Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 45 of 66
Found at i:16192602 original size:15 final size:15
Alignment explanation
Indices: 16192582--16192615 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
16192572 AAAAAAATTG
16192582 AAAAGGCAAGAAAAC
1 AAAAGGCAAGAAAAC
* *
16192597 AAAAGGGAAGAAAAG
1 AAAAGGCAAGAAAAC
16192612 AAAA
1 AAAA
16192616 AGTTGAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.06, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAAGGCAAGAAAAC
Found at i:16197909 original size:23 final size:23
Alignment explanation
Indices: 16197882--16197931 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
16197872 TCTTTAAATT
* *
16197882 ACATTATCTTCTTGATAA-ATCCC
1 ACATTATCATCTAGATAATAT-CC
16197905 ACATTATCATCTAGATAATATCC
1 ACATTATCATCTAGATAATATCC
16197928 ACAT
1 ACAT
16197932 GTAGATGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (23 bp):
ACATTATCATCTAGATAATATCC
Found at i:16210074 original size:20 final size:19
Alignment explanation
Indices: 16210042--16210079 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
16210032 ACCTAGAGCA
16210042 AAAATAATGTAAACTTAACC
1 AAAATAATGTAAA-TTAACC
16210062 AAAATAACT-TAAATTAAC
1 AAAATAA-TGTAAATTAAC
16210080 TACTCAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 11 0.65
21 1 0.06
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (19 bp):
AAAATAATGTAAATTAACC
Found at i:16210151 original size:21 final size:22
Alignment explanation
Indices: 16210115--16210156 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
16210105 CTTGAAAAAT
* *
16210115 ACCTAAAATGTTAAAG-TCTAA
1 ACCTAAAATCTCAAAGATCTAA
16210136 ACCTAAAATCTCAAAGATCTA
1 ACCTAAAATCTCAAAGATCTA
16210157 GCTACTTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.26
Consensus pattern (22 bp):
ACCTAAAATCTCAAAGATCTAA
Found at i:16217636 original size:13 final size:13
Alignment explanation
Indices: 16217618--16217643 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16217608 AAGAGAAATT
16217618 ATGATTTTATAAA
1 ATGATTTTATAAA
16217631 ATGATTTTATAAA
1 ATGATTTTATAAA
16217644 TTTTCTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
ATGATTTTATAAA
Found at i:16221875 original size:15 final size:15
Alignment explanation
Indices: 16221855--16221892 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
16221845 AAGATATTTT
16221855 GATTTTAAAGCTTTG
1 GATTTTAAAGCTTTG
* *
16221870 GATTTTAAAGTTTTT
1 GATTTTAAAGCTTTG
16221885 GATTTTAA
1 GATTTTAA
16221893 GGTTGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (15 bp):
GATTTTAAAGCTTTG
Found at i:16221968 original size:5 final size:5
Alignment explanation
Indices: 16221938--16221967 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
16221928 CCCCAAGTCC
*
16221938 AGTTA AGTTA AGTTA AGTTA AGTTA GGTTA
1 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA
16221968 GATTGAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (5 bp):
AGTTA
Found at i:16229944 original size:21 final size:21
Alignment explanation
Indices: 16229920--16229963 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
16229910 AGGTACATAT
*
16229920 GTTGTTTTAATTAAGACAAGA
1 GTTGTTTAAATTAAGACAAGA
* *
16229941 GTTGTTTAAATTTAGATAAGA
1 GTTGTTTAAATTAAGACAAGA
16229962 GT
1 GT
16229964 ATATGTGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.41
Consensus pattern (21 bp):
GTTGTTTAAATTAAGACAAGA
Found at i:16241573 original size:42 final size:42
Alignment explanation
Indices: 16241473--16241590 Score: 150
Period size: 42 Copynumber: 2.8 Consensus size: 42
16241463 GTGGACCCAG
* * *
16241473 CTAAGTGCGAGTAGGAGTGTACATAAGCCGATGATGACCCCT
1 CTAAGTGCGAGTGGGAGTGCACATAAGCTGATGATGACCCCT
16241515 CTAAGTGCGAGTGGGAGTGCACATAAGCTGATGATGACCCAC-
1 CTAAGTGCGAGTGGGAGTGCACATAAGCTGATGATGACCC-CT
* * *
16241557 C-ACGTGCTAGTGGGGAGTGCACATGAGCTGATGA
1 CTAAGTGCGAGT-GGGAGTGCACATAAGCTGATGA
16241591 CGATGGGAGA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
41 8 0.12
42 59 0.87
43 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.20
Consensus pattern (42 bp):
CTAAGTGCGAGTGGGAGTGCACATAAGCTGATGATGACCCCT
Found at i:16241624 original size:2 final size:2
Alignment explanation
Indices: 16241617--16241651 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16241607 ATGATGATGA
16241617 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16241652 AATGTATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16242674 original size:2 final size:2
Alignment explanation
Indices: 16242667--16242692 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16242657 ATAATGTATG
16242667 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
16242693 CTTGATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16248281 original size:18 final size:18
Alignment explanation
Indices: 16248235--16248281 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
16248225 AAAGAAGAAG
*
16248235 AAGAAGAATAAGACAAGA
1 AAGAAGAAAAAGACAAGA
* *
16248253 GAGAAGCAAAAGA-AAGA
1 AAGAAGAAAAAGACAAGA
16248270 AAGAAAGAAAAA
1 AAG-AAGAAAAA
16248282 CATTGCCTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.70, C:0.04, G:0.23, T:0.02
Consensus pattern (18 bp):
AAGAAGAAAAAGACAAGA
Found at i:16252570 original size:13 final size:13
Alignment explanation
Indices: 16252552--16252576 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16252542 GGAAAATGGG
16252552 ATTTTATAAAATA
1 ATTTTATAAAATA
16252565 ATTTTATAAAAT
1 ATTTTATAAAAT
16252577 TTTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:16260457 original size:21 final size:19
Alignment explanation
Indices: 16260428--16260466 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
16260418 TTGATGACAA
16260428 AAAGAGGGAGAAATAGAAAGC
1 AAAGAGGGAG--ATAGAAAGC
*
16260449 AAAGGGGGAGATAGAAAG
1 AAAGAGGGAGATAGAAAG
16260467 TAGAAGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.54, C:0.03, G:0.38, T:0.05
Consensus pattern (19 bp):
AAAGAGGGAGATAGAAAGC
Found at i:16260487 original size:22 final size:22
Alignment explanation
Indices: 16260461--16260504 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
16260451 AGGGGGAGAT
*
16260461 AGAAAGTAGAAGAAATTTAGGG
1 AGAAAGCAGAAGAAATTTAGGG
*
16260483 AGAAAGCAGAAGTAATTTAGGG
1 AGAAAGCAGAAGAAATTTAGGG
16260505 GTAATTTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.32, T:0.18
Consensus pattern (22 bp):
AGAAAGCAGAAGAAATTTAGGG
Found at i:16314387 original size:35 final size:33
Alignment explanation
Indices: 16314352--16314667 Score: 310
Period size: 35 Copynumber: 9.3 Consensus size: 33
16314342 GGGAAGACTA
* *
16314352 GTGAGAGCGGCTAAGAGAGAGGGGCATACCCAC
1 GTGAGAGCGGCTGAGAGAGAGGGGCAGACCCAC
16314385 TAGTGAGAGCGGCTGAGAGAGAGGGGCAGACCCACC
1 --GTGAGAGCGGCTGAGAGAGAGGGGCAGACCCA-C
* *
16314421 GGTGAGAGCAGTTGAGAGAGAGGGGCAGACCCAC
1 -GTGAGAGCGGCTGAGAGAGAGGGGCAGACCCAC
* * * * * *
16314455 GGGTGAGTGGTTGAGAAAGAGGGGCAAACCCAC
1 GTGAGAGCGGCTGAGAGAGAGGGGCAGACCCAC
* * *
16314488 GGGTGAGCGGCTGAGAGAGAAGGGCAGACCCACC
1 GTGAGAGCGGCTGAGAGAGAGGGGCAGACCCA-C
*
16314522 GGTGAGAGCGGATGAGAGAGAGGGGCAGACCCAC
1 -GTGAGAGCGGCTGAGAGAGAGGGGCAGACCCAC
* * *
16314556 TAGTGAGATCGGTTGAGAGAGAAGGGCAGACCCAC
1 --GTGAGAGCGGCTGAGAGAGAGGGGCAGACCCAC
* * *
16314591 GGGTGAGCAGG-TGAAAGAGAGGGGCAGACCCAC
1 GTGAGAGC-GGCTGAGAGAGAGGGGCAGACCCAC
* * * *
16314624 GGGTGAGCGGCTAAGAGAGAGGGGCAAACCCAC
1 GTGAGAGCGGCTGAGAGAGAGGGGCAGACCCAC
16314657 GGGTGAGAGCG
1 --GTGAGAGCG
16314668 AGGGGAAGAC
Statistics
Matches: 239, Mismatches: 34, Indels: 16
0.83 0.12 0.06
Matches are distributed among these distances:
32 2 0.01
33 106 0.44
34 5 0.02
35 125 0.52
36 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.43, T:0.09
Consensus pattern (33 bp):
GTGAGAGCGGCTGAGAGAGAGGGGCAGACCCAC
Found at i:16314612 original size:136 final size:136
Alignment explanation
Indices: 16314356--16314667 Score: 457
Period size: 136 Copynumber: 2.3 Consensus size: 136
16314346 AGACTAGTGA
* ** *
16314356 GAGCGGCTAAGAGAGAGGGGCATACCCACTAGTGAGAGCGGCTGAGAGAGAGGGGCAGACCCACC
1 GAGCGGCTAAGAGAGAGGGGCAAACCCACCGGTGAGAGCGGATGAGAGAGAGGGGCAGACCCACC
* * *
16314421 GGTGAGAGCAGTTGAGAGAGAGGGGCAGACCCACGGGTGAGTGGTTGAGAAAGAGGGGCAAACCC
66 AGTGAGAGCAGTTGAGAGAGAAGGGCAGACCCACGGGTGAGAGGTTGAGAAAGAGGGGCAAACCC
16314486 ACGGGT
131 ACGGGT
* * * *
16314492 GAGCGGCTGAGAGAGAAGGGCAGACCCACCGGTGAGAGCGGATGAGAGAGAGGGGCAGACCCACT
1 GAGCGGCTAAGAGAGAGGGGCAAACCCACCGGTGAGAGCGGATGAGAGAGAGGGGCAGACCCACC
* * *
16314557 AGTGAGATCGGTTGAGAGAGAAGGGCAGACCCACGGGTGAGCAGG-TGA-AAGAGAGGGGCAGAC
66 AGTGAGAGCAGTTGAGAGAGAAGGGCAGACCCACGGGTGAG-AGGTTGAGAA-AGAGGGGCAAAC
16314620 CCACGGGT
129 CCACGGGT
*
16314628 GAGCGGCTAAGAGAGAGGGGCAAACCCACGGGTGAGAGCG
1 GAGCGGCTAAGAGAGAGGGGCAAACCCACCGGTGAGAGCG
16314668 AGGGGAAGAC
Statistics
Matches: 157, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
135 2 0.01
136 153 0.97
137 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.43, T:0.08
Consensus pattern (136 bp):
GAGCGGCTAAGAGAGAGGGGCAAACCCACCGGTGAGAGCGGATGAGAGAGAGGGGCAGACCCACC
AGTGAGAGCAGTTGAGAGAGAAGGGCAGACCCACGGGTGAGAGGTTGAGAAAGAGGGGCAAACCC
ACGGGT
Found at i:16314670 original size:25 final size:25
Alignment explanation
Indices: 16314637--16314795 Score: 162
Period size: 25 Copynumber: 6.4 Consensus size: 25
16314627 TGAGCGGCTA
16314637 AGAGAGAGGGGCAA-ACCCACGGGTG
1 AGAGAGAGGGG-AAGACCCACGGGTG
* * * *
16314662 AGAGCGAGGGGAAGACCCACTGCTA
1 AGAGAGAGGGGAAGACCCACGGGTG
*
16314687 AGAGAGAGGGGTAA-ACCCACAGGTG
1 AGAGAGAGGGG-AAGACCCACGGGTG
* *
16314712 AGAGCA-AGGGGAAGACCCACGGCTA
1 AGAG-AGAGGGGAAGACCCACGGGTG
* *
16314737 AGAGAGAGGGGCAGACCCACAGGTG
1 AGAGAGAGGGGAAGACCCACGGGTG
* **
16314762 AGAGCGAGGGGAAGACCCACGATTG
1 AGAGAGAGGGGAAGACCCACGGGTG
16314787 AGAGAGAGG
1 AGAGAGAGG
16314796 AAGCTGACCA
Statistics
Matches: 108, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
24 5 0.05
25 100 0.93
26 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.41, T:0.06
Consensus pattern (25 bp):
AGAGAGAGGGGAAGACCCACGGGTG
Found at i:16314692 original size:50 final size:50
Alignment explanation
Indices: 16314631--16314782 Score: 259
Period size: 50 Copynumber: 3.0 Consensus size: 50
16314621 CACGGGTGAG
*
16314631 CGGCTAAGAGAGAGGGGCAAACCCACGGGTGAGAGCGAGGGGAAGACCCA
1 CGGCTAAGAGAGAGGGGCAAACCCACAGGTGAGAGCGAGGGGAAGACCCA
* * *
16314681 CTGCTAAGAGAGAGGGGTAAACCCACAGGTGAGAGCAAGGGGAAGACCCA
1 CGGCTAAGAGAGAGGGGCAAACCCACAGGTGAGAGCGAGGGGAAGACCCA
*
16314731 CGGCTAAGAGAGAGGGGCAGACCCACAGGTGAGAGCGAGGGGAAGACCCA
1 CGGCTAAGAGAGAGGGGCAAACCCACAGGTGAGAGCGAGGGGAAGACCCA
16314781 CG
1 CG
16314783 ATTGAGAGAG
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 94 1.00
ACGTcount: A:0.33, C:0.22, G:0.40, T:0.05
Consensus pattern (50 bp):
CGGCTAAGAGAGAGGGGCAAACCCACAGGTGAGAGCGAGGGGAAGACCCA
Found at i:16315221 original size:22 final size:22
Alignment explanation
Indices: 16315193--16315244 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
16315183 CAAGGGAAAC
16315193 GGAATGGCATGGGAATAGAGGG
1 GGAATGGCATGGGAATAGAGGG
16315215 GGAATGGCATGGGAATAGAGGG
1 GGAATGGCATGGGAATAGAGGG
16315237 GGAATGGC
1 GGAATGGC
16315245 TTAGCCATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.31, C:0.06, G:0.50, T:0.13
Consensus pattern (22 bp):
GGAATGGCATGGGAATAGAGGG
Found at i:16316986 original size:29 final size:29
Alignment explanation
Indices: 16316954--16317011 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
16316944 GAAGAAGTTG
*
16316954 TACGTGAACAGTTACAAGAGAAAAAGCTA
1 TACGTGAACAGGTACAAGAGAAAAAGCTA
*
16316983 TACGTGAACAGGTACAAGAGAATAAGCTA
1 TACGTGAACAGGTACAAGAGAAAAAGCTA
16317012 AAGGTGACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.47, C:0.14, G:0.22, T:0.17
Consensus pattern (29 bp):
TACGTGAACAGGTACAAGAGAAAAAGCTA
Found at i:16317018 original size:29 final size:29
Alignment explanation
Indices: 16316955--16317018 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
16316945 AAGAAGTTGT
* *
16316955 ACGTGAACAGTTACAAGAGAAAAAGCTAT
1 ACGTGAACAGGTACAAGAGAAAAAGCTAA
*
16316984 ACGTGAACAGGTACAAGAGAATAAGCTAA
1 ACGTGAACAGGTACAAGAGAAAAAGCTAA
*
16317013 AGGTGA
1 ACGTGA
16317019 CAGAGAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.16
Consensus pattern (29 bp):
ACGTGAACAGGTACAAGAGAAAAAGCTAA
Found at i:16317194 original size:18 final size:17
Alignment explanation
Indices: 16317167--16317200 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
16317157 TTCTTTCACT
*
16317167 GCTATCTATGTAAAGTG
1 GCTATCTATGAAAAGTG
16317184 GCTATTCTATGAAAAGT
1 GCTA-TCTATGAAAAGT
16317201 AGTTGCTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (17 bp):
GCTATCTATGAAAAGTG
Found at i:16317823 original size:36 final size:35
Alignment explanation
Indices: 16317710--16317824 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 35
16317700 AAGGAATCTT
* * * *
16317710 GCTTTTTAATGGGATCAAGTAATAACTCTCACAATA-
1 GCTTTTTCATGGGATC-AGCAATAACCCTTAC-ATAG
* *
16317746 GCTTTTTCATGAGATCAACAGATAACCCTTTA-A-ACG
1 GCTTTTTCATGGGATCAGCA-ATAACCC-TTACATA-G
*
16317782 ACTTTTTCATGGGATCGAGCAATAACCCTTACATAG
1 GCTTTTTCATGGGATC-AGCAATAACCCTTACATAG
16317818 GCTTTTT
1 GCTTTTT
16317825 TACGTGATCA
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
34 1 0.02
35 6 0.10
36 49 0.79
37 6 0.10
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (35 bp):
GCTTTTTCATGGGATCAGCAATAACCCTTACATAG
Found at i:16317834 original size:72 final size:72
Alignment explanation
Indices: 16317711--16317846 Score: 175
Period size: 72 Copynumber: 1.9 Consensus size: 72
16317701 AGGAATCTTG
* * *
16317711 CTTTTTAATGGGATCAAGTAATAACTCTCACAATAGCTTTTTCATGAGATCAACAGATAACCCTT
1 CTTTTTAATGGGATCAAGCAATAACCCTCACAATAGCTTTTTCACGAGATCAACAGATAACCCTT
16317776 TAAACGA
66 TAAACGA
* * * * * *
16317783 CTTTTTCATGGGATCGAGCAATAACCCTTAC-ATAGGCTTTTTTACGTGATCAAGAGATAACCCT
1 CTTTTTAATGGGATCAAGCAATAACCCTCACAATA-GCTTTTTCACGAGATCAACAGATAACCCT
16317847 CACTAACTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 3 0.06
72 51 0.94
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (72 bp):
CTTTTTAATGGGATCAAGCAATAACCCTCACAATAGCTTTTTCACGAGATCAACAGATAACCCTT
TAAACGA
Found at i:16319002 original size:10 final size:10
Alignment explanation
Indices: 16318987--16319016 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
16318977 CAAATGCATG
16318987 AAGTTTCAAA
1 AAGTTTCAAA
16318997 AAGTTTTCAAA
1 AAG-TTTCAAA
16319008 AAGTTTCAA
1 AAGTTTCAA
16319017 CTTTATCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (10 bp):
AAGTTTCAAA
Found at i:16319279 original size:2 final size:2
Alignment explanation
Indices: 16319272--16319308 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
16319262 AGAATGCCAC
*
16319272 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16319309 AGCAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:16323017 original size:34 final size:34
Alignment explanation
Indices: 16322976--16323053 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
16322966 GAAGGAAAAG
*
16322976 AGAGCCATTTAAGGGCTGGCTTTGGAGGCTGAAA
1 AGAGCCATTTAACGGCTGGCTTTGGAGGCTGAAA
** * *
16323010 AGAGCCATTTTTCTGCTGGTTTTGGAGGCTGAAA
1 AGAGCCATTTAACGGCTGGCTTTGGAGGCTGAAA
*
16323044 AGTGCCATTT
1 AGAGCCATTT
16323054 TTTTTGCTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (34 bp):
AGAGCCATTTAACGGCTGGCTTTGGAGGCTGAAA
Found at i:16323054 original size:34 final size:35
Alignment explanation
Indices: 16322990--16323083 Score: 127
Period size: 35 Copynumber: 2.7 Consensus size: 35
16322980 CCATTTAAGG
* *
16322990 GCTGGCTTTGGAGGCTGAAAAGAGCCA-TTTTTCT
1 GCTGGTTTTGGAGGCTGAAAAGTGCCATTTTTTCT
*
16323024 GCTGGTTTTGGAGGCTGAAAAGTGCCATTTTTTTT
1 GCTGGTTTTGGAGGCTGAAAAGTGCCATTTTTTCT
* **
16323059 GCTAGTTTTGGAGGCCAAAAAGTGC
1 GCTGGTTTTGGAGGCTGAAAAGTGC
16323084 AGAATTTTGC
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 25 0.47
35 28 0.53
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.34
Consensus pattern (35 bp):
GCTGGTTTTGGAGGCTGAAAAGTGCCATTTTTTCT
Found at i:16323220 original size:35 final size:35
Alignment explanation
Indices: 16323175--16323261 Score: 117
Period size: 34 Copynumber: 2.5 Consensus size: 35
16323165 AGGGAAAGGT
*
16323175 GCAGCTTAGCTGCTGAAATTTT-AAGGAAAAATAGA
1 GCAGCTTAGCTGCTGAAATTTTGAAGCAAAAATA-A
*
16323210 GCAGCATAGCTGCTG--ATTTTGAAGCAAAAATAA
1 GCAGCTTAGCTGCTGAAATTTTGAAGCAAAAATAA
16323243 GCAGCCTTAGCTGCTGAAA
1 GCAG-CTTAGCTGCTGAAA
16323262 AATTAAAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
33 10 0.22
34 20 0.44
35 14 0.31
36 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (35 bp):
GCAGCTTAGCTGCTGAAATTTTGAAGCAAAAATAA
Found at i:16323412 original size:10 final size:10
Alignment explanation
Indices: 16323389--16323433 Score: 67
Period size: 10 Copynumber: 4.7 Consensus size: 10
16323379 GGTGGGAGAG
16323389 AAAGAAA-G-
1 AAAGAAAGGA
16323397 AAAGAAAGGA
1 AAAGAAAGGA
*
16323407 AAAGAAAAGA
1 AAAGAAAGGA
16323417 AAAGAAAGGA
1 AAAGAAAGGA
16323427 AAAGAAA
1 AAAGAAA
16323434 ATAACAAGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 25 0.76
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (10 bp):
AAAGAAAGGA
Found at i:16323413 original size:5 final size:5
Alignment explanation
Indices: 16323389--16323434 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
16323379 GGTGGGAGAG
* *
16323389 AAAG- AAAG- AAAGA AAGGA AAAGA AAAGA AAAGA AAGGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
16323435 TAACAAGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
4 8 0.22
5 29 0.78
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:16323422 original size:20 final size:19
Alignment explanation
Indices: 16323389--16323434 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
16323379 GGTGGGAGAG
16323389 AAAG-AAAGAAAGAAAGGA
1 AAAGAAAAGAAAGAAAGGA
16323407 AAAGAAAAGAAAAGAAAGGA
1 AAAGAAAAG-AAAGAAAGGA
16323427 AAAGAAAA
1 AAAGAAAA
16323435 TAACAAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 4 0.15
19 4 0.15
20 18 0.69
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
AAAGAAAAGAAAGAAAGGA
Found at i:16323524 original size:25 final size:24
Alignment explanation
Indices: 16323466--16323526 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 24
16323456 CCCAACAAGC
16323466 AAGAAAAATGGACATGGTCCAATA
1 AAGAAAAATGGACATGGTCCAATA
16323490 AAGGAAAAATGGACATGGTCCAATTA
1 AA-GAAAAATGGACATGGTCCAA-TA
16323516 AA-AAGAAATGG
1 AAGAA-AAATGG
16323527 GAGAAGTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
24 4 0.12
25 26 0.76
26 4 0.12
ACGTcount: A:0.51, C:0.10, G:0.23, T:0.16
Consensus pattern (24 bp):
AAGAAAAATGGACATGGTCCAATA
Found at i:16326383 original size:20 final size:20
Alignment explanation
Indices: 16326366--16326403 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16326356 CCTCAAATCT
*
16326366 TACTCTAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
16326386 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
16326404 GGGGCCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:16332348 original size:11 final size:11
Alignment explanation
Indices: 16332313--16332351 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
16332303 AGCTTTTGAG
16332313 TTTAAAGTTAG-
1 TTTAAAGTT-GT
16332324 TTTAAAGTTGT
1 TTTAAAGTTGT
16332335 TTTAAAGTTGT
1 TTTAAAGTTGT
16332346 TTTAAA
1 TTTAAA
16332352 ATTTACAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 1 0.04
11 26 0.96
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (11 bp):
TTTAAAGTTGT
Found at i:16332416 original size:5 final size:5
Alignment explanation
Indices: 16332381--16332415 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
16332371 CCCTAAGTCC
* *
16332381 AGTTA AGTTA AGATA AGTTA AGTTA AGTTA GGTTA
1 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA
16332416 GATTGAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (5 bp):
AGTTA
Found at i:16334032 original size:16 final size:16
Alignment explanation
Indices: 16334011--16334041 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16334001 AGTTTTTTTA
16334011 AAATAAATATGTAAAT
1 AAATAAATATGTAAAT
*
16334027 AAATAAATATTTAAA
1 AAATAAATATGTAAA
16334042 AATATCAGAA
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:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATAAATATGTAAAT
Found at i:16334519 original size:17 final size:15
Alignment explanation
Indices: 16334457--16334524 Score: 50
Period size: 17 Copynumber: 4.3 Consensus size: 15
16334447 TAAAAATAAC
*
16334457 AAATAAATAATAAATA
1 AAATAAA-AATAATTA
16334473 AAGATAAAAAGATAA-T-
1 AA-AT-AAAA-ATAATTA
*
16334489 AAATAAAAATAATTC
1 AAATAAAAATAATTA
16334504 AAATATAAAATAAATTA
1 AAATA-AAAAT-AATTA
16334521 AAAT
1 AAAT
16334525 TGTGAAAATG
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
13 4 0.09
14 5 0.11
15 7 0.16
16 9 0.20
17 12 0.27
18 7 0.16
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (15 bp):
AAATAAAAATAATTA
Found at i:16334723 original size:7 final size:7
Alignment explanation
Indices: 16334649--16334728 Score: 53
Period size: 7 Copynumber: 11.9 Consensus size: 7
16334639 AAATTACTTG
16334649 ATAAA-A
1 ATAAATA
16334655 ATAACA-A
1 ATAA-ATA
16334662 ATAAATA
1 ATAAATA
*
16334669 ATAAATG
1 ATAAATA
*
16334676 A-AGATA
1 ATAAATA
*
16334682 AAAAGATA
1 ATAA-ATA
16334690 ATAAATA
1 ATAAATA
16334697 A-AAATA
1 ATAAATA
**
16334703 ATTCA-A
1 ATAAATA
*
16334709 ATATATA
1 ATAAATA
16334716 ATAAATA
1 ATAAATA
16334723 ATAAAT
1 ATAAAT
16334729 TTGTGAAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
6 19 0.33
7 33 0.57
8 6 0.10
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.25
Consensus pattern (7 bp):
ATAAATA
Found at i:16334777 original size:21 final size:22
Alignment explanation
Indices: 16334753--16334796 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
16334743 TATACATGAC
16334753 ATTAAATAAA-A-AAACAAAAAT
1 ATTAAATAAATAGAAA-AAAAAT
16334774 ATTAAATAAATAGAAAAAAAAT
1 ATTAAATAAATAGAAAAAAAAT
16334796 A
1 A
16334797 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 8 0.38
23 3 0.14
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (22 bp):
ATTAAATAAATAGAAAAAAAAT
Found at i:16347018 original size:37 final size:36
Alignment explanation
Indices: 16346971--16347280 Score: 325
Period size: 37 Copynumber: 8.3 Consensus size: 36
16346961 GGTTTTGTTA
* * *
16346971 CCTCAATTTTGAGGAATTCATTTTTAAAGGTACGTTG
1 CCTCAGTTTTGAGGAGTTCATTTTTAAA-GTTCGTTG
* * *
16347008 CCTCATTTTTGAGGAGCTCACTTTTAAAAGTTTTCGTTG
1 CCTCAGTTTTGAGGAGTTCA-TTTTTAAAG--TTCGTTG
* *
16347047 CCTCAGTTTTGAGGAGTTCATTTTTTAAAGTCTTGGTG
1 CCTCAGTTTTGAGGAGTTCA-TTTTTAAAGT-TCGTTG
**
16347085 CCTCAACTTTGAGGAGTTCATTTTTAAAGTCTCGTTG
1 CCTCAGTTTTGAGGAGTTCATTTTTAAAGT-TCGTTG
*
16347122 CCTCAGTTTTGAGGAGTTCATTTTTAAAATCTCGTTG
1 CCTCAGTTTTGAGGAGTTCATTTTTAAAGT-TCGTTG
* * *
16347159 CCTCAGTTTTGCGGAGTTCA-TTTTAAAATCTCGGTG
1 CCTCAGTTTTGAGGAGTTCATTTTTAAAGT-TCGTTG
* * * **
16347195 ACTCAATTTTGAGGAGTTCATTTTAAAAGTCTAATTG
1 CCTCAGTTTTGAGGAGTTCATTTTTAAAGT-TCGTTG
* *
16347232 CCTCAGTTTTGAGGAGTTCATTTTAAAAGTCTCGTGG
1 CCTCAGTTTTGAGGAGTTCATTTTTAAAGT-TCGTTG
16347269 CCTCAGTTTTGA
1 CCTCAGTTTTGA
16347281 AGAATTTATT
Statistics
Matches: 235, Mismatches: 33, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
36 32 0.14
37 142 0.60
38 29 0.12
39 32 0.14
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (36 bp):
CCTCAGTTTTGAGGAGTTCATTTTTAAAGTTCGTTG
Found at i:16347233 original size:73 final size:76
Alignment explanation
Indices: 16346971--16347280 Score: 366
Period size: 73 Copynumber: 4.2 Consensus size: 76
16346961 GGTTTTGTTA
* * * *
16346971 CCTCAATTTTGAGGAATTCATTTTT-AAAG-GTACGTTGCCTCATTTTTGAGGAGCTCACTTTTA
1 CCTCAATTTTGAGGAGTTCATTTTTAAAAGTCTA-GTTGCCTCAGTTTTGAGGAGTTCACTTTTA
*
16347034 AAAGTTTTCGTTG
65 AAAG-TCTCGTTG
* * * * ** *
16347047 CCTCAGTTTTGAGGAGTTCATTTTTTAAAGTCTTGGTGCCTCAACTTTGAGGAGTTCA-TTTTTA
1 CCTCAATTTTGAGGAGTTCATTTTTAAAAGTCTAGTTGCCTCAGTTTTGAGGAGTTCACTTTTAA
16347111 AAGTCTCGTTG
66 AAGTCTCGTTG
* * *
16347122 CCTCAGTTTTGAGGAGTTCATTTTTAAAA-TCTCGTTGCCTCAGTTTTGCGGAGTTCA-TTTTAA
1 CCTCAATTTTGAGGAGTTCATTTTTAAAAGTCTAGTTGCCTCAGTTTTGAGGAGTTCACTTTTAA
*
16347185 AA-TCTCGGTG
66 AAGTCTCGTTG
* *
16347195 ACTCAATTTTGAGGAGTTCA-TTTTAAAAGTCTAATTGCCTCAGTTTTGAGGAGTTCA-TTTTAA
1 CCTCAATTTTGAGGAGTTCATTTTTAAAAGTCTAGTTGCCTCAGTTTTGAGGAGTTCACTTTTAA
*
16347258 AAGTCTCGTGG
66 AAGTCTCGTTG
*
16347269 CCTCAGTTTTGA
1 CCTCAATTTTGA
16347281 AGAATTTATT
Statistics
Matches: 203, Mismatches: 27, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
72 8 0.04
73 58 0.29
74 46 0.23
75 35 0.17
76 31 0.15
77 24 0.12
78 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (76 bp):
CCTCAATTTTGAGGAGTTCATTTTTAAAAGTCTAGTTGCCTCAGTTTTGAGGAGTTCACTTTTAA
AAGTCTCGTTG
Found at i:16347233 original size:110 final size:111
Alignment explanation
Indices: 16346972--16347280 Score: 426
Period size: 110 Copynumber: 2.8 Consensus size: 111
16346962 GTTTTGTTAC
* * * *
16346972 CTCAATTTTGAGGAATTCATTTTTAAAG-GTACGTTGCCTCATTTTTGAGGAGCTCACTTTTAAA
1 CTCAATTTTGAGGAGTTCATTTTTAAAGTCTA-GTTGCCTCAGTTTTGAGGAGTTCA-TTTTAAA
* * * *
16347036 AGTTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTTAAAGTCTTGGTGC
64 AG-TCTCGTTGCCTCAGTTTTGAGGAGTTCA-TTTTTAAAATCTCGGTGA
* *
16347086 CTCAACTTTGAGGAGTTCATTTTTAAAGTCTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAA
1 CTCAATTTTGAGGAGTTCATTTTTAAAGTCTAGTTGCCTCAGTTTTGAGGAGTTCA-TTTTAAAA
*
16347151 -TCTCGTTGCCTCAGTTTTGCGGAGTTCA-TTTTAAAATCTCGGTGA
65 GTCTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAATCTCGGTGA
* *
16347196 CTCAATTTTGAGGAGTTCATTTTAAAAGTCTAATTGCCTCAGTTTTGAGGAGTTCATTTTAAAAG
1 CTCAATTTTGAGGAGTTCATTTTTAAAGTCTAGTTGCCTCAGTTTTGAGGAGTTCATTTTAAAAG
*
16347261 TCTCGTGGCCTCAGTTTTGA
66 TCTCGTTGCCTCAGTTTTGA
16347281 AGAATTTATT
Statistics
Matches: 175, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
109 8 0.05
110 84 0.48
112 26 0.15
114 56 0.32
115 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (111 bp):
CTCAATTTTGAGGAGTTCATTTTTAAAGTCTAGTTGCCTCAGTTTTGAGGAGTTCATTTTAAAAG
TCTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAATCTCGGTGA
Found at i:16347968 original size:28 final size:28
Alignment explanation
Indices: 16347932--16347985 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
16347922 GCAGAAGTCG
*
16347932 CCGGCAGGTGAGAGAGAAAGAGAAGCCT
1 CCGGAAGGTGAGAGAGAAAGAGAAGCCT
16347960 CCGGAAGGTGAGAGAGAAAGAGAAGC
1 CCGGAAGGTGAGAGAGAAAGAGAAGC
16347986 TTGATTCAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.39, C:0.15, G:0.41, T:0.06
Consensus pattern (28 bp):
CCGGAAGGTGAGAGAGAAAGAGAAGCCT
Found at i:16348645 original size:16 final size:16
Alignment explanation
Indices: 16348624--16348654 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16348614 AGTTTTTTTA
16348624 AAATAAATATGTAAAT
1 AAATAAATATGTAAAT
*
16348640 AAATAAATATTTAAA
1 AAATAAATATGTAAA
16348655 AATATCAGAA
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:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATAAATATGTAAAT
Found at i:16349190 original size:22 final size:21
Alignment explanation
Indices: 16349165--16349223 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
16349155 TATACATGAC
16349165 ATTAAATAAAAAAAACAAAAAT
1 ATTAAATAAAAAAAA-AAAAAT
*
16349187 ATTAAATAAATAGAAAAAAAAT
1 ATTAAATAAA-AAAAAAAAAAT
* *
16349209 AAT-AATAATAAAAAA
1 ATTAAATAAAAAAAAA
16349224 TCTAAGATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.16
21 5 0.16
22 18 0.56
23 4 0.12
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
ATTAAATAAAAAAAAAAAAAT
Found at i:16349204 original size:28 final size:27
Alignment explanation
Indices: 16349172--16349224 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
16349162 GACATTAAAT
*
16349172 AAAAAAAACAAAAATATTAAATAAATAG
1 AAAAAAAACAAAAATAATAAA-AAATAG
* *
16349200 AAAAAAAATAATAATAATAAAAAAT
1 AAAAAAAACAAAAATAATAAAAAAT
16349225 CTAAGATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (27 bp):
AAAAAAAACAAAAATAATAAAAAATAG
Found at i:16349404 original size:25 final size:25
Alignment explanation
Indices: 16349335--16349407 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 25
16349325 GTAAGGTGTA
* *
16349335 AAAAATAATAATTAGACATAA-AATAG
1 AAAAATGATAATTA-A-ATAATAAAAG
*
16349361 AAAACATGATAA--AAA-AATAAAAT
1 AAAA-ATGATAATTAAATAATAAAAG
16349384 AAAAATGATAATTAAATAATAAAA
1 AAAAATGATAATTAAATAATAAAA
16349408 AATGACAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
22 9 0.23
23 8 0.21
24 4 0.10
25 8 0.21
26 4 0.10
27 6 0.15
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (25 bp):
AAAAATGATAATTAAATAATAAAAG
Found at i:16355322 original size:24 final size:23
Alignment explanation
Indices: 16355281--16355326 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
16355271 GAAAAATCAA
*
16355281 TTTTCTTTCATTTTCTTTCTTTG
1 TTTTCTTTCATTTCCTTTCTTTG
*
16355304 TTTTCTTTTCCTTTCCTTTCTTT
1 TTTTC-TTTCATTTCCTTTCTTT
16355327 TCTTACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTTCTTTCATTTCCTTTCTTTG
Found at i:16355335 original size:24 final size:24
Alignment explanation
Indices: 16355286--16355336 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
16355276 ATCAATTTTC
* *
16355286 TTTCATTTTCTTTCTTTGTTTTCT
1 TTTCATTTCCTTTCTTTGTTTACT
*
16355310 TTTCCTTTCCTTTCTTT-TCTTACT
1 TTTCATTTCCTTTCTTTGT-TTACT
16355334 TTT
1 TTT
16355337 TTCTTCTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTCATTTCCTTTCTTTGTTTACT
Found at i:16355675 original size:33 final size:34
Alignment explanation
Indices: 16355609--16355686 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 34
16355599 TTAAGGGCTA
16355609 GTTTTGGAGGCTGAAAAGAGCCATTTTTCTACTG
1 GTTTTGGAGGCTGAAAAGAGCCATTTTTCTACTG
* *
16355643 GTTTTGGAGGTTGAAAAGTGCCA-TTTTCTACTG
1 GTTTTGGAGGCTGAAAAGAGCCATTTTTCTACTG
16355676 GTTTTGGAGGC
1 GTTTTGGAGGC
16355687 CAAAAAGTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 20 0.49
34 21 0.51
ACGTcount: A:0.21, C:0.13, G:0.29, T:0.37
Consensus pattern (34 bp):
GTTTTGGAGGCTGAAAAGAGCCATTTTTCTACTG
Found at i:16355693 original size:33 final size:34
Alignment explanation
Indices: 16355609--16355695 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 34
16355599 TTAAGGGCTA
*
16355609 GTTTTGGAGGCTGAAAAGAGCCATTTTTCTACTG
1 GTTTTGGAGGCTGAAAAGTGCCATTTTTCTACTG
*
16355643 GTTTTGGAGGTTGAAAAGTGCCA-TTTTCTACTG
1 GTTTTGGAGGCTGAAAAGTGCCATTTTTCTACTG
**
16355676 GTTTTGGAGGCCAAAAAGTG
1 GTTTTGGAGGCTGAAAAGTG
16355696 TAAAATTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 27 0.56
34 21 0.44
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (34 bp):
GTTTTGGAGGCTGAAAAGTGCCATTTTTCTACTG
Found at i:16355841 original size:33 final size:34
Alignment explanation
Indices: 16355804--16355871 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
16355794 AGTTGTTGAA
16355804 ATTTT-AAGAAAAAACAGAGCAG-CATAGCTGCTG
1 ATTTTGAAGAAAAAACA-AGCAGCCATAGCTGCTG
* * *
16355837 ATTTTGAAGCAAAAATAAGCAGCCTTAGCTGCTG
1 ATTTTGAAGAAAAAACAAGCAGCCATAGCTGCTG
16355871 A
1 A
16355872 AAAATTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 10 0.33
34 20 0.67
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (34 bp):
ATTTTGAAGAAAAAACAAGCAGCCATAGCTGCTG
Found at i:16362950 original size:36 final size:36
Alignment explanation
Indices: 16362910--16362987 Score: 84
Period size: 37 Copynumber: 2.1 Consensus size: 36
16362900 GATCAAGTTG
16362910 TAACCTTTTCAATGACCTTTGCACAAGATCAAGCGA
1 TAACCTTTTCAATGACCTTTGCACAAGATCAAGCGA
* * * * ** *
16362946 TAACCCTTTTTACTGACTTTTTCATGAGATTAAGCGA
1 TAA-CCTTTTCAATGACCTTTGCACAAGATCAAGCGA
16362983 TAACC
1 TAACC
16362988 CTCACTAACT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
36 5 0.15
37 29 0.85
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (36 bp):
TAACCTTTTCAATGACCTTTGCACAAGATCAAGCGA
Found at i:16365540 original size:21 final size:21
Alignment explanation
Indices: 16365516--16365557 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16365506 AATGCAAGAT
*
16365516 AAAAGAAAGAAAATAAAACAA
1 AAAACAAAGAAAATAAAACAA
* *
16365537 AAAACAAAGTAAATGAAACAA
1 AAAACAAAGAAAATAAAACAA
16365558 CAGAATCTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.76, C:0.07, G:0.10, T:0.07
Consensus pattern (21 bp):
AAAACAAAGAAAATAAAACAA
Found at i:16365689 original size:22 final size:20
Alignment explanation
Indices: 16365651--16365694 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
16365641 ACCGGTGATA
16365651 TTTACAAGCTTTCACCAAGC
1 TTTACAAGCTTTCACCAAGC
*
16365671 TTTACAATGGCTTTTACCAAGC
1 TTTACAA--GCTTTCACCAAGC
16365693 TT
1 TT
16365695 AGCCAAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
22 14 0.67
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.36
Consensus pattern (20 bp):
TTTACAAGCTTTCACCAAGC
Found at i:16370266 original size:43 final size:43
Alignment explanation
Indices: 16370218--16370299 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
16370208 TTGACTCGGC
*
16370218 TATGTGCTAGTAGGGAGTACGCATAAGCCGATGATGACCCGAT
1 TATGTGCTAGTAGGGAGTACGCATAACCCGATGATGACCCGAT
* *
16370261 TATGTGCTAGTTGGGAGTGCGCATAACCCGATGATGACC
1 TATGTGCTAGTAGGGAGTACGCATAACCCGATGATGACC
16370300 TAGCCATGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (43 bp):
TATGTGCTAGTAGGGAGTACGCATAACCCGATGATGACCCGAT
Found at i:16370309 original size:43 final size:43
Alignment explanation
Indices: 16370219--16370323 Score: 131
Period size: 43 Copynumber: 2.4 Consensus size: 43
16370209 TGACTCGGCT
* * * **
16370219 ATGTGCTAGTAGGGAGTACGCATAAGCCGATGATGACCCGATT
1 ATGTGCTAGTAGGGAGTGCGCATAACCCGATGATGACCAGACC
*
16370262 ATGTGCTAGTTGGGAGTGCGCATAACCCGATGATGACCTAG-CC
1 ATGTGCTAGTAGGGAGTGCGCATAACCCGATGATGACC-AGACC
*
16370305 ATGTGCGAGTAGGGAGTGC
1 ATGTGCTAGTAGGGAGTGC
16370324 ACATGAGCTG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 52 0.98
44 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (43 bp):
ATGTGCTAGTAGGGAGTGCGCATAACCCGATGATGACCAGACC
Found at i:16370368 original size:23 final size:23
Alignment explanation
Indices: 16370336--16370386 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
16370326 ATGAGCTGGG
*
16370336 GATGATGGGATGGTGTGCATGAT
1 GATGACGGGATGGTGTGCATGAT
16370359 GATGACGGGATGGTGTGCATGAT
1 GATGACGGGATGGTGTGCATGAT
16370382 GATGA
1 GATGA
16370387 TGGGTATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.06, G:0.43, T:0.27
Consensus pattern (23 bp):
GATGACGGGATGGTGTGCATGAT
Found at i:16375685 original size:42 final size:42
Alignment explanation
Indices: 16375617--16375776 Score: 189
Period size: 43 Copynumber: 3.8 Consensus size: 42
16375607 CCTCGCTATA
*
16375617 TGCGAGTAGGGAGTGCACATGAGCTGATGATGACTCAGTTACG
1 TGCGAGTAGGGAGTGCACATGAGCTGATGATGACTAAGTTA-G
** *
16375660 TGCGAGTA-GGAGTGCACATGAGCTGATGATGACTTGGCTATG
1 TGCGAGTAGGGAGTGCACATGAGCTGATGATGACTAAGTTA-G
* * *
16375702 TGCGAGTAGGGAGTGCACATGAGCCGATGATGGCCTAACTATA-
1 TGCGAGTAGGGAGTGCACATGAGCTGATGAT-GACTAAGT-TAG
* *
16375745 TGCGAGTAAGGAGTGCACATGAGTTGATGATG
1 TGCGAGTAGGGAGTGCACATGAGCTGATGATG
16375777 TTGAAATGTG
Statistics
Matches: 101, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
42 39 0.39
43 57 0.56
44 3 0.03
45 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (42 bp):
TGCGAGTAGGGAGTGCACATGAGCTGATGATGACTAAGTTAG
Found at i:16375716 original size:85 final size:85
Alignment explanation
Indices: 16375598--16375806 Score: 248
Period size: 85 Copynumber: 2.5 Consensus size: 85
16375588 AATTATGTGT
* * * * *
16375598 TGATGATGACCTCGCTATATGCGAGTAGGGAGTGCACATGAGCTGATGAT-GACTCAGT-TACGT
1 TGATGATGA-CTTGCTATGTGCGAGTAGGGAGTGCACATGAGCCGATGATGGACTAACTATA--T
16375661 GCGAGT-AGGAGTGCACATGAGC
63 GCGAGTAAGGAGTGCACATGAGC
*
16375683 TGATGATGACTTGGCTATGTGCGAGTAGGGAGTGCACATGAGCCGATGATGGCCTAACTATATGC
1 TGATGATGACTT-GCTATGTGCGAGTAGGGAGTGCACATGAGCCGATGATGGACTAACTATATGC
*
16375748 GAGTAAGGAGTGCACATGAGT
65 GAGTAAGGAGTGCACATGAGC
** * *
16375769 TGATGATG--TTGAAATGTGCAAGTAAGGAGTGCACATGA
1 TGATGATGACTTGCTATGTGCGAGTAGGGAGTGCACATGA
16375807 CGATGAATGA
Statistics
Matches: 109, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
83 24 0.22
84 4 0.04
85 51 0.47
86 28 0.26
87 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.24
Consensus pattern (85 bp):
TGATGATGACTTGCTATGTGCGAGTAGGGAGTGCACATGAGCCGATGATGGACTAACTATATGCG
AGTAAGGAGTGCACATGAGC
Found at i:16375793 original size:40 final size:41
Alignment explanation
Indices: 16375617--16375806 Score: 179
Period size: 43 Copynumber: 4.5 Consensus size: 41
16375607 CCTCGCTATA
* * ** *
16375617 TGCGAGTAGGGAGTGCACATGAGCTGATGATGACTCAGTTACG
1 TGCGAGTAAGGAGTGCACATGAGCTGATGATG-CT-TGAAATG
**
16375660 TGCGAGT-AGGAGTGCACATGAGCTGATGATGACTTGGCTATG
1 TGCGAGTAAGGAGTGCACATGAGCTGATGATG-CTT-GAAATG
* * * *
16375702 TGCGAGTAGGGAGTGCACATGAGCCGATGATGGCCT-AACTATA
1 TGCGAGTAAGGAGTGCACATGAGCTGATGAT-GCTTGAA--ATG
*
16375745 TGCGAGTAAGGAGTGCACATGAGTTGATGATG-TTGAAATG
1 TGCGAGTAAGGAGTGCACATGAGCTGATGATGCTTGAAATG
*
16375785 TGCAAGTAAGGAGTGCACATGA
1 TGCGAGTAAGGAGTGCACATGA
16375807 CGATGAATGA
Statistics
Matches: 125, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
40 23 0.18
41 1 0.01
42 40 0.32
43 60 0.48
44 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.24
Consensus pattern (41 bp):
TGCGAGTAAGGAGTGCACATGAGCTGATGATGCTTGAAATG
Found at i:16382979 original size:43 final size:43
Alignment explanation
Indices: 16382889--16383023 Score: 209
Period size: 43 Copynumber: 3.2 Consensus size: 43
16382879 ATTATGTGAT
* *
16382889 GATGATGACCCGACTATGTGCGAATA-GGAGTGCACATGAGCC
1 GATGATGACCCAACTATGTGCGAGTAGGGAGTGCACATGAGCC
*
16382931 AATGATGACCCAACTATGTGCGAGTAGGGAGTGCACATGAGCC
1 GATGATGACCCAACTATGTGCGAGTAGGGAGTGCACATGAGCC
* * *
16382974 GATGATGACCCAGCTATGTGCGAGTAGAGAGTGCACATGAGCT
1 GATGATGACCCAACTATGTGCGAGTAGGGAGTGCACATGAGCC
16383017 GATGATG
1 GATGATG
16383024 TTGAAATGTG
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 23 0.27
43 62 0.73
ACGTcount: A:0.29, C:0.19, G:0.32, T:0.20
Consensus pattern (43 bp):
GATGATGACCCAACTATGTGCGAGTAGGGAGTGCACATGAGCC
Found at i:16383033 original size:40 final size:41
Alignment explanation
Indices: 16382904--16383053 Score: 144
Period size: 43 Copynumber: 3.6 Consensus size: 41
16382894 TGACCCGACT
* * *
16382904 ATGTGCGAATAG-GAGTGCACATGAGCCAATGATGACCCA-ACT
1 ATGTGCGAGTAGAGAGTGCACATGAGCCGATGATG--CCAGA-A
* **
16382946 ATGTGCGAGTAGGGAGTGCACATGAGCCGATGATGACCCAGCT
1 ATGTGCGAGTAGAGAGTGCACATGAGCCGATGATG--CCAGAA
* **
16382989 ATGTGCGAGTAGAGAGTGCACATGAGCTGATGATG-TTGAA
1 ATGTGCGAGTAGAGAGTGCACATGAGCCGATGATGCCAGAA
*
16383029 ATGTGCAAGTAGAGAGTGCACATGA
1 ATGTGCGAGTAGAGAGTGCACATGA
16383054 TGATGAATGA
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
40 25 0.26
42 11 0.11
43 60 0.62
ACGTcount: A:0.31, C:0.17, G:0.32, T:0.21
Consensus pattern (41 bp):
ATGTGCGAGTAGAGAGTGCACATGAGCCGATGATGCCAGAA
Found at i:16383046 original size:83 final size:84
Alignment explanation
Indices: 16382889--16383053 Score: 210
Period size: 85 Copynumber: 2.0 Consensus size: 84
16382879 ATTATGTGAT
*
16382889 GATGATGACCCGACTATGTGCGAATAGGAGTGCACATGAGCCAATGATGACCCAACTATGTGCGA
1 GATGATGACCCGACTATGTGCGAATAGGAGTGCACATGAGCCAATGATGACCCAAC-ATGTGCAA
*
16382954 GTAGGGAGTGCACATGAGCC
65 GTAGAGAGTGCACATGAGCC
* ** ***
16382974 GATGATGACCC-AGCTATGTGCGAGTAGAGAGTGCACATGAGCTGATGATG-TTGAA-ATGTGCA
1 GATGATGACCCGA-CTATGTGCGAATAG-GAGTGCACATGAGCCAATGATGACCCAACATGTGCA
16383036 AGTAGAGAGTGCACATGA
64 AGTAGAGAGTGCACATGA
16383054 TGATGAATGA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
83 23 0.33
84 1 0.01
85 26 0.37
86 20 0.29
ACGTcount: A:0.30, C:0.18, G:0.32, T:0.21
Consensus pattern (84 bp):
GATGATGACCCGACTATGTGCGAATAGGAGTGCACATGAGCCAATGATGACCCAACATGTGCAAG
TAGAGAGTGCACATGAGCC
Found at i:16386657 original size:22 final size:20
Alignment explanation
Indices: 16386619--16386662 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
16386609 ACTGGTGAAA
16386619 TTTACAAGCTTTCACCAAGC
1 TTTACAAGCTTTCACCAAGC
*
16386639 TTTACAATGGCTTTTACCAAGC
1 TTTACAA--GCTTTCACCAAGC
16386661 TT
1 TT
16386663 AGCCAAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
22 14 0.67
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.36
Consensus pattern (20 bp):
TTTACAAGCTTTCACCAAGC
Found at i:16398913 original size:2 final size:2
Alignment explanation
Indices: 16398906--16398935 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16398896 TTATGACATA
16398906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16398936 CAATATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16407691 original size:2 final size:2
Alignment explanation
Indices: 16407679--16407722 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
16407669 CGTAAAGTAC
*
16407679 TA TA T- TA TA TA TA TA TA TA TA -A TA TA -A TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16407718 TA TA T
1 TA TA T
16407723 CATTGAAGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16410861 original size:2 final size:2
Alignment explanation
Indices: 16410854--16410880 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16410844 ACATAATCAT
16410854 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
16410881 TATACACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16415410 original size:38 final size:39
Alignment explanation
Indices: 16415312--16415417 Score: 126
Period size: 38 Copynumber: 2.7 Consensus size: 39
16415302 CACGCCCGGC
* *
16415312 TCATGTACATCCCCCCACATCTTGCACATAGCCGGCACCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAGG-ACCA
** * *
16415352 TTGTGTGCATCCCCCCACATCGTGCACA-ATCAGTG-CCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAG-GACCA
16415390 TCATGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
16415418 CGGGCATTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 28 0.50
39 3 0.05
40 25 0.45
ACGTcount: A:0.24, C:0.41, G:0.14, T:0.22
Consensus pattern (39 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCAGGACCA
Found at i:16415559 original size:2 final size:2
Alignment explanation
Indices: 16415554--16415581 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16415544 ACACACACAC
16415554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16415582 CATCATATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16418720 original size:8 final size:8
Alignment explanation
Indices: 16418707--16418736 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
16418697 TACCTAGTAG
16418707 CCCATTTA
1 CCCATTTA
*
16418715 CCCATTTG
1 CCCATTTA
16418723 CCCATTTA
1 CCCATTTA
16418731 CCCATT
1 CCCATT
16418737 ACTCACTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.03, T:0.37
Consensus pattern (8 bp):
CCCATTTA
Found at i:16418725 original size:16 final size:16
Alignment explanation
Indices: 16418706--16418736 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16418696 CTACCTAGTA
16418706 GCCCATTTACCCATTT
1 GCCCATTTACCCATTT
16418722 GCCCATTTACCCATT
1 GCCCATTTACCCATT
16418737 ACTCACTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.39, G:0.06, T:0.35
Consensus pattern (16 bp):
GCCCATTTACCCATTT
Found at i:16418856 original size:32 final size:33
Alignment explanation
Indices: 16418814--16418890 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 33
16418804 AACCCTTTTC
* **
16418814 TTTATTTATTTTCTTT-TCATATATTTTTATTTA
1 TTTATTTATTTTATTTCTC-TATATTAATATTTA
*
16418847 -TTATTTATTTTATTTCTCTATATTAATCTTTA
1 TTTATTTATTTTATTTCTCTATATTAATATTTA
16418879 TTTATTTATTTT
1 TTTATTTATTTT
16418891 TTTGTAGCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 25 0.66
33 13 0.34
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (33 bp):
TTTATTTATTTTATTTCTCTATATTAATATTTA
Found at i:16421189 original size:38 final size:40
Alignment explanation
Indices: 16421099--16421203 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 40
16421089 CACACCTAAC
*
16421099 TCATGTACATCCCCCCTACATCGTGCATATAGTCGGCACCA
1 TCATGTACATCCCCCC-ACATCGTGCATATAGTCAGCACCA
* **
16421140 TCATGTGCATCCCCCCACATCGTGCATA-A-TCAGTGCCA
1 TCATGTACATCCCCCCACATCGTGCATATAGTCAGCACCA
* *
16421178 TCGTGTACATCCCCCCACATTGTGCA
1 TCATGTACATCCCCCCACATCGTGCA
16421204 CATGAGCACT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
38 29 0.51
39 1 0.02
40 12 0.21
41 15 0.26
ACGTcount: A:0.23, C:0.37, G:0.15, T:0.25
Consensus pattern (40 bp):
TCATGTACATCCCCCCACATCGTGCATATAGTCAGCACCA
Found at i:16433039 original size:20 final size:20
Alignment explanation
Indices: 16433014--16433059 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
16433004 TTTTGGCCCC
16433014 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
16433034 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
16433054 ATTTGA
1 ATTTGA
16433060 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:16433135 original size:28 final size:27
Alignment explanation
Indices: 16433104--16433156 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
16433094 TTTGGAGTAA
*
16433104 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
16433132 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
16433157 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:16433162 original size:28 final size:28
Alignment explanation
Indices: 16433104--16433162 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
16433094 TTTGGAGTAA
* *
16433104 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
16433132 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
16433160 AGG
1 AGG
16433163 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:16440982 original size:49 final size:48
Alignment explanation
Indices: 16440875--16441020 Score: 141
Period size: 49 Copynumber: 3.0 Consensus size: 48
16440865 ATATACCTTA
* * *
16440875 TCCAAAATCATCCTCGGATGGAACATACATATCTCATATCATATTATCT
1 TCCAAAATCATCCT-GGATGGAACATACATATATCACATCATATCATCT
*
16440924 TCCAAAATCATCCATGGATGGAACTTACATATATCACATCATATCATCGT
1 TCCAAAATCATCC-TGGATGGAACATACATATATCACATCATATCATC-T
* * * ** * * *
16440974 T-TAGAATCATGCTTGGACAGAACATACTTATTTAACATCATATCATC
1 TCCAAAATCAT-CCTGGATGGAACATACATATATCACATCATATCATC
16441021 ATTCATCATG
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
49 77 0.95
50 4 0.05
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.32
Consensus pattern (48 bp):
TCCAAAATCATCCTGGATGGAACATACATATATCACATCATATCATCT
Found at i:16443062 original size:2 final size:2
Alignment explanation
Indices: 16443055--16443091 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
16443045 ACCTTGGTGT
16443055 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16443092 TTCATTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16445502 original size:3 final size:3
Alignment explanation
Indices: 16445489--16445535 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
16445479 GAAACAAAAA
* *
16445489 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16445536 ATACAAAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:16448544 original size:19 final size:20
Alignment explanation
Indices: 16448517--16448562 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
16448507 AGGAGACAAG
*
16448517 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
16448536 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
16448555 ATAATATT
1 ATAATATT
16448563 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:16453060 original size:12 final size:12
Alignment explanation
Indices: 16453043--16453067 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16453033 CTGAATAAGC
16453043 TTTAAAAAAAAT
1 TTTAAAAAAAAT
16453055 TTTAAAAAAAAT
1 TTTAAAAAAAAT
16453067 T
1 T
16453068 GTGCTATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTTAAAAAAAAT
Found at i:16453565 original size:27 final size:27
Alignment explanation
Indices: 16453527--16453593 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
16453517 ATTGTAAATG
16453527 AATTCTAAATGAAGAAAGCCAAGGATT
1 AATTCTAAATGAAGAAAGCCAAGGATT
* *
16453554 AATTCTAAATGAAGAAGGCCGAGGATT
1 AATTCTAAATGAAGAAAGCCAAGGATT
16453581 AATTCTAAATGAA
1 AATTCTAAATGAA
16453594 TTAACCAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.24
Consensus pattern (27 bp):
AATTCTAAATGAAGAAAGCCAAGGATT
Found at i:16459081 original size:27 final size:27
Alignment explanation
Indices: 16459043--16459128 Score: 163
Period size: 27 Copynumber: 3.2 Consensus size: 27
16459033 TTTTTCACAT
*
16459043 ATGAAAAAGGCCGAGGATTAATTCTAA
1 ATGAAGAAGGCCGAGGATTAATTCTAA
16459070 ATGAAGAAGGCCGAGGATTAATTCTAA
1 ATGAAGAAGGCCGAGGATTAATTCTAA
16459097 ATGAAGAAGGCCGAGGATTAATTCTAA
1 ATGAAGAAGGCCGAGGATTAATTCTAA
16459124 ATGAA
1 ATGAA
16459129 TTAACCAAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.22
Consensus pattern (27 bp):
ATGAAGAAGGCCGAGGATTAATTCTAA
Found at i:16473080 original size:31 final size:31
Alignment explanation
Indices: 16473027--16473085 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
16473017 CCCCTAACAA
*
16473027 TTTTAAAATTTTTATAACTTACCTTTACTTT
1 TTTTAAAATTTTTATAACTTACCCTTACTTT
* *
16473058 TTTTGAAA-TTTTATAATTTTACCCTTAC
1 TTTTAAAATTTTTATAA-CTTACCCTTAC
16473086 AAAAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.29, C:0.14, G:0.02, T:0.56
Consensus pattern (31 bp):
TTTTAAAATTTTTATAACTTACCCTTACTTT
Found at i:16475653 original size:45 final size:45
Alignment explanation
Indices: 16475593--16475686 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 45
16475583 AATATATTAA
* * * *
16475593 TATTATTTCACTATAATAAATATTATGAAGCATATTATTTAATAT
1 TATTATTTCAATATAATAAATATAATAAAGAATATTATTTAATAT
* * *
16475638 TATTATTTGAATATAATAAATGTAATAAAGAATATTATTTAGTAT
1 TATTATTTCAATATAATAAATATAATAAAGAATATTATTTAATAT
16475683 TATT
1 TATT
16475687 TAAATTTAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (45 bp):
TATTATTTCAATATAATAAATATAATAAAGAATATTATTTAATAT
Found at i:16475727 original size:22 final size:21
Alignment explanation
Indices: 16475701--16475779 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 21
16475691 TTTAATGAAG
16475701 AAAATATTTTTTATTTTAATA
1 AAAATATTTTTTATTTTAATA
* ** *
16475722 TTAAATATTATTAAATTATAATA
1 -AAAATATT-TTTTATTTTAATA
**
16475745 AAAATATGTTTTTATTTTGGTA
1 AAAATAT-TTTTTATTTTAATA
*
16475767 AAAATATTATTTA
1 AAAATATTTTTTA
16475780 ATTATAGTAA
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
21 5 0.11
22 28 0.64
23 11 0.25
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (21 bp):
AAAATATTTTTTATTTTAATA
Found at i:16475751 original size:44 final size:44
Alignment explanation
Indices: 16475701--16475791 Score: 121
Period size: 44 Copynumber: 2.1 Consensus size: 44
16475691 TTTAATGAAG
*
16475701 AAAATAT-TTTTTATTTTAATATTAAATATTATTAAATTATAATA
1 AAAATATGTTTTTATTTTAATA-AAAATATTATTAAATTATAATA
** * *
16475745 AAAATATGTTTTTATTTTGGTAAAAATATTATTTAATTATAGTA
1 AAAATATGTTTTTATTTTAATAAAAATATTATTAAATTATAATA
16475789 AAA
1 AAA
16475792 GTTATTTTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
44 29 0.71
45 12 0.29
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (44 bp):
AAAATATGTTTTTATTTTAATAAAAATATTATTAAATTATAATA
Found at i:16475789 original size:22 final size:22
Alignment explanation
Indices: 16475724--16475791 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
16475714 TTTTAATATT
* *
16475724 AAATATTATTAAATTATAATAA
1 AAATATTATTTAATTATAGTAA
* * *
16475746 AAATATGT-TTTTATTTTGGTAA
1 AAATAT-TATTTAATTATAGTAA
16475768 AAATATTATTTAATTATAGTAA
1 AAATATTATTTAATTATAGTAA
16475790 AA
1 AA
16475792 GTTATTTTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (22 bp):
AAATATTATTTAATTATAGTAA
Found at i:16476741 original size:20 final size:20
Alignment explanation
Indices: 16476716--16476761 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
16476706 TTTTGGCCCC
16476716 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
16476736 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
16476756 ATTTGA
1 ATTTGA
16476762 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:16476837 original size:28 final size:27
Alignment explanation
Indices: 16476806--16476858 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
16476796 TTTGGAGTAT
*
16476806 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
16476834 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
16476859 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:16476864 original size:28 final size:28
Alignment explanation
Indices: 16476806--16476864 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
16476796 TTTGGAGTAT
* *
16476806 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
16476834 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
16476862 AGG
1 AGG
16476865 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:16484780 original size:20 final size:20
Alignment explanation
Indices: 16484755--16484800 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
16484745 TTTTGACCCC
*
16484755 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGAAGTATA
*
16484775 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
16484795 ATTTGA
1 ATTTGA
16484801 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:16484876 original size:28 final size:27
Alignment explanation
Indices: 16484845--16484897 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
16484835 TTTGGAGTAT
*
16484845 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
16484873 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
16484898 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:16484903 original size:28 final size:28
Alignment explanation
Indices: 16484845--16484903 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
16484835 TTTGGAGTAT
* *
16484845 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
16484873 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
16484901 AGG
1 AGG
16484904 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:16490656 original size:32 final size:32
Alignment explanation
Indices: 16490596--16490656 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
16490586 AAAATTTGGC
**
16490596 TATTTCCAACGGAAATTTCCGTTAGAAATGTT
1 TATTTCCAACGGAAAAGTCCGTTAGAAATGTT
* * *
16490628 TATTTGCAACGGAAAAGTCTGTTGGAAAT
1 TATTTCCAACGGAAAAGTCCGTTAGAAAT
16490657 TTCGTCGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (32 bp):
TATTTCCAACGGAAAAGTCCGTTAGAAATGTT
Found at i:16491555 original size:35 final size:36
Alignment explanation
Indices: 16491493--16491568 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 36
16491483 ATTTTCTTCC
* *
16491493 ACAAAAATATTAAAATTTAAATTTAAATAA-TCAAAA
1 ACAAAAATATTAAAACTTAAAATTAAATAACT-AAAA
*
16491529 ACAAAAATCTT-AAACTTAAAATTAAATAACTAAAA
1 ACAAAAATATTAAAACTTAAAATTAAATAACTAAAA
16491564 ACAAA
1 ACAAA
16491569 TATTTGGGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 25 0.69
36 11 0.31
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.26
Consensus pattern (36 bp):
ACAAAAATATTAAAACTTAAAATTAAATAACTAAAA
Found at i:16492436 original size:20 final size:21
Alignment explanation
Indices: 16492392--16492438 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
16492382 TTTTTGGGCC
* *
16492392 CATTTTACTTATTGGAGTATA
1 CATTTGACTTATTAGAGTATA
16492413 -ATTTGACTTATTAGAGTA-A
1 CATTTGACTTATTAGAGTATA
16492432 CATTTGA
1 CATTTGA
16492439 GGTTTAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.45
Consensus pattern (21 bp):
CATTTGACTTATTAGAGTATA
Found at i:16501343 original size:21 final size:21
Alignment explanation
Indices: 16501317--16501360 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
16501307 TCTGTGTGAA
16501317 AAATATCAATACTTGTTACCC
1 AAATATCAATACTTGTTACCC
*
16501338 AAATATCGATACTTGTTACCC
1 AAATATCAATACTTGTTACCC
16501359 AA
1 AA
16501361 GAGACTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.32
Consensus pattern (21 bp):
AAATATCAATACTTGTTACCC
Found at i:16508648 original size:20 final size:21
Alignment explanation
Indices: 16508623--16508669 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
16508613 CTTCTAAACC
16508623 TCAAATGT-TACTCCAATAAG
1 TCAAATGTATACTCCAATAAG
16508643 TCAAAT-TATACTCCAATAAG
1 TCAAATGTATACTCCAATAAG
16508663 TCAAATG
1 TCAAATG
16508670 GAGCCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.30
Consensus pattern (21 bp):
TCAAATGTATACTCCAATAAG
Found at i:16513368 original size:14 final size:14
Alignment explanation
Indices: 16513349--16513375 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16513339 AATCAAAAAA
16513349 AAATTAAAACTAAT
1 AAATTAAAACTAAT
16513363 AAATTAAAACTAA
1 AAATTAAAACTAA
16513376 AATTAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATTAAAACTAAT
Found at i:16525780 original size:28 final size:29
Alignment explanation
Indices: 16525722--16525781 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
16525712 TTTTTGAAAT
*
16525722 TTACACTTTTGCCCCTGTAAAAGTCAAAAA
1 TTACACTTTTGCCCC-GAAAAAGTCAAAAA
*
16525752 TTACATTTTTGCCCC-AAAAAGTCAAAAA
1 TTACACTTTTGCCCCGAAAAAGTCAAAAA
16525780 TT
1 TT
16525782 GCCCATAGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 14 0.50
30 14 0.50
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (29 bp):
TTACACTTTTGCCCCGAAAAAGTCAAAAA
Found at i:16527977 original size:2 final size:2
Alignment explanation
Indices: 16527970--16528087 Score: 80
Period size: 2 Copynumber: 60.0 Consensus size: 2
16527960 GTATGTATGA
* * * * *
16527970 AT AT AT AT AT AT AT AT AC AC AC AC AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
16528012 AT AT AT AT AT -T GT -T GT NT GT AT GA- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
* * * * *
16528052 AC AC AC AC AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16528088 TGTGTCAAGA
Statistics
Matches: 105, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
1 3 0.03
2 101 0.96
3 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (2 bp):
AT
Found at i:16528069 original size:66 final size:65
Alignment explanation
Indices: 16527963--16528090 Score: 247
Period size: 66 Copynumber: 2.0 Consensus size: 65
16527953 TATGTATGTA
16527963 TGTATGAATATATATATATATATACACACACACATATATATATATATATATATATATATTGTTGT
1 TGTATGAATATATATATATATATACACACACACATATATATATATATATATATATATATTGTTGT
16528028 NTGTATGAATATATATATATATATACACACACACATATATATATATATATATATATATATTGT
1 -TGTATGAATATATATATATATATACACACACACATATATATATATATATATATATATATTGT
16528091 GTCAAGACAC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (65 bp):
TGTATGAATATATATATATATATACACACACACATATATATATATATATATATATATATTGTTGT
Found at i:16530118 original size:20 final size:21
Alignment explanation
Indices: 16530095--16530134 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
16530085 AAGTGAGTTA
*
16530095 TTTTAATTTTA-TGTTATTTC
1 TTTTAATTTGATTGTTATTTC
16530115 TTTTAATTTGATTGTTATTT
1 TTTTAATTTGATTGTTATTT
16530135 ATTAGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTAATTTGATTGTTATTTC
Found at i:16530901 original size:13 final size:13
Alignment explanation
Indices: 16530883--16530910 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16530873 AATTTAAAGT
16530883 AAACTAAAATTAG
1 AAACTAAAATTAG
16530896 AAACTAAAATTAG
1 AAACTAAAATTAG
16530909 AA
1 AA
16530911 TAGTATATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AAACTAAAATTAG
Found at i:16536370 original size:13 final size:13
Alignment explanation
Indices: 16536352--16536389 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
16536342 TTCTAGAAAA
16536352 TTTATAAAATCAT
1 TTTATAAAATCAT
16536365 TTTATAAAATCAT
1 TTTATAAAATCAT
16536378 TTTATAAAATCA
1 TTTATAAAATCA
16536390 CAATTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:16539297 original size:26 final size:26
Alignment explanation
Indices: 16539268--16539353 Score: 83
Period size: 26 Copynumber: 3.5 Consensus size: 26
16539258 TTGTCTATAG
16539268 GCATTACGTGACTGAATATTTGTTTA
1 GCATTACGTGACTGAATATTTGTTTA
* * *
16539294 GCATTGCGTGAC---AT-GTT-TATA
1 GCATTACGTGACTGAATATTTGTTTA
*
16539315 GGCATTACGTGACTGAATATTTGTTGA
1 -GCATTACGTGACTGAATATTTGTTTA
*
16539342 GCATTGCGTGAC
1 GCATTACGTGAC
16539354 CTATTTGTAG
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
21 3 0.07
22 13 0.28
23 2 0.04
25 2 0.04
26 24 0.52
27 2 0.04
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (26 bp):
GCATTACGTGACTGAATATTTGTTTA
Found at i:16539300 original size:48 final size:48
Alignment explanation
Indices: 16539222--16539376 Score: 229
Period size: 48 Copynumber: 3.2 Consensus size: 48
16539212 GTGCCTGAAT
* * * *
16539222 ATTACGTGACTAAATATTTGTTGAGTATTGCGTGACTTGTCTATAGGC
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACATGTTTATAGGC
*
16539270 ATTACGTGACTGAATATTTGTTTAGCATTGCGTGACATGTTTATAGGC
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACATGTTTATAGGC
* * *
16539318 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACCTATTTGTAGGC
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACATGTTTATAGGC
*
16539366 ATTGCGTGACT
1 ATTACGTGACT
16539377 TTATCTACTT
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 97 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.39
Consensus pattern (48 bp):
ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACATGTTTATAGGC
Found at i:16539370 original size:22 final size:22
Alignment explanation
Indices: 16539294--16539375 Score: 83
Period size: 22 Copynumber: 3.5 Consensus size: 22
16539284 TATTTGTTTA
* *
16539294 GCATTGCGTGACATGTTTATAG
1 GCATTGCGTGACATATTTGTAG
* *
16539316 GCATTACGTGACTGAATATTTGTTG
1 GCATTGCGTGAC---ATATTTGTAG
*
16539341 AGCATTGCGTGACCTATTTGTAG
1 -GCATTGCGTGACATATTTGTAG
16539364 GCATTGCGTGAC
1 GCATTGCGTGAC
16539376 TTTATCTACT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
22 23 0.47
23 8 0.16
25 7 0.14
26 11 0.22
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (22 bp):
GCATTGCGTGACATATTTGTAG
Found at i:16544455 original size:78 final size:78
Alignment explanation
Indices: 16544171--16544463 Score: 376
Period size: 76 Copynumber: 3.8 Consensus size: 78
16544161 GATGATACTC
* * * * *
16544171 TGACCAGTACAATGAAGAAAACTGAGTGGTGTGATTGGGGGAGAAGCAAATCTAAAACACAAGAT
1 TGACCAGTACAACGAAGCAAACTGAGTGGGGTGATTAGGGGACAAGCAAATCTAAAACACAAGAT
16544236 GTTGCAGCAGCTG
66 GTTGCAGCAGCTG
* * *
16544249 TAACCAGTACAACGAAGCAAAATGAGT--GGTGATTGGGGGACAAGCAAATCTAAAACACAAGAT
1 TGACCAGTACAACGAAGCAAACTGAGTGGGGTGATTAGGGGACAAGCAAATCTAAAACACAAGAT
* * *
16544312 ATTGCAACAACTG
66 GTTGCAGCAGCTG
* * * * * * * *
16544325 TGACCAGTATAGCGGAGCATA-TGAGTGGCGTGATTAAGGGACAAGTAAATCTAAAACAGAAGAT
1 TGACCAGTACAACGAAGCAAACTGAGTGGGGTGATTAGGGGACAAGCAAATCTAAAACACAAGAT
16544389 GTTGCAGCAGCTG
66 GTTGCAGCAGCTG
* *
16544402 TGACAAGTACAACAAAGCAAACTGAGTGGGGTGATTAGGGGACAAGCAAATCTAAAACACAA
1 TGACCAGTACAACGAAGCAAACTGAGTGGGGTGATTAGGGGACAAGCAAATCTAAAACACAA
16544464 TATTTTACTT
Statistics
Matches: 180, Mismatches: 32, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
75 5 0.03
76 60 0.33
77 56 0.31
78 59 0.33
ACGTcount: A:0.40, C:0.15, G:0.27, T:0.18
Consensus pattern (78 bp):
TGACCAGTACAACGAAGCAAACTGAGTGGGGTGATTAGGGGACAAGCAAATCTAAAACACAAGAT
GTTGCAGCAGCTG
Found at i:16548509 original size:23 final size:23
Alignment explanation
Indices: 16548479--16548656 Score: 153
Period size: 23 Copynumber: 7.7 Consensus size: 23
16548469 ACGATAAATG
*
16548479 AGTCACGCGATCCCATATCAACT
1 AGTCACGCGATTCCATATCAACT
*
16548502 AGTCACGCGATTCCATATCAATT
1 AGTCACGCGATTCCATATCAACT
* *
16548525 AGTCACGTGATTTCATATCAACT
1 AGTCACGCGATTCCATATCAACT
* *
16548548 AGTCACGCGATTCCATAACAAGT
1 AGTCACGCGATTCCATATCAACT
* * * * *
16548571 GGTAACGCCAATCCATA-GATACT
1 AGTCACGCGATTCCATATCA-ACT
* * * * *
16548594 ACTGACGCGACTCAATATAAACT
1 AGTCACGCGATTCCATATCAACT
*
16548617 AGTAACGCGATTCCATAAT-AACT
1 AGTCACGCGATTCCAT-ATCAACT
* *
16548640 AATCACACGATTCCATA
1 AGTCACGCGATTCCATA
16548657 ATAAATACTA
Statistics
Matches: 123, Mismatches: 29, Indels: 7
0.77 0.18 0.04
Matches are distributed among these distances:
22 2 0.02
23 118 0.96
24 3 0.02
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.25
Consensus pattern (23 bp):
AGTCACGCGATTCCATATCAACT
Found at i:16548670 original size:23 final size:23
Alignment explanation
Indices: 16548610--16548670 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
16548600 GCGACTCAAT
* *
16548610 ATAAACTAGTAACGCGATTCCATA
1 ATAAA-TAATAACACGATTCCATA
* *
16548634 ATAACTAATCACACGATTCCATA
1 ATAAATAATAACACGATTCCATA
*
16548657 ATAAATACTAACAC
1 ATAAATAATAACAC
16548671 CACTTCATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.25
Consensus pattern (23 bp):
ATAAATAATAACACGATTCCATA
Found at i:16548794 original size:46 final size:46
Alignment explanation
Indices: 16548736--16548843 Score: 128
Period size: 46 Copynumber: 2.3 Consensus size: 46
16548726 TCTTAACGGT
* * * *
16548736 TCAGGCAATTCCATACTTAA-TAGTCACGCGATTCAAAATCGATTAG
1 TCAGGCGATTCCATA-TTAACTAATCACACGATTCAAAATCGAGTAG
* *
16548782 TCAGGCGATTCCATATTAACTAATCACATGATTCAAAATTGAGTAG
1 TCAGGCGATTCCATATTAACTAATCACACGATTCAAAATCGAGTAG
* *
16548828 TCACGTGATTCCATAT
1 TCAGGCGATTCCATAT
16548844 CAAATACTCG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 4 0.08
46 49 0.92
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (46 bp):
TCAGGCGATTCCATATTAACTAATCACACGATTCAAAATCGAGTAG
Found at i:16548814 original size:23 final size:23
Alignment explanation
Indices: 16548788--16548843 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
16548778 TTAGTCAGGC
16548788 GATTCCATATTAACTAATCACAT
1 GATTCCATATTAACTAATCACAT
* * * * * *
16548811 GATTCAAAATTGAGTAGTCACGT
1 GATTCCATATTAACTAATCACAT
16548834 GATTCCATAT
1 GATTCCATAT
16548844 CAAATACTCG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (23 bp):
GATTCCATATTAACTAATCACAT
Found at i:16549233 original size:61 final size:61
Alignment explanation
Indices: 16549127--16549583 Score: 689
Period size: 61 Copynumber: 7.5 Consensus size: 61
16549117 TCTATGAGCA
* * * * * *
16549127 AAATATCTATCGATAGATTCTAAATATATCAATAGATACCGTTTCATCTTCCAAGCATTCA
1 AAATATCTATCGATAGATTTTAAATATATCGATAGCTGCCATTTCATCTTCCAAGCATTCG
16549188 AAATATCTATCGATAGATTTTAAATATATCGATAGCTGCCATTTCATCTTCCAAGCATTCG
1 AAATATCTATCGATAGATTTTAAATATATCGATAGCTGCCATTTCATCTTCCAAGCATTCG
* * *
16549249 AAATATCTATCGATAGCTTTTAAATATATCGATAGATACCATTTCATCTTCCAAGCATTCG
1 AAATATCTATCGATAGATTTTAAATATATCGATAGCTGCCATTTCATCTTCCAAGCATTCG
* * * *
16549310 AAATATCTATCAATAGATTTTAAACATATCGATAGCTGCCATTTCATCTTCTAACCATTCG
1 AAATATCTATCGATAGATTTTAAATATATCGATAGCTGCCATTTCATCTTCCAAGCATTCG
* * * *
16549371 AAATATCTATCGATAGATTTTAAAGATATCGATAGATGCCCTTTCATCTTACAAGCATTCG
1 AAATATCTATCGATAGATTTTAAATATATCGATAGCTGCCATTTCATCTTCCAAGCATTCG
* ** *
16549432 AAATATCTATCGATAGATTTTAAATATATCGATAGCTACTGTTTCATCTTCCAAGCATTCA
1 AAATATCTATCGATAGATTTTAAATATATCGATAGCTGCCATTTCATCTTCCAAGCATTCG
* * * *
16549493 AAATATGTATCAATAGATTTTAAATATATCGATAGCTGGCGTTTCATCTTCCAAGCATTCG
1 AAATATCTATCGATAGATTTTAAATATATCGATAGCTGCCATTTCATCTTCCAAGCATTCG
16549554 AAATATCTATCGATAGATTTTAAATATATC
1 AAATATCTATCGATAGATTTTAAATATATC
16549584 AACTAGTAGC
Statistics
Matches: 358, Mismatches: 38, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 358 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (61 bp):
AAATATCTATCGATAGATTTTAAATATATCGATAGCTGCCATTTCATCTTCCAAGCATTCG
Found at i:16553788 original size:23 final size:23
Alignment explanation
Indices: 16553758--16553813 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
16553748 TAACATTAAA
16553758 TCACGCAATGATCTATAAACAAG
1 TCACGCAATGATCTATAAACAAG
* *
16553781 TCACGCAATGATCTTTAAACATG
1 TCACGCAATGATCTATAAACAAG
16553804 TCACGCAATG
1 TCACGCAATG
16553814 CTAAGAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (23 bp):
TCACGCAATGATCTATAAACAAG
Found at i:16564846 original size:2 final size:2
Alignment explanation
Indices: 16564839--16564865 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16564829 TATTAGTATG
16564839 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
16564866 AACTAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.