Multiple sequence alignment - TraesCS6A01G151900

Loading Multiple Alignment...

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 TraesCS6A01G151900 chr6A 100.000 2351 0 0 1 2351 136164438 136162088 0.000000e+00 4342
1 TraesCS6A01G151900 chr6A 95.934 2238 84 5 119 2351 204306933 204304698 0.000000e+00 3622
2 TraesCS6A01G151900 chr6A 95.501 2245 100 1 107 2351 328875916 328878159 0.000000e+00 3585
3 TraesCS6A01G151900 chr6A 95.402 2240 101 2 112 2351 518075644 518073407 0.000000e+00 3565
4 TraesCS6A01G151900 chr6A 95.255 2255 96 6 99 2351 213994247 213992002 0.000000e+00 3561
5 TraesCS6A01G151900 chr6A 96.373 1985 68 4 368 2351 473515388 473517369 0.000000e+00 3264
6 TraesCS6A01G151900 chr6A 88.462 208 19 4 1 204 93641415 93641621 1.800000e-61 246
7 TraesCS6A01G151900 chr2A 95.252 2359 103 8 1 2351 616456474 616454117 0.000000e+00 3727
8 TraesCS6A01G151900 chr2A 87.864 206 22 2 1 204 374906293 374906497 3.020000e-59 239
9 TraesCS6A01G151900 chr2A 89.091 165 15 3 1 163 340535847 340536010 3.960000e-48 202
10 TraesCS6A01G151900 chr2A 95.798 119 5 0 1 119 90406818 90406700 2.380000e-45 193
11 TraesCS6A01G151900 chr5A 96.435 2244 77 3 109 2351 268344297 268346538 0.000000e+00 3698
12 TraesCS6A01G151900 chr5A 96.333 2236 76 4 116 2351 109667608 109669837 0.000000e+00 3670
13 TraesCS6A01G151900 chr5A 88.995 209 20 3 1 209 309381754 309381549 3.000000e-64 255
14 TraesCS6A01G151900 chr3A 94.486 2267 97 8 107 2351 134617324 134619584 0.000000e+00 3469
15 TraesCS6A01G151900 chr3A 86.869 198 20 5 7 203 539232437 539232245 1.410000e-52 217
16 TraesCS6A01G151900 chr1A 96.127 1833 69 2 519 2351 465251795 465253625 0.000000e+00 2990
17 TraesCS6A01G151900 chr4A 91.489 188 14 2 1 187 288777940 288778126 8.340000e-65 257
18 TraesCS6A01G151900 chr4B 89.375 160 17 0 7 166 73545300 73545141 3.960000e-48 202


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 TraesCS6A01G151900 chr6A 136162088 136164438 2350 True 4342 4342 100.000 1 2351 1 chr6A.!!$R1 2350
1 TraesCS6A01G151900 chr6A 204304698 204306933 2235 True 3622 3622 95.934 119 2351 1 chr6A.!!$R2 2232
2 TraesCS6A01G151900 chr6A 328875916 328878159 2243 False 3585 3585 95.501 107 2351 1 chr6A.!!$F2 2244
3 TraesCS6A01G151900 chr6A 518073407 518075644 2237 True 3565 3565 95.402 112 2351 1 chr6A.!!$R4 2239
4 TraesCS6A01G151900 chr6A 213992002 213994247 2245 True 3561 3561 95.255 99 2351 1 chr6A.!!$R3 2252
5 TraesCS6A01G151900 chr6A 473515388 473517369 1981 False 3264 3264 96.373 368 2351 1 chr6A.!!$F3 1983
6 TraesCS6A01G151900 chr2A 616454117 616456474 2357 True 3727 3727 95.252 1 2351 1 chr2A.!!$R2 2350
7 TraesCS6A01G151900 chr5A 268344297 268346538 2241 False 3698 3698 96.435 109 2351 1 chr5A.!!$F2 2242
8 TraesCS6A01G151900 chr5A 109667608 109669837 2229 False 3670 3670 96.333 116 2351 1 chr5A.!!$F1 2235
9 TraesCS6A01G151900 chr3A 134617324 134619584 2260 False 3469 3469 94.486 107 2351 1 chr3A.!!$F1 2244
10 TraesCS6A01G151900 chr1A 465251795 465253625 1830 False 2990 2990 96.127 519 2351 1 chr1A.!!$F1 1832

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
825 860 0.03601 CATGAACCTGGCCTTCGACT 60.036 55.0 3.32 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 1916 0.892755 AAGCACGAACGGGATCACTA 59.107 50.0 0.0 0.0 0.0 2.74 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 4.468951 CGAAAGCCGAAATCGAAAAATG 57.531 40.909 4.04 0.00 43.02 2.32
52 53 4.872691 CACATGTTTGGAGATAGAGGTGTC 59.127 45.833 0.00 0.00 0.00 3.67
84 85 4.508551 AATACAGACATGAGGGCATCAA 57.491 40.909 5.73 0.00 42.53 2.57
85 86 4.719026 ATACAGACATGAGGGCATCAAT 57.281 40.909 5.73 0.00 42.53 2.57
87 88 4.719026 ACAGACATGAGGGCATCAATAT 57.281 40.909 5.73 0.00 42.53 1.28
96 97 7.610692 ACATGAGGGCATCAATATCATTCTTAG 59.389 37.037 5.73 0.00 42.53 2.18
101 102 8.000709 AGGGCATCAATATCATTCTTAGAACAA 58.999 33.333 0.00 0.00 0.00 2.83
260 268 2.121042 ACCCCACCCACTTCCCAT 60.121 61.111 0.00 0.00 0.00 4.00
288 296 1.173444 CCACTACCCTCTCCCGATCG 61.173 65.000 8.51 8.51 0.00 3.69
338 346 1.218047 CGCCGATGAACTTCTCCCA 59.782 57.895 0.00 0.00 0.00 4.37
362 373 3.849951 CACCGCCGCCCTACATCT 61.850 66.667 0.00 0.00 0.00 2.90
473 484 4.899239 CTCCCGCCACCAGATCGC 62.899 72.222 0.00 0.00 0.00 4.58
571 583 3.770040 CCACACGCCTCGGATCCA 61.770 66.667 13.41 0.00 0.00 3.41
635 647 2.722487 GCGAGATCCGTCCATCGT 59.278 61.111 5.66 0.00 41.15 3.73
726 761 1.217244 GGCGCGAACTTCCCTCTAA 59.783 57.895 12.10 0.00 0.00 2.10
751 786 0.910088 CTCGACCTTCCCTCCCCTTT 60.910 60.000 0.00 0.00 0.00 3.11
825 860 0.036010 CATGAACCTGGCCTTCGACT 60.036 55.000 3.32 0.00 0.00 4.18
854 889 0.553819 TTGGCCCGCCCATATACTTT 59.446 50.000 0.00 0.00 44.89 2.66
987 1022 4.523943 TCCGGCTGTACTGAACTTTTACTA 59.476 41.667 0.00 0.00 0.00 1.82
1095 1130 1.209127 GCAACCCGTTCATGAACCG 59.791 57.895 28.40 22.55 38.03 4.44
1146 1181 3.205784 GGACATCATCCCCTTCTTCTG 57.794 52.381 0.00 0.00 42.46 3.02
1433 1482 4.330620 GCGTATACCGGTTTCTTCAATTCA 59.669 41.667 15.04 0.00 36.94 2.57
1443 1492 7.023575 CGGTTTCTTCAATTCATAGGTTCAAG 58.976 38.462 0.00 0.00 0.00 3.02
1466 1515 3.009723 CGTGCATCAGGTATTCAGGTTT 58.990 45.455 0.00 0.00 0.00 3.27
1505 1554 4.107622 CAAAACATTAGCTGCCTGTATGC 58.892 43.478 0.00 0.00 0.00 3.14
1814 1863 4.828072 AGCGTCTTCTTCCTAATTTCCT 57.172 40.909 0.00 0.00 0.00 3.36
2090 2140 3.695556 TCGATGTCCGTTGTGTTATCCTA 59.304 43.478 0.00 0.00 39.75 2.94
2135 2186 2.031157 CAGGTGGTTTCGTTTGCCTAAG 60.031 50.000 0.00 0.00 0.00 2.18
2175 2226 8.316640 ACATTCAGTTTTGATTCTCTGTAGTC 57.683 34.615 0.00 0.00 32.27 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.832248 TCTATCTCCAAACATGTGGACAC 58.168 43.478 0.00 0.00 42.97 3.67
38 39 9.760077 TTTTATTTTATCGACACCTCTATCTCC 57.240 33.333 0.00 0.00 0.00 3.71
67 68 4.648651 TGATATTGATGCCCTCATGTCTG 58.351 43.478 0.00 0.00 32.72 3.51
68 69 4.987963 TGATATTGATGCCCTCATGTCT 57.012 40.909 0.00 0.00 32.72 3.41
260 268 0.335361 GAGGGTAGTGGAGGGAGTCA 59.665 60.000 0.00 0.00 0.00 3.41
288 296 0.321034 TGTGAGGAGTGTGCAGATGC 60.321 55.000 0.00 0.00 42.50 3.91
318 326 1.218316 GGAGAAGTTCATCGGCGGT 59.782 57.895 7.21 0.00 0.00 5.68
726 761 1.152096 AGGGAAGGTCGAGGTGGTT 60.152 57.895 0.00 0.00 0.00 3.67
987 1022 6.867816 CACCTGCACACATACACAAATTATTT 59.132 34.615 0.00 0.00 0.00 1.40
1095 1130 1.840635 AGATGCCCTTGTACTCCTTCC 59.159 52.381 0.00 0.00 0.00 3.46
1146 1181 2.357034 TTGTCAGCTTCGCGACCC 60.357 61.111 9.15 1.94 33.64 4.46
1409 1458 3.598019 TTGAAGAAACCGGTATACGCT 57.402 42.857 8.00 0.00 42.52 5.07
1429 1478 2.017049 GCACGCCTTGAACCTATGAAT 58.983 47.619 0.00 0.00 0.00 2.57
1433 1482 1.065491 TGATGCACGCCTTGAACCTAT 60.065 47.619 0.00 0.00 0.00 2.57
1443 1492 0.940126 CTGAATACCTGATGCACGCC 59.060 55.000 0.00 0.00 0.00 5.68
1466 1515 5.672503 TGTTTTGTAGTACACAACAGCCTA 58.327 37.500 24.39 7.73 46.80 3.93
1505 1554 8.574196 AAATAAGAAACAACATGGTTTTCTCG 57.426 30.769 16.26 0.00 40.85 4.04
1709 1758 1.457346 CTTTTTGCTGCCGAGGAGAT 58.543 50.000 0.00 0.00 0.00 2.75
1778 1827 1.727335 GACGCTAAGAACTCTGTTGCC 59.273 52.381 0.00 0.00 0.00 4.52
1866 1916 0.892755 AAGCACGAACGGGATCACTA 59.107 50.000 0.00 0.00 0.00 2.74
2090 2140 5.509670 GCTCCTTTTGAATTGCTTGGTTAGT 60.510 40.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.