Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold713
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: 40853
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:7257 original size:15 final size:16
Alignment explanation
Indices: 7219--7255 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
7209 TAGCTTCTTC
7219 TTTTTTCACGAATTTT
1 TTTTTTCACGAATTTT
7235 TTTTTTCACGAATTTT
1 TTTTTTCACGAATTTT
7251 TTTTT
1 TTTTT
7256 CAACTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.16, C:0.11, G:0.05, T:0.68
Consensus pattern (16 bp):
TTTTTTCACGAATTTT
Found at i:7355 original size:11 final size:12
Alignment explanation
Indices: 7295--7352 Score: 116
Period size: 12 Copynumber: 4.8 Consensus size: 12
7285 ATGGAAACCA
7295 AATTTTTTTTTG
1 AATTTTTTTTTG
7307 AATTTTTTTTTG
1 AATTTTTTTTTG
7319 AATTTTTTTTTG
1 AATTTTTTTTTG
7331 AATTTTTTTTTG
1 AATTTTTTTTTG
7343 AATTTTTTTT
1 AATTTTTTTT
7353 GAAGAAACTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:8791 original size:21 final size:22
Alignment explanation
Indices: 8767--8815 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
8757 TGTTAAAACA
8767 AATGAGGAAAA-AG-AAAAAGAG
1 AATGA-GAAAAGAGCAAAAAGAG
8788 AATGA-AAAAGAGCAAAAAGAG
1 AATGAGAAAAGAGCAAAAAGAG
*
8809 ATTGAGA
1 AATGAGA
8816 GTGAAAAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 2 0.08
21 17 0.71
22 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.27, T:0.08
Consensus pattern (22 bp):
AATGAGAAAAGAGCAAAAAGAG
Found at i:14105 original size:17 final size:17
Alignment explanation
Indices: 14081--14123 Score: 79
Period size: 16 Copynumber: 2.6 Consensus size: 17
14071 TAGACCGTAT
14081 AATTTTTTTTCTTTTC-
1 AATTTTTTTTCTTTTCA
14097 AATTTTTTTTCTTTTCA
1 AATTTTTTTTCTTTTCA
14114 AATTTTTTTT
1 AATTTTTTTT
14124 GATTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 16 0.62
17 10 0.38
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
AATTTTTTTTCTTTTCA
Found at i:18520 original size:20 final size:19
Alignment explanation
Indices: 18456--18520 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
18446 AAATAAACGC
18456 GAATGAGCTTAAAATGAGCT
1 GAATGAGC-TAAAATGAGCT
*
18476 G-ATCGAGCTACAAGTGAGCT
1 GAAT-GAGCTA-AAATGAGCT
*
18496 CAATGAGCTAAAATTGAGCT
1 GAATGAGCTAAAA-TGAGCT
18516 GAATG
1 GAATG
18521 CACTTGAAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 6 0.16
20 29 0.78
21 2 0.05
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (19 bp):
GAATGAGCTAAAATGAGCT
Found at i:18845 original size:19 final size:20
Alignment explanation
Indices: 18821--18864 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
18811 TTTTCACTCA
18821 CTTTTT-TCGAGTTTTC-TTT
1 CTTTTTCTC-AGTTTTCTTTT
*
18840 CTTTTTCTCATTTTTCTTTT
1 CTTTTTCTCAGTTTTCTTTT
18860 CTTTT
1 CTTTT
18865 GTAGTTTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.05, C:0.18, G:0.05, T:0.73
Consensus pattern (20 bp):
CTTTTTCTCAGTTTTCTTTT
Found at i:26746 original size:21 final size:21
Alignment explanation
Indices: 26701--26763 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
26691 TTTGAACCAT
* *
26701 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
26723 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
26744 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
26764 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:28557 original size:30 final size:29
Alignment explanation
Indices: 28458--28559 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 29
28448 CGAGTTTAAA
*
28458 CTAAAATGAGCTAA-GTTTAGCTCGTGAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
* * * * * *
28486 CTAAAGTTGAGCTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTAAGGTTTAGCTCGTGAG
*
28516 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
28546 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
28560 GGAGTGAGCT
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
28 5 0.09
29 10 0.18
30 38 0.69
31 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:30727 original size:12 final size:12
Alignment explanation
Indices: 30712--30742 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
30702 TTCTTTTTGC
30712 TTTTCAAAGGCT
1 TTTTCAAAGGCT
30724 TTTTCAAAGGCT
1 TTTTCAAAGGCT
30736 TTTTCAA
1 TTTTCAA
30743 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:30819 original size:6 final size:6
Alignment explanation
Indices: 30803--30852 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
30793 TTTCTTTTTA
*
30803 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
30852 T
1 T
30853 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:30835 original size:37 final size:37
Alignment explanation
Indices: 30792--30862 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
30782 CTTGCCTCTC
30792 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
30829 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
30863 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:30863 original size:16 final size:16
Alignment explanation
Indices: 30788--30848 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
30778 GCCTCTTGCC
*
30788 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
30804 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
30820 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
30836 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
30849 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:31779 original size:11 final size:11
Alignment explanation
Indices: 31763--31803 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
31753 TATACTTCGA
31763 TTTTTTTTAAT
1 TTTTTTTTAAT
**
31774 TTTTTTTCGAT
1 TTTTTTTTAAT
*
31785 TTTTTTTAAAT
1 TTTTTTTTAAT
31796 TTTTTTTT
1 TTTTTTTT
31804 CGAATTTCCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTTTTTAAT
Found at i:31782 original size:21 final size:22
Alignment explanation
Indices: 31758--31802 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
31748 TTTTTTATAC
31758 TTCGATTTTTTTT-AATTTTTT
1 TTCGATTTTTTTTAAATTTTTT
31779 TTCGATTTTTTTTAAATTTTTT
1 TTCGATTTTTTTTAAATTTTTT
31801 TT
1 TT
31803 TCGAATTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (22 bp):
TTCGATTTTTTTTAAATTTTTT
Found at i:33530 original size:30 final size:30
Alignment explanation
Indices: 33496--33592 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33486 TAAACTAAAA
*
33496 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
33526 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
33556 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
33585 ATGAGCTA
1 -TGAGCTA
33593 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:36187 original size:17 final size:17
Alignment explanation
Indices: 36141--36189 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
36131 AGAAAAGAGC
*
36141 GAAAATACAAAAGAAAA
1 GAAAATACAAAAAAAAA
36158 GAAAAATGA-AAAAAAAAA
1 G-AAAAT-ACAAAAAAAAA
*
36176 GAAAATTCAAAAAA
1 GAAAATACAAAAAA
36190 GAGAATGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 12 0.44
18 14 0.52
19 1 0.04
ACGTcount: A:0.78, C:0.04, G:0.10, T:0.08
Consensus pattern (17 bp):
GAAAATACAAAAAAAAA
Found at i:40350 original size:21 final size:21
Alignment explanation
Indices: 40305--40367 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
40295 TTTGAACCAT
* *
40305 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
40327 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
40348 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
40368 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Done.