Multiple sequence alignment - TraesCS7D01G550500

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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 TraesCS7D01G550500 chr7D 100.000 2558 0 0 1 2558 634669049 634671606 0.000000e+00 4724.0
1 TraesCS7D01G550500 chr7D 84.859 2054 223 41 456 2448 634677541 634679567 0.000000e+00 1989.0
2 TraesCS7D01G550500 chr7D 85.981 1712 199 29 456 2144 634710134 634708441 0.000000e+00 1794.0
3 TraesCS7D01G550500 chr7D 87.607 234 23 3 6 235 634711159 634710928 1.510000e-67 267.0
4 TraesCS7D01G550500 chr7B 92.199 2474 144 19 6 2461 741620683 741618241 0.000000e+00 3454.0
5 TraesCS7D01G550500 chr7B 92.935 2024 124 15 459 2472 741548872 741550886 0.000000e+00 2928.0
6 TraesCS7D01G550500 chr7B 82.969 2061 257 52 456 2450 741588860 741586828 0.000000e+00 1775.0
7 TraesCS7D01G550500 chr7B 83.087 1827 208 46 456 2224 741558454 741560237 0.000000e+00 1568.0
8 TraesCS7D01G550500 chr7B 90.227 440 36 4 2039 2471 741554162 741554601 3.690000e-158 568.0
9 TraesCS7D01G550500 chr7B 100.000 42 0 0 2514 2555 741550893 741550934 7.590000e-11 78.7
10 TraesCS7D01G550500 chr7B 95.556 45 2 0 2514 2558 741618235 741618191 3.530000e-09 73.1
11 TraesCS7D01G550500 chr7B 97.500 40 1 0 2514 2553 741554609 741554648 4.570000e-08 69.4
12 TraesCS7D01G550500 chr7A 94.007 2069 103 10 498 2558 731389588 731387533 0.000000e+00 3114.0
13 TraesCS7D01G550500 chr7A 86.157 1712 193 27 456 2144 731252555 731254245 0.000000e+00 1808.0
14 TraesCS7D01G550500 chr7A 85.631 1712 186 29 860 2558 731236443 731238107 0.000000e+00 1744.0
15 TraesCS7D01G550500 chr7A 85.309 1552 162 30 456 1990 731017269 731018771 0.000000e+00 1543.0
16 TraesCS7D01G550500 chr7A 85.979 1455 178 16 1009 2448 731283067 731281624 0.000000e+00 1533.0
17 TraesCS7D01G550500 chr7A 92.994 471 26 5 6 474 731390046 731389581 0.000000e+00 680.0
18 TraesCS7D01G550500 chr7A 83.878 490 56 10 2075 2555 731019029 731019504 1.810000e-121 446.0
19 TraesCS7D01G550500 chr7A 78.902 583 79 20 458 1011 731292445 731291878 3.130000e-94 355.0
20 TraesCS7D01G550500 chr7A 86.765 272 28 5 6 271 731422129 731421860 1.920000e-76 296.0
21 TraesCS7D01G550500 chr7A 86.022 279 29 6 1 271 731016995 731017271 8.950000e-75 291.0
22 TraesCS7D01G550500 chr7A 84.615 247 25 7 1 235 731234395 731234640 1.530000e-57 233.0
23 TraesCS7D01G550500 chr7A 84.925 199 22 4 454 648 731235716 731235910 7.220000e-46 195.0
24 TraesCS7D01G550500 chr4B 87.035 1558 159 20 456 1994 625077765 625079298 0.000000e+00 1718.0
25 TraesCS7D01G550500 chr4B 83.032 277 32 7 1 271 625077500 625077767 1.180000e-58 237.0


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 TraesCS7D01G550500 chr7D 634669049 634671606 2557 False 4724.00 4724 100.000000 1 2558 1 chr7D.!!$F1 2557
1 TraesCS7D01G550500 chr7D 634677541 634679567 2026 False 1989.00 1989 84.859000 456 2448 1 chr7D.!!$F2 1992
2 TraesCS7D01G550500 chr7D 634708441 634711159 2718 True 1030.50 1794 86.794000 6 2144 2 chr7D.!!$R1 2138
3 TraesCS7D01G550500 chr7B 741586828 741588860 2032 True 1775.00 1775 82.969000 456 2450 1 chr7B.!!$R1 1994
4 TraesCS7D01G550500 chr7B 741618191 741620683 2492 True 1763.55 3454 93.877500 6 2558 2 chr7B.!!$R2 2552
5 TraesCS7D01G550500 chr7B 741548872 741560237 11365 False 1042.42 2928 92.749800 456 2555 5 chr7B.!!$F1 2099
6 TraesCS7D01G550500 chr7A 731387533 731390046 2513 True 1897.00 3114 93.500500 6 2558 2 chr7A.!!$R4 2552
7 TraesCS7D01G550500 chr7A 731252555 731254245 1690 False 1808.00 1808 86.157000 456 2144 1 chr7A.!!$F1 1688
8 TraesCS7D01G550500 chr7A 731281624 731283067 1443 True 1533.00 1533 85.979000 1009 2448 1 chr7A.!!$R1 1439
9 TraesCS7D01G550500 chr7A 731016995 731019504 2509 False 760.00 1543 85.069667 1 2555 3 chr7A.!!$F2 2554
10 TraesCS7D01G550500 chr7A 731234395 731238107 3712 False 724.00 1744 85.057000 1 2558 3 chr7A.!!$F3 2557
11 TraesCS7D01G550500 chr7A 731291878 731292445 567 True 355.00 355 78.902000 458 1011 1 chr7A.!!$R2 553
12 TraesCS7D01G550500 chr4B 625077500 625079298 1798 False 977.50 1718 85.033500 1 1994 2 chr4B.!!$F1 1993

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
819 1948 0.172578 GGGCACAATTAAAGTCGGGC 59.827 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 13343 0.179067 TCTCCCAACACACGACCAAC 60.179 55.0 0.0 0.0 0.0 3.77 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
137 151 8.634475 TTATCTCATCTTAGTCAATCACAACG 57.366 34.615 0.00 0.00 0.00 4.10
231 251 2.785562 TGTTATCCGGTTGGTGAAAGG 58.214 47.619 0.00 0.00 36.30 3.11
235 255 0.536460 TCCGGTTGGTGAAAGGCTTC 60.536 55.000 0.00 0.00 36.30 3.86
245 1312 4.837860 TGGTGAAAGGCTTCCAAAACATAT 59.162 37.500 0.00 0.00 0.00 1.78
290 1357 3.549827 GGACAACAATGCAACATTCACGA 60.550 43.478 0.00 0.00 0.00 4.35
299 1366 3.940852 TGCAACATTCACGAGCTCAATAT 59.059 39.130 15.40 0.00 0.00 1.28
321 1388 3.181434 TGGGGCTTTTACATTGTCACTCT 60.181 43.478 0.00 0.00 0.00 3.24
322 1389 3.440522 GGGGCTTTTACATTGTCACTCTC 59.559 47.826 0.00 0.00 0.00 3.20
344 1411 0.482446 AGTTGGCAGGGGTTGATTGA 59.518 50.000 0.00 0.00 0.00 2.57
345 1412 1.077663 AGTTGGCAGGGGTTGATTGAT 59.922 47.619 0.00 0.00 0.00 2.57
531 1610 5.038033 GCGATGTGGTTTTTGTTCAAGTAA 58.962 37.500 0.00 0.00 0.00 2.24
660 1744 2.853210 CATTGCGACGCGTGAAGT 59.147 55.556 20.70 0.00 0.00 3.01
692 1788 3.576078 TCGTGGGGAAATCATTAGCAT 57.424 42.857 0.00 0.00 0.00 3.79
698 1794 3.058224 GGGGAAATCATTAGCATGCGTAC 60.058 47.826 13.01 0.00 0.00 3.67
819 1948 0.172578 GGGCACAATTAAAGTCGGGC 59.827 55.000 0.00 0.00 0.00 6.13
876 2290 9.384764 ACAAGTACTAAATAAGGCAATCTTCTC 57.615 33.333 0.00 0.00 36.93 2.87
879 2293 4.816925 ACTAAATAAGGCAATCTTCTCCGC 59.183 41.667 0.00 0.00 36.93 5.54
934 11965 6.008331 GGTAACCCCTCCATTATAAATCCAC 58.992 44.000 0.00 0.00 0.00 4.02
975 12006 5.420725 AACCAGCAACTTTCTTTTCCTTT 57.579 34.783 0.00 0.00 0.00 3.11
977 12008 4.222810 ACCAGCAACTTTCTTTTCCTTTGT 59.777 37.500 0.00 0.00 0.00 2.83
1012 12074 1.659233 CCAACAATGCCTCGCAACA 59.341 52.632 0.00 0.00 43.62 3.33
1259 12322 0.755686 GAGGCGATGAACCAGGAGAT 59.244 55.000 0.00 0.00 0.00 2.75
1390 12453 4.796231 CGGTCCTCGTTGGCCTCG 62.796 72.222 3.32 9.57 35.26 4.63
1432 12495 2.319136 TGGCTACAAAGTGAACGTGT 57.681 45.000 0.00 0.00 0.00 4.49
1447 12510 2.061773 ACGTGTTTCTCAAGAGCATCG 58.938 47.619 0.00 0.00 42.67 3.84
1651 12715 1.472201 CCAGCTTCTCTTGCAGCGATA 60.472 52.381 0.00 0.00 41.24 2.92
1652 12716 2.481854 CAGCTTCTCTTGCAGCGATAT 58.518 47.619 0.00 0.00 41.24 1.63
1716 12789 1.339631 CCTTTCGCTCCCATGTACCAA 60.340 52.381 0.00 0.00 0.00 3.67
1785 12859 4.281435 TGGTGGTTAGTACGAGACATTCAA 59.719 41.667 0.00 0.00 0.00 2.69
1847 12925 8.015087 GTCATTGTAATCATCGTGTTCTTTGAA 58.985 33.333 0.00 0.00 0.00 2.69
1850 12928 4.766404 AATCATCGTGTTCTTTGAACCC 57.234 40.909 7.81 0.00 0.00 4.11
1853 12931 3.948473 TCATCGTGTTCTTTGAACCCAAA 59.052 39.130 7.81 0.00 39.74 3.28
1914 12992 3.198853 AGTTGATCTCTTCCCTAGGTTGC 59.801 47.826 8.29 0.00 0.00 4.17
1930 13008 6.825721 CCTAGGTTGCTTGTTTGATCTCTATT 59.174 38.462 0.00 0.00 0.00 1.73
1931 13009 6.506500 AGGTTGCTTGTTTGATCTCTATTG 57.493 37.500 0.00 0.00 0.00 1.90
1999 13300 2.262572 GCCGTGTTTTCTTAGGCATG 57.737 50.000 0.00 0.00 46.48 4.06
2042 13343 5.396484 AGACAATTGATTGATTGCTGAACG 58.604 37.500 13.59 0.00 39.97 3.95
2066 13367 2.431057 GGTCGTGTGTTGGGAGATCTAT 59.569 50.000 0.00 0.00 0.00 1.98
2162 13466 4.759782 TCCTAGAGCAAGCTAAATGTGAC 58.240 43.478 0.00 0.00 0.00 3.67
2194 13504 8.199449 ACTTGCCTGGATAAATATTTGTGAATG 58.801 33.333 11.05 0.00 0.00 2.67
2238 13548 2.031163 GGTGACAGCTCGCCAAGT 59.969 61.111 0.83 0.00 45.39 3.16
2253 13563 2.796593 GCCAAGTGCAAACATCAGAAAC 59.203 45.455 0.00 0.00 40.77 2.78
2268 13578 2.743664 CAGAAACAGCGATGATCCACAA 59.256 45.455 8.12 0.00 0.00 3.33
2289 13599 6.202762 CACAATGTGCTCTTGTTAGTTGTAGA 59.797 38.462 0.00 0.00 34.69 2.59
2325 13635 2.329267 TCAGACCATCCTCTGTTGTGT 58.671 47.619 0.00 0.00 39.08 3.72
2457 13777 0.548682 AGGAGACATGGTGGCCTCTT 60.549 55.000 3.32 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 151 7.967890 ATCAAAAAGTTTCCATGTTTGATCC 57.032 32.000 10.69 0.00 42.40 3.36
263 1330 6.646240 GTGAATGTTGCATTGTTGTCCTATTT 59.354 34.615 0.00 0.00 0.00 1.40
290 1357 4.249638 TGTAAAAGCCCCATATTGAGCT 57.750 40.909 0.00 0.00 37.10 4.09
299 1366 3.153919 GAGTGACAATGTAAAAGCCCCA 58.846 45.455 0.00 0.00 0.00 4.96
321 1388 1.059584 TCAACCCCTGCCAACTCAGA 61.060 55.000 0.00 0.00 36.19 3.27
322 1389 0.038744 ATCAACCCCTGCCAACTCAG 59.961 55.000 0.00 0.00 0.00 3.35
484 1558 4.161377 TGGAAGGAACAAAAAGGTCAAAGG 59.839 41.667 0.00 0.00 34.85 3.11
485 1559 5.337578 TGGAAGGAACAAAAAGGTCAAAG 57.662 39.130 0.00 0.00 34.85 2.77
489 1563 2.287608 CGCTGGAAGGAACAAAAAGGTC 60.288 50.000 0.00 0.00 0.00 3.85
490 1564 1.681264 CGCTGGAAGGAACAAAAAGGT 59.319 47.619 0.00 0.00 0.00 3.50
660 1744 1.376166 CCCACGATGTGCCCGTAAA 60.376 57.895 0.00 0.00 38.29 2.01
692 1788 3.449789 GCGAGACATATCGTACGCA 57.550 52.632 11.24 0.48 46.06 5.24
698 1794 0.386100 CACGGGAGCGAGACATATCG 60.386 60.000 0.00 0.00 45.48 2.92
819 1948 6.471841 CGATCGAATATCTAGCAGATCTTTGG 59.528 42.308 10.26 0.00 36.20 3.28
876 2290 0.865769 GTTTACTGTGACAGGTGCGG 59.134 55.000 17.92 0.00 35.51 5.69
879 2293 4.989168 GGTAAGAGTTTACTGTGACAGGTG 59.011 45.833 17.92 0.00 39.30 4.00
975 12006 3.838565 TGGCAAGAGGATAAAACCAACA 58.161 40.909 0.00 0.00 0.00 3.33
977 12008 4.219115 TGTTGGCAAGAGGATAAAACCAA 58.781 39.130 0.00 0.00 33.50 3.67
1012 12074 1.695989 GGGGATGTACTGGAGGGTCAT 60.696 57.143 0.00 0.00 0.00 3.06
1259 12322 1.469703 CAATGCGCTTGGTGATGAAGA 59.530 47.619 9.73 0.00 0.00 2.87
1390 12453 2.370281 TTGGTGAGCTTCTCGATGTC 57.630 50.000 0.00 0.00 32.35 3.06
1426 12489 2.476619 CGATGCTCTTGAGAAACACGTT 59.523 45.455 1.30 0.00 0.00 3.99
1432 12495 3.184379 CGTTCAACGATGCTCTTGAGAAA 59.816 43.478 3.01 0.00 46.05 2.52
1447 12510 2.157474 GGATTTTTGCCATGCGTTCAAC 59.843 45.455 0.00 0.00 0.00 3.18
1651 12715 4.708576 AGGACTGCATCTTCATCATCAT 57.291 40.909 0.00 0.00 0.00 2.45
1652 12716 4.498894 AAGGACTGCATCTTCATCATCA 57.501 40.909 0.00 0.00 0.00 3.07
1716 12789 2.503061 CGCATGTAGCTGGCCTCT 59.497 61.111 3.32 3.53 42.61 3.69
1930 13008 6.762187 TCAAGATTTACGACCAACTAAACACA 59.238 34.615 0.00 0.00 0.00 3.72
1931 13009 7.042254 ACTCAAGATTTACGACCAACTAAACAC 60.042 37.037 0.00 0.00 0.00 3.32
2042 13343 0.179067 TCTCCCAACACACGACCAAC 60.179 55.000 0.00 0.00 0.00 3.77
2066 13367 3.033659 TGAAACTAAAGGCCCCAACAA 57.966 42.857 0.00 0.00 0.00 2.83
2162 13466 2.620251 TTATCCAGGCAAGTCATCCG 57.380 50.000 0.00 0.00 0.00 4.18
2206 13516 6.418101 AGCTGTCACCATGTAATTAAGTCAT 58.582 36.000 0.00 0.00 0.00 3.06
2237 13547 2.046313 CGCTGTTTCTGATGTTTGCAC 58.954 47.619 0.00 0.00 0.00 4.57
2238 13548 1.946081 TCGCTGTTTCTGATGTTTGCA 59.054 42.857 0.00 0.00 0.00 4.08
2253 13563 1.268386 GCACATTGTGGATCATCGCTG 60.268 52.381 18.05 0.00 33.64 5.18
2268 13578 5.853936 TGTCTACAACTAACAAGAGCACAT 58.146 37.500 0.00 0.00 0.00 3.21
2289 13599 6.611613 TGGTCTGAAGAATAGAGAACATGT 57.388 37.500 0.00 0.00 28.28 3.21
2457 13777 0.677414 TGATTGCATGAAGGCGAGCA 60.677 50.000 0.00 0.00 41.02 4.26


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

AutoCloner maintained by Alex Coulton.