Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022393.1 Corchorus olitorius cultivar O-4 contig22426, 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: 10726
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37


Found at i:1638 original size:24 final size:23

Alignment explanation


    Indices: 1611--1658  Score: 60
    Period size: 24  Copynumber: 2.0  Consensus size: 23

       1601 ATACTACAAA

                   *          *     
       1611 TTAATATGTGATTTATTATATTAT
          1 TTAATATATGATTTA-TAAATTAT

                 *                 
       1635 TTAATTTATGATTTATAAATTAT
          1 TTAATATATGATTTATAAATTAT

             
       1658 T
          1 T

       1659 AACATACGTG


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  23    8  0.38
  24   13  0.62

ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58


Consensus pattern (23 bp):   
TTAATATATGATTTATAAATTAT

Found at i:1696 original size:2 final size:2

Alignment explanation


    Indices: 1689--1730  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       1679 ACTTTAACTC

                                                                          
       1689 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1731 GTCAATGTCT


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:7560 original size:38 final size:37

Alignment explanation


    Indices: 7446--7562  Score: 95
    Period size: 38  Copynumber: 3.2  Consensus size: 37

       7436 CTTCTTTTGT

                                          *        
       7446 TGATTTCGTTTTCTTCAGTTTTAACTTCCCATCTGGATC
          1 TGATTTCG-TTTCTTCAGTTTTAACTTCCCTTCT-GATC

                         *            *         *  
       7485 TGATTTC-TTGTGTTTC--TTTT--CAT--CTTCTGTTC
          1 TGATTTCGTT-T-CTTCAGTTTTAACTTCCCTTCTGATC

                                                   
       7517 TTGATTTCGTTTCTTCAGTTTTAACTTCCCTTCTAGATC
          1 -TGATTTCGTTTCTTCAGTTTTAACTTCCCTTCT-GATC

                   
       7556 TGATTTC
          1 TGATTTC

       7563 TTGTATTTCT


Statistics
Matches: 60,  Mismatches: 7, Indels: 23
        0.67            0.08        0.26

Matches are distributed among these distances:
  32    6  0.10
  33   12  0.20
  34    6  0.10
  35    2  0.03
  36    2  0.03
  37    6  0.10
  38   13  0.22
  39   13  0.22

ACGTcount: A:0.13, C:0.21, G:0.12, T:0.54


Consensus pattern (37 bp):   
TGATTTCGTTTCTTCAGTTTTAACTTCCCTTCTGATC

Found at i:7562 original size:71 final size:72

Alignment explanation


    Indices: 7402--7592  Score: 303
    Period size: 71  Copynumber: 2.7  Consensus size: 72

       7392 TCTCTCTATT

                             **                       *                      
       7402 CCTTCTAGATCTGATTTAGTGTATTTCTTTTCATCTTCTTTTGTTGATTTCGTTTTCTTCAGTTT
          1 CCTTCTAGATCTGATTTCTTGTATTTCTTTTCATCTTCTTTTCTTGATTTCGTTTTCTTCAGTTT

                   
       7467 TAACTTC
         66 TAACTTC

              *   *               *                *                         
       7474 CCATCTGGATCTGATTTCTTGTGTTTCTTTTCATCTTCTGTTCTTGATTTCG-TTTCTTCAGTTT
          1 CCTTCTAGATCTGATTTCTTGTATTTCTTTTCATCTTCTTTTCTTGATTTCGTTTTCTTCAGTTT

                   
       7538 TAACTTC
         66 TAACTTC

                                           *                
       7545 CCTTCTAGATCTGATTTCTTGTATTTCTTTTTATCTTCTTTTCTTGAT
          1 CCTTCTAGATCTGATTTCTTGTATTTCTTTTCATCTTCTTTTCTTGAT

       7593 AGCTTTGTTT


Statistics
Matches: 107,  Mismatches: 12, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  71   62  0.58
  72   45  0.42

ACGTcount: A:0.13, C:0.19, G:0.11, T:0.57


Consensus pattern (72 bp):   
CCTTCTAGATCTGATTTCTTGTATTTCTTTTCATCTTCTTTTCTTGATTTCGTTTTCTTCAGTTT
TAACTTC

Found at i:9761 original size:13 final size:13

Alignment explanation


    Indices: 9743--9768  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       9733 TTTGCCTAAG

                         
       9743 CTTTTAGTTTTGC
          1 CTTTTAGTTTTGC

                         
       9756 CTTTTAGTTTTGC
          1 CTTTTAGTTTTGC

       9769 AAAAGATACT


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:0.08, C:0.15, G:0.15, T:0.62


Consensus pattern (13 bp):   
CTTTTAGTTTTGC
Done.