Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001098.1 Corchorus olitorius cultivar O-4 contig01098, 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: 2449
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37


Found at i:922 original size:174 final size:174

Alignment explanation


    Indices: 596--958  Score: 554
    Period size: 174  Copynumber: 2.1  Consensus size: 174

        586 ATACACTCAT

                                            *  *                             
        596 GTAATTTAGTACCCTTTGATCTATAATGAAGGTTTTTGGACTTTTTTTCCCCTTAATCTCCCCAC
          1 GTAATTTAGTACCCTTTGATCTATAATGAAGGATTATGGACTTTTTTTCCCCTTAATCTCCCCAC

                                                                             
        661 TTCATTTATAAAACAAAAATTTAAAACACAACTTTTTTTCACATATAGGTAAAATAAATTGAATA
         66 TTCATTTATAAAACAAAAATTTAAAACACAACTTTTTTTCACATATAGGTAAAATAAATTGAATA

                           *                      *     
        726 TGTAGATAATAAATATTATCAACAAATTCC-ACTTACATTTTTA
        131 TGTAGATAATAAATACTATCAACAAATTCCAACTTACACTTTTA

                                                                     *       
        769 GTAATTTAGTACCCTTTGATCTATAATGAA-GATTAT-GACCTTTGTTTT-CCCTTATTCTCCCC
          1 GTAATTTAGTACCCTTTGATCTATAATGAAGGATTATGGA-CTTT-TTTTCCCCTTAATCTCCCC

                                                                  *          
        831 ACTTCATTTATAAAACAAAAATTTAAAACACAACGTTTTTTTTCACATATAGGTTAAATAAATTG
         64 ACTTCATTTATAAAACAAAAATTTAAAACACAAC--TTTTTTTCACATATAGGTAAAATAAATTG

               *     *                                         
        896 AATGTGTAGGTAATAAATACTATCAACAAATTCCATAAACTTACACTTTTA
        127 AATATGTAGATAATAAATACTATCAACAAATTCC---AACTTACACTTTTA

                        
        947 GTAATTATAGTA
          1 GTAATT-TAGTA

        959 ATAGTACAAC


Statistics
Matches: 173,  Mismatches: 8, Indels: 12
        0.90            0.04        0.06

Matches are distributed among these distances:
 171    2  0.01
 172   55  0.32
 173   34  0.20
 174   59  0.34
 178   18  0.10
 179    5  0.03

ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39


Consensus pattern (174 bp):   
GTAATTTAGTACCCTTTGATCTATAATGAAGGATTATGGACTTTTTTTCCCCTTAATCTCCCCAC
TTCATTTATAAAACAAAAATTTAAAACACAACTTTTTTTCACATATAGGTAAAATAAATTGAATA
TGTAGATAATAAATACTATCAACAAATTCCAACTTACACTTTTA

Found at i:1324 original size:24 final size:23

Alignment explanation


    Indices: 1296--1346  Score: 68
    Period size: 22  Copynumber: 2.2  Consensus size: 23

       1286 AAAAATTAAT

                                    
       1296 AAGGTTATACCAATCTTCTTATTC
          1 AAGGTT-TACCAATCTTCTTATTC

                       *          *
       1320 AAGG-TTACCATTCTTCTTATTT
          1 AAGGTTTACCAATCTTCTTATTC

                 
       1342 AAGGT
          1 AAGGT

       1347 CACTAAAAGA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  22   19  0.79
  23    1  0.04
  24    4  0.17

ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43


Consensus pattern (23 bp):   
AAGGTTTACCAATCTTCTTATTC

Found at i:1334 original size:22 final size:22

Alignment explanation


    Indices: 1303--1346  Score: 70
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1293 AATAAGGTTA

                                  
       1303 TACCAATCTTCTTATTCAAGGT
          1 TACCAATCTTCTTATTCAAGGT

                 *          *     
       1325 TACCATTCTTCTTATTTAAGGT
          1 TACCAATCTTCTTATTCAAGGT

       1347 CACTAAAAGA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.25, C:0.20, G:0.09, T:0.45


Consensus pattern (22 bp):   
TACCAATCTTCTTATTCAAGGT

Found at i:2001 original size:27 final size:27

Alignment explanation


    Indices: 1971--2025  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       1961 CACAAATTCT

                                       
       1971 AATTACCACAAATTGCTCCAAGTAATG
          1 AATTACCACAAATTGCTCCAAGTAATG

                                       
       1998 AATTACCACAAATTGCTCCAAGTAATG
          1 AATTACCACAAATTGCTCCAAGTAATG

             
       2025 A
          1 A

       2026 CGTTTTTTTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25


Consensus pattern (27 bp):   
AATTACCACAAATTGCTCCAAGTAATG
Done.