Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023914.1 Corchorus olitorius cultivar O-4 contig23947, 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: 8903
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:3030 original size:2 final size:2

Alignment explanation


    Indices: 3023--3053  Score: 53
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       3013 GGTTGGAAAT

                                                         
       3023 TA TA TA TA GTA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA

       3054 AAAGAGAGAG


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2   26  0.93
   3    2  0.07

ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:4040 original size:31 final size:32

Alignment explanation


    Indices: 3971--4036  Score: 100
    Period size: 32  Copynumber: 2.1  Consensus size: 32

       3961 CTAAAGACTA

                             *  *           
       3971 AATTGTCTTGAATTTGGGAATTTTAGGGGGCT
          1 AATTGTCTTGAATTTGGAAAATTTAGGGGGCT

                                            
       4003 AATTGTCTTGAATTT-GAAAATTTAGGGGGC-
          1 AATTGTCTTGAATTTGGAAAATTTAGGGGGCT

                
       4033 AATT
          1 AATT

       4037 TGTCACGATG


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  30    4  0.12
  31   13  0.41
  32   15  0.47

ACGTcount: A:0.27, C:0.06, G:0.27, T:0.39


Consensus pattern (32 bp):   
AATTGTCTTGAATTTGGAAAATTTAGGGGGCT

Found at i:4767 original size:23 final size:23

Alignment explanation


    Indices: 4740--4786  Score: 94
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       4730 ATCTCATCAA

                                   
       4740 TCCGACTAGTTTAGATTAAATCC
          1 TCCGACTAGTTTAGATTAAATCC

                                   
       4763 TCCGACTAGTTTAGATTAAATCC
          1 TCCGACTAGTTTAGATTAAATCC

             
       4786 T
          1 T

       4787 AATGCTCCCT


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

Matches are distributed among these distances:
  23   24  1.00

ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36


Consensus pattern (23 bp):   
TCCGACTAGTTTAGATTAAATCC

Found at i:8354 original size:60 final size:59

Alignment explanation


    Indices: 8243--8366  Score: 203
    Period size: 60  Copynumber: 2.1  Consensus size: 59

       8233 CTCCTCGGAA

                                    *                                  
       8243 AAGTAAAATTGGCTCCCCCAATCAGTAAAAAATTAACCATGTTAATATGAATATCTTAG
          1 AAGTAAAATTGGCTCCCCCAATCAATAAAAAATTAACCATGTTAATATGAATATCTTAG

                                       *    *              *            
       8302 AAGTAAAATTGGCTCCCCCCAATCAATCAAAATTTAACCATGTTAATTTGAATATCTTAG
          1 AAGTAAAATTGGCT-CCCCCAATCAATAAAAAATTAACCATGTTAATATGAATATCTTAG

                 
       8362 AAGTA
          1 AAGTA

       8367 GACTTAGAAA


Statistics
Matches: 60,  Mismatches: 4, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  59   14  0.23
  60   46  0.77

ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30


Consensus pattern (59 bp):   
AAGTAAAATTGGCTCCCCCAATCAATAAAAAATTAACCATGTTAATATGAATATCTTAG
Done.