Multiple sequence alignment - TraesCS2D01G286900

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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 TraesCS2D01G286900 chr2D 100.000 2789 0 0 1 2789 367088039 367090827 0.000000e+00 5151.0
1 TraesCS2D01G286900 chr2D 98.752 561 5 1 2231 2789 469708181 469708741 0.000000e+00 996.0
2 TraesCS2D01G286900 chr2D 98.390 559 7 1 2233 2789 136364782 136364224 0.000000e+00 981.0
3 TraesCS2D01G286900 chr2D 86.705 173 19 4 1129 1299 67496767 67496597 3.670000e-44 189.0
4 TraesCS2D01G286900 chr2D 82.667 150 22 3 1125 1272 538055273 538055126 2.250000e-26 130.0
5 TraesCS2D01G286900 chr2B 94.554 1928 77 14 1 1907 435628354 435630274 0.000000e+00 2953.0
6 TraesCS2D01G286900 chr2B 93.354 316 10 5 1919 2232 435630258 435630564 9.100000e-125 457.0
7 TraesCS2D01G286900 chr2B 80.791 177 26 7 1125 1297 640765313 640765141 6.270000e-27 132.0
8 TraesCS2D01G286900 chr2A 93.264 1722 72 19 193 1907 496562015 496563699 0.000000e+00 2497.0
9 TraesCS2D01G286900 chr2A 94.357 319 5 5 1919 2232 496563683 496563993 6.990000e-131 477.0
10 TraesCS2D01G286900 chr2A 91.964 112 9 0 1 112 496561898 496562009 1.030000e-34 158.0
11 TraesCS2D01G286900 chr2A 82.781 151 20 5 1125 1272 680357725 680357578 2.250000e-26 130.0
12 TraesCS2D01G286900 chr2A 85.227 88 12 1 245 332 745142397 745142311 3.830000e-14 89.8
13 TraesCS2D01G286900 chr2A 88.571 70 7 1 263 332 288987093 288987025 1.780000e-12 84.2
14 TraesCS2D01G286900 chr5D 98.748 559 5 1 2233 2789 272536348 272535790 0.000000e+00 992.0
15 TraesCS2D01G286900 chr4D 98.571 560 6 1 2232 2789 150896050 150895491 0.000000e+00 989.0
16 TraesCS2D01G286900 chr4D 98.569 559 6 1 2233 2789 201744928 201744370 0.000000e+00 987.0
17 TraesCS2D01G286900 chr4D 98.393 560 7 1 2232 2789 42744108 42743549 0.000000e+00 983.0
18 TraesCS2D01G286900 chr4D 98.390 559 7 1 2233 2789 42751491 42750933 0.000000e+00 981.0
19 TraesCS2D01G286900 chr4D 97.064 579 12 4 2214 2789 307961731 307961155 0.000000e+00 970.0
20 TraesCS2D01G286900 chr3D 98.390 559 7 1 2233 2789 127535098 127535656 0.000000e+00 981.0
21 TraesCS2D01G286900 chr3D 80.808 99 16 2 236 332 581366185 581366282 1.070000e-09 75.0
22 TraesCS2D01G286900 chr6B 82.857 140 24 0 1122 1261 239729257 239729396 2.920000e-25 126.0
23 TraesCS2D01G286900 chr6A 82.857 140 24 0 1122 1261 183188183 183188322 2.920000e-25 126.0
24 TraesCS2D01G286900 chr6D 82.609 138 24 0 1124 1261 139916322 139916459 3.770000e-24 122.0
25 TraesCS2D01G286900 chr1D 85.227 88 12 1 245 332 49924312 49924226 3.830000e-14 89.8
26 TraesCS2D01G286900 chr4A 83.908 87 12 2 246 332 688963824 688963908 6.400000e-12 82.4
27 TraesCS2D01G286900 chr3A 85.366 82 9 3 248 328 568455412 568455333 6.400000e-12 82.4
28 TraesCS2D01G286900 chr3A 87.143 70 8 1 263 332 650058621 650058553 8.280000e-11 78.7
29 TraesCS2D01G286900 chr3A 87.143 70 8 1 263 332 650058834 650058766 8.280000e-11 78.7
30 TraesCS2D01G286900 chr7A 100.000 28 0 0 2150 2177 20188446 20188419 5.000000e-03 52.8
31 TraesCS2D01G286900 chr7A 100.000 28 0 0 2150 2177 20196503 20196476 5.000000e-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 TraesCS2D01G286900 chr2D 367088039 367090827 2788 False 5151 5151 100.000 1 2789 1 chr2D.!!$F1 2788
1 TraesCS2D01G286900 chr2D 469708181 469708741 560 False 996 996 98.752 2231 2789 1 chr2D.!!$F2 558
2 TraesCS2D01G286900 chr2D 136364224 136364782 558 True 981 981 98.390 2233 2789 1 chr2D.!!$R2 556
3 TraesCS2D01G286900 chr2B 435628354 435630564 2210 False 1705 2953 93.954 1 2232 2 chr2B.!!$F1 2231
4 TraesCS2D01G286900 chr2A 496561898 496563993 2095 False 1044 2497 93.195 1 2232 3 chr2A.!!$F1 2231
5 TraesCS2D01G286900 chr5D 272535790 272536348 558 True 992 992 98.748 2233 2789 1 chr5D.!!$R1 556
6 TraesCS2D01G286900 chr4D 150895491 150896050 559 True 989 989 98.571 2232 2789 1 chr4D.!!$R3 557
7 TraesCS2D01G286900 chr4D 201744370 201744928 558 True 987 987 98.569 2233 2789 1 chr4D.!!$R4 556
8 TraesCS2D01G286900 chr4D 42743549 42744108 559 True 983 983 98.393 2232 2789 1 chr4D.!!$R1 557
9 TraesCS2D01G286900 chr4D 42750933 42751491 558 True 981 981 98.390 2233 2789 1 chr4D.!!$R2 556
10 TraesCS2D01G286900 chr4D 307961155 307961731 576 True 970 970 97.064 2214 2789 1 chr4D.!!$R5 575
11 TraesCS2D01G286900 chr3D 127535098 127535656 558 False 981 981 98.390 2233 2789 1 chr3D.!!$F1 556

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
420 439 0.175760 TAAGTGGAGGCGCATGAGAC 59.824 55.0 10.83 0.0 0.00 3.36 F
959 981 0.465705 CTCCCACACAGTCACACACT 59.534 55.0 0.00 0.0 34.67 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 1575 2.202866 GGAGAAGTCCATCTCGCCA 58.797 57.895 0.00 0.0 45.54 5.69 R
1923 1950 4.217118 ACCACGAGACGTATCAAAGTAAGT 59.783 41.667 11.25 0.0 38.32 2.24 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
119 120 5.389859 TCGTTAGGTTTCTTATGACGGAA 57.610 39.130 0.00 0.00 0.00 4.30
158 159 4.223700 TCATGTCTTAGACTTGGCACTGAT 59.776 41.667 22.39 0.34 37.98 2.90
208 211 5.105752 ACTCTCTGACGATGTTCATTTAGC 58.894 41.667 0.00 0.00 0.00 3.09
212 215 3.845178 TGACGATGTTCATTTAGCGAGT 58.155 40.909 0.00 0.00 0.00 4.18
241 246 2.649331 CGTTGATTACGGAGGTGTCT 57.351 50.000 0.00 0.00 46.42 3.41
260 265 5.911280 GTGTCTGTGTCAATCTCAAAATGTG 59.089 40.000 0.00 0.00 0.00 3.21
279 284 3.515502 TGTGTTGCCAGCTTAGTATCTCT 59.484 43.478 0.00 0.00 0.00 3.10
281 286 3.769300 TGTTGCCAGCTTAGTATCTCTGA 59.231 43.478 0.00 0.00 0.00 3.27
295 300 6.073981 AGTATCTCTGAATGTGCTCATAGGA 58.926 40.000 0.93 0.80 33.49 2.94
301 306 5.069648 TCTGAATGTGCTCATAGGAGTAAGG 59.930 44.000 6.23 0.00 43.37 2.69
306 311 2.168521 TGCTCATAGGAGTAAGGTGTGC 59.831 50.000 6.23 0.00 43.37 4.57
335 353 6.384015 TGTGTTCATAGGGATGAGTGTAGATT 59.616 38.462 0.00 0.00 43.03 2.40
375 393 1.328069 TCTGCGTTTGTACCGTGTTTG 59.672 47.619 0.00 0.00 0.00 2.93
420 439 0.175760 TAAGTGGAGGCGCATGAGAC 59.824 55.000 10.83 0.00 0.00 3.36
422 441 4.147449 TGGAGGCGCATGAGACGG 62.147 66.667 10.83 0.00 0.00 4.79
458 477 5.180492 TGTTCCCAAGATTTAACTTGCTACG 59.820 40.000 0.00 0.00 43.83 3.51
566 585 1.076332 GTCGTCCCCACAAAGAATCG 58.924 55.000 0.00 0.00 0.00 3.34
639 658 3.314331 CCTCGCCGCCCCATCTAT 61.314 66.667 0.00 0.00 0.00 1.98
746 768 2.665649 AGCACATAACGACGGATCAA 57.334 45.000 0.00 0.00 0.00 2.57
747 769 2.967362 AGCACATAACGACGGATCAAA 58.033 42.857 0.00 0.00 0.00 2.69
761 783 7.332430 ACGACGGATCAAATTGTTAACTAATCA 59.668 33.333 7.22 0.00 0.00 2.57
825 847 1.170290 CCCTTTTCACTTTCCCGCGT 61.170 55.000 4.92 0.00 0.00 6.01
894 916 3.424703 CACCATTTCAACCACCTCTGAT 58.575 45.455 0.00 0.00 0.00 2.90
901 923 1.065854 CAACCACCTCTGATCTCCCAC 60.066 57.143 0.00 0.00 0.00 4.61
943 965 1.066143 ACGACCAACACATCCATCTCC 60.066 52.381 0.00 0.00 0.00 3.71
948 970 2.086869 CAACACATCCATCTCCCACAC 58.913 52.381 0.00 0.00 0.00 3.82
959 981 0.465705 CTCCCACACAGTCACACACT 59.534 55.000 0.00 0.00 34.67 3.55
1017 1044 6.739331 AGGAAGATGAATTTCTCGTCCTAT 57.261 37.500 20.61 8.11 44.99 2.57
1050 1077 1.222387 CTCCTCGTCCTCGTCCTCT 59.778 63.158 0.00 0.00 38.33 3.69
1053 1080 1.378124 CCTCGTCCTCGTCCTCTTCC 61.378 65.000 0.00 0.00 38.33 3.46
1362 1389 2.751913 CGACCTCACCTCCGACGAG 61.752 68.421 0.00 0.00 35.72 4.18
1405 1432 4.720902 TCTACGCCGACCCCGTCA 62.721 66.667 0.00 0.00 39.88 4.35
1548 1575 4.221422 CCCATGATCGACGGCGGT 62.221 66.667 12.58 1.25 38.28 5.68
1797 1824 8.164070 TCTTCCTACTACTACTGATATGATGCA 58.836 37.037 0.00 0.00 0.00 3.96
1902 1929 9.280174 TGTGCTTAGCAGTTAATTTACTTACTT 57.720 29.630 7.34 0.00 40.08 2.24
1909 1936 8.957466 AGCAGTTAATTTACTTACTTTGATCCC 58.043 33.333 0.00 0.00 0.00 3.85
1910 1937 8.188799 GCAGTTAATTTACTTACTTTGATCCCC 58.811 37.037 0.00 0.00 0.00 4.81
1911 1938 8.395633 CAGTTAATTTACTTACTTTGATCCCCG 58.604 37.037 0.00 0.00 0.00 5.73
1912 1939 5.830000 AATTTACTTACTTTGATCCCCGC 57.170 39.130 0.00 0.00 0.00 6.13
1913 1940 3.985019 TTACTTACTTTGATCCCCGCA 57.015 42.857 0.00 0.00 0.00 5.69
1914 1941 2.871096 ACTTACTTTGATCCCCGCAA 57.129 45.000 0.00 0.00 0.00 4.85
1915 1942 3.149005 ACTTACTTTGATCCCCGCAAA 57.851 42.857 0.00 0.00 34.40 3.68
1916 1943 3.492337 ACTTACTTTGATCCCCGCAAAA 58.508 40.909 0.00 0.00 35.09 2.44
1917 1944 3.892588 ACTTACTTTGATCCCCGCAAAAA 59.107 39.130 0.00 0.00 35.09 1.94
2050 2078 1.499007 TCTGGGCTGTTTCCTTTTCCT 59.501 47.619 0.00 0.00 0.00 3.36
2051 2079 2.091333 TCTGGGCTGTTTCCTTTTCCTT 60.091 45.455 0.00 0.00 0.00 3.36
2052 2080 2.700371 CTGGGCTGTTTCCTTTTCCTTT 59.300 45.455 0.00 0.00 0.00 3.11
2053 2081 3.111484 TGGGCTGTTTCCTTTTCCTTTT 58.889 40.909 0.00 0.00 0.00 2.27
2054 2082 3.133901 TGGGCTGTTTCCTTTTCCTTTTC 59.866 43.478 0.00 0.00 0.00 2.29
2055 2083 3.494398 GGGCTGTTTCCTTTTCCTTTTCC 60.494 47.826 0.00 0.00 0.00 3.13
2056 2084 3.388024 GGCTGTTTCCTTTTCCTTTTCCT 59.612 43.478 0.00 0.00 0.00 3.36
2057 2085 4.141711 GGCTGTTTCCTTTTCCTTTTCCTT 60.142 41.667 0.00 0.00 0.00 3.36
2158 2187 3.807622 GCTGGCGCTTCAGTGTAATATTA 59.192 43.478 7.64 0.00 37.12 0.98
2201 2234 5.477984 ACCTGTTCGTTGTTATGTACTCCTA 59.522 40.000 0.00 0.00 0.00 2.94
2288 2321 3.266772 TGCTTAAGTGTCATCCCTGGATT 59.733 43.478 4.02 0.00 31.62 3.01
2290 2323 4.626287 GCTTAAGTGTCATCCCTGGATTGA 60.626 45.833 4.02 0.00 31.62 2.57
2292 2325 3.572632 AGTGTCATCCCTGGATTGATG 57.427 47.619 0.00 0.00 39.75 3.07
2568 2603 7.951347 AGAGAAATGATGAACAAAGGCTATT 57.049 32.000 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 7.707464 CGTCTTACCTTTGGTTAATTTGGTTTT 59.293 33.333 0.00 0.00 37.09 2.43
98 99 4.328169 GGTTCCGTCATAAGAAACCTAACG 59.672 45.833 0.00 0.00 0.00 3.18
119 120 2.105477 ACATGAACTCTGTTGAGCTGGT 59.895 45.455 0.00 0.00 43.85 4.00
184 187 5.578727 GCTAAATGAACATCGTCAGAGAGTT 59.421 40.000 0.00 0.00 33.23 3.01
188 191 4.105486 TCGCTAAATGAACATCGTCAGAG 58.895 43.478 0.00 0.00 0.00 3.35
208 211 0.037697 TCAACGGGAACATCCACTCG 60.038 55.000 0.00 0.00 38.64 4.18
233 238 3.667497 TGAGATTGACACAGACACCTC 57.333 47.619 0.00 0.00 0.00 3.85
241 246 5.042593 GCAACACATTTTGAGATTGACACA 58.957 37.500 0.00 0.00 0.00 3.72
260 265 4.392921 TCAGAGATACTAAGCTGGCAAC 57.607 45.455 0.00 0.00 0.00 4.17
279 284 4.716784 ACCTTACTCCTATGAGCACATTCA 59.283 41.667 0.83 0.00 42.74 2.57
281 286 4.471386 ACACCTTACTCCTATGAGCACATT 59.529 41.667 0.83 0.00 42.74 2.71
295 300 0.177141 ACACACACGCACACCTTACT 59.823 50.000 0.00 0.00 0.00 2.24
301 306 1.194547 CCTATGAACACACACGCACAC 59.805 52.381 0.00 0.00 0.00 3.82
306 311 3.190079 CTCATCCCTATGAACACACACG 58.810 50.000 0.00 0.00 41.57 4.49
348 366 3.119245 ACGGTACAAACGCAGATACTCAT 60.119 43.478 0.00 0.00 34.00 2.90
353 371 2.728690 ACACGGTACAAACGCAGATA 57.271 45.000 0.00 0.00 34.00 1.98
359 377 3.661758 AAGTCAAACACGGTACAAACG 57.338 42.857 0.00 0.00 37.36 3.60
393 412 4.475051 TGCGCCTCCACTTATTACTTAA 57.525 40.909 4.18 0.00 0.00 1.85
420 439 4.822036 TGGGAACAATATTAATTCGCCG 57.178 40.909 18.41 0.00 37.44 6.46
458 477 7.600752 GGAGTAACAGCATCTCCAATTATAGAC 59.399 40.741 5.69 0.00 44.85 2.59
469 488 9.425577 GGTTTTATATAGGAGTAACAGCATCTC 57.574 37.037 0.00 0.00 0.00 2.75
566 585 1.578206 GCAGAGGTCGCTTTGGGTTC 61.578 60.000 0.00 0.00 0.00 3.62
761 783 3.382546 GGCCATGACAAGCTCATTAACAT 59.617 43.478 0.00 0.00 37.53 2.71
825 847 6.876789 CGGTGTTGCATGGGAGTATATATAAA 59.123 38.462 0.00 0.00 0.00 1.40
894 916 1.216678 GGAGATGAGAGAGGTGGGAGA 59.783 57.143 0.00 0.00 0.00 3.71
901 923 3.095332 TGACAAGTGGAGATGAGAGAGG 58.905 50.000 0.00 0.00 0.00 3.69
959 981 3.969287 ACAGAGCAAGCAATAGAGACA 57.031 42.857 0.00 0.00 0.00 3.41
1017 1044 3.027412 CGAGGAGGATGAGGAGAAGAAA 58.973 50.000 0.00 0.00 0.00 2.52
1386 1413 3.690108 GACGGGGTCGGCGTAGAAC 62.690 68.421 6.85 0.00 41.39 3.01
1513 1540 4.838152 CAGGTCGTCGGGCATGGG 62.838 72.222 0.00 0.00 0.00 4.00
1548 1575 2.202866 GGAGAAGTCCATCTCGCCA 58.797 57.895 0.00 0.00 45.54 5.69
1917 1944 9.415544 ACGAGACGTATCAAAGTAAGTAATTTT 57.584 29.630 11.25 0.00 38.73 1.82
1918 1945 8.857216 CACGAGACGTATCAAAGTAAGTAATTT 58.143 33.333 11.25 0.00 38.32 1.82
1919 1946 7.487189 CCACGAGACGTATCAAAGTAAGTAATT 59.513 37.037 11.25 0.00 38.32 1.40
1920 1947 6.971184 CCACGAGACGTATCAAAGTAAGTAAT 59.029 38.462 11.25 0.00 38.32 1.89
1921 1948 6.072508 ACCACGAGACGTATCAAAGTAAGTAA 60.073 38.462 11.25 0.00 38.32 2.24
1922 1949 5.412594 ACCACGAGACGTATCAAAGTAAGTA 59.587 40.000 11.25 0.00 38.32 2.24
1923 1950 4.217118 ACCACGAGACGTATCAAAGTAAGT 59.783 41.667 11.25 0.00 38.32 2.24
1924 1951 4.730657 ACCACGAGACGTATCAAAGTAAG 58.269 43.478 11.25 0.00 38.32 2.34
1925 1952 4.771590 ACCACGAGACGTATCAAAGTAA 57.228 40.909 11.25 0.00 38.32 2.24
1926 1953 5.878332 TTACCACGAGACGTATCAAAGTA 57.122 39.130 11.25 5.19 38.32 2.24
1927 1954 4.771590 TTACCACGAGACGTATCAAAGT 57.228 40.909 11.25 6.15 38.32 2.66
1928 1955 7.567048 GCATTATTACCACGAGACGTATCAAAG 60.567 40.741 11.25 0.00 38.32 2.77
1929 1956 6.199531 GCATTATTACCACGAGACGTATCAAA 59.800 38.462 11.25 0.00 38.32 2.69
2158 2187 9.071276 GAACAGGTAAATCATCATAACATGGAT 57.929 33.333 0.00 0.00 0.00 3.41
2201 2234 8.141909 GGCAGTGAAAGAAAAAGTAAAATAGGT 58.858 33.333 0.00 0.00 0.00 3.08
2568 2603 5.338300 CCACCAGCCATATATGCATGTAGTA 60.338 44.000 10.16 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.