Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020200.1 Corchorus olitorius cultivar O-4 contig20233, 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: 4130
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39


Found at i:718 original size:2 final size:2

Alignment explanation


    Indices: 711--760  Score: 73
    Period size: 2  Copynumber: 24.5  Consensus size: 2

        701 GAAGAATTTG

                                             *                    *       
        711 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT CT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                       
        753 ACT AT AT A
          1 A-T AT AT A

        761 AGTTTAAACT


Statistics
Matches: 43,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
   2   41  0.95
   3    2  0.05

ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:948 original size:21 final size:19

Alignment explanation


    Indices: 902--953  Score: 59
    Period size: 21  Copynumber: 2.6  Consensus size: 19

        892 AAATAATAAC

                   *           
        902 AATTATTTTTACATTAAAA
          1 AATTATTATTACATTAAAA

                               *  
        921 AACTTATTATTACAATTATTAA
          1 AA-TTATTATTAC-ATTA-AAA

                       
        943 AATTATTATTA
          1 AATTATTATTA

        954 GTTATATATA


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  19    2  0.07
  20    9  0.32
  21   13  0.46
  22    4  0.14

ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48


Consensus pattern (19 bp):   
AATTATTATTACATTAAAA

Found at i:1132 original size:116 final size:113

Alignment explanation


    Indices: 994--1220  Score: 357
    Period size: 116  Copynumber: 2.0  Consensus size: 113

        984 TTTTTGAGGA

                                                                 *           
        994 ATTAATCATTACGTTTTTCTTTCCATATTACAAAAGTCTT-AAATAATACTAATAATTTTTTTAC
          1 ATTAATCATTACGTTTTTCTTTCCATATTACAAAAGT-TTAAAATAATACTAACAA-TTTTTTAC

                                                                
       1058 GTTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATATATATC
         64 GTTAAACAACTTATTATTATAATTATTAAAATTATTATTA-TTAT-TATATC

                *      *                                                     
       1110 ATTAGTCATTATGTTTTTCTTTCCATATTACAAAAGTTTAAAATAATACTAACAATTTTTTACGT
          1 ATTAATCATTACGTTTTTCTTTCCATATTACAAAAGTTTAAAATAATACTAACAATTTTTTACGT

                  *   *                 *                 
       1175 TAAACATCTTCTTATTATAATTATTAAACTTATTATTATTATTATA
         66 TAAACAACTTATTATTATAATTATTAAAATTATTATTATTATTATA

       1221 ACAATTATTA


Statistics
Matches: 104,  Mismatches: 6, Indels: 5
        0.90            0.05        0.04

Matches are distributed among these distances:
 113    4  0.04
 114    4  0.04
 115   47  0.45
 116   49  0.47

ACGTcount: A:0.38, C:0.11, G:0.04, T:0.48


Consensus pattern (113 bp):   
ATTAATCATTACGTTTTTCTTTCCATATTACAAAAGTTTAAAATAATACTAACAATTTTTTACGT
TAAACAACTTATTATTATAATTATTAAAATTATTATTATTATTATATC

Found at i:1212 original size:21 final size:21

Alignment explanation


    Indices: 1186--1233  Score: 62
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       1176 AAACATCTTC

                              *   
       1186 TTATTATAATTATTAA-ACTTA
          1 TTATTATAATTA-TAACAATTA

                   *             
       1207 TTATTATTATTATAACAATTA
          1 TTATTATAATTATAACAATTA

                  
       1228 TTATTA
          1 TTATTA

       1234 GTTATATGAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  20    3  0.12
  21   21  0.88

ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54


Consensus pattern (21 bp):   
TTATTATAATTATAACAATTA

Found at i:1227 original size:18 final size:19

Alignment explanation


    Indices: 1188--1239  Score: 63
    Period size: 18  Copynumber: 2.8  Consensus size: 19

       1178 ACATCTTCTT

                 *            *
       1188 ATTATAATTATTA-AACTT
          1 ATTATTATTATTATAACTA

                               
       1206 ATTATTATTATTATAAC-A
          1 ATTATTATTATTATAACTA

                            
       1224 ATTATTATTAGTTATA
          1 ATTATTATTA-TTATA

       1240 TGATCACTAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
  18   22  0.73
  19    8  0.27

ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52


Consensus pattern (19 bp):   
ATTATTATTATTATAACTA
Done.