Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010238.1 Corchorus olitorius cultivar O-4 contig10270, 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: 4534
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39


Found at i:631 original size:131 final size:131

Alignment explanation


    Indices: 455--823  Score: 657
    Period size: 131  Copynumber: 2.9  Consensus size: 131

        445 AAATATATTC

                                                                             
        455 AAAAATTCTAATATATATAAG-TTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATA
          1 AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATA

               *                                                             
        519 AGGTTATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTGTAACAGTATATTT
         66 AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTGTAACAGTATATTT

             
        584 A
        131 A

                                                                             
        585 AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATA
          1 AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATA

                                                                             
        650 AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTGTAACAGTATATTT
         66 AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTGTAACAGTATATTT

             
        715 A
        131 A

                                                                             
        716 AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT----TA--TA-A
          1 AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATA

                                                       *       
        774 A-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACT
         66 AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACT

        824 ATAAAAGTTT


Statistics
Matches: 236,  Mismatches: 2, Indels: 9
        0.96            0.01        0.04

Matches are distributed among these distances:
 123   48  0.20
 124    2  0.01
 125    2  0.01
 127    2  0.01
 130   21  0.09
 131  161  0.68

ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37


Consensus pattern (131 bp):   
AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATA
AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTGTAACAGTATATTT
A

Found at i:1238 original size:150 final size:153

Alignment explanation


    Indices: 1058--1366  Score: 507
    Period size: 153  Copynumber: 2.0  Consensus size: 153

       1048 ATTTTTATTA

                                                               *             
       1058 TTTTAAAAATAAATATCAATAACTTTTAATAATATC-ATATTAAC-AAAAAGGAGATAATATTCC
          1 TTTTAAAAATAAATATCAATAACTTTTAATAATATCAATATTAACAAAAAAAGAGATAATATTCC

                       *                  *                       *  *       
       1121 TACTATAACTCTCTCCCTCCCATCGTCTCCCAAATCTTCAATTCTCCAATTTTGGTCGATCC-TT
         66 TACTATAACTCCCTCCCTCCCATCGTCTCCAAAATCTTCAATTCTCCAATTTTGATCAATCCATT

                 *                 
       1185 CCATTGATTGTATTTGGGTGATT
        131 CCATTCATTGTATTTGGGTGATT

                                                                             
       1208 TTTTAAAAATAAATATCAATAACTTTTAATAATATCATATATTAACAAAAAAAGAGATAATATTC
          1 TTTTAAAAATAAATATCAATAACTTTTAATAATATCA-ATATTAACAAAAAAAGAGATAATATTC

                           *                                                 
       1273 CTACTATAACTCCCTTCCTCCCATCGTCTCCAAAATCTTCAATTCTCCAATTTTGATCAATCCTA
         65 CTACTATAACTCCCTCCCTCCCATCGTCTCCAAAATCTTCAATTCTCCAATTTTGATCAATCC-A

                         *           
       1338 TTCCATTCATTGTTTTTGGGTGATT
        129 TTCCATTCATTGTATTTGGGTGATT

                
       1363 TTTT
          1 TTTT

       1367 TTTTTTGGAG


Statistics
Matches: 146,  Mismatches: 8, Indels: 5
        0.92            0.05        0.03

Matches are distributed among these distances:
 150   36  0.25
 152    8  0.05
 153   75  0.51
 155   27  0.18

ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39


Consensus pattern (153 bp):   
TTTTAAAAATAAATATCAATAACTTTTAATAATATCAATATTAACAAAAAAAGAGATAATATTCC
TACTATAACTCCCTCCCTCCCATCGTCTCCAAAATCTTCAATTCTCCAATTTTGATCAATCCATT
CCATTCATTGTATTTGGGTGATT

Found at i:2042 original size:14 final size:15

Alignment explanation


    Indices: 2011--2042  Score: 57
    Period size: 14  Copynumber: 2.2  Consensus size: 15

       2001 TTTATCAATT

                           
       2011 AAATTAAATATATTA
          1 AAATTAAATATATTA

                           
       2026 AAATTAAA-ATATTA
          1 AAATTAAATATATTA

               
       2040 AAA
          1 AAA

       2043 GTTATAATTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    9  0.53
  15    8  0.47

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (15 bp):   
AAATTAAATATATTA

Found at i:2690 original size:14 final size:13

Alignment explanation


    Indices: 2654--2692  Score: 51
    Period size: 14  Copynumber: 2.9  Consensus size: 13

       2644 TATATATTAG

                         
       2654 AATTTTTTAAATA
          1 AATTTTTTAAATA

            *    *        
       2667 TATTTCTTAAATGA
          1 AATTTTTTAAAT-A

                        
       2681 AATTTTTTAAAT
          1 AATTTTTTAAAT

       2693 TTTACAATTT


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  13   10  0.48
  14   11  0.52

ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54


Consensus pattern (13 bp):   
AATTTTTTAAATA
Done.