Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015071.1 Corchorus capsularis cultivar CVL-1 contig15092, 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: 12108
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30


Found at i:1576 original size:33 final size:33

Alignment explanation


    Indices: 1539--1646  Score: 96
    Period size: 33  Copynumber: 3.3  Consensus size: 33

       1529 CCGAGTTGTT

                                 *           
       1539 TGGCCGGTTGTAGCCGGACATGGCCATGTCGCG
          1 TGGCCGGTTGTAGCCGGACATCGCCATGTCGCG

                             *      *         *
       1572 TGGCCGG-TG-ATGACCAGACATCTCCATGTCGCA
          1 TGGCCGGTTGTA-G-CCGGACATCGCCATGTCGCG

                       *      *    *   *      
       1605 TGGCCGG-TGTTGCGCGGGCATCTCCAAGTCGCG
          1 TGGCCGGTTGTAGC-CGGACATCGCCATGTCGCG

                     
       1638 TGGCCGGTT
          1 TGGCCGGTT

       1647 CTCCAAGTCG


Statistics
Matches: 61,  Mismatches: 9, Indels: 9
        0.77            0.11        0.11

Matches are distributed among these distances:
  31    1  0.02
  32    4  0.07
  33   55  0.90
  34    1  0.02

ACGTcount: A:0.13, C:0.29, G:0.36, T:0.22


Consensus pattern (33 bp):   
TGGCCGGTTGTAGCCGGACATCGCCATGTCGCG

Found at i:1651 original size:21 final size:21

Alignment explanation


    Indices: 1625--1666  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1615 TGCGCGGGCA

                        *        
       1625 TCTCCAAGTCGCGTGGCCGGT
          1 TCTCCAAGTCGCATGGCCGGT

                                 
       1646 TCTCCAAGTCGCATGGCCGGT
          1 TCTCCAAGTCGCATGGCCGGT

       1667 CACTTGTGCT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.12, C:0.33, G:0.31, T:0.24


Consensus pattern (21 bp):   
TCTCCAAGTCGCATGGCCGGT

Found at i:7141 original size:9 final size:8

Alignment explanation


    Indices: 7104--7137  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       7094 GAATCGGCTA

                    
       7104 TGAATTTT
          1 TGAATTTT

                    *
       7112 TGAAGTTTC
          1 TGAA-TTTT

                    
       7121 TGAATTTT
          1 TGAATTTT

                    
       7129 TGAATTTT
          1 TGAATTTT

             
       7137 T
          1 T

       7138 TGAAGAAGGT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59


Consensus pattern (8 bp):   
TGAATTTT

Found at i:8096 original size:33 final size:32

Alignment explanation


    Indices: 8059--8162  Score: 100
    Period size: 33  Copynumber: 3.2  Consensus size: 32

       8049 GCCGAGTCAA

                                  *          
       8059 GTGGCCGGGTGTGGCCGGGCATGGCCATGTCGC
          1 GTGGCC-GGTGTGGCCGGGCATCGCCATGTCGC

                 *       *         *  *      
       8092 GTGGCTGGTGATGACCGGGCATCTCCTTGTCGC
          1 GTGGCCGGTG-TGGCCGGGCATCGCCATGTCGC

            *          *           *   *     
       8125 ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGC
          1 GTGGCCGGTGTGGC-CGGGCATCGCCATGTCGC

                 
       8158 GTGGC
          1 GTGGC

       8163 TGGTTCTCCA


Statistics
Matches: 57,  Mismatches: 12, Indels: 4
        0.78            0.16        0.05

Matches are distributed among these distances:
  32    6  0.11
  33   51  0.89

ACGTcount: A:0.09, C:0.28, G:0.41, T:0.22


Consensus pattern (32 bp):   
GTGGCCGGTGTGGCCGGGCATCGCCATGTCGC

Found at i:11984 original size:22 final size:22

Alignment explanation


    Indices: 11959--12003  Score: 81
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      11949 GAGTTGCAGC

                          *       
      11959 GGTGAGGGTTGAGACAGAAGGA
          1 GGTGAGGGTTGAGAAAGAAGGA

                                  
      11981 GGTGAGGGTTGAGAAAGAAGGA
          1 GGTGAGGGTTGAGAAAGAAGGA

             
      12003 G
          1 G

      12004 ACGTCGGGAG


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.33, C:0.02, G:0.51, T:0.13


Consensus pattern (22 bp):   
GGTGAGGGTTGAGAAAGAAGGA
Done.