Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008560.1 Corchorus capsularis cultivar CVL-1 contig08581, 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: 10723
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:6985 original size:16 final size:16

Alignment explanation


    Indices: 6966--7009  Score: 79
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       6956 ATTTTTGGGT

                            
       6966 ACCCGAACCCGAAATG
          1 ACCCGAACCCGAAATG

                      *     
       6982 ACCCGAACCCAAAATG
          1 ACCCGAACCCGAAATG

                        
       6998 ACCCGAACCCGA
          1 ACCCGAACCCGA

       7010 TCAACCCGAC


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   26  1.00

ACGTcount: A:0.39, C:0.41, G:0.16, T:0.05


Consensus pattern (16 bp):   
ACCCGAACCCGAAATG

Found at i:8066 original size:15 final size:15

Alignment explanation


    Indices: 8012--8068  Score: 53
    Period size: 15  Copynumber: 3.6  Consensus size: 15

       8002 TCCGAACCGT

                          *  
       8012 ATGACCCGAAACCGAAA
          1 ATGACCCG-AACC-CAA

             *              
       8029 ACGACCC-AACCCAGA
          1 ATGACCCGAACCCA-A

                            
       8044 ATTGACCCGAACCCAA
          1 A-TGACCCGAACCCAA

                     
       8060 ATGACCCGA
          1 ATGACCCGA

       8069 CATTTGAACG


Statistics
Matches: 34,  Mismatches: 3, Indels: 8
        0.76            0.07        0.18

Matches are distributed among these distances:
  14    1  0.03
  15   14  0.41
  16    7  0.21
  17   12  0.35

ACGTcount: A:0.40, C:0.37, G:0.16, T:0.07


Consensus pattern (15 bp):   
ATGACCCGAACCCAA

Found at i:8492 original size:31 final size:30

Alignment explanation


    Indices: 8457--8528  Score: 83
    Period size: 29  Copynumber: 2.4  Consensus size: 30

       8447 CGTCCAATTT

                  *                        
       8457 TATCCTTAATTGAATGGATTAGGTAACGTTA
          1 TATCCTGAATTGAAT-GATTAGGTAACGTTA

                           **  **         
       8488 TATCCTGAATT-AATTTTTTTGTAACGTTA
          1 TATCCTGAATTGAATGATTAGGTAACGTTA

                        
       8517 TATCCTGAATTG
          1 TATCCTGAATTG

       8529 TGTTTTTCGT


Statistics
Matches: 35,  Mismatches: 5, Indels: 3
        0.81            0.12        0.07

Matches are distributed among these distances:
  29   22  0.63
  30    3  0.09
  31   10  0.29

ACGTcount: A:0.29, C:0.11, G:0.15, T:0.44


Consensus pattern (30 bp):   
TATCCTGAATTGAATGATTAGGTAACGTTA

Found at i:8511 original size:29 final size:29

Alignment explanation


    Indices: 8479--8558  Score: 99
    Period size: 29  Copynumber: 2.7  Consensus size: 29

       8469 AATGGATTAG

                                         *
       8479 GTAACGTTATATCCTGAATTAAT-TTTTTT
          1 GTAACGTTATATCCTGAATT-ATGTTTTTC

                                *        
       8508 GTAACGTTATATCCTGAATTGTGTTTTTC
          1 GTAACGTTATATCCTGAATTATGTTTTTC

                   *              
       8537 GTCAAACCTTATATCCTGAATT
          1 GT--AACGTTATATCCTGAATT

       8559 GATTATTTAG


Statistics
Matches: 45,  Mismatches: 3, Indels: 4
        0.87            0.06        0.08

Matches are distributed among these distances:
  28    1  0.02
  29   27  0.60
  31   17  0.38

ACGTcount: A:0.26, C:0.15, G:0.12, T:0.46


Consensus pattern (29 bp):   
GTAACGTTATATCCTGAATTATGTTTTTC

Done.