Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_564 ID=scaffold_564-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: 5660
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:4195 original size:21 final size:19

Alignment explanation


    Indices: 4170--4220  Score: 50
    Period size: 20  Copynumber: 2.6  Consensus size: 19

       4160 AAAACTCAAA

                               * 
       4170 CCCAATACCCAACCACCCTGG
          1 CCCAATACCCAA--ACCCTAG

                    *           
       4191 CCCAACTAACCAAACCCTAG
          1 CCCAA-TACCCAAACCCTAG

                       
       4211 CCCAA-ACCCA
          1 CCCAATACCCA

       4221 TAACAGAAAG


Statistics
Matches: 26,  Mismatches: 3, Indels: 5
        0.76            0.09        0.15

Matches are distributed among these distances:
  18    4  0.15
  20   11  0.42
  21    5  0.19
  22    6  0.23

ACGTcount: A:0.35, C:0.51, G:0.06, T:0.08


Consensus pattern (19 bp):   
CCCAATACCCAAACCCTAG

Found at i:4552 original size:14 final size:13

Alignment explanation


    Indices: 4533--4574  Score: 50
    Period size: 13  Copynumber: 3.2  Consensus size: 13

       4523 AGATTCAAGG

                          
       4533 TTGTTTTCTTATTT
          1 TTGTTTT-TTATTT

                          
       4547 TTGTTTTTGT-TTT
          1 TTGTTTTT-TATTT

                     *   
       4560 TTGTTTTTTGTTT
          1 TTGTTTTTTATTT

              
       4573 TT
          1 TT

       4575 TTTCTTCTTG


Statistics
Matches: 26,  Mismatches: 0, Indels: 5
        0.84            0.00        0.16

Matches are distributed among these distances:
  12    1  0.04
  13   17  0.65
  14    8  0.31

ACGTcount: A:0.02, C:0.02, G:0.12, T:0.83


Consensus pattern (13 bp):   
TTGTTTTTTATTT

Found at i:4558 original size:20 final size:21

Alignment explanation


    Indices: 4533--4590  Score: 75
    Period size: 20  Copynumber: 2.8  Consensus size: 21

       4523 AGATTCAAGG

                                 
       4533 TTGTTTTCTT-ATTTTTGTTT
          1 TTGTTTTCTTGATTTTTGTTT

                       *         
       4553 TTGTTTT-TTGTTTTTTGTTT
          1 TTGTTTTCTTGATTTTTGTTT

              *               
       4573 TTTTTCTTCTTGATTTTT
          1 TTGTT-TTCTTGATTTTT

       4591 TTATTTCGAA


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  19    2  0.06
  20   20  0.62
  21    2  0.06
  22    8  0.25

ACGTcount: A:0.03, C:0.05, G:0.10, T:0.81


Consensus pattern (21 bp):   
TTGTTTTCTTGATTTTTGTTT

Found at i:4560 original size:7 final size:7

Alignment explanation


    Indices: 4544--4575  Score: 57
    Period size: 7  Copynumber: 4.7  Consensus size: 7

       4534 TGTTTTCTTA

                   
       4544 TTTTTG-
          1 TTTTTGT

                   
       4550 TTTTTGT
          1 TTTTTGT

                   
       4557 TTTTTGT
          1 TTTTTGT

                   
       4564 TTTTTGT
          1 TTTTTGT

                 
       4571 TTTTT
          1 TTTTT

       4576 TTCTTCTTGA


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6    6  0.24
   7   19  0.76

ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88


Consensus pattern (7 bp):   
TTTTTGT

Done.