Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015051.1 Corchorus capsularis cultivar CVL-1 contig15072, 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: 21467
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:1041 original size:28 final size:28

Alignment explanation


    Indices: 1006--1085  Score: 115
    Period size: 28  Copynumber: 2.9  Consensus size: 28

        996 TTCGTCATAT

                              *         
       1006 TAGTTTATACTCGATCGCGGAGTTCATG
          1 TAGTTTATACTCGATCGCAGAGTTCATG

                        *              *
       1034 TAGTTTATACTCAATCGCAGAGTTCATT
          1 TAGTTTATACTCGATCGCAGAGTTCATG

                       *    *       
       1062 TAGTTTATACTTGATCACAGAGTT
          1 TAGTTTATACTCGATCGCAGAGTT

       1086 ATGCTCGACG


Statistics
Matches: 46,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  28   46  1.00

ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39


Consensus pattern (28 bp):   
TAGTTTATACTCGATCGCAGAGTTCATG

Found at i:5290 original size:21 final size:21

Alignment explanation


    Indices: 5264--5304  Score: 73
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5254 TTAACTTAGA

                           *     
       5264 TTTTTTAGAAGTATCGGATTT
          1 TTTTTTAGAAGTATCAGATTT

                                
       5285 TTTTTTAGAAGTATCAGATT
          1 TTTTTTAGAAGTATCAGATT

       5305 GATGATTAGC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.27, C:0.05, G:0.17, T:0.51


Consensus pattern (21 bp):   
TTTTTTAGAAGTATCAGATTT

Found at i:7263 original size:31 final size:31

Alignment explanation


    Indices: 7223--7301  Score: 115
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       7213 AATTTTAGCC

                                           
       7223 ACCAATTTGAGTCTAAACCTTTCAAAAGTTG
          1 ACCAATTTGAGTCTAAACCTTTCAAAAGTTG

                              **    *       
       7254 -CTCAATTTGAGTCTAAATTTTTCCAAAGTTG
          1 AC-CAATTTGAGTCTAAACCTTTCAAAAGTTG

                             
       7285 ACCAATTTGAGTCTAAA
          1 ACCAATTTGAGTCTAAA

       7302 AAAACAGAAA


Statistics
Matches: 43,  Mismatches: 3, Indels: 4
        0.86            0.06        0.08

Matches are distributed among these distances:
  30    1  0.02
  31   41  0.95
  32    1  0.02

ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35


Consensus pattern (31 bp):   
ACCAATTTGAGTCTAAACCTTTCAAAAGTTG

Found at i:11083 original size:22 final size:22

Alignment explanation


    Indices: 11047--11088  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

      11037 AGGAAATAAA

                  *               
      11047 TTAAATTCAGATTTAGCCCCAC
          1 TTAAATCCAGATTTAGCCCCAC

                      *         
      11069 TTAAATCCAGGTTTAGCCCC
          1 TTAAATCCAGATTTAGCCCC

      11089 TTGTTATAAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31


Consensus pattern (22 bp):   
TTAAATCCAGATTTAGCCCCAC

Found at i:13440 original size:27 final size:27

Alignment explanation


    Indices: 13409--13465  Score: 71
    Period size: 27  Copynumber: 2.1  Consensus size: 27

      13399 TAGTTTTTTT

                       *              * 
      13409 TTTTTTG-GCACAAGATCACTTTTTTGG
          1 TTTTTTGAGCAAAAGATCA-TTTTTTAG

                     *                 
      13436 TTTTTTGAGGAAAAGATCATTTTTTAG
          1 TTTTTTGAGCAAAAGATCATTTTTTAG

               
      13463 TTT
          1 TTT

      13466 AATAACTACT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  27   17  0.65
  28    9  0.35

ACGTcount: A:0.23, C:0.09, G:0.18, T:0.51


Consensus pattern (27 bp):   
TTTTTTGAGCAAAAGATCATTTTTTAG

Found at i:16327 original size:20 final size:19

Alignment explanation


    Indices: 16299--16337  Score: 51
    Period size: 20  Copynumber: 2.0  Consensus size: 19

      16289 CACGTGGCAT

                     *    *    
      16299 TTTTGACACGTGGCGTGCC
          1 TTTTGACACATGGCATGCC

                                
      16318 TTTTGTACACATGGCATGCC
          1 TTTTG-ACACATGGCATGCC

      16338 ACGTGTCATT


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  19    5  0.29
  20   12  0.71

ACGTcount: A:0.15, C:0.26, G:0.26, T:0.33


Consensus pattern (19 bp):   
TTTTGACACATGGCATGCC

Found at i:20025 original size:19 final size:19

Alignment explanation


    Indices: 19989--20024  Score: 65
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      19979 TGGTTCTCTA

                               
      19989 ATAAAATTATTGCTTTTTC
          1 ATAAAATTATTGCTTTTTC

                              
      20008 ATAAAATTA-TGCTTTTT
          1 ATAAAATTATTGCTTTTT

      20025 TGTCAATTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  18    8  0.47
  19    9  0.53

ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53


Consensus pattern (19 bp):   
ATAAAATTATTGCTTTTTC
Done.