Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014808.1 Corchorus olitorius cultivar O-4 contig14841, 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: 8471
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:1491 original size:11 final size:12

Alignment explanation


    Indices: 1477--1508  Score: 50
    Period size: 11  Copynumber: 2.8  Consensus size: 12

       1467 AATTTATAAT

                        
       1477 TAATTTATTT-A
          1 TAATTTATTTGA

                        
       1488 TAA-TTATTTGA
          1 TAATTTATTTGA

                      
       1499 TAATTTATTT
          1 TAATTTATTT

       1509 TATATAGGAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  10    6  0.32
  11    7  0.37
  12    6  0.32

ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62


Consensus pattern (12 bp):   
TAATTTATTTGA

Found at i:2504 original size:78 final size:78

Alignment explanation


    Indices: 2336--2497  Score: 252
    Period size: 78  Copynumber: 2.1  Consensus size: 78

       2326 TTTTTTTAAT

                                *      *       **                            
       2336 TAAAATAGTAAAATGGTAAACTAAAATTGTTATAAGGATATTAGATTTAATTAAATAAAAAAAGA
          1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAAAAGA

                         
       2401 GTATTTAGTTGAG
         66 GTATTTAGTTGAG

                                                                *      * *   
       2414 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAAATATTAGATTTAATTGAATAAATATAGA
          1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAAAAGA

              *          
       2479 GTTTTTAGTTGAG
         66 GTATTTAGTTGAG

                  
       2492 TAAAAT
          1 TAAAAT

       2498 TATAAAAGTT


Statistics
Matches: 76,  Mismatches: 8, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  78   76  1.00

ACGTcount: A:0.51, C:0.01, G:0.14, T:0.35


Consensus pattern (78 bp):   
TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAAAAGA
GTATTTAGTTGAG

Found at i:3136 original size:132 final size:131

Alignment explanation


    Indices: 2987--3255  Score: 439
    Period size: 132  Copynumber: 2.0  Consensus size: 131

       2977 ATGTCATTTA

                *       *                *  *              *                 
       2987 AAAAATATATTTTAAAAATTCTAATATATCTACGTTTTTTAATTAAATTAGTAAAATGATAAAAA
          1 AAAAGTATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAA

                                                      *                      
       3052 TAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAAATGGAGTTTTTAGTTGAGTAAAACT
         66 TAAAATAGGTATAAGGATATTAGATTTAATTAAAT-AAAAATAGAGTTTTTAGTTGAGTAAAACT

              
       3117 AT
        130 AT

                                *                                     *      
       3119 AAAAGTATATTTAAAAAATTTTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAA
          1 AAAAGTATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAA

             *      *                                                        
       3184 TTAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTA
         66 TAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTA

             
       3249 T
        131 T

                  
       3250 AAAAGT
          1 AAAAGT

       3256 TTAAAAAATG


Statistics
Matches: 127,  Mismatches: 10, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
 131   36  0.28
 132   91  0.72

ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38


Consensus pattern (131 bp):   
AAAAGTATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAA
TAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTA
T

Found at i:4751 original size:19 final size:18

Alignment explanation


    Indices: 4727--4762  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       4717 TGAAGATTTA

                               
       4727 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       4746 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       4763 ATTATTTCCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:6131 original size:22 final size:22

Alignment explanation


    Indices: 6081--6133  Score: 56
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       6071 TGCTTTCTGA

                              *   
       6081 TTAATTGTTTTCTTTAATTTAC
          1 TTAATTGTTTTCTTTAATGTAC

              *                     
       6103 TTGATTGTTTTC-TTAGATAGT-C
          1 TTAATTGTTTTCTTTA-AT-GTAC

                     
       6125 TTAATTGTT
          1 TTAATTGTT

       6134 AGTTTGATTT


Statistics
Matches: 26,  Mismatches: 3, Indels: 4
        0.79            0.09        0.12

Matches are distributed among these distances:
  21    3  0.12
  22   22  0.85
  23    1  0.04

ACGTcount: A:0.21, C:0.08, G:0.11, T:0.60


Consensus pattern (22 bp):   
TTAATTGTTTTCTTTAATGTAC

Found at i:7162 original size:12 final size:12

Alignment explanation


    Indices: 7145--7175  Score: 62
    Period size: 12  Copynumber: 2.6  Consensus size: 12

       7135 AAATGATCTC

                        
       7145 GAATCAAATGGT
          1 GAATCAAATGGT

                        
       7157 GAATCAAATGGT
          1 GAATCAAATGGT

                   
       7169 GAATCAA
          1 GAATCAA

       7176 CCTCAAGTTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.45, C:0.10, G:0.23, T:0.23


Consensus pattern (12 bp):   
GAATCAAATGGT
Done.