Multiple sequence alignment - TraesCS2D01G320200

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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 TraesCS2D01G320200 chr2D 100.000 3073 0 0 1 3073 411418559 411415487 0.000000e+00 5675.0
1 TraesCS2D01G320200 chr2D 97.832 2814 48 9 1 2805 411704652 411701843 0.000000e+00 4846.0
2 TraesCS2D01G320200 chr2D 97.059 272 8 0 2802 3073 411701731 411701460 2.790000e-125 459.0
3 TraesCS2D01G320200 chr2A 94.257 1515 67 4 1 1507 579211697 579210195 0.000000e+00 2298.0
4 TraesCS2D01G320200 chr2A 93.544 1425 70 14 1497 2900 579143474 579142051 0.000000e+00 2102.0
5 TraesCS2D01G320200 chr2A 96.591 176 6 0 2896 3071 579076924 579076749 3.000000e-75 292.0
6 TraesCS2D01G320200 chr5A 96.774 31 1 0 2807 2837 143033959 143033989 6.000000e-03 52.8


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 TraesCS2D01G320200 chr2D 411415487 411418559 3072 True 5675.0 5675 100.0000 1 3073 1 chr2D.!!$R1 3072
1 TraesCS2D01G320200 chr2D 411701460 411704652 3192 True 2652.5 4846 97.4455 1 3073 2 chr2D.!!$R2 3072
2 TraesCS2D01G320200 chr2A 579210195 579211697 1502 True 2298.0 2298 94.2570 1 1507 1 chr2A.!!$R3 1506
3 TraesCS2D01G320200 chr2A 579142051 579143474 1423 True 2102.0 2102 93.5440 1497 2900 1 chr2A.!!$R2 1403

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
605 606 0.625316 TATGGCCCTGCAAGATGTGT 59.375 50.0 0.0 0.0 34.07 3.72 F
1460 1469 0.613777 CCTCCTCTAGGCCGTTTTGT 59.386 55.0 0.0 0.0 38.97 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 1661 1.202557 TGGCCACGACCGAAATATACC 60.203 52.381 0.0 0.0 0.0 2.73 R
3018 3162 1.619654 TGGGTGATCCTTTGTTGCTG 58.380 50.000 0.0 0.0 36.2 4.41 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
142 143 9.244292 TGTGGGTGTGCTTATGTTTAAATTATA 57.756 29.630 0.00 0.00 0.00 0.98
285 286 5.774498 AGTTAGGTTTCTGGAAAAGCAAG 57.226 39.130 0.00 0.00 31.33 4.01
605 606 0.625316 TATGGCCCTGCAAGATGTGT 59.375 50.000 0.00 0.00 34.07 3.72
712 713 3.266772 AGATGGATTGCACTACTCCCAAA 59.733 43.478 0.00 0.00 0.00 3.28
826 835 2.746279 TTTGAGGGTGACAACATGGT 57.254 45.000 0.00 0.00 0.00 3.55
976 985 0.774276 TGGTATTGGAACTGTGCCCA 59.226 50.000 1.39 0.00 0.00 5.36
1317 1326 2.418368 AGTTTGCTCAGTTGGTGACA 57.582 45.000 0.00 0.00 39.83 3.58
1412 1421 4.210331 GTGAATATGATTCCCACCAAGCT 58.790 43.478 0.00 0.00 0.00 3.74
1460 1469 0.613777 CCTCCTCTAGGCCGTTTTGT 59.386 55.000 0.00 0.00 38.97 2.83
1652 1661 0.326927 ACCGAACCTAATGTGGTGGG 59.673 55.000 0.00 0.00 40.73 4.61
1728 1737 6.415573 AGTCTTCAAGTTGACCTACTTTGTT 58.584 36.000 4.68 0.00 36.24 2.83
2055 2065 0.112218 TACAAACCTGCTGCCCATGT 59.888 50.000 0.00 0.00 0.00 3.21
2498 2516 1.991121 TGTACACTCTGACGGAACCT 58.009 50.000 0.00 0.00 0.00 3.50
2563 2581 1.572085 AAGCGTGCACATCACTCTGC 61.572 55.000 18.64 9.31 39.64 4.26
2600 2618 5.736486 AACGACTCTTCAACTTTTCTTCC 57.264 39.130 0.00 0.00 0.00 3.46
2652 2670 6.247229 TGCATAAGAAACAGGGCTATCTTA 57.753 37.500 0.00 0.00 38.38 2.10
2805 2834 5.072741 ACCTCTAGTGACCTAAAACGTACA 58.927 41.667 0.00 0.00 0.00 2.90
2963 3107 6.976636 TGTCGCTTGTTGATTATGTTCATA 57.023 33.333 0.00 0.00 0.00 2.15
2992 3136 5.529060 AGAACTTTAGCTTGGAGAACAACAG 59.471 40.000 0.00 0.00 34.76 3.16
3018 3162 6.371809 TTGGATCTTGTTTGTGTTACTGTC 57.628 37.500 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 6.071784 TGCTAGCAGTTGAATGACAATGAAAT 60.072 34.615 14.93 0.0 40.76 2.17
142 143 4.817318 ACAAAATTAATGGCCAACGGAT 57.183 36.364 10.96 0.0 0.00 4.18
308 309 2.742774 ACTTGCGAATTTCAAGGCAAC 58.257 42.857 19.15 0.0 43.77 4.17
712 713 7.815068 GCTTCACTATTTCATCATACCGAGTAT 59.185 37.037 0.00 0.0 0.00 2.12
783 792 2.235898 CTGAGACTGGAAGAAAGGGGAG 59.764 54.545 0.00 0.0 37.43 4.30
826 835 3.725754 GGTTGGCAGACCTCTCAAA 57.274 52.632 10.41 0.0 36.73 2.69
976 985 0.036010 CCAGTCTGAAGCCGACCAAT 60.036 55.000 0.00 0.0 31.83 3.16
1317 1326 2.636830 CCAGATCGCCTGTCAATCTTT 58.363 47.619 4.40 0.0 41.33 2.52
1412 1421 3.773119 GGTGAAGGTCTCCACTACCATAA 59.227 47.826 0.00 0.0 39.64 1.90
1460 1469 4.377943 CCGTTTGCTTCATATCACGAACAA 60.378 41.667 0.00 0.0 0.00 2.83
1652 1661 1.202557 TGGCCACGACCGAAATATACC 60.203 52.381 0.00 0.0 0.00 2.73
2055 2065 3.359033 ACACCTATGCTTCGTAGTACCA 58.641 45.455 0.00 0.0 0.00 3.25
2498 2516 2.672874 CGCAGCAAGCAGAGTGTATTAA 59.327 45.455 0.00 0.0 46.13 1.40
2563 2581 9.241317 TGAAGAGTCGTTTTAGTAGTTAAGTTG 57.759 33.333 0.00 0.0 0.00 3.16
2652 2670 8.225603 AGTTGTCATGAAGAACTGTAAATGTT 57.774 30.769 16.85 0.0 0.00 2.71
2963 3107 5.552870 TCTCCAAGCTAAAGTTCTGAACT 57.447 39.130 17.00 17.0 45.46 3.01
2992 3136 7.033185 ACAGTAACACAAACAAGATCCAAAAC 58.967 34.615 0.00 0.0 0.00 2.43
3018 3162 1.619654 TGGGTGATCCTTTGTTGCTG 58.380 50.000 0.00 0.0 36.20 4.41


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

AutoCloner maintained by Alex Coulton.