Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013810.1 Corchorus capsularis cultivar CVL-1 contig13831, 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: 20050
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:1787 original size:1 final size:1

Alignment explanation


    Indices: 1781--1815  Score: 70
    Period size: 1  Copynumber: 35.0  Consensus size: 1

       1771 TTTTCTCTGC

                                               
       1781 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       1816 CCAGTTGCAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   34  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:4931 original size:31 final size:32

Alignment explanation


    Indices: 4896--4957  Score: 99
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       4886 TTGGGTTATC

                    *                       
       4896 AGTCTCCATA-TCTTTAGATCTTGGATGTTTT
          1 AGTCTCCAGATTCTTTAGATCTTGGATGTTTT

                        *                  
       4927 AGTCTCCAGATTTTTTAGATCTTGGATGTTT
          1 AGTCTCCAGATTCTTTAGATCTTGGATGTTT

       4958 GACTTAATTC


Statistics
Matches: 28,  Mismatches: 2, Indels: 1
        0.90            0.06        0.03

Matches are distributed among these distances:
  31    9  0.32
  32   19  0.68

ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48


Consensus pattern (32 bp):   
AGTCTCCAGATTCTTTAGATCTTGGATGTTTT

Found at i:5029 original size:20 final size:20

Alignment explanation


    Indices: 5001--5045  Score: 81
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       4991 TGTGCTAGGG

                *               
       5001 ACTCATGGGAAAGGTTCAGA
          1 ACTCCTGGGAAAGGTTCAGA

                                
       5021 ACTCCTGGGAAAGGTTCAGA
          1 ACTCCTGGGAAAGGTTCAGA

                 
       5041 ACTCC
          1 ACTCC

       5046 GATTCAAAGG


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  20   24  1.00

ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20


Consensus pattern (20 bp):   
ACTCCTGGGAAAGGTTCAGA

Found at i:6934 original size:31 final size:31

Alignment explanation


    Indices: 6896--6957  Score: 124
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       6886 AATAATGCAT

                                           
       6896 CAATTCTCAAAGGATATTAACCAGTCACCTA
          1 CAATTCTCAAAGGATATTAACCAGTCACCTA

                                           
       6927 CAATTCTCAAAGGATATTAACCAGTCACCTA
          1 CAATTCTCAAAGGATATTAACCAGTCACCTA

       6958 ATAAGACACC


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   31  1.00

ACGTcount: A:0.39, C:0.26, G:0.10, T:0.26


Consensus pattern (31 bp):   
CAATTCTCAAAGGATATTAACCAGTCACCTA

Found at i:8740 original size:23 final size:24

Alignment explanation


    Indices: 8695--8746  Score: 61
    Period size: 23  Copynumber: 2.2  Consensus size: 24

       8685 AAGACTTATT

                             **     
       8695 CCATAAAAAAGCAAGGTGGATAGG
          1 CCATAAAAAAGCAAGGTCAATAGG

                 *                 *
       8719 CCATACAAAA-CAAGGTCAATAGT
          1 CCATAAAAAAGCAAGGTCAATAGG

                 
       8742 CCATA
          1 CCATA

       8747 GAACTGTATT


Statistics
Matches: 24,  Mismatches: 4, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  23   15  0.62
  24    9  0.38

ACGTcount: A:0.46, C:0.19, G:0.19, T:0.15


Consensus pattern (24 bp):   
CCATAAAAAAGCAAGGTCAATAGG

Found at i:14625 original size:6 final size:6

Alignment explanation


    Indices: 14614--14648  Score: 70
    Period size: 6  Copynumber: 5.8  Consensus size: 6

      14604 AATTTGCTGC

                                                    
      14614 TTGAAG TTGAAG TTGAAG TTGAAG TTGAAG TTGAA
          1 TTGAAG TTGAAG TTGAAG TTGAAG TTGAAG TTGAA

      14649 CCCTTGTTAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   29  1.00

ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34


Consensus pattern (6 bp):   
TTGAAG

Found at i:16346 original size:6 final size:6

Alignment explanation


    Indices: 16331--16362  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

      16321 TTTGTTTTCC

                                                  
      16331 TTTC-T TTTCTT TTTCTT TTTCTT TTTCTT TTT
          1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT

      16363 TCAATTTTTA


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

Matches are distributed among these distances:
   5    4  0.15
   6   22  0.85

ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84


Consensus pattern (6 bp):   
TTTCTT

Done.