Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008840.1 Corchorus capsularis cultivar CVL-1 contig08861, 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: 18105
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:1203 original size:71 final size:73

Alignment explanation


    Indices: 1109--1256  Score: 194
    Period size: 75  Copynumber: 2.0  Consensus size: 73

       1099 TCGAAAGTCG

                   *                   *                        *  *       * 
       1109 AAACTTGGTTTGGAAACTTTACATAATGCACATT-A-ACG-GTTGGGGATAATTGGTTTCTGTGT
          1 AAACTTGATTTGGAAACTTTACATAATACACATTAACACGAGTTGGGGATAACTGATTTCTGTAT

                    
       1171 TGAACTCC
         66 TGAACTCC

                                         **                                  
       1179 AAACTTGATTTGGGAAACTTTACATAATATTCATTAACTACGAGTTGGGGATAACTGATTTCTGT
          1 AAACTTGATTT-GGAAACTTTACATAATACACATTAAC-ACGAGTTGGGGATAACTGATTTCTGT

                      
       1244 ATTGAACTCC
         64 ATTGAACTCC

               
       1254 AAA
          1 AAA

       1257 TTTGTTTTTT


Statistics
Matches: 66,  Mismatches: 7, Indels: 5
        0.85            0.09        0.06

Matches are distributed among these distances:
  70   10  0.15
  71   20  0.30
  72    1  0.02
  74    3  0.05
  75   32  0.48

ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35


Consensus pattern (73 bp):   
AAACTTGATTTGGAAACTTTACATAATACACATTAACACGAGTTGGGGATAACTGATTTCTGTAT
TGAACTCC

Found at i:3358 original size:28 final size:30

Alignment explanation


    Indices: 3284--3358  Score: 82
    Period size: 28  Copynumber: 2.5  Consensus size: 30

       3274 CTAAAATCTC

                  *         *              
       3284 AATTAGGGCCTGAACTTTGCCAAAAGGGTCA
          1 AATTAGTGCCTGAACTATG-CAAAAGGGTCA

               *      **                  
       3315 AATAAGTGCCCAAACTATG-AAAA-GGTCA
          1 AATTAGTGCCTGAACTATGCAAAAGGGTCA

                            
       3343 AATTAGTGCCTGAACT
          1 AATTAGTGCCTGAACT

       3359 TTTCGATTTG


Statistics
Matches: 36,  Mismatches: 8, Indels: 3
        0.77            0.17        0.06

Matches are distributed among these distances:
  28   18  0.50
  29    4  0.11
  31   14  0.39

ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23


Consensus pattern (30 bp):   
AATTAGTGCCTGAACTATGCAAAAGGGTCA

Found at i:8302 original size:1 final size:1

Alignment explanation


    Indices: 8298--8326  Score: 58
    Period size: 1  Copynumber: 29.0  Consensus size: 1

       8288 CCCCCCCCCC

                                         
       8298 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       8327 CATACAGCTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   28  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:9385 original size:1 final size:1

Alignment explanation


    Indices: 9375--9413  Score: 60
    Period size: 1  Copynumber: 39.0  Consensus size: 1

       9365 ACTGCCGACC

                 *                           *     
       9375 AAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       9414 GATTAGTAAC


Statistics
Matches: 34,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   1   34  1.00

ACGTcount: A:0.95, C:0.03, G:0.03, T:0.00


Consensus pattern (1 bp):   
A

Found at i:11908 original size:30 final size:27

Alignment explanation


    Indices: 11873--11940  Score: 82
    Period size: 29  Copynumber: 2.3  Consensus size: 27

      11863 TTTTTACCAT

                                          
      11873 ACTATAACATTTCAAAAACTTATTTCCCAA
          1 ACTATAACATTT---AAACTTATTTCCCAA

            *                            
      11903 TCTATAACACATTTAAACTTATTTCCCAA
          1 ACTAT-A-ACATTTAAACTTATTTCCCAA

                     
      11932 ACTATAACA
          1 ACTATAACA

      11941 AATCATGCCA


Statistics
Matches: 34,  Mismatches: 2, Indels: 7
        0.79            0.05        0.16

Matches are distributed among these distances:
  27    3  0.09
  28    1  0.03
  29   19  0.56
  30    4  0.12
  31    1  0.03
  32    6  0.18

ACGTcount: A:0.43, C:0.24, G:0.00, T:0.34


Consensus pattern (27 bp):   
ACTATAACATTTAAACTTATTTCCCAA
Done.