Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018834.1 Corchorus olitorius cultivar O-4 contig18867, 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: 17188
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3064 original size:69 final size:69
Alignment explanation
Indices: 2969--3198 Score: 361
Period size: 69 Copynumber: 3.3 Consensus size: 69
2959 ATTTCCCGCA
* *
2969 ACAACTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCGCTCCTCAA
1 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCGCTCCTCAA
3034 CAGC
66 CAGC
* * *
3038 ACAAGTCCGGGACAGGACTTGGGTAACTCCCGCCCAGGTCTTGTCCTATAATTTGCGCTCTTCAA
1 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCGCTCCTCAA
3103 CAGC
66 CAGC
* **
3107 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTTTGCATTCCTCA
1 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTA-ATTTGCGCTCCTCA
3172 ACAGC
65 ACAGC
* *
3177 CCAAGTCCTGGACAGGACTTGG
1 ACAAGTCCGGGACAGGACTTGG
3199 CCAAGATCTG
Statistics
Matches: 147, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
69 112 0.76
70 35 0.24
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (69 bp):
ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCGCTCCTCAA
CAGC
Found at i:3209 original size:22 final size:22
Alignment explanation
Indices: 3184--3238 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
3174 AGCCCAAGTC
3184 CTGGACAGGACTTGGCCAAGAT
1 CTGGACAGGACTTGGCCAAGAT
3206 CTGGACAGGACTTGGCCAAGAT
1 CTGGACAGGACTTGGCCAAGAT
3228 CTGGACAGGAC
1 CTGGACAGGAC
3239 GTGTTCTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.27, C:0.24, G:0.33, T:0.16
Consensus pattern (22 bp):
CTGGACAGGACTTGGCCAAGAT
Found at i:10864 original size:12 final size:12
Alignment explanation
Indices: 10847--10875 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
10837 GGTTTTCACC
10847 ATATAACAAACT
1 ATATAACAAACT
10859 ATATAACAAACT
1 ATATAACAAACT
10871 ATATA
1 ATATA
10876 GCGGTTCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (12 bp):
ATATAACAAACT
Found at i:11939 original size:27 final size:27
Alignment explanation
Indices: 11873--11998 Score: 87
Period size: 27 Copynumber: 5.1 Consensus size: 27
11863 GTGGGGCGGG
*
11873 GACTTGTAGACGTAAGGCGGTGGAGGT
1 GACTTGTAGACGTAAGGTGGTGGAGGT
* * *
11900 GA--TG--GA-G-ATGGTGGCGGTGGT
1 GACTTGTAGACGTAAGGTGGTGGAGGT
*
11921 GACTTGTAGACGTAAGGTGGTGGAGGA
1 GACTTGTAGACGTAAGGTGGTGGAGGT
* * *
11948 GA--TG--GA-G-AGGGAGGTGGTGGT
1 GACTTGTAGACGTAAGGTGGTGGAGGT
*
11969 GACTTGTAGACGTAAGGTGGAGGAGGT
1 GACTTGTAGACGTAAGGTGGTGGAGGT
11996 GAC
1 GAC
11999 GGAGATGGTG
Statistics
Matches: 71, Mismatches: 16, Indels: 24
0.64 0.14 0.22
Matches are distributed among these distances:
21 24 0.34
22 2 0.03
23 8 0.11
25 8 0.11
26 2 0.03
27 27 0.38
ACGTcount: A:0.22, C:0.07, G:0.49, T:0.21
Consensus pattern (27 bp):
GACTTGTAGACGTAAGGTGGTGGAGGT
Found at i:11942 original size:24 final size:24
Alignment explanation
Indices: 11915--11988 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
11905 AGATGGTGGC
11915 GGTGGTGACTTGTAGACGTAAGGT
1 GGTGGTGACTTGTAGACGTAAGGT
* ** * **
11939 GGTGGAGGAGATGGAGA-GGGAGGT
1 GGTGG-TGACTTGTAGACGTAAGGT
11963 GGTGGTGACTTGTAGACGTAAGGT
1 GGTGGTGACTTGTAGACGTAAGGT
11987 GG
1 GG
11989 AGGAGGTGAC
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
23 7 0.19
24 22 0.61
25 7 0.19
ACGTcount: A:0.22, C:0.05, G:0.50, T:0.23
Consensus pattern (24 bp):
GGTGGTGACTTGTAGACGTAAGGT
Found at i:12318 original size:48 final size:48
Alignment explanation
Indices: 11745--12382 Score: 555
Period size: 48 Copynumber: 13.3 Consensus size: 48
11735 GTAGTAATAT
* * * * *
11745 GGAGGAGGAGGCGATGGTGAAGGAGGTGGCGGTGACTTGTAATA-ATAA
1 GGAGGAGGAGGTGATGGAGATGGTGGTGGAGGTGACTTGTAA-ACATAA
* * * * *
11793 GGAGGAGGAGGGGATGGTGATGGTGGTGGAGGAGATTTGTAAACATAG
1 GGAGGAGGAGGTGATGGAGATGGTGGTGGAGGTGACTTGTAAACATAA
* * * *
11841 GGAGGAGGAGGTGATGGAGATGGTGG-GGCGGGGACTTGTAGACGTAA
1 GGAGGAGGAGGTGATGGAGATGGTGGTGGAGGTGACTTGTAAACATAA
* * * * * *
11888 GGCGGTGGAGGTGATGGAGATGGTGGCGGTGGTGACTTGTAGACGTAA
1 GGAGGAGGAGGTGATGGAGATGGTGGTGGAGGTGACTTGTAAACATAA
* * * * * * * *
11936 GGTGGTGGAGGAGATGGAGAGGGAGGTGGTGGTGACTTGTAGACGTAA
1 GGAGGAGGAGGTGATGGAGATGGTGGTGGAGGTGACTTGTAAACATAA
* * * * * * *
11984 GGTGGAGGAGGTGACGGAGATGGTGGGGGAGGTGATTTATAGACATAG
1 GGAGGAGGAGGTGATGGAGATGGTGGTGGAGGTGACTTGTAAACATAA
* * * * * *
12032 GGAGGTGGAGGTGATGGTGAGGGAGGAGGAGGGGACTTGTAAACAT-A
1 GGAGGAGGAGGTGATGGAGATGGTGGTGGAGGTGACTTGTAAACATAA
* * * * * * *
12079 TGATGGAGGTGGTGATGGTGAAGGTGGTGGGGGTGATTTGTAAACGTAA
1 GGA-GGAGGAGGTGATGGAGATGGTGGTGGAGGTGACTTGTAAACATAA
* * * *
12128 GGAGGAGGGGGTGACGGAGATGGTGGAGGTGGTGACTTGTAAACATAA
1 GGAGGAGGAGGTGATGGAGATGGTGGTGGAGGTGACTTGTAAACATAA
* * * *
12176 GGAGGAGGAGGTGAGGGAGATGGTGGCGGAGGGGACTTGTAAACATAG
1 GGAGGAGGAGGTGATGGAGATGGTGGTGGAGGTGACTTGTAAACATAA
* * * * * * *
12224 GGAGGAGGAGGTGATGGAGACGGTGGAGGTGGTGATTTATAGACGTAA
1 GGAGGAGGAGGTGATGGAGATGGTGGTGGAGGTGACTTGTAAACATAA
* * * * * * *
12272 GGAGGAGGGGGTGATGGTGATGGTGGTGGTGGGGATTTGTAAACGTAT
1 GGAGGAGGAGGTGATGGAGATGGTGGTGGAGGTGACTTGTAAACATAA
* * *
12320 GGCGGAGGTA-GTGAAGGAGATGGTGGTGGAGGTGACTTGTAGACATAA
1 GGAGGAGG-AGGTGATGGAGATGGTGGTGGAGGTGACTTGTAAACATAA
*
12368 GGAGGAGGTGGTGAT
1 GGAGGAGGAGGTGAT
12383 TTGTATTCGG
Statistics
Matches: 481, Mismatches: 103, Indels: 12
0.81 0.17 0.02
Matches are distributed among these distances:
47 42 0.09
48 436 0.91
49 3 0.01
ACGTcount: A:0.25, C:0.05, G:0.50, T:0.21
Consensus pattern (48 bp):
GGAGGAGGAGGTGATGGAGATGGTGGTGGAGGTGACTTGTAAACATAA
Found at i:15403 original size:71 final size:72
Alignment explanation
Indices: 15299--15442 Score: 184
Period size: 71 Copynumber: 2.0 Consensus size: 72
15289 TCTTGGGTTA
* * * *
15299 TGGGATTCTAATTTTGATGCAAAGTTTTTTGCTGAAGTCTTAAGATTGTC-AAAATTGA-CTTTG
1 TGGGATTCTAATTTAGATGCAAAATTTTCTGCTGAAATCTTAAGATTGTCAAAAATTGATC-TTG
15362 AAGGTTTG
65 AAGGTTTG
** * *
15370 TGGGATTCTGGTTTAGATGCAAAATTTTCTGCTGAAATTTTTAGATTGTCAAAAATTGATCTTGA
1 TGGGATTCTAATTTAGATGCAAAATTTTCTGCTGAAATCTTAAGATTGTCAAAAATTGATCTTGA
*
15435 TGGTTTG
66 AGGTTTG
15442 T
1 T
15443 TTGCAAAAGC
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
71 42 0.68
72 19 0.31
73 1 0.02
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.43
Consensus pattern (72 bp):
TGGGATTCTAATTTAGATGCAAAATTTTCTGCTGAAATCTTAAGATTGTCAAAAATTGATCTTGA
AGGTTTG
Found at i:16067 original size:27 final size:29
Alignment explanation
Indices: 16031--16102 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 29
16021 ATCTAGGGTT
*
16031 TTAGGTGAGGCTCAAAG-AAGCTTC-AGG
1 TTAGGTGAGGCTCAAAGAAAGCTCCAAGG
* *
16058 TTAGGTGAGGCTAAAAGAAAGCTCCAAGT
1 TTAGGTGAGGCTCAAAGAAAGCTCCAAGG
*
16087 TTAGGAGAGGCTCAAA
1 TTAGGTGAGGCTCAAA
16103 AGCTATGTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 16 0.42
28 6 0.16
29 16 0.42
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.21
Consensus pattern (29 bp):
TTAGGTGAGGCTCAAAGAAAGCTCCAAGG
Found at i:17067 original size:20 final size:20
Alignment explanation
Indices: 17032--17069 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17022 TATTACTCAT
*
17032 AAGTTGGTGACGATTCAAAA
1 AAGTTGGTGACAATTCAAAA
*
17052 AAGTTGGTGATAATTCAA
1 AAGTTGGTGACAATTCAA
17070 CTCATAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (20 bp):
AAGTTGGTGACAATTCAAAA
Found at i:17152 original size:2 final size:2
Alignment explanation
Indices: 17145--17186 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
17135 TTATACATGA
* *
17145 AT AT AT AT AT AT AT AT AT AT AT AT CT AT CT 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 AT AT
17187 GT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.