Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006120.1 Corchorus olitorius cultivar O-4 contig06145, 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: 2264
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35


Found at i:729 original size:109 final size:105

Alignment explanation


    Indices: 543--767  Score: 353
    Period size: 109  Copynumber: 2.1  Consensus size: 105

        533 GCCATGCTTG

                                                                      *      
        543 TAGTG-AATTAATTATATATTTTATTTCTAAAACCCTATAACAATATTATTAATTATGGAATTTA
          1 TAGTGAAATTAATTATATATTTTATTTCTAAAACCCTATAACAATATTATTAATTATGAAATTTA

                                        **          
        607 CCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACT
         66 CCCTTAAAATAAAAATAAAATTTTAATTAAGGGCTAAACT

                          * *                                          *     
        647 TAGTGAAATTAATTTTGTATTTTATTTCTAAAAAACCCTATAACAATAAATTATTAATTTTGAAA
          1 TAGTGAAATTAATTATATATTTTATTTCT--AAAACCCTATAACAAT--ATTATTAATTATGAAA

                                                        
        712 TTTACCCTTAAAATAAAAATAAAATTTTAATTAAGGGCTAAACT
         62 TTTACCCTTAAAATAAAAATAAAATTTTAATTAAGGGCTAAACT

                        
        756 TAGTGAAATTAA
          1 TAGTGAAATTAA

        768 AGCTAAACTT


Statistics
Matches: 110,  Mismatches: 6, Indels: 5
        0.91            0.05        0.04

Matches are distributed among these distances:
 104    5  0.05
 105   21  0.19
 107   16  0.15
 109   68  0.62

ACGTcount: A:0.44, C:0.09, G:0.08, T:0.40


Consensus pattern (105 bp):   
TAGTGAAATTAATTATATATTTTATTTCTAAAACCCTATAACAATATTATTAATTATGAAATTTA
CCCTTAAAATAAAAATAAAATTTTAATTAAGGGCTAAACT

Found at i:1338 original size:15 final size:15

Alignment explanation


    Indices: 1318--1349  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1308 AATTACATAA

                           
       1318 TTCAACCATAATTCT
          1 TTCAACCATAATTCT

                           
       1333 TTCAACCATAATTCT
          1 TTCAACCATAATTCT

              
       1348 TT
          1 TT

       1350 TCCATGTAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44


Consensus pattern (15 bp):   
TTCAACCATAATTCT

Found at i:1408 original size:51 final size:51

Alignment explanation


    Indices: 1348--1451  Score: 208
    Period size: 51  Copynumber: 2.0  Consensus size: 51

       1338 CCATAATTCT

                                                               
       1348 TTTCCATGTAAAACACCTATAATCTATAGTGATTATTGGCCCAAGTTGATC
          1 TTTCCATGTAAAACACCTATAATCTATAGTGATTATTGGCCCAAGTTGATC

                                                               
       1399 TTTCCATGTAAAACACCTATAATCTATAGTGATTATTGGCCCAAGTTGATC
          1 TTTCCATGTAAAACACCTATAATCTATAGTGATTATTGGCCCAAGTTGATC

              
       1450 TT
          1 TT

       1452 GAAGGCATCA


Statistics
Matches: 53,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  51   53  1.00

ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37


Consensus pattern (51 bp):   
TTTCCATGTAAAACACCTATAATCTATAGTGATTATTGGCCCAAGTTGATC

Found at i:1527 original size:58 final size:58

Alignment explanation


    Indices: 1437--1550  Score: 228
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       1427 GTGATTATTG

                                                                      
       1437 GCCCAAGTTGATCTTGAAGGCATCACCAATATATATATACTAGGTTTTTTTCCCGCAA
          1 GCCCAAGTTGATCTTGAAGGCATCACCAATATATATATACTAGGTTTTTTTCCCGCAA

                                                                    
       1495 GCCCAAGTTGATCTTGAAGGCATCACCAATATATATATACTAGGTTTTTTTCCCGC
          1 GCCCAAGTTGATCTTGAAGGCATCACCAATATATATATACTAGGTTTTTTTCCCGC

       1551 GCTCCGTTGC


Statistics
Matches: 56,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  58   56  1.00

ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33


Consensus pattern (58 bp):   
GCCCAAGTTGATCTTGAAGGCATCACCAATATATATATACTAGGTTTTTTTCCCGCAA
Done.