Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_371 ID=scaffold_371-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: 7778
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29


Found at i:1130 original size:27 final size:27

Alignment explanation


    Indices: 1100--1156  Score: 78
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       1090 CTGCACCTTC

                 *     *           *   
       1100 GAATCTTCAATGTCCAGCTGAGGCTTT
          1 GAATCATCAATCTCCAGCTGAGGATTT

                     *                 
       1127 GAATCATCACTCTCCAGCTGAGGATTT
          1 GAATCATCAATCTCCAGCTGAGGATTT

               
       1154 GAA
          1 GAA

       1157 CCCTGCAGTT


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30


Consensus pattern (27 bp):   
GAATCATCAATCTCCAGCTGAGGATTT

Found at i:3318 original size:20 final size:20

Alignment explanation


    Indices: 3293--3337  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 20

       3283 GCTCCCCGTC

                                 
       3293 TATTTATAAC-ATAAAAAAAA
          1 TATTTA-AACTATAAAAAAAA

                  *              
       3313 TATTTAGACTTATAAAAAAAA
          1 TATTTAAAC-TATAAAAAAAA

                
       3334 TATT
          1 TATT

       3338 AACATAATTA


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  19    2  0.09
  20    6  0.27
  21   14  0.64

ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36


Consensus pattern (20 bp):   
TATTTAAACTATAAAAAAAA

Found at i:3349 original size:21 final size:21

Alignment explanation


    Indices: 3303--3354  Score: 63
    Period size: 20  Copynumber: 2.5  Consensus size: 21

       3293 TATTTATAAC

                                *
       3303 ATAAAAAAAATATTTAGACTT
          1 ATAAAAAAAATATTTAGACTA

                                  
       3324 ATAAAAAAAATA-TTA-ACATA
          1 ATAAAAAAAATATTTAGAC-TA

              *        
       3344 ATTAAAAAAAT
          1 ATAAAAAAAAT

       3355 GAAATTTTAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  19    2  0.07
  20   14  0.50
  21   12  0.43

ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29


Consensus pattern (21 bp):   
ATAAAAAAAATATTTAGACTA

Found at i:6955 original size:27 final size:27

Alignment explanation


    Indices: 6846--6956  Score: 107
    Period size: 27  Copynumber: 4.1  Consensus size: 27

       6836 GCAGCTGGCC

                   * *         *    * *
       6846 CTTTGGATCATCATTCTCCCCCTCAGC
          1 CTTTGGACCCTCATTCTCCACCTCGGG

                *        *             
       6873 CTTTAGACCCTCACTCTCCACCTCGGG
          1 CTTTGGACCCTCATTCTCCACCTCGGG

                 *           *      *  
       6900 CTTTGAACCCTCATTCTTCACCTCAGG
          1 CTTTGGACCCTCATTCTCCACCTCGGG

                      *                 
       6927 CTTTGGACCCACATTCTCCAACCT-GGG
          1 CTTTGGACCCTCATTCTCC-ACCTCGGG

               
       6954 CTT
          1 CTT

       6957 GGGATCAGAC


Statistics
Matches: 67,  Mismatches: 16, Indels: 2
        0.79            0.19        0.02

Matches are distributed among these distances:
  27   63  0.94
  28    4  0.06

ACGTcount: A:0.16, C:0.40, G:0.14, T:0.31


Consensus pattern (27 bp):   
CTTTGGACCCTCATTCTCCACCTCGGG
Done.