Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001701.1 Corchorus capsularis cultivar CVL-1 contig01701, 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: 3352
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--60  Score: 120
    Period size: 2  Copynumber: 30.0  Consensus size: 2

                                                                          
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                      
         43 TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC

         61 CTTGTAGGTG


Statistics
Matches: 58,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   58  1.00

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


Consensus pattern (2 bp):   
TC

Found at i:706 original size:20 final size:18

Alignment explanation


    Indices: 681--725  Score: 54
    Period size: 18  Copynumber: 2.4  Consensus size: 18

        671 ACATATGTTT

                                
        681 TACTAATAAATAATAATATA
          1 TACTAATAAAT-A-AATATA

                  *          *
        701 TACTAACAAATAAATATT
          1 TACTAATAAATAAATATA

                   
        719 TACTAAT
          1 TACTAAT

        726 TTTGCTTAAA


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  18   11  0.50
  19    1  0.05
  20   10  0.45

ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36


Consensus pattern (18 bp):   
TACTAATAAATAAATATA

Found at i:1423 original size:22 final size:22

Alignment explanation


    Indices: 1312--1499  Score: 127
    Period size: 22  Copynumber: 8.7  Consensus size: 22

       1302 TTAGTTGTGA

                                  
       1312 TTATCAAAATTTCATAGGGAGG
          1 TTATCAAAATTTCATAGGGAGG

                        *     *     
       1334 -TA-CAAAATTTGATA-GTATGAG
          1 TTATCAAAATTTCATAGGGA-G-G

                 *  *       **    
       1355 -TATCGAATTTTCATACAGAGG
          1 TTATCAAAATTTCATAGGGAGG

                        *   ***    
       1376 TTATCAAAATTTTAT-TTTATGG
          1 TTATCAAAATTTCATAGGGA-GG

                                **
       1398 TTATCAAAATTTCATAGGGATA
          1 TTATCAAAATTTCATAGGGAGG

                *            *    
       1420 TTATTAAAATTTCATAGCGAGG
          1 TTATCAAAATTTCATAGGGAGG

            *          * *        
       1442 CTATCAAAATTACTTAGGGAGG
          1 TTATCAAAATTTCATAGGGAGG

                 *      *         
       1464 TTATCGAAATTTTATAGGGA-G
          1 TTATCAAAATTTCATAGGGAGG

                 *         
       1485 TTATCGAAATTTCAT
          1 TTATCAAAATTTCAT

       1500 TGTGTGGTTA


Statistics
Matches: 125,  Mismatches: 34, Indels: 15
        0.72            0.20        0.09

Matches are distributed among these distances:
  19    2  0.02
  20   12  0.10
  21   22  0.18
  22   87  0.70
  23    2  0.02

ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37


Consensus pattern (22 bp):   
TTATCAAAATTTCATAGGGAGG

Found at i:1489 original size:21 final size:22

Alignment explanation


    Indices: 1396--1518  Score: 81
    Period size: 22  Copynumber: 5.7  Consensus size: 22

       1386 TTTATTTTAT

                   *      *       
       1396 GGTTATCAAAATTTCATAGGGA
          1 GGTTATCGAAATTTTATAGGGA

            **    **      *    *  
       1418 TATTATTAAAATTTCATAGCGA
          1 GGTTATCGAAATTTTATAGGGA

              *    *      *        
       1440 GGCTATCAAAATTACT-TAGGGA
          1 GGTTATCGAAATT-TTATAGGGA

                                  
       1462 GGTTATCGAAATTTTATAGGGA
          1 GGTTATCGAAATTTTATAGGGA

                          *  * * *
       1484 -GTTATCGAAATTTCATTGTGT
          1 GGTTATCGAAATTTTATAGGGA

                           
       1505 GGTTAT-GAAATTTT
          1 GGTTATCGAAATTTT

       1519 TATAAGTTAT


Statistics
Matches: 79,  Mismatches: 19, Indels: 7
        0.75            0.18        0.07

Matches are distributed among these distances:
  21   25  0.32
  22   54  0.68

ACGTcount: A:0.33, C:0.08, G:0.20, T:0.38


Consensus pattern (22 bp):   
GGTTATCGAAATTTTATAGGGA

Found at i:2935 original size:15 final size:16

Alignment explanation


    Indices: 2915--2950  Score: 56
    Period size: 16  Copynumber: 2.3  Consensus size: 16

       2905 CTCAAATGTC

                            
       2915 GGGTC-ATTTGGGTTT
          1 GGGTCAATTTGGGTTT

                      *     
       2930 GGGTCAATTTTGGTTT
          1 GGGTCAATTTGGGTTT

                 
       2946 GGGTC
          1 GGGTC

       2951 TTTTTCAGTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  15    5  0.26
  16   14  0.74

ACGTcount: A:0.08, C:0.08, G:0.39, T:0.44


Consensus pattern (16 bp):   
GGGTCAATTTGGGTTT

Done.