Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019980.1 Corchorus olitorius cultivar O-4 contig20013, 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: 2815
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:973 original size:13 final size:13

Alignment explanation


    Indices: 955--979  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        945 TGGTCGAAAC

                         
        955 TTTTTTTATTTTG
          1 TTTTTTTATTTTG

                        
        968 TTTTTTTATTTT
          1 TTTTTTTATTTT

        980 TTTGATATTT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.08, C:0.00, G:0.04, T:0.88


Consensus pattern (13 bp):   
TTTTTTTATTTTG

Found at i:1134 original size:26 final size:23

Alignment explanation


    Indices: 1104--1150  Score: 67
    Period size: 26  Copynumber: 1.9  Consensus size: 23

       1094 CTTGAAAATT

                                      
       1104 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAAC-TTGAT-GAT-AGATGGA

                                 
       1130 TGAAAAACTTGATGATAGATG
          1 TGAAAAACTTGATGATAGATG

       1151 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (23 bp):   
TGAAAAACTTGATGATAGATGGA

Found at i:1448 original size:21 final size:21

Alignment explanation


    Indices: 1422--1538  Score: 173
    Period size: 21  Copynumber: 5.6  Consensus size: 21

       1412 AAGATGCTAG

                                  
       1422 AAGTTCATTGGAGCAA-GTTCC
          1 AAGTTCATTGGAG-AAGGTTCC

                                 
       1443 AAGTTCATTGGAGAAGGTTCC
          1 AAGTTCATTGGAGAAGGTTCC

                                *
       1464 AAGTTCATTGGAGAAGGTTCA
          1 AAGTTCATTGGAGAAGGTTCC

                           *     
       1485 AAGTTCATTGGAGAATGTTCC
          1 AAGTTCATTGGAGAAGGTTCC

               *               * 
       1506 AAGATCATTGGAGAAGGTTTC
          1 AAGTTCATTGGAGAAGGTTCC

               *        
       1527 AAGCTCATTGGA
          1 AAGTTCATTGGA

       1539 ATTGCCTAAG


Statistics
Matches: 88,  Mismatches: 7, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   86  0.98

ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29


Consensus pattern (21 bp):   
AAGTTCATTGGAGAAGGTTCC

Done.