Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010675.1 Corchorus olitorius cultivar O-4 contig10707, 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: 12823
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35


Found at i:364 original size:2 final size:2

Alignment explanation


    Indices: 357--382  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

        347 ATTTAGACTT

                                                  
        357 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

        383 AGAAAAGAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:3551 original size:34 final size:34

Alignment explanation


    Indices: 3503--3570  Score: 100
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       3493 TTTTGGTCAT

                                  *           
       3503 TTGGGCTTTCTTTCAATCGGCCTGTTTATTAAGC
          1 TTGGGCTTTCTTTCAATCGGCCCGTTTATTAAGC

                 *   *     *                  
       3537 TTGGGTTTTGTTTCACTCGGCCCGTTTATTAAGC
          1 TTGGGCTTTCTTTCAATCGGCCCGTTTATTAAGC

       3571 CCTTCTCAAT


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

Matches are distributed among these distances:
  34   30  1.00

ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44


Consensus pattern (34 bp):   
TTGGGCTTTCTTTCAATCGGCCCGTTTATTAAGC

Found at i:3923 original size:23 final size:23

Alignment explanation


    Indices: 3897--3943  Score: 76
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       3887 TTCTTCTTCT

                                   
       3897 GTTTCTCTCTCTACTCCGACGCC
          1 GTTTCTCTCTCTACTCCGACGCC

                           **      
       3920 GTTTCTCTCTCTACTTTGACGCC
          1 GTTTCTCTCTCTACTCCGACGCC

             
       3943 G
          1 G

       3944 CTCCTTCCGT


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.09, C:0.38, G:0.15, T:0.38


Consensus pattern (23 bp):   
GTTTCTCTCTCTACTCCGACGCC

Found at i:7248 original size:1 final size:1

Alignment explanation


    Indices: 7242--7269  Score: 56
    Period size: 1  Copynumber: 28.0  Consensus size: 1

       7232 ATGTTTCTTG

                                        
       7242 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT

       7270 AGTTTCATAC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   27  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:9742 original size:15 final size:15

Alignment explanation


    Indices: 9712--9753  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       9702 TTACTTTGCT

                            
       9712 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       9728 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       9743 TTGCTTTCTGT
          1 TTGTTTTCTGT

       9754 CAATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:10229 original size:25 final size:25

Alignment explanation


    Indices: 10188--10258  Score: 87
    Period size: 25  Copynumber: 2.9  Consensus size: 25

      10178 CCTTGTTCTG

                                      
      10188 TGTTT-TGCGTCGA-AAAAAAAAACT
          1 TGTTTCTGCGTC-ATAAAAAAAAACT

                                       
      10212 AT-TTT-TAGCGTCATAAAAAAAAACT
          1 -TGTTTCT-GCGTCATAAAAAAAAACT

                                  
      10237 TGTTTCTGCGTCATAAAAAAAA
          1 TGTTTCTGCGTCATAAAAAAAA

      10259 GTTTTTGCGA


Statistics
Matches: 42,  Mismatches: 0, Indels: 8
        0.84            0.00        0.16

Matches are distributed among these distances:
  24    6  0.14
  25   35  0.83
  26    1  0.02

ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31


Consensus pattern (25 bp):   
TGTTTCTGCGTCATAAAAAAAAACT

Found at i:10390 original size:19 final size:19

Alignment explanation


    Indices: 10350--10389  Score: 55
    Period size: 19  Copynumber: 2.2  Consensus size: 19

      10340 AAATATTTTC

                *          *   
      10350 TTTATTTTTTGTCTTTAAT
          1 TTTAATTTTTGTCTTAAAT

                               
      10369 TTTAATTTTTGT-TTAAAT
          1 TTTAATTTTTGTCTTAAAT

               
      10387 TTT
          1 TTT

      10390 TTACTACTAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  18    8  0.42
  19   11  0.58

ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72


Consensus pattern (19 bp):   
TTTAATTTTTGTCTTAAAT
Done.