Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013264.1 Corchorus olitorius cultivar O-4 contig13297, 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: 6101
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34


Found at i:1599 original size:18 final size:19

Alignment explanation


    Indices: 1568--1609  Score: 50
    Period size: 18  Copynumber: 2.2  Consensus size: 19

       1558 CATAATTTGC

                               
       1568 GTGTATATCATCT-CAAAA
          1 GTGTATATCATCTCCAAAA

                    **          
       1586 GTGTATATTGTCTCGCAAAA
          1 GTGTATATCATCTC-CAAAA

                
       1606 GTGT
          1 GTGT

       1610 GTAATTGCTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  18   11  0.55
  20    9  0.45

ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36


Consensus pattern (19 bp):   
GTGTATATCATCTCCAAAA

Found at i:2022 original size:30 final size:30

Alignment explanation


    Indices: 1983--2041  Score: 82
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       1973 TTTCTTTTAA

                        *                 
       1983 TTTACAGTTTGCCACGGGCCTTGCCACGGT
          1 TTTACAGTTTGCAACGGGCCTTGCCACGGT

                *     *        *         
       2013 TTTAGAGTTTTCAACGGGCTTTGCCACGG
          1 TTTACAGTTTGCAACGGGCCTTGCCACGG

       2042 ATGATTTGTT


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  30   25  1.00

ACGTcount: A:0.15, C:0.25, G:0.27, T:0.32


Consensus pattern (30 bp):   
TTTACAGTTTGCAACGGGCCTTGCCACGGT

Found at i:2288 original size:21 final size:21

Alignment explanation


    Indices: 2262--2302  Score: 73
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2252 CAAAAACCCG

                                 
       2262 ACTCACCGATCACCACTCACC
          1 ACTCACCGATCACCACTCACC

                          *     
       2283 ACTCACCGATCACCGCTCAC
          1 ACTCACCGATCACCACTCAC

       2303 TGGTTTACGG


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

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.27, C:0.51, G:0.07, T:0.15


Consensus pattern (21 bp):   
ACTCACCGATCACCACTCACC

Found at i:4150 original size:22 final size:22

Alignment explanation


    Indices: 4125--4166  Score: 75
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       4115 ACTATTTTTT

                      *           
       4125 TTGTTTAGATTATCTTATATTC
          1 TTGTTTAGATGATCTTATATTC

                                
       4147 TTGTTTAGATGATCTTATAT
          1 TTGTTTAGATGATCTTATAT

       4167 GCAGACTGTT


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

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.24, C:0.07, G:0.12, T:0.57


Consensus pattern (22 bp):   
TTGTTTAGATGATCTTATATTC
Done.