Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1458
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: 16068
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2232 original size:20 final size:20
Alignment explanation
Indices: 2186--2232 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2176 AGCTCGTTTC
*
2186 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
2206 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
2226 CAGCTCA
1 CAGCTCA
2233 ATCTTAACCC
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:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:6347 original size:20 final size:20
Alignment explanation
Indices: 6324--6370 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
6314 GGGTTAAGAT
*
6324 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
6344 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
6364 TGAGCTG
1 TGAGCTG
6371 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:9188 original size:10 final size:9
Alignment explanation
Indices: 9175--9210 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
9165 ACTTTTAACT
9175 TTTTTTGTTC
1 TTTTTT-TTC
9185 TTTTTTTTAC
1 TTTTTTTT-C
9195 TTTTTTTTC
1 TTTTTTTTC
9204 TTTTTTT
1 TTTTTTT
9211 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:10770 original size:20 final size:20
Alignment explanation
Indices: 10747--10793 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
10737 GGGTTAAGAT
*
10747 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
10767 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
10787 TGAGCTG
1 TGAGCTG
10794 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:12602 original size:11 final size:12
Alignment explanation
Indices: 12586--12620 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
12576 AAAGAAATTG
12586 AAAGAAAAC-AA
1 AAAGAAAACGAA
12597 AAAGAAAACGAA
1 AAAGAAAACGAA
12609 AAAGAAAA-GAA
1 AAAGAAAACGAA
12620 A
1 A
12621 TTGCAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:12616 original size:17 final size:17
Alignment explanation
Indices: 12596--12637 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
12586 AAAGAAAACA
12596 AAAAGAAAACGAAAAAG
1 AAAAGAAAACGAAAAAG
** *
12613 AAAAGAAATTGCAAAAG
1 AAAAGAAAACGAAAAAG
12630 AAAAGAAA
1 AAAAGAAA
12638 TCAAAATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.74, C:0.05, G:0.17, T:0.05
Consensus pattern (17 bp):
AAAAGAAAACGAAAAAG
Found at i:12688 original size:12 final size:13
Alignment explanation
Indices: 12650--12693 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
12640 AAAATAGTGA
*
12650 GAGAAAAGAAAAT
1 GAGAAAAGAAATT
12663 GAAGAAAAGAAAATT
1 G-AGAAAAG-AAATT
12678 GA-AAAAGAAATT
1 GAGAAAAGAAATT
12690 GAGA
1 GAGA
12694 TTGAGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 7 0.26
13 7 0.26
14 8 0.30
15 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (13 bp):
GAGAAAAGAAATT
Found at i:12707 original size:17 final size:18
Alignment explanation
Indices: 12675--12708 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12665 AGAAAAGAAA
12675 ATTGAAAAAGAAATTGAG
1 ATTGAAAAAGAAATTGAG
*
12693 ATTGAGAAA-AAATTGA
1 ATTGAAAAAGAAATTGA
12709 AAAAGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (18 bp):
ATTGAAAAAGAAATTGAG
Found at i:14788 original size:10 final size:10
Alignment explanation
Indices: 14772--14829 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
14762 CAACTCCGAC
14772 CAGCTCAATT
1 CAGCTCAATT
* *
14782 GAGCTCATTT
1 CAGCTCAATT
14792 CAGCTCAA-T
1 CAGCTCAATT
14801 CGAGCTCAATT
1 C-AGCTCAATT
*
14812 TAGCTACAATT
1 CAGCT-CAATT
14823 CAGCTCA
1 CAGCTCA
14830 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:14795 original size:20 final size:20
Alignment explanation
Indices: 14772--14832 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
14762 CAACTCCGAC
14772 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
14792 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
14813 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
14833 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Done.