Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012187.1 Corchorus capsularis cultivar CVL-1 contig12208, 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: 34802
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35


Found at i:1700 original size:2 final size:2

Alignment explanation


    Indices: 1693--1718  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       1683 ACATACATAC

                                                  
       1693 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       1719 TCTGTGAAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:4303 original size:2 final size:2

Alignment explanation


    Indices: 4298--4326  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       4288 CACATATGTA

                                                       
       4298 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
          1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T

       4327 ATATATATAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52


Consensus pattern (2 bp):   
TG

Found at i:8643 original size:17 final size:17

Alignment explanation


    Indices: 8607--8661  Score: 58
    Period size: 17  Copynumber: 3.2  Consensus size: 17

       8597 ATCATCCCCC

                   *         
       8607 AGATCACTAGTGATCTA
          1 AGATCACCAGTGATCTA

                              
       8624 AGATCACCAGTGATGC-A
          1 AGATCACCAGTGAT-CTA

                 *  *      * 
       8641 AGATCGCCGGTGATCAA
          1 AGATCACCAGTGATCTA

                
       8658 AGAT
          1 AGAT

       8662 TACATGGATT


Statistics
Matches: 33,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  16    1  0.03
  17   31  0.94
  18    1  0.03

ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22


Consensus pattern (17 bp):   
AGATCACCAGTGATCTA

Found at i:16165 original size:2 final size:2

Alignment explanation


    Indices: 16158--16192  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      16148 ACTTCAAGAA

                                                                
      16158 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 A

      16193 ATAAACATGG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:33431 original size:23 final size:24

Alignment explanation


    Indices: 33399--33450  Score: 79
    Period size: 23  Copynumber: 2.2  Consensus size: 24

      33389 AAGACAATAA

                                    
      33399 AAAAAGCTCTCACAAAGGAGTCCC
          1 AAAAAGCTCTCACAAAGGAGTCCC

                         *       *  
      33423 AAAAA-CTCTCACTAAGGAGTTCC
          1 AAAAAGCTCTCACAAAGGAGTCCC

                 
      33446 AAAAA
          1 AAAAA

      33451 AAAAATAGAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  23   21  0.81
  24    5  0.19

ACGTcount: A:0.46, C:0.25, G:0.13, T:0.15


Consensus pattern (24 bp):   
AAAAAGCTCTCACAAAGGAGTCCC
Done.