Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3081
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: 17820
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1888 original size:20 final size:20
Alignment explanation
Indices: 1865--1918 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1855 AGTTTTTCCC
*
1865 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
1885 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
1905 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
1919 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:1900 original size:30 final size:30
Alignment explanation
Indices: 1865--1938 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
1855 AGTTTTTCCC
1865 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
1895 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
1925 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
1939 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:1928 original size:20 final size:20
Alignment explanation
Indices: 1865--1929 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
1855 AGTTTTTCCC
* * * *
1865 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
1885 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
1904 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
1925 AGCTC
1 AGCTC
1930 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:3508 original size:10 final size:11
Alignment explanation
Indices: 3494--3551 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 11
3484 TAACAAAAAA
3494 AAAAAAAATTG
1 AAAAAAAATTG
3505 AAAAAAAATTGATTG
1 -AAAAAAA---ATTG
*
3520 AAAAAAAAATTC
1 -AAAAAAAATTG
*
3532 AAAAAAAAGTG
1 AAAAAAAATTG
3543 AAAAAAAAT
1 AAAAAAAAT
3552 CGAGCAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 17 0.44
12 10 0.26
15 12 0.31
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:3510 original size:11 final size:12
Alignment explanation
Indices: 3493--3550 Score: 64
Period size: 12 Copynumber: 4.7 Consensus size: 12
3483 GTAACAAAAA
3493 AAAAAAAAATTG
1 AAAAAAAAATTG
3505 AAAAAAAATTGATTG
1 AAAAAAAA---ATTG
3520 AAAAAAAAATT-
1 AAAAAAAAATTG
* *
3531 CAAAAAAAAGTG
1 AAAAAAAAATTG
3543 AAAAAAAA
1 AAAAAAAA
3551 TCGAGCAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 9 0.23
12 18 0.46
15 12 0.31
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.16
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:3510 original size:15 final size:15
Alignment explanation
Indices: 3490--3528 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3480 GGAGTAACAA
3490 AAAAAAAAAAAATTG
1 AAAAAAAAAAAATTG
***
3505 AAAAAAAATTGATTG
1 AAAAAAAAAAAATTG
3520 AAAAAAAAA
1 AAAAAAAAA
3529 TTCAAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (15 bp):
AAAAAAAAAAAATTG
Found at i:3550 original size:27 final size:27
Alignment explanation
Indices: 3489--3550 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
3479 TGGAGTAACA
* *
3489 AAAAAAAAAAAAATTGAAAAAAAATTG
1 AAAAAAAAAAAAATTCAAAAAAAAGTG
***
3516 ATTGAAAAAAAAATTCAAAAAAAAGTG
1 AAAAAAAAAAAAATTCAAAAAAAAGTG
3543 AAAAAAAA
1 AAAAAAAA
3551 TCGAGCAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.15
Consensus pattern (27 bp):
AAAAAAAAAAAAATTCAAAAAAAAGTG
Found at i:4650 original size:12 final size:12
Alignment explanation
Indices: 4624--4742 Score: 66
Period size: 12 Copynumber: 9.6 Consensus size: 12
4614 AAAGAAATTG
4624 AAAGAAAAC-AA
1 AAAGAAAACGAA
4635 AAAGAAAACGAA
1 AAAGAAAACGAA
*
4647 AAAGAAAAAGAA
1 AAAGAAAACGAA
**
4659 ATTGCAAAA-GAA
1 AAAG-AAAACGAA
*
4671 AAAGAAATC-AA
1 AAAGAAAACGAA
* *
4682 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
4694 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
4708 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
4721 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
4736 AAAGAAA
1 AAAGAAA
4743 TTGAAAGAGA
Statistics
Matches: 84, Mismatches: 13, Indels: 19
0.72 0.11 0.16
Matches are distributed among these distances:
11 20 0.24
12 28 0.33
13 10 0.12
14 18 0.21
15 8 0.10
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:4654 original size:18 final size:18
Alignment explanation
Indices: 4628--4730 Score: 73
Period size: 18 Copynumber: 5.6 Consensus size: 18
4618 AAATTGAAAG
*
4628 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
4646 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
4664 AAAAGAAAAAGAAATC-A
1 AAAAGAAAAAGAAAACGA
** * *
4681 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
4699 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
4720 AAAAGAAAAAG
1 AAAAGAAAAAG
4731 CGAAAAAAGA
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
17 11 0.17
18 34 0.53
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:4656 original size:6 final size:6
Alignment explanation
Indices: 4624--4730 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
4614 AAAGAAATTG
* * ** *
4624 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
4671 AAAG-A AATCAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
4721 AAAGAA AAAG
1 AAAGAA AAAG
4731 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 24, Indels: 9
0.69 0.23 0.08
Matches are distributed among these distances:
5 6 0.08
6 56 0.77
7 7 0.10
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:4712 original size:14 final size:13
Alignment explanation
Indices: 4691--4728 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
4681 AAAAGTGAGA
4691 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
4703 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
4718 GAAAAAGAAAA
1 GAAAAAGAAAA
4729 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:4742 original size:21 final size:21
Alignment explanation
Indices: 4692--4742 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
4682 AAAGTGAGAG
*
4692 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
4713 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
4734 AAAAAGAAA
1 AAAAAGAAA
4743 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:4782 original size:33 final size:33
Alignment explanation
Indices: 4745--4807 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
4735 AAAAGAAATT
4745 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
4778 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
4808 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:6607 original size:20 final size:20
Alignment explanation
Indices: 6584--6637 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
6574 AGTTTTTCCC
*
6584 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
6604 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
6624 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
6638 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:6619 original size:30 final size:30
Alignment explanation
Indices: 6584--6657 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
6574 AGTTTTTCCC
6584 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
6614 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
6644 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
6658 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:6647 original size:20 final size:20
Alignment explanation
Indices: 6584--6648 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
6574 AGTTTTTCCC
* * * *
6584 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
6604 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
6623 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
6644 AGCTC
1 AGCTC
6649 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:9640 original size:14 final size:15
Alignment explanation
Indices: 9621--9659 Score: 71
Period size: 14 Copynumber: 2.7 Consensus size: 15
9611 AGCTTCTTCT
9621 TTTTTTTTCACG-AA
1 TTTTTTTTCACGAAA
9635 TTTTTTTTCACGAAA
1 TTTTTTTTCACGAAA
9650 TTTTTTTTCA
1 TTTTTTTTCA
9660 ACTTGATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTTTTTTCACGAAA
Found at i:14786 original size:20 final size:20
Alignment explanation
Indices: 14763--14808 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
14753 GGGTTAAGAT
*
14763 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
14783 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
14803 TGAGCT
1 TGAGCT
14809 AGAAACAAGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Done.