Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001875.1 Corchorus olitorius cultivar O-4 contig01875, 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, 863

Length: 1439
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28


Found at i:1258 original size:33 final size:31

Alignment explanation


    Indices: 1193--1421  Score: 134
    Period size: 33  Copynumber: 6.9  Consensus size: 31

       1183 TATTTTCAAG

                               ** *          
       1193 AGATTTGTTTTCATCACAATTAGCATCCAAAAC
          1 AGATTTG-TTTCATCACAAACAACA-CCAAAAC

                                             
       1226 AGAATTTGTTTCATCACAAACAACACCTAAAAC
          1 AG-ATTTGTTTCATCACAAACAACACC-AAAAC

                     *                     **
       1259 AGATTTAGTGTCATCACAAACAACACTCAAATT
          1 AGATTT-GTTTCATCACAAACAACAC-CAAAAC

              *      *       *         * *   
       1292 AGTTTTAGTATCATCACTAACAACATCTAGAAC
          1 AGATTT-GTTTCATCACAAACAACA-CCAAAAC

             *       *     *               **
       1325 ATATTTAGTGTCATCGCAAACAACACTCAAATT
          1 AGATTT-GTTTCATCACAAACAACAC-CAAAAC

              *      *       *               
       1358 AGGTTTAGTATCATCACTAACAACACTCAAAAC
          1 AGATTT-GTTTCATCACAAACAACAC-CAAAAC

                     *    **               
       1391 AGATTTCGTGTCATTGCAAACAACACTCAAA
          1 AGATTT-GTTTCATCACAAACAACAC-CAAA

       1422 TTAGGTTCAG


Statistics
Matches: 155,  Mismatches: 35, Indels: 12
        0.77            0.17        0.06

Matches are distributed among these distances:
  32    7  0.05
  33  141  0.91
  34    7  0.05

ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28


Consensus pattern (31 bp):   
AGATTTGTTTCATCACAAACAACACCAAAAC

Found at i:1306 original size:66 final size:65

Alignment explanation


    Indices: 1236--1428  Score: 296
    Period size: 66  Copynumber: 2.9  Consensus size: 65

       1226 AGAATTTGTT

                   *                              *                   *      
       1236 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGTTTTAGT
          1 TCATCACTAACAACA-CTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT

             
       1301 A
         65 A

                               *    *                                        
       1302 TCATCACTAACAACATCTAGAACATATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT
          1 TCATCACTAACAACA-CTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT

             
       1367 A
         65 A

                                         *       *                       
       1368 TCATCACTAACAACACTCAAAACAGATTTCGTGTCATTGCAAACAACACTCAAATTAGGTT
          1 TCATCACTAACAACACT-AAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTT

       1429 CAGAATTACT


Statistics
Matches: 116,  Mismatches: 10, Indels: 2
        0.91            0.08        0.02

Matches are distributed among these distances:
  65    2  0.02
  66  114  0.98

ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27


Consensus pattern (65 bp):   
TCATCACTAACAACACTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGTA

Found at i:1413 original size:99 final size:99

Alignment explanation


    Indices: 1236--1415  Score: 218
    Period size: 99  Copynumber: 1.8  Consensus size: 99

       1226 AGAATTTGTT

                                            *                     **  *      
       1236 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGTTTTAGT
          1 TCATCACAAACAACACCTAAAACAGATTTAGTATCATCACAAACAACACTCAAAACAGATTTAGT

                    *                         
       1301 ATCATCACTAACAACATCTAGAACATATTTAGTG
         66 ATCATCACAAACAACATCTAGAACATATTTAGTG

                 *                **  *              *                     * 
       1335 TCATCGCAAACAACA-CTCAAATTAGGTTTAGTATCATCACTAACAACACTCAAAACAGATTTCG
          1 TCATCACAAACAACACCT-AAAACAGATTTAGTATCATCACAAACAACACTCAAAACAGATTTAG

             *    **         
       1399 TGTCATTGCAAACAACA
         65 TATCATCACAAACAACA

       1416 CTCAAATTAG


Statistics
Matches: 66,  Mismatches: 14, Indels: 2
        0.80            0.17        0.02

Matches are distributed among these distances:
  98    2  0.03
  99   64  0.97

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


Consensus pattern (99 bp):   
TCATCACAAACAACACCTAAAACAGATTTAGTATCATCACAAACAACACTCAAAACAGATTTAGT
ATCATCACAAACAACATCTAGAACATATTTAGTG
Done.