Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012323.1 Corchorus olitorius cultivar O-4 contig12356, 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: 10801
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Found at i:664 original size:30 final size:31

Alignment explanation


    Indices: 623--690  Score: 84
    Period size: 32  Copynumber: 2.2  Consensus size: 31

        613 ATGAAAGTTT

                  *       *  *             
        623 AAATAATGGTAT-TTAAGAAATATATTCGAA
          1 AAATAAGGGTATATGAACAAATATATTCGAA

                            *               
        653 AAATAAGGGTATAATGGACAAATATATTCGAA
          1 AAATAAGGGTAT-ATGAACAAATATATTCGAA

                  
        685 AAATAA
          1 AAATAA

        691 TGATATAATA


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  30   11  0.34
  32   21  0.66

ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28


Consensus pattern (31 bp):   
AAATAAGGGTATATGAACAAATATATTCGAA

Found at i:1306 original size:20 final size:20

Alignment explanation


    Indices: 1283--1334  Score: 61
    Period size: 20  Copynumber: 2.6  Consensus size: 20

       1273 ACCCGGCCGG

                *                
       1283 TTCACCGGGTTA-ATCCGGGT
          1 TTCAACGGGTTACA-CCGGGT

                    * *         
       1303 TTCAACGGATCACACCGGGT
          1 TTCAACGGGTTACACCGGGT

                        
       1323 TTCAACGGGTTA
          1 TTCAACGGGTTA

       1335 TTTCCTTGAA


Statistics
Matches: 26,  Mismatches: 5, Indels: 2
        0.79            0.15        0.06

Matches are distributed among these distances:
  20   25  0.96
  21    1  0.04

ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27


Consensus pattern (20 bp):   
TTCAACGGGTTACACCGGGT

Found at i:6884 original size:35 final size:35

Alignment explanation


    Indices: 6844--6918  Score: 134
    Period size: 35  Copynumber: 2.1  Consensus size: 35

       6834 AGTTCGTTTA

                                                
       6844 TGTTCACGAACATG-CTCGTTTATTGTTCATTTAAG
          1 TGTTCACGAACA-GACTCGTTTATTGTTCATTTAAG

                                               
       6879 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
          1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG

                 
       6914 TGTTC
          1 TGTTC

       6919 GTTTATATAA


Statistics
Matches: 39,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  34    1  0.03
  35   38  0.97

ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43


Consensus pattern (35 bp):   
TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG

Found at i:6982 original size:16 final size:16

Alignment explanation


    Indices: 6961--6993  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       6951 ATAATTATTT

                            
       6961 ATATATTAATAATAAA
          1 ATATATTAATAATAAA

                    *       
       6977 ATATATTATTAATAAA
          1 ATATATTAATAATAAA

             
       6993 A
          1 A

       6994 ATTATAAAAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (16 bp):   
ATATATTAATAATAAA

Found at i:7070 original size:15 final size:14

Alignment explanation


    Indices: 7043--7084  Score: 61
    Period size: 15  Copynumber: 3.1  Consensus size: 14

       7033 AATTAAAATT

                          
       7043 TAATTAT-TATATA
          1 TAATTATATATATA

                           
       7056 TAATATATATATATA
          1 TAAT-TATATATATA

                          
       7071 TAATTATATA-ATA
          1 TAATTATATATATA

             
       7084 T
          1 T

       7085 TTTGTTCGTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  13    8  0.30
  14    9  0.33
  15   10  0.37

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


Consensus pattern (14 bp):   
TAATTATATATATA

Found at i:10774 original size:2 final size:2

Alignment explanation


    Indices: 10769--10801  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      10759 AAAAAAAAAC

                                                             
      10769 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

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


Consensus pattern (2 bp):   
TA

Done.