Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020992.1 Corchorus olitorius cultivar O-4 contig21025, 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: 2470
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:234 original size:35 final size:35
Alignment explanation
Indices: 188--258 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
178 GTCTACAGCT
188 GCCCCTCTTTGTGCATTTGCTAGCTATCAGAAGAG
1 GCCCCTCTTTGTGCATTTGCTAGCTATCAGAAGAG
223 GCCCCTCTTTGTGCATTTGCTAGCTATCAGAAGAG
1 GCCCCTCTTTGTGCATTTGCTAGCTATCAGAAGAG
258 G
1 G
259 TGCAAAGGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (35 bp):
GCCCCTCTTTGTGCATTTGCTAGCTATCAGAAGAG
Found at i:460 original size:39 final size:38
Alignment explanation
Indices: 396--809 Score: 285
Period size: 39 Copynumber: 10.7 Consensus size: 38
386 TATTGTAAAG
* * *
396 AGAGACCTCAGCAGGTTTACTTTAAACGAAACTATTAGC
1 AGAGACCTAAGCAGGTTTAC-TTAAACGAAACTCTAAGC
* * **
435 AGAGATCCTAAGCAGGTTTACTTAAATGATAATTCTAAAT
1 AGAGA-CCTAAGCAGGTTTACTTAAACGA-AACTCTAAGC
* ** * * *
475 AGTGACCTAAATAAGTTTACTTAAACGAAAATTCTAAAC
1 AGAGACCTAAGCAGGTTTACTTAAACG-AAACTCTAAGC
*** * *
514 AGAGACCTAAGCAGGTTTAAACAAACGAGATTCTAAGC
1 AGAGACCTAAGCAGGTTTACTTAAACGAAACTCTAAGC
* * * * * *
552 GGGGACCTAAGCAGGTTTTCTTAAGCAGAAATTCTAGGC
1 AGAGACCTAAGCAGGTTTACTTAAAC-GAAACTCTAAGC
* * * * * *
591 CGGGACCTAAGCAGGTTTTCTTAAATGAAATTCTAAAC
1 AGAGACCTAAGCAGGTTTACTTAAACGAAACTCTAAGC
* *
629 ATAGACCTAAGCAGG-TTACTTAAACGAAGCTCTAAGC
1 AGAGACCTAAGCAGGTTTACTTAAACGAAACTCTAAGC
* * * * * *
666 AAAGGCCTAAGCAGGTTTACTAAAATGGAAATTCTAAAGG
1 AGAGACCTAAGCAGGTTTACTTAAA-CGAAACTCT-AAGC
* * * *
706 AG-GACCTAAGCAGGTTTACTTAAATGGCAACTTTATA-T
1 AGAGACCTAAGCAGGTTTACTTAAA-CGAAACTCTA-AGC
* * * *
744 AGGGACCTAAGCAGGTTTACTTGACCAAAACTCTAAGC
1 AGAGACCTAAGCAGGTTTACTTAAACGAAACTCTAAGC
* *
782 AGGGATCCTAAACAGGTTTACTTAAACG
1 AGAGA-CCTAAGCAGGTTTACTTAAACG
810 GAACAGAGAC
Statistics
Matches: 295, Mismatches: 69, Indels: 22
0.76 0.18 0.06
Matches are distributed among these distances:
37 31 0.11
38 72 0.24
39 164 0.56
40 28 0.09
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (38 bp):
AGAGACCTAAGCAGGTTTACTTAAACGAAACTCTAAGC
Found at i:697 original size:114 final size:113
Alignment explanation
Indices: 391--879 Score: 349
Period size: 116 Copynumber: 4.3 Consensus size: 113
381 ATTTTTATTG
* * * * * *
391 TAAAGAGAGACCTCAGCAGGTTTACTTTAAACGAAACTATTAGCAGAGATCCTAAGCAGGTTTAC
1 TAAACAGAGACCTAAGCAGGTTTAC-TTAAACGAAGCTCTAAGCAGAG-GCCTAAGCAGGTTTAC
** * ** * *
456 TTAAATGATAATTCTAAATAGTGACCTAAATAAGTTTACTTAAACGAAAATTC
64 TTAAATGA-AATTCT--AGGGGGACCTAAGCAGGTTTACTTAAATGAAAATTC
*** * * *
509 TAAACAGAGACCTAAGCAGGTTTAAACAAACG-AGATTCTAAGC-GGGGACCTAAGCAGGTTTTC
1 TAAACAGAGACCTAAGCAGGTTTACTTAAACGAAG-CTCTAAGCAGAGG-CCTAAGCAGGTTTAC
*
572 TTAAGCA-GAAATTCTAGGCCGGGACCTAAGCAGGTTTTCTTAAATG-AAATTC
64 TTAA--ATGAAATTCTAGG--GGGACCTAAGCAGGTTTACTTAAATGAAAATTC
* * *
624 TAAACATAGACCTAAGCAGG-TTACTTAAACGAAGCTCTAAGCAAAGGCCTAAGCAGGTTTACTA
1 TAAACAGAGACCTAAGCAGGTTTACTTAAACGAAGCTCTAAGCAGAGGCCTAAGCAGGTTTACTT
* * *
688 AAATGGAAATTCTAAAGGAGGACCTAAGCAGGTTTACTTAAATGGCAACTT-
66 AAAT-GAAATTCT--AGGGGGACCTAAGCAGGTTTACTTAAAT-GAAAATTC
* * * * * * * *
739 TATATAGGGACCTAAGCAGGTTTACTTGACCAAAACTCTAAGCAG-GGATCCTAAACAGGTTTAC
1 TAAACAGAGACCTAAGCAGGTTTACTTAAACGAAGCTCTAAGCAGAGG--CCTAAGCAGGTTTAC
* * * * * *
803 TTAAACGGAA--C-A--GAGACCTAAGCAGGTTTGCTTAAATGGAGATTC
64 TTAAATGAAATTCTAGGGGGACCTAAGCAGGTTTACTTAAATGAAAATTC
848 TAAACA-AGGACCTAAGCAGGTTTTA-TTAAACG
1 TAAACAGA-GACCTAAGCAGG-TTTACTTAAACG
880 CAAATTCTGA
Statistics
Matches: 294, Mismatches: 57, Indels: 49
0.74 0.14 0.12
Matches are distributed among these distances:
108 4 0.01
109 42 0.14
110 4 0.01
111 1 0.00
112 1 0.00
114 65 0.22
115 48 0.16
116 76 0.26
117 30 0.10
118 23 0.08
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (113 bp):
TAAACAGAGACCTAAGCAGGTTTACTTAAACGAAGCTCTAAGCAGAGGCCTAAGCAGGTTTACTT
AAATGAAATTCTAGGGGGACCTAAGCAGGTTTACTTAAATGAAAATTC
Found at i:919 original size:50 final size:50
Alignment explanation
Indices: 841--970 Score: 163
Period size: 50 Copynumber: 2.6 Consensus size: 50
831 TGCTTAAATG
** *
841 GAGATTCTAAACAAGGACCTAAGCAGGTTTTATTAAAC-GCAAATTCTGAT
1 GAGATTCTAAACGGGGGCCTAAGCAGGTTTTATTAAACAG-AAATTCTGAT
* * *
891 GAGATTTTAAACGGGGGCCTAAGTAGGTTTTCTTAAACAGAAATTCTGAT
1 GAGATTCTAAACGGGGGCCTAAGCAGGTTTTATTAAACAGAAATTCTGAT
** *
941 GAGATTCTAAACGTAGACCTAAGCAGGTTT
1 GAGATTCTAAACGGGGGCCTAAGCAGGTTT
971 ACTAAGTTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
50 67 0.99
51 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (50 bp):
GAGATTCTAAACGGGGGCCTAAGCAGGTTTTATTAAACAGAAATTCTGAT
Done.