Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1912
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: 12702
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:1383 original size:20 final size:20
Alignment explanation
Indices: 1353--1399 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
1343 AGGGGGAGAG
*
1353 GGGGAGAAATT-TTTGATTAAA
1 GGGG-GAAATTCTTTAATT-AA
1374 GGGGGAAATTCTTTAATTAA
1 GGGGGAAATTCTTTAATTAA
1394 GGGGGA
1 GGGGGA
1400 GAAAAATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.34, C:0.02, G:0.34, T:0.30
Consensus pattern (20 bp):
GGGGGAAATTCTTTAATTAA
Found at i:2057 original size:13 final size:13
Alignment explanation
Indices: 2036--2089 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
2026 CGATACATGG
*
2036 TACAATGTATCGA
1 TACATTGTATCGA
2049 TACATTGTATCGA
1 TACATTGTATCGA
2062 TACA-TG-AT-G-
1 TACATTGTATCGA
*
2071 GA-ATTGTATCGA
1 TACATTGTATCGA
2083 TACATTG
1 TACATTG
2090 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
8 1 0.03
9 3 0.09
10 3 0.09
11 3 0.09
12 3 0.09
13 20 0.61
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:2062 original size:33 final size:34
Alignment explanation
Indices: 2020--2089 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 34
2010 CCTACCACTG
*
2020 TTGTATCGATACATGGTACAA-TGTATCGATACA
1 TTGTATCGATACATGATACAATTGTATCGATACA
**
2053 TTGTATCGATACATGATGGAATTGTATCGATACA
1 TTGTATCGATACATGATACAATTGTATCGATACA
2087 TTG
1 TTG
2090 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 18 0.55
34 15 0.45
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (34 bp):
TTGTATCGATACATGATACAATTGTATCGATACA
Found at i:2532 original size:13 final size:13
Alignment explanation
Indices: 2514--2539 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2504 TACAGCAAGT
2514 ATGTATCGATACA
1 ATGTATCGATACA
2527 ATGTATCGATACA
1 ATGTATCGATACA
2540 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:7924 original size:15 final size:15
Alignment explanation
Indices: 7904--7934 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7894 TAAAAATGTC
*
7904 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
7919 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
7934 C
1 C
7935 TAAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:9805 original size:8 final size:8
Alignment explanation
Indices: 9792--9821 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
9782 TTGATTAAAC
9792 TTTGTGAT
1 TTTGTGAT
9800 TTTGTGAT
1 TTTGTGAT
9808 TTTGTGAT
1 TTTGTGAT
9816 TTTGTG
1 TTTGTG
9822 TTGAATGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.10, C:0.00, G:0.27, T:0.63
Consensus pattern (8 bp):
TTTGTGAT
Found at i:10042 original size:13 final size:13
Alignment explanation
Indices: 10024--10059 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
10014 CATTTTTCTT
10024 TGTATCGATACAA
1 TGTATCGATACAA
*
10037 TGTATCGATACAC
1 TGTATCGATACAA
10050 TGTATCGATA
1 TGTATCGATA
10060 TAGGGGGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:11930 original size:38 final size:40
Alignment explanation
Indices: 11888--11974 Score: 106
Period size: 42 Copynumber: 2.2 Consensus size: 40
11878 ATTAAAAAAA
*
11888 GGGGAGA-TAAG-GGGAGAATGCGTGAATTATCTATTAAG
1 GGGGAGAGTAAGAAGGAGAATGCGTGAATTATCTATTAAG
* * *
11926 GGGGAGAATGTACGAATGAGAATGCGTGAATTATTTATTAAG
1 GGGGAG-A-GTAAGAAGGAGAATGCGTGAATTATCTATTAAG
11968 GGGGAGA
1 GGGGAGA
11975 ATGTACGAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 6 0.15
39 1 0.02
41 4 0.10
42 30 0.73
ACGTcount: A:0.34, C:0.05, G:0.37, T:0.24
Consensus pattern (40 bp):
GGGGAGAGTAAGAAGGAGAATGCGTGAATTATCTATTAAG
Found at i:11947 original size:42 final size:42
Alignment explanation
Indices: 11901--11984 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
11891 GAGATAAGGG
11901 GAGAATGCGTGAATTATCTATTAAGGGGGAGAATGTACGAAT
1 GAGAATGCGTGAATTATCTATTAAGGGGGAGAATGTACGAAT
*
11943 GAGAATGCGTGAATTATTTATTAAGGGGGAGAATGTACGAAT
1 GAGAATGCGTGAATTATCTATTAAGGGGGAGAATGTACGAAT
11985 TTGTTAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.36, C:0.06, G:0.31, T:0.27
Consensus pattern (42 bp):
GAGAATGCGTGAATTATCTATTAAGGGGGAGAATGTACGAAT
Found at i:12567 original size:20 final size:19
Alignment explanation
Indices: 12513--12568 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
12503 AAACCCTTTA
*
12513 AAAGTATCGATACACAGTTC
1 AAAGTATCGATACA-TGTTC
12533 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
12553 AATGTATCGATACATG
1 AAAGTATCGATACATG
12569 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:12689 original size:13 final size:13
Alignment explanation
Indices: 12671--12696 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12661 CACAAAAAAT
12671 ATGTATCGATACA
1 ATGTATCGATACA
12684 ATGTATCGATACA
1 ATGTATCGATACA
12697 CAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Done.