Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_5483

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: 10801
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31


Found at i:708 original size:23 final size:24

Alignment explanation


    Indices: 681--728  Score: 62
    Period size: 23  Copynumber: 2.0  Consensus size: 24

        671 ACTCGTTTAT

                  *      *          
        681 ATGTTTGCAAACATTAAA-CAAAC
          1 ATGTTTACAAACAGTAAATCAAAC

                       *            
        704 ATGTTTACAAATAGTAAATCAAAC
          1 ATGTTTACAAACAGTAAATCAAAC

             
        728 A
          1 A

        729 AACGAACAAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  23   15  0.71
  24    6  0.29

ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27


Consensus pattern (24 bp):   
ATGTTTACAAACAGTAAATCAAAC

Found at i:1061 original size:26 final size:26

Alignment explanation


    Indices: 1032--1139  Score: 180
    Period size: 26  Copynumber: 4.2  Consensus size: 26

       1022 TGGTACAAAT

                                      
       1032 TGATAATGGGTTAGGTAAATGTTCCA
          1 TGATAATGGGTTAGGTAAATGTTCCA

                     *          *     
       1058 TGATAATGGATTAGGTAAATATTCCA
          1 TGATAATGGGTTAGGTAAATGTTCCA

                    *                 
       1084 TGATAATGTGTTAGGTAAATGTTCCA
          1 TGATAATGGGTTAGGTAAATGTTCCA

                     *                
       1110 TGATAATGGTTTAGGTAAATGTTCCA
          1 TGATAATGGGTTAGGTAAATGTTCCA

                
       1136 TGAT
          1 TGAT

       1140 GGGAATTTCA


Statistics
Matches: 75,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  26   75  1.00

ACGTcount: A:0.32, C:0.07, G:0.23, T:0.37


Consensus pattern (26 bp):   
TGATAATGGGTTAGGTAAATGTTCCA

Found at i:8103 original size:26 final size:26

Alignment explanation


    Indices: 8074--8181  Score: 171
    Period size: 26  Copynumber: 4.2  Consensus size: 26

       8064 TGGTACAAAT

                          *           
       8074 TGATAATGGGTTAGCTAAATGTTCCA
          1 TGATAATGGGTTAGGTAAATGTTCCA

                     *          *     
       8100 TGATAATGGATTAGGTAAATATTCCA
          1 TGATAATGGGTTAGGTAAATGTTCCA

                                      
       8126 TGATAATGGGTTAGGTAAATGTTCCA
          1 TGATAATGGGTTAGGTAAATGTTCCA

             *       *                
       8152 TTATAATGGTTTAGGTAAATGTTCCA
          1 TGATAATGGGTTAGGTAAATGTTCCA

                
       8178 TGAT
          1 TGAT

       8182 GGGAATTTTA


Statistics
Matches: 74,  Mismatches: 8, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  26   74  1.00

ACGTcount: A:0.32, C:0.08, G:0.22, T:0.37


Consensus pattern (26 bp):   
TGATAATGGGTTAGGTAAATGTTCCA

Done.