Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018076.1 Corchorus olitorius cultivar O-4 contig18109, 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: 25360
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:7419 original size:26 final size:26

Alignment explanation


    Indices: 7390--7441  Score: 86
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       7380 GGAGCCTAGC

                          *           
       7390 TTTTCAATGAAATAGTAAGTGATTGT
          1 TTTTCAATGAAATAATAAGTGATTGT

                *                     
       7416 TTTTTAATGAAATAATAAGTGATTGT
          1 TTTTCAATGAAATAATAAGTGATTGT

       7442 CTGTATTTTT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44


Consensus pattern (26 bp):   
TTTTCAATGAAATAATAAGTGATTGT

Found at i:9278 original size:27 final size:27

Alignment explanation


    Indices: 9248--9299  Score: 104
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       9238 ATCACTATTT

                                       
       9248 ATTTTCGAACATGCAGCCATTTCCCTC
          1 ATTTTCGAACATGCAGCCATTTCCCTC

                                     
       9275 ATTTTCGAACATGCAGCCATTTCCC
          1 ATTTTCGAACATGCAGCCATTTCCC

       9300 CCGCGGGGTA


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

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.23, C:0.33, G:0.12, T:0.33


Consensus pattern (27 bp):   
ATTTTCGAACATGCAGCCATTTCCCTC

Found at i:9426 original size:68 final size:68

Alignment explanation


    Indices: 9317--9453  Score: 229
    Period size: 68  Copynumber: 2.0  Consensus size: 68

       9307 GTAGCGCCGG

                     *            *                   *                      
       9317 GCAAATTCTGGTTGGGTCTTAATATCTCCACAAAATATGTCACTTTATTACTTGATGATCACTGA
          1 GCAAATTCTAGTTGGGTCTTAAAATCTCCACAAAATATGTCAATTTATTACTTGATGATCACTGA

               
       9382 TCA
         66 TCA

                                            *             *                  
       9385 GCAAATTCTAGTTGGGTCTTAAAATCTCCACAGAATATGTCAATTTGTTACTTGATGATCACTGA
          1 GCAAATTCTAGTTGGGTCTTAAAATCTCCACAAAATATGTCAATTTATTACTTGATGATCACTGA

               
       9450 TCA
         66 TCA

             
       9453 G
          1 G

       9454 GCGAAACTAT


Statistics
Matches: 64,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  68   64  1.00

ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36


Consensus pattern (68 bp):   
GCAAATTCTAGTTGGGTCTTAAAATCTCCACAAAATATGTCAATTTATTACTTGATGATCACTGA
TCA

Found at i:9718 original size:96 final size:95

Alignment explanation


    Indices: 9554--9823  Score: 414
    Period size: 96  Copynumber: 2.8  Consensus size: 95

       9544 ACATGAAATA

                       *                    *                                
       9554 GGGTTAGGTTCATGAGGGAGAGTTCCATTATCCATGGCATAATCAAGTGCTCGATAACCCCAATT
          1 GGGTTAGGTTCCTGAGGGAGAGTTCCATT-TCTATGGCATAATCAAGTGCTCGATAACCCCAATT

                                           
       9619 ATCAAAAGCCCAATTTGATCCGGATAACAAT
         65 ATCAAAAGCCCAATTTGATCCGGATAACAAT

                                                               *             
       9650 GGGTTAGGTTCCTGAGGGAGAGTTCCATCTTCTATGGCATAATCAAGTGCTTGATAACCCCAATT
          1 GGGTTAGGTTCCTGAGGGAGAGTTCCAT-TTCTATGGCATAATCAAGTGCTCGATAACCCCAATT

                      ***            *     
       9715 ATCAAAAGCCTGTTTTGATCCGGATGACAAT
         65 ATCAAAAGCCCAATTTGATCCGGATAACAAT

             *                              *                       *        
       9746 GAGTTAGGTTCCTGAGGGAGAGTTCCATTTTTTTATGGCATAATCAAGTGCTCGATGACCCCAAT
          1 GGGTTAGGTTCCTGAGGGAGAGTTCCA--TTTCTATGGCATAATCAAGTGCTCGATAACCCCAAT

                         
       9811 TATCAAAAGCCCA
         64 TATCAAAAGCCCA

       9824 TTTAGCATCT


Statistics
Matches: 158,  Mismatches: 13, Indels: 5
        0.90            0.07        0.03

Matches are distributed among these distances:
  96  113  0.72
  97   44  0.28
  98    1  0.01

ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29


Consensus pattern (95 bp):   
GGGTTAGGTTCCTGAGGGAGAGTTCCATTTCTATGGCATAATCAAGTGCTCGATAACCCCAATTA
TCAAAAGCCCAATTTGATCCGGATAACAAT

Found at i:10691 original size:12 final size:12

Alignment explanation


    Indices: 10676--10701  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      10666 CGGACCATAA

                        
      10676 CCATCACCATGT
          1 CCATCACCATGT

                        
      10688 CCATCACCATGT
          1 CCATCACCATGT

              
      10700 CC
          1 CC

      10702 CTATATATTC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.23, C:0.46, G:0.08, T:0.23


Consensus pattern (12 bp):   
CCATCACCATGT

Found at i:19831 original size:22 final size:23

Alignment explanation


    Indices: 19806--19848  Score: 70
    Period size: 23  Copynumber: 1.9  Consensus size: 23

      19796 AAATAGAATG

                                   
      19806 TTTTC-TTTGATTTTTCCTTTTT
          1 TTTTCTTTTGATTTTTCCTTTTT

                      *          
      19828 TTTTCTTTTGTTTTTTCCTTT
          1 TTTTCTTTTGATTTTTCCTTT

      19849 CTAAAAAGGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  22    5  0.26
  23   14  0.74

ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79


Consensus pattern (23 bp):   
TTTTCTTTTGATTTTTCCTTTTT

Done.