Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012091.1 Corchorus olitorius cultivar O-4 contig12124, 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: 17421
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29


Found at i:4060 original size:19 final size:19

Alignment explanation


    Indices: 4033--4078  Score: 56
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       4023 GGCTCATGAG

                *        *     
       4033 CCGGCTTGGCCGGTCCGAA
          1 CCGGTTTGGCCGGACCGAA

                     *        *
       4052 CCGGTTTGGTCGGACCGAG
          1 CCGGTTTGGCCGGACCGAA

                    
       4071 CCGGTTTG
          1 CCGGTTTG

       4079 ACCCGATCCG


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  19   23  1.00

ACGTcount: A:0.09, C:0.30, G:0.39, T:0.22


Consensus pattern (19 bp):   
CCGGTTTGGCCGGACCGAA

Found at i:4567 original size:12 final size:12

Alignment explanation


    Indices: 4552--4600  Score: 55
    Period size: 13  Copynumber: 4.0  Consensus size: 12

       4542 TTGAGGAAAC

                       *
       4552 TGTTTTTATTAC
          1 TGTTTTTATTAA

                        
       4564 TG-TTTTATTAA
          1 TGTTTTTATTAA

                      *  
       4575 TGTGTTTTATAAA
          1 TGT-TTTTATTAA

                         
       4588 TGATTTTTATTAA
          1 TG-TTTTTATTAA

       4601 AATATCTTTG


Statistics
Matches: 31,  Mismatches: 3, Indels: 5
        0.79            0.08        0.13

Matches are distributed among these distances:
  11   10  0.32
  12    2  0.06
  13   18  0.58
  14    1  0.03

ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61


Consensus pattern (12 bp):   
TGTTTTTATTAA

Found at i:10154 original size:18 final size:19

Alignment explanation


    Indices: 10115--10154  Score: 55
    Period size: 21  Copynumber: 2.1  Consensus size: 19

      10105 GTGCTCCCGT

                                 
      10115 TGTGATGCACCCACTTTTCAA
          1 TGTGATGCACCCA--TTTCAA

                               
      10136 TGTGATGCACCCA-TTCAA
          1 TGTGATGCACCCATTTCAA

             
      10154 T
          1 T

      10155 TCTGACCATT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    6  0.32
  21   13  0.68

ACGTcount: A:0.25, C:0.28, G:0.15, T:0.33


Consensus pattern (19 bp):   
TGTGATGCACCCATTTCAA

Found at i:12503 original size:51 final size:50

Alignment explanation


    Indices: 12402--12503  Score: 118
    Period size: 51  Copynumber: 2.0  Consensus size: 50

      12392 GTTCTTCATA

                                                     * **     
      12402 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
          1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

                                      *     *                    
      12452 TTTTCTCTTGTTTCA-ATCTTGTCTCTGGACATACAAACACT-GTACACGTGT
          1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT

             
      12503 T
          1 T

      12504 CTTCATTCAG


Statistics
Matches: 44,  Mismatches: 5, Indels: 5
        0.81            0.09        0.09

Matches are distributed among these distances:
  50    7  0.16
  51   36  0.82
  52    1  0.02

ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42


Consensus pattern (50 bp):   
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Done.