Multiple sequence alignment - TraesCS3D01G212500

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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 TraesCS3D01G212500 chr3D 100.000 3224 0 0 1 3224 285728476 285731699 0.000000e+00 5954.0
1 TraesCS3D01G212500 chr3B 94.302 3282 94 33 1 3224 377914330 377911084 0.000000e+00 4939.0
2 TraesCS3D01G212500 chr3A 96.818 2231 51 9 644 2869 374317802 374320017 0.000000e+00 3709.0
3 TraesCS3D01G212500 chr3A 87.615 654 65 6 4 641 374314154 374314807 0.000000e+00 745.0
4 TraesCS3D01G212500 chr3A 89.130 230 8 3 2868 3080 374320186 374320415 1.470000e-68 270.0
5 TraesCS3D01G212500 chr1D 83.588 262 36 7 400 659 20292104 20291848 4.160000e-59 239.0
6 TraesCS3D01G212500 chr7B 83.951 243 35 4 400 639 636645813 636645572 2.500000e-56 230.0
7 TraesCS3D01G212500 chr5B 87.324 142 17 1 497 637 600114586 600114727 9.260000e-36 161.0
8 TraesCS3D01G212500 chr5B 95.946 74 3 0 1986 2059 184778080 184778007 1.570000e-23 121.0
9 TraesCS3D01G212500 chr6A 94.595 74 4 0 1986 2059 66383015 66383088 7.310000e-22 115.0
10 TraesCS3D01G212500 chr6A 93.243 74 5 0 1986 2059 330038521 330038594 3.400000e-20 110.0
11 TraesCS3D01G212500 chr4A 94.595 74 4 0 1986 2059 362070976 362071049 7.310000e-22 115.0
12 TraesCS3D01G212500 chr4A 94.595 74 4 0 1986 2059 521816963 521817036 7.310000e-22 115.0
13 TraesCS3D01G212500 chr4D 86.813 91 7 3 573 663 497242754 497242669 2.650000e-16 97.1


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 TraesCS3D01G212500 chr3D 285728476 285731699 3223 False 5954.000000 5954 100.000000 1 3224 1 chr3D.!!$F1 3223
1 TraesCS3D01G212500 chr3B 377911084 377914330 3246 True 4939.000000 4939 94.302000 1 3224 1 chr3B.!!$R1 3223
2 TraesCS3D01G212500 chr3A 374314154 374320415 6261 False 1574.666667 3709 91.187667 4 3080 3 chr3A.!!$F1 3076

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
95 96 0.391793 CAAAGAGAGGAAGGGACGGC 60.392 60.0 0.00 0.0 0.00 5.68 F
1892 4930 0.391263 CGGGTCTTCAAGTACCAGGC 60.391 60.0 7.93 0.0 37.51 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 5117 0.759436 ACGACCTCCTGTTGTCCACT 60.759 55.0 0.0 0.0 36.89 4.00 R
2712 5751 0.524862 CTGAACAGATGGCAGGCAAC 59.475 55.0 0.0 0.0 0.00 4.17 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
47 48 1.600511 TAGGGTTCGTCGCATGCAGA 61.601 55.000 19.57 13.08 0.00 4.26
95 96 0.391793 CAAAGAGAGGAAGGGACGGC 60.392 60.000 0.00 0.00 0.00 5.68
152 153 7.750947 ATGGGTCTACTTATAGAAAGTTGGT 57.249 36.000 0.00 0.00 39.20 3.67
226 238 0.526211 TACACACGAATCTCTGCGCT 59.474 50.000 9.73 0.00 0.00 5.92
229 241 1.520174 CACACGAATCTCTGCGCTATG 59.480 52.381 9.73 0.00 0.00 2.23
233 249 3.120947 CACGAATCTCTGCGCTATGATTC 59.879 47.826 25.23 25.23 40.51 2.52
322 339 8.270744 ACCTATCTAGCTCAAACTTCATTCATT 58.729 33.333 0.00 0.00 0.00 2.57
339 356 6.268158 TCATTCATTGGCCAATATATTGCTGT 59.732 34.615 30.19 2.49 36.48 4.40
353 370 6.857777 ATATTGCTGTCATTGAAGTAGCTC 57.142 37.500 15.49 0.00 35.50 4.09
366 383 8.820933 CATTGAAGTAGCTCGAAAAATAGATCA 58.179 33.333 0.00 0.00 0.00 2.92
367 384 7.757097 TGAAGTAGCTCGAAAAATAGATCAC 57.243 36.000 0.00 0.00 0.00 3.06
368 385 6.757010 TGAAGTAGCTCGAAAAATAGATCACC 59.243 38.462 0.00 0.00 0.00 4.02
369 386 5.282510 AGTAGCTCGAAAAATAGATCACCG 58.717 41.667 0.00 0.00 0.00 4.94
370 387 2.866762 AGCTCGAAAAATAGATCACCGC 59.133 45.455 0.00 0.00 0.00 5.68
371 388 2.607635 GCTCGAAAAATAGATCACCGCA 59.392 45.455 0.00 0.00 0.00 5.69
372 389 3.248602 GCTCGAAAAATAGATCACCGCAT 59.751 43.478 0.00 0.00 0.00 4.73
375 392 5.597806 TCGAAAAATAGATCACCGCATACT 58.402 37.500 0.00 0.00 0.00 2.12
389 413 2.741553 CGCATACTGCTATTCCACACCA 60.742 50.000 0.00 0.00 42.25 4.17
539 564 6.289745 TGTTTACGTGTTAGCGAAGAATTT 57.710 33.333 0.00 0.00 35.59 1.82
567 592 4.106197 CGAAAAATGTTCCGTGTTTTGGA 58.894 39.130 0.00 0.00 0.00 3.53
571 596 7.043325 CGAAAAATGTTCCGTGTTTTGGAAATA 60.043 33.333 0.00 0.00 46.53 1.40
601 626 7.703058 TCCCTGATTTTATTTCTCAAACTCC 57.297 36.000 0.00 0.00 0.00 3.85
929 3946 1.713647 ACACAAGGGGAGAGAGAGAGA 59.286 52.381 0.00 0.00 0.00 3.10
930 3947 2.291540 ACACAAGGGGAGAGAGAGAGAG 60.292 54.545 0.00 0.00 0.00 3.20
931 3948 2.025416 CACAAGGGGAGAGAGAGAGAGA 60.025 54.545 0.00 0.00 0.00 3.10
932 3949 2.242196 ACAAGGGGAGAGAGAGAGAGAG 59.758 54.545 0.00 0.00 0.00 3.20
933 3950 2.509548 CAAGGGGAGAGAGAGAGAGAGA 59.490 54.545 0.00 0.00 0.00 3.10
934 3951 3.080660 AGGGGAGAGAGAGAGAGAGAT 57.919 52.381 0.00 0.00 0.00 2.75
935 3952 4.228237 AGGGGAGAGAGAGAGAGAGATA 57.772 50.000 0.00 0.00 0.00 1.98
936 3953 4.779386 AGGGGAGAGAGAGAGAGAGATAT 58.221 47.826 0.00 0.00 0.00 1.63
1608 4646 1.148157 CCGATGACGTGTGGATGAGC 61.148 60.000 0.00 0.00 37.88 4.26
1892 4930 0.391263 CGGGTCTTCAAGTACCAGGC 60.391 60.000 7.93 0.00 37.51 4.85
2014 5052 3.701604 ATCGAGGTCGCGCAGTTCC 62.702 63.158 8.75 3.45 39.60 3.62
2532 5570 8.613482 GTTACTTCCTATATTTGGCTTCTTGTC 58.387 37.037 0.00 0.00 0.00 3.18
2601 5639 2.614520 GCTGTCTCGCATCAGTAGTAGA 59.385 50.000 0.00 0.00 34.57 2.59
2637 5675 3.130633 GTTGTTGCAACTGGAAATTCCC 58.869 45.455 28.61 0.00 35.03 3.97
2652 5690 6.071221 TGGAAATTCCCATTCAGTTTCTGATG 60.071 38.462 9.87 2.45 36.64 3.07
2712 5751 5.532557 TCGTGGATATTGTTAGCTCTCATG 58.467 41.667 0.00 0.00 0.00 3.07
2713 5752 5.069119 TCGTGGATATTGTTAGCTCTCATGT 59.931 40.000 0.00 0.00 0.00 3.21
2748 5788 6.482308 TCTGTTCAGGTTACTTTAGTGCTTTC 59.518 38.462 0.00 0.00 0.00 2.62
2759 5801 0.820891 AGTGCTTTCCTGTGCAGTGG 60.821 55.000 0.00 0.00 40.80 4.00
2835 5877 3.061322 CCATGCAATTTGTGTTCCACAG 58.939 45.455 0.00 0.00 45.39 3.66
2849 5891 0.954452 CCACAGGCTCTTTGGTGTTC 59.046 55.000 1.86 0.00 0.00 3.18
2862 5904 3.558931 TGGTGTTCTTGTCAGACATGT 57.441 42.857 14.47 0.00 0.00 3.21
2927 6147 5.365605 CCTTGGTGTGTATTGATAGGTAGGA 59.634 44.000 0.00 0.00 0.00 2.94
3024 6246 1.815421 GCCCACGCTGATGTGTAGG 60.815 63.158 0.00 0.00 38.27 3.18
3083 6315 1.202348 GTGAATTGCCAGTGCTTACCC 59.798 52.381 0.00 0.00 38.71 3.69
3085 6317 1.474077 GAATTGCCAGTGCTTACCCTG 59.526 52.381 0.00 0.00 38.71 4.45
3105 6337 2.634940 TGGAACTAGCAAGCTTCAGACT 59.365 45.455 0.00 0.00 0.00 3.24
3107 6339 3.056179 GGAACTAGCAAGCTTCAGACTCT 60.056 47.826 0.00 0.00 0.00 3.24
3108 6340 4.562552 GGAACTAGCAAGCTTCAGACTCTT 60.563 45.833 0.00 0.00 0.00 2.85
3109 6341 5.336849 GGAACTAGCAAGCTTCAGACTCTTA 60.337 44.000 0.00 0.00 0.00 2.10
3149 6381 9.942850 TGATAGTTTACATGAAGTTCTCAATGA 57.057 29.630 0.00 0.00 37.67 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 1.673033 CCTCTCTTTGATCGTTGCCGT 60.673 52.381 0.00 0.00 35.01 5.68
95 96 1.039068 ATCCATCAGACTCGGCTCTG 58.961 55.000 4.38 4.38 39.35 3.35
152 153 6.660800 TCCCCATTTTATGTTGTTCGGTATA 58.339 36.000 0.00 0.00 0.00 1.47
194 195 9.678941 GAGATTCGTGTGTACATTCTTCATATA 57.321 33.333 0.00 0.00 0.00 0.86
226 238 3.909776 ATCGGTTAGTCGCGAATCATA 57.090 42.857 14.32 0.00 0.00 2.15
229 241 3.532892 TCTATCGGTTAGTCGCGAATC 57.467 47.619 14.32 0.00 0.00 2.52
233 249 2.114825 GGTTTCTATCGGTTAGTCGCG 58.885 52.381 0.00 0.00 0.00 5.87
322 339 5.139001 TCAATGACAGCAATATATTGGCCA 58.861 37.500 23.57 0.00 38.21 5.36
339 356 8.948631 ATCTATTTTTCGAGCTACTTCAATGA 57.051 30.769 0.00 0.00 0.00 2.57
353 370 5.670097 CAGTATGCGGTGATCTATTTTTCG 58.330 41.667 0.00 0.00 0.00 3.46
370 387 4.260985 TGTTGGTGTGGAATAGCAGTATG 58.739 43.478 0.00 0.00 36.63 2.39
371 388 4.568072 TGTTGGTGTGGAATAGCAGTAT 57.432 40.909 0.00 0.00 36.63 2.12
372 389 4.568072 ATGTTGGTGTGGAATAGCAGTA 57.432 40.909 0.00 0.00 36.63 2.74
375 392 4.148079 TGAAATGTTGGTGTGGAATAGCA 58.852 39.130 0.00 0.00 32.20 3.49
389 413 4.219288 GTCTCCCTGCTGAATTGAAATGTT 59.781 41.667 0.00 0.00 0.00 2.71
539 564 7.578169 AAACACGGAACATTTTTCGTTAAAA 57.422 28.000 0.00 1.81 39.88 1.52
559 584 9.659135 AATCAGGGATCATATATTTCCAAAACA 57.341 29.630 11.75 0.00 0.00 2.83
661 3678 2.181525 GGCAAAATGTCGGCGCAT 59.818 55.556 10.83 6.50 0.00 4.73
929 3946 5.396057 AGGCCGATGAGGTATATATCTCT 57.604 43.478 21.04 9.03 43.70 3.10
930 3947 5.182380 GCTAGGCCGATGAGGTATATATCTC 59.818 48.000 15.07 15.07 43.70 2.75
931 3948 5.074115 GCTAGGCCGATGAGGTATATATCT 58.926 45.833 0.00 0.00 43.70 1.98
932 3949 5.074115 AGCTAGGCCGATGAGGTATATATC 58.926 45.833 0.00 0.00 43.70 1.63
933 3950 5.068215 AGCTAGGCCGATGAGGTATATAT 57.932 43.478 0.00 0.00 43.70 0.86
934 3951 4.521536 AGCTAGGCCGATGAGGTATATA 57.478 45.455 0.00 0.00 43.70 0.86
935 3952 3.390175 AGCTAGGCCGATGAGGTATAT 57.610 47.619 0.00 0.00 43.70 0.86
936 3953 2.901338 AGCTAGGCCGATGAGGTATA 57.099 50.000 0.00 0.00 43.70 1.47
1794 4832 1.377725 GGAGTCCACGAGGTACCGA 60.378 63.158 6.18 0.00 35.89 4.69
1863 4901 2.905415 TGAAGACCCGGAACCTAGTA 57.095 50.000 0.73 0.00 0.00 1.82
2014 5052 3.787001 GGAGCCCTCGAACCCCTG 61.787 72.222 0.00 0.00 0.00 4.45
2079 5117 0.759436 ACGACCTCCTGTTGTCCACT 60.759 55.000 0.00 0.00 36.89 4.00
2513 5551 3.251004 GCCGACAAGAAGCCAAATATAGG 59.749 47.826 0.00 0.00 0.00 2.57
2532 5570 3.354089 ACAAGAACATGAAAACTGCCG 57.646 42.857 0.00 0.00 0.00 5.69
2564 5602 1.336517 ACAGCAGCATCACATTTGTGC 60.337 47.619 5.81 0.00 45.25 4.57
2601 5639 3.004734 GCAACAACTAGAACCTGCAATGT 59.995 43.478 0.00 0.00 0.00 2.71
2637 5675 5.390673 GCACAGAGTCATCAGAAACTGAATG 60.391 44.000 5.57 5.53 44.04 2.67
2712 5751 0.524862 CTGAACAGATGGCAGGCAAC 59.475 55.000 0.00 0.00 0.00 4.17
2713 5752 0.609957 CCTGAACAGATGGCAGGCAA 60.610 55.000 0.00 0.00 42.30 4.52
2748 5788 0.594602 CAACATCACCACTGCACAGG 59.405 55.000 2.21 0.00 0.00 4.00
2759 5801 2.472695 TCTGGTACCAGCAACATCAC 57.527 50.000 33.39 0.00 43.31 3.06
2835 5877 2.291741 CTGACAAGAACACCAAAGAGCC 59.708 50.000 0.00 0.00 0.00 4.70
2849 5891 9.850628 ATGAAATTAAATGACATGTCTGACAAG 57.149 29.630 25.55 13.07 31.03 3.16
2946 6168 6.488683 TCATTCGGGTTTGATTTACTCTGTTT 59.511 34.615 0.00 0.00 0.00 2.83
2964 6186 5.356751 TGAATTTGGAACCTACATCATTCGG 59.643 40.000 0.00 0.00 0.00 4.30
3024 6246 5.363939 CAGGAGGATTACCATCAGAAGAAC 58.636 45.833 0.00 0.00 38.94 3.01
3083 6315 2.999355 GTCTGAAGCTTGCTAGTTCCAG 59.001 50.000 2.10 2.07 0.00 3.86
3085 6317 3.056179 AGAGTCTGAAGCTTGCTAGTTCC 60.056 47.826 2.10 0.00 0.00 3.62
3088 6320 5.930837 ATAAGAGTCTGAAGCTTGCTAGT 57.069 39.130 2.10 0.00 0.00 2.57
3089 6321 8.763356 CAATAATAAGAGTCTGAAGCTTGCTAG 58.237 37.037 2.10 0.00 0.00 3.42
3090 6322 8.478066 TCAATAATAAGAGTCTGAAGCTTGCTA 58.522 33.333 2.10 0.00 0.00 3.49
3132 6364 5.573219 TGGGAATCATTGAGAACTTCATGT 58.427 37.500 0.00 0.00 35.27 3.21


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

AutoCloner maintained by Alex Coulton.