Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2064
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: 29406
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:5984 original size:23 final size:22
Alignment explanation
Indices: 5958--6009 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
5948 GAAAATTGAA
*
5958 AAAAGAAGTT-GAAGAAAGAAGAG
1 AAAAGAAGTTAGAA-AAAGAA-AC
5981 AAAATG-AGTTAGAAAAAGAAAC
1 AAAA-GAAGTTAGAAAAAGAAAC
6003 AAAAGAA
1 AAAAGAA
6010 AAGATGAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 6 0.24
23 14 0.56
24 4 0.16
ACGTcount: A:0.65, C:0.02, G:0.23, T:0.10
Consensus pattern (22 bp):
AAAAGAAGTTAGAAAAAGAAAC
Found at i:12635 original size:19 final size:20
Alignment explanation
Indices: 12611--12648 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
12601 TGAGCTGGTT
12611 GGAGCTGAAA-TGAGCTAAG
1 GGAGCTGAAATTGAGCTAAG
12630 GGAGCTGAAATTGAGCTAA
1 GGAGCTGAAATTGAGCTAA
12649 AATCAGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.18
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAG
Found at i:14297 original size:10 final size:10
Alignment explanation
Indices: 14282--14330 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
14272 TTGGGTTAAG
14282 ATTGAGCTGA
1 ATTGAGCTGA
14292 ATTGAGCTCGA
1 ATTGAGCT-GA
14303 A-TGAGCTGA
1 ATTGAGCTGA
* *
14312 CTTGAGCTCA
1 ATTGAGCTGA
*
14322 AGTGAGCTG
1 ATTGAGCTG
14331 GAAACGAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:14307 original size:20 final size:20
Alignment explanation
Indices: 14284--14330 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
14274 GGGTTAAGAT
14284 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
14304 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
14324 TGAGCTG
1 TGAGCTG
14331 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:16232 original size:12 final size:12
Alignment explanation
Indices: 16199--16279 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
16189 TTTCCACTCG
16199 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
16210 AGCTCTCTTTCA
1 ATTTCTTTTTCA
16222 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
16235 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
16248 --TTCTCTTTCA
1 ATTTCTTTTTCA
16258 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
16270 ATCTCTTTTT
1 ATTTCTTTTT
16280 GCTTTTCACT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 30 0.57
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.25, G:0.01, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:16240 original size:21 final size:20
Alignment explanation
Indices: 16214--16269 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
16204 TTTTCAAGCT
16214 CTCTTTCAATTTCTTTTTCCA
1 CTCTTTCAATTTCTTTTT-CA
*
16235 CTCTTTC--TTT-TTCTT--
1 CTCTTTCAATTTCTTTTTCA
16250 CTCTTTCAATTTCTTTTTCA
1 CTCTTTCAATTTCTTTTTCA
16270 ATCTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.25
17 3 0.11
18 8 0.29
19 3 0.11
21 7 0.25
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTTCAATTTCTTTTTCA
Found at i:16332 original size:15 final size:15
Alignment explanation
Indices: 16309--16355 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
16299 TTTTGAAATC
16309 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
16324 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
16339 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
16355 T
1 T
16356 ATTCTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:17621 original size:14 final size:14
Alignment explanation
Indices: 17602--17629 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17592 TGGATAGCTC
17602 ACAATTCAAATATT
1 ACAATTCAAATATT
17616 ACAATTCAAATATT
1 ACAATTCAAATATT
17630 TCATCTATAT
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:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (14 bp):
ACAATTCAAATATT
Found at i:18961 original size:9 final size:9
Alignment explanation
Indices: 18927--18961 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
18917 TTCACTTCTT
18927 TTTTTTCTTC
1 TTTTTT-TTC
18937 TTTTTTTTAC
1 TTTTTTTT-C
18947 TTTTTTTTC
1 TTTTTTTTC
18956 TTTTTT
1 TTTTTT
18962 GCTCACTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:22079 original size:10 final size:10
Alignment explanation
Indices: 22064--22112 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
22054 TTGGGTTAAG
22064 ATTGAGCTGA
1 ATTGAGCTGA
22074 ATTGAGCTCGA
1 ATTGAGCT-GA
22085 A-TGAGCTGA
1 ATTGAGCTGA
* *
22094 CTTGAGCTCA
1 ATTGAGCTGA
*
22104 AGTGAGCTG
1 ATTGAGCTG
22113 GAAACGAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:22089 original size:20 final size:20
Alignment explanation
Indices: 22066--22112 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
22056 GGGTTAAGAT
22066 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
22086 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
22106 TGAGCTG
1 TGAGCTG
22113 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Done.