Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014016.1 Corchorus capsularis cultivar CVL-1 contig14037, 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: 19051
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33


Found at i:2715 original size:33 final size:33

Alignment explanation


    Indices: 2660--2733  Score: 96
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       2650 TTAGGGCTGG

                    *                 * *    
       2660 TCGCGACCCGCCCATGGCTGGGTCGCGCGCAGA
          1 TCGCGACCAGCCCATGGCTGGGTCGCACACAGA

                                           *  
       2693 TCGCGACCAG-CCATGGCATGGGTCGCACACGGA
          1 TCGCGACCAGCCCATGGC-TGGGTCGCACACAGA

                    
       2726 TCGCGACC
          1 TCGCGACC

       2734 TGGGTTGCGA


Statistics
Matches: 36,  Mismatches: 4, Indels: 2
        0.86            0.10        0.05

Matches are distributed among these distances:
  32    7  0.19
  33   29  0.81

ACGTcount: A:0.16, C:0.38, G:0.34, T:0.12


Consensus pattern (33 bp):   
TCGCGACCAGCCCATGGCTGGGTCGCACACAGA

Found at i:3192 original size:21 final size:22

Alignment explanation


    Indices: 3168--3212  Score: 58
    Period size: 21  Copynumber: 2.1  Consensus size: 22

       3158 ATTAAGGGGG

                                   
       3168 TTGCTAAAT-ACCGCCCC-CTTT
          1 TTGCT-AATCACCGCCCCACTTT

                  *               
       3189 TTGCTATTCACCGCCCCACTTT
          1 TTGCTAATCACCGCCCCACTTT

              
       3211 TT
          1 TT

       3213 ACACTTTTGC


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  20    2  0.10
  21   13  0.62
  22    6  0.29

ACGTcount: A:0.16, C:0.38, G:0.09, T:0.38


Consensus pattern (22 bp):   
TTGCTAATCACCGCCCCACTTT

Found at i:18553 original size:6 final size:6

Alignment explanation


    Indices: 18542--18570  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

      18532 GTATACTTAA

                                             
      18542 AATTTT AATTTT AATTTT AATTTT AATTT
          1 AATTTT AATTTT AATTTT AATTTT AATTT

      18571 AAACATATTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

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


Consensus pattern (6 bp):   
AATTTT

Done.