Multiple sequence alignment - TraesCS6D01G210700

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 TraesCS6D01G210700 chr6D 100.000 3248 0 0 1 3248 297173825 297170578 0.000000e+00 5999.0
1 TraesCS6D01G210700 chr4D 96.229 3235 105 12 1 3222 125888955 125892185 0.000000e+00 5282.0
2 TraesCS6D01G210700 chr4D 96.166 3234 109 10 1 3222 125920307 125917077 0.000000e+00 5271.0
3 TraesCS6D01G210700 chr4D 96.012 3235 113 11 1 3222 125841322 125838091 0.000000e+00 5245.0
4 TraesCS6D01G210700 chr7D 94.940 3261 123 19 1 3248 103539098 103542329 0.000000e+00 5070.0
5 TraesCS6D01G210700 chr4A 95.288 3056 118 11 100 3145 549631896 549634935 0.000000e+00 4822.0
6 TraesCS6D01G210700 chr7B 94.990 3054 127 12 100 3145 553274164 553271129 0.000000e+00 4769.0
7 TraesCS6D01G210700 chr5B 94.894 3055 130 12 100 3145 682906781 682909818 0.000000e+00 4754.0
8 TraesCS6D01G210700 chr5B 94.861 3055 132 11 99 3145 703926595 703929632 0.000000e+00 4748.0
9 TraesCS6D01G210700 chr5B 94.695 3054 137 11 100 3145 672334576 672331540 0.000000e+00 4719.0
10 TraesCS6D01G210700 chr5B 88.287 2749 225 56 556 3239 399762684 399765400 0.000000e+00 3203.0
11 TraesCS6D01G210700 chr5B 86.772 189 17 5 6 188 133707181 133707367 1.530000e-48 204.0
12 TraesCS6D01G210700 chr5B 100.000 30 0 0 3219 3248 61819915 61819944 4.530000e-04 56.5
13 TraesCS6D01G210700 chr5B 100.000 30 0 0 3219 3248 62357344 62357315 4.530000e-04 56.5
14 TraesCS6D01G210700 chr5B 100.000 30 0 0 3219 3248 117471747 117471776 4.530000e-04 56.5
15 TraesCS6D01G210700 chr6B 95.745 94 1 1 3158 3248 429916075 429915982 7.260000e-32 148.0
16 TraesCS6D01G210700 chr7A 92.553 94 4 1 3158 3248 387062336 387062429 7.310000e-27 132.0
17 TraesCS6D01G210700 chr5A 92.553 94 4 1 3158 3248 545036814 545036907 7.310000e-27 132.0
18 TraesCS6D01G210700 chr2B 89.362 94 7 2 3158 3248 316250228 316250135 7.360000e-22 115.0


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 TraesCS6D01G210700 chr6D 297170578 297173825 3247 True 5999 5999 100.000 1 3248 1 chr6D.!!$R1 3247
1 TraesCS6D01G210700 chr4D 125888955 125892185 3230 False 5282 5282 96.229 1 3222 1 chr4D.!!$F1 3221
2 TraesCS6D01G210700 chr4D 125917077 125920307 3230 True 5271 5271 96.166 1 3222 1 chr4D.!!$R2 3221
3 TraesCS6D01G210700 chr4D 125838091 125841322 3231 True 5245 5245 96.012 1 3222 1 chr4D.!!$R1 3221
4 TraesCS6D01G210700 chr7D 103539098 103542329 3231 False 5070 5070 94.940 1 3248 1 chr7D.!!$F1 3247
5 TraesCS6D01G210700 chr4A 549631896 549634935 3039 False 4822 4822 95.288 100 3145 1 chr4A.!!$F1 3045
6 TraesCS6D01G210700 chr7B 553271129 553274164 3035 True 4769 4769 94.990 100 3145 1 chr7B.!!$R1 3045
7 TraesCS6D01G210700 chr5B 682906781 682909818 3037 False 4754 4754 94.894 100 3145 1 chr5B.!!$F5 3045
8 TraesCS6D01G210700 chr5B 703926595 703929632 3037 False 4748 4748 94.861 99 3145 1 chr5B.!!$F6 3046
9 TraesCS6D01G210700 chr5B 672331540 672334576 3036 True 4719 4719 94.695 100 3145 1 chr5B.!!$R2 3045
10 TraesCS6D01G210700 chr5B 399762684 399765400 2716 False 3203 3203 88.287 556 3239 1 chr5B.!!$F4 2683

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
232 238 2.734079 GCTTGCTGTCAGACTGTCTAAC 59.266 50.0 10.47 7.11 0.0 2.34 F
1237 1247 0.110486 GTCTTGCTTGGAGGGTTGGA 59.890 55.0 0.00 0.00 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 1427 1.142688 ACCCTTCCTGGAGGCATTGT 61.143 55.0 0.00 0.00 38.35 2.71 R
2372 2416 0.530870 GTTAGATCTGGCACCGGAGC 60.531 60.0 16.31 16.31 37.95 4.70 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
56 62 7.015226 TGAATGTCTTAACTTGTGTGTCTTG 57.985 36.000 0.00 0.00 0.00 3.02
75 81 8.347035 GTGTCTTGTAGTTTGTAGCCATTTTTA 58.653 33.333 0.00 0.00 0.00 1.52
78 84 9.781633 TCTTGTAGTTTGTAGCCATTTTTAGTA 57.218 29.630 0.00 0.00 0.00 1.82
195 201 4.628074 TCTAGTTGTTTTGAAGGTCCTCG 58.372 43.478 0.00 0.00 0.00 4.63
206 212 4.788679 TGAAGGTCCTCGTGATATACTCA 58.211 43.478 0.00 0.00 0.00 3.41
232 238 2.734079 GCTTGCTGTCAGACTGTCTAAC 59.266 50.000 10.47 7.11 0.00 2.34
421 427 7.170393 TCAATAGTACTTGCTTGCTTCTCTA 57.830 36.000 0.00 0.00 0.00 2.43
422 428 7.261325 TCAATAGTACTTGCTTGCTTCTCTAG 58.739 38.462 0.00 0.00 0.00 2.43
571 581 3.910568 TCACTGTATGTGCATGATGGA 57.089 42.857 0.00 0.00 45.81 3.41
821 831 8.623903 CAATCTGAATAAGCTGGCTTAATTGTA 58.376 33.333 17.23 6.01 41.21 2.41
832 842 3.127030 GGCTTAATTGTACCTGTGTGCTC 59.873 47.826 0.00 0.00 0.00 4.26
961 971 7.231317 TGTTTCCTTTATCATGCAAAGAAGAGT 59.769 33.333 16.73 0.00 35.43 3.24
1237 1247 0.110486 GTCTTGCTTGGAGGGTTGGA 59.890 55.000 0.00 0.00 0.00 3.53
1300 1311 8.627208 TTCTCTTGTGATCTAATGCTTTTTCT 57.373 30.769 0.00 0.00 0.00 2.52
1318 1329 7.519328 GCTTTTTCTGTGTTGTTTATACGAGGA 60.519 37.037 0.00 0.00 0.00 3.71
1365 1391 3.665190 CCTGGTGTTAAGAAGACAGTCC 58.335 50.000 0.00 0.00 0.00 3.85
1367 1393 4.310769 CTGGTGTTAAGAAGACAGTCCAG 58.689 47.826 0.00 0.00 35.95 3.86
1398 1427 4.465660 AGAAGAGCTCAGAAACATCTGCTA 59.534 41.667 17.77 0.00 37.63 3.49
1539 1568 1.701847 ACCATCAGGAAAGTCTGCTGT 59.298 47.619 0.00 0.00 43.69 4.40
1789 1818 5.622007 GCAAGTTGACCTTTGCAATGCTATA 60.622 40.000 7.16 0.00 31.79 1.31
1834 1864 9.104965 CAAATGGAATGATCATGTATGCTTTTT 57.895 29.630 9.46 1.90 0.00 1.94
2161 2204 7.930513 AAGCTACTTGTTTCAAAGTTAATGC 57.069 32.000 0.00 0.00 40.77 3.56
2293 2336 1.595489 CGCGTGCAAAGATATTCTGCC 60.595 52.381 0.00 0.00 35.13 4.85
2372 2416 3.670055 CGCAAACAAAGTCAGCATTAAGG 59.330 43.478 0.00 0.00 0.00 2.69
2461 2505 4.335315 CACAAGGTTTGTCTCTGCTTTGTA 59.665 41.667 0.00 0.00 43.23 2.41
2570 2614 3.788434 TGAATCGAGAAAAAGTCGTGC 57.212 42.857 0.00 0.00 38.60 5.34
2621 2667 2.129607 CAGCACACATTTTTGCCACTC 58.870 47.619 0.00 0.00 39.75 3.51
2810 2858 3.431725 CGGGTTTTCGGAGCCAGC 61.432 66.667 4.08 0.00 37.01 4.85
2811 2859 2.034221 GGGTTTTCGGAGCCAGCT 59.966 61.111 0.00 0.00 37.16 4.24
2879 2956 6.462552 TTGATTCACAACCAACTTTGATGA 57.537 33.333 0.00 0.00 33.18 2.92
2897 2974 5.106442 TGATGATGTTTGATGCTTTGATGC 58.894 37.500 0.00 0.00 0.00 3.91
3071 3160 1.668101 GATCGGCTCACTCGGGAAGT 61.668 60.000 0.00 0.00 39.44 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.950680 ACACAAGTTAAGACATTCAACAATTAG 57.049 29.630 0.00 0.00 0.00 1.73
25 26 9.729023 CACACAAGTTAAGACATTCAACAATTA 57.271 29.630 0.00 0.00 0.00 1.40
26 27 8.250332 ACACACAAGTTAAGACATTCAACAATT 58.750 29.630 0.00 0.00 0.00 2.32
27 28 7.771183 ACACACAAGTTAAGACATTCAACAAT 58.229 30.769 0.00 0.00 0.00 2.71
28 29 7.120579 AGACACACAAGTTAAGACATTCAACAA 59.879 33.333 0.00 0.00 0.00 2.83
30 31 7.016361 AGACACACAAGTTAAGACATTCAAC 57.984 36.000 0.00 0.00 0.00 3.18
31 32 7.120579 ACAAGACACACAAGTTAAGACATTCAA 59.879 33.333 0.00 0.00 0.00 2.69
33 34 7.016361 ACAAGACACACAAGTTAAGACATTC 57.984 36.000 0.00 0.00 0.00 2.67
75 81 9.261035 ACTAATATTATGCTGCCTCTACATACT 57.739 33.333 0.00 0.00 0.00 2.12
78 84 8.597167 TCAACTAATATTATGCTGCCTCTACAT 58.403 33.333 0.00 0.00 0.00 2.29
158 164 4.844349 AACTAGATGTTGCCACTGGTAT 57.156 40.909 0.00 0.00 37.52 2.73
195 201 6.686630 ACAGCAAGCTAGATGAGTATATCAC 58.313 40.000 0.00 0.00 41.91 3.06
206 212 2.830923 ACAGTCTGACAGCAAGCTAGAT 59.169 45.455 10.88 0.00 0.00 1.98
246 252 5.182001 AGCAACATGAACTAGTGAATTGGTC 59.818 40.000 0.00 0.00 0.00 4.02
343 349 3.876274 TCTTCTCCATGTGCTACTGAC 57.124 47.619 0.00 0.00 0.00 3.51
421 427 5.221581 ACAAGCAAGCAATGAAGGAAATTCT 60.222 36.000 5.12 0.00 38.83 2.40
422 428 4.992951 ACAAGCAAGCAATGAAGGAAATTC 59.007 37.500 5.12 0.00 38.50 2.17
571 581 8.133024 TGTATCAATAAAGGAAAGCATTTGGT 57.867 30.769 0.00 0.00 39.27 3.67
651 661 1.699083 TGATCTTGAGGTGGTGCTTGA 59.301 47.619 0.00 0.00 0.00 3.02
821 831 2.300437 GGAAGACTAAGAGCACACAGGT 59.700 50.000 0.00 0.00 0.00 4.00
1046 1056 6.432783 ACCATTTGTTTTCCTAATCATCGACA 59.567 34.615 0.00 0.00 0.00 4.35
1237 1247 8.299570 CAAGGAAACACATAGCATAAAAGAACT 58.700 33.333 0.00 0.00 0.00 3.01
1300 1311 5.845103 TCAGTTCCTCGTATAAACAACACA 58.155 37.500 0.00 0.00 0.00 3.72
1318 1329 5.017490 TCTTCGTCCTAGATTCCTTCAGTT 58.983 41.667 0.00 0.00 0.00 3.16
1365 1391 5.389859 TCTGAGCTCTTCTTCTTCTTCTG 57.610 43.478 16.19 0.00 0.00 3.02
1367 1393 5.988561 TGTTTCTGAGCTCTTCTTCTTCTTC 59.011 40.000 16.19 0.00 0.00 2.87
1398 1427 1.142688 ACCCTTCCTGGAGGCATTGT 61.143 55.000 0.00 0.00 38.35 2.71
1539 1568 1.189752 GAGGTCTCAGAGTCCATGCA 58.810 55.000 15.27 0.00 0.00 3.96
1789 1818 8.592809 TCCATTTGGAAAATGCACTAGTAAAAT 58.407 29.630 0.00 0.00 42.18 1.82
1834 1864 2.694213 TCGACAAATGCAGGAATCGAA 58.306 42.857 11.97 0.00 35.80 3.71
2019 2061 1.952296 ACACTCAGAAGCAAGCTTTGG 59.048 47.619 8.91 4.73 36.26 3.28
2152 2195 8.438676 ACAGAAAATAGATAGCGCATTAACTT 57.561 30.769 11.47 0.00 0.00 2.66
2161 2204 8.916654 CATAGGTGTAACAGAAAATAGATAGCG 58.083 37.037 0.00 0.00 39.98 4.26
2204 2247 5.316987 CAAGACAGGAAACAAGGTAGGAAT 58.683 41.667 0.00 0.00 0.00 3.01
2219 2262 6.490040 TCTCAAAATTTTCCTACCAAGACAGG 59.510 38.462 0.00 0.00 0.00 4.00
2293 2336 5.780192 TGCGTTTGTTCTTTGAATTTTTCG 58.220 33.333 0.00 0.00 0.00 3.46
2372 2416 0.530870 GTTAGATCTGGCACCGGAGC 60.531 60.000 16.31 16.31 37.95 4.70
2570 2614 3.743521 TGGAACCAGTTCTCTGATTGTG 58.256 45.455 10.19 0.00 43.76 3.33
2713 2761 5.163814 CCTTACGCTCTTCTTTCTGAAATGG 60.164 44.000 2.88 0.00 33.79 3.16
2810 2858 7.499563 TGGAGTGACTTACTATAGCAGTCTTAG 59.500 40.741 23.61 3.90 40.53 2.18
2811 2859 7.344134 TGGAGTGACTTACTATAGCAGTCTTA 58.656 38.462 23.61 9.85 40.53 2.10
2879 2956 5.543714 TCAAAGCATCAAAGCATCAAACAT 58.456 33.333 0.00 0.00 36.85 2.71
2897 2974 4.618489 GCTCCGAATCAAACAACATCAAAG 59.382 41.667 0.00 0.00 0.00 2.77
3169 3302 9.862371 GAAGAAGATGATGACTAGTAACTTGAA 57.138 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.