Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_552 ID=scaffold_552-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: 5815
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.35


Found at i:1729 original size:45 final size:45

Alignment explanation


    Indices: 1665--1803  Score: 242
    Period size: 45  Copynumber: 3.1  Consensus size: 45

       1655 AACAGATACT

                   *                *     *              
       1665 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
          1 CGGTGGAATCAGCACATAGCAACCTCCTTACTAATCAATGATGTC

                                                         
       1710 CGGTGGAATCAGCACATAGCAACCTCCTTACTAATCAATGATGTC
          1 CGGTGGAATCAGCACATAGCAACCTCCTTACTAATCAATGATGTC

                                                        *
       1755 CGGTGGAATCAGCACATAGCAACCTCCTTACTAATCAATGATGTT
          1 CGGTGGAATCAGCACATAGCAACCTCCTTACTAATCAATGATGTC

                
       1800 CGGT
          1 CGGT

       1804 TCACATAGTA


Statistics
Matches: 90,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  45   90  1.00

ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26


Consensus pattern (45 bp):   
CGGTGGAATCAGCACATAGCAACCTCCTTACTAATCAATGATGTC

Found at i:1867 original size:51 final size:51

Alignment explanation


    Indices: 1800--1994  Score: 234
    Period size: 51  Copynumber: 3.8  Consensus size: 51

       1790 CAATGATGTT

                *   *                                          
       1800 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCACTACCATC
          1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCACTACCATC

              *                        *       *      *  *  *   
       1851 CGATACACGTAGTAGCCTGCACATAGTTCTACACACGTGATCGA-AACTATC
          1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCACTACCATC

                  * *                            *        *     
       1902 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGA-C-CTATCATTC
          1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCACTACCA-TC

                            *                          
       1952 CGGTACACGTAGTAGCTTGCACATAGTACTACACATGTGACCA
          1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA

       1995 TCATTTTCAC


Statistics
Matches: 117,  Mismatches: 22, Indels: 9
        0.79            0.15        0.06

Matches are distributed among these distances:
  49    2  0.02
  50   38  0.32
  51   75  0.64
  52    2  0.02

ACGTcount: A:0.30, C:0.29, G:0.18, T:0.24


Consensus pattern (51 bp):   
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCACTACCATC

Found at i:1986 original size:101 final size:102

Alignment explanation


    Indices: 1807--1991  Score: 293
    Period size: 101  Copynumber: 1.8  Consensus size: 102

       1797 GTTCGGTTCA

                                          *                                  
       1807 CATAGTAGCCTGCACATAGTACTACACATGTGACCACTACCATCCGATACACGTAGTAGCCTGCA
          1 CATAGTAGCCTGCACATAGTACTACACATGCGACCACTACCATCCGATACACGTAGTAGCCTGCA

                  *                              
       1872 CATAGTTCTACACACGTGATCGAAACTATCCGGTACG
         66 CATAGTACTACACACGTGATCGAAACTATCCGGTACG

                                                   *       *             *   
       1909 CATAGTAGCCTGCACATAGTACTACACATGCGA-C-CTATCATTCCGGTACACGTAGTAGCTTGC
          1 CATAGTAGCCTGCACATAGTACTACACATGCGACCACTACCA-TCCGATACACGTAGTAGCCTGC

                           *    
       1972 ACATAGTACTACACATGTGA
         65 ACATAGTACTACACACGTGA

       1992 CCATCATTTT


Statistics
Matches: 76,  Mismatches: 6, Indels: 3
        0.89            0.07        0.04

Matches are distributed among these distances:
 100    5  0.07
 101   39  0.51
 102   32  0.42

ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24


Consensus pattern (102 bp):   
CATAGTAGCCTGCACATAGTACTACACATGCGACCACTACCATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAACTATCCGGTACG

Done.