Multiple sequence alignment - TraesCS2B01G061800

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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 TraesCS2B01G061800 chr2B 100.000 2318 0 0 1 2318 29549173 29551490 0.000000e+00 4281.0
1 TraesCS2B01G061800 chr2B 83.714 1621 222 28 5 1598 29263053 29264658 0.000000e+00 1493.0
2 TraesCS2B01G061800 chr2B 83.529 1621 225 28 5 1598 29318290 29319895 0.000000e+00 1476.0
3 TraesCS2B01G061800 chr2B 83.477 1622 224 30 5 1598 29349409 29351014 0.000000e+00 1471.0
4 TraesCS2B01G061800 chr2B 87.681 276 30 4 5 280 29218183 29218454 3.720000e-83 318.0
5 TraesCS2B01G061800 chr2D 95.009 2324 103 11 1 2318 17612935 17610619 0.000000e+00 3637.0
6 TraesCS2B01G061800 chr2D 95.009 2324 103 11 1 2318 17640306 17637990 0.000000e+00 3637.0
7 TraesCS2B01G061800 chr2D 83.007 1530 212 30 5 1500 17775303 17773788 0.000000e+00 1341.0
8 TraesCS2B01G061800 chr2A 94.710 2325 110 11 1 2318 19035146 19032828 0.000000e+00 3600.0
9 TraesCS2B01G061800 chr2A 83.524 874 115 17 5 857 19054938 19054073 0.000000e+00 789.0
10 TraesCS2B01G061800 chr2A 82.911 790 100 15 832 1606 19054064 19053295 0.000000e+00 678.0
11 TraesCS2B01G061800 chr3B 96.756 1449 44 1 190 1638 765017784 765019229 0.000000e+00 2412.0
12 TraesCS2B01G061800 chr3B 95.198 354 15 2 1630 1982 765019255 765019607 2.010000e-155 558.0
13 TraesCS2B01G061800 chr7B 82.573 614 82 9 1007 1607 745128184 745128785 3.410000e-143 518.0
14 TraesCS2B01G061800 chr7B 89.011 91 8 2 1957 2046 584033195 584033106 6.770000e-21 111.0
15 TraesCS2B01G061800 chr6B 83.000 100 14 3 1942 2038 288424061 288423962 1.140000e-13 87.9
16 TraesCS2B01G061800 chr7A 83.516 91 13 2 1949 2038 99345135 99345046 1.480000e-12 84.2
17 TraesCS2B01G061800 chr7A 82.558 86 13 2 1954 2038 107191990 107192074 8.880000e-10 75.0


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 TraesCS2B01G061800 chr2B 29549173 29551490 2317 False 4281.0 4281 100.0000 1 2318 1 chr2B.!!$F5 2317
1 TraesCS2B01G061800 chr2B 29263053 29264658 1605 False 1493.0 1493 83.7140 5 1598 1 chr2B.!!$F2 1593
2 TraesCS2B01G061800 chr2B 29318290 29319895 1605 False 1476.0 1476 83.5290 5 1598 1 chr2B.!!$F3 1593
3 TraesCS2B01G061800 chr2B 29349409 29351014 1605 False 1471.0 1471 83.4770 5 1598 1 chr2B.!!$F4 1593
4 TraesCS2B01G061800 chr2D 17610619 17612935 2316 True 3637.0 3637 95.0090 1 2318 1 chr2D.!!$R1 2317
5 TraesCS2B01G061800 chr2D 17637990 17640306 2316 True 3637.0 3637 95.0090 1 2318 1 chr2D.!!$R2 2317
6 TraesCS2B01G061800 chr2D 17773788 17775303 1515 True 1341.0 1341 83.0070 5 1500 1 chr2D.!!$R3 1495
7 TraesCS2B01G061800 chr2A 19032828 19035146 2318 True 3600.0 3600 94.7100 1 2318 1 chr2A.!!$R1 2317
8 TraesCS2B01G061800 chr2A 19053295 19054938 1643 True 733.5 789 83.2175 5 1606 2 chr2A.!!$R2 1601
9 TraesCS2B01G061800 chr3B 765017784 765019607 1823 False 1485.0 2412 95.9770 190 1982 2 chr3B.!!$F1 1792
10 TraesCS2B01G061800 chr7B 745128184 745128785 601 False 518.0 518 82.5730 1007 1607 1 chr7B.!!$F1 600

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
42 43 1.540146 CGTGCCGGACATCCATTATCA 60.540 52.381 5.05 0.0 35.14 2.15 F
868 932 3.379057 TCAACCTTTCCGTTTGACTTTCC 59.621 43.478 0.00 0.0 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1053 1119 1.338769 ACGCCCTCCAAGACATTGTAC 60.339 52.381 0.0 0.0 34.39 2.9 R
2196 2322 2.180159 TGTAGGGACAAAGCGGGAGC 62.180 60.000 0.0 0.0 45.11 4.7 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
42 43 1.540146 CGTGCCGGACATCCATTATCA 60.540 52.381 5.05 0.00 35.14 2.15
121 124 8.630917 CCTATATATAGGTATGTTAACTGCGCT 58.369 37.037 25.28 0.00 43.95 5.92
337 351 6.854496 ACAAACTAATACATGTGTGTTCGT 57.146 33.333 9.11 0.00 39.77 3.85
667 690 6.017400 TCTGGAATGCAGAAACAAATCTTC 57.983 37.500 0.85 0.00 0.00 2.87
868 932 3.379057 TCAACCTTTCCGTTTGACTTTCC 59.621 43.478 0.00 0.00 0.00 3.13
1053 1119 4.418013 TGTCCTTGCAATTGTGTTATCG 57.582 40.909 7.40 0.00 0.00 2.92
1119 1185 4.105486 TCTCTCGCAAAGTGATGAATACG 58.895 43.478 0.00 0.00 0.00 3.06
1301 1367 2.030628 GGATTAACCACAAACCACCACG 60.031 50.000 0.00 0.00 38.79 4.94
1433 1506 9.389570 GTTCTTTGTTATGTGTGTAATGTAACC 57.610 33.333 0.00 0.00 0.00 2.85
1617 1706 9.414295 ACAAGTAAACCAACTTTCAAAAACTAC 57.586 29.630 0.00 0.00 37.61 2.73
1756 1881 6.824196 GGAATTAATTAGTGGCTAGCTATCCC 59.176 42.308 15.72 7.32 0.00 3.85
1807 1932 0.178964 CCAAACCAGGCAGGAAAGGA 60.179 55.000 1.67 0.00 41.22 3.36
1905 2030 5.904941 TGCACTTCAACAAGATGAACAAAT 58.095 33.333 0.00 0.00 35.55 2.32
1970 2096 8.993424 ACTACCTCAGATCCATAAATAAGTGTT 58.007 33.333 0.00 0.00 0.00 3.32
2038 2164 4.149046 CACTTATTTTAGATCGGAGCGAGC 59.851 45.833 0.00 0.00 42.87 5.03
2106 2232 7.721399 GTGAACCACTCCCTGATAATTAATCAT 59.279 37.037 0.00 0.00 43.70 2.45
2114 2240 9.381033 CTCCCTGATAATTAATCATCATCAGAC 57.619 37.037 20.21 0.00 43.70 3.51
2123 2249 2.621338 TCATCATCAGACACGGCTTTC 58.379 47.619 0.00 0.00 0.00 2.62
2177 2303 5.041287 GCTGTGATGATCAACAATTCCATG 58.959 41.667 7.30 0.00 0.00 3.66
2206 2332 1.692411 AGTTTTTCAGCTCCCGCTTT 58.308 45.000 0.00 0.00 46.47 3.51
2207 2333 1.338020 AGTTTTTCAGCTCCCGCTTTG 59.662 47.619 0.00 0.00 46.47 2.77
2208 2334 1.067060 GTTTTTCAGCTCCCGCTTTGT 59.933 47.619 0.00 0.00 46.47 2.83
2211 2337 2.747855 CAGCTCCCGCTTTGTCCC 60.748 66.667 0.00 0.00 46.47 4.46
2212 2338 2.930562 AGCTCCCGCTTTGTCCCT 60.931 61.111 0.00 0.00 46.47 4.20
2213 2339 1.612442 AGCTCCCGCTTTGTCCCTA 60.612 57.895 0.00 0.00 46.47 3.53
2214 2340 1.449778 GCTCCCGCTTTGTCCCTAC 60.450 63.158 0.00 0.00 0.00 3.18
2217 2343 0.834687 TCCCGCTTTGTCCCTACACT 60.835 55.000 0.00 0.00 34.61 3.55
2234 2360 8.772250 TCCCTACACTCTCTATGAAAAATGAAT 58.228 33.333 0.00 0.00 0.00 2.57
2281 2408 7.421599 TCAAAAGAATATGAAACTTTGCGACA 58.578 30.769 0.00 0.00 34.70 4.35
2282 2409 7.378461 TCAAAAGAATATGAAACTTTGCGACAC 59.622 33.333 0.00 0.00 34.70 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 122 3.334691 TGGCAAGTATGTAACACTCAGC 58.665 45.455 0.00 0.00 0.00 4.26
121 124 3.244387 TGCTGGCAAGTATGTAACACTCA 60.244 43.478 0.00 0.00 0.00 3.41
557 575 8.850452 GCATTAAATTGTGCAAGTTTCTAGTAC 58.150 33.333 3.00 0.00 40.94 2.73
667 690 9.196552 GAAGTGGTTTTCAAAATTATCTCTTGG 57.803 33.333 0.00 0.00 0.00 3.61
868 932 4.320667 TGCGATAAGAATGTTGACAACG 57.679 40.909 13.46 0.00 0.00 4.10
922 986 8.348285 TGCAATTAAGCTAGAAAACAAGGTAT 57.652 30.769 0.00 0.00 34.99 2.73
1053 1119 1.338769 ACGCCCTCCAAGACATTGTAC 60.339 52.381 0.00 0.00 34.39 2.90
1119 1185 4.881920 TGCTAAAGGATGCTTTTTGTTCC 58.118 39.130 17.87 1.67 0.00 3.62
1164 1230 1.846007 TTGTTGCACCAAGAACCTGT 58.154 45.000 0.00 0.00 0.00 4.00
1433 1506 2.224079 CACAATCCAGGTCTGACAAACG 59.776 50.000 10.38 0.00 0.00 3.60
1639 1762 2.224606 TGACAGAAAAGGCTTCAGCTG 58.775 47.619 7.63 7.63 41.70 4.24
1756 1881 3.242903 CGCACATCCCTAGCTCTATATCG 60.243 52.174 0.00 0.00 0.00 2.92
1905 2030 8.686334 GGATAAAATCATTTTCCTTGCTACTGA 58.314 33.333 0.00 0.00 34.19 3.41
1961 2087 7.920682 CCTTACTTCAAAACTGCAACACTTATT 59.079 33.333 0.00 0.00 0.00 1.40
1970 2096 4.947388 AGTTCACCTTACTTCAAAACTGCA 59.053 37.500 0.00 0.00 0.00 4.41
2025 2151 3.393089 AAATATTGCTCGCTCCGATCT 57.607 42.857 0.00 0.00 34.61 2.75
2106 2232 2.542020 TTGAAAGCCGTGTCTGATGA 57.458 45.000 0.00 0.00 0.00 2.92
2114 2240 5.920273 AGACAATACATTTTTGAAAGCCGTG 59.080 36.000 0.00 0.00 0.00 4.94
2123 2249 9.986833 TCATGATACGAAGACAATACATTTTTG 57.013 29.630 0.00 0.00 0.00 2.44
2177 2303 7.852516 CGGGAGCTGAAAAACTAATCTTATAC 58.147 38.462 0.00 0.00 0.00 1.47
2196 2322 2.180159 TGTAGGGACAAAGCGGGAGC 62.180 60.000 0.00 0.00 45.11 4.70
2206 2332 6.928348 TTTTTCATAGAGAGTGTAGGGACA 57.072 37.500 0.00 0.00 0.00 4.02
2207 2333 7.556844 TCATTTTTCATAGAGAGTGTAGGGAC 58.443 38.462 0.00 0.00 0.00 4.46
2208 2334 7.733773 TCATTTTTCATAGAGAGTGTAGGGA 57.266 36.000 0.00 0.00 0.00 4.20
2276 2403 3.119849 AGTTTGAGCATATTTGGTGTCGC 60.120 43.478 0.00 0.00 32.62 5.19
2281 2408 6.041979 ACCTTCAAAGTTTGAGCATATTTGGT 59.958 34.615 17.36 12.89 41.38 3.67
2282 2409 6.366877 CACCTTCAAAGTTTGAGCATATTTGG 59.633 38.462 17.36 12.40 41.38 3.28


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

AutoCloner maintained by Alex Coulton.