Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013329.1 Corchorus olitorius cultivar O-4 contig13362, 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: 3532
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34


Found at i:1379 original size:13 final size:12

Alignment explanation


    Indices: 1361--1405  Score: 54
    Period size: 14  Copynumber: 3.5  Consensus size: 12

       1351 ATTTTATTAC

                         
       1361 TGTTTTATCAAAT
          1 TGTTTTAT-AAAT

                        
       1374 TGTTTTATAAAT
          1 TGTTTTATAAAT

            *             
       1386 GGTTTTAAATAAAT
          1 TGTTTT--ATAAAT

                  
       1400 TGTTTT
          1 TGTTTT

       1406 GGGTGCATGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  12    9  0.32
  13    8  0.29
  14   11  0.39

ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56


Consensus pattern (12 bp):   
TGTTTTATAAAT

Found at i:2456 original size:22 final size:22

Alignment explanation


    Indices: 2428--2469  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       2418 CGTGACAATC

                       *   *      
       2428 AAAGTGCAAAAGCTATATGATT
          1 AAAGTGCAAAAACTAAATGATT

                                
       2450 AAAGTGCAAAAACTAAATGA
          1 AAAGTGCAAAAACTAAATGA

       2470 AGCTAAATCA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.52, C:0.10, G:0.17, T:0.21


Consensus pattern (22 bp):   
AAAGTGCAAAAACTAAATGATT

Found at i:2623 original size:27 final size:29

Alignment explanation


    Indices: 2592--2668  Score: 104
    Period size: 29  Copynumber: 2.7  Consensus size: 29

       2582 GCGTGGCCTT

                                         
       2592 AAAATGACCAAAATGCCCCT-GA-ATATG
          1 AAAATGACCAAAATGCCCCTAGATATATG

            *       *               * *  
       2619 CAAATGACTAAAATGCCCCTAGATTTTTG
          1 AAAATGACCAAAATGCCCCTAGATATATG

                                 
       2648 AAAATGACCAAAATGCCCCTA
          1 AAAATGACCAAAATGCCCCTA

       2669 CGTGATCCTA


Statistics
Matches: 42,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  27   18  0.43
  28    2  0.05
  29   22  0.52

ACGTcount: A:0.42, C:0.23, G:0.13, T:0.22


Consensus pattern (29 bp):   
AAAATGACCAAAATGCCCCTAGATATATG

Found at i:3332 original size:82 final size:84

Alignment explanation


    Indices: 3195--3351  Score: 239
    Period size: 82  Copynumber: 1.9  Consensus size: 84

       3185 AAATATATAT

                                                       *                     
       3195 TTAAAAAATTATAATATATCTAAGTTTTGCAATTAAAATAGTTTAATGGTAAAAATAAAATAGTT
          1 TTAAAAAATTATAATATATCTAAGTTTTGCAATTAAAATAGTTAAATGGTAAAAATAAAATAGTT

                 *             
       3260 ATAAAGAGATTAGATTTAA
         66 ATAAAAAGATTAGATTTAA

                      *                 **                                   
       3279 TTAAAAAATTCTAATATATC-AA-TTTTTTAATTAAAATAG-TAAACTGGTAAAAATAAAATAGT
          1 TTAAAAAATTATAATATATCTAAGTTTTGCAATTAAAATAGTTAAA-TGGTAAAAATAAAATAGT

                       
       3341 TATAAAAAGAT
         65 TATAAAAAGAT

       3352 CAAAAAGTGT


Statistics
Matches: 67,  Mismatches: 5, Indels: 4
        0.88            0.07        0.05

Matches are distributed among these distances:
  81    3  0.04
  82   43  0.64
  83    2  0.03
  84   19  0.28

ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36


Consensus pattern (84 bp):   
TTAAAAAATTATAATATATCTAAGTTTTGCAATTAAAATAGTTAAATGGTAAAAATAAAATAGTT
ATAAAAAGATTAGATTTAA
Done.