Multiple sequence alignment - TraesCS1A01G001100

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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 TraesCS1A01G001100 chr1A 100.000 2297 0 0 1 2297 280247 277951 0 4242
1 TraesCS1A01G001100 chrUn 97.426 2292 58 1 3 2294 291535442 291537732 0 3904
2 TraesCS1A01G001100 chrUn 97.251 2292 61 2 3 2294 245706070 245708359 0 3882
3 TraesCS1A01G001100 chrUn 97.209 2293 62 2 3 2294 274341280 274338989 0 3879
4 TraesCS1A01G001100 chrUn 97.208 2292 63 1 3 2294 199874826 199877116 0 3877
5 TraesCS1A01G001100 chrUn 97.208 2292 63 1 3 2294 229310225 229307935 0 3877
6 TraesCS1A01G001100 chrUn 97.077 2292 66 1 3 2294 3845812 3843522 0 3860
7 TraesCS1A01G001100 chr1B 97.208 2292 61 2 3 2294 544593699 544595987 0 3875
8 TraesCS1A01G001100 chr1B 97.120 2292 65 1 3 2294 544623638 544625928 0 3866
9 TraesCS1A01G001100 chr5D 97.120 2292 65 1 3 2294 18998926 19001216 0 3866


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 TraesCS1A01G001100 chr1A 277951 280247 2296 True 4242 4242 100.000 1 2297 1 chr1A.!!$R1 2296
1 TraesCS1A01G001100 chrUn 291535442 291537732 2290 False 3904 3904 97.426 3 2294 1 chrUn.!!$F3 2291
2 TraesCS1A01G001100 chrUn 245706070 245708359 2289 False 3882 3882 97.251 3 2294 1 chrUn.!!$F2 2291
3 TraesCS1A01G001100 chrUn 274338989 274341280 2291 True 3879 3879 97.209 3 2294 1 chrUn.!!$R3 2291
4 TraesCS1A01G001100 chrUn 199874826 199877116 2290 False 3877 3877 97.208 3 2294 1 chrUn.!!$F1 2291
5 TraesCS1A01G001100 chrUn 229307935 229310225 2290 True 3877 3877 97.208 3 2294 1 chrUn.!!$R2 2291
6 TraesCS1A01G001100 chrUn 3843522 3845812 2290 True 3860 3860 97.077 3 2294 1 chrUn.!!$R1 2291
7 TraesCS1A01G001100 chr1B 544593699 544595987 2288 False 3875 3875 97.208 3 2294 1 chr1B.!!$F1 2291
8 TraesCS1A01G001100 chr1B 544623638 544625928 2290 False 3866 3866 97.120 3 2294 1 chr1B.!!$F2 2291
9 TraesCS1A01G001100 chr5D 18998926 19001216 2290 False 3866 3866 97.120 3 2294 1 chr5D.!!$F1 2291

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
655 656 0.034574 TGCACATGGGTAAGCCGATT 60.035 50.0 0.0 0.0 30.32 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 1875 1.11593 AAGGATCGATAGGCCACGCT 61.116 55.0 5.01 0.0 34.1 5.07 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 1.254026 ATCGTTCGTCTGACTTGGGA 58.746 50.000 6.21 0.00 0.00 4.37
63 64 6.062749 AGACTAATCGAACCATCTAGTAGCA 58.937 40.000 0.00 0.00 0.00 3.49
98 99 1.709578 TTCGCTCAGGATAGCTGGAT 58.290 50.000 0.00 0.00 40.49 3.41
148 149 4.263816 CCAATGATTAGAGGCATCTGGGAT 60.264 45.833 11.96 2.24 36.96 3.85
373 374 0.036306 GGACGGTGGTCATGGAAGTT 59.964 55.000 0.00 0.00 45.28 2.66
412 413 1.346395 TGTAACAACTCACCTGCCGAT 59.654 47.619 0.00 0.00 0.00 4.18
425 426 1.223487 GCCGATTCAACTAGCCCCA 59.777 57.895 0.00 0.00 0.00 4.96
477 478 4.864334 CGGCCATCTGGGTGAGCC 62.864 72.222 2.24 0.00 39.65 4.70
478 479 3.731728 GGCCATCTGGGTGAGCCA 61.732 66.667 2.31 2.31 43.32 4.75
479 480 2.599597 GCCATCTGGGTGAGCCAT 59.400 61.111 2.84 0.00 39.65 4.40
655 656 0.034574 TGCACATGGGTAAGCCGATT 60.035 50.000 0.00 0.00 30.32 3.34
665 666 2.433239 GGTAAGCCGATTCTAAGGGACA 59.567 50.000 0.00 0.00 0.00 4.02
730 731 4.166246 GGGAATCGGGTTAAGATTTCCT 57.834 45.455 8.58 0.00 45.83 3.36
745 746 3.402681 CCTGAGCCGGGATGTGGT 61.403 66.667 2.18 0.00 29.82 4.16
746 747 2.063979 CCTGAGCCGGGATGTGGTA 61.064 63.158 2.18 0.00 29.82 3.25
755 756 0.611714 GGGATGTGGTAGTTGACGGT 59.388 55.000 0.00 0.00 0.00 4.83
838 839 1.152567 CCTGCCAACCCTGGAAACA 60.153 57.895 0.00 0.00 46.92 2.83
877 878 2.925170 AGTGGCCGGAAGAGCACT 60.925 61.111 5.05 0.00 0.00 4.40
943 944 2.270959 GGAGGACCGAGTACCGTTT 58.729 57.895 0.00 0.00 36.31 3.60
965 966 0.743097 GCCCGGTCGTACTCATAACT 59.257 55.000 0.00 0.00 0.00 2.24
1040 1041 0.250553 AAGTCGGCAAAACGGATCCA 60.251 50.000 13.41 0.00 0.00 3.41
1423 1424 4.401202 TGCCTCGTCATCTAATTAGTGACA 59.599 41.667 28.21 20.45 41.69 3.58
1424 1425 5.069119 TGCCTCGTCATCTAATTAGTGACAT 59.931 40.000 28.21 11.48 41.69 3.06
1453 1454 6.099125 TGAATGGATTAACGAGATTCCCACTA 59.901 38.462 0.00 0.00 0.00 2.74
1478 1479 3.381908 CCTGTCTACTATCCAGCGAAACT 59.618 47.826 0.00 0.00 0.00 2.66
1502 1503 3.897122 AAGGGAACGGGCTTGGCA 61.897 61.111 0.00 0.00 0.00 4.92
1538 1539 2.439507 AGAAGACCCTGTTGAGCTTGAA 59.560 45.455 0.00 0.00 0.00 2.69
1542 1543 3.006247 GACCCTGTTGAGCTTGAATCTC 58.994 50.000 0.00 0.00 0.00 2.75
1707 1710 2.132352 GTCTTACCGGGCCGATCCT 61.132 63.158 30.79 9.11 34.39 3.24
1745 1748 3.264845 GGGGAGTTTGGCTGGGGA 61.265 66.667 0.00 0.00 0.00 4.81
1808 1811 3.990469 GCTCAACGAGAACAGAAATCTCA 59.010 43.478 4.62 0.00 42.79 3.27
1872 1875 4.382457 CAGTACGAATACGAACCGTGAAAA 59.618 41.667 1.93 0.00 41.39 2.29
1922 1925 3.555168 CGGAGTTTGAAGCTAGAGGTGTT 60.555 47.826 0.00 0.00 0.00 3.32
1953 1956 1.474077 CCACAAGGATAACTGGCTTGC 59.526 52.381 0.00 0.00 36.89 4.01
2120 2123 6.729569 AGGTTAGTTTTACCCTACTGATGACT 59.270 38.462 0.00 0.00 36.27 3.41
2131 2134 1.067565 ACTGATGACTGTGTCGCGATT 60.068 47.619 14.06 0.00 34.95 3.34
2147 2150 5.063060 GTCGCGATTGTAATTCAACCTAGTT 59.937 40.000 14.06 0.00 38.97 2.24
2224 2227 2.048597 CGAAGCTACCGTGTGCCA 60.049 61.111 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.157668 GTCAGACGAACGATTTGCACAT 59.842 45.455 0.14 0.00 0.00 3.21
1 2 1.525197 GTCAGACGAACGATTTGCACA 59.475 47.619 0.14 0.00 0.00 4.57
27 28 3.640029 TCGATTAGTCTTTCGCCCCTATT 59.360 43.478 1.16 0.00 35.39 1.73
82 83 0.612744 GGGATCCAGCTATCCTGAGC 59.387 60.000 15.23 0.00 44.64 4.26
98 99 4.543689 ACCTGATAGAACTCGTAATGGGA 58.456 43.478 0.00 0.00 0.00 4.37
142 143 1.811266 CGAGGACGTTGCATCCCAG 60.811 63.158 1.05 0.00 36.86 4.45
143 144 2.264480 CGAGGACGTTGCATCCCA 59.736 61.111 1.05 0.00 36.86 4.37
148 149 0.892755 AATAGGTCGAGGACGTTGCA 59.107 50.000 0.00 0.00 40.69 4.08
373 374 2.301870 ACACACTCCTTAGCGGATTTCA 59.698 45.455 0.00 0.00 42.12 2.69
412 413 3.850752 TCCATTTTTGGGGCTAGTTGAA 58.149 40.909 0.00 0.00 0.00 2.69
425 426 1.404583 GCTTCAGCGCCATCCATTTTT 60.405 47.619 2.29 0.00 0.00 1.94
477 478 2.167281 CTCCTACTCATCGGGGCATATG 59.833 54.545 0.00 0.00 0.00 1.78
478 479 2.461695 CTCCTACTCATCGGGGCATAT 58.538 52.381 0.00 0.00 0.00 1.78
479 480 1.550179 CCTCCTACTCATCGGGGCATA 60.550 57.143 0.00 0.00 0.00 3.14
559 560 6.821665 TGAATATTTGCTACTACCACCAAGAC 59.178 38.462 0.00 0.00 0.00 3.01
630 631 1.538047 CTTACCCATGTGCAAGTGCT 58.462 50.000 4.69 0.00 42.66 4.40
655 656 2.259014 GGGTTACCCTGTCCCTTAGA 57.741 55.000 14.22 0.00 41.34 2.10
730 731 0.907704 AACTACCACATCCCGGCTCA 60.908 55.000 0.00 0.00 0.00 4.26
755 756 1.171308 CTCCGGACTTCCTAACGTCA 58.829 55.000 0.00 0.00 31.88 4.35
838 839 1.686110 CCCTACCTCCGGCTGAACT 60.686 63.158 0.00 0.00 0.00 3.01
905 906 2.044451 ATTTTCATGGGCCGCCGA 60.044 55.556 2.55 0.00 0.00 5.54
943 944 0.179059 TATGAGTACGACCGGGCGTA 60.179 55.000 37.96 37.96 43.61 4.42
965 966 0.325933 CACCTTGGAGACCTGATGCA 59.674 55.000 0.00 0.00 0.00 3.96
1019 1020 1.439679 GATCCGTTTTGCCGACTTCT 58.560 50.000 0.00 0.00 0.00 2.85
1040 1041 3.699538 GCCAATCCTTTTCCCGAAGTTAT 59.300 43.478 0.00 0.00 0.00 1.89
1201 1202 1.269723 AGTCGACTGTTTCATGCTCGA 59.730 47.619 19.30 0.00 0.00 4.04
1423 1424 6.072286 GGAATCTCGTTAATCCATTCATGCAT 60.072 38.462 0.00 0.00 32.08 3.96
1424 1425 5.239306 GGAATCTCGTTAATCCATTCATGCA 59.761 40.000 0.00 0.00 32.08 3.96
1453 1454 2.108425 TCGCTGGATAGTAGACAGGGAT 59.892 50.000 15.33 0.00 45.40 3.85
1478 1479 3.074281 CCCGTTCCCTTGGCTGTA 58.926 61.111 0.00 0.00 0.00 2.74
1502 1503 1.909302 TCTTCTTTCCCCGCTGATTCT 59.091 47.619 0.00 0.00 0.00 2.40
1538 1539 3.380479 TTTCACAAAGTCGGACGAGAT 57.620 42.857 1.89 0.00 0.00 2.75
1542 1543 2.800544 AGTCATTTCACAAAGTCGGACG 59.199 45.455 1.89 0.00 0.00 4.79
1707 1710 1.421268 ACCTGACAATGTCTTCTGCCA 59.579 47.619 14.97 0.00 33.15 4.92
1711 1714 1.352352 CCCCACCTGACAATGTCTTCT 59.648 52.381 14.97 0.00 33.15 2.85
1745 1748 5.163754 GCGTTATCTTTTAACAGATGTGCCT 60.164 40.000 13.31 0.00 35.08 4.75
1808 1811 4.653801 AGCTTTTACCCTTTTGTTCCACAT 59.346 37.500 0.00 0.00 0.00 3.21
1872 1875 1.115930 AAGGATCGATAGGCCACGCT 61.116 55.000 5.01 0.00 34.10 5.07
1922 1925 7.881232 CCAGTTATCCTTGTGGTAACTTTTCTA 59.119 37.037 0.00 0.00 37.70 2.10
1953 1956 2.040213 CTATGAACGCTTGGCTGCCG 62.040 60.000 14.98 4.23 0.00 5.69
2120 2123 3.120477 GGTTGAATTACAATCGCGACACA 60.120 43.478 12.93 0.00 40.76 3.72
2131 2134 5.713389 TCCTCTCGAACTAGGTTGAATTACA 59.287 40.000 0.00 0.00 34.30 2.41
2147 2150 3.320826 TGTGAATCAACAGTTCCTCTCGA 59.679 43.478 0.00 0.00 0.00 4.04
2158 2161 5.562501 CGATGACCAATTGTGTGAATCAACA 60.563 40.000 4.43 0.00 0.00 3.33
2224 2227 5.361285 ACTTAGAGGCGTTCAGTCATAATCT 59.639 40.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.