Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007509.1 Corchorus capsularis cultivar CVL-1 contig07530, 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: 16157
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26


Found at i:7648 original size:37 final size:37

Alignment explanation


    Indices: 7582--7653  Score: 108
    Period size: 37  Copynumber: 1.9  Consensus size: 37

       7572 TGAAGAAGTC

                                  * *     *      
       7582 TTGTAAAAAGGGGAATCCCCCCGATACTTTGCATGTT
          1 TTGTAAAAAGGGGAATCCCCCCAACACTTTACATGTT

                 *                             
       7619 TTGTAGAAAGGGGAATCCCCCCAACACTTTACATG
          1 TTGTAAAAAGGGGAATCCCCCCAACACTTTACATG

       7654 AATACAAAAC


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  37   31  1.00

ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26


Consensus pattern (37 bp):   
TTGTAAAAAGGGGAATCCCCCCAACACTTTACATGTT

Found at i:7794 original size:28 final size:28

Alignment explanation


    Indices: 7741--7794  Score: 72
    Period size: 28  Copynumber: 1.9  Consensus size: 28

       7731 TACAGCTTAC

                                 *      
       7741 CTTAAAGGCATAAAGCCTAGATAAAATT
          1 CTTAAAGGCATAAAGCCTAGACAAAATT

                        **     *      
       7769 CTTAAAGGCATACTGCCTATACAAAA
          1 CTTAAAGGCATAAAGCCTAGACAAAA

       7795 ATTTCAAAAG


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  28   22  1.00

ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24


Consensus pattern (28 bp):   
CTTAAAGGCATAAAGCCTAGACAAAATT

Found at i:9469 original size:20 final size:21

Alignment explanation


    Indices: 9441--9479  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 21

       9431 TTATAGCTAT

                *                
       9441 TTTTCTATAC-TTTTTACCAC
          1 TTTTATATACATTTTTACCAC

                               
       9461 TTTTATATACATTTTTACC
          1 TTTTATATACATTTTTACC

       9480 TTATTTTCTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    9  0.53
  21    8  0.47

ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56


Consensus pattern (21 bp):   
TTTTATATACATTTTTACCAC

Found at i:16120 original size:13 final size:13

Alignment explanation


    Indices: 16102--16127  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      16092 GGCAACCCAA

                         
      16102 TTTTTAATTTTTG
          1 TTTTTAATTTTTG

                         
      16115 TTTTTAATTTTTG
          1 TTTTTAATTTTTG

      16128 AATTTTCATA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77


Consensus pattern (13 bp):   
TTTTTAATTTTTG
Done.