Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015279.1 Corchorus olitorius cultivar O-4 contig15312, 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: 8243
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38


Found at i:1944 original size:59 final size:59

Alignment explanation


    Indices: 1872--2048  Score: 327
    Period size: 59  Copynumber: 3.0  Consensus size: 59

       1862 TTAGCAGTTC

                    *                                                  
       1872 TTTTTTTTTTCCAAAACCAACTTCTACATAAACTTTCTCCTGATAGAGATATTGACTTA
          1 TTTTTTTTCTCCAAAACCAACTTCTACATAAACTTTCTCCTGATAGAGATATTGACTTA

                                                                   *   
       1931 TTTTTTTTCTCCAAAACCAACTTCTACATAAACTTTCTCCTGATAGAGATATTGAATTA
          1 TTTTTTTTCTCCAAAACCAACTTCTACATAAACTTTCTCCTGATAGAGATATTGACTTA

                                *                                      
       1990 TTTTTTTTCTCCAAAACCAATTTCTACATAAACTTTCTCCTGATAGAGATATTGACTTA
          1 TTTTTTTTCTCCAAAACCAACTTCTACATAAACTTTCTCCTGATAGAGATATTGACTTA

       2049 ACGGCCTTCA


Statistics
Matches: 114,  Mismatches: 4, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  59  114  1.00

ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42


Consensus pattern (59 bp):   
TTTTTTTTCTCCAAAACCAACTTCTACATAAACTTTCTCCTGATAGAGATATTGACTTA

Found at i:2253 original size:37 final size:37

Alignment explanation


    Indices: 2203--2275  Score: 137
    Period size: 37  Copynumber: 2.0  Consensus size: 37

       2193 GATCTTAGAG

                                                 
       2203 TATAATTCCTATGGAATCTTGGATTATGCCCATTTCT
          1 TATAATTCCTATGGAATCTTGGATTATGCCCATTTCT

                                          *     
       2240 TATAATTCCTATGGAATCTTGGATTATGCCTATTTC
          1 TATAATTCCTATGGAATCTTGGATTATGCCCATTTC

       2276 AATGTTCTTA


Statistics
Matches: 35,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  37   35  1.00

ACGTcount: A:0.25, C:0.18, G:0.14, T:0.44


Consensus pattern (37 bp):   
TATAATTCCTATGGAATCTTGGATTATGCCCATTTCT

Found at i:2271 original size:21 final size:21

Alignment explanation


    Indices: 2210--2272  Score: 55
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       2200 GAGTATAATT

                                 
       2210 CCTATGGAATCTTGGATTATG
          1 CCTATGGAATCTTGGATTATG

              *     *        *  *
       2231 CCCAT---TTCTT--ATAATT
          1 CCTATGGAATCTTGGATTATG

                                 
       2247 CCTATGGAATCTTGGATTATG
          1 CCTATGGAATCTTGGATTATG

                 
       2268 CCTAT
          1 CCTAT

       2273 TTCAATGTTC


Statistics
Matches: 29,  Mismatches: 8, Indels: 10
        0.62            0.17        0.21

Matches are distributed among these distances:
  16    8  0.28
  18    4  0.14
  19    4  0.14
  21   13  0.45

ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41


Consensus pattern (21 bp):   
CCTATGGAATCTTGGATTATG
Done.