Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022928.1 Corchorus olitorius cultivar O-4 contig22961, 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: 1841
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34


Found at i:1149 original size:2 final size:2

Alignment explanation


    Indices: 1142--1187  Score: 65
    Period size: 2  Copynumber: 22.5  Consensus size: 2

       1132 TCTTAAAACG

                                                            *  *           
       1142 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT TT AT ACT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT

                
       1185 AT A
          1 AT A

       1188 AGTCTAAACT


Statistics
Matches: 40,  Mismatches: 3, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
   2   38  0.95
   3    2  0.05

ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:1377 original size:24 final size:24

Alignment explanation


    Indices: 1347--1397  Score: 75
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       1337 TATTTTTACG

                    *             * 
       1347 TTAAACATTTTATCATTATAATTA
          1 TTAAACATCTTATCATTATAATAA

                         *          
       1371 TTAAACATCTTATTATTATAATAA
          1 TTAAACATCTTATCATTATAATAA

               
       1395 TTA
          1 TTA

       1398 TTAGTAGTAG


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49


Consensus pattern (24 bp):   
TTAAACATCTTATCATTATAATAA

Found at i:1559 original size:15 final size:15

Alignment explanation


    Indices: 1541--1569  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       1531 ATTATTTCAT

                           
       1541 GAATCAAGACTTACC
          1 GAATCAAGACTTACC

                          
       1556 GAATCAAGACTTAC
          1 GAATCAAGACTTAC

       1570 TTTGATGTAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21


Consensus pattern (15 bp):   
GAATCAAGACTTACC

Found at i:1640 original size:3 final size:3

Alignment explanation


    Indices: 1634--1666  Score: 57
    Period size: 3  Copynumber: 11.0  Consensus size: 3

       1624 ACTTCTTATT

                                    *                  
       1634 ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

       1667 GTAAAATTAT


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   28  1.00

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


Consensus pattern (3 bp):   
ATA

Found at i:1658 original size:15 final size:15

Alignment explanation


    Indices: 1638--1670  Score: 66
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       1628 CTTATTATAA

                           
       1638 TAATAATAATAATAG
          1 TAATAATAATAATAG

                           
       1653 TAATAATAATAATAG
          1 TAATAATAATAATAG

               
       1668 TAA
          1 TAA

       1671 AATTATTATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33


Consensus pattern (15 bp):   
TAATAATAATAATAG
Done.