Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021358.1 Corchorus olitorius cultivar O-4 contig21391, 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: 52562
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:4302 original size:7 final size:8

Alignment explanation


    Indices: 4285--4312  Score: 56
    Period size: 8  Copynumber: 3.5  Consensus size: 8

       4275 CAGATTAACA

                    
       4285 TTTCTTTT
          1 TTTCTTTT

                    
       4293 TTTCTTTT
          1 TTTCTTTT

                    
       4301 TTTCTTTT
          1 TTTCTTTT

                
       4309 TTTC
          1 TTTC

       4313 CACCGACTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   20  1.00

ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86


Consensus pattern (8 bp):   
TTTCTTTT

Found at i:23858 original size:1 final size:1

Alignment explanation


    Indices: 23852--23876  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

      23842 ACTGTAATGC

                                     
      23852 AAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAA

      23877 GTTTCAAGCC


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

Matches are distributed among these distances:
   1   24  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:26196 original size:29 final size:30

Alignment explanation


    Indices: 26154--26212  Score: 102
    Period size: 29  Copynumber: 2.0  Consensus size: 30

      26144 TCTATCTGGT

                     *                    
      26154 CAAAATTGGTAGTTCAGGGGCTTATTTGAC
          1 CAAAATTGGAAGTTCAGGGGCTTATTTGAC

                                          
      26184 CAAAATT-GAAGTTCAGGGGCTTATTTGAC
          1 CAAAATTGGAAGTTCAGGGGCTTATTTGAC

      26213 AATTGACGGA


Statistics
Matches: 28,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  29   21  0.75
  30    7  0.25

ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32


Consensus pattern (30 bp):   
CAAAATTGGAAGTTCAGGGGCTTATTTGAC

Found at i:34236 original size:21 final size:21

Alignment explanation


    Indices: 34212--34260  Score: 57
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      34202 CTCTCATCTC

                                   
      34212 TTTTCTTATGAAAATTT-T-ATT
          1 TTTTCTTA--AAAATTTCTAATT

                *                
      34233 TTTTGTTAAAAATTTCTAATT
          1 TTTTCTTAAAAATTTCTAATT

                   
      34254 TTTTCTT
          1 TTTTCTT

      34261 TTATTTTTTA


Statistics
Matches: 24,  Mismatches: 2, Indels: 4
        0.80            0.07        0.13

Matches are distributed among these distances:
  19    7  0.29
  20    1  0.04
  21   16  0.67

ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63


Consensus pattern (21 bp):   
TTTTCTTAAAAATTTCTAATT

Found at i:34494 original size:5 final size:5

Alignment explanation


    Indices: 34486--34515  Score: 51
    Period size: 5  Copynumber: 6.0  Consensus size: 5

      34476 ACTTCCCTCC

                                  *            
      34486 CCTTT CCTTT CCTTT CCTTC CCTTT CCTTT
          1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT

      34516 AATTACTTGA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   5   23  1.00

ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57


Consensus pattern (5 bp):   
CCTTT

Found at i:35019 original size:23 final size:23

Alignment explanation


    Indices: 34989--35040  Score: 104
    Period size: 23  Copynumber: 2.3  Consensus size: 23

      34979 GTTGAATATA

                                   
      34989 TATATCCACTCTTCATCATGATT
          1 TATATCCACTCTTCATCATGATT

                                   
      35012 TATATCCACTCTTCATCATGATT
          1 TATATCCACTCTTCATCATGATT

                  
      35035 TATATC
          1 TATATC

      35041 GTTTCCCTTG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   29  1.00

ACGTcount: A:0.27, C:0.25, G:0.04, T:0.44


Consensus pattern (23 bp):   
TATATCCACTCTTCATCATGATT

Found at i:47590 original size:51 final size:50

Alignment explanation


    Indices: 47489--47591  Score: 118
    Period size: 51  Copynumber: 2.0  Consensus size: 50

      47479 GTTCTTCATA

                                           **         *       
      47489 TTTTTCTTGTTTAGATCTTGTCTCAGGACACCCAAACACTCTTTTAGTGT
          1 TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT

                                      *     *         *    *    
      47539 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAAAAACACTGTATTCGTGT
          1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT

              
      47590 TT
          1 TT

      47592 CTCTTTCAGA


Statistics
Matches: 44,  Mismatches: 7, Indels: 3
        0.81            0.13        0.06

Matches are distributed among these distances:
  50    4  0.09
  51   39  0.89
  52    1  0.02

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


Consensus pattern (50 bp):   
TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
Done.