Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019097.1 Corchorus olitorius cultivar O-4 contig19130, 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: 15719
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:2626 original size:29 final size:29
Alignment explanation
Indices: 2590--2645 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
2580 AATCTATGAG
*
2590 AAAAGGTATAGGGTGAGAAACAAATCTAT
1 AAAAGGTATAGAGTGAGAAACAAATCTAT
2619 AAAAGGTATAGAGTGAGAAACAAATCT
1 AAAAGGTATAGAGTGAGAAACAAATCT
2646 TTAGTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.20
Consensus pattern (29 bp):
AAAAGGTATAGAGTGAGAAACAAATCTAT
Found at i:11666 original size:6 final size:6
Alignment explanation
Indices: 11645--11685 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
11635 CTCTTGATCC
* *
11645 TCCTCT TCTTCT TCCTCC TCCTCT TCCTCT TCCTCT TCCTC
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTC
11686 CTCCCCTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (6 bp):
TCCTCT
Found at i:11688 original size:15 final size:15
Alignment explanation
Indices: 11630--11670 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
11620 GCTCGACTCG
*
11630 TCCTCCTCTTGATCC
1 TCCTCCTCTTCATCC
* *
11645 TCCTCTTCTTCTTCC
1 TCCTCCTCTTCATCC
11660 TCCTCCTCTTC
1 TCCTCCTCTTC
11671 CTCTTCCTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.02, C:0.49, G:0.02, T:0.46
Consensus pattern (15 bp):
TCCTCCTCTTCATCC
Found at i:11694 original size:12 final size:12
Alignment explanation
Indices: 11654--11694 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
11644 CTCCTCTTCT
11654 TCTTCCTCCTCC
1 TCTTCCTCCTCC
*
11666 TCTTCCTCTTCC
1 TCTTCCTCCTCC
11678 TCTTCCTCCTCC
1 TCTTCCTCCTCC
*
11690 CCTTC
1 TCTTC
11695 TTCGAGTACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (12 bp):
TCTTCCTCCTCC
Found at i:11694 original size:18 final size:18
Alignment explanation
Indices: 11655--11694 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11645 TCCTCTTCTT
* *
11655 CTTCCTCCTCCTCTTCCT
1 CTTCCTCCTCCTCCTCCC
*
11673 CTTCCTCTTCCTCCTCCC
1 CTTCCTCCTCCTCCTCCC
11691 CTTC
1 CTTC
11695 TTCGAGTACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.42
Consensus pattern (18 bp):
CTTCCTCCTCCTCCTCCC
Found at i:13232 original size:14 final size:14
Alignment explanation
Indices: 13191--13232 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
13181 AGATTGTAAA
13191 ATTTAAAAAATT-T
1 ATTTAAAAAATTAT
*
13204 CATTTAAGAAA-TAT
1 -ATTTAAAAAATTAT
13218 ATTTAAAAAATTAT
1 ATTTAAAAAATTAT
13232 A
1 A
13233 ATATATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (14 bp):
ATTTAAAAAATTAT
Found at i:13449 original size:125 final size:128
Alignment explanation
Indices: 13215--13471 Score: 373
Period size: 125 Copynumber: 2.0 Consensus size: 128
13205 ATTTAAGAAA
13215 TATATTTAAAAAATTATAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTATAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGT---AATAAAA
* *
13280 TAGATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 TACATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
13345 G
128 G
* * *
13346 TATATTTAAAAAATTCTAATATATATATAAGTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT
1 TATATTTAAAAAATTAT-A-ATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAATAAAAT
13409 -CATA-AA-GATATTAGATTTAATTAAAT-AAAATAAGAGTTTTTAGTTGAGTAAAACTATAAAA
64 ACATATAAGGATATTAGATTTAATTAAATAAAAAT-AGAGTTTTTAGTTGAGTAAAACTATAAAA
13470 G
128 G
13471 T
1 T
13472 TTAAATGATG
Statistics
Matches: 118, Mismatches: 5, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
124 5 0.04
125 50 0.42
126 2 0.02
127 3 0.03
128 5 0.04
129 1 0.01
131 16 0.14
132 1 0.01
133 35 0.30
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.37
Consensus pattern (128 bp):
TATATTTAAAAAATTATAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAATAAAATAC
ATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:14977 original size:31 final size:31
Alignment explanation
Indices: 14932--15003 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
14922 CCAGACATGC
* *
14932 ATGACCCTAAATCCAGCA-GACCCGAGACCCGA
1 ATGA-CCTGAATCCAG-ATGACCCGAAACCCGA
*
14964 ATGACCTGAATCCAGATGAGCCGAAACCCGA
1 ATGACCTGAATCCAGATGACCCGAAACCCGA
*
14995 ATGATCTGA
1 ATGACCTGA
15004 GAAAATTACC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.03
31 30 0.86
32 4 0.11
ACGTcount: A:0.35, C:0.31, G:0.21, T:0.14
Consensus pattern (31 bp):
ATGACCTGAATCCAGATGACCCGAAACCCGA
Done.