Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004160.1 Corchorus capsularis cultivar CVL-1 contig04168, 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: 9944
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Found at i:2223 original size:14 final size:14

Alignment explanation


    Indices: 2200--2236  Score: 58
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       2190 AACTAGTAGA

                           
       2200 TTTTCTTTTTCTTTT
          1 TTTTC-TTTTCTTTT

                          
       2215 TTTTCTTTTCTTTT
          1 TTTTCTTTTCTTTT

                     
       2229 TTTT-TTTT
          1 TTTTCTTTT

       2237 AATATGTCTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  13    4  0.18
  14   13  0.59
  15    5  0.23

ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89


Consensus pattern (14 bp):   
TTTTCTTTTCTTTT

Found at i:4127 original size:23 final size:23

Alignment explanation


    Indices: 4087--4130  Score: 61
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       4077 TAAAATAATT

                     *             
       4087 ATAAAAATATTGAATTCAATTAA
          1 ATAAAAATAGTGAATTCAATTAA

                        **       
       4110 ATAAAAATAGTGTTTTCAATT
          1 ATAAAAATAGTGAATTCAATT

       4131 GCAAAAGTTT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   18  1.00

ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39


Consensus pattern (23 bp):   
ATAAAAATAGTGAATTCAATTAA

Found at i:4406 original size:78 final size:78

Alignment explanation


    Indices: 4226--4476  Score: 324
    Period size: 78  Copynumber: 3.2  Consensus size: 78

       4216 TTTTTTTAAT

                          **                     *  *                    *   
       4226 TAAAATAGTAAAATATTAAAATATAATAGTTATAAGGTTAATAGATTTAATCATATAAAATTAAA
          1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAAT--TAT---ATAAAA

               *             *
       4291 ATAAAGTTTTTAGTTGAA
         61 ATAGAGTTTTTAGTTGAG

                                                                             
       4309 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
          1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA

                         
       4374 GTTTTTAGTTGAG
         66 GTTTTTAGTTGAG

                                   *           *   *   *         *    *      
       4387 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATGTTATATTTAATTAAATAATAATAGA
          1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA

                         
       4452 GTTTTTAGTTGAG
         66 GTTTTTAGTTGAG

                *        
       4465 TAAACTA-TAAAA
          1 TAAAATAGTAAAA

       4477 ACCTAAACAA


Statistics
Matches: 154,  Mismatches: 14, Indels: 6
        0.89            0.08        0.03

Matches are distributed among these distances:
  77    5  0.03
  78   99  0.64
  81    3  0.02
  83   47  0.31

ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37


Consensus pattern (78 bp):   
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG

Found at i:4951 original size:21 final size:21

Alignment explanation


    Indices: 4925--4965  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       4915 GCGATACATA

                  *  *           
       4925 ATACATTTATCGTATCGTACG
          1 ATACATGTAGCGTATCGTACG

                    *           
       4946 ATACATGTCGCGTATCGTAC
          1 ATACATGTAGCGTATCGTAC

       4966 AATATTGATA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34


Consensus pattern (21 bp):   
ATACATGTAGCGTATCGTACG

Found at i:9627 original size:2 final size:2

Alignment explanation


    Indices: 9620--9650  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       9610 ATTAGATAGC

                                        *                 
       9620 AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       9651 AATGTAAAAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (2 bp):   
AT

Found at i:9651 original size:12 final size:12

Alignment explanation


    Indices: 9620--9653  Score: 59
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       9610 ATTAGATAGC

                   *    
       9620 ATATATATATAT
          1 ATATATAAATAT

                        
       9632 ATATATAAATAT
          1 ATATATAAATAT

                      
       9644 ATATATAAAT
          1 ATATATAAAT

       9654 GTAAAAGTAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   21  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (12 bp):   
ATATATAAATAT
Done.