Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017483.1 Corchorus olitorius cultivar O-4 contig17516, 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: 12001
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Found at i:692 original size:16 final size:16

Alignment explanation


    Indices: 651--694  Score: 54
    Period size: 15  Copynumber: 2.8  Consensus size: 16

        641 GTCGGGTTGA

                        **  
        651 TCGGGTTCGGGTCGTT
          1 TCGGGTTCGGGTAATT

                *           
        667 T-GGATTCGGGTAATT
          1 TCGGGTTCGGGTAATT

                         
        682 TCGGGTTCGGGTA
          1 TCGGGTTCGGGTA

        695 CCCAAAATTT


Statistics
Matches: 23,  Mismatches: 4, Indels: 2
        0.79            0.14        0.07

Matches are distributed among these distances:
  15   12  0.52
  16   11  0.48

ACGTcount: A:0.09, C:0.14, G:0.41, T:0.36


Consensus pattern (16 bp):   
TCGGGTTCGGGTAATT

Found at i:742 original size:17 final size:17

Alignment explanation


    Indices: 702--742  Score: 50
    Period size: 16  Copynumber: 2.5  Consensus size: 17

        692 GTACCCAAAA

                             
        702 TTTCGGGTCATTTCTGG
          1 TTTCGGGTCATTTCTGG

            *                 
        719 GTT-GGGTCAGTTTC-GG
          1 TTTCGGGTCA-TTTCTGG

                    
        735 TTTCGGGT
          1 TTTCGGGT

        743 TGGGCGGATT


Statistics
Matches: 20,  Mismatches: 2, Indels: 4
        0.77            0.08        0.15

Matches are distributed among these distances:
  16   10  0.50
  17   10  0.50

ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44


Consensus pattern (17 bp):   
TTTCGGGTCATTTCTGG

Found at i:4437 original size:19 final size:18

Alignment explanation


    Indices: 4413--4448  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       4403 TGGGCCTTAA

                               
       4413 CCCATTATCTCTTCTTTTC
          1 CCCATT-TCTCTTCTTTTC

                   *         
       4432 CCCATTTTTCTTCTTTT
          1 CCCATTTCTCTTCTTTT

       4449 TTTTTTGATT


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

Matches are distributed among these distances:
  18   10  0.62
  19    6  0.38

ACGTcount: A:0.08, C:0.33, G:0.00, T:0.58


Consensus pattern (18 bp):   
CCCATTTCTCTTCTTTTC

Found at i:8533 original size:107 final size:105

Alignment explanation


    Indices: 8311--8562  Score: 402
    Period size: 107  Copynumber: 2.4  Consensus size: 105

       8301 AGTTTAGCCT

                                                                     *       
       8311 TAATTTCACTAAGTTTAGCCCCAAATTAAAAATTTATTTTTATTTTAAGGGTAAATTTCAAAATT
          1 TAATTTCACTAAGTTTAGCCCCAAATT-AAAATTTATTTTTATTTTAAGGGTAAATTCCAAAATT

                                                      
       8376 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
         65 AATAA-TTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC

                                                                             
       8418 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATATTA
          1 TAATTTCACTAAGTTTAGCCCCAAATTAAAA-TTTATTTTTATTTTAAGGGTAAATTCCA-A--A

                                                  * *   
       8483 ATTAATAA-TATTGTTATAGGGTTTTAGAAATAAAATATATAAC
         62 ATTAATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC

                                                   
       8526 TAA-TTCACTAAGTTTAG-CCCAAATTAAAATTTATTTT
          1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTATTTT

       8563 AAGGGTTAGA


Statistics
Matches: 138,  Mismatches: 3, Indels: 10
        0.91            0.02        0.07

Matches are distributed among these distances:
 105    8  0.06
 106   16  0.12
 107   68  0.49
 108   37  0.27
 110    9  0.07

ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42


Consensus pattern (105 bp):   
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC

Found at i:8964 original size:18 final size:19

Alignment explanation


    Indices: 8925--8964  Score: 55
    Period size: 21  Copynumber: 2.1  Consensus size: 19

       8915 GTGCTCCCGT

                                 
       8925 TGTGATGCTCCCATTTTTCAA
          1 TGTGATGCTCCCA--TTTCAA

                               
       8946 TGTGATGCTCCCA-TTCAA
          1 TGTGATGCTCCCATTTCAA

             
       8964 T
          1 T

       8965 TCTAACCATT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    6  0.32
  21   13  0.68

ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40


Consensus pattern (19 bp):   
TGTGATGCTCCCATTTCAA
Done.