Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023143.1 Corchorus olitorius cultivar O-4 contig23176, 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: 13464
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27


Found at i:1021 original size:35 final size:35

Alignment explanation


    Indices: 975--1044  Score: 106
    Period size: 35  Copynumber: 2.0  Consensus size: 35

        965 AGTTAGATCA

                          *           *         
        975 AATTGATCAATTTAGC-TACTTTAACTAATTTTCTT
          1 AATTGATCAATTTAACTTA-TTTAACCAATTTTCTT

                                               
       1010 AATTGATCAATTTAACTTATTTAACCAATTTTCTT
          1 AATTGATCAATTTAACTTATTTAACCAATTTTCTT

       1045 GATATGTACA


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  35   30  0.94
  36    2  0.06

ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49


Consensus pattern (35 bp):   
AATTGATCAATTTAACTTATTTAACCAATTTTCTT

Found at i:1105 original size:13 final size:13

Alignment explanation


    Indices: 1087--1114  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       1077 ATGGAGGGAG

                         
       1087 TAATAGCTAATAT
          1 TAATAGCTAATAT

                         
       1100 TAATAGCTAATAT
          1 TAATAGCTAATAT

              
       1113 TA
          1 TA

       1115 TATCGAATTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39


Consensus pattern (13 bp):   
TAATAGCTAATAT

Found at i:11866 original size:66 final size:65

Alignment explanation


    Indices: 11796--11988  Score: 314
    Period size: 66  Copynumber: 2.9  Consensus size: 65

      11786 AGAATTTGTT

                   *                              *                   *      
      11796 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGTTTTAGT
          1 TCATCACTAACAACA-CTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT

             
      11861 A
         65 A

                                                                             
      11862 TCATCACTAACAACATCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT
          1 TCATCACTAACAACA-CTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT

             
      11927 A
         65 A

                                         *       *                       
      11928 TCATCACTAACAACACTCAAAACAGATTTCGTGTCATTGCAAACAACACTCAAATTAGGTT
          1 TCATCACTAACAACACT-AAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTT

      11989 CAGAATTACT


Statistics
Matches: 120,  Mismatches: 6, Indels: 2
        0.94            0.05        0.02

Matches are distributed among these distances:
  65    2  0.02
  66  118  0.98

ACGTcount: A:0.41, C:0.23, G:0.09, T:0.26


Consensus pattern (65 bp):   
TCATCACTAACAACACTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGTA

Found at i:11977 original size:33 final size:33

Alignment explanation


    Indices: 11780--11981  Score: 221
    Period size: 33  Copynumber: 6.1  Consensus size: 33

      11770 AATTAGCTTC

                            *                 
      11780 CAAAACAGAATTT-GTTTCATCACAAACAACAC-
          1 CAAAACAG-ATTTAGTGTCATCACAAACAACACT

                                              
      11812 CTAAAACAGATTTAGTGTCATCACAAACAACACT
          1 C-AAAACAGATTTAGTGTCATCACAAACAACACT

                **  *      *       *         
      11846 CAAATTAGTTTTAGTATCATCACTAACAACA-T
          1 CAAAACAGATTTAGTGTCATCACAAACAACACT

                                  *           
      11878 CTAAAACAGATTTAGTGTCATCGCAAACAACACT
          1 C-AAAACAGATTTAGTGTCATCACAAACAACACT

                **  *      *       *         
      11912 CAAATTAGGTTTAGTATCATCACTAACAACACT
          1 CAAAACAGATTTAGTGTCATCACAAACAACACT

                        *       **           
      11945 CAAAACAGATTTCGTGTCATTGCAAACAACACT
          1 CAAAACAGATTTAGTGTCATCACAAACAACACT

                
      11978 CAAA
          1 CAAA

      11982 TTAGGTTCAG


Statistics
Matches: 139,  Mismatches: 26, Indels: 9
        0.80            0.15        0.05

Matches are distributed among these distances:
  32    7  0.05
  33  129  0.93
  34    3  0.02

ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26


Consensus pattern (33 bp):   
CAAAACAGATTTAGTGTCATCACAAACAACACT

Found at i:12594 original size:15 final size:15

Alignment explanation


    Indices: 12574--12605  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      12564 AAACTAAGTG

                           
      12574 GAGCTTGTCGATTTT
          1 GAGCTTGTCGATTTT

                    *      
      12589 GAGCTTGTTGATTTT
          1 GAGCTTGTCGATTTT

              
      12604 GA
          1 GA

      12606 ACCCCCAAGG


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

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.16, C:0.09, G:0.28, T:0.47


Consensus pattern (15 bp):   
GAGCTTGTCGATTTT
Done.