Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014027.1 Corchorus olitorius cultivar O-4 contig14060, 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: 3542
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.39


Found at i:1057 original size:28 final size:28

Alignment explanation


    Indices: 1017--1073  Score: 105
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       1007 CTACCATCCC

                                        
       1017 ACCTCCCCCCATTGTAAAATAAAACGAA
          1 ACCTCCCCCCATTGTAAAATAAAACGAA

                *                       
       1045 ACCTTCCCCCATTGTAAAATAAAACGAA
          1 ACCTCCCCCCATTGTAAAATAAAACGAA

             
       1073 A
          1 A

       1074 GAGAGATTAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  28   28  1.00

ACGTcount: A:0.44, C:0.30, G:0.07, T:0.19


Consensus pattern (28 bp):   
ACCTCCCCCCATTGTAAAATAAAACGAA

Found at i:2076 original size:2 final size:2

Alignment explanation


    Indices: 2069--2097  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       2059 ATTCTCTTTG

                                                       
       2069 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 T

       2098 TTTTATTTTG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:2505 original size:17 final size:16

Alignment explanation


    Indices: 2483--2535  Score: 56
    Period size: 17  Copynumber: 3.2  Consensus size: 16

       2473 CTATGAAAAA

                             
       2483 TTATTAATTTAGAGAGG
          1 TTATTAATTTAG-GAGG

                        *    
       2500 TTATTAATTTATTGA-G
          1 TTATTAATTTA-GGAGG

                             
       2516 -TATTAATTTATGGAGG
          1 TTATTAATTTA-GGAGG

                
       2532 TTAT
          1 TTAT

       2536 ACTGTATACT


Statistics
Matches: 31,  Mismatches: 2, Indels: 6
        0.79            0.05        0.15

Matches are distributed among these distances:
  15   13  0.42
  16    2  0.06
  17   16  0.52

ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49


Consensus pattern (16 bp):   
TTATTAATTTAGGAGG

Found at i:2505 original size:76 final size:76

Alignment explanation


    Indices: 2379--2526  Score: 237
    Period size: 76  Copynumber: 1.9  Consensus size: 76

       2369 AAACCTCTAT

                                                                          *  
       2379 AAATTAATAATGTTGGGATCATGAAAAATTTTCAATTTAGAGAGGTTATTAATTTATCGAGTGTT
          1 AAATTAATAATGTTGGGATCATGAAAAATTTTCAATTTAGAGAGGTTATTAATTTATCGAGTATT

                       
       2444 AATTTATATAA
         66 AATTTATATAA

                              *                                        *     
       2455 AAATTAATAATGTTGGG-GCTATGAAAAATTATT-AATTTAGAGAGGTTATTAATTTATTGAGTA
          1 AAATTAATAATGTTGGGATC-ATGAAAAATT-TTCAATTTAGAGAGGTTATTAATTTATCGAGTA

                     
       2518 TTAATTTAT
         64 TTAATTTAT

       2527 GGAGGTTATA


Statistics
Matches: 67,  Mismatches: 3, Indels: 4
        0.91            0.04        0.05

Matches are distributed among these distances:
  75    1  0.01
  76   64  0.96
  77    2  0.03

ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42


Consensus pattern (76 bp):   
AAATTAATAATGTTGGGATCATGAAAAATTTTCAATTTAGAGAGGTTATTAATTTATCGAGTATT
AATTTATATAA
Done.