Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016100.1 Corchorus olitorius cultivar O-4 contig16133, 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: 5369
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37


Found at i:435 original size:39 final size:40

Alignment explanation


    Indices: 379--459  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        369 TTTAATTCCT

                                                    
        379 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

                     *          *                   
        419 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

              
        458 AT
          1 AT

        460 TCTTAGGTAT


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

Found at i:795 original size:191 final size:194

Alignment explanation


    Indices: 571--967  Score: 667
    Period size: 202  Copynumber: 2.0  Consensus size: 194

        561 TTCCTTAATA

                                                                             
        571 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
          1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA

                         *                            *           *          
        636 ATTTAATAAATCATCCAC-T-A-A-TTTTTTTTGGTATAGTTCTATATATAATAGTAATGTGTTG
         66 ATTTAATAAATCAACCACTTCACACTTTTTTTTGGTATAGTTATATATATAATAATAATGTGTTG

                                                                            
        697 TATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTG
        131 TATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTG

                                                                             
        761 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
          1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT

                                                                             
        826 AATTTAATAAATCAACCACTAATGTTCAGCTACTTTTTTTTGGTATAGTTATATATATAATAATA
         65 AATTTAATAAATCAACCAC-----TTCA-C-ACTTTTTTTTGGTATAGTTATATATATAATAATA

                                                                             
        891 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
        123 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC

                   
        956 ACCATTG
        188 ACCATTG

                 
        963 ATAAA
          1 ATAAA

        968 GTTATTAAGC


Statistics
Matches: 192,  Mismatches: 3, Indels: 12
        0.93            0.01        0.06

Matches are distributed among these distances:
 190   16  0.08
 191   66  0.34
 197    1  0.01
 198    1  0.01
 201    1  0.01
 202  107  0.56

ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44


Consensus pattern (194 bp):   
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTTCACACTTTTTTTTGGTATAGTTATATATATAATAATAATGTGTTG
TATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTG

Found at i:1526 original size:36 final size:36

Alignment explanation


    Indices: 1479--1548  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1469 GAGATTTTGG

                         *      *               
       1479 AGAAATATGATAATCAAAATTACAAAAAATGTAACA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAACA

                                       *      
       1515 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

       1549 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAACA

Found at i:4358 original size:16 final size:16

Alignment explanation


    Indices: 4337--4369  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       4327 TACACATGTG

                            
       4337 TGGAATATATTATTTA
          1 TGGAATATATTATTTA

                            
       4353 TGGAATATATTATTTA
          1 TGGAATATATTATTTA

             
       4369 T
          1 T

       4370 CAATTATTAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52


Consensus pattern (16 bp):   
TGGAATATATTATTTA

Found at i:4414 original size:25 final size:25

Alignment explanation


    Indices: 4386--4437  Score: 104
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       4376 TTAACTGCAC

                                     
       4386 GTGCTTTAACTAGTATATATATATT
          1 GTGCTTTAACTAGTATATATATATT

                                     
       4411 GTGCTTTAACTAGTATATATATATT
          1 GTGCTTTAACTAGTATATATATATT

              
       4436 GT
          1 GT

       4438 TAGGATTCAT


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

Matches are distributed among these distances:
  25   27  1.00

ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48


Consensus pattern (25 bp):   
GTGCTTTAACTAGTATATATATATT
Done.