Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold229

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: 44889
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32


Found at i:1726 original size:21 final size:22

Alignment explanation


    Indices: 1702--1744  Score: 70
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       1692 AAAAAAGTTT

                                  
       1702 GAAAAAAAAATCG-AAAAAAAA
          1 GAAAAAAAAATCGCAAAAAAAA

                       *          
       1723 GAAAAAAAAATTGCAAAAAAAA
          1 GAAAAAAAAATCGCAAAAAAAA

       1745 AATTGCATAC


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  21   12  0.60
  22    8  0.40

ACGTcount: A:0.79, C:0.05, G:0.09, T:0.07


Consensus pattern (22 bp):   
GAAAAAAAAATCGCAAAAAAAA

Found at i:1741 original size:14 final size:14

Alignment explanation


    Indices: 1724--1751  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       1714 GAAAAAAAAG

                          
       1724 AAAAAAAAATTGCA
          1 AAAAAAAAATTGCA

                          
       1738 AAAAAAAAATTGCA
          1 AAAAAAAAATTGCA

       1752 TACGGTCTAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14


Consensus pattern (14 bp):   
AAAAAAAAATTGCA

Found at i:1747 original size:35 final size:34

Alignment explanation


    Indices: 1677--1745  Score: 95
    Period size: 35  Copynumber: 2.0  Consensus size: 34

       1667 AATCGTAGCT

                                 **            
       1677 TCGAAAAAAAAGTTAAAAAAAGTTTGAAAAAAAAA
          1 TCGAAAAAAAAG-TAAAAAAAAATTGAAAAAAAAA

                                               
       1712 TCGAAAAAAAAG-AAAAAAAAATTGCAAAAAAAAA
          1 TCGAAAAAAAAGTAAAAAAAAATTG-AAAAAAAAA

       1746 ATTGCATACG


Statistics
Matches: 31,  Mismatches: 2, Indels: 3
        0.86            0.06        0.08

Matches are distributed among these distances:
  33   10  0.32
  34    9  0.29
  35   12  0.39

ACGTcount: A:0.72, C:0.04, G:0.10, T:0.13


Consensus pattern (34 bp):   
TCGAAAAAAAAGTAAAAAAAAATTGAAAAAAAAA

Found at i:16737 original size:21 final size:21

Alignment explanation


    Indices: 16711--16754  Score: 70
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      16701 GTACCAAATA

                                 
      16711 CCATACCATTTCAAACCAATT
          1 CCATACCATTTCAAACCAATT

                        **       
      16732 CCATACCATTTCGTACCAATT
          1 CCATACCATTTCAAACCAATT

              
      16753 CC
          1 CC

      16755 CAAATACCAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.32, C:0.36, G:0.02, T:0.30


Consensus pattern (21 bp):   
CCATACCATTTCAAACCAATT

Found at i:18882 original size:21 final size:22

Alignment explanation


    Indices: 18853--18903  Score: 61
    Period size: 21  Copynumber: 2.4  Consensus size: 22

      18843 TCTCTCTCTC

                *                 
      18853 TTTCCTTTTCACCTTTTTCA-T
          1 TTTCATTTTCACCTTTTTCACT

                      **          
      18874 TTTCATTTTCTTCTTTTTCACT
          1 TTTCATTTTCACCTTTTTCACT

                     
      18896 TTT-ATTTT
          1 TTTCATTTT

      18904 TCTATTCTCT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  21   22  0.85
  22    4  0.15

ACGTcount: A:0.10, C:0.22, G:0.00, T:0.69


Consensus pattern (22 bp):   
TTTCATTTTCACCTTTTTCACT

Found at i:24956 original size:23 final size:22

Alignment explanation


    Indices: 24904--24956  Score: 56
    Period size: 23  Copynumber: 2.4  Consensus size: 22

      24894 TCCACGTCTT

                    *             
      24904 TTTCTTTTGTTTCTTTTTCTAA
          1 TTTCTTTTCTTTCTTTTTCTAA

                                     
      24926 -TTCATTTTCTCTTCTTTCTTC-AA
          1 TTTC-TTTTCT-TTCTTT-TTCTAA

                    
      24949 TTTCTTTT
          1 TTTCTTTT

      24957 TCACTCTCAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 7
        0.76            0.03        0.21

Matches are distributed among these distances:
  21    3  0.12
  22    5  0.19
  23   12  0.46
  24    6  0.23

ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70


Consensus pattern (22 bp):   
TTTCTTTTCTTTCTTTTTCTAA

Found at i:29171 original size:18 final size:18

Alignment explanation


    Indices: 29148--29184  Score: 74
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      29138 TAATCTCGTG

                              
      29148 TTAGGGCATTCCCTACTA
          1 TTAGGGCATTCCCTACTA

                              
      29166 TTAGGGCATTCCCTACTA
          1 TTAGGGCATTCCCTACTA

             
      29184 T
          1 T

      29185 AATGACCACG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35


Consensus pattern (18 bp):   
TTAGGGCATTCCCTACTA
Done.