Multiple sequence alignment - TraesCS6A01G200500

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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 TraesCS6A01G200500 chr6A 100.000 2836 0 0 1 2836 322997919 322995084 0.000000e+00 5238
1 TraesCS6A01G200500 chr6D 92.271 2303 86 27 2 2232 262271062 262273344 0.000000e+00 3182
2 TraesCS6A01G200500 chr6D 93.027 631 29 5 2217 2833 262273412 262274041 0.000000e+00 907
3 TraesCS6A01G200500 chr6B 91.705 1941 75 36 775 2663 348696758 348694852 0.000000e+00 2614
4 TraesCS6A01G200500 chr6B 92.647 748 28 6 2 727 348704507 348703765 0.000000e+00 1051
5 TraesCS6A01G200500 chr6B 87.069 116 6 2 2701 2816 348694841 348694735 3.840000e-24 122


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 TraesCS6A01G200500 chr6A 322995084 322997919 2835 True 5238.0 5238 100.000 1 2836 1 chr6A.!!$R1 2835
1 TraesCS6A01G200500 chr6D 262271062 262274041 2979 False 2044.5 3182 92.649 2 2833 2 chr6D.!!$F1 2831
2 TraesCS6A01G200500 chr6B 348694735 348696758 2023 True 1368.0 2614 89.387 775 2816 2 chr6B.!!$R2 2041
3 TraesCS6A01G200500 chr6B 348703765 348704507 742 True 1051.0 1051 92.647 2 727 1 chr6B.!!$R1 725

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
560 600 1.025812 GTCTCGATCCCGATCACTGT 58.974 55.0 5.59 0.0 44.62 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 2264 0.526524 CGTGAGCAGTCGGAATCCTC 60.527 60.0 0.0 0.0 0.0 3.71 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
223 224 1.475213 GGACTCATCACCGATTTCCCC 60.475 57.143 0.00 0.00 0.00 4.81
290 323 3.076621 CAGTTCACCATGCATGTAGTGT 58.923 45.455 25.68 15.46 0.00 3.55
291 324 3.503363 CAGTTCACCATGCATGTAGTGTT 59.497 43.478 25.68 15.21 0.00 3.32
292 325 4.694982 CAGTTCACCATGCATGTAGTGTTA 59.305 41.667 25.68 16.79 0.00 2.41
293 326 5.355071 CAGTTCACCATGCATGTAGTGTTAT 59.645 40.000 25.68 15.00 0.00 1.89
295 328 5.357742 TCACCATGCATGTAGTGTTATCT 57.642 39.130 25.68 0.00 0.00 1.98
296 329 5.744171 TCACCATGCATGTAGTGTTATCTT 58.256 37.500 25.68 0.00 0.00 2.40
297 330 5.585844 TCACCATGCATGTAGTGTTATCTTG 59.414 40.000 25.68 11.08 0.00 3.02
298 331 5.355071 CACCATGCATGTAGTGTTATCTTGT 59.645 40.000 24.58 8.10 0.00 3.16
299 332 5.355071 ACCATGCATGTAGTGTTATCTTGTG 59.645 40.000 24.58 6.44 0.00 3.33
305 345 6.035435 GCATGTAGTGTTATCTTGTGAGTGAG 59.965 42.308 0.00 0.00 0.00 3.51
560 600 1.025812 GTCTCGATCCCGATCACTGT 58.974 55.000 5.59 0.00 44.62 3.55
607 647 4.610333 TCTGCTTATCTGAGGACCACTAA 58.390 43.478 0.00 0.00 0.00 2.24
619 659 7.234782 TCTGAGGACCACTAAGTCATTCTTTTA 59.765 37.037 0.00 0.00 38.59 1.52
620 660 7.741785 TGAGGACCACTAAGTCATTCTTTTAA 58.258 34.615 0.00 0.00 38.59 1.52
952 1007 4.025401 CCGCCGGTTGCTTGTGTC 62.025 66.667 1.90 0.00 38.05 3.67
1028 1083 4.814294 CTCTACGCCCACGCCCAC 62.814 72.222 0.00 0.00 45.53 4.61
1132 1187 0.595310 GATGTCTTCGGCCTACTCGC 60.595 60.000 0.00 0.00 0.00 5.03
1218 1291 1.635487 CAGGTGAGGGAAGGAAATCCA 59.365 52.381 1.67 0.00 41.55 3.41
1278 1352 2.599578 CTTGGCTGGCTTGCAGGT 60.600 61.111 2.00 0.00 34.04 4.00
1320 1394 1.339151 GGTGTTCGATTTCCAGCCTCT 60.339 52.381 0.00 0.00 0.00 3.69
1322 1396 1.281899 GTTCGATTTCCAGCCTCTCG 58.718 55.000 0.00 0.00 0.00 4.04
1437 1511 6.784176 TGCTTGGAATTTTCTTTTTCTTTGC 58.216 32.000 0.00 0.00 0.00 3.68
1460 1537 4.022849 CCAAGAAACGGAAGCAGAATTCTT 60.023 41.667 4.86 0.00 37.54 2.52
1603 1686 2.878429 GAGAGGTTCAGCGAGCGA 59.122 61.111 0.00 0.00 0.00 4.93
1693 1783 3.566322 TGCCGCTTTACTTACACAACATT 59.434 39.130 0.00 0.00 0.00 2.71
1694 1784 3.911964 GCCGCTTTACTTACACAACATTG 59.088 43.478 0.00 0.00 0.00 2.82
1695 1785 3.911964 CCGCTTTACTTACACAACATTGC 59.088 43.478 0.00 0.00 0.00 3.56
1778 1874 3.126703 TTCGCAAGGGCTGGTGGAA 62.127 57.895 0.00 0.00 38.10 3.53
1799 1895 2.354821 AGTCTTGACAGGACAAAAACGC 59.645 45.455 18.77 0.00 36.29 4.84
1809 1905 0.529119 ACAAAAACGCGTCCTCGACT 60.529 50.000 14.44 0.00 39.71 4.18
1936 2033 0.171231 TTGCTCCAGACATCGTCTCG 59.829 55.000 0.00 0.00 41.37 4.04
2066 2166 2.357034 TTGCTTGTCCGACGGAGC 60.357 61.111 18.98 17.93 32.64 4.70
2075 2175 1.300465 CCGACGGAGCTCATCATGG 60.300 63.158 17.19 6.46 0.00 3.66
2156 2264 5.207768 GCCGTTTCACTTTGCAGATATATG 58.792 41.667 0.00 0.00 0.00 1.78
2173 2281 1.489481 ATGAGGATTCCGACTGCTCA 58.511 50.000 11.52 11.52 43.83 4.26
2177 2285 1.153745 GATTCCGACTGCTCACGCT 60.154 57.895 0.00 0.00 36.97 5.07
2214 2322 7.321153 TCTTCTAATCCTAGACCAAGAAAACG 58.679 38.462 0.00 0.00 33.73 3.60
2456 2652 6.977213 TGTTTACTAACAAAATGGAGGAAGC 58.023 36.000 0.00 0.00 41.15 3.86
2568 2777 4.273005 TGAGAGACGTTTTTGCAGTTTC 57.727 40.909 0.00 0.00 0.00 2.78
2573 2782 5.516339 AGAGACGTTTTTGCAGTTTCAATTG 59.484 36.000 0.00 0.00 0.00 2.32
2621 2830 5.699097 TTACATTTAGAAACACAGGGTGC 57.301 39.130 0.00 0.00 36.98 5.01
2705 2918 4.164822 GCTCAAGCTTTTTGTGCATCTA 57.835 40.909 0.00 0.00 38.40 1.98
2720 2933 2.224161 GCATCTACCTGCTGACCCTAAG 60.224 54.545 0.00 0.00 39.12 2.18
2796 3009 1.302431 CATCGTTGGCTGTCCACCA 60.302 57.895 0.00 0.00 43.33 4.17
2819 3032 2.673523 CTCTGGCCCCACCTTCAG 59.326 66.667 0.00 0.00 40.22 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.346722 ACTCTGGGTAAACGGACTTGG 59.653 52.381 0.00 0.00 0.00 3.61
79 80 5.068329 CAGCAGATACACATAGACTGGAAGA 59.932 44.000 0.00 0.00 37.43 2.87
223 224 1.065928 GTATCTGTGAGCCGTCCCG 59.934 63.158 0.00 0.00 0.00 5.14
290 323 7.439356 CACAAGAAGAACTCACTCACAAGATAA 59.561 37.037 0.00 0.00 0.00 1.75
291 324 6.925718 CACAAGAAGAACTCACTCACAAGATA 59.074 38.462 0.00 0.00 0.00 1.98
292 325 5.757320 CACAAGAAGAACTCACTCACAAGAT 59.243 40.000 0.00 0.00 0.00 2.40
293 326 5.111989 CACAAGAAGAACTCACTCACAAGA 58.888 41.667 0.00 0.00 0.00 3.02
295 328 4.832248 ACACAAGAAGAACTCACTCACAA 58.168 39.130 0.00 0.00 0.00 3.33
296 329 4.471904 ACACAAGAAGAACTCACTCACA 57.528 40.909 0.00 0.00 0.00 3.58
297 330 5.563842 CAAACACAAGAAGAACTCACTCAC 58.436 41.667 0.00 0.00 0.00 3.51
298 331 4.094887 GCAAACACAAGAAGAACTCACTCA 59.905 41.667 0.00 0.00 0.00 3.41
299 332 4.592179 GCAAACACAAGAAGAACTCACTC 58.408 43.478 0.00 0.00 0.00 3.51
305 345 2.111756 CTGCGCAAACACAAGAAGAAC 58.888 47.619 13.05 0.00 0.00 3.01
393 433 4.718961 CTTTATCCTGTATGACCCCAAGG 58.281 47.826 0.00 0.00 40.04 3.61
394 434 4.137543 GCTTTATCCTGTATGACCCCAAG 58.862 47.826 0.00 0.00 0.00 3.61
560 600 1.143838 CATAGCACTAGCACCGCCA 59.856 57.895 0.00 0.00 45.49 5.69
607 647 3.443681 CGGGTGGCATTAAAAGAATGACT 59.556 43.478 4.84 0.00 36.63 3.41
619 659 4.141482 ACATAGAATAGAACGGGTGGCATT 60.141 41.667 0.00 0.00 0.00 3.56
620 660 3.391296 ACATAGAATAGAACGGGTGGCAT 59.609 43.478 0.00 0.00 0.00 4.40
655 699 4.513442 AGACCCAAAGCAAAAGGAAAAAC 58.487 39.130 0.00 0.00 0.00 2.43
893 948 0.817654 TCGCCGTCAGATGTCAATCT 59.182 50.000 0.00 0.00 44.35 2.40
1218 1291 0.172803 CGGAGTCGAAAAGGACGGAT 59.827 55.000 0.00 0.00 41.81 4.18
1287 1361 4.657824 ACACCAACGACGGCTCCG 62.658 66.667 6.79 6.79 46.03 4.63
1320 1394 2.833582 GAGCATCCTCCGGGTCGA 60.834 66.667 0.00 0.00 31.68 4.20
1322 1396 2.851071 CGAGAGCATCCTCCGGGTC 61.851 68.421 0.00 0.00 38.96 4.46
1437 1511 3.503748 AGAATTCTGCTTCCGTTTCTTGG 59.496 43.478 7.30 0.00 0.00 3.61
1460 1537 5.072040 TCGCAGACAAGATGAATCACTAA 57.928 39.130 0.00 0.00 0.00 2.24
1523 1600 1.075970 TCCTCCTGTCAGGGATCCG 60.076 63.158 19.11 2.60 35.59 4.18
1664 1747 2.723124 AAGTAAAGCGGCAATTGTGG 57.277 45.000 7.40 0.37 0.00 4.17
1693 1783 3.144657 TGAAAAGAAGAGATGGCAGCA 57.855 42.857 5.19 0.00 0.00 4.41
1694 1784 3.693085 TGATGAAAAGAAGAGATGGCAGC 59.307 43.478 0.00 0.00 0.00 5.25
1695 1785 5.823570 AGATGATGAAAAGAAGAGATGGCAG 59.176 40.000 0.00 0.00 0.00 4.85
1778 1874 2.354821 GCGTTTTTGTCCTGTCAAGACT 59.645 45.455 3.32 0.00 35.21 3.24
1799 1895 1.433053 ATCTCAGCGAGTCGAGGACG 61.433 60.000 18.61 6.82 37.67 4.79
1965 2062 8.882736 CACCATTGACGCATATGTATACATAAT 58.117 33.333 25.41 13.81 41.60 1.28
1984 2081 4.160065 TCTTTCAACCATATGGCACCATTG 59.840 41.667 22.18 17.06 39.32 2.82
2066 2166 5.702670 ACAGTAACACAAGAACCATGATGAG 59.297 40.000 0.00 0.00 0.00 2.90
2156 2264 0.526524 CGTGAGCAGTCGGAATCCTC 60.527 60.000 0.00 0.00 0.00 3.71
2214 2322 4.755411 TCATTAGTAGTTGCAGGCAGTAC 58.245 43.478 7.44 7.44 0.00 2.73
2456 2652 9.896645 ATATAATCCAAGTGCTACTGGATATTG 57.103 33.333 12.52 0.00 36.10 1.90
2483 2682 4.386652 GTGTTTGTTTGCTGAAGCCATATG 59.613 41.667 0.00 0.00 41.18 1.78
2568 2777 7.410800 TTTGCAGCTTAAATCAGTTCAATTG 57.589 32.000 0.00 0.00 0.00 2.32
2573 2782 5.107875 CCGTTTTTGCAGCTTAAATCAGTTC 60.108 40.000 0.00 0.00 0.00 3.01
2705 2918 0.910088 GGGTCTTAGGGTCAGCAGGT 60.910 60.000 0.00 0.00 0.00 4.00
2720 2933 1.337118 TGTTTGGAAGGCATTGGGTC 58.663 50.000 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.