Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000683.1 Corchorus olitorius cultivar O-4 contig00683, 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, 696

Length: 1161
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.35


Found at i:628 original size:31 final size:29

Alignment explanation


    Indices: 553--629  Score: 84
    Period size: 29  Copynumber: 2.6  Consensus size: 29

        543 TTTGGCCAGA

                 *                     * 
        553 TGTTCGATTTGGTACCAAACCTTTAAACC
          1 TGTTCAATTTGGTACCAAACCTTTAAAAC

                     **                    
        582 TGTTCAATTCAGTACCAAACCTTTCAAAAAC
          1 TGTTCAATTTGGTACCAAACCTTT--AAAAC

                              
        613 -GATTCAATTTGGTACCA
          1 TG-TTCAATTTGGTACCA

        630 TTTATGACGT


Statistics
Matches: 39,  Mismatches: 6, Indels: 4
        0.80            0.12        0.08

Matches are distributed among these distances:
  29   21  0.54
  30    1  0.03
  31   17  0.44

ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32


Consensus pattern (29 bp):   
TGTTCAATTTGGTACCAAACCTTTAAAAC

Found at i:912 original size:2 final size:2

Alignment explanation


    Indices: 899--941  Score: 68
    Period size: 2  Copynumber: 20.5  Consensus size: 2

        889 TTTAAAACAT

                                                                           
        899 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA T
          1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T

        942 TAAAACTATA


Statistics
Matches: 39,  Mismatches: 0, Indels: 4
        0.91            0.00        0.09

Matches are distributed among these distances:
   2   35  0.90
   3    4  0.10

ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:1125 original size:4 final size:4

Alignment explanation


    Indices: 1116--1142  Score: 54
    Period size: 4  Copynumber: 6.8  Consensus size: 4

       1106 ATGATATTAA

                                             
       1116 ATTG ATTG ATTG ATTG ATTG ATTG ATT
          1 ATTG ATTG ATTG ATTG ATTG ATTG ATT

       1143 TGAATATCTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   23  1.00

ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52


Consensus pattern (4 bp):   
ATTG

Done.