Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003028.1 Corchorus capsularis cultivar CVL-1 contig03036, 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, 944

Length: 1574
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30


Found at i:475 original size:33 final size:33

Alignment explanation


    Indices: 399--489  Score: 103
    Period size: 33  Copynumber: 2.7  Consensus size: 33

        389 TAGACAAAGG

                             *     *         
        399 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA
          1 GTCGCGTGGCCGGTTGTAGCCGGCCATGGCCGA

                **                      *    
        432 GTCGTTTGGCCGGTTGTAGCCGGCCATGTCC-A
          1 GTCGCGTGGCCGGTTGTAGCCGGCCATGGCCGA

                                      
        464 TGTCGCGTGGCCGGTCTTGTAGCCGG
          1 -GTCGCGTGGCCGG--TTGTAGCCGG

        490 TGTTGCGCGG


Statistics
Matches: 48,  Mismatches: 7, Indels: 4
        0.81            0.12        0.07

Matches are distributed among these distances:
  32    1  0.02
  33   37  0.77
  35   10  0.21

ACGTcount: A:0.07, C:0.27, G:0.42, T:0.24


Consensus pattern (33 bp):   
GTCGCGTGGCCGGTTGTAGCCGGCCATGGCCGA

Found at i:1118 original size:33 final size:33

Alignment explanation


    Indices: 1053--1166  Score: 119
    Period size: 33  Copynumber: 3.5  Consensus size: 33

       1043 CTCGTCACCT

                                              
       1053 AAAACA-GATTTATTTTCAATGC--T-ATCAACC
          1 AAAACAGGA-TTATTTTCAATGCTATGATCAACC

                           *                 
       1083 AAAACAGGATTATTTGCAATGCTATGATCAACC
          1 AAAACAGGATTATTTTCAATGCTATGATCAACC

                * **        *         *      
       1116 AAAATAAAATTATTTTTAATGCTATGTTCAACC
          1 AAAACAGGATTATTTTCAATGCTATGATCAACC

                   *   *      
       1149 AAAACAGAATTGTTTTCA
          1 AAAACAGGATTATTTTCA

       1167 TCACAATTAG


Statistics
Matches: 69,  Mismatches: 11, Indels: 5
        0.81            0.13        0.06

Matches are distributed among these distances:
  30   18  0.26
  31    2  0.03
  32    1  0.01
  33   48  0.70

ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33


Consensus pattern (33 bp):   
AAAACAGGATTATTTTCAATGCTATGATCAACC

Found at i:1227 original size:33 final size:33

Alignment explanation


    Indices: 1202--1310  Score: 130
    Period size: 33  Copynumber: 3.3  Consensus size: 33

       1192 TAGTTTTATT

                                             
       1202 GCAAACAACACTCAAATTAGGTTTAGTATCATC
          1 GCAAACAACACTCAAATTAGGTTTAGTATCATC

                             **  *      *    *
       1235 GCAAACAACA-TCTAAAACAGATTTAGTGTCATT
          1 GCAAACAACACTC-AAATTAGGTTTAGTATCATC

                           *  *      *       
       1268 GCAAACAACACTCAATTTTGGTTTACTATCATC
          1 GCAAACAACACTCAAATTAGGTTTAGTATCATC

                      
       1301 GCAAACAACA
          1 GCAAACAACA

       1311 TCTAAAAGAC


Statistics
Matches: 61,  Mismatches: 13, Indels: 4
        0.78            0.17        0.05

Matches are distributed among these distances:
  32    2  0.03
  33   57  0.93
  34    2  0.03

ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27


Consensus pattern (33 bp):   
GCAAACAACACTCAAATTAGGTTTAGTATCATC

Found at i:1260 original size:66 final size:66

Alignment explanation


    Indices: 1177--1317  Score: 219
    Period size: 66  Copynumber: 2.1  Consensus size: 66

       1167 TCACAATTAG

                *              * *                            *              
       1177 CATCCAAAACAAATTTAGTTTTATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGCAAACA
          1 CATCTAAAACAAATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTACTATCATCGCAAACA

             
       1242 A
         66 A

                       *                            *  *                     
       1243 CATCTAAAACAGATTTAGTGTCATTGCAAACAACACTCAATTTTGGTTTACTATCATCGCAAACA
          1 CATCTAAAACAAATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTACTATCATCGCAAACA

             
       1308 A
         66 A

                     
       1309 CATCTAAAA
          1 CATCTAAAA

       1318 GACTCTTTTC


Statistics
Matches: 68,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  66   68  1.00

ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29


Consensus pattern (66 bp):   
CATCTAAAACAAATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTACTATCATCGCAAACA
A
Done.