Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001362.1 Corchorus capsularis cultivar CVL-1 contig01362, 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: 6454
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30


Found at i:1568 original size:20 final size:21

Alignment explanation


    Indices: 1543--1585  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1533 GACATTGATT

                                 
       1543 AATAATAATA-AAAATAAAAA
          1 AATAATAATACAAAATAAAAA

                   *   *         
       1563 AATAATATTACTAAATAAAAA
          1 AATAATAATACAAAATAAAAA

              
       1584 AA
          1 AA

       1586 AAAATTAAAG


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    9  0.45
  21   11  0.55

ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23


Consensus pattern (21 bp):   
AATAATAATACAAAATAAAAA

Found at i:1577 original size:23 final size:24

Alignment explanation


    Indices: 1542--1588  Score: 60
    Period size: 23  Copynumber: 2.0  Consensus size: 24

       1532 AGACATTGAT

                            *       
       1542 TAATAATAATAAA-AATAAAAAAA
          1 TAATAATAATAAATAAAAAAAAAA

                 *  *               
       1565 TAATATTACTAAATAAAAAAAAAA
          1 TAATAATAATAAATAAAAAAAAAA

       1589 ATTAAAGTAT


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  23   11  0.55
  24    9  0.45

ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23


Consensus pattern (24 bp):   
TAATAATAATAAATAAAAAAAAAA

Found at i:6405 original size:21 final size:21

Alignment explanation


    Indices: 6381--6429  Score: 57
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       6371 TCTCACTAAA

                    *             
       6381 TCTGATTTGAAT-TTGAAAACC
          1 TCTGATTTAAATCTTGAAAA-C

                                 
       6402 TCTGA-TTAAATCTTGAAAAC
          1 TCTGATTTAAATCTTGAAAAC

                    
       6422 TCTTGATT
          1 TC-TGATT

       6430 ACCCATTTTA


Statistics
Matches: 24,  Mismatches: 1, Indels: 5
        0.80            0.03        0.17

Matches are distributed among these distances:
  20    8  0.33
  21   15  0.62
  22    1  0.04

ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41


Consensus pattern (21 bp):   
TCTGATTTAAATCTTGAAAAC
Done.