Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010300.1 Corchorus capsularis cultivar CVL-1 contig10321, 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: 41093
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:284 original size:2 final size:2

Alignment explanation


    Indices: 279--304  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

        269 TTAATAAAAT

                                                  
        279 GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA

        305 CAGTAGCAAA


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

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
GA

Found at i:830 original size:31 final size:32

Alignment explanation


    Indices: 792--857  Score: 89
    Period size: 33  Copynumber: 2.1  Consensus size: 32

        782 AAGGAAAATG

                              *             
        792 AATTCCCTATATATG-TTGGCTCTGAATTCTT
          1 AATTCCCTATATATGTTTAGCTCTGAATTCTT

                      *          *           
        823 AATTCCCTATGTATGTTTTAGTTCTGAATTCTT
          1 AATTCCCTATATATG-TTTAGCTCTGAATTCTT

              
        856 AA
          1 AA

        858 CAAAAACCAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  31   14  0.47
  33   16  0.53

ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47


Consensus pattern (32 bp):   
AATTCCCTATATATGTTTAGCTCTGAATTCTT

Found at i:17376 original size:3 final size:3

Alignment explanation


    Indices: 17370--17394  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

      17360 TGAAAAAAAA

                                             
      17370 AAG AAG AAG AAG AAG AAG AAG AAG A
          1 AAG AAG AAG AAG AAG AAG AAG AAG A

      17395 TAACAATAAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:25956 original size:2 final size:2

Alignment explanation


    Indices: 25949--25991  Score: 86
    Period size: 2  Copynumber: 21.5  Consensus size: 2

      25939 AAAGGGAATC

                                                                          
      25949 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

             
      25991 T
          1 T

      25992 GTAAAGGAAA


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   41  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:30179 original size:2 final size:2

Alignment explanation


    Indices: 30157--30201  Score: 65
    Period size: 2  Copynumber: 22.0  Consensus size: 2

      30147 GTAGGGGACA

                                                                            
      30157 AT AT -T AT ACT AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT

              
      30200 AT
          1 AT

      30202 CATGGAAATG


Statistics
Matches: 40,  Mismatches: 0, Indels: 6
        0.87            0.00        0.13

Matches are distributed among these distances:
   1    1  0.03
   2   35  0.88
   3    4  0.10

ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49


Consensus pattern (2 bp):   
AT

Done.