Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013600.1 Corchorus olitorius cultivar O-4 contig13633, 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: 25212
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30


Found at i:34 original size:19 final size:18

Alignment explanation


    Indices: 11--52  Score: 57
    Period size: 19  Copynumber: 2.3  Consensus size: 18

          1 ATCTTTTTAT

                              
         11 TTATTAATTTAGTTATTA
          1 TTATTAATTTAGTTATTA

                  *     *      
         29 TCTATTTATTTATTTATTA
          1 T-TATTAATTTAGTTATTA

                 
         48 TTATT
          1 TTATT

         53 TCTTAGCTAC


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  18    5  0.24
  19   16  0.76

ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67


Consensus pattern (18 bp):   
TTATTAATTTAGTTATTA

Found at i:14537 original size:40 final size:40

Alignment explanation


    Indices: 14476--14714  Score: 347
    Period size: 40  Copynumber: 6.0  Consensus size: 40

      14466 TGTTTAGCCC

                *                                   
      14476 AAATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTT
          1 AAATACCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTT

                            *                       
      14516 AAATACCCAATTTGCCATTCCCCACCGGAAGGTGTTGTTT
          1 AAATACCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTT

                                  *                 
      14556 AAATACCCAATTTGCCCTTCCCTACCGGAAGGTGTTGTTT
          1 AAATACCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTT

                                     *               
      14596 AAATACCCAATTTGCCCTTCCCCA-TGTGAAGGTGTTGTTT
          1 AAATACCCAATTTGCCCTTCCCCACCG-GAAGGTGTTGTTT

                                           *      ** 
      14636 AAATA-CCAAGTTTGCCCTTCCCCACCGGAAAGTGTTGACT
          1 AAATACCCAA-TTTGCCCTTCCCCACCGGAAGGTGTTGTTT

                *                *  *   *          
      14676 AAATTCCCAATTTGCCCTTCCTCATCGGGAGGTGTTGTT
          1 AAATACCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTT

      14715 CTTATTCATT


Statistics
Matches: 178,  Mismatches: 17, Indels: 8
        0.88            0.08        0.04

Matches are distributed among these distances:
  39    5  0.03
  40  168  0.94
  41    5  0.03

ACGTcount: A:0.23, C:0.28, G:0.18, T:0.32


Consensus pattern (40 bp):   
AAATACCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTT

Found at i:18152 original size:11 final size:11

Alignment explanation


    Indices: 18136--18161  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

      18126 AGCCCTAAAA

                       
      18136 AAAACTAGAAG
          1 AAAACTAGAAG

                       
      18147 AAAACTAGAAG
          1 AAAACTAGAAG

                
      18158 AAAA
          1 AAAA

      18162 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG

Found at i:18783 original size:19 final size:18

Alignment explanation


    Indices: 18750--18785  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      18740 TTGAAATAGA

                              
      18750 TCTTCAAAAATCTTCAAG
          1 TCTTCAAAAATCTTCAAG

                     *        
      18768 TCTTCAAATTATCTTCAA
          1 TCTTCAAA-AATCTTCAA

      18786 ATGGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    8  0.50
  19    8  0.50

ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39


Consensus pattern (18 bp):   
TCTTCAAAAATCTTCAAG

Found at i:20452 original size:16 final size:15

Alignment explanation


    Indices: 20431--20477  Score: 53
    Period size: 16  Copynumber: 3.1  Consensus size: 15

      20421 AGAAATAGGC

                           
      20431 AATCAATCAAAGCAA
          1 AATCAATCAAAGCAA

                      *     
      20446 TAATCAATCAGAGCAA
          1 -AATCAATCAAAGCAA

                            
      20462 AA-CAATGCAAAG-AA
          1 AATCAAT-CAAAGCAA

              
      20476 AA
          1 AA

      20478 AGTAAATGGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  14    8  0.29
  15    6  0.21
  16   14  0.50

ACGTcount: A:0.60, C:0.17, G:0.11, T:0.13


Consensus pattern (15 bp):   
AATCAATCAAAGCAA
Done.