Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011828.1 Corchorus capsularis cultivar CVL-1 contig11849, 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: 14440
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:1691 original size:17 final size:17

Alignment explanation


    Indices: 1664--1712  Score: 64
    Period size: 17  Copynumber: 2.9  Consensus size: 17

       1654 TGTAATTTTT

                  *          
       1664 GATCACCGGTGATCTT-
          1 GATCACTGGTGATCTTA

                              
       1680 GCATCACTGGTGATCTTA
          1 G-ATCACTGGTGATCTTA

                   *       
       1698 GATCACTAGTGATCT
          1 GATCACTGGTGATCT

       1713 GGGGGGTGAT


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  16    1  0.03
  17   27  0.93
  18    1  0.03

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


Consensus pattern (17 bp):   
GATCACTGGTGATCTTA

Found at i:2182 original size:37 final size:35

Alignment explanation


    Indices: 2105--2190  Score: 92
    Period size: 34  Copynumber: 2.5  Consensus size: 35

       2095 CTAAGCAATG

                                               
       2105 GTATAAGGTTTGGTG----TTTTTTTTTGGGCACA
          1 GTATAAGGTTTGGTGTTTTTTTTTTTTTGGGCACA

                *                       *       
       2136 GTATGAGG-TTGGTGTTTTTTTTTTTTTTGGCACAA
          1 GTATAAGGTTTGGTGTTTTTTTTTTTTTGGGCAC-A

                                
       2171 TTGTATAAGGTTTGGTGTTT
          1 --GTATAAGGTTTGGTGTTT

       2191 AGGCAATTGA


Statistics
Matches: 44,  Mismatches: 3, Indels: 9
        0.79            0.05        0.16

Matches are distributed among these distances:
  30    6  0.14
  31    7  0.16
  34   14  0.32
  35    1  0.02
  37    7  0.16
  38    9  0.20

ACGTcount: A:0.15, C:0.05, G:0.28, T:0.52


Consensus pattern (35 bp):   
GTATAAGGTTTGGTGTTTTTTTTTTTTTGGGCACA

Found at i:2943 original size:16 final size:16

Alignment explanation


    Indices: 2922--2956  Score: 70
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       2912 CGAGTTTGAG

                            
       2922 ATTTCATATTTCCTTA
          1 ATTTCATATTTCCTTA

                            
       2938 ATTTCATATTTCCTTA
          1 ATTTCATATTTCCTTA

               
       2954 ATT
          1 ATT

       2957 AGTTCTAATA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57


Consensus pattern (16 bp):   
ATTTCATATTTCCTTA
Done.