Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 230 of 230
Found at i:68642552 original size:21 final size:20
Alignment explanation
Indices: 68642512--68642552 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
68642502 TTCAATTTTG
68642512 TTTGTTTGTTTAATAATTTA
1 TTTGTTTGTTTAATAATTTA
68642532 TTTGTTTTGTTTAATAATTTA
1 TTTG-TTTGTTTAATAATTTA
68642553 CTTAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (20 bp):
TTTGTTTGTTTAATAATTTA
Found at i:68643916 original size:23 final size:23
Alignment explanation
Indices: 68643884--68643928 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
68643874 GCCTGCACAC
*
68643884 TTAACCCATTCCCATGCTACCCA
1 TTAACACATTCCCATGCTACCCA
68643907 TTAACACATTCCCATGCTACCC
1 TTAACACATTCCCATGCTACCC
68643929 GCAGCCCTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.42, G:0.04, T:0.27
Consensus pattern (23 bp):
TTAACACATTCCCATGCTACCCA
Found at i:68645346 original size:20 final size:23
Alignment explanation
Indices: 68645321--68645365 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 23
68645311 AGTTCGTATG
68645321 GTTAAACTG-T-AATGATA-TAT
1 GTTAAACTGATGAATGATATTAT
*
68645341 GTTAAATTGATGAATGATATTAT
1 GTTAAACTGATGAATGATATTAT
68645364 GT
1 GT
68645366 ATTTATTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 1 0.05
22 7 0.33
23 5 0.24
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (23 bp):
GTTAAACTGATGAATGATATTAT
Found at i:68650518 original size:40 final size:40
Alignment explanation
Indices: 68650474--68650557 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
68650464 AATTCCTCAG
68650474 ATTTTCTTATTTAATATGATTTAATATGCTTAGTCCTACA
1 ATTTTCTTATTTAATATGATTTAATATGCTTAGTCCTACA
68650514 ATTTTCTTATTTAATATGATTTAATATGCTTAGTCCTACA
1 ATTTTCTTATTTAATATGATTTAATATGCTTAGTCCTACA
68650554 ATTT
1 ATTT
68650558 ATTAATATGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (40 bp):
ATTTTCTTATTTAATATGATTTAATATGCTTAGTCCTACA
Found at i:68651942 original size:24 final size:24
Alignment explanation
Indices: 68651906--68651977 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
68651896 TTGAAACCAG
68651906 TTCCACAGCTCCTCTCTTCACCCT
1 TTCCACAGCTCCTCTCTTCACCCT
* *
68651930 TTCCACTGTTCCTCTCTTCACCCT
1 TTCCACAGCTCCTCTCTTCACCCT
*
68651954 TTCCACAGCTCTTCTCTTCACCCT
1 TTCCACAGCTCCTCTCTTCACCCT
68651978 ATCGATTGCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.11, C:0.47, G:0.04, T:0.38
Consensus pattern (24 bp):
TTCCACAGCTCCTCTCTTCACCCT
Found at i:68655638 original size:78 final size:78
Alignment explanation
Indices: 68655538--68655688 Score: 230
Period size: 78 Copynumber: 1.9 Consensus size: 78
68655528 CTCATTTTCT
* *
68655538 ACCATTAAACCATGATCCCTTGATCTCACCAACTGGGAGAGTCGGTGATCATGTTAATAATGATC
1 ACCATTAAACCATGATCCCTTGATCTCACCAACTAGGAGAGTCGGTGATCATGTTAATAACGATC
68655603 ACCATGGAGTTCG
66 ACCATGGAGTTCG
* * * * * *
68655616 ACCATTAAACCATGATCCCTTGATCTCATCAGCTAGGAGAGTTGGTGATCATGTTGATAGCGGTC
1 ACCATTAAACCATGATCCCTTGATCTCACCAACTAGGAGAGTCGGTGATCATGTTAATAACGATC
68655681 ACCATGGA
66 ACCATGGA
68655689 CTTTGTGTAC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (78 bp):
ACCATTAAACCATGATCCCTTGATCTCACCAACTAGGAGAGTCGGTGATCATGTTAATAACGATC
ACCATGGAGTTCG
Found at i:68657970 original size:13 final size:13
Alignment explanation
Indices: 68657952--68657977 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
68657942 ATTTTGACTT
68657952 AGGCTCATTTTTC
1 AGGCTCATTTTTC
68657965 AGGCTCATTTTTC
1 AGGCTCATTTTTC
68657978 TATAGGGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
AGGCTCATTTTTC
Found at i:68661206 original size:9 final size:9
Alignment explanation
Indices: 68661146--68661222 Score: 77
Period size: 9 Copynumber: 8.6 Consensus size: 9
68661136 TTTGGTTAAA
*
68661146 AATTACCCG
1 AATTACTCG
*
68661155 AATTACCCG
1 AATTACTCG
68661164 AATTA-TCCG
1 AATTACT-CG
68661173 AATTA-TCCG
1 AATTACT-CG
*
68661182 AATTAATCG
1 AATTACTCG
68661191 AATTACTCG
1 AATTACTCG
*
68661200 AATTACTTG
1 AATTACTCG
*
68661209 AATTAATCG
1 AATTACTCG
68661218 AATTA
1 AATTA
68661223 ACCTAATTGA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
9 60 0.98
10 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (9 bp):
AATTACTCG
Found at i:68661230 original size:18 final size:18
Alignment explanation
Indices: 68661146--68661235 Score: 67
Period size: 18 Copynumber: 4.9 Consensus size: 18
68661136 TTTGGTTAAA
* **
68661146 AATTACCCGAATTACCCG
1 AATTAACCGAATTAATCG
*
68661164 AATTATCCGAATT-ATCCG
1 AATTAACCGAATTAAT-CG
* *
68661182 AATTAATCGAATTACTCG
1 AATTAACCGAATTAATCG
*
68661200 AATT-ACTTGAATTAATCG
1 AATTAAC-CGAATTAATCG
*
68661218 AATTAACCTAATTGAATC
1 AATTAACCGAATT-AATC
68661236 ATACATAATT
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
17 1 0.02
18 48 0.86
19 7 0.12
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (18 bp):
AATTAACCGAATTAATCG
Found at i:68661320 original size:18 final size:19
Alignment explanation
Indices: 68661297--68661335 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
68661287 TTATAGAATT
* *
68661297 TTATTTTTATTTTTTA-AA
1 TTATTTGTAATTTTTATAA
68661315 TTATTTGTAATTTTTATAA
1 TTATTTGTAATTTTTATAA
68661334 TT
1 TT
68661336 GGGATGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTATTTGTAATTTTTATAA
Found at i:68661702 original size:20 final size:20
Alignment explanation
Indices: 68661677--68661718 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
68661667 CATAGCAAAA
68661677 GGACATTAGTGAAATGTTGT
1 GGACATTAGTGAAATGTTGT
*
68661697 GGACATTAGTGCAATGTTGT
1 GGACATTAGTGAAATGTTGT
68661717 GG
1 GG
68661719 TCAGCTACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.33
Consensus pattern (20 bp):
GGACATTAGTGAAATGTTGT
Done.