Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016538.1 Corchorus olitorius cultivar O-4 contig16571, 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: 8294
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31


Found at i:4438 original size:14 final size:15

Alignment explanation


    Indices: 4414--4442  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

       4404 GTGTACAATA

                           
       4414 TCTTCTTTCTTTCTT
          1 TCTTCTTTCTTTCTT

                           
       4429 TCTT-TTTCTTTCTT
          1 TCTTCTTTCTTTCTT

       4443 AATTCTTACT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14   10  0.71
  15    4  0.29

ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76


Consensus pattern (15 bp):   
TCTTCTTTCTTTCTT

Found at i:4448 original size:25 final size:25

Alignment explanation


    Indices: 4420--4467  Score: 62
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       4410 AATATCTTCT

                 *  *                 
       4420 TTCTTTCTTTCTT-TTTCTTTCTTAA
          1 TTCTTACTGTCTTCTTT-TTTCTTAA

                                   
       4445 TTCTTACTGTCTTCTTTTTTCTT
          1 TTCTTACTGTCTTCTTTTTTCTT

       4468 TTTATTTTTC


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  25   17  0.85
  26    3  0.15

ACGTcount: A:0.06, C:0.21, G:0.02, T:0.71


Consensus pattern (25 bp):   
TTCTTACTGTCTTCTTTTTTCTTAA

Found at i:5194 original size:104 final size:106

Alignment explanation


    Indices: 4977--5236  Score: 388
    Period size: 104  Copynumber: 2.5  Consensus size: 106

       4967 AAGTTCAGTC

                                                                      *      
       4977 TTAATTTCACTAAGTTTAGCCCCAAATT--AATTTT-TTTTTATTTTAAGGGTAAATTTCAAAAT
          1 TTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAAT

                                                      
       5039 TAATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAA
         66 TAATAA-TTATTGTTATAGGGTTTTAGAAATAAAATACAAAA

            *                                                            *   
       5081 CTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAAT
          1 TTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAAT

                                                * *  
       5146 TAATAA-TATTGTTATAGGGTTTTAGAAATAAAATATATAA
         66 TAATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAA

                                *             ** *               
       5186 TTAA-TTCACTAAGTTTAG-TCCAAATTAAAATTAAAATTTTATTTTAAGGGT
          1 TTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT

       5237 TAGAAAAATT


Statistics
Matches: 143,  Mismatches: 10, Indels: 7
        0.89            0.06        0.04

Matches are distributed among these distances:
 103   29  0.20
 104   41  0.29
 105   35  0.24
 106    6  0.04
 107   32  0.22

ACGTcount: A:0.40, C:0.08, G:0.10, T:0.43


Consensus pattern (106 bp):   
TTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAAT
TAATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAA

Found at i:6906 original size:15 final size:15

Alignment explanation


    Indices: 6888--6920  Score: 50
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       6878 AACAGAGGTG

                            
       6888 AGAGGAACA-AGAAGA
          1 AGAGG-ACAGAGAAGA

                           
       6903 AGAGGACAGAGAAGA
          1 AGAGGACAGAGAAGA

               
       6918 AGA
          1 AGA

       6921 AGAAGATTTG


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  14    3  0.18
  15   14  0.82

ACGTcount: A:0.58, C:0.06, G:0.36, T:0.00


Consensus pattern (15 bp):   
AGAGGACAGAGAAGA

Found at i:7569 original size:108 final size:108

Alignment explanation


    Indices: 7409--7724  Score: 431
    Period size: 108  Copynumber: 2.9  Consensus size: 108

       7399 ACTCAAAAAA

                                 *                                           
       7409 AATTTTATTATTAATAGAGTTATGGTTTCTAAAATTACAAAATAAATTTAAAACAAAGTTTAGCC
          1 AATTTTATTATTAATAGAGTTTTGGTTTCTAAAATTA-AAAATAAATTTAAAACAAAGTTTAGCC

             *                                          
       7474 CTAAATAAAAAAAATATTATATATAGGGTAAGCCTTGTAA-TTT
         65 CCAAATAAAAAAAATATTATATATAGGGTAAGCCTTGTAATTTT

                     *  *                                           *        
       7517 AATTTTATTGTTTATAGAGTTTTGGTTTCTAAAATTAAAAATTAAATTTAAAACAAGGTTTAGCC
          1 AATTTTATTATTAATAGAGTTTTGGTTTCTAAAATTAAAAA-TAAATTTAAAACAAAGTTTAGCC

               *        *                                 
       7582 CCAGATAAAAAATATATTATATATATAGGGTAAGCCTTGTAATTTT
         65 CCAAATAAAAAAAATA-T-TATATATAGGGTAAGCCTTGTAATTTT

                                                         *   *               
       7628 ATTTTATTTTATTATTAATAGAGTTTTGGTTTCTAAAATTAAAAAAAAAATTAAAACAAAGTTTA
          1 A----ATTTTATTATTAATAGAGTTTTGGTTTCTAAAATTAAAAATAAATTTAAAACAAAGTTTA

            *             * *                 
       7693 ACCCCAAAT-AAAATATTA-TATATATAGGGTAA
         62 GCCCCAAATAAAAAAAATATTATATATAGGGTAA

       7725 CCATCAAAGT


Statistics
Matches: 183,  Mismatches: 17, Indels: 14
        0.86            0.08        0.07

Matches are distributed among these distances:
 107    4  0.02
 108   69  0.38
 109    1  0.01
 110   37  0.20
 111    4  0.02
 113    6  0.03
 114   24  0.13
 115   38  0.21

ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39


Consensus pattern (108 bp):   
AATTTTATTATTAATAGAGTTTTGGTTTCTAAAATTAAAAATAAATTTAAAACAAAGTTTAGCCC
CAAATAAAAAAAATATTATATATAGGGTAAGCCTTGTAATTTT

Done.