Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001906.1 Corchorus olitorius cultivar O-4 contig01906, 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: 10308
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31


Found at i:1273 original size:41 final size:41

Alignment explanation


    Indices: 1189--1273  Score: 109
    Period size: 41  Copynumber: 2.1  Consensus size: 41

       1179 ATAAAAATTC

                                                 **  
       1189 ATTACCACATAATAATCAATTTGAAAAATCAATTAATTTTT
          1 ATTACCACATAATAATCAATTTGAAAAATCAATTAATGGTT

                *                  * *                
       1230 ATTAGCACATAATAATCAATTTGTATAAT-AATTTAATGGTT
          1 ATTACCACATAATAATCAATTTGAAAAATCAA-TTAATGGTT

               
       1271 ATT
          1 ATT

       1274 TCAATTTGAC


Statistics
Matches: 38,  Mismatches: 5, Indels: 2
        0.84            0.11        0.04

Matches are distributed among these distances:
  40    2  0.05
  41   36  0.95

ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41


Consensus pattern (41 bp):   
ATTACCACATAATAATCAATTTGAAAAATCAATTAATGGTT

Found at i:3085 original size:26 final size:28

Alignment explanation


    Indices: 3056--3116  Score: 81
    Period size: 30  Copynumber: 2.2  Consensus size: 28

       3046 TCAAATCAAC

                                        
       3056 TAATTA-AT-CAATCAATCTAAAGTAAT
          1 TAATTATATCCAATCAATCTAAAGTAAT

                    *                     
       3082 TAATATATTTCCCAATCAATCTAAAGTAAT
          1 TAAT-TATAT-CCAATCAATCTAAAGTAAT

                 
       3112 TAATT
          1 TAATT

       3117 TATTTCCTTT


Statistics
Matches: 30,  Mismatches: 1, Indels: 5
        0.83            0.03        0.14

Matches are distributed among these distances:
  26    4  0.13
  27    2  0.07
  28    1  0.03
  29    1  0.03
  30   22  0.73

ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38


Consensus pattern (28 bp):   
TAATTATATCCAATCAATCTAAAGTAAT

Found at i:3098 original size:30 final size:30

Alignment explanation


    Indices: 3064--3123  Score: 111
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       3054 ACTAATTAAT

                                          
       3064 CAATCAATCTAAAGTAATTAATATATTTCC
          1 CAATCAATCTAAAGTAATTAATATATTTCC

                                  *       
       3094 CAATCAATCTAAAGTAATTAATTTATTTCC
          1 CAATCAATCTAAAGTAATTAATATATTTCC

       3124 TTTTGTCCAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38


Consensus pattern (30 bp):   
CAATCAATCTAAAGTAATTAATATATTTCC

Found at i:3677 original size:6 final size:6

Alignment explanation


    Indices: 3666--3692  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       3656 GGGGCTGCTA

                                           
       3666 GAGAAG GAGAAG GAGAAG GAGAAG GAG
          1 GAGAAG GAGAAG GAGAAG GAGAAG GAG

       3693 CGAGGGAAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00


Consensus pattern (6 bp):   
GAGAAG

Found at i:9990 original size:21 final size:21

Alignment explanation


    Indices: 9964--10006  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       9954 TTTAAGGGTA

                                 
       9964 TTACTAAATACCGCCCCCCTT
          1 TTACTAAATACCGCCCCCCTT

                  **             
       9985 TTACTAGCTACCGCCCCCCTT
          1 TTACTAAATACCGCCCCCCTT

             
      10006 T
          1 T

      10007 GGACTATTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.19, C:0.44, G:0.07, T:0.30


Consensus pattern (21 bp):   
TTACTAAATACCGCCCCCCTT

Found at i:10012 original size:22 final size:21

Alignment explanation


    Indices: 9972--10012  Score: 64
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       9962 TATTACTAAA

                          *      
       9972 TACCGCCCCCCTTTTACTAGC
          1 TACCGCCCCCCTTTGACTAGC

                                
       9993 TACCGCCCCCCTTTGGACTA
          1 TACCGCCCCCCTTT-GACTA

      10013 TTTTGCCCTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21   14  0.78
  22    4  0.22

ACGTcount: A:0.15, C:0.46, G:0.12, T:0.27


Consensus pattern (21 bp):   
TACCGCCCCCCTTTGACTAGC
Done.