Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002768.1 Corchorus olitorius cultivar O-4 contig02770, 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: 1719
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38


Found at i:1161 original size:14 final size:15

Alignment explanation


    Indices: 1130--1162  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       1120 AGCAAGAGAC

                       *   
       1130 TCTCCCTCAGGGGAG
          1 TCTCCCTCAGGCGAG

                           
       1145 TCTCCCTCA-GCGAG
          1 TCTCCCTCAGGCGAG

                
       1159 TCTC
          1 TCTC

       1163 TCCCCTAGCG


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14    8  0.47
  15    9  0.53

ACGTcount: A:0.12, C:0.39, G:0.24, T:0.24


Consensus pattern (15 bp):   
TCTCCCTCAGGCGAG

Found at i:1480 original size:40 final size:40

Alignment explanation


    Indices: 1425--1527  Score: 161
    Period size: 40  Copynumber: 2.5  Consensus size: 40

       1415 CGAGGGAGTC

                                       *   *        
       1425 TCTCCCTCAGGGGAGTCTCCTCTAGCGTGGAGCAAGAGAG
          1 TCTCCCTCAGGGGAGTCTCCTCTAGCGCGGAACAAGAGAG

                                                    
       1465 TCTCCCTCAGGGGAGTCTCCTCTAGCGCGGAACAAGAGAG
          1 TCTCCCTCAGGGGAGTCTCCTCTAGCGCGGAACAAGAGAG

               *     *             
       1505 TCTTCCTCAAGGGAGTCTTCCTC
          1 TCTCCCTCAGGGGAGTC-TCCTC

       1528 AAGGGAGTCT


Statistics
Matches: 58,  Mismatches: 4, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  40   53  0.91
  41    5  0.09

ACGTcount: A:0.19, C:0.30, G:0.28, T:0.22


Consensus pattern (40 bp):   
TCTCCCTCAGGGGAGTCTCCTCTAGCGCGGAACAAGAGAG

Found at i:1520 original size:15 final size:15

Alignment explanation


    Indices: 1497--1545  Score: 80
    Period size: 15  Copynumber: 3.3  Consensus size: 15

       1487 TAGCGCGGAA

                *          
       1497 CAAGAGAGTCTTCCT
          1 CAAGGGAGTCTTCCT

                           
       1512 CAAGGGAGTCTTCCT
          1 CAAGGGAGTCTTCCT

                        *  
       1527 CAAGGGAGTCTTGCT
          1 CAAGGGAGTCTTCCT

                
       1542 CAAG
          1 CAAG

       1546 TTAAATTGCA


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   32  1.00

ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24


Consensus pattern (15 bp):   
CAAGGGAGTCTTCCT

Found at i:1585 original size:33 final size:34

Alignment explanation


    Indices: 1548--1667  Score: 100
    Period size: 34  Copynumber: 3.4  Consensus size: 34

       1538 TGCTCAAGTT

                                *             
       1548 AAATTGCAAGGGGG-ATAACCCCTCCCCCATTAA
          1 AAATTGCAAGGGGGCATAACACCTCCCCCATTAA

                  *        *      *            
       1581 AAATTGGAAGGGGGCGTAACACTTCCCCCATTAAA
          1 AAATTGCAAGGGGGCATAACACCTCCCCCATT-AA

                   *          *    *             *
       1616 AAATTTGGAAGGGGGGGCGTAACGCCTCCCCCA-TATT
          1 AAA-TTGCAA--GGGGGCATAACACCTCCCCCATTA-A

                  *        
       1653 AAATTGGAAGGGGGC
          1 AAATTGCAAGGGGGC

       1668 GTGCCCCGTT


Statistics
Matches: 74,  Mismatches: 7, Indels: 11
        0.80            0.08        0.12

Matches are distributed among these distances:
  33   13  0.18
  34   20  0.27
  35    5  0.07
  36   13  0.18
  37    4  0.05
  38   19  0.26

ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19


Consensus pattern (34 bp):   
AAATTGCAAGGGGGCATAACACCTCCCCCATTAA

Found at i:1660 original size:36 final size:36

Alignment explanation


    Indices: 1563--1666  Score: 115
    Period size: 38  Copynumber: 2.9  Consensus size: 36

       1553 GCAAGGGGGA

                *                                
       1563 TAACCCCTCCCCCAT-TAAAAATTGGAA--GGGGGCG
          1 TAACACCTCCCCCATAT-AAAATTGGAAGGGGGGGCG

                  *          *                    
       1597 TAACACTTCCCCCATTAAAAAATTTGGAAGGGGGGGCG
          1 TAACACCTCCCCCA-TATAAAA-TTGGAAGGGGGGGCG

                *            *              
       1635 TAACGCCTCCCCCATATTAAATTGGAAGGGGG
          1 TAACACCTCCCCCATATAAAATTGGAAGGGGG

       1667 CGTGCCCCGT


Statistics
Matches: 58,  Mismatches: 7, Indels: 8
        0.79            0.10        0.11

Matches are distributed among these distances:
  34   12  0.21
  35    5  0.09
  36   17  0.29
  37    5  0.09
  38   19  0.33

ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20


Consensus pattern (36 bp):   
TAACACCTCCCCCATATAAAATTGGAAGGGGGGGCG
Done.