Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012279.1 Corchorus capsularis cultivar CVL-1 contig12300, 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: 13857
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:1208 original size:3 final size:3

Alignment explanation


    Indices: 1200--1231  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       1190 CTTTAGTTTT

                                                      
       1200 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA

       1232 TATTATCATT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
TAA

Found at i:6054 original size:3 final size:3

Alignment explanation


    Indices: 6046--6084  Score: 78
    Period size: 3  Copynumber: 13.0  Consensus size: 3

       6036 GTTCGTACCA

                                                               
       6046 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

       6085 GATGATAATT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   36  1.00

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


Consensus pattern (3 bp):   
AAT

Found at i:6350 original size:3 final size:3

Alignment explanation


    Indices: 6342--6388  Score: 76
    Period size: 3  Copynumber: 15.7  Consensus size: 3

       6332 AGAGGGAGTA

                                     *            *                       
       6342 ATT ATT ATT ATT ATT ATT AGT ATT ATT ATC ATT ATT ATT ATT ATT AT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT

       6389 GATATATGAT


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   3   40  1.00

ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62


Consensus pattern (3 bp):   
ATT

Found at i:7238 original size:33 final size:33

Alignment explanation


    Indices: 7200--7274  Score: 116
    Period size: 33  Copynumber: 2.3  Consensus size: 33

       7190 CCGCCCCAGT

                       *     *                
       7200 GGGAGGCTCCGTCGTGGTTGAGCC-TCCCTAGTG
          1 GGGAGGCTCCGCCGTGGCTGAGCCGT-CCTAGTG

                                             
       7233 GGGAGGCTCCGCCGTGGCTGAGCCGTCCTAGTG
          1 GGGAGGCTCCGCCGTGGCTGAGCCGTCCTAGTG

                     
       7266 GGGAGGCTC
          1 GGGAGGCTC

       7275 AGTGTAAAAG


Statistics
Matches: 39,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  33   38  0.97
  34    1  0.03

ACGTcount: A:0.09, C:0.28, G:0.43, T:0.20


Consensus pattern (33 bp):   
GGGAGGCTCCGCCGTGGCTGAGCCGTCCTAGTG

Found at i:9189 original size:6 final size:6

Alignment explanation


    Indices: 9178--9213  Score: 72
    Period size: 6  Copynumber: 6.0  Consensus size: 6

       9168 TTGGCTCAAA

                                                     
       9178 CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG
          1 CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG

       9214 TAGGAAATAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   30  1.00

ACGTcount: A:0.00, C:0.33, G:0.17, T:0.50


Consensus pattern (6 bp):   
CTCTTG

Found at i:12051 original size:7 final size:7

Alignment explanation


    Indices: 12041--12067  Score: 54
    Period size: 7  Copynumber: 3.9  Consensus size: 7

      12031 AATGAATATC

                   
      12041 ATCATAA
          1 ATCATAA

                   
      12048 ATCATAA
          1 ATCATAA

                   
      12055 ATCATAA
          1 ATCATAA

                  
      12062 ATCATA
          1 ATCATA

      12068 CTCCCTCAGT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   20  1.00

ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30


Consensus pattern (7 bp):   
ATCATAA

Done.