Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010163.1 Corchorus capsularis cultivar CVL-1 contig10184, 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: 20008
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35


Found at i:623 original size:2 final size:2

Alignment explanation


    Indices: 616--646  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

        606 TGTTCGGAAG

                                                          
        616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        647 GCAGAAGTTG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:1112 original size:20 final size:20

Alignment explanation


    Indices: 1087--1127  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1077 TTATTTTTTA

                      **        
       1087 AAAATAAATTTCAATAAAAT
          1 AAAATAAATTAAAATAAAAT

                  *             
       1107 AAAATATATTAAAATAAAAT
          1 AAAATAAATTAAAATAAAAT

             
       1127 A
          1 A

       1128 TTTAAATTTT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29


Consensus pattern (20 bp):   
AAAATAAATTAAAATAAAAT

Found at i:1134 original size:13 final size:15

Alignment explanation


    Indices: 1101--1133  Score: 59
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       1091 TAAATTTCAA

                           
       1101 TAAAATAAAATATAT
          1 TAAAATAAAATATAT

                           
       1116 TAAAATAAAATAT-T
          1 TAAAATAAAATATAT

                
       1130 TAAA
          1 TAAA

       1134 TTTTATTCCA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  14    5  0.28
  15   13  0.72

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (15 bp):   
TAAAATAAAATATAT

Found at i:9993 original size:22 final size:21

Alignment explanation


    Indices: 9968--10009  Score: 57
    Period size: 22  Copynumber: 2.0  Consensus size: 21

       9958 AGGAAATAAA

                                  
       9968 TTAAATACAGGTTTAGTCCCCC
          1 TTAAATACAGGTTTAG-CCCCC

                  *  *          
       9990 TTAAATCCATGTTTAGCCCC
          1 TTAAATACAGGTTTAGCCCC

      10010 TAGTTATAAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  21    4  0.22
  22   14  0.78

ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33


Consensus pattern (21 bp):   
TTAAATACAGGTTTAGCCCCC

Found at i:16351 original size:21 final size:20

Alignment explanation


    Indices: 16318--16356  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 20

      16308 CAATAAAATT

                    *            
      16318 TGTACTATTGTTATAATTTTA
          1 TGTACTATGGTTA-AATTTTA

                *             
      16339 TGTATTATGGTTAAATTT
          1 TGTACTATGGTTAAATTT

      16357 GCTAAATTTC


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    5  0.31
  21   11  0.69

ACGTcount: A:0.28, C:0.03, G:0.13, T:0.56


Consensus pattern (20 bp):   
TGTACTATGGTTAAATTTTA

Found at i:17962 original size:3 final size:3

Alignment explanation


    Indices: 17954--18005  Score: 86
    Period size: 3  Copynumber: 17.0  Consensus size: 3

      17944 TTAGTAAATA

                        *                                               
      17954 ATT ATT ATT TTGT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

                   
      18000 ATT ATT
          1 ATT ATT

      18006 CTTAAGTTTG


Statistics
Matches: 46,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
   3   44  0.96
   4    2  0.04

ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67


Consensus pattern (3 bp):   
ATT

Found at i:19795 original size:21 final size:21

Alignment explanation


    Indices: 19769--19813  Score: 72
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      19759 TTGAACTGAA

                                 
      19769 TTGCTAAATACCGTCCCCTTT
          1 TTGCTAAATACCGTCCCCTTT

                  **             
      19790 TTGCTAGTTACCGTCCCCTTT
          1 TTGCTAAATACCGTCCCCTTT

               
      19811 TTG
          1 TTG

      19814 ACACTTTTGC


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.13, C:0.31, G:0.13, T:0.42


Consensus pattern (21 bp):   
TTGCTAAATACCGTCCCCTTT
Done.