Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012182.1 Corchorus olitorius cultivar O-4 contig12215, 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: 16521
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:3034 original size:20 final size:21

Alignment explanation


    Indices: 2999--3039  Score: 66
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       2989 ATGAACAAAG

                 *               
       2999 ATAGATAAATAGCACAGGGCT
          1 ATAGAGAAATAGCACAGGGCT

                                 
       3020 ATAGAGAAA-AGCACAGGGCT
          1 ATAGAGAAATAGCACAGGGCT

       3040 TCGGTTTTTG


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20   11  0.58
  21    8  0.42

ACGTcount: A:0.44, C:0.15, G:0.27, T:0.15


Consensus pattern (21 bp):   
ATAGAGAAATAGCACAGGGCT

Found at i:4702 original size:2 final size:2

Alignment explanation


    Indices: 4697--4732  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       4687 TCTTATTTCA

                                                                 
       4697 AT AT AT AT 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 AT AT AT AT

       4733 CCCTTTGGGG


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):   
AT

Found at i:9088 original size:51 final size:52

Alignment explanation


    Indices: 8987--9088  Score: 120
    Period size: 51  Copynumber: 2.0  Consensus size: 52

       8977 GTTCATCAAA

                                                     * **       
       8987 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTT
          1 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT

                                     *     *                     
       9039 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
          1 TTCTCCTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT

       9089 CTTCATTCAG


Statistics
Matches: 43,  Mismatches: 5, Indels: 5
        0.81            0.09        0.09

Matches are distributed among these distances:
  50    2  0.05
  51   36  0.84
  52    5  0.12

ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40


Consensus pattern (52 bp):   
TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT

Found at i:11315 original size:16 final size:15

Alignment explanation


    Indices: 11277--11318  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      11267 ACAGAGATTG

                   *       
      11277 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
      11292 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      11307 ACTAGAAAACAA
          1 AC-AGAAAACAA

      11319 AACAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:12094 original size:11 final size:11

Alignment explanation


    Indices: 12078--12103  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

      12068 CCTTTGCCTA

                       
      12078 AAAACTAGAAG
          1 AAAACTAGAAG

                       
      12089 AAAACTAGAAG
          1 AAAACTAGAAG

                
      12100 AAAA
          1 AAAA

      12104 GAAATTATAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG
Done.