Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008670.1 Corchorus capsularis cultivar CVL-1 contig08691, 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: 10628
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:1331 original size:11 final size:11

Alignment explanation


    Indices: 1315--1343  Score: 58
    Period size: 11  Copynumber: 2.6  Consensus size: 11

       1305 TAGGTCGATG

                       
       1315 GCCGGGCTGCA
          1 GCCGGGCTGCA

                       
       1326 GCCGGGCTGCA
          1 GCCGGGCTGCA

                   
       1337 GCCGGGC
          1 GCCGGGC

       1344 ATACTGTCTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.07, C:0.38, G:0.48, T:0.07


Consensus pattern (11 bp):   
GCCGGGCTGCA

Found at i:4387 original size:12 final size:12

Alignment explanation


    Indices: 4355--4387  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       4345 AAAAACGGAA

                        
       4355 AAAGAAAAA-TT
          1 AAAGAAAAATTT

               *        
       4366 AAAAAAAAATTT
          1 AAAGAAAAATTT

                      
       4378 AAAGAAAAAT
          1 AAAGAAAAAT

       4388 CGGAAACCCT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  11    8  0.42
  12   11  0.58

ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18


Consensus pattern (12 bp):   
AAAGAAAAATTT

Found at i:4840 original size:6 final size:6

Alignment explanation


    Indices: 4829--4855  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       4819 AAAGCAAAGC

                                           
       4829 AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAA

       4856 ACAGAATTAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:7022 original size:13 final size:13

Alignment explanation


    Indices: 7004--7029  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       6994 CTAAGATGTT

                         
       7004 CCTTTGTTATCTA
          1 CCTTTGTTATCTA

                         
       7017 CCTTTGTTATCTA
          1 CCTTTGTTATCTA

       7030 TCCATATTTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.15, C:0.23, G:0.08, T:0.54


Consensus pattern (13 bp):   
CCTTTGTTATCTA

Found at i:7885 original size:60 final size:61

Alignment explanation


    Indices: 7753--7892  Score: 210
    Period size: 60  Copynumber: 2.3  Consensus size: 61

       7743 TCAACTCTCA

                          *                        *                     
       7753 ACCTCAGACAGGTCCTTCTCAATTTCAATATCGACCACATACTGGTCTTCTTCAATTCCAG
          1 ACCTCAGACAGGTCTTTCTCAATTTCAATATCGACCACAGACTGGTCTTCTTCAATTCCAG

                                *            *    *               *    * 
       7814 ACCTCAGACAGGTCTTTCTCGATTTCAAT-TCGGCCACGGACTGGTCTTCTTCAGTTCCGG
          1 ACCTCAGACAGGTCTTTCTCAATTTCAATATCGACCACAGACTGGTCTTCTTCAATTCCAG

                               
       7874 ACCTCAGACAGGTCTTTCT
          1 ACCTCAGACAGGTCTTTCT

       7893 TAGTTTTCAG


Statistics
Matches: 72,  Mismatches: 7, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  60   45  0.62
  61   27  0.38

ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31


Consensus pattern (61 bp):   
ACCTCAGACAGGTCTTTCTCAATTTCAATATCGACCACAGACTGGTCTTCTTCAATTCCAG

Found at i:8352 original size:2 final size:2

Alignment explanation


    Indices: 8345--8369  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       8335 ATTAGTCATG

                                                 
       8345 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       8370 TTTGATGTGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
TA

Done.