Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008547.1 Corchorus capsularis cultivar CVL-1 contig08568, 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, 874

Length: 1457
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40


Found at i:880 original size:32 final size:32

Alignment explanation


    Indices: 836--896  Score: 104
    Period size: 32  Copynumber: 1.9  Consensus size: 32

        826 ATGTACCAAA

                   *                        
        836 AAGATTATCAATTTTCTATCTAATTTTTTATG
          1 AAGATTACCAATTTTCTATCTAATTTTTTATG

                                  *      
        868 AAGATTACCAATTTTCTATCTATTTTTTT
          1 AAGATTACCAATTTTCTATCTAATTTTTT

        897 TTTTTGAAAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  32   27  1.00

ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54


Consensus pattern (32 bp):   
AAGATTACCAATTTTCTATCTAATTTTTTATG

Found at i:1248 original size:32 final size:31

Alignment explanation


    Indices: 1212--1275  Score: 83
    Period size: 32  Copynumber: 2.0  Consensus size: 31

       1202 TTCATTAATG

                       *                    
       1212 GTGAAGATCACTAATTTTCTATCTAATTTTTT
          1 GTGAAGATCACCAATTTTCTATCT-ATTTTTT

                    **              *      
       1244 GTGAAGATTGCCAATTTTCTATCTTTTTTTT
          1 GTGAAGATCACCAATTTTCTATCTATTTTTT

             
       1275 G
          1 G

       1276 AAAAAAAATC


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  31    7  0.25
  32   21  0.75

ACGTcount: A:0.23, C:0.12, G:0.12, T:0.52


Consensus pattern (31 bp):   
GTGAAGATCACCAATTTTCTATCTATTTTTT

Found at i:1383 original size:374 final size:374

Alignment explanation


    Indices: 656--1409  Score: 1095
    Period size: 374  Copynumber: 2.0  Consensus size: 374

        646 AAAAATGTTG

                                      *      *                               
        656 TACTTTATATTTTTTGAGAAAAATATTGTCAAATTTGAAGATTGGTTAACCAAAATGTGACAAAT
          1 TACTTTATATTTTTTGAGAAAAATATGGTCAAACTTGAAGATTGGTTAACCAAAATGTGACAAAT

                    ***              *                          *    *       
        721 AAAAGGAACGTAGGGAGTATCAATTGAAGGTTATTAAAACAATTATGATACTTTGAATAAATTCA
         66 AAAAGGAAAAAAGGGAGTATCAATTAAAGGTTATTAAAACAATTATGATACTATGAACAAATTCA

                                                                   *         
        786 ATAACCTTACATTATTATTAACTTTAGTAAACTTTCATGAATGTACCAAAAAGATTATCAATTTT
        131 ATAACCTTACATTATTATTAACTTTAGTAAACTTTCATGAATGT----AAAAGATCATCAATTTT

                                                             ***             
        851 CTATCTAATTTTTTATGAAGATTACCAATTTTCTATCTATTTTTTTTTTTTGAAAAAACTATAAT
        192 CTATCTAATTTTTTATGAAGATTACCAATTTTCTATC---TTTTTTTTTGAAAAAAAACTATAAT

                                                                            *
        916 GATTATAAAAAGAAAGGCATAGTACTATCAACTAATCTAATAACCTTACATTCTCAATATTTTTG
        254 GATTAT-AAAAGAAAGGCATAGTACTATCAACTAATCTAATAACCTTACATTCTCAATATTTTTA

            *       *                         *          *   *       
        981 GTTATCAAGTTTCTTATTTATATTTACTAAAATTTCTTTTGTAAATGAAGATTATTT
        318 ATTATCAAATTTCTTATTTATATTTACTAAAATTGCTTTTGTAAACGAAAATTATTT

                           *                                                 
       1038 TACTTTATATTTTTTTAGAAAAATATGGTCAAACTTGAAGATTGGTTAACCAAAATGTGACAAAT
          1 TACTTTATATTTTTTGAGAAAAATATGGTCAAACTTGAAGATTGGTTAACCAAAATGTGACAAAT

                                         *                                   
       1103 AAATAGGAAAAAAGGGAGTATCAATTAAATGTTATTAAAACAATTATGATACTATGAACAAATTC
         66 AAA-AGGAAAAAAGGGAGTATCAATTAAAGGTTATTAAAACAATTATGATACTATGAACAAATTC

                  *       *                        *       *                 
       1168 AATAACTTTACATTCTTATTAACTTTAGTAAACTTTCATTAATGGT-GAAGATCA-CTAATTTTC
        130 AATAACCTTACATTATTATTAACTTTAGTAAACTTTCATGAAT-GTAAAAGATCATC-AATTTTC

                         *        *                                          
       1231 TATCTAATTTTTTGTGAAGATTGCCAATTTTCTATC-TTTTTTTTGAAAAAAAATCCTATAATGA
        193 TATCTAATTTTTTATGAAGATTACCAATTTTCTATCTTTTTTTTTGAAAAAAAA--CTATAATGA

                        * *                          *                       
       1295 TTAT-AAA-AAATGTATAGTACTATCAACTAATCTAATAACTTTACATTCTCAATATTTTTAATT
        256 TTATAAAAGAAAGGCATAGTACTATCAACTAATCTAATAACCTTACATTCTCAATATTTTTAATT

                                                                
       1358 ATCAAATTTCTTATTTATATTTACTAAAATTGCTTTTGTAAACGAAAATTAT
        321 ATCAAATTTCTTATTTATATTTACTAAAATTGCTTTTGTAAACGAAAATTAT

       1410 ACCAAATTTT


Statistics
Matches: 338,  Mismatches: 29, Indels: 18
        0.88            0.08        0.05

Matches are distributed among these distances:
 374   99  0.29
 375   17  0.05
 377   13  0.04
 378    1  0.00
 379   47  0.14
 382   65  0.19
 383   94  0.28
 384    2  0.01

ACGTcount: A:0.39, C:0.11, G:0.10, T:0.41


Consensus pattern (374 bp):   
TACTTTATATTTTTTGAGAAAAATATGGTCAAACTTGAAGATTGGTTAACCAAAATGTGACAAAT
AAAAGGAAAAAAGGGAGTATCAATTAAAGGTTATTAAAACAATTATGATACTATGAACAAATTCA
ATAACCTTACATTATTATTAACTTTAGTAAACTTTCATGAATGTAAAAGATCATCAATTTTCTAT
CTAATTTTTTATGAAGATTACCAATTTTCTATCTTTTTTTTTGAAAAAAAACTATAATGATTATA
AAAGAAAGGCATAGTACTATCAACTAATCTAATAACCTTACATTCTCAATATTTTTAATTATCAA
ATTTCTTATTTATATTTACTAAAATTGCTTTTGTAAACGAAAATTATTT
Done.