Multiple sequence alignment - TraesCS4D01G146300

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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 TraesCS4D01G146300 chr4D 100.000 2378 0 0 1 2378 135005821 135003444 0 4392
1 TraesCS4D01G146300 chr4D 97.397 2382 54 6 1 2378 483696759 483699136 0 4048
2 TraesCS4D01G146300 chr4D 96.136 2381 87 5 1 2378 241142845 241140467 0 3882
3 TraesCS4D01G146300 chr5D 95.672 2380 100 3 1 2378 79865655 79868033 0 3821
4 TraesCS4D01G146300 chr5D 93.910 2381 134 11 1 2378 197839498 197837126 0 3583
5 TraesCS4D01G146300 chr1B 95.380 2381 94 7 1 2378 286167000 286169367 0 3773
6 TraesCS4D01G146300 chr1B 95.203 2022 92 5 361 2378 286025634 286023614 0 3192
7 TraesCS4D01G146300 chr7A 95.112 2189 101 5 195 2378 571648029 571650216 0 3445
8 TraesCS4D01G146300 chr7A 98.043 920 18 0 1459 2378 4954288 4955207 0 1600
9 TraesCS4D01G146300 chr6B 95.660 1636 54 8 1 1626 53079407 53081035 0 2612
10 TraesCS4D01G146300 chr3A 97.532 1499 34 3 1 1496 191855949 191857447 0 2560
11 TraesCS4D01G146300 chr1D 97.284 1215 31 2 1165 2378 185763599 185764812 0 2060


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 TraesCS4D01G146300 chr4D 135003444 135005821 2377 True 4392 4392 100.000 1 2378 1 chr4D.!!$R1 2377
1 TraesCS4D01G146300 chr4D 483696759 483699136 2377 False 4048 4048 97.397 1 2378 1 chr4D.!!$F1 2377
2 TraesCS4D01G146300 chr4D 241140467 241142845 2378 True 3882 3882 96.136 1 2378 1 chr4D.!!$R2 2377
3 TraesCS4D01G146300 chr5D 79865655 79868033 2378 False 3821 3821 95.672 1 2378 1 chr5D.!!$F1 2377
4 TraesCS4D01G146300 chr5D 197837126 197839498 2372 True 3583 3583 93.910 1 2378 1 chr5D.!!$R1 2377
5 TraesCS4D01G146300 chr1B 286167000 286169367 2367 False 3773 3773 95.380 1 2378 1 chr1B.!!$F1 2377
6 TraesCS4D01G146300 chr1B 286023614 286025634 2020 True 3192 3192 95.203 361 2378 1 chr1B.!!$R1 2017
7 TraesCS4D01G146300 chr7A 571648029 571650216 2187 False 3445 3445 95.112 195 2378 1 chr7A.!!$F2 2183
8 TraesCS4D01G146300 chr7A 4954288 4955207 919 False 1600 1600 98.043 1459 2378 1 chr7A.!!$F1 919
9 TraesCS4D01G146300 chr6B 53079407 53081035 1628 False 2612 2612 95.660 1 1626 1 chr6B.!!$F1 1625
10 TraesCS4D01G146300 chr3A 191855949 191857447 1498 False 2560 2560 97.532 1 1496 1 chr3A.!!$F1 1495
11 TraesCS4D01G146300 chr1D 185763599 185764812 1213 False 2060 2060 97.284 1165 2378 1 chr1D.!!$F1 1213

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
297 306 0.767375 TTGAGCAAGCTCCTCCACTT 59.233 50.0 18.54 0.0 42.09 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 1903 1.423921 GGAAGGTCAGAGGTGGGAAAA 59.576 52.381 0.0 0.0 0.0 2.29 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
87 88 2.092375 GGGTTCGAATCCCATTTCCTCT 60.092 50.000 17.16 0.00 44.05 3.69
104 105 1.546476 CTCTGGCACGGAAGTAGAACT 59.454 52.381 0.00 0.00 46.55 3.01
114 115 2.202756 GTAGAACTGGCGGGCGAG 60.203 66.667 0.00 0.88 0.00 5.03
154 163 1.137675 CTCAGATTGATGGAGTCCGCA 59.862 52.381 4.30 2.29 0.00 5.69
272 281 3.618855 TAGTCCCTGGCCGGCTCTT 62.619 63.158 28.56 7.82 0.00 2.85
297 306 0.767375 TTGAGCAAGCTCCTCCACTT 59.233 50.000 18.54 0.00 42.09 3.16
474 483 6.597832 TTTTTCTTGTTTCAGTGGGAAGAA 57.402 33.333 0.00 0.00 36.72 2.52
482 491 0.771127 CAGTGGGAAGAACAAGGGGA 59.229 55.000 0.00 0.00 0.00 4.81
654 667 3.129638 AGTGATCAGTCCGCTAGTTTCTC 59.870 47.826 0.00 0.00 0.00 2.87
880 893 8.910944 CAAGATTGATCTATTTGGATCTTGGTT 58.089 33.333 13.36 0.00 43.07 3.67
1198 1213 6.638168 ATCGACATGATATATTTGCTCACG 57.362 37.500 0.00 0.00 34.83 4.35
1274 1289 1.731720 AGAGTGAAAGATTCGCCAGC 58.268 50.000 0.35 0.00 40.99 4.85
1363 1378 9.282569 GAAGATCTAAATATGGTGCAGAAAGAT 57.717 33.333 0.00 0.00 0.00 2.40
1431 1447 0.396974 TGGGGGCAATATGGAAGCAC 60.397 55.000 0.00 0.00 0.00 4.40
1468 1484 7.270047 TCCCTTATTACGTTACCATTTCTCTG 58.730 38.462 0.00 0.00 0.00 3.35
1848 1864 2.415625 CCTCTTCCCTTCAACTCGTACG 60.416 54.545 9.53 9.53 0.00 3.67
1887 1903 7.340487 CCAGTAAGCATTTCCTCTATTTCCTTT 59.660 37.037 0.00 0.00 0.00 3.11
2120 2137 3.011517 GGGAGGAGCCAGGAAGCA 61.012 66.667 0.00 0.00 38.95 3.91
2275 2292 7.851472 CCACTCTCTTTCTTCTTTCGTTTTAAC 59.149 37.037 0.00 0.00 0.00 2.01
2358 2378 9.810231 GTCTAGCTCTACTTTACAACGATATAC 57.190 37.037 0.00 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 0.320374 CCAGTTCTACTTCCGTGCCA 59.680 55.000 0.00 0.0 0.00 4.92
104 105 3.454573 ACGTAATCTCGCCCGCCA 61.455 61.111 0.00 0.0 0.00 5.69
114 115 5.710984 TGAGGTTCTTTCTCTCACGTAATC 58.289 41.667 0.00 0.0 33.21 1.75
154 163 1.479709 AGCAGCTATTCTGTCCGACT 58.520 50.000 0.00 0.0 44.66 4.18
254 263 3.618855 AAGAGCCGGCCAGGGACTA 62.619 63.158 26.15 0.0 41.48 2.59
272 281 0.767375 AGGAGCTTGCTCAAGAACCA 59.233 50.000 21.97 0.0 40.79 3.67
297 306 5.003096 TCATCTATGAGCATCCTACCTGA 57.997 43.478 0.00 0.0 32.11 3.86
482 491 4.020839 CACTGAAGGATTTCAAGGGCAATT 60.021 41.667 0.00 0.0 42.48 2.32
564 576 1.377333 TTCTCTCGCTCTCCTCGCA 60.377 57.895 0.00 0.0 0.00 5.10
654 667 1.276421 AGGAACACCGAGTGGAATCAG 59.724 52.381 8.57 0.0 37.94 2.90
880 893 8.319881 TCAAAATCAATAAAAAGGCCATCATGA 58.680 29.630 5.01 0.0 0.00 3.07
1198 1213 2.396590 TTATGACCTTCGCCTGGAAC 57.603 50.000 0.00 0.0 0.00 3.62
1274 1289 4.368315 TCGAATACGATGGGATTTCACAG 58.632 43.478 0.00 0.0 43.81 3.66
1301 1316 2.169144 GGAATTCCCAGCAAATCCTTGG 59.831 50.000 14.03 0.0 31.90 3.61
1363 1378 7.255242 GGCATCTTCCATTCATTTCGATTTAGA 60.255 37.037 0.00 0.0 0.00 2.10
1431 1447 4.262506 CGTAATAAGGGAAAGGGAGCTAGG 60.263 50.000 0.00 0.0 0.00 3.02
1487 1503 5.554070 GGTAAGTTAAGTAAGTCAAGCCCA 58.446 41.667 0.00 0.0 0.00 5.36
1848 1864 3.206964 GCTTACTGGGACATAGCCTTTC 58.793 50.000 0.00 0.0 38.20 2.62
1887 1903 1.423921 GGAAGGTCAGAGGTGGGAAAA 59.576 52.381 0.00 0.0 0.00 2.29
2120 2137 2.231721 GTCTCTTCCTCACTAAACGCCT 59.768 50.000 0.00 0.0 0.00 5.52
2154 2171 6.863275 TCGAAAGCACTCATCTTTATCTACA 58.137 36.000 0.00 0.0 34.24 2.74
2157 2174 5.689514 CGATCGAAAGCACTCATCTTTATCT 59.310 40.000 10.26 0.0 34.24 1.98


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

AutoCloner maintained by Alex Coulton.