Multiple sequence alignment - TraesCS7D01G021500

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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 TraesCS7D01G021500 chr7D 100.000 2810 0 0 1 2810 10056017 10058826 0.000000e+00 5190.0
1 TraesCS7D01G021500 chr4A 95.552 2136 72 8 1 2113 729653493 729655628 0.000000e+00 3397.0
2 TraesCS7D01G021500 chr4A 92.621 2087 117 15 1 2061 729797851 729799926 0.000000e+00 2966.0
3 TraesCS7D01G021500 chr4A 89.482 1873 152 23 432 2266 729151967 729153832 0.000000e+00 2326.0
4 TraesCS7D01G021500 chr4A 90.751 1319 91 18 587 1897 729213131 729214426 0.000000e+00 1731.0
5 TraesCS7D01G021500 chr4A 89.101 1046 66 19 1281 2279 729120520 729119476 0.000000e+00 1256.0
6 TraesCS7D01G021500 chr4A 86.496 822 62 19 1496 2270 729921293 729922112 0.000000e+00 857.0
7 TraesCS7D01G021500 chr4A 89.143 700 56 7 682 1367 729857232 729857925 0.000000e+00 854.0
8 TraesCS7D01G021500 chr4A 91.341 589 41 2 698 1286 730007204 730006626 0.000000e+00 797.0
9 TraesCS7D01G021500 chr4A 88.372 602 42 10 642 1217 729920322 729920921 0.000000e+00 699.0
10 TraesCS7D01G021500 chr4A 91.557 379 24 6 1 378 729151371 729151742 1.490000e-142 516.0
11 TraesCS7D01G021500 chr4A 92.035 339 19 5 41 378 729212686 729213017 1.180000e-128 470.0
12 TraesCS7D01G021500 chr4A 87.402 381 32 6 1906 2270 729214791 729215171 9.310000e-115 424.0
13 TraesCS7D01G021500 chr4A 89.236 288 20 5 372 650 729904238 729904523 1.600000e-92 350.0
14 TraesCS7D01G021500 chr4A 92.683 205 11 2 1 205 729903651 729903851 2.740000e-75 292.0
15 TraesCS7D01G021500 chr4A 97.872 94 2 0 1 94 729857123 729857216 2.240000e-36 163.0
16 TraesCS7D01G021500 chr4A 85.859 99 14 0 1802 1900 728834112 728834210 3.830000e-19 106.0
17 TraesCS7D01G021500 chr4A 94.286 70 2 1 2113 2182 729655654 729655721 3.830000e-19 106.0
18 TraesCS7D01G021500 chr4A 86.441 59 5 3 365 422 729151787 729151843 8.400000e-06 62.1
19 TraesCS7D01G021500 chr4A 100.000 28 0 0 739 766 729857212 729857239 5.000000e-03 52.8
20 TraesCS7D01G021500 chr7A 89.734 1958 154 21 203 2113 9684196 9682239 0.000000e+00 2459.0
21 TraesCS7D01G021500 chr7A 90.217 1615 94 17 702 2270 9363816 9365412 0.000000e+00 2049.0
22 TraesCS7D01G021500 chr7A 93.140 379 23 2 1 378 9507718 9508094 1.140000e-153 553.0
23 TraesCS7D01G021500 chr7A 93.814 291 17 1 1 291 9684885 9684596 1.200000e-118 436.0
24 TraesCS7D01G021500 chr7A 83.898 354 29 13 365 713 9362146 9362476 2.100000e-81 313.0
25 TraesCS7D01G021500 chr7A 93.617 188 8 1 372 555 9508145 9508332 7.670000e-71 278.0
26 TraesCS7D01G021500 chr7A 96.875 32 0 1 108 139 9684257 9684227 5.000000e-03 52.8
27 TraesCS7D01G021500 chr4D 99.417 515 3 0 2296 2810 127560365 127560879 0.000000e+00 935.0
28 TraesCS7D01G021500 chr4D 99.225 516 4 0 2295 2810 293539143 293538628 0.000000e+00 931.0
29 TraesCS7D01G021500 chr4D 99.225 516 4 0 2295 2810 488033678 488033163 0.000000e+00 931.0
30 TraesCS7D01G021500 chr4D 98.476 525 5 2 2287 2810 179928559 179928037 0.000000e+00 922.0
31 TraesCS7D01G021500 chr5D 99.226 517 4 0 2294 2810 35127118 35127634 0.000000e+00 933.0
32 TraesCS7D01G021500 chr3D 98.669 526 6 1 2286 2810 491627743 491628268 0.000000e+00 931.0
33 TraesCS7D01G021500 chr2D 99.037 519 5 0 2292 2810 587258384 587258902 0.000000e+00 931.0
34 TraesCS7D01G021500 chr2D 99.225 516 4 0 2295 2810 640992347 640991832 0.000000e+00 931.0
35 TraesCS7D01G021500 chr2D 81.741 942 143 17 867 1797 564438285 564439208 0.000000e+00 760.0
36 TraesCS7D01G021500 chr1D 99.223 515 4 0 2296 2810 75872229 75871715 0.000000e+00 929.0
37 TraesCS7D01G021500 chr2A 77.787 1166 193 44 638 1769 705268193 705269326 0.000000e+00 658.0


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 TraesCS7D01G021500 chr7D 10056017 10058826 2809 False 5190.000000 5190 100.000000 1 2810 1 chr7D.!!$F1 2809
1 TraesCS7D01G021500 chr4A 729797851 729799926 2075 False 2966.000000 2966 92.621000 1 2061 1 chr4A.!!$F2 2060
2 TraesCS7D01G021500 chr4A 729653493 729655721 2228 False 1751.500000 3397 94.919000 1 2182 2 chr4A.!!$F5 2181
3 TraesCS7D01G021500 chr4A 729119476 729120520 1044 True 1256.000000 1256 89.101000 1281 2279 1 chr4A.!!$R1 998
4 TraesCS7D01G021500 chr4A 729151371 729153832 2461 False 968.033333 2326 89.160000 1 2266 3 chr4A.!!$F3 2265
5 TraesCS7D01G021500 chr4A 729212686 729215171 2485 False 875.000000 1731 90.062667 41 2270 3 chr4A.!!$F4 2229
6 TraesCS7D01G021500 chr4A 730006626 730007204 578 True 797.000000 797 91.341000 698 1286 1 chr4A.!!$R2 588
7 TraesCS7D01G021500 chr4A 729920322 729922112 1790 False 778.000000 857 87.434000 642 2270 2 chr4A.!!$F8 1628
8 TraesCS7D01G021500 chr4A 729857123 729857925 802 False 356.600000 854 95.671667 1 1367 3 chr4A.!!$F6 1366
9 TraesCS7D01G021500 chr4A 729903651 729904523 872 False 321.000000 350 90.959500 1 650 2 chr4A.!!$F7 649
10 TraesCS7D01G021500 chr7A 9362146 9365412 3266 False 1181.000000 2049 87.057500 365 2270 2 chr7A.!!$F1 1905
11 TraesCS7D01G021500 chr7A 9682239 9684885 2646 True 982.600000 2459 93.474333 1 2113 3 chr7A.!!$R1 2112
12 TraesCS7D01G021500 chr7A 9507718 9508332 614 False 415.500000 553 93.378500 1 555 2 chr7A.!!$F2 554
13 TraesCS7D01G021500 chr4D 127560365 127560879 514 False 935.000000 935 99.417000 2296 2810 1 chr4D.!!$F1 514
14 TraesCS7D01G021500 chr4D 293538628 293539143 515 True 931.000000 931 99.225000 2295 2810 1 chr4D.!!$R2 515
15 TraesCS7D01G021500 chr4D 488033163 488033678 515 True 931.000000 931 99.225000 2295 2810 1 chr4D.!!$R3 515
16 TraesCS7D01G021500 chr4D 179928037 179928559 522 True 922.000000 922 98.476000 2287 2810 1 chr4D.!!$R1 523
17 TraesCS7D01G021500 chr5D 35127118 35127634 516 False 933.000000 933 99.226000 2294 2810 1 chr5D.!!$F1 516
18 TraesCS7D01G021500 chr3D 491627743 491628268 525 False 931.000000 931 98.669000 2286 2810 1 chr3D.!!$F1 524
19 TraesCS7D01G021500 chr2D 587258384 587258902 518 False 931.000000 931 99.037000 2292 2810 1 chr2D.!!$F2 518
20 TraesCS7D01G021500 chr2D 640991832 640992347 515 True 931.000000 931 99.225000 2295 2810 1 chr2D.!!$R1 515
21 TraesCS7D01G021500 chr2D 564438285 564439208 923 False 760.000000 760 81.741000 867 1797 1 chr2D.!!$F1 930
22 TraesCS7D01G021500 chr1D 75871715 75872229 514 True 929.000000 929 99.223000 2296 2810 1 chr1D.!!$R1 514
23 TraesCS7D01G021500 chr2A 705268193 705269326 1133 False 658.000000 658 77.787000 638 1769 1 chr2A.!!$F1 1131

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
635 1477 5.758784 CGGATAAGTTTTCTTCCACCTATCC 59.241 44.0 0.0 0.0 40.91 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 4928 0.167251 GCATTGGTTTGGTACGTCCG 59.833 55.0 0.0 0.0 39.52 4.79 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
635 1477 5.758784 CGGATAAGTTTTCTTCCACCTATCC 59.241 44.000 0.00 0.00 40.91 2.59
1683 4184 0.828677 GGCGGTATGTCTACCAAGGT 59.171 55.000 0.00 0.00 46.80 3.50
1844 4346 3.175133 CCTTCGGGCAGCAATTAGT 57.825 52.632 0.00 0.00 0.00 2.24
1965 4826 8.981724 TGTACTATTGTATTGAGAGTGTTGAC 57.018 34.615 0.00 0.00 0.00 3.18
2006 4868 6.510478 GCTTGTGAAGTTGTACGTTACATTCA 60.510 38.462 0.00 2.16 38.68 2.57
2012 4874 7.385478 TGAAGTTGTACGTTACATTCATGCTTA 59.615 33.333 0.00 0.00 38.68 3.09
2033 4895 7.277539 TGCTTATTTTCTGGCCGAATAATTTTG 59.722 33.333 10.19 3.44 0.00 2.44
2071 4933 6.890558 TCTTTTTAATCACTTAAACCGGACG 58.109 36.000 9.46 0.00 36.73 4.79
2093 4955 3.159213 ACCAAACCAATGCTCAGATGA 57.841 42.857 0.00 0.00 0.00 2.92
2281 5179 8.301730 ACGAAACATCGTGTAAGATTAAAAGA 57.698 30.769 2.72 0.00 45.30 2.52
2282 5180 8.932791 ACGAAACATCGTGTAAGATTAAAAGAT 58.067 29.630 2.72 0.00 45.30 2.40
2283 5181 9.755064 CGAAACATCGTGTAAGATTAAAAGATT 57.245 29.630 0.00 0.00 0.00 2.40
2290 5188 9.893634 TCGTGTAAGATTAAAAGATTATTGGGA 57.106 29.630 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1683 4184 9.252635 AGCTGTGATAGATCAATGTAGATATCA 57.747 33.333 5.32 0.00 38.75 2.15
1844 4346 2.060383 CCGACAGCTCCATCTCCCA 61.060 63.158 0.00 0.00 0.00 4.37
1875 4377 2.711922 CGAGTCCCTCCCGTGAAGG 61.712 68.421 0.00 0.00 40.63 3.46
2006 4868 6.655078 ATTATTCGGCCAGAAAATAAGCAT 57.345 33.333 12.83 0.00 42.91 3.79
2012 4874 7.607250 TGTACAAAATTATTCGGCCAGAAAAT 58.393 30.769 12.83 10.86 42.91 1.82
2066 4928 0.167251 GCATTGGTTTGGTACGTCCG 59.833 55.000 0.00 0.00 39.52 4.79
2071 4933 4.009675 TCATCTGAGCATTGGTTTGGTAC 58.990 43.478 0.00 0.00 0.00 3.34
2093 4955 5.615289 AGCGGCTAAGAAATCATAAGACAT 58.385 37.500 0.00 0.00 0.00 3.06
2170 5067 6.656270 TGTACATCAACAAGCAATCTCTGAAT 59.344 34.615 0.00 0.00 0.00 2.57
2173 5070 5.868043 TGTACATCAACAAGCAATCTCTG 57.132 39.130 0.00 0.00 0.00 3.35
2270 5168 9.413734 CAGACCTCCCAATAATCTTTTAATCTT 57.586 33.333 0.00 0.00 0.00 2.40
2271 5169 8.781951 TCAGACCTCCCAATAATCTTTTAATCT 58.218 33.333 0.00 0.00 0.00 2.40
2276 5174 6.153510 GCTTTCAGACCTCCCAATAATCTTTT 59.846 38.462 0.00 0.00 0.00 2.27
2279 5177 4.476479 AGCTTTCAGACCTCCCAATAATCT 59.524 41.667 0.00 0.00 0.00 2.40
2280 5178 4.578105 CAGCTTTCAGACCTCCCAATAATC 59.422 45.833 0.00 0.00 0.00 1.75
2281 5179 4.228210 TCAGCTTTCAGACCTCCCAATAAT 59.772 41.667 0.00 0.00 0.00 1.28
2282 5180 3.587061 TCAGCTTTCAGACCTCCCAATAA 59.413 43.478 0.00 0.00 0.00 1.40
2283 5181 3.181329 TCAGCTTTCAGACCTCCCAATA 58.819 45.455 0.00 0.00 0.00 1.90
2284 5182 1.988107 TCAGCTTTCAGACCTCCCAAT 59.012 47.619 0.00 0.00 0.00 3.16
2285 5183 1.434188 TCAGCTTTCAGACCTCCCAA 58.566 50.000 0.00 0.00 0.00 4.12
2286 5184 1.434188 TTCAGCTTTCAGACCTCCCA 58.566 50.000 0.00 0.00 0.00 4.37
2287 5185 2.797177 ATTCAGCTTTCAGACCTCCC 57.203 50.000 0.00 0.00 0.00 4.30
2288 5186 5.707764 AGTTTTATTCAGCTTTCAGACCTCC 59.292 40.000 0.00 0.00 0.00 4.30
2289 5187 6.809630 AGTTTTATTCAGCTTTCAGACCTC 57.190 37.500 0.00 0.00 0.00 3.85
2290 5188 8.734386 CAATAGTTTTATTCAGCTTTCAGACCT 58.266 33.333 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.