Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012562.1 Corchorus olitorius cultivar O-4 contig12595, 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: 2824
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29


Found at i:1429 original size:12 final size:12

Alignment explanation


    Indices: 1412--1444  Score: 66
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       1402 CAAGTTCTTT

                        
       1412 AAAACGTTTATC
          1 AAAACGTTTATC

                        
       1424 AAAACGTTTATC
          1 AAAACGTTTATC

                     
       1436 AAAACGTTT
          1 AAAACGTTT

       1445 TATAAATCAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   21  1.00

ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33


Consensus pattern (12 bp):   
AAAACGTTTATC

Found at i:1457 original size:24 final size:24

Alignment explanation


    Indices: 1412--1458  Score: 60
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       1402 CAAGTTCTTT

                             *      
       1412 AAAACGTTTATCAAAACGTTTATC
          1 AAAACGTTTATCAAAACATTTATC

                            *       
       1436 AAAACGTTTTAT-AAATCATTTAT
          1 AAAACG-TTTATCAAAACATTTAT

       1459 GTAAAACTGT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  24   15  0.75
  25    5  0.25

ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38


Consensus pattern (24 bp):   
AAAACGTTTATCAAAACATTTATC

Found at i:2700 original size:47 final size:47

Alignment explanation


    Indices: 2648--2738  Score: 114
    Period size: 47  Copynumber: 1.9  Consensus size: 47

       2638 CTAATCTTTA

                                                *            
       2648 TTTTCTTAT-TATTATTTTCCTATTTCCCTTTCTT-TCTTTTTTTTCCT
          1 TTTTCTTATCTATTATTTTCCT-TTTCCCTTT-TTCCCTTTTTTTTCCT

                   *   *  *                             
       2695 TTTTCTTTTCTTTTGTTTTCCTTTTCCCTTTTTCCCTTTTTTTT
          1 TTTTCTTATCTATTATTTTCCTTTTCCCTTTTTCCCTTTTTTTT

       2739 TTCCTTTCCT


Statistics
Matches: 38,  Mismatches: 4, Indels: 4
        0.83            0.09        0.09

Matches are distributed among these distances:
  46    2  0.05
  47   26  0.68
  48   10  0.26

ACGTcount: A:0.04, C:0.22, G:0.01, T:0.73


Consensus pattern (47 bp):   
TTTTCTTATCTATTATTTTCCTTTTCCCTTTTTCCCTTTTTTTTCCT

Found at i:2713 original size:16 final size:17

Alignment explanation


    Indices: 2680--2750  Score: 56
    Period size: 16  Copynumber: 4.1  Consensus size: 17

       2670 TTTCCCTTTC

                             
       2680 TTTCTTTT-TTTTCCTT
          1 TTTCTTTTCTTTTCCTT

                          *  
       2696 TTTCTTTTCTTTT-GTT
          1 TTTCTTTTCTTTTCCTT

              *                  
       2712 TTCCTTTTCCCTTTTTCCCTT
          1 TTTCTTTT--C-TTTT-CCTT

               *     *       
       2733 TTTTTTTTCCTTTCCTT
          1 TTTCTTTTCTTTTCCTT

             
       2750 T
          1 T

       2751 CCTTTCCCCG


Statistics
Matches: 43,  Mismatches: 6, Indels: 11
        0.72            0.10        0.18

Matches are distributed among these distances:
  16   17  0.40
  17    9  0.21
  18    4  0.09
  19    5  0.12
  21    8  0.19

ACGTcount: A:0.00, C:0.24, G:0.01, T:0.75


Consensus pattern (17 bp):   
TTTCTTTTCTTTTCCTT
Done.