Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011787.1 Corchorus olitorius cultivar O-4 contig11820, 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: 2483
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31


Found at i:124 original size:11 final size:11

Alignment explanation


    Indices: 110--143  Score: 68
    Period size: 11  Copynumber: 3.1  Consensus size: 11

        100 TAAAGGAAAA

                       
        110 AGCTAGGAAGG
          1 AGCTAGGAAGG

                       
        121 AGCTAGGAAGG
          1 AGCTAGGAAGG

                       
        132 AGCTAGGAAGG
          1 AGCTAGGAAGG

             
        143 A
          1 A

        144 CCCTACTCCT


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

Matches are distributed among these distances:
  11   23  1.00

ACGTcount: A:0.38, C:0.09, G:0.44, T:0.09


Consensus pattern (11 bp):   
AGCTAGGAAGG

Found at i:537 original size:21 final size:21

Alignment explanation


    Indices: 513--625  Score: 165
    Period size: 21  Copynumber: 5.4  Consensus size: 21

        503 CTTAGGCAAT

                         *       
        513 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        534 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        555 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
        576 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                             * * 
        597 TCCAATGAGCTTGGAACATGC
          1 TCCAATGAGCTTGGAACCTTC

                    
        618 TCCAATGA
          1 TCCAATGA

        626 ACTTCTAGCA


Statistics
Matches: 84,  Mismatches: 6, Indels: 4
        0.89            0.06        0.04

Matches are distributed among these distances:
  20    3  0.04
  21   80  0.95
  22    1  0.01

ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:1012 original size:154 final size:154

Alignment explanation


    Indices: 732--1410  Score: 1036
    Period size: 154  Copynumber: 4.4  Consensus size: 154

        722 TGGCGCATCA

                                              **                 *           
        732 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCCATTTGGCAACC
          1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC

                            *  *                                             
        797 CTCAATGCTTTTCTTTTCAATGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTT
         66 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTT

                                    
        862 TGAAGTTTTTAGCTCATTTGGAAC
        131 TGAAGTTTTTAGCTCATTTGGAAC

                      *           *                                        * 
        886 ACTTGTTATTATGGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
          1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC

                                         * *                  *             *
        951 CTCAATGCTTTTCTTTCCATTGTTTATGGTCAAACTATAATCATTTTGGTGAGATTAGTCCACTC
         66 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTT

               *               *    
       1016 TGATGTTTTTAGCTCATTTTGAAC
        131 TGAAGTTTTTAGCTCATTTGGAAC

                  *                                     *                *   
       1040 ACTTGTCATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGATTCGTCTTCGATTTGGCCACC
          1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC

                               *            *          *      *             *
       1105 CTCAATGCTTTTCTTTCCACTGTTTATGGCCTTACTATAATCACTTTGGTGAGATTAGTCCACTG
         66 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTT

                                    
       1170 TGAAGTTTTTAGCTCATTTGGAAC
        131 TGAAGTTTTTAGCTCATTTGGAAC

                          *  *         *       **    *            *          
       1194 ACTT-TATATTTTGAGCTTATCGGGGCGCATTAGTGACGTTGTGAATCGTCTTCCATTTGGCAAC
          1 ACTTGT-TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAC

                     *        *                                              
       1258 CCTCAATGCCTTTCTTTCGATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACT
         65 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACT

                 *                   
       1323 TTGAATTTTTTAGCTCATTTGGAAC
        130 TTGAAGTTTTTAGCTCATTTGGAAC

                                 *                                   *     
       1348 ACTTGTTATTTTGGGCCTATCTGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTAGGCAA
          1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAA

       1411 ACTGCAATGA


Statistics
Matches: 468,  Mismatches: 55, Indels: 4
        0.89            0.10        0.01

Matches are distributed among these distances:
 153    1  0.00
 154  466  1.00
 155    1  0.00

ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41


Consensus pattern (154 bp):   
ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTT
TGAAGTTTTTAGCTCATTTGGAAC

Found at i:2231 original size:21 final size:21

Alignment explanation


    Indices: 2207--2253  Score: 78
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       2197 CTTAGGCAAT

                                  
       2207 TCCAATGAGCTTGGAACCTT-C
          1 TCCAATGAGCTTGGAA-CTTCC

                                 
       2228 TCCAATGAGCTTGGAACTTCC
          1 TCCAATGAGCTTGGAACTTCC

                 
       2249 TCCAA
          1 TCCAA

       2254 CGATCTCCTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  20    3  0.12
  21   22  0.88

ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACTTCC
Done.