Multiple sequence alignment - TraesCS3D01G358800

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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 TraesCS3D01G358800 chr3D 100.000 3086 0 0 625 3710 472399514 472402599 0.000000e+00 5699
1 TraesCS3D01G358800 chr3D 100.000 146 0 0 1 146 472398890 472399035 1.700000e-68 270
2 TraesCS3D01G358800 chr3D 91.892 185 11 2 625 808 509243842 509244023 4.750000e-64 255
3 TraesCS3D01G358800 chr3D 91.912 136 10 1 1 135 509243157 509243292 4.890000e-44 189
4 TraesCS3D01G358800 chr3A 96.355 1015 35 2 1942 2954 614758284 614759298 0.000000e+00 1668
5 TraesCS3D01G358800 chr3A 93.456 1085 51 8 848 1926 614756450 614757520 0.000000e+00 1592
6 TraesCS3D01G358800 chr3A 97.500 760 10 2 2952 3710 614759403 614760154 0.000000e+00 1290
7 TraesCS3D01G358800 chr3B 94.338 1095 48 7 839 1926 627904264 627905351 0.000000e+00 1666
8 TraesCS3D01G358800 chr3B 93.732 1037 47 10 1944 2972 627905517 627906543 0.000000e+00 1539
9 TraesCS3D01G358800 chr3B 88.253 647 49 13 3072 3710 627906558 627907185 0.000000e+00 749
10 TraesCS3D01G358800 chr3B 89.785 186 14 3 625 808 64502659 64502477 2.230000e-57 233
11 TraesCS3D01G358800 chr1D 91.892 185 12 2 625 808 59015860 59016042 4.750000e-64 255
12 TraesCS3D01G358800 chrUn 90.957 188 13 2 625 811 88056862 88056678 2.210000e-62 250
13 TraesCS3D01G358800 chrUn 88.889 144 15 1 1 143 88057601 88057458 3.810000e-40 176
14 TraesCS3D01G358800 chr2B 90.625 192 12 3 625 815 683382385 683382571 2.210000e-62 250
15 TraesCS3D01G358800 chr2B 89.781 137 11 3 1 135 683381751 683381886 4.930000e-39 172
16 TraesCS3D01G358800 chr6D 91.351 185 11 3 625 808 380949122 380948942 7.960000e-62 248
17 TraesCS3D01G358800 chr6D 90.811 185 13 2 625 808 19713558 19713739 1.030000e-60 244
18 TraesCS3D01G358800 chr6A 90.476 189 14 2 625 812 461807226 461807041 2.860000e-61 246
19 TraesCS3D01G358800 chr7A 90.270 185 14 2 625 808 718315045 718315226 4.790000e-59 239
20 TraesCS3D01G358800 chr5D 90.278 144 12 2 1 143 44142032 44142174 1.760000e-43 187


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 TraesCS3D01G358800 chr3D 472398890 472402599 3709 False 2984.500000 5699 100.000000 1 3710 2 chr3D.!!$F1 3709
1 TraesCS3D01G358800 chr3D 509243157 509244023 866 False 222.000000 255 91.902000 1 808 2 chr3D.!!$F2 807
2 TraesCS3D01G358800 chr3A 614756450 614760154 3704 False 1516.666667 1668 95.770333 848 3710 3 chr3A.!!$F1 2862
3 TraesCS3D01G358800 chr3B 627904264 627907185 2921 False 1318.000000 1666 92.107667 839 3710 3 chr3B.!!$F1 2871
4 TraesCS3D01G358800 chrUn 88056678 88057601 923 True 213.000000 250 89.923000 1 811 2 chrUn.!!$R1 810
5 TraesCS3D01G358800 chr2B 683381751 683382571 820 False 211.000000 250 90.203000 1 815 2 chr2B.!!$F1 814

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
821 1602 0.685785 TGCTCTGAGGCTCTACAGGG 60.686 60.0 16.72 6.63 37.63 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2768 4311 0.520404 CTGCTGCACCACTCATGAAC 59.48 55.0 0.0 0.0 0.0 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
689 1469 1.618616 CCGGGTTGGGCCTCTAAAAAT 60.619 52.381 4.53 0.00 37.43 1.82
694 1474 5.279556 CGGGTTGGGCCTCTAAAAATTTTTA 60.280 40.000 19.58 19.58 37.43 1.52
733 1513 2.159268 GGGGTCTAGTCTACGCACTTTC 60.159 54.545 0.00 0.00 0.00 2.62
741 1521 3.318275 AGTCTACGCACTTTCTTCTGTCA 59.682 43.478 0.00 0.00 0.00 3.58
749 1529 5.220586 CGCACTTTCTTCTGTCAAAACTGTA 60.221 40.000 0.00 0.00 0.00 2.74
750 1530 6.551736 GCACTTTCTTCTGTCAAAACTGTAA 58.448 36.000 0.00 0.00 0.00 2.41
751 1531 7.027161 GCACTTTCTTCTGTCAAAACTGTAAA 58.973 34.615 0.00 0.00 0.00 2.01
798 1579 7.902941 AGATTTGGGAGTTTAGGGTACTACTAA 59.097 37.037 6.51 6.51 0.00 2.24
808 1589 7.584122 TTAGGGTACTACTAAAGATGCTCTG 57.416 40.000 7.73 0.00 0.00 3.35
811 1592 5.010213 GGGTACTACTAAAGATGCTCTGAGG 59.990 48.000 6.83 0.00 0.00 3.86
812 1593 4.664150 ACTACTAAAGATGCTCTGAGGC 57.336 45.455 6.83 0.00 0.00 4.70
813 1594 4.285863 ACTACTAAAGATGCTCTGAGGCT 58.714 43.478 6.83 0.00 0.00 4.58
814 1595 3.817709 ACTAAAGATGCTCTGAGGCTC 57.182 47.619 7.79 7.79 0.00 4.70
815 1596 3.373830 ACTAAAGATGCTCTGAGGCTCT 58.626 45.455 16.72 0.00 0.00 4.09
816 1597 4.541705 ACTAAAGATGCTCTGAGGCTCTA 58.458 43.478 16.72 2.97 0.00 2.43
817 1598 3.817709 AAAGATGCTCTGAGGCTCTAC 57.182 47.619 16.72 3.04 0.00 2.59
818 1599 2.450867 AGATGCTCTGAGGCTCTACA 57.549 50.000 16.72 8.74 0.00 2.74
819 1600 2.309613 AGATGCTCTGAGGCTCTACAG 58.690 52.381 16.72 9.51 35.72 2.74
820 1601 1.340889 GATGCTCTGAGGCTCTACAGG 59.659 57.143 16.72 2.98 35.20 4.00
821 1602 0.685785 TGCTCTGAGGCTCTACAGGG 60.686 60.000 16.72 6.63 37.63 4.45
822 1603 2.123409 CTCTGAGGCTCTACAGGGC 58.877 63.158 16.72 0.00 35.20 5.19
823 1604 1.733402 CTCTGAGGCTCTACAGGGCG 61.733 65.000 16.72 0.00 35.20 6.13
824 1605 3.438017 CTGAGGCTCTACAGGGCGC 62.438 68.421 16.72 0.00 0.00 6.53
825 1606 4.577246 GAGGCTCTACAGGGCGCG 62.577 72.222 7.40 0.00 0.00 6.86
942 1724 1.132453 CGCACTGGATAGAGTCGAACA 59.868 52.381 0.00 0.00 0.00 3.18
945 1727 3.377485 GCACTGGATAGAGTCGAACACTA 59.623 47.826 0.00 0.00 34.41 2.74
973 1761 3.691342 CCTCCTGTTCACCGGCGA 61.691 66.667 9.30 0.00 0.00 5.54
1047 1835 1.142748 CCTCCTGCAACCTCTAGCG 59.857 63.158 0.00 0.00 0.00 4.26
1054 1842 1.450312 CAACCTCTAGCGCCCAAGG 60.450 63.158 15.76 15.76 34.94 3.61
1071 1859 4.483243 GCCCATCGCCCTTTCGGA 62.483 66.667 0.00 0.00 0.00 4.55
1074 1862 2.584608 CATCGCCCTTTCGGACCT 59.415 61.111 0.00 0.00 0.00 3.85
1260 2048 2.680352 GGGCAGGACTCCGACTCA 60.680 66.667 0.00 0.00 0.00 3.41
1326 2114 1.149101 AGAAGTCCCCAAAGCAGGAA 58.851 50.000 0.00 0.00 32.81 3.36
1339 2127 1.593296 GCAGGAAGCCAAGAAGCAGG 61.593 60.000 0.00 0.00 37.23 4.85
1340 2128 0.037303 CAGGAAGCCAAGAAGCAGGA 59.963 55.000 0.00 0.00 34.23 3.86
1341 2129 0.327591 AGGAAGCCAAGAAGCAGGAG 59.672 55.000 0.00 0.00 34.23 3.69
1342 2130 0.679321 GGAAGCCAAGAAGCAGGAGG 60.679 60.000 0.00 0.00 34.23 4.30
1346 2134 1.557269 GCCAAGAAGCAGGAGGAGGA 61.557 60.000 0.00 0.00 0.00 3.71
1356 2144 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1362 2150 2.766229 GAGGAGGAGGAGGCCCAC 60.766 72.222 0.00 0.00 33.88 4.61
1406 2194 4.194720 CGAGGAGGACGCGGGAAG 62.195 72.222 12.47 0.00 38.81 3.46
1778 2566 1.002624 GGATGAAGGTGGCGTTCCA 60.003 57.895 0.00 0.00 40.85 3.53
1899 2687 0.464036 TGAAAGAGGTGAGTGCGTGT 59.536 50.000 0.00 0.00 0.00 4.49
1902 2690 0.753262 AAGAGGTGAGTGCGTGTTCT 59.247 50.000 0.00 0.00 0.00 3.01
1919 2707 6.913673 GCGTGTTCTTTGTGGTAAAAGATTTA 59.086 34.615 0.58 0.00 43.75 1.40
1928 3248 8.810652 TTGTGGTAAAAGATTTAGTTTGATGC 57.189 30.769 0.00 0.00 0.00 3.91
1929 3249 7.375053 TGTGGTAAAAGATTTAGTTTGATGCC 58.625 34.615 0.00 0.00 0.00 4.40
1930 3250 6.526674 GTGGTAAAAGATTTAGTTTGATGCCG 59.473 38.462 0.00 0.00 0.00 5.69
1932 3252 6.745907 GGTAAAAGATTTAGTTTGATGCCGTC 59.254 38.462 0.00 0.00 0.00 4.79
1935 3255 4.192317 AGATTTAGTTTGATGCCGTCTCC 58.808 43.478 0.00 0.00 0.00 3.71
1938 3258 4.746535 TTAGTTTGATGCCGTCTCCATA 57.253 40.909 0.00 0.00 0.00 2.74
1940 3260 2.158900 AGTTTGATGCCGTCTCCATAGG 60.159 50.000 0.00 0.00 0.00 2.57
2040 3583 5.106987 GGCGAAAATGTTGCATTTCAATTCT 60.107 36.000 10.29 0.00 36.99 2.40
2073 3616 2.469847 CCGTCAATGCACGACACG 59.530 61.111 16.11 9.82 42.69 4.49
2232 3775 1.280421 GAGGTGTCAAGGGATGAGCTT 59.720 52.381 0.00 0.00 39.19 3.74
2235 3778 2.553028 GGTGTCAAGGGATGAGCTTGAA 60.553 50.000 0.00 0.00 39.19 2.69
2478 4021 2.546795 GGAGGATGCACTCATAACTCCG 60.547 54.545 6.66 0.00 42.22 4.63
2496 4039 1.444250 GACCACAACTGACCGGACA 59.556 57.895 9.46 7.70 0.00 4.02
2589 4132 2.301583 GGATACATTGGAGAGGGAGCTC 59.698 54.545 4.71 4.71 0.00 4.09
2751 4294 3.340814 TCTGATGAAGGAGGCAGAAAC 57.659 47.619 0.00 0.00 34.71 2.78
2768 4311 2.611974 AACTTATTTTGCGAGCGTGG 57.388 45.000 0.00 0.00 0.00 4.94
2913 4456 4.373156 ACTTCAGTAGGAAAATGTGCCT 57.627 40.909 0.00 0.00 34.44 4.75
2938 4482 6.599244 TGTCAAGAAAGACTTATATTGCCTGG 59.401 38.462 0.00 0.00 39.27 4.45
3382 5041 8.692110 ATAAACGAAGTACAAACATGTATCGA 57.308 30.769 15.05 0.00 45.00 3.59
3459 5118 4.238514 ACTCGAAATCTCTTTGTCTTCCG 58.761 43.478 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.163713 GCCTTTTGTAGATGGAGATGAACAC 60.164 44.000 0.00 0.00 0.00 3.32
689 1469 7.897030 CCCCTTTAATCCTTAGACCCTTAAAAA 59.103 37.037 0.00 0.00 0.00 1.94
694 1474 4.455161 ACCCCTTTAATCCTTAGACCCTT 58.545 43.478 0.00 0.00 0.00 3.95
706 1486 4.099113 GTGCGTAGACTAGACCCCTTTAAT 59.901 45.833 0.00 0.00 0.00 1.40
758 1538 8.706322 ACTCCCAAATCTGTAAAAATAACTGT 57.294 30.769 0.00 0.00 0.00 3.55
781 1561 7.974730 AGCATCTTTAGTAGTACCCTAAACT 57.025 36.000 9.96 5.17 32.49 2.66
808 1589 4.577246 CGCGCCCTGTAGAGCCTC 62.577 72.222 0.00 0.00 0.00 4.70
827 1608 0.106217 ACAAGTTGTCAACCCCCTGG 60.106 55.000 12.17 0.00 37.80 4.45
828 1609 1.032014 CACAAGTTGTCAACCCCCTG 58.968 55.000 12.17 7.46 0.00 4.45
829 1610 0.923358 TCACAAGTTGTCAACCCCCT 59.077 50.000 12.17 0.00 0.00 4.79
830 1611 1.029681 GTCACAAGTTGTCAACCCCC 58.970 55.000 12.17 0.00 0.00 5.40
831 1612 1.757682 TGTCACAAGTTGTCAACCCC 58.242 50.000 12.17 0.00 0.00 4.95
832 1613 3.145212 GTTGTCACAAGTTGTCAACCC 57.855 47.619 21.50 8.34 44.09 4.11
835 1616 3.417101 ACCAGTTGTCACAAGTTGTCAA 58.583 40.909 5.27 5.79 31.74 3.18
836 1617 3.006940 GACCAGTTGTCACAAGTTGTCA 58.993 45.455 19.90 0.00 43.85 3.58
837 1618 3.675467 GACCAGTTGTCACAAGTTGTC 57.325 47.619 12.52 12.52 43.85 3.18
957 1739 2.432628 GTCGCCGGTGAACAGGAG 60.433 66.667 21.49 0.23 32.68 3.69
963 1745 1.738830 GGAATTCGTCGCCGGTGAA 60.739 57.895 21.49 11.01 33.95 3.18
973 1761 1.201647 TCTCTTCTTCGCGGAATTCGT 59.798 47.619 6.13 0.00 41.72 3.85
1066 1854 0.613853 CTGGGGTGTAGAGGTCCGAA 60.614 60.000 0.00 0.00 0.00 4.30
1071 1859 1.306226 GAGGCTGGGGTGTAGAGGT 60.306 63.158 0.00 0.00 0.00 3.85
1074 1862 1.001760 GAGGAGGCTGGGGTGTAGA 59.998 63.158 0.00 0.00 0.00 2.59
1254 2042 2.438614 TCCTCGCCCTCTGAGTCG 60.439 66.667 3.66 7.04 0.00 4.18
1260 2048 4.851214 GGCTCCTCCTCGCCCTCT 62.851 72.222 0.00 0.00 40.43 3.69
1317 2105 0.964700 GCTTCTTGGCTTCCTGCTTT 59.035 50.000 0.00 0.00 42.39 3.51
1326 2114 1.560866 CCTCCTCCTGCTTCTTGGCT 61.561 60.000 0.00 0.00 0.00 4.75
1333 2121 1.002792 CCTCCTCCTCCTCCTGCTT 59.997 63.158 0.00 0.00 0.00 3.91
1339 2127 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1340 2128 2.710826 GCCTCCTCCTCCTCCTCCT 61.711 68.421 0.00 0.00 0.00 3.69
1341 2129 2.123033 GCCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
1342 2130 2.123033 GGCCTCCTCCTCCTCCTC 60.123 72.222 0.00 0.00 0.00 3.71
1346 2134 4.787280 CGTGGGCCTCCTCCTCCT 62.787 72.222 4.53 0.00 0.00 3.69
1716 2504 2.745884 TCAAACCTGATGGCGCGG 60.746 61.111 8.83 0.00 36.63 6.46
1778 2566 2.752238 CGCCGTCCTCTCTGTCCT 60.752 66.667 0.00 0.00 0.00 3.85
1879 2667 1.143305 CACGCACTCACCTCTTTCAG 58.857 55.000 0.00 0.00 0.00 3.02
1902 2690 9.255304 GCATCAAACTAAATCTTTTACCACAAA 57.745 29.630 0.00 0.00 0.00 2.83
1919 2707 2.158900 CCTATGGAGACGGCATCAAACT 60.159 50.000 0.00 0.00 0.00 2.66
1927 3247 1.735376 TTCTCGCCTATGGAGACGGC 61.735 60.000 0.00 0.00 40.09 5.68
1928 3248 0.744874 TTTCTCGCCTATGGAGACGG 59.255 55.000 0.00 0.00 40.09 4.79
1929 3249 1.405821 AGTTTCTCGCCTATGGAGACG 59.594 52.381 0.00 0.00 40.09 4.18
1930 3250 2.815478 CAGTTTCTCGCCTATGGAGAC 58.185 52.381 0.00 0.00 40.09 3.36
1932 3252 1.134699 TGCAGTTTCTCGCCTATGGAG 60.135 52.381 0.00 0.00 0.00 3.86
1935 3255 6.974932 ATATAATGCAGTTTCTCGCCTATG 57.025 37.500 0.00 0.00 0.00 2.23
1938 3258 5.221641 TGGTATATAATGCAGTTTCTCGCCT 60.222 40.000 0.00 0.00 0.00 5.52
1940 3260 6.727824 ATGGTATATAATGCAGTTTCTCGC 57.272 37.500 0.00 0.00 0.00 5.03
2019 3562 8.553696 ACTTCAGAATTGAAATGCAACATTTTC 58.446 29.630 6.97 3.97 42.48 2.29
2073 3616 2.419324 CAGCTCAATGGTTCTGAAGAGC 59.581 50.000 16.42 16.42 46.47 4.09
2115 3658 9.760077 AATGGCAAATTGAGATCAAAGAATATC 57.240 29.630 0.00 0.00 39.55 1.63
2232 3775 3.515502 ACTTGTGATCGAGGAGGAATTCA 59.484 43.478 7.93 0.00 0.00 2.57
2235 3778 5.878406 AATACTTGTGATCGAGGAGGAAT 57.122 39.130 0.00 0.00 0.00 3.01
2478 4021 0.600255 CTGTCCGGTCAGTTGTGGTC 60.600 60.000 19.16 0.00 0.00 4.02
2496 4039 4.012374 CAACAATAGCATCACCAGAACCT 58.988 43.478 0.00 0.00 0.00 3.50
2751 4294 2.095969 TGAACCACGCTCGCAAAATAAG 60.096 45.455 0.00 0.00 0.00 1.73
2768 4311 0.520404 CTGCTGCACCACTCATGAAC 59.480 55.000 0.00 0.00 0.00 3.18
2885 4428 8.082242 GCACATTTTCCTACTGAAGTTTACATT 58.918 33.333 0.00 0.00 33.63 2.71
2888 4431 6.206829 AGGCACATTTTCCTACTGAAGTTTAC 59.793 38.462 0.00 0.00 33.63 2.01
2913 4456 6.599244 CCAGGCAATATAAGTCTTTCTTGACA 59.401 38.462 8.95 0.00 39.27 3.58
2972 4631 5.763204 TGGCTTTAACAGTAGCATATAAGGC 59.237 40.000 0.00 0.00 39.15 4.35
3015 4674 4.887655 GCTTAGTGGGTAGGCATTAAACAT 59.112 41.667 0.00 0.00 33.86 2.71
3382 5041 6.120507 AGGATTAGCAAGACAGAAGACTTT 57.879 37.500 0.00 0.00 0.00 2.66
3459 5118 6.046593 TGGTTATTCAAGTGTACGATGGATC 58.953 40.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.