Multiple sequence alignment - TraesCS3B01G450800

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 TraesCS3B01G450800 chr3B 100.000 3298 0 0 1 3298 691342236 691338939 0.000000e+00 6091
1 TraesCS3B01G450800 chr3B 96.863 1020 32 0 2279 3298 786464728 786465747 0.000000e+00 1707
2 TraesCS3B01G450800 chr3B 93.269 104 5 2 2178 2279 678531640 678531537 5.700000e-33 152
3 TraesCS3B01G450800 chr7D 97.105 2280 62 4 1 2279 30312808 30315084 0.000000e+00 3842
4 TraesCS3B01G450800 chr1D 97.016 2279 64 4 1 2279 58485513 58483239 0.000000e+00 3829
5 TraesCS3B01G450800 chr1D 96.713 2282 70 4 1 2279 108798530 108796251 0.000000e+00 3794
6 TraesCS3B01G450800 chr1D 96.519 2241 67 7 47 2279 10804205 10801968 0.000000e+00 3696
7 TraesCS3B01G450800 chrUn 96.361 2281 76 4 1 2279 52473335 52475610 0.000000e+00 3746
8 TraesCS3B01G450800 chr4B 96.280 2285 77 6 1 2279 539964047 539961765 0.000000e+00 3742
9 TraesCS3B01G450800 chr4D 95.744 2279 68 9 1 2279 65876431 65874182 0.000000e+00 3644
10 TraesCS3B01G450800 chr3D 95.940 2192 82 7 90 2279 175422130 175419944 0.000000e+00 3548
11 TraesCS3B01G450800 chr6B 95.898 2194 81 7 1 2191 680526233 680524046 0.000000e+00 3544
12 TraesCS3B01G450800 chr1B 97.059 1020 30 0 2279 3298 559602249 559603268 0.000000e+00 1718
13 TraesCS3B01G450800 chr1B 96.663 1019 34 0 2280 3298 348793470 348792452 0.000000e+00 1694
14 TraesCS3B01G450800 chr5B 96.860 1019 32 0 2280 3298 362536832 362535814 0.000000e+00 1705
15 TraesCS3B01G450800 chr5B 96.673 1022 34 0 2277 3298 539123797 539124818 0.000000e+00 1700
16 TraesCS3B01G450800 chr5B 96.667 1020 33 1 2279 3298 277592514 277591496 0.000000e+00 1694
17 TraesCS3B01G450800 chr5B 96.667 1020 33 1 2279 3298 575834792 575833774 0.000000e+00 1694
18 TraesCS3B01G450800 chr7B 96.765 1020 33 0 2279 3298 566566332 566565313 0.000000e+00 1701
19 TraesCS3B01G450800 chr7B 96.762 1019 33 0 2280 3298 18891153 18892171 0.000000e+00 1700


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 TraesCS3B01G450800 chr3B 691338939 691342236 3297 True 6091 6091 100.000 1 3298 1 chr3B.!!$R2 3297
1 TraesCS3B01G450800 chr3B 786464728 786465747 1019 False 1707 1707 96.863 2279 3298 1 chr3B.!!$F1 1019
2 TraesCS3B01G450800 chr7D 30312808 30315084 2276 False 3842 3842 97.105 1 2279 1 chr7D.!!$F1 2278
3 TraesCS3B01G450800 chr1D 58483239 58485513 2274 True 3829 3829 97.016 1 2279 1 chr1D.!!$R2 2278
4 TraesCS3B01G450800 chr1D 108796251 108798530 2279 True 3794 3794 96.713 1 2279 1 chr1D.!!$R3 2278
5 TraesCS3B01G450800 chr1D 10801968 10804205 2237 True 3696 3696 96.519 47 2279 1 chr1D.!!$R1 2232
6 TraesCS3B01G450800 chrUn 52473335 52475610 2275 False 3746 3746 96.361 1 2279 1 chrUn.!!$F1 2278
7 TraesCS3B01G450800 chr4B 539961765 539964047 2282 True 3742 3742 96.280 1 2279 1 chr4B.!!$R1 2278
8 TraesCS3B01G450800 chr4D 65874182 65876431 2249 True 3644 3644 95.744 1 2279 1 chr4D.!!$R1 2278
9 TraesCS3B01G450800 chr3D 175419944 175422130 2186 True 3548 3548 95.940 90 2279 1 chr3D.!!$R1 2189
10 TraesCS3B01G450800 chr6B 680524046 680526233 2187 True 3544 3544 95.898 1 2191 1 chr6B.!!$R1 2190
11 TraesCS3B01G450800 chr1B 559602249 559603268 1019 False 1718 1718 97.059 2279 3298 1 chr1B.!!$F1 1019
12 TraesCS3B01G450800 chr1B 348792452 348793470 1018 True 1694 1694 96.663 2280 3298 1 chr1B.!!$R1 1018
13 TraesCS3B01G450800 chr5B 362535814 362536832 1018 True 1705 1705 96.860 2280 3298 1 chr5B.!!$R2 1018
14 TraesCS3B01G450800 chr5B 539123797 539124818 1021 False 1700 1700 96.673 2277 3298 1 chr5B.!!$F1 1021
15 TraesCS3B01G450800 chr5B 277591496 277592514 1018 True 1694 1694 96.667 2279 3298 1 chr5B.!!$R1 1019
16 TraesCS3B01G450800 chr5B 575833774 575834792 1018 True 1694 1694 96.667 2279 3298 1 chr5B.!!$R3 1019
17 TraesCS3B01G450800 chr7B 566565313 566566332 1019 True 1701 1701 96.765 2279 3298 1 chr7B.!!$R1 1019
18 TraesCS3B01G450800 chr7B 18891153 18892171 1018 False 1700 1700 96.762 2280 3298 1 chr7B.!!$F1 1018

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
494 499 2.095853 CCACACCTATTGCAAAGCTACG 59.904 50.0 1.71 0.0 0.00 3.51 F
1284 1303 1.398958 CCAGGACTGAGCTAGGAGCC 61.399 65.0 0.00 0.0 43.77 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 1432 0.981183 AGAAACCCATCCGTAGTGCA 59.019 50.0 0.00 0.0 0.0 4.57 R
3275 3330 0.178958 TAATCTCTCTCGGGAGGGCC 60.179 60.0 13.54 0.0 39.8 5.80 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
38 39 6.219473 CAAACCTAAAACATGCATTGTACCA 58.781 36.000 0.00 0.00 37.68 3.25
79 80 5.504665 GCATGCTAGCCAAAACTGTAGTATG 60.505 44.000 13.29 5.41 38.15 2.39
133 136 2.172851 ACATGCATGTTGGCCAAAAG 57.827 45.000 26.61 14.05 37.90 2.27
187 190 7.928706 ACATCTATTCTAGCCAACTGAATACAC 59.071 37.037 0.00 0.00 33.24 2.90
213 216 2.553602 TGTCCAACTGAACATGCATGTC 59.446 45.455 31.45 23.19 40.80 3.06
242 245 7.012232 CCAAAAACTGAAATAAATGCAACCTGT 59.988 33.333 0.00 0.00 0.00 4.00
393 398 3.497118 CGACAGCAAAAACACAAGAACA 58.503 40.909 0.00 0.00 0.00 3.18
439 444 8.194104 GCCACAAACCATATTAACATATTCACA 58.806 33.333 0.00 0.00 0.00 3.58
493 498 2.423538 CCCACACCTATTGCAAAGCTAC 59.576 50.000 1.71 0.00 0.00 3.58
494 499 2.095853 CCACACCTATTGCAAAGCTACG 59.904 50.000 1.71 0.00 0.00 3.51
542 548 5.005586 CGGAACTAAAAACATAACGGCGATA 59.994 40.000 16.62 6.62 0.00 2.92
752 762 4.753516 TGCTCTTGCCAGCTATTTACTA 57.246 40.909 0.00 0.00 40.39 1.82
1192 1211 2.815684 ATCAGACCGTGGTGCCCCTA 62.816 60.000 0.00 0.00 0.00 3.53
1284 1303 1.398958 CCAGGACTGAGCTAGGAGCC 61.399 65.000 0.00 0.00 43.77 4.70
1289 1308 4.075793 TGAGCTAGGAGCCGGGGT 62.076 66.667 2.18 0.00 43.77 4.95
1329 1351 4.557899 AGGAGAAGAAGGAGAGGATGAT 57.442 45.455 0.00 0.00 0.00 2.45
1396 1418 4.774200 ACAGCCTTCAAATTGCTAAGGATT 59.226 37.500 15.18 2.63 42.01 3.01
1410 1432 7.361457 TGCTAAGGATTACTACAACAGCTAT 57.639 36.000 0.00 0.00 0.00 2.97
1607 1629 3.710677 AGTGATGAGGAGATGGAAGAAGG 59.289 47.826 0.00 0.00 0.00 3.46
1734 1757 1.836166 CTGATAGATGGGCGATGGGAT 59.164 52.381 0.00 0.00 0.00 3.85
1983 2010 6.449635 AAAATGACTTAACTGTGCAACTGA 57.550 33.333 0.00 0.00 39.30 3.41
2000 2027 2.644299 ACTGATGTCCAACTTCCCATGA 59.356 45.455 0.00 0.00 0.00 3.07
2009 2036 4.039004 TCCAACTTCCCATGATGTTTTGTG 59.961 41.667 0.00 0.00 36.91 3.33
2114 2141 6.040247 AGTGTTTTTAAAAAGGTGCAGCTAC 58.960 36.000 20.51 11.37 0.00 3.58
2163 2190 3.377172 GTGCCAACACATGTCCTATTACC 59.623 47.826 0.00 0.00 46.61 2.85
2174 2201 0.532862 CCTATTACCGTGCAGCTGGG 60.533 60.000 17.12 11.00 0.00 4.45
2542 2597 8.951787 TTGTAGTGATTGTAACAGTAACAACT 57.048 30.769 0.00 0.00 39.51 3.16
2573 2628 9.826574 AGTAAATAAGCGAAAACCAGTATATGA 57.173 29.630 0.00 0.00 0.00 2.15
2649 2704 8.923270 TCATCATGTAACAGTCATAACATAGGA 58.077 33.333 0.00 0.00 31.55 2.94
2704 2759 7.817478 TGTAATGTAGGCATGTATTCCGAATAG 59.183 37.037 0.81 0.00 35.15 1.73
2706 2761 5.779922 TGTAGGCATGTATTCCGAATAGTC 58.220 41.667 0.81 0.00 0.00 2.59
3150 3205 0.253044 CATCCAACCCATCACCGTCT 59.747 55.000 0.00 0.00 0.00 4.18
3275 3330 0.028242 CTCGAACGGACTCCAGATCG 59.972 60.000 10.96 10.96 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 5.160641 GTGTGGTACAATGCATGTTTTAGG 58.839 41.667 0.00 0.00 44.16 2.69
38 39 1.736645 GCATGCCGAGTACACGTGT 60.737 57.895 26.52 26.52 0.00 4.49
79 80 7.639461 CCAGAAAACATGTTTTTATTTGCACAC 59.361 33.333 31.42 17.43 42.26 3.82
133 136 3.620488 TGGCCAGGATACATTTTCTCAC 58.380 45.455 0.00 0.00 41.41 3.51
187 190 3.814842 TGCATGTTCAGTTGGACAGTTAG 59.185 43.478 0.00 0.00 0.00 2.34
213 216 4.450419 TGCATTTATTTCAGTTTTTGGCCG 59.550 37.500 0.00 0.00 0.00 6.13
242 245 5.303078 GGCTAGAATAGATGTCTCAGTTGGA 59.697 44.000 0.00 0.00 42.77 3.53
393 398 4.660789 GCTTCATTAGCCATGGACAAAT 57.339 40.909 18.40 8.36 44.48 2.32
451 456 4.263068 GGGACCAGAATATATGTGTGGGAG 60.263 50.000 11.21 0.00 32.13 4.30
493 498 9.313323 CGCTATATTGAACATATTTTTACACCG 57.687 33.333 0.00 0.00 0.00 4.94
494 499 9.607285 CCGCTATATTGAACATATTTTTACACC 57.393 33.333 0.00 0.00 0.00 4.16
517 522 3.165890 GCCGTTATGTTTTTAGTTCCGC 58.834 45.455 0.00 0.00 0.00 5.54
561 567 8.697507 AACAAGAAAGAAGAATTGTAGGACAT 57.302 30.769 0.00 0.00 34.92 3.06
752 762 6.443934 TGTTATGTTAGTTGCACAGTTTGT 57.556 33.333 0.00 0.00 0.00 2.83
960 974 2.034687 GCCACACACTCCCTGCAT 59.965 61.111 0.00 0.00 0.00 3.96
1192 1211 3.324846 TCTGACTGCAAAGACACCACTAT 59.675 43.478 0.00 0.00 0.00 2.12
1284 1303 3.047877 GCTCCGTCAACAACCCCG 61.048 66.667 0.00 0.00 0.00 5.73
1289 1308 0.746204 TTGCACAGCTCCGTCAACAA 60.746 50.000 0.00 0.00 0.00 2.83
1396 1418 4.201980 CCGTAGTGCATAGCTGTTGTAGTA 60.202 45.833 0.00 0.00 0.00 1.82
1410 1432 0.981183 AGAAACCCATCCGTAGTGCA 59.019 50.000 0.00 0.00 0.00 4.57
1547 1569 4.834406 TCTGGAATAGGGTCTAGGACAT 57.166 45.455 0.14 0.00 33.68 3.06
1554 1576 5.674035 AGATTTTGGATCTGGAATAGGGTCT 59.326 40.000 0.00 0.00 0.00 3.85
1607 1629 4.578105 CCTCTTCAGCAAATATTGGAGGTC 59.422 45.833 0.00 0.00 35.66 3.85
1734 1757 2.413796 GTCACGAACAAAGTGTGTCACA 59.586 45.455 0.18 0.18 40.60 3.58
1841 1866 2.905075 TGCAGTTATACAAGATGCGCT 58.095 42.857 9.73 0.00 39.74 5.92
1983 2010 3.744940 ACATCATGGGAAGTTGGACAT 57.255 42.857 0.00 0.00 0.00 3.06
2000 2027 7.847557 AAGCACCAAAAGTGATACACAAAACAT 60.848 33.333 4.75 0.00 46.71 2.71
2009 2036 4.739716 CACAACAAGCACCAAAAGTGATAC 59.260 41.667 0.00 0.00 46.71 2.24
2114 2141 1.086696 AATCGCAGGAAATGGACACG 58.913 50.000 0.00 0.00 0.00 4.49
2386 2440 3.316308 GGTTGAATTGACAACTCAGCTGT 59.684 43.478 14.67 0.00 46.17 4.40
2542 2597 7.708998 ACTGGTTTTCGCTTATTTACTTTTCA 58.291 30.769 0.00 0.00 0.00 2.69
2573 2628 0.393820 TCCGGTGCCTACGAGTTTTT 59.606 50.000 0.00 0.00 0.00 1.94
2649 2704 3.169099 ACTGGAGCTAGTTCTGTGTCAT 58.831 45.455 6.54 0.00 0.00 3.06
2704 2759 5.810587 TCTTTTCCATAAGCACGTATGAGAC 59.189 40.000 5.32 0.00 33.97 3.36
2706 2761 6.313905 AGTTCTTTTCCATAAGCACGTATGAG 59.686 38.462 5.32 0.00 33.97 2.90
2941 2996 5.879223 AGTTCTTGATCCTATCTTGCAAGTG 59.121 40.000 25.19 15.92 37.71 3.16
3150 3205 3.838244 AATTCCATCGTAGGCTTGCTA 57.162 42.857 0.00 0.00 0.00 3.49
3202 3257 2.644299 TCATCAACCATCCTCCAACACT 59.356 45.455 0.00 0.00 0.00 3.55
3206 3261 3.682436 CGTCATCATCAACCATCCTCCAA 60.682 47.826 0.00 0.00 0.00 3.53
3275 3330 0.178958 TAATCTCTCTCGGGAGGGCC 60.179 60.000 13.54 0.00 39.80 5.80


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

AutoCloner maintained by Alex Coulton.