Multiple sequence alignment - TraesCS5D01G126500

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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 TraesCS5D01G126500 chr5D 100.000 2806 0 0 1 2806 193511918 193509113 0 5182
1 TraesCS5D01G126500 chr5A 94.752 2839 85 18 1 2806 248531926 248534733 0 4359
2 TraesCS5D01G126500 chr5B 92.161 1416 53 14 1 1393 216400064 216398684 0 1947
3 TraesCS5D01G126500 chr5B 94.815 810 17 5 2016 2806 216395420 216394617 0 1240
4 TraesCS5D01G126500 chr5B 97.222 576 16 0 1449 2024 216397014 216396439 0 976


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 TraesCS5D01G126500 chr5D 193509113 193511918 2805 True 5182.000000 5182 100.000000 1 2806 1 chr5D.!!$R1 2805
1 TraesCS5D01G126500 chr5A 248531926 248534733 2807 False 4359.000000 4359 94.752000 1 2806 1 chr5A.!!$F1 2805
2 TraesCS5D01G126500 chr5B 216394617 216400064 5447 True 1387.666667 1947 94.732667 1 2806 3 chr5B.!!$R1 2805

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
605 609 1.713297 GTAGGGATGGTGGTATCCGT 58.287 55.000 0.0 0.0 46.19 4.69 F
1247 1275 1.455217 GCAGGCATTGGAGCTGGAT 60.455 57.895 0.0 0.0 34.17 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 3170 0.984995 ACAAGGGAGAAGTAGTGCCC 59.015 55.00 0.0 0.0 41.0 5.36 R
2462 5146 5.545063 TCTACAGTCTCAAACCACAATGA 57.455 39.13 0.0 0.0 0.0 2.57 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
79 80 3.182341 TGTGAAAGCAGCAAAGCATTT 57.818 38.095 0.00 0.00 40.26 2.32
207 208 2.344950 CATGTGAGACAGAAGCTCCAC 58.655 52.381 0.00 0.00 0.00 4.02
227 228 2.354656 TGACTCGTCGCACACTGC 60.355 61.111 0.00 0.00 40.69 4.40
311 315 4.137543 GGGAATGATGTGTTCCATAGACC 58.862 47.826 7.16 0.00 45.56 3.85
338 342 3.209410 CTGTCTGAGCAAAGGAAACACT 58.791 45.455 0.00 0.00 0.00 3.55
339 343 2.945008 TGTCTGAGCAAAGGAAACACTG 59.055 45.455 0.00 0.00 0.00 3.66
436 440 3.567478 AACAGACTTAGATGGGCATCC 57.433 47.619 0.00 0.00 38.58 3.51
594 598 2.037772 CCTCCAAGAATCGGTAGGGATG 59.962 54.545 0.00 0.00 0.00 3.51
605 609 1.713297 GTAGGGATGGTGGTATCCGT 58.287 55.000 0.00 0.00 46.19 4.69
646 650 2.499693 TCGAAGCTCTCTCTCTCTCTCA 59.500 50.000 0.00 0.00 0.00 3.27
650 668 2.840038 AGCTCTCTCTCTCTCTCACTCA 59.160 50.000 0.00 0.00 0.00 3.41
720 738 2.887889 CTCTCGCTAGTCGCCTCGG 61.888 68.421 2.24 0.00 38.27 4.63
768 786 3.052082 CTCGGCTGGCCACACAAG 61.052 66.667 0.00 0.00 35.37 3.16
769 787 3.535629 CTCGGCTGGCCACACAAGA 62.536 63.158 0.00 0.00 35.37 3.02
770 788 3.357079 CGGCTGGCCACACAAGAC 61.357 66.667 0.00 0.00 35.37 3.01
771 789 2.203337 GGCTGGCCACACAAGACA 60.203 61.111 0.00 0.00 35.81 3.41
772 790 2.555547 GGCTGGCCACACAAGACAC 61.556 63.158 0.00 0.00 35.81 3.67
773 791 1.823470 GCTGGCCACACAAGACACA 60.823 57.895 0.00 0.00 0.00 3.72
809 827 2.436109 GGCCAGTCAGAGCCCAAA 59.564 61.111 0.00 0.00 43.76 3.28
935 958 5.816919 TCTTTGACTTGTTGGTTCGATTTC 58.183 37.500 0.00 0.00 0.00 2.17
963 986 1.940242 AAAGGAACCCCCAACACCGT 61.940 55.000 0.00 0.00 37.41 4.83
1124 1152 1.642952 CCTTCTCTTGGCTCTTGCGC 61.643 60.000 0.00 0.00 40.82 6.09
1131 1159 3.052082 GGCTCTTGCGCTTGCTGA 61.052 61.111 9.73 0.00 40.82 4.26
1185 1213 1.753078 GGGTTGGGGAATTCGAGCC 60.753 63.158 0.00 1.29 0.00 4.70
1247 1275 1.455217 GCAGGCATTGGAGCTGGAT 60.455 57.895 0.00 0.00 34.17 3.41
1309 1337 3.371965 ACACGGTGGACTTCCTACATAT 58.628 45.455 13.48 0.00 36.82 1.78
1310 1338 4.539726 ACACGGTGGACTTCCTACATATA 58.460 43.478 13.48 0.00 36.82 0.86
1311 1339 5.145564 ACACGGTGGACTTCCTACATATAT 58.854 41.667 13.48 0.00 36.82 0.86
1312 1340 5.601313 ACACGGTGGACTTCCTACATATATT 59.399 40.000 13.48 0.00 36.82 1.28
1313 1341 6.099269 ACACGGTGGACTTCCTACATATATTT 59.901 38.462 13.48 0.00 36.82 1.40
1314 1342 6.990349 CACGGTGGACTTCCTACATATATTTT 59.010 38.462 0.00 0.00 36.82 1.82
1529 3171 9.109393 TCTTGGAGATTTTTCATAAGAATACGG 57.891 33.333 0.00 0.00 32.89 4.02
1577 3219 3.008835 AGCTCAAATAATGCTGCTCCA 57.991 42.857 0.00 0.00 34.88 3.86
1697 3339 9.143631 GAGTGCTAATCATGTTTGCTTTTTAAT 57.856 29.630 12.59 0.00 0.00 1.40
1912 3555 9.533831 TCCATCTATGTTTCTATATCAGCACTA 57.466 33.333 0.00 0.00 0.00 2.74
1970 3613 5.409826 GTGTGGTTGAGGTTTCTATCTGAAG 59.590 44.000 0.00 0.00 35.89 3.02
1973 3616 6.370166 GTGGTTGAGGTTTCTATCTGAAGAAG 59.630 42.308 3.68 0.00 36.85 2.85
2006 3649 3.252458 GCCCGCTTACAGAAAAAGAAAGA 59.748 43.478 0.00 0.00 0.00 2.52
2009 3652 5.858581 CCCGCTTACAGAAAAAGAAAGATTG 59.141 40.000 0.00 0.00 0.00 2.67
2087 4757 8.154203 TGAATCTCTACTTTGGTTACAATGACA 58.846 33.333 0.00 0.00 36.29 3.58
2185 4869 2.820178 TCTATCAAGACCAGGCACAGA 58.180 47.619 0.00 0.00 0.00 3.41
2383 5067 6.174720 ACTTTCAAGACTGATGGAAGTGTA 57.825 37.500 0.73 0.00 31.75 2.90
2388 5072 3.931578 AGACTGATGGAAGTGTAAGTGC 58.068 45.455 0.00 0.00 0.00 4.40
2392 5076 5.072741 ACTGATGGAAGTGTAAGTGCAATT 58.927 37.500 4.23 4.23 0.00 2.32
2462 5146 6.264067 GGCAAGCAGAATCAACCTCTTATTAT 59.736 38.462 0.00 0.00 0.00 1.28
2512 5201 5.590259 GCACCATAACAACTTGACCATAGAT 59.410 40.000 0.00 0.00 0.00 1.98
2513 5202 6.095440 GCACCATAACAACTTGACCATAGATT 59.905 38.462 0.00 0.00 0.00 2.40
2514 5203 7.679638 GCACCATAACAACTTGACCATAGATTC 60.680 40.741 0.00 0.00 0.00 2.52
2515 5204 6.828785 ACCATAACAACTTGACCATAGATTCC 59.171 38.462 0.00 0.00 0.00 3.01
2756 5447 0.898320 AGTGGATCCTGTTGACTCCG 59.102 55.000 14.23 0.00 0.00 4.63
2777 5468 4.582656 CCGGCCTATCATATTTGGTTTCAA 59.417 41.667 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.747355 GATGCTGGGTGATTTGAGGTG 59.253 52.381 0.00 0.00 0.00 4.00
79 80 5.428253 GTCATAACAAGGTAAGCCATCTCA 58.572 41.667 0.00 0.00 37.19 3.27
227 228 4.096003 AATGGGGGTCGGTCTGCG 62.096 66.667 0.00 0.00 0.00 5.18
311 315 1.673033 CCTTTGCTCAGACAGTACCGG 60.673 57.143 0.00 0.00 0.00 5.28
338 342 1.345741 CTGCCACTTCTCTCAGGAACA 59.654 52.381 0.00 0.00 0.00 3.18
339 343 1.338579 CCTGCCACTTCTCTCAGGAAC 60.339 57.143 1.09 0.00 46.80 3.62
436 440 4.911390 ACCAGAGTTCTTGGTATCCTTTG 58.089 43.478 0.00 0.00 33.61 2.77
594 598 1.340568 GGAGCTTCTACGGATACCACC 59.659 57.143 0.00 0.00 0.00 4.61
605 609 3.027412 GACTGAGGTGATGGAGCTTCTA 58.973 50.000 0.00 0.00 30.42 2.10
646 650 3.117284 GGGAGGATAAGAGGAGAGTGAGT 60.117 52.174 0.00 0.00 0.00 3.41
650 668 2.107552 CGAGGGAGGATAAGAGGAGAGT 59.892 54.545 0.00 0.00 0.00 3.24
729 747 0.173708 CCAGAGAGGTAGTGGCGAAC 59.826 60.000 0.00 0.00 0.00 3.95
768 786 2.248431 GCGCTCCGTTGTTGTGTC 59.752 61.111 0.00 0.00 0.00 3.67
769 787 3.636043 CGCGCTCCGTTGTTGTGT 61.636 61.111 5.56 0.00 0.00 3.72
770 788 4.368808 CCGCGCTCCGTTGTTGTG 62.369 66.667 5.56 0.00 34.38 3.33
773 791 4.388499 ATCCCGCGCTCCGTTGTT 62.388 61.111 5.56 0.00 34.38 2.83
796 814 2.050144 TGAGAGTTTTGGGCTCTGACT 58.950 47.619 0.00 0.00 42.74 3.41
798 816 2.037772 GAGTGAGAGTTTTGGGCTCTGA 59.962 50.000 0.00 0.00 42.74 3.27
809 827 0.972883 GCCCAGAGTGAGTGAGAGTT 59.027 55.000 0.00 0.00 0.00 3.01
904 925 7.306167 CGAACCAACAAGTCAAAGAATCAATTG 60.306 37.037 0.00 0.00 0.00 2.32
906 927 6.039270 TCGAACCAACAAGTCAAAGAATCAAT 59.961 34.615 0.00 0.00 0.00 2.57
935 958 1.004862 GGGGGTTCCTTTGAGAAGAGG 59.995 57.143 0.00 0.00 34.71 3.69
1131 1159 6.138263 TCCAGAATTATGCATGAATCCCTTT 58.862 36.000 10.16 0.00 0.00 3.11
1185 1213 3.474806 GACATGTCCAAGCGTCGG 58.525 61.111 15.31 0.00 0.00 4.79
1232 1260 1.271271 CCTAGATCCAGCTCCAATGCC 60.271 57.143 0.00 0.00 0.00 4.40
1247 1275 6.183361 GCTCCTAAATCCCAATTCTTCCTAGA 60.183 42.308 0.00 0.00 0.00 2.43
1288 1316 1.640917 ATGTAGGAAGTCCACCGTGT 58.359 50.000 0.00 0.00 38.89 4.49
1433 3017 8.850156 ACACCAGCATATAAAACAGGAAATATC 58.150 33.333 0.00 0.00 0.00 1.63
1499 3141 9.846248 ATTCTTATGAAAAATCTCCAAGAAACG 57.154 29.630 0.00 0.00 35.63 3.60
1528 3170 0.984995 ACAAGGGAGAAGTAGTGCCC 59.015 55.000 0.00 0.00 41.00 5.36
1529 3171 2.861147 AACAAGGGAGAAGTAGTGCC 57.139 50.000 0.00 0.00 0.00 5.01
1577 3219 1.833492 TGGTGCCACAATGCTGCTT 60.833 52.632 0.00 0.00 0.00 3.91
1613 3255 3.797353 GCCTCATCCGCCCTTGGA 61.797 66.667 0.00 0.00 43.58 3.53
1697 3339 7.990886 AGTGACTGAATAACTTTCAAACACCTA 59.009 33.333 14.77 0.00 36.33 3.08
1862 3504 6.833342 ATTTGTGAACTGCAGAATTTGAAC 57.167 33.333 23.35 8.84 28.99 3.18
1865 3507 5.754406 TGGAATTTGTGAACTGCAGAATTTG 59.246 36.000 23.35 0.00 28.99 2.32
1970 3613 5.526111 TGTAAGCGGGCTAATGATAAACTTC 59.474 40.000 0.00 0.00 0.00 3.01
1973 3616 5.054477 TCTGTAAGCGGGCTAATGATAAAC 58.946 41.667 0.00 0.00 0.00 2.01
2087 4757 8.122472 ACCAAAATAGACATTCGAAAAAGGAT 57.878 30.769 0.00 0.00 0.00 3.24
2388 5072 8.313227 CACGCTGCAATTTAGTTATGTTAATTG 58.687 33.333 0.00 0.00 39.68 2.32
2392 5076 6.729391 TCACGCTGCAATTTAGTTATGTTA 57.271 33.333 0.00 0.00 0.00 2.41
2462 5146 5.545063 TCTACAGTCTCAAACCACAATGA 57.455 39.130 0.00 0.00 0.00 2.57
2515 5204 7.846593 TGTATATAACATAATGGCTAGCCCACG 60.847 40.741 30.81 16.40 38.91 4.94
2756 5447 8.253113 CCATATTGAAACCAAATATGATAGGCC 58.747 37.037 14.68 0.00 0.00 5.19
2777 5468 7.997223 CCTTTCATCATATCATAGCACCCATAT 59.003 37.037 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.