Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008088.1 Corchorus capsularis cultivar CVL-1 contig08109, 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: 66503
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6655 original size:2 final size:2
Alignment explanation
Indices: 6648--6674 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6638 GCATGACATT
6648 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6675 TGATGCCTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22063 original size:2 final size:2
Alignment explanation
Indices: 22056--22091 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
22046 GGCCTTCCTA
22056 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
22092 TTTAACTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33904 original size:17 final size:17
Alignment explanation
Indices: 33882--33920 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
33872 AACTGTACTT
33882 AAGAAAATGAAAA-AAAA
1 AAGAAAA-GAAAAGAAAA
33899 AAGAAAAGAAAAGAAAA
1 AAGAAAAGAAAAGAAAA
33916 AAGAA
1 AAGAA
33921 GCAGCAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (17 bp):
AAGAAAAGAAAAGAAAA
Found at i:43251 original size:21 final size:21
Alignment explanation
Indices: 43222--43261 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
43212 TCATGCGGTA
43222 ATTTCATC-ATCTCCTTTTATC
1 ATTTCATCAATCT-CTTTTATC
*
43243 ATTTTATCAATCTCTTTTA
1 ATTTCATCAATCTCTTTTA
43262 GGAAACTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTCATCAATCTCTTTTATC
Found at i:48090 original size:14 final size:17
Alignment explanation
Indices: 48071--48105 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
48061 AAAGAAACTG
48071 TTTTT-TTT-TTCCTTT
1 TTTTTATTTCTTCCTTT
48086 TTTTTATTTCTTCCTTT
1 TTTTTATTTCTTCCTTT
48103 TTT
1 TTT
48106 GCAGCCACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 3 0.17
17 10 0.56
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTATTTCTTCCTTT
Found at i:58969 original size:5 final size:4
Alignment explanation
Indices: 58939--58973 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
58929 GGTTGGTGAG
58939 ATTC ATTC ATTC ATTC ATTC AATTC ATTTC ATTC A
1 ATTC ATTC ATTC ATTC ATTC -ATTC A-TTC ATTC A
58974 ATTGATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 21 0.72
5 8 0.28
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.49
Consensus pattern (4 bp):
ATTC
Found at i:58971 original size:14 final size:14
Alignment explanation
Indices: 58940--58986 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
58930 GTTGGTGAGA
58940 TTCATTC-ATTCA-
1 TTCATTCAATTCAT
58952 TTCATTCAATTCAT
1 TTCATTCAATTCAT
*
58966 TTCATTCAATTGAT
1 TTCATTCAATTCAT
*
58980 TTGATTC
1 TTCATTC
58987 TACGCTCGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
12 7 0.23
13 5 0.16
14 19 0.61
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.51
Consensus pattern (14 bp):
TTCATTCAATTCAT
Done.