Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold912
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: 22324
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1113 original size:20 final size:20
Alignment explanation
Indices: 1090--1136 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1080 GGGTTAAGAT
*
1090 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
1110 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
1130 TGAGCTG
1 TGAGCTG
1137 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:5379 original size:20 final size:20
Alignment explanation
Indices: 5356--5402 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
5346 GGGTTAAGAT
*
5356 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
5376 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
5396 TGAGCTG
1 TGAGCTG
5403 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:8322 original size:18 final size:18
Alignment explanation
Indices: 8301--8358 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
8291 CCTCACTCTT
8301 TTTTTTGATTTCTTTTTC
1 TTTTTTGATTTCTTTTTC
** *
8319 TTTTTCAATCTCTTTTTC
1 TTTTTTGATTTCTTTTTC
8337 TTTTCTTTTGATTTCTTTTTC
1 --TT-TTTTGATTTCTTTTTC
8358 T
1 T
8359 CGCTCGCACT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
18 15 0.48
19 1 0.03
20 2 0.06
21 13 0.42
ACGTcount: A:0.07, C:0.16, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTTTGATTTCTTTTTC
Found at i:9313 original size:13 final size:13
Alignment explanation
Indices: 9289--9328 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
9279 AAAAAAAAAA
9289 TTTGAA-TTTTTT
1 TTTGAATTTTTTT
9301 TTTGAATTTTTTT
1 TTTGAATTTTTTT
9314 TTTGAATTTTTTT
1 TTTGAATTTTTTT
9327 TT
1 TT
9329 CAAATTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 6 0.22
13 21 0.78
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (13 bp):
TTTGAATTTTTTT
Found at i:9335 original size:13 final size:12
Alignment explanation
Indices: 9289--9328 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
9279 AAAAAAAAAA
9289 TTTGAATTTTTT
1 TTTGAATTTTTT
9301 TTTGAATTTTTTT
1 TTTGAA-TTTTTT
9314 TTTGAATTTTTT
1 TTTGAATTTTTT
9326 TTT
1 TTT
9329 CAAATTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTGAATTTTTT
Found at i:17803 original size:11 final size:11
Alignment explanation
Indices: 17787--17822 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
17777 AAAAGAGAAG
17787 AAATTCAAAAA
1 AAATTCAAAAA
17798 AAATTCAAAAA
1 AAATTCAAAAA
*
17809 AAAATCAAAAA
1 AAATTCAAAAA
17820 AAA
1 AAA
17823 AGAAAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:17833 original size:22 final size:22
Alignment explanation
Indices: 17773--17834 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
17763 TATTGGATTT
* *
17773 AAAAAAAAGAGAAG-AAATTCA
1 AAAAAAAAGAAAAGAAAAATCA
**
17794 AAAAAAATTCAAAA-AAAAATCA
1 AAAAAAA-AGAAAAGAAAAATCA
17816 AAAAAAAAGAAAAGAAAAA
1 AAAAAAAAGAAAAGAAAAA
17835 AAAAGGTGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 11 0.34
22 21 0.66
ACGTcount: A:0.79, C:0.05, G:0.08, T:0.08
Consensus pattern (22 bp):
AAAAAAAAGAAAAGAAAAATCA
Found at i:18909 original size:6 final size:6
Alignment explanation
Indices: 18877--18984 Score: 76
Period size: 6 Copynumber: 17.7 Consensus size: 6
18867 AAAGAAATTG
* * ** *
18877 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * *
18924 AAAGAA ATCA-AA AAAGTG AAAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
18975 AAAGAA AAAG
1 AAAGAA AAAG
18985 CGAAAAAAGA
Statistics
Matches: 77, Mismatches: 20, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
5 4 0.05
6 61 0.79
7 8 0.10
8 4 0.05
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:18964 original size:14 final size:13
Alignment explanation
Indices: 18945--18982 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
18935 AAAAGTGAAA
18945 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
18957 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
18972 GAAAAAGAAAA
1 GAAAAAGAAAA
18983 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:18989 original size:26 final size:27
Alignment explanation
Indices: 18945--19005 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
18935 AAAAGTGAAA
*
18945 GAAAAAGAAAATGAAGAAAAGAA-AATT
1 GAAAAAGAAAAAGAAGAAAA-AAGAATT
*
18972 GAAAAAGAAAAAG-CGAAAAAAGAATT
1 GAAAAAGAAAAAGAAGAAAAAAGAATT
*
18998 TAAAAAGA
1 GAAAAAGA
19006 GTTTGAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 2 0.07
26 16 0.53
27 12 0.40
ACGTcount: A:0.70, C:0.02, G:0.18, T:0.10
Consensus pattern (27 bp):
GAAAAAGAAAAAGAAGAAAAAAGAATT
Done.