Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010261.1 Corchorus olitorius cultivar O-4 contig10293, 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: 5210
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30


Found at i:722 original size:6 final size:6

Alignment explanation


    Indices: 711--761  Score: 61
    Period size: 6  Copynumber: 8.7  Consensus size: 6

        701 CAATTTCCCT

                               *                                  * 
        711 TTTTTC TTTTTC TTTTTT TTTTTCC TTTTTC -TTTTC -TTTTC TTTTCC
          1 TTTTTC TTTTTC TTTTTC TTTTT-C TTTTTC TTTTTC TTTTTC TTTTTC

                
        758 TTTT
          1 TTTT

        762 CCCTTTTTTC


Statistics
Matches: 40,  Mismatches: 3, Indels: 4
        0.85            0.06        0.09

Matches are distributed among these distances:
   5   10  0.25
   6   25  0.62
   7    5  0.12

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (6 bp):   
TTTTTC

Found at i:726 original size:5 final size:5

Alignment explanation


    Indices: 712--762  Score: 52
    Period size: 5  Copynumber: 10.0  Consensus size: 5

        702 AATTTCCCTT

                                        *                           
        712 TTTTC TTTTTC TTTT- TTTT- TTTCC TTTTTC TTTTC TTTTC TTTTCC
          1 TTTTC -TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTTT-C

                 
        758 TTTTC
          1 TTTTC

        763 CCTTTTTTCC


Statistics
Matches: 40,  Mismatches: 2, Indels: 7
        0.82            0.04        0.14

Matches are distributed among these distances:
   4    7  0.17
   5   19  0.47
   6   14  0.35

ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80


Consensus pattern (5 bp):   
TTTTC

Found at i:751 original size:29 final size:30

Alignment explanation


    Indices: 712--792  Score: 87
    Period size: 29  Copynumber: 2.8  Consensus size: 30

        702 AATTTCCCTT

                           **    *        
        712 TTTTCTTTTTCTTTTTTTTTTTCCTTTTTC
          1 TTTTCTTTTTCTTTTCCTTTTCCCTTTTTC

                                           
        742 TTTTC-TTTTCTTTTCCTTTTCCCTTTTTTC
          1 TTTTCTTTTTCTTTTCCTTTTCCC-TTTTTC

            *                 *    
        772 CTTT-TTTTT-TTTTCCTCTTCC
          1 TTTTCTTTTTCTTTTCCTTTTCC

        793 TTCCTTCCTT


Statistics
Matches: 44,  Mismatches: 5, Indels: 5
        0.81            0.09        0.09

Matches are distributed among these distances:
  29   26  0.59
  30   18  0.41

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (30 bp):   
TTTTCTTTTTCTTTTCCTTTTCCCTTTTTC

Found at i:1855 original size:20 final size:22

Alignment explanation


    Indices: 1830--1870  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       1820 GCGTTTTATT

                                  
       1830 CTTGTT-AACTCTTT-AACTTC
          1 CTTGTTCAACTCTTTCAACTTC

                    *            
       1850 CTTGTTCATCTCTTTCAACTT
          1 CTTGTTCAACTCTTTCAACTT

       1871 AAACGGTTGT


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

Matches are distributed among these distances:
  20    6  0.33
  21    7  0.39
  22    5  0.28

ACGTcount: A:0.17, C:0.27, G:0.05, T:0.51


Consensus pattern (22 bp):   
CTTGTTCAACTCTTTCAACTTC

Found at i:2080 original size:25 final size:25

Alignment explanation


    Indices: 2046--2093  Score: 78
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       2036 TAATAGGCTT

                                     
       2046 AACCATGTACTACAAAGCTTATCTG
          1 AACCATGTACTACAAAGCTTATCTG

                        *   *      
       2071 AACCATGTACTATAAATCTTATC
          1 AACCATGTACTACAAAGCTTATC

       2094 CATTCACCAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  25   21  1.00

ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31


Consensus pattern (25 bp):   
AACCATGTACTACAAAGCTTATCTG
Done.