Multiple sequence alignment - TraesCS3A01G479600

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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 TraesCS3A01G479600 chr3A 100.000 2905 0 0 1 2905 711079848 711076944 0.000000e+00 5365.0
1 TraesCS3A01G479600 chr3D 97.695 1952 26 9 1 1934 575598426 575596476 0.000000e+00 3338.0
2 TraesCS3A01G479600 chr3D 86.242 974 65 35 1932 2864 526481143 526482088 0.000000e+00 992.0
3 TraesCS3A01G479600 chr3D 94.937 158 8 0 1932 2089 397770092 397770249 6.220000e-62 248.0
4 TraesCS3A01G479600 chr3D 94.937 158 8 0 1932 2089 486146279 486146436 6.220000e-62 248.0
5 TraesCS3A01G479600 chr3B 96.245 1944 43 15 1 1934 766377463 766379386 0.000000e+00 3158.0
6 TraesCS3A01G479600 chr3B 87.748 857 54 21 2089 2903 498353899 498354746 0.000000e+00 953.0
7 TraesCS3A01G479600 chr5D 91.148 836 36 6 2089 2891 326744802 326743972 0.000000e+00 1099.0
8 TraesCS3A01G479600 chr5D 90.942 828 39 18 2090 2890 493362960 493362142 0.000000e+00 1081.0
9 TraesCS3A01G479600 chr5D 90.154 843 50 13 2089 2904 434725188 434724352 0.000000e+00 1066.0
10 TraesCS3A01G479600 chr5D 95.541 157 7 0 1933 2089 359548046 359547890 4.810000e-63 252.0
11 TraesCS3A01G479600 chr5D 94.410 161 9 0 1929 2089 357075978 357076138 6.220000e-62 248.0
12 TraesCS3A01G479600 chr5D 84.483 58 7 2 1329 1385 365121858 365121802 4.040000e-04 56.5
13 TraesCS3A01G479600 chrUn 90.224 849 44 8 2089 2904 79925260 79926102 0.000000e+00 1072.0
14 TraesCS3A01G479600 chrUn 90.798 815 36 8 2089 2864 108948296 108949110 0.000000e+00 1053.0
15 TraesCS3A01G479600 chrUn 84.536 97 13 1 1319 1413 211006520 211006424 8.570000e-16 95.3
16 TraesCS3A01G479600 chr7B 90.335 807 45 12 2089 2862 518466375 518467181 0.000000e+00 1027.0
17 TraesCS3A01G479600 chr4B 89.937 795 46 11 2089 2864 347391906 347391127 0.000000e+00 994.0
18 TraesCS3A01G479600 chr2B 88.530 837 64 14 2090 2904 74214716 74213890 0.000000e+00 985.0
19 TraesCS3A01G479600 chr2B 89.335 797 47 19 2089 2848 212306320 212305525 0.000000e+00 966.0
20 TraesCS3A01G479600 chr6B 89.219 807 56 10 2089 2864 114516164 114516970 0.000000e+00 979.0
21 TraesCS3A01G479600 chr2D 90.526 760 33 12 2089 2815 489652212 489651459 0.000000e+00 968.0
22 TraesCS3A01G479600 chr1A 87.587 862 57 13 2091 2902 478633543 478632682 0.000000e+00 953.0
23 TraesCS3A01G479600 chr1A 75.510 1666 336 47 245 1891 551531802 551533414 0.000000e+00 750.0
24 TraesCS3A01G479600 chr1A 74.564 1663 354 47 249 1895 554880714 554882323 0.000000e+00 664.0
25 TraesCS3A01G479600 chr1A 75.892 701 131 22 1203 1891 551787028 551786354 1.000000e-84 324.0
26 TraesCS3A01G479600 chr1A 83.158 95 16 0 1319 1413 552964479 552964385 1.430000e-13 87.9
27 TraesCS3A01G479600 chr1D 86.006 929 68 30 1921 2816 479342229 479343128 0.000000e+00 939.0
28 TraesCS3A01G479600 chr1D 75.406 1663 341 45 245 1891 459521580 459523190 0.000000e+00 743.0
29 TraesCS3A01G479600 chr1D 75.102 1719 353 50 201 1891 459626544 459624873 0.000000e+00 734.0
30 TraesCS3A01G479600 chr1D 74.684 1663 349 46 249 1895 463007638 463009244 0.000000e+00 673.0
31 TraesCS3A01G479600 chr1D 74.661 221 43 7 1198 1413 461502236 461502024 5.160000e-13 86.1
32 TraesCS3A01G479600 chr7D 86.264 910 70 26 1932 2814 147576167 147577048 0.000000e+00 937.0
33 TraesCS3A01G479600 chr1B 87.234 846 70 17 2089 2904 363214312 363213475 0.000000e+00 929.0
34 TraesCS3A01G479600 chr1B 85.073 824 78 21 2089 2888 581348700 581347898 0.000000e+00 798.0
35 TraesCS3A01G479600 chr1B 74.985 1715 356 49 201 1891 631716565 631718230 0.000000e+00 723.0
36 TraesCS3A01G479600 chr1B 74.498 647 144 17 303 936 634608125 634608763 7.980000e-66 261.0
37 TraesCS3A01G479600 chr1B 79.878 164 26 4 1257 1418 634114485 634114327 2.370000e-21 113.0
38 TraesCS3A01G479600 chr1B 72.980 396 75 22 1319 1692 634498394 634498009 3.060000e-20 110.0
39 TraesCS3A01G479600 chr6D 80.569 633 55 35 1931 2530 58721071 58721668 2.680000e-115 425.0
40 TraesCS3A01G479600 chr6D 90.536 317 12 3 2089 2390 98075691 98076004 1.250000e-108 403.0
41 TraesCS3A01G479600 chr5B 88.421 285 12 11 2091 2354 697576113 697575829 1.000000e-84 324.0
42 TraesCS3A01G479600 chr4D 96.178 157 6 0 1933 2089 76609114 76608958 1.030000e-64 257.0


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 TraesCS3A01G479600 chr3A 711076944 711079848 2904 True 5365 5365 100.000 1 2905 1 chr3A.!!$R1 2904
1 TraesCS3A01G479600 chr3D 575596476 575598426 1950 True 3338 3338 97.695 1 1934 1 chr3D.!!$R1 1933
2 TraesCS3A01G479600 chr3D 526481143 526482088 945 False 992 992 86.242 1932 2864 1 chr3D.!!$F3 932
3 TraesCS3A01G479600 chr3B 766377463 766379386 1923 False 3158 3158 96.245 1 1934 1 chr3B.!!$F2 1933
4 TraesCS3A01G479600 chr3B 498353899 498354746 847 False 953 953 87.748 2089 2903 1 chr3B.!!$F1 814
5 TraesCS3A01G479600 chr5D 326743972 326744802 830 True 1099 1099 91.148 2089 2891 1 chr5D.!!$R1 802
6 TraesCS3A01G479600 chr5D 493362142 493362960 818 True 1081 1081 90.942 2090 2890 1 chr5D.!!$R5 800
7 TraesCS3A01G479600 chr5D 434724352 434725188 836 True 1066 1066 90.154 2089 2904 1 chr5D.!!$R4 815
8 TraesCS3A01G479600 chrUn 79925260 79926102 842 False 1072 1072 90.224 2089 2904 1 chrUn.!!$F1 815
9 TraesCS3A01G479600 chrUn 108948296 108949110 814 False 1053 1053 90.798 2089 2864 1 chrUn.!!$F2 775
10 TraesCS3A01G479600 chr7B 518466375 518467181 806 False 1027 1027 90.335 2089 2862 1 chr7B.!!$F1 773
11 TraesCS3A01G479600 chr4B 347391127 347391906 779 True 994 994 89.937 2089 2864 1 chr4B.!!$R1 775
12 TraesCS3A01G479600 chr2B 74213890 74214716 826 True 985 985 88.530 2090 2904 1 chr2B.!!$R1 814
13 TraesCS3A01G479600 chr2B 212305525 212306320 795 True 966 966 89.335 2089 2848 1 chr2B.!!$R2 759
14 TraesCS3A01G479600 chr6B 114516164 114516970 806 False 979 979 89.219 2089 2864 1 chr6B.!!$F1 775
15 TraesCS3A01G479600 chr2D 489651459 489652212 753 True 968 968 90.526 2089 2815 1 chr2D.!!$R1 726
16 TraesCS3A01G479600 chr1A 478632682 478633543 861 True 953 953 87.587 2091 2902 1 chr1A.!!$R1 811
17 TraesCS3A01G479600 chr1A 551531802 551533414 1612 False 750 750 75.510 245 1891 1 chr1A.!!$F1 1646
18 TraesCS3A01G479600 chr1A 554880714 554882323 1609 False 664 664 74.564 249 1895 1 chr1A.!!$F2 1646
19 TraesCS3A01G479600 chr1A 551786354 551787028 674 True 324 324 75.892 1203 1891 1 chr1A.!!$R2 688
20 TraesCS3A01G479600 chr1D 479342229 479343128 899 False 939 939 86.006 1921 2816 1 chr1D.!!$F3 895
21 TraesCS3A01G479600 chr1D 459521580 459523190 1610 False 743 743 75.406 245 1891 1 chr1D.!!$F1 1646
22 TraesCS3A01G479600 chr1D 459624873 459626544 1671 True 734 734 75.102 201 1891 1 chr1D.!!$R1 1690
23 TraesCS3A01G479600 chr1D 463007638 463009244 1606 False 673 673 74.684 249 1895 1 chr1D.!!$F2 1646
24 TraesCS3A01G479600 chr7D 147576167 147577048 881 False 937 937 86.264 1932 2814 1 chr7D.!!$F1 882
25 TraesCS3A01G479600 chr1B 363213475 363214312 837 True 929 929 87.234 2089 2904 1 chr1B.!!$R1 815
26 TraesCS3A01G479600 chr1B 581347898 581348700 802 True 798 798 85.073 2089 2888 1 chr1B.!!$R2 799
27 TraesCS3A01G479600 chr1B 631716565 631718230 1665 False 723 723 74.985 201 1891 1 chr1B.!!$F1 1690
28 TraesCS3A01G479600 chr1B 634608125 634608763 638 False 261 261 74.498 303 936 1 chr1B.!!$F2 633
29 TraesCS3A01G479600 chr6D 58721071 58721668 597 False 425 425 80.569 1931 2530 1 chr6D.!!$F1 599

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
84 85 1.127951 CGGGCATACAACTTTGACGAC 59.872 52.381 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 2111 1.133823 TGGAGCTGCTCTTTTGAACCA 60.134 47.619 27.09 13.31 0.0 3.67 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
84 85 1.127951 CGGGCATACAACTTTGACGAC 59.872 52.381 0.00 0.00 0.00 4.34
90 91 4.377431 GCATACAACTTTGACGACAGGAAG 60.377 45.833 0.00 0.00 0.00 3.46
574 590 6.121590 AGAACCGTTAAGTCTGGGTTTAAAA 58.878 36.000 0.00 0.00 42.54 1.52
802 819 8.349983 GCACTTGTTTTCAAAATCTTCTACCTA 58.650 33.333 0.00 0.00 39.47 3.08
849 867 4.812626 GCCATGGGATAATTTGCTTGAAAG 59.187 41.667 15.13 0.00 0.00 2.62
865 883 3.247442 TGAAAGTACCTTGTACGATGCG 58.753 45.455 0.00 0.00 0.00 4.73
1194 1223 6.699204 CAGTGTATAGGAGTAGTTTGATGCAG 59.301 42.308 0.00 0.00 0.00 4.41
1200 1229 4.018960 AGGAGTAGTTTGATGCAGGAACAT 60.019 41.667 10.89 0.00 0.00 2.71
1201 1230 4.095483 GGAGTAGTTTGATGCAGGAACATG 59.905 45.833 10.89 0.00 0.00 3.21
1549 1591 4.202274 TGGAGATAATTACGAATGCCCGAA 60.202 41.667 0.00 0.00 0.00 4.30
1929 1981 5.989477 TCTATGTCAGGGTGGTTTATCTTG 58.011 41.667 0.00 0.00 0.00 3.02
2022 2074 3.733443 AAAAATGCGTTTTGGAGCTCT 57.267 38.095 17.08 0.00 38.04 4.09
2060 2112 5.866335 CCAACAAATGGTCCAAATTGATG 57.134 39.130 21.44 19.25 44.85 3.07
2061 2113 4.696402 CCAACAAATGGTCCAAATTGATGG 59.304 41.667 23.75 23.75 44.85 3.51
2062 2114 5.307204 CAACAAATGGTCCAAATTGATGGT 58.693 37.500 21.44 1.87 41.46 3.55
2063 2115 5.565455 ACAAATGGTCCAAATTGATGGTT 57.435 34.783 21.44 2.67 41.46 3.67
2064 2116 5.550290 ACAAATGGTCCAAATTGATGGTTC 58.450 37.500 21.44 0.00 41.46 3.62
2065 2117 5.071519 ACAAATGGTCCAAATTGATGGTTCA 59.928 36.000 21.44 0.00 41.46 3.18
2066 2118 5.822132 AATGGTCCAAATTGATGGTTCAA 57.178 34.783 0.00 0.00 45.57 2.69
2067 2119 5.822132 ATGGTCCAAATTGATGGTTCAAA 57.178 34.783 0.00 0.00 44.70 2.69
2068 2120 5.620738 TGGTCCAAATTGATGGTTCAAAA 57.379 34.783 0.00 0.00 44.70 2.44
2069 2121 5.609423 TGGTCCAAATTGATGGTTCAAAAG 58.391 37.500 0.00 0.00 44.70 2.27
2070 2122 5.365025 TGGTCCAAATTGATGGTTCAAAAGA 59.635 36.000 0.00 0.00 44.70 2.52
2071 2123 5.928264 GGTCCAAATTGATGGTTCAAAAGAG 59.072 40.000 0.00 0.00 44.70 2.85
2072 2124 5.406477 GTCCAAATTGATGGTTCAAAAGAGC 59.594 40.000 0.00 0.00 44.70 4.09
2073 2125 5.070180 TCCAAATTGATGGTTCAAAAGAGCA 59.930 36.000 0.00 0.00 44.70 4.26
2074 2126 5.407387 CCAAATTGATGGTTCAAAAGAGCAG 59.593 40.000 0.00 0.00 44.70 4.24
2075 2127 3.648339 TTGATGGTTCAAAAGAGCAGC 57.352 42.857 0.00 0.00 38.90 5.25
2076 2128 2.867624 TGATGGTTCAAAAGAGCAGCT 58.132 42.857 0.00 0.00 32.61 4.24
2077 2129 2.816087 TGATGGTTCAAAAGAGCAGCTC 59.184 45.455 15.25 15.25 32.61 4.09
2078 2130 1.609208 TGGTTCAAAAGAGCAGCTCC 58.391 50.000 19.40 1.97 0.00 4.70
2079 2131 1.133823 TGGTTCAAAAGAGCAGCTCCA 60.134 47.619 19.40 4.89 0.00 3.86
2080 2132 1.956477 GGTTCAAAAGAGCAGCTCCAA 59.044 47.619 19.40 1.80 0.00 3.53
2081 2133 2.560105 GGTTCAAAAGAGCAGCTCCAAT 59.440 45.455 19.40 2.85 0.00 3.16
2082 2134 3.758554 GGTTCAAAAGAGCAGCTCCAATA 59.241 43.478 19.40 0.00 0.00 1.90
2083 2135 4.142513 GGTTCAAAAGAGCAGCTCCAATAG 60.143 45.833 19.40 6.01 0.00 1.73
2084 2136 4.558226 TCAAAAGAGCAGCTCCAATAGA 57.442 40.909 19.40 8.28 0.00 1.98
2085 2137 5.108187 TCAAAAGAGCAGCTCCAATAGAT 57.892 39.130 19.40 0.00 0.00 1.98
2086 2138 4.880120 TCAAAAGAGCAGCTCCAATAGATG 59.120 41.667 19.40 8.82 44.75 2.90
2279 2352 2.056906 AACTGCGCCCAGAACTCCTT 62.057 55.000 4.18 0.00 41.77 3.36
2288 2364 0.977395 CAGAACTCCTTCTCCGGGTT 59.023 55.000 0.00 0.00 34.20 4.11
2440 2590 0.681564 CTCAGCCTGGACGTACTCCT 60.682 60.000 0.00 0.00 40.26 3.69
2449 2599 0.029567 GACGTACTCCTGATGCTCCG 59.970 60.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.038603 TGTGCCAGCAGTTATGATAAAGAATC 59.961 38.462 0.00 0.00 34.93 2.52
64 65 1.127951 GTCGTCAAAGTTGTATGCCCG 59.872 52.381 0.00 0.00 0.00 6.13
84 85 3.248602 CAGTCGGTTTGTTCTTCTTCCTG 59.751 47.826 0.00 0.00 0.00 3.86
227 230 9.787435 AAACAAGGTTCATCAGTTATACTGTAA 57.213 29.630 6.71 0.00 46.03 2.41
574 590 7.503902 GGATAAAGGCATCTCCAAGTAAAGATT 59.496 37.037 0.00 0.00 37.29 2.40
802 819 3.386078 TGCGAATATTCTGAGCTCCTCTT 59.614 43.478 12.15 0.00 0.00 2.85
849 867 2.267188 TGTCGCATCGTACAAGGTAC 57.733 50.000 0.00 0.00 0.00 3.34
865 883 8.386606 GTTGAACATCAAGTATCTTGAGATGTC 58.613 37.037 15.59 11.04 46.02 3.06
1054 1072 1.445410 CGTGCGATGGACGGAAGAA 60.445 57.895 2.77 0.00 44.90 2.52
1218 1247 5.918011 GTGTTGGCATTCTGAAAAACGATAA 59.082 36.000 0.00 0.00 0.00 1.75
1219 1248 5.240623 AGTGTTGGCATTCTGAAAAACGATA 59.759 36.000 0.00 0.00 0.00 2.92
1220 1249 4.037923 AGTGTTGGCATTCTGAAAAACGAT 59.962 37.500 0.00 0.00 0.00 3.73
2044 2096 5.822132 TTGAACCATCAATTTGGACCATT 57.178 34.783 3.10 0.00 40.59 3.16
2056 2108 2.816087 GAGCTGCTCTTTTGAACCATCA 59.184 45.455 21.93 0.00 0.00 3.07
2057 2109 2.163211 GGAGCTGCTCTTTTGAACCATC 59.837 50.000 27.09 4.18 0.00 3.51
2058 2110 2.165998 GGAGCTGCTCTTTTGAACCAT 58.834 47.619 27.09 0.00 0.00 3.55
2059 2111 1.133823 TGGAGCTGCTCTTTTGAACCA 60.134 47.619 27.09 13.31 0.00 3.67
2060 2112 1.609208 TGGAGCTGCTCTTTTGAACC 58.391 50.000 27.09 10.83 0.00 3.62
2061 2113 3.930634 ATTGGAGCTGCTCTTTTGAAC 57.069 42.857 27.09 10.73 0.00 3.18
2062 2114 4.910195 TCTATTGGAGCTGCTCTTTTGAA 58.090 39.130 27.09 13.41 0.00 2.69
2063 2115 4.558226 TCTATTGGAGCTGCTCTTTTGA 57.442 40.909 27.09 16.26 0.00 2.69
2064 2116 5.171147 CATCTATTGGAGCTGCTCTTTTG 57.829 43.478 27.09 14.50 0.00 2.44
2078 2130 5.887598 TCTTTTGGACCATCACCATCTATTG 59.112 40.000 0.00 0.00 37.26 1.90
2079 2131 6.078456 TCTTTTGGACCATCACCATCTATT 57.922 37.500 0.00 0.00 37.26 1.73
2080 2132 5.688807 CTCTTTTGGACCATCACCATCTAT 58.311 41.667 0.00 0.00 37.26 1.98
2081 2133 4.626287 GCTCTTTTGGACCATCACCATCTA 60.626 45.833 0.00 0.00 37.26 1.98
2082 2134 3.875369 GCTCTTTTGGACCATCACCATCT 60.875 47.826 0.00 0.00 37.26 2.90
2083 2135 2.424956 GCTCTTTTGGACCATCACCATC 59.575 50.000 0.00 0.00 37.26 3.51
2084 2136 2.225091 TGCTCTTTTGGACCATCACCAT 60.225 45.455 0.00 0.00 37.26 3.55
2085 2137 1.144708 TGCTCTTTTGGACCATCACCA 59.855 47.619 0.00 0.00 35.47 4.17
2086 2138 1.815003 CTGCTCTTTTGGACCATCACC 59.185 52.381 0.00 0.00 0.00 4.02
2087 2139 1.200948 GCTGCTCTTTTGGACCATCAC 59.799 52.381 0.00 0.00 0.00 3.06
2279 2352 3.998672 GGTGCGACAACCCGGAGA 61.999 66.667 0.73 0.00 33.79 3.71
2299 2375 0.033011 TTCTCGAAGGAGGAGGAGGG 60.033 60.000 0.00 0.00 40.85 4.30
2449 2599 2.464459 CGATGGCGAGGTTTGCTCC 61.464 63.158 0.00 0.00 40.82 4.70
2783 2934 3.264897 CGATGGCGCCGAAGAAGG 61.265 66.667 23.90 2.28 0.00 3.46


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

AutoCloner maintained by Alex Coulton.