Multiple sequence alignment - TraesCS5B01G039000

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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 TraesCS5B01G039000 chr5B 100.000 2551 0 0 1 2551 43978848 43976298 0 4711
1 TraesCS5B01G039000 chr6D 96.748 2552 76 3 1 2551 389245798 389243253 0 4246
2 TraesCS5B01G039000 chr5D 96.748 2552 76 3 1 2551 503245296 503247841 0 4246
3 TraesCS5B01G039000 chr5D 96.630 2552 79 3 1 2551 503264752 503262207 0 4229
4 TraesCS5B01G039000 chr3A 96.748 2552 76 3 1 2551 66005109 66002564 0 4246
5 TraesCS5B01G039000 chr3D 96.669 2552 77 4 1 2551 589263502 589260958 0 4235
6 TraesCS5B01G039000 chr2D 96.591 2552 80 3 1 2551 591984633 591987178 0 4224
7 TraesCS5B01G039000 chr2A 96.591 2552 80 3 1 2551 726906431 726903886 0 4224
8 TraesCS5B01G039000 chr7B 96.395 2552 85 3 1 2551 663099401 663096856 0 4196
9 TraesCS5B01G039000 chr3B 96.317 2552 85 4 1 2551 201539546 201542089 0 4183


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 TraesCS5B01G039000 chr5B 43976298 43978848 2550 True 4711 4711 100.000 1 2551 1 chr5B.!!$R1 2550
1 TraesCS5B01G039000 chr6D 389243253 389245798 2545 True 4246 4246 96.748 1 2551 1 chr6D.!!$R1 2550
2 TraesCS5B01G039000 chr5D 503245296 503247841 2545 False 4246 4246 96.748 1 2551 1 chr5D.!!$F1 2550
3 TraesCS5B01G039000 chr5D 503262207 503264752 2545 True 4229 4229 96.630 1 2551 1 chr5D.!!$R1 2550
4 TraesCS5B01G039000 chr3A 66002564 66005109 2545 True 4246 4246 96.748 1 2551 1 chr3A.!!$R1 2550
5 TraesCS5B01G039000 chr3D 589260958 589263502 2544 True 4235 4235 96.669 1 2551 1 chr3D.!!$R1 2550
6 TraesCS5B01G039000 chr2D 591984633 591987178 2545 False 4224 4224 96.591 1 2551 1 chr2D.!!$F1 2550
7 TraesCS5B01G039000 chr2A 726903886 726906431 2545 True 4224 4224 96.591 1 2551 1 chr2A.!!$R1 2550
8 TraesCS5B01G039000 chr7B 663096856 663099401 2545 True 4196 4196 96.395 1 2551 1 chr7B.!!$R1 2550
9 TraesCS5B01G039000 chr3B 201539546 201542089 2543 False 4183 4183 96.317 1 2551 1 chr3B.!!$F1 2550

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
815 816 0.6112 CACGGACCAACCATAGACCA 59.389 55.0 0.0 0.0 38.9 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1634 1636 0.179 CCGCTTGTATTGCTCTCCCT 59.821 55.0 0.0 0.0 0.0 4.2 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 1.512735 GGCCAGGAGGGTCTCTTAAT 58.487 55.000 0.00 0.00 38.65 1.40
139 140 1.078497 CGGGGAGTTGTATGCTGCA 60.078 57.895 4.13 4.13 0.00 4.41
182 183 6.038714 GCTCCCGAAAATGAGTCTATTGATTT 59.961 38.462 0.00 0.00 0.00 2.17
290 291 5.124617 CCAGGGAAAAGAATAGAAGAAGCAC 59.875 44.000 0.00 0.00 0.00 4.40
293 294 6.215636 AGGGAAAAGAATAGAAGAAGCACCTA 59.784 38.462 0.00 0.00 0.00 3.08
317 318 6.299805 ACTCTTTCATGCATACTCCACTTA 57.700 37.500 0.00 0.00 0.00 2.24
322 323 2.871182 TGCATACTCCACTTAGCTCG 57.129 50.000 0.00 0.00 0.00 5.03
323 324 1.409064 TGCATACTCCACTTAGCTCGG 59.591 52.381 0.00 0.00 0.00 4.63
437 438 6.124340 TGATAGTATCTTGTACCTGAACCGA 58.876 40.000 11.40 0.00 0.00 4.69
508 509 7.168972 CACTGAAAGACTCTACTGAGACAAAAG 59.831 40.741 0.00 0.00 39.08 2.27
528 529 1.970640 GGATGGGCTGTCAAAAAGGTT 59.029 47.619 0.00 0.00 0.00 3.50
533 534 1.269778 GGCTGTCAAAAAGGTTGAGGC 60.270 52.381 0.00 0.00 0.00 4.70
653 654 0.622665 AGAGGATCAAGTTGGCCCTG 59.377 55.000 17.77 0.00 37.82 4.45
815 816 0.611200 CACGGACCAACCATAGACCA 59.389 55.000 0.00 0.00 38.90 4.02
829 830 6.721318 ACCATAGACCATGTTCAATAAGTGT 58.279 36.000 0.00 0.00 32.21 3.55
842 843 6.995511 TCAATAAGTGTAACACATTAGCCC 57.004 37.500 0.00 0.00 41.43 5.19
870 871 1.674322 CGGTTGGGCAGTAAGGGTG 60.674 63.158 0.00 0.00 0.00 4.61
1025 1026 4.079253 GGATTCCAACTCAGCACCTTTTA 58.921 43.478 0.00 0.00 0.00 1.52
1030 1031 6.084326 TCCAACTCAGCACCTTTTATTTTC 57.916 37.500 0.00 0.00 0.00 2.29
1086 1087 7.064609 GCACAGTATGATGAAAGTTGTAAGCTA 59.935 37.037 0.00 0.00 39.69 3.32
1094 1095 4.693566 TGAAAGTTGTAAGCTATGTTCGGG 59.306 41.667 0.00 0.00 0.00 5.14
1095 1096 3.261981 AGTTGTAAGCTATGTTCGGGG 57.738 47.619 0.00 0.00 0.00 5.73
1096 1097 2.093128 AGTTGTAAGCTATGTTCGGGGG 60.093 50.000 0.00 0.00 0.00 5.40
1097 1098 1.868713 TGTAAGCTATGTTCGGGGGA 58.131 50.000 0.00 0.00 0.00 4.81
1186 1187 0.691078 ACCCTATGGCGGATGTCAGT 60.691 55.000 0.00 0.00 29.87 3.41
1188 1189 0.752658 CCTATGGCGGATGTCAGTGA 59.247 55.000 0.00 0.00 29.87 3.41
1275 1276 2.566952 CCAATTCGGCAGTTCAATCC 57.433 50.000 0.00 0.00 0.00 3.01
1335 1336 5.071788 CCATTTAGTAGCACCTTAGGATGGA 59.928 44.000 4.77 0.00 33.81 3.41
1539 1540 1.629043 AGAGACAACCTGGCGAACTA 58.371 50.000 0.00 0.00 0.00 2.24
1576 1578 4.202151 GCCAGAGGAAAAGAAAGAAAAGCA 60.202 41.667 0.00 0.00 0.00 3.91
1581 1583 7.924947 CAGAGGAAAAGAAAGAAAAGCAATTCT 59.075 33.333 0.00 0.00 41.34 2.40
1626 1628 2.488153 GAGCAGCCTAAACCGTGAAAAT 59.512 45.455 0.00 0.00 0.00 1.82
1634 1636 2.074729 AACCGTGAAAATGGGGTTGA 57.925 45.000 0.00 0.00 41.04 3.18
1653 1655 0.179000 AGGGAGAGCAATACAAGCGG 59.821 55.000 0.00 0.00 37.01 5.52
1767 1769 4.041762 GGGGCACGTGGAATCCCA 62.042 66.667 24.73 0.00 40.53 4.37
1858 1860 2.518407 AGGGAAAGGTGAAAAGAACCCT 59.482 45.455 0.00 0.00 41.17 4.34
1926 1928 2.045885 AGTGGGAGGGGAAAGTGATCTA 59.954 50.000 0.00 0.00 0.00 1.98
1954 1956 2.549754 CGTGCCTGTTGAAGAATGAGTT 59.450 45.455 0.00 0.00 0.00 3.01
1989 1991 1.497286 AGTGGCTTGGTTAAGGGAACA 59.503 47.619 0.00 0.00 40.09 3.18
2031 2033 3.737047 CGAAAGCGAGTCTTAATAGGGCA 60.737 47.826 0.00 0.00 40.82 5.36
2077 2079 3.246301 CCTGGGTGATCTATCCATGACT 58.754 50.000 0.00 0.00 0.00 3.41
2125 2127 1.810030 GGTCCGAACCGACTGATGC 60.810 63.158 0.00 0.00 35.36 3.91
2171 2173 1.367346 TAGGGGTGAAATGCCACTCA 58.633 50.000 0.00 0.00 39.36 3.41
2186 2188 1.002430 CACTCAAACCCAGAGCTAGCA 59.998 52.381 18.83 0.00 36.58 3.49
2195 2197 1.189752 CAGAGCTAGCAGGTTCTCCA 58.810 55.000 18.83 0.00 35.89 3.86
2252 2254 6.157994 ACATCTAGGGGTAAAGCACTATTTCA 59.842 38.462 0.00 0.00 0.00 2.69
2336 2338 4.760047 CAGGGGTCAAGGTCGGCG 62.760 72.222 0.00 0.00 0.00 6.46
2365 2367 2.038952 CGATGGGGGATAAGCTTCATCA 59.961 50.000 18.34 6.04 32.88 3.07
2380 2382 4.507710 CTTCATCATCGAGAGGGAAACAA 58.492 43.478 0.00 0.00 0.00 2.83
2383 2385 1.974957 TCATCGAGAGGGAAACAACCA 59.025 47.619 0.00 0.00 0.00 3.67
2386 2388 0.396811 CGAGAGGGAAACAACCAGGT 59.603 55.000 0.00 0.00 0.00 4.00
2393 2395 2.104170 GGAAACAACCAGGTTCACCAA 58.896 47.619 0.12 0.00 46.07 3.67
2446 2448 2.600470 GGTGGGGGTGCAAAGACC 60.600 66.667 0.00 0.00 34.96 3.85
2472 2474 0.674895 AGGTTTGCCTAGAAGCAGCG 60.675 55.000 0.00 0.00 44.90 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.105760 TGGGCAGAAAAAGGAAGGCA 60.106 50.000 0.00 0.00 0.00 4.75
139 140 1.417890 AGCGATTCATCCTTCCCGAAT 59.582 47.619 0.00 0.00 32.15 3.34
168 169 7.340232 CCAATTGGGAGAAAATCAATAGACTCA 59.660 37.037 17.36 0.00 40.01 3.41
290 291 5.525378 GTGGAGTATGCATGAAAGAGTTAGG 59.475 44.000 10.16 0.00 39.99 2.69
293 294 5.171339 AGTGGAGTATGCATGAAAGAGTT 57.829 39.130 10.16 0.00 39.99 3.01
437 438 6.378280 CCCATTACTTAGAAAAAGTGAGCCAT 59.622 38.462 0.74 0.00 0.00 4.40
508 509 1.632589 ACCTTTTTGACAGCCCATCC 58.367 50.000 0.00 0.00 0.00 3.51
528 529 3.161450 GCCCATCCTACCGCCTCA 61.161 66.667 0.00 0.00 0.00 3.86
533 534 1.153168 CCAACTGCCCATCCTACCG 60.153 63.158 0.00 0.00 0.00 4.02
570 571 4.023107 CGACTCCAACTATCGTCCATGTAT 60.023 45.833 0.00 0.00 0.00 2.29
629 630 1.283321 GCCAACTTGATCCTCTTCCCT 59.717 52.381 0.00 0.00 0.00 4.20
653 654 4.752101 AGATAGTGCATCAAGTTATTCGCC 59.248 41.667 0.00 0.00 35.96 5.54
804 805 7.175104 ACACTTATTGAACATGGTCTATGGTT 58.825 34.615 16.66 0.00 36.66 3.67
815 816 8.458843 GGCTAATGTGTTACACTTATTGAACAT 58.541 33.333 16.79 0.00 34.54 2.71
829 830 3.772619 GCGGAGGGCTAATGTGTTA 57.227 52.632 0.00 0.00 39.11 2.41
842 843 4.148825 CCCAACCGGAGAGCGGAG 62.149 72.222 9.46 0.00 0.00 4.63
870 871 0.462759 CGAGTGATTGCCCTTCTCCC 60.463 60.000 0.00 0.00 0.00 4.30
1025 1026 7.949434 AGCAACTCTTCTCAAAATCTGAAAAT 58.051 30.769 0.00 0.00 32.17 1.82
1030 1031 6.557291 AAGAGCAACTCTTCTCAAAATCTG 57.443 37.500 4.02 0.00 46.42 2.90
1086 1087 4.033251 TCCCCCTCCCCCGAACAT 62.033 66.667 0.00 0.00 0.00 2.71
1094 1095 1.894699 AGACAATAACTCCCCCTCCC 58.105 55.000 0.00 0.00 0.00 4.30
1095 1096 3.258622 CGATAGACAATAACTCCCCCTCC 59.741 52.174 0.00 0.00 39.76 4.30
1096 1097 3.896272 ACGATAGACAATAACTCCCCCTC 59.104 47.826 0.00 0.00 41.38 4.30
1097 1098 3.924922 ACGATAGACAATAACTCCCCCT 58.075 45.455 0.00 0.00 41.38 4.79
1172 1173 1.807755 CGAATCACTGACATCCGCCAT 60.808 52.381 0.00 0.00 0.00 4.40
1186 1187 2.293677 GGAGATAAGCGGACTCGAATCA 59.706 50.000 0.00 0.00 39.00 2.57
1188 1189 2.294791 CTGGAGATAAGCGGACTCGAAT 59.705 50.000 0.00 0.00 39.00 3.34
1335 1336 4.444536 TCGCCATTAACGTTAAGGCTATT 58.555 39.130 33.67 16.91 43.07 1.73
1539 1540 6.374417 TTCCTCTGGCTACTAAGATGTTTT 57.626 37.500 0.00 0.00 0.00 2.43
1576 1578 1.019673 TCGCCGCTACTACGAGAATT 58.980 50.000 0.00 0.00 34.06 2.17
1581 1583 0.460811 TTCTCTCGCCGCTACTACGA 60.461 55.000 0.00 0.00 34.06 3.43
1597 1599 2.621668 GGTTTAGGCTGCTCCCATTTCT 60.622 50.000 0.00 0.00 34.51 2.52
1626 1628 0.846427 ATTGCTCTCCCTCAACCCCA 60.846 55.000 0.00 0.00 0.00 4.96
1634 1636 0.179000 CCGCTTGTATTGCTCTCCCT 59.821 55.000 0.00 0.00 0.00 4.20
1653 1655 2.744768 GCTTCGCCTAGCAGCACAC 61.745 63.158 0.00 0.00 40.89 3.82
1767 1769 2.440409 GTGGTCCTTGCTGATTCACAT 58.560 47.619 0.00 0.00 0.00 3.21
1858 1860 3.449737 CGTTCTATTTCCCTACCCACTGA 59.550 47.826 0.00 0.00 0.00 3.41
1869 1871 3.666111 GCACGGTTTCACGTTCTATTTCC 60.666 47.826 0.00 0.00 46.25 3.13
1926 1928 3.049674 CAACAGGCACGCGGTCAT 61.050 61.111 12.47 0.00 0.00 3.06
1954 1956 1.399714 CCACTACCTATGAGTCGCCA 58.600 55.000 0.00 0.00 0.00 5.69
1968 1970 2.712087 TGTTCCCTTAACCAAGCCACTA 59.288 45.455 0.00 0.00 37.27 2.74
1989 1991 3.892104 TACGGCTCCGGTGGGTTCT 62.892 63.158 13.31 0.00 44.69 3.01
2031 2033 3.356290 GGGTCCATAAGCAGTGACAATT 58.644 45.455 0.00 0.00 0.00 2.32
2077 2079 5.441718 AGTTTCATCCAAGCTTCATCCTA 57.558 39.130 0.00 0.00 0.00 2.94
2171 2173 1.003696 GAACCTGCTAGCTCTGGGTTT 59.996 52.381 24.20 13.27 39.92 3.27
2186 2188 2.840974 CGCATTTCGTGGAGAACCT 58.159 52.632 0.00 0.00 38.83 3.50
2216 2218 3.012502 ACCCCTAGATGTCCAGTCAACTA 59.987 47.826 0.00 0.00 0.00 2.24
2271 2273 3.941483 CAGAGTTTGCCTCGATTTGGTAT 59.059 43.478 0.00 0.00 45.44 2.73
2336 2338 1.996798 TATCCCCCATCGTCTCACTC 58.003 55.000 0.00 0.00 0.00 3.51
2365 2367 1.279271 CCTGGTTGTTTCCCTCTCGAT 59.721 52.381 0.00 0.00 0.00 3.59
2380 2382 1.202891 GCCTTAGTTGGTGAACCTGGT 60.203 52.381 0.00 0.00 36.82 4.00
2383 2385 0.404426 GGGCCTTAGTTGGTGAACCT 59.596 55.000 0.84 0.00 36.82 3.50
2386 2388 2.047769 TAGGGGCCTTAGTTGGTGAA 57.952 50.000 0.84 0.00 0.00 3.18
2393 2395 1.489230 CGGTCATTTAGGGGCCTTAGT 59.511 52.381 0.84 0.00 0.00 2.24
2446 2448 1.450312 CTAGGCAAACCTCCTGGCG 60.450 63.158 0.00 0.00 46.34 5.69
2472 2474 5.006455 GCTATTACGCACTCTTTAAAGGGTC 59.994 44.000 18.05 11.67 37.74 4.46


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

AutoCloner maintained by Alex Coulton.