Multiple sequence alignment - TraesCS7A01G275000

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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 TraesCS7A01G275000 chr7A 100.000 2702 0 0 1 2702 287804242 287806943 0.000000e+00 4990.0
1 TraesCS7A01G275000 chr7D 94.614 2692 93 21 61 2702 264311011 264313700 0.000000e+00 4120.0
2 TraesCS7A01G275000 chr7D 90.925 1763 87 18 261 1965 264306132 264307879 0.000000e+00 2302.0
3 TraesCS7A01G275000 chr7D 81.794 1137 159 24 801 1904 264315198 264316319 0.000000e+00 909.0
4 TraesCS7A01G275000 chr7D 93.103 58 4 0 1 58 264303129 264303186 4.790000e-13 86.1
5 TraesCS7A01G275000 chr7B 94.830 2476 102 15 61 2513 244624102 244626574 0.000000e+00 3840.0
6 TraesCS7A01G275000 chr7B 88.287 1921 126 36 440 2276 244600422 244602327 0.000000e+00 2209.0
7 TraesCS7A01G275000 chr7B 89.568 1390 107 16 490 1842 244566050 244567438 0.000000e+00 1729.0
8 TraesCS7A01G275000 chr7B 81.074 1136 157 25 801 1904 244631498 244632607 0.000000e+00 854.0
9 TraesCS7A01G275000 chr7B 81.464 1079 149 25 795 1840 244635719 244636779 0.000000e+00 837.0
10 TraesCS7A01G275000 chr7B 93.878 196 7 3 2505 2699 244629645 244629836 9.460000e-75 291.0
11 TraesCS7A01G275000 chr7B 86.345 249 15 5 61 309 244598000 244598229 1.240000e-63 254.0
12 TraesCS7A01G275000 chr7B 89.888 89 7 2 301 387 244599829 244599917 2.200000e-21 113.0
13 TraesCS7A01G275000 chr3D 81.372 1079 160 22 797 1857 583027005 583025950 0.000000e+00 841.0
14 TraesCS7A01G275000 chr3D 80.075 1069 168 28 801 1842 583222923 583221873 0.000000e+00 752.0
15 TraesCS7A01G275000 chr3B 79.563 1145 183 32 728 1843 780300029 780298907 0.000000e+00 771.0
16 TraesCS7A01G275000 chr3B 80.865 1040 146 30 838 1841 780301924 780300902 0.000000e+00 769.0
17 TraesCS7A01G275000 chr6B 80.896 1005 150 20 804 1787 62676316 62675333 0.000000e+00 754.0
18 TraesCS7A01G275000 chr6B 80.263 912 138 20 804 1694 62680863 62679973 0.000000e+00 649.0
19 TraesCS7A01G275000 chr6B 80.263 912 138 20 804 1694 62685482 62684592 0.000000e+00 649.0
20 TraesCS7A01G275000 chrUn 80.210 1046 159 28 820 1836 352585812 352586838 0.000000e+00 741.0
21 TraesCS7A01G275000 chr6A 80.697 1005 145 30 816 1792 34392737 34391754 0.000000e+00 736.0


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 TraesCS7A01G275000 chr7A 287804242 287806943 2701 False 4990.000000 4990 100.000000 1 2702 1 chr7A.!!$F1 2701
1 TraesCS7A01G275000 chr7D 264303129 264316319 13190 False 1854.275000 4120 90.109000 1 2702 4 chr7D.!!$F1 2701
2 TraesCS7A01G275000 chr7B 244566050 244567438 1388 False 1729.000000 1729 89.568000 490 1842 1 chr7B.!!$F1 1352
3 TraesCS7A01G275000 chr7B 244624102 244636779 12677 False 1455.500000 3840 87.811500 61 2699 4 chr7B.!!$F3 2638
4 TraesCS7A01G275000 chr7B 244598000 244602327 4327 False 858.666667 2209 88.173333 61 2276 3 chr7B.!!$F2 2215
5 TraesCS7A01G275000 chr3D 583025950 583027005 1055 True 841.000000 841 81.372000 797 1857 1 chr3D.!!$R1 1060
6 TraesCS7A01G275000 chr3D 583221873 583222923 1050 True 752.000000 752 80.075000 801 1842 1 chr3D.!!$R2 1041
7 TraesCS7A01G275000 chr3B 780298907 780301924 3017 True 770.000000 771 80.214000 728 1843 2 chr3B.!!$R1 1115
8 TraesCS7A01G275000 chr6B 62675333 62685482 10149 True 684.000000 754 80.474000 804 1787 3 chr6B.!!$R1 983
9 TraesCS7A01G275000 chrUn 352585812 352586838 1026 False 741.000000 741 80.210000 820 1836 1 chrUn.!!$F1 1016
10 TraesCS7A01G275000 chr6A 34391754 34392737 983 True 736.000000 736 80.697000 816 1792 1 chr6A.!!$R1 976

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
58 59 0.475906 AGCAAACAGGGAAGACAGCT 59.524 50.0 0.0 0.0 0.0 4.24 F
59 60 0.877743 GCAAACAGGGAAGACAGCTC 59.122 55.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 11610 0.394565 CCACCCCATTCTCGAGATCC 59.605 60.000 17.44 0.0 0.0 3.36 R
1858 11853 3.798202 AGGACATCGAAAGGAAGTATGC 58.202 45.455 0.00 0.0 0.0 3.14 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
46 47 1.610038 CAGCTCATGTCCAAGCAAACA 59.390 47.619 6.86 0.00 41.06 2.83
58 59 0.475906 AGCAAACAGGGAAGACAGCT 59.524 50.000 0.00 0.00 0.00 4.24
59 60 0.877743 GCAAACAGGGAAGACAGCTC 59.122 55.000 0.00 0.00 0.00 4.09
369 9803 2.911120 TGACTAAAAACACGATTGCGC 58.089 42.857 0.00 0.00 42.48 6.09
473 10384 5.096443 AGGTAGCTCAATCTGAAAGGAAG 57.904 43.478 0.00 0.00 0.00 3.46
582 10493 6.507958 TCCAAAGCATGACGATTCAATTAA 57.492 33.333 0.00 0.00 34.61 1.40
612 10523 3.312736 ACACTTCCCACCAAAGAACAT 57.687 42.857 0.00 0.00 0.00 2.71
657 10588 4.260538 GCTCACAGCTAGATGTTGCATTAC 60.261 45.833 23.00 3.96 38.45 1.89
977 10952 4.082190 TCTCCTCTCTTCAACCACAATACG 60.082 45.833 0.00 0.00 0.00 3.06
1147 11122 2.363018 CCGGTCTGAGGAGGCTCA 60.363 66.667 17.69 0.00 0.00 4.26
1278 11268 3.005554 CACCATGCAAGAGATCTTCGTT 58.994 45.455 0.00 0.00 33.11 3.85
1383 11373 1.886861 CTCGTTTGGTGAAGACGGCG 61.887 60.000 4.80 4.80 37.39 6.46
1407 11397 3.565482 AGAAACATTTCAAGAAGAGCGCA 59.435 39.130 11.47 0.00 39.61 6.09
1430 11420 4.623932 AGAAGGCTAATGTTGTGTCTGA 57.376 40.909 0.00 0.00 0.00 3.27
1450 11440 1.076024 AGGGTTGCAAGATGGTCATGT 59.924 47.619 0.00 0.00 0.00 3.21
1570 11560 5.593909 TCAAAGGCATTTCACAAGAAGAAGA 59.406 36.000 0.00 0.00 34.71 2.87
1620 11610 5.452077 GCAGGAGTTAGAGTGTAGTATTGGG 60.452 48.000 0.00 0.00 0.00 4.12
1798 11793 5.464057 TGCCATATGTATACAGTACAAACGC 59.536 40.000 11.91 5.41 0.00 4.84
1858 11853 8.890124 ATCTATTTCATGTCTTGTGATCTCTG 57.110 34.615 0.00 0.00 0.00 3.35
2001 12007 1.081892 CACATGGCTGTACAGTCTGC 58.918 55.000 26.75 12.32 33.14 4.26
2108 12114 4.943705 AGCTCCATATCGTTCAAACATGTT 59.056 37.500 4.92 4.92 0.00 2.71
2110 12116 4.980590 TCCATATCGTTCAAACATGTTGC 58.019 39.130 12.82 2.50 0.00 4.17
2162 12190 2.205022 TCTGCTTGTTCTTGGGGATG 57.795 50.000 0.00 0.00 0.00 3.51
2316 12344 4.344102 TGGTAAGAAAGCACAGTGTAGACT 59.656 41.667 1.61 0.00 0.00 3.24
2347 12375 2.237643 ACTTCAGAGGCTAGAGAGTCGA 59.762 50.000 0.00 0.00 30.20 4.20
2392 12420 2.677524 GCAGGTTGGATGCTGGCA 60.678 61.111 0.00 0.00 40.59 4.92
2464 12492 0.249197 CTCCGCTGCTTCGATCATCA 60.249 55.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.037446 AGCTGCAATTTTGGTTCGAAAGTA 59.963 37.500 0.00 0.00 0.00 2.24
13 14 2.420628 TGAGCTGCAATTTTGGTTCG 57.579 45.000 1.02 0.00 0.00 3.95
46 47 1.968310 GACACGAGCTGTCTTCCCT 59.032 57.895 0.00 0.00 45.38 4.20
58 59 3.698250 CCTTGAAAGGTGGACACGA 57.302 52.632 0.57 0.00 41.41 4.35
117 156 9.690913 TTGATTTTTAGTGATGGAGATCTTCAT 57.309 29.630 16.84 16.84 33.08 2.57
473 10384 4.381185 GGTTCAACGTTTTATCCCCCATTC 60.381 45.833 0.00 0.00 0.00 2.67
582 10493 3.245229 TGGTGGGAAGTGTTGCTAATCAT 60.245 43.478 0.00 0.00 0.00 2.45
633 10544 1.012841 GCAACATCTAGCTGTGAGCC 58.987 55.000 11.36 0.00 43.77 4.70
757 10699 9.672673 ATGTTTAGTGCATATTTTAGAGTGTCT 57.327 29.630 0.00 0.00 0.00 3.41
977 10952 7.811713 CCATTTCTGATCTTGAAGTTTTTCTCC 59.188 37.037 0.00 0.00 34.31 3.71
1095 11070 0.475632 TGGTGGTGGTGGAGGAAGAT 60.476 55.000 0.00 0.00 0.00 2.40
1147 11122 5.745312 TCAACACCATTGTAGATGTCTCT 57.255 39.130 0.00 0.00 33.55 3.10
1383 11373 4.614702 GCGCTCTTCTTGAAATGTTTCTTC 59.385 41.667 0.00 0.00 38.02 2.87
1407 11397 5.376625 TCAGACACAACATTAGCCTTCTTT 58.623 37.500 0.00 0.00 0.00 2.52
1430 11420 1.076024 ACATGACCATCTTGCAACCCT 59.924 47.619 0.00 0.00 0.00 4.34
1450 11440 6.814954 AATCTCTCTAGCCTTGGTCAATAA 57.185 37.500 0.00 0.00 0.00 1.40
1570 11560 0.550914 TCCTCCTGGCAAACAACTGT 59.449 50.000 0.00 0.00 0.00 3.55
1620 11610 0.394565 CCACCCCATTCTCGAGATCC 59.605 60.000 17.44 0.00 0.00 3.36
1796 11791 9.107367 CTTTTTCTTTCTATAAGTTTCTGTGCG 57.893 33.333 0.00 0.00 0.00 5.34
1858 11853 3.798202 AGGACATCGAAAGGAAGTATGC 58.202 45.455 0.00 0.00 0.00 3.14
1921 11918 4.263550 TGCTAATAACAACCTTAGGCACCA 60.264 41.667 0.00 0.00 0.00 4.17
2108 12114 5.798125 TTTGGAATATTTTGGTCACTGCA 57.202 34.783 0.00 0.00 0.00 4.41
2110 12116 8.606040 ATGTTTTTGGAATATTTTGGTCACTG 57.394 30.769 0.00 0.00 0.00 3.66
2316 12344 9.696572 TCTCTAGCCTCTGAAGTTAACTAATTA 57.303 33.333 8.92 0.00 0.00 1.40
2392 12420 2.031616 CATGCCGCCAGGATCGAT 59.968 61.111 0.00 0.00 41.02 3.59
2515 15622 3.577848 ACAGCCCTATGCACAAAAATGAA 59.422 39.130 0.00 0.00 44.83 2.57


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

AutoCloner maintained by Alex Coulton.