Multiple sequence alignment - TraesCS3D01G512800

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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 TraesCS3D01G512800 chr3D 100.000 2522 0 0 1 2522 597209198 597206677 0.000000e+00 4658
1 TraesCS3D01G512800 chr1D 95.417 2553 84 3 1 2522 490894229 490891679 0.000000e+00 4036
2 TraesCS3D01G512800 chr2B 93.610 2582 103 25 1 2522 47381887 47384466 0.000000e+00 3797
3 TraesCS3D01G512800 chr2B 95.573 1988 87 1 1 1988 155036736 155038722 0.000000e+00 3182
4 TraesCS3D01G512800 chr7D 94.334 2418 97 21 1 2388 16793650 16796057 0.000000e+00 3670
5 TraesCS3D01G512800 chr7D 88.281 256 9 2 2277 2512 21070776 21071030 1.140000e-73 287
6 TraesCS3D01G512800 chr3A 92.512 2564 128 20 1 2512 145552776 145555327 0.000000e+00 3613
7 TraesCS3D01G512800 chr3A 91.482 2524 146 30 4 2470 635318238 635315727 0.000000e+00 3406
8 TraesCS3D01G512800 chr4A 92.292 2504 147 25 1 2470 637829730 637832221 0.000000e+00 3513
9 TraesCS3D01G512800 chr7A 92.329 2490 144 17 1 2470 16873120 16875582 0.000000e+00 3496
10 TraesCS3D01G512800 chr7A 92.403 2422 137 28 1 2388 509520829 509518421 0.000000e+00 3410
11 TraesCS3D01G512800 chr7A 90.372 2524 144 32 1 2470 134602280 134599802 0.000000e+00 3223
12 TraesCS3D01G512800 chr5B 94.279 2290 116 7 1 2278 641177043 641179329 0.000000e+00 3489
13 TraesCS3D01G512800 chr5B 95.423 1988 88 2 1 1988 530934843 530936827 0.000000e+00 3164
14 TraesCS3D01G512800 chr1A 91.703 2531 148 15 3 2481 559595631 559593111 0.000000e+00 3454
15 TraesCS3D01G512800 chr6A 92.261 2455 147 12 48 2470 516292050 516294493 0.000000e+00 3441
16 TraesCS3D01G512800 chr6A 92.197 2422 143 26 1 2388 74985955 74988364 0.000000e+00 3384
17 TraesCS3D01G512800 chr5A 91.165 2524 157 28 1 2470 606694704 606692193 0.000000e+00 3365
18 TraesCS3D01G512800 chr6D 92.066 2357 162 11 1 2341 293056426 293058773 0.000000e+00 3293
19 TraesCS3D01G512800 chr7B 96.278 1988 73 1 1 1988 27332644 27330658 0.000000e+00 3260
20 TraesCS3D01G512800 chr7B 90.391 2352 200 11 3 2338 315275927 315278268 0.000000e+00 3068
21 TraesCS3D01G512800 chr7B 95.922 564 22 1 1959 2522 34254503 34255065 0.000000e+00 913
22 TraesCS3D01G512800 chr6B 95.687 1971 83 2 4 1974 425601957 425599989 0.000000e+00 3168
23 TraesCS3D01G512800 chr3B 95.272 1988 87 2 1 1988 16193179 16195159 0.000000e+00 3144


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 TraesCS3D01G512800 chr3D 597206677 597209198 2521 True 4658 4658 100.000 1 2522 1 chr3D.!!$R1 2521
1 TraesCS3D01G512800 chr1D 490891679 490894229 2550 True 4036 4036 95.417 1 2522 1 chr1D.!!$R1 2521
2 TraesCS3D01G512800 chr2B 47381887 47384466 2579 False 3797 3797 93.610 1 2522 1 chr2B.!!$F1 2521
3 TraesCS3D01G512800 chr2B 155036736 155038722 1986 False 3182 3182 95.573 1 1988 1 chr2B.!!$F2 1987
4 TraesCS3D01G512800 chr7D 16793650 16796057 2407 False 3670 3670 94.334 1 2388 1 chr7D.!!$F1 2387
5 TraesCS3D01G512800 chr3A 145552776 145555327 2551 False 3613 3613 92.512 1 2512 1 chr3A.!!$F1 2511
6 TraesCS3D01G512800 chr3A 635315727 635318238 2511 True 3406 3406 91.482 4 2470 1 chr3A.!!$R1 2466
7 TraesCS3D01G512800 chr4A 637829730 637832221 2491 False 3513 3513 92.292 1 2470 1 chr4A.!!$F1 2469
8 TraesCS3D01G512800 chr7A 16873120 16875582 2462 False 3496 3496 92.329 1 2470 1 chr7A.!!$F1 2469
9 TraesCS3D01G512800 chr7A 509518421 509520829 2408 True 3410 3410 92.403 1 2388 1 chr7A.!!$R2 2387
10 TraesCS3D01G512800 chr7A 134599802 134602280 2478 True 3223 3223 90.372 1 2470 1 chr7A.!!$R1 2469
11 TraesCS3D01G512800 chr5B 641177043 641179329 2286 False 3489 3489 94.279 1 2278 1 chr5B.!!$F2 2277
12 TraesCS3D01G512800 chr5B 530934843 530936827 1984 False 3164 3164 95.423 1 1988 1 chr5B.!!$F1 1987
13 TraesCS3D01G512800 chr1A 559593111 559595631 2520 True 3454 3454 91.703 3 2481 1 chr1A.!!$R1 2478
14 TraesCS3D01G512800 chr6A 516292050 516294493 2443 False 3441 3441 92.261 48 2470 1 chr6A.!!$F2 2422
15 TraesCS3D01G512800 chr6A 74985955 74988364 2409 False 3384 3384 92.197 1 2388 1 chr6A.!!$F1 2387
16 TraesCS3D01G512800 chr5A 606692193 606694704 2511 True 3365 3365 91.165 1 2470 1 chr5A.!!$R1 2469
17 TraesCS3D01G512800 chr6D 293056426 293058773 2347 False 3293 3293 92.066 1 2341 1 chr6D.!!$F1 2340
18 TraesCS3D01G512800 chr7B 27330658 27332644 1986 True 3260 3260 96.278 1 1988 1 chr7B.!!$R1 1987
19 TraesCS3D01G512800 chr7B 315275927 315278268 2341 False 3068 3068 90.391 3 2338 1 chr7B.!!$F2 2335
20 TraesCS3D01G512800 chr7B 34254503 34255065 562 False 913 913 95.922 1959 2522 1 chr7B.!!$F1 563
21 TraesCS3D01G512800 chr6B 425599989 425601957 1968 True 3168 3168 95.687 4 1974 1 chr6B.!!$R1 1970
22 TraesCS3D01G512800 chr3B 16193179 16195159 1980 False 3144 3144 95.272 1 1988 1 chr3B.!!$F1 1987

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
413 415 0.325933 TGTGGATGTTCCTGGAGCTG 59.674 55.000 11.95 0.0 37.46 4.24 F
1101 1103 1.625818 GAGGAGAGCAAGGAGGAAACA 59.374 52.381 0.00 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1472 1474 0.537188 ATAGTCAACGTGAGCCCCTG 59.463 55.000 0.0 0.0 0.00 4.45 R
2167 2223 1.077501 CCTCCGCATCATTGGTGGT 60.078 57.895 0.0 0.0 37.22 4.16 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 1.535444 TTGGAGGCCGGAGACTCAA 60.535 57.895 5.05 0.00 34.00 3.02
98 99 3.426615 GGAGATGACGATGACCCTAGAT 58.573 50.000 0.00 0.00 0.00 1.98
100 101 3.161067 AGATGACGATGACCCTAGATGG 58.839 50.000 0.00 0.00 0.00 3.51
196 197 6.348458 CGAGAACAGACTGGCATTTTAATTGA 60.348 38.462 7.51 0.00 0.00 2.57
242 243 3.224324 ATGGCCGATACCGCGAGT 61.224 61.111 8.23 6.57 0.00 4.18
292 293 1.003839 GAGACACCAATCCGTGCCA 60.004 57.895 0.00 0.00 37.25 4.92
413 415 0.325933 TGTGGATGTTCCTGGAGCTG 59.674 55.000 11.95 0.00 37.46 4.24
609 611 1.799933 TTGGCTGGGTTTGTTTGGAT 58.200 45.000 0.00 0.00 0.00 3.41
679 681 2.028561 AGAACCCCAACATGCCAAAT 57.971 45.000 0.00 0.00 0.00 2.32
697 699 3.943671 AATCCACGGGGTAATCATGAA 57.056 42.857 2.12 0.00 34.93 2.57
806 808 5.462068 GTGCGATACAAGTGCTATATGAACA 59.538 40.000 0.00 0.00 0.00 3.18
1101 1103 1.625818 GAGGAGAGCAAGGAGGAAACA 59.374 52.381 0.00 0.00 0.00 2.83
1323 1325 2.255406 AGACCTCACAATCAGTCAGCT 58.745 47.619 0.00 0.00 0.00 4.24
1354 1356 2.779755 TCAAGTGTGGTATGCGGATT 57.220 45.000 0.00 0.00 0.00 3.01
1557 1563 9.264719 TCTAACATACTTGCATCATATTGTCTG 57.735 33.333 0.00 0.00 0.00 3.51
1640 1646 0.038343 AACGATGCCAATGTTGCACC 60.038 50.000 0.00 0.00 42.38 5.01
1892 1900 2.858344 CCAGAGTTAATAGACGGCGTTG 59.142 50.000 16.19 3.78 0.00 4.10
2041 2097 2.202388 CACAAGGCAATGCTCGCG 60.202 61.111 4.82 0.00 0.00 5.87
2167 2223 4.578516 CCACGGGAATGCAAATATACAAGA 59.421 41.667 0.00 0.00 0.00 3.02
2232 2312 0.187361 AGGCTAGCGAAGAGGAGGAT 59.813 55.000 9.00 0.00 0.00 3.24
2482 2619 6.947258 TCTGTGAAATGTTCATATATGTGCG 58.053 36.000 12.42 0.00 42.47 5.34
2503 2640 6.036083 GTGCGATATTCTGTGTTGTATGAACT 59.964 38.462 0.00 0.00 0.00 3.01
2517 2654 9.549078 TGTTGTATGAACTTGTTGATACTTGTA 57.451 29.630 18.56 2.33 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.602267 TCTCCGGCCTCCAACGAA 60.602 61.111 0.00 0.00 0.00 3.85
56 57 2.113860 CACATGGAAGGTGGAACGAT 57.886 50.000 0.00 0.00 46.42 3.73
98 99 1.611410 CCGCTTATCATAGCCATGCCA 60.611 52.381 0.00 0.00 37.90 4.92
100 101 0.449388 GCCGCTTATCATAGCCATGC 59.551 55.000 0.00 0.00 37.90 4.06
226 227 4.201679 CACTCGCGGTATCGGCCA 62.202 66.667 6.13 0.00 36.79 5.36
242 243 2.877097 TTAGCCAAGAATGCCTCACA 57.123 45.000 0.00 0.00 0.00 3.58
292 293 0.677731 CACGTCATTGGCACCCTCAT 60.678 55.000 0.00 0.00 0.00 2.90
570 572 4.934001 CCAATGAGGATGTATCTCCATTCG 59.066 45.833 8.30 0.00 41.22 3.34
574 576 3.321039 AGCCAATGAGGATGTATCTCCA 58.679 45.455 0.00 0.00 41.22 3.86
655 657 1.273327 GGCATGTTGGGGTTCTTGAAG 59.727 52.381 0.00 0.00 0.00 3.02
679 681 1.488812 CCTTCATGATTACCCCGTGGA 59.511 52.381 0.00 0.00 34.81 4.02
697 699 1.075050 GGATCATCATCATGCACCCCT 59.925 52.381 0.00 0.00 0.00 4.79
759 761 1.201647 GCGAGCTTCCTGTGTACACTA 59.798 52.381 25.60 11.91 0.00 2.74
903 905 1.550072 GGCAACCAATGTACCTGCAAT 59.450 47.619 0.00 0.00 34.66 3.56
1101 1103 1.339610 GCTCACCGATGCAGAGATAGT 59.660 52.381 4.21 0.00 0.00 2.12
1180 1182 4.150897 ACCTACAAATGATGCACGGTAT 57.849 40.909 0.00 0.00 0.00 2.73
1323 1325 7.710907 GCATACCACACTTGATACTTCTGATAA 59.289 37.037 0.00 0.00 0.00 1.75
1354 1356 3.752747 GGCTTTAGCTTTAACCGGTAACA 59.247 43.478 8.00 0.00 41.70 2.41
1472 1474 0.537188 ATAGTCAACGTGAGCCCCTG 59.463 55.000 0.00 0.00 0.00 4.45
1557 1563 7.651704 ACACACCAAACTTATGTATTTGAAAGC 59.348 33.333 0.00 0.00 37.91 3.51
1640 1646 4.919653 CACCAGGTGGATGACTCG 57.080 61.111 12.40 0.00 38.94 4.18
1877 1885 2.492881 TGGAGACAACGCCGTCTATTAA 59.507 45.455 7.27 0.00 46.26 1.40
1892 1900 3.753294 TGTCCTCTTTGTTCTGGAGAC 57.247 47.619 0.00 0.00 0.00 3.36
2167 2223 1.077501 CCTCCGCATCATTGGTGGT 60.078 57.895 0.00 0.00 37.22 4.16
2232 2312 1.961394 ACGAGAGTTGCAAGTGTAGGA 59.039 47.619 12.53 0.00 46.40 2.94
2482 2619 9.546909 CAACAAGTTCATACAACACAGAATATC 57.453 33.333 0.00 0.00 0.00 1.63


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

AutoCloner maintained by Alex Coulton.