Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019992.1 Corchorus olitorius cultivar O-4 contig20025, 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: 19927
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:453 original size:15 final size:15
Alignment explanation
Indices: 435--465 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
425 CAAGGGCTGA
*
435 AATTAATTAATTATT
1 AATTAAATAATTATT
450 AATTAAATAATTATT
1 AATTAAATAATTATT
465 A
1 A
466 TTTTATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTAAATAATTATT
Found at i:1949 original size:11 final size:11
Alignment explanation
Indices: 1930--1959 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1920 TTTTCACCCT
*
1930 GTTCATCACTC
1 GTTCTTCACTC
1941 GTTCTTCACTC
1 GTTCTTCACTC
1952 GTTCTTCA
1 GTTCTTCA
1960 TATTTTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.13, C:0.33, G:0.10, T:0.43
Consensus pattern (11 bp):
GTTCTTCACTC
Found at i:3668 original size:14 final size:13
Alignment explanation
Indices: 3649--3687 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
3639 AAATTGTAAA
3649 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
3662 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
3676 ATTTAAAAAATT
1 ATTTAAAAAATT
3688 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:3904 original size:124 final size:127
Alignment explanation
Indices: 3673--3928 Score: 367
Period size: 124 Copynumber: 2.0 Consensus size: 127
3663 ATTTAAGAAA
3673 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAAT---A
* *
3738 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAAAGTTTTTAGTTGAGTAAAACTGTAAAA
63 CA-GTATAAGGATATTAGATTTAATTAAATAAAAATAAAGTTTTTAGTTGAGTAAAACTATAAAA
3803 G
127 G
* * *
3804 TATATTTAAAAAATTCTAATATATATAATTTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-CA
1 TATATTTAAAAAATTCTAATATATATAA-GTTTTTAAAATAAAATAGTAAAATGGTAAAAATACA
* * *
3868 -TA-AA-GATATTGGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
65 GTATAAGGATATTAGATTTAATTAAATAAAAATAAAGTTTTTAGTTGAGTAAAACTATAAAAG
3928 T
1 T
3929 TTAAACAATG
Statistics
Matches: 116, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
124 53 0.46
125 2 0.02
126 2 0.02
128 1 0.01
131 28 0.24
132 30 0.26
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATACAG
TATAAGGATATTAGATTTAATTAAATAAAAATAAAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:8918 original size:46 final size:46
Alignment explanation
Indices: 8866--8959 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
8856 TTTATACAAT
8866 CATTTATAAATACTAGTTTTAACTTTCACGTGCGTTGCACGTGGCC
1 CATTTATAAATACTAGTTTTAACTTTCACGTGCGTTGCACGTGGCC
8912 CATTTATAAATACTAGTTTTAACTTTCACGTGCGTTGCACGTGGCC
1 CATTTATAAATACTAGTTTTAACTTTCACGTGCGTTGCACGTGGCC
8958 CA
1 CA
8960 ACATATTTCG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.36
Consensus pattern (46 bp):
CATTTATAAATACTAGTTTTAACTTTCACGTGCGTTGCACGTGGCC
Found at i:9006 original size:22 final size:22
Alignment explanation
Indices: 8981--9041 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
8971 TTGAATATTT
8981 TTATGAAATTTTGATAACCACC
1 TTATGAAATTTTGATAACCACC
* **
9003 TTATTAAATTTTGATAACCATG
1 TTATGAAATTTTGATAACCACC
9025 TTATGAAATTTTGATAA
1 TTATGAAATTTTGATAA
9042 TTTACCTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCACC
Found at i:9081 original size:29 final size:29
Alignment explanation
Indices: 9026--9084 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
9016 ATAACCATGT
* * *
9026 TATGAAATTTTGATAATTTACCTATGAAA
1 TATGAAACTTTGATAACTAACCTATGAAA
9055 TATGAAACTTTGATAACCTAACC-ATGAAA
1 TATGAAACTTTGATAA-CTAACCTATGAAA
9084 T
1 T
9085 TTTAATAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (29 bp):
TATGAAACTTTGATAACTAACCTATGAAA
Found at i:9118 original size:21 final size:21
Alignment explanation
Indices: 9055--9125 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 21
9045 ACCTATGAAA
* *
9055 TATGAAACTTTGATAACCTAACC
1 TATGAAATTTTG-TAACCT-TCC
*
9078 -ATGAAATTTTAATAAACCTTCC
1 TATGAAATTTT-GT-AACCTTCC
9100 TATGAAATTTTGTAACCTTCC
1 TATGAAATTTTGTAACCTTCC
9121 TATGA
1 TATGA
9126 TTTTTTATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 13 0.32
22 13 0.32
23 15 0.37
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (21 bp):
TATGAAATTTTGTAACCTTCC
Found at i:9131 original size:21 final size:21
Alignment explanation
Indices: 9055--9138 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
9045 ACCTATGAAA
* *
9055 TATGAAACTTTGATAACCTAACC
1 TATGAAA-TTTTATAACCT-TCC
9078 -ATGAAATTTTAATAAACCTTCC
1 TATGAAATTTT-AT-AACCTTCC
*
9100 TATGAAATTTTGTAACCTTCC
1 TATGAAATTTTATAACCTTCC
**
9121 TATGATTTTTTATAACCT
1 TATGAAATTTTATAACCT
9139 CTCTGTGAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
21 26 0.50
22 11 0.21
23 15 0.29
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (21 bp):
TATGAAATTTTATAACCTTCC
Found at i:11648 original size:29 final size:28
Alignment explanation
Indices: 11612--11680 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
11602 GGTTTTAAGT
11612 GAGACTCAAAGAAAGCTCCAGGTTTAGGA
1 GAGACTCAAA-AAAGCTCCAGGTTTAGGA
* * *
11641 GAGGCTCAAATAAGCTCCAGGTTTAGGT
1 GAGACTCAAAAAAGCTCCAGGTTTAGGA
11669 GAGACTCAAAAA
1 GAGACTCAAAAA
11681 CCTATGTGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 26 0.74
29 9 0.26
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (28 bp):
GAGACTCAAAAAAGCTCCAGGTTTAGGA
Done.