Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005231.1 Corchorus capsularis cultivar CVL-1 contig05249, 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: 5403
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.33


Found at i:1746 original size:2 final size:2

Alignment explanation


    Indices: 1739--1767  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       1729 TGAATTTGCA

                                                       
       1739 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       1768 CCACATATTA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:2047 original size:45 final size:44

Alignment explanation


    Indices: 1959--2091  Score: 212
    Period size: 45  Copynumber: 3.0  Consensus size: 44

       1949 AATAGAGTAA

                               * *   *                  
       1959 TGGAATTACTAAAAGATCCCTACCCAAATTAATGATGAGCTGGG
          1 TGGAATTACTAAAAGATCCTTCCCCGAATTAATGATGAGCTGGG

                                                         
       2003 TGGAATTACTAAAAGATCTCTTCCCCGAATTAATGATGAGCTGGG
          1 TGGAATTACTAAAAGATC-CTTCCCCGAATTAATGATGAGCTGGG

                                       *                
       2048 TGGAATTACTAAAAGATCCTTACCCCGGATTAATGATGAGCTGG
          1 TGGAATTACTAAAAGATCCTT-CCCCGAATTAATGATGAGCTGG

       2092 AGAAGTAATC


Statistics
Matches: 83,  Mismatches: 4, Indels: 3
        0.92            0.04        0.03

Matches are distributed among these distances:
  44   21  0.25
  45   62  0.75

ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27


Consensus pattern (44 bp):   
TGGAATTACTAAAAGATCCTTCCCCGAATTAATGATGAGCTGGG

Found at i:2528 original size:21 final size:21

Alignment explanation


    Indices: 2504--2543  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2494 TAAATGAAGA

                                  
       2504 ATTAGT-TTATATATATATATT
          1 ATTAGTATTAT-TATATATATT

                *              
       2525 ATTATTATTATTATATATA
          1 ATTAGTATTATTATATATA

       2544 AATGAATTAG


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  21   13  0.76
  22    4  0.24

ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57


Consensus pattern (21 bp):   
ATTAGTATTATTATATATATT

Found at i:2649 original size:2 final size:2

Alignment explanation


    Indices: 2636--2727  Score: 77
    Period size: 2  Copynumber: 48.0  Consensus size: 2

       2626 TTTTAATTGA

                      *                                         *    **  *
       2636 AT AT AT AA AT AT AT AT AT AT AT AT AT AT A- AT AT AA AT GG AG
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                         *                                                 
       2677 A- AT -T AGT TT AT AT AT -T AT AT AT AT A- AT AT AT AT AT AT AT
          1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                  *          
       2716 AT AT TT AT AT AT
          1 AT AT AT AT AT AT

       2728 TCAATTTATG


Statistics
Matches: 73,  Mismatches: 11, Indels: 12
        0.76            0.11        0.12

Matches are distributed among these distances:
   1    5  0.07
   2   67  0.92
   3    1  0.01

ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47


Consensus pattern (2 bp):   
AT

Done.