Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2124

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: 13779
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35


Found at i:4724 original size:13 final size:13

Alignment explanation


    Indices: 4706--4731  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       4696 TACAAGCTAA

                         
       4706 TGTATCGATACAT
          1 TGTATCGATACAT

                         
       4719 TGTATCGATACAT
          1 TGTATCGATACAT

       4732 ACTTGGTGTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38


Consensus pattern (13 bp):   
TGTATCGATACAT

Found at i:5746 original size:15 final size:15

Alignment explanation


    Indices: 5728--5758  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       5718 GTCACTAGAA

                           
       5728 CTACTCGAACTAGGG
          1 CTACTCGAACTAGGG

                           
       5743 CTACTCGAACTAGGG
          1 CTACTCGAACTAGGG

             
       5758 C
          1 C

       5759 GAAGTCGATG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.26, C:0.29, G:0.26, T:0.19


Consensus pattern (15 bp):   
CTACTCGAACTAGGG

Found at i:6868 original size:21 final size:20

Alignment explanation


    Indices: 6839--6881  Score: 59
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       6829 GACTAGTGTG

                         *       
       6839 GGGACTGCCCGGTTGCGACCT
          1 GGGACTG-CCGGTCGCGACCT

                *               
       6860 GGGAGTGCCGGTCGCGACCT
          1 GGGACTGCCGGTCGCGACCT

              
       6880 GG
          1 GG

       6882 TGGGTGCTGC


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20   14  0.70
  21    6  0.30

ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16


Consensus pattern (20 bp):   
GGGACTGCCGGTCGCGACCT

Found at i:7181 original size:21 final size:21

Alignment explanation


    Indices: 7157--7203  Score: 62
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       7147 TTTGAAGCTG

                                  
       7157 ATTTTG-A-TGAAAAACGAAGT
          1 ATTTTGAAGTGAAAAAC-AAGT

             *                   
       7177 AATTTGAAGTGAAAAACAAGT
          1 ATTTTGAAGTGAAAAACAAGT

                  
       7198 ATTTTG
          1 ATTTTG

       7204 CAAAAGATTT


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  20    5  0.22
  21   10  0.43
  22    8  0.35

ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32


Consensus pattern (21 bp):   
ATTTTGAAGTGAAAAACAAGT

Found at i:7344 original size:13 final size:13

Alignment explanation


    Indices: 7326--7350  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       7316 ATAATCCCCC

                         
       7326 TGTATCGATACAG
          1 TGTATCGATACAG

                        
       7339 TGTATCGATACA
          1 TGTATCGATACA

       7351 AAGAAAGATG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32


Consensus pattern (13 bp):   
TGTATCGATACAG

Found at i:7528 original size:13 final size:14

Alignment explanation


    Indices: 7510--7549  Score: 55
    Period size: 13  Copynumber: 2.9  Consensus size: 14

       7500 AATAAAAACA

                          
       7510 CAAAATCATTCA-T
          1 CAAAATCATTCATT

                           
       7523 CAAAATCATTCATTT
          1 CAAAATCATTCA-TT

               *        
       7538 CAACATCATTCA
          1 CAAAATCATTCA

       7550 ACATAAAATC


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  13   12  0.50
  15   12  0.50

ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33


Consensus pattern (14 bp):   
CAAAATCATTCATT

Done.