Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008742.1 Corchorus capsularis cultivar CVL-1 contig08763, 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: 7278
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:3101 original size:29 final size:29
Alignment explanation
Indices: 3059--3139 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
3049 TGGTTCCGAT
* **
3059 TTTGTGGAGAAGGCGAAGCATAGTCGGTG
1 TTTGTGGAGAAGGCGAAGCAGAGAAGGTG
* *
3088 TTTGTGGAGAAGGCGAAACAGCGAAGGTG
1 TTTGTGGAGAAGGCGAAGCAGAGAAGGTG
3117 TTTGTGGA-ACAGGCGAAGCAGAG
1 TTTGTGGAGA-AGGCGAAGCAGAG
3140 GCGGCGCTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 1 0.02
29 43 0.98
ACGTcount: A:0.28, C:0.11, G:0.41, T:0.20
Consensus pattern (29 bp):
TTTGTGGAGAAGGCGAAGCAGAGAAGGTG
Found at i:3235 original size:14 final size:13
Alignment explanation
Indices: 3218--3256 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
3208 GAAATTAGGA
3218 AAAGAAAAAGAAAG
1 AAAGAAAAA-AAAG
3232 AAAGAAAAAAAA-
1 AAAGAAAAAAAAG
*
3244 ACAGAAAAAAAAG
1 AAAGAAAAAAAAG
3257 CTTTAGATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 11 0.48
13 3 0.13
14 9 0.39
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAG
Found at i:3238 original size:19 final size:19
Alignment explanation
Indices: 3201--3250 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
3191 AGGAAGAAGG
** *
3201 AGAAAAAGAAATTAGGAAA
1 AGAAAAAGAAAGAAAGAAA
3220 AGAAAAAGAAAGAAAGAAA
1 AGAAAAAGAAAGAAAGAAA
*
3239 AAAAAACAGAAA
1 AGAAAA-AGAAA
3251 AAAAAGCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (19 bp):
AGAAAAAGAAAGAAAGAAA
Found at i:4104 original size:7 final size:7
Alignment explanation
Indices: 4092--4121 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4082 TTTGAATGTC
4092 TTCTTTT
1 TTCTTTT
4099 TTCTTTT
1 TTCTTTT
*
4106 TTCCTTT
1 TTCTTTT
4113 TTCTTTT
1 TTCTTTT
4120 TT
1 TT
4122 TTCTTTGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTCTTTT
Found at i:7049 original size:11 final size:11
Alignment explanation
Indices: 7033--7075 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
7023 TACACTATAT
7033 CTAATTAATAG
1 CTAATTAATAG
*
7044 CTAATTAATAT
1 CTAATTAATAG
7055 CTAATTAATAG
1 CTAATTAATAG
*
7066 TTAATTAATA
1 CTAATTAATA
7076 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:7057 original size:22 final size:22
Alignment explanation
Indices: 7029--7075 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
7019 CCATTACACT
7029 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
7051 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
7073 ATA
1 ATA
7076 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Done.