Multiple sequence alignment - TraesCS6B01G143400

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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 TraesCS6B01G143400 chr6B 100.000 2378 0 0 1 2378 142990760 142993137 0.000000e+00 4392.0
1 TraesCS6B01G143400 chr6B 92.308 52 4 0 2224 2275 135579575 135579524 9.120000e-10 75.0
2 TraesCS6B01G143400 chr6D 92.760 1464 51 17 142 1578 68080785 68082220 0.000000e+00 2065.0
3 TraesCS6B01G143400 chr6D 91.935 620 34 7 1562 2170 68082245 68082859 0.000000e+00 854.0
4 TraesCS6B01G143400 chr6D 90.909 121 1 3 1 114 68080673 68080790 1.140000e-33 154.0
5 TraesCS6B01G143400 chr6D 89.000 100 5 4 2238 2335 68083299 68083394 4.150000e-23 119.0
6 TraesCS6B01G143400 chr6A 93.304 1374 57 7 144 1505 85572167 85573517 0.000000e+00 1995.0
7 TraesCS6B01G143400 chr6A 91.888 789 37 10 1562 2336 85573618 85574393 0.000000e+00 1077.0
8 TraesCS6B01G143400 chr6A 86.777 121 2 5 1 114 85572055 85572168 3.210000e-24 122.0
9 TraesCS6B01G143400 chr5A 85.915 71 10 0 2213 2283 663727769 663727699 2.530000e-10 76.8
10 TraesCS6B01G143400 chr7B 78.302 106 19 4 2034 2136 666330782 666330886 5.490000e-07 65.8
11 TraesCS6B01G143400 chr4A 100.000 30 0 0 2227 2256 727127347 727127318 3.300000e-04 56.5
12 TraesCS6B01G143400 chr4A 96.970 33 1 0 2224 2256 727194447 727194479 3.300000e-04 56.5
13 TraesCS6B01G143400 chr4A 96.970 33 1 0 2224 2256 727202867 727202899 3.300000e-04 56.5
14 TraesCS6B01G143400 chr2D 86.275 51 3 3 2219 2269 426009434 426009480 4.000000e-03 52.8


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 TraesCS6B01G143400 chr6B 142990760 142993137 2377 False 4392.000000 4392 100.000000 1 2378 1 chr6B.!!$F1 2377
1 TraesCS6B01G143400 chr6D 68080673 68083394 2721 False 798.000000 2065 91.151000 1 2335 4 chr6D.!!$F1 2334
2 TraesCS6B01G143400 chr6A 85572055 85574393 2338 False 1064.666667 1995 90.656333 1 2336 3 chr6A.!!$F1 2335

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
489 502 0.822164 ACCTACTCCACACATACGCC 59.178 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 1976 0.183492 TTTCAGTTGTCCCAGCTGCT 59.817 50.0 8.66 0.0 41.36 4.24 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
63 65 4.006319 AGAGGGAACGTGTGTACTACTAC 58.994 47.826 0.00 0.00 0.00 2.73
64 66 4.006319 GAGGGAACGTGTGTACTACTACT 58.994 47.826 0.00 0.00 0.00 2.57
65 67 5.046304 AGAGGGAACGTGTGTACTACTACTA 60.046 44.000 0.00 0.00 0.00 1.82
120 128 3.591196 TGTATTGGGTACACCGTACAC 57.409 47.619 5.79 3.24 44.64 2.90
121 129 2.896044 TGTATTGGGTACACCGTACACA 59.104 45.455 5.14 5.14 44.64 3.72
122 130 2.460757 ATTGGGTACACCGTACACAC 57.539 50.000 8.69 0.00 44.64 3.82
123 131 4.217466 GTATTGGGTACACCGTACACACG 61.217 52.174 8.69 0.00 44.64 4.49
184 192 4.210120 CAGATCTGCGGTTAATTAGACTGC 59.790 45.833 10.38 17.57 46.94 4.40
398 407 2.080693 ACGTGTAACCGTATCACCGTA 58.919 47.619 0.00 0.00 39.73 4.02
482 495 3.695830 TTCCATTGACCTACTCCACAC 57.304 47.619 0.00 0.00 0.00 3.82
483 496 2.615391 TCCATTGACCTACTCCACACA 58.385 47.619 0.00 0.00 0.00 3.72
489 502 0.822164 ACCTACTCCACACATACGCC 59.178 55.000 0.00 0.00 0.00 5.68
527 540 1.610522 GACAGCCAGCTGAACATTTGT 59.389 47.619 25.66 9.59 46.30 2.83
564 577 4.723309 AGCATACCCATCCAAGAGAAATC 58.277 43.478 0.00 0.00 0.00 2.17
568 581 6.716628 GCATACCCATCCAAGAGAAATCATAA 59.283 38.462 0.00 0.00 0.00 1.90
569 582 7.395489 GCATACCCATCCAAGAGAAATCATAAT 59.605 37.037 0.00 0.00 0.00 1.28
570 583 9.964354 CATACCCATCCAAGAGAAATCATAATA 57.036 33.333 0.00 0.00 0.00 0.98
777 790 0.951558 CTTTGTCTCCAACCCCAACG 59.048 55.000 0.00 0.00 0.00 4.10
809 826 1.631388 CCCCATAATATACACCCGCCA 59.369 52.381 0.00 0.00 0.00 5.69
853 870 1.281925 TGCTTTGATCCCTCCCCCTC 61.282 60.000 0.00 0.00 0.00 4.30
854 871 2.000825 GCTTTGATCCCTCCCCCTCC 62.001 65.000 0.00 0.00 0.00 4.30
855 872 1.308746 TTTGATCCCTCCCCCTCCC 60.309 63.158 0.00 0.00 0.00 4.30
856 873 1.848835 TTTGATCCCTCCCCCTCCCT 61.849 60.000 0.00 0.00 0.00 4.20
857 874 2.205749 GATCCCTCCCCCTCCCTC 59.794 72.222 0.00 0.00 0.00 4.30
858 875 3.462501 ATCCCTCCCCCTCCCTCC 61.463 72.222 0.00 0.00 0.00 4.30
859 876 4.761304 TCCCTCCCCCTCCCTCCT 62.761 72.222 0.00 0.00 0.00 3.69
860 877 4.179599 CCCTCCCCCTCCCTCCTC 62.180 77.778 0.00 0.00 0.00 3.71
861 878 4.179599 CCTCCCCCTCCCTCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
862 879 3.039526 CTCCCCCTCCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
863 880 3.036959 TCCCCCTCCCTCCTCCTC 61.037 72.222 0.00 0.00 0.00 3.71
864 881 4.179599 CCCCCTCCCTCCTCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
865 882 3.039526 CCCCTCCCTCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
866 883 2.612251 CCCTCCCTCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
867 884 2.612251 CCTCCCTCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
956 983 1.374758 CGACCAACCAGCCACTCTC 60.375 63.158 0.00 0.00 0.00 3.20
958 985 2.352805 CCAACCAGCCACTCTCCC 59.647 66.667 0.00 0.00 0.00 4.30
959 986 2.352805 CAACCAGCCACTCTCCCC 59.647 66.667 0.00 0.00 0.00 4.81
960 987 2.936032 AACCAGCCACTCTCCCCC 60.936 66.667 0.00 0.00 0.00 5.40
1398 1425 2.430248 TGATCAAGCTCATGCATGGT 57.570 45.000 25.97 8.94 42.74 3.55
1444 1471 1.296715 GTCATGTGGAAGGACGCCT 59.703 57.895 0.00 0.00 33.87 5.52
1458 1485 3.657537 CGCCTTGTCTTTGCGTAAG 57.342 52.632 0.00 0.00 43.12 2.34
1536 1563 4.022242 TCGGTTTGCCAGTAGATAGATAGC 60.022 45.833 0.00 0.00 34.09 2.97
1551 1589 4.374689 AGATAGCCTCGAGTCTGGAATA 57.625 45.455 12.31 0.00 0.00 1.75
1579 1660 3.135348 TGATGATCTTGTAAGGGCTCTGG 59.865 47.826 0.00 0.00 0.00 3.86
1588 1669 0.689623 AAGGGCTCTGGAACTGACAG 59.310 55.000 0.00 0.00 37.30 3.51
1924 2005 1.956477 GACAACTGAAACTGGTGGCAT 59.044 47.619 0.00 0.00 28.16 4.40
1932 2013 5.772672 ACTGAAACTGGTGGCATAATTAACA 59.227 36.000 0.00 0.00 0.00 2.41
1978 2060 7.255173 GGACTTCTCCTCCTTTTACTGTTTTTC 60.255 40.741 0.00 0.00 33.07 2.29
1980 2062 7.834681 ACTTCTCCTCCTTTTACTGTTTTTCTT 59.165 33.333 0.00 0.00 0.00 2.52
1981 2063 8.589701 TTCTCCTCCTTTTACTGTTTTTCTTT 57.410 30.769 0.00 0.00 0.00 2.52
1984 2066 7.778083 TCCTCCTTTTACTGTTTTTCTTTTCC 58.222 34.615 0.00 0.00 0.00 3.13
2014 2104 4.511826 CAGGAGAAACACAACCTTCTGTAC 59.488 45.833 0.00 0.00 32.01 2.90
2027 2117 7.093289 ACAACCTTCTGTACATGAATAGCTAGT 60.093 37.037 0.00 0.00 0.00 2.57
2048 2138 6.248569 AGTCCCCACACTAACCTATTTATG 57.751 41.667 0.00 0.00 0.00 1.90
2082 2172 2.705220 CCACATCAGCATGCGACG 59.295 61.111 13.01 8.01 34.76 5.12
2148 2238 6.655078 AAAAGTTCACCTCACTATGCAAAT 57.345 33.333 0.00 0.00 0.00 2.32
2294 2756 9.972106 TCAAAATATCCATGTACCATATATGCA 57.028 29.630 7.24 0.76 0.00 3.96
2296 2758 8.437360 AAATATCCATGTACCATATATGCACG 57.563 34.615 7.24 0.00 0.00 5.34
2305 2767 8.623310 TGTACCATATATGCACGTAAATATCG 57.377 34.615 7.24 0.00 0.00 2.92
2310 2774 8.813282 CCATATATGCACGTAAATATCGCTAAA 58.187 33.333 7.24 0.00 0.00 1.85
2318 2782 9.377383 GCACGTAAATATCGCTAAAATATGTTT 57.623 29.630 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 137 2.791849 GCGTGTGTACTTTCCGCAAAAA 60.792 45.455 12.52 0.00 43.53 1.94
130 138 1.268133 GCGTGTGTACTTTCCGCAAAA 60.268 47.619 12.52 0.00 43.53 2.44
131 139 0.305313 GCGTGTGTACTTTCCGCAAA 59.695 50.000 12.52 0.00 43.53 3.68
132 140 1.500512 GGCGTGTGTACTTTCCGCAA 61.501 55.000 16.98 0.00 45.70 4.85
133 141 1.957186 GGCGTGTGTACTTTCCGCA 60.957 57.895 16.98 0.00 45.70 5.69
134 142 1.226030 AAGGCGTGTGTACTTTCCGC 61.226 55.000 10.02 10.02 43.35 5.54
135 143 2.068837 TAAGGCGTGTGTACTTTCCG 57.931 50.000 0.00 0.00 0.00 4.30
136 144 3.396560 AGTTAAGGCGTGTGTACTTTCC 58.603 45.455 0.00 0.00 0.00 3.13
137 145 4.304939 AGAGTTAAGGCGTGTGTACTTTC 58.695 43.478 0.00 0.00 0.00 2.62
138 146 4.332428 AGAGTTAAGGCGTGTGTACTTT 57.668 40.909 0.00 0.00 0.00 2.66
139 147 4.279169 TGTAGAGTTAAGGCGTGTGTACTT 59.721 41.667 0.00 0.00 0.00 2.24
140 148 3.822735 TGTAGAGTTAAGGCGTGTGTACT 59.177 43.478 0.00 0.00 0.00 2.73
141 149 4.083110 TCTGTAGAGTTAAGGCGTGTGTAC 60.083 45.833 0.00 0.00 0.00 2.90
142 150 4.074259 TCTGTAGAGTTAAGGCGTGTGTA 58.926 43.478 0.00 0.00 0.00 2.90
143 151 2.889045 TCTGTAGAGTTAAGGCGTGTGT 59.111 45.455 0.00 0.00 0.00 3.72
184 192 6.315393 ACCGACTAATGTTAGCTGGTTAATTG 59.685 38.462 0.00 0.00 37.96 2.32
289 298 2.173569 AGCTGTTCTTCCACCAGTTCTT 59.826 45.455 0.00 0.00 0.00 2.52
328 337 6.237861 GGAATGAACGAGTCAATTAGCTGTAC 60.238 42.308 0.00 0.00 40.50 2.90
398 407 2.127708 GGACTTGGATCCATGTAGGGT 58.872 52.381 28.10 14.56 38.77 4.34
482 495 4.180817 TGACAGTGTAATGAAGGCGTATG 58.819 43.478 0.00 0.00 0.00 2.39
483 496 4.465632 TGACAGTGTAATGAAGGCGTAT 57.534 40.909 0.00 0.00 0.00 3.06
527 540 8.995027 ATGGGTATGCTTTCTTGATTATTGTA 57.005 30.769 0.00 0.00 0.00 2.41
568 581 9.595823 TCTCTACTTTACGCAAAAAGCTATTAT 57.404 29.630 7.50 0.00 39.59 1.28
569 582 8.991243 TCTCTACTTTACGCAAAAAGCTATTA 57.009 30.769 7.50 0.00 39.59 0.98
570 583 7.900782 TCTCTACTTTACGCAAAAAGCTATT 57.099 32.000 7.50 0.00 39.59 1.73
571 584 7.900782 TTCTCTACTTTACGCAAAAAGCTAT 57.099 32.000 7.50 0.00 39.59 2.97
572 585 7.718272 TTTCTCTACTTTACGCAAAAAGCTA 57.282 32.000 7.50 1.05 39.59 3.32
573 586 6.613755 TTTCTCTACTTTACGCAAAAAGCT 57.386 33.333 7.50 0.00 39.59 3.74
574 587 8.944212 TTATTTCTCTACTTTACGCAAAAAGC 57.056 30.769 7.50 0.00 39.59 3.51
589 602 9.645059 GTGCACATATCAGCTATTATTTCTCTA 57.355 33.333 13.17 0.00 0.00 2.43
788 801 1.680860 GGCGGGTGTATATTATGGGGC 60.681 57.143 0.00 0.00 0.00 5.80
809 826 0.889186 GGTGTGGTGGTTCTTGCGAT 60.889 55.000 0.00 0.00 0.00 4.58
825 842 1.747355 GGGATCAAAGCATGTGAGGTG 59.253 52.381 0.00 0.00 34.53 4.00
853 870 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
854 871 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
855 872 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
856 873 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
857 874 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
858 875 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
859 876 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
860 877 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
861 878 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
862 879 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
863 880 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
864 881 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
865 882 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
866 883 0.998945 AGAGGAGGAGGAGGAGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
867 884 0.933700 AAGAGGAGGAGGAGGAGGAG 59.066 60.000 0.00 0.00 0.00 3.69
956 983 3.370231 CAAAGAAACGGCCGGGGG 61.370 66.667 31.76 7.47 0.00 5.40
958 985 4.050934 GCCAAAGAAACGGCCGGG 62.051 66.667 31.76 19.86 42.82 5.73
1385 1412 0.536724 TACGTCACCATGCATGAGCT 59.463 50.000 28.31 6.96 42.74 4.09
1444 1471 1.144969 CTCGCCTTACGCAAAGACAA 58.855 50.000 0.00 0.00 43.23 3.18
1457 1484 4.827087 CGACAGCCATGCTCGCCT 62.827 66.667 0.00 0.00 36.40 5.52
1536 1563 8.090831 TCATCATTAATTATTCCAGACTCGAGG 58.909 37.037 18.41 0.00 0.00 4.63
1551 1589 8.223330 AGAGCCCTTACAAGATCATCATTAATT 58.777 33.333 0.00 0.00 0.00 1.40
1588 1669 8.036575 TCATGGGAATCAAAATCATCTTTGAAC 58.963 33.333 3.13 1.87 45.75 3.18
1591 1672 9.472361 GTATCATGGGAATCAAAATCATCTTTG 57.528 33.333 0.00 0.00 37.59 2.77
1888 1969 1.003355 GTCCCAGCTGCTGCAAGTA 60.003 57.895 23.86 4.04 42.74 2.24
1889 1970 2.282040 GTCCCAGCTGCTGCAAGT 60.282 61.111 23.86 0.00 42.74 3.16
1890 1971 1.900016 TTGTCCCAGCTGCTGCAAG 60.900 57.895 23.86 14.14 42.74 4.01
1892 1973 2.595463 GTTGTCCCAGCTGCTGCA 60.595 61.111 23.86 13.70 42.74 4.41
1893 1974 2.282040 AGTTGTCCCAGCTGCTGC 60.282 61.111 23.86 11.17 40.05 5.25
1894 1975 0.535780 TTCAGTTGTCCCAGCTGCTG 60.536 55.000 22.44 22.44 41.36 4.41
1895 1976 0.183492 TTTCAGTTGTCCCAGCTGCT 59.817 50.000 8.66 0.00 41.36 4.24
1924 2005 8.108378 TCTCCCAGGAATTATGGTGTTAATTA 57.892 34.615 8.07 0.00 35.96 1.40
1932 2013 3.051032 TCCTCTCTCCCAGGAATTATGGT 60.051 47.826 8.07 0.00 37.09 3.55
1978 2060 5.580691 GTGTTTCTCCTGGTTTTTGGAAAAG 59.419 40.000 0.00 0.00 31.23 2.27
1980 2062 4.528596 TGTGTTTCTCCTGGTTTTTGGAAA 59.471 37.500 0.00 0.00 31.23 3.13
1981 2063 4.090090 TGTGTTTCTCCTGGTTTTTGGAA 58.910 39.130 0.00 0.00 31.23 3.53
1984 2066 4.081697 AGGTTGTGTTTCTCCTGGTTTTTG 60.082 41.667 0.00 0.00 0.00 2.44
2014 2104 3.389329 AGTGTGGGGACTAGCTATTCATG 59.611 47.826 12.61 0.00 0.00 3.07
2027 2117 5.727279 TGACATAAATAGGTTAGTGTGGGGA 59.273 40.000 0.00 0.00 0.00 4.81
2148 2238 9.926158 AACAAAATGTAAATTCTCATGCACATA 57.074 25.926 0.00 0.00 0.00 2.29
2291 2753 8.078959 ACATATTTTAGCGATATTTACGTGCA 57.921 30.769 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.