Multiple sequence alignment - TraesCS7D01G119200

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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 TraesCS7D01G119200 chr7D 100.000 2378 0 0 1 2378 74082953 74085330 0.000000e+00 4392.0
1 TraesCS7D01G119200 chrUn 97.106 1762 51 0 617 2378 220751136 220752897 0.000000e+00 2972.0
2 TraesCS7D01G119200 chrUn 97.106 1762 51 0 617 2378 245706208 245704447 0.000000e+00 2972.0
3 TraesCS7D01G119200 chrUn 96.992 1762 53 0 617 2378 67510633 67512394 0.000000e+00 2961.0
4 TraesCS7D01G119200 chrUn 96.992 1762 53 0 617 2378 291535580 291533819 0.000000e+00 2961.0
5 TraesCS7D01G119200 chrUn 96.935 1762 54 0 617 2378 67492169 67493930 0.000000e+00 2955.0
6 TraesCS7D01G119200 chrUn 96.879 1762 55 0 617 2378 67500868 67502629 0.000000e+00 2950.0
7 TraesCS7D01G119200 chrUn 96.879 1762 55 0 617 2378 237320538 237318777 0.000000e+00 2950.0
8 TraesCS7D01G119200 chrUn 96.879 1762 55 0 617 2378 342573963 342575724 0.000000e+00 2950.0
9 TraesCS7D01G119200 chrUn 87.500 632 65 12 1 626 309507836 309507213 0.000000e+00 717.0
10 TraesCS7D01G119200 chrUn 87.809 607 60 12 1 601 318597270 318597868 0.000000e+00 699.0
11 TraesCS7D01G119200 chrUn 87.809 607 60 12 1 601 323562141 323561543 0.000000e+00 699.0
12 TraesCS7D01G119200 chrUn 87.809 607 60 12 1 601 328977245 328977843 0.000000e+00 699.0
13 TraesCS7D01G119200 chr5D 96.992 1762 53 0 617 2378 18999064 18997303 0.000000e+00 2961.0
14 TraesCS7D01G119200 chr7B 90.172 641 37 9 1 617 677110487 677111125 0.000000e+00 811.0
15 TraesCS7D01G119200 chr7B 87.678 633 63 13 1 626 649129836 649129212 0.000000e+00 723.0
16 TraesCS7D01G119200 chr7B 87.460 630 63 13 1 617 649251915 649251289 0.000000e+00 712.0
17 TraesCS7D01G119200 chr7A 88.504 635 47 3 6 615 84134703 84134070 0.000000e+00 745.0
18 TraesCS7D01G119200 chr3A 91.837 49 3 1 576 624 62763811 62763858 1.530000e-07 67.6


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 TraesCS7D01G119200 chr7D 74082953 74085330 2377 False 4392 4392 100.000 1 2378 1 chr7D.!!$F1 2377
1 TraesCS7D01G119200 chrUn 220751136 220752897 1761 False 2972 2972 97.106 617 2378 1 chrUn.!!$F4 1761
2 TraesCS7D01G119200 chrUn 245704447 245706208 1761 True 2972 2972 97.106 617 2378 1 chrUn.!!$R2 1761
3 TraesCS7D01G119200 chrUn 67510633 67512394 1761 False 2961 2961 96.992 617 2378 1 chrUn.!!$F3 1761
4 TraesCS7D01G119200 chrUn 291533819 291535580 1761 True 2961 2961 96.992 617 2378 1 chrUn.!!$R3 1761
5 TraesCS7D01G119200 chrUn 67492169 67493930 1761 False 2955 2955 96.935 617 2378 1 chrUn.!!$F1 1761
6 TraesCS7D01G119200 chrUn 67500868 67502629 1761 False 2950 2950 96.879 617 2378 1 chrUn.!!$F2 1761
7 TraesCS7D01G119200 chrUn 237318777 237320538 1761 True 2950 2950 96.879 617 2378 1 chrUn.!!$R1 1761
8 TraesCS7D01G119200 chrUn 342573963 342575724 1761 False 2950 2950 96.879 617 2378 1 chrUn.!!$F7 1761
9 TraesCS7D01G119200 chrUn 309507213 309507836 623 True 717 717 87.500 1 626 1 chrUn.!!$R4 625
10 TraesCS7D01G119200 chrUn 318597270 318597868 598 False 699 699 87.809 1 601 1 chrUn.!!$F5 600
11 TraesCS7D01G119200 chrUn 323561543 323562141 598 True 699 699 87.809 1 601 1 chrUn.!!$R5 600
12 TraesCS7D01G119200 chrUn 328977245 328977843 598 False 699 699 87.809 1 601 1 chrUn.!!$F6 600
13 TraesCS7D01G119200 chr5D 18997303 18999064 1761 True 2961 2961 96.992 617 2378 1 chr5D.!!$R1 1761
14 TraesCS7D01G119200 chr7B 677110487 677111125 638 False 811 811 90.172 1 617 1 chr7B.!!$F1 616
15 TraesCS7D01G119200 chr7B 649129212 649129836 624 True 723 723 87.678 1 626 1 chr7B.!!$R1 625
16 TraesCS7D01G119200 chr7B 649251289 649251915 626 True 712 712 87.460 1 617 1 chr7B.!!$R2 616
17 TraesCS7D01G119200 chr7A 84134070 84134703 633 True 745 745 88.504 6 615 1 chr7A.!!$R1 609

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
593 622 1.16527 GCAAAATGACTAGCCCGTGT 58.835 50.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 2217 1.153449 TGTCATCCAATCCGTCGGC 60.153 57.895 6.34 0.0 0.0 5.54 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
95 96 2.376109 TGTACCGCCAAAAAGGACAAA 58.624 42.857 0.00 0.00 41.22 2.83
211 214 3.824133 TGATCCAATGGCTCCTAATGTG 58.176 45.455 0.18 0.00 0.00 3.21
222 225 4.270325 GGCTCCTAATGTGTTATGTTCGTC 59.730 45.833 0.00 0.00 0.00 4.20
329 333 9.498176 AATAAGGTTAAGTAAAACAGTGACGAT 57.502 29.630 0.00 0.00 0.00 3.73
402 430 5.277058 GCTACTTTTGCAATCGTAGATGAGG 60.277 44.000 26.86 10.66 45.12 3.86
406 434 4.670896 TTGCAATCGTAGATGAGGATGA 57.329 40.909 0.00 0.00 45.12 2.92
408 436 5.219343 TGCAATCGTAGATGAGGATGAAT 57.781 39.130 0.00 0.00 45.12 2.57
482 510 7.906527 GTGTACATCCACGGTTGTATTATTTTC 59.093 37.037 9.61 0.00 34.24 2.29
593 622 1.165270 GCAAAATGACTAGCCCGTGT 58.835 50.000 0.00 0.00 0.00 4.49
878 907 3.107601 CCCTTCACAGAAGATCAGGGTA 58.892 50.000 8.26 0.00 36.88 3.69
1178 1207 1.600916 GGACCAGCAAGAGCCGTTT 60.601 57.895 0.00 0.00 43.56 3.60
1499 1528 4.521256 GCCTCTCTAGACTACAATTCGGAT 59.479 45.833 0.00 0.00 0.00 4.18
1587 1616 2.464157 AAGTTTCTTCTCCTCCGCTG 57.536 50.000 0.00 0.00 0.00 5.18
1590 1619 2.167487 AGTTTCTTCTCCTCCGCTGATC 59.833 50.000 0.00 0.00 0.00 2.92
1608 1637 6.865726 CGCTGATCTATATGCTTAAACTCAGT 59.134 38.462 0.00 0.00 32.27 3.41
1686 1715 1.599542 GTCGTTCTGAGGCCATAATGC 59.400 52.381 5.01 0.00 0.00 3.56
1844 1873 1.553690 CGATGAGGGTGGTTGGGAGT 61.554 60.000 0.00 0.00 0.00 3.85
1859 1888 0.951558 GGAGTGTGTTTTGGCGTGAT 59.048 50.000 0.00 0.00 0.00 3.06
1943 1972 0.451383 TTCGCGGGATTCTGCAATTG 59.549 50.000 6.13 0.00 45.28 2.32
1957 1986 2.290008 TGCAATTGACACCAGGTATCGT 60.290 45.455 10.34 0.00 0.00 3.73
2092 2121 3.412386 GTTAGGCACAGTGTTCCTTGAT 58.588 45.455 19.93 0.00 30.73 2.57
2099 2128 2.158623 ACAGTGTTCCTTGATGCCTTCA 60.159 45.455 0.00 0.00 0.00 3.02
2166 2195 2.185310 GAGGTGGTCGAGGCATTGGT 62.185 60.000 0.00 0.00 0.00 3.67
2167 2196 1.303317 GGTGGTCGAGGCATTGGTT 60.303 57.895 0.00 0.00 0.00 3.67
2175 2204 0.955428 GAGGCATTGGTTGAGCGACA 60.955 55.000 0.00 0.00 0.00 4.35
2176 2205 0.322816 AGGCATTGGTTGAGCGACAT 60.323 50.000 0.00 0.00 0.00 3.06
2178 2207 1.949525 GGCATTGGTTGAGCGACATAT 59.050 47.619 0.00 0.00 0.00 1.78
2179 2208 2.287188 GGCATTGGTTGAGCGACATATG 60.287 50.000 0.00 0.00 0.00 1.78
2188 2217 3.612919 CGACATATGGTGCCGTCG 58.387 61.111 7.80 2.23 44.34 5.12
2206 2235 1.153449 GCCGACGGATTGGATGACA 60.153 57.895 20.50 0.00 0.00 3.58
2215 2244 3.850095 TTGGATGACACGTGCGCGA 62.850 57.895 28.73 3.44 42.00 5.87
2297 2326 5.182760 TGTTACGACTTCTCCTTCCTCTAAC 59.817 44.000 0.00 0.00 0.00 2.34
2309 2338 5.661759 TCCTTCCTCTAACTGATAAGGTTCC 59.338 44.000 0.00 0.00 38.18 3.62
2321 2350 4.782691 TGATAAGGTTCCATGGACTTCTCA 59.217 41.667 20.47 20.47 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.937436 ACCAAACTCCGTCCATTATTAATC 57.063 37.500 0.00 0.00 0.00 1.75
121 122 8.362639 AGCAATAACTTGAAACATTTCATCACT 58.637 29.630 7.83 0.00 45.65 3.41
211 214 8.736742 CAATATGCAAATCAAGACGAACATAAC 58.263 33.333 0.00 0.00 0.00 1.89
222 225 8.067784 GCATGAATTTCCAATATGCAAATCAAG 58.932 33.333 12.19 0.00 42.63 3.02
326 330 6.603095 AGTTGCAAGAGCTTTAACTTAATCG 58.397 36.000 0.00 0.00 42.74 3.34
338 342 4.072131 TCCGATTTTAAGTTGCAAGAGCT 58.928 39.130 0.00 0.00 42.74 4.09
593 622 1.149401 TTGTCAACCCGTGCATCCA 59.851 52.632 0.00 0.00 0.00 3.41
812 841 2.076863 GACCCGAAAGATGGTGAACTG 58.923 52.381 0.00 0.00 34.20 3.16
948 977 1.874019 GACATGCGTGCGAGTCGAT 60.874 57.895 18.61 0.00 0.00 3.59
1483 1512 3.449377 TGTGCCATCCGAATTGTAGTCTA 59.551 43.478 0.00 0.00 0.00 2.59
1587 1616 7.445945 ACCCACTGAGTTTAAGCATATAGATC 58.554 38.462 0.00 0.00 0.00 2.75
1590 1619 7.727181 ACTACCCACTGAGTTTAAGCATATAG 58.273 38.462 0.00 0.00 0.00 1.31
1652 1681 1.164041 AACGACCCAGCAAACGAAGG 61.164 55.000 0.00 0.00 0.00 3.46
1796 1825 3.785859 GCGGCATCTGGTCCCTCA 61.786 66.667 0.00 0.00 0.00 3.86
1943 1972 2.793232 GCGAAATACGATACCTGGTGTC 59.207 50.000 13.07 13.07 45.77 3.67
1957 1986 4.912214 TCGATGAAGAACGTAGCGAAATA 58.088 39.130 0.00 0.00 0.00 1.40
2099 2128 1.173913 GTAAAAGAACCCATGGCGCT 58.826 50.000 6.09 0.00 0.00 5.92
2166 2195 3.079131 GGCACCATATGTCGCTCAA 57.921 52.632 11.96 0.00 0.00 3.02
2167 2196 4.855105 GGCACCATATGTCGCTCA 57.145 55.556 11.96 0.00 0.00 4.26
2188 2217 1.153449 TGTCATCCAATCCGTCGGC 60.153 57.895 6.34 0.00 0.00 5.54
2206 2235 1.204062 CAAAACAGATCGCGCACGT 59.796 52.632 8.75 0.00 41.18 4.49
2215 2244 2.810400 CGTGACCCTGACCAAAACAGAT 60.810 50.000 0.00 0.00 37.54 2.90
2260 2289 3.805971 AGTCGTAACAAGGTTTGTGTAGC 59.194 43.478 0.00 0.00 44.59 3.58
2266 2295 4.377897 AGGAGAAGTCGTAACAAGGTTTG 58.622 43.478 0.00 0.00 0.00 2.93
2297 2326 5.104776 TGAGAAGTCCATGGAACCTTATCAG 60.105 44.000 26.58 0.00 32.11 2.90
2356 2385 1.967779 TCCGGTGAAGTGTTCAGATCA 59.032 47.619 0.00 0.00 41.01 2.92


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

AutoCloner maintained by Alex Coulton.