Multiple sequence alignment - TraesCS7B01G256400

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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 TraesCS7B01G256400 chr7B 100.000 2900 0 0 1 2900 475366294 475369193 0 5356
1 TraesCS7B01G256400 chr7B 96.103 2925 78 8 1 2900 99712350 99709437 0 4737
2 TraesCS7B01G256400 chr7B 95.321 2928 107 11 1 2900 5959061 5956136 0 4621
3 TraesCS7B01G256400 chr7B 94.496 2925 130 11 1 2900 570096188 570093270 0 4481
4 TraesCS7B01G256400 chr7B 94.399 2928 125 16 1 2900 606777096 606774180 0 4462
5 TraesCS7B01G256400 chr7B 94.049 2924 136 14 3 2900 709392524 709389613 0 4401
6 TraesCS7B01G256400 chr7B 92.844 2222 123 13 1 2194 34309328 34307115 0 3190
7 TraesCS7B01G256400 chr2B 95.725 2924 95 6 1 2900 747121814 747118897 0 4680
8 TraesCS7B01G256400 chr3B 95.557 2926 96 8 1 2899 103311908 103308990 0 4652
9 TraesCS7B01G256400 chr3B 94.803 2925 116 12 1 2900 177745888 177748801 0 4527
10 TraesCS7B01G256400 chr3B 95.997 2448 73 3 1 2424 678534086 678531640 0 3954
11 TraesCS7B01G256400 chr3B 95.491 2218 75 3 1 2194 694806887 694804671 0 3518
12 TraesCS7B01G256400 chr3B 85.288 1441 153 33 372 1787 237214803 237213397 0 1432
13 TraesCS7B01G256400 chr6B 90.248 2820 211 42 109 2900 680526126 680523343 0 3626
14 TraesCS7B01G256400 chr1B 94.644 1307 43 6 1 1282 588839769 588838465 0 2001


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 TraesCS7B01G256400 chr7B 475366294 475369193 2899 False 5356 5356 100.000 1 2900 1 chr7B.!!$F1 2899
1 TraesCS7B01G256400 chr7B 99709437 99712350 2913 True 4737 4737 96.103 1 2900 1 chr7B.!!$R3 2899
2 TraesCS7B01G256400 chr7B 5956136 5959061 2925 True 4621 4621 95.321 1 2900 1 chr7B.!!$R1 2899
3 TraesCS7B01G256400 chr7B 570093270 570096188 2918 True 4481 4481 94.496 1 2900 1 chr7B.!!$R4 2899
4 TraesCS7B01G256400 chr7B 606774180 606777096 2916 True 4462 4462 94.399 1 2900 1 chr7B.!!$R5 2899
5 TraesCS7B01G256400 chr7B 709389613 709392524 2911 True 4401 4401 94.049 3 2900 1 chr7B.!!$R6 2897
6 TraesCS7B01G256400 chr7B 34307115 34309328 2213 True 3190 3190 92.844 1 2194 1 chr7B.!!$R2 2193
7 TraesCS7B01G256400 chr2B 747118897 747121814 2917 True 4680 4680 95.725 1 2900 1 chr2B.!!$R1 2899
8 TraesCS7B01G256400 chr3B 103308990 103311908 2918 True 4652 4652 95.557 1 2899 1 chr3B.!!$R1 2898
9 TraesCS7B01G256400 chr3B 177745888 177748801 2913 False 4527 4527 94.803 1 2900 1 chr3B.!!$F1 2899
10 TraesCS7B01G256400 chr3B 678531640 678534086 2446 True 3954 3954 95.997 1 2424 1 chr3B.!!$R3 2423
11 TraesCS7B01G256400 chr3B 694804671 694806887 2216 True 3518 3518 95.491 1 2194 1 chr3B.!!$R4 2193
12 TraesCS7B01G256400 chr3B 237213397 237214803 1406 True 1432 1432 85.288 372 1787 1 chr3B.!!$R2 1415
13 TraesCS7B01G256400 chr6B 680523343 680526126 2783 True 3626 3626 90.248 109 2900 1 chr6B.!!$R1 2791
14 TraesCS7B01G256400 chr1B 588838465 588839769 1304 True 2001 2001 94.644 1 1282 1 chr1B.!!$R1 1281

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
596 710 1.820519 TCACCTGGATTTTGCATCTGC 59.179 47.619 0.0 0.0 42.5 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2435 2903 2.483714 GGCACAGAAGATAATCGCAGGA 60.484 50.0 0.0 0.0 0.0 3.86 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
71 72 9.186837 GCTGATATATGGATCCATGAAAATTCT 57.813 33.333 33.41 10.53 37.82 2.40
596 710 1.820519 TCACCTGGATTTTGCATCTGC 59.179 47.619 0.00 0.00 42.50 4.26
751 881 6.770785 AGTCAAGTTCTTGCCAACTATTTACA 59.229 34.615 7.58 0.00 35.45 2.41
794 929 4.361451 ACAACTCTGTGCAGAAACAAAG 57.639 40.909 3.36 0.00 36.94 2.77
949 1099 9.552114 GATTAACAACTGATCATCACTTTCTTG 57.448 33.333 0.00 0.00 0.00 3.02
983 1136 2.771089 CAGTGAGTGTGTGGTAGCATT 58.229 47.619 0.00 0.00 0.00 3.56
1196 1350 2.426023 CCGTGGTGCCCCTATAGC 59.574 66.667 0.00 0.00 0.00 2.97
1204 1358 1.113517 TGCCCCTATAGCGGTGTCTC 61.114 60.000 5.34 0.00 0.00 3.36
1241 1395 4.219507 CCATACTCTAGATGACGCAGGAAT 59.780 45.833 0.00 0.00 0.00 3.01
1282 1436 3.913799 TCCAACCAGGATTGAGTTAGGAA 59.086 43.478 0.00 0.00 43.07 3.36
1314 1468 2.008329 GATGGAGCTGTGCAAGAAGAG 58.992 52.381 0.00 0.00 0.00 2.85
1584 1739 7.504911 CCTATTCCAGATCCAAAATCTGTTGAT 59.495 37.037 12.62 7.07 42.88 2.57
1780 1939 1.428448 TCATCCGCTCGTGAACAAAG 58.572 50.000 0.00 0.00 0.00 2.77
1789 1948 2.975851 CTCGTGAACAAAGCTTCATTGC 59.024 45.455 0.00 0.00 32.78 3.56
1866 2025 5.631026 CGCATCTTGTATAACTGCAACTTT 58.369 37.500 0.00 0.00 33.13 2.66
1960 2119 6.209986 ACTGTTATGGTACTACTGTGCAACTA 59.790 38.462 0.00 0.00 38.04 2.24
2089 2555 7.039784 ACACAATGTCCTATATGCAAAAAGTGT 60.040 33.333 0.00 0.00 0.00 3.55
2111 2577 9.767228 AGTGTAAAAGTGTTTTTAAAAAGGTGT 57.233 25.926 13.58 0.00 39.69 4.16
2184 2650 3.052082 GTGCAGCTGGATGTGCGT 61.052 61.111 17.12 0.00 42.96 5.24
2213 2679 3.005155 GCACATGATCCATCCCTTAAAGC 59.995 47.826 0.00 0.00 0.00 3.51
2435 2903 2.644798 AGGTTCAGCTAGGTGTCCATTT 59.355 45.455 26.87 13.40 0.00 2.32
2752 3224 8.324306 TGAAATATGATGAAGAGGACAGAGTTT 58.676 33.333 0.00 0.00 0.00 2.66
2859 3331 4.593956 TGACCAACATGTACAATATGCCA 58.406 39.130 0.00 0.00 0.00 4.92
2863 3335 5.655974 ACCAACATGTACAATATGCCATTCA 59.344 36.000 0.00 0.00 0.00 2.57
2864 3336 6.324512 ACCAACATGTACAATATGCCATTCAT 59.675 34.615 0.00 0.00 39.17 2.57
2876 3348 2.175284 TGCCATTCATGCCCTTCATAGA 59.825 45.455 0.00 0.00 33.19 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 8.726988 GTGTTCAGTTGGCTAAAATAGATGTTA 58.273 33.333 0.00 0.00 0.00 2.41
596 710 6.146021 GGGACACAATTTGATGCTACTTTTTG 59.854 38.462 2.79 0.00 0.00 2.44
1196 1350 1.959848 TCTGACTGCAGAGACACCG 59.040 57.895 23.35 6.92 45.88 4.94
1204 1358 1.755959 AGTATGGCTCTCTGACTGCAG 59.244 52.381 13.48 13.48 43.67 4.41
1234 1388 1.098050 ACATTTGCCTCGATTCCTGC 58.902 50.000 0.00 0.00 0.00 4.85
1241 1395 0.400213 ACCAGGAACATTTGCCTCGA 59.600 50.000 0.00 0.00 30.41 4.04
1271 1425 1.351017 CAGCCCCAGTTCCTAACTCAA 59.649 52.381 0.00 0.00 40.46 3.02
1282 1436 1.687612 CTCCATCAACAGCCCCAGT 59.312 57.895 0.00 0.00 0.00 4.00
1314 1468 0.758123 CAGCCTCATCCTCTCCTTCC 59.242 60.000 0.00 0.00 0.00 3.46
1584 1739 5.333581 TCTTCTTCCATCTCCTTGTCACTA 58.666 41.667 0.00 0.00 0.00 2.74
1780 1939 4.158394 TCTCAAGTATTTGGGCAATGAAGC 59.842 41.667 0.00 0.00 34.63 3.86
1789 1948 3.053693 TGGTGGGATCTCAAGTATTTGGG 60.054 47.826 0.00 0.00 36.04 4.12
1866 2025 5.362105 AGAAAAACACCACACCTGTAGTA 57.638 39.130 0.00 0.00 0.00 1.82
1960 2119 7.014230 ACACCAGTTGCATAGTTAAGTCATTTT 59.986 33.333 0.00 0.00 0.00 1.82
2111 2577 3.197766 CACAGGAAATGGACACCTAGCTA 59.802 47.826 0.00 0.00 32.35 3.32
2184 2650 3.306989 GGGATGGATCATGTGCTCGAATA 60.307 47.826 0.00 0.00 0.00 1.75
2213 2679 5.586643 GGACTGCCTAGAGGAAAACTTAATG 59.413 44.000 0.00 0.00 37.39 1.90
2435 2903 2.483714 GGCACAGAAGATAATCGCAGGA 60.484 50.000 0.00 0.00 0.00 3.86
2720 3192 7.987458 TGTCCTCTTCATCATATTTCACCTTAC 59.013 37.037 0.00 0.00 0.00 2.34
2752 3224 4.081198 GCCATCCACCCAAAATATGTTGAA 60.081 41.667 7.23 0.00 0.00 2.69
2859 3331 8.636213 CAGTTTATTTCTATGAAGGGCATGAAT 58.364 33.333 0.00 0.00 37.87 2.57
2863 3335 7.118723 TGTCAGTTTATTTCTATGAAGGGCAT 58.881 34.615 0.00 0.00 41.08 4.40
2864 3336 6.480763 TGTCAGTTTATTTCTATGAAGGGCA 58.519 36.000 0.00 0.00 0.00 5.36
2876 3348 6.610075 AAGATTGGCCATGTCAGTTTATTT 57.390 33.333 6.09 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.