Multiple sequence alignment - TraesCS7B01G051100

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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 TraesCS7B01G051100 chr7B 100.000 2471 0 0 1 2471 52971637 52969167 0.000000e+00 4564
1 TraesCS7B01G051100 chr7B 94.103 2018 77 17 1 1994 139532997 139530998 0.000000e+00 3029
2 TraesCS7B01G051100 chr7B 96.633 594 19 1 1879 2471 139531077 139530484 0.000000e+00 985
3 TraesCS7B01G051100 chr7B 95.946 148 6 0 1811 1958 139531109 139530962 8.830000e-60 241
4 TraesCS7B01G051100 chr7B 100.000 116 0 0 1843 1958 52969759 52969644 5.350000e-52 215
5 TraesCS7B01G051100 chr3A 95.900 2512 52 18 1 2471 633121748 633124249 0.000000e+00 4021
6 TraesCS7B01G051100 chr6A 95.990 2494 52 23 1 2471 64687549 64685081 0.000000e+00 4008
7 TraesCS7B01G051100 chr1B 95.496 2509 68 16 1 2471 672580368 672577867 0.000000e+00 3965
8 TraesCS7B01G051100 chr7A 95.664 2491 63 23 1 2471 60253082 60255547 0.000000e+00 3960
9 TraesCS7B01G051100 chr7A 94.415 1325 41 21 1154 2471 120866201 120864903 0.000000e+00 2006
10 TraesCS7B01G051100 chr4B 95.303 2491 72 23 1 2471 209133129 209135594 0.000000e+00 3910
11 TraesCS7B01G051100 chrUn 95.476 2100 46 23 1 2076 86468008 86465934 0.000000e+00 3306
12 TraesCS7B01G051100 chrUn 96.774 1488 29 4 1 1471 189419837 189418352 0.000000e+00 2464
13 TraesCS7B01G051100 chrUn 96.946 1015 18 2 1 1002 419931691 419930677 0.000000e+00 1690
14 TraesCS7B01G051100 chr6D 96.040 1894 54 7 1 1880 102373355 102375241 0.000000e+00 3062
15 TraesCS7B01G051100 chr6D 94.702 151 8 0 1844 1994 153924031 153923881 4.110000e-58 235
16 TraesCS7B01G051100 chr4A 95.095 1896 63 13 1 1886 275492688 275490813 0.000000e+00 2959
17 TraesCS7B01G051100 chr3B 93.944 1288 58 17 1199 2471 669841305 669840023 0.000000e+00 1929
18 TraesCS7B01G051100 chr3B 97.643 594 13 1 1879 2471 483376343 483376936 0.000000e+00 1018
19 TraesCS7B01G051100 chr3B 98.701 154 2 0 1805 1958 483376305 483376458 8.710000e-70 274
20 TraesCS7B01G051100 chr3B 94.595 148 8 0 1811 1958 669840646 669840499 1.910000e-56 230
21 TraesCS7B01G051100 chr6B 97.315 596 13 2 1879 2471 625627480 625626885 0.000000e+00 1009
22 TraesCS7B01G051100 chr6B 96.633 594 19 1 1879 2471 297448755 297449348 0.000000e+00 985
23 TraesCS7B01G051100 chr6B 95.966 595 22 1 1879 2471 215778908 215779502 0.000000e+00 965
24 TraesCS7B01G051100 chr6B 99.324 148 1 0 1811 1958 625627512 625627365 4.050000e-68 268
25 TraesCS7B01G051100 chr6B 97.403 154 4 0 1805 1958 215778870 215779023 1.880000e-66 263
26 TraesCS7B01G051100 chr6B 96.104 154 6 0 1805 1958 297448717 297448870 4.080000e-63 252
27 TraesCS7B01G051100 chr2D 95.953 593 23 1 1880 2471 189921712 189922304 0.000000e+00 961
28 TraesCS7B01G051100 chr1A 95.863 556 10 2 1 543 94735373 94735928 0.000000e+00 887
29 TraesCS7B01G051100 chr4D 97.006 167 4 1 1 166 450952659 450952825 1.870000e-71 279


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 TraesCS7B01G051100 chr7B 52969167 52971637 2470 True 2389.500000 4564 100.000000 1 2471 2 chr7B.!!$R1 2470
1 TraesCS7B01G051100 chr7B 139530484 139532997 2513 True 1418.333333 3029 95.560667 1 2471 3 chr7B.!!$R2 2470
2 TraesCS7B01G051100 chr3A 633121748 633124249 2501 False 4021.000000 4021 95.900000 1 2471 1 chr3A.!!$F1 2470
3 TraesCS7B01G051100 chr6A 64685081 64687549 2468 True 4008.000000 4008 95.990000 1 2471 1 chr6A.!!$R1 2470
4 TraesCS7B01G051100 chr1B 672577867 672580368 2501 True 3965.000000 3965 95.496000 1 2471 1 chr1B.!!$R1 2470
5 TraesCS7B01G051100 chr7A 60253082 60255547 2465 False 3960.000000 3960 95.664000 1 2471 1 chr7A.!!$F1 2470
6 TraesCS7B01G051100 chr7A 120864903 120866201 1298 True 2006.000000 2006 94.415000 1154 2471 1 chr7A.!!$R1 1317
7 TraesCS7B01G051100 chr4B 209133129 209135594 2465 False 3910.000000 3910 95.303000 1 2471 1 chr4B.!!$F1 2470
8 TraesCS7B01G051100 chrUn 86465934 86468008 2074 True 3306.000000 3306 95.476000 1 2076 1 chrUn.!!$R1 2075
9 TraesCS7B01G051100 chrUn 189418352 189419837 1485 True 2464.000000 2464 96.774000 1 1471 1 chrUn.!!$R2 1470
10 TraesCS7B01G051100 chrUn 419930677 419931691 1014 True 1690.000000 1690 96.946000 1 1002 1 chrUn.!!$R3 1001
11 TraesCS7B01G051100 chr6D 102373355 102375241 1886 False 3062.000000 3062 96.040000 1 1880 1 chr6D.!!$F1 1879
12 TraesCS7B01G051100 chr4A 275490813 275492688 1875 True 2959.000000 2959 95.095000 1 1886 1 chr4A.!!$R1 1885
13 TraesCS7B01G051100 chr3B 669840023 669841305 1282 True 1079.500000 1929 94.269500 1199 2471 2 chr3B.!!$R1 1272
14 TraesCS7B01G051100 chr3B 483376305 483376936 631 False 646.000000 1018 98.172000 1805 2471 2 chr3B.!!$F1 666
15 TraesCS7B01G051100 chr6B 625626885 625627512 627 True 638.500000 1009 98.319500 1811 2471 2 chr6B.!!$R1 660
16 TraesCS7B01G051100 chr6B 297448717 297449348 631 False 618.500000 985 96.368500 1805 2471 2 chr6B.!!$F2 666
17 TraesCS7B01G051100 chr6B 215778870 215779502 632 False 614.000000 965 96.684500 1805 2471 2 chr6B.!!$F1 666
18 TraesCS7B01G051100 chr2D 189921712 189922304 592 False 961.000000 961 95.953000 1880 2471 1 chr2D.!!$F1 591
19 TraesCS7B01G051100 chr1A 94735373 94735928 555 False 887.000000 887 95.863000 1 543 1 chr1A.!!$F1 542

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
780 794 0.318107 CCAACAAAGGCTTGCTCGTG 60.318 55.0 0.0 0.0 35.84 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2398 1.040646 TATCAGTGGCCTCGTGATCC 58.959 55.0 15.65 0.0 33.05 3.36 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
402 416 5.874261 GTCTCTTCTCAAAAGCTTATCTGCT 59.126 40.000 0.00 0.0 46.40 4.24
701 715 0.461961 GTCTATCTTCGCACCTGGCT 59.538 55.000 0.00 0.0 41.67 4.75
709 723 2.753029 GCACCTGGCTCTTCTGGT 59.247 61.111 0.00 0.0 40.25 4.00
718 732 2.371841 TGGCTCTTCTGGTGCTTTCTTA 59.628 45.455 0.00 0.0 35.10 2.10
741 755 3.254093 TCCACCTTCCTCTTGTACTCA 57.746 47.619 0.00 0.0 0.00 3.41
753 767 1.263356 TGTACTCAACTCTTCCCCGG 58.737 55.000 0.00 0.0 0.00 5.73
780 794 0.318107 CCAACAAAGGCTTGCTCGTG 60.318 55.000 0.00 0.0 35.84 4.35
850 864 0.991920 GATGACTTGGGAGGGTTCCA 59.008 55.000 0.00 0.0 45.98 3.53
903 917 6.288941 TCATTCACATCAGAAATGGCAAAT 57.711 33.333 0.00 0.0 0.00 2.32
1152 1173 3.711842 CAACTGCTTTCGCGCCGA 61.712 61.111 0.00 0.0 39.65 5.54
1188 1215 3.967987 GGAGCAAGGACCCTAAGAATCTA 59.032 47.826 0.00 0.0 0.00 1.98
1285 1312 4.379813 GGTGTAAGACCGTCGACTATTTGA 60.380 45.833 14.70 0.0 34.02 2.69
1379 1406 8.474025 ACAGATTCTCTATTTGATCTCGAAGTT 58.526 33.333 0.00 0.0 0.00 2.66
1652 1680 1.062810 ACTTGGCTTTGGGGTGGTTTA 60.063 47.619 0.00 0.0 0.00 2.01
1730 1760 7.984617 CCCTTGTTCTTCCTTTTGATTTAAACA 59.015 33.333 0.00 0.0 0.00 2.83
1738 1768 6.919721 TCCTTTTGATTTAAACATTCTCCCG 58.080 36.000 0.00 0.0 0.00 5.14
1806 1839 5.807909 TCATGAAAATGTGGAGAGTGATGA 58.192 37.500 0.00 0.0 0.00 2.92
1807 1840 6.420638 TCATGAAAATGTGGAGAGTGATGAT 58.579 36.000 0.00 0.0 0.00 2.45
1808 1841 6.888088 TCATGAAAATGTGGAGAGTGATGATT 59.112 34.615 0.00 0.0 0.00 2.57
1809 1842 6.748333 TGAAAATGTGGAGAGTGATGATTC 57.252 37.500 0.00 0.0 0.00 2.52
1828 1861 4.553668 TCGGATCTCGACACGGAT 57.446 55.556 2.65 0.0 43.74 4.18
1829 1862 2.789842 TCGGATCTCGACACGGATT 58.210 52.632 2.65 0.0 43.74 3.01
1830 1863 1.957668 TCGGATCTCGACACGGATTA 58.042 50.000 2.65 0.0 43.74 1.75
1831 1864 2.501261 TCGGATCTCGACACGGATTAT 58.499 47.619 2.65 0.0 43.74 1.28
1832 1865 2.225727 TCGGATCTCGACACGGATTATG 59.774 50.000 2.65 0.0 43.74 1.90
1833 1866 2.225727 CGGATCTCGACACGGATTATGA 59.774 50.000 0.00 0.0 42.43 2.15
1834 1867 3.119814 CGGATCTCGACACGGATTATGAT 60.120 47.826 0.00 0.0 42.43 2.45
1835 1868 4.169508 GGATCTCGACACGGATTATGATG 58.830 47.826 0.00 0.0 0.00 3.07
1836 1869 4.082733 GGATCTCGACACGGATTATGATGA 60.083 45.833 0.00 0.0 0.00 2.92
1837 1870 4.489679 TCTCGACACGGATTATGATGAG 57.510 45.455 0.00 0.0 0.00 2.90
1838 1871 2.983136 CTCGACACGGATTATGATGAGC 59.017 50.000 0.00 0.0 0.00 4.26
1839 1872 2.623416 TCGACACGGATTATGATGAGCT 59.377 45.455 0.00 0.0 0.00 4.09
1840 1873 3.818773 TCGACACGGATTATGATGAGCTA 59.181 43.478 0.00 0.0 0.00 3.32
1841 1874 4.277423 TCGACACGGATTATGATGAGCTAA 59.723 41.667 0.00 0.0 0.00 3.09
1842 1875 4.383052 CGACACGGATTATGATGAGCTAAC 59.617 45.833 0.00 0.0 0.00 2.34
1843 1876 5.533482 GACACGGATTATGATGAGCTAACT 58.467 41.667 0.00 0.0 0.00 2.24
1844 1877 5.292765 ACACGGATTATGATGAGCTAACTG 58.707 41.667 0.00 0.0 0.00 3.16
1845 1878 5.069119 ACACGGATTATGATGAGCTAACTGA 59.931 40.000 0.00 0.0 0.00 3.41
1846 1879 6.162079 CACGGATTATGATGAGCTAACTGAT 58.838 40.000 0.00 0.0 0.00 2.90
1847 1880 6.090493 CACGGATTATGATGAGCTAACTGATG 59.910 42.308 0.00 0.0 0.00 3.07
2177 2397 6.908870 TTGTGTAGTGATCTATGTTCATGC 57.091 37.500 0.00 0.0 0.00 4.06
2178 2398 5.043248 TGTGTAGTGATCTATGTTCATGCG 58.957 41.667 0.00 0.0 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 117 7.103641 CCTTAGAGCTGAAAACCTACATACAA 58.896 38.462 0.00 0.00 0.00 2.41
302 316 1.475034 GGAGAATAGCATGCACGGGAA 60.475 52.381 21.98 0.00 0.00 3.97
664 678 4.437682 AGACCATCAAAGAACTCCACAA 57.562 40.909 0.00 0.00 0.00 3.33
701 715 4.102524 TGGAAGTAAGAAAGCACCAGAAGA 59.897 41.667 0.00 0.00 0.00 2.87
709 723 3.394606 AGGAAGGTGGAAGTAAGAAAGCA 59.605 43.478 0.00 0.00 0.00 3.91
718 732 3.579151 GAGTACAAGAGGAAGGTGGAAGT 59.421 47.826 0.00 0.00 0.00 3.01
741 755 1.192803 GGAGTGACCGGGGAAGAGTT 61.193 60.000 6.32 0.00 0.00 3.01
753 767 0.178990 AGCCTTTGTTGGGGAGTGAC 60.179 55.000 0.00 0.00 0.00 3.67
780 794 5.927115 AGAAAGAGTTTGGACTATGACGAAC 59.073 40.000 0.00 0.00 35.88 3.95
1152 1173 4.924187 CTCCGGATCTCGCCCCCT 62.924 72.222 3.57 0.00 37.59 4.79
1285 1312 6.605119 TCAGAGTGATTTTCCTCCTTTTTCT 58.395 36.000 0.00 0.00 0.00 2.52
1379 1406 6.183360 CCGACTGGAAGAAGTGTTATATGAGA 60.183 42.308 0.00 0.00 37.43 3.27
1652 1680 4.319133 GTGGCATTGTCCACGGAT 57.681 55.556 12.42 0.00 45.95 4.18
1738 1768 2.439156 AATTCTGCAGCTCCCGGC 60.439 61.111 9.47 0.00 42.19 6.13
1825 1858 8.789825 AATCATCAGTTAGCTCATCATAATCC 57.210 34.615 0.00 0.00 0.00 3.01
1826 1859 9.433153 TGAATCATCAGTTAGCTCATCATAATC 57.567 33.333 0.00 0.00 0.00 1.75
1827 1860 9.961264 ATGAATCATCAGTTAGCTCATCATAAT 57.039 29.630 0.00 0.00 39.39 1.28
1828 1861 9.433153 GATGAATCATCAGTTAGCTCATCATAA 57.567 33.333 17.60 0.00 40.28 1.90
1829 1862 8.591072 TGATGAATCATCAGTTAGCTCATCATA 58.409 33.333 20.85 0.00 44.60 2.15
1830 1863 7.450903 TGATGAATCATCAGTTAGCTCATCAT 58.549 34.615 20.85 0.00 44.60 2.45
1831 1864 6.823497 TGATGAATCATCAGTTAGCTCATCA 58.177 36.000 20.85 7.55 44.60 3.07
2106 2326 7.699812 GCTTGCTTCTTCAAATCTCGAAATAAT 59.300 33.333 0.00 0.00 0.00 1.28
2168 2388 1.575244 CTCGTGATCCGCATGAACAT 58.425 50.000 0.00 0.00 41.77 2.71
2177 2397 2.021068 ATCAGTGGCCTCGTGATCCG 62.021 60.000 3.32 0.00 38.13 4.18
2178 2398 1.040646 TATCAGTGGCCTCGTGATCC 58.959 55.000 15.65 0.00 33.05 3.36
2343 2563 3.503748 AGCATTGAACAACCTACTTCAGC 59.496 43.478 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.