Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001163.1 Corchorus capsularis cultivar CVL-1 contig01163, 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: 12242
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:3988 original size:29 final size:29

Alignment explanation


    Indices: 3946--4005  Score: 120
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       3936 AGGGGCAACT

                                         
       3946 GCGTACGCTAGGTCTCGATGGAACAAACC
          1 GCGTACGCTAGGTCTCGATGGAACAAACC

                                         
       3975 GCGTACGCTAGGTCTCGATGGAACAAACC
          1 GCGTACGCTAGGTCTCGATGGAACAAACC

              
       4004 GC
          1 GC

       4006 TTACCACTTG


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:0.27, C:0.28, G:0.28, T:0.17


Consensus pattern (29 bp):   
GCGTACGCTAGGTCTCGATGGAACAAACC

Found at i:4156 original size:30 final size:29

Alignment explanation


    Indices: 4122--4186  Score: 94
    Period size: 30  Copynumber: 2.2  Consensus size: 29

       4112 TTTTAGTATT

                     *            *     * 
       4122 TAACTCAATGGTCTTTTTTTTTTTGGCACC
          1 TAACTCAATAGTCTTTTTTTTTATGG-AAC

                                         
       4152 TAACTCAATAGTCTTTTTTTTTATGGAAC
          1 TAACTCAATAGTCTTTTTTTTTATGGAAC

                  
       4181 TAACTC
          1 TAACTC

       4187 TAGTTGAGAT


Statistics
Matches: 32,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  29    8  0.25
  30   24  0.75

ACGTcount: A:0.23, C:0.18, G:0.11, T:0.48


Consensus pattern (29 bp):   
TAACTCAATAGTCTTTTTTTTTATGGAAC

Found at i:4169 original size:29 final size:30

Alignment explanation


    Indices: 4122--4186  Score: 89
    Period size: 29  Copynumber: 2.2  Consensus size: 30

       4112 TTTTAGTATT

                     *                   * 
       4122 TAACTCAATGGTCTTTTTTTTTT-TGGCACC
          1 TAACTCAATAGTCTTTTTTTTTTATGG-AAC

                                          
       4152 TAACTCAATAGTC-TTTTTTTTTATGGAAC
          1 TAACTCAATAGTCTTTTTTTTTTATGGAAC

                  
       4181 TAACTC
          1 TAACTC

       4187 TAGTTGAGAT


Statistics
Matches: 32,  Mismatches: 2, Indels: 3
        0.86            0.05        0.08

Matches are distributed among these distances:
  29   17  0.53
  30   15  0.47

ACGTcount: A:0.23, C:0.18, G:0.11, T:0.48


Consensus pattern (30 bp):   
TAACTCAATAGTCTTTTTTTTTTATGGAAC

Found at i:6269 original size:2 final size:2

Alignment explanation


    Indices: 6262--6288  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       6252 TATGATATGC

                                                    
       6262 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

       6289 GTGAAGCAAA


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


Consensus pattern (2 bp):   
AT

Found at i:8383 original size:13 final size:13

Alignment explanation


    Indices: 8365--8400  Score: 56
    Period size: 13  Copynumber: 2.8  Consensus size: 13

       8355 TGGCAAGATA

                         
       8365 TATATATAAATAT
          1 TATATATAAATAT

                         
       8378 TATATAT-AATAT
          1 TATATATAAATAT

                       
       8390 TATACTATAAA
          1 TATA-TATAAA

       8401 AAGGGCATGT


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  12    9  0.43
  13   10  0.48
  14    2  0.10

ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44


Consensus pattern (13 bp):   
TATATATAAATAT
Done.