Multiple sequence alignment - TraesCS3B01G400300

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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 TraesCS3B01G400300 chr3B 100.000 2952 0 0 1 2952 632150079 632153030 0 5452
1 TraesCS3B01G400300 chr3B 98.273 2953 49 2 1 2952 717600213 717597262 0 5169
2 TraesCS3B01G400300 chr2B 98.341 2953 46 3 1 2951 106932257 106935208 0 5179
3 TraesCS3B01G400300 chr2B 98.307 2953 47 3 1 2952 563765202 563768152 0 5173
4 TraesCS3B01G400300 chr2B 98.104 2953 53 3 1 2952 257723679 257720729 0 5140
5 TraesCS3B01G400300 chr2B 98.037 2954 55 3 1 2952 327771545 327768593 0 5131
6 TraesCS3B01G400300 chr2B 97.934 2953 59 2 1 2952 63584121 63587072 0 5114
7 TraesCS3B01G400300 chr1B 98.273 2953 49 2 1 2952 26649548 26652499 0 5169
8 TraesCS3B01G400300 chr5B 98.172 2954 51 3 1 2952 36453512 36450560 0 5153
9 TraesCS3B01G400300 chr4B 98.138 2954 50 5 1 2952 11627592 11624642 0 5145


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 TraesCS3B01G400300 chr3B 632150079 632153030 2951 False 5452 5452 100.000 1 2952 1 chr3B.!!$F1 2951
1 TraesCS3B01G400300 chr3B 717597262 717600213 2951 True 5169 5169 98.273 1 2952 1 chr3B.!!$R1 2951
2 TraesCS3B01G400300 chr2B 106932257 106935208 2951 False 5179 5179 98.341 1 2951 1 chr2B.!!$F2 2950
3 TraesCS3B01G400300 chr2B 563765202 563768152 2950 False 5173 5173 98.307 1 2952 1 chr2B.!!$F3 2951
4 TraesCS3B01G400300 chr2B 257720729 257723679 2950 True 5140 5140 98.104 1 2952 1 chr2B.!!$R1 2951
5 TraesCS3B01G400300 chr2B 327768593 327771545 2952 True 5131 5131 98.037 1 2952 1 chr2B.!!$R2 2951
6 TraesCS3B01G400300 chr2B 63584121 63587072 2951 False 5114 5114 97.934 1 2952 1 chr2B.!!$F1 2951
7 TraesCS3B01G400300 chr1B 26649548 26652499 2951 False 5169 5169 98.273 1 2952 1 chr1B.!!$F1 2951
8 TraesCS3B01G400300 chr5B 36450560 36453512 2952 True 5153 5153 98.172 1 2952 1 chr5B.!!$R1 2951
9 TraesCS3B01G400300 chr4B 11624642 11627592 2950 True 5145 5145 98.138 1 2952 1 chr4B.!!$R1 2951

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
900 901 0.254747 CCCAAACCCCGCTCATCTTA 59.745 55.0 0.0 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2425 2429 1.559682 GGGCTGGAACCATAGTCAGAA 59.44 52.381 0.0 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
84 85 7.920682 TGTTTCAGGCTTTCTCTAAAATGAAAC 59.079 33.333 16.47 16.47 43.21 2.78
787 788 9.784531 CAATATATGGTAGTTTCCACTCTTCAT 57.215 33.333 0.00 0.00 40.51 2.57
900 901 0.254747 CCCAAACCCCGCTCATCTTA 59.745 55.000 0.00 0.00 0.00 2.10
1141 1142 3.370366 GTGCTCTGCTCATGTTGTTAGAG 59.630 47.826 0.00 0.00 35.84 2.43
1294 1295 2.315925 ATCACCTTCGGCATGTACAG 57.684 50.000 0.33 0.00 0.00 2.74
1302 1303 1.765161 CGGCATGTACAGCATCACCG 61.765 60.000 15.90 11.34 43.48 4.94
1358 1359 1.656587 TGTCCTGGAGTGCCATTAGT 58.343 50.000 0.00 0.00 44.91 2.24
1439 1440 0.756294 TTGTGTGTCCATCCGTCTGT 59.244 50.000 0.00 0.00 0.00 3.41
1480 1481 5.765182 CCCCATTGATGTCCTACTAATGTTC 59.235 44.000 0.00 0.00 0.00 3.18
1640 1641 8.679100 ACTGCTAACACAGAGAGTATTTACTAG 58.321 37.037 0.00 0.00 40.25 2.57
1898 1900 2.126346 GGATGCAACAGCGGCAAC 60.126 61.111 1.45 0.00 45.60 4.17
1997 1999 1.329599 TCGTCGACACTATCATCCACG 59.670 52.381 17.16 0.00 0.00 4.94
2011 2013 2.241281 TCCACGGGTATCTTCCTTGA 57.759 50.000 0.00 0.00 0.00 3.02
2101 2103 3.334691 CCAGTTGAATGTATGGTCGTGT 58.665 45.455 0.00 0.00 0.00 4.49
2128 2130 8.644374 AGTAGAATGGTATTTTGTTTTAGGCA 57.356 30.769 0.00 0.00 0.00 4.75
2346 2349 6.500684 TCTTTTCTGATTCATGTAACAGGC 57.499 37.500 9.24 0.00 0.00 4.85
2369 2373 1.630369 ACAGAGGAAGCCATGTTGCTA 59.370 47.619 0.00 0.00 41.80 3.49
2425 2429 1.300697 GAGTCCGGCGTGTTGTTCT 60.301 57.895 6.01 0.00 0.00 3.01
2463 2467 3.325716 AGCCCTGACTACCGAAGTTTTTA 59.674 43.478 0.00 0.00 39.07 1.52
2678 2682 6.451064 TTGTCTCTGCGAATCTGAATACTA 57.549 37.500 0.00 0.00 0.00 1.82
2761 2765 4.039973 CCTGTTACCAGAACCTGACAACTA 59.960 45.833 0.00 0.00 41.50 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 7.680730 AGTATTGGTGACTAATAGGCCTATTG 58.319 38.462 37.67 29.48 36.52 1.90
176 177 5.425217 TGTATATGGATCACTGTGGACAAGT 59.575 40.000 8.11 1.74 0.00 3.16
504 505 2.634815 ACATGAGGCAGATGGATGAC 57.365 50.000 0.00 0.00 0.00 3.06
679 680 9.676861 TCACAGAGATAAGATGAAAATCAACAT 57.323 29.630 0.00 0.00 0.00 2.71
787 788 2.092484 TGCAGCATACTAATCTTGGGCA 60.092 45.455 0.00 0.00 0.00 5.36
1141 1142 2.795329 TGGCAGGAAGTGAAAATCCTC 58.205 47.619 0.00 0.00 44.26 3.71
1294 1295 4.197498 GCATGCCCACGGTGATGC 62.197 66.667 14.85 14.85 35.02 3.91
1333 1334 0.962356 GGCACTCCAGGACATGTTGG 60.962 60.000 9.92 9.92 35.74 3.77
1439 1440 4.978438 TGGGGCACAACTTAGTTAACTA 57.022 40.909 11.38 11.38 0.00 2.24
1480 1481 4.260985 TCAGCACCATGGTAGTAACAATG 58.739 43.478 19.28 2.64 36.86 2.82
1640 1641 2.017049 ACAAAGTCTCTGTGTTGGCAC 58.983 47.619 0.00 0.00 45.44 5.01
1997 1999 4.797912 AAGGGAATCAAGGAAGATACCC 57.202 45.455 0.00 0.00 36.67 3.69
2011 2013 4.050757 AGGCAGGAGAGAATAAAGGGAAT 58.949 43.478 0.00 0.00 0.00 3.01
2346 2349 2.082231 CAACATGGCTTCCTCTGTCAG 58.918 52.381 0.00 0.00 0.00 3.51
2369 2373 2.629617 CAGGGCTGAGACCAAACAAAAT 59.370 45.455 7.31 0.00 29.21 1.82
2425 2429 1.559682 GGGCTGGAACCATAGTCAGAA 59.440 52.381 0.00 0.00 0.00 3.02
2463 2467 8.627403 CATATTTCTATGCAACTTCAACAGGAT 58.373 33.333 0.00 0.00 0.00 3.24
2712 2716 4.104102 TCAATTTGTCAGGTAAGTGGGTCT 59.896 41.667 0.00 0.00 0.00 3.85
2761 2765 1.646447 TCCACTAGTCAGATGGGTCCT 59.354 52.381 0.00 0.00 34.03 3.85


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

AutoCloner maintained by Alex Coulton.