Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010755.1 Corchorus capsularis cultivar CVL-1 contig10776, 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: 34001
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:5552 original size:42 final size:43

Alignment explanation


    Indices: 5495--5577  Score: 116
    Period size: 42  Copynumber: 2.0  Consensus size: 43

       5485 CGTGTTTGGC

                                          *             
       5495 TTATCGTGTCTCGTGTC-TGAATCGTGTC-GGACACGATTAAGA
          1 TTATCGTGTCTCGTGTCGT-AATCGTGTCAAGACACGATTAAGA

                *    *                               
       5537 TTATTGTGTTTCGTGTCGTAATCGTGTCAAGACACGATTAA
          1 TTATCGTGTCTCGTGTCGTAATCGTGTCAAGACACGATTAA

       5578 CACGTTTAAG


Statistics
Matches: 36,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  42   24  0.67
  43   12  0.33

ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36


Consensus pattern (43 bp):   
TTATCGTGTCTCGTGTCGTAATCGTGTCAAGACACGATTAAGA

Found at i:5590 original size:20 final size:21

Alignment explanation


    Indices: 5565--5607  Score: 61
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       5555 TAATCGTGTC

                     *           
       5565 AAGACACGATTAACACG-TTT
          1 AAGACACGAGTAACACGCTTT

                       *         
       5585 AAGACACGAGTGACACGCTTT
          1 AAGACACGAGTAACACGCTTT

              
       5606 AA
          1 AA

       5608 TTAACGGGTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20   15  0.75
  21    5  0.25

ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21


Consensus pattern (21 bp):   
AAGACACGAGTAACACGCTTT

Found at i:5757 original size:2 final size:2

Alignment explanation


    Indices: 5750--5786  Score: 53
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       5740 TATCTTTAAT

                                                                       
       5750 TA TA TA TA TA -A TA TA TA TA -A T- 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 TA TA

       5787 CAATGTTTTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 6
        0.84            0.00        0.16

Matches are distributed among these distances:
   1    3  0.09
   2   29  0.91

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:5772 original size:21 final size:20

Alignment explanation


    Indices: 5746--5786  Score: 73
    Period size: 21  Copynumber: 2.0  Consensus size: 20

       5736 AAATTATCTT

                                 
       5746 TAATTATATATATAATATATA
          1 TAATTATATATAT-ATATATA

                                
       5767 TAATTATATATATATATATA
          1 TAATTATATATATATATATA

       5787 CAATGTTTTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  20    7  0.35
  21   13  0.65

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (20 bp):   
TAATTATATATATATATATA

Found at i:14042 original size:2 final size:2

Alignment explanation


    Indices: 14035--14062  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      14025 TAGCACGTGC

                                                     
      14035 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA

      14063 AAATAAAATC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
GA

Done.