Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001935.1 Corchorus capsularis cultivar CVL-1 contig01937, 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: 2705
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32


Found at i:436 original size:31 final size:28

Alignment explanation


    Indices: 401--593  Score: 111
    Period size: 31  Copynumber: 6.5  Consensus size: 28

        391 AAAGGCTAAT

                                           
        401 TGCTCAAATAAGGGCCTAACGTTTAGCAAAA
          1 TGCTCAAATAAGGGCCTAACG-TT--CAAAA

                          *  * * *  *  **
        432 TGCTCAAATAAGGACCCGACCTTTTAATT
          1 TGCTCAAATAAGG-GCCTAACGTTCAAAA

                                    *    
        461 TGGC-CAAATAAGGGCCTAACGTTGAAAA
          1 T-GCTCAAATAAGGGCCTAACGTTCAAAA

                             * * *  *  **
        489 TGCTCAAATAAGGGTCCGATCTTTTAATT
          1 TGCTCAAATAAGGG-CCTAACGTTCAAAA

                        *                   
        518 TGGC-CAAATAAAGGCCTAACGTTATCCAAAA
          1 T-GCTCAAATAAGGGCCTAACG-T-T-CAAAA

                                           
        549 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
          1 TGCTCAAATAAGGGCCTAACG-T-TC-AAAA

              *           
        580 TGTTCAAATAAGGG
          1 TGCTCAAATAAGGG

        594 TCTGGTGTCA


Statistics
Matches: 123,  Mismatches: 29, Indels: 20
        0.72            0.17        0.12

Matches are distributed among these distances:
  27    2  0.02
  28   23  0.19
  29   31  0.25
  30    8  0.07
  31   55  0.45
  32    4  0.03

ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25


Consensus pattern (28 bp):   
TGCTCAAATAAGGGCCTAACGTTCAAAA

Found at i:473 original size:60 final size:59

Alignment explanation


    Indices: 405--561  Score: 237
    Period size: 57  Copynumber: 2.7  Consensus size: 59

        395 GCTAATTGCT

                                                                        
        405 CAAATAAGGGCCTAACGTTTAGCAAAATGCTCAAATAAGGACCCGACCTTTTAATTTGGC
          1 CAAATAAGGGCCTAACG-TTAGCAAAATGCTCAAATAAGGACCCGACCTTTTAATTTGGC

                                                   **    *             
        465 CAAATAAGGGCCTAACGTT-G-AAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
          1 CAAATAAGGGCCTAACGTTAGCAAAATGCTCAAATAAGGACCCGACCTTTTAATTTGGC

                   *             *                  
        522 CAAATAAAGGCCTAACGTTATCCAAAATGCTCAAATAAGG
          1 CAAATAAGGGCCTAACGTTA-GCAAAATGCTCAAATAAGG

        562 GCCTAACGTT


Statistics
Matches: 89,  Mismatches: 5, Indels: 6
        0.89            0.05        0.06

Matches are distributed among these distances:
  57   52  0.58
  58    1  0.01
  59    2  0.02
  60   34  0.38

ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25


Consensus pattern (59 bp):   
CAAATAAGGGCCTAACGTTAGCAAAATGCTCAAATAAGGACCCGACCTTTTAATTTGGC

Found at i:659 original size:31 final size:31

Alignment explanation


    Indices: 624--731  Score: 123
    Period size: 31  Copynumber: 3.5  Consensus size: 31

        614 CGCGTGAGAC

                                           
        624 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
          1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT

                 *            **        ** *
        655 AGGCCTTTATTTG-GCCAAATT--CAAAAATG
          1 AGGCCCTTATTTGAG-CATTTTGGCAAACGTT

                                   *       
        684 AGGCCCTTATTTGAGCATTTTGGAAAACGTT
          1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT

                             
        715 AGGCCCTTATTTGAGCA
          1 AGGCCCTTATTTGAGCA

        732 ATTAGCCTGA


Statistics
Matches: 60,  Mismatches: 13, Indels: 8
        0.74            0.16        0.10

Matches are distributed among these distances:
  29   21  0.35
  30    2  0.03
  31   37  0.62

ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33


Consensus pattern (31 bp):   
AGGCCCTTATTTGAGCATTTTGGCAAACGTT

Found at i:1443 original size:19 final size:19

Alignment explanation


    Indices: 1419--1457  Score: 78
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       1409 TCCTTGCATG

                               
       1419 ACACAATTGAAATCTCTTA
          1 ACACAATTGAAATCTCTTA

                               
       1438 ACACAATTGAAATCTCTTA
          1 ACACAATTGAAATCTCTTA

             
       1457 A
          1 A

       1458 ACTTCTATCT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31


Consensus pattern (19 bp):   
ACACAATTGAAATCTCTTA

Found at i:2665 original size:17 final size:17

Alignment explanation


    Indices: 2645--2678  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       2635 CCATGTAAAA

                             
       2645 GAGTGAAACTATTTCAT
          1 GAGTGAAACTATTTCAT

                             
       2662 GAGTGAAACTATTTCAT
          1 GAGTGAAACTATTTCAT

       2679 TTCTTCCGAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35


Consensus pattern (17 bp):   
GAGTGAAACTATTTCAT
Done.