Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012900.1 Corchorus olitorius cultivar O-4 contig12933, 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: 6847
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:1041 original size:30 final size:30

Alignment explanation


    Indices: 1007--1064  Score: 82
    Period size: 30  Copynumber: 1.9  Consensus size: 30

        997 GTGTCGTCGA

                             *             
       1007 TTTCGGTGCCATC-AGTTTTGGTGCCATCAT
          1 TTTCGGTGCCATCGA-TGTTGGTGCCATCAT

                      *                 
       1037 TTTCGGTGCCGTCGATGTTGGTGCCATC
          1 TTTCGGTGCCATCGATGTTGGTGCCATC

       1065 GATGCTGGTG


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  30   24  0.96
  31    1  0.04

ACGTcount: A:0.10, C:0.24, G:0.28, T:0.38


Consensus pattern (30 bp):   
TTTCGGTGCCATCGATGTTGGTGCCATCAT

Found at i:1050 original size:45 final size:45

Alignment explanation


    Indices: 982--1084  Score: 122
    Period size: 45  Copynumber: 2.3  Consensus size: 45

        972 AACACTTTCA

                              *                        **  
        982 GTGCCATCATCTTTAGTGTCGTCGAT-TTCGGTGCCATC-AGTTTTG
          1 GTGCCATCATCTTTAGTGCCGTCGATGTT-GGTGCCATCGA-TGCTG

                           *                              
       1027 GTGCCATCAT-TTTCGGTGCCGTCGATGTTGGTGCCATCGATGCTG
          1 GTGCCATCATCTTT-AGTGCCGTCGATGTTGGTGCCATCGATGCTG

                         
       1072 GTGCCATCATCTT
          1 GTGCCATCATCTT

       1085 CTTCCATGAC


Statistics
Matches: 50,  Mismatches: 4, Indels: 7
        0.82            0.07        0.11

Matches are distributed among these distances:
  44    3  0.06
  45   42  0.84
  46    5  0.10

ACGTcount: A:0.13, C:0.24, G:0.26, T:0.37


Consensus pattern (45 bp):   
GTGCCATCATCTTTAGTGCCGTCGATGTTGGTGCCATCGATGCTG

Found at i:1066 original size:15 final size:14

Alignment explanation


    Indices: 1011--1081  Score: 70
    Period size: 15  Copynumber: 4.8  Consensus size: 14

       1001 CGTCGATTTC

                        *  
       1011 GGTGCCATCAGTTTT
          1 GGTGCCATCA-TGTT

                       *  
       1026 GGTGCCATCATTTT
          1 GGTGCCATCATGTT

                   *        
       1040 CGGTGCCGTCGATGTT
          1 -GGTGCCATC-ATGTT

                         * 
       1056 GGTGCCATCGATGCT
          1 GGTGCCATC-ATGTT

                       
       1071 GGTGCCATCAT
          1 GGTGCCATCAT

       1082 CTTCTTCCAT


Statistics
Matches: 50,  Mismatches: 4, Indels: 5
        0.85            0.07        0.08

Matches are distributed among these distances:
  14    6  0.12
  15   40  0.80
  16    4  0.08

ACGTcount: A:0.13, C:0.24, G:0.30, T:0.34


Consensus pattern (14 bp):   
GGTGCCATCATGTT

Found at i:2328 original size:18 final size:18

Alignment explanation


    Indices: 2305--2374  Score: 104
    Period size: 18  Copynumber: 3.9  Consensus size: 18

       2295 AAGTGTGGCA

                              
       2305 ACTTGGTGCGGTGCGACC
          1 ACTTGGTGCGGTGCGACC

                    *         
       2323 ACTTGGTGTGGTGCGACC
          1 ACTTGGTGCGGTGCGACC

             *              **
       2341 ATTTGGTGCGGTGCGAAT
          1 ACTTGGTGCGGTGCGACC

                            
       2359 ACTTGGTGCGGTGCGA
          1 ACTTGGTGCGGTGCGA

       2375 TTTGTTGTTG


Statistics
Matches: 46,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   46  1.00

ACGTcount: A:0.13, C:0.20, G:0.40, T:0.27


Consensus pattern (18 bp):   
ACTTGGTGCGGTGCGACC

Found at i:3023 original size:50 final size:48

Alignment explanation


    Indices: 2910--3050  Score: 135
    Period size: 50  Copynumber: 2.9  Consensus size: 48

       2900 CGTGCCAATC

                      *         *             *    *      *   
       2910 AATTTTGTC-AAAAAATTGATAAAAAGTGC-GATGAAAATTAAAAGATC-
          1 AATTTTGTCGTAAAAATTGAGAAAAAGTGCAG-TAAAAAAT-AAAGTTCA

                     *                                        
       2957 AATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAAATAAAGTTCA
          1 AATTTTGTCGTAAAAATTGAGAAAAAG-TGC-AGTAAAAAATAAAGTTCA

                    *          *             *    *     
       3007 AATTTTGTGGTAAAAATTGTGAAAAAGTGCAGTGAAAAGTAAAG
          1 AATTTTGTCGTAAAAATTGAGAAAAAGTGCAGTAAAAAATAAAG

       3051 GATTGCTTTA


Statistics
Matches: 79,  Mismatches: 10, Indels: 9
        0.81            0.10        0.09

Matches are distributed among these distances:
  47    9  0.11
  48   27  0.34
  49   12  0.15
  50   30  0.38
  51    1  0.01

ACGTcount: A:0.50, C:0.05, G:0.18, T:0.28


Consensus pattern (48 bp):   
AATTTTGTCGTAAAAATTGAGAAAAAGTGCAGTAAAAAATAAAGTTCA
Done.