Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: evm.model.Scaffold1961.26

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: 2418
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23


Found at i:994 original size:27 final size:27

Alignment explanation


    Indices: 964--1018  Score: 83
    Period size: 27  Copynumber: 2.0  Consensus size: 27

        954 TAGATATCGG

                     *                 
        964 TCACCTATCGGACATCATAGATCACCA
          1 TCACCTATCAGACATCATAGATCACCA

                  *      *             
        991 TCACCTGTCAGACGTCATAGATCACCA
          1 TCACCTATCAGACATCATAGATCACCA

             
       1018 T
          1 T

       1019 TATCGATTCG


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.31, C:0.33, G:0.13, T:0.24


Consensus pattern (27 bp):   
TCACCTATCAGACATCATAGATCACCA

Found at i:1084 original size:27 final size:26

Alignment explanation


    Indices: 978--1085  Score: 101
    Period size: 27  Copynumber: 4.0  Consensus size: 26

        968 CTATCGGACA

                             *         
        978 TCATAGATCACCATCACCTGTCAGACG
          1 TCATAGATCACCATCACATGTC-GACG

                          *             
       1005 TCATAGATCACCATTATCGAT-TCGACG
          1 TCATAGATCACCATCA-C-ATGTCGACG

              **           * *         
       1032 TCGCAGATCACCATCTCCTGTTCGACG
          1 TCATAGATCACCATCACATG-TCGACG

                     *                 
       1059 TCATAGATCTCCATCACATGTGCGACG
          1 TCATAGATCACCATCACATGT-CGACG

       1086 CAGATCTCCT


Statistics
Matches: 64,  Mismatches: 12, Indels: 10
        0.74            0.14        0.12

Matches are distributed among these distances:
  25    1  0.02
  26    2  0.03
  27   57  0.89
  28    3  0.05
  29    1  0.02

ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26


Consensus pattern (26 bp):   
TCATAGATCACCATCACATGTCGACG

Found at i:1114 original size:48 final size:48

Alignment explanation


    Indices: 1055--1149  Score: 120
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       1045 TCTCCTGTTC

                                                     *       
       1055 GACGTCATAGATCTCCATCACAT-GTGCGACGCAGATCTCCTTCACCCA
          1 GACGTCATAGATCTCCATCACATGGT-CGACGCAGATCTCCATCACCCA

                  *     *        *      *  *               
       1103 GACGTCGTAGATGTCCATCACCTGGTCGCCGTAGATCTCCATCACCC
          1 GACGTCATAGATCTCCATCACATGGTCGACGCAGATCTCCATCACCC

       1150 TTGCGACGTA


Statistics
Matches: 40,  Mismatches: 6, Indels: 2
        0.83            0.12        0.04

Matches are distributed among these distances:
  48   38  0.95
  49    2  0.05

ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23


Consensus pattern (48 bp):   
GACGTCATAGATCTCCATCACATGGTCGACGCAGATCTCCATCACCCA

Found at i:1159 original size:24 final size:24

Alignment explanation


    Indices: 1062--1163  Score: 82
    Period size: 24  Copynumber: 4.2  Consensus size: 24

       1052 TTCGACGTCA

                          *          
       1062 TAGATCTCCATCACATGTG-CGACG
          1 TAGATCTCCATCACCT-TGACGACG

            *        *     **    *  
       1086 CAGATCTCCTTCACCCAGACGTCG
          1 TAGATCTCCATCACCTTGACGACG

                 *          * *  *  
       1110 TAGATGTCCATCACCTGGTCGCCG
          1 TAGATCTCCATCACCTTGACGACG

                                     
       1134 TAGATCTCCATCACCCTTG-CGACG
          1 TAGATCTCCATCA-CCTTGACGACG

                  
       1158 TAGATC
          1 TAGATC

       1164 ACCCTCTCCT


Statistics
Matches: 60,  Mismatches: 16, Indels: 4
        0.75            0.20        0.05

Matches are distributed among these distances:
  23    1  0.02
  24   55  0.92
  25    4  0.07

ACGTcount: A:0.22, C:0.34, G:0.20, T:0.25


Consensus pattern (24 bp):   
TAGATCTCCATCACCTTGACGACG
Done.