Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006374.1 Corchorus capsularis cultivar CVL-1 contig06395, 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: 10275
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31


Found at i:3010 original size:18 final size:18

Alignment explanation


    Indices: 2976--3010  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2966 AACTTTTATA

                        *     
       2976 AAAATAAATATATAAATC
          1 AAAATAAATATAAAAATC

                     *       
       2994 AAAATAAATTTAAAAAT
          1 AAAATAAATATAAAAAT

       3011 AATACTCATA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29


Consensus pattern (18 bp):   
AAAATAAATATAAAAATC

Found at i:5672 original size:15 final size:15

Alignment explanation


    Indices: 5654--5683  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       5644 AATAAATTTC

                           
       5654 AATAAAAAGATTTAA
          1 AATAAAAAGATTTAA

                    *      
       5669 AATAAAAATATTTAA
          1 AATAAAAAGATTTAA

       5684 TTTTTATGCC


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30


Consensus pattern (15 bp):   
AATAAAAAGATTTAA

Found at i:6121 original size:29 final size:29

Alignment explanation


    Indices: 6079--6138  Score: 120
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       6069 CATGTACAAA

                                         
       6079 AATCAATCCAATCAATCAACACAATTTAT
          1 AATCAATCCAATCAATCAACACAATTTAT

                                         
       6108 AATCAATCCAATCAATCAACACAATTTAT
          1 AATCAATCCAATCAATCAACACAATTTAT

              
       6137 AA
          1 AA

       6139 GACCAACATT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   31  1.00

ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27


Consensus pattern (29 bp):   
AATCAATCCAATCAATCAACACAATTTAT

Found at i:8843 original size:3 final size:3

Alignment explanation


    Indices: 8835--8874  Score: 71
    Period size: 3  Copynumber: 13.3  Consensus size: 3

       8825 TTTAGTATAT

                                          *                      
       8835 ATA ATA ATA ATA ATA ATA ATA ATC ATA ATA ATA ATA ATA A
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A

       8875 ATTTTGATAT


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

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATA

Found at i:10247 original size:2 final size:2

Alignment explanation


    Indices: 10240--10275  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      10230 AAACTCAGGC

                                                                 
      10240 AT AT AT AT AT 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 AT AT AT AT AT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
AT

Done.