Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007265.1 Corchorus olitorius cultivar O-4 contig07290, 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: 1958
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37


Found at i:1428 original size:29 final size:31

Alignment explanation


    Indices: 1396--1462  Score: 93
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       1386 TGCAATTTGG

                                           
       1396 GATATAGCGTTAC-AAAACA-AGCAATTAAA
          1 GATATAGCGTTACGAAAACAGAGCAATTAAA

                  *           *           *
       1425 GATATAACGTTACGAAAAGAGAGCAATTAAG
          1 GATATAGCGTTACGAAAACAGAGCAATTAAA

                   
       1456 GATATAG
          1 GATATAG

       1463 TCCGTTAGAA


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  29   12  0.38
  30    5  0.16
  31   15  0.47

ACGTcount: A:0.49, C:0.10, G:0.19, T:0.21


Consensus pattern (31 bp):   
GATATAGCGTTACGAAAACAGAGCAATTAAA

Found at i:1627 original size:31 final size:31

Alignment explanation


    Indices: 1592--1670  Score: 131
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       1582 CTAACTGATT

                                 *         
       1592 ATATCCTTAATTGCTTGAAATCGAAAACGTC
          1 ATATCCTTAATTGCTTGAAATAGAAAACGTC

                                          *
       1623 ATATCCTTAATTGCTTGAAATAGAAAACGTT
          1 ATATCCTTAATTGCTTGAAATAGAAAACGTC

                 *           
       1654 ATATCATTAATTGCTTG
          1 ATATCCTTAATTGCTTG

       1671 TTTTGTAACG


Statistics
Matches: 45,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   45  1.00

ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37


Consensus pattern (31 bp):   
ATATCCTTAATTGCTTGAAATAGAAAACGTC

Found at i:1715 original size:31 final size:31

Alignment explanation


    Indices: 1590--1726  Score: 129
    Period size: 31  Copynumber: 4.5  Consensus size: 31

       1580 GCCTAACTGA

                                            
       1590 TTATATCCTTAATTGCTTGAAATC-GAAAACG
          1 TTATATCCTTAATTGCTTG-AATCAGAAAACG

             *                              
       1621 TCATATCCTTAATTGCTTGAAAT-AGAAAACG
          1 TTATATCCTTAATTGCTTG-AATCAGAAAACG

                   *            * **  *    
       1652 TTATATCATTAATTGCTTG-TTTTG-TAACG
          1 TTATATCCTTAATTGCTTGAATCAGAAAACG

                               ***   *     
       1681 TTATATCCTTAATTGCTTGTGGCAGCAAACG
          1 TTATATCCTTAATTGCTTGAATCAGAAAACG

                     *     
       1712 TTATATCCTAAATTG
          1 TTATATCCTTAATTG

       1727 ATTATTTGAC


Statistics
Matches: 89,  Mismatches: 13, Indels: 8
        0.81            0.12        0.07

Matches are distributed among these distances:
  29   23  0.26
  30    2  0.02
  31   64  0.72

ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39


Consensus pattern (31 bp):   
TTATATCCTTAATTGCTTGAATCAGAAAACG
Done.