Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021560.1 Corchorus olitorius cultivar O-4 contig21593, 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: 10677
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33


Found at i:1338 original size:38 final size:35

Alignment explanation


    Indices: 1276--1345  Score: 95
    Period size: 38  Copynumber: 1.9  Consensus size: 35

       1266 GCAACGTACC

                                               
       1276 TTTTAATATTGATTTTTCTTCTTCTTTATAGTAGT
          1 TTTTAATATTGATTTTTCTTCTTCTTTATAGTAGT

                         *     *               
       1311 TTTTAATTATTGGTTTTTTTTTCCTTCTTTATAGT
          1 TTTTAA-TATT-GATTTTTCTT-CTTCTTTATAGT

       1346 TACCAAAGTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
  35    6  0.20
  36    4  0.13
  37    8  0.27
  38   12  0.40

ACGTcount: A:0.17, C:0.09, G:0.09, T:0.66


Consensus pattern (35 bp):   
TTTTAATATTGATTTTTCTTCTTCTTTATAGTAGT

Found at i:3718 original size:132 final size:130

Alignment explanation


    Indices: 3567--3831  Score: 363
    Period size: 132  Copynumber: 2.0  Consensus size: 130

       3557 TTCATTGAAG

                                 *   **                 **                   
       3567 AAATAATTTTAAAATTCTAATGTATCTAAG-TTTT-TTAATTAAGTTAGTAAAATGGTAAAAATA
          1 AAATAATTTTAAAATTCTAATATATAAAAGTTTTTCTTAATTAAAATAGTAAAATGGTAAAAATA

                        *       *                                            
       3630 AAATAGGTATACGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTAC
         66 AAATAGGTATA-AGATATTACATTTAATTAAAT-AAAAATAGAGTTTTTAGTTGAGTAAAACTAC

              
       3695 AA
        129 AA

                                                                     *       
       3697 AAATATATTTTAAAAATTCTAATATATAAAAGTTTTTCTTAATTAAAATAGTAAAATTGTAAAAA
          1 AAATA-ATTTT-AAAATTCTAATATATAAAAGTTTTTCTTAATTAAAATAGTAAAATGGTAAAAA

             *      *     *                                       *         *
       3762 TTAAATAGTTATAATATATTACATTTAATTAAATAAAAATAGAGTTTTTAGTTGCGTAAAACTAT
         64 TAAAATAGGTATAAGATATTACATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAC

              
       3827 AA
        129 AA

               
       3829 AAA
          1 AAA

       3832 CTTTAAACAA


Statistics
Matches: 118,  Mismatches: 13, Indels: 6
        0.86            0.09        0.04

Matches are distributed among these distances:
 130    5  0.04
 131    5  0.04
 132   51  0.43
 133   22  0.19
 134   35  0.30

ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38


Consensus pattern (130 bp):   
AAATAATTTTAAAATTCTAATATATAAAAGTTTTTCTTAATTAAAATAGTAAAATGGTAAAAATA
AAATAGGTATAAGATATTACATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTACAA

Found at i:4429 original size:133 final size:132

Alignment explanation


    Indices: 4086--4481  Score: 582
    Period size: 131  Copynumber: 3.0  Consensus size: 132

       4076 TTTAATTAAA

                                   *                                *        
       4086 ATATTTTAAAAATTCTAATATATTTAAGTTTTTTATTAATT-AAATCAGTAAAATGATAAAAATA
          1 ATATTTTAAAAATTCTAATATATATAAG-TTTTT-TTAATTAAAAT-AGTAAAATGGTAAAAATA

                  *             *                     *                      
       4150 AAATAGGTATAAGGATATTATATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATA
         63 AAATAGTTATAAGGATATTACATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTA-A

                  
       4215 AAAAAT
        127 AAAAAT

                  *                                                      *   
       4221 ATATTTAAAAAATTCTAATATATATAAG--TTTTTAATTAAAATAGTAAAATGGTAAAAATGAAA
          1 ATATTTTAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAA

                             *                                           *   
       4284 TAGTTATAAGGATATTAGATTTAATTAAATTAAAAATAGAGTTTTTAGTTGAGTAAAACTACAAA
         66 TAGTTATAAGGATATTACATTTAATTAAA-TAAAAATAGAGTTTTTAGTTGAGTAAAACTAAAAA

             * 
       4349 AGT
        130 AAT

                       *                                                 *   
       4352 ATATTTTAAAATTTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAA
          1 ATATTTTAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAA

                   *                             *              *       *    
       4417 TAGTTATGAGGATATTACATTTAATTAAATAAAAATATAGTTTTTAGTTGAGCAAAACTATAAAA
         66 TAGTTATAAGGATATTACATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAAAAAA

       4482 TGTTTAAGAA


Statistics
Matches: 240,  Mismatches: 17, Indels: 11
        0.90            0.06        0.04

Matches are distributed among these distances:
 131   83  0.35
 132   70  0.29
 133   61  0.25
 135   26  0.11

ACGTcount: A:0.49, C:0.03, G:0.10, T:0.39


Consensus pattern (132 bp):   
ATATTTTAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAA
TAGTTATAAGGATATTACATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAAAAAA
AT

Found at i:5842 original size:18 final size:18

Alignment explanation


    Indices: 5819--5854  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       5809 TCTCCATCTC

                              
       5819 TACTCAAAGTGCTATTCA
          1 TACTCAAAGTGCTATTCA

                              
       5837 TACTCAAAGTGCTATTCA
          1 TACTCAAAGTGCTATTCA

       5855 AGCTTTCCCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33


Consensus pattern (18 bp):   
TACTCAAAGTGCTATTCA

Found at i:9472 original size:13 final size:13

Alignment explanation


    Indices: 9454--9479  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       9444 TGTAATGATA

                         
       9454 AATTATGTGTTTT
          1 AATTATGTGTTTT

                         
       9467 AATTATGTGTTTT
          1 AATTATGTGTTTT

       9480 TTTCAGCATT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62


Consensus pattern (13 bp):   
AATTATGTGTTTT
Done.