Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold420
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: 186816
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
File 2 of 2
Found at i:178230 original size:122 final size:122
Alignment explanation
Indices: 178092--178331 Score: 306
Period size: 122 Copynumber: 2.0 Consensus size: 122
178082 TCTAATTGAT
* * * **
178092 AATTAGTAAAAAAATATATTTGACTTTATGATATGAT-TTTCAATATAGAAGTAAGAGGTTAAAA
1 AATTAATAAAAAAATATATTTGACTTTATGATATGATCATT-AATATAAAAGTAAGAAATTAAAA
*
178156 ATTTAAATCTCATTAACCATAAATAAAAGTTT-AAGAAAA-ATAAAAACATATATACTTG
65 ATTCAAATCTCATTAACCATAAATAAAA-TTTAAAGAAAATATAAAAA-ATATATACTTG
* * * * *
178214 AATTAATAAAAAAATATATTTGATTTTATGGTATGATCATTAATATAAAATTTAGAAATTAAAAG
1 AATTAATAAAAAAATATATTTGACTTTATGATATGATCATTAATATAAAAGTAAGAAATTAAAAA
** *
178279 TTCAAATCTCATTAATTATAGATAAAATTTAAAGAAAATATAAAAAATATATA
66 TTCAAATCTCATTAACCATAAATAAAATTTAAAGAAAATATAAAAAATATATA
178332 AAACTGTTTT
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
121 3 0.03
122 89 0.88
123 9 0.09
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (122 bp):
AATTAATAAAAAAATATATTTGACTTTATGATATGATCATTAATATAAAAGTAAGAAATTAAAAA
TTCAAATCTCATTAACCATAAATAAAATTTAAAGAAAATATAAAAAATATATACTTG
Found at i:179909 original size:35 final size:35
Alignment explanation
Indices: 179839--179933 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 35
179829 TCAATTTATT
*
179839 TAAATAAAATTTTAAATATTTTTAAAAAAATTTAATAG
1 TAAAT-AAATTTTTAATA-TTTT-AAAAAATTTAATAG
*
179877 TAAATAAATTTTTAATATTTTAAAAAATTTAATTG
1 TAAATAAATTTTTAATATTTTAAAAAATTTAATAG
*
179912 TAAATAAA-TTTTAATATATTAA
1 TAAATAAATTTTTAATATTTTAA
179934 GTTGTTAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
34 13 0.24
35 21 0.39
36 4 0.07
37 11 0.20
38 5 0.09
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (35 bp):
TAAATAAATTTTTAATATTTTAAAAAATTTAATAG
Found at i:179924 original size:17 final size:17
Alignment explanation
Indices: 179869--179926 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
179859 TTTAAAAAAA
*
179869 TTTAATAGTAAATAAATT
1 TTTAATTGTAAATAAA-T
*
179887 TTTAATATTTTAAA-AAA-
1 TTT-A-ATTGTAAATAAAT
179904 TTTAATTGTAAATAAAT
1 TTTAATTGTAAATAAAT
179921 TTTAAT
1 TTTAAT
179927 ATATTAAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
15 7 0.21
16 4 0.12
17 9 0.27
18 3 0.09
19 4 0.12
20 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATTGTAAATAAAT
Found at i:182298 original size:17 final size:18
Alignment explanation
Indices: 182271--182306 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
182261 TATCTTTCGT
182271 TATTGTTATTATAACTGA
1 TATTGTTATTATAACTGA
*
182289 TATT-TTATTATAATTGA
1 TATTGTTATTATAACTGA
182306 T
1 T
182307 TACGATAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (18 bp):
TATTGTTATTATAACTGA
Found at i:183095 original size:28 final size:30
Alignment explanation
Indices: 183056--183124 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
183046 ATTTGTAGAT
183056 AAAAACT--AAGATG-AAAT-AAGAAGAAA
1 AAAAACTAAAAGATGAAAATGAAGAAGAAA
*
183082 AAAAA-TATAAAGATGAAAATGAAGAGGAAA
1 AAAAACTA-AAAGATGAAAATGAAGAAGAAA
183112 AAAAACTAAAAGA
1 AAAAACTAAAAGA
183125 AAGAATAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
25 1 0.03
26 5 0.14
28 6 0.17
29 4 0.11
30 18 0.50
31 2 0.06
ACGTcount: A:0.70, C:0.03, G:0.16, T:0.12
Consensus pattern (30 bp):
AAAAACTAAAAGATGAAAATGAAGAAGAAA
Found at i:183126 original size:27 final size:26
Alignment explanation
Indices: 183056--183139 Score: 64
Period size: 27 Copynumber: 3.0 Consensus size: 26
183046 ATTTGTAGAT
*
183056 AAAAACTAAGATG-AAATAAGAAGAAA
1 AAAAACTAA-AAGAAAATAAGAAGAAA
* *
183082 AAAAATATAAAGATGAAAATGAAGAGGAAA
1 AAAAA-CTAAA-A-GAAAAT-AAGAAGAAA
183112 AAAAACTAAAAGAAAGA-ATAGAAGAAA
1 AAAAACTAAAAGAAA-ATA-AGAAGAAA
183139 A
1 A
183140 CTACCTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
26 7 0.15
27 15 0.33
28 3 0.07
29 8 0.17
30 13 0.28
ACGTcount: A:0.70, C:0.02, G:0.17, T:0.11
Consensus pattern (26 bp):
AAAAACTAAAAGAAAATAAGAAGAAA
Found at i:183136 original size:30 final size:29
Alignment explanation
Indices: 183069--183137 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 29
183059 AACTAAGATG
183069 AAAT-AAGAAGAAAAAAAATATAAAGATGA
1 AAATGAAGAAGAAAAAAAATATAAAGA-GA
*
183098 AAATGAAGAGGAAAAAAAACTA-AAAGA-A
1 AAATGAAGAAGAAAAAAAA-TATAAAGAGA
183126 AGAATAGAAGAA
1 A-AAT-GAAGAA
183138 AACTACCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
28 2 0.06
29 7 0.21
30 23 0.68
31 2 0.06
ACGTcount: A:0.71, C:0.01, G:0.17, T:0.10
Consensus pattern (29 bp):
AAATGAAGAAGAAAAAAAATATAAAGAGA
Found at i:186310 original size:34 final size:33
Alignment explanation
Indices: 186272--186336 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 33
186262 TTAAATTTCA
*
186272 ATTATTAAATT-AATAATAATAATATATTTTTAAC
1 ATTATT-AATTAAATAATAA-AATAAATTTTTAAC
**
186306 ATTATTTTTTAAATAATAAAATAAATTTTTA
1 ATTATTAATTAAATAATAAAATAAATTTTTA
186337 GATCAAGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 13 0.48
34 14 0.52
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (33 bp):
ATTATTAATTAAATAATAAAATAAATTTTTAAC
Done.