Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017381.1 Corchorus olitorius cultivar O-4 contig17414, 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: 19152
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:627 original size:24 final size:24

Alignment explanation


    Indices: 581--627  Score: 69
    Period size: 25  Copynumber: 2.0  Consensus size: 24

        571 ACTTAATTTG

                            *       
        581 TTAATATTGTCAAAGTTTGTTTTT
          1 TTAATATTGTCAAAGTATGTTTTT

                                    
        605 TTAATAATTGTCAAAGTAT-TTTT
          1 TTAAT-ATTGTCAAAGTATGTTTT

        628 CTATAACATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  24    9  0.43
  25   12  0.57

ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55


Consensus pattern (24 bp):   
TTAATATTGTCAAAGTATGTTTTT

Found at i:10776 original size:12 final size:12

Alignment explanation


    Indices: 10759--10783  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      10749 CATGACGTGA

                        
      10759 TTCAAATTATCT
          1 TTCAAATTATCT

                        
      10771 TTCAAATTATCT
          1 TTCAAATTATCT

             
      10783 T
          1 T

      10784 CCCTCTTGCC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52


Consensus pattern (12 bp):   
TTCAAATTATCT

Found at i:11546 original size:12 final size:13

Alignment explanation


    Indices: 11524--11553  Score: 53
    Period size: 12  Copynumber: 2.4  Consensus size: 13

      11514 ACTAGCAATT

                         
      11524 AAAATCAATCAAG
          1 AAAATCAATCAAG

                         
      11537 AAAA-CAATCAAG
          1 AAAATCAATCAAG

                 
      11549 AAAAT
          1 AAAAT

      11554 TAAAGAAAAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  12   12  0.75
  13    4  0.25

ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13


Consensus pattern (13 bp):   
AAAATCAATCAAG

Found at i:14884 original size:15 final size:16

Alignment explanation


    Indices: 14864--14905  Score: 68
    Period size: 15  Copynumber: 2.7  Consensus size: 16

      14854 ACAGAGGTTG

                            
      14864 ACAGAAAACAATT-AA
          1 ACAGAAAACAATTAAA

                            
      14879 ACAGAAAACAATTAAA
          1 ACAGAAAACAATTAAA

             *         
      14895 ATAGAAAACAA
          1 ACAGAAAACAA

      14906 AGCAGAGTAA


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

Matches are distributed among these distances:
  15   13  0.52
  16   12  0.48

ACGTcount: A:0.69, C:0.12, G:0.07, T:0.12


Consensus pattern (16 bp):   
ACAGAAAACAATTAAA

Found at i:16323 original size:30 final size:31

Alignment explanation


    Indices: 16277--16336  Score: 95
    Period size: 30  Copynumber: 2.0  Consensus size: 31

      16267 CAATTATTCC

                *                          
      16277 TCTTGAAATAAATCTTC-AATGGTCTTCAAG
          1 TCTTCAAATAAATCTTCAAATGGTCTTCAAG

                       *                  
      16307 TCTTCAAATAAGTCTTCAAATGGTCTTCAA
          1 TCTTCAAATAAATCTTCAAATGGTCTTCAA

      16337 ACACGAACTT


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  30   15  0.56
  31   12  0.44

ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37


Consensus pattern (31 bp):   
TCTTCAAATAAATCTTCAAATGGTCTTCAAG

Found at i:16334 original size:11 final size:11

Alignment explanation


    Indices: 16289--16337  Score: 52
    Period size: 12  Copynumber: 4.7  Consensus size: 11

      16279 TTGAAATAAA

                       
      16289 TCTTC-AATGG
          1 TCTTCAAATGG

                       
      16299 TCTTC-AA--G
          1 TCTTCAAATGG

                      * 
      16307 TCTTCAAATAAG
          1 TCTTCAAAT-GG

                       
      16319 TCTTCAAATGG
          1 TCTTCAAATGG

                    
      16330 TCTTCAAA
          1 TCTTCAAA

      16338 CACGAACTTC


Statistics
Matches: 34,  Mismatches: 1, Indels: 7
        0.81            0.02        0.17

Matches are distributed among these distances:
   8    6  0.18
   9    2  0.06
  10    7  0.21
  11    9  0.26
  12   10  0.29

ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37


Consensus pattern (11 bp):   
TCTTCAAATGG
Done.