Multiple sequence alignment - TraesCS3B01G192000

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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 TraesCS3B01G192000 chr3B 100.000 2996 0 0 1 2996 205693524 205690529 0.000000e+00 5533.0
1 TraesCS3B01G192000 chr3B 95.620 1781 21 18 195 1966 205466736 205465004 0.000000e+00 2804.0
2 TraesCS3B01G192000 chr3B 89.867 829 63 15 2177 2996 597855430 597854614 0.000000e+00 1046.0
3 TraesCS3B01G192000 chr3B 97.044 203 6 0 1 203 205475510 205475308 2.860000e-90 342.0
4 TraesCS3B01G192000 chr3B 95.876 97 4 0 1967 2063 597855827 597855731 1.110000e-34 158.0
5 TraesCS3B01G192000 chr3D 91.717 1666 69 34 335 1966 145202632 145201002 0.000000e+00 2248.0
6 TraesCS3B01G192000 chr3D 97.420 659 16 1 1308 1966 144779374 144780031 0.000000e+00 1122.0
7 TraesCS3B01G192000 chr3D 82.152 818 96 25 2196 2996 612524821 612524037 0.000000e+00 656.0
8 TraesCS3B01G192000 chr3D 93.472 337 15 3 1 337 145203844 145203515 7.460000e-136 494.0
9 TraesCS3B01G192000 chr3D 87.324 213 20 4 1967 2174 109028058 109028268 1.390000e-58 237.0
10 TraesCS3B01G192000 chr2B 91.778 827 48 14 2177 2996 158878711 158877898 0.000000e+00 1133.0
11 TraesCS3B01G192000 chr2B 91.052 827 53 13 2177 2996 158888757 158887945 0.000000e+00 1098.0
12 TraesCS3B01G192000 chr2B 91.837 196 14 1 1967 2162 158890679 158890486 3.810000e-69 272.0
13 TraesCS3B01G192000 chr2B 83.333 72 10 2 706 776 31437503 31437573 6.930000e-07 65.8
14 TraesCS3B01G192000 chr7B 91.198 818 48 14 2177 2987 637621744 637622544 0.000000e+00 1090.0
15 TraesCS3B01G192000 chr7B 94.931 217 8 2 1962 2177 637620101 637620315 1.330000e-88 337.0
16 TraesCS3B01G192000 chr7B 74.160 476 72 35 586 1041 44116322 44116766 1.860000e-32 150.0
17 TraesCS3B01G192000 chr5D 90.194 826 58 12 2177 2996 137998 137190 0.000000e+00 1055.0
18 TraesCS3B01G192000 chr5D 85.507 828 80 19 2177 2993 420315141 420315939 0.000000e+00 828.0
19 TraesCS3B01G192000 chr5D 88.462 208 19 3 1967 2174 138423 138221 2.310000e-61 246.0
20 TraesCS3B01G192000 chr3A 89.102 835 57 20 2177 2996 629679644 629678829 0.000000e+00 1007.0
21 TraesCS3B01G192000 chr4D 91.304 736 50 10 2264 2993 2991931 2992658 0.000000e+00 992.0
22 TraesCS3B01G192000 chrUn 90.999 711 47 11 2289 2993 27693788 27694487 0.000000e+00 942.0
23 TraesCS3B01G192000 chrUn 81.633 98 14 4 200 296 402855697 402855791 8.900000e-11 78.7
24 TraesCS3B01G192000 chr7D 85.835 826 80 15 2177 2993 21686661 21687458 0.000000e+00 843.0
25 TraesCS3B01G192000 chr7D 83.721 215 23 5 1965 2168 65639486 65639273 3.050000e-45 193.0
26 TraesCS3B01G192000 chr7D 75.455 220 36 13 832 1042 104915639 104915849 1.140000e-14 91.6
27 TraesCS3B01G192000 chr5B 90.122 658 51 11 2343 2993 700310922 700311572 0.000000e+00 843.0
28 TraesCS3B01G192000 chr5B 92.742 124 7 1 1966 2089 700310259 700310380 8.530000e-41 178.0
29 TraesCS3B01G192000 chr7A 74.817 818 122 53 311 1108 678595194 678594441 2.920000e-75 292.0
30 TraesCS3B01G192000 chr7A 77.428 381 68 13 477 847 604260003 604260375 8.410000e-51 211.0
31 TraesCS3B01G192000 chr7A 77.256 277 52 10 482 752 604289259 604289530 5.170000e-33 152.0
32 TraesCS3B01G192000 chr7A 81.633 98 14 4 200 296 5249225 5249131 8.900000e-11 78.7
33 TraesCS3B01G192000 chr7A 82.716 81 10 4 217 296 5275791 5275714 5.360000e-08 69.4
34 TraesCS3B01G192000 chr7A 82.716 81 10 4 217 296 5305188 5305111 5.360000e-08 69.4
35 TraesCS3B01G192000 chr7A 79.592 98 16 4 200 296 5262027 5261933 1.930000e-07 67.6
36 TraesCS3B01G192000 chr2A 88.372 215 11 8 1967 2177 52202006 52202210 2.310000e-61 246.0
37 TraesCS3B01G192000 chr2A 90.116 172 9 3 1967 2134 52226099 52226266 1.810000e-52 217.0
38 TraesCS3B01G192000 chr2A 77.714 175 31 7 876 1046 227561289 227561119 1.900000e-17 100.0
39 TraesCS3B01G192000 chr2D 72.229 875 162 54 307 1159 510221637 510222452 8.470000e-46 195.0
40 TraesCS3B01G192000 chr6D 81.967 183 27 6 980 1159 454741037 454741216 1.860000e-32 150.0
41 TraesCS3B01G192000 chr4A 77.178 241 42 10 862 1096 736916686 736916919 8.720000e-26 128.0
42 TraesCS3B01G192000 chr1D 73.697 403 60 28 471 863 478338934 478339300 6.790000e-22 115.0
43 TraesCS3B01G192000 chr5A 93.478 46 2 1 1006 1051 510184321 510184277 1.930000e-07 67.6


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 TraesCS3B01G192000 chr3B 205690529 205693524 2995 True 5533.0 5533 100.0000 1 2996 1 chr3B.!!$R3 2995
1 TraesCS3B01G192000 chr3B 205465004 205466736 1732 True 2804.0 2804 95.6200 195 1966 1 chr3B.!!$R1 1771
2 TraesCS3B01G192000 chr3B 597854614 597855827 1213 True 602.0 1046 92.8715 1967 2996 2 chr3B.!!$R4 1029
3 TraesCS3B01G192000 chr3D 145201002 145203844 2842 True 1371.0 2248 92.5945 1 1966 2 chr3D.!!$R2 1965
4 TraesCS3B01G192000 chr3D 144779374 144780031 657 False 1122.0 1122 97.4200 1308 1966 1 chr3D.!!$F2 658
5 TraesCS3B01G192000 chr3D 612524037 612524821 784 True 656.0 656 82.1520 2196 2996 1 chr3D.!!$R1 800
6 TraesCS3B01G192000 chr2B 158877898 158878711 813 True 1133.0 1133 91.7780 2177 2996 1 chr2B.!!$R1 819
7 TraesCS3B01G192000 chr2B 158887945 158890679 2734 True 685.0 1098 91.4445 1967 2996 2 chr2B.!!$R2 1029
8 TraesCS3B01G192000 chr7B 637620101 637622544 2443 False 713.5 1090 93.0645 1962 2987 2 chr7B.!!$F2 1025
9 TraesCS3B01G192000 chr5D 420315141 420315939 798 False 828.0 828 85.5070 2177 2993 1 chr5D.!!$F1 816
10 TraesCS3B01G192000 chr5D 137190 138423 1233 True 650.5 1055 89.3280 1967 2996 2 chr5D.!!$R1 1029
11 TraesCS3B01G192000 chr3A 629678829 629679644 815 True 1007.0 1007 89.1020 2177 2996 1 chr3A.!!$R1 819
12 TraesCS3B01G192000 chr4D 2991931 2992658 727 False 992.0 992 91.3040 2264 2993 1 chr4D.!!$F1 729
13 TraesCS3B01G192000 chrUn 27693788 27694487 699 False 942.0 942 90.9990 2289 2993 1 chrUn.!!$F1 704
14 TraesCS3B01G192000 chr7D 21686661 21687458 797 False 843.0 843 85.8350 2177 2993 1 chr7D.!!$F1 816
15 TraesCS3B01G192000 chr5B 700310259 700311572 1313 False 510.5 843 91.4320 1966 2993 2 chr5B.!!$F1 1027
16 TraesCS3B01G192000 chr7A 678594441 678595194 753 True 292.0 292 74.8170 311 1108 1 chr7A.!!$R5 797

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
415 1301 2.799017 AGTTTATTCCCCACCGGTTTC 58.201 47.619 2.97 0.0 0.0 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 5026 0.331278 TGGTTATGTGGCAAGGGAGG 59.669 55.0 0.0 0.0 0.0 4.3 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
168 169 4.481112 GATGTTTGCCAGCGCCCG 62.481 66.667 2.29 0.00 0.00 6.13
290 291 6.826668 TCGGTGAATCCATGACTATATTTGT 58.173 36.000 0.00 0.00 35.57 2.83
309 310 4.436998 GTCGACGGACTGGGCAGG 62.437 72.222 0.00 0.00 40.15 4.85
415 1301 2.799017 AGTTTATTCCCCACCGGTTTC 58.201 47.619 2.97 0.00 0.00 2.78
612 1536 6.820470 TTTGCGATTTTTCGTTTCAAATCT 57.180 29.167 0.00 0.00 37.28 2.40
692 1618 7.760437 TCAAGAATGCAAATAATGTTCATCGA 58.240 30.769 0.00 0.00 0.00 3.59
712 1638 6.384258 TCGAACTCAATTTTTGGTTCATCA 57.616 33.333 15.41 0.00 39.07 3.07
1096 2041 9.801873 CTTGTTGTGATCCCGAATTATTTTAAT 57.198 29.630 0.00 0.00 0.00 1.40
1942 2911 3.264947 GGATTTGTACTTCCACCCGTAC 58.735 50.000 0.00 0.00 37.19 3.67
2033 3002 4.696455 TCAGATGACGTATGCATGACATT 58.304 39.130 10.16 0.00 40.38 2.71
2047 3058 4.219288 GCATGACATTCCCTTTTCTTGTCT 59.781 41.667 0.00 0.00 38.00 3.41
2087 3115 1.674057 CCGCACTGTCCTTCTCCTT 59.326 57.895 0.00 0.00 0.00 3.36
2125 3154 0.755327 ACGGGCCTCTTTTGCTTGTT 60.755 50.000 0.84 0.00 0.00 2.83
2213 4989 7.490402 CACTTTGATCATCATAAAAAGCCCTTC 59.510 37.037 0.00 0.00 32.33 3.46
2242 5022 3.762288 GAGAAACACCTAAAATCACCCCC 59.238 47.826 0.00 0.00 0.00 5.40
2341 5123 4.627467 ACTTGCTGTACAATTTCTCTAGCG 59.373 41.667 0.00 0.00 37.72 4.26
2374 5242 7.699878 ACTTCTACCAAATAGAAATTCCTGGT 58.300 34.615 10.24 10.24 46.96 4.00
2389 5257 8.977267 AAATTCCTGGTTCAATGAATCAAAAA 57.023 26.923 10.40 7.72 31.94 1.94
2395 5263 7.065120 TGGTTCAATGAATCAAAAACCTCAT 57.935 32.000 6.45 0.00 37.60 2.90
2429 5300 0.903454 ACCCCCTACTCCAACGTGAG 60.903 60.000 1.56 1.56 38.37 3.51
2476 5351 4.142902 CCGACGCATTCTACAGTTCAATTT 60.143 41.667 0.00 0.00 0.00 1.82
2481 5356 4.379394 GCATTCTACAGTTCAATTTGCGGA 60.379 41.667 0.00 0.00 0.00 5.54
2508 5383 2.045561 TGAACAGAGCGGAACCAAAA 57.954 45.000 0.00 0.00 0.00 2.44
2536 5412 6.019881 GGAACTCTGCATACAAACAAACAAAC 60.020 38.462 0.00 0.00 0.00 2.93
2736 5613 2.757099 GAAGACGACGGGGGCCTA 60.757 66.667 0.84 0.00 0.00 3.93
2808 5700 2.969238 GACATCGCAGGCCATCGG 60.969 66.667 5.01 0.00 0.00 4.18
2872 5766 0.592637 CGATTCAAACAGTGCCAGCA 59.407 50.000 0.00 0.00 0.00 4.41
2936 5838 4.111916 CGTTGCAAACTTTGGACATCTTT 58.888 39.130 0.00 0.00 46.99 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 4.953579 GTGCCCCAGTTTCTTTATTCCATA 59.046 41.667 0.00 0.00 0.00 2.74
168 169 0.247854 GAGCTCCAATTTCGCGCTTC 60.248 55.000 5.56 0.00 0.00 3.86
170 171 2.109126 GGAGCTCCAATTTCGCGCT 61.109 57.895 28.43 0.00 35.64 5.92
309 310 3.937062 CCGCGCGCCAAATAGGAC 61.937 66.667 27.36 0.00 41.22 3.85
415 1301 6.273071 AGAAAACATTGAAAAGAACTTCCCG 58.727 36.000 0.00 0.00 0.00 5.14
1995 2964 7.554118 ACGTCATCTGAATGAGACCATTTTATT 59.446 33.333 0.00 0.00 42.53 1.40
2033 3002 1.073923 GGGCTGAGACAAGAAAAGGGA 59.926 52.381 0.00 0.00 0.00 4.20
2047 3058 4.388499 GCGAGGGAAACGGGCTGA 62.388 66.667 0.00 0.00 0.00 4.26
2198 4972 4.519906 CCTAGGGAAGGGCTTTTTATGA 57.480 45.455 0.00 0.00 42.32 2.15
2213 4989 4.921644 TTTTAGGTGTTTCTCCCTAGGG 57.078 45.455 23.22 23.22 34.87 3.53
2243 5023 1.580066 TTATGTGGCAAGGGAGGGGG 61.580 60.000 0.00 0.00 0.00 5.40
2244 5024 0.395724 GTTATGTGGCAAGGGAGGGG 60.396 60.000 0.00 0.00 0.00 4.79
2245 5025 0.395724 GGTTATGTGGCAAGGGAGGG 60.396 60.000 0.00 0.00 0.00 4.30
2246 5026 0.331278 TGGTTATGTGGCAAGGGAGG 59.669 55.000 0.00 0.00 0.00 4.30
2247 5027 1.271871 TGTGGTTATGTGGCAAGGGAG 60.272 52.381 0.00 0.00 0.00 4.30
2374 5242 7.160726 GGGAATGAGGTTTTTGATTCATTGAA 58.839 34.615 0.75 0.75 39.60 2.69
2389 5257 2.679716 GCAGCAGGGGAATGAGGT 59.320 61.111 0.00 0.00 0.00 3.85
2395 5263 4.299796 GGTTGGGCAGCAGGGGAA 62.300 66.667 0.00 0.00 0.00 3.97
2429 5300 2.979813 CGCTGGTGAATTTTTGTGTAGC 59.020 45.455 0.00 0.00 0.00 3.58
2476 5351 0.601046 CTGTTCAACTCAGCTCCGCA 60.601 55.000 0.00 0.00 0.00 5.69
2481 5356 0.320247 CCGCTCTGTTCAACTCAGCT 60.320 55.000 8.98 0.00 33.48 4.24
2508 5383 4.085357 TGTTTGTATGCAGAGTTCCACT 57.915 40.909 0.00 0.00 0.00 4.00
2549 5426 3.525537 CAAGTCCACATCACGCTATCTT 58.474 45.455 0.00 0.00 0.00 2.40
2720 5597 2.758737 CTAGGCCCCCGTCGTCTT 60.759 66.667 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.