Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002203.1 Corchorus olitorius cultivar O-4 contig02203, 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, 621
Length: 1036
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Found at i:200 original size:57 final size:57
Alignment explanation
Indices: 112--303 Score: 186
Period size: 57 Copynumber: 3.4 Consensus size: 57
102 CTGACTTTCG
* * * **
112 CTTGTAAGTGTCTGGCTCTGCACCCTAGTTAGCCGTTACGTCTACTTCGAGTTTTGC
1 CTTGTAAGTGTCTGGCTTTGCACCATAGTTAGCCGTTACATCTACTTCGAGCCTTGC
* * * * * * *
169 CTTGTAAGTGTCTGACTTTGAACCATAGTTAGGCTTTACATCTCCTTCGGGCCTTGG
1 CTTGTAAGTGTCTGGCTTTGCACCATAGTTAGCCGTTACATCTACTTCGAGCCTTGC
* * * * * * * * *
226 CTTGTAACTGTCTGGCTTTGCACCATAGTCAGGCTTTGCATCTCCTTCGGGCTTTGT
1 CTTGTAAGTGTCTGGCTTTGCACCATAGTTAGCCGTTACATCTACTTCGAGCCTTGC
*
283 CTCGTAAGTGTCTGGCTTTGC
1 CTTGTAAGTGTCTGGCTTTGC
304 TTCTCCTTCG
Statistics
Matches: 114, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 114 1.00
ACGTcount: A:0.14, C:0.25, G:0.23, T:0.38
Consensus pattern (57 bp):
CTTGTAAGTGTCTGGCTTTGCACCATAGTTAGCCGTTACATCTACTTCGAGCCTTGC
Found at i:302 original size:39 final size:39
Alignment explanation
Indices: 257--343 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
247 ACCATAGTCA
* * *
257 GGCTTTGCATCTCCTTCGGGCTTTGTCTCGTAAGTGTCT
1 GGCTTTGCATCTCCTTCGAGCTTTGACTCGTAACTGTCT
* *
296 GGCTTTGCTTCTCCTTCGAGCTTTGACTTGTAACTGTCT
1 GGCTTTGCATCTCCTTCGAGCTTTGACTCGTAACTGTCT
335 GGCTTTGCA
1 GGCTTTGCA
344 CCATAATTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.41
Consensus pattern (39 bp):
GGCTTTGCATCTCCTTCGAGCTTTGACTCGTAACTGTCT
Found at i:333 original size:96 final size:96
Alignment explanation
Indices: 200--400 Score: 285
Period size: 96 Copynumber: 2.1 Consensus size: 96
190 ACCATAGTTA
* * * * *
200 GGCTTTACATCTCCTTCGGGCCTTGGCTTGTAACTGTCTGGCTTTGCACCATAGTCAGGCTTTGC
1 GGCTTTGCATCTCCTTCGAGCCTTGACTTGTAACTGTCTGGCTTTGCACCATAATCAGACTTTGC
* *
265 ATCTCCTTCGGGCTTTGTCTCGTAAGTGTCT
66 ATCTCCTTCGGGCTTTGGCTCGTAACTGTCT
* * *
296 GGCTTTGCTTCTCCTTCGAGCTTTGACTTGTAACTGTCTGGCTTTGCACCATAATTAGACTTTGC
1 GGCTTTGCATCTCCTTCGAGCCTTGACTTGTAACTGTCTGGCTTTGCACCATAATCAGACTTTGC
* *
361 TTCTCCTTCGGGCTTTGGCTTGTAACTGTCT
66 ATCTCCTTCGGGCTTTGGCTCGTAACTGTCT
*
392 TGCTTTGCA
1 GGCTTTGCA
401 CCATAGTCAT
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 91 1.00
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (96 bp):
GGCTTTGCATCTCCTTCGAGCCTTGACTTGTAACTGTCTGGCTTTGCACCATAATCAGACTTTGC
ATCTCCTTCGGGCTTTGGCTCGTAACTGTCT
Found at i:359 original size:57 final size:56
Alignment explanation
Indices: 297--499 Score: 262
Period size: 57 Copynumber: 3.6 Consensus size: 56
287 TAAGTGTCTG
* *
297 GCTTTGCTTCTCCTTCGAGCTTTGACTTGTAACTGTCTGGCTTTGCACCATAATTA
1 GCTTTGCTTCTCCTTCGGGCTTTGACTTGTAACTGTCTGGCTTTGCACCATAGTTA
* * *
353 GACTTTGCTTCTCCTTCGGGCTTTGGCTTGTAACTGTCTTGCTTTGCACCATAGTCA
1 G-CTTTGCTTCTCCTTCGGGCTTTGACTTGTAACTGTCTGGCTTTGCACCATAGTTA
** * * * * *
410 TGCTTTGCTTCTCCTTTTGGCTTTGCCTTGTAAGTGTCTGGCTTTGCGCCGTGGTTA
1 -GCTTTGCTTCTCCTTCGGGCTTTGACTTGTAACTGTCTGGCTTTGCACCATAGTTA
*
467 GGCTTTGGTTCTCCTTCGGGCTTTGACTTGTAA
1 -GCTTTGCTTCTCCTTCGGGCTTTGACTTGTAA
500 TTTTGTTCAG
Statistics
Matches: 126, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
56 1 0.01
57 124 0.98
58 1 0.01
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (56 bp):
GCTTTGCTTCTCCTTCGGGCTTTGACTTGTAACTGTCTGGCTTTGCACCATAGTTA
Found at i:434 original size:153 final size:153
Alignment explanation
Indices: 156--456 Score: 449
Period size: 153 Copynumber: 2.0 Consensus size: 153
146 GTTACGTCTA
* * * * *
156 CTTCGAGTTTTGCCTTGTAAGTGTCTGACTTTGAACCATAGTTAGGCTTTACATCTCCTTCGGGC
1 CTTCGAGCTTTGACTTGTAACTGTCTGACTTTGAACCATAATTAGACTTTACATCTCCTTCGGGC
*
221 CTTGGCTTGTAACTGTCTGGCTTTGCACCATAGTCAGGCTTTGCATCTCCTTCGGGCTTTGTCTC
66 CTTGGCTTGTAACTGTCTGGCTTTGCACCATAGTCAGGCTTTGCATCTCCTTCGGGCTTTGCCTC
286 GTAAGTGTCTGGCTTTGCTTCTC
131 GTAAGTGTCTGGCTTTGCTTCTC
* * * *
309 CTTCGAGCTTTGACTTGTAACTGTCTGGCTTTGCACCATAATTAGACTTTGCTTCTCCTTCGGGC
1 CTTCGAGCTTTGACTTGTAACTGTCTGACTTTGAACCATAATTAGACTTTACATCTCCTTCGGGC
* * * * ** *
374 TTTGGCTTGTAACTGTCTTGCTTTGCACCATAGTCATGCTTTGCTTCTCCTTTTGGCTTTGCCTT
66 CTTGGCTTGTAACTGTCTGGCTTTGCACCATAGTCAGGCTTTGCATCTCCTTCGGGCTTTGCCTC
439 GTAAGTGTCTGGCTTTGC
131 GTAAGTGTCTGGCTTTGC
457 GCCGTGGTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
153 131 1.00
ACGTcount: A:0.13, C:0.25, G:0.22, T:0.41
Consensus pattern (153 bp):
CTTCGAGCTTTGACTTGTAACTGTCTGACTTTGAACCATAATTAGACTTTACATCTCCTTCGGGC
CTTGGCTTGTAACTGTCTGGCTTTGCACCATAGTCAGGCTTTGCATCTCCTTCGGGCTTTGCCTC
GTAAGTGTCTGGCTTTGCTTCTC
Found at i:913 original size:20 final size:20
Alignment explanation
Indices: 894--930 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
884 AATTAATTAT
894 TTTA-ATATTAAATTTTTTA
1 TTTATATATTAAATTTTTTA
*
913 TTTATATATTATATTTTT
1 TTTATATATTAAATTTTT
931 ACTTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATATATTAAATTTTTTA
Done.