Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007563.1 Corchorus capsularis cultivar CVL-1 contig07584, 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: 27485
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:8059 original size:19 final size:19
Alignment explanation
Indices: 8035--8110 Score: 68
Period size: 19 Copynumber: 4.1 Consensus size: 19
8025 ACTTTTTCTT
8035 TTTTTTTTATTATTATTAA
1 TTTTTTTTATTATTATTAA
****
8054 TTTTTTTT-TGGCGA-TAA
1 TTTTTTTTATTATTATTAA
*
8071 TTTTTTTTTTTATTATTAA
1 TTTTTTTTATTATTATTAA
*
8090 -TTTTTTTAGTATTAATTAA
1 TTTTTTTTATTATT-ATTAA
8109 TT
1 TT
8111 AATTTATTAG
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
17 11 0.26
18 15 0.35
19 16 0.37
20 1 0.02
ACGTcount: A:0.24, C:0.01, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTTTTTATTATTATTAA
Found at i:8093 original size:15 final size:15
Alignment explanation
Indices: 8075--8106 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
8065 CGATAATTTT
*
8075 TTTTTTTATTATTAA
1 TTTTTTTAGTATTAA
8090 TTTTTTTAGTATTAA
1 TTTTTTTAGTATTAA
8105 TT
1 TT
8107 AATTAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
TTTTTTTAGTATTAA
Found at i:9159 original size:38 final size:38
Alignment explanation
Indices: 9108--9182 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
9098 ATTGTTCTTC
*
9108 TTGGTGATATTCAATCCTTTAACC-AGACGATCTTATTA
1 TTGGTGATATTCAATCCTCTAACCGA-ACGATCTTATTA
*
9146 TTGGTGATATTCAATTCTCTAACCGAACGATCTTATT
1 TTGGTGATATTCAATCCTCTAACCGAACGATCTTATT
9183 GGTTAAGATC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 33 0.97
39 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (38 bp):
TTGGTGATATTCAATCCTCTAACCGAACGATCTTATTA
Found at i:11901 original size:42 final size:42
Alignment explanation
Indices: 11855--11941 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
11845 TATGTACTCT
11855 AGATATCTAAGCCTCACAAAACTCTGTCAATTCTTAGCTAGA
1 AGATATCTAAGCCTCACAAAACTCTGTCAATTCTTAGCTAGA
*
11897 AGATATCTAAGCCTCACAAAACTCTGTCAATTCTTAGCTTGA
1 AGATATCTAAGCCTCACAAAACTCTGTCAATTCTTAGCTAGA
11939 AGA
1 AGA
11942 AGCACACTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.29
Consensus pattern (42 bp):
AGATATCTAAGCCTCACAAAACTCTGTCAATTCTTAGCTAGA
Found at i:12147 original size:21 final size:21
Alignment explanation
Indices: 12121--12170 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
12111 TGTCAAATCA
*
12121 GTGCCCCAAGAATACAGTGTT
1 GTGCCCCAAGAATACAGTATT
12142 GTGCCCCAAGAATACAGTATT
1 GTGCCCCAAGAATACAGTATT
12163 GTGCCCCA
1 GTGCCCCA
12171 TCCTGGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (21 bp):
GTGCCCCAAGAATACAGTATT
Found at i:13609 original size:61 final size:60
Alignment explanation
Indices: 13515--13630 Score: 207
Period size: 61 Copynumber: 1.9 Consensus size: 60
13505 GGTTACTAAC
13515 TGTACCCTATCCGAACCGTGATGGATAATAATACTCCCTCAG-TCTCATATTATCTATCCA
1 TGTACCCTATCCGAACCGTGATGGATAATAATACTCCCTCAGTTC-CATATTATCTATCCA
13575 TGTACCCTATCCGAACCCGTGATGGATAATAATACTCCCTCAGTTCCATATTATCT
1 TGTACCCTATCCGAA-CCGTGATGGATAATAATACTCCCTCAGTTCCATATTATCT
13631 GTCCCCTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
60 15 0.28
61 37 0.69
62 2 0.04
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (60 bp):
TGTACCCTATCCGAACCGTGATGGATAATAATACTCCCTCAGTTCCATATTATCTATCCA
Done.