Multiple sequence alignment - TraesCS1B01G016200

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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 TraesCS1B01G016200 chr1B 100.000 4497 0 0 1 4497 7902813 7898317 0.000000e+00 8305
1 TraesCS1B01G016200 chr1B 97.244 4499 120 4 1 4497 567735587 567731091 0.000000e+00 7618
2 TraesCS1B01G016200 chr1B 97.088 4499 124 7 1 4497 676864401 676859908 0.000000e+00 7576
3 TraesCS1B01G016200 chr6B 97.399 4498 112 5 1 4497 572516290 572511797 0.000000e+00 7653
4 TraesCS1B01G016200 chr4A 97.065 4498 128 4 2 4497 673171281 673166786 0.000000e+00 7572
5 TraesCS1B01G016200 chr2B 96.821 4498 137 5 1 4497 785300765 785296273 0.000000e+00 7509
6 TraesCS1B01G016200 chr2B 96.333 4499 124 11 1 4497 662568065 662572524 0.000000e+00 7356
7 TraesCS1B01G016200 chr5B 96.777 4499 136 5 1 4497 18261522 18257031 0.000000e+00 7496
8 TraesCS1B01G016200 chr5B 96.503 2002 55 3 2497 4497 568809872 568811859 0.000000e+00 3295
9 TraesCS1B01G016200 chr3B 96.577 4499 143 7 1 4497 667633189 667637678 0.000000e+00 7444
10 TraesCS1B01G016200 chr3B 91.617 167 12 2 3964 4129 13141464 13141629 3.500000e-56 230
11 TraesCS1B01G016200 chr7B 96.087 4498 149 6 1 4497 629987599 629992070 0.000000e+00 7306
12 TraesCS1B01G016200 chr2A 94.520 3960 213 4 1 3958 773697694 773693737 0.000000e+00 6107


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 TraesCS1B01G016200 chr1B 7898317 7902813 4496 True 8305 8305 100.000 1 4497 1 chr1B.!!$R1 4496
1 TraesCS1B01G016200 chr1B 567731091 567735587 4496 True 7618 7618 97.244 1 4497 1 chr1B.!!$R2 4496
2 TraesCS1B01G016200 chr1B 676859908 676864401 4493 True 7576 7576 97.088 1 4497 1 chr1B.!!$R3 4496
3 TraesCS1B01G016200 chr6B 572511797 572516290 4493 True 7653 7653 97.399 1 4497 1 chr6B.!!$R1 4496
4 TraesCS1B01G016200 chr4A 673166786 673171281 4495 True 7572 7572 97.065 2 4497 1 chr4A.!!$R1 4495
5 TraesCS1B01G016200 chr2B 785296273 785300765 4492 True 7509 7509 96.821 1 4497 1 chr2B.!!$R1 4496
6 TraesCS1B01G016200 chr2B 662568065 662572524 4459 False 7356 7356 96.333 1 4497 1 chr2B.!!$F1 4496
7 TraesCS1B01G016200 chr5B 18257031 18261522 4491 True 7496 7496 96.777 1 4497 1 chr5B.!!$R1 4496
8 TraesCS1B01G016200 chr5B 568809872 568811859 1987 False 3295 3295 96.503 2497 4497 1 chr5B.!!$F1 2000
9 TraesCS1B01G016200 chr3B 667633189 667637678 4489 False 7444 7444 96.577 1 4497 1 chr3B.!!$F2 4496
10 TraesCS1B01G016200 chr7B 629987599 629992070 4471 False 7306 7306 96.087 1 4497 1 chr7B.!!$F1 4496
11 TraesCS1B01G016200 chr2A 773693737 773697694 3957 True 6107 6107 94.520 1 3958 1 chr2A.!!$R1 3957


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
86 87 1.000274 TCACATCGATCCTGCATACCG 60.000 52.381 0.0 0.0 0.00 4.02 F
329 330 1.224592 CCAAGCCGCCATTACCTCT 59.775 57.895 0.0 0.0 0.00 3.69 F
1769 1776 1.072648 CCTAAACGGAAAGGTGGTGGA 59.927 52.381 0.0 0.0 33.16 4.02 F
2314 2322 2.513897 CCCGAACCCCGCAGAATC 60.514 66.667 0.0 0.0 36.84 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1690 1.344942 GCACGTCTGTACTCTTGGCG 61.345 60.000 0.00 0.0 0.00 5.69 R
2299 2307 0.391130 TCAAGATTCTGCGGGGTTCG 60.391 55.000 0.00 0.0 42.76 3.95 R
2791 2800 0.527565 ACAGCGCCATTCAACCATTC 59.472 50.000 2.29 0.0 0.00 2.67 R
3595 3606 2.105128 GCGATCTCCGTCCCAGTG 59.895 66.667 0.00 0.0 41.15 3.66 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
84 85 3.005261 AGACTCACATCGATCCTGCATAC 59.995 47.826 0.00 0.00 0.00 2.39
86 87 1.000274 TCACATCGATCCTGCATACCG 60.000 52.381 0.00 0.00 0.00 4.02
101 102 3.639538 CATACCGTCCAAATAGAGTCCG 58.360 50.000 0.00 0.00 0.00 4.79
329 330 1.224592 CCAAGCCGCCATTACCTCT 59.775 57.895 0.00 0.00 0.00 3.69
398 399 4.124351 GATCCGACGGTCGCACCA 62.124 66.667 24.26 8.40 38.47 4.17
849 850 6.712998 TGTTGAGAATTCCTTCCGTGAAAATA 59.287 34.615 0.65 0.00 31.27 1.40
958 960 7.443879 TCAGTGTGCTTAATGAAGATGTTTACA 59.556 33.333 0.00 0.00 34.25 2.41
1080 1084 4.870021 AAGAACAGGCCTAATCCTCATT 57.130 40.909 3.98 0.00 33.25 2.57
1192 1196 2.158971 GCACCACAATCCACCAAGTTTT 60.159 45.455 0.00 0.00 0.00 2.43
1357 1361 4.141482 ACTTGGCTCTTCTTCAGGTACAAA 60.141 41.667 0.00 0.00 0.00 2.83
1411 1417 5.408880 TTTATGTGACCTATGTGTCCGAA 57.591 39.130 0.00 0.00 34.25 4.30
1428 1435 7.874016 TGTGTCCGAATAGTTGTGTTTACTATT 59.126 33.333 7.72 7.72 46.28 1.73
1497 1504 4.692625 ACATTTGATCCTTTGTCTCGTGAG 59.307 41.667 0.00 0.00 0.00 3.51
1510 1517 3.693085 GTCTCGTGAGTACCCACTAATGA 59.307 47.826 5.94 0.00 34.21 2.57
1683 1690 6.034044 TGTTGTACAACTTGAAAATTGCGTTC 59.966 34.615 32.58 7.05 41.67 3.95
1769 1776 1.072648 CCTAAACGGAAAGGTGGTGGA 59.927 52.381 0.00 0.00 33.16 4.02
1971 1978 9.906660 TTTCATTTGTGTTTGTAGATGGTAATC 57.093 29.630 0.00 0.00 0.00 1.75
2035 2042 9.699410 ATAAGAGGGACAACAATGATGAATTTA 57.301 29.630 0.00 0.00 0.00 1.40
2299 2307 3.889520 AAGAGTTTCCGTCTATGTCCC 57.110 47.619 0.00 0.00 0.00 4.46
2314 2322 2.513897 CCCGAACCCCGCAGAATC 60.514 66.667 0.00 0.00 36.84 2.52
2609 2618 6.930164 TGCATTGTTTTAGATCTGTTTGCATT 59.070 30.769 5.18 0.00 32.01 3.56
2791 2800 4.161333 GCTTCACGATGTCCTGAATTTTG 58.839 43.478 0.00 0.00 0.00 2.44
2858 2867 9.778741 AATACTCTCATTTGAACTTCACAAGTA 57.221 29.630 0.00 0.00 41.91 2.24
2912 2921 9.410556 GATAATCAATGCATATTGTAAACACCC 57.589 33.333 0.00 0.00 43.33 4.61
2928 2937 1.407258 CACCCACAACACCGTGATTTT 59.593 47.619 5.28 0.00 39.34 1.82
2986 2995 2.881266 TATGTTGGGTAGGGCTAGGT 57.119 50.000 0.00 0.00 0.00 3.08
3077 3086 8.311395 AGAGTAATGGATGAGTATTTCAGACA 57.689 34.615 0.00 0.00 39.68 3.41
3595 3606 6.257630 ACTTTTTGTGATGTGGTGCATAAAAC 59.742 34.615 0.00 0.00 38.06 2.43
3667 3678 1.346395 AGTCAAGGCCACGTATTGTCA 59.654 47.619 5.01 0.00 0.00 3.58
3758 3770 4.625607 AGGAGTAGGTATTAGCATTGGC 57.374 45.455 0.00 0.00 41.61 4.52
3857 3869 6.094881 GGGATAGATTTCGACAATTTTCCACA 59.905 38.462 0.00 0.00 0.00 4.17
3884 3896 8.810652 TTTATTTATTGCTTTTGTGAGACACC 57.189 30.769 0.00 0.00 32.73 4.16
3966 3980 3.897325 TCTGCGATATTACGGACATGTC 58.103 45.455 17.91 17.91 0.00 3.06
4017 4031 1.106351 TGTGCCGTGCCACATCTTTT 61.106 50.000 0.00 0.00 40.55 2.27
4061 4075 2.107552 ACTAAGGTTAGGCTTGCCACAA 59.892 45.455 14.54 4.63 35.08 3.33
4169 4211 8.330247 TGTAGAAATTTGCCCCTAAATGTAGTA 58.670 33.333 0.00 0.00 31.05 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.836898 AGGTTCACATGGATCATGCATATTT 59.163 36.000 0.00 0.00 44.80 1.40
84 85 1.533338 CGTCGGACTCTATTTGGACGG 60.533 57.143 6.57 0.00 42.35 4.79
86 87 3.119566 AGTTCGTCGGACTCTATTTGGAC 60.120 47.826 0.00 0.00 0.00 4.02
101 102 2.543848 TGCACAAACATCTCAGTTCGTC 59.456 45.455 0.00 0.00 0.00 4.20
274 275 2.098871 CGTACGGCGTCATCGACA 59.901 61.111 19.21 0.00 46.73 4.35
329 330 3.081409 GCTAGGCGGTCTTGGGGA 61.081 66.667 0.00 0.00 0.00 4.81
398 399 3.819877 GAGTTTGGACGGCCACGGT 62.820 63.158 11.33 0.00 45.94 4.83
499 500 2.275380 GGGTGCCGGTGAATTTGCT 61.275 57.895 1.90 0.00 0.00 3.91
893 895 9.997482 TTGGTCAAATAATAAATCGCTTTCTAC 57.003 29.630 0.00 0.00 0.00 2.59
913 915 2.027653 TGATGCCGTCTGTATTTGGTCA 60.028 45.455 0.00 0.00 0.00 4.02
958 960 3.066621 TCGTTACGTAGCCCGAATATGTT 59.933 43.478 4.24 0.00 40.70 2.71
1398 1404 4.755411 ACACAACTATTCGGACACATAGG 58.245 43.478 1.50 0.00 0.00 2.57
1497 1504 4.820173 GGCCAGTTAATCATTAGTGGGTAC 59.180 45.833 0.00 0.00 0.00 3.34
1510 1517 2.871096 TCCGTTTCTGGCCAGTTAAT 57.129 45.000 31.58 0.00 0.00 1.40
1572 1579 5.007682 ACTTATTGACTTACATTGCCGGTT 58.992 37.500 1.90 0.00 0.00 4.44
1683 1690 1.344942 GCACGTCTGTACTCTTGGCG 61.345 60.000 0.00 0.00 0.00 5.69
1769 1776 2.784347 GTGCTTGGCTTTCTACTCCTT 58.216 47.619 0.00 0.00 0.00 3.36
1936 1943 6.096036 ACAAACACAAATGAAACACGATCAA 58.904 32.000 0.00 0.00 0.00 2.57
1971 1978 2.353579 ACCTTCCGTGTTCAACTTTTCG 59.646 45.455 0.00 0.00 0.00 3.46
2035 2042 6.969043 TCCCAACTCCTTGATGTACATTAAT 58.031 36.000 12.91 0.00 0.00 1.40
2045 2052 2.850833 TCTCCATCCCAACTCCTTGAT 58.149 47.619 0.00 0.00 0.00 2.57
2299 2307 0.391130 TCAAGATTCTGCGGGGTTCG 60.391 55.000 0.00 0.00 42.76 3.95
2314 2322 8.373981 ACCCATAGACTCATCAGAAATATCAAG 58.626 37.037 0.00 0.00 0.00 3.02
2791 2800 0.527565 ACAGCGCCATTCAACCATTC 59.472 50.000 2.29 0.00 0.00 2.67
2912 2921 4.035017 GTCAGAAAAATCACGGTGTTGTG 58.965 43.478 8.17 4.24 41.28 3.33
2928 2937 5.107259 CGTTGTTGATATGAAACGGTCAGAA 60.107 40.000 0.00 0.00 40.43 3.02
3595 3606 2.105128 GCGATCTCCGTCCCAGTG 59.895 66.667 0.00 0.00 41.15 3.66
3637 3648 3.941483 CGTGGCCTTGACTCATTAATCTT 59.059 43.478 3.32 0.00 0.00 2.40
3758 3770 3.369157 CCTTCTACGGGACTAAAACCCTG 60.369 52.174 0.00 0.00 44.72 4.45
3966 3980 3.118629 TGGCTAGCTAAGTCATGAACCAG 60.119 47.826 15.72 0.00 33.94 4.00
4039 4053 2.907696 TGTGGCAAGCCTAACCTTAGTA 59.092 45.455 12.96 0.00 36.94 1.82
4061 4075 5.888982 TCTACAGAAAAACCTCTTCCAGT 57.111 39.130 0.00 0.00 0.00 4.00
4169 4211 2.478894 CGCGAGTAGGAACAACAACAAT 59.521 45.455 0.00 0.00 0.00 2.71
4350 4392 3.826754 CTAGCTGGAGTGCGCGGA 61.827 66.667 8.83 0.00 38.13 5.54



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

AutoCloner maintained by Alex Coulton.