Multiple sequence alignment - TraesCS3D01G253700

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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 TraesCS3D01G253700 chr3D 100.000 3779 0 0 1 3779 355321162 355317384 0.000000e+00 6979.0
1 TraesCS3D01G253700 chr3B 91.794 2547 87 36 636 3123 456325231 456322748 0.000000e+00 3434.0
2 TraesCS3D01G253700 chr3B 93.484 1811 48 20 901 2688 463203000 463204763 0.000000e+00 2627.0
3 TraesCS3D01G253700 chr3B 92.663 627 21 9 1 608 456326101 456325481 0.000000e+00 880.0
4 TraesCS3D01G253700 chr3B 91.379 580 17 13 2950 3529 463211132 463211678 0.000000e+00 763.0
5 TraesCS3D01G253700 chr3B 96.165 339 3 3 1 335 463200499 463200831 2.570000e-151 545.0
6 TraesCS3D01G253700 chr3B 89.823 452 4 7 489 898 463201136 463201587 3.320000e-150 542.0
7 TraesCS3D01G253700 chr3B 97.122 278 2 3 2692 2963 463210830 463211107 7.390000e-127 464.0
8 TraesCS3D01G253700 chr3B 87.611 339 10 6 3156 3490 456322751 456322441 7.710000e-97 364.0
9 TraesCS3D01G253700 chr3B 93.820 178 4 2 334 504 463200946 463201123 1.040000e-65 261.0
10 TraesCS3D01G253700 chr3B 91.720 157 7 6 3604 3755 463212194 463212349 2.960000e-51 213.0
11 TraesCS3D01G253700 chr3A 91.858 1916 58 20 762 2625 474210867 474208998 0.000000e+00 2584.0
12 TraesCS3D01G253700 chr3A 90.714 840 26 16 2617 3438 474208978 474208173 0.000000e+00 1072.0
13 TraesCS3D01G253700 chr3A 88.933 750 36 24 1 718 474211603 474210869 0.000000e+00 881.0
14 TraesCS3D01G253700 chr3A 88.710 186 11 6 3604 3779 474208037 474207852 6.360000e-53 219.0
15 TraesCS3D01G253700 chr1B 91.371 197 17 0 1999 2195 376072616 376072812 1.730000e-68 270.0
16 TraesCS3D01G253700 chr1D 90.863 197 18 0 1999 2195 277094382 277094578 8.050000e-67 265.0
17 TraesCS3D01G253700 chr1A 90.355 197 19 0 1999 2195 349360255 349360451 3.740000e-65 259.0
18 TraesCS3D01G253700 chr7D 86.697 218 16 9 1146 1351 234656763 234656979 2.940000e-56 230.0
19 TraesCS3D01G253700 chr7D 89.404 151 15 1 1430 1580 234656974 234657123 4.980000e-44 189.0
20 TraesCS3D01G253700 chr2D 87.234 47 6 0 2045 2091 477238231 477238277 2.000000e-03 54.7


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 TraesCS3D01G253700 chr3D 355317384 355321162 3778 True 6979.000000 6979 100.000000 1 3779 1 chr3D.!!$R1 3778
1 TraesCS3D01G253700 chr3B 456322441 456326101 3660 True 1559.333333 3434 90.689333 1 3490 3 chr3B.!!$R1 3489
2 TraesCS3D01G253700 chr3B 463200499 463204763 4264 False 993.750000 2627 93.323000 1 2688 4 chr3B.!!$F1 2687
3 TraesCS3D01G253700 chr3B 463210830 463212349 1519 False 480.000000 763 93.407000 2692 3755 3 chr3B.!!$F2 1063
4 TraesCS3D01G253700 chr3A 474207852 474211603 3751 True 1189.000000 2584 90.053750 1 3779 4 chr3A.!!$R1 3778

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
402 561 1.659954 TCATTTTTGGTGCGTGCGC 60.660 52.632 9.85 9.85 42.35 6.09 F
1811 3697 0.535797 GGATCTTCGGGAAGGACGTT 59.464 55.000 8.46 0.00 38.88 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 3849 1.011794 GCGTCGCTGAAGCTTATGC 60.012 57.895 10.68 5.99 39.32 3.14 R
3463 5553 0.183492 TAATGGCACTGGATGGGAGC 59.817 55.000 0.00 0.00 0.00 4.70 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
402 561 1.659954 TCATTTTTGGTGCGTGCGC 60.660 52.632 9.85 9.85 42.35 6.09
1520 3397 1.478510 CTGGCGTCCATGTACTTCTCT 59.521 52.381 0.00 0.00 30.82 3.10
1811 3697 0.535797 GGATCTTCGGGAAGGACGTT 59.464 55.000 8.46 0.00 38.88 3.99
1960 3849 1.994507 AGCAGGAGCCTCCCAAGAG 60.995 63.158 7.26 0.00 43.56 2.85
2413 4311 2.957489 CGACACCGTCACGCACAA 60.957 61.111 0.00 0.00 32.09 3.33
2560 4476 0.872388 GGCAACTGTCAACCGTTAGG 59.128 55.000 0.00 0.00 45.13 2.69
2636 4597 2.841442 AGGTGAAACTCCTTTCCTCG 57.159 50.000 0.00 0.00 35.75 4.63
3186 5215 2.124403 ATCGGCTCGGGTACTCGT 60.124 61.111 16.07 0.00 0.00 4.18
3330 5367 1.072965 CAACCCTTTCAGCTCAGGACT 59.927 52.381 4.88 0.00 30.81 3.85
3331 5368 1.439543 ACCCTTTCAGCTCAGGACTT 58.560 50.000 4.88 0.00 30.81 3.01
3332 5369 1.072965 ACCCTTTCAGCTCAGGACTTG 59.927 52.381 4.88 0.00 30.81 3.16
3333 5370 1.349026 CCCTTTCAGCTCAGGACTTGA 59.651 52.381 4.88 0.00 30.81 3.02
3369 5406 4.218578 CGGCTGGCTCATCTCGCT 62.219 66.667 0.00 0.00 0.00 4.93
3370 5407 2.588314 GGCTGGCTCATCTCGCTG 60.588 66.667 0.00 0.00 0.00 5.18
3391 5428 1.192534 CGCCTTTTCGTGAACTCACTC 59.807 52.381 8.16 0.00 44.34 3.51
3392 5429 1.192534 GCCTTTTCGTGAACTCACTCG 59.807 52.381 8.16 0.00 44.34 4.18
3441 5531 7.900352 GCTTTAATCAAGTTACAATCAGTCGAG 59.100 37.037 0.00 0.00 34.56 4.04
3463 5553 3.001330 GGTCGCGAAATCTTAATCACCAG 59.999 47.826 12.06 0.00 0.00 4.00
3525 6036 1.812922 GGCAGCAGTGATCGTCTGG 60.813 63.158 15.99 5.28 33.98 3.86
3528 6039 0.799917 CAGCAGTGATCGTCTGGTCG 60.800 60.000 15.97 10.22 40.86 4.79
3537 6048 2.631418 TCGTCTGGTCGTGAAATCTC 57.369 50.000 0.00 0.00 0.00 2.75
3540 6051 2.478031 CGTCTGGTCGTGAAATCTCGAT 60.478 50.000 10.30 0.00 42.56 3.59
3552 6063 7.276878 TCGTGAAATCTCGATGCAACTTTTATA 59.723 33.333 3.69 0.00 37.02 0.98
3588 6099 5.066117 GCCTTGTCTTTAATAACCTAGTGCC 59.934 44.000 0.00 0.00 0.00 5.01
3589 6100 6.177610 CCTTGTCTTTAATAACCTAGTGCCA 58.822 40.000 0.00 0.00 0.00 4.92
3590 6101 6.316390 CCTTGTCTTTAATAACCTAGTGCCAG 59.684 42.308 0.00 0.00 0.00 4.85
3594 6105 6.421202 GTCTTTAATAACCTAGTGCCAGATCG 59.579 42.308 0.00 0.00 0.00 3.69
3601 6112 3.389329 ACCTAGTGCCAGATCGATTGAAT 59.611 43.478 0.00 0.00 0.00 2.57
3602 6113 4.141620 ACCTAGTGCCAGATCGATTGAATT 60.142 41.667 0.00 0.00 0.00 2.17
3603 6114 4.818546 CCTAGTGCCAGATCGATTGAATTT 59.181 41.667 0.00 0.00 0.00 1.82
3604 6115 4.627611 AGTGCCAGATCGATTGAATTTG 57.372 40.909 0.00 0.00 0.00 2.32
3605 6116 4.012374 AGTGCCAGATCGATTGAATTTGT 58.988 39.130 0.00 0.00 0.00 2.83
3607 6118 4.560035 GTGCCAGATCGATTGAATTTGTTG 59.440 41.667 0.00 0.00 0.00 3.33
3691 6231 3.000041 CTGCTAATGCTTCACCGTGTAA 59.000 45.455 0.00 0.00 40.48 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
194 216 2.934932 TGCTCTGGACCATGCCCA 60.935 61.111 14.57 5.17 0.00 5.36
898 1337 2.982470 GCGCCAAGAAGTTGATTTTCTG 59.018 45.455 0.00 0.00 35.20 3.02
1900 3786 4.785453 CCTCCTGCTTGGTCGGGC 62.785 72.222 0.00 0.00 37.07 6.13
1901 3787 4.785453 GCCTCCTGCTTGGTCGGG 62.785 72.222 0.00 0.00 36.87 5.14
1960 3849 1.011794 GCGTCGCTGAAGCTTATGC 60.012 57.895 10.68 5.99 39.32 3.14
2516 4414 0.374758 CGCGATTGTTACAGCTGCAT 59.625 50.000 15.27 0.00 0.00 3.96
2560 4476 3.610911 AGCATGCTCACCTAAACTTACC 58.389 45.455 16.30 0.00 0.00 2.85
2636 4597 2.843701 CAATCTGGGATACTGCCACTC 58.156 52.381 0.00 0.00 30.85 3.51
3186 5215 1.958715 CCATCAACCGTGCACGACA 60.959 57.895 39.10 19.74 43.02 4.35
3330 5367 3.589579 GCCACGGCACATCATCAA 58.410 55.556 2.36 0.00 41.49 2.57
3369 5406 0.812014 TGAGTTCACGAAAAGGCGCA 60.812 50.000 10.83 0.00 33.86 6.09
3370 5407 0.384353 GTGAGTTCACGAAAAGGCGC 60.384 55.000 0.00 0.00 37.10 6.53
3441 5531 2.933906 TGGTGATTAAGATTTCGCGACC 59.066 45.455 9.15 2.79 0.00 4.79
3463 5553 0.183492 TAATGGCACTGGATGGGAGC 59.817 55.000 0.00 0.00 0.00 4.70
3512 5608 0.521735 TCACGACCAGACGATCACTG 59.478 55.000 9.18 9.18 37.03 3.66
3525 6036 2.668457 AGTTGCATCGAGATTTCACGAC 59.332 45.455 2.27 0.00 41.31 4.34
3528 6039 9.722056 ATTATAAAAGTTGCATCGAGATTTCAC 57.278 29.630 0.00 0.00 0.00 3.18
3540 6051 9.748708 GGCATCTCAAATATTATAAAAGTTGCA 57.251 29.630 14.08 0.00 32.39 4.08
3574 6085 6.266786 TCAATCGATCTGGCACTAGGTTATTA 59.733 38.462 0.00 0.00 0.00 0.98
3588 6099 9.611284 TTTTCTACAACAAATTCAATCGATCTG 57.389 29.630 0.00 0.00 0.00 2.90
3691 6231 1.348775 GCTCCATAGCCCCCACTCTT 61.349 60.000 0.00 0.00 43.40 2.85


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

AutoCloner maintained by Alex Coulton.