Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g02456.P2

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: 4618
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Found at i:2125 original size:14 final size:14

Alignment explanation


    Indices: 2100--2147  Score: 55
    Period size: 14  Copynumber: 3.4  Consensus size: 14

       2090 TTTGTGCTCA

                          
       2100 TTTTTTCT--TTTT
          1 TTTTTTCTGATTTT

                          
       2112 TTTTTTCTGATTTT
          1 TTTTTTCTGATTTT

            *              
       2126 CTTTTTCTGAATTTT
          1 TTTTTTCTG-ATTTT

                   
       2141 TATTTTT
          1 T-TTTTT

       2148 TTTAAAATTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  12    8  0.27
  14   12  0.40
  15    5  0.17
  16    5  0.17

ACGTcount: A:0.08, C:0.08, G:0.04, T:0.79


Consensus pattern (14 bp):   
TTTTTTCTGATTTT

Found at i:4146 original size:42 final size:42

Alignment explanation


    Indices: 4096--4222  Score: 161
    Period size: 42  Copynumber: 3.0  Consensus size: 42

       4086 CTTCATTTTC

                        **  *                *         
       4096 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
          1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A

                                           *      *   
       4139 T-GATGCCATAGCCCAGCTATGGTCTTACACCTATTCATATA
          1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA

                                                       
       4180 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
          1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA

              
       4221 TC
          1 TC

       4223 TCACTGATGC


Statistics
Matches: 74,  Mismatches: 8, Indels: 6
        0.84            0.09        0.07

Matches are distributed among these distances:
  41   10  0.14
  42   63  0.85
  43    1  0.01

ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30


Consensus pattern (42 bp):   
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA

Found at i:4284 original size:47 final size:47

Alignment explanation


    Indices: 4181--4307  Score: 166
    Period size: 47  Copynumber: 2.7  Consensus size: 47

       4171 ATTCATATAT

                      *     *          *      *        *   
       4181 CGATGCCATAGCCCAGCTATGGTCTTACAC-GAATCACATATCTCAC
          1 CGATGCCATATCCCAGATATGGTCTTATACAGAAGCACATATCACAC

            *                               *    *         
       4227 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
          1 CGATGCCATATCCCAGATATGGTCTTATACAGAAGCACATATCACAC

                                   *          
       4274 CGATGCCATATCCCAGATATGGTTTTATACAGAA
          1 CGATGCCATATCCCAGATATGGTCTTATACAGAA

       4308 ATCACTTGTC


Statistics
Matches: 69,  Mismatches: 11, Indels: 1
        0.85            0.14        0.01

Matches are distributed among these distances:
  46   26  0.38
  47   43  0.62

ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28


Consensus pattern (47 bp):   
CGATGCCATATCCCAGATATGGTCTTATACAGAAGCACATATCACAC

Found at i:4364 original size:31 final size:31

Alignment explanation


    Indices: 4329--4477  Score: 253
    Period size: 31  Copynumber: 4.8  Consensus size: 31

       4319 CTTGTCACTT

                              *            
       4329 GTAGCCGAAGCTACCACTATTCACTGATCAG
          1 GTAGCCGAAGCTACCACTTTTCACTGATCAG

                   *        *              
       4360 GTAGCCGGAGCTACCATTTTTCACTGATCAG
          1 GTAGCCGAAGCTACCACTTTTCACTGATCAG

                                           
       4391 GTAGCCGAAGCTACCACTTTTCACTGATCAG
          1 GTAGCCGAAGCTACCACTTTTCACTGATCAG

                 *                      *  
       4422 GTAGCAGAAGCTACCACTTTTCACTGATTAG
          1 GTAGCCGAAGCTACCACTTTTCACTGATCAG

                                     
       4453 GTAGCCGAAGCTACCACTTTTCACT
          1 GTAGCCGAAGCTACCACTTTTCACT

       4478 TGTCATTGAT


Statistics
Matches: 110,  Mismatches: 8, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  31  110  1.00

ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27


Consensus pattern (31 bp):   
GTAGCCGAAGCTACCACTTTTCACTGATCAG

Done.