Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010622.1 Corchorus olitorius cultivar O-4 contig10654, 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: 3005
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31


Found at i:71 original size:33 final size:32

Alignment explanation


    Indices: 1--142  Score: 135
    Period size: 33  Copynumber: 4.3  Consensus size: 32

                                     ** *    *
          1 AAAACAGATTT-GTTTTCATCACAATTAGCATCC
          1 AAAACAGATTTAG-TTTCATCACAAACAACA-CT

                                              
         34 AAAACAGAATTT-GTTTCATCACAAACAACACCT
          1 AAAACAG-ATTTAGTTTCATCACAAACAACA-CT

                          *                 
         67 AAAACAGATTTAGTGTCATCACAAACAACACT
          1 AAAACAGATTTAGTTTCATCACAAACAACACT

                **  *      *       *         
         99 CAAATTAGGTTTAGTATCATCACTAACAACACT
          1 -AAAACAGATTTAGTTTCATCACAAACAACACT

                       
        132 AAAACAGATTT
          1 AAAACAGATTT

        143 CATGTCATTG


Statistics
Matches: 92,  Mismatches: 14, Indels: 7
        0.81            0.12        0.06

Matches are distributed among these distances:
  32   14  0.15
  33   73  0.79
  34    5  0.05

ACGTcount: A:0.43, C:0.21, G:0.08, T:0.27


Consensus pattern (32 bp):   
AAAACAGATTTAGTTTCATCACAAACAACACT

Found at i:157 original size:65 final size:66

Alignment explanation


    Indices: 49--174  Score: 193
    Period size: 65  Copynumber: 1.9  Consensus size: 66

         39 AGAATTTGTT

                                                                   *         
         49 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGGTTTAGT
          1 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATCAGGTTTAGT

             
        114 A
         66 A

                   *                              **                      
        115 TCATCACTAACAACA-CTAAAACAGATTTCA-TGTCATTGCAAACAACACTCAAATCAGGTT
          1 TCATCACAAACAACACCTAAAACAGATTT-AGTGTCATCACAAACAACACTCAAATCAGGTT

        175 CAGAATTACT


Statistics
Matches: 55,  Mismatches: 4, Indels: 3
        0.89            0.06        0.05

Matches are distributed among these distances:
  65   40  0.73
  66   15  0.27

ACGTcount: A:0.43, C:0.24, G:0.09, T:0.25


Consensus pattern (66 bp):   
TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATCAGGTTTAGT
A

Found at i:163 original size:32 final size:32

Alignment explanation


    Indices: 34--163  Score: 138
    Period size: 33  Copynumber: 4.0  Consensus size: 32

         24 ATTAGCATCC

                           *                  
         34 AAAACAGAATTT-GTTTCATCACAAACAACACCT
          1 AAAACAG-ATTTAGTGTCATCACAAACAACA-CT

                                            
         67 AAAACAGATTTAGTGTCATCACAAACAACACT
          1 AAAACAGATTTAGTGTCATCACAAACAACACT

                **  *      *       *         
         99 CAAATTAGGTTTAGTATCATCACTAACAACACT
          1 -AAAACAGATTTAGTGTCATCACAAACAACACT

                                **           
        132 AAAACAGATTTCA-TGTCATTGCAAACAACACT
          1 AAAACAGATTT-AGTGTCATCACAAACAACACT

        164 CAAATCAGGT


Statistics
Matches: 81,  Mismatches: 13, Indels: 7
        0.80            0.13        0.07

Matches are distributed among these distances:
  32   29  0.36
  33   52  0.64

ACGTcount: A:0.44, C:0.22, G:0.08, T:0.25


Consensus pattern (32 bp):   
AAAACAGATTTAGTGTCATCACAAACAACACT

Found at i:1754 original size:25 final size:24

Alignment explanation


    Indices: 1717--1763  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       1707 TTAGAAAATT

                                      
       1717 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       1743 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       1764 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:2687 original size:21 final size:21

Alignment explanation


    Indices: 2632--2693  Score: 106
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       2622 CTTAGGCAAT

                         *       
       2632 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       2653 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                           *    
       2674 TCCAATGAGCTTGGAGCCTT
          1 TCCAATGAGCTTGGAACCTT

       2694 GTTTGGGTTG


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   39  1.00

ACGTcount: A:0.24, C:0.27, G:0.19, T:0.29


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC
Done.