Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015031.1 Corchorus olitorius cultivar O-4 contig15064, 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: 37230
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:2214 original size:29 final size:28

Alignment explanation


    Indices: 2180--2256  Score: 109
    Period size: 29  Copynumber: 2.7  Consensus size: 28

       2170 ATGTGAACTT

                          *              
       2180 AAAATGACCAAAATACCCCTGAATGTGCA
          1 AAAATGACCAAAATGCCCCTGAAT-TGCA

                                     * *
       2209 AAAATGACCAAAATGCCCCTGAATTTCG
          1 AAAATGACCAAAATGCCCCTGAATTGCA

                     *          
       2237 AAAATGACCGAAATGCCCCT
          1 AAAATGACCAAAATGCCCCT

       2257 AGATGACCCT


Statistics
Matches: 44,  Mismatches: 4, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  28   21  0.48
  29   23  0.52

ACGTcount: A:0.42, C:0.26, G:0.14, T:0.18


Consensus pattern (28 bp):   
AAAATGACCAAAATGCCCCTGAATTGCA

Found at i:3085 original size:19 final size:18

Alignment explanation


    Indices: 3061--3119  Score: 75
    Period size: 18  Copynumber: 3.2  Consensus size: 18

       3051 ATCATCATTA

                               
       3061 AATTGAAACACTAAAACAG
          1 AATTGAAACAC-AAAACAG

                        *     
       3080 AATTGAAACACATAACAG
          1 AATTGAAACACAAAACAG

                       *       
       3098 AATTGGAAA-AAAAAACAG
          1 AATT-GAAACACAAAACAG

                
       3116 AATT
          1 AATT

       3120 ACTAGTATCA


Statistics
Matches: 36,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  18   21  0.58
  19   15  0.42

ACGTcount: A:0.59, C:0.12, G:0.12, T:0.17


Consensus pattern (18 bp):   
AATTGAAACACAAAACAG

Found at i:21999 original size:18 final size:18

Alignment explanation


    Indices: 21964--21998  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      21954 CTCCTCTATC

                     *        
      21964 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                              
      21982 ATGAAAACAATT-TTTTT
          1 ATGAAAACAATTCTTTTT

      21999 TTAATTACCC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    5  0.31
  18   11  0.69

ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT

Found at i:27455 original size:19 final size:18

Alignment explanation


    Indices: 27422--27457  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      27412 TTGAAATTAT

                              
      27422 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
      27440 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

      27458 TAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA
Done.