Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012366.1 Corchorus capsularis cultivar CVL-1 contig12387, 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: 4618
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37


Found at i:88 original size:29 final size:29

Alignment explanation


    Indices: 35--97  Score: 90
    Period size: 29  Copynumber: 2.2  Consensus size: 29

         25 TAATCATTAA

                         *   *       *   
         35 AATTCCATCTACCCATATACATGCTGCAT
          1 AATTCCATCTACCAATAAACATGCTACAT

                                *        
         64 AATTCCATCTACCAATAAACGTGCTACAT
          1 AATTCCATCTACCAATAAACATGCTACAT

                 
         93 AATTC
          1 AATTC

         98 TTTAGTTTGT


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  29   30  1.00

ACGTcount: A:0.35, C:0.29, G:0.06, T:0.30


Consensus pattern (29 bp):   
AATTCCATCTACCAATAAACATGCTACAT

Found at i:3097 original size:18 final size:18

Alignment explanation


    Indices: 3052--3123  Score: 65
    Period size: 18  Copynumber: 3.8  Consensus size: 18

       3042 AATGATCATA

                               
       3052 TATAACTAATAATAATT-T
          1 TATAA-TAATAATAATTAT

               * *             
       3070 TACCACTAATAATAATTAT
          1 TA-TAATAATAATAATTAT

                               *
       3089 TATAATAATAATAAGTTTAA
          1 TATAATAATAATAA--TTAT

                  *        
       3109 TATAATTATAATAAT
          1 TATAATAATAATAAT

       3124 AAGATATTTA


Statistics
Matches: 44,  Mismatches: 6, Indels: 8
        0.76            0.10        0.14

Matches are distributed among these distances:
  18   24  0.55
  19    4  0.09
  20   16  0.36

ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42


Consensus pattern (18 bp):   
TATAATAATAATAATTAT

Found at i:4597 original size:2 final size:2

Alignment explanation


    Indices: 4592--4618  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       4582 TTCACACTTC

                                                    
       4592 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.