Multiple sequence alignment - TraesCS6D01G119100

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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 TraesCS6D01G119100 chr6D 100.000 3209 0 0 1 3209 84231879 84228671 0.000000e+00 5927
1 TraesCS6D01G119100 chr6D 87.528 2205 264 6 13 2216 84631028 84628834 0.000000e+00 2538
2 TraesCS6D01G119100 chr6D 85.967 2316 285 15 13 2328 84224431 84222156 0.000000e+00 2440
3 TraesCS6D01G119100 chr6D 86.649 2217 271 17 1 2211 84474074 84471877 0.000000e+00 2431
4 TraesCS6D01G119100 chr6D 86.667 105 13 1 2253 2357 84628838 84628735 7.270000e-22 115
5 TraesCS6D01G119100 chr6B 96.633 3237 65 10 1 3209 159989857 159986637 0.000000e+00 5334
6 TraesCS6D01G119100 chr6B 89.124 2363 234 14 1 2358 160683166 160680822 0.000000e+00 2918
7 TraesCS6D01G119100 chr6B 87.286 2218 269 8 1 2216 160716998 160714792 0.000000e+00 2521
8 TraesCS6D01G119100 chr6B 85.128 780 93 11 1581 2358 160685827 160685069 0.000000e+00 776
9 TraesCS6D01G119100 chr6A 96.511 3239 75 12 1 3208 101562696 101559465 0.000000e+00 5321
10 TraesCS6D01G119100 chr6A 88.708 2214 225 15 2 2211 101865419 101863227 0.000000e+00 2680
11 TraesCS6D01G119100 chr6A 86.572 2316 284 12 13 2328 101554789 101552501 0.000000e+00 2529


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 TraesCS6D01G119100 chr6D 84228671 84231879 3208 True 5927.0 5927 100.0000 1 3209 1 chr6D.!!$R2 3208
1 TraesCS6D01G119100 chr6D 84222156 84224431 2275 True 2440.0 2440 85.9670 13 2328 1 chr6D.!!$R1 2315
2 TraesCS6D01G119100 chr6D 84471877 84474074 2197 True 2431.0 2431 86.6490 1 2211 1 chr6D.!!$R3 2210
3 TraesCS6D01G119100 chr6D 84628735 84631028 2293 True 1326.5 2538 87.0975 13 2357 2 chr6D.!!$R4 2344
4 TraesCS6D01G119100 chr6B 159986637 159989857 3220 True 5334.0 5334 96.6330 1 3209 1 chr6B.!!$R1 3208
5 TraesCS6D01G119100 chr6B 160714792 160716998 2206 True 2521.0 2521 87.2860 1 2216 1 chr6B.!!$R2 2215
6 TraesCS6D01G119100 chr6B 160680822 160685827 5005 True 1847.0 2918 87.1260 1 2358 2 chr6B.!!$R3 2357
7 TraesCS6D01G119100 chr6A 101559465 101562696 3231 True 5321.0 5321 96.5110 1 3208 1 chr6A.!!$R2 3207
8 TraesCS6D01G119100 chr6A 101863227 101865419 2192 True 2680.0 2680 88.7080 2 2211 1 chr6A.!!$R3 2209
9 TraesCS6D01G119100 chr6A 101552501 101554789 2288 True 2529.0 2529 86.5720 13 2328 1 chr6A.!!$R1 2315

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
993 3674 0.695462 ATGTCTGGGGAGCTGCCATA 60.695 55.0 26.95 13.25 38.95 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2562 5264 0.037326 TGTGCACCTCATCGAAGACC 60.037 55.0 15.69 0.0 42.51 3.85 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
716 3397 2.363680 CCAAACACACTGGGTAATTGCA 59.636 45.455 0.00 0.00 0.00 4.08
724 3405 1.895131 CTGGGTAATTGCACCAAGCTT 59.105 47.619 0.00 0.00 45.94 3.74
904 3585 2.243736 TGACCTTGGAGGGAACAGTTTT 59.756 45.455 0.00 0.00 40.58 2.43
993 3674 0.695462 ATGTCTGGGGAGCTGCCATA 60.695 55.000 26.95 13.25 38.95 2.74
994 3675 0.695462 TGTCTGGGGAGCTGCCATAT 60.695 55.000 26.95 0.00 38.95 1.78
1949 4630 4.513318 CCTTCACTTCCTTTCAGAGTTCAC 59.487 45.833 0.00 0.00 0.00 3.18
2082 4763 2.159707 CCATTGTAGTTCGGTTGAAGCG 60.160 50.000 10.91 10.91 40.97 4.68
2360 5042 8.810652 TTAATATTGTTGAGCAAACCAAGTTC 57.189 30.769 0.00 0.00 40.91 3.01
2393 5075 7.214467 TCACAGCAAAAATTTAAGACCCTAG 57.786 36.000 0.00 0.00 0.00 3.02
2402 5084 8.608844 AAAATTTAAGACCCTAGATAGCATCG 57.391 34.615 0.00 0.00 0.00 3.84
2422 5104 4.127171 TCGTAGAATCAGGCCTTAATTGC 58.873 43.478 13.66 6.83 0.00 3.56
2582 5284 1.608025 GGTCTTCGATGAGGTGCACAA 60.608 52.381 20.43 3.64 0.00 3.33
2617 5319 1.207089 AGGAATTTGGCGACGAGATGA 59.793 47.619 0.00 0.00 0.00 2.92
2735 5440 3.338676 GCCGCCGCTGCTACATAC 61.339 66.667 0.00 0.00 34.43 2.39
2853 5558 2.976692 TATCATCTGCGGCAGCCACG 62.977 60.000 24.78 12.35 44.33 4.94
2868 5573 1.290203 CCACGACATGATTTCCCTCG 58.710 55.000 0.00 0.00 0.00 4.63
2906 5611 3.323403 CCCTCTCCTGTGGATAGATCAAC 59.677 52.174 0.00 0.00 28.78 3.18
2937 5642 8.357796 ACATGTTTCGAGATGTTAGATGTATG 57.642 34.615 0.00 0.00 27.94 2.39
2957 5664 0.677731 ATGTGCCGGAACATCACTGG 60.678 55.000 23.34 0.00 35.92 4.00
2995 5706 1.072266 TACTTGGATGGGTTGGCAGT 58.928 50.000 0.00 0.00 0.00 4.40
3027 5738 1.293924 AGCATACAAGCGTCTGCATC 58.706 50.000 5.86 0.00 45.20 3.91
3030 5741 0.530650 ATACAAGCGTCTGCATCGGG 60.531 55.000 12.11 0.00 46.23 5.14
3044 5755 1.948403 ATCGGGGTGCCAATTGGGAT 61.948 55.000 25.73 14.99 40.01 3.85
3060 5771 1.476471 GGGATGAGTTCATGGGAGCAG 60.476 57.143 0.00 0.00 36.57 4.24
3094 5806 0.179108 GGTCAGGACGAGTATGTGGC 60.179 60.000 0.00 0.00 0.00 5.01
3119 5831 6.073003 CCAGATGACCAAAGTCTTCAGTTAAC 60.073 42.308 0.00 0.00 45.29 2.01
3121 5833 6.708054 AGATGACCAAAGTCTTCAGTTAACAG 59.292 38.462 8.61 0.00 45.29 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
406 3087 3.525537 GACGATGATGCTTCTGGAGAAA 58.474 45.455 0.88 0.00 33.07 2.52
646 3327 1.683385 AGGTCAAGCAAAGCCAAAGAC 59.317 47.619 0.00 0.00 0.00 3.01
716 3397 2.887152 CCTTGAGCACTTTAAGCTTGGT 59.113 45.455 9.86 0.00 43.58 3.67
904 3585 0.339859 ACTCTGGGATGGCTCCACTA 59.660 55.000 5.54 0.00 44.08 2.74
993 3674 3.678289 TGTGCAGTTGCTCATAGTTGAT 58.322 40.909 5.62 0.00 39.29 2.57
994 3675 3.124578 TGTGCAGTTGCTCATAGTTGA 57.875 42.857 5.62 0.00 39.29 3.18
1949 4630 7.281100 GTCCTTCTAGGTCATTGTTAGAAATGG 59.719 40.741 0.00 7.62 36.53 3.16
2082 4763 2.107901 AGAAATGATGGAGATGGGAGCC 59.892 50.000 0.00 0.00 0.00 4.70
2360 5042 6.774354 AAATTTTTGCTGTGATTGTGCTAG 57.226 33.333 0.00 0.00 0.00 3.42
2393 5075 3.194542 AGGCCTGATTCTACGATGCTATC 59.805 47.826 3.11 0.00 0.00 2.08
2422 5104 0.111001 CGCGACCTTGTAAAACACGG 60.111 55.000 0.00 1.35 42.60 4.94
2562 5264 0.037326 TGTGCACCTCATCGAAGACC 60.037 55.000 15.69 0.00 42.51 3.85
2567 5269 4.693532 GGTTGTGCACCTCATCGA 57.306 55.556 15.69 0.00 43.29 3.59
2586 5288 2.711542 CCAAATTCCTCTACCTTGCGT 58.288 47.619 0.00 0.00 0.00 5.24
2595 5297 0.895530 TCTCGTCGCCAAATTCCTCT 59.104 50.000 0.00 0.00 0.00 3.69
2617 5319 0.250467 ACGAGGTGCTTGATGCTGTT 60.250 50.000 0.00 0.00 43.37 3.16
2694 5396 3.365265 CCCTTGTCGGCTTGTGGC 61.365 66.667 0.00 0.00 40.90 5.01
2769 5474 2.203126 CATGAGGCGAGGAAGGGC 60.203 66.667 0.00 0.00 0.00 5.19
2770 5475 1.445095 CTCATGAGGCGAGGAAGGG 59.555 63.158 15.38 0.00 0.00 3.95
2853 5558 5.278169 CCATGAAATCGAGGGAAATCATGTC 60.278 44.000 16.56 0.00 42.19 3.06
2868 5573 2.025887 AGAGGGGTCACACCATGAAATC 60.026 50.000 0.00 0.00 41.02 2.17
2906 5611 1.325640 CATCTCGAAACATGTCAGGCG 59.674 52.381 0.00 0.88 0.00 5.52
2957 5664 2.556534 ATAGTGTCGTCGTGCTTACC 57.443 50.000 0.00 0.00 0.00 2.85
2995 5706 2.591923 TGTATGCTTGGAACCAAAGCA 58.408 42.857 22.28 22.28 40.93 3.91
3027 5738 2.043046 ATCCCAATTGGCACCCCG 60.043 61.111 19.75 4.36 0.00 5.73
3030 5741 1.478105 GAACTCATCCCAATTGGCACC 59.522 52.381 19.75 0.00 0.00 5.01
3044 5755 0.325933 CCACTGCTCCCATGAACTCA 59.674 55.000 0.00 0.00 0.00 3.41
3060 5771 2.554032 CCTGACCAAATTCAGTCACCAC 59.446 50.000 6.44 0.00 41.40 4.16
3094 5806 4.013267 ACTGAAGACTTTGGTCATCTGG 57.987 45.455 10.94 4.47 44.36 3.86


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

AutoCloner maintained by Alex Coulton.