Multiple sequence alignment - TraesCS7B01G308100

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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 TraesCS7B01G308100 chr7B 100.000 2228 0 0 1 2228 551952474 551954701 0.000000e+00 4115
1 TraesCS7B01G308100 chr7A 95.612 2256 61 8 1 2228 593463158 593465403 0.000000e+00 3583
2 TraesCS7B01G308100 chr7D 94.062 1600 54 18 634 2228 518641383 518642946 0.000000e+00 2390
3 TraesCS7B01G308100 chr7D 96.799 656 11 5 1 647 518640611 518641265 0.000000e+00 1086
4 TraesCS7B01G308100 chr4B 87.786 262 26 5 1760 2019 25784335 25784078 3.600000e-78 302
5 TraesCS7B01G308100 chr4B 87.786 262 26 5 1760 2019 25787787 25787530 3.600000e-78 302
6 TraesCS7B01G308100 chr4D 87.786 262 22 8 1760 2019 15253207 15252954 4.650000e-77 298


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 TraesCS7B01G308100 chr7B 551952474 551954701 2227 False 4115 4115 100.0000 1 2228 1 chr7B.!!$F1 2227
1 TraesCS7B01G308100 chr7A 593463158 593465403 2245 False 3583 3583 95.6120 1 2228 1 chr7A.!!$F1 2227
2 TraesCS7B01G308100 chr7D 518640611 518642946 2335 False 1738 2390 95.4305 1 2228 2 chr7D.!!$F1 2227
3 TraesCS7B01G308100 chr4B 25784078 25787787 3709 True 302 302 87.7860 1760 2019 2 chr4B.!!$R1 259

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
995 1143 3.252215 CCACTAGCTACTTCTCTCATCGG 59.748 52.174 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1866 3560 0.90891 TGCCCGTACATGGATGTTCT 59.091 50.0 0.0 0.0 41.97 3.01 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
39 40 3.564352 GGGGATCCACAGAAAAGGAACAT 60.564 47.826 15.23 0.00 37.48 2.71
142 147 5.376625 ACACAATTAGAAGCTCCAACTTGA 58.623 37.500 0.00 0.00 0.00 3.02
179 184 5.174395 CACCTAAGACTTGATGAGTTCTGG 58.826 45.833 0.00 0.00 39.19 3.86
252 257 4.573900 AGTGAGGCACTTTGATAGTTCAG 58.426 43.478 0.00 0.00 42.59 3.02
405 416 5.698545 GCTGGTGACTAGATGATTCATAACC 59.301 44.000 0.00 2.50 0.00 2.85
541 552 4.808414 TGAAAGTATCACTCTGACTGGG 57.192 45.455 0.00 0.00 31.50 4.45
573 584 8.969260 AACAATATCACACTGATACATGTCAT 57.031 30.769 0.00 0.00 41.62 3.06
949 1097 4.019860 TGTCTTCAGCTCTTATTCTTGCCT 60.020 41.667 0.00 0.00 0.00 4.75
959 1107 5.018809 TCTTATTCTTGCCTGCTTCCATTT 58.981 37.500 0.00 0.00 0.00 2.32
995 1143 3.252215 CCACTAGCTACTTCTCTCATCGG 59.748 52.174 0.00 0.00 0.00 4.18
1235 1383 0.038744 CCACCAAACTGAGATGGCCT 59.961 55.000 3.32 0.00 40.51 5.19
1247 1395 0.750546 GATGGCCTGATGCTGCTTCA 60.751 55.000 16.14 16.14 40.92 3.02
1723 1872 8.776376 ATTGGTCAAGGCTAAAATAATTGTTG 57.224 30.769 0.00 0.00 0.00 3.33
1745 1894 5.155161 TGAGCAAGCCCTTAGAATATAGGA 58.845 41.667 0.00 0.00 33.13 2.94
1828 3522 5.473162 TGTTGTTGGTGGTCTTATCAATGAG 59.527 40.000 0.00 0.00 0.00 2.90
1881 3576 4.811024 ACATTAGCAGAACATCCATGTACG 59.189 41.667 0.00 0.00 40.80 3.67
1981 3677 9.797642 TGTACATTCCTAATCTATGATGCAAAT 57.202 29.630 0.00 0.00 0.00 2.32
2073 3769 2.294791 CCTTGGAGCTCTATGTACTCGG 59.705 54.545 14.64 0.00 0.00 4.63
2087 3783 2.640316 ACTCGGCCATCTATTTTCCC 57.360 50.000 2.24 0.00 0.00 3.97
2116 3812 7.128331 CAGTTTCATTCTTATGGCTGTATTCG 58.872 38.462 0.00 0.00 32.40 3.34
2182 3897 3.059306 CGTTGCACAATTATTTTGCCTCG 59.941 43.478 12.69 12.51 35.26 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 147 3.655777 TCTTAGGTGGAGGGAACAAACAT 59.344 43.478 0.00 0.00 0.00 2.71
179 184 5.241662 AGAACAGCAAGTTGGATCTTCTAC 58.758 41.667 4.75 0.00 41.51 2.59
405 416 2.737252 GTTACCAAAGACTGAAGAGGCG 59.263 50.000 0.00 0.00 29.20 5.52
541 552 5.565592 TCAGTGTGATATTGTTTCCATGC 57.434 39.130 0.00 0.00 0.00 4.06
567 578 3.244318 TGAACTCTGTGACAGCATGACAT 60.244 43.478 7.93 0.00 43.59 3.06
573 584 0.250038 GCCTGAACTCTGTGACAGCA 60.250 55.000 7.93 0.00 0.00 4.41
949 1097 3.828451 AGCTAGCTTGAAAAATGGAAGCA 59.172 39.130 12.68 0.00 43.78 3.91
995 1143 4.734398 TTTGATGAAATGGCCATGGTAC 57.266 40.909 21.63 11.50 0.00 3.34
1235 1383 3.216800 GGTATGGAATGAAGCAGCATCA 58.783 45.455 2.13 2.13 0.00 3.07
1247 1395 3.624777 CTGCAAAGTCCTGGTATGGAAT 58.375 45.455 0.00 0.00 37.93 3.01
1723 1872 5.729510 CTCCTATATTCTAAGGGCTTGCTC 58.270 45.833 0.00 0.00 33.40 4.26
1828 3522 4.853050 AGCCGGATCAGCTGCAGC 62.853 66.667 31.53 31.53 39.69 5.25
1866 3560 0.908910 TGCCCGTACATGGATGTTCT 59.091 50.000 0.00 0.00 41.97 3.01
2073 3769 3.365472 ACTGGTTGGGAAAATAGATGGC 58.635 45.455 0.00 0.00 0.00 4.40
2087 3783 5.047802 ACAGCCATAAGAATGAAACTGGTTG 60.048 40.000 0.00 0.00 34.84 3.77
2182 3897 5.662211 AATTGCAAATGAAAACACTCAGC 57.338 34.783 1.71 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.