Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3359
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: 30103
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Found at i:1081 original size:18 final size:17
Alignment explanation
Indices: 1048--1086 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1038 TTGTATAAAT
1048 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
1066 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
1083 TGTG
1 TGTG
1087 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:1339 original size:23 final size:23
Alignment explanation
Indices: 1312--1387 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
1302 AGTGTTATTG
1312 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
1335 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1358 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1381 ATCAGTG
1 ATCAGTG
1388 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:8387 original size:18 final size:17
Alignment explanation
Indices: 8354--8392 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
8344 TTGTATAAAT
8354 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
8372 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
8389 TGTG
1 TGTG
8393 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:8645 original size:23 final size:23
Alignment explanation
Indices: 8618--8715 Score: 155
Period size: 23 Copynumber: 4.3 Consensus size: 23
8608 AGTGTTATTG
8618 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
8641 TTCAGTGGTAGCTT-GGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
8663 CTACA-TGGTAGCTTCGGCTACAT
1 AT-CAGTGGTAGCTTCGGCTACAT
8686 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
8709 ATCAGTG
1 ATCAGTG
8716 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:15734 original size:18 final size:17
Alignment explanation
Indices: 15701--15739 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
15691 TTGTATAAAT
15701 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
15719 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
15736 TGTG
1 TGTG
15740 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:15996 original size:23 final size:23
Alignment explanation
Indices: 15969--16044 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
15959 AGTGTTATTG
15969 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
15992 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16015 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16038 ATCAGTG
1 ATCAGTG
16045 TGCACTTATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:19631 original size:19 final size:20
Alignment explanation
Indices: 19607--19646 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
19597 AACGGTGTCT
* *
19607 AATGCATATG-ATGTAATGA
1 AATGCAAATGCATGAAATGA
19626 AATGCAAATGCATGAAATGA
1 AATGCAAATGCATGAAATGA
19646 A
1 A
19647 TGCGAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.25
Consensus pattern (20 bp):
AATGCAAATGCATGAAATGA
Found at i:21665 original size:19 final size:19
Alignment explanation
Indices: 21628--21666 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
21618 TTATAAAGGC
*
21628 TTAAAAATATATACATATA
1 TTAAAAATATACACATATA
* *
21647 TTAAAAATATGCACCTATA
1 TTAAAAATATACACATATA
21666 T
1 T
21667 ATTATATGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (19 bp):
TTAAAAATATACACATATA
Found at i:23490 original size:22 final size:22
Alignment explanation
Indices: 23465--23514 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
23455 GTATACTTAA
23465 ATAACATTAAGATAGATGCAAT
1 ATAACATTAAGATAGATGCAAT
23487 ATAACATTAAGATAGATGCAAT
1 ATAACATTAAGATAGATGCAAT
*
23509 TTAACA
1 ATAACA
23515 AACAAATACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (22 bp):
ATAACATTAAGATAGATGCAAT
Done.