Multiple sequence alignment - TraesCS1D01G156500

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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 TraesCS1D01G156500 chr1D 100.000 3813 0 0 1 3813 220600439 220604251 0 7042
1 TraesCS1D01G156500 chr4D 97.823 3813 83 0 1 3813 218284244 218288056 0 6582
2 TraesCS1D01G156500 chr4D 96.879 3813 116 3 3 3813 385545535 385549346 0 6379
3 TraesCS1D01G156500 chr7D 97.640 3813 88 2 1 3813 75363646 75367456 0 6541
4 TraesCS1D01G156500 chr7D 97.640 3813 88 2 1 3813 75374938 75378748 0 6541
5 TraesCS1D01G156500 chr7D 97.535 3813 92 2 1 3813 75405617 75409427 0 6519
6 TraesCS1D01G156500 chr7D 97.036 3812 110 3 3 3813 333147050 333143241 0 6410
7 TraesCS1D01G156500 chr5D 96.986 3815 106 3 1 3813 67895157 67898964 0 6399
8 TraesCS1D01G156500 chr3D 96.933 3815 115 1 1 3813 76500017 76503831 0 6396
9 TraesCS1D01G156500 chr2D 96.774 3813 121 1 1 3813 323527783 323531593 0 6359


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 TraesCS1D01G156500 chr1D 220600439 220604251 3812 False 7042 7042 100.000 1 3813 1 chr1D.!!$F1 3812
1 TraesCS1D01G156500 chr4D 218284244 218288056 3812 False 6582 6582 97.823 1 3813 1 chr4D.!!$F1 3812
2 TraesCS1D01G156500 chr4D 385545535 385549346 3811 False 6379 6379 96.879 3 3813 1 chr4D.!!$F2 3810
3 TraesCS1D01G156500 chr7D 75363646 75367456 3810 False 6541 6541 97.640 1 3813 1 chr7D.!!$F1 3812
4 TraesCS1D01G156500 chr7D 75374938 75378748 3810 False 6541 6541 97.640 1 3813 1 chr7D.!!$F2 3812
5 TraesCS1D01G156500 chr7D 75405617 75409427 3810 False 6519 6519 97.535 1 3813 1 chr7D.!!$F3 3812
6 TraesCS1D01G156500 chr7D 333143241 333147050 3809 True 6410 6410 97.036 3 3813 1 chr7D.!!$R1 3810
7 TraesCS1D01G156500 chr5D 67895157 67898964 3807 False 6399 6399 96.986 1 3813 1 chr5D.!!$F1 3812
8 TraesCS1D01G156500 chr3D 76500017 76503831 3814 False 6396 6396 96.933 1 3813 1 chr3D.!!$F1 3812
9 TraesCS1D01G156500 chr2D 323527783 323531593 3810 False 6359 6359 96.774 1 3813 1 chr2D.!!$F1 3812

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
757 758 0.478507 CCACCCAAAGGACTGGAACT 59.521 55.0 0.00 0.00 38.96 3.01 F
1830 1834 1.064825 GGAAACCTCACCTTCCTCCA 58.935 55.0 0.00 0.00 38.48 3.86 F
2171 2175 0.391228 ACCCGGACCAAATTTGTTGC 59.609 50.0 16.73 7.29 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2045 0.179018 GTGGTTTCTGGAGCTGGTGT 60.179 55.000 0.00 0.00 0.00 4.16 R
2765 2770 1.202359 GCGGGTCTTCAGATCAGAGAC 60.202 57.143 12.22 12.22 0.00 3.36 R
3391 3405 1.674057 CGTCTTCCTTCAGGCTGGT 59.326 57.895 15.73 0.00 34.44 4.00 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
120 121 8.523915 ACTTGAATTGCTTATGATATCCACAA 57.476 30.769 0.00 0.00 0.00 3.33
142 143 2.798499 CGGCTTAGATAACCCGACACAG 60.798 54.545 0.90 0.00 43.20 3.66
265 266 1.880027 GGCTTCCGTCTTTCACAATGT 59.120 47.619 0.00 0.00 0.00 2.71
351 352 4.523173 ACCTTAGATGACTTCGTGAAGACA 59.477 41.667 16.10 15.55 44.39 3.41
531 532 1.173913 TCGATCTGCGACCTCAAGAA 58.826 50.000 0.00 0.00 45.59 2.52
538 539 2.813754 CTGCGACCTCAAGAAATTGGAA 59.186 45.455 0.00 0.00 0.00 3.53
627 628 4.416179 AGCCTACTACTCTTTAGGGAGCTA 59.584 45.833 0.00 0.00 36.16 3.32
757 758 0.478507 CCACCCAAAGGACTGGAACT 59.521 55.000 0.00 0.00 38.96 3.01
1088 1089 3.498397 GTCGTTGATGACATGACCAAGTT 59.502 43.478 0.00 0.00 38.75 2.66
1272 1274 3.601443 ATGAGAAGTTCTGGAAGGTCG 57.399 47.619 10.90 0.00 0.00 4.79
1513 1517 1.087771 GCGAGTAACCCGGTGATTGG 61.088 60.000 0.00 0.00 0.00 3.16
1635 1639 8.469309 TCAAGATCCTCAATTTCTTTTGAAGT 57.531 30.769 0.00 0.00 39.88 3.01
1643 1647 7.806960 CCTCAATTTCTTTTGAAGTGACAGATC 59.193 37.037 0.00 0.00 39.88 2.75
1766 1770 7.125391 ACTTATATCCTTTTCATCCTTTGGCA 58.875 34.615 0.00 0.00 0.00 4.92
1817 1821 7.607991 TCTTCTGATTCAAACTATCAGGAAACC 59.392 37.037 11.65 0.00 45.78 3.27
1830 1834 1.064825 GGAAACCTCACCTTCCTCCA 58.935 55.000 0.00 0.00 38.48 3.86
1888 1892 1.548719 CGCTCCCGGGTAATGATGATA 59.451 52.381 22.86 0.00 0.00 2.15
1917 1921 6.992063 ACTTTGTGCTTATCTTACTCATGG 57.008 37.500 0.00 0.00 0.00 3.66
2041 2045 2.829003 CCTCTGAGCCGCCGTCTA 60.829 66.667 0.00 0.00 0.00 2.59
2161 2165 0.836830 TGTGGTGATTACCCGGACCA 60.837 55.000 0.73 4.25 46.96 4.02
2171 2175 0.391228 ACCCGGACCAAATTTGTTGC 59.609 50.000 16.73 7.29 0.00 4.17
2174 2178 1.068434 CCGGACCAAATTTGTTGCACT 59.932 47.619 16.73 0.00 0.00 4.40
2307 2311 5.105269 TGTCGCTGGTTATATTGGTCAAGTA 60.105 40.000 0.00 0.00 0.00 2.24
2360 2364 6.815089 TGGTGAAGCAGATACAACAAAAATT 58.185 32.000 0.00 0.00 0.00 1.82
2484 2488 1.373812 GTAACACTCAAGGGCCGGT 59.626 57.895 1.90 0.00 0.00 5.28
2504 2508 4.395625 GGTTTAAACAGCCTAGGTGAACT 58.604 43.478 19.57 0.00 34.87 3.01
2765 2770 4.470462 CTGCAAGAAACTTGAATCGGAAG 58.530 43.478 14.44 0.00 34.07 3.46
3190 3198 1.448013 GAGCAACTCTACACCGGGC 60.448 63.158 6.32 0.00 0.00 6.13
3231 3239 1.555075 GTGGCTCTGTCCAATGAGGTA 59.445 52.381 0.00 0.00 37.96 3.08
3391 3405 1.067060 CCGACATCGCTCTTGGATACA 59.933 52.381 0.00 0.00 41.57 2.29
3490 3504 3.765511 CACCTTGATTGGGAATGACACAT 59.234 43.478 0.00 0.00 0.00 3.21
3806 3820 0.843309 TGCCTCACCTTTTGGACTCA 59.157 50.000 0.00 0.00 44.07 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 5.132816 AGGGGCCTAATGATATATGGCTAAC 59.867 44.000 0.84 3.08 42.84 2.34
351 352 3.108376 CTCCTTCTTAGGCAGGTAACCT 58.892 50.000 0.00 0.00 41.69 3.50
550 551 5.212194 CACTTGGAAGTTACAAATGTTCGG 58.788 41.667 1.35 0.00 37.08 4.30
627 628 3.374058 CGTTCTGGCGGTTCAGATAAAAT 59.626 43.478 0.00 0.00 42.57 1.82
684 685 3.259064 TCTCCGTCGTTGGATTGAAATC 58.741 45.455 0.00 0.00 37.41 2.17
757 758 2.766263 CCTGGCAGTAGAACCATGTCTA 59.234 50.000 14.43 0.00 34.82 2.59
1088 1089 3.762288 TGCTAAGCTCTCGTTTAGAAGGA 59.238 43.478 0.00 0.00 36.41 3.36
1164 1165 3.383185 GGTGCTCAGATCAGTAGCTTACT 59.617 47.826 13.12 0.00 40.28 2.24
1272 1274 0.536006 GCAGCCTCATGGTCATACCC 60.536 60.000 0.00 0.00 37.50 3.69
1336 1338 0.744771 CTTACTCCCCTTCTTGCGGC 60.745 60.000 0.00 0.00 0.00 6.53
1635 1639 0.749049 CGGCTCTCATGGATCTGTCA 59.251 55.000 0.00 0.00 0.00 3.58
1766 1770 2.338984 GGTTGACGAGTGACGCCT 59.661 61.111 0.00 0.00 46.94 5.52
1817 1821 4.896979 TCCCTGGAGGAAGGTGAG 57.103 61.111 0.00 0.00 43.78 3.51
1830 1834 3.118531 AGTTAGATTGCATGGAGTCCCT 58.881 45.455 6.74 0.00 0.00 4.20
1917 1921 6.588373 TGAAAGTCAAAAGGTTAGTGCAAAAC 59.412 34.615 4.91 4.91 0.00 2.43
2041 2045 0.179018 GTGGTTTCTGGAGCTGGTGT 60.179 55.000 0.00 0.00 0.00 4.16
2161 2165 3.181466 GGTCTTCCCAGTGCAACAAATTT 60.181 43.478 0.00 0.00 41.43 1.82
2307 2311 3.168528 AGGTCCCGGCTGTTGTGT 61.169 61.111 0.00 0.00 0.00 3.72
2360 2364 7.187824 AGTAAGCAAGAGAATCATACCTCAA 57.812 36.000 0.00 0.00 37.82 3.02
2484 2488 4.141344 ACCAGTTCACCTAGGCTGTTTAAA 60.141 41.667 9.30 0.00 0.00 1.52
2765 2770 1.202359 GCGGGTCTTCAGATCAGAGAC 60.202 57.143 12.22 12.22 0.00 3.36
3190 3198 2.870372 GGCTAAAGCACGCTGTGG 59.130 61.111 4.07 0.00 44.36 4.17
3231 3239 2.122413 TCTGCCAGGTGAGTGGGT 60.122 61.111 0.00 0.00 38.14 4.51
3391 3405 1.674057 CGTCTTCCTTCAGGCTGGT 59.326 57.895 15.73 0.00 34.44 4.00
3490 3504 4.280174 GCCCGACTGATACTTGGTAAGATA 59.720 45.833 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.