Multiple sequence alignment - TraesCS6B01G274700

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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 TraesCS6B01G274700 chr6B 100.000 2825 0 0 1 2825 496412442 496415266 0 5217
1 TraesCS6B01G274700 chr6D 94.478 2825 151 5 1 2825 326296525 326293706 0 4348
2 TraesCS6B01G274700 chr7D 90.011 2823 269 10 3 2823 208835818 208833007 0 3639
3 TraesCS6B01G274700 chr7A 89.526 2826 283 11 1 2824 221976269 221973455 0 3567
4 TraesCS6B01G274700 chrUn 88.645 2827 308 12 1 2824 86158831 86161647 0 3430


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 TraesCS6B01G274700 chr6B 496412442 496415266 2824 False 5217 5217 100.000 1 2825 1 chr6B.!!$F1 2824
1 TraesCS6B01G274700 chr6D 326293706 326296525 2819 True 4348 4348 94.478 1 2825 1 chr6D.!!$R1 2824
2 TraesCS6B01G274700 chr7D 208833007 208835818 2811 True 3639 3639 90.011 3 2823 1 chr7D.!!$R1 2820
3 TraesCS6B01G274700 chr7A 221973455 221976269 2814 True 3567 3567 89.526 1 2824 1 chr7A.!!$R1 2823
4 TraesCS6B01G274700 chrUn 86158831 86161647 2816 False 3430 3430 88.645 1 2824 1 chrUn.!!$F1 2823

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
704 708 0.320374 GTGATCCTCGTGGTGGAACA 59.680 55.0 2.99 0.12 39.98 3.18 F
1093 1097 0.531532 AATCTCCAATCGGCTGCTCG 60.532 55.0 0.00 1.60 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 1643 1.201429 ATCGCCCTCCAAAGGTCACT 61.201 55.0 0.0 0.0 41.59 3.41 R
1903 1908 1.656587 ACCTCAAGCACCTCCATACA 58.343 50.0 0.0 0.0 0.00 2.29 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
22 23 4.423732 CCCTTTTGAGTTAATGCATTCGG 58.576 43.478 16.86 3.88 0.00 4.30
72 73 4.320494 GGTTGCTTGTTTGACCATCACTAG 60.320 45.833 0.00 0.00 32.41 2.57
116 117 8.594550 AGTAGTAAATAAGAACTGAAAGGAGCA 58.405 33.333 0.00 0.00 39.30 4.26
325 329 6.881602 TGCAACCACAAAGTGTACATGATATA 59.118 34.615 0.00 0.00 0.00 0.86
512 516 1.229359 CATCTTGATGGGCCAGCCT 59.771 57.895 20.74 0.00 36.10 4.58
528 532 1.855451 CCTGGTTACCCACCCCCTT 60.855 63.158 0.00 0.00 46.68 3.95
545 549 1.298859 CTTCCCCTTGCGTGCACTAC 61.299 60.000 16.19 7.56 0.00 2.73
634 638 1.883084 GCCGCCACCTAGAATGACG 60.883 63.158 0.00 0.00 0.00 4.35
687 691 5.703978 TCACCACCAAACATCTATTTGTG 57.296 39.130 0.00 0.00 37.79 3.33
704 708 0.320374 GTGATCCTCGTGGTGGAACA 59.680 55.000 2.99 0.12 39.98 3.18
720 724 1.178534 AACAAGCCCACCACCAATCG 61.179 55.000 0.00 0.00 0.00 3.34
730 734 1.623811 ACCACCAATCGCACTCTAGTT 59.376 47.619 0.00 0.00 0.00 2.24
731 735 2.002586 CCACCAATCGCACTCTAGTTG 58.997 52.381 0.00 0.00 0.00 3.16
734 738 3.123621 CACCAATCGCACTCTAGTTGTTC 59.876 47.826 0.00 0.00 0.00 3.18
794 798 2.829120 AGAAAGGAAGAAGAGGTCTCCG 59.171 50.000 0.00 0.00 34.56 4.63
795 799 1.562783 AAGGAAGAAGAGGTCTCCGG 58.437 55.000 0.00 0.00 34.56 5.14
831 835 4.360951 AACCAAATCCAGAGGTACGAAA 57.639 40.909 0.00 0.00 34.63 3.46
832 836 4.569719 ACCAAATCCAGAGGTACGAAAT 57.430 40.909 0.00 0.00 32.92 2.17
958 962 5.410355 AAAACATATGCAGTGCCTTGATT 57.590 34.783 13.72 5.76 0.00 2.57
962 966 5.628130 ACATATGCAGTGCCTTGATTAGAT 58.372 37.500 13.72 0.00 0.00 1.98
1026 1030 3.548793 TTTTTGGTCCCATGCCAGT 57.451 47.368 0.00 0.00 37.31 4.00
1073 1077 5.273208 ACTATGTACAGATCTTGTGGAGGT 58.727 41.667 0.33 0.00 41.10 3.85
1089 1093 2.760374 GAGGTAATCTCCAATCGGCTG 58.240 52.381 0.00 0.00 36.52 4.85
1093 1097 0.531532 AATCTCCAATCGGCTGCTCG 60.532 55.000 0.00 1.60 0.00 5.03
1125 1129 1.469251 GCAGACTACATCCGCTTTCGA 60.469 52.381 0.00 0.00 38.10 3.71
1154 1158 3.909662 GCCATGGCGTGACTTCAT 58.090 55.556 23.48 0.00 0.00 2.57
1209 1214 1.444212 CTTTCGCCCACGCAATTGG 60.444 57.895 7.72 0.00 39.84 3.16
1213 1218 2.114670 CGCCCACGCAATTGGATCT 61.115 57.895 7.72 0.00 39.24 2.75
1215 1220 1.031571 GCCCACGCAATTGGATCTCA 61.032 55.000 7.72 0.00 39.24 3.27
1224 1229 3.464907 CAATTGGATCTCACTCGCTCAT 58.535 45.455 0.00 0.00 0.00 2.90
1262 1267 1.522668 CGCACCCTTCTCAATGTCAA 58.477 50.000 0.00 0.00 0.00 3.18
1263 1268 2.086869 CGCACCCTTCTCAATGTCAAT 58.913 47.619 0.00 0.00 0.00 2.57
1323 1328 2.665000 CACCATCACCTCGGCACT 59.335 61.111 0.00 0.00 0.00 4.40
1369 1374 6.782000 TGGCCATAAGCTCAATAATACCATTT 59.218 34.615 0.00 0.00 43.05 2.32
1389 1394 4.649267 TTGTCTTATCCACCCATTCACA 57.351 40.909 0.00 0.00 0.00 3.58
1468 1473 3.126831 CGAGTGAACTTATCTGCCATCC 58.873 50.000 0.00 0.00 0.00 3.51
1638 1643 0.178903 AGGTTAGAGGCCACTCACCA 60.179 55.000 28.56 1.40 46.44 4.17
1679 1684 0.179181 TACTTCACGACATCGGACGC 60.179 55.000 6.21 0.00 44.95 5.19
1822 1827 2.696989 TGATCGAATGCTCATGGTGT 57.303 45.000 0.00 0.00 0.00 4.16
1824 1829 2.093553 TGATCGAATGCTCATGGTGTGA 60.094 45.455 0.00 0.00 35.05 3.58
1855 1860 3.587061 TGGTATGAGCCTTCTCCAGAAAA 59.413 43.478 0.00 0.00 38.58 2.29
1863 1868 4.476479 AGCCTTCTCCAGAAAAGTGGATAT 59.524 41.667 0.00 0.00 45.87 1.63
1889 1894 5.482006 TGAAGAGGATATATTCATGTGGCG 58.518 41.667 0.00 0.00 34.25 5.69
1926 1931 2.254152 TGGAGGTGCTTGAGGTAGAT 57.746 50.000 0.00 0.00 0.00 1.98
2052 2057 4.261155 CGAATCATTTCCAATGCGGTGTAT 60.261 41.667 0.00 0.00 35.57 2.29
2106 2111 2.205022 TTGCTGCCTACTGCTTTGAT 57.795 45.000 0.00 0.00 41.07 2.57
2154 2159 4.315803 ACTTTCAAGATCGTCGATTTGGT 58.684 39.130 20.21 12.79 0.00 3.67
2522 2529 7.450074 AGCCATATCTTACCATCGTGATTTAA 58.550 34.615 0.00 0.00 0.00 1.52
2617 2624 5.921004 TGCCATGTTTTTACTGCATTTTC 57.079 34.783 0.00 0.00 0.00 2.29
2618 2625 5.363101 TGCCATGTTTTTACTGCATTTTCA 58.637 33.333 0.00 0.00 0.00 2.69
2749 2757 3.896888 TGGGGCTGCAAATATATTTCCTG 59.103 43.478 7.76 4.84 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 9.507280 TTTACTACTAGATGTGTACGCATTAAC 57.493 33.333 22.18 10.45 0.00 2.01
177 180 8.226819 TCATGACAACAAAAGTACAACCATTA 57.773 30.769 0.00 0.00 0.00 1.90
325 329 9.995003 TCAGTGATGCAAATAATAAAACCTTTT 57.005 25.926 0.00 0.00 0.00 2.27
528 532 2.046009 TTGTAGTGCACGCAAGGGGA 62.046 55.000 20.52 4.35 45.01 4.81
538 542 5.470368 GTGAGAGTCACTATTTGTAGTGCA 58.530 41.667 10.03 0.00 45.20 4.57
634 638 3.156288 AGGGAAGAACAAGTTTAGGGC 57.844 47.619 0.00 0.00 0.00 5.19
687 691 1.726853 CTTGTTCCACCACGAGGATC 58.273 55.000 5.68 0.00 38.69 3.36
704 708 2.676471 GCGATTGGTGGTGGGCTT 60.676 61.111 0.00 0.00 0.00 4.35
720 724 7.016361 TCAAAGAAAAGAACAACTAGAGTGC 57.984 36.000 0.00 0.00 0.00 4.40
730 734 9.447157 AATTGACCAAATTCAAAGAAAAGAACA 57.553 25.926 0.00 0.00 38.95 3.18
734 738 8.344831 GGGAAATTGACCAAATTCAAAGAAAAG 58.655 33.333 11.31 0.00 38.95 2.27
794 798 1.338973 TGGTTACGATCTATGTCCGCC 59.661 52.381 0.00 0.00 0.00 6.13
795 799 2.787601 TGGTTACGATCTATGTCCGC 57.212 50.000 0.00 0.00 0.00 5.54
831 835 9.927081 AAAACTTCTCATATATTGAACAGGGAT 57.073 29.630 0.00 0.00 32.78 3.85
958 962 9.784531 CAAAAATAGATAGCTCCCTTTCATCTA 57.215 33.333 0.00 0.00 33.87 1.98
962 966 6.731467 ACCAAAAATAGATAGCTCCCTTTCA 58.269 36.000 0.00 0.00 0.00 2.69
1014 1018 2.166254 CCATTTTGTACTGGCATGGGAC 59.834 50.000 0.00 0.00 32.18 4.46
1026 1030 2.026262 GGCCCAGTCTCTCCATTTTGTA 60.026 50.000 0.00 0.00 0.00 2.41
1073 1077 1.269778 CGAGCAGCCGATTGGAGATTA 60.270 52.381 1.98 0.00 37.49 1.75
1089 1093 1.703438 CTGCAATGTGAGAGGCGAGC 61.703 60.000 0.00 0.00 0.00 5.03
1093 1097 2.275318 GTAGTCTGCAATGTGAGAGGC 58.725 52.381 0.00 0.00 0.00 4.70
1097 1101 2.862536 CGGATGTAGTCTGCAATGTGAG 59.137 50.000 0.00 0.00 0.00 3.51
1125 1129 1.669440 CCATGGCTTGCAAGTTGCT 59.331 52.632 27.17 4.26 45.31 3.91
1154 1158 0.776810 ACATGTGTGGGGGTCATCAA 59.223 50.000 0.00 0.00 0.00 2.57
1209 1214 1.592081 GCACAATGAGCGAGTGAGATC 59.408 52.381 0.00 0.00 35.33 2.75
1213 1218 1.362768 GATGCACAATGAGCGAGTGA 58.637 50.000 0.00 0.00 35.33 3.41
1215 1220 0.745845 GGGATGCACAATGAGCGAGT 60.746 55.000 0.00 0.00 33.85 4.18
1224 1229 2.358125 CGTGACGGGGATGCACAA 60.358 61.111 0.00 0.00 32.96 3.33
1262 1267 0.251073 GTTGGTACAGGCACCGGTAT 59.749 55.000 6.87 0.00 42.39 2.73
1263 1268 1.120184 TGTTGGTACAGGCACCGGTA 61.120 55.000 6.87 0.00 42.39 4.02
1369 1374 3.618752 CGTGTGAATGGGTGGATAAGACA 60.619 47.826 0.00 0.00 0.00 3.41
1375 1380 2.569853 TCTTACGTGTGAATGGGTGGAT 59.430 45.455 0.00 0.00 0.00 3.41
1389 1394 3.288964 AGGGAACTCGATGATCTTACGT 58.711 45.455 0.00 0.00 32.90 3.57
1638 1643 1.201429 ATCGCCCTCCAAAGGTCACT 61.201 55.000 0.00 0.00 41.59 3.41
1679 1684 7.816031 GGCTCAAATCCAATGTCATTATTATGG 59.184 37.037 0.00 0.00 32.40 2.74
1841 1846 2.568623 TCCACTTTTCTGGAGAAGGC 57.431 50.000 5.98 0.00 35.23 4.35
1863 1868 7.765819 CGCCACATGAATATATCCTCTTCATTA 59.234 37.037 0.00 0.00 37.48 1.90
1902 1907 1.985159 ACCTCAAGCACCTCCATACAA 59.015 47.619 0.00 0.00 0.00 2.41
1903 1908 1.656587 ACCTCAAGCACCTCCATACA 58.343 50.000 0.00 0.00 0.00 2.29
1980 1985 2.357034 TGAGAGGCGCCAACGAAC 60.357 61.111 31.54 17.51 43.93 3.95
2052 2057 5.809001 ACTCCTTGCATTGAATAGTTCAGA 58.191 37.500 0.00 0.00 41.38 3.27
2106 2111 9.136323 TCTCTTGCAGATATAGTTGTCTTATCA 57.864 33.333 0.00 0.00 0.00 2.15
2154 2159 3.317993 GGCAAGCACAAGGAGAGTTTTTA 59.682 43.478 0.00 0.00 0.00 1.52
2452 2459 9.797556 CTCTGAAGCAAATTATTCAAATGATCA 57.202 29.630 0.00 0.00 35.14 2.92
2468 2475 5.649395 CACCAAGAATATTCCTCTGAAGCAA 59.351 40.000 11.92 0.00 33.05 3.91
2522 2529 7.772332 GACAAATGGTCATCGACTTAATAGT 57.228 36.000 0.00 0.00 46.19 2.12
2749 2757 9.384764 GAAAATACTGGGGCTATTATAGATCAC 57.615 37.037 3.04 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.