Multiple sequence alignment - TraesCS6A01G315500

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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 TraesCS6A01G315500 chr6A 100.000 2136 0 0 771 2906 552207698 552209833 0.000000e+00 3945.0
1 TraesCS6A01G315500 chr6A 100.000 67 0 0 1 67 552206928 552206994 1.090000e-24 124.0
2 TraesCS6A01G315500 chr6A 78.030 132 25 3 1713 1842 487770715 487770844 2.400000e-11 80.5
3 TraesCS6A01G315500 chr6D 92.219 2159 111 31 771 2906 405649747 405651871 0.000000e+00 3003.0
4 TraesCS6A01G315500 chr6D 87.179 195 13 8 879 1065 405649216 405649406 8.160000e-51 211.0
5 TraesCS6A01G315500 chr6B 92.582 2103 106 23 771 2862 609853758 609855821 0.000000e+00 2974.0
6 TraesCS6A01G315500 chr6B 78.030 132 25 3 1713 1842 523880887 523881016 2.400000e-11 80.5


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 TraesCS6A01G315500 chr6A 552206928 552209833 2905 False 2034.5 3945 100.000 1 2906 2 chr6A.!!$F2 2905
1 TraesCS6A01G315500 chr6D 405649216 405651871 2655 False 1607.0 3003 89.699 771 2906 2 chr6D.!!$F1 2135
2 TraesCS6A01G315500 chr6B 609853758 609855821 2063 False 2974.0 2974 92.582 771 2862 1 chr6B.!!$F2 2091

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
66 67 1.769295 TTGGGGGTGGACACGGTTA 60.769 57.895 0.00 0.00 0.00 2.85 F
1194 1211 1.261089 CCTCTAATCCTCGTCGACGAC 59.739 57.143 34.97 18.04 44.22 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 1640 0.390603 CCAGCGAAATCACCGTGGTA 60.391 55.0 0.00 0.00 0.00 3.25 R
2709 2733 0.037326 TGGTCGACCACTTGATCTGC 60.037 55.0 33.23 3.01 42.01 4.26 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
64 65 3.566210 CTTGGGGGTGGACACGGT 61.566 66.667 0.00 0.00 0.00 4.83
66 67 1.769295 TTGGGGGTGGACACGGTTA 60.769 57.895 0.00 0.00 0.00 2.85
982 993 9.601217 TTACAGTCTCTTTCTTGGATTAATAGC 57.399 33.333 0.00 0.00 0.00 2.97
1033 1044 5.185249 AGAACACCGCTTCTAGTAGATTCAA 59.815 40.000 0.00 0.00 0.00 2.69
1040 1051 5.520649 CGCTTCTAGTAGATTCAAAAGTCCC 59.479 44.000 0.00 0.00 0.00 4.46
1164 1181 4.832608 AGGAAATCGACGGCGGCC 62.833 66.667 12.58 9.54 38.28 6.13
1194 1211 1.261089 CCTCTAATCCTCGTCGACGAC 59.739 57.143 34.97 18.04 44.22 4.34
1308 1325 2.588314 CATCTGCCGGCTCTCTGC 60.588 66.667 29.70 0.00 41.94 4.26
1541 1558 2.439104 GCTCCATCGCCTCCTTCCT 61.439 63.158 0.00 0.00 0.00 3.36
1620 1637 2.263741 GCTGTCTGCTTGGTGGTGG 61.264 63.158 0.00 0.00 38.95 4.61
1623 1640 3.872603 TCTGCTTGGTGGTGGCGT 61.873 61.111 0.00 0.00 0.00 5.68
1645 1662 1.741770 ACGGTGATTTCGCTGGAGC 60.742 57.895 5.05 0.00 37.07 4.70
2106 2123 1.656095 GCGAGGATGAAGAAGAACACG 59.344 52.381 0.00 0.00 0.00 4.49
2169 2186 3.461773 ATCTCCTGGTCGGCCACG 61.462 66.667 3.51 0.11 40.46 4.94
2178 2195 3.902086 TCGGCCACGTCGTTGTCA 61.902 61.111 2.24 0.00 41.85 3.58
2373 2394 2.267006 CTGACTGGCTGCGGATGT 59.733 61.111 0.00 0.00 0.00 3.06
2377 2398 1.078848 ACTGGCTGCGGATGTTCTC 60.079 57.895 0.00 0.00 0.00 2.87
2378 2399 2.125552 TGGCTGCGGATGTTCTCG 60.126 61.111 0.00 0.00 0.00 4.04
2411 2435 0.386985 GTCCGTCGACTGTGGAGTTC 60.387 60.000 14.70 0.00 35.99 3.01
2430 2454 3.451402 TCGGGCTATATAGAGGCAGAA 57.549 47.619 18.75 5.50 41.88 3.02
2431 2455 3.357203 TCGGGCTATATAGAGGCAGAAG 58.643 50.000 18.75 9.20 41.88 2.85
2432 2456 2.159170 CGGGCTATATAGAGGCAGAAGC 60.159 54.545 20.95 4.03 43.66 3.86
2433 2457 2.834549 GGGCTATATAGAGGCAGAAGCA 59.165 50.000 20.95 0.00 43.66 3.91
2434 2458 3.118811 GGGCTATATAGAGGCAGAAGCAG 60.119 52.174 20.95 0.00 43.66 4.24
2435 2459 3.766591 GGCTATATAGAGGCAGAAGCAGA 59.233 47.826 15.45 0.00 44.61 4.26
2442 2466 2.667418 GCAGAAGCAGAGGAGCCA 59.333 61.111 0.00 0.00 41.58 4.75
2445 2469 2.124778 GAAGCAGAGGAGCCAGCC 60.125 66.667 0.00 0.00 34.23 4.85
2669 2693 3.745803 GCAGCAGGCTGGCAGTTC 61.746 66.667 21.63 9.03 43.77 3.01
2843 2875 2.188817 AGGGTGTGGGTAGATCTCAAC 58.811 52.381 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.770749 TAACCGTGTCCACCCCCAAG 61.771 60.000 0.00 0.00 0.00 3.61
48 49 1.769295 TAACCGTGTCCACCCCCAA 60.769 57.895 0.00 0.00 0.00 4.12
49 50 2.122503 TAACCGTGTCCACCCCCA 60.123 61.111 0.00 0.00 0.00 4.96
791 792 6.056884 TGTGTTTTACTAACGAATTGGGACT 58.943 36.000 0.00 0.00 0.00 3.85
906 917 3.624777 CTGTGGAGGCACCTGAATTATT 58.375 45.455 1.84 0.00 39.86 1.40
908 919 1.281867 CCTGTGGAGGCACCTGAATTA 59.718 52.381 1.84 0.00 39.86 1.40
982 993 0.107508 ATGCGGGGAATCTGTCTGTG 60.108 55.000 0.00 0.00 0.00 3.66
1033 1044 4.445453 ACGTAGAAAAGAAACGGGACTTT 58.555 39.130 0.00 0.00 40.81 2.66
1040 1051 4.207841 AGGTTCGAACGTAGAAAAGAAACG 59.792 41.667 21.10 0.00 42.17 3.60
1164 1181 0.876342 GGATTAGAGGGAAGCGCGTG 60.876 60.000 8.43 0.00 0.00 5.34
1308 1325 4.939915 AGCTCGTATCGTCGCGCG 62.940 66.667 26.76 26.76 44.50 6.86
1603 1620 2.263741 GCCACCACCAAGCAGACAG 61.264 63.158 0.00 0.00 0.00 3.51
1604 1621 2.203337 GCCACCACCAAGCAGACA 60.203 61.111 0.00 0.00 0.00 3.41
1605 1622 2.725203 TACGCCACCACCAAGCAGAC 62.725 60.000 0.00 0.00 0.00 3.51
1620 1637 1.705727 CGAAATCACCGTGGTACGC 59.294 57.895 0.00 0.00 40.91 4.42
1623 1640 0.390603 CCAGCGAAATCACCGTGGTA 60.391 55.000 0.00 0.00 0.00 3.25
1671 1688 4.666728 GACGACGAGGCGAGTAAG 57.333 61.111 4.95 0.00 34.83 2.34
2169 2186 4.534401 GGGGGCTATGACAACGAC 57.466 61.111 0.00 0.00 0.00 4.34
2308 2328 4.253257 CTAGCGACGACGAGCCCC 62.253 72.222 12.29 0.00 42.66 5.80
2309 2329 4.908877 GCTAGCGACGACGAGCCC 62.909 72.222 12.29 0.00 42.66 5.19
2322 2342 4.266070 TTAGGCGCGGCGAGCTAG 62.266 66.667 32.75 8.81 45.59 3.42
2341 2361 0.386113 GTCAGCTAGCTAGGTTCCCG 59.614 60.000 22.58 11.70 30.45 5.14
2353 2373 2.060383 ATCCGCAGCCAGTCAGCTA 61.060 57.895 0.00 0.00 42.61 3.32
2411 2435 2.159170 GCTTCTGCCTCTATATAGCCCG 60.159 54.545 4.75 0.00 0.00 6.13
2442 2466 1.098712 TTTTCTTCAACACGCGGGCT 61.099 50.000 9.12 0.00 0.00 5.19
2445 2469 1.451651 GCAATTTTCTTCAACACGCGG 59.548 47.619 12.47 1.27 0.00 6.46
2450 2474 3.119316 ACACGGTGCAATTTTCTTCAACA 60.119 39.130 8.30 0.00 0.00 3.33
2571 2595 2.042435 CTCCTCTTCCTCCCGCCT 60.042 66.667 0.00 0.00 0.00 5.52
2604 2628 3.521126 AGTCCAAGTGCCAGATAACTCAT 59.479 43.478 0.00 0.00 0.00 2.90
2622 2646 1.517832 CCTGGATGGTCGACAGTCC 59.482 63.158 23.97 23.97 0.00 3.85
2658 2682 3.357079 CACACCGAACTGCCAGCC 61.357 66.667 0.00 0.00 0.00 4.85
2668 2692 0.834612 AGTCCAAAAGTCCACACCGA 59.165 50.000 0.00 0.00 0.00 4.69
2669 2693 1.226746 GAGTCCAAAAGTCCACACCG 58.773 55.000 0.00 0.00 0.00 4.94
2709 2733 0.037326 TGGTCGACCACTTGATCTGC 60.037 55.000 33.23 3.01 42.01 4.26
2729 2753 1.756375 CGATACAAGCACTCTGCCGC 61.756 60.000 0.00 0.00 46.52 6.53


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

AutoCloner maintained by Alex Coulton.