Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014348.1 Corchorus capsularis cultivar CVL-1 contig14369, 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: 12600
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26


Found at i:501 original size:38 final size:38

Alignment explanation


    Indices: 470--774  Score: 431
    Period size: 38  Copynumber: 8.1  Consensus size: 38

        460 ATTAAGGACA

                                                  
        470 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTC
          1 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTC

                                                  
        508 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTC
          1 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTC

                **                              * 
        546 -AAGGGAT--TAATCAGTAAAATTGATAATTAAGAGGC
          1 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTC

                                *               * 
        581 AAAGTAATAGTAATCAGTAAGATTGATAATTAAGAGGC
          1 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTC

                                                * 
        619 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGCC
          1 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTC

                                                  
        657 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTC
          1 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTC

                      *                   *   *   
        695 AAAGTAATAGCAATCAGTAAAATTGATAATCAAGGGTC
          1 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTC

              *                  *     *              
        733 AAGGTAAAAATAGTAATCAG-CAAA-TCAGTAATTAAGAGTC
          1 AAAGT---AATAGTAATCAGTAAAATTGA-TAATTAAGAGTC

              
        773 AA
          1 AA

        775 GGGTTTAATC


Statistics
Matches: 242,  Mismatches: 18, Indels: 12
        0.89            0.07        0.04

Matches are distributed among these distances:
  35   27  0.11
  36    5  0.02
  37    5  0.02
  38  177  0.73
  39    2  0.01
  40   15  0.06
  41   11  0.05

ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26


Consensus pattern (38 bp):   
AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTC

Found at i:1135 original size:14 final size:13

Alignment explanation


    Indices: 1113--1198  Score: 59
    Period size: 14  Copynumber: 6.3  Consensus size: 13

       1103 CAGTAAAAAG

                         
       1113 GTAAAAGTAATCA
          1 GTAAAAGTAATCA

                          
       1126 GTAAAGAGTAATCA
          1 GTAAA-AGTAATCA

                       ** 
       1140 GTAAAAAGTAAAAA
          1 GT-AAAAGTAATCA

               *        *   
       1154 TGGCAAAGAGTAGT-A
          1 --GTAAA-AGTAATCA

             *           
       1169 -AAAAAGTAATCA
          1 GTAAAAGTAATCA

                          
       1181 GGTAAAAGTAATCA
          1 -GTAAAAGTAATCA

                
       1195 GTAA
          1 GTAA

       1199 GAAGGTCAAA


Statistics
Matches: 57,  Mismatches: 8, Indels: 16
        0.70            0.10        0.20

Matches are distributed among these distances:
  11    5  0.09
  12    4  0.07
  13    9  0.16
  14   27  0.47
  15    7  0.12
  16    5  0.09

ACGTcount: A:0.55, C:0.06, G:0.20, T:0.20


Consensus pattern (13 bp):   
GTAAAAGTAATCA

Found at i:1289 original size:26 final size:25

Alignment explanation


    Indices: 1260--1311  Score: 68
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       1250 AAAATGGTGT

                        *             
       1260 AGAGTAAAAAAATGGTATTAAGTAAA
          1 AGAGT-AAAAAACGGTATTAAGTAAA

                    *           *    
       1286 AGAGTAAAGAACGGTATTAATTAAA
          1 AGAGTAAAAAACGGTATTAAGTAAA

             
       1311 A
          1 A

       1312 AATGGTGTTA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  25   18  0.78
  26    5  0.22

ACGTcount: A:0.56, C:0.02, G:0.19, T:0.23


Consensus pattern (25 bp):   
AGAGTAAAAAACGGTATTAAGTAAA

Found at i:1386 original size:16 final size:16

Alignment explanation


    Indices: 1334--1386  Score: 52
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       1324 TAAAAGGGTC

                       **   
       1334 AAAAATGGTATCCAGT
          1 AAAAATGGTATTAAGT

                *          **
       1350 AAGAGATGGTATTAAAC
          1 AA-AAATGGTATTAAGT

                            
       1367 AAAAATGGTATTAAGT
          1 AAAAATGGTATTAAGT

                
       1383 AAAA
          1 AAAA

       1387 GAGTAAGAAA


Statistics
Matches: 28,  Mismatches: 8, Indels: 2
        0.74            0.21        0.05

Matches are distributed among these distances:
  16   17  0.61
  17   11  0.39

ACGTcount: A:0.51, C:0.06, G:0.19, T:0.25


Consensus pattern (16 bp):   
AAAAATGGTATTAAGT

Found at i:1414 original size:15 final size:15

Alignment explanation


    Indices: 1394--1424  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1384 AAAGAGTAAG

                   *       
       1394 AAAAATGGTAAAAGT
          1 AAAAATGATAAAAGT

                           
       1409 AAAAATGATAAAAGT
          1 AAAAATGATAAAAGT

             
       1424 A
          1 A

       1425 GCAAAAGTAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19


Consensus pattern (15 bp):   
AAAAATGATAAAAGT
Done.