Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold664
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: 33494
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2080 original size:23 final size:22
Alignment explanation
Indices: 2028--2081 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
2018 TCCACGTCTT
*
2028 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
2050 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
2073 TTTCTTTTC
1 TTTCTTTTC
2082 ACTCTCAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 3 0.11
22 5 0.19
23 13 0.48
24 6 0.22
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:5855 original size:13 final size:13
Alignment explanation
Indices: 5837--5861 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5827 GTATTGATCA
5837 TGTGTTCACACCT
1 TGTGTTCACACCT
5850 TGTGTTCACACC
1 TGTGTTCACACC
5862 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:11641 original size:20 final size:20
Alignment explanation
Indices: 11599--11642 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
11589 AAAATCAGTC
* *
11599 AAAAAAGTCAAAATCGAAAA
1 AAAAAAGACAAAATCCAAAA
* *
11619 AAAAAAGACGAAATCCAATA
1 AAAAAAGACAAAATCCAAAA
11639 AAAA
1 AAAA
11643 TTAAAAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.70, C:0.11, G:0.09, T:0.09
Consensus pattern (20 bp):
AAAAAAGACAAAATCCAAAA
Found at i:14305 original size:12 final size:13
Alignment explanation
Indices: 14283--14311 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
14273 GTTGTAAAGT
14283 TTTATTTTATTTA
1 TTTATTTTATTTA
14296 TTTA-TTTATTTA
1 TTTATTTTATTTA
14308 TTTA
1 TTTA
14312 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:14978 original size:21 final size:22
Alignment explanation
Indices: 14954--14994 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
14944 TTCTATTCTC
14954 ATTTGATTC-TTACTGTTTTCA
1 ATTTGATTCTTTACTGTTTTCA
14975 ATTTGATTCTTTACTGTTTT
1 ATTTGATTCTTTACTGTTTT
14995 GGGGATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.61
Consensus pattern (22 bp):
ATTTGATTCTTTACTGTTTTCA
Found at i:15136 original size:33 final size:33
Alignment explanation
Indices: 15094--15160 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
15084 GAGTTTCTCG
15094 TGACTTGGCAACTCGATCTTGGTCCGCGCGCAA
1 TGACTTGGCAACTCGATCTTGGTCCGCGCGCAA
15127 TGACTTGGCAACTCGATCTTGGTCCGCGCGCAA
1 TGACTTGGCAACTCGATCTTGGTCCGCGCGCAA
15160 T
1 T
15161 CCCGTATCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.18, C:0.30, G:0.27, T:0.25
Consensus pattern (33 bp):
TGACTTGGCAACTCGATCTTGGTCCGCGCGCAA
Found at i:18769 original size:15 final size:15
Alignment explanation
Indices: 18749--18796 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
18739 TCAAAGATGG
18749 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
18764 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
18779 -TTTATGGATATAAA
1 GTTTATGGATATGAA
18793 GTTT
1 GTTT
18797 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:18776 original size:29 final size:29
Alignment explanation
Indices: 18743--18802 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
18733 AAGGATTCAA
* *
18743 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
18772 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
18801 AG
1 AG
18803 GTTTGTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:19821 original size:14 final size:14
Alignment explanation
Indices: 19779--19823 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
19769 TTAAAGAAGC
19779 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
19793 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
19806 AACTCATTTAATTA
1 AACTCATTAAATTA
19820 AACT
1 AACT
19824 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:22326 original size:18 final size:18
Alignment explanation
Indices: 22305--22354 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
22295 AAACTCTTTT
22305 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
22323 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
22341 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
22355 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:22360 original size:24 final size:24
Alignment explanation
Indices: 22280--22357 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
22270 CTTGTTCACA
*
22280 TTCTTTCTCTCTCTCAAACTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
* * * *
22304 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTCTCTCTCTCAATCTCTTT
* *
22328 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
22352 TTCTTT
1 TTCTTT
22358 TTCTTTCATT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59
Consensus pattern (24 bp):
TTCTTTCTCTCTCTCAATCTCTTT
Done.