Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016979.1 Corchorus olitorius cultivar O-4 contig17012, 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: 24846
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Found at i:4369 original size:22 final size:22
Alignment explanation
Indices: 4339--4383 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
4329 GTTCTTAAAG
*
4339 TACCCAAATCTGCCTTAATTAC
1 TACCAAAATCTGCCTTAATTAC
*
4361 TACCAAAATCTGCTTTAATTAC
1 TACCAAAATCTGCCTTAATTAC
4383 T
1 T
4384 GCCCAATCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (22 bp):
TACCAAAATCTGCCTTAATTAC
Found at i:13864 original size:23 final size:23
Alignment explanation
Indices: 13832--13954 Score: 175
Period size: 23 Copynumber: 5.5 Consensus size: 23
13822 TTAATAACAC
*
13832 CTTGGGCCATTTTATTTTCTTTA
1 CTTGGTCCATTTTATTTTCTTTA
13855 CTTGGTCCATTTTATTTTCTTTA
1 CTTGGTCCATTTTATTTTCTTTA
13878 CTTGGTCCATTTTATTTTTCTTTA
1 CTTGGTCCATTTTA-TTTTCTTTA
*
13902 CTTGGTCCGTTTTA--TTC---A
1 CTTGGTCCATTTTATTTTCTTTA
*
13920 CTTGGTCCGTTTTATTTTCTTTA
1 CTTGGTCCATTTTATTTTCTTTA
13943 CTTGGTCCATTT
1 CTTGGTCCATTT
13955 CTTTATTTCC
Statistics
Matches: 91, Mismatches: 3, Indels: 12
0.86 0.03 0.11
Matches are distributed among these distances:
18 15 0.16
20 3 0.03
21 3 0.03
23 48 0.53
24 22 0.24
ACGTcount: A:0.11, C:0.19, G:0.12, T:0.58
Consensus pattern (23 bp):
CTTGGTCCATTTTATTTTCTTTA
Found at i:13922 original size:18 final size:18
Alignment explanation
Indices: 13901--13935 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
13891 ATTTTTCTTT
13901 ACTTGGTCCGTTTTATTC
1 ACTTGGTCCGTTTTATTC
13919 ACTTGGTCCGTTTTATT
1 ACTTGGTCCGTTTTATT
13936 TTCTTTACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.20, G:0.17, T:0.51
Consensus pattern (18 bp):
ACTTGGTCCGTTTTATTC
Found at i:13954 original size:18 final size:18
Alignment explanation
Indices: 13893--13959 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 18
13883 TCCATTTTAT
*
13893 TTTTCTTTACTTGGTCCG
1 TTTTCTTTACTTGGTCCA
* *
13911 TTTTATTCACTTGGTCCGTTTTA
1 TTTTCTTTACTTGGTCC-----A
13934 TTTTCTTTACTTGGTCCA
1 TTTTCTTTACTTGGTCCA
13952 -TTTCTTTA
1 TTTTCTTTA
13960 TTTCCATGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
17 8 0.21
18 16 0.41
23 15 0.38
ACGTcount: A:0.10, C:0.19, G:0.12, T:0.58
Consensus pattern (18 bp):
TTTTCTTTACTTGGTCCA
Found at i:15144 original size:22 final size:19
Alignment explanation
Indices: 15098--15135 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
15088 AGATCCCAAG
15098 AAAAAACAACAGTTCATAC
1 AAAAAACAACAGTTCATAC
*
15117 AAAAAAGAACAGTTCATAC
1 AAAAAACAACAGTTCATAC
15136 CCAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.58, C:0.18, G:0.08, T:0.16
Consensus pattern (19 bp):
AAAAAACAACAGTTCATAC
Found at i:15195 original size:17 final size:17
Alignment explanation
Indices: 15161--15223 Score: 94
Period size: 17 Copynumber: 3.8 Consensus size: 17
15151 AAAACAGAAT
*
15161 CATACA-AT-CCATACA
1 CATACAGATCCCAAACA
15176 CATACAGATCCCAAACA
1 CATACAGATCCCAAACA
*
15193 CATACAGACCCCAAACA
1 CATACAGATCCCAAACA
15210 CATACAGATCCCAA
1 CATACAGATCCCAA
15224 GAACAACAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
15 6 0.14
16 2 0.05
17 35 0.81
ACGTcount: A:0.46, C:0.37, G:0.05, T:0.13
Consensus pattern (17 bp):
CATACAGATCCCAAACA
Found at i:15239 original size:30 final size:32
Alignment explanation
Indices: 15173--15241 Score: 81
Period size: 34 Copynumber: 2.2 Consensus size: 32
15163 TACAATCCAT
*
15173 ACACATACAGATCCCAAACACATACAGACCCCAA
1 ACACATACAGATCCCAAACACATACAGA--CAAA
15207 ACACATACAGATCCCAAGA-ACA-ACAGA-AAA
1 ACACATACAGATCCCAA-ACACATACAGACAAA
15237 ACACA
1 ACACA
15242 CTTTCAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
30 7 0.21
33 5 0.15
34 20 0.61
35 1 0.03
ACGTcount: A:0.52, C:0.33, G:0.07, T:0.07
Consensus pattern (32 bp):
ACACATACAGATCCCAAACACATACAGACAAA
Found at i:16247 original size:2 final size:2
Alignment explanation
Indices: 16240--16264 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16230 CTTGTGGATT
16240 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
16265 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16295 original size:2 final size:2
Alignment explanation
Indices: 16290--16316 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16280 GTGTGTTATA
16290 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
16317 ATGTTATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Done.