Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006085.1 Corchorus capsularis cultivar CVL-1 contig06103, 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: 5008
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38


Found at i:280 original size:2 final size:2

Alignment explanation


    Indices: 269--307  Score: 62
    Period size: 2  Copynumber: 20.0  Consensus size: 2

        259 TAGAAAAGTT

                                                *                      
        269 TA TA -A TA TA TA TA TA TA TA TA TA CA 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

        308 GCTTTAGCAG


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   33  0.97

ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46


Consensus pattern (2 bp):   
TA

Found at i:3362 original size:59 final size:61

Alignment explanation


    Indices: 3267--3382  Score: 173
    Period size: 59  Copynumber: 1.9  Consensus size: 61

       3257 TACTCTGATA

                                                     **                   
       3267 TTTTTGGAACTTTGTTGGTTCTGATACAAGTTAGACCATAATCGAAATCAATTGTCATTGTC
          1 TTTTTGGAACTTTGTT-GTTCTGATACAAGTTAGACCATAAAAGAAATCAATTGTCATTGTC

                                     * *                            
       3329 TTTTTGGAACTTTG-T-TTCTGATATATGTTAGACCATAAAAGAAATCAATTGTCA
          1 TTTTTGGAACTTTGTTGTTCTGATACAAGTTAGACCATAAAAGAAATCAATTGTCA

       3383 CCACTTTTCA


Statistics
Matches: 50,  Mismatches: 4, Indels: 3
        0.88            0.07        0.05

Matches are distributed among these distances:
  59   35  0.70
  61    1  0.02
  62   14  0.28

ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41


Consensus pattern (61 bp):   
TTTTTGGAACTTTGTTGTTCTGATACAAGTTAGACCATAAAAGAAATCAATTGTCATTGTC

Found at i:3968 original size:5 final size:5

Alignment explanation


    Indices: 3953--3987  Score: 54
    Period size: 5  Copynumber: 7.2  Consensus size: 5

       3943 CTCTGCCATC

                   *                                   
       3953 ATTTT AGTTT ATTTT ATTTT ATTTT ATTTT -TTTT A
          1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A

       3988 GTAAAAATAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
   4    4  0.15
   5   23  0.85

ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77


Consensus pattern (5 bp):   
ATTTT

Found at i:4118 original size:15 final size:15

Alignment explanation


    Indices: 4094--4124  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       4084 TAATTCAGTA

                           
       4094 TATAACGTTATTGGG
          1 TATAACGTTATTGGG

                 *         
       4109 TATAATGTTATTGGG
          1 TATAACGTTATTGGG

             
       4124 T
          1 T

       4125 TGTGTCAATT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.26, C:0.03, G:0.26, T:0.45


Consensus pattern (15 bp):   
TATAACGTTATTGGG
Done.