Multiple sequence alignment - TraesCS5D01G077000

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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 TraesCS5D01G077000 chr5D 100.000 3643 0 0 1 3643 76692210 76688568 0.000000e+00 6728.0
1 TraesCS5D01G077000 chr5D 97.661 3549 52 12 1 3542 76756435 76752911 0.000000e+00 6065.0
2 TraesCS5D01G077000 chr5D 76.407 462 87 16 2120 2571 79106211 79106660 2.830000e-56 230.0
3 TraesCS5D01G077000 chr5D 82.775 209 26 8 226 433 79104303 79104502 1.040000e-40 178.0
4 TraesCS5D01G077000 chr5D 84.615 143 13 5 760 899 459581952 459582088 2.280000e-27 134.0
5 TraesCS5D01G077000 chr5B 95.302 3661 119 22 1 3643 85116422 85120047 0.000000e+00 5758.0
6 TraesCS5D01G077000 chr5B 95.039 3487 116 23 182 3643 85178696 85182150 0.000000e+00 5428.0
7 TraesCS5D01G077000 chr5B 92.217 681 48 4 1 679 85285444 85286121 0.000000e+00 959.0
8 TraesCS5D01G077000 chr5B 85.670 321 41 4 398 715 564092896 564093214 2.100000e-87 333.0
9 TraesCS5D01G077000 chr5B 84.735 321 45 3 398 715 564302890 564303209 5.870000e-83 318.0
10 TraesCS5D01G077000 chr5B 84.112 321 47 3 398 715 564423866 564424185 1.270000e-79 307.0
11 TraesCS5D01G077000 chr5B 83.178 321 50 3 398 715 564361667 564361986 1.280000e-74 291.0
12 TraesCS5D01G077000 chr5B 77.778 468 88 11 2123 2580 88781313 88781774 1.290000e-69 274.0
13 TraesCS5D01G077000 chr5B 93.642 173 10 1 7 179 85147875 85148046 1.300000e-64 257.0
14 TraesCS5D01G077000 chr5B 85.345 232 22 8 398 619 563864262 563864491 2.830000e-56 230.0
15 TraesCS5D01G077000 chr5A 92.813 3534 161 35 153 3643 72230537 72227054 0.000000e+00 5033.0
16 TraesCS5D01G077000 chr5A 94.925 2069 82 12 1587 3643 72388938 72386881 0.000000e+00 3217.0
17 TraesCS5D01G077000 chr5A 94.045 1696 81 10 1911 3595 72330698 72329012 0.000000e+00 2555.0
18 TraesCS5D01G077000 chr5A 94.821 1120 42 4 783 1890 72331807 72330692 0.000000e+00 1733.0
19 TraesCS5D01G077000 chr5A 89.044 1433 96 22 153 1558 72390334 72388936 0.000000e+00 1720.0
20 TraesCS5D01G077000 chr5A 86.969 353 22 6 783 1115 72260105 72259757 3.430000e-100 375.0
21 TraesCS5D01G077000 chr5A 76.582 474 89 16 2123 2580 75050051 75050518 1.310000e-59 241.0
22 TraesCS5D01G077000 chr7B 92.424 66 3 2 2933 2998 131743966 131744029 3.870000e-15 93.5
23 TraesCS5D01G077000 chr7D 90.000 70 7 0 2924 2993 463883623 463883554 1.390000e-14 91.6
24 TraesCS5D01G077000 chr2B 86.420 81 8 3 2933 3013 416830046 416829969 6.480000e-13 86.1
25 TraesCS5D01G077000 chr2B 100.000 30 0 0 717 746 21856951 21856922 5.080000e-04 56.5
26 TraesCS5D01G077000 chr2A 100.000 30 0 0 717 746 13878746 13878775 5.080000e-04 56.5


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 TraesCS5D01G077000 chr5D 76688568 76692210 3642 True 6728.0 6728 100.0000 1 3643 1 chr5D.!!$R1 3642
1 TraesCS5D01G077000 chr5D 76752911 76756435 3524 True 6065.0 6065 97.6610 1 3542 1 chr5D.!!$R2 3541
2 TraesCS5D01G077000 chr5D 79104303 79106660 2357 False 204.0 230 79.5910 226 2571 2 chr5D.!!$F2 2345
3 TraesCS5D01G077000 chr5B 85116422 85120047 3625 False 5758.0 5758 95.3020 1 3643 1 chr5B.!!$F1 3642
4 TraesCS5D01G077000 chr5B 85178696 85182150 3454 False 5428.0 5428 95.0390 182 3643 1 chr5B.!!$F3 3461
5 TraesCS5D01G077000 chr5B 85285444 85286121 677 False 959.0 959 92.2170 1 679 1 chr5B.!!$F4 678
6 TraesCS5D01G077000 chr5A 72227054 72230537 3483 True 5033.0 5033 92.8130 153 3643 1 chr5A.!!$R1 3490
7 TraesCS5D01G077000 chr5A 72386881 72390334 3453 True 2468.5 3217 91.9845 153 3643 2 chr5A.!!$R4 3490
8 TraesCS5D01G077000 chr5A 72329012 72331807 2795 True 2144.0 2555 94.4330 783 3595 2 chr5A.!!$R3 2812

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
622 650 0.106708 ACGCCTTCTCTTCTGCAACA 59.893 50.0 0.0 0.0 0.0 3.33 F
623 651 1.229428 CGCCTTCTCTTCTGCAACAA 58.771 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 2780 7.325097 CGACAAACCAAATACATAACAACTTCC 59.675 37.037 0.00 0.0 0.0 3.46 R
3293 3808 8.172352 TCTCATCTAGCTAGGAATTTGACTAC 57.828 38.462 20.58 0.0 0.0 2.73 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
187 188 5.850557 AATTTGCGACATGATATTTCCCA 57.149 34.783 0.00 0.00 0.00 4.37
329 342 2.844348 GTTGGGGAGGGATGAGAAGTAA 59.156 50.000 0.00 0.00 0.00 2.24
336 350 5.189934 GGGAGGGATGAGAAGTAAAGAGAAA 59.810 44.000 0.00 0.00 0.00 2.52
338 352 6.306643 AGGGATGAGAAGTAAAGAGAAAGG 57.693 41.667 0.00 0.00 0.00 3.11
395 413 0.738389 CAGAAAACAAGCACCGGTGT 59.262 50.000 33.92 18.91 0.00 4.16
398 416 0.681564 AAAACAAGCACCGGTGTGGA 60.682 50.000 33.92 0.00 42.99 4.02
399 417 1.101049 AAACAAGCACCGGTGTGGAG 61.101 55.000 33.92 22.88 42.99 3.86
400 418 2.669569 CAAGCACCGGTGTGGAGG 60.670 66.667 33.92 16.37 42.99 4.30
402 420 2.448582 AAGCACCGGTGTGGAGGAA 61.449 57.895 33.92 0.00 42.99 3.36
403 421 1.990160 AAGCACCGGTGTGGAGGAAA 61.990 55.000 33.92 0.00 42.99 3.13
404 422 2.258726 GCACCGGTGTGGAGGAAAC 61.259 63.158 33.92 11.69 42.99 2.78
405 423 1.599797 CACCGGTGTGGAGGAAACC 60.600 63.158 26.95 0.00 42.00 3.27
406 424 2.073716 ACCGGTGTGGAGGAAACCA 61.074 57.895 6.12 0.00 42.00 3.67
407 425 1.378762 CCGGTGTGGAGGAAACCAT 59.621 57.895 0.00 0.00 42.17 3.55
559 586 0.909610 TCCCTCATTCCCGACTTGCT 60.910 55.000 0.00 0.00 0.00 3.91
615 643 1.802069 AGCTTTGACGCCTTCTCTTC 58.198 50.000 0.00 0.00 0.00 2.87
621 649 0.793250 GACGCCTTCTCTTCTGCAAC 59.207 55.000 0.00 0.00 0.00 4.17
622 650 0.106708 ACGCCTTCTCTTCTGCAACA 59.893 50.000 0.00 0.00 0.00 3.33
623 651 1.229428 CGCCTTCTCTTCTGCAACAA 58.771 50.000 0.00 0.00 0.00 2.83
624 652 1.603802 CGCCTTCTCTTCTGCAACAAA 59.396 47.619 0.00 0.00 0.00 2.83
625 653 2.033299 CGCCTTCTCTTCTGCAACAAAA 59.967 45.455 0.00 0.00 0.00 2.44
626 654 3.304928 CGCCTTCTCTTCTGCAACAAAAT 60.305 43.478 0.00 0.00 0.00 1.82
627 655 4.083324 CGCCTTCTCTTCTGCAACAAAATA 60.083 41.667 0.00 0.00 0.00 1.40
628 656 5.562696 CGCCTTCTCTTCTGCAACAAAATAA 60.563 40.000 0.00 0.00 0.00 1.40
629 657 5.860716 GCCTTCTCTTCTGCAACAAAATAAG 59.139 40.000 0.00 0.00 0.00 1.73
630 658 6.385033 CCTTCTCTTCTGCAACAAAATAAGG 58.615 40.000 0.00 0.00 0.00 2.69
683 733 1.523154 TTGTTGGAAGCATGCGTCCC 61.523 55.000 38.63 28.08 42.61 4.46
2285 2780 7.518161 TGCTTTATTGATCTACTTGTTGTTCG 58.482 34.615 0.00 0.00 0.00 3.95
2891 3395 4.876107 ACACTCGGCATAGACAATTTTAGG 59.124 41.667 0.00 0.00 0.00 2.69
3293 3808 8.768955 GCAGTGATATCATTAAACTCTAACCAG 58.231 37.037 9.02 0.00 0.00 4.00
3318 3833 8.001875 AGTAGTCAAATTCCTAGCTAGATGAGA 58.998 37.037 22.70 7.81 0.00 3.27
3325 3840 8.450578 AATTCCTAGCTAGATGAGATCTATCG 57.549 38.462 22.70 0.50 40.82 2.92
3602 4117 1.503800 GGGGTAATCCTCCTTTCCGA 58.496 55.000 0.00 0.00 35.33 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.032680 AGGCTTGTACGTGTGTTGTT 57.967 45.000 0.00 0.0 0.00 2.83
187 188 8.692110 TCACGTAATTAACAACGATAAGACAT 57.308 30.769 15.96 0.0 41.55 3.06
235 246 2.484417 CGAAGCTCCACATAGCCAAGAT 60.484 50.000 0.00 0.0 43.86 2.40
283 294 6.923199 ATCCAGTTCTCCATCAAACAAAAT 57.077 33.333 0.00 0.0 0.00 1.82
329 342 2.418669 TGGTTCCTCCACCTTTCTCTT 58.581 47.619 0.00 0.0 41.93 2.85
336 350 1.350310 AACCGTTGGTTCCTCCACCT 61.350 55.000 0.00 0.0 43.05 4.00
338 352 0.179040 TCAACCGTTGGTTCCTCCAC 60.179 55.000 11.35 0.0 43.05 4.02
395 413 0.486879 AAGGGCAATGGTTTCCTCCA 59.513 50.000 0.00 0.0 42.01 3.86
398 416 1.428912 TGAGAAGGGCAATGGTTTCCT 59.571 47.619 0.00 0.0 0.00 3.36
399 417 1.923356 TGAGAAGGGCAATGGTTTCC 58.077 50.000 0.00 0.0 0.00 3.13
400 418 3.091545 TCATGAGAAGGGCAATGGTTTC 58.908 45.455 0.00 0.0 0.00 2.78
402 420 2.905415 TCATGAGAAGGGCAATGGTT 57.095 45.000 0.00 0.0 0.00 3.67
403 421 2.423947 GGATCATGAGAAGGGCAATGGT 60.424 50.000 0.09 0.0 0.00 3.55
404 422 2.158505 AGGATCATGAGAAGGGCAATGG 60.159 50.000 0.09 0.0 0.00 3.16
405 423 3.225177 AGGATCATGAGAAGGGCAATG 57.775 47.619 0.09 0.0 0.00 2.82
406 424 3.967467 AAGGATCATGAGAAGGGCAAT 57.033 42.857 0.09 0.0 0.00 3.56
407 425 3.744940 AAAGGATCATGAGAAGGGCAA 57.255 42.857 0.09 0.0 0.00 4.52
615 643 7.534918 GCTTTAATTTGCCTTATTTTGTTGCAG 59.465 33.333 0.00 0.0 32.88 4.41
621 649 7.131498 TGCAGCTTTAATTTGCCTTATTTTG 57.869 32.000 0.00 0.0 37.03 2.44
622 650 6.128200 GCTGCAGCTTTAATTTGCCTTATTTT 60.128 34.615 31.33 0.0 37.03 1.82
623 651 5.352293 GCTGCAGCTTTAATTTGCCTTATTT 59.648 36.000 31.33 0.0 37.03 1.40
624 652 4.872124 GCTGCAGCTTTAATTTGCCTTATT 59.128 37.500 31.33 0.0 37.03 1.40
625 653 4.436332 GCTGCAGCTTTAATTTGCCTTAT 58.564 39.130 31.33 0.0 37.03 1.73
626 654 3.848726 GCTGCAGCTTTAATTTGCCTTA 58.151 40.909 31.33 0.0 37.03 2.69
627 655 2.691927 GCTGCAGCTTTAATTTGCCTT 58.308 42.857 31.33 0.0 37.03 4.35
628 656 2.375173 GCTGCAGCTTTAATTTGCCT 57.625 45.000 31.33 0.0 37.03 4.75
2285 2780 7.325097 CGACAAACCAAATACATAACAACTTCC 59.675 37.037 0.00 0.0 0.00 3.46
3293 3808 8.172352 TCTCATCTAGCTAGGAATTTGACTAC 57.828 38.462 20.58 0.0 0.00 2.73
3318 3833 8.701895 TCAATACCTTGAAAGTTACCGATAGAT 58.298 33.333 0.00 0.0 38.43 1.98
3581 4096 0.472898 GGAAAGGAGGATTACCCCCG 59.527 60.000 0.00 0.0 36.73 5.73


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

AutoCloner maintained by Alex Coulton.