Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001710.1 Corchorus capsularis cultivar CVL-1 contig01710, 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, 681

Length: 1136
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33


Found at i:81 original size:24 final size:24

Alignment explanation


    Indices: 49--131  Score: 73
    Period size: 24  Copynumber: 3.4  Consensus size: 24

         39 CATATAATAA

                *                   
         49 TCAATAATGATGAAATTCTAAATT
          1 TCAAAAATGATGAAATTCTAAATT

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

                *                   
         98 TCAATAATGATGAAATTCTAAATT
          1 TCAAAAATGATGAAATTCTAAATT

                      
        122 TCAAAAATGA
          1 TCAAAAATGA

        132 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:95 original size:49 final size:49

Alignment explanation


    Indices: 23--147  Score: 250
    Period size: 49  Copynumber: 2.6  Consensus size: 49

         13 AAAATCATCA

                                                             
         23 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT
          1 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT

                                                             
         72 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT
          1 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT

                                       
        121 TTCAAAAATGAATTATCATATAATAAT
          1 TTCAAAAATGAATTATCATATAATAAT

        148 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:172 original size:21 final size:18

Alignment explanation


    Indices: 131--165  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        121 TTCAAAAATG

                              
        131 AATTATCATATAATAATT
          1 AATTATCATATAATAATT

                             
        149 AATTATCATATAATAAT
          1 AATTATCATATAATAAT

        166 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

Found at i:260 original size:21 final size:21

Alignment explanation


    Indices: 236--277  Score: 50
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        226 AGGATATAAT

                                  
        236 TAAA-AAAATTAATACATAAAA
          1 TAAATAAAA-TAATACATAAAA

                  *       *      
        257 TAAATACAATAATAGATAAAA
          1 TAAATAAAATAATACATAAAA

        278 AGAGATGCGA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  21   15  0.83
  22    3  0.17

ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24


Consensus pattern (21 bp):   
TAAATAAAATAATACATAAAA
Done.