Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009058.1 Corchorus olitorius cultivar O-4 contig09086, 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, 812

Length: 1354
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Found at i:812 original size:14 final size:15

Alignment explanation


    Indices: 782--814  Score: 50
    Period size: 16  Copynumber: 2.2  Consensus size: 15

        772 AGAAAAAATG

                            
        782 AAAAAAAAAACGTGTA
          1 AAAAAAAAAACG-GTA

                           
        798 AAAAAAAAAAC-GTA
          1 AAAAAAAAAACGGTA

               
        812 AAA
          1 AAA

        815 GTAAGTCCTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  14    6  0.35
  16   11  0.65

ACGTcount: A:0.76, C:0.06, G:0.09, T:0.09


Consensus pattern (15 bp):   
AAAAAAAAAACGGTA

Found at i:961 original size:23 final size:23

Alignment explanation


    Indices: 935--986  Score: 70
    Period size: 23  Copynumber: 2.3  Consensus size: 23

        925 ATTCAAAAGG

                                    
        935 TTCTTGACAGCTTAC-AATAAGTT
          1 TTCTT-ACAGCTTACTAATAAGTT

                  * *              
        958 TTCTTATATCTTACTAATAAGTT
          1 TTCTTACAGCTTACTAATAAGTT

                  
        981 TTCTTA
          1 TTCTTA

        987 TATATATGCT


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  22    7  0.27
  23   19  0.73

ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48


Consensus pattern (23 bp):   
TTCTTACAGCTTACTAATAAGTT

Found at i:971 original size:22 final size:23

Alignment explanation


    Indices: 945--989  Score: 83
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        935 TTCTTGACAG

                                   
        945 CTTAC-AATAAGTTTTCTTATAT
          1 CTTACTAATAAGTTTTCTTATAT

                                   
        967 CTTACTAATAAGTTTTCTTATAT
          1 CTTACTAATAAGTTTTCTTATAT

        990 ATATGCTGTC


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  22    5  0.23
  23   17  0.77

ACGTcount: A:0.31, C:0.13, G:0.04, T:0.51


Consensus pattern (23 bp):   
CTTACTAATAAGTTTTCTTATAT

Found at i:1086 original size:49 final size:49

Alignment explanation


    Indices: 1030--1127  Score: 196
    Period size: 49  Copynumber: 2.0  Consensus size: 49

       1020 CTTAGCCTTT

                                                             
       1030 TTTTATTCAATTCAATTAGATGTTAATGTAAATGAACCATAACTATGTA
          1 TTTTATTCAATTCAATTAGATGTTAATGTAAATGAACCATAACTATGTA

                                                             
       1079 TTTTATTCAATTCAATTAGATGTTAATGTAAATGAACCATAACTATGTA
          1 TTTTATTCAATTCAATTAGATGTTAATGTAAATGAACCATAACTATGTA

       1128 AACCTATTCC


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  49   49  1.00

ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41


Consensus pattern (49 bp):   
TTTTATTCAATTCAATTAGATGTTAATGTAAATGAACCATAACTATGTA
Done.