Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00159.N1

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: 3916
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34


Found at i:1237 original size:63 final size:63

Alignment explanation


    Indices: 1138--1263  Score: 243
    Period size: 63  Copynumber: 2.0  Consensus size: 63

       1128 TGTGGTTTAA

                                                                           
       1138 GTCTGATAAGTTGCGAGGCCAATGGTGCTTGGTTGATGTGGGCACTATAGAAATGGTACTTTG
          1 GTCTGATAAGTTGCGAGGCCAATGGTGCTTGGTTGATGTGGGCACTATAGAAATGGTACTTTG

                                                                     *     
       1201 GTCTGATAAGTTGCGAGGCCAATGGTGCTTGGTTGATGTGGGCACTATAGAAATGGTTCTTTG
          1 GTCTGATAAGTTGCGAGGCCAATGGTGCTTGGTTGATGTGGGCACTATAGAAATGGTACTTTG

       1264 TGTAGCAGGC


Statistics
Matches: 62,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  63   62  1.00

ACGTcount: A:0.21, C:0.13, G:0.33, T:0.33


Consensus pattern (63 bp):   
GTCTGATAAGTTGCGAGGCCAATGGTGCTTGGTTGATGTGGGCACTATAGAAATGGTACTTTG

Found at i:1256 original size:31 final size:31

Alignment explanation


    Indices: 1158--1257  Score: 82
    Period size: 31  Copynumber: 3.2  Consensus size: 31

       1148 TTGCGAGGCC

                                           
       1158 AATGGTGCTTGGTTGATGTGGGCACTATAGA
          1 AATGGTGCTTGGTTGATGTGGGCACTATAGA

                  *                 *    *  *  *
       1189 AATGGTACTTTGGTCTGATAAGT-TG--CGA-GGCC
          1 AATGGTGC-TTGGT-TGAT--GTGGGCACTATAG-A

                                           
       1221 AATGGTGCTTGGTTGATGTGGGCACTATAGA
          1 AATGGTGCTTGGTTGATGTGGGCACTATAGA

                  
       1252 AATGGT
          1 AATGGT

       1258 TCTTTGTGTA


Statistics
Matches: 50,  Mismatches: 10, Indels: 18
        0.64            0.13        0.23

Matches are distributed among these distances:
  28    2  0.04
  29    1  0.02
  30    4  0.08
  31   21  0.42
  32   15  0.30
  33    4  0.08
  34    1  0.02
  35    2  0.04

ACGTcount: A:0.23, C:0.11, G:0.34, T:0.32


Consensus pattern (31 bp):   
AATGGTGCTTGGTTGATGTGGGCACTATAGA

Found at i:3668 original size:14 final size:15

Alignment explanation


    Indices: 3635--3673  Score: 53
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       3625 TTTCCTTCAT

                           
       3635 TAAGTTTTTATTACA
          1 TAAGTTTTTATTACA

            *        *     
       3650 CAAGTTTTTCTTA-A
          1 TAAGTTTTTATTACA

                      
       3664 TAAGTTTTTA
          1 TAAGTTTTTA

       3674 ATTTCGTTGA


Statistics
Matches: 20,  Mismatches: 4, Indels: 1
        0.80            0.16        0.04

Matches are distributed among these distances:
  14    9  0.45
  15   11  0.55

ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54


Consensus pattern (15 bp):   
TAAGTTTTTATTACA
Done.