Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008678.1 Corchorus capsularis cultivar CVL-1 contig08699, 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: 34112
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:6622 original size:16 final size:16

Alignment explanation


    Indices: 6600--6641  Score: 52
    Period size: 14  Copynumber: 2.8  Consensus size: 16

       6590 TTGTAGTTTG

                         *  
       6600 AATTCAGTACTTTTAA
          1 AATTCAGTACTTTAAA

            *               
       6616 GATTCAGTA--TTAAA
          1 AATTCAGTACTTTAAA

                        
       6630 AATTCAGTACTT
          1 AATTCAGTACTT

       6642 AATCTTTCAG


Statistics
Matches: 21,  Mismatches: 3, Indels: 4
        0.75            0.11        0.14

Matches are distributed among these distances:
  14   12  0.57
  16    9  0.43

ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40


Consensus pattern (16 bp):   
AATTCAGTACTTTAAA

Found at i:6665 original size:14 final size:15

Alignment explanation


    Indices: 6632--6666  Score: 63
    Period size: 15  Copynumber: 2.4  Consensus size: 15

       6622 GTATTAAAAA

                           
       6632 TTCAGTACTTAATCT
          1 TTCAGTACTTAATCT

                           
       6647 TTCAGTACTTAAT-T
          1 TTCAGTACTTAATCT

                  
       6661 TTCAGT
          1 TTCAGT

       6667 TTTATCAAAC


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  14    7  0.35
  15   13  0.65

ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49


Consensus pattern (15 bp):   
TTCAGTACTTAATCT

Found at i:10008 original size:17 final size:17

Alignment explanation


    Indices: 9986--10022  Score: 65
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       9976 ATTATCCAGC

                             
       9986 ACCTCATGCTACCTAGT
          1 ACCTCATGCTACCTAGT

                          *  
      10003 ACCTCATGCTACCTGGT
          1 ACCTCATGCTACCTAGT

               
      10020 ACC
          1 ACC

      10023 ATGAGGAGGG


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

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.22, C:0.38, G:0.14, T:0.27


Consensus pattern (17 bp):   
ACCTCATGCTACCTAGT

Found at i:22604 original size:17 final size:17

Alignment explanation


    Indices: 22582--22618  Score: 65
    Period size: 17  Copynumber: 2.2  Consensus size: 17

      22572 GGTATCCAGC

                             
      22582 ACCTCATGCTACCTAGT
          1 ACCTCATGCTACCTAGT

                          *  
      22599 ACCTCATGCTACCTGGT
          1 ACCTCATGCTACCTAGT

               
      22616 ACC
          1 ACC

      22619 ATGAGGGACG


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

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.22, C:0.38, G:0.14, T:0.27


Consensus pattern (17 bp):   
ACCTCATGCTACCTAGT

Found at i:25128 original size:24 final size:24

Alignment explanation


    Indices: 25094--25141  Score: 71
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      25084 CTAAGCTACC

                  *                  
      25094 TCTCTCTTTCT-CTTTCTTTGTTTT
          1 TCTCTCCTTCTGCTTT-TTTGTTTT

                                    
      25118 TCTCTCCTTCTGCTTTTTTGTTTT
          1 TCTCTCCTTCTGCTTTTTTGTTTT

      25142 AGGTATTAAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  24   18  0.82
  25    4  0.18

ACGTcount: A:0.00, C:0.25, G:0.06, T:0.69


Consensus pattern (24 bp):   
TCTCTCCTTCTGCTTTTTTGTTTT

Found at i:25704 original size:2 final size:2

Alignment explanation


    Indices: 25699--25734  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      25689 AATGAGCATC

                                                                 
      25699 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

      25735 CTTTGCCGGA


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:32728 original size:2 final size:2

Alignment explanation


    Indices: 32721--32765  Score: 81
    Period size: 2  Copynumber: 22.0  Consensus size: 2

      32711 TGCCATCATG

                                                                           
      32721 AT AT AT AT AT CAT 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 AT AT AT

              
      32764 AT
          1 AT

      32766 GATGAGGGTT


Statistics
Matches: 42,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   40  0.95
   3    2  0.05

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.