Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003267.1 Kokia drynarioides strain JFW-HI SEQ_115924, whole genome shotgun sequence

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: 8194
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32


Found at i:2243 original size:21 final size:23

Alignment explanation


    Indices: 2214--2264  Score: 61
    Period size: 24  Copynumber: 2.3  Consensus size: 23

       2204 TTTTGTCCCA

                                   
       2214 CTCCATCTCAC-C-TCCTTATTT
          1 CTCCATCTCACGCTTCCTTATTT

                *    *              
       2235 CTCCTTCTCTCGTCTTCCTTATTT
          1 CTCCATCTCACG-CTTCCTTATTT

                  
       2259 CTCCAT
          1 CTCCAT

       2265 ATTTAGGAGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  21    9  0.38
  23    1  0.04
  24   14  0.58

ACGTcount: A:0.10, C:0.41, G:0.02, T:0.47


Consensus pattern (23 bp):   
CTCCATCTCACGCTTCCTTATTT

Found at i:6572 original size:26 final size:26

Alignment explanation


    Indices: 6543--6626  Score: 105
    Period size: 26  Copynumber: 3.2  Consensus size: 26

       6533 ATCTTATACA

                        *      *      
       6543 AGCCCAGACAGAGTTTAGCCCTTACG
          1 AGCCCAGACAGAATTTAGCTCTTACG

                  *           *     * 
       6569 AGCCCAAACAGAATTTAGTTCTTATG
          1 AGCCCAGACAGAATTTAGCTCTTACG

            *       *                 
       6595 TGCCCAGATAGAATTTAGCTCTTACG
          1 AGCCCAGACAGAATTTAGCTCTTACG

                  
       6621 AGCCCA
          1 AGCCCA

       6627 AACAAAATAA


Statistics
Matches: 47,  Mismatches: 11, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  26   47  1.00

ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25


Consensus pattern (26 bp):   
AGCCCAGACAGAATTTAGCTCTTACG

Found at i:6644 original size:52 final size:52

Alignment explanation


    Indices: 6544--6644  Score: 132
    Period size: 52  Copynumber: 1.9  Consensus size: 52

       6534 TCTTATACAA

                       *                       *   *   *        
       6544 GCCCAGACAGAGTTTAGCCCTTACGAGCCCAAACAGAATTTAGTTCTTATGT
          1 GCCCAGACAGAATTTAGCCCTTACGAGCCCAAACAAAATATAGCTCTTATGT

                   *          *                               
       6596 GCCCAGATAGAATTTAGCTCTTACGAGCCCAAACAAAATA-ATGCTCTTA
          1 GCCCAGACAGAATTTAGCCCTTACGAGCCCAAACAAAATATA-GCTCTTA

       6645 CAAGTCTGAC


Statistics
Matches: 42,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  51    1  0.02
  52   41  0.98

ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26


Consensus pattern (52 bp):   
GCCCAGACAGAATTTAGCCCTTACGAGCCCAAACAAAATATAGCTCTTATGT

Found at i:6666 original size:25 final size:25

Alignment explanation


    Indices: 6632--6693  Score: 83
    Period size: 24  Copynumber: 2.5  Consensus size: 25

       6622 GCCCAAACAA

                 *           *        
       6632 AATAATGCTCTTACAAGTCT-GACAG
          1 AATAACGCTCTTACAA-ACTAGACAG

                                     
       6657 AATAACGCTC-TACAAACTAGACAG
          1 AATAACGCTCTTACAAACTAGACAG

                         
       6681 AATAACGCTCTTA
          1 AATAACGCTCTTA

       6694 TGTGCCAGAG


Statistics
Matches: 33,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  23    2  0.06
  24   20  0.61
  25   11  0.33

ACGTcount: A:0.40, C:0.23, G:0.13, T:0.24


Consensus pattern (25 bp):   
AATAACGCTCTTACAAACTAGACAG

Found at i:7169 original size:154 final size:154

Alignment explanation


    Indices: 6916--7209  Score: 518
    Period size: 154  Copynumber: 1.9  Consensus size: 154

       6906 CACGATCCTA

                               *                                       *    *
       6916 ATCTATCACAACAAAGCATTCAAATTTCTTATTAAAGTATGAAATTCAAATCATTTATTGCATTT
          1 ATCTATCACAACAAAGCATACAAATTTCTTATTAAAGTATGAAATTCAAATCATTTATTCCATTA

                *                    *                                       
       6981 AAGTTATTTTGGGGAAATTTACAAAGTTACCCCTAACATTTCATTTTTATTCAATTTAGTCCTTA
         66 AAGTCATTTTGGGGAAATTTACAAAATTACCCCTAACATTTCATTTTTATTCAATTTAGTCCTTA

                                     
       7046 -AACCTTAAATTTAGCATGATCTTG
        131 GAA-CTTAAATTTAGCATGATCTTG

                                                                             
       7070 ATCTATCACAACAAAGCATACAAATTTCTTATTAAAGTATGAAATTCAAATCATTTATTCCATTA
          1 ATCTATCACAACAAAGCATACAAATTTCTTATTAAAGTATGAAATTCAAATCATTTATTCCATTA

                                         *                                   
       7135 AAGTCATTTTGGGGAAATTTACAAAATTATCCCTAACATTTCATTTTTATTCAATTTAGTCCTTA
         66 AAGTCATTTTGGGGAAATTTACAAAATTACCCCTAACATTTCATTTTTATTCAATTTAGTCCTTA

                      
       7200 GAACTTAAAT
        131 GAACTTAAAT

       7210 ATGCAAAATA


Statistics
Matches: 133,  Mismatches: 6, Indels: 2
        0.94            0.04        0.01

Matches are distributed among these distances:
 154  131  0.98
 155    2  0.02

ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39


Consensus pattern (154 bp):   
ATCTATCACAACAAAGCATACAAATTTCTTATTAAAGTATGAAATTCAAATCATTTATTCCATTA
AAGTCATTTTGGGGAAATTTACAAAATTACCCCTAACATTTCATTTTTATTCAATTTAGTCCTTA
GAACTTAAATTTAGCATGATCTTG
Done.