Multiple sequence alignment - TraesCS6B01G464600

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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 TraesCS6B01G464600 chr6B 100.000 2167 0 0 578 2744 715991505 715989339 0 4002
1 TraesCS6B01G464600 chr6B 99.031 2167 20 1 578 2744 596602291 596600126 0 3884
2 TraesCS6B01G464600 chr6B 100.000 396 0 0 1 396 715992082 715991687 0 732
3 TraesCS6B01G464600 chr6B 98.741 397 4 1 1 396 596602604 596602208 0 704
4 TraesCS6B01G464600 chr7A 98.939 2167 22 1 578 2744 638508098 638505933 0 3873
5 TraesCS6B01G464600 chr7A 98.800 2167 22 3 578 2744 708245194 708247356 0 3855
6 TraesCS6B01G464600 chr7A 98.237 397 6 1 1 396 638508411 638508015 0 693
7 TraesCS6B01G464600 chr7A 98.237 397 6 1 1 396 708244881 708245277 0 693
8 TraesCS6B01G464600 chrUn 98.847 2168 21 4 578 2744 171007853 171010017 0 3862
9 TraesCS6B01G464600 chrUn 98.237 397 6 1 1 396 171007540 171007936 0 693
10 TraesCS6B01G464600 chrUn 98.237 397 6 1 1 396 432741607 432742003 0 693
11 TraesCS6B01G464600 chr1B 98.478 2168 30 2 578 2744 672540790 672542955 0 3818
12 TraesCS6B01G464600 chr5B 98.293 2168 36 1 578 2744 567279562 567281729 0 3797
13 TraesCS6B01G464600 chr5B 98.489 397 5 1 1 396 567279249 567279645 0 699
14 TraesCS6B01G464600 chr4B 98.200 2167 32 4 578 2744 495567533 495569692 0 3779
15 TraesCS6B01G464600 chr2B 98.109 2168 38 3 578 2744 391225676 391223511 0 3773
16 TraesCS6B01G464600 chr2B 97.600 2167 49 1 578 2744 391144372 391146535 0 3711
17 TraesCS6B01G464600 chr7B 98.485 396 6 0 1 396 54050611 54050216 0 699
18 TraesCS6B01G464600 chr7B 98.237 397 6 1 1 396 54050026 54049630 0 693
19 TraesCS6B01G464600 chr7D 97.980 396 8 0 1 396 382089054 382089449 0 688


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 TraesCS6B01G464600 chr6B 715989339 715992082 2743 True 2367.0 4002 100.0000 1 2744 2 chr6B.!!$R2 2743
1 TraesCS6B01G464600 chr6B 596600126 596602604 2478 True 2294.0 3884 98.8860 1 2744 2 chr6B.!!$R1 2743
2 TraesCS6B01G464600 chr7A 638505933 638508411 2478 True 2283.0 3873 98.5880 1 2744 2 chr7A.!!$R1 2743
3 TraesCS6B01G464600 chr7A 708244881 708247356 2475 False 2274.0 3855 98.5185 1 2744 2 chr7A.!!$F1 2743
4 TraesCS6B01G464600 chrUn 171007540 171010017 2477 False 2277.5 3862 98.5420 1 2744 2 chrUn.!!$F2 2743
5 TraesCS6B01G464600 chr1B 672540790 672542955 2165 False 3818.0 3818 98.4780 578 2744 1 chr1B.!!$F1 2166
6 TraesCS6B01G464600 chr5B 567279249 567281729 2480 False 2248.0 3797 98.3910 1 2744 2 chr5B.!!$F1 2743
7 TraesCS6B01G464600 chr4B 495567533 495569692 2159 False 3779.0 3779 98.2000 578 2744 1 chr4B.!!$F1 2166
8 TraesCS6B01G464600 chr2B 391223511 391225676 2165 True 3773.0 3773 98.1090 578 2744 1 chr2B.!!$R1 2166
9 TraesCS6B01G464600 chr2B 391144372 391146535 2163 False 3711.0 3711 97.6000 578 2744 1 chr2B.!!$F1 2166
10 TraesCS6B01G464600 chr7B 54049630 54050611 981 True 696.0 699 98.3610 1 396 2 chr7B.!!$R1 395

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
320 322 0.108377 TCGGAGCTGCTATTGCGAAA 60.108 50.000 0.15 0.0 43.34 3.46 F
390 392 0.177141 TTCATAGAAAGGCGACCGGG 59.823 55.000 6.32 0.0 0.00 5.73 F
391 393 1.887707 CATAGAAAGGCGACCGGGC 60.888 63.158 6.32 0.0 42.69 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1237 1246 3.055675 ACCACGAATAGGAATGAAACGGA 60.056 43.478 0.0 0.0 0.00 4.69 R
1594 1603 4.330944 AGGCATTTCGTCGGAATACATA 57.669 40.909 0.0 0.0 30.88 2.29 R
2327 2378 5.698545 GGGCAAGTGAGTTCTACATGATATC 59.301 44.000 0.0 0.0 0.00 1.63 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
112 114 1.006832 GACACACTTGCGCGGATTAT 58.993 50.000 8.83 0.00 0.00 1.28
182 184 2.039418 TCAGGGATGAATGTAGACCCG 58.961 52.381 0.00 0.00 44.57 5.28
314 316 3.677002 GCTTCTCGGAGCTGCTATT 57.323 52.632 0.15 0.00 39.57 1.73
315 317 1.216122 GCTTCTCGGAGCTGCTATTG 58.784 55.000 0.15 0.00 39.57 1.90
316 318 1.216122 CTTCTCGGAGCTGCTATTGC 58.784 55.000 0.15 0.00 40.20 3.56
317 319 0.528466 TTCTCGGAGCTGCTATTGCG 60.528 55.000 0.15 0.00 43.34 4.85
318 320 1.066422 CTCGGAGCTGCTATTGCGA 59.934 57.895 0.15 2.66 43.34 5.10
319 321 0.528466 CTCGGAGCTGCTATTGCGAA 60.528 55.000 0.15 0.00 43.34 4.70
320 322 0.108377 TCGGAGCTGCTATTGCGAAA 60.108 50.000 0.15 0.00 43.34 3.46
321 323 0.940126 CGGAGCTGCTATTGCGAAAT 59.060 50.000 0.15 0.00 43.34 2.17
322 324 2.135139 CGGAGCTGCTATTGCGAAATA 58.865 47.619 0.15 0.00 43.34 1.40
323 325 2.096713 CGGAGCTGCTATTGCGAAATAC 60.097 50.000 0.15 0.00 43.34 1.89
324 326 2.096713 GGAGCTGCTATTGCGAAATACG 60.097 50.000 0.15 0.00 43.34 3.06
325 327 1.867233 AGCTGCTATTGCGAAATACGG 59.133 47.619 0.00 0.00 43.34 4.02
326 328 1.660333 GCTGCTATTGCGAAATACGGC 60.660 52.381 11.41 11.41 43.34 5.68
327 329 1.867233 CTGCTATTGCGAAATACGGCT 59.133 47.619 8.41 0.00 43.34 5.52
328 330 2.285083 TGCTATTGCGAAATACGGCTT 58.715 42.857 8.41 0.00 43.34 4.35
329 331 2.286833 TGCTATTGCGAAATACGGCTTC 59.713 45.455 8.41 0.00 43.34 3.86
330 332 2.349532 GCTATTGCGAAATACGGCTTCC 60.350 50.000 0.00 0.00 42.83 3.46
331 333 2.038387 ATTGCGAAATACGGCTTCCT 57.962 45.000 0.00 0.00 42.83 3.36
332 334 1.816074 TTGCGAAATACGGCTTCCTT 58.184 45.000 0.00 0.00 42.83 3.36
333 335 2.676632 TGCGAAATACGGCTTCCTTA 57.323 45.000 0.00 0.00 42.83 2.69
334 336 2.975266 TGCGAAATACGGCTTCCTTAA 58.025 42.857 0.00 0.00 42.83 1.85
335 337 3.537580 TGCGAAATACGGCTTCCTTAAT 58.462 40.909 0.00 0.00 42.83 1.40
336 338 4.695396 TGCGAAATACGGCTTCCTTAATA 58.305 39.130 0.00 0.00 42.83 0.98
337 339 5.302360 TGCGAAATACGGCTTCCTTAATAT 58.698 37.500 0.00 0.00 42.83 1.28
338 340 5.407387 TGCGAAATACGGCTTCCTTAATATC 59.593 40.000 0.00 0.00 42.83 1.63
339 341 5.163884 GCGAAATACGGCTTCCTTAATATCC 60.164 44.000 0.00 0.00 42.83 2.59
340 342 5.929992 CGAAATACGGCTTCCTTAATATCCA 59.070 40.000 0.00 0.00 38.46 3.41
341 343 6.425721 CGAAATACGGCTTCCTTAATATCCAA 59.574 38.462 0.00 0.00 38.46 3.53
342 344 7.041644 CGAAATACGGCTTCCTTAATATCCAAA 60.042 37.037 0.00 0.00 38.46 3.28
343 345 8.706322 AAATACGGCTTCCTTAATATCCAAAT 57.294 30.769 0.00 0.00 0.00 2.32
344 346 8.706322 AATACGGCTTCCTTAATATCCAAATT 57.294 30.769 0.00 0.00 0.00 1.82
345 347 8.706322 ATACGGCTTCCTTAATATCCAAATTT 57.294 30.769 0.00 0.00 0.00 1.82
346 348 7.039313 ACGGCTTCCTTAATATCCAAATTTC 57.961 36.000 0.00 0.00 0.00 2.17
347 349 6.605594 ACGGCTTCCTTAATATCCAAATTTCA 59.394 34.615 0.00 0.00 0.00 2.69
348 350 7.123547 ACGGCTTCCTTAATATCCAAATTTCAA 59.876 33.333 0.00 0.00 0.00 2.69
349 351 7.435192 CGGCTTCCTTAATATCCAAATTTCAAC 59.565 37.037 0.00 0.00 0.00 3.18
350 352 8.257306 GGCTTCCTTAATATCCAAATTTCAACA 58.743 33.333 0.00 0.00 0.00 3.33
351 353 9.651913 GCTTCCTTAATATCCAAATTTCAACAA 57.348 29.630 0.00 0.00 0.00 2.83
354 356 8.757877 TCCTTAATATCCAAATTTCAACAAGGG 58.242 33.333 0.00 0.00 0.00 3.95
355 357 7.986889 CCTTAATATCCAAATTTCAACAAGGGG 59.013 37.037 0.00 0.00 0.00 4.79
356 358 5.955961 ATATCCAAATTTCAACAAGGGGG 57.044 39.130 0.00 0.00 0.00 5.40
357 359 3.053359 TCCAAATTTCAACAAGGGGGT 57.947 42.857 0.00 0.00 0.00 4.95
358 360 3.388913 TCCAAATTTCAACAAGGGGGTT 58.611 40.909 0.00 0.00 0.00 4.11
360 362 3.475575 CAAATTTCAACAAGGGGGTTGG 58.524 45.455 6.24 0.00 46.29 3.77
361 363 1.728323 ATTTCAACAAGGGGGTTGGG 58.272 50.000 6.24 0.00 46.29 4.12
362 364 1.051556 TTTCAACAAGGGGGTTGGGC 61.052 55.000 6.24 0.00 46.29 5.36
363 365 1.955458 TTCAACAAGGGGGTTGGGCT 61.955 55.000 6.24 0.00 46.29 5.19
364 366 2.201210 AACAAGGGGGTTGGGCTG 59.799 61.111 0.00 0.00 40.90 4.85
365 367 4.621087 ACAAGGGGGTTGGGCTGC 62.621 66.667 0.00 0.00 40.90 5.25
366 368 4.305956 CAAGGGGGTTGGGCTGCT 62.306 66.667 0.00 0.00 31.82 4.24
367 369 3.984732 AAGGGGGTTGGGCTGCTC 61.985 66.667 0.00 0.00 0.00 4.26
379 381 3.369381 GCTGCTCGCCTTCATAGAA 57.631 52.632 0.00 0.00 0.00 2.10
380 382 1.656652 GCTGCTCGCCTTCATAGAAA 58.343 50.000 0.00 0.00 0.00 2.52
381 383 1.596727 GCTGCTCGCCTTCATAGAAAG 59.403 52.381 0.00 0.00 0.00 2.62
388 390 1.571919 CCTTCATAGAAAGGCGACCG 58.428 55.000 0.00 0.00 39.47 4.79
389 391 1.571919 CTTCATAGAAAGGCGACCGG 58.428 55.000 0.00 0.00 0.00 5.28
390 392 0.177141 TTCATAGAAAGGCGACCGGG 59.823 55.000 6.32 0.00 0.00 5.73
391 393 1.887707 CATAGAAAGGCGACCGGGC 60.888 63.158 6.32 0.00 42.69 6.13
1046 1054 2.716424 AGTTCCATTTCAAGGGAGGACA 59.284 45.455 0.00 0.00 40.36 4.02
1109 1117 4.385825 GTCTCTGGTTTGATGGTTGTACA 58.614 43.478 0.00 0.00 0.00 2.90
1237 1246 7.181125 CCCCAGTAGTTCATATAGGAGCTATTT 59.819 40.741 13.06 4.04 33.94 1.40
1594 1603 5.104485 AGGACTACAAAGGTGAAAAGACAGT 60.104 40.000 0.00 0.00 0.00 3.55
2004 2053 5.535333 TGGTAGGTTTCTCGAAGTAGTTTG 58.465 41.667 0.00 0.00 0.00 2.93
2107 2156 1.394917 GCTTCCTTCACAGTGCATACG 59.605 52.381 0.00 0.00 0.00 3.06
2327 2378 2.544267 GGAAGGCTCGTTTCATTATCGG 59.456 50.000 0.00 0.00 0.00 4.18
2378 2429 5.279506 CCTTTTGCTAGGAGAGTGTAGTTCA 60.280 44.000 0.00 0.00 37.50 3.18
2638 2689 7.216494 TCGCCATCTTGTATTCATGATCTTAA 58.784 34.615 0.00 0.00 36.67 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 114 3.618019 GCCATTCTTGTAACCGTCACCTA 60.618 47.826 0.00 0.0 0.00 3.08
182 184 0.036306 AATGATTATCCCCGCCCGAC 59.964 55.000 0.00 0.0 0.00 4.79
312 314 2.038387 AGGAAGCCGTATTTCGCAAT 57.962 45.000 0.00 0.0 38.35 3.56
313 315 1.816074 AAGGAAGCCGTATTTCGCAA 58.184 45.000 0.00 0.0 38.35 4.85
314 316 2.676632 TAAGGAAGCCGTATTTCGCA 57.323 45.000 0.00 0.0 38.35 5.10
315 317 5.163884 GGATATTAAGGAAGCCGTATTTCGC 60.164 44.000 0.00 0.0 38.35 4.70
316 318 5.929992 TGGATATTAAGGAAGCCGTATTTCG 59.070 40.000 0.00 0.0 39.52 3.46
317 319 7.739498 TTGGATATTAAGGAAGCCGTATTTC 57.261 36.000 0.00 0.0 0.00 2.17
318 320 8.706322 ATTTGGATATTAAGGAAGCCGTATTT 57.294 30.769 0.00 0.0 0.00 1.40
319 321 8.706322 AATTTGGATATTAAGGAAGCCGTATT 57.294 30.769 0.00 0.0 0.00 1.89
320 322 8.706322 AAATTTGGATATTAAGGAAGCCGTAT 57.294 30.769 0.00 0.0 0.00 3.06
321 323 7.776030 TGAAATTTGGATATTAAGGAAGCCGTA 59.224 33.333 0.00 0.0 0.00 4.02
322 324 6.605594 TGAAATTTGGATATTAAGGAAGCCGT 59.394 34.615 0.00 0.0 0.00 5.68
323 325 7.038154 TGAAATTTGGATATTAAGGAAGCCG 57.962 36.000 0.00 0.0 0.00 5.52
324 326 8.257306 TGTTGAAATTTGGATATTAAGGAAGCC 58.743 33.333 0.00 0.0 0.00 4.35
325 327 9.651913 TTGTTGAAATTTGGATATTAAGGAAGC 57.348 29.630 0.00 0.0 0.00 3.86
328 330 8.757877 CCCTTGTTGAAATTTGGATATTAAGGA 58.242 33.333 0.00 0.0 33.42 3.36
329 331 7.986889 CCCCTTGTTGAAATTTGGATATTAAGG 59.013 37.037 0.00 0.0 0.00 2.69
330 332 7.986889 CCCCCTTGTTGAAATTTGGATATTAAG 59.013 37.037 0.00 0.0 0.00 1.85
331 333 7.459444 ACCCCCTTGTTGAAATTTGGATATTAA 59.541 33.333 0.00 0.0 0.00 1.40
332 334 6.962902 ACCCCCTTGTTGAAATTTGGATATTA 59.037 34.615 0.00 0.0 0.00 0.98
333 335 5.790096 ACCCCCTTGTTGAAATTTGGATATT 59.210 36.000 0.00 0.0 0.00 1.28
334 336 5.349690 ACCCCCTTGTTGAAATTTGGATAT 58.650 37.500 0.00 0.0 0.00 1.63
335 337 4.757692 ACCCCCTTGTTGAAATTTGGATA 58.242 39.130 0.00 0.0 0.00 2.59
336 338 3.597182 ACCCCCTTGTTGAAATTTGGAT 58.403 40.909 0.00 0.0 0.00 3.41
337 339 3.053359 ACCCCCTTGTTGAAATTTGGA 57.947 42.857 0.00 0.0 0.00 3.53
338 340 3.475575 CAACCCCCTTGTTGAAATTTGG 58.524 45.455 0.00 0.0 46.77 3.28
339 341 3.475575 CCAACCCCCTTGTTGAAATTTG 58.524 45.455 0.00 0.0 46.77 2.32
340 342 2.441375 CCCAACCCCCTTGTTGAAATTT 59.559 45.455 5.53 0.0 46.77 1.82
341 343 2.054021 CCCAACCCCCTTGTTGAAATT 58.946 47.619 5.53 0.0 46.77 1.82
342 344 1.728323 CCCAACCCCCTTGTTGAAAT 58.272 50.000 5.53 0.0 46.77 2.17
343 345 1.051556 GCCCAACCCCCTTGTTGAAA 61.052 55.000 5.53 0.0 46.77 2.69
344 346 1.458588 GCCCAACCCCCTTGTTGAA 60.459 57.895 5.53 0.0 46.77 2.69
345 347 2.200092 GCCCAACCCCCTTGTTGA 59.800 61.111 5.53 0.0 46.77 3.18
346 348 2.201210 AGCCCAACCCCCTTGTTG 59.799 61.111 0.00 0.0 44.12 3.33
347 349 2.201210 CAGCCCAACCCCCTTGTT 59.799 61.111 0.00 0.0 0.00 2.83
348 350 4.621087 GCAGCCCAACCCCCTTGT 62.621 66.667 0.00 0.0 0.00 3.16
349 351 4.305956 AGCAGCCCAACCCCCTTG 62.306 66.667 0.00 0.0 0.00 3.61
350 352 3.984732 GAGCAGCCCAACCCCCTT 61.985 66.667 0.00 0.0 0.00 3.95
362 364 2.208431 CCTTTCTATGAAGGCGAGCAG 58.792 52.381 0.00 0.0 39.75 4.24
363 365 2.315925 CCTTTCTATGAAGGCGAGCA 57.684 50.000 0.00 0.0 39.75 4.26
370 372 1.571919 CCGGTCGCCTTTCTATGAAG 58.428 55.000 0.00 0.0 0.00 3.02
371 373 0.177141 CCCGGTCGCCTTTCTATGAA 59.823 55.000 0.00 0.0 0.00 2.57
372 374 1.820581 CCCGGTCGCCTTTCTATGA 59.179 57.895 0.00 0.0 0.00 2.15
373 375 1.887707 GCCCGGTCGCCTTTCTATG 60.888 63.158 0.00 0.0 0.00 2.23
374 376 2.504519 GCCCGGTCGCCTTTCTAT 59.495 61.111 0.00 0.0 0.00 1.98
375 377 3.777910 GGCCCGGTCGCCTTTCTA 61.778 66.667 13.98 0.0 46.10 2.10
1046 1054 7.227910 ACAAAACAGAAAGTATCATGGTACGTT 59.772 33.333 15.90 15.9 0.00 3.99
1109 1117 5.767816 GGAATGTACCGGATTTTTAGCAT 57.232 39.130 9.46 0.0 0.00 3.79
1237 1246 3.055675 ACCACGAATAGGAATGAAACGGA 60.056 43.478 0.00 0.0 0.00 4.69
1594 1603 4.330944 AGGCATTTCGTCGGAATACATA 57.669 40.909 0.00 0.0 30.88 2.29
2004 2053 7.648039 TCTCTATTTCCTGAGAAACCTACTC 57.352 40.000 0.00 0.0 44.57 2.59
2107 2156 7.912773 CCAGAAAAACTCAAAAGAGAAAGAGAC 59.087 37.037 0.00 0.0 32.59 3.36
2327 2378 5.698545 GGGCAAGTGAGTTCTACATGATATC 59.301 44.000 0.00 0.0 0.00 1.63
2397 2448 1.286501 GCTTTGCGTATCACGGATCA 58.713 50.000 0.44 0.0 42.59 2.92
2638 2689 5.297776 GCTATGCATTTGTGACCAATAGAGT 59.702 40.000 3.54 0.0 0.00 3.24


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

AutoCloner maintained by Alex Coulton.