Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015635.1 Corchorus capsularis cultivar CVL-1 contig15656, 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: 25869
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:1519 original size:21 final size:22

Alignment explanation


    Indices: 1493--1535  Score: 79
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       1483 AACAGCTCTA

                                  
       1493 GCCAGTGCAACTCA-TAAGCCT
          1 GCCAGTGCAACTCAGTAAGCCT

                                  
       1514 GCCAGTGCAACTCAGTAAGCCT
          1 GCCAGTGCAACTCAGTAAGCCT

       1536 CTGGAAAGTG


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  21   14  0.67
  22    7  0.33

ACGTcount: A:0.28, C:0.33, G:0.21, T:0.19


Consensus pattern (22 bp):   
GCCAGTGCAACTCAGTAAGCCT

Found at i:3284 original size:7 final size:7

Alignment explanation


    Indices: 3272--3301  Score: 60
    Period size: 7  Copynumber: 4.3  Consensus size: 7

       3262 CAAGCAAAAA

                   
       3272 TGGATTT
          1 TGGATTT

                   
       3279 TGGATTT
          1 TGGATTT

                   
       3286 TGGATTT
          1 TGGATTT

                   
       3293 TGGATTT
          1 TGGATTT

              
       3300 TG
          1 TG

       3302 AAATATAGGA


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

Matches are distributed among these distances:
   7   23  1.00

ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57


Consensus pattern (7 bp):   
TGGATTT

Found at i:7610 original size:99 final size:100

Alignment explanation


    Indices: 7428--7626  Score: 292
    Period size: 99  Copynumber: 2.0  Consensus size: 100

       7418 CTAACCACGT

                *                                      *                     
       7428 ACTCGCATATATGATAAGAACCGAGAGAAAAAAACAAACTCTATAACTAAAATGATTTGCTAGCC
          1 ACTCACATATATGATAAGAACCGAGAGAAAAAAACAAACTCTAAAACTAAAATGATTTGCTAGCC

               *                               
       7493 ACACATCAAGAATACTCGACACGCCAGCGCGAGCC
         66 ACAAATCAAGAATACTCGACACGCCAGCGCGAGCC

                               * *                *                          
       7528 ACTCACATATATGATAAGAGCTGAGAGAAAAAAA-AAAGTCTAAAACTAAAATGATTTGCTAGCC
          1 ACTCACATATATGATAAGAACCGAGAGAAAAAAACAAACTCTAAAACTAAAATGATTTGCTAGCC

                     *   *      *  *     *     
       7592 ACAAATCAATAATGCTCGACGCGTCAGCGTGAGCC
         66 ACAAATCAAGAATACTCGACACGCCAGCGCGAGCC

       7627 GATCAACTTA


Statistics
Matches: 88,  Mismatches: 11, Indels: 1
        0.88            0.11        0.01

Matches are distributed among these distances:
  99   57  0.65
 100   31  0.35

ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19


Consensus pattern (100 bp):   
ACTCACATATATGATAAGAACCGAGAGAAAAAAACAAACTCTAAAACTAAAATGATTTGCTAGCC
ACAAATCAAGAATACTCGACACGCCAGCGCGAGCC

Found at i:14790 original size:24 final size:25

Alignment explanation


    Indices: 14732--14788  Score: 91
    Period size: 25  Copynumber: 2.4  Consensus size: 25

      14722 TTCAAACCCT

                             *       
      14732 ACTTCATTTCTAACAACTTCTTCAA
          1 ACTTCATTTCTAACAACATCTTCAA

                                     
      14757 ACTTCATTTCTAACAA-ATCTTCAA
          1 ACTTCATTTCTAACAACATCTTCAA

                     
      14781 AC-TCATTT
          1 ACTTCATTT

      14789 TCCTTCATTT


Statistics
Matches: 31,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  23    6  0.19
  24    9  0.29
  25   16  0.52

ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40


Consensus pattern (25 bp):   
ACTTCATTTCTAACAACATCTTCAA

Found at i:20342 original size:2 final size:2

Alignment explanation


    Indices: 20335--20364  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      20325 AAGCATCAAC

                                                        
      20335 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      20365 CGTGAACAAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.