Multiple sequence alignment - TraesCS3D01G278600

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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 TraesCS3D01G278600 chr3D 100.000 3726 0 0 1 3726 386303963 386300238 0.000000e+00 6881.0
1 TraesCS3D01G278600 chr3A 95.441 3663 144 11 1 3648 507772547 507768893 0.000000e+00 5818.0
2 TraesCS3D01G278600 chr3A 89.655 87 8 1 3640 3726 507766678 507766593 3.930000e-20 110.0
3 TraesCS3D01G278600 chr3B 94.345 3360 129 16 1 3321 501988665 501985328 0.000000e+00 5096.0
4 TraesCS3D01G278600 chr3B 96.279 215 7 1 3313 3526 501981095 501980881 5.920000e-93 351.0
5 TraesCS3D01G278600 chr3B 93.064 173 11 1 3554 3726 501980821 501980650 6.180000e-63 252.0
6 TraesCS3D01G278600 chr6A 93.590 156 8 1 1870 2023 91902412 91902567 8.050000e-57 231.0
7 TraesCS3D01G278600 chr1B 92.121 165 9 3 1863 2024 325812708 325812545 2.890000e-56 230.0
8 TraesCS3D01G278600 chr4B 90.854 164 12 3 1870 2031 103804485 103804647 2.250000e-52 217.0
9 TraesCS3D01G278600 chr2A 90.798 163 13 1 1870 2030 184561309 184561147 2.250000e-52 217.0
10 TraesCS3D01G278600 chr1D 89.080 174 15 3 1863 2033 225704947 225704775 2.920000e-51 213.0
11 TraesCS3D01G278600 chr1A 89.143 175 13 6 1864 2034 487486462 487486290 2.920000e-51 213.0
12 TraesCS3D01G278600 chr7B 91.139 158 10 3 1870 2024 644193606 644193450 1.050000e-50 211.0
13 TraesCS3D01G278600 chr4D 87.952 83 9 1 713 795 425699103 425699184 3.060000e-16 97.1


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 TraesCS3D01G278600 chr3D 386300238 386303963 3725 True 6881 6881 100.000 1 3726 1 chr3D.!!$R1 3725
1 TraesCS3D01G278600 chr3A 507766593 507772547 5954 True 2964 5818 92.548 1 3726 2 chr3A.!!$R1 3725
2 TraesCS3D01G278600 chr3B 501985328 501988665 3337 True 5096 5096 94.345 1 3321 1 chr3B.!!$R1 3320

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
218 220 0.179124 GGCAGCTTACCTCTCGTCAG 60.179 60.0 0.00 0.0 0.00 3.51 F
594 598 0.457851 CACAACAAGAAACGGGCCAA 59.542 50.0 4.39 0.0 0.00 4.52 F
1411 1416 2.235898 GTCTTGCTGGATCTCCTTGACT 59.764 50.0 0.00 0.0 36.82 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 1416 1.271871 ACATTTCCACGCCTCATCCAA 60.272 47.619 0.0 0.0 0.00 3.53 R
2047 2084 1.413077 GGCCATACGCTAAGAGGAAGT 59.587 52.381 0.0 0.0 37.74 3.01 R
3383 3433 0.684535 AAATTCCCCCTGGTTTTGCG 59.315 50.000 0.0 0.0 0.00 4.85 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
56 57 1.417288 TGCATCACCATCGAGATCCT 58.583 50.000 0.00 0.00 0.00 3.24
81 82 2.224159 GCTCCCAGACCACCTCCAA 61.224 63.158 0.00 0.00 0.00 3.53
99 100 1.255667 AACCCGTGCTAGTCGGTGAT 61.256 55.000 20.71 9.36 45.63 3.06
130 131 1.689243 CCGCCTGGACATCATCTCCA 61.689 60.000 0.00 0.00 37.49 3.86
143 144 1.557269 ATCTCCACCGCTTCAAGCCT 61.557 55.000 3.08 0.00 38.18 4.58
181 182 4.361971 TCGTCTCCTCCGTGGCCT 62.362 66.667 3.32 0.00 35.26 5.19
218 220 0.179124 GGCAGCTTACCTCTCGTCAG 60.179 60.000 0.00 0.00 0.00 3.51
224 226 1.751924 CTTACCTCTCGTCAGAAGGGG 59.248 57.143 0.00 0.00 0.00 4.79
265 267 4.227300 TGGATAAGGTAGAACCAGTGCAAT 59.773 41.667 0.00 0.00 41.95 3.56
268 270 1.073763 AGGTAGAACCAGTGCAATGCA 59.926 47.619 9.04 2.72 41.95 3.96
375 377 3.334583 TCCAACAGTTGCTAGGATGTC 57.665 47.619 7.88 0.00 0.00 3.06
381 383 1.204941 AGTTGCTAGGATGTCCGTGTC 59.795 52.381 0.00 0.00 42.08 3.67
461 464 4.864334 CCTGGCCAGATGGTCCGC 62.864 72.222 34.91 0.00 39.61 5.54
496 499 1.290955 CTAAACGGGCCAGACACGA 59.709 57.895 10.86 0.00 0.00 4.35
587 590 3.798337 CCAAGCACATCACAACAAGAAAC 59.202 43.478 0.00 0.00 0.00 2.78
594 598 0.457851 CACAACAAGAAACGGGCCAA 59.542 50.000 4.39 0.00 0.00 4.52
620 624 2.332654 GCACGTTTAGCCCACCAGG 61.333 63.158 0.00 0.00 39.47 4.45
849 854 2.270850 GTTATCGGGCCAGCACCA 59.729 61.111 4.39 0.00 0.00 4.17
1237 1242 2.819595 GCTCAGATTTGGCGCGGA 60.820 61.111 8.83 0.00 0.00 5.54
1396 1401 9.476202 AAGGTAAAATGACTTAATTTGTCTTGC 57.524 29.630 11.02 3.60 35.63 4.01
1411 1416 2.235898 GTCTTGCTGGATCTCCTTGACT 59.764 50.000 0.00 0.00 36.82 3.41
1465 1470 6.034044 CAGAAAACGAACTACAGTCATCTAGC 59.966 42.308 0.00 0.00 0.00 3.42
1499 1504 8.454894 GTCAGAATTAGATTTTGTTCTCCCTTC 58.545 37.037 0.00 0.00 0.00 3.46
1500 1505 8.386264 TCAGAATTAGATTTTGTTCTCCCTTCT 58.614 33.333 0.00 0.00 0.00 2.85
1501 1506 9.672673 CAGAATTAGATTTTGTTCTCCCTTCTA 57.327 33.333 0.00 0.00 0.00 2.10
1616 1621 4.585070 GCTATTCATGGCCAGGCA 57.415 55.556 13.87 0.85 0.00 4.75
1873 1908 9.444600 GTACAAACCTTGAAATTATCTACTCCA 57.555 33.333 0.00 0.00 0.00 3.86
1999 2036 8.138074 GTCCATAATGAAATCTCTTAAAAGGCC 58.862 37.037 0.00 0.00 0.00 5.19
2047 2084 8.997621 AATTGTTATGTTCTTTAGTCGAGCTA 57.002 30.769 0.00 0.00 0.00 3.32
2172 2209 7.274447 TCTTGCTTGGTTGATTTCATCTTTTT 58.726 30.769 0.00 0.00 0.00 1.94
2348 2393 7.962995 TGCAATCCTTATACCAAAATAACCA 57.037 32.000 0.00 0.00 0.00 3.67
2378 2423 7.976734 AGTTGTTATAGACTGTCAGTAATGCTC 59.023 37.037 5.21 0.00 0.00 4.26
2584 2630 4.705023 GCCTTTCACTAAAAGCCATCCTTA 59.295 41.667 0.00 0.00 42.63 2.69
2856 2904 4.739137 GCTGATGGAATCTGTAGTCTCACC 60.739 50.000 0.00 0.00 45.81 4.02
2907 2955 4.458397 CAGTCATCTTATTGCCCTGTGAT 58.542 43.478 0.00 0.00 0.00 3.06
3064 3112 4.458989 GCTCAATGGAAAGTGATACACCAA 59.541 41.667 0.00 0.00 34.49 3.67
3081 3129 9.701098 GATACACCAAATCATTTGCATGAATAT 57.299 29.630 15.87 7.22 42.93 1.28
3118 3166 5.470098 AGCGTACACTGACTGATTTGATTTT 59.530 36.000 0.00 0.00 0.00 1.82
3132 3180 4.898829 TTGATTTTCAGTGGATATGCCG 57.101 40.909 0.00 0.00 40.66 5.69
3133 3181 4.149511 TGATTTTCAGTGGATATGCCGA 57.850 40.909 0.00 0.00 40.66 5.54
3226 3276 0.969149 CTGTGTCTAGTCTGCCCACA 59.031 55.000 0.00 0.00 35.02 4.17
3280 3330 7.307101 GCGGGTTACATGCCATAAAAATTTATG 60.307 37.037 15.71 15.71 45.96 1.90
3341 3391 2.833943 ACTGTCTACATCACATGGCTCA 59.166 45.455 0.00 0.00 33.60 4.26
3398 3448 1.502527 ATACCGCAAAACCAGGGGGA 61.503 55.000 0.00 0.00 42.86 4.81
3415 3465 6.481643 CAGGGGGAATTTACTCTTTCACTTA 58.518 40.000 0.00 0.00 0.00 2.24
3479 3529 6.728200 TGAGTTTGATTTGTGACACATCTTC 58.272 36.000 9.55 7.44 0.00 2.87
3491 3541 9.515020 TTGTGACACATCTTCAGAAAATAAAAC 57.485 29.630 9.55 0.00 0.00 2.43
3572 3623 9.990360 TTTTAAAGTTCCAAGACAAGTTTTTCT 57.010 25.926 0.00 0.00 30.63 2.52
3623 3674 8.610035 GTCAAAAGGTTATCTTACTTATTCGGG 58.390 37.037 0.00 0.00 34.78 5.14
3629 3680 6.541278 GGTTATCTTACTTATTCGGGTTTGCT 59.459 38.462 0.00 0.00 0.00 3.91
3644 3695 5.741982 CGGGTTTGCTCTTTTATTATTTCCG 59.258 40.000 0.00 0.00 0.00 4.30
3700 5974 1.497991 TGAGACTTTTCTTGCGACCG 58.502 50.000 0.00 0.00 29.47 4.79
3715 5989 2.032808 GCGACCGGATCTTTTTATGCTC 60.033 50.000 9.46 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 3.319198 GGTCTGGGAGCCACCGAA 61.319 66.667 0.00 0.00 40.11 4.30
115 116 0.531532 GCGGTGGAGATGATGTCCAG 60.532 60.000 12.05 2.54 45.00 3.86
130 131 2.048127 GACGAGGCTTGAAGCGGT 60.048 61.111 11.48 8.87 43.62 5.68
143 144 2.595878 CGAGCGGCGATAGAGACGA 61.596 63.158 12.98 0.00 44.57 4.20
181 182 2.084101 CGATTTCGGTGTCGACGCA 61.084 57.895 28.67 10.28 45.92 5.24
218 220 2.433970 CACTCATCTTCTCTCCCCCTTC 59.566 54.545 0.00 0.00 0.00 3.46
224 226 5.549742 ATCCATTCACTCATCTTCTCTCC 57.450 43.478 0.00 0.00 0.00 3.71
295 297 3.291585 GTCAGATGCAACAAAGTGTTCG 58.708 45.455 0.00 0.00 38.77 3.95
554 557 1.302192 GTGCTTGGGCCAACGAGTA 60.302 57.895 16.66 2.01 37.74 2.59
594 598 1.743995 GCTAAACGTGCCGATGGGT 60.744 57.895 0.00 0.00 34.97 4.51
620 624 0.246360 ACTGCCCAAAATTAAGCGGC 59.754 50.000 0.00 0.00 40.16 6.53
627 631 1.478471 GGCCCAAAACTGCCCAAAATT 60.478 47.619 0.00 0.00 0.00 1.82
829 834 3.012119 TGCTGGCCCGATAACCCA 61.012 61.111 0.00 0.00 0.00 4.51
1051 1056 2.043227 GGACAGAGTAGATGGGGAAGG 58.957 57.143 0.00 0.00 0.00 3.46
1179 1184 3.071479 CGACCAATCCGAGGAAAAGAAA 58.929 45.455 0.00 0.00 0.00 2.52
1237 1242 2.186826 GCACCCTGCACAACGAAGT 61.187 57.895 0.00 0.00 44.45 3.01
1396 1401 3.453717 TCATCCAAGTCAAGGAGATCCAG 59.546 47.826 0.92 0.00 38.83 3.86
1411 1416 1.271871 ACATTTCCACGCCTCATCCAA 60.272 47.619 0.00 0.00 0.00 3.53
1616 1621 8.579850 TCATATTTGAAGTGCACCTTATTTCT 57.420 30.769 14.63 0.00 32.03 2.52
2041 2078 1.671845 ACGCTAAGAGGAAGTAGCTCG 59.328 52.381 0.00 0.00 40.51 5.03
2047 2084 1.413077 GGCCATACGCTAAGAGGAAGT 59.587 52.381 0.00 0.00 37.74 3.01
2172 2209 9.241919 TCAAGCTATTTGACCTGATCATTTAAA 57.758 29.630 0.00 0.00 40.82 1.52
2378 2423 5.047092 AGGTGAACCAAAATAAGCAAGATGG 60.047 40.000 1.62 0.00 38.89 3.51
2584 2630 4.457466 CCAACTACCAAAGTACAGTGGTT 58.543 43.478 21.51 11.84 46.17 3.67
2688 2736 5.111293 CAAAACCTGAAGTTGCAAATGAGT 58.889 37.500 0.00 0.00 39.19 3.41
2856 2904 6.688385 CACCATGTCATCATAAGTTTTAAGCG 59.312 38.462 0.00 0.00 32.47 4.68
3064 3112 7.724506 AGAGAGTCCATATTCATGCAAATGATT 59.275 33.333 0.00 0.00 0.00 2.57
3081 3129 2.030185 GTGTACGCTGAAAGAGAGTCCA 60.030 50.000 0.00 0.00 37.13 4.02
3118 3166 2.036346 CTGTGATCGGCATATCCACTGA 59.964 50.000 0.00 0.00 34.01 3.41
3216 3264 1.507141 CCTGAAACGTGTGGGCAGAC 61.507 60.000 0.00 0.00 0.00 3.51
3226 3276 3.485463 TGATCTTGAACCCTGAAACGT 57.515 42.857 0.00 0.00 0.00 3.99
3383 3433 0.684535 AAATTCCCCCTGGTTTTGCG 59.315 50.000 0.00 0.00 0.00 4.85
3557 3608 9.918630 ATGATGGAAATAGAAAAACTTGTCTTG 57.081 29.630 0.00 0.00 0.00 3.02
3566 3617 9.265862 ACCCATGTTATGATGGAAATAGAAAAA 57.734 29.630 0.00 0.00 45.24 1.94
3609 3660 5.416271 AGAGCAAACCCGAATAAGTAAGA 57.584 39.130 0.00 0.00 0.00 2.10
3621 3672 6.627243 ACGGAAATAATAAAAGAGCAAACCC 58.373 36.000 0.00 0.00 0.00 4.11
3623 3674 9.836076 AGTTACGGAAATAATAAAAGAGCAAAC 57.164 29.630 0.00 0.00 0.00 2.93
3692 5966 2.096819 GCATAAAAAGATCCGGTCGCAA 59.903 45.455 0.00 0.00 0.00 4.85
3700 5974 6.183360 GGTTCCAAGAGAGCATAAAAAGATCC 60.183 42.308 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.