Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_3067

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: 20393
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34


Found at i:2941 original size:17 final size:17

Alignment explanation


    Indices: 2919--2951  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       2909 ATATTTAATA

                             
       2919 TATATTTGATTAAAAAG
          1 TATATTTGATTAAAAAG

                            
       2936 TATATTTGATTAAAAA
          1 TATATTTGATTAAAAA

       2952 TAGAAATATA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42


Consensus pattern (17 bp):   
TATATTTGATTAAAAAG

Found at i:4072 original size:24 final size:23

Alignment explanation


    Indices: 4042--4088  Score: 67
    Period size: 24  Copynumber: 2.0  Consensus size: 23

       4032 TCTTTATGTT

                   *                
       4042 TATAAATTATATAATATATCTATA
          1 TATAAATAATATAATATAT-TATA

                         *         
       4066 TATAAATAATATATTATATTATA
          1 TATAAATAATATAATATATTATA

       4089 AACATAGAAC


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  23    4  0.19
  24   17  0.81

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (23 bp):   
TATAAATAATATAATATATTATA

Found at i:4076 original size:19 final size:19

Alignment explanation


    Indices: 4052--4090  Score: 62
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       4042 TATAAATTAT

                                
       4052 ATAATATATCTATA-TATAA
          1 ATAATATAT-TATATTATAA

                               
       4071 ATAATATATTATATTATAA
          1 ATAATATATTATATTATAA

             
       4090 A
          1 A

       4091 CATAGAACAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  18    4  0.21
  19   15  0.79

ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44


Consensus pattern (19 bp):   
ATAATATATTATATTATAA

Found at i:8364 original size:17 final size:17

Alignment explanation


    Indices: 8342--8379  Score: 51
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       8332 TTCCCACTCA

                              
       8342 TAATAA-AATAATAATAC
          1 TAATAATAA-AATAATAC

                      *      
       8359 TAATAATAAATTAATAC
          1 TAATAATAAAATAATAC

                
       8376 TAAT
          1 TAAT

       8380 TTTATACTAC


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  17   17  0.89
  18    2  0.11

ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34


Consensus pattern (17 bp):   
TAATAATAAAATAATAC

Found at i:9100 original size:17 final size:16

Alignment explanation


    Indices: 9068--9101  Score: 50
    Period size: 17  Copynumber: 2.1  Consensus size: 16

       9058 TTTGGCATTC

                     *      
       9068 TGTTTCTTTCTTCTTT
          1 TGTTTCTTTATTCTTT

                             
       9084 TGTTTCTTTTATTCTTT
          1 TGTTTC-TTTATTCTTT

             
       9101 T
          1 T

       9102 ATTTTAACTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    6  0.38
  17   10  0.62

ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76


Consensus pattern (16 bp):   
TGTTTCTTTATTCTTT

Found at i:9149 original size:14 final size:14

Alignment explanation


    Indices: 9090--9140  Score: 50
    Period size: 14  Copynumber: 3.6  Consensus size: 14

       9080 CTTTTGTTTC

                     *    
       9090 TTTTA-TTCTTTTA
          1 TTTTATTTCCTTTA

                  *  *     
       9103 TTTTAACTTACTTTA
          1 TTTT-ATTTCCTTTA

            *             
       9118 CTTTATTTCCTTTA
          1 TTTTATTTCCTTTA

                     
       9132 TTTTATTTC
          1 TTTTATTTC

       9141 TTTTGTTTTT


Statistics
Matches: 30,  Mismatches: 6, Indels: 3
        0.77            0.15        0.08

Matches are distributed among these distances:
  13    4  0.13
  14   17  0.57
  15    9  0.30

ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69


Consensus pattern (14 bp):   
TTTTATTTCCTTTA

Found at i:17027 original size:23 final size:23

Alignment explanation


    Indices: 16987--17033  Score: 60
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      16977 CCCAAGTATT

                               *   
      16987 ACCCAACCCAAAGTAAAATTAAA
          1 ACCCAACCCAAAGTAAAATGAAA

                        *           
      17010 ACCCAACCC-AATTAAAAATGAAA
          1 ACCCAACCCAAAGT-AAAATGAAA

             
      17033 A
          1 A

      17034 TAAAACACAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  22    3  0.14
  23   18  0.86

ACGTcount: A:0.57, C:0.26, G:0.04, T:0.13


Consensus pattern (23 bp):   
ACCCAACCCAAAGTAAAATGAAA
Done.