Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010463.1 Corchorus capsularis cultivar CVL-1 contig10484, 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: 12851
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:1447 original size:23 final size:23

Alignment explanation


    Indices: 1402--1450  Score: 62
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       1392 AAAAGAGAAA

                        * * * *    
       1402 ATACATAATATTTTTTTTGAGGT
          1 ATACATAATATTATATATAAGGT

                                   
       1425 ATACATAATATTATATATAAGGT
          1 ATACATAATATTATATATAAGGT

               
       1448 ATA
          1 ATA

       1451 ACGGTCTTCA


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45


Consensus pattern (23 bp):   
ATACATAATATTATATATAAGGT

Found at i:3376 original size:13 final size:13

Alignment explanation


    Indices: 3350--3388  Score: 53
    Period size: 13  Copynumber: 3.0  Consensus size: 13

       3340 TTTACATCCC

                          
       3350 CTTC-CATTGATTT
          1 CTTCTCATTG-TTT

                         
       3363 CTTCTCATTGTTT
          1 CTTCTCATTGTTT

                  *      
       3376 CTTCTCTTTGTTT
          1 CTTCTCATTGTTT

       3389 TGGATTTACT


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  13   19  0.79
  14    5  0.21

ACGTcount: A:0.08, C:0.23, G:0.08, T:0.62


Consensus pattern (13 bp):   
CTTCTCATTGTTT

Found at i:5051 original size:2 final size:2

Alignment explanation


    Indices: 4999--5035  Score: 51
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       4989 TTATTTGTAA

                                                    *                 
       4999 AT AT AT AT AT AT AT AT AT AT A- AT AT AA AT AT A- AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       5036 ACATCACAAT


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   1    2  0.06
   2   29  0.94

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (2 bp):   
AT

Found at i:9048 original size:16 final size:16

Alignment explanation


    Indices: 9027--9057  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       9017 CCCTATGAAT

                            
       9027 TATCACTACATATATA
          1 TATCACTACATATATA

                    *      
       9043 TATCACTATATATAT
          1 TATCACTACATATAT

       9058 TAATGGCCGG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42


Consensus pattern (16 bp):   
TATCACTACATATATA
Done.