Multiple sequence alignment - TraesCS7A01G127900

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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 TraesCS7A01G127900 chr7A 100.000 3062 0 0 1 3062 82118578 82121639 0 5655
1 TraesCS7A01G127900 chr2D 96.719 3078 70 25 1 3062 431013075 431010013 0 5096
2 TraesCS7A01G127900 chr6D 96.528 3082 77 25 1 3062 1925043 1921972 0 5072
3 TraesCS7A01G127900 chr6D 96.301 3082 77 29 1 3062 60329319 60332383 0 5025
4 TraesCS7A01G127900 chr6A 96.087 3092 74 13 1 3062 588563071 588559997 0 4996
5 TraesCS7A01G127900 chr1D 95.974 3080 77 25 1 3062 70138974 70135924 0 4957
6 TraesCS7A01G127900 chr4D 95.964 3072 83 13 1 3062 20321598 20324638 0 4948
7 TraesCS7A01G127900 chr4D 96.412 2843 70 16 228 3062 143323381 143320563 0 4656
8 TraesCS7A01G127900 chr3A 95.632 3068 102 15 1 3062 637909266 637912307 0 4894
9 TraesCS7A01G127900 chr5D 96.174 2718 71 27 1 2699 458878418 458881121 0 4412
10 TraesCS7A01G127900 chr3D 96.690 2477 63 14 1 2466 547240121 547242589 0 4102
11 TraesCS7A01G127900 chr7D 95.484 1240 35 5 1826 3062 120716720 120715499 0 1960


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 TraesCS7A01G127900 chr7A 82118578 82121639 3061 False 5655 5655 100.000 1 3062 1 chr7A.!!$F1 3061
1 TraesCS7A01G127900 chr2D 431010013 431013075 3062 True 5096 5096 96.719 1 3062 1 chr2D.!!$R1 3061
2 TraesCS7A01G127900 chr6D 1921972 1925043 3071 True 5072 5072 96.528 1 3062 1 chr6D.!!$R1 3061
3 TraesCS7A01G127900 chr6D 60329319 60332383 3064 False 5025 5025 96.301 1 3062 1 chr6D.!!$F1 3061
4 TraesCS7A01G127900 chr6A 588559997 588563071 3074 True 4996 4996 96.087 1 3062 1 chr6A.!!$R1 3061
5 TraesCS7A01G127900 chr1D 70135924 70138974 3050 True 4957 4957 95.974 1 3062 1 chr1D.!!$R1 3061
6 TraesCS7A01G127900 chr4D 20321598 20324638 3040 False 4948 4948 95.964 1 3062 1 chr4D.!!$F1 3061
7 TraesCS7A01G127900 chr4D 143320563 143323381 2818 True 4656 4656 96.412 228 3062 1 chr4D.!!$R1 2834
8 TraesCS7A01G127900 chr3A 637909266 637912307 3041 False 4894 4894 95.632 1 3062 1 chr3A.!!$F1 3061
9 TraesCS7A01G127900 chr5D 458878418 458881121 2703 False 4412 4412 96.174 1 2699 1 chr5D.!!$F1 2698
10 TraesCS7A01G127900 chr3D 547240121 547242589 2468 False 4102 4102 96.690 1 2466 1 chr3D.!!$F1 2465
11 TraesCS7A01G127900 chr7D 120715499 120716720 1221 True 1960 1960 95.484 1826 3062 1 chr7D.!!$R1 1236

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
287 312 1.221021 CTCCCTAGGGCAAACGACC 59.779 63.158 24.42 0.0 34.68 4.79 F
316 341 1.334960 GCTTGTGTTTGATGTGTCCCG 60.335 52.381 0.00 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 1592 0.109532 TTGCGACCTGATCAAACCCA 59.890 50.0 0.00 0.0 0.0 4.51 R
2144 2193 2.026542 TCCCAACTACACTCGAGCTAGA 60.027 50.0 19.69 0.0 0.0 2.43 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
22 23 3.204467 TTCTTTCCCAGGGCACGGG 62.204 63.158 9.35 9.35 46.03 5.28
287 312 1.221021 CTCCCTAGGGCAAACGACC 59.779 63.158 24.42 0.00 34.68 4.79
298 323 2.902457 AAACGACCATTCCGGGGCT 61.902 57.895 0.00 0.00 40.22 5.19
316 341 1.334960 GCTTGTGTTTGATGTGTCCCG 60.335 52.381 0.00 0.00 0.00 5.14
460 489 5.233225 TCTGTTTTTGTGTTGTTGCAATGA 58.767 33.333 0.59 0.00 0.00 2.57
498 527 1.740332 TTGCACGAGACAACCGAGGA 61.740 55.000 0.00 0.00 0.00 3.71
615 644 3.937814 AGATTAAGGTTGATGCACACGA 58.062 40.909 0.00 0.00 0.00 4.35
884 915 6.318144 ACATCTCTCGAGAATTTTCATGCATT 59.682 34.615 17.36 0.00 41.36 3.56
956 987 8.200120 CCTGAAGACATTCAACTATGATCAGTA 58.800 37.037 0.09 0.00 44.68 2.74
1132 1170 4.344968 TCTCCATCAGTTGAAACTCAGTGA 59.655 41.667 0.00 0.00 37.08 3.41
1325 1369 4.399934 TGATGCATTGCAGCTATTCTTCAA 59.600 37.500 25.47 1.26 45.80 2.69
1351 1395 6.127004 TTGTACACAAAAAGCACTGGGCAA 62.127 41.667 4.01 0.00 37.74 4.52
1489 1533 2.879002 TGGCGCAACAAATCTTTTCA 57.121 40.000 10.83 0.00 0.00 2.69
1546 1592 6.373774 TGCATTTTGTTTGTCCATGTTTTCTT 59.626 30.769 0.00 0.00 0.00 2.52
1733 1779 7.032377 AGACATTTTTCTCTTTGTTCACCTC 57.968 36.000 0.00 0.00 0.00 3.85
2050 2099 2.034879 CCCGCGCATCAGTTGAAGT 61.035 57.895 8.75 0.00 0.00 3.01
2059 2108 4.614946 GCATCAGTTGAAGTTGCTTCTTT 58.385 39.130 9.82 0.00 40.73 2.52
2102 2151 1.544314 GCTTCTGCAACAGGAGGAGTT 60.544 52.381 5.09 0.00 37.56 3.01
2181 2230 1.630369 TGGGAGCATGTTCTTGTAGCT 59.370 47.619 9.57 0.00 38.43 3.32
2277 2326 7.815840 TGAAGTTCACAGGAATGTTTCATTA 57.184 32.000 0.08 0.00 35.05 1.90
2623 2685 2.283604 GGGGTTGGGGCGATTGTT 60.284 61.111 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.736400 GCAGTTACCATCATTGCTTGCC 60.736 50.000 0.00 0.0 0.00 4.52
26 27 2.756760 CAAGGCAGTTACCATCATTGCT 59.243 45.455 0.00 0.0 35.23 3.91
287 312 0.038343 CAAACACAAGCCCCGGAATG 60.038 55.000 0.73 0.0 0.00 2.67
298 323 0.665835 GCGGGACACATCAAACACAA 59.334 50.000 0.00 0.0 0.00 3.33
316 341 3.609807 GGAAGCGTTTTTGAATGAGATGC 59.390 43.478 0.00 0.0 0.00 3.91
460 489 4.949238 TGCAAATCCATTACTACTGCACAT 59.051 37.500 0.00 0.0 33.65 3.21
473 502 1.812571 GGTTGTCTCGTGCAAATCCAT 59.187 47.619 0.00 0.0 0.00 3.41
498 527 1.002134 CCCCTGACCGCAACATTCT 60.002 57.895 0.00 0.0 0.00 2.40
805 836 7.406553 GGCCTGTAAAAAGAAAATTTGTGTTC 58.593 34.615 0.00 0.0 0.00 3.18
884 915 1.899814 TCTCCGCTCTTGGCTTTAGAA 59.100 47.619 0.00 0.0 39.13 2.10
956 987 6.530019 TTTTTGGCTTCTTCTTCTTCACTT 57.470 33.333 0.00 0.0 0.00 3.16
1061 1095 2.439507 AGGGCAGACCACAACTATATGG 59.560 50.000 0.00 0.0 43.89 2.74
1132 1170 3.285484 GGATCAAACACATCTGGCTCAT 58.715 45.455 0.00 0.0 0.00 2.90
1325 1369 3.130340 CCAGTGCTTTTTGTGTACAACCT 59.870 43.478 0.00 0.0 35.28 3.50
1351 1395 5.950544 TGGGTGATGTTAGCAACTACTAT 57.049 39.130 0.00 0.0 0.00 2.12
1546 1592 0.109532 TTGCGACCTGATCAAACCCA 59.890 50.000 0.00 0.0 0.00 4.51
1725 1771 2.735823 CAAAAGCAGCTTGAGGTGAAC 58.264 47.619 8.88 0.0 45.66 3.18
1733 1779 7.355332 AGTTATAAAATGCAAAAGCAGCTTG 57.645 32.000 8.88 0.0 0.00 4.01
2059 2108 2.419021 CGAAAACCCCCATCTAACGCTA 60.419 50.000 0.00 0.0 0.00 4.26
2144 2193 2.026542 TCCCAACTACACTCGAGCTAGA 60.027 50.000 19.69 0.0 0.00 2.43
2181 2230 2.678836 GCTCTCAACTACACTCGAGCTA 59.321 50.000 13.61 1.0 40.37 3.32
2277 2326 5.012239 ACAAATCCTTGCATACAGTCACAT 58.988 37.500 0.00 0.0 35.84 3.21
2623 2685 2.727123 TGAAGAGAAACAACAGCCCA 57.273 45.000 0.00 0.0 0.00 5.36
2682 2744 7.505248 TGCCACATAGAAAGGATATTGCATTAA 59.495 33.333 0.00 0.0 0.00 1.40


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

AutoCloner maintained by Alex Coulton.