Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1877
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: 187756
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 2
Found at i:172877 original size:17 final size:17
Alignment explanation
Indices: 172828--172879 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
172818 TAACTATTTT
172828 AATTTATATA-ATATAA
1 AATTTATATATATATAA
*
172844 ATTATTAT-TATAT-TAA
1 AAT-TTATATATATATAA
172860 AATTTATATATATATAA
1 AATTTATATATATATAA
172877 AAT
1 AAT
172880 ATTTCAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 4 0.13
16 14 0.47
17 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTATATATATATAA
Found at i:172892 original size:34 final size:32
Alignment explanation
Indices: 172793--172882 Score: 85
Period size: 32 Copynumber: 2.8 Consensus size: 32
172783 AAATATATTA
* *
172793 TAAAATATAATATAACAT-AAATA-TATAACTAT
1 TAAAAT-TTATATAATATAAAATATTATAA-TAT
** * *
172825 TTTAATTTATATAATATAAATTATTATTATAT
1 TAAAATTTATATAATATAAAATATTATAATAT
172857 TAAAATTTATATATATATAAAATATT
1 TAAAATTTATATA-ATATAAAATATT
172883 TCAAATATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
31 9 0.20
32 22 0.48
33 15 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (32 bp):
TAAAATTTATATAATATAAAATATTATAATAT
Found at i:173149 original size:13 final size:13
Alignment explanation
Indices: 173133--173157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
173123 ATTTAAAATT
173133 ATAAATTAATTAC
1 ATAAATTAATTAC
173146 ATAAATTAATTA
1 ATAAATTAATTA
173158 AATTTTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAAATTAATTAC
Found at i:173856 original size:13 final size:13
Alignment explanation
Indices: 173838--173864 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
173828 ACTATTTACT
173838 TAAAAATAAAAAA
1 TAAAAATAAAAAA
173851 TAAAAATAAAAAA
1 TAAAAATAAAAAA
173864 T
1 T
173865 TGGTTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:176240 original size:2 final size:2
Alignment explanation
Indices: 176233--176269 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
176223 CTTGTAACAT
176233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
176270 TCATATACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:177564 original size:22 final size:23
Alignment explanation
Indices: 177536--177583 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 23
177526 ATAATTTAAA
177536 AATTTTAAAA-ATTTTATTATTT
1 AATTTTAAAATATTTTATTATTT
177558 AATTTTAAAATTTATTTTATTATTT
1 AATTTTAAAA--TATTTTATTATTT
177583 A
1 A
177584 TTATATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.43
25 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
AATTTTAAAATATTTTATTATTT
Found at i:177582 original size:12 final size:12
Alignment explanation
Indices: 177546--177592 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
177536 AATTTTAAAA
177546 ATTTTATTATTT
1 ATTTTATTATTT
**
177558 AATTTTAAAATTT
1 -ATTTTATTATTT
177571 ATTTTATTATTT
1 ATTTTATTATTT
*
177583 ATTATATTAT
1 ATTTTATTAT
177593 ATAAAAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATTTTATTATTT
Found at i:177950 original size:95 final size:98
Alignment explanation
Indices: 177831--178025 Score: 290
Period size: 95 Copynumber: 2.0 Consensus size: 98
177821 ATTGATGTTT
* *
177831 ACATAATTTTATATACCTAATTTTTTCTATGATTGATGATTTGATAAATA-TAAATAAAAAGAAT
1 ACATAATTTTATATACCTAATTTTTTCTATAATTGATGATTTGACAAATACTAAA-AAAAAGAAT
*
177895 AAAGAAATGA-C-C-TAGGTTATTATTGAGTATA
65 AAAGAAATGACCTCATAAGTTATTATTGAGTATA
* * *
177926 ACATTATTTTATATGCCTAATTTTTTCTATAATTGATGATTTGACAAATACTAAACAAAAGAATA
1 ACATAATTTTATATACCTAATTTTTTCTATAATTGATGATTTGACAAATACTAAAAAAAAGAATA
177991 AAGAAATGACCTCTATAAGTTATTATTGAGTATA
66 AAGAAATGACCTC-ATAAGTTATTATTGAGTATA
178025 A
1 A
178026 AACTTATCAT
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
95 64 0.72
96 5 0.06
97 1 0.01
99 19 0.21
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (98 bp):
ACATAATTTTATATACCTAATTTTTTCTATAATTGATGATTTGACAAATACTAAAAAAAAGAATA
AAGAAATGACCTCATAAGTTATTATTGAGTATA
Found at i:178736 original size:22 final size:21
Alignment explanation
Indices: 178704--178750 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
178694 ATTTAAAATA
* *
178704 ATTT-AAAATTTTATTTTACT
1 ATTTAAAAATTTTATATTAAT
178724 ATTTAAAATATTTTATATTAAT
1 ATTTAAAA-ATTTTATATTAAT
178746 ATTTA
1 ATTTA
178751 TAATTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 3 0.13
22 16 0.70
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTAAAAATTTTATATTAAT
Found at i:179837 original size:22 final size:23
Alignment explanation
Indices: 179807--179850 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
179797 AAATTTTTAT
179807 TTATATTATATATAT-AATATAC
1 TTATATTATATATATAAATATAC
* *
179829 TTATGTTATATATCTAAATATA
1 TTATATTATATATATAAATATA
179851 TAATATACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (23 bp):
TTATATTATATATATAAATATAC
Found at i:179851 original size:30 final size:29
Alignment explanation
Indices: 179808--179876 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 29
179798 AATTTTTATT
* *
179808 TATATTATATATATAATATACTTATGTTA
1 TATATTAAATATATAATATACTTAAGTTA
179837 TATATCTAAATATATAATATACTTAAGTTA
1 TATAT-TAAATATATAATATACTTAAGTTA
*
179867 TATATAAAAT
1 TATATTAAAT
179877 TATCGAGCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 9 0.25
30 27 0.75
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (29 bp):
TATATTAAATATATAATATACTTAAGTTA
Found at i:180161 original size:33 final size:35
Alignment explanation
Indices: 180116--180187 Score: 112
Period size: 33 Copynumber: 2.1 Consensus size: 35
180106 ATAAGAAGAG
180116 AAATTATAATTTAAAATAGTAA-TTTTTTTAAA-A
1 AAATTATAATTTAAAATAGTAATTTTTTTTAAACA
* *
180149 AAATTATCATTTAAAATGGTAATTTTTTTTAAACA
1 AAATTATAATTTAAAATAGTAATTTTTTTTAAACA
180184 AAAT
1 AAAT
180188 AAAATTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 20 0.57
34 10 0.29
35 5 0.14
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (35 bp):
AAATTATAATTTAAAATAGTAATTTTTTTTAAACA
Found at i:180196 original size:33 final size:33
Alignment explanation
Indices: 180116--180197 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
180106 ATAAGAAGAG
*
180116 AAATTATAATTTAAAATAGTAATTTTTTTAAAA
1 AAATTATAAATTAAAATAGTAATTTTTTTAAAA
* * *
180149 AAATTATCATTTAAAATGGTAATTTTTTTTAAACA
1 AAATTATAAATTAAAATAGTAA-TTTTTTTAAA-A
180184 AAA-TA-AAATTAAAA
1 AAATTATAAATTAAAA
180198 ATGAAAAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 27 0.63
34 12 0.28
35 4 0.09
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (33 bp):
AAATTATAAATTAAAATAGTAATTTTTTTAAAA
Found at i:180199 original size:34 final size:33
Alignment explanation
Indices: 180116--180200 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 33
180106 ATAAGAAGAG
* *
180116 AAATTATAATTTAAAATAGTAATTTTTTTAAAA
1 AAATTAAAATTTAAAATGGTAATTTTTTTAAAA
**
180149 AAATTATCATTTAAAATGGTAATTTTTTTTAAACA
1 AAATTAAAATTTAAAATGGTAA-TTTTTTTAAA-A
*
180184 AAA-TAAAATTAAAAATG
1 AAATTAAAATTTAAAATG
180201 AAAAAAGATA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
33 20 0.44
34 21 0.47
35 4 0.09
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (33 bp):
AAATTAAAATTTAAAATGGTAATTTTTTTAAAA
Found at i:180953 original size:22 final size:22
Alignment explanation
Indices: 180928--180971 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
180918 TAATTTTATT
180928 AATT-TATATAATTATTTTTAAA
1 AATTATATATAA-TATTTTTAAA
*
180950 AATTAATATTTAATATTTTTAA
1 AATT-ATATATAATATTTTTAA
180972 TTTTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 9 0.47
24 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATTATATATAATATTTTTAAA
Found at i:182628 original size:14 final size:14
Alignment explanation
Indices: 182594--182628 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
182584 TTAGCTGAGA
*
182594 TTTTGTTCTTTTCT
1 TTTTTTTCTTTTCT
*
182608 CTTTTTTCTTTTCT
1 TTTTTTTCTTTTCT
182622 TTTTTTT
1 TTTTTTT
182629 ATTAATACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTTTTCTTTTCT
Found at i:183817 original size:14 final size:15
Alignment explanation
Indices: 183784--183819 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
183774 TTACTATTAC
183784 TATTTATGACAAGTT
1 TATTTATGACAAGTT
*
183799 TATTTATGGCAAG-T
1 TATTTATGACAAGTT
183813 TATTTAT
1 TATTTAT
183820 CTGGTATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.50
Consensus pattern (15 bp):
TATTTATGACAAGTT
Found at i:184894 original size:40 final size:38
Alignment explanation
Indices: 184839--184918 Score: 99
Period size: 40 Copynumber: 2.1 Consensus size: 38
184829 AATATCACAC
*
184839 AAAAATAATTAAAATATAATACAATATACATAAAACATAA
1 AAAAATAATTAAAATACAATA-AA-ATACATAAAACATAA
* *
184879 AAAAATAA-TATAAATACAATAAAATATATATAACATAA
1 AAAAATAATTA-AAATACAATAAAATACATAAAACATAA
184917 AA
1 AA
184919 TATTAATCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 15 0.42
39 4 0.11
40 17 0.47
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (38 bp):
AAAAATAATTAAAATACAATAAAATACATAAAACATAA
Found at i:184911 original size:11 final size:10
Alignment explanation
Indices: 184839--184911 Score: 62
Period size: 10 Copynumber: 7.2 Consensus size: 10
184829 AATATCACAC
184839 AAAA-ATAATT
1 AAAATATAA-T
184849 AAAATATAAT
1 AAAATATAAT
*
184859 ACAATATACAT
1 AAAATATA-AT
*
184870 AAAACATAA-
1 AAAATATAAT
184879 AAAA-ATAAT
1 AAAATATAAT
*
184888 ATAAATACAAT
1 A-AAATATAAT
184899 AAAATATATAT
1 AAAATATA-AT
184910 AA
1 AA
184912 CATAAAATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
8 4 0.08
9 5 0.10
10 22 0.42
11 21 0.40
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAATATAAT
Found at i:185417 original size:14 final size:15
Alignment explanation
Indices: 185393--185425 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
185383 ATATTTTAAA
185393 TTAATAATATATTTT
1 TTAATAATATATTTT
185408 TTAA-AATATATTTT
1 TTAATAATATATTTT
185422 TTAA
1 TTAA
185426 CATTCTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATAATATATTTT
Done.