Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001028.1 Corchorus olitorius cultivar O-4 contig01028, 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, 820

Length: 1367
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40


Found at i:784 original size:21 final size:21

Alignment explanation


    Indices: 760--822  Score: 90
    Period size: 21  Copynumber: 2.9  Consensus size: 21

        750 ATTGGGGTAT

                                 
        760 TATTTGCATGGTTTTTTGGTC
          1 TATTTGCATGGTTTTTTGGTC

                                 
        781 TATTTGCATGGTTTTTTGGTC
          1 TATTTGCATGGTTTTTTGGTC

             *                   
        802 TTTTTGCCATCGGCTTTTTTG
          1 TATTTG-CAT-GG-TTTTTTG

        823 TTATTTCGTT


Statistics
Matches: 38,  Mismatches: 1, Indels: 3
        0.90            0.02        0.07

Matches are distributed among these distances:
  21   26  0.68
  22    3  0.08
  23    2  0.05
  24    7  0.18

ACGTcount: A:0.08, C:0.13, G:0.22, T:0.57


Consensus pattern (21 bp):   
TATTTGCATGGTTTTTTGGTC

Found at i:1106 original size:25 final size:25

Alignment explanation


    Indices: 1078--1163  Score: 77
    Period size: 25  Copynumber: 3.4  Consensus size: 25

       1068 TTAGGGTTTG

                                     
       1078 TCATGTCATGGTTAGGGTTTAGATT
          1 TCATGTCATGGTTAGGGTTTAGATT

                        * ***   *     
       1103 TCATGTCAT-GTCATTTTTTTG-TCT
          1 TCATGTCATGGTTAGGGTTTAGAT-T

             *                         
       1127 CCCTATGTCATGGTTAGGGTTTAGATT
          1 -TC-ATGTCATGGTTAGGGTTTAGATT

                      
       1154 TCATGTCATG
          1 TCATGTCATG

       1164 TCATTTTTTT


Statistics
Matches: 44,  Mismatches: 12, Indels: 10
        0.67            0.18        0.15

Matches are distributed among these distances:
  23    1  0.02
  24    8  0.18
  25   18  0.41
  26    8  0.18
  27    8  0.18
  28    1  0.02

ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47


Consensus pattern (25 bp):   
TCATGTCATGGTTAGGGTTTAGATT

Found at i:1110 original size:30 final size:30

Alignment explanation


    Indices: 1076--1167  Score: 85
    Period size: 30  Copynumber: 3.4  Consensus size: 30

       1066 ACTTAGGGTT

                                          
       1076 TGTCATGTCATGGTTAGGGTTTAGATTTCA
          1 TGTCATGTCATGGTTAGGGTTTAGATTTCA

                                  *   *   
       1106 TGTCATGTCAT--TT----TTTTG-TCTC-
          1 TGTCATGTCATGGTTAGGGTTTAGATTTCA

            **                            
       1128 CCT-ATGTCATGGTTAGGGTTTAGATTTCA
          1 TGTCATGTCATGGTTAGGGTTTAGATTTCA

                       
       1157 TGTCATGTCAT
          1 TGTCATGTCAT

       1168 TTTTTTGTCT


Statistics
Matches: 45,  Mismatches: 8, Indels: 18
        0.63            0.11        0.25

Matches are distributed among these distances:
  21    7  0.16
  22    1  0.02
  23    5  0.11
  24    4  0.09
  27    4  0.09
  28    5  0.11
  29    1  0.02
  30   18  0.40

ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47


Consensus pattern (30 bp):   
TGTCATGTCATGGTTAGGGTTTAGATTTCA

Found at i:1145 original size:51 final size:51

Alignment explanation


    Indices: 1080--1181  Score: 204
    Period size: 51  Copynumber: 2.0  Consensus size: 51

       1070 AGGGTTTGTC

                                                               
       1080 ATGTCATGGTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTGTCTCCCT
          1 ATGTCATGGTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTGTCTCCCT

                                                               
       1131 ATGTCATGGTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTGTCTCCCT
          1 ATGTCATGGTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTGTCTCCCT

       1182 TAATATTTAT


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  51   51  1.00

ACGTcount: A:0.16, C:0.16, G:0.20, T:0.49


Consensus pattern (51 bp):   
ATGTCATGGTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTGTCTCCCT
Done.