Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017156.1 Corchorus olitorius cultivar O-4 contig17189, 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: 3213
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38


Found at i:81 original size:18 final size:17

Alignment explanation


    Indices: 52--100  Score: 57
    Period size: 15  Copynumber: 2.9  Consensus size: 17

         42 GTAGTGATCA

                               
         52 TATAACTAATAATAATTGT
          1 TATAA-TAATAATAA-TGT

                             
         71 TATAATAATAATAA-GT
          1 TATAATAATAATAATGT

                     *     
         87 T-TAATAATTATAAT
          1 TATAATAATAATAAT

        101 AAGAAGATGT


Statistics
Matches: 28,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  15   11  0.39
  16    3  0.11
  18    9  0.32
  19    5  0.18

ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43


Consensus pattern (17 bp):   
TATAATAATAATAATGT

Found at i:670 original size:39 final size:40

Alignment explanation


    Indices: 614--694  Score: 121
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        604 TTTAATTCCT

                                                     
        614 ATGTAATATATATAATAACTAAAATACTTTA-ATTAATTAA
          1 ATGTAATATATATAATAACTAAAATAC-TTACATTAATTAA

                     *          *                   
        654 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

              
        693 AT
          1 AT

        695 TCTTAGGTAT


Statistics
Matches: 38,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  38    3  0.08
  39   27  0.71
  40    8  0.21

ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

Found at i:1049 original size:204 final size:201

Alignment explanation


    Indices: 811--1203  Score: 696
    Period size: 204  Copynumber: 1.9  Consensus size: 201

        801 TTAATAATAA

                   *                                                         
        811 ATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
          1 ATAAATCAGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTT

                                 *                                     **    
        876 AATAAATCAACCACTAATGTTTAACTAATTTTTTTTGGTATAGTTCTATATATATAATAGTAATG
         66 AATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTT-T-TATATATAATAACAATG

            *                                   *                            
        941 TGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTGACC
        129 CGTTGTATCTTATTCACTACAACTTTGTTAGTAATCCTAGACTTAAAAAATTAATAACATTGACC

                    
       1006 ATTGATAT
        194 ATTGATAT

                                                                             
       1014 ATAAATCAGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT
          1 ATAAATCAGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT

                                        *                                    
       1079 TAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTTTTATATATAATAACAATGC
         65 TAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTTTATATATAATAACAATGC

                                                                        
       1144 GTTGTATCTTATTCACTACAACTTTGTTAGTAATCCTAGACTTAAAAAATTAATAACATT
        130 GTTGTATCTTATTCACTACAACTTTGTTAGTAATCCTAGACTTAAAAAATTAATAACATT

       1204 CATCATCGAT


Statistics
Matches: 182,  Mismatches: 7, Indels: 3
        0.95            0.04        0.02

Matches are distributed among these distances:
 202   74  0.41
 203   12  0.07
 204   96  0.53

ACGTcount: A:0.36, C:0.11, G:0.09, T:0.45


Consensus pattern (201 bp):   
ATAAATCAGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
AATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTTTATATATAATAACAATGCG
TTGTATCTTATTCACTACAACTTTGTTAGTAATCCTAGACTTAAAAAATTAATAACATTGACCAT
TGATAT

Found at i:1700 original size:36 final size:36

Alignment explanation


    Indices: 1653--1722  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1643 GAGATTTTGG

                         *      *               
       1653 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
       1689 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

       1723 GGTTAATGAA


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:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA

Found at i:3101 original size:58 final size:58

Alignment explanation


    Indices: 3000--3109  Score: 159
    Period size: 58  Copynumber: 1.9  Consensus size: 58

       2990 ATCATGCCTC

                 *                                *                   
       3000 GGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAATATGTCACTCGATAAGTTTT
          1 GGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGTTTT

                                  *             *           *    
       3058 GGTCCGAAAACGTCTTTTTTTATGCATCTAAT-AAAGAACATGTCACTTGATA
          1 GGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATA

       3110 TTTGATTAAT


Statistics
Matches: 46,  Mismatches: 5, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  58   30  0.65
  59   16  0.35

ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Consensus pattern (58 bp):   
GGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGTTTT
Done.