Multiple sequence alignment - TraesCS2B01G081600

Loading Multiple Alignment...

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 TraesCS2B01G081600 chr2B 100.000 2351 0 0 1 2351 45616563 45618913 0.000000e+00 4342.0
1 TraesCS2B01G081600 chr2B 97.067 716 21 0 1 716 44926954 44926239 0.000000e+00 1206.0
2 TraesCS2B01G081600 chr2B 96.648 716 24 0 1 716 45625608 45624893 0.000000e+00 1190.0
3 TraesCS2B01G081600 chr2B 89.055 201 22 0 512 712 45690651 45690451 1.390000e-62 250.0
4 TraesCS2B01G081600 chr2B 88.060 201 24 0 510 710 45031140 45031340 3.020000e-59 239.0
5 TraesCS2B01G081600 chr2A 90.417 1607 82 26 712 2267 30313523 30311938 0.000000e+00 2049.0
6 TraesCS2B01G081600 chr2A 91.667 492 41 0 2 493 30303440 30302949 0.000000e+00 682.0
7 TraesCS2B01G081600 chr2A 90.669 493 46 0 1 493 30253990 30254482 0.000000e+00 656.0
8 TraesCS2B01G081600 chr2A 90.467 493 47 0 1 493 30269638 30270130 0.000000e+00 651.0
9 TraesCS2B01G081600 chr2A 90.061 493 49 0 1 493 30244388 30244880 7.080000e-180 640.0
10 TraesCS2B01G081600 chr2A 93.659 205 13 0 512 716 30302957 30302753 8.160000e-80 307.0
11 TraesCS2B01G081600 chr2A 88.060 201 24 0 510 710 30162926 30163126 3.020000e-59 239.0
12 TraesCS2B01G081600 chr2A 81.739 115 14 5 1446 1555 30312280 30312168 3.220000e-14 89.8
13 TraesCS2B01G081600 chr2D 88.933 1518 89 30 876 2351 28429256 28427776 0.000000e+00 1799.0
14 TraesCS2B01G081600 chr2D 90.467 493 47 0 1 493 28416112 28416604 0.000000e+00 651.0
15 TraesCS2B01G081600 chr2D 87.440 207 26 0 504 710 27977077 27977283 3.020000e-59 239.0
16 TraesCS2B01G081600 chr2D 88.060 201 24 0 510 710 27999774 27999974 3.020000e-59 239.0
17 TraesCS2B01G081600 chr2D 87.065 201 26 0 510 710 27958791 27958591 6.540000e-56 228.0
18 TraesCS2B01G081600 chr7D 90.061 493 49 0 2 494 302746052 302745560 7.080000e-180 640.0
19 TraesCS2B01G081600 chr7A 85.153 229 27 3 1079 1300 469981671 469981443 6.540000e-56 228.0


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 TraesCS2B01G081600 chr2B 45616563 45618913 2350 False 4342.0 4342 100.000 1 2351 1 chr2B.!!$F2 2350
1 TraesCS2B01G081600 chr2B 44926239 44926954 715 True 1206.0 1206 97.067 1 716 1 chr2B.!!$R1 715
2 TraesCS2B01G081600 chr2B 45624893 45625608 715 True 1190.0 1190 96.648 1 716 1 chr2B.!!$R2 715
3 TraesCS2B01G081600 chr2A 30311938 30313523 1585 True 1069.4 2049 86.078 712 2267 2 chr2A.!!$R2 1555
4 TraesCS2B01G081600 chr2A 30302753 30303440 687 True 494.5 682 92.663 2 716 2 chr2A.!!$R1 714
5 TraesCS2B01G081600 chr2D 28427776 28429256 1480 True 1799.0 1799 88.933 876 2351 1 chr2D.!!$R2 1475

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
797 798 0.543277 TCCACTTAGCAGATGGGCTG 59.457 55.0 0.0 0.0 45.44 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 1719 0.855349 GCTTGCAGTATCATCGGTCG 59.145 55.0 0.0 0.0 0.0 4.79 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
86 87 3.864789 ATCATATCCACCAGGTTCACC 57.135 47.619 0.00 0.00 35.89 4.02
126 127 1.134670 GCAACTAGGCTCTTGTCGGAT 60.135 52.381 0.00 0.00 0.00 4.18
148 149 7.334921 CGGATTTGAACCTACCAACATAAACTA 59.665 37.037 0.00 0.00 0.00 2.24
157 158 8.608598 ACCTACCAACATAAACTAAACCAGTAT 58.391 33.333 0.00 0.00 36.04 2.12
171 172 4.844349 ACCAGTATAGGTTGTGCTGATT 57.156 40.909 0.00 0.00 39.34 2.57
190 191 5.556915 TGATTGTATGGACCGAAGAAAACT 58.443 37.500 0.00 0.00 0.00 2.66
721 722 5.788533 TGGGTTGATACTAGTATATTGGGGG 59.211 44.000 15.42 0.00 0.00 5.40
734 735 3.855255 ATTGGGGGTTTTGTTTTGGAG 57.145 42.857 0.00 0.00 0.00 3.86
751 752 5.736951 TTGGAGAAAATGTATTGGGGTTG 57.263 39.130 0.00 0.00 0.00 3.77
756 757 5.899278 AGAAAATGTATTGGGGTTGTAGGT 58.101 37.500 0.00 0.00 0.00 3.08
775 776 2.976840 GCCGCTCATTTGCCGAACA 61.977 57.895 0.00 0.00 0.00 3.18
782 783 3.244976 CTCATTTGCCGAACATTTCCAC 58.755 45.455 0.00 0.00 0.00 4.02
789 790 2.159517 GCCGAACATTTCCACTTAGCAG 60.160 50.000 0.00 0.00 0.00 4.24
797 798 0.543277 TCCACTTAGCAGATGGGCTG 59.457 55.000 0.00 0.00 45.44 4.85
799 800 1.340405 CCACTTAGCAGATGGGCTGTT 60.340 52.381 0.00 0.00 46.62 3.16
817 818 1.666189 GTTAGAAGGTCAATCTGCGGC 59.334 52.381 0.00 0.00 0.00 6.53
848 849 5.180680 ACTTAGCCGAACATTTCCACTTTAC 59.819 40.000 0.00 0.00 0.00 2.01
852 853 5.766174 AGCCGAACATTTCCACTTTACTTTA 59.234 36.000 0.00 0.00 0.00 1.85
938 961 3.873805 GCAAAAGGCAACAGAGGTC 57.126 52.632 0.00 0.00 43.97 3.85
994 1023 4.527583 GGAGCAGAGCCGCCAGAG 62.528 72.222 0.00 0.00 0.00 3.35
1376 1414 2.672908 GGTTAGTTCCCACCCCCG 59.327 66.667 0.00 0.00 0.00 5.73
1388 1427 3.781307 CCCCCGGTGATGCTTCGA 61.781 66.667 0.00 0.00 0.00 3.71
1396 1435 2.910482 CGGTGATGCTTCGATTTGTTTG 59.090 45.455 0.00 0.00 0.00 2.93
1397 1436 2.663119 GGTGATGCTTCGATTTGTTTGC 59.337 45.455 0.00 0.00 0.00 3.68
1398 1437 3.568538 GTGATGCTTCGATTTGTTTGCT 58.431 40.909 0.00 0.00 0.00 3.91
1440 1493 3.289704 TTCGACGCAATGCCTCGGA 62.290 57.895 22.16 14.00 37.59 4.55
1480 1533 8.956426 TCCTTTTTAATAGAAATGCTGTAGTGG 58.044 33.333 0.00 0.00 0.00 4.00
1499 1552 5.865085 AGTGGTCTGTAGCAACTTGAATTA 58.135 37.500 0.00 0.00 34.25 1.40
1525 1578 5.951747 TGGGAATAAGTGAAGAATTTCCTGG 59.048 40.000 0.00 0.00 30.65 4.45
1609 1662 2.034432 TGTTGCGTGATGCTTTGAATGT 59.966 40.909 0.00 0.00 46.63 2.71
1628 1681 9.797642 TTGAATGTTGAATATAGATATGCCTGT 57.202 29.630 0.00 0.00 0.00 4.00
1659 1712 5.566826 CGTTGGAAGGACTCTCTAAATGTGA 60.567 44.000 0.00 0.00 0.00 3.58
1666 1719 5.104735 AGGACTCTCTAAATGTGATTCCCAC 60.105 44.000 0.00 0.00 45.88 4.61
1727 1780 3.157087 TCTTGATTTTGAGGCCCAGTTC 58.843 45.455 0.00 0.00 0.00 3.01
1764 1817 7.617041 AGCAGATTTCATTTAGGTACTGTTC 57.383 36.000 0.00 0.00 41.52 3.18
1775 1836 7.886629 TTTAGGTACTGTTCGTATGATAGGT 57.113 36.000 0.00 0.00 41.52 3.08
1821 1885 5.945144 ATTTAGATTTGGGAAATGCAGCT 57.055 34.783 0.00 0.00 0.00 4.24
1837 1901 4.516323 TGCAGCTATCAAGACATGCTTTA 58.484 39.130 0.00 0.00 33.60 1.85
1924 1989 6.677781 TTTAGATTGATTTTAGCACCCTCG 57.322 37.500 0.00 0.00 0.00 4.63
1936 2001 1.737793 GCACCCTCGTTCCAATACAAG 59.262 52.381 0.00 0.00 0.00 3.16
1938 2003 3.670625 CACCCTCGTTCCAATACAAGAA 58.329 45.455 0.00 0.00 0.00 2.52
1940 2005 3.326880 ACCCTCGTTCCAATACAAGAAGT 59.673 43.478 0.00 0.00 0.00 3.01
1944 2009 5.238650 CCTCGTTCCAATACAAGAAGTTGTT 59.761 40.000 0.00 0.00 45.00 2.83
1945 2010 6.425721 CCTCGTTCCAATACAAGAAGTTGTTA 59.574 38.462 0.00 0.00 45.00 2.41
1946 2011 7.181143 TCGTTCCAATACAAGAAGTTGTTAC 57.819 36.000 0.00 0.00 45.00 2.50
1947 2012 6.987992 TCGTTCCAATACAAGAAGTTGTTACT 59.012 34.615 0.00 0.00 45.00 2.24
1948 2013 7.170320 TCGTTCCAATACAAGAAGTTGTTACTC 59.830 37.037 0.00 0.00 45.00 2.59
1949 2014 7.042321 CGTTCCAATACAAGAAGTTGTTACTCA 60.042 37.037 0.00 0.00 45.00 3.41
1950 2015 8.784043 GTTCCAATACAAGAAGTTGTTACTCAT 58.216 33.333 0.00 0.00 45.00 2.90
1951 2016 8.918202 TCCAATACAAGAAGTTGTTACTCATT 57.082 30.769 0.00 0.00 45.00 2.57
1952 2017 8.999431 TCCAATACAAGAAGTTGTTACTCATTC 58.001 33.333 0.00 0.00 45.00 2.67
1953 2018 8.237267 CCAATACAAGAAGTTGTTACTCATTCC 58.763 37.037 0.00 0.00 45.00 3.01
1954 2019 5.924475 ACAAGAAGTTGTTACTCATTCCG 57.076 39.130 0.00 0.00 45.00 4.30
1955 2020 4.755123 ACAAGAAGTTGTTACTCATTCCGG 59.245 41.667 0.00 0.00 45.00 5.14
1956 2021 4.884668 AGAAGTTGTTACTCATTCCGGA 57.115 40.909 0.00 0.00 31.99 5.14
1957 2022 4.822026 AGAAGTTGTTACTCATTCCGGAG 58.178 43.478 3.34 0.00 40.79 4.63
1958 2023 2.973945 AGTTGTTACTCATTCCGGAGC 58.026 47.619 3.34 0.00 38.50 4.70
2090 2156 1.065401 TGTTGTAACTGTTGCAGCTGC 59.935 47.619 31.89 31.89 42.50 5.25
2092 2158 1.172180 TGTAACTGTTGCAGCTGCCC 61.172 55.000 34.64 24.78 41.18 5.36
2100 2166 0.179078 TTGCAGCTGCCCTGTTTTTG 60.179 50.000 34.64 0.00 43.71 2.44
2137 2206 2.867109 AGTTGCAGACTGGCTGTTAT 57.133 45.000 12.93 0.00 46.62 1.89
2139 2208 1.470098 GTTGCAGACTGGCTGTTATGG 59.530 52.381 12.93 0.00 46.62 2.74
2194 2263 0.531657 TGATTTGGGAAATGCAGCCG 59.468 50.000 0.00 0.00 0.00 5.52
2208 2277 1.470890 GCAGCCGTGCCTAACAAATTA 59.529 47.619 0.00 0.00 44.72 1.40
2283 2352 9.645059 TGTAAATTTTTGTGTGAGATGTTTGAA 57.355 25.926 0.00 0.00 0.00 2.69
2311 2380 4.522789 TGCCTAGAAAATTCCTTGGAACAC 59.477 41.667 4.00 0.00 39.29 3.32
2327 2396 1.279025 ACACTTGGTGGAGGTGTGGT 61.279 55.000 2.75 0.00 41.75 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.700213 GCACCCGCCATAGAAATATAATGT 59.300 41.667 0.00 0.00 0.00 2.71
126 127 8.631797 GGTTTAGTTTATGTTGGTAGGTTCAAA 58.368 33.333 0.00 0.00 0.00 2.69
157 158 4.513442 GTCCATACAATCAGCACAACCTA 58.487 43.478 0.00 0.00 0.00 3.08
171 172 5.733620 ACTAGTTTTCTTCGGTCCATACA 57.266 39.130 0.00 0.00 0.00 2.29
190 191 7.103641 CAGGACATTCTTAAAGCTACCAACTA 58.896 38.462 0.00 0.00 0.00 2.24
721 722 8.341903 CCCAATACATTTTCTCCAAAACAAAAC 58.658 33.333 0.00 0.00 34.24 2.43
734 735 5.623596 GCACCTACAACCCCAATACATTTTC 60.624 44.000 0.00 0.00 0.00 2.29
751 752 1.429423 GCAAATGAGCGGCACCTAC 59.571 57.895 1.45 0.00 0.00 3.18
756 757 2.671276 TTCGGCAAATGAGCGGCA 60.671 55.556 1.45 0.00 35.13 5.69
775 776 2.243221 AGCCCATCTGCTAAGTGGAAAT 59.757 45.455 0.00 0.00 40.56 2.17
782 783 3.827008 TCTAACAGCCCATCTGCTAAG 57.173 47.619 0.00 0.00 46.76 2.18
789 790 3.350219 TTGACCTTCTAACAGCCCATC 57.650 47.619 0.00 0.00 0.00 3.51
797 798 1.666189 GCCGCAGATTGACCTTCTAAC 59.334 52.381 0.00 0.00 0.00 2.34
799 800 0.178068 GGCCGCAGATTGACCTTCTA 59.822 55.000 0.00 0.00 0.00 2.10
848 849 4.308265 GGCTATAAGAAGGCCGACTAAAG 58.692 47.826 0.00 1.19 36.37 1.85
909 928 2.434331 CTTTTGCCGGAGTGGGGA 59.566 61.111 5.05 0.00 38.63 4.81
961 984 2.509336 CCTCCGTGTGGTGCGATC 60.509 66.667 0.00 0.00 36.30 3.69
965 988 4.314440 TGCTCCTCCGTGTGGTGC 62.314 66.667 10.26 10.26 42.44 5.01
988 1017 2.828145 GCTCATCTCCCCTCTGGC 59.172 66.667 0.00 0.00 0.00 4.85
989 1018 2.506061 CCGCTCATCTCCCCTCTGG 61.506 68.421 0.00 0.00 0.00 3.86
993 1022 2.123077 CTCCCGCTCATCTCCCCT 60.123 66.667 0.00 0.00 0.00 4.79
994 1023 3.934962 GCTCCCGCTCATCTCCCC 61.935 72.222 0.00 0.00 0.00 4.81
1023 1061 3.723348 GGCACCCGCGACTTGAAC 61.723 66.667 8.23 0.00 39.92 3.18
1185 1223 1.028868 GCTTGACCTGGGTGAGCATC 61.029 60.000 15.44 0.00 35.37 3.91
1376 1414 2.663119 GCAAACAAATCGAAGCATCACC 59.337 45.455 0.00 0.00 0.00 4.02
1388 1427 1.948834 GGCAGGCAAAAGCAAACAAAT 59.051 42.857 0.00 0.00 0.00 2.32
1480 1533 6.374333 TCCCATTAATTCAAGTTGCTACAGAC 59.626 38.462 0.13 0.00 0.00 3.51
1499 1552 7.124750 CCAGGAAATTCTTCACTTATTCCCATT 59.875 37.037 0.00 0.00 37.61 3.16
1525 1578 8.665685 ACAATCAGTAGTAAAATTGAACGATCC 58.334 33.333 0.00 0.00 34.12 3.36
1628 1681 5.014858 AGAGAGTCCTTCCAACGTGTATTA 58.985 41.667 0.00 0.00 0.00 0.98
1659 1712 2.035961 CAGTATCATCGGTCGTGGGAAT 59.964 50.000 0.00 0.00 0.00 3.01
1666 1719 0.855349 GCTTGCAGTATCATCGGTCG 59.145 55.000 0.00 0.00 0.00 4.79
1764 1817 7.603651 AGTATAGCCAAAAGACCTATCATACG 58.396 38.462 0.00 0.00 0.00 3.06
1805 1869 4.957954 TCTTGATAGCTGCATTTCCCAAAT 59.042 37.500 1.02 0.00 0.00 2.32
1813 1877 3.552875 AGCATGTCTTGATAGCTGCATT 58.447 40.909 1.02 0.00 33.67 3.56
1915 1980 0.981183 TGTATTGGAACGAGGGTGCT 59.019 50.000 0.00 0.00 0.00 4.40
1924 1989 8.149973 TGAGTAACAACTTCTTGTATTGGAAC 57.850 34.615 0.00 0.00 39.88 3.62
1936 2001 3.371285 GCTCCGGAATGAGTAACAACTTC 59.629 47.826 5.23 0.00 34.74 3.01
1938 2003 2.301870 TGCTCCGGAATGAGTAACAACT 59.698 45.455 5.23 0.00 34.74 3.16
1940 2005 2.301870 ACTGCTCCGGAATGAGTAACAA 59.698 45.455 5.23 0.00 34.74 2.83
1944 2009 4.038042 CAGATTACTGCTCCGGAATGAGTA 59.962 45.833 5.23 9.11 37.33 2.59
1945 2010 3.034635 AGATTACTGCTCCGGAATGAGT 58.965 45.455 5.23 10.16 34.74 3.41
1946 2011 3.181471 ACAGATTACTGCTCCGGAATGAG 60.181 47.826 5.23 3.91 46.95 2.90
1947 2012 2.766263 ACAGATTACTGCTCCGGAATGA 59.234 45.455 5.23 0.00 46.95 2.57
1948 2013 2.868583 CACAGATTACTGCTCCGGAATG 59.131 50.000 5.23 0.53 46.95 2.67
1949 2014 2.766263 TCACAGATTACTGCTCCGGAAT 59.234 45.455 5.23 0.00 46.95 3.01
1950 2015 2.176045 TCACAGATTACTGCTCCGGAA 58.824 47.619 5.23 0.00 46.95 4.30
1951 2016 1.847328 TCACAGATTACTGCTCCGGA 58.153 50.000 2.93 2.93 46.95 5.14
1952 2017 2.159043 ACATCACAGATTACTGCTCCGG 60.159 50.000 0.00 0.00 46.95 5.14
1953 2018 3.119291 GACATCACAGATTACTGCTCCG 58.881 50.000 0.00 0.00 46.95 4.63
1954 2019 4.399004 AGACATCACAGATTACTGCTCC 57.601 45.455 0.00 0.00 46.95 4.70
1955 2020 5.290643 GTCAAGACATCACAGATTACTGCTC 59.709 44.000 0.00 0.00 46.95 4.26
1956 2021 5.046735 AGTCAAGACATCACAGATTACTGCT 60.047 40.000 2.72 0.00 46.95 4.24
1957 2022 5.174395 AGTCAAGACATCACAGATTACTGC 58.826 41.667 2.72 0.00 46.95 4.40
2062 2128 5.666462 TGCAACAGTTACAACAGACTTAGA 58.334 37.500 0.00 0.00 0.00 2.10
2090 2156 3.304659 CGAACTGGACATCAAAAACAGGG 60.305 47.826 0.00 0.00 33.63 4.45
2092 2158 4.811555 TCGAACTGGACATCAAAAACAG 57.188 40.909 0.00 0.00 35.40 3.16
2100 2166 5.106712 TGCAACTTTTATCGAACTGGACATC 60.107 40.000 0.00 0.00 0.00 3.06
2137 2206 3.953612 CCATGAAGTATAGGCAAAAGCCA 59.046 43.478 9.42 0.00 0.00 4.75
2139 2208 3.969899 GCCATGAAGTATAGGCAAAAGC 58.030 45.455 0.00 0.00 46.26 3.51
2194 2263 7.422399 TGAACTTCTTGTAATTTGTTAGGCAC 58.578 34.615 0.00 0.00 0.00 5.01
2208 2277 8.682936 AAACACATTCTAGATGAACTTCTTGT 57.317 30.769 0.00 0.00 37.52 3.16
2283 2352 6.731467 TCCAAGGAATTTTCTAGGCATTACT 58.269 36.000 0.00 0.00 0.00 2.24
2311 2380 1.133792 AGAAACCACACCTCCACCAAG 60.134 52.381 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.