Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003097.1 Kokia drynarioides strain JFW-HI SEQ_115660, 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: 8792
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30


Found at i:1151 original size:44 final size:44

Alignment explanation


    Indices: 1053--1157  Score: 138
    Period size: 44  Copynumber: 2.4  Consensus size: 44

       1043 GTCTTTAGTC

                     *              *               **  
       1053 CGCCATTTTAGCTTGCACCCACTCGGGCTTGCATTTAGACTGTT
          1 CGCCATTTTGGCTTGCACCCACTCAGGCTTGCATTTAGACCATT

                 *                         *            
       1097 CGCCACTTTGGCTTGCACCCACTCAGGCTTGTATTTAGACCATT
          1 CGCCATTTTGGCTTGCACCCACTCAGGCTTGCATTTAGACCATT

            **               
       1141 TTCCATTTTGGCTTGCA
          1 CGCCATTTTGGCTTGCA

       1158 TTTCGGCAGG


Statistics
Matches: 52,  Mismatches: 9, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  44   52  1.00

ACGTcount: A:0.16, C:0.30, G:0.19, T:0.35


Consensus pattern (44 bp):   
CGCCATTTTGGCTTGCACCCACTCAGGCTTGCATTTAGACCATT

Found at i:1316 original size:18 final size:18

Alignment explanation


    Indices: 1293--1373  Score: 78
    Period size: 18  Copynumber: 4.6  Consensus size: 18

       1283 CTTTGATTGA

                       *  *   
       1293 TCGCACATTTTCCAAAGC
          1 TCGCACATTTTGCAGAGC

                  *      *    
       1311 TCGCACCTTTTGCTGAGC
          1 TCGCACATTTTGCAGAGC

              *               
       1329 TCACACATTTTGCAGAGC
          1 TCGCACATTTTGCAGAGC

                       *       
       1347 TCGCAC-TTTGAGCAGAG-
          1 TCGCACATTT-TGCAGAGC

                       
       1364 TCGCAC-TTTT
          1 TCGCACATTTT

       1374 TACTAAGCTC


Statistics
Matches: 52,  Mismatches: 10, Indels: 4
        0.79            0.15        0.06

Matches are distributed among these distances:
  17   12  0.23
  18   40  0.77

ACGTcount: A:0.21, C:0.30, G:0.19, T:0.31


Consensus pattern (18 bp):   
TCGCACATTTTGCAGAGC

Found at i:1316 original size:33 final size:33

Alignment explanation


    Indices: 1234--1357  Score: 97
    Period size: 33  Copynumber: 3.7  Consensus size: 33

       1224 GGTTCCCACC

                *                  * *      *
       1234 TTTTACAGAGCTCGCACTTTGATAGCTCGCACC
          1 TTTTCCAGAGCTCGCACTTTGATTGATCGCACA

                * * *  *                     
       1267 TTTTTCTGTGCCCGCACTTTGATTGATCGCACA
          1 TTTTCCAGAGCTCGCACTTTGATTGATCGCACA

                   *                *       *    
       1300 TTTTCCAAAGCTCGCACCTTTTG-CTGAGCTCACACA
          1 TTTTCCAGAGCTCGCA-C-TTTGATTGA--TCGCACA

                *                 
       1336 TTTTGCAGAGCTCGCACTTTGA
          1 TTTTCCAGAGCTCGCACTTTGA

       1358 GCAGAGTCGC


Statistics
Matches: 70,  Mismatches: 16, Indels: 8
        0.74            0.17        0.09

Matches are distributed among these distances:
  33   37  0.53
  34    8  0.11
  35    5  0.07
  36   20  0.29

ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34


Consensus pattern (33 bp):   
TTTTCCAGAGCTCGCACTTTGATTGATCGCACA
Done.