Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014744.1 Corchorus olitorius cultivar O-4 contig14777, 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: 25162
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:2660 original size:35 final size:35

Alignment explanation


    Indices: 2544--2649  Score: 194
    Period size: 35  Copynumber: 3.0  Consensus size: 35

       2534 GAGAAAAAAC

                                  *            
       2544 ATTTTAAGTGTTAGGAAGAAAAAAGACTTAGGCAA
          1 ATTTTAAGTGTTAGGAAGAAAAGAGACTTAGGCAA

                                               
       2579 ATTTTAAGTGTTAGGAAGAAAAGAGACTTAGGCAA
          1 ATTTTAAGTGTTAGGAAGAAAAGAGACTTAGGCAA

                                           *   
       2614 ATTTTAAGTGTTAGGAAGAAAAGAGACTTAGACAA
          1 ATTTTAAGTGTTAGGAAGAAAAGAGACTTAGGCAA

             
       2649 A
          1 A

       2650 ACGACAGTGT


Statistics
Matches: 69,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  35   69  1.00

ACGTcount: A:0.45, C:0.06, G:0.24, T:0.25


Consensus pattern (35 bp):   
ATTTTAAGTGTTAGGAAGAAAAGAGACTTAGGCAA

Found at i:3109 original size:32 final size:32

Alignment explanation


    Indices: 3042--3137  Score: 115
    Period size: 32  Copynumber: 3.0  Consensus size: 32

       3032 GAAATTATAT

                    *             *     *     
       3042 ATAGCGGCATCTTGTTT-AATAAACGCCACTAAA
          1 ATAGCGGCGT-TTGTTTCAATAGACGCCGCT-AA

                                            
       3075 ATAGCGGCGTTTGTTTCAATAGACGCCGCTAA
          1 ATAGCGGCGTTTGTTTCAATAGACGCCGCTAA

                              *             
       3107 ATAAG-GGCGTTTGTTTCTATAGACGCCGCTA
          1 AT-AGCGGCGTTTGTTTCAATAGACGCCGCTA

       3138 TTTTCCAGCA


Statistics
Matches: 57,  Mismatches: 4, Indels: 5
        0.86            0.06        0.08

Matches are distributed among these distances:
  32   35  0.61
  33   22  0.39

ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29


Consensus pattern (32 bp):   
ATAGCGGCGTTTGTTTCAATAGACGCCGCTAA

Found at i:9790 original size:21 final size:20

Alignment explanation


    Indices: 9764--9808  Score: 72
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       9754 GGCACTATTG

                       *         
       9764 ATTTTTTTTAGTCATTTTATA
          1 ATTTTTTTT-GGCATTTTATA

                                
       9785 ATTTTTTTTGGCATTTTATA
          1 ATTTTTTTTGGCATTTTATA

                
       9805 ATTT
          1 ATTT

       9809 AGTTTGAGTA


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  20   14  0.61
  21    9  0.39

ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67


Consensus pattern (20 bp):   
ATTTTTTTTGGCATTTTATA

Found at i:9814 original size:20 final size:20

Alignment explanation


    Indices: 9776--9814  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       9766 TTTTTTTAGT

                         **     
       9776 CATTTTATAATTTTTTTTGG
          1 CATTTTATAATTTAGTTTGG

                               
       9796 CATTTTATAATTTAGTTTG
          1 CATTTTATAATTTAGTTTG

       9815 AGTATATTAC


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62


Consensus pattern (20 bp):   
CATTTTATAATTTAGTTTGG

Found at i:19271 original size:18 final size:16

Alignment explanation


    Indices: 19235--19265  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      19225 TGATGATATT

                            
      19235 GTTTTTATAATTGTTG
          1 GTTTTTATAATTGTTG

                  *        
      19251 GTTTTTCTAATTGTT
          1 GTTTTTATAATTGTT

      19266 TTGGTTATGA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.16, C:0.03, G:0.16, T:0.65


Consensus pattern (16 bp):   
GTTTTTATAATTGTTG

Found at i:24012 original size:16 final size:15

Alignment explanation


    Indices: 23993--24026  Score: 59
    Period size: 16  Copynumber: 2.2  Consensus size: 15

      23983 GATTGAAATA

                            
      23993 AAAAGGAAAAGAAAAG
          1 AAAAGGAAAA-AAAAG

                           
      24009 AAAAGGAAAAAAAAG
          1 AAAAGGAAAAAAAAG

               
      24024 AAA
          1 AAA

      24027 TAAGAGAATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  15    8  0.44
  16   10  0.56

ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00


Consensus pattern (15 bp):   
AAAAGGAAAAAAAAG
Done.