Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001937.1 Corchorus capsularis cultivar CVL-1 contig01939, 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, 617

Length: 1029
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38


Found at i:116 original size:49 final size:49

Alignment explanation


    Indices: 25--148  Score: 241
    Period size: 49  Copynumber: 2.6  Consensus size: 49

         15 AAAATCATCA

                                                             
         25 TTCAAAAATGAATTATCATAT-ATAATCAATAATGATGAAATTCTAAAT
          1 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT

                                                             
         73 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT
          1 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT

                                       
        122 TTCAAAAATGAATTATCATATAATAAT
          1 TTCAAAAATGAATTATCATATAATAAT

        149 TAATTATCAT


Statistics
Matches: 75,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  48   21  0.28
  49   54  0.72

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


Consensus pattern (49 bp):   
TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT

Found at i:131 original size:24 final size:24

Alignment explanation


    Indices: 50--132  Score: 73
    Period size: 24  Copynumber: 3.4  Consensus size: 24

         40 TCATATATAA

                *                   
         50 TCAATAATGATGAAATTCTAAATT
          1 TCAAAAATGATGAAATTCTAAATT

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

                *                   
         99 TCAATAATGATGAAATTCTAAATT
          1 TCAAAAATGATGAAATTCTAAATT

                      
        123 TCAAAAATGA
          1 TCAAAAATGA

        133 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:173 original size:21 final size:18

Alignment explanation


    Indices: 132--166  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        122 TTCAAAAATG

                              
        132 AATTATCATATAATAATT
          1 AATTATCATATAATAATT

                             
        150 AATTATCATATAATAAT
          1 AATTATCATATAATAAT

        167 CAATAATGAT


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.