Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007001.1 Corchorus capsularis cultivar CVL-1 contig07022, 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: 3864
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.35


Found at i:136 original size:53 final size:53

Alignment explanation


    Indices: 45--185  Score: 219
    Period size: 53  Copynumber: 2.7  Consensus size: 53

         35 AAGGTGTAAG

                *     *                   *  *                   
         45 CAAACAGGGTAATCTGAGATCACCACCCAAAATTACCAATAGGTTATCCCAAC
          1 CAAATAGGGTGATCTGAGATCACCACCCAAGATCACCAATAGGTTATCCCAAC

                         *        *  *                           
         98 CAAATAGGGTGATTTGAGATCATCATCCAAGATCACCAATAGGTTATCCCAAC
          1 CAAATAGGGTGATCTGAGATCACCACCCAAGATCACCAATAGGTTATCCCAAC

                                               
        151 CAAATAGGGTGATCTGAGATCACCACCCAAGATCA
          1 CAAATAGGGTGATCTGAGATCACCACCCAAGATCA

        186 GCACAGGTGA


Statistics
Matches: 78,  Mismatches: 10, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  53   78  1.00

ACGTcount: A:0.38, C:0.26, G:0.16, T:0.21


Consensus pattern (53 bp):   
CAAATAGGGTGATCTGAGATCACCACCCAAGATCACCAATAGGTTATCCCAAC

Found at i:1121 original size:131 final size:132

Alignment explanation


    Indices: 902--1144  Score: 380
    Period size: 131  Copynumber: 1.8  Consensus size: 132

        892 TAAAAATTAT

                              *                                       *      
        902 AATATATCTAAGTTTTTTGATTAAAATAGTAAAATGATAAAAAATAAAATAGTTATAAGGATATT
          1 AATATATCTAAGTTTTTTAATTAAAATAGTAAAATGATAAAAAATAAAATAGTTATAAAGATATT

                                               *                             
        967 AGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAACAGTATATTCAAAAATTT
         66 AGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAACAGTATATTCAAAAATTT

              
       1032 CG
        131 CG

                                            *   *      * *                *  
       1034 AATATATCTAAGTTTTTTAATTAAAATAGTAAGATGGT-AAAAGTGAAATAGTTATAAAGATGTT
          1 AATATATCTAAGTTTTTTAATTAAAATAGTAAAATGATAAAAAATAAAATAGTTATAAAGATATT

                          **  *                            
       1098 AGATTTAATTAAATGTAAGTAGAGTTTTTAGTTGAATAAAACTATAA
         66 AGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAA

       1145 AAATTTAAAC


Statistics
Matches: 100,  Mismatches: 11, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
 131   65  0.65
 132   35  0.35

ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37


Consensus pattern (132 bp):   
AATATATCTAAGTTTTTTAATTAAAATAGTAAAATGATAAAAAATAAAATAGTTATAAAGATATT
AGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAACAGTATATTCAAAAATTT
CG

Found at i:3461 original size:21 final size:22

Alignment explanation


    Indices: 3437--3479  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       3427 TATAAGTGAA

                                  
       3437 TTACTAAATACCGCCC-CCTTT
          1 TTACTAAATACCGCCCTCCTTT

                  **              
       3458 TTACTAGGTACCGCCCTCCTTT
          1 TTACTAAATACCGCCCTCCTTT

       3480 GGACAATTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   14  0.74
  22    5  0.26

ACGTcount: A:0.19, C:0.37, G:0.09, T:0.35


Consensus pattern (22 bp):   
TTACTAAATACCGCCCTCCTTT

Found at i:3834 original size:15 final size:16

Alignment explanation


    Indices: 3807--3844  Score: 67
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       3797 AAAGCCTTTT

                            
       3807 AAAGAAGGAAAAAAAA
          1 AAAGAAGGAAAAAAAA

                   *        
       3823 AAAGAAGAAAAAAAAA
          1 AAAGAAGGAAAAAAAA

                  
       3839 AAAGAA
          1 AAAGAA

       3845 CAGCGGGTCG


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   21  1.00

ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00


Consensus pattern (16 bp):   
AAAGAAGGAAAAAAAA
Done.