Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015543.1 Corchorus olitorius cultivar O-4 contig15576, 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: 5985
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36


Found at i:106 original size:39 final size:40

Alignment explanation


    Indices: 50--130  Score: 128
    Period size: 39  Copynumber: 2.0  Consensus size: 40

         40 TTTAATTCCT

                                                    
         50 ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA

                     *          *         *         
         90 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA

              
        129 AT
          1 AT

        131 TCTTAGGTAT


Statistics
Matches: 38,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  39   30  0.79
  40    8  0.21

ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA

Found at i:157 original size:25 final size:24

Alignment explanation


    Indices: 121--167  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

        111 AATACTTACA

                                    
        121 TTAATTAAATTCTTAGGTATTTTT
          1 TTAATTAAATTCTTAGGTATTTTT

                                   
        145 TTAATTCAAATTCTTAGGTATTT
          1 TTAATT-AAATTCTTAGGTATTT

        168 GTGCAAACGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55


Consensus pattern (24 bp):   
TTAATTAAATTCTTAGGTATTTTT

Found at i:2609 original size:56 final size:58

Alignment explanation


    Indices: 2502--2614  Score: 158
    Period size: 56  Copynumber: 2.0  Consensus size: 58

       2492 ATAGCAACAT

                      *                                               
       2502 GCCTCGGTCCTAAAACGTCTTTTTTAGGCAACTAATAAAAAAACATGTCACTCGATAA
          1 GCCTCGGTCCGAAAACGTCTTTTTTAGGCAACTAATAAAAAAACATGTCACTCGATAA

                *                     *   *         *           *    
       2560 GCCTTGGTCCGAAAACGT-TTTTTTATGCATCTAAT-AAAGAACATGTCACTTGATA
          1 GCCTCGGTCCGAAAACGTCTTTTTTAGGCAACTAATAAAAAAACATGTCACTCGATA

       2615 TTTGATTAAT


Statistics
Matches: 49,  Mismatches: 6, Indels: 2
        0.86            0.11        0.04

Matches are distributed among these distances:
  56   18  0.37
  57   15  0.31
  58   16  0.33

ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31


Consensus pattern (58 bp):   
GCCTCGGTCCGAAAACGTCTTTTTTAGGCAACTAATAAAAAAACATGTCACTCGATAA

Found at i:5294 original size:2 final size:2

Alignment explanation


    Indices: 5287--5311  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       5277 AGGAAGGAAA

                                                 
       5287 TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC T

       5312 ATATATATAT


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

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (2 bp):   
TC

Found at i:5316 original size:2 final size:2

Alignment explanation


    Indices: 5311--5339  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       5301 TCTCTCTCTC

                                                       
       5311 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       5340 GATCTAAAAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.