Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018123.1 Corchorus olitorius cultivar O-4 contig18156, 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: 4968
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:1491 original size:19 final size:18

Alignment explanation


    Indices: 1467--1506  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       1457 TTGAAGATTT

                    *          
       1467 ATTGAAGATAATTTGAAGA
          1 ATTGAAGACAA-TTGAAGA

                     *        
       1486 ATTGAAGACCATTGAAGA
          1 ATTGAAGACAATTGAAGA

               
       1504 ATT
          1 ATT

       1507 ATTTCAAGAG


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  18   10  0.53
  19    9  0.47

ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30


Consensus pattern (18 bp):   
ATTGAAGACAATTGAAGA

Found at i:3913 original size:21 final size:21

Alignment explanation


    Indices: 3887--3927  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3877 TCATCTCCAT

                                 
       3887 TTATTGCATTGCGTTGATTGA
          1 TTATTGCATTGCGTTGATTGA

                   *    *       
       3908 TTATTGCTTTGCTTTGATTG
          1 TTATTGCATTGCGTTGATTG

       3928 CCTATTCCTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.15, C:0.10, G:0.22, T:0.54


Consensus pattern (21 bp):   
TTATTGCATTGCGTTGATTGA

Found at i:3933 original size:21 final size:21

Alignment explanation


    Indices: 3888--3933  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       3878 CATCTCCATT

                                *
       3888 TATTGCATTGCGTTGATTGAT
          1 TATTGCATTGCGTTGATTGAC

                  *    *       * 
       3909 TATTGCTTTGCTTTGATTGCC
          1 TATTGCATTGCGTTGATTGAC

                
       3930 TATT
          1 TATT

       3934 CCTTGATTTG


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.15, C:0.13, G:0.20, T:0.52


Consensus pattern (21 bp):   
TATTGCATTGCGTTGATTGAC

Found at i:4293 original size:22 final size:22

Alignment explanation


    Indices: 4268--4320  Score: 56
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       4258 TAATTAAACT

                                    
       4268 AACAATTAA-AATTAACT-AAGAA
          1 AACAATTAAGAA--AACTAAAGAA

                  *       *       
       4290 AACAATCAAGAAAATTAAAGAA
          1 AACAATTAAGAAAACTAAAGAA

                     
       4312 AACAATTAA
          1 AACAATTAA

       4321 TAAGAAAGCA


Statistics
Matches: 26,  Mismatches: 3, Indels: 4
        0.79            0.09        0.12

Matches are distributed among these distances:
  21    3  0.12
  22   21  0.81
  23    2  0.08

ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19


Consensus pattern (22 bp):   
AACAATTAAGAAAACTAAAGAA
Done.