Multiple sequence alignment - TraesCS7D01G363800

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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 TraesCS7D01G363800 chr7D 100.00 3608 0 0 1 3608 467999109 467995502 0 6663
1 TraesCS7D01G363800 chr7B 98.92 3611 33 5 1 3608 491400285 491396678 0 6447


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 TraesCS7D01G363800 chr7D 467995502 467999109 3607 True 6663 6663 100.00 1 3608 1 chr7D.!!$R1 3607
1 TraesCS7D01G363800 chr7B 491396678 491400285 3607 True 6447 6447 98.92 1 3608 1 chr7B.!!$R1 3607

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
132 135 0.170339 GGTATCTGCAAACGCCAACC 59.830 55.000 0.00 0.00 0.0 3.77 F
150 153 1.541310 CCAAGGACAGGTGAGGCGTA 61.541 60.000 0.00 0.00 0.0 4.42 F
1407 1410 1.134280 AGAAGGGCCGAACATCTGATG 60.134 52.381 15.83 15.83 0.0 3.07 F
1666 1669 0.178915 AGGTGTGGGTGTACTGGCTA 60.179 55.000 0.00 0.00 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1310 1313 1.055849 TGGCAGTGCACCTTTCTCTA 58.944 50.0 18.61 0.0 0.00 2.43 R
1666 1669 2.603075 ACACCACCAATGCCAGTTAT 57.397 45.0 0.00 0.0 0.00 1.89 R
2525 2528 0.034896 GTATGTATCAGGTGCCCCCG 59.965 60.0 0.00 0.0 38.74 5.73 R
3234 3238 1.343069 CTATCAGAGGTGCCCCTACC 58.657 60.0 0.00 0.0 42.86 3.18 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
78 81 1.372087 GGAACCCTGAAGCAGCATCG 61.372 60.000 0.00 0.00 0.00 3.84
132 135 0.170339 GGTATCTGCAAACGCCAACC 59.830 55.000 0.00 0.00 0.00 3.77
150 153 1.541310 CCAAGGACAGGTGAGGCGTA 61.541 60.000 0.00 0.00 0.00 4.42
319 322 9.177608 CATGTTTGAATTGTAGAGGAAGGATTA 57.822 33.333 0.00 0.00 0.00 1.75
409 412 7.115378 GCACTTCAAATTTCATGAAACTGTAGG 59.885 37.037 25.88 19.91 36.43 3.18
420 423 3.197766 TGAAACTGTAGGCTAGGATGGTG 59.802 47.826 0.00 0.00 0.00 4.17
478 481 2.496470 AGTGGTTATCCAGTTCGTCCTC 59.504 50.000 0.00 0.00 44.20 3.71
660 663 6.980397 CCTGCTCATTTTTGTACTTCTGTTTT 59.020 34.615 0.00 0.00 0.00 2.43
661 664 7.168135 CCTGCTCATTTTTGTACTTCTGTTTTC 59.832 37.037 0.00 0.00 0.00 2.29
663 666 7.915397 TGCTCATTTTTGTACTTCTGTTTTCTC 59.085 33.333 0.00 0.00 0.00 2.87
880 883 8.853469 TTAAACTAACAATTAAACGTGGTTGG 57.147 30.769 0.00 0.00 0.00 3.77
1184 1187 3.035363 TGCCAATGATGCAGGAAATGAT 58.965 40.909 0.00 0.00 34.05 2.45
1246 1249 7.484140 AGCAAAACTTTTAGAAGAACTCAAGG 58.516 34.615 0.00 0.00 36.69 3.61
1310 1313 7.849804 ACTATTACGTGCTGAAATCAAAGAT 57.150 32.000 0.00 0.00 0.00 2.40
1407 1410 1.134280 AGAAGGGCCGAACATCTGATG 60.134 52.381 15.83 15.83 0.00 3.07
1666 1669 0.178915 AGGTGTGGGTGTACTGGCTA 60.179 55.000 0.00 0.00 0.00 3.93
1744 1747 3.131223 TCCTCTGGTAGAAGCTCATTTCG 59.869 47.826 0.00 0.00 32.33 3.46
1823 1826 0.323542 CTCGTACAGTCCTCAGGGGT 60.324 60.000 0.00 0.00 36.25 4.95
1944 1947 5.049474 CGATGTTCTGACTGAAAATGGACAA 60.049 40.000 2.67 0.00 32.99 3.18
2096 2099 1.988107 TGATGCCTTCTGGGAGTTCTT 59.012 47.619 0.00 0.00 37.02 2.52
2271 2274 6.922957 GGAGAAATGTCTTAGATAGTGAGCTG 59.077 42.308 0.00 0.00 32.80 4.24
2346 2349 6.037830 GCTACATTTATCTGCCTTTCCGTTTA 59.962 38.462 0.00 0.00 0.00 2.01
2525 2528 2.095819 GCTCACTCTTTCAAGAAGCTGC 60.096 50.000 4.97 0.00 34.03 5.25
2670 2674 3.561310 GCATTTGTCACTGTTCACAGAGA 59.439 43.478 14.00 8.41 46.59 3.10
2738 2742 5.329035 AGCTGCGGACAATTTTTATCAAT 57.671 34.783 0.00 0.00 0.00 2.57
2769 2773 5.023452 TGAACCAGACTGCTCTTATTCCTA 58.977 41.667 0.00 0.00 0.00 2.94
2970 2974 1.908066 GCAAACGTTCGTGGGGCTAG 61.908 60.000 0.00 0.00 0.00 3.42
3090 3094 2.433868 TTCTGTTCCTTCCGAGTTCG 57.566 50.000 0.00 0.00 39.44 3.95
3234 3238 8.406297 GGAAACTAATATTAGCTTTTGACCAGG 58.594 37.037 20.24 0.00 34.09 4.45
3296 3300 0.413037 TTTGCCCCCATCCAGATGTT 59.587 50.000 6.87 0.00 37.11 2.71
3576 3580 1.754201 GCCCAGAGTTGGTGAACCTTT 60.754 52.381 0.37 0.00 43.40 3.11
3577 3581 2.666317 CCCAGAGTTGGTGAACCTTTT 58.334 47.619 0.37 0.00 43.40 2.27
3591 3595 6.874664 GGTGAACCTTTTTGTTGAAACCTTTA 59.125 34.615 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 81 3.462021 AGAAGCTTCGAGATGCCAATAC 58.538 45.455 20.43 0.0 32.53 1.89
132 135 0.389948 GTACGCCTCACCTGTCCTTG 60.390 60.000 0.00 0.0 0.00 3.61
150 153 2.713154 GTGCGACCAACAAAGCGT 59.287 55.556 0.00 0.0 0.00 5.07
409 412 2.012673 CTTCACAAGCACCATCCTAGC 58.987 52.381 0.00 0.0 0.00 3.42
420 423 2.095364 CAGCAGGATTCACTTCACAAGC 60.095 50.000 0.00 0.0 0.00 4.01
478 481 7.443575 AGCTGTTAGGACATTCAAGCAATATAG 59.556 37.037 0.00 0.0 34.72 1.31
660 663 6.876257 GCAGAGATAACAAGAAAAAGGAGAGA 59.124 38.462 0.00 0.0 0.00 3.10
661 664 6.652481 TGCAGAGATAACAAGAAAAAGGAGAG 59.348 38.462 0.00 0.0 0.00 3.20
663 666 6.808008 TGCAGAGATAACAAGAAAAAGGAG 57.192 37.500 0.00 0.0 0.00 3.69
880 883 2.147150 GAACTGTGACTCCAAAGCTCC 58.853 52.381 0.00 0.0 30.52 4.70
1184 1187 3.258372 ACTTGACCACTCTGCTTTATCGA 59.742 43.478 0.00 0.0 0.00 3.59
1310 1313 1.055849 TGGCAGTGCACCTTTCTCTA 58.944 50.000 18.61 0.0 0.00 2.43
1407 1410 6.638468 GTGAAACCATGAAATTCAACTGAGTC 59.362 38.462 0.00 0.0 35.07 3.36
1666 1669 2.603075 ACACCACCAATGCCAGTTAT 57.397 45.000 0.00 0.0 0.00 1.89
1744 1747 3.758554 ACACATATCCAAAGCTGTTGGTC 59.241 43.478 20.22 0.0 40.40 4.02
1823 1826 5.559770 TCAGGTTATCTGACAATGCTTTCA 58.440 37.500 0.00 0.0 46.71 2.69
1944 1947 2.641815 AGCACAGAAGTTCTCCCATTCT 59.358 45.455 1.26 0.0 33.62 2.40
2096 2099 4.678622 GCAATTGAATGCACATGATCTGA 58.321 39.130 10.34 0.0 45.70 3.27
2134 2137 6.040209 TGCAATGGTTTCTAAATCTGCATT 57.960 33.333 0.00 0.0 0.00 3.56
2271 2274 6.096673 TCCTTTTCTTGCTTTAATTCCCAC 57.903 37.500 0.00 0.0 0.00 4.61
2525 2528 0.034896 GTATGTATCAGGTGCCCCCG 59.965 60.000 0.00 0.0 38.74 5.73
2539 2542 6.767423 TGGATCAAATCATGAATGACGTATGT 59.233 34.615 14.65 0.0 42.54 2.29
2738 2742 4.005650 GAGCAGTCTGGTTCAATGATTCA 58.994 43.478 5.91 0.0 0.00 2.57
2970 2974 5.437060 TGGTAAGTTCTGGAATATGAAGCC 58.563 41.667 0.00 0.0 0.00 4.35
3090 3094 4.026356 ACCTTAGCAATCTGATATGGGC 57.974 45.455 8.25 0.0 37.72 5.36
3234 3238 1.343069 CTATCAGAGGTGCCCCTACC 58.657 60.000 0.00 0.0 42.86 3.18
3386 3390 9.459640 ACTGTACGTATATCACATGTTATGAAC 57.540 33.333 0.00 0.0 0.00 3.18


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

AutoCloner maintained by Alex Coulton.