Multiple sequence alignment - TraesCS3D01G204200

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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 TraesCS3D01G204200 chr3D 100.000 3472 0 0 1 3472 254419845 254416374 0 6412
1 TraesCS3D01G204200 chr3D 96.380 2845 94 4 630 3472 421480451 421483288 0 4674
2 TraesCS3D01G204200 chr2D 95.666 3507 109 8 1 3472 259243883 259240385 0 5594
3 TraesCS3D01G204200 chr4D 96.759 3240 95 7 1 3235 426266280 426263046 0 5393
4 TraesCS3D01G204200 chr7A 94.077 3512 160 21 1 3472 458658706 458655203 0 5289
5 TraesCS3D01G204200 chr7A 94.330 3245 154 20 1 3232 421609604 421612831 0 4946
6 TraesCS3D01G204200 chr6D 96.543 3182 100 8 59 3232 249264292 249267471 0 5258
7 TraesCS3D01G204200 chr1D 95.917 3233 122 4 6 3232 285939050 285942278 0 5230
8 TraesCS3D01G204200 chr7D 96.379 3176 104 4 59 3232 387292997 387296163 0 5217
9 TraesCS3D01G204200 chr2A 93.732 3510 162 27 1 3472 160670688 160667199 0 5210
10 TraesCS3D01G204200 chr3A 94.451 3244 160 10 1 3235 204342961 204339729 0 4975
11 TraesCS3D01G204200 chr3A 94.324 3242 167 9 1 3235 204308732 204305501 0 4951
12 TraesCS3D01G204200 chr3A 94.474 2244 88 13 1264 3472 84729562 84731804 0 3424
13 TraesCS3D01G204200 chr6A 93.698 3253 170 20 1 3232 118303830 118307068 0 4839


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 TraesCS3D01G204200 chr3D 254416374 254419845 3471 True 6412 6412 100.000 1 3472 1 chr3D.!!$R1 3471
1 TraesCS3D01G204200 chr3D 421480451 421483288 2837 False 4674 4674 96.380 630 3472 1 chr3D.!!$F1 2842
2 TraesCS3D01G204200 chr2D 259240385 259243883 3498 True 5594 5594 95.666 1 3472 1 chr2D.!!$R1 3471
3 TraesCS3D01G204200 chr4D 426263046 426266280 3234 True 5393 5393 96.759 1 3235 1 chr4D.!!$R1 3234
4 TraesCS3D01G204200 chr7A 458655203 458658706 3503 True 5289 5289 94.077 1 3472 1 chr7A.!!$R1 3471
5 TraesCS3D01G204200 chr7A 421609604 421612831 3227 False 4946 4946 94.330 1 3232 1 chr7A.!!$F1 3231
6 TraesCS3D01G204200 chr6D 249264292 249267471 3179 False 5258 5258 96.543 59 3232 1 chr6D.!!$F1 3173
7 TraesCS3D01G204200 chr1D 285939050 285942278 3228 False 5230 5230 95.917 6 3232 1 chr1D.!!$F1 3226
8 TraesCS3D01G204200 chr7D 387292997 387296163 3166 False 5217 5217 96.379 59 3232 1 chr7D.!!$F1 3173
9 TraesCS3D01G204200 chr2A 160667199 160670688 3489 True 5210 5210 93.732 1 3472 1 chr2A.!!$R1 3471
10 TraesCS3D01G204200 chr3A 204339729 204342961 3232 True 4975 4975 94.451 1 3235 1 chr3A.!!$R2 3234
11 TraesCS3D01G204200 chr3A 204305501 204308732 3231 True 4951 4951 94.324 1 3235 1 chr3A.!!$R1 3234
12 TraesCS3D01G204200 chr3A 84729562 84731804 2242 False 3424 3424 94.474 1264 3472 1 chr3A.!!$F1 2208
13 TraesCS3D01G204200 chr6A 118303830 118307068 3238 False 4839 4839 93.698 1 3232 1 chr6A.!!$F1 3231

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
983 1010 0.473694 TCTCTCTCCCAAGCCCACAA 60.474 55.0 0.0 0.0 0.0 3.33 F
986 1013 0.622665 CTCTCCCAAGCCCACAATCT 59.377 55.0 0.0 0.0 0.0 2.40 F
2238 2310 1.315690 CTACGACTCCTTGGCCGATA 58.684 55.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2395 2470 0.238289 CCAACCTGTCACGATGTTGC 59.762 55.000 0.0 0.0 37.38 4.17 R
2432 2507 1.078159 TGGTAGTAAGGGTCAGCCTCA 59.922 52.381 0.0 0.0 34.45 3.86 R
3207 3336 3.445008 TCTAGGCTGTGGTTCTTCTCAT 58.555 45.455 0.0 0.0 0.00 2.90 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
393 413 2.081725 TCAAAACCGCACGCTGTATA 57.918 45.000 0.00 0.00 0.00 1.47
683 707 1.539388 CGTGCAAGTGGGATTTAGCAA 59.461 47.619 0.00 0.00 33.37 3.91
764 789 1.719063 TTGCTTCTTCCAGGCCACCT 61.719 55.000 5.01 0.00 0.00 4.00
929 956 1.786937 TTGCCAGAAACCACCATTGT 58.213 45.000 0.00 0.00 0.00 2.71
944 971 2.947652 CCATTGTCGCTTCAATCTCCAT 59.052 45.455 1.22 0.00 36.10 3.41
983 1010 0.473694 TCTCTCTCCCAAGCCCACAA 60.474 55.000 0.00 0.00 0.00 3.33
986 1013 0.622665 CTCTCCCAAGCCCACAATCT 59.377 55.000 0.00 0.00 0.00 2.40
1043 1070 1.815421 GTCATCATGGCGAGCCGTT 60.815 57.895 6.03 0.00 39.42 4.44
1150 1177 1.404717 GCAAAGAGACGCTGGAGATCA 60.405 52.381 0.00 0.00 0.00 2.92
1248 1275 3.599343 CTTCATCGGAGTTGATGTGGAA 58.401 45.455 3.90 0.00 44.82 3.53
1469 1497 2.348666 GTGGATGCACGAGTACATGTTC 59.651 50.000 2.30 0.00 0.00 3.18
1526 1554 6.318648 GTGGATTGTTTCACCAGATTAGCATA 59.681 38.462 0.00 0.00 34.21 3.14
1596 1625 5.922053 TCTGAACTTGATGTGCTAGCATAT 58.078 37.500 25.04 25.04 0.00 1.78
1729 1759 8.302965 TCTGAACTTGATATAGAATTGATGCG 57.697 34.615 0.00 0.00 0.00 4.73
1865 1932 5.855395 GTGAAGCACTGAAGATAGCAAAAAG 59.145 40.000 0.00 0.00 0.00 2.27
1883 1950 7.012232 AGCAAAAAGGAAAAATAACATGGTGTG 59.988 33.333 0.00 0.00 0.00 3.82
2238 2310 1.315690 CTACGACTCCTTGGCCGATA 58.684 55.000 0.00 0.00 0.00 2.92
2344 2419 2.549563 CGCTGCCAGATAACCTCATCAT 60.550 50.000 0.00 0.00 0.00 2.45
2395 2470 3.338249 ACAAGTCATGGAAGACAATCGG 58.662 45.455 0.00 0.00 40.98 4.18
2432 2507 5.960202 AGGTTGGGATATTTCAAAAGAGCAT 59.040 36.000 0.00 0.00 0.00 3.79
2467 2542 4.389576 CCACTGCAACTTCGCGGC 62.390 66.667 6.13 0.79 42.32 6.53
2688 2765 8.689061 TCCTATTTTGTTCATCCATCATTTGAG 58.311 33.333 0.00 0.00 0.00 3.02
3207 3336 6.128486 ACTATGATCATACCAAACATTGCCA 58.872 36.000 11.49 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
223 226 3.192844 AGATCGTTCGTTGAGGTGTGTAT 59.807 43.478 0.00 0.0 0.00 2.29
683 707 6.159988 GTCTTGTCAAGCTGTACTTATGACT 58.840 40.000 7.78 0.0 36.04 3.41
791 816 2.644992 CCGTTTGCAGTCCCTTGC 59.355 61.111 0.00 0.0 44.33 4.01
929 956 1.739466 GTGCAATGGAGATTGAAGCGA 59.261 47.619 0.00 0.0 41.49 4.93
944 971 3.006323 AGAAGTTTGTGGTTTGTGTGCAA 59.994 39.130 0.00 0.0 0.00 4.08
1043 1070 0.250467 GAGGTTGCTGCTCTTGTCCA 60.250 55.000 0.00 0.0 0.00 4.02
1150 1177 1.376424 CTGGTTCGCTGGTGCAGAT 60.376 57.895 0.00 0.0 39.64 2.90
1248 1275 1.359848 GTTCATCGTCGCTGGTGAAT 58.640 50.000 5.84 0.0 33.65 2.57
1361 1388 7.968956 AGTACTAGTACAACAGATGAATGAACG 59.031 37.037 29.87 0.0 38.48 3.95
1469 1497 5.885230 TCAGAAATGCATGTAACTTGAGG 57.115 39.130 0.00 0.0 0.00 3.86
1729 1759 3.441572 ACCAGTGCTTGATACATCTTTGC 59.558 43.478 0.00 0.0 0.00 3.68
1865 1932 5.848406 TCAACCACACCATGTTATTTTTCC 58.152 37.500 0.00 0.0 0.00 3.13
1883 1950 8.764287 CACAAAGTCCTGAAATTAAATTCAACC 58.236 33.333 7.35 0.0 38.75 3.77
2238 2310 0.466543 TGGATTACGCCGCCTACAAT 59.533 50.000 0.00 0.0 0.00 2.71
2333 2408 3.028130 TCCTGCGTACATGATGAGGTTA 58.972 45.455 0.00 0.0 0.00 2.85
2395 2470 0.238289 CCAACCTGTCACGATGTTGC 59.762 55.000 0.00 0.0 37.38 4.17
2432 2507 1.078159 TGGTAGTAAGGGTCAGCCTCA 59.922 52.381 0.00 0.0 34.45 3.86
2444 2519 2.409975 GCGAAGTTGCAGTGGTAGTAA 58.590 47.619 0.00 0.0 34.15 2.24
2467 2542 4.142469 TGCAGACTTTCATGCATCTTCATG 60.142 41.667 0.00 0.0 46.97 3.07
2688 2765 6.095021 AGTTTCAACTTCAACCTACTTCAACC 59.905 38.462 0.00 0.0 35.21 3.77
3207 3336 3.445008 TCTAGGCTGTGGTTCTTCTCAT 58.555 45.455 0.00 0.0 0.00 2.90


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

AutoCloner maintained by Alex Coulton.