Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022693.1 Corchorus olitorius cultivar O-4 contig22726, 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: 10886
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31


Found at i:1179 original size:41 final size:40

Alignment explanation


    Indices: 1075--1194  Score: 111
    Period size: 41  Copynumber: 3.0  Consensus size: 40

       1065 AGGACACATA

                             *          *            
       1075 AATTAAAAACA-AAATCTTAAATCAGGGGCAAAATTGAACC
          1 AATTAAAAACATAAA-CCTAAATCAGGGACAAAATTGAACC

                           *    *                    * 
       1115 AA-TAAATAA-ATACTACTCCAAATCAGGGACAAAATTGAATC
          1 AATTAAA-AACATA-AAC-CTAAATCAGGGACAAAATTGAACC

                                          * *      
       1156 AATTAACAAACATAAACCTAAATCAGGGACTATATTGAA
          1 AATTAA-AAACATAAACCTAAATCAGGGACAAAATTGAA

       1195 AACGGAAAAA


Statistics
Matches: 64,  Mismatches: 9, Indels: 13
        0.74            0.10        0.15

Matches are distributed among these distances:
  39    5  0.08
  40    6  0.09
  41   42  0.66
  42    7  0.11
  43    4  0.06

ACGTcount: A:0.52, C:0.16, G:0.11, T:0.22


Consensus pattern (40 bp):   
AATTAAAAACATAAACCTAAATCAGGGACAAAATTGAACC

Found at i:3007 original size:27 final size:27

Alignment explanation


    Indices: 2939--3041  Score: 116
    Period size: 27  Copynumber: 3.8  Consensus size: 27

       2929 AGTGGGCTTA

                   * *     *   *        
       2939 AAATGACCACAATGCGCCTTGAGTGTGC
          1 AAATGACTAAAATGCCCCTAGA-TGTGC

                   *           *       
       2967 AAATGACCAAAATGCCCCTGGATGTGC
          1 AAATGACTAAAATGCCCCTAGATGTGC

                *    *            *    
       2994 AAATAACTAGAATGCCCCTAGACGTGC
          1 AAATGACTAAAATGCCCCTAGATGTGC

                                 
       3021 AAATGACTAAAATGCCCCTAG
          1 AAATGACTAAAATGCCCCTAG

       3042 TGACCCTAAA


Statistics
Matches: 65,  Mismatches: 10, Indels: 1
        0.86            0.13        0.01

Matches are distributed among these distances:
  27   46  0.71
  28   19  0.29

ACGTcount: A:0.35, C:0.25, G:0.20, T:0.19


Consensus pattern (27 bp):   
AAATGACTAAAATGCCCCTAGATGTGC

Found at i:4982 original size:20 final size:21

Alignment explanation


    Indices: 4941--4984  Score: 79
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       4931 TATAATTTAT

                       *         
       4941 AATCCCAATTTTTTTAAAAAA
          1 AATCCCAATTTCTTTAAAAAA

                                 
       4962 AATCCCAATTTCTTTAAAAAA
          1 AATCCCAATTTCTTTAAAAAA

              
       4983 AA
          1 AA

       4985 AAACAAAAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34


Consensus pattern (21 bp):   
AATCCCAATTTCTTTAAAAAA

Found at i:8948 original size:21 final size:21

Alignment explanation


    Indices: 8924--8978  Score: 74
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       8914 CGCCCATTCA

                           **    
       8924 CCGTGCCACCACCGGTTAAGC
          1 CCGTGCCACCACCGGCCAAGC

                              *  
       8945 CCGTGCCACCACCGGCCATGC
          1 CCGTGCCACCACCGGCCAAGC

                    *    
       8966 CCGTGCCATCACC
          1 CCGTGCCACCACC

       8979 ATTCCAAGCC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCCAAGC

Found at i:9361 original size:15 final size:16

Alignment explanation


    Indices: 9330--9363  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       9320 TATCTTTTTA

                            
       9330 ATTTTTCCCTTGCATT
          1 ATTTTTCCCTTGCATT

                  *         
       9346 ATTTTTTCCTTG-ATT
          1 ATTTTTCCCTTGCATT

               
       9361 ATT
          1 ATT

       9364 GCTTTTAATT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    6  0.35
  16   11  0.65

ACGTcount: A:0.15, C:0.18, G:0.06, T:0.62


Consensus pattern (16 bp):   
ATTTTTCCCTTGCATT

Found at i:9369 original size:17 final size:17

Alignment explanation


    Indices: 9331--9363  Score: 52
    Period size: 15  Copynumber: 2.1  Consensus size: 17

       9321 ATCTTTTTAA

                             
       9331 TTTTTCCCTTGCATTAT
          1 TTTTTCCCTTGCATTAT

                             
       9348 TTTTT-CCTTG-ATTAT
          1 TTTTTCCCTTGCATTAT

             
       9363 T
          1 T

       9364 GCTTTTAATT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    6  0.38
  16    5  0.31
  17    5  0.31

ACGTcount: A:0.12, C:0.18, G:0.06, T:0.64


Consensus pattern (17 bp):   
TTTTTCCCTTGCATTAT

Found at i:9580 original size:26 final size:26

Alignment explanation


    Indices: 9551--9604  Score: 108
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       9541 GAGAGTCTGC

                                      
       9551 ATGCATCAAGATCTAAATATGCCATA
          1 ATGCATCAAGATCTAAATATGCCATA

                                      
       9577 ATGCATCAAGATCTAAATATGCCATA
          1 ATGCATCAAGATCTAAATATGCCATA

              
       9603 AT
          1 AT

       9605 TTTTTCAAAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   28  1.00

ACGTcount: A:0.43, C:0.19, G:0.11, T:0.28


Consensus pattern (26 bp):   
ATGCATCAAGATCTAAATATGCCATA
Done.