Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001502.1 Corchorus capsularis cultivar CVL-1 contig01502, 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: 5500
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29


Found at i:856 original size:235 final size:233

Alignment explanation


    Indices: 412--883  Score: 854
    Period size: 235  Copynumber: 2.0  Consensus size: 233

        402 AAAATCCATG

                                *   *                                        
        412 ATGATGGTAAAGGAACTTAATTGCGCGTGTATTTCACTTGCTAACAGCAGTCTGAAAAAAGTACT
          1 ATGATGGTAAAGGAACTTAACTGCACGTGTATTTCACTTGCTAACAGCAGTCTGAAAAAAGTACT

                 *  *                                *                       
        477 AAATTGAGTCAATTTTGTAATGTTTAATATCAATTATGGTGCAAAAAAATCAATTTGACCACGAT
         66 AAATTAAGCCAATTTTGTAATGTTTAATATCAATTATGGTGAAAAAAAATCAATTTGACCACGAT

                 *                                                           
        542 TTAAATTTTGGTATCAAGTTGAAAATTGAGATTTTAGCCTGTGGTAAATTGGTAGAGCTTTCTAG
        131 TTAAAATTTGGTATCAAGTTGAAAATTGAGATTTTAGCCTGTGGTAAATTGGTAGAGCTTTCTAG

                                         *        
        607 GTGCACTTTGGATGTCACTCATTGCAAGATGTAAACCA
        196 GTGCACTTTGGATGTCACTCATTGCAAGACGTAAACCA

                                                           *                 
        645 ATGATGGTAAAGGAACTTAACTGCACGTGTATTTCACTTGCTAACAGTAGTCTGAAAAAAGTACT
          1 ATGATGGTAAAGGAACTTAACTGCACGTGTATTTCACTTGCTAACAGCAGTCTGAAAAAAGTACT

                                                                             
        710 AAATTAAGCCAATTTTGTAATGTTTAATATCAATTATGGTGAATAAAAATATCAATTTGACCACG
         66 AAATTAAGCCAATTTTGTAATGTTTAATATCAATTATGGTGAA-AAAAA-ATCAATTTGACCACG

                                                                             
        775 ATTTAAAATTTGGTATCAAGTTGAAAATTGAGATTTTAGCCTGTGGTAAATTGGTAGAGCTTTCT
        129 ATTTAAAATTTGGTATCAAGTTGAAAATTGAGATTTTAGCCTGTGGTAAATTGGTAGAGCTTTCT

                                                    
        840 AGGTGCACTTTGGATGTCACTCATTGCAAGACGTAAACCA
        194 AGGTGCACTTTGGATGTCACTCATTGCAAGACGTAAACCA

                
        880 ATGA
          1 ATGA

        884 GAGGGGAATG


Statistics
Matches: 229,  Mismatches: 8, Indels: 2
        0.96            0.03        0.01

Matches are distributed among these distances:
 233  102  0.45
 234    5  0.02
 235  122  0.53

ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33


Consensus pattern (233 bp):   
ATGATGGTAAAGGAACTTAACTGCACGTGTATTTCACTTGCTAACAGCAGTCTGAAAAAAGTACT
AAATTAAGCCAATTTTGTAATGTTTAATATCAATTATGGTGAAAAAAAATCAATTTGACCACGAT
TTAAAATTTGGTATCAAGTTGAAAATTGAGATTTTAGCCTGTGGTAAATTGGTAGAGCTTTCTAG
GTGCACTTTGGATGTCACTCATTGCAAGACGTAAACCA

Found at i:992 original size:31 final size:29

Alignment explanation


    Indices: 947--1026  Score: 106
    Period size: 29  Copynumber: 2.7  Consensus size: 29

        937 GCTTAATATC

                  *  *              *      
        947 CAAATTAGCTCCTTAACTATTTATTTTGGGA
          1 CAAATTGGCCCCTTAACT-TTT-TCTTGGGA

                                         
        978 CAAATTGGCCCCTTAACTTTTTCTTGGGA
          1 CAAATTGGCCCCTTAACTTTTTCTTGGGA

                   *            
       1007 CAAATTGACCCCTTAACTTT
          1 CAAATTGGCCCCTTAACTTT

       1027 AAAAAACGAG


Statistics
Matches: 45,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  29   26  0.58
  30    3  0.07
  31   16  0.36

ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39


Consensus pattern (29 bp):   
CAAATTGGCCCCTTAACTTTTTCTTGGGA

Found at i:2550 original size:2 final size:2

Alignment explanation


    Indices: 2543--2571  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       2533 TGTCCCTGAA

                                                       
       2543 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
          1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A

       2572 TATATATATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Found at i:4115 original size:2 final size:2

Alignment explanation


    Indices: 4108--4135  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       4098 TCAAGCGTCT

                                                     
       4108 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       4136 ACATGATTGA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:4452 original size:14 final size:15

Alignment explanation


    Indices: 4430--4464  Score: 54
    Period size: 14  Copynumber: 2.4  Consensus size: 15

       4420 TAAAAGGCAC

                *          
       4430 AGAATAAAAAAGAAA
          1 AGAAAAAAAAAGAAA

                           
       4445 A-AAAAAAAAAGAAA
          1 AGAAAAAAAAAGAAA

                  
       4459 AGAAAA
          1 AGAAAA

       4465 CCTATCAAGT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  14   13  0.72
  15    5  0.28

ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03


Consensus pattern (15 bp):   
AGAAAAAAAAAGAAA
Done.