Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014994.1 Corchorus capsularis cultivar CVL-1 contig15015, 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: 17938
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:1573 original size:31 final size:31

Alignment explanation


    Indices: 1529--1616  Score: 140
    Period size: 31  Copynumber: 2.8  Consensus size: 31

       1519 CATGATTACT

                                            
       1529 CACCAAAAGGTATACCGTAAATACTCCATACC
          1 CACC-AAAGGTATACCGTAAATACTCCATACC

                  *              *         
       1561 CACCAAGGGTATACCGTAAATGCTCCATACC
          1 CACCAAAGGTATACCGTAAATACTCCATACC

                                *    
       1592 CACCAAAGGTATACCGTAAACACTC
          1 CACCAAAGGTATACCGTAAATACTC

       1617 ACCAAGTATT


Statistics
Matches: 51,  Mismatches: 5, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  31   47  0.92
  32    4  0.08

ACGTcount: A:0.38, C:0.32, G:0.12, T:0.18


Consensus pattern (31 bp):   
CACCAAAGGTATACCGTAAATACTCCATACC

Found at i:1704 original size:45 final size:45

Alignment explanation


    Indices: 1640--1725  Score: 172
    Period size: 45  Copynumber: 1.9  Consensus size: 45

       1630 AAGCCAATAG

                                                         
       1640 GCAGTTACTTCATCAAGAATGAGGTAACCACCCACGTTCTTCAAA
          1 GCAGTTACTTCATCAAGAATGAGGTAACCACCCACGTTCTTCAAA

                                                     
       1685 GCAGTTACTTCATCAAGAATGAGGTAACCACCCACGTTCTT
          1 GCAGTTACTTCATCAAGAATGAGGTAACCACCCACGTTCTT

       1726 ATTTGAAGAA


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  45   41  1.00

ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26


Consensus pattern (45 bp):   
GCAGTTACTTCATCAAGAATGAGGTAACCACCCACGTTCTTCAAA

Found at i:14246 original size:23 final size:23

Alignment explanation


    Indices: 14220--14264  Score: 90
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      14210 GTAGTTTTTC

                                   
      14220 CAGAATACATTATGAGTTGTGTA
          1 CAGAATACATTATGAGTTGTGTA

                                  
      14243 CAGAATACATTATGAGTTGTGT
          1 CAGAATACATTATGAGTTGTGT

      14265 TTGACATGTC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36


Consensus pattern (23 bp):   
CAGAATACATTATGAGTTGTGTA

Found at i:17336 original size:25 final size:25

Alignment explanation


    Indices: 17280--17329  Score: 93
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      17270 GGTGACTGCG

                                     
      17280 TACCTAA-GTCTCGAACCTAAAACT
          1 TACCTAAGGTCTCGAACCTAAAACT

                                     
      17304 TACCTAAGGTCTCGAACCTAAAACT
          1 TACCTAAGGTCTCGAACCTAAAACT

             
      17329 T
          1 T

      17330 GTTTAAGCAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    7  0.28
  25   18  0.72

ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26


Consensus pattern (25 bp):   
TACCTAAGGTCTCGAACCTAAAACT

Found at i:17450 original size:21 final size:22

Alignment explanation


    Indices: 17424--17466  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 22

      17414 AAAAAGGGGA

                                  
      17424 TTACTAAATACCGCCC-CCTTT
          1 TTACTAAATACCGCCCTCCTTT

                  **              
      17445 TTACTAGGTACCGCCCTCCTTT
          1 TTACTAAATACCGCCCTCCTTT

      17467 GGACAATTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   14  0.74
  22    5  0.26

ACGTcount: A:0.19, C:0.37, G:0.09, T:0.35


Consensus pattern (22 bp):   
TTACTAAATACCGCCCTCCTTT
Done.