Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012836.1 Corchorus capsularis cultivar CVL-1 contig12857, 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: 27865
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:5141 original size:5 final size:5

Alignment explanation


    Indices: 5131--5159  Score: 58
    Period size: 5  Copynumber: 5.8  Consensus size: 5

       5121 ATGAATATAG

                                              
       5131 GGGAA GGGAA GGGAA GGGAA GGGAA GGGA
          1 GGGAA GGGAA GGGAA GGGAA GGGAA GGGA

       5160 GGTGGGTTTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   24  1.00

ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00


Consensus pattern (5 bp):   
GGGAA

Found at i:8878 original size:20 final size:21

Alignment explanation


    Indices: 8841--8883  Score: 52
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       8831 AACCCGTTAA

                         *    *  
       8841 TTAAAGCGTGTCACTCGTGTC
          1 TTAAAGCGTGTCAATCGTATC

                       *         
       8862 TTAAA-CGTGTTAATCGTATC
          1 TTAAAGCGTGTCAATCGTATC

              
       8882 TT
          1 TT

       8884 GACGATTAGG


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  20   14  0.74
  21    5  0.26

ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40


Consensus pattern (21 bp):   
TTAAAGCGTGTCAATCGTATC

Found at i:17995 original size:24 final size:26

Alignment explanation


    Indices: 17963--18012  Score: 61
    Period size: 24  Copynumber: 2.0  Consensus size: 26

      17953 TATAAAAAAG

                        *              
      17963 ATTGCAATTGCATAT-ATAAG-AAATT
          1 ATTGCAATT-CAGATAATAAGTAAATT

                                      
      17988 ATTG-AATTCAGATAATAAGTAAATT
          1 ATTGCAATTCAGATAATAAGTAAATT

      18013 TTAATCTAAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  23    4  0.18
  24    9  0.41
  25    9  0.41

ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36


Consensus pattern (26 bp):   
ATTGCAATTCAGATAATAAGTAAATT

Found at i:22153 original size:30 final size:30

Alignment explanation


    Indices: 22112--22170  Score: 100
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      22102 CACGGTGTAC

                  *                       
      22112 CTACCAGTTGAACTAACAACTCGGATGCAT
          1 CTACCAATTGAACTAACAACTCGGATGCAT

                                    *    
      22142 CTACCAATTGAACTAACAACTCGGGTGCA
          1 CTACCAATTGAACTAACAACTCGGATGCA

      22171 CTCAATATGA


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22


Consensus pattern (30 bp):   
CTACCAATTGAACTAACAACTCGGATGCAT

Found at i:22519 original size:12 final size:12

Alignment explanation


    Indices: 22502--22530  Score: 58
    Period size: 12  Copynumber: 2.4  Consensus size: 12

      22492 AAAATTAATA

                        
      22502 ATAAATTTCTAC
          1 ATAAATTTCTAC

                        
      22514 ATAAATTTCTAC
          1 ATAAATTTCTAC

                 
      22526 ATAAA
          1 ATAAA

      22531 GTACGAAACA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38


Consensus pattern (12 bp):   
ATAAATTTCTAC

Found at i:26079 original size:20 final size:21

Alignment explanation


    Indices: 26042--26080  Score: 55
    Period size: 20  Copynumber: 1.9  Consensus size: 21

      26032 AAGAAAAGAA

                                 
      26042 TTTCAATTTACTTCTTTTTTT
          1 TTTCAATTTACTTCTTTTTTT

                                
      26063 TTTC-ATTTAACTT-TTTTT
          1 TTTCAATTT-ACTTCTTTTT

      26081 AGTAGTAGTA


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  20    9  0.53
  21    8  0.47

ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72


Consensus pattern (21 bp):   
TTTCAATTTACTTCTTTTTTT
Done.