Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017906.1 Corchorus olitorius cultivar O-4 contig17939, 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: 62940
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:28160 original size:1 final size:1

Alignment explanation


    Indices: 28154--28178  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

      28144 AATCTATTGA

                                     
      28154 TTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTT

      28179 ATTATCTTAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   24  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:39500 original size:19 final size:19

Alignment explanation


    Indices: 39476--39514  Score: 78
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      39466 AAGGAGACAG

                               
      39476 AAACACCAGGTACTACCAT
          1 AAACACCAGGTACTACCAT

                               
      39495 AAACACCAGGTACTACCAT
          1 AAACACCAGGTACTACCAT

             
      39514 A
          1 A

      39515 CAGTCACAGC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.44, C:0.31, G:0.10, T:0.15


Consensus pattern (19 bp):   
AAACACCAGGTACTACCAT

Found at i:48067 original size:98 final size:96

Alignment explanation


    Indices: 47954--48229  Score: 359
    Period size: 98  Copynumber: 2.9  Consensus size: 96

      47944 CACAGACTTA

                                                                             
      47954 ATTGTAGGATCTTGTTTGTCATAAATACGTAATCTCTACATTTAAGTACTAAATCACATAATTAA
          1 ATTGTAGGATCTTGTTTGTCATAAATAC-TAATCTCTACATTTAAGTACTAAATCACATAATTAA

                *   *                         
      48019 TCAACAATTCCTATGATTAATTAGTTAGAGAA-T
         65 TCAAGAATCCCTATGATTAA--AGTTAGAGAATT

                             *                          *   *                
      48052 ATTGTAGGATCTTGTTTTTCATAAATACATAATCTCTACAATTAAACACTACTAAATCACATAAT
          1 ATTGTAGGATCTTGTTTGTCATAAATAC-TAATCTCTAC-ATT-TA-AGTACTAAATCACATAAT

                            *                  
      48117 TAATCAAGAATCCCTACGATT-AAGTTAGAGAATT
         62 TAATCAAGAATCCCTATGATTAAAGTTAGAGAATT

                                                   *                         
      48151 ATTGTAGGATCTTGTTTGTCATAAATA-TAATCTCTACAATTAAGTA-T--ATCACATAATTAA-
          1 ATTGTAGGATCTTGTTTGTCATAAATACTAATCTCTACATTTAAGTACTAAATCACATAATTAAT

                   *  *        
      48211 CAAGAATGCCGATGATTAA
         66 CAAGAATCCCTATGATTAA

      48230 GTCAGAGCAT


Statistics
Matches: 159,  Mismatches: 14, Indels: 17
        0.84            0.07        0.09

Matches are distributed among these distances:
  90   14  0.09
  91   14  0.09
  93    1  0.01
  94    3  0.02
  95    1  0.01
  96    2  0.01
  97   10  0.06
  98   47  0.30
  99   30  0.19
 100    2  0.01
 101   35  0.22

ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36


Consensus pattern (96 bp):   
ATTGTAGGATCTTGTTTGTCATAAATACTAATCTCTACATTTAAGTACTAAATCACATAATTAAT
CAAGAATCCCTATGATTAAAGTTAGAGAATT

Found at i:48933 original size:14 final size:16

Alignment explanation


    Indices: 48907--48943  Score: 51
    Period size: 15  Copynumber: 2.4  Consensus size: 16

      48897 ATTAAGTAGC

                            
      48907 AAAAAAAGTTAT-ACT
          1 AAAAAAAGTTATAACT

                          * 
      48922 AAAAAAAG-TATAATT
          1 AAAAAAAGTTATAACT

                   
      48937 AAAAAAA
          1 AAAAAAA

      48944 AATAGTTGTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  14    3  0.15
  15   17  0.85

ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22


Consensus pattern (16 bp):   
AAAAAAAGTTATAACT

Found at i:52938 original size:2 final size:2

Alignment explanation


    Indices: 52931--52967  Score: 65
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      52921 GATTCGTACA

                                                      *            
      52931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      52968 CTAGTTTTAA


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
AT

Done.