Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_128 ID=scaffold_128-JGI_221_v2.0

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: 11798
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:3485 original size:3 final size:3

Alignment explanation


    Indices: 3477--3502  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       3467 CTCCATGAGA

                                              
       3477 TCT TCT TCT TCT TCT TCT TCT TCT TC
          1 TCT TCT TCT TCT TCT TCT TCT TCT TC

       3503 GAGATCCTTG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65


Consensus pattern (3 bp):   
TCT

Found at i:5148 original size:22 final size:22

Alignment explanation


    Indices: 5123--5164  Score: 63
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       5113 TGCAAAGTTG

                                  
       5123 ATAAT-AAT-TAA-TATATATT
          1 ATAATAAATATAATTATATATT

                                  
       5142 ATAATAAATATAATTATATATT
          1 ATAATAAATATAATTATATATT

             
       5164 A
          1 A

       5165 GTTATTATCA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  19    5  0.25
  20    3  0.15
  21    3  0.15
  22    9  0.45

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (22 bp):   
ATAATAAATATAATTATATATT

Found at i:5151 original size:16 final size:15

Alignment explanation


    Indices: 5126--5159  Score: 50
    Period size: 16  Copynumber: 2.2  Consensus size: 15

       5116 AAAGTTGATA

                 *          
       5126 ATAATTAATATATATT
          1 ATAATAAATATA-ATT

                           
       5142 ATAATAAATATAATT
          1 ATAATAAATATAATT

               
       5157 ATA
          1 ATA

       5160 TATTAGTTAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    6  0.35
  16   11  0.65

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (15 bp):   
ATAATAAATATAATT

Found at i:5284 original size:29 final size:30

Alignment explanation


    Indices: 5225--5285  Score: 88
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       5215 TGCCATTGAA

                                * *  *    
       5225 AATATTTACAAAAAGAGACATCTAATTTTT
          1 AATATTTACAAAAAGAGACAACCAAATTTT

                                          
       5255 AATATTTACAAAAAGAG-CAACCAAATTTT
          1 AATATTTACAAAAAGAGACAACCAAATTTT

              
       5284 AA
          1 AA

       5286 AAATAATTCA


Statistics
Matches: 28,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  29   11  0.39
  30   17  0.61

ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31


Consensus pattern (30 bp):   
AATATTTACAAAAAGAGACAACCAAATTTT
Done.