Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013653.1 Corchorus capsularis cultivar CVL-1 contig13674, 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: 31128
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33


Found at i:3562 original size:11 final size:10

Alignment explanation


    Indices: 3545--3569  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       3535 CCAGGCAGTA

                      
       3545 ATTTTTTTTT
          1 ATTTTTTTTT

                      
       3555 ATTTTTTTTT
          1 ATTTTTTTTT

                 
       3565 ATTTT
          1 ATTTT

       3570 CTCGATGCTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88


Consensus pattern (10 bp):   
ATTTTTTTTT

Found at i:7946 original size:30 final size:30

Alignment explanation


    Indices: 7912--7973  Score: 97
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       7902 TCTTCTAAAC

                    *                 *   
       7912 TTTTAAACTAAGAAATTTATCACATATATA
          1 TTTTAAACAAAGAAATTTATCACATAAATA

                   *                      
       7942 TTTTAAAGAAAGAAATTTATCACATAAATA
          1 TTTTAAACAAAGAAATTTATCACATAAATA

              
       7972 TT
          1 TT

       7974 CTAAGATATT


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39


Consensus pattern (30 bp):   
TTTTAAACAAAGAAATTTATCACATAAATA

Found at i:15175 original size:13 final size:13

Alignment explanation


    Indices: 15157--15181  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      15147 GAGAGGTATG

                         
      15157 ATTCAAAATATAT
          1 ATTCAAAATATAT

                        
      15170 ATTCAAAATATA
          1 ATTCAAAATATA

      15182 AATTAATTTT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36


Consensus pattern (13 bp):   
ATTCAAAATATAT

Found at i:23162 original size:2 final size:2

Alignment explanation


    Indices: 23155--23202  Score: 75
    Period size: 2  Copynumber: 25.5  Consensus size: 2

      23145 GTGCAAAACC

                                                                          
      23155 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                         
      23195 AT AT -T AT A
          1 AT AT AT AT A

      23203 AAGGCGATTG


Statistics
Matches: 43,  Mismatches: 0, Indels: 6
        0.88            0.00        0.12

Matches are distributed among these distances:
   1    3  0.07
   2   40  0.93

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


Consensus pattern (2 bp):   
AT

Found at i:30327 original size:55 final size:55

Alignment explanation


    Indices: 30090--30583  Score: 608
    Period size: 53  Copynumber: 9.2  Consensus size: 55

      30080 TCTAGTTAAT

                  *   *                                       *     
      30090 AGTTGTTAGGCATATT-CCTCGAATCTTC-TTTTTATGACTA-ATAATTTTTACAC
          1 AGTTGTCAGGTATATTCCCTCGAATCTTCTTTTTTATGAC-AGATAATTTGTACAC

                               *      *                       *     
      30143 --TCTGTCAGGTATATTCCTTCGAATATT-TTTTTTATGACAGATAATTTTTACAC
          1 AGT-TGTCAGGTATATTCCCTCGAATCTTCTTTTTTATGACAGATAATTTGTACAC

                     *        **                              *     
      30196 --TCTGTCAAGTATATTCTTTCGAATCTTC-TTTTTATGACAGATAATTTTTACAC
          1 AGT-TGTCAGGTATATTCCCTCGAATCTTCTTTTTTATGACAGATAATTTGTACAC

                              *  *           **                    
      30249 ---TGTCAGGTATATTCCTTCAAATCTTCTTTTCCATGACAGATAATTTGTACAC
          1 AGTTGTCAGGTATATTCCCTCGAATCTTCTTTTTTATGACAGATAATTTGTACAC

                                                              *   *
      30301 AGTTGTCAGGTATATTCCCTCGAATCTT-TTTTTTATGACAGATAATTTGCACAT
          1 AGTTGTCAGGTATATTCCCTCGAATCTTCTTTTTTATGACAGATAATTTGTACAC

                                *                          *       
      30355 AGTTGTCAGGTATATTCCCTTGAATCTTCTTTTTTATGACAGATAATCTGTACAC
          1 AGTTGTCAGGTATATTCCCTCGAATCTTCTTTTTTATGACAGATAATTTGTACAC

                        *  **                                     *
      30410 AGTTGTCA-G-ACATAACCTCGAATCTTCTTTTTTATGACAGATAATTTGTACAT
          1 AGTTGTCAGGTATATTCCCTCGAATCTTCTTTTTTATGACAGATAATTTGTACAC

                      *                                            
      30463 AGTTGTCAGGCATATTCCCTCGAATC-T-TTTTTTATGACAGATAATTTGTACAC
          1 AGTTGTCAGGTATATTCCCTCGAATCTTCTTTTTTATGACAGATAATTTGTACAC

                             *                             *       
      30516 AGTTGTCAGGTATATTCACTCGAATCTTCTTTTTTATGACAGATAATCTGTACAC
          1 AGTTGTCAGGTATATTCCCTCGAATCTTCTTTTTTATGACAGATAATTTGTACAC

                    *    
      30571 AGTTGTCAAGTAT
          1 AGTTGTCAGGTAT

      30584 CAGGGATAGA


Statistics
Matches: 390,  Mismatches: 37, Indels: 26
        0.86            0.08        0.06

Matches are distributed among these distances:
  51   24  0.06
  52   34  0.09
  53  176  0.45
  54   53  0.14
  55  103  0.26

ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43


Consensus pattern (55 bp):   
AGTTGTCAGGTATATTCCCTCGAATCTTCTTTTTTATGACAGATAATTTGTACAC
Done.