Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3878

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, 381

Length: 635
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31


Found at i:125 original size:44 final size:44

Alignment explanation


    Indices: 1--147  Score: 208
    Period size: 43  Copynumber: 3.4  Consensus size: 44

                               *                      * 
          1 TGGTCTATAGTGGCGTTTTGT-GGCTAAGCGCCGCTAAAGACTA
          1 TGGTCTATAGTGGCGTTTTTTAGGCTAAGCGCCGCTAAAGACCA

              *           *     *                       
         44 TGATCTATAGTGGCATTTTTCA-GCTAAGCGCCGCTAAAGACCA
          1 TGGTCTATAGTGGCGTTTTTTAGGCTAAGCGCCGCTAAAGACCA

                                             *     *    
         87 TGGTCTATAGTGGCGTTTTTTAGGCTAAGCGCCACTAAAAACCA
          1 TGGTCTATAGTGGCGTTTTTTAGGCTAAGCGCCGCTAAAGACCA

                      *      
        131 TGGTCTATAGCGGCGTT
          1 TGGTCTATAGTGGCGTT

        148 GCAAAGAAAA


Statistics
Matches: 91,  Mismatches: 11, Indels: 3
        0.87            0.10        0.03

Matches are distributed among these distances:
  43   56  0.62
  44   35  0.38

ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30


Consensus pattern (44 bp):   
TGGTCTATAGTGGCGTTTTTTAGGCTAAGCGCCGCTAAAGACCA

Found at i:545 original size:22 final size:23

Alignment explanation


    Indices: 501--554  Score: 58
    Period size: 22  Copynumber: 2.4  Consensus size: 23

        491 ATTATGAAAG

                              **   
        501 AAAAT-TATATTATAAATCTTAA
          1 AAAATATATATTATAAATAATAA

                                   
        523 AAAATATATATTATAAA-AATAA
          1 AAAATATATATTATAAATAATAA

             **       
        545 ATTATATATA
          1 AAAATATATA

        555 GTAAACAGAA


Statistics
Matches: 27,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  22   16  0.59
  23   11  0.41

ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39


Consensus pattern (23 bp):   
AAAATATATATTATAAATAATAA

Found at i:559 original size:20 final size:21

Alignment explanation


    Indices: 522--572  Score: 54
    Period size: 20  Copynumber: 2.5  Consensus size: 21

        512 ATAAATCTTA

                *                
        522 AAAAATATATATTATAAA-A-
          1 AAAATTATATATTATAAACAG

                                   
        541 ATAAATTATATA-TAGTAAACAG
          1 A-AAATTATATATTA-TAAACAG

                      
        563 AAAATTATAT
          1 AAAATTATAT

        573 TATTTAATTT


Statistics
Matches: 27,  Mismatches: 1, Indels: 6
        0.79            0.03        0.18

Matches are distributed among these distances:
  19    3  0.11
  20   13  0.48
  21   10  0.37
  22    1  0.04

ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33


Consensus pattern (21 bp):   
AAAATTATATATTATAAACAG
Done.