Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006062.1 Corchorus capsularis cultivar CVL-1 contig06080, 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: 14983
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:2468 original size:31 final size:31

Alignment explanation


    Indices: 2433--2503  Score: 124
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       2423 AAATTGCCAA

                             *  *          
       2433 TTGACCCCATTAAAATGGTAGGTTTATAGTT
          1 TTGACCCCATTAAAATGATAAGTTTATAGTT

                                           
       2464 TTGACCCCATTAAAATGATAAGTTTATAGTT
          1 TTGACCCCATTAAAATGATAAGTTTATAGTT

                     
       2495 TTGACCCCA
          1 TTGACCCCA

       2504 CTATTTTTTT


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  31   38  1.00

ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37


Consensus pattern (31 bp):   
TTGACCCCATTAAAATGATAAGTTTATAGTT

Found at i:7227 original size:10 final size:10

Alignment explanation


    Indices: 7212--7244  Score: 57
    Period size: 10  Copynumber: 3.3  Consensus size: 10

       7202 GGTTAAGATA

                      
       7212 TATCTTATTT
          1 TATCTTATTT

                      
       7222 TATCTTATTT
          1 TATCTTATTT

               *      
       7232 TATTTTATTT
          1 TATCTTATTT

               
       7242 TAT
          1 TAT

       7245 ACTATATAAA


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

Matches are distributed among these distances:
  10   22  1.00

ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73


Consensus pattern (10 bp):   
TATCTTATTT

Found at i:11189 original size:48 final size:48

Alignment explanation


    Indices: 11116--11213  Score: 187
    Period size: 48  Copynumber: 2.0  Consensus size: 48

      11106 TTCACGAATT

                                                            
      11116 TTTGTCCAAAACATTCTCCAAGTTGGAGAAATTATTACATGGACCGGG
          1 TTTGTCCAAAACATTCTCCAAGTTGGAGAAATTATTACATGGACCGGG

                                *                           
      11164 TTTGTCCAAAACATTCTCCATGTTGGAGAAATTATTACATGGACCGGG
          1 TTTGTCCAAAACATTCTCCAAGTTGGAGAAATTATTACATGGACCGGG

              
      11212 TT
          1 TT

      11214 CACCACGCCA


Statistics
Matches: 49,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  48   49  1.00

ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32


Consensus pattern (48 bp):   
TTTGTCCAAAACATTCTCCAAGTTGGAGAAATTATTACATGGACCGGG

Found at i:13978 original size:26 final size:26

Alignment explanation


    Indices: 13935--13985  Score: 77
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      13925 ATTATTAAAA

                                      
      13935 TATTTTATATTGAAAAATTCAATTTT
          1 TATTTTATATTGAAAAATTCAATTTT

                          *           
      13961 TATTTTAT-TTAGAGAAATTCAATTT
          1 TATTTTATATT-GAAAAATTCAATTT

      13986 CTACATTACC


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  25    2  0.09
  26   21  0.91

ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53


Consensus pattern (26 bp):   
TATTTTATATTGAAAAATTCAATTTT

Found at i:14840 original size:4 final size:4

Alignment explanation


    Indices: 14831--14857  Score: 54
    Period size: 4  Copynumber: 6.8  Consensus size: 4

      14821 TTGCCTCTAT

                                             
      14831 ATAA ATAA ATAA ATAA ATAA ATAA ATA
          1 ATAA ATAA ATAA ATAA ATAA ATAA ATA

      14858 TATATATATA


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

Matches are distributed among these distances:
   4   23  1.00

ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26


Consensus pattern (4 bp):   
ATAA

Found at i:14862 original size:2 final size:2

Alignment explanation


    Indices: 14855--14883  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      14845 AAATAAATAA

                                                       
      14855 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 A

      14884 ACTTGGAGAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.