Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021516.1 Corchorus olitorius cultivar O-4 contig21549, 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: 3574
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30


Found at i:365 original size:66 final size:65

Alignment explanation


    Indices: 293--485  Score: 305
    Period size: 66  Copynumber: 2.9  Consensus size: 65

        283 AGAATTTGTT

                   *                *             *                   *      
        293 TCATCACAAACAACACCTAAAACAAATTTAGTGTCATCACAAACAACACTCAAATTAGTTTTAGT
          1 TCATCACTAACAACA-CTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT

             
        358 A
         65 A

                                                                             
        359 TCATCACTAACAACATCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT
          1 TCATCACTAACAACA-CTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT

             
        424 A
         65 A

                                         *       *                       
        425 TCATCACTAACAACACTCAAAACAGATTTCGTGTCATTGCAAACAACACTCAAATTAGGTT
          1 TCATCACTAACAACACT-AAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTT

        486 CAGAATTACT


Statistics
Matches: 119,  Mismatches: 7, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  65    2  0.02
  66  117  0.98

ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26


Consensus pattern (65 bp):   
TCATCACTAACAACACTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGTA

Found at i:474 original size:33 final size:33

Alignment explanation


    Indices: 277--478  Score: 212
    Period size: 33  Copynumber: 6.1  Consensus size: 33

        267 AATTAGCATC

                            *                 
        277 CAAAACAGAATTT-GTTTCATCACAAACAACAC-
          1 CAAAACAG-ATTTAGTGTCATCACAAACAACACT

                    *                         
        309 CTAAAACAAATTTAGTGTCATCACAAACAACACT
          1 C-AAAACAGATTTAGTGTCATCACAAACAACACT

                **  *      *       *         
        343 CAAATTAGTTTTAGTATCATCACTAACAACA-T
          1 CAAAACAGATTTAGTGTCATCACAAACAACACT

                                  *           
        375 CTAAAACAGATTTAGTGTCATCGCAAACAACACT
          1 C-AAAACAGATTTAGTGTCATCACAAACAACACT

                **  *      *       *         
        409 CAAATTAGGTTTAGTATCATCACTAACAACACT
          1 CAAAACAGATTTAGTGTCATCACAAACAACACT

                        *       **           
        442 CAAAACAGATTTCGTGTCATTGCAAACAACACT
          1 CAAAACAGATTTAGTGTCATCACAAACAACACT

                
        475 CAAA
          1 CAAA

        479 TTAGGTTCAG


Statistics
Matches: 137,  Mismatches: 28, Indels: 9
        0.79            0.16        0.05

Matches are distributed among these distances:
  32    7  0.05
  33  127  0.93
  34    3  0.02

ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26


Consensus pattern (33 bp):   
CAAAACAGATTTAGTGTCATCACAAACAACACT

Found at i:3154 original size:16 final size:16

Alignment explanation


    Indices: 3133--3173  Score: 64
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       3123 TTGGAACTCC

                            
       3133 GGCGGAGGCCCGACGT
          1 GGCGGAGGCCCGACGT

                  *   *     
       3149 GGCGGACGCCTGACGT
          1 GGCGGAGGCCCGACGT

                     
       3165 GGCGGAGGC
          1 GGCGGAGGC

       3174 GATTCCCAAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  16   22  1.00

ACGTcount: A:0.12, C:0.29, G:0.51, T:0.07


Consensus pattern (16 bp):   
GGCGGAGGCCCGACGT
Done.