Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014596.1 Corchorus capsularis cultivar CVL-1 contig14617, 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: 15495
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:1162 original size:2 final size:2

Alignment explanation


    Indices: 1157--1183  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       1147 ATACATACAC

                                                    
       1157 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

       1184 AATTAAAAGT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:1630 original size:3 final size:3

Alignment explanation


    Indices: 1622--1679  Score: 107
    Period size: 3  Copynumber: 19.0  Consensus size: 3

       1612 TACATCACAC

                                                                           
       1622 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

                        
       1670 AAT AGAT AAT
          1 AAT A-AT AAT

       1680 TGAAGGAATT


Statistics
Matches: 54,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
   3   51  0.94
   4    3  0.06

ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:5436 original size:91 final size:87

Alignment explanation


    Indices: 5285--5449  Score: 204
    Period size: 91  Copynumber: 1.9  Consensus size: 87

       5275 TTTTTTGATA

                              *                            *   * *       *   
       5285 TGTTTTAACTATTGATGATCGGTAAAGCAGATTTGTGTATTATCCTTGGATTAGCTGTTGTTAAG
          1 TGTTTTAACTATTGATGACCGGTAAAGCAGATTTGTGTATTATCCTTAGATCAACTGTTGTCAAG

                *                 
       5350 TTTTTCTTTATACAATGGATTT
         66 TTTTACTTTATACAATGGATTT

                                            *     * * *                      
       5372 TGTTTTAACTATTGAAATTTGACCGGTAAAGCTGATTTTTTTGTTATCCTTAGATCAACTGTTGT
          1 TGTTTTAACTATTG--A--TGACCGGTAAAGCAGATTTGTGTATTATCCTTAGATCAACTGTTGT

                         
       5437 CAAGTTTTACTTT
         62 CAAGTTTTACTTT

       5450 CTTTAATGCA


Statistics
Matches: 64,  Mismatches: 10, Indels: 4
        0.82            0.13        0.05

Matches are distributed among these distances:
  87   14  0.22
  89    1  0.02
  91   49  0.77

ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47


Consensus pattern (87 bp):   
TGTTTTAACTATTGATGACCGGTAAAGCAGATTTGTGTATTATCCTTAGATCAACTGTTGTCAAG
TTTTACTTTATACAATGGATTT

Found at i:14657 original size:12 final size:13

Alignment explanation


    Indices: 14640--14680  Score: 50
    Period size: 12  Copynumber: 3.3  Consensus size: 13

      14630 TTATTATTTA

                         
      14640 ATATATTATAGAT
          1 ATATATTATAGAT

                      *  
      14653 A-ATATTA-ATAT
          1 ATATATTATAGAT

                      *  
      14664 ATATATTATATAT
          1 ATATATTATAGAT

                
      14677 ATAT
          1 ATAT

      14681 GATAAGCTGA


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  11    4  0.16
  12   12  0.48
  13    9  0.36

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (13 bp):   
ATATATTATAGAT
Done.