Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g00002.C10

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: 13993
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35


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:625 original size:16 final size:16

Alignment explanation


    Indices: 604--634  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

        594 ATTTGGTTTA

                            
        604 CTGTTTCCCTCTTTTT
          1 CTGTTTCCCTCTTTTT

                  *        
        620 CTGTTTTCCTCTTTT
          1 CTGTTTCCCTCTTTT

        635 GTATATATTA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.00, C:0.29, G:0.06, T:0.65


Consensus pattern (16 bp):   
CTGTTTCCCTCTTTTT

Found at i:1715 original size:5 final size:5

Alignment explanation


    Indices: 1682--1714  Score: 50
    Period size: 5  Copynumber: 6.8  Consensus size: 5

       1672 TTTACTTTCT

                *                                   
       1682 TTTTC TTTTG TTTTG TTTTG TTTTG TTTT- TTTT
          1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT

       1715 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:2895 original size:78 final size:78

Alignment explanation


    Indices: 2753--2897  Score: 220
    Period size: 78  Copynumber: 1.9  Consensus size: 78

       2743 TATTCTACCG

                                          *                         *  *     
       2753 TTAAACCATGATCCCTTGATCTCACCAGCTGGGAGAGTCGGTGATCATGTTGATAATGATCACCA
          1 TTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGACCACCA

                         
       2818 TGGAGTTCGACCA
         66 TGGAGTTCGACCA

                   *                               *                *        
       2831 TTAAACCCTGATCCCTTGATCTCATCC-GCTAGGAGAGTTGGTGATCATGTTGATAGCGACCACC
          1 TTAAACCATGATCCCTTGATCTCA-CCAGCTAGGAGAGTCGGTGATCATGTTGATAACGACCACC

               
       2895 ATG
         65 ATG

       2898 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

Found at i:7632 original size:39 final size:39

Alignment explanation


    Indices: 7587--7668  Score: 119
    Period size: 39  Copynumber: 2.1  Consensus size: 39

       7577 CACCGACCAC

                   *                               
       7587 CACCATCGTCGTTCACCAGTCAGGCAGTCACCACCGGTA
          1 CACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTA

                                 *  *        *    *
       7626 CACCATCATCGTTCACCAGTCTGGTAGTCACCATCGGTC
          1 CACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTA

                
       7665 CACC
          1 CACC

       7669 CGTCACCACG


Statistics
Matches: 38,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  39   38  1.00

ACGTcount: A:0.22, C:0.39, G:0.18, T:0.21


Consensus pattern (39 bp):   
CACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTA
Done.