Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009694.1 Corchorus olitorius cultivar O-4 contig09726, 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: 21549
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2256 original size:43 final size:42
Alignment explanation
Indices: 2180--2269 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 42
2170 TTTTTATAAG
* * *
2180 GTTGTTACGAATAGTTTATGATTTTGCAGCAACTTAAAAAGTT
1 GTTGTTACGAATAGTTTATGATTTGGCAACAACTAAAAAAG-T
2223 GTTGTTACGAATA-TTGTATGCA-TTGGCAACAACTAAAAAAGT
1 GTTGTTACGAATAGTT-TATG-ATTTGGCAACAACTAAAAAAGT
2265 GTTGT
1 GTTGT
2270 GTAAAATACC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 8 0.19
43 33 0.79
44 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (42 bp):
GTTGTTACGAATAGTTTATGATTTGGCAACAACTAAAAAAGT
Found at i:2429 original size:65 final size:64
Alignment explanation
Indices: 2252--2429 Score: 302
Period size: 64 Copynumber: 2.8 Consensus size: 64
2242 GCATTGGCAA
2252 CAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATTACTTAGACAACGTTTATATTAAGTTGT
1 CAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATTACTTAGACAACGTTTATATTAAGTTGT
* *
2316 CAACTAAAAAAGTGTTGTGTAAAATTCCATCAAAATTACTTAGACAACGTTTTTATTAAGTTGT
1 CAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATTACTTAGACAACGTTTATATTAAGTTGT
* * *
2380 CAACTAAAAAAAGTGTTGTGAAAAATACCATCAAAATCACTTAGGCAACG
1 CAACT-AAAAAAGTGTTGTGTAAAATACCATCAAAATTACTTAGACAACG
2430 GCATTATAAA
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
64 67 0.63
65 40 0.37
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (64 bp):
CAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATTACTTAGACAACGTTTATATTAAGTTGT
Found at i:2545 original size:131 final size:130
Alignment explanation
Indices: 2386--2641 Score: 406
Period size: 131 Copynumber: 2.0 Consensus size: 130
2376 TTGTCAACTA
* * *
2386 AAAAAAGTGTTGTGAAAAATACCATCAAAATCACTTAGGCAACGGCATTAT-AAAGTTGTTATGA
1 AAAAAAGTGTTGTGAAAAATAACATCAAAATCACTTAGGCAACGACATTATGAAA-TTGTTACGA
*
2450 ATAGATTATGATTTCGCAACGACTTTTGTTTTTGTTGTTACGAAAAATGTAAGCATTGGCAATGA
65 ATAGATTATGATTTCGCAAAGAC-TTTGTTTTTGTTGTTACGAAAAATGTAAGCATTGGCAATGA
2515 AT
129 AT
* *
2517 AAAAAAGTGTTGTGTAAAATAACATCAAAATCACTTAGGCAACGACTTTATGAAATTGTTACGAA
1 AAAAAAGTGTTGTGAAAAATAACATCAAAATCACTTAGGCAACGACATTATGAAATTGTTACGAA
** *
2582 TAGATTATGATTTCGCAAAGACTTTGTTTTTGTTGTTGTGAAAACTGTAAGCATTGGCAA
66 TAGATTATGATTTCGCAAAGACTTTGTTTTTGTTGTTACGAAAAATGTAAGCATTGGCAA
2642 CTTAAAAAGG
Statistics
Matches: 115, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
130 35 0.30
131 77 0.67
132 3 0.03
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.33
Consensus pattern (130 bp):
AAAAAAGTGTTGTGAAAAATAACATCAAAATCACTTAGGCAACGACATTATGAAATTGTTACGAA
TAGATTATGATTTCGCAAAGACTTTGTTTTTGTTGTTACGAAAAATGTAAGCATTGGCAATGAAT
Found at i:9234 original size:36 final size:36
Alignment explanation
Indices: 9187--9258 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
9177 TTTATTCAAT
9187 TTCATGCTCTTCAAGATCTAATTCAAAAGTTAGAAA
1 TTCATGCTCTTCAAGATCTAATTCAAAAGTTAGAAA
9223 TTCATGCTCTTCAAGATCTAATTCAAAAGTTAGAAA
1 TTCATGCTCTTCAAGATCTAATTCAAAAGTTAGAAA
9259 GGAAGATCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (36 bp):
TTCATGCTCTTCAAGATCTAATTCAAAAGTTAGAAA
Found at i:12688 original size:60 final size:60
Alignment explanation
Indices: 12488--12672 Score: 289
Period size: 60 Copynumber: 3.0 Consensus size: 60
12478 CCTTAACAAT
* * *
12488 TAATATATACGAAAATGCTCAATTTAGGGCCTATTCTTTTAATTTGGTTAAATAGGCCCC
1 TAATGTATACGAAAATGCTCAATTTAGGGCCTATGCTTTTAATTTGGTTAAATAGGGCCC
12548 TAATGTATACGAAAATGCTCAATTTAGGGCTCATATGCTTTTAATTTGGTTAAATAGGGCCC
1 TAATGTATACGAAAATGCTCAATTTAGGGC-C-TATGCTTTTAATTTGGTTAAATAGGGCCC
* * * *
12610 TAATGTATACGGAAATGCTCAATTTAGGGCCCATGCTTTGAATTTGGTTAAATAGGGTCC
1 TAATGTATACGAAAATGCTCAATTTAGGGCCTATGCTTTTAATTTGGTTAAATAGGGCCC
12670 TAA
1 TAA
12673 CACATGCGAA
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
60 58 0.50
61 2 0.02
62 56 0.48
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (60 bp):
TAATGTATACGAAAATGCTCAATTTAGGGCCTATGCTTTTAATTTGGTTAAATAGGGCCC
Found at i:17163 original size:36 final size:36
Alignment explanation
Indices: 17116--17224 Score: 209
Period size: 36 Copynumber: 3.0 Consensus size: 36
17106 GCTTGTCTCG
*
17116 TTAGCCATGGATCAAATCAGCAATTCCCTTTTAGGC
1 TTAGCTATGGATCAAATCAGCAATTCCCTTTTAGGC
17152 TTAGCTATGGATCAAATCAGCAATTCCCTTTTAGGC
1 TTAGCTATGGATCAAATCAGCAATTCCCTTTTAGGC
17188 TTAGCTATGGATCAAATCAGCAATTCCCTTTTAGGC
1 TTAGCTATGGATCAAATCAGCAATTCCCTTTTAGGC
17224 T
1 T
17225 GTTTATCAAC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 72 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.33
Consensus pattern (36 bp):
TTAGCTATGGATCAAATCAGCAATTCCCTTTTAGGC
Found at i:19172 original size:4 final size:4
Alignment explanation
Indices: 19155--19188 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
19145 AAAACAGGAC
*
19155 TAGT TAGT TGGT TAGT TAGT TAGT TAGT TAGT TA
1 TAGT TAGT TAGT TAGT TAGT TAGT TAGT TAGT TA
19189 TTTCTTTCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
TAGT
Done.