Multiple sequence alignment - TraesCS6A01G256700

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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 TraesCS6A01G256700 chr6A 100.000 3224 0 0 1 3224 478311068 478307845 0.000000e+00 5954.0
1 TraesCS6A01G256700 chr6D 95.717 3105 86 21 143 3224 337843264 337840184 0.000000e+00 4953.0
2 TraesCS6A01G256700 chr6D 85.294 136 16 4 8 141 402325186 402325319 1.560000e-28 137.0
3 TraesCS6A01G256700 chr6D 86.885 122 13 3 8 128 117362013 117362132 2.020000e-27 134.0
4 TraesCS6A01G256700 chr6B 93.673 3256 119 34 2 3224 482470042 482473243 0.000000e+00 4791.0
5 TraesCS6A01G256700 chr4A 79.842 253 44 6 1053 1300 71166237 71166487 9.190000e-41 178.0
6 TraesCS6A01G256700 chr4A 85.294 136 16 4 8 141 261914283 261914150 1.560000e-28 137.0
7 TraesCS6A01G256700 chr2D 85.294 136 16 4 8 141 627516577 627516444 1.560000e-28 137.0
8 TraesCS6A01G256700 chr2D 84.559 136 17 4 8 141 10206121 10206254 7.260000e-27 132.0
9 TraesCS6A01G256700 chr4D 84.672 137 16 5 8 142 428481948 428481815 7.260000e-27 132.0
10 TraesCS6A01G256700 chr4B 83.824 136 18 4 8 141 357958188 357958055 3.380000e-25 126.0
11 TraesCS6A01G256700 chr1D 83.824 136 18 4 8 141 276797466 276797333 3.380000e-25 126.0
12 TraesCS6A01G256700 chr1D 94.737 57 3 0 494 550 275139273 275139217 4.430000e-14 89.8
13 TraesCS6A01G256700 chr1B 94.737 57 3 0 494 550 374330031 374329975 4.430000e-14 89.8
14 TraesCS6A01G256700 chr1A 94.737 57 3 0 494 550 347635533 347635477 4.430000e-14 89.8
15 TraesCS6A01G256700 chr3B 92.982 57 4 0 494 550 823473651 823473707 2.060000e-12 84.2
16 TraesCS6A01G256700 chrUn 89.474 57 6 0 494 550 239745238 239745294 4.460000e-09 73.1
17 TraesCS6A01G256700 chr7B 93.750 48 2 1 655 701 675380180 675380227 1.600000e-08 71.3


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 TraesCS6A01G256700 chr6A 478307845 478311068 3223 True 5954 5954 100.000 1 3224 1 chr6A.!!$R1 3223
1 TraesCS6A01G256700 chr6D 337840184 337843264 3080 True 4953 4953 95.717 143 3224 1 chr6D.!!$R1 3081
2 TraesCS6A01G256700 chr6B 482470042 482473243 3201 False 4791 4791 93.673 2 3224 1 chr6B.!!$F1 3222

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
837 864 0.821711 CCCACCAGTCCGCTTTTTCA 60.822 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2719 2758 1.79517 TTTTGAGGAGCAGCAACGGC 61.795 55.0 0.0 0.0 41.61 5.68 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
56 57 6.932947 TGATTTGGCATTGTGAATGTTGATA 58.067 32.000 0.00 0.00 41.01 2.15
60 61 7.598189 TTGGCATTGTGAATGTTGATATTTG 57.402 32.000 0.00 0.00 41.01 2.32
97 98 8.475331 TTGGTCAAAGTAGAGATATTTTCGAC 57.525 34.615 0.00 0.00 0.00 4.20
99 100 7.759886 TGGTCAAAGTAGAGATATTTTCGACTG 59.240 37.037 5.23 0.00 32.04 3.51
102 103 7.981789 TCAAAGTAGAGATATTTTCGACTGCAT 59.018 33.333 0.00 0.00 32.04 3.96
110 111 6.540189 AGATATTTTCGACTGCATGCTAAACT 59.460 34.615 20.33 8.27 0.00 2.66
115 116 7.603963 TTTCGACTGCATGCTAAACTTATAA 57.396 32.000 20.33 0.00 0.00 0.98
220 224 3.533606 AGCAGCTACTACTGGTCAATG 57.466 47.619 0.00 0.00 44.83 2.82
337 349 1.140804 GGCTCGAGAACCTCTCTGC 59.859 63.158 18.75 0.00 41.26 4.26
736 763 3.775654 GGCCCGACTGGTCTGAGG 61.776 72.222 0.00 0.00 35.10 3.86
820 847 0.825840 CCCTCGATCTCCACTCTCCC 60.826 65.000 0.00 0.00 0.00 4.30
829 856 2.650116 CCACTCTCCCACCAGTCCG 61.650 68.421 0.00 0.00 0.00 4.79
837 864 0.821711 CCCACCAGTCCGCTTTTTCA 60.822 55.000 0.00 0.00 0.00 2.69
1554 1592 1.856539 ATGTGGTGGGCAGGGAAGAG 61.857 60.000 0.00 0.00 0.00 2.85
1731 1769 3.059982 CTGGTGGACGAGAAGGCA 58.940 61.111 0.00 0.00 0.00 4.75
1818 1856 4.873129 CGCGCCGTATCAGCTGGT 62.873 66.667 15.13 9.93 0.00 4.00
1899 1937 3.826754 CTAGCAGCGGTGGAGCGA 61.827 66.667 17.54 0.00 43.00 4.93
2296 2334 3.396951 GGCGGTGCCTGTATGTAAT 57.603 52.632 0.00 0.00 46.69 1.89
2413 2451 8.798859 AGTATGATTTTATTGACACTCTTGCT 57.201 30.769 0.00 0.00 0.00 3.91
2687 2726 4.080129 ACATAGGAGTTGCAGGATGTTGAT 60.080 41.667 0.00 0.00 39.31 2.57
2697 2736 6.409524 TGCAGGATGTTGATTTTTCTCTTT 57.590 33.333 0.00 0.00 39.31 2.52
2724 2763 3.505835 TTTCCAGGTGAAAGCCGTT 57.494 47.368 0.00 0.00 38.04 4.44
2779 2818 7.360269 GCTTTAATTTTTGGTGTGATGTCATGG 60.360 37.037 0.00 0.00 0.00 3.66
2807 2846 5.010922 TGCAAGTCACATCTTAAGGCAATTT 59.989 36.000 1.85 0.00 0.00 1.82
2831 2870 4.517453 TGTTTCTTTTACCTGGAATCACGG 59.483 41.667 0.00 0.00 0.00 4.94
2847 2886 8.243426 TGGAATCACGGAGATTATTTCTTTTTG 58.757 33.333 5.49 0.00 46.76 2.44
2976 3015 2.370349 TCGTTTTGTTCAGGAGCCAAA 58.630 42.857 0.00 0.00 0.00 3.28
2993 3032 4.921547 GCCAAATGCTACTAGCTTTTACC 58.078 43.478 17.25 10.23 43.77 2.85
3097 3136 9.811995 TGACACCATATTTGTACAGTTATAGAC 57.188 33.333 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.315525 CAACATTCACAATGCCAAATCAATATA 57.684 29.630 0.00 0.00 42.69 0.86
90 91 4.829064 AAGTTTAGCATGCAGTCGAAAA 57.171 36.364 21.98 7.28 0.00 2.29
91 92 7.603963 TTATAAGTTTAGCATGCAGTCGAAA 57.396 32.000 21.98 8.83 0.00 3.46
97 98 6.259608 AGTCTGCTTATAAGTTTAGCATGCAG 59.740 38.462 21.98 11.65 43.33 4.41
99 100 6.610741 AGTCTGCTTATAAGTTTAGCATGC 57.389 37.500 10.51 10.51 43.33 4.06
337 349 0.803117 TCACGTGCGTTAGAGAGAGG 59.197 55.000 11.67 0.00 0.00 3.69
492 507 2.506061 CGGAGGAGGATCTGCAGGG 61.506 68.421 15.13 0.00 33.73 4.45
533 548 3.449227 TAGCGAGACCCAGTGGCG 61.449 66.667 2.61 2.75 33.59 5.69
534 549 2.184579 GTAGCGAGACCCAGTGGC 59.815 66.667 2.61 0.00 33.59 5.01
535 550 2.893398 GGTAGCGAGACCCAGTGG 59.107 66.667 0.63 0.63 32.88 4.00
541 556 2.493501 GGTTCGGGTAGCGAGACC 59.506 66.667 0.00 0.00 38.93 3.85
542 557 2.493501 GGGTTCGGGTAGCGAGAC 59.506 66.667 0.00 0.00 0.00 3.36
543 558 2.757099 GGGGTTCGGGTAGCGAGA 60.757 66.667 0.00 0.00 0.00 4.04
544 559 3.072468 TGGGGTTCGGGTAGCGAG 61.072 66.667 0.00 0.00 0.00 5.03
820 847 1.264288 GAGTGAAAAAGCGGACTGGTG 59.736 52.381 0.00 0.00 0.00 4.17
829 856 2.554462 GGTGGAAGGAGAGTGAAAAAGC 59.446 50.000 0.00 0.00 0.00 3.51
869 897 2.280592 GTGGTGGGTGGACACGAC 60.281 66.667 0.00 0.00 41.58 4.34
941 975 3.135348 TGATTTGGATCTGGCCTACTCTG 59.865 47.826 3.32 0.00 33.28 3.35
1113 1151 2.753043 TCGTAGGTCTGGCCGGTC 60.753 66.667 12.43 5.74 43.70 4.79
1359 1397 2.588989 GCCCTGAGCTTCCTGAGG 59.411 66.667 0.00 0.00 41.62 3.86
1554 1592 2.352805 CCAAGCCTGGTGACCCTC 59.647 66.667 0.00 0.00 38.00 4.30
2296 2334 2.377531 TCCTATGATCCTACTACCGCCA 59.622 50.000 0.00 0.00 0.00 5.69
2687 2726 7.363793 CCTGGAAAGGAAGACAAAAGAGAAAAA 60.364 37.037 0.00 0.00 0.00 1.94
2697 2736 3.943671 TTCACCTGGAAAGGAAGACAA 57.056 42.857 0.00 0.00 30.98 3.18
2719 2758 1.795170 TTTTGAGGAGCAGCAACGGC 61.795 55.000 0.00 0.00 41.61 5.68
2779 2818 3.120060 CCTTAAGATGTGACTTGCAGTGC 60.120 47.826 8.58 8.58 0.00 4.40
2807 2846 5.009210 CCGTGATTCCAGGTAAAAGAAACAA 59.991 40.000 0.00 0.00 0.00 2.83
2976 3015 4.189231 CCAACGGTAAAAGCTAGTAGCAT 58.811 43.478 23.77 9.68 45.56 3.79
2992 3031 3.674955 GCCCTAACTAAAATTGCCAACGG 60.675 47.826 0.00 0.00 0.00 4.44
2993 3032 3.057174 TGCCCTAACTAAAATTGCCAACG 60.057 43.478 0.00 0.00 0.00 4.10
3097 3136 6.419413 TGAAAGCCGCAAAAACTATAACAAAG 59.581 34.615 0.00 0.00 0.00 2.77
3143 3183 7.609532 AGACTTATCAAACCAAGAGAATGGAAG 59.390 37.037 0.00 0.00 43.54 3.46


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

AutoCloner maintained by Alex Coulton.