Multiple sequence alignment - TraesCS3A01G201400

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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 TraesCS3A01G201400 chr3A 100.000 2993 0 0 1 2993 336599249 336596257 0.000000e+00 5528
1 TraesCS3A01G201400 chr3A 93.846 130 7 1 2410 2539 336596451 336596323 8.470000e-46 195
2 TraesCS3A01G201400 chr3A 93.846 130 7 1 2799 2927 336596840 336596711 8.470000e-46 195
3 TraesCS3A01G201400 chr3A 94.393 107 3 1 2264 2370 336596558 336596455 8.590000e-36 161
4 TraesCS3A01G201400 chr3A 94.393 107 3 1 2692 2795 336596986 336596880 8.590000e-36 161
5 TraesCS3A01G201400 chr3D 96.036 2800 64 19 1 2795 253520890 253518133 0.000000e+00 4512
6 TraesCS3A01G201400 chr3D 92.657 572 22 2 2224 2795 253518266 253517715 0.000000e+00 806
7 TraesCS3A01G201400 chr3D 90.217 276 17 3 2264 2539 253517818 253517553 4.750000e-93 351
8 TraesCS3A01G201400 chr3D 95.679 162 6 1 2796 2956 253517685 253517524 2.960000e-65 259
9 TraesCS3A01G201400 chr3D 93.023 129 8 1 2799 2926 253518100 253517972 1.420000e-43 187
10 TraesCS3A01G201400 chr3D 93.023 129 8 1 2799 2926 253518492 253518364 1.420000e-43 187
11 TraesCS3A01G201400 chr3D 94.393 107 3 1 2692 2795 253518631 253518525 8.590000e-36 161
12 TraesCS3A01G201400 chr3B 95.846 1950 44 9 856 2795 309614951 309616873 0.000000e+00 3118
13 TraesCS3A01G201400 chr3B 96.283 861 26 1 1 861 309420633 309421487 0.000000e+00 1408
14 TraesCS3A01G201400 chr3B 89.568 278 17 4 2264 2539 309616770 309617037 2.860000e-90 342
15 TraesCS3A01G201400 chr3B 93.902 164 7 3 2796 2956 309616903 309617066 8.290000e-61 244
16 TraesCS3A01G201400 chr3B 93.182 132 7 2 2796 2926 309616486 309616616 3.040000e-45 193
17 TraesCS3A01G201400 chr3B 94.231 104 4 1 2692 2795 309616355 309616456 1.110000e-34 158


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 TraesCS3A01G201400 chr3A 336596257 336599249 2992 True 1248.000000 5528 95.295600 1 2993 5 chr3A.!!$R1 2992
1 TraesCS3A01G201400 chr3D 253517524 253520890 3366 True 923.285714 4512 93.575429 1 2956 7 chr3D.!!$R1 2955
2 TraesCS3A01G201400 chr3B 309420633 309421487 854 False 1408.000000 1408 96.283000 1 861 1 chr3B.!!$F1 860
3 TraesCS3A01G201400 chr3B 309614951 309617066 2115 False 811.000000 3118 93.345800 856 2956 5 chr3B.!!$F2 2100

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
792 793 1.003839 GACACGGCCTTGGACATGA 60.004 57.895 14.57 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2410 2427 1.003464 TGCAGCTCTTTCTACATGCCA 59.997 47.619 0.0 0.0 32.77 4.92 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
111 112 1.198713 CTCCTCTAAGAAGCCCTGCA 58.801 55.000 0.00 0.00 0.00 4.41
574 575 2.683933 GAGGAAGCGGAGGGTGGA 60.684 66.667 0.00 0.00 0.00 4.02
660 661 4.816984 GGCCGGAGAGGTCGAGGA 62.817 72.222 5.05 0.00 43.70 3.71
792 793 1.003839 GACACGGCCTTGGACATGA 60.004 57.895 14.57 0.00 0.00 3.07
861 867 1.511768 GAAACCCTCCGACTCCGAG 59.488 63.158 0.00 0.00 38.22 4.63
979 985 1.581447 GCCGCCACCAGAGAAAAAG 59.419 57.895 0.00 0.00 0.00 2.27
983 989 2.494059 CGCCACCAGAGAAAAAGAGAA 58.506 47.619 0.00 0.00 0.00 2.87
1030 1036 2.292794 GATTCCGGCTAGGTCACGCA 62.293 60.000 0.00 0.00 41.99 5.24
1524 1539 2.354704 CCTCTGCAAGAACGGATTGGTA 60.355 50.000 0.00 0.00 46.34 3.25
1743 1758 1.954362 GCGACAGACTGGATGAGGCT 61.954 60.000 7.51 0.00 43.08 4.58
2064 2079 5.234972 GGTTAAATCAAAATGGCTAGCATGC 59.765 40.000 18.24 10.51 0.00 4.06
2349 2366 8.816894 TGAACAATCTTGAGAGAACTAATAGGT 58.183 33.333 0.00 0.00 35.07 3.08
2405 2422 0.401356 TGCAAGTTGGCATCCTCTGA 59.599 50.000 4.75 0.00 39.25 3.27
2407 2424 1.457346 CAAGTTGGCATCCTCTGACC 58.543 55.000 0.00 0.00 28.32 4.02
2409 2426 0.908198 AGTTGGCATCCTCTGACCTC 59.092 55.000 0.00 0.00 28.32 3.85
2410 2427 0.908198 GTTGGCATCCTCTGACCTCT 59.092 55.000 0.00 0.00 28.32 3.69
2411 2428 0.907486 TTGGCATCCTCTGACCTCTG 59.093 55.000 0.00 0.00 28.32 3.35
2412 2429 0.979709 TGGCATCCTCTGACCTCTGG 60.980 60.000 0.00 0.00 28.32 3.86
2413 2430 1.145819 GCATCCTCTGACCTCTGGC 59.854 63.158 0.00 0.00 0.00 4.85
2414 2431 1.620739 GCATCCTCTGACCTCTGGCA 61.621 60.000 0.00 0.00 0.00 4.92
2415 2432 1.129917 CATCCTCTGACCTCTGGCAT 58.870 55.000 0.00 0.00 0.00 4.40
2416 2433 1.129917 ATCCTCTGACCTCTGGCATG 58.870 55.000 0.00 0.00 0.00 4.06
2417 2434 0.252421 TCCTCTGACCTCTGGCATGT 60.252 55.000 0.00 0.00 0.00 3.21
2496 2513 2.806745 GCTCACCGGCAAGCTAATATGA 60.807 50.000 18.78 3.00 35.60 2.15
2511 2920 6.836527 AGCTAATATGACTTACTCTCCACTGT 59.163 38.462 0.00 0.00 0.00 3.55
2574 2983 7.239563 TGATTTTTCTATCCATATGGGCTAGGA 59.760 37.037 21.78 14.07 36.21 2.94
2721 3130 7.639039 TGTTAATTCAAGCTGTTGAGTTGTAG 58.361 34.615 6.45 0.00 43.66 2.74
2761 3170 7.854557 TTCCTACATGATGAACAATCTTGAG 57.145 36.000 0.00 2.80 41.03 3.02
2856 3294 1.003233 GTTCACCCTCCAGCCAGAC 60.003 63.158 0.00 0.00 0.00 3.51
2872 3310 1.115467 AGACTATCCTTGCTCACCGG 58.885 55.000 0.00 0.00 0.00 5.28
2933 3374 9.706691 CCACATCTAGTATATGTTAACGGAATT 57.293 33.333 0.26 0.00 35.39 2.17
2989 3430 6.817765 TGACATCAGATTTTTACCACTTCC 57.182 37.500 0.00 0.00 0.00 3.46
2990 3431 5.411361 TGACATCAGATTTTTACCACTTCCG 59.589 40.000 0.00 0.00 0.00 4.30
2991 3432 5.313712 ACATCAGATTTTTACCACTTCCGT 58.686 37.500 0.00 0.00 0.00 4.69
2992 3433 5.181245 ACATCAGATTTTTACCACTTCCGTG 59.819 40.000 0.00 0.00 40.89 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
341 342 4.070552 GTCAAGGCGCTCCTCCGT 62.071 66.667 7.64 0.00 43.40 4.69
551 552 2.656651 CTCCGCTTCCTCATCGCG 60.657 66.667 0.00 0.00 45.86 5.87
574 575 2.032681 GCCACTCTCACCCGCTTT 59.967 61.111 0.00 0.00 0.00 3.51
660 661 2.046314 CGCGGAACCCACCAAGAT 60.046 61.111 0.00 0.00 0.00 2.40
739 740 2.177518 ACCCTGACCTCCCTCCTCA 61.178 63.158 0.00 0.00 0.00 3.86
861 867 4.485163 GGCCAACATGTCATACAAAGAAC 58.515 43.478 0.00 0.00 0.00 3.01
961 967 0.889186 TCTTTTTCTCTGGTGGCGGC 60.889 55.000 0.00 0.00 0.00 6.53
964 970 4.137543 TCTTTCTCTTTTTCTCTGGTGGC 58.862 43.478 0.00 0.00 0.00 5.01
965 971 5.615289 TCTCTTTCTCTTTTTCTCTGGTGG 58.385 41.667 0.00 0.00 0.00 4.61
966 972 6.520272 TCTCTCTTTCTCTTTTTCTCTGGTG 58.480 40.000 0.00 0.00 0.00 4.17
967 973 6.553100 TCTCTCTCTTTCTCTTTTTCTCTGGT 59.447 38.462 0.00 0.00 0.00 4.00
968 974 6.991938 TCTCTCTCTTTCTCTTTTTCTCTGG 58.008 40.000 0.00 0.00 0.00 3.86
969 975 7.092716 CCTCTCTCTCTTTCTCTTTTTCTCTG 58.907 42.308 0.00 0.00 0.00 3.35
970 976 6.211384 CCCTCTCTCTCTTTCTCTTTTTCTCT 59.789 42.308 0.00 0.00 0.00 3.10
971 977 6.210584 TCCCTCTCTCTCTTTCTCTTTTTCTC 59.789 42.308 0.00 0.00 0.00 2.87
979 985 4.503714 TCTCTCCCTCTCTCTCTTTCTC 57.496 50.000 0.00 0.00 0.00 2.87
983 989 3.435601 GCTCATCTCTCCCTCTCTCTCTT 60.436 52.174 0.00 0.00 0.00 2.85
1115 1121 3.461773 CCTCATCCCGTGCCTCGT 61.462 66.667 0.00 0.00 37.94 4.18
1524 1539 3.011517 AGCTTCATGGCCTCCGGT 61.012 61.111 3.32 0.00 0.00 5.28
1743 1758 2.708216 TCTCCACACAGAAAGCAACA 57.292 45.000 0.00 0.00 0.00 3.33
2064 2079 4.522405 TGGGTGGACATCATGTAAAAACAG 59.478 41.667 0.00 0.00 0.00 3.16
2349 2366 8.388656 ACCTAGAATTCAGAAACACCCTATTA 57.611 34.615 8.44 0.00 0.00 0.98
2352 2369 7.989947 ATACCTAGAATTCAGAAACACCCTA 57.010 36.000 8.44 0.00 0.00 3.53
2354 2371 9.930693 CTATATACCTAGAATTCAGAAACACCC 57.069 37.037 8.44 0.00 0.00 4.61
2405 2422 2.093235 GCTCTTTCTACATGCCAGAGGT 60.093 50.000 0.00 0.00 32.99 3.85
2407 2424 3.196463 CAGCTCTTTCTACATGCCAGAG 58.804 50.000 0.00 0.00 35.11 3.35
2409 2426 1.669779 GCAGCTCTTTCTACATGCCAG 59.330 52.381 0.00 0.00 0.00 4.85
2410 2427 1.003464 TGCAGCTCTTTCTACATGCCA 59.997 47.619 0.00 0.00 32.77 4.92
2411 2428 1.742761 TGCAGCTCTTTCTACATGCC 58.257 50.000 0.00 0.00 32.77 4.40
2412 2429 3.190118 AGTTTGCAGCTCTTTCTACATGC 59.810 43.478 0.00 0.00 0.00 4.06
2413 2430 5.368256 AAGTTTGCAGCTCTTTCTACATG 57.632 39.130 0.00 0.00 0.00 3.21
2414 2431 6.881065 TGATAAGTTTGCAGCTCTTTCTACAT 59.119 34.615 0.00 0.00 0.00 2.29
2415 2432 6.230472 TGATAAGTTTGCAGCTCTTTCTACA 58.770 36.000 0.00 0.00 0.00 2.74
2416 2433 6.727824 TGATAAGTTTGCAGCTCTTTCTAC 57.272 37.500 0.00 0.00 0.00 2.59
2417 2434 7.065085 GTGATGATAAGTTTGCAGCTCTTTCTA 59.935 37.037 0.00 0.00 0.00 2.10
2496 2513 5.601313 TGGAACTTAACAGTGGAGAGTAAGT 59.399 40.000 0.00 0.00 31.60 2.24
2602 3011 8.385898 TCTTACATTTGTAGTAAAACAGTGGG 57.614 34.615 0.00 0.00 31.66 4.61
2640 3049 4.854173 AGTGTGTATTCATGGGTGCAATA 58.146 39.130 0.00 0.00 0.00 1.90
2721 3130 7.981789 TCATGTAGGAAACTGATAGTGATGAAC 59.018 37.037 0.00 0.00 43.88 3.18
2761 3170 6.051179 ACACCCTGTTTCCTATTAGTTCTC 57.949 41.667 0.00 0.00 0.00 2.87
2856 3294 1.522092 TGCCGGTGAGCAAGGATAG 59.478 57.895 1.90 0.00 40.56 2.08
2872 3310 5.921408 CGGAGAGTAAGACATATTACCTTGC 59.079 44.000 0.00 0.00 36.49 4.01
2875 3313 5.241949 CAGCGGAGAGTAAGACATATTACCT 59.758 44.000 0.00 0.00 36.49 3.08
2876 3314 5.009811 ACAGCGGAGAGTAAGACATATTACC 59.990 44.000 0.00 0.00 36.49 2.85
2877 3315 6.074544 ACAGCGGAGAGTAAGACATATTAC 57.925 41.667 0.00 0.00 36.16 1.89
2884 3324 4.437772 ACTTAACAGCGGAGAGTAAGAC 57.562 45.455 0.00 0.00 0.00 3.01
2965 3406 6.402550 CGGAAGTGGTAAAAATCTGATGTCAG 60.403 42.308 3.61 3.61 45.08 3.51
2966 3407 5.411361 CGGAAGTGGTAAAAATCTGATGTCA 59.589 40.000 0.00 0.00 0.00 3.58
2967 3408 5.411669 ACGGAAGTGGTAAAAATCTGATGTC 59.588 40.000 0.00 0.00 46.97 3.06
2968 3409 5.313712 ACGGAAGTGGTAAAAATCTGATGT 58.686 37.500 0.00 0.00 46.97 3.06
2969 3410 5.880054 ACGGAAGTGGTAAAAATCTGATG 57.120 39.130 0.00 0.00 46.97 3.07


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

AutoCloner maintained by Alex Coulton.