5.28 0.0 0.00 3.93 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
22 23 0.546122 ATATTTCCGAGCCTGCACCA 59.454 50.000 0.00 0.0 0.00 4.17
40 41 2.360801 ACCATTTCCGGTTCAAACTGTG 59.639 45.455 0.00 0.0 34.91 3.66
53 54 2.116983 AACTGTGCTGGCCTCGATGT 62.117 55.000 3.32 0.0 0.00 3.06
536 566 1.484444 AAGCAGAAAGGAGGACGGCT 61.484 55.000 0.00 0.0 36.74 5.52
887 932 2.330372 CGACGTCCGGGAACTCTCA 61.330 63.158 10.58 0.0 33.91 3.27
911 956 4.980805 GCGAAGTGGTGCCCGTCA 62.981 66.667 0.00 0.0 0.00 4.35
1381 1430 2.195567 GGCAAGCTCACCAACTGCA 61.196 57.895 6.63 0.0 0.00 4.41
1734 1783 1.380524 CGTGGGAGACAGACTACGAT 58.619 55.000 0.00 0.0 33.78 3.73
2056 2110 4.058124 GGCGCAATCTCATCAACTGTATA 58.942 43.478 10.83 0.0 0.00 1.47
2057 2111 4.692625 GGCGCAATCTCATCAACTGTATAT 59.307 41.667 10.83 0.0 0.00 0.86
2177 2231 3.940852 CCAATGATTCTCGAATGACACCA 59.059 43.478 0.00 0.0 0.00 4.17
2215 2269 1.455383 AAGTTCCAACAAGCCGCCTG 61.455 55.000 0.00 0.0 0.00 4.85
2216 2270 3.294493 TTCCAACAAGCCGCCTGC 61.294 61.111 0.00 0.0 41.71 4.85
2268 2322 2.035155 TTCTCCCGCCAGTCGAGA 59.965 61.111 0.00 0.0 41.67 4.04
2409 2463 2.992689 TAGAACCAGGCGCCGACA 60.993 61.111 23.20 0.0 0.00 4.35
2934 2989 1.153597 CGCGCTCTAATCATGTGCCA 61.154 55.000 5.56 0.0 34.16 4.92
2963 3018 6.519761 CGATAACTGCAAACATAACAGTGAAC 59.480 38.462 0.00 0.0 43.63 3.18
2998 3053 4.811555 TGGCATGTAAAACTATCGCATC 57.188 40.909 0.00 0.0 0.00 3.91
3000 3055 4.511454 TGGCATGTAAAACTATCGCATCTC 59.489 41.667 0.00 0.0 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.034558 CAGCACAGTTTGAACCGGAAAT 59.965 45.455 9.46 0.00 0.00 2.17
40 41 1.520342 GTCAGACATCGAGGCCAGC 60.520 63.158 5.01 0.00 0.00 4.85
53 54 2.338015 GGTAGTCCGCGGTGTCAGA 61.338 63.158 27.15 0.06 0.00 3.27
97 98 1.950630 CGTGATCATCGCGGCATGA 60.951 57.895 13.00 12.26 45.61 3.07
256 257 0.387929 ACACGCGGAAGAAGAAGTCA 59.612 50.000 12.47 0.00 0.00 3.41
692 737 3.827898 GAGAGCTCCCGGTCGTGG 61.828 72.222 10.93 0.00 42.35 4.94
811 856 1.659794 GCAAACAGATTGGCCGTGT 59.340 52.632 0.00 0.00 39.54 4.49
881 926 3.329688 CTTCGCCGCGAGTGAGAGT 62.330 63.158 16.14 0.00 37.14 3.24
911 956 4.919653 TCGTACGACGAGCCTAGT 57.080 55.556 15.28 0.00 46.73 2.57
1204 1253 0.675083 TTGACGTCGGCAAGGTAAGA 59.325 50.000 10.09 0.00 0.00 2.10
1734 1783 1.618837 CTTCCGAGAACTTCCTCACCA 59.381 52.381 0.00 0.00 32.86 4.17
1932 1986 3.702529 TACTCCGGGCCGACGATGA 62.703 63.158 30.79 14.87 35.47 2.92
2016 2070 2.413502 CGCCGCTTTTTAGTGCATACAA 60.414 45.455 0.00 0.00 0.00 2.41
2069 2123 4.338964 TGAACTTGTGATTTGACATGCAGT 59.661 37.500 0.00 0.00 0.00 4.40
2070 2124 4.678287 GTGAACTTGTGATTTGACATGCAG 59.322 41.667 0.00 0.00 0.00 4.41
2071 2125 4.097589 TGTGAACTTGTGATTTGACATGCA 59.902 37.500 0.00 0.00 0.00 3.96
2072 2126 4.442073 GTGTGAACTTGTGATTTGACATGC 59.558 41.667 0.00 0.00 0.00 4.06
2073 2127 4.671964 CGTGTGAACTTGTGATTTGACATG 59.328 41.667 0.00 0.00 0.00 3.21
2880 2934 2.671619 GTTTGCGTGCAGGGCCTA 60.672 61.111 5.28 0.00 0.00 3.93
2934 2989 6.007936 TGTTATGTTTGCAGTTATCGCTTT 57.992 33.333 0.00 0.00 0.00 3.51
2963 3018 7.712264 TTTACATGCCAAACAGAGATTTTTG 57.288 32.000 0.00 0.00 33.30 2.44


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

AutoCloner maintained by Alex Coulton.