Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016705.1 Corchorus olitorius cultivar O-4 contig16738, 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: 10027
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32


Found at i:4126 original size:16 final size:15

Alignment explanation


    Indices: 4088--4129  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       4078 ACAGAGGTTG

                           
       4088 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
       4103 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       4118 ACTAGAAAACAA
          1 AC-AGAAAACAA

       4130 AGCAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:6974 original size:14 final size:15

Alignment explanation


    Indices: 6955--6984  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       6945 CAATCAAAGC

                           
       6955 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       6969 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       6984 A
          1 A

       6985 TTAAAGAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:7361 original size:21 final size:21

Alignment explanation


    Indices: 7337--7412  Score: 107
    Period size: 21  Copynumber: 3.6  Consensus size: 21

       7327 GGCTTGGAAT

                *          *  *  
       7337 GGTGATGGCACGGGCATGGCC
          1 GGTGGTGGCACGGGCTTGACC

                             *   
       7358 GGTGGTGGCACGGGCTTAACC
          1 GGTGGTGGCACGGGCTTGACC

             *                   
       7379 GATGGTGGCACGGGCTTGACC
          1 GGTGGTGGCACGGGCTTGACC

                         
       7400 GGTGGTGGCACGG
          1 GGTGGTGGCACGG

       7413 TGAATGGGCG


Statistics
Matches: 48,  Mismatches: 7, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  21   48  1.00

ACGTcount: A:0.13, C:0.22, G:0.47, T:0.17


Consensus pattern (21 bp):   
GGTGGTGGCACGGGCTTGACC
Done.