Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001152.1 Corchorus capsularis cultivar CVL-1 contig01152, 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, 627

Length: 1046
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:939 original size:25 final size:25

Alignment explanation


    Indices: 905--1028  Score: 102
    Period size: 25  Copynumber: 5.0  Consensus size: 25

        895 AAATCATCAT

                                     
        905 TCAAAAATGAATTATCATATAATAA
          1 TCAAAAATGAATTATCATATAATAA

                          *            *
        930 TCAATAATGATGAAAT-TC-TA-AAT-T
          1 TCAA-AA--ATGAATTATCATATAATAA

                                     
        954 TCAAAAATGAATTATCATATAATAA
          1 TCAAAAATGAATTATCATATAATAA

                          *            *
        979 TCAATAATGATGAAAT-TC-TA-AAT-T
          1 TCAA-AA--ATGAATTATCATATAATAA

                                     
       1003 TCAAAAATGAATTATCATATAATAA
          1 TCAAAAATGAATTATCATATAATAA

             
       1028 T
          1 T

       1029 TAATTATCAT


Statistics
Matches: 77,  Mismatches: 8, Indels: 28
        0.68            0.07        0.25

Matches are distributed among these distances:
  21   12  0.16
  22    4  0.05
  23    8  0.10
  24   14  0.18
  25   15  0.19
  26    8  0.10
  27    4  0.05
  28   12  0.16

ACGTcount: A:0.52, C:0.08, G:0.06, T:0.35


Consensus pattern (25 bp):   
TCAAAAATGAATTATCATATAATAA

Found at i:962 original size:24 final size:24

Alignment explanation


    Indices: 930--1012  Score: 73
    Period size: 24  Copynumber: 3.4  Consensus size: 24

        920 CATATAATAA

                *                   
        930 TCAATAATGATGAAATTCTAAATT
          1 TCAAAAATGATGAAATTCTAAATT

                          *            *
        954 TC-AAAA--ATGAATTATCATATAATAA
          1 TCAAAAATGATGAAAT-TC-TA-AAT-T

                *                   
        979 TCAATAATGATGAAATTCTAAATT
          1 TCAAAAATGATGAAATTCTAAATT

                      
       1003 TCAAAAATGA
          1 TCAAAAATGA

       1013 ATTATCATAT


Statistics
Matches: 45,  Mismatches: 7, Indels: 14
        0.68            0.11        0.21

Matches are distributed among these distances:
  21    6  0.13
  22    2  0.04
  23    5  0.11
  24   14  0.31
  25    5  0.11
  26    5  0.11
  27    2  0.04
  28    6  0.13

ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34


Consensus pattern (24 bp):   
TCAAAAATGATGAAATTCTAAATT

Found at i:976 original size:49 final size:49

Alignment explanation


    Indices: 904--1028  Score: 250
    Period size: 49  Copynumber: 2.6  Consensus size: 49

        894 AAAATCATCA

                                                             
        904 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT
          1 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT

                                                             
        953 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT
          1 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT

                                       
       1002 TTCAAAAATGAATTATCATATAATAAT
          1 TTCAAAAATGAATTATCATATAATAAT

       1029 TAATTATCAT


Statistics
Matches: 76,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  49   76  1.00

ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35


Consensus pattern (49 bp):   
TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT

Found at i:1035 original size:18 final size:18

Alignment explanation


    Indices: 1012--1046  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1002 TTCAAAAATG

                              
       1012 AATTATCATATAATAATT
          1 AATTATCATATAATAATT

                             
       1030 AATTATCATATAATAAT
          1 AATTATCATATAATAAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43


Consensus pattern (18 bp):   
AATTATCATATAATAATT
Done.