Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009598.1 Corchorus olitorius cultivar O-4 contig09630, 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: 7107
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:8 original size:2 final size:2

Alignment explanation


    Indices: 2--38  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

          1 C

                                                                   
          2 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

         39 CTATGAATTG


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:3063 original size:2 final size:2

Alignment explanation


    Indices: 3056--3091  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       3046 ATAATATTCC

                                                                 
       3056 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

       3092 AAGCAGAATT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:4670 original size:21 final size:20

Alignment explanation


    Indices: 4607--4670  Score: 58
    Period size: 21  Copynumber: 3.1  Consensus size: 20

       4597 TTGACACTGT

                         *       
       4607 TTAGATACTGTACTGATGAGA
          1 TTAG-TACTGTACAGATGAGA

                *           * * 
       4628 TTA-CACTGTACAGATTAAA
          1 TTAGTACTGTACAGATGAGA

                          *      
       4647 TTAGGTACTGTACAAATGAGA
          1 TTA-GTACTGTACAGATGAGA

               
       4668 TTA
          1 TTA

       4671 TTAGAGCAGC


Statistics
Matches: 33,  Mismatches: 8, Indels: 4
        0.73            0.18        0.09

Matches are distributed among these distances:
  19   15  0.45
  21   18  0.55

ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33


Consensus pattern (20 bp):   
TTAGTACTGTACAGATGAGA

Found at i:6494 original size:29 final size:29

Alignment explanation


    Indices: 6461--6517  Score: 71
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       6451 TGTTGGTAGA

                                           
       6461 AAAAATATAATTAGTTGG-TATTTCCGTCGC
          1 AAAAA-ATAATTAG-TGGATATTTCCGTCGC

                   *              *    
       6491 AAAAAATTATTAGTGGATATTTTCGTC
          1 AAAAAATAATTAGTGGATATTTCCGTC

       6518 ACTTATAATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  28    3  0.12
  29   16  0.67
  30    5  0.21

ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39


Consensus pattern (29 bp):   
AAAAAATAATTAGTGGATATTTCCGTCGC

Found at i:7034 original size:3 final size:3

Alignment explanation


    Indices: 7026--7107  Score: 164
    Period size: 3  Copynumber: 27.3  Consensus size: 3

       7016 NCNCNCACAC

                                                                           
       7026 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
          1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT

                                                         
       7074 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT A
          1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT A


Statistics
Matches: 79,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   79  1.00

ACGTcount: A:0.34, C:0.33, G:0.00, T:0.33


Consensus pattern (3 bp):   
ACT

Done.