Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1738
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: 37217
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:15546 original size:44 final size:44
Alignment explanation
Indices: 15432--15548 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 44
15422 TTTTAACCCA
* * ** * *
15432 CTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTG
1 CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
*
15475 CTCCGCTGTAA-TCTC-GGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGG-GATAAGATCTCTGGCTTCAATCTG
*
15519 CTCCACTGTAACTTCAGGGGGACAAGATCT
1 CTCCACTGTAACTTCAGGGGGATAAGATCT
15549 GTAATTTCCA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
42 4 0.07
43 19 0.32
44 32 0.53
45 5 0.08
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
Found at i:15788 original size:86 final size:86
Alignment explanation
Indices: 15682--15937 Score: 336
Period size: 86 Copynumber: 2.9 Consensus size: 86
15672 AATCTGTAAC
*
15682 CTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCGCTGTTAAT
1 CTTTAACCAGCTCC-ATGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAAT
15747 GCAGGAAGGCAAGATCTGCT-T
65 GCAGGAAGGCAAGATCTGCTGT
* * *
15768 CTTTAACTAGCTCCACTGCAATCGATGGATGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAAT
1 CTTTAACCAGCTCCA-TGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAAT
* **
15833 GTAGGAAGGCAAGATCTTTTGT
65 GCAGGAAGGCAAGATCTGCTGT
* * * ** *
15855 CTTCAACCAGCTCTATCACAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCA
1 CTTTAACCAGCTCCAT-GCAACCGATGGAGGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTA
15919 ATGCAGGAAGGCAAGATCT
63 ATGCAGGAAGGCAAGATCT
15938 TTAACTTCAT
Statistics
Matches: 148, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
85 1 0.01
86 82 0.55
87 28 0.19
88 37 0.25
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (86 bp):
CTTTAACCAGCTCCATGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATG
CAGGAAGGCAAGATCTGCTGT
Found at i:24592 original size:17 final size:17
Alignment explanation
Indices: 24570--24612 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
24560 TTTTTTAAAA
* *
24570 TATAAATTTTGAAATTT
1 TATAAATTTTAAAAATT
24587 TATAAATATTTAAAAATT
1 TATAAAT-TTTAAAAATT
*
24605 TAAAAATT
1 TATAAATT
24613 ATTTTGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TATAAATTTTAAAAATT
Found at i:25071 original size:40 final size:40
Alignment explanation
Indices: 25027--25107 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
25017 TTTAGGTTTT
25027 AAAAAAATATATAACTTA-TTTTTAAAA-TTTAAAATTATTA
1 AAAAAAATATATAA-TTATTTTTTAAAACTTTAAAA-TATTA
* * *
25067 AAAAATATTTATTATTATTTTTTAAAACTTTAAAATATTA
1 AAAAAAATATATAATTATTTTTTAAAACTTTAAAATATTA
25107 A
1 A
25108 TTAAATGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 3 0.08
40 26 0.72
41 7 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (40 bp):
AAAAAAATATATAATTATTTTTTAAAACTTTAAAATATTA
Found at i:25638 original size:37 final size:37
Alignment explanation
Indices: 25597--25681 Score: 107
Period size: 38 Copynumber: 2.3 Consensus size: 37
25587 TAAAACATCT
** *
25597 TAGCAAATTTCAATAAAACTTGCAGCGGACAGCATTA
1 TAGCAAATTTCAATAAAACTTGCAGCAAAAAGCATTA
* **
25634 TAGCAAATTGACCTTAAAACTTGCAGCAAAAAGCATTA
1 TAGCAAATT-TCAATAAAACTTGCAGCAAAAAGCATTA
25672 TAGCAAATTT
1 TAGCAAATTT
25682 ACCTTATAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
37 9 0.22
38 31 0.77
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (37 bp):
TAGCAAATTTCAATAAAACTTGCAGCAAAAAGCATTA
Found at i:25656 original size:38 final size:38
Alignment explanation
Indices: 25610--25692 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
25600 CAAATTTCAA
** *
25610 TAAAACTTGCAGCGGACAGCATTATAGCAAATTGACCT
1 TAAAACTTGCAGCAAAAAGCATTATAGCAAATTGACCT
*
25648 TAAAACTTGCAGCAAAAAGCATTATAGCAAATTTACCT
1 TAAAACTTGCAGCAAAAAGCATTATAGCAAATTGACCT
*
25686 TATAACT
1 TAAAACT
25693 ATGGTTTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (38 bp):
TAAAACTTGCAGCAAAAAGCATTATAGCAAATTGACCT
Found at i:31096 original size:32 final size:32
Alignment explanation
Indices: 31055--31119 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
31045 TTGCCCTTTT
31055 CAGCTAACCAGACATGGAGGGCTCGAGACAAA
1 CAGCTAACCAGACATGGAGGGCTCGAGACAAA
31087 CAGCTAACCAGACATGGAGGGCTCGAGACAAA
1 CAGCTAACCAGACATGGAGGGCTCGAGACAAA
31119 C
1 C
31120 TTGAGTTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.26, G:0.28, T:0.09
Consensus pattern (32 bp):
CAGCTAACCAGACATGGAGGGCTCGAGACAAA
Done.