Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3039
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: 52439
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:880 original size:12 final size:12
Alignment explanation
Indices: 863--892 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
853 TCAGGCTATT
863 ACACGGCCTAGC
1 ACACGGCCTAGC
*
875 ACACGGCCTGGC
1 ACACGGCCTAGC
887 ACACGG
1 ACACGG
893 GCTTGTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:1034 original size:21 final size:20
Alignment explanation
Indices: 995--1036 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
985 CTCTGTAGTA
*
995 TTGAAAAATTTTAATGTTTT
1 TTGAAAAATTTTAAGGTTTT
*
1015 TTGAAAAATGTTTAGGGTTTT
1 TTGAAAAAT-TTTAAGGTTTT
1036 T
1 T
1037 GATTTAGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (20 bp):
TTGAAAAATTTTAAGGTTTT
Found at i:16249 original size:33 final size:34
Alignment explanation
Indices: 16195--16259 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 34
16185 ATTTAAGTAT
*
16195 AAATATATTTTTTAATTTATTTTCAATTTATTAGG
1 AAATATATTTTTTAA-TTATTTTCAATATATTAGG
*
16230 AAATAT-TTATTTTAA-TATTTTTAATATATT
1 AAATATATT-TTTTAATTATTTTCAATATATT
16260 TTGTGATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 13 0.48
34 2 0.07
35 12 0.44
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (34 bp):
AAATATATTTTTTAATTATTTTCAATATATTAGG
Found at i:19370 original size:23 final size:24
Alignment explanation
Indices: 19306--19382 Score: 93
Period size: 23 Copynumber: 3.2 Consensus size: 24
19296 GGAAACTCAT
* *
19306 AAGAGCCATAATTAGGAAGTTCACA
1 AAGAGCCAT-ATCAGGAAGCTCACA
* * *
19331 AAGAACCATATCGGGAAGCTCACG
1 AAGAGCCATATCAGGAAGCTCACA
19355 AAGAGCC-TATCAGGAAGCTCACA
1 AAGAGCCATATCAGGAAGCTCACA
19378 AAGAG
1 AAGAG
19383 TCATGCAACG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 19 0.43
24 17 0.39
25 8 0.18
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (24 bp):
AAGAGCCATATCAGGAAGCTCACA
Found at i:22052 original size:3 final size:3
Alignment explanation
Indices: 22044--22069 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
22034 GCCTGTTCTA
22044 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
22070 CAACAACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:23494 original size:19 final size:20
Alignment explanation
Indices: 23472--23509 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23462 ATAATACAAT
23472 TTTAG-GACAATTAAAAGTA
1 TTTAGAGACAATTAAAAGTA
*
23491 TTTAGAGACAATTTAAAGT
1 TTTAGAGACAATTAAAAGT
23510 TTTTTTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (20 bp):
TTTAGAGACAATTAAAAGTA
Found at i:24137 original size:25 final size:25
Alignment explanation
Indices: 24103--24152 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
24093 ATGAAAGTTT
24103 GATGTATGATAAACATCTTTTACTA
1 GATGTATGATAAACATCTTTTACTA
24128 GATGTATGATAAACATCTTTTACTA
1 GATGTATGATAAACATCTTTTACTA
24153 AGTGGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (25 bp):
GATGTATGATAAACATCTTTTACTA
Found at i:25798 original size:13 final size:13
Alignment explanation
Indices: 25780--25806 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25770 AATGTGTAAG
25780 TGCTCAATTATGC
1 TGCTCAATTATGC
25793 TGCTCAATTATGC
1 TGCTCAATTATGC
25806 T
1 T
25807 ATGTAGGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (13 bp):
TGCTCAATTATGC
Found at i:26284 original size:40 final size:40
Alignment explanation
Indices: 26229--26315 Score: 174
Period size: 40 Copynumber: 2.2 Consensus size: 40
26219 ACACGGGCGT
26229 AGTAATGGATCCCAATCAAGTTGAACCTGATGATGTAGAA
1 AGTAATGGATCCCAATCAAGTTGAACCTGATGATGTAGAA
26269 AGTAATGGATCCCAATCAAGTTGAACCTGATGATGTAGAA
1 AGTAATGGATCCCAATCAAGTTGAACCTGATGATGTAGAA
26309 AGTAATG
1 AGTAATG
26316 CGTCAGCTCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (40 bp):
AGTAATGGATCCCAATCAAGTTGAACCTGATGATGTAGAA
Found at i:33047 original size:13 final size:13
Alignment explanation
Indices: 33029--33054 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33019 ATGTGTAAGG
33029 GCTCAATTATGCT
1 GCTCAATTATGCT
33042 GCTCAATTATGCT
1 GCTCAATTATGCT
33055 ATGTAGGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
GCTCAATTATGCT
Found at i:33294 original size:13 final size:13
Alignment explanation
Indices: 33276--33300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33266 CGGGCAGAGA
33276 CACGGCCGTGTGT
1 CACGGCCGTGTGT
33289 CACGGCCGTGTG
1 CACGGCCGTGTG
33301 AGGGACACGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.32, G:0.40, T:0.20
Consensus pattern (13 bp):
CACGGCCGTGTGT
Found at i:37803 original size:51 final size:51
Alignment explanation
Indices: 37748--37847 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
37738 CTACCACATA
* *
37748 ACATGTAA-CACATCCATAACGAACTCGGACCTCTTAATGAGCTCGGATGTT
1 ACATG-AATCACATCCATAACGAACTCGGACCTCTCAATGAGCCCGGATGTT
** * * *
37799 ACATGAATTGCATCCATTATGAACTTGGACCTCTCAATGAGCCCGGATG
1 ACATGAATCACATCCATAACGAACTCGGACCTCTCAATGAGCCCGGATG
37848 CTCACATCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 2 0.05
51 39 0.95
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (51 bp):
ACATGAATCACATCCATAACGAACTCGGACCTCTCAATGAGCCCGGATGTT
Done.