Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015512.1 Corchorus olitorius cultivar O-4 contig15545, 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: 8516
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:1277 original size:76 final size:76

Alignment explanation


    Indices: 1141--1293  Score: 168
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       1131 CAAGGGCCCC

                                                              *  *        *  
       1141 GACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGGGAACCCAGGTG
          1 GACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGATG

                       
       1206 GGCAATGTCAT
         66 GGCAATGTCAT

                   *     *              *                            **      
       1217 GACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCAG
          1 GACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCAG

                  **      
       1279 ATGGGCTGTGTCAT
         63 ATGGGCAATGTCAT

             
       1293 G
          1 G

       1294 GCTCGGTACT


Statistics
Matches: 64,  Mismatches: 10, Indels: 6
        0.80            0.12        0.08

Matches are distributed among these distances:
  75    4  0.06
  76   54  0.84
  77    6  0.09

ACGTcount: A:0.17, C:0.28, G:0.29, T:0.25


Consensus pattern (76 bp):   
GACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGATG
GGCAATGTCAT

Found at i:7001 original size:15 final size:16

Alignment explanation


    Indices: 6981--7011  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       6971 CAATCAAAGC

                            
       6981 AATAAT-CAAGGAAAA
          1 AATAATGCAAGGAAAA

                            
       6996 AATAATGCAAGGAAAA
          1 AATAATGCAAGGAAAA

       7012 TTAAAGAGAT


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

Matches are distributed among these distances:
  15    6  0.40
  16    9  0.60

ACGTcount: A:0.65, C:0.06, G:0.16, T:0.13


Consensus pattern (16 bp):   
AATAATGCAAGGAAAA

Found at i:7389 original size:24 final size:21

Alignment explanation


    Indices: 7371--7417  Score: 76
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       7361 ATGGTGATGC

                      *          
       7371 CACGGGCATGGCCGGTGGTGG
          1 CACGGGCATGACCGGTGGTGG

                   *             
       7392 CACGGGCTTGACCGGTGGTGG
          1 CACGGGCATGACCGGTGGTGG

                 
       7413 CACGG
          1 CACGG

       7418 TAATGGGCGG


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.11, C:0.26, G:0.49, T:0.15


Consensus pattern (21 bp):   
CACGGGCATGACCGGTGGTGG

Found at i:7637 original size:21 final size:21

Alignment explanation


    Indices: 7613--7661  Score: 80
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       7603 CGGGCAGGCA

                 *          *    
       7613 GCGCGTATGGCCGGTTGTGGC
          1 GCGCGGATGGCCGGTTCTGGC

                                 
       7634 GCGCGGATGGCCGGTTCTGGC
          1 GCGCGGATGGCCGGTTCTGGC

                   
       7655 GCGCGGA
          1 GCGCGGA

       7662 GGAGTCCGGG


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.06, C:0.27, G:0.49, T:0.18


Consensus pattern (21 bp):   
GCGCGGATGGCCGGTTCTGGC

Done.