Multiple sequence alignment - TraesCS3D01G271000

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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 TraesCS3D01G271000 chr3D 100.000 2957 0 0 1 2957 375724338 375721382 0.000000e+00 5461
1 TraesCS3D01G271000 chr3A 93.443 3050 84 36 1 2957 500528369 500525343 0.000000e+00 4418
2 TraesCS3D01G271000 chr3B 93.026 3040 91 34 1 2957 489982388 489979387 0.000000e+00 4327
3 TraesCS3D01G271000 chr1B 86.253 371 48 1 988 1358 643567705 643567338 1.650000e-107 399
4 TraesCS3D01G271000 chr1D 86.517 356 48 0 1003 1358 467002361 467002716 2.760000e-105 392
5 TraesCS3D01G271000 chr1D 78.313 249 39 11 196 436 387470234 387469993 2.370000e-31 147
6 TraesCS3D01G271000 chr1A 86.517 356 48 0 1003 1358 558954615 558954970 2.760000e-105 392
7 TraesCS3D01G271000 chr5A 81.780 236 30 11 196 423 594138032 594138262 5.030000e-43 185
8 TraesCS3D01G271000 chr5A 83.152 184 27 3 242 423 143575960 143576141 6.560000e-37 165
9 TraesCS3D01G271000 chr7A 79.339 242 38 9 196 429 669666616 669666379 3.050000e-35 159
10 TraesCS3D01G271000 chr6A 79.661 236 36 8 196 423 421524846 421525077 3.050000e-35 159
11 TraesCS3D01G271000 chr2A 82.703 185 26 5 247 429 11647441 11647261 3.050000e-35 159
12 TraesCS3D01G271000 chr2A 82.258 186 25 5 242 423 676404239 676404058 1.420000e-33 154
13 TraesCS3D01G271000 chr4D 79.464 224 34 9 193 407 257403736 257403956 6.600000e-32 148


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 TraesCS3D01G271000 chr3D 375721382 375724338 2956 True 5461 5461 100.000 1 2957 1 chr3D.!!$R1 2956
1 TraesCS3D01G271000 chr3A 500525343 500528369 3026 True 4418 4418 93.443 1 2957 1 chr3A.!!$R1 2956
2 TraesCS3D01G271000 chr3B 489979387 489982388 3001 True 4327 4327 93.026 1 2957 1 chr3B.!!$R1 2956

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
923 1013 0.032540 CGACTCGCATCCATCCATCA 59.967 55.0 0.0 0.0 0.0 3.07 F
995 1085 0.178935 GAGAGAGATCTGGGAGGGGG 60.179 65.0 0.0 0.0 0.0 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 1983 2.166664 GAGCATCTCTGAGGTACCGTTT 59.833 50.000 6.18 0.0 0.0 3.60 R
2355 2455 3.475566 TCGCCTATAAGCAGAGCAATT 57.524 42.857 0.00 0.0 0.0 2.32 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
75 78 2.263540 CATGCAAAGGGCCTGTGC 59.736 61.111 36.86 36.86 44.36 4.57
97 105 1.387295 TTTGTGTGTGCATTCGGGCA 61.387 50.000 0.00 0.00 42.53 5.36
98 106 1.387295 TTGTGTGTGCATTCGGGCAA 61.387 50.000 0.00 0.00 46.93 4.52
141 149 4.380444 CGAAATCGTTTGGTGGGATTGATT 60.380 41.667 0.00 0.00 31.21 2.57
155 163 2.442212 TTGATTGCTCGTACCGAACA 57.558 45.000 0.00 0.00 34.74 3.18
159 167 2.736144 TTGCTCGTACCGAACATCTT 57.264 45.000 0.00 0.00 32.12 2.40
204 237 3.162666 ACGAACATGTAGACTCCCTTCA 58.837 45.455 0.00 0.00 0.00 3.02
227 260 5.752892 TTTTGTTTAGTCCGCACATTACA 57.247 34.783 0.00 0.00 0.00 2.41
467 502 2.125269 GCCTCAATACACGGCGGT 60.125 61.111 13.24 9.14 33.64 5.68
482 517 2.423898 CGGTCCCACCTCTACGCAT 61.424 63.158 0.00 0.00 35.66 4.73
584 628 0.613777 TTCTCTCTCCTTTTCGGCCC 59.386 55.000 0.00 0.00 0.00 5.80
585 629 1.153549 CTCTCTCCTTTTCGGCCCG 60.154 63.158 0.00 0.00 0.00 6.13
751 825 4.280019 AGTCAAACCCGCCCCCAC 62.280 66.667 0.00 0.00 0.00 4.61
921 1011 1.368950 CCGACTCGCATCCATCCAT 59.631 57.895 0.00 0.00 0.00 3.41
922 1012 0.668706 CCGACTCGCATCCATCCATC 60.669 60.000 0.00 0.00 0.00 3.51
923 1013 0.032540 CGACTCGCATCCATCCATCA 59.967 55.000 0.00 0.00 0.00 3.07
972 1062 4.072839 GTCCAGACTTTTAGGGTTTCCTG 58.927 47.826 0.00 0.00 44.61 3.86
973 1063 3.977999 TCCAGACTTTTAGGGTTTCCTGA 59.022 43.478 0.00 0.00 44.61 3.86
994 1084 0.859760 AGAGAGAGATCTGGGAGGGG 59.140 60.000 0.00 0.00 0.00 4.79
995 1085 0.178935 GAGAGAGATCTGGGAGGGGG 60.179 65.000 0.00 0.00 0.00 5.40
996 1086 0.631998 AGAGAGATCTGGGAGGGGGA 60.632 60.000 0.00 0.00 0.00 4.81
1260 1350 2.996621 CCTCAAGAAGAAGTACAAGGCG 59.003 50.000 0.00 0.00 0.00 5.52
1512 1602 0.983378 ACCTCTTCCATAAGGCCGCT 60.983 55.000 0.00 0.00 36.01 5.52
1693 1789 1.850755 AAAAGGAAGAGGGGCGGGA 60.851 57.895 0.00 0.00 0.00 5.14
1887 1983 1.202830 TCGAGGGTAAAGCAAGCCAAA 60.203 47.619 5.00 0.00 39.59 3.28
1899 1995 1.950909 CAAGCCAAAAACGGTACCTCA 59.049 47.619 10.90 0.00 0.00 3.86
2000 2096 5.964958 TTTGGCCTCTTAAAGTCAGATTG 57.035 39.130 3.32 0.00 0.00 2.67
2033 2129 6.769512 TGTAATAGACTTAGGGGATTGATGC 58.230 40.000 0.00 0.00 0.00 3.91
2126 2224 5.336690 CCCATTTTGAACATGTAACCAGAGG 60.337 44.000 0.00 0.00 0.00 3.69
2338 2438 4.719369 GCGTCGTCTGGTCGGCTT 62.719 66.667 0.00 0.00 33.02 4.35
2342 2442 4.680237 CGTCTGGTCGGCTTGCCA 62.680 66.667 12.45 0.00 0.00 4.92
2366 2466 1.577922 CACACGCAATTGCTCTGCT 59.422 52.632 26.86 10.40 37.67 4.24
2544 2644 8.038862 AGATACATAGGTTTCTGATTCATGGT 57.961 34.615 0.00 0.00 34.57 3.55
2545 2645 8.497745 AGATACATAGGTTTCTGATTCATGGTT 58.502 33.333 0.00 0.00 34.57 3.67
2546 2646 9.125026 GATACATAGGTTTCTGATTCATGGTTT 57.875 33.333 0.00 0.00 0.00 3.27
2547 2647 7.781324 ACATAGGTTTCTGATTCATGGTTTT 57.219 32.000 0.00 0.00 0.00 2.43
2548 2648 7.830739 ACATAGGTTTCTGATTCATGGTTTTC 58.169 34.615 0.00 0.00 0.00 2.29
2549 2649 7.671398 ACATAGGTTTCTGATTCATGGTTTTCT 59.329 33.333 0.00 0.00 0.00 2.52
2550 2650 6.581171 AGGTTTCTGATTCATGGTTTTCTC 57.419 37.500 0.00 0.00 0.00 2.87
2660 2763 7.729116 TGGAAGCATTTGAAGATCTTCTTTTT 58.271 30.769 30.45 17.79 36.73 1.94
2702 2805 8.718102 TTAGATTAGTTAAGCTGGTGATGAAC 57.282 34.615 0.18 0.00 33.48 3.18
2785 2889 1.248486 GCCGCCTTCCTTCTTCTTTT 58.752 50.000 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 65 0.388907 CAAATCGCACAGGCCCTTTG 60.389 55.000 0.00 0.00 36.38 2.77
74 77 0.976963 CGAATGCACACACAAATCGC 59.023 50.000 0.00 0.00 0.00 4.58
75 78 1.605500 CCGAATGCACACACAAATCG 58.394 50.000 0.00 0.00 34.57 3.34
128 136 0.327924 ACGAGCAATCAATCCCACCA 59.672 50.000 0.00 0.00 0.00 4.17
155 163 0.546747 TCCCCCAGACCGAACAAGAT 60.547 55.000 0.00 0.00 0.00 2.40
159 167 0.976073 GAGATCCCCCAGACCGAACA 60.976 60.000 0.00 0.00 0.00 3.18
204 237 6.320494 TGTAATGTGCGGACTAAACAAAAT 57.680 33.333 8.99 0.00 0.00 1.82
401 436 7.962918 CCTCGTATTAGGTTTTGTCTGAAATTG 59.037 37.037 0.00 0.00 31.46 2.32
416 451 4.794655 GCTCTTCAGCTTCCTCGTATTAGG 60.795 50.000 0.00 0.00 43.09 2.69
467 502 0.398522 ATGGATGCGTAGAGGTGGGA 60.399 55.000 0.00 0.00 0.00 4.37
482 517 1.706866 GGATGGATGGTCATGGATGGA 59.293 52.381 0.00 0.00 0.00 3.41
584 628 0.721483 GCGTCTCTTTGGTTTTCGCG 60.721 55.000 0.00 0.00 33.59 5.87
585 629 0.306533 TGCGTCTCTTTGGTTTTCGC 59.693 50.000 0.00 0.00 41.98 4.70
921 1011 1.000359 TCTCGGTGGCTGGAGATGA 60.000 57.895 0.00 0.00 34.52 2.92
922 1012 1.440893 CTCTCGGTGGCTGGAGATG 59.559 63.158 3.81 0.00 38.53 2.90
923 1013 1.760086 CCTCTCGGTGGCTGGAGAT 60.760 63.158 3.81 0.00 38.53 2.75
972 1062 2.224867 CCCTCCCAGATCTCTCTCTCTC 60.225 59.091 0.00 0.00 0.00 3.20
973 1063 1.782752 CCCTCCCAGATCTCTCTCTCT 59.217 57.143 0.00 0.00 0.00 3.10
994 1084 2.190578 CTTCCCGTCCATGGCTCC 59.809 66.667 6.96 0.00 0.00 4.70
995 1085 2.514824 GCTTCCCGTCCATGGCTC 60.515 66.667 6.96 1.49 0.00 4.70
996 1086 3.011517 AGCTTCCCGTCCATGGCT 61.012 61.111 6.96 0.00 0.00 4.75
1348 1438 4.803908 CGGGGAGGGCTTCTTGGC 62.804 72.222 0.00 0.00 40.96 4.52
1349 1439 4.803908 GCGGGGAGGGCTTCTTGG 62.804 72.222 0.00 0.00 0.00 3.61
1350 1440 4.803908 GGCGGGGAGGGCTTCTTG 62.804 72.222 0.00 0.00 0.00 3.02
1545 1635 7.826744 TCATAGTTGTTGTTATTGTAGCCATCA 59.173 33.333 0.00 0.00 0.00 3.07
1693 1789 3.167414 CTCCCCAAAACCTCCGGT 58.833 61.111 0.00 0.00 37.65 5.28
1887 1983 2.166664 GAGCATCTCTGAGGTACCGTTT 59.833 50.000 6.18 0.00 0.00 3.60
2000 2096 8.001292 TCCCCTAAGTCTATTACAGTAACCTAC 58.999 40.741 0.00 0.00 0.00 3.18
2033 2129 6.484643 AGGCAATATAGCATACAAAGACACAG 59.515 38.462 0.00 0.00 35.83 3.66
2126 2224 4.766375 TGCACAAATAAGGTAGCCTAGAC 58.234 43.478 0.00 0.00 31.13 2.59
2178 2278 4.591929 TGGTCTCTCATCATGCAAAATCA 58.408 39.130 0.00 0.00 0.00 2.57
2355 2455 3.475566 TCGCCTATAAGCAGAGCAATT 57.524 42.857 0.00 0.00 0.00 2.32
2366 2466 8.740906 TCAACAAATTAAACCATTCGCCTATAA 58.259 29.630 0.00 0.00 0.00 0.98
2415 2515 7.918076 AGGACCTGATAACTAAGAATTTGACA 58.082 34.615 0.00 0.00 0.00 3.58
2544 2644 7.335627 TCCTACTCACAACAGAAAAGAGAAAA 58.664 34.615 0.00 0.00 0.00 2.29
2545 2645 6.884832 TCCTACTCACAACAGAAAAGAGAAA 58.115 36.000 0.00 0.00 0.00 2.52
2546 2646 6.479972 TCCTACTCACAACAGAAAAGAGAA 57.520 37.500 0.00 0.00 0.00 2.87
2547 2647 6.479972 TTCCTACTCACAACAGAAAAGAGA 57.520 37.500 0.00 0.00 0.00 3.10
2548 2648 7.579726 CATTTCCTACTCACAACAGAAAAGAG 58.420 38.462 0.00 0.00 0.00 2.85
2549 2649 6.017109 GCATTTCCTACTCACAACAGAAAAGA 60.017 38.462 0.00 0.00 0.00 2.52
2550 2650 6.016777 AGCATTTCCTACTCACAACAGAAAAG 60.017 38.462 0.00 0.00 0.00 2.27
2660 2763 4.919774 TCTAAGCATGAAACCCCAGTAA 57.080 40.909 0.00 0.00 0.00 2.24
2702 2805 8.916654 CATAATCTACCAAGCTAACAATACTCG 58.083 37.037 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.