Multiple sequence alignment - TraesCS3A01G329900

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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 TraesCS3A01G329900 chr3A 100.000 2416 0 0 1 2416 574865319 574867734 0.000000e+00 4462.0
1 TraesCS3A01G329900 chr3A 82.329 249 38 6 130 376 439278499 439278743 6.770000e-51 211.0
2 TraesCS3A01G329900 chr3A 83.190 232 33 5 141 371 501028793 501028567 8.750000e-50 207.0
3 TraesCS3A01G329900 chr3D 96.159 2421 86 5 1 2416 436043575 436045993 0.000000e+00 3949.0
4 TraesCS3A01G329900 chr3D 95.047 2423 111 6 1 2416 436162789 436165209 0.000000e+00 3801.0
5 TraesCS3A01G329900 chr3B 93.858 2426 127 14 1 2416 571810746 571813159 0.000000e+00 3635.0
6 TraesCS3A01G329900 chr5D 87.854 247 27 3 140 385 542699524 542699280 1.090000e-73 287.0
7 TraesCS3A01G329900 chr2D 83.913 230 26 7 156 384 509751350 509751569 2.430000e-50 209.0
8 TraesCS3A01G329900 chr7D 81.600 250 40 5 131 378 628130391 628130636 4.070000e-48 202.0
9 TraesCS3A01G329900 chr6A 80.455 220 35 6 160 378 6585422 6585210 6.910000e-36 161.0
10 TraesCS3A01G329900 chr2B 81.325 166 27 3 2254 2416 447484132 447483968 5.420000e-27 132.0
11 TraesCS3A01G329900 chr2A 81.366 161 27 2 2258 2416 508581476 508581635 7.010000e-26 128.0
12 TraesCS3A01G329900 chr2A 89.706 68 7 0 2 69 724512148 724512081 1.190000e-13 87.9


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 TraesCS3A01G329900 chr3A 574865319 574867734 2415 False 4462 4462 100.000 1 2416 1 chr3A.!!$F2 2415
1 TraesCS3A01G329900 chr3D 436043575 436045993 2418 False 3949 3949 96.159 1 2416 1 chr3D.!!$F1 2415
2 TraesCS3A01G329900 chr3D 436162789 436165209 2420 False 3801 3801 95.047 1 2416 1 chr3D.!!$F2 2415
3 TraesCS3A01G329900 chr3B 571810746 571813159 2413 False 3635 3635 93.858 1 2416 1 chr3B.!!$F1 2415

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
504 507 0.389426 CTGCAAATGCCTTGGTCTGC 60.389 55.0 2.46 0.0 41.18 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 2285 2.514803 GAGCTACTTCCTTTTTGGGCA 58.485 47.619 0.0 0.0 36.2 5.36 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
27 28 7.865820 TGAATCCTTGAATAGACCTGAAGAAT 58.134 34.615 0.00 0.00 0.00 2.40
32 33 7.346698 TCCTTGAATAGACCTGAAGAATCTGAT 59.653 37.037 0.00 0.00 0.00 2.90
46 47 6.808008 AGAATCTGATACCAAATATTGCCG 57.192 37.500 0.00 0.00 0.00 5.69
79 82 4.915667 CACGACAAGAAACGAATCTCACTA 59.084 41.667 0.00 0.00 0.00 2.74
93 96 0.406750 TCACTACCCCGAGGAGTCAA 59.593 55.000 0.00 0.00 36.73 3.18
152 155 2.561419 GGACTCTAGTAAGTGCCACACA 59.439 50.000 0.00 0.00 36.74 3.72
177 180 2.753055 TACGAGCACATGCCAACTTA 57.247 45.000 0.00 0.00 43.38 2.24
289 292 1.651987 AACTTGTCGTGTGTCACTGG 58.348 50.000 4.27 0.00 31.34 4.00
336 339 5.009010 GGAATTGCCATCGAATAATGTCAGT 59.991 40.000 0.00 0.00 36.34 3.41
504 507 0.389426 CTGCAAATGCCTTGGTCTGC 60.389 55.000 2.46 0.00 41.18 4.26
520 523 4.096833 TGGTCTGCATTCATAGTTTGCATC 59.903 41.667 0.00 0.00 44.65 3.91
553 556 5.132648 ACATCATACATGTATCCAACCTGGT 59.867 40.000 15.60 0.00 39.03 4.00
584 587 7.452880 TGGATGTATTCATTAAATAGCTGCC 57.547 36.000 0.00 0.00 34.06 4.85
626 629 5.574891 ACAACAAACATAAGTGCTCACAA 57.425 34.783 2.63 0.00 0.00 3.33
654 657 6.931838 ACTATAAGACAAACAGAATGGACGA 58.068 36.000 0.00 0.00 43.62 4.20
743 746 4.698583 GACACGTGTCTACATAGGAACT 57.301 45.455 35.51 3.21 41.65 3.01
780 783 3.119463 GTCAATGTAACAAACGCATGTGC 59.881 43.478 6.08 0.00 32.81 4.57
805 808 6.806739 CGTACATCTGTCTACATGAGAAACAA 59.193 38.462 0.00 0.00 35.37 2.83
851 854 2.224670 ACCACCTACGCCTTGATTGAAA 60.225 45.455 0.00 0.00 0.00 2.69
990 993 3.714391 GGTAGCCAACCGATTACTACTG 58.286 50.000 2.79 0.00 38.88 2.74
1052 1055 4.402155 TCTTGCCTTTGTTCTTGTTGTGAT 59.598 37.500 0.00 0.00 0.00 3.06
1160 1163 1.126846 GTCGAGTGCATGTTGTAGTGC 59.873 52.381 0.00 0.00 41.61 4.40
1287 1290 0.036010 CACTCAAACCTGGCTCCGAT 60.036 55.000 0.00 0.00 0.00 4.18
1454 1457 8.655935 ATCTGGTAATCAAAGGAGAAATGTTT 57.344 30.769 0.00 0.00 0.00 2.83
1490 1493 3.135530 GCCTCTATGTTGACTGGATTCCT 59.864 47.826 3.95 0.00 0.00 3.36
1663 1667 6.703165 CCTTTTCTGGTTTTGATTCCTTTGAG 59.297 38.462 0.00 0.00 0.00 3.02
1854 1861 2.562738 GGCTAAATTGGTTGGTGCTTCT 59.437 45.455 0.00 0.00 0.00 2.85
2061 2068 9.599866 ACATTTATTGAGATCGATCAGTACAAA 57.400 29.630 26.47 18.79 0.00 2.83
2104 2115 1.995376 AGACAAACCCAATGGACCAC 58.005 50.000 0.00 0.00 34.81 4.16
2237 2248 4.436998 CGGGAGCACTCGGACCAC 62.437 72.222 0.00 0.00 36.22 4.16
2250 2261 1.534385 CGGACCACGCGTCATATTACA 60.534 52.381 9.86 0.00 43.95 2.41
2274 2285 6.092533 CACTTTGGTTGCTCTGTTGAATTTTT 59.907 34.615 0.00 0.00 0.00 1.94
2353 2364 5.698104 TCTTCCATATGTTCATTCCTGCAT 58.302 37.500 1.24 0.00 0.00 3.96
2358 2369 6.882678 TCCATATGTTCATTCCTGCATATCAG 59.117 38.462 1.24 0.00 42.49 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.036262 GCAACGGCAATATTTGGTATCAGA 59.964 41.667 0.00 0.00 40.72 3.27
32 33 2.085320 ACGCAACGGCAATATTTGGTA 58.915 42.857 0.00 0.00 41.24 3.25
62 63 3.368116 CGGGGTAGTGAGATTCGTTTCTT 60.368 47.826 0.00 0.00 0.00 2.52
79 82 2.640826 TGTATTTTTGACTCCTCGGGGT 59.359 45.455 0.00 0.00 0.00 4.95
128 131 3.006537 TGTGGCACTTACTAGAGTCCAAC 59.993 47.826 19.83 0.00 32.50 3.77
152 155 3.751479 TGGCATGTGCTCGTATCTTAT 57.249 42.857 4.84 0.00 41.70 1.73
205 208 2.722094 ACTAAAATTGCCATCCTCGCA 58.278 42.857 0.00 0.00 0.00 5.10
240 243 7.476667 TCGAAAAATAAACTGAAGCACAAAGA 58.523 30.769 0.00 0.00 0.00 2.52
289 292 4.614284 CAGTCACGCAAAGATGACAAATTC 59.386 41.667 7.10 0.00 46.34 2.17
584 587 4.641396 TGTACTGACCCATCTCAACAAAG 58.359 43.478 0.00 0.00 0.00 2.77
626 629 9.167311 GTCCATTCTGTTTGTCTTATAGTCAAT 57.833 33.333 0.00 0.00 0.00 2.57
780 783 6.322491 TGTTTCTCATGTAGACAGATGTACG 58.678 40.000 0.00 0.00 32.51 3.67
826 829 2.034879 CAAGGCGTAGGTGGTGCTG 61.035 63.158 0.00 0.00 0.00 4.41
851 854 7.782644 TGAATTCACCCGAGGGAAAATAATTAT 59.217 33.333 16.26 0.00 38.96 1.28
988 991 5.938125 AGTGTTTTGCCATAACTACTACCAG 59.062 40.000 0.00 0.00 0.00 4.00
990 993 6.812879 AAGTGTTTTGCCATAACTACTACC 57.187 37.500 0.00 0.00 0.00 3.18
1052 1055 1.403647 CGACGGTACAATCTTCAGCCA 60.404 52.381 0.00 0.00 0.00 4.75
1160 1163 1.197721 GTGCATTGACCTTCTGAACCG 59.802 52.381 0.00 0.00 0.00 4.44
1287 1290 8.397575 TCAAAATATAACACTTACTGCCACAA 57.602 30.769 0.00 0.00 0.00 3.33
1324 1327 5.524971 TCATGACAAGTATTAGGGGTACG 57.475 43.478 0.00 0.00 0.00 3.67
1454 1457 7.787904 TCAACATAGAGGCCTAGGAACTAAATA 59.212 37.037 14.75 4.50 42.17 1.40
1663 1667 4.599047 TGTTTTCAATCCCCATTCACAC 57.401 40.909 0.00 0.00 0.00 3.82
1929 1936 8.011844 AGATCGAGGCATTTGTAGCATATATA 57.988 34.615 0.00 0.00 0.00 0.86
2061 2068 8.154856 TCTTGTAGTAACCTATGAGCACTTTTT 58.845 33.333 0.00 0.00 0.00 1.94
2104 2115 3.826157 ACACCAATTCACAACCATACCAG 59.174 43.478 0.00 0.00 0.00 4.00
2237 2248 4.331137 CAACCAAAGTGTAATATGACGCG 58.669 43.478 3.53 3.53 34.94 6.01
2250 2261 5.343307 AAATTCAACAGAGCAACCAAAGT 57.657 34.783 0.00 0.00 0.00 2.66
2274 2285 2.514803 GAGCTACTTCCTTTTTGGGCA 58.485 47.619 0.00 0.00 36.20 5.36
2316 2327 8.415950 ACATATGGAAGAAAACCAATGTACAA 57.584 30.769 7.80 0.00 40.93 2.41
2320 2331 7.537596 TGAACATATGGAAGAAAACCAATGT 57.462 32.000 7.80 0.00 40.93 2.71
2321 2332 9.090692 GAATGAACATATGGAAGAAAACCAATG 57.909 33.333 7.80 0.00 40.93 2.82
2384 2395 6.091437 CGTCTTTCTAACACTAATCCTTCGT 58.909 40.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.