Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022967.1 Corchorus olitorius cultivar O-4 contig23000, 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: 7220
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42


Found at i:1123 original size:8 final size:8

Alignment explanation


    Indices: 1081--1129  Score: 50
    Period size: 8  Copynumber: 6.2  Consensus size: 8

       1071 TTAGTAATAT

                    
       1081 ATAGATAA
          1 ATAGATAA

                    
       1089 ATAGA-AA
          1 ATAGATAA

                    *
       1096 GATAGATAG
          1 -ATAGATAA

                    
       1105 AT--ATAA
          1 ATAGATAA

                     
       1111 GATAGATAA
          1 -ATAGATAA

                    
       1120 ATAGATAA
          1 ATAGATAA

              
       1128 AT
          1 AT

       1130 TTCGATAGGA


Statistics
Matches: 34,  Mismatches: 2, Indels: 10
        0.74            0.04        0.22

Matches are distributed among these distances:
   6    3  0.09
   7    4  0.12
   8   22  0.65
   9    5  0.15

ACGTcount: A:0.59, C:0.00, G:0.16, T:0.24


Consensus pattern (8 bp):   
ATAGATAA

Found at i:1320 original size:16 final size:16

Alignment explanation


    Indices: 1299--1331  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       1289 TGATACTTTG

                            
       1299 AAGAATAATAAAAGTA
          1 AAGAATAATAAAAGTA

                  *         
       1315 AAGAATGATAAAAGTA
          1 AAGAATAATAAAAGTA

             
       1331 A
          1 A

       1332 GAAAATTGAA


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

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18


Consensus pattern (16 bp):   
AAGAATAATAAAAGTA

Found at i:1551 original size:20 final size:22

Alignment explanation


    Indices: 1526--1585  Score: 79
    Period size: 22  Copynumber: 2.8  Consensus size: 22

       1516 ATAATTGGAA

                                  
       1526 TGCAGAG-ATT-CTTTCTACTT
          1 TGCAGAGCATTACTTTCTACTT

                        *         
       1546 TGCAGAGCATTATTTTCTACTT
          1 TGCAGAGCATTACTTTCTACTT

                    *   *     
       1568 TGCAGAGCGTTATTTTCT
          1 TGCAGAGCATTACTTTCT

       1586 TCAGCTTCAG


Statistics
Matches: 36,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  20    7  0.19
  21    3  0.08
  22   26  0.72

ACGTcount: A:0.20, C:0.18, G:0.17, T:0.45


Consensus pattern (22 bp):   
TGCAGAGCATTACTTTCTACTT

Found at i:1565 original size:22 final size:22

Alignment explanation


    Indices: 1537--1585  Score: 89
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       1527 GCAGAGATTC

                                  
       1537 TTTCTACTTTGCAGAGCATTAT
          1 TTTCTACTTTGCAGAGCATTAT

                             *    
       1559 TTTCTACTTTGCAGAGCGTTAT
          1 TTTCTACTTTGCAGAGCATTAT

                 
       1581 TTTCT
          1 TTTCT

       1586 TCAGCTTCAG


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   26  1.00

ACGTcount: A:0.18, C:0.18, G:0.14, T:0.49


Consensus pattern (22 bp):   
TTTCTACTTTGCAGAGCATTAT

Found at i:1668 original size:22 final size:22

Alignment explanation


    Indices: 1626--1701  Score: 102
    Period size: 22  Copynumber: 3.5  Consensus size: 22

       1616 TGAAAACATC

                        *         
       1626 TTGCAGAG-ATTCTTTT-CACT
          1 TTGCAGAGCATTATTTTCCACT

             *    *               
       1646 TGGCAGGGCATTATTTTCCACT
          1 TTGCAGAGCATTATTTTCCACT

                                  
       1668 TTGCAGAGCATTATTTTCCACT
          1 TTGCAGAGCATTATTTTCCACT

                   *    
       1690 TTGCAGAACATT
          1 TTGCAGAGCATT

       1702 TTCTTCAATC


Statistics
Matches: 48,  Mismatches: 6, Indels: 2
        0.86            0.11        0.04

Matches are distributed among these distances:
  20    6  0.12
  21    7  0.15
  22   35  0.73

ACGTcount: A:0.22, C:0.21, G:0.17, T:0.39


Consensus pattern (22 bp):   
TTGCAGAGCATTATTTTCCACT

Done.