Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000089.1 Corchorus olitorius cultivar O-4 contig00089, 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, 805

Length: 1343
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28


Found at i:529 original size:14 final size:14

Alignment explanation


    Indices: 510--572  Score: 56
    Period size: 14  Copynumber: 4.4  Consensus size: 14

        500 TGAAGCGAAG

                          
        510 CCCTAAAACGAAAC
          1 CCCTAAAACGAAAC

                    *  *     
        524 CCCTAAATCCAAAAACC
          1 CCCTAAA-AC-GAAA-C

                   *     *
        541 CCCTAAATCG-AAG
          1 CCCTAAAACGAAAC

                          
        554 CCCTAAAACGAAAC
          1 CCCTAAAACGAAAC

                 
        568 CCCTA
          1 CCCTA

        573 CCCCCAAATC


Statistics
Matches: 38,  Mismatches: 7, Indels: 8
        0.72            0.13        0.15

Matches are distributed among these distances:
  13    9  0.24
  14   16  0.42
  15    1  0.03
  16    4  0.11
  17    8  0.21

ACGTcount: A:0.44, C:0.38, G:0.06, T:0.11


Consensus pattern (14 bp):   
CCCTAAAACGAAAC

Found at i:1122 original size:29 final size:31

Alignment explanation


    Indices: 1090--1156  Score: 111
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       1080 ATGCAATTTG

                                           
       1090 GGATATAACGTTAC-AAAA-CAAGCAATTAA
          1 GGATATAACGTTACGAAAAGCAAGCAATTAA

                                 *         
       1119 GGATATAACGTTACGAAAAGCGAGCAATTAA
          1 GGATATAACGTTACGAAAAGCAAGCAATTAA

                   
       1150 GGATATA
          1 GGATATA

       1157 GTCCGTTAAA


Statistics
Matches: 35,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  29   14  0.40
  30    4  0.11
  31   17  0.49

ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21


Consensus pattern (31 bp):   
GGATATAACGTTACGAAAAGCAAGCAATTAA

Found at i:1334 original size:31 final size:31

Alignment explanation


    Indices: 1276--1343  Score: 100
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       1266 CTAACTAATT

                                 **        
       1276 ATATCCTTAATTGCTTGAAATCGAAAACCTC
          1 ATATCCTTAATTGCTTGAAATAAAAAACCTC

                                        * *
       1307 ATATCCTTAATTGCTTGAAATAAAAAACGTT
          1 ATATCCTTAATTGCTTGAAATAAAAAACCTC

                  
       1338 ATATCC
          1 ATATCC


Statistics
Matches: 33,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  31   33  1.00

ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34


Consensus pattern (31 bp):   
ATATCCTTAATTGCTTGAAATAAAAAACCTC
Done.