Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000122.1 Corchorus olitorius cultivar O-4 contig00122, 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, 734

Length: 1224
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31


Found at i:1132 original size:46 final size:46

Alignment explanation


    Indices: 1082--1224  Score: 252
    Period size: 46  Copynumber: 3.1  Consensus size: 46

       1072 TGCAACGTCA

                                                          
       1082 CCCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTTT
          1 CCCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTTT

                                                          
       1128 CCCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAA-TTT
          1 CCCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTTT

                     *                                     
       1173 CTCCATCCTTATGGTATAAATTTCTTCACACCATCAGGACCAATTTT
          1 C-CCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTTT

            *    
       1220 GCCAT
          1 CCCAT


Statistics
Matches: 93,  Mismatches: 2, Indels: 4
        0.94            0.02        0.04

Matches are distributed among these distances:
  45    4  0.04
  46   86  0.92
  47    3  0.03

ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33


Consensus pattern (46 bp):   
CCCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTTT

Found at i:1171 original size:23 final size:23

Alignment explanation


    Indices: 1099--1218  Score: 81
    Period size: 23  Copynumber: 5.2  Consensus size: 23

       1089 TGATGGTATA

                                   
       1099 AATTTCTTCACACCATCAGGACC
          1 AATTTCTTCACACCATCAGGACC

                     *       *      **
       1122 AA-TT-TTCCCATCC-TGATGGTATA
          1 AATTTCTTCACA-CCATCA-GG-ACC

                                   
       1145 AATTTCTTCACACCATCAGGACC
          1 AATTTCTTCACACCATCAGGACC

                             *      **
       1168 AATTTC-TC-CATCC-TTATGGTATA
          1 AATTTCTTCACA-CCATCA-GG-ACC

                                   
       1191 AATTTCTTCACACCATCAGGACC
          1 AATTTCTTCACACCATCAGGACC

                 
       1214 AATTT
          1 AATTT

       1219 TGCCAT


Statistics
Matches: 71,  Mismatches: 14, Indels: 24
        0.65            0.13        0.22

Matches are distributed among these distances:
  21   11  0.15
  22   12  0.17
  23   25  0.35
  24   12  0.17
  25   11  0.15

ACGTcount: A:0.29, C:0.28, G:0.09, T:0.33


Consensus pattern (23 bp):   
AATTTCTTCACACCATCAGGACC
Done.