Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold93

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: 1685797
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32

Warning! 216 characters in sequence are not A, C, G, or T


File 14 of 14

Found at i:1683239 original size:13 final size:13

Alignment explanation


    Indices: 1683221--1683246  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

    1683211 ACTAAAGAAA

                         
    1683221 TGTATCGATACAT
          1 TGTATCGATACAT

                         
    1683234 TGTATCGATACAT
          1 TGTATCGATACAT

    1683247 CAATCTTTGT


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:1685684 original size:50 final size:51

Alignment explanation


    Indices: 1685607--1685716  Score: 138
    Period size: 50  Copynumber: 2.2  Consensus size: 51

    1685597 TTTCATCTTG

                             *                           *      
    1685607 GGGATACTCCAATCCCGGTTTCTTTTCCAAAACA-TCAA-TTTTCTCAATCA
          1 GGGATACTCCAATCCCGATTTCTTTTCCAAAACACT-AATTTTTCACAATCA

                                                                *
    1685657 GGGATACTCCAA-CTCCGATTT-TATTTCCAAAACACTAATTTTTCACAATCG
          1 GGGATACTCCAATC-CCGATTTCT-TTTCCAAAACACTAATTTTTCACAATCA

                     
    1685708 GGGATACTC
          1 GGGATACTC

    1685717 TAGCCTTGTT


Statistics
Matches: 53,  Mismatches: 3, Indels: 7
        0.84            0.05        0.11

Matches are distributed among these distances:
  49    2  0.04
  50   31  0.58
  51   20  0.38

ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33


Consensus pattern (51 bp):   
GGGATACTCCAATCCCGATTTCTTTTCCAAAACACTAATTTTTCACAATCA

Found at i:1685755 original size:28 final size:27

Alignment explanation


    Indices: 1685704--1685777  Score: 78
    Period size: 28  Copynumber: 2.7  Consensus size: 27

    1685694 ATTTTTCACA

                         * *  **       
    1685704 ATCGGGGATACTCTAGCCTTGTTATTT
          1 ATCGGGGATACTCCAACCCCGTTATTT

                                        
    1685731 CATCGGGGATACTCCAACCCCGTTATTT
          1 -ATCGGGGATACTCCAACCCCGTTATTT

                                
    1685759 -TCGAGGGGATACTCCAACC
          1 ATC--GGGGATACTCCAACC

    1685778 TCGGCGTTAT


Statistics
Matches: 40,  Mismatches: 4, Indels: 4
        0.83            0.08        0.08

Matches are distributed among these distances:
  26    2  0.05
  28   38  0.95

ACGTcount: A:0.22, C:0.27, G:0.22, T:0.30


Consensus pattern (27 bp):   
ATCGGGGATACTCCAACCCCGTTATTT

Done.