Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009844.1 Corchorus olitorius cultivar O-4 contig09876, 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: 4703
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30


Found at i:566 original size:21 final size:21

Alignment explanation


    Indices: 542--583  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        532 TACCGTCACG

                                 
        542 TTTCCGTCGTCACGTTTCTGT
          1 TTTCCGTCGTCACGTTTCTGT

                                 
        563 TTTCCGTCGTCACGTTTCTGT
          1 TTTCCGTCGTCACGTTTCTGT

        584 CAAGCCTCAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.05, C:0.29, G:0.19, T:0.48


Consensus pattern (21 bp):   
TTTCCGTCGTCACGTTTCTGT

Found at i:3192 original size:22 final size:24

Alignment explanation


    Indices: 3125--3192  Score: 70
    Period size: 22  Copynumber: 2.9  Consensus size: 24

       3115 AAACATAACA

                                      
       3125 GAAAGAGCAAGAAGAAAAGAAAAATG
          1 GAAAGAGC-AGAAGAAAAG-AAAATG

             *           *  *       
       3151 GGAAGAG-AGAAGGAAGGAAAAT-
          1 GAAAGAGCAGAAGAAAAGAAAATG

                                 
       3173 GAAAG-GCAGAAGAAAAGAAA
          1 GAAAGAGCAGAAGAAAAGAAA

       3193 TATCTAGAAT


Statistics
Matches: 35,  Mismatches: 6, Indels: 6
        0.74            0.13        0.13

Matches are distributed among these distances:
  21    1  0.03
  22   15  0.43
  23    5  0.14
  24    8  0.23
  26    6  0.17

ACGTcount: A:0.62, C:0.03, G:0.32, T:0.03


Consensus pattern (24 bp):   
GAAAGAGCAGAAGAAAAGAAAATG

Found at i:3695 original size:20 final size:19

Alignment explanation


    Indices: 3670--3710  Score: 64
    Period size: 20  Copynumber: 2.1  Consensus size: 19

       3660 GTACACCCCT

                                
       3670 TTATGGTGCACCCCTTATAA
          1 TTATGGTGCACCCCTTA-AA

                      *        
       3690 TTATGGTGCATCCCTTAAA
          1 TTATGGTGCACCCCTTAAA

              
       3709 TT
          1 TT

       3711 CTGGCACTTG


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  19    4  0.20
  20   16  0.80

ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39


Consensus pattern (19 bp):   
TTATGGTGCACCCCTTAAA

Found at i:4493 original size:2 final size:2

Alignment explanation


    Indices: 4405--4482  Score: 86
    Period size: 2  Copynumber: 39.5  Consensus size: 2

       4395 AGCCTACTAT

                         *  *                                         *  *
       4405 TA TA TA TA TG TT TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

             *  *  *                                               
       4447 TG TG TG T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       4483 TGTTAATATA


Statistics
Matches: 71,  Mismatches: 4, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
   1    1  0.01
   2   70  0.99

ACGTcount: A:0.40, C:0.00, G:0.08, T:0.53


Consensus pattern (2 bp):   
TA
Done.