Multiple sequence alignment - TraesCS4D01G086300

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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 TraesCS4D01G086300 chr4D 100.000 3170 0 0 1 3170 61850477 61853646 0.000000e+00 5854.0
1 TraesCS4D01G086300 chr4B 91.224 3236 110 56 43 3145 90894159 90890965 0.000000e+00 4242.0
2 TraesCS4D01G086300 chr4B 100.000 33 0 0 1 33 90894220 90894188 9.490000e-06 62.1
3 TraesCS4D01G086300 chr4A 90.053 3026 98 64 276 3145 535034088 535037066 0.000000e+00 3733.0
4 TraesCS4D01G086300 chr4A 88.211 246 4 8 1 230 535033851 535034087 1.450000e-68 270.0
5 TraesCS4D01G086300 chr5A 81.959 194 35 0 1825 2018 459775651 459775458 7.030000e-37 165.0
6 TraesCS4D01G086300 chr5A 79.348 184 34 4 1821 2002 443289623 443289804 3.320000e-25 126.0
7 TraesCS4D01G086300 chr5A 87.500 80 8 2 1339 1417 443289054 443289132 1.210000e-14 91.6
8 TraesCS4D01G086300 chr5B 80.435 184 32 4 1821 2002 401667829 401668010 1.530000e-28 137.0
9 TraesCS4D01G086300 chr5B 77.564 156 25 9 1339 1486 401667251 401667404 5.630000e-13 86.1
10 TraesCS4D01G086300 chr5D 79.891 184 33 4 1821 2002 342175354 342175535 7.130000e-27 132.0
11 TraesCS4D01G086300 chr5D 76.374 182 31 11 1313 1486 342174761 342174938 1.570000e-13 87.9
12 TraesCS4D01G086300 chr1B 78.488 172 37 0 1828 1999 667750250 667750421 2.580000e-21 113.0
13 TraesCS4D01G086300 chr1D 77.907 172 38 0 1828 1999 479540798 479540969 1.200000e-19 108.0
14 TraesCS4D01G086300 chr3D 77.326 172 37 2 1828 1998 305622630 305622800 2.010000e-17 100.0


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 TraesCS4D01G086300 chr4D 61850477 61853646 3169 False 5854.00 5854 100.000 1 3170 1 chr4D.!!$F1 3169
1 TraesCS4D01G086300 chr4B 90890965 90894220 3255 True 2152.05 4242 95.612 1 3145 2 chr4B.!!$R1 3144
2 TraesCS4D01G086300 chr4A 535033851 535037066 3215 False 2001.50 3733 89.132 1 3145 2 chr4A.!!$F1 3144

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
415 461 0.035458 TCCACACACACACACACACA 59.965 50.0 0.0 0.0 0.0 3.72 F
416 462 0.167908 CCACACACACACACACACAC 59.832 55.0 0.0 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2123 0.107459 GCATCCAGACCTTGAGGACC 60.107 60.000 3.59 0.0 38.94 4.46 R
2211 2397 2.131183 CTAACGCTAGCAGAATCAGCC 58.869 52.381 16.45 0.0 31.43 4.85 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
41 65 1.420891 CTAGACCCTAGACGCCCTAGT 59.579 57.143 10.40 0.00 42.63 2.57
70 94 0.607489 GAAGCTGCAAAGGCTGGAGA 60.607 55.000 1.02 0.00 46.07 3.71
71 95 0.608582 AAGCTGCAAAGGCTGGAGAG 60.609 55.000 1.02 0.00 46.07 3.20
202 238 0.250467 TCCTCCACTGTTCAAGCAGC 60.250 55.000 0.00 0.00 39.96 5.25
225 261 3.470709 CAGTGCAGGACAAGAAGAAGAA 58.529 45.455 0.00 0.00 0.00 2.52
226 262 3.497640 CAGTGCAGGACAAGAAGAAGAAG 59.502 47.826 0.00 0.00 0.00 2.85
269 305 7.062371 GTCTCTCTATCACACACATAAACACAC 59.938 40.741 0.00 0.00 0.00 3.82
333 371 4.866921 GCTTAGCTAGCTCTTAGTCCTTC 58.133 47.826 23.26 0.98 46.77 3.46
334 372 4.583073 GCTTAGCTAGCTCTTAGTCCTTCT 59.417 45.833 23.26 0.00 46.77 2.85
408 454 2.831685 TAGTCCATCCACACACACAC 57.168 50.000 0.00 0.00 0.00 3.82
410 456 0.944386 GTCCATCCACACACACACAC 59.056 55.000 0.00 0.00 0.00 3.82
412 458 0.662619 CCATCCACACACACACACAC 59.337 55.000 0.00 0.00 0.00 3.82
413 459 1.377536 CATCCACACACACACACACA 58.622 50.000 0.00 0.00 0.00 3.72
414 460 1.063912 CATCCACACACACACACACAC 59.936 52.381 0.00 0.00 0.00 3.82
415 461 0.035458 TCCACACACACACACACACA 59.965 50.000 0.00 0.00 0.00 3.72
416 462 0.167908 CCACACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
417 463 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
418 464 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
419 465 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
420 466 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
421 467 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
422 468 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
423 469 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
424 470 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
443 489 1.421646 ACAAACCACTCCTAGCAGCTT 59.578 47.619 0.00 0.00 0.00 3.74
455 501 4.245054 CAGCTTGCTTGCTTGCTG 57.755 55.556 18.98 18.98 45.15 4.41
506 575 0.759346 GCATCCACGGGAGGAGTAAT 59.241 55.000 8.51 0.00 41.90 1.89
517 586 2.074729 AGGAGTAATCCCTCACTCGG 57.925 55.000 5.39 0.00 41.75 4.63
566 651 4.040047 ACTGTTCATCATCCATCCTACCA 58.960 43.478 0.00 0.00 0.00 3.25
590 675 3.054802 CCTTCCTTCCTGCATCTAGTTGT 60.055 47.826 2.85 0.00 0.00 3.32
627 712 4.130857 GCTACCCATCTTCTAAAGCTTCC 58.869 47.826 0.00 0.00 0.00 3.46
630 715 2.511637 CCCATCTTCTAAAGCTTCCCCT 59.488 50.000 0.00 0.00 0.00 4.79
807 894 5.181748 GGCTAGATTATGTATGCTCTTGGG 58.818 45.833 0.00 0.00 0.00 4.12
2032 2190 3.905678 CGCTCCCTACCTCGCCTG 61.906 72.222 0.00 0.00 0.00 4.85
2052 2210 3.108289 CAGCCGCAGTCACAGTCG 61.108 66.667 0.00 0.00 0.00 4.18
2211 2397 4.101790 GTCAACGGCGCCATGGTG 62.102 66.667 28.98 21.43 0.00 4.17
2327 2517 5.684550 AAAAACAAACCCGAGTCTATCAC 57.315 39.130 0.00 0.00 0.00 3.06
2336 2526 3.161067 CCGAGTCTATCACCATCTCCAT 58.839 50.000 0.00 0.00 0.00 3.41
2556 2777 6.769341 TCATGGATCAGAGGTTGTATGAAATG 59.231 38.462 0.00 0.00 27.80 2.32
2610 2832 1.213296 TCAGTTCCCTGGGCTAATCC 58.787 55.000 8.22 0.00 39.31 3.01
2616 2838 1.227674 CCTGGGCTAATCCGCAGAC 60.228 63.158 7.66 0.00 36.07 3.51
2625 2847 3.308323 GCTAATCCGCAGACTCTGAAAAG 59.692 47.826 10.45 0.00 32.44 2.27
2627 2849 3.685139 ATCCGCAGACTCTGAAAAGAA 57.315 42.857 10.45 0.00 32.44 2.52
2809 3036 1.348250 CGGCGATGTGAATTCACCG 59.652 57.895 30.66 27.16 45.88 4.94
2824 3051 1.893808 ACCGCTCACAAGCCACAAG 60.894 57.895 0.00 0.00 46.34 3.16
2825 3052 2.253452 CGCTCACAAGCCACAAGC 59.747 61.111 0.00 0.00 46.34 4.01
2826 3053 2.647297 GCTCACAAGCCACAAGCC 59.353 61.111 0.00 0.00 45.47 4.35
2827 3054 2.195567 GCTCACAAGCCACAAGCCA 61.196 57.895 0.00 0.00 45.47 4.75
2828 3055 1.656441 CTCACAAGCCACAAGCCAC 59.344 57.895 0.00 0.00 45.47 5.01
2830 3057 0.682532 TCACAAGCCACAAGCCACAA 60.683 50.000 0.00 0.00 45.47 3.33
2834 3061 0.746659 AAGCCACAAGCCACAAAGAC 59.253 50.000 0.00 0.00 45.47 3.01
2836 3063 0.459489 GCCACAAGCCACAAAGACAA 59.541 50.000 0.00 0.00 34.35 3.18
2837 3064 1.802508 GCCACAAGCCACAAAGACAAC 60.803 52.381 0.00 0.00 34.35 3.32
2838 3065 1.533756 CCACAAGCCACAAAGACAACG 60.534 52.381 0.00 0.00 0.00 4.10
2839 3066 1.400142 CACAAGCCACAAAGACAACGA 59.600 47.619 0.00 0.00 0.00 3.85
2849 3076 3.380320 ACAAAGACAACGAAAAGGGAAGG 59.620 43.478 0.00 0.00 0.00 3.46
2892 3141 5.859648 TCGGGAGCGTGAAAATTAAAATTTC 59.140 36.000 9.15 9.15 37.62 2.17
2894 3143 5.061684 GGGAGCGTGAAAATTAAAATTTCGG 59.938 40.000 1.36 7.57 39.17 4.30
2933 3182 5.441718 TTTGGAGCAGATGATAGTCCTTT 57.558 39.130 0.00 0.00 0.00 3.11
3036 3290 3.736224 AGGGGAGCATGTGGCCAG 61.736 66.667 5.11 0.00 46.50 4.85
3136 3390 3.868077 CCTGCAGGAGATTTTTCTACGAG 59.132 47.826 29.88 0.00 37.39 4.18
3139 3393 6.032956 TGCAGGAGATTTTTCTACGAGTTA 57.967 37.500 0.00 0.00 0.00 2.24
3145 3399 9.589111 AGGAGATTTTTCTACGAGTTATTCTTC 57.411 33.333 0.00 0.00 0.00 2.87
3146 3400 9.589111 GGAGATTTTTCTACGAGTTATTCTTCT 57.411 33.333 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 65 1.114119 TTGCAGCTTCCACCATTGCA 61.114 50.000 0.00 0.00 42.44 4.08
70 94 1.688211 GAAGGAAGGAGCAAGGCCT 59.312 57.895 0.00 0.00 37.35 5.19
71 95 1.379176 GGAAGGAAGGAGCAAGGCC 60.379 63.158 0.00 0.00 0.00 5.19
202 238 0.601046 TCTTCTTGTCCTGCACTGCG 60.601 55.000 0.00 0.00 0.00 5.18
237 273 5.755849 TGTGTGTGATAGAGAGACCATCTA 58.244 41.667 0.00 0.00 38.84 1.98
250 286 6.927294 TGTTGTGTGTTTATGTGTGTGATA 57.073 33.333 0.00 0.00 0.00 2.15
269 305 3.128242 GCTTCCTTCATGGACAGATGTTG 59.872 47.826 0.00 0.00 46.14 3.33
333 371 0.764890 TTCCTCTCCCACACACCAAG 59.235 55.000 0.00 0.00 0.00 3.61
334 372 0.764890 CTTCCTCTCCCACACACCAA 59.235 55.000 0.00 0.00 0.00 3.67
408 454 2.315011 GTTTGTGTGTGTGTGTGTGTG 58.685 47.619 0.00 0.00 0.00 3.82
410 456 1.268079 TGGTTTGTGTGTGTGTGTGTG 59.732 47.619 0.00 0.00 0.00 3.82
412 458 1.539388 AGTGGTTTGTGTGTGTGTGTG 59.461 47.619 0.00 0.00 0.00 3.82
413 459 1.810151 GAGTGGTTTGTGTGTGTGTGT 59.190 47.619 0.00 0.00 0.00 3.72
414 460 1.132262 GGAGTGGTTTGTGTGTGTGTG 59.868 52.381 0.00 0.00 0.00 3.82
415 461 1.004277 AGGAGTGGTTTGTGTGTGTGT 59.996 47.619 0.00 0.00 0.00 3.72
416 462 1.750193 AGGAGTGGTTTGTGTGTGTG 58.250 50.000 0.00 0.00 0.00 3.82
417 463 2.745152 GCTAGGAGTGGTTTGTGTGTGT 60.745 50.000 0.00 0.00 0.00 3.72
418 464 1.873591 GCTAGGAGTGGTTTGTGTGTG 59.126 52.381 0.00 0.00 0.00 3.82
419 465 1.488812 TGCTAGGAGTGGTTTGTGTGT 59.511 47.619 0.00 0.00 0.00 3.72
420 466 2.146342 CTGCTAGGAGTGGTTTGTGTG 58.854 52.381 2.51 0.00 0.00 3.82
421 467 1.543429 GCTGCTAGGAGTGGTTTGTGT 60.543 52.381 13.28 0.00 0.00 3.72
422 468 1.160137 GCTGCTAGGAGTGGTTTGTG 58.840 55.000 13.28 0.00 0.00 3.33
423 469 1.059913 AGCTGCTAGGAGTGGTTTGT 58.940 50.000 13.28 0.00 0.00 2.83
424 470 1.808945 CAAGCTGCTAGGAGTGGTTTG 59.191 52.381 13.28 8.82 0.00 2.93
506 575 1.906824 AAAGCGACCGAGTGAGGGA 60.907 57.895 0.00 0.00 35.02 4.20
514 583 3.353836 GGCAAGCAAAGCGACCGA 61.354 61.111 0.00 0.00 0.00 4.69
515 584 3.192954 TTGGCAAGCAAAGCGACCG 62.193 57.895 0.00 0.00 0.00 4.79
516 585 1.372128 CTTGGCAAGCAAAGCGACC 60.372 57.895 15.25 0.00 0.00 4.79
517 586 0.030638 TTCTTGGCAAGCAAAGCGAC 59.969 50.000 22.31 0.00 0.00 5.19
566 651 3.663198 ACTAGATGCAGGAAGGAAGGAT 58.337 45.455 0.00 0.00 0.00 3.24
590 675 1.819288 GGTAGCTGCTGTACTCACTCA 59.181 52.381 13.43 0.00 0.00 3.41
627 712 2.916269 AGAAGAGAAAAGGGAAGGAGGG 59.084 50.000 0.00 0.00 0.00 4.30
630 715 7.017651 ACAAGATTAGAAGAGAAAAGGGAAGGA 59.982 37.037 0.00 0.00 0.00 3.36
751 838 9.541143 TCAATTACACCATACATACACACATAG 57.459 33.333 0.00 0.00 0.00 2.23
757 844 6.511767 GCTGCTCAATTACACCATACATACAC 60.512 42.308 0.00 0.00 0.00 2.90
807 894 4.518970 TCAAGAAGATACCACTTGCAAACC 59.481 41.667 0.00 0.00 40.20 3.27
1764 1919 2.087462 CTCTGCCGTCGCCCATGATA 62.087 60.000 0.00 0.00 0.00 2.15
1965 2123 0.107459 GCATCCAGACCTTGAGGACC 60.107 60.000 3.59 0.00 38.94 4.46
2036 2194 2.640302 ATCGACTGTGACTGCGGCT 61.640 57.895 0.00 0.00 0.00 5.52
2211 2397 2.131183 CTAACGCTAGCAGAATCAGCC 58.869 52.381 16.45 0.00 31.43 4.85
2349 2542 6.884295 CCCAACCTTATGACAAGATAAACAGA 59.116 38.462 0.00 0.00 0.00 3.41
2556 2777 9.399403 GGAGAAATTGTAAACAAGTCAGAATTC 57.601 33.333 0.00 0.00 39.47 2.17
2597 2818 2.111878 CTGCGGATTAGCCCAGGG 59.888 66.667 0.00 0.00 33.69 4.45
2610 2832 4.747108 TCTCTTTTCTTTTCAGAGTCTGCG 59.253 41.667 15.72 4.04 36.27 5.18
2616 2838 6.488006 TCCCATGTTCTCTTTTCTTTTCAGAG 59.512 38.462 0.00 0.00 36.19 3.35
2625 2847 4.789012 TTGCATCCCATGTTCTCTTTTC 57.211 40.909 0.00 0.00 0.00 2.29
2627 2849 3.703052 GGATTGCATCCCATGTTCTCTTT 59.297 43.478 0.00 0.00 43.88 2.52
2649 2872 2.182516 AGATACAAGACCTGGGGAGG 57.817 55.000 0.00 0.00 0.00 4.30
2824 3051 2.459934 CCTTTTCGTTGTCTTTGTGGC 58.540 47.619 0.00 0.00 0.00 5.01
2825 3052 2.685897 TCCCTTTTCGTTGTCTTTGTGG 59.314 45.455 0.00 0.00 0.00 4.17
2826 3053 4.351192 CTTCCCTTTTCGTTGTCTTTGTG 58.649 43.478 0.00 0.00 0.00 3.33
2827 3054 3.380320 CCTTCCCTTTTCGTTGTCTTTGT 59.620 43.478 0.00 0.00 0.00 2.83
2828 3055 3.243401 CCCTTCCCTTTTCGTTGTCTTTG 60.243 47.826 0.00 0.00 0.00 2.77
2830 3057 2.173996 TCCCTTCCCTTTTCGTTGTCTT 59.826 45.455 0.00 0.00 0.00 3.01
2834 3061 2.561478 TCTCCCTTCCCTTTTCGTTG 57.439 50.000 0.00 0.00 0.00 4.10
2836 3063 1.560146 GGATCTCCCTTCCCTTTTCGT 59.440 52.381 0.00 0.00 0.00 3.85
2837 3064 1.840635 AGGATCTCCCTTCCCTTTTCG 59.159 52.381 0.00 0.00 44.85 3.46
2849 3076 3.873952 CCGAATTCTTGACAAGGATCTCC 59.126 47.826 15.13 4.75 0.00 3.71
2894 3143 1.539827 CAAATGGAGAAACGGGGACAC 59.460 52.381 0.00 0.00 0.00 3.67
2974 3227 3.243301 CCCCAAGAATGATTGATTGCTCG 60.243 47.826 0.00 0.00 31.55 5.03
2975 3228 3.492137 GCCCCAAGAATGATTGATTGCTC 60.492 47.826 0.00 0.00 31.55 4.26
2976 3229 2.433239 GCCCCAAGAATGATTGATTGCT 59.567 45.455 0.00 0.00 31.55 3.91
2977 3230 2.484241 GGCCCCAAGAATGATTGATTGC 60.484 50.000 0.00 0.00 31.55 3.56


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

AutoCloner maintained by Alex Coulton.