Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1961
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: 25929
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:3603 original size:22 final size:22
Alignment explanation
Indices: 3575--3618 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3565 TTTTGAACCA
3575 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
3597 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
3619 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:6202 original size:17 final size:17
Alignment explanation
Indices: 6157--6210 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
6147 AGAAAAGAGC
* *
6157 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* *
6174 GAAAAATGAAAAAAAAA
1 GAAAATTCAAAAAAAAA
*
6191 GAAAATTCAAAAAAAGA
1 GAAAATTCAAAAAAAAA
6208 GAA
1 GAA
6211 TGAAAAGAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:9039 original size:20 final size:21
Alignment explanation
Indices: 9004--9062 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
8994 AATTAAATTA
*
9004 AATGAGCT-AGTGAGCT-AAT
1 AATGAGCTCAATGAGCTGAAT
9023 AATGAGCTCAATGAGCTGAAT
1 AATGAGCTCAATGAGCTGAAT
9044 --TGAGCTCGAATGAGCTGAA
1 AATGAGCTC-AATGAGCTGAA
9063 CCAAAAATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 15 0.42
20 18 0.50
21 3 0.08
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.24
Consensus pattern (21 bp):
AATGAGCTCAATGAGCTGAAT
Found at i:9049 original size:10 final size:9
Alignment explanation
Indices: 9023--9062 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
9013 GTGAGCTAAT
*
9023 AATGAGCTC
1 AATGAGCTG
9032 AATGAGCTG
1 AATGAGCTG
9041 AATTGAGCTCG
1 AA-TGAGCT-G
9052 AATGAGCTG
1 AATGAGCTG
9061 AA
1 AA
9063 CCAAAAATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 13 0.46
10 12 0.43
11 3 0.11
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.23
Consensus pattern (9 bp):
AATGAGCTG
Found at i:12370 original size:22 final size:22
Alignment explanation
Indices: 12342--12385 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12332 TTTCGAACCA
12342 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
12364 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
12386 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:16940 original size:11 final size:11
Alignment explanation
Indices: 16924--16980 Score: 69
Period size: 11 Copynumber: 4.7 Consensus size: 11
16914 TCGGTATTGT
16924 AAAAAAAATTC
1 AAAAAAAATTC
16935 AAAAAAAATTC
1 AAAAAAAATTC
16946 AAAAAATAATTTC
1 AAAAAA-AA-TTC
16959 AAAAAAAAAAATTC
1 ---AAAAAAAATTC
16973 AAAAAAAA
1 AAAAAAAA
16981 AAGTTTGTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
11 25 0.61
12 2 0.05
13 3 0.07
14 3 0.07
15 2 0.05
16 6 0.15
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:16942 original size:13 final size:13
Alignment explanation
Indices: 16924--16982 Score: 77
Period size: 13 Copynumber: 4.6 Consensus size: 13
16914 TCGGTATTGT
16924 AAAAAAAATTC--
1 AAAAAAAATTCAA
16935 AAAAAAAATTCAA
1 AAAAAAAATTCAA
* *
16948 AAAATAATTTCAAA
1 AAAAAAAATTC-AA
16962 AAAAAAAATTCAA
1 AAAAAAAATTCAA
16975 AAAAAAAA
1 AAAAAAAA
16983 GTTTGTATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.27
13 19 0.46
14 11 0.27
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:16966 original size:15 final size:14
Alignment explanation
Indices: 16924--16982 Score: 72
Period size: 14 Copynumber: 4.5 Consensus size: 14
16914 TCGGTATTGT
16924 AAAAAAAATTC---
1 AAAAAAAATTCAAA
16935 AAAAAAAATTC-AA
1 AAAAAAAATTCAAA
* *
16948 AAAATAATTTCAAA
1 AAAAAAAATTCAAA
16962 AAAAAAAATTCAAA
1 AAAAAAAATTCAAA
16976 AAAAAAA
1 AAAAAAA
16983 GTTTGTATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
11 11 0.27
13 9 0.22
14 21 0.51
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAAAAATTCAAA
Found at i:17041 original size:13 final size:13
Alignment explanation
Indices: 17023--17047 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17013 ATTTAGTATT
17023 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
17036 GAAGAAAAAAAA
1 GAAGAAAAAAAA
17048 TTCGGAATTA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAAAA
Found at i:17084 original size:28 final size:30
Alignment explanation
Indices: 17027--17096 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
17017 AGTATTGAAG
*
17027 AAAAAAAAAGAAGAAAAAAAATTCGGAATT
1 AAAAAAAAAGAAGAAAAAAAATTCGAAATT
17057 AAAAAAAAA-AAGAAAAAAAATT-GAAATT
1 AAAAAAAAAGAAGAAAAAAAATTCGAAATT
*
17085 GAAAAAAGAAGA
1 -AAAAAAAAAGA
17097 GTGATTGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 5 0.14
29 21 0.58
30 10 0.28
ACGTcount: A:0.74, C:0.01, G:0.13, T:0.11
Consensus pattern (30 bp):
AAAAAAAAAGAAGAAAAAAAATTCGAAATT
Found at i:18013 original size:17 final size:15
Alignment explanation
Indices: 17993--18031 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
17983 GCGAGCGAGA
17993 AAATGAACACGAAAAAG
1 AAATGAA-A-GAAAAAG
18010 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
18025 AAGATGA
1 AA-ATGA
18032 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.05, G:0.21, T:0.08
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:23021 original size:15 final size:15
Alignment explanation
Indices: 23003--23036 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22993 AAAGAAATTG
* *
23003 AAGAAAGAAGAGAAA
1 AAGAAACAAAAGAAA
23018 AAGAAACAAAAGAAA
1 AAGAAACAAAAGAAA
23033 AAGA
1 AAGA
23037 CGTGGAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAACAAAAGAAA
Done.