Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005323.1 Corchorus capsularis cultivar CVL-1 contig05341, 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: 3701
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37


Found at i:1226 original size:20 final size:19

Alignment explanation


    Indices: 1179--1227  Score: 53
    Period size: 20  Copynumber: 2.5  Consensus size: 19

       1169 AAAAAGCTTC

                   *           
       1179 AATTATTGTTCTAAAAAAT
          1 AATTATTATTCTAAAAAAT

                *             * 
       1198 AAGTGATTATTCTAAAAACT
          1 AA-TTATTATTCTAAAAAAT

                      
       1218 ATATTATTAT
          1 A-ATTATTAT

       1228 ATTTATTTTT


Statistics
Matches: 24,  Mismatches: 4, Indels: 3
        0.77            0.13        0.10

Matches are distributed among these distances:
  19    2  0.08
  20   21  0.88
  21    1  0.04

ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43


Consensus pattern (19 bp):   
AATTATTATTCTAAAAAAT

Found at i:1351 original size:30 final size:31

Alignment explanation


    Indices: 1291--1359  Score: 131
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       1281 ACATTTAGTT

                                           
       1291 AACAATTTTTGTTTTATTTTCACAAAAAAAA
          1 AACAATTTTTGTTTTATTTTCACAAAAAAAA

                                           
       1322 AACAATTTTTGTTTTATTTTCAC-AAAAAAA
          1 AACAATTTTTGTTTTATTTTCACAAAAAAAA

                    
       1352 AACAATTT
          1 AACAATTT

       1360 ATTTTTTTTA


Statistics
Matches: 38,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  30   15  0.39
  31   23  0.61

ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42


Consensus pattern (31 bp):   
AACAATTTTTGTTTTATTTTCACAAAAAAAA

Found at i:2834 original size:122 final size:119

Alignment explanation


    Indices: 2693--2910  Score: 285
    Period size: 122  Copynumber: 1.8  Consensus size: 119

       2683 TAATAATAAC

                                              *             *            *   
       2693 TATAATAATAACAAGTTTAATAATGATAATAATATATAAGATGTTTAACGTAA-AAAAATTGTTA
          1 TATAATAATAACAAGTTTAATAATGATAATAAT-GATAAGATGTTTAAAGTAAGAAAAATTCTTA

              *                                                      
       2757 GTGTTATTAGACTTTTTGTAATATGGAAAGAAAAAAAGTAAAAAACGTAATGAAATA
         65 GTATT-TTAGACTTTTT-TAATATGGAAAGAAAAAAAGTAAAAAACGTAATGAAATA

                        *  *         *  *           *               *        
       2814 TATAACTAATAATAATTTTAATAATTATTATAATGATAAGTTGTTTAAAGTAAGAATAATTCTTA
          1 TATAA-TAATAACAAGTTTAATAATGATAATAATGATAAGATGTTTAAAGTAAGAAAAATTCTTA

            *                          *    
       2879 TTATTTTAGACTTTTTTAATATGGAAATAAAA
         65 GTATTTTAGACTTTTTTAATATGGAAAGAAAA

       2911 TCTGGTTGGA


Statistics
Matches: 83,  Mismatches: 12, Indels: 5
        0.83            0.12        0.05

Matches are distributed among these distances:
 120   15  0.18
 121   32  0.39
 122   36  0.43

ACGTcount: A:0.48, C:0.03, G:0.11, T:0.38


Consensus pattern (119 bp):   
TATAATAATAACAAGTTTAATAATGATAATAATGATAAGATGTTTAAAGTAAGAAAAATTCTTAG
TATTTTAGACTTTTTTAATATGGAAAGAAAAAAAGTAAAAAACGTAATGAAATA

Found at i:3335 original size:23 final size:23

Alignment explanation


    Indices: 3256--3338  Score: 62
    Period size: 23  Copynumber: 3.7  Consensus size: 23

       3246 TTCTTGGGGA

                      *      *     
       3256 GAGC-TCCGCACAAGAGTTGGGT
          1 GAGCGTCCGCGCAAGAGCTGGGT

            *   *             ***  
       3278 TAGCCTCCGCGCAAGAGCAAAG-
          1 GAGCGTCCGCGCAAGAGCTGGGT

               *    *               
       3300 GAGTGCTCAGCGCAAGAGCTGGGT
          1 GAGCG-TCCGCGCAAGAGCTGGGT

                           
       3324 GAGCGTCCGCGCAAG
          1 GAGCGTCCGCGCAAG

       3339 GAGTAAGGGA


Statistics
Matches: 43,  Mismatches: 15, Indels: 5
        0.68            0.24        0.08

Matches are distributed among these distances:
  22    5  0.12
  23   34  0.79
  24    4  0.09

ACGTcount: A:0.24, C:0.27, G:0.36, T:0.13


Consensus pattern (23 bp):   
GAGCGTCCGCGCAAGAGCTGGGT

Found at i:3601 original size:18 final size:18

Alignment explanation


    Indices: 3578--3614  Score: 74
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       3568 GACTCCCCTA

                              
       3578 GGTGCAAGTGGGGGCGAC
          1 GGTGCAAGTGGGGGCGAC

                              
       3596 GGTGCAAGTGGGGGCGAC
          1 GGTGCAAGTGGGGGCGAC

             
       3614 G
          1 G

       3615 CACCCCTCAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.16, C:0.16, G:0.57, T:0.11


Consensus pattern (18 bp):   
GGTGCAAGTGGGGGCGAC

Found at i:3645 original size:30 final size:33

Alignment explanation


    Indices: 3598--3677  Score: 89
    Period size: 30  Copynumber: 2.5  Consensus size: 33

       3588 GGGGCGACGG

                         *                    
       3598 TGCAAGTGGGG-GCGACGCACCCC-T-CATTAT-
          1 TGCAAG-GGGGCGTGACGCACCCCTTGCATTATA

                                              
       3628 TGCAAGGGGGCGTGACGCACCCCTTGCATTATAA
          1 TGCAAGGGGGCGTGACGCACCCCTTGCATTAT-A

                             
       3662 TG-AAGGGGGCCGTGAC
          1 TGCAAGGGGG-CGTGAC

       3678 ACTCCCCTGT


Statistics
Matches: 43,  Mismatches: 1, Indels: 8
        0.83            0.02        0.15

Matches are distributed among these distances:
  29    4  0.09
  30   17  0.40
  31    1  0.02
  32    6  0.14
  33    7  0.16
  34    8  0.19

ACGTcount: A:0.21, C:0.26, G:0.34, T:0.19


Consensus pattern (33 bp):   
TGCAAGGGGGCGTGACGCACCCCTTGCATTATA
Done.