Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011274.1 Corchorus olitorius cultivar O-4 contig11307, 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: 11504
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:1184 original size:2 final size:2

Alignment explanation


    Indices: 1177--1221  Score: 76
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       1167 GAAAATATGC

                                                                          
       1177 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT A- AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                   
       1217 AT AT A
          1 AT AT A

       1222 AAGAGATTGA


Statistics
Matches: 41,  Mismatches: 0, Indels: 4
        0.91            0.00        0.09

Matches are distributed among these distances:
   1    2  0.05
   2   39  0.95

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:1199 original size:19 final size:19

Alignment explanation


    Indices: 1177--1221  Score: 90
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       1167 GAAAATATGC

                               
       1177 ATATATATATATAATATAT
          1 ATATATATATATAATATAT

                               
       1196 ATATATATATATAATATAT
          1 ATATATATATATAATATAT

                   
       1215 ATATATA
          1 ATATATA

       1222 AAGAGATTGA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   26  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (19 bp):   
ATATATATATATAATATAT

Found at i:1428 original size:2 final size:2

Alignment explanation


    Indices: 1421--1447  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       1411 AATAATACAC

                                                    
       1421 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

       1448 AGAAAAGGAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:3017 original size:10 final size:10

Alignment explanation


    Indices: 3002--3042  Score: 55
    Period size: 10  Copynumber: 4.1  Consensus size: 10

       2992 ATTTAATATA

                      
       3002 GATATTTACG
          1 GATATTTACG

                    * 
       3012 GATATTTATG
          1 GATATTTACG

                   ** 
       3022 GATATTTGTG
          1 GATATTTACG

                      
       3032 GATATTTACG
          1 GATATTTACG

             
       3042 G
          1 G

       3043 GTATATCGAG


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  10   27  1.00

ACGTcount: A:0.27, C:0.05, G:0.24, T:0.44


Consensus pattern (10 bp):   
GATATTTACG

Found at i:5859 original size:65 final size:67

Alignment explanation


    Indices: 5731--5875  Score: 242
    Period size: 65  Copynumber: 2.2  Consensus size: 67

       5721 GCATTTAAGT

                *                                                            
       5731 ATTCTAAAGTTAAATAAGAGCACGTTTCAACATATAGTACTAAATAAGTACTAAATCCCAATTCC
          1 ATTCAAAAGTTAAATAAGAGCACGTTTCAACATATA-TACTAAATAAGTACTAAATCCCAATTCC

               
       5796 AGC
         65 AGC

                                  *                                          
       5799 ATTCAAAAGTTAAATAAGAGCAGGTTTCAACAT-T-TACTAAATAAGTACTAAATCCCAATTCCA
          1 ATTCAAAAGTTAAATAAGAGCACGTTTCAACATATATACTAAATAAGTACTAAATCCCAATTCCA

              
       5862 GC
         66 GC

                         
       5864 ATTCAAAA-TTAA
          1 ATTCAAAAGTTAA

       5876 TCACTTCGAG


Statistics
Matches: 75,  Mismatches: 2, Indels: 4
        0.93            0.02        0.05

Matches are distributed among these distances:
  64    4  0.05
  65   39  0.52
  67    1  0.01
  68   31  0.41

ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28


Consensus pattern (67 bp):   
ATTCAAAAGTTAAATAAGAGCACGTTTCAACATATATACTAAATAAGTACTAAATCCCAATTCCA
GC

Found at i:7839 original size:25 final size:24

Alignment explanation


    Indices: 7803--7849  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       7793 TCCTTCTATT

                                    
       7803 CATCTATCATC-AAGTTTTTCATC
          1 CATCTATCATCAAAGTTTTTCATC

                                    
       7826 CATCTCATCCATCAAAGTTTTTCA
          1 CATCT-AT-CATCAAAGTTTTTCA

       7850 AATTTTCAAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    2  0.10
  25    4  0.19
  26   10  0.48

ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40


Consensus pattern (24 bp):   
CATCTATCATCAAAGTTTTTCATC

Done.