Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009113.1 Corchorus olitorius cultivar O-4 contig09141, 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, 859

Length: 1433
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38


Found at i:483 original size:19 final size:20

Alignment explanation


    Indices: 459--497  Score: 62
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        449 CCCATCGCCC

                                
        459 ATTTGTTA-TGTTATAATTA
          1 ATTTGTTATTGTTATAATTA

                      *         
        478 ATTTGTTATTTTTATAATTA
          1 ATTTGTTATTGTTATAATTA

        498 TTCTAATTTA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  19    8  0.44
  20   10  0.56

ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62


Consensus pattern (20 bp):   
ATTTGTTATTGTTATAATTA

Found at i:1091 original size:19 final size:18

Alignment explanation


    Indices: 1053--1088  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       1043 ATAAGCCCTT

                              
       1053 TTTTATAGATTCATAAAA
          1 TTTTATAGATTCATAAAA

                              
       1071 TTTTATAGATTCATAAAA
          1 TTTTATAGATTCATAAAA

       1089 ATTATATAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44


Consensus pattern (18 bp):   
TTTTATAGATTCATAAAA

Found at i:1096 original size:19 final size:18

Alignment explanation


    Indices: 1056--1096  Score: 64
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       1046 AGCCCTTTTT

                             *
       1056 TATAGATTCATAAAATTT
          1 TATAGATTCATAAAATTA

                               
       1074 TATAGATTCATAAAAATTA
          1 TATAGATTCAT-AAAATTA

                
       1093 TATA
          1 TATA

       1097 AAAAAATGAG


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  18   11  0.52
  19   10  0.48

ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41


Consensus pattern (18 bp):   
TATAGATTCATAAAATTA

Found at i:1290 original size:22 final size:21

Alignment explanation


    Indices: 1255--1306  Score: 70
    Period size: 22  Copynumber: 2.5  Consensus size: 21

       1245 TCCGTTGACG

                             *   
       1255 AAATAAT-AAAATAAAAGGAT
          1 AAATAATAAAAATAAAACGAT

              *                   
       1275 AATTAAATAAAAATAAAACGAT
          1 AAAT-AATAAAAATAAAACGAT

                      
       1297 AAATAATAAA
          1 AAATAATAAA

       1307 GATTCTTTTT


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  20    3  0.11
  21    9  0.33
  22   15  0.56

ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21


Consensus pattern (21 bp):   
AAATAATAAAAATAAAACGAT
Done.