Multiple sequence alignment - TraesCS3D01G182800

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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 TraesCS3D01G182800 chr3D 100.000 2972 0 0 1 2972 167461464 167464435 0.000000e+00 5489.0
1 TraesCS3D01G182800 chrUn 95.522 2814 120 6 162 2972 97537309 97534499 0.000000e+00 4494.0
2 TraesCS3D01G182800 chr1D 95.600 2068 88 3 5 2069 290260732 290262799 0.000000e+00 3312.0
3 TraesCS3D01G182800 chr1D 94.879 2070 103 3 1 2067 465662780 465664849 0.000000e+00 3232.0
4 TraesCS3D01G182800 chr1D 95.200 2021 92 4 54 2069 472667870 472665850 0.000000e+00 3190.0
5 TraesCS3D01G182800 chr1D 95.243 883 39 2 2093 2972 366400530 366401412 0.000000e+00 1395.0
6 TraesCS3D01G182800 chr1D 95.103 878 43 0 2093 2970 290262892 290263769 0.000000e+00 1384.0
7 TraesCS3D01G182800 chr1D 94.904 883 42 2 2093 2972 465664944 465665826 0.000000e+00 1378.0
8 TraesCS3D01G182800 chr6D 95.171 2071 98 2 1 2069 327915126 327917196 0.000000e+00 3269.0
9 TraesCS3D01G182800 chr6D 94.836 2072 100 4 1 2069 411319895 411321962 0.000000e+00 3227.0
10 TraesCS3D01G182800 chr6D 96.136 880 33 1 2093 2972 327917289 327918167 0.000000e+00 1435.0
11 TraesCS3D01G182800 chr7D 94.932 2072 101 4 1 2069 166280167 166278097 0.000000e+00 3241.0
12 TraesCS3D01G182800 chr7D 95.568 880 39 0 2093 2972 166278004 166277125 0.000000e+00 1410.0
13 TraesCS3D01G182800 chr2D 94.892 2075 100 5 1 2069 534835532 534837606 0.000000e+00 3240.0
14 TraesCS3D01G182800 chr2D 95.362 884 37 3 2093 2972 533551932 533552815 0.000000e+00 1402.0
15 TraesCS3D01G182800 chr2D 94.886 880 45 0 2093 2972 491280385 491281264 0.000000e+00 1376.0
16 TraesCS3D01G182800 chr5D 95.103 2042 90 4 1 2032 539362926 539364967 0.000000e+00 3208.0
17 TraesCS3D01G182800 chr5D 95.455 880 40 0 2093 2972 419533415 419532536 0.000000e+00 1404.0
18 TraesCS3D01G182800 chr2A 82.619 443 50 11 1 428 492776949 492777379 1.680000e-97 366.0
19 TraesCS3D01G182800 chr2B 93.478 46 3 0 1 46 635825084 635825129 5.320000e-08 69.4
20 TraesCS3D01G182800 chr2B 93.478 46 3 0 1 46 764626742 764626787 5.320000e-08 69.4


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 TraesCS3D01G182800 chr3D 167461464 167464435 2971 False 5489.0 5489 100.0000 1 2972 1 chr3D.!!$F1 2971
1 TraesCS3D01G182800 chrUn 97534499 97537309 2810 True 4494.0 4494 95.5220 162 2972 1 chrUn.!!$R1 2810
2 TraesCS3D01G182800 chr1D 472665850 472667870 2020 True 3190.0 3190 95.2000 54 2069 1 chr1D.!!$R1 2015
3 TraesCS3D01G182800 chr1D 290260732 290263769 3037 False 2348.0 3312 95.3515 5 2970 2 chr1D.!!$F2 2965
4 TraesCS3D01G182800 chr1D 465662780 465665826 3046 False 2305.0 3232 94.8915 1 2972 2 chr1D.!!$F3 2971
5 TraesCS3D01G182800 chr1D 366400530 366401412 882 False 1395.0 1395 95.2430 2093 2972 1 chr1D.!!$F1 879
6 TraesCS3D01G182800 chr6D 411319895 411321962 2067 False 3227.0 3227 94.8360 1 2069 1 chr6D.!!$F1 2068
7 TraesCS3D01G182800 chr6D 327915126 327918167 3041 False 2352.0 3269 95.6535 1 2972 2 chr6D.!!$F2 2971
8 TraesCS3D01G182800 chr7D 166277125 166280167 3042 True 2325.5 3241 95.2500 1 2972 2 chr7D.!!$R1 2971
9 TraesCS3D01G182800 chr2D 534835532 534837606 2074 False 3240.0 3240 94.8920 1 2069 1 chr2D.!!$F3 2068
10 TraesCS3D01G182800 chr2D 533551932 533552815 883 False 1402.0 1402 95.3620 2093 2972 1 chr2D.!!$F2 879
11 TraesCS3D01G182800 chr2D 491280385 491281264 879 False 1376.0 1376 94.8860 2093 2972 1 chr2D.!!$F1 879
12 TraesCS3D01G182800 chr5D 539362926 539364967 2041 False 3208.0 3208 95.1030 1 2032 1 chr5D.!!$F1 2031
13 TraesCS3D01G182800 chr5D 419532536 419533415 879 True 1404.0 1404 95.4550 2093 2972 1 chr5D.!!$R1 879

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
122 131 0.040692 CTCGACAAGAACGACGACCA 60.041 55.0 0.0 0.0 35.88 4.02 F
573 584 0.534412 CTTCATCTCCGTGCCTCACT 59.466 55.0 0.0 0.0 31.34 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1020 1033 0.318955 GTGCACATTGTGGGTTCTGC 60.319 55.0 18.05 2.8 33.64 4.26 R
2221 2306 0.904649 AGGATCGTGATGCAAGGACA 59.095 50.0 4.16 0.0 0.00 4.02 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
97 98 3.749954 GCATAGGCTCCATCATTCACCTT 60.750 47.826 0.00 0.00 36.96 3.50
122 131 0.040692 CTCGACAAGAACGACGACCA 60.041 55.000 0.00 0.00 35.88 4.02
197 206 2.236146 TCAGACATGACCGTGCCTATTT 59.764 45.455 0.00 0.00 0.00 1.40
211 220 2.550978 CCTATTTCGTCGGCACATTCT 58.449 47.619 0.00 0.00 0.00 2.40
418 429 3.235481 TCGAACCCACCTTGCGGA 61.235 61.111 0.00 0.00 0.00 5.54
441 452 2.589540 CATGGAGGCCGGTGCTTA 59.410 61.111 1.90 0.00 37.74 3.09
539 550 2.094182 ACCATAGCACGAATTGACGTCT 60.094 45.455 17.92 0.00 44.76 4.18
573 584 0.534412 CTTCATCTCCGTGCCTCACT 59.466 55.000 0.00 0.00 31.34 3.41
585 596 3.458189 GTGCCTCACTTAGCATCGTATT 58.542 45.455 0.00 0.00 41.86 1.89
766 777 9.507280 CAGCGAATGTATCACTGAAAATAATTT 57.493 29.630 0.00 0.00 40.03 1.82
788 799 3.054434 TCCACTCCCAATGAATGTACCAG 60.054 47.826 0.00 0.00 0.00 4.00
936 947 3.585862 ACTACGCAAGACAACGATCATT 58.414 40.909 0.00 0.00 43.62 2.57
981 992 6.183360 ACGACGGTTGTTAAAAACATAACTGT 60.183 34.615 10.65 8.20 41.81 3.55
1031 1044 1.302431 CCACGATGCAGAACCCACA 60.302 57.895 0.00 0.00 0.00 4.17
1103 1116 3.118000 CCCGCCCTTAAATTTAGACTCCT 60.118 47.826 0.00 0.00 0.00 3.69
1105 1118 4.514401 CGCCCTTAAATTTAGACTCCTGT 58.486 43.478 0.00 0.00 0.00 4.00
1280 1294 0.105224 ACGTGATCCACACCAACGAA 59.895 50.000 6.51 0.00 45.73 3.85
1336 1350 1.666011 GACACCTCCAGTTCGAGCA 59.334 57.895 1.01 0.00 0.00 4.26
1674 1688 2.100197 TCCTTGTCCATGACGTAGAGG 58.900 52.381 0.00 0.00 34.95 3.69
1862 1876 1.693627 CTAGGTCCTGTGGCGACTAT 58.306 55.000 0.00 0.00 0.00 2.12
1916 1930 8.887717 ACAAAAGTATCTAGAACATTGCTCATC 58.112 33.333 0.00 0.00 0.00 2.92
1995 2009 9.685828 GTTATAAATTTAGGTTTGCTTGTGTCA 57.314 29.630 3.94 0.00 0.00 3.58
2051 2066 7.981225 ACATGTCTTTTGCACAAGTTTATTTCT 59.019 29.630 12.16 0.00 0.00 2.52
2075 2091 2.203538 CCACATAGGCATGCCCCC 60.204 66.667 33.14 8.89 35.39 5.40
2114 2199 7.670140 TGTCTTCACCTTCTCTCTGATAAGTTA 59.330 37.037 0.00 0.00 0.00 2.24
2244 2330 2.027285 TCCTTGCATCACGATCCTTTCA 60.027 45.455 0.00 0.00 0.00 2.69
2275 2365 2.165845 CTCCCTTAGAATCACGTCCGTT 59.834 50.000 0.00 0.00 0.00 4.44
2290 2380 2.094338 GTCCGTTCCTCCAGTTCGTTAT 60.094 50.000 0.00 0.00 0.00 1.89
2308 2398 1.873270 ATGTGCGTGCCTCTACGTCA 61.873 55.000 0.00 0.00 45.36 4.35
2331 2421 4.179298 GGTAAAACCATACCTCTGTCGTC 58.821 47.826 0.00 0.00 41.80 4.20
2336 2426 2.228059 CCATACCTCTGTCGTCCGTAT 58.772 52.381 0.00 0.00 0.00 3.06
2542 2633 1.289160 TAGGCTCCATGCTTCACCTT 58.711 50.000 0.00 0.00 42.39 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 131 6.403200 CCAATACGCTTTACAGTTACAAGCAT 60.403 38.462 10.76 0.89 42.65 3.79
145 154 1.080498 AGGTCATCCCTAAGGTGTCCA 59.920 52.381 0.00 0.00 43.87 4.02
197 206 3.561429 GCAAGAATGTGCCGACGA 58.439 55.556 0.00 0.00 38.66 4.20
418 429 1.155155 ACCGGCCTCCATGGTTTTT 59.845 52.632 12.58 0.00 38.35 1.94
441 452 3.430042 AGCCACAGATGTGTTTCTGAT 57.570 42.857 11.76 0.00 44.88 2.90
539 550 2.162319 TGAAGCTACGTGATTGCACA 57.838 45.000 0.00 0.14 45.41 4.57
573 584 4.137116 AGAGGCACAAATACGATGCTAA 57.863 40.909 0.00 0.00 39.38 3.09
585 596 2.721231 GCGCAACAAGAGGCACAA 59.279 55.556 0.30 0.00 0.00 3.33
766 777 2.916269 TGGTACATTCATTGGGAGTGGA 59.084 45.455 0.00 0.00 37.54 4.02
788 799 2.100879 AACTCTCAGACACACGGGCC 62.101 60.000 0.00 0.00 0.00 5.80
936 947 3.064958 CGTATCTCTAGCAAGTCGTGGAA 59.935 47.826 0.00 0.00 0.00 3.53
1020 1033 0.318955 GTGCACATTGTGGGTTCTGC 60.319 55.000 18.05 2.80 33.64 4.26
1103 1116 3.611674 TGTGAGAAGGCCGCGACA 61.612 61.111 8.23 0.00 0.00 4.35
1105 1118 3.611674 TGTGTGAGAAGGCCGCGA 61.612 61.111 8.23 0.00 0.00 5.87
1280 1294 3.737172 GTCGCCGCCTTGTGCAAT 61.737 61.111 0.00 0.00 41.33 3.56
1336 1350 0.966920 AACTCCGACGATCTTGTGGT 59.033 50.000 0.00 0.00 0.00 4.16
1560 1574 2.183679 GAAGTGGGTGATCTCCAGTCT 58.816 52.381 15.46 7.33 36.98 3.24
1603 1617 0.905357 CTTGGTAGCTGTAGGCACCT 59.095 55.000 0.00 0.00 44.79 4.00
1674 1688 2.248431 GCGTTCTGCGTTGGTGAC 59.752 61.111 0.00 0.00 43.66 3.67
1862 1876 1.618837 GACCACCTGCTTCAGTAGTCA 59.381 52.381 0.00 0.00 0.00 3.41
1916 1930 9.656040 CAGATCTAATGAGAAATCTAGAATGGG 57.344 37.037 0.00 0.00 34.61 4.00
1940 1954 2.985809 CGACAGTCTTGAGAGAAAGCAG 59.014 50.000 0.00 0.00 32.66 4.24
1995 2009 5.449999 GCAAGCAAACTACAAGGTTAACTGT 60.450 40.000 5.42 5.68 0.00 3.55
2051 2066 1.746861 GCATGCCTATGTGGTGCACTA 60.747 52.381 17.98 8.10 37.65 2.74
2075 2091 2.076100 TGAAGACATGTAAGCTTGCGG 58.924 47.619 9.86 6.85 0.00 5.69
2076 2092 2.159653 GGTGAAGACATGTAAGCTTGCG 60.160 50.000 9.86 0.00 0.00 4.85
2082 2098 6.071672 TCAGAGAGAAGGTGAAGACATGTAAG 60.072 42.308 0.00 0.00 0.00 2.34
2221 2306 0.904649 AGGATCGTGATGCAAGGACA 59.095 50.000 4.16 0.00 0.00 4.02
2244 2330 3.446442 TTCTAAGGGAGGTACAGACGT 57.554 47.619 0.00 0.00 0.00 4.34
2275 2365 1.403647 CGCACATAACGAACTGGAGGA 60.404 52.381 0.00 0.00 0.00 3.71
2290 2380 2.257371 GACGTAGAGGCACGCACA 59.743 61.111 0.00 0.00 45.77 4.57
2331 2421 6.092122 TCAGCAACTTTCTTAACATGATACGG 59.908 38.462 0.00 0.00 0.00 4.02
2336 2426 6.691754 TTGTCAGCAACTTTCTTAACATGA 57.308 33.333 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.