Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_538 ID=scaffold_538-JGI_221_v2.0
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: 5924
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1657 original size:25 final size:25
Alignment explanation
Indices: 1618--1762 Score: 89
Period size: 25 Copynumber: 5.7 Consensus size: 25
1608 CGTACATAAT
* * *
1618 AACATA-ACAACTTACATTATACAT
1 AACATACATAACTTACATAATACAA
*
1642 AGCATACATAACTTACATAATACAA
1 AACATACATAACTTACATAATACAA
* * * *
1667 AACTTACATAACTTAAATATCTTACAC
1 AACATACATAACTTACATA--ATACAA
* * * *
1694 AACTTACACAACCTACATAATACAT
1 AACATACATAACTTACATAATACAA
* *
1719 AACTTACATAA--TACATAATAACTTAC
1 AACATACATAACTTACATAAT-AC--AA
*
1745 AACATACATAACATACAT
1 AACATACATAACTTACAT
1763 TAGTTTGATA
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
23 8 0.08
24 7 0.07
25 45 0.47
26 11 0.11
27 20 0.21
28 5 0.05
ACGTcount: A:0.50, C:0.22, G:0.01, T:0.28
Consensus pattern (25 bp):
AACATACATAACTTACATAATACAA
Found at i:1658 original size:9 final size:9
Alignment explanation
Indices: 1646--1800 Score: 108
Period size: 9 Copynumber: 17.8 Consensus size: 9
1636 ATACATAGCA
1646 TACATAACT
1 TACATAACT
1655 TACATAA--
1 TACATAACT
*
1662 TACAAAACT
1 TACATAACT
1671 TACATAACT
1 TACATAACT
* *
1680 TAAATATCT
1 TACATAACT
*
1689 TACACAACT
1 TACATAACT
* *
1698 TACACAACC
1 TACATAACT
1707 TACATAA--
1 TACATAACT
1714 TACATAACT
1 TACATAACT
*
1723 TACATAATACA
1 TACAT-A-ACT
1734 TA-ATAACT
1 TACATAACT
*
1742 TAC--AACA
1 TACATAACT
*
1749 TACATAACA
1 TACATAACT
* *
1758 TACATTAGT
1 TACATAACT
**
1767 TTGATAACT
1 TACATAACT
* *
1776 TACGTAAGT
1 TACATAACT
1785 TACATAACT
1 TACATAACT
1794 TACATAA
1 TACATAA
1801 TACATAAAAA
Statistics
Matches: 112, Mismatches: 25, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
7 19 0.17
8 4 0.04
9 82 0.73
10 3 0.03
11 4 0.04
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (9 bp):
TACATAACT
Found at i:1664 original size:16 final size:16
Alignment explanation
Indices: 1645--1807 Score: 112
Period size: 16 Copynumber: 9.5 Consensus size: 16
1635 TATACATAGC
1645 ATACATAACTTACATA
1 ATACATAACTTACATA
*
1661 ATACAAAACTTACATA
1 ATACATAACTTACATA
* * *
1677 ACTTAAATATCTTACACA
1 A--TACATAACTTACATA
* *
1695 ACTTACACAACCTACATA
1 A--TACATAACTTACATA
1713 ATACATAACTTACATA
1 ATACATAACTTACATA
1729 ATACATAATAACTTACA-A
1 ATAC---ATAACTTACATA
*
1747 CATACATAACATACATTA
1 -ATACATAACTTACA-TA
* ** *
1765 GTTTGATAACTTACGTA
1 -ATACATAACTTACATA
1782 AGTTACATAACTTACATA
1 A--TACATAACTTACATA
1800 ATACATAA
1 ATACATAA
1808 AAATATATCA
Statistics
Matches: 114, Mismatches: 23, Indels: 20
0.73 0.15 0.13
Matches are distributed among these distances:
16 49 0.43
17 2 0.02
18 49 0.43
19 14 0.12
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (16 bp):
ATACATAACTTACATA
Found at i:1740 original size:87 final size:88
Alignment explanation
Indices: 1644--1807 Score: 197
Period size: 87 Copynumber: 1.9 Consensus size: 88
1634 TTATACATAG
* *
1644 CATACATAACTTACATA-ATACAAAACTTACATAACTTAAATATCTTACACAACTTACACAACCT
1 CATACATAACTTACA-ACATACAAAACATACATAACTTAAATAACTTACACAACTTACACAACCT
1708 ACATAATACATAACTTACATAATA
65 ACATAATACATAACTTACATAATA
* * * ** ** * * *
1732 CATA-ATAACTTACAACATACATAACATACATTAGTTTGATAACTTACGTAAGTTACATAACTTA
1 CATACATAACTTACAACATACAAAACATACATAACTTAAATAACTTACACAACTTACACAACCTA
1796 CATAATACATAA
66 CATAATACATAA
1808 AAATATATCA
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
86 1 0.02
87 58 0.92
88 4 0.06
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (88 bp):
CATACATAACTTACAACATACAAAACATACATAACTTAAATAACTTACACAACTTACACAACCTA
CATAATACATAACTTACATAATA
Done.