Multiple sequence alignment - TraesCS4A01G169600

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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 TraesCS4A01G169600 chr4A 100.000 2774 0 0 1 2774 428134874 428137647 0 5123
1 TraesCS4A01G169600 chr4A 95.228 985 44 1 971 1955 589099142 589098161 0 1555
2 TraesCS4A01G169600 chr7A 95.736 985 42 0 971 1955 642988075 642987091 0 1587
3 TraesCS4A01G169600 chr7A 95.710 979 31 8 1 968 87762423 87763401 0 1565
4 TraesCS4A01G169600 chr1A 95.736 985 39 1 971 1955 498219683 498218702 0 1583
5 TraesCS4A01G169600 chr1A 95.403 979 42 1 971 1949 23400448 23401423 0 1555
6 TraesCS4A01G169600 chr1A 94.958 952 28 10 1 934 62667512 62668461 0 1474
7 TraesCS4A01G169600 chr5A 95.436 986 41 2 971 1955 99544018 99543036 0 1568
8 TraesCS4A01G169600 chr6A 95.330 985 43 1 971 1955 396286574 396285593 0 1561
9 TraesCS4A01G169600 chr6A 95.399 978 41 2 973 1949 37847899 37848873 0 1554
10 TraesCS4A01G169600 chr6A 96.608 796 27 0 1979 2774 592295055 592295850 0 1321
11 TraesCS4A01G169600 chr3A 95.228 985 44 1 971 1955 717936170 717935189 0 1555
12 TraesCS4A01G169600 chr3A 94.320 986 37 11 1 970 596887369 596888351 0 1493
13 TraesCS4A01G169600 chr3A 94.320 986 37 11 1 970 596938322 596939304 0 1493
14 TraesCS4A01G169600 chr3A 93.441 991 42 11 1 971 596865094 596866081 0 1448
15 TraesCS4A01G169600 chr2A 95.306 980 42 2 971 1949 202057225 202058201 0 1552
16 TraesCS4A01G169600 chr2A 94.630 987 36 7 1 971 376910985 376911970 0 1513
17 TraesCS4A01G169600 chr2A 94.416 985 41 10 1 972 376917725 376918708 0 1502
18 TraesCS4A01G169600 chr2A 89.180 878 40 24 126 973 228216496 228215644 0 1044
19 TraesCS4A01G169600 chr6D 94.534 988 36 11 1 971 330608786 330609772 0 1509
20 TraesCS4A01G169600 chr6D 94.260 993 33 11 1 970 330656628 330657619 0 1496
21 TraesCS4A01G169600 chr5D 97.111 796 21 1 1979 2774 384429563 384428770 0 1341
22 TraesCS4A01G169600 chr5D 96.859 796 25 0 1979 2774 174300752 174299957 0 1332
23 TraesCS4A01G169600 chr5D 96.742 798 26 0 1977 2774 371075657 371076454 0 1330
24 TraesCS4A01G169600 chr5D 96.734 796 26 0 1979 2774 193610385 193611180 0 1327
25 TraesCS4A01G169600 chr3D 96.985 796 24 0 1979 2774 550987391 550986596 0 1338
26 TraesCS4A01G169600 chr3D 96.985 796 24 0 1979 2774 552271435 552272230 0 1338
27 TraesCS4A01G169600 chr3D 96.859 796 25 0 1979 2774 2391650 2390855 0 1332
28 TraesCS4A01G169600 chr7D 96.608 796 27 0 1979 2774 501412696 501413491 0 1321


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 TraesCS4A01G169600 chr4A 428134874 428137647 2773 False 5123 5123 100.000 1 2774 1 chr4A.!!$F1 2773
1 TraesCS4A01G169600 chr4A 589098161 589099142 981 True 1555 1555 95.228 971 1955 1 chr4A.!!$R1 984
2 TraesCS4A01G169600 chr7A 642987091 642988075 984 True 1587 1587 95.736 971 1955 1 chr7A.!!$R1 984
3 TraesCS4A01G169600 chr7A 87762423 87763401 978 False 1565 1565 95.710 1 968 1 chr7A.!!$F1 967
4 TraesCS4A01G169600 chr1A 498218702 498219683 981 True 1583 1583 95.736 971 1955 1 chr1A.!!$R1 984
5 TraesCS4A01G169600 chr1A 23400448 23401423 975 False 1555 1555 95.403 971 1949 1 chr1A.!!$F1 978
6 TraesCS4A01G169600 chr1A 62667512 62668461 949 False 1474 1474 94.958 1 934 1 chr1A.!!$F2 933
7 TraesCS4A01G169600 chr5A 99543036 99544018 982 True 1568 1568 95.436 971 1955 1 chr5A.!!$R1 984
8 TraesCS4A01G169600 chr6A 396285593 396286574 981 True 1561 1561 95.330 971 1955 1 chr6A.!!$R1 984
9 TraesCS4A01G169600 chr6A 37847899 37848873 974 False 1554 1554 95.399 973 1949 1 chr6A.!!$F1 976
10 TraesCS4A01G169600 chr6A 592295055 592295850 795 False 1321 1321 96.608 1979 2774 1 chr6A.!!$F2 795
11 TraesCS4A01G169600 chr3A 717935189 717936170 981 True 1555 1555 95.228 971 1955 1 chr3A.!!$R1 984
12 TraesCS4A01G169600 chr3A 596887369 596888351 982 False 1493 1493 94.320 1 970 1 chr3A.!!$F2 969
13 TraesCS4A01G169600 chr3A 596938322 596939304 982 False 1493 1493 94.320 1 970 1 chr3A.!!$F3 969
14 TraesCS4A01G169600 chr3A 596865094 596866081 987 False 1448 1448 93.441 1 971 1 chr3A.!!$F1 970
15 TraesCS4A01G169600 chr2A 202057225 202058201 976 False 1552 1552 95.306 971 1949 1 chr2A.!!$F1 978
16 TraesCS4A01G169600 chr2A 376910985 376911970 985 False 1513 1513 94.630 1 971 1 chr2A.!!$F2 970
17 TraesCS4A01G169600 chr2A 376917725 376918708 983 False 1502 1502 94.416 1 972 1 chr2A.!!$F3 971
18 TraesCS4A01G169600 chr2A 228215644 228216496 852 True 1044 1044 89.180 126 973 1 chr2A.!!$R1 847
19 TraesCS4A01G169600 chr6D 330608786 330609772 986 False 1509 1509 94.534 1 971 1 chr6D.!!$F1 970
20 TraesCS4A01G169600 chr6D 330656628 330657619 991 False 1496 1496 94.260 1 970 1 chr6D.!!$F2 969
21 TraesCS4A01G169600 chr5D 384428770 384429563 793 True 1341 1341 97.111 1979 2774 1 chr5D.!!$R2 795
22 TraesCS4A01G169600 chr5D 174299957 174300752 795 True 1332 1332 96.859 1979 2774 1 chr5D.!!$R1 795
23 TraesCS4A01G169600 chr5D 371075657 371076454 797 False 1330 1330 96.742 1977 2774 1 chr5D.!!$F2 797
24 TraesCS4A01G169600 chr5D 193610385 193611180 795 False 1327 1327 96.734 1979 2774 1 chr5D.!!$F1 795
25 TraesCS4A01G169600 chr3D 550986596 550987391 795 True 1338 1338 96.985 1979 2774 1 chr3D.!!$R2 795
26 TraesCS4A01G169600 chr3D 552271435 552272230 795 False 1338 1338 96.985 1979 2774 1 chr3D.!!$F1 795
27 TraesCS4A01G169600 chr3D 2390855 2391650 795 True 1332 1332 96.859 1979 2774 1 chr3D.!!$R1 795
28 TraesCS4A01G169600 chr7D 501412696 501413491 795 False 1321 1321 96.608 1979 2774 1 chr7D.!!$F1 795

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
109 110 3.477210 AAGAAGTGGAAAGAGCGAACT 57.523 42.857 0.0 0.0 0.00 3.01 F
1292 1342 1.167851 CATCAACCCGATGTGCTTGT 58.832 50.000 0.0 0.0 45.61 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 1646 0.179089 CTGCTACGAGCTTGCTCCAT 60.179 55.0 15.87 7.91 42.97 3.41 R
2226 2276 0.037590 TTGTCTTAGGCGGCAATGGT 59.962 50.0 13.08 0.00 0.00 3.55 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
109 110 3.477210 AAGAAGTGGAAAGAGCGAACT 57.523 42.857 0.00 0.00 0.00 3.01
180 187 6.928979 TCTGTTCTCCAAATTGAAACGTAA 57.071 33.333 0.00 0.00 0.00 3.18
403 431 6.761099 ACACGTAATTATAATTTGGTGCCA 57.239 33.333 25.65 6.06 35.53 4.92
581 612 8.455598 AATTTGGAAATATTTAAACGACGGTG 57.544 30.769 0.00 0.00 0.00 4.94
601 632 9.878599 GACGGTGAAACTCCAAATAATATAATG 57.121 33.333 0.00 0.00 36.74 1.90
1004 1053 6.646267 AGCGTCAAGTTTAATCCTTGGTATA 58.354 36.000 12.78 0.00 39.78 1.47
1292 1342 1.167851 CATCAACCCGATGTGCTTGT 58.832 50.000 0.00 0.00 45.61 3.16
1401 1451 1.484444 GGTCTGTTCCAGCCTCACCT 61.484 60.000 0.00 0.00 0.00 4.00
1590 1640 1.903860 TGTATGTTACCCGCTTCCAGT 59.096 47.619 0.00 0.00 0.00 4.00
1596 1646 3.140623 GTTACCCGCTTCCAGTTTTGTA 58.859 45.455 0.00 0.00 0.00 2.41
1623 1673 2.430751 CTCGTAGCAGTGCACGCA 60.431 61.111 27.05 16.97 34.81 5.24
1652 1702 1.373570 GTGAGCATAGTCCACTTGCC 58.626 55.000 9.08 4.26 37.07 4.52
1656 1706 3.263170 TGAGCATAGTCCACTTGCCTTTA 59.737 43.478 9.08 0.00 37.07 1.85
1688 1738 6.597672 ACATACGATGGCTTCTTGAAAATACA 59.402 34.615 0.00 0.00 33.60 2.29
1703 1753 8.996024 TTGAAAATACACGAGTTGAGATATGA 57.004 30.769 0.00 0.00 0.00 2.15
1708 1758 2.025155 ACGAGTTGAGATATGACCGCT 58.975 47.619 0.00 0.00 0.00 5.52
1775 1825 6.621514 AGGATCTATCAAAGGGGAAGTACAAT 59.378 38.462 0.00 0.00 0.00 2.71
1813 1863 1.534235 ACGGAGTCCCTGCTGTTCT 60.534 57.895 2.80 0.00 29.74 3.01
1862 1912 2.943036 TCTTTACTTTCCCGTTGGCT 57.057 45.000 0.00 0.00 0.00 4.75
1931 1981 2.807967 CAGTGCACCGAGATCAAGAAAA 59.192 45.455 14.63 0.00 0.00 2.29
1949 1999 1.273759 AACAGCTGATGAGAGCCAGA 58.726 50.000 23.35 0.00 40.08 3.86
1951 2001 0.179078 CAGCTGATGAGAGCCAGACC 60.179 60.000 8.42 0.00 40.08 3.85
1955 2005 2.683152 GCTGATGAGAGCCAGACCATTT 60.683 50.000 0.00 0.00 32.35 2.32
1956 2006 3.204526 CTGATGAGAGCCAGACCATTTC 58.795 50.000 0.00 0.00 32.37 2.17
1957 2007 2.092753 TGATGAGAGCCAGACCATTTCC 60.093 50.000 0.00 0.00 0.00 3.13
1958 2008 0.620556 TGAGAGCCAGACCATTTCCC 59.379 55.000 0.00 0.00 0.00 3.97
1959 2009 0.106967 GAGAGCCAGACCATTTCCCC 60.107 60.000 0.00 0.00 0.00 4.81
1960 2010 0.846427 AGAGCCAGACCATTTCCCCA 60.846 55.000 0.00 0.00 0.00 4.96
1961 2011 0.259938 GAGCCAGACCATTTCCCCAT 59.740 55.000 0.00 0.00 0.00 4.00
1962 2012 0.259938 AGCCAGACCATTTCCCCATC 59.740 55.000 0.00 0.00 0.00 3.51
1963 2013 0.259938 GCCAGACCATTTCCCCATCT 59.740 55.000 0.00 0.00 0.00 2.90
1964 2014 1.342374 GCCAGACCATTTCCCCATCTT 60.342 52.381 0.00 0.00 0.00 2.40
1965 2015 2.381911 CCAGACCATTTCCCCATCTTG 58.618 52.381 0.00 0.00 0.00 3.02
1966 2016 2.291800 CCAGACCATTTCCCCATCTTGT 60.292 50.000 0.00 0.00 0.00 3.16
1967 2017 3.019564 CAGACCATTTCCCCATCTTGTC 58.980 50.000 0.00 0.00 0.00 3.18
1968 2018 2.649312 AGACCATTTCCCCATCTTGTCA 59.351 45.455 0.00 0.00 0.00 3.58
1969 2019 2.755103 GACCATTTCCCCATCTTGTCAC 59.245 50.000 0.00 0.00 0.00 3.67
1970 2020 1.745087 CCATTTCCCCATCTTGTCACG 59.255 52.381 0.00 0.00 0.00 4.35
1971 2021 2.436417 CATTTCCCCATCTTGTCACGT 58.564 47.619 0.00 0.00 0.00 4.49
1972 2022 1.890876 TTTCCCCATCTTGTCACGTG 58.109 50.000 9.94 9.94 0.00 4.49
1973 2023 0.605319 TTCCCCATCTTGTCACGTGC 60.605 55.000 11.67 6.86 0.00 5.34
1974 2024 2.040544 CCCCATCTTGTCACGTGCC 61.041 63.158 11.67 0.00 0.00 5.01
1975 2025 2.390599 CCCATCTTGTCACGTGCCG 61.391 63.158 11.67 0.00 0.00 5.69
2020 2070 0.460311 CACCGAAGCGAAGTCCCTAT 59.540 55.000 0.00 0.00 0.00 2.57
2060 2110 0.251297 CCCCTTCTTGTCACATGCCA 60.251 55.000 0.00 0.00 0.00 4.92
2064 2114 3.411446 CCTTCTTGTCACATGCCAAGTA 58.589 45.455 15.77 8.86 39.25 2.24
2161 2211 2.829120 CCTCTCCTCCTCTCGTTTCTTT 59.171 50.000 0.00 0.00 0.00 2.52
2186 2236 2.091610 TCCATCCTCTCCTTCTGACGAT 60.092 50.000 0.00 0.00 0.00 3.73
2281 2331 3.558505 CTTTTTGACATCTTCTGGCACG 58.441 45.455 0.00 0.00 44.75 5.34
2491 2541 3.000041 CGTCCATGATTTCTTTCGGTCA 59.000 45.455 0.00 0.00 0.00 4.02
2742 2792 4.282496 ACCCTAACACCAACATCAAACAA 58.718 39.130 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.004086 TCCACTTTGATGTCTTAATTGTTCCT 58.996 34.615 0.00 0.00 0.00 3.36
109 110 3.261897 CCTCTCCCTCTAGCACTTGAAAA 59.738 47.826 0.00 0.00 0.00 2.29
180 187 2.270858 GAACCCCTTCTTCCTCCTCTT 58.729 52.381 0.00 0.00 0.00 2.85
1004 1053 6.237942 CGCTGTAATTCGTCATCTTCATCTTT 60.238 38.462 0.00 0.00 0.00 2.52
1108 1157 1.403780 GGCGTAATCGTGTCCAACTCT 60.404 52.381 0.00 0.00 39.49 3.24
1292 1342 0.870313 AGCCAGAGATCCCTATCCCA 59.130 55.000 0.00 0.00 31.98 4.37
1342 1392 4.557296 CGATGTGGCAAATGAAACTCAACT 60.557 41.667 0.00 0.00 0.00 3.16
1401 1451 1.529796 GTATCCACCCATTCCGGCA 59.470 57.895 0.00 0.00 0.00 5.69
1516 1566 0.397941 CTGCCTTCTCCTGTCCAACA 59.602 55.000 0.00 0.00 0.00 3.33
1590 1640 2.778299 ACGAGCTTGCTCCATACAAAA 58.222 42.857 15.87 0.00 0.00 2.44
1596 1646 0.179089 CTGCTACGAGCTTGCTCCAT 60.179 55.000 15.87 7.91 42.97 3.41
1652 1702 9.477484 AGAAGCCATCGTATGTAGTTATTAAAG 57.523 33.333 0.00 0.00 0.00 1.85
1656 1706 7.497595 TCAAGAAGCCATCGTATGTAGTTATT 58.502 34.615 0.00 0.00 0.00 1.40
1688 1738 2.025155 AGCGGTCATATCTCAACTCGT 58.975 47.619 0.00 0.00 0.00 4.18
1703 1753 1.977854 TCCTCATTATATGCCAGCGGT 59.022 47.619 0.00 0.00 0.00 5.68
1708 1758 9.676861 CTTCAAGAATATCCTCATTATATGCCA 57.323 33.333 0.00 0.00 0.00 4.92
1775 1825 1.573857 TGCCCTACCCTGACATCTCTA 59.426 52.381 0.00 0.00 0.00 2.43
1813 1863 7.455058 ACACTTTACCACATAGTTAATCACCA 58.545 34.615 0.00 0.00 0.00 4.17
1862 1912 6.832520 AGCCATTCAAACATGTGTAATACA 57.167 33.333 0.00 0.00 44.87 2.29
1931 1981 0.536260 GTCTGGCTCTCATCAGCTGT 59.464 55.000 14.67 0.00 39.58 4.40
1949 1999 2.807676 GTGACAAGATGGGGAAATGGT 58.192 47.619 0.00 0.00 0.00 3.55
1951 2001 2.162208 CACGTGACAAGATGGGGAAATG 59.838 50.000 10.90 0.00 0.00 2.32
1955 2005 1.003839 GCACGTGACAAGATGGGGA 60.004 57.895 22.23 0.00 0.00 4.81
1956 2006 2.040544 GGCACGTGACAAGATGGGG 61.041 63.158 22.23 0.00 0.00 4.96
1957 2007 3.578456 GGCACGTGACAAGATGGG 58.422 61.111 22.23 0.00 0.00 4.00
1970 2020 4.352887 GTCAACTATCTTCTACTCGGCAC 58.647 47.826 0.00 0.00 0.00 5.01
1971 2021 3.064958 CGTCAACTATCTTCTACTCGGCA 59.935 47.826 0.00 0.00 0.00 5.69
1972 2022 3.311871 TCGTCAACTATCTTCTACTCGGC 59.688 47.826 0.00 0.00 0.00 5.54
1973 2023 4.550447 CGTCGTCAACTATCTTCTACTCGG 60.550 50.000 0.00 0.00 0.00 4.63
1974 2024 4.267214 TCGTCGTCAACTATCTTCTACTCG 59.733 45.833 0.00 0.00 0.00 4.18
1975 2025 5.291614 ACTCGTCGTCAACTATCTTCTACTC 59.708 44.000 0.00 0.00 0.00 2.59
2020 2070 1.195115 AATGGCCTCGCTCTACTCAA 58.805 50.000 3.32 0.00 0.00 3.02
2060 2110 0.533032 GAGGCGCAAGAGGAGTACTT 59.467 55.000 10.83 0.00 43.02 2.24
2086 2136 3.706086 AGAGGGAAAGAAAGCTTGCAAAA 59.294 39.130 7.33 0.00 33.79 2.44
2161 2211 0.260230 AGAAGGAGAGGATGGAGCGA 59.740 55.000 0.00 0.00 0.00 4.93
2186 2236 0.546267 AGAGGCTTGGAGGAAGAGCA 60.546 55.000 0.00 0.00 38.14 4.26
2226 2276 0.037590 TTGTCTTAGGCGGCAATGGT 59.962 50.000 13.08 0.00 0.00 3.55
2281 2331 5.000012 ACTTCACGTGGATAGATCTTGAC 58.000 43.478 17.00 0.00 0.00 3.18
2491 2541 0.179018 GCAAGGTGAAGGTGTCCACT 60.179 55.000 0.00 0.00 33.99 4.00
2742 2792 5.909417 AGTATGCTAGGGTTAGGGTTATGTT 59.091 40.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.