Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g00002.C14

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: 3108
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31


Found at i:171 original size:39 final size:39

Alignment explanation


    Indices: 121--199  Score: 104
    Period size: 39  Copynumber: 2.0  Consensus size: 39

        111 CCGGCCACCC

                 *            *               *    
        121 CCATCGTCGTTCACCAGTTAGGCAGTCACCACCGTTCCA
          1 CCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTCCA

                        *         *        *       
        160 CCATCATCGTTCTCCAGTCAGGTAGTCACCATCGGTCCA
          1 CCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTCCA

             
        199 C
          1 C

        200 GCGTCACCAC


Statistics
Matches: 34,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  39   34  1.00

ACGTcount: A:0.20, C:0.38, G:0.18, T:0.24


Consensus pattern (39 bp):   
CCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTCCA

Found at i:1305 original size:5 final size:5

Alignment explanation


    Indices: 1272--1304  Score: 50
    Period size: 5  Copynumber: 6.8  Consensus size: 5

       1262 TTTACTTTCT

                *                                   
       1272 TTTTC TTTTG TTTTG TTTTG TTTTG TTTT- TTTT
          1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT

       1305 TAATTTTCTC


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
   4    4  0.15
   5   23  0.85

ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85


Consensus pattern (5 bp):   
TTTTG

Found at i:2523 original size:78 final size:78

Alignment explanation


    Indices: 2381--2525  Score: 220
    Period size: 78  Copynumber: 1.9  Consensus size: 78

       2371 TATTCTACCG

                                          *                         *  *     
       2381 TTAAACCATGATCCCTTGATCTCACCAGCTGGGAGAGTCGGTGATCATGTTGATAATGATCACCA
          1 TTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGACCACCA

                         
       2446 TGGAGTTCGACCA
         66 TGGAGTTCGACCA

                   *                               *                *        
       2459 TTAAACCCTGATCCCTTGATCTCATCC-GCTAGGAGAGTTGGTGATCATGTTGATAGCGACCACC
          1 TTAAACCATGATCCCTTGATCTCA-CCAGCTAGGAGAGTCGGTGATCATGTTGATAACGACCACC

               
       2523 ATG
         65 ATG

       2526 ACGTTGTGCA


Statistics
Matches: 60,  Mismatches: 6, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  78   58  0.97
  79    2  0.03

ACGTcount: A:0.26, C:0.24, G:0.23, T:0.28


Consensus pattern (78 bp):   
TTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGACCACCA
TGGAGTTCGACCA
Done.