Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 93 of 240
Found at i:29212717 original size:12 final size:12
Alignment explanation
Indices: 29212697--29212736 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
29212687 AACAGAGGCC
*
29212697 GCAGAGAGAGAA
1 GCAGCGAGAGAA
29212709 GCAGCGAGAGAA
1 GCAGCGAGAGAA
*
29212721 GCAGCGATAGAA
1 GCAGCGAGAGAA
29212733 GCAG
1 GCAG
29212737 AGGTTCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.40, T:0.03
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:29213203 original size:42 final size:42
Alignment explanation
Indices: 29213157--29213249 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
29213147 ATCAAATAGT
* *
29213157 GGCGTTTTTGACC-AAGCGCCGCTATAGAAAATTA-CTTTTAGC
1 GGCGTTTTT-ACCTAAGCGCCGCTAAAGAAAATGATC-TTTAGC
* * *
29213199 GGCGTTTTTTCCTAAGCGCTGCTAAAGAACATGATCTTTAGC
1 GGCGTTTTTACCTAAGCGCCGCTAAAGAAAATGATCTTTAGC
29213241 GGCGTTTTT
1 GGCGTTTTT
29213250 TTCTGTAAGC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 2 0.05
42 41 0.93
43 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (42 bp):
GGCGTTTTTACCTAAGCGCCGCTAAAGAAAATGATCTTTAGC
Found at i:29214354 original size:15 final size:16
Alignment explanation
Indices: 29214326--29214359 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
29214316 ATACATATTT
29214326 AAATGAAATGAGAAAA
1 AAATGAAATGAGAAAA
*
29214342 AAAT-AAATTAGAAAA
1 AAATGAAATGAGAAAA
29214357 AAA
1 AAA
29214360 GATAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (16 bp):
AAATGAAATGAGAAAA
Found at i:29214386 original size:5 final size:5
Alignment explanation
Indices: 29214368--29214440 Score: 92
Period size: 5 Copynumber: 13.6 Consensus size: 5
29214358 AAGATAATTT
*
29214368 AAATG AAATGG AAATG AAATG AGATGG AAATAG AAATG AAATG AAATGG
1 AAATG AAAT-G AAATG AAATG AAAT-G AAAT-G AAATG AAATG AAAT-G
29214417 AAATAG AAATG AAATG AAATG AAA
1 AAAT-G AAATG AAATG AAATG AAA
29214441 AAAAAAAGTT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
5 37 0.61
6 24 0.39
ACGTcount: A:0.59, C:0.00, G:0.23, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:29214398 original size:27 final size:27
Alignment explanation
Indices: 29214369--29214440 Score: 101
Period size: 27 Copynumber: 2.6 Consensus size: 27
29214359 AGATAATTTA
* *
29214369 AATGAAATGGAAATGAAAT-GAGATGGA
1 AATGAAAT-GAAATGAAATGGAAATAGA
29214396 AATAGAAATGAAATGAAATGGAAATAGA
1 AAT-GAAATGAAATGAAATGGAAATAGA
29214424 AATGAAATGAAATGAAA
1 AATGAAATGAAATGAAA
29214441 AAAAAAAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 27 0.66
28 14 0.34
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (27 bp):
AATGAAATGAAATGAAATGGAAATAGA
Found at i:29214403 original size:22 final size:22
Alignment explanation
Indices: 29214368--29214437 Score: 115
Period size: 22 Copynumber: 3.2 Consensus size: 22
29214358 AAGATAATTT
*
29214368 AAAT-GAAATGGAAATGAAATG
1 AAATGGAAATAGAAATGAAATG
*
29214389 AGATGGAAATAGAAATGAAATG
1 AAATGGAAATAGAAATGAAATG
29214411 AAATGGAAATAGAAATGAAATG
1 AAATGGAAATAGAAATGAAATG
29214433 AAATG
1 AAATG
29214438 AAAAAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 3 0.07
22 42 0.93
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.19
Consensus pattern (22 bp):
AAATGGAAATAGAAATGAAATG
Found at i:29214977 original size:25 final size:26
Alignment explanation
Indices: 29214927--29214980 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
29214917 AGGAAATGAG
*
29214927 AAAATTTTGAAATTTAAATGAAATTT
1 AAAATTTTGAAATTGAAATGAAATTT
* *
29214953 AAAATTTTGAAA-TGGAATGATATTT
1 AAAATTTTGAAATTGAAATGAAATTT
29214978 AAA
1 AAA
29214981 TTGAGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (26 bp):
AAAATTTTGAAATTGAAATGAAATTT
Found at i:29215178 original size:21 final size:21
Alignment explanation
Indices: 29215148--29215199 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
29215138 TTGTATATTA
29215148 GGAAA-AAAATAAATTTAAAT
1 GGAAATAAAATAAATTTAAAT
29215168 GGAAATAAAATAAATTTAAAT
1 GGAAATAAAATAAATTTAAAT
*
29215189 GGAAATGAAAT
1 GGAAATAAAAT
29215200 GAAAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (21 bp):
GGAAATAAAATAAATTTAAAT
Found at i:29221410 original size:19 final size:20
Alignment explanation
Indices: 29221384--29221432 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
29221374 AGGTAGGTAA
29221384 CTTTTTTTTTGCGGTTTTTG
1 CTTTTTTTTTGCGGTTTTTG
29221404 CTTTTTTTTTGCGGTTTTTG
1 CTTTTTTTTTGCGGTTTTTG
29221424 CTTTTTTTT
1 CTTTTTTTT
29221433 AAAGAATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.00, C:0.10, G:0.16, T:0.73
Consensus pattern (20 bp):
CTTTTTTTTTGCGGTTTTTG
Found at i:29221637 original size:3 final size:3
Alignment explanation
Indices: 29221629--29221663 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
29221619 AAATTAGTTA
29221629 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29221664 AAGGATAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:29222001 original size:31 final size:31
Alignment explanation
Indices: 29221963--29222024 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
29221953 AGGCAAATTA
29221963 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
29221994 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
29222025 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:29223391 original size:90 final size:89
Alignment explanation
Indices: 29223247--29223575 Score: 416
Period size: 90 Copynumber: 3.7 Consensus size: 89
29223237 ATTCTACAAT
* * * * * * *
29223247 ATTAATACAC-AAAATTATAAAATTCAAATAAAAATATTACG-TACTAAGTTAAATTTAAGCACC
1 ATTAATACACGAAAATT-TTAAATTCAAATACATATAATACGAGACTAAATTAAATTTAAACACC
*
29223310 CAACAAACTACAAACATATAGGTAAA
65 CAACAAACTACAAACAGAT-GGTAAA
*
29223336 ATTAATATACGAAAATTTTAAATTCAAACTACATATAATACGA-ACTAAATTAAATTTAAACACC
1 ATTAATACACGAAAATTTTAAATTCAAA-TACATATAATACGAGACTAAATTAAATTTAAACACC
29223400 CAACAAACTACAAACAGATGGATAAA
65 CAACAAACTACAAACAGATGG-TAAA
* * * * * *
29223426 ATTAGTGCATGAAATTTTTAAATTCAAATGATATATAACAC-AGACTAAATTAAATTTAAACACC
1 ATTAATACACGAAAATTTTAAATTCAAAT-ACATATAATACGAGACTAAATTAAATTTAAACACC
29223490 CAACAAACTACAAACAGATGGGTAAA
65 CAACAAACTACAAACAGAT-GGTAAA
*
29223516 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATA-TAGACTAAATTAAATTTAAA
1 ATTAATACACGAAAATTTTAAATTCAAA-TACATATAATACGAGACTAAATTAAATTTAAA
29223576 GATACAAAAA
Statistics
Matches: 210, Mismatches: 21, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
89 23 0.11
90 184 0.88
91 3 0.01
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.27
Consensus pattern (89 bp):
ATTAATACACGAAAATTTTAAATTCAAATACATATAATACGAGACTAAATTAAATTTAAACACCC
AACAAACTACAAACAGATGGTAAA
Found at i:29224496 original size:112 final size:111
Alignment explanation
Indices: 29224231--29224560 Score: 380
Period size: 112 Copynumber: 2.9 Consensus size: 111
29224221 GAAAAAGGTA
* **
29224231 ATGTCGGCCATCAGTGTCCCAAAGTAAAAAGAAAATTG-CATTGGGAGAC-AAAAATGTATTTGG
1 ATGTCGGCCATCAGTGTCCCAAAGTAAAAAG--AATTGTC-TTGGGACACGAAAAATGTACCTGG
* ** *
29224294 TGCCGGCCATCTACTGGCCAGCACTCCAAAAAAATATTTTT-AATAGACACTG
63 TGCCGACCATCTACTGGCCAGCAC-CC---AATTTTTTTTTAAATAGACACTG
* * * *
29224346 ATG-CTGGCTATCAGTGTCCCAAAGTAAAAAAAAATGTCTTGGGACTCGAAAAATGTACCTGGTG
1 ATGTC-GGCCATCAGTGTCCCAAAGTAAAAAGAATTGTCTTGGGACACGAAAAATGTACCTGGTG
* * *
29224410 TCGACCATCTATTGGCCAGCACCCAATTTTTTTTTTAAATTGACACTG
65 CCGACCATCTACTGGCCAGCACCCAA-TTTTTTTTTAAATAGACACTG
* * *
29224458 GTGTCGACCATCAGTGTCCCAAAGTAAAAAGAATTGTCTTGGGACCCGAAAAATGTACCTGGTGC
1 ATGTCGGCCATCAGTGTCCCAAAGTAAAAAGAATTGTCTTGGGACACGAAAAATGTACCTGGTGC
* *
29224523 CGACCACCTACTGGCTAGCACCCAATTTTTTTTTAAAT
66 CGACCATCTACTGGCCAGCACCCAATTTTTTTTTAAAT
29224561 GTCTCTGGTG
Statistics
Matches: 185, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
110 2 0.01
111 19 0.10
112 88 0.48
113 14 0.08
114 35 0.19
115 27 0.15
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (111 bp):
ATGTCGGCCATCAGTGTCCCAAAGTAAAAAGAATTGTCTTGGGACACGAAAAATGTACCTGGTGC
CGACCATCTACTGGCCAGCACCCAATTTTTTTTTAAATAGACACTG
Found at i:29225593 original size:9 final size:9
Alignment explanation
Indices: 29225581--29225623 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
29225571 TAAAAATTAA
29225581 TAAAAAAAT
1 TAAAAAAAT
29225590 TAAATAAAAT
1 TAAA-AAAAT
* *
29225600 TCAAAAAGT
1 TAAAAAAAT
29225609 TAAAAAAA-
1 TAAAAAAAT
29225617 TAAAAAA
1 TAAAAAA
29225624 TGAATCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 7 0.24
9 14 0.48
10 8 0.28
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:29225623 original size:18 final size:18
Alignment explanation
Indices: 29225579--29225623 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
29225569 TTTAAAAATT
29225579 AATAAAAAAATTAAATAA
1 AATAAAAAAATTAAATAA
* *
29225597 AATTCAAAAAGTTAAA-AA
1 AA-TAAAAAAATTAAATAA
29225615 AATAAAAAA
1 AATAAAAAA
29225624 TGAATCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.26
18 6 0.26
19 11 0.48
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (18 bp):
AATAAAAAAATTAAATAA
Found at i:29226859 original size:20 final size:20
Alignment explanation
Indices: 29226836--29226875 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29226826 AAAAATCTAA
29226836 ATAAACAAA-TTAAAAAATAT
1 ATAAA-AAATTTAAAAAATAT
*
29226856 ATAAAAAATTTAAATAATAT
1 ATAAAAAATTTAAAAAATAT
29226876 GTACAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAAAAAATTTAAAAAATAT
Found at i:29231045 original size:26 final size:26
Alignment explanation
Indices: 29231016--29231072 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
29231006 CCATTTTTTT
* * *
29231016 AATAAACACCAAAAAGTTATTTTAAA
1 AATAAAAACAAAAAAATTATTTTAAA
*
29231042 AATAAAAAATAAAAAAATTATTTTAAA
1 AAT-AAAAACAAAAAAATTATTTTAAA
29231069 AATA
1 AATA
29231073 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (26 bp):
AATAAAAACAAAAAAATTATTTTAAA
Found at i:29244017 original size:21 final size:22
Alignment explanation
Indices: 29243967--29244018 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
29243957 AAAAAAAACC
* * *
29243967 CCTTACACCCATCACATCCTAA
1 CCTTTCACCCATCAAATCCAAA
29243989 CCTTTCACCCATCAAAT-CAAA
1 CCTTTCACCCATCAAATCCAAA
*
29244010 CTTTTCACC
1 CCTTTCACC
29244019 TAGAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.31, C:0.42, G:0.00, T:0.27
Consensus pattern (22 bp):
CCTTTCACCCATCAAATCCAAA
Found at i:29255860 original size:21 final size:23
Alignment explanation
Indices: 29255834--29255875 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
29255824 TTCACTGGAT
*
29255834 ACGACGGTG-CCTA-TGGTTGCA
1 ACGACGGCGTCCTAGTGGTTGCA
29255855 ACGACGGCGTCCTAGTGGTTG
1 ACGACGGCGTCCTAGTGGTTG
29255876 GTGGCAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 4 0.22
23 6 0.33
ACGTcount: A:0.17, C:0.24, G:0.36, T:0.24
Consensus pattern (23 bp):
ACGACGGCGTCCTAGTGGTTGCA
Found at i:29259518 original size:42 final size:42
Alignment explanation
Indices: 29259472--29259609 Score: 204
Period size: 42 Copynumber: 3.3 Consensus size: 42
29259462 ATAGTCAGCT
*
29259472 ATGGTCTTACACGAATCTCATATCGATGCCATTGTCCCAAAC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAAAC
*
29259514 ATGGTCTTACATGAATCTCATATCGATGCCAATGTCCCAAAC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAAAC
* * * * *
29259556 ATGGTCTTACATGAATCACATAACAATGCCAATGTCCCAGAC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAAAC
*
29259598 ATGGTTTTACAC
1 ATGGTCTTACAC
29259610 ATAATCACAT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.28
Consensus pattern (42 bp):
ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAAAC
Found at i:29259560 original size:84 final size:84
Alignment explanation
Indices: 29259430--29259608 Score: 213
Period size: 84 Copynumber: 2.1 Consensus size: 84
29259420 GATCCCATAT
* * * *
29259430 ATGGTCTTACATGCTATCATATATCGATGCCAATAGTCAGCTATGGTCTTACACGAATCTCATAT
1 ATGGTCTTACATGCAATCATATATCGATGCCAATAGTCAACTATGGTCTTACACGAATCACATAA
* *
29259495 CGATGCCATTGTCCCAAAC
66 CAATGCCAATGTCCCAAAC
*
29259514 ATGGTCTTACATG-AATC-TCATATCGATGCCAAT-GTCCCAAAC-ATGGTCTTACATGAATCAC
1 ATGGTCTTACATGCAATCAT-ATATCGATGCCAATAGT--C-AACTATGGTCTTACACGAATCAC
*
29259575 ATAACAATGCCAATGTCCCAGAC
62 ATAACAATGCCAATGTCCCAAAC
*
29259598 ATGGTTTTACA
1 ATGGTCTTACA
29259609 CATAATCACA
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
82 3 0.04
83 17 0.21
84 60 0.73
85 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (84 bp):
ATGGTCTTACATGCAATCATATATCGATGCCAATAGTCAACTATGGTCTTACACGAATCACATAA
CAATGCCAATGTCCCAAAC
Found at i:29268105 original size:30 final size:30
Alignment explanation
Indices: 29268035--29268112 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
29268025 AAAGAATAAG
* * * *
29268035 AAATGAAATGGAAA-AAGAAAATTTGAGAA
1 AAATGAAGTGAAAAGAAAAAAAGTTGAGAA
29268064 AAATGAAGTG-AAAGAAAAAAAGTTGAGAA
1 AAATGAAGTGAAAAGAAAAAAAGTTGAGAA
29268093 AAGA-GAAAGTGAAAAGAAAA
1 AA-ATG-AAGTGAAAAGAAAA
29268113 CAAAAATTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 3 0.07
29 25 0.60
30 6 0.14
31 8 0.19
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.13
Consensus pattern (30 bp):
AAATGAAGTGAAAAGAAAAAAAGTTGAGAA
Found at i:29272636 original size:29 final size:30
Alignment explanation
Indices: 29272601--29272668 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 30
29272591 TGAAAACTTC
29272601 ATGTATAAAATTACACA-AAATCAAAGTTT
1 ATGTATAAAATTACACATAAATCAAAGTTT
* *
29272630 ATTTATAACATTACACATTAAATCAAAGTTT
1 ATGTATAAAATTACACA-TAAATCAAAGTTT
29272661 ATGTATAA
1 ATGTATAA
29272669 TTTTGAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 15 0.44
31 19 0.56
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (30 bp):
ATGTATAAAATTACACATAAATCAAAGTTT
Found at i:29278266 original size:26 final size:23
Alignment explanation
Indices: 29278215--29278268 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 23
29278205 TGTTTATGCT
**
29278215 AATTACTTTAAATAGTAAAAGTA
1 AATTACTTTAAATAGTAAAACAA
29278238 AATTACTATTAAATAGAATAAAACAA
1 AATTACT-TTAAATAG--TAAAACAA
29278264 AATTA
1 AATTA
29278269 TTAGTATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.27
24 8 0.31
26 11 0.42
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (23 bp):
AATTACTTTAAATAGTAAAACAA
Found at i:29279939 original size:2 final size:2
Alignment explanation
Indices: 29279932--29279986 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
29279922 TTTATAACAT
29279932 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
29279974 TG TG TG TG TG TG T
1 TG TG TG TG TG TG T
29279987 CTAACTTATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:29281376 original size:21 final size:21
Alignment explanation
Indices: 29281334--29281376 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
29281324 AGGGAAAATG
*
29281334 AAATAAGGAAAAGAAGACAAA
1 AAATAAGGAAAAGAAGAAAAA
*
29281355 AAATAATGTAAAAGAA-AAAAA
1 AAATAA-GGAAAAGAAGAAAAA
29281376 A
1 A
29281377 TATGTTCAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.09
Consensus pattern (21 bp):
AAATAAGGAAAAGAAGAAAAA
Found at i:29290667 original size:18 final size:18
Alignment explanation
Indices: 29290646--29290684 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
29290636 AAAGGAAGAT
29290646 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
29290664 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
29290682 AGA
1 AGA
29290685 GCCAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:29292499 original size:33 final size:34
Alignment explanation
Indices: 29292455--29292529 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
29292445 GAGTTAGTTT
*
29292455 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
* * *
29292488 ATTCATTTTAGTTCAGCTTAAATAATTGTTAGTA
1 ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
29292522 ATTAATTT
1 ATTAATTT
29292530 GTTTAAATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 28 0.78
34 8 0.22
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (34 bp):
ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:29308500 original size:20 final size:19
Alignment explanation
Indices: 29308477--29308522 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
29308467 AAAATCATTT
29308477 AAAATATTAAAAAAGTTGTA
1 AAAATATTAAAAAA-TTGTA
*
29308497 AAAATTCTTAAAAAATTGTA
1 AAAA-TATTAAAAAATTGTA
29308517 ACAAAT
1 A-AAAT
29308523 TGTTAAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (19 bp):
AAAATATTAAAAAATTGTA
Found at i:29308530 original size:20 final size:21
Alignment explanation
Indices: 29308483--29308531 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
29308473 ATTTAAAATA
29308483 TTAAAAAAGTTGTAAAAATTC
1 TTAAAAAAGTTGTAAAAATTC
*
29308504 TTAAAAAA-TTGTAACAAATTG
1 TTAAAAAAGTTGTAA-AAATTC
29308525 TTAAAAA
1 TTAAAAA
29308532 CTATAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (21 bp):
TTAAAAAAGTTGTAAAAATTC
Found at i:29308641 original size:18 final size:19
Alignment explanation
Indices: 29308602--29308651 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
29308592 TTATTTTTAA
*
29308602 AAAAATGATTAAACATTGT
1 AAAAATGATTAAACATTAT
29308621 AAAAATGA-TAAGA-ATTAT
1 AAAAATGATTAA-ACATTAT
* *
29308639 AAACATTATTAAA
1 AAAAATGATTAAA
29308652 GAATTGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (19 bp):
AAAAATGATTAAACATTAT
Found at i:29308907 original size:18 final size:18
Alignment explanation
Indices: 29308875--29308909 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29308865 GTAAAATTAT
**
29308875 TATAATTTTTTCAATTTA
1 TATAATTTTCACAATTTA
29308893 TATAATTTTCACAATTT
1 TATAATTTTCACAATTT
29308910 TTAAATAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (18 bp):
TATAATTTTCACAATTTA
Found at i:29309314 original size:19 final size:18
Alignment explanation
Indices: 29309254--29309315 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
29309244 AAAAAATATA
*
29309254 TTTATATATATTGCAATT
1 TTTATATATATTACAATT
* * * *
29309272 TTTCATTTAAATTAAAAATA
1 TTT-ATATATATT-ACAATT
29309292 TTTATATATATTACTAATT
1 TTTATATATATTAC-AATT
29309311 TTTAT
1 TTTAT
29309316 TCTATGTGGT
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
18 4 0.12
19 22 0.69
20 6 0.19
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTATATATATTACAATT
Found at i:29309430 original size:133 final size:133
Alignment explanation
Indices: 29309175--29309415 Score: 299
Period size: 133 Copynumber: 1.8 Consensus size: 133
29309165 CAAGAAAGAT
* *
29309175 ATTTTTATCCTATGTGATGCACAAATTTAATTACATGTATCAATTAATATATATTATACTAATTT
1 ATTTTTATCCTATGTGATGCACAAATTTAATTACATGTATCAATTAAAATATAATATACTAATTT
* * ** **** *
29309240 CTTAAAAAAATATATTTATATATATTGCAATTTTTCATTTAAATTAAAAATATTTATATATATTA
66 CTTAAAAAAATATATTGAGATATATTAAAAAAAATAATTTAAATTAAAAATATTTATATATATTA
29309305 CTA
131 CTA
* * * * *
29309308 ATTTTTATTCTATGTGGTGCACCAATTTAATTATATGTATTAATTAAAATATAATATACTAATTT
1 ATTTTTATCCTATGTGATGCACAAATTTAATTACATGTATCAATTAAAATATAATATACTAATTT
29309373 CTTAAAAAAAT-TATTGAGA-A-ATTAAAAACAAAATAATTTAAAT
66 CTTAAAAAAATATATTGAGATATATT-AAAA-AAAATAATTTAAAT
29309416 GTTAAATTTT
Statistics
Matches: 90, Mismatches: 16, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
130 3 0.03
131 3 0.03
132 15 0.17
133 69 0.77
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (133 bp):
ATTTTTATCCTATGTGATGCACAAATTTAATTACATGTATCAATTAAAATATAATATACTAATTT
CTTAAAAAAATATATTGAGATATATTAAAAAAAATAATTTAAATTAAAAATATTTATATATATTA
CTA
Found at i:29311143 original size:3 final size:3
Alignment explanation
Indices: 29311129--29311175 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
29311119 GTGAGGTAAG
* * *
29311129 TAT TAG TAT TAT TAT TAG TAT TAT TAT TAG TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29311176 AGATGAGTGG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:29311146 original size:12 final size:12
Alignment explanation
Indices: 29311129--29311175 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
29311119 GTGAGGTAAG
29311129 TATTAGTATTAT
1 TATTAGTATTAT
29311141 TATTAGTATTAT
1 TATTAGTATTAT
29311153 TATTAGTATTAT
1 TATTAGTATTAT
*
29311165 TATTATTATTA
1 TATTAGTATTA
29311176 AGATGAGTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (12 bp):
TATTAGTATTAT
Found at i:29316232 original size:4 final size:4
Alignment explanation
Indices: 29316217--29316247 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
29316207 ATTGCAATCA
29316217 AATT ATATT AATT AATT AATT AATT AATT AA
1 AATT A-ATT AATT AATT AATT AATT AATT AA
29316248 ACTTATAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:29323949 original size:29 final size:29
Alignment explanation
Indices: 29323917--29323985 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
29323907 GTTGGGCTCG
* * * *
29323917 TTTTAATAAAATTGACCCATTTCTGTTAA
1 TTTTAAAAAAAGTGACACATTTCTATTAA
* * *
29323946 TTTTAACAAAAGTGACATATTTCTATTAT
1 TTTTAAAAAAAGTGACACATTTCTATTAA
29323975 TTTTAAAAAAA
1 TTTTAAAAAAA
29323986 ATGAGATTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (29 bp):
TTTTAAAAAAAGTGACACATTTCTATTAA
Found at i:29324551 original size:21 final size:22
Alignment explanation
Indices: 29324522--29324565 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
29324512 AAAGATTAAT
*
29324522 TATTATATCATTCATA-AAAAAA
1 TATTATATC-TGCATATAAAAAA
29324544 TATT-TATCTGCATATAAAAAA
1 TATTATATCTGCATATAAAAAA
29324565 T
1 T
29324566 TCTTTGTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (22 bp):
TATTATATCTGCATATAAAAAA
Found at i:29325653 original size:24 final size:24
Alignment explanation
Indices: 29325610--29325655 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
29325600 AAAATTTAAG
*
29325610 TCGAGTTAAATCAAATAAAATTGT
1 TCGAGTTAAATCAAAAAAAATTGT
29325634 TCGAGTTAAA-CTAAAAAAAATT
1 TCGAGTTAAATC-AAAAAAAATT
29325656 AAACATGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (24 bp):
TCGAGTTAAATCAAAAAAAATTGT
Found at i:29325790 original size:20 final size:19
Alignment explanation
Indices: 29325767--29325811 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
29325757 TTCTAGAAAT
* *
29325767 TTTTTTATATATTTTTTAGA
1 TTTTTTATA-ATATTTTAAA
29325787 TTTTTT-TAATATTTTAAA
1 TTTTTTATAATATTTTAAA
29325805 TTTTTTA
1 TTTTTTA
29325812 AAAATACAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 14 0.64
19 2 0.09
20 6 0.27
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTTATAATATTTTAAA
Found at i:29332668 original size:21 final size:22
Alignment explanation
Indices: 29332625--29332670 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
29332615 TTTATTAAAA
29332625 TAATAAATTATATTAATCATAT
1 TAATAAATTATATTAATCATAT
*
29332647 TAAT-AATT-TATTATATCTTAT
1 TAATAAATTATATTA-ATCATAT
29332668 TAA
1 TAA
29332671 ATATAAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATAAATTATATTAATCATAT
Found at i:29344274 original size:20 final size:21
Alignment explanation
Indices: 29344230--29344276 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
29344220 TAATTGTTAT
*
29344230 ATTTTA-ATATTTAAAATATA
1 ATTTTATATATTCAAAATATA
*
29344250 A-TTTATATATTCAAATTA-A
1 ATTTTATATATTCAAAATATA
29344269 ATTTTATA
1 ATTTTATA
29344277 AATAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTATATATTCAAAATATA
Found at i:29346170 original size:31 final size:31
Alignment explanation
Indices: 29346132--29346247 Score: 94
Period size: 31 Copynumber: 3.6 Consensus size: 31
29346122 AATTTAATAA
29346132 AAATATATAATTTAATAAAATTCTTAATATT
1 AAATATATAATTTAATAAAATTCTTAATATT
* *
29346163 AAATATATGAATTTACTAAAA-TCATAATATAT
1 AAATATAT-AATTTAATAAAATTCTTAATAT-T
* * ** *
29346195 AATACTATAAAATATAATTTAAAATAATTATTATT
1 AA-A-TATATAATTTAA--TAAAATTCTTAATATT
29346230 -AA-ATATAATTTAATAAAA
1 AAATATATAATTTAATAAAA
29346248 ATATATAATT
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
29 5 0.07
31 25 0.37
32 14 0.21
33 7 0.10
34 5 0.07
35 6 0.09
36 5 0.07
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (31 bp):
AAATATATAATTTAATAAAATTCTTAATATT
Found at i:29349400 original size:23 final size:23
Alignment explanation
Indices: 29349371--29349418 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
29349361 CATGGGTTGC
*
29349371 TGTTTTTTTTCTCTTTTCTGGGT
1 TGTTTTTTTTCTCTTTTATGGGT
29349394 TGTTTTTTTTCTCTTTTATGGGT
1 TGTTTTTTTTCTCTTTTATGGGT
29349417 TG
1 TG
29349419 CTGTTTCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.02, C:0.10, G:0.19, T:0.69
Consensus pattern (23 bp):
TGTTTTTTTTCTCTTTTATGGGT
Found at i:29349586 original size:25 final size:26
Alignment explanation
Indices: 29349548--29349701 Score: 176
Period size: 25 Copynumber: 6.2 Consensus size: 26
29349538 GGCGATGCGG
*
29349548 CAGAGGACTGTCGATGGCAATGTAGA
1 CAGAGGACTGTCGATGGCAATGCAGA
*
29349574 -AGAGGACTATCGATGGCAATGC-GA
1 CAGAGGACTGTCGATGGCAATGCAGA
* *
29349598 TAGAGGACTTTCGATGGCAATGCA-A
1 CAGAGGACTGTCGATGGCAATGCAGA
* * * *
29349623 CAGAGGACTTTCGATGACGATGC-GG
1 CAGAGGACTGTCGATGGCAATGCAGA
**
29349648 CAGAGGACTGTCGATGGTGATGCA-A
1 CAGAGGACTGTCGATGGCAATGCAGA
29349673 CAGAGGACTGTCGATGGCAATGCAG-
1 CAGAGGACTGTCGATGGCAATGCAGA
29349698 CAGA
1 CAGA
29349702 CGTTCAGGGA
Statistics
Matches: 110, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
24 2 0.02
25 108 0.98
ACGTcount: A:0.30, C:0.18, G:0.34, T:0.19
Consensus pattern (26 bp):
CAGAGGACTGTCGATGGCAATGCAGA
Found at i:29349701 original size:50 final size:50
Alignment explanation
Indices: 29349542--29349701 Score: 205
Period size: 50 Copynumber: 3.2 Consensus size: 50
29349532 TTACACGGCG
*
29349542 ATGCGGCAGAGGACTGTCGATGGCAATGTAGA-AGAGGACTATCGATGGCA
1 ATGCGGCAGAGGACTGTCGATGGCAATGCA-ACAGAGGACTATCGATGGCA
** * * * *
29349592 ATGCGATAGAGGACTTTCGATGGCAATGCAACAGAGGACTTTCGATGACG
1 ATGCGGCAGAGGACTGTCGATGGCAATGCAACAGAGGACTATCGATGGCA
** *
29349642 ATGCGGCAGAGGACTGTCGATGGTGATGCAACAGAGGACTGTCGATGGCA
1 ATGCGGCAGAGGACTGTCGATGGCAATGCAACAGAGGACTATCGATGGCA
*
29349692 ATGCAGCAGA
1 ATGCGGCAGA
29349702 CGTTCAGGGA
Statistics
Matches: 93, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 1 0.01
50 92 0.99
ACGTcount: A:0.29, C:0.17, G:0.34, T:0.19
Consensus pattern (50 bp):
ATGCGGCAGAGGACTGTCGATGGCAATGCAACAGAGGACTATCGATGGCA
Found at i:29350538 original size:39 final size:37
Alignment explanation
Indices: 29350480--29350616 Score: 127
Period size: 39 Copynumber: 3.5 Consensus size: 37
29350470 CCCATCCCTT
*
29350480 TCCTTCTTCCCACCATCCCTCCCCCTTACTTCGATTCTC
1 TCCTTCTCCCCACCATCCCT-CCCCTTAC-TCGATTCTC
*
29350519 TCCTTCTCCCCACCGTCCCTCCCCTTACTCTGATTCTCAC
1 TCCTTCTCCCCACCATCCCTCCCCTTACTC-GATTCT--C
*
29350559 TCTCTTCT--CCACCATCCCTCACCTTACTC-ATCTTCTC
1 TC-CTTCTCCCCACCATCCCTCCCCTTACTCGA--TTCTC
* *
29350596 TCCCTCTCTCCCACCGTCCCT
1 TCCTTCTC-CCCACCATCCCT
29350617 TTCTCTCTAC
Statistics
Matches: 83, Mismatches: 6, Indels: 18
0.78 0.06 0.17
Matches are distributed among these distances:
36 4 0.05
37 6 0.07
38 14 0.17
39 51 0.61
40 3 0.04
41 5 0.06
ACGTcount: A:0.10, C:0.53, G:0.03, T:0.34
Consensus pattern (37 bp):
TCCTTCTCCCCACCATCCCTCCCCTTACTCGATTCTC
Found at i:29352007 original size:29 final size:32
Alignment explanation
Indices: 29351972--29352054 Score: 104
Period size: 30 Copynumber: 2.7 Consensus size: 32
29351962 AATCTCAAAG
29351972 TTATATAT-TAATTTTGATTTAAAGT-TAAAT
1 TTATATATATAATTTTGATTTAAAGTATAAAT
*
29352002 TT-TATATATAAATTTTGATTT--TGTATAAAT
1 TTATATATAT-AATTTTGATTTAAAGTATAAAT
*
29352032 TTATATATAAAATTTTGATTTAA
1 TTATATATATAATTTTGATTTAA
29352055 TGTAATTCTC
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
29 7 0.16
30 21 0.47
31 17 0.38
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (32 bp):
TTATATATATAATTTTGATTTAAAGTATAAAT
Found at i:29352010 original size:31 final size:31
Alignment explanation
Indices: 29351972--29352054 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
29351962 AATCTCAAAG
*
29351972 TTATATATTAATTTTGATTTAAAGT-TAAATT
1 TTATATATAAATTTTGATTTAAAGTATAAA-T
*
29352003 TTATATATAAATTTTGATTT--TGTATAAAT
1 TTATATATAAATTTTGATTTAAAGTATAAAT
29352032 TTATATATAAAATTTTGATTTAA
1 TTATATAT-AAATTTTGATTTAA
29352055 TGTAATTCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
29 11 0.24
30 16 0.35
31 19 0.41
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (31 bp):
TTATATATAAATTTTGATTTAAAGTATAAAT
Found at i:29352912 original size:22 final size:22
Alignment explanation
Indices: 29352887--29352967 Score: 99
Period size: 22 Copynumber: 3.7 Consensus size: 22
29352877 ATTTTGTATT
*
29352887 ATATAACATATCAGAGAATATA
1 ATATAACATATCAGAGAATATC
** *
29352909 ATATAACATATTGGAGCATATC
1 ATATAACATATCAGAGAATATC
** *
29352931 ATATAACATATTGGAGTATATC
1 ATATAACATATCAGAGAATATC
29352953 ATATAACATATCAGA
1 ATATAACATATCAGA
29352968 ACATATCTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (22 bp):
ATATAACATATCAGAGAATATC
Found at i:29352973 original size:44 final size:44
Alignment explanation
Indices: 29352887--29352974 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
29352877 ATTTTGTATT
** *
29352887 ATATAACATATCAGAGAATATAATATAACATATTGGAGCATATC
1 ATATAACATATCAGAGAATATAATATAACATATCAGAACATATC
** * *
29352931 ATATAACATATTGGAGTATATCATATAACATATCAGAACATATC
1 ATATAACATATCAGAGAATATAATATAACATATCAGAACATATC
29352975 TTACTCCCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (44 bp):
ATATAACATATCAGAGAATATAATATAACATATCAGAACATATC
Found at i:29365325 original size:16 final size:16
Alignment explanation
Indices: 29365299--29365345 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
29365289 CAGCTATTTT
*
29365299 ATTCAAATAATAATAAC
1 ATTC-AATAATAATAAA
*
29365316 ATTCAATAATATTAAA
1 ATTCAATAATAATAAA
*
29365332 ATTCATTAATAATA
1 ATTCAATAATAATA
29365346 TTATAACTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTCAATAATAATAAA
Found at i:29369176 original size:75 final size:76
Alignment explanation
Indices: 29369096--29369239 Score: 220
Period size: 76 Copynumber: 1.9 Consensus size: 76
29369086 ATTGATGTAA
* * * *
29369096 AATACAGTAGAATACAATATAAATTATTT-TT-CTTTTTTTCCGTAGATTGTAAATAAGTATATA
1 AATACAATAGAATACAATACAAATAATTTCTTAATTTTTTT-CGTAGATTGTAAATAAGTATATA
29369159 TTATTGACATGG
65 TTATTGACATGG
*
29369171 AATACAATAGAATACAATACAAATAATTTCTTAATTTTTTTCTTAGATTGTAAATAAGTATATAT
1 AATACAATAGAATACAATACAAATAATTTCTTAATTTTTTTCGTAGATTGTAAATAAGTATATAT
29369236 TATT
66 TATT
29369240 TATGTAAAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 26 0.42
76 29 0.47
77 7 0.11
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (76 bp):
AATACAATAGAATACAATACAAATAATTTCTTAATTTTTTTCGTAGATTGTAAATAAGTATATAT
TATTGACATGG
Found at i:29369251 original size:76 final size:75
Alignment explanation
Indices: 29369079--29369259 Score: 238
Period size: 75 Copynumber: 2.4 Consensus size: 75
29369069 GTAAGTATTG
* * * *
29369079 ATATATTATTGATGTAAAATACAGTAGAATACAATATAAATTATTTTTCTTTTTTTCCGTAGATT
1 ATATATTATTGATGTAAAATACAATAGAATACAATACAAATAATTTTTATTTTTTTCCGTAGATT
29369144 GTAAATAAGT
66 GTAAATAAGT
** ** *
29369154 ATATATTATTGACATGGAATACAATAGAATACAATACAAATAATTTCTTAATTTTTTT-CTTAGA
1 ATATATTATTGATGTAAAATACAATAGAATACAATACAAATAATTT-TT-ATTTTTTTCCGTAGA
29369218 TTGTAAATAAGT
64 TTGTAAATAAGT
*
29369230 ATATATTATTTATGTAAAATACAAATAGAA
1 ATATATTATTGATGTAAAATAC-AATAGAA
29369260 CAATTTTTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
75 39 0.44
76 36 0.40
77 14 0.16
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (75 bp):
ATATATTATTGATGTAAAATACAATAGAATACAATACAAATAATTTTTATTTTTTTCCGTAGATT
GTAAATAAGT
Found at i:29370358 original size:27 final size:27
Alignment explanation
Indices: 29370322--29370385 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
29370312 TAAAAAAATA
*
29370322 ACCAAAATATTATAATTTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
*
29370349 ATCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
29370376 ACCAAAATAT
1 ACCAAAATAT
29370386 GCAAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (27 bp):
ACCAAAATATTATAAATTTTTTTATTT
Found at i:29370418 original size:16 final size:17
Alignment explanation
Indices: 29370392--29370423 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29370382 ATATGCAAAA
29370392 AAAAAACAAAAACCTGC
1 AAAAAACAAAAACCTGC
29370409 AAAAAA-AAAAACCTG
1 AAAAAACAAAAACCTG
29370424 TGGCGGCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.69, C:0.19, G:0.06, T:0.06
Consensus pattern (17 bp):
AAAAAACAAAAACCTGC
Found at i:29370926 original size:23 final size:23
Alignment explanation
Indices: 29370900--29370971 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 23
29370890 ACTCTATTTT
29370900 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
*
29370923 AATTACTTAATAACTCTATT-T--T--
1 AA-T--TTAATAA-ACTATTCTCATCA
29370945 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
29370968 AATT
1 AATT
29370972 ACCAAAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
18 5 0.13
19 8 0.21
21 2 0.05
22 2 0.05
23 6 0.16
24 2 0.05
26 8 0.21
27 5 0.13
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTTAATAAACTATTCTCATCA
Found at i:29370934 original size:45 final size:45
Alignment explanation
Indices: 29370885--29370973 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
29370875 TCTAATTAAG
29370885 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
29370930 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTAC
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTAC
29370974 CAAAATAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (45 bp):
TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
Found at i:29370999 original size:15 final size:15
Alignment explanation
Indices: 29370979--29371028 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
29370969 ATTACCAAAA
29370979 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
29370994 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
*
29371009 GAGAATAGTTTATTAAAT
1 TAG---AGTTTATTAAAT
29371027 TA
1 TA
29371029 AAATAGAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 17 0.57
18 13 0.43
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (15 bp):
TAGAGTTTATTAAAT
Found at i:29371033 original size:18 final size:18
Alignment explanation
Indices: 29370997--29371034 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29370987 ATTAAATTAG
*
29370997 AGTTTATTAAATGAGAAT
1 AGTTTATTAAATGAAAAT
*
29371015 AGTTTATTAAATTAAAAT
1 AGTTTATTAAATGAAAAT
29371033 AG
1 AG
29371035 AGTTATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (18 bp):
AGTTTATTAAATGAAAAT
Found at i:29371367 original size:26 final size:26
Alignment explanation
Indices: 29371338--29371399 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
29371328 ATTTTTTGGT
29371338 ATATTTTGGTAAATAAAAAAATTATA
1 ATATTTTGGTAAATAAAAAAATTATA
29371364 ATATTTTGGTAAATAAAAAAATTATA
1 ATATTTTGGTAAATAAAAAAATTATA
29371390 ATATTTTGGT
1 ATATTTTGGT
29371400 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (26 bp):
ATATTTTGGTAAATAAAAAAATTATA
Found at i:29374089 original size:34 final size:35
Alignment explanation
Indices: 29374031--29374097 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 35
29374021 CAAACACCAG
29374031 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
29374066 AAAATATTTTTCC-G-AAATCATTTTACGGAAAA
1 AAAATA-TTTTCCAGTAAATCATTTTACAGAAAA
29374098 TATTTTACTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 17 0.57
35 7 0.23
36 6 0.20
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:29375431 original size:48 final size:48
Alignment explanation
Indices: 29375360--29375454 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
29375350 TTCTTTGCTT
29375360 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAGC
1 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAGC
* *
29375408 AAAAACGCCTAAGTCGGCCTAACTTGCAATGATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAG
29375455 AATTCCCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAGC
Found at i:29375711 original size:36 final size:36
Alignment explanation
Indices: 29375659--29375729 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
29375649 GTCAAAGGCT
29375659 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
* * *
29375695 ACAATTAGAAGTTGTATACAATTAGAACTCTAAGA
1 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGA
29375730 TTACATAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
Found at i:29380577 original size:48 final size:48
Alignment explanation
Indices: 29380500--29380593 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
29380490 TTCTTTGCTT
*
29380500 AAAACGCCTAAGTTAGCCTAACTCACAATGATAAAGGATTCAACAGCA
1 AAAACGCCTAAGTCAGCCTAACTCACAATGATAAAGGATTCAACAGCA
* **
29380548 AAAACGCCTAAGTCGGCCTAACTTGCAATGATAAAGGATTCAACAG
1 AAAACGCCTAAGTCAGCCTAACTCACAATGATAAAGGATTCAACAG
29380594 AATTCCCTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.19
Consensus pattern (48 bp):
AAAACGCCTAAGTCAGCCTAACTCACAATGATAAAGGATTCAACAGCA
Found at i:29380819 original size:17 final size:17
Alignment explanation
Indices: 29380797--29380857 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
29380787 CATCAAAGGC
29380797 TACAATTAAAAGCTGTA
1 TACAATTAAAAGCTGTA
*
29380814 TACAATTAAAA-CTCTAAGA
1 TACAATTAAAAGCTGT---A
* *
29380833 CACAATTAGAAGCTGTA
1 TACAATTAAAAGCTGTA
29380850 TACAATTA
1 TACAATTA
29380858 GAACTTTAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 3 0.09
17 19 0.54
19 10 0.29
20 3 0.09
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.28
Consensus pattern (17 bp):
TACAATTAAAAGCTGTA
Found at i:29380846 original size:36 final size:36
Alignment explanation
Indices: 29380798--29380868 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
29380788 ATCAAAGGCT
29380798 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
* * *
29380834 ACAATTAGAAGCTGTATACAATTAGAACTTTAAGA
1 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGA
29380869 TTACATAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
Found at i:29383498 original size:13 final size:12
Alignment explanation
Indices: 29383480--29383517 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
29383470 TTTTACATAT
29383480 ATATTAATTTTAA
1 ATATTAA-TTTAA
29383493 ATATTAA-TTAA
1 ATATTAATTTAA
29383504 ATATTAATATTAA
1 ATATTAAT-TTAA
29383517 A
1 A
29383518 ATTTCGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.48
13 12 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATTAATTTAA
Found at i:29384352 original size:7 final size:7
Alignment explanation
Indices: 29384330--29384408 Score: 69
Period size: 7 Copynumber: 11.6 Consensus size: 7
29384320 AGCCCGAAGG
29384330 AGAA-AA
1 AGAAGAA
29384336 AGAA-ATA
1 AGAAGA-A
*
29384343 AGAAGGA
1 AGAAGAA
29384350 AGAAGAA
1 AGAAGAA
*
29384357 AAAAGAA
1 AGAAGAA
29384364 AGAAGAA
1 AGAAGAA
29384371 AGAAGAA
1 AGAAGAA
29384378 A-AAGAGA
1 AGAAGA-A
*
29384385 AAAAGGAA
1 AGAA-GAA
29384393 AGAA-AA
1 AGAAGAA
29384399 AGAA-AA
1 AGAAGAA
29384405 AGAA
1 AGAA
29384409 AAAATATATA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
6 21 0.33
7 34 0.54
8 6 0.10
9 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (7 bp):
AGAAGAA
Found at i:29384357 original size:17 final size:17
Alignment explanation
Indices: 29384330--29384409 Score: 64
Period size: 16 Copynumber: 5.1 Consensus size: 17
29384320 AGCCCGAAGG
* *
29384330 AGAAAAAGAAATAAGAA
1 AGAAGAAGAAAAAAGAA
*
29384347 GGAAGAAGAAAAAAG--
1 AGAAGAAGAAAAAAGAA
*
29384362 A-AAGAAGAAAGAAGAA
1 AGAAGAAGAAAAAAGAA
*
29384378 A-AAG-AGAAAAAGGAA
1 AGAAGAAGAAAAAAGAA
*
29384393 AGAAAAAG-AAAAAGAA
1 AGAAGAAGAAAAAAGAA
29384409 A
1 A
29384410 AAATATATAT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
14 12 0.24
15 10 0.20
16 14 0.28
17 14 0.28
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (17 bp):
AGAAGAAGAAAAAAGAA
Found at i:29384364 original size:24 final size:23
Alignment explanation
Indices: 29384332--29384411 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 23
29384322 CCCGAAGGAG
29384332 AAAAAGAAATAAGAAGGAAGAAGA
1 AAAAAGAAA-AAGAAGGAAGAAGA
*
29384356 AAAAAG--AAAGAAGAAAGAAGA
1 AAAAAGAAAAAGAAGGAAGAAGA
* *
29384377 AAAAGAGAAAAAGGAAAGAAAAAG-
1 AAAA-AGAAAAA-GAAGGAAGAAGA
29384401 AAAAAGAAAAA
1 AAAAAGAAAAA
29384412 ATATATATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
21 17 0.35
22 3 0.06
23 7 0.15
24 13 0.27
25 8 0.17
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (23 bp):
AAAAAGAAAAAGAAGGAAGAAGA
Found at i:29384366 original size:28 final size:28
Alignment explanation
Indices: 29384334--29384402 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 28
29384324 CGAAGGAGAA
*
29384334 AAAGAAATAAGAAGGAAGAAGA-AAAAA-G
1 AAAGAAA-AAGAA-GAAAAAGAGAAAAAGG
29384362 AAAGAAGAAAGAAGAAAAAGAGAAAAAGG
1 AAAGAA-AAAGAAGAAAAAGAGAAAAAGG
29384391 AAAGAAAAAGAA
1 AAAGAAAAAGAA
29384403 AAAGAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 7 0.19
28 22 0.59
29 8 0.22
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (28 bp):
AAAGAAAAAGAAGAAAAAGAGAAAAAGG
Found at i:29385217 original size:17 final size:17
Alignment explanation
Indices: 29385174--29385221 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
29385164 TTTTAAAAAA
29385174 TCGTGTTTCAAAAGTTT
1 TCGTGTTTCAAAAGTTT
*
29385191 TCATGTTTTCAAAA-TTT
1 TCGTG-TTTCAAAAGTTT
29385208 CTCGTGTTTCAAAA
1 -TCGTGTTTCAAAA
29385222 AATAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (17 bp):
TCGTGTTTCAAAAGTTT
Found at i:29385328 original size:18 final size:17
Alignment explanation
Indices: 29385279--29385551 Score: 91
Period size: 18 Copynumber: 15.1 Consensus size: 17
29385269 TTTTAAAAAT
29385279 AATTTTCGTGTTTC--A
1 AATTTTCGTGTTTCAAA
*
29385294 AACTTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTCAAA
29385312 AATTTCTCGTGTTTCAAAA
1 AATTT-TCGTGTTTC-AAA
29385331 AATTTT-G-G---C---
1 AATTTTCGTGTTTCAAA
* *
29385340 -CTTTTCGCGTTTTCAAA
1 AATTTTCGTG-TTTCAAA
29385357 AATTTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTCAAA
* *
29385375 ATTTTCTCGTGTTTTAAA
1 AATTT-TCGTGTTTCAAA
*
29385393 AATTTTCGACTTTTCGCGTTTTAAAA
1 AATTTTCG-----T---G-TTTCAAA
29385419 AATTTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTCAAA
* * *
29385437 AATTTCTCCTATTTTAAA
1 AATTT-TCGTGTTTCAAA
29385455 AATTTTCGACTTTTTGCGTTTTCAAA
1 AATTTTCG------T--GTT-TCAAA
* *
29385481 AATTTTCGTGTTTTAGA
1 AATTTTCGTGTTTCAAA
*
29385498 AATTTTCGTGTTTCTAA
1 AATTTTCGTGTTTCAAA
* *
29385515 AATTCTCGTATTTCAAA
1 AATTTTCGTGTTTCAAA
*
29385532 AATTTCCGTGTTCTCAAA
1 AATTTTCGTGTT-TCAAA
29385550 AA
1 AA
29385552 AATTATTATC
Statistics
Matches: 195, Mismatches: 27, Indels: 69
0.67 0.09 0.24
Matches are distributed among these distances:
8 4 0.02
9 1 0.01
10 1 0.01
13 1 0.01
14 1 0.01
15 9 0.05
16 5 0.03
17 46 0.24
18 73 0.37
19 21 0.11
20 1 0.01
21 1 0.01
22 1 0.01
23 1 0.01
25 3 0.02
26 26 0.13
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.48
Consensus pattern (17 bp):
AATTTTCGTGTTTCAAA
Found at i:29385330 original size:17 final size:16
Alignment explanation
Indices: 29385279--29385330 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 16
29385269 TTTTAAAAAT
29385279 AATTTTCGTGTTTC-A
1 AATTTTCGTGTTTCAA
*
29385294 AACTTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTC-AA
29385312 AATTTCTCGTGTTTCAA
1 AATTT-TCGTGTTTCAA
29385329 AA
1 AA
29385331 AATTTTGGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 9 0.29
16 4 0.13
17 4 0.13
18 9 0.29
19 5 0.16
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (16 bp):
AATTTTCGTGTTTCAA
Found at i:29385407 original size:62 final size:63
Alignment explanation
Indices: 29385297--29385516 Score: 331
Period size: 62 Copynumber: 3.6 Consensus size: 63
29385287 TGTTTCAAAC
* * *
29385297 TTTCGTGTTTTCAAAAATTTCTCGTGTTTCAAAAAATTTTGGCCTTTTCGCGTTTTCAAAAAT
1 TTTCGTGTTTTCAAAAATTTCTCGTGTTTCTAAAAATTTTCGACTTTTCGCGTTTTCAAAAAT
* *
29385360 TTTCGTGTTTTCAAAATTTTCTCGTGTTT-TAAAAATTTTCGACTTTTCGCGTTTTAAAAAAT
1 TTTCGTGTTTTCAAAAATTTCTCGTGTTTCTAAAAATTTTCGACTTTTCGCGTTTTCAAAAAT
* * *
29385422 TTTCGTGTTTTCAAAAATTTCTCCTATTT-TAAAAATTTTCGACTTTTTGCGTTTTCAAAAAT
1 TTTCGTGTTTTCAAAAATTTCTCGTGTTTCTAAAAATTTTCGACTTTTCGCGTTTTCAAAAAT
*
29385484 TTTCGTGTTTT-AGAAATTT-TCGTGTTTCTAAAA
1 TTTCGTGTTTTCAAAAATTTCTCGTGTTTCTAAAA
29385517 TTCTCGTATT
Statistics
Matches: 143, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
60 6 0.04
61 12 0.08
62 97 0.68
63 28 0.20
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (63 bp):
TTTCGTGTTTTCAAAAATTTCTCGTGTTTCTAAAAATTTTCGACTTTTCGCGTTTTCAAAAAT
Found at i:29385486 original size:17 final size:17
Alignment explanation
Indices: 29385474--29385551 Score: 93
Period size: 17 Copynumber: 4.5 Consensus size: 17
29385464 CTTTTTGCGT
29385474 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
* *
29385491 TTTTAGAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
* * *
29385508 TTTCTAAAATTCTCGTA
1 TTTCAAAAATTTTCGTG
*
29385525 TTTCAAAAATTTCCGTG
1 TTTCAAAAATTTTCGTG
29385542 TTCTCAAAAA
1 TT-TCAAAAA
29385552 AATTATTATC
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 42 0.86
18 7 0.14
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (17 bp):
TTTCAAAAATTTTCGTG
Found at i:29386670 original size:25 final size:25
Alignment explanation
Indices: 29386641--29386791 Score: 92
Period size: 25 Copynumber: 6.1 Consensus size: 25
29386631 CTTTCTCTCA
*
29386641 AGCCATATAACGGGAAGCTCATGTG
1 AGCCATATAACGGGAAGCTCATGAG
* * **
29386666 AGCCATGTAACGGGAAGCTAATTCG
1 AGCCATATAACGGGAAGCTCATGAG
** * * *
29386691 AGCTGTATAATGAGAAGCTCATAAG
1 AGCCATATAACGGGAAGCTCATGAG
* * * *
29386716 AGCCATAATTA--GGAAGTTCAAGCG
1 AGCCAT-ATAACGGGAAGCTCATGAG
* **
29386740 AGCCA-ATATCGGGAAGCTCCGGAG
1 AGCCATATAACGGGAAGCTCATGAG
* * *
29386764 AGCCATATATCAGGAAGCTCATAAG
1 AGCCATATAACGGGAAGCTCATGAG
29386789 AGC
1 AGC
29386792 TATGGTGTGT
Statistics
Matches: 92, Mismatches: 30, Indels: 8
0.71 0.23 0.06
Matches are distributed among these distances:
22 2 0.02
24 27 0.29
25 60 0.65
26 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATGAG
Found at i:29395130 original size:29 final size:32
Alignment explanation
Indices: 29395088--29395146 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
29395078 ATTATTTGTG
*
29395088 AAAATTGAATC-AAATCAAAATTT-TATATTT
1 AAAATCGAATCAAAATCAAAATTTGTATATTT
*
29395118 AAAATCGAA-CAAAATCAAAGTTTGTATAT
1 AAAATCGAATCAAAATCAAAATTTGTATAT
29395147 GATATTACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 19 0.76
31 5 0.20
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (32 bp):
AAAATCGAATCAAAATCAAAATTTGTATATTT
Found at i:29395185 original size:43 final size:43
Alignment explanation
Indices: 29395138--29395231 Score: 181
Period size: 43 Copynumber: 2.2 Consensus size: 43
29395128 AAAATCAAAG
29395138 TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
1 TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
29395181 TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
1 TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
29395224 TTT-TATAT
1 TTTGTATAT
29395232 TTATCCTAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 5 0.10
43 46 0.90
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (43 bp):
TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
Found at i:29398941 original size:20 final size:20
Alignment explanation
Indices: 29398893--29398943 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
29398883 AAAACCTCAG
**
29398893 TGGTATCGATATTTTTCCAC
1 TGGTATCGATATTTTTAAAC
*
29398913 -GAGTGTCGATATTTTTAAAC
1 TG-GTATCGATATTTTTAAAC
29398933 TGGTATCGATA
1 TGGTATCGATA
29398944 CCAAATTACC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 23 0.92
21 1 0.04
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (20 bp):
TGGTATCGATATTTTTAAAC
Found at i:29416706 original size:13 final size:12
Alignment explanation
Indices: 29416688--29416725 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
29416678 TTTTACATAT
29416688 ATATTAATTTTAA
1 ATATTAA-TTTAA
29416701 ATATTAA-TTAA
1 ATATTAATTTAA
29416712 ATATTAATATTAA
1 ATATTAAT-TTAA
29416725 A
1 A
29416726 ATTTCGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.48
13 12 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATTAATTTAA
Found at i:29417563 original size:7 final size:7
Alignment explanation
Indices: 29417541--29417616 Score: 61
Period size: 7 Copynumber: 11.1 Consensus size: 7
29417531 AGCCCGAAGG
29417541 AGAAA-A
1 AGAAAGA
*
29417547 AGAAATA
1 AGAAAGA
*
29417554 AGAAGGA
1 AGAAAGA
29417561 AG-AAGA
1 AGAAAGA
*
29417567 AAAAAGA
1 AGAAAGA
29417574 AGAAAGA
1 AGAAAGA
*
29417581 AGAAAAA
1 AGAAAGA
*
29417588 AGAGAAAA
1 AGA-AAGA
29417596 AGGAAAGA
1 A-GAAAGA
29417604 A-AAAGA
1 AGAAAGA
29417610 A-AAAGA
1 AGAAAGA
29417616 A
1 A
29417617 AAAAATATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
6 21 0.36
7 27 0.46
8 9 0.15
9 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (7 bp):
AGAAAGA
Found at i:29417568 original size:17 final size:17
Alignment explanation
Indices: 29417541--29417620 Score: 89
Period size: 17 Copynumber: 4.9 Consensus size: 17
29417531 AGCCCGAAGG
*
29417541 AGAAA-AAGAAATAAGA
1 AGAAAGAAGAAAAAAGA
*
29417557 AGGAAGAAGAAAAAAGA
1 AGAAAGAAGAAAAAAGA
29417574 AGAAAGAAGAAAAAAG-
1 AGAAAGAAGAAAAAAGA
29417590 AGAAA-AAGGAAAGAAA-A
1 AGAAAGAA-GAAA-AAAGA
29417607 AGAAA-AAGAAAAAA
1 AGAAAGAAGAAAAAA
29417621 ATATATAAAC
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.09
16 17 0.30
17 35 0.61
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (17 bp):
AGAAAGAAGAAAAAAGA
Found at i:29417606 original size:11 final size:12
Alignment explanation
Indices: 29417541--29417619 Score: 58
Period size: 11 Copynumber: 6.6 Consensus size: 12
29417531 AGCCCGAAGG
29417541 AGAAAAAGAAATA
1 AGAAAAAGAAA-A
* *
29417554 AG--AAGGAAGA
1 AGAAAAAGAAAA
29417564 AGAAAAAAGAAGAA
1 AG-AAAAAGAA-AA
*
29417578 AGAAGAAA-AAAG
1 AGAA-AAAGAAAA
*
29417590 AGAAAAAG-GAA
1 AGAAAAAGAAAA
29417601 AGAAAAAGAAAA
1 AGAAAAAGAAAA
29417613 AGAAAAA
1 AGAAAAA
29417620 AATATATAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
10 3 0.06
11 17 0.33
12 14 0.27
13 11 0.22
14 6 0.12
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (12 bp):
AGAAAAAGAAAA
Found at i:29417611 original size:10 final size:10
Alignment explanation
Indices: 29417541--29417611 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
29417531 AGCCCGAAGG
29417541 AGAAAAAGAA
1 AGAAAAAGAA
* * *
29417551 ATAAGAAGGA
1 AGAAAAAGAA
29417561 AGAAGAAA-AA
1 AGAA-AAAGAA
29417571 AGAAGAAAG-A
1 AGAA-AAAGAA
*
29417581 AGAAAAA-AG
1 AGAAAAAGAA
29417590 AGAAAAAGGAA
1 AGAAAAA-GAA
29417601 AGAAAAAGAA
1 AGAAAAAGAA
29417611 A
1 A
29417612 AAGAAAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 10 0.21
10 28 0.58
11 10 0.21
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (10 bp):
AGAAAAAGAA
Found at i:29418428 original size:17 final size:18
Alignment explanation
Indices: 29418385--29418430 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
29418375 TTTTAAAAAA
29418385 TCGTGTTTCAAAAGTTTC
1 TCGTGTTTCAAAAGTTTC
*
29418403 -AGT-TTTCAAAA-TTTC
1 TCGTGTTTCAAAAGTTTC
29418418 TCGTGTTTCAAAA
1 TCGTGTTTCAAAA
29418431 AATAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 4 0.17
16 10 0.42
17 10 0.42
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (18 bp):
TCGTGTTTCAAAAGTTTC
Found at i:29418521 original size:17 final size:18
Alignment explanation
Indices: 29418499--29418739 Score: 97
Period size: 17 Copynumber: 12.8 Consensus size: 18
29418489 CGTTTCAAAT
29418499 TCGTG-TTCAAAAATTTC
1 TCGTGTTTCAAAAATTTC
29418516 TCGTGTTTCAAAAATTTTGGCC
1 TCGTGTTTCAAAAA-TTT---C
*
29418538 TTTTCGCGTTTTCAAAAATTT-
1 ---TCGTG-TTTCAAAAATTTC
*
29418559 TCGTGTTTC-AAAATTTT
1 TCGTGTTTCAAAAATTTC
29418576 TCGTGTTT-AAAAATTTCGAC
1 TCGTGTTTCAAAAATTT---C
* * *
29418596 TTTTCGCGTTTTAAAAAATT-
1 ---TCGTGTTTCAAAAATTTC
29418616 TCGTGTTTCAAAAATTTC
1 TCGTGTTTCAAAAATTTC
* * *
29418634 TCCTATTTTAAAAATTTCGAC
1 TCGTGTTTCAAAAATTT---C
* *
29418655 TTTTTGCGTTTCAAAAA-TT-
1 ---TCGTGTTTCAAAAATTTC
* *
29418674 TCGTGTTTTAGAAATTT-
1 TCGTGTTTCAAAAATTTC
*
29418691 TCGTGTTTCTAAAA-TTC
1 TCGTGTTTCAAAAATTTC
*
29418708 TCGTATTTCAAAAATTTC
1 TCGTGTTTCAAAAATTTC
29418726 -CGTGTTCTCAAAAA
1 TCGTGTT-TCAAAAA
29418740 AATTATTATC
Statistics
Matches: 169, Mismatches: 26, Indels: 57
0.67 0.10 0.23
Matches are distributed among these distances:
16 19 0.11
17 68 0.40
18 36 0.21
19 3 0.02
21 1 0.01
22 1 0.01
23 9 0.05
24 16 0.09
25 7 0.04
26 9 0.05
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.46
Consensus pattern (18 bp):
TCGTGTTTCAAAAATTTC
Found at i:29418607 original size:58 final size:58
Alignment explanation
Indices: 29418498--29418698 Score: 257
Period size: 58 Copynumber: 3.5 Consensus size: 58
29418488 TCGTTTCAAA
* *
29418498 TTCGTG-TTCAAAAATTTCTCGTGTTTCAAAAATTTTGGCCTTTTCGCGTTTTCAAAAATT
1 TTCGTGTTTCAAAAATTTCTCGTGTTT-AAAAA-TTTCGACTTTTCGCGTTTTCAAAAA-T
* *
29418558 TTCGTGTTTC-AAAATTTTTCGTGTTTAAAAATTTCGACTTTTCGCGTTTTAAAAAAT
1 TTCGTGTTTCAAAAATTTCTCGTGTTTAAAAATTTCGACTTTTCGCGTTTTCAAAAAT
* * *
29418615 TTCGTGTTTCAAAAATTTCTCCTATTTTAAAAATTTCGACTTTTTGCG-TTTCAAAAAT
1 TTCGTGTTTCAAAAATTTCTCGT-GTTTAAAAATTTCGACTTTTCGCGTTTTCAAAAAT
* *
29418673 TTCGTGTTTTAGAAATTT-TCGTGTTT
1 TTCGTGTTTCAAAAATTTCTCGTGTTT
29418699 CTAAAATTCT
Statistics
Matches: 125, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
56 3 0.02
57 14 0.11
58 57 0.46
59 27 0.22
60 21 0.17
61 3 0.02
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (58 bp):
TTCGTGTTTCAAAAATTTCTCGTGTTTAAAAATTTCGACTTTTCGCGTTTTCAAAAAT
Found at i:29418618 original size:40 final size:41
Alignment explanation
Indices: 29418556--29418633 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
29418546 TTTTCAAAAA
* **
29418556 TTTTCGTGTTTCAAAATTTTTCGTGTTT-AAAAATTTCGAC
1 TTTTCGCGTTTCAAAAAATTTCGTGTTTCAAAAATTTCGAC
*
29418596 TTTTCGCGTTTTAAAAAATTTCGTGTTTCAAAAATTTC
1 TTTTCGCGTTTCAAAAAATTTCGTGTTTCAAAAATTTC
29418634 TCCTATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
40 24 0.73
41 9 0.27
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.49
Consensus pattern (41 bp):
TTTTCGCGTTTCAAAAAATTTCGTGTTTCAAAAATTTCGAC
Found at i:29419845 original size:25 final size:25
Alignment explanation
Indices: 29419816--29419966 Score: 92
Period size: 25 Copynumber: 6.1 Consensus size: 25
29419806 CTTTCTCTCA
*
29419816 AGCCATATAACGGGAAGCTCATGTG
1 AGCCATATAACGGGAAGCTCATGAG
* * **
29419841 AGCCATGTAACGGGAAGCTAATTCG
1 AGCCATATAACGGGAAGCTCATGAG
** * * *
29419866 AGCTGTATAATGAGAAGCTCATAAG
1 AGCCATATAACGGGAAGCTCATGAG
* * * *
29419891 AGCCATAATTA--GGAAGTTCAAGCG
1 AGCCAT-ATAACGGGAAGCTCATGAG
* **
29419915 AGCCA-ATATCGGGAAGCTCCGGAG
1 AGCCATATAACGGGAAGCTCATGAG
* * *
29419939 AGCCATATATCAGGAAGCTCATAAG
1 AGCCATATAACGGGAAGCTCATGAG
29419964 AGC
1 AGC
29419967 TATGGTGTGT
Statistics
Matches: 92, Mismatches: 30, Indels: 8
0.71 0.23 0.06
Matches are distributed among these distances:
22 2 0.02
24 27 0.29
25 60 0.65
26 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATGAG
Found at i:29428280 original size:29 final size:32
Alignment explanation
Indices: 29428238--29428296 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
29428228 ATTATTTGTG
*
29428238 AAAATTGAATC-AAATCAAAATTT-TATATTT
1 AAAATCGAATCAAAATCAAAATTTGTATATTT
*
29428268 AAAATCGAA-CAAAATCAAAGTTTGTATAT
1 AAAATCGAATCAAAATCAAAATTTGTATAT
29428297 GATATTACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 19 0.76
31 5 0.20
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (32 bp):
AAAATCGAATCAAAATCAAAATTTGTATATTT
Found at i:29428335 original size:43 final size:43
Alignment explanation
Indices: 29428288--29428381 Score: 181
Period size: 43 Copynumber: 2.2 Consensus size: 43
29428278 AAAATCAAAG
29428288 TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
1 TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
29428331 TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
1 TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
29428374 TTT-TATAT
1 TTTGTATAT
29428382 TTATCCTAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 5 0.10
43 46 0.90
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (43 bp):
TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
Found at i:29432203 original size:20 final size:20
Alignment explanation
Indices: 29432178--29432232 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
29432168 AAAACCTCTG
*
29432178 GTATCGATATTTTTACACTA
1 GTATCGATATTTTTACAATA
*
29432198 GTATCGATATTTTTATAATA
1 GTATCGATATTTTTACAATA
*
29432218 GTATCAATATTTTTA
1 GTATCGATATTTTTA
29432233 AGTTGGTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (20 bp):
GTATCGATATTTTTACAATA
Found at i:29442334 original size:17 final size:18
Alignment explanation
Indices: 29442307--29442343 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
29442297 GTGGAGTTTG
29442307 TCTTCTTCCTTCTTCTTT
1 TCTTCTTCCTTCTTCTTT
*
29442325 TCTT-TTCCTTTTTCTTT
1 TCTTCTTCCTTCTTCTTT
29442342 TC
1 TC
29442344 CAAACTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
TCTTCTTCCTTCTTCTTT
Found at i:29445321 original size:62 final size:59
Alignment explanation
Indices: 29445213--29445330 Score: 182
Period size: 62 Copynumber: 1.9 Consensus size: 59
29445203 TATAATGCCT
*
29445213 AGGGTAGCTTAAAGGAGAAGATCCTGTTATCATCATGCCTTAGGGTATTTATAGGGCCC
1 AGGGTAGCTTAAAGGAGAAGAGCCTGTTATCATCATGCCTTAGGGTATTTATAGGGCCC
* *
29445272 AGGGTAGCTTAAAGAAGAAGAAGAGCCTGTTATCATCGTGCCTTGGGGTATTTATAGGG
1 AGGGTAGCTTAAAG--G-AGAAGAGCCTGTTATCATCATGCCTTAGGGTATTTATAGGG
29445331 GGAAGGTCCT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
59 14 0.26
61 1 0.02
62 38 0.72
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (59 bp):
AGGGTAGCTTAAAGGAGAAGAGCCTGTTATCATCATGCCTTAGGGTATTTATAGGGCCC
Found at i:29453935 original size:22 final size:22
Alignment explanation
Indices: 29453896--29453942 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
29453886 ATAATAGTTC
**
29453896 AAAAATTTTCTTTTCATTTATTA
1 AAAAATTTTCTTGACATTTA-TA
29453919 AAAAATTTTC-TGACATTTATA
1 AAAAATTTTCTTGACATTTATA
29453940 AAA
1 AAA
29453943 CCTATGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 7 0.32
23 10 0.45
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (22 bp):
AAAAATTTTCTTGACATTTATA
Found at i:29461165 original size:2 final size:2
Alignment explanation
Indices: 29461158--29461205 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
29461148 ATGCTACATT
29461158 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
29461200 TG TG TG
1 TG TG TG
29461206 AAGCTGTCTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:29469842 original size:164 final size:164
Alignment explanation
Indices: 29469571--29469932 Score: 634
Period size: 164 Copynumber: 2.2 Consensus size: 164
29469561 CCTCTGCCGA
* * *
29469571 TTTCCTTGTTGGTAAGTTAATCCCCTTCAGATTTCCTTGTTGCTGAAGCCTTAGTTGCAGCTTCT
1 TTTCCTTGTTGGTAAGTTAATCCCCTTCAAATTTCCTTGTTGCTGAAGCCTTAGCTGCAGCCTCT
*
29469636 TCAAGCTTTCGAACTGTACTTTCTGATTTCCTTGTTGGTAAGTTAATGGGTTCTTCAAGTTTTAT
66 TCAAGCTTTCGAACTGTACTTTCTAATTTCCTTGTTGGTAAGTTAATGGGTTCTTCAAGTTTTAT
29469701 TCTTTTATGATATTATTGGCATAACTGAGTAGTT
131 TCTTTTATGATATTATTGGCATAACTGAGTAGTT
* *
29469735 TTTCCTTATTGGTAAGTTAATCCCCTTTAAATTTCCTTGTTGCTGAAGCCTTAGCTGCAGCCTCT
1 TTTCCTTGTTGGTAAGTTAATCCCCTTCAAATTTCCTTGTTGCTGAAGCCTTAGCTGCAGCCTCT
* *
29469800 TCAAGCTTTCGAACTGTACTTTCTAATTTCTTTGTTGGTAAGTTAATGGGTTCTTCAAGTTTTCT
66 TCAAGCTTTCGAACTGTACTTTCTAATTTCCTTGTTGGTAAGTTAATGGGTTCTTCAAGTTTTAT
29469865 TCTTTTATGATATTATTGGCATAACTGAGTAGTT
131 TCTTTTATGATATTATTGGCATAACTGAGTAGTT
* *
29469899 TTTCCTTGTTGGTAAGTTAATCTCCTTCAGATTT
1 TTTCCTTGTTGGTAAGTTAATCCCCTTCAAATTT
29469933 GTTTCACTCT
Statistics
Matches: 186, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
164 186 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (164 bp):
TTTCCTTGTTGGTAAGTTAATCCCCTTCAAATTTCCTTGTTGCTGAAGCCTTAGCTGCAGCCTCT
TCAAGCTTTCGAACTGTACTTTCTAATTTCCTTGTTGGTAAGTTAATGGGTTCTTCAAGTTTTAT
TCTTTTATGATATTATTGGCATAACTGAGTAGTT
Found at i:29481507 original size:47 final size:45
Alignment explanation
Indices: 29481456--29481620 Score: 121
Period size: 47 Copynumber: 3.6 Consensus size: 45
29481446 TATTTAATAT
29481456 TAATTATTTTAAATTGTATAAATTCATATAAGAAAAATTATTATCAA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAAATTATTAT-AA
* * **
29481503 TAATT-TTATGAAA-TTATATATT-AT-T-A-AATTA-TATGTAATAA
1 TAATTATT-TTAAATTTATAAATTCATATAAGAAAAATTAT-T-ATAA
* * * *
29481544 TAATTATTTTAAATTATACAAATTCATATAAGATAATTTATTAGTTA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAAATTATTA-TAA
29481591 TAATTATTTTAAATTTTATTAAA-TCATATA
1 TAATTATTTTAAA-TTTA-TAAATTCATATA
29481621 TTTTAATTAA
Statistics
Matches: 91, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
40 3 0.03
41 15 0.16
42 6 0.07
43 7 0.08
44 4 0.04
45 8 0.09
46 5 0.05
47 35 0.38
48 8 0.09
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (45 bp):
TAATTATTTTAAATTTATAAATTCATATAAGAAAAATTATTATAA
Found at i:29481532 original size:25 final size:24
Alignment explanation
Indices: 29481504--29481561 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
29481494 TATTATCAAT
* *
29481504 AATTTTATGAAATTATATATTATTA
1 AATTATATGAAATAATA-ATTATTA
*
29481529 AATTATATGTAATAATAATTATTTTA
1 AATTATATGAAATAATAATTA--TTA
29481555 AATTATA
1 AATTATA
29481562 CAAATTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 14 0.50
26 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (24 bp):
AATTATATGAAATAATAATTATTA
Found at i:29481542 original size:88 final size:91
Alignment explanation
Indices: 29481382--29481586 Score: 299
Period size: 88 Copynumber: 2.3 Consensus size: 91
29481372 TTGATTTTAG
* *
29481382 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
29481447 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* *
29481474 TAAATTCATATAAGAAAAATTATTATCAATAATTTTATGAAA-T-TATAT-ATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
29481536 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
29481562 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
29481587 GTTATAATTA
Statistics
Matches: 103, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
88 59 0.57
89 5 0.05
90 1 0.01
91 22 0.21
92 16 0.16
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:29481628 original size:47 final size:49
Alignment explanation
Indices: 29481504--29481629 Score: 123
Period size: 47 Copynumber: 2.6 Consensus size: 49
29481494 TATTATCAAT
* *
29481504 AATTTTATGAAATTATATATTATTAAATTATATGTAATAATAATTATTTTA
1 AATTTTATCAAATCATATATT-TT-AATTATATGTAATAATAATTATTTTA
* *** * *
29481555 AATTATA-CAAATTCATATAAGATAATT-TAT-TAGTTATAATTATTTTA
1 AATTTTATCAAA-TCATATATTTTAATTATATGTAATAATAATTATTTTA
*
29481602 AATTTTATTAAATCATATATTTTAATTA
1 AATTTTATCAAATCATATATTTTAATTA
29481630 AAATATATTT
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
47 33 0.56
48 6 0.10
49 4 0.07
50 4 0.07
51 12 0.20
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (49 bp):
AATTTTATCAAATCATATATTTTAATTATATGTAATAATAATTATTTTA
Found at i:29481757 original size:16 final size:16
Alignment explanation
Indices: 29481736--29481777 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
29481726 TTATTAAATT
*
29481736 ATATATTTTAATTATA
1 ATATATTTTAATAATA
29481752 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
29481767 AT-TATGTTTAA
1 ATATAT-TTTAA
29481778 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:29481762 original size:15 final size:15
Alignment explanation
Indices: 29481727--29481768 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29481717 TTAAGAATTT
*
29481727 TATTAAATTAT-ATA
1 TATTTAATTATAATA
29481741 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
29481755 TATTTAATAATAAT
1 TATTTAATTATAAT
29481769 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:29482012 original size:16 final size:16
Alignment explanation
Indices: 29481991--29482028 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
29481981 TTGATTTGCT
*
29481991 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
29482007 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
29482023 AATACA
1 ATTACA
29482029 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:29486124 original size:19 final size:19
Alignment explanation
Indices: 29486100--29486136 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29486090 ATTCAAGCCC
*
29486100 CAAGATTAAATAATAAAAG
1 CAAGATTAAATAAGAAAAG
29486119 CAAGATTAAATAAGAAAA
1 CAAGATTAAATAAGAAAA
29486137 AAATTCACCA
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:0.65, C:0.05, G:0.11, T:0.19
Consensus pattern (19 bp):
CAAGATTAAATAAGAAAAG
Found at i:29489010 original size:38 final size:39
Alignment explanation
Indices: 29488914--29489035 Score: 112
Period size: 38 Copynumber: 3.2 Consensus size: 39
29488904 CTTTGAATGC
** * *
29488914 ATATATATA-TTATTCAAATACATATGCCAAAAGCAA-AT
1 ATATATATACTTA-TCAACCACATATGCCGAATGCAACAT
* *
29488952 A-AT-TATACTTATCAACCACATGTGCTGAATGC-ACAT
1 ATATATATACTTATCAACCACATATGCCGAATGCAACAT
*
29488988 ATATATATACTTAT-AATTCACATATGCCGAATGCATACAT
1 ATATATATACTTATCAA-CCACATATGCCGAATGCA-ACAT
29489028 ATATATAT
1 ATATATAT
29489036 CCAACAATTT
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
35 1 0.01
36 22 0.32
37 9 0.13
38 24 0.35
40 12 0.18
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (39 bp):
ATATATATACTTATCAACCACATATGCCGAATGCAACAT
Found at i:29495439 original size:21 final size:19
Alignment explanation
Indices: 29495414--29495454 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29495404 AAAATTCAGA
29495414 AAATAAATAAAACAAACAAAG
1 AAATAAA-AAAA-AAACAAAG
*
29495435 AAATAAAAAAAAAACTAAG
1 AAATAAAAAAAAAACAAAG
29495454 A
1 A
29495455 TGAAATTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 4 0.21
21 7 0.37
ACGTcount: A:0.78, C:0.07, G:0.05, T:0.10
Consensus pattern (19 bp):
AAATAAAAAAAAAACAAAG
Found at i:29498131 original size:18 final size:21
Alignment explanation
Indices: 29498078--29498132 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
29498068 TGCGATTGGT
29498078 TATTGTAGTGGTGAGATTAAA
1 TATTGTAGTGGTGAGATTAAA
**
29498099 TATTGTAGTAATGAGATTAAA
1 TATTGTAGTGGTGAGATTAAA
29498120 -A-T-TAGTGGTGAGA
1 TATTGTAGTGGTGAGA
29498133 CATGTGTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 9 0.30
19 1 0.03
20 1 0.03
21 19 0.63
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (21 bp):
TATTGTAGTGGTGAGATTAAA
Found at i:29500750 original size:16 final size:16
Alignment explanation
Indices: 29500731--29500761 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29500721 ATTGATGGAA
*
29500731 AATTCACAGATACATG
1 AATTCACACATACATG
29500747 AATTCACACATACAT
1 AATTCACACATACAT
29500762 TGTTTTTTTT
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:0.45, C:0.23, G:0.06, T:0.26
Consensus pattern (16 bp):
AATTCACACATACATG
Found at i:29501517 original size:19 final size:17
Alignment explanation
Indices: 29501490--29501540 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
29501480 AATTTTTTAA
*
29501490 ATTATATATAAAATTTT
1 ATTAAATATAAAATTTT
29501507 AATTAACATAT-AAATGTTT
1 -ATTAA-ATATAAAAT-TTT
*
29501526 ATTAAAAATAAAATT
1 ATTAAATATAAAATT
29501541 AAATCTTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 4 0.14
18 17 0.61
19 7 0.25
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTAAATATAAAATTTT
Found at i:29501521 original size:18 final size:19
Alignment explanation
Indices: 29501495--29501539 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
29501485 TTTAAATTAT
29501495 ATATAAAAT-TTTAATTAAC
1 ATATAAAATGTTT-ATTAAC
29501514 ATAT-AAATGTTTATTAA-
1 ATATAAAATGTTTATTAAC
*
29501531 AAATAAAAT
1 ATATAAAAT
29501540 TAAATCTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 3 0.13
18 13 0.57
19 7 0.30
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
ATATAAAATGTTTATTAAC
Found at i:29524455 original size:3 final size:3
Alignment explanation
Indices: 29524449--29524483 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
29524439 TCTATTATTT
29524449 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
29524484 TCCATTCCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:29531433 original size:61 final size:58
Alignment explanation
Indices: 29531363--29531478 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 58
29531353 AGTAATTATC
* * *
29531363 TTAATATTAAATTTAATTTAATATTTATCTTGTAGATAGATATTCTATTAATTTAATAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATAGAT
29531424 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
29531479 TTAAAGTGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 22 0.42
59 1 0.02
60 1 0.02
61 28 0.54
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (58 bp):
TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAGAT
Found at i:29531497 original size:58 final size:60
Alignment explanation
Indices: 29531365--29531498 Score: 168
Period size: 58 Copynumber: 2.2 Consensus size: 60
29531355 TAATTATCTT
* * * *
29531365 AATATTAAATTTAATTTAATATTTATCTTGTAGATAGATATTCTATTAATTTAATAGATTT
1 AATATTAAATTTAATCTAATATTTATCTTGTAGATAAATATTATATTAATTTAATA-ATTA
29531426 AATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAAT-ATTA
1 AATATTAAATTTAATCTAATATTTATCTTGTAGATAAATATTATATTAATTTAATAATTA
*
29531482 AAGTGATTAAGTTTAAT
1 AA-T-ATTAAATTTAAT
29531499 TATAATTGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
56 5 0.08
57 1 0.02
58 32 0.48
59 1 0.02
60 1 0.02
61 26 0.39
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (60 bp):
AATATTAAATTTAATCTAATATTTATCTTGTAGATAAATATTATATTAATTTAATAATTA
Found at i:29535143 original size:53 final size:53
Alignment explanation
Indices: 29535076--29535336 Score: 283
Period size: 53 Copynumber: 4.9 Consensus size: 53
29535066 AGCACTAAAG
* * * * *
29535076 GACCATATCATGTAAAATCATAATTGGTGGGTTATGACATCATATGGAATGAA
1 GACCATATCGTGTAAGACCATAACTGGTGGGTTATGACATCATATGGAAAGAA
* **
29535129 GACCATATCGTGTAAGACCATAACTGGTGAGTTATGGTATCATATGGAAAGAA
1 GACCATATCGTGTAAGACCATAACTGGTGGGTTATGACATCATATGGAAAGAA
* * * * *
29535182 AAACATATCATGTAAGACCATAACTGGTGGGTTAAGGCATCATATGGAAAGAA
1 GACCATATCGTGTAAGACCATAACTGGTGGGTTATGACATCATATGGAAAGAA
* * * * **
29535235 GATCATATTGTGTAAGACCGTAACTGATGGGTTAT-AGCAT-ATTATATAAAGAA
1 GACCATATCGTGTAAGACCATAACTGGTGGGTTATGA-CATCA-TATGGAAAGAA
* * * *
29535288 GACCATATCGTGTAAGACCGTAACTAGTGGGTTATCATATCATATGGAA
1 GACCATATCGTGTAAGACCATAACTGGTGGGTTATGACATCATATGGAA
29535337 GAACTTAAGA
Statistics
Matches: 173, Mismatches: 31, Indels: 8
0.82 0.15 0.04
Matches are distributed among these distances:
52 1 0.01
53 170 0.98
54 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (53 bp):
GACCATATCGTGTAAGACCATAACTGGTGGGTTATGACATCATATGGAAAGAA
Found at i:29539921 original size:15 final size:14
Alignment explanation
Indices: 29539890--29539930 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
29539880 TGTTTCATTG
*
29539890 AAAATAATTTTTGA
1 AAAATGATTTTTGA
29539904 AAAATGATTTTTGA
1 AAAATGATTTTTGA
29539918 AAAATGATATTTT
1 AAAATGAT-TTTT
29539931 CTGATGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (14 bp):
AAAATGATTTTTGA
Found at i:29541091 original size:20 final size:20
Alignment explanation
Indices: 29541068--29541151 Score: 57
Period size: 20 Copynumber: 4.0 Consensus size: 20
29541058 AAATTTTATT
29541068 AAAAATCATAAAAA-TATAGAA
1 AAAAAT-ATAAAAATTATA-AA
*
29541089 AAAAATTTAAAAATTATAAA
1 AAAAATATAAAAATTATAAA
* *
29541109 AAAATTAATATAAAA-GAT-AA
1 AAAAAT-ATA-AAAATTATAAA
*
29541129 AAAAATACAGAAAATTATTAAA
1 AAAAATATA-AAAATTA-TAAA
29541151 A
1 A
29541152 TTTTATTAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
19 6 0.12
20 21 0.43
21 15 0.31
22 7 0.14
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (20 bp):
AAAAATATAAAAATTATAAA
Done.