Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008724.1 Hibiscus syriacus cultivar Beakdansim tig00111783_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: 5289199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 23
Found at i:3826499 original size:54 final size:54
Alignment explanation
Indices: 3826430--3827265 Score: 725
Period size: 54 Copynumber: 15.3 Consensus size: 54
3826420 AATTTATTAG
3826430 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
3826484 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * *
3826538 TATAGATTTATTTATTTTAAATAATTTATTTGTATTGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * *
3826592 TATGGATTGCTTTA--TT--AT--TGTAGTT-TTATGGATTGATTTATTTTAAATAATTTA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT--A-AA---A
* * * * ***
3826646 TTTGTATGGATTGATTTATTTT-AA-AA--TA-TA-AATTGATTTA-TTATTGTAGTTG
1 ----TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAA
3826698 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * * * * ***
3826751 TA---ATTTATTT-GTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTTTAGTTG
1 TATGGATTGATTTATTTTA-AATAATTTA--TT--AGTATGGATTGA--T-TTATTTTA-AAA
3826810 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
** ** * ** * * * ***
3826863 TAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTAGTTG
1 T-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAA
*
3826922 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
3826976 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
3827030 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * ** * * * ***
3827083 TA---ATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAA
3827142 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
3827196 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATGGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
3827250 TATGGATTGATTTATT
1 TATGGATTGATTTATT
3827266 ATTGTAGTTG
Statistics
Matches: 627, Mismatches: 95, Indels: 120
0.74 0.11 0.14
Matches are distributed among these distances:
48 38 0.06
49 7 0.01
50 35 0.06
51 2 0.00
52 8 0.01
53 10 0.02
54 341 0.54
55 30 0.05
56 16 0.03
57 27 0.04
58 66 0.11
59 5 0.01
60 8 0.01
61 1 0.00
62 30 0.05
63 3 0.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:3826643 original size:80 final size:80
Alignment explanation
Indices: 3826542--3826750 Score: 355
Period size: 80 Copynumber: 2.6 Consensus size: 80
3826532 TTAAAATATA
* * ** *
3826542 GATTTATTTATTTTAAATAATTTATTTGTATTGATTGATTTATTTTAAAATATGGATTGCTTTAT
1 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATAAATTGATTTAT
*
3826607 TATTGTAGTTTTATG
66 TATTGTAGTTGTATG
3826622 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATAAATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATAAATTGATTTAT
3826687 TATTGTAGTTGTATG
66 TATTGTAGTTGTATG
*
3826702 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAA
3826751 TAATTTATTT
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 122 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (80 bp):
GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATAAATTGATTTAT
TATTGTAGTTGTATG
Found at i:3826738 original size:32 final size:32
Alignment explanation
Indices: 3826697--3826782 Score: 154
Period size: 32 Copynumber: 2.7 Consensus size: 32
3826687 TATTGTAGTT
3826697 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
3826729 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
3826761 GTATAGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
3826783 ATATGGATTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:3826744 original size:112 final size:112
Alignment explanation
Indices: 3826618--3827194 Score: 909
Period size: 112 Copynumber: 5.2 Consensus size: 112
3826608 ATTGTAGTTT
**
3826618 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATAAATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
3826683 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
*
3826730 TATGGATTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
3826795 TTATTATTTTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
*
3826842 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
3826907 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
* * * * ** * * *
3826954 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA--TT--AGTATGGAT
1 TATGGATTGATTTATTTT-AAATA---ATTTATTTGTATGGATTGATTTATTTTAAAATATGGAT
***
3827015 TGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAG
62 TGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
3827062 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
3827127 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
3827174 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
3827195 ATATGGATTG
Statistics
Matches: 421, Mismatches: 32, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
104 16 0.04
106 2 0.00
107 5 0.01
108 64 0.15
109 3 0.01
110 4 0.01
111 3 0.01
112 302 0.72
113 5 0.01
114 2 0.00
116 15 0.04
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (112 bp):
TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:3826847 original size:32 final size:32
Alignment explanation
Indices: 3826809--3827114 Score: 234
Period size: 32 Copynumber: 9.7 Consensus size: 32
3826799 TATTTTAGTT
3826809 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
3826841 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
**
3826873 GTATGGATTGATTTATTTTAAA-ATATGGATT-
1 GTATGGATTGATTTATTTTAAATA-ATTTATTA
** * * *
3826904 G-ATTTATT-ATTGTAGTTGTATGGATTGATTTATT-
1 GTATGGATTGATT-TA-TT-T-T-AAATAATTTATTA
* * * * *
3826938 -T-T-AAATAATTTATTAGTATGAATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-T-AAATAATTTA--TT--A
*
3826975 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
3827007 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
3827030 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
3827061 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
3827093 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
3827115 ATATGGATTG
Statistics
Matches: 227, Mismatches: 19, Indels: 56
0.75 0.06 0.19
Matches are distributed among these distances:
22 14 0.06
23 4 0.02
25 1 0.00
26 3 0.01
28 3 0.01
29 4 0.02
30 7 0.03
31 10 0.04
32 145 0.64
33 5 0.02
34 10 0.04
36 8 0.04
37 1 0.00
38 2 0.01
39 1 0.00
40 9 0.04
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:3826979 original size:22 final size:22
Alignment explanation
Indices: 3826954--3826996 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3826944 AATTTATTAG
3826954 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
3826976 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
3826997 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:3827033 original size:22 final size:22
Alignment explanation
Indices: 3827008--3827050 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3826998 AATTTATTAG
3827008 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
3827030 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
3827051 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:3827145 original size:134 final size:131
Alignment explanation
Indices: 3826873--3827296 Score: 531
Period size: 134 Copynumber: 3.2 Consensus size: 131
3826863 TAATTTATTA
*
3826873 GTATGGATTGATTTATTTTAAAATATGGATTGATTTA-TT-AT-TGTAGTT-GTATGGATTGATT
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTAATATTTA-TTAGTATGGATTGATT
*
3826934 TATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATA
65 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT-
*
3826999 ATTTA-TT
125 -TGTAGTT
3827006 AGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 -GTATGGATTGATTTATTTTAAAATATGGATTGATTTA-TTT-AAT-ATTTATTAGTATGGATTG
*
3827071 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
62 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
3827136 TAGTT
127 TAGTT
* * * * *
3827141 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTT-AT-TTTA-AAATATGGAT
1 GTATGGATTGATTTATTTT-AA-AA--TA-T-GGATTGATTTATTTAATATTTATTAGTATGGAT
*
3827203 TGATTTATTTTAAATAATTTATTAGTATGGATGGATTTATTTTAAAATATGGATTGATTTATTAT
60 TGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTAT
3827268 TGTAGTT
125 TGTAGTT
**
3827275 GTATAAATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
3827297 TAATTTATTA
Statistics
Matches: 263, Mismatches: 13, Indels: 30
0.86 0.04 0.10
Matches are distributed among these distances:
132 1 0.00
133 2 0.01
134 154 0.59
135 8 0.03
136 6 0.02
137 2 0.01
138 6 0.02
139 6 0.02
140 78 0.30
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (131 bp):
GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTAATATTTATTAGTATGGATTGATTT
ATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGT
T
Found at i:3827182 original size:32 final size:32
Alignment explanation
Indices: 3827141--3827248 Score: 137
Period size: 32 Copynumber: 3.7 Consensus size: 32
3827131 TATTGTAGTT
3827141 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
3827173 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
3827196 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
3827227 GTATGGATGGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
3827249 ATATGGATTG
Statistics
Matches: 65, Mismatches: 1, Indels: 20
0.76 0.01 0.23
Matches are distributed among these distances:
22 14 0.22
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.06
32 35 0.54
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:3827199 original size:22 final size:22
Alignment explanation
Indices: 3827174--3827216 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3827164 AATTTATTAG
3827174 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
3827196 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
3827217 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:3827232 original size:112 final size:109
Alignment explanation
Indices: 3826434--3827243 Score: 745
Period size: 112 Copynumber: 7.4 Consensus size: 109
3826424 TATTAGTATG
* ***
3826434 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TTTA-AAATATGGATTGATT
1 GATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATTATTTAGTTGTATGGATTGATT
3826496 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT
66 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATAT
* ** * *** *
3826541 AGATTTATTTATTTTAAATAATTTATTTGTATTGATTGATTTA-T-TTTA-AAATATGGATTGCT
1 -GATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATTATTTAGTTGTATGGATTGAT
* *
3826603 TTA--TT--AT--TGTAGTT-TTATGGATTGATTTATTTTAAATA-
65 TTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAATAT
* * * ** * * **
3826641 -ATTTATTTGTATGGATTGATTTATTTTAAAATATAAATTGATTTATTATTGTAGTTGTATGGAT
1 GATTGATTTATTTTAAATAATTTA--TT--AATATGGATTGATTTATTATT-TAGTTGTATGGAT
3826705 TGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATA-
61 TGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAT
* * * * *
3826753 -ATTTATTT-GTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTTTAGTTGTATGGA
1 GATTGATTTATTTTA-AATAATTTA--TT--AATATGGATTGATTTATTA-TTTAGTTGTATGGA
3826816 TTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATA-
60 TTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAT
* * * * * *
3826865 -ATTTATTAGTATGGATTGATTTATTT-TAAAATATGGATTGATTTATTATTGTAGTTGTATGGA
1 GATTGATT--TAT--TTTAAATAATTTAT-TAATATGGATTGATTTATTATT-TAGTTGTATGGA
*
3826928 TTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATAT
60 TTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATAT
* ***
3826979 GGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TTTA-AAATATGGATTGAT
1 -GATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATTATTTAGTTGTATGGATTGAT
3827041 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATA-
65 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAT
* * * ** * *
3827085 -ATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGAT
1 GATTGATTTATTTTAAATAATTTA--TT--AATATGGATTGATTTATTATT-TAGTTGTATGGAT
3827149 TGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT
61 TGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATAT
* *
3827199 GGATTGATTTATTTTAAATAATTTATTAGTATGGATGGATTTATT
1 -GATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATT
3827244 TTAAAATATG
Statistics
Matches: 593, Mismatches: 67, Indels: 80
0.80 0.09 0.11
Matches are distributed among these distances:
98 17 0.03
100 2 0.00
101 5 0.01
102 33 0.06
103 3 0.01
104 20 0.03
105 2 0.00
106 17 0.03
107 5 0.01
108 126 0.21
109 3 0.01
110 6 0.01
111 7 0.01
112 297 0.50
113 14 0.02
114 6 0.01
116 29 0.05
117 1 0.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (109 bp):
GATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATTATTTAGTTGTATGGATTGATT
TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAT
Found at i:3827302 original size:134 final size:134
Alignment explanation
Indices: 3826922--3827328 Score: 552
Period size: 134 Copynumber: 3.0 Consensus size: 134
3826912 ATTGTAGTTG
*
3826922 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
* ** ** *
3826987 TTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTT
66 TTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTG
** * * *
3827048 AAATAATTTATTAG
122 ATTTATTTTA-AAA
*
3827062 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
3827127 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
3827192 AAAA
131 AAAA
*
3827196 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATGGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
**
3827261 TTATTATTGTAGTTGTATAAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
3827326 AAA
131 AAA
3827329 TAATTTATTA
Statistics
Matches: 246, Mismatches: 17, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
134 160 0.65
135 13 0.05
136 5 0.02
138 2 0.01
140 66 0.27
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (134 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
AAAA
Found at i:3827388 original size:30 final size:30
Alignment explanation
Indices: 3827352--3827408 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
3827342 TAGTTGTATG
* *
3827352 AATTATTTAAATTTCAGTATTGTAAAATAA
1 AATTATTTAAATCTCAGTATTGCAAAATAA
3827382 AATTATTTAAATCTCAGTATTGCAAAA
1 AATTATTTAAATCTCAGTATTGCAAAA
3827409 CTCTTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (30 bp):
AATTATTTAAATCTCAGTATTGCAAAATAA
Found at i:3828670 original size:24 final size:24
Alignment explanation
Indices: 3828643--3828715 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
3828633 AAGGATGCCA
3828643 TAAATGAAATGCATAACGGTACAT
1 TAAATGAAATGCATAACGGTACAT
* * * *
3828667 TAAA-GACATG-A-AATGATGCCA-
1 TAAATGAAATGCATAACGGT-ACAT
*
3828688 TAAATGAAATGCATAACGGTGCAT
1 TAAATGAAATGCATAACGGTACAT
3828712 TAAA
1 TAAA
3828716 GGAATGAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
21 8 0.22
22 8 0.22
23 8 0.22
24 12 0.33
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (24 bp):
TAAATGAAATGCATAACGGTACAT
Found at i:3828671 original size:45 final size:45
Alignment explanation
Indices: 3828620--3829113 Score: 603
Period size: 45 Copynumber: 10.7 Consensus size: 45
3828610 TAAAAAGCAT
*
3828620 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTAC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* *
3828665 ATTAAAGACATGAAATGATGCCATAAATGAAATGCATAACGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* * *
3828710 ATTAAAGGAATGAAATGATGCCATAAATGAAATGCATAATGACATGCATAACAATGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCAT-A--AC--G-------GTGC
* **
3828767 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATTGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* * **
3828812 ATTAAAAGCATGAAAGGATGCCATAAATTAAATGCATAAAAGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* * * *
3828857 ATTAAAGGCATTAAAGGATGTCATAAATAAAATGTATAACGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* *
3828902 ATTAAAGGCATGAAAGGATGTCATAAATGAAATGAATAACGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* * *
3828947 ATTAAAGGCATGAAAGGATACCATAAATAAAATGTGA-AACGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATG-CATAACGGTGC
* * *
3828992 ATTAAAGGCGTGAAAGGATGCCATAAATTAAATGCATAACGGTGT
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* *
3829037 ATTAAAGGCATGAAAGGATGCCATAAATGAAGTGCATAACGGTAC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* *
3829082 ATTAAAGGCATGGAAGGATGTCATAAATGAAA
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAA
3829114 ATAATGAATA
Statistics
Matches: 391, Mismatches: 44, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
44 1 0.00
45 346 0.88
46 2 0.01
48 2 0.01
50 1 0.00
54 1 0.00
56 1 0.00
57 37 0.09
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.23
Consensus pattern (45 bp):
ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
Found at i:3828691 original size:21 final size:21
Alignment explanation
Indices: 3828674--3828736 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
3828664 CATTAAAGAC
*
3828674 ATGAAATGATGCCATAAATGAA
1 ATGAAATGATGCCATAAA-GGA
* *
3828696 ATGCATAACGGTG-CATTAAAGGA
1 ATG-A-AATGATGCCA-TAAAGGA
3828719 ATGAAATGATGCCATAAA
1 ATGAAATGATGCCATAAA
3828737 TGAAATGCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 9
0.70 0.11 0.20
Matches are distributed among these distances:
21 9 0.28
22 6 0.19
23 8 0.25
24 9 0.28
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.22
Consensus pattern (21 bp):
ATGAAATGATGCCATAAAGGA
Found at i:3828757 original size:57 final size:57
Alignment explanation
Indices: 3828690--3828806 Score: 180
Period size: 57 Copynumber: 2.1 Consensus size: 57
3828680 TGATGCCATA
** *
3828690 AATGAAATGCATAACGGTGCATTAAAGGAATGAAATGATGCCATAAATGAAATGCAT
1 AATGAAATGCATAACAATGCATTAAAGGAATGAAAGGATGCCATAAATGAAATGCAT
* * *
3828747 AATGACATGCATAACAATGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGTAT
1 AATGAAATGCATAACAATGCATTAAAGGAATGAAAGGATGCCATAAATGAAATGCAT
3828804 AAT
1 AAT
3828807 TGTGCATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (57 bp):
AATGAAATGCATAACAATGCATTAAAGGAATGAAAGGATGCCATAAATGAAATGCAT
Found at i:3830498 original size:21 final size:22
Alignment explanation
Indices: 3830457--3830498 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3830447 TAATCTTTAA
*
3830457 ATTTACTATATTTTAATATTTT
1 ATTTACTATATTATAATATTTT
3830479 ATTTA-TATAGTTATAA-ATTT
1 ATTTACTATA-TTATAATATTT
3830499 ATTATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTACTATATTATAATATTTT
Found at i:3831510 original size:15 final size:15
Alignment explanation
Indices: 3831483--3831526 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
3831473 AATAAAATAT
3831483 ATAAAT-ATAAATAAA
1 ATAAATAAT-AATAAA
* *
3831498 ATTAATAATAATAAC
1 ATAAATAATAATAAA
3831513 ATAAATAATAATAA
1 ATAAATAATAATAA
3831527 TAGTATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 23 0.92
16 2 0.08
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAATAATAATAAA
Found at i:3831511 original size:19 final size:18
Alignment explanation
Indices: 3831472--3831548 Score: 68
Period size: 19 Copynumber: 4.1 Consensus size: 18
3831462 AAACAAAACA
3831472 AAATAAAATATATAA-ATAT
1 AAATAAAATA-ATAATA-AT
3831491 AAATAAAATTAATAATAAT
1 AAATAAAA-TAATAATAAT
3831510 AACAT-AAATAATAATAAT
1 AA-ATAAAATAATAATAAT
* * *
3831528 AGTATTAAATATTAATAAT
1 A-AATAAAATAATAATAAT
3831547 AA
1 AA
3831549 CCCAGACAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
18 13 0.26
19 32 0.64
20 5 0.10
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (18 bp):
AAATAAAATAATAATAAT
Found at i:3832279 original size:42 final size:42
Alignment explanation
Indices: 3832181--3832279 Score: 180
Period size: 42 Copynumber: 2.4 Consensus size: 42
3832171 TATCATCTCT
*
3832181 CTCGAAAGACTTACAGATGACCCAAAGGATTTAATCATCATG
1 CTCGAAAGACTTACTGATGACCCAAAGGATTTAATCATCATG
*
3832223 CTCGAAAGACTTACTGATGACCCGAAGGATTTAATCATCATG
1 CTCGAAAGACTTACTGATGACCCAAAGGATTTAATCATCATG
3832265 CTCGAAAGACTTACT
1 CTCGAAAGACTTACT
3832280 TATGGCCCTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (42 bp):
CTCGAAAGACTTACTGATGACCCAAAGGATTTAATCATCATG
Found at i:3832475 original size:299 final size:299
Alignment explanation
Indices: 3831917--3832536 Score: 924
Period size: 299 Copynumber: 2.1 Consensus size: 299
3831907 AATGACTTAC
* * * * *
3831917 CATCTTGCTTGAAAGACTGACAGATGACCGGAAGGATTTAATCATCATGCTCGAAAGACTTACTG
1 CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTG
* * * *
3831982 ATGGCTCGAATGACTTACCAATTTGGGAAATAGTTTATTGGGTAAGAAACTTTGGAAATCACTTT
66 ATGGCCCGAATGACTTACCAATTTGGGAAATAGTTTACTAGGTAAAAAACTTTGGAAATCACTTT
*
3832047 CTTACTTTTCAAAAAATTCATTTTCTAAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCA
131 CTTACTTTTCAAAAAATTCATTTTCTAAAAATACTAAATGAGAAACTTTGGAAATCACTTTCTCA
*
3832112 TTTTTCAAATTCATGTGAAAAAATCCTACTCGAAGCTCTTACGGATAGCCAGAAGGAATTATCAT
196 TTTTTCAAATTCATGTGAAAAAATCCTACCCGAAGCTCTTACGGATAGCCAGAAGGAATTATCAT
* *
3832177 CTCTCTCGAAAGACTTACAGATGACCCAAAGGATTTAAT
261 CTCTCTCAAAAGACTTACAGATAACCCAAAGGATTTAAT
*
3832216 CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTT
1 CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTG
* * * **
3832281 ATGGCCCTAA-GAACTTACTAATTTTGGAAATAGTTTACTAGGTAAAAAACTTTGGAAATCGTTT
66 ATGGCCCGAATG-ACTTACCAATTTGGGAAATAGTTTACTAGGTAAAAAACTTTGGAAATCACTT
* *
3832345 TCTTACTTTT-AAAAAATTTCATTTTCTGAAAATTCTAAATGAGAAACTTTGGAAATCACTTTCT
130 TCTTACTTTTCAAAAAA-TTCATTTTCTAAAAATACTAAATGAGAAACTTTGGAAATCACTTTCT
* * * * *
3832409 CATTTTTCAAATTCAT-TTAGAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAA-GAACTTA
194 CATTTTTCAAATTCATGTGA-AAAAATCCTACCCGAAGCTCTTACGGATAGCCAGAAGGAA-TTA
* *
3832472 TCATCTTTCTCAAAAGACTTACAGATAACCCGAAGGATTTAAT
257 TCATCTCTCTCAAAAGACTTACAGATAACCCAAAGGATTTAAT
3832515 CATCATGCTCGAAAGACTTACT
1 CATCATGCTCGAAAGACTTACT
3832537 AATGGCCTGA
Statistics
Matches: 289, Mismatches: 28, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
298 12 0.04
299 277 0.96
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (299 bp):
CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTG
ATGGCCCGAATGACTTACCAATTTGGGAAATAGTTTACTAGGTAAAAAACTTTGGAAATCACTTT
CTTACTTTTCAAAAAATTCATTTTCTAAAAATACTAAATGAGAAACTTTGGAAATCACTTTCTCA
TTTTTCAAATTCATGTGAAAAAATCCTACCCGAAGCTCTTACGGATAGCCAGAAGGAATTATCAT
CTCTCTCAAAAGACTTACAGATAACCCAAAGGATTTAAT
Found at i:3835392 original size:13 final size:13
Alignment explanation
Indices: 3835374--3835405 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3835364 GCCTTTGTGC
3835374 CTTCAAACGAAGT
1 CTTCAAACGAAGT
*
3835387 CTTCAAAGGAAGT
1 CTTCAAACGAAGT
3835400 CTTCAA
1 CTTCAA
3835406 TCAGCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (13 bp):
CTTCAAACGAAGT
Found at i:3838567 original size:17 final size:16
Alignment explanation
Indices: 3838533--3838583 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
3838523 TTAGGCCTGC
3838533 AAAAAAAATAAAAAAT
1 AAAAAAAATAAAAAAT
*
3838549 AAAAAAAATATAAATAT
1 AAAAAAAATA-AAAAAT
* * *
3838566 AAATAATATAAATAAT
1 AAAAAAAATAAAAAAT
3838582 AA
1 AA
3838584 TAATAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAAAAATAAAAAAT
Found at i:3838585 original size:15 final size:15
Alignment explanation
Indices: 3838545--3838588 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
3838535 AAAAAATAAA
* *
3838545 AAATAAAAAAAATAT
1 AAATAATAATAATAT
3838560 AAAT-ATAAATAATAT
1 AAATAAT-AATAATAT
3838575 AAATAATAATAATA
1 AAATAATAATAATA
3838589 ATATTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 22 0.88
16 2 0.08
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAATAATAATAT
Found at i:3838610 original size:9 final size:9
Alignment explanation
Indices: 3838561--3838610 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
3838551 AAAAAATATA
*
3838561 AATATAAAT
1 AATATTAAT
*
3838570 AATATAAAT
1 AATATTAAT
*
3838579 AATAATAAT
1 AATATTAAT
*
3838588 AATATTATT
1 AATATTAAT
3838597 AAATATTAAT
1 -AATATTAAT
3838607 AATA
1 AATA
3838611 ACCCGGAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
9 27 0.77
10 8 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AATATTAAT
Found at i:3841056 original size:2 final size:2
Alignment explanation
Indices: 3841049--3841086 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3841039 AACAATTACA
3841049 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3841087 GATTGATGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3841164 original size:22 final size:22
Alignment explanation
Indices: 3841125--3841223 Score: 74
Period size: 22 Copynumber: 4.4 Consensus size: 22
3841115 ATGATGCATG
* * *
3841125 TATATATAAGTATTAAACTACA
1 TATATAAAACTATAAAACTACA
*
3841147 TATATAAAACTATAAAACTATA
1 TATATAAAACTATAAAACTACA
* *
3841169 TA-ATATAAAGTATTAAACTACA
1 TATATA-AAACTATAAAACTACA
* * *
3841191 TAATACAAAACTAATATAACTATA
1 T-ATATAAAACT-ATAAAACTACA
3841215 TTATATAAA
1 -TATATAAA
3841224 GTATATAGTT
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
21 3 0.05
22 34 0.58
23 5 0.08
24 16 0.27
25 1 0.02
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (22 bp):
TATATAAAACTATAAAACTACA
Found at i:3841184 original size:44 final size:46
Alignment explanation
Indices: 3841126--3841227 Score: 154
Period size: 46 Copynumber: 2.2 Consensus size: 46
3841116 TGATGCATGT
*
3841126 ATATATAAGTATTAAACTACAT-ATATAAAACT-ATAAAACTATATA
1 ATATA-AAGTATTAAACTACATAATACAAAACTAATAAAACTATATA
* *
3841171 ATATAAAGTATTAAACTACATAATACAAAACTAATATAACTATATT
1 ATATAAAGTATTAAACTACATAATACAAAACTAATAAAACTATATA
3841217 ATATAAAGTAT
1 ATATAAAGTAT
3841228 ATAGTTATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
44 16 0.31
45 14 0.27
46 22 0.42
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (46 bp):
ATATAAAGTATTAAACTACATAATACAAAACTAATAAAACTATATA
Found at i:3841317 original size:4 final size:4
Alignment explanation
Indices: 3841308--3841334 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3841298 TTTATACATA
3841308 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
3841335 TGAACTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:3841365 original size:10 final size:9
Alignment explanation
Indices: 3841337--3841586 Score: 135
Period size: 8 Copynumber: 30.2 Consensus size: 9
3841327 GTATGTATTG
3841337 AACTAATATA
1 AACT-ATATA
*
3841347 AAGTAT-TA
1 AACTATATA
3841355 AACTATATTA
1 AACTATA-TA
*
3841365 AACTACAT-
1 AACTATATA
3841373 AA-TATA-A
1 AACTATATA
3841380 AACTATA-A
1 AACTATATA
3841388 AACTATAT-
1 AACTATATA
3841396 -A--ATATA
1 AACTATATA
*
3841402 AAGTAT-TA
1 AACTATATA
*
3841410 AAATAATATTA
1 AACT-ATA-TA
*
3841421 CACTATATA
1 AACTATATA
*
3841430 AAGTATTATAA
1 AACTA-TAT-A
3841441 AACTATAT-
1 AACTATATA
3841449 AA-TATA-A
1 AACTATATA
3841456 AACTATA-A
1 AACTATATA
3841464 AACTATAT-
1 AACTATATA
3841472 AA-TATA-A
1 AACTATATA
3841479 AACTATA-A
1 AACTATATA
3841487 AACTATATA
1 AACTATATA
*
3841496 AAGTATATA
1 AACTATATA
*
3841505 AA-TA-ATT
1 AACTATATA
3841512 AA--ATAT-
1 AACTATATA
*
3841518 AAGTAT-TA
1 AACTATATA
3841526 AACTATATTA
1 AACTATA-TA
3841536 AACTATAT-
1 AACTATATA
3841544 AA-TATA-A
1 AACTATATA
*
3841551 AACTAGA-A
1 AACTATATA
3841559 AACTATA-A
1 AACTATATA
3841567 AACTATATA
1 AACTATATA
*
3841576 AAGTATATA
1 AACTATATA
3841585 AA
1 AA
3841587 TAATTAAATA
Statistics
Matches: 195, Mismatches: 16, Indels: 59
0.72 0.06 0.22
Matches are distributed among these distances:
5 4 0.02
6 3 0.02
7 32 0.16
8 83 0.43
9 35 0.18
10 29 0.15
11 9 0.05
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (9 bp):
AACTATATA
Found at i:3841368 original size:28 final size:27
Alignment explanation
Indices: 3841332--3841598 Score: 83
Period size: 23 Copynumber: 10.1 Consensus size: 27
3841322 TGTATGTATG
*
3841332 TATTGAACTAATATAAAGTATTAAACTA
1 TATTAAACT-ATATAAAGTATTAAACTA
* *
3841360 TATTAAACTACAT-AA-TATAAAACTA
1 TATTAAACTATATAAAGTATTAAACTA
*
3841385 TA--AAACTATATAATATAAAGTATTAAAATAA
1 TATTAAAC----T-ATATAAAGTATTAAACT-A
*
3841416 TATTACACTATATAAAGTATTATAAAACTA
1 TATTAAACTATATAAAGTA-T-T-AAACTA
* *
3841446 TA-T-AA-TATA-AAACTATAAAACTA
1 TATTAAACTATATAAAGTATTAAACTA
* *
3841469 TA-T-AA-TATA-AAACTATAAAACTA
1 TATTAAACTATATAAAGTATTAAACTA
* *
3841492 TA-TAAAGTATATAAA-TAATTAAATATAA
1 TATTAAACTATATAAAGT-ATTAAA-CT-A
*
3841520 GTATTAAACTATATTAAACTA-TATAA-TA
1 -TATTAAACTATA-TAAAGTATTA-AACTA
* * *
3841548 TA--AAACTAGA-AAACTATAAAACTA
1 TATTAAACTATATAAAGTATTAAACTA
*
3841572 TA-TAAAGTATATAAA-TAATTAAA-TA
1 TATTAAACTATATAAAGT-ATTAAACTA
3841597 TA
1 TA
3841599 AGTATTAAGT
Statistics
Matches: 191, Mismatches: 19, Indels: 61
0.70 0.07 0.23
Matches are distributed among these distances:
23 44 0.23
24 7 0.04
25 35 0.18
26 23 0.12
27 11 0.06
28 24 0.13
29 8 0.04
30 21 0.11
31 14 0.07
32 1 0.01
33 3 0.02
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (27 bp):
TATTAAACTATATAAAGTATTAAACTA
Found at i:3841397 original size:23 final size:23
Alignment explanation
Indices: 3841354--3841565 Score: 173
Period size: 23 Copynumber: 8.7 Consensus size: 23
3841344 ATAAAGTATT
*
3841354 AAACTATATTAAACTACATAATATA
1 AAACTATA--AAACTATATAATATA
3841379 AAACTATAAAACTATATAATAT-
1 AAACTATAAAACTATATAATATA
*
3841401 AAAGTATTAAAA-TAATATTACACTATATA
1 AAACTA-TAAAACT-ATA-T--A--ATATA
*
3841430 AAGTATTATAAAACTATATAATATA
1 AA--ACTATAAAACTATATAATATA
3841455 AAACTATAAAACTATATAATATA
1 AAACTATAAAACTATATAATATA
3841478 AAACTATAAAACTATATAAAGTATA
1 AAACTATAAAACTATAT-AA-TATA
* * *
3841503 TAAA-TAATTAAA-TATA-AGTATT
1 -AAACT-ATAAAACTATATAATATA
3841525 AAACTATATTAAACTATATAATATA
1 AAACTATA--AAACTATATAATATA
*
3841550 AAACTAGAAAACTATA
1 AAACTATAAAACTATA
3841566 AAACTATATA
Statistics
Matches: 156, Mismatches: 11, Indels: 42
0.75 0.05 0.20
Matches are distributed among these distances:
21 5 0.03
22 10 0.06
23 70 0.45
24 7 0.04
25 35 0.22
26 9 0.06
27 1 0.01
28 4 0.03
29 3 0.02
30 8 0.05
31 4 0.03
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (23 bp):
AAACTATAAAACTATATAATATA
Found at i:3841452 original size:53 final size:54
Alignment explanation
Indices: 3841340--3841509 Score: 158
Period size: 53 Copynumber: 3.1 Consensus size: 54
3841330 TGTATTGAAC
*
3841340 TAATATAAAGTATTAAACTATATTAAACTACATAATATAAAACTATAAAACTATA
1 TAATATAAAGTATTAAAATATATT-AACTACATAATATAAAACTATAAAACTATA
*
3841395 TAATATAAAGTATTAAAATAATATT-AC-AC-T-ATATAAAGTATTATAAAACTATA
1 TAATATAAAGTATTAAAAT-ATATTAACTACATAATATAAA--ACTATAAAACTATA
* * * *
3841448 TAATATAAAACTA-TAAAACTATA-TAA-TATAAAACTATAAAACTATATAAAGTATA
1 TAATAT-AAAGTATTAAAA-TATATTAACTACATAA-TATAAAACTATA-AAACTATA
3841503 TAA-ATAA
1 TAATATAA
3841510 TTAAATATAA
Statistics
Matches: 97, Mismatches: 7, Indels: 24
0.76 0.05 0.19
Matches are distributed among these distances:
51 7 0.07
52 2 0.02
53 33 0.34
54 15 0.15
55 29 0.30
56 11 0.11
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (54 bp):
TAATATAAAGTATTAAAATATATTAACTACATAATATAAAACTATAAAACTATA
Found at i:3841489 original size:31 final size:32
Alignment explanation
Indices: 3841340--3841576 Score: 168
Period size: 33 Copynumber: 7.1 Consensus size: 32
3841330 TGTATTGAAC
* * *
3841340 TAATAT-AAAGTATTAAACTATATTAAACTACA
1 TAATATAAAACTATAAAACTATA-TAAACTATA
3841372 TAATATAAAACTATAAAACTATAT-AA-TATA
1 TAATATAAAACTATAAAACTATATAAACTATA
* *
3841402 -AAGTATTAAAA-TAATATTACACTATATAAAGTATTA
1 TAA-TA-TAAAACT-ATA--AAACTATATAAACTA-TA
*
3841438 TAAAACTATATAA-TATAAAACTATA-AAACTATA
1 T--AA-TATAAAACTATAAAACTATATAAACTATA
*
3841471 TAATATAAAACTATAAAACTATATAAAGTATA
1 TAATATAAAACTATAAAACTATATAAACTATA
3841503 TAAATAATTAAATA-TAAGTATTAAACTATATTAAACTATA
1 T-AAT-A-TAAA-ACT-A-TA--AAACTATA-TAAACTATA
*
3841543 TAATATAAAACTAGAAAACTATA-AAACTATA
1 TAATATAAAACTATAAAACTATATAAACTATA
3841574 TAA
1 TAA
3841577 AGTATATAAA
Statistics
Matches: 169, Mismatches: 12, Indels: 49
0.73 0.05 0.21
Matches are distributed among these distances:
29 2 0.01
30 12 0.07
31 35 0.21
32 15 0.09
33 36 0.21
34 8 0.05
35 15 0.09
36 6 0.04
37 10 0.06
38 6 0.04
39 15 0.09
40 9 0.05
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (32 bp):
TAATATAAAACTATAAAACTATATAAACTATA
Found at i:3841561 original size:80 final size:80
Alignment explanation
Indices: 3841450--3841606 Score: 262
Period size: 80 Copynumber: 2.0 Consensus size: 80
3841440 AAACTATATA
* *
3841450 ATATAAAACTATAAAACTATATAATATAAAACTATAAAACTATATAAAGTATATAAATAATTAAA
1 ATATAAAACTATAAAACTATAAAATAGAAAACTATAAAACTATATAAAGTATATAAATAATTAAA
3841515 TATAAGTATTAAACT
66 TATAAGTATTAAACT
* *
3841530 ATATTAAACTATATAA-TATAAAACTAGAAAACTATAAAACTATATAAAGTATATAAATAATTAA
1 ATATAAAACTATAAAACTATAAAA-TAGAAAACTATAAAACTATATAAAGTATATAAATAATTAA
3841594 ATATAAGTATTAA
65 ATATAAGTATTAA
3841607 GTAATAAATT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
79 6 0.08
80 66 0.92
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (80 bp):
ATATAAAACTATAAAACTATAAAATAGAAAACTATAAAACTATATAAAGTATATAAATAATTAAA
TATAAGTATTAAACT
Found at i:3841832 original size:17 final size:17
Alignment explanation
Indices: 3841810--3841843 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3841800 ATTTTGGAAA
3841810 ATTTTATGATTTTTTTC
1 ATTTTATGATTTTTTTC
*
3841827 ATTTTATTATTTTTTTC
1 ATTTTATGATTTTTTTC
3841844 TCTCTCTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTATGATTTTTTTC
Found at i:3842449 original size:157 final size:155
Alignment explanation
Indices: 3842154--3842459 Score: 402
Period size: 157 Copynumber: 2.0 Consensus size: 155
3842144 TCCTCGTTTA
* * *
3842154 ATCCTTACAAACACCAAATATTTTCCCCAATATATTTTTCAAGATCAGAACCCCTAAATCAAATC
1 ATCCTTACAAACACCAAATATTTTCCCCAATATATTTTTCAAGATCAGAACCCCCAAACCAAAGC
* * *
3842219 ACTATTTATCTTCTTCCCAACCCTAAATCCCAAATCTCACTATTCATCCCCCTTCCCCTTCTTCG
66 ACTATTCATCTTATTCCCAACCCTAAATCCCAAATCTCACTATTCATCCCCCTTCCCCTTCTTCA
* *
3842284 ACATAGACTCTTCCCCTTCTATTTG
131 ACAGAGACTATTCCCCTTCTATTTG
* * *
3842309 ATCCTTACAAACACCAAGA-ATTTTCCCCAATTTGTTTTTCAAGATCTA-AACCTCCCAAACCGA
1 ATCCTTACAAACACCAA-ATATTTTCCCCAATATATTTTTCAAGATC-AGAACC-CCCAAACCAA
* * *
3842372 AGCACT-TTCATCTTATTCTCGTAACCCTAATTCCCAAATCTCACTATTCATCCCCTTTCCCCTT
63 AGCACTATTCATCTTATTC-C-CAACCCTAAATCCCAAATCTCACTATTCATCCCCCTTCCCCTT
* *
3842436 CTTCAACCGAGACTATTCCTCTTC
126 CTTCAACAGAGACTATTCCCCTTC
3842460 CCCTTCTTCA
Statistics
Matches: 130, Mismatches: 16, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
155 56 0.43
156 15 0.12
157 59 0.45
ACGTcount: A:0.28, C:0.34, G:0.04, T:0.33
Consensus pattern (155 bp):
ATCCTTACAAACACCAAATATTTTCCCCAATATATTTTTCAAGATCAGAACCCCCAAACCAAAGC
ACTATTCATCTTATTCCCAACCCTAAATCCCAAATCTCACTATTCATCCCCCTTCCCCTTCTTCA
ACAGAGACTATTCCCCTTCTATTTG
Found at i:3843242 original size:16 final size:15
Alignment explanation
Indices: 3843221--3843279 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 15
3843211 CTGCTAATTG
3843221 TTTTATGTTTTATGTT
1 TTTTAT-TTTTATGTT
3843237 TTTTATTTTT-TGTTTT
1 TTTTATTTTTATG--TT
3843253 GTTTTATTTTATATGTT
1 -TTTTATTTT-TATGTT
3843270 TTTTATTTTT
1 TTTTATTTTT
3843280 TTTCTGTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.05
15 5 0.13
16 17 0.45
17 11 0.29
18 1 0.03
19 2 0.05
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (15 bp):
TTTTATTTTTATGTT
Found at i:3843255 original size:33 final size:33
Alignment explanation
Indices: 3843218--3843280 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
3843208 TTTCTGCTAA
3843218 TTGTTTTATGTTT-TATGTTTTTTATTTTTTGTT
1 TTGTTTTAT-TTTATATGTTTTTTATTTTTTGTT
3843251 TTGTTTTATTTTATATGTTTTTTATTTTTT
1 TTGTTTTATTTTATATGTTTTTTATTTTTT
3843281 TTCTGTATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.11, C:0.00, G:0.10, T:0.79
Consensus pattern (33 bp):
TTGTTTTATTTTATATGTTTTTTATTTTTTGTT
Found at i:3843298 original size:32 final size:33
Alignment explanation
Indices: 3843231--3843298 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
3843221 TTTTATGTTT
* * * *
3843231 TATGTTTTTTATTTTTTGTTTTGTTTTATTTTA
1 TATGTTTTTTATTTTTTGTTCTGTATGATTGTA
3843264 TATGTTTTTTATTTTTT-TTCTGTATGATTGTA
1 TATGTTTTTTATTTTTTGTTCTGTATGATTGTA
3843296 TAT
1 TAT
3843299 ATTATATGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.15, C:0.01, G:0.10, T:0.74
Consensus pattern (33 bp):
TATGTTTTTTATTTTTTGTTCTGTATGATTGTA
Found at i:3843386 original size:29 final size:28
Alignment explanation
Indices: 3843354--3843421 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 28
3843344 TTATATAGTT
3843354 TTTATTTTTT-ATTCGTGTTCTGTTATTTA
1 TTTATTTTTTCA-T-GTGTTCTGTTATTTA
*
3843383 TTTATTTATTTCATGTTTTCTGTTATTTA
1 TTTATTT-TTTCATGTGTTCTGTTATTTA
3843412 TTTATTTTTT
1 TTTATTTTTT
3843422 GCTTTTTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
28 3 0.08
29 28 0.78
30 4 0.11
31 1 0.03
ACGTcount: A:0.15, C:0.06, G:0.07, T:0.72
Consensus pattern (28 bp):
TTTATTTTTTCATGTGTTCTGTTATTTA
Found at i:3844246 original size:35 final size:36
Alignment explanation
Indices: 3844196--3844269 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 36
3844186 AAAAACCCAC
*
3844196 TGTTTATTATTTGTTTTTT-TTTTGCTAATTGTTTTA
1 TGTTTATTATATGTTTTTTATTTT-CTAATTGTTTTA
* *
3844232 TGTTT-TTATATGTTTTTTATTTTTTATTTGTTTTA
1 TGTTTATTATATGTTTTTTATTTTCTAATTGTTTTA
3844267 TGT
1 TGT
3844270 ATGATTGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 25 0.74
36 9 0.26
ACGTcount: A:0.14, C:0.01, G:0.11, T:0.74
Consensus pattern (36 bp):
TGTTTATTATATGTTTTTTATTTTCTAATTGTTTTA
Found at i:3844248 original size:18 final size:18
Alignment explanation
Indices: 3844227--3844269 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3844217 TTGCTAATTG
3844227 TTTTATGTTTTTATATGTT
1 TTTTATGTTTTTATATG-T
*
3844246 TTTTAT-TTTTTATTTG-
1 TTTTATGTTTTTATATGT
3844262 TTTTATGT
1 TTTTATGT
3844270 ATGATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.27
17 1 0.05
18 9 0.41
19 6 0.27
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (18 bp):
TTTTATGTTTTTATATGT
Found at i:3844414 original size:29 final size:29
Alignment explanation
Indices: 3844353--3844412 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
3844343 TTTAAATTTG
*
3844353 TTTT-ATGTTATTTATTTGTTTATTTCTT
1 TTTTAATGTTATTTATTTATTTATTTCTT
* *
3844381 GTTTAATGTTATTTATTTATTT-TTTGTT
1 TTTTAATGTTATTTATTTATTTATTTCTT
3844409 TTTT
1 TTTT
3844413 TATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75
Consensus pattern (29 bp):
TTTTAATGTTATTTATTTATTTATTTCTT
Found at i:3846637 original size:47 final size:47
Alignment explanation
Indices: 3846583--3846677 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
3846573 GAAATTGTAG
*
3846583 TACTTTGATTGTTATTAAAGTATAAATGTTAGGAATATACAAACATT
1 TACTTTGATTGTTATTAAAGTATAAATGTTAGAAATATACAAACATT
*
3846630 TACTTTGATTGTTATTAAAGTATAAATGTTAGAAATATACTAACATT
1 TACTTTGATTGTTATTAAAGTATAAATGTTAGAAATATACAAACATT
3846677 T
1 T
3846678 GGTATGGTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (47 bp):
TACTTTGATTGTTATTAAAGTATAAATGTTAGAAATATACAAACATT
Found at i:3846958 original size:21 final size:21
Alignment explanation
Indices: 3846932--3847048 Score: 58
Period size: 21 Copynumber: 5.3 Consensus size: 21
3846922 AAAAGCATAT
3846932 TAAATGCATGAAAGGATTCCA
1 TAAATGCATGAAAGGATTCCA
* * *
3846953 TAAATGAAATGTATAACGA-TGCA
1 TAAATG-CATG-A-AAGGATTCCA
* *
3846976 TTAAAGGCATGAAAAGATTCCA
1 -TAAATGCATGAAAGGATTCCA
* * *
3846998 TAAATGAAATGCAAAATGA-TGCA
1 TAAATG-CATG--AAAGGATTCCA
* *
3847021 TTAAAGGCATGAAAGGATGCCA
1 -TAAATGCATGAAAGGATTCCA
3847043 TAAATG
1 TAAATG
3847049 AAATGCATAA
Statistics
Matches: 69, Mismatches: 17, Indels: 20
0.65 0.16 0.19
Matches are distributed among these distances:
21 25 0.36
22 12 0.17
23 13 0.19
24 19 0.28
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (21 bp):
TAAATGCATGAAAGGATTCCA
Found at i:3846995 original size:45 final size:45
Alignment explanation
Indices: 3846930--3847591 Score: 1000
Period size: 45 Copynumber: 14.7 Consensus size: 45
3846920 TGAAAAGCAT
* * * *
3846930 ATTAAATGCATGAAAGGATTCCATAAATGAAATGTATAACGATGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* * * * *
3846975 ATTAAAGGCATGAAAAGATTCCATAAATGAAATGCAAAATGATGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
*
3847020 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACTGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
*
3847065 ATTAAAGGCATAAAAGGATGCCATAAATGAAATGCATAACGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
*
3847110 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGCGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
3847155 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
3847200 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
3847245 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* * * * *
3847290 ATTAAATGAATGAAAGGATACGATAAATGAAATGCATAATGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* **
3847335 ATTAAAGGCATGAAAGGATGCCATAAATTAAATGCATAAAAGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* * * ** *
3847380 ATTAAAGGCATTAAAGGATGTCATTAATGAAATGCATAATAGCGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* * * * *
3847425 ATTAAAGGCATGAAATGATACCATAAATAAAATGCATAACAGCGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* *
3847470 ATTAAAGGCATGAAAGGATGCCATAGATGAAATGCATAATGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* *
3847515 ATTAAAGGCATGAAAGGATGCCATAGATGAAATGCATAATGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
*
3847560 ATTAAAGGCATGAAATGATGCCATAAATGAAA
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAA
3847592 ATAATGAATA
Statistics
Matches: 567, Mismatches: 50, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 567 1.00
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (45 bp):
ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
Found at i:3847576 original size:21 final size:21
Alignment explanation
Indices: 3847507--3847576 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
3847497 TGAAATGCAT
3847507 AATGGTGCATTAAAGGCATGA
1 AATGGTGCATTAAAGGCATGA
*
3847528 AA-GGATGCCATAGATGAAATGCAT--
1 AATGG-TG-CAT---T-AAAGGCATGA
3847552 AATGGTGCATTAAAGGCATGA
1 AATGGTGCATTAAAGGCATGA
3847573 AATG
1 AATG
3847577 ATGCCATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
19 7 0.18
20 3 0.08
21 8 0.21
22 3 0.08
23 3 0.08
24 4 0.11
25 3 0.08
26 7 0.18
ACGTcount: A:0.40, C:0.10, G:0.27, T:0.23
Consensus pattern (21 bp):
AATGGTGCATTAAAGGCATGA
Found at i:3848154 original size:2 final size:2
Alignment explanation
Indices: 3848149--3848206 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
3848139 GAGTTTGTTA
3848149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3848191 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3848207 CAAAATATGC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3849043 original size:56 final size:57
Alignment explanation
Indices: 3848972--3849083 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 57
3848962 TTGCAGGGTT
* *
3848972 CTACTGCTTTTACATTTACTATTTTTTCATTAATTTTCATGAATTTCAGCAAGCATG
1 CTACTGCTTTTACATTTACTACTTTTTCATTAATTTTCATAAATTTCAGCAAGCATG
* *
3849029 CTACT-CTTTTACATTTACTGCTTTTTGATTAATTTTCATAAATTTCAGCAAGCAT
1 CTACTGCTTTTACATTTACTACTTTTTCATTAATTTTCATAAATTTCAGCAAGCAT
3849084 ATAAATGAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
56 46 0.90
57 5 0.10
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (57 bp):
CTACTGCTTTTACATTTACTACTTTTTCATTAATTTTCATAAATTTCAGCAAGCATG
Found at i:3850574 original size:54 final size:54
Alignment explanation
Indices: 3850440--3850571 Score: 203
Period size: 54 Copynumber: 2.4 Consensus size: 54
3850430 TATGTGGGGC
* *
3850440 GCACATATAGTGTCAATACGAAAATTCATAAACTAATTATGAATTTCTTATGTT
1 GCACATATAGTGCCAATACGAAAATTGATAAACTAATTATGAATTTCTTATGTT
*
3850494 GCACATATAGTGCCAATACGAAAATTGATAAACTTATTATGAATTTCTTA-GATT
1 GCACATATAGTGCCAATACGAAAATTGATAAACTAATTATGAATTTCTTATG-TT
*
3850548 GCACACATAGTGCCAATACAGAAA
1 GCACATATAGTGCCAATAC-GAAA
3850572 TTGCAAAACA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
53 1 0.01
54 67 0.93
55 4 0.06
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (54 bp):
GCACATATAGTGCCAATACGAAAATTGATAAACTAATTATGAATTTCTTATGTT
Found at i:3856869 original size:107 final size:108
Alignment explanation
Indices: 3856730--3856967 Score: 372
Period size: 107 Copynumber: 2.2 Consensus size: 108
3856720 ACATGGGGTG
* *
3856730 CACACATAGTGCCAATAC-AGAAATTCATAAACTGATTATGAATTTCTTATATTGCACATATATT
1 CACACATAGTGCCAATACGA-AAATTCATAAACTGATTATGAATTTCTTAGATTGCACATATAGT
*
3856794 GCTAATACGAAAATTCATAAACTTATTACGAATTTCTTAGGTTA
65 GCCAATACGAAAATTCATAAACTTATTACGAATTTCTTAGGTTA
* * *
3856838 CA-ATATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACATATAGTG
1 CACACATAGTGCCAATACGAAAATTCATAAACTGATTATGAATTTCTTAGATTGCACATATAGTG
* *
3856902 CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTG
66 CCAATACGAAAATTCATAAACTTATTACGAATTTCTTAGGTTA
3856945 CACACATAGTGCCAATACAGAAA
1 CACACATAGTGCCAATAC-GAAA
3856968 TTGCAAAACA
Statistics
Matches: 118, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
107 97 0.82
108 17 0.14
109 4 0.03
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (108 bp):
CACACATAGTGCCAATACGAAAATTCATAAACTGATTATGAATTTCTTAGATTGCACATATAGTG
CCAATACGAAAATTCATAAACTTATTACGAATTTCTTAGGTTA
Found at i:3856969 original size:54 final size:54
Alignment explanation
Indices: 3856675--3856967 Score: 374
Period size: 54 Copynumber: 5.4 Consensus size: 54
3856665 AGTGGTTTTC
* * ** * * * * * *
3856675 GCACACGTAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACATGGGGT
1 GCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTT
* **
3856729 GCACACATAGTGCCAATAC-AGAAATTCATAAACTGATTATGAATTTCTTATATT
1 GCACACATAGTGCCAATACGA-AAATTCATAAACTTATTATGAATTTCTTAGGTT
* * * *
3856783 GCACATATATTGCTAATACGAAAATTCATAAACTTATTACGAATTTCTTAGGTT
1 GCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTT
* *
3856837 ACA-ATATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTT
1 GCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTT
*
3856890 GCACATATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTT
1 GCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTT
3856944 GCACACATAGTGCCAATACAGAAA
1 GCACACATAGTGCCAATAC-GAAA
3856968 TTGCAAAACA
Statistics
Matches: 210, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
53 49 0.23
54 156 0.74
55 5 0.02
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.32
Consensus pattern (54 bp):
GCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTT
Found at i:3859786 original size:25 final size:25
Alignment explanation
Indices: 3859735--3859786 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
3859725 CCCAAACACC
* * *
3859735 ATTCACACTAGTAGCAGATTTAGAA
1 ATTCACACCAGTAGCAGATCTAAAA
*
3859760 ATTCACACCAGTAGCATATCTAAAA
1 ATTCACACCAGTAGCAGATCTAAAA
3859785 AT
1 AT
3859787 AAAAAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (25 bp):
ATTCACACCAGTAGCAGATCTAAAA
Found at i:3871502 original size:3 final size:3
Alignment explanation
Indices: 3871462--3871519 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
3871452 AAGTTCGTTA
* * *
3871462 TAT TTT TAT TAT TTT TAT TAC TAT TAAT TAT T-T TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
3871507 TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TA
3871520 ACAATTAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3874986 original size:15 final size:16
Alignment explanation
Indices: 3874961--3874997 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
3874951 TCCTAAGGCG
*
3874961 ATGAGAAGAGCCGAGA
1 ATGAGAAGAGCCAAGA
3874977 ATGA-AAGAGCCAAGA
1 ATGAGAAGAGCCAAGA
3874992 ATGAGA
1 ATGAGA
3874998 TCCCTGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.49, C:0.11, G:0.32, T:0.08
Consensus pattern (16 bp):
ATGAGAAGAGCCAAGA
Found at i:3889421 original size:22 final size:23
Alignment explanation
Indices: 3889381--3889423 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3889371 AGATCGAATC
**
3889381 TGGGGCAAAAGAAGCCAAATTTT
1 TGGGGCAAAAGAAAACAAATTTT
3889404 TGGGGC-AAAGAAAACAAATT
1 TGGGGCAAAAGAAAACAAATT
3889424 GTCTCAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.44, C:0.12, G:0.26, T:0.19
Consensus pattern (23 bp):
TGGGGCAAAAGAAAACAAATTTT
Found at i:3889568 original size:16 final size:16
Alignment explanation
Indices: 3889531--3889572 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3889521 CAGATCGAGA
*
3889531 AAACATACATCAATAC
1 AAACATACATCAACAC
*
3889547 AAACATACATCAACAT
1 AAACATACATCAACAC
*
3889563 ATACATACAT
1 AAACATACAT
3889573 GATACATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (16 bp):
AAACATACATCAACAC
Found at i:3889984 original size:37 final size:36
Alignment explanation
Indices: 3889922--3890044 Score: 142
Period size: 36 Copynumber: 3.4 Consensus size: 36
3889912 ACCAAGTGTC
* * *
3889922 GTCTCGCTAGAGATAGTTTCT-TAAAAACATATTTT
1 GTCTCGCTAGAGACAATTTCTCTAAAAACAAATTTT
3889957 GTCTCGCTAGAGACAACTTTCTCTAAAAACAAATTTT
1 GTCTCGCTAGAGACAA-TTTCTCTAAAAACAAATTTT
* * * *
3889994 GTTTTGCTTGAGACAATTTCTCTCAAAACAAATTTCT
1 GTCTCGCTAGAGACAATTTCTCTAAAAACAAATTT-T
*
3890031 -TCTCGCTTGAGACA
1 GTCTCGCTAGAGACA
3890045 TTTTTCTTTG
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
35 14 0.18
36 35 0.46
37 27 0.36
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (36 bp):
GTCTCGCTAGAGACAATTTCTCTAAAAACAAATTTT
Found at i:3890277 original size:32 final size:33
Alignment explanation
Indices: 3890177--3890288 Score: 86
Period size: 37 Copynumber: 3.2 Consensus size: 33
3890167 TATTTTACTA
* *
3890177 AAAACAAAATTGACAATCTTTGAATCTTTTTCTCTT
1 AAAACAAAATT--C-ATCTTTGAGTCTGTTTCTCTT
* *
3890213 AAAACAAAATTGTGTC-TCTCTTGAGACAGTTTCTCTT
1 AAAACAAAA---T-TCATCT-TTGAGTCTGTTTCTCTT
3890250 AAAACAAAA-TCATCTTTGAGTCTGTTTC-CTT
1 AAAACAAAATTCATCTTTGAGTCTGTTTCTCTT
*
3890281 GAAACAAA
1 AAAACAAA
3890289 TCCCTAAAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
31 10 0.16
32 13 0.21
33 3 0.05
36 12 0.19
37 22 0.35
38 1 0.02
39 1 0.02
40 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.37
Consensus pattern (33 bp):
AAAACAAAATTCATCTTTGAGTCTGTTTCTCTT
Found at i:3890495 original size:40 final size:42
Alignment explanation
Indices: 3890440--3890626 Score: 118
Period size: 40 Copynumber: 4.4 Consensus size: 42
3890430 TGGCATTCCG
*
3890440 TCCTCATCGCGTAGGAACCTTGTCATCCCCT-GACCAGA-CC
1 TCCTCATCACGTAGGAACCTTGTCATCCCCTAGACCAGATCC
* * *
3890480 TCCTCATCACGTAGGAGCCTTGCCA-CCCCTAGATAACCA-ATCG
1 TCCTCATCACGTAGGAACCTTGTCATCCCCTAG---ACCAGATCC
* * ** *
3890523 TCCTCATCACGTAGGAACCATGTTATCATCCCTA-AATATGGTATATCA
1 TCCTCATCACGTAGGAACCTTGTCATC--CCCTAGACCA--G---ATCC
* * * *
3890571 TCCTCATCGCGTAAGAACCGTGTCAT-CCCTCGACCAGA-CC
1 TCCTCATCACGTAGGAACCTTGTCATCCCCTAGACCAGATCC
3890611 TCCTCATCACGTAGGA
1 TCCTCATCACGTAGGA
3890627 GTTGTGTCAC
Statistics
Matches: 111, Mismatches: 21, Indels: 30
0.69 0.13 0.19
Matches are distributed among these distances:
39 5 0.05
40 38 0.34
41 1 0.01
42 3 0.03
43 26 0.23
44 2 0.02
45 4 0.04
46 7 0.06
48 25 0.23
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24
Consensus pattern (42 bp):
TCCTCATCACGTAGGAACCTTGTCATCCCCTAGACCAGATCC
Found at i:3890527 original size:131 final size:131
Alignment explanation
Indices: 3890292--3890724 Score: 505
Period size: 131 Copynumber: 3.3 Consensus size: 131
3890282 AAACAAATCC
* * *
3890292 CTAAAGATGGCCTGCCATCCTCATCGTGTAGGAA-CTGTGTCATCCCCCGACCAGACCTCCAT-A
1 CTAAAGATGGCATGCCATCCTCATCGCGTAGGAACCT-TGTCATCCCCTGACCAGACCTCC-TCA
* * * *
3890355 TCACGTAGGAGCCTTGTCACCCCTAGATAACTAGTCTTCCTCATCACGTAGGAATTGTGATATCA
64 TCACGTAGGAGCCTTGTCACCCCTAGATAACCAGTCATCCTCATCACGTAGGAACTGTGTTATCA
3890420 TCT
129 TCT
* *
3890423 CTAAAGATGGCATTCCGTCCTCATCGCGTAGGAACCTTGTCATCCCCTGACCAGACCTCCTCATC
1 CTAAAGATGGCATGCCATCCTCATCGCGTAGGAACCTTGTCATCCCCTGACCAGACCTCCTCATC
* * * **
3890488 ACGTAGGAGCCTTGCCACCCCTAGATAACCAATCGTCCTCATCACGTAGGAACCATGTTATCATC
66 ACGTAGGAGCCTTGTCACCCCTAGATAACCAGTCATCCTCATCACGTAGGAACTGTGTTATCATC
*
3890553 C
131 T
* * ** * *
3890554 CTAAATATGGTATATCATCCTCATCGCGTAAGAACCGTGTCAT-CCCTCGACCAGACCTCCTCAT
1 CTAAAGATGGCATGCCATCCTCATCGCGTAGGAACCTTGTCATCCCCT-GACCAGACCTCCTCAT
* * *
3890618 CACGTAGGAG-TTGTGTCACCCTTAGATAACCAGTCATCCTCTTCACGTAGGAACTGTGTTATCA
65 CACGTAGGAGCCT-TGTCACCCCTAGATAACCAGTCATCCTCATCACGTAGGAACTGTGTTATCA
*
3890682 CCATT
129 TC--T
* * *
3890687 CCTTAAAGATGGTCAAGCCGTCCTCATCACGTAGGAAC
1 -C-TAAAGATGG-CATGCCATCCTCATCGCGTAGGAAC
3890725 TGTGTCACTC
Statistics
Matches: 254, Mismatches: 39, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
130 6 0.02
131 219 0.86
132 2 0.01
134 1 0.00
135 8 0.03
136 18 0.07
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (131 bp):
CTAAAGATGGCATGCCATCCTCATCGCGTAGGAACCTTGTCATCCCCTGACCAGACCTCCTCATC
ACGTAGGAGCCTTGTCACCCCTAGATAACCAGTCATCCTCATCACGTAGGAACTGTGTTATCATC
T
Found at i:3890969 original size:3 final size:3
Alignment explanation
Indices: 3890929--3890985 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
3890919 AAATTCGTTA
* * * *
3890929 TAT TTT TAT TAT TTT TAT TAC TAT TAAT TAT T-T TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
3890974 TAT TAT ATAT TA
1 TAT TAT -TAT TA
3890986 ACTATTAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3893744 original size:44 final size:44
Alignment explanation
Indices: 3893652--3893749 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 44
3893642 AGAACAAAAT
* * * *
3893652 ATAAGCTATATGATATGATCTACGTGATTACATGAACATGTGAT
1 ATAAGCTATATGACATGACCTACGTGATTACATGAACATGTAAA
*
3893696 ATAAGCTATGA-GACATGACCTACGTGATTACTTG-ACTATGTAAA
1 ATAAGCTAT-ATGACATGACCTACGTGATTACATGAAC-ATGTAAA
*
3893740 ATAAGATATA
1 ATAAGCTATA
3893750 ATATATGATA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
43 3 0.07
44 42 0.91
45 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (44 bp):
ATAAGCTATATGACATGACCTACGTGATTACATGAACATGTAAA
Found at i:3893896 original size:21 final size:22
Alignment explanation
Indices: 3893828--3893913 Score: 120
Period size: 23 Copynumber: 3.9 Consensus size: 22
3893818 GAGTCGATAC
3893828 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGGGAC-ATTCTACGT
*
3893851 GGTCCTTCGGGAGATTTCTACGT
1 GGTCCTTCGGGACA-TTCTACGT
*
3893874 GGTCCTTCGGGACA-TCTATGT
1 GGTCCTTCGGGACATTCTACGT
*
3893895 GGTCCTTAGGGACATTCTA
1 GGTCCTTCGGGACATTCTA
3893914 TATGGCTCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
21 19 0.33
22 5 0.09
23 33 0.58
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (22 bp):
GGTCCTTCGGGACATTCTACGT
Found at i:3894736 original size:14 final size:14
Alignment explanation
Indices: 3894717--3894747 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3894707 CCGAAGTGAA
3894717 GCAGGAGATGATAG
1 GCAGGAGATGATAG
3894731 GCAGGAGATGATAG
1 GCAGGAGATGATAG
3894745 GCA
1 GCA
3894748 AGAAGGTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.42, T:0.13
Consensus pattern (14 bp):
GCAGGAGATGATAG
Found at i:3898010 original size:22 final size:22
Alignment explanation
Indices: 3897952--3898004 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
3897942 GGTTCTACGC
3897952 GGTCCTTCGGGACA-TCTATGT
1 GGTCCTTCGGGACATTCTATGT
3897973 GGTCCTTCGGGACATTCTATGT
1 GGTCCTTCGGGACATTCTATGT
3897995 GG-CACTTCGG
1 GGTC-CTTCGG
3898005 TGCATTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.13, C:0.25, G:0.30, T:0.32
Consensus pattern (22 bp):
GGTCCTTCGGGACATTCTATGT
Found at i:3901725 original size:23 final size:23
Alignment explanation
Indices: 3901695--3901741 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3901685 ATATCCTAAG
3901695 TAATTTTAATTCTAAGTTGAAGC
1 TAATTTTAATTCTAAGTTGAAGC
3901718 TAATTTTAATTCTAAGTTGAAGC
1 TAATTTTAATTCTAAGTTGAAGC
3901741 T
1 T
3901742 CAAATTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.45
Consensus pattern (23 bp):
TAATTTTAATTCTAAGTTGAAGC
Found at i:3909104 original size:19 final size:19
Alignment explanation
Indices: 3909072--3909110 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3909062 TATAATTTTT
** *
3909072 TTATTTTTTTAGAATTATA
1 TTATTTTTAAAGAAATATA
3909091 TTATTTTTAAAGAAATATA
1 TTATTTTTAAAGAAATATA
3909110 T
1 T
3909111 AGAAAAAATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TTATTTTTAAAGAAATATA
Found at i:3909309 original size:39 final size:39
Alignment explanation
Indices: 3909265--3909373 Score: 134
Period size: 39 Copynumber: 2.8 Consensus size: 39
3909255 TTAAAAATAT
3909265 TTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAGAA
1 TTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAGAA
* * *
3909304 TTTAGAATGCT-ATGGTGGCAA-AATTTAAGAAATTAGGAA
1 TTTAGAATGTTAAT-GT-GAAATAATTTAAGAAATTAAGAA
*
3909343 TTTAGAATGTTAGA-GTGAAATAATTTGAGAA
1 TTTAGAATGTTA-ATGTGAAATAATTTAAGAA
3909374 TTATATATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
38 5 0.08
39 50 0.85
40 3 0.05
41 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (39 bp):
TTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAGAA
Found at i:3911739 original size:21 final size:20
Alignment explanation
Indices: 3911714--3911816 Score: 143
Period size: 20 Copynumber: 5.1 Consensus size: 20
3911704 CCGTTAGACA
*
3911714 GGGGGAATCAGTACCCCCTGG
1 GGGGGAATCTGTACCCCCT-G
*
3911735 GGGGGAATCTGTTCCCCCTG
1 GGGGGAATCTGTACCCCCTG
* * *
3911755 GGGGGAATCGGTACCCCTTA
1 GGGGGAATCTGTACCCCCTG
*
3911775 GGGGGAATCTGTTCCCCCTG
1 GGGGGAATCTGTACCCCCTG
3911795 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
3911815 GG
1 GG
3911817 CAATCTGATT
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
20 54 0.76
21 17 0.24
ACGTcount: A:0.15, C:0.28, G:0.37, T:0.20
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:3911772 original size:40 final size:41
Alignment explanation
Indices: 3911714--3911816 Score: 163
Period size: 40 Copynumber: 2.5 Consensus size: 41
3911704 CCGTTAGACA
3911714 GGGGGAATCAGTACCCCCTGGGGGGGAATCTGTTCCCCCTG
1 GGGGGAATCAGTACCCCCTGGGGGGGAATCTGTTCCCCCTG
* **
3911755 GGGGGAATCGGTA-CCCCTTAGGGGGAATCTGTTCCCCCTG
1 GGGGGAATCAGTACCCCCTGGGGGGGAATCTGTTCCCCCTG
*
3911795 GGGGGAATCTGTACCCCCTGGG
1 GGGGGAATCAGTACCCCCTGGG
3911817 CAATCTGATT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 37 0.67
41 18 0.33
ACGTcount: A:0.15, C:0.28, G:0.37, T:0.20
Consensus pattern (41 bp):
GGGGGAATCAGTACCCCCTGGGGGGGAATCTGTTCCCCCTG
Found at i:3915038 original size:16 final size:16
Alignment explanation
Indices: 3915007--3915063 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
3914997 TCATGTCTTT
3915007 TTTTTTTCTTTCGAACAG
1 TTTTTTT-TTT-GAACAG
*
3915025 TTTTTTTTTTGAACTG
1 TTTTTTTTTTGAACAG
* * *
3915041 CTATTTTTTTCAACA-
1 TTTTTTTTTTGAACAG
3915056 TTTTTTTT
1 TTTTTTTT
3915064 GATGGAGAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 6 0.19
16 16 0.50
17 3 0.09
18 7 0.22
ACGTcount: A:0.16, C:0.12, G:0.07, T:0.65
Consensus pattern (16 bp):
TTTTTTTTTTGAACAG
Found at i:3920196 original size:20 final size:20
Alignment explanation
Indices: 3920160--3920220 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
3920150 CCGTTAGACA
*
3920160 GGGGGAATCGGTA-CCCCTG
1 GGGGGAATAGGTACCCCCTG
* *
3920179 GGGGGAATATGTTCCCCCTG
1 GGGGGAATAGGTACCCCCTG
*
3920199 GGGGGAATCGGTACCCCCTG
1 GGGGGAATAGGTACCCCCTG
3920219 GG
1 GG
3920221 CAATCTGATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
19 10 0.29
20 25 0.71
ACGTcount: A:0.15, C:0.26, G:0.41, T:0.18
Consensus pattern (20 bp):
GGGGGAATAGGTACCCCCTG
Found at i:3922388 original size:26 final size:26
Alignment explanation
Indices: 3922348--3922397 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3922338 ATTGAGACAG
* *
3922348 TCAATGGGTCTGGTCAAAGTCAACAA
1 TCAACGGGTCGGGTCAAAGTCAACAA
*
3922374 TCAACGGGTCGGGTCAATGTCAAC
1 TCAACGGGTCGGGTCAAAGTCAAC
3922398 GGATCGGGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (26 bp):
TCAACGGGTCGGGTCAAAGTCAACAA
Found at i:3922803 original size:29 final size:30
Alignment explanation
Indices: 3922770--3922881 Score: 128
Period size: 32 Copynumber: 3.8 Consensus size: 30
3922760 AAAATAATAT
*
3922770 TATATTATTATATATTTAATTATTAT-TAG
1 TATATTATTATATATTTAATTATTATGTAA
3922799 TATATTATTATATA-TT--TTA-TATGTAA
1 TATATTATTATATATTTAATTATTATGTAA
* *
3922825 AATATTATTATAT-TATTAATTATTAATAGTAT
1 TATATTATTATATAT-TTAATTATT-AT-GTAA
3922857 TATATTATTATATATTTAATTATTA
1 TATATTATTATATATTTAATTATTA
3922882 ATAATATTAT
Statistics
Matches: 70, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
25 3 0.04
26 17 0.24
27 2 0.03
28 2 0.03
29 17 0.24
30 1 0.01
31 3 0.04
32 24 0.34
33 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (30 bp):
TATATTATTATATATTTAATTATTATGTAA
Found at i:3922819 original size:7 final size:7
Alignment explanation
Indices: 3922766--3922894 Score: 69
Period size: 8 Copynumber: 18.4 Consensus size: 7
3922756 ATATAAAATA
3922766 ATATTAT
1 ATATTAT
3922773 ATTATTAT
1 A-TATTAT
3922781 ATATT-T
1 ATATTAT
3922787 A-ATTAT
1 ATATTAT
3922793 -TATTAGT
1 ATATTA-T
3922800 ATATTAT
1 ATATTAT
3922807 -TA-TAT
1 ATATTAT
*
3922812 ATTTTAT
1 ATATTAT
* * *
3922819 ATGTAAA
1 ATATTAT
3922826 ATATTATT
1 ATATTA-T
3922834 ATATTATT
1 ATATTA-T
3922842 AATTATTAAT
1 -A-TATT-AT
3922852 AGTATTAT
1 A-TATTAT
3922860 ATTATTAT
1 A-TATTAT
3922868 ATATT-T
1 ATATTAT
3922874 A-ATTAT
1 ATATTAT
*
3922880 -TAATA-
1 ATATTAT
3922885 ATATTAT
1 ATATTAT
3922892 ATA
1 ATA
3922895 CACATTTAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
5 9 0.09
6 20 0.21
7 25 0.26
8 30 0.31
9 6 0.06
10 5 0.05
11 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (7 bp):
ATATTAT
Found at i:3922867 original size:32 final size:32
Alignment explanation
Indices: 3922762--3922893 Score: 158
Period size: 29 Copynumber: 4.4 Consensus size: 32
3922752 TTATATATAA
3922762 AATAATATTATATTATTATATATTTAATTATT
1 AATAATATTATATTATTATATATTTAATTATT
* *
3922794 -AT--TAGTATATTATTATATATTTTA-TATGT
1 AATAATATTATATTATTATATATTTAATTAT-T
3922823 AA-AATA-T-TATTA-TAT-TA-TTAATTATT
1 AATAATATTATATTATTATATATTTAATTATT
*
3922849 AATAGTATTATATTATTATATATTTAATTATT
1 AATAATATTATATTATTATATATTTAATTATT
3922881 AATAATATTATAT
1 AATAATATTATAT
3922894 ACACATTTAA
Statistics
Matches: 84, Mismatches: 5, Indels: 22
0.76 0.05 0.20
Matches are distributed among these distances:
26 6 0.07
27 8 0.10
28 7 0.08
29 31 0.37
30 5 0.06
31 6 0.07
32 21 0.25
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (32 bp):
AATAATATTATATTATTATATATTTAATTATT
Found at i:3926746 original size:75 final size:75
Alignment explanation
Indices: 3926659--3927487 Score: 387
Period size: 75 Copynumber: 11.2 Consensus size: 75
3926649 CGATCAAAAA
* **
3926659 TCTAAATTTCCTGATCCTGAACCTCAAGCCATGCCTTGTGAACATTCTGGAATCAACATGTTCGG
1 TCTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCCTCTGGAATCAACATGTTCGG
3926724 AAAACAGGCT
66 AAAACAGGCT
* ** * *
3926734 TCTAAATTTCCTG-A----AA-CTCAAGCGATGAATTGTGAACCCACTGGAA-CAAACATGTTTG
1 TCTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCCTCTGGAATC-AACATGTTCG
**
3926792 GGCAACAGGCT
65 GAAAACAGGCT
* * ** *
3926803 TCTAAATTTCTTGAACCTGAAACTCAAGTTATGCCCTGTGAACCC-CTGGAATCAACATGTTCGG
1 TCTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCCTCTGGAATCAACATGTTCGG
**
3926867 AAAACAAACT
66 AAAACAGGCT
* * * ** * * * * * *
3926877 TTTAAGTTTCCTGGACCCCAATCTCAAGCTATACCCTCTGAACCC-CTTGGAATCAACATGTTTG
1 TCTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCCTC-TGGAATCAACATGTTCG
* *
3926941 GGAAACAAGCT
65 GAAAACAGGCT
** ** * * * *
3926952 TCTAAATTTCCTGGTCCTGAATCC-CAAGCTTTTCCCTGTGAACCCCCT-CAGATCAACATGTTC
1 TCTAAATTTCCTGAACCTGAA-CCTCAAGCCATGCCTTGTGAACCCTCTGGA-ATCAACATGTTC
* *
3927015 GAAAAACAGCCT
64 GGAAAACAGGCT
* * ** * * * * * * *
3927027 ACTAAATTTCCTGAATCTGGTCCTCAAGCCATGCCCTCTGATCCCACTGGGATCAACATTTTTGG
1 TCTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCCTCTGGAATCAACATGTTCGG
* * **
3927092 GAATCAAACT
66 AAAACAGGCT
* * * * * * * * * * *
3927102 TCTAAGTTTCATGAACTTGAACCACAAGGCATTCGTTGTGAA-CTTACCGGAATGAACATGTTTG
1 TCTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCCT-CTGGAATCAACATGTTCG
* *
3927166 GCAAGCAAGG-T
65 GAAAAC-AGGCT
* * * * * * *
3927177 TCTAAATTTCCTGAACCT----CT--ACCCATGCTTTGTGAA-CCTGCTAGAAACAATATTTTTG
1 TCTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCCT-CTGGAATCAACATGTTCG
* * **
3927235 GGAAGCAAACT
65 GAAAACAGGCT
* * ** ** ** *
3927246 TCCAAATTTCCCGAACCTGATTCTCAAGCCATATCTTACGAACCCAT-TGGATTCAACATGTTCG
1 TCTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCC-TCTGGAATCAACATGTTCG
*
3927310 GAAAACAGACT
65 GAAAACAGGCT
* * * * * * *
3927321 TCTAAA-TTCCTTGAACCTGGACCCCAAGCGATACC--GTGCAAACTTACTGGATTCAACATGTT
1 TCTAAATTTCC-TGAACCTGAACCTCAAGCCATGCCTTGTG-AACCCT-CTGGAATCAACATGTT
* *
3927383 CAGAAATCAGGCT
63 CGGAAAACAGGCT
* * * * * * *
3927396 CCTAAATTTCCGGAACTTGAACCCCAAGCCATACCATCTGAA-CCTACTGGAATCAACATGCTT-
1 TCTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCCT-CTGGAATCAACATG-TTC
3927459 GGAAAACAGGCT
64 GGAAAACAGGCT
** *
3927471 TCCCAATTTCCCGAACC
1 TCTAAATTTCCTGAACC
3927488 CAAGCCATAC
Statistics
Matches: 561, Mismatches: 160, Indels: 66
0.71 0.20 0.08
Matches are distributed among these distances:
68 2 0.00
69 102 0.18
70 3 0.01
71 1 0.00
73 4 0.01
74 71 0.13
75 362 0.65
76 13 0.02
77 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (75 bp):
TCTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCCTCTGGAATCAACATGTTCGG
AAAACAGGCT
Found at i:3926767 original size:69 final size:69
Alignment explanation
Indices: 3926673--3926817 Score: 175
Period size: 69 Copynumber: 2.1 Consensus size: 69
3926663 AATTTCCTGA
* ** **
3926673 TCCTGAACCTCAAGCCATGCCTTGTGAACATTCTGGAATC-AACATGTTCGGAAAACAGGCTTCT
1 TCCTGAAACTCAAGCCATGAATTGTGAACACACTGGAA-CAAACATGTTCGGAAAACAGGCTTCT
3926737 AAATT
65 AAATT
* * * **
3926742 TCCTGAAACTCAAGCGATGAATTGTGAACCCACTGGAACAAACATGTTTGGGCAACAGGCTTCTA
1 TCCTGAAACTCAAGCCATGAATTGTGAACACACTGGAACAAACATGTTCGGAAAACAGGCTTCTA
3926807 AATT
66 AATT
*
3926811 TCTTGAA
1 TCCTGAA
3926818 CCTGAAACTC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
68 1 0.02
69 63 0.98
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (69 bp):
TCCTGAAACTCAAGCCATGAATTGTGAACACACTGGAACAAACATGTTCGGAAAACAGGCTTCTA
AATT
Found at i:3926953 original size:149 final size:143
Alignment explanation
Indices: 3926659--3927041 Score: 371
Period size: 149 Copynumber: 2.6 Consensus size: 143
3926649 CGATCAAAAA
* ** * **
3926659 TCTAAATTTCCTGATCCTGAACCTCAAGCCATGCCTTGTGAACATTCTGGAATCAACATGTTCGG
1 TCTAAATTTCCTGATCCTGAAACTCAAGTTATGCCCTGTGAAC-CCCTGGAATCAACATGTTCGG
** * *
3926724 AAAACAGGCTTCTAAATTTCCTGAAACTCAAGCGATGAATTGTGAACCCACTGGAACAAACATGT
65 AAAACAAACTTCTAAATTTCCTGAAACTCAAGCGATGAACTCTGAACCCACTGGAACAAACATGT
* *
3926789 TTGGGCAACAGGCT
130 TTGGGAAACAAGCT
* *
3926803 TCTAAATTTCTTGAACCTGAAACTCAAGTTATGCCCTGTGAACCCCTGGAATCAACATGTTCGGA
1 TCTAAATTTCCTGATCCTGAAACTCAAGTTATGCCCTGTGAACCCCTGGAATCAACATGTTCGGA
* * * *
3926868 AAACAAACTTTTAAGTTTCCTGGACCCCAATCTCAAGCTAT-ACCCTCTGAACCC-CTTGGAATC
66 AAACAAACTTCTAAATTTCCT-GA----AA-CTCAAGCGATGA-ACTCTGAACCCAC-TGGAA-C
3926931 -AACATGTTTGGGAAACAAGCT
122 AAACATGTTTGGGAAACAAGCT
* * * * *
3926952 TCTAAATTTCCTGGTCCTGAATCCCAAGCTT-TTCCCTGTGAACCCCCT-CAGATCAACATGTTC
1 TCTAAATTTCCTGATCCTGAAACTCAAG-TTATGCCCTGTGAA-CCCCTGGA-ATCAACATGTTC
* ** *
3927015 GAAAAACAGCCTACTAAATTTCCTGAA
63 GGAAAACAAACTTCTAAATTTCCTGAA
3927042 TCTGGTCCTC
Statistics
Matches: 196, Mismatches: 31, Indels: 23
0.78 0.12 0.09
Matches are distributed among these distances:
143 37 0.19
144 39 0.20
145 1 0.01
148 4 0.02
149 77 0.39
150 38 0.19
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (143 bp):
TCTAAATTTCCTGATCCTGAAACTCAAGTTATGCCCTGTGAACCCCTGGAATCAACATGTTCGGA
AAACAAACTTCTAAATTTCCTGAAACTCAAGCGATGAACTCTGAACCCACTGGAACAAACATGTT
TGGGAAACAAGCT
Found at i:3927593 original size:69 final size:68
Alignment explanation
Indices: 3927418--3927605 Score: 245
Period size: 68 Copynumber: 2.8 Consensus size: 68
3927408 GAACTTGAAC
*
3927418 CCCAAGCCATACCATC-TGAACCTACTGGAATCAACATGCTT-GGAAAACAGGCTTCCCAATTTC
1 CCCAAGCCATACC-TCATGAACCTACTGGAATCAACATG-TTCGGAAAACAGGATTCCCAATTTC
3927481 CCGAA
64 CCGAA
* * * * *
3927486 CCCAAGCCATACCTCATGAACCTACTGGAATCAGCATGTTCGAAAAACATGATTCCCATTTTCCT
1 CCCAAGCCATACCTCATGAACCTACTGGAATCAACATGTTCGGAAAACAGGATTCCCAATTTCCC
3927551 GAA
66 GAA
* * * *
3927554 CCCAAATCTATACCTTATGAAACTACTGGAATCAACATGTTCGGAAAACAGG
1 CCC-AAGCCATACCTCATGAACCTACTGGAATCAACATGTTCGGAAAACAGG
3927606 TGCCTTCAAG
Statistics
Matches: 104, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
67 4 0.04
68 59 0.57
69 41 0.39
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (68 bp):
CCCAAGCCATACCTCATGAACCTACTGGAATCAACATGTTCGGAAAACAGGATTCCCAATTTCCC
GAA
Found at i:3934684 original size:55 final size:54
Alignment explanation
Indices: 3934615--3935054 Score: 369
Period size: 55 Copynumber: 8.1 Consensus size: 54
3934605 TAGATAAGCG
* * * * * *
3934615 AGACTTGAAAAATCTTCAAATGACGGGTCCGCTCCCTATTCTTTTAGGTAGTATA
1 AGACTCGAACAATCTTCAAA-AACGGGTCCGCTCCCTATTCGTTCAGGGAGTATA
* ** * * *
3934670 AGACTCGGACAATCTTCGGTAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
1 AGACTCGAACAATCTTC-AAAAACGGGTCCGCTCCCTATTCGTTCAGGGAGTATA
* * ** *
3934725 AGACTCAAACAATCTTCAACAAACGTGTTTGCTCCCTGTTCGTTCAGGGAGTATA
1 AGACTCGAACAATCTTCAA-AAACGGGTCCGCTCCCTATTCGTTCAGGGAGTATA
* * * *
3934780 AGACTTGAATAATCTTCAACAAACGGGTCTGCTCCCTATTTC-TTCAGAGAGTATA
1 AGACTCGAACAATCTTCAA-AAACGGGTCCGCTCCCTA-TTCGTTCAGGGAGTATA
* * *
3934835 AGACTCG----ATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTCGAACAATCTTCAA-AAACGGGTCCGCTCCCTATTCGTTCAGGGAGTATA
* * *
3934886 AGACTCAAACAATTTTCAACAAACAGGTCCGCTCCCTATTCGTTCAGGGAGTAT-
1 AGACTCGAACAATCTTCAA-AAACGGGTCCGCTCCCTATTCGTTCAGGGAGTATA
* * * *
3934940 AGAACTCGAATAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
1 AG-ACTCGAACAATCTTCA-AAAACGGGTCCGCTCCCTATTCGTTCAGGGAGTATA
* * * * * * *
3934996 GGACT-G---GATCTTCACCAAACAGGTCCGCTCTCTATTCCTTCAGAGAGTATA
1 AGACTCGAACAATCTTCA-AAAACGGGTCCGCTCCCTATTCGTTCAGGGAGTATA
*
3935047 GGACTCGA
1 AGACTCGA
3935055 TCTTCATAAA
Statistics
Matches: 324, Mismatches: 48, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
50 3 0.01
51 89 0.27
52 1 0.00
54 3 0.01
55 222 0.69
56 6 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (54 bp):
AGACTCGAACAATCTTCAAAAACGGGTCCGCTCCCTATTCGTTCAGGGAGTATA
Found at i:3934904 original size:106 final size:105
Alignment explanation
Indices: 3934641--3935064 Score: 378
Period size: 106 Copynumber: 4.0 Consensus size: 105
3934631 CAAATGACGG
* * * *** *
3934641 GTCCGCTCCCTATTCTTTTAG-GTAGTATAAGACTCGGACAATCTTCGGTAAAC-GTGTCTGCTC
1 GTCCGCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCAACAAACAG-GTCCGCTC
* * *
3934704 CCTATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAACAAACGT
64 CCTATTCATTCAGAGAGTATAAGACT----CGATCTTC-ATAAACGT
** * * * * * * *
3934751 GTTTGCTCCCTGTTCGTTCAGGGAGTATAAGACTTGAATAATCTTCAACAAACGGGTCTGCTCCC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACAGGTCCGCTCCC
3934816 TATTTC-TTCAGAGAGTATAAGACTCGATCTTCAATAAACGT
66 TA-TTCATTCAGAGAGTATAAGACTCGATCTTC-ATAAACGT
* *
3934857 GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAATTTTCAACAAACAGGTCCGCTCCC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACAGGTCCGCTCCC
* * *
3934922 TATTCGTTCAGGGAGTAT-AGAACTCGAATAATCTTCATAAAACGG
66 TATTCATTCAGAGAGTATAAG-ACTCG----ATCTTCAT-AAACGT
* * * * *
3934967 GTCCGCTCTCTATTCCTTCAGAGAGTATAGGACT-G---GATCTTCACCAAACAGGTCCGCTCTC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACAGGTCCGCTCCC
* *
3935028 TATTCCTTCAGAGAGTATAGGACTCGATCTTCATAAA
66 TATTCATTCAGAGAGTATAAGACTCGATCTTCATAAA
3935065 ATGAGTTTGC
Statistics
Matches: 266, Mismatches: 37, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
101 3 0.01
102 8 0.03
105 5 0.02
106 130 0.49
107 1 0.00
109 2 0.01
110 112 0.42
111 5 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (105 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACAGGTCCGCTCCC
TATTCATTCAGAGAGTATAAGACTCGATCTTCATAAACGT
Found at i:3934906 original size:161 final size:159
Alignment explanation
Indices: 3934615--3935052 Score: 533
Period size: 161 Copynumber: 2.7 Consensus size: 159
3934605 TAGATAAGCG
* * *
3934615 AGACTTGAAAAATCTTCAAATGACGGGTCCGCTCCCTA-TTCTTTTAG-GTAGTATAAGACTCGG
1 AGACTTGAATAATCTTCAAA-AACGGGTCCGCTCCCTATTTC-TTCAGAG-AGTATAAGACTC-G
** * * *
3934678 ACAATCTTCGGTAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAACAATCTTCA
62 ---ATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCA
** *
3934743 ACAAAC-GTGTTTGCTCCCTGTTCGTTCAGGGAGTAT
124 ACAAACAG-GTCCGCTCCCTATTCGTTCAGGGAGTAT
*
3934779 AAGACTTGAATAATCTTCAACAAACGGGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAT
1 -AGACTTGAATAATCTTCAA-AAACGGGTCCGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAT
*
3934844 CTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAATTTTCAACAAA
64 CTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAAA
3934909 CAGGTCCGCTCCCTATTCGTTCAGGGAGTAT
129 CAGGTCCGCTCCCTATTCGTTCAGGGAGTAT
* * * * *
3934940 AGAACTCGAATAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGGACTGGAT
1 AG-ACTTGAATAATCTTCA-AAAACGGGTCCGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAT
** * *
3935005 CTTCACCAAACAG-GTCCGCTCTCTATTCCTTCAGAGAGTATAGGACTC
64 CTTCAATAAAC-GTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTC
3935053 GATCTTCATA
Statistics
Matches: 243, Mismatches: 23, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
160 2 0.01
161 183 0.75
162 3 0.01
164 1 0.00
165 49 0.20
166 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (159 bp):
AGACTTGAATAATCTTCAAAAACGGGTCCGCTCCCTATTTCTTCAGAGAGTATAAGACTCGATCT
TCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAAACA
GGTCCGCTCCCTATTCGTTCAGGGAGTAT
Found at i:3935112 original size:37 final size:38
Alignment explanation
Indices: 3935063--3935136 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 38
3935053 GATCTTCATA
3935063 AAATGAGTTTGCTTCACAACTCTTCCGTGAAGGCTTAT
1 AAATGAGTTTGCTTCACAACTCTTCCGTGAAGGCTTAT
*
3935101 AAATGA-TTTGCTTCACTACTCTTCCGTGAAGGCTTA
1 AAATGAGTTTGCTTCACAACTCTTCCGTGAAGGCTTA
3935137 AGATTGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 29 0.83
38 6 0.17
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.35
Consensus pattern (38 bp):
AAATGAGTTTGCTTCACAACTCTTCCGTGAAGGCTTAT
Found at i:3936438 original size:17 final size:17
Alignment explanation
Indices: 3936408--3936513 Score: 110
Period size: 17 Copynumber: 6.2 Consensus size: 17
3936398 TCCTTTTATT
**
3936408 TTTTTTTTTTTTTTTC-
1 TTTTTTTTCATTTTTCA
3936424 TTCTTTTTTCATTTTTCA
1 TT-TTTTTTCATTTTTCA
3936442 TTTTTTTTCA-TTTTCA
1 TTTTTTTTCATTTTTCA
3936458 TTTTTTTCTCA-TTTTCA
1 TTTTTTT-TCATTTTTCA
* *
3936475 TTTTCTTTCATTTTCCTCC
1 TTTTTTTTCATTTT--TCA
*
3936494 TTTTTTTTCTTTTTTCA
1 TTTTTTTTCATTTTTCA
3936511 TTT
1 TTT
3936514 CTTCTTCAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
16 18 0.23
17 43 0.56
18 2 0.03
19 14 0.18
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTTTCATTTTTCA
Found at i:3936448 original size:10 final size:10
Alignment explanation
Indices: 3936401--3936455 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
3936391 TGAACCCTCC
3936401 TTTT-ATTTT
1 TTTTCATTTT
*
3936410 TTTT-TTTTT
1 TTTTCATTTT
3936419 TTTTC-TTCTT
1 TTTTCATT-TT
3936429 TTTTCA---T
1 TTTTCATTTT
3936436 TTTTCATTTT
1 TTTTCATTTT
3936446 TTTTCATTTT
1 TTTTCATTTT
3936456 CATTTTTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
7 7 0.18
9 14 0.36
10 18 0.46
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTCATTTT
Found at i:3936456 original size:33 final size:32
Alignment explanation
Indices: 3936409--3936513 Score: 104
Period size: 33 Copynumber: 3.1 Consensus size: 32
3936399 CCTTTTATTT
**
3936409 TTTTTTTTTTTTTTCTTCTTTTTTCATTTTTCA
1 TTTTTTTTCATTTTCTT-TTTTTTCATTTTTCA
3936442 TTTTTTTTCATTTTCATTTTTTTCTCA-TTTTCA
1 TTTTTTTTCATTTTC-TTTTTTT-TCATTTTTCA
* *
3936475 TTTTCTTTCATTTTCCTCCTTTTTTTTCTTTTTTCA
1 TTTTTTTTCA-TTT--T-CTTTTTTTTCATTTTTCA
3936511 TTT
1 TTT
3936514 CTTCTTCAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
33 33 0.54
34 8 0.13
35 2 0.03
36 17 0.28
37 1 0.02
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (32 bp):
TTTTTTTTCATTTTCTTTTTTTTCATTTTTCA
Found at i:3943047 original size:45 final size:45
Alignment explanation
Indices: 3942988--3943131 Score: 243
Period size: 45 Copynumber: 3.1 Consensus size: 45
3942978 TGTTATTAAC
*
3942988 AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCA
1 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCTTATTCA
3943034 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTATTCA
1 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTATTCA
*
3943079 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC--TTATTCA
3943126 AAAAAT
1 AAAAAT
3943132 GAAAATAAAT
Statistics
Matches: 94, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
45 73 0.78
46 9 0.10
47 12 0.13
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (45 bp):
AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTATTCA
Found at i:3947570 original size:31 final size:31
Alignment explanation
Indices: 3947386--3947555 Score: 331
Period size: 31 Copynumber: 5.5 Consensus size: 31
3947376 GGGTCGAGGG
3947386 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
3947417 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
3947448 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
3947479 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
3947510 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
3947541 TTACCTAGGTTCTTC
1 TTACCTATGTTCTTC
3947556 AGAATCTATG
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 138 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:3951930 original size:31 final size:31
Alignment explanation
Indices: 3951749--3951920 Score: 335
Period size: 31 Copynumber: 5.5 Consensus size: 31
3951739 GGGTCGAGGG
3951749 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
3951780 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
3951811 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
3951842 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
3951873 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
3951904 TTACCTAGGTTCTTCGG
1 TTACCTATGTTCTTCGG
3951921 AATCTATGGA
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 140 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:3955444 original size:31 final size:32
Alignment explanation
Indices: 3955409--3955470 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
3955399 TATACTAGCA
* * *
3955409 AAGCAGATTT-ATAAGTAATGTATAAGGAAAC
1 AAGCAGATTTAACAAGTAATATATAAAGAAAC
3955440 AAGCAGATTTAACAAGTAATATATAAAGAAA
1 AAGCAGATTTAACAAGTAATATATAAAGAAA
3955471 TAAGATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 10 0.37
32 17 0.63
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.24
Consensus pattern (32 bp):
AAGCAGATTTAACAAGTAATATATAAAGAAAC
Found at i:3958950 original size:29 final size:29
Alignment explanation
Indices: 3958890--3958966 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
3958880 TACGTCCATG
*
3958890 ATAACAAATATTAAAGAAATTAGGCCCCTA
1 ATAACAAATATTAAA-AAATTAGACCCCTA
* *
3958920 ATAACAAGTATTAAAAAATTAGACCCTTA
1 ATAACAAATATTAAAAAATTAGACCCCTA
*
3958949 ATAATAAATATTAAAAAA
1 ATAACAAATATTAAAAAA
3958967 ATATTGGTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 28 0.67
30 14 0.33
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (29 bp):
ATAACAAATATTAAAAAATTAGACCCCTA
Found at i:3959148 original size:17 final size:18
Alignment explanation
Indices: 3959126--3959160 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3959116 ATAATTGGGC
3959126 CCCATA-ATTTATATAAA
1 CCCATATATTTATATAAA
*
3959143 CCCATATGTTTATATAAA
1 CCCATATATTTATATAAA
3959161 TATAGTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (18 bp):
CCCATATATTTATATAAA
Found at i:3960488 original size:4 final size:4
Alignment explanation
Indices: 3960479--3960746 Score: 509
Period size: 4 Copynumber: 67.0 Consensus size: 4
3960469 ATTGACAAAG
3960479 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3960527 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3960575 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3960623 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
3960671 CATA CATA CATA CATA CATA CATA CATA CATG CATA CATG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
3960719 CATA CATA CATA CATA CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA
3960747 TTGCTGATTG
Statistics
Matches: 258, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 258 1.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:3978251 original size:24 final size:24
Alignment explanation
Indices: 3978217--3978301 Score: 143
Period size: 24 Copynumber: 3.5 Consensus size: 24
3978207 TGAATTCTGT
3978217 TATGATACTTGACATGGATTTTGA
1 TATGATACTTGACATGGATTTTGA
* *
3978241 TTTGATACTTGACCTGGATTTTGA
1 TATGATACTTGACATGGATTTTGA
*
3978265 TCTGATACTTGACATGGATTTTGA
1 TATGATACTTGACATGGATTTTGA
3978289 TATGATACTTGAC
1 TATGATACTTGAC
3978302 CTGAATTAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (24 bp):
TATGATACTTGACATGGATTTTGA
Found at i:3981684 original size:27 final size:27
Alignment explanation
Indices: 3981646--3981714 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
3981636 TCTAAATTAT
*
3981646 ATTATTTGGTTAAGAGTTAATACCGAA
1 ATTATTTGGTTAAGAGTTAATACCAAA
3981673 ATTATTTGGTTAAGAGTTAATACCAAA
1 ATTATTTGGTTAAGAGTTAATACCAAA
3981700 ATTATTTGGTTAAGA
1 ATTATTTGGTTAAGA
3981715 AATTATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (27 bp):
ATTATTTGGTTAAGAGTTAATACCAAA
Found at i:3984523 original size:15 final size:15
Alignment explanation
Indices: 3984503--3984531 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3984493 ACTTTGATCA
3984503 AAAAGTCATTTTTTG
1 AAAAGTCATTTTTTG
3984518 AAAAGTCATTTTTT
1 AAAAGTCATTTTTT
3984532 ATGTTTTTCG
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:0.34, C:0.07, G:0.10, T:0.48
Consensus pattern (15 bp):
AAAAGTCATTTTTTG
Found at i:3986544 original size:124 final size:124
Alignment explanation
Indices: 3986340--3986583 Score: 332
Period size: 124 Copynumber: 2.0 Consensus size: 124
3986330 TTTCCTAAAA
* * * *
3986340 AATAATTTAAATAAAACTAGATTAAATATAATATTTTATTTATTAAAAAATATCAGAAAATGACA
1 AATAATTTAAATAAAACTAAAGTAAAGATAATATTTTATTTATTAAAAAATATCAAAAAATGACA
** * *
3986405 TCCAGTTATTTTAAGACAGCCA-ATTTCTTTGATATTAAAAAAATAAATAAATATTAATAAC
66 TCCAGTTACCTTAAGAC-GACACATTTC-TTAATATT-AAAAAATAAATAAATATTAATAAC
* *
3986466 AATAGTTTAAATAAAACTAAAGTAAAGATAATA-TTT-TTTATTTAAAAATATCAAAAAATGACA
1 AATAATTTAAATAAAACTAAAGTAAAGATAATATTTTATTTATTAAAAAATATCAAAAAATGACA
* *
3986529 TCTAGTTACCTTAAGACGACACCTTTCTTAATATTAAAAAATAAATAAATATTAA
66 TCCAGTTACCTTAAGACGACACATTTCTTAATATTAAAAAATAAATAAATATTAA
3986584 AATTTAATTA
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
122 20 0.19
123 10 0.10
124 43 0.41
125 3 0.03
126 29 0.28
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.35
Consensus pattern (124 bp):
AATAATTTAAATAAAACTAAAGTAAAGATAATATTTTATTTATTAAAAAATATCAAAAAATGACA
TCCAGTTACCTTAAGACGACACATTTCTTAATATTAAAAAATAAATAAATATTAATAAC
Found at i:3987210 original size:3 final size:3
Alignment explanation
Indices: 3987202--3987272 Score: 115
Period size: 3 Copynumber: 23.0 Consensus size: 3
3987192 AATATAAATT
*
3987202 TAA TAA TAA TAA TAA TAA TAA TATA TAA TAT TAA TAA TAA TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A
3987249 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
3987273 CAAAATCATA
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 58 0.91
4 6 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3987230 original size:22 final size:22
Alignment explanation
Indices: 3987204--3987272 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
3987194 TATAAATTTA
3987204 ATAATAATAATAATAATAATAT
1 ATAATAATAATAATAATAATAT
*
3987226 ATAATATTAATAATAATAATAT
1 ATAATAATAATAATAATAATAT
3987248 ATAATAATAATAATAATAATA-
1 ATAATAATAATAATAATAATAT
3987269 ATAA
1 ATAA
3987273 CAAAATCATA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
21 4 0.09
22 41 0.91
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAATAATAATAATAATAATAT
Found at i:3987528 original size:39 final size:39
Alignment explanation
Indices: 3987473--3987904 Score: 526
Period size: 39 Copynumber: 11.1 Consensus size: 39
3987463 ATGTTGAATA
* * * * * *
3987473 AGTTCTTTAGACTATGAACTTCATCTTCCTCTTTAAATG
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
* *
3987512 AGTTCTTGAAATTATGAACTCCTTCTTCCTCTTCAGATG
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
* * *
3987551 AGCTCTTCAGACTATGAACTCCTT-TTCCTCTTCATATG
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
* *
3987589 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
* *
3987628 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCATATG
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
* *
3987667 AGTTCTTCAGATTATGAACTCATTCTTCCTCTTCAGACG
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
* * ** * * *
3987706 AGTTCTTCAGACTATGAACTCCTTTTTTTTATTCAAACG
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
* *
3987745 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
* *
3987784 AGTTCTTCAGATTATGAACTCCTTCTGCCTTTTCAGATG
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
* * * * *
3987823 AGTTCTTCAGATTATGAACTCCTTTTTTCTTTTTAGACG
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
* *
3987862 AGTTCTTCAGATTATGAACTCATT-TTCCCTCTTCAGACG
1 AGTTCTTCAGATTATGAACTCCTTCTT-CCTCTTCAGATG
3987901 AGTT
1 AGTT
3987905 ATTTCATATG
Statistics
Matches: 343, Mismatches: 48, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
38 38 0.11
39 305 0.89
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (39 bp):
AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGATG
Found at i:3988076 original size:37 final size:36
Alignment explanation
Indices: 3988035--3988156 Score: 120
Period size: 37 Copynumber: 3.3 Consensus size: 36
3988025 AAGAAAACAA
*
3988035 TCTCAAGTGAGATAAATTATTATTTAAAGTGAAACTT
1 TCTCAAGCGAGATAAATT-TTATTTAAAGTGAAACTT
* * ** **
3988072 TCTCAAGCGAGA-AATAGTTTATTTTAAGAAAAACAA
1 TCTCAAGCGAGATAA-ATTTTATTTAAAGTGAAACTT
* * *
3988108 TCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTT
1 TCTCAAGCGAGATAAATT-TTATTTAAAGTGAAACTT
3988145 TCTCAAGCGAGA
1 TCTCAAGCGAGA
3988157 AACAGTTTGT
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
36 28 0.42
37 38 0.58
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (36 bp):
TCTCAAGCGAGATAAATTTTATTTAAAGTGAAACTT
Found at i:3988112 original size:36 final size:35
Alignment explanation
Indices: 3988007--3988192 Score: 142
Period size: 36 Copynumber: 5.1 Consensus size: 35
3987997 TTTTCTCCAA
*
3988007 CGAGAAACAGTTTGTTTTAAG-AAAACAATCTCAAG
1 CGAGAAA-AGTTTATTTTAAGAAAAACAATCTCAAG
* * * ** **
3988042 TGAGATAAATTATTATTTAAAGTGAAACTTTCTCAAG
1 CGAGA-AAAGT-TTATTTTAAGAAAAACAATCTCAAG
3988079 CGAGAAATAGTTTATTTTAAGAAAAACAATCTCAAG
1 CGAGAAA-AGTTTATTTTAAGAAAAACAATCTCAAG
* * ** **
3988115 TGAGATAAA-TTGCTATTTCAAGTGAAACTTTCTCAAG
1 CGAGA-AAAGTT--TATTTTAAGAAAAACAATCTCAAG
*
3988152 CGAGAAACAGTTTGTTTTAAGAAAAACAATCTCAAG
1 CGAGAAA-AGTTTATTTTAAGAAAAACAATCTCAAG
*
3988188 TGAGA
1 CGAGA
3988193 TAAATTGCTA
Statistics
Matches: 114, Mismatches: 28, Indels: 17
0.72 0.18 0.11
Matches are distributed among these distances:
35 8 0.07
36 61 0.54
37 43 0.38
38 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (35 bp):
CGAGAAAAGTTTATTTTAAGAAAAACAATCTCAAG
Found at i:3988139 original size:73 final size:73
Alignment explanation
Indices: 3987946--3988205 Score: 425
Period size: 73 Copynumber: 3.6 Consensus size: 73
3987936 CTTCTGGAAA
* *
3987946 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCGAGTGAAATTTTCTCCAA-CGA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTTTCT-CAAGCGA
3988010 GAAACAGTT
65 GAAACAGTT
* *
3988019 TGTTTTAAG-AAAACAATCTCAAGTGAGATAAATTATTATTTAAAGTGAAACTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTTTCTCAAGCGAG
*
3988083 AAATAGTT
66 AAACAGTT
* *
3988091 TATTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTTTCTCAAGCGAG
3988156 AAACAGTT
66 AAACAGTT
*
3988164 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTT
3988206 GAAAACATCA
Statistics
Matches: 174, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
71 3 0.02
72 62 0.36
73 109 0.63
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (73 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTTTCTCAAGCGAG
AAACAGTT
Found at i:3988993 original size:22 final size:22
Alignment explanation
Indices: 3988916--3988997 Score: 123
Period size: 22 Copynumber: 3.7 Consensus size: 22
3988906 AATAAAGCTT
3988916 TCATCTTTGAA-AATAGAATCTA
1 TCATCTTTGAAGAAT-GAATCTA
*
3988938 TCATCTTTGAAAAGAT-AATCTA
1 TCATCTTTGAAGA-ATGAATCTA
3988960 TCATCTTTGAAGAATGAATCTA
1 TCATCTTTGAAGAATGAATCTA
3988982 TCATCTTTGAAGAATG
1 TCATCTTTGAAGAATG
3988998 TAGATGTAGA
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
21 2 0.04
22 51 0.91
23 1 0.02
24 2 0.04
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (22 bp):
TCATCTTTGAAGAATGAATCTA
Found at i:3989446 original size:55 final size:55
Alignment explanation
Indices: 3989348--3989453 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 55
3989338 ATAACTGGTT
* * *
3989348 CGTAAAACATTTGACAATACAATCATCATTTTCTGTGGCTTCTGCACATATGTTC
1 CGTAAAACATTTGACAACACAATCATCATTTCCTATGGCTTCTGCACATATGTTC
* * * *
3989403 CGTAAAACATTTGACAACACATTCATCCTTTCCTATGGTTTCTGCCCATAT
1 CGTAAAACATTTGACAACACAATCATCATTTCCTATGGCTTCTGCACATAT
3989454 TTCTCAATCA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (55 bp):
CGTAAAACATTTGACAACACAATCATCATTTCCTATGGCTTCTGCACATATGTTC
Found at i:3996262 original size:23 final size:24
Alignment explanation
Indices: 3996236--3996292 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
3996226 AAGTTAGAGC
*
3996236 AAAATAAAATGTATAAAA-AA-TAA
1 AAAATAAAATGTA-AAAATAAGAAA
*
3996259 AAAATAAAA-ATAAAAATAAGAAA
1 AAAATAAAATGTAAAAATAAGAAA
3996282 AAAATAAAATG
1 AAAATAAAATG
3996293 GTTAGTACCA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 4 0.14
22 4 0.14
23 20 0.71
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (24 bp):
AAAATAAAATGTAAAAATAAGAAA
Found at i:3996267 original size:6 final size:6
Alignment explanation
Indices: 3996251--3996290 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
3996241 AAAATGTATA
*
3996251 AAAAAT AAAAAAT AAAAAT AAAAAT AAGAA- AAAAAT AAAA
1 AAAAAT -AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
3996291 TGGTTAGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
5 4 0.13
6 20 0.67
7 6 0.20
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:3996282 original size:14 final size:13
Alignment explanation
Indices: 3996251--3996290 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
3996241 AAAATGTATA
3996251 AAAAATAAAAAAT
1 AAAAATAAAAAAT
3996264 AAAAAT-AAAAAT
1 AAAAATAAAAAAT
*
3996276 -AAGA-AAAAAAT
1 AAAAATAAAAAAT
3996287 AAAA
1 AAAA
3996291 TGGTTAGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 9 0.39
12 8 0.35
13 6 0.26
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:3997723 original size:125 final size:124
Alignment explanation
Indices: 3997593--3997837 Score: 361
Period size: 125 Copynumber: 2.0 Consensus size: 124
3997583 TTTTCCTAAA
*
3997593 AATAATTTAAATAAAACT--AGATTAATAATAATATTTTAATTATTTAAAAATATCAGAAAATG-
1 AATAATTTAAATAAAACTCAAG-TAAAT-ATAATATTTTAATTATTTAAAAATATCAGAAAA-GA
** *
3997655 ACATATAGTTATTTTAAGACAACCCATTTCATTGATATTAAAAAATAAATAAATATTAATAAC
63 ACATATAGTTACCTTAAGACAACCCATTTC-TTAATATTAAAAAATAAATAAATATTAATAAC
*
3997718 AATAATTTAAATAAAACTCAAGTAAATATAATATTTTATTTATTTAAAAATATCAGAAAAGAACA
1 AATAATTTAAATAAAACTCAAGTAAATATAATATTTTAATTATTTAAAAATATCAGAAAAGAACA
* * *
3997783 TCTAGTTACCTTAAGACGACCCCTTTCTTAATATTAAAAAATAAATAAATATTAA
66 TATAGTTACCTTAAGACAACCCATTTCTTAATATTAAAAAATAAATAAATATTAA
3997838 AATTGAATTA
Statistics
Matches: 109, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
124 28 0.26
125 75 0.69
126 4 0.04
127 2 0.02
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (124 bp):
AATAATTTAAATAAAACTCAAGTAAATATAATATTTTAATTATTTAAAAATATCAGAAAAGAACA
TATAGTTACCTTAAGACAACCCATTTCTTAATATTAAAAAATAAATAAATATTAATAAC
Found at i:3999112 original size:3 final size:3
Alignment explanation
Indices: 3999104--3999176 Score: 76
Period size: 3 Copynumber: 23.0 Consensus size: 3
3999094 AATATAAATT
3999104 TAA TAA TAA TAA TAA TATA TATA TATA TATA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TA-A TA-A TA-A TAA TAA TAA TAA TAA TAA
* *
3999153 TAA TAA -AA TCA TAAA TAA AAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA
3999177 ATGGGCAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
2 2 0.03
3 44 0.70
4 17 0.27
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3999137 original size:25 final size:23
Alignment explanation
Indices: 3999093--3999176 Score: 75
Period size: 23 Copynumber: 3.6 Consensus size: 23
3999083 TTTGGGCCTG
*
3999093 TAATATAAATTTAATAATAATAA
1 TAATATAAATATAATAATAATAA
*
3999116 TAATATATATATATATATATAATAA
1 TAATATAAATATA-ATA-ATAATAA
*
3999141 TAATA-ATAATAATAATAA-AATCA
1 TAATATA-AAT-ATAATAATAATAA
*
3999164 TAA-ATAAAAATAA
1 TAATATAAATATAA
3999177 ATGGGCAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
21 4 0.08
22 3 0.06
23 19 0.37
24 5 0.10
25 17 0.33
26 3 0.06
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (23 bp):
TAATATAAATATAATAATAATAA
Found at i:4003630 original size:32 final size:31
Alignment explanation
Indices: 4003588--4003649 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
4003578 TTTAAATATG
4003588 TTTTAATATTTTA-ATTAAGTTTTAGGATATTA
1 TTTTAATATTTTATATT-AGTTTTAGG-TATTA
* *
4003620 TTTTTATATTTTATATTTGTTTTAGGTATT
1 TTTTAATATTTTATATTAGTTTTAGGTATT
4003650 TTAGTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 4 0.15
32 20 0.74
33 3 0.11
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (31 bp):
TTTTAATATTTTATATTAGTTTTAGGTATTA
Found at i:4004324 original size:19 final size:18
Alignment explanation
Indices: 4004273--4004321 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
4004263 AATCTCTTTA
4004273 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
* *
4004292 TTTCTTTTATTTAATTCTT
1 ATT-TTTTATTTAATTATT
4004311 ATTTTTTATTT
1 ATTTTTTATTT
4004322 TAAAAACAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:4016161 original size:2 final size:2
Alignment explanation
Indices: 4016154--4016207 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
4016144 AATAAAATTG
4016154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4016196 AT AT AT AT AT AT
1 AT AT AT AT AT AT
4016208 TACTAATTCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4019812 original size:43 final size:43
Alignment explanation
Indices: 4019764--4020072 Score: 313
Period size: 43 Copynumber: 7.1 Consensus size: 43
4019754 GTAATTAGCT
* * *
4019764 GCGTTTATATCCAAAAACGCCACTATAGATCTGACCTTTTGCA
1 GCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCG
* * * *
4019807 GCGTTTGTGTCAAAAAACGCCGCTATATATCTAACCTTTTGCG
1 GCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCG
* ** *
4019850 GCGTATTTTCCCCAAAAAC-CCAGC-ATAGATCTTGACCTTTTGTG
1 GCGT-TTGTATCCAAAAACGCC-GCTATAGATC-TGACCTTTTGCG
* *
4019894 GCGTTTGTATCCAACAACGCCGCTATATATCT-ACCCTTTTGCG
1 GCGTTTGTATCCAAAAACGCCGCTATAGATCTGA-CCTTTTGCG
* * * * * *
4019937 GTGTTTTTA-GCAAAAACGCCGCTAGAGAACTTGACATTTTGCG
1 GCGTTTGTATCCAAAAACGCCGCTATAGATC-TGACCTTTTGCG
*
4019980 GCGTTTGTATCCAAAAACGCCGCTATAGATCTCAACCTTTTGCG
1 GCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTTGCG
* * *
4020024 GCGTTTGT-TCCAAAAACGACACTATAGATCTTGACTTTTTGCG
1 GCGTTTGTATCCAAAAACGCCGCTATAGATC-TGACCTTTTGCG
4020067 GCGTTT
1 GCGTTT
4020073 TTATATCACA
Statistics
Matches: 216, Mismatches: 39, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
42 17 0.08
43 128 0.59
44 71 0.33
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (43 bp):
GCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCG
Found at i:4019920 original size:87 final size:85
Alignment explanation
Indices: 4019764--4020072 Score: 381
Period size: 87 Copynumber: 3.6 Consensus size: 85
4019754 GTAATTAGCT
* * *
4019764 GCGTTTATATCCAAAAACGCCACTATAGATC-TGACCTTTTGCAGCGTTTGTGTCAAAAAACGCC
1 GCGTTT-T-TCCAAAAACGCCACTATAGATCTTGACCTTTTGCGGCGTTTGTATCCAAAAACGCC
4019828 GCTATATATCTAACCTTTTGCG
64 GCTATATATCTAACCTTTTGCG
* *
4019850 GCGTATTTTCCCCAAAAAC-CCAGC-ATAGATCTTGACCTTTTGTGGCGTTTGTATCCAACAACG
1 GCGT-TTTT--CCAAAAACGCCA-CTATAGATCTTGACCTTTTGCGGCGTTTGTATCCAAAAACG
*
4019913 CCGCTATATATCTACCCTTTTGCG
62 CCGCTATATATCTAACCTTTTGCG
* * * * * *
4019937 GTGTTTTTAGCAAAAACGCCGCTAGAGAACTTGACATTTTGCGGCGTTTGTATCCAAAAACGCCG
1 GCGTTTTT-CCAAAAACGCCACTATAGATCTTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCG
*
4020002 CTATAGATCTCAACCTTTTGCG
65 CTATATATCT-AACCTTTTGCG
* *
4020024 GCGTTTGTTCCAAAAACGACACTATAGATCTTGACTTTTTGCGGCGTTT
1 GCGTTT-TTCCAAAAACGCCACTATAGATCTTGACCTTTTGCGGCGTTT
4020073 TTATATCACA
Statistics
Matches: 190, Mismatches: 24, Indels: 17
0.82 0.10 0.07
Matches are distributed among these distances:
85 9 0.05
86 67 0.35
87 112 0.59
88 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (85 bp):
GCGTTTTTCCAAAAACGCCACTATAGATCTTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGC
TATATATCTAACCTTTTGCG
Done.