Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023479.1 Corchorus olitorius cultivar O-4 contig23512, 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: 3374
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37


Found at i:710 original size:35 final size:33

Alignment explanation


    Indices: 648--731  Score: 143
    Period size: 35  Copynumber: 2.5  Consensus size: 33

        638 GGGCACTGTT

                                             
        648 GAGAGTGATTGTTTGC-TTTTTTTTTTATAGAA
          1 GAGAGTGATTGTTTGCTTTTTTTTTTTATAGAA

                                               
        680 GAGAGTGATTGTTTGCTTTTTTTTTTTTTATAGAA
          1 GAGAGTGATTGTTTGC--TTTTTTTTTTTATAGAA

                             
        715 GAGAGTGATTGTTTGCT
          1 GAGAGTGATTGTTTGCT

        732 AGCCATCAAA


Statistics
Matches: 49,  Mismatches: 0, Indels: 5
        0.91            0.00        0.09

Matches are distributed among these distances:
  32   16  0.33
  33    1  0.02
  35   32  0.65

ACGTcount: A:0.20, C:0.04, G:0.24, T:0.52


Consensus pattern (33 bp):   
GAGAGTGATTGTTTGCTTTTTTTTTTTATAGAA

Found at i:1026 original size:35 final size:35

Alignment explanation


    Indices: 985--1065  Score: 162
    Period size: 35  Copynumber: 2.3  Consensus size: 35

        975 TCCGAACTCA

                                               
        985 AAAATACCCTTGAAAATCTTAATTAGTCAATTACT
          1 AAAATACCCTTGAAAATCTTAATTAGTCAATTACT

                                               
       1020 AAAATACCCTTGAAAATCTTAATTAGTCAATTACT
          1 AAAATACCCTTGAAAATCTTAATTAGTCAATTACT

                       
       1055 AAAATACCCTT
          1 AAAATACCCTT

       1066 AATATTATAA


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   46  1.00

ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33


Consensus pattern (35 bp):   
AAAATACCCTTGAAAATCTTAATTAGTCAATTACT

Found at i:1252 original size:30 final size:30

Alignment explanation


    Indices: 1216--1277  Score: 88
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       1206 TATAATTTTT

                   *  *  *    *           
       1216 AATCATTTAATTTTTATTTATTAATTATAA
          1 AATCATTCAAATTCTATTCATTAATTATAA

                                          
       1246 AATCATTCAAATTCTATTCATTAATTATAA
          1 AATCATTCAAATTCTATTCATTAATTATAA

              
       1276 AA
          1 AA

       1278 AGATATTATA


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  30   28  1.00

ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48


Consensus pattern (30 bp):   
AATCATTCAAATTCTATTCATTAATTATAA

Found at i:1691 original size:3 final size:3

Alignment explanation


    Indices: 1685--1725  Score: 82
    Period size: 3  Copynumber: 13.7  Consensus size: 3

       1675 TAACTTTATT

                                                                  
       1685 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT

       1726 TTTAATCATG


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   38  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATA

Done.