Multiple sequence alignment - TraesCS5D01G559600

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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 TraesCS5D01G559600 chr5D 100.000 2132 0 0 1 2132 560874659 560872528 0.000000e+00 3938.0
1 TraesCS5D01G559600 chr5D 98.290 2105 33 3 1 2104 6199091 6201193 0.000000e+00 3685.0
2 TraesCS5D01G559600 chr5D 98.100 2105 35 5 1 2104 329164365 329162265 0.000000e+00 3661.0
3 TraesCS5D01G559600 chr1D 98.480 2105 31 1 1 2104 254500189 254498085 0.000000e+00 3709.0
4 TraesCS5D01G559600 chr1D 93.097 2028 90 30 84 2104 244481977 244483961 0.000000e+00 2924.0
5 TraesCS5D01G559600 chr4D 97.196 2104 56 3 1 2104 19918683 19916583 0.000000e+00 3555.0
6 TraesCS5D01G559600 chr4D 96.875 32 0 1 2101 2132 489234204 489234234 4.000000e-03 52.8
7 TraesCS5D01G559600 chr1A 97.196 2104 53 5 1 2104 168448382 168450479 0.000000e+00 3554.0
8 TraesCS5D01G559600 chr7A 95.204 2106 95 6 1 2104 352191835 352193936 0.000000e+00 3325.0
9 TraesCS5D01G559600 chr6B 97.272 1393 36 2 713 2104 22427423 22426032 0.000000e+00 2361.0
10 TraesCS5D01G559600 chr3B 98.144 1293 20 4 1 1291 201516870 201515580 0.000000e+00 2252.0
11 TraesCS5D01G559600 chr3B 96.496 1170 13 5 936 2104 201514356 201513214 0.000000e+00 1908.0
12 TraesCS5D01G559600 chr3B 95.259 675 28 4 1 675 524776894 524777564 0.000000e+00 1066.0
13 TraesCS5D01G559600 chr3B 94.118 85 5 0 673 757 152335419 152335335 1.720000e-26 130.0
14 TraesCS5D01G559600 chr7B 95.858 676 27 1 1 676 102631440 102632114 0.000000e+00 1092.0
15 TraesCS5D01G559600 chr2B 94.231 52 3 0 739 790 113026772 113026823 1.750000e-11 80.5
16 TraesCS5D01G559600 chr7D 100.000 29 0 0 2104 2132 43665560 43665588 1.000000e-03 54.7
17 TraesCS5D01G559600 chr2D 94.444 36 1 1 2097 2132 582927593 582927559 1.000000e-03 54.7
18 TraesCS5D01G559600 chr2D 100.000 29 0 0 2104 2132 646416774 646416802 1.000000e-03 54.7
19 TraesCS5D01G559600 chr2D 100.000 28 0 0 2105 2132 512471790 512471763 4.000000e-03 52.8
20 TraesCS5D01G559600 chrUn 100.000 28 0 0 2105 2132 9969796 9969823 4.000000e-03 52.8
21 TraesCS5D01G559600 chrUn 100.000 28 0 0 2105 2132 19124628 19124601 4.000000e-03 52.8
22 TraesCS5D01G559600 chrUn 100.000 28 0 0 2105 2132 19836352 19836379 4.000000e-03 52.8
23 TraesCS5D01G559600 chrUn 100.000 28 0 0 2105 2132 19836431 19836458 4.000000e-03 52.8


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 TraesCS5D01G559600 chr5D 560872528 560874659 2131 True 3938 3938 100.000 1 2132 1 chr5D.!!$R2 2131
1 TraesCS5D01G559600 chr5D 6199091 6201193 2102 False 3685 3685 98.290 1 2104 1 chr5D.!!$F1 2103
2 TraesCS5D01G559600 chr5D 329162265 329164365 2100 True 3661 3661 98.100 1 2104 1 chr5D.!!$R1 2103
3 TraesCS5D01G559600 chr1D 254498085 254500189 2104 True 3709 3709 98.480 1 2104 1 chr1D.!!$R1 2103
4 TraesCS5D01G559600 chr1D 244481977 244483961 1984 False 2924 2924 93.097 84 2104 1 chr1D.!!$F1 2020
5 TraesCS5D01G559600 chr4D 19916583 19918683 2100 True 3555 3555 97.196 1 2104 1 chr4D.!!$R1 2103
6 TraesCS5D01G559600 chr1A 168448382 168450479 2097 False 3554 3554 97.196 1 2104 1 chr1A.!!$F1 2103
7 TraesCS5D01G559600 chr7A 352191835 352193936 2101 False 3325 3325 95.204 1 2104 1 chr7A.!!$F1 2103
8 TraesCS5D01G559600 chr6B 22426032 22427423 1391 True 2361 2361 97.272 713 2104 1 chr6B.!!$R1 1391
9 TraesCS5D01G559600 chr3B 201513214 201516870 3656 True 2080 2252 97.320 1 2104 2 chr3B.!!$R2 2103
10 TraesCS5D01G559600 chr3B 524776894 524777564 670 False 1066 1066 95.259 1 675 1 chr3B.!!$F1 674
11 TraesCS5D01G559600 chr7B 102631440 102632114 674 False 1092 1092 95.858 1 676 1 chr7B.!!$F1 675

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
317 319 4.511454 GGCAAACAAAATTGGAAGGAAGAC 59.489 41.667 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 3698 0.247185 CGTGGCTAACCGGGACTAAA 59.753 55.0 6.32 0.0 39.7 1.85 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
232 234 4.562082 TCTTCGAATAAGAACCGCTTGAA 58.438 39.130 0.00 0.00 37.42 2.69
317 319 4.511454 GGCAAACAAAATTGGAAGGAAGAC 59.489 41.667 0.00 0.00 0.00 3.01
823 1359 5.067805 ACTTTCCCATATTCCGAATTCAAGC 59.932 40.000 6.22 0.00 0.00 4.01
1239 2289 3.700038 GGTGGTTCTCGGAAGAAGATAGA 59.300 47.826 0.00 0.00 42.14 1.98
1893 3483 5.536916 TCATCTACCAAAACAACCGGAAATT 59.463 36.000 9.46 0.00 0.00 1.82
2104 3696 7.984617 AGACCAAGCTTCTGATAAACTAAGATC 59.015 37.037 0.00 0.00 0.00 2.75
2105 3697 7.051000 ACCAAGCTTCTGATAAACTAAGATCC 58.949 38.462 0.00 0.00 0.00 3.36
2106 3698 7.092668 ACCAAGCTTCTGATAAACTAAGATCCT 60.093 37.037 0.00 0.00 0.00 3.24
2107 3699 7.772757 CCAAGCTTCTGATAAACTAAGATCCTT 59.227 37.037 0.00 0.00 0.00 3.36
2108 3700 9.171877 CAAGCTTCTGATAAACTAAGATCCTTT 57.828 33.333 0.00 0.00 0.00 3.11
2111 3703 9.825109 GCTTCTGATAAACTAAGATCCTTTAGT 57.175 33.333 2.35 2.35 43.77 2.24
2114 3706 8.925338 TCTGATAAACTAAGATCCTTTAGTCCC 58.075 37.037 7.60 0.95 41.70 4.46
2115 3707 7.723324 TGATAAACTAAGATCCTTTAGTCCCG 58.277 38.462 7.60 0.00 41.70 5.14
2116 3708 5.354842 AAACTAAGATCCTTTAGTCCCGG 57.645 43.478 7.60 0.00 41.70 5.73
2117 3709 3.991683 ACTAAGATCCTTTAGTCCCGGT 58.008 45.455 0.00 0.00 39.10 5.28
2118 3710 4.359996 ACTAAGATCCTTTAGTCCCGGTT 58.640 43.478 0.00 0.00 39.10 4.44
2119 3711 5.522641 ACTAAGATCCTTTAGTCCCGGTTA 58.477 41.667 0.00 0.00 39.10 2.85
2120 3712 5.597594 ACTAAGATCCTTTAGTCCCGGTTAG 59.402 44.000 0.00 0.00 39.10 2.34
2121 3713 2.699321 AGATCCTTTAGTCCCGGTTAGC 59.301 50.000 0.00 0.00 0.00 3.09
2122 3714 1.197812 TCCTTTAGTCCCGGTTAGCC 58.802 55.000 0.00 0.00 0.00 3.93
2123 3715 0.906775 CCTTTAGTCCCGGTTAGCCA 59.093 55.000 0.00 0.00 34.09 4.75
2124 3716 1.406477 CCTTTAGTCCCGGTTAGCCAC 60.406 57.143 0.00 0.00 34.09 5.01
2125 3717 0.247185 TTTAGTCCCGGTTAGCCACG 59.753 55.000 0.00 0.00 34.09 4.94
2126 3718 0.611618 TTAGTCCCGGTTAGCCACGA 60.612 55.000 0.00 0.00 34.09 4.35
2127 3719 1.033746 TAGTCCCGGTTAGCCACGAG 61.034 60.000 0.00 0.00 34.09 4.18
2128 3720 2.036098 TCCCGGTTAGCCACGAGA 59.964 61.111 0.00 0.00 34.09 4.04
2129 3721 1.607178 TCCCGGTTAGCCACGAGAA 60.607 57.895 0.00 0.00 34.09 2.87
2130 3722 1.447314 CCCGGTTAGCCACGAGAAC 60.447 63.158 0.00 0.00 34.09 3.01
2131 3723 1.447314 CCGGTTAGCCACGAGAACC 60.447 63.158 0.00 0.00 39.44 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1960 3551 5.437060 GAATAGCTGTTGGATGGTTAGGAA 58.563 41.667 0.00 0.0 0.0 3.36
2104 3696 0.906775 TGGCTAACCGGGACTAAAGG 59.093 55.000 6.32 0.0 39.7 3.11
2105 3697 1.738030 CGTGGCTAACCGGGACTAAAG 60.738 57.143 6.32 0.0 39.7 1.85
2106 3698 0.247185 CGTGGCTAACCGGGACTAAA 59.753 55.000 6.32 0.0 39.7 1.85
2107 3699 0.611618 TCGTGGCTAACCGGGACTAA 60.612 55.000 6.32 0.0 39.7 2.24
2108 3700 1.001020 TCGTGGCTAACCGGGACTA 60.001 57.895 6.32 0.0 39.7 2.59
2109 3701 2.283388 TCGTGGCTAACCGGGACT 60.283 61.111 6.32 0.0 39.7 3.85
2110 3702 1.880819 TTCTCGTGGCTAACCGGGAC 61.881 60.000 6.32 0.0 39.7 4.46
2111 3703 1.607178 TTCTCGTGGCTAACCGGGA 60.607 57.895 6.32 0.0 39.7 5.14
2112 3704 1.447314 GTTCTCGTGGCTAACCGGG 60.447 63.158 6.32 0.0 39.7 5.73
2113 3705 1.447314 GGTTCTCGTGGCTAACCGG 60.447 63.158 0.00 0.0 39.7 5.28
2114 3706 4.180496 GGTTCTCGTGGCTAACCG 57.820 61.111 0.00 0.0 39.7 4.44


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

AutoCloner maintained by Alex Coulton.