Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001840.1 Corchorus capsularis cultivar CVL-1 contig01841, 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, 940

Length: 1568
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31


Found at i:1308 original size:20 final size:21

Alignment explanation


    Indices: 1269--1312  Score: 70
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1259 GTAAACTGGA

                                 
       1269 TTGCTAAACACCGCCCCCCTT
          1 TTGCTAAACACCGCCCCCCTT

                    *         *  
       1290 TTGCTAAATACCGCCCCCTTT
          1 TTGCTAAACACCGCCCCCCTT

              
       1311 TT
          1 TT

       1313 ACACTTTTGC


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.18, C:0.41, G:0.09, T:0.32


Consensus pattern (21 bp):   
TTGCTAAACACCGCCCCCCTT

Found at i:1411 original size:10 final size:10

Alignment explanation


    Indices: 1398--1423  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       1388 CATTTCTAAC

                      
       1398 AACTTCTTCA
          1 AACTTCTTCA

                      
       1408 AACTTCTTCA
          1 AACTTCTTCA

                  
       1418 AACTTC
          1 AACTTC

       1424 ATTTCTAACA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38


Consensus pattern (10 bp):   
AACTTCTTCA

Found at i:1489 original size:26 final size:26

Alignment explanation


    Indices: 1460--1527  Score: 109
    Period size: 26  Copynumber: 2.6  Consensus size: 26

       1450 TTCCTTCATT

                                      
       1460 TTAATCATAAACTAATTAAATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                 *            *       
       1486 TTAATAATAAACTAATTAGATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                *           
       1512 TTAAACATAAACTAAT
          1 TTAATCATAAACTAAT

       1528 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:1551 original size:52 final size:51

Alignment explanation


    Indices: 1460--1563  Score: 122
    Period size: 52  Copynumber: 2.0  Consensus size: 51

       1450 TTCCTTCATT

                *                                         *     
       1460 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTAGATACTAA
          1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA

                                    *      *    *                
       1512 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
          1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA

             
       1563 T
          1 T

       1564 CATAA


Statistics
Matches: 45,  Mismatches: 5, Indels: 5
        0.82            0.09        0.09

Matches are distributed among these distances:
  51   11  0.24
  52   28  0.62
  53    6  0.13

ACGTcount: A:0.54, C:0.10, G:0.02, T:0.35


Consensus pattern (51 bp):   
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA
Done.