Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 44 of 106
Found at i:16664836 original size:42 final size:42
Alignment explanation
Indices: 16664787--16664948 Score: 191
Period size: 42 Copynumber: 3.8 Consensus size: 42
16664777 TGTGGACCAG
* *
16664787 GCTATGTGCGAGTAGGAGTGTACATAAATCGATGATGACCCA
1 GCTATGTGCGAGTAGGAGTGCACATAAGTCGATGATGACCCA
* * *
16664829 GCTATGTGCGAGTAGGAGTGCGCATAAGCCAATGATGA-CCA
1 GCTATGTGCGAGTAGGAGTGCACATAAGTCGATGATGACCCA
*
16664870 GGCTATGTGCGAGTGGGAGTGCACATAAGTCGATGATGACCCA
1 -GCTATGTGCGAGTAGGAGTGCACATAAGTCGATGATGACCCA
* ** * * *
16664913 GCCATGTGTTAGTGGGGAGTGCACATGAGTTGATGA
1 GCTATGTGCGAGT-AGGAGTGCACATAAGTCGATGA
16664949 CGATGGGAGA
Statistics
Matches: 103, Mismatches: 14, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
41 3 0.03
42 77 0.75
43 23 0.22
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (42 bp):
GCTATGTGCGAGTAGGAGTGCACATAAGTCGATGATGACCCA
Found at i:16664982 original size:2 final size:2
Alignment explanation
Indices: 16664975--16665015 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
16664965 ATGATGATGA
16664975 AT AT AT 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 AT AT AT A
16665016 GTATNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16665080 original size:2 final size:2
Alignment explanation
Indices: 16665073--16665107 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16665063 NNNNNNNNNN
16665073 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
16665108 CATGTATAGA
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:16671701 original size:38 final size:40
Alignment explanation
Indices: 16671659--16671761 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 40
16671649 ATAGTTCTCG
*
16671659 TGTGCACGATGTGGGGGGATGTACACAATAGC-ACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACAATAGCGACGGATA
* * * * * * *
16671697 TGTGCACGATGTGAGGGGATGCACGCGATGGCGTCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACAATAGCGACGGATA
16671737 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
16671762 TGAGCCGGGT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
38 27 0.52
39 3 0.06
40 22 0.42
ACGTcount: A:0.21, C:0.17, G:0.40, T:0.22
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACAATAGCGACGGATA
Found at i:16674108 original size:189 final size:189
Alignment explanation
Indices: 16673788--16674143 Score: 588
Period size: 189 Copynumber: 1.9 Consensus size: 189
16673778 ATTTCGGCTG
* * *
16673788 CTGAAATGGTTAAAGGTGTTCCCTTCGAGGGAAACAAAAGGCCTCGGGTTCGAATCCTGGGTACG
1 CTGAAATGGTTAAAGGCGTTCCCTTCGAGGGAAACAAAAGGCCTCGAGTTCGAATCCTGGGTAAG
16673853 CAGCTGCAGCTGGGACGTACCGCAGGGAACGAGAGATCGAACAATACCTTGGAGTGGACCCCGGA
66 CAGCTGCAGCTGGGACGTACCGCAGGGAACGAGAGATCGAACAATACCTTGGAGTGGACCCCGGA
*
16673918 TGGGGAGGCCACATGGGTGGGCCCCGAGGGGGATGTCCCAAAAAAGTGCCTTTTTACAA
131 TGGAGAGGCCACATGGGTGGGCCCCGAGGGGGATGTCCCAAAAAAGTGCCTTTTTACAA
* * * *
16673977 CTGAAATGGTTAAAGGCGTTCCCTTCGGGGGAAACAAAAGGTCTTGAGTTCGAATCTTGGGTAAG
1 CTGAAATGGTTAAAGGCGTTCCCTTCGAGGGAAACAAAAGGCCTCGAGTTCGAATCCTGGGTAAG
* * * *
16674042 TAGCTGCAGCTGGGACGTATCGCAGGGAACGGGAGA-CGGAACAATACCTTGGAGTGGGCCCCGG
66 CAGCTGCAGCTGGGACGTACCGCAGGGAACGAGAGATC-GAACAATACCTTGGAGTGGACCCCGG
16674106 ATGGAGAGGCCACATGGGTGGGCCCCGAGGGGGATGTC
130 ATGGAGAGGCCACATGGGTGGGCCCCGAGGGGGATGTC
16674144 ACACATTTCA
Statistics
Matches: 154, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
188 1 0.01
189 153 0.99
ACGTcount: A:0.25, C:0.21, G:0.35, T:0.18
Consensus pattern (189 bp):
CTGAAATGGTTAAAGGCGTTCCCTTCGAGGGAAACAAAAGGCCTCGAGTTCGAATCCTGGGTAAG
CAGCTGCAGCTGGGACGTACCGCAGGGAACGAGAGATCGAACAATACCTTGGAGTGGACCCCGGA
TGGAGAGGCCACATGGGTGGGCCCCGAGGGGGATGTCCCAAAAAAGTGCCTTTTTACAA
Found at i:16674228 original size:14 final size:14
Alignment explanation
Indices: 16674209--16674268 Score: 67
Period size: 14 Copynumber: 4.6 Consensus size: 14
16674199 AGGCTAAACG
16674209 CTTCTTTCTCTTTT
1 CTTCTTTCTCTTTT
* *
16674223 CTTCTTCCTCCTTT
1 CTTCTTTCTCTTTT
16674237 CTTCTTT-TC---T
1 CTTCTTTCTCTTTT
16674247 -TTCTTTCTCTTTT
1 CTTCTTTCTCTTTT
16674260 CTTCTTTCT
1 CTTCTTTCT
16674269 TTCAAACCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
9 6 0.16
10 3 0.08
13 3 0.08
14 26 0.68
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (14 bp):
CTTCTTTCTCTTTT
Found at i:16674243 original size:7 final size:7
Alignment explanation
Indices: 16674209--16674269 Score: 54
Period size: 7 Copynumber: 8.4 Consensus size: 7
16674199 AGGCTAAACG
16674209 CTTCTTT
1 CTTCTTT
16674216 C-TCTTTT
1 CTTC-TTT
*
16674223 CTTCTTC
1 CTTCTTT
*
16674230 CTCCTTT
1 CTTCTTT
16674237 CTTCTTTT
1 CTTC-TTT
16674245 CTTTCTTT
1 C-TTCTTT
16674253 C-TCTTTT
1 CTTC-TTT
16674260 CTTCTTT
1 CTTCTTT
16674267 CTT
1 CTT
16674270 TCAAACCAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
6 4 0.09
7 25 0.57
8 12 0.27
9 3 0.07
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (7 bp):
CTTCTTT
Found at i:16674267 original size:22 final size:23
Alignment explanation
Indices: 16674212--16674271 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
16674202 CTAAACGCTT
16674212 CTTTC-TCTTTTC-TTCTTCCTC
1 CTTTCTTCTTTTCTTTCTTCCTC
*
16674233 CTTTCTTCTTTTCTTTCTTTCTC
1 CTTTCTTCTTTTCTTTCTTCCTC
*
16674256 TTTTCTTC-TTTCTTTC
1 CTTTCTTCTTTTCTTTC
16674272 AAACCAATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 5 0.14
22 15 0.43
23 15 0.43
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (23 bp):
CTTTCTTCTTTTCTTTCTTCCTC
Found at i:16674571 original size:5 final size:5
Alignment explanation
Indices: 16674552--16674584 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
16674542 TCACATCTTT
*
16674552 TTTTC -TTTA TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
16674585 TCTTCTCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:16681388 original size:38 final size:38
Alignment explanation
Indices: 16681258--16681396 Score: 117
Period size: 36 Copynumber: 3.7 Consensus size: 38
16681248 ACCCAGCTCA
* *
16681258 TGTGTATCCCCCCACATCGTGCACA--TAGCCGGAGTCATCG
1 TGTGCATCCCCCCACATCGTGCACAGGTA--C--AGACATCG
* * *
16681298 CGTGCATCCCCCCACATCGTGCATAGGTACAGACATCA
1 TGTGCATCCCCCCACATCGTGCACAGGTACAGACATCG
* * * *
16681336 TGTGC-T-CCCCCACATCGCGCACAGTTGA-TGCCATCG
1 TGTGCATCCCCCCACATCGTGCACAGGT-ACAGACATCG
16681372 TGTGCATCCCCCCACATCGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
16681397 CGGGTAATAT
Statistics
Matches: 81, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
36 27 0.33
37 3 0.04
38 26 0.32
40 23 0.28
42 2 0.02
ACGTcount: A:0.21, C:0.38, G:0.20, T:0.21
Consensus pattern (38 bp):
TGTGCATCCCCCCACATCGTGCACAGGTACAGACATCG
Found at i:16682696 original size:42 final size:43
Alignment explanation
Indices: 16682615--16682772 Score: 221
Period size: 42 Copynumber: 3.7 Consensus size: 43
16682605 ATCATTATCA
* * *
16682615 GCTTATGCGCACTCCCTACTCGCACATAGTCTGATCAGCATCG
1 GCTTATGCGCACTCCCTACTCGCACATAGCCAGGTCAGCATCG
*
16682658 GCTTATGCGCACTCCC-ACTCTCACATAGCCAGGTCAGCATCG
1 GCTTATGCGCACTCCCTACTCGCACATAGCCAGGTCAGCATCG
* * **
16682700 GCTTATGCGCACT-CCTACTAGCACATAGCTAGGTCAGCATTA
1 GCTTATGCGCACTCCCTACTCGCACATAGCCAGGTCAGCATCG
*
16682742 GCTTATGTGCACTCCCTACTCGCACATAGCC
1 GCTTATGCGCACTCCCTACTCGCACATAGCC
16682773 GAGTCAATAT
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
41 2 0.02
42 68 0.67
43 31 0.31
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.25
Consensus pattern (43 bp):
GCTTATGCGCACTCCCTACTCGCACATAGCCAGGTCAGCATCG
Found at i:16685070 original size:20 final size:19
Alignment explanation
Indices: 16685025--16685071 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
16685015 AGAGTGGAGG
*
16685025 AAGAA-GAAGAAGTTGCTA
1 AAGAATGAAGAAGCTGCTA
*
16685043 GAGAAATGAAGAAGCTGCTGA
1 AAG-AATGAAGAAGCTGCT-A
16685064 AAGAATGA
1 AAGAATGA
16685072 GATCCTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.09
19 2 0.09
20 16 0.70
21 3 0.13
ACGTcount: A:0.49, C:0.06, G:0.30, T:0.15
Consensus pattern (19 bp):
AAGAATGAAGAAGCTGCTA
Found at i:16686729 original size:35 final size:33
Alignment explanation
Indices: 16686681--16686785 Score: 101
Period size: 35 Copynumber: 3.2 Consensus size: 33
16686671 GCTAAACTAA
*
16686681 AACCT-AAAGTGGTTTCTCAAAGGCTCAACCAC
1 AACCTCAAAGTGGTTTTTCAAAGGCTCAACCAC
* * *
16686713 AACCTTTCACAA-TGGTTTTTC-ACGAGCTCAACAAA
1 AACC--TCA-AAGTGGTTTTTCAAAG-GCTCAACCAC
16686748 AACC-CAAAGTGGTTTTTTCAAAGGCTCAACCAC
1 AACCTCAAAGTGG-TTTTTCAAAGGCTCAACCAC
16686781 AACCT
1 AACCT
16686786 ACAACAATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
31 2 0.04
32 9 0.16
33 18 0.32
34 5 0.09
35 21 0.37
36 2 0.04
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (33 bp):
AACCTCAAAGTGGTTTTTCAAAGGCTCAACCAC
Found at i:16686731 original size:67 final size:68
Alignment explanation
Indices: 16686633--16686785 Score: 200
Period size: 67 Copynumber: 2.3 Consensus size: 68
16686623 TGGCTTTTAC
* * * * * * *
16686633 AAGGCTCAGCCAAAACCTTTTACACTAGTTTTTTACAAGCTAAACTAAAACCTAAAGTGG-TTTC
1 AAGGCTCAACCACAACCTTTCACAATAGTTTTTCACAAGCTAAACAAAAACCCAAAGTGGTTTTC
16686697 TCA
66 TCA
* * * *
16686700 AAGGCTCAACCACAACCTTTCACAATGGTTTTTCACGAGCTCAACAAAAACCCAAAGTGGTTTTT
1 AAGGCTCAACCACAACCTTTCACAATAGTTTTTCACAAGCTAAACAAAAACCCAAAGTGGTTTTC
16686765 TCA
66 TCA
16686768 AAGGCTCAACCACAACCT
1 AAGGCTCAACCACAACCT
16686786 ACAACAATGA
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
67 50 0.68
68 24 0.32
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.26
Consensus pattern (68 bp):
AAGGCTCAACCACAACCTTTCACAATAGTTTTTCACAAGCTAAACAAAAACCCAAAGTGGTTTTC
TCA
Found at i:16686793 original size:68 final size:66
Alignment explanation
Indices: 16686662--16686822 Score: 189
Period size: 68 Copynumber: 2.4 Consensus size: 66
16686652 TTACACTAGT
* * * *
16686662 TTTTTACAAGCTAAACTAAAACCTAAAGTGGTTTCTCAAAGGCTCAACCACAACCTTTCACAATG
1 TTTTTACAAGCTCAACAAAAACCCAAAGTGGTTTCTCAAAGGCTCAACCACAACCTTACACAATG
16686727 G
66 G
* *
16686728 TTTTTCACGAGCTCAACAAAAACCCAAAGTGGTTTTTTCAAAGGCTCAACCACAACC-TACAACA
1 TTTTT-ACAAGCTCAACAAAAACCCAAAGTGG-TTTCTCAAAGGCTCAACCACAACCTTAC-ACA
*
16686792 ATGA
63 ATGG
* * *
16686796 TTTTTACCAGGATCAACCAAAACCCAA
1 TTTTTA-CAAGCTCAACAAAAACCCAA
16686823 CAACAAATTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
66 5 0.06
67 25 0.31
68 50 0.62
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.25
Consensus pattern (66 bp):
TTTTTACAAGCTCAACAAAAACCCAAAGTGGTTTCTCAAAGGCTCAACCACAACCTTACACAATG
G
Found at i:16690106 original size:38 final size:39
Alignment explanation
Indices: 16690020--16690114 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 39
16690010 ACCCGGCTCA
*
16690020 TGTACATCCCCCCACATCGTGCACATAGCCGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAGG-ACCATCG
* *
16690060 TGTGCATCCCCCCACATCGTGCACA-ATCAGTG-CCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAG-GACCATCG
16690098 TGTACATCCCCCCACAT
1 TGTACATCCCCCCACAT
16690115 TGGGCACACG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
38 22 0.44
39 3 0.06
40 25 0.50
ACGTcount: A:0.22, C:0.42, G:0.16, T:0.20
Consensus pattern (39 bp):
TGTACATCCCCCCACATCGTGCACATAGCAGGACCATCG
Found at i:16692510 original size:38 final size:40
Alignment explanation
Indices: 16692468--16692542 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
16692458 GGAGATGAAT
*
16692468 GATGA-TATTGCT-TGTGCACGATGTGGGGGGATGCACAC
1 GATGACTATGGCTATGTGCACGATGTGGGGGGATGCACAC
*
16692506 GATGACTCTGGCTATGTGCACGATGTGGGGGGATGCA
1 GATGACTATGGCTATGTGCACGATGTGGGGGGATGCA
16692543 TATGAGCTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 5 0.15
39 5 0.15
40 23 0.70
ACGTcount: A:0.20, C:0.16, G:0.39, T:0.25
Consensus pattern (40 bp):
GATGACTATGGCTATGTGCACGATGTGGGGGGATGCACAC
Found at i:16692667 original size:54 final size:54
Alignment explanation
Indices: 16692515--16692675 Score: 241
Period size: 54 Copynumber: 3.0 Consensus size: 54
16692505 CGATGACTCT
* * * *
16692515 GGCTATGTGCACGATGTGGGGGGATGCATATGAGCTAGGTGAGACGGGGTATCC
1 GGCTATGTGCACGATGTGGGGGGATGCACATGAGCTGGGTGAGATGGGGTGTCC
*
16692569 GACTATGTGCACGATGTGGGGGGATGCACATGAGCTGGGTGAGATGGGGTGTCC
1 GGCTATGTGCACGATGTGGGGGGATGCACATGAGCTGGGTGAGATGGGGTGTCC
* * *
16692623 GGCTATGTGCACAATGTGGAGGGATGTACATGAGCTGGGTGAGATGGTGGTGT
1 GGCTATGTGCACGATGTGGGGGGATGCACATGAGCTGGGTGAGATGG-GGTGT
16692676 ATGTGCTTAT
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
54 92 0.95
55 5 0.05
ACGTcount: A:0.20, C:0.13, G:0.43, T:0.24
Consensus pattern (54 bp):
GGCTATGTGCACGATGTGGGGGGATGCACATGAGCTGGGTGAGATGGGGTGTCC
Found at i:16711324 original size:31 final size:31
Alignment explanation
Indices: 16711274--16711359 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
16711264 AAATGTTTTG
* * *
16711274 CAAACACCGCCTTTTCAAGCATAACCATAATT
1 CAAAC-CCGCCTCTCCAAGCATAACCATAAAT
* * *
16711306 TAAACCCGCCTCTCCAAGCGTAATCATAAAT
1 CAAACCCGCCTCTCCAAGCATAACCATAAAT
* *
16711337 CATTACCCACCTCTCCAAGCATA
1 CA-AACCCGCCTCTCCAAGCATA
16711360 TTCATAAAAC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
31 22 0.51
32 21 0.49
ACGTcount: A:0.35, C:0.35, G:0.07, T:0.23
Consensus pattern (31 bp):
CAAACCCGCCTCTCCAAGCATAACCATAAAT
Found at i:16711355 original size:32 final size:32
Alignment explanation
Indices: 16711309--16711372 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
16711299 CATAATTTAA
* * *
16711309 ACCCGCCTCTCCAAGCGTAATCATAAATCATT
1 ACCCACCTCTCCAAGCATAATCATAAAACATT
*
16711341 ACCCACCTCTCCAAGCATATTCATAAAACATT
1 ACCCACCTCTCCAAGCATAATCATAAAACATT
16711373 CCTGCTTAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.34, C:0.34, G:0.06, T:0.25
Consensus pattern (32 bp):
ACCCACCTCTCCAAGCATAATCATAAAACATT
Found at i:16719705 original size:4 final size:4
Alignment explanation
Indices: 16719696--16719787 Score: 94
Period size: 4 Copynumber: 23.0 Consensus size: 4
16719686 ACATTTCGCT
* * * * * *
16719696 TATA TATA TATA TATG TACA TATA TATA TGTA TGTA TATA TACA TACA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
16719744 TATA TATA TATA TATG TACA TATA TATA TGTA TGTA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
16719788 CGTGTGGCTT
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 74 1.00
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (4 bp):
TATA
Found at i:16719718 original size:10 final size:10
Alignment explanation
Indices: 16719705--16719768 Score: 51
Period size: 10 Copynumber: 6.6 Consensus size: 10
16719695 TTATATATAT
16719705 ATATATGTAC
1 ATATATGTAC
*
16719715 ATATA--TAT
1 ATATATGTAC
* *
16719723 ATGTATGTAT
1 ATATATGTAC
**
16719733 ATATACATAC
1 ATATATGTAC
* *
16719743 ATATATATAT
1 ATATATGTAC
16719753 ATATATGTAC
1 ATATATGTAC
16719763 ATATAT
1 ATATAT
16719769 ATATGTATGT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
8 6 0.14
10 36 0.86
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (10 bp):
ATATATGTAC
Found at i:16719720 original size:14 final size:14
Alignment explanation
Indices: 16719701--16719786 Score: 80
Period size: 14 Copynumber: 6.7 Consensus size: 14
16719691 TCGCTTATAT
16719701 ATATATATATGTAC
1 ATATATATATGTAC
16719715 ATATATATATGT--
1 ATATATATATGTAC
*
16719727 ATGTATATA--TAC
1 ATATATATATGTAC
*
16719739 ATACATATA--T--
1 ATATATATATGTAC
16719749 ATATATATATGTAC
1 ATATATATATGTAC
*
16719763 ATATATATATGTAT
1 ATATATATATGTAC
*
16719777 GTATATATAT
1 ATATATATAT
16719787 ACGTGTGGCT
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
10 9 0.15
12 17 0.28
14 34 0.57
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (14 bp):
ATATATATATGTAC
Found at i:16719720 original size:18 final size:17
Alignment explanation
Indices: 16719697--16719787 Score: 93
Period size: 18 Copynumber: 5.5 Consensus size: 17
16719687 CATTTCGCTT
16719697 ATATATATATATATGTA
1 ATATATATATATATGTA
*
16719714 CATATATATATGTATGT-
1 -ATATATATATATATGTA
* *
16719731 ATATATACATACA--T-
1 ATATATATATATATGTA
16719745 ATATATATATATATGTA
1 ATATATATATATATGTA
*
16719762 CATATATATATGTATGT-
1 -ATATATATATATATGTA
16719779 ATATATATA
1 ATATATATA
16719788 CGTGTGGCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
14 12 0.19
16 20 0.32
18 30 0.48
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (17 bp):
ATATATATATATATGTA
Found at i:16723150 original size:20 final size:19
Alignment explanation
Indices: 16723087--16723162 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 19
16723077 TCTAGGCCTA
*
16723087 ATCTATTGATAGATTGAGTC
1 ATCTATCGATAGA-TGAGTC
*
16723107 TATCTATCGATAGATTTG-GCC
1 -ATCTATCGATAGA--TGAGTC
16723128 ATCTATCGATAGATGAGATC
1 ATCTATCGATAGATGAG-TC
* *
16723148 ATCTGTCCATAGATG
1 ATCTATCGATAGATG
16723163 TTCTTCAGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 27 0.57
21 14 0.30
22 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (19 bp):
ATCTATCGATAGATGAGTC
Found at i:16724180 original size:13 final size:13
Alignment explanation
Indices: 16724162--16724186 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16724152 AATAATTGTT
16724162 ATAATGATGTATA
1 ATAATGATGTATA
16724175 ATAATGATGTAT
1 ATAATGATGTAT
16724187 GATGACAACC
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:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
ATAATGATGTATA
Found at i:16728484 original size:27 final size:27
Alignment explanation
Indices: 16728446--16728499 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
16728436 GTTATTGGAC
16728446 TTTAATCTTGGTACAATTAAATAGATT
1 TTTAATCTTGGTACAATTAAATAGATT
16728473 TTTAATCTTGGTACAATTAAATAGATT
1 TTTAATCTTGGTACAATTAAATAGATT
16728500 ATGGATGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (27 bp):
TTTAATCTTGGTACAATTAAATAGATT
Found at i:16730932 original size:57 final size:57
Alignment explanation
Indices: 16730844--16730955 Score: 197
Period size: 57 Copynumber: 2.0 Consensus size: 57
16730834 AGATAGTGCT
* *
16730844 AAGTGATTGATTCTAGTCTATTATTTAACAATTAAATCTTATGCTGGCTTCTTTCCC
1 AAGTGATGGATTCTAGTCTATTATTTAACAATTAAATCTTATGCAGGCTTCTTTCCC
*
16730901 AAGTGATGGGTTCTAGTCTATTATTTAACAATTAAATCTTATGCAGGCTTCTTTC
1 AAGTGATGGATTCTAGTCTATTATTTAACAATTAAATCTTATGCAGGCTTCTTTC
16730956 TTGAAAGGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (57 bp):
AAGTGATGGATTCTAGTCTATTATTTAACAATTAAATCTTATGCAGGCTTCTTTCCC
Found at i:16733004 original size:13 final size:14
Alignment explanation
Indices: 16732980--16733010 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
16732970 TTTTGAGTTC
16732980 TTTATTTGTTTATT
1 TTTATTTGTTTATT
16732994 TTTATTT-TTTATT
1 TTTATTTGTTTATT
16733007 TTTA
1 TTTA
16733011 AATTTTGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (14 bp):
TTTATTTGTTTATT
Found at i:16745241 original size:15 final size:15
Alignment explanation
Indices: 16745221--16745259 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
16745211 CACTTAGAAG
16745221 TGGAAAAAAGGTAAA
1 TGGAAAAAAGGTAAA
* *
16745236 TGGAAAAGAGGTAAG
1 TGGAAAAAAGGTAAA
16745251 TGGTAAAAA
1 TGG-AAAAA
16745260 TTTAAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.54, C:0.00, G:0.31, T:0.15
Consensus pattern (15 bp):
TGGAAAAAAGGTAAA
Found at i:16750834 original size:20 final size:20
Alignment explanation
Indices: 16750809--16750863 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
16750799 TATTGAAGGC
*
16750809 AATCTATCGATAGATCGAGA
1 AATCTATCGATAGATCGACA
* *
16750829 AATCTATCAATAGGTCGACA
1 AATCTATCGATAGATCGACA
*
16750849 AATTTATCGATAGAT
1 AATCTATCGATAGAT
16750864 GATGATCGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (20 bp):
AATCTATCGATAGATCGACA
Found at i:16751831 original size:2 final size:2
Alignment explanation
Indices: 16751824--16751882 Score: 82
Period size: 2 Copynumber: 29.0 Consensus size: 2
16751814 TGTTATGTTG
* *
16751824 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
16751866 AA AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT -AT AT
16751883 GTATTGATAG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 50 0.96
3 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16752133 original size:2 final size:2
Alignment explanation
Indices: 16752120--16752212 Score: 150
Period size: 2 Copynumber: 46.5 Consensus size: 2
16752110 TATTGGTGGT
*
16752120 TA TA TA TG TA TA TA TA 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 TA TA TA TA TA TA TA TA
* **
16752162 TA TA TA TN NN TA TA TA 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 TA TA TA TA TA TA TA TA
16752204 TA TA TA TA T
1 TA TA TA TA T
16752213 TTATGCAATA
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16765766 original size:36 final size:36
Alignment explanation
Indices: 16765724--16765794 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
16765714 AAGGTAGAGT
*
16765724 GGTTGTGCTTTAACCATATAA-GGCAGTGTATTGAAA
1 GGTTGTGCTTGAACCATA-AAGGGCAGTGTATTGAAA
* *
16765760 GGTTGTGCTTGATCCATAAAGGGCATTGTATTGAA
1 GGTTGTGCTTGAACCATAAAGGGCAGTGTATTGAA
16765795 TTCTATTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 2 0.06
36 29 0.94
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.34
Consensus pattern (36 bp):
GGTTGTGCTTGAACCATAAAGGGCAGTGTATTGAAA
Found at i:16768303 original size:50 final size:50
Alignment explanation
Indices: 16768247--16768348 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
16768237 TGACGACTCT
16768247 CAAGATGAAGAAGATGAAGTTACTAACCTTTACTTCATGGCACTTGAGGA
1 CAAGATGAAGAAGATGAAGTTACTAACCTTTACTTCATGGCACTTGAGGA
16768297 CAAGATGAAGAAGATGAAGTTACTAACCTTTACTTCATGGCACTTGAGGA
1 CAAGATGAAGAAGATGAAGTTACTAACCTTTACTTCATGGCACTTGAGGA
16768347 CA
1 CA
16768349 TTAAGGTACG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (50 bp):
CAAGATGAAGAAGATGAAGTTACTAACCTTTACTTCATGGCACTTGAGGA
Found at i:16769811 original size:17 final size:17
Alignment explanation
Indices: 16769785--16769830 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
16769775 AATTTATAAA
16769785 AATTCAATTTATTTTAT
1 AATTCAATTTATTTTAT
*
16769802 AATTCCATTTATTTTAT
1 AATTCAATTTATTTTAT
16769819 AAATTCATATTT
1 -AATTCA-ATTT
16769831 TTCTCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 16 0.64
18 5 0.20
19 4 0.16
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTCAATTTATTTTAT
Found at i:16771085 original size:19 final size:19
Alignment explanation
Indices: 16771061--16771098 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16771051 ACTTCTAAAC
16771061 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
16771080 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
16771099 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:16772294 original size:21 final size:21
Alignment explanation
Indices: 16772268--16772311 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
16772258 GTTAAGTAAG
16772268 CATTGAAAGCTTTTATTTAAA
1 CATTGAAAGCTTTTATTTAAA
16772289 CATTGAAAGCTTTTATTTAAA
1 CATTGAAAGCTTTTATTTAAA
16772310 CA
1 CA
16772312 ATGGGAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (21 bp):
CATTGAAAGCTTTTATTTAAA
Found at i:16781199 original size:38 final size:40
Alignment explanation
Indices: 16781157--16781259 Score: 129
Period size: 38 Copynumber: 2.6 Consensus size: 40
16781147 AAAGTGCCCG
* *
16781157 TGTGCACGATGTGGGGGGATGTACACGATGGCACTA-AT-
1 TGTGCACGATGTGGGGGGATGCACACGATGACACTAGATA
* * * *
16781195 TGTGCACGATGTGGGGGAATACACACGATGACTCTAGTTA
1 TGTGCACGATGTGGGGGGATGCACACGATGACACTAGATA
*
16781235 TGTGCACGATGTGAGGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
16781260 TGAGTTGGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 31 0.57
39 1 0.02
40 22 0.41
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGCACACGATGACACTAGATA
Found at i:16787601 original size:14 final size:14
Alignment explanation
Indices: 16787578--16787632 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
16787568 TCGAACCTTC
16787578 CTTTCTCTTTTTTT
1 CTTTCTCTTTTTTT
* *
16787592 CTTCCTCTTTTCTT
1 CTTTCTCTTTTTTT
* *
16787606 CTTTCTCCTTTCTTC
1 CTTTCT-CTTTTTTT
16787621 CTTTCTCTTTTT
1 CTTTCTCTTTTT
16787633 GCTTCCAAGC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
14 22 0.67
15 11 0.33
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
CTTTCTCTTTTTTT
Found at i:16790537 original size:28 final size:28
Alignment explanation
Indices: 16790462--16790667 Score: 286
Period size: 28 Copynumber: 7.2 Consensus size: 28
16790452 TTATCTTCTG
* * * **
16790462 AGACAAATATGTTTTCTAGTTTGTATTA
1 AGACAAACATGTTTTCTTGTCTAAATTA
* *
16790490 AGACAAAATATGTTTTCTTGTCCAAATTA
1 AGAC-AAACATGTTTTCTTGTCTAAATTA
*
16790519 AGACAAACATGTTTTCTTGTCCAAATTA
1 AGACAAACATGTTTTCTTGTCTAAATTA
16790547 AGACAAACATGTTTTTCTTGTCTAAATTA
1 AGACAAACATG-TTTTCTTGTCTAAATTA
*
16790576 AGACAAACATGTTTTCTTGTCTACATTA
1 AGACAAACATGTTTTCTTGTCTAAATTA
* *
16790604 AGACATAACATGTTATCTTGTTTAAATTA
1 AGACA-AACATGTTTTCTTGTCTAAATTA
16790633 AGACAAACATGTTTTCTTGTCTAAATTA
1 AGACAAACATGTTTTCTTGTCTAAATTA
16790661 AGACAAA
1 AGACAAA
16790668 ACCTTTTAAA
Statistics
Matches: 162, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
28 87 0.54
29 75 0.46
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (28 bp):
AGACAAACATGTTTTCTTGTCTAAATTA
Found at i:16790550 original size:57 final size:57
Alignment explanation
Indices: 16790462--16790669 Score: 292
Period size: 57 Copynumber: 3.6 Consensus size: 57
16790452 TTATCTTCTG
* * * ** * *
16790462 AGACAAATATGTTTTCTAGTTTGTATTAAGACAAAATATGTTTTCTTGTCCAAATTA
1 AGACAAACATGTTTTCTTGTCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTA
*
16790519 AGACAAACATGTTTTCTTGTCCAAATTAAGAC-AAACATGTTTTTCTTGTCTAAATTA
1 AGACAAACATGTTTTCTTGTCTAAATTAAGACAAAACATG-TTTTCTTGTCTAAATTA
* * * *
16790576 AGACAAACATGTTTTCTTGTCTACATTAAGACATAACATGTTATCTTGTTTAAATTA
1 AGACAAACATGTTTTCTTGTCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTA
16790633 AGACAAACATGTTTTCTTGTCTAAATTAAGACAAAAC
1 AGACAAACATGTTTTCTTGTCTAAATTAAGACAAAAC
16790670 CTTTTAAAGT
Statistics
Matches: 134, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
56 6 0.04
57 122 0.91
58 6 0.04
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (57 bp):
AGACAAACATGTTTTCTTGTCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTA
Found at i:16792211 original size:54 final size:54
Alignment explanation
Indices: 16792120--16792298 Score: 304
Period size: 54 Copynumber: 3.3 Consensus size: 54
16792110 AAAACATTTT
* *
16792120 ATCTCACCCAGCTCATGTGCATCCCACCACATAGTGCACATAGCCGGACACCAC
1 ATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
* * *
16792174 GTCGCACCCAACTCATATGCATCCCACCACATCGTGCACATAGCCGGACACCAC
1 ATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
*
16792228 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
1 ATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
16792282 ATCTCACCCAACTCATG
1 ATCTCACCCAACTCATG
16792299 CATGGTTACA
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 115 1.00
ACGTcount: A:0.27, C:0.42, G:0.14, T:0.17
Consensus pattern (54 bp):
ATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACACCAC
Found at i:16792225 original size:24 final size:24
Alignment explanation
Indices: 16792198--16792284 Score: 70
Period size: 24 Copynumber: 3.4 Consensus size: 24
16792188 ATATGCATCC
16792198 CACCACATCGTGCACATAGCCGGA
1 CACCACATCGTGCACATAGCCGGA
**
16792222 CACCACATC-T-CACCCAGCTCATGTGCA
1 CACCACATCGTGCACATAGC-C--G-G-A
16792249 TCCCACCACATCGTGCACATAGCCGGA
1 ---CACCACATCGTGCACATAGCCGGA
16792276 CACCACATC
1 CACCACATC
16792285 TCACCCAACT
Statistics
Matches: 49, Mismatches: 4, Indels: 20
0.67 0.05 0.27
Matches are distributed among these distances:
22 6 0.12
23 2 0.04
24 18 0.37
25 1 0.02
26 1 0.02
27 2 0.04
28 1 0.02
29 1 0.02
30 9 0.18
31 2 0.04
32 6 0.12
ACGTcount: A:0.28, C:0.43, G:0.15, T:0.15
Consensus pattern (24 bp):
CACCACATCGTGCACATAGCCGGA
Found at i:16805002 original size:19 final size:19
Alignment explanation
Indices: 16804978--16805014 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16804968 TTAAATTATC
*
16804978 AACTAGCTGAGGGTTTCTT
1 AACTAGCCGAGGGTTTCTT
16804997 AACTAGCCGAGGGTTTCT
1 AACTAGCCGAGGGTTTCT
16805015 CACCAAACCT
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:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (19 bp):
AACTAGCCGAGGGTTTCTT
Found at i:16805275 original size:30 final size:30
Alignment explanation
Indices: 16805204--16805280 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
16805194 AATAGAAAGT
** *
16805204 TTCTCACTATAGCGAAAAGCTACAGTAACA
1 TTCTCACTGCAGCGAGAAGCTACAGTAACA
16805234 TTCTCACTGCAGCGAGAAGCTACAGTAACA
1 TTCTCACTGCAGCGAGAAGCTACAGTAACA
**
16805264 TTCTCGTTGCAGCGAGA
1 TTCTCACTGCAGCGAGA
16805281 TTTTCGGCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (30 bp):
TTCTCACTGCAGCGAGAAGCTACAGTAACA
Found at i:16854311 original size:33 final size:35
Alignment explanation
Indices: 16854233--16854396 Score: 172
Period size: 36 Copynumber: 4.6 Consensus size: 35
16854223 TCAACTAAGC
* * * *
16854233 TCATGTGCACTCCTACACCGCACATAGCTAATATCC
1 TCATGTGCACTCCCACACCGCACATGGC-AATGTCA
*
16854269 TCATGTGCACTCCCACACCCCACATGGCAAT-T-A
1 TCATGTGCACTCCCACACCGCACATGGCAATGTCA
* * *
16854302 TCATGTGCACTTCAACACCACACATGGCATATGTCA
1 TCATGTGCACTCCCACACCGCACATGGCA-ATGTCA
16854338 TCATGTGCACTCCCACACCGCACATGGC-ATGTATCA
1 TCATGTGCACTCCCACACCGCACATGGCAATG--TCA
16854374 TCAGCGTGTGCACTCCCACACCG
1 TCA---TGTGCACTCCCACACCG
16854397 TACACCACCA
Statistics
Matches: 110, Mismatches: 10, Indels: 13
0.83 0.08 0.10
Matches are distributed among these distances:
33 26 0.24
34 6 0.05
35 4 0.04
36 57 0.52
39 17 0.15
ACGTcount: A:0.26, C:0.37, G:0.15, T:0.23
Consensus pattern (35 bp):
TCATGTGCACTCCCACACCGCACATGGCAATGTCA
Found at i:16854344 original size:69 final size:69
Alignment explanation
Indices: 16854233--16854374 Score: 189
Period size: 69 Copynumber: 2.1 Consensus size: 69
16854223 TCAACTAAGC
* * *
16854233 TCATGTGCACTCCTACACCGCACATAGCTAATATCCTCATGTGCACTCCCACACCCCACATGGCA
1 TCATGTGCACTCCAACACCACACATAGCTAATATCATCATGTGCACTCCCACACCCCACATGGC-
16854298 AT-TA
65 ATGTA
* * * *
16854302 TCATGTGCACTTCAACACCACACATGGC-ATATGTCATCATGTGCACTCCCACACCGCACATGGC
1 TCATGTGCACTCCAACACCACACATAGCTA-ATATCATCATGTGCACTCCCACACCCCACATGGC
16854366 ATGTA
65 ATGTA
16854371 TCAT
1 TCAT
16854375 CAGCGTGTGC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
68 3 0.05
69 61 0.95
ACGTcount: A:0.27, C:0.35, G:0.13, T:0.24
Consensus pattern (69 bp):
TCATGTGCACTCCAACACCACACATAGCTAATATCATCATGTGCACTCCCACACCCCACATGGCA
TGTA
Found at i:16856530 original size:10 final size:10
Alignment explanation
Indices: 16856515--16856540 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
16856505 ACCATATATC
16856515 ATATATGTAT
1 ATATATGTAT
16856525 ATATATGTAT
1 ATATATGTAT
16856535 ATATAT
1 ATATAT
16856541 AGATATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (10 bp):
ATATATGTAT
Found at i:16856649 original size:42 final size:42
Alignment explanation
Indices: 16856586--16856703 Score: 173
Period size: 42 Copynumber: 2.8 Consensus size: 42
16856576 CATCTCATAT
*
16856586 GCAACGGCTTATGCGCACTCCCACTCGCACATAGTCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGTCGGGTCA
* * *
16856628 GCAACGGCTTATGTGCCCTCCCACTCACACATAGTCGGGTTA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGTCGGGTCA
* * *
16856670 ACAACGGCTTATGTGCACTTCTACTCGCACATAG
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAG
16856704 CCGAGTCCAC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGTCGGGTCA
Found at i:16859702 original size:19 final size:20
Alignment explanation
Indices: 16859675--16859720 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
16859665 AGGAGACAAG
*
16859675 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
16859694 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
16859713 ATAATATT
1 ATAATATT
16859721 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:16861552 original size:13 final size:13
Alignment explanation
Indices: 16861534--16861558 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16861524 AGAGAAATTG
16861534 TGATTTTATAAAA
1 TGATTTTATAAAA
16861547 TGATTTTATAAA
1 TGATTTTATAAA
16861559 TTTTCTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:16863790 original size:43 final size:43
Alignment explanation
Indices: 16863728--16863838 Score: 152
Period size: 43 Copynumber: 2.6 Consensus size: 43
16863718 ATTGACTCGG
*
16863728 CTATGTGCGAGTAGGGAGTACGCATAAGCCGAG-GATGACCCAA
1 CTATGTGCGAGTAGGGAGTACGCATAACCCG-GTGATGACCCAA
* * *
16863771 TTATGTGCGAGTAAGGAGTACGCATAACCCGGTGATGACCCAG
1 CTATGTGCGAGTAGGGAGTACGCATAACCCGGTGATGACCCAA
* *
16863814 CCATGTGCGAGTAGGGAGTGCGCAT
1 CTATGTGCGAGTAGGGAGTACGCAT
16863839 GAGCTAGTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 1 0.02
43 58 0.98
ACGTcount: A:0.27, C:0.21, G:0.33, T:0.19
Consensus pattern (43 bp):
CTATGTGCGAGTAGGGAGTACGCATAACCCGGTGATGACCCAA
Found at i:16863849 original size:43 final size:43
Alignment explanation
Indices: 16863730--16863851 Score: 147
Period size: 43 Copynumber: 2.8 Consensus size: 43
16863720 TGACTCGGCT
**
16863730 ATGTGCGAGTAGGGAGTACGCATAAGCCGAG-GATGACCCAATT
1 ATGTGCGAGTAGGGAGTACGCATAAGCC-AGTGATGACCCAACC
* * * *
16863773 ATGTGCGAGTAAGGAGTACGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTACGCATAAGCCAGTGATGACCCAACC
* * *
16863816 ATGTGCGAGTAGGGAGTGCGCATGAGCTAGTGATGA
1 ATGTGCGAGTAGGGAGTACGCATAAGCCAGTGATGA
16863852 TGATGATGGC
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 1 0.02
43 65 0.98
ACGTcount: A:0.28, C:0.19, G:0.34, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTACGCATAAGCCAGTGATGACCCAACC
Found at i:16864285 original size:39 final size:39
Alignment explanation
Indices: 16864231--16864314 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
16864221 ATTCTCGCTG
* *
16864231 CAGCGAGAAACTTTCTATTTCTGGTTTACAATTTCACTA
1 CAGCGAAAAACTTTCTATTTCTGGGTTACAATTTCACTA
* * *
16864270 CAGCGAAAAACTTTCTGTTTCTGGGTTACAATTTCGCTG
1 CAGCGAAAAACTTTCTATTTCTGGGTTACAATTTCACTA
16864309 CAGCGA
1 CAGCGA
16864315 GATTCAATCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (39 bp):
CAGCGAAAAACTTTCTATTTCTGGGTTACAATTTCACTA
Found at i:16877447 original size:5 final size:5
Alignment explanation
Indices: 16877434--16877492 Score: 64
Period size: 5 Copynumber: 11.6 Consensus size: 5
16877424 TGTTGAATAG
* * * * *
16877434 TTAAA TTAAG TTAAT TTAAT TTAAT TTAAT TTAATT TTACT TTATT TTAGT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAA-T TTAAT TTAAT TTAAT
16877485 TTAAT TTA
1 TTAAT TTA
16877493 CTCTAAGAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
5 43 0.91
6 4 0.09
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (5 bp):
TTAAT
Found at i:16888129 original size:19 final size:18
Alignment explanation
Indices: 16888101--16888138 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
16888091 ATCATTTTCT
16888101 TCCAGCAGCTTCTTCATTC
1 TCCAGCAGCTTCTTC-TTC
*
16888120 TCCAGTAGCTTCTTCTTC
1 TCCAGCAGCTTCTTCTTC
16888138 T
1 T
16888139 TCTTCCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.13, C:0.34, G:0.11, T:0.42
Consensus pattern (18 bp):
TCCAGCAGCTTCTTCTTC
Found at i:16891462 original size:21 final size:22
Alignment explanation
Indices: 16891429--16891470 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
16891419 TACCTTTTTT
*
16891429 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
16891451 CACTT-TTCCCTTGAATTTTC
1 CACTTGTTCCCTTGAATTTTC
16891471 CACCTAGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.17, C:0.26, G:0.07, T:0.50
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:16906379 original size:23 final size:23
Alignment explanation
Indices: 16906330--16906386 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
16906320 TACTTTAGAA
**
16906330 ATCATCATTT-ATTTTTATTTCC
1 ATCATCATTTAATCCTTATTTCC
* *
16906352 TTCATCATTTAATCCTTATTTTC
1 ATCATCATTTAATCCTTATTTCC
16906375 ATCATTCATTTA
1 ATCA-TCATTTA
16906387 TGCTTTAGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 9 0.32
23 12 0.43
24 7 0.25
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (23 bp):
ATCATCATTTAATCCTTATTTCC
Found at i:16906433 original size:42 final size:42
Alignment explanation
Indices: 16906385--16906470 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
16906375 ATCATTCATT
*
16906385 TATGCTTTAGGCCTACTTAGGCCTTAAAAATGTTTGAAAGCA
1 TATGCTTTAGGCCTACTTAAGCCTTAAAAATGTTTGAAAGCA
16906427 TATGCTTTAGGCCTACTTAAGCCTTAAAAATGTTTGAAAGCA
1 TATGCTTTAGGCCTACTTAAGCCTTAAAAATGTTTGAAAGCA
16906469 TA
1 TA
16906471 CTTCTAGGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (42 bp):
TATGCTTTAGGCCTACTTAAGCCTTAAAAATGTTTGAAAGCA
Found at i:16908694 original size:31 final size:31
Alignment explanation
Indices: 16908627--16908686 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
16908617 TAAAAATACC
* *
16908627 CAATTTAGTCTTTGTACTGTAAAATTTTAAT
1 CAATTTAATCTTTATACTGTAAAATTTTAAT
* *
16908658 CAATTTAATCTTTATACTTTACAATTTTA
1 CAATTTAATCTTTATACTGTAAAATTTTA
16908687 TTTAATTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (31 bp):
CAATTTAATCTTTATACTGTAAAATTTTAAT
Found at i:16915244 original size:19 final size:19
Alignment explanation
Indices: 16915220--16915322 Score: 64
Period size: 19 Copynumber: 5.3 Consensus size: 19
16915210 GATAGTGCCC
16915220 ATGTACACGATGTGGGGGG
1 ATGTACACGATGTGGGGGG
****
16915239 ATGTACACGATG-GCACTG
1 ATGTACACGATGTGGGGGG
*
16915257 ATTGTGCACGATGTGGGGGG
1 A-TGTACACGATGTGGGGGG
** * **
16915277 ATACACACGATGGTGCCGGCT
1 ATGTACACGAT-GTG-GGGGG
* *
16915298 ATGTGCACGATGTGGGGAG
1 ATGTACACGATGTGGGGGG
16915317 ATGTAC
1 ATGTAC
16915323 GTGAGCCGAG
Statistics
Matches: 58, Mismatches: 22, Indels: 8
0.66 0.25 0.09
Matches are distributed among these distances:
18 3 0.05
19 36 0.62
20 9 0.16
21 10 0.17
ACGTcount: A:0.22, C:0.17, G:0.39, T:0.22
Consensus pattern (19 bp):
ATGTACACGATGTGGGGGG
Found at i:16915267 original size:38 final size:40
Alignment explanation
Indices: 16915220--16915322 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 40
16915210 GATAGTGCCC
* *
16915220 ATGTACACGATGTGGGGGGATGTACACGAT-G-GCACTGAT
1 ATGTGCACGATGTGGGGGGATGTACACGATGGTGC-CGGAT
** *
16915259 -TGTGCACGATGTGGGGGGATACACACGATGGTGCCGGCT
1 ATGTGCACGATGTGGGGGGATGTACACGATGGTGCCGGAT
*
16915298 ATGTGCACGATGTGGGGAGATGTAC
1 ATGTGCACGATGTGGGGGGATGTAC
16915323 GTGAGCCGAG
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
38 26 0.49
39 4 0.08
40 23 0.43
ACGTcount: A:0.22, C:0.17, G:0.39, T:0.22
Consensus pattern (40 bp):
ATGTGCACGATGTGGGGGGATGTACACGATGGTGCCGGAT
Found at i:16917342 original size:10 final size:10
Alignment explanation
Indices: 16917327--16917401 Score: 57
Period size: 10 Copynumber: 7.4 Consensus size: 10
16917317 ATATTCAAAG
16917327 AATAATATTA
1 AATAATATTA
*
16917337 AATAATATTCTT
1 AATAATA-T-TA
*
16917349 TATAATATT-
1 AATAATATTA
* *
16917358 TATTATAGTTA
1 AATAATA-TTA
16917369 AATAATATT-
1 AATAATATTA
16917378 AAT-ATATTA
1 AATAATATTA
16917387 AATAATATTTA
1 AATAATA-TTA
16917398 AATA
1 AATA
16917402 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
8 5 0.09
9 12 0.23
10 15 0.28
11 14 0.26
12 7 0.13
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (10 bp):
AATAATATTA
Found at i:16917389 original size:18 final size:19
Alignment explanation
Indices: 16917350--16917395 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
16917340 AATATTCTTT
*
16917350 ATAATATTTATTATAGTTAA
1 ATAATA-TTAATATAGTTAA
16917370 ATAATATTAATATA-TTAA
1 ATAATATTAATATAGTTAA
16917388 ATAATATT
1 ATAATATT
16917396 TAAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.48
19 7 0.28
20 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATAATATTAATATAGTTAA
Found at i:16917394 original size:12 final size:11
Alignment explanation
Indices: 16917327--16917401 Score: 56
Period size: 11 Copynumber: 7.4 Consensus size: 11
16917317 ATATTCAAAG
16917327 AATAATA-TTA
1 AATAATATTTA
*
16917337 AATAATATTCTT
1 AATAATATT-TA
*
16917349 TATAATATTT-
1 AATAATATTTA
* *
16917359 -ATTATAGTTA
1 AATAATATTTA
16917369 AATAATA-TT-
1 AATAATATTTA
16917378 AAT-ATA-TTA
1 AATAATATTTA
16917387 AATAATATTTA
1 AATAATATTTA
16917398 AATA
1 AATA
16917402 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
8 5 0.09
9 13 0.25
10 12 0.23
11 14 0.26
12 9 0.17
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (11 bp):
AATAATATTTA
Found at i:16917402 original size:18 final size:18
Alignment explanation
Indices: 16917350--16917403 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
16917340 AATATTCTTT
*
16917350 ATAATATTTATTATAGTTAA
1 ATAATATTTA-AATA-TTAA
16917370 ATAATA-TTAATATATTAA
1 ATAATATTTAA-ATATTAA
16917388 ATAATATTTAAATATT
1 ATAATATTTAAATATT
16917404 TTCATTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 15 0.48
19 10 0.32
20 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATAATATTTAAATATTAA
Found at i:16917967 original size:22 final size:23
Alignment explanation
Indices: 16917930--16917989 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
16917920 ACTAATTTTT
* *
16917930 AAGCATTGCGTAACTGATT-G-A
1 AAGCATTGTGTGACTGATTAGTA
* *
16917951 TAAGTATTGTGTGACTGGTTAGTA
1 -AAGCATTGTGTGACTGATTAGTA
16917975 AAGCATTGTGTGACT
1 AAGCATTGTGTGACT
16917990 TAGGCATTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 15 0.48
23 15 0.48
24 1 0.03
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.35
Consensus pattern (23 bp):
AAGCATTGTGTGACTGATTAGTA
Found at i:16918137 original size:44 final size:44
Alignment explanation
Indices: 16918073--16918159 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
16918063 TGATTAAGTC
* * *
16918073 ACACAATGCCTAAAACCCAGT-CTCGCAATACCTACA-AACTAATG
1 ACACAACGCCTAAAAACCAGTAAT-GCAATACCTA-ATAACTAATG
16918117 ACACAACGCCTAAAAACCAGTAATGCAATACCTAATAACTAAT
1 ACACAACGCCTAAAAACCAGTAATGCAATACCTAATAACTAAT
16918160 TGATTTACCT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 1 0.03
44 36 0.95
45 1 0.03
ACGTcount: A:0.45, C:0.29, G:0.08, T:0.18
Consensus pattern (44 bp):
ACACAACGCCTAAAAACCAGTAATGCAATACCTAATAACTAATG
Found at i:16920078 original size:25 final size:26
Alignment explanation
Indices: 16920050--16920104 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
16920040 ATTCGTTCAG
*
16920050 AAAAC-TTTACT-ATTTGATATTTTTT
1 AAAACTTTTACTAAATTG-TATTTTTT
*
16920075 AAAACTTTTTCTAAATTGTATTTTTT
1 AAAACTTTTACTAAATTGTATTTTTT
16920101 AAAA
1 AAAA
16920105 AAAATATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 5 0.19
26 17 0.65
27 4 0.15
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (26 bp):
AAAACTTTTACTAAATTGTATTTTTT
Found at i:16931965 original size:21 final size:21
Alignment explanation
Indices: 16931935--16932002 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
16931925 GGATATATTC
*
16931935 ATGCAATTCATGACAAAGATTG
1 ATGC-ATTCATGACAAAGACTG
*
16931957 ATGCATTCATAACAAAGACTG
1 ATGCATTCATGACAAAGACTG
* *
16931978 ATGCATTTATGACAAGGACTG
1 ATGCATTCATGACAAAGACTG
16931999 ATGC
1 ATGC
16932003 CTCCATTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 37 0.90
22 4 0.10
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (21 bp):
ATGCATTCATGACAAAGACTG
Found at i:16933417 original size:11 final size:11
Alignment explanation
Indices: 16933378--16933426 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
16933368 TAATTTACTC
16933378 TATTTTATT-T
1 TATTTTATTAT
16933388 TATTTTATTAT
1 TATTTTATTAT
** *
16933399 TAAATTATTAA
1 TATTTTATTAT
*
16933410 TATTTTATTTT
1 TATTTTATTAT
16933421 TATTTT
1 TATTTT
16933427 GCAAAAACAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 9 0.29
11 22 0.71
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:16934312 original size:15 final size:14
Alignment explanation
Indices: 16934263--16934326 Score: 55
Period size: 15 Copynumber: 4.6 Consensus size: 14
16934253 TCAATATTTA
16934263 TTTA-TTTTC-TCT
1 TTTATTTTTCTTCT
*
16934275 TTT-TATTTCTTC-
1 TTTATTTTTCTTCT
16934287 TTTACTTTTTTCTTCT
1 TTTA--TTTTTCTTCT
*
16934303 TTTATCTTTTCTTGT
1 TTTAT-TTTTCTTCT
16934318 TTTATTTTT
1 TTTATTTTT
16934327 ATTATTGTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
12 10 0.24
13 2 0.05
14 5 0.12
15 21 0.50
16 4 0.10
ACGTcount: A:0.08, C:0.14, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTATTTTTCTTCT
Found at i:16942831 original size:11 final size:11
Alignment explanation
Indices: 16942815--16942859 Score: 67
Period size: 11 Copynumber: 4.3 Consensus size: 11
16942805 TATGGCCGGC
16942815 CAAAGGAAGAA
1 CAAAGGAAGAA
16942826 CAAAGGAAGAA
1 CAAAGGAAGAA
16942837 CAAAGGAAG-A
1 CAAAGGAAGAA
*
16942847 -AAAGAAAGAA
1 CAAAGGAAGAA
16942857 CAA
1 CAA
16942860 GAACCCTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 7 0.23
10 2 0.06
11 22 0.71
ACGTcount: A:0.67, C:0.09, G:0.24, T:0.00
Consensus pattern (11 bp):
CAAAGGAAGAA
Found at i:16947916 original size:37 final size:37
Alignment explanation
Indices: 16947867--16947941 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
16947857 ATAGGAAGTA
*
16947867 AAAACTATCTAGGGGTAGATTGGGAACATTAACTGTT
1 AAAACTATCTAGGGGTAGATTAGGAACATTAACTGTT
* *
16947904 AAAACTATCTAGGGGTAGTTTAGGAACATTAATTGTT
1 AAAACTATCTAGGGGTAGATTAGGAACATTAACTGTT
16947941 A
1 A
16947942 CTTTTTGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (37 bp):
AAAACTATCTAGGGGTAGATTAGGAACATTAACTGTT
Found at i:16948453 original size:17 final size:17
Alignment explanation
Indices: 16948431--16948467 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16948421 AGCAAAATAT
16948431 GCACACACTAAGAGGGA
1 GCACACACTAAGAGGGA
* *
16948448 GCACACACTTAGGGGGA
1 GCACACACTAAGAGGGA
16948465 GCA
1 GCA
16948468 ATCCTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.24, G:0.32, T:0.08
Consensus pattern (17 bp):
GCACACACTAAGAGGGA
Found at i:16949425 original size:32 final size:32
Alignment explanation
Indices: 16949383--16949485 Score: 118
Period size: 32 Copynumber: 3.1 Consensus size: 32
16949373 CATTATTGTA
*
16949383 GGTTGTGGTTGAGCCTTTGAAAAATCACTTTG
1 GGTTGTGGTTGAGCCTTTGAAAAACCACTTTG
* **
16949415 GGTTTTGGTTGAGCCCGTGAAAAACCA-TTGTG
1 GGTTGTGGTTGAGCCTTTGAAAAACCACTT-TG
*
16949447 AAAGGTTGTGGTTGAACCTTTGAAAAACCACTTTG
1 ---GGTTGTGGTTGAGCCTTTGAAAAACCACTTTG
16949482 GGTT
1 GGTT
16949486 TTATTTGCTC
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
31 2 0.03
32 29 0.50
35 25 0.43
36 2 0.03
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (32 bp):
GGTTGTGGTTGAGCCTTTGAAAAACCACTTTG
Found at i:16953204 original size:42 final size:42
Alignment explanation
Indices: 16953104--16953223 Score: 143
Period size: 42 Copynumber: 2.8 Consensus size: 42
16953094 ACCATCCCAC
* * * * *
16953104 CATCATCAGCTCATGTACATTTCCCACTCGCGCATAGCTGGGT
1 CATCATCAGCTCATGTGCA-CTCCCACTCGCACATAACTAGGT
*
16953147 CATCATCAGCGCATGTGCACTCCACACT-GCACATAACTAGGT
1 CATCATCAGCTCATGTGCACTCC-CACTCGCACATAACTAGGT
**
16953189 CATCATCAGCTCATGTGCACTCCCACAAGCACATA
1 CATCATCAGCTCATGTGCACTCCCACTCGCACATA
16953224 GTTGAGTCAT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
41 3 0.04
42 43 0.64
43 21 0.31
ACGTcount: A:0.27, C:0.34, G:0.16, T:0.23
Consensus pattern (42 bp):
CATCATCAGCTCATGTGCACTCCCACTCGCACATAACTAGGT
Found at i:16955171 original size:21 final size:21
Alignment explanation
Indices: 16955126--16955172 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
16955116 ACCTAGAGAA
* *
16955126 TTGAGAACCTTGAGCACCTAG
1 TTGAGAACCTTGAGCAACAAG
* *
16955147 TTGAGAACCTTGGGCAACAAT
1 TTGAGAACCTTGAGCAACAAG
16955168 TTGAG
1 TTGAG
16955173 CAACACATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (21 bp):
TTGAGAACCTTGAGCAACAAG
Found at i:16956227 original size:39 final size:39
Alignment explanation
Indices: 16956183--16956262 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
16956173 AAAAGAGAGA
16956183 TAAATAATTCAGACTATATATTGTGTTTAATCATAATCT
1 TAAATAATTCAGACTATATATTGTGTTTAATCATAATCT
16956222 TAAATAATTCAGACTATATATTGTGTTTAATCATAATCT
1 TAAATAATTCAGACTATATATTGTGTTTAATCATAATCT
16956261 TA
1 TA
16956263 GATTAACAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (39 bp):
TAAATAATTCAGACTATATATTGTGTTTAATCATAATCT
Found at i:16963673 original size:5 final size:5
Alignment explanation
Indices: 16963664--16963704 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
16963654 TCTATTCAAT
* *
16963664 TTAAC CTAAC TTAAC TTAAC TTAAC TTATC TTAAC TTAAC T
1 TTAAC TTAAC TTAAC TTAAC TTAAC TTAAC TTAAC TTAAC T
16963705 GGACTTGGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (5 bp):
TTAAC
Found at i:16963766 original size:15 final size:15
Alignment explanation
Indices: 16963746--16963790 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
16963736 TTCTTAAAAC
16963746 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
16963761 AACTTTAAAATCC-AA
1 AACTTTAAAA-CCAAA
*
16963776 AGCTTTAAAACCAAA
1 AACTTTAAAACCAAA
16963791 TTCTTTGATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 2 0.07
15 23 0.85
16 2 0.07
ACGTcount: A:0.56, C:0.20, G:0.02, T:0.22
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:16965386 original size:14 final size:14
Alignment explanation
Indices: 16965367--16965402 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
16965357 GCACAATCTT
16965367 TGTACTTTTACCTG
1 TGTACTTTTACCTG
16965381 TGTACTTTTACCTG
1 TGTACTTTTACCTG
16965395 TGTACTTT
1 TGTACTTT
16965403 GCTCACCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.14, T:0.53
Consensus pattern (14 bp):
TGTACTTTTACCTG
Found at i:16973022 original size:2 final size:2
Alignment explanation
Indices: 16973017--16973055 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
16973007 GCATTTTTTC
16973017 AT AT 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 AT AT A
16973056 CCAAATGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16977631 original size:20 final size:20
Alignment explanation
Indices: 16977614--16977651 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
16977604 CCTCAAATCT
16977614 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
16977634 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
16977652 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:16979123 original size:30 final size:30
Alignment explanation
Indices: 16979082--16979235 Score: 124
Period size: 28 Copynumber: 5.3 Consensus size: 30
16979072 TCTTATCTTT
* *
16979082 AATTTAGACAAAAATATGTTATCTTGTCTA
1 AATTAAGACAAAAATATGTTTTCTTGTCTA
* *
16979112 AATTGAGAC--AAATATGTTTTGTTGTCTA
1 AATTAAGACAAAAATATGTTTTCTTGTCTA
*
16979140 GATTAAGACAAAACATAT-TTTTCTTGTCTTA
1 AATTAAGACAAAA-ATATGTTTTCTTGTC-TA
* * *
16979171 AATTAAGACAAACATA--TTTTCTTATTTA
1 AATTAAGACAAAAATATGTTTTCTTGTCTA
* * *
16979199 AATTAAAACTAAACATAT-TTTT-TTATCTA
1 AATTAAGAC-AAAAATATGTTTTCTTGTCTA
*
16979228 AACTAAGA
1 AATTAAGA
16979236 TAAATATGTT
Statistics
Matches: 104, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
28 34 0.33
29 27 0.26
30 26 0.25
31 17 0.16
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.41
Consensus pattern (30 bp):
AATTAAGACAAAAATATGTTTTCTTGTCTA
Found at i:16979204 original size:59 final size:58
Alignment explanation
Indices: 16979072--16979235 Score: 161
Period size: 59 Copynumber: 2.8 Consensus size: 58
16979062 TTAAGATAAC
* * * * * *
16979072 TCTTATCTTTAATTTAGACAAAA-ATATGTTATCTTGTCTAAATTGAGACAAATATGTTT
1 TCTTAT-TTAAATTAAGACAAAACATAT-TTTTCTTGTCTAAATTAAGACAAACATATTT
* * * *
16979131 TGTTGTCTAGATTAAGACAAAACATATTTTTCTTGTCTTAAATTAAGACAAACATATTT
1 TCTTATTTAAATTAAGACAAAACATATTTTTCTTGTC-TAAATTAAGACAAACATATTT
* * * *
16979190 TCTTATTTAAATTAAAACTAAACATATTTTT-TTATCTAAACTAAGA
1 TCTTATTTAAATTAAGACAAAACATATTTTTCTTGTCTAAATTAAGA
16979236 TAAATATGTT
Statistics
Matches: 85, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
57 9 0.11
58 25 0.29
59 51 0.60
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (58 bp):
TCTTATTTAAATTAAGACAAAACATATTTTTCTTGTCTAAATTAAGACAAACATATTT
Found at i:16979212 original size:29 final size:28
Alignment explanation
Indices: 16979072--16979235 Score: 112
Period size: 29 Copynumber: 5.6 Consensus size: 28
16979062 TTAAGATAAC
* * *
16979072 TCTTATCTTTAATTTAGACAAAAATATGTT
1 TCTTAT-TTAAATTAAGACAAACATAT-TT
* * * * *
16979102 ATCTTGTCTAAATTGAGACAAATATGTTT
1 -TCTTATTTAAATTAAGACAAACATATTT
* * * *
16979131 TGTTGTCTAGATTAAGACAAAACATATTTT
1 TCTTATTTAAATTAAGAC-AAACATA-TTT
*
16979161 TCTTGTCTTAAATTAAGACAAACATATTT
1 TCTTAT-TTAAATTAAGACAAACATATTT
*
16979190 TCTTATTTAAATTAAAACTAAACATATTT
1 TCTTATTTAAATTAAGAC-AAACATATTT
* * *
16979219 TTTTATCTAAACTAAGA
1 TCTTATTTAAATTAAGA
16979236 TAAATATGTT
Statistics
Matches: 109, Mismatches: 20, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
28 26 0.24
29 38 0.35
30 30 0.28
31 15 0.14
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (28 bp):
TCTTATTTAAATTAAGACAAACATATTT
Found at i:16984437 original size:2 final size:2
Alignment explanation
Indices: 16984430--16984459 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16984420 GCTTTGTCTT
16984430 TA TA 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 TA TA
16984460 GTATTAGGTT
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):
TA
Found at i:16988076 original size:34 final size:32
Alignment explanation
Indices: 16987982--16988086 Score: 92
Period size: 34 Copynumber: 3.1 Consensus size: 32
16987972 AATATTAATA
16987982 ATTATAATTTAGATGTTA-ATATT-TTATTTGT
1 ATTATAATTTAGATGTTATATATTATTATTT-T
16988013 AATT-TAATCATTAGTAT-TATATAATATTATTATTTT
1 -ATTATAAT--TTAG-ATGT-TAT-ATATTATTATTTT
16988049 ATTATAATTTAGATGTTATTATGATTATTTATTTT
1 ATTATAATTTAGATGTTA-TAT-ATTA-TTATTTT
16988084 ATT
1 ATT
16988087 TTATTTTTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 21
0.74 0.00 0.26
Matches are distributed among these distances:
31 4 0.07
32 3 0.05
33 11 0.18
34 14 0.23
35 13 0.21
36 10 0.16
37 6 0.10
ACGTcount: A:0.34, C:0.01, G:0.07, T:0.58
Consensus pattern (32 bp):
ATTATAATTTAGATGTTATATATTATTATTTT
Found at i:16988163 original size:22 final size:24
Alignment explanation
Indices: 16988118--16988163 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
16988108 TTGATAATTT
*
16988118 ATTTAAAATAATTAATAATTTTTA
1 ATTTAAAATAATTAATAATGTTTA
*
16988142 ATTT-AAAT-ATTAATACTGTTTA
1 ATTTAAAATAATTAATAATGTTTA
16988164 TTATATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 4 0.20
24 4 0.20
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTTAAAATAATTAATAATGTTTA
Found at i:16988218 original size:69 final size:68
Alignment explanation
Indices: 16988135--16988312 Score: 159
Period size: 69 Copynumber: 2.6 Consensus size: 68
16988125 ATAATTAATA
* * *
16988135 ATTTTTAATTTAAATATTAATACTG-TTTATTATATT-TTAATCA-TTA-ATATTTAAAAATATT
1 ATTTATAATTTAAATATTAATA-TGATATATT-TATTATTAATAATTTACA-ATTT--AAATATT
16988196 AATATTTT
61 AATATTTT
* * * *
16988204 ATTTATAAGTTAAATGTTATTATGATATATTTATTNATTAATAATTTACAATTTAAATGTTAATA
1 ATTTATAATTTAAATATTAATATGATATATTTATT-ATTAATAATTTACAATTTAAATATTAATA
16988269 TTTT
65 TTTT
* *
16988273 ATTTATAATTT-AATCATTAGTATTATATAATATTATTATT
1 ATTTATAATTTAAAT-ATTAATATGATAT-AT-TTATTATT
16988313 TTATTATAAT
Statistics
Matches: 90, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
68 9 0.10
69 57 0.63
70 11 0.12
71 12 0.13
72 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.54
Consensus pattern (68 bp):
ATTTATAATTTAAATATTAATATGATATATTTATTATTAATAATTTACAATTTAAATATTAATAT
TTT
Found at i:16988277 original size:155 final size:152
Alignment explanation
Indices: 16987919--16988325 Score: 375
Period size: 155 Copynumber: 2.6 Consensus size: 152
16987909 ATATCTATTG
* * * *
16987919 TTATTTATTTTTATTTTATCATTTTAAATACT-AATAA-TATATAATTTATTGAAAATATTAATA
1 TTATTTA-TTTTATTTAAT-AATTTAAAT-TTAAATAATTA-ATAATTTATTTAAAATATTAATA
* * * * * *
16987982 ATTATAATTTAGATGTTAATATTTTATTTGTAATTTAATCATTAGTATTATATAATATTATTATT
62 ATTATAATTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATATTAATATT
* *
16988047 TTATTATAATTTAGATGTTATTATGA
127 TTATTATAAGTTAAATGTTATTATGA
* ** ** *
16988073 TTATTTATTTTATTTTATTTTTTAAATTTTTATAATTGATAATTTATTTAAAATAATTAATAATT
1 TTATTTATTTTATTTAATAATTTAAATTTAAATAATTAATAATTTATTTAAAAT-ATTAATAA-T
* *
16988138 TTTAATTTAAATATTAATACTGTTTA-TTATATTTTAATCATTAATATT-TAAAAATATTAATAT
64 TATAATTTAAATATTAATA-T-TTTATTTATAATTTAATCATTAATATTAT-AAAATATTAATAT
16988201 TTTATTTATAAGTTAAATGTTATTATGA
126 TTTA-TTATAAGTTAAATGTTATTATGA
* * * * *
16988229 TATATTTA-TTNA-TTAATAATTTACAATTTAAAT-GTTAATATTTTATTTATAAT-TTAATCAT
1 T-TATTTATTTTATTTAATAATTTA-AATTTAAATAATTAATAATTTATTTAAAATATTAATAAT
*
16988290 TAGT-ATTATATAATATTATTATTTTA-TTATAATTTA
64 TA-TAATT-TA-AATATTAATATTTTATTTATAATTTA
16988326 GATGTTATTA
Statistics
Matches: 211, Mismatches: 29, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
151 1 0.00
152 45 0.21
153 30 0.14
154 34 0.16
155 59 0.28
156 36 0.17
157 6 0.03
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (152 bp):
TTATTTATTTTATTTAATAATTTAAATTTAAATAATTAATAATTTATTTAAAATATTAATAATTA
TAATTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATATTAATATTTTAT
TATAAGTTAAATGTTATTATGA
Found at i:16988391 original size:27 final size:28
Alignment explanation
Indices: 16988352--16988408 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
16988342 TTTATTTTAT
* * * *
16988352 TTTATTTTTAAATTTTTATAATTTATAA
1 TTTATTTTAAAATATTAATAATTGATAA
16988380 TTTA-TTTAAAATATTAATAATTGATAA
1 TTTATTTTAAAATATTAATAATTGATAA
16988407 TT
1 TT
16988409 AAAATATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTATTTTAAAATATTAATAATTGATAA
Found at i:16988397 original size:111 final size:109
Alignment explanation
Indices: 16988128--16988436 Score: 274
Period size: 110 Copynumber: 2.8 Consensus size: 109
16988118 ATTTAAAATA
** * * * * * *
16988128 ATTAATAATTTTTAATTTAAATATTAATACTGTT-TATTATATTTTAATCATTAATATTTAAAAA
1 ATTAATAATTTACAATTTAAATGTTAATAAT-TTAT-TTAAAATTTAATCATTAGTA-TTATAAA
* *
16988192 TATTAATATTTTATTTATAAGTTAAATGTTATTATGATATATTTATTN
63 TATTAATATTTTA-TTATAATTTAAATGTTATTATGATATATTTATTT
* *
16988240 ATTAATAATTTACAATTTAAATGTTAATATTTTATTTATAATTTAATCATTAGTATTATATAATA
1 ATTAATAATTTACAATTTAAATGTTAATAATTTATTTAAAATTTAATCATTAGTATTATA-AATA
* *
16988305 TTATTATTTTATTATAATTTAGATGTTATTATGAT-TATTTATTTT
65 TTAATATTTTATTATAATTTAAATGTTATTATGATATATTTA-TTT
* * *
16988350 ATT-TTATTTTTA-AATTTTTATAAT-TT-ATAATTTATTTAAAATATTAATAATT-GATAATTA
1 ATTAATA-ATTTACAA--TTTA-AATGTTAATAATTTATTTAAAAT-TTAATCATTAG-T-ATTA
* *
16988410 -AAATATTAATACTTTATTATATTTTAA
59 TAAATATTAATATTTTATTATAATTTAA
16988437 TCATTAATAT
Statistics
Matches: 167, Mismatches: 20, Indels: 22
0.80 0.10 0.11
Matches are distributed among these distances:
109 10 0.06
110 72 0.43
111 50 0.30
112 35 0.21
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (109 bp):
ATTAATAATTTACAATTTAAATGTTAATAATTTATTTAAAATTTAATCATTAGTATTATAAATAT
TAATATTTTATTATAATTTAAATGTTATTATGATATATTTATTT
Found at i:16988512 original size:266 final size:265
Alignment explanation
Indices: 16987971--16988524 Score: 938
Period size: 266 Copynumber: 2.1 Consensus size: 265
16987961 AATTTATTGA
* *
16987971 AAATATTAATAA-TTATAATTTAGATGTTAATATTTTATTTGTAATTTAATCATTAGTATTATAT
1 AAATATTAATAATTTATAATTTAAATGTTAATATTTTATTTATAATTTAATCATTAGTATTATAT
16988035 AATATTATTATTTTATTATAATTTAGATGTTATTATGATTATTTATTTTATTTTATTTTTTAAAT
66 AATATTATTATTTTATTATAATTTAGATGTTATTATGATTATTTATTTTATTTTATTTTTTAAAT
** *
16988100 TTTTATAATTGATAATTTATTTAAAATAATTAATAATTTTTAATTTAAATATTAATACTGTTTAT
131 TTTTATAATTGATAATTTATTTAAAATAATTAATAATTGATAATTAAAATATTAATAC-GTTTAT
*
16988165 TATATTTTAATCATTAATATTTAAAAATATTAATATTTTATTTATAAGTTAAATGTTATTATGAT
195 TATATTTTAATCATTAATATTTAAAAATATTAATATTTTATTTATAAGTTAAATGCTATTATGAT
16988230 ATATTT
260 ATATTT
* *
16988236 -ATTNATTAATAATTTACAATTTAAATGTTAATATTTTATTTATAATTTAATCATTAGTATTATA
1 AAAT-ATTAATAATTTATAATTTAAATGTTAATATTTTATTTATAATTTAATCATTAGTATTATA
16988300 TAATATTATTATTTTATTATAATTTAGATGTTATTATGATTATTTATTTTATTTTA-TTTTTAAA
65 TAATATTATTATTTTATTATAATTTAGATGTTATTATGATTATTTATTTTATTTTATTTTTTAAA
*
16988364 TTTTTATAATTTATAATTTATTTAAAAT-ATTAATAATTGATAATTAAAATATTAATAC-TTTAT
130 TTTTTATAATTGATAATTTATTTAAAATAATTAATAATTGATAATTAAAATATTAATACGTTTAT
16988427 TATATTTTAATCATTAATATTTAAAAATATTAATATTTTATTTATAAGTTAAATGCTATTATGAT
195 TATATTTTAATCATTAATATTTAAAAATATTAATATTTTATTTATAAGTTAAATGCTATTATGA-
16988492 TATTAATTTT
259 TA-T-A-TTT
16988502 AAATATTAATAATTTATAATTTA
1 AAATATTAATAATTTATAATTTA
16988525 TTTAGGATTA
Statistics
Matches: 271, Mismatches: 11, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
262 68 0.25
263 2 0.01
264 30 0.11
265 44 0.16
266 125 0.46
267 2 0.01
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (265 bp):
AAATATTAATAATTTATAATTTAAATGTTAATATTTTATTTATAATTTAATCATTAGTATTATAT
AATATTATTATTTTATTATAATTTAGATGTTATTATGATTATTTATTTTATTTTATTTTTTAAAT
TTTTATAATTGATAATTTATTTAAAATAATTAATAATTGATAATTAAAATATTAATACGTTTATT
ATATTTTAATCATTAATATTTAAAAATATTAATATTTTATTTATAAGTTAAATGCTATTATGATA
TATTT
Found at i:16988578 original size:50 final size:50
Alignment explanation
Indices: 16988451--16988579 Score: 124
Period size: 50 Copynumber: 2.6 Consensus size: 50
16988441 TAATATTTAA
* *
16988451 AAATATTAATATTTTATTTATAAGTTAAATGCTATTATGATTATTAATTTT
1 AAATATTAATATTTTATTTATAATTTAAAT-CTATTATAATTATTAATTTT
* * *
16988502 AAATATTAATAATTTATAATT-T-ATTTAGGAT-TATTAATAATTGA-TCA-TTT
1 AAATATTAAT-ATTT-TATTTATAATTTA-AATCTATT-ATAATT-ATTAATTTT
16988552 AAATATTAATATTTTATTTATAATTTAA
1 AAATATTAATATTTTATTTATAATTTAA
16988580 TCATTAATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
48 4 0.06
49 5 0.08
50 22 0.34
51 21 0.33
52 8 0.12
53 4 0.06
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (50 bp):
AAATATTAATATTTTATTTATAATTTAAATCTATTATAATTATTAATTTT
Found at i:16991436 original size:30 final size:31
Alignment explanation
Indices: 16991394--16991509 Score: 150
Period size: 30 Copynumber: 3.9 Consensus size: 31
16991384 TAATCAAACC
16991394 CTTATA-TTTTATTTTGAATCAAATAAGTCT
1 CTTATATTTTTATTTTGAATCAAATAAGTCT
* *
16991424 -TTATATTTTTATTTTGAATTAAATAA-ACT
1 CTTATATTTTTATTTTGAATCAAATAAGTCT
*
16991453 CTTATATTTTTATTTTGAGTCAAATAAG-CT
1 CTTATATTTTTATTTTGAATCAAATAAGTCT
* * *
16991483 CTTATACTTTTATTTTGAGTTAAATAA
1 CTTATATTTTTATTTTGAATCAAATAA
16991510 ATTTTTATAA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
29 7 0.09
30 70 0.91
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.52
Consensus pattern (31 bp):
CTTATATTTTTATTTTGAATCAAATAAGTCT
Found at i:16991479 original size:60 final size:58
Alignment explanation
Indices: 16991354--16991510 Score: 201
Period size: 60 Copynumber: 2.7 Consensus size: 58
16991344 TCTAAAAAAT
* * *
16991354 TCAAATAAGTTTTTATATTTTTATTGTG-TTTAATCAAACCCTTATATTTTATTTTGAA
1 TCAAATAAGTCTTTATATTTTTATTTTGATTAAAT-AAACCCTTATATTTTATTTTGAA
* *
16991412 TCAAATAAGTCTTTATATTTTTATTTTGAATTAAATAAACTCTTATATTTTTATTTTGAG
1 TCAAATAAGTCTTTATATTTTTATTTTG-ATTAAATAAACCCTTATA-TTTTATTTTGAA
*
16991472 TCAAATAAG-CTCTTATACTTTTATTTTGAGTTAAATAAA
1 TCAAATAAGTCT-TTATATTTTTATTTTGA-TTAAATAAA
16991511 TTTTTATAAC
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
58 26 0.30
59 13 0.15
60 49 0.56
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (58 bp):
TCAAATAAGTCTTTATATTTTTATTTTGATTAAATAAACCCTTATATTTTATTTTGAA
Found at i:16992559 original size:2 final size:2
Alignment explanation
Indices: 16992552--16992599 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
16992542 ACCAAACCAC
16992552 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
16992594 CT CT CT
1 CT CT CT
16992600 TCCAACAACC
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:16993460 original size:29 final size:28
Alignment explanation
Indices: 16993428--16993567 Score: 154
Period size: 29 Copynumber: 4.8 Consensus size: 28
16993418 ATTTTATCTC
* * *
16993428 GTCTAAATTTGAGACAAATATGTATTCTT
1 GTCTAAA-TTAAGACAAACATGTTTTCTT
* * *
16993457 GTCTAGATTAAGACAAAAAATATTTTTCTT
1 GTCTAAATTAAGAC-AAACAT-GTTTTCTT
*
16993487 GTCTTAAATTAAGACAAACATATTTTCTT
1 GTC-TAAATTAAGACAAACATGTTTTCTT
*
16993516 ATCTAAATTAAGACCAAACATGTTTTCTT
1 GTCTAAATTAAGA-CAAACATGTTTTCTT
*
16993545 GTTTAAATTAAGACAAACATGTT
1 GTCTAAATTAAGACAAACATGTT
16993568 AAAGCTGCCA
Statistics
Matches: 95, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
28 26 0.27
29 45 0.47
30 14 0.15
31 10 0.11
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (28 bp):
GTCTAAATTAAGACAAACATGTTTTCTT
Found at i:16993526 original size:59 final size:59
Alignment explanation
Indices: 16993402--16993564 Score: 197
Period size: 59 Copynumber: 2.8 Consensus size: 59
16993392 TCTTATCCGT
* * * * *
16993402 AATTAAGACAAAAAATATTTTATCTCGTC-TAAATTTGAGACAAATATGTATTCTTGTCTA
1 AATTAAGACAAAAAATATTTT-TCTTGTCTTAAA-TTAAGACAAACATATATTCTTATCTA
* *
16993462 GATTAAGACAAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTATCTA
1 AATTAAGACAAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATATATTCTTATCTA
* * *
16993521 AATTAAGACCAAACAT-GTTTTCTTGT-TTAAATTAAGACAAACAT
1 AATTAAGACAAAAAATATTTTTCTTGTCTTAAATTAAGACAAACAT
16993565 GTTAAAGCTG
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
57 18 0.20
58 9 0.10
59 40 0.44
60 24 0.26
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (59 bp):
AATTAAGACAAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATATATTCTTATCTA
Found at i:16998860 original size:38 final size:40
Alignment explanation
Indices: 16998771--16998877 Score: 137
Period size: 38 Copynumber: 2.7 Consensus size: 40
16998761 CACACCCGGC
* *
16998771 TCATGTACATCCTCCCACATCGTGCACATAGCCGACACCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAGACACCA
* * * **
16998811 TCGTGTGCATCCCCCCACATCGTGCACA-ATCAG-TGCCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAGACACCA
16998849 TCATGTACATCCCCCCACATCGTGCACAT
1 TCATGTACATCCCCCCACATCGTGCACAT
16998878 GGGCACTATC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
38 29 0.51
39 3 0.05
40 25 0.44
ACGTcount: A:0.24, C:0.40, G:0.14, T:0.21
Consensus pattern (40 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCAGACACCA
Found at i:17001148 original size:15 final size:15
Alignment explanation
Indices: 17001119--17001147 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17001109 ATATATTGAA
17001119 ATATATATATATTTT
1 ATATATATATATTTT
17001134 ATATAT-TATATTTT
1 ATATATATATATTTT
17001148 TGCTTTACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATATATATATTTT
Found at i:17003892 original size:24 final size:24
Alignment explanation
Indices: 17003832--17003926 Score: 70
Period size: 24 Copynumber: 4.0 Consensus size: 24
17003822 TTCTCTTCTC
*
17003832 CTTGCCTTCTTC-ACTTTCTT-CTT
1 CTTGCCTTCTTCTCCTTT-TTCCTT
* * *
17003855 CCTGTCTTCGTCTCCTTTTTCCTT
1 CTTGCCTTCTTCTCCTTTTTCCTT
* * **
17003879 CTTGCCTTTTTCTCCTTCTTCTCAC
1 CTTGCCTTCTTCTCCTTTTTC-CTT
*
17003904 CTTGCCTTCTTCT-CTTTCTCCTT
1 CTTGCCTTCTTCTCCTTTTTCCTT
17003927 ACTATCCGCA
Statistics
Matches: 53, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
23 12 0.23
24 28 0.53
25 13 0.25
ACGTcount: A:0.02, C:0.38, G:0.05, T:0.55
Consensus pattern (24 bp):
CTTGCCTTCTTCTCCTTTTTCCTT
Found at i:17003923 original size:22 final size:25
Alignment explanation
Indices: 17003831--17003922 Score: 73
Period size: 25 Copynumber: 3.8 Consensus size: 25
17003821 CTTCTCTTCT
* * *
17003831 CCTTGCCTTCTTCACTTTCTTCT-T
1 CCTTGCCTTCTTCTCCTTCTTCTCA
* * * *
17003855 CC-TGTCTTCGTCTCCTTTTTC-CT
1 CCTTGCCTTCTTCTCCTTCTTCTCA
* *
17003878 TCTTGCCTTTTTCTCCTTCTTCTCA
1 CCTTGCCTTCTTCTCCTTCTTCTCA
*
17003903 CCTTGCCTTCTTCTCTTTCT
1 CCTTGCCTTCTTCTCCTTCT
17003923 CCTTACTATC
Statistics
Matches: 51, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
23 16 0.31
24 17 0.33
25 18 0.35
ACGTcount: A:0.02, C:0.38, G:0.05, T:0.54
Consensus pattern (25 bp):
CCTTGCCTTCTTCTCCTTCTTCTCA
Found at i:17004311 original size:20 final size:20
Alignment explanation
Indices: 17004268--17004316 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
17004258 GATGATATTT
* **
17004268 ATCTATCTATAGATGGTATA
1 ATCTATCGATAGATAATATA
*
17004288 ATCTATCGATAGATAATATG
1 ATCTATCGATAGATAATATA
17004308 ATCTATCGA
1 ATCTATCGA
17004317 CAGAATTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (20 bp):
ATCTATCGATAGATAATATA
Found at i:17004484 original size:21 final size:22
Alignment explanation
Indices: 17004447--17004487 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
17004437 AAAATAAAAA
*
17004447 TATTATGTTATTTTTTTAATGT
1 TATTATGTTATTATTTTAATGT
17004469 TATTAT-TTATTATTTTAAT
1 TATTATGTTATTATTTTAAT
17004488 AGCTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (22 bp):
TATTATGTTATTATTTTAATGT
Found at i:17004715 original size:15 final size:15
Alignment explanation
Indices: 17004695--17004751 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
17004685 GCAAAGTTAT
*
17004695 ATTCTCATCAATCAC
1 ATTCTCAACAATCAC
*
17004710 ATTCTCAACAATCAT
1 ATTCTCAACAATCAC
*
17004725 ATAC-CTAACAATCAC
1 ATTCTC-AACAATCAC
*
17004740 ATTCCCAACAAT
1 ATTCTCAACAAT
17004752 ATACTAAACG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 1 0.03
15 33 0.94
16 1 0.03
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (15 bp):
ATTCTCAACAATCAC
Found at i:17013788 original size:21 final size:21
Alignment explanation
Indices: 17013747--17013791 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
17013737 TAACTATTCT
*
17013747 TAAAGTAAATTAAGGCAAAAA
1 TAAAGTAAATTAAGACAAAAA
*
17013768 TAAAGTAAAATTAA-ACTAAAA
1 TAAAGT-AAATTAAGACAAAAA
17013789 TAA
1 TAA
17013792 CTTATTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.22
Consensus pattern (21 bp):
TAAAGTAAATTAAGACAAAAA
Found at i:17021679 original size:16 final size:15
Alignment explanation
Indices: 17021614--17021680 Score: 50
Period size: 16 Copynumber: 4.5 Consensus size: 15
17021604 TTTATTTGTA
17021614 TTAATATATATAATAT
1 TTAATATATAT-ATAT
* *
17021630 TTTATATATATTATTT
1 TTAATATATA-TATAT
17021646 TTAA-AT-T-TATAT
1 TTAATATATATATAT
**
17021658 AAAATATAATATATAT
1 TTAATAT-ATATATAT
17021674 TTAATAT
1 TTAATAT
17021681 TTTCAATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
12 6 0.16
13 2 0.05
14 1 0.03
15 3 0.08
16 25 0.66
17 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAATATATATATAT
Found at i:17022360 original size:36 final size:36
Alignment explanation
Indices: 17022310--17022427 Score: 96
Period size: 36 Copynumber: 3.3 Consensus size: 36
17022300 ATTAGACCAC
** * *
17022310 GCGATAACTTTTACATCGACTTTTTCATGGGATCAA
1 GCGATAACCCTTACATCAACTTTTTAATGGGATCAA
* ** * *
17022346 GTGATAACCCTTACA-CTTTCTTTTTAACGGGATTAA
1 GCGATAACCCTTACATC-AACTTTTTAATGGGATCAA
* * *
17022382 GCGATAACCCTTACTTTAACTTTTTAATGGGATTAA
1 GCGATAACCCTTACATCAACTTTTTAATGGGATCAA
17022418 GCAGA-AACCC
1 GC-GATAACCC
17022428 ACACACTAAC
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
35 1 0.02
36 62 0.95
37 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (36 bp):
GCGATAACCCTTACATCAACTTTTTAATGGGATCAA
Found at i:17022438 original size:36 final size:36
Alignment explanation
Indices: 17022328--17022441 Score: 95
Period size: 36 Copynumber: 3.2 Consensus size: 36
17022318 TTTTACATCG
* * * * ** *
17022328 ACTTTTTCATGGGATCAAGTGATAACCCTTACACTT
1 ACTTTTTAACGGGATTAAGCGATAACCCACACACTA
* ** **
17022364 TCTTTTTAACGGGATTAAGCGATAACCCTTACTTTA
1 ACTTTTTAACGGGATTAAGCGATAACCCACACACTA
*
17022400 ACTTTTTAATGGGATTAAGCAGA-AACCCACACACTA
1 ACTTTTTAACGGGATTAAGC-GATAACCCACACACTA
17022436 ACTTTT
1 ACTTTT
17022442 CAAGGTTAAG
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
36 61 0.97
37 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (36 bp):
ACTTTTTAACGGGATTAAGCGATAACCCACACACTA
Found at i:17027984 original size:35 final size:35
Alignment explanation
Indices: 17027939--17028009 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
17027929 TTCCACCAAG
* * *
17027939 CTTTTACAATG-GTTTTTCACAAGCTCAACCACAAC
1 CTTTAACAATGAGTTTTTC-CAAGATCAACCAAAAC
*
17027974 CTTTAACAATGATTTTTTCCAAGATCAACCAAAAC
1 CTTTAACAATGAGTTTTTCCAAGATCAACCAAAAC
17028009 C
1 C
17028010 CAAAACTAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 25 0.81
36 6 0.19
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.31
Consensus pattern (35 bp):
CTTTAACAATGAGTTTTTCCAAGATCAACCAAAAC
Found at i:17030770 original size:22 final size:23
Alignment explanation
Indices: 17030745--17030796 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
17030735 CTCGGTGCAT
*
17030745 AAAGGAT-TTG-GATTTTGTGCTC
1 AAAGGATCTTGTGATTTTG-ACTC
17030767 AAA-GATCTTGTGATTTTGACTC
1 AAAGGATCTTGTGATTTTGACTC
17030789 AAA-GATCT
1 AAAGGATCT
17030797 AAAAGGTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 3 0.11
22 17 0.63
23 7 0.26
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (23 bp):
AAAGGATCTTGTGATTTTGACTC
Found at i:17036030 original size:62 final size:62
Alignment explanation
Indices: 17035923--17036376 Score: 615
Period size: 62 Copynumber: 7.3 Consensus size: 62
17035913 ATGACATTAT
* * * *
17035923 ATGTTTGAGTATAGT-AATGACTTTAGTTAGTAGCTAAGACTTAATCAAGTTATCCATTCAC
1 ATGTTTGAGTATAGTAAATGACTTTAATTAGTAGTTGAGACCTAATCAAGTTATCCATTCAC
17035984 ATGTTTGAGTATAGTAAATGACTTTAATTAGTAGTTGAGACCTAATCAAGTTATCCATTCAC
1 ATGTTTGAGTATAGTAAATGACTTTAATTAGTAGTTGAGACCTAATCAAGTTATCCATTCAC
17036046 ATGTTTGAGTATAGTAAATGACTTTAATTAGTAGTTGAGACCTAATCAAGTTATCCATTCAC
1 ATGTTTGAGTATAGTAAATGACTTTAATTAGTAGTTGAGACCTAATCAAGTTATCCATTCAC
* *
17036108 ATGTTTGAGTATAGTAAATGACTTTAATTAGTTGTTGAGACCTAATCAAGTTATCCGTTCAC
1 ATGTTTGAGTATAGTAAATGACTTTAATTAGTAGTTGAGACCTAATCAAGTTATCCATTCAC
* * * * * **
17036170 ATGTTTGAGTATAGTAAATGACCTTAATTAATAATTGAGA-CTGAACCAAGTTATTCACCCAC
1 ATGTTTGAGTATAGTAAATGACTTTAATTAGTAGTTGAGACCT-AATCAAGTTATCCATTCAC
* * * * * * *** *
17036232 ATGTCTAAGTATAGTAAATGACTATAATTAATAGTTGAGATCTAACCAAGTTATTGTTTCAA
1 ATGTTTGAGTATAGTAAATGACTTTAATTAGTAGTTGAGACCTAATCAAGTTATCCATTCAC
* * * * * *
17036294 ATGTTTGAGCATCGTAAATGACTTTGATTAGTAGCTGAGACCTAATCAAATTATCCATTCAT
1 ATGTTTGAGTATAGTAAATGACTTTAATTAGTAGTTGAGACCTAATCAAGTTATCCATTCAC
*
17036356 ATGTTTGAGTGTAGTAAATGA
1 ATGTTTGAGTATAGTAAATGA
17036377 TCTTCATTGT
Statistics
Matches: 347, Mismatches: 43, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
61 17 0.05
62 328 0.95
63 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (62 bp):
ATGTTTGAGTATAGTAAATGACTTTAATTAGTAGTTGAGACCTAATCAAGTTATCCATTCAC
Found at i:17036707 original size:21 final size:22
Alignment explanation
Indices: 17036674--17036716 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
17036664 AATACCTTTT
* *
17036674 ATTATAATTTTTAAT-TTTTAA
1 ATTAAAATATTTAATATTTTAA
*
17036695 ATTAAAATATTTATTATTTTAA
1 ATTAAAATATTTAATATTTTAA
17036717 TAATTTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTAAAATATTTAATATTTTAA
Found at i:17036937 original size:27 final size:27
Alignment explanation
Indices: 17036690--17036955 Score: 129
Period size: 27 Copynumber: 10.2 Consensus size: 27
17036680 ATTTTTAATT
* * *
17036690 TTTAAATTAAAATATTTATTATTTTAATAA
1 TTTAATTTAAAATA-TTAATAATTT-AT-A
17036720 TTT-ATTTAAAATATTAATAAATTT-TA
1 TTTAATTTAAAATATTAAT-AATTTATA
** * *
17036746 TTTAATTT-TTATA-TGATTATTTAT-
1 TTTAATTTAAAATATTAATAATTTATA
17036770 TTTAATTTATAGAATATTAATAATTTATA
1 TTTAATTTA-A-AATATTAATAATTTATA
* **
17036799 TTTCATTTTTAA-ATTAA-AA--TAT-
1 TTTAATTTAAAATATTAATAATTTATA
* *
17036821 TTATAA-TTAAAACATTAA-CA--T-TA
1 TT-TAATTTAAAATATTAATAATTTATA
* *
17036844 -TTANTTTAAAATATTAATAAATTTTTA
1 TTTAATTTAAAATATTAAT-AATTTATA
* * * *
17036871 TTGAATTT-TAATA-TGATTATTTAT-
1 TTTAATTTAAAATATTAATAATTTATA
17036895 TTTAATTTATAGAATATTAATAATTTATA
1 TTTAATTTA-A-AATATTAATAATTTATA
*
17036924 TTTCATTTAAAATATTAATAATTTATA
1 TTTAATTTAAAATATTAATAATTTATA
*
17036951 ATTAA
1 TTTAA
17036956 AACATTAACA
Statistics
Matches: 179, Mismatches: 34, Indels: 49
0.68 0.13 0.19
Matches are distributed among these distances:
21 2 0.01
22 19 0.11
23 12 0.07
24 20 0.11
25 11 0.06
26 16 0.09
27 40 0.22
28 28 0.16
29 28 0.16
30 3 0.02
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
TTTAATTTAAAATATTAATAATTTATA
Found at i:17036984 original size:125 final size:124
Alignment explanation
Indices: 17036724--17036976 Score: 418
Period size: 125 Copynumber: 2.0 Consensus size: 124
17036714 TAATAATTTA
* *
17036724 TTTAAAATATTAATAAATTTTATTTAATTTTTATATGATTATTTATTTTAATTTATAGAATATTA
1 TTTAAAATATTAATAAATTTTATTGAATTTTAATATGATTATTTATTTTAATTTATAGAATATTA
** * *
17036789 ATAATTTATATTTCATTTTTAAATTAAAATATTTATAATTAAAACATTAACATTATTAN
66 ATAATTTATATTTCATTTAAAAATTAAAATATTTATAATTAAAACATTAACATCATTAT
17036848 TTTAAAATATTAATAAATTTTTATTGAATTTTAATATGATTATTTATTTTAATTTATAGAATATT
1 TTTAAAATATTAATAAA-TTTTATTGAATTTTAATATGATTATTTATTTTAATTTATAGAATATT
*
17036913 AATAATTTATATTTCATTTAAAATATTAATA-ATTTATAATTAAAACATTAACATCATTAT
65 AATAATTTATATTTCATTTAAAA-ATTAAAATATTTATAATTAAAACATTAACATCATTAT
17036973 TTTA
1 TTTA
17036977 TTTTATTATT
Statistics
Matches: 120, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
124 17 0.14
125 97 0.81
126 6 0.05
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (124 bp):
TTTAAAATATTAATAAATTTTATTGAATTTTAATATGATTATTTATTTTAATTTATAGAATATTA
ATAATTTATATTTCATTTAAAAATTAAAATATTTATAATTAAAACATTAACATCATTAT
Found at i:17037046 original size:30 final size:31
Alignment explanation
Indices: 17037012--17037070 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
17037002 AAAATATTAC
*
17037012 AAATTTATAATTAA-AA-TTTTAATAATTTTT
1 AAATTTA-AAATAATAACTTTTAATAATTTTT
*
17037042 AAATTTAAAATAATAACTTTTTATAATTT
1 AAATTTAAAATAATAACTTTTAATAATTT
17037071 AGAATTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 9 0.36
31 11 0.44
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (31 bp):
AAATTTAAAATAATAACTTTTAATAATTTTT
Done.