Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3520
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: 35368
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:5583 original size:29 final size:31
Alignment explanation
Indices: 5536--5597 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 31
5526 AAAGGATCAA
*
5536 AGATGGGGTTTAATGGATATGAAGTTTATGT
1 AGATGGGGTTTAATGGATATAAAGTTTATGT
*
5567 AGAT-GGGTTT-ATGGATATAAAGTTTTTGT
1 AGATGGGGTTTAATGGATATAAAGTTTATGT
5596 AG
1 AG
5598 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 19 0.66
30 6 0.21
31 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (31 bp):
AGATGGGGTTTAATGGATATAAAGTTTATGT
Found at i:8960 original size:23 final size:22
Alignment explanation
Indices: 8908--8960 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
8898 TCCACGTCTT
*
8908 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
8930 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
8953 TTTCTTTT
1 TTTCTTTT
8961 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:12714 original size:23 final size:22
Alignment explanation
Indices: 12662--12714 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
12652 TCCACGTCTT
*
12662 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
12684 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
12707 TTTCTTTT
1 TTTCTTTT
12715 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:16033 original size:13 final size:13
Alignment explanation
Indices: 16015--16039 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16005 TGGTCATCAT
16015 GGTGTGAACACAA
1 GGTGTGAACACAA
16028 GGTGTGAACACA
1 GGTGTGAACACA
16040 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:17225 original size:30 final size:30
Alignment explanation
Indices: 17140--17236 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
17130 TAAACTAAAA
* * *
17140 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
17170 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
17200 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
17229 ATGAGCTA
1 -TGAGCTA
17237 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:19288 original size:11 final size:11
Alignment explanation
Indices: 19272--19310 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
19262 TTGAACCATA
19272 ACCAATTTCAT
1 ACCAATTTCAT
*
19283 ACCAATTCCAT
1 ACCAATTTCAT
*
19294 ACC-ATTTCGT
1 ACCAATTTCAT
19304 ACCAATT
1 ACCAATT
19311 CCCAAATACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (11 bp):
ACCAATTTCAT
Found at i:19301 original size:21 final size:23
Alignment explanation
Indices: 19267--19312 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
19257 ACCTCTTGAA
19267 CCATAACCAATTTCATACCAATT
1 CCATAACCAATTTCATACCAATT
*
19290 CCAT-ACC-ATTTCGTACCAATT
1 CCATAACCAATTTCATACCAATT
19311 CC
1 CC
19313 CAAATACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.68
22 3 0.14
23 4 0.18
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.30
Consensus pattern (23 bp):
CCATAACCAATTTCATACCAATT
Found at i:25503 original size:30 final size:30
Alignment explanation
Indices: 25432--25514 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
25422 CTTTTGTTTC
* *
25432 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
25463 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
25492 ATTTTCTTTTTCTTTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
25515 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.12, C:0.22, G:0.01, T:0.65
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:25609 original size:21 final size:20
Alignment explanation
Indices: 25583--25631 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
25573 CTCTTGCCTC
* *
25583 TCTTTTCTTTTTATTTCGTTT
1 TCTTTTCTTCTT-TTGCGTTT
*
25604 TCTTTTTCTTCTTTTGCTTTT
1 TC-TTTTCTTCTTTTGCGTTT
25625 TCTTTTC
1 TCTTTTC
25632 ATTTCTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.21
21 10 0.42
22 9 0.38
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (20 bp):
TCTTTTCTTCTTTTGCGTTT
Found at i:25623 original size:15 final size:14
Alignment explanation
Indices: 25583--25628 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
25573 CTCTTGCCTC
*
25583 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
25598 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
25613 TCTTTTGCTTTTTCT
1 TCTTTT-CTTTTTCT
25628 T
1 T
25629 TTCATTTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 4 0.14
15 14 0.50
16 10 0.36
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.76
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:26576 original size:10 final size:10
Alignment explanation
Indices: 26553--26593 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
26543 ATTAAACACT
*
26553 TTTTTTTCATA
1 TTTTTTTGA-A
26564 TTTTTTTGAA
1 TTTTTTTGAA
26574 TTTTTTTTGAA
1 -TTTTTTTGAA
26585 TTTTTTTGA
1 TTTTTTTGA
26594 CTTGTATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.73
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:26579 original size:21 final size:21
Alignment explanation
Indices: 26552--26593 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
26542 CATTAAACAC
26552 TTTTTTTTCATATTTTTTTGAA
1 TTTTTTTTCA-ATTTTTTTGAA
*
26574 TTTTTTTTGAATTTTTTTGA
1 TTTTTTTTCAATTTTTTTGA
26594 CTTGTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (21 bp):
TTTTTTTTCAATTTTTTTGAA
Found at i:28169 original size:17 final size:18
Alignment explanation
Indices: 28124--28170 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
28114 TTAGCTCCCG
28124 AAATTTATGTGTCTAAAT
1 AAATTTATGTGTCTAAAT
*
28142 AAATTAATGTG-CTAAAT
1 AAATTTATGTGTCTAAAT
* *
28159 TAATTTGTGTGT
1 AAATTTATGTGT
28171 GCAGGTGCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (18 bp):
AAATTTATGTGTCTAAAT
Found at i:30157 original size:28 final size:28
Alignment explanation
Indices: 30094--30191 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
30084 ATATTAAGTC
*
30094 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
30121 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
30149 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
30178 CGCACACTTAGTGC
1 CGCACACTTAGTGC
30192 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Done.