Multiple sequence alignment - TraesCS5B01G112000

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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 TraesCS5B01G112000 chr5B 100.000 2729 0 0 1 2729 170658537 170661265 0 5040
1 TraesCS5B01G112000 chr5B 92.693 2737 186 11 1 2729 197849213 197851943 0 3934
2 TraesCS5B01G112000 chr5D 93.114 2730 172 10 4 2729 248977055 248974338 0 3986
3 TraesCS5B01G112000 chr5D 92.988 2738 174 10 1 2729 49712723 49715451 0 3976
4 TraesCS5B01G112000 chr7B 92.975 2733 177 10 1 2729 107284669 107287390 0 3969
5 TraesCS5B01G112000 chr7B 92.865 2733 178 8 1 2729 478025061 478027780 0 3951
6 TraesCS5B01G112000 chr3B 92.959 2727 181 9 7 2729 244462980 244460261 0 3962
7 TraesCS5B01G112000 chr3D 92.944 2721 180 9 1 2716 169270245 169272958 0 3951
8 TraesCS5B01G112000 chr6B 92.815 2728 180 11 4 2729 289634295 289631582 0 3938
9 TraesCS5B01G112000 chr6D 92.787 2731 179 14 1 2725 294362562 294365280 0 3936


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 TraesCS5B01G112000 chr5B 170658537 170661265 2728 False 5040 5040 100.000 1 2729 1 chr5B.!!$F1 2728
1 TraesCS5B01G112000 chr5B 197849213 197851943 2730 False 3934 3934 92.693 1 2729 1 chr5B.!!$F2 2728
2 TraesCS5B01G112000 chr5D 248974338 248977055 2717 True 3986 3986 93.114 4 2729 1 chr5D.!!$R1 2725
3 TraesCS5B01G112000 chr5D 49712723 49715451 2728 False 3976 3976 92.988 1 2729 1 chr5D.!!$F1 2728
4 TraesCS5B01G112000 chr7B 107284669 107287390 2721 False 3969 3969 92.975 1 2729 1 chr7B.!!$F1 2728
5 TraesCS5B01G112000 chr7B 478025061 478027780 2719 False 3951 3951 92.865 1 2729 1 chr7B.!!$F2 2728
6 TraesCS5B01G112000 chr3B 244460261 244462980 2719 True 3962 3962 92.959 7 2729 1 chr3B.!!$R1 2722
7 TraesCS5B01G112000 chr3D 169270245 169272958 2713 False 3951 3951 92.944 1 2716 1 chr3D.!!$F1 2715
8 TraesCS5B01G112000 chr6B 289631582 289634295 2713 True 3938 3938 92.815 4 2729 1 chr6B.!!$R1 2725
9 TraesCS5B01G112000 chr6D 294362562 294365280 2718 False 3936 3936 92.787 1 2725 1 chr6D.!!$F1 2724

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
939 949 0.038526 CGGACACGACCACTAAGCTT 60.039 55.0 3.48 3.48 44.6 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 1834 0.527565 CACAAGGGCATACAAGTGGC 59.472 55.0 0.0 0.0 43.34 5.01 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
142 143 2.106187 AGTGGGTTGTAGGTGGTACA 57.894 50.000 0.00 0.00 40.06 2.90
225 226 1.553248 TGTATTCGAGTCTTGTGGGGG 59.447 52.381 0.00 0.00 0.00 5.40
270 273 8.774586 GCAGTGTATAAACTAATCATGGTTAGG 58.225 37.037 25.79 11.01 36.27 2.69
304 307 6.239036 CGGTTATGGACATCTTGAGTATCTGA 60.239 42.308 0.00 0.00 34.92 3.27
417 422 7.040062 CCTTCTCAATGTTTAACAACCACCATA 60.040 37.037 0.66 0.00 31.02 2.74
552 559 9.639601 TTCTGTTCATTACTCTATGTGTTACAG 57.360 33.333 0.00 0.00 0.00 2.74
594 601 3.685435 CCATTTCGGGCTGCAACT 58.315 55.556 0.50 0.00 0.00 3.16
605 612 2.483538 GGGCTGCAACTTTTCATGTTGT 60.484 45.455 0.50 0.00 44.54 3.32
641 648 1.754803 CGAGTAAGGTGCCATAGGTCA 59.245 52.381 0.00 0.00 0.00 4.02
698 705 4.287067 TGGACTCACTTTATCTTCCAAGCT 59.713 41.667 0.00 0.00 30.08 3.74
704 711 4.010349 ACTTTATCTTCCAAGCTTTCCGG 58.990 43.478 0.00 0.00 0.00 5.14
791 800 8.882736 TCAATGTAATAAGTGTGTGATTGCTAG 58.117 33.333 0.00 0.00 0.00 3.42
905 915 6.953101 TGGTTGCTACAAGATGGTATTAGAA 58.047 36.000 0.00 0.00 0.00 2.10
914 924 5.847111 AGATGGTATTAGAACACACGCTA 57.153 39.130 0.00 0.00 0.00 4.26
920 930 5.287992 GGTATTAGAACACACGCTAACTGTC 59.712 44.000 0.00 0.00 30.17 3.51
939 949 0.038526 CGGACACGACCACTAAGCTT 60.039 55.000 3.48 3.48 44.60 3.74
953 963 6.069615 ACCACTAAGCTTAAACCATAGGTCAT 60.070 38.462 7.74 0.00 33.12 3.06
1036 1047 4.312443 GAACAAGTTCACTCAACCGGATA 58.688 43.478 9.46 0.00 39.31 2.59
1091 1104 5.259632 AGTTACTAGGTACCTGAACATCGT 58.740 41.667 25.33 11.36 0.00 3.73
1101 1114 5.670792 ACCTGAACATCGTAATACCAAGA 57.329 39.130 0.00 0.00 0.00 3.02
1129 1142 2.093341 GGGACCTACATCGCCACTTTAA 60.093 50.000 0.00 0.00 0.00 1.52
1130 1143 3.433173 GGGACCTACATCGCCACTTTAAT 60.433 47.826 0.00 0.00 0.00 1.40
1382 1398 1.952296 GGATAGGTCCATTGCAGCTTG 59.048 52.381 0.00 0.00 44.42 4.01
1392 1408 4.007457 GCAGCTTGCATCCAGGAA 57.993 55.556 0.00 0.00 44.26 3.36
1449 1465 1.895131 TGCGCAGGCATGATAGATCTA 59.105 47.619 5.66 4.57 46.21 1.98
1457 1473 6.519721 GCAGGCATGATAGATCTAAAGAAGGA 60.520 42.308 6.52 0.00 0.00 3.36
1471 1487 3.941704 AGAAGGAAATGACCAGGATCC 57.058 47.619 2.48 2.48 0.00 3.36
1579 1595 5.458595 TGAGGAAGCTAGGAGTATTCATGA 58.541 41.667 0.00 0.00 0.00 3.07
1642 1664 4.038042 GTCCGGAGAACTACATCATCATCA 59.962 45.833 3.06 0.00 0.00 3.07
1650 1672 5.330455 ACTACATCATCATCAACGACACT 57.670 39.130 0.00 0.00 0.00 3.55
1738 1761 5.873164 TCTTCCACCGATTAAAACTTCTAGC 59.127 40.000 0.00 0.00 0.00 3.42
1765 1788 7.174426 TGACCACCATATCAGTAGTAGTATTCG 59.826 40.741 0.00 0.00 0.00 3.34
1898 1921 4.095211 GGGTAGTGTTTTCCCTCTAGACT 58.905 47.826 0.00 0.00 38.29 3.24
1907 1930 7.762159 GTGTTTTCCCTCTAGACTTCATTCTAG 59.238 40.741 1.38 1.38 44.59 2.43
1951 1974 0.975135 CCATCAGATGCCTCCGAGAT 59.025 55.000 4.68 0.00 0.00 2.75
2023 2046 5.938710 CAGCAGAATACCTTGATGCAGATAT 59.061 40.000 0.00 0.00 39.34 1.63
2064 2108 1.550976 GGGAACAACAACAACAACCCA 59.449 47.619 0.00 0.00 36.47 4.51
2065 2109 2.612604 GGAACAACAACAACAACCCAC 58.387 47.619 0.00 0.00 0.00 4.61
2066 2110 2.612604 GAACAACAACAACAACCCACC 58.387 47.619 0.00 0.00 0.00 4.61
2067 2111 1.633774 ACAACAACAACAACCCACCA 58.366 45.000 0.00 0.00 0.00 4.17
2068 2112 1.273886 ACAACAACAACAACCCACCAC 59.726 47.619 0.00 0.00 0.00 4.16
2069 2113 0.899019 AACAACAACAACCCACCACC 59.101 50.000 0.00 0.00 0.00 4.61
2070 2114 0.251832 ACAACAACAACCCACCACCA 60.252 50.000 0.00 0.00 0.00 4.17
2110 2157 3.244422 TGTTGATCACTTAGCCCGTTTCT 60.244 43.478 0.00 0.00 0.00 2.52
2283 2330 2.710377 TCATGGTGGGAGAATTTCACG 58.290 47.619 0.00 0.00 32.65 4.35
2317 2364 0.033366 CGACACTGTCACATGGGACA 59.967 55.000 28.41 28.41 45.06 4.02
2502 2549 4.097589 GCCGCTAAGTAGGAGAAGTTTCTA 59.902 45.833 0.00 0.00 37.73 2.10
2509 2556 9.416284 CTAAGTAGGAGAAGTTTCTAGAAGGAT 57.584 37.037 5.12 0.00 37.73 3.24
2560 2607 2.685897 GTGGCAACCTTCAACAACTACA 59.314 45.455 0.00 0.00 0.00 2.74
2561 2608 2.685897 TGGCAACCTTCAACAACTACAC 59.314 45.455 0.00 0.00 0.00 2.90
2575 2622 4.715527 AACTACACGGAGTTGGTAGATC 57.284 45.455 0.00 0.00 41.61 2.75
2687 2734 0.612744 CCCCGTTTTACCCCGAACTA 59.387 55.000 0.00 0.00 0.00 2.24
2702 2749 1.477295 GAACTAGGGAGGACACCTTCG 59.523 57.143 0.00 0.00 39.54 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
225 226 1.758783 CAGAGGTTTGCGCACTTTTC 58.241 50.000 11.12 6.30 0.00 2.29
270 273 2.512974 CCATAACCGGGGACACGC 60.513 66.667 6.32 0.00 0.00 5.34
304 307 9.809395 ATGAGATCAACATGATAATCCAAGAAT 57.191 29.630 0.00 0.00 37.20 2.40
353 357 9.419297 CAATCCCAATTAAGCATCATCATTAAG 57.581 33.333 0.00 0.00 0.00 1.85
552 559 3.549299 GCACATGGAATATGCTAGCAC 57.451 47.619 22.07 7.08 36.40 4.40
594 601 7.279090 TCGTCTGAAAAGTCTACAACATGAAAA 59.721 33.333 0.00 0.00 0.00 2.29
605 612 5.106791 CCTTACTCGTCGTCTGAAAAGTCTA 60.107 44.000 0.00 0.00 0.00 2.59
641 648 3.944015 GGCATAGCTGAGTGAAAGACAAT 59.056 43.478 0.00 0.00 0.00 2.71
698 705 5.389859 TCTAAGAACGATAACACCGGAAA 57.610 39.130 9.46 0.00 0.00 3.13
704 711 4.694339 AGGCCATCTAAGAACGATAACAC 58.306 43.478 5.01 0.00 0.00 3.32
791 800 8.969267 CACAATACTCGAGGATTTATAACAGAC 58.031 37.037 20.58 0.00 0.00 3.51
814 824 2.217750 GGTAATGCTGACACACACACA 58.782 47.619 0.00 0.00 0.00 3.72
815 825 1.194547 CGGTAATGCTGACACACACAC 59.805 52.381 0.00 0.00 0.00 3.82
905 915 0.318445 GTCCGACAGTTAGCGTGTGT 60.318 55.000 0.00 0.00 0.00 3.72
920 930 0.038526 AAGCTTAGTGGTCGTGTCCG 60.039 55.000 0.00 0.00 0.00 4.79
953 963 5.186797 GGAGTCAGAAATGAGAAGAGAGGAA 59.813 44.000 0.00 0.00 0.00 3.36
1036 1047 4.514066 GTGTCGTCCAAAAGGTGTATCTTT 59.486 41.667 0.00 0.00 38.48 2.52
1091 1104 3.135167 GGTCCCGGTGAATCTTGGTATTA 59.865 47.826 0.00 0.00 0.00 0.98
1101 1114 0.750850 CGATGTAGGTCCCGGTGAAT 59.249 55.000 0.00 0.00 0.00 2.57
1129 1142 3.300388 TCATCCAACGCTCCTCTTCTAT 58.700 45.455 0.00 0.00 0.00 1.98
1130 1143 2.735151 TCATCCAACGCTCCTCTTCTA 58.265 47.619 0.00 0.00 0.00 2.10
1382 1398 2.760092 TGCTGGTTTAATTCCTGGATGC 59.240 45.455 0.00 0.00 0.00 3.91
1392 1408 2.159572 GCGTCGAATGTGCTGGTTTAAT 60.160 45.455 0.00 0.00 0.00 1.40
1449 1465 4.293368 AGGATCCTGGTCATTTCCTTCTTT 59.707 41.667 15.29 0.00 32.94 2.52
1457 1473 3.390639 CAGCTCTAGGATCCTGGTCATTT 59.609 47.826 25.28 4.74 0.00 2.32
1471 1487 3.360867 TGAGTTCTTCCTCCAGCTCTAG 58.639 50.000 0.00 0.00 0.00 2.43
1579 1595 4.316823 TCCTGGCGTGGGGTCTCT 62.317 66.667 0.00 0.00 0.00 3.10
1642 1664 1.658673 GGTCCGAGTCAGTGTCGTT 59.341 57.895 2.89 0.00 35.59 3.85
1650 1672 2.091830 ACTATCATCAGGGTCCGAGTCA 60.092 50.000 0.00 0.00 0.00 3.41
1738 1761 8.410673 AATACTACTACTGATATGGTGGTCAG 57.589 38.462 1.14 1.14 45.65 3.51
1765 1788 6.294065 GCTCGGACTATACTATATACATGGGC 60.294 46.154 0.00 0.00 0.00 5.36
1811 1834 0.527565 CACAAGGGCATACAAGTGGC 59.472 55.000 0.00 0.00 43.34 5.01
1898 1921 7.962995 AGGTGAGAATACAGACTAGAATGAA 57.037 36.000 0.00 0.00 0.00 2.57
1907 1930 7.119407 GGGTTTAGAAAAGGTGAGAATACAGAC 59.881 40.741 0.00 0.00 0.00 3.51
1913 1936 6.552008 TGATGGGTTTAGAAAAGGTGAGAAT 58.448 36.000 0.00 0.00 0.00 2.40
1951 1974 2.352617 GGAAAGCAAATCCATTGTCGCA 60.353 45.455 0.00 0.00 41.32 5.10
2023 2046 3.519510 CCCTGGTTCTGATTCTGGACTAA 59.480 47.826 2.42 0.00 0.00 2.24
2064 2108 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
2065 2109 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
2066 2110 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
2067 2111 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
2068 2112 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
2069 2113 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
2070 2114 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
2127 2174 0.603569 CGGTGCTACTGGAGAACACT 59.396 55.000 0.00 0.00 34.97 3.55
2283 2330 1.153229 GTCGATGGGGTAAGTGGCC 60.153 63.158 0.00 0.00 0.00 5.36
2317 2364 1.269257 GCGAAAAGCCTGCTGAAACTT 60.269 47.619 0.00 0.00 40.81 2.66
2391 2438 4.835927 CGTCCTCCTTAGCGCAAT 57.164 55.556 11.47 0.00 0.00 3.56
2398 2445 1.541310 CCCACTGTGCGTCCTCCTTA 61.541 60.000 1.29 0.00 0.00 2.69
2502 2549 5.369409 TCAGCTCATCATTCAATCCTTCT 57.631 39.130 0.00 0.00 0.00 2.85
2509 2556 2.357952 GCATGCTCAGCTCATCATTCAA 59.642 45.455 11.37 0.00 0.00 2.69
2560 2607 0.739561 GCTCGATCTACCAACTCCGT 59.260 55.000 0.00 0.00 0.00 4.69
2561 2608 1.002251 GAGCTCGATCTACCAACTCCG 60.002 57.143 0.00 0.00 0.00 4.63
2575 2622 4.327982 TCCCTTCAATCATAAGAGCTCG 57.672 45.455 8.37 0.00 0.00 5.03
2687 2734 3.003763 GGCGAAGGTGTCCTCCCT 61.004 66.667 0.00 0.00 30.89 4.20


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

AutoCloner maintained by Alex Coulton.