Multiple sequence alignment - TraesCS3B01G251600

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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 TraesCS3B01G251600 chr3B 100.000 5312 0 0 1 5312 403904303 403909614 0.000000e+00 9810
1 TraesCS3B01G251600 chr3D 96.562 5323 145 18 1 5312 316171883 316166588 0.000000e+00 8781
2 TraesCS3B01G251600 chr3A 97.262 3031 61 7 2287 5312 413680050 413683063 0.000000e+00 5118
3 TraesCS3B01G251600 chr3A 94.278 2237 95 14 1 2231 413677844 413680053 0.000000e+00 3391
4 TraesCS3B01G251600 chr1D 79.556 631 99 20 1256 1877 484419147 484418538 1.770000e-114 424
5 TraesCS3B01G251600 chr1A 79.556 631 96 22 1256 1877 581832371 581831765 2.290000e-113 420
6 TraesCS3B01G251600 chr1B 79.365 630 90 28 1256 1877 674671206 674670609 1.780000e-109 407


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 TraesCS3B01G251600 chr3B 403904303 403909614 5311 False 9810.0 9810 100.000 1 5312 1 chr3B.!!$F1 5311
1 TraesCS3B01G251600 chr3D 316166588 316171883 5295 True 8781.0 8781 96.562 1 5312 1 chr3D.!!$R1 5311
2 TraesCS3B01G251600 chr3A 413677844 413683063 5219 False 4254.5 5118 95.770 1 5312 2 chr3A.!!$F1 5311
3 TraesCS3B01G251600 chr1D 484418538 484419147 609 True 424.0 424 79.556 1256 1877 1 chr1D.!!$R1 621
4 TraesCS3B01G251600 chr1A 581831765 581832371 606 True 420.0 420 79.556 1256 1877 1 chr1A.!!$R1 621
5 TraesCS3B01G251600 chr1B 674670609 674671206 597 True 407.0 407 79.365 1256 1877 1 chr1B.!!$R1 621

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
521 526 0.944386 CCACAAGGTCCAAGAACACG 59.056 55.000 0.0 0.0 0.00 4.49 F
1167 1181 0.933700 CCTCCTCCTCCTCCTCTTCT 59.066 60.000 0.0 0.0 0.00 2.85 F
1418 1444 0.107831 GCCGGTAACATCTGCCCATA 59.892 55.000 1.9 0.0 0.00 2.74 F
2406 2435 1.140652 TCAGACCACACAATGCTGACA 59.859 47.619 0.0 0.0 31.24 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1397 0.249447 CATTGGTCATCGGCGAGCTA 60.249 55.000 17.22 3.2 34.46 3.32 R
2293 2322 0.889994 GCATTGTGTGATGGGAAGCA 59.110 50.000 0.00 0.0 0.00 3.91 R
3177 3206 2.406616 CCCAACTTCCGCATTCCCG 61.407 63.158 0.00 0.0 0.00 5.14 R
4320 4350 0.106669 GGAGCCCTATGTTCCAACCC 60.107 60.000 0.00 0.0 43.50 4.11 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
82 83 8.729756 TCAATTCTATCGTTGAAATGTTGTCAT 58.270 29.630 0.00 0.00 31.85 3.06
84 85 7.905604 TTCTATCGTTGAAATGTTGTCATCT 57.094 32.000 0.00 0.00 32.56 2.90
107 108 8.681486 TCTCATCATCAATATTTACCTTGTGG 57.319 34.615 0.00 0.00 39.83 4.17
237 241 9.905713 ATACATGTCATTTACATCACTTAGGTT 57.094 29.630 0.00 0.00 46.15 3.50
250 254 5.607477 TCACTTAGGTTGTACCAGTCAAAG 58.393 41.667 0.00 0.00 41.95 2.77
256 260 3.317993 GGTTGTACCAGTCAAAGCACATT 59.682 43.478 0.00 0.00 38.42 2.71
321 325 7.106663 AGTAAAATCGCTATAACTCATTCGC 57.893 36.000 0.00 0.00 0.00 4.70
485 490 9.667989 GTAGTTCTAAGAAATCTCGATAACTCC 57.332 37.037 0.00 0.00 0.00 3.85
521 526 0.944386 CCACAAGGTCCAAGAACACG 59.056 55.000 0.00 0.00 0.00 4.49
596 605 3.019564 CCAAACAGCCCCATAGAAGAAG 58.980 50.000 0.00 0.00 0.00 2.85
597 606 3.308402 CCAAACAGCCCCATAGAAGAAGA 60.308 47.826 0.00 0.00 0.00 2.87
598 607 4.335416 CAAACAGCCCCATAGAAGAAGAA 58.665 43.478 0.00 0.00 0.00 2.52
629 638 3.778954 TTTTTGTATTTTGCCCCCTGG 57.221 42.857 0.00 0.00 0.00 4.45
700 709 2.406002 TTTCTTCCCCTGACGCCCAC 62.406 60.000 0.00 0.00 0.00 4.61
729 742 3.332187 CCCCTTTCTTCTTCCTTCCTTCT 59.668 47.826 0.00 0.00 0.00 2.85
1167 1181 0.933700 CCTCCTCCTCCTCCTCTTCT 59.066 60.000 0.00 0.00 0.00 2.85
1245 1259 2.037367 AGCCACTCCGGTGAGCTA 59.963 61.111 19.35 0.00 45.61 3.32
1418 1444 0.107831 GCCGGTAACATCTGCCCATA 59.892 55.000 1.90 0.00 0.00 2.74
1677 1706 2.537143 GAGTGGTACAAGAAGGGGAGA 58.463 52.381 0.00 0.00 44.16 3.71
2056 2085 1.581447 CTTGCCAGCTTTTCCGGTC 59.419 57.895 0.00 0.00 0.00 4.79
2122 2151 6.364976 CGTTGTTCCTCTTTCTTTTTGTTTGT 59.635 34.615 0.00 0.00 0.00 2.83
2155 2184 4.046286 TGATTGGGGATTGTTACTGCTT 57.954 40.909 0.00 0.00 0.00 3.91
2156 2185 3.763360 TGATTGGGGATTGTTACTGCTTG 59.237 43.478 0.00 0.00 0.00 4.01
2184 2213 1.827969 CTGTTTGATCGTCCCTCTCCT 59.172 52.381 0.00 0.00 0.00 3.69
2188 2217 5.205821 TGTTTGATCGTCCCTCTCCTATTA 58.794 41.667 0.00 0.00 0.00 0.98
2190 2219 4.035612 TGATCGTCCCTCTCCTATTAGG 57.964 50.000 3.07 3.07 36.46 2.69
2262 2291 1.875009 TGAGCTGTGAGTGAGCAAAG 58.125 50.000 0.00 0.00 39.05 2.77
2278 2307 2.363683 CAAAGGCCAGGATCTTGTCTC 58.636 52.381 5.01 0.00 0.00 3.36
2295 2324 3.553039 CGCAAGCAAATTGGGTGC 58.447 55.556 0.00 0.00 44.58 5.01
2356 2385 6.564328 AGCTGTATTATTTTGTAAGCTTGCC 58.436 36.000 9.86 0.00 36.13 4.52
2406 2435 1.140652 TCAGACCACACAATGCTGACA 59.859 47.619 0.00 0.00 31.24 3.58
2485 2514 9.453572 AGAGCAATTCAGTGTTATTATTCAGAA 57.546 29.630 0.00 0.00 0.00 3.02
2685 2714 5.713861 CAGGAAAATTGGAGATTGGAAGAGT 59.286 40.000 0.00 0.00 0.00 3.24
2795 2824 6.147864 TCTTTCAAGTGTTGGAAAATGGAG 57.852 37.500 0.00 0.00 33.05 3.86
3177 3206 3.007398 AGAATGCCAGACTTATCGATCCC 59.993 47.826 0.00 0.00 0.00 3.85
3847 3876 2.839486 TGAAGAACGAGAACTGCCAT 57.161 45.000 0.00 0.00 0.00 4.40
4094 4123 8.978564 AAGCTACTTGATATATGACTCAATCG 57.021 34.615 0.00 0.00 31.39 3.34
4302 4332 2.290916 AGTGAGACACTATGCCGTATCG 59.709 50.000 2.43 0.00 43.46 2.92
4320 4350 5.220117 CGTATCGAGTTCTTGAGAAGCTTTG 60.220 44.000 0.00 0.00 34.27 2.77
4327 4357 2.174639 TCTTGAGAAGCTTTGGGTTGGA 59.825 45.455 0.00 0.00 32.93 3.53
4385 4415 3.238597 TGCTTTAGGTCCCAAATTTGCT 58.761 40.909 12.92 6.94 0.00 3.91
4462 4492 0.767375 GAGCATAATGAGCCTCCCCA 59.233 55.000 0.00 0.00 0.00 4.96
4680 4716 4.618378 ATATCATAGAGGGAGAGGGGAC 57.382 50.000 0.00 0.00 0.00 4.46
4701 4737 1.299850 GGTTGCTGGTTGCGGTTTC 60.300 57.895 0.00 0.00 46.63 2.78
4817 4853 5.144359 GTTGTGTTACTGTCATTTTAGCGG 58.856 41.667 0.00 0.00 0.00 5.52
4830 4866 7.980099 TGTCATTTTAGCGGTAAAAAGGAAAAA 59.020 29.630 29.74 17.80 40.65 1.94
5018 5054 3.634397 TCCTTTCTGTAATGAGCTGGG 57.366 47.619 0.00 0.00 0.00 4.45
5063 5099 4.927978 TCACTAATCCTAGCTTGCTCTC 57.072 45.455 0.00 0.00 0.00 3.20
5140 5176 3.134879 CATGGCATGGCATGACCC 58.865 61.111 43.62 21.62 37.55 4.46
5159 5195 1.404717 CCGTGAGAGTCATTGGGAGTG 60.405 57.143 0.00 0.00 0.00 3.51
5306 5342 5.986135 TGAGAAAGAAGAGACTTTTTCCTCG 59.014 40.000 0.00 0.00 38.99 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 9.559958 GACAACATTTCAACGATAGAATTGAAT 57.440 29.630 13.59 0.00 42.72 2.57
64 65 6.372381 TGATGAGATGACAACATTTCAACGAT 59.628 34.615 7.34 0.00 45.85 3.73
82 83 8.493607 TCCACAAGGTAAATATTGATGATGAGA 58.506 33.333 0.00 0.00 35.89 3.27
84 85 9.473007 TTTCCACAAGGTAAATATTGATGATGA 57.527 29.630 0.00 0.00 35.89 2.92
146 147 5.673514 TGTTCTACAACCGAGTTACCTTTT 58.326 37.500 0.00 0.00 0.00 2.27
147 148 5.280654 TGTTCTACAACCGAGTTACCTTT 57.719 39.130 0.00 0.00 0.00 3.11
235 239 4.568152 AATGTGCTTTGACTGGTACAAC 57.432 40.909 0.00 0.00 38.70 3.32
237 241 6.264292 ACATAAAATGTGCTTTGACTGGTACA 59.736 34.615 0.00 0.00 43.01 2.90
250 254 9.173939 GCAATACAATCTAGACATAAAATGTGC 57.826 33.333 0.00 0.00 45.03 4.57
297 301 6.700081 TGCGAATGAGTTATAGCGATTTTACT 59.300 34.615 0.00 0.00 0.00 2.24
485 490 2.244695 GTGGGTTTTTGGAGGGTTAGG 58.755 52.381 0.00 0.00 0.00 2.69
518 523 3.627577 CCATAGAGTTTTGGGATTCCGTG 59.372 47.826 0.00 0.00 35.24 4.94
521 526 3.381590 GTGCCATAGAGTTTTGGGATTCC 59.618 47.826 0.00 0.00 35.67 3.01
597 606 9.875691 GGCAAAATACAAAAATCTCTATCCTTT 57.124 29.630 0.00 0.00 0.00 3.11
598 607 8.478066 GGGCAAAATACAAAAATCTCTATCCTT 58.522 33.333 0.00 0.00 0.00 3.36
629 638 1.369448 CGAGACGCTGCGAGTATCC 60.369 63.158 30.47 9.85 0.00 2.59
657 666 3.568743 GTGCGCACACCGACACAA 61.569 61.111 34.52 0.00 41.21 3.33
700 709 2.503765 GGAAGAAGAAAGGGGAGAGGAG 59.496 54.545 0.00 0.00 0.00 3.69
729 742 2.567615 CGGAGAAAGAGGGGAGAAGAAA 59.432 50.000 0.00 0.00 0.00 2.52
1299 1313 1.666011 GCCGGAGAATATCAGCGGA 59.334 57.895 5.05 0.00 35.44 5.54
1371 1397 0.249447 CATTGGTCATCGGCGAGCTA 60.249 55.000 17.22 3.20 34.46 3.32
2053 2082 2.297701 TCAAGTTGGACTTTGCTGACC 58.702 47.619 2.34 0.00 36.03 4.02
2056 2085 4.276678 TCATCTTCAAGTTGGACTTTGCTG 59.723 41.667 2.34 0.00 36.03 4.41
2122 2151 1.321805 CCCAATCAAATCGGGCAGCA 61.322 55.000 0.00 0.00 31.89 4.41
2155 2184 1.140052 ACGATCAAACAGACCACACCA 59.860 47.619 0.00 0.00 0.00 4.17
2156 2185 1.798813 GACGATCAAACAGACCACACC 59.201 52.381 0.00 0.00 0.00 4.16
2197 2226 7.970614 GTGATAATTCTGTCACCAAAATTCCTC 59.029 37.037 7.10 0.00 37.64 3.71
2235 2264 3.351740 TCACTCACAGCTCAAACCAAAA 58.648 40.909 0.00 0.00 0.00 2.44
2238 2267 1.811558 GCTCACTCACAGCTCAAACCA 60.812 52.381 0.00 0.00 33.75 3.67
2240 2269 1.586422 TGCTCACTCACAGCTCAAAC 58.414 50.000 0.00 0.00 37.79 2.93
2241 2270 2.330440 TTGCTCACTCACAGCTCAAA 57.670 45.000 0.00 0.00 37.79 2.69
2262 2291 1.522580 GCGAGACAAGATCCTGGCC 60.523 63.158 0.00 0.00 0.00 5.36
2278 2307 3.553039 GCACCCAATTTGCTTGCG 58.447 55.556 5.12 0.00 37.00 4.85
2293 2322 0.889994 GCATTGTGTGATGGGAAGCA 59.110 50.000 0.00 0.00 0.00 3.91
2295 2324 2.439409 TCAGCATTGTGTGATGGGAAG 58.561 47.619 0.00 0.00 44.27 3.46
2356 2385 5.065218 GTGTACCTAAAGACAATGGCATCAG 59.935 44.000 0.00 0.00 0.00 2.90
2406 2435 9.816354 CGGAATTAGGATTAAAATTCATGGTTT 57.184 29.630 10.84 0.00 41.70 3.27
2795 2824 8.784043 ACCAAGAATCTACAATGTAAAACTGTC 58.216 33.333 0.00 0.00 0.00 3.51
3177 3206 2.406616 CCCAACTTCCGCATTCCCG 61.407 63.158 0.00 0.00 0.00 5.14
3599 3628 1.405526 GCTTCGGCAACCTCAGTATCA 60.406 52.381 0.00 0.00 41.33 2.15
3773 3802 4.037858 ACGGATATCGGAACTGTAACAC 57.962 45.455 16.44 0.00 44.45 3.32
4085 4114 5.398416 GCAAAAAGTTGTAACCGATTGAGTC 59.602 40.000 7.67 0.00 37.06 3.36
4094 4123 5.407502 AGTGACTTGCAAAAAGTTGTAACC 58.592 37.500 0.00 0.00 34.82 2.85
4302 4332 3.481453 ACCCAAAGCTTCTCAAGAACTC 58.519 45.455 0.00 0.00 0.00 3.01
4320 4350 0.106669 GGAGCCCTATGTTCCAACCC 60.107 60.000 0.00 0.00 43.50 4.11
4385 4415 1.817740 GCTGTGGAGGCTGGTGTTTTA 60.818 52.381 0.00 0.00 0.00 1.52
4462 4492 2.745968 TGGGTGGAAAGCAGAAAACTT 58.254 42.857 0.00 0.00 0.00 2.66
4701 4737 7.696755 TGCTATATGGTATATACACGTAACGG 58.303 38.462 14.70 6.09 0.00 4.44
5018 5054 9.337396 TGATTCTTGACAACATACCATAATACC 57.663 33.333 0.00 0.00 0.00 2.73
5063 5099 5.291858 TGCTGACAAATAGTAGAAGAATGCG 59.708 40.000 0.00 0.00 0.00 4.73
5137 5173 0.544357 TCCCAATGACTCTCACGGGT 60.544 55.000 7.96 0.00 41.15 5.28
5140 5176 1.404717 CCACTCCCAATGACTCTCACG 60.405 57.143 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.