Multiple sequence alignment - TraesCS5D01G120600

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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 TraesCS5D01G120600 chr5D 100.000 3161 0 0 1 3161 170710585 170713745 0 5838
1 TraesCS5D01G120600 chr6D 96.364 3163 113 2 1 3161 343521720 343524882 0 5203
2 TraesCS5D01G120600 chr7D 96.110 3162 104 5 1 3161 59692741 59689598 0 5140
3 TraesCS5D01G120600 chr2D 95.003 3162 112 13 1 3160 621171286 621168169 0 4922
4 TraesCS5D01G120600 chr3D 96.562 2938 89 8 235 3161 482587959 482590895 0 4855
5 TraesCS5D01G120600 chr6A 93.095 2795 149 18 255 3038 298324264 298327025 0 4052
6 TraesCS5D01G120600 chr5B 95.879 2014 79 4 1151 3161 658347010 658349022 0 3256
7 TraesCS5D01G120600 chr5B 90.372 1049 87 5 1 1038 658345960 658347005 0 1365
8 TraesCS5D01G120600 chr1B 95.236 2015 88 6 1151 3161 198113642 198111632 0 3182
9 TraesCS5D01G120600 chr1B 89.704 1049 93 8 1 1038 198114691 198113647 0 1325
10 TraesCS5D01G120600 chr1B 89.569 1045 95 5 5 1038 149122773 149121732 0 1314
11 TraesCS5D01G120600 chr6B 95.233 2014 89 5 1151 3161 651661139 651659130 0 3181
12 TraesCS5D01G120600 chr6B 90.325 1230 103 10 1 1218 396295844 396297069 0 1598
13 TraesCS5D01G120600 chr6B 89.704 1049 94 6 1 1038 651662189 651661144 0 1327
14 TraesCS5D01G120600 chr1A 95.848 1951 79 2 1213 3161 365222534 365224484 0 3153
15 TraesCS5D01G120600 chr1A 90.650 1230 98 8 1 1218 365221022 365222246 0 1618
16 TraesCS5D01G120600 chr7B 91.200 1500 128 3 207 1704 241348024 241346527 0 2036
17 TraesCS5D01G120600 chr2B 89.710 1137 88 14 107 1218 86850189 86849057 0 1424


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 TraesCS5D01G120600 chr5D 170710585 170713745 3160 False 5838.0 5838 100.0000 1 3161 1 chr5D.!!$F1 3160
1 TraesCS5D01G120600 chr6D 343521720 343524882 3162 False 5203.0 5203 96.3640 1 3161 1 chr6D.!!$F1 3160
2 TraesCS5D01G120600 chr7D 59689598 59692741 3143 True 5140.0 5140 96.1100 1 3161 1 chr7D.!!$R1 3160
3 TraesCS5D01G120600 chr2D 621168169 621171286 3117 True 4922.0 4922 95.0030 1 3160 1 chr2D.!!$R1 3159
4 TraesCS5D01G120600 chr3D 482587959 482590895 2936 False 4855.0 4855 96.5620 235 3161 1 chr3D.!!$F1 2926
5 TraesCS5D01G120600 chr6A 298324264 298327025 2761 False 4052.0 4052 93.0950 255 3038 1 chr6A.!!$F1 2783
6 TraesCS5D01G120600 chr5B 658345960 658349022 3062 False 2310.5 3256 93.1255 1 3161 2 chr5B.!!$F1 3160
7 TraesCS5D01G120600 chr1B 198111632 198114691 3059 True 2253.5 3182 92.4700 1 3161 2 chr1B.!!$R2 3160
8 TraesCS5D01G120600 chr1B 149121732 149122773 1041 True 1314.0 1314 89.5690 5 1038 1 chr1B.!!$R1 1033
9 TraesCS5D01G120600 chr6B 651659130 651662189 3059 True 2254.0 3181 92.4685 1 3161 2 chr6B.!!$R1 3160
10 TraesCS5D01G120600 chr6B 396295844 396297069 1225 False 1598.0 1598 90.3250 1 1218 1 chr6B.!!$F1 1217
11 TraesCS5D01G120600 chr1A 365221022 365224484 3462 False 2385.5 3153 93.2490 1 3161 2 chr1A.!!$F1 3160
12 TraesCS5D01G120600 chr7B 241346527 241348024 1497 True 2036.0 2036 91.2000 207 1704 1 chr7B.!!$R1 1497
13 TraesCS5D01G120600 chr2B 86849057 86850189 1132 True 1424.0 1424 89.7100 107 1218 1 chr2B.!!$R1 1111

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
98 99 0.744281 CAAAGAGGGTGTTTGCCGTT 59.256 50.0 0.00 0.00 0.00 4.44 F
501 502 0.902516 GTCACCTCTCCCTGCTCACT 60.903 60.0 0.00 0.00 0.00 3.41 F
1366 1693 0.676184 AGTTCAGAGCACTGCTTCGA 59.324 50.0 4.67 2.16 39.88 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1366 1693 1.303155 GGCTTTCTGGAGCTGCTGT 60.303 57.895 7.01 0.0 42.32 4.40 R
1895 2229 1.813753 CCATAGCCACAACCGGACG 60.814 63.158 9.46 0.0 0.00 4.79 R
2641 2981 0.250124 CCGTGGTACAACAAGAGGCA 60.250 55.000 0.35 0.0 44.16 4.75 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 64 1.728971 CTTACAGAAAGCTGACGGCAG 59.271 52.381 15.93 15.93 45.17 4.85
98 99 0.744281 CAAAGAGGGTGTTTGCCGTT 59.256 50.000 0.00 0.00 0.00 4.44
171 172 2.388347 GCAGACGGCAAAGAGGATC 58.612 57.895 0.00 0.00 43.97 3.36
191 192 2.099405 CGGTGGCCCATTAACAAGAAT 58.901 47.619 0.00 0.00 0.00 2.40
426 427 3.172106 TTTCTCCACCCCACGCCA 61.172 61.111 0.00 0.00 0.00 5.69
501 502 0.902516 GTCACCTCTCCCTGCTCACT 60.903 60.000 0.00 0.00 0.00 3.41
528 529 1.511768 CGACCGGTTTCTCTCCTCC 59.488 63.158 9.42 0.00 0.00 4.30
552 553 1.682684 GAGAGTCCCGCCTCCTTGA 60.683 63.158 0.00 0.00 31.53 3.02
659 683 2.431771 CCCGCGTTGACATCGACA 60.432 61.111 4.92 0.00 0.00 4.35
713 737 2.942796 ATCAGCTCGACCAACGGCA 61.943 57.895 0.00 0.00 42.82 5.69
848 872 0.923358 AACCACTTCTCAACCCCACA 59.077 50.000 0.00 0.00 0.00 4.17
851 875 1.609208 CACTTCTCAACCCCACAAGG 58.391 55.000 0.00 0.00 0.00 3.61
1059 1093 5.420725 TTGCTCAATTAACTGCCTCTCTA 57.579 39.130 0.00 0.00 0.00 2.43
1102 1136 2.286833 CGCGTAATTCTGTAATGTGGGG 59.713 50.000 0.00 0.00 0.00 4.96
1161 1195 8.844244 AGATTAGGTGATAAACTGATGAATTGC 58.156 33.333 0.00 0.00 0.00 3.56
1173 1207 5.884232 ACTGATGAATTGCTGCTTGATTCTA 59.116 36.000 17.85 9.77 32.41 2.10
1186 1220 4.498682 GCTTGATTCTAATGGTCATGGTGC 60.499 45.833 0.00 0.00 0.00 5.01
1366 1693 0.676184 AGTTCAGAGCACTGCTTCGA 59.324 50.000 4.67 2.16 39.88 3.71
1401 1728 0.739813 GCCTTCGCGTCACAGGTTAT 60.740 55.000 5.77 0.00 0.00 1.89
1411 1738 4.671766 GCGTCACAGGTTATGGATCAAAAC 60.672 45.833 0.00 0.00 0.00 2.43
1425 1752 4.328712 GGATCAAAACGCAACACAAAACTT 59.671 37.500 0.00 0.00 0.00 2.66
1642 1969 3.055819 GCACTCCTCCTACTGATGAAACA 60.056 47.826 0.00 0.00 0.00 2.83
1671 1998 8.565896 TTCAAATGTCTCTACATGCAAATACT 57.434 30.769 0.00 0.00 45.79 2.12
1895 2229 6.756542 GGTCATATTTAGTTGCATTTTGGTCC 59.243 38.462 0.00 0.00 0.00 4.46
2344 2681 8.901793 TGCTGCTATTCATTTATGTATGTGAAA 58.098 29.630 0.00 0.00 34.62 2.69
2429 2768 7.719633 TGGGAATAATTAGTCCTTGCTATCAAC 59.280 37.037 26.40 10.21 40.17 3.18
2442 2781 6.201806 CCTTGCTATCAACTGTAGTAGCATTC 59.798 42.308 16.94 0.00 46.11 2.67
2472 2811 1.936547 GAGTGTGAGGGAATTCGATGC 59.063 52.381 0.00 0.00 0.00 3.91
2544 2883 3.976942 CACGTGATCTTCCTTTGCTTTTG 59.023 43.478 10.90 0.00 0.00 2.44
2641 2981 8.697507 AACTGAGATTTAGTTTGATTTGGAGT 57.302 30.769 0.00 0.00 34.91 3.85
2702 3043 7.281098 TGTACTTGTACAACAGGTTTTGGATA 58.719 34.615 3.59 0.00 39.28 2.59
2705 3046 5.570205 TGTACAACAGGTTTTGGATAGGA 57.430 39.130 0.00 0.00 0.00 2.94
2876 3218 1.754621 TAGGAGGACGAGCAGCAGG 60.755 63.158 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 3.341823 TCTTTGCCATCTGCTCTTTCTC 58.658 45.455 0.00 0.00 42.00 2.87
98 99 1.079127 GACGGCAAAGAGCAGGCTA 60.079 57.895 0.00 0.00 43.80 3.93
171 172 1.540267 TTCTTGTTAATGGGCCACCG 58.460 50.000 9.28 0.00 40.75 4.94
230 231 1.228245 TGCTTTCGGGCTCTTTGCT 60.228 52.632 0.00 0.00 42.39 3.91
606 621 3.900892 CGAGGTCTATGGCGCGGT 61.901 66.667 8.83 0.00 0.00 5.68
614 629 2.913060 GCGGGAGGCGAGGTCTAT 60.913 66.667 0.00 0.00 0.00 1.98
648 672 0.250124 GTGGGTGGTGTCGATGTCAA 60.250 55.000 0.00 0.00 0.00 3.18
713 737 2.103143 CTGCGCGTCCTCGATCTT 59.897 61.111 8.43 0.00 39.71 2.40
830 854 0.923358 TTGTGGGGTTGAGAAGTGGT 59.077 50.000 0.00 0.00 0.00 4.16
1059 1093 5.450688 GCGACTCTCCAACTCATATACAACT 60.451 44.000 0.00 0.00 0.00 3.16
1102 1136 3.932710 TCACACAGAAACTGAGACAACAC 59.067 43.478 5.76 0.00 35.18 3.32
1161 1195 4.885907 ACCATGACCATTAGAATCAAGCAG 59.114 41.667 0.00 0.00 0.00 4.24
1173 1207 2.703798 GCAGCGCACCATGACCATT 61.704 57.895 11.47 0.00 0.00 3.16
1321 1648 3.695606 GCAGCCAGGGTCTCGTCA 61.696 66.667 0.00 0.00 0.00 4.35
1366 1693 1.303155 GGCTTTCTGGAGCTGCTGT 60.303 57.895 7.01 0.00 42.32 4.40
1401 1728 3.510388 TTTGTGTTGCGTTTTGATCCA 57.490 38.095 0.00 0.00 0.00 3.41
1411 1738 7.760750 CATAACTAGTAAGTTTTGTGTTGCG 57.239 36.000 0.00 0.00 43.60 4.85
1425 1752 7.116662 CGTTTTGCTTGTACCACATAACTAGTA 59.883 37.037 0.00 0.00 0.00 1.82
1642 1969 6.882610 TGCATGTAGAGACATTTGAAGTTT 57.117 33.333 0.00 0.00 44.18 2.66
1895 2229 1.813753 CCATAGCCACAACCGGACG 60.814 63.158 9.46 0.00 0.00 4.79
2429 2768 6.159293 TCAACAGTGAAGAATGCTACTACAG 58.841 40.000 0.00 0.00 0.00 2.74
2472 2811 8.584157 AGTAGATGATAGGCAAAAGTAGATGAG 58.416 37.037 0.00 0.00 0.00 2.90
2544 2883 9.482627 AAGCAGTTATCATACTATCAGCTAAAC 57.517 33.333 0.00 0.00 0.00 2.01
2641 2981 0.250124 CCGTGGTACAACAAGAGGCA 60.250 55.000 0.35 0.00 44.16 4.75
2702 3043 2.291865 GGAAGAGCATTTTCCCCTTCCT 60.292 50.000 11.08 0.00 45.66 3.36
2705 3046 3.181418 TGAAGGAAGAGCATTTTCCCCTT 60.181 43.478 9.47 0.00 44.19 3.95
2804 3146 6.712179 TGAATGGCATGCATGATAAAACTA 57.288 33.333 30.64 9.47 0.00 2.24
2814 3156 4.751060 CAAGTTAGTTGAATGGCATGCAT 58.249 39.130 21.36 8.40 38.60 3.96
2876 3218 4.025896 CGTCATCATCAGTCTGATTTGCTC 60.026 45.833 12.88 9.04 34.28 4.26
3067 3409 4.454678 ACATACTGATTTGCGACCATGAT 58.545 39.130 0.00 0.00 0.00 2.45
3071 3413 4.180817 CACTACATACTGATTTGCGACCA 58.819 43.478 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.