Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012830.1 Corchorus olitorius cultivar O-4 contig12863, 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: 12856
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:2688 original size:16 final size:16

Alignment explanation


    Indices: 2667--2700  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       2657 ATAATACTTG

                             
       2667 TAATATTAATTA-ATAA
          1 TAATA-TAATTAGATAA

                            
       2683 TAATATAATTAGATAA
          1 TAATATAATTAGATAA

              
       2699 TA
          1 TA

       2701 CATGTAATAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    6  0.35
  16   11  0.65

ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41


Consensus pattern (16 bp):   
TAATATAATTAGATAA

Found at i:2729 original size:38 final size:38

Alignment explanation


    Indices: 2635--2719  Score: 125
    Period size: 38  Copynumber: 2.2  Consensus size: 38

       2625 CATAAAAATT

                   *                     *        *
       2635 AATTTATGATAATAATAATTAGATAATACTTGTAATATT
          1 AATTTATAATAAT-ATAATTAGATAATACATGTAATATA

                *                                 
       2674 AATTAATAATAATATAATTAGATAATACATGTAATATA
          1 AATTTATAATAATATAATTAGATAATACATGTAATATA

                    
       2712 AATTTATA
          1 AATTTATA

       2720 TATTCATAAT


Statistics
Matches: 41,  Mismatches: 5, Indels: 1
        0.87            0.11        0.02

Matches are distributed among these distances:
  38   30  0.73
  39   11  0.27

ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41


Consensus pattern (38 bp):   
AATTTATAATAATATAATTAGATAATACATGTAATATA

Found at i:5136 original size:50 final size:48

Alignment explanation


    Indices: 5034--5164  Score: 169
    Period size: 49  Copynumber: 2.7  Consensus size: 48

       5024 GAGCGTGCCA

                         *         *                *       
       5034 ATCAATTTTGTC-CAAAAATTGATAAAAAGTGCAATAAAAGTAAAAAG
          1 ATCAATTTTGTCTTAAAAATTGAGAAAAAGTGCAATAAAAATAAAAAG

                                                               
       5081 ATCAATTTTGTCTTAAAAAATTGAGAAAAAGGTGCAAGTAAAAAT-AAAAG
          1 ATCAATTTTGTCTT-AAAAATTGAGAAAAA-GTGCAA-TAAAAATAAAAAG

            *                                  
       5131 TTCAATTTTGT-TGTAAAAATTGAGAAAAAGTGCA
          1 ATCAATTTTGTCT-TAAAAATTGAGAAAAAGTGCA

       5165 GGAAATGTAA


Statistics
Matches: 75,  Mismatches: 4, Indels: 9
        0.85            0.05        0.10

Matches are distributed among these distances:
  47   12  0.16
  48    5  0.07
  49   30  0.40
  50   22  0.29
  51    6  0.08

ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28


Consensus pattern (48 bp):   
ATCAATTTTGTCTTAAAAATTGAGAAAAAGTGCAATAAAAATAAAAAG

Found at i:7008 original size:61 final size:61

Alignment explanation


    Indices: 6913--7032  Score: 213
    Period size: 61  Copynumber: 2.0  Consensus size: 61

       6903 AGCTCGTTTG

                          *                                              
       6913 GCATCGTTTCCGTTTCCTGTTTTCTGTTGCCAATTTTATGTTTTTGGAAACAAAACAGTAA
          1 GCATCGTTTCCGTTCCCTGTTTTCTGTTGCCAATTTTATGTTTTTGGAAACAAAACAGTAA

                                         *       *                     
       6974 GCATCGTTTCCGTTCCCTGTTTTCTGTTGTCAATTTTCTGTTTTTGGAAACAAAACAGT
          1 GCATCGTTTCCGTTCCCTGTTTTCTGTTGCCAATTTTATGTTTTTGGAAACAAAACAGT

       7033 GAAAACATGT


Statistics
Matches: 56,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  61   56  1.00

ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43


Consensus pattern (61 bp):   
GCATCGTTTCCGTTCCCTGTTTTCTGTTGCCAATTTTATGTTTTTGGAAACAAAACAGTAA

Done.