Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000915.1 Corchorus olitorius cultivar O-4 contig00915, 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: 3164
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:95 original size:30 final size:29

Alignment explanation


    Indices: 23--96  Score: 85
    Period size: 29  Copynumber: 2.5  Consensus size: 29

         13 TTGTAGCATT

                      *    *    *        
         23 TGGACGTTTTGCCCCTTGAATTTCAATTC
          1 TGGACGTTTTACCCCCTGAACTTCAATTC

                 *  *                   *
         52 TGGACATTCTACCCCCTGAACTTCAATTT
          1 TGGACGTTTTACCCCCTGAACTTCAATTC

                            
         81 TGGGACGTTTTACCCC
          1 T-GGACGTTTTACCCC

         97 TCAGCCTAAT


Statistics
Matches: 36,  Mismatches: 8, Indels: 1
        0.80            0.18        0.02

Matches are distributed among these distances:
  29   24  0.67
  30   12  0.33

ACGTcount: A:0.19, C:0.28, G:0.16, T:0.36


Consensus pattern (29 bp):   
TGGACGTTTTACCCCCTGAACTTCAATTC

Found at i:393 original size:29 final size:29

Alignment explanation


    Indices: 357--431  Score: 114
    Period size: 29  Copynumber: 2.6  Consensus size: 29

        347 TTGTAGCATT

                      *                  
        357 TGGACGTTTTGCCCCTTGAACTTCAATTC
          1 TGGACGTTTTACCCCTTGAACTTCAATTC

                           *            *
        386 TGGACGTTTTACCCCATGAACTTCAATTT
          1 TGGACGTTTTACCCCTTGAACTTCAATTC

                             
        415 TGGGACGTTTTACCCCT
          1 T-GGACGTTTTACCCCT

        432 CAGCCTAATG


Statistics
Matches: 41,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  29   27  0.66
  30   14  0.34

ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37


Consensus pattern (29 bp):   
TGGACGTTTTACCCCTTGAACTTCAATTC

Found at i:621 original size:29 final size:29

Alignment explanation


    Indices: 586--641  Score: 94
    Period size: 29  Copynumber: 1.9  Consensus size: 29

        576 GGCAAAACGT

                        *    *           
        586 TCCAAAATTGAAGTTCATGGGACAAAATG
          1 TCCAAAATTGAAATTCAGGGGACAAAATG

                                       
        615 TCCAAAATTGAAATTCAGGGGACAAAA
          1 TCCAAAATTGAAATTCAGGGGACAAAA

        642 CGTCAAATGC


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

Matches are distributed among these distances:
  29   25  1.00

ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21


Consensus pattern (29 bp):   
TCCAAAATTGAAATTCAGGGGACAAAATG

Found at i:2684 original size:21 final size:20

Alignment explanation


    Indices: 2646--2684  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2636 CAAGTAAATC

                    *    *      
       2646 GGACCCATTAAATGCGATTT
          1 GGACCCATCAAATCCGATTT

                               
       2666 GGACCCATCCAAATCCGAT
          1 GGACCCAT-CAAATCCGAT

       2685 CCAAGCGGCC


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    8  0.50
  21    8  0.50

ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23


Consensus pattern (20 bp):   
GGACCCATCAAATCCGATTT

Found at i:3074 original size:2 final size:2

Alignment explanation


    Indices: 3050--3110  Score: 54
    Period size: 2  Copynumber: 30.5  Consensus size: 2

       3040 ATATAATCAG

                              *                        *  *      *          
       3050 AT AT AT -T AT AT CT GAT AT A- AT AT AT AT TT TT AGT TT AT AT AT
          1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT A-T AT AT AT AT

                                        
       3092 AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT A

       3111 CTAAAATAAC


Statistics
Matches: 49,  Mismatches: 6, Indels: 8
        0.78            0.10        0.13

Matches are distributed among these distances:
   1    2  0.04
   2   45  0.92
   3    2  0.04

ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52


Consensus pattern (2 bp):   
AT

Done.