Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3787

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: 7001
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31


Found at i:1513 original size:46 final size:46

Alignment explanation


    Indices: 1463--1638  Score: 200
    Period size: 46  Copynumber: 3.8  Consensus size: 46

       1453 TGATTGAGCA

                                                          
       1463 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

                                          * *        *       
       1509 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G

                   *                                      * 
       1554 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
          1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

                  *                       *       
       1602 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
          1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG

       1639 GCGGGTTACA


Statistics
Matches: 111,  Mismatches: 9, Indels: 20
        0.79            0.06        0.14

Matches are distributed among these distances:
  42    2  0.02
  43    5  0.05
  45    5  0.05
  46   62  0.56
  47   28  0.25
  48    3  0.03
  50    4  0.04
  51    2  0.02

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


Consensus pattern (46 bp):   
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

Found at i:1619 original size:93 final size:93

Alignment explanation


    Indices: 1460--1631  Score: 301
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       1450 GGATGATTGA

                                                           *                 
       1460 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT

                                        
       1525 TGAGTCCGAGTTCGTGAGATGTAACTAG
         66 TGAGTCCGAGTTCGTGAGATGTAACTAG

                    *                                              *         
       1553 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG

                           
       1617 TTGAGTCCGAGTTCG
         65 TTGAGTCCGAGTTCG

       1632 CTTATGGGCG


Statistics
Matches: 75,  Mismatches: 3, Indels: 2
        0.94            0.04        0.03

Matches are distributed among these distances:
  92    2  0.03
  93   73  0.97

ACGTcount: A:0.20, C:0.21, G:0.30, T:0.28


Consensus pattern (93 bp):   
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG

Found at i:6021 original size:40 final size:39

Alignment explanation


    Indices: 5977--6106  Score: 124
    Period size: 39  Copynumber: 3.3  Consensus size: 39

       5967 GGACTAAGAT

                                *                   
       5977 CCGAAGGCATTTTGTACGAGATACTAATTCCGGGCTAAGC
          1 CCGAAGGCATTTTGT-CGAGTTACTAATTCCGGGCTAAGC

                        *              *      *    *
       6017 CCGAAGGCATTGGTGT-GAGTTACTAAATCCGGGTTAAGT
          1 CCGAAGGCATT-TTGTCGAGTTACTAATTCCGGGCTAAGC

                                         *        *   
       6056 CCG-AGGCA-TTTGTGCGAGTTACT-ATAACCGGGCTATGTC
          1 CCGAAGGCATTTTGT-CGAGTTACTAAT-TCCGGGCTAAG-C

                        
       6095 CCGAAGGCATTT
          1 CCGAAGGCATTT

       6107 GAACGAGTAG


Statistics
Matches: 72,  Mismatches: 11, Indels: 13
        0.75            0.11        0.14

Matches are distributed among these distances:
  36    3  0.04
  37    2  0.03
  38   21  0.29
  39   25  0.35
  40   16  0.22
  41    5  0.07

ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27


Consensus pattern (39 bp):   
CCGAAGGCATTTTGTCGAGTTACTAATTCCGGGCTAAGC

Found at i:6075 original size:38 final size:39

Alignment explanation


    Indices: 5924--6107  Score: 176
    Period size: 40  Copynumber: 4.6  Consensus size: 39

       5914 TCAAATGATG

                                          *   *  * * 
       5924 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
          1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA

                 *                      *    *      *
       5964 TCCGGACTAAGATCCGAAGGCATTTTGTACGAGATACTAAT
          1 TCCGGGCTAAG-TCCGAAGGCA-TTTGTGCGAGTTACTAAA

                       *           *   *           
       6005 TCCGGGCTAAGCCCGAAGGCATTGGTGTGAGTTACTAAA
          1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA

                  *                                 
       6044 TCCGGGTTAAGTCCG-AGGCATTTGTGCGAGTTACTATAA
          1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTA-AA

                     *                
       6083 -CCGGGCTATGTCCCGAAGGCATTTG
          1 TCCGGGCTAAGT-CCGAAGGCATTTG

       6108 AACGAGTAGC


Statistics
Matches: 117,  Mismatches: 21, Indels: 12
        0.78            0.14        0.08

Matches are distributed among these distances:
  38   28  0.24
  39   31  0.26
  40   36  0.31
  41   16  0.14
  42    6  0.05

ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26


Consensus pattern (39 bp):   
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA

Done.