Multiple sequence alignment - TraesCS2A01G234500

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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 TraesCS2A01G234500 chr2A 100.000 2484 0 0 1 2484 284782265 284784748 0.000000e+00 4588
1 TraesCS2A01G234500 chr2A 94.966 437 20 2 2049 2484 528783375 528782940 0.000000e+00 684
2 TraesCS2A01G234500 chr2A 93.043 460 29 2 2023 2481 482546045 482546502 0.000000e+00 669
3 TraesCS2A01G234500 chr7A 96.140 2487 80 3 1 2484 347383184 347385657 0.000000e+00 4047
4 TraesCS2A01G234500 chr7A 96.014 2484 98 1 1 2484 401494982 401497464 0.000000e+00 4037
5 TraesCS2A01G234500 chr7A 90.476 420 38 2 1476 1894 458555683 458555265 1.000000e-153 553
6 TraesCS2A01G234500 chr6A 96.055 2484 98 0 1 2484 242010628 242008145 0.000000e+00 4045
7 TraesCS2A01G234500 chr2D 94.279 874 48 2 1025 1898 64941660 64940789 0.000000e+00 1336
8 TraesCS2A01G234500 chr2D 90.000 740 47 10 28 767 64942371 64941659 0.000000e+00 931
9 TraesCS2A01G234500 chr2D 86.100 259 35 1 1892 2150 64940608 64940351 6.770000e-71 278
10 TraesCS2A01G234500 chr1B 91.166 815 44 11 1032 1844 227793850 227794638 0.000000e+00 1081
11 TraesCS2A01G234500 chr1B 91.667 768 58 4 1 764 226904477 226905242 0.000000e+00 1059
12 TraesCS2A01G234500 chr1B 94.953 634 29 3 1024 1656 226905242 226905873 0.000000e+00 990
13 TraesCS2A01G234500 chr1B 90.390 718 44 10 50 767 227793151 227793843 0.000000e+00 920
14 TraesCS2A01G234500 chr1B 89.663 416 40 3 1480 1894 310676592 310676179 6.080000e-146 527
15 TraesCS2A01G234500 chr1B 86.099 223 30 1 1892 2114 606148591 606148812 3.190000e-59 239
16 TraesCS2A01G234500 chr1B 85.714 224 29 3 1892 2114 412239677 412239456 1.490000e-57 233
17 TraesCS2A01G234500 chr1B 85.446 213 29 1 317 527 197788773 197788985 1.160000e-53 220
18 TraesCS2A01G234500 chr5D 94.783 575 23 7 909 1481 534638075 534638644 0.000000e+00 889
19 TraesCS2A01G234500 chr5D 94.783 575 23 7 909 1481 534857968 534858537 0.000000e+00 889
20 TraesCS2A01G234500 chr5D 94.435 575 25 7 909 1481 534866092 534866661 0.000000e+00 878
21 TraesCS2A01G234500 chr5D 86.613 620 52 17 317 935 534856425 534857014 0.000000e+00 656
22 TraesCS2A01G234500 chr5D 94.022 368 19 3 1476 1842 198493533 198493168 2.790000e-154 555
23 TraesCS2A01G234500 chr5D 76.660 497 82 23 460 935 534864655 534865138 6.860000e-61 244
24 TraesCS2A01G234500 chr5D 86.854 213 26 1 317 527 228445898 228445686 1.150000e-58 237
25 TraesCS2A01G234500 chr5B 94.609 575 24 7 909 1481 674893292 674893861 0.000000e+00 883
26 TraesCS2A01G234500 chr5B 87.290 417 36 11 317 732 675079413 675079813 6.260000e-126 460
27 TraesCS2A01G234500 chr5B 90.099 202 15 4 735 935 675080110 675080307 8.810000e-65 257
28 TraesCS2A01G234500 chr5B 92.188 128 10 0 808 935 675423366 675423493 5.460000e-42 182
29 TraesCS2A01G234500 chr5B 82.199 191 31 2 1892 2081 113020446 113020634 7.110000e-36 161
30 TraesCS2A01G234500 chr5B 93.684 95 5 1 673 767 280176329 280176422 9.260000e-30 141
31 TraesCS2A01G234500 chr4A 94.977 438 21 1 2048 2484 123476666 123477103 0.000000e+00 686
32 TraesCS2A01G234500 chr4A 86.301 292 30 6 646 935 636687360 636687077 2.400000e-80 309
33 TraesCS2A01G234500 chr4A 86.411 287 26 6 317 602 636687636 636687362 4.010000e-78 302
34 TraesCS2A01G234500 chr4A 76.553 499 84 22 462 935 636965290 636964800 2.470000e-60 243
35 TraesCS2A01G234500 chr4A 80.745 322 42 18 626 935 636680299 636679986 1.490000e-57 233
36 TraesCS2A01G234500 chr1A 92.641 462 32 2 2023 2484 288306435 288306894 0.000000e+00 664
37 TraesCS2A01G234500 chr3D 93.607 438 27 1 2048 2484 225806867 225806430 0.000000e+00 652
38 TraesCS2A01G234500 chr4D 90.467 493 38 7 1995 2484 234847184 234846698 2.080000e-180 641
39 TraesCS2A01G234500 chr4D 83.893 149 22 2 317 464 280924958 280925105 9.260000e-30 141
40 TraesCS2A01G234500 chr4D 89.157 83 8 1 379 460 148512885 148512803 4.370000e-18 102
41 TraesCS2A01G234500 chr2B 91.473 387 32 1 1508 1894 51451679 51451294 4.700000e-147 531
42 TraesCS2A01G234500 chr2B 83.556 225 33 4 1892 2114 51451366 51451144 9.000000e-50 207
43 TraesCS2A01G234500 chr2B 79.087 263 51 3 1892 2152 501130856 501130596 7.060000e-41 178
44 TraesCS2A01G234500 chr3B 87.764 237 28 1 1892 2128 410849461 410849226 2.430000e-70 276
45 TraesCS2A01G234500 chr7D 77.645 501 74 22 457 935 568598107 568598591 1.130000e-68 270
46 TraesCS2A01G234500 chr7B 80.757 317 45 14 623 935 624350911 624351215 1.490000e-57 233
47 TraesCS2A01G234500 chr7B 83.158 190 29 3 1881 2068 714749790 714749978 1.180000e-38 171
48 TraesCS2A01G234500 chr4B 86.385 213 27 1 317 527 426877414 426877626 5.340000e-57 231
49 TraesCS2A01G234500 chr4B 79.245 265 47 6 1892 2152 458242898 458243158 7.060000e-41 178


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 TraesCS2A01G234500 chr2A 284782265 284784748 2483 False 4588.000000 4588 100.000000 1 2484 1 chr2A.!!$F1 2483
1 TraesCS2A01G234500 chr7A 347383184 347385657 2473 False 4047.000000 4047 96.140000 1 2484 1 chr7A.!!$F1 2483
2 TraesCS2A01G234500 chr7A 401494982 401497464 2482 False 4037.000000 4037 96.014000 1 2484 1 chr7A.!!$F2 2483
3 TraesCS2A01G234500 chr6A 242008145 242010628 2483 True 4045.000000 4045 96.055000 1 2484 1 chr6A.!!$R1 2483
4 TraesCS2A01G234500 chr2D 64940351 64942371 2020 True 848.333333 1336 90.126333 28 2150 3 chr2D.!!$R1 2122
5 TraesCS2A01G234500 chr1B 226904477 226905873 1396 False 1024.500000 1059 93.310000 1 1656 2 chr1B.!!$F3 1655
6 TraesCS2A01G234500 chr1B 227793151 227794638 1487 False 1000.500000 1081 90.778000 50 1844 2 chr1B.!!$F4 1794
7 TraesCS2A01G234500 chr5D 534638075 534638644 569 False 889.000000 889 94.783000 909 1481 1 chr5D.!!$F1 572
8 TraesCS2A01G234500 chr5D 534856425 534858537 2112 False 772.500000 889 90.698000 317 1481 2 chr5D.!!$F2 1164
9 TraesCS2A01G234500 chr5D 534864655 534866661 2006 False 561.000000 878 85.547500 460 1481 2 chr5D.!!$F3 1021
10 TraesCS2A01G234500 chr5B 674893292 674893861 569 False 883.000000 883 94.609000 909 1481 1 chr5B.!!$F3 572
11 TraesCS2A01G234500 chr5B 675079413 675080307 894 False 358.500000 460 88.694500 317 935 2 chr5B.!!$F5 618
12 TraesCS2A01G234500 chr4A 636687077 636687636 559 True 305.500000 309 86.356000 317 935 2 chr4A.!!$R3 618
13 TraesCS2A01G234500 chr2B 51451144 51451679 535 True 369.000000 531 87.514500 1508 2114 2 chr2B.!!$R2 606

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
928 1256 1.019673 GCTGGTGATGTTCGCATGAT 58.98 50.0 0.0 0.0 38.08 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 3470 0.106335 TCCGAAACTAAACCGTGCCA 59.894 50.0 0.0 0.0 0.0 4.92 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
40 41 1.836604 GCTCTCTGCCCTCCCCTAG 60.837 68.421 0.00 0.00 35.15 3.02
41 42 1.934410 CTCTCTGCCCTCCCCTAGA 59.066 63.158 0.00 0.00 0.00 2.43
99 104 2.660802 CCGCAAACTACCTCCGGT 59.339 61.111 0.00 0.00 40.16 5.28
127 132 4.504596 GCATGTCCATCCCCGGCA 62.505 66.667 0.00 0.00 0.00 5.69
142 147 2.027625 GGCAGCTCGCGTACAGTTT 61.028 57.895 5.77 0.00 43.84 2.66
208 213 1.304381 GACCTTCCCTGGCATGCAA 60.304 57.895 21.36 7.49 0.00 4.08
327 332 6.495872 TGTAGTTTCTCTCCTTTTGTAGCCTA 59.504 38.462 0.00 0.00 0.00 3.93
361 366 6.071334 TGTGCCATATTATTTCCAAAAACCGA 60.071 34.615 0.00 0.00 0.00 4.69
544 549 1.423541 TCTGCCCAGTTTGGTGTATGT 59.576 47.619 0.00 0.00 35.17 2.29
579 610 9.619316 GTTGCTGAATGTATTACAATTTACACA 57.381 29.630 0.00 0.00 31.55 3.72
928 1256 1.019673 GCTGGTGATGTTCGCATGAT 58.980 50.000 0.00 0.00 38.08 2.45
936 2241 5.008019 GGTGATGTTCGCATGATTGATACTT 59.992 40.000 0.00 0.00 38.08 2.24
1083 2389 6.379988 TGAAGAGTGTCCAGCATACTGTTATA 59.620 38.462 0.00 0.00 42.81 0.98
1420 2726 5.713389 TGAAATCTGTTTGAAGGATCTGCAT 59.287 36.000 0.00 0.00 0.00 3.96
1678 2985 1.134848 ACATTGCAGTGCGGTTTTTGT 60.135 42.857 11.20 4.77 0.00 2.83
1818 3127 2.481449 GGTTCACTCGCTTCGTCCATAT 60.481 50.000 0.00 0.00 0.00 1.78
1887 3196 9.442047 TGAAAAAGGTTAACAAAAATGTCATGT 57.558 25.926 8.10 0.00 0.00 3.21
1906 3402 1.175983 TGGTTCCATGCGTTTGGTCC 61.176 55.000 5.80 9.47 38.01 4.46
1957 3453 9.442047 TGAAAAAGGTTAACAAAAATGTCATGT 57.558 25.926 8.10 0.00 0.00 3.21
1974 3470 3.562232 TGGTTCCCTTTCGGCGGT 61.562 61.111 7.21 0.00 0.00 5.68
2040 3536 1.871039 GTGAAGCGCACTCCACTTTTA 59.129 47.619 11.47 0.00 44.27 1.52
2093 3590 2.837532 TCATGCACTGCACTTGTCTA 57.162 45.000 5.67 0.00 43.04 2.59
2098 3595 2.005451 GCACTGCACTTGTCTATCCAG 58.995 52.381 0.00 0.00 0.00 3.86
2116 3613 2.604614 CCAGTGAAGTGCGGTTTTTAGC 60.605 50.000 0.00 0.00 0.00 3.09
2166 3663 3.719924 CAGTACGGCCCATTTACGATAA 58.280 45.455 0.00 0.00 0.00 1.75
2387 3884 4.036852 CCATGCAGTTCTCTATCACGTCTA 59.963 45.833 0.00 0.00 0.00 2.59
2442 3940 4.562963 GGTTTTCAGTCGGATGAAGTACCT 60.563 45.833 18.63 0.00 40.16 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 64 1.912731 AGAGGAGGAAGAAGGAAAGGC 59.087 52.381 0.00 0.00 0.00 4.35
99 104 1.937191 TGGACATGCACTAGACCTCA 58.063 50.000 0.00 0.00 0.00 3.86
127 132 2.027625 GCCAAACTGTACGCGAGCT 61.028 57.895 15.93 0.00 0.00 4.09
136 141 2.340427 CCATCGTTGGCCAAACTGT 58.660 52.632 22.47 3.74 35.85 3.55
203 208 2.100846 CACGCTAGTGGCATTGCAT 58.899 52.632 11.39 0.00 44.34 3.96
215 220 2.031012 AAGCTGCACTGCACGCTA 59.969 55.556 21.04 0.00 40.21 4.26
263 268 2.223829 GCATGGACGAGCTACACTACAT 60.224 50.000 0.00 0.00 0.00 2.29
422 427 0.906756 CTCCAGGAGACAGCAAGGGA 60.907 60.000 11.62 0.00 0.00 4.20
544 549 7.880713 TGTAATACATTCAGCAACTAACAGGAA 59.119 33.333 0.00 0.00 0.00 3.36
624 655 6.014327 ACAAAATCTAGTGGGACATTGCAAAT 60.014 34.615 1.71 0.00 44.52 2.32
786 1114 9.060347 AGCATCCATATTAATAGTTGAACACAG 57.940 33.333 0.00 0.00 0.00 3.66
804 1132 0.527565 GACGGTGCAAAAGCATCCAT 59.472 50.000 0.00 0.00 0.00 3.41
866 1194 0.896940 CAGCTGCCACAAGGGAATGT 60.897 55.000 0.00 0.00 40.01 2.71
867 1195 1.888018 CAGCTGCCACAAGGGAATG 59.112 57.895 0.00 0.00 40.01 2.67
928 1256 4.263462 ACCCTTGTCAGATGCAAGTATCAA 60.263 41.667 0.00 0.00 41.08 2.57
936 2241 3.776969 AGAATCTACCCTTGTCAGATGCA 59.223 43.478 0.00 0.00 28.07 3.96
1083 2389 5.297776 CGATTCTTGCTTCTTTACCATCCAT 59.702 40.000 0.00 0.00 0.00 3.41
1420 2726 1.616725 GCACCACCCATGAAATCCTCA 60.617 52.381 0.00 0.00 38.81 3.86
1678 2985 5.299028 ACATATCACACACACTGCTTCAAAA 59.701 36.000 0.00 0.00 0.00 2.44
1818 3127 0.687920 TAGACCAAACGCATGGACCA 59.312 50.000 13.55 0.00 43.54 4.02
1887 3196 1.175983 GGACCAAACGCATGGAACCA 61.176 55.000 13.55 0.00 43.54 3.67
1906 3402 9.779237 CATACTTAATATTTTTCTACGAGCGTG 57.221 33.333 5.69 0.00 0.00 5.34
1974 3470 0.106335 TCCGAAACTAAACCGTGCCA 59.894 50.000 0.00 0.00 0.00 4.92
1978 3474 3.183793 ACACTTCCGAAACTAAACCGT 57.816 42.857 0.00 0.00 0.00 4.83
2040 3536 6.527423 TGTGGGACGTAAATTTTCTTAGACT 58.473 36.000 0.00 0.00 0.00 3.24
2081 3578 3.599730 TCACTGGATAGACAAGTGCAG 57.400 47.619 0.00 0.00 39.38 4.41
2093 3590 1.981256 AAAACCGCACTTCACTGGAT 58.019 45.000 0.00 0.00 0.00 3.41
2098 3595 1.607148 AGGCTAAAAACCGCACTTCAC 59.393 47.619 0.00 0.00 0.00 3.18
2116 3613 7.444183 TCAGACAGAAAACCACACTTATTTAGG 59.556 37.037 0.00 0.00 0.00 2.69
2166 3663 4.712337 ACTATGGAAAGTGAACCTCGAGAT 59.288 41.667 15.71 1.50 0.00 2.75
2183 3680 1.338674 TGGTGAACCGCAAGACTATGG 60.339 52.381 0.00 0.00 39.43 2.74
2387 3884 0.383949 ACGAAAAACCGCACTGCATT 59.616 45.000 1.11 0.00 0.00 3.56
2442 3940 0.733566 GCGACACCCAAATCGACGTA 60.734 55.000 0.00 0.00 40.86 3.57


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

AutoCloner maintained by Alex Coulton.