Multiple sequence alignment - TraesCS6A01G346400

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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 TraesCS6A01G346400 chr6A 100.000 2288 0 0 1 2288 579516962 579519249 0.000000e+00 4226
1 TraesCS6A01G346400 chr6A 93.843 2290 125 12 1 2281 579753840 579756122 0.000000e+00 3434
2 TraesCS6A01G346400 chr6A 94.822 2028 96 5 1 2022 579758855 579760879 0.000000e+00 3155
3 TraesCS6A01G346400 chr6D 94.272 2287 106 5 1 2281 433547460 433549727 0.000000e+00 3474
4 TraesCS6A01G346400 chr6D 94.272 2287 105 5 1 2281 433562585 433564851 0.000000e+00 3474
5 TraesCS6A01G346400 chr6D 95.219 2029 72 5 1 2022 433568286 433570296 0.000000e+00 3186
6 TraesCS6A01G346400 chr6B 93.997 1999 108 9 1 1996 655053299 655055288 0.000000e+00 3016
7 TraesCS6A01G346400 chr6B 93.422 1946 119 4 1 1939 654917437 654919380 0.000000e+00 2876
8 TraesCS6A01G346400 chr6B 94.134 1790 99 4 1 1786 654853921 654855708 0.000000e+00 2719
9 TraesCS6A01G346400 chr6B 93.966 1790 102 4 1 1786 654878018 654879805 0.000000e+00 2702
10 TraesCS6A01G346400 chr6B 93.956 1787 105 3 1 1786 654888141 654889925 0.000000e+00 2699
11 TraesCS6A01G346400 chr6B 89.556 450 35 6 1786 2235 654902680 654903117 5.520000e-156 560
12 TraesCS6A01G346400 chr6B 89.333 450 36 7 1786 2235 654886016 654886453 2.570000e-154 555


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 TraesCS6A01G346400 chr6A 579516962 579519249 2287 False 4226.0 4226 100.0000 1 2288 1 chr6A.!!$F1 2287
1 TraesCS6A01G346400 chr6A 579753840 579760879 7039 False 3294.5 3434 94.3325 1 2281 2 chr6A.!!$F2 2280
2 TraesCS6A01G346400 chr6D 433547460 433549727 2267 False 3474.0 3474 94.2720 1 2281 1 chr6D.!!$F1 2280
3 TraesCS6A01G346400 chr6D 433562585 433570296 7711 False 3330.0 3474 94.7455 1 2281 2 chr6D.!!$F2 2280
4 TraesCS6A01G346400 chr6B 655053299 655055288 1989 False 3016.0 3016 93.9970 1 1996 1 chr6B.!!$F5 1995
5 TraesCS6A01G346400 chr6B 654917437 654919380 1943 False 2876.0 2876 93.4220 1 1939 1 chr6B.!!$F4 1938
6 TraesCS6A01G346400 chr6B 654853921 654855708 1787 False 2719.0 2719 94.1340 1 1786 1 chr6B.!!$F1 1785
7 TraesCS6A01G346400 chr6B 654878018 654879805 1787 False 2702.0 2702 93.9660 1 1786 1 chr6B.!!$F2 1785
8 TraesCS6A01G346400 chr6B 654886016 654889925 3909 False 1627.0 2699 91.6445 1 2235 2 chr6B.!!$F6 2234

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
598 2725 0.11319 CCCATCAAGGATTAGGGCCC 59.887 60.0 16.46 16.46 41.22 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 14529 0.320374 GTTGAGGGACCATGACGACA 59.68 55.0 0.0 0.0 0.0 4.35 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
53 2179 3.703001 ACGTTGGAGACCATCTCAATT 57.297 42.857 8.06 0.00 45.12 2.32
68 2194 7.015877 ACCATCTCAATTCCCCATATTCAAATG 59.984 37.037 0.00 0.00 0.00 2.32
69 2195 7.015877 CCATCTCAATTCCCCATATTCAAATGT 59.984 37.037 0.00 0.00 0.00 2.71
116 2242 3.888930 CACCCAGTACCATTCACAAAACT 59.111 43.478 0.00 0.00 0.00 2.66
203 2330 3.604875 AAAGCTTTGATCCTTGGCATG 57.395 42.857 11.80 0.00 0.00 4.06
466 2593 2.084546 GTTCAAGGCAACGAAGGCTAT 58.915 47.619 8.16 0.00 44.47 2.97
497 2624 1.207791 AACCGAGCATGGAGAGGATT 58.792 50.000 0.69 0.00 0.00 3.01
503 2630 3.238597 GAGCATGGAGAGGATTCCTACT 58.761 50.000 4.86 4.85 38.12 2.57
569 2696 2.415625 CGTAGACTGGAGAACGAAAGGG 60.416 54.545 0.00 0.00 37.53 3.95
591 2718 1.285962 CAGTCACCCCCATCAAGGATT 59.714 52.381 0.00 0.00 41.22 3.01
598 2725 0.113190 CCCATCAAGGATTAGGGCCC 59.887 60.000 16.46 16.46 41.22 5.80
954 3081 4.868116 ACCAACGGTGCCGCAACT 62.868 61.111 10.87 0.00 44.19 3.16
976 3103 9.330063 CAACTATCAAAAGCTATGAGGATGTTA 57.670 33.333 8.00 0.00 0.00 2.41
1003 3130 0.179089 CAACGAGGGAGCTCTCATGG 60.179 60.000 17.82 6.69 33.59 3.66
1017 3144 2.034879 CATGGAAGCCGTCGCAAGT 61.035 57.895 0.00 0.00 37.52 3.16
1044 3171 1.043116 TCTCGGTGGCTGTAGATGGG 61.043 60.000 0.00 0.00 0.00 4.00
1056 3183 4.682563 CTGTAGATGGGGGAGATATGACT 58.317 47.826 0.00 0.00 0.00 3.41
1089 3216 2.030027 AAGGTGGAGTGATGACAGGA 57.970 50.000 0.00 0.00 0.00 3.86
1197 9025 0.252193 CATGGGGAACAACATGGGGT 60.252 55.000 0.00 0.00 40.11 4.95
1399 9227 9.800433 ATTTCGTGAATACAATGCAAATTATGA 57.200 25.926 0.00 0.00 0.00 2.15
1476 9304 2.855660 ACCCGTTGTGTTTTGTAAGC 57.144 45.000 0.00 0.00 0.00 3.09
1499 9327 2.550978 ACTGTGTTGTCTCTTGTTCCG 58.449 47.619 0.00 0.00 0.00 4.30
1501 9329 3.131577 ACTGTGTTGTCTCTTGTTCCGTA 59.868 43.478 0.00 0.00 0.00 4.02
1680 14529 2.450886 ACTTTTCCCTCCACCAATTCCT 59.549 45.455 0.00 0.00 0.00 3.36
1703 14552 0.321653 GTCATGGTCCCTCAACGCTT 60.322 55.000 0.00 0.00 0.00 4.68
1859 14713 6.480763 TGGTAGAGCACATAAATGGAGAAAA 58.519 36.000 0.00 0.00 0.00 2.29
1892 14746 4.938226 GCTTTCTGCTAGTAATGAACAGGT 59.062 41.667 0.00 0.00 38.95 4.00
1913 14767 1.351350 AGGCTAACAACTCCTTCCCAC 59.649 52.381 0.00 0.00 0.00 4.61
2007 14862 9.191995 CAACTTCACCACATAATAAGGAAAAAC 57.808 33.333 0.00 0.00 0.00 2.43
2034 14889 6.590656 TTTGGTCCCAAGGTAATCATCTAT 57.409 37.500 0.00 0.00 37.24 1.98
2040 14895 8.437575 GGTCCCAAGGTAATCATCTATAGAAAA 58.562 37.037 6.52 0.00 0.00 2.29
2077 14932 0.954452 CTCACCTCACCTGCAAAACC 59.046 55.000 0.00 0.00 0.00 3.27
2079 14934 1.101049 CACCTCACCTGCAAAACCGT 61.101 55.000 0.00 0.00 0.00 4.83
2085 14940 0.536460 ACCTGCAAAACCGTCGGAAT 60.536 50.000 20.51 3.04 0.00 3.01
2091 14946 3.425122 AAACCGTCGGAATGGGTTT 57.575 47.368 20.51 13.33 46.33 3.27
2096 14951 1.816224 CCGTCGGAATGGGTTTGATTT 59.184 47.619 4.91 0.00 0.00 2.17
2120 14975 3.505464 AACCACGACAGTATAGTGCTC 57.495 47.619 7.51 4.23 34.79 4.26
2123 14978 3.447586 ACCACGACAGTATAGTGCTCAAT 59.552 43.478 7.51 0.00 34.79 2.57
2134 14989 7.924947 CAGTATAGTGCTCAATGAGAAGATGAA 59.075 37.037 15.38 0.00 0.00 2.57
2144 14999 9.767228 CTCAATGAGAAGATGAAATGTAGAGAT 57.233 33.333 3.77 0.00 0.00 2.75
2145 15000 9.543783 TCAATGAGAAGATGAAATGTAGAGATG 57.456 33.333 0.00 0.00 0.00 2.90
2174 15029 7.231317 TGAGATGGTCAGTGAGCTTTAATTTTT 59.769 33.333 22.08 0.00 0.00 1.94
2175 15030 7.597386 AGATGGTCAGTGAGCTTTAATTTTTC 58.403 34.615 22.08 3.15 0.00 2.29
2177 15032 7.288810 TGGTCAGTGAGCTTTAATTTTTCAT 57.711 32.000 22.08 0.00 0.00 2.57
2178 15033 7.370383 TGGTCAGTGAGCTTTAATTTTTCATC 58.630 34.615 22.08 0.00 0.00 2.92
2238 15093 8.251750 TGTTAGTACTTTGATGAGTGTTATGC 57.748 34.615 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 2179 7.994539 TGGATGTATACATTTGAATATGGGGA 58.005 34.615 19.19 0.00 36.57 4.81
203 2330 1.226128 GAAGCAAACGCATCCGAGC 60.226 57.895 0.00 0.00 38.29 5.03
455 2582 1.286248 ACCCCTTGATAGCCTTCGTT 58.714 50.000 0.00 0.00 0.00 3.85
466 2593 0.035739 GCTCGGTTTGTACCCCTTGA 59.964 55.000 0.00 0.00 41.75 3.02
497 2624 8.228206 ACATTCTCATACCTGAATCTAGTAGGA 58.772 37.037 10.54 0.00 35.55 2.94
569 2696 1.379044 CTTGATGGGGGTGACTGCC 60.379 63.158 0.00 0.00 0.00 4.85
591 2718 2.572229 TACTTACCACATGGGCCCTA 57.428 50.000 25.70 10.18 42.05 3.53
682 2809 9.988815 ACAACAACCTGCAAATATTTACATTTA 57.011 25.926 0.00 0.00 0.00 1.40
692 2819 2.224161 GCCCAACAACAACCTGCAAATA 60.224 45.455 0.00 0.00 0.00 1.40
698 2825 2.689553 AAAAGCCCAACAACAACCTG 57.310 45.000 0.00 0.00 0.00 4.00
853 2980 6.197276 CGCCATTCTTGATTATGAACTTGAG 58.803 40.000 0.00 0.00 0.00 3.02
954 3081 7.442364 GCTGTAACATCCTCATAGCTTTTGATA 59.558 37.037 0.00 0.00 0.00 2.15
976 3103 1.071471 CTCCCTCGTTGTTGGCTGT 59.929 57.895 0.00 0.00 0.00 4.40
1003 3130 1.204312 GTTGACTTGCGACGGCTTC 59.796 57.895 0.00 0.00 40.82 3.86
1044 3171 8.519799 TGTAAAATTGGAAAGTCATATCTCCC 57.480 34.615 0.00 0.00 0.00 4.30
1056 3183 6.381420 TCACTCCACCTTTGTAAAATTGGAAA 59.619 34.615 7.58 0.00 31.85 3.13
1089 3216 0.034767 CCAGGTCTGTGCCACATGAT 60.035 55.000 0.00 0.00 0.00 2.45
1197 9025 8.018537 TCTCCATTCTTAAATATCCGTTCTCA 57.981 34.615 0.00 0.00 0.00 3.27
1399 9227 9.376075 CTTCTTCATCAGTCTTAACATATGTGT 57.624 33.333 9.63 2.63 41.28 3.72
1414 9242 7.840342 ATAGCTAACACAACTTCTTCATCAG 57.160 36.000 0.00 0.00 0.00 2.90
1476 9304 3.001330 GGAACAAGAGACAACACAGTTCG 59.999 47.826 0.00 0.00 35.86 3.95
1634 14483 5.698545 CCATCCTATTTCAATTCCTCGAGAC 59.301 44.000 15.71 0.00 0.00 3.36
1680 14529 0.320374 GTTGAGGGACCATGACGACA 59.680 55.000 0.00 0.00 0.00 4.35
1703 14552 1.056660 GGGAGAGGAGGTTGTTGTCA 58.943 55.000 0.00 0.00 0.00 3.58
1892 14746 2.570302 GTGGGAAGGAGTTGTTAGCCTA 59.430 50.000 0.00 0.00 0.00 3.93
1913 14767 3.572632 ATGTGGACCATCTCTTCCATG 57.427 47.619 0.00 0.00 43.85 3.66
2007 14862 4.599041 TGATTACCTTGGGACCAAATCAG 58.401 43.478 10.58 0.00 35.33 2.90
2034 14889 6.323739 AGCCCTTTGATTGAAGTTGTTTTCTA 59.676 34.615 0.00 0.00 0.00 2.10
2040 14895 3.319122 GTGAGCCCTTTGATTGAAGTTGT 59.681 43.478 0.00 0.00 0.00 3.32
2077 14932 4.893424 ATAAATCAAACCCATTCCGACG 57.107 40.909 0.00 0.00 0.00 5.12
2079 14934 6.663953 TGGTTAATAAATCAAACCCATTCCGA 59.336 34.615 1.30 0.00 41.66 4.55
2085 14940 5.768662 TGTCGTGGTTAATAAATCAAACCCA 59.231 36.000 1.30 0.00 41.66 4.51
2091 14946 9.524106 CACTATACTGTCGTGGTTAATAAATCA 57.476 33.333 0.00 0.00 0.00 2.57
2096 14951 6.319405 TGAGCACTATACTGTCGTGGTTAATA 59.681 38.462 9.69 0.00 39.22 0.98
2120 14975 8.775527 CCATCTCTACATTTCATCTTCTCATTG 58.224 37.037 0.00 0.00 0.00 2.82
2123 14978 7.666063 TCCATCTCTACATTTCATCTTCTCA 57.334 36.000 0.00 0.00 0.00 3.27
2134 14989 5.842874 TGACCATCTCATCCATCTCTACATT 59.157 40.000 0.00 0.00 0.00 2.71
2144 14999 1.483827 GCTCACTGACCATCTCATCCA 59.516 52.381 0.00 0.00 0.00 3.41
2145 15000 1.761784 AGCTCACTGACCATCTCATCC 59.238 52.381 0.00 0.00 0.00 3.51
2208 15063 9.783256 AACACTCATCAAAGTACTAACAAAAAC 57.217 29.630 0.00 0.00 0.00 2.43
2216 15071 8.478066 AGATGCATAACACTCATCAAAGTACTA 58.522 33.333 0.00 0.00 39.12 1.82


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

AutoCloner maintained by Alex Coulton.