Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006006.1 Corchorus olitorius cultivar O-4 contig06031, 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: 6380
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38


Found at i:449 original size:28 final size:31

Alignment explanation


    Indices: 348--429  Score: 148
    Period size: 30  Copynumber: 2.7  Consensus size: 31

        338 ACTAAATACT

                        *                  
        348 AAAAAAATCCCTAATGTTTTTCTTTTGGGAC
          1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC

                                           
        379 -AAAAAATCCCTTATGTTTTTCTTTTGGGAC
          1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC

                                 
        409 AAAAAAATCCCTTATGTTTTT
          1 AAAAAAATCCCTTATGTTTTT

        430 TTTGGACAAA


Statistics
Matches: 49,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  30   29  0.59
  31   20  0.41

ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41


Consensus pattern (31 bp):   
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC

Found at i:625 original size:29 final size:30

Alignment explanation


    Indices: 583--656  Score: 96
    Period size: 29  Copynumber: 2.5  Consensus size: 30

        573 CTCATTTTTG

                *                   *     
        583 AAACGTAAGGGATTAATTTATCCCGAAA-A
          1 AAACATAAGGGATTAATTTATCCCAAAACA

                           *   *           
        612 AAACATAAGGGATTATTTTGTCCCAAAAGCA
          1 AAACATAAGGGATTAATTTATCCCAAAA-CA

                          
        643 AAACATAAGGGATT
          1 AAACATAAGGGATT

        657 TTTCTGGGTA


Statistics
Matches: 39,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  29   24  0.62
  31   15  0.38

ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24


Consensus pattern (30 bp):   
AAACATAAGGGATTAATTTATCCCAAAACA

Found at i:1254 original size:3 final size:3

Alignment explanation


    Indices: 1222--1290  Score: 84
    Period size: 3  Copynumber: 21.3  Consensus size: 3

       1212 GGTTCTAACC

                                     *                                     
       1222 TAA TAA TATA TATA TATA TAT TATA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TA-A TA-A TA-A TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA

                                      
       1271 TAA TATA TAA TAA TAA TAA T
          1 TAA TA-A TAA TAA TAA TAA T

       1291 GAAATAATGA


Statistics
Matches: 61,  Mismatches: 2, Indels: 6
        0.88            0.03        0.09

Matches are distributed among these distances:
   3   45  0.74
   4   16  0.26

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (3 bp):   
TAA

Found at i:1260 original size:31 final size:31

Alignment explanation


    Indices: 1222--1298  Score: 102
    Period size: 31  Copynumber: 2.4  Consensus size: 31

       1212 GGTTCTAACC

                                *             
       1222 TAATAATATATATATATATATTATATAATAATAA
          1 TAATAATA-ATA-ATA-ATAATATATAATAATAA

                                           
       1256 TAATAATAATAATAATAATATATAATAATAA
          1 TAATAATAATAATAATAATATATAATAATAA

                *        
       1287 TAATGA-AATAAT
          1 TAATAATAATAAT

       1299 GATGACAGCT


Statistics
Matches: 41,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
  30    6  0.15
  31   21  0.51
  32    3  0.07
  33    3  0.07
  34    8  0.20

ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39


Consensus pattern (31 bp):   
TAATAATAATAATAATAATATATAATAATAA

Found at i:2476 original size:60 final size:62

Alignment explanation


    Indices: 2403--2527  Score: 227
    Period size: 60  Copynumber: 2.0  Consensus size: 62

       2393 ACAGATAAGT

                                                                          
       2403 TACTGAGCTGTTGAGTTTGATTTTCTTGAAAAACACTGTCACTGT-ATATTCTTAT-TTGCG
          1 TACTGAGCTGTTGAGTTTGATTTTCTTGAAAAACACTGTCACTGTAATATTCTTATATTGCG

                                                                           
       2463 TACTGAGCTGTTGAGTTTGATTTTCTTGAAAAACACTGTCACTGTACATATTCTTATATTGCG
          1 TACTGAGCTGTTGAGTTTGATTTTCTTGAAAAACACTGTCACTGTA-ATATTCTTATATTGCG

              
       2526 TA
          1 TA

       2528 GATTCTAATA


Statistics
Matches: 62,  Mismatches: 0, Indels: 3
        0.95            0.00        0.05

Matches are distributed among these distances:
  60   45  0.73
  62   10  0.16
  63    7  0.11

ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42


Consensus pattern (62 bp):   
TACTGAGCTGTTGAGTTTGATTTTCTTGAAAAACACTGTCACTGTAATATTCTTATATTGCG
Done.