Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009914.1 Corchorus olitorius cultivar O-4 contig09946, 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: 14852
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36


Found at i:234 original size:14 final size:13

Alignment explanation


    Indices: 203--247  Score: 54
    Period size: 13  Copynumber: 3.2  Consensus size: 13

        193 GTCGGGTTTT

                         
        203 AGTCAGTTTGTTG
          1 AGTCAGTTTGTTG

                     *    
        216 AGTCAGTTTTTTCG
          1 AGTCAGTTTGTT-G

                           
        230 AGTCAGTTAGTGTTG
          1 AGTCAGTT--TGTTG

               
        245 AGT
          1 AGT

        248 ATGAGTCTGG


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  13   11  0.41
  14    9  0.33
  15    4  0.15
  16    3  0.11

ACGTcount: A:0.18, C:0.09, G:0.29, T:0.44


Consensus pattern (13 bp):   
AGTCAGTTTGTTG

Found at i:1133 original size:34 final size:37

Alignment explanation


    Indices: 1090--1176  Score: 117
    Period size: 38  Copynumber: 2.4  Consensus size: 37

       1080 TGACTCTTTT

                             *      *            
       1090 AAACTCTTGAGTTTC-TGGTGCC-TAAAA-AAAAAAA
          1 AAACTCTTGAGTTTCTTAGTGCCAAAAAAGAAAAAAA

                              *                   
       1124 AAACTCTTGAGTTTCTTATTGCCAAAAAAGGAAAAAAA
          1 AAACTCTTGAGTTTCTTAGTGCCAAAAAA-GAAAAAAA

                           
       1162 AAACTCTTGAGTTTC
          1 AAACTCTTGAGTTTC

       1177 CATTATAAAG


Statistics
Matches: 46,  Mismatches: 3, Indels: 4
        0.87            0.06        0.08

Matches are distributed among these distances:
  34   15  0.33
  35    5  0.11
  36    4  0.09
  38   22  0.48

ACGTcount: A:0.43, C:0.15, G:0.14, T:0.29


Consensus pattern (37 bp):   
AAACTCTTGAGTTTCTTAGTGCCAAAAAAGAAAAAAA

Found at i:2042 original size:19 final size:21

Alignment explanation


    Indices: 2018--2059  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2008 AAACTCAATC

                              *  
       2018 ATATAAAAA-T-CTAATTGTT
          1 ATATAAAAACTCCTAATTATT

                                 
       2037 ATATAAAAACTCCTAATTATT
          1 ATATAAAAACTCCTAATTATT

              
       2058 AT
          1 AT

       2060 GTCAACTTCA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  19    9  0.45
  20    1  0.05
  21   10  0.50

ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40


Consensus pattern (21 bp):   
ATATAAAAACTCCTAATTATT

Done.