Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold486

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: 10149
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32


Found at i:3888 original size:18 final size:18

Alignment explanation


    Indices: 3865--3900  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       3855 CTAGTGATTT

                              
       3865 TATCCGGGTTAAGACCCG
          1 TATCCGGGTTAAGACCCG

                              
       3883 TATCCGGGTTAAGACCCG
          1 TATCCGGGTTAAGACCCG

       3901 AAGGCATTTG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.22, C:0.28, G:0.28, T:0.22


Consensus pattern (18 bp):   
TATCCGGGTTAAGACCCG

Found at i:3915 original size:58 final size:58

Alignment explanation


    Indices: 3825--3940  Score: 205
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       3815 ATTTGAATGA

                         *                                  *         
       3825 TATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGTTAAGACCCG
          1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCG

                    *                                                 
       3883 TATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCG
          1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCG

       3941 AAGGCATTTG


Statistics
Matches: 55,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  58   55  1.00

ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28


Consensus pattern (58 bp):   
TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCG

Found at i:3938 original size:40 final size:41

Alignment explanation


    Indices: 3883--4033  Score: 218
    Period size: 40  Copynumber: 3.8  Consensus size: 41

       3873 TTAAGACCCG

                    *                      *        *
       3883 TATCCGGGTTAAGACCCGAAGGCATTTGTGCTAG-TGATTT
          1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATTA

                                                     
       3923 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
          1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATTA

                                                  *  
       3963 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
          1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATTA

              *     *               *      
       4003 TACCCGGGTTAAGACCCGAAGGCAATTGTGC
          1 TATCCGGGCTAAGACCCGAAGGCATTTGTGC

       4034 TTGTGGTTAT


Statistics
Matches: 103,  Mismatches: 6, Indels: 4
        0.91            0.05        0.04

Matches are distributed among these distances:
  40  100  0.97
  41    3  0.03

ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26


Consensus pattern (41 bp):   
TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATTA

Found at i:4045 original size:80 final size:80

Alignment explanation


    Indices: 3883--4053  Score: 220
    Period size: 80  Copynumber: 2.1  Consensus size: 80

       3873 TTAAGACCCG

                    *                      *     * *  *                     *
       3883 TATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCAT
          1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCAA

                      *    
       3948 TTGTGCGAGTTGATA
         66 TTGTGCGAGTGGATA

                                                             *               
       3963 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGCA
          1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGACTATACCCGGGCTAAGACCCGAAGGCA

                   **    *  
       4027 ATTGTGCTTGTGGTTA
         65 ATTGTGCGAGTGGATA

                        
       4043 TATCC-GGCTAA
          1 TATCCGGGCTAA

       4054 ATTTCGAAGA


Statistics
Matches: 79,  Mismatches: 11, Indels: 3
        0.85            0.12        0.03

Matches are distributed among these distances:
  79    6  0.08
  80   71  0.90
  81    2  0.03

ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27


Consensus pattern (80 bp):   
TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCAA
TTGTGCGAGTGGATA

Found at i:6832 original size:40 final size:39

Alignment explanation


    Indices: 6775--7001  Score: 332
    Period size: 39  Copynumber: 5.8  Consensus size: 39

       6765 ATTTGAATAC

                        *             *            * 
       6775 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTTT
          1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC-AGTTGA-TAT

                                                    
       6815 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
          1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC-AGTTGATAT

                                                   
       6855 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAGTTGATAT
          1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAGTTGATAT

                                            *      
       6894 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAGATGATAT
          1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAGTTGATAT

                                     *          *   
       6933 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
          1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC-AGTTGATAT

                   *               *      
       6973 A-CCGGGTTAAGACCCGAAGGCAATTGTGC
          1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC

       7002 TTGTGGTTAT


Statistics
Matches: 174,  Mismatches: 11, Indels: 5
        0.92            0.06        0.03

Matches are distributed among these distances:
  39  101  0.58
  40   70  0.40
  41    3  0.02

ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25


Consensus pattern (39 bp):   
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAGTTGATAT

Done.