Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold6719.1

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: 10212
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.29

Warning! 672 characters in sequence are not A, C, G, or T


Found at i:6488 original size:12 final size:12

Alignment explanation


    Indices: 6473--6503  Score: 62
    Period size: 12  Copynumber: 2.6  Consensus size: 12

       6463 TTCTTTTTGC

                        
       6473 TTTTCAAAGGCT
          1 TTTTCAAAGGCT

                        
       6485 TTTTCAAAGGCT
          1 TTTTCAAAGGCT

                   
       6497 TTTTCAA
          1 TTTTCAA

       6504 GTTCTCTCAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45


Consensus pattern (12 bp):   
TTTTCAAAGGCT

Found at i:6573 original size:6 final size:6

Alignment explanation


    Indices: 6564--6613  Score: 50
    Period size: 6  Copynumber: 8.2  Consensus size: 6

       6554 TTTCTTTTTA

                                             *                        
       6564 TTTCTT TTTCTT TTTCTT CTCTTGCTT TTCCTT TTTC-T TTTC-T TTTCTT
          1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT

             
       6613 T
          1 T

       6614 GTTTTCTCTT


Statistics
Matches: 38,  Mismatches: 2, Indels: 8
        0.79            0.04        0.17

Matches are distributed among these distances:
   5   10  0.26
   6   20  0.53
   7    2  0.05
   8    3  0.08
   9    3  0.08

ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76


Consensus pattern (6 bp):   
TTTCTT

Found at i:6575 original size:21 final size:23

Alignment explanation


    Indices: 6551--6609  Score: 59
    Period size: 26  Copynumber: 2.5  Consensus size: 23

       6541 CTCTTGCCTC

                                   
       6551 TCTTTTCTTTTT-ATTT-CTTTT
          1 TCTTTTCTTTTTCATTTCCTTTT

                             *         
       6572 TCTTTTTCTTCTCTTGCTTTTCCTTTT
          1 TC-TTTTCTT-T-TT-CATTTCCTTTT

                       
       6599 TCTTTTCTTTT
          1 TCTTTTCTTTT

       6610 CTTTGTTTTC


Statistics
Matches: 31,  Mismatches: 1, Indels: 9
        0.76            0.02        0.22

Matches are distributed among these distances:
  21    2  0.06
  22    7  0.23
  23    1  0.03
  24    3  0.10
  25    1  0.03
  26   10  0.32
  27    7  0.23

ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76


Consensus pattern (23 bp):   
TCTTTTCTTTTTCATTTCCTTTT

Found at i:6610 original size:37 final size:36

Alignment explanation


    Indices: 6552--6623  Score: 94
    Period size: 37  Copynumber: 2.0  Consensus size: 36

       6542 TCTTGCCTCT

                                                 
       6552 CTTTTCTTTTTATTTCTTTTTCTTT-TTCTTCTCTTG
          1 CTTTTCTTTTTATTTCTTTTTCTTTGTT-TTCTCTTG

                        *                        
       6588 CTTTTCCTTTTTCTTT-TCTTTTCTTTGTTTTCTCTT
          1 CTTTT-CTTTTTATTTCT-TTTTCTTTGTTTTCTCTT

       6624 TACAAGAATG


Statistics
Matches: 32,  Mismatches: 1, Indels: 5
        0.84            0.03        0.13

Matches are distributed among these distances:
  36    6  0.19
  37   24  0.75
  38    2  0.06

ACGTcount: A:0.01, C:0.21, G:0.03, T:0.75


Consensus pattern (36 bp):   
CTTTTCTTTTTATTTCTTTTTCTTTGTTTTCTCTTG

Found at i:7200 original size:69 final size:69

Alignment explanation


    Indices: 7066--7200  Score: 180
    Period size: 69  Copynumber: 2.0  Consensus size: 69

       7056 GAACCATGTA

                   *                        *                          **    
       7066 ACACCCCGAACCCGAGACCGACACCGGAGTCGGACACGAGATGTTAACAAACTTTGAAATTTTTT
          1 ACACCCCAAACCCGAGACCGACACCGGAGTCGAACACGAGATGTTAACAAACTTTGAAAAATTTT

                
       7131 TTTT
         66 TTTT

                                *             *     *    *   *     *         
       7135 ACACCCCAAACCCGAGACCGTCACCGGAGTCGAATACGAGGTGTTGACAGACTTTTAAAAATTTT
          1 ACACCCCAAACCCGAGACCGACACCGGAGTCGAACACGAGATGTTAACAAACTTTGAAAAATTTT

             
       7200 T
         66 T

       7201 CCAGACACTG


Statistics
Matches: 56,  Mismatches: 10, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  69   56  1.00

ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24


Consensus pattern (69 bp):   
ACACCCCAAACCCGAGACCGACACCGGAGTCGAACACGAGATGTTAACAAACTTTGAAAAATTTT
TTTT

Found at i:8604 original size:40 final size:40

Alignment explanation


    Indices: 8513--8682  Score: 198
    Period size: 40  Copynumber: 4.3  Consensus size: 40

       8503 TCCTCGTTCA

                          *  *     *    *      *    
       8513 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

            *             *              *          
       8552 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

                                   *                
       8592 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

                  *  *                  *  *       *
       8632 AATGCCCTCAGGACTTAACCCGGATTTAGTATCTCGCACA
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

              *        
       8672 AAGGCCTTCGG
          1 AATGCCTTCGG

       8683 ATCTTAGTCC


Statistics
Matches: 110,  Mismatches: 20, Indels: 1
        0.84            0.15        0.01

Matches are distributed among these distances:
  39   32  0.29
  40   78  0.71

ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24


Consensus pattern (40 bp):   
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

Done.