Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009718.1 Corchorus olitorius cultivar O-4 contig09750, 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: 3549
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35


Found at i:213 original size:33 final size:33

Alignment explanation


    Indices: 190--287  Score: 160
    Period size: 33  Copynumber: 3.0  Consensus size: 33

        180 GAGGCATGAT

                                             
        190 CATGGTCATGCCGCCCAAGGAGGGTGGCACCGC
          1 CATGGTCATGCCGCCCAAGGAGGGTGGCACCGC

                            *       *        
        223 CATGGTCATGCCGCCCTAGGAGGGCGGCACCGC
          1 CATGGTCATGCCGCCCAAGGAGGGTGGCACCGC

                      *     *               
        256 CATGGTCATGTCGCCCTAGGAGGGTGGCACCG
          1 CATGGTCATGCCGCCCAAGGAGGGTGGCACCG

        288 GTTATTTTTT


Statistics
Matches: 61,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   61  1.00

ACGTcount: A:0.16, C:0.33, G:0.37, T:0.14


Consensus pattern (33 bp):   
CATGGTCATGCCGCCCAAGGAGGGTGGCACCGC

Found at i:349 original size:29 final size:25

Alignment explanation


    Indices: 310--379  Score: 77
    Period size: 26  Copynumber: 2.6  Consensus size: 25

        300 TTTTTTAATT

                  *                      
        310 ATTAATTATAATTAATAATAACAATTTAA
          1 ATTAATAATAATTAATAATAA-AA--T-A

                                *     
        339 ATTAATAATAATTAAATAATTAAATA
          1 ATTAATAATAATT-AATAATAAAATA

                           
        365 ATTAATAATAATTAA
          1 ATTAATAATAATTAA

        380 AAAAATATAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 6
        0.83            0.04        0.13

Matches are distributed among these distances:
  25    2  0.05
  26   14  0.37
  27    1  0.03
  29   14  0.37
  30    7  0.18

ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40


Consensus pattern (25 bp):   
ATTAATAATAATTAATAATAAAATA

Found at i:358 original size:8 final size:8

Alignment explanation


    Indices: 345--380  Score: 54
    Period size: 8  Copynumber: 4.2  Consensus size: 8

        335 TTAAATTAAT

                    
        345 AATAATTA
          1 AATAATTA

                    
        353 AATAATTA
          1 AATAATTA

                     
        361 AATAATTAA
          1 AATAATT-A

                     
        370 TAATAATTA
          1 -AATAATTA

              
        379 AA
          1 AA

        381 AAAATATAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
   8   17  0.65
   9    2  0.08
  10    7  0.27

ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (8 bp):   
AATAATTA

Found at i:397 original size:26 final size:26

Alignment explanation


    Indices: 342--399  Score: 66
    Period size: 26  Copynumber: 2.2  Consensus size: 26

        332 AATTTAAATT

                         *           *
        342 AATAATAATTAAATAATTAAATAATT
          1 AATAATAATTAAAAAATTAAATAATA

                                        
        368 AATAATAATTAAAAAAATATAAA-AA-A
          1 AATAATAATT-AAAAAAT-TAAATAATA

                  
        394 AATAAT
          1 AATAAT

        400 TGGAGTCTTG


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  26   16  0.57
  27    8  0.29
  28    4  0.14

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (26 bp):   
AATAATAATTAAAAAATTAAATAATA

Found at i:1183 original size:35 final size:35

Alignment explanation


    Indices: 1137--1204  Score: 127
    Period size: 35  Copynumber: 1.9  Consensus size: 35

       1127 AAAGGTAAAA

                                *              
       1137 GTAAGAGTATGGGGGAGATAGAGTCATGTTTCTAG
          1 GTAAGAGTATGGGGGAGATAAAGTCATGTTTCTAG

                                             
       1172 GTAAGAGTATGGGGGAGATAAAGTCATGTTTCT
          1 GTAAGAGTATGGGGGAGATAAAGTCATGTTTCT

       1205 GTCTTTGTGT


Statistics
Matches: 32,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  35   32  1.00

ACGTcount: A:0.29, C:0.06, G:0.35, T:0.29


Consensus pattern (35 bp):   
GTAAGAGTATGGGGGAGATAAAGTCATGTTTCTAG

Done.