Multiple sequence alignment - TraesCS1D01G100400

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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 TraesCS1D01G100400 chr1D 100.000 3485 0 0 1 3485 88009178 88005694 0 6436
1 TraesCS1D01G100400 chr1D 95.878 3251 127 5 1 3248 78750932 78747686 0 5254
2 TraesCS1D01G100400 chr5D 96.390 3490 100 13 1 3485 108666113 108662645 0 5723
3 TraesCS1D01G100400 chr4D 96.827 3435 92 13 60 3485 79267678 79264252 0 5723
4 TraesCS1D01G100400 chr2D 95.838 3508 115 6 1 3485 259243884 259240385 0 5640
5 TraesCS1D01G100400 chr7A 94.278 3513 165 19 1 3485 458658707 458655203 0 5341
6 TraesCS1D01G100400 chr2A 93.935 3512 165 26 1 3485 160670689 160667199 0 5262
7 TraesCS1D01G100400 chr2A 94.031 3267 161 28 1 3248 109291159 109287908 0 4922
8 TraesCS1D01G100400 chr2A 94.024 3263 162 23 1 3245 230716167 230719414 0 4915
9 TraesCS1D01G100400 chr3D 96.206 3189 116 4 60 3245 353285025 353288211 0 5214
10 TraesCS1D01G100400 chr6A 94.653 3254 146 13 1 3248 490173673 490170442 0 5020
11 TraesCS1D01G100400 chr3A 94.128 3253 170 16 1 3245 665589535 665592774 0 4929
12 TraesCS1D01G100400 chr3A 95.187 2244 85 11 1264 3485 84729562 84731804 0 3524
13 TraesCS1D01G100400 chr1A 93.471 3002 184 10 249 3246 435194874 435197867 0 4447


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 TraesCS1D01G100400 chr1D 88005694 88009178 3484 True 6436 6436 100.000 1 3485 1 chr1D.!!$R2 3484
1 TraesCS1D01G100400 chr1D 78747686 78750932 3246 True 5254 5254 95.878 1 3248 1 chr1D.!!$R1 3247
2 TraesCS1D01G100400 chr5D 108662645 108666113 3468 True 5723 5723 96.390 1 3485 1 chr5D.!!$R1 3484
3 TraesCS1D01G100400 chr4D 79264252 79267678 3426 True 5723 5723 96.827 60 3485 1 chr4D.!!$R1 3425
4 TraesCS1D01G100400 chr2D 259240385 259243884 3499 True 5640 5640 95.838 1 3485 1 chr2D.!!$R1 3484
5 TraesCS1D01G100400 chr7A 458655203 458658707 3504 True 5341 5341 94.278 1 3485 1 chr7A.!!$R1 3484
6 TraesCS1D01G100400 chr2A 160667199 160670689 3490 True 5262 5262 93.935 1 3485 1 chr2A.!!$R2 3484
7 TraesCS1D01G100400 chr2A 109287908 109291159 3251 True 4922 4922 94.031 1 3248 1 chr2A.!!$R1 3247
8 TraesCS1D01G100400 chr2A 230716167 230719414 3247 False 4915 4915 94.024 1 3245 1 chr2A.!!$F1 3244
9 TraesCS1D01G100400 chr3D 353285025 353288211 3186 False 5214 5214 96.206 60 3245 1 chr3D.!!$F1 3185
10 TraesCS1D01G100400 chr6A 490170442 490173673 3231 True 5020 5020 94.653 1 3248 1 chr6A.!!$R1 3247
11 TraesCS1D01G100400 chr3A 665589535 665592774 3239 False 4929 4929 94.128 1 3245 1 chr3A.!!$F2 3244
12 TraesCS1D01G100400 chr3A 84729562 84731804 2242 False 3524 3524 95.187 1264 3485 1 chr3A.!!$F1 2221
13 TraesCS1D01G100400 chr1A 435194874 435197867 2993 False 4447 4447 93.471 249 3246 1 chr1A.!!$F1 2997

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
369 379 1.067974 CCACTCACACCACTACGACAA 59.932 52.381 0.0 0.0 0.0 3.18 F
660 673 2.516930 GCCATCATCACCACCCCG 60.517 66.667 0.0 0.0 0.0 5.73 F
2416 2445 2.290260 TGGAAGACAATCGCCAACATCT 60.290 45.455 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 1562 5.534207 TTGGTGCATCAAGTTCAGAATTT 57.466 34.783 8.71 0.0 0.0 1.82 R
2449 2478 1.895866 GCAGTGGTAGTAGGGGTCAGT 60.896 57.143 0.00 0.0 0.0 3.41 R
3223 3328 4.431416 TTTTCTAGGCTGTGGTTCTTCA 57.569 40.909 0.00 0.0 0.0 3.02 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
369 379 1.067974 CCACTCACACCACTACGACAA 59.932 52.381 0.00 0.00 0.00 3.18
660 673 2.516930 GCCATCATCACCACCCCG 60.517 66.667 0.00 0.00 0.00 5.73
1397 1414 9.650539 TCTGTTGTACTAGTACTACTCACTAAG 57.349 37.037 32.84 24.69 40.64 2.18
1523 1541 5.256474 AGTGGATTGTTTCACCAGATTAGG 58.744 41.667 0.00 0.00 34.67 2.69
1585 1604 9.638239 GCACCAAATTAATTTCTGAACTTGATA 57.362 29.630 10.53 0.00 0.00 2.15
1700 1721 6.864685 TCTTGATGCACATGTTTCTCAAATTC 59.135 34.615 0.00 0.00 0.00 2.17
1765 1786 8.313944 TCAAGCACTGGTATAGGTCTTTTATA 57.686 34.615 0.00 0.00 0.00 0.98
1824 1847 9.445878 AGCACATATATCATTGAATCTGGTAAG 57.554 33.333 0.00 0.00 0.00 2.34
1863 1886 3.253188 GTGAAGCATTTGGTGAAGCACTA 59.747 43.478 0.00 0.00 34.40 2.74
1902 1927 9.744468 AAGAAAAATAACATGGTGTAGTTGAAC 57.256 29.630 0.00 0.00 0.00 3.18
1997 2022 8.421249 ACCTCATGGATTATCACTTTCAAAAA 57.579 30.769 0.00 0.00 37.04 1.94
2408 2437 2.744202 ACAAGTCATGGAAGACAATCGC 59.256 45.455 0.00 0.00 40.98 4.58
2416 2445 2.290260 TGGAAGACAATCGCCAACATCT 60.290 45.455 0.00 0.00 0.00 2.90
2449 2478 5.044919 TGGGATATTTCAAAAGAGCAGGAGA 60.045 40.000 0.00 0.00 0.00 3.71
2475 2504 2.835764 CCCCTACTACCACTGCAACTTA 59.164 50.000 0.00 0.00 0.00 2.24
2478 2507 3.056107 CCTACTACCACTGCAACTTAGCA 60.056 47.826 0.00 0.00 43.35 3.49
2805 2902 4.286032 TGGCAGACTAACTAAGGACAACAT 59.714 41.667 0.00 0.00 0.00 2.71
3001 3102 4.391523 GCAACAGGAAAAGCAAAGAACAAA 59.608 37.500 0.00 0.00 0.00 2.83
3056 3157 5.477637 AGGACTAAGAGTTCTGGTACACTTC 59.522 44.000 0.00 0.00 31.41 3.01
3181 3285 8.677148 ACAACTGAAATGTGAGTACAACTTAT 57.323 30.769 0.00 0.00 40.84 1.73
3223 3328 4.771577 TGATCATACCAAACATTGCCTTGT 59.228 37.500 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
334 343 0.252421 AGTGGCCTGACTGATCCTGA 60.252 55.000 3.32 0.00 0.00 3.86
369 379 1.590698 GCGTGCGGTTTTGAAATTTGT 59.409 42.857 0.00 0.00 0.00 2.83
660 673 0.321653 AATCCCACTTGCACGTCTCC 60.322 55.000 0.00 0.00 0.00 3.71
847 863 3.338250 GGGGATGTGTGGGAGGCA 61.338 66.667 0.00 0.00 0.00 4.75
1027 1044 2.335011 CGACGGCTCGCCATGATA 59.665 61.111 8.87 0.00 35.37 2.15
1397 1414 8.847196 AGTTGGGAAACTAGTTTAATGAAGTTC 58.153 33.333 20.58 5.32 31.15 3.01
1543 1562 5.534207 TTGGTGCATCAAGTTCAGAATTT 57.466 34.783 8.71 0.00 0.00 1.82
1585 1604 7.242322 TCAAGATCAGAATCTATGCTAGCAT 57.758 36.000 31.60 31.60 41.54 3.79
1824 1847 6.392354 TGCTTCACCAAATTCAAGAATCATC 58.608 36.000 0.00 0.00 0.00 2.92
2416 2445 6.780031 TCTTTTGAAATATCCCAACCTGTCAA 59.220 34.615 0.00 0.00 0.00 3.18
2449 2478 1.895866 GCAGTGGTAGTAGGGGTCAGT 60.896 57.143 0.00 0.00 0.00 3.41
2475 2504 3.292492 TTCATGCATCTTCATCCTGCT 57.708 42.857 0.00 0.00 36.84 4.24
2478 2507 5.623824 GCAAACTTTCATGCATCTTCATCCT 60.624 40.000 0.00 0.00 42.12 3.24
2805 2902 5.972935 TGAGCGTCCAATTCTACTATTTGA 58.027 37.500 0.00 0.00 0.00 2.69
3001 3102 5.416271 AGTGACTGGGAAATACGTATTGT 57.584 39.130 21.00 13.76 0.00 2.71
3056 3157 6.893759 TGTAGAATGAATGTACCGTTTGTTG 58.106 36.000 0.00 0.00 0.00 3.33
3169 3273 7.603024 ACTTGCCTTACAGAATAAGTTGTACTC 59.397 37.037 0.00 0.00 30.03 2.59
3181 3285 7.418337 TGATCATAGTACTTGCCTTACAGAA 57.582 36.000 0.00 0.00 0.00 3.02
3223 3328 4.431416 TTTTCTAGGCTGTGGTTCTTCA 57.569 40.909 0.00 0.00 0.00 3.02
3378 3484 6.939730 TGAGATTTCAATTGTGCTGGTACTTA 59.060 34.615 5.13 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.