Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2317

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: 12690
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35


Found at i:1139 original size:21 final size:21

Alignment explanation


    Indices: 1110--1154  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1100 AAGTTTTCAT

                      *          
       1110 TTTTCTTAGCTAAC-TCATTA
          1 TTTTCTTAGCCAACTTCATTA

                              *   
       1130 TTTTCATTAGCCAACTTCTTTA
          1 TTTTC-TTAGCCAACTTCATTA

               
       1152 TTT
          1 TTT

       1155 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:3346 original size:13 final size:13

Alignment explanation


    Indices: 3328--3353  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       3318 ATTTTTTTTG

                         
       3328 TGTATCGATACAT
          1 TGTATCGATACAT

                         
       3341 TGTATCGATACAT
          1 TGTATCGATACAT

       3354 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:7335 original size:22 final size:22

Alignment explanation


    Indices: 7293--7336  Score: 70
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       7283 ATGTGAAAAT

                          * *     
       7293 AAATTTTTTATAAAGGGGGAGA
          1 AAATTTTTTATAAAAGAGGAGA

                                  
       7315 AAATTTTTTATAAAAGAGGAGA
          1 AAATTTTTTATAAAAGAGGAGA

       7337 TAATCGTTTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32


Consensus pattern (22 bp):   
AAATTTTTTATAAAAGAGGAGA

Found at i:7925 original size:13 final size:13

Alignment explanation


    Indices: 7907--7933  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       7897 ACATGCTGCT

                         
       7907 TTGTATCGATACA
          1 TTGTATCGATACA

                         
       7920 TTGTATCGATACA
          1 TTGTATCGATACA

             
       7933 T
          1 T

       7934 GTTCATTGTA


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

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41


Consensus pattern (13 bp):   
TTGTATCGATACA

Found at i:7930 original size:33 final size:32

Alignment explanation


    Indices: 7888--7952  Score: 103
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       7878 CACACCCAGA

                              *              
       7888 TGTATCGATACATGCTGCTTTGTATCGATACAT
          1 TGTATCGATACATG-TGCATTGTATCGATACAT

                           *                
       7921 TGTATCGATACATGTTCATTGTATCGATACAT
          1 TGTATCGATACATGTGCATTGTATCGATACAT

       7953 GGACAATTGT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  32   16  0.53
  33   14  0.47

ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40


Consensus pattern (32 bp):   
TGTATCGATACATGTGCATTGTATCGATACAT

Found at i:7963 original size:20 final size:19

Alignment explanation


    Indices: 7917--7973  Score: 87
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       7907 TTGTATCGAT

                              *
       7917 ACATTGTATCGATACATGT
          1 ACATTGTATCGATACATGG

            *                  
       7936 TCATTGTATCGATACATGG
          1 ACATTGTATCGATACATGG

                               
       7955 ACAATTGTATCGATACATG
          1 AC-ATTGTATCGATACATG

       7974 AAACTGGCAG


Statistics
Matches: 34,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  19   18  0.53
  20   16  0.47

ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35


Consensus pattern (19 bp):   
ACATTGTATCGATACATGG
Done.