Multiple sequence alignment - TraesCS2D01G400800

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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 TraesCS2D01G400800 chr2D 100.000 4280 0 0 1 4280 515578924 515583203 0.000000e+00 7904.0
1 TraesCS2D01G400800 chr2B 97.145 3608 83 10 93 3690 607053349 607056946 0.000000e+00 6074.0
2 TraesCS2D01G400800 chr2B 92.883 548 35 3 3735 4280 607056929 607057474 0.000000e+00 793.0
3 TraesCS2D01G400800 chr2B 95.455 44 1 1 440 483 746593582 746593624 7.680000e-08 69.4
4 TraesCS2D01G400800 chr2B 93.333 45 2 1 432 476 657793304 657793261 9.930000e-07 65.8
5 TraesCS2D01G400800 chr2A 93.348 3713 168 31 29 3717 659275911 659279568 0.000000e+00 5415.0
6 TraesCS2D01G400800 chr2A 91.595 583 30 8 3701 4280 659279789 659280355 0.000000e+00 787.0
7 TraesCS2D01G400800 chr7D 93.878 49 0 3 432 479 571471715 571471669 2.140000e-08 71.3
8 TraesCS2D01G400800 chr3D 97.561 41 0 1 443 483 420811479 420811440 7.680000e-08 69.4
9 TraesCS2D01G400800 chr3D 91.667 48 4 0 429 476 567408816 567408769 2.760000e-07 67.6
10 TraesCS2D01G400800 chr3B 97.561 41 0 1 443 483 547572947 547572908 7.680000e-08 69.4
11 TraesCS2D01G400800 chr4A 93.478 46 1 2 435 479 634836847 634836891 2.760000e-07 67.6
12 TraesCS2D01G400800 chr1A 83.099 71 8 4 408 477 511307724 511307657 1.290000e-05 62.1


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 TraesCS2D01G400800 chr2D 515578924 515583203 4279 False 7904.0 7904 100.0000 1 4280 1 chr2D.!!$F1 4279
1 TraesCS2D01G400800 chr2B 607053349 607057474 4125 False 3433.5 6074 95.0140 93 4280 2 chr2B.!!$F2 4187
2 TraesCS2D01G400800 chr2A 659275911 659280355 4444 False 3101.0 5415 92.4715 29 4280 2 chr2A.!!$F1 4251

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
307 317 1.154131 CACTCGTCCACTCTCAGCG 60.154 63.158 0.0 0.0 0.0 5.18 F
1577 1600 1.281899 GACTACAACAGCATCTCCGC 58.718 55.000 0.0 0.0 0.0 5.54 F
2141 2164 0.546122 ACAGGTCAAAGTGGTGCTGA 59.454 50.000 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1676 1699 0.321298 CACCAAGGTACTGTTCCCGG 60.321 60.0 0.0 0.0 40.86 5.73 R
2894 2918 0.577269 GTTGTGACTCGTGACTGTGC 59.423 55.0 0.0 0.0 0.00 4.57 R
3618 3647 0.168128 GCCGTGCCATCAAGTAACAC 59.832 55.0 0.0 0.0 0.00 3.32 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
23 24 6.174720 TGAGTTTATGGGTATCATGACCTC 57.825 41.667 0.00 0.00 39.66 3.85
24 25 5.905331 TGAGTTTATGGGTATCATGACCTCT 59.095 40.000 0.00 0.00 39.66 3.69
25 26 6.386927 TGAGTTTATGGGTATCATGACCTCTT 59.613 38.462 0.00 0.00 39.66 2.85
26 27 7.092444 TGAGTTTATGGGTATCATGACCTCTTT 60.092 37.037 0.00 0.00 39.66 2.52
27 28 8.331931 AGTTTATGGGTATCATGACCTCTTTA 57.668 34.615 0.00 0.00 39.66 1.85
44 45 9.538508 GACCTCTTTACTTTTGTTAGACTTACA 57.461 33.333 0.00 0.00 0.00 2.41
165 171 5.799213 CTCTGGTACTGATTTTTCAGGTCT 58.201 41.667 7.80 0.00 41.76 3.85
185 191 4.639310 GTCTCAGATCTCCAAATTGCATGT 59.361 41.667 0.00 0.00 0.00 3.21
186 192 5.125097 GTCTCAGATCTCCAAATTGCATGTT 59.875 40.000 0.00 0.00 0.00 2.71
187 193 5.713389 TCTCAGATCTCCAAATTGCATGTTT 59.287 36.000 0.00 0.00 0.00 2.83
188 194 6.209986 TCTCAGATCTCCAAATTGCATGTTTT 59.790 34.615 0.00 0.00 0.00 2.43
307 317 1.154131 CACTCGTCCACTCTCAGCG 60.154 63.158 0.00 0.00 0.00 5.18
370 382 1.626686 CTCTCCACAGTCCACACTCT 58.373 55.000 0.00 0.00 0.00 3.24
386 398 3.445450 ACACTCTCACAGTATACAGCCTG 59.555 47.826 5.50 0.00 32.21 4.85
452 464 4.058817 GCATCATTTTAGTACTCCCTCCG 58.941 47.826 0.00 0.00 0.00 4.63
465 477 6.960542 AGTACTCCCTCCGATCCATATTAATT 59.039 38.462 0.00 0.00 0.00 1.40
625 646 5.773575 CAGTAGAACTGCTTACTGAAGTCA 58.226 41.667 5.90 0.00 39.62 3.41
629 650 5.293560 AGAACTGCTTACTGAAGTCAACTC 58.706 41.667 0.00 0.00 32.06 3.01
722 743 5.542779 CCTGTAGCAAGTACATTCCTATCC 58.457 45.833 0.00 0.00 40.99 2.59
774 795 4.947388 TCTTGATATTGGTTTCTTTCCCGG 59.053 41.667 0.00 0.00 0.00 5.73
903 924 3.764434 AGAAGTAGATCGCTCAAGGTCAA 59.236 43.478 0.00 0.00 0.00 3.18
1577 1600 1.281899 GACTACAACAGCATCTCCGC 58.718 55.000 0.00 0.00 0.00 5.54
1676 1699 3.015312 GCTCTCCACCGGTGTACCC 62.015 68.421 31.80 13.00 0.00 3.69
2095 2118 8.847196 TCTACAATCTACCTGTGTACATATGAC 58.153 37.037 10.38 4.14 0.00 3.06
2141 2164 0.546122 ACAGGTCAAAGTGGTGCTGA 59.454 50.000 0.00 0.00 0.00 4.26
2229 2252 6.436027 AGATACTTCAAGTAGATCACCTCCA 58.564 40.000 3.12 0.00 33.66 3.86
2676 2700 7.602644 CCATGTAAATACGTCCTGTAGCATAAT 59.397 37.037 0.00 0.00 36.25 1.28
2677 2701 9.634163 CATGTAAATACGTCCTGTAGCATAATA 57.366 33.333 0.00 0.00 36.25 0.98
2689 2713 9.725019 TCCTGTAGCATAATAAAGATACAATGG 57.275 33.333 0.00 0.00 36.35 3.16
2782 2806 0.894141 TTGTTGGCGGATTTCCATGG 59.106 50.000 4.97 4.97 35.14 3.66
3010 3035 5.748402 TGATTTGGACAGCTATTGAGTGAT 58.252 37.500 0.00 0.00 0.00 3.06
3059 3087 6.259608 CGAGGTAGCATTGAATTTCAGAGATT 59.740 38.462 0.00 0.00 0.00 2.40
3174 3202 4.141597 GGTAAAGAGGAGGATTTGAGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
3314 3342 5.235186 CGCATGTTTCCTTTATCACCTCTAG 59.765 44.000 0.00 0.00 0.00 2.43
3345 3373 1.000717 CACGAATTGGTTGGGGTGTTC 60.001 52.381 0.00 0.00 0.00 3.18
3357 3385 1.269726 GGGGTGTTCACGACTTTACGA 60.270 52.381 0.00 0.00 37.03 3.43
3435 3463 2.319136 TCCGGTGTATTGTATGGTGC 57.681 50.000 0.00 0.00 0.00 5.01
3490 3518 4.762251 GGTCTTAGATCTTTGGCTTTGTGT 59.238 41.667 0.00 0.00 0.00 3.72
3501 3529 1.135228 GGCTTTGTGTGAAAACGGTGT 60.135 47.619 0.00 0.00 0.00 4.16
3515 3543 0.530650 CGGTGTCGATGCAGGCTTAT 60.531 55.000 0.00 0.00 39.00 1.73
3535 3563 3.965292 TCACTCGCTATTAGGAGAACG 57.035 47.619 13.08 0.44 34.40 3.95
3542 3571 6.658391 ACTCGCTATTAGGAGAACGGTATAAT 59.342 38.462 13.08 0.00 34.40 1.28
3618 3647 6.171921 TGGCATTTTACCCTTTGATTTGATG 58.828 36.000 0.00 0.00 0.00 3.07
3621 3650 6.650390 GCATTTTACCCTTTGATTTGATGTGT 59.350 34.615 0.00 0.00 0.00 3.72
3640 3669 0.676466 TTACTTGATGGCACGGCTGG 60.676 55.000 0.00 0.00 0.00 4.85
3803 4066 2.943449 GACCTGCGTCTAAACTAGCT 57.057 50.000 0.00 0.00 35.99 3.32
3805 4068 4.571372 GACCTGCGTCTAAACTAGCTAT 57.429 45.455 0.00 0.00 35.99 2.97
3806 4069 4.934515 GACCTGCGTCTAAACTAGCTATT 58.065 43.478 0.00 0.00 35.99 1.73
3848 4118 6.352516 ACATCTGGACTTCTGATAACCATTC 58.647 40.000 0.00 0.00 33.52 2.67
3855 4125 0.813610 CTGATAACCATTCGGCCGCA 60.814 55.000 23.51 11.40 34.57 5.69
3858 4128 0.179032 ATAACCATTCGGCCGCATCA 60.179 50.000 23.51 0.00 34.57 3.07
3874 4144 2.093341 GCATCATGGGCCTGTTTGAAAT 60.093 45.455 4.53 0.00 0.00 2.17
3939 4210 2.766313 GCCTTTTAGCCCTTGTTTTGG 58.234 47.619 0.00 0.00 0.00 3.28
4155 4429 8.928733 GTTAGATCGTTAACAACAACTTATGGA 58.071 33.333 6.39 0.00 34.43 3.41
4211 4485 6.391227 AAGTGGTTTGAGTGGATTGTAAAG 57.609 37.500 0.00 0.00 0.00 1.85
4237 4511 8.752254 GTTCTTTCATTTTCCCTTTTAAACTCG 58.248 33.333 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.905331 AGAGGTCATGATACCCATAAACTCA 59.095 40.000 0.00 0.00 40.71 3.41
1 2 6.426646 AGAGGTCATGATACCCATAAACTC 57.573 41.667 0.00 0.00 40.71 3.01
2 3 6.831664 AAGAGGTCATGATACCCATAAACT 57.168 37.500 0.00 0.00 40.71 2.66
3 4 8.211629 AGTAAAGAGGTCATGATACCCATAAAC 58.788 37.037 0.00 0.00 40.71 2.01
4 5 8.331931 AGTAAAGAGGTCATGATACCCATAAA 57.668 34.615 0.00 0.00 40.71 1.40
5 6 7.931015 AGTAAAGAGGTCATGATACCCATAA 57.069 36.000 0.00 0.00 40.71 1.90
6 7 7.931015 AAGTAAAGAGGTCATGATACCCATA 57.069 36.000 0.00 0.00 40.71 2.74
7 8 6.831664 AAGTAAAGAGGTCATGATACCCAT 57.168 37.500 0.00 0.00 40.71 4.00
8 9 6.636454 AAAGTAAAGAGGTCATGATACCCA 57.364 37.500 0.00 0.00 40.71 4.51
9 10 6.884836 ACAAAAGTAAAGAGGTCATGATACCC 59.115 38.462 0.00 0.00 40.71 3.69
10 11 7.923414 ACAAAAGTAAAGAGGTCATGATACC 57.077 36.000 0.00 0.00 40.06 2.73
13 14 9.220767 GTCTAACAAAAGTAAAGAGGTCATGAT 57.779 33.333 0.00 0.00 0.00 2.45
14 15 8.429641 AGTCTAACAAAAGTAAAGAGGTCATGA 58.570 33.333 0.00 0.00 0.00 3.07
15 16 8.608844 AGTCTAACAAAAGTAAAGAGGTCATG 57.391 34.615 0.00 0.00 0.00 3.07
17 18 9.538508 GTAAGTCTAACAAAAGTAAAGAGGTCA 57.461 33.333 0.00 0.00 0.00 4.02
18 19 9.538508 TGTAAGTCTAACAAAAGTAAAGAGGTC 57.461 33.333 0.00 0.00 0.00 3.85
19 20 9.543783 CTGTAAGTCTAACAAAAGTAAAGAGGT 57.456 33.333 0.00 0.00 0.00 3.85
165 171 5.988310 AAACATGCAATTTGGAGATCTGA 57.012 34.783 0.00 0.00 0.00 3.27
307 317 1.620323 AGAAAGACCCTGCCATTTTGC 59.380 47.619 0.00 0.00 0.00 3.68
370 382 3.260632 TCTTTGCAGGCTGTATACTGTGA 59.739 43.478 17.16 0.00 37.07 3.58
386 398 2.841442 AGGGACACTACAGTCTTTGC 57.159 50.000 0.00 0.00 38.57 3.68
481 493 3.639561 TCCCTGAAAAGTTTAAAGTGGCC 59.360 43.478 0.00 0.00 0.00 5.36
492 504 8.934023 TTTGTACTCATATTTCCCTGAAAAGT 57.066 30.769 0.00 0.00 35.11 2.66
550 562 1.728971 CAATGTCGAGTGACTCAAGCC 59.271 52.381 13.67 0.00 45.70 4.35
551 563 2.156504 CACAATGTCGAGTGACTCAAGC 59.843 50.000 13.67 2.48 45.70 4.01
625 646 1.591594 CGTCGTGCACCACAGAGTT 60.592 57.895 15.06 0.00 33.40 3.01
722 743 8.749841 TTTTGGTGGAAAATCATTATGTTACG 57.250 30.769 0.00 0.00 0.00 3.18
774 795 6.000840 GGAGGGAATTTCAGATCCTAATGAC 58.999 44.000 0.00 0.00 35.95 3.06
859 880 7.762588 TCTAGTAATCACTAATCAGTAGGGC 57.237 40.000 0.00 0.00 36.81 5.19
903 924 6.655078 ACTTTTACTTGGCATGAGTTCATT 57.345 33.333 7.45 0.00 33.61 2.57
1476 1499 1.215382 CATCACCGTCCTCGCTTCA 59.785 57.895 0.00 0.00 35.54 3.02
1577 1600 4.701651 TGTCAAAACCATAGGAAGCTGATG 59.298 41.667 0.00 0.00 0.00 3.07
1676 1699 0.321298 CACCAAGGTACTGTTCCCGG 60.321 60.000 0.00 0.00 40.86 5.73
2095 2118 2.559668 TCCTTGCCTGCAAATTCAAGAG 59.440 45.455 14.59 7.95 38.45 2.85
2141 2164 7.922382 TGATTTTCTCTTCTTAGGATCACCTT 58.078 34.615 0.00 0.00 45.36 3.50
2676 2700 6.370442 CGGTGTGAGTTTCCATTGTATCTTTA 59.630 38.462 0.00 0.00 0.00 1.85
2677 2701 5.181245 CGGTGTGAGTTTCCATTGTATCTTT 59.819 40.000 0.00 0.00 0.00 2.52
2678 2702 4.695455 CGGTGTGAGTTTCCATTGTATCTT 59.305 41.667 0.00 0.00 0.00 2.40
2689 2713 1.259770 GAAACCGTCGGTGTGAGTTTC 59.740 52.381 19.67 12.86 39.44 2.78
2782 2806 6.525976 CCTCATTCTCGAAAGAAAAAGAATGC 59.474 38.462 15.63 0.00 44.49 3.56
2894 2918 0.577269 GTTGTGACTCGTGACTGTGC 59.423 55.000 0.00 0.00 0.00 4.57
3010 3035 5.692115 TTGTGCTATTCTTCATGTAGGGA 57.308 39.130 0.00 0.00 0.00 4.20
3069 3097 7.198306 GTTTGAGACGATTTAGAAAAGGGAA 57.802 36.000 0.00 0.00 0.00 3.97
3089 3117 5.447279 GCAAGTCATTACCAGGTATCGTTTG 60.447 44.000 0.00 4.00 0.00 2.93
3314 3342 1.398451 CCAATTCGTGAGCGTGACAAC 60.398 52.381 0.00 0.00 39.49 3.32
3357 3385 3.124636 CGCAAGCAAAATAACCGACTACT 59.875 43.478 0.00 0.00 0.00 2.57
3413 3441 3.630312 GCACCATACAATACACCGGAAAT 59.370 43.478 9.46 0.00 0.00 2.17
3435 3463 6.387041 TGTTATTCTAGACTACACATCGGG 57.613 41.667 0.00 0.00 0.00 5.14
3490 3518 0.865111 CTGCATCGACACCGTTTTCA 59.135 50.000 0.00 0.00 37.05 2.69
3501 3529 1.269257 CGAGTGATAAGCCTGCATCGA 60.269 52.381 0.00 0.00 0.00 3.59
3515 3543 2.617308 CCGTTCTCCTAATAGCGAGTGA 59.383 50.000 0.00 0.00 0.00 3.41
3535 3563 8.565416 CCTTCAAAAGACGGGAATAATTATACC 58.435 37.037 0.00 3.94 0.00 2.73
3542 3571 5.378332 TCAACCTTCAAAAGACGGGAATAA 58.622 37.500 0.00 0.00 0.00 1.40
3547 3576 2.034179 GGTTCAACCTTCAAAAGACGGG 59.966 50.000 0.00 0.00 34.73 5.28
3618 3647 0.168128 GCCGTGCCATCAAGTAACAC 59.832 55.000 0.00 0.00 0.00 3.32
3621 3650 0.676466 CCAGCCGTGCCATCAAGTAA 60.676 55.000 0.00 0.00 0.00 2.24
3717 3749 7.639945 TCCTCTTTTGATTCTCGAAAAGAAAC 58.360 34.615 8.58 0.00 46.85 2.78
3718 3750 7.801716 TCCTCTTTTGATTCTCGAAAAGAAA 57.198 32.000 8.58 0.00 46.85 2.52
3759 4022 1.686355 TGGCCCATAATTTGCCTACG 58.314 50.000 0.00 0.00 45.56 3.51
3800 4063 4.214971 CGCAAATGAGAATGGCTAATAGCT 59.785 41.667 12.41 0.00 41.99 3.32
3801 4064 4.214119 TCGCAAATGAGAATGGCTAATAGC 59.786 41.667 3.17 3.17 41.46 2.97
3802 4065 5.237127 TGTCGCAAATGAGAATGGCTAATAG 59.763 40.000 0.00 0.00 0.00 1.73
3803 4066 5.122519 TGTCGCAAATGAGAATGGCTAATA 58.877 37.500 0.00 0.00 0.00 0.98
3804 4067 3.947196 TGTCGCAAATGAGAATGGCTAAT 59.053 39.130 0.00 0.00 0.00 1.73
3805 4068 3.342719 TGTCGCAAATGAGAATGGCTAA 58.657 40.909 0.00 0.00 0.00 3.09
3806 4069 2.984562 TGTCGCAAATGAGAATGGCTA 58.015 42.857 0.00 0.00 0.00 3.93
3855 4125 2.093341 GCATTTCAAACAGGCCCATGAT 60.093 45.455 0.00 0.00 0.00 2.45
3858 4128 1.276989 CTGCATTTCAAACAGGCCCAT 59.723 47.619 0.00 0.00 0.00 4.00
3991 4262 5.499004 AGCACATACTCCCTCTGTAAAAA 57.501 39.130 0.00 0.00 0.00 1.94
4175 4449 5.350633 TCAAACCACTTTCTTGCATTTCTG 58.649 37.500 0.00 0.00 0.00 3.02
4211 4485 8.752254 CGAGTTTAAAAGGGAAAATGAAAGAAC 58.248 33.333 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.