Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016399.1 Corchorus capsularis cultivar CVL-1 contig16420, 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: 5289
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31


Found at i:1087 original size:33 final size:32

Alignment explanation


    Indices: 1048--1159  Score: 118
    Period size: 33  Copynumber: 3.4  Consensus size: 32

       1038 GGCCACAAGC

                                             
       1048 CCGGCCACGCGACATGGACATGTCCGGCCATCA
          1 CCGGCCACGCGACATGGACATGTCCGGCCA-CA

                      *                 *    
       1081 CCGGCCACGCAACATGGACATGTCCGGCTACAA
          1 CCGGCCACGCGACATGGACATGTCCGGCCAC-A

                   **         *    *          
       1114 CCGGCCAAACGAC-TCGGCCATGCCCGGCCACCA
          1 CCGGCCACGCGACAT-GGACATGTCCGGCCA-CA

               *         
       1147 CCGTCCACGCGAC
          1 CCGGCCACGCGAC

       1160 CCTTTGTCTA


Statistics
Matches: 65,  Mismatches: 11, Indels: 6
        0.79            0.13        0.07

Matches are distributed among these distances:
  32    2  0.03
  33   62  0.95
  34    1  0.02

ACGTcount: A:0.22, C:0.43, G:0.25, T:0.10


Consensus pattern (32 bp):   
CCGGCCACGCGACATGGACATGTCCGGCCACA

Found at i:1420 original size:17 final size:19

Alignment explanation


    Indices: 1388--1423  Score: 58
    Period size: 17  Copynumber: 2.0  Consensus size: 19

       1378 ATTGGGCCTT

                               
       1388 TTATTCTATCTTAGTTTAG
          1 TTATTCTATCTTAGTTTAG

                               
       1407 TTATT-TAT-TTAGTTTAG
          1 TTATTCTATCTTAGTTTAG

       1424 AAGACATTGG


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    9  0.53
  18    3  0.18
  19    5  0.29

ACGTcount: A:0.22, C:0.06, G:0.11, T:0.61


Consensus pattern (19 bp):   
TTATTCTATCTTAGTTTAG

Found at i:4232 original size:21 final size:21

Alignment explanation


    Indices: 4208--4256  Score: 57
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       4198 TCTAACTAAG

                    *             
       4208 TCTGATTTGAAT-TTGAAAACC
          1 TCTGATTTAAATCTTGAAAA-C

                                 
       4229 TCTGA-TTAAATCTTGAAAAC
          1 TCTGATTTAAATCTTGAAAAC

                    
       4249 TCTTGATT
          1 TC-TGATT

       4257 ACCAATTTCA


Statistics
Matches: 24,  Mismatches: 1, Indels: 5
        0.80            0.03        0.17

Matches are distributed among these distances:
  20    8  0.33
  21   15  0.62
  22    1  0.04

ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41


Consensus pattern (21 bp):   
TCTGATTTAAATCTTGAAAAC
Done.