Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold174

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: 2085601
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35

Warning! 25 characters in sequence are not A, C, G, or T


File 15 of 15

Found at i:2062520 original size:15 final size:14

Alignment explanation


    Indices: 2062497--2062526  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

    2062487 AAAAATTAAA

                          
    2062497 TATTTTAAAAAAAT
          1 TATTTTAAAAAAAT

                           
    2062511 TATTTATAAAAAAAT
          1 TATTT-TAAAAAAAT

             
    2062526 T
          1 T

    2062527 TACTCTCATG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (14 bp):   
TATTTTAAAAAAAT

Found at i:2063952 original size:2 final size:2

Alignment explanation


    Indices: 2063917--2063944  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

    2063907 AAGCTTATTT

                                                     
    2063917 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

    2063945 AGTATATAGA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:2069232 original size:11 final size:10

Alignment explanation


    Indices: 2069201--2069234  Score: 50
    Period size: 10  Copynumber: 3.3  Consensus size: 10

    2069191 ATCAGTAAGA

                      
    2069201 AGGGGGGGGG
          1 AGGGGGGGGG

            *         
    2069211 GGGGGGGGGG
          1 AGGGGGGGGG

                       
    2069221 AGGGTGGGGGG
          1 AGGG-GGGGGG

               
    2069232 AGG
          1 AGG

    2069235 TCTTATATAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  10   12  0.57
  11    9  0.43

ACGTcount: A:0.09, C:0.00, G:0.88, T:0.03


Consensus pattern (10 bp):   
AGGGGGGGGG

Found at i:2070933 original size:20 final size:20

Alignment explanation


    Indices: 2070908--2070959  Score: 68
    Period size: 20  Copynumber: 2.6  Consensus size: 20

    2070898 TACCCTGATG

                         *      
    2070908 TATCGATACATTTTTCAATA
          1 TATCGATACATTTATCAATA

                       *   *   *
    2070928 TATCGATACATGTATGAATG
          1 TATCGATACATTTATCAATA

                        
    2070948 TATCGATACATT
          1 TATCGATACATT

    2070960 ATGTCTTTTT


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  20   27  1.00

ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40


Consensus pattern (20 bp):   
TATCGATACATTTATCAATA

Found at i:2084900 original size:1 final size:1

Alignment explanation


    Indices: 2084896--2084965  Score: 77
    Period size: 1  Copynumber: 70.0  Consensus size: 1

    2084886 ATTTTTGCTA

                  *               *    *          *       *          *      *
    2084896 TTTTTTCTTTTTTTTTTTTTTTGTTTTGTTTTTTTTTTGTTTTTTTATTTTTTTTTTGTTTTTTG
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

                 
    2084961 TTTTT
          1 TTTTT

    2084966 GGGTGTAAAG


Statistics
Matches: 55,  Mismatches: 14, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
   1   55  1.00

ACGTcount: A:0.01, C:0.01, G:0.07, T:0.90


Consensus pattern (1 bp):   
T

Found at i:2084915 original size:16 final size:16

Alignment explanation


    Indices: 2084896--2084966  Score: 90
    Period size: 16  Copynumber: 4.4  Consensus size: 16

    2084886 ATTTTTGCTA

                  *         
    2084896 TTTTTTCTTTTTTTTT
          1 TTTTTTGTTTTTTTTT

                       *    
    2084912 TTTTTTGTTTTGTTTT
          1 TTTTTTGTTTTTTTTT

                             
    2084928 TTTTTTGTTTTTTTATT
          1 TTTTTTGTTTTTTT-TT

                     *      
    2084945 TTTTTT-TTGTTTTTT
          1 TTTTTTGTTTTTTTTT

            *      
    2084960 GTTTTTG
          1 TTTTTTG

    2084967 GGTGTAAAGG


Statistics
Matches: 48,  Mismatches: 5, Indels: 4
        0.84            0.09        0.07

Matches are distributed among these distances:
  15    7  0.15
  16   33  0.69
  17    8  0.17

ACGTcount: A:0.01, C:0.01, G:0.08, T:0.89


Consensus pattern (16 bp):   
TTTTTTGTTTTTTTTT

Found at i:2084927 original size:19 final size:18

Alignment explanation


    Indices: 2084896--2084965  Score: 88
    Period size: 18  Copynumber: 3.9  Consensus size: 18

    2084886 ATTTTTGCTA

                  *           
    2084896 TTTTTTCTTT-TTTTTTT
          1 TTTTTTTTTTGTTTTTTT

                 *            
    2084913 TTTTTGTTTTGTTTTTTT
          1 TTTTTTTTTTGTTTTTTT

                       *       
    2084931 TTTGTTTTTTTATTTTTTT
          1 TTT-TTTTTTTGTTTTTTT

               *            
    2084950 TTTGTTTTTTGTTTTT
          1 TTTTTTTTTTGTTTTT

    2084966 GGGTGTAAAG


Statistics
Matches: 45,  Mismatches: 6, Indels: 3
        0.83            0.11        0.06

Matches are distributed among these distances:
  17    8  0.18
  18   21  0.47
  19   16  0.36

ACGTcount: A:0.01, C:0.01, G:0.07, T:0.90


Consensus pattern (18 bp):   
TTTTTTTTTTGTTTTTTT


Done.