Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014227.1 Corchorus olitorius cultivar O-4 contig14260, 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: 2637
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38


Found at i:1473 original size:29 final size:30

Alignment explanation


    Indices: 1412--1491  Score: 99
    Period size: 29  Copynumber: 2.7  Consensus size: 30

       1402 GCTAAATACC

                 *                    **   
       1412 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
          1 CAAAATAATCCCTTATGTTTT-CTTTCAGGA

                                          
       1443 CAAAATAATCCCTTATGTTTT-TTTCAGGA
          1 CAAAATAATCCCTTATGTTTTCTTTCAGGA

                *          *    
       1472 CAAATTAATCCCTTACGTTT
          1 CAAAATAATCCCTTATGTTT

       1492 CAAAAATGAG


Statistics
Matches: 44,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  29   24  0.55
  31   20  0.45

ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40


Consensus pattern (30 bp):   
CAAAATAATCCCTTATGTTTTCTTTCAGGA

Found at i:1650 original size:31 final size:31

Alignment explanation


    Indices: 1615--1711  Score: 158
    Period size: 31  Copynumber: 3.1  Consensus size: 31

       1605 AAGGGACTGA

                  *                        
       1615 TTTGTCTCAAAAGAAAAACATAAGGGATTTT
          1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT

                                           
       1646 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
          1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT

                              *       *     
       1677 TTTGTCCCAAAAGAAAAATATAAGAGAATTTT
          1 TTTGTCCCAAAAGAAAAACATAAG-GGATTTT

               
       1709 TTT
          1 TTT

       1712 AGTATTTAGT


Statistics
Matches: 62,  Mismatches: 3, Indels: 1
        0.94            0.05        0.02

Matches are distributed among these distances:
  31   53  0.85
  32    9  0.15

ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33


Consensus pattern (31 bp):   
TTTGTCCCAAAAGAAAAACATAAGGGATTTT

Found at i:2503 original size:126 final size:125

Alignment explanation


    Indices: 2317--2555  Score: 336
    Period size: 126  Copynumber: 1.9  Consensus size: 125

       2307 CTTATTTTTC

                      *       *                             **               
       2317 AAATATATTTTTTAAATGCCATTTTTAAACTTTTACAATTTTACTCAATTAAAAACTCTATTTTT
          1 AAATATATTTCTTAAATGACATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT

                                                 *                       
       2382 ATTTAATCAAACTT-AATATATTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT
         66 ATTTAATCAAA-TTCAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT

                                                 **     * **        *        
       2442 AAATATATTTCTTAAATGACATTATTTAAACTTTTACGGTTTTATTTTACCAAAAATTCTATTTT
          1 AAATATATTTCTTAAATGACATT-TTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTT

                    *           *                            
       2507 TATTTAATTAAATTCAATATTTTTATAACTATTTTATCTTTACCATTTT
         65 TATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTT

       2556 TTAGGGAATT


Statistics
Matches: 99,  Mismatches: 13, Indels: 3
        0.86            0.11        0.03

Matches are distributed among these distances:
 125   23  0.23
 126   76  0.77

ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52


Consensus pattern (125 bp):   
AAATATATTTCTTAAATGACATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
ATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
Done.