Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005788.1 Corchorus capsularis cultivar CVL-1 contig05806, 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: 4715
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:1501 original size:27 final size:27

Alignment explanation


    Indices: 1471--1546  Score: 107
    Period size: 27  Copynumber: 2.8  Consensus size: 27

       1461 AGGTGAACCT

                     *                 
       1471 AAAAATGACTAAAATGCCCTTGAGTAC
          1 AAAAATGACCAAAATGCCCTTGAGTAC

                               *  *  * 
       1498 AAAAATGACCAAAATGCCCCTGGGTGC
          1 AAAAATGACCAAAATGCCCTTGAGTAC

                           *      
       1525 AAAAATGACCAAAATACCCTTG
          1 AAAAATGACCAAAATGCCCTTG

       1547 GACGACCCTA


Statistics
Matches: 43,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  27   43  1.00

ACGTcount: A:0.43, C:0.22, G:0.16, T:0.18


Consensus pattern (27 bp):   
AAAAATGACCAAAATGCCCTTGAGTAC

Found at i:2559 original size:29 final size:29

Alignment explanation


    Indices: 2521--2576  Score: 94
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       2511 CTGCAGAGAG

                           *             
       2521 TTTGAAAGAAAGCACGGAGCTTGAGATAA
          1 TTTGAAAGAAAGCACAGAGCTTGAGATAA

                 *                     
       2550 TTTGAGAGAAAGCACAGAGCTTGAGAT
          1 TTTGAAAGAAAGCACAGAGCTTGAGAT

       2577 TTTGCGCGGA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   25  1.00

ACGTcount: A:0.39, C:0.11, G:0.29, T:0.21


Consensus pattern (29 bp):   
TTTGAAAGAAAGCACAGAGCTTGAGATAA

Found at i:4541 original size:16 final size:17

Alignment explanation


    Indices: 4506--4547  Score: 68
    Period size: 16  Copynumber: 2.5  Consensus size: 17

       4496 TTATTAGATA

                              
       4506 ATTAATAATTTAGAAAAT
          1 ATTAA-AATTTAGAAAAT

                             
       4524 ATTAAAATTTAG-AAAT
          1 ATTAAAATTTAGAAAAT

                    
       4540 ATTAAAAT
          1 ATTAAAAT

       4548 AATTAATAAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  16   12  0.50
  17    7  0.29
  18    5  0.21

ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38


Consensus pattern (17 bp):   
ATTAAAATTTAGAAAAT
Done.