Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3189

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: 45155
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:441 original size:6 final size:6

Alignment explanation


    Indices: 432--458  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

        422 CACCTTTTAA

                                           
        432 TTTTCT TTTTCT TTTTCT TTTTCT TTT
          1 TTTTCT TTTTCT TTTTCT TTTTCT TTT

        459 CCAATTAAAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85


Consensus pattern (6 bp):   
TTTTCT

Found at i:5277 original size:30 final size:31

Alignment explanation


    Indices: 5218--5277  Score: 88
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       5208 GCCTAATGTC

                                           
       5218 TTAAATAAAAATTTACGAATAGTTTAGTGAT
          1 TTAAATAAAAATTTACGAATAGTTTAGTGAT

                  *                        
       5249 TTAAATGAAAATTT-CGAATA-TTTCAGTGA
          1 TTAAATAAAAATTTACGAATAGTTT-AGTGA

       5278 CTATTTTATA


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  29    3  0.11
  30   11  0.41
  31   13  0.48

ACGTcount: A:0.43, C:0.05, G:0.13, T:0.38


Consensus pattern (31 bp):   
TTAAATAAAAATTTACGAATAGTTTAGTGAT

Found at i:5856 original size:13 final size:14

Alignment explanation


    Indices: 5829--5857  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       5819 TATATTATAT

                          
       5829 TAAAATTTAAATTA
          1 TAAAATTTAAATTA

                          
       5843 TAAAATTT-AATTA
          1 TAAAATTTAAATTA

              
       5856 TA
          1 TA

       5858 CTTATTTAAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    7  0.47
  14    8  0.53

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (14 bp):   
TAAAATTTAAATTA

Found at i:10032 original size:31 final size:29

Alignment explanation


    Indices: 9962--10041  Score: 90
    Period size: 29  Copynumber: 2.7  Consensus size: 29

       9952 GAATTTGATC

                                     *    
       9962 AAATTAAAATTTCATGTATAAAATTGTACA
          1 AAATTAAAA-TTCATGTATAAAATTATACA

                               *       * 
       9992 AAATTAAAATTCATGTATATAATTATATA
          1 AAATTAAAATTCATGTATAAAATTATACA

                  *               
      10021 TTAAATCAAAATT-ATGTATAA
          1 --AAATTAAAATTCATGTATAA

      10042 TTTTAAGATT


Statistics
Matches: 43,  Mismatches: 5, Indels: 4
        0.83            0.10        0.08

Matches are distributed among these distances:
  29   17  0.40
  30   16  0.37
  31   10  0.23

ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39


Consensus pattern (29 bp):   
AAATTAAAATTCATGTATAAAATTATACA

Found at i:25820 original size:24 final size:24

Alignment explanation


    Indices: 25805--25855  Score: 75
    Period size: 24  Copynumber: 2.1  Consensus size: 24

      25795 AATCAAAGTC

                                    
      25805 AAATATATTATGCTAATAAATGCT
          1 AAATATATTATGCTAATAAATGCT

                       *  *      *  
      25829 AAATATATTATACTCATAAATACT
          1 AAATATATTATGCTAATAAATGCT

               
      25853 AAA
          1 AAA

      25856 GCTTTTAGAA


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35


Consensus pattern (24 bp):   
AAATATATTATGCTAATAAATGCT

Found at i:30860 original size:16 final size:16

Alignment explanation


    Indices: 30839--30876  Score: 76
    Period size: 16  Copynumber: 2.4  Consensus size: 16

      30829 TTAATTATTG

                            
      30839 ATTACAGCTCTATTCC
          1 ATTACAGCTCTATTCC

                            
      30855 ATTACAGCTCTATTCC
          1 ATTACAGCTCTATTCC

                  
      30871 ATTACA
          1 ATTACA

      30877 TTGAACCAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   22  1.00

ACGTcount: A:0.29, C:0.29, G:0.05, T:0.37


Consensus pattern (16 bp):   
ATTACAGCTCTATTCC

Found at i:36455 original size:21 final size:22

Alignment explanation


    Indices: 36415--36455  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

      36405 AAATAATTAA

                      *           
      36415 TCATATTATATTAATCACATAC
          1 TCATATTATAATAATCACATAC

                         *      
      36437 TCATATT-TAATATTCACAT
          1 TCATATTATAATAATCACAT

      36456 TTAAATTTAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21   10  0.59
  22    7  0.41

ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44


Consensus pattern (22 bp):   
TCATATTATAATAATCACATAC

Found at i:42975 original size:3 final size:3

Alignment explanation


    Indices: 42969--43003  Score: 63
    Period size: 3  Copynumber: 12.0  Consensus size: 3

      42959 TTCTCTTGTT

                                                           
      42969 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

      43004 CACATTTAGT


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2    2  0.06
   3   29  0.94

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
TTA

Done.