Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014073.1 Corchorus capsularis cultivar CVL-1 contig14094, 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: 31731
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:1672 original size:17 final size:17

Alignment explanation


    Indices: 1650--1683  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       1640 ATTGGATTTA

                             
       1650 GTTTTAGATGTATCTGG
          1 GTTTTAGATGTATCTGG

                             
       1667 GTTTTAGATGTATCTGG
          1 GTTTTAGATGTATCTGG

       1684 ATTTCTTCAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.18, C:0.06, G:0.29, T:0.47


Consensus pattern (17 bp):   
GTTTTAGATGTATCTGG

Found at i:2603 original size:12 final size:12

Alignment explanation


    Indices: 2586--2615  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       2576 CTTGAGAAAA

                    *   
       2586 TATTTTCCTTAG
          1 TATTTTCCATAG

                        
       2598 TATTTTCCATAG
          1 TATTTTCCATAG

                  
       2610 TATTTT
          1 TATTTT

       2616 TCTTGACACC


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

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60


Consensus pattern (12 bp):   
TATTTTCCATAG

Found at i:4768 original size:20 final size:20

Alignment explanation


    Indices: 4743--4780  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4733 ATTTTGTGAA

                                
       4743 TTACTAAATACCGCCCCCTT
          1 TTACTAAATACCGCCCCCTT

                  **          
       4763 TTACTAGCTACCGCCCCC
          1 TTACTAAATACCGCCCCC

       4781 CCTTTGGATT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.21, C:0.45, G:0.08, T:0.26


Consensus pattern (20 bp):   
TTACTAAATACCGCCCCCTT

Found at i:5741 original size:5 final size:5

Alignment explanation


    Indices: 5733--5760  Score: 56
    Period size: 5  Copynumber: 5.6  Consensus size: 5

       5723 TTTTCTTTTT

                                             
       5733 GTTTA GTTTA GTTTA GTTTA GTTTA GTT
          1 GTTTA GTTTA GTTTA GTTTA GTTTA GTT

       5761 AAATTTTAAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   23  1.00

ACGTcount: A:0.18, C:0.00, G:0.21, T:0.61


Consensus pattern (5 bp):   
GTTTA

Found at i:7403 original size:21 final size:22

Alignment explanation


    Indices: 7353--7405  Score: 56
    Period size: 21  Copynumber: 2.4  Consensus size: 22

       7343 TGCTTGCCGC

                       *          
       7353 AAGCGGGGAGGTCAGCTTGACA
          1 AAGCGGGGAGGCCAGCTTGACA

               *                   
       7375 AGAACGGGGA-GCCA-CTTGACA
          1 A-AGCGGGGAGGCCAGCTTGACA

                      
       7396 TAAGCGGGGA
          1 -AAGCGGGGA

       7406 TGTTACCTTG


Statistics
Matches: 26,  Mismatches: 3, Indels: 5
        0.76            0.09        0.15

Matches are distributed among these distances:
  21   14  0.54
  22    5  0.19
  23    7  0.27

ACGTcount: A:0.30, C:0.19, G:0.40, T:0.11


Consensus pattern (22 bp):   
AAGCGGGGAGGCCAGCTTGACA

Found at i:15263 original size:15 final size:15

Alignment explanation


    Indices: 15239--15282  Score: 54
    Period size: 15  Copynumber: 2.9  Consensus size: 15

      15229 ATCACAAGAT

                 *         
      15239 TATAGGCCATTTCCA
          1 TATAGTCCATTTCCA

                         * 
      15254 TATAGTCCATTT-GA
          1 TATAGTCCATTTCCA

                           
      15268 TCATAGTCCATTTCC
          1 T-ATAGTCCATTTCC

      15283 TAGCCCTAAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  14    2  0.08
  15   22  0.92

ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39


Consensus pattern (15 bp):   
TATAGTCCATTTCCA

Found at i:19614 original size:89 final size:89

Alignment explanation


    Indices: 19463--19645  Score: 330
    Period size: 89  Copynumber: 2.1  Consensus size: 89

      19453 CACCGAGCAG

                         *             *                                     
      19463 CCCATATACATGTTGGACACCAATCCTGAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTT
          1 CCCATATACATGTCGGACACCAATCCTAAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTT

                                    
      19528 CATGTATATAAGCTACTCCAACAA
         66 CATGTATATAAGCTACTCCAACAA

                    *                                                        
      19552 CCCATATATATGTCGGACACCAATCCTAAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTT
          1 CCCATATACATGTCGGACACCAATCCTAAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTT

                        *           
      19617 CATGTATATAAGTTACTCCAACAA
         66 CATGTATATAAGCTACTCCAACAA

                 
      19641 CCCAT
          1 CCCAT

      19646 CTCTTCATGA


Statistics
Matches: 90,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  89   90  1.00

ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28


Consensus pattern (89 bp):   
CCCATATACATGTCGGACACCAATCCTAAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTT
CATGTATATAAGCTACTCCAACAA
Done.