Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002336.1 Corchorus capsularis cultivar CVL-1 contig02342, 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, 841

Length: 1403
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23


Found at i:1347 original size:30 final size:30

Alignment explanation


    Indices: 1311--1379  Score: 101
    Period size: 26  Copynumber: 2.4  Consensus size: 30

       1301 TGACGCCAAG

                                          
       1311 GCCAAGTGCCATCCATCAGCAAGTGCCGAT
          1 GCCAAGTGCCATCCATCAGCAAGTGCCGAT

                                          
       1341 GCCAAGTG----CCATCAGCAAGTGCCGAT
          1 GCCAAGTGCCATCCATCAGCAAGTGCCGAT

                         
       1367 GCCAAGTGTCCAT
          1 GCCAAGTG-CCAT

       1380 ACGGAGAATG


Statistics
Matches: 34,  Mismatches: 0, Indels: 9
        0.79            0.00        0.21

Matches are distributed among these distances:
  26   26  0.76
  30    8  0.24

ACGTcount: A:0.26, C:0.32, G:0.25, T:0.17


Consensus pattern (30 bp):   
GCCAAGTGCCATCCATCAGCAAGTGCCGAT

Found at i:1348 original size:13 final size:13

Alignment explanation


    Indices: 1330--1374  Score: 58
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       1320 CATCCATCAG

                         
       1330 CAAGTGCCGATGC
          1 CAAGTGCCGATGC

                         
       1343 CAAGTGCC-AT-C
          1 CAAGTGCCGATGC

                           
       1354 AGCAAGTGCCGATGC
          1 --CAAGTGCCGATGC

                  
       1369 CAAGTG
          1 CAAGTG

       1375 TCCATACGGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 8
        0.78            0.00        0.22

Matches are distributed among these distances:
  11    1  0.04
  12    2  0.07
  13   22  0.79
  14    2  0.07
  15    1  0.04

ACGTcount: A:0.27, C:0.29, G:0.29, T:0.16


Consensus pattern (13 bp):   
CAAGTGCCGATGC

Found at i:1356 original size:26 final size:27

Alignment explanation


    Indices: 1322--1379  Score: 109
    Period size: 26  Copynumber: 2.2  Consensus size: 27

       1312 CCAAGTGCCA

                                       
       1322 TCCATCAGCAAGTGCCGATGCCAAGTG
          1 TCCATCAGCAAGTGCCGATGCCAAGTG

                                       
       1349 -CCATCAGCAAGTGCCGATGCCAAGTG
          1 TCCATCAGCAAGTGCCGATGCCAAGTG

                 
       1375 TCCAT
          1 TCCAT

       1380 ACGGAGAATG


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  26   26  0.87
  27    4  0.13

ACGTcount: A:0.26, C:0.31, G:0.24, T:0.19


Consensus pattern (27 bp):   
TCCATCAGCAAGTGCCGATGCCAAGTG
Done.