Multiple sequence alignment - TraesCS5D01G348800

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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 TraesCS5D01G348800 chr5D 100.000 2273 0 0 1 2273 434332635 434330363 0.000000e+00 4198.0
1 TraesCS5D01G348800 chr5D 95.876 2037 46 8 247 2273 434381011 434383019 0.000000e+00 3262.0
2 TraesCS5D01G348800 chr5D 80.274 877 139 21 724 1580 435238218 435237356 4.120000e-177 630.0
3 TraesCS5D01G348800 chr5D 80.068 878 142 25 724 1590 434569822 434568967 2.480000e-174 621.0
4 TraesCS5D01G348800 chr5D 74.198 655 130 24 1327 1957 434673997 434674636 1.050000e-58 237.0
5 TraesCS5D01G348800 chr5A 95.815 2294 70 10 1 2273 548225391 548227679 0.000000e+00 3681.0
6 TraesCS5D01G348800 chr5B 94.852 2292 61 12 1 2273 527038783 527041036 0.000000e+00 3526.0
7 TraesCS5D01G348800 chr5B 79.884 860 140 22 724 1567 527060221 527061063 1.160000e-167 599.0
8 TraesCS5D01G348800 chr5B 79.475 877 147 21 724 1590 527608369 527607516 1.940000e-165 592.0
9 TraesCS5D01G348800 chr5B 75.687 1201 225 44 777 1957 527773381 527772228 2.570000e-149 538.0
10 TraesCS5D01G348800 chr5B 78.303 825 147 20 726 1532 528525313 528524503 9.370000e-139 503.0
11 TraesCS5D01G348800 chr5B 79.201 726 130 16 724 1436 527058364 527059081 3.390000e-133 484.0
12 TraesCS5D01G348800 chr5B 89.041 73 7 1 1885 1957 527495036 527494965 3.110000e-14 89.8


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 TraesCS5D01G348800 chr5D 434330363 434332635 2272 True 4198.0 4198 100.0000 1 2273 1 chr5D.!!$R1 2272
1 TraesCS5D01G348800 chr5D 434381011 434383019 2008 False 3262.0 3262 95.8760 247 2273 1 chr5D.!!$F1 2026
2 TraesCS5D01G348800 chr5D 435237356 435238218 862 True 630.0 630 80.2740 724 1580 1 chr5D.!!$R3 856
3 TraesCS5D01G348800 chr5D 434568967 434569822 855 True 621.0 621 80.0680 724 1590 1 chr5D.!!$R2 866
4 TraesCS5D01G348800 chr5D 434673997 434674636 639 False 237.0 237 74.1980 1327 1957 1 chr5D.!!$F2 630
5 TraesCS5D01G348800 chr5A 548225391 548227679 2288 False 3681.0 3681 95.8150 1 2273 1 chr5A.!!$F1 2272
6 TraesCS5D01G348800 chr5B 527038783 527041036 2253 False 3526.0 3526 94.8520 1 2273 1 chr5B.!!$F1 2272
7 TraesCS5D01G348800 chr5B 527607516 527608369 853 True 592.0 592 79.4750 724 1590 1 chr5B.!!$R2 866
8 TraesCS5D01G348800 chr5B 527058364 527061063 2699 False 541.5 599 79.5425 724 1567 2 chr5B.!!$F2 843
9 TraesCS5D01G348800 chr5B 527772228 527773381 1153 True 538.0 538 75.6870 777 1957 1 chr5B.!!$R3 1180
10 TraesCS5D01G348800 chr5B 528524503 528525313 810 True 503.0 503 78.3030 726 1532 1 chr5B.!!$R4 806

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
24 25 1.126846 CAGAATGGTTCAGACGTTCGC 59.873 52.381 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 3361 0.322008 GTCCCTGGCCAACTCTTCAG 60.322 60.0 7.01 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
24 25 1.126846 CAGAATGGTTCAGACGTTCGC 59.873 52.381 0.00 0.00 0.00 4.70
26 27 2.230508 AGAATGGTTCAGACGTTCGCTA 59.769 45.455 0.00 0.00 0.00 4.26
100 101 7.323656 GTGATTGTGCTTAATGTGTGTTCTTAC 59.676 37.037 0.00 0.00 0.00 2.34
147 153 3.067106 ACTAGTTGATGCAAGGAACACG 58.933 45.455 0.00 0.00 0.00 4.49
216 225 3.181483 GGCATCCATTTCTTAGTGCCTTG 60.181 47.826 6.92 0.00 46.44 3.61
228 237 2.719376 TGCCTTGTCTGCACTTTCC 58.281 52.632 0.00 0.00 32.85 3.13
229 238 1.165907 TGCCTTGTCTGCACTTTCCG 61.166 55.000 0.00 0.00 32.85 4.30
239 248 1.557371 TGCACTTTCCGATGGGTCATA 59.443 47.619 0.00 0.00 33.83 2.15
699 710 6.449635 AAGTAAAACAATGACAGCTTGTGA 57.550 33.333 0.00 0.00 36.95 3.58
797 2666 9.601810 TTCCTATTGCCTATTATCTAACTCTCA 57.398 33.333 0.00 0.00 0.00 3.27
965 2834 3.151912 AGAACTCAGCAATGCCTTCTT 57.848 42.857 0.00 0.00 0.00 2.52
1156 3025 4.403137 TTCCGTCGGCCGTGTACG 62.403 66.667 27.15 26.37 39.44 3.67
1251 3121 4.974721 CCAAGTGCCGCCACCCTT 62.975 66.667 0.00 0.00 43.09 3.95
1264 3134 1.341209 CCACCCTTTGCCACTTCTTTC 59.659 52.381 0.00 0.00 0.00 2.62
1300 3170 4.631813 GTCTCTTCGTGCTAATCATGGTTT 59.368 41.667 0.00 0.00 32.54 3.27
1369 3244 1.070134 TGTAGTGCTCAGTTGGTGGTC 59.930 52.381 0.00 0.00 0.00 4.02
1464 3361 4.551388 CTGGTGAAGAGTAGTTGTCACTC 58.449 47.826 12.00 0.00 42.30 3.51
1598 3527 4.694760 AGTGGTAGCAATAGCATCATGA 57.305 40.909 0.00 0.00 45.49 3.07
1650 3579 6.534436 GGATGGATTCAGTTGAGATATCATCG 59.466 42.308 5.32 0.00 0.00 3.84
1779 3717 2.357034 TCGCCGCTGAACCTTCAC 60.357 61.111 0.00 0.00 32.90 3.18
2042 3990 6.123651 TGTCCAAAGTTGTACCATGTTTAGT 58.876 36.000 0.00 0.00 0.00 2.24
2084 4033 5.953183 TGCAACTTGCCATAAATTACTGAG 58.047 37.500 11.29 0.00 44.23 3.35
2086 4035 5.801947 GCAACTTGCCATAAATTACTGAGTG 59.198 40.000 1.95 0.00 37.42 3.51
2155 4114 5.836358 AGTAATTTTGGCAACTAGTTTCCCA 59.164 36.000 19.84 18.28 37.61 4.37
2191 4150 4.223923 TCTCTCTCCCCTGTTTCTGATTTC 59.776 45.833 0.00 0.00 0.00 2.17
2202 4161 1.603456 TCTGATTTCCGCAGTTTGCA 58.397 45.000 1.69 0.00 45.36 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.672714 CGAACGTCTGAACCATTCTGA 58.327 47.619 0.00 0.0 35.61 3.27
24 25 9.125026 ACCTGCTAAAATAAGACCATTGAATAG 57.875 33.333 0.00 0.0 0.00 1.73
26 27 7.615365 TCACCTGCTAAAATAAGACCATTGAAT 59.385 33.333 0.00 0.0 0.00 2.57
147 153 7.948278 ACTAAGATACAACACTGTTCAAGTC 57.052 36.000 0.00 0.0 36.83 3.01
216 225 0.321653 ACCCATCGGAAAGTGCAGAC 60.322 55.000 0.00 0.0 0.00 3.51
239 248 0.892755 CATGGTTTGCAGCTGGTCAT 59.107 50.000 17.12 0.0 0.00 3.06
1156 3025 0.811281 GTAAAGGGCCACTGCATCAC 59.189 55.000 6.18 0.0 40.13 3.06
1251 3121 2.031120 CAACTGGGAAAGAAGTGGCAA 58.969 47.619 0.00 0.0 0.00 4.52
1264 3134 2.421619 GAAGAGACTTGCTCAACTGGG 58.578 52.381 0.00 0.0 46.45 4.45
1369 3244 2.801111 CCATCACTTCATCAGCTCATCG 59.199 50.000 0.00 0.0 0.00 3.84
1464 3361 0.322008 GTCCCTGGCCAACTCTTCAG 60.322 60.000 7.01 0.0 0.00 3.02
1598 3527 2.223805 TGCATCGCAGAATAGATCGTGT 60.224 45.455 0.00 0.0 43.58 4.49
1779 3717 5.236282 ACTGATCAACAACACATCTGAGAG 58.764 41.667 0.00 0.0 0.00 3.20
2042 3990 2.038557 GCAGAACACTTGACCCTCCTAA 59.961 50.000 0.00 0.0 0.00 2.69
2084 4033 2.009774 ACACACTCAGCAGAAACACAC 58.990 47.619 0.00 0.0 0.00 3.82
2086 4035 2.420022 ACAACACACTCAGCAGAAACAC 59.580 45.455 0.00 0.0 0.00 3.32
2155 4114 6.099990 CAGGGGAGAGAGAATATATGATGCAT 59.900 42.308 0.00 0.0 0.00 3.96


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

AutoCloner maintained by Alex Coulton.