Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017364.1 Corchorus olitorius cultivar O-4 contig17397, 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: 30360
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:5226 original size:51 final size:51
Alignment explanation
Indices: 5165--5261 Score: 160
Period size: 51 Copynumber: 1.9 Consensus size: 51
5155 GTGCTAATTG
*
5165 ATTTTAATTTGAGT-AAAATATTCAAATTAATCAATCAATCAATCAAATAGC
1 ATTTTAATTTGA-TCAAAATATTCAAATCAATCAATCAATCAATCAAATAGC
*
5216 ATTTTTATTTGATCAAAATATTCAAATCAATCAATCAATCAATCAA
1 ATTTTAATTTGATCAAAATATTCAAATCAATCAATCAATCAATCAA
5262 TCAATCAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
50 1 0.02
51 42 0.98
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.36
Consensus pattern (51 bp):
ATTTTAATTTGATCAAAATATTCAAATCAATCAATCAATCAATCAAATAGC
Found at i:5249 original size:4 final size:4
Alignment explanation
Indices: 5240--5271 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
5230 AAAATATTCA
5240 AATC AATC AATC AATC AATC AATC AATC AATC
1 AATC AATC AATC AATC AATC AATC AATC AATC
5272 TAATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
AATC
Found at i:9156 original size:51 final size:50
Alignment explanation
Indices: 9055--9157 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
9045 GTTCTTCATA
** *
9055 TTTTTCTTGTTTAGATCTTGTCTCAGGACACCCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
* * * *
9105 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAAAAACACTGTATTCGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
9156 TT
1 TT
9158 CTCTTTCGGA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
50 4 0.09
51 39 0.89
52 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
Found at i:10959 original size:5 final size:5
Alignment explanation
Indices: 10929--10983 Score: 64
Period size: 5 Copynumber: 11.4 Consensus size: 5
10919 TACAGTTTTA
10929 ATAT- ATAT- ATAT- ATATG ATGTATG ATATG ATATG ATAT- ATATG ATATG
1 ATATG ATATG ATATG ATATG A--TATG ATATG ATATG ATATG ATATG ATATG
10977 ATATG AT
1 ATATG AT
10984 TATATTAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
4 16 0.34
5 26 0.55
7 5 0.11
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (5 bp):
ATATG
Found at i:10966 original size:24 final size:23
Alignment explanation
Indices: 10933--10988 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 23
10923 GTTTTAATAT
10933 ATATATATATATGATGTATGATATG
1 ATATATATATATGA--TATGATATG
10958 ATATGATATATATGATATGATATG
1 ATAT-ATATATATGATATGATATG
10982 AT-TATAT
1 ATATATAT
10989 TAAAATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.13
23 1 0.03
24 11 0.37
25 4 0.13
26 10 0.33
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (23 bp):
ATATATATATATGATATGATATG
Found at i:10970 original size:14 final size:14
Alignment explanation
Indices: 10929--10980 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
10919 TACAGTTTTA
10929 ATAT-ATATATAT-
1 ATATGATATATATG
10941 ATATGATGTATGATATG
1 ATATGA--TAT-ATATG
10958 ATATGATATATATG
1 ATATGATATATATG
10972 ATATGATAT
1 ATATGATAT
10981 GATTATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.11
13 1 0.03
14 14 0.40
15 6 0.17
16 4 0.11
17 6 0.17
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (14 bp):
ATATGATATATATG
Found at i:10971 original size:19 final size:19
Alignment explanation
Indices: 10929--10988 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
10919 TACAGTTTTA
10929 ATATATAT-ATAT-ATATG
1 ATATATATGATATGATATG
*
10946 --ATGTATGATATGATATG
1 ATATATATGATATGATATG
10963 ATATATATGATATGATATG
1 ATATATATGATATGATATG
10982 AT-TATAT
1 ATATATAT
10989 TAAAATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
15 5 0.14
16 4 0.11
17 5 0.14
18 5 0.14
19 18 0.49
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (19 bp):
ATATATATGATATGATATG
Found at i:11061 original size:2 final size:2
Alignment explanation
Indices: 11054--11098 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
11044 GGAAGATACA
11054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
11097 AT
1 AT
11099 TAATTTTAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19718 original size:13 final size:13
Alignment explanation
Indices: 19700--19727 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19690 AGCTTTATCA
19700 TATTTATATATAC
1 TATTTATATATAC
19713 TATTTATATATAC
1 TATTTATATATAC
19726 TA
1 TA
19728 ATACTTTGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (13 bp):
TATTTATATATAC
Done.