Multiple sequence alignment - TraesCS4D01G161000

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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 TraesCS4D01G161000 chr4D 100.000 2243 0 0 1 2243 240994780 240992538 0 4143
1 TraesCS4D01G161000 chr4D 96.446 2251 72 5 1 2243 123350116 123352366 0 3707
2 TraesCS4D01G161000 chr4D 95.828 2253 84 4 1 2243 134979418 134981670 0 3631
3 TraesCS4D01G161000 chr4D 96.652 1643 49 4 607 2243 123561662 123563304 0 2724
4 TraesCS4D01G161000 chr5D 95.909 2249 83 6 1 2243 301054395 301056640 0 3635
5 TraesCS4D01G161000 chr6D 95.861 2247 76 9 1 2243 370022512 370024745 0 3618
6 TraesCS4D01G161000 chr6D 96.891 1158 36 0 1086 2243 369972795 369971638 0 1940
7 TraesCS4D01G161000 chr1D 95.763 2242 78 5 1 2239 269426754 269424527 0 3598
8 TraesCS4D01G161000 chr6A 93.336 2251 111 15 1 2243 79195944 79198163 0 3290
9 TraesCS4D01G161000 chr7B 97.027 1312 34 2 1 1307 716784602 716785913 0 2202
10 TraesCS4D01G161000 chr7B 96.654 1315 39 2 1 1310 742948743 742947429 0 2180
11 TraesCS4D01G161000 chr7A 96.875 1312 36 2 1 1307 60084931 60086242 0 2191
12 TraesCS4D01G161000 chr7D 97.535 1217 29 1 1028 2243 382029169 382027953 0 2080


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 TraesCS4D01G161000 chr4D 240992538 240994780 2242 True 4143 4143 100.000 1 2243 1 chr4D.!!$R1 2242
1 TraesCS4D01G161000 chr4D 123350116 123352366 2250 False 3707 3707 96.446 1 2243 1 chr4D.!!$F1 2242
2 TraesCS4D01G161000 chr4D 134979418 134981670 2252 False 3631 3631 95.828 1 2243 1 chr4D.!!$F3 2242
3 TraesCS4D01G161000 chr4D 123561662 123563304 1642 False 2724 2724 96.652 607 2243 1 chr4D.!!$F2 1636
4 TraesCS4D01G161000 chr5D 301054395 301056640 2245 False 3635 3635 95.909 1 2243 1 chr5D.!!$F1 2242
5 TraesCS4D01G161000 chr6D 370022512 370024745 2233 False 3618 3618 95.861 1 2243 1 chr6D.!!$F1 2242
6 TraesCS4D01G161000 chr6D 369971638 369972795 1157 True 1940 1940 96.891 1086 2243 1 chr6D.!!$R1 1157
7 TraesCS4D01G161000 chr1D 269424527 269426754 2227 True 3598 3598 95.763 1 2239 1 chr1D.!!$R1 2238
8 TraesCS4D01G161000 chr6A 79195944 79198163 2219 False 3290 3290 93.336 1 2243 1 chr6A.!!$F1 2242
9 TraesCS4D01G161000 chr7B 716784602 716785913 1311 False 2202 2202 97.027 1 1307 1 chr7B.!!$F1 1306
10 TraesCS4D01G161000 chr7B 742947429 742948743 1314 True 2180 2180 96.654 1 1310 1 chr7B.!!$R1 1309
11 TraesCS4D01G161000 chr7A 60084931 60086242 1311 False 2191 2191 96.875 1 1307 1 chr7A.!!$F1 1306
12 TraesCS4D01G161000 chr7D 382027953 382029169 1216 True 2080 2080 97.535 1028 2243 1 chr7D.!!$R1 1215

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
740 744 0.120377 TTCAGGATACCCCACCCAGT 59.88 55.0 0.0 0.0 37.41 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2024 1.293924 CAGAATGGCGTCCTTAGCAG 58.706 55.0 0.0 0.0 36.08 4.24 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
96 97 7.346751 TGTTTGGAAACAGAGCTCTTTTATT 57.653 32.000 15.27 6.64 43.45 1.40
99 100 4.826733 TGGAAACAGAGCTCTTTTATTGCA 59.173 37.500 15.27 14.41 35.01 4.08
139 140 1.403647 CGTTGGCTTATCCGTCAGTCA 60.404 52.381 0.00 0.00 37.80 3.41
150 151 1.293963 CGTCAGTCACGTCGGGTCTA 61.294 60.000 0.00 0.00 44.07 2.59
180 181 6.017109 TCAGTTGAAAGCTATGAAACAAGTCC 60.017 38.462 0.00 0.00 0.00 3.85
183 184 2.472695 AGCTATGAAACAAGTCCGCA 57.527 45.000 0.00 0.00 0.00 5.69
256 257 4.081406 CAATTTGGGTCAGACCTTGATGA 58.919 43.478 19.57 0.87 38.64 2.92
282 283 5.777802 CGACTCAGGCATTACTCAATAGAT 58.222 41.667 0.00 0.00 0.00 1.98
303 304 2.222027 GTGCAAGGCTTACAGAAGTGT 58.778 47.619 0.00 0.00 41.06 3.55
537 539 5.337578 AAAAGAAAGCACTTTGCCTTACA 57.662 34.783 0.00 0.00 46.52 2.41
538 540 5.337578 AAAGAAAGCACTTTGCCTTACAA 57.662 34.783 0.00 0.00 46.52 2.41
551 555 9.830975 ACTTTGCCTTACAAGTGAATTAAAAAT 57.169 25.926 0.00 0.00 40.06 1.82
568 572 4.668138 AAAATAGGTTGCCCCTTACTCA 57.332 40.909 0.00 0.00 42.73 3.41
666 670 5.664294 AAGATAGATTTTTGTGCCATGCA 57.336 34.783 0.00 0.00 35.60 3.96
740 744 0.120377 TTCAGGATACCCCACCCAGT 59.880 55.000 0.00 0.00 37.41 4.00
759 763 2.429930 CCACAAGGGCTGACGGAA 59.570 61.111 0.00 0.00 0.00 4.30
935 939 2.093447 AGGCCCAAGTACTTCGAATCAG 60.093 50.000 4.77 0.00 0.00 2.90
1040 1049 0.833834 ATAGGTGCCGGAGCTGCTAT 60.834 55.000 5.05 0.00 40.80 2.97
1101 1110 2.029244 CCTCGGTTCGTTGATTCATTCG 59.971 50.000 5.72 5.72 0.00 3.34
1165 1174 1.403249 CCATTTTGGGCTTTGCTCTCG 60.403 52.381 0.00 0.00 32.67 4.04
1569 1587 1.550524 CCCTCCTTGATCGTGACAGAA 59.449 52.381 0.00 0.00 0.00 3.02
1641 1659 4.344359 TTTGATATATGGTGCCACGCTA 57.656 40.909 0.00 0.00 0.00 4.26
1717 1735 4.745116 GGGGGCTTGAAACTCCTC 57.255 61.111 0.00 0.00 0.00 3.71
1889 1907 1.030488 CACTCTACTCCGGCCGAAGA 61.030 60.000 30.73 21.08 0.00 2.87
2035 2053 1.224069 CGCCATTCTGGGTATGCTCG 61.224 60.000 0.00 0.00 38.19 5.03
2056 2074 9.168451 TGCTCGAATTAAATACCAGTTTGAATA 57.832 29.630 0.00 0.00 0.00 1.75
2064 2082 6.469782 AATACCAGTTTGAATAGGGCATTG 57.530 37.500 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 5.753438 CGTTAATAGCTGGTCTAATTCTGCA 59.247 40.000 0.00 0.00 0.00 4.41
99 100 6.761714 CCAACGTTAATAGCTGGTCTAATTCT 59.238 38.462 0.00 0.00 0.00 2.40
150 151 2.028112 TCATAGCTTTCAACTGAGCGGT 60.028 45.455 0.00 0.00 43.53 5.68
180 181 4.749245 ATTCCAGTTTTGAACTACTGCG 57.251 40.909 0.00 0.00 40.46 5.18
183 184 4.892934 TGCCAATTCCAGTTTTGAACTACT 59.107 37.500 0.00 0.00 40.46 2.57
282 283 2.221169 CACTTCTGTAAGCCTTGCACA 58.779 47.619 0.00 0.00 36.05 4.57
303 304 4.895889 TGGTTCATATTGTGGTTGTTTGGA 59.104 37.500 0.00 0.00 0.00 3.53
465 466 7.498570 TCTTTCGTTAGTTAAGCCACCTTTTTA 59.501 33.333 0.00 0.00 32.47 1.52
568 572 4.917906 AAAGCCTTCTTCCTACATCTGT 57.082 40.909 0.00 0.00 0.00 3.41
666 670 3.262915 AGACTCTCAGCAGCTTGGTTTAT 59.737 43.478 0.00 0.00 0.00 1.40
751 755 2.083628 ATAGGTAGGGGTTCCGTCAG 57.916 55.000 0.00 0.00 38.33 3.51
759 763 5.436842 TCAGGTATAGGTATAGGTAGGGGT 58.563 45.833 0.00 0.00 0.00 4.95
798 802 5.988310 TGAGCTGTGGATTGAAAATCATT 57.012 34.783 0.00 0.00 0.00 2.57
935 939 5.173854 CGTTGTTCTTTCTTGGATTTCTTGC 59.826 40.000 0.00 0.00 0.00 4.01
991 1000 3.119459 GCACCTTCTAACATCTCGAGTCA 60.119 47.826 13.13 0.00 0.00 3.41
1089 1098 0.523335 GCGCCACCGAATGAATCAAC 60.523 55.000 0.00 0.00 36.29 3.18
1101 1110 1.447317 ATGATGGATTTCGCGCCACC 61.447 55.000 0.00 2.65 36.92 4.61
1165 1174 2.566952 AACAATGCAATAGCTTCGGC 57.433 45.000 0.00 0.00 42.74 5.54
1190 1199 4.863548 TGAGATCAGAAAGGCCATCATTT 58.136 39.130 5.01 0.00 0.00 2.32
1355 1365 0.825840 CCGAAGCACCCCTTTTCCAA 60.826 55.000 0.00 0.00 32.78 3.53
1569 1587 1.978580 AGTAGTGCTTGCCTAACCTGT 59.021 47.619 0.00 0.00 0.00 4.00
1641 1659 2.758423 GGCCGGTACCATTTCTTCAATT 59.242 45.455 13.54 0.00 0.00 2.32
1815 1833 2.659610 GGCTGTTCCTGCTCGAGT 59.340 61.111 15.13 0.00 0.00 4.18
1889 1907 5.130145 TCAAGTTGTTGGTGGAATGGATTTT 59.870 36.000 2.11 0.00 34.09 1.82
2006 2024 1.293924 CAGAATGGCGTCCTTAGCAG 58.706 55.000 0.00 0.00 36.08 4.24
2035 2053 8.691797 TGCCCTATTCAAACTGGTATTTAATTC 58.308 33.333 0.00 0.00 0.00 2.17
2056 2074 7.094205 CGATCCTAAATAAAATAGCAATGCCCT 60.094 37.037 0.00 0.00 0.00 5.19
2064 2082 7.997071 GCTTTTGCGATCCTAAATAAAATAGC 58.003 34.615 0.00 0.00 34.86 2.97


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

AutoCloner maintained by Alex Coulton.