Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001034.1 Corchorus capsularis cultivar CVL-1 contig01034, 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: 2826
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37


Found at i:1354 original size:34 final size:34

Alignment explanation


    Indices: 1316--1384  Score: 129
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       1306 CCTAAGCTAT

                                   *          
       1316 TTTACATACAATACAACAACACACATCAGATTTC
          1 TTTACATACAATACAACAACACAAATCAGATTTC

                                              
       1350 TTTACATACAATACAACAACACAAATCAGATTTC
          1 TTTACATACAATACAACAACACAAATCAGATTTC

             
       1384 T
          1 T

       1385 GTATTCTCTT


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  34   34  1.00

ACGTcount: A:0.45, C:0.25, G:0.03, T:0.28


Consensus pattern (34 bp):   
TTTACATACAATACAACAACACAAATCAGATTTC

Found at i:1473 original size:2 final size:2

Alignment explanation


    Indices: 1466--1511  Score: 74
    Period size: 2  Copynumber: 22.5  Consensus size: 2

       1456 GTTTAATAAC

                                                            *              
       1466 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT

                
       1509 AT A
          1 AT A

       1512 AAAGTATGAG


Statistics
Matches: 41,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
   2   39  0.95
   3    2  0.05

ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:1804 original size:176 final size:176

Alignment explanation


    Indices: 1510--1865  Score: 622
    Period size: 176  Copynumber: 2.0  Consensus size: 176

       1500 ATACTATATA

                    *                        *                              *
       1510 TAAAAGTATGAGTTTTGAGAAACTTTTGAAATGTCTATTGTACCCTTATTTAACTTTTAAAAGAT
          1 TAAAAGTACGAGTTTTGAGAAACTTTTGAAATGCCTATTGTACCCTTATTTAACTTTTAAAAGAC

                      *                            *                         
       1575 CTATTATATCTTTACTTATCTAACATATTTCTAAAAATTGCCATTATATAATTAATTTTTAATTT
         66 CTATTATATCCTTACTTATCTAACATATTTCTAAAAATTACCATTATATAATTAATTTTTAATTT

                                                  * *     
       1640 TGTTAATTTGCATTTAATTAAATCTACAAAATATATAGTTTTTCAT
        131 TGTTAATTTGCATTTAATTAAATCTACAAAATATATAGCTCTTCAT

                                        *                                 *  
       1686 TAAAAGTACGAGTTTTGAGAAACTTTTGGAATGCCTATTGTACCCTTATTTAACTTTTAAAATAC
          1 TAAAAGTACGAGTTTTGAGAAACTTTTGAAATGCCTATTGTACCCTTATTTAACTTTTAAAAGAC

                                                                             
       1751 CTATTATATCCTTACTTATCTAACATATTTCTAAAAATTACCATTATATAATTAATTTTTAATTT
         66 CTATTATATCCTTACTTATCTAACATATTTCTAAAAATTACCATTATATAATTAATTTTTAATTT

                      *                                   
       1816 TGTTAATTTGTATTTAATTAAATCTACAAAATATATAGCTCTTCAT
        131 TGTTAATTTGCATTTAATTAAATCTACAAAATATATAGCTCTTCAT

                
       1862 TAAA
          1 TAAA

       1866 CAAATTACTT


Statistics
Matches: 170,  Mismatches: 10, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 176  170  1.00

ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45


Consensus pattern (176 bp):   
TAAAAGTACGAGTTTTGAGAAACTTTTGAAATGCCTATTGTACCCTTATTTAACTTTTAAAAGAC
CTATTATATCCTTACTTATCTAACATATTTCTAAAAATTACCATTATATAATTAATTTTTAATTT
TGTTAATTTGCATTTAATTAAATCTACAAAATATATAGCTCTTCAT

Found at i:2664 original size:98 final size:97

Alignment explanation


    Indices: 2536--2713  Score: 259
    Period size: 98  Copynumber: 1.8  Consensus size: 97

       2526 TAACAATTTT

                     *               *        *                          *   
       2536 TTTTGTTTTTTTGTTTTCGAATATCTCAACCTTATAATTTATAATATAAAGTCGGATTATTTTGT
          1 TTTTGTTTTCTTGTTTTCGAATATCCCAACCTTAAAATTTATAATATAAAGTCGGATTATTGTGT

                *                           
       2601 TCAAGAATTAATATAATTAATTAACAATATCC
         66 TCAAAAATTAATATAATTAATTAACAATATCC

                                                           *      *          
       2633 TTTTGATTTTCTT-TTTTCTGAATATCCCAACCTTAAAATTTATAATGTAAAGTTGGATTATTGT
          1 TTTTG-TTTTCTTGTTTTC-GAATATCCCAACCTTAAAATTTATAATATAAAGTCGGATTATTGT

               *             
       2697 GTTGAAAAATTAATATA
         64 GTTCAAAAATTAATATA

       2714 TCCGATTAAT


Statistics
Matches: 71,  Mismatches: 8, Indels: 3
        0.87            0.10        0.04

Matches are distributed among these distances:
  97   10  0.14
  98   61  0.86

ACGTcount: A:0.34, C:0.10, G:0.10, T:0.47


Consensus pattern (97 bp):   
TTTTGTTTTCTTGTTTTCGAATATCCCAACCTTAAAATTTATAATATAAAGTCGGATTATTGTGT
TCAAAAATTAATATAATTAATTAACAATATCC

Found at i:2793 original size:17 final size:17

Alignment explanation


    Indices: 2771--2803  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       2761 TATTATACAT

                             
       2771 TAATATAGATGAAATTC
          1 TAATATAGATGAAATTC

                            
       2788 TAATATAGATGAAATT
          1 TAATATAGATGAAATT

       2804 TTATACTCAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36


Consensus pattern (17 bp):   
TAATATAGATGAAATTC
Done.