Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold323
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: 39576
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2607 original size:17 final size:18
Alignment explanation
Indices: 2585--2619 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2575 ATGACACTCG
*
2585 TTTCTTT-TACACTCTCA
1 TTTCTTTATACAATCTCA
2602 TTTCTTTATACAATCTCA
1 TTTCTTTATACAATCTCA
2620 CTCTCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTCTTTATACAATCTCA
Found at i:5897 original size:50 final size:52
Alignment explanation
Indices: 5839--5954 Score: 157
Period size: 50 Copynumber: 2.3 Consensus size: 52
5829 TTAATAAAGT
* * *
5839 CATGCATTATGTAACTCTCATGTTAG-TTAAGTTTGCATCA-TAAA-TTATGA
1 CATGCATTATGTAACTCCCATGTTAGTTTAAATCTGCATCATTAAATTTA-GA
*
5889 CATGCATTATGTAACTCCCATGTTAGTTTAAATCTGCATCATTAAATTTAGT
1 CATGCATTATGTAACTCCCATGTTAGTTTAAATCTGCATCATTAAATTTAGA
*
5941 CATGCATTAAGTAA
1 CATGCATTATGTAA
5955 ATCATTTATT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 25 0.43
51 12 0.21
52 18 0.31
53 3 0.05
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (52 bp):
CATGCATTATGTAACTCCCATGTTAGTTTAAATCTGCATCATTAAATTTAGA
Found at i:12536 original size:47 final size:48
Alignment explanation
Indices: 12479--12573 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 48
12469 TTATTAGCTA
* * *
12479 CTGCTATTTAATTTGTCCAGCTGAATTTAGTCATT-AATTTGTCTTTG
1 CTGCTATTTAATTTGTCCAGCCGAATCTAGTCATTAAACTTGTCTTTG
12526 CTGCTATTTAATTTGTCCAGCCGAATCTAGTCATTAAACTTGTCTTTG
1 CTGCTATTTAATTTGTCCAGCCGAATCTAGTCATTAAACTTGTCTTTG
12574 TTGCAGCTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 33 0.75
48 11 0.25
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45
Consensus pattern (48 bp):
CTGCTATTTAATTTGTCCAGCCGAATCTAGTCATTAAACTTGTCTTTG
Found at i:22909 original size:20 final size:20
Alignment explanation
Indices: 22884--22938 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
22874 TAACACATGT
22884 ATTAAATTAAGACAAACTTA
1 ATTAAATTAAGACAAACTTA
* * *
22904 ATTAAATCAAGACATATTTA
1 ATTAAATTAAGACAAACTTA
* *
22924 ATTTAACTAAGACAA
1 ATTAAATTAAGACAA
22939 GACAACTTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (20 bp):
ATTAAATTAAGACAAACTTA
Found at i:31374 original size:12 final size:12
Alignment explanation
Indices: 31357--31381 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31347 AAAATCTGAT
31357 TTCAATGTGTAA
1 TTCAATGTGTAA
31369 TTCAATGTGTAA
1 TTCAATGTGTAA
31381 T
1 T
31382 GTGTATAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCAATGTGTAA
Found at i:32858 original size:20 final size:20
Alignment explanation
Indices: 32833--32872 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
32823 TTAGAAACTA
**
32833 AATTGAGCTTGAATGAGCTG
1 AATTGAGCTCAAATGAGCTG
32853 AATTGAGCTCAAATGAGCTG
1 AATTGAGCTCAAATGAGCTG
32873 GTTGGAGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.28
Consensus pattern (20 bp):
AATTGAGCTCAAATGAGCTG
Found at i:32880 original size:20 final size:20
Alignment explanation
Indices: 32833--32904 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
32823 TTAGAAACTA
**
32833 AATTGAGCTTGAATGAGCTG
1 AATTGAGCTAAAATGAGCTG
*
32853 AATTGAGCTCAAATGAGCTG
1 AATTGAGCTAAAATGAGCTG
* *
32873 -GTTGGAGCTAAAACGAGCT-
1 AATT-GAGCTAAAATGAGCTG
**
32892 AAAGGAGCTAAAA
1 AATTGAGCTAAAA
32905 CCGAGCTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 11 0.26
20 31 0.74
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (20 bp):
AATTGAGCTAAAATGAGCTG
Found at i:32890 original size:10 final size:10
Alignment explanation
Indices: 32877--32915 Score: 53
Period size: 11 Copynumber: 3.9 Consensus size: 10
32867 GAGCTGGTTG
32877 GAGCTAAAAC
1 GAGCTAAAAC
*
32887 GAGCT-AAAG
1 GAGCTAAAAC
32896 GAGCTAAAACC
1 GAGCTAAAA-C
32907 GAGCTAAAA
1 GAGCTAAAA
32916 TCAGCTTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.32
10 8 0.32
11 9 0.36
ACGTcount: A:0.49, C:0.18, G:0.23, T:0.10
Consensus pattern (10 bp):
GAGCTAAAAC
Found at i:32900 original size:19 final size:20
Alignment explanation
Indices: 32876--32914 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
32866 TGAGCTGGTT
32876 GGAGCTAAAA-CGAGCTAAA
1 GGAGCTAAAACCGAGCTAAA
32895 GGAGCTAAAACCGAGCTAAA
1 GGAGCTAAAACCGAGCTAAA
32915 ATCAGCTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.46, C:0.18, G:0.26, T:0.10
Consensus pattern (20 bp):
GGAGCTAAAACCGAGCTAAA
Found at i:35290 original size:25 final size:26
Alignment explanation
Indices: 35221--35290 Score: 61
Period size: 25 Copynumber: 2.7 Consensus size: 26
35211 CTTATTAATT
* * *
35221 TGTCTTTAATTAATATAAATGTTTAATT
1 TGTCTTGAATTAAT-TAAA-GTTAAATA
** *
35249 TGTCTTGTCTTAGTTAAA-TTAAATA
1 TGTCTTGAATTAATTAAAGTTAAATA
35274 TGTCTTGAATTAATTAA
1 TGTCTTGAATTAATTAA
35291 GTTTGTCTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
25 19 0.58
27 4 0.12
28 10 0.30
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.50
Consensus pattern (26 bp):
TGTCTTGAATTAATTAAAGTTAAATA
Found at i:35306 original size:20 final size:20
Alignment explanation
Indices: 35253--35307 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
35243 TTAATTTGTC
* *
35253 TTGTCTTAGTTAAATTAAAT
1 TTGTCTTAATTTAATTAAAT
* *
35273 ATGTCTTGAA-TTAATTAAGT
1 TTGTCTT-AATTTAATTAAAT
35293 TTGTCTTAATTTAAT
1 TTGTCTTAATTTAAT
35308 ACATGTGTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 25 0.89
21 1 0.04
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (20 bp):
TTGTCTTAATTTAATTAAAT
Found at i:38770 original size:19 final size:20
Alignment explanation
Indices: 38729--38785 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
38719 CAAATGAAAG
38729 AAAAGAAAAGATTGAAAACAGA
1 AAAAGAAAAG--TGAAAACAGA
*
38751 AGAGAGAAAA-TGAAAA-AGA
1 A-AAAGAAAAGTGAAAACAGA
38770 AAAAGAAAAGTGAAAA
1 AAAAGAAAAGTGAAAA
38786 TAAAAGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 7 0.23
19 10 0.32
20 6 0.19
22 1 0.03
23 7 0.23
ACGTcount: A:0.70, C:0.02, G:0.21, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGTGAAAACAGA
Found at i:38784 original size:25 final size:25
Alignment explanation
Indices: 38742--38790 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
38732 AGAAAAGATT
*
38742 GAAAACAGAAGAGAGAAAATGAAAAA
1 GAAAACAGAAAAGAGAAAAT-AAAAA
*
38768 GAAAA-AGAAAAGTGAAAATAAAA
1 GAAAACAGAAAAGAGAAAATAAAA
38791 GTCAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 12 0.57
26 5 0.24
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.06
Consensus pattern (25 bp):
GAAAACAGAAAAGAGAAAATAAAAA
Done.