Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1509
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: 21807
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Found at i:305 original size:27 final size:26
Alignment explanation
Indices: 212--304 Score: 132
Period size: 27 Copynumber: 3.5 Consensus size: 26
202 GCATAGGTTG
* *
212 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
238 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
266 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
*
293 CCAGATCAGATA
1 CCAGAACAGATA
305 TTTGGTGCAT
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
26 5 0.08
27 39 0.64
28 17 0.28
ACGTcount: A:0.39, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:4131 original size:26 final size:26
Alignment explanation
Indices: 4094--4229 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
4084 TGATACAAAT
* *
4094 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* * *
4120 GGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
4146 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
4172 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
4198 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
4224 TGATAA
1 TGATAA
4230 GAATTTCATG
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 106 1.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:5942 original size:27 final size:26
Alignment explanation
Indices: 5838--5952 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
5828 TGGAGGAAGC
* *
5838 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
*
5865 GGTCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTCTGCCACAT-TATCT
5892 GTTCTGGTGGCTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* * *
5919 GTATCTGGTGACTTTGTCACATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
5946 GTTCTGG
1 GTTCTGG
5953 CAGCTATGCT
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.08
27 56 0.72
28 16 0.21
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:6047 original size:21 final size:20
Alignment explanation
Indices: 6014--6053 Score: 55
Period size: 19 Copynumber: 1.9 Consensus size: 20
6004 TTCCCCACAC
6014 GGTGTAAGGTTGG-TATGGA
1 GGTGTAAGGTTGGATATGGA
6033 GGTGTATACGGTTGGATATGG
1 GGTGTA-A-GGTTGGATATGG
6054 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.20, C:0.03, G:0.45, T:0.33
Consensus pattern (20 bp):
GGTGTAAGGTTGGATATGGA
Found at i:9583 original size:26 final size:27
Alignment explanation
Indices: 9533--9585 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
9523 CTAATTCATA
* *
9533 AAATTAAACAACAGTAAAATGAAAAAT
1 AAATTAAACAACAATAAAAAGAAAAAT
*
9560 AAATTAAAGAA-AATAAAAAGAAAAAT
1 AAATTAAACAACAATAAAAAGAAAAAT
9586 TGTAATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.72, C:0.04, G:0.08, T:0.17
Consensus pattern (27 bp):
AAATTAAACAACAATAAAAAGAAAAAT
Found at i:11106 original size:46 final size:45
Alignment explanation
Indices: 11053--11228 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 45
11043 TATTTGGGCA
11053 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
11099 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
11146 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*
11192 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11229 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 4 0.04
46 64 0.59
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:11208 original size:93 final size:93
Alignment explanation
Indices: 11049--11220 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
11039 AGGATATTTG
* *
11049 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAG
11114 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
*
11142 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCAAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAA-CTCGTTGA
11206 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
11221 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 4 0.05
93 71 0.95
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:16686 original size:45 final size:45
Alignment explanation
Indices: 16529--16702 Score: 215
Period size: 45 Copynumber: 3.8 Consensus size: 45
16519 ATTTGGGCAT
*
16529 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GC
*** * * * *
16575 CCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGAAGC
*
16620 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGC
*
16667 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
16703 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
45 37 0.34
46 35 0.32
47 36 0.33
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGC
Found at i:18104 original size:11 final size:11
Alignment explanation
Indices: 18079--18117 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
18069 GCCCGGCCCG
*
18079 AAAAATAAACGA
1 AAAAAAAAAC-A
18091 AAAAAAAAACA
1 AAAAAAAAACA
*
18102 AAAACAAAACA
1 AAAAAAAAACA
18113 AAAAA
1 AAAAA
18118 TCAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.03
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:18115 original size:18 final size:19
Alignment explanation
Indices: 18085--18124 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
18075 CCCGAAAAAT
18085 AAACGAAAAAAAAAA-CAA
1 AAACGAAAAAAAAAATCAA
18103 AAAC-AAAACAAAAAATCAA
1 AAACGAAAA-AAAAAATCAA
18122 AAA
1 AAA
18125 ATAATAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 10 0.50
19 6 0.30
ACGTcount: A:0.82, C:0.12, G:0.03, T:0.03
Consensus pattern (19 bp):
AAACGAAAAAAAAAATCAA
Found at i:19828 original size:16 final size:16
Alignment explanation
Indices: 19798--19849 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
19788 CCTTTTACTC
19798 TTTATTATATTATATAT
1 TTTATTAT-TTATATAT
19815 TTTATTATTTATAT-T
1 TTTATTATTTATATAT
*
19830 TATTATTATGTATA-AT
1 T-TTATTATTTATATAT
19846 TTTA
1 TTTA
19850 AAATTTGCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.16
16 19 0.59
17 8 0.25
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTATTATTTATATAT
Done.