Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005217.1 Corchorus capsularis cultivar CVL-1 contig05235, 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: 3619
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30


Found at i:709 original size:33 final size:33

Alignment explanation


    Indices: 672--744  Score: 87
    Period size: 33  Copynumber: 2.2  Consensus size: 33

        662 CGCCTAGCGA

                                  *         *  
        672 TGGCCGGT-TATGGCCGGACATGTCC-ATGTCGCG
          1 TGGCCGGTGT-TGGCCGGACATCTCCGA-GTCACG

                             *               
        705 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCACG
          1 TGGCCGGTGTTGGCCGGACATCTCCGAGTCACG

                   
        738 TGGCCGG
          1 TGGCCGG

        745 ACTTCTCCAA


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

Matches are distributed among these distances:
  33   33  0.94
  34    2  0.06

ACGTcount: A:0.10, C:0.29, G:0.40, T:0.22


Consensus pattern (33 bp):   
TGGCCGGTGTTGGCCGGACATCTCCGAGTCACG

Found at i:751 original size:23 final size:23

Alignment explanation


    Indices: 715--767  Score: 61
    Period size: 23  Copynumber: 2.3  Consensus size: 23

        705 TGGCCGGTGT

                   *       *      *
        715 TGGCCGGGCATCTCCGAGTCACG
          1 TGGCCGGACATCTCCAAGTCACA

                     *          *  
        738 TGGCCGGACTTCTCCAAGTCGCA
          1 TGGCCGGACATCTCCAAGTCACA

                   
        761 TGGCCGG
          1 TGGCCGG

        768 TCACTAGTGC


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  23   25  1.00

ACGTcount: A:0.13, C:0.34, G:0.34, T:0.19


Consensus pattern (23 bp):   
TGGCCGGACATCTCCAAGTCACA

Found at i:2556 original size:30 final size:30

Alignment explanation


    Indices: 2520--2576  Score: 98
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       2510 TTTTCGTCAC

                                           
       2520 CCAAAAC-AGATTTATTTTCAATGCTATCTA
          1 CCAAAACAAGA-TTATTTTCAATGCTATCTA

                                       
       2550 CCAAAACAAGATTATTTTCAATGCTAT
          1 CCAAAACAAGATTATTTTCAATGCTAT

       2577 GTTCAACCAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  30   23  0.88
  31    3  0.12

ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35


Consensus pattern (30 bp):   
CCAAAACAAGATTATTTTCAATGCTATCTA

Found at i:2660 original size:33 final size:33

Alignment explanation


    Indices: 2618--2722  Score: 131
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       2608 ATTAGCATCC

                *               *            
       2618 AAAATAGATTTAGTATCATCACAAACAACACTT
          1 AAAACAGATTTAGTATCATCGCAAACAACACTT

                          *    *             
       2651 AAAACAGATTTAGTGTCATTGCAAACAACACTT
          1 AAAACAGATTTAGTATCATCGCAAACAACACTT

               **  *                          
       2684 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
          1 AAAACAGATTTAGTATCATCGCAAACAACACT-T

                  
       2717 AAAACA
          1 AAAACA

       2723 TTCTTTTCAA


Statistics
Matches: 60,  Mismatches: 11, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  32    1  0.02
  33   59  0.98

ACGTcount: A:0.46, C:0.18, G:0.10, T:0.27


Consensus pattern (33 bp):   
AAAACAGATTTAGTATCATCGCAAACAACACTT
Done.