Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022841.1 Corchorus olitorius cultivar O-4 contig22874, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8768
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:3808 original size:21 final size:22
Alignment explanation
Indices: 3784--3824 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3774 TTGCCTCATA
*
3784 CATTCATTCAT-CATGCCATGG
1 CATTCATTCATGCATCCCATGG
3805 CATTCATTCATGCATCCCAT
1 CATTCATTCATGCATCCCAT
3825 TAAACTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.34
Consensus pattern (22 bp):
CATTCATTCATGCATCCCATGG
Found at i:5820 original size:6 final size:6
Alignment explanation
Indices: 5809--5834 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5799 TTTCCCAAAA
5809 AAAATG AAAATG AAAATG AAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AA
5835 GAAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:6299 original size:12 final size:12
Alignment explanation
Indices: 6242--6282 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
6232 GAAATTCAAA
6242 AAAAAAATCATC
1 AAAAAAATCATC
*
6254 AAAAACATCATC
1 AAAAAAATCATC
6266 AAAAAAATCATC
1 AAAAAAATCATC
6278 AAAAA
1 AAAAA
6283 GAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.68, C:0.17, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAATCATC
Found at i:6967 original size:50 final size:50
Alignment explanation
Indices: 6891--7032 Score: 203
Period size: 50 Copynumber: 2.8 Consensus size: 50
6881 AATGAGATTT
* *
6891 CTTTCCATTTATGAGTTCAAGATCAAAATTCACTTTTCAAAGTAAAACTG
1 CTTTCCATTTGTGAGTTCAAGATCAAAATTCACTTTTCAAAGTAAAACTA
* ** *
6941 CTTTCCATTTGTGAGTTCAAGGTCAAAATTCACTTTTCAAAGTAGGATTA
1 CTTTCCATTTGTGAGTTCAAGATCAAAATTCACTTTTCAAAGTAAAACTA
* * *
6991 CATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 CTTTCCATTTGTGAGTTCAAGATCAAAATTCACTTTTCAAAG
7033 GGCATTTAAG
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 82 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.36
Consensus pattern (50 bp):
CTTTCCATTTGTGAGTTCAAGATCAAAATTCACTTTTCAAAGTAAAACTA
Found at i:7712 original size:50 final size:49
Alignment explanation
Indices: 7635--7822 Score: 304
Period size: 50 Copynumber: 3.8 Consensus size: 49
7625 CGAATGCTTC
*
7635 GGCTTTTCCACAAACCAAACTCGTTTCCATACGAGTCAATTATCAACAT
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
*
7684 GGACTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACG
1 GG-CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA-T
7735 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
* * *
7784 AGGCTTTTCCACAAGCCGAAGTCGTTCCCATACGAGTCA
1 -GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
7823 TTTCAAACCT
Statistics
Matches: 130, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
49 2 0.02
50 126 0.97
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (49 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAT
Found at i:8018 original size:50 final size:50
Alignment explanation
Indices: 7881--8038 Score: 253
Period size: 50 Copynumber: 3.1 Consensus size: 50
7871 TTACTTTTTT
* * *
7881 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATTAGTGGAAGACGATCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
7931 TTTTATAGAATTGAATTGGTAGACAGTTCAAACGATAAGCGGAAGACGGTCC
1 TTTTA-AG-ATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
7983 TTTTAAGATTAAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
8033 TTTTAA
1 TTTTAA
8039 TATATTAGAG
Statistics
Matches: 100, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
50 52 0.52
51 4 0.04
52 44 0.44
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:8057 original size:102 final size:102
Alignment explanation
Indices: 7881--8064 Score: 264
Period size: 102 Copynumber: 1.8 Consensus size: 102
7871 TTACTTTTTT
* * *
7881 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATTAGTGGAAGACGATCCTTTTATAGAATTGAA
1 TTTTAAGATTAAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTATAGAATTGAA
* * *
7946 TTGGTAGACAGTTCAAACGATAAGCGGAAGACGGTCC
66 GTGGAAGACAATTCAAACGATAAGCGGAAGACGGTCC
* *
7983 TTTTAAGATTAAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAATA-TATT-A
1 TTTTAAGATTAAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTT-ATAGAATTGA
8046 GAGTGGAAGACAATTCAAA
65 -AGTGGAAGACAATTCAAA
8065 GAAATTGATC
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
101 1 0.01
102 68 0.94
103 3 0.04
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (102 bp):
TTTTAAGATTAAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTATAGAATTGAA
GTGGAAGACAATTCAAACGATAAGCGGAAGACGGTCC
Found at i:8471 original size:21 final size:21
Alignment explanation
Indices: 8445--8488 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
8435 TTTTGTCTCT
8445 ATTTCGTTCACCGTAAGTTGC
1 ATTTCGTTCACCGTAAGTTGC
8466 ATTTCGTTCACCGTAAGTTGC
1 ATTTCGTTCACCGTAAGTTGC
8487 AT
1 AT
8489 GGTATTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (21 bp):
ATTTCGTTCACCGTAAGTTGC
Done.