Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006893.1 Corchorus olitorius cultivar O-4 contig06918, 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, 771

Length: 1285
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.38


Found at i:676 original size:7 final size:7

Alignment explanation


    Indices: 666--756  Score: 50
    Period size: 7  Copynumber: 13.1  Consensus size: 7

        656 TTTTTTTATT

                   
        666 TTATATA
          1 TTATATA

                   
        673 TTATATA
          1 TTATATA

                   
        680 TTATATA
          1 TTATATA

                     
        687 TATAATATA
          1 T-T-ATATA

                   
        696 TT-TAT-
          1 TTATATA

                   
        701 TT-T-T-
          1 TTATATA

                    
        705 TTATATAA
          1 TTATAT-A

              *     *
        713 TTTTCATTT
          1 TTAT-A-TA

              *   *
        722 TTTTATT
          1 TTATATA

                   
        729 TTATATA
          1 TTATATA

                   
        736 TTATATA
          1 TTATATA

             *     
        743 TAATATA
          1 TTATATA

                   
        750 TT-TATA
          1 TTATATA

             
        756 T
          1 T

        757 AAATATGTGG


Statistics
Matches: 70,  Mismatches: 6, Indels: 17
        0.75            0.06        0.18

Matches are distributed among these distances:
   4    3  0.04
   5    4  0.06
   6    9  0.13
   7   36  0.51
   8    6  0.09
   9   11  0.16
  10    1  0.01

ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63


Consensus pattern (7 bp):   
TTATATA

Found at i:721 original size:19 final size:21

Alignment explanation


    Indices: 647--737  Score: 71
    Period size: 21  Copynumber: 4.3  Consensus size: 21

        637 TATTCCTTTT

                *             * *
        647 ATATTTTCATTTTTTTATTTT
          1 ATATATTCATTTTTTTATATA

                             *      
        668 ATATATT-ATATATTATATATATA
          1 ATATATTCAT-T-TT-TTTATATA

                   *             
        691 ATATATTTATTTTTTTATATA
          1 ATATATTCATTTTTTTATATA

                              * *
        712 AT-T-TTCATTTTTTTATTTT
          1 ATATATTCATTTTTTTATATA

                   
        731 ATATATT
          1 ATATATT

        738 ATATATAATA


Statistics
Matches: 56,  Mismatches: 8, Indels: 12
        0.74            0.11        0.16

Matches are distributed among these distances:
  19   15  0.27
  20    4  0.07
  21   18  0.32
  22    4  0.07
  23   13  0.23
  24    2  0.04

ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67


Consensus pattern (21 bp):   
ATATATTCATTTTTTTATATA

Found at i:761 original size:14 final size:16

Alignment explanation


    Indices: 730--762  Score: 52
    Period size: 15  Copynumber: 2.2  Consensus size: 16

        720 TTTTTTATTT

                            
        730 TATATATTATATATAA
          1 TATATATTATATATAA

                            
        746 TATAT-TTATATA-AA
          1 TATATATTATATATAA

               
        760 TAT
          1 TAT

        763 GTGGATGCCC


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

Matches are distributed among these distances:
  14    5  0.29
  15    7  0.41
  16    5  0.29

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


Consensus pattern (16 bp):   
TATATATTATATATAA

Found at i:1165 original size:33 final size:33

Alignment explanation


    Indices: 1123--1191  Score: 120
    Period size: 33  Copynumber: 2.1  Consensus size: 33

       1113 AGAAAGTTTA

                        *       *            
       1123 TTTATCATGCATGATCTCCTTCTTCTACCTTTC
          1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC

                                             
       1156 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
          1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC

               
       1189 TTT
          1 TTT

       1192 TATTATTAAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.16, C:0.30, G:0.04, T:0.49


Consensus pattern (33 bp):   
TTTATCATGCATAATCTCCTCCTTCTACCTTTC

Done.