Multiple sequence alignment - TraesCS7B01G467400

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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 TraesCS7B01G467400 chr7B 100.000 3347 0 0 1 3347 724955867 724952521 0.000000e+00 6181.0
1 TraesCS7B01G467400 chr7B 86.406 2479 289 28 1 2467 466668962 466671404 0.000000e+00 2667.0
2 TraesCS7B01G467400 chr7B 86.879 2355 283 14 1 2349 723902882 723900548 0.000000e+00 2614.0
3 TraesCS7B01G467400 chr7B 83.740 2171 312 27 1 2149 723907755 723909906 0.000000e+00 2015.0
4 TraesCS7B01G467400 chr7B 87.707 423 20 15 2945 3336 23678578 23678999 6.540000e-127 464.0
5 TraesCS7B01G467400 chr7D 96.781 3386 65 19 1 3347 625355333 625351953 0.000000e+00 5609.0
6 TraesCS7B01G467400 chr7D 87.097 2356 276 17 1 2349 625250600 625252934 0.000000e+00 2641.0
7 TraesCS7B01G467400 chr7D 85.391 2478 312 28 1 2467 448855489 448857927 0.000000e+00 2525.0
8 TraesCS7B01G467400 chr7D 85.554 2402 303 27 1 2388 625227632 625225261 0.000000e+00 2473.0
9 TraesCS7B01G467400 chr7A 87.012 2356 273 20 1 2349 720864278 720861949 0.000000e+00 2625.0
10 TraesCS7B01G467400 chr7A 84.094 2477 345 27 4 2467 547114064 547111624 0.000000e+00 2346.0
11 TraesCS7B01G467400 chr1B 86.752 2355 272 20 1 2340 623547595 623549924 0.000000e+00 2584.0
12 TraesCS7B01G467400 chr1B 93.878 98 5 1 3240 3336 33322878 33322781 2.690000e-31 147.0
13 TraesCS7B01G467400 chr1D 86.480 2352 284 14 1 2340 453113412 453115741 0.000000e+00 2551.0
14 TraesCS7B01G467400 chr1D 83.253 830 103 21 1441 2260 452681527 452680724 0.000000e+00 730.0
15 TraesCS7B01G467400 chr1D 81.667 120 13 5 2257 2376 452675659 452675549 1.280000e-14 91.6
16 TraesCS7B01G467400 chr6A 84.615 2392 323 29 1 2377 608493722 608491361 0.000000e+00 2337.0
17 TraesCS7B01G467400 chr2B 87.707 423 20 11 2945 3336 642414460 642414881 6.540000e-127 464.0
18 TraesCS7B01G467400 chrUn 87.470 423 21 15 2945 3336 200831425 200831846 3.040000e-125 459.0
19 TraesCS7B01G467400 chr5B 86.998 423 23 15 2945 3336 594290790 594291211 6.590000e-122 448.0
20 TraesCS7B01G467400 chr3B 86.480 429 20 16 2945 3336 34313358 34312931 1.430000e-118 436.0
21 TraesCS7B01G467400 chr3B 86.525 423 25 15 2945 3336 34317914 34318335 1.430000e-118 436.0
22 TraesCS7B01G467400 chr6B 87.246 345 13 14 3023 3336 31387746 31387402 6.820000e-97 364.0
23 TraesCS7B01G467400 chr1A 86.503 163 15 4 2219 2379 547567654 547567497 4.440000e-39 172.0


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 TraesCS7B01G467400 chr7B 724952521 724955867 3346 True 6181 6181 100.000 1 3347 1 chr7B.!!$R2 3346
1 TraesCS7B01G467400 chr7B 466668962 466671404 2442 False 2667 2667 86.406 1 2467 1 chr7B.!!$F2 2466
2 TraesCS7B01G467400 chr7B 723900548 723902882 2334 True 2614 2614 86.879 1 2349 1 chr7B.!!$R1 2348
3 TraesCS7B01G467400 chr7B 723907755 723909906 2151 False 2015 2015 83.740 1 2149 1 chr7B.!!$F3 2148
4 TraesCS7B01G467400 chr7D 625351953 625355333 3380 True 5609 5609 96.781 1 3347 1 chr7D.!!$R2 3346
5 TraesCS7B01G467400 chr7D 625250600 625252934 2334 False 2641 2641 87.097 1 2349 1 chr7D.!!$F2 2348
6 TraesCS7B01G467400 chr7D 448855489 448857927 2438 False 2525 2525 85.391 1 2467 1 chr7D.!!$F1 2466
7 TraesCS7B01G467400 chr7D 625225261 625227632 2371 True 2473 2473 85.554 1 2388 1 chr7D.!!$R1 2387
8 TraesCS7B01G467400 chr7A 720861949 720864278 2329 True 2625 2625 87.012 1 2349 1 chr7A.!!$R2 2348
9 TraesCS7B01G467400 chr7A 547111624 547114064 2440 True 2346 2346 84.094 4 2467 1 chr7A.!!$R1 2463
10 TraesCS7B01G467400 chr1B 623547595 623549924 2329 False 2584 2584 86.752 1 2340 1 chr1B.!!$F1 2339
11 TraesCS7B01G467400 chr1D 453113412 453115741 2329 False 2551 2551 86.480 1 2340 1 chr1D.!!$F1 2339
12 TraesCS7B01G467400 chr1D 452680724 452681527 803 True 730 730 83.253 1441 2260 1 chr1D.!!$R2 819
13 TraesCS7B01G467400 chr6A 608491361 608493722 2361 True 2337 2337 84.615 1 2377 1 chr6A.!!$R1 2376

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
982 1012 7.182817 AGGTAATGATCAAAGTAGCAGTACA 57.817 36.0 0.0 0.0 34.56 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2507 2566 0.526211 TCGATCAGACACTTGGACGG 59.474 55.0 0.0 0.0 0.0 4.79 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
982 1012 7.182817 AGGTAATGATCAAAGTAGCAGTACA 57.817 36.000 0.00 0.00 34.56 2.90
1005 1035 5.823209 TCAGTTTCATTCCATACATGCAG 57.177 39.130 0.00 0.00 0.00 4.41
1054 1084 3.119708 GCAAAGGTTTCTCATACTGGCAG 60.120 47.826 14.16 14.16 0.00 4.85
1373 1413 1.761449 TGCTGGTTTGTGCTGAGAAA 58.239 45.000 0.00 0.00 0.00 2.52
2393 2445 6.751514 CAGTATGCATACTACCAACCAAAA 57.248 37.500 33.27 0.00 41.44 2.44
2454 2513 7.704047 GCTTATTCTTGGATCCAAAACAAGATC 59.296 37.037 26.97 15.80 46.82 2.75
2482 2541 5.868257 TGATGTGTTAGAAATAAAGCGCAG 58.132 37.500 11.47 0.00 0.00 5.18
2483 2542 4.678509 TGTGTTAGAAATAAAGCGCAGG 57.321 40.909 11.47 0.00 0.00 4.85
2507 2566 6.457528 GGTCACTTTGCATAAGTAGATTCTGC 60.458 42.308 12.06 0.00 40.47 4.26
2598 2657 2.213499 GAGTTGGTGTCCTGTTGAGTG 58.787 52.381 0.00 0.00 0.00 3.51
2659 2725 4.712337 AGCACTAGCCTTGTAACTGATACT 59.288 41.667 0.00 0.00 43.56 2.12
2720 2786 1.900237 GCTAGCTGCACCAAAAATCG 58.100 50.000 7.70 0.00 42.31 3.34
2764 2830 3.242549 TCTGTGCATGTCTAGCTTCTG 57.757 47.619 0.00 0.00 0.00 3.02
2842 2908 2.481952 AGCTTCATGCACGAAAGACTTC 59.518 45.455 0.00 0.00 45.94 3.01
2855 2921 3.840890 AAGACTTCTCAGCTAGTCACG 57.159 47.619 15.10 0.00 42.51 4.35
2889 2955 5.221621 TGGTGTATCAGTGACTTGATCAACA 60.222 40.000 3.38 0.00 39.72 3.33
2905 2971 0.037590 AACACCAAGCGGGCTCAATA 59.962 50.000 0.00 0.00 42.05 1.90
2915 2981 2.544267 GCGGGCTCAATACTAACATGAC 59.456 50.000 0.00 0.00 0.00 3.06
2938 3004 4.213270 CGTGTGTCCATGTAAATCAACTGT 59.787 41.667 0.00 0.00 0.00 3.55
3009 3075 3.429207 GTCTCCTCTAACGTTTGTGCTTC 59.571 47.826 5.91 0.00 0.00 3.86
3010 3076 2.737252 CTCCTCTAACGTTTGTGCTTCC 59.263 50.000 5.91 0.00 0.00 3.46
3013 3079 3.502211 CCTCTAACGTTTGTGCTTCCATT 59.498 43.478 5.91 0.00 0.00 3.16
3014 3080 4.466828 CTCTAACGTTTGTGCTTCCATTG 58.533 43.478 5.91 0.00 0.00 2.82
3058 3124 3.339093 GGGACCCTGGACCCTTGG 61.339 72.222 15.43 0.00 44.68 3.61
3200 3270 0.108615 CGTCTACTCCTGTTGGCCAG 60.109 60.000 5.11 0.00 41.15 4.85
3211 3281 3.555324 TGGCCAGCACGAGGTCAA 61.555 61.111 0.00 0.00 37.92 3.18
3212 3282 2.743928 GGCCAGCACGAGGTCAAG 60.744 66.667 0.00 0.00 0.00 3.02
3233 3303 2.825387 GGTGGCGCTCATGCATCA 60.825 61.111 7.64 0.00 39.64 3.07
3234 3304 2.191513 GGTGGCGCTCATGCATCAT 61.192 57.895 7.64 0.00 39.64 2.45
3235 3305 1.281960 GTGGCGCTCATGCATCATC 59.718 57.895 7.64 0.00 39.64 2.92
3238 3308 1.441732 GGCGCTCATGCATCATCACA 61.442 55.000 7.64 0.00 39.64 3.58
3288 3384 3.715097 GGACCCTGCTGCTGCTCT 61.715 66.667 17.00 0.00 40.48 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
278 279 4.338118 ACTTGTTCGGCTTTTGATGAAGAA 59.662 37.500 0.00 0.00 0.00 2.52
982 1012 5.301045 CCTGCATGTATGGAATGAAACTGAT 59.699 40.000 0.00 0.00 0.00 2.90
1005 1035 4.156556 TGCAGTTGTTCAAGCATATCTTCC 59.843 41.667 0.00 0.00 31.27 3.46
1054 1084 1.559682 TGGATAGCACTTCCACTTCCC 59.440 52.381 0.00 0.00 38.35 3.97
1373 1413 0.771127 TGTTAACTGCTTGCCCTCCT 59.229 50.000 7.22 0.00 0.00 3.69
2454 2513 8.006590 GCGCTTTATTTCTAACACATCATAGAG 58.993 37.037 0.00 0.00 30.33 2.43
2478 2537 1.806542 ACTTATGCAAAGTGACCTGCG 59.193 47.619 11.78 0.00 41.63 5.18
2482 2541 7.009568 CAGAATCTACTTATGCAAAGTGACC 57.990 40.000 18.57 11.66 0.00 4.02
2507 2566 0.526211 TCGATCAGACACTTGGACGG 59.474 55.000 0.00 0.00 0.00 4.79
2544 2603 5.923684 TCTGGACGAAATGCCAAAATAAAAC 59.076 36.000 0.00 0.00 32.95 2.43
2598 2657 3.185246 ACACATCTATACAGCAGCACC 57.815 47.619 0.00 0.00 0.00 5.01
2720 2786 5.886960 ACTGGCTAACAAACAGATTGATC 57.113 39.130 0.00 0.00 41.85 2.92
2842 2908 1.515088 CCGCACGTGACTAGCTGAG 60.515 63.158 22.23 0.00 0.00 3.35
2855 2921 1.521681 GATACACCAGAGCCCGCAC 60.522 63.158 0.00 0.00 0.00 5.34
2889 2955 1.200519 TAGTATTGAGCCCGCTTGGT 58.799 50.000 0.00 0.00 36.04 3.67
2905 2971 3.244078 ACATGGACACACGTCATGTTAGT 60.244 43.478 12.57 3.67 44.54 2.24
2915 2981 4.213270 ACAGTTGATTTACATGGACACACG 59.787 41.667 0.00 0.00 0.00 4.49
2978 3044 2.561419 CGTTAGAGGAGACTTTGTCCCA 59.439 50.000 0.00 0.00 44.43 4.37
3041 3107 3.339093 CCAAGGGTCCAGGGTCCC 61.339 72.222 12.16 12.16 42.55 4.46
3058 3124 1.005450 TCCCCCTTCTATTTGTGGCAC 59.995 52.381 11.55 11.55 0.00 5.01
3091 3157 7.387265 ACCCATGTATGTATCTGTATTCCAA 57.613 36.000 0.00 0.00 0.00 3.53
3200 3270 2.743928 CCAGCCTTGACCTCGTGC 60.744 66.667 0.00 0.00 0.00 5.34
3211 3281 4.790962 CATGAGCGCCACCAGCCT 62.791 66.667 2.29 0.00 38.78 4.58
3233 3303 4.827087 CCTCGCGGCAGCTGTGAT 62.827 66.667 17.96 0.00 42.32 3.06
3288 3384 1.000060 GGTGTAGCCGCGGTGATATAA 60.000 52.381 28.70 7.58 0.00 0.98


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

AutoCloner maintained by Alex Coulton.