Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2709

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: 6064
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34


Found at i:1200 original size:21 final size:21

Alignment explanation


    Indices: 1171--1215  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1161 AAGTTTTCAT

                      *          
       1171 TTTTCTTAGCTAAC-TCATTA
          1 TTTTCTTAGCCAACTTCATTA

                              *   
       1191 TTTTCATTAGCCAACTTCTTTA
          1 TTTTC-TTAGCCAACTTCATTA

               
       1213 TTT
          1 TTT

       1216 CAACTTGCAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  20    5  0.24
  21    8  0.38
  22    8  0.38

ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53


Consensus pattern (21 bp):   
TTTTCTTAGCCAACTTCATTA

Found at i:3478 original size:13 final size:13

Alignment explanation


    Indices: 3460--3485  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       3450 CAATTTTTTG

                         
       3460 TGTATCGATACAT
          1 TGTATCGATACAT

                         
       3473 TGTATCGATACAT
          1 TGTATCGATACAT

       3486 ACTTGCTGTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38


Consensus pattern (13 bp):   
TGTATCGATACAT

Found at i:3592 original size:21 final size:19

Alignment explanation


    Indices: 3566--3608  Score: 68
    Period size: 21  Copynumber: 2.2  Consensus size: 19

       3556 ACATGCAACA

                                 
       3566 TGTATCGATACTTTTGAAGTG
          1 TGTATCGATACTTTT-AAG-G

                               
       3587 TGTATCGATACTTTTAAGG
          1 TGTATCGATACTTTTAAGG

               
       3606 TGT
          1 TGT

       3609 TTTGACAATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  19    4  0.18
  20    3  0.14
  21   15  0.68

ACGTcount: A:0.23, C:0.09, G:0.23, T:0.44


Consensus pattern (19 bp):   
TGTATCGATACTTTTAAGG

Found at i:5881 original size:21 final size:21

Alignment explanation


    Indices: 5857--5903  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       5847 TTTGATGCTG

                                  
       5857 ATTTTG-A-TGAAAAACGAAGT
          1 ATTTTGAAGTGAAAAAC-AAGT

                                  
       5877 -TATTTGAAGTGAAAAACAAGT
          1 AT-TTTGAAGTGAAAAACAAGT

                  
       5898 ATTTTG
          1 ATTTTG

       5904 CAAAAGATTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 7
        0.77            0.00        0.23

Matches are distributed among these distances:
  19    1  0.04
  20    4  0.17
  21    9  0.39
  22    9  0.39

ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34


Consensus pattern (21 bp):   
ATTTTGAAGTGAAAAACAAGT

Found at i:6040 original size:13 final size:13

Alignment explanation


    Indices: 6022--6060  Score: 69
    Period size: 13  Copynumber: 3.0  Consensus size: 13

       6012 ATAATCACCC

                        *
       6022 TGTATCGATACAG
          1 TGTATCGATACAA

                         
       6035 TGTATCGATACAA
          1 TGTATCGATACAA

                         
       6048 TGTATCGATACAA
          1 TGTATCGATACAA

       6061 AGAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  13   25  1.00

ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31


Consensus pattern (13 bp):   
TGTATCGATACAA
Done.