Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023902.1 Corchorus olitorius cultivar O-4 contig23935, 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: 3666
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Found at i:1708 original size:7 final size:7
Alignment explanation
Indices: 1689--1771 Score: 53
Period size: 7 Copynumber: 11.3 Consensus size: 7
1679 ACTAAATTAG
1689 TTCT-AA
1 TTCTAAA
1695 TTACTAAA
1 TT-CTAAA
*
1703 TTCTAAT
1 TTCTAAA
1710 TTCTAAA
1 TTCTAAA
*
1717 TTACT-TA
1 TT-CTAAA
*
1724 TTCTAAT
1 TTCTAAA
1731 TTCTAAAAA
1 TTCT--AAA
*
1740 TACTTAAA
1 TTC-TAAA
*
1748 TTCTAAT
1 TTCTAAA
1755 TTCTAAA
1 TTCTAAA
1762 TTACTAAA
1 TT-CTAAA
1770 TT
1 TT
1772 AGTTCTAATT
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
6 4 0.07
7 32 0.54
8 18 0.31
9 4 0.07
10 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (7 bp):
TTCTAAA
Found at i:1708 original size:14 final size:14
Alignment explanation
Indices: 1689--1788 Score: 64
Period size: 14 Copynumber: 7.1 Consensus size: 14
1679 ACTAAATTAG
1689 TTCTAATTACTAAA
1 TTCTAATTACTAAA
*
1703 TTCTAATTTCTAAA
1 TTCTAATTACTAAA
* *
1717 TTACTTATT-CTAAT
1 TT-CTAATTACTAAA
*
1731 TTCTAAAAATACTTAAA
1 TTCT--AATTAC-TAAA
*
1748 TTCTAATTTCTAAA
1 TTCTAATTACTAAA
* *
1762 TTACTAA--A-TTAG
1 TT-CTAATTACTAAA
1774 TTCTAATTACTAAA
1 TTCTAATTACTAAA
1788 T
1 T
1789 GAGTACTCCT
Statistics
Matches: 64, Mismatches: 13, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
11 4 0.06
12 4 0.06
13 3 0.05
14 30 0.47
15 15 0.23
16 1 0.02
17 7 0.11
ACGTcount: A:0.40, C:0.13, G:0.01, T:0.46
Consensus pattern (14 bp):
TTCTAATTACTAAA
Found at i:1755 original size:24 final size:24
Alignment explanation
Indices: 1699--1761 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
1689 TTCTAATTAC
*
1699 TAAATTCTAATTTCT-AAATTACT
1 TAAATTCTAATTTCTAAAAATACT
1722 T--ATTCTAATTTCTAAAAATACT
1 TAAATTCTAATTTCTAAAAATACT
1744 TAAATTCTAATTTCTAAA
1 TAAATTCTAATTTCTAAA
1762 TTACTAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 12 0.33
22 8 0.22
23 1 0.03
24 15 0.42
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAATTCTAATTTCTAAAAATACT
Found at i:2837 original size:17 final size:17
Alignment explanation
Indices: 2797--2848 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2787 TTTCAATGTG
*
2797 TGATTTCTTGGCTC-CT
1 TGATTTTTTGGCTCTCT
*
2813 CTGTTTTTTTGGCTCTCT
1 -TGATTTTTTGGCTCTCT
2831 TGA-TTTTTGGCTTCTCT
1 TGATTTTTTGGC-TCTCT
2848 T
1 T
2849 CCGTTCAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 8 0.27
17 20 0.67
18 2 0.07
ACGTcount: A:0.04, C:0.21, G:0.17, T:0.58
Consensus pattern (17 bp):
TGATTTTTTGGCTCTCT
Found at i:3140 original size:21 final size:21
Alignment explanation
Indices: 3114--3184 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
3104 TGCTAGGAGA
*
3114 TCATTGGAGCAA-ATTCGAAGC
1 TCATTGGAG-AAGATTCCAAGC
*
3135 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGATTCCAAGC
* *
3156 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGATTCCAAGC
3177 TCATTGGA
1 TCATTGGA
3185 ATTGCCTAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 2 0.04
21 44 0.96
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGATTCCAAGC
Done.