Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022511.1 Corchorus olitorius cultivar O-4 contig22544, 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: 8432
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36


Found at i:1416 original size:59 final size:58

Alignment explanation


    Indices: 1319--1429  Score: 177
    Period size: 59  Copynumber: 1.9  Consensus size: 58

       1309 ATAGCATCAT

                 *    *                                               
       1319 GCCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCCATAA
          1 GCCTCAGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCCATAA

                                       *             *           
       1377 GCCTCAGTCCGAAAACGTCTTTTTTTATGCATCTAATAAAAGAACATGTCACT
          1 GCCTCAGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAAACATGTCACT

       1430 TGATGTTTGA


Statistics
Matches: 48,  Mismatches: 4, Indels: 1
        0.91            0.08        0.02

Matches are distributed among these distances:
  58   17  0.35
  59   31  0.65

ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31


Consensus pattern (58 bp):   
GCCTCAGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCCATAA

Found at i:2266 original size:98 final size:97

Alignment explanation


    Indices: 2097--2294  Score: 387
    Period size: 98  Copynumber: 2.0  Consensus size: 97

       2087 AAAAAGTTAC

                                                                             
       2097 TAAAATCATCCAAGAGGGCAATTAGGTTTGTAGAGAGCATTATAGCTATTTTAATACCTTTTATA
          1 TAAAATCATCCAAGAGGGCAATTAGGTTTGTAGAGAGCATTATAGCTATTTTAATACCTTTTATA

                                             
       2162 ATTTTTTTTAGTAATTTTAGATTACAAGATTAA
         66 A-TTTTTTTAGTAATTTTAGATTACAAGATTAA

                                                                             
       2195 TAAAATCATCCAAGAGGGCAATTAGGTTTGTAGAGAGCATTATAGCTATTTTAATACCTTTTATA
          1 TAAAATCATCCAAGAGGGCAATTAGGTTTGTAGAGAGCATTATAGCTATTTTAATACCTTTTATA

                                            
       2260 ATTTTTTTAGTAATTTTAGATTACAAGATTAA
         66 ATTTTTTTAGTAATTTTAGATTACAAGATTAA

               
       2292 TAA
          1 TAA

       2295 CATTCATAAT


Statistics
Matches: 100,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  97   34  0.34
  98   66  0.66

ACGTcount: A:0.36, C:0.09, G:0.14, T:0.40


Consensus pattern (97 bp):   
TAAAATCATCCAAGAGGGCAATTAGGTTTGTAGAGAGCATTATAGCTATTTTAATACCTTTTATA
ATTTTTTTAGTAATTTTAGATTACAAGATTAA

Found at i:2467 original size:19 final size:21

Alignment explanation


    Indices: 2445--2484  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2435 CCTTATACTA

                                 
       2445 TATAA-ATTTTT-ATAACCTT
          1 TATAACATTTTTAATAACCTT

                  *              
       2464 TATAACTTTTTTAATAACCTT
          1 TATAACATTTTTAATAACCTT

       2485 AAAGAAGAAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  19    5  0.28
  20    5  0.28
  21    8  0.44

ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53


Consensus pattern (21 bp):   
TATAACATTTTTAATAACCTT

Found at i:3039 original size:15 final size:16

Alignment explanation


    Indices: 2997--3039  Score: 70
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       2987 GGGTCCCAAG

                            
       2997 TACTCAAAACTTTAAT
          1 TACTCAAAACTTTAAT

                            
       3013 TACTCAAAACTTTAAT
          1 TACTCAAAACTTTAAT

                 *      
       3029 TA-TCCAAACTT
          1 TACTCAAAACTT

       3040 GGGAGCATGA


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15    8  0.31
  16   18  0.69

ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37


Consensus pattern (16 bp):   
TACTCAAAACTTTAAT

Found at i:4877 original size:15 final size:15

Alignment explanation


    Indices: 4859--4891  Score: 57
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       4849 ATTAAATTGG

                           
       4859 TGACAATTCAATTCA
          1 TGACAATTCAATTCA

                *          
       4874 TGACGATTCAATTCA
          1 TGACAATTCAATTCA

               
       4889 TGA
          1 TGA

       4892 TTGAAATATG


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33


Consensus pattern (15 bp):   
TGACAATTCAATTCA
Done.