Multiple sequence alignment - TraesCS5B01G176800

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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 TraesCS5B01G176800 chr5B 100.000 2120 0 0 1 2120 322864513 322862394 0.000000e+00 3916.0
1 TraesCS5B01G176800 chr5A 94.601 2130 93 12 1 2120 377125231 377123114 0.000000e+00 3277.0
2 TraesCS5B01G176800 chr5A 83.333 222 19 5 1 211 377127232 377127018 2.780000e-44 189.0
3 TraesCS5B01G176800 chr5D 95.504 1646 70 4 477 2120 285252593 285250950 0.000000e+00 2627.0
4 TraesCS5B01G176800 chr5D 93.995 433 11 2 1 424 285253297 285252871 1.770000e-180 641.0
5 TraesCS5B01G176800 chr1D 88.235 68 8 0 1054 1121 452898583 452898650 4.850000e-12 82.4
6 TraesCS5B01G176800 chr1D 94.118 51 3 0 1054 1104 453288109 453288159 6.270000e-11 78.7
7 TraesCS5B01G176800 chr1B 88.060 67 8 0 1054 1120 623194814 623194748 1.740000e-11 80.5
8 TraesCS5B01G176800 chr1A 94.118 51 3 0 1054 1104 547959127 547959177 6.270000e-11 78.7
9 TraesCS5B01G176800 chr1A 94.118 51 3 0 1054 1104 547978064 547978114 6.270000e-11 78.7
10 TraesCS5B01G176800 chr1A 86.765 68 9 0 1054 1121 547687372 547687305 2.260000e-10 76.8
11 TraesCS5B01G176800 chr3A 86.957 69 8 1 1053 1120 34580240 34580172 2.260000e-10 76.8


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 TraesCS5B01G176800 chr5B 322862394 322864513 2119 True 3916 3916 100.0000 1 2120 1 chr5B.!!$R1 2119
1 TraesCS5B01G176800 chr5A 377123114 377127232 4118 True 1733 3277 88.9670 1 2120 2 chr5A.!!$R1 2119
2 TraesCS5B01G176800 chr5D 285250950 285253297 2347 True 1634 2627 94.7495 1 2120 2 chr5D.!!$R1 2119

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
885 3120 0.1078 CCCTCATCAGCTGACACAGG 60.108 60.0 20.97 22.02 31.21 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1828 4072 0.681733 AGCACCTACACACTGACCAG 59.318 55.0 0.0 0.0 0.0 4.0 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
77 2079 6.939622 AGATTCTTTGGATCCAAACATTTCC 58.060 36.000 31.75 19.03 40.51 3.13
78 2080 5.482163 TTCTTTGGATCCAAACATTTCCC 57.518 39.130 31.75 0.00 40.51 3.97
79 2081 4.750941 TCTTTGGATCCAAACATTTCCCT 58.249 39.130 31.75 0.00 40.51 4.20
80 2082 5.154418 TCTTTGGATCCAAACATTTCCCTT 58.846 37.500 31.75 0.00 40.51 3.95
81 2083 5.606329 TCTTTGGATCCAAACATTTCCCTTT 59.394 36.000 31.75 0.00 40.51 3.11
82 2084 5.482163 TTGGATCCAAACATTTCCCTTTC 57.518 39.130 25.13 0.00 32.44 2.62
136 2138 2.751259 CAGCAGCCAACATGTAACTGAT 59.249 45.455 20.78 14.54 0.00 2.90
203 2214 1.148310 TGTCTGCTAAGCTTGCGTTC 58.852 50.000 9.86 5.83 0.00 3.95
316 2327 5.852282 ACAAGTAATTGGTGCTGACTTTT 57.148 34.783 7.93 0.00 0.00 2.27
325 2336 2.038557 GGTGCTGACTTTTCTACCTCCA 59.961 50.000 0.00 0.00 0.00 3.86
469 2480 4.024302 CAGATACATGCTGTGCTTACCATG 60.024 45.833 0.00 0.00 40.54 3.66
482 2493 4.754618 TGCTTACCATGTTGTGTTACTCAG 59.245 41.667 0.00 0.00 0.00 3.35
483 2494 4.755123 GCTTACCATGTTGTGTTACTCAGT 59.245 41.667 0.00 0.00 0.00 3.41
866 3101 2.053627 CAAGCATGGCGTTGAAAGAAC 58.946 47.619 0.00 0.00 0.00 3.01
885 3120 0.107800 CCCTCATCAGCTGACACAGG 60.108 60.000 20.97 22.02 31.21 4.00
886 3121 0.107800 CCTCATCAGCTGACACAGGG 60.108 60.000 20.97 12.94 31.21 4.45
887 3122 0.107800 CTCATCAGCTGACACAGGGG 60.108 60.000 20.97 2.50 31.21 4.79
888 3123 1.748122 CATCAGCTGACACAGGGGC 60.748 63.158 20.97 0.00 31.21 5.80
889 3124 2.226315 ATCAGCTGACACAGGGGCA 61.226 57.895 20.97 0.00 31.21 5.36
890 3125 1.569030 ATCAGCTGACACAGGGGCAT 61.569 55.000 20.97 0.00 31.21 4.40
891 3126 2.044555 CAGCTGACACAGGGGCATG 61.045 63.158 8.42 0.00 31.21 4.06
892 3127 2.753043 GCTGACACAGGGGCATGG 60.753 66.667 0.00 0.00 31.21 3.66
893 3128 2.753043 CTGACACAGGGGCATGGC 60.753 66.667 11.56 11.56 0.00 4.40
896 3131 2.601367 ACACAGGGGCATGGCAAC 60.601 61.111 22.06 13.11 0.00 4.17
897 3132 2.283388 CACAGGGGCATGGCAACT 60.283 61.111 22.06 15.26 37.61 3.16
935 3171 7.446013 CCATACTACTACAAACTCCAAAAACCA 59.554 37.037 0.00 0.00 0.00 3.67
952 3188 2.365582 ACCACAACACAAACCAGAGTC 58.634 47.619 0.00 0.00 0.00 3.36
975 3211 2.529632 GGATTCCAAACCCAAGAAGCT 58.470 47.619 0.00 0.00 0.00 3.74
1011 3247 2.277008 ATCAGAAGATGAGGGTGGGT 57.723 50.000 0.00 0.00 42.53 4.51
1086 3322 0.664767 GGCTCTACATCATCCGTCGC 60.665 60.000 0.00 0.00 0.00 5.19
1179 3415 3.445008 ACTTCTCTATCTGACTGGCCAA 58.555 45.455 7.01 0.00 0.00 4.52
1348 3584 7.014230 TGTCCCTTTTCTTCTTCTAAAACATGG 59.986 37.037 0.00 0.00 0.00 3.66
1457 3698 1.079256 TGGAGGGAGGTGAGACCAG 59.921 63.158 0.00 0.00 41.95 4.00
1664 3907 2.918802 TACTGCAACGGACCCGGT 60.919 61.111 13.43 2.69 44.69 5.28
1687 3930 2.662527 GGGTTTTCGACGCGACCA 60.663 61.111 15.93 0.00 34.89 4.02
1719 3962 3.322254 TGCCCTAGCAGTCTAATTAGCTC 59.678 47.826 7.67 3.85 46.52 4.09
1787 4031 5.356751 ACACACATTTCTTTGCTTGAGTACA 59.643 36.000 0.00 0.00 0.00 2.90
1805 4049 8.555896 TGAGTACACCAATAATATCCTAACCA 57.444 34.615 0.00 0.00 0.00 3.67
1828 4072 8.084684 ACCACAATTAGAAAAGATCTCAAAAGC 58.915 33.333 0.00 0.00 39.71 3.51
1844 4088 1.424638 AAGCTGGTCAGTGTGTAGGT 58.575 50.000 0.00 0.00 0.00 3.08
1865 4109 0.911769 CTTGTGGGAGGGAGCACATA 59.088 55.000 0.00 0.00 0.00 2.29
1914 4158 5.633601 GCCTTCCTCGTTTTTGAAATAAAGG 59.366 40.000 0.00 0.00 34.13 3.11
2096 4342 3.393800 TCTCAGAAACTCTTCGCCTTTG 58.606 45.455 0.00 0.00 36.61 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 2080 8.258007 AGTGTTTTCCTTTCCCTTTTTAGAAAG 58.742 33.333 5.68 5.68 45.55 2.62
79 2081 8.038351 CAGTGTTTTCCTTTCCCTTTTTAGAAA 58.962 33.333 0.00 0.00 0.00 2.52
80 2082 7.397761 TCAGTGTTTTCCTTTCCCTTTTTAGAA 59.602 33.333 0.00 0.00 0.00 2.10
81 2083 6.893005 TCAGTGTTTTCCTTTCCCTTTTTAGA 59.107 34.615 0.00 0.00 0.00 2.10
82 2084 7.107639 TCAGTGTTTTCCTTTCCCTTTTTAG 57.892 36.000 0.00 0.00 0.00 1.85
136 2138 0.908910 ATGTACATCGAACCTGCCCA 59.091 50.000 1.41 0.00 0.00 5.36
203 2214 0.111253 AACTGAAACCCTGCTCCCAG 59.889 55.000 0.00 0.00 38.85 4.45
257 2268 8.873830 CACAATAACTTCCATAGTCAACTACTG 58.126 37.037 0.00 0.00 39.39 2.74
258 2269 8.812972 TCACAATAACTTCCATAGTCAACTACT 58.187 33.333 0.00 0.00 42.62 2.57
469 2480 6.307077 GGTTGACAAAAACTGAGTAACACAAC 59.693 38.462 0.00 0.00 34.19 3.32
578 2813 8.627403 CCAAAGAAATCTCATGTTATAGTGCAT 58.373 33.333 0.00 0.00 0.00 3.96
684 2919 1.875009 CAGTATCATCTGCACCGCAT 58.125 50.000 0.00 0.00 38.13 4.73
856 3091 3.190118 CAGCTGATGAGGGTTCTTTCAAC 59.810 47.826 8.42 0.00 0.00 3.18
866 3101 0.107800 CCTGTGTCAGCTGATGAGGG 60.108 60.000 21.47 15.71 39.07 4.30
892 3127 8.095169 AGTAGTATGGTTTATATAGGCAGTTGC 58.905 37.037 0.00 0.00 41.14 4.17
911 3147 7.994334 TGTGGTTTTTGGAGTTTGTAGTAGTAT 59.006 33.333 0.00 0.00 0.00 2.12
935 3171 2.643551 CCAGACTCTGGTTTGTGTTGT 58.356 47.619 16.18 0.00 45.82 3.32
965 3201 3.690460 AGAAATGTGGTAGCTTCTTGGG 58.310 45.455 0.00 0.00 0.00 4.12
972 3208 6.552725 TCTGATGATCTAGAAATGTGGTAGCT 59.447 38.462 0.00 0.00 0.00 3.32
975 3211 8.539117 TCTTCTGATGATCTAGAAATGTGGTA 57.461 34.615 0.00 0.00 32.96 3.25
1011 3247 3.532542 CTTGAGCTTCAGATCATGAGCA 58.467 45.455 14.38 0.00 40.42 4.26
1086 3322 0.179137 TTAGGAGCATCACGACGCAG 60.179 55.000 0.00 0.00 36.25 5.18
1150 3386 7.468631 GCCAGTCAGATAGAGAAGTAAGAGAAG 60.469 44.444 0.00 0.00 0.00 2.85
1179 3415 3.165071 CCCAAAATTTCAGCCACTAGGT 58.835 45.455 0.00 0.00 37.19 3.08
1319 3555 8.466798 TGTTTTAGAAGAAGAAAAGGGACAAAG 58.533 33.333 0.00 0.00 0.00 2.77
1348 3584 3.181538 CGAACACACATCAAAATGCATGC 60.182 43.478 11.82 11.82 36.26 4.06
1441 3682 1.610673 TGCTGGTCTCACCTCCCTC 60.611 63.158 0.00 0.00 39.58 4.30
1457 3698 7.597743 GGATGACAAATTCCATATCAAATCTGC 59.402 37.037 0.00 0.00 31.99 4.26
1664 3907 0.797542 CGCGTCGAAAACCCCATAAA 59.202 50.000 0.00 0.00 0.00 1.40
1687 3930 1.072159 GCTAGGGCAAGCCGATCAT 59.928 57.895 4.80 0.00 36.45 2.45
1719 3962 5.810080 TGTTTTGTAATTTTGGGGTAGGG 57.190 39.130 0.00 0.00 0.00 3.53
1761 4004 4.202050 ACTCAAGCAAAGAAATGTGTGTCC 60.202 41.667 0.00 0.00 0.00 4.02
1805 4049 8.302438 CCAGCTTTTGAGATCTTTTCTAATTGT 58.698 33.333 0.00 0.00 33.74 2.71
1828 4072 0.681733 AGCACCTACACACTGACCAG 59.318 55.000 0.00 0.00 0.00 4.00
1844 4088 2.853542 TGCTCCCTCCCACAAGCA 60.854 61.111 0.00 0.00 42.16 3.91
2090 4336 7.031226 TGTATCAGCTTAATCATTCAAAGGC 57.969 36.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.