Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015140.1 Corchorus olitorius cultivar O-4 contig15173, 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: 4092
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30


Found at i:2027 original size:48 final size:47

Alignment explanation


    Indices: 1952--2086  Score: 157
    Period size: 49  Copynumber: 2.8  Consensus size: 47

       1942 GAGCGTGCCA

                     *  *         *                 *      
       1952 ATCAATTTTATCAAAAAATTGATAAAAAGTGCAGTGAAAATTAAAAG
          1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGTGAAAAATAAAAG

                                                              
       1999 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGT-AAAAATAAAAG
          1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGC-AGTGAAAAATAAAAG

            *           *                *          
       2048 TTCAATTTTGTAGTAAAAATTGAGAAAAAATGCAG-GAAA
          1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAGTGAAA

       2087 TGTAAAGGAT


Statistics
Matches: 76,  Mismatches: 7, Indels: 10
        0.82            0.08        0.11

Matches are distributed among these distances:
  47   16  0.21
  48   18  0.24
  49   39  0.51
  50    3  0.04

ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27


Consensus pattern (47 bp):   
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGTGAAAAATAAAAG

Found at i:2053 original size:49 final size:50

Alignment explanation


    Indices: 1965--2081  Score: 161
    Period size: 49  Copynumber: 2.4  Consensus size: 50

       1955 AATTTTATCA

                     *                   *                 ** 
       1965 AAAAATTGATAAAAAG-TGC-AGTGAAAATTAAAAGATCAATTTTGTCTT
          1 AAAAATTGAGAAAAAGATGCAAGTGAAAAATAAAAGATCAATTTTGTAGT

                                                *             
       2013 AAAAATTGAGAAAAAGATGCAAGT-AAAAATAAAAGTTCAATTTTGTAGT
          1 AAAAATTGAGAAAAAGATGCAAGTGAAAAATAAAAGATCAATTTTGTAGT

                                 
       2062 AAAAATTGAGAAAAA-ATGCA
          1 AAAAATTGAGAAAAAGATGCA

       2082 GGAAATGTAA


Statistics
Matches: 62,  Mismatches: 5, Indels: 4
        0.87            0.07        0.06

Matches are distributed among these distances:
  48   20  0.32
  49   39  0.63
  50    3  0.05

ACGTcount: A:0.53, C:0.05, G:0.15, T:0.26


Consensus pattern (50 bp):   
AAAAATTGAGAAAAAGATGCAAGTGAAAAATAAAAGATCAATTTTGTAGT

Found at i:3379 original size:18 final size:17

Alignment explanation


    Indices: 3350--3387  Score: 58
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       3340 TTAATTCATT

                             
       3350 TAATTTCCTAATTCCCA
          1 TAATTTCCTAATTCCCA

                          *   
       3367 TAATTTCCCTAATTTCCA
          1 TAATTT-CCTAATTCCCA

               
       3385 TAA
          1 TAA

       3388 GTAATTTGGG


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17    6  0.32
  18   13  0.68

ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42


Consensus pattern (17 bp):   
TAATTTCCTAATTCCCA
Done.