Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002453.1 Corchorus capsularis cultivar CVL-1 contig02459, 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, 856

Length: 1427
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:32 original size:23 final size:23

Alignment explanation


    Indices: 4--56  Score: 106
    Period size: 23  Copynumber: 2.3  Consensus size: 23

          1 ATT

                                   
          4 TATTTATATTTATTGATTATTTA
          1 TATTTATATTTATTGATTATTTA

                                   
         27 TATTTATATTTATTGATTATTTA
          1 TATTTATATTTATTGATTATTTA

                   
         50 TATTTAT
          1 TATTTAT

         57 CGTATATTTA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   30  1.00

ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66


Consensus pattern (23 bp):   
TATTTATATTTATTGATTATTTA

Found at i:64 original size:17 final size:17

Alignment explanation


    Indices: 25--66  Score: 59
    Period size: 17  Copynumber: 2.5  Consensus size: 17

         15 ATTGATTATT

                           * 
         25 TATATTTATATTTATTG
          1 TATATTTATATTTATCG

                              
         42 -ATTATTTATATTTATCG
          1 TA-TATTTATATTTATCG

                    
         59 TATATTTA
          1 TATATTTA

         67 CTTTTAAATA


Statistics
Matches: 22,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  16    1  0.05
  17   20  0.91
  18    1  0.05

ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62


Consensus pattern (17 bp):   
TATATTTATATTTATCG

Found at i:957 original size:24 final size:24

Alignment explanation


    Indices: 925--1007  Score: 73
    Period size: 24  Copynumber: 3.4  Consensus size: 24

        915 CATATAATAA

                *                   
        925 TCAATAATGATGAAATTCTAAATT
          1 TCAAAAATGATGAAATTCTAAATT

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

                *                   
        974 TCAATAATGATGAAATTCTAAATT
          1 TCAAAAATGATGAAATTCTAAATT

                      
        998 TCAAAAATGA
          1 TCAAAAATGA

       1008 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:971 original size:49 final size:49

Alignment explanation


    Indices: 899--1023  Score: 250
    Period size: 49  Copynumber: 2.6  Consensus size: 49

        889 AAAATCATCA

                                                             
        899 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT
          1 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT

                                                             
        948 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT
          1 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT

                                       
        997 TTCAAAAATGAATTATCATATAATAAT
          1 TTCAAAAATGAATTATCATATAATAAT

       1024 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:1048 original size:21 final size:18

Alignment explanation


    Indices: 1007--1041  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        997 TTCAAAAATG

                              
       1007 AATTATCATATAATAATT
          1 AATTATCATATAATAATT

                             
       1025 AATTATCATATAATAAT
          1 AATTATCATATAATAAT

       1042 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.