Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001526.1 Corchorus capsularis cultivar CVL-1 contig01526, 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, 913

Length: 1523
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32


Found at i:1034 original size:262 final size:261

Alignment explanation


    Indices: 620--1143  Score: 732
    Period size: 262  Copynumber: 2.0  Consensus size: 261

        610 GAATATAGAT

                           *   *         *     *            *                
        620 ATTTCAAGAAGTCTTTACGCAAAAAATCATGCAAACCTGAGACAGGGCTCCGAACGCCTTTTTAG
          1 ATTTCAAGAAGTCTTGACGAAAAAAATCAGGCAAAACTGAGACAGGGCCCCGAACGCCTTTTTAG

                    *               *     *                         *        
        685 CTAAAAACTGTGATGGTTAGTACATGATTTCGGCTAAAATTTAACAAAACTTGCCCTGAAATAGT
         66 CTAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAATTTAACAAAACTTGCCCCGAAATAGT

                        *  *           *          *                          
        750 TTTCATCAATTTTTTGGCAAAATACTCGTAA-AATATATATAATTCAACTCCAAAAATATTGAAA
        131 TTTCATCAATTTCTTAGCAAAATACTCATAAGAA-ATACATAATTCAACTCCAAAAATATTGAAA

                                                                          *  
        814 GCCTTTTCACGCTTAAAAATATCA-TTTTCTTATTTTATTCTGAATTAATTTCAAAATAAATTGA
        195 GCCTTTTCACGCTT-AAAATATCATTTTTCTTATTTTATTCTGAATTAATTTCAAAATAAATCGA

               
        878 AAC
        259 AAC

                            *                        * *           *         
        881 ATTTCAAGAAGTCTTGGCGAAAAAAATCAGGCAAAACTGAGTCGGGGCCCCGGAATGCGC-TTTT
          1 ATTTCAAGAAGTCTTGACGAAAAAAATCAGGCAAAACTGAGACAGGGCCCC-GAACGC-CTTTTT

                                    *                    *                   
        945 AGCTAAAAACCGTGATGGTTAGTAGACGATTTAGGCTAAAATTTAGCAAAAAC-TGCCCCGAAAT
         64 AGCTAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAATTTAAC-AAAACTTGCCCCGAAAT

             *       *                                                       
       1009 ATTTTTCATTAATTTCTTAGCAAAATACTCATAAGAAATACATAATTCAACTCCAAAAATATTGA
        128 AGTTTTCATCAATTTCTTAGCAAAATACTCATAAGAAATACATAATTCAACTCCAAAAATATTGA

             * *                                  *              *      *    
       1074 AGGTCTTTTCACGCTTAAAATATCATTTTTCTTATTTTTTTCTGAATTAATTTTAAAATATATCG
        193 AAGCCTTTTCACGCTTAAAATATCATTTTTCTTATTTTATTCTGAATTAATTTCAAAATAAATCG

                
       1139 AAAC
        258 AAAC

             
       1143 A
          1 A

       1144 AGATTCTGAT


Statistics
Matches: 231,  Mismatches: 27, Indels: 9
        0.87            0.10        0.03

Matches are distributed among these distances:
 261   52  0.23
 262  171  0.74
 263    8  0.03

ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33


Consensus pattern (261 bp):   
ATTTCAAGAAGTCTTGACGAAAAAAATCAGGCAAAACTGAGACAGGGCCCCGAACGCCTTTTTAG
CTAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAATTTAACAAAACTTGCCCCGAAATAGT
TTTCATCAATTTCTTAGCAAAATACTCATAAGAAATACATAATTCAACTCCAAAAATATTGAAAG
CCTTTTCACGCTTAAAATATCATTTTTCTTATTTTATTCTGAATTAATTTCAAAATAAATCGAAA
C

Found at i:1481 original size:323 final size:325

Alignment explanation


    Indices: 883--1497  Score: 862
    Period size: 323  Copynumber: 1.9  Consensus size: 325

        873 ATTGAAACAT

                                                *  *             *           
        883 TTCAAGAAGTCTTGGCGAAAAAAATCAGGCAAAACTGAGTCGGGGCCCCGGAATGCGCTTTTAGC
          1 TTCAAGAAGTCTTGGCGAAAAAAATCAGGCAAAACTAAGCCGGGGCCCCGGAACGCGCTTTTAGC

                      *          *                                      *    
        948 TAAAAACCGTGATGGTTAGTAGACGATTTAGGCTAAAATTTAGCAAAAACTGCCCCGAAATATTT
         66 TAAAAACCGTAATGGTTAGTACACG---TA-G-T---ATTTAGCAAAAACTGCCCCGAAAGATTT

                 *                        *                        *        *
       1013 TTCATTAATTTCTTAGCAAAATACTCATAAGAAATACATAATTCAACTCCAAAAATATTGAAGGT
        123 TTCATCAATTTCTTAGCAAAATACTCATAAAAAATACATAATTCAACTCCAAAAAGATTGAAGGG

                *                            *               *      *        
       1078 CTTTTCACGCTTAAAATATCATTTTTCTTATTTTTTTCTGAATTAATTTTAAAATATATCGAAAC
        188 CTTTACACGCTTAAAATATCATTTTTCTTATTTCTTTCTGAATTAATTTCAAAATAAATCGAAAC

                                                                             
       1143 AAGATTCTGATGCTCATAAAAACAGATCCTTATATGCAACGTGGCTGAAAATTTATTAGATGAAT
        253 AAGATTCTGATGCTCATAAAAACAGATCCTTATATGCAACGTGGCTGAAAATTTATTAGATGAAT

                    
       1208 ATAGATAC
        318 ATAGATAC

                                     *                   *           *       
       1216 TTCAAGAAGTCTTGGCGAAAAAAATTAGGCAAAACTAAGCCGGGGTCCCGGAACGCGTTTTTAGC
          1 TTCAAGAAGTCTTGGCGAAAAAAATCAGGCAAAACTAAGCCGGGGCCCCGGAACGCGCTTTTAGC

                                   *          *       *     *                
       1281 -AAAAACCAGTAATGGTTAGTACCCG-A-T-TTTGGCAAAAATTGCCCTGAAAGATTTTTCATCA
         66 TAAAAACC-GTAATGGTTAGTACACGTAGTATTTAGCAAAAACTGCCCCGAAAGATTTTTCATCA

                   *                       *      *  *                       
       1342 ATTT-TTTGCCCAAAATACTCATAAAAAATATATAATTTAATTCCAAAAAGATTGAAGGGCTTTA
        130 ATTTCTTAG--CAAAATACTCATAAAAAATACATAATTCAACTCCAAAAAGATTGAAGGGCTTTA

              *                                                              
       1406 CATGCTTAAAATATCATTTTTCTTATTTCTTTCTGAATTAATTTCAAAATAAATCGAAACAAGAT
        193 CACGCTTAAAATATCATTTTTCTTATTTCTTTCTGAATTAATTTCAAAATAAATCGAAACAAGAT

                                       
       1471 TCTGATGCTCATAAAAACAGATCCTTA
        258 TCTGATGCTCATAAAAACAGATCCTTA

       1498 AATCCAACAA


Statistics
Matches: 253,  Mismatches: 26, Indels: 16
        0.86            0.09        0.05

Matches are distributed among these distances:
 321    3  0.01
 322   33  0.13
 323  135  0.53
 326    1  0.00
 329    1  0.00
 332    7  0.03
 333   73  0.29

ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32


Consensus pattern (325 bp):   
TTCAAGAAGTCTTGGCGAAAAAAATCAGGCAAAACTAAGCCGGGGCCCCGGAACGCGCTTTTAGC
TAAAAACCGTAATGGTTAGTACACGTAGTATTTAGCAAAAACTGCCCCGAAAGATTTTTCATCAA
TTTCTTAGCAAAATACTCATAAAAAATACATAATTCAACTCCAAAAAGATTGAAGGGCTTTACAC
GCTTAAAATATCATTTTTCTTATTTCTTTCTGAATTAATTTCAAAATAAATCGAAACAAGATTCT
GATGCTCATAAAAACAGATCCTTATATGCAACGTGGCTGAAAATTTATTAGATGAATATAGATAC
Done.