Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_224
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: 125177
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7008 original size:22 final size:21
Alignment explanation
Indices: 6978--7035 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
6968 GAATGGTATC
6978 TACAAATCAAATCTCTAAGAT
1 TACAAATCAAATCTCTAAGAT
* *
6999 TACAAAATCATACCTTCTAAGAT
1 TAC-AAATCAAATC-TCTAAGAT
*
7022 TACATATCAAATCT
1 TACAAATCAAATCT
7036 ACGATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 15 0.50
23 11 0.37
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.31
Consensus pattern (21 bp):
TACAAATCAAATCTCTAAGAT
Found at i:9534 original size:20 final size:20
Alignment explanation
Indices: 9509--9592 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 20
9499 TACAGGATTG
*
9509 GCACTTCGGTGCTCATGTTT
1 GCACTTCGGTGCTCCTGTTT
** * *
9529 GCACTTCTTTGCCCCTGTAT
1 GCACTTCGGTGCTCCTGTTT
* *
9549 ACACTTCGGTG-TCCTTGTTC
1 GCACTTCGGTGCTCC-TGTTT
*
9569 GCACTACGGTGCTCCTGTTT
1 GCACTTCGGTGCTCCTGTTT
9589 GCAC
1 GCAC
9593 ATTTGTACAC
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
19 2 0.04
20 43 0.90
21 3 0.06
ACGTcount: A:0.11, C:0.31, G:0.21, T:0.37
Consensus pattern (20 bp):
GCACTTCGGTGCTCCTGTTT
Found at i:12289 original size:30 final size:30
Alignment explanation
Indices: 12248--12307 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
12238 AATTTACAAG
12248 CTTTAGGGT-AAAATCATAATTTT-GTCAAA
1 CTTTAGGGTAAAAAT-ATAATTTTCGTCAAA
*
12277 CTTTAGGGGTAAAAATGTAATTTTCGTCAAA
1 CTTTA-GGGTAAAAATATAATTTTCGTCAAA
12308 GTGTGATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 5 0.19
30 11 0.41
31 11 0.41
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (30 bp):
CTTTAGGGTAAAAATATAATTTTCGTCAAA
Found at i:12850 original size:84 final size:85
Alignment explanation
Indices: 12589--12915 Score: 471
Period size: 85 Copynumber: 3.9 Consensus size: 85
12579 ATTCTTTGAA
* ** **
12589 TGAAAGGGGTTGCTATGTGCTAATTCCCTGTATCATTGAATATAAAGGTGGTTGCTCTGTGCTGA
1 TGAAAGGGGTTGCTATGTGCTGATTCCCCATATCATTGAATATAAAGGTGGTTGCTAAGTGCTGA
*
12654 TTCCACCGTATCCTTAACTG
66 TTCCACCGTATCCTTGACTG
* *
12674 TGAAAGGGGTTGCTATGTGCTGATT-CCCATTATCATTGAATATAAAGGTGATTGCTATGTGCTG
1 TGAAAGGGGTTGCTATGTGCTGATTCCCCA-TATCATTGAATATAAAGGTGGTTGCTAAGTGCTG
12738 ATTCCACCGTATCCTTGACTG
65 ATTCCACCGTATCCTTGACTG
* *
12759 TGAAAGGGGTTGCTATGTGTTGATTCCCCATATCATTGATTAT-AAGGTGGTTGCTAAGTGCTGA
1 TGAAAGGGGTTGCTATGTGCTGATTCCCCATATCATTGAATATAAAGGTGGTTGCTAAGTGCTGA
* *
12823 TTTCACCGTATCCTTGATTG
66 TTCCACCGTATCCTTGACTG
* * * * *
12843 TGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTTATTAT-AATGTGGTTGCTAAGTGTTGA
1 TGAAAGGGGTTGCTATGTGCTGATTCCCCATATCATTGAATATAAAGGTGGTTGCTAAGTGCTGA
12907 TTCCACCGT
66 TTCCACCGT
12916 GTAACGGTTA
Statistics
Matches: 222, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
84 106 0.48
85 112 0.50
86 4 0.02
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (85 bp):
TGAAAGGGGTTGCTATGTGCTGATTCCCCATATCATTGAATATAAAGGTGGTTGCTAAGTGCTGA
TTCCACCGTATCCTTGACTG
Found at i:12869 original size:169 final size:169
Alignment explanation
Indices: 12589--12915 Score: 476
Period size: 169 Copynumber: 1.9 Consensus size: 169
12579 ATTCTTTGAA
** **
12589 TGAAAGGGGTTGCTATGTGCTAATTCCCTGTATCATTGAATATAAAGGTGGTTGCTCTGTGCTGA
1 TGAAAGGGGTTGCTATGTGCTAATTCCCCATATCATTGAATATAAAGGTGGTTGCTAAGTGCTGA
*
12654 TTCCACCGTATCCTTAACTGTGAAAGGGGTTGCTATGTGCTGATTCCCATTATCATTGAATATAA
66 TTCCACCGTATCCTTAACTGTGAAAGGGGTTGCTATGTGCTGATTCCCAGTATCATTGAATAT-A
*
12719 AGGTGATTGCTATGTGCTGATTCCACCGTATCCTTGACTG
130 AGGTGATTGCTAAGTGCTGATTCCACCGTATCCTTGACTG
* * *
12759 TGAAAGGGGTTGCTATGTGTTGATTCCCCATATCATTGATTAT-AAGGTGGTTGCTAAGTGCTGA
1 TGAAAGGGGTTGCTATGTGCTAATTCCCCATATCATTGAATATAAAGGTGGTTGCTAAGTGCTGA
* * * * * *
12823 TTTCACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTTATTATAA
66 TTCCACCGTATCCTTAACTGTGAAAGGGGTTGCTATGTGCTGATTCCCAGTATCATTGAATATAA
* * *
12888 TGTGGTTGCTAAGTGTTGATTCCACCGT
131 GGTGATTGCTAAGTGCTGATTCCACCGT
12916 GTAACGGTTA
Statistics
Matches: 139, Mismatches: 18, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
168 26 0.19
169 75 0.54
170 38 0.27
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (169 bp):
TGAAAGGGGTTGCTATGTGCTAATTCCCCATATCATTGAATATAAAGGTGGTTGCTAAGTGCTGA
TTCCACCGTATCCTTAACTGTGAAAGGGGTTGCTATGTGCTGATTCCCAGTATCATTGAATATAA
GGTGATTGCTAAGTGCTGATTCCACCGTATCCTTGACTG
Found at i:16535 original size:13 final size:14
Alignment explanation
Indices: 16517--16550 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
16507 ATAATAAATA
16517 TATTTTTT-ATTTT
1 TATTTTTTAATTTT
16530 TATTTTTTAATTTT
1 TATTTTTTAATTTT
*
16544 TAATTTT
1 TATTTTT
16551 AAAATACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:16542 original size:14 final size:13
Alignment explanation
Indices: 16517--16550 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
16507 ATAATAAATA
16517 TATTTTTTATTTT
1 TATTTTTTATTTT
16530 TATTTTTTAATTTT
1 TATTTTTT-ATTTT
16544 TAATTTT
1 T-ATTTT
16551 AAAATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 6 0.32
15 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:18943 original size:38 final size:38
Alignment explanation
Indices: 18895--18971 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
18885 TCTTGACAAA
18895 TATAGCATGCATGAGAAACGG-AAACTACTCAAACTTTG
1 TATAGCATGCATGAGAAA-GGCAAACTACTCAAACTTTG
* *
18933 TATAGGATGCATGAGAAAGGCAAACTACTCAACCTTTG
1 TATAGCATGCATGAGAAAGGCAAACTACTCAAACTTTG
18971 T
1 T
18972 GCTGCTATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 2 0.06
38 34 0.94
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (38 bp):
TATAGCATGCATGAGAAAGGCAAACTACTCAAACTTTG
Found at i:27571 original size:20 final size:20
Alignment explanation
Indices: 27482--27577 Score: 72
Period size: 20 Copynumber: 4.8 Consensus size: 20
27472 TGTTCGCATA
*
27482 TATGTGTCTCTATTTGCACAT
1 TATGTGCCTCTATTTGCAC-T
*
27503 T-CGTGCCT-TGATTTGCACT
1 TATGTGCCTCT-ATTTGCACT
* *
27522 TAAGTGCCTCCATTTGCACT
1 TATGTGCCTCTATTTGCACT
** *
27542 TCGGTACCTCTATTTGCACAT
1 TATGTGCCTCTATTTGCAC-T
*
27563 T-TGTGCCTCTGTTTG
1 TATGTGCCTCTATTTG
27578 TGTCACATCC
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.05
20 54 0.90
21 3 0.05
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.43
Consensus pattern (20 bp):
TATGTGCCTCTATTTGCACT
Found at i:34056 original size:21 final size:21
Alignment explanation
Indices: 34024--34064 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
34014 GAACATTTGG
34024 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
34045 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
34065 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:37738 original size:22 final size:20
Alignment explanation
Indices: 37662--37749 Score: 63
Period size: 21 Copynumber: 4.2 Consensus size: 20
37652 ATTTTTTATT
*
37662 TTTTTAAAAAGAAAGTTTAGA
1 TTTTTAAAAAAAAAGTTTA-A
*
37683 TTTTTAGAAATAAAAA-TCT-A
1 TTTTTA-AAA-AAAAAGTTTAA
*
37703 TTTTTAAAGGAAAAAGTTTAA
1 TTTTTAAA-AAAAAAGTTTAA
* * *
37724 TATTTTAAAACAAAATTTTGA
1 T-TTTTAAAAAAAAAGTTTAA
37745 TTTTT
1 TTTTT
37750 TTCAACTATT
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
19 7 0.13
20 13 0.25
21 17 0.32
22 12 0.23
23 4 0.08
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (20 bp):
TTTTTAAAAAAAAAGTTTAA
Found at i:40473 original size:13 final size:13
Alignment explanation
Indices: 40455--40488 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
40445 GGAGCACGCA
*
40455 TAAAACATATCTT
1 TAAAACATAGCTT
40468 TAAAACATAGCTT
1 TAAAACATAGCTT
*
40481 TAGAACAT
1 TAAAACAT
40489 GACTTGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (13 bp):
TAAAACATAGCTT
Found at i:41962 original size:9 final size:9
Alignment explanation
Indices: 41948--41977 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
41938 GAAGATCACA
41948 TTGGCCATG
1 TTGGCCATG
41957 TTGGCCATG
1 TTGGCCATG
41966 TTGGCCATG
1 TTGGCCATG
41975 TTG
1 TTG
41978 ATGGCACAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.20, G:0.33, T:0.37
Consensus pattern (9 bp):
TTGGCCATG
Found at i:61603 original size:29 final size:29
Alignment explanation
Indices: 61540--61607 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
61530 TAATCAACCA
61540 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
61569 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
61598 CGCACACTTA
1 CGCACACTTA
61608 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:61722 original size:29 final size:30
Alignment explanation
Indices: 61675--61753 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
61665 TAGAAAATAC
61675 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
61705 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
61734 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
61754 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:64119 original size:19 final size:19
Alignment explanation
Indices: 64095--64131 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
64085 CATACCATGC
*
64095 ACTTAGAAATATGCTAGCT
1 ACTTAGAAATAAGCTAGCT
64114 ACTTAGAAATAAGCTAGC
1 ACTTAGAAATAAGCTAGC
64132 CAAATATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (19 bp):
ACTTAGAAATAAGCTAGCT
Found at i:75942 original size:615 final size:615
Alignment explanation
Indices: 74772--76622 Score: 3621
Period size: 615 Copynumber: 3.0 Consensus size: 615
74762 ATGGATAAGG
74772 TGCGTGATTAGCTTGAGTTGTGGTAGTATAAGCGTTATAAAAGAATGATGAACCAAATATGGGGT
1 TGCGTGATTAGCTTGAGTTGTGGTAGTATAAGCGTTATAAAAGAATGATGAACCAAATATGGGGT
* *
74837 CTGAAGAGGAAGATCAATCAGCTTGTGGATGGTCCAAACAGGGATAACACAACTAACCTCCTTAA
66 CTGAAGAGGAAGATCAATCAACTTGTAGATGGTCCAAACAGGGATAACACAACTAACCTCCTTAA
*
74902 AATGGCTCGCTTCAAGCTTGGGCACTTGTATGTTGTGGATGAGGACTATTGGGCACAAAGGGCTC
131 AATGGCTCGCTTCAAGCTTGGGCACTTGTATGCTGTGGATGAGGACTATTGGGCACAAAGGGCTC
74967 ACATTAAGTGGCTCACGGAGGGTGATAGAAACACCCGTTATTTTCACATGCACGCTACTGGCAGA
196 ACATTAAGTGGCTCACGGAGGGTGATAGAAACACCCGTTATTTTCACATGCACGCTACTGGCAGA
75032 AGAAAGAACACAATATAGAAAAGTTAAAAGATTCTAATGGGACGTGGCAAAAAGACAAGAGGGAC
261 AGAAAGAACACAATATAGAAAAGTTAAAAGATTCTAATGGGACGTGGCAAAAAGACAAGAGGGAC
75097 ATCTGTAAAGTTGCATGGGACTATTTTAATGATCTTTTTAAGTCAACCATTGTTTCTTGTAATGA
326 ATCTGTAAAGTTGCATGGGACTATTTTAATGATCTTTTTAAGTCAACCATTGTTTCTTGTAATGA
75162 ACCTGACATGCATTATATCCAAACGTGCATTACTGACAATATGAACTCTTGCTTGGACAGGGACT
391 ACCTGACATGCATTATATCCAAACGTGCATTACTGACAATATGAACTCTTGCTTGGACAGGGACT
*
75227 TTATTGATGAAGAAATTGTTGCTGCTTTTAACCATATGGACCAGCGAAAAGCTCCGGGGAGTGAT
456 TTACTGATGAAGAAATTGTTGCTGCTTTTAACCATATGGACCAGCGAAAAGCTCCGGGGAGTGAT
75292 GGTTTATCAGGTTGCTTCTTCAAAAAGCACTGGGCCGTAGTTGGAAAAGATGTCTTAAAGTTGTG
521 GGTTTATCAGGTTGCTTCTTCAAAAAGCACTGGGCCGTAGTTGGAAAAGATGTCTTAAAGTTGTG
75357 TCACGATGTGCTCAATGGCAACAAGGATGT
586 TCACGATGTGCTCAATGGCAACAAGGATGT
75387 TGCGTGATTAGCTTGAGTTGTGGTAGTATAAGCGTTATAAAAGAATGATGAACCAAATATGGGGT
1 TGCGTGATTAGCTTGAGTTGTGGTAGTATAAGCGTTATAAAAGAATGATGAACCAAATATGGGGT
75452 CTGAAGAGGAAGATCAATCAACTTGTAGATGGTCCAAACAGGGATAACACAACTAACCTCCTTAA
66 CTGAAGAGGAAGATCAATCAACTTGTAGATGGTCCAAACAGGGATAACACAACTAACCTCCTTAA
75517 AATGGCTCGCTTCAAGCTTGGGCACTTGTATGCTGTGGATGAGGACTATTGGGCACAAAGGGCTC
131 AATGGCTCGCTTCAAGCTTGGGCACTTGTATGCTGTGGATGAGGACTATTGGGCACAAAGGGCTC
*
75582 ACATTAAGTGGCTCACGGAGGGTGATAGAAACACCCGTTATTTTCATATGCACGCTACTGGCAGA
196 ACATTAAGTGGCTCACGGAGGGTGATAGAAACACCCGTTATTTTCACATGCACGCTACTGGCAGA
75647 AGAAAGAACACAATATAGAAAAGTTAAAAGATTCTAATGGGACGTGGCAAAAAGACAAGAGGGAC
261 AGAAAGAACACAATATAGAAAAGTTAAAAGATTCTAATGGGACGTGGCAAAAAGACAAGAGGGAC
75712 ATCTGTAAAGTTGCATGGGACTATTTTAATGATCTTTTTAAGTCAACCATTGTTTCTTGTAATGA
326 ATCTGTAAAGTTGCATGGGACTATTTTAATGATCTTTTTAAGTCAACCATTGTTTCTTGTAATGA
75777 ACCTGACATGCATTATATCCAAACGTGCATTACTGACAATATGAACTCTTGCTTGGACAGGGACT
391 ACCTGACATGCATTATATCCAAACGTGCATTACTGACAATATGAACTCTTGCTTGGACAGGGACT
75842 TTACTGATGAAGAAATTGTTGCTGCTTTTAACCATATGGACCAGCGAAAAGCTCCGGGGAGTGAT
456 TTACTGATGAAGAAATTGTTGCTGCTTTTAACCATATGGACCAGCGAAAAGCTCCGGGGAGTGAT
75907 GGTTTATCAGGTTGCTTCTTCAAAAAGCACTGGGCCGTAGTTGGAAAAGATGTCTTAAAGTTGTG
521 GGTTTATCAGGTTGCTTCTTCAAAAAGCACTGGGCCGTAGTTGGAAAAGATGTCTTAAAGTTGTG
75972 TCACGATGTGCTCAATGGCAACAAGGATGT
586 TCACGATGTGCTCAATGGCAACAAGGATGT
76002 TGCGTGATTAGCTTGAGTTGTGGTAGTATAAGCGTTATAAAAGAATGATGAACCAAATATGGGGT
1 TGCGTGATTAGCTTGAGTTGTGGTAGTATAAGCGTTATAAAAGAATGATGAACCAAATATGGGGT
*
76067 CTGAAAAGGAAGATCAATCAACTTGTAGATGGTCCAAACAGGGATAACACAACTAACCTCCTTAA
66 CTGAAGAGGAAGATCAATCAACTTGTAGATGGTCCAAACAGGGATAACACAACTAACCTCCTTAA
76132 AATGGCTCGCTTCAAGCTTGGGCACTTGTATGCTGTGGATGAGGACTATTGGGCACAAAGGGCTC
131 AATGGCTCGCTTCAAGCTTGGGCACTTGTATGCTGTGGATGAGGACTATTGGGCACAAAGGGCTC
76197 ACATTAAGTGGCTCACGGAGGGTGATAGAAACACCCGTTATTTTCACATGCACGCTACTGGCAGA
196 ACATTAAGTGGCTCACGGAGGGTGATAGAAACACCCGTTATTTTCACATGCACGCTACTGGCAGA
*
76262 AGAAAGAACACAATATAGAAAAGTTAAAAGATTCTAATGGGGCGTGGCAAAAAGACAAGAGGGAC
261 AGAAAGAACACAATATAGAAAAGTTAAAAGATTCTAATGGGACGTGGCAAAAAGACAAGAGGGAC
76327 ATCTGTAAAGTTGCATGGGACTATTTTAATGATCTTTTTAAGTCAACCATTGTTTCTTGTAATGA
326 ATCTGTAAAGTTGCATGGGACTATTTTAATGATCTTTTTAAGTCAACCATTGTTTCTTGTAATGA
*
76392 ACCTGACATGCATTATATCCAACCGTGCATTACTGACAATATGAACTCTTGCTTGGACAGGGACT
391 ACCTGACATGCATTATATCCAAACGTGCATTACTGACAATATGAACTCTTGCTTGGACAGGGACT
76457 TTACTGATGAAGAAATTGTTGCTGCTTTTAACCATATGGACCAGCGAAAAGCTCCGGGGAGTGAT
456 TTACTGATGAAGAAATTGTTGCTGCTTTTAACCATATGGACCAGCGAAAAGCTCCGGGGAGTGAT
76522 GGTTTATCAGGTTGCTTCTTCAAAAAGCACTGGGCCGTAGTTGGAAAAGATGTCTTAAAGTTGTG
521 GGTTTATCAGGTTGCTTCTTCAAAAAGCACTGGGCCGTAGTTGGAAAAGATGTCTTAAAGTTGTG
*
76587 TCACGATATGCTCAATGGCAACAAGGATGT
586 TCACGATGTGCTCAATGGCAACAAGGATGT
76617 TGCGTG
1 TGCGTG
76623 CCTTAATGAT
Statistics
Matches: 1226, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
615 1226 1.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.27
Consensus pattern (615 bp):
TGCGTGATTAGCTTGAGTTGTGGTAGTATAAGCGTTATAAAAGAATGATGAACCAAATATGGGGT
CTGAAGAGGAAGATCAATCAACTTGTAGATGGTCCAAACAGGGATAACACAACTAACCTCCTTAA
AATGGCTCGCTTCAAGCTTGGGCACTTGTATGCTGTGGATGAGGACTATTGGGCACAAAGGGCTC
ACATTAAGTGGCTCACGGAGGGTGATAGAAACACCCGTTATTTTCACATGCACGCTACTGGCAGA
AGAAAGAACACAATATAGAAAAGTTAAAAGATTCTAATGGGACGTGGCAAAAAGACAAGAGGGAC
ATCTGTAAAGTTGCATGGGACTATTTTAATGATCTTTTTAAGTCAACCATTGTTTCTTGTAATGA
ACCTGACATGCATTATATCCAAACGTGCATTACTGACAATATGAACTCTTGCTTGGACAGGGACT
TTACTGATGAAGAAATTGTTGCTGCTTTTAACCATATGGACCAGCGAAAAGCTCCGGGGAGTGAT
GGTTTATCAGGTTGCTTCTTCAAAAAGCACTGGGCCGTAGTTGGAAAAGATGTCTTAAAGTTGTG
TCACGATGTGCTCAATGGCAACAAGGATGT
Found at i:79458 original size:20 final size:20
Alignment explanation
Indices: 79433--79474 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
79423 ATTCAAATTA
79433 GCTCAGAAGTATCAATACTT
1 GCTCAGAAGTATCAATACTT
79453 GCTCAGAAGTATCAATACTT
1 GCTCAGAAGTATCAATACTT
79473 GC
1 GC
79475 GCCCAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (20 bp):
GCTCAGAAGTATCAATACTT
Found at i:82436 original size:27 final size:27
Alignment explanation
Indices: 82381--82464 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
82371 GGTATAACAG
*
82381 TCATTTTACCCTAT-AGGGTATTTCAA
1 TCATTTTACCCTATGGGGGTATTTCAA
*
82407 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCAA
*
82434 TCATTTTACCCTATGGGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCAA
82461 TCAT
1 TCAT
82465 AACAGTGTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 14 0.26
27 39 0.74
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCAA
Found at i:88610 original size:20 final size:21
Alignment explanation
Indices: 88573--88611 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
88563 CGAATATCCT
*
88573 TTTAAAATCAAAATAATAAGA
1 TTTAAAATCAAAAAAATAAGA
88594 TTTAAAAT-AAAAAAATAA
1 TTTAAAATCAAAAAAATAA
88612 AGGCAAGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (21 bp):
TTTAAAATCAAAAAAATAAGA
Found at i:98948 original size:35 final size:35
Alignment explanation
Indices: 98896--98988 Score: 107
Period size: 35 Copynumber: 2.7 Consensus size: 35
98886 GATTTAACAC
* * * * *
98896 AGTGGCATGTTTTACATGCGAATCAGAATA-AGTAT
1 AGTGGCATGCTTAACATGCAAACCAGAA-ACAATAT
98931 AGTGGCATGCTTAACATGCAAACCAGAAACAATAT
1 AGTGGCATGCTTAACATGCAAACCAGAAACAATAT
* *
98966 AGTGACATACTTAACATGCAAAC
1 AGTGGCATGCTTAACATGCAAAC
98989 TAAAATATCA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
34 1 0.02
35 49 0.98
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (35 bp):
AGTGGCATGCTTAACATGCAAACCAGAAACAATAT
Found at i:123787 original size:23 final size:23
Alignment explanation
Indices: 123742--123796 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
123732 TAATAATAAA
123742 GAAAAAAAAAAAAAATAGAAAAT
1 GAAAAAAAAAAAAAATAGAAAAT
123765 GTAAAAAAAAAAAAAA-A-ACAAAT
1 G-AAAAAAAAAAAAAATAGA-AAAT
*
123788 GAAACAAAA
1 GAAAAAAAA
123797 CTTATTCTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 8 0.28
23 7 0.24
24 14 0.48
ACGTcount: A:0.82, C:0.04, G:0.07, T:0.07
Consensus pattern (23 bp):
GAAAAAAAAAAAAAATAGAAAAT
Found at i:124485 original size:38 final size:38
Alignment explanation
Indices: 124421--124637 Score: 199
Period size: 38 Copynumber: 5.6 Consensus size: 38
124411 TAGAAATATA
* * * * *
124421 GTGATTATTCGAGCTATTTGCTTAGCAAGTTGTGTGCCG
1 GTGATTATTAG-GCTATGTGCCTAGCAGGCTGTGTGCCG
* *
124460 GTAATTATTTGGCTATGTGCCTAGCAGGCTGTGTGCCG
1 GTGATTATTAGGCTATGTGCCTAGCAGGCTGTGTGCCG
*
124498 TTGATTATTCGAGGC-ATGTGCCTAGCAGGCTG-GTGCCG
1 GTGATTATT--AGGCTATGTGCCTAGCAGGCTGTGTGCCG
* *
124536 GTGATTATTCAGGCTATGTGCCTAGCAAG-TAGTGTGTCG
1 GTGATTATT-AGGCTATGTGCCTAGCAGGCT-GTGTGCCG
* * * *
124575 GTAATTATTTCGGGCTTTGTGCCTAGCAGGCTCTGTGCCG
1 GTGATTA-TT-AGGCTATGTGCCTAGCAGGCTGTGTGCCG
* *
124615 GTGA-TATTCGGCTATATGCCTAG
1 GTGATTATTAGGCTATGTGCCTAG
124638 TAGGTTGTAT
Statistics
Matches: 148, Mismatches: 23, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
37 17 0.11
38 60 0.41
39 39 0.26
40 31 0.21
41 1 0.01
ACGTcount: A:0.17, C:0.18, G:0.30, T:0.34
Consensus pattern (38 bp):
GTGATTATTAGGCTATGTGCCTAGCAGGCTGTGTGCCG
Found at i:124551 original size:77 final size:77
Alignment explanation
Indices: 124421--124637 Score: 237
Period size: 77 Copynumber: 2.8 Consensus size: 77
124411 TAGAAATATA
* * * * * *
124421 GTGATTATTCGA-GCTATTTGCTTAGCAAGTTGTGTGCCGGTAATTATTTGGCTATGTGCCTAGC
1 GTGATTATTCGAGGCTATGTGCCTAGCAGGCTG-GTGCCGGTGATTATTCGGCTATGTGCCTAGC
*
124485 AGGCT-GTGTGCCG
65 AAG-TAGTGTGCCG
*
124498 TTGATTATTCGAGGC-ATGTGCCTAGCAGGCTGGTGCCGGTGATTATTCAGGCTATGTGCCTAGC
1 GTGATTATTCGAGGCTATGTGCCTAGCAGGCTGGTGCCGGTGATTATTC-GGCTATGTGCCTAGC
*
124562 AAGTAGTGTGTCG
65 AAGTAGTGTGCCG
* * * *
124575 GTAATTATTTCG-GGCTTTGTGCCTAGCAGGCTCTGTGCCGGTGA-TATTCGGCTATATGCCTAG
1 GTGATTA-TTCGAGGCTATGTGCCTAGCAGGCT-GGTGCCGGTGATTATTCGGCTATGTGCCTAG
124638 TAGGTTGTAT
Statistics
Matches: 120, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
76 15 0.12
77 69 0.57
78 26 0.22
79 10 0.08
ACGTcount: A:0.17, C:0.18, G:0.30, T:0.34
Consensus pattern (77 bp):
GTGATTATTCGAGGCTATGTGCCTAGCAGGCTGGTGCCGGTGATTATTCGGCTATGTGCCTAGCA
AGTAGTGTGCCG
Found at i:124635 original size:115 final size:114
Alignment explanation
Indices: 124421--124637 Score: 296
Period size: 115 Copynumber: 1.9 Consensus size: 114
124411 TAGAAATATA
* * *
124421 GTGATTATTCGAGCTATTTGCTTAGCAAGTTGTGTGCCGGTAATTATTTGGCTATGTGCCTAGCA
1 GTGATTATTCGAGCTATGTGCCTAGCAAGTAGTGTGCCGGTAATTATTTGGCTATGTGCCTAGCA
* * *
124486 GGCTGTGTGCCGTTGATTATTCGAGGCATGTGCCTAGCAGGCTGGTGCCG
66 GGCTCTGTGCCGGTGATTATTC-AGGCATATGCCTAGCAGGCTGGTGCCG
* *
124536 GTGATTATTC-AGGCTATGTGCCTAGCAAGTAGTGTGTCGGTAATTATTTCGGGCTTTGTGCCTA
1 GTGATTATTCGA-GCTATGTGCCTAGCAAGTAGTGTGCCGGTAATTATTT--GGCTATGTGCCTA
124600 GCAGGCTCTGTGCCGGTGA-TATTC-GGCTATATGCCTAG
63 GCAGGCTCTGTGCCGGTGATTATTCAGGC-ATATGCCTAG
124638 TAGGTTGTAT
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
114 4 0.04
115 52 0.58
116 5 0.06
117 29 0.32
ACGTcount: A:0.17, C:0.18, G:0.30, T:0.34
Consensus pattern (114 bp):
GTGATTATTCGAGCTATGTGCCTAGCAAGTAGTGTGCCGGTAATTATTTGGCTATGTGCCTAGCA
GGCTCTGTGCCGGTGATTATTCAGGCATATGCCTAGCAGGCTGGTGCCG
Done.