Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009243.1 Corchorus capsularis cultivar CVL-1 contig09264, 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: 25627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:2546 original size:19 final size:19

Alignment explanation


    Indices: 2523--2565  Score: 63
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       2513 TCATTTATAA

                               
       2523 ATATAATTAT-TTATTTAT
          1 ATATAATTATATTATTTAT

                                
       2541 AT-TATATTATATTATTTAT
          1 ATATA-ATTATATTATTTAT

                  
       2560 ATATAA
          1 ATATAA

       2566 ATACGGGCCA


Statistics
Matches: 22,  Mismatches: 0, Indels: 5
        0.81            0.00        0.19

Matches are distributed among these distances:
  17    2  0.09
  18    7  0.32
  19   11  0.50
  20    2  0.09

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (19 bp):   
ATATAATTATATTATTTAT

Found at i:3915 original size:23 final size:24

Alignment explanation


    Indices: 3867--3914  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       3857 TGTAAAAAGT

                                    
       3867 GAGGCGGTGAATAGCAAAAATGGG
          1 GAGGCGGTGAATAGCAAAAATGGG

                                    
       3891 GAGGCGGTGAATAGCAAAAATGGG
          1 GAGGCGGTGAATAGCAAAAATGGG

       3915 ACGGTATTTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.38, C:0.08, G:0.42, T:0.12


Consensus pattern (24 bp):   
GAGGCGGTGAATAGCAAAAATGGG

Found at i:6265 original size:11 final size:11

Alignment explanation


    Indices: 6251--6288  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       6241 ATTCATAACA

                       
       6251 AATTTATAATT
          1 AATTTATAATT

                       
       6262 AATTTATAATT
          1 AATTTATAATT

                        
       6273 -ATTTGATAATT
          1 AATTT-ATAATT

            *    
       6284 TATTT
          1 AATTT

       6289 TATATAGGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  10    4  0.16
  11   17  0.68
  12    4  0.16

ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58


Consensus pattern (11 bp):   
AATTTATAATT

Found at i:7363 original size:31 final size:30

Alignment explanation


    Indices: 7320--7386  Score: 80
    Period size: 31  Copynumber: 2.2  Consensus size: 30

       7310 TGTACTAAAG

                *        *                 
       7320 TAGTTCATGTACTTATAATATTGGATCAATT
          1 TAGTCCATGTACTCATAA-ATTGGATCAATT

                              *    *      
       7351 TAGTCCATGTACTCATAAGTTGGGTCAATT
          1 TAGTCCATGTACTCATAAATTGGATCAATT

            *     
       7381 GAGTCC
          1 TAGTCC

       7387 TTATTGTGCC


Statistics
Matches: 31,  Mismatches: 5, Indels: 1
        0.84            0.14        0.03

Matches are distributed among these distances:
  30   15  0.48
  31   16  0.52

ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39


Consensus pattern (30 bp):   
TAGTCCATGTACTCATAAATTGGATCAATT

Found at i:7386 original size:30 final size:31

Alignment explanation


    Indices: 7325--7386  Score: 81
    Period size: 30  Copynumber: 2.0  Consensus size: 31

       7315 TAAAGTAGTT

                    *                 *    
       7325 CATGTACTTATAATATTGGATCAATTTAGTC
          1 CATGTACTCATAATATTGGATCAATTGAGTC

                          *    *           
       7356 CATGTACTCATAA-GTTGGGTCAATTGAGTC
          1 CATGTACTCATAATATTGGATCAATTGAGTC

             
       7386 C
          1 C

       7387 TTATTGTGCC


Statistics
Matches: 27,  Mismatches: 4, Indels: 1
        0.84            0.12        0.03

Matches are distributed among these distances:
  30   15  0.56
  31   12  0.44

ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37


Consensus pattern (31 bp):   
CATGTACTCATAATATTGGATCAATTGAGTC

Found at i:7448 original size:31 final size:30

Alignment explanation


    Indices: 7406--7527  Score: 102
    Period size: 31  Copynumber: 4.0  Consensus size: 30

       7396 CTTTATCGAT

                  *               *        
       7406 TGGACTCAATTGATACAATTTTTTGAGTACA
          1 TGGACTAAATTGA-ACAATTTTGTGAGTACA

                         *     *      *  * 
       7437 TGGACTAAATTGACCAAATCTTGTGAATATA
          1 TGGACTAAATTGAAC-AATTTTGTGAGTACA

                         *  *             
       7468 TGGACTAAATTGATCACTTTT-TGAGTACA
          1 TGGACTAAATTGAACAATTTTGTGAGTACA

            **   *          *              
       7497 AAGACGAAATTGAACACTTTTGTGCAGTACA
          1 TGGACTAAATTGAACAATTTTGTG-AGTACA

       7528 AGAACCTCCC


Statistics
Matches: 73,  Mismatches: 15, Indels: 6
        0.78            0.16        0.06

Matches are distributed among these distances:
  29   23  0.32
  30    7  0.10
  31   43  0.59

ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34


Consensus pattern (30 bp):   
TGGACTAAATTGAACAATTTTGTGAGTACA
Done.