Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010276.1 Corchorus olitorius cultivar O-4 contig10308, 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: 1848
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:776 original size:42 final size:43

Alignment explanation


    Indices: 729--811  Score: 125
    Period size: 42  Copynumber: 2.0  Consensus size: 43

        719 CGTGTTTGAC

                                          *             
        729 TTATCGTGTCTCGTGT-CTGAATCGTGTC-GGACACGATTAAGA
          1 TTATCGTGTCTCGTGTCCT-AATCGTGTCAAGACACGATTAAGA

                     *                               
        771 TTATCGTGTTTCGTGTCCTAATCGTGTCAAGACACGATTAA
          1 TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAA

        812 CACGTTTAAG


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  42   24  0.65
  43   13  0.35

ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35


Consensus pattern (43 bp):   
TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAAGA

Found at i:824 original size:20 final size:21

Alignment explanation


    Indices: 799--841  Score: 61
    Period size: 20  Copynumber: 2.1  Consensus size: 21

        789 TAATCGTGTC

                     *           
        799 AAGACACGATTAACACG-TTT
          1 AAGACACGAGTAACACGCTTT

                       *         
        819 AAGACACGAGTGACACGCTTT
          1 AAGACACGAGTAACACGCTTT

              
        840 AA
          1 AA

        842 TTAACGGGTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20   15  0.75
  21    5  0.25

ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21


Consensus pattern (21 bp):   
AAGACACGAGTAACACGCTTT

Found at i:1325 original size:12 final size:12

Alignment explanation


    Indices: 1308--1339  Score: 55
    Period size: 12  Copynumber: 2.7  Consensus size: 12

       1298 TACCCTATGT

                        
       1308 AAACACGACACG
          1 AAACACGACACG

                        
       1320 AAACACGACACG
          1 AAACACGACACG

            *       
       1332 GAACACGA
          1 AAACACGA

       1340 ATTGCCAGGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.50, C:0.31, G:0.19, T:0.00


Consensus pattern (12 bp):   
AAACACGACACG
Done.