Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold866

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: 27563
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31


Found at i:21421 original size:26 final size:26

Alignment explanation


    Indices: 21350--21430  Score: 83
    Period size: 26  Copynumber: 3.1  Consensus size: 26

      21340 GGCCACATAT

                                      
      21350 ATACTGATACTAGCAGCTTTGCTGCG
          1 ATACTGATACTAGCAGCTTTGCTGCG

                  *  * *   *          
      21376 ATACTGCTATTGGCAACTTTGCTGC-
          1 ATACTGATACTAGCAGCTTTGCTGCG

                   *     *          *  
      21401 ACTACTGGTACTAACAGCTTTGCTACG
          1 A-TACTGATACTAGCAGCTTTGCTGCG

               
      21428 ATA
          1 ATA

      21431 TTGGTATATT


Statistics
Matches: 43,  Mismatches: 10, Indels: 4
        0.75            0.18        0.07

Matches are distributed among these distances:
  25    1  0.02
  26   41  0.95
  27    1  0.02

ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32


Consensus pattern (26 bp):   
ATACTGATACTAGCAGCTTTGCTGCG

Found at i:22012 original size:16 final size:17

Alignment explanation


    Indices: 21991--22023  Score: 50
    Period size: 18  Copynumber: 1.9  Consensus size: 17

      21981 CACATTGAAG

                             
      21991 TGTTTT-TTGAAAACCT
          1 TGTTTTATTGAAAACCT

                             
      22007 TGTTTTCATTGAAAACC
          1 TGTTTT-ATTGAAAACC

      22024 CTTCTTGAAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    6  0.40
  18    9  0.60

ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45


Consensus pattern (17 bp):   
TGTTTTATTGAAAACCT

Found at i:23549 original size:16 final size:16

Alignment explanation


    Indices: 23528--23558  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      23518 CCAAACTTCT

                            
      23528 GGCTTTTCAGCATTTC
          1 GGCTTTTCAGCATTTC

                      *    
      23544 GGCTTTTCAGGATTT
          1 GGCTTTTCAGCATTT

      23559 GTCAGTCTAC


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45


Consensus pattern (16 bp):   
GGCTTTTCAGCATTTC

Found at i:25759 original size:46 final size:48

Alignment explanation


    Indices: 25641--25816  Score: 190
    Period size: 46  Copynumber: 3.8  Consensus size: 48

      25631 TGTAACCCGC

                                           *      *     *   
      25641 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCG--GGC-GTTGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGATGCCAGTTACAT

                   *                                         
      25686 CCAT-AGTGAACTCGGACTCAACTCAACGAGTTCGATGCCTAGTTACAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGATGCC-AGTTACAT

                *                                 *  *  *   
      25734 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCG--GACATTTGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGATGCCAGTTACAT

                   *                                
      25777 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GATGC

      25817 TCAACCATCC


Statistics
Matches: 109,  Mismatches: 11, Indels: 18
        0.79            0.08        0.13

Matches are distributed among these distances:
  43    6  0.06
  44   31  0.28
  45    6  0.06
  46   56  0.51
  47    3  0.03
  48    6  0.06
  49    1  0.01

ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22


Consensus pattern (48 bp):   
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGATGCCAGTTACAT

Found at i:25805 original size:92 final size:91

Alignment explanation


    Indices: 25648--25816  Score: 286
    Period size: 90  Copynumber: 1.8  Consensus size: 91

      25638 CGCCCATAAG

                                         *                                   
      25648 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTGCATCCATAGTGAACTCGGACTCAACTCAAC
          1 CGAACTCGGACTCAACTCAACGAGCTCGGACGTTGCATCCATAGTGAACTCGGACTCAACTCAAC

                                      
      25713 GAGTTC-GATGCCTAGTTACATCTCA
         66 GAGTTCGGATGCCTAGTTACATCTCA

                                    *       *                                
      25738 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
          1 CGAACTCGGACTCAACTCAACGAGCTCGGAC-GTTGCATCCAT-AGTGAACTCGGACTCAACTCA

                          
      25803 ACGAGTTCGGATGC
         64 ACGAGTTCGGATGC

      25817 TCAACCATCC


Statistics
Matches: 73,  Mismatches: 3, Indels: 3
        0.92            0.04        0.04

Matches are distributed among these distances:
  90   29  0.40
  91   10  0.14
  92   29  0.40
  93    5  0.07

ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22


Consensus pattern (91 bp):   
CGAACTCGGACTCAACTCAACGAGCTCGGACGTTGCATCCATAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCA

Done.