Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019736.1 Corchorus olitorius cultivar O-4 contig19769, 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: 14627
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32


Found at i:616 original size:6 final size:6

Alignment explanation


    Indices: 605--629  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

        595 TTATCTTATC

                                         
        605 TTACTA TTACTA TTACTA TTACTA T
          1 TTACTA TTACTA TTACTA TTACTA T

        630 ATATATATAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52


Consensus pattern (6 bp):   
TTACTA

Found at i:1388 original size:2 final size:2

Alignment explanation


    Indices: 1383--1414  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       1373 GTAAAGGAGT

                                                           
       1383 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1415 AGTACGAATA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:2165 original size:2 final size:2

Alignment explanation


    Indices: 2158--2182  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       2148 ACTTTAATGT

                                                 
       2158 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 T

       2183 TATGGACCAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:3015 original size:22 final size:22

Alignment explanation


    Indices: 2994--3169  Score: 119
    Period size: 22  Copynumber: 7.9  Consensus size: 22

       2984 AATTACAGGG

                  *                
       2994 AGATTAACAAAATTTCATAGGGA
          1 AGATTATCAAAATTTCATA-GGA

              *                   
       3017 AGGTTA-CAAAATTTCATAGGA
          1 AGATTATCAAAATTTCATAGGA

               *    *              
       3038 AGGTTTATTAAAATTTCATAGGA
          1 A-GATTATCAAAATTTCATAGGA

               *    *            **
       3061 AGGTTTATTAAAATTTCATAGTT
          1 A-GATTATCAAAATTTCATAGGA

                       *           
       3084 AGATTATCAAAGTTTCATATGGA
          1 AGATTATCAAAATTTCATA-GGA

              *      *    *       
       3107 A-TTTATCACAATTGCATA-GA
          1 AGATTATCAAAATTTCATAGGA

                                     *
       3127 TA-ATTATCAAAATTTTTCATAGCGT
          1 -AGATTATCAAAA--TTTCATAG-GA

              *                
       3152 A-TTTATCAAAATTTCATA
          1 AGATTATCAAAATTTCATA

       3170 AAAATATTCA


Statistics
Matches: 126,  Mismatches: 19, Indels: 17
        0.78            0.12        0.10

Matches are distributed among these distances:
  20    2  0.02
  21   13  0.10
  22   51  0.40
  23   49  0.39
  24   10  0.08
  25    1  0.01

ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38


Consensus pattern (22 bp):   
AGATTATCAAAATTTCATAGGA

Found at i:3054 original size:23 final size:23

Alignment explanation


    Indices: 3002--3081  Score: 128
    Period size: 23  Copynumber: 3.5  Consensus size: 23

       2992 GGAGATTAAC

                                   *
       3002 AAAATTTCATAGGGAAGG-TTA-C
          1 AAAATTTCATA-GGAAGGTTTATT

                                   
       3024 AAAATTTCATAGGAAGGTTTATT
          1 AAAATTTCATAGGAAGGTTTATT

                                   
       3047 AAAATTTCATAGGAAGGTTTATT
          1 AAAATTTCATAGGAAGGTTTATT

                        
       3070 AAAATTTCATAG
          1 AAAATTTCATAG

       3082 TTAGATTATC


Statistics
Matches: 55,  Mismatches: 1, Indels: 3
        0.93            0.02        0.05

Matches are distributed among these distances:
  21    6  0.11
  22   14  0.25
  23   35  0.64

ACGTcount: A:0.41, C:0.06, G:0.17, T:0.35


Consensus pattern (23 bp):   
AAAATTTCATAGGAAGGTTTATT

Found at i:3100 original size:45 final size:46

Alignment explanation


    Indices: 2994--3169  Score: 154
    Period size: 45  Copynumber: 3.9  Consensus size: 46

       2984 AATTACAGGG

                  *                                        
       2994 AGATTAACAAAATTTCATAGGGAAGG-TTA-CAAAATTTCATAGGA-
          1 AGATTATCAAAATTTCATAGGGAAGGTTTATCAAAATTTCATA-GAT

               *    *                       *            * 
       3038 AGGTTTATTAAAATTTCATA-GGAAGGTTTATTAAAATTTCATAGTT
          1 A-GATTATCAAAATTTCATAGGGAAGGTTTATCAAAATTTCATAGAT

                       *       *             *    *       
       3084 AGATTATCAAAGTTTCATATGGAA--TTTATCACAATTGCATAGAT
          1 AGATTATCAAAATTTCATAGGGAAGGTTTATCAAAATTTCATAGAT

                                  * *                    
       3128 A-ATTATCAAAATTTTTCATAGCGTA--TTTATCAAAATTTCATA
          1 AGATTATCAAAA--TTTCATAGGGAAGGTTTATCAAAATTTCATA

       3170 AAAATATTCA


Statistics
Matches: 107,  Mismatches: 18, Indels: 13
        0.78            0.13        0.09

Matches are distributed among these distances:
  43    9  0.08
  44   24  0.22
  45   58  0.54
  46   16  0.15

ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38


Consensus pattern (46 bp):   
AGATTATCAAAATTTCATAGGGAAGGTTTATCAAAATTTCATAGAT
Done.