Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018383.1 Corchorus olitorius cultivar O-4 contig18416, 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: 7444
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32


Found at i:952 original size:22 final size:21

Alignment explanation


    Indices: 908--955  Score: 60
    Period size: 22  Copynumber: 2.2  Consensus size: 21

        898 GTTTAAACTA

                       *   *     
        908 TTTTTAGACATTTTGTTTATG
          1 TTTTTAGACATCTTGATTATG

                               *  
        929 TTTTTAGACATCCTTGATTCTG
          1 TTTTTAGACAT-CTTGATTATG

                 
        951 TTTTT
          1 TTTTT

        956 CTGTTTCCAT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  21   11  0.48
  22   12  0.52

ACGTcount: A:0.17, C:0.10, G:0.12, T:0.60


Consensus pattern (21 bp):   
TTTTTAGACATCTTGATTATG

Found at i:1153 original size:18 final size:18

Alignment explanation


    Indices: 1130--1172  Score: 86
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       1120 GGGAGGAGGT

                              
       1130 TGCTGCACCACCTCCACC
          1 TGCTGCACCACCTCCACC

                              
       1148 TGCTGCACCACCTCCACC
          1 TGCTGCACCACCTCCACC

                   
       1166 TGCTGCA
          1 TGCTGCA

       1173 GTTCAAAGTC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   25  1.00

ACGTcount: A:0.16, C:0.51, G:0.14, T:0.19


Consensus pattern (18 bp):   
TGCTGCACCACCTCCACC

Found at i:2213 original size:49 final size:50

Alignment explanation


    Indices: 2080--2226  Score: 199
    Period size: 49  Copynumber: 2.9  Consensus size: 50

       2070 GGAACTTTCC

                      *        *   *                           
       2080 CTAAATTGAAAAC-TAAAACCTGGTGGGAACTTTCCCAATTTGCAAAAGAG
          1 CTAAATTGAATACTTAAAAACTGATGGGAACTTTCCCAATTTG-AAAAGAG

                            *                     *           *
       2130 CTAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCGATTTGAAAA-AT
          1 CTAAATTGAATAC-TTAAAAACTGATGGGAACTTTCCCAATTTGAAAAGAG

            *                                              
       2180 TTAAATTGAATACTTAAAAACTGATGGGAACTTTCCCAATTTGAAAA
          1 CTAAATTGAATACTTAAAAACTGATGGGAACTTTCCCAATTTGAAAA

       2227 CTTAAACCTG


Statistics
Matches: 86,  Mismatches: 9, Indels: 5
        0.86            0.09        0.05

Matches are distributed among these distances:
  49   32  0.37
  50   25  0.29
  51    4  0.05
  52   25  0.29

ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29


Consensus pattern (50 bp):   
CTAAATTGAATACTTAAAAACTGATGGGAACTTTCCCAATTTGAAAAGAG

Found at i:6180 original size:66 final size:66

Alignment explanation


    Indices: 6030--6225  Score: 308
    Period size: 66  Copynumber: 3.0  Consensus size: 66

       6020 CCGCATTAAC

                         *              *                            *      *
       6030 TTGATTCACCGAACCATCCTGAACTGTTCGAAAATGTGCTGCACCGAGCT--CCGAATTCCAATT
          1 TTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAAATCCAATC

             
       6093 T
         66 T

                                                    ***                      
       6094 TTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGCTATGCCGAGCTCACCGAAATCCAATC
          1 TTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAAATCCAATC

             
       6159 T
         66 T

                                                                             
       6160 TTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCG-AATCCAATC
          1 TTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAAATCCAATC

             
       6224 T
         66 T

             
       6225 T
          1 T

       6226 GAAGATGTAA


Statistics
Matches: 120,  Mismatches: 10, Indels: 3
        0.90            0.08        0.02

Matches are distributed among these distances:
  64   45  0.38
  65   11  0.09
  66   64  0.53

ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29


Consensus pattern (66 bp):   
TTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAAATCCAATC
T
Done.