Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004982.1 Corchorus capsularis cultivar CVL-1 contig05000, 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: 8525
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37


Found at i:5282 original size:27 final size:27

Alignment explanation


    Indices: 5252--5304  Score: 106
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       5242 ATGAAGTTTA

                                       
       5252 ATGGGTTTAGTAGAAATAGCTCTTTTG
          1 ATGGGTTTAGTAGAAATAGCTCTTTTG

                                      
       5279 ATGGGTTTAGTAGAAATAGCTCTTTT
          1 ATGGGTTTAGTAGAAATAGCTCTTTT

       5305 ATATGGCCAC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.26, C:0.08, G:0.25, T:0.42


Consensus pattern (27 bp):   
ATGGGTTTAGTAGAAATAGCTCTTTTG

Found at i:6844 original size:36 final size:35

Alignment explanation


    Indices: 6737--6846  Score: 93
    Period size: 33  Copynumber: 3.2  Consensus size: 35

       6727 AAATTGTATG

                              *       *        
       6737 ATTTTTTACCTTATTAAGGATTTC-ACATTCAATA
          1 ATTTTTTACCTTATTAAGAATTTCTAAATTCAATA

                       * *          *      **  *
       6771 ATTTTTT--CTAACTACA-AATTTGTAAATTGTATG
          1 ATTTTTTACCTTATTA-AGAATTTCTAAATTCAATA

                                       *        
       6804 ATTTTTTACCTTATTAAGAATTTCATATATTCAATA
          1 ATTTTTTACCTTATTAAGAATTTC-TAAATTCAATA

                   
       6840 ATTTTTT
          1 ATTTTTT

       6847 CAGCATTATA


Statistics
Matches: 55,  Mismatches: 15, Indels: 10
        0.69            0.19        0.12

Matches are distributed among these distances:
  32    9  0.16
  33   14  0.25
  34    8  0.15
  35   10  0.18
  36   14  0.25

ACGTcount: A:0.33, C:0.11, G:0.05, T:0.51


Consensus pattern (35 bp):   
ATTTTTTACCTTATTAAGAATTTCTAAATTCAATA

Found at i:6954 original size:22 final size:22

Alignment explanation


    Indices: 6928--6971  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       6918 ATTACCATTT

                                  
       6928 TACTAATATTAATCAATTATTC
          1 TACTAATATTAATCAATTATTC

                                  
       6950 TACTAATATTAATCAATTATTC
          1 TACTAATATTAATCAATTATTC

       6972 GCATACACCC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45


Consensus pattern (22 bp):   
TACTAATATTAATCAATTATTC

Found at i:8427 original size:16 final size:17

Alignment explanation


    Indices: 8406--8437  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

       8396 TTCGATTAGC

                             
       8406 TTTCCCTT-TATTACAT
          1 TTTCCCTTCTATTACAT

                            
       8422 TTTCCCTTCTATTACA
          1 TTTCCCTTCTATTACA

       8438 CATTATTTAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    8  0.53
  17    7  0.47

ACGTcount: A:0.19, C:0.28, G:0.00, T:0.53


Consensus pattern (17 bp):   
TTTCCCTTCTATTACAT

Found at i:8477 original size:2 final size:2

Alignment explanation


    Indices: 8472--8525  Score: 83
    Period size: 2  Copynumber: 27.0  Consensus size: 2

       8462 ACACACACAC

                                          *                                
       8472 AT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT AT AT AT AT AT -T
          1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT

                             
       8514 AT AT AT AT AT AT
          1 AT AT AT AT AT AT


Statistics
Matches: 48,  Mismatches: 2, Indels: 4
        0.89            0.04        0.07

Matches are distributed among these distances:
   1    1  0.02
   2   45  0.94
   3    2  0.04

ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.