Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012645.1 Corchorus capsularis cultivar CVL-1 contig12666, 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: 6877
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39


Found at i:1514 original size:40 final size:41

Alignment explanation


    Indices: 1442--1518  Score: 104
    Period size: 40  Copynumber: 1.9  Consensus size: 41

       1432 TAAGGTAACA

                        *           *  *             
       1442 AATTAAATCTAGTTTTAGTCCCTAGTTCTAAATATGGGGAG
          1 AATTAAATCTAGGTTTAGTCCCTAATTATAAATATGGGGAG

                                                  
       1483 AATTAAATCT-GGTTTA-TCCCCTAATTATAAATATGG
          1 AATTAAATCTAGGTTTAGT-CCCTAATTATAAATATGG

       1519 AGAATTTGTA


Statistics
Matches: 32,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  39    1  0.03
  40   21  0.66
  41   10  0.31

ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38


Consensus pattern (41 bp):   
AATTAAATCTAGGTTTAGTCCCTAATTATAAATATGGGGAG

Found at i:3435 original size:17 final size:18

Alignment explanation


    Indices: 3413--3450  Score: 60
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       3403 TTTTTTAAAC

                           *  
       3413 TTACA-TTTTAAAAAGAA
          1 TTACATTTTTAAAAAAAA

                              
       3430 TTACATTTTTAAAAAAAA
          1 TTACATTTTTAAAAAAAA

               
       3448 TTA
          1 TTA

       3451 AAGAAAAAGA


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

Matches are distributed among these distances:
  17    5  0.26
  18   14  0.74

ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39


Consensus pattern (18 bp):   
TTACATTTTTAAAAAAAA

Found at i:3871 original size:21 final size:21

Alignment explanation


    Indices: 3847--3893  Score: 60
    Period size: 22  Copynumber: 2.2  Consensus size: 21

       3837 TAGGAAGTTC

                                  
       3847 ATAAGCAC-TTTTAGTAATCGT
          1 ATAAGC-CTTTTTAGTAATCGT

                                * 
       3868 ATAAGCCTTTTTTAGTAATCTT
          1 ATAAGCC-TTTTTAGTAATCGT

                
       3890 ATAA
          1 ATAA

       3894 AATATTTTAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  20    1  0.04
  21    6  0.26
  22   16  0.70

ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43


Consensus pattern (21 bp):   
ATAAGCCTTTTTAGTAATCGT

Found at i:4104 original size:33 final size:34

Alignment explanation


    Indices: 4040--4104  Score: 80
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       4030 AAATGACCTT

                                     **       
       4040 ATAAGTTTTTGAACTAGCATTATAATTTTTTAGA
          1 ATAAGTTTTTGAACTAGCATTATAACATTTTAGA

                *                            
       4074 ATAATTTTTTGAACTA-C-TTGATAACATTTTA
          1 ATAAGTTTTTGAACTAGCATT-ATAACATTTTA

       4105 ATCAATCTTA


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  32    2  0.07
  33   10  0.37
  34   15  0.56

ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48


Consensus pattern (34 bp):   
ATAAGTTTTTGAACTAGCATTATAACATTTTAGA

Found at i:4135 original size:32 final size:32

Alignment explanation


    Indices: 4099--4160  Score: 124
    Period size: 32  Copynumber: 1.9  Consensus size: 32

       4089 ACTTGATAAC

                                            
       4099 ATTTTAATCAATCTTATAAGATTTTTTAATCA
          1 ATTTTAATCAATCTTATAAGATTTTTTAATCA

                                          
       4131 ATTTTAATCAATCTTATAAGATTTTTTAAT
          1 ATTTTAATCAATCTTATAAGATTTTTTAAT

       4161 TAAGCTTAGT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   30  1.00

ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52


Consensus pattern (32 bp):   
ATTTTAATCAATCTTATAAGATTTTTTAATCA

Found at i:4223 original size:21 final size:21

Alignment explanation


    Indices: 4201--4241  Score: 64
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       4191 AGTTTTCTTT

                                  
       4201 AATAACTCTTATAAAATTTTTA
          1 AATAA-TCTTATAAAATTTTTA

                     *         
       4223 AATAATCTTTTAAAATTTT
          1 AATAATCTTATAAAATTTT

       4242 AGTACTCCTA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21   13  0.72
  22    5  0.28

ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49


Consensus pattern (21 bp):   
AATAATCTTATAAAATTTTTA

Found at i:6363 original size:17 final size:16

Alignment explanation


    Indices: 6323--6365  Score: 59
    Period size: 17  Copynumber: 2.6  Consensus size: 16

       6313 CATATAATCT

                    *       
       6323 TTGATCACCGGTGATC
          1 TTGATCACTGGTGATC

                             
       6339 TTGCATCACTGGTGATC
          1 TTG-ATCACTGGTGATC

                      
       6356 TTAGATCACT
          1 TT-GATCACT

       6366 AGTAATCTGA


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  16    3  0.12
  17   20  0.83
  18    1  0.04

ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35


Consensus pattern (16 bp):   
TTGATCACTGGTGATC
Done.