Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2200
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: 114701
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
File 2 of 2
Found at i:97551 original size:15 final size:14
Alignment explanation
Indices: 97506--97551 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
97496 ATATTTTATA
97506 TTTATA-TAAAAAT
1 TTTATATTAAAAAT
*
97519 TATTATATTAATAA-
1 T-TTATATTAAAAAT
97533 TTTATATTATAAAAT
1 TTTATATTA-AAAAT
97548 TTTA
1 TTTA
97552 AAAAATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 9 0.33
14 9 0.33
15 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTATATTAAAAAT
Found at i:98135 original size:26 final size:23
Alignment explanation
Indices: 98106--98180 Score: 71
Period size: 26 Copynumber: 3.1 Consensus size: 23
98096 CATAAAAAGA
98106 AAAAAATAAAATTAATATATTATTTT
1 AAAAAATAAAATTAA-A-ATT-TTTT
* *
98132 AAAAAATTAAATTAAACTTTTTT
1 AAAAAATAAAATTAAAATTTTTT
*
98155 -AAAAATAATAATTAAATAATTTTT
1 AAAAAATAA-AATTAAA-ATTTTTT
98179 AA
1 AA
98181 CTGAATTCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
22 7 0.17
23 11 0.27
24 7 0.17
25 2 0.05
26 14 0.34
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAAAATAAAATTAAAATTTTTT
Found at i:98158 original size:22 final size:23
Alignment explanation
Indices: 98128--98170 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
98118 TAATATATTA
*
98128 TTTTAAAAAATTA-AATTAAACT
1 TTTTAAAAAATAATAATTAAACT
*
98150 TTTTTAAAAATAATAATTAAA
1 TTTTAAAAAATAATAATTAAA
98171 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTTAAAAAATAATAATTAAACT
Found at i:98177 original size:23 final size:23
Alignment explanation
Indices: 98107--98177 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 23
98097 ATAAAAAGAA
98107 AAAAATAA-AATTAATATATTATTTT
1 AAAAATAATAATTAA-ATA--ATTTT
* *
98132 AAAAA-ATTAAATTAAACT-TTTTT
1 AAAAATAAT-AATTAAA-TAATTTT
98155 AAAAATAATAATTAAATAATTTT
1 AAAAATAATAATTAAATAATTTT
98178 TAACTGAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
22 1 0.03
23 20 0.54
24 3 0.08
25 6 0.16
26 7 0.19
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (23 bp):
AAAAATAATAATTAAATAATTTT
Found at i:99986 original size:14 final size:14
Alignment explanation
Indices: 99935--99990 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 14
99925 ATTTATATAA
99935 TAAAATATTATTTT
1 TAAAATATTATTTT
* * *
99949 AATTAAAT-TTAATTG
1 --TAAAATATTATTTT
99964 TAAAA-ATTATTTT
1 TAAAATATTATTTT
99977 TAAAATATTATTTT
1 TAAAATATTATTTT
99991 AAATAATTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
13 14 0.44
14 8 0.25
15 5 0.16
16 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
TAAAATATTATTTT
Found at i:99990 original size:13 final size:12
Alignment explanation
Indices: 99935--100000 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 12
99925 ATTTATATAA
99935 TAAAATATTATTT
1 TAAAA-ATTATTT
*
99948 TAATTAAATTTAATTG
1 TAA--AAA-TT-ATTT
99964 TAAAAATTATTTT
1 TAAAAATTA-TTT
99977 TAAAATATTATTT
1 TAAAA-ATTATTT
99990 TAAATAATTAT
1 TAAA-AATTAT
100001 ATAAACTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
12 1 0.02
13 24 0.55
14 9 0.20
15 4 0.09
16 6 0.14
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
TAAAAATTATTT
Found at i:102928 original size:21 final size:21
Alignment explanation
Indices: 102889--102928 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
102879 TTGAAATGAA
*
102889 TATTATTTTATTATCAAAACT
1 TATTATTTTATTATAAAAACT
102910 TATTATTTTGATT-TAAAAA
1 TATTATTTT-ATTATAAAAA
102929 AATTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
TATTATTTTATTATAAAAACT
Found at i:102973 original size:18 final size:19
Alignment explanation
Indices: 102933--102975 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
102923 TAAAAAAATT
*
102933 TAAATTTTTTAAATATTAGA
1 TAAA-TTTTTAAATATTAAA
102953 TAAATTTTTAAAT-TTAAA
1 TAAATTTTTAAATATTAAA
102971 TAAAT
1 TAAAT
102976 AAAATACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 9 0.41
20 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TAAATTTTTAAATATTAAA
Found at i:103311 original size:22 final size:23
Alignment explanation
Indices: 103267--103314 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
103257 TAATCCTTAC
* *
103267 TATATGATATGAATTTAGTAAAAA
1 TATATGATATAAATATAG-AAAAA
103291 TATATGATATAAATATA-AAAAA
1 TATATGATATAAATATAGAAAAA
103313 TA
1 TA
103315 ATTAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
24 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (23 bp):
TATATGATATAAATATAGAAAAA
Found at i:103320 original size:11 final size:12
Alignment explanation
Indices: 103302--103334 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
103292 ATATGATATA
103302 AATATAAAAAAT
1 AATATAAAAAAT
*
103314 AAT-TAAAATAT
1 AATATAAAAAAT
103325 AATATAAAAA
1 AATATAAAAA
103335 TAAAATAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AATATAAAAAAT
Found at i:103350 original size:29 final size:29
Alignment explanation
Indices: 103287--103363 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 29
103277 GAATTTAGTA
* *
103287 AAAATATATGATATAAATATAAAAAATAATT
1 AAAATATA--ATATAAAAATAAAAAATAATG
*
103318 AAAATATAATATAAAAATAAAATAA-CATG
1 AAAATATAATATAAAAATAAAA-AATAATG
*
103347 AAAA-A-AATAAAAAAATA
1 AAAATATAATATAAAAATA
103364 TATGAACAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 11 0.27
28 1 0.02
29 19 0.46
30 2 0.05
31 8 0.20
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (29 bp):
AAAATATAATATAAAAATAAAAAATAATG
Found at i:103404 original size:22 final size:24
Alignment explanation
Indices: 103374--103425 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
103364 TATGAACAAT
*
103374 AAATATATAT-TTA-AAAATATTA
1 AAATATATATAATATAAAATATTA
*
103396 AAATTTATATAATATAAAATATTA
1 AAATATATATAATATAAAATATTA
*
103420 ATATAT
1 AAATAT
103426 TAAAATTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 9 0.38
23 2 0.08
24 13 0.54
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATATATATAATATAAAATATTA
Found at i:103413 original size:16 final size:17
Alignment explanation
Indices: 103389--103453 Score: 73
Period size: 16 Copynumber: 3.8 Consensus size: 17
103379 TATATTTAAA
103389 AATATTAAAATTTATAT
1 AATATTAAAATTTATAT
103406 AATA-TAAAATATTA-AT
1 AATATTAAAAT-TTATAT
103422 -ATATTAAAATTTATAT
1 AATATTAAAATTTATAT
103438 AAAATATATAAAATTT
1 --AATAT-TAAAATTT
103454 TAAATACAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
15 6 0.15
16 16 0.39
17 7 0.17
19 4 0.10
20 8 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATATTAAAATTTATAT
Found at i:104445 original size:20 final size:20
Alignment explanation
Indices: 104422--104485 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 20
104412 ACATTATATA
104422 TTAAA-TTTATTGATAAATTT
1 TTAAACTTTATT-ATAAATTT
*
104442 TTAAACTTTACTATAAATTT
1 TTAAACTTTATTATAAATTT
*
104462 TTAAACTTTATTAAAATATTT
1 TTAAACTTTATTATAA-ATTT
104483 TTA
1 TTA
104486 TCGTAAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
20 27 0.69
21 12 0.31
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (20 bp):
TTAAACTTTATTATAAATTT
Found at i:104658 original size:28 final size:29
Alignment explanation
Indices: 104602--104658 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
104592 TCGAATAATT
* *
104602 ATTTAATTAATAAAAATATTTTTATTTAA
1 ATTTAATTAATAAAAATATTTTAAATTAA
104631 ATTTAATT-AT-AAAATATTTATAAATTAA
1 ATTTAATTAATAAAAATATTT-TAAATTAA
104659 TATAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.36
28 8 0.32
29 8 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTAATTAATAAAAATATTTTAAATTAA
Found at i:104668 original size:22 final size:21
Alignment explanation
Indices: 104624--104665 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
104614 AAAATATTTT
*
104624 TATTTAAATTTAATTATAAAA
1 TATTTAAAATTAATTATAAAA
104645 TATTTATAAATTAA-TATAAAA
1 TATTTA-AAATTAATTATAAAA
104666 ATAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTTAAAATTAATTATAAAA
Found at i:105305 original size:21 final size:19
Alignment explanation
Indices: 105268--105308 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
105258 TGATAAAATC
105268 ATTTAATTCAATAAATTTA
1 ATTTAATTCAATAAATTTA
*
105287 ATTTATATTGAATCAAATTTA
1 ATTTA-ATTCAAT-AAATTTA
105308 A
1 A
105309 ATATTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 6 0.32
21 8 0.42
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (19 bp):
ATTTAATTCAATAAATTTA
Found at i:105920 original size:19 final size:19
Alignment explanation
Indices: 105896--105934 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
105886 ATACTGACAC
105896 CGATATATATAATAGATAT
1 CGATATATATAATAGATAT
105915 CGATATATATAATAGATAT
1 CGATATATATAATAGATAT
105934 C
1 C
105935 TACCGATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (19 bp):
CGATATATATAATAGATAT
Found at i:105941 original size:23 final size:21
Alignment explanation
Indices: 105894--105944 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 21
105884 ACATACTGAC
105894 ACCGATATATATAATAGATAT
1 ACCGATATATATAATAGATAT
105915 --CGATATATATAATAGATATCT
1 ACCGATATATATAATAGATA--T
105936 ACCGATATA
1 ACCGATATA
105945 ACATTGAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 18 0.69
21 1 0.04
23 7 0.27
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (21 bp):
ACCGATATATATAATAGATAT
Found at i:112249 original size:21 final size:21
Alignment explanation
Indices: 112169--112262 Score: 66
Period size: 24 Copynumber: 4.2 Consensus size: 21
112159 CTGATTTTTT
*
112169 ATTTTTAATTTTTATATATTTAA
1 ATTTATAATTTTTATA-A-TTAA
* *
112192 ATTTGATTATTTTTATTATT--
1 ATTT-ATAATTTTTATAATTAA
* *
112212 ATTTAAAAATTATTTTTATATTAA
1 ATTT-ATAATT-TTTATA-ATTAA
112236 CATTTATAATTTTTATAATTAA
1 -ATTTATAATTTTTATAATTAA
112258 ATTTA
1 ATTTA
112263 AATAAAAATA
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
20 8 0.15
21 9 0.16
22 10 0.18
23 10 0.18
24 14 0.25
25 4 0.07
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (21 bp):
ATTTATAATTTTTATAATTAA
Done.