Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019742.1 Corchorus olitorius cultivar O-4 contig19775, 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: 25080
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33


Found at i:1093 original size:58 final size:58

Alignment explanation


    Indices: 1003--1115  Score: 181
    Period size: 58  Copynumber: 1.9  Consensus size: 58

        993 AGCATCATGC

                    *     *                                           
       1003 CTCGGTCCTAAAACGTCTTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGT
          1 CTCGGTCCGAAAACATCTTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGT

                                     *            *           *    
       1061 CTCGGTCCGAAAACATCTTTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
          1 CTCGGTCCGAAAACATCTTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA

       1116 TTTGATTAAT


Statistics
Matches: 50,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  58   50  1.00

ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34


Consensus pattern (58 bp):   
CTCGGTCCGAAAACATCTTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGT

Found at i:4906 original size:22 final size:22

Alignment explanation


    Indices: 4881--4924  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4871 ATGTATATTC

                                  
       4881 ATAACAAATTGATAATTAATTT
          1 ATAACAAATTGATAATTAATTT

                ** *         *    
       4903 ATAATTATTTGATAATTTATTT
          1 ATAACAAATTGATAATTAATTT

       4925 TATATAGGAA


Statistics
Matches: 18,  Mismatches: 4, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50


Consensus pattern (22 bp):   
ATAACAAATTGATAATTAATTT

Found at i:10411 original size:13 final size:13

Alignment explanation


    Indices: 10393--10420  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

      10383 AATGATATCG

                         
      10393 ATGTACTTGATCA
          1 ATGTACTTGATCA

                         
      10406 ATGTACTTGATCA
          1 ATGTACTTGATCA

              
      10419 AT
          1 AT

      10421 TGAATTTCCA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39


Consensus pattern (13 bp):   
ATGTACTTGATCA

Found at i:19293 original size:20 final size:21

Alignment explanation


    Indices: 19260--19306  Score: 53
    Period size: 19  Copynumber: 2.3  Consensus size: 21

      19250 AAATCAAAAG

                  *       *      
      19260 AAAAAATTAGAAATTTTCAAC
          1 AAAAAAATAGAAATCTTCAAC

                                 
      19281 AAAAAAATA-AAATCTTC-AC
          1 AAAAAAATAGAAATCTTCAAC

              *    
      19300 AAGAAAA
          1 AAAAAAA

      19307 GAGATGAGAG


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  19    8  0.35
  20    7  0.30
  21    8  0.35

ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21


Consensus pattern (21 bp):   
AAAAAAATAGAAATCTTCAAC

Found at i:21287 original size:55 final size:56

Alignment explanation


    Indices: 21183--21290  Score: 164
    Period size: 55  Copynumber: 1.9  Consensus size: 56

      21173 CCCTTTCTCG

                            *                       *               
      21183 ATCAGGCTAAAATCATTAAATCAGAAAGAGGAATCAAGCACATATTGATGAAAGCT
          1 ATCAGGCTAAAATCATCAAATCAGAAAGAGGAATCAAGCAAATATTGATGAAAGCT

                             **               *                  
      21239 ATCAGGCTAAAATCATCCGATCAG-AAGAGGAATGAAGCAAATATTGATGAAA
          1 ATCAGGCTAAAATCATCAAATCAGAAAGAGGAATCAAGCAAATATTGATGAAA

      21291 ATTGAAAGCT


Statistics
Matches: 47,  Mismatches: 5, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  55   26  0.55
  56   21  0.45

ACGTcount: A:0.46, C:0.14, G:0.19, T:0.20


Consensus pattern (56 bp):   
ATCAGGCTAAAATCATCAAATCAGAAAGAGGAATCAAGCAAATATTGATGAAAGCT

Found at i:25014 original size:2 final size:2

Alignment explanation


    Indices: 24990--25055  Score: 57
    Period size: 2  Copynumber: 33.5  Consensus size: 2

      24980 TTTTAATTAA

                                    *     *                                
      24990 AT AT AT A- AT AT -T AT GT AT GT AT AT AT AT AT AT AT AT AT AGT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T

               *              *                   
      25031 -T GT AT AT AT AT CT AT AT ACT AT AT A
          1 AT AT AT AT AT AT AT AT AT A-T AT AT A

      25056 AGTCTAAACT


Statistics
Matches: 52,  Mismatches: 7, Indels: 10
        0.75            0.10        0.14

Matches are distributed among these distances:
   1    3  0.06
   2   46  0.88
   3    3  0.06

ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:25020 original size:24 final size:24

Alignment explanation


    Indices: 24990--25053  Score: 80
    Period size: 24  Copynumber: 2.7  Consensus size: 24

      24980 TTTTAATTAA

                                     
      24990 ATATATA-ATAT-TAT-GTATGTAT
          1 ATATATATATATATATAGT-TGTAT

                                    
      25012 ATATATATATATATATAGTTGTAT
          1 ATATATATATATATATAGTTGTAT

                  *           
      25036 ATATATCTATATACTATA
          1 ATATATATATATA-TATA

      25054 TAAGTCTAAA


Statistics
Matches: 37,  Mismatches: 1, Indels: 5
        0.86            0.02        0.12

Matches are distributed among these distances:
  22    7  0.19
  23    4  0.11
  24   20  0.54
  25    6  0.16

ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48


Consensus pattern (24 bp):   
ATATATATATATATATAGTTGTAT
Done.