Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011960.1 Corchorus capsularis cultivar CVL-1 contig11981, 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: 10172
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:6195 original size:37 final size:38

Alignment explanation


    Indices: 6145--6223  Score: 124
    Period size: 37  Copynumber: 2.1  Consensus size: 38

       6135 ATATAATTAT

                              *  *                
       6145 TCATAAAGTTATGTCTATTTGGAAAGACA-TATGTTGA
          1 TCATAAAGTTATGTCTATATGAAAAGACAGTATGTTGA

                                                   
       6182 TCATAAAGTTATGTCTATATGAAAAGACATGTATGTTGA
          1 TCATAAAGTTATGTCTATATGAAAAGACA-GTATGTTGA

               
       6221 TCA
          1 TCA

       6224 AGTATATAAG


Statistics
Matches: 38,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  37   27  0.71
  39   11  0.29

ACGTcount: A:0.37, C:0.09, G:0.18, T:0.37


Consensus pattern (38 bp):   
TCATAAAGTTATGTCTATATGAAAAGACAGTATGTTGA

Found at i:7450 original size:31 final size:32

Alignment explanation


    Indices: 7412--7473  Score: 90
    Period size: 31  Copynumber: 2.0  Consensus size: 32

       7402 TGGGGGTGTC

                            *               
       7412 TTGGTTTCTTAAAGAACCAAAA-AGATATATG
          1 TTGGTTTCTTAAAGAAACAAAAGAGATATATG

                       *             *     
       7443 TTGGTTTCTTAGAGAAACAAAAGAGTTATAT
          1 TTGGTTTCTTAAAGAAACAAAAGAGATATAT

       7474 CATCGATTTC


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  31   20  0.74
  32    7  0.26

ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34


Consensus pattern (32 bp):   
TTGGTTTCTTAAAGAAACAAAAGAGATATATG

Found at i:7739 original size:33 final size:33

Alignment explanation


    Indices: 7692--7813  Score: 217
    Period size: 33  Copynumber: 3.7  Consensus size: 33

       7682 TCCGGATGGC

                *     *                      
       7692 CCAATCGATGTCCGGTTGTGGCCGGTTGGTGCG
          1 CCAAGCGATGGCCGGTTGTGGCCGGTTGGTGCG

                      *                      
       7725 CCAAGCGATGTCCGGTTGTGGCCGGTTGGTGCG
          1 CCAAGCGATGGCCGGTTGTGGCCGGTTGGTGCG

                                             
       7758 CCAAGCGATGGCCGGTTGTGGCCGGTTGGTGCG
          1 CCAAGCGATGGCCGGTTGTGGCCGGTTGGTGCG

                                   
       7791 CCAAGCGATGGCCGGTTGTGGCC
          1 CCAAGCGATGGCCGGTTGTGGCC

       7814 AGATGCCCCA


Statistics
Matches: 87,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  33   87  1.00

ACGTcount: A:0.10, C:0.25, G:0.42, T:0.23


Consensus pattern (33 bp):   
CCAAGCGATGGCCGGTTGTGGCCGGTTGGTGCG

Found at i:9746 original size:33 final size:33

Alignment explanation


    Indices: 9651--9752  Score: 129
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       9641 ATCAGATTTA

                                        *   *
       9651 TTTTCAATGC--T-ATCAACCAAAACAGGATTA
          1 TTTTCAATGCTATAATCAACCAAAACAGAATTG

               *                             
       9681 TTTGCAATGCTATAATCAACCAAAACAGAATTG
          1 TTTTCAATGCTATAATCAACCAAAACAGAATTG

                *        **                  
       9714 TTTTTAATGCTATGTTCAACCAAAACAGAATTG
          1 TTTTCAATGCTATAATCAACCAAAACAGAATTG

                  
       9747 TTTTCA
          1 TTTTCA

       9753 TCACAATTAG


Statistics
Matches: 61,  Mismatches: 8, Indels: 3
        0.85            0.11        0.04

Matches are distributed among these distances:
  30    9  0.15
  32    1  0.02
  33   51  0.84

ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33


Consensus pattern (33 bp):   
TTTTCAATGCTATAATCAACCAAAACAGAATTG

Found at i:9813 original size:33 final size:33

Alignment explanation


    Indices: 9788--9896  Score: 141
    Period size: 33  Copynumber: 3.3  Consensus size: 33

       9778 TAGTTTTATT

                                             
       9788 GCAAACAACACTCAAATTAGGTTTAGTATCATC
          1 GCAAACAACACTCAAATTAGGTTTAGTATCATC

                 *       *    *          *    *
       9821 GCAAAGAACATCTAAAACATA--TTTAGTGTCATT
          1 GCAAACAACA-CTCAAA-TTAGGTTTAGTATCATC

                                             
       9854 GCAAACAACACTCAAATTAGGTTTAGTATCATC
          1 GCAAACAACACTCAAATTAGGTTTAGTATCATC

                      
       9887 GCAAACAACA
          1 GCAAACAACA

       9897 TCTAAAACAC


Statistics
Matches: 62,  Mismatches: 10, Indels: 8
        0.77            0.12        0.10

Matches are distributed among these distances:
  31    2  0.03
  32    5  0.08
  33   48  0.77
  34    5  0.08
  35    2  0.03

ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26


Consensus pattern (33 bp):   
GCAAACAACACTCAAATTAGGTTTAGTATCATC

Found at i:9820 original size:66 final size:66

Alignment explanation


    Indices: 9763--9905  Score: 214
    Period size: 66  Copynumber: 2.2  Consensus size: 66

       9753 TCACAATTAG

                               * *                                    *      
       9763 CATCCAAAACAGATTTAGTTTTATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGCAAAGA
          1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAAGA

             
       9828 A
         66 A

                *      *                                              *    * 
       9829 CATCTAAAACATATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGCAAACA
          1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAAGA

             
       9894 A
         66 A

                *      
       9895 CATCTAAAACA
          1 CATCCAAAACA

       9906 CTCTTTTCAA


Statistics
Matches: 72,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  66   72  1.00

ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28


Consensus pattern (66 bp):   
CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAAGA
A
Done.