Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024342.1 Corchorus olitorius cultivar O-4 contig24375, 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: 13827
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Found at i:3908 original size:30 final size:30
Alignment explanation
Indices: 3874--3979 Score: 176
Period size: 30 Copynumber: 3.5 Consensus size: 30
3864 GGCTGACACC
*
3874 TCAAATTCCTCCTCAGGATCTTCATCCGGG
1 TCAAAATCCTCCTCAGGATCTTCATCCGGG
*
3904 TCAAAATCCTCCTCGGGATCTTCATCCGGG
1 TCAAAATCCTCCTCAGGATCTTCATCCGGG
*
3934 TCAAAATCCTCCTCAGGATCCTCATCCGGG
1 TCAAAATCCTCCTCAGGATCTTCATCCGGG
*
3964 TCAAAATCATCCTCAG
1 TCAAAATCCTCCTCAG
3980 AATCCGAATC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (30 bp):
TCAAAATCCTCCTCAGGATCTTCATCCGGG
Found at i:5831 original size:2 final size:2
Alignment explanation
Indices: 5824--5853 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5814 TTCCCTTGAC
5824 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5854 TAAAAAGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11203 original size:74 final size:74
Alignment explanation
Indices: 11121--11294 Score: 203
Period size: 73 Copynumber: 2.4 Consensus size: 74
11111 AAAAACGCTT
* *
11121 TTGATGGGAACTTTCCCACTTTGAAAACTAAAAATGAAAATG-ACGGGAACTTTCCCTAAATTG-
1 TTGATGGGAACTTTCCCAATTTAAAAACTAAAAA--AAAATGAACGGGAACTTTCCC-AAATTGA
11184 AAAAC-TAAAAC
63 AAAACTTAAAAC
*** * * *
11195 TTGATGGGAACTTTCCCAATTTAAAAACTTTGAAAAACTGAATGGGAACTTTCCCAATTTGAAAA
1 TTGATGGGAACTTTCCCAATTTAAAAACTAAAAAAAAATGAACGGGAACTTTCCCAAATTGAAAA
11260 ACTTAAAAC
66 ACTTAAAAC
* *
11269 -TGGTGGGAACTTTCCCAATTAAAAAA
1 TTGATGGGAACTTTCCCAATTTAAAAA
11295 ACTTTGAACA
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
72 10 0.11
73 42 0.48
74 35 0.40
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (74 bp):
TTGATGGGAACTTTCCCAATTTAAAAACTAAAAAAAAATGAACGGGAACTTTCCCAAATTGAAAA
ACTTAAAAC
Found at i:11211 original size:35 final size:34
Alignment explanation
Indices: 11157--11288 Score: 151
Period size: 35 Copynumber: 3.7 Consensus size: 34
11147 ACTAAAAATG
* *
11157 AAAA-TGACGGGAACTTTCCCTAAATTGAAAAC-T
1 AAAACTGATGGGAACTTTCCC-AATTTGAAAACTT
*
11190 AAAACTTGATGGGAACTTTCCCAATTTAAAAACTTT
1 AAAAC-TGATGGGAACTTTCCCAATTTGAAAAC-TT
11226 GAAAAACTGAATGGGAACTTTCCCAATTTGAAAAACTT
1 --AAAACTG-ATGGGAACTTTCCCAATTTG-AAAACTT
*
11264 AAAACTGGTGGGAACTTTCCCAATT
1 AAAACTGATGGGAACTTTCCCAATT
11289 AAAAAAACTT
Statistics
Matches: 86, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
33 4 0.05
34 9 0.10
35 32 0.37
36 8 0.09
37 2 0.02
38 26 0.30
39 5 0.06
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28
Consensus pattern (34 bp):
AAAACTGATGGGAACTTTCCCAATTTGAAAACTT
Found at i:11241 original size:38 final size:37
Alignment explanation
Indices: 11190--11302 Score: 151
Period size: 38 Copynumber: 3.0 Consensus size: 37
11180 ATTGAAAACT
11190 AAAACTTGATGGGAACTTTCCCAATTTAAAAACTTTGA
1 AAAAC-TGATGGGAACTTTCCCAATTTAAAAACTTTGA
11228 AAAACTGAATGGGAACTTTCCCAATTTGAAAAAC-TT--
1 AAAACTG-ATGGGAACTTTCCCAATTT-AAAAACTTTGA
* *
11264 AAAACTGGTGGGAACTTTCCCAATTAAAAAAACTTTGA
1 AAAACTGATGGGAACTTTCCCAATT-TAAAAACTTTGA
11302 A
1 A
11303 CATGATGAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
35 23 0.34
36 9 0.13
37 2 0.03
38 27 0.40
39 6 0.09
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (37 bp):
AAAACTGATGGGAACTTTCCCAATTTAAAAACTTTGA
Found at i:11284 original size:73 final size:74
Alignment explanation
Indices: 11165--11302 Score: 210
Period size: 73 Copynumber: 1.9 Consensus size: 74
11155 TGAAAATGAC
*
11165 GGGAACTTTCCCTAAATTGAAAACTAAAACTTGATGGGAACTTTCCCAATT-TAAAAACTTTGAA
1 GGGAACTTTCCCTAAATTGAAAACTAAAACTTGATGGGAACTTTCCCAATTAAAAAAACTTTGAA
11229 AAACTGAAT
66 AAACTGAAT
* *
11238 GGGAACTTTCCC-AATTTGAAAAACTTAAAAC-TGGTGGGAACTTTCCCAATTAAAAAAACTTTG
1 GGGAACTTTCCCTAAATTG-AAAAC-TAAAACTTGATGGGAACTTTCCCAATTAAAAAAACTTTG
11301 AA
64 AA
11303 CATGATGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
72 5 0.08
73 36 0.61
74 18 0.31
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (74 bp):
GGGAACTTTCCCTAAATTGAAAACTAAAACTTGATGGGAACTTTCCCAATTAAAAAAACTTTGAA
AAACTGAAT
Found at i:12164 original size:19 final size:19
Alignment explanation
Indices: 12140--12178 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
12130 GGGTTTAGTA
12140 TAAATGCTAAATTTTCCAT
1 TAAATGCTAAATTTTCCAT
12159 TAAATGCTAAATTTTCCAT
1 TAAATGCTAAATTTTCCAT
12178 T
1 T
12179 CTTCTTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (19 bp):
TAAATGCTAAATTTTCCAT
Done.