Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_3140

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: 20018
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:1404 original size:42 final size:41

Alignment explanation


    Indices: 1282--1428  Score: 149
    Period size: 41  Copynumber: 3.6  Consensus size: 41

       1272 TCCAATTCCG

                          *           **     *        
       1282 TTCACCCGGCACTTTGCCTGCTAGGCCCATA-CGCTGATTCA
          1 TTCA-CCGGCACTTAGCCTGCTAGGCATATAGCCCTGATTCA

                                     * *             
       1323 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCCTGATTCA
          1 TTCACCGGCACTTAGCCTGCTAGGCATATAGCCCTGATTCA

            *                                 *          
       1364 GTCACCGGCATCTTAGCCTGCT-GGACAATATAGTCC-GATTCAA
          1 TTCACCGGCA-CTTAGCCTGCTAGG-C-ATATAGCCCTGATTC-A

                                   
       1407 TTCACCGGCACTT-GCCTGCTAG
          1 TTCACCGGCACTTAGCCTGCTAG

       1429 ACGTACAGTC


Statistics
Matches: 90,  Mismatches: 10, Indels: 11
        0.81            0.09        0.10

Matches are distributed among these distances:
  40   22  0.24
  41   31  0.34
  42   21  0.23
  43   16  0.18

ACGTcount: A:0.19, C:0.33, G:0.21, T:0.27


Consensus pattern (41 bp):   
TTCACCGGCACTTAGCCTGCTAGGCATATAGCCCTGATTCA

Found at i:8302 original size:17 final size:16

Alignment explanation


    Indices: 8280--8312  Score: 57
    Period size: 17  Copynumber: 2.0  Consensus size: 16

       8270 GGAAGTCGTG

                             
       8280 ATAATTATACATTTAAA
          1 ATAATTATA-ATTTAAA

                            
       8297 ATAATTATAATTTAAA
          1 ATAATTATAATTTAAA

       8313 TTTATAATTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    7  0.44
  17    9  0.56

ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42


Consensus pattern (16 bp):   
ATAATTATAATTTAAA

Found at i:8325 original size:22 final size:23

Alignment explanation


    Indices: 8280--8325  Score: 58
    Period size: 22  Copynumber: 2.0  Consensus size: 23

       8270 GGAAGTCGTG

                     *             
       8280 ATAATTATACATTTAAAATAATT
          1 ATAATTATAAATTTAAAATAATT

                           *   *   
       8303 ATAATT-TAAATTTATAATTATT
          1 ATAATTATAAATTTAAAATAATT

             
       8325 A
          1 A

       8326 GCTAAAAGGT


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  22   14  0.70
  23    6  0.30

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (23 bp):   
ATAATTATAAATTTAAAATAATT

Found at i:8434 original size:19 final size:18

Alignment explanation


    Indices: 8396--8434  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 18

       8386 ATATAAGAAA

                          **  
       8396 AATTATAATTTAAATTAT
          1 AATTATAATTTAAAAAAT

                               
       8414 AATTATTAATTTAAAAAAT
          1 AATTA-TAATTTAAAAAAT

              
       8433 AA
          1 AA

       8435 GTTGTGCTAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  18    5  0.28
  19   13  0.72

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (18 bp):   
AATTATAATTTAAAAAAT

Found at i:14444 original size:12 final size:14

Alignment explanation


    Indices: 14422--14460  Score: 51
    Period size: 14  Copynumber: 2.7  Consensus size: 14

      14412 AGGAAAATTT

                         * 
      14422 TAATAATAATATAAA
          1 TAATAAT-ATATACA

             *            
      14437 TGATAATATATACA
          1 TAATAATATATACA

                      
      14451 TAATAATATA
          1 TAATAATATA

      14461 CAAAAGTTGA


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  14   15  0.71
  15    6  0.29

ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36


Consensus pattern (14 bp):   
TAATAATATATACA

Found at i:16858 original size:39 final size:39

Alignment explanation


    Indices: 16815--16892  Score: 156
    Period size: 39  Copynumber: 2.0  Consensus size: 39

      16805 ACTATAGAGT

                                                   
      16815 ACCATCCCGATAAGGCTAATATTGTGGCTGATGCTCTTA
          1 ACCATCCCGATAAGGCTAATATTGTGGCTGATGCTCTTA

                                                   
      16854 ACCATCCCGATAAGGCTAATATTGTGGCTGATGCTCTTA
          1 ACCATCCCGATAAGGCTAATATTGTGGCTGATGCTCTTA

      16893 GTTGTAGAGT


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  39   39  1.00

ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31


Consensus pattern (39 bp):   
ACCATCCCGATAAGGCTAATATTGTGGCTGATGCTCTTA

Found at i:19550 original size:29 final size:29

Alignment explanation


    Indices: 19508--19572  Score: 85
    Period size: 29  Copynumber: 2.2  Consensus size: 29

      19498 ATGTGATGAG

                   * *                 * 
      19508 CCACACGGCTGTGTGCCAGGTCTTGTGGA
          1 CCACACGACCGTGTGCCAGGTCTTGTGAA

                            *            
      19537 CCACACGACCGTGTGCTAGGTCTTGTGAA
          1 CCACACGACCGTGTGCCAGGTCTTGTGAA

             *     
      19566 CTACACG
          1 CCACACG

      19573 GGCCAGCCAT


Statistics
Matches: 31,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  29   31  1.00

ACGTcount: A:0.18, C:0.29, G:0.29, T:0.23


Consensus pattern (29 bp):   
CCACACGACCGTGTGCCAGGTCTTGTGAA
Done.