Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 42 of 132
Found at i:11370989 original size:72 final size:71
Alignment explanation
Indices: 11370904--11371168 Score: 413
Period size: 72 Copynumber: 3.7 Consensus size: 71
11370894 CAATGCTAAA
11370904 CTAGTTTTATCAATAGTTGTTTATATTTGGTTTTTAGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATATTTGGTTTTT-GATATTGAATTTATGTTCTACTTATTTAT
11370969 GTGTAAT
65 GTGTAAT
* *
11370976 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAGTTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATATTTGGTTTTT-GATATTGAATTTATGTTCTACTTATTTAT
*
11371041 GTGCAAT
65 GTGTAAT
* * *
11371048 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGAATATTGAATTTATTTTTTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATATTTGGTTTTTG-ATATTGAATTTATGTTCTACTTATTTAT
11371113 GTGTAAT
65 GTGTAAT
* * **
11371120 TTAGTTTTATCAATAGTTGTTTATATTTGATTTTTGATATAAAATTTAT
1 CTAGTTTTATCAATAGTTGTTTATATTTGGTTTTTGATATTGAATTTAT
11371169 TCACAAGTGA
Statistics
Matches: 179, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
71 12 0.07
72 167 0.93
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.56
Consensus pattern (71 bp):
CTAGTTTTATCAATAGTTGTTTATATTTGGTTTTTGATATTGAATTTATGTTCTACTTATTTATG
TGTAAT
Found at i:11372955 original size:21 final size:20
Alignment explanation
Indices: 11372875--11372955 Score: 58
Period size: 21 Copynumber: 4.0 Consensus size: 20
11372865 TATTTAAATA
* *
11372875 TAAATATTTAATGATTAAATT
1 TAAATAATTAAT-ATTAATTT
* *
11372896 TAAATATTTAAAATATAA-TT
1 TAAATAATTAATAT-TAATTT
* *
11372916 TATATAATCTAAT-TAAATTTT
1 TAAATAAT-TAATATTAA-TTT
11372937 TAAATAATTAATATTAATT
1 TAAATAATTAATATTAATT
11372956 ACTTAGAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
19 2 0.04
20 17 0.35
21 29 0.60
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (20 bp):
TAAATAATTAATATTAATTT
Found at i:11372977 original size:30 final size:30
Alignment explanation
Indices: 11372897--11372998 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 30
11372887 GATTAAATTT
* *
11372897 AAATATTTAAAATATAATTTATATAATCTAATT-
1 AAATATTTAAAAT-TAA--TATTTAATAT-ATTA
*
11372930 AAATTTTTAAATAATTAATA-TTAAT-TACTTA
1 AAATATTT-AA-AATTAATATTTAATATA-TTA
11372961 GAAATATTTAAAATTAATATTTAATATATTA
1 -AAATATTTAAAATTAATATTTAATATATTA
11372992 AAATATT
1 AAATATT
11372999 AACAATAAGT
Statistics
Matches: 59, Mismatches: 3, Indels: 17
0.75 0.04 0.22
Matches are distributed among these distances:
29 1 0.02
30 18 0.31
31 14 0.24
32 11 0.19
33 7 0.12
34 5 0.08
35 3 0.05
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (30 bp):
AAATATTTAAAATTAATATTTAATATATTA
Found at i:11373197 original size:13 final size:13
Alignment explanation
Indices: 11373176--11373218 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
11373166 ATTTAACCAA
*
11373176 ACTTTTCAAAAGT
1 ACTTCTCAAAAGT
11373189 ACTTCTCAAAAGT
1 ACTTCTCAAAAGT
*
11373202 ACTTCTCAAAAGC
1 ACTTCTCAAAAGT
11373215 ACTT
1 ACTT
11373219 TTCCACCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (13 bp):
ACTTCTCAAAAGT
Found at i:11375124 original size:21 final size:21
Alignment explanation
Indices: 11375100--11375176 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
11375090 TAGTGCAGTT
*
11375100 TTCTACCGATACAAGTGTCAA
1 TTCTACCGATACAAGTCTCAA
* * *
11375121 TTCTACCAAAACAAGTCTCAC
1 TTCTACCGATACAAGTCTCAA
* * *
11375142 TTCTACCGATACAACTCTTAC
1 TTCTACCGATACAAGTCTCAA
*
11375163 TTCTACCGACACAA
1 TTCTACCGATACAA
11375177 AAAACTCTAG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.34, C:0.31, G:0.08, T:0.27
Consensus pattern (21 bp):
TTCTACCGATACAAGTCTCAA
Found at i:11375941 original size:36 final size:36
Alignment explanation
Indices: 11375838--11375941 Score: 136
Period size: 36 Copynumber: 2.9 Consensus size: 36
11375828 CGTTCGTTAT
* * *
11375838 TCGTTTTACTCCCTGTTGACCTAAAGGTCATAATGT
1 TCGTTTTACTCCCTATTGACCTAAAGGTCATGATGC
* *
11375874 TCATTTTACTCCCTATTGACCTAGAGGTCATGATGC
1 TCGTTTTACTCCCTATTGACCTAAAGGTCATGATGC
* * *
11375910 TCGTTTTACTCCCTATTAACCCAAAAGTCATG
1 TCGTTTTACTCCCTATTGACCTAAAGGTCATG
11375942 CCTGTTACCA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (36 bp):
TCGTTTTACTCCCTATTGACCTAAAGGTCATGATGC
Found at i:11380943 original size:22 final size:24
Alignment explanation
Indices: 11380918--11380968 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
11380908 AATTAAATTG
*
11380918 TGTATTTTT-AC-GATAATGAAAA
1 TGTATTTTTAACAAATAATGAAAA
*
11380940 TGTAATTTTTAACAAATTATGAAAA
1 TGT-ATTTTTAACAAATAATGAAAA
11380965 TGTA
1 TGTA
11380969 ATTAGTGGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 3 0.12
23 6 0.25
24 3 0.12
25 12 0.50
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (24 bp):
TGTATTTTTAACAAATAATGAAAA
Found at i:11382649 original size:26 final size:24
Alignment explanation
Indices: 11382620--11382669 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 24
11382610 TTAAAAAAAA
11382620 TTAGGTACCAAATTGAGCAAAAAAGT
1 TTAGGTACCAAATT-AG-AAAAAAGT
11382646 TTAGGTACCAAATTAGAAAAAAGT
1 TTAGGTACCAAATTAGAAAAAAGT
11382670 GTCAAGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.33
25 2 0.08
26 14 0.58
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (24 bp):
TTAGGTACCAAATTAGAAAAAAGT
Found at i:11382666 original size:25 final size:25
Alignment explanation
Indices: 11382612--11382667 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
11382602 AATTGAATTT
11382612 AAAAAAAATTAGGTACCAAATTGAG
1 AAAAAAAATTAGGTACCAAATTGAG
**
11382637 CAAAAAAGTTTAGGTACCAAATT-AG
1 -AAAAAAAATTAGGTACCAAATTGAG
11382662 AAAAAA
1 AAAAAA
11382668 GTGTCAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 6 0.21
25 2 0.07
26 20 0.71
ACGTcount: A:0.57, C:0.09, G:0.14, T:0.20
Consensus pattern (25 bp):
AAAAAAAATTAGGTACCAAATTGAG
Found at i:11384761 original size:26 final size:26
Alignment explanation
Indices: 11384725--11384780 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
11384715 AATATTTTTA
11384725 TAATTTTAGTTTTTGTTTAGATTAAT
1 TAATTTTAGTTTTTGTTTAGATTAAT
11384751 TAATTTTAGTTTTTGTTTAGATTAAT
1 TAATTTTAGTTTTTGTTTAGATTAAT
11384777 TAAT
1 TAAT
11384781 GATATTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (26 bp):
TAATTTTAGTTTTTGTTTAGATTAAT
Found at i:11386961 original size:18 final size:20
Alignment explanation
Indices: 11386932--11386969 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
11386922 ATAGGTCAAA
11386932 CATGCTTACATA-TCAAAAT
1 CATGCTTACATACTCAAAAT
11386951 CATGC-TACATACTCAAAAT
1 CATGCTTACATACTCAAAAT
11386970 TTTCATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29
Consensus pattern (20 bp):
CATGCTTACATACTCAAAAT
Found at i:11402809 original size:7 final size:7
Alignment explanation
Indices: 11402797--11402840 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
11402787 AATGACATCA
11402797 TTAATAT
1 TTAATAT
11402804 TTAATAT
1 TTAATAT
11402811 TTAATAT
1 TTAATAT
11402818 TT-ATAT
1 TTAATAT
*
11402824 TTAATAA
1 TTAATAT
11402831 TTAATAT
1 TTAATAT
11402838 TTA
1 TTA
11402841 TGACTCGACT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTAATAT
Found at i:11402825 original size:20 final size:20
Alignment explanation
Indices: 11402800--11402841 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
11402790 GACATCATTA
*
11402800 ATATTTAATATTTAATATTT
1 ATATTTAATAATTAATATTT
11402820 ATATTTAATAATTAATATTT
1 ATATTTAATAATTAATATTT
11402840 AT
1 AT
11402842 GACTCGACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTTAATAATTAATATTT
Found at i:11406784 original size:26 final size:25
Alignment explanation
Indices: 11406753--11406801 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
11406743 TAGTAATTTG
11406753 TTTTATATTCTAATTTTAATTTCTCT
1 TTTTATATTCTAA-TTTAATTTCTCT
* *
11406779 TTTTATATTTTGATTTAATTTCT
1 TTTTATATTCTAATTTAATTTCT
11406802 TATGTCCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTTATATTCTAATTTAATTTCTCT
Found at i:11407710 original size:22 final size:22
Alignment explanation
Indices: 11407679--11407730 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
11407669 TGGCTTTGCT
11407679 AGCTGATGGATTCACTGCCCTC
1 AGCTGATGGATTCACTGCCCTC
*
11407701 AGTTGATGGATTCACTGCCCTC
1 AGCTGATGGATTCACTGCCCTC
11407723 AGCTGATG
1 AGCTGATG
11407731 TAATGGGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.27, G:0.25, T:0.29
Consensus pattern (22 bp):
AGCTGATGGATTCACTGCCCTC
Found at i:11414252 original size:20 final size:21
Alignment explanation
Indices: 11414229--11414267 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
11414219 ATAATGAAGT
11414229 TTAATTAAG-GTAATGATGGG
1 TTAATTAAGCGTAATGATGGG
*
11414249 TTAATTAAGCTTAATGATG
1 TTAATTAAGCGTAATGATG
11414268 AAAGTTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (21 bp):
TTAATTAAGCGTAATGATGGG
Found at i:11419153 original size:14 final size:14
Alignment explanation
Indices: 11419129--11419177 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
11419119 GTTGTAATGT
* *
11419129 AATTAAAATTTGAA
1 AATTTAAATTTTAA
*
11419143 AACTTAAATTTTAA
1 AATTTAAATTTTAA
*
11419157 AATTTGAATTTTAA
1 AATTTAAATTTTAA
11419171 AATTTAA
1 AATTTAA
11419178 TTGGTCGTCC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (14 bp):
AATTTAAATTTTAA
Found at i:11419246 original size:22 final size:22
Alignment explanation
Indices: 11419221--11419264 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11419211 TGGAAAGTTG
*
11419221 TAATGTAATTCAAATTTGAAAA
1 TAATGTAATTAAAATTTGAAAA
11419243 TAATGTAATTAAAATTTGAAAA
1 TAATGTAATTAAAATTTGAAAA
11419265 CTTAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.36
Consensus pattern (22 bp):
TAATGTAATTAAAATTTGAAAA
Found at i:11419271 original size:14 final size:14
Alignment explanation
Indices: 11419254--11419305 Score: 77
Period size: 14 Copynumber: 3.7 Consensus size: 14
11419244 AATGTAATTA
11419254 AAATTTGAAAACTT
1 AAATTTGAAAACTT
* *
11419268 AAATTTTAAAATTT
1 AAATTTGAAAACTT
*
11419282 GAATTTGAAAACTT
1 AAATTTGAAAACTT
11419296 AAATTTGAAA
1 AAATTTGAAA
11419306 GCTAAAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (14 bp):
AAATTTGAAAACTT
Found at i:11419271 original size:28 final size:28
Alignment explanation
Indices: 11419240--11419299 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
11419230 TCAAATTTGA
**
11419240 AAATAATGTAATTAAAATTTGAAAACTT
1 AAATAATAAAATTAAAATTTGAAAACTT
** **
11419268 AAATTTTAAAATTTGAATTTGAAAACTT
1 AAATAATAAAATTAAAATTTGAAAACTT
11419296 AAAT
1 AAAT
11419300 TTGAAAGCTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (28 bp):
AAATAATAAAATTAAAATTTGAAAACTT
Found at i:11419272 original size:98 final size:97
Alignment explanation
Indices: 11419089--11419276 Score: 263
Period size: 98 Copynumber: 1.9 Consensus size: 97
11419079 TCCCGAGGAT
11419089 CTGAGGATCTGAGGATCAGAGAAATGGAAAGTTGTAATGTAATTAAAATTTGAAAACTTAAATTT
1 CTGAGGATCTGAGGATCAGAGAAATGGAAAGTTGTAATGTAATTAAAATTTGAAAAC-TAAATTT
**
11419154 TAAAATTTGAATTTTAAAATTTAATTGGTCGTC
65 TAAAATTTGAAACTTAAAATTTAATTGGTCGTC
* * *
11419187 CTGAGGATCTGAGGATCGGAGAGATGGAAAGTTGTAATGTAATTCAAATTTGAAAA-T-AATGTA
1 CTGAGGATCTGAGGATCAGAGAAATGGAAAGTTGTAATGTAATTAAAATTTGAAAACTAAAT-T-
*
11419250 ATTAAAATTTGAAAACTTAAATTTTAA
64 -TTAAAATTTG-AAACTTAAAATTTAA
11419277 AATTTGAATT
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
95 3 0.04
96 2 0.03
98 63 0.79
99 12 0.15
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (97 bp):
CTGAGGATCTGAGGATCAGAGAAATGGAAAGTTGTAATGTAATTAAAATTTGAAAACTAAATTTT
AAAATTTGAAACTTAAAATTTAATTGGTCGTC
Found at i:11428489 original size:72 final size:72
Alignment explanation
Indices: 11428402--11428575 Score: 183
Period size: 72 Copynumber: 2.4 Consensus size: 72
11428392 GAAAGTACAA
* * * *
11428402 AAATAGTGAGTTACACGGCCTAGACACATGGACGTGTGCCAGACCGTGTG-GATA-TGCTCTTTG
1 AAATAGTGAGTTACACGGCCTAGACACATGGACGAGTGCCAGACCATGTGCCATACCG-T-TTTG
* *
11428465 TGGAATCAG
64 TGCAAACAG
* * * *
11428474 AAATAGTGAGTTACACAGGAC-GGACACACGGACGAGTGTCAGACCATGTGCCCATACCGTTTTG
1 AAATAGTGAGTTACAC-GGCCTAGACACATGGACGAGTGCCAGACCATGTG-CCATACCGTTTTG
11428538 TGCAAACAG
64 TGCAAACAG
* *
11428547 AAACAGTGAGTTACACGACCTAGACACAT
1 AAATAGTGAGTTACACGGCCTAGACACAT
11428576 AGGCCTAATA
Statistics
Matches: 82, Mismatches: 15, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
72 42 0.51
73 35 0.43
74 4 0.05
75 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (72 bp):
AAATAGTGAGTTACACGGCCTAGACACATGGACGAGTGCCAGACCATGTGCCATACCGTTTTGTG
CAAACAG
Found at i:11428741 original size:38 final size:39
Alignment explanation
Indices: 11428647--11428744 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
11428637 TTATCAAATA
*
11428647 ACTGAACTGGTAGTGACACTATAAACACTACAATTCGCT
1 ACTGAACTGGTAGTGACACTATAAACACTACAATACGCT
** *
11428686 ACTGAACTGACAATGACACTATAAACACTACAATACGCT
1 ACTGAACTGGTAGTGACACTATAAACACTACAATACGCT
11428725 -CTGAACTGGTAGTGACACTA
1 ACTGAACTGGTAGTGACACTA
11428745 AAAGTACTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
38 17 0.33
39 35 0.67
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (39 bp):
ACTGAACTGGTAGTGACACTATAAACACTACAATACGCT
Found at i:11434599 original size:55 final size:55
Alignment explanation
Indices: 11434504--11434617 Score: 183
Period size: 55 Copynumber: 2.1 Consensus size: 55
11434494 CGAAGGATAG
* *
11434504 CTCGGTTAGAGCATAAAGCTATTATAGCTCAGGTAAAGCTTTGGACTTCTTATGT
1 CTCGGTTAAAGCATAAAGCTATTATAGCTCAGGTAAAGCTTTGGACTACTTATGT
** *
11434559 CTCGGTTAAAGCATAAAGCTATTATAGCTTGGGTAGAGCTTTGGACTACTTATGT
1 CTCGGTTAAAGCATAAAGCTATTATAGCTCAGGTAAAGCTTTGGACTACTTATGT
11434614 CTCG
1 CTCG
11434618 ATTACAGCGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (55 bp):
CTCGGTTAAAGCATAAAGCTATTATAGCTCAGGTAAAGCTTTGGACTACTTATGT
Found at i:11439298 original size:22 final size:23
Alignment explanation
Indices: 11439273--11439315 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
11439263 GCAACCTAAA
* *
11439273 TTTATTTTTATTTC-ATTTAATT
1 TTTAATTTTAGTTCAATTTAATT
11439295 TTTAATTTTAGTTCAATTTAA
1 TTTAATTTTAGTTCAATTTAA
11439316 GTTGAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTAATTTTAGTTCAATTTAATT
Found at i:11441091 original size:21 final size:21
Alignment explanation
Indices: 11441065--11441105 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
11441055 ATGTACCTAT
11441065 ACTACTCCGATAGAAGCACGA
1 ACTACTCCGATAGAAGCACGA
11441086 ACTACTCCGATAGAAGCACG
1 ACTACTCCGATAGAAGCACG
11441106 TCTTCGTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.29, G:0.20, T:0.15
Consensus pattern (21 bp):
ACTACTCCGATAGAAGCACGA
Found at i:11442521 original size:10 final size:10
Alignment explanation
Indices: 11442506--11442545 Score: 64
Period size: 10 Copynumber: 4.0 Consensus size: 10
11442496 TGAATATATT
11442506 GAAAAAAAAA
1 GAAAAAAAAA
11442516 GAAAAAAAAA
1 GAAAAAAAAA
11442526 G-AAAAAAAA
1 GAAAAAAAAA
11442535 GAAGAAAAAAA
1 GAA-AAAAAAA
11442546 TACATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.32
10 12 0.43
11 7 0.25
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:11442524 original size:12 final size:12
Alignment explanation
Indices: 11442507--11442545 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
11442497 GAATATATTG
11442507 AAAAAAAAAG--
1 AAAAAAAAAGAA
11442517 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
11442529 AAAAAAGAAGAA
1 AAAAAAAAAGAA
11442541 AAAAA
1 AAAAA
11442546 TACATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
12 16 0.62
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:11448052 original size:8 final size:10
Alignment explanation
Indices: 11448024--11448055 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
11448014 TAAGGATTAA
*
11448024 AACAATATAT
1 AACATTATAT
11448034 AACATTATAT
1 AACATTATAT
11448044 AACATTATAT
1 AACATTATAT
11448054 AA
1 AA
11448056 ACTAATTGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (10 bp):
AACATTATAT
Found at i:11451924 original size:27 final size:26
Alignment explanation
Indices: 11451880--11451941 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
11451870 ATTTTTTTAA
* * * *
11451880 ATTTAAAATAATCCAAATATATATATT
1 ATTTAAAAAAATCAAAATATA-AAAAT
* *
11451907 ATTTAAAAAAATTAAAATTTAAAAAT
1 ATTTAAAAAAATCAAAATATAAAAAT
11451933 ATTTAAAAA
1 ATTTAAAAA
11451942 TTATAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (26 bp):
ATTTAAAAAAATCAAAATATAAAAAT
Found at i:11454282 original size:676 final size:678
Alignment explanation
Indices: 11452991--11454351 Score: 2690
Period size: 676 Copynumber: 2.0 Consensus size: 678
11452981 TGGATCGGGC
11452991 ATTAGGGAATACAGTCTAGGTCCAAACCTTTCCGAAGTGTTTAATAACGCACCTTGTAAGATTGA
1 ATTAGGGAATACAGTCTAGGTCCAAACCTTTCCGAAGTGTTTAATAACGCACCTTGTAAGATTGA
11453056 AGTCGGACCATAGACCCCTTCTTCTCACCTTTTGCCTTGTGATCAATATGTTGAGAGGTTGTCCA
66 AGTCGGACCATAGACCCCTTCTTCTCACCTTTTGCCTTGTGATCAATATGTTGAGAGGTTGTCCA
11453121 TTCTGTTTCTTTGCAGGTTGGACTTAACATTAGAGTTTTTCTAGCACCGTGGAAGATCTGTGGGA
131 TTCTGTTTCTTTGCAGGTTGGACTTAACATTAGAGTTTTTCTAGCACCGTGGAAGATCTGTGGGA
11453186 ATATAACGGGGGCATGACTAAAACATTGAAGGACCAGACCGGAGGACTCAAGGAATGGAATAAGA
196 ATATAACGGGGGCATGACTAAAACATTGAAGGACCAGACCGGAGGACTCAAGGAATGGAATAAGA
11453251 ACATCTATGGTCATATTGGGCAACGAAAACGAAAACTTCTACAAACCCTCCGTCGAACTCAAGAA
261 ACATCTATGGTCATATTGGGCAACGAAAACGAAAACTTCTACAAACCCTCCGTCGAACTCAAGAA
11453316 AAGTTAGAAAAGACCAATTCAAAAGCTTTAGTCGCAAGAGAAATGGAAATTGTAAAGGAGCTTGA
326 AAGTTAGAAAAGACCAATTCAAAAGCTTTAGTCGCAAGAGAAATGGAAATTGTAAAGGAGCTTGA
11453381 AGAGGTGCTTAATCATGAGGAACTACTATGGAAACAGAAATCCAGGTGTGATTAGCTTAAACTAG
391 AGAGGTGCTTAATCATGAGGAACTACTATGGAAACAGAAATCCAGGTGTGATTAGCTTAAACTAG
11453446 GCGATAGAAACACTAATTTTTTTCATAGTCGCACGATGTTCCGAAGGTAAATAAATTGCATCACT
456 GCGATAGAAACACTAATTTTTTTCATAGTCGCACGATGTTCCGAAGGTAAATAAATTGCATCACT
11453511 ACACTACGAAATCGAAATGGAGATTGGTTATATGATTCATATGCAGTTCAAACTGAGGCGGTCAA
521 ACACTACGAAATCGAAATGGAGATTGGTTATATGATTCATATGCAGTTCAAACTGAGGCGGTCAA
11453576 CTATTTTCAGCAAATTTTTGGAGAGTTACCAGATAAGATGGGTGAGCTCCCTCCTAATCGTTTT-
586 CTATTTTCAGCAAATTTTTGGAGAGTTACCAGATAAGATGGGTGAGCTCCCTCCTAATCGTTTTC
*
11453640 CCC-CCAAAACTAGAGTGGCTTGAACTT
651 CCCACCAAAACTAGAGTGACTTGAACTT
11453667 ATTAGGGAATACAGTCTAGGTCCAAACCTTTCCGAAGTGTTTAATAACGCACCTTGTAAGATTGA
1 ATTAGGGAATACAGTCTAGGTCCAAACCTTTCCGAAGTGTTTAATAACGCACCTTGTAAGATTGA
11453732 AGTCGGACCATAGACCCCTTCTTCTCACCTTTTGCCTTGTGATCAATATGTTGAGAGGTTGTCCA
66 AGTCGGACCATAGACCCCTTCTTCTCACCTTTTGCCTTGTGATCAATATGTTGAGAGGTTGTCCA
11453797 TTCTGTTTCTTTGCAGGTTGGACTTAACATTAGAGTTTTTCTAGCACCGTGGAAGATCTGTGGGA
131 TTCTGTTTCTTTGCAGGTTGGACTTAACATTAGAGTTTTTCTAGCACCGTGGAAGATCTGTGGGA
11453862 ATATAACGGGGGCATGACTAAAACATTGAAGGACCAGACCGGAGGACTCAAGGAATGGAATAAGA
196 ATATAACGGGGGCATGACTAAAACATTGAAGGACCAGACCGGAGGACTCAAGGAATGGAATAAGA
11453927 ACATCTATGGTCATATTGGGCAACGAAAACGAAAACTTCTACAAACCCTCCGTCGAACTCAAGAA
261 ACATCTATGGTCATATTGGGCAACGAAAACGAAAACTTCTACAAACCCTCCGTCGAACTCAAGAA
11453992 AAGTTAGAAAAGACCAATTCAAAAGCTTTAGTCGCAAGAGAAATGGAAATTGTAAAGGAGCTTGA
326 AAGTTAGAAAAGACCAATTCAAAAGCTTTAGTCGCAAGAGAAATGGAAATTGTAAAGGAGCTTGA
11454057 AGAGGTGCTTAATCATGAGGAACTACTATGGAAACAGAAATCCAGGTGTGATTAGCTTAAACTAG
391 AGAGGTGCTTAATCATGAGGAACTACTATGGAAACAGAAATCCAGGTGTGATTAGCTTAAACTAG
11454122 GCGATAGAAACACTAATTTTTTTCATAGTCGCACGATGTTCCGAAGGTAAATAAATTGCATCACT
456 GCGATAGAAACACTAATTTTTTTCATAGTCGCACGATGTTCCGAAGGTAAATAAATTGCATCACT
11454187 ACACTACGAAATCGAAATGGAGATTGGTTATATGATTCATATGCAGTTCAAACTGAGGCGGTCAA
521 ACACTACGAAATCGAAATGGAGATTGGTTATATGATTCATATGCAGTTCAAACTGAGGCGGTCAA
11454252 CTATTTTCAGCAAATTTTTGGAGAGTTACCAGATAAGATGGGTGAGCTCCCTCCTAATCGTTTTC
586 CTATTTTCAGCAAATTTTTGGAGAGTTACCAGATAAGATGGGTGAGCTCCCTCCTAATCGTTTTC
*
11454317 CCCACCAAAACTAGAGTGACTTGGACTT
651 CCCACCAAAACTAGAGTGACTTGAACTT
11454345 ATTAGGG
1 ATTAGGG
11454352 GGAAAGGTCT
Statistics
Matches: 681, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
676 649 0.95
677 3 0.00
678 29 0.04
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (678 bp):
ATTAGGGAATACAGTCTAGGTCCAAACCTTTCCGAAGTGTTTAATAACGCACCTTGTAAGATTGA
AGTCGGACCATAGACCCCTTCTTCTCACCTTTTGCCTTGTGATCAATATGTTGAGAGGTTGTCCA
TTCTGTTTCTTTGCAGGTTGGACTTAACATTAGAGTTTTTCTAGCACCGTGGAAGATCTGTGGGA
ATATAACGGGGGCATGACTAAAACATTGAAGGACCAGACCGGAGGACTCAAGGAATGGAATAAGA
ACATCTATGGTCATATTGGGCAACGAAAACGAAAACTTCTACAAACCCTCCGTCGAACTCAAGAA
AAGTTAGAAAAGACCAATTCAAAAGCTTTAGTCGCAAGAGAAATGGAAATTGTAAAGGAGCTTGA
AGAGGTGCTTAATCATGAGGAACTACTATGGAAACAGAAATCCAGGTGTGATTAGCTTAAACTAG
GCGATAGAAACACTAATTTTTTTCATAGTCGCACGATGTTCCGAAGGTAAATAAATTGCATCACT
ACACTACGAAATCGAAATGGAGATTGGTTATATGATTCATATGCAGTTCAAACTGAGGCGGTCAA
CTATTTTCAGCAAATTTTTGGAGAGTTACCAGATAAGATGGGTGAGCTCCCTCCTAATCGTTTTC
CCCACCAAAACTAGAGTGACTTGAACTT
Found at i:11455937 original size:22 final size:23
Alignment explanation
Indices: 11455910--11455952 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
11455900 TTACAGTTTC
*
11455910 AATTTAGTCCCTTTA-TTTATTT
1 AATTTAATCCCTTTACTTTATTT
*
11455932 AATTTAATTCCTTTACTTTAT
1 AATTTAATCCCTTTACTTTAT
11455953 GTTTTTTAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.26, C:0.14, G:0.02, T:0.58
Consensus pattern (23 bp):
AATTTAATCCCTTTACTTTATTT
Found at i:11456066 original size:3 final size:3
Alignment explanation
Indices: 11456060--11456201 Score: 119
Period size: 3 Copynumber: 48.3 Consensus size: 3
11456050 TTAAATACGA
* * * * * * * * *
11456060 TAT TAT TAT TAT TAT TAT TGT TTT TGT TGT TGT TGT TGT TGT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
11456108 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
11456156 TAT T-T TAC TAT CAT GAC TAT TGT TAT T-T TAT TCT T-T TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11456201 T
1 T
11456202 TTACTATAGT
Statistics
Matches: 118, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
2 6 0.05
3 112 0.95
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:11456481 original size:9 final size:9
Alignment explanation
Indices: 11456467--11456544 Score: 58
Period size: 9 Copynumber: 10.2 Consensus size: 9
11456457 ACAAATGATT
11456467 TTAAAATTA
1 TTAAAATTA
11456476 TTAAAATTA
1 TTAAAATTA
11456485 TT----TT-
1 TTAAAATTA
11456489 TTAAAA-TA
1 TTAAAATTA
11456497 -TAAAATTA
1 TTAAAATTA
11456505 TTAAAATTA
1 TTAAAATTA
11456514 TT----TT-
1 TTAAAATTA
11456518 TTAAAA-TA
1 TTAAAATTA
11456526 -TAAAATTA
1 TTAAAATTA
11456534 TTAAAATTA
1 TTAAAATTA
11456543 TT
1 TT
11456545 TGTTTGAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 28
0.66 0.00 0.34
Matches are distributed among these distances:
4 4 0.07
5 4 0.07
7 12 0.22
8 4 0.07
9 31 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TTAAAATTA
Found at i:11456487 original size:20 final size:20
Alignment explanation
Indices: 11456459--11456515 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
11456449 CCACATCAAC
*
11456459 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
11456479 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
11456499 AAATTA--TTAAAATTATT
1 AAATTATTTTAAAATTATT
11456516 TTTTAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 1 0.03
20 13 0.41
21 2 0.06
22 8 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:11456494 original size:13 final size:13
Alignment explanation
Indices: 11456476--11456524 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
11456466 TTTAAAATTA
11456476 TTAAAATTATTTT
1 TTAAAATTATTTT
* *
11456489 TTAAAATATAAAATTA
1 TTAAAAT-T--ATTTT
11456505 TTAAAATTATTTT
1 TTAAAATTATTTT
11456518 TTAAAAT
1 TTAAAAT
11456525 ATAAAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 17 0.59
14 1 0.03
15 1 0.03
16 10 0.34
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAAAATTATTTT
Found at i:11456500 original size:29 final size:29
Alignment explanation
Indices: 11456468--11456569 Score: 177
Period size: 29 Copynumber: 3.4 Consensus size: 29
11456458 CAAATGATTT
11456468 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
11456497 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
*
11456526 TAAAATTATTAAAATTATTTGTTTGAAATAA
1 TAAAATTATTAAAATTATTT-TTTAAAAT-A
11456557 TAAAATTATTAAA
1 TAAAATTATTAAA
11456570 TAATTTTAAT
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 49 0.70
30 7 0.10
31 14 0.20
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:11459049 original size:87 final size:89
Alignment explanation
Indices: 11458925--11459116 Score: 232
Period size: 91 Copynumber: 2.2 Consensus size: 89
11458915 TTAAGGGTGT
* * *
11458925 AAAAA-GCCCTCAAATTTTTTCAAAAAAAATAATTAAGCCCCT-TTTTTTT-GCACTCAATT-GA
1 AAAAAGGCCCTCAAACTTCTTCAAAAAAAATAATTAAGCCCCTCTTTTTTTCCCACTCAATTGGA
*
11458986 GCACTTGAA-TTTTCAAAATACATAA
66 -CACTTAAACTTTT-AAAATACATAA
*
11459011 AAAAAGGCCCTCAAACTTCTTCAAAAAAAGTAATTAAGCCCCTGCTTTTTTTCCCCACTCAATTG
1 AAAAAGGCCCTCAAACTTCTTCAAAAAAAATAATTAAGCCCCT-CTTTTTTT-CCCACTCAATTG
* *
11459076 GATACTTAAACTTTTAAAATGCATAA
64 GACACTTAAACTTTTAAAATACATAA
* *
11459102 AAAAAGACCTTCAAA
1 AAAAAGGCCCTCAAA
11459117 ATTTTTAAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
86 5 0.06
87 34 0.38
89 7 0.08
91 38 0.42
92 6 0.07
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (89 bp):
AAAAAGGCCCTCAAACTTCTTCAAAAAAAATAATTAAGCCCCTCTTTTTTTCCCACTCAATTGGA
CACTTAAACTTTTAAAATACATAA
Found at i:11459599 original size:27 final size:27
Alignment explanation
Indices: 11459569--11459679 Score: 102
Period size: 28 Copynumber: 4.1 Consensus size: 27
11459559 AAATTCTATA
*
11459569 ATTTTTTTATATTTCTATATATTTTAT
1 ATTTTTTTATATTTTTATATATTTTAT
* * *
11459596 A-TTTTTTACGATTTTTATAAAATTTTAC
1 ATTTTTTTA-TATTTTTAT-ATATTTTAT
* *
11459624 AATTTTTTATATTTTTTATATTTTTTAT
1 ATTTTTTTATA-TTTTTATATATTTTAT
* *
11459652 ATTTTTCTA-ATTTTTA-ATATTTTTT
1 ATTTTTTTATATTTTTATATATTTTAT
11459677 ATT
1 ATT
11459680 AAAATTTAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
25 10 0.15
26 13 0.19
27 9 0.13
28 22 0.32
29 14 0.21
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (27 bp):
ATTTTTTTATATTTTTATATATTTTAT
Found at i:11459602 original size:9 final size:9
Alignment explanation
Indices: 11459571--11459678 Score: 96
Period size: 9 Copynumber: 11.9 Consensus size: 9
11459561 ATTCTATAAT
11459571 TTTTTTATA
1 TTTTTTATA
*
11459580 -TTTCTATA
1 TTTTTTATA
*
11459588 TATTTTATA
1 TTTTTTATA
*
11459597 TTTTTTACGA
1 TTTTTTA-TA
11459607 -TTTTTATAA
1 TTTTTTAT-A
** *
11459616 AATTTTACAA
1 TTTTTTA-TA
11459626 TTTTTTATA
1 TTTTTTATA
11459635 TTTTTTATA
1 TTTTTTATA
11459644 TTTTTTATA
1 TTTTTTATA
11459653 TTTTTCTA-A
1 TTTTT-TATA
*
11459662 TTTTTAATA
1 TTTTTTATA
11459671 TTTTTTAT
1 TTTTTTAT
11459679 TAAAATTTAA
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
8 8 0.10
9 57 0.72
10 14 0.18
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.69
Consensus pattern (9 bp):
TTTTTTATA
Found at i:11459644 original size:56 final size:55
Alignment explanation
Indices: 11459522--11459657 Score: 166
Period size: 56 Copynumber: 2.4 Consensus size: 55
11459512 TTTTTTCGAA
*
11459522 TTTTATATTTCTTTATATTTTGTATTACGACTTTATAAAATTCTATAATTTTTTTATAT
1 TTTTATATTT-TTTATA-TTT-T-TTACGACTTTATAAAATTCTACAATTTTTTTATAT
* * * *
11459581 TTCTATATATTTTATATTTTTTACGATTTTTATAAAATTTTACAA-TTTTTTATATT
1 TTTTATATTTTTTATATTTTTTACGA-CTTTATAAAATTCTACAATTTTTTTATA-T
11459637 TTTTATATTTTTTATATTTTT
1 TTTTATATTTTTTATATTTTT
11459658 CTAATTTTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
55 15 0.22
56 36 0.53
57 3 0.04
58 6 0.09
59 8 0.12
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (55 bp):
TTTTATATTTTTTATATTTTTTACGACTTTATAAAATTCTACAATTTTTTTATAT
Found at i:11459676 original size:65 final size:62
Alignment explanation
Indices: 11459571--11459744 Score: 156
Period size: 65 Copynumber: 2.7 Consensus size: 62
11459561 ATTCTATAAT
* * ** * *
11459571 TTTTTTATATTTCTATATATTTTATATTTTTTACGA-TTTTTATAAAATTTTACAATTTTTTATA
1 TTTTTTATATTT-T-TATATTTTTTAATTTTTAATATTTTTTATAAAATTTAACAA-TATTTATA
*
11459635 TTTTTTATATTTTTTATATTTTTCTAATTTTTAATATTTTTTATTAAAATTTAATAATATTTATA
1 TTTTTTATA-TTTTTATATTTTT-TAATTTTTAATATTTTTTA-TAAAATTTAACAATATTTATA
*** * *
11459700 ACCTTTATAGATTTTA-ATTTTTTAATTTTT-ATATTTTTAATAAAA
1 TTTTTTATA-TTTTTATATTTTTTAATTTTTAATATTTTTTATAAAA
11459745 GTAAGGGCTT
Statistics
Matches: 93, Mismatches: 13, Indels: 11
0.79 0.11 0.09
Matches are distributed among these distances:
61 5 0.05
62 9 0.10
63 16 0.17
64 25 0.27
65 27 0.29
66 11 0.12
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (62 bp):
TTTTTTATATTTTTATATTTTTTAATTTTTAATATTTTTTATAAAATTTAACAATATTTATA
Found at i:11459868 original size:89 final size:88
Alignment explanation
Indices: 11459741--11459964 Score: 292
Period size: 89 Copynumber: 2.5 Consensus size: 88
11459731 TATTTTTAAT
* **
11459741 AAAAGTAAGGGCTTAATTGCTTTTGTTTTTAAGTTTGAGGGTCTTTTTT-ATGCATTTTAAAAGT
1 AAAAGTAGGGGCTTAATTGCTTTT-TTTAAAAGTTTGAGGGTCTTTTTTGATGCATTTTAAAAGT
* * *
11459805 TCAAGTATTCAATTGAGTATAAAA
65 TCAAGTATCCAAATGAGTACAAAA
*
11459829 AAAATGTAGGGGCTTAATTGCTTTTTTTAAAAGGTTTGAGAG-CTTTTTTGATGCATTTTAAAAG
1 AAAA-GTAGGGGCTTAATTGCTTTTTTTAAAA-GTTTGAGGGTCTTTTTTGATGCATTTTAAAAG
*
11459893 TTCAAGTATCCAAATGAGTGCAAAA
64 TTCAAGTATCCAAATGAGTACAAAA
* * *
11459918 AAAAGAAGGGGTTTAATTGCTTTTTTGAGAAAGTTTGAGGGT-TTTTT
1 AAAAGTAGGGGCTTAATTGCTTTTTTTA-AAAGTTTGAGGGTCTTTTT
11459965 ACACCCTTAA
Statistics
Matches: 119, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
88 50 0.42
89 69 0.58
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.41
Consensus pattern (88 bp):
AAAAGTAGGGGCTTAATTGCTTTTTTTAAAAGTTTGAGGGTCTTTTTTGATGCATTTTAAAAGTT
CAAGTATCCAAATGAGTACAAAA
Found at i:11481835 original size:21 final size:21
Alignment explanation
Indices: 11481809--11481862 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
11481799 GGAGTTTTTG
**
11481809 GTATCGGTAGATGTATAACTT
1 GTATCGGTAGAAATATAACTT
* * *
11481830 GTATCGATAGAAATCTTACTT
1 GTATCGGTAGAAATATAACTT
11481851 GTATCGGTAGAA
1 GTATCGGTAGAA
11481863 CTAATGCAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAAATATAACTT
Found at i:11487017 original size:13 final size:14
Alignment explanation
Indices: 11486979--11487019 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
11486969 TAGTTTAGCA
11486979 TTGCTTTTGAAAA-
1 TTGCTTTTGAAAAG
11486992 TTGCTTTTGAAAAG
1 TTGCTTTTGAAAAG
*
11487006 TT-CTTTTAAAAAG
1 TTGCTTTTGAAAAG
11487019 T
1 T
11487020 GTGGTGGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 24 0.92
14 2 0.08
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (14 bp):
TTGCTTTTGAAAAG
Found at i:11487065 original size:13 final size:13
Alignment explanation
Indices: 11486980--11487071 Score: 51
Period size: 13 Copynumber: 7.1 Consensus size: 13
11486970 AGTTTAGCAT
* *
11486980 TGCTTTTGAAAAT
1 TGCTTTTGAGAAG
*
11486993 TGCTTTTGAAAAG
1 TGCTTTTGAGAAG
* * *
11487006 TTCTTTTAAAAAG
1 TGCTTTTGAGAAG
* * *
11487019 TG-TGGTGGAAAAG
1 TGCT-TTTGAGAAG
*
11487032 TGCTTTTTAGAAG
1 TGCTTTTGAGAAG
*
11487045 TGTTTTTGAGAAG
1 TGCTTTTGAGAAG
* *
11487058 TACTTTTGAAAAG
1 TGCTTTTGAGAAG
11487071 T
1 T
11487072 TTGGTTTAAG
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
12 1 0.02
13 59 0.97
14 1 0.02
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.41
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:11487071 original size:26 final size:26
Alignment explanation
Indices: 11486982--11487071 Score: 81
Period size: 26 Copynumber: 3.5 Consensus size: 26
11486972 TTTAGCATTG
* * *
11486982 CTTTTGAAAATTGCTTTTGAAAAGTT
1 CTTTTGAAAAGTGTTTTTGAAAAGTA
* ** * *
11487008 CTTTTAAAAAGTGTGGTGGAAAAGTG
1 CTTTTGAAAAGTGTTTTTGAAAAGTA
* * *
11487034 CTTTTTAGAAGTGTTTTTGAGAAGTA
1 CTTTTGAAAAGTGTTTTTGAAAAGTA
11487060 CTTTTGAAAAGT
1 CTTTTGAAAAGT
11487072 TTGGTTTAAG
Statistics
Matches: 48, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (26 bp):
CTTTTGAAAAGTGTTTTTGAAAAGTA
Found at i:11488060 original size:43 final size:43
Alignment explanation
Indices: 11488006--11488349 Score: 373
Period size: 43 Copynumber: 8.0 Consensus size: 43
11487996 GGAAAACGAT
* * * *
11488006 GCTATAAAACATGATCTTTAGTGGCGCTTTTCCCACAAACGTC
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* ** *
11488049 GCTATAGAACATGGGCTTTAGCGATGCTTTTCCCACAAAAGCC
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * * ** *
11488092 GCTGTAAAACATGTTCTTTAGTTGTGCTTTTCCCACAAACGCC
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * * * *
11488135 GCTATAGAACATGATCTTTAGCGACGTTTTTTCCACAAACACC
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * * * *
11488178 ACTATAGAGCATGGTCTTTAGCAGTGCTTTACCCACAAACGCC
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * ** *
11488221 GCTATAGAGCATGGTCTTAAGCGGCATTTTTCCCACAAACGTC
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* *
11488264 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCATAAATGCC
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * **
11488307 GCTACAGAACATGGTCTTTAGCAGCGCTTTTCTTACAAACGCC
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
11488350 ACTAACATTA
Statistics
Matches: 244, Mismatches: 57, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 244 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (43 bp):
GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
Found at i:11495588 original size:29 final size:28
Alignment explanation
Indices: 11495556--11495627 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
11495546 GGCCCGAGGT
*
11495556 AAAACGGTAATTTTGAACACTTCGGGGGC
1 AAAACGGTAATTTTGAACACTT-GAGGGC
*
11495585 AAAACGGTAATTTTTGGACACTTGAGGGC
1 AAAACGGTAA-TTTTGAACACTTGAGGGC
**
11495614 AAAAATGTAATTTT
1 AAAACGGTAATTTT
11495628 TAGATATTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 4 0.11
29 23 0.61
30 11 0.29
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (28 bp):
AAAACGGTAATTTTGAACACTTGAGGGC
Found at i:11495624 original size:58 final size:59
Alignment explanation
Indices: 11495562--11495779 Score: 196
Period size: 58 Copynumber: 3.7 Consensus size: 59
11495552 AGGTAAAACG
* * * *
11495562 GTAATTTTGA-ACACTTCGGGGGCAAAACGGTAATTTTTGGACACTT--GAGGGCAAAAAT
1 GTAATTTTTAGACA-TTCGGGGGTAAAATGGTAATTTTTGGAAACTTCGGA-GGCAAAAAT
* * * *
11495620 GTAATTTTTAGATATTCAGGGGTAAAATGGTAATTTTTGGAAAGTTCGGAGTCAAAAAT
1 GTAATTTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAACTTCGGAGGCAAAAAT
* * ** *
11495679 GTAATTTTTAGACA-TCTGGGGGTAAAATGGTAATTTTTGAAAAGTTATG-GTCAAAAAT
1 GTAATTTTTAGACATTC-GGGGGTAAAATGGTAATTTTTGGAAACTTCGGAGGCAAAAAT
* * * * *
11495737 GAAATTTTT-GAAAATTTGAGTGTAAAATGGTAATTTTTGGAAA
1 GTAATTTTTAG-ACATTCGGGGGTAAAATGGTAATTTTTGGAAA
11495780 GTTTGAGGTT
Statistics
Matches: 135, Mismatches: 19, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
57 1 0.01
58 80 0.59
59 52 0.39
60 2 0.01
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.34
Consensus pattern (59 bp):
GTAATTTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAACTTCGGAGGCAAAAAT
Found at i:11495628 original size:29 final size:28
Alignment explanation
Indices: 11495581--11495923 Score: 133
Period size: 29 Copynumber: 11.7 Consensus size: 28
11495571 AACACTTCGG
** *
11495581 GGGCAAAACGGTAATTTTTGGACACTTGA
1 GGGCAAAAATGTAATTTTTGGA-AATTGA
* * *
11495610 GGGCAAAAATGTAATTTTTAGATATTCA
1 GGGCAAAAATGTAATTTTTGGAAATTGA
**
11495638 GGGGTAAAATGGTAATTTTTGGAAAGTTCG-
1 GGGCAAAAAT-GTAATTTTTGGAAA-TT-GA
* * *
11495668 GAGTCAAAAATGTAATTTTTAGACATCTG-
1 G-GGCAAAAATGTAATTTTTGGAAAT-TGA
** *
11495697 GGGGTAAAATGGTAATTTTTGAAAAGTT-A
1 GGGCAAAAAT-GTAATTTTTGGAAA-TTGA
* * *
11495726 TGGTCAAAAATGAAATTTTTGAAAATTTGA
1 -GGGCAAAAATGTAATTTTTGGAAA-TTGA
* *
11495756 GTG-TAAAATGGTAATTTTTGGAAAGTTTGA
1 GGGCAAAAAT-GTAATTTTTGGAAA--TTGA
** * *
11495786 GGTTAAAAATGGAATTTTT-GAAAGTTTAA
1 GGGCAAAAATGTAATTTTTGGAAA--TTGA
* * * * *
11495815 GGG-TACAATGGTGATTTTGGGAAGTTCGA
1 GGGCAAAAAT-GTAATTTTTGGAAATT-GA
* *
11495844 GGG-TAAAATGGTAATTTTTGGAAAGTTCAA
1 GGGCAAAAAT-GTAATTTTTGGAAA-TT-GA
** *
11495874 GGGTTAAAATGTAATTTTTGTGAAGTTTGA
1 GGGCAAAAATGTAATTTTTG-GAA-ATTGA
*
11495904 GGGTAAAAATGTAATTTTTG
1 GGGCAAAAATGTAATTTTTG
11495924 AAAAGTTTAA
Statistics
Matches: 241, Mismatches: 53, Indels: 39
0.72 0.16 0.12
Matches are distributed among these distances:
28 28 0.12
29 112 0.46
30 79 0.33
31 22 0.09
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (28 bp):
GGGCAAAAATGTAATTTTTGGAAATTGA
Found at i:11495908 original size:60 final size:61
Alignment explanation
Indices: 11495585--11495943 Score: 270
Period size: 59 Copynumber: 6.1 Consensus size: 61
11495575 CTTCGGGGGC
* * * * * * *
11495585 AAAACGGTAATTTTTGGACA-CTTGAGGGCAAAAAT-GTAATTTTTAGATA--TTCAGGGGT
1 AAAATGGTAATTTTTGGA-AGTTTGAGGGTAAAAATGGTAATTTTTGGAAAGTTTAAGGGTT
* * * * * * *
11495643 AAAATGGTAATTTTTGGAAAGTTCG-GAGTCAAAAAT-GTAATTTTTAGACA-TCT-GGGGGT
1 AAAATGGTAATTTTTGG-AAGTTTGAGGGT-AAAAATGGTAATTTTTGGAAAGTTTAAGGGTT
* * * * * *
11495702 AAAATGGTAATTTTTGAAAAG-TT-ATGGTCAAAAAT-GAAATTTTT-GAAAATTTGAGTG-T
1 AAAATGGTAATTTTTG-GAAGTTTGAGGGT-AAAAATGGTAATTTTTGGAAAGTTTAAGGGTT
*
11495760 AAAATGGTAATTTTTGGAAAGTTTGAGGTTAAAAATGG-AATTTTT-GAAAGTTTAAGGG-T
1 AAAATGGTAATTTTTGG-AAGTTTGAGGGTAAAAATGGTAATTTTTGGAAAGTTTAAGGGTT
* * * * *
11495819 ACAATGGTGATTTTGGGAAGTTCGAGGGT-AAAATGGTAATTTTTGGAAAGTTCAAGGGTT
1 AAAATGGTAATTTTTGGAAGTTTGAGGGTAAAAATGGTAATTTTTGGAAAGTTTAAGGGTT
* *
11495879 AAAAT-GTAATTTTTGTGAAGTTTGAGGGTAAAAAT-GTAATTTTTGAAAAGTTTAAGGGTC
1 AAAATGGTAATTTTTG-GAAGTTTGAGGGTAAAAATGGTAATTTTTGGAAAGTTTAAGGGTT
11495939 AAAAT
1 AAAAT
11495944 ATAATTTCTA
Statistics
Matches: 248, Mismatches: 36, Indels: 32
0.78 0.11 0.10
Matches are distributed among these distances:
57 10 0.04
58 76 0.31
59 108 0.44
60 49 0.20
61 5 0.02
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (61 bp):
AAAATGGTAATTTTTGGAAGTTTGAGGGTAAAAATGGTAATTTTTGGAAAGTTTAAGGGTT
Found at i:11495937 original size:30 final size:29
Alignment explanation
Indices: 11495639--11495950 Score: 217
Period size: 30 Copynumber: 10.6 Consensus size: 29
11495629 AGATATTCAG
* *
11495639 GGGTAAAATGGTAATTTTTGGAAAGTTCG-
1 GGGTAAAAT-GTAATTTTTGAAAAGTTTGA
* * * *
11495668 GAGTCAAAAATGTAATTTTT-AGACA-TCTGG
1 GGGT--AAAATGTAATTTTTGA-AAAGTTTGA
11495698 GGGTAAAATGGTAATTTTTGAAAAG-TT-A
1 GGGTAAAAT-GTAATTTTTGAAAAGTTTGA
* *
11495726 TGGTCAAAAATGAAATTTTTGAAAA-TTTGA
1 GGGT--AAAATGTAATTTTTGAAAAGTTTGA
* *
11495756 GTGTAAAATGGTAATTTTTGGAAAGTTTGA
1 GGGTAAAAT-GTAATTTTTGAAAAGTTTGA
* * *
11495786 GGTTAAAAATGGAATTTTTG-AAAGTTTAA
1 GGGT-AAAATGTAATTTTTGAAAAGTTTGA
* * ** *
11495815 GGGTACAATGGTGA-TTTTGGGAAGTTCGA
1 GGGTAAAAT-GTAATTTTTGAAAAGTTTGA
* **
11495844 GGGTAAAATGGTAATTTTTGGAAAGTTCAA
1 GGGTAAAAT-GTAATTTTTGAAAAGTTTGA
**
11495874 GGGTTAAAATGTAATTTTTGTGAAGTTTGA
1 GGG-TAAAATGTAATTTTTGAAAAGTTTGA
*
11495904 GGGTAAAAATGTAATTTTTGAAAAGTTTAA
1 GGGT-AAAATGTAATTTTTGAAAAGTTTGA
*
11495934 GGGTCAAAATATAATTT
1 GGGT-AAAATGTAATTT
11495951 CTAGAGAATT
Statistics
Matches: 225, Mismatches: 39, Indels: 37
0.75 0.13 0.12
Matches are distributed among these distances:
28 22 0.10
29 76 0.34
30 111 0.49
31 16 0.07
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGTAAAATGTAATTTTTGAAAAGTTTGA
Found at i:11500984 original size:30 final size:30
Alignment explanation
Indices: 11500948--11501221 Score: 116
Period size: 29 Copynumber: 9.3 Consensus size: 30
11500938 GTAAAATAGT
*
11500948 AATTTTTGGAAAGTTCAGGGTCAAAAATAA
1 AATTTTTGGAAAGTTCAGGGTCAAAAATGA
* * * *
11500978 AATTTTTAGACA-TCCGAGGGT-AAAAATGGT
1 AATTTTTGGAAAGTTC-AGGGTCAAAAAT-GA
* *
11501008 AATTTTTGG-AAGTTCATGGTCAAAAATGG
1 AATTTTTGGAAAGTTCAGGGTCAAAAATGA
* *
11501037 AATTTTTGG-AACTTCGAGGGT--AAAATGGT
1 AATTTTTGGAAAGTTC-AGGGTCAAAAAT-GA
* * *
11501066 GATTTTTGGAATGTTC-GGAGTCAAAAATGT
1 AATTTTTGGAAAGTTCAGG-GTCAAAAATGA
* * * *
11501096 GATTTTTAG-AGGTTCGGGGGT-AAAAAT-A
1 AATTTTTGGAAAGTTC-AGGGTCAAAAATGA
* *
11501124 CGATTTTTGG-AAGTTCAAGGGT--AAAATGGT
1 -AATTTTTGGAAAGTTC-AGGGTCAAAAAT-GA
*
11501154 AA-TTTTGG-AAGTTCGAGGGT-AAAAATGC
1 AATTTTTGGAAAGTTC-AGGGTCAAAAATGA
* * *
11501182 AATTTTTGAAAACTTTAGGGGTCAAAATATG-
1 AATTTTTGGAAAGTTCA-GGGTCAAAA-ATGA
11501213 -ATTTTTGGA
1 AATTTTTGGA
11501222 GAATTTAAGG
Statistics
Matches: 192, Mismatches: 31, Indels: 42
0.72 0.12 0.16
Matches are distributed among these distances:
28 32 0.17
29 79 0.41
30 67 0.35
31 11 0.06
32 3 0.02
ACGTcount: A:0.34, C:0.07, G:0.26, T:0.34
Consensus pattern (30 bp):
AATTTTTGGAAAGTTCAGGGTCAAAAATGA
Found at i:11501094 original size:59 final size:58
Alignment explanation
Indices: 11500907--11501177 Score: 233
Period size: 59 Copynumber: 4.7 Consensus size: 58
11500897 TTTGGATGCC
* *
11500907 CAGGGTAAAAAAT--AA-TTTTGG-ACATTCGAGGGTAAAATAGTAATTTTTGGAAAGTT
1 CAGGGTCAAAAATGGAATTTTTGGAAC-TTCGAGGGTAAAATGGTAATTTTTGG-AAGTT
** * *
11500963 CAGGGTCAAAAATAAAATTTTTAG-ACATCCGAGGGTAAAAATGGTAATTTTTGGAAGTT
1 CAGGGTCAAAAATGGAATTTTTGGAAC-TTCGAGGGT-AAAATGGTAATTTTTGGAAGTT
* *
11501022 CATGGTCAAAAATGGAATTTTTGGAACTTCGAGGGTAAAATGGTGATTTTTGGAATGTT
1 CAGGGTCAAAAATGGAATTTTTGGAACTTCGAGGGTAAAATGGTAATTTTTGGAA-GTT
* ** * *
11501081 C-GGAGTCAAAAATGTG-ATTTTTAGAGGTTCGGGGGTAAAA--ATACGATTTTTGGAAGTT
1 CAGG-GTCAAAAATG-GAATTTTTGGAACTTCGAGGGTAAAATGGTA--ATTTTTGGAAGTT
*
11501139 CAAGGGT--AAAATGGTAA-TTTTGGAAGTTCGAGGGTAAAA
1 C-AGGGTCAAAAATGG-AATTTTTGGAACTTCGAGGGTAAAA
11501178 ATGCAATTTT
Statistics
Matches: 181, Mismatches: 20, Indels: 27
0.79 0.09 0.12
Matches are distributed among these distances:
56 13 0.07
57 26 0.14
58 26 0.14
59 95 0.52
60 21 0.12
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (58 bp):
CAGGGTCAAAAATGGAATTTTTGGAACTTCGAGGGTAAAATGGTAATTTTTGGAAGTT
Found at i:11501188 original size:29 final size:29
Alignment explanation
Indices: 11500908--11501189 Score: 217
Period size: 29 Copynumber: 9.7 Consensus size: 29
11500898 TTGGATGCCC
*
11500908 AGGGTAAAAA-ATAA-TTTTGGACA-TTCG
1 AGGGTAAAAATGTAATTTTTGGA-AGTTCG
11500935 AGGGT-AAAATAGTAATTTTTGGAAAGTTC-
1 AGGGTAAAAAT-GTAATTTTTGG-AAGTTCG
** * *
11500964 AGGGTCAAAAATAAAATTTTTAGACA-TCCG
1 AGGGT-AAAAATGTAATTTTTGGA-AGTTCG
11500994 AGGGTAAAAATGGTAATTTTTGGAAGTTC-
1 AGGGTAAAAAT-GTAATTTTTGGAAGTTCG
* * *
11501023 ATGGTCAAAAATGGAATTTTTGGAACTTCG
1 AGGGT-AAAAATGTAATTTTTGGAAGTTCG
*
11501053 AGGGT-AAAATGGTGATTTTTGGAATGTTCG
1 AGGGTAAAAAT-GTAATTTTTGGAA-GTTCG
* * * *
11501083 -GAGTCAAAAATGTGATTTTTAGAGGTTCG
1 AGGGT-AAAAATGTAATTTTTGGAAGTTCG
* *** *
11501112 GGGGTAAAAATACGATTTTTGGAAGTTCA
1 AGGGTAAAAATGTAATTTTTGGAAGTTCG
11501141 AGGGT-AAAATGGTAA-TTTTGGAAGTTCG
1 AGGGTAAAAAT-GTAATTTTTGGAAGTTCG
*
11501169 AGGGTAAAAATGCAATTTTTG
1 AGGGTAAAAATGTAATTTTTG
11501190 AAAACTTTAG
Statistics
Matches: 203, Mismatches: 31, Indels: 40
0.74 0.11 0.15
Matches are distributed among these distances:
26 4 0.02
27 5 0.02
28 33 0.16
29 94 0.46
30 57 0.28
31 10 0.05
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (29 bp):
AGGGTAAAAATGTAATTTTTGGAAGTTCG
Found at i:11503156 original size:11 final size:11
Alignment explanation
Indices: 11503142--11503225 Score: 53
Period size: 11 Copynumber: 7.5 Consensus size: 11
11503132 TAAATTCAAA
11503142 TTAAAATAAAT
1 TTAAAATAAAT
* *
11503153 TTAAACTAAAAA
1 TTAAAAT-AAAT
**
11503165 TTAATTTAAAT
1 TTAAAATAAAT
*
11503176 TTATAATAAAT
1 TTAAAATAAAT
*
11503187 TTAAACTTAAA-
1 TTAAA-ATAAAT
* *
11503198 ATAAATTAAAAT
1 TTAAAAT-AAAT
*
11503210 TTATAATAAAT
1 TTAAAATAAAT
11503221 TTAAA
1 TTAAA
11503226 CTTAAAATAA
Statistics
Matches: 54, Mismatches: 15, Indels: 8
0.70 0.19 0.10
Matches are distributed among these distances:
10 2 0.04
11 36 0.67
12 16 0.30
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
TTAAAATAAAT
Found at i:11503170 original size:17 final size:17
Alignment explanation
Indices: 11503132--11503250 Score: 141
Period size: 17 Copynumber: 7.1 Consensus size: 17
11503122 ATTTTTTAAT
*
11503132 TAAATTCAAA-TTAAAA
1 TAAATTTAAACTTAAAA
*
11503148 TAAATTTAAACTAAAAA
1 TAAATTTAAACTTAAAA
* * *
11503165 TTAATTTAAATTTATAA
1 TAAATTTAAACTTAAAA
11503182 TAAATTTAAACTTAAAA
1 TAAATTTAAACTTAAAA
* * *
11503199 TAAATTAAAATTTATAA
1 TAAATTTAAACTTAAAA
11503216 TAAATTTAAACTTAAAA
1 TAAATTTAAACTTAAAA
* *
11503233 TAAATTAAAATTTAAAA
1 TAAATTTAAACTTAAAA
11503250 T
1 T
11503251 CTGGGCTTGG
Statistics
Matches: 85, Mismatches: 17, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
16 9 0.11
17 76 0.89
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:11503184 original size:34 final size:34
Alignment explanation
Indices: 11503132--11503246 Score: 178
Period size: 34 Copynumber: 3.4 Consensus size: 34
11503122 ATTTTTTAAT
* * *
11503132 TAAATTCAAA-TTAAAATAAATTTAAACTAAAAA
1 TAAATTAAAATTTATAATAAATTTAAACTTAAAA
* *
11503165 TTAATTTAAATTTATAATAAATTTAAACTTAAAA
1 TAAATTAAAATTTATAATAAATTTAAACTTAAAA
11503199 TAAATTAAAATTTATAATAAATTTAAACTTAAAA
1 TAAATTAAAATTTATAATAAATTTAAACTTAAAA
11503233 TAAATTAAAATTTA
1 TAAATTAAAATTTA
11503247 AAATCTGGGC
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
33 8 0.11
34 67 0.89
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (34 bp):
TAAATTAAAATTTATAATAAATTTAAACTTAAAA
Found at i:11503433 original size:8 final size:8
Alignment explanation
Indices: 11503434--11503532 Score: 53
Period size: 8 Copynumber: 12.4 Consensus size: 8
11503424 AAATATTTAA
*
11503434 TTAAATAA
1 TTAAATAT
11503442 TTAAATAT
1 TTAAATAT
*
11503450 AGTTAAATAA
1 --TTAAATAT
11503460 TTAAATAT
1 TTAAATAT
*
11503468 TTTAA-A-
1 TTAAATAT
11503474 TTAAATAT
1 TTAAATAT
* *
11503482 TTGGATTATT
1 TT-AAATA-T
* *
11503492 TTTAATAA
1 TTAAATAT
*
11503500 TTAAATAA
1 TTAAATAT
11503508 TTAAATAT
1 TTAAATAT
*
11503516 TTTAA-A-
1 TTAAATAT
11503522 TTAAATAT
1 TTAAATAT
11503530 TTA
1 TTA
11503533 GATTGTTTTT
Statistics
Matches: 69, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
6 8 0.12
7 4 0.06
8 41 0.59
9 6 0.09
10 10 0.14
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (8 bp):
TTAAATAT
Found at i:11503457 original size:18 final size:18
Alignment explanation
Indices: 11503417--11503467 Score: 75
Period size: 18 Copynumber: 2.7 Consensus size: 18
11503407 AGTTATTTTT
11503417 AATAATTAAATATTTAATTA
1 AATAATTAAATA--TAATTA
*
11503437 AATAATTAAATATAGTTA
1 AATAATTAAATATAATTA
11503455 AATAATTAAATAT
1 AATAATTAAATAT
11503468 TTTAAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 18 0.60
20 12 0.40
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AATAATTAAATATAATTA
Found at i:11503511 original size:48 final size:48
Alignment explanation
Indices: 11503452--11503562 Score: 195
Period size: 48 Copynumber: 2.3 Consensus size: 48
11503442 TTAAATATAG
*
11503452 TTAAATAATTAAATATTTTAAATTAAATATTTGGATTATTTTTAATAA
1 TTAAATAATTAAATATTTTAAATTAAATATTTAGATTATTTTTAATAA
*
11503500 TTAAATAATTAAATATTTTAAATTAAATATTTAGATTGTTTTTAATAA
1 TTAAATAATTAAATATTTTAAATTAAATATTTAGATTATTTTTAATAA
*
11503548 TTAAATAATAAAATA
1 TTAAATAATTAAATA
11503563 ATTAAATAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.48
Consensus pattern (48 bp):
TTAAATAATTAAATATTTTAAATTAAATATTTAGATTATTTTTAATAA
Found at i:11503551 original size:26 final size:25
Alignment explanation
Indices: 11503472--11503554 Score: 91
Period size: 26 Copynumber: 3.4 Consensus size: 25
11503462 AAATATTTTA
*
11503472 AATTAAATATTTGGATTATTTTTAAT
1 AATTAAATATTTAGATT-TTTTTAAT
* * *
11503498 AATTAAATAATTA-AATATTTT-A-
1 AATTAAATATTTAGATTTTTTTAAT
11503520 AATTAAATATTTAGATTGTTTTTAAT
1 AATTAAATATTTAGATT-TTTTTAAT
11503546 AATTAAATA
1 AATTAAATA
11503555 ATAAAATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
22 12 0.26
23 3 0.07
24 8 0.17
25 3 0.07
26 20 0.43
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (25 bp):
AATTAAATATTTAGATTTTTTTAAT
Found at i:11503556 original size:8 final size:8
Alignment explanation
Indices: 11503543--11503572 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
11503533 GATTGTTTTT
11503543 AATAATTA
1 AATAATTA
*
11503551 AATAATAA
1 AATAATTA
11503559 AATAATTA
1 AATAATTA
11503567 AATAAT
1 AATAAT
11503573 CAATTCTGTT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AATAATTA
Found at i:11506015 original size:2 final size:2
Alignment explanation
Indices: 11506008--11506033 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11505998 TATATTCATT
11506008 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
11506034 CATGTGTGTG
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:11507066 original size:29 final size:29
Alignment explanation
Indices: 11507002--11507454 Score: 238
Period size: 29 Copynumber: 15.7 Consensus size: 29
11506992 TGTTCTCTTT
* * *
11507002 AAAAATCACATTTTAACCCTTAAACGTT-TC
1 AAAAATTACATTTTGACCC-CAAAC-TTCTC
* *
11507032 TAAAATTATATTTTGACCCCAAACTTCTC
1 AAAAATTACATTTTGACCCCAAACTTCTC
**
11507061 AAAAATTACATTTTGACCCTTAA-TT-TC
1 AAAAATTACATTTTGACCCCAAACTTCTC
*
11507088 AAAAATTACATTTTGCCCCCAAACTTCT-
1 AAAAATTACATTTTGACCCCAAACTTCTC
* *
11507116 TAAAATTACATTTT-ACCCCTAAACTT-AC
1 AAAAATTACATTTTGACCCC-AAACTTCTC
* * *
11507144 AAAAATTTCATTTTGACCCCTAAACTTTTT
1 AAAAATTACATTTTGACCCC-AAACTTCTC
**
11507174 AAAAATTACATTTTTG-CCTTGAAACTTC-C
1 AAAAATTACA-TTTTGACC-CCAAACTTCTC
* * *
11507203 AAAGATTACATTTT-ACCCTCAAGCTT-AC
1 AAAAATTACATTTTGACCC-CAAACTTCTC
* * * *
11507231 AAAAATTTCATTTTGACTCCGAAACTTTTT
1 AAAAATTACATTTTGAC-CCCAAACTTCTC
* ***
11507261 AAAAATTATATTTTTG-CTCTTGAACTT-TC
1 AAAAATTACA-TTTTGAC-CCCAAACTTCTC
* * * * *
11507290 AAAAATCACATTTTTACCCCCGATCTTC-G
1 AAAAATTACATTTTGA-CCCCAAACTTCTC
*
11507319 AAAAAATACAATTTT-ACCCCTAAACTTCT-
1 AAAAATTAC-ATTTTGACCCC-AAACTTCTC
* * *
11507348 AAAAATCATATTTTTACCCCAAACTTCTC
1 AAAAATTACATTTTGACCCCAAACTTCTC
* ** * *
11507377 AAAAATCACATTTTTTCCCCGAAC-TCTTT
1 AAAAATTACATTTTGACCCCAAACTTC-TC
* * *
11507406 GAAAATGACATTTTTACCCCTAAAACTT-TC
1 AAAAATTACATTTTGACCCC--AAACTTCTC
* *
11507436 TAAAATTACATTTTAACCC
1 AAAAATTACATTTTGACCC
11507455 TGAACTCTCT
Statistics
Matches: 329, Mismatches: 66, Indels: 56
0.73 0.15 0.12
Matches are distributed among these distances:
27 26 0.08
28 84 0.26
29 132 0.40
30 73 0.22
31 13 0.04
32 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (29 bp):
AAAAATTACATTTTGACCCCAAACTTCTC
Found at i:11507216 original size:87 final size:86
Alignment explanation
Indices: 11507033--11507309 Score: 298
Period size: 87 Copynumber: 3.2 Consensus size: 86
11507023 AAACGTTTCT
* * * * *
11507033 AAAATTATATTTTGACCCC-AAACTTCTCAAAAATTACATTTTGA-CCCTTAA--TTTCAAAAAT
1 AAAATTACATTTT-ACCCCTAAACTT-ACAAAAATTTCATTTTGACCCCTAAACTTTTTAAAAAT
*** *
11507094 TACA-TTTTGCCCCCAAACTTCTT
64 TACATTTTTGCCTTGAAACTTC-C
11507117 AAAATTACATTTTACCCCTAAACTTACAAAAATTTCATTTTGACCCCTAAACTTTTTAAAAATTA
1 AAAATTACATTTTACCCCTAAACTTACAAAAATTTCATTTTGACCCCTAAACTTTTTAAAAATTA
11507182 CATTTTTGCCTTGAAACTTCC
66 CATTTTTGCCTTGAAACTTCC
* * *
11507203 AAAGATTACATTTTA-CCCTCAAGCTTACAAAAATTTCATTTTGACTCCGAAACTTTTTAAAAAT
1 AAA-ATTACATTTTACCCCT-AAACTTACAAAAATTTCATTTTGACCCCTAAACTTTTTAAAAAT
* *
11507267 TATATTTTTGCTCTTG-AACTTTCA
64 TACATTTTTGC-CTTGAAAC-TTCC
*
11507291 AAAATCACATTTTTACCCC
1 AAAATTACA-TTTTACCCC
11507310 CGATCTTCGA
Statistics
Matches: 167, Mismatches: 15, Indels: 17
0.84 0.08 0.09
Matches are distributed among these distances:
83 21 0.13
84 24 0.14
86 20 0.12
87 84 0.50
88 15 0.09
89 3 0.02
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.38
Consensus pattern (86 bp):
AAAATTACATTTTACCCCTAAACTTACAAAAATTTCATTTTGACCCCTAAACTTTTTAAAAATTA
CATTTTTGCCTTGAAACTTCC
Found at i:11507624 original size:16 final size:14
Alignment explanation
Indices: 11507589--11507628 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
11507579 AATTCGTTTT
*
11507589 TTTTCTTATATTTA
1 TTTTCGTATATTTA
11507603 TTTTCGTATATTTA
1 TTTTCGTATATTTA
11507617 TTCATTCGTATA
1 TT--TTCGTATA
11507629 ATTGTTCACG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 15 0.65
16 8 0.35
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (14 bp):
TTTTCGTATATTTA
Found at i:11512318 original size:9 final size:9
Alignment explanation
Indices: 11512285--11512340 Score: 69
Period size: 9 Copynumber: 6.0 Consensus size: 9
11512275 GGATTCAATG
11512285 AAGAAAAAA
1 AAGAAAAAA
11512294 ATA-AATAAATA
1 A-AGAA-AAA-A
11512305 AAGAAAAAA
1 AAGAAAAAA
11512314 AAGAAAAAA
1 AAGAAAAAA
*
11512323 AAGAGAAAA
1 AAGAAAAAA
11512332 AAGAAAAAA
1 AAGAAAAAA
11512341 GGAAAAGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 29 0.71
10 8 0.20
11 4 0.10
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:11512329 original size:20 final size:20
Alignment explanation
Indices: 11512288--11512357 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
11512278 TTCAATGAAG
*
11512288 AAAAAAATAAATAAATAA-AGA
1 AAAAAAAGAAA-AAA-AAGAGA
11512309 AAAAAAAGAAAAAAAAGAG-
1 AAAAAAAGAAAAAAAAGAGA
*
11512328 -AAAAAAG-AAAAAAGGA-A
1 AAAAAAAGAAAAAAAAGAGA
11512345 AAGAAAAAGAAAA
1 AA-AAAAAGAAAA
11512358 TATAAAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
17 8 0.19
18 8 0.19
19 8 0.19
20 8 0.19
21 10 0.24
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (20 bp):
AAAAAAAGAAAAAAAAGAGA
Found at i:11512338 original size:6 final size:6
Alignment explanation
Indices: 11512311--11512357 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
11512301 AATAAAGAAA
* *
11512311 AAAAAG AAAAA- AAAGAG AAAAAAG AAAAAAG GAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG -AAAAAG -AAAAAG AAAAAG AAAAAG AAAA
11512358 TATAAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 4 0.11
6 19 0.54
7 12 0.34
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:11512338 original size:26 final size:25
Alignment explanation
Indices: 11512289--11512366 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 25
11512279 TCAATGAAGA
*
11512289 AAAAAATAAATAAATAAAGAAAAAAAAG
1 AAAAAA-AAAGAAA-AAAG-AAAAAAAG
*
11512317 AAAAAAAAGAGAAAAAAGAAAAAAGG
1 AAAAAAAA-AGAAAAAAGAAAAAAAG
* *
11512343 AAAAGAAAAAGAAAATATAAAAAA
1 AAAA-AAAAAGAAAAAAGAAAAAA
11512367 GGGGAAAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
26 24 0.55
27 10 0.23
28 10 0.23
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (25 bp):
AAAAAAAAAGAAAAAAGAAAAAAAG
Found at i:11512364 original size:18 final size:17
Alignment explanation
Indices: 11512289--11512357 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 17
11512279 TCAATGAAGA
*
11512289 AAAAAATAAATAAATAAAG
1 AAAAAA-AAAGAAA-AAAG
11512308 -AAAAAAAAGAAAAAA-
1 AAAAAAAAAGAAAAAAG
11512323 AAGAGAAAAAAGAAAAAAGG
1 AA-A-AAAAAAGAAAAAA-G
11512343 AAAAGAAAAAGAAAA
1 AAAA-AAAAAGAAAA
11512358 TATAAAAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
16 4 0.09
17 7 0.16
18 19 0.44
19 11 0.26
20 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAAG
Found at i:11512366 original size:20 final size:18
Alignment explanation
Indices: 11512285--11512367 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 18
11512275 GGATTCAATG
11512285 AAGAAAAAAATAAATAAATA
1 AAGAAAAAAA-AAATAAA-A
11512305 AAGAAAAAAAAGAA-AAAA
1 AAGAAAAAAAA-AATAAAA
*
11512323 AAGAGAAAAAAGAAAAAAGGAA
1 AAGA-AAAAAA-AAATAA--AA
11512345 AAGAAAAAGAAAATATAAAA
1 AAGAAAAA-AAAA-ATAAAA
11512365 AAG
1 AAG
11512368 GGGAAAAAGA
Statistics
Matches: 54, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
18 5 0.09
19 12 0.22
20 20 0.37
21 6 0.11
22 11 0.20
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (18 bp):
AAGAAAAAAAAAATAAAA
Found at i:11512367 original size:26 final size:26
Alignment explanation
Indices: 11512304--11512368 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
11512294 ATAAATAAAT
*
11512304 AAAGAAAAAAAAGAAAAAAAAGAGAAA
1 AAAG-AAAAAAGGAAAAAAAAGAGAAA
11512331 AAAGAAAAAAGGAAAAGAAAA-AGAAA
1 AAAGAAAAAAGGAAAA-AAAAGAGAAA
* *
11512357 ATATAAAAAAGG
1 AAAGAAAAAAGG
11512369 GGAAAAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 26 0.76
27 8 0.24
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (26 bp):
AAAGAAAAAAGGAAAAAAAAGAGAAA
Found at i:11513372 original size:50 final size:50
Alignment explanation
Indices: 11513288--11513995 Score: 450
Period size: 50 Copynumber: 14.6 Consensus size: 50
11513278 CAGATTTCAA
* * * * * * *
11513288 GGGAAAGGTTAAGGCCGTAACGGTGAATCAGGTACCTTAAAAGATGTGAC
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * *
11513338 GAGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCTCAGAAGATATGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
** ** * *** *
11513388 AAGAAATATTGAGG-TG-AA-TTTG-A-----TACCAT-GAA-ATGTGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * ** * * *
11513427 AGGAAAGGTTTAGGCCGCAACAGCGAACCTAGTACCAT-GAAGATTTGAA
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * * * *
11513476 GGGAAAAGTTAAGGTCGCAACGACGAACCCGGTACCTTAAAAGATGTGAC
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* *
11513526 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTCAGAAGATGTGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * * * ** *
11513576 GGGAAAGATTGAAGCCGTAACGACGAATCTAGTACCAT-GAA-ATGTGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
** ** * * *
11513624 GGGAAAGGTTGAGGCCGCAATAGCGAACCCAATACCAT-GAAG-T-TAAA
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * * *
11513671 GGG-AAGGATTGAGGCCGCAACGGTGAATCTGGTACCTTAAAAGATGTGAC
1 GGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* *
11513721 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTCAGAAGATGTGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * * * *
11513771 GGGAAAGATTGAGACCGTAATGGCGAATCCGGTACCAT-GAA-ATGTGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * * * * * * *
11513819 TGGAAAGGTTGAGGCCGCAATGGCGAACTCAGTTCCAT-GAAGATTTTAA
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * * * *
11513868 GGGAAAGGTTGAGGCTGCAATGGCGAACCTGGTACCTTAAAAGATATGAA
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * * * **
11513918 GGGCAATGTTGAGGCTGCAACGGCGAACCCGGTACCTTAAAAAATAAGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * *
11513968 GGAAAAGATTGAAGCCGCAATGGCGAAC
1 GGGAAAGGTTGAGGCCGCAACGGCGAAC
11513996 TTATACCATA
Statistics
Matches: 508, Mismatches: 131, Indels: 38
0.75 0.19 0.06
Matches are distributed among these distances:
39 16 0.03
40 4 0.01
41 6 0.01
42 1 0.00
43 1 0.00
46 5 0.01
47 28 0.06
48 94 0.19
49 77 0.15
50 272 0.54
51 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (50 bp):
GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
Found at i:11513738 original size:195 final size:196
Alignment explanation
Indices: 11513286--11513984 Score: 787
Period size: 195 Copynumber: 3.6 Consensus size: 196
11513276 TACAGATTTC
* * * * * *
11513286 AAGGGAAAGG-TTAAGGCCGTAACGGTGAATCAGGTACCTTAAAAGATGTGACGAGAAAGGTTGA
1 AAGGG-AAGGATTGAGGCCGCAACGGCGAACCTGGTACCTTAAAAGATGTGACGGGAAAGGTTGA
** * ** * *
11513350 GGCCGCAACGACGAACCCGGTACCTCAGAAGATATGATAAGAAATATTG-AG--GT---GA--AT
65 GGCCGCAACGGTGAACCCGGTACCTCAGAAGATGTGATGGGAAAGATTGAAGCCGTAACGACGAA
** * * *
11513407 TTGA-TACCATGAAATGTGATAGGAAAGGTTTAGGCCGCAACAGCGAACCTAGTACCATGAAGAT
130 TCCAGTACCATGAAATGTGATAGGAAAGGTTGAGGCCGCAATAGCGAACCCAGTACCATGAAGA-
*
11513471 TTG
194 TTA
* * * * *
11513474 AAGGGAA-AAGTTAAGGTCGCAACGACGAACCCGGTACCTTAAAAGATGTGACGGGAAAGGTTGA
1 AAGGGAAGGA-TTGAGGCCGCAACGGCGAACCTGGTACCTTAAAAGATGTGACGGGAAAGGTTGA
11513538 GGCCGCAACGGTGAACCCGGTACCTCAGAAGATGTGATGGGAAAGATTGAAGCCGTAACGACGAA
65 GGCCGCAACGGTGAACCCGGTACCTCAGAAGATGTGATGGGAAAGATTGAAGCCGTAACGACGAA
* * *
11513603 TCTAGTACCATGAAATGTGATGGGAAAGGTTGAGGCCGCAATAGCGAACCCAATACCATGAAG-T
130 TCCAGTACCATGAAATGTGATAGGAAAGGTTGAGGCCGCAATAGCGAACCCAGTACCATGAAGAT
11513667 TA
195 TA
* *
11513669 AAGGGAAGGATTGAGGCCGCAACGGTGAATCTGGTACCTTAAAAGATGTGACGGGAAAGGTTGAG
1 AAGGGAAGGATTGAGGCCGCAACGGCGAACCTGGTACCTTAAAAGATGTGACGGGAAAGGTTGAG
* *
11513734 GCCGCAACGGTGAACCCGGTACCTCAGAAGATGTGATGGGAAAGATTG-AGACCGTAATGGCGAA
66 GCCGCAACGGTGAACCCGGTACCTCAGAAGATGTGATGGGAAAGATTGAAG-CCGTAACGACGAA
* * * * *
11513798 TCCGGTACCATGAAATGTGATTGGAAAGGTTGAGGCCGCAATGGCGAACTCAGTTCCATGAAGAT
130 TCCAGTACCATGAAATGTGATAGGAAAGGTTGAGGCCGCAATAGCGAACCCAGTACCATGAAGA-
*
11513863 TTT
194 TTA
* * * * * *
11513866 AAGGGAAAGG-TTGAGGCTGCAATGGCGAACCTGGTACCTTAAAAGATATGAAGGGCAATGTTGA
1 AAGGG-AAGGATTGAGGCCGCAACGGCGAACCTGGTACCTTAAAAGATGTGACGGGAAAGGTTGA
* * * * * ** *
11513930 GGCTGCAACGGCGAACCCGGTACCTTAAAAAATAAGATGGAAAAGATTGAAGCCG
65 GGCCGCAACGGTGAACCCGGTACCTCAGAAGATGTGATGGGAAAGATTGAAGCCG
11513985 CAATGGCGAA
Statistics
Matches: 438, Mismatches: 56, Indels: 25
0.84 0.11 0.05
Matches are distributed among these distances:
187 2 0.00
188 95 0.22
189 2 0.00
191 2 0.00
194 4 0.01
195 173 0.39
196 4 0.01
197 150 0.34
198 6 0.01
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (196 bp):
AAGGGAAGGATTGAGGCCGCAACGGCGAACCTGGTACCTTAAAAGATGTGACGGGAAAGGTTGAG
GCCGCAACGGTGAACCCGGTACCTCAGAAGATGTGATGGGAAAGATTGAAGCCGTAACGACGAAT
CCAGTACCATGAAATGTGATAGGAAAGGTTGAGGCCGCAATAGCGAACCCAGTACCATGAAGATT
A
Found at i:11513756 original size:145 final size:145
Alignment explanation
Indices: 11513530--11513838 Score: 343
Period size: 145 Copynumber: 2.1 Consensus size: 145
11513520 TGTGACGGGA
* * *
11513530 AAGGTTGAGGCCGCAACGGTGAACCCGGTACCTCAGAAGATGTGATGGGAAAGATTGAAGCCGTA
1 AAGGTTGAGGCCGCAACGGTGAACCCGGTACCTCAAAAGATGTGACGGGAAAGATTGAAGCCGCA
* * * *
11513595 ACGACGAATCTAGTACC-ATGAA-ATGTGATGGGAAAGGTTGAGGCCGCAATAGCGAACCCAATA
66 ACGACGAACCCAGTACCTA-GAAGATGTGATGGGAAAGATTGAGACCGCAATAGCGAACCCAATA
11513658 CCATGAAGTTAAAGGG
130 CCATGAAGTTAAAGGG
* * * * *
11513674 AAGGATTGAGGCCGCAACGGTGAATCTGGTACCTTAAAAGATGTGACGGGAAAGGTTGAGGCCGC
1 AAGG-TTGAGGCCGCAACGGTGAACCCGGTACCTCAAAAGATGTGACGGGAAAGATTGAAGCCGC
** * * * * **
11513739 AACGGTGAACCCGGTACCTCAGAAGATGTGATGGGAAAGATTGAGACCGTAATGGCGAATCCGGT
65 AACGACGAACCCAGTACCT-AGAAGATGTGATGGGAAAGATTGAGACCGCAATAGCGAACCCAAT
* ** *
11513804 ACCATGAAATGTGATTGGA
129 ACCATG-AA-GTTAAAGGG
11513823 AAGGTTGAGGCCGCAA
1 AAGGTTGAGGCCGCAA
11513839 TGGCGAACTC
Statistics
Matches: 135, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
144 4 0.03
145 65 0.48
146 3 0.02
147 40 0.30
148 14 0.10
149 9 0.07
ACGTcount: A:0.32, C:0.17, G:0.32, T:0.18
Consensus pattern (145 bp):
AAGGTTGAGGCCGCAACGGTGAACCCGGTACCTCAAAAGATGTGACGGGAAAGATTGAAGCCGCA
ACGACGAACCCAGTACCTAGAAGATGTGATGGGAAAGATTGAGACCGCAATAGCGAACCCAATAC
CATGAAGTTAAAGGG
Found at i:11514204 original size:41 final size:41
Alignment explanation
Indices: 11514120--11514209 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 41
11514110 TCATTCAGTA
* * *
11514120 TTTTACCCTTAATCAAGAAGGGCAGATTGAAGATTCTAATC
1 TTTTACCCTTAATCAAGAAGGACAGAATGAAGATTCCAATC
* **
11514161 TTTTACCCTTAATCAAGAAGGATAGAATGAAGATTCCGGTC
1 TTTTACCCTTAATCAAGAAGGACAGAATGAAGATTCCAATC
11514202 TTTTACCC
1 TTTTACCC
11514210 CGAGCCTGGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (41 bp):
TTTTACCCTTAATCAAGAAGGACAGAATGAAGATTCCAATC
Found at i:11514258 original size:39 final size:39
Alignment explanation
Indices: 11514204--11515074 Score: 396
Period size: 39 Copynumber: 22.3 Consensus size: 39
11514194 TTCCGGTCTT
*
11514204 TTACCCCGAGCCTGGGGTAGATCACCATCAGTCAATCTC
1 TTACCCCGAGCCTGGGGCAGATCACCATCAGTCAATCTC
* * *
11514243 TTACCCCGAGCCTGGGGCAGATTGA--AGTCA-TCCGATCTTT
1 TTACCCCGAGCCTGGGGCAGA-TCACCA-TCAGT-CAATC-TC
** * * * * *
11514283 TTACCCTAAGCTTGGGGTAGTTCACCAACAATCAATCTC
1 TTACCCCGAGCCTGGGGCAGATCACCATCAGTCAATCTC
* * * * *
11514322 TTACCCTGAGCCTGGGGTAGATTGAAGCCATC--T-GATCTT
1 TTACCCCGAGCCTGGGGCAGA-T-CA-CCATCAGTCAATCTC
* * * *
11514361 TTACCCCAAGCCTGGGGCAAATAATCATCA-TCTAATCTC
1 TTACCCCGAGCCTGGGGCAGATCACCATCAGTC-AATCTC
* * * *
11514400 TTACCCCGAGCCTGGGGTAGATTGCAGCA--ATTCGATCTC
1 TTACCCCGAGCCTGGGGCAGA-T-CACCATCAGTCAATCTC
* * * **
11514439 TTACCCCGAGCTTGGGGCGGATCATCATCAACCAATCTC
1 TTACCCCGAGCCTGGGGCAGATCACCATCAGTCAATCTC
** * * *
11514478 TTACCCCGAGCCTGGGGCAGAT-TGCAGTCATTCGATCTA
1 TTACCCCGAGCCTGGGGCAGATCACCA-TCAGTCAATCTC
* * *
11514517 TTACCTCGAGCCTAGGGTAGATCACCATCAGTCAATCTC
1 TTACCCCGAGCCTGGGGCAGATCACCATCAGTCAATCTC
* * * * * * * *
11514556 TTACCCCGAGCCTAGGGAAAATTA-AAGTCATTCGATCTT
1 TTACCCCGAGCCTGGGGCAGATCACCA-TCAGTCAATCTC
* * * * *
11514595 TTACCTCGAGCTTGGGGCAGATTATCATCAGCCAATCTC
1 TTACCCCGAGCCTGGGGCAGATCACCATCAGTCAATCTC
* ** ** * * *
11514634 TTACCCCGAGCTTTAGGCAGATTGCAATCATTCGATCTC
1 TTACCCCGAGCCTGGGGCAGATCACCATCAGTCAATCTC
* * * * * *
11514673 TTACCCCTAGCCTGAGACAAATCATCATCAGCCAATCTC
1 TTACCCCGAGCCTGGGGCAGATCACCATCAGTCAATCTC
* * * * * * * * * *
11514712 TTACCCCGAGCCTAGGGTAAATTACAACCATTCGATATT
1 TTACCCCGAGCCTGGGGCAGATCACCATCAGTCAATCTC
* * *
11514751 TTACCCCGAGCCTGGGGCAGATAGAAGCCATC---CGATCTT
1 TTACCCCGAGCCTGGGGCAGAT--CA-CCATCAGTCAATCTC
** * *
11514790 TTACCTTGAG-CTGGGGGCAGATCATCATCAGCCAATCTC
1 TTACCCCGAGCCT-GGGGCAGATCACCATCAGTCAATCTC
* * * * *
11514829 TTACCCCGAGCCTAGGGCAAATTGAAGCCATC---CGATCTT
1 TTACCCCGAGCCTGGGGCAGA-T-CA-CCATCAGTCAATCTC
* * * *
11514868 TTACCTCGAGCCTAGGGCAAATCACCATCAGCCAATCTC
1 TTACCCCGAGCCTGGGGCAGATCACCATCAGTCAATCTC
* * * * * * *
11514907 TTACCTCGAGCCTGGGGCAAATTA-TAGCCATTCGATCTC
1 TTACCCCGAGCCTGGGGCAGATCACCA-TCAGTCAATCTC
* * * **
11514946 TTACCCCGAGCTTGAGGCAAATCACCATCAACCAATCTC
1 TTACCCCGAGCCTGGGGCAGATCACCATCAGTCAATCTC
* * * * * * * *
11514985 TTACCCCGAGCCTAGGGCATATTACAACCATTCGATCTT
1 TTACCCCGAGCCTGGGGCAGATCACCATCAGTCAATCTC
* * *
11515024 TTACCCCGAG-CTTGGGCAGATCATCATCAGCCAATCTC
1 TTACCCCGAGCCTGGGGCAGATCACCATCAGTCAATCTC
*
11515062 TTACCTCGAGCCT
1 TTACCCCGAGCCT
11515075 AGGGTAAATT
Statistics
Matches: 621, Mismatches: 172, Indels: 78
0.71 0.20 0.09
Matches are distributed among these distances:
36 13 0.02
37 9 0.01
38 38 0.06
39 505 0.81
40 37 0.06
41 8 0.01
42 11 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (39 bp):
TTACCCCGAGCCTGGGGCAGATCACCATCAGTCAATCTC
Found at i:11514411 original size:78 final size:77
Alignment explanation
Indices: 11514200--11514772 Score: 551
Period size: 78 Copynumber: 7.3 Consensus size: 77
11514190 AAGATTCCGG
* *
11514200 TCTTTTACCCCGAGCCTGGGGTAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGCAGAT
1 TCTTTTACCCCGAGCCTGGGGCAGATCATCATCA-TCAATCTCTTACCCCGAGCCTGGGGCAGAT
*
11514265 TGAAGTCATCCGA
65 TGAAGTCATTCGA
** * * * * * * *
11514278 TCTTTTTACCCTAAGCTTGGGGTAGTTCACCAACAATCAATCTCTTACCCTGAGCCTGGGGTAGA
1 TC-TTTTACCCCGAGCCTGGGGCAGATCATCATC-ATCAATCTCTTACCCCGAGCCTGGGGCAGA
*
11514343 TTGAAGCCA-TCTGA
64 TTGAAGTCATTC-GA
* * * *
11514357 TCTTTTACCCCAAGCCTGGGGCAAATAATCATCATCTAATCTCTTACCCCGAGCCTGGGGTAGAT
1 TCTTTTACCCCGAGCCTGGGGCAGATCATCATCATC-AATCTCTTACCCCGAGCCTGGGGCAGAT
*
11514422 TGCAG-CAATTCGA
65 TGAAGTC-ATTCGA
* * * *
11514435 TCTCTTACCCCGAGCTTGGGGCGGATCATCATCAACCAATCTCTTACCCCGAGCCTGGGGCAGAT
1 TCTTTTACCCCGAGCCTGGGGCAGATCATCATC-ATCAATCTCTTACCCCGAGCCTGGGGCAGAT
*
11514500 TGCAGTCATTCGA
65 TGAAGTCATTCGA
* * * * * * * *
11514513 TCTATTACCTCGAGCCTAGGGTAGATCACCATCAGTCAATCTCTTACCCCGAGCCTAGGGAAAAT
1 TCTTTTACCCCGAGCCTGGGGCAGATCATCATCA-TCAATCTCTTACCCCGAGCCTGGGGCAGAT
*
11514578 TAAAGTCATTCGA
65 TGAAGTCATTCGA
* * * * * **
11514591 TCTTTTACCTCGAGCTTGGGGCAGATTATCATCAGCCAATCTCTTACCCCGAGCTTTAGGCAGAT
1 TCTTTTACCCCGAGCCTGGGGCAGATCATCATCA-TCAATCTCTTACCCCGAGCCTGGGGCAGAT
11514656 TGCAA-TCATTCGA
65 TG-AAGTCATTCGA
* * * * * * * * *
11514669 TCTCTTACCCCTAGCCTGAGACAAATCATCATCAGCCAATCTCTTACCCCGAGCCTAGGGTAAAT
1 TCTTTTACCCCGAGCCTGGGGCAGATCATCATCA-TCAATCTCTTACCCCGAGCCTGGGGCAGAT
**
11514734 T-ACAACCATTCGA
65 TGA-AGTCATTCGA
*
11514747 TATTTTACCCCGAGCCTGGGGCAGAT
1 TCTTTTACCCCGAGCCTGGGGCAGAT
11514773 AGAAGCCATC
Statistics
Matches: 410, Mismatches: 73, Indels: 24
0.81 0.14 0.05
Matches are distributed among these distances:
76 1 0.00
77 6 0.01
78 330 0.80
79 72 0.18
80 1 0.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (77 bp):
TCTTTTACCCCGAGCCTGGGGCAGATCATCATCATCAATCTCTTACCCCGAGCCTGGGGCAGATT
GAAGTCATTCGA
Found at i:11514529 original size:156 final size:156
Alignment explanation
Indices: 11514204--11514772 Score: 624
Period size: 156 Copynumber: 3.6 Consensus size: 156
11514194 TTCCGGTCTT
* * * * * *
11514204 TTACCCCGAGCCTGGGGTAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGCAGATTGAA
1 TTACCCCGAGCCTGGGGCAAATCACCATCAGTCAATCTCTTACCCCGAGCCTAGGGTAAATTAAA
* ** * * * * * *
11514269 GTCATCCGATCTTTTTACCCTAAGCTTGGGGTAGTTCACCAACAATCAATCTCTTACCCTGAGCC
66 GTCATTCGATC-TTTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCC
* * * *
11514334 TGGGGTAGATTGAAGCCA-TCTGATCTT
130 TGGGGCAGATTGCAGTCATTC-GATCTA
* * * * * **
11514361 TTACCCCAAGCCTGGGGCAAATAATCATCA-TCTAATCTCTTACCCCGAGCCTGGGGTAGATTGC
1 TTACCCCGAGCCTGGGGCAAATCACCATCAGTC-AATCTCTTACCCCGAGCCTAGGGTAAATTAA
* *
11514425 AG-CAATTCGATCTCTTACCCCGAGCTTGGGGCGGATCATCATCAACCAATCTCTTACCCCGAGC
65 AGTC-ATTCGATCTTTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGC
11514489 CTGGGGCAGATTGCAGTCATTCGATCTA
129 CTGGGGCAGATTGCAGTCATTCGATCTA
* * * * *
11514517 TTACCTCGAGCCTAGGGTAGATCACCATCAGTCAATCTCTTACCCCGAGCCTAGGGAAAATTAAA
1 TTACCCCGAGCCTGGGGCAAATCACCATCAGTCAATCTCTTACCCCGAGCCTAGGGTAAATTAAA
* * * *
11514582 GTCATTCGATCTTTTACCTCGAGCTTGGGGCAGATTATCATCAGCCAATCTCTTACCCCGAGCTT
66 GTCATTCGATCTTTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCT
** * *
11514647 TAGGCAGATTGCAATCATTCGATCTC
131 GGGGCAGATTGCAGTCATTCGATCTA
* * * * *
11514673 TTACCCCTAGCCTGAGACAAATCATCATCAGCCAATCTCTTACCCCGAGCCTAGGGTAAATTACA
1 TTACCCCGAGCCTGGGGCAAATCACCATCAGTCAATCTCTTACCCCGAGCCTAGGGTAAATTA-A
* * *
11514738 A-CCATTCGATATTTTACCCCGAGCCTGGGGCAGAT
65 AGTCATTCGATCTTTTACCCCGAGCTTGGGGCAGAT
11514773 AGAAGCCATC
Statistics
Matches: 348, Mismatches: 58, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
156 278 0.80
157 70 0.20
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (156 bp):
TTACCCCGAGCCTGGGGCAAATCACCATCAGTCAATCTCTTACCCCGAGCCTAGGGTAAATTAAA
GTCATTCGATCTTTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCT
GGGGCAGATTGCAGTCATTCGATCTA
Found at i:11514794 original size:78 final size:77
Alignment explanation
Indices: 11514707--11515116 Score: 346
Period size: 78 Copynumber: 5.3 Consensus size: 77
11514697 TCATCAGCCA
* * * ** * * * *
11514707 ATCTCTTACCCCGAGCCTAGGGTAAATTACAACCATTCGATATTTTACCCCGAGCCTGGGGCAGA
1 ATCTCTTACCCCGAGCCTAGGGCAAATCAC-ATCAGCCAATCTCTTACCCCGAGCCTGGGGCAAA
11514772 TAGAAGCCATCCG
65 TAGAAGCCATCCG
* ** * * *
11514785 ATCTTTTACCTTGAG-CTGGGGGCAGATCATCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAA
1 ATCTCTTACCCCGAGCCT-AGGGCAAATCA-CATCAGCCAATCTCTTACCCCGAGCCTGGGGCAA
*
11514849 ATTGAAGCCATCCG
64 ATAGAAGCCATCCG
* * *
11514863 ATCTTTTACCTCGAGCCTAGGGCAAATCACCATCAGCCAATCTCTTACCTCGAGCCTGGGGCAAA
1 ATCTCTTACCCCGAGCCTAGGGCAAATCA-CATCAGCCAATCTCTTACCCCGAGCCTGGGGCAAA
* *
11514928 TTA-TAGCCATTCG
65 -TAGAAGCCATCCG
* * *
11514941 ATCTCTTACCCCGAG-CTTGAGGCAAATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGCAT
1 ATCTCTTACCCCGAGCCTAG-GGCAAATCA-CATCAGCCAATCTCTTACCCCGAGCCTGGGGCA-
* * *
11515005 ATTACAA-CCATTCG
63 AATAGAAGCCATCCG
* * * * * *
11515019 ATCTTTTACCCCGAG-CTTGGGCAGATCATCATCAGCCAATCTCTTACCTCGAGCCTAGGGTAAA
1 ATCTCTTACCCCGAGCCTAGGGCAAATCA-CATCAGCCAATCTCTTACCCCGAGCCTGGGGCAAA
* * * *
11515083 TTGCAGTCATTCG
65 TAGAAGCCATCCG
* *
11515096 ATCTTTTACTCCGAGCC-AGGG
1 ATCTCTTACCCCGAGCCTAGGG
11515117 TCAGATTGCA
Statistics
Matches: 277, Mismatches: 46, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
76 3 0.01
77 66 0.24
78 202 0.73
79 6 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (77 bp):
ATCTCTTACCCCGAGCCTAGGGCAAATCACATCAGCCAATCTCTTACCCCGAGCCTGGGGCAAAT
AGAAGCCATCCG
Found at i:11514850 original size:156 final size:155
Alignment explanation
Indices: 11514204--11515003 Score: 522
Period size: 156 Copynumber: 5.1 Consensus size: 155
11514194 TTCCGGTCTT
* * * * * * * *
11514204 TTACCCCGAGCCTGGGGTAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGCAGATTGA-
1 TTACCCCGAGCCTAGGGCAAATCATCATCAGCCAATCTCTTACCCCGAGCCTAGGGTAAATT-AC
** * * ** * * * * *
11514268 AGTCATCCGATCTTTTTACCCTAAGCTTGGGGTAG-TTCACCAACAAT-CAATCTCTTACCCTGA
65 AACCATTCGATC-TCTTACCCCGAGCCTGGGGCAGATT-ATC-ACCATCCAATCTCTTACCCCGA
* * * * * ** *
11514331 GCCTGGGGTAGATTGAAGCCATCTGATCTT
127 GCTTGAGGCAGATTGCA-TCATCCAATCTC
* * * * * * * *
11514361 TTACCCCAAGCCTGGGGCAAATAATCATCATCTAATCTCTTACCCCGAGCCTGGGGTAGATTGCA
1 TTACCCCGAGCCTAGGGCAAATCATCATCAGCCAATCTCTTACCCCGAGCCTAGGGTAAATTACA
* * * * * * * *
11514426 GCAATTCGATCTCTTACCCCGAGCTTGGGGCGGATCATCATCAACCAATCTCTTACCCCGAGCCT
66 ACCATTCGATCTCTTACCCCGAGCCTGGGGCAGATTATCACCATCCAATCTCTTACCCCGAGCTT
* * * *
11514491 GGGGCAGATTGCAGTCATTCGATCTA
131 GAGGCAGATTGCA-TCATCCAATCTC
* * * * * *
11514517 TTACCTCGAGCCTAGGGTAGATCACCATCAGTCAATCTCTTACCCCGAGCCTAGGGAAAATTA-A
1 TTACCCCGAGCCTAGGGCAAATCATCATCAGCCAATCTCTTACCCCGAGCCTAGGGTAAATTACA
* * * * * *
11514581 AGTCATTCGATCTTTTACCTCGAGCTTGGGGCAGATTATCATCAGCCAATCTCTTACCCCGAGCT
66 A-CCATTCGATCTCTTACCCCGAGCCTGGGGCAGATTATCACCATCCAATCTCTTACCCCGAGCT
* * *
11514646 TTAGGCAGATTGCAATCATTCGATCTC
130 TGAGGCAGATTGC-ATCATCCAATCTC
* *
11514673 TTACCCCTAGCCT-GAGACAAATCATCATCAGCCAATCTCTTACCCCGAGCCTAGGGTAAATTAC
1 TTACCCCGAGCCTAG-GGCAAATCATCATCAGCCAATCTCTTACCCCGAGCCTAGGGTAAATTAC
* * ** * * **
11514737 AACCATTCGATATTTTACCCCGAGCCTGGGGCAGA-TAGAAGCCATCCGATCTTTTACCTTGAGC
65 AACCATTCGATCTCTTACCCCGAGCCTGGGGCAGATTATCA-CCATCCAATCTCTTACCCCGAGC
* * *
11514801 TGGGGGCAGATCAT-CATCAGCCAATCTC
129 TTGAGGCAGAT--TGCATCATCCAATCTC
* * * * * * * *
11514829 TTACCCCGAGCCTAGGGCAAAT--TGAAGCCATCCGATCTTTTACCTCGAGCCTAGGGCAAATCA
1 TTACCCCGAGCCTAGGGCAAATCAT-CA-TCAGCCAATCTCTTACCCCGAGCCTAGGGTAAATTA
* * ** * * * * *
11514892 CCATCAGCCAATCTCTTACCTCGAGCCTGGGGCAAATTAT-AGCCATTCGATCTCTTACCCCGAG
64 CAACCATTCGATCTCTTACCCCGAGCCTGGGGCAGATTATCA-CCATCCAATCTCTTACCCCGAG
* ** *
11514956 CTTGAGGCAAATCACCATCAACCAATCTC
128 CTTGAGGCAGAT-TGCATCATCCAATCTC
11514985 TTACCCCGAGCCTAGGGCA
1 TTACCCCGAGCCTAGGGCA
11515004 TATTACAACC
Statistics
Matches: 516, Mismatches: 112, Indels: 31
0.78 0.17 0.05
Matches are distributed among these distances:
154 1 0.00
155 8 0.02
156 436 0.84
157 70 0.14
158 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (155 bp):
TTACCCCGAGCCTAGGGCAAATCATCATCAGCCAATCTCTTACCCCGAGCCTAGGGTAAATTACA
ACCATTCGATCTCTTACCCCGAGCCTGGGGCAGATTATCACCATCCAATCTCTTACCCCGAGCTT
GAGGCAGATTGCATCATCCAATCTC
Found at i:11515021 original size:156 final size:155
Alignment explanation
Indices: 11514751--11515111 Score: 456
Period size: 156 Copynumber: 2.3 Consensus size: 155
11514741 ATTCGATATT
* * * ** * * *
11514751 TTACCCCGAGCCTGGGGCAGA-TAGAAGCCATCCGATCTTTTACCTTGAGCTGGGGGCAGATCAT
1 TTACCTCGAGCCTGGGGCAAATTA-AAGCCATTCGATCTTTTACCCCGAGCTGGAGGCAAATCAC
* * *
11514815 CATCAGCCAATCTCTTACCCCGAGCCTAGGGCAAATTGAAGCCATCCGATCTTTTACCTCGAGCC
65 CATCAACCAATCTCTTACCCCGAGCCTAGGGCAAATTGAAACCATCCGATCTTTTACCCCGAG-C
11514880 TAGGGCAAATCACCATCAGCCAATCTC
129 TAGGGCAAATCACCATCAGCCAATCTC
* * *
11514907 TTACCTCGAGCCTGGGGCAAATTATAGCCATTCGATCTCTTACCCCGAGCTTGAGGCAAATCACC
1 TTACCTCGAGCCTGGGGCAAATTAAAGCCATTCGATCTTTTACCCCGAGCTGGAGGCAAATCACC
* *
11514972 ATCAACCAATCTCTTACCCCGAGCCTAGGGCATATT-ACAACCATTCGATCTTTTACCCCGAGCT
66 ATCAACCAATCTCTTACCCCGAGCCTAGGGCAAATTGA-AACCATCCGATCTTTTACCCCGAGCT
* * *
11515036 TGGGCAGATCATCATCAGCCAATCTC
130 AGGGCAAATCACCATCAGCCAATCTC
* * ** * *
11515062 TTACCTCGAGCCTAGGGTAAATTGCAGTCATTCGATCTTTTACTCCGAGC
1 TTACCTCGAGCCTGGGGCAAATTAAAGCCATTCGATCTTTTACCCCGAGC
11515112 CAGGGTCAGA
Statistics
Matches: 177, Mismatches: 26, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
155 69 0.39
156 106 0.60
157 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (155 bp):
TTACCTCGAGCCTGGGGCAAATTAAAGCCATTCGATCTTTTACCCCGAGCTGGAGGCAAATCACC
ATCAACCAATCTCTTACCCCGAGCCTAGGGCAAATTGAAACCATCCGATCTTTTACCCCGAGCTA
GGGCAAATCACCATCAGCCAATCTC
Found at i:11517075 original size:29 final size:30
Alignment explanation
Indices: 11517037--11517241 Score: 211
Period size: 30 Copynumber: 6.9 Consensus size: 30
11517027 GTTCTCTTTA
* *
11517037 AAAATCACATTTTGACCTTTAAACTTTT-C
1 AAAATTACATTTTGACCCTTAAACTTTTCC
* * **
11517066 AAAATTACATTTTAACTCTCGAACTTTTCC
1 AAAATTACATTTTGACCCTTAAACTTTTCC
*
11517096 AAAATTACATTTTGA-CCTTAAAATTTTCCC
1 AAAATTACATTTTGACCCTTAAACTTTT-CC
11517126 AAAATTACATTTTGACCCTTAAACTTTTCC
1 AAAATTACATTTTGACCCTTAAACTTTTCC
* * * **
11517156 AAAATTACATTTTAACCCCT-AATTTTTTT
1 AAAATTACATTTTGACCCTTAAACTTTTCC
* * * *
11517185 AAAATTTCATTTTAACCCCTAAACTTTTCA
1 AAAATTACATTTTGACCCTTAAACTTTTCC
*
11517215 AAAATTACATTTTTG-CCCTTAGACTTT
1 AAAATTACA-TTTTGACCCTTAAACTTT
11517242 CAAAAAACAT
Statistics
Matches: 146, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
29 55 0.38
30 76 0.52
31 15 0.10
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTTAAACTTTTCC
Found at i:11517189 original size:89 final size:89
Alignment explanation
Indices: 11517036--11517246 Score: 250
Period size: 89 Copynumber: 2.4 Consensus size: 89
11517026 TGTTCTCTTT
* * *
11517036 AAAAATCACATTTTGACCTTTAAACTTTTCAAAATTACATTTTAACTCTCGAACTTTTCCAAAAT
1 AAAAATTACATTTTGACCCTTAAACTTTTCAAAATTACATTTTAACTCCCGAACTTTTCCAAAAT
* *
11517101 TACATTTTGA-CCTTAAAATTTTCC
66 TACATTTTAACCCCTAAAATTTT-C
* * * **
11517125 CAAAATTACATTTTGACCCTTAAACTTTTCCAAAATTACATTTTAAC-CCCTAATTTTTTTAAAA
1 AAAAATTACATTTTGACCCTTAAACTTTT-CAAAATTACATTTTAACTCCCGAACTTTTCCAAAA
* *
11517189 TTTCATTTTAACCCCTAAACTTTTC
65 TTACATTTTAACCCCTAAAATTTTC
*
11517214 AAAAATTACATTTTTG-CCCTTAGAC-TTTCAAAA
1 AAAAATTACA-TTTTGACCCTTAAACTTTTCAAAA
11517247 AACATATTTT
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
87 5 0.05
88 3 0.03
89 65 0.62
90 32 0.30
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.41
Consensus pattern (89 bp):
AAAAATTACATTTTGACCCTTAAACTTTTCAAAATTACATTTTAACTCCCGAACTTTTCCAAAAT
TACATTTTAACCCCTAAAATTTTC
Found at i:11517332 original size:57 final size:58
Alignment explanation
Indices: 11517201--11517382 Score: 208
Period size: 57 Copynumber: 3.2 Consensus size: 58
11517191 TCATTTTAAC
* * * * *
11517201 CCCTAAACTTTTCAAAAATTACATTTTTGCCCTTAGACTTTCAAAAAACATATTTTTA
1 CCCTAAACTTCTCAAAAATTACATTTTTGCCCTCAAACTTCCAAAAATCATATTTTTA
* ** * * *
11517259 CCCCTAATCTTC-CAAAAATTACA-TTTCACCCTCGAACTTCCAAAAATCACATTTTTG
1 -CCCTAAACTTCTCAAAAATTACATTTTTGCCCTCAAACTTCCAAAAATCATATTTTTA
* *
11517316 CCCAAAACTTCTCAAAAATAACATTTTTGCCC-CAAACTTCTCAAAAATCATATTTTTA
1 CCCTAAACTTCTCAAAAATTACATTTTTGCCCTCAAACTTC-CAAAAATCATATTTTTA
11517374 CCCTAAACT
1 CCCTAAACT
11517383 CTTCCAGACT
Statistics
Matches: 100, Mismatches: 20, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
56 9 0.09
57 42 0.42
58 40 0.40
59 9 0.09
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (58 bp):
CCCTAAACTTCTCAAAAATTACATTTTTGCCCTCAAACTTCCAAAAATCATATTTTTA
Found at i:11517435 original size:30 final size:29
Alignment explanation
Indices: 11517032--11517440 Score: 201
Period size: 29 Copynumber: 14.1 Consensus size: 29
11517022 CCTCTGTTCT
* * **
11517032 CTTT-AAAAATCACATTTTGACCTTTAAA
1 CTTTCAAAAATTACATTTTAACCCCTAAA
* *
11517060 CTTTTC-AAAATTACATTTTAA-CTCTCGAA
1 C-TTTCAAAAATTACATTTTAACCCCT-AAA
* * *
11517089 CTTTTCCAAAATTACATTTTGA-CCTTAAAA
1 C-TTTCAAAAATTACATTTTAACCCCT-AAA
* * * *
11517119 TTTTCCCAAAATTACATTTTGACCCTTAAA
1 CTTT-CAAAAATTACATTTTAACCCCTAAA
* *
11517149 CTTTTCCAAAATTACATTTTAACCCCTAAT
1 C-TTTCAAAAATTACATTTTAACCCCTAAA
* ** *
11517179 TTTTTTAAAATTTCATTTTAACCCCTAAA
1 CTTTCAAAAATTACATTTTAACCCCTAAA
** * *
11517208 CTTTTCAAAAATTACATTTTTGCCCTTAGA
1 C-TTTCAAAAATTACATTTTAACCCCTAAA
** * * *
11517238 CTTTCAAAAAACATATTTTTACCCCTAAT
1 CTTTCAAAAATTACATTTTAACCCCTAAA
* * *
11517267 CTTCCAAAAATTACA-TTTCA-CCCTCGAA
1 CTTTCAAAAATTACATTTTAACCCCT-AAA
* * ** *
11517295 CTTCCAAAAATCACATTTT-TGCCCAAAA
1 CTTTCAAAAATTACATTTTAACCCCTAAA
* **
11517323 CTTCTCAAAAATAACATTTTTGCCCC-AAA
1 CTT-TCAAAAATTACATTTTAACCCCTAAA
* * *
11517352 CTTCTCAAAAATCATATTTTTA-CCCTAAA
1 CTT-TCAAAAATTACATTTTAACCCCTAAA
* * * * *
11517381 CTCTTCCAGACTGAC-TTTTTACCCCTAAAA
1 CT-TTCAAAAATTACATTTTAACCCCT-AAA
*
11517411 CTTTCTAAAATTACATTTTAACCCC-AAA
1 CTTTCAAAAATTACATTTTAACCCCTAAA
11517439 CT
1 CT
11517441 CTCCGAATCT
Statistics
Matches: 301, Mismatches: 62, Indels: 36
0.75 0.16 0.09
Matches are distributed among these distances:
27 4 0.01
28 42 0.14
29 148 0.49
30 100 0.33
31 7 0.02
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
CTTTCAAAAATTACATTTTAACCCCTAAA
Found at i:11517591 original size:14 final size:14
Alignment explanation
Indices: 11517563--11517613 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
11517553 TCATAATTCG
*
11517563 TATTT-TTTTCTTA
1 TATTTATTTTCGTA
11517576 TATTTATTTTCGTA
1 TATTTATTTTCGTA
11517590 TATTTATTCATTCGTA
1 TATTTATT--TTCGTA
*
11517606 TAATTATT
1 TATTTATT
11517614 CACGCTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
13 5 0.15
14 15 0.45
16 13 0.39
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.65
Consensus pattern (14 bp):
TATTTATTTTCGTA
Found at i:11517603 original size:16 final size:16
Alignment explanation
Indices: 11517574--11517615 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
11517564 ATTTTTTTCT
11517574 TATATTTATT--TTCG
1 TATATTTATTCATTCG
11517588 TATATTTATTCATTCG
1 TATATTTATTCATTCG
*
11517604 TATAATTATTCA
1 TATATTTATTCA
11517616 CGCTTTGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 10 0.40
16 15 0.60
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.57
Consensus pattern (16 bp):
TATATTTATTCATTCG
Found at i:11518895 original size:42 final size:41
Alignment explanation
Indices: 11518810--11518937 Score: 132
Period size: 41 Copynumber: 3.1 Consensus size: 41
11518800 GTTTATGTGA
* * * * * *
11518810 AAACGCCACTATTGCTTAACCTTTAGCGGTGTTTTTCTCAT
1 AAACACCACTATTTCTTTACCTTTTGCGGCGTTTTTCCCAT
*
11518851 AAACACCATTAATTCTCTTTACCTTTTGCGGCG-TTTTCCCAT
1 AAACACCACT-ATT-TCTTTACCTTTTGCGGCGTTTTTCCCAT
** * *
11518893 AAACACTGCTATTTCTTTACCTTTTGCGACGTTTTTGCCAT
1 AAACACCACTATTTCTTTACCTTTTGCGGCGTTTTTCCCAT
11518934 AAAC
1 AAAC
11518938 TCCGATATTG
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
40 17 0.24
41 23 0.32
42 18 0.25
43 14 0.19
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.40
Consensus pattern (41 bp):
AAACACCACTATTTCTTTACCTTTTGCGGCGTTTTTCCCAT
Found at i:11518957 original size:40 final size:40
Alignment explanation
Indices: 11518867--11518957 Score: 112
Period size: 41 Copynumber: 2.3 Consensus size: 40
11518857 CATTAATTCT
* * * *
11518867 CTTTACCTTTTGCGGCGTTTTCCCATAAACACTGCTATTT
1 CTTTACCTTTTGCGACGTTTTCCCATAAACACCGATATTG
* *
11518907 CTTTACCTTTTGCGACGTTTTTGCCATAAACTCCGATATTG
1 CTTTACCTTTTGCGACG-TTTTCCCATAAACACCGATATTG
11518948 CTTTA-CTTTT
1 CTTTACCTTTT
11518958 ACAGTGTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
40 21 0.48
41 23 0.52
ACGTcount: A:0.18, C:0.25, G:0.12, T:0.45
Consensus pattern (40 bp):
CTTTACCTTTTGCGACGTTTTCCCATAAACACCGATATTG
Found at i:11520762 original size:40 final size:40
Alignment explanation
Indices: 11520718--11520815 Score: 153
Period size: 40 Copynumber: 2.5 Consensus size: 40
11520708 TAAAATGCCA
*
11520718 CTATTGCTTTACCTTTTGTGGCATTTTT-CCATAAACGCTC
1 CTATTGCTTTACCTTTTGTGGC-TTTTTCCCATAAACGCAC
* *
11520758 CTATTGCTTTACCTTTTGTGGCTTTTTCCCATAAATGCAG
1 CTATTGCTTTACCTTTTGTGGCTTTTTCCCATAAACGCAC
11520798 CTATTGCTTTACCTTTTG
1 CTATTGCTTTACCTTTTG
11520816 CAATGTTTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 5 0.09
40 49 0.91
ACGTcount: A:0.16, C:0.23, G:0.13, T:0.47
Consensus pattern (40 bp):
CTATTGCTTTACCTTTTGTGGCTTTTTCCCATAAACGCAC
Found at i:11522197 original size:72 final size:72
Alignment explanation
Indices: 11522090--11522353 Score: 397
Period size: 72 Copynumber: 3.7 Consensus size: 72
11522080 AACAAATTTT
* * *
11522090 ATATCC-AAAATCAAATACAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
11522154 AAATTCA
66 AAATTCA
** * *
11522161 ATATTTAAAAACCAAACATAAACAACTATTGTTAAAACGAGATTACACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
11522226 AAATTCA
66 AAATTCA
* * *
11522233 ATATCCAAAAACCAAACATAAACAACTATTAATAAAACTGGATTACTCATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
*
11522298 AAATTTA
66 AAATTCA
* *
11522305 ATATCCAAAAACCAAACATAAACAACTAATGATAAAACTAGTTTA-ACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACAT
11522354 TGTTGTTTAG
Statistics
Matches: 172, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
71 7 0.04
72 165 0.96
ACGTcount: A:0.55, C:0.16, G:0.06, T:0.24
Consensus pattern (72 bp):
ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
AAATTCA
Found at i:11524617 original size:25 final size:25
Alignment explanation
Indices: 11524580--11524628 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
11524570 AAGTATTTCA
* *
11524580 TTAATAAATTGGGTTTATTAAATTG
1 TTAATAAAGTGGGTTAATTAAATTG
* *
11524605 TTAATTAAGTGGGTTAATTTAATT
1 TTAATAAAGTGGGTTAATTAAATT
11524629 ACTTTGACCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (25 bp):
TTAATAAAGTGGGTTAATTAAATTG
Found at i:11535345 original size:24 final size:24
Alignment explanation
Indices: 11535291--11535348 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 24
11535281 GTGGGCCATG
11535291 CATAAATTA-ATTAAATATTAAAA
1 CATAAATTATATTAAATATTAAAA
11535314 CATAAAATTATATTAAATAATT-AAA
1 CAT-AAATTATATTAAAT-ATTAAAA
11535339 CATAAATTAT
1 CATAAATTAT
11535349 TTCATTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 3 0.09
24 13 0.41
25 13 0.41
26 3 0.09
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (24 bp):
CATAAATTATATTAAATATTAAAA
Found at i:11536261 original size:21 final size:21
Alignment explanation
Indices: 11536237--11536278 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11536227 CATCTTAACC
11536237 CGATTAAATTGCAGGATTCAT
1 CGATTAAATTGCAGGATTCAT
*
11536258 CGATTAAATTGTAGGATTCAT
1 CGATTAAATTGCAGGATTCAT
11536279 AACAACTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (21 bp):
CGATTAAATTGCAGGATTCAT
Found at i:11541923 original size:386 final size:386
Alignment explanation
Indices: 11541210--11541985 Score: 1480
Period size: 386 Copynumber: 2.0 Consensus size: 386
11541200 AGAAAATGTG
11541210 TTTTGTGTAATATGTTATATACCTACATGTTAATGTGAAATATGCTTAAAGGCTAATGAGATTAT
1 TTTTGTGTAATATGTTATATACCTACATGTTAATGTGAAATATGCTTAAAGGCTAATGAGATTAT
*
11541275 TATGTGAATGAACTACTAAGTTATGCATGAGTTGATGTAACATGACACTAAAGATGAGACTGCTG
66 TATGTGAATGAACTACTAAGTTATGCATGAGTTGATGTAACATGACACTAAAGATGAGACTGATG
11541340 TAACTAATTTATTCAATTATTGATAATGCATGATGACTTGTTTGCGTGGTAGTTATTCTAAGCAT
131 TAACTAATTTATTCAATTATTGATAATGCATGATGACTTGTTTGCGTGGTAGTTATTCTAAGCAT
* *
11541405 TCACTGAGCTTGTTTAAGCTCATCCACTCCTTTTAAACCATTGTAGATCAGTAGTAACGGTGTGA
196 TCACTGAGCTTGTTTAAGCTCACCCACTCCTTTTAAACCATTGCAGATCAGTAGTAACGGTGTGA
11541470 GCGATGTGATATCCGAGGGGTGATCCAAGCCAAAAAACTTTAGTAGTCATTCATAGGTGTTTATT
261 GCGATGTGATATCCGAGGGGTGATCCAAGCCAAAAAACTTTAGTAGTCATTCATAGGTGTTTATT
11541535 TGATTATTTATGTTTTGGGAATAAAGACAATGTGGTAGACTTTATGTTAGTTATGCTATGA
326 TGATTATTTATGTTTTGGGAATAAAGACAATGTGGTAGACTTTATGTTAGTTATGCTATGA
11541596 TTTTGTGTAATATGTTATATACCTACATGTTAATGTGAAATATGCTTAAAGGCTAATGAGATTAT
1 TTTTGTGTAATATGTTATATACCTACATGTTAATGTGAAATATGCTTAAAGGCTAATGAGATTAT
11541661 TATGTGAATGAACTACTAAGTTATGCATGAGTTGATGTAACATGACACTAAAGATGAGACTGATG
66 TATGTGAATGAACTACTAAGTTATGCATGAGTTGATGTAACATGACACTAAAGATGAGACTGATG
* *
11541726 TAACTAATTTATTCACTTATTGATAATGCATGATGACTTGTTTGCGTGGTAGTTATTCTGAGCAT
131 TAACTAATTTATTCAATTATTGATAATGCATGATGACTTGTTTGCGTGGTAGTTATTCTAAGCAT
**
11541791 TCACTGAGCTTGTTTAAGCTCACCCACTGTTTTTAAACCATTGCAGATCAGTAGTAACGGTGTGA
196 TCACTGAGCTTGTTTAAGCTCACCCACTCCTTTTAAACCATTGCAGATCAGTAGTAACGGTGTGA
*
11541856 GCGATGTGATATCCGAGGGGTGATCCAAGCCAAAAAATTTTAGTAGTCATTCATAGGTGTTTATT
261 GCGATGTGATATCCGAGGGGTGATCCAAGCCAAAAAACTTTAGTAGTCATTCATAGGTGTTTATT
11541921 TGATTATTTATGTTTTGGGAATAAAGACAATGTGGTAGACTTTATGTTAGTTATGCTATGA
326 TGATTATTTATGTTTTGGGAATAAAGACAATGTGGTAGACTTTATGTTAGTTATGCTATGA
11541982 TTTT
1 TTTT
11541986 AAGTTATTTA
Statistics
Matches: 382, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
386 382 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (386 bp):
TTTTGTGTAATATGTTATATACCTACATGTTAATGTGAAATATGCTTAAAGGCTAATGAGATTAT
TATGTGAATGAACTACTAAGTTATGCATGAGTTGATGTAACATGACACTAAAGATGAGACTGATG
TAACTAATTTATTCAATTATTGATAATGCATGATGACTTGTTTGCGTGGTAGTTATTCTAAGCAT
TCACTGAGCTTGTTTAAGCTCACCCACTCCTTTTAAACCATTGCAGATCAGTAGTAACGGTGTGA
GCGATGTGATATCCGAGGGGTGATCCAAGCCAAAAAACTTTAGTAGTCATTCATAGGTGTTTATT
TGATTATTTATGTTTTGGGAATAAAGACAATGTGGTAGACTTTATGTTAGTTATGCTATGA
Found at i:11548552 original size:88 final size:88
Alignment explanation
Indices: 11548414--11548682 Score: 367
Period size: 88 Copynumber: 3.0 Consensus size: 88
11548404 TTAAATTAAT
* * *
11548414 AAGTTCGGAGTTCAATTAAAAAAAAAAGTACTAATTTCAAGTATAAAGGTGAAAAGGAAAATTAC
1 AAGTTCGGAGTTCAATTGAAAAAAAAAGTACTGATTTCAAGTATAAAGGTGAAAAGAAAAATTAC
*
11548479 CATTTGAAATCCAAATTAAGTAC
66 CATTTGAACTCCAAATTAAGTAC
* * * *
11548502 AAGTTCGGACTTCAATTGAAAAAAAAAGTATTGATATCAAGTATAAAGGTGAAAAGAAAAATAAC
1 AAGTTCGGAGTTCAATTGAAAAAAAAAGTACTGATTTCAAGTATAAAGGTGAAAAGAAAAATTAC
* * *
11548567 TATTTGATCTCCAAATTAAGTAT
66 CATTTGAACTCCAAATTAAGTAC
*
11548590 AAGTTCGGAGTTTAATTGAAAAATAAAAGAATACTGATTTCAAGTATAAAGGTGAAAAGAAAAAT
1 AAGTTCGGAGTTCAATTGAAAAA-AAAAG--TACTGATTTCAAGTATAAAGGTGAAAAGAAAAAT
* * * *
11548655 TATCATTTTAACTCTAAATTAAATAC
63 TACCATTTGAACTCCAAATTAAGTAC
11548681 AA
1 AA
11548683 CTAGGTTAAA
Statistics
Matches: 155, Mismatches: 23, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
88 98 0.63
89 5 0.03
91 52 0.34
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (88 bp):
AAGTTCGGAGTTCAATTGAAAAAAAAAGTACTGATTTCAAGTATAAAGGTGAAAAGAAAAATTAC
CATTTGAACTCCAAATTAAGTAC
Found at i:11551387 original size:24 final size:24
Alignment explanation
Indices: 11551355--11551402 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
11551345 AAATCTAGGT
11551355 ACATATAAGCATGTGAAGTGATAA
1 ACATATAAGCATGTGAAGTGATAA
*
11551379 ACATATAAGCATGTGATGTGATAA
1 ACATATAAGCATGTGAAGTGATAA
11551403 GTAAATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (24 bp):
ACATATAAGCATGTGAAGTGATAA
Found at i:11564881 original size:49 final size:48
Alignment explanation
Indices: 11564758--11564889 Score: 126
Period size: 50 Copynumber: 2.7 Consensus size: 48
11564748 TCTGATACCC
* * **
11564758 TGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCATGTACCT
1 TGAAGATATGAAGGGAAAGGTTGAGGCCACAACGACAAACCATG-ACAA
* * *
11564807 TAGAAGATGT-AATGGG-AAGGATTGAGGCCACAATGGCAAATCCGATG-CAA
1 T-GAAGATATGAA-GGGAAAGG-TTGAGGCCACAACGACAAA-CC-ATGACAA
11564857 TGAAGATATGAAGGGAAAGGTTGAGGCCACAAC
1 TGAAGATATGAAGGGAAAGGTTGAGGCCACAAC
11564890 AGCGAACCCT
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
49 29 0.43
50 33 0.49
51 2 0.03
52 3 0.04
ACGTcount: A:0.37, C:0.15, G:0.31, T:0.17
Consensus pattern (48 bp):
TGAAGATATGAAGGGAAAGGTTGAGGCCACAACGACAAACCATGACAA
Found at i:11564903 original size:99 final size:98
Alignment explanation
Indices: 11564722--11565383 Score: 396
Period size: 99 Copynumber: 6.7 Consensus size: 98
11564712 AGGTTTGAAA
** * * * **
11564722 GGGAA-GATTGAGGCCGTAACGGCGAATCTGATACCCTGAAGATATGAAGGGAAAGGTTGAGGCC
1 GGGAAGGATTGAGGCCACAACGGCAAATCCGACACAATGAAGATATGAAGGGAAAGGTTGAGGCC
* *
11564786 GCAACGACGAACCATGTACCTTAGAAGATGTAAT
66 GCAACG-CGAACCCTGTACCTTAGAAGATGTGAT
* **
11564820 GGGAAGGATTGAGGCCACAATGGCAAATCCGATGCAATGAAGATATGAAGGGAAAGGTTGAGGCC
1 GGGAAGGATTGAGGCCACAACGGCAAATCCGACACAATGAAGATATGAAGGGAAAGGTTGAGGCC
*
11564885 ACAACAGCGAACCCTGTACCTTAGAAGATGTGAT
66 GCAAC-GCGAACCCTGTACCTTAGAAGATGTGAT
* * * ** * * * *
11564919 GGGAAGGATTGAAGTCGCAACGGTGAATCTGACACCATGAAGATATGAAAGGAAAGGATGAGGCC
1 GGGAAGGATTGAGGCCACAACGGCAAATCCGACACAATGAAGATATGAAGGGAAAGGTTGAGGCC
11564984 GCAACTGCGAACCC-GATACCTTAGAAGATGTGAT
66 GCAAC-GCGAACCCTG-TACCTTAGAAGATGTGAT
* *** * ** * * *
11565018 GGGAAGGATCGAGGCTGTAACGACGGATCTAGTA-TC-ATGGAA-ATATAAAGGAGAAAGGTTGA
1 GGGAAGGATTGAGGCCACAACGGCAAATC-CG-ACACAAT-GAAGATATGAAGG-GAAAGGTTGA
* * * **
11565080 GGCTGCAACGACGAACCTTGTACCCTAGAA-ACATGAT
62 GGCCGCAACG-CGAACCCTGTACCTTAGAAGATGTGAT
* ** ** ** * ** * *
11565117 GGGAAGGATTGAGGCCATAACGGTGAATTTGGTACTATGAAGATATGAAGGGAAAAATTAAGGTC
1 GGGAAGGATTGAGGCCACAACGGCAAATCCGACACAATGAAGATATGAAGGGAAAGGTTGAGGCC
* * * *
11565182 GTAAAGGTGAACCC-GATACCTCAGAAGATGTGAT
66 G-CAACGCGAACCCTG-TACCTTAGAAGATGTGAT
* * * * * ** * * *
11565216 GGAAAGGATCGAGGTCGCAACGACGGAT-CTAGTACAATGGAA-ATATAAAGGGGAAAGGTTGAG
1 GGGAAGGATTGAGGCCACAACGGCAAATCCGA-CACAAT-GAAGATATGAA-GGGAAAGGTTGAG
* * * * **
11565279 GCCGCAACGATGAACCTTGTACCCTA-AAAACATGAT
63 GCCGCAACG-CGAACCCTGTACCTTAGAAGATGTGAT
* * * * * *
11565315 GGGAAGGATTGAGGTCGCAACGGCGAATCTGGA-ATC-ATGAAGAT-TTAAGGAGAAAGATTGAG
1 GGGAAGGATTGAGGCCACAACGGCAAATC-CGACA-CAATGAAGATATGAAGG-GAAAGGTTGAG
11565377 GCCGCAA
63 GCCGCAA
11565384 TGACGAATCA
Statistics
Matches: 439, Mismatches: 100, Indels: 50
0.75 0.17 0.08
Matches are distributed among these distances:
97 3 0.01
98 57 0.13
99 309 0.70
100 66 0.15
101 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.18
Consensus pattern (98 bp):
GGGAAGGATTGAGGCCACAACGGCAAATCCGACACAATGAAGATATGAAGGGAAAGGTTGAGGCC
GCAACGCGAACCCTGTACCTTAGAAGATGTGAT
Found at i:11564987 original size:49 final size:50
Alignment explanation
Indices: 11564717--11565392 Score: 211
Period size: 49 Copynumber: 13.7 Consensus size: 50
11564707 TCTATAGGTT
* * *
11564717 TGAAAGGGAA-GATTGAGGCCGTAACGGCGAATCTGATACCCTGAAGATA
1 TGAAAGGAAAGGATTGAGGCCGCAACGGCGAATCTGATACCATGAAGATA
* * * * *
11564766 TGAAGGGAAAGG-TTGAGGCCGCAACGACGAACCATG-TACCTTAGAAGATG
1 TGAAAGGAAAGGATTGAGGCCGCAACGGCGAATC-TGATACCAT-GAAGATA
* * * * * * * *
11564816 T-AATGGGAAGGATTGAGGCCACAATGGCAAATCCGATGCAATGAAGATA
1 TGAAAGGAAAGGATTGAGGCCGCAACGGCGAATCTGATACCATGAAGATA
* * * * * *
11564865 TGAAGGGAAAGG-TTGAGGCCACAACAGCGAACCCTG-TACCTTAGAAGATG
1 TGAAAGGAAAGGATTGAGGCCGCAACGGCGAA-TCTGATACCAT-GAAGATA
* * * * * *
11564915 TG-ATGGGAAGGATTGAAGTCGCAACGGTGAATCTGACACCATGAAGATA
1 TGAAAGGAAAGGATTGAGGCCGCAACGGCGAATCTGATACCATGAAGATA
* * * * *
11564964 TGAAAGGAAAGGA-TGAGGCCGCAACTGCGAACCCGATACCTTAGAAGATG
1 TGAAAGGAAAGGATTGAGGCCGCAACGGCGAATCTGATACCAT-GAAGATA
* * * * * * * *
11565014 TG-ATGGGAAGGATCGAGGCTGTAACGACGGATCT-AGTATCATGGAA-ATA
1 TGAAAGGAAAGGATTGAGGCCGCAACGGCGAATCTGA-TACCAT-GAAGATA
* * * * *
11565063 T-AAAGGAGAAAGG-TTGAGGCTGCAACGACGAACCTTG-TACCCTAGAA-ACA
1 TGAAA-G-GAAAGGATTGAGGCCGCAACGGCGAATC-TGATACCAT-GAAGATA
* * ** * * * *
11565113 TG-ATGGGAAGGATTGAGGCCATAACGGTGAATTTGGTACTATGAAGATA
1 TGAAAGGAAAGGATTGAGGCCGCAACGGCGAATCTGATACCATGAAGATA
* * * * * * * * * *
11565162 TGAAGGGAAA-AATTAAGGTCGTAAAGGTGAACCCGATACC-TCAGAAGATG
1 TGAAAGGAAAGGATTGAGGCCGCAACGGCGAATCTGATACCAT--GAAGATA
* * * * * *
11565212 TG-ATGGAAAGGATCGAGGTCGCAACGACGGATCT-AGTACAATGGAA-ATA
1 TGAAAGGAAAGGATTGAGGCCGCAACGGCGAATCTGA-TACCAT-GAAGATA
** * * * * *
11565261 T-AAAGGGGAAAGG-TTGAGGCCGCAACGATGAACCTTG-TACCCTAAAAACA
1 TGAAA--GGAAAGGATTGAGGCCGCAACGGCGAATC-TGATACCATGAAGATA
* * * *
11565311 TG-ATGGGAAGGATTGAGGTCGCAACGGCGAATCTGGA-ATCATGAAGAT-
1 TGAAAGGAAAGGATTGAGGCCGCAACGGCGAATCT-GATACCATGAAGATA
* * * *
11565359 T-TAAGGAGAAAGATTGAGGCCGCAATGACGAATC
1 TGAAAGGA-AAGGATTGAGGCCGCAACGGCGAATC
11565393 AGGAACCACA
Statistics
Matches: 444, Mismatches: 142, Indels: 82
0.66 0.21 0.12
Matches are distributed among these distances:
48 22 0.05
49 220 0.50
50 187 0.42
51 15 0.03
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.18
Consensus pattern (50 bp):
TGAAAGGAAAGGATTGAGGCCGCAACGGCGAATCTGATACCATGAAGATA
Found at i:11565119 original size:198 final size:198
Alignment explanation
Indices: 11564722--11565383 Score: 688
Period size: 198 Copynumber: 3.4 Consensus size: 198
11564712 AGGTTTGAAA
* * *
11564722 GGGAA-GATTGAGGCCGTAACGGCGAATCTGATACCCTGAAGATATGAAGGGAAAGG-TTGAGGC
1 GGGAAGGATTGAGGCCGCAACGGCGAATCTGATACCATGAAGATATGAAAGGAAAGGATTGAGGC
* * * ** * * **
11564785 CGCAACGACGAACCATG-TACCTTAGAAGATGTAATGGGAAGGATTGAGGCCACAATGGCAAATC
66 CGCAACG-CGAACC-CGATACCTTAGAAGATGTGATGGGAAGGATCGAGGCTGCAACGACGGATC
* * * * *
11564849 -CG-ATGCAAT-GAAGATATGAAGGGAAAGGTTGAGGCCACAAC-AGCGAACCCTGTACCTTAGA
129 TAGTAT-CAATGGAA-ATATAAAGGGAAAGGTTGAGGCCGCAACGA-CGAACCTTGTACCCTAGA
**
11564910 AGATGTGAT
191 A-ACATGAT
* * * *
11564919 GGGAAGGATTGAAGTCGCAACGGTGAATCTGACACCATGAAGATATGAAAGGAAAGGA-TGAGGC
1 GGGAAGGATTGAGGCCGCAACGGCGAATCTGATACCATGAAGATATGAAAGGAAAGGATTGAGGC
*
11564983 CGCAACTGCGAACCCGATACCTTAGAAGATGTGATGGGAAGGATCGAGGCTGTAACGACGGATCT
66 CGCAAC-GCGAACCCGATACCTTAGAAGATGTGATGGGAAGGATCGAGGCTGCAACGACGGATCT
*
11565048 AGTATC-ATGGAAATATAAAGGAGAAAGGTTGAGGCTGCAACGACGAACCTTGTACCCTAGAAAC
130 AGTATCAATGGAAATATAAAGG-GAAAGGTTGAGGCCGCAACGACGAACCTTGTACCCTAGAAAC
11565112 ATGAT
194 ATGAT
** * * * * * * * *
11565117 GGGAAGGATTGAGGCCATAACGGTGAATTTGGTACTATGAAGATATGAAGGGAAA-AATTAAGGT
1 GGGAAGGATTGAGGCCGCAACGGCGAATCTGATACCATGAAGATATGAAAGGAAAGGATTGAGGC
* * * * *
11565181 CGTAAAGGTGAACCCGATACCTCAGAAGATGTGATGGAAAGGATCGAGG-TCGCAACGACGGATC
66 CG-CAACGCGAACCCGATACCTTAGAAGATGTGATGGGAAGGATCGAGGCT-GCAACGACGGATC
* *
11565245 TAGTA-CAATGGAAATATAAAGGGGAAAGGTTGAGGCCGCAACGATGAACCTTGTACCCTAAAAA
129 TAGTATCAATGGAAATATAAA-GGGAAAGGTTGAGGCCGCAACGACGAACCTTGTACCCTAGAAA
11565309 CATGAT
193 CATGAT
* * * *
11565315 GGGAAGGATTGAGGTCGCAACGGCGAATCTGGA-ATCATGAAGAT-T-TAAGGAGAAAGATTGAG
1 GGGAAGGATTGAGGCCGCAACGGCGAATCT-GATACCATGAAGATATGAAAGGA-AAGGATTGAG
11565377 GCCGCAA
64 GCCGCAA
11565384 TGACGAATCA
Statistics
Matches: 388, Mismatches: 60, Indels: 34
0.80 0.12 0.07
Matches are distributed among these distances:
196 4 0.01
197 14 0.04
198 322 0.83
199 45 0.12
200 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.18
Consensus pattern (198 bp):
GGGAAGGATTGAGGCCGCAACGGCGAATCTGATACCATGAAGATATGAAAGGAAAGGATTGAGGC
CGCAACGCGAACCCGATACCTTAGAAGATGTGATGGGAAGGATCGAGGCTGCAACGACGGATCTA
GTATCAATGGAAATATAAAGGGAAAGGTTGAGGCCGCAACGACGAACCTTGTACCCTAGAAACAT
GAT
Found at i:11565317 original size:297 final size:296
Alignment explanation
Indices: 11564758--11565390 Score: 653
Period size: 297 Copynumber: 2.1 Consensus size: 296
11564748 TCTGATACCC
* * *
11564758 TGAAGATATGAAGG-GAAAGGTTGAGGCCGCAACGACGAACCATGTACCTTAGAAGATGTAATGG
1 TGAAGATATAAAGGAGAAAGGTTGAGGCCGCAACGACGAACCATGTACCCTAGAACATG-AATGG
* * ** *
11564822 GAAGGATTGAGGCCACAATGGCAAATCCGATGCAATGAAGATATGAAGGGAAAGGTTGAGGCCAC
65 GAAGGATTGAGGCCACAACGGCAAATCCGATACAATGAAGATATGAAGGGAAAAATTAAGGCCAC
* * * **
11564887 AACAGCGAACCCTGTACCTTAGAAGATGTGATGGGAAGGATTGAAGTCGCAACGGTGAATCTGAC
130 AACAGCGAACCCTGTACCTCAGAAGATGTGATGGAAAGGATCGAAGTCGCAACGACGAATCTGAC
* * **
11564952 ACCATGAAGATATGAAAGGAAAGGATGAGGCCGCAACTGCGAACCCGATACCTTAGAAGATGTGA
195 A-CATGAAGATATGAAAGGAAAGGATGAGGCCGCAACTGCGAACCCGATACCCTAGAAAACATGA
* * *
11565017 TGGGAAGGATCGAGG-CTGTAACGACGGATCTAGTATCA
259 TGGGAAGGATCGAGGTC-GCAACGACGAATCTAGAATCA
* *
11565055 TGGAA-ATATAAAGGAGAAAGGTTGAGGCTGCAACGACGAACCTTGTACCCTAGAAACATG-ATG
1 T-GAAGATATAAAGGAGAAAGGTTGAGGCCGCAACGACGAACCATGTACCCTAG-AACATGAATG
* ** ** * * * *
11565118 GGAAGGATTGAGGCCATAACGGTGAATTTGGTACTATGAAGATATGAAGGGAAAAATTAAGGTCG
64 GGAAGGATTGAGGCCACAACGGCAAATCCGATACAATGAAGATATGAAGGGAAAAATTAAGGCCA
* * * *
11565183 TAA-AGGTGAACCC-GATACCTCAGAAGATGTGATGGAAAGGATCGAGGTCGCAACGACGGATCT
129 CAACA-GCGAACCCTG-TACCTCAGAAGATGTGATGGAAAGGATCGAAGTCGCAACGACGAATCT
* * *
11565246 AGTACA-ATGGAA-ATAT-AAAGGGGAAAGGTTGAGGCCGCAAC-GATGAACCTTG-TACCCTA-
192 -G-ACACAT-GAAGATATGAAA--GGAAAGGATGAGGCCGCAACTG-CGAACC-CGATACCCTAG
* * *
11565305 AAAACATGATGGGAAGGATTGAGGTCGCAACGGCGAATCTGGAATCA
250 AAAACATGATGGGAAGGATCGAGGTCGCAACGACGAATCTAGAATCA
* * *
11565352 TGAAGAT-TTAAGGAGAAAGATTGAGGCCGCAATGACGAA
1 TGAAGATATAAAGGAGAAAGGTTGAGGCCGCAACGACGAA
11565391 TCAGGAACCA
Statistics
Matches: 277, Mismatches: 45, Indels: 29
0.79 0.13 0.08
Matches are distributed among these distances:
296 36 0.13
297 159 0.57
298 73 0.26
299 9 0.03
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.18
Consensus pattern (296 bp):
TGAAGATATAAAGGAGAAAGGTTGAGGCCGCAACGACGAACCATGTACCCTAGAACATGAATGGG
AAGGATTGAGGCCACAACGGCAAATCCGATACAATGAAGATATGAAGGGAAAAATTAAGGCCACA
ACAGCGAACCCTGTACCTCAGAAGATGTGATGGAAAGGATCGAAGTCGCAACGACGAATCTGACA
CATGAAGATATGAAAGGAAAGGATGAGGCCGCAACTGCGAACCCGATACCCTAGAAAACATGATG
GGAAGGATCGAGGTCGCAACGACGAATCTAGAATCA
Found at i:11574737 original size:12 final size:12
Alignment explanation
Indices: 11574720--11574744 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11574710 ATTCCTCTTA
11574720 TAATATGTATTT
1 TAATATGTATTT
11574732 TAATATGTATTT
1 TAATATGTATTT
11574744 T
1 T
11574745 TTATTTCATG
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:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (12 bp):
TAATATGTATTT
Found at i:11591000 original size:17 final size:17
Alignment explanation
Indices: 11590972--11591008 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
11590962 TGGGTTTGAG
11590972 TTTTAAGAGTA-TTAAA
1 TTTTAAGAGTATTTAAA
11590988 TTTTAATGAGTATTTAAA
1 TTTTAA-GAGTATTTAAA
11591006 TTT
1 TTT
11591009 AAGGTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 5 0.26
18 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (17 bp):
TTTTAAGAGTATTTAAA
Found at i:11596225 original size:185 final size:185
Alignment explanation
Indices: 11595913--11596280 Score: 727
Period size: 185 Copynumber: 2.0 Consensus size: 185
11595903 GGGTAAAATC
11595913 ATAATTTTACCAAAAAGGGGTTTGATTGTGTTAAATGAATTGATTGTGTGATTTAATATGAGAAA
1 ATAATTTTACCAAAAAGGGGTTTGATTGTGTTAAATGAATTGATTGTGTGATTTAATATGAGAAA
11595978 TTGAATGATTTGTGAATGTAGACTACGATCGTGCCACCAATCATGGAAAGGGAAAATTAGCAGCA
66 TTGAATGATTTGTGAATGTAGACTACGATCGTGCCACCAATCATGGAAAGGGAAAATTAGCAGCA
*
11596043 TAGTTCCTAAGATCCATTCACAACTGCAATCCAGTCCGGTAAGTTCGTATGATCA
131 TAGTCCCTAAGATCCATTCACAACTGCAATCCAGTCCGGTAAGTTCGTATGATCA
11596098 ATAATTTTACCAAAAAGGGGTTTGATTGTGTTAAATGAATTGATTGTGTGATTTAATATGAGAAA
1 ATAATTTTACCAAAAAGGGGTTTGATTGTGTTAAATGAATTGATTGTGTGATTTAATATGAGAAA
11596163 TTGAATGATTTGTGAATGTAGACTACGATCGTGCCACCAATCATGGAAAGGGAAAATTAGCAGCA
66 TTGAATGATTTGTGAATGTAGACTACGATCGTGCCACCAATCATGGAAAGGGAAAATTAGCAGCA
11596228 TAGTCCCTAAGATCCATTCACAACTGCAATCCAGTCCGGTAAGTTCGTATGAT
131 TAGTCCCTAAGATCCATTCACAACTGCAATCCAGTCCGGTAAGTTCGTATGAT
11596281 TAAATTCCAA
Statistics
Matches: 182, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 182 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (185 bp):
ATAATTTTACCAAAAAGGGGTTTGATTGTGTTAAATGAATTGATTGTGTGATTTAATATGAGAAA
TTGAATGATTTGTGAATGTAGACTACGATCGTGCCACCAATCATGGAAAGGGAAAATTAGCAGCA
TAGTCCCTAAGATCCATTCACAACTGCAATCCAGTCCGGTAAGTTCGTATGATCA
Found at i:11596575 original size:53 final size:52
Alignment explanation
Indices: 11596407--11596593 Score: 218
Period size: 51 Copynumber: 3.6 Consensus size: 52
11596397 CTATAAACGA
* * * *
11596407 AAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATT-CTTTACGGATT
1 AAAGGTCCGATGACTATGTGTCATCGTGAGTAAATGAATTCCTATATGGATT
* *
11596458 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAA-TCC-ATGATGGATT
1 AAAGGTCCGATGACTATGTGTCATCGTGAGTAAATGAATTCCTAT-ATGGATT
* ** * **
11596509 AAAGGTCCGATGACTTTGTGTTGTCGTGAGTATATGAATTCCTATATGGAAC
1 AAAGGTCCGATGACTATGTGTCATCGTGAGTAAATGAATTCCTATATGGATT
*
11596561 AAGAGGTCCGATGACTATATGTCATCGTGAGTA
1 AA-AGGTCCGATGACTATGTGTCATCGTGAGTA
11596594 TTAAATGAAA
Statistics
Matches: 115, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
50 2 0.02
51 75 0.65
52 10 0.09
53 28 0.24
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (52 bp):
AAAGGTCCGATGACTATGTGTCATCGTGAGTAAATGAATTCCTATATGGATT
Found at i:11609048 original size:41 final size:41
Alignment explanation
Indices: 11608992--11609075 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
11608982 TGAGTTATAT
11608992 TATTAAAGTCATGAAATTTATCACCCTCGTAGGCATGGTCA
1 TATTAAAGTCATGAAATTTATCACCCTCGTAGGCATGGTCA
11609033 TATTAAAGTCATGAAATTTATCACCCTCGTAGGCATGGTCA
1 TATTAAAGTCATGAAATTTATCACCCTCGTAGGCATGGTCA
11609074 TA
1 TA
11609076 GTGAATATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (41 bp):
TATTAAAGTCATGAAATTTATCACCCTCGTAGGCATGGTCA
Found at i:11612677 original size:96 final size:98
Alignment explanation
Indices: 11612511--11612691 Score: 233
Period size: 96 Copynumber: 1.9 Consensus size: 98
11612501 ATACATTGGA
* **
11612511 CCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCATCCCGGTTACTCAACCCAACATGCTCT
1 CCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCATCCCGATTACTCAACCCAACACACTCT
*
11612576 CAATTT-TTTCTTT-TTTTTAGAATGTGTTAGC
66 CAATTTGTTTATTTATTTTTAGAATGTGTTAGC
* * * ** *
11612607 CCTTTTGACGCGAAGTGAAATGATAACCAAGCACTCCA-CCTCGATTACTTAGTCTAACACACTC
1 CCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCATCC-CGATTACTCAACCCAACACACTC
*
11612671 TGAATTTGTTTATTTATTTTT
65 TCAATTTGTTTATTTATTTTT
11612692 TTCTTTTCTT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
95 2 0.03
96 58 0.82
97 6 0.08
98 5 0.07
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (98 bp):
CCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCATCCCGATTACTCAACCCAACACACTCT
CAATTTGTTTATTTATTTTTAGAATGTGTTAGC
Found at i:11613228 original size:14 final size:16
Alignment explanation
Indices: 11613201--11613234 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
11613191 TATACTTAAA
11613201 AAAATAAAACAGGTAG
1 AAAATAAAACAGGTAG
11613217 AAAA-AAAA-AGGTAG
1 AAAATAAAACAGGTAG
11613231 AAAA
1 AAAA
11613235 CACACTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 4 0.22
16 4 0.22
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.09
Consensus pattern (16 bp):
AAAATAAAACAGGTAG
Found at i:11616263 original size:22 final size:22
Alignment explanation
Indices: 11616238--11616279 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
11616228 GATTTAAGGA
11616238 AAAAAAAAACAGAATTAAAAAT
1 AAAAAAAAACAGAATTAAAAAT
* *
11616260 AAAATAAAATAGAATTAAAA
1 AAAAAAAAACAGAATTAAAA
11616280 GAAATAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (22 bp):
AAAAAAAAACAGAATTAAAAAT
Found at i:11616290 original size:22 final size:22
Alignment explanation
Indices: 11616238--11616294 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
11616228 GATTTAAGGA
* *
11616238 AAAAAAAAACAGAATTAAAAAT
1 AAAAGAAAATAGAATTAAAAAT
*
11616260 AAAATAAAATAGAATTAAAAGA-
1 AAAAGAAAATAGAATTAAAA-AT
*
11616282 AATAGAAAATAGA
1 AAAAGAAAATAGA
11616295 GGTGTCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.16
Consensus pattern (22 bp):
AAAAGAAAATAGAATTAAAAAT
Found at i:11619253 original size:16 final size:16
Alignment explanation
Indices: 11619232--11619262 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11619222 TTCATTGTTA
*
11619232 TGTCTTTTATATTTTT
1 TGTCTTTCATATTTTT
11619248 TGTCTTTCATATTTT
1 TGTCTTTCATATTTT
11619263 GCATGCATAG
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:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (16 bp):
TGTCTTTCATATTTTT
Found at i:11620631 original size:68 final size:68
Alignment explanation
Indices: 11620546--11620743 Score: 191
Period size: 68 Copynumber: 3.0 Consensus size: 68
11620536 ATTTTAATAG
11620546 TTTAATATTAAATTTAATTTAATACTTATTTTAATAAA-ATTTTATTAATTTAATATTAAAGTGA
1 TTTAATATTAAATTTAATTTAATACTTATTTTAATAAACATTTTATTAATTTAATATTAAAGTGA
11620610 TTA
66 TTA
* ** *
11620613 TCTTAATATTAAATTTAATTCAATGTTTATATTGTAGATAAACATTTTATT-ATTT--TAAT-AA
1 T-TTAATATTAAATTTAATTTAATACTTAT-TT-TA-ATAAACATTTTATTAATTTAATATTAAA
11620674 --G---A
62 GTGATTA
* * * * * * *
11620676 TTTAATATTAAATTTAATCTAATAGTTATCTTAATAAATATTATGTTAGTTTAATATTAAAGTGA
1 TTTAATATTAAATTTAATTTAATACTTATTTTAATAAACATTTTATTAATTTAATATTAAAGTGA
11620741 TTA
66 TTA
11620744 AGTTTAATCA
Statistics
Matches: 103, Mismatches: 14, Indels: 27
0.72 0.10 0.19
Matches are distributed among these distances:
59 11 0.11
60 5 0.05
61 1 0.01
62 27 0.26
63 4 0.04
65 1 0.01
66 1 0.01
67 1 0.01
68 28 0.27
69 5 0.05
70 2 0.02
71 9 0.09
72 8 0.08
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (68 bp):
TTTAATATTAAATTTAATTTAATACTTATTTTAATAAACATTTTATTAATTTAATATTAAAGTGA
TTA
Found at i:11625465 original size:36 final size:36
Alignment explanation
Indices: 11625436--11625655 Score: 173
Period size: 36 Copynumber: 6.1 Consensus size: 36
11625426 GTGAAAGCTG
* *
11625436 ATATGTGAGTTTCTTATTCATGCAATGTGATAGTAA
1 ATATGTGAGTATCTTATTCATGCAATGTGAAAGTAA
* * *
11625472 ATATGTGGGTATGTTATTCATGCCATGTGACAA-TAA
1 ATATGTGAGTATCTTATTCATGCAATGTGA-AAGTAA
* *
11625508 ATATGTTG-GTATGTTATTCATGTC-ATGTGACAGTAA
1 ATATG-TGAGTATCTTATTCATG-CAATGTGAAAGTAA
* *
11625544 ATATGTGGGTATGTTATTCATGTC-ATGTGACAA-TAA
1 ATATGTGAGTATCTTATTCATG-CAATGTGA-AAGTAA
* * * * *
11625580 ATATGTAAGTA-CGTTATTCATGCCATGAGACAGAAA
1 ATATGTGAGTATC-TTATTCATGCAATGTGAAAGTAA
* * * * *
11625616 ATATCTGGGTATGTTATTCATGCCATGTGATAGTAA
1 ATATGTGAGTATCTTATTCATGCAATGTGAAAGTAA
11625652 ATAT
1 ATAT
11625656 ATTGTGTTGA
Statistics
Matches: 154, Mismatches: 20, Indels: 20
0.79 0.10 0.10
Matches are distributed among these distances:
35 5 0.03
36 144 0.94
37 5 0.03
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (36 bp):
ATATGTGAGTATCTTATTCATGCAATGTGAAAGTAA
Found at i:11625543 original size:72 final size:71
Alignment explanation
Indices: 11625449--11625655 Score: 297
Period size: 72 Copynumber: 2.9 Consensus size: 71
11625439 TGTGAGTTTC
*
11625449 TTATTCATGCAATGTGATAGTAAATATGTGGGTATGTTATTCATGCCATGTGACAATAAATATGT
1 TTATTCATGC-ATGTGACAGTAAATATGTGGGTATGTTATTCATGCCATGTGACAATAAATATGT
** *
11625514 TGGTATG
65 AAGTACG
*
11625521 TTATTCATGTCATGTGACAGTAAATATGTGGGTATGTTATTCATGTCATGTGACAATAAATATGT
1 TTATTCATG-CATGTGACAGTAAATATGTGGGTATGTTATTCATGCCATGTGACAATAAATATGT
11625586 AAGTACG
65 AAGTACG
* * * * *
11625593 TTATTCATGCCATGAGACAGAAAATATCTGGGTATGTTATTCATGCCATGTGATAGTAAATAT
1 TTATTCATG-CATGTGACAGTAAATATGTGGGTATGTTATTCATGCCATGTGACAATAAATAT
11625656 ATTGTGTTGA
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
72 121 0.99
73 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (71 bp):
TTATTCATGCATGTGACAGTAAATATGTGGGTATGTTATTCATGCCATGTGACAATAAATATGTA
AGTACG
Found at i:11625618 original size:108 final size:108
Alignment explanation
Indices: 11625449--11625655 Score: 292
Period size: 108 Copynumber: 1.9 Consensus size: 108
11625439 TGTGAGTTTC
* * ** * * *
11625449 TTATTCATGCAATGTGATAGTAAATATGTGGGTATGTTATTCATGCCATGTGACAATAAATATGT
1 TTATTCATGCAATGTGACAATAAATATGTAAGTACGTTATTCATGCCATGAGACAATAAATATCT
* *
11625514 TGGTATGTTATTCATGTCATGTGACAGTAAATATGTGGGTATG
66 GGGTATGTTATTCATGCCATGTGACAGTAAATATGTGGGTATG
11625557 TTATTCATGTC-ATGTGACAATAAATATGTAAGTACGTTATTCATGCCATGAGACAGA-AAATAT
1 TTATTCATG-CAATGTGACAATAAATATGTAAGTACGTTATTCATGCCATGAGACA-ATAAATAT
*
11625620 CTGGGTATGTTATTCATGCCATGTGATAGTAAATAT
64 CTGGGTATGTTATTCATGCCATGTGACAGTAAATAT
11625656 ATTGTGTTGA
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
108 85 0.98
109 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (108 bp):
TTATTCATGCAATGTGACAATAAATATGTAAGTACGTTATTCATGCCATGAGACAATAAATATCT
GGGTATGTTATTCATGCCATGTGACAGTAAATATGTGGGTATG
Done.