Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005308.1 Corchorus capsularis cultivar CVL-1 contig05326, 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: 4964
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34


Found at i:2451 original size:2 final size:2

Alignment explanation


    Indices: 2436--2469  Score: 54
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       2426 CTATCCTCAG

                                                                 
       2436 TA TA T- TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       2470 ATTTCTTAAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   1    2  0.07
   2   28  0.93

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:3447 original size:26 final size:26

Alignment explanation


    Indices: 3418--3485  Score: 109
    Period size: 26  Copynumber: 2.6  Consensus size: 26

       3408 TTCCTTCATT

                                      
       3418 TTAATCATAAACTAATTAAATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                 *            *       
       3444 TTAATAATAAACTAATTAGATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                *           
       3470 TTAAACATAAACTAAT
          1 TTAATCATAAACTAAT

       3486 AAACTAAGTA


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  26   38  1.00

ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34


Consensus pattern (26 bp):   
TTAATCATAAACTAATTAAATACTAA

Found at i:3509 original size:52 final size:51

Alignment explanation


    Indices: 3418--3535  Score: 122
    Period size: 52  Copynumber: 2.4  Consensus size: 51

       3408 TTCCTTCATT

                *                                         *     
       3418 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTAGATACTAA
          1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA

                                    *      *    *                
       3470 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
          1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA

                               
       3521 -T---CATAAACTAATTAA
          1 TTAAACATAAACTAATTAA

       3536 TATTAAAAAA


Statistics
Matches: 58,  Mismatches: 5, Indels: 10
        0.79            0.07        0.14

Matches are distributed among these distances:
  47   10  0.17
  48    3  0.05
  50    1  0.02
  51   10  0.17
  52   28  0.48
  53    6  0.10

ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34


Consensus pattern (51 bp):   
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA

Found at i:3775 original size:21 final size:21

Alignment explanation


    Indices: 3746--3790  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       3736 AAAAATTATA

                           **    
       3746 AAAAAGGGGGCGGTATTTAGC
          1 AAAAAGGGGGCGGTAAATAGC

                *                
       3767 AAAAGGGGGGCGGTAAATAGC
          1 AAAAAGGGGGCGGTAAATAGC

               
       3788 AAA
          1 AAA

       3791 CCCCATTCTT


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.40, C:0.09, G:0.38, T:0.13


Consensus pattern (21 bp):   
AAAAAGGGGGCGGTAAATAGC
Done.