Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001862.1 Corchorus capsularis cultivar CVL-1 contig01863, 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: 2756
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36


Found at i:1360 original size:15 final size:15

Alignment explanation


    Indices: 1304--1359  Score: 67
    Period size: 16  Copynumber: 3.6  Consensus size: 15

       1294 GATTTTTTAA

                            
       1304 GTGAGTATCTCACCAG
          1 GTGAGTAT-TCACCAG

                           *
       1320 GTGAGTATTACACCAA
          1 GTGAGTATT-CACCAG

                     *   * 
       1336 GTGAGTATTTACCGG
          1 GTGAGTATTCACCAG

                     
       1351 GTGAGTATT
          1 GTGAGTATT

       1360 TGTATTGGGT


Statistics
Matches: 35,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  15   13  0.37
  16   22  0.63

ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30


Consensus pattern (15 bp):   
GTGAGTATTCACCAG

Found at i:1813 original size:23 final size:22

Alignment explanation


    Indices: 1787--1850  Score: 65
    Period size: 23  Copynumber: 2.8  Consensus size: 22

       1777 CTGGATGAGC

                                   
       1787 CTCCGCGCAAGAGCAAGAGAATT
          1 CTCCGCGCAAGAGCAAG-GAATT

                    *     *      * 
       1810 CTCCGCGCGAGAGCTAGGTAAGT
          1 CTCCGCGCAAGAGCAAGG-AATT

                   *     *    
       1833 CTCCGCGTAAGAGTAAGG
          1 CTCCGCGCAAGAGCAAGG

       1851 GAATAATACA


Statistics
Matches: 33,  Mismatches: 7, Indels: 2
        0.79            0.17        0.05

Matches are distributed among these distances:
  22    1  0.03
  23   32  0.97

ACGTcount: A:0.28, C:0.25, G:0.31, T:0.16


Consensus pattern (22 bp):   
CTCCGCGCAAGAGCAAGGAATT

Found at i:2036 original size:31 final size:31

Alignment explanation


    Indices: 2001--2071  Score: 124
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       1991 AAATTACCAA

                                *          
       2001 TTGACCCCATTAAAATGATAGGTTTATAGTT
          1 TTGACCCCATTAAAATGATAAGTTTATAGTT

                                           
       2032 TTGACCCCATTAAAATGATAAGTTTATAGTT
          1 TTGACCCCATTAAAATGATAAGTTTATAGTT

                *    
       2063 TTGATCCCA
          1 TTGACCCCA

       2072 CTATTTATTT


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  31   38  1.00

ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38


Consensus pattern (31 bp):   
TTGACCCCATTAAAATGATAAGTTTATAGTT

Found at i:2561 original size:3 final size:3

Alignment explanation


    Indices: 2541--2601  Score: 79
    Period size: 3  Copynumber: 20.3  Consensus size: 3

       2531 ATATGTATAC

                    *   *                                               
       2541 ATT ATT TTT TTT AGTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

                        *        
       2587 ATT ATT -TT TTT ATT A
          1 ATT ATT ATT ATT ATT A

       2602 ATTTTTTTTA


Statistics
Matches: 53,  Mismatches: 3, Indels: 4
        0.88            0.05        0.07

Matches are distributed among these distances:
   2    2  0.04
   3   48  0.91
   4    3  0.06

ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70


Consensus pattern (3 bp):   
ATT

Found at i:2605 original size:12 final size:11

Alignment explanation


    Indices: 2561--2609  Score: 53
    Period size: 12  Copynumber: 4.2  Consensus size: 11

       2551 TTAGTTATTA

                       *
       2561 TTATTATTATTA
          1 TTATTATT-TTT

                       *
       2573 TTATTATTATTA
          1 TTATTATT-TTT

                       
       2585 TTATTATTTTT
          1 TTATTATTTTT

                        
       2596 TTATTAATTTTT
          1 TTATT-ATTTTT

              
       2608 TT
          1 TT

       2610 TAGACGAAGG


Statistics
Matches: 35,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  11    7  0.20
  12   28  0.80

ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73


Consensus pattern (11 bp):   
TTATTATTTTT

Done.