Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009740.1 Corchorus olitorius cultivar O-4 contig09772, 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: 2699
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34


Found at i:1066 original size:25 final size:25

Alignment explanation


    Indices: 1038--1129  Score: 130
    Period size: 25  Copynumber: 3.7  Consensus size: 25

       1028 GTAGCCTATG

                   *                 
       1038 CGTTTTCTAAACGCAAGCACAGGCT
          1 CGTTTTCCAAACGCAAGCACAGGCT

                 * *               * 
       1063 CGTTTGCTAAACGCAAGCACAGGTT
          1 CGTTTTCCAAACGCAAGCACAGGCT

            *                        
       1088 TGTTTTCCAAACGCAAGCACAGGCT
          1 CGTTTTCCAAACGCAAGCACAGGCT

                        *    
       1113 CGTTTTCCAAACACAAG
          1 CGTTTTCCAAACGCAAG

       1130 AACATGAGCG


Statistics
Matches: 59,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  25   59  1.00

ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24


Consensus pattern (25 bp):   
CGTTTTCCAAACGCAAGCACAGGCT

Found at i:1141 original size:25 final size:25

Alignment explanation


    Indices: 1089--1142  Score: 63
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       1079 GCACAGGTTT

                       *    *     ** 
       1089 GTTTTCCAAACGCAAGCACAGGCTC
          1 GTTTTCCAAACACAAGAACAGGAGC

                                *    
       1114 GTTTTCCAAACACAAGAACATGAGC
          1 GTTTTCCAAACACAAGAACAGGAGC

                
       1139 GTTT
          1 GTTT

       1143 ACCCAGCGCA


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24


Consensus pattern (25 bp):   
GTTTTCCAAACACAAGAACAGGAGC

Found at i:2378 original size:25 final size:24

Alignment explanation


    Indices: 2341--2391  Score: 66
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       2331 TAATGCAATA

                           *         
       2341 TTTTGGCCATCTTCTGTTTTCTTTG
          1 TTTTGGCCATCTT-TCTTTTCTTTG

                  * *               
       2366 TTTTGGTCTTCTTTCTTTTCTTTG
          1 TTTTGGCCATCTTTCTTTTCTTTG

              
       2390 TT
          1 TT

       2392 GCCTGAAGAG


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  24   12  0.52
  25   11  0.48

ACGTcount: A:0.02, C:0.18, G:0.14, T:0.67


Consensus pattern (24 bp):   
TTTTGGCCATCTTTCTTTTCTTTG
Done.