Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010214.1 Corchorus olitorius cultivar O-4 contig10246, 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: 5573
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:932 original size:31 final size:31

Alignment explanation


    Indices: 894--993  Score: 109
    Period size: 31  Copynumber: 3.3  Consensus size: 31

        884 AAAGGCTAAT

                                           
        894 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
          1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA

                          **           *  **
        925 TGCTCAAATAAGGGTTTAATC-TTT--TAATT
          1 TGCTCAAATAAGGGCCTAA-CGTTTGCCAAAA

                                            
        954 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
          1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA

                     
        985 TGCTCAAAT
          1 TGCTCAAAT

        994 TTGGGTCCGA


Statistics
Matches: 53,  Mismatches: 10, Indels: 12
        0.71            0.13        0.16

Matches are distributed among these distances:
  28    1  0.02
  29   19  0.36
  30    4  0.08
  31   28  0.53
  32    1  0.02

ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29


Consensus pattern (31 bp):   
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA

Found at i:965 original size:60 final size:60

Alignment explanation


    Indices: 898--1025  Score: 202
    Period size: 60  Copynumber: 2.1  Consensus size: 60

        888 GCTAATTGCT

                                                      **                
        898 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTTTAATCTTTTAATTTGGC
          1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGC

                                                **      *               
        958 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATTTGGGTCCGATCTTTTAATTTGGC
          1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGC

            *       
       1018 TAAATAAG
          1 CAAATAAG

       1026 AGCGTTATCG


Statistics
Matches: 62,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  60   62  1.00

ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Consensus pattern (60 bp):   
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGC

Found at i:1170 original size:60 final size:60

Alignment explanation


    Indices: 1095--1262  Score: 187
    Period size: 60  Copynumber: 2.8  Consensus size: 60

       1085 ACGCCAGGCC

                              *                    *                    
       1095 CTTATTTGAGCATTTTCGTTAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGATT
          1 CTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCAGATT

                      *            *      *                       **  **
       1155 CTTATTTGAGTATTTTCGATAACGTTAGGCTCTTATTTGACCAAATTAAAAGATTGGACC
          1 CTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCAGATT

                     *      *       *     *          *        
       1215 CTTATTTGAACATTTTGGCA-AACGTTAGGTCCTTATTTGAGC-AATTAA
          1 CTTATTTGAGCATTTTCG-ATAACATTAGGCCCTTATTTGACCAAATTAA

       1263 CCAAATATGA


Statistics
Matches: 92,  Mismatches: 15, Indels: 3
        0.84            0.14        0.03

Matches are distributed among these distances:
  59    6  0.07
  60   85  0.92
  61    1  0.01

ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39


Consensus pattern (60 bp):   
CTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCAGATT

Found at i:1408 original size:15 final size:16

Alignment explanation


    Indices: 1389--1425  Score: 58
    Period size: 15  Copynumber: 2.4  Consensus size: 16

       1379 TATAAATAAT

                            
       1389 AATATTATAAT-TAAA
          1 AATATTATAATCTAAA

            *               
       1404 TATATTATAATCTAAA
          1 AATATTATAATCTAAA

                  
       1420 AATATT
          1 AATATT

       1426 TATTAGAAGT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  15   10  0.53
  16    9  0.47

ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43


Consensus pattern (16 bp):   
AATATTATAATCTAAA

Done.