Multiple sequence alignment - TraesCS5D01G119600

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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 TraesCS5D01G119600 chr5D 100.000 2732 0 0 1 2732 165250423 165253154 0 5046
1 TraesCS5D01G119600 chr5D 96.824 2739 78 6 1 2732 210479993 210477257 0 4567
2 TraesCS5D01G119600 chr5D 96.495 2739 84 9 1 2732 107838693 107835960 0 4516
3 TraesCS5D01G119600 chr6D 97.074 2734 75 5 1 2732 298652369 298655099 0 4601
4 TraesCS5D01G119600 chr6D 96.928 2734 78 4 1 2732 305891572 305894301 0 4578
5 TraesCS5D01G119600 chr1D 97.075 2735 73 5 1 2732 179488160 179490890 0 4601
6 TraesCS5D01G119600 chr1D 96.637 2736 76 10 1 2732 146890214 146892937 0 4529
7 TraesCS5D01G119600 chr1D 96.425 2741 82 11 1 2732 369966209 369968942 0 4505
8 TraesCS5D01G119600 chr2D 96.678 2739 77 7 1 2732 324193960 324196691 0 4542
9 TraesCS5D01G119600 chr4D 96.455 2736 88 6 1 2732 353946253 353943523 0 4506


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 TraesCS5D01G119600 chr5D 165250423 165253154 2731 False 5046 5046 100.000 1 2732 1 chr5D.!!$F1 2731
1 TraesCS5D01G119600 chr5D 210477257 210479993 2736 True 4567 4567 96.824 1 2732 1 chr5D.!!$R2 2731
2 TraesCS5D01G119600 chr5D 107835960 107838693 2733 True 4516 4516 96.495 1 2732 1 chr5D.!!$R1 2731
3 TraesCS5D01G119600 chr6D 298652369 298655099 2730 False 4601 4601 97.074 1 2732 1 chr6D.!!$F1 2731
4 TraesCS5D01G119600 chr6D 305891572 305894301 2729 False 4578 4578 96.928 1 2732 1 chr6D.!!$F2 2731
5 TraesCS5D01G119600 chr1D 179488160 179490890 2730 False 4601 4601 97.075 1 2732 1 chr1D.!!$F2 2731
6 TraesCS5D01G119600 chr1D 146890214 146892937 2723 False 4529 4529 96.637 1 2732 1 chr1D.!!$F1 2731
7 TraesCS5D01G119600 chr1D 369966209 369968942 2733 False 4505 4505 96.425 1 2732 1 chr1D.!!$F3 2731
8 TraesCS5D01G119600 chr2D 324193960 324196691 2731 False 4542 4542 96.678 1 2732 1 chr2D.!!$F1 2731
9 TraesCS5D01G119600 chr4D 353943523 353946253 2730 True 4506 4506 96.455 1 2732 1 chr4D.!!$R1 2731

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
222 224 0.310854 GTCTTGTGGGGAAAAGTGCG 59.689 55.0 0.0 0.0 0.0 5.34 F
925 933 0.313987 CACGCTGACTGTAGGACACA 59.686 55.0 0.0 0.0 35.3 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1322 1330 0.249447 CCATTGCTCATCTCGGCGTA 60.249 55.0 6.85 0.0 0.00 4.42 R
2113 2149 0.739462 CAACAATCGGCTCGGTGCTA 60.739 55.0 1.77 0.0 42.39 3.49 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
202 203 2.978452 AATCAAGCGGAGGCGATCGG 62.978 60.000 18.30 0.01 46.35 4.18
222 224 0.310854 GTCTTGTGGGGAAAAGTGCG 59.689 55.000 0.00 0.00 0.00 5.34
332 334 8.886719 TCATGTGAATCTCATCATGTTACTTTC 58.113 33.333 13.76 0.00 37.28 2.62
519 524 8.093307 AGCCATATATGCATGTAGTATAGCATC 58.907 37.037 10.16 0.00 43.67 3.91
520 525 7.062722 GCCATATATGCATGTAGTATAGCATCG 59.937 40.741 10.16 0.00 43.67 3.84
682 687 2.427506 GTTGGAGTTGATGGACTCACC 58.572 52.381 7.27 0.00 46.21 4.02
687 692 3.070302 GGAGTTGATGGACTCACCTATCC 59.930 52.174 7.27 0.00 46.21 2.59
801 807 9.448438 TGTGTGATTGCTACTCTGTTATAAATT 57.552 29.630 0.00 0.00 0.00 1.82
835 843 2.094026 TGCGTGTCAGCATTACAGATCT 60.094 45.455 0.00 0.00 42.92 2.75
899 907 2.303600 TGGTCGCTACAAAGGTGGTATT 59.696 45.455 0.00 0.00 0.00 1.89
925 933 0.313987 CACGCTGACTGTAGGACACA 59.686 55.000 0.00 0.00 35.30 3.72
954 962 8.092687 CACTAAGCTTAAACCCTAGAACACTAA 58.907 37.037 7.74 0.00 0.00 2.24
1069 1077 2.992124 TGGACGACACTTGAAGGAAA 57.008 45.000 0.00 0.00 0.00 3.13
1122 1130 1.053424 TCACCGGGACTTACAAAGCT 58.947 50.000 6.32 0.00 0.00 3.74
1204 1212 2.295909 CCAGTCACTGAGCCTATAGAGC 59.704 54.545 6.30 3.20 32.44 4.09
1252 1260 2.274760 GGAAGAGCATGGCAGCCT 59.725 61.111 14.15 0.00 34.23 4.58
1451 1459 3.244156 GCGCAGACATGATAGATCTGAG 58.756 50.000 12.99 10.87 42.07 3.35
1493 1501 2.234908 CGGAGTTGGAGGAAGAACTCAT 59.765 50.000 12.56 0.00 46.69 2.90
1504 1512 1.809619 GAACTCATGGCTACGCGCA 60.810 57.895 5.73 0.00 41.67 6.09
1527 1535 6.431234 GCAAGGATTATATGGAGGAAATCGTT 59.569 38.462 0.00 0.00 37.08 3.85
1566 1574 2.351835 CGACGACCTGACACAGAAGATT 60.352 50.000 0.00 0.00 32.44 2.40
2113 2149 0.476771 ATCCACCGGTGTTTTCCAGT 59.523 50.000 31.80 6.64 0.00 4.00
2345 2381 1.453235 GCAGGAGCTATGGCCATGA 59.547 57.895 29.04 11.24 39.73 3.07
2424 2460 6.212791 TGTGGAGGACTTTAGTAAGTTAGCAT 59.787 38.462 0.00 0.00 44.51 3.79
2610 2647 5.952347 AAACCGTAAGAGGAAGTATGGAT 57.048 39.130 0.00 0.00 43.02 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 203 0.673985 GCACTTTTCCCCACAAGACC 59.326 55.000 0.00 0.00 0.00 3.85
222 224 2.169832 TACACTCTGCAGAGGTTTGC 57.830 50.000 39.42 0.00 46.13 3.68
332 334 8.945481 TCATCATTAACCCAGCAAAATTAATG 57.055 30.769 13.29 13.29 42.47 1.90
343 345 8.796475 CCCAATTAAGTATCATCATTAACCCAG 58.204 37.037 0.00 0.00 0.00 4.45
445 449 3.519908 GCGAAAAGCCAATTTTTCCAC 57.480 42.857 5.85 0.00 41.24 4.02
519 524 7.142021 ACACATAGAGAGTAATGAGCATAACG 58.858 38.462 0.00 0.00 0.00 3.18
520 525 8.879342 AACACATAGAGAGTAATGAGCATAAC 57.121 34.615 0.00 0.00 0.00 1.89
526 531 8.759641 GCAATGTAACACATAGAGAGTAATGAG 58.240 37.037 0.00 0.00 37.97 2.90
592 597 6.211515 GTCTGAAAAGTCTGCAACATGAAAT 58.788 36.000 0.00 0.00 0.00 2.17
682 687 2.035632 AGCGGAAGACTTGGAGGATAG 58.964 52.381 0.00 0.00 0.00 2.08
687 692 2.743636 TAACAGCGGAAGACTTGGAG 57.256 50.000 0.00 0.00 0.00 3.86
801 807 1.000607 GACACGCACAGTACTTGGAGA 60.001 52.381 0.00 0.00 0.00 3.71
830 838 3.303938 CACCAGTGTCATCCCTAGATCT 58.696 50.000 0.00 0.00 0.00 2.75
835 843 0.613260 GTGCACCAGTGTCATCCCTA 59.387 55.000 5.22 0.00 0.00 3.53
925 933 6.183361 TGTTCTAGGGTTTAAGCTTAGTGGTT 60.183 38.462 11.90 0.00 39.89 3.67
954 962 6.197168 AGAGGAGTCAGAAATGAGAAGAGAT 58.803 40.000 0.00 0.00 0.00 2.75
1069 1077 4.954202 TCCGATGTTCAGGTACTTAGTGAT 59.046 41.667 0.00 0.00 34.60 3.06
1122 1130 2.366533 CGCTCCTCTTCTGGTAGTGTA 58.633 52.381 0.00 0.00 0.00 2.90
1204 1212 2.629617 AGGTTGGTGCATCAAAGGAAAG 59.370 45.455 15.37 0.00 0.00 2.62
1252 1260 3.006859 CCAATGCGTCCCATAGAGATGTA 59.993 47.826 0.00 0.00 32.67 2.29
1322 1330 0.249447 CCATTGCTCATCTCGGCGTA 60.249 55.000 6.85 0.00 0.00 4.42
1451 1459 2.424956 GTGATCTTGGTCAATGCCTTCC 59.575 50.000 0.00 0.00 0.00 3.46
1504 1512 6.431234 GCAACGATTTCCTCCATATAATCCTT 59.569 38.462 0.00 0.00 0.00 3.36
1527 1535 2.030185 GTCGTTCTTCCTCACTAGTGCA 60.030 50.000 18.45 6.44 0.00 4.57
1566 1574 2.408565 GGGTCTCCCATGAATACTCCA 58.591 52.381 0.00 0.00 44.65 3.86
1593 1601 2.621055 AGAATCGTCATCTTCTCCTCCG 59.379 50.000 0.00 0.00 0.00 4.63
2113 2149 0.739462 CAACAATCGGCTCGGTGCTA 60.739 55.000 1.77 0.00 42.39 3.49
2424 2460 3.261580 CAACGTCATCTGGAGCATAACA 58.738 45.455 0.00 0.00 0.00 2.41
2610 2647 4.783227 AGCTCCAGAATTGTACTTCCCTTA 59.217 41.667 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.