Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2024
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: 36192
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:11078 original size:18 final size:18
Alignment explanation
Indices: 11032--11080 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 18
11022 ATTTTTATTT
*
11032 AAATAA-TTATAAAATAA
1 AAATAATTTATAATATAA
* *
11049 ATA-AATAT-TAATATAA
1 AAATAATTTATAATATAA
11065 AAATAATTTATAATAT
1 AAATAATTTATAATAT
11081 TTTAATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
16 11 0.46
17 7 0.29
18 6 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATAATTTATAATATAA
Found at i:12675 original size:22 final size:22
Alignment explanation
Indices: 12650--12691 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12640 GTTAAAATAA
*
12650 AAATATTATATATATTAAATTT
1 AAATATTAAATATATTAAATTT
* *
12672 AAATTTTAAATTTATTAAAT
1 AAATATTAAATATATTAAAT
12692 ATCATCTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATATTAAATATATTAAATTT
Found at i:13452 original size:20 final size:22
Alignment explanation
Indices: 13429--13469 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
13419 AATATTATTT
13429 AAAAA-TTATTTAAT-TATTAA
1 AAAAATTTATTTAATATATTAA
13449 AAAAATTTATTTAATATATTA
1 AAAAATTTATTTAATATATTA
13470 CTTTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAAATTTATTTAATATATTAA
Found at i:16768 original size:13 final size:12
Alignment explanation
Indices: 16741--16840 Score: 57
Period size: 13 Copynumber: 8.3 Consensus size: 12
16731 CTTCGAATTG
*
16741 ATAATTTTATAT
1 ATAATTATATAT
16753 ATAATTATATTAT
1 ATAATTATA-TAT
*
16766 ATAAATATAATAT
1 ATAATTAT-ATAT
*
16779 AAAATTAATATATT
1 ATAATT-ATATA-T
*
16793 AAAATT-TATAT
1 ATAATTATATAT
16804 A-AA-TATATA-
1 ATAATTATATAT
* *
16813 AT-ATTTTAAAT
1 ATAATTATATAT
*
16824 ATATTTATAATAT
1 ATAATTAT-ATAT
16837 ATAA
1 ATAA
16841 AAATATTAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
9 3 0.04
10 10 0.15
11 4 0.06
12 15 0.22
13 26 0.38
14 10 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATAATTATATAT
Found at i:16820 original size:20 final size:20
Alignment explanation
Indices: 16797--16836 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16787 TATATTAAAA
*
16797 TTTATATAAATATATAATAT
1 TTTAAATAAATATATAATAT
* *
16817 TTTAAATATATTTATAATAT
1 TTTAAATAAATATATAATAT
16837 ATAAAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAAATAAATATATAATAT
Found at i:16822 original size:27 final size:29
Alignment explanation
Indices: 16747--16849 Score: 91
Period size: 27 Copynumber: 3.8 Consensus size: 29
16737 ATTGATAATT
*
16747 TTATATATAAT-TATATTATA-TAAATATA
1 TTATATA-AATATATAATATATTAAATATA
16775 --ATATAAA-AT-TAATATATTAAA-AT-
1 TTATATAAATATATAATATATTAAATATA
*
16798 TTATATAAATATATAATATTTTAAATATA
1 TTATATAAATATATAATATATTAAATATA
*
16827 TT-TAT-AATATATAAAAATATTAA
1 TTATATAAATATAT-AATATATTAA
16850 TTTATCCGCA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
24 8 0.13
25 14 0.23
26 7 0.11
27 18 0.29
28 13 0.21
29 2 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTATATAAATATATAATATATTAAATATA
Found at i:19170 original size:18 final size:18
Alignment explanation
Indices: 19147--19184 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
19137 TGATTAATAG
19147 ACGAAAAGCCTCAATAAT
1 ACGAAAAGCCTCAATAAT
19165 ACGAAAAGCCTCAATAAT
1 ACGAAAAGCCTCAATAAT
19183 AC
1 AC
19185 AACATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.24, G:0.11, T:0.16
Consensus pattern (18 bp):
ACGAAAAGCCTCAATAAT
Found at i:23079 original size:16 final size:15
Alignment explanation
Indices: 23025--23079 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
23015 TAATTCGAGT
*
23025 TTCAAATTTAAATTA
1 TTCAAATTTAAAATA
*
23040 TTCAAATTTAAGATGA
1 TTCAAATTTAAAAT-A
*
23056 TTCGAATTTAAAATA
1 TTCAAATTTAAAATA
23071 TTCTAAATT
1 TTC-AAATT
23080 CGAAGAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
15 16 0.48
16 17 0.52
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (15 bp):
TTCAAATTTAAAATA
Found at i:23131 original size:16 final size:15
Alignment explanation
Indices: 23086--23146 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 15
23076 AATTCGAAGA
*
23086 AATTTTAATTAAAAGT
1 AATTTAAATTAAAA-T
*
23102 AACTTAAATCTAAAAT
1 AATTTAAAT-TAAAAT
23118 AATTTAAACTTAAAAT
1 AATTTAAA-TTAAAAT
*
23134 AATCTAAAATTAA
1 AAT-TTAAATTAA
23147 TCTAAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
16 28 0.74
17 10 0.26
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (15 bp):
AATTTAAATTAAAAT
Done.