Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012861.1 Corchorus capsularis cultivar CVL-1 contig12882, 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: 42937
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:1671 original size:18 final size:18

Alignment explanation


    Indices: 1648--1722  Score: 60
    Period size: 18  Copynumber: 3.7  Consensus size: 18

       1638 TAATAAAAAC

                              
       1648 ATATATAATATATTTTAA
          1 ATATATAATATATTTTAA

                               *      
       1666 ATATATTTATATAAAATACATTTATA
          1 ATATA--TA-AT---ATA-TTTTA-A

                              
       1692 ATATATAATATATTTTAA
          1 ATATATAATATATTTTAA

                   *     
       1710 ATATATATTATAT
          1 ATATATAATATAT

       1723 AAAAATATCT


Statistics
Matches: 46,  Mismatches: 3, Indels: 16
        0.71            0.05        0.25

Matches are distributed among these distances:
  18   18  0.39
  19    4  0.09
  20    5  0.11
  21    2  0.04
  23    2  0.04
  24    5  0.11
  25    4  0.09
  26    6  0.13

ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49


Consensus pattern (18 bp):   
ATATATAATATATTTTAA

Found at i:14433 original size:15 final size:15

Alignment explanation


    Indices: 14413--14441  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

      14403 TGGGCAGTTT

                           
      14413 CAGAATTTATTGAAC
          1 CAGAATTTATTGAAC

                          
      14428 CAGAATTTATTGAA
          1 CAGAATTTATTGAA

      14442 TCTATTAGTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34


Consensus pattern (15 bp):   
CAGAATTTATTGAAC

Found at i:18421 original size:1 final size:1

Alignment explanation


    Indices: 18415--18440  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

      18405 TCATCAAATT

                                      
      18415 AAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA

      18441 GAAGCAACAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:31766 original size:166 final size:167

Alignment explanation


    Indices: 31491--31825  Score: 480
    Period size: 166  Copynumber: 2.0  Consensus size: 167

      31481 CTTAAATGTC

                    *                  *           *           * **     *    
      31491 ATAAACTTTAACAGAGTAGTGGAATTACTAAAAGATCCCTATCAAGACTTGTTTTTGGAGTTAGA
          1 ATAAACTTGAACAGAGTAGTGGAATTAATAAAAGATCCCCATCAAGACTTGATGATGGAGCTAGA

                 * *             *                                           
      31556 GAACTTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTG
         66 GAACTAAATTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTG

                          *                       
      31621 AGGGGATTAAATAAGT-AATCTTTTTGGTCATTTCTCA
        131 AGGGGATTAAATAACTAAAT-TTTTTGGTCATTTCTCA

                       *                    *                                
      31658 ATAAACTTGAATAGAGTAGTGGAATTAATAAATGATCCCCATCAAGGA-TTGATGAT-GAGCTAG
          1 ATAAACTTGAACAGAGTAGTGGAATTAATAAAAGATCCCCATCAA-GACTTGATGATGGAGCTAG

                                                                  *    *     
      31721 AGAACTAACATTTTTT-GTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAATTTTTTATTCT
         65 AGAACTAA-ATTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCT

                                                   
      31785 TGAGGGGATTAAATAACTAAATTTTTTGGTCATTTCTCA
        129 TGAGGGGATTAAATAACTAAATTTTTTGGTCATTTCTCA

              
      31824 AT
          1 AT

      31826 TGACAAATGA


Statistics
Matches: 150,  Mismatches: 15, Indels: 7
        0.87            0.09        0.04

Matches are distributed among these distances:
 166   94  0.63
 167   54  0.36
 168    2  0.01

ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39


Consensus pattern (167 bp):   
ATAAACTTGAACAGAGTAGTGGAATTAATAAAAGATCCCCATCAAGACTTGATGATGGAGCTAGA
GAACTAAATTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTG
AGGGGATTAAATAACTAAATTTTTTGGTCATTTCTCA

Found at i:42899 original size:2 final size:2

Alignment explanation


    Indices: 42892--42929  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      42882 AAACTTTTTA

                                                                    
      42892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      42930 CATTACAT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

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


Consensus pattern (2 bp):   
AT

Done.