Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010587.1 Corchorus capsularis cultivar CVL-1 contig10608, 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: 42194
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31


Found at i:5458 original size:23 final size:23

Alignment explanation


    Indices: 5420--5463  Score: 70
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       5410 GGATGAGGTA

                   *               
       5420 AAAAAAATTTACATTAATTATCC
          1 AAAAAAAGTTACATTAATTATCC

                       *         
       5443 AAAAAAAGTTAGATTAATTAT
          1 AAAAAAAGTTACATTAATTAT

       5464 TGAGTAATTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  23   19  1.00

ACGTcount: A:0.55, C:0.07, G:0.05, T:0.34


Consensus pattern (23 bp):   
AAAAAAAGTTACATTAATTATCC

Found at i:23549 original size:20 final size:21

Alignment explanation


    Indices: 23519--23563  Score: 83
    Period size: 20  Copynumber: 2.2  Consensus size: 21

      23509 TTAAGTAAAT

                                 
      23519 ATCTCGAGTTATGTAATTGAG
          1 ATCTCGAGTTATGTAATTGAG

                                 
      23540 ATCT-GAGTTATGTAATTGAG
          1 ATCTCGAGTTATGTAATTGAG

                
      23560 ATCT
          1 ATCT

      23564 AACACGGTTT


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

Matches are distributed among these distances:
  20   20  0.83
  21    4  0.17

ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40


Consensus pattern (21 bp):   
ATCTCGAGTTATGTAATTGAG

Found at i:23615 original size:38 final size:38

Alignment explanation


    Indices: 23567--23646  Score: 160
    Period size: 38  Copynumber: 2.1  Consensus size: 38

      23557 GAGATCTAAC

                                                  
      23567 ACGGTTTGACTCTGGATTAGAAAGACTCAATGTAACTA
          1 ACGGTTTGACTCTGGATTAGAAAGACTCAATGTAACTA

                                                  
      23605 ACGGTTTGACTCTGGATTAGAAAGACTCAATGTAACTA
          1 ACGGTTTGACTCTGGATTAGAAAGACTCAATGTAACTA

                
      23643 ACGG
          1 ACGG

      23647 GTGAAGACTC


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  38   42  1.00

ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28


Consensus pattern (38 bp):   
ACGGTTTGACTCTGGATTAGAAAGACTCAATGTAACTA

Found at i:33176 original size:14 final size:14

Alignment explanation


    Indices: 33157--33184  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      33147 CAGAGAGTAA

                          
      33157 ACTCCAAAATAGTG
          1 ACTCCAAAATAGTG

                          
      33171 ACTCCAAAATAGTG
          1 ACTCCAAAATAGTG

      33185 TATAAGAAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21


Consensus pattern (14 bp):   
ACTCCAAAATAGTG
Done.