Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001998.1 Corchorus capsularis cultivar CVL-1 contig02001, 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, 607

Length: 1013
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38


Found at i:235 original size:18 final size:18

Alignment explanation


    Indices: 212--247  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

        202 TTTCGTTGGA

                              
        212 TCTTTATCAGAGGATTGT
          1 TCTTTATCAGAGGATTGT

                              
        230 TCTTTATCAGAGGATTGT
          1 TCTTTATCAGAGGATTGT

        248 AGTTTAAATC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44


Consensus pattern (18 bp):   
TCTTTATCAGAGGATTGT

Found at i:253 original size:18 final size:18

Alignment explanation


    Indices: 213--253  Score: 64
    Period size: 18  Copynumber: 2.3  Consensus size: 18

        203 TTCGTTGGAT

                             *
        213 CTTTATCAGAGGATTGTT
          1 CTTTATCAGAGGATTGTA

                              
        231 CTTTATCAGAGGATTGTA
          1 CTTTATCAGAGGATTGTA

            *    
        249 GTTTA
          1 CTTTA

        254 AATCTGTGCC


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44


Consensus pattern (18 bp):   
CTTTATCAGAGGATTGTA

Found at i:932 original size:9 final size:9

Alignment explanation


    Indices: 915--958  Score: 70
    Period size: 9  Copynumber: 4.9  Consensus size: 9

        905 GTCCTTAGGC

                *    
        915 TCATTGGTA
          1 TCATCGGTA

                     
        924 TCATCGGTA
          1 TCATCGGTA

                    *
        933 TCATCGGTC
          1 TCATCGGTA

                     
        942 TCATCGGTA
          1 TCATCGGTA

                    
        951 TCATCGGT
          1 TCATCGGT

        959 TTTAGTATAA


Statistics
Matches: 32,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   9   32  1.00

ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36


Consensus pattern (9 bp):   
TCATCGGTA

Found at i:974 original size:27 final size:27

Alignment explanation


    Indices: 944--1004  Score: 122
    Period size: 27  Copynumber: 2.3  Consensus size: 27

        934 CATCGGTCTC

                                       
        944 ATCGGTATCATCGGTTTTAGTATAAGT
          1 ATCGGTATCATCGGTTTTAGTATAAGT

                                       
        971 ATCGGTATCATCGGTTTTAGTATAAGT
          1 ATCGGTATCATCGGTTTTAGTATAAGT

                   
        998 ATCGGTA
          1 ATCGGTA

       1005 CCCTTGGTA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   34  1.00

ACGTcount: A:0.26, C:0.11, G:0.23, T:0.39


Consensus pattern (27 bp):   
ATCGGTATCATCGGTTTTAGTATAAGT

Done.