Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2088

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: 6144
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28


Found at i:138 original size:14 final size:13

Alignment explanation


    Indices: 83--142  Score: 53
    Period size: 12  Copynumber: 5.1  Consensus size: 13

         73 CCCTTACTGT

                         
         83 TTGTATCGATACA
          1 TTGTATCGATACA

                       * 
         96 TT-TATCGATATA
          1 TTGTATCGATACA

                         
        108 -TG-A-CG--A-A
          1 TTGTATCGATACA

                         
        115 TTGTATCGATACA
          1 TTGTATCGATACA

                          
        128 TTGTAATCGATACA
          1 TTGT-ATCGATACA

             
        142 T
          1 T

        143 GATGGGCTTG


Statistics
Matches: 38,  Mismatches: 1, Indels: 15
        0.70            0.02        0.28

Matches are distributed among these distances:
   7    1  0.03
   8    3  0.08
   9    1  0.03
  10    4  0.11
  11    2  0.05
  12   10  0.26
  13    7  0.18
  14   10  0.26

ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38


Consensus pattern (13 bp):   
TTGTATCGATACA

Found at i:4063 original size:50 final size:54

Alignment explanation


    Indices: 3937--4080  Score: 181
    Period size: 56  Copynumber: 2.7  Consensus size: 54

       3927 ATTGGGGTAT

                  *                                *  *            
       3937 TTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGATGCG
          1 TTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATT-GAGAAAAATTGATGCG

                            *                                    * 
       3992 TTTTTGGAAAATAAAACCGGAGTTGGAGTATCCCCGATTGAGAAAAATT-A-GTG
          1 TTTTT-GAAAATAAAATCGGAGTTGGAGTATCCCCGATTGAGAAAAATTGATGCG

                                      *            
       4045 -TTTTGAAAAT-AAATCGGAGTTGGAATAT-CCCGATTG
          1 TTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTG

       4081 TGGAGAATTG


Statistics
Matches: 81,  Mismatches: 7, Indels: 8
        0.84            0.07        0.08

Matches are distributed among these distances:
  49    8  0.10
  50   16  0.20
  51    6  0.07
  52    4  0.05
  53    2  0.02
  54    1  0.01
  55   13  0.16
  56   31  0.38

ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30


Consensus pattern (54 bp):   
TTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTGAGAAAAATTGATGCG
Done.