Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011301.1 Corchorus capsularis cultivar CVL-1 contig11322, 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: 36121
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:1388 original size:30 final size:29

Alignment explanation


    Indices: 1328--1390  Score: 90
    Period size: 30  Copynumber: 2.1  Consensus size: 29

       1318 AAAGCAGAGT

                                 *        
       1328 AAAATTCATTAATAGATTTTATTTCAAAAA
          1 AAAATTCATTAATAGATTTTAGTT-AAAAA

                                           
       1358 AAAATTCATTAATAGATTTACTAGTTAAAAA
          1 AAAATTCATTAATAGATTT--TAGTTAAAAA

              
       1389 AA
          1 AA

       1391 TAAAGAAAGA


Statistics
Matches: 30,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  30   19  0.63
  31    7  0.23
  32    4  0.13

ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37


Consensus pattern (29 bp):   
AAAATTCATTAATAGATTTTAGTTAAAAA

Found at i:6900 original size:50 final size:50

Alignment explanation


    Indices: 6833--6944  Score: 206
    Period size: 50  Copynumber: 2.2  Consensus size: 50

       6823 AACAAAAATA

                   **                                         
       6833 TATTTTCCCATATATGGTTTTTATATCTCATCATCTTGCCTTAAAATATG
          1 TATTTTCTAATATATGGTTTTTATATCTCATCATCTTGCCTTAAAATATG

                                                              
       6883 TATTTTCTAATATATGGTTTTTATATCTCATCATCTTGCCTTAAAATATG
          1 TATTTTCTAATATATGGTTTTTATATCTCATCATCTTGCCTTAAAATATG

                        
       6933 TATTTTCTAATA
          1 TATTTTCTAATA

       6945 AGATGCATTT


Statistics
Matches: 60,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  50   60  1.00

ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50


Consensus pattern (50 bp):   
TATTTTCTAATATATGGTTTTTATATCTCATCATCTTGCCTTAAAATATG

Found at i:8543 original size:2 final size:2

Alignment explanation


    Indices: 8536--8560  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       8526 GTCCGATAAA

                                                 
       8536 AC AC AC AC AC AC AC AC AC AC AC AC A
          1 AC AC AC AC AC AC AC AC AC AC AC AC A

       8561 ATTGTCATAC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Found at i:16912 original size:24 final size:24

Alignment explanation


    Indices: 16880--16927  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      16870 GTATTCATAT

                                    
      16880 TTTCCTGGGTAAACTTTCCCAAAC
          1 TTTCCTGGGTAAACTTTCCCAAAC

                                    
      16904 TTTCCTGGGTAAACTTTCCCAAAC
          1 TTTCCTGGGTAAACTTTCCCAAAC

      16928 GTAACTCATA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.25, C:0.29, G:0.12, T:0.33


Consensus pattern (24 bp):   
TTTCCTGGGTAAACTTTCCCAAAC

Found at i:29952 original size:12 final size:12

Alignment explanation


    Indices: 29937--29961  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      29927 AATTATGAAC

                        
      29937 TTAATTAAGTAA
          1 TTAATTAAGTAA

                        
      29949 TTAATTAAGTAA
          1 TTAATTAAGTAA

             
      29961 T
          1 T

      29962 AAACTCCGGC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44


Consensus pattern (12 bp):   
TTAATTAAGTAA

Found at i:30175 original size:10 final size:9

Alignment explanation


    Indices: 30156--30204  Score: 55
    Period size: 10  Copynumber: 5.2  Consensus size: 9

      30146 ACCGAATAAG

                     
      30156 ATATTATAT
          1 ATATTATAT

                      
      30165 ATATATATAT
          1 ATAT-TATAT

             *        
      30175 ACATGTATAT
          1 ATAT-TATAT

                     
      30185 -TATTATAT
          1 ATATTATAT

                      
      30193 ATACTTATAT
          1 ATA-TTATAT

              
      30203 AT
          1 AT

      30205 TGATGCCACA


Statistics
Matches: 34,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
   8    5  0.15
   9    8  0.24
  10   21  0.62

ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51


Consensus pattern (9 bp):   
ATATTATAT

Done.