Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007002.1 Corchorus capsularis cultivar CVL-1 contig07023, 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: 11939
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:391 original size:2 final size:2

Alignment explanation


    Indices: 379--418  Score: 73
    Period size: 2  Copynumber: 20.5  Consensus size: 2

        369 GTAATTCACT

                                                                         
        379 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        419 CTTCATTAAT


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   36  0.97

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:8915 original size:17 final size:16

Alignment explanation


    Indices: 8861--8922  Score: 65
    Period size: 16  Copynumber: 3.8  Consensus size: 16

       8851 ACACAAACTG

                             
       8861 AACCCGAACCCGAATT-
          1 AACCCGAACCCG-ATTC

                *       *    
       8877 AACCTG-ACCCAAATTC
          1 AACCCGAACCC-GATTC

                            
       8893 AACCCGAACCCGATTC
          1 AACCCGAACCCGATTC

                          
       8909 AAGCCCGAACCCGA
          1 AA-CCCGAACCCGA

       8923 CGACCCGAGC


Statistics
Matches: 38,  Mismatches: 4, Indels: 7
        0.78            0.08        0.14

Matches are distributed among these distances:
  15    7  0.18
  16   16  0.42
  17   15  0.39

ACGTcount: A:0.35, C:0.40, G:0.13, T:0.11


Consensus pattern (16 bp):   
AACCCGAACCCGATTC

Found at i:9649 original size:116 final size:113

Alignment explanation


    Indices: 9412--9653  Score: 297
    Period size: 116  Copynumber: 2.1  Consensus size: 113

       9402 AAATAGTGAG

                        * *                                                  
       9412 TTTCAGTCGACTATGCTTGGTGTTGAAACTGCAGTCGCATGGTTGTCAACACTGCCACTTTTAGG
          1 TTTCAGTCGACTGTCCTTGGTGTTGAAACTGCAGTCGCATGGTTGTCAACACTGCCACTTTTAGG

              **                                            
       9477 AAGGACTGATTAAAATTTCAGTCGACTAAAGAAAGTATTGAAAATCAC
         66 AAAAACTGATTAAAATTTCAGTCGACTAAAGAAAGTATTGAAAATCAC

                                                *  *                        *
       9525 TTTCAGTCGACTGTCCTTGGTGTTGAAACTGCAGTCTCTTTGGTTGTCAACACTGCCACTTTTCT
          1 TTTCAGTCGACTGTCCTTGGTGTTGAAACTGCAGTCGC-ATGGTTGTCAACACTGCCACTTTT-A

            *       *     *  *          *  *   *    *           
       9590 TGAACAAAGTGATTGAACTTTCAGTCGATTGTAA-CAAGTGTTGAAAATCAC
         64 GGAA-AAACTGATTAAAATTTCAGTCGACT-AAAGAAAGTATTGAAAATCAC

               *         
       9641 TTTTAGTCGACTG
          1 TTTCAGTCGACTG

       9654 AAAATATTTC


Statistics
Matches: 109,  Mismatches: 16, Indels: 5
        0.84            0.12        0.04

Matches are distributed among these distances:
 113   35  0.32
 114   23  0.21
 115    3  0.03
 116   46  0.42
 117    2  0.02

ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33


Consensus pattern (113 bp):   
TTTCAGTCGACTGTCCTTGGTGTTGAAACTGCAGTCGCATGGTTGTCAACACTGCCACTTTTAGG
AAAAACTGATTAAAATTTCAGTCGACTAAAGAAAGTATTGAAAATCAC

Found at i:9734 original size:21 final size:21

Alignment explanation


    Indices: 9710--9765  Score: 60
    Period size: 20  Copynumber: 2.7  Consensus size: 21

       9700 CTAGTTTGAA

                            *    
       9710 GCTAGGAACATGTGAAGAACG
          1 GCTAGGAACATGTGAACAACG

                     *   ***     
       9731 GCTA-GAACTTGTCTCCAACG
          1 GCTAGGAACATGTGAACAACG

                           
       9751 GCTAGGAACATGTGA
          1 GCTAGGAACATGTGA

       9766 GAGACTATAA


Statistics
Matches: 26,  Mismatches: 8, Indels: 2
        0.72            0.22        0.06

Matches are distributed among these distances:
  20   15  0.58
  21   11  0.42

ACGTcount: A:0.32, C:0.20, G:0.29, T:0.20


Consensus pattern (21 bp):   
GCTAGGAACATGTGAACAACG
Done.