Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013548.1 Corchorus capsularis cultivar CVL-1 contig13569, 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: 19904
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:2105 original size:26 final size:27

Alignment explanation


    Indices: 2048--2118  Score: 99
    Period size: 26  Copynumber: 2.7  Consensus size: 27

       2038 AAGTGAACTT

                                     **
       2048 AAAATGACCAAAATGCCCTTGAGTATG
          1 AAAATGACCAAAATGCCCTTGAGTACA

            *                          
       2075 CAAATGACCAAAATGCCCTT-AGTACA
          1 AAAATGACCAAAATGCCCTTGAGTACA

                    *         
       2101 AAAATGACAAAAATGCCC
          1 AAAATGACCAAAATGCCC

       2119 CCTAGGTGAC


Statistics
Matches: 39,  Mismatches: 5, Indels: 1
        0.87            0.11        0.02

Matches are distributed among these distances:
  26   20  0.51
  27   19  0.49

ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18


Consensus pattern (27 bp):   
AAAATGACCAAAATGCCCTTGAGTACA

Found at i:7280 original size:23 final size:23

Alignment explanation


    Indices: 7248--7299  Score: 68
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       7238 GGCAAAAATG

                 *       *         
       7248 GCATCGCAAGCTATATACAAAAA
          1 GCATCACAAGCTACATACAAAAA

                        *          
       7271 GCATCACAAGCTCCATACAAAAA
          1 GCATCACAAGCTACATACAAAAA

             *    
       7294 GAATCA
          1 GCATCA

       7300 TCATCATCTT


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   25  1.00

ACGTcount: A:0.48, C:0.25, G:0.12, T:0.15


Consensus pattern (23 bp):   
GCATCACAAGCTACATACAAAAA

Found at i:7898 original size:2 final size:2

Alignment explanation


    Indices: 7885--7954  Score: 51
    Period size: 2  Copynumber: 36.5  Consensus size: 2

       7875 TTTTAATTGA

                      *                          *         *              * 
       7885 AT AT AT AA AT AT AT AT AT AT AT AT AA AT GA- AG A- AT -T AGT TT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT A-T AT

                                                          
       7926 AT AT AT AT AT AT AT AT AT -T AT -T AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       7955 ATTGAATTAG


Statistics
Matches: 55,  Mismatches: 6, Indels: 14
        0.73            0.08        0.19

Matches are distributed among these distances:
   1    5  0.09
   2   48  0.87
   3    2  0.04

ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:8450 original size:19 final size:18

Alignment explanation


    Indices: 8426--8461  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       8416 TGAAGATTTC

                               
       8426 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       8445 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       8462 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT
Done.