Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1784
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: 31882
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:5198 original size:12 final size:12
Alignment explanation
Indices: 5178--5209 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5168 TGGAACCTGC
*
5178 TAGTGCCTACCA
1 TAGTACCTACCA
5190 TAGTACCTACCA
1 TAGTACCTACCA
5202 TAGTACCT
1 TAGTACCT
5210 TGTAGGTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.31, G:0.12, T:0.28
Consensus pattern (12 bp):
TAGTACCTACCA
Found at i:13763 original size:17 final size:17
Alignment explanation
Indices: 13732--13765 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13722 CATGGTAAAT
* *
13732 AATAAAAAGTCAACAAA
1 AATAAAAAATAAACAAA
13749 AATAAAAAATAAACAAA
1 AATAAAAAATAAACAAA
13766 TAAGAATAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (17 bp):
AATAAAAAATAAACAAA
Found at i:15792 original size:44 final size:43
Alignment explanation
Indices: 15696--16299 Score: 310
Period size: 44 Copynumber: 14.1 Consensus size: 43
15686 TTTTAACCCA
* * *
15696 CTCCACTGTAA-CTTCAGGGAGATAGGATAGTGT-CTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGAT-CTCTACTTCGATCTG
* * *
15739 CTCCGCTGTAATCTCGGGGAGATAAGATCTCTGACTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCT-ACTTCGATCTG
* * * *
15783 CTCCACTGTAA-CTTCAGGGGGATAAGATCTGCAATTCTTCGGTCTA
1 CTCCACTGTAATC-TCAGGGAGATAAGATCT-C--TACTTCGATCTG
* * * *
15829 CTCCACTGTAACCTCAGAGAGATAAGA-C-CTGA-TGCGATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCT-ACTTCGATCTG
* * * * ** *
15870 CTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGAT-CTCTACTTCGATCTG
* *
15914 CTCCACTGTAA-CTTCAGGGAGATAGGAT-TATATCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTCTA-CTTCGATCTG
* * * * * *
15957 CTCCGCTGTAACCTCAGGGAGACAAGGTCTGCAATTCTTCGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT-C--TACTTCGATCTG
* *
16003 TTCCACTGTAATCTCAGGGAGATAAGA-C-CTGA-TGT-GATCTT
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCT-ACT-TCGATCTG
* * * *
16044 CTCTACTGTAA-CTTCAGAGAGATAAGATC-CT--TT-AATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTCTACTTCGATCTG
* * * *
16083 CTCCATTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT-CTA-CTTCGATCTG
* * *
16127 CTCCGCTGTAATCTCAGGGAGATAAGATCT-GA-TGT-GATCTT
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCTACT-TCGATCTG
* * * *
16168 CTCTACTGTAA-CTTCAGAGAGATAAGATC-CT--TT-AATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTCTACTTCGATCTG
* * * *
16207 CTCCATTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT-CTA-CTTCGATCTG
* * *
16251 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCT-ACTTCGATCTG
16295 CTCCA
1 CTCCA
16300 ATGCAACCTA
Statistics
Matches: 428, Mismatches: 89, Indels: 87
0.71 0.15 0.14
Matches are distributed among these distances:
39 50 0.12
40 11 0.03
41 90 0.21
42 10 0.02
43 61 0.14
44 137 0.32
45 5 0.01
46 61 0.14
47 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (43 bp):
CTCCACTGTAATCTCAGGGAGATAAGATCTCTACTTCGATCTG
Found at i:15960 original size:174 final size:170
Alignment explanation
Indices: 15738--16157 Score: 553
Period size: 174 Copynumber: 2.4 Consensus size: 170
15728 TCTTCGATCT
* ** * * *
15738 GCTCCGCTGTAATCTCGGGGAGATAAGATCT-CTGA-CTTCAATCTGCTCCACTGTAACTTCAGG
1 GCTCCACTGTAATCTCAAGGAGATAGGAT-TACT-ATCTTCGATCTGCTCCGCTGTAACTTCAGG
*
15801 GGGATAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGA
64 GAGATAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGA
15866 TCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
129 TCTACTCTACTGTAACTTCAGAGAGATAAGATCC-----TTTAATCC
* *
15913 GCTCCACTGTAA-CTTCAGGGAGATAGGATTA-TATCTTCGATCTGCTCCGCTGTAACCTCAGGG
1 GCTCCACTGTAATC-TCAAGGAGATAGGATTACTATCTTCGATCTGCTCCGCTGTAACTTCAGGG
* * ** * * *
15976 AGACAAGGTCTGCAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGTGAT
65 AGATAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGAT
*
16041 CTTCTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
130 CTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
* *
16082 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAA-TCTCAGGG
1 GCTCCACTGTAATCTCAAGGAGATAGGATTACTATCTTCGATCTGCTCCGCTGTAACT-TCAGGG
16146 AGATAAGATCTG
65 AGATAAGATCTG
16158 ATGTGATCTT
Statistics
Matches: 218, Mismatches: 21, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
169 35 0.16
170 40 0.18
173 1 0.00
174 118 0.54
175 24 0.11
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (170 bp):
GCTCCACTGTAATCTCAAGGAGATAGGATTACTATCTTCGATCTGCTCCGCTGTAACTTCAGGGA
GATAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGATC
TACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
Found at i:16278 original size:124 final size:124
Alignment explanation
Indices: 15999--16280 Score: 537
Period size: 124 Copynumber: 2.3 Consensus size: 124
15989 AATTCTTCGG
* * *
15999 TCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGATGTGATCTTCTCTACTGTAACTTCAGAGA
16064 GATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGA
66 GATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGA
16123 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGATGTGATCTTCTCTACTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGATGTGATCTTCTCTACTGTAACTTCAGAGA
16188 GATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGA
66 GATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGA
16247 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
16281 CTGGCTTCAA
Statistics
Matches: 155, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 155 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (124 bp):
TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGATGTGATCTTCTCTACTGTAACTTCAGAGA
GATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGA
Found at i:28400 original size:17 final size:17
Alignment explanation
Indices: 28369--28402 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28359 CATGGTAAAT
* *
28369 AATAAAAAGTCAACAAA
1 AATAAAAAATAAACAAA
28386 AATAAAAAATAAACAAA
1 AATAAAAAATAAACAAA
28403 TAAGAATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (17 bp):
AATAAAAAATAAACAAA
Found at i:28874 original size:24 final size:24
Alignment explanation
Indices: 28829--28892 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 24
28819 ATAATTTTAG
* *
28829 ACATATATATTATAGTATATAAGT
1 ACATATATATAATAATATATAAGT
28853 ACATATATAT-A-AATA-ATAA-T
1 ACATATATATAATAATATATAAGT
*
28873 A-ATATA-ATAATAATAAATAA
1 ACATATATATAATAATATATAA
28893 ATGAGCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
18 2 0.06
19 6 0.17
20 6 0.17
21 8 0.22
22 3 0.08
23 1 0.03
24 10 0.28
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (24 bp):
ACATATATATAATAATATATAAGT
Found at i:28881 original size:11 final size:11
Alignment explanation
Indices: 28861--28892 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
28851 GTACATATAT
28861 ATAA-ATAATA
1 ATAATATAATA
28871 ATAATATAATA
1 ATAATATAATA
28882 ATAATA-AATA
1 ATAATATAATA
28892 A
1 A
28893 ATGAGCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAATATAATA
Done.