Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012568.1 Corchorus olitorius cultivar O-4 contig12601, 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: 13961
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:316 original size:3 final size:3

Alignment explanation


    Indices: 303--361  Score: 66
    Period size: 3  Copynumber: 19.3  Consensus size: 3

        293 AATTATATAT

                               *                                *        
        303 ATA ACTA ATA ATA ATT ATA ATA AT- ATA ACTA ATA ATA ATT ATA ATA
          1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA

              *              
        349 ATT ATA ATA ATA A
          1 ATA ATA ATA ATA A

        362 GTTGTTTAAC


Statistics
Matches: 47,  Mismatches: 6, Indels: 6
        0.80            0.10        0.10

Matches are distributed among these distances:
   2    2  0.04
   3   39  0.83
   4    6  0.13

ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37


Consensus pattern (3 bp):   
ATA

Found at i:332 original size:24 final size:24

Alignment explanation


    Indices: 292--361  Score: 110
    Period size: 24  Copynumber: 3.0  Consensus size: 24

        282 AAGGAAAACG

                                    
        292 TAATTAT-AT-ATATAACTAATAA
          1 TAATTATAATAATATAACTAATAA

                                    
        314 TAATTATAATAATATAACTAATAA
          1 TAATTATAATAATATAACTAATAA

                                     
        338 TAATTATAATAATTATAA-TAATAA
          1 TAATTATAATAA-TATAACTAATAA

        362 GTTGTTTAAC


Statistics
Matches: 45,  Mismatches: 0, Indels: 4
        0.92            0.00        0.08

Matches are distributed among these distances:
  22    7  0.16
  23    2  0.04
  24   31  0.69
  25    5  0.11

ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40


Consensus pattern (24 bp):   
TAATTATAATAATATAACTAATAA

Found at i:633 original size:14 final size:14

Alignment explanation


    Indices: 592--633  Score: 52
    Period size: 14  Copynumber: 3.1  Consensus size: 14

        582 GGTAGTCAAA

                          
        592 AATAAAATATTAAT
          1 AATAAAATATTAAT

                    *  *  
        606 -A-AAAATTTTTAT
          1 AATAAAATATTAAT

                          
        618 AATAAAATATTAAT
          1 AATAAAATATTAAT

              
        632 AA
          1 AA

        634 AAGTCAAGAA


Statistics
Matches: 22,  Mismatches: 4, Indels: 4
        0.73            0.13        0.13

Matches are distributed among these distances:
  12    9  0.41
  13    2  0.09
  14   11  0.50

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (14 bp):   
AATAAAATATTAAT

Found at i:1172 original size:22 final size:22

Alignment explanation


    Indices: 1143--1341  Score: 110
    Period size: 22  Copynumber: 9.1  Consensus size: 22

       1133 TGAACATTTT

                                  
       1143 TATGAAATTTTGATAACTACCC
          1 TATGAAATTTTGATAACTACCC

               *             *  **
       1165 TATTAAATTTTGATAACCACGT
          1 TATGAAATTTTGATAACTACCC

                               *  
       1187 TATGAAATTTTGATAA-TAACC
          1 TATGAAATTTTGATAACTACCC

                     *            *
       1208 TATGAAATTGTGATAAACT-CCA
          1 TATGAAATTTTGAT-AACTACCC

               *   *  *          * 
       1230 TATAAAACTTCGATAACCTA-AC
          1 TATGAAATTTTGATAA-CTACCC

               *       *         *  
       1252 TATTAAATTTTAATAAACCT-TCC
          1 TATGAAATTTTGAT-AA-CTACCC

                                   
       1275 TATGAAATTTTG-TAACCT-CCC
          1 TATGAAATTTTGATAA-CTACCC

                  *              * 
       1296 TATG-AGTTTTGATAACCT-CAC
          1 TATGAAATTTTGATAA-CTACCC

                 *      *          
       1317 TATGAGATTTTGTTAATCT-CCC
          1 TATGAAATTTTGATAA-CTACCC

               
       1339 TAT
          1 TAT

       1342 AATTTTTTGA


Statistics
Matches: 136,  Mismatches: 33, Indels: 16
        0.74            0.18        0.09

Matches are distributed among these distances:
  20    6  0.04
  21   39  0.29
  22   74  0.54
  23   17  0.12

ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38


Consensus pattern (22 bp):   
TATGAAATTTTGATAACTACCC
Done.