Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016694.1 Corchorus olitorius cultivar O-4 contig16727, 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: 1981
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--29  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

                                                       
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

         30 CTACATATTA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:1364 original size:12 final size:13

Alignment explanation


    Indices: 1347--1386  Score: 57
    Period size: 12  Copynumber: 3.2  Consensus size: 13

       1337 TTATGCACCC

                         
       1347 AAAACATTTAT-T
          1 AAAACATTTATAT

                         
       1359 AAAACATTT-TAT
          1 AAAACATTTATAT

               *         
       1371 AAAGCATTTATAT
          1 AAAACATTTATAT

               
       1384 AAA
          1 AAA

       1387 GCAGTTATGA


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  11    1  0.04
  12   18  0.72
  13    6  0.24

ACGTcount: A:0.53, C:0.07, G:0.03, T:0.38


Consensus pattern (13 bp):   
AAAACATTTATAT

Found at i:1382 original size:11 final size:11

Alignment explanation


    Indices: 1347--1403  Score: 51
    Period size: 12  Copynumber: 4.8  Consensus size: 11

       1337 TTATGCACCC

                        
       1347 AAAACATTTATT
          1 AAAACATTTA-T

                        
       1359 AAAACATTTTAT
          1 AAAACA-TTTAT

               *       
       1371 AAAGCATTTAT
          1 AAAACATTTAT

                    *    
       1382 ATAAAGCAGTTAT
          1 A-AAA-CATTTAT

            *        
       1395 GAAACATTT
          1 AAAACATTT

       1404 CCTCAACGGG


Statistics
Matches: 37,  Mismatches: 5, Indels: 7
        0.76            0.10        0.14

Matches are distributed among these distances:
  11   10  0.27
  12   17  0.46
  13   10  0.27

ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37


Consensus pattern (11 bp):   
AAAACATTTAT

Found at i:1384 original size:13 final size:13

Alignment explanation


    Indices: 1351--1394  Score: 56
    Period size: 12  Copynumber: 3.5  Consensus size: 13

       1341 GCACCCAAAA

                        *
       1351 CATTTAT-TAAAA
          1 CATTTATATAAAG

                         
       1363 CATTT-TATAAAG
          1 CATTTATATAAAG

                         
       1375 CATTTATATAAAG
          1 CATTTATATAAAG

              *    
       1388 CAGTTAT
          1 CATTTAT

       1395 GAAACATTTC


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  11    1  0.04
  12   14  0.50
  13   13  0.46

ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41


Consensus pattern (13 bp):   
CATTTATATAAAG
Done.