Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001743.1 Corchorus olitorius cultivar O-4 contig01743, 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, 637

Length: 1063
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42


Found at i:59 original size:15 final size:15

Alignment explanation


    Indices: 39--72  Score: 68
    Period size: 15  Copynumber: 2.3  Consensus size: 15

         29 TATCTATATC

                           
         39 TATATCCATATACTA
          1 TATATCCATATACTA

                           
         54 TATATCCATATACTA
          1 TATATCCATATACTA

                
         69 TATA
          1 TATA

         73 AGTCTAAACT


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

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41


Consensus pattern (15 bp):   
TATATCCATATACTA

Found at i:344 original size:39 final size:40

Alignment explanation


    Indices: 288--368  Score: 128
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        278 TTTAATTCCT

                                                    
        288 ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA

                     *          *         *         
        328 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA

              
        367 AT
          1 AT

        369 TTTTAGGTAT


Statistics
Matches: 38,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  39   30  0.79
  40    8  0.21

ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA

Found at i:399 original size:25 final size:24

Alignment explanation


    Indices: 359--405  Score: 76
    Period size: 25  Copynumber: 1.9  Consensus size: 24

        349 AATACTTACA

                       *            
        359 TTAATTAAATTTTTAGGTATTTTT
          1 TTAATTAAATTCTTAGGTATTTTT

                                   
        383 TTAATTCAAATTCTTAGGTATTT
          1 TTAATT-AAATTCTTAGGTATTT

        406 GTGCAAACGT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  24    6  0.29
  25   15  0.71

ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57


Consensus pattern (24 bp):   
TTAATTAAATTCTTAGGTATTTTT

Found at i:737 original size:212 final size:204

Alignment explanation


    Indices: 483--897  Score: 672
    Period size: 212  Copynumber: 2.0  Consensus size: 204

        473 TTAATAATAA

                                                                             
        483 ATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGACCTAATTTAATTT
          1 ATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGACCTAATTTAATTT

                                            *          *                     
        548 AATAAATCAACCACTAATGTTCAACTAATTTTTTTTTTTTTTGGGTTATAGTTCTATATATATAA
         66 AATAAATCAACCACTAATGTTCAACT-A----CTTTTTTTTT-AG-TATAGTT-T-TATATATAA

              *                                                              
        613 TAGTAATGTGTTGTATCTTATTCACTACAACTTTGTT-AGTAATCTTAGACTTAAAAAA-TTAAT
        122 TAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAAGTAATCTTAGACTTAAAAAACTTAAT

                        *     
        676 AACATTCACCATTGATAT
        187 AACATTCACCATCGATAT

                                                                 *           
        694 ATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT
          1 ATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGACCTAATTTAATT

                                                                             
        759 TAATAAATCAACCACTAATGTTCAACTACTTTTTTTTTAGTATAGTTTTATATATAATAATAATG
         65 TAATAAATCAACCACTAATGTTCAACTACTTTTTTTTTAGTATAGTTTTATATATAATAATAATG

                                                                             
        824 TGTTGTATCTTATTCACTACAACTTTGTTAAGTAATCTTAGACTTAAAAAACTTAATAACATTCA
        130 TGTTGTATCTTATTCACTACAACTTTGTTAAGTAATCTTAGACTTAAAAAACTTAATAACATTCA

            *        
        889 TCATCGATA
        195 CCATCGATA

        898 AAATTATTAA


Statistics
Matches: 195,  Mismatches: 6, Indels: 12
        0.92            0.03        0.06

Matches are distributed among these distances:
 203   45  0.23
 204   22  0.11
 205   27  0.14
 206    1  0.01
 207    9  0.05
 211   13  0.07
 212   78  0.40

ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45


Consensus pattern (204 bp):   
ATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGACCTAATTTAATTT
AATAAATCAACCACTAATGTTCAACTACTTTTTTTTTAGTATAGTTTTATATATAATAATAATGT
GTTGTATCTTATTCACTACAACTTTGTTAAGTAATCTTAGACTTAAAAAACTTAATAACATTCAC
CATCGATAT
Done.