Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022002.1 Corchorus olitorius cultivar O-4 contig22035, 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: 2858
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31


Found at i:1379 original size:39 final size:39

Alignment explanation


    Indices: 1331--1408  Score: 106
    Period size: 39  Copynumber: 2.0  Consensus size: 39

       1321 TCTTAAGAGA

                *                                    
       1331 CCCTTTGCGGTCTTTCA-TAGAAGCTT-TCAGAAATCTAAG
          1 CCCTGTGCGGTCTTTCACT-GAAG-TTCTCAGAAATCTAAG

                                           *       
       1370 CCCTGTGCGGTCTTTCACTGAAGTTCTCAGAGATCTAAG
          1 CCCTGTGCGGTCTTTCACTGAAGTTCTCAGAAATCTAAG

       1409 TTGATTTTAA


Statistics
Matches: 35,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  38    2  0.06
  39   32  0.91
  40    1  0.03

ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32


Consensus pattern (39 bp):   
CCCTGTGCGGTCTTTCACTGAAGTTCTCAGAAATCTAAG

Found at i:1420 original size:92 final size:93

Alignment explanation


    Indices: 1278--1454  Score: 286
    Period size: 92  Copynumber: 1.9  Consensus size: 93

       1268 CCTTCAAGCA

                                     *        *                              
       1278 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGATGATCTTAAGA-GACCCTTTGCGGT
          1 CCCTGTGCGGTCTTTCATAGAAGTTCTCAGAGATCTAAGATGATCTTAAGATGACCCTTTGCGGT

             *                          
       1342 CTTTCATAGAAGCTTTCAGAAATCTAAG
         66 CATTCATAGAAGCTTTCAGAAATCTAAG

                                                    *    *                   
       1370 CCCTGTGCGGTCTTTCACT-GAAGTTCTCAGAGATCTAAGTTGATTTTAAGATGACCCTTTGCGG
          1 CCCTGTGCGGTCTTTCA-TAGAAGTTCTCAGAGATCTAAGATGATCTTAAGATGACCCTTTGCGG

                                 
       1434 TCATTCATAGAAGCTTTCAGA
         65 TCATTCATAGAAGCTTTCAGA

       1455 GATAAGTTGA


Statistics
Matches: 78,  Mismatches: 5, Indels: 3
        0.91            0.06        0.03

Matches are distributed among these distances:
  92   45  0.58
  93   33  0.42

ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34


Consensus pattern (93 bp):   
CCCTGTGCGGTCTTTCATAGAAGTTCTCAGAGATCTAAGATGATCTTAAGATGACCCTTTGCGGT
CATTCATAGAAGCTTTCAGAAATCTAAG

Found at i:1475 original size:52 final size:53

Alignment explanation


    Indices: 1370--1476  Score: 130
    Period size: 54  Copynumber: 2.0  Consensus size: 53

       1360 GAAATCTAAG

                        *                               *         
       1370 CCCTGTGCGGTCTTTCACTGAAGTTCTCAGAGATCTAAGTTGATTTTAAGATGA
          1 CCCTGTGCGGTCATTCACTGAAGTTCTCAGAGA-CTAAGTTGATCTTAAGATGA

                *                                           *      
       1424 CCCTTTGCGGTCATTCA-TAGAAGCTT-TCAGAGA-TAAGTTGATCTTCAGATGA
          1 CCCTGTGCGGTCATTCACT-GAAG-TTCTCAGAGACTAAGTTGATCTTAAGATGA

             
       1476 C
          1 C

       1477 TCGGTGTTGT


Statistics
Matches: 47,  Mismatches: 4, Indels: 6
        0.82            0.07        0.11

Matches are distributed among these distances:
  52   18  0.38
  53    1  0.02
  54   26  0.55
  55    2  0.04

ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34


Consensus pattern (53 bp):   
CCCTGTGCGGTCATTCACTGAAGTTCTCAGAGACTAAGTTGATCTTAAGATGA

Found at i:1552 original size:54 final size:54

Alignment explanation


    Indices: 1494--2082  Score: 443
    Period size: 54  Copynumber: 11.0  Consensus size: 54

       1484 TGTCTTTCAT

                                               *    *  * *        
       1494 AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGGTCCAATGAGATCATTCCA
          1 AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCA

                     *       *              *      *      *     *  
       1548 AGAAGTTTTGA-ATGATTAGAGTTGATCCCCAAATGATCTAGTGCGATCATTTCA
          1 AGAAGTTTTTAGA-GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCA

                     *  *                *                        
       1602 AGAAGTTTTCAGTGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTCCA
          1 AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCA

                        **              *       **                *
       1656 AGAAGTTTTCT-TTGATCAGAGTTGAT-TCCAGATGGCCCAGTGCGGTCATTCCT
          1 AGAAGTTTT-TAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCA

             *                         *     *                    
       1709 ATAAG-TTTTAGAGATCAGAGTTGATCGCCA-AAGATCCAGTGCGGTCATTCCA
          1 AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCA

             *          *               * *        *        *     
       1761 AAAAG-TTTTA-TGATCAGAGTTGATCCTCGGATGATCCCGTGCGGTCGTTCCA
          1 AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCA

                                        *   *                *      
       1813 AGAAGTTTTT-GATGATCAGAGTTGATCTCCAAATGATCCAGTGCGGTCCTTCCGA
          1 AGAAGTTTTTAGA-GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC-A

                      *    *           **                      *   *
       1868 A-AAG-TTTTCGAAGTTCAGAGTTGATGTCCAGATGATCCAGTGCGGTTC-CTCCT
          1 AGAAGTTTTTAG-AGATCAGAGTTGATCCCCAGATGATCCAGTGCGG-TCATTCCA

                     * *      *        *           *   ** * *  *  
       1921 AGAAGTTTTCAAAGATCAAAGTTGATCTCCAGATGATCCGGTGTTGACGTTTCA
          1 AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCA

                 *    *                 **          *  **    *     
       1975 AGAA-ATTTTCGAAGATCAGAGTTGATCTTCAGATGATCCGGTATGGTCGTT-CA
          1 AGAAGTTTTTAG-AGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCA

                     **                 *                **          
       2028 AGAAG-TTTCCGATGATCAGAGTTGATCTCCA-ATTTGATCCAGTATGGTCATTCCA
          1 AGAAGTTTTTAGA-GATCAGAGTTGATCCCCAGA--TGATCCAGTGCGGTCATTCCA

       2083 GGAAAGGTTT


Statistics
Matches: 435,  Mismatches: 78, Indels: 43
        0.78            0.14        0.08

Matches are distributed among these distances:
  51   16  0.04
  52   68  0.16
  53   71  0.16
  54  270  0.62
  55   10  0.02

ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31


Consensus pattern (54 bp):   
AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCA

Done.