Multiple sequence alignment - TraesCS2B01G285600

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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 TraesCS2B01G285600 chr2B 100.000 3278 0 0 1 3278 393462199 393465476 0 6054
1 TraesCS2B01G285600 chr2B 85.278 1277 184 4 1004 2278 472898500 472899774 0 1314
2 TraesCS2B01G285600 chr2D 96.562 3287 62 15 1 3278 324592248 324595492 0 5397
3 TraesCS2B01G285600 chr2A 96.251 2534 64 10 1 2516 394023795 394021275 0 4124
4 TraesCS2B01G285600 chr2A 84.977 1278 186 6 1004 2278 536623656 536624930 0 1291
5 TraesCS2B01G285600 chr2A 93.634 754 20 6 2551 3278 394021163 394020412 0 1101


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 TraesCS2B01G285600 chr2B 393462199 393465476 3277 False 6054.0 6054 100.0000 1 3278 1 chr2B.!!$F1 3277
1 TraesCS2B01G285600 chr2B 472898500 472899774 1274 False 1314.0 1314 85.2780 1004 2278 1 chr2B.!!$F2 1274
2 TraesCS2B01G285600 chr2D 324592248 324595492 3244 False 5397.0 5397 96.5620 1 3278 1 chr2D.!!$F1 3277
3 TraesCS2B01G285600 chr2A 394020412 394023795 3383 True 2612.5 4124 94.9425 1 3278 2 chr2A.!!$R1 3277
4 TraesCS2B01G285600 chr2A 536623656 536624930 1274 False 1291.0 1291 84.9770 1004 2278 1 chr2A.!!$F1 1274

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
264 268 0.322546 CTGAAGGCTTGGGGTACACC 60.323 60.0 7.4 7.4 39.11 4.16 F
274 278 0.614812 GGGGTACACCGTACAATGGT 59.385 55.0 0.0 0.0 41.60 3.55 F
948 954 0.687354 ACACTGCCTTCTTGGTCGAT 59.313 50.0 0.0 0.0 38.35 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1821 0.032815 GGCCTGCCTTAGACGAGATC 59.967 60.000 0.00 0.0 0.0 2.75 R
1902 1908 4.319549 CCAAGAGCGGTTTCAAAGTACTTC 60.320 45.833 8.95 0.0 0.0 3.01 R
2717 2830 0.171231 CGCATGTCTCGTCTTCTCCA 59.829 55.000 0.00 0.0 0.0 3.86 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 57 4.715297 GGGGATTCTCAGTTCTAGGTTGTA 59.285 45.833 0.00 0.00 0.00 2.41
214 218 3.900941 ACGCCATTAGCAACTTCTTTTG 58.099 40.909 0.00 0.00 44.04 2.44
260 264 3.087065 GGCTGAAGGCTTGGGGTA 58.913 61.111 3.46 0.00 41.46 3.69
261 265 1.378646 GGCTGAAGGCTTGGGGTAC 60.379 63.158 3.46 0.00 41.46 3.34
262 266 1.378762 GCTGAAGGCTTGGGGTACA 59.621 57.895 3.46 0.00 38.06 2.90
263 267 0.960861 GCTGAAGGCTTGGGGTACAC 60.961 60.000 3.46 0.00 38.06 2.90
264 268 0.322546 CTGAAGGCTTGGGGTACACC 60.323 60.000 7.40 7.40 39.11 4.16
265 269 1.376812 GAAGGCTTGGGGTACACCG 60.377 63.158 10.24 0.00 41.60 4.94
274 278 0.614812 GGGGTACACCGTACAATGGT 59.385 55.000 0.00 0.00 41.60 3.55
305 309 9.016438 TCGCCCAATTTTCTTAACTTTACTTAT 57.984 29.630 0.00 0.00 0.00 1.73
306 310 9.634163 CGCCCAATTTTCTTAACTTTACTTATT 57.366 29.630 0.00 0.00 0.00 1.40
390 394 2.307496 TGACGGTGGTAGGGTTTAGA 57.693 50.000 0.00 0.00 0.00 2.10
409 413 2.272146 CATGCCCGCTACCAAGGT 59.728 61.111 0.00 0.00 0.00 3.50
477 481 4.321527 GCTATTCCAAAATGCATAGGAGCC 60.322 45.833 13.23 0.00 0.00 4.70
526 530 5.752955 TGTTCTTTTGCATTTTAAGTGGCTC 59.247 36.000 0.00 0.00 0.00 4.70
735 739 7.768120 AGATGGTGAATTTAGTGTCTGATCTTC 59.232 37.037 0.00 0.00 0.00 2.87
740 744 7.544566 GTGAATTTAGTGTCTGATCTTCGGTTA 59.455 37.037 0.00 0.00 0.00 2.85
894 900 1.126329 ATGCCCTCCAGATGCTCGAT 61.126 55.000 0.00 0.00 0.00 3.59
948 954 0.687354 ACACTGCCTTCTTGGTCGAT 59.313 50.000 0.00 0.00 38.35 3.59
949 955 1.899814 ACACTGCCTTCTTGGTCGATA 59.100 47.619 0.00 0.00 38.35 2.92
1198 1204 2.810852 CTCACAAAAGAGAACAGAGCCC 59.189 50.000 0.00 0.00 37.87 5.19
1815 1821 1.400846 GCTGATGATGTTGCAGGAGTG 59.599 52.381 0.00 0.00 0.00 3.51
1902 1908 2.097629 TGCCTACTCGAAACGATCTCTG 59.902 50.000 0.00 0.00 34.61 3.35
2193 2199 2.812499 GCCAAGACGGAGGCGATA 59.188 61.111 0.00 0.00 41.70 2.92
2310 2328 7.519032 TTTGTTCCCCAGTTAAATCTTACAG 57.481 36.000 0.00 0.00 0.00 2.74
2326 2344 4.767409 TCTTACAGTTGAGCTCTGCTAGAA 59.233 41.667 16.19 8.84 39.88 2.10
2384 2402 8.592105 TTATTTCTTCCTTGCAAATTGTCTTG 57.408 30.769 0.00 0.00 0.00 3.02
2389 2407 4.431809 TCCTTGCAAATTGTCTTGTGTTG 58.568 39.130 0.00 0.00 0.00 3.33
2411 2430 6.731292 TGGCTCTATAAAATGTCTAGCTCA 57.269 37.500 0.00 0.00 0.00 4.26
2422 2441 4.890158 TGTCTAGCTCATGGACAAGAAA 57.110 40.909 0.00 0.00 45.42 2.52
2424 2443 4.997395 TGTCTAGCTCATGGACAAGAAAAC 59.003 41.667 0.00 0.00 45.42 2.43
2427 2446 2.549754 AGCTCATGGACAAGAAAACACG 59.450 45.455 0.00 0.00 0.00 4.49
2492 2511 1.722011 ACCATTTCCGTTCTAGTGCG 58.278 50.000 0.00 0.00 0.00 5.34
2498 2517 0.885879 TCCGTTCTAGTGCGATGTGT 59.114 50.000 9.54 0.00 0.00 3.72
2510 2529 4.515191 AGTGCGATGTGTAATGTTCTGTTT 59.485 37.500 0.00 0.00 0.00 2.83
2582 2683 4.877823 TCACTGCAGTAATGCAAGATTAGG 59.122 41.667 21.20 7.97 44.88 2.69
2596 2698 5.600696 CAAGATTAGGTTGCTTGTTTGGTT 58.399 37.500 0.00 0.00 35.49 3.67
2609 2722 5.535783 GCTTGTTTGGTTAAAGGGGTTAGTA 59.464 40.000 0.00 0.00 0.00 1.82
2635 2748 1.833630 TGAGGTGGCAGATTAGTGGAG 59.166 52.381 0.00 0.00 0.00 3.86
2636 2749 2.111384 GAGGTGGCAGATTAGTGGAGA 58.889 52.381 0.00 0.00 0.00 3.71
2717 2830 2.539081 GGGTCAAGGGTCAAGGGCT 61.539 63.158 0.00 0.00 0.00 5.19
2822 2935 1.706305 CCCCCACCCGCCTTTATATAA 59.294 52.381 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 7.630242 AACGAACAAATCCATATGAAGATGT 57.370 32.000 3.65 1.54 0.00 3.06
161 165 3.831323 TCTTGATGGAAAGCAACAAGGA 58.169 40.909 0.00 0.00 38.56 3.36
214 218 0.961019 TCAAATGCCAACAGGTGAGC 59.039 50.000 0.00 0.00 0.00 4.26
262 266 1.735571 GCGAAATCACCATTGTACGGT 59.264 47.619 0.00 0.00 37.16 4.83
263 267 1.063469 GGCGAAATCACCATTGTACGG 59.937 52.381 0.00 0.00 0.00 4.02
264 268 1.063469 GGGCGAAATCACCATTGTACG 59.937 52.381 0.00 0.00 0.00 3.67
265 269 2.088423 TGGGCGAAATCACCATTGTAC 58.912 47.619 0.00 0.00 0.00 2.90
274 278 6.339587 AGTTAAGAAAATTGGGCGAAATCA 57.660 33.333 0.00 0.00 0.00 2.57
308 312 9.832445 AGTAAGAAAAAGACTTGTGAGATACAA 57.168 29.630 0.00 0.00 46.62 2.41
328 332 9.907229 TGATTAGAGTTGAGAGATACAGTAAGA 57.093 33.333 0.00 0.00 0.00 2.10
390 394 2.272146 CTTGGTAGCGGGCATGGT 59.728 61.111 0.00 0.00 0.00 3.55
409 413 9.438228 TGAAAATTAGAACATATGTACCGACAA 57.562 29.630 9.21 2.91 39.59 3.18
477 481 5.120363 GCTTAAGGTTTCAGAAGGTAAGTCG 59.880 44.000 4.29 0.00 0.00 4.18
683 687 4.744631 GGCAACCAACAAAACATCTAGTTG 59.255 41.667 0.00 0.00 41.19 3.16
1198 1204 4.187694 GTCAACAGATTCCTAAGCTCCTG 58.812 47.826 0.00 0.00 0.00 3.86
1815 1821 0.032815 GGCCTGCCTTAGACGAGATC 59.967 60.000 0.00 0.00 0.00 2.75
1902 1908 4.319549 CCAAGAGCGGTTTCAAAGTACTTC 60.320 45.833 8.95 0.00 0.00 3.01
2310 2328 3.131933 TGGAGATTCTAGCAGAGCTCAAC 59.868 47.826 17.77 7.23 40.44 3.18
2326 2344 3.137913 CAGGGATTTCATGTCCTGGAGAT 59.862 47.826 0.00 0.00 42.12 2.75
2384 2402 6.763610 AGCTAGACATTTTATAGAGCCAACAC 59.236 38.462 0.00 0.00 0.00 3.32
2389 2407 6.593382 CCATGAGCTAGACATTTTATAGAGCC 59.407 42.308 0.00 0.00 0.00 4.70
2411 2430 3.020984 ACAACCGTGTTTTCTTGTCCAT 58.979 40.909 0.00 0.00 32.58 3.41
2424 2443 2.605338 CCATCAAGCAGAAACAACCGTG 60.605 50.000 0.00 0.00 0.00 4.94
2427 2446 4.320608 TTTCCATCAAGCAGAAACAACC 57.679 40.909 0.00 0.00 0.00 3.77
2439 2458 6.349280 GCAAGTGCTAACTGTATTTCCATCAA 60.349 38.462 0.00 0.00 36.51 2.57
2519 2543 0.250945 ACCCACACACACACACACAA 60.251 50.000 0.00 0.00 0.00 3.33
2582 2683 3.118555 ACCCCTTTAACCAAACAAGCAAC 60.119 43.478 0.00 0.00 0.00 4.17
2596 2698 4.100498 CCTCAATCGCTACTAACCCCTTTA 59.900 45.833 0.00 0.00 0.00 1.85
2609 2722 0.254178 AATCTGCCACCTCAATCGCT 59.746 50.000 0.00 0.00 0.00 4.93
2635 2748 1.017387 CTAATTTGGACCTGCGCCTC 58.983 55.000 4.18 0.00 0.00 4.70
2636 2749 1.032114 GCTAATTTGGACCTGCGCCT 61.032 55.000 4.18 0.00 0.00 5.52
2717 2830 0.171231 CGCATGTCTCGTCTTCTCCA 59.829 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.