Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g01726.C5

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: 6010
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34


Found at i:3812 original size:117 final size:116

Alignment explanation


    Indices: 3607--3840  Score: 396
    Period size: 117  Copynumber: 2.0  Consensus size: 116

       3597 AAGTATCCAA

                  * *      *                                           *     
       3607 TCGTCCGATTTTCCCGTTCTCCTCTGAATAGACTCCCGTTCATGCCTTCCATTCTCTTTTATTCC
          1 TCGTCCAAATTTCCCATTCTCCTCTGAATAGACTCCCGTTCATGCCTTCCATTCTCTTTGATTCC

                                                               
       3672 AGCTTCCATCAACATTTAGCTTGGCAATTCCTGTTTCCAGGTTGTCCCAGT
         66 AGCTTCCATCAACATTTAGCTTGGCAATTCCTGTTTCCAGGTTGTCCCAGT

                                   *             *                           
       3723 TCGTCCAAATTTCCCATTCTCCTTTGAATAGACTGCCTGTTCATGCCTTCCATTCTCTTTGATTC
          1 TCGTCCAAATTTCCCATTCTCCTCTGAATAGACT-CCCGTTCATGCCTTCCATTCTCTTTGATTC

                                                   *            
       3788 CAGCTTCCATCAACATTTAGCTTGGCAATTCCTGTTTCCGGGTTGTCCCAGT
         65 CAGCTTCCATCAACATTTAGCTTGGCAATTCCTGTTTCCAGGTTGTCCCAGT

             
       3840 T
          1 T

       3841 TAGAAGAATT


Statistics
Matches: 110,  Mismatches: 7, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
 116   30  0.27
 117   80  0.73

ACGTcount: A:0.16, C:0.31, G:0.14, T:0.39


Consensus pattern (116 bp):   
TCGTCCAAATTTCCCATTCTCCTCTGAATAGACTCCCGTTCATGCCTTCCATTCTCTTTGATTCC
AGCTTCCATCAACATTTAGCTTGGCAATTCCTGTTTCCAGGTTGTCCCAGT

Found at i:3979 original size:66 final size:66

Alignment explanation


    Indices: 3873--4004  Score: 248
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       3863 GATTTAGGAA

                                                                             
       3873 TCTTGCTGTCGGTATTCTTTGACCACTTTAACAATGTTGTCCTGTTTATAATCGGAATCGCTCTG
          1 TCTTGCTGTCGGTATTCTTTGACCACTTTAACAATGTTGTCCTGTTTATAATCGGAATCGCTCTG

             
       3938 T
         66 T

                                                                             
       3939 TCTTGCTGTCGCG-ATTCTTTGACCACTTTAACAATGTTGTCCTGTTTATAATCGGAATCGCTCT
          1 TCTTGCTGTCG-GTATTCTTTGACCACTTTAACAATGTTGTCCTGTTTATAATCGGAATCGCTCT

              
       4003 GT
         65 GT

       4005 AACTTTGGAT


Statistics
Matches: 65,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
  66   64  0.98
  67    1  0.02

ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42


Consensus pattern (66 bp):   
TCTTGCTGTCGGTATTCTTTGACCACTTTAACAATGTTGTCCTGTTTATAATCGGAATCGCTCTG
T

Found at i:5146 original size:24 final size:24

Alignment explanation


    Indices: 5118--5165  Score: 87
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       5108 ATTTTTTTAC

                              *     
       5118 CCATTGGTTCTGGTTATTTATCTT
          1 CCATTGGTTCTGGTTATTCATCTT

                                    
       5142 CCATTGGTTCTGGTTATTCATCTT
          1 CCATTGGTTCTGGTTATTCATCTT

       5166 TTGTTTTTGC


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.12, C:0.19, G:0.17, T:0.52


Consensus pattern (24 bp):   
CCATTGGTTCTGGTTATTCATCTT
Done.