Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011018.1 Corchorus capsularis cultivar CVL-1 contig11039, 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: 9607
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36


Found at i:3228 original size:3 final size:3

Alignment explanation


    Indices: 3215--3253  Score: 69
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       3205 CATTTTAATG

                                                               
       3215 CTT CTTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
          1 CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT

       3254 CTCTCTCCTC


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   3   32  0.91
   4    3  0.09

ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67


Consensus pattern (3 bp):   
CTT

Found at i:9357 original size:21 final size:20

Alignment explanation


    Indices: 9298--9359  Score: 65
    Period size: 19  Copynumber: 3.1  Consensus size: 20

       9288 AGGAAAATAT

                   *            
       9298 GATCAATGTTTGGTGTAAT-
          1 GATCAATATTTGGTGTAATG

                 *         *    
       9317 GATCATTATTTGGTGCAATG
          1 GATCAATATTTGGTGTAATG

                                  
       9337 GCATCAAT-TTTGAGTGTAATG
          1 G-ATCAATATTTG-GTGTAATG

              
       9358 GA
          1 GA

       9360 AAATCACTCT


Statistics
Matches: 35,  Mismatches: 5, Indels: 5
        0.78            0.11        0.11

Matches are distributed among these distances:
  19   16  0.46
  20    6  0.17
  21   13  0.37

ACGTcount: A:0.27, C:0.08, G:0.26, T:0.39


Consensus pattern (20 bp):   
GATCAATATTTGGTGTAATG

Found at i:9447 original size:21 final size:23

Alignment explanation


    Indices: 9423--9469  Score: 71
    Period size: 24  Copynumber: 2.1  Consensus size: 23

       9413 ATCTGCAATT

                                   
       9423 CTCTCCC-TCT-CCATCTTCTTC
          1 CTCTCCCATCTCCCATCTTCTTC

                                    
       9444 CTCTCCCATCTCCCCATCTTCTTC
          1 CTCTCCCATCT-CCCATCTTCTTC

              
       9468 CT
          1 CT

       9470 TTCCTTGTAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  21    7  0.30
  22    3  0.13
  24   13  0.57

ACGTcount: A:0.06, C:0.53, G:0.00, T:0.40


Consensus pattern (23 bp):   
CTCTCCCATCTCCCATCTTCTTC

Found at i:9500 original size:2 final size:2

Alignment explanation


    Indices: 9493--9526  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       9483 CACCTTCTTG

                                                                
       9493 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       9527 TTCCAGCAAC


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.97

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Done.