Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024881.1 Corchorus olitorius cultivar O-4 contig24914, 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: 6581
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:165 original size:15 final size:15

Alignment explanation


    Indices: 145--182  Score: 67
    Period size: 15  Copynumber: 2.5  Consensus size: 15

        135 AAAACAGAAT

                           
        145 ACAGAAAGCAATTAA
          1 ACAGAAAGCAATTAA

                           
        160 ACAGAAAGCAATTAA
          1 ACAGAAAGCAATTAA

                    
        175 ACTAGAAA
          1 AC-AGAAA

        183 ACAAAGCAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.77
  16    5  0.23

ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13


Consensus pattern (15 bp):   
ACAGAAAGCAATTAA

Found at i:1592 original size:20 final size:18

Alignment explanation


    Indices: 1559--1595  Score: 56
    Period size: 20  Copynumber: 1.9  Consensus size: 18

       1549 TTGAAATAAA

                              
       1559 TCTTCAATAGTCTTCAAG
          1 TCTTCAATAGTCTTCAAG

                               
       1577 TCTTCAATTAAGTCTTCAA
          1 TCTTCAA-T-AGTCTTCAA

       1596 ATGGTCTTCA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  18    7  0.41
  19    1  0.06
  20    9  0.53

ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41


Consensus pattern (18 bp):   
TCTTCAATAGTCTTCAAG

Found at i:3489 original size:22 final size:21

Alignment explanation


    Indices: 3446--3497  Score: 68
    Period size: 22  Copynumber: 2.4  Consensus size: 21

       3436 GGCACTGAAT

                          *      
       3446 GGTGATGGCACGGGCATGGCC
          1 GGTGATGGCACGGGAATGGCC

                *                 
       3467 GGTGGTGGCACGGTGAATGGCC
          1 GGTGATGGCACGG-GAATGGCC

               *     
       3489 GGTAATGGC
          1 GGTGATGGC

       3498 TTGGTAGTGG


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  21   12  0.46
  22   14  0.54

ACGTcount: A:0.15, C:0.19, G:0.48, T:0.17


Consensus pattern (21 bp):   
GGTGATGGCACGGGAATGGCC
Done.