Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2291

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: 10005
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31


Found at i:1633 original size:40 final size:40

Alignment explanation


    Indices: 1554--1730  Score: 234
    Period size: 40  Copynumber: 4.5  Consensus size: 40

       1544 CGGATGATAA

                *      *           *          *     
       1554 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT

                    * *             *   *            
       1594 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT

                                              *     
       1634 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT

                                                    
       1674 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT

                               
       1714 CC-GGCTAA-ATCCCGAAG
          1 CCGGGCTAAGA-CCCGAAG

       1731 ATACTTGGGT


Statistics
Matches: 120,  Mismatches: 14, Indels: 7
        0.85            0.10        0.05

Matches are distributed among these distances:
  38    1  0.01
  39   15  0.12
  40  102  0.85
  41    2  0.02

ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26


Consensus pattern (40 bp):   
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT

Found at i:1996 original size:22 final size:22

Alignment explanation


    Indices: 1956--1997  Score: 59
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       1946 GAATGTGCAT

                        *         
       1956 ATATGAAGTTATTCATTTAGCC
          1 ATATGAAGTTATACATTTAGCC

                                 
       1978 ATATGAATGTTATAC-TTTAG
          1 ATATGAA-GTTATACATTTAG

       1998 TCAAAACTAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  22   12  0.67
  23    6  0.33

ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43


Consensus pattern (22 bp):   
ATATGAAGTTATACATTTAGCC

Found at i:9653 original size:39 final size:40

Alignment explanation


    Indices: 9513--9656  Score: 163
    Period size: 39  Copynumber: 3.6  Consensus size: 40

       9503 CGGATGATAA

                *      *           *                 
       9513 CCGGACTAAGATCCGAAGGCATTCGTGCGAGT-TGCTATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGCG-GTATGCTATAT

                    *  *            *           *     
       9553 CCGGGCTATG-TCCGAAGGCATTTATGC--TAGTGATTATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGCGGTA-TG-CTATAT

                                                    
       9592 CCGGGCTAAGACCCGAAGGCATTTGTGCGGTATGCTATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGCGGTATGCTATAT

                                      
       9632 CCGGGC-AAGACCCGAAGGCATTTGT
          1 CCGGGCTAAGACCCGAAGGCATTTGT

       9657 ACGATTGTTA


Statistics
Matches: 89,  Mismatches: 9, Indels: 13
        0.80            0.08        0.12

Matches are distributed among these distances:
  36    1  0.01
  38    2  0.02
  39   48  0.54
  40   34  0.38
  41    2  0.02
  42    2  0.02

ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26


Consensus pattern (40 bp):   
CCGGGCTAAGACCCGAAGGCATTTGTGCGGTATGCTATAT

Found at i:9954 original size:22 final size:22

Alignment explanation


    Indices: 9914--9955  Score: 59
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       9904 GAATGTGCAT

                        *         
       9914 ATATGAAGTTATTCATTTAGCC
          1 ATATGAAGTTATACATTTAGCC

                                 
       9936 ATATGAATGTTATAC-TTTAG
          1 ATATGAA-GTTATACATTTAG

       9956 TCAAAACTAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  22   12  0.67
  23    6  0.33

ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43


Consensus pattern (22 bp):   
ATATGAAGTTATACATTTAGCC
Done.