Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1131
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: 37282
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Found at i:225 original size:6 final size:6
Alignment explanation
Indices: 214--239 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
204 AGTTGTAAAG
214 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
240 ATTTACTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:12578 original size:22 final size:23
Alignment explanation
Indices: 12547--12591 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
12537 ATGTATATTT
*
12547 TTTTTAATTTCGAATTTTTTTTA
1 TTTTTAATTTCGAAATTTTTTTA
*
12570 TTTTT-ATTTTGAAATTTTTTTA
1 TTTTTAATTTCGAAATTTTTTTA
12592 CGTAGCTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTTTAATTTCGAAATTTTTTTA
Found at i:14306 original size:20 final size:20
Alignment explanation
Indices: 14283--14328 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
14273 CCAGCTCGAA
*
14283 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
14303 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
14323 TTAGCT
1 TTAGCT
14329 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:14310 original size:30 final size:30
Alignment explanation
Indices: 14275--14348 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
14265 AGTTTTTCCC
14275 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
14305 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
14335 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
14349 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:15926 original size:13 final size:13
Alignment explanation
Indices: 15896--15929 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
15886 TGGATTTAAA
15896 AAAAAAGAAAATTC
1 AAAAAA-AAAATTC
15910 -AAAAAAAAATTC
1 AAAAAAAAAATTC
15922 AAAAAAAA
1 AAAAAAAA
15930 TCGAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAAAAAAAATTC
Found at i:15930 original size:11 final size:12
Alignment explanation
Indices: 15897--15929 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
15887 GGATTTAAAA
15897 AAAAAGAAAATTC
1 AAAAA-AAAATTC
15910 AAAAAAAAATTC
1 AAAAAAAAATTC
15922 AAAAAAAA
1 AAAAAAAA
15930 TCGAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:15936 original size:11 final size:11
Alignment explanation
Indices: 15898--15939 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
15888 GATTTAAAAA
15898 AAAAGAAAATTC
1 AAAA-AAAATTC
15910 AAAAAAAAATTC
1 -AAAAAAAATTC
15922 AAAAAAAA-TC
1 AAAAAAAATTC
15932 GAAAAAAA
1 -AAAAAAA
15940 GAAGTGACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.07
11 15 0.54
12 7 0.25
13 4 0.14
ACGTcount: A:0.76, C:0.07, G:0.05, T:0.12
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:17029 original size:6 final size:6
Alignment explanation
Indices: 16996--17103 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
16986 AAAGAAATTG
* * * ** *
16996 AAAG-A AAACAA AAAGAA AACGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
17043 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
17094 AAAGAA AAAG
1 AAAGAA AAAG
17104 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 26, Indels: 7
0.69 0.25 0.07
Matches are distributed among these distances:
5 3 0.04
6 59 0.81
7 7 0.10
8 4 0.05
ACGTcount: A:0.70, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:17057 original size:18 final size:18
Alignment explanation
Indices: 17000--17058 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
16990 AAATTGAAAG
* *
17000 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* * *
17018 AGAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
17036 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
17054 AAAAG
1 AAAAG
17059 TGAGAGAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.71, C:0.07, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:17085 original size:14 final size:13
Alignment explanation
Indices: 17064--17101 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
17054 AAAAGTGAGA
17064 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
17076 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
17091 GAAAAAGAAAA
1 GAAAAAGAAAA
17102 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:17115 original size:21 final size:21
Alignment explanation
Indices: 17065--17115 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
17055 AAAGTGAGAG
*
17065 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
17086 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
17107 AAAAAGAAA
1 AAAAAGAAA
17116 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:17119 original size:27 final size:27
Alignment explanation
Indices: 17017--17121 Score: 77
Period size: 27 Copynumber: 3.8 Consensus size: 27
17007 AAAGAAAACG
* *
17017 AAGAAGAAAAAGAAATTGCAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*** **
17044 AAGAAATCGAAAAAGTGAGAGAAAAAGAAA
1 AAG-AA--GAAAAAAAAATTGAAAAAGAAA
* *
17074 ATGAAGAAAAGAAAATTGAAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*
17101 AAG-CGAAAAAAGAAATTGAAA
1 AAGAAGAAAAAA-AAATTGAAA
17122 GAGAGCTTGA
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
26 6 0.10
27 30 0.51
28 2 0.03
29 2 0.03
30 19 0.32
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.09
Consensus pattern (27 bp):
AAGAAGAAAAAAAAATTGAAAAAGAAA
Found at i:17155 original size:33 final size:33
Alignment explanation
Indices: 17118--17180 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
17108 AAAAGAAATT
17118 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
17151 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
17181 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:18978 original size:20 final size:20
Alignment explanation
Indices: 18955--19008 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
18945 AGTTTTTCCC
*
18955 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
18975 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
18995 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
19009 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:18990 original size:30 final size:30
Alignment explanation
Indices: 18955--19028 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
18945 AGTTTTTCCC
18955 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
18985 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
19015 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
19029 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:19018 original size:20 final size:20
Alignment explanation
Indices: 18955--19019 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
18945 AGTTTTTCCC
* * * *
18955 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
18975 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
18994 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
19015 AGCTC
1 AGCTC
19020 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Done.