Multiple sequence alignment - TraesCS7B01G115800

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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 TraesCS7B01G115800 chr7B 100.000 4073 0 0 1 4073 134329174 134325102 0 7522
1 TraesCS7B01G115800 chr7B 97.718 4076 89 4 1 4073 678100228 678104302 0 7009
2 TraesCS7B01G115800 chr1B 97.841 4076 85 3 1 4073 618191519 618187444 0 7036
3 TraesCS7B01G115800 chr1B 97.770 4080 83 6 1 4073 615476444 615480522 0 7023
4 TraesCS7B01G115800 chr1B 97.211 3657 93 5 419 4073 122762247 122765896 0 6180
5 TraesCS7B01G115800 chr2B 95.315 4098 165 16 1 4073 631383056 631378961 0 6479
6 TraesCS7B01G115800 chr3B 94.641 4105 173 25 1 4073 542642261 542638172 0 6318
7 TraesCS7B01G115800 chr3B 93.649 4094 188 35 1 4073 28344445 28348487 0 6054
8 TraesCS7B01G115800 chr3B 95.013 3369 144 13 728 4073 737835837 737832470 0 5269
9 TraesCS7B01G115800 chr3B 94.766 3305 150 13 361 3652 81550607 81547313 0 5123
10 TraesCS7B01G115800 chr5B 94.169 3687 161 22 1 3661 351453123 351449465 0 5568
11 TraesCS7B01G115800 chr5B 95.848 3131 106 12 1 3118 109899684 109896565 0 5040
12 TraesCS7B01G115800 chr5B 95.345 623 27 2 3453 4073 351449556 351448934 0 989


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 TraesCS7B01G115800 chr7B 134325102 134329174 4072 True 7522.0 7522 100.000 1 4073 1 chr7B.!!$R1 4072
1 TraesCS7B01G115800 chr7B 678100228 678104302 4074 False 7009.0 7009 97.718 1 4073 1 chr7B.!!$F1 4072
2 TraesCS7B01G115800 chr1B 618187444 618191519 4075 True 7036.0 7036 97.841 1 4073 1 chr1B.!!$R1 4072
3 TraesCS7B01G115800 chr1B 615476444 615480522 4078 False 7023.0 7023 97.770 1 4073 1 chr1B.!!$F2 4072
4 TraesCS7B01G115800 chr1B 122762247 122765896 3649 False 6180.0 6180 97.211 419 4073 1 chr1B.!!$F1 3654
5 TraesCS7B01G115800 chr2B 631378961 631383056 4095 True 6479.0 6479 95.315 1 4073 1 chr2B.!!$R1 4072
6 TraesCS7B01G115800 chr3B 542638172 542642261 4089 True 6318.0 6318 94.641 1 4073 1 chr3B.!!$R2 4072
7 TraesCS7B01G115800 chr3B 28344445 28348487 4042 False 6054.0 6054 93.649 1 4073 1 chr3B.!!$F1 4072
8 TraesCS7B01G115800 chr3B 737832470 737835837 3367 True 5269.0 5269 95.013 728 4073 1 chr3B.!!$R3 3345
9 TraesCS7B01G115800 chr3B 81547313 81550607 3294 True 5123.0 5123 94.766 361 3652 1 chr3B.!!$R1 3291
10 TraesCS7B01G115800 chr5B 109896565 109899684 3119 True 5040.0 5040 95.848 1 3118 1 chr5B.!!$R1 3117
11 TraesCS7B01G115800 chr5B 351448934 351453123 4189 True 3278.5 5568 94.757 1 4073 2 chr5B.!!$R2 4072

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
62 63 4.740934 GCGTTTCTGGGCTAGATGAAGTAT 60.741 45.833 0.0 0.0 34.8 2.12 F
1239 1287 0.320374 CTAGTCCGGCTGTTGTGGAA 59.680 55.000 0.0 0.0 32.6 3.53 F
2550 2601 0.320421 GCGCACCTGGTAGAGAAACA 60.320 55.000 0.3 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 1617 0.179200 GCAATGGTCAAGTTACGGCG 60.179 55.0 4.80 4.8 0.0 6.46 R
2873 2952 0.591659 CGGATCCGCATCGAAGTCTA 59.408 55.0 23.37 0.0 0.0 2.59 R
3406 3492 1.068474 CAGAAGAAACGCCAGGTACG 58.932 55.0 0.00 0.0 0.0 3.67 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
62 63 4.740934 GCGTTTCTGGGCTAGATGAAGTAT 60.741 45.833 0.00 0.00 34.80 2.12
513 540 7.231467 AGAATTAGTGTTGGTAATGTGGTTCT 58.769 34.615 0.00 0.00 0.00 3.01
515 542 7.833285 ATTAGTGTTGGTAATGTGGTTCTTT 57.167 32.000 0.00 0.00 0.00 2.52
1037 1085 3.092301 AGGATATTGCGATGATCTCCGA 58.908 45.455 10.65 0.00 0.00 4.55
1239 1287 0.320374 CTAGTCCGGCTGTTGTGGAA 59.680 55.000 0.00 0.00 32.60 3.53
1248 1296 2.162681 GCTGTTGTGGAAAGGTATGCT 58.837 47.619 0.00 0.00 0.00 3.79
1653 1702 3.130516 CGGTATCCCACTATCGCATACAT 59.869 47.826 0.00 0.00 0.00 2.29
1775 1824 7.503230 TCAAATGCCTTGCTATCAATTCAGATA 59.497 33.333 0.00 0.00 34.76 1.98
2223 2273 0.533032 TCACACACCTGACAACGACA 59.467 50.000 0.00 0.00 0.00 4.35
2505 2555 3.306364 GCACGGAGCTATGGAGATGTATT 60.306 47.826 0.00 0.00 41.15 1.89
2550 2601 0.320421 GCGCACCTGGTAGAGAAACA 60.320 55.000 0.30 0.00 0.00 2.83
2748 2800 3.935872 GTGCGTGCACGTGCTCAA 61.936 61.111 37.59 23.18 42.66 3.02
2802 2860 0.392193 CTTCGAGCCAAGCATGTCCT 60.392 55.000 0.00 0.00 0.00 3.85
2803 2861 0.674581 TTCGAGCCAAGCATGTCCTG 60.675 55.000 0.00 0.00 0.00 3.86
2871 2950 5.427806 TGAACAGGAAGATGAAGATGAGGAT 59.572 40.000 0.00 0.00 0.00 3.24
2873 2952 7.291885 TGAACAGGAAGATGAAGATGAGGATAT 59.708 37.037 0.00 0.00 0.00 1.63
2950 3029 1.347707 CTCCACAGCCAACTCAACCTA 59.652 52.381 0.00 0.00 0.00 3.08
3038 3117 0.320374 CCTGAGGGCTACGTCAACAA 59.680 55.000 0.00 0.00 40.59 2.83
3339 3425 2.228822 CTGTACTTGGCATGGTTTGGTC 59.771 50.000 5.31 0.00 0.00 4.02
3355 3441 3.116096 TGGTCTGGTAGGCATAGAAGT 57.884 47.619 0.00 0.00 0.00 3.01
3431 3517 2.213499 CTGGCGTTTCTTCTGTGAACT 58.787 47.619 0.00 0.00 0.00 3.01
3441 3527 3.438781 TCTTCTGTGAACTGCAACGTTTT 59.561 39.130 0.00 0.00 0.00 2.43
3487 3573 2.882761 GTCTTAAAGGAACGCCAAACCT 59.117 45.455 0.00 0.00 36.29 3.50
3509 3595 2.987149 CGTGAAGCGTTTCTGTGTAGAT 59.013 45.455 13.36 0.00 34.31 1.98
3541 3627 0.033781 GACCTTTGGCATTGCAAGCA 59.966 50.000 18.36 0.00 0.00 3.91
3562 3765 0.951558 ACAGCCAACGTTTCATGGAC 59.048 50.000 8.20 0.03 39.12 4.02
3581 3784 1.899437 CGAACCCCAGGCAGCTTCTA 61.899 60.000 0.00 0.00 0.00 2.10
3637 3840 2.047274 TAGGTCTGCAACGCCAGC 60.047 61.111 4.07 0.00 32.87 4.85
3829 4032 8.424918 CCACATAAAAGAGTACACATAGAGGAT 58.575 37.037 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.591170 AAGGACATTGGCGTTTCACG 59.409 50.000 0.00 0.0 45.88 4.35
112 117 1.300620 CGTCAAGAACTGCCCGACA 60.301 57.895 0.00 0.0 0.00 4.35
215 229 0.543410 TACCTCAAGCAACTCGGGGA 60.543 55.000 0.00 0.0 0.00 4.81
886 934 5.358442 TGCCTTTAAAGTTGAGCACAAACTA 59.642 36.000 14.03 0.0 37.77 2.24
1239 1287 5.013183 CCATAAGTAAGCCCTAGCATACCTT 59.987 44.000 0.00 0.0 42.77 3.50
1248 1296 7.773690 GTCAAAAGATTCCATAAGTAAGCCCTA 59.226 37.037 0.00 0.0 0.00 3.53
1289 1337 1.003839 GTGTCTCCCGTGCCATCAA 60.004 57.895 0.00 0.0 0.00 2.57
1472 1521 3.028130 TCATACATGCTCCGTCCAACTA 58.972 45.455 0.00 0.0 0.00 2.24
1568 1617 0.179200 GCAATGGTCAAGTTACGGCG 60.179 55.000 4.80 4.8 0.00 6.46
1653 1702 1.423541 ACACTTGGACATTAGCCCACA 59.576 47.619 0.00 0.0 31.11 4.17
1775 1824 4.062677 AGCTCATGCACAACAACAAAAT 57.937 36.364 0.00 0.0 42.74 1.82
2223 2273 3.636018 ATGCCTTAAATATGCCCCCTT 57.364 42.857 0.00 0.0 0.00 3.95
2505 2555 5.530915 GCCAAGCACCACATTACTATCATTA 59.469 40.000 0.00 0.0 0.00 1.90
2748 2800 9.282569 GCAGAAGAAAGAACATCCATTCTATAT 57.717 33.333 0.00 0.0 37.99 0.86
2802 2860 2.048222 CGAGCGGAAGAAGCACCA 60.048 61.111 0.00 0.0 37.01 4.17
2803 2861 2.048127 ACGAGCGGAAGAAGCACC 60.048 61.111 0.00 0.0 37.01 5.01
2842 2921 7.170277 TCATCTTCATCTTCCTGTTCATCAAA 58.830 34.615 0.00 0.0 0.00 2.69
2871 2950 2.418976 CGGATCCGCATCGAAGTCTATA 59.581 50.000 23.37 0.0 0.00 1.31
2873 2952 0.591659 CGGATCCGCATCGAAGTCTA 59.408 55.000 23.37 0.0 0.00 2.59
3038 3117 1.852157 TTTCGCAGGCATCTTCCCCT 61.852 55.000 0.00 0.0 0.00 4.79
3295 3377 7.287005 ACAGCAACAGATTATCAATGATCCAAT 59.713 33.333 0.00 0.0 0.00 3.16
3339 3425 5.344743 TTCTGAACTTCTATGCCTACCAG 57.655 43.478 0.00 0.0 0.00 4.00
3355 3441 3.689161 CCAACATCTATGGCGTTTCTGAA 59.311 43.478 0.00 0.0 0.00 3.02
3406 3492 1.068474 CAGAAGAAACGCCAGGTACG 58.932 55.000 0.00 0.0 0.00 3.67
3441 3527 1.532078 TGCCTGGGACACGTACAGA 60.532 57.895 9.45 0.0 34.21 3.41
3487 3573 3.305131 ATCTACACAGAAACGCTTCACGA 60.305 43.478 0.78 0.0 38.07 4.35
3509 3595 2.517959 CAAAGGTCCTGGCATTTCTGA 58.482 47.619 0.00 0.0 0.00 3.27
3532 3618 1.135315 CGTTGGCTGTATGCTTGCAAT 60.135 47.619 0.00 0.0 42.39 3.56
3541 3627 2.747446 GTCCATGAAACGTTGGCTGTAT 59.253 45.455 0.00 0.0 32.80 2.29
3562 3765 1.899437 TAGAAGCTGCCTGGGGTTCG 61.899 60.000 0.00 0.0 43.33 3.95
3581 3784 2.092323 GGCTTGGCGTTCCTTTAAGAT 58.908 47.619 0.00 0.0 0.00 2.40
3647 3850 3.817238 CGTTTTACTACGCTTTGGCAAT 58.183 40.909 0.00 0.0 38.60 3.56
3829 4032 3.125146 GTGATGTCACAATTGCGCTAGAA 59.875 43.478 9.73 0.0 45.75 2.10


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

AutoCloner maintained by Alex Coulton.