Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012404.1 Corchorus capsularis cultivar CVL-1 contig12425, 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: 10022
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:1255 original size:21 final size:22

Alignment explanation


    Indices: 1229--1272  Score: 56
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       1219 ATTTATGGGG

                                   
       1229 TTGCTAAAT-ACCGCCCC-CTTT
          1 TTGCT-AATCACCGCCCCACTTT

                  *               
       1250 TTGCTATTCACCGCCCCACTTT
          1 TTGCTAATCACCGCCCCACTTT

             
       1272 T
          1 T

       1273 GCCCTTTGCT


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  20    2  0.10
  21   13  0.65
  22    5  0.25

ACGTcount: A:0.16, C:0.39, G:0.09, T:0.36


Consensus pattern (22 bp):   
TTGCTAATCACCGCCCCACTTT

Found at i:2330 original size:132 final size:135

Alignment explanation


    Indices: 2084--2390  Score: 480
    Period size: 132  Copynumber: 2.3  Consensus size: 135

       2074 ATAGAATCCA

                                                                             
       2084 AGAAGAAGATTGAA-AGAGGAGGAGGAACGGAGGATGAGGTGAGATCGCAGAGAGGGTGAGCGGC
          1 AGAAGAAGATTGAAGA-AGGAGGAGGAACGGAGGATGAGGTGAGATCGCAGAGAGGGTGAGCGGC

                                *                   * *                      
       2148 GGGTTTGTTTTGTTTATGCTTGAAGATGATGAGATCTAATTGGATATGGAGAAAAATACAGG-T-
         65 GGGTTTGTTTTGTTTATGCTCGAAGATGATGAGATCTAATAGAATATGGAGAAAAATACAGGTTG

                  
       2211 TTTAAG
        130 TTTAAG

                   *                                     *                   
       2217 AGAAGAAAATTGAAGAAGGAGGAGGAACGGAGGATGAGGTGAGA-GGCAGAGAGGGTGAGCGGCG
          1 AGAAGAAGATTGAAGAAGGAGGAGGAACGGAGGATGAGGTGAGATCGCAGAGAGGGTGAGCGGCG

                                  *                                          
       2281 GGTTTGTTTTGTTTATGCTCGAGGATGATGAGATCTAATCAGAAT-TGGAGAAAAATACAGGTTT
         66 GGTTTGTTTTGTTTATGCTCGAAGATGATGAGATCTAAT-AGAATATGGAGAAAAATACAGG--T

                    
       2345 TGTTTAAG
        128 TGTTTAAG

                                             *    
       2353 AGAAGAAGATTGAAGAAGGAGGAGGAACGGAGGTTGAG
          1 AGAAGAAGATTGAAGAAGGAGGAGGAACGGAGGATGAG

       2391 CCGATGGGGT


Statistics
Matches: 160,  Mismatches: 8, Indels: 9
        0.90            0.05        0.05

Matches are distributed among these distances:
 132   72  0.45
 133   44  0.28
 134    1  0.01
 135    1  0.01
 136   42  0.26

ACGTcount: A:0.34, C:0.06, G:0.38, T:0.22


Consensus pattern (135 bp):   
AGAAGAAGATTGAAGAAGGAGGAGGAACGGAGGATGAGGTGAGATCGCAGAGAGGGTGAGCGGCG
GGTTTGTTTTGTTTATGCTCGAAGATGATGAGATCTAATAGAATATGGAGAAAAATACAGGTTGT
TTAAG

Found at i:4107 original size:16 final size:15

Alignment explanation


    Indices: 4086--4115  Score: 51
    Period size: 16  Copynumber: 1.9  Consensus size: 15

       4076 CTGTCATCTT

                            
       4086 TTATTATTATTTTTAA
          1 TTATTATT-TTTTTAA

                          
       4102 TTATTATTTTTTTA
          1 TTATTATTTTTTTA

       4116 GATAAAATTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    6  0.43
  16    8  0.57

ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73


Consensus pattern (15 bp):   
TTATTATTTTTTTAA

Found at i:4273 original size:31 final size:29

Alignment explanation


    Indices: 4185--4281  Score: 106
    Period size: 29  Copynumber: 3.2  Consensus size: 29

       4175 ACCTAATTAA

                 *                        
       4185 TCCCTGTACTAATGAAAAAGATCAATTTAG
          1 TCCCTCTACT-ATGAAAAAGATCAATTTAG

                  * *        **           
       4215 TCCCTCAATTATGAAATCTG-TCAATTTAG
          1 TCCCTCTACTATGAAA-AAGATCAATTTAG

                                           
       4244 TCCCTCTACTATTGAAAAGAGATCAATTTAG
          1 TCCCTCTACTA-TGAAAA-AGATCAATTTAG

                   
       4275 TCCCTCT
          1 TCCCTCT

       4282 GTGAAATGGG


Statistics
Matches: 54,  Mismatches: 9, Indels: 7
        0.77            0.13        0.10

Matches are distributed among these distances:
  29   24  0.44
  30   14  0.26
  31   16  0.30

ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34


Consensus pattern (29 bp):   
TCCCTCTACTATGAAAAAGATCAATTTAG

Found at i:10000 original size:23 final size:24

Alignment explanation


    Indices: 9970--10016  Score: 87
    Period size: 23  Copynumber: 2.0  Consensus size: 24

       9960 ATAGAAGATT

                                    
       9970 TCCACTTTCAAGA-TTTGGGGGGG
          1 TCCACTTTCAAGATTTTGGGGGGG

                                    
       9993 TCCACTTTCAAGATTTTGGGGGGG
          1 TCCACTTTCAAGATTTTGGGGGGG

      10017 GGGGGG


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  23   13  0.57
  24   10  0.43

ACGTcount: A:0.17, C:0.17, G:0.34, T:0.32


Consensus pattern (24 bp):   
TCCACTTTCAAGATTTTGGGGGGG

Done.