Multiple sequence alignment - TraesCS3D01G521200

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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 TraesCS3D01G521200 chr3D 100.000 2666 0 0 1 2666 603115266 603117931 0.000000e+00 4924
1 TraesCS3D01G521200 chr3D 97.397 2113 46 6 1 2108 603150837 603152945 0.000000e+00 3589
2 TraesCS3D01G521200 chr3D 96.325 517 19 0 2150 2666 603163132 603163648 0.000000e+00 850
3 TraesCS3D01G521200 chr3B 92.793 2442 138 17 119 2553 810622975 810620565 0.000000e+00 3500
4 TraesCS3D01G521200 chr3B 92.589 1066 70 5 1606 2666 810598106 810597045 0.000000e+00 1522
5 TraesCS3D01G521200 chr3B 91.686 421 33 1 722 1142 810602627 810602209 1.380000e-162 582
6 TraesCS3D01G521200 chr3B 92.010 413 28 5 1141 1551 810598515 810598106 2.300000e-160 575
7 TraesCS3D01G521200 chr3B 85.748 421 47 7 2024 2434 815163936 815164353 1.470000e-117 433
8 TraesCS3D01G521200 chr3A 94.229 2010 101 9 119 2121 732913007 732911006 0.000000e+00 3055
9 TraesCS3D01G521200 chr3A 89.744 546 40 6 2124 2666 732910688 732910156 0.000000e+00 684
10 TraesCS3D01G521200 chr3A 78.293 410 81 7 2038 2442 597083614 597083208 9.470000e-65 257
11 TraesCS3D01G521200 chr5A 82.326 430 61 6 2024 2442 645417915 645418340 2.520000e-95 359
12 TraesCS3D01G521200 chr6D 80.896 424 70 7 2024 2442 341114982 341114565 9.210000e-85 324
13 TraesCS3D01G521200 chr7A 80.861 418 64 12 2024 2435 736508009 736507602 5.540000e-82 315
14 TraesCS3D01G521200 chr6A 79.343 426 64 16 2026 2435 2055632 2055215 7.270000e-71 278
15 TraesCS3D01G521200 chr2D 78.588 425 77 10 2019 2434 626635774 626635355 4.370000e-68 268


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 TraesCS3D01G521200 chr3D 603115266 603117931 2665 False 4924.0 4924 100.0000 1 2666 1 chr3D.!!$F1 2665
1 TraesCS3D01G521200 chr3D 603150837 603152945 2108 False 3589.0 3589 97.3970 1 2108 1 chr3D.!!$F2 2107
2 TraesCS3D01G521200 chr3D 603163132 603163648 516 False 850.0 850 96.3250 2150 2666 1 chr3D.!!$F3 516
3 TraesCS3D01G521200 chr3B 810620565 810622975 2410 True 3500.0 3500 92.7930 119 2553 1 chr3B.!!$R1 2434
4 TraesCS3D01G521200 chr3B 810597045 810602627 5582 True 893.0 1522 92.0950 722 2666 3 chr3B.!!$R2 1944
5 TraesCS3D01G521200 chr3A 732910156 732913007 2851 True 1869.5 3055 91.9865 119 2666 2 chr3A.!!$R2 2547

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
414 418 2.249309 TCTTACTCCCACTCCCCTTC 57.751 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2346 6370 2.061773 GCATTGCTCGTATATGCTCGT 58.938 47.619 0.16 0.0 41.04 4.18 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
311 312 8.737168 TTTTCTAGATACTGTGCTGCATAAAT 57.263 30.769 5.27 0.00 0.00 1.40
389 393 2.856222 CTGGGGCTCACTTTCCATATC 58.144 52.381 0.00 0.00 0.00 1.63
414 418 2.249309 TCTTACTCCCACTCCCCTTC 57.751 55.000 0.00 0.00 0.00 3.46
943 951 3.076621 TGCCATGTCATTCTTCTGTCAC 58.923 45.455 0.00 0.00 0.00 3.67
1117 1125 5.128827 TCCGATCTCCTAAAGTTGCAATACT 59.871 40.000 0.59 0.00 0.00 2.12
1139 4842 5.647658 ACTTTCGTTGCATAATCATGGAGAA 59.352 36.000 0.00 0.00 33.63 2.87
1147 4850 4.274459 GCATAATCATGGAGAAGCTTCGTT 59.726 41.667 20.43 4.20 32.36 3.85
1326 5030 7.549488 CCAGAAAGGTACTAAGTATGAAACCAG 59.451 40.741 0.00 0.00 38.49 4.00
1327 5031 8.095169 CAGAAAGGTACTAAGTATGAAACCAGT 58.905 37.037 0.00 0.00 38.49 4.00
1349 5054 8.846211 CCAGTCTTCTCTGTTTATTTTGGTTTA 58.154 33.333 0.00 0.00 34.02 2.01
1373 5078 4.871513 TGGAAGTGCTTATATGAGTAGCG 58.128 43.478 0.00 0.00 37.73 4.26
1644 5349 2.710096 AACCCCGTCAATCTATGGTG 57.290 50.000 0.00 0.00 0.00 4.17
1668 5373 8.500773 GTGACTCTTCTTTCGGAGATATAGTAG 58.499 40.741 0.00 0.00 35.04 2.57
1873 5578 8.177119 TGAATGCCACCATATAACTTAAATCC 57.823 34.615 0.00 0.00 0.00 3.01
1926 5631 9.515020 GTGTTGACATTTTTAATTCAGAACAGA 57.485 29.630 0.00 0.00 0.00 3.41
1950 5655 8.959548 AGATGTGTGTTTGATCATTTGCTTATA 58.040 29.630 0.00 0.00 0.00 0.98
2043 5749 3.746045 AAACACGATGAGTACACACCT 57.254 42.857 0.00 0.00 0.00 4.00
2091 5797 4.230863 AACACCAACGCGCACACG 62.231 61.111 5.73 0.00 44.07 4.49
2121 5827 5.581605 ACATGCCAATAAATAGCAAAGTCG 58.418 37.500 0.00 0.00 40.46 4.18
2126 6149 8.439993 TGCCAATAAATAGCAAAGTCGTATAA 57.560 30.769 0.00 0.00 32.56 0.98
2145 6168 5.986004 ATAAAGACCAAAGCTATACGCAC 57.014 39.130 0.00 0.00 42.61 5.34
2220 6243 6.372381 TCATATTCGCACCAATTATCTCATGG 59.628 38.462 0.00 0.00 40.16 3.66
2282 6305 2.963782 ACGAAGGGAGTGACACTTAAGT 59.036 45.455 10.01 1.12 42.92 2.24
2321 6344 0.325577 ACCATCCAGGGCCAAAATCC 60.326 55.000 6.18 0.00 43.89 3.01
2346 6370 6.881065 CAGATTTTCATCCTGAAGAACCAGTA 59.119 38.462 0.00 0.00 37.70 2.74
2619 6643 4.065789 CCGACAATTATTTCCTCTAGGGC 58.934 47.826 0.00 0.00 35.41 5.19
2635 6664 1.768870 AGGGCTACGGATTGCTTGTAT 59.231 47.619 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
303 304 9.752961 CTTCATCATTGGAAATGTATTTATGCA 57.247 29.630 0.00 0.00 0.00 3.96
311 312 8.821686 AACATACCTTCATCATTGGAAATGTA 57.178 30.769 0.26 0.00 33.86 2.29
356 357 0.111253 GCCCCAGCATTGGTATAGCT 59.889 55.000 3.20 0.00 43.40 3.32
389 393 2.436173 GGGAGTGGGAGTAAGAAGATGG 59.564 54.545 0.00 0.00 0.00 3.51
414 418 7.731054 AGCTAGGAAAGGAACAACATATAGAG 58.269 38.462 0.00 0.00 0.00 2.43
784 791 5.835113 AACATGGCCACACTATACATTTC 57.165 39.130 8.16 0.00 0.00 2.17
943 951 1.518133 CTTCGAGGGCGCTCTTCAG 60.518 63.158 26.13 15.56 37.46 3.02
1117 1125 5.449041 GCTTCTCCATGATTATGCAACGAAA 60.449 40.000 0.00 0.00 32.79 3.46
1139 4842 0.537143 TGGTGGATGCAAACGAAGCT 60.537 50.000 0.00 0.00 0.00 3.74
1147 4850 0.106268 AGTGGTGTTGGTGGATGCAA 60.106 50.000 0.00 0.00 0.00 4.08
1326 5030 9.665264 CAGTAAACCAAAATAAACAGAGAAGAC 57.335 33.333 0.00 0.00 0.00 3.01
1327 5031 8.846211 CCAGTAAACCAAAATAAACAGAGAAGA 58.154 33.333 0.00 0.00 0.00 2.87
1349 5054 5.508153 CGCTACTCATATAAGCACTTCCAGT 60.508 44.000 0.00 0.00 35.98 4.00
1622 5327 3.875134 CACCATAGATTGACGGGGTTTAC 59.125 47.826 0.00 0.00 0.00 2.01
1644 5349 8.611654 ACTACTATATCTCCGAAAGAAGAGTC 57.388 38.462 0.00 0.00 37.61 3.36
1668 5373 2.742053 ACAGCCATGTGTTCGACAATAC 59.258 45.455 0.00 0.00 38.57 1.89
2015 5720 8.653338 GTGTGTACTCATCGTGTTTATGTAAAT 58.347 33.333 0.24 0.00 0.00 1.40
2043 5749 4.025040 CATCCTAATTATGCAGAGGCCA 57.975 45.455 5.01 0.00 40.13 5.36
2091 5797 5.353678 TGCTATTTATTGGCATGTTTTTGGC 59.646 36.000 0.00 0.00 42.20 4.52
2172 6195 7.264221 TGATCATTGTTGTAGTTTGTTGCTTT 58.736 30.769 0.00 0.00 0.00 3.51
2220 6243 4.634133 TCGTCGTCCGTGTGGTGC 62.634 66.667 0.00 0.00 37.94 5.01
2346 6370 2.061773 GCATTGCTCGTATATGCTCGT 58.938 47.619 0.16 0.00 41.04 4.18
2619 6643 4.268644 CACAGTCATACAAGCAATCCGTAG 59.731 45.833 0.00 0.00 0.00 3.51
2635 6664 3.146066 GGCATAACCTTTCACACAGTCA 58.854 45.455 0.00 0.00 34.51 3.41


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

AutoCloner maintained by Alex Coulton.