Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015107.1 Corchorus olitorius cultivar O-4 contig15140, 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: 18113
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31


Found at i:467 original size:21 final size:21

Alignment explanation


    Indices: 412--482  Score: 108
    Period size: 21  Copynumber: 3.4  Consensus size: 21

        402 TTTAGGCAAT

                         *      *
        412 TCCAATGAGCTTGAAACCTTA
          1 TCCAATGAGCTTGGAACCTTC

                                 
        433 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
        454 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
        475 TCCAATGA
          1 TCCAATGA

        483 ACTCCTAGCA


Statistics
Matches: 47,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
  20    3  0.06
  21   44  0.94

ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:2358 original size:33 final size:31

Alignment explanation


    Indices: 2285--2389  Score: 102
    Period size: 33  Copynumber: 3.2  Consensus size: 31

       2275 GCTATGATCA

                     *                 ** * 
       2285 ACCAAAACAGATTTGTTTTCATCACAATTAGC
          1 ACCAAAACAAATTTG-TTTCATCACAAACAAC

                                             
       2317 ATCCAAAACAAAATTTGTTTCATCACAAACAAC
          1 A-CCAAAAC-AAATTTGTTTCATCACAAACAAC

                      *       *              
       2350 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
          1 ACC-AAAACAAATTT-GTTTCATCACAAACAAC

                   
       2383 ACTCAAA
          1 AC-CAAA

       2390 TTAGTTTTAG


Statistics
Matches: 62,  Mismatches: 6, Indels: 9
        0.81            0.08        0.12

Matches are distributed among these distances:
  32    8  0.13
  33   47  0.76
  34    7  0.11

ACGTcount: A:0.45, C:0.24, G:0.07, T:0.25


Consensus pattern (31 bp):   
ACCAAAACAAATTTGTTTCATCACAAACAAC

Found at i:2399 original size:33 final size:33

Alignment explanation


    Indices: 2336--2425  Score: 110
    Period size: 33  Copynumber: 2.7  Consensus size: 33

       2326 AAAATTTGTT

                                            *
       2336 TCATCACAAACAACACCTAAAACAGATTTAGTG
          1 TCATCACAAACAACACCTAAAACAGATTTAGTA

                                  **  *       
       2369 TCATCACAAACAACA-CTCAAATTAGTTTTAGTA
          1 TCATCACAAACAACACCT-AAAACAGATTTAGTA

                 *         *        
       2402 TCATCGCAAACAACATCTAAAACA
          1 TCATCACAAACAACACCTAAAACA

       2426 TTCTTTGCAA


Statistics
Matches: 48,  Mismatches: 7, Indels: 4
        0.81            0.12        0.07

Matches are distributed among these distances:
  32    2  0.04
  33   44  0.92
  34    2  0.04

ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23


Consensus pattern (33 bp):   
TCATCACAAACAACACCTAAAACAGATTTAGTA

Found at i:3927 original size:25 final size:24

Alignment explanation


    Indices: 3890--3936  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       3880 CTAGAAAATT

                                      
       3890 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       3916 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       3937 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:5423 original size:2 final size:2

Alignment explanation


    Indices: 5416--5446  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       5406 AGAATTTAAC

                                                          
       5416 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       5447 CACCAACAAG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.