Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001553.1 Corchorus capsularis cultivar CVL-1 contig01553, 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: 5930
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29


Found at i:42 original size:2 final size:2

Alignment explanation


    Indices: 1--28  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

                                                     
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         29 CACTAAGATA


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

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:4085 original size:20 final size:19

Alignment explanation


    Indices: 4027--4099  Score: 60
    Period size: 20  Copynumber: 3.6  Consensus size: 19

       4017 AATTATTAAC

                                 
       4027 ATATATAA-ATAATAATATCA
          1 ATATATAATATAA-AATAT-A

                           *     
       4047 GATATATAAT-TATATATATA
          1 -ATATATAATATA-AAATATA

                                
       4067 TATATATAATATAAAATATA
          1 -ATATATAATATAAAATATA

             *           
       4087 AGATTATAATATA
          1 ATA-TATAATATA

       4100 TATATCATGA


Statistics
Matches: 44,  Mismatches: 4, Indels: 9
        0.77            0.07        0.16

Matches are distributed among these distances:
  19    2  0.05
  20   25  0.57
  21   16  0.36
  22    1  0.02

ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40


Consensus pattern (19 bp):   
ATATATAATATAAAATATA

Found at i:4085 original size:41 final size:39

Alignment explanation


    Indices: 4027--4104  Score: 113
    Period size: 41  Copynumber: 1.9  Consensus size: 39

       4017 AATTATTAAC

                              *                      
       4027 ATATATAAATAATAATATCAGATATATAATTATATATATAT
          1 ATATATAAATAATAATATAAGAT-TATAA-TATATATATAT

                                                  
       4068 ATATATAATATAA-AATATAAGATTATAATATATATAT
          1 ATATATAA-ATAATAATATAAGATTATAATATATATAT

       4105 CATGATTTGG


Statistics
Matches: 35,  Mismatches: 1, Indels: 4
        0.88            0.03        0.10

Matches are distributed among these distances:
  39    9  0.26
  40    5  0.14
  41   17  0.49
  42    4  0.11

ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41


Consensus pattern (39 bp):   
ATATATAAATAATAATATAAGATTATAATATATATATAT

Found at i:4111 original size:20 final size:20

Alignment explanation


    Indices: 4047--4110  Score: 69
    Period size: 20  Copynumber: 3.1  Consensus size: 20

       4037 AATAATATCA

                                 
       4047 GATATATAATTATATATATAT
          1 GATATATAA-TATATATATAT

                          *     *
       4068 -ATATATAATATAAAATATAA
          1 GATATATAATAT-ATATATAT

                                 
       4088 GAT-TATAATATATATATCAT
          1 GATATATAATATATATAT-AT

               
       4108 GAT
          1 GAT

       4111 TTGGTCGGTT


Statistics
Matches: 36,  Mismatches: 4, Indels: 7
        0.77            0.09        0.15

Matches are distributed among these distances:
  19    8  0.22
  20   26  0.72
  21    2  0.06

ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42


Consensus pattern (20 bp):   
GATATATAATATATATATAT
Done.