Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2835
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: 65902
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:6248 original size:32 final size:32
Alignment explanation
Indices: 6207--6268 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
6197 CATCTATTTT
6207 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
6239 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
6269 ACCAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:13565 original size:13 final size:13
Alignment explanation
Indices: 13547--13574 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
13537 TGAAAATTCG
13547 TTAATGGTACATT
1 TTAATGGTACATT
13560 TTAATGGTACATT
1 TTAATGGTACATT
13573 TT
1 TT
13575 CCCCTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (13 bp):
TTAATGGTACATT
Found at i:23511 original size:21 final size:21
Alignment explanation
Indices: 23487--23530 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
23477 GAATCTTTAG
*
23487 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
23508 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
23529 TA
1 TA
23531 ATTAGGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:25782 original size:22 final size:22
Alignment explanation
Indices: 25755--25798 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
25745 CTCTCGATTT
25755 TTTTATTGCTCCTTTTCAATCA
1 TTTTATTGCTCCTTTTCAATCA
25777 TTTTATTGCTCCTTTTCAATCA
1 TTTTATTGCTCCTTTTCAATCA
25799 AAAGAGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.55
Consensus pattern (22 bp):
TTTTATTGCTCCTTTTCAATCA
Found at i:29953 original size:32 final size:32
Alignment explanation
Indices: 29917--29978 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
29907 AGCTTTTGGT
29917 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
29949 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
29979 AAAATAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Found at i:38162 original size:6 final size:6
Alignment explanation
Indices: 38151--38224 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
38141 GGGATCACTA
38151 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
*
38194 A-GAAT ACTAAT -CTAAT ACTCTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT A--CTAAT ACTAAT A
38225 GAATAGAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
4 3 0.05
5 22 0.38
6 27 0.47
8 6 0.10
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (6 bp):
ACTAAT
Found at i:38168 original size:5 final size:5
Alignment explanation
Indices: 38148--38209 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
38138 GCCGGGATCA
38148 CTAA- CTAAT ACTAAT CTAAT CTAA- CTAAT ACTAAT CTAAT ACTAAT
1 CTAAT CTAAT -CTAAT CTAAT CTAAT CTAAT -CTAAT CTAAT -CTAAT
**
38194 AGAAT ACTAAT CTAAT
1 CTAAT -CTAAT CTAAT
38210 ACTCTAATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
4 8 0.17
5 22 0.46
6 18 0.38
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.34
Consensus pattern (5 bp):
CTAAT
Found at i:38186 original size:11 final size:11
Alignment explanation
Indices: 38147--38223 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
38137 AGCCGGGATC
38147 ACTAA-CTAAT
1 ACTAATCTAAT
38157 ACTAATCTAAT
1 ACTAATCTAAT
38168 -CTAA-CTAAT
1 ACTAATCTAAT
38177 ACTAATCTAAT
1 ACTAATCTAAT
**
38188 ACTAATAGAAT
1 ACTAATCTAAT
38199 ACTAATCTAAT
1 ACTAATCTAAT
38210 AC---TCTAAT
1 ACTAATCTAAT
38218 ACTAAT
1 ACTAAT
38224 AGAATAGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
8 8 0.14
9 5 0.09
10 13 0.23
11 31 0.54
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (11 bp):
ACTAATCTAAT
Found at i:38202 original size:22 final size:21
Alignment explanation
Indices: 38147--38223 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
38137 AGCCGGGATC
38147 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
38168 -CTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
38188 ACTAA-TAGAATACTAATCTAAT
1 ACTAACT--AATACTAATCTAAT
38210 ACT--CTAATACTAAT
1 ACTAACTAATACTAAT
38224 AGAATAGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.17
20 21 0.40
21 5 0.10
22 17 0.33
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (21 bp):
ACTAACTAATACTAATCTAAT
Found at i:38238 original size:14 final size:14
Alignment explanation
Indices: 38221--38248 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38211 CTCTAATACT
38221 AATAGAATAGAAAA
1 AATAGAATAGAAAA
38235 AATAGAATAGAAAA
1 AATAGAATAGAAAA
38249 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:46582 original size:18 final size:18
Alignment explanation
Indices: 46503--46596 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
46493 CAAGGTCACG
*
46503 ATCAATAGCGTCACTATC
1 ATCAATATCGTCACTATC
* *
46521 ATCAATAGCGTCACTAGC
1 ATCAATATCGTCACTATC
*
46539 ATCAATATCGTCACTAGC
1 ATCAATATCGTCACTATC
46557 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTATC
46575 ATCAATATCG--A-TATC
1 ATCAATATCGTCACTATC
46590 ATCAATA
1 ATCAATA
46597 AGAAAACCTT
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29
Consensus pattern (18 bp):
ATCAATATCGTCACTATC
Found at i:46583 original size:9 final size:9
Alignment explanation
Indices: 46503--46583 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
46493 CAAGGTCACG
*
46503 ATCAATAGC
1 ATCAATATC
* *
46512 GTCACTATC
1 ATCAATATC
*
46521 ATCAATAGC
1 ATCAATATC
* * *
46530 GTCACTAGC
1 ATCAATATC
46539 ATCAATATC
1 ATCAATATC
* * *
46548 GTCACTAGC
1 ATCAATATC
46557 ATCAATATC
1 ATCAATATC
* *
46566 GTCACTATC
1 ATCAATATC
46575 ATCAATATC
1 ATCAATATC
46584 GATATCATCA
Statistics
Matches: 51, Mismatches: 21, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (9 bp):
ATCAATATC
Found at i:48986 original size:21 final size:21
Alignment explanation
Indices: 48956--49044 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
48946 CTCACAAAGA
* *
48956 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
48976 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
48997 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
49018 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
49042 AAA
1 AAA
49045 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:49037 original size:24 final size:21
Alignment explanation
Indices: 48956--49024 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
48946 CTCACAAAGA
* * *
48956 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
48976 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
48997 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
49018 AAAAAGA
1 AAAAAGA
49025 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:53201 original size:14 final size:14
Alignment explanation
Indices: 53182--53210 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
53172 TACAATATAT
53182 ATAAGAATTATACG
1 ATAAGAATTATACG
53196 ATAAGAATTATACG
1 ATAAGAATTATACG
53210 A
1 A
53211 ATCCATCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:55991 original size:13 final size:15
Alignment explanation
Indices: 55966--56005 Score: 66
Period size: 13 Copynumber: 2.8 Consensus size: 15
55956 TATTTTATTA
55966 AATAAATATTAAATT
1 AATAAATATTAAATT
55981 AA-AAA-ATTAAATT
1 AATAAATATTAAATT
55994 AATAAATATTAA
1 AATAAATATTAA
56006 TAAATTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.43
14 6 0.26
15 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAAATATTAAATT
Done.