Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007546.1 Corchorus capsularis cultivar CVL-1 contig07567, 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: 28162
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33


Found at i:1556 original size:1 final size:1

Alignment explanation


    Indices: 1552--1578  Score: 54
    Period size: 1  Copynumber: 27.0  Consensus size: 1

       1542 ATATATATAT

                                       
       1552 AAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAA

       1579 GAGAGAGAGA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   26  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:13985 original size:18 final size:18

Alignment explanation


    Indices: 13962--14001  Score: 80
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      13952 CATAACTAGG

                              
      13962 TTCGCGAAGCGGATCAGA
          1 TTCGCGAAGCGGATCAGA

                              
      13980 TTCGCGAAGCGGATCAGA
          1 TTCGCGAAGCGGATCAGA

                
      13998 TTCG
          1 TTCG

      14002 AATTAGTAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   22  1.00

ACGTcount: A:0.25, C:0.23, G:0.33, T:0.20


Consensus pattern (18 bp):   
TTCGCGAAGCGGATCAGA

Found at i:16164 original size:2 final size:2

Alignment explanation


    Indices: 16157--16210  Score: 65
    Period size: 2  Copynumber: 26.5  Consensus size: 2

      16147 ACTAGTTAAG

                            *                *                              
      16157 TA TA TA TA CTA CA TA TA T- TA GTG TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA

                            
      16200 TA TA TA TA TA T
          1 TA TA TA TA TA T

      16211 GTAGCTTTCA


Statistics
Matches: 45,  Mismatches: 4, Indels: 6
        0.82            0.07        0.11

Matches are distributed among these distances:
   1    1  0.02
   2   41  0.91
   3    3  0.07

ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:27824 original size:2 final size:2

Alignment explanation


    Indices: 27817--27858  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

      27807 CAAGAAACTC

                                                                          
      27817 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

      27859 GCAACAAATG


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
CT

Done.