Multiple sequence alignment - TraesCS5D01G157500

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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 TraesCS5D01G157500 chr5D 100.000 4621 0 0 1 4621 245206744 245202124 0.000000e+00 8534
1 TraesCS5D01G157500 chr5D 87.500 112 12 1 1840 1951 91631904 91632013 1.350000e-25 128
2 TraesCS5D01G157500 chr5D 85.714 126 13 3 1841 1966 91850108 91850228 1.350000e-25 128
3 TraesCS5D01G157500 chr5B 94.960 4663 172 24 1 4620 278476912 278472270 0.000000e+00 7251
4 TraesCS5D01G157500 chr5B 88.462 286 31 2 4336 4621 455170863 455170580 1.230000e-90 344
5 TraesCS5D01G157500 chr5A 93.994 4246 187 26 27 4240 329252447 329248238 0.000000e+00 6366
6 TraesCS5D01G157500 chr5A 93.830 389 21 2 4235 4621 329245175 329244788 2.400000e-162 582
7 TraesCS5D01G157500 chr5A 90.625 96 9 0 1840 1935 85264337 85264432 1.350000e-25 128
8 TraesCS5D01G157500 chr6D 91.417 501 19 6 2923 3399 100198930 100198430 0.000000e+00 665
9 TraesCS5D01G157500 chr6D 88.153 287 32 2 4335 4621 267532810 267533094 1.590000e-89 340
10 TraesCS5D01G157500 chr4D 91.417 501 19 7 2923 3399 329012202 329012702 0.000000e+00 665
11 TraesCS5D01G157500 chr4D 91.218 501 19 7 2923 3399 105942803 105942304 0.000000e+00 658
12 TraesCS5D01G157500 chr4D 81.971 477 82 4 1 475 502107154 502107628 7.200000e-108 401
13 TraesCS5D01G157500 chr4D 81.974 466 82 2 1 465 497182377 497181913 1.210000e-105 394
14 TraesCS5D01G157500 chr2D 82.636 478 73 9 3 475 38062902 38062430 9.250000e-112 414
15 TraesCS5D01G157500 chr2D 81.612 484 83 6 1 481 400495112 400495592 3.350000e-106 396
16 TraesCS5D01G157500 chr2D 80.962 478 85 6 1 475 462791974 462792448 1.570000e-99 374
17 TraesCS5D01G157500 chr2D 89.399 283 27 3 4339 4621 380416529 380416808 2.050000e-93 353
18 TraesCS5D01G157500 chr2D 88.502 287 31 2 4333 4619 243656317 243656033 3.420000e-91 346
19 TraesCS5D01G157500 chr3B 82.231 484 73 7 1 480 749867974 749868448 5.570000e-109 405
20 TraesCS5D01G157500 chr4B 81.590 478 80 6 1 475 514576763 514576291 5.610000e-104 388
21 TraesCS5D01G157500 chr6A 89.199 287 29 2 4335 4621 381088703 381088987 1.580000e-94 357
22 TraesCS5D01G157500 chr3A 89.399 283 29 1 4339 4621 561107241 561106960 5.690000e-94 355
23 TraesCS5D01G157500 chr7B 88.502 287 31 2 4335 4621 445663374 445663658 3.420000e-91 346


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 TraesCS5D01G157500 chr5D 245202124 245206744 4620 True 8534 8534 100.000 1 4621 1 chr5D.!!$R1 4620
1 TraesCS5D01G157500 chr5B 278472270 278476912 4642 True 7251 7251 94.960 1 4620 1 chr5B.!!$R1 4619
2 TraesCS5D01G157500 chr5A 329244788 329252447 7659 True 3474 6366 93.912 27 4621 2 chr5A.!!$R1 4594
3 TraesCS5D01G157500 chr6D 100198430 100198930 500 True 665 665 91.417 2923 3399 1 chr6D.!!$R1 476
4 TraesCS5D01G157500 chr4D 329012202 329012702 500 False 665 665 91.417 2923 3399 1 chr4D.!!$F1 476

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
407 408 0.250727 GTGCAGTGCTTTCTACCCCA 60.251 55.000 17.60 0.00 0.0 4.96 F
830 832 3.497332 AGGGAAGGGTTGAAACTAAAGC 58.503 45.455 0.00 0.00 0.0 3.51 F
2024 2058 0.530211 TGTTGGTGTTGCTTGCATGC 60.530 50.000 17.19 17.19 0.0 4.06 F
2060 2094 2.094390 CGGTGATTCTTCCTTGTACGGA 60.094 50.000 0.00 0.00 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1253 1287 1.600636 CAGAAGTTTCCGGGCTGCA 60.601 57.895 0.00 0.0 0.00 4.41 R
2131 2165 3.007831 CAGGGCCTTAAGCAAAATTTGGA 59.992 43.478 1.32 0.0 46.50 3.53 R
3523 3586 0.794473 CAAGTTCGCCGGTAACTTCC 59.206 55.000 25.19 0.0 43.52 3.46 R
3902 3975 2.043115 AGGAGACACATACAGAGGTGGA 59.957 50.000 0.00 0.0 41.73 4.02 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
21 22 1.446016 AGAACAAGCCTAACCTGGGT 58.554 50.000 0.00 0.00 39.84 4.51
32 33 4.382541 CCTGGGTGGGGAAAGGGC 62.383 72.222 0.00 0.00 0.00 5.19
123 124 7.817418 CTCTAAGGCTAGAGTGTCTAAGATT 57.183 40.000 0.00 0.00 44.33 2.40
153 154 2.488528 CCCGTGCAGTCCTAGGATAGTA 60.489 54.545 16.27 7.43 36.82 1.82
173 174 6.279513 AGTAACTGGAGAGAACTCATTCAG 57.720 41.667 4.64 9.92 44.22 3.02
207 208 0.761323 TCCTGAAGGGTGGACGAACA 60.761 55.000 0.00 0.00 36.25 3.18
250 251 6.319911 GCAAGCATCTCCTAGGTAGAATTTTT 59.680 38.462 9.08 2.80 0.00 1.94
255 256 7.716998 GCATCTCCTAGGTAGAATTTTTCATCA 59.283 37.037 9.08 0.00 0.00 3.07
256 257 9.618890 CATCTCCTAGGTAGAATTTTTCATCAA 57.381 33.333 9.08 0.00 0.00 2.57
313 314 4.553323 GGCAAGAATGTTATCATCATGGC 58.447 43.478 0.00 0.00 32.56 4.40
315 316 4.560108 GCAAGAATGTTATCATCATGGCCC 60.560 45.833 0.00 0.00 32.56 5.80
407 408 0.250727 GTGCAGTGCTTTCTACCCCA 60.251 55.000 17.60 0.00 0.00 4.96
440 441 3.715495 CATGTGATCTCTGGCACTCTAC 58.285 50.000 0.00 0.00 36.05 2.59
546 547 7.385752 TGTTTCTTGAATGATTTGAAGATTGCC 59.614 33.333 2.60 0.00 35.43 4.52
579 581 4.742659 TGCTGCGGTAAATTCTTTGTTTTC 59.257 37.500 0.00 0.00 0.00 2.29
612 614 8.046708 ACTATGTCAAACACCTAATGCTATTGA 58.953 33.333 0.00 0.00 0.00 2.57
830 832 3.497332 AGGGAAGGGTTGAAACTAAAGC 58.503 45.455 0.00 0.00 0.00 3.51
834 836 4.217767 GGAAGGGTTGAAACTAAAGCGATT 59.782 41.667 0.00 0.00 0.00 3.34
1086 1112 4.761058 TTCGCCTCCCGCCTCTCT 62.761 66.667 0.00 0.00 36.73 3.10
1274 1308 2.668550 GCCCGGAAACTTCTGCGT 60.669 61.111 0.73 0.00 32.15 5.24
1406 1440 1.277495 GGACAAATTGCGCACACTGC 61.277 55.000 11.12 3.84 40.69 4.40
1416 1450 4.602259 CACACTGCGTGGTCCGGT 62.602 66.667 0.00 0.00 42.34 5.28
1597 1631 1.603739 GGGGTGCAGTTTCAGGGTC 60.604 63.158 0.00 0.00 0.00 4.46
1642 1676 3.681874 GCTTCAGTTCAGTATACACCCCC 60.682 52.174 5.50 0.00 0.00 5.40
2024 2058 0.530211 TGTTGGTGTTGCTTGCATGC 60.530 50.000 17.19 17.19 0.00 4.06
2060 2094 2.094390 CGGTGATTCTTCCTTGTACGGA 60.094 50.000 0.00 0.00 0.00 4.69
2131 2165 6.042781 TGTCAGTAGTTTGAATGTCCTTAGGT 59.957 38.462 0.00 0.00 0.00 3.08
2184 2218 5.872070 GAGTCTTACTCATGCTTAACAGCTT 59.128 40.000 2.22 0.00 44.54 3.74
2200 2234 4.298332 ACAGCTTATTTTGGCTTTCGTTG 58.702 39.130 0.00 0.00 36.59 4.10
2224 2258 6.719370 TGTAGCTTTGTCCAAAAGGAATACAT 59.281 34.615 0.00 0.00 0.00 2.29
2226 2260 7.775053 AGCTTTGTCCAAAAGGAATACATAA 57.225 32.000 0.46 0.00 0.00 1.90
2247 2281 8.752187 ACATAATTAACCTCAAGCATCATTTGT 58.248 29.630 0.00 0.00 0.00 2.83
2628 2665 4.034510 GTGCTGCCTTACTCACATATTGAC 59.965 45.833 0.00 0.00 0.00 3.18
2955 2993 4.216257 TGATCAGCTCTTTGTGGTTAAAGC 59.784 41.667 0.00 0.00 37.53 3.51
3029 3067 6.126409 TGACCCCTGATTGTATTGTTAATCC 58.874 40.000 0.00 0.00 33.43 3.01
3500 3563 5.767816 AAACTTCAGGCGTTAGTGAAAAT 57.232 34.783 0.00 0.00 32.36 1.82
3523 3586 6.804534 TTGCAATTTACACTCAGAAAAACG 57.195 33.333 0.00 0.00 0.00 3.60
3715 3778 6.968263 TGGTACAAAAGGTGAATTTCATGA 57.032 33.333 1.78 0.00 31.92 3.07
3746 3809 2.696707 TCTTGTCGTTTCCCACAGTAGT 59.303 45.455 0.00 0.00 0.00 2.73
3751 3814 1.796459 CGTTTCCCACAGTAGTTTCGG 59.204 52.381 0.00 0.00 0.00 4.30
3882 3955 4.312443 GTTGTTCCTCTCCGTCATTAACA 58.688 43.478 0.00 0.00 0.00 2.41
4240 7381 3.498774 ATCACCTCTTGCTTGAACTGT 57.501 42.857 0.00 0.00 0.00 3.55
4354 7496 6.870965 ACTAGCAATCAACAACAACAACAAAA 59.129 30.769 0.00 0.00 0.00 2.44
4395 7537 1.414550 GGGGTAGGCTAGAGCTGAAAG 59.585 57.143 0.00 0.00 41.70 2.62
4408 7550 2.442189 CTGAAAGCGGTAAGATTGCG 57.558 50.000 0.00 0.00 0.00 4.85
4471 7613 0.982852 CACCCCTGTCCATGGCTAGA 60.983 60.000 6.96 0.00 0.00 2.43
4503 7645 7.293299 TGGTGATATTCCACTCCTTCAGATATT 59.707 37.037 0.00 0.00 37.24 1.28
4529 7671 3.766068 ATAGACTCCTGCCATGTCATG 57.234 47.619 5.79 5.79 33.56 3.07
4578 7720 6.044046 ACATTATCAACACGCTTTATCCGTA 58.956 36.000 0.00 0.00 37.12 4.02
4579 7721 6.535865 ACATTATCAACACGCTTTATCCGTAA 59.464 34.615 0.00 0.00 37.12 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.235028 TCATTCCGCCCTTTCCCCA 61.235 57.895 0.00 0.00 0.00 4.96
70 71 4.842531 TGAGAATGCATTTGGAGGTCTA 57.157 40.909 14.33 0.00 0.00 2.59
120 121 2.213499 CTGCACGGGGATAGTTCAATC 58.787 52.381 0.00 0.00 0.00 2.67
123 124 0.535335 GACTGCACGGGGATAGTTCA 59.465 55.000 0.00 0.00 0.00 3.18
153 154 5.338219 CCATCTGAATGAGTTCTCTCCAGTT 60.338 44.000 1.53 0.14 39.75 3.16
173 174 4.446371 CTTCAGGACAATCAGGTACCATC 58.554 47.826 15.94 1.44 0.00 3.51
202 203 2.047274 ATGTCGGCCTGGTGTTCG 60.047 61.111 0.00 0.00 0.00 3.95
207 208 1.146930 CTATGCATGTCGGCCTGGT 59.853 57.895 10.16 0.00 0.00 4.00
304 305 0.397941 GAAGGATCGGGCCATGATGA 59.602 55.000 13.91 0.00 0.00 2.92
313 314 0.106894 GTTAGCTGGGAAGGATCGGG 59.893 60.000 0.00 0.00 0.00 5.14
315 316 3.132289 TGTTAGTTAGCTGGGAAGGATCG 59.868 47.826 0.00 0.00 0.00 3.69
382 383 0.752743 AGAAAGCACTGCACAAGCCA 60.753 50.000 3.30 0.00 41.13 4.75
383 384 1.068954 GTAGAAAGCACTGCACAAGCC 60.069 52.381 3.30 0.00 41.13 4.35
407 408 2.172082 AGATCACATGCTGCACCATACT 59.828 45.455 3.57 0.00 0.00 2.12
413 414 1.015109 CCAGAGATCACATGCTGCAC 58.985 55.000 3.57 0.00 0.00 4.57
420 421 2.697751 GGTAGAGTGCCAGAGATCACAT 59.302 50.000 0.00 0.00 35.76 3.21
440 441 5.798125 ATAGATGGTACTCATGTGACTGG 57.202 43.478 0.94 0.00 35.97 4.00
553 554 3.317993 ACAAAGAATTTACCGCAGCAAGT 59.682 39.130 0.00 0.00 35.03 3.16
559 560 7.921214 TGTTATGAAAACAAAGAATTTACCGCA 59.079 29.630 0.00 0.00 35.03 5.69
579 581 9.773328 CATTAGGTGTTTGACATAGTTGTTATG 57.227 33.333 0.00 0.00 43.96 1.90
664 666 8.626526 TCTTATAGGAACCAAAAACACTGAAAC 58.373 33.333 0.00 0.00 0.00 2.78
703 705 6.660521 AGGAAGAATGTAGCATTTCAATGTCA 59.339 34.615 1.59 0.52 38.65 3.58
809 811 3.497332 GCTTTAGTTTCAACCCTTCCCT 58.503 45.455 0.00 0.00 0.00 4.20
816 818 3.896122 TGCAATCGCTTTAGTTTCAACC 58.104 40.909 0.00 0.00 39.64 3.77
852 856 6.146021 CACTTCCATGGCAAATTGTTTAGTTC 59.854 38.462 6.96 0.00 0.00 3.01
1054 1080 2.943978 CGAACAGGGAGAGGGCGTT 61.944 63.158 0.00 0.00 0.00 4.84
1086 1112 2.337170 CGTGCGTACCTGTGGTGA 59.663 61.111 0.00 0.00 36.19 4.02
1120 1154 0.393132 GGAGGTTGTAGAAGCTGGCC 60.393 60.000 9.30 0.00 40.07 5.36
1121 1155 0.393132 GGGAGGTTGTAGAAGCTGGC 60.393 60.000 9.30 0.00 40.07 4.85
1177 1211 2.888464 TACCCGGAGCTCCTCGTCTG 62.888 65.000 29.73 13.29 0.00 3.51
1253 1287 1.600636 CAGAAGTTTCCGGGCTGCA 60.601 57.895 0.00 0.00 0.00 4.41
1416 1450 2.922740 AGAGCGAAAACAACAGGGTA 57.077 45.000 0.00 0.00 0.00 3.69
1597 1631 5.268544 CACTGAAACAGCATCATAAATCGG 58.731 41.667 0.00 0.00 34.37 4.18
1642 1676 6.795593 GTCATCATTGATAAATGATCTGTGCG 59.204 38.462 14.53 4.21 45.35 5.34
2024 2058 9.781834 GAAGAATCACCGATAGACTGAATATAG 57.218 37.037 0.00 0.00 39.76 1.31
2131 2165 3.007831 CAGGGCCTTAAGCAAAATTTGGA 59.992 43.478 1.32 0.00 46.50 3.53
2184 2218 5.699097 AAGCTACAACGAAAGCCAAAATA 57.301 34.783 0.00 0.00 39.64 1.40
2224 2258 9.421806 CAAACAAATGATGCTTGAGGTTAATTA 57.578 29.630 0.00 0.00 37.30 1.40
2226 2260 7.444299 ACAAACAAATGATGCTTGAGGTTAAT 58.556 30.769 0.00 0.00 37.30 1.40
2247 2281 5.046159 CACCCTGGACCATTAGTAGTACAAA 60.046 44.000 2.52 0.00 0.00 2.83
2368 2404 8.589338 AGAGAAATACTTGCTAACTCTTGAGAA 58.411 33.333 4.49 0.00 30.61 2.87
2378 2414 5.447683 CGCAATGCAGAGAAATACTTGCTAA 60.448 40.000 5.91 0.00 36.31 3.09
2628 2665 8.225603 ACTAACATGCTGAGGTATTAAAATGG 57.774 34.615 0.00 0.00 0.00 3.16
3236 3295 2.286418 GCAGGAACAGTTTCTCAACACG 60.286 50.000 0.00 0.00 35.05 4.49
3415 3478 5.639506 ACAGTACACAAGCAGCAGTATTAAG 59.360 40.000 0.00 0.00 0.00 1.85
3500 3563 5.746245 CCGTTTTTCTGAGTGTAAATTGCAA 59.254 36.000 0.00 0.00 0.00 4.08
3523 3586 0.794473 CAAGTTCGCCGGTAACTTCC 59.206 55.000 25.19 0.00 43.52 3.46
3715 3778 5.648960 TGGGAAACGACAAGAAAAACTAAGT 59.351 36.000 0.00 0.00 0.00 2.24
3746 3809 7.951347 AAGTACTAGACTAGGAAATCCGAAA 57.049 36.000 14.03 0.00 37.44 3.46
3751 3814 9.902196 GCTCAATAAGTACTAGACTAGGAAATC 57.098 37.037 14.03 0.00 37.44 2.17
3821 3894 3.817647 GCCTGTAAAGATCCAGCCAATAG 59.182 47.826 0.00 0.00 0.00 1.73
3882 3955 9.927081 AGGTGGAGATGTATTTAATGAAGAAAT 57.073 29.630 0.00 0.00 0.00 2.17
3902 3975 2.043115 AGGAGACACATACAGAGGTGGA 59.957 50.000 0.00 0.00 41.73 4.02
3903 3976 2.461695 AGGAGACACATACAGAGGTGG 58.538 52.381 0.00 0.00 41.73 4.61
3904 3977 3.766591 AGAAGGAGACACATACAGAGGTG 59.233 47.826 0.00 0.00 43.10 4.00
3954 4027 5.459536 AAAGATCAAAGTGGCCTTCTTTC 57.540 39.130 18.65 11.28 33.58 2.62
4378 7520 1.537135 CCGCTTTCAGCTCTAGCCTAC 60.537 57.143 0.00 0.00 43.38 3.18
4397 7539 1.539827 AGTTGGTTGCGCAATCTTACC 59.460 47.619 31.66 25.28 0.00 2.85
4398 7540 2.225491 TGAGTTGGTTGCGCAATCTTAC 59.775 45.455 31.66 26.79 0.00 2.34
4405 7547 3.353600 CCATGAGTTGGTTGCGCA 58.646 55.556 5.66 5.66 40.99 6.09
4471 7613 6.332976 AGGAGTGGAATATCACCAAAAGAT 57.667 37.500 3.62 0.00 39.22 2.40
4503 7645 5.425217 TGACATGGCAGGAGTCTATAAAGAA 59.575 40.000 5.99 0.00 32.16 2.52
4529 7671 4.095211 AGAGAGGTTAGGGTAGACCAAAC 58.905 47.826 0.21 4.56 43.89 2.93


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

AutoCloner maintained by Alex Coulton.