Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019796.1 Corchorus olitorius cultivar O-4 contig19829, 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: 8322
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31


Found at i:1128 original size:26 final size:27

Alignment explanation


    Indices: 1073--1143  Score: 99
    Period size: 26  Copynumber: 2.6  Consensus size: 27

       1063 GGTGAATTTC

                 *                   *  
       1073 TGGTCATTTGTACTTCAGGGGGGCATTT
          1 TGGTCTTTTGTACTTCA-GGGGGCACTT

                        *              
       1101 TGGTCTTTTGTATTTCA-GGGGCACTT
          1 TGGTCTTTTGTACTTCAGGGGGCACTT

                             
       1127 TGGTCTTTTGTACTTCA
          1 TGGTCTTTTGTACTTCA

       1144 TTACTAGCTT


Statistics
Matches: 39,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  26   24  0.62
  28   15  0.38

ACGTcount: A:0.13, C:0.15, G:0.27, T:0.45


Consensus pattern (27 bp):   
TGGTCTTTTGTACTTCAGGGGGCACTT

Found at i:1266 original size:22 final size:22

Alignment explanation


    Indices: 1241--1283  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1231 TTATGTTCTC

                 *        *       
       1241 TTGCATATTTATATTACATTTT
          1 TTGCAGATTTATATCACATTTT

                        *        
       1263 TTGCAGATTTATCTCACATTT
          1 TTGCAGATTTATATCACATTT

       1284 GCACTTGCCT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.26, C:0.14, G:0.07, T:0.53


Consensus pattern (22 bp):   
TTGCAGATTTATATCACATTTT

Found at i:4252 original size:21 final size:21

Alignment explanation


    Indices: 4227--4267  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       4217 TTAGAAACCC

                                  
       4227 TAGTACCACTTAG-ATCCAATT
          1 TAGTACCACTT-GTATCCAATT

                                
       4248 TAGTACCACTTGTATCCAAT
          1 TAGTACCACTTGTATCCAAT

       4268 AGGGCTTCAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    1  0.05
  21   18  0.95

ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34


Consensus pattern (21 bp):   
TAGTACCACTTGTATCCAATT

Found at i:7489 original size:2 final size:2

Alignment explanation


    Indices: 7482--7518  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       7472 CATGGTCATA

                                                                   
       7482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       7519 CTTAATAGAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.