Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017497.1 Corchorus olitorius cultivar O-4 contig17530, 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: 22319
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


Found at i:920 original size:128 final size:128

Alignment explanation


    Indices: 706--961  Score: 485
    Period size: 128  Copynumber: 2.0  Consensus size: 128

        696 TTTTGGATGA

                                                                             
        706 AAATTTTTGGCGGAAGTTGGTTATTAGTTGTAGCATACATTGATCAGTTTGGAATGTCTACAGCA
          1 AAATTTTTGGCGGAAGTTGGTTATTAGTTGTAGCATACATTGATCAGTTTGGAATGTCTACAGCA

                                             *                             
        771 ATGATTAAGGACCACTGATCGTAAATCCGGCAGTTGTGTACACAAATTATTTATTGGAGGATC
         66 ATGATTAAGGACCACTGATCGTAAATCCGGCAGCTGTGTACACAAATTATTTATTGGAGGATC

                      *                                                      
        834 AAATTTTTGGTGGAAGTTGGTTATTAGTTGTAGCATACATTGATCAGTTTGGAATGTCTACAGCA
          1 AAATTTTTGGCGGAAGTTGGTTATTAGTTGTAGCATACATTGATCAGTTTGGAATGTCTACAGCA

                                       *                                   
        899 ATGATTAAGGACCACTGATCGTAAATCTGGCAGCTGTGTACACAAATTATTTATTGGAGGATC
         66 ATGATTAAGGACCACTGATCGTAAATCCGGCAGCTGTGTACACAAATTATTTATTGGAGGATC

        962 CGTGGGGCTC


Statistics
Matches: 125,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 128  125  1.00

ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34


Consensus pattern (128 bp):   
AAATTTTTGGCGGAAGTTGGTTATTAGTTGTAGCATACATTGATCAGTTTGGAATGTCTACAGCA
ATGATTAAGGACCACTGATCGTAAATCCGGCAGCTGTGTACACAAATTATTTATTGGAGGATC

Found at i:1769 original size:36 final size:36

Alignment explanation


    Indices: 1722--1791  Score: 131
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1712 ACATGGAGAT

                                                
       1722 TTAGCCAATGTCTTGAGACATTGATGAAATAAATGA
          1 TTAGCCAATGTCTTGAGACATTGATGAAATAAATGA

                          *                   
       1758 TTAGCCAATGTCTTTAGACATTGATGAAATAAAT
          1 TTAGCCAATGTCTTGAGACATTGATGAAATAAAT

       1792 TGGAGAAAAT


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  36   33  1.00

ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33


Consensus pattern (36 bp):   
TTAGCCAATGTCTTGAGACATTGATGAAATAAATGA

Found at i:4924 original size:22 final size:22

Alignment explanation


    Indices: 4896--4944  Score: 98
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       4886 TATGAATACA

                                  
       4896 CAAATGTGTTGGAAGAGAAACT
          1 CAAATGTGTTGGAAGAGAAACT

                                  
       4918 CAAATGTGTTGGAAGAGAAACT
          1 CAAATGTGTTGGAAGAGAAACT

                 
       4940 CAAAT
          1 CAAAT

       4945 CTCTCGTATT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   27  1.00

ACGTcount: A:0.43, C:0.10, G:0.24, T:0.22


Consensus pattern (22 bp):   
CAAATGTGTTGGAAGAGAAACT

Found at i:7006 original size:27 final size:26

Alignment explanation


    Indices: 6943--7023  Score: 90
    Period size: 27  Copynumber: 3.0  Consensus size: 26

       6933 GTGGATGCCA

                    *         *        
       6943 CAGGAAAATCTGGAGAATCAATTACCG
          1 CAGGAAAAACTGGAG-ATGAATTACCG

                 *                     
       6970 CAGGAGAAACTGGAGATGAATTCACCG
          1 CAGGAAAAACTGGAGATGAATT-ACCG

                       **              
       6997 CAGGAAAAACTTAAGATGAACTTACCG
          1 CAGGAAAAACTGGAGATGAA-TTACCG

       7024 GTGGCTATAC


Statistics
Matches: 46,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  26    6  0.13
  27   38  0.83
  28    2  0.04

ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17


Consensus pattern (26 bp):   
CAGGAAAAACTGGAGATGAATTACCG

Found at i:12105 original size:21 final size:21

Alignment explanation


    Indices: 12057--12103  Score: 87
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      12047 CTCCTAGTTG

                                 
      12057 CTAGGGAAAGATGGGTATTTA
          1 CTAGGGAAAGATGGGTATTTA

                                 
      12078 CTAGGGAAAGATGGGTATTTA
          1 CTAGGGAAAGATGGGTATTTA

                  
      12099 -TAGGG
          1 CTAGGG

      12104 GATGCCTAGG


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  20    5  0.19
  21   21  0.81

ACGTcount: A:0.32, C:0.04, G:0.36, T:0.28


Consensus pattern (21 bp):   
CTAGGGAAAGATGGGTATTTA

Found at i:20982 original size:20 final size:20

Alignment explanation


    Indices: 20957--20995  Score: 78
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      20947 GTCTTTCCCT

                                
      20957 TTTCTAAACCCATCAAATTG
          1 TTTCTAAACCCATCAAATTG

                               
      20977 TTTCTAAACCCATCAAATT
          1 TTTCTAAACCCATCAAATT

      20996 TTTGTTGAGA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36


Consensus pattern (20 bp):   
TTTCTAAACCCATCAAATTG
Done.