Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023494.1 Corchorus olitorius cultivar O-4 contig23527, 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: 24444
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:250 original size:19 final size:19

Alignment explanation


    Indices: 226--262  Score: 74
    Period size: 19  Copynumber: 1.9  Consensus size: 19

        216 ATTCTAATGT

                               
        226 CTATTCAAATAATTATCTG
          1 CTATTCAAATAATTATCTG

                              
        245 CTATTCAAATAATTATCT
          1 CTATTCAAATAATTATCT

        263 ACTGGATCCC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.38, C:0.16, G:0.03, T:0.43


Consensus pattern (19 bp):   
CTATTCAAATAATTATCTG

Found at i:7125 original size:31 final size:31

Alignment explanation


    Indices: 7087--7145  Score: 118
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       7077 AAAAAAAATC

                                           
       7087 GAGATTGAAAGTTGAATCATACAAGTCTACA
          1 GAGATTGAAAGTTGAATCATACAAGTCTACA

                                        
       7118 GAGATTGAAAGTTGAATCATACAAGTCT
          1 GAGATTGAAAGTTGAATCATACAAGTCT

       7146 TATGTTAGAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27


Consensus pattern (31 bp):   
GAGATTGAAAGTTGAATCATACAAGTCTACA

Found at i:7218 original size:33 final size:34

Alignment explanation


    Indices: 7176--7250  Score: 109
    Period size: 33  Copynumber: 2.2  Consensus size: 34

       7166 ACAAAGTTTA

                *       *                      
       7176 TTTAGCATGCATGATCTCCTT-CTTCTACCTTTC-
          1 TTTATCATGCATAATCT-CTTCCTTCTACCTTTCT

                                              
       7209 TTTATCATGCATAATCTCTTCCTTCTACCTTTCT
          1 TTTATCATGCATAATCTCTTCCTTCTACCTTTCT

                    
       7243 TTTATCAT
          1 TTTATCAT

       7251 TAAAAATTAT


Statistics
Matches: 38,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  32    3  0.08
  33   27  0.71
  34    8  0.21

ACGTcount: A:0.17, C:0.28, G:0.05, T:0.49


Consensus pattern (34 bp):   
TTTATCATGCATAATCTCTTCCTTCTACCTTTCT

Found at i:8725 original size:35 final size:35

Alignment explanation


    Indices: 8686--8815  Score: 188
    Period size: 35  Copynumber: 3.7  Consensus size: 35

       8676 CTATATCGGG

                     *                         
       8686 TGAAGGCTAGAGAAGAGCCAGTATTCAAATTTGAT
          1 TGAAGGCTACAGAAGAGCCAGTATTCAAATTTGAT

                     *                         
       8721 TGAAGGCTAAAGAAGAGCCAGTATTCAAATTTGAT
          1 TGAAGGCTACAGAAGAGCCAGTATTCAAATTTGAT

                    *        *    *            
       8756 TGAAGGCTCCAGAAGAGTCAGTGTTCAAATTTGAT
          1 TGAAGGCTACAGAAGAGCCAGTATTCAAATTTGAT

                  * *         *      
       8791 TGAAGGTTCCAGAAGAGCTAGTATT
          1 TGAAGGCTACAGAAGAGCCAGTATT

       8816 ATTTTATCTG


Statistics
Matches: 86,  Mismatches: 9, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  35   86  1.00

ACGTcount: A:0.35, C:0.12, G:0.25, T:0.27


Consensus pattern (35 bp):   
TGAAGGCTACAGAAGAGCCAGTATTCAAATTTGAT

Found at i:16553 original size:27 final size:28

Alignment explanation


    Indices: 16515--16583  Score: 95
    Period size: 27  Copynumber: 2.5  Consensus size: 28

      16505 AAGATGAGCC

                   *                    
      16515 AAAAATGGCCAAAATGCCCCT-GAATGT
          1 AAAAATGACCAAAATGCCCCTGGAATGT

                                    * * 
      16542 AAAAATGACCAAAATGCCCCTGGATTTT
          1 AAAAATGACCAAAATGCCCCTGGAATGT

            *             
      16570 GAAAATGACCAAAA
          1 AAAAATGACCAAAA

      16584 AATCCCCTAG


Statistics
Matches: 37,  Mismatches: 4, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  27   20  0.54
  28   17  0.46

ACGTcount: A:0.45, C:0.20, G:0.16, T:0.19


Consensus pattern (28 bp):   
AAAAATGACCAAAATGCCCCTGGAATGT

Found at i:18351 original size:17 final size:17

Alignment explanation


    Indices: 18331--18363  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      18321 TTTTCTCCCC

                             
      18331 TTCTCCATATTCTCTTG
          1 TTCTCCATATTCTCTTG

                 *          
      18348 TTCTCTATATTCTCTT
          1 TTCTCCATATTCTCTT

      18364 TTTTTTTTTT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.12, C:0.27, G:0.03, T:0.58


Consensus pattern (17 bp):   
TTCTCCATATTCTCTTG

Found at i:19847 original size:15 final size:16

Alignment explanation


    Indices: 19819--19850  Score: 57
    Period size: 15  Copynumber: 2.1  Consensus size: 16

      19809 GAAAATATTC

                            
      19819 GTAAATGTTGGGTTTT
          1 GTAAATGTTGGGTTTT

                            
      19835 GTAAATG-TGGGTTTT
          1 GTAAATGTTGGGTTTT

             
      19850 G
          1 G

      19851 AACTCATTAA


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

Matches are distributed among these distances:
  15    9  0.56
  16    7  0.44

ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47


Consensus pattern (16 bp):   
GTAAATGTTGGGTTTT
Done.