Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013704.1 Corchorus olitorius cultivar O-4 contig13737, 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: 11634
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--41  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

                                                                         
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         42 CAGAGTTGGG


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:1292 original size:24 final size:24

Alignment explanation


    Indices: 1251--1302  Score: 77
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       1241 ATGGTGAGCA

                      *  *          
       1251 CCAAGTCAACTTCTTGACAGACTT
          1 CCAAGTCAACATCATGACAGACTT

                    *               
       1275 CCAAGTCATCATCATGACAGACTT
          1 CCAAGTCAACATCATGACAGACTT

                
       1299 CCAA
          1 CCAA

       1303 AAACACAAAT


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.33, C:0.31, G:0.12, T:0.25


Consensus pattern (24 bp):   
CCAAGTCAACATCATGACAGACTT

Found at i:2911 original size:38 final size:38

Alignment explanation


    Indices: 2857--3042  Score: 248
    Period size: 38  Copynumber: 4.9  Consensus size: 38

       2847 GCTATGCAAT

                     *                    *       
       2857 AGTGGACCCATGCCTCAGGGGGTTAAACTGATGGTAAG
          1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG

            *          *      *                   
       2895 TGTGGACCCGTACCTCAGAGGGTTAAACTGTTGGTAAG
          1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG

            *          *           *              
       2933 TGTGGACCCGTACCTCAGGGGGTCAAACTGTTGGTAAG
          1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG

                   *        *                      
       2971 AGTGGACTCGTGCCTCTGGGGGTTAAACTGTTGGTAAAG
          1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGT-AAG

                *          *                  
       3010 AGTGAACCCGTGCCTTAGGGGGTT-AACTGTTGG
          1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGG

       3043 CTAGACTCGA


Statistics
Matches: 131,  Mismatches: 16, Indels: 2
        0.88            0.11        0.01

Matches are distributed among these distances:
  38  108  0.82
  39   23  0.18

ACGTcount: A:0.22, C:0.18, G:0.34, T:0.25


Consensus pattern (38 bp):   
AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG

Found at i:4367 original size:20 final size:20

Alignment explanation


    Indices: 4342--4380  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4332 CAAAAGTTTT

                                
       4342 GCTATAAAGTAATGGGATAC
          1 GCTATAAAGTAATGGGATAC

                  *            
       4362 GCTATACAGTAATGGGATA
          1 GCTATAAAGTAATGGGATA

       4381 TAATATATAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26


Consensus pattern (20 bp):   
GCTATAAAGTAATGGGATAC

Found at i:4387 original size:20 final size:20

Alignment explanation


    Indices: 4344--4387  Score: 52
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       4334 AAAGTTTTGC

                              **
       4344 TATAAAGTAATGGGATACGC
          1 TATAAAGTAATGGGATACAA

                *            *  
       4364 TATACAGTAATGGGATATAA
          1 TATAAAGTAATGGGATACAA

                
       4384 TATA
          1 TATA

       4388 TAATATAGCA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30


Consensus pattern (20 bp):   
TATAAAGTAATGGGATACAA

Found at i:8138 original size:53 final size:51

Alignment explanation


    Indices: 8000--8143  Score: 182
    Period size: 51  Copynumber: 2.8  Consensus size: 51

       7990 CCACCAGCAG

                *                   *           *          *  *
       8000 CAGTGTCATATTTGTTTTCTAAGCCCTCGTAATTAGCTTCTGTCCTGCCAG
          1 CAGTATCATATTTGTTTTCTAAGCGCTCGTAATTAGTTTCTGTCCTGACAA

                                        **                     
       8051 CAGTATCATATTTGTTTTCTAAGCGCTCAAAATTAGTTTCTGTCCTGACAA
          1 CAGTATCATATTTGTTTTCTAAGCGCTCGTAATTAGTTTCTGTCCTGACAA

                     *                                 
       8102 CAGTAT-ATCTTTGTAATTTTCTAAGCGCTCGTAATTAGTTTC
          1 CAGTATCATATTTG---TTTTCTAAGCGCTCGTAATTAGTTTC

       8144 AAAACCTGCC


Statistics
Matches: 80,  Mismatches: 10, Indels: 4
        0.85            0.11        0.04

Matches are distributed among these distances:
  50    6  0.08
  51   50  0.62
  53   24  0.30

ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41


Consensus pattern (51 bp):   
CAGTATCATATTTGTTTTCTAAGCGCTCGTAATTAGTTTCTGTCCTGACAA

Found at i:9470 original size:10 final size:10

Alignment explanation


    Indices: 9449--9477  Score: 51
    Period size: 10  Copynumber: 3.0  Consensus size: 10

       9439 TTAAAAAAGG

                      
       9449 AAATAAAA-T
          1 AAATAAAATT

                      
       9458 AAATAAAATT
          1 AAATAAAATT

                      
       9468 AAATAAAATT
          1 AAATAAAATT

       9478 GTTAATATGG


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
   9    8  0.42
  10   11  0.58

ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28


Consensus pattern (10 bp):   
AAATAAAATT
Done.