Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2720

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: 15226
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:1735 original size:60 final size:60

Alignment explanation


    Indices: 1613--1728  Score: 169
    Period size: 60  Copynumber: 1.9  Consensus size: 60

       1603 CGATACATCT

                               *                *      * *              
       1613 TCATGTTTCGATTATTTCAGGACCTGGAGTGCAATTGTATCGATATAATTGCATGTCATA
          1 TCATGTTTCGATTATTTCAAGACCTGGAGTGCAATTATATCGAAACAATTGCATGTCATA

                    *           *                   *               
       1673 TCATGTTTTGATTATTTCAATACCTGGAGTGCAATTATATTGAAACAATTGCATGT
          1 TCATGTTTCGATTATTTCAAGACCTGGAGTGCAATTATATCGAAACAATTGCATGT

       1729 TGTATCAATA


Statistics
Matches: 49,  Mismatches: 7, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  60   49  1.00

ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40


Consensus pattern (60 bp):   
TCATGTTTCGATTATTTCAAGACCTGGAGTGCAATTATATCGAAACAATTGCATGTCATA

Found at i:8145 original size:2 final size:2

Alignment explanation


    Indices: 8138--8191  Score: 108
    Period size: 2  Copynumber: 27.0  Consensus size: 2

       8128 CATCTTCCAT

                                                                          
       8138 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                             
       8180 TA TA TA TA TA TA
          1 TA TA TA TA TA TA

       8192 ACATAAGATG


Statistics
Matches: 52,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   52  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:8853 original size:17 final size:18

Alignment explanation


    Indices: 8822--8858  Score: 51
    Period size: 17  Copynumber: 2.1  Consensus size: 18

       8812 CTACTGCATC

                              
       8822 TTTATAGACTATTAC-AT
          1 TTTATAGACTATTACTAT

                               
       8839 TTTATAGA-TATTTACTAT
          1 TTTATAGACTA-TTACTAT

              
       8857 TT
          1 TT

       8859 AGGCATCAAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  16    2  0.11
  17   12  0.67
  18    4  0.22

ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54


Consensus pattern (18 bp):   
TTTATAGACTATTACTAT

Found at i:10882 original size:72 final size:72

Alignment explanation


    Indices: 10784--10918  Score: 175
    Period size: 72  Copynumber: 1.9  Consensus size: 72

      10774 TATATGGTTT

                                                *                    *       
      10784 CTTTCCACGCCGTACATAAACCATCTCATG-AGGTTTATTCCTATGCTGGGAATAAAGTATCTCA
          1 CTTTCCACGCCGTACATAAACCATCTCA-GCAGGTTCATTCCTATGCTGGGAATAAACTATCTCA

                    
      10848 CTCGCTTG
         65 CTCGCTTG

                 *                *        *     *  *                       
      10856 CTTTCTACGCCG-AGCATAAACTATCTCAGCTGGTTCCTTTCTATGCTGGGAATAAACTATCTC
          1 CTTTCCACGCCGTA-CATAAACCATCTCAGCAGGTTCATTCCTATGCTGGGAATAAACTATCTC

      10919 TGTTGGTTCT


Statistics
Matches: 54,  Mismatches: 7, Indels: 4
        0.83            0.11        0.06

Matches are distributed among these distances:
  71    2  0.04
  72   52  0.96

ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33


Consensus pattern (72 bp):   
CTTTCCACGCCGTACATAAACCATCTCAGCAGGTTCATTCCTATGCTGGGAATAAACTATCTCAC
TCGCTTG

Found at i:10896 original size:36 final size:36

Alignment explanation


    Indices: 10833--10927  Score: 93
    Period size: 36  Copynumber: 2.6  Consensus size: 36

      10823 CCTATGCTGG

                   *            *  *             
      10833 GAATAAAGTATCTCA-CTCGCTTGCTTTCTACGCCGA
          1 GAATAAACTATCTCAGCT-GGTTCCTTTCTACGCCGA

             *                            *  * *
      10869 GCATAAACTATCTCAGCTGGTTCCTTTCTATGCTGG
          1 GAATAAACTATCTCAGCTGGTTCCTTTCTACGCCGA

                          * *      
      10905 GAATAAACTATCTCTGTTGGTTC
          1 GAATAAACTATCTCAGCTGGTTC

      10928 TATCTCAGCT


Statistics
Matches: 48,  Mismatches: 10, Indels: 2
        0.80            0.17        0.03

Matches are distributed among these distances:
  36   46  0.96
  37    2  0.04

ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35


Consensus pattern (36 bp):   
GAATAAACTATCTCAGCTGGTTCCTTTCTACGCCGA

Found at i:10936 original size:51 final size:51

Alignment explanation


    Indices: 10876--10977  Score: 150
    Period size: 51  Copynumber: 2.0  Consensus size: 51

      10866 CGAGCATAAA

                                   *  *                *       
      10876 CTATCTCAGCTGGTTCCTTTCTATGCTGGGAATAAACTATCTCTGTTGGTT
          1 CTATCTCAGCTGGTTCCTTTCTACGCCGGGAATAAACTATCTCCGTTGGTT

                           *              *         *          
      10927 CTATCTCAGCTGGTTTCTTTCTACGCCGGGCATAAACTATTTCCGTTGGTT
          1 CTATCTCAGCTGGTTCCTTTCTACGCCGGGAATAAACTATCTCCGTTGGTT

      10978 TCAAACAACT


Statistics
Matches: 45,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  51   45  1.00

ACGTcount: A:0.17, C:0.24, G:0.20, T:0.40


Consensus pattern (51 bp):   
CTATCTCAGCTGGTTCCTTTCTACGCCGGGAATAAACTATCTCCGTTGGTT
Done.