Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006391.1 Corchorus olitorius cultivar O-4 contig06416, 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, 984

Length: 1641
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34


Found at i:1015 original size:29 final size:30

Alignment explanation


    Indices: 983--1049  Score: 109
    Period size: 31  Copynumber: 2.2  Consensus size: 30

        973 ATGCAATTTG

                                          
        983 GGATATAACGTTAC-AAAACAAGCAATTAA
          1 GGATATAACGTTACAAAAACAAGCAATTAA

                                 *         
       1012 GGATATAACGTTACGAAAAACGAGCAATTAA
          1 GGATATAACGTTAC-AAAAACAAGCAATTAA

                   
       1043 GGATATA
          1 GGATATA

       1050 GTCCGTTAGG


Statistics
Matches: 35,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  29   14  0.40
  31   21  0.60

ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21


Consensus pattern (30 bp):   
GGATATAACGTTACAAAAACAAGCAATTAA

Found at i:1208 original size:31 final size:31

Alignment explanation


    Indices: 1170--1247  Score: 129
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       1160 CTAACTGATT

                                **         
       1170 TATCCTTAATTGCTTGAAATCGAAAACGTCA
          1 TATCCTTAATTGCTTGAAATAAAAAACGTCA

                                         * 
       1201 TATCCTTAATTGCTTGAAATAAAAAACGTTA
          1 TATCCTTAATTGCTTGAAATAAAAAACGTCA

                            
       1232 TATCCTTAATTGCTTG
          1 TATCCTTAATTGCTTG

       1248 TTTTGTAACG


Statistics
Matches: 44,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   44  1.00

ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37


Consensus pattern (31 bp):   
TATCCTTAATTGCTTGAAATAAAAAACGTCA

Found at i:1297 original size:31 final size:29

Alignment explanation


    Indices: 1193--1303  Score: 89
    Period size: 31  Copynumber: 3.7  Consensus size: 29

       1183 TTGAAATCGA

                  *                      * *
       1193 AAACGTCATATCCTTAATTGCTTGAAAT-AAA
          1 AAACGTTATATCCTTAATTGCTTG---TGCAG

                                     *** 
       1224 AAACGTTATATCCTTAATTGCTTGTTTTG
          1 AAACGTTATATCCTTAATTGCTTGTGCAG

            *                             
       1253 TAACGTTATATCCTTAATTGCTTGTGGCAG
          1 AAACGTTATATCCTTAATTGCTTGT-GCAG

                     *     *     
       1283 CAAACGTTAAATCCTAAATTG
          1 -AAACGTTATATCCTTAATTG

       1304 ATTATTTGAC


Statistics
Matches: 66,  Mismatches: 11, Indels: 6
        0.80            0.13        0.07

Matches are distributed among these distances:
  28    1  0.02
  29   24  0.36
  30    1  0.02
  31   40  0.61

ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38


Consensus pattern (29 bp):   
AAACGTTATATCCTTAATTGCTTGTGCAG
Done.