Multiple sequence alignment - TraesCS4B01G309700

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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 TraesCS4B01G309700 chr4B 100.000 2627 0 0 1 2627 600432677 600430051 0.000000e+00 4852
1 TraesCS4B01G309700 chr4B 87.507 1825 201 15 3 1812 600376921 600378733 0.000000e+00 2082
2 TraesCS4B01G309700 chr4B 92.806 278 20 0 1865 2142 600424199 600423922 1.130000e-108 403
3 TraesCS4B01G309700 chr4D 95.610 1845 71 5 1 1836 476198896 476197053 0.000000e+00 2950
4 TraesCS4B01G309700 chr4D 87.638 1715 197 9 3 1711 475954016 475952311 0.000000e+00 1978
5 TraesCS4B01G309700 chr4A 94.869 1871 76 10 1 1864 683258481 683256624 0.000000e+00 2905
6 TraesCS4B01G309700 chr4A 87.588 1853 187 27 1 1816 682991706 682989860 0.000000e+00 2108
7 TraesCS4B01G309700 chr5B 78.440 1192 236 14 3 1179 420012260 420013445 0.000000e+00 758
8 TraesCS4B01G309700 chr5A 78.072 1172 235 14 3 1158 413220731 413221896 0.000000e+00 721
9 TraesCS4B01G309700 chr1B 81.593 766 130 10 1865 2624 435753855 435754615 7.980000e-175 623
10 TraesCS4B01G309700 chr1D 79.716 774 134 22 1865 2624 231012212 231012976 2.980000e-149 538
11 TraesCS4B01G309700 chr5D 79.275 772 141 17 1863 2624 553047972 553048734 3.000000e-144 521
12 TraesCS4B01G309700 chr5D 78.506 656 125 14 1979 2624 123943874 123944523 1.450000e-112 416


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 TraesCS4B01G309700 chr4B 600430051 600432677 2626 True 4852 4852 100.000 1 2627 1 chr4B.!!$R2 2626
1 TraesCS4B01G309700 chr4B 600376921 600378733 1812 False 2082 2082 87.507 3 1812 1 chr4B.!!$F1 1809
2 TraesCS4B01G309700 chr4D 476197053 476198896 1843 True 2950 2950 95.610 1 1836 1 chr4D.!!$R2 1835
3 TraesCS4B01G309700 chr4D 475952311 475954016 1705 True 1978 1978 87.638 3 1711 1 chr4D.!!$R1 1708
4 TraesCS4B01G309700 chr4A 683256624 683258481 1857 True 2905 2905 94.869 1 1864 1 chr4A.!!$R2 1863
5 TraesCS4B01G309700 chr4A 682989860 682991706 1846 True 2108 2108 87.588 1 1816 1 chr4A.!!$R1 1815
6 TraesCS4B01G309700 chr5B 420012260 420013445 1185 False 758 758 78.440 3 1179 1 chr5B.!!$F1 1176
7 TraesCS4B01G309700 chr5A 413220731 413221896 1165 False 721 721 78.072 3 1158 1 chr5A.!!$F1 1155
8 TraesCS4B01G309700 chr1B 435753855 435754615 760 False 623 623 81.593 1865 2624 1 chr1B.!!$F1 759
9 TraesCS4B01G309700 chr1D 231012212 231012976 764 False 538 538 79.716 1865 2624 1 chr1D.!!$F1 759
10 TraesCS4B01G309700 chr5D 553047972 553048734 762 False 521 521 79.275 1863 2624 1 chr5D.!!$F2 761
11 TraesCS4B01G309700 chr5D 123943874 123944523 649 False 416 416 78.506 1979 2624 1 chr5D.!!$F1 645


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
27 28 1.707632 CTGCTGTTCCTTGTCGAGAG 58.292 55.0 0.0 0.00 0.0 3.20 F
1223 1239 0.252057 TCCATCACGGTGGAGAAGGA 60.252 55.0 8.5 6.13 43.2 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 1598 0.596600 TCCAACGCTGACTTGACGAC 60.597 55.0 0.00 0.0 0.00 4.34 R
2034 2107 0.034477 CCGAAATGGGCCTAACTGGT 60.034 55.0 4.53 0.0 38.35 4.00 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
27 28 1.707632 CTGCTGTTCCTTGTCGAGAG 58.292 55.000 0.00 0.00 0.00 3.20
709 716 1.841302 TTGTCAAGAGGCTGGCCGAT 61.841 55.000 5.93 0.00 41.95 4.18
1057 1073 1.211703 TCATATTGGCTCTTGGCGGAA 59.788 47.619 0.00 0.00 42.94 4.30
1163 1179 3.753434 CGACGAGTGGCAGCTCCT 61.753 66.667 10.22 0.00 35.26 3.69
1179 1195 0.487325 TCCTTCTGAGAGGGGTCACA 59.513 55.000 10.97 0.00 37.41 3.58
1223 1239 0.252057 TCCATCACGGTGGAGAAGGA 60.252 55.000 8.50 6.13 43.20 3.36
1481 1497 1.989508 TGGAGCTCGGCATGGAGAA 60.990 57.895 7.83 0.00 36.08 2.87
1582 1598 2.022129 GACACCAGCGTCTGTTCCG 61.022 63.158 6.19 0.00 32.92 4.30
1647 1672 4.862641 AGCCCTCAAACTACCACATATT 57.137 40.909 0.00 0.00 0.00 1.28
1651 1676 6.069615 AGCCCTCAAACTACCACATATTTACT 60.070 38.462 0.00 0.00 0.00 2.24
1653 1678 7.110155 CCCTCAAACTACCACATATTTACTGT 58.890 38.462 0.00 0.00 0.00 3.55
1654 1679 8.262227 CCCTCAAACTACCACATATTTACTGTA 58.738 37.037 0.00 0.00 0.00 2.74
1655 1680 9.832445 CCTCAAACTACCACATATTTACTGTAT 57.168 33.333 0.00 0.00 0.00 2.29
1739 1788 5.114785 GTGTATCATCTCACGCTACTCAT 57.885 43.478 0.00 0.00 0.00 2.90
1881 1942 4.347607 TCATCTGTGAGGTCTCAATCTCA 58.652 43.478 1.86 0.00 41.85 3.27
1900 1961 1.661617 CAAATTGCATTCACCATGGCG 59.338 47.619 13.04 1.26 32.81 5.69
1906 1967 1.536709 GCATTCACCATGGCGGAATTC 60.537 52.381 22.97 17.29 38.63 2.17
1927 1990 1.475213 GCTTACAAGGAAGGGGATCGG 60.475 57.143 0.00 0.00 0.00 4.18
1928 1991 2.116238 CTTACAAGGAAGGGGATCGGA 58.884 52.381 0.00 0.00 0.00 4.55
1945 2012 1.491668 GGAGGAGAGGAGGAAGAACC 58.508 60.000 0.00 0.00 39.35 3.62
1949 2016 1.828595 GGAGAGGAGGAAGAACCACTC 59.171 57.143 0.00 0.00 41.79 3.51
1956 2023 2.894126 GAGGAAGAACCACTCTCTCACA 59.106 50.000 0.00 0.00 42.04 3.58
1957 2024 3.513515 GAGGAAGAACCACTCTCTCACAT 59.486 47.826 0.00 0.00 42.04 3.21
1965 2032 4.865905 ACCACTCTCTCACATCATCTACT 58.134 43.478 0.00 0.00 0.00 2.57
1969 2036 5.050159 CACTCTCTCACATCATCTACTCTCG 60.050 48.000 0.00 0.00 0.00 4.04
2004 2073 3.204467 TTTGCCAGCCGCCTACCTT 62.204 57.895 0.00 0.00 36.24 3.50
2005 2074 2.706952 TTTGCCAGCCGCCTACCTTT 62.707 55.000 0.00 0.00 36.24 3.11
2006 2075 2.824489 GCCAGCCGCCTACCTTTC 60.824 66.667 0.00 0.00 0.00 2.62
2008 2077 2.670148 CCAGCCGCCTACCTTTCCT 61.670 63.158 0.00 0.00 0.00 3.36
2009 2078 1.335132 CCAGCCGCCTACCTTTCCTA 61.335 60.000 0.00 0.00 0.00 2.94
2010 2079 0.179081 CAGCCGCCTACCTTTCCTAC 60.179 60.000 0.00 0.00 0.00 3.18
2011 2080 1.145598 GCCGCCTACCTTTCCTACC 59.854 63.158 0.00 0.00 0.00 3.18
2012 2081 1.619807 GCCGCCTACCTTTCCTACCA 61.620 60.000 0.00 0.00 0.00 3.25
2013 2082 0.464452 CCGCCTACCTTTCCTACCAG 59.536 60.000 0.00 0.00 0.00 4.00
2014 2083 0.179081 CGCCTACCTTTCCTACCAGC 60.179 60.000 0.00 0.00 0.00 4.85
2016 2085 0.464452 CCTACCTTTCCTACCAGCCG 59.536 60.000 0.00 0.00 0.00 5.52
2018 2087 1.136500 CTACCTTTCCTACCAGCCGTC 59.864 57.143 0.00 0.00 0.00 4.79
2021 2090 1.136500 CCTTTCCTACCAGCCGTCTAC 59.864 57.143 0.00 0.00 0.00 2.59
2022 2091 1.822990 CTTTCCTACCAGCCGTCTACA 59.177 52.381 0.00 0.00 0.00 2.74
2030 2103 5.243283 CCTACCAGCCGTCTACAATATAAGT 59.757 44.000 0.00 0.00 0.00 2.24
2032 2105 6.081872 ACCAGCCGTCTACAATATAAGTAC 57.918 41.667 0.00 0.00 0.00 2.73
2033 2106 5.595542 ACCAGCCGTCTACAATATAAGTACA 59.404 40.000 0.00 0.00 0.00 2.90
2034 2107 6.097270 ACCAGCCGTCTACAATATAAGTACAA 59.903 38.462 0.00 0.00 0.00 2.41
2074 2147 3.003173 AGCCAGCTGAGCGGGTAA 61.003 61.111 23.98 0.00 45.32 2.85
2097 2170 2.743928 GCTGCCTCTTGGACCACG 60.744 66.667 0.00 0.00 34.57 4.94
2162 2235 3.508952 ATCCCTCCTCCCTTAGAAACA 57.491 47.619 0.00 0.00 0.00 2.83
2163 2236 3.285290 TCCCTCCTCCCTTAGAAACAA 57.715 47.619 0.00 0.00 0.00 2.83
2168 2241 4.202472 CCTCCTCCCTTAGAAACAACTTGT 60.202 45.833 0.00 0.00 0.00 3.16
2192 2265 4.162690 GCCGGTGCTCTCGGGAAT 62.163 66.667 1.90 0.00 46.86 3.01
2238 2311 1.064463 CCCAAGTAGCCATGTCCACAT 60.064 52.381 0.00 0.00 36.96 3.21
2260 2333 1.271001 TGCATCACTCCACTTGACCAG 60.271 52.381 0.00 0.00 0.00 4.00
2291 2364 2.711922 GGAGTCAGATCCACGCCGT 61.712 63.158 0.19 0.00 39.34 5.68
2293 2366 0.454600 GAGTCAGATCCACGCCGTAA 59.545 55.000 0.00 0.00 0.00 3.18
2297 2370 0.527817 CAGATCCACGCCGTAAGACC 60.528 60.000 0.00 0.00 43.02 3.85
2348 2426 3.539604 GAACTGATCATCAGGTGAAGGG 58.460 50.000 19.17 0.00 45.99 3.95
2414 2492 2.816087 CAAGGAGACATGAAACACTGGG 59.184 50.000 0.00 0.00 0.00 4.45
2424 2502 0.923358 AAACACTGGGTGGACCTTGA 59.077 50.000 2.75 0.00 41.11 3.02
2501 2579 6.773976 TCAAATGGCCCATAGAACTTAAAG 57.226 37.500 0.00 0.00 0.00 1.85
2504 2582 2.580783 TGGCCCATAGAACTTAAAGGCT 59.419 45.455 0.00 0.00 38.95 4.58
2513 2591 7.389053 CCATAGAACTTAAAGGCTAGCTTATGG 59.611 40.741 15.72 9.63 0.00 2.74
2549 2627 1.079503 CTGAAGCTTGAAGGTACGGC 58.920 55.000 2.10 0.00 0.00 5.68
2558 2636 1.079503 GAAGGTACGGCTGAAGCTTG 58.920 55.000 2.10 0.00 41.70 4.01
2606 2684 4.758688 ACTCATGATCAGTGCGATGTTTA 58.241 39.130 0.09 0.00 33.17 2.01
2624 2702 5.744171 TGTTTATCAGCTTGGCTCTTCATA 58.256 37.500 0.00 0.00 36.40 2.15
2625 2703 5.586243 TGTTTATCAGCTTGGCTCTTCATAC 59.414 40.000 0.00 0.00 36.40 2.39
2626 2704 2.299993 TCAGCTTGGCTCTTCATACG 57.700 50.000 0.00 0.00 36.40 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.666596 CTTCCACTCCCATAGCGCCC 62.667 65.000 2.29 0.00 0.00 6.13
206 207 1.811266 CCGCGGTGATGAGGTCTTG 60.811 63.158 19.50 0.00 0.00 3.02
208 209 3.461773 CCCGCGGTGATGAGGTCT 61.462 66.667 26.12 0.00 0.00 3.85
404 405 1.807165 CGGTGAGCATGGACACGAG 60.807 63.158 0.00 0.00 37.82 4.18
465 466 3.092192 GACGCGACGGACTCGATGA 62.092 63.158 15.93 0.00 46.14 2.92
1042 1058 1.852157 ATCCTTCCGCCAAGAGCCAA 61.852 55.000 0.00 0.00 38.78 4.52
1163 1179 1.633774 GACTGTGACCCCTCTCAGAA 58.366 55.000 6.76 0.00 39.46 3.02
1223 1239 5.114780 CGATGAAGATGTTGAGGATCTTGT 58.885 41.667 0.00 0.00 39.72 3.16
1481 1497 3.753434 CCACGCTCCTCAGCTCGT 61.753 66.667 0.00 0.00 44.40 4.18
1582 1598 0.596600 TCCAACGCTGACTTGACGAC 60.597 55.000 0.00 0.00 0.00 4.34
1695 1723 8.492673 ACACGATGAGTAACAAATCATAATGT 57.507 30.769 0.00 0.00 36.30 2.71
1842 1903 8.100164 TCACAGATGATTAGTTGTGTTAATCCA 58.900 33.333 3.73 0.00 41.19 3.41
1844 1905 8.607459 CCTCACAGATGATTAGTTGTGTTAATC 58.393 37.037 3.73 0.00 41.19 1.75
1881 1942 1.405797 CCGCCATGGTGAATGCAATTT 60.406 47.619 27.12 0.00 36.07 1.82
1900 1961 2.683362 CCCTTCCTTGTAAGCGAATTCC 59.317 50.000 0.00 0.00 0.00 3.01
1906 1967 1.806623 CGATCCCCTTCCTTGTAAGCG 60.807 57.143 0.00 0.00 0.00 4.68
1927 1990 1.828595 GTGGTTCTTCCTCCTCTCCTC 59.171 57.143 0.00 0.00 37.07 3.71
1928 1991 1.435168 AGTGGTTCTTCCTCCTCTCCT 59.565 52.381 0.00 0.00 37.07 3.69
1945 2012 5.050159 CGAGAGTAGATGATGTGAGAGAGTG 60.050 48.000 0.00 0.00 0.00 3.51
1949 2016 3.563390 TGCGAGAGTAGATGATGTGAGAG 59.437 47.826 0.00 0.00 0.00 3.20
1950 2017 3.545703 TGCGAGAGTAGATGATGTGAGA 58.454 45.455 0.00 0.00 0.00 3.27
1956 2023 6.810911 AGTTTGTAATGCGAGAGTAGATGAT 58.189 36.000 0.00 0.00 0.00 2.45
1957 2024 6.208988 AGTTTGTAATGCGAGAGTAGATGA 57.791 37.500 0.00 0.00 0.00 2.92
1965 2032 2.094390 ACGGCTAGTTTGTAATGCGAGA 60.094 45.455 0.00 0.00 0.00 4.04
2004 2073 1.927487 TTGTAGACGGCTGGTAGGAA 58.073 50.000 0.00 0.00 0.00 3.36
2005 2074 2.154567 ATTGTAGACGGCTGGTAGGA 57.845 50.000 0.00 0.00 0.00 2.94
2006 2075 5.243283 ACTTATATTGTAGACGGCTGGTAGG 59.757 44.000 0.00 0.00 0.00 3.18
2008 2077 6.772233 TGTACTTATATTGTAGACGGCTGGTA 59.228 38.462 0.00 0.00 0.00 3.25
2009 2078 5.595542 TGTACTTATATTGTAGACGGCTGGT 59.404 40.000 0.00 0.00 0.00 4.00
2010 2079 6.080648 TGTACTTATATTGTAGACGGCTGG 57.919 41.667 0.00 0.00 0.00 4.85
2011 2080 6.420008 GGTTGTACTTATATTGTAGACGGCTG 59.580 42.308 0.00 0.00 0.00 4.85
2012 2081 6.097270 TGGTTGTACTTATATTGTAGACGGCT 59.903 38.462 0.00 0.00 0.00 5.52
2013 2082 6.275335 TGGTTGTACTTATATTGTAGACGGC 58.725 40.000 0.00 0.00 0.00 5.68
2014 2083 7.486647 ACTGGTTGTACTTATATTGTAGACGG 58.513 38.462 0.00 0.00 0.00 4.79
2018 2087 9.257651 GCCTAACTGGTTGTACTTATATTGTAG 57.742 37.037 0.00 0.00 38.35 2.74
2021 2090 6.485648 GGGCCTAACTGGTTGTACTTATATTG 59.514 42.308 0.84 0.00 38.35 1.90
2022 2091 6.159046 TGGGCCTAACTGGTTGTACTTATATT 59.841 38.462 4.53 0.00 38.35 1.28
2030 2103 3.692690 GAAATGGGCCTAACTGGTTGTA 58.307 45.455 4.53 0.00 38.35 2.41
2032 2105 1.472480 CGAAATGGGCCTAACTGGTTG 59.528 52.381 4.53 0.00 38.35 3.77
2033 2106 1.615919 CCGAAATGGGCCTAACTGGTT 60.616 52.381 4.53 0.00 38.35 3.67
2034 2107 0.034477 CCGAAATGGGCCTAACTGGT 60.034 55.000 4.53 0.00 38.35 4.00
2060 2133 2.887568 CGCTTACCCGCTCAGCTG 60.888 66.667 7.63 7.63 0.00 4.24
2097 2170 2.427410 CGCAGTTCAAACCAGCGC 60.427 61.111 14.47 0.00 43.40 5.92
2192 2265 2.989840 CAAGGTGACGTTGCAACAAAAA 59.010 40.909 28.01 8.61 0.00 1.94
2238 2311 1.543208 GGTCAAGTGGAGTGATGCACA 60.543 52.381 2.75 0.00 36.74 4.57
2291 2364 0.759959 TCCTGCAACAACGGGTCTTA 59.240 50.000 0.00 0.00 37.37 2.10
2293 2366 0.110486 AATCCTGCAACAACGGGTCT 59.890 50.000 0.00 0.00 37.37 3.85
2348 2426 3.017232 CGAGGTACTGTCGCAACTC 57.983 57.895 5.44 0.00 41.55 3.01
2414 2492 2.039879 ACCACCAACTATCAAGGTCCAC 59.960 50.000 0.00 0.00 32.15 4.02
2424 2502 5.250774 ACAAACTGGATCTACCACCAACTAT 59.749 40.000 0.00 0.00 44.64 2.12
2501 2579 2.485814 GCATGCTAACCATAAGCTAGCC 59.514 50.000 12.13 0.00 40.73 3.93
2504 2582 2.766313 CCGCATGCTAACCATAAGCTA 58.234 47.619 17.13 0.00 40.73 3.32
2513 2591 2.040544 AGTGGTGCCGCATGCTAAC 61.041 57.895 17.13 10.66 42.00 2.34
2526 2604 2.548067 CGTACCTTCAAGCTTCAGTGGT 60.548 50.000 0.00 5.61 0.00 4.16
2549 2627 2.866156 TCGTGTGTTTCTCAAGCTTCAG 59.134 45.455 0.00 0.00 0.00 3.02
2558 2636 3.059597 CAGTTGGTGATCGTGTGTTTCTC 60.060 47.826 0.00 0.00 0.00 2.87
2606 2684 2.831333 CGTATGAAGAGCCAAGCTGAT 58.169 47.619 0.00 0.00 39.88 2.90



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

AutoCloner maintained by Alex Coulton.