Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2290
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: 23053
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Found at i:2693 original size:20 final size:20
Alignment explanation
Indices: 2668--2707 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2658 TAATAATTGT
*
2668 TTTAACTACAATATTTTACA
1 TTTAACTACAATATTGTACA
2688 TTTAACTACAATATTGTACA
1 TTTAACTACAATATTGTACA
2708 GAATTGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (20 bp):
TTTAACTACAATATTGTACA
Found at i:4761 original size:2 final size:2
Alignment explanation
Indices: 4754--4783 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4744 CTCCAATTTC
4754 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4784 TTAACAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4946 original size:16 final size:16
Alignment explanation
Indices: 4925--4955 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4915 ATTTGGATGG
4925 ATTTAAATAATTTTAA
1 ATTTAAATAATTTTAA
4941 ATTTAAATAATTTTA
1 ATTTAAATAATTTTA
4956 TTTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTAAATAATTTTAA
Found at i:4953 original size:25 final size:26
Alignment explanation
Indices: 4925--4981 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
4915 ATTTGGATGG
4925 ATTTAAATAATTTT-AAATTTAAATA
1 ATTTAAATAATTTTAAAATTTAAATA
* ** *
4950 ATTT-TATTTTTTTAAAATTTAAATT
1 ATTTAAATAATTTTAAAATTTAAATA
4975 ATTTAAA
1 ATTTAAA
4982 ATTTAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 6 0.24
25 18 0.72
26 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTAAATAATTTTAAAATTTAAATA
Found at i:4968 original size:16 final size:16
Alignment explanation
Indices: 4960--5035 Score: 91
Period size: 16 Copynumber: 4.7 Consensus size: 16
4950 ATTTTATTTT
4960 TTTAAAATTTAAATTA
1 TTTAAAATTTAAATTA
4976 TTTAAAATTTAAATTA
1 TTTAAAATTTAAATTA
*
4992 TTTAAAATATAAATT-
1 TTTAAAATTTAAATTA
**
5007 TTTATGAGCTTTAAATTA
1 TTTA--AAATTTAAATTA
*
5025 TTTTAAATTTA
1 TTTAAAATTTA
5036 GTTTAATTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
15 4 0.08
16 35 0.70
17 8 0.16
18 3 0.06
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (16 bp):
TTTAAAATTTAAATTA
Found at i:5392 original size:20 final size:22
Alignment explanation
Indices: 5351--5396 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
5341 TATTCCTTAC
*
5351 TATTTTGTAATAATTATATATT
1 TATTTTGTAAAAATTATATATT
5373 TATTTT-TAAAAATT-TATATT
1 TATTTTGTAAAAATTATATATT
5393 TATT
1 TATT
5397 ATAATTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 7 0.30
22 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TATTTTGTAAAAATTATATATT
Found at i:5800 original size:16 final size:15
Alignment explanation
Indices: 5781--5814 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
5771 TTTTTTAATT
5781 TTAAAATTAAATCAAA
1 TTAAAATTAAAT-AAA
*
5797 TTAAATTTAAATAAA
1 TTAAAATTAAATAAA
5812 TTA
1 TTA
5815 TTTGATTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAAAATTAAATAAA
Found at i:5892 original size:24 final size:23
Alignment explanation
Indices: 5845--5896 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
5835 TTAAAATTTT
*
5845 ATAAA-AATATTGAAAATAAGTA
1 ATAAATAATATTAAAAATAAGTA
5867 ATAAATAATATTTAAAAATCAA-TA
1 ATAAATAATA-TTAAAAAT-AAGTA
5891 ATAAAT
1 ATAAAT
5897 TGTAATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 5 0.19
23 4 0.15
24 15 0.58
25 2 0.08
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (23 bp):
ATAAATAATATTAAAAATAAGTA
Found at i:7071 original size:95 final size:95
Alignment explanation
Indices: 6961--7199 Score: 315
Period size: 94 Copynumber: 2.5 Consensus size: 95
6951 CTTTTGGTTG
* * *
6961 AAAAATGGGGCTGGAGTATCCCTTCGAAGTATTGGGGTTGGAGTATCCCTGATGATGACAATTTA
1 AAAAATAGGGTTGGAGTATCCCTTCGAAGTAATGGGGTTGGAGTATCCCTGATGATGACAATTTA
7026 AGCAAAAATAAGAATTATCTTAACAAGTTT
66 AGCAAAAATAAGAATTATCTTAACAAGTTT
*
7056 AAAAATAGGGTTGGAGTATCCCCTCAGAAG-AATGGGGTTGGAGTAT-CCTGATGATGACAATTT
1 AAAAATAGGGTTGGAGTATCCCTTC-GAAGTAATGGGGTTGGAGTATCCCTGATGATGACAATTT
* * *
7119 AAGTAAAACTAAGAATTATCTTGACAAGTTT
65 AAGCAAAAATAAGAATTATCTTAACAAGTTT
* * * * *
7150 AAAAA-CGGAGTTAGAGTATCTCCTTAGAA-TAATAGGGTTGGAGTCTCCCT
1 AAAAATAGG-GTTGGAGTATC-CCTTCGAAGTAATGGGGTTGGAGTATCCCT
7200 AATAAAAGAA
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
93 2 0.02
94 77 0.61
95 43 0.34
96 4 0.03
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (95 bp):
AAAAATAGGGTTGGAGTATCCCTTCGAAGTAATGGGGTTGGAGTATCCCTGATGATGACAATTTA
AGCAAAAATAAGAATTATCTTAACAAGTTT
Found at i:9060 original size:13 final size:13
Alignment explanation
Indices: 9042--9067 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9032 TACACCAAGT
9042 ATGTATCGATACA
1 ATGTATCGATACA
9055 ATGTATCGATACA
1 ATGTATCGATACA
9068 CCAAAAATTG
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:9065 original size:32 final size:33
Alignment explanation
Indices: 9024--9087 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
9014 TAGCCAAAAT
**
9024 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
9056 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
9088 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:10758 original size:20 final size:22
Alignment explanation
Indices: 10733--10788 Score: 80
Period size: 20 Copynumber: 2.6 Consensus size: 22
10723 AAAAACCCAG
10733 AATGTATCGATACAA-TG-AAA
1 AATGTATCGATACAATTGTAAA
*
10753 AATGTATCGATACAATTGTAAG
1 AATGTATCGATACAATTGTAAA
*
10775 CATGTATCGATACA
1 AATGTATCGATACA
10789 TTTAGTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 15 0.47
21 2 0.06
22 15 0.47
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (22 bp):
AATGTATCGATACAATTGTAAA
Found at i:11604 original size:33 final size:31
Alignment explanation
Indices: 11558--11622 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
11548 CCATAATAAT
* *
11558 TAAAATATATAATTTATTCTAA-ATTTTATTA
1 TAAAATATATAA-TTAATATAACATTTTATTA
11589 TAAAATTATCATAATTAATATAACATTTTATTA
1 TAAAA-TAT-ATAATTAATATAACATTTTATTA
11622 T
1 T
11623 TTATTTAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 5 0.17
32 10 0.34
33 14 0.48
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (31 bp):
TAAAATATATAATTAATATAACATTTTATTA
Found at i:11661 original size:22 final size:22
Alignment explanation
Indices: 11616--11661 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
11606 ATATAACATT
* * **
11616 TTATTATTTATTTAAGAGTTTA
1 TTATTATATATTTAAAAGACTA
11638 TTATTATATATTTAAAAGACTA
1 TTATTATATATTTAAAAGACTA
11660 TT
1 TT
11662 TTAATCTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (22 bp):
TTATTATATATTTAAAAGACTA
Found at i:19652 original size:13 final size:13
Alignment explanation
Indices: 19634--19690 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
19624 CATAAAGTAT
19634 TGTATCGATACAA
1 TGTATCGATACAA
19647 TGTATCGATACATAA
1 TGTATCGATAC--AA
19662 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
19679 TGTATCGATACA
1 TGTATCGATACA
19691 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:19671 original size:19 final size:17
Alignment explanation
Indices: 19612--19713 Score: 85
Period size: 19 Copynumber: 6.1 Consensus size: 17
19602 ATTTCAACGA
19612 TTTGTATCGATACATAAAG
1 TTTGTATCGATAC--AAAG
19631 TATTGTATCGATAC-AA-
1 T-TTGTATCGATACAAAG
19647 --TGTATCGATACATAAG
1 TTTGTATCGATACA-AAG
19663 TGTTGTATCGATAC-AA-
1 T-TTGTATCGATACAAAG
19679 --TGTATCGATACATAAG
1 TTTGTATCGATACA-AAG
19695 TTTTGTATCGATACAAAG
1 -TTTGTATCGATACAAAG
19713 T
1 T
19714 AAGCTACTGC
Statistics
Matches: 70, Mismatches: 0, Indels: 28
0.71 0.00 0.29
Matches are distributed among these distances:
13 22 0.31
15 4 0.06
17 5 0.07
18 3 0.04
19 24 0.34
20 12 0.17
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (17 bp):
TTTGTATCGATACAAAG
Found at i:19674 original size:32 final size:32
Alignment explanation
Indices: 19614--19710 Score: 167
Period size: 32 Copynumber: 3.0 Consensus size: 32
19604 TTCAACGATT
19614 TGTATCGATACATAAAGTATTGTATCGATACAA
1 TGTATCGATACAT-AAGTATTGTATCGATACAA
*
19647 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
*
19679 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
19711 AGTAAGCTAC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 49 0.79
33 13 0.21
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:19770 original size:13 final size:13
Alignment explanation
Indices: 19752--19776 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19742 ATTACTCAAA
19752 TGTATCGATACAT
1 TGTATCGATACAT
19765 TGTATCGATACA
1 TGTATCGATACA
19777 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:19827 original size:52 final size:52
Alignment explanation
Indices: 19785--19913 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
19775 CACTGATCTT
*
19785 TGTATCGATACTTGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
19837 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
19889 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
19914 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Done.