Multiple sequence alignment - TraesCS6B01G255700

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 TraesCS6B01G255700 chr6B 100.000 3449 0 0 1 3449 459690962 459694410 0 6370
1 TraesCS6B01G255700 chr5B 95.055 3438 151 14 1 3434 547745193 547748615 0 5389
2 TraesCS6B01G255700 chr5B 94.881 3438 156 15 2 3434 547789109 547792531 0 5356
3 TraesCS6B01G255700 chr5B 94.852 3438 158 14 1 3434 547750735 547754157 0 5350
4 TraesCS6B01G255700 chr5B 94.793 3438 159 15 1 3434 547755797 547759218 0 5339
5 TraesCS6B01G255700 chr5B 94.793 3438 160 14 1 3434 547766244 547769666 0 5339
6 TraesCS6B01G255700 chr4B 93.210 3461 215 14 1 3449 78830608 78827156 0 5072
7 TraesCS6B01G255700 chr4B 92.009 3454 262 11 1 3449 443187667 443184223 0 4837
8 TraesCS6B01G255700 chr4A 92.317 3462 235 26 1 3449 721638035 721641478 0 4891
9 TraesCS6B01G255700 chr6D 93.229 3308 204 12 1 3303 283636546 283633254 0 4850


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 TraesCS6B01G255700 chr6B 459690962 459694410 3448 False 6370.000000 6370 100.000 1 3449 1 chr6B.!!$F1 3448
1 TraesCS6B01G255700 chr5B 547745193 547759218 14025 False 5359.333333 5389 94.900 1 3434 3 chr5B.!!$F3 3433
2 TraesCS6B01G255700 chr5B 547789109 547792531 3422 False 5356.000000 5356 94.881 2 3434 1 chr5B.!!$F2 3432
3 TraesCS6B01G255700 chr5B 547766244 547769666 3422 False 5339.000000 5339 94.793 1 3434 1 chr5B.!!$F1 3433
4 TraesCS6B01G255700 chr4B 78827156 78830608 3452 True 5072.000000 5072 93.210 1 3449 1 chr4B.!!$R1 3448
5 TraesCS6B01G255700 chr4B 443184223 443187667 3444 True 4837.000000 4837 92.009 1 3449 1 chr4B.!!$R2 3448
6 TraesCS6B01G255700 chr4A 721638035 721641478 3443 False 4891.000000 4891 92.317 1 3449 1 chr4A.!!$F1 3448
7 TraesCS6B01G255700 chr6D 283633254 283636546 3292 True 4850.000000 4850 93.229 1 3303 1 chr6D.!!$R1 3302

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
41 42 2.886523 GGTGTAAAAACCCCACTGTACC 59.113 50.000 0.0 0.0 33.79 3.34 F
1526 1528 3.069443 CCAAGGAGAGAGATACAAGAGGC 59.931 52.174 0.0 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 1674 1.834263 GGGTGCTGAGATCACTACCTT 59.166 52.381 0.0 0.0 34.97 3.50 R
3159 8723 1.037493 CCACCGATCCCGAGAACATA 58.963 55.000 0.0 0.0 38.22 2.29 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
41 42 2.886523 GGTGTAAAAACCCCACTGTACC 59.113 50.000 0.00 0.00 33.79 3.34
498 500 4.444876 GCCAATACAGTCCAGTATCATGGT 60.445 45.833 0.00 0.00 41.43 3.55
855 857 4.549458 CTGGTGGAACAATCATGAACAAC 58.451 43.478 0.00 0.00 44.16 3.32
1166 1168 8.415950 ACTACTATAGATCAGATGGAAACCAG 57.584 38.462 6.78 0.00 36.75 4.00
1369 1371 5.235616 CACACTTGTGTTACAACGGTATCTT 59.764 40.000 3.39 0.00 40.96 2.40
1393 1395 6.218019 TGGCAATTTGTCAAGAAGAAATCAG 58.782 36.000 0.15 0.00 0.00 2.90
1526 1528 3.069443 CCAAGGAGAGAGATACAAGAGGC 59.931 52.174 0.00 0.00 0.00 4.70
1620 1622 3.258372 GGTGGAAGTCATCAGTGTCACTA 59.742 47.826 4.85 0.00 0.00 2.74
1672 1674 4.098349 AGAACATTGCTCAAAAAGACAGCA 59.902 37.500 0.00 0.00 41.45 4.41
1820 1822 8.840321 TCAACTTGAAGAAGATTTACAAGAAGG 58.160 33.333 0.00 0.00 39.84 3.46
1910 1912 4.588951 TCCTGAAGAAGTACAAGAAGCTGA 59.411 41.667 0.00 0.00 0.00 4.26
1932 1934 6.586344 TGATGTAGATGAAGATGAAGAACCC 58.414 40.000 0.00 0.00 0.00 4.11
2343 7888 4.154918 CCTACCACTTGCATTGTCTCTTTC 59.845 45.833 0.00 0.00 0.00 2.62
2347 7892 4.213270 CCACTTGCATTGTCTCTTTCGTTA 59.787 41.667 0.00 0.00 0.00 3.18
2364 7909 4.056050 TCGTTAAGTGCTCTTTCAGGTTC 58.944 43.478 6.31 0.00 35.36 3.62
2383 7928 2.112928 TGCTTGTGCACGGTCCAT 59.887 55.556 13.13 0.00 45.31 3.41
2478 8023 2.358737 GGGCACACACGAGGAAGG 60.359 66.667 0.00 0.00 0.00 3.46
2651 8197 7.957002 TCAAATGTTATTTGGGTTGCTTAAGA 58.043 30.769 6.67 0.00 0.00 2.10
2784 8333 6.476380 TGCTTTGCTGAAATTAGTGAAAGTTG 59.524 34.615 0.00 0.00 0.00 3.16
2947 8497 4.712051 TGGATTAGCATGCTATGTTCCT 57.288 40.909 31.39 16.18 0.00 3.36
3159 8723 5.416271 AATTGTCGAACCAGGTGTATACT 57.584 39.130 4.17 0.00 0.00 2.12
3205 8769 3.028130 TCCTTTGGGGAGACAAACAAAC 58.972 45.455 0.00 0.00 39.58 2.93
3206 8770 3.031013 CCTTTGGGGAGACAAACAAACT 58.969 45.455 0.00 0.00 35.57 2.66
3207 8771 4.079672 TCCTTTGGGGAGACAAACAAACTA 60.080 41.667 0.00 0.00 39.58 2.24
3208 8772 4.647399 CCTTTGGGGAGACAAACAAACTAA 59.353 41.667 0.00 0.00 35.57 2.24
3407 14035 4.102367 GGATCATGCTCTCTTTAGGAACCT 59.898 45.833 0.00 0.00 0.00 3.50
3414 14042 4.398319 CTCTCTTTAGGAACCTTTTGGCA 58.602 43.478 0.00 0.00 45.59 4.92
3421 14049 1.338020 GGAACCTTTTGGCACAGTCAG 59.662 52.381 0.00 0.00 45.59 3.51
3427 14055 2.512485 TTTGGCACAGTCAGCATTTG 57.488 45.000 0.00 0.00 42.39 2.32
3434 14062 3.047796 CACAGTCAGCATTTGAACTTGC 58.952 45.455 0.00 0.00 37.61 4.01
3443 14071 5.634896 AGCATTTGAACTTGCTAATCTTCG 58.365 37.500 0.37 0.00 46.92 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.798337 GGCGCCAAAATGATCAATTGTAG 59.202 43.478 24.80 13.73 0.00 2.74
498 500 4.701651 CACTTGATAGCATCTTGGGAAACA 59.298 41.667 0.00 0.00 0.00 2.83
949 951 1.986575 GCTTCTGATTGCACGAGGCC 61.987 60.000 0.00 0.00 43.89 5.19
991 993 7.697946 TGAATATTAGGCACCATGGATGATTA 58.302 34.615 21.47 6.46 0.00 1.75
1147 1149 6.014669 GCTACTCTGGTTTCCATCTGATCTAT 60.015 42.308 0.00 0.00 30.82 1.98
1166 1168 5.477510 CATGAGGTATTGGATCTGCTACTC 58.522 45.833 0.00 0.00 0.00 2.59
1369 1371 6.159299 TGATTTCTTCTTGACAAATTGCCA 57.841 33.333 0.00 0.00 0.00 4.92
1620 1622 5.316167 TCACCATCACTGCTAAGTTTCAAT 58.684 37.500 0.00 0.00 32.98 2.57
1672 1674 1.834263 GGGTGCTGAGATCACTACCTT 59.166 52.381 0.00 0.00 34.97 3.50
1770 1772 4.142038 GACTCTCTTCCTCTGGATCTACC 58.858 52.174 0.00 0.00 39.54 3.18
1772 1774 4.051478 AGGACTCTCTTCCTCTGGATCTA 58.949 47.826 0.00 0.00 42.98 1.98
1820 1822 4.438472 GCTCTTGATCATCTTGTTCCTTGC 60.438 45.833 0.00 0.00 0.00 4.01
1910 1912 6.566079 TGGGTTCTTCATCTTCATCTACAT 57.434 37.500 0.00 0.00 0.00 2.29
1932 1934 5.840243 TGACAATAGGCCAATGAATCTTG 57.160 39.130 5.01 0.00 0.00 3.02
2289 2292 5.104527 ACCCTCCAAGTCATCAATCGAATAA 60.105 40.000 0.00 0.00 0.00 1.40
2343 7888 4.058817 AGAACCTGAAAGAGCACTTAACG 58.941 43.478 0.00 0.00 35.05 3.18
2347 7892 2.620585 GCAAGAACCTGAAAGAGCACTT 59.379 45.455 0.00 0.00 38.05 3.16
2383 7928 3.556213 CCTCGAACCTGGTCAACATGTAA 60.556 47.826 0.00 0.00 0.00 2.41
2478 8023 2.124778 GCCTGCTCCAGCTTCTCC 60.125 66.667 0.00 0.00 42.66 3.71
2651 8197 3.258123 GTGGGGCAACATTTAAGACATGT 59.742 43.478 0.00 0.00 36.36 3.21
2833 8382 4.406003 AGGTGTATCGAGGTAAAAGCAGAT 59.594 41.667 0.00 0.00 0.00 2.90
2947 8497 2.627945 GTTCACATGCTACCGATCCAA 58.372 47.619 0.00 0.00 0.00 3.53
3091 8647 1.396996 CCAAGCTAACCCGATTTCACG 59.603 52.381 0.00 0.00 0.00 4.35
3159 8723 1.037493 CCACCGATCCCGAGAACATA 58.963 55.000 0.00 0.00 38.22 2.29
3372 13999 4.942483 AGAGCATGATCCTGAGAACAAAAG 59.058 41.667 7.49 0.00 0.00 2.27
3383 14011 4.102367 GGTTCCTAAAGAGAGCATGATCCT 59.898 45.833 7.49 1.59 0.00 3.24
3407 14035 2.429971 TCAAATGCTGACTGTGCCAAAA 59.570 40.909 0.00 0.00 0.00 2.44
3414 14042 3.360249 GCAAGTTCAAATGCTGACTGT 57.640 42.857 0.00 0.00 39.46 3.55
3421 14049 5.393962 ACGAAGATTAGCAAGTTCAAATGC 58.606 37.500 0.00 0.00 42.87 3.56


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

AutoCloner maintained by Alex Coulton.