Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004925.1 Corchorus capsularis cultivar CVL-1 contig04943, 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: 8758
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:6278 original size:1 final size:1

Alignment explanation


    Indices: 6274--6309  Score: 72
    Period size: 1  Copynumber: 36.0  Consensus size: 1

       6264 TACAAAAATG

                                                
       6274 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       6310 CCATGGTAAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   35  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:7199 original size:60 final size:60

Alignment explanation


    Indices: 7123--7263  Score: 203
    Period size: 60  Copynumber: 2.4  Consensus size: 60

       7113 GAGTGAGACA

                *                                        *      *      * 
       7123 GGCCTTTATTTGAGCATTTTGGCAAACGTTAGGC-CTTTATTTGGTCAAATTCAAAGATGG
          1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCTC-TTATTTGGCCAAATTAAAAGATCG

              *    *            *                                       
       7183 GGTCCTTGTTTGAGCATTTTAGCAAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCG
          1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCG

                                 
       7243 GGCCCTTATTTGAGCATTTTG
          1 GGCCCTTATTTGAGCATTTTG

       7264 ATAAACATTA


Statistics
Matches: 70,  Mismatches: 10, Indels: 2
        0.85            0.12        0.02

Matches are distributed among these distances:
  60   69  0.99
  61    1  0.01

ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37


Consensus pattern (60 bp):   
GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCG

Found at i:7282 original size:60 final size:60

Alignment explanation


    Indices: 7123--7285  Score: 202
    Period size: 60  Copynumber: 2.7  Consensus size: 60

       7113 GAGTGAGACA

                *                *             *        *      *      * 
       7123 GGCCTTTATTTGAGCATTTTGGCAAACGTTAGGCCTTTATTTGGTCAAATTCAAAGATGG
          1 GGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG

              *    *                           *                         
       7183 GGTCCTTGTTTGAGCATTTT-AGCAAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCG
          1 GGCCCTTATTTGAGCATTTTGA-CAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG

                                  *    *   *           
       7243 GGCCCTTATTTGAGCATTTTGATAAACATTAAGCCCTTATTTG
          1 GGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTG

       7286 AGCAATTAGC


Statistics
Matches: 86,  Mismatches: 15, Indels: 4
        0.82            0.14        0.04

Matches are distributed among these distances:
  60   85  0.99
  61    1  0.01

ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37


Consensus pattern (60 bp):   
GGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG

Found at i:7604 original size:31 final size:31

Alignment explanation


    Indices: 7542--7604  Score: 83
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       7532 ACCCCTGCCT

                   *  *               *    
       7542 TTTTTTATTTTTAAATTTTATATTAATTTAA
          1 TTTTTTAATTGTAAATTTTATATTAAGTTAA

                                            
       7573 TTTTTTAATTGTAAATTTTA-ATTAAGGTTAA
          1 TTTTTTAATTGTAAATTTTATATTAA-GTTAA

             
       7604 T
          1 T

       7605 AATAATTACC


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  30    5  0.18
  31   23  0.82

ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62


Consensus pattern (31 bp):   
TTTTTTAATTGTAAATTTTATATTAAGTTAA

Found at i:7737 original size:20 final size:21

Alignment explanation


    Indices: 7702--7741  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       7692 AAATTAACAA

                       *         
       7702 TAATTATTATATTTGTAATTT
          1 TAATTATTATAATTGTAATTT

                                
       7723 TAATTA-TATAATTGTAATT
          1 TAATTATTATAATTGTAATT

       7742 ATCATAAAAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20   12  0.67
  21    6  0.33

ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57


Consensus pattern (21 bp):   
TAATTATTATAATTGTAATTT

Found at i:7995 original size:24 final size:24

Alignment explanation


    Indices: 7963--8010  Score: 87
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       7953 AGTTAAAAAT

                            *       
       7963 TTAGAAAGTTAGAAATTATTTGAG
          1 TTAGAAAGTTAGAAATGATTTGAG

                                    
       7987 TTAGAAAGTTAGAAATGATTTGAG
          1 TTAGAAAGTTAGAAATGATTTGAG

       8011 AGAATTTTAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35


Consensus pattern (24 bp):   
TTAGAAAGTTAGAAATGATTTGAG

Found at i:8728 original size:2 final size:2

Alignment explanation


    Indices: 8721--8755  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       8711 AATATGACTA

                                                                
       8721 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       8756 CTA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.