Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010682.1 Corchorus olitorius cultivar O-4 contig10714, 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: 17474
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24


Found at i:2691 original size:40 final size:40

Alignment explanation


    Indices: 2639--2737  Score: 155
    Period size: 40  Copynumber: 2.5  Consensus size: 40

       2629 ACATTCCAAC

                          *                          
       2639 TGATTGATTGTTACGAAAGAGTGT-GATAGATAAAACTGAT
          1 TGATTGATTGTTACAAAAGA-TGTCGATAGATAAAACTGAT

                                 *            *     
       2679 TGATTGATTGTTACAAAAGATTTCGATAGATAAATCTGAT
          1 TGATTGATTGTTACAAAAGATGTCGATAGATAAAACTGAT

                               
       2719 TGATTGATTGTTACAAAAG
          1 TGATTGATTGTTACAAAAG

       2738 TCTGGCCAAC


Statistics
Matches: 55,  Mismatches: 3, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  39    2  0.04
  40   53  0.96

ACGTcount: A:0.37, C:0.06, G:0.21, T:0.35


Consensus pattern (40 bp):   
TGATTGATTGTTACAAAAGATGTCGATAGATAAAACTGAT

Found at i:2696 original size:23 final size:23

Alignment explanation


    Indices: 2670--2736  Score: 56
    Period size: 19  Copynumber: 3.2  Consensus size: 23

       2660 TGTGATAGAT

                                   
       2670 AAAACTGATTGATTGATTGTTAC
          1 AAAACTGATTGATTGATTGTTAC

                         *   *    *
       2693 AAAA--GATT--TCGATAG--AT
          1 AAAACTGATTGATTGATTGTTAC

               *                   
       2710 AAATCTGATTGATTGATTGTTAC
          1 AAAACTGATTGATTGATTGTTAC

                
       2733 AAAA
          1 AAAA

       2737 GTCTGGCCAA


Statistics
Matches: 30,  Mismatches: 8, Indels: 12
        0.60            0.16        0.24

Matches are distributed among these distances:
  17    4  0.13
  19    9  0.30
  21    9  0.30
  23    8  0.27

ACGTcount: A:0.40, C:0.07, G:0.16, T:0.36


Consensus pattern (23 bp):   
AAAACTGATTGATTGATTGTTAC

Found at i:11082 original size:148 final size:148

Alignment explanation


    Indices: 10814--11110  Score: 576
    Period size: 148  Copynumber: 2.0  Consensus size: 148

      10804 ATGACCATGC

                                                                             
      10814 AAGCGCAGAAACATAAAATACTCAAGGTTATGAAGACACCATATTGATGAGTAACACATAGTTCC
          1 AAGCGCAGAAACATAAAATACTCAAGGTTATGAAGACACCATATTGATGAGTAACACATAGTTCC

                                                                             
      10879 ACTAAACTGTTTTCTTTTAAAGCCCAAATAGGAATTTTGCACACAAAAATGATTGGCGAGGAACT
         66 ACTAAACTGTTTTCTTTTAAAGCCCAAATAGGAATTTTGCACACAAAAATGATTGGCGAGGAACT

                 *            
      10944 AACTTGATATATATATAT
        131 AACTTAATATATATATAT

                                                                       *     
      10962 AAGCGCAGAAACATAAAATACTCAAGGTTATGAAGACACCATATTGATGAGTAACACATTGTTCC
          1 AAGCGCAGAAACATAAAATACTCAAGGTTATGAAGACACCATATTGATGAGTAACACATAGTTCC

                                                                             
      11027 ACTAAACTGTTTTCTTTTAAAGCCCAAATAGGAATTTTGCACACAAAAATGATTGGCGAGGAACT
         66 ACTAAACTGTTTTCTTTTAAAGCCCAAATAGGAATTTTGCACACAAAAATGATTGGCGAGGAACT

                              
      11092 AACTTAATATATATATAT
        131 AACTTAATATATATATAT

             
      11110 A
          1 A

      11111 TATATATATA


Statistics
Matches: 147,  Mismatches: 2, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 148  147  1.00

ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28


Consensus pattern (148 bp):   
AAGCGCAGAAACATAAAATACTCAAGGTTATGAAGACACCATATTGATGAGTAACACATAGTTCC
ACTAAACTGTTTTCTTTTAAAGCCCAAATAGGAATTTTGCACACAAAAATGATTGGCGAGGAACT
AACTTAATATATATATAT

Found at i:12418 original size:67 final size:65

Alignment explanation


    Indices: 12307--12440  Score: 214
    Period size: 67  Copynumber: 2.0  Consensus size: 65

      12297 AATATGTATG

                                     *     *                     *           
      12307 AACATAAATTAAAAATACATATGAGGTAATATATATGAAGGTAACTATATTGCTAATGAAGTACC
          1 AACATAAATTAAAAATACATATGAGCTAATAAATATGAAGGTAAC--TATTGCCAATGAAGTACC

              
      12372 AT
         64 AT

                                                   *                         
      12374 AACATAAATTAAAAATACATATGAGCTAATAAATATGAATGTAACTATTGCCAATGAAGTACCAT
          1 AACATAAATTAAAAATACATATGAGCTAATAAATATGAAGGTAACTATTGCCAATGAAGTACCAT

              
      12439 AA
          1 AA

      12441 AAGGGTCTCG


Statistics
Matches: 63,  Mismatches: 4, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
  65   21  0.33
  67   42  0.67

ACGTcount: A:0.49, C:0.10, G:0.12, T:0.28


Consensus pattern (65 bp):   
AACATAAATTAAAAATACATATGAGCTAATAAATATGAAGGTAACTATTGCCAATGAAGTACCAT

Found at i:15043 original size:151 final size:151

Alignment explanation


    Indices: 14769--15060  Score: 521
    Period size: 151  Copynumber: 1.9  Consensus size: 151

      14759 ATGACCGAGT

                                                                             
      14769 ATCCCAAATATACATAGCTATGGAAAGCATTAAGCATGGACGACATATGGCTGAGTACGTTAAAC
          1 ATCCCAAATATACATAGCTATGGAAAGCATTAAGCATGGACGACATATGGCTGAGTACGTTAAAC

                            *                           *                    
      14834 ATACATAGATATAAAATTGATAATGAATTATATAAGAACTTCAATAGGTAAGAGATATACATGAG
         66 ATACATAGATATAAAAATGATAATGAATTATATAAGAACTTCAACAGGTAAGAGATATACATGAG

               *                 
      14899 GTCGAATTTGATATGGAAAGC
        131 GTCAAATTTGATATGGAAAGC

                                       *   *                          *    * 
      14920 ATCCCAAATATACATAGCTATGGAAAGTATTCAGCATGGACGACATATGGCTGAGTACTTTAAGC
          1 ATCCCAAATATACATAGCTATGGAAAGCATTAAGCATGGACGACATATGGCTGAGTACGTTAAAC

                                                                             
      14985 ATACATAGATATAAAAATGATAATGAATTATATAAGAACTTCAACAGGTAAGAGATATACATGAG
         66 ATACATAGATATAAAAATGATAATGAATTATATAAGAACTTCAACAGGTAAGAGATATACATGAG

                       
      15050 GTCAAATTTGA
        131 GTCAAATTTGA

      15061 CTCAACTTTC


Statistics
Matches: 134,  Mismatches: 7, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 151  134  1.00

ACGTcount: A:0.42, C:0.12, G:0.18, T:0.27


Consensus pattern (151 bp):   
ATCCCAAATATACATAGCTATGGAAAGCATTAAGCATGGACGACATATGGCTGAGTACGTTAAAC
ATACATAGATATAAAAATGATAATGAATTATATAAGAACTTCAACAGGTAAGAGATATACATGAG
GTCAAATTTGATATGGAAAGC
Done.