Multiple sequence alignment - TraesCS6A01G164000

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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 TraesCS6A01G164000 chr6A 100.000 3014 0 0 1 3014 161157707 161154694 0 5566
1 TraesCS6A01G164000 chr6A 96.282 1506 52 3 255 1756 161412694 161411189 0 2468
2 TraesCS6A01G164000 chr6A 88.342 935 106 3 2081 3014 127556089 127557021 0 1120
3 TraesCS6A01G164000 chr6A 89.316 833 87 2 2183 3014 99821737 99822568 0 1044
4 TraesCS6A01G164000 chr1A 97.568 2056 39 3 1 2054 106532221 106534267 0 3509
5 TraesCS6A01G164000 chr1A 94.750 1162 61 0 894 2055 433526031 433527192 0 1808
6 TraesCS6A01G164000 chr1A 94.108 1171 60 2 894 2055 433736978 433738148 0 1772
7 TraesCS6A01G164000 chr1A 95.525 1095 49 0 961 2055 399893488 399892394 0 1751
8 TraesCS6A01G164000 chr1A 94.328 952 52 2 2063 3014 552877264 552876315 0 1458
9 TraesCS6A01G164000 chr1A 95.698 860 31 5 1 856 481215888 481216745 0 1378
10 TraesCS6A01G164000 chr1A 97.667 600 11 2 1 597 399895130 399894531 0 1027
11 TraesCS6A01G164000 chr5D 94.762 2062 88 6 1 2055 88142359 88144407 0 3192
12 TraesCS6A01G164000 chr3B 86.377 1703 178 30 362 2054 728776623 728778281 0 1810
13 TraesCS6A01G164000 chr1B 94.836 1162 51 1 894 2055 510208201 510209353 0 1805
14 TraesCS6A01G164000 chr1B 96.475 766 24 3 86 848 510207428 510208193 0 1262
15 TraesCS6A01G164000 chr3A 86.256 1688 177 29 362 2036 686662407 686664052 0 1781
16 TraesCS6A01G164000 chr1D 95.302 1043 46 3 371 1410 82303783 82304825 0 1652
17 TraesCS6A01G164000 chr1D 94.787 1055 35 8 1 1051 83126010 83127048 0 1626
18 TraesCS6A01G164000 chr1D 94.245 556 26 6 2 553 400412661 400412108 0 845
19 TraesCS6A01G164000 chr7A 89.112 946 100 3 2064 3008 260021028 260020085 0 1173
20 TraesCS6A01G164000 chr7A 87.633 938 110 4 2081 3014 184620961 184620026 0 1085
21 TraesCS6A01G164000 chr4B 94.241 764 25 5 1292 2055 451335689 451334945 0 1149
22 TraesCS6A01G164000 chr4B 94.110 764 26 2 1292 2055 451311090 451310346 0 1144
23 TraesCS6A01G164000 chr4B 93.979 764 26 6 1292 2055 451261759 451261016 0 1138
24 TraesCS6A01G164000 chr4A 87.799 836 100 2 2173 3007 627305379 627306213 0 977
25 TraesCS6A01G164000 chr4A 88.000 800 91 5 2216 3014 17985979 17986774 0 941
26 TraesCS6A01G164000 chr6B 84.467 779 112 8 2238 3010 47135470 47134695 0 760
27 TraesCS6A01G164000 chr5B 81.296 957 155 18 2065 3014 613656999 613657938 0 754


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 TraesCS6A01G164000 chr6A 161154694 161157707 3013 True 5566.0 5566 100.0000 1 3014 1 chr6A.!!$R1 3013
1 TraesCS6A01G164000 chr6A 161411189 161412694 1505 True 2468.0 2468 96.2820 255 1756 1 chr6A.!!$R2 1501
2 TraesCS6A01G164000 chr6A 127556089 127557021 932 False 1120.0 1120 88.3420 2081 3014 1 chr6A.!!$F2 933
3 TraesCS6A01G164000 chr6A 99821737 99822568 831 False 1044.0 1044 89.3160 2183 3014 1 chr6A.!!$F1 831
4 TraesCS6A01G164000 chr1A 106532221 106534267 2046 False 3509.0 3509 97.5680 1 2054 1 chr1A.!!$F1 2053
5 TraesCS6A01G164000 chr1A 433526031 433527192 1161 False 1808.0 1808 94.7500 894 2055 1 chr1A.!!$F2 1161
6 TraesCS6A01G164000 chr1A 433736978 433738148 1170 False 1772.0 1772 94.1080 894 2055 1 chr1A.!!$F3 1161
7 TraesCS6A01G164000 chr1A 552876315 552877264 949 True 1458.0 1458 94.3280 2063 3014 1 chr1A.!!$R1 951
8 TraesCS6A01G164000 chr1A 399892394 399895130 2736 True 1389.0 1751 96.5960 1 2055 2 chr1A.!!$R2 2054
9 TraesCS6A01G164000 chr1A 481215888 481216745 857 False 1378.0 1378 95.6980 1 856 1 chr1A.!!$F4 855
10 TraesCS6A01G164000 chr5D 88142359 88144407 2048 False 3192.0 3192 94.7620 1 2055 1 chr5D.!!$F1 2054
11 TraesCS6A01G164000 chr3B 728776623 728778281 1658 False 1810.0 1810 86.3770 362 2054 1 chr3B.!!$F1 1692
12 TraesCS6A01G164000 chr1B 510207428 510209353 1925 False 1533.5 1805 95.6555 86 2055 2 chr1B.!!$F1 1969
13 TraesCS6A01G164000 chr3A 686662407 686664052 1645 False 1781.0 1781 86.2560 362 2036 1 chr3A.!!$F1 1674
14 TraesCS6A01G164000 chr1D 82303783 82304825 1042 False 1652.0 1652 95.3020 371 1410 1 chr1D.!!$F1 1039
15 TraesCS6A01G164000 chr1D 83126010 83127048 1038 False 1626.0 1626 94.7870 1 1051 1 chr1D.!!$F2 1050
16 TraesCS6A01G164000 chr1D 400412108 400412661 553 True 845.0 845 94.2450 2 553 1 chr1D.!!$R1 551
17 TraesCS6A01G164000 chr7A 260020085 260021028 943 True 1173.0 1173 89.1120 2064 3008 1 chr7A.!!$R2 944
18 TraesCS6A01G164000 chr7A 184620026 184620961 935 True 1085.0 1085 87.6330 2081 3014 1 chr7A.!!$R1 933
19 TraesCS6A01G164000 chr4B 451334945 451335689 744 True 1149.0 1149 94.2410 1292 2055 1 chr4B.!!$R3 763
20 TraesCS6A01G164000 chr4B 451310346 451311090 744 True 1144.0 1144 94.1100 1292 2055 1 chr4B.!!$R2 763
21 TraesCS6A01G164000 chr4B 451261016 451261759 743 True 1138.0 1138 93.9790 1292 2055 1 chr4B.!!$R1 763
22 TraesCS6A01G164000 chr4A 627305379 627306213 834 False 977.0 977 87.7990 2173 3007 1 chr4A.!!$F2 834
23 TraesCS6A01G164000 chr4A 17985979 17986774 795 False 941.0 941 88.0000 2216 3014 1 chr4A.!!$F1 798
24 TraesCS6A01G164000 chr6B 47134695 47135470 775 True 760.0 760 84.4670 2238 3010 1 chr6B.!!$R1 772
25 TraesCS6A01G164000 chr5B 613656999 613657938 939 False 754.0 754 81.2960 2065 3014 1 chr5B.!!$F1 949

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
547 565 1.649633 ACAGGAGGGTCCAGGTACATA 59.35 52.381 0.0 0.0 39.61 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 2886 0.533755 CCAGAGCCATCGAATCACCC 60.534 60.0 0.0 0.0 0.0 4.61 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
69 70 3.347216 AGTGAAATCCACCTCGAATTGG 58.653 45.455 5.72 5.72 46.87 3.16
399 416 6.775629 AGTTGCCTACACTAAATTTCTCCAAA 59.224 34.615 0.00 0.00 0.00 3.28
547 565 1.649633 ACAGGAGGGTCCAGGTACATA 59.350 52.381 0.00 0.00 39.61 2.29
705 1451 5.661458 CTCTTGTATGTTTAGTCGGTGGAT 58.339 41.667 0.00 0.00 0.00 3.41
849 1597 3.181423 ACCAGGGAAGCCTTAACAAATCA 60.181 43.478 0.00 0.00 0.00 2.57
1052 1840 4.987285 CGAGCTACATCTTGCATCTACAAT 59.013 41.667 0.00 0.00 0.00 2.71
1058 1846 4.141846 ACATCTTGCATCTACAATCGAGGT 60.142 41.667 0.00 0.00 0.00 3.85
1295 2083 0.395173 GAGAGAGGAGGCGAGGAAGT 60.395 60.000 0.00 0.00 0.00 3.01
1302 2090 0.247736 GAGGCGAGGAAGTGACACAT 59.752 55.000 8.59 0.00 0.00 3.21
1316 2104 3.072944 TGACACATGAACATGCGAATCA 58.927 40.909 13.71 9.67 42.39 2.57
1614 2444 5.896073 AGCAATACTTAGGTCTATGCCTT 57.104 39.130 6.11 0.00 39.94 4.35
1644 2474 3.557264 CGCTCTTTTTCTAGGGTCTGGTT 60.557 47.826 0.00 0.00 0.00 3.67
1690 2521 0.251077 CAAGGCTCAAGGGAAGCAGT 60.251 55.000 0.00 0.00 0.00 4.40
1729 2560 7.715249 TCTTTGTATGCTTATGGTATCTTGGAC 59.285 37.037 0.00 0.00 0.00 4.02
1823 2654 6.307800 CCCTTATGTTTGTGCTTTACATTTCG 59.692 38.462 0.00 0.00 39.48 3.46
2056 2887 9.865321 ATCTTTCTTTTGAAATCACATACATGG 57.135 29.630 0.00 0.00 46.05 3.66
2057 2888 8.306038 TCTTTCTTTTGAAATCACATACATGGG 58.694 33.333 0.00 0.00 46.05 4.00
2058 2889 7.537596 TTCTTTTGAAATCACATACATGGGT 57.462 32.000 0.00 0.00 35.17 4.51
2059 2890 6.923012 TCTTTTGAAATCACATACATGGGTG 58.077 36.000 0.00 2.78 36.36 4.61
2060 2891 6.718912 TCTTTTGAAATCACATACATGGGTGA 59.281 34.615 16.18 16.18 46.92 4.02
2567 3436 3.073735 CTCTGCTCCGGCCTGTCT 61.074 66.667 0.00 0.00 37.74 3.41
2575 3444 3.062466 CGGCCTGTCTGACTCCGA 61.062 66.667 22.53 0.00 42.43 4.55
2941 3810 3.470888 CGGCCCAATCTCGTCCCT 61.471 66.667 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.289072 ACACAGTTCAGATAGCAACGCT 60.289 45.455 0.00 0.00 43.41 5.07
69 70 4.149396 GCATCAATGCGATCCAAAAATAGC 59.851 41.667 0.00 0.00 44.67 2.97
376 393 7.589958 TTTTGGAGAAATTTAGTGTAGGCAA 57.410 32.000 0.00 0.00 0.00 4.52
547 565 4.082571 GCAACATCAGCCAAGTTTATGAGT 60.083 41.667 0.00 0.00 0.00 3.41
597 615 3.627395 TCTTGTTCATAGAACCGGCAT 57.373 42.857 0.00 0.00 0.00 4.40
1052 1840 1.153208 GAGCCTAGGTCGACCTCGA 60.153 63.158 39.49 22.91 44.77 4.04
1134 1922 0.660595 CTATCGCGTCCAGCCGTTAG 60.661 60.000 5.77 0.00 44.76 2.34
1295 2083 3.072944 TGATTCGCATGTTCATGTGTCA 58.927 40.909 20.67 16.30 33.99 3.58
1302 2090 2.413796 GGTACGTTGATTCGCATGTTCA 59.586 45.455 0.00 0.00 0.00 3.18
1316 2104 2.633967 TGATGGTAGGTTGTGGTACGTT 59.366 45.455 0.00 0.00 0.00 3.99
1596 2426 8.376270 GGAATTGTAAGGCATAGACCTAAGTAT 58.624 37.037 0.00 0.00 39.93 2.12
1614 2444 5.183228 CCCTAGAAAAAGAGCGGAATTGTA 58.817 41.667 0.00 0.00 0.00 2.41
1644 2474 6.119536 CCCTTGCTATCAACATAGTACCAAA 58.880 40.000 0.00 0.00 35.28 3.28
1690 2521 4.927425 GCATACAAAGAACTACAGAACCGA 59.073 41.667 0.00 0.00 0.00 4.69
2055 2886 0.533755 CCAGAGCCATCGAATCACCC 60.534 60.000 0.00 0.00 0.00 4.61
2056 2887 1.162800 GCCAGAGCCATCGAATCACC 61.163 60.000 0.00 0.00 0.00 4.02
2057 2888 1.493950 CGCCAGAGCCATCGAATCAC 61.494 60.000 0.00 0.00 34.57 3.06
2058 2889 1.227350 CGCCAGAGCCATCGAATCA 60.227 57.895 0.00 0.00 34.57 2.57
2059 2890 1.068083 TCGCCAGAGCCATCGAATC 59.932 57.895 0.00 0.00 34.57 2.52
2060 2891 1.227380 GTCGCCAGAGCCATCGAAT 60.227 57.895 0.00 0.00 34.57 3.34
2061 2892 2.184322 GTCGCCAGAGCCATCGAA 59.816 61.111 0.00 0.00 34.57 3.71
2191 3052 4.779733 GCCAGAGGGAGGGGTCGA 62.780 72.222 0.00 0.00 35.59 4.20
2311 3177 4.082523 GGCGTGGTCAGGCAGCTA 62.083 66.667 15.91 0.00 43.38 3.32
2382 3251 3.838271 GCATGAGGGAGACGCCGA 61.838 66.667 0.00 0.00 37.63 5.54
2424 3293 2.983592 GACCCAAAGGCCACACCG 60.984 66.667 5.01 0.00 46.52 4.94
2567 3436 3.515286 GCGGGATCGTCGGAGTCA 61.515 66.667 8.74 0.00 38.89 3.41


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

AutoCloner maintained by Alex Coulton.