Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021323.1 Corchorus olitorius cultivar O-4 contig21356, 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: 17979
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35


Found at i:2208 original size:51 final size:50

Alignment explanation


    Indices: 2107--2208  Score: 127
    Period size: 51  Copynumber: 2.0  Consensus size: 50

       2097 GTTCTTCATA

                                                     * **     
       2107 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
          1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

                                            *                    
       2157 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
          1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT

             
       2208 T
          1 T

       2209 CTTCATTTAG


Statistics
Matches: 45,  Mismatches: 4, Indels: 5
        0.83            0.07        0.09

Matches are distributed among these distances:
  50    7  0.16
  51   37  0.82
  52    1  0.02

ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41


Consensus pattern (50 bp):   
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

Found at i:6510 original size:17 final size:17

Alignment explanation


    Indices: 6488--6528  Score: 82
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       6478 TAAATATCTA

                             
       6488 CTACATGATAGGCAATC
          1 CTACATGATAGGCAATC

                             
       6505 CTACATGATAGGCAATC
          1 CTACATGATAGGCAATC

                   
       6522 CTACATG
          1 CTACATG

       6529 CTAGAAATTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   24  1.00

ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24


Consensus pattern (17 bp):   
CTACATGATAGGCAATC

Found at i:6548 original size:15 final size:15

Alignment explanation


    Indices: 6528--6558  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       6518 AATCCTACAT

                           
       6528 GCTAGAAATTTTCTA
          1 GCTAGAAATTTTCTA

                           
       6543 GCTAGAAATTTTCTA
          1 GCTAGAAATTTTCTA

             
       6558 G
          1 G

       6559 ACAATTCTAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39


Consensus pattern (15 bp):   
GCTAGAAATTTTCTA

Found at i:14698 original size:36 final size:36

Alignment explanation


    Indices: 14651--14720  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

      14641 TTAAATAACC

                         *      *               
      14651 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

                  *                           
      14687 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCT

      14721 CCAAAATCTC


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

Found at i:15737 original size:24 final size:23

Alignment explanation


    Indices: 15705--15750  Score: 83
    Period size: 24  Copynumber: 2.0  Consensus size: 23

      15695 ACGTTTGCAC

                                    
      15705 AAATACCTAAGAATTTGAATTAAA
          1 AAATACCTAAGAATTT-AATTAAA

                                  
      15729 AAATACCTAAGAATTTAATTAA
          1 AAATACCTAAGAATTTAATTAA

      15751 TGTAAGTATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  23    6  0.27
  24   16  0.73

ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30


Consensus pattern (23 bp):   
AAATACCTAAGAATTTAATTAAA
Done.