Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold11250.1

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: 2969
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33


Found at i:159 original size:27 final size:27

Alignment explanation


    Indices: 129--220  Score: 130
    Period size: 27  Copynumber: 3.4  Consensus size: 27

        119 ATTACCAAAG

                         * *           
        129 TACCCTCGATTTATAGAATTACTATTT
          1 TACCCTCGATTTAAAAAATTACTATTT

                  *      *             
        156 TACCCTTGATTTACAAAATTACTATTT
          1 TACCCTCGATTTAAAAAATTACTATTT

                                 * *   
        183 TACCCTCGATTTAAAAAATTATTGTTT
          1 TACCCTCGATTTAAAAAATTACTATTT

                       
        210 TACCCTCGATT
          1 TACCCTCGATT

        221 GTGAAATTAC


Statistics
Matches: 58,  Mismatches: 7, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  27   58  1.00

ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43


Consensus pattern (27 bp):   
TACCCTCGATTTAAAAAATTACTATTT

Found at i:286 original size:27 final size:27

Alignment explanation


    Indices: 252--375  Score: 119
    Period size: 27  Copynumber: 4.6  Consensus size: 27

        242 TATAGGGTAG

                                       
        252 AATTACCAAAATACCCCTAGTTTGTAA
          1 AATTACCAAAATACCCCTAGTTTGTAA

               *           *  *      * 
        279 AATAACCAAAATACCACTGGTTTGTGA
          1 AATTACCAAAATACCCCTAGTTTGTAA

                   **           *       
        306 AATTACCGTAATA-CCCTCAATTTGTAA
          1 AATTACCAAAATACCCCT-AGTTTGTAA

                                    **  
        333 AATTACCAAAATACCCCT-GATTTACAA
          1 AATTACCAAAATACCCCTAG-TTTGTAA

                             
        360 AATTA-CAGAAATACCC
          1 AATTACCA-AAATACCC

        376 TTGACTTTCT


Statistics
Matches: 77,  Mismatches: 16, Indels: 8
        0.76            0.16        0.08

Matches are distributed among these distances:
  26    5  0.06
  27   68  0.88
  28    4  0.05

ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27


Consensus pattern (27 bp):   
AATTACCAAAATACCCCTAGTTTGTAA

Found at i:363 original size:54 final size:54

Alignment explanation


    Indices: 272--432  Score: 144
    Period size: 54  Copynumber: 2.9  Consensus size: 54

        262 ATACCCCTAG

                                      *   ***       * *           
        272 TTTGTAAAATAACCAAAATACCACTGGTTTGTGAAATTACCGTAATACCCTCAA
          1 TTTGTAAAATAACCAAAATACCACTGATTTACAAAATTACAGAAATACCCTCAA

                      *           *                             * *
        326 TTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAAATACCCTTGAC
          1 TTTGTAAAATAACCAAAATACCACTGATTTACAAAATTACAGAAATACCC-TCAA

               *       *  *          *  *             *          
        381 TTTCTAAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCCT
          1 TTTGT-AAAATAACCA-AAATACCACTGATTTACAAAATTACAGAAATACCCT

        433 TGGTTTGTAG


Statistics
Matches: 88,  Mismatches: 16, Indels: 5
        0.81            0.15        0.05

Matches are distributed among these distances:
  54   42  0.48
  55    8  0.09
  56   38  0.43

ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31


Consensus pattern (54 bp):   
TTTGTAAAATAACCAAAATACCACTGATTTACAAAATTACAGAAATACCCTCAA

Found at i:426 original size:27 final size:27

Alignment explanation


    Indices: 331--438  Score: 103
    Period size: 27  Copynumber: 3.9  Consensus size: 27

        321 CTCAATTTGT

                    **        *  *     
        331 AAAATTACCAAAATACCCCTGATTTAC
          1 AAAATTACTGAAATACCCTTGGTTTAC

                    *             *     
        358 AAAATTACAGAAATACCCTTGACTTT-C
          1 AAAATTACTGAAATACCCTTG-GTTTAC

                                *         
        385 TAAAAATTA-TAGAAATACCATTGGTTTAC
          1 --AAAATTACT-GAAATACCCTTGGTTTAC

                                     
        414 AAAATTACTGAAATACCCTTGGTTT
          1 AAAATTACTGAAATACCCTTGGTTT

        439 GTAGATTTAC


Statistics
Matches: 67,  Mismatches: 8, Indels: 12
        0.77            0.09        0.14

Matches are distributed among these distances:
  27   41  0.61
  28    7  0.10
  29   19  0.28

ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31


Consensus pattern (27 bp):   
AAAATTACTGAAATACCCTTGGTTTAC

Found at i:1341 original size:25 final size:26

Alignment explanation


    Indices: 1307--1376  Score: 90
    Period size: 25  Copynumber: 2.8  Consensus size: 26

       1297 AGGAAGTGCT

                      *             * 
       1307 AAAAGGGCTCCGCCCCAGTTTA-CCG
          1 AAAAGGGCTCTGCCCCAGTTTATCAG

                           *          
       1332 AAAAGGGCTCTGCCCTAGTTTATCAG
          1 AAAAGGGCTCTGCCCCAGTTTATCAG

                     *          
       1358 AAAA-GGCTTTGCCCCAGTT
          1 AAAAGGGCTCTGCCCCAGTT

       1377 ATTAAAAGAG


Statistics
Matches: 39,  Mismatches: 5, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  25   33  0.85
  26    6  0.15

ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23


Consensus pattern (26 bp):   
AAAAGGGCTCTGCCCCAGTTTATCAG
Done.