Multiple sequence alignment - TraesCS5B01G145600

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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 TraesCS5B01G145600 chr5B 100.000 2294 0 0 1 2294 272829766 272832059 0.000000e+00 4237
1 TraesCS5B01G145600 chr5B 94.965 2304 103 8 1 2294 338718466 338720766 0.000000e+00 3600
2 TraesCS5B01G145600 chr5B 94.400 2232 110 9 74 2294 480059538 480057311 0.000000e+00 3415
3 TraesCS5B01G145600 chr6B 96.054 2281 80 5 22 2294 704096450 704094172 0.000000e+00 3705
4 TraesCS5B01G145600 chr3D 95.832 2303 79 7 1 2294 605958866 605961160 0.000000e+00 3705
5 TraesCS5B01G145600 chr7B 93.829 2301 129 8 1 2293 118130954 118133249 0.000000e+00 3450
6 TraesCS5B01G145600 chr7B 91.964 336 19 5 1 331 692983036 692983368 4.460000e-127 464
7 TraesCS5B01G145600 chr4B 93.310 2317 127 18 1 2294 524004268 524001957 0.000000e+00 3395
8 TraesCS5B01G145600 chr5D 93.241 2323 124 20 1 2294 351392589 351390271 0.000000e+00 3389
9 TraesCS5B01G145600 chr3B 94.060 2155 116 5 148 2294 735208589 735206439 0.000000e+00 3260
10 TraesCS5B01G145600 chr3B 93.985 2078 118 5 221 2294 217103184 217101110 0.000000e+00 3138
11 TraesCS5B01G145600 chr3B 92.035 339 15 8 1 331 37296909 37296575 1.240000e-127 466
12 TraesCS5B01G145600 chr1B 90.828 338 19 9 1 330 551878367 551878034 2.090000e-120 442


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 TraesCS5B01G145600 chr5B 272829766 272832059 2293 False 4237 4237 100.000 1 2294 1 chr5B.!!$F1 2293
1 TraesCS5B01G145600 chr5B 338718466 338720766 2300 False 3600 3600 94.965 1 2294 1 chr5B.!!$F2 2293
2 TraesCS5B01G145600 chr5B 480057311 480059538 2227 True 3415 3415 94.400 74 2294 1 chr5B.!!$R1 2220
3 TraesCS5B01G145600 chr6B 704094172 704096450 2278 True 3705 3705 96.054 22 2294 1 chr6B.!!$R1 2272
4 TraesCS5B01G145600 chr3D 605958866 605961160 2294 False 3705 3705 95.832 1 2294 1 chr3D.!!$F1 2293
5 TraesCS5B01G145600 chr7B 118130954 118133249 2295 False 3450 3450 93.829 1 2293 1 chr7B.!!$F1 2292
6 TraesCS5B01G145600 chr4B 524001957 524004268 2311 True 3395 3395 93.310 1 2294 1 chr4B.!!$R1 2293
7 TraesCS5B01G145600 chr5D 351390271 351392589 2318 True 3389 3389 93.241 1 2294 1 chr5D.!!$R1 2293
8 TraesCS5B01G145600 chr3B 735206439 735208589 2150 True 3260 3260 94.060 148 2294 1 chr3B.!!$R3 2146
9 TraesCS5B01G145600 chr3B 217101110 217103184 2074 True 3138 3138 93.985 221 2294 1 chr3B.!!$R2 2073

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
125 127 0.527817 CTCCGATCCCCTCGTTTTCG 60.528 60.000 0.0 0.0 46.18 3.46 F
714 742 1.822990 ACGGTTGCGGAATCTCTAGAA 59.177 47.619 0.0 0.0 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1211 1240 0.320697 ACGGTGAGAACTTGGCCTAC 59.679 55.0 3.32 0.0 0.00 3.18 R
1657 1688 0.457337 CTTGAATGCGGCTTGCTTCC 60.457 55.0 0.00 0.0 46.63 3.46 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
20 21 0.633921 CCTCCTCTCTTCCCCTCTCA 59.366 60.000 0.00 0.00 0.00 3.27
76 78 3.687698 CGGAGTATTTGACCGTGGATTTT 59.312 43.478 0.00 0.00 41.47 1.82
125 127 0.527817 CTCCGATCCCCTCGTTTTCG 60.528 60.000 0.00 0.00 46.18 3.46
212 218 5.355596 TGGAAATTTGTGTTGATGTTGGTC 58.644 37.500 0.00 0.00 0.00 4.02
263 283 2.801077 AGGGTTAGGGTTATGTGTGC 57.199 50.000 0.00 0.00 0.00 4.57
606 634 5.277154 CCAAAGTAACGTTGTTGAGTTCGAT 60.277 40.000 11.99 0.00 0.00 3.59
714 742 1.822990 ACGGTTGCGGAATCTCTAGAA 59.177 47.619 0.00 0.00 0.00 2.10
741 769 4.400567 GCTCTTGAGTTATTTGCCTCCAAT 59.599 41.667 0.00 0.00 0.00 3.16
747 775 5.885912 TGAGTTATTTGCCTCCAATAAGGTC 59.114 40.000 0.00 0.00 38.79 3.85
873 902 3.030291 ACAAGTTTGGCCAACATTGAGA 58.970 40.909 33.22 13.07 37.93 3.27
921 950 7.765695 AGCTTTTGAAGAGGACAATTATGAA 57.234 32.000 0.00 0.00 0.00 2.57
939 968 4.655762 TGAATACGAGGAGGATGACAAG 57.344 45.455 0.00 0.00 0.00 3.16
983 1012 3.801114 TGTGGGTGATCTCGAGTAATG 57.199 47.619 13.13 0.00 0.00 1.90
1069 1098 3.199727 TGATGATGGTCCCGATGAAGAAA 59.800 43.478 0.00 0.00 0.00 2.52
1130 1159 1.979619 AAGAAGGTATTCGGGCGGGG 61.980 60.000 0.00 0.00 40.58 5.73
1151 1180 3.003689 GGTCACAAGACACCATTGTTCAG 59.996 47.826 0.00 0.00 46.80 3.02
1211 1240 6.072286 GGTGGCAAATGTATATCTCTTGGATG 60.072 42.308 0.00 0.00 35.98 3.51
1262 1291 2.897969 ACGGCAAGAACGGGATATATCT 59.102 45.455 12.42 0.00 35.23 1.98
1315 1345 5.127194 TGAAGATATGGCTCGACAACTACTT 59.873 40.000 0.00 0.00 0.00 2.24
1325 1355 3.991773 TCGACAACTACTTGGTTATGCAC 59.008 43.478 0.00 0.00 0.00 4.57
1559 1590 9.289782 GAGTTCATTGCTTATAGGTTATCCAAT 57.710 33.333 0.00 0.00 35.89 3.16
1587 1618 8.757982 AATATTCACACTTCCAATAATGAGCT 57.242 30.769 0.00 0.00 0.00 4.09
1623 1654 3.960102 TGACCTTGTGAAAGCCATCTTTT 59.040 39.130 0.00 0.00 42.24 2.27
1657 1688 2.550699 TACGGCAAGGCATGGAAGGG 62.551 60.000 0.00 0.00 0.00 3.95
1702 1733 2.310538 GTATGGCAATTGGGAGGAAGG 58.689 52.381 7.72 0.00 0.00 3.46
1877 1911 0.883833 CTTTTGAGCATTGTCGGCCT 59.116 50.000 0.00 0.00 0.00 5.19
2048 2084 5.390567 GCGTCAACTAAGAACAAGGGTATTG 60.391 44.000 0.00 0.00 0.00 1.90
2089 2125 2.094494 GTGTCATATCGGATCGCCATCT 60.094 50.000 0.00 0.00 0.00 2.90
2240 2280 5.585390 CAAGATTGTTGTCTTGCTTTCACT 58.415 37.500 3.97 0.00 45.89 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.921221 TGAGAAGGATTTGAGAGGGGT 58.079 47.619 0.00 0.00 0.00 4.95
76 78 0.476808 TAAGGGAGGGGTTGGCTTCA 60.477 55.000 0.00 0.00 0.00 3.02
125 127 5.643379 TGAGCAAAACAATTCCTATGGAC 57.357 39.130 0.00 0.00 0.00 4.02
212 218 5.367945 TGAAGCCTAACCATAACCCTAAG 57.632 43.478 0.00 0.00 0.00 2.18
263 283 5.393027 GCATAACCCTAACACCAACATCAAG 60.393 44.000 0.00 0.00 0.00 3.02
584 612 5.277154 CCATCGAACTCAACAACGTTACTTT 60.277 40.000 0.00 0.00 0.00 2.66
589 617 2.828877 TCCATCGAACTCAACAACGTT 58.171 42.857 0.00 0.00 0.00 3.99
606 634 4.262808 CCAAAACCAACATTATGCCTTCCA 60.263 41.667 0.00 0.00 0.00 3.53
714 742 4.790765 GGCAAATAACTCAAGAGCCTTT 57.209 40.909 0.00 0.00 37.67 3.11
741 769 5.401531 AATGCAAACTAGACTCGACCTTA 57.598 39.130 0.00 0.00 0.00 2.69
747 775 5.551760 AATCCAAATGCAAACTAGACTCG 57.448 39.130 0.00 0.00 0.00 4.18
921 950 3.314307 TCCTTGTCATCCTCCTCGTAT 57.686 47.619 0.00 0.00 0.00 3.06
939 968 4.326826 TGTTGTCATGGAGATCAACTTCC 58.673 43.478 0.00 0.00 38.23 3.46
983 1012 3.076621 TCCATTGTCTCTTGCACATGAC 58.923 45.455 0.00 0.00 0.00 3.06
1069 1098 1.210478 CGTGAACCCCTCCTCATCAAT 59.790 52.381 0.00 0.00 0.00 2.57
1130 1159 3.003689 CCTGAACAATGGTGTCTTGTGAC 59.996 47.826 0.00 0.00 43.20 3.67
1151 1180 5.359194 TTCATCCACAAGACTAAGATCCC 57.641 43.478 0.00 0.00 0.00 3.85
1211 1240 0.320697 ACGGTGAGAACTTGGCCTAC 59.679 55.000 3.32 0.00 0.00 3.18
1262 1291 5.200483 AGAAGGATTGAAACTCACAACCAA 58.800 37.500 0.00 0.00 0.00 3.67
1298 1328 1.623811 ACCAAGTAGTTGTCGAGCCAT 59.376 47.619 9.42 0.00 30.95 4.40
1567 1598 5.559770 TGAAGCTCATTATTGGAAGTGTGA 58.440 37.500 0.00 0.00 0.00 3.58
1587 1618 4.576053 CACAAGGTCAATGACACTCTTGAA 59.424 41.667 26.19 0.00 34.97 2.69
1623 1654 4.804868 TGCCGTACTTCACCTTGTAATA 57.195 40.909 0.00 0.00 0.00 0.98
1657 1688 0.457337 CTTGAATGCGGCTTGCTTCC 60.457 55.000 0.00 0.00 46.63 3.46
1702 1733 2.664015 ACCTAGGGAGTCGGTTGTATC 58.336 52.381 14.81 0.00 0.00 2.24
1799 1833 1.929860 ATACTCGGACGGTCCTCCCA 61.930 60.000 23.86 8.05 33.30 4.37
2048 2084 0.608130 AAATTTCCCTTTCAGCCGGC 59.392 50.000 21.89 21.89 0.00 6.13
2089 2125 4.196193 CACCACCGCATTTAGAATTCCTA 58.804 43.478 0.65 0.00 0.00 2.94
2240 2280 6.471800 AACAATGTGGCAAACCGCTTGTTA 62.472 41.667 17.02 0.00 45.47 2.41


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

AutoCloner maintained by Alex Coulton.