Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008460.1 Corchorus olitorius cultivar O-4 contig08487, 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: 5806
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36


Found at i:1993 original size:3 final size:3

Alignment explanation


    Indices: 1985--2030  Score: 92
    Period size: 3  Copynumber: 15.3  Consensus size: 3

       1975 AAATTTTCAT

                                                                         
       1985 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

       2031 ATATGTCCGC


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   43  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:2055 original size:30 final size:30

Alignment explanation


    Indices: 2021--2080  Score: 102
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       2011 ATTATTATTA

                         *                
       2021 TTATTATTATATATGTCCGCTTTGTCCTTG
          1 TTATTATTATATAGGTCCGCTTTGTCCTTG

                        *                 
       2051 TTATTATTATATGGGTCCGCTTTGTCCTTG
          1 TTATTATTATATAGGTCCGCTTTGTCCTTG

       2081 GATTATTCAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  30   28  1.00

ACGTcount: A:0.15, C:0.17, G:0.17, T:0.52


Consensus pattern (30 bp):   
TTATTATTATATAGGTCCGCTTTGTCCTTG

Found at i:2620 original size:45 final size:45

Alignment explanation


    Indices: 2552--2648  Score: 153
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       2542 AGTGCATTAC

                                       *                 
       2552 CTAA-ATTCTACTCACTCATCTCTAGGTAATTCATCAAAATAAAG
          1 CTAATATTCTACTCACTCATCTCTAGGCAATTCATCAAAATAAAG

                                                         *
       2596 CTAATATTCTACTC-CTTCATCTCTAGGCAATTCATCAAAATAAAT
          1 CTAATATTCTACTCAC-TCATCTCTAGGCAATTCATCAAAATAAAG

                    
       2641 CTAATATT
          1 CTAATATT

       2649 ATATGTTACT


Statistics
Matches: 49,  Mismatches: 2, Indels: 3
        0.91            0.04        0.06

Matches are distributed among these distances:
  44    5  0.10
  45   44  0.90

ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35


Consensus pattern (45 bp):   
CTAATATTCTACTCACTCATCTCTAGGCAATTCATCAAAATAAAG

Found at i:3299 original size:55 final size:55

Alignment explanation


    Indices: 3213--3322  Score: 211
    Period size: 55  Copynumber: 2.0  Consensus size: 55

       3203 ACATTAAAAA

                                                                   
       3213 TTGATGAGATCCTTTAGTAAATTTCCCAGTAGTTTCAAATAATATATAGTATAGT
          1 TTGATGAGATCCTTTAGTAAATTTCCCAGTAGTTTCAAATAATATATAGTATAGT

                                      *                            
       3268 TTGATGAGATCCTTTAGTAAATTTCCTAGTAGTTTCAAATAATATATAGTATAGT
          1 TTGATGAGATCCTTTAGTAAATTTCCCAGTAGTTTCAAATAATATATAGTATAGT

       3323 ACTATAATAT


Statistics
Matches: 54,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  55   54  1.00

ACGTcount: A:0.35, C:0.10, G:0.15, T:0.41


Consensus pattern (55 bp):   
TTGATGAGATCCTTTAGTAAATTTCCCAGTAGTTTCAAATAATATATAGTATAGT

Found at i:3334 original size:2 final size:2

Alignment explanation


    Indices: 3309--3356  Score: 62
    Period size: 2  Copynumber: 23.0  Consensus size: 2

       3299 GTTTCAAATA

                                                                          
       3309 AT AT AT AGT AT AGT ACT AT A- AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT A-T AT A-T A-T AT AT AT AT AT AT AT AT AT AT AT AT AT

                    
       3351 AT AT AT
          1 AT AT AT

       3357 TAGGTTAGTG


Statistics
Matches: 42,  Mismatches: 1, Indels: 6
        0.86            0.02        0.12

Matches are distributed among these distances:
   1    1  0.02
   2   35  0.83
   3    6  0.14

ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:4007 original size:11 final size:11

Alignment explanation


    Indices: 3991--4042  Score: 68
    Period size: 11  Copynumber: 4.5  Consensus size: 11

       3981 ACTTATGGTG

                    *  
       3991 TTTTTTATGTA
          1 TTTTTTATTTA

                       
       4002 TTTTTTATTTA
          1 TTTTTTATTTA

              *        
       4013 TTATTTATTTA
          1 TTTTTTATTTA

                         
       4024 TTTATTTATTTAA
          1 TTT-TTTATTT-A

                  
       4037 TTTTTT
          1 TTTTTT

       4043 TTTTTTGGTA


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

Matches are distributed among these distances:
  11   22  0.61
  12   10  0.28
  13    4  0.11

ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77


Consensus pattern (11 bp):   
TTTTTTATTTA

Found at i:4014 original size:4 final size:4

Alignment explanation


    Indices: 3994--4035  Score: 61
    Period size: 4  Copynumber: 11.0  Consensus size: 4

       3984 TATGGTGTTT

                  *                                               
       3994 TTTA TGTA TTT- TTTA TTTA -TTA TTTA TTTA TTTA TTTA TTTA
          1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA

       4036 ATTTTTTTTT


Statistics
Matches: 34,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
   3    6  0.18
   4   28  0.82

ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74


Consensus pattern (4 bp):   
TTTA

Done.