Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009610.1 Hibiscus syriacus cultivar Beakdansim tig00116996_pilon, whole genome shotgun sequence
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: 3811333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 18
Found at i:1931096 original size:33 final size:34
Alignment explanation
Indices: 1931053--1931117 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
1931043 ATATCATACC
* * *
1931053 TGATAAAGTTTATTTAGTTCTTTAGGGAAAGTGG
1 TGATAAAGTTTATTCACTTCTTTAGAGAAAGTGG
1931087 TGAT-AAGTTTATTCACTTCTTTAGAGAAAGT
1 TGATAAAGTTTATTCACTTCTTTAGAGAAAGT
1931118 AGATTGATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (34 bp):
TGATAAAGTTTATTCACTTCTTTAGAGAAAGTGG
Found at i:1932964 original size:64 final size:64
Alignment explanation
Indices: 1932884--1933100 Score: 249
Period size: 64 Copynumber: 3.4 Consensus size: 64
1932874 TTGAAGGTGT
** **
1932884 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATG
1932947 C
64 C
* * **
1932948 ATCGATGCATAAGTAGTACATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* * * * ** *
1933012 ATCGATGCATAAGGAGTGCATCGATGCATCCCATCAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* *
1933076 ACCGATGCATCAGTAGTGCATCGAT
1 ATCGATGCATAAGTAGTGCATCGAT
1933101 TCATACCTTC
Statistics
Matches: 130, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
64 126 0.97
65 4 0.03
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:1933430 original size:12 final size:12
Alignment explanation
Indices: 1933412--1933447 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1933402 TATATATGTT
1933412 CATGTGATATGA
1 CATGTGATATGA
*
1933424 TATGTGATATGA
1 CATGTGATATGA
1933436 CATGTGATATGA
1 CATGTGATATGA
1933448 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:1933456 original size:25 final size:24
Alignment explanation
Indices: 1933428--1933480 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
1933418 ATATGATATG
*
1933428 TGATATGACATGTGATATGAGA-ACA
1 TGATATGA-A-GTGACATGAGATACA
1933453 TGATATGAAGTGACATGAGATACA
1 TGATATGAAGTGACATGAGATACA
1933477 TGAT
1 TGAT
1933481 CACAAGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.38
24 8 0.31
25 8 0.31
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.28
Consensus pattern (24 bp):
TGATATGAAGTGACATGAGATACA
Found at i:1939855 original size:64 final size:64
Alignment explanation
Indices: 1939775--1939995 Score: 246
Period size: 64 Copynumber: 3.5 Consensus size: 64
1939765 TTGAAGGTGT
** * **
1939775 ATCGATGCATTGGTAGTGCATCGATGCATTCTTTTAA-AATAAAAACATCAAATGCAATTCATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAT-AAAACATCAAATGCAATTCATGC
* * **
1939839 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCATGC
* ** * * * ** *
1939903 ATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCATGC
* *
1939967 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
1939996 ACATTCATTA
Statistics
Matches: 134, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
64 131 0.98
65 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCATGC
Found at i:1940321 original size:12 final size:12
Alignment explanation
Indices: 1940303--1940338 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1940293 TATATATGTT
1940303 CATGTGATATGA
1 CATGTGATATGA
*
1940315 TATGTGATATGA
1 CATGTGATATGA
1940327 CATGTGATATGA
1 CATGTGATATGA
1940339 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:1940360 original size:23 final size:26
Alignment explanation
Indices: 1940303--1940371 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
1940293 TATATATGTT
**
1940303 CATGTGATAT--GATATGTGATATGA
1 CATGTGATATGAGATACATGATATGA
1940327 CATGTGATATGAGA-ACATGATATGA
1 CATGTGATATGAGATACATGATATGA
1940352 -A-GTGATATGAGATACATGAT
1 CATGTGATATGAGATACATGAT
1940372 CACAAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 18 0.45
25 9 0.22
26 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (26 bp):
CATGTGATATGAGATACATGATATGA
Found at i:1943858 original size:16 final size:16
Alignment explanation
Indices: 1943834--1943865 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1943824 TGTGTGAGTG
*
1943834 AGTTTAATTTAGGTTT
1 AGTTAAATTTAGGTTT
1943850 AGTTAAATTTAGGTTT
1 AGTTAAATTTAGGTTT
1943866 CATATTAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (16 bp):
AGTTAAATTTAGGTTT
Found at i:1944497 original size:14 final size:14
Alignment explanation
Indices: 1944474--1944519 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
1944464 CATAATCAGA
*
1944474 TTTATGGTTTAGGG
1 TTTATAGTTTAGGG
1944488 TTTATAGTTTAGGG
1 TTTATAGTTTAGGG
*
1944502 TTTATAGCTTAGGG
1 TTTATAGTTTAGGG
1944516 TTTA
1 TTTA
1944520 GGATTCATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.20, C:0.02, G:0.28, T:0.50
Consensus pattern (14 bp):
TTTATAGTTTAGGG
Found at i:1944657 original size:11 final size:11
Alignment explanation
Indices: 1944641--1944703 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
1944631 GTATTATAGA
1944641 ATTTTTAATAT
1 ATTTTTAATAT
1944652 ATTTTTAA-A-
1 ATTTTTAATAT
1944661 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
1944672 ATCAATAGTGT
1 ATTTTTAATAT
1944683 ATTTTTAATAT
1 ATTTTTAATAT
1944694 ATTTTTAATA
1 ATTTTTAATA
1944704 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:1945941 original size:17 final size:18
Alignment explanation
Indices: 1945919--1945952 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1945909 TTTTATTATT
*
1945919 ATTTAATATA-AAAAATA
1 ATTTAAAATATAAAAATA
1945936 ATTTAAAATATAAAAAT
1 ATTTAAAATATAAAAAT
1945953 TAAAATCGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTTAAAATATAAAAATA
Found at i:1946943 original size:21 final size:18
Alignment explanation
Indices: 1946917--1946959 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 18
1946907 TTTAAAGATT
1946917 TTTAAAAATTTATTATTTTTA
1 TTTAAAAA-TTA-T-TTTTTA
1946938 TTTAAAAATTATTTTTTA
1 TTTAAAAATTATTTTTTA
1946956 TTTA
1 TTTA
1946960 TTTTAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.45
19 1 0.05
20 3 0.14
21 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTAAAAATTATTTTTTA
Found at i:1946959 original size:22 final size:21
Alignment explanation
Indices: 1946917--1946979 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1946907 TTTAAAGATT
*
1946917 TTTAAAAATT-TATTATTTTTA
1 TTTAAAAATTAT-TTTTTTTTA
1946938 TTTAAAAATTATTTTTTATTTA
1 TTTAAAAATTATTTTTT-TTTA
* *
1946960 TTT-TAAATTATTTTATTTTA
1 TTTAAAAATTATTTTTTTTTA
1946980 ATTATGATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.11
21 25 0.68
22 8 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTAAAAATTATTTTTTTTTA
Found at i:1951306 original size:5 final size:5
Alignment explanation
Indices: 1951296--1951332 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
1951286 CTTTATTAGT
1951296 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
1951333 ATTATTTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:1957197 original size:21 final size:21
Alignment explanation
Indices: 1957155--1957197 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1957145 TTTTCGGGCT
* * *
1957155 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1957176 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1957197 A
1 A
1957198 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1957332 original size:21 final size:22
Alignment explanation
Indices: 1957292--1957333 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1957282 AAAGAAAGAC
*
1957292 TAAGCTATTAATTTCTTAATTAG
1 TAAGCTATTAA-TGCTTAATTAG
1957315 TAAGCTATTAA-GCTTAATT
1 TAAGCTATTAATGCTTAATT
1957334 TCAAGACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (22 bp):
TAAGCTATTAATGCTTAATTAG
Found at i:1957999 original size:150 final size:149
Alignment explanation
Indices: 1957729--1958036 Score: 535
Period size: 150 Copynumber: 2.1 Consensus size: 149
1957719 GGGTAGAGGG
* * *
1957729 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCAGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
* * *
1957794 GCTTGATCCTTAGTATATGTATATAATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
1957859 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
1957878 TCTACGCGGTCCTTCAGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCAGGACATATATATATTCTGTGGAACATGTGTGAAGTCTT-GAAAGACACA
*
1957943 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
65 TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
1958008 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
1958028 TCTACGCGG
1 TCTACGCGG
1958037 CACTTCGGTG
Statistics
Matches: 150, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
149 50 0.33
150 100 0.67
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCAGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1958056 original size:23 final size:23
Alignment explanation
Indices: 1958012--1958056 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1958002 ATCATTATAT
*
1958012 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1958035 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1958057 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1964871 original size:149 final size:150
Alignment explanation
Indices: 1964683--1964987 Score: 531
Period size: 150 Copynumber: 2.0 Consensus size: 150
1964673 GGGTAGAGGG
* *
1964683 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* * *
1964747 TGCTTGATCCTTAGTATATGTATATAATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
1964812 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
1964832 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
*
1964897 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
*
1964962 ATATGGCACTACGGTGTAAT
131 ATATGGCACTACGGTGCAAT
1964982 TCTACG
1 TCTACG
1964988 TGGCACTTCG
Statistics
Matches: 147, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
149 51 0.35
150 96 0.65
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:1965010 original size:23 final size:23
Alignment explanation
Indices: 1964965--1965010 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1964955 CATCATTATA
* *
1964965 TGGCACTACGGTGTAATTCTACG
1 TGGCACTACGGTGCAATTATACG
* *
1964988 TGGCACTTCGGTGCATTTATACG
1 TGGCACTACGGTGCAATTATACG
1965011 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.33
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:1965246 original size:23 final size:23
Alignment explanation
Indices: 1965202--1965246 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1965192 ATCATTATAT
*
1965202 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1965225 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1965247 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1965323 original size:236 final size:236
Alignment explanation
Indices: 1964910--1965392 Score: 905
Period size: 236 Copynumber: 2.0 Consensus size: 236
1964900 TTGATCCCTA
*
1964910 GTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTATATGGCACTACG
1 GTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTATATGGCACTACG
* *
1964975 GTGTAATTCTACGTGGCACTTCGGTGCATTTATACGAGCTGTGGTGACAGCATAGTGCACAACCT
66 GTGCAATTCTACGCGGCACTTCGGTGCATTTATACGAGCTGTGGTGACAGCATAGTGCACAACCT
1965040 CACATTACTCAGATACCTTAGGTTCTCAATATGCTATCATGGGCCAATAAACTTATTAATACAGA
131 CACATTACTCAGATACCTTAGGTTCTCAATATGCTATCATGGGCCAATAAACTTATTAATACAGA
1965105 TTCATGAATGTTACAGTCATACGCTTACAGGTATGGATATT
196 TTCATGAATGTTACAGTCATACGCTTACAGGTATGGATATT
1965146 GTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTATATGGCACTACG
1 GTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTATATGGCACTACG
*
1965211 GTGCAATTCTACGCGGCACTTCGGTGCATTTATACGAGCTGTGGTGACAGCATAGTGTACAACCT
66 GTGCAATTCTACGCGGCACTTCGGTGCATTTATACGAGCTGTGGTGACAGCATAGTGCACAACCT
*
1965276 CACATTACTTAGATACCTTAGGTTCTCAATATGCTATCATGGGCCAATAAACTTATTAATACAGA
131 CACATTACTCAGATACCTTAGGTTCTCAATATGCTATCATGGGCCAATAAACTTATTAATACAGA
1965341 TTCATGAATGTTACAGTCATACGCTTACAGGTATGGATATT
196 TTCATGAATGTTACAGTCATACGCTTACAGGTATGGATATT
1965382 G-ATGATGTATA
1 GTAT-ATGTATA
1965393 CTACATTGAT
Statistics
Matches: 241, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
235 2 0.01
236 239 0.99
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (236 bp):
GTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTATATGGCACTACG
GTGCAATTCTACGCGGCACTTCGGTGCATTTATACGAGCTGTGGTGACAGCATAGTGCACAACCT
CACATTACTCAGATACCTTAGGTTCTCAATATGCTATCATGGGCCAATAAACTTATTAATACAGA
TTCATGAATGTTACAGTCATACGCTTACAGGTATGGATATT
Found at i:1967276 original size:23 final size:23
Alignment explanation
Indices: 1967250--1967308 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 23
1967240 GACATTTTGT
*
1967250 TTTTCGATGGATTTTAAATCCAC
1 TTTTCGGTGGATTTTAAATCCAC
*
1967273 TTTTCGGTGGA--TTAATTCCAC
1 TTTTCGGTGGATTTTAAATCCAC
*
1967294 CTTTCGGTGGATTTT
1 TTTTCGGTGGATTTT
1967309 CAACACATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 19 0.61
23 12 0.39
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.46
Consensus pattern (23 bp):
TTTTCGGTGGATTTTAAATCCAC
Found at i:1971343 original size:27 final size:27
Alignment explanation
Indices: 1971299--1971365 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
1971289 TGAATAACTC
*
1971299 AAACTTGACTCGGTCAAAGCTCGATAA
1 AAACTCGACTCGGTCAAAGCTCGATAA
* *
1971326 AAATTCGACTCGGTCAAAGTTCGATAA
1 AAACTCGACTCGGTCAAAGCTCGATAA
1971353 AAACTCGACTCGG
1 AAACTCGACTCGG
1971366 GATGACTCGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (27 bp):
AAACTCGACTCGGTCAAAGCTCGATAA
Found at i:1978516 original size:38 final size:38
Alignment explanation
Indices: 1978436--1978508 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
1978426 TTATGCATCG
1978436 ATGCACTCAGGTTTTTATGAAAACATCAAATGCATAAA
1 ATGCACTCAGGTTTTTATGAAAACATCAAATGCATAAA
*
1978474 ATGCACTCAGGTTTTTATGAAAACATCGAATGCAT
1 ATGCACTCAGGTTTTTATGAAAACATCAAATGCAT
1978509 TTTATGCATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (38 bp):
ATGCACTCAGGTTTTTATGAAAACATCAAATGCATAAA
Found at i:1988260 original size:20 final size:19
Alignment explanation
Indices: 1988237--1988283 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1988227 CGATATAACA
1988237 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
* *
1988257 GGTATCAAAATGATGAAACC
1 GGTA-AAAAATGATAAAACC
1988277 GGTAAAA
1 GGTAAAA
1988284 CGCTACCAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1988393 original size:183 final size:182
Alignment explanation
Indices: 1988024--1988497 Score: 736
Period size: 181 Copynumber: 2.6 Consensus size: 182
1988014 GATCCAAATT
* * * * **
1988024 AAAAATGTATTGATCCACAACGATATAACAGGTAAAACTATGACAAAATCGGTATTGAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
1988089 AAACCGGTAAAGCGGTACCGAATATATTTAAAGTGTCGGTACTTTAATATAAAGATCGACACTTC
66 AAACCGGTAAAACGCTACCG-ATATATTGAAAGTGTCGATACTTTAATATAAAGATCGACACTTC
*
1988154 GTTAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
130 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
* *
1988207 AAAAATGTATCGATGCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATG
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
1988272 AAACCGGTAAAACGCTACCAGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGCTACC-GATATATTGAAAGTGTCGATACTTTAATATAAAGATCGACACTTC
*
1988336 GTGAATTTAAAAGAGAAGCAGTTTTAGCGTCTATAAAGTGTCGATACTTTAAA
130 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
*
1988389 AAAAA-ATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
1988453 AAACCGATAAAACGCTATCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGCTA-CCGATATATTGAAAGTGTCGATACTTT
1988498 CGTAAGTACG
Statistics
Matches: 268, Mismatches: 21, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
181 97 0.36
182 74 0.28
183 96 0.36
184 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGCTACCGATATATTGAAAGTGTCGATACTTTAATATAAAGATCGACACTTCG
TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
Found at i:1988441 original size:20 final size:19
Alignment explanation
Indices: 1988418--1988464 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1988408 CGATATAACA
1988418 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1988438 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
*
1988458 GATAAAA
1 GGTAAAA
1988465 CGCTATCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1990621 original size:15 final size:15
Alignment explanation
Indices: 1990601--1990633 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1990591 TGGTTGTATT
*
1990601 GGGGGATGGCGGTGA
1 GGGGGACGGCGGTGA
1990616 GGGGGACGGCGGTGA
1 GGGGGACGGCGGTGA
1990631 GGG
1 GGG
1990634 AAAACAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.09, G:0.70, T:0.09
Consensus pattern (15 bp):
GGGGGACGGCGGTGA
Found at i:1990742 original size:21 final size:21
Alignment explanation
Indices: 1990716--1990780 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
1990706 AAGACAATCA
*
1990716 AGAGTCGAAGAAAAACTTGAT
1 AGAGTCGAAGAAAAACTTGAG
*
1990737 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAAAAACTTGAG
* *
1990758 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAAAAACTTGAG
1990779 AG
1 AG
1990781 GCATAAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.43, C:0.11, G:0.29, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAAAAACTTGAG
Found at i:1990851 original size:33 final size:33
Alignment explanation
Indices: 1990814--1990879 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1990804 AAATAGATGG
*
1990814 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
1990847 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1990880 TCTTAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1991089 original size:18 final size:18
Alignment explanation
Indices: 1991066--1991146 Score: 98
Period size: 18 Copynumber: 4.6 Consensus size: 18
1991056 AAAATATGAA
*
1991066 GAAGAAAAGAGGGAGGAT
1 GAAGAAAAGAGGGAGGAG
*
1991084 GAAGAAGAAGA--GA--TG
1 GAAGAA-AAGAGGGAGGAG
1991099 GAAGAAAAGAGGGAGGAG
1 GAAGAAAAGAGGGAGGAG
1991117 GAAGAAAAGAGGGAGGAG
1 GAAGAAAAGAGGGAGGAG
1991135 GAAGAATAAGAG
1 GAAGAA-AAGAG
1991147 ATGGAAGAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
14 4 0.07
15 6 0.11
16 2 0.04
17 2 0.04
18 31 0.57
19 9 0.17
ACGTcount: A:0.52, C:0.00, G:0.44, T:0.04
Consensus pattern (18 bp):
GAAGAAAAGAGGGAGGAG
Found at i:1991108 original size:33 final size:32
Alignment explanation
Indices: 1991066--1991127 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
1991056 AAAATATGAA
*
1991066 GAAGAAAAGAGGGAGGATGAAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAA-AAGAGATG
1991099 GAAGAAAAGAGGGAGGAGGAAGAAAAGAG
1 GAAGAAAAGAGGGAGGAGGAAGAAAAGAG
1991128 GGAGGAGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 5 0.18
33 23 0.82
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.03
Consensus pattern (32 bp):
GAAGAAAAGAGGGAGGAGGAAGAAAAGAGATG
Found at i:1992745 original size:19 final size:19
Alignment explanation
Indices: 1992721--1992769 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1992711 AATGTAGGGT
1992721 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1992740 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1992759 TAATTTTGTAT
1 TAATTTTGTAT
1992770 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1993344 original size:200 final size:200
Alignment explanation
Indices: 1992999--1993784 Score: 1419
Period size: 200 Copynumber: 3.9 Consensus size: 200
1992989 AATTTACAAT
*
1992999 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
*
1993064 CGAAACCCATAAGTAAAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* * *
1993129 ATGAGAGATTAGGTGTAATATATGTATCGATACTTTTTAATTTTGTGTCGATACTATTGGTCTAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
1993194 AATGA
196 AATGA
*
1993199 ATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
*
1993264 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* *
1993329 ATGAGAGAATAGGTGTAATATATGTATCGCCACTTTTTAATTTTGTGTTGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
1993394 AATGA
196 AATGA
*
1993399 ATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
** *
1993464 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACATGTATAAGTATATCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
*
1993529 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTATCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
1993594 AATGA
196 AATGA
*
1993599 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
*
1993664 CGAAACCCATAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
*
1993729 ATGAGAGAATATGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
1993785 ATTTAAATAT
Statistics
Matches: 560, Mismatches: 26, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
200 560 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (200 bp):
ATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:1996870 original size:184 final size:184
Alignment explanation
Indices: 1996561--1997666 Score: 1791
Period size: 184 Copynumber: 5.9 Consensus size: 184
1996551 ATATCAGCAT
*
1996561 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACTCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
* *
1996626 ATAGGTAATTTTGTAATATAACCGGTTTAGATATACCGATTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
*
1996691 TATATCGACACTTTTTAATATTGTGTCACTACTTTATGTCCAGAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
*
1996745 AAAGTGTCGATACCTTTTCAAAAAGTGTCAATTGAAAAAACATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
1996810 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
*
1996875 TATATCGAAACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
*
1996929 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAATATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
* *
1996994 ATAGGTAATTTTGTAATAAAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
1997059 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
*
1997113 AAAGTGTCGACACCTTTTCAAAAAGTGTCGACACCTTTTCAAAAAGTGTCGATTGAAAAAACATC
1 AAAGTGTCGATACCTTTTCAAAAA-----G--------T--------GTCGATTGAAAAAACATC
**
1997178 GGAACCCATAATTATAATACAATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTA
45 GGAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTA
*
1997243 TGAGAGAATAGGTCTACAACCTATATCGACACATTTTAATATTGTGTCGCTACTTTATGTCCAGA
110 TGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGA
1997308 ATGGATGAAA
175 ATGGATGAAA
* * * **
1997318 AAAGTATCGATAACTTTTCAAAAAGTATCGATTGAAAAAACATCAAAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
* *
1997383 ATAGGTAATTTTGTAATATAACCGGTATAGATATACTGGTTTTATGAGAGAATAAGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
*
1997448 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCATAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
*
1997502 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTAAAAAAACATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
* *
1997567 ATAGGTAATTTTGTAATATAACAGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
1997632 TATATCGACACTTTTTAATATTGTGTC-CATACTTT
131 TATATCGACACTTTTTAATATTGTGTCGC-TACTTT
1997667 TAAGTAACGC
Statistics
Matches: 860, Mismatches: 40, Indels: 44
0.91 0.04 0.05
Matches are distributed among these distances:
183 1 0.00
184 682 0.79
189 1 0.00
192 1 0.00
197 1 0.00
200 1 0.00
205 173 0.20
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (184 bp):
AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
Found at i:1997135 original size:21 final size:21
Alignment explanation
Indices: 1997111--1997164 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1997101 GAATGGATGA
1997111 AAAAAGTGTCGACACCTTTTC
1 AAAAAGTGTCGACACCTTTTC
1997132 AAAAAGTGTCGACACCTTTTC
1 AAAAAGTGTCGACACCTTTTC
1997153 AAAAAGTGTCGA
1 AAAAAGTGTCGA
1997165 TTGAAAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (21 bp):
AAAAAGTGTCGACACCTTTTC
Found at i:1997282 original size:389 final size:378
Alignment explanation
Indices: 1996561--1997666 Score: 1678
Period size: 389 Copynumber: 2.9 Consensus size: 378
1996551 ATATCAGCAT
* * * ** *
1996561 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACTCATAATTATAATGTA
1 AAAGTATCGATAACTTTTCAAAAAGTATCGATTGAAAAAACATCAAAACCCATAATTATAATGTA
* * * * *
1996626 ATAGGTAATTTTGTAATATAACCGGTTTAGATATACCGATTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATAAAACCGGTATAAATATACCGGTTTTATGAGAGAATAAGTCTACAACC
*
1996691 TATATCGACACTTTTTAATATTGTGTCACTACTTTATGTCCAGAATGGATGAAAAAAGTGTCG--
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAAAAAGTGTCGAA
*
1996754 --A---T---ACCTTTTCAAAAAGTGTCAATTGAAAAAACATCGGAACCCATAATTATAATGTAA
196 AAAGTGTCGAACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAA
1996811 TAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACCT
261 TAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACCT
*
1996876 ATATCGAAACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
326 ATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
* * * * **
1996929 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAATATCGGAACCCATAATTATAATGTA
1 AAAGTATCGATAACTTTTCAAAAAGTATCGATTGAAAAAACATCAAAACCCATAATTATAATGTA
*
1996994 ATAGGTAATTTTGTAATAAAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATAAAACCGGTATAAATATACCGGTTTTATGAGAGAATAAGTCTACAACC
1997059 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAAAAAGTGTCGAC
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAAAAAGTGTCG--
1997124 ACCTTTTCAAAAAGTGTCGACACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAA
194 --------AAAAAGTGTCGA-ACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAA
**
1997189 TTATAATACAATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAG
250 TTATAATGTAATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAG
*
1997254 GTCTACAACCTATATCGACACATTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
315 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
1997318 AAAGTATCGATAACTTTTCAAAAAGTATCGATTGAAAAAACATCAAAACCCATAATTATAATGTA
1 AAAGTATCGATAACTTTTCAAAAAGTATCGATTGAAAAAACATCAAAACCCATAATTATAATGTA
* * *
1997383 ATAGGTAATTTTGTAATATAACCGGTATAGATATACTGGTTTTATGAGAGAATAAGTCTACAACC
66 ATAGGTAATTTTGTAATAAAACCGGTATAAATATACCGGTTTTATGAGAGAATAAGTCTACAACC
*
1997448 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCATAATGGATGAAAAAAGTGTCG--
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAAAAAGTGTCGAA
*
1997511 --A---T---ACCTTTTCAAAAAGTGTCGATTAAAAAAACATCGGAACCCATAATTATAATGTAA
196 AAAGTGTCGAACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAA
* *
1997568 TAGGTAATTTTGTAATATAACAGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCT
261 TAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACCT
1997633 ATATCGACACTTTTTAATATTGTGTC-CATACTTT
326 ATATCGACACTTTTTAATATTGTGTCGC-TACTTT
1997667 TAAGTAACGC
Statistics
Matches: 687, Mismatches: 29, Indels: 44
0.90 0.04 0.06
Matches are distributed among these distances:
367 1 0.00
368 332 0.48
372 1 0.00
375 1 0.00
382 1 0.00
385 1 0.00
389 350 0.51
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (378 bp):
AAAGTATCGATAACTTTTCAAAAAGTATCGATTGAAAAAACATCAAAACCCATAATTATAATGTA
ATAGGTAATTTTGTAATAAAACCGGTATAAATATACCGGTTTTATGAGAGAATAAGTCTACAACC
TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAAAAAGTGTCGAA
AAAGTGTCGAACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAA
TAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACCT
ATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
Found at i:1997649 original size:573 final size:573
Alignment explanation
Indices: 1996561--1997666 Score: 1998
Period size: 573 Copynumber: 1.9 Consensus size: 573
1996551 ATATCAGCAT
* * **
1996561 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACTCATAATTATAATGTA
1 AAAGTGTCGACACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATACA
*
1996626 ATAGGTAATTTTGTAATATAACCGGTTTAGATATACCGATTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGATTTTATGAGAGAATAGGTCTACAACC
* *
1996691 TATATCGACACTTTTTAATATTGTGTCACTACTTTATGTCCAGAATGGATGAAAAAAGTGTCGAT
131 TATATCGACACATTTTAATATTGTGTCACTACTTTATGTCCAGAATGGATGAAAAAAGTATCGAT
* * **
1996756 ACCTTTTCAAAAAGTGTCAATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTT
196 AACTTTTCAAAAAGTATCAATTGAAAAAACATCAAAACCCATAATTATAATGTAATAGGTAATTT
*
1996821 TGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGAAAC
261 TGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAAGTCTACAACCTATATCGAAAC
1996886 TTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAAAAAGTGTCGATACCTTTTCAAA
326 TTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAAAAAGTGTCGATACCTTTTCAAA
* *
1996951 AAGTGTCGATTGAAAAAATATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATAAAAC
391 AAGTGTCGATTAAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATAAAAC
*
1997016 CGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
456 AGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1997081 GTGTCGC-TACTTTATGTCCAGAATGGATGAAAAAAGTGTCGACACCTTTTCAA
521 GTGTC-CATACTTTATGTCCAGAATGGATGAAAAAAGTGTCGACACCTTTTCAA
1997134 AAAGTGTCGACACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATACA
1 AAAGTGTCGACACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATACA
*
1997199 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGATTTTATGAGAGAATAGGTCTACAACC
*
1997264 TATATCGACACATTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAAAAAGTATCGAT
131 TATATCGACACATTTTAATATTGTGTCACTACTTTATGTCCAGAATGGATGAAAAAAGTATCGAT
*
1997329 AACTTTTCAAAAAGTATCGATTGAAAAAACATCAAAACCCATAATTATAATGTAATAGGTAATTT
196 AACTTTTCAAAAAGTATCAATTGAAAAAACATCAAAACCCATAATTATAATGTAATAGGTAATTT
* *
1997394 TGTAATATAACCGGTATAGATATACTGGTTTTATGAGAGAATAAGTCTACAACCTATATCGACAC
261 TGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAAGTCTACAACCTATATCGAAAC
*
1997459 TTTTTAATATTGTGTCGCTACTTTATGTCCATAATGGATGAAAAAAGTGTCGATACCTTTTCAAA
326 TTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAAAAAGTGTCGATACCTTTTCAAA
*
1997524 AAGTGTCGATTAAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAAC
391 AAGTGTCGATTAAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATAAAAC
1997589 AGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
456 AGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1997654 GTGTCCATACTTT
521 GTGTCCATACTTT
1997667 TAAGTAACGC
Statistics
Matches: 510, Mismatches: 22, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
572 1 0.00
573 509 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (573 bp):
AAAGTGTCGACACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATACA
ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGATTTTATGAGAGAATAGGTCTACAACC
TATATCGACACATTTTAATATTGTGTCACTACTTTATGTCCAGAATGGATGAAAAAAGTATCGAT
AACTTTTCAAAAAGTATCAATTGAAAAAACATCAAAACCCATAATTATAATGTAATAGGTAATTT
TGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAAGTCTACAACCTATATCGAAAC
TTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAAAAAGTGTCGATACCTTTTCAAA
AAGTGTCGATTAAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATAAAAC
AGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
GTGTCCATACTTTATGTCCAGAATGGATGAAAAAAGTGTCGACACCTTTTCAA
Found at i:2001170 original size:23 final size:23
Alignment explanation
Indices: 2001097--2001154 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
2001087 TACATATTTT
2001097 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTATCTATTAC
2001120 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTATCTATTAC
2001143 ATTATATAAGCG
1 ATTATATAAGCG
2001155 TTACCTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTATCTATTAC
Found at i:2004104 original size:26 final size:29
Alignment explanation
Indices: 2004043--2004110 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 29
2004033 TTTTGGTGAG
*
2004043 TTTAACGAGCAACGAGTCGAGCAACAAGTTTT
1 TTTAACGAGCAACGAGTCGAGCAACAA---TA
2004075 TTTAACGAGC-ACGAGTCGAGCAA-AA-A
1 TTTAACGAGCAACGAGTCGAGCAACAATA
*
2004101 TTTAATGAGC
1 TTTAACGAGC
2004111 TTAACTTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 9 0.26
30 2 0.06
31 13 0.38
32 10 0.29
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (29 bp):
TTTAACGAGCAACGAGTCGAGCAACAATA
Found at i:2004534 original size:3 final size:3
Alignment explanation
Indices: 2004526--2004555 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2004516 AATGAATAAT
2004526 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2004556 AATAGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2004780 original size:20 final size:20
Alignment explanation
Indices: 2004755--2004806 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
2004745 AGAGTGACAC
*
2004755 GGTTGACCTAAAAATTTAAA
1 GGTTGACCGAAAAATTTAAA
*
2004775 GGTTGACCGGAAAATTTAAA
1 GGTTGACCGAAAAATTTAAA
2004795 GGTTGACTCGAA
1 GGTTGAC-CGAA
2004807 TTAAAATCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (20 bp):
GGTTGACCGAAAAATTTAAA
Found at i:2007944 original size:23 final size:23
Alignment explanation
Indices: 2007914--2007972 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 23
2007904 AAAATTTTGT
2007914 TTTTCGGTGGATTTTAAATCCAC
1 TTTTCGGTGGATTTTAAATCCAC
* *
2007937 TTTTCGGTGGA--TTAATTCTAC
1 TTTTCGGTGGATTTTAAATCCAC
*
2007958 CTTTCGGTGGATTTT
1 TTTTCGGTGGATTTT
2007973 CAACACATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 18 0.58
23 13 0.42
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.47
Consensus pattern (23 bp):
TTTTCGGTGGATTTTAAATCCAC
Found at i:2009176 original size:64 final size:64
Alignment explanation
Indices: 2009075--2009203 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
2009065 AGCAGATCTA
2009075 GAGTGGTCCTAATCGGGACGGACGTATGATTTTATATTAAAGAGGTGAAATTCTTAAATTTTAG
1 GAGTGGTCCTAATCGGGACGGACGTATGATTTTATATTAAAGAGGTGAAATTCTTAAATTTTAG
*
2009139 GAGTGGTCCTAATCGGGACGGACGTATGATTTTATATTAAAGAGGTGGAATTCTTAAATTTTAG
1 GAGTGGTCCTAATCGGGACGGACGTATGATTTTATATTAAAGAGGTGAAATTCTTAAATTTTAG
2009203 G
1 G
2009204 GGAGCAAGCT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.34
Consensus pattern (64 bp):
GAGTGGTCCTAATCGGGACGGACGTATGATTTTATATTAAAGAGGTGAAATTCTTAAATTTTAG
Found at i:2012078 original size:27 final size:27
Alignment explanation
Indices: 2012036--2012102 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
2012026 TGAATAACTC
2012036 AAACTCGACTCGGTCAAAGCTCGATAA
1 AAACTCGACTCGGTCAAAGCTCGATAA
*
2012063 AAATTCGACTCGGTCAAAGCTCGATAA
1 AAACTCGACTCGGTCAAAGCTCGATAA
2012090 AAACTCGACTCGG
1 AAACTCGACTCGG
2012103 GATGACTCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (27 bp):
AAACTCGACTCGGTCAAAGCTCGATAA
Found at i:2012471 original size:99 final size:99
Alignment explanation
Indices: 2012364--2012562 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
2012354 TTGTTACTTT
2012364 GGAGTTTAGAGTTTAAAATTATTTCTTACACTCTTTTGATAATATGTTTGGTTAAATTTATTAAT
1 GGAGTTTAGAGTTTAAAATTATTTCTTACACTCTTTTGATAATATGTTTGGTTAAATTTATTAAT
2012429 TTATGTTTATATTAAGCACTGTATAGTATTAATA
66 TTATGTTTATATTAAGCACTGTATAGTATTAATA
2012463 GGAGTTTAGAGTTTAAAATTATTTCTTACACTCTTTTGATAATATGTTTGGTTAAATTTATTAAT
1 GGAGTTTAGAGTTTAAAATTATTTCTTACACTCTTTTGATAATATGTTTGGTTAAATTTATTAAT
2012528 TTATGTTTATATTAAGCACTGTATAGTATTAATA
66 TTATGTTTATATTAAGCACTGTATAGTATTAATA
2012562 G
1 G
2012563 ATTTTACTTA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (99 bp):
GGAGTTTAGAGTTTAAAATTATTTCTTACACTCTTTTGATAATATGTTTGGTTAAATTTATTAAT
TTATGTTTATATTAAGCACTGTATAGTATTAATA
Found at i:2019295 original size:46 final size:46
Alignment explanation
Indices: 2019228--2019342 Score: 165
Period size: 38 Copynumber: 2.7 Consensus size: 46
2019218 GAATAAATTG
2019228 AACATCGAATGCATTTTATGCATCGATGCACTCAGGTTTTTATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACTCAGGTTTTTATGAA
*
2019274 AACATCGAATGCA---TA---A--AATGCACTCAGGTTTTTATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACTCAGGTTTTTATGAA
2019312 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
2019343 AAGCCATGCA
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
38 34 0.58
40 1 0.02
41 2 0.03
43 2 0.03
44 1 0.02
46 19 0.32
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (46 bp):
AACATCGAATGCATTTTATGCATCGATGCACTCAGGTTTTTATGAA
Found at i:2029121 original size:180 final size:180
Alignment explanation
Indices: 2028788--2029254 Score: 683
Period size: 180 Copynumber: 2.6 Consensus size: 180
2028778 GATCCAAATT
* * * *
2028788 AAAAATGTATTGATCCACAACGATATAACAGGTAAAACTATGACAAAATCGGTATTGAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAATCGGTA-TCAAATGATA
* * * *
2028853 AAACCGGTAAAGCGGTACCGAATATATTTAAAGTGTCGGTACTTTAATATAAAGATCGACACTTC
65 AAACCGGTAAAACGCTACCG-ATATATTGAAAGTGTCGATAC-TTAATATAAAGATCGACACTTC
*
2028918 GTTAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
128 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
* * *
2028971 AAAAATGTATCGATGCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATG
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAATCGGTATC-AAATGATA
* *
2029036 AAA-CGGTAAAACGCTACCAGATATATTGAAAGTGTCGATACTT-ATATAAGGATCGACACTTTG
65 AAACCGGTAAAACGCTACC-GATATATTGAAAGTGTCGATACTTAATATAAAGATCGACACTTCG
*
2029099 TGAATTTAAAAGAGAAGCAGTTTTAGCGTCTATAAAGTGTCGATACTTTAAA
129 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
*
2029151 AAAAA-ATATCGATCCACAACGA-ATAACAGGTAAAAATATGATAAAATCGGTATCAAATGATAA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAATCGGTATCAAATGATAA
* * *
2029214 AACCGATAAAACGCTATCG-GATATTGAAAGTGTCGATACTT
66 AACCGGTAAAACGCTACCGATATATTGAAAGTGTCGATACTT
2029255 TCGTAAGTAC
Statistics
Matches: 259, Mismatches: 22, Indels: 13
0.88 0.07 0.04
Matches are distributed among these distances:
176 21 0.08
177 11 0.04
178 44 0.17
179 15 0.06
180 73 0.28
181 2 0.01
182 33 0.13
183 60 0.23
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (180 bp):
AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAATCGGTATCAAATGATAA
AACCGGTAAAACGCTACCGATATATTGAAAGTGTCGATACTTAATATAAAGATCGACACTTCGTG
AATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
Found at i:2031420 original size:15 final size:15
Alignment explanation
Indices: 2031400--2031432 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2031390 TGGTTGTATT
*
2031400 GGGGGATGGCGGTGA
1 GGGGGACGGCGGTGA
2031415 GGGGGACGGCGGTGA
1 GGGGGACGGCGGTGA
2031430 GGG
1 GGG
2031433 AAAACAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.09, G:0.70, T:0.09
Consensus pattern (15 bp):
GGGGGACGGCGGTGA
Found at i:2031559 original size:20 final size:20
Alignment explanation
Indices: 2031513--2031575 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
2031503 AAAACAATCA
*
2031513 AGAGTCGAAGAAAAACTTGAT
1 AGAGTCGAAGAAAAAC-TGAG
*
2031534 AGAGTCGAAGAGAAACTGAG
1 AGAGTCGAAGAAAAACTGAG
* *
2031554 AGAGTCGAAGATACACTGAG
1 AGAGTCGAAGAAAAACTGAG
2031574 AG
1 AG
2031576 GCATAAGGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
20 23 0.61
21 15 0.39
ACGTcount: A:0.44, C:0.11, G:0.30, T:0.14
Consensus pattern (20 bp):
AGAGTCGAAGAAAAACTGAG
Found at i:2031574 original size:18 final size:19
Alignment explanation
Indices: 2031513--2031564 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
2031503 AAAACAATCA
* *
2031513 AGAGTCGAAGAAAAACTTGAT
1 AGAGTCGAAGAGAAAC-T-AG
2031534 AGAGTCGAAGAGAAACTGAG
1 AGAGTCGAAGAGAAACT-AG
2031554 AGAGTCGAAGA
1 AGAGTCGAAGA
2031565 TACACTGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.46, C:0.10, G:0.31, T:0.13
Consensus pattern (19 bp):
AGAGTCGAAGAGAAACTAG
Found at i:2031645 original size:32 final size:32
Alignment explanation
Indices: 2031608--2031671 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
2031598 AAATAGATGG
*
2031608 AGTGGTGAAAGAAGTAGA-GTGTTGAGGGGTGA
1 AGTGGTG-AAGAAGTAGAGGTGTTAAGGGGTGA
*
2031640 AGTGGTGAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAGAAGTAGAGGTGTTAAGGGGTGA
2031672 TCTTAAGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (32 bp):
AGTGGTGAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2031903 original size:16 final size:17
Alignment explanation
Indices: 2031882--2031921 Score: 66
Period size: 15 Copynumber: 2.5 Consensus size: 17
2031872 GAGAAGAGAT
2031882 GGAAGAAAGAGGGAGG-
1 GGAAGAAAGAGGGAGGA
2031898 GGAAG-AAGAGGGAGGA
1 GGAAGAAAGAGGGAGGA
2031914 GGAAGAAA
1 GGAAGAAA
2031922 AGAGATGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.45
16 10 0.45
17 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (17 bp):
GGAAGAAAGAGGGAGGA
Found at i:2031908 original size:15 final size:16
Alignment explanation
Indices: 2031882--2031920 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
2031872 GAGAAGAGAT
2031882 GGAAGAAAGAGGGAGG-
1 GGAAG-AAGAGGGAGGA
2031898 GGAAGAAGAGGGAGGA
1 GGAAGAAGAGGGAGGA
2031914 GGAAGAA
1 GGAAGAA
2031921 AAGAGATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (16 bp):
GGAAGAAGAGGGAGGA
Found at i:2033518 original size:19 final size:19
Alignment explanation
Indices: 2033494--2033542 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2033484 AATGTAGGGT
2033494 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
2033513 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
2033532 TAATTTTGTAT
1 TAATTTTGTAT
2033543 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2034317 original size:200 final size:200
Alignment explanation
Indices: 2033772--2034556 Score: 1428
Period size: 200 Copynumber: 3.9 Consensus size: 200
2033762 AATTTACAAT
*
2033772 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
* *
2033837 CGAAACCCATAAGTAAAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATATCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
*
2033902 ATGAGAGATTAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
2033967 AATGA
196 AATGA
*
2033972 ATGGCAAACAGGGTGCAACCATAAAGTATCGATCCATATAT-AAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
*
2034036 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
*
2034101 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTTGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
2034166 AATGA
196 AATGA
* * *
2034171 ATGGCAAACAAGGTGCAACCATAAAGTGTAGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
* *
2034236 CGAAACACATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATATCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
*
2034301 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGCCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
2034366 AATGA
196 AATGA
2034371 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
*
2034436 CGAAACCCATAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
*
2034501 ATGAGAGAATATGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
2034557 ATTTAAATAT
Statistics
Matches: 561, Mismatches: 23, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
199 191 0.34
200 370 0.66
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:2037657 original size:184 final size:184
Alignment explanation
Indices: 2037347--2038431 Score: 1893
Period size: 184 Copynumber: 5.9 Consensus size: 184
2037337 ATATCAGCAT
* * *
2037347 AAAGTGTCGATACATTTTCAAAAAGTGTCGATTGAAAAAACATCGAAACTCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
* * * *
2037412 ATATGTAATTTTGTAATATAACCGGTTTAGATATACCGATTTTATGAGAGAATATGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
2037477 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
*
2037531 AAAGTGTCGATACCTTTTCAAAAAGTGTCAATTGAAAAAACATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
2037596 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
2037661 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
* *
2037715 AAAGTGTCGATACATTTTCAAAAAGTGTCGATTGAAAAAATATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
* * *
2037780 ATAGGTAATTTTGTAATAAAACTGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
*
2037845 TATATCGACACTTTTTAATATTGTGTTGCTACTTTATGTCCAGAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
* *
2037899 AAAGTGTCGACACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATATA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
*
2037964 ATATGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
* *
2038029 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCATAATAGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
* * **
2038083 AAAGTATCGATACCTTTTCAAAAAGTATCGATTGAAAAAACATCAAAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
* * *
2038148 ATAGGTAATTTTGTAATATAACCGGTATAGATATACTGGTTTTATGAGAAAATAAGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
*
2038213 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCATAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
2038267 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
* *
2038332 ATAGGTAATTTTGTAATATAACAGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
2038397 TATATCGACACTTTTTAATATTGTGTC-CATACTTT
131 TATATCGACACTTTTTAATATTGTGTCGC-TACTTT
2038432 TAAGTAACGC
Statistics
Matches: 854, Mismatches: 46, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
183 1 0.00
184 853 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (184 bp):
AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
Found at i:2041926 original size:23 final size:23
Alignment explanation
Indices: 2041853--2041910 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
2041843 TACATATTTT
2041853 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTATCTATTAC
2041876 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTATCTATTAC
2041899 ATTATATAAGCG
1 ATTATATAAGCG
2041911 TTACCTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTATCTATTAC
Found at i:2044863 original size:26 final size:29
Alignment explanation
Indices: 2044802--2044869 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 29
2044792 TTTCGGTGAG
*
2044802 TTTAACGAGCAACGAGTCGAGCAACAAGTTTT
1 TTTAACGAGCAACGAGTCGAGCAACAA---TA
2044834 TTTAACGAGC-ACGAGTCGAGCAA-AA-A
1 TTTAACGAGCAACGAGTCGAGCAACAATA
*
2044860 TTTAATGAGC
1 TTTAACGAGC
2044870 TTAACTTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 9 0.26
30 2 0.06
31 13 0.38
32 10 0.29
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (29 bp):
TTTAACGAGCAACGAGTCGAGCAACAATA
Found at i:2045300 original size:3 final size:3
Alignment explanation
Indices: 2045292--2045330 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2045282 ATTTATTTAT
2045292 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2045331 GCATTGATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2046693 original size:23 final size:24
Alignment explanation
Indices: 2046667--2046712 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
2046657 CCTAATACCA
2046667 TTAT-CATCATATTATAATTTTTT
1 TTATACATCATATTATAATTTTTT
*
2046690 TTATAAGATCATATTATAATTTT
1 TTAT-ACATCATATTATAATTTT
2046713 ACAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
25 16 0.80
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATACATCATATTATAATTTTTT
Found at i:2051604 original size:16 final size:16
Alignment explanation
Indices: 2051585--2051618 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2051575 GTAGGAGATT
2051585 ATTGAAAATTCAAAGC
1 ATTGAAAATTCAAAGC
2051601 ATTGAAAATTCAAAGC
1 ATTGAAAATTCAAAGC
2051617 AT
1 AT
2051619 CTAGATGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (16 bp):
ATTGAAAATTCAAAGC
Found at i:2052427 original size:16 final size:16
Alignment explanation
Indices: 2052406--2052438 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2052396 TGCTATCTAG
2052406 ATGCTTTGAATTTTCA
1 ATGCTTTGAATTTTCA
2052422 ATGCTTTGAATTTTCA
1 ATGCTTTGAATTTTCA
2052438 A
1 A
2052439 CAAGATAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (16 bp):
ATGCTTTGAATTTTCA
Found at i:2052769 original size:2 final size:2
Alignment explanation
Indices: 2052762--2052789 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2052752 AAAACTCTTT
2052762 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2052790 CCCAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2059147 original size:106 final size:107
Alignment explanation
Indices: 2058897--2059185 Score: 300
Period size: 106 Copynumber: 2.7 Consensus size: 107
2058887 TTTATTCGAA
* * * * * * *
2058897 ATAATATTATTGGGCGCAACCTAGTATGTTAATATTTATTTATAACAAAATAAGAAATTAA-ACT
1 ATAATATT-TTAGGCGCTACCTAATATGTTGATA-ATATTAATAACAAAATAAGTAATTAACA-T
* * * * *
2058961 ATTTTGTTGTTGTGGGATTTCAAAAGCCCATCATCTTAAATTTTG
63 ATTTTGTTATCGTAGGATTTCAAAAGCCCATCAGCTTAAACTTTG
* ** *
2059006 GTAATATTTTAGG-TTTCACTTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATAT
1 ATAATATTTTAGGCGCT-ACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATAT
* * *
2059070 TTTGTTATCGTATGATTTC-TAAGGCCAGT-AGCTTAAACTTTG
65 TTTGTTATCGTAGGATTTCAAAAGCCCA-TCAGCTTAAACTTTG
* * *
2059112 ATAATATTTTAGGCGCTACCTAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCTA-T
1 ATAATATTTTAGGCGCTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATT
2059176 TTGTTATCGT
66 TTGTTATCGT
2059186 CAGATTTTTA
Statistics
Matches: 150, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
105 11 0.07
106 71 0.47
107 43 0.29
108 18 0.12
109 7 0.05
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (107 bp):
ATAATATTTTAGGCGCTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATT
TTGTTATCGTAGGATTTCAAAAGCCCATCAGCTTAAACTTTG
Found at i:2059434 original size:107 final size:107
Alignment explanation
Indices: 2059280--2059640 Score: 314
Period size: 108 Copynumber: 3.3 Consensus size: 107
2059270 AATATTTCCG
* * *
2059280 GTAATTAACCTATTTTTTATCGTCGGATTTCTAATGCTCCATTAGCTTAAACTTTGGTAACATTT
1 GTAATTAACCTATTTTTTATCGTCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACATTT
**
2059345 TAGGCGTTACCTAATATGTTGATAATATCGATAACAAATCAA
66 TAGGCGTTATTTAATATGTTGATAATATCGATAACAAATCAA
* * *
2059387 GTAATTAACCTATTTTTTATCGTCGAATTTCTAAGGCCCCATCAGCTTTAAAAAAACTACCT-AT
1 GTAATTAACCTATTTTTTATCGTCGAATTTCTAAGGCTCCATCAGC-TT----AAACT--TTGGT
* * * ** * ** * ** *
2059451 TACATTAAATAAGCGTTATTTGTTATGTT-ATTATGATTAATAATATTTCCA
59 AACATT--TTAGGCGTTATTTAATATGTTGATAAT-ATCGATAACAAATCAA
* * * * * *
2059502 GTAATTAA-CTGATTATGTTATCGTCAAATTTATAAGGTTCTATCAGCTTAAATTTTGGTAACAT
1 GTAATTAACCT-ATT-TTTTATCGTCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* *
2059566 TTTAGACGCTATTTAATATGTTGATAATATCGATAACAAATCAA
64 TTTAGGCGTTATTTAATATGTTGATAATATCGATAACAAATCAA
* *
2059610 GTAATTAACATATTTTGTTATCGTTGAATTT
1 GTAATTAACCTATTTT-TTATCGTCGAATTT
2059641 TAATGACACA
Statistics
Matches: 191, Mismatches: 47, Indels: 31
0.71 0.17 0.12
Matches are distributed among these distances:
107 43 0.23
108 50 0.26
109 6 0.03
110 6 0.03
111 4 0.02
112 5 0.03
113 6 0.03
114 7 0.04
115 38 0.20
116 26 0.14
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Consensus pattern (107 bp):
GTAATTAACCTATTTTTTATCGTCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACATTT
TAGGCGTTATTTAATATGTTGATAATATCGATAACAAATCAA
Found at i:2059608 original size:223 final size:223
Alignment explanation
Indices: 2059099--2059746 Score: 818
Period size: 223 Copynumber: 2.9 Consensus size: 223
2059089 TAAGGCCAGT
* * * *
2059099 AGCTTAAACTTTGATAATATTTTAGGCGCTACCTAATATGTTGATAATATTGATAACAAATTAAG
1 AGCTTAAACTTTGGTAACATTTTAGGCGCTACCTAATATGTTGATAATATCGATAACAAATCAAG
* * * * *
2059164 TAATTAACCTATTTGTTATCGTCAGATTTTTAAAACTCCGTCAGCTTTAAAAATACGCTACCTAT
66 TAATTAACCTATTTTTTATCGTC-GAATTTTAAAGCCCCATCAGCTTTAAAAATA-GCTACCTAT
* *
2059229 TATATTAAATAAGCGTTATTTGTTATGTTATTATGGTTGATAATATTTCCGGTAATTAACCT-AT
129 TACATTAAATAAGCGTTATTTGTTATGTTATTATGGTTGATAATATTTCCAGTAATTAA-CTGAT
* ** * * *
2059293 T-TTTTATCGTCGGATTTCTAATGCTCCATT
193 TATGTTATCGTCAAATTTATAAGGCTCCATC
*
2059323 AGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATATCGATAACAAATCAAG
1 AGCTTAAACTTTGGTAACATTTTAGGCGCTACCTAATATGTTGATAATATCGATAACAAATCAAG
* *
2059388 TAATTAACCTATTTTTTATCGTCGAATTTCTAAGGCCCCATCAGCTTTAAAAA-AACTACCTATT
66 TAATTAACCTATTTTTTATCGTCGAATTT-TAAAGCCCCATCAGCTTTAAAAATAGCTACCTATT
* *
2059452 ACATTAAATAAGCGTTATTTGTTATGTTATTATGATTAATAATATTTCCAGTAATTAACTGATTA
130 ACATTAAATAAGCGTTATTTGTTATGTTATTATGGTTGATAATATTTCCAGTAATTAACTGATTA
* *
2059517 TGTTATCGTCAAATTTATAAGGTTCTATC
195 TGTTATCGTCAAATTTATAAGGCTCCATC
* * **
2059546 AGCTTAAATTTTGGTAACATTTTAGACGCTATTTAATATGTTGATAATATCGATAACAAATCAAG
1 AGCTTAAACTTTGGTAACATTTTAGGCGCTACCTAATATGTTGATAATATCGATAACAAATCAAG
* * * * * * * *
2059611 TAATTAACATATTTTGTTATCGTTGAATTTTAATGACACATCAGTTTTAAAAATGTGTTACCTAT
66 TAATTAACCTATTTT-TTATCGTCGAATTTTAAAGCCCCATCAGCTTTAAAAAT-AGCTACCTAT
* * * ** * *
2059676 TACGTTATATAAGCGCTACCTGTTATGTTATTATGGTTGATAATATTTCTATTAATTAA-TCGAT
129 TACATTAAATAAGCGTTATTTGTTATGTTATTATGGTTGATAATATTTCCAGTAATTAACT-GAT
2059740 TATGTTA
193 TATGTTA
2059747 AAGTTAATAT
Statistics
Matches: 370, Mismatches: 47, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
221 2 0.01
222 66 0.18
223 120 0.32
224 115 0.31
225 67 0.18
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (223 bp):
AGCTTAAACTTTGGTAACATTTTAGGCGCTACCTAATATGTTGATAATATCGATAACAAATCAAG
TAATTAACCTATTTTTTATCGTCGAATTTTAAAGCCCCATCAGCTTTAAAAATAGCTACCTATTA
CATTAAATAAGCGTTATTTGTTATGTTATTATGGTTGATAATATTTCCAGTAATTAACTGATTAT
GTTATCGTCAAATTTATAAGGCTCCATC
Found at i:2061978 original size:20 final size:20
Alignment explanation
Indices: 2061949--2062059 Score: 135
Period size: 20 Copynumber: 5.8 Consensus size: 20
2061939 AGAATAGTTT
* * *
2061949 ACTATTGCAATACAAAAATG
1 ACTATCGCAATGCGAAAATG
*
2061969 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2061989 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
2062005 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
2062023 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
2062043 ACTATCGCAATGCGAAA
1 ACTATCGCAATGCGAAA
2062060 TGAAAATCGC
Statistics
Matches: 79, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
14 7 0.09
16 4 0.05
17 4 0.05
18 4 0.05
20 60 0.76
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:2062128 original size:20 final size:20
Alignment explanation
Indices: 2062083--2062131 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2062073 GTGATTCTCT
2062083 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTTG
* * *
2062103 CATTGCGATATTC-ATTTTCG
1 CGTTGCGATAGTCAAATTT-G
2062123 CGTTGCGAT
1 CGTTGCGAT
2062132 TTTGTTGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTTG
Found at i:2062175 original size:33 final size:34
Alignment explanation
Indices: 2062105--2062198 Score: 91
Period size: 33 Copynumber: 2.8 Consensus size: 34
2062095 CAAATTTGCA
* * * * *
2062105 TTGCGATATTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATATTCATTTTCACATTGCGATTCTCTCG
*
2062139 TTGCGATTTTCA-TTTCACATTGCGATTCTCTCG
1 TTGCGATATTCATTTTCACATTGCGATTCTCTCG
* ** *
2062172 TTGCGATAGTCAAATTCGCATTGCGAT
1 TTGCGATATTCATTTTCACATTGCGAT
2062199 AGTCATTTTC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
33 26 0.53
34 23 0.47
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (34 bp):
TTGCGATATTCATTTTCACATTGCGATTCTCTCG
Found at i:2062197 original size:20 final size:20
Alignment explanation
Indices: 2062172--2062258 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
2062162 GATTCTCTCG
**
2062172 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
2062192 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
2062212 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* * *
2062232 TTACGATAGACATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
2062252 TTGCGAT
1 TTGCGAT
2062259 TTTAAGTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:2064197 original size:14 final size:14
Alignment explanation
Indices: 2064178--2064213 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2064168 ATTGTTTAAT
2064178 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2064192 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2064206 TGATTTGT
1 TGATTTGT
2064214 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2064392 original size:33 final size:33
Alignment explanation
Indices: 2064350--2064417 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
2064340 AACGAGAGAA
* **
2064350 TCGCATTGCGATTCACTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCACTCGTTACGATAGTCATT
*
2064383 TCGCATTGCGATTCTCTCGTTACGATAGTCATT
1 TCGCATTGCGATTCACTCGTTACGATAGTCATT
2064416 TC
1 TC
2064418 CGCGTTGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (33 bp):
TCGCATTGCGATTCACTCGTTACGATAGTCATT
Found at i:2064430 original size:20 final size:20
Alignment explanation
Indices: 2064400--2064488 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
2064390 GCGATTCTCT
*
2064400 CGTTACGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
2064420 CGTTGCAATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* *
2064440 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
*
2064460 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
2064480 CGTTGCGAT
1 CGTTGCGAT
2064489 TTCCGCGTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 56 0.97
21 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:2066953 original size:24 final size:24
Alignment explanation
Indices: 2066919--2066972 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2066909 CTGAAAAATC
2066919 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
2066943 ATCAAAGTCCGGGTATTGATCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2066967 ATCAAA
1 ATCAAA
2066973 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2067856 original size:20 final size:20
Alignment explanation
Indices: 2067833--2067919 Score: 120
Period size: 20 Copynumber: 4.3 Consensus size: 20
2067823 CAGAATCTCG
2067833 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
2067853 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
2067873 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
2067894 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
2067914 TTGCGA
1 TTGCGA
2067920 ATTAGGAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 41 0.73
21 15 0.27
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:2067940 original size:21 final size:21
Alignment explanation
Indices: 2067916--2067961 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2067906 TATTCGCATT
2067916 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
2067937 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
2067958 GCGA
1 GCGA
2067962 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:2069271 original size:31 final size:30
Alignment explanation
Indices: 2069207--2069286 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 30
2069197 AAATAATTTA
* * *
2069207 TTTATT-ATTAAAATATT-ATTTTTATAAT
1 TTTATTGATAAAAATATTAATATTGATAAT
2069235 TTTATTGATAAAAATATTAATATTGATATAT
1 TTTATTGATAAAAATATTAATATTGATA-AT
2069266 TTTATTGAAATAAAAATATTA
1 TTTATTG--ATAAAAATATTA
2069287 TAAATTATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
28 6 0.14
29 10 0.23
30 7 0.16
31 9 0.20
33 12 0.27
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (30 bp):
TTTATTGATAAAAATATTAATATTGATAAT
Found at i:2069296 original size:31 final size:29
Alignment explanation
Indices: 2069198--2069297 Score: 75
Period size: 31 Copynumber: 3.4 Consensus size: 29
2069188 AAAATATCAA
*
2069198 AATAATT-TA-TTTATT-ATTAAAATATT
1 AATAATTATATTTTATTGATAAAAATATT
**
2069224 -ATTTTTATAATTTTATTGATAAAAATATT
1 AATAATTAT-ATTTTATTGATAAAAATATT
*
2069253 AATATTGATATATTTTATTGAAATAAAAATATT
1 AATAAT--TATATTTTATTG--ATAAAAATATT
2069286 -ATAAATTATATT
1 AAT-AATTATATT
2069298 AATTAGTTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
25 4 0.07
26 1 0.02
27 1 0.02
28 6 0.10
29 10 0.17
30 4 0.07
31 15 0.25
32 5 0.08
33 13 0.22
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
AATAATTATATTTTATTGATAAAAATATT
Found at i:2069377 original size:23 final size:23
Alignment explanation
Indices: 2069328--2069378 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2069318 ATGTTATATT
**
2069328 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
2069351 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
2069374 ATATT
1 ATATT
2069379 ATTAGATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:2069459 original size:27 final size:26
Alignment explanation
Indices: 2069392--2069463 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
2069382 AGATTAATGT
2069392 TAAATATATAAATAATATTATTCATTA
1 TAAATA-ATAAATAATATTATTCATTA
* * *
2069419 TTAATAATTTAATAATATTATTTA-TA
1 TAAATAA-TAAATAATATTATTCATTA
2069445 TGAAATTAATAAATAATAT
1 T-AAA-TAATAAATAATAT
2069464 AAATTTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
26 4 0.11
27 30 0.81
28 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (26 bp):
TAAATAATAAATAATATTATTCATTA
Found at i:2069533 original size:23 final size:23
Alignment explanation
Indices: 2069503--2069552 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2069493 TTAAAATAAA
2069503 AATATAATAT-CTTATATTATTAT
1 AATATAAT-TGCTTATATTATTAT
* *
2069526 AATATAATTGGTTATTTTATTAT
1 AATATAATTGCTTATATTATTAT
2069549 AATA
1 AATA
2069553 CTAAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (23 bp):
AATATAATTGCTTATATTATTAT
Found at i:2069571 original size:22 final size:23
Alignment explanation
Indices: 2069543--2069589 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
2069533 TTGGTTATTT
2069543 TATTATAATACTAAAAATA-TAA
1 TATTATAATACTAAAAATATTAA
* * *
2069565 TATTATATTATTAGAAATATTAA
1 TATTATAATACTAAAAATATTAA
2069588 TA
1 TA
2069590 AATATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TATTATAATACTAAAAATATTAA
Found at i:2069658 original size:24 final size:24
Alignment explanation
Indices: 2069589--2069664 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 24
2069579 AAATATTAAT
* *
2069589 AAATATATTT-TTAATATTTTAATA
1 AAATAT-TTTATTAATATTATATTA
*
2069613 ATTAATATTTTGATTAAAATTATATTA
1 A--AATATTTT-ATTAATATTATATTA
*
2069640 AAATATTTTATTAATATTAAATTA
1 AAATATTTTATTAATATTATATTA
2069664 A
1 A
2069665 TAAAATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
24 15 0.35
25 11 0.26
26 5 0.12
27 12 0.28
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (24 bp):
AAATATTTTATTAATATTATATTA
Found at i:2071757 original size:16 final size:18
Alignment explanation
Indices: 2071732--2071778 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
2071722 ATATGGAATT
2071732 AGATTCTAATTCC-T-AC
1 AGATTCTAATTCCTTCAC
*
2071748 AGATTTTAATTCCTTCAC
1 AGATTCTAATTCCTTCAC
2071766 AGATTCTAATTCC
1 AGATTCTAATTCC
2071779 ATCATAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 14 0.52
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.40
Consensus pattern (18 bp):
AGATTCTAATTCCTTCAC
Found at i:2072222 original size:8 final size:10
Alignment explanation
Indices: 2072215--2072250 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
2072205 TAAATTTTAT
2072215 TATAT-TATA
1 TATATATATA
2072224 T-TATATATA
1 TATATATATA
2072233 TATATATATA
1 TATATATATA
2072243 TA-ATATAT
1 TATATATAT
2072251 TTTTTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 3 0.12
9 12 0.48
10 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TATATATATA
Found at i:2072232 original size:2 final size:2
Alignment explanation
Indices: 2072215--2072250 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2072205 TAAATTTTAT
2072215 TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2072251 TTTTTTTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2072348 original size:11 final size:11
Alignment explanation
Indices: 2072329--2072388 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
2072319 TATTGTATAG
2072329 TTTTGAAAATA
1 TTTTGAAAATA
*
2072340 TTTTTAAAATA
1 TTTTGAAAATA
*
2072351 TATAT-AATATATA
1 T-TTTGAA-A-ATA
*
2072364 TTTCGAAAATA
1 TTTTGAAAATA
2072375 TTTTGAAAATA
1 TTTTGAAAATA
2072386 TTT
1 TTT
2072389 ATATATTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
11 29 0.73
12 5 0.12
13 6 0.15
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:2072423 original size:39 final size:36
Alignment explanation
Indices: 2072311--2072671 Score: 269
Period size: 39 Copynumber: 9.8 Consensus size: 36
2072301 ACGGTTTTCG
* * *
2072311 AAAA-TATATATTGTATAGTTTTGAAAAT-ATTTTT
1 AAAATTATATATTATATAGTTTTTAAAATCATTTTA
* **
2072345 AAAATATATATAATATATA-TTTCGAAAAT-ATTTTGA
1 AAAAT-TATATATTATATAGTTTTTAAAATCATTTT-A
2072381 AAATATTTATATATTATATAGTTTTTAAAAGTCATTTTA
1 AAA-A-TTATATATTATATAGTTTTTAAAA-TCATTTTA
* * *
2072420 AAATATATATATATAATATAATTTTTAAAA-CATTTCA
1 AAA-AT-TATATATTATATAGTTTTTAAAATCATTTTA
* * *
2072457 AAAATTATATAATATGTAGTTTTTGAAA-CATTTGTGA
1 AAAATTATATATTATATAGTTTTTAAAATCATTT-T-A
*
2072494 AAACA-TATATATTATATAGTTTTGAAAAT-ATTTTTGA
1 AAA-ATTATATATTATATAGTTTTTAAAATCA-TTTT-A
2072531 AAACATTTATATATTATATAGTTTTTAAAAT-ATTTTTTA
1 AAA-A-TTATATATTATATAGTTTTTAAAATCA--TTTTA
* * * *
2072570 AAAACTTATATAATACATAATTTTGAAAA-CATTTTGA
1 AAAA-TTATATATTATATAGTTTTTAAAATCATTTT-A
* *
2072607 AAACATTTATATATTATATAATTTTTAAAAGCATTTT-
1 AAA-A-TTATATATTATATAGTTTTTAAAATCATTTTA
* *
2072644 GAAATTATATATTATAT-GTTTTTGAAAT
1 AAAATTATATATTATATAGTTTTTAAAAT
2072672 TACTTTTTTA
Statistics
Matches: 272, Mismatches: 34, Indels: 42
0.78 0.10 0.12
Matches are distributed among these distances:
34 12 0.04
35 50 0.18
36 21 0.08
37 60 0.22
38 57 0.21
39 62 0.23
40 10 0.04
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (36 bp):
AAAATTATATATTATATAGTTTTTAAAATCATTTTA
Found at i:2072429 original size:37 final size:36
Alignment explanation
Indices: 2072314--2072671 Score: 245
Period size: 37 Copynumber: 9.7 Consensus size: 36
2072304 GTTTTCGAAA
* *
2072314 ATATATATTGTATAGTTTTGAAAAT-ATTTTTAAAAT
1 ATATATATTATATAGTTTTTAAAATCA-TTTTAAAAT
* **
2072350 ATATATAATATATA-TTTCGAAAAT-ATTTTGAAAAT
1 ATATATATTATATAGTTTTTAAAATCATTTT-AAAAT
2072385 ATTTATATATTATATAGTTTTTAAAAGTCATTTTAAAAT
1 A--TATATATTATATAGTTTTTAAAA-TCATTTTAAAAT
* *
2072424 ATATATATATAATATAATTTTTAAAA-CATTTCAAAA-
1 ATATATAT-T-ATATAGTTTTTAAAATCATTTTAAAAT
* * * *
2072460 ATTATATAATATGTAGTTTTTGAAA-CATTTGTGAAAAC
1 A-TATATATTATATAGTTTTTAAAATCATTT-T-AAAAT
*
2072498 ATATATATTATATAGTTTTGAAAAT-ATTTTTGAAAACAT
1 ATATATATTATATAGTTTTTAAAATCA-TTTT--AAA-AT
*
2072537 TTATATATTATATAGTTTTTAAAAT-ATTTTTTAAAA-
1 ATATATATTATATAGTTTTTAAAATCA--TTTTAAAAT
* * * *
2072573 ACTTATATAATACATAATTTTGAAAA-CATTTTGAAAACAT
1 A--TATATATTATATAGTTTTTAAAATCATTTT--AAA-AT
* * * *
2072613 TTATATATTATATAATTTTTAAAAGCATTTTGAAAT
1 ATATATATTATATAGTTTTTAAAATCATTTTAAAAT
*
2072649 -TATATATTATAT-GTTTTTGAAAT
1 ATATATATTATATAGTTTTTAAAAT
2072672 TACTTTTTTA
Statistics
Matches: 263, Mismatches: 34, Indels: 52
0.75 0.10 0.15
Matches are distributed among these distances:
34 12 0.05
35 45 0.17
36 20 0.08
37 62 0.24
38 61 0.23
39 53 0.20
40 10 0.04
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (36 bp):
ATATATATTATATAGTTTTTAAAATCATTTTAAAAT
Found at i:2072543 original size:150 final size:150
Alignment explanation
Indices: 2072339--2072679 Score: 389
Period size: 150 Copynumber: 2.3 Consensus size: 150
2072329 TTTTGAAAAT
* * * *
2072339 ATTTTTAAAATATATATAATATATA-TTTCGAAAATA-TTTTGAAAATATTTATATATTATATAG
1 ATTTTGAAAA-ATATATATTATATAGTTTTGAAAATATTTTTGAAAACATTTATATATTATATAG
* *
2072402 TTTTTAAAAGTCA-TTTT-AAAA-TATATATATATAATATAATTTTTAAAACA-TTTCAAAA-A-
65 TTTTTAAAA-T-ATTTTTAAAAACT-TATATA-AT-ACATAATTTTGAAAACATTTTCAAAACAT
* * *
2072461 TTATATAATATGTAGTTTTTGAAA-C
125 TTATATAATATATAATTTTTAAAAGC
2072486 ATTTGTGAAAACATATATATTATATAGTTTTGAAAATATTTTTGAAAACATTTATATATTATATA
1 ATTT-TGAAAA-ATATATATTATATAGTTTTGAAAATATTTTTGAAAACATTTATATATTATATA
*
2072551 GTTTTTAAAATATTTTTTAAAAACTTATATAATACATAATTTTGAAAACATTTTGAAAACATTTA
64 GTTTTTAAAATA-TTTTTAAAAACTTATATAATACATAATTTTGAAAACATTTTCAAAACATTTA
*
2072616 TATATTATATAATTTTTAAAAGC
128 TATAATATATAATTTTTAAAAGC
* *
2072639 ATTTTG-AAATTATATATTATAT-GTTTTTGAAATTACTTTTT
1 ATTTTGAAAAATATATATTATATAG-TTTTGAAAATA-TTTTT
2072680 TATATTTATT
Statistics
Matches: 167, Mismatches: 14, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
147 4 0.02
148 19 0.11
149 27 0.16
150 70 0.42
151 19 0.11
152 23 0.14
153 5 0.03
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (150 bp):
ATTTTGAAAAATATATATTATATAGTTTTGAAAATATTTTTGAAAACATTTATATATTATATAGT
TTTTAAAATATTTTTAAAAACTTATATAATACATAATTTTGAAAACATTTTCAAAACATTTATAT
AATATATAATTTTTAAAAGC
Found at i:2072604 original size:38 final size:37
Alignment explanation
Indices: 2072284--2072647 Score: 214
Period size: 38 Copynumber: 9.7 Consensus size: 37
2072274 AAAGTATAAT
*
2072284 ATATATAATTTTAGAAAACGGTTTTCG-AAAA--TATATA
1 ATATATAATTTT-GAAAAC-ATTTT-GAAAAACTTATATA
* * * * *
2072321 TTGTATAGTTTTGAAAATATTTT-TAAAA-TATATATA
1 ATATATAATTTTGAAAACATTTTGAAAAACT-TATATA
* * *
2072357 ATATAT-ATTTCGAAAATATTTTGAAAATATTTATATA
1 ATATATAATTTTGAAAACATTTTGAAAA-ACTTATATA
* * *
2072394 TTATATAGTTTTTAAAAGTCATTTT--AAAA-TATATATA
1 ATATATAATTTTGAAAA--CATTTTGAAAAACT-TATATA
* *
2072431 TATAATATAATTTTTAAAACA-TTTCAAAAA-TTATATA
1 -AT-ATATAATTTTGAAAACATTTTGAAAAACTTATATA
* * *
2072468 ATATGTAGTTTTTG-AAACATTTGTG-AAAACATATATA
1 ATATATA-ATTTTGAAAACATTT-TGAAAAACTTATATA
* * * *
2072505 TTATATAGTTTTGAAAATATTTTTGAAAACATTTATATA
1 ATATATAATTTTGAAAACA-TTTTGAAAA-ACTTATATA
* * * * *
2072544 TTATATAGTTTTTAAAATATTTTTTAAAAACTTATATA
1 ATATATAATTTTGAAAACA-TTTTGAAAAACTTATATA
* *
2072582 ATACATAATTTTGAAAACATTTTGAAAACATTTATATA
1 ATATATAATTTTGAAAACATTTTGAAAA-ACTTATATA
* *
2072620 TTATATAATTTTTAAAAGCATTTTGAAA
1 ATATATAATTTTGAAAA-CATTTTGAAA
2072648 TTATATATTA
Statistics
Matches: 262, Mismatches: 41, Indels: 46
0.75 0.12 0.13
Matches are distributed among these distances:
34 4 0.02
35 27 0.10
36 39 0.15
37 62 0.24
38 67 0.26
39 58 0.22
40 5 0.02
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
ATATATAATTTTGAAAACATTTTGAAAAACTTATATA
Found at i:2072605 original size:11 final size:11
Alignment explanation
Indices: 2072589--2072614 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2072579 ATAATACATA
2072589 ATTTTGAAAAC
1 ATTTTGAAAAC
2072600 ATTTTGAAAAC
1 ATTTTGAAAAC
2072611 ATTT
1 ATTT
2072615 ATATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (11 bp):
ATTTTGAAAAC
Found at i:2072733 original size:16 final size:17
Alignment explanation
Indices: 2072712--2072745 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2072702 TTATTATTTC
*
2072712 TTTTATTTCTTTT-TTT
1 TTTTATTTATTTTGTTT
2072728 TTTTATTTATTTTGTTT
1 TTTTATTTATTTTGTTT
2072745 T
1 T
2072746 GTTTCAGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.09, C:0.03, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTATTTATTTTGTTT
Found at i:2075046 original size:182 final size:182
Alignment explanation
Indices: 2074738--2075311 Score: 839
Period size: 182 Copynumber: 3.2 Consensus size: 182
2074728 TACGCGTACT
* * * * *
2074738 TATTAAAGTATCGACACTTTAAATATATCCGATAGTGCT-T-TACCGGTTTTGTCATTTCGAGAC
1 TATTAAAGTATCGACACTTTCAATATATTCGAT--TGCTCTATACCGTTTTTGTCCTTTAGAGAC
* * * * *
2074801 CGGTTTTGTCATATTTTTACCTATTATATCGTTGTAGACCAATACATTGTTATAAAATATCGACA
64 CGATTTTGTCATATTTTTACCTGTTATATCGTTGTAGATCGATACATTGTTATAAAGTATCGACA
**
2074866 CTTTATAGGCGCTAAAACTAATTCTCTTTTAAATTCACAAAGTGTCGATACTTA
129 CTTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * *
2074920 TATTAAAGTAACGACACTTTCAATATATTCGGTTGCTCTATACCATTTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATTCGATTGCTCTATACCGTTTTTGTCCTTTAGAGACCG
* * *
2074985 ATTTTGTCATATTTTTATCTGTTATATCGTTGTGGATTGATACATTGTTATAAAGTATCGACACT
66 ATTTTGTCATATTTTTACCTGTTATATCGTTGTAGATCGATACATTGTTATAAAGTATCGACACT
*
2075050 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCTATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* **
2075102 TATTAAAGTATCGACACTTTCAATATATTTGATCACTCTATACCGGTTTTT-TCCTTTAGAGACC
1 TATTAAAGTATCGACACTTTCAATATATTCGATTGCTCTATACC-GTTTTTGTCCTTTAGAGACC
*
2075166 GATTTTGTCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTGTTATAAAGTATCGACAC
65 GATTTTGTCATATTTTTACCTGTTATATCGTTGTAGATCGATACATTGTTATAAAGTATCGACAC
** * * *
2075231 TTTATAGGTTCTGAAACTGCTTCTCTTTTAAATTCGCAAAGTGTTGATACTTA
130 TTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
*
2075284 TATTAAAGTATCGATACTTTCAATATAT
1 TATTAAAGTATCGACACTTTCAATATAT
2075312 CTGGTACGTT
Statistics
Matches: 354, Mismatches: 35, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
180 4 0.01
181 1 0.00
182 344 0.97
183 5 0.01
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAATATATTCGATTGCTCTATACCGTTTTTGTCCTTTAGAGACCG
ATTTTGTCATATTTTTACCTGTTATATCGTTGTAGATCGATACATTGTTATAAAGTATCGACACT
TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Found at i:2080564 original size:17 final size:17
Alignment explanation
Indices: 2080530--2080580 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
2080520 TAAAAGTAAT
*
2080530 ATTAAATT-TTATTCTAA
1 ATTAAATTATT-TTTTAA
2080547 ATTAAATTATTTTTTAA
1 ATTAAATTATTTTTTAA
* * *
2080564 ATTTATTTACTTTTTAA
1 ATTAAATTATTTTTTAA
2080581 TAGTATGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 27 0.93
18 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTAAATTATTTTTTAA
Found at i:2082352 original size:2 final size:2
Alignment explanation
Indices: 2082345--2082369 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2082335 ATGAATTTAT
2082345 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2082370 TTATTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2097086 original size:20 final size:20
Alignment explanation
Indices: 2097057--2097098 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2097047 TCCAAATTCA
2097057 CAACGCGAATATGTAAATCG
1 CAACGCGAATATGTAAATCG
* * *
2097077 CAACGTGAATCTGTAATTCG
1 CAACGCGAATATGTAAATCG
2097097 CA
1 CA
2097099 GCACATAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (20 bp):
CAACGCGAATATGTAAATCG
Found at i:2097114 original size:20 final size:20
Alignment explanation
Indices: 2097091--2097136 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2097081 GTGAATCTGT
* *
2097091 AATTCGCAGCACATAAGTCA
1 AATTCGCAACACAGAAGTCA
2097111 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
2097131 AATTCG
1 AATTCG
2097137 TAAAGCGCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:2097322 original size:22 final size:22
Alignment explanation
Indices: 2097287--2097340 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
2097277 TCACTCTCTA
* *
2097287 CGACGACATCTGTCCCCATTTC
1 CGACGAAATCTGTCCCCATCTC
*
2097309 CGATGAAATCTGTCCCCATCTC
1 CGACGAAATCTGTCCCCATCTC
2097331 CGACGAAATC
1 CGACGAAATC
2097341 CGTCTATCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.24
Consensus pattern (22 bp):
CGACGAAATCTGTCCCCATCTC
Found at i:2097733 original size:19 final size:20
Alignment explanation
Indices: 2097709--2097761 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
2097699 AAATCGTAAC
2097709 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
*
2097728 GCGATTTTCA-TTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
2097747 GCGATTTTAAGTTTC
1 GCGATTTTAAGTTTC
2097762 AGAAATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 26 0.84
20 5 0.16
ACGTcount: A:0.13, C:0.17, G:0.23, T:0.47
Consensus pattern (20 bp):
GCGATTTTAAGTTTCGCGTT
Found at i:2099572 original size:21 final size:21
Alignment explanation
Indices: 2099548--2099599 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
2099538 GACAATGGTG
* *
2099548 CTTTACGTGGTGAGGTATCTA
1 CTTTACGTGATGAGGTAGCTA
2099569 CTTTACGTGATGAGGTAGCTA
1 CTTTACGTGATGAGGTAGCTA
*
2099590 CTCTACGTGA
1 CTTTACGTGA
2099600 GATTGTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (21 bp):
CTTTACGTGATGAGGTAGCTA
Found at i:2099907 original size:21 final size:21
Alignment explanation
Indices: 2099879--2099955 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
2099869 GAAGCACCTG
*
2099879 TCATCGTTCAAGAGGCCTCTC
1 TCATCGTTCAAGAGGCCCCTC
*
2099900 -CTATCGTTCAAGAGGCCCCTG
1 TC-ATCGTTCAAGAGGCCCCTC
*
2099921 TCATCGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
2099942 CCACCGTTCGAGAG
1 TCATCGTTCAAGAG
2099956 CCTGATTCAC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.02
21 45 0.96
22 1 0.02
ACGTcount: A:0.19, C:0.34, G:0.22, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:2099950 original size:42 final size:42
Alignment explanation
Indices: 2099875--2099955 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
2099865 GCCTGAAGCA
* *
2099875 CCTGTCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCCTCTCCCACCGTTCAAGAGGCC
*
2099917 CCTGTCATCGTTCAAGAGGTCC-CTCCCACCGTTCGAGAG
1 CCTGTCATCGTTCAAGAGG-CCTCTCCCACCGTTCAAGAG
2099956 CCTGATTCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.19, C:0.35, G:0.22, T:0.25
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGGCCTCTCCCACCGTTCAAGAGGCC
Found at i:2101328 original size:13 final size:14
Alignment explanation
Indices: 2101303--2101335 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
2101293 AAATTGATGT
2101303 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
2101317 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
2101330 ATTTGT
1 ATTTGT
2101336 TTAATTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:2101497 original size:20 final size:20
Alignment explanation
Indices: 2101467--2101530 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
2101457 CTTTCACAAC
2101467 GCGAAAGTCAAATTCGCGTT
1 GCGAAAGTCAAATTCGCGTT
***
2101487 GC-AATAGTCAAATTCGCAAC
1 GCGAA-AGTCAAATTCGCGTT
2101507 GCGAAAGTCAAATTCGCGTT
1 GCGAAAGTCAAATTCGCGTT
2101527 GCGA
1 GCGA
2101531 TTTTCACGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCGTT
Found at i:2103798 original size:12 final size:12
Alignment explanation
Indices: 2103783--2103823 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2103773 AAGCCGGTTG
2103783 TGATTGAGATTT
1 TGATTGAGATTT
**
2103795 TGATTTTGATTT
1 TGATTGAGATTT
*
2103807 TGATTGCGATTT
1 TGATTGAGATTT
2103819 TGATT
1 TGATT
2103824 TCCTTTTGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.20, C:0.02, G:0.22, T:0.56
Consensus pattern (12 bp):
TGATTGAGATTT
Found at i:2103799 original size:6 final size:6
Alignment explanation
Indices: 2103790--2103824 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2103780 TTGTGATTGA
**
2103790 GATTTT GATTTT GATTTT GATTGC GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
2103825 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:2106063 original size:24 final size:24
Alignment explanation
Indices: 2106029--2106082 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2106019 CTGAAACATC
2106029 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2106053 ATCAAAGTCCGAGTATTGACTAAG
1 ATCAAAATCCGAGTATTGACCAAG
2106077 ATCAAA
1 ATCAAA
2106083 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2106096 original size:24 final size:24
Alignment explanation
Indices: 2106029--2106098 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
2106019 CTGAAACATC
* * * *
2106029 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACTAAG
* *
2106053 ATCAAAGTCCGAGTATTGACTAAG
1 ATCAAAGTCCGAATACTGACTAAG
* *
2106077 ATCAAATTTCGAATACTGACTA
1 ATCAAAGTCCGAATACTGACTA
2106099 GTACTCACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACTAAG
Found at i:2107041 original size:20 final size:19
Alignment explanation
Indices: 2106997--2107085 Score: 65
Period size: 20 Copynumber: 4.5 Consensus size: 19
2106987 CAAAACATTT
*
2106997 GTGTTGCGAAAATAAAA-C
1 GTGTTGCGAAATTAAAATC
*
2107015 ATGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAA-TC
2107035 GTGTTGCG-AATTCGAAAATC
1 GTGTTGCGAAATT--AAAATC
* * * *
2107055 GAGTTTCGAATTTGAAATTC
1 GTGTTGCGAAATT-AAAATC
2107075 AGTGTTGCGAA
1 -GTGTTGCGAA
2107086 TTTGTAAATC
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
18 15 0.27
19 4 0.07
20 22 0.39
21 15 0.27
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.31
Consensus pattern (19 bp):
GTGTTGCGAAATTAAAATC
Found at i:2107086 original size:21 final size:21
Alignment explanation
Indices: 2107016--2107094 Score: 83
Period size: 20 Copynumber: 3.8 Consensus size: 21
2107006 AAATAAAACA
* *
2107016 TGTTGCGAAATTAAAATTC-G
1 TGTTGCGAATTTGAAATTCAG
* *
2107036 TGTTGCGAATTCGAAAATCGAG
1 TGTTGCGAATTTGAAATTC-AG
2107058 T-TT-CGAATTTGAAATTCAG
1 TGTTGCGAATTTGAAATTCAG
2107077 TGTTGCGAATTTGTAAAT
1 TGTTGCGAATTTG-AAAT
2107095 CACAACGCGA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 3 0.06
20 29 0.60
21 10 0.21
22 6 0.12
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (21 bp):
TGTTGCGAATTTGAAATTCAG
Found at i:2107124 original size:20 final size:20
Alignment explanation
Indices: 2107037--2107149 Score: 86
Period size: 20 Copynumber: 5.6 Consensus size: 20
2107027 TAAAATTCGT
* *
2107037 GTTGCGAATTCGAAAATCGA-
1 GTTGCGAATTTGTAAATC-AC
* *
2107057 GTTTCGAATTTG-AAATTCAGT
1 GTTGCGAATTTGTAAA-TCA-C
2107078 GTTGCGAATTTGTAAATCAC
1 GTTGCGAATTTGTAAATCAC
***
2107098 AACGCGAATTTGTAAATCAC
1 GTTGCGAATTTGTAAATCAC
* *
2107118 GTTGCGAATTTGGAAATCGC
1 GTTGCGAATTTGTAAATCAC
* *
2107138 ATTGTGAATTTG
1 GTTGCGAATTTG
2107150 ACTTATGTGT
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
19 4 0.05
20 54 0.72
21 14 0.19
22 3 0.04
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTGTAAATCAC
Found at i:2107201 original size:20 final size:20
Alignment explanation
Indices: 2107156--2107204 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2107146 TTTGACTTAT
2107156 GTGTTGCGATTTACAGATTC
1 GTGTTGCGATTTACAGATTC
** *
2107176 ACGTTGCGATTTACATATTC
1 GTGTTGCGATTTACAGATTC
2107196 GTGTTGCGA
1 GTGTTGCGA
2107205 ATTTGGAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.39
Consensus pattern (20 bp):
GTGTTGCGATTTACAGATTC
Found at i:2118401 original size:22 final size:23
Alignment explanation
Indices: 2118365--2118416 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2118355 TTTAGATATT
*
2118365 TTTATACAATAA-TTTC-AAAAA
1 TTTATAAAATAATTTTCTAAAAA
*
2118386 GTTTATAAAATCATTTTCTAAAAA
1 -TTTATAAAATAATTTTCTAAAAA
2118410 TTTATAA
1 TTTATAA
2118417 TTTATCTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 11 0.42
24 5 0.19
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (23 bp):
TTTATAAAATAATTTTCTAAAAA
Found at i:2120627 original size:14 final size:13
Alignment explanation
Indices: 2120595--2120646 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 13
2120585 ATTTCGTAAA
2120595 ATATTTTTAATA-
1 ATATTTTTAATAT
2120607 ATCATATTTTAATAT
1 AT-AT-TTTTAATAT
* *
2120622 ATATATAT-ATAT
1 ATATTTTTAATAT
2120634 ATATTTTTAATAT
1 ATATTTTTAATAT
2120647 TAAGAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
12 12 0.38
13 8 0.25
14 10 0.31
15 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATTTTTAATAT
Found at i:2120724 original size:15 final size:15
Alignment explanation
Indices: 2120688--2120716 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2120678 GTATGTTTTC
2120688 TGATATTTTTAAATA
1 TGATATTTTTAAATA
2120703 TGATATTTTTAAAT
1 TGATATTTTTAAAT
2120717 TATATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
TGATATTTTTAAATA
Found at i:2120737 original size:20 final size:19
Alignment explanation
Indices: 2120707--2120755 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
2120697 TAAATATGAT
*
2120707 ATTTTTAAATTATATATTA
1 ATTTTTTAATTATATATTA
* *
2120726 ATTGTTTTAATTATTTATTT
1 ATT-TTTTAATTATATATTA
2120746 ATTTTTTAAT
1 ATTTTTTAAT
2120756 ATCAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTTTTAATTATATATTA
Found at i:2123025 original size:14 final size:14
Alignment explanation
Indices: 2122987--2123040 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
2122977 ATTTTAAATA
*
2122987 ATTTACATTTACAT
1 ATTTACATTTGCAT
* *
2123001 TTTTACATTTGCGT
1 ATTTACATTTGCAT
2123015 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
2123030 CTTTGCATTTG
1 ATTTACATTTG
2123041 TATTGCACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Done.