Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023410.1 Corchorus olitorius cultivar O-4 contig23443, 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: 5743
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:1112 original size:14 final size:15

Alignment explanation


    Indices: 1093--1122  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1083 CAATCAAAGC

                           
       1093 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       1107 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       1122 A
          1 A

       1123 TTAAAAAGAT


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:1499 original size:21 final size:21

Alignment explanation


    Indices: 1475--1547  Score: 65
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       1465 GGCTTGGAAT

                                 
       1475 GGTGATGGCACGGGCATGGCC
          1 GGTGATGGCACGGGCATGGCC

                *          * **  
       1496 GGTGGTGGCACGGGCTTAACC
          1 GGTGATGGCACGGGCATGGCC

                *        * *      
       1517 GGTGGTGGCACAGTGAATGGCC
          1 GGTGATGGCAC-GGGCATGGCC

               *     
       1539 GGTAATGGC
          1 GGTGATGGC

       1548 TTGGTAGTGG


Statistics
Matches: 40,  Mismatches: 11, Indels: 1
        0.77            0.21        0.02

Matches are distributed among these distances:
  21   28  0.70
  22   12  0.30

ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18


Consensus pattern (21 bp):   
GGTGATGGCACGGGCATGGCC

Found at i:3391 original size:15 final size:14

Alignment explanation


    Indices: 3367--3398  Score: 55
    Period size: 15  Copynumber: 2.2  Consensus size: 14

       3357 ATCAAAGCAA

                          
       3367 TAATCAAGGAAAAT
          1 TAATCAAGGAAAAT

                           
       3381 TAATGCAAGGAAAAT
          1 TAAT-CAAGGAAAAT

               
       3396 TAA
          1 TAA

       3399 AAAGATAGAG


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    4  0.24
  15   13  0.76

ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22


Consensus pattern (14 bp):   
TAATCAAGGAAAAT
Done.