Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1377
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: 32021
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:6669 original size:2 final size:2
Alignment explanation
Indices: 6657--6693 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
6647 ACAGACACAT
* *
6657 TA TA AA TA TA TA TA TA TA TA TG 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
6694 CTTACAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16770 original size:3 final size:3
Alignment explanation
Indices: 16762--16794 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
16752 TGATGTTTGA
16762 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16795 CTTATGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17171 original size:11 final size:11
Alignment explanation
Indices: 17157--17198 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
17147 TAGTATAATT
17157 ATAAAAATATA
1 ATAAAAATATA
*
17168 ATAAAAATTTA
1 ATAAAAATATA
17179 ATAAAAATA-A
1 ATAAAAATATA
*
17189 ATAAATATAT
1 ATAAAAATAT
17199 CATACTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAAAAATATA
Found at i:17326 original size:11 final size:12
Alignment explanation
Indices: 17308--17338 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
17298 TAATATTCTA
17308 TCTTTCTTTTTT
1 TCTTTCTTTTTT
17320 T-TTTCTTTTTT
1 TCTTTCTTTTTT
17331 TCTTTCTT
1 TCTTTCTT
17339 GATTTGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TCTTTCTTTTTT
Found at i:18369 original size:16 final size:16
Alignment explanation
Indices: 18345--18375 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18335 ATTTTTTATA
*
18345 TATTTTTTATTCTTTT
1 TATTCTTTATTCTTTT
18361 TATTCTTTATTCTTT
1 TATTCTTTATTCTTT
18376 AACCAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTCTTTATTCTTTT
Found at i:19554 original size:27 final size:28
Alignment explanation
Indices: 19507--19562 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
19497 TAAAAAATTT
*
19507 ATTTTTAATTTATTTATATATATATTAA
1 ATTTTTAATTTATTTAAATATATATTAA
19535 ATTTTT-ATTT-TTTAAAATATATATTAA
1 ATTTTTAATTTATTT-AAATATATATTAA
19562 A
1 A
19563 ATATTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 3 0.12
27 17 0.65
28 6 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTTTTAATTTATTTAAATATATATTAA
Found at i:20239 original size:16 final size:17
Alignment explanation
Indices: 20199--20244 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
20189 ATTAATAATA
20199 ATATCTTAATTT-AAATT
1 ATAT-TTAATTTAAAATT
20216 AGTATTTAATTTAAAATT
1 A-TATTTAATTTAAAATT
20234 -TATTTAATTTA
1 ATATTTAATTTA
20245 TTTAAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 11 0.41
17 8 0.30
18 8 0.30
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
ATATTTAATTTAAAATT
Found at i:20246 original size:25 final size:24
Alignment explanation
Indices: 20218--20266 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
20208 TTTAAATTAG
*
20218 TATTTAATTTAAAATTTATTTAATT
1 TATTTAAATTAAAA-TTATTTAATT
*
20243 TATTTAAATTAATATTATTTAATT
1 TATTTAAATTAAAATTATTTAATT
20267 CATTATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTAAATTAAAATTATTTAATT
Found at i:21049 original size:7 final size:7
Alignment explanation
Indices: 21039--21071 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
21029 AAAATTTAAA
*
21039 AAATTAT
1 AAATTTT
21046 AAATTTT
1 AAATTTT
21053 AAATTTT
1 AAATTTT
21060 AAATTTT
1 AAATTTT
21067 AAATT
1 AAATT
21072 AATCAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
AAATTTT
Found at i:21956 original size:47 final size:48
Alignment explanation
Indices: 21902--22082 Score: 130
Period size: 47 Copynumber: 3.8 Consensus size: 48
21892 AAAATACTTC
21902 ATATATAAATTTA-ATTTAATATATATAAATTTATATATTTATAATGA
1 ATATATAAATTTATATTTAATATATATAAATTTATATATTTATAATGA
* ***
21949 ATATATAAA--TATCATGT-ATAT-TATGGGTTTATTATATTTATATATGA
1 ATATATAAATTTAT-ATTTAATATATATAAATTTA-TATATTTATA-ATGA
* * * *
21996 ATATAT--A-TTATTTTTAATATATATTAATTTAT-TATTTTTAATTTAA
1 ATATATAAATTTATATTTAATATATATAAATTTATATATTTATAA--TGA
* * *
22042 TATATATAAATTTATATATTTATA-ATGTATATTTATATATT
1 -ATATATAAATTTATAT-TTAATATATATAAATTTATATATT
22083 ATGGGTTTAT
Statistics
Matches: 103, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
44 1 0.01
45 19 0.18
46 24 0.23
47 35 0.34
49 1 0.01
50 14 0.14
51 9 0.09
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (48 bp):
ATATATAAATTTATATTTAATATATATAAATTTATATATTTATAATGA
Found at i:21988 original size:9 final size:8
Alignment explanation
Indices: 21976--22118 Score: 58
Period size: 8 Copynumber: 18.9 Consensus size: 8
21966 ATATTATGGG
21976 TTTATTATA
1 TTTA-TATA
21985 TTTATATA
1 TTTATATA
**
21993 TGAATATA
1 TTTATATA
22001 TATTAT-T-
1 T-TTATATA
22008 TTTA-ATA
1 TTTATATA
*
22015 TATAT-TAA
1 TTTATAT-A
22023 TTTAT-TA
1 TTTATATA
*
22030 TTTTTA-A
1 TTTATATA
22037 TTTA-ATA
1 TTTATATA
* *
22044 TATATAAA
1 TTTATATA
22052 TTTATATA
1 TTTATATA
22060 TTTATA-A
1 TTTATATA
*
22067 --TGTATA
1 TTTATATA
22073 TTTATATA
1 TTTATATA
***
22081 -TTATGGG
1 TTTATATA
22088 TTTATAATA
1 TTTAT-ATA
22097 TTTATATA
1 TTTATATA
**
22105 TGAATAT-
1 TTTATATA
22112 TTTATAT
1 TTTATAT
22119 GAAGTATTTT
Statistics
Matches: 97, Mismatches: 24, Indels: 28
0.65 0.16 0.19
Matches are distributed among these distances:
5 3 0.03
6 6 0.06
7 28 0.29
8 49 0.51
9 11 0.11
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (8 bp):
TTTATATA
Found at i:22015 original size:24 final size:23
Alignment explanation
Indices: 21978--22048 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 23
21968 ATTATGGGTT
*
21978 TATTATATTT-ATATATGAATATA
1 TATTATTTTTAATATAT-AATATA
* *
22001 TATTATTTTTAATATATATTAATT
1 TATTATTTTTAATATATAAT-ATA
22025 TATTATTTTTAAT-T-TAATATA
1 TATTATTTTTAATATATAATATA
22046 TAT
1 TAT
22049 AAATTTATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
21 5 0.12
22 3 0.07
23 12 0.29
24 21 0.51
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (23 bp):
TATTATTTTTAATATATAATATA
Found at i:22043 original size:29 final size:30
Alignment explanation
Indices: 22008--22067 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
21998 ATATATTATT
* *
22008 TTTAATATATATTAATTTAT-TATTTTTAA
1 TTTAATATATATAAATTTATATATTTATAA
22037 TTTAATATATATAAATTTATATATTTATAA
1 TTTAATATATATAAATTTATATATTTATAA
22067 T
1 T
22068 GTATATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTAATATATATAAATTTATATATTTATAA
Found at i:22058 original size:14 final size:14
Alignment explanation
Indices: 21996--22060 Score: 60
Period size: 14 Copynumber: 4.4 Consensus size: 14
21986 TTATATATGA
*
21996 ATATATATTATTTTT
1 ATATATATTA-ATTT
22011 AATATATATTAATTT
1 -ATATATATTAATTT
*
22026 AT-TATTTTTAATTT
1 ATATA-TATTAATTT
*
22040 AATATATATAAATTT
1 -ATATATATTAATTT
22055 ATATAT
1 ATATAT
22061 TTATAATGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
13 2 0.05
14 16 0.38
15 12 0.29
16 12 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATATATATTAATTT
Found at i:22073 original size:29 final size:29
Alignment explanation
Indices: 22010--22080 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
22000 ATATTATTTT
* * *
22010 TAATATATATTAATTTATTATTTTTAATT
1 TAATATATATAAATTTATTATTTATAATG
22039 TAATATATATAAATTTATATATTTATAATG
1 TAATATATATAAATTTAT-TATTTATAATG
*
22069 TATATTTATATA
1 TA-ATATATATA
22081 TTATGGGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 17 0.47
30 11 0.31
31 8 0.22
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
TAATATATATAAATTTATTATTTATAATG
Found at i:22119 original size:13 final size:13
Alignment explanation
Indices: 22093--22131 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 13
22083 ATGGGTTTAT
22093 AATATTTATATATG
1 AATATTT-TATATG
22107 AATATTTTATATG
1 AATATTTTATATG
22120 AAGTATTTTATA
1 AA-TATTTTATA
22132 ACACATGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (13 bp):
AATATTTTATATG
Found at i:22187 original size:28 final size:28
Alignment explanation
Indices: 22147--22204 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
22137 TGATATTTTT
*
22147 TAAATATAAATTTAAATT-ATTATAAATA
1 TAAATATAAATTT-AATTCATGATAAATA
* * *
22175 TAAATTTATATTTGATTCATGATAAATA
1 TAAATATAAATTTAATTCATGATAAATA
22203 TA
1 TA
22205 TAAATGTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (28 bp):
TAAATATAAATTTAATTCATGATAAATA
Found at i:24672 original size:31 final size:30
Alignment explanation
Indices: 24637--24695 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
24627 AAAATTTATA
24637 TAAA-TATAAATATATTTTATTTTTATTTACT
1 TAAATTATAAA-ATA-TTTATTTTTATTTACT
* *
24668 TAAATTTTTAAATATTTATTTTTATTTA
1 TAAATTATAAAATATTTATTTTTATTTA
24696 ATTCAACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 14 0.56
31 7 0.28
32 4 0.16
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (30 bp):
TAAATTATAAAATATTTATTTTTATTTACT
Found at i:24711 original size:29 final size:30
Alignment explanation
Indices: 24652--24713 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
24642 ATAAATATAT
* *
24652 TTTATTTTTATTTACTTAAATTTTTAAATA
1 TTTATTTTTATTTAATTAAACTTTTAAATA
*
24682 TTTATTTTTATTTAATTCAACTTTT-AATA
1 TTTATTTTTATTTAATTAAACTTTTAAATA
24711 TTT
1 TTT
24714 TTATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (30 bp):
TTTATTTTTATTTAATTAAACTTTTAAATA
Found at i:25435 original size:2 final size:2
Alignment explanation
Indices: 25428--25453 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25418 CACATAATGT
25428 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
25454 AATTACCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26464 original size:3 final size:3
Alignment explanation
Indices: 26456--26491 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
26446 ATTGTTTAAA
26456 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
26492 TATTATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:31348 original size:4 final size:4
Alignment explanation
Indices: 31339--31363 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
31329 CTGGGTATTG
31339 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
31364 CGCTTGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Done.