Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013554.1 Corchorus olitorius cultivar O-4 contig13587, 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: 112299
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:34 original size:15 final size:15
Alignment explanation
Indices: 2--49 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1 A
* *
2 AAAAAAAAAGTAAGTT
1 AAAAAAAAA-TTATTT
* *
18 AAAAATAAATTTTTT
1 AAAAAAAAATTATTT
33 AAAAAAAAATTATTT
1 AAAAAAAAATTATTT
48 AA
1 AA
50 TTTTAACTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (15 bp):
AAAAAAAAATTATTT
Found at i:26891 original size:2 final size:2
Alignment explanation
Indices: 26884--26917 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
26874 AGTACCAAAC
26884 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26918 ATCATTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30290 original size:50 final size:50
Alignment explanation
Indices: 30210--30309 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
30200 TGGTTCAAAT
30210 TTACCAAAGGGTCGCCATCAATAGGAAAGGCAAAAAGAAAGCTAAAAGAA
1 TTACCAAAGGGTCGCCATCAATAGGAAAGGCAAAAAGAAAGCTAAAAGAA
*
30260 TTACCAAAGGGTCGCCATCAATAGGGAAGGCAAAAAGAAAGCTAAAAGAA
1 TTACCAAAGGGTCGCCATCAATAGGAAAGGCAAAAAGAAAGCTAAAAGAA
30310 GAACAGAAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.49, C:0.16, G:0.23, T:0.12
Consensus pattern (50 bp):
TTACCAAAGGGTCGCCATCAATAGGAAAGGCAAAAAGAAAGCTAAAAGAA
Found at i:45058 original size:2 final size:2
Alignment explanation
Indices: 45051--45090 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
45041 TACTGAGATC
45051 AT AT AT AT AT 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 AT AT AT AT AT
45091 TAAGTTCCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48186 original size:1 final size:1
Alignment explanation
Indices: 48180--48206 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
48170 ATTGTCAAGG
48180 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
48207 GCATTATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:59039 original size:19 final size:19
Alignment explanation
Indices: 59015--59051 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
59005 GCCGGTGTAT
59015 TGTATAATTTGCCATAAAG
1 TGTATAATTTGCCATAAAG
59034 TGTATAATTTGCCATAAA
1 TGTATAATTTGCCATAAA
59052 TTATATGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (19 bp):
TGTATAATTTGCCATAAAG
Found at i:63082 original size:6 final size:6
Alignment explanation
Indices: 63071--63096 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
63061 CTCAACTCCG
63071 TCTTCA TCTTCA TCTTCA TCTTCA TC
1 TCTTCA TCTTCA TCTTCA TCTTCA TC
63097 CCCGCTATAG
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:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTTCA
Found at i:68316 original size:5 final size:5
Alignment explanation
Indices: 68306--68332 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
68296 TTAAGGCCAG
68306 CCAAA CCAAA CCAAA CCAAA CCAAA CC
1 CCAAA CCAAA CCAAA CCAAA CCAAA CC
68333 GATTCTCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.56, C:0.44, G:0.00, T:0.00
Consensus pattern (5 bp):
CCAAA
Found at i:73644 original size:10 final size:10
Alignment explanation
Indices: 73629--73663 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
73619 ATTAGTTTAG
73629 TTTTAGTTTT
1 TTTTAGTTTT
73639 TTTTAGTTTTT
1 TTTTAG-TTTT
73650 TTTTAGTTTT
1 TTTTAGTTTT
73660 TTTT
1 TTTT
73664 TTTTTTAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.83
Consensus pattern (10 bp):
TTTTAGTTTT
Found at i:73665 original size:12 final size:11
Alignment explanation
Indices: 73629--73664 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
73619 ATTAGTTTAG
73629 TTTTAG-TTTT
1 TTTTAGTTTTT
73639 TTTTAGTTTTT
1 TTTTAGTTTTT
73650 TTTTAGTTTTT
1 TTTTAGTTTTT
73661 TTTT
1 TTTT
73665 TTTTTAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.83
Consensus pattern (11 bp):
TTTTAGTTTTT
Found at i:73669 original size:21 final size:21
Alignment explanation
Indices: 73620--73663 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
73610 TACTAGAAAA
**
73620 TTAGTTTAGTTTTAGTTTTTT
1 TTAGTTTTTTTTTAGTTTTTT
73641 TTAGTTTTTTTTTAGTTTTTT
1 TTAGTTTTTTTTTAGTTTTTT
73662 TT
1 TT
73664 TTTTTTAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.77
Consensus pattern (21 bp):
TTAGTTTTTTTTTAGTTTTTT
Found at i:101057 original size:2 final size:2
Alignment explanation
Indices: 101052--101086 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
101042 CACACACTTC
101052 CT CT CT CT CT CT CT CT CT CT CT CT CT C- CT C- CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
101087 ACACACACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:107716 original size:21 final size:21
Alignment explanation
Indices: 107692--107731 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
107682 CTAACAAACA
*
107692 TTCTACAGCTTCTAAATGACC
1 TTCTACAGCTGCTAAATGACC
**
107713 TTCTTGAGCTGCTAAATGA
1 TTCTACAGCTGCTAAATGA
107732 AGTGGAGTGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (21 bp):
TTCTACAGCTGCTAAATGACC
Found at i:109538 original size:21 final size:19
Alignment explanation
Indices: 109483--109540 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
109473 CTGTTTAACA
109483 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* * * *
109502 ACTATACATATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
109523 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
109541 TTAGAGCAGC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 15 0.50
21 15 0.50
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Done.