Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016047.1 Corchorus olitorius cultivar O-4 contig16080, 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: 6854
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30


Found at i:534 original size:26 final size:23

Alignment explanation


    Indices: 504--550  Score: 67
    Period size: 26  Copynumber: 1.9  Consensus size: 23

        494 CTTGAAAATT

                                      
        504 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAAC-TTGAT-GAT-AGATGGA

                                 
        530 TGAAAAACTTGATGATAGATG
          1 TGAAAAACTTGATGATAGATG

        551 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (23 bp):   
TGAAAAACTTGATGATAGATGGA

Found at i:3290 original size:33 final size:34

Alignment explanation


    Indices: 3253--3359  Score: 121
    Period size: 33  Copynumber: 3.2  Consensus size: 34

       3243 ATTAGCATCC

                           *                  
       3253 AAAACAGAATTT-GTTTCATCACAAACAACACCT
          1 AAAACAGAATTTAGTATCATCACAAACAACACCT

                           *                * 
       3286 AAAACA-AATTTAGTGTCATCACAAACAACACTT
          1 AAAACAGAATTTAGTATCATCACAAACAACACCT

               **   *              *       *  
       3319 AAATTAG-GTTTAGTATCATCACTAACAACATCT
          1 AAAACAGAATTTAGTATCATCACAAACAACACCT

                    
       3352 AAAACAGA
          1 AAAACAGA

       3360 TTTCATGTCA


Statistics
Matches: 60,  Mismatches: 11, Indels: 5
        0.79            0.14        0.07

Matches are distributed among these distances:
  32    5  0.08
  33   55  0.92

ACGTcount: A:0.47, C:0.21, G:0.07, T:0.25


Consensus pattern (34 bp):   
AAAACAGAATTTAGTATCATCACAAACAACACCT

Found at i:3340 original size:66 final size:66

Alignment explanation


    Indices: 3268--3394  Score: 175
    Period size: 66  Copynumber: 1.9  Consensus size: 66

       3258 AGAATTTGTT

                                                               *    *        
       3268 TCATCACAAACAACACCTAAAACAAATTT-AGTGTCATCACAAACAACACTTAAATTAGGTTTAG
          1 TCATCACAAACAACACCTAAAACAAATTTCA-TGTCATCACAAACAACACTCAAATCAGGTTTAG

              
       3332 TA
         65 TA

                   *       *        *            **                      
       3334 TCATCACTAACAACATCTAAAACAGATTTCATGTCATTGCAAACAACACTCAAATCAGGTT
          1 TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTCAAATCAGGTT

       3395 CAGAATTACT


Statistics
Matches: 53,  Mismatches: 7, Indels: 2
        0.85            0.11        0.03

Matches are distributed among these distances:
  66   52  0.98
  67    1  0.02

ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26


Consensus pattern (66 bp):   
TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTCAAATCAGGTTTAGT
A

Found at i:4000 original size:15 final size:15

Alignment explanation


    Indices: 3980--4011  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3970 AAACTAAGTG

                           
       3980 GAGCTTGTCGATTTT
          1 GAGCTTGTCGATTTT

                    *      
       3995 GAGCTTGTTGATTTT
          1 GAGCTTGTCGATTTT

              
       4010 GA
          1 GA

       4012 ACCCCCAAGG


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

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.16, C:0.09, G:0.28, T:0.47


Consensus pattern (15 bp):   
GAGCTTGTCGATTTT

Found at i:4993 original size:25 final size:24

Alignment explanation


    Indices: 4956--5002  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       4946 CTAGAAAATT

                                      
       4956 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       4982 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       5003 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA
Done.