Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006683.1 Corchorus capsularis cultivar CVL-1 contig06704, 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: 17299
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:1717 original size:3 final size:3

Alignment explanation


    Indices: 1705--1744  Score: 64
    Period size: 3  Copynumber: 13.3  Consensus size: 3

       1695 GAAACTGACC

                                                                  
       1705 TTA TTA -TA TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA T

       1745 GGTAATTGTT


Statistics
Matches: 35,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   2    2  0.06
   3   30  0.86
   4    3  0.09

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
TTA

Found at i:2346 original size:20 final size:18

Alignment explanation


    Indices: 2313--2351  Score: 60
    Period size: 20  Copynumber: 2.1  Consensus size: 18

       2303 ATGAAAGTTA

                              
       2313 TTTCCTTTTCTCTTTCTC
          1 TTTCCTTTTCTCTTTCTC

                                
       2331 TTTCACTTTCTCTCTTTCTC
          1 TTTC-CTTT-TCTCTTTCTC

             
       2351 T
          1 T

       2352 ATATACCAAC


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  18    4  0.21
  19    4  0.21
  20   11  0.58

ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64


Consensus pattern (18 bp):   
TTTCCTTTTCTCTTTCTC

Found at i:7586 original size:24 final size:24

Alignment explanation


    Indices: 7554--7668  Score: 149
    Period size: 24  Copynumber: 4.8  Consensus size: 24

       7544 GAATGTGCCT

                            *       
       7554 GTACAGATGAACACTCCATATCCA
          1 GTACAGATGAACACTCAATATCCA

                      *  *          
       7578 GTACAGATGAGCAGTCAATATCCA
          1 GTACAGATGAACACTCAATATCCA

                                   *
       7602 GTACAGATGAACACTCAATATCCG
          1 GTACAGATGAACACTCAATATCCA

                         *  *      *
       7626 GTACAGATGAACAATCGATATCCT
          1 GTACAGATGAACACTCAATATCCA

             *           *     
       7650 GCACAGATGAACAATCAAT
          1 GTACAGATGAACACTCAAT

       7669 GTTACATGCA


Statistics
Matches: 80,  Mismatches: 11, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   80  1.00

ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21


Consensus pattern (24 bp):   
GTACAGATGAACACTCAATATCCA

Found at i:12326 original size:32 final size:32

Alignment explanation


    Indices: 12259--12342  Score: 100
    Period size: 32  Copynumber: 2.6  Consensus size: 32

      12249 CGTGGCGAAA

                                             
      12259 CCGCCCTCATGGGGCGGCTTCACCATGGGCAGG
          1 CCGCCC-CATGGGGCGGCTTCACCATGGGCAGG

                                              
      12292 CCGCCCCACTGGGGCGGCTT-AGCCA-GGGCAGG
          1 CCGCCCCA-TGGGGCGGCTTCA-CCATGGGCAGG

                   **          
      12324 CCGTCCCGGTGGGGCGGCT
          1 CCG-CCCCATGGGGCGGCT

      12343 CGGCTATTTT


Statistics
Matches: 46,  Mismatches: 2, Indels: 7
        0.84            0.04        0.13

Matches are distributed among these distances:
  32   23  0.50
  33   23  0.50

ACGTcount: A:0.10, C:0.37, G:0.40, T:0.13


Consensus pattern (32 bp):   
CCGCCCCATGGGGCGGCTTCACCATGGGCAGG

Found at i:12468 original size:33 final size:33

Alignment explanation


    Indices: 12415--12527  Score: 92
    Period size: 33  Copynumber: 3.4  Consensus size: 33

      12405 GGTGCCGTCC

                                         *     
      12415 CCCTGGGGCGG--CTGAGCCATGGCCAAGTCGCC-
          1 CCCTGGGGCGGCACT-A-CCATGGCCAAGCCGCCT

               *                      *       
      12447 CTCTTGGGGCGGCACTACCATGGCCAGGCCGCCT
          1 C-CCTGGGGCGGCACTACCATGGCCAAGCCGCCT

                        *                     *
      12481 CCCTGGGGCGGCCCTACCATGG--ATAGACCGCCC
          1 CCCTGGGGCGGCACTACCATGGCCA-AG-CCGCCT

                *         
      12514 CCCTAGGGCGGCAC
          1 CCCTGGGGCGGCAC

      12528 CGGTACTAAA


Statistics
Matches: 66,  Mismatches: 9, Indels: 11
        0.77            0.10        0.13

Matches are distributed among these distances:
  31    1  0.02
  32    2  0.03
  33   59  0.89
  34    2  0.03
  35    2  0.03

ACGTcount: A:0.13, C:0.40, G:0.34, T:0.13


Consensus pattern (33 bp):   
CCCTGGGGCGGCACTACCATGGCCAAGCCGCCT
Done.