Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, 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: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 9 of 22
Found at i:3548659 original size:13 final size:13
Alignment explanation
Indices: 3548637--3548675 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
3548627 CAACGTGACA
3548637 AGGG-TAGGTTTT
1 AGGGTTAGGTTTT
*
3548649 GGGGTTAGGTTTT
1 AGGGTTAGGTTTT
3548662 AGGGTTAGGTTTT
1 AGGGTTAGGTTTT
3548675 A
1 A
3548676 ATGCCATTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 3 0.12
13 21 0.88
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (13 bp):
AGGGTTAGGTTTT
Found at i:3567601 original size:117 final size:117
Alignment explanation
Indices: 3567395--3567626 Score: 437
Period size: 117 Copynumber: 2.0 Consensus size: 117
3567385 TTATTTGATA
3567395 AATTATGCATATGGACATTCATGGAATTGATTAATTAACATACTGAATGATTGTCCTGATTTTGT
1 AATTATGCATATGGACATTCATGGAATTGATTAATTAACATACTGAATGATTGTCCTGATTTTGT
3567460 ATTATGTCTGTGGGAGGATCCTCCAGATTTATGCTTCAAGCTGGTAATTAGC
66 ATTATGTCTGTGGGAGGATCCTCCAGATTTATGCTTCAAGCTGGTAATTAGC
* *
3567512 AATTATGCATGTGGACATTCATGGAATTGATTAATTAAGATACTGAATGATTGTCCTGATTTTGT
1 AATTATGCATATGGACATTCATGGAATTGATTAATTAACATACTGAATGATTGTCCTGATTTTGT
*
3567577 ATTATGTCTGTGGGAGGATCCTCCAGATTTATGCTTGAAGCTGGTAATTA
66 ATTATGTCTGTGGGAGGATCCTCCAGATTTATGCTTCAAGCTGGTAATTA
3567627 TCCTGTCAGA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 112 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (117 bp):
AATTATGCATATGGACATTCATGGAATTGATTAATTAACATACTGAATGATTGTCCTGATTTTGT
ATTATGTCTGTGGGAGGATCCTCCAGATTTATGCTTCAAGCTGGTAATTAGC
Found at i:3570851 original size:2 final size:2
Alignment explanation
Indices: 3570844--3570869 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3570834 TGTTTTGTCC
3570844 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
3570870 GGAGGGGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3572028 original size:7 final size:7
Alignment explanation
Indices: 3572004--3572044 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
3571994 TAAGGTTCCA
3572004 TTTG-TT
1 TTTGCTT
3572010 TTATGC-T
1 TT-TGCTT
3572017 TTTGCTT
1 TTTGCTT
3572024 TTTGCTT
1 TTTGCTT
3572031 TTTGCTT
1 TTTGCTT
3572038 TTTGCTT
1 TTTGCTT
3572045 CTTTTGCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.02, C:0.12, G:0.15, T:0.71
Consensus pattern (7 bp):
TTTGCTT
Found at i:3585066 original size:26 final size:26
Alignment explanation
Indices: 3585037--3585091 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
3585027 TTCTACTCTT
*
3585037 TAAATAAAAAA-TTATATATTAATTAA
1 TAAATAAAAAATTTAAATA-TAATTAA
* *
3585063 TAAATTAAATATTTAAATATAATTAA
1 TAAATAAAAAATTTAAATATAATTAA
3585089 TAA
1 TAA
3585092 TTGTTGATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TAAATAAAAAATTTAAATATAATTAA
Found at i:3585084 original size:19 final size:20
Alignment explanation
Indices: 3585035--3585081 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
3585025 AATTCTACTC
* *
3585035 TTTAAATAAAAAATTATATA
1 TTTAAATAATAAATTAAATA
*
3585055 -TTAATTAATAAATTAAATA
1 TTTAAATAATAAATTAAATA
3585074 TTTAAATA
1 TTTAAATA
3585082 TAATTAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTAAATAATAAATTAAATA
Found at i:3587121 original size:2 final size:2
Alignment explanation
Indices: 3587114--3587151 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3587104 AAGAACTATC
3587114 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
3587152 TCTAGGTGCT
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:3587419 original size:2 final size:2
Alignment explanation
Indices: 3587412--3587441 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3587402 ATTTGTTGTA
3587412 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
3587442 TCATAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3589194 original size:2 final size:2
Alignment explanation
Indices: 3589189--3589227 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
3589179 TGTGTGTGTG
*
3589189 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3589228 AATTAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3595630 original size:22 final size:22
Alignment explanation
Indices: 3595624--3595667 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3595614 AGGAAGAAAA
3595624 GAGAAAGGAAGAAAGAAATAAAG
1 GAGAAA-GAAGAAAGAAATAAAG
*
3595647 GAGAAAGAAGAAA-AAAAAAAG
1 GAGAAAGAAGAAAGAAATAAAG
3595668 ACAAGGTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.02
Consensus pattern (22 bp):
GAGAAAGAAGAAAGAAATAAAG
Found at i:3596486 original size:2 final size:2
Alignment explanation
Indices: 3596479--3596505 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3596469 TATCTTGATC
3596479 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3596506 CAAGTTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3600472 original size:14 final size:14
Alignment explanation
Indices: 3600455--3600560 Score: 59
Period size: 14 Copynumber: 7.3 Consensus size: 14
3600445 CCCCACCCAC
3600455 TTTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
*** *
3600469 TTTTTAATTCAAAG
1 TTTTCCCTCCAAAG
* *
3600483 TATTCCCCCCAAAAG
1 TTTTCCCTCC-AAAG
*
3600498 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
** *
3600512 TTTTCAATTCAAAG
1 TTTTCCCTCCAAAG
* *
3600526 TATTCCCCCCCCAAAAG
1 T-TT-TCCCTCC-AAAG
*
3600543 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
3600557 TTTT
1 TTTT
3600561 GGAAGGTTCT
Statistics
Matches: 62, Mismatches: 26, Indels: 8
0.65 0.27 0.08
Matches are distributed among these distances:
14 36 0.58
15 18 0.29
16 4 0.06
17 4 0.06
ACGTcount: A:0.29, C:0.30, G:0.07, T:0.34
Consensus pattern (14 bp):
TTTTCCCTCCAAAG
Found at i:3600504 original size:43 final size:44
Alignment explanation
Indices: 3600456--3600560 Score: 185
Period size: 43 Copynumber: 2.4 Consensus size: 44
3600446 CCCACCCACT
*
3600456 TTTCCCTCCAAAGTTTTTAATTCAAAGTATT-CCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCCAAAAGA
3600499 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTTCAATTCAAAGTATT-CCCCCCCAAAAGA
3600544 TTTCCCTCCAAAGTTTT
1 TTTCCCTCCAAAGTTTT
3600561 GGAAGGTTCT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
43 30 0.51
45 29 0.49
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (44 bp):
TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCCAAAAGA
Found at i:3615686 original size:167 final size:166
Alignment explanation
Indices: 3615407--3615745 Score: 563
Period size: 167 Copynumber: 2.0 Consensus size: 166
3615397 TAGGTATATT
* *
3615407 AACTAGTCCTGCTTACTTGTTTGCCGTGTACTATGGTTTATGGATACTATTGATGATTGTTTCTC
1 AACTAGTCCTGCTTACTTGTTTACCATGTACTATGGTTTATGGATACTATTGATGATTGTTTCTC
* *
3615472 TAGGCCTCTTGGATATTACTGTTTCCTCCCTTTTTCTCCCTTTTCTCTCTTGAGTCT-CCTCTAG
66 TAGGCCTCTTGGATATGACTGTTTCCTCCCTTTTTCTCCCCTTTCTCTC-TGAGT-TGCCTCTAG
3615536 TAGCCTCTTTTCTCTCTACCCCTTCATCACAAGTTACA
129 TAGCCTCTTTTCTCTCTACCCCTTCATCACAAGTTACA
*
3615574 AACTAGTCCTGTTTACTTGTTTACCATGTACTATGGTTTATGGATACTATTGATGATTGTTTCTC
1 AACTAGTCCTGCTTACTTGTTTACCATGTACTATGGTTTATGGATACTATTGATGATTGTTTCTC
* * *
3615639 TAGGCCTCTTGGATATGACTGTTTCCTCTCTTTTTCTCCCCTTTCTCTCTGGGTTGCCTCTGGTA
66 TAGGCCTCTTGGATATGACTGTTTCCTCCCTTTTTCTCCCCTTTCTCTCTGAGTTGCCTCTAGTA
* *
3615704 GCGTCTTTTCTCTCTACCCCTTCATCACATGTTACA
131 GCCTCTTTTCTCTCTACCCCTTCATCACAAGTTACA
3615740 AACTAG
1 AACTAG
3615746 GTGTGTAACG
Statistics
Matches: 161, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
165 1 0.01
166 52 0.32
167 108 0.67
ACGTcount: A:0.16, C:0.26, G:0.15, T:0.43
Consensus pattern (166 bp):
AACTAGTCCTGCTTACTTGTTTACCATGTACTATGGTTTATGGATACTATTGATGATTGTTTCTC
TAGGCCTCTTGGATATGACTGTTTCCTCCCTTTTTCTCCCCTTTCTCTCTGAGTTGCCTCTAGTA
GCCTCTTTTCTCTCTACCCCTTCATCACAAGTTACA
Found at i:3618216 original size:53 final size:53
Alignment explanation
Indices: 3618153--3618258 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
3618143 CCTCTGATCA
3618153 TCTAGTTATAATTGAACCACATAAACTAAGTTAAAGTAAATAGTGGTGTAGTC
1 TCTAGTTATAATTGAACCACATAAACTAAGTTAAAGTAAATAGTGGTGTAGTC
*
3618206 TCTAGTTATAATTGCACCACATAAACTAAGTTAAAGTAAATAGTGGTGTAGTC
1 TCTAGTTATAATTGAACCACATAAACTAAGTTAAAGTAAATAGTGGTGTAGTC
3618259 AAACTTTCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (53 bp):
TCTAGTTATAATTGAACCACATAAACTAAGTTAAAGTAAATAGTGGTGTAGTC
Found at i:3621533 original size:25 final size:27
Alignment explanation
Indices: 3621496--3621557 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
3621486 AATATTATTT
*
3621496 AATTAATAAATTAATT-A-AAAAAATA
1 AATTTATAAATTAATTAATAAAAAATA
* *
3621521 AATTTATATATTAATTAATAAAAAATT
1 AATTTATAAATTAATTAATAAAAAATA
3621548 AATTTATAAA
1 AATTTATAAA
3621558 AAATATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 14 0.45
26 1 0.03
27 16 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AATTTATAAATTAATTAATAAAAAATA
Found at i:3621565 original size:13 final size:15
Alignment explanation
Indices: 3621503--3621561 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 15
3621493 TTTAATTAAT
3621503 AAATTAA-TTA-AAA
1 AAATTAATTTATAAA
*
3621516 AAATAAATTTAT---
1 AAATTAATTTATAAA
* *
3621528 ATATTAATTAATAAA
1 AAATTAATTTATAAA
3621543 AAATTAATTTATAAA
1 AAATTAATTTATAAA
3621558 AAAT
1 AAAT
3621562 ATTTTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
12 9 0.26
13 6 0.17
14 3 0.09
15 17 0.49
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTAATTTATAAA
Found at i:3622068 original size:17 final size:17
Alignment explanation
Indices: 3622046--3622095 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
3622036 CTCAAGATCG
3622046 ATTAAAAATATT-ATTT
1 ATTAAAAATATTAATTT
*
3622062 AATTAAAATTATTAATTT
1 -ATTAAAAATATTAATTT
3622080 ATT--AAATATTAATTT
1 ATTAAAAATATTAATTT
3622095 A
1 A
3622096 GAGATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 12 0.40
17 14 0.47
18 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTAAAAATATTAATTT
Found at i:3622091 original size:15 final size:16
Alignment explanation
Indices: 3622050--3622095 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
3622040 AGATCGATTA
3622050 AAAATATT-ATTTAATT
1 AAAATATTAATTT-ATT
3622066 AAAATTATTAATTTATT
1 AAAA-TATTAATTTATT
3622083 -AAATATTAATTTA
1 AAAATATTAATTTA
3622096 GAGATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 10 0.36
16 7 0.25
17 7 0.25
18 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAAATATTAATTTATT
Found at i:3622719 original size:12 final size:12
Alignment explanation
Indices: 3622702--3622727 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3622692 AGACAGAGAA
3622702 TCAATCCAAGTT
1 TCAATCCAAGTT
3622714 TCAATCCAAGTT
1 TCAATCCAAGTT
3622726 TC
1 TC
3622728 CTTTCCAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
TCAATCCAAGTT
Found at i:3637020 original size:33 final size:33
Alignment explanation
Indices: 3636978--3637043 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
3636968 CTTGATGCGT
3636978 GCTGTAACGTACTTTCTTTTAAGAGTTGTTGTC
1 GCTGTAACGTACTTTCTTTTAAGAGTTGTTGTC
3637011 GCTGTAACGTACTTTCTTTTAAGAGTTGTTGTC
1 GCTGTAACGTACTTTCTTTTAAGAGTTGTTGTC
3637044 TACTTTGGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.45
Consensus pattern (33 bp):
GCTGTAACGTACTTTCTTTTAAGAGTTGTTGTC
Found at i:3639855 original size:27 final size:27
Alignment explanation
Indices: 3639825--3639911 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 27
3639815 TAATATACTT
3639825 ATATTTTTTATTATTAATTTTTATATA
1 ATATTTTTTATTATTAATTTTTATATA
* *
3639852 ATATTATTTT-TTAAATATATTTTTAATATC
1 ATATT-TTTTATT-ATTA-ATTTTT-ATATA
* *
3639882 ATATATTTTATT-TTTATTTATTATTATA
1 ATATTTTTTATTATTAATTT-TTA-TATA
3639910 AT
1 AT
3639912 CTTATATATT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
27 12 0.26
28 15 0.32
29 10 0.21
30 10 0.21
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (27 bp):
ATATTTTTTATTATTAATTTTTATATA
Found at i:3639874 original size:13 final size:16
Alignment explanation
Indices: 3639836--3639931 Score: 56
Period size: 18 Copynumber: 5.8 Consensus size: 16
3639826 TATTTTTTAT
3639836 TATTAATTTTTATATAA
1 TATT-ATTTTTATATAA
3639853 TATTATTTTT-TA-AA
1 TATTATTTTTATATAA
3639867 TA-TATTTTTAATATCATA
1 TATTATTTTT-ATAT-A-A
* *
3639885 TATTTTATTTTTATTTAT
1 TA--TTATTTTTATATAA
*
3639903 TATTATAATCTTATAT-A
1 TATTAT--TTTTATATAA
*
3639920 TTTTATTTTTAT
1 TATTATTTTTAT
3639932 TTCTTAATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 22
0.68 0.08 0.24
Matches are distributed among these distances:
13 7 0.11
14 4 0.06
15 9 0.15
16 10 0.16
17 10 0.16
18 11 0.18
19 1 0.02
20 3 0.05
21 7 0.11
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTATTTTTATATAA
Found at i:3639877 original size:60 final size:61
Alignment explanation
Indices: 3639795--3639909 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 61
3639785 AAATTATCTA
* *
3639795 TATTTATTAAAATATAAATTTAATATACTTATATTTT-TTATTATTAATTTTTATATAATAT
1 TATTTATTAAAATATAAATTTAATAT-CATATATTTTATTATTATTAATTATTATATAATAT
* ** * *
3639856 TATTT-TTTAAATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATA
1 TATTTATTAAAATATAAATTTAATATCATATATTTTATTATTATTAATTATTATA
3639910 ATCTTATATA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
59 9 0.20
60 32 0.70
61 5 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (61 bp):
TATTTATTAAAATATAAATTTAATATCATATATTTTATTATTATTAATTATTATATAATAT
Found at i:3639919 original size:33 final size:33
Alignment explanation
Indices: 3639882--3639954 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
3639872 TTTTAATATC
*
3639882 ATATATTTTATTTTTATTTATTATTATAATCTT
1 ATATATTTTATTTTTATTTATTAATATAATCTT
* *
3639915 ATATATTTTATTTTTATTTCTTAATATAATTTT
1 ATATATTTTATTTTTATTTATTAATATAATCTT
*
3639948 TTATATT
1 ATATATT
3639955 ATCTATCTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTATTAATATAATCTT
Found at i:3640352 original size:15 final size:15
Alignment explanation
Indices: 3640332--3640361 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3640322 CATAATTGAC
3640332 TGCTTGACCTTATAT
1 TGCTTGACCTTATAT
*
3640347 TGCTTGACTTTATAT
1 TGCTTGACCTTATAT
3640362 CAGAGCTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (15 bp):
TGCTTGACCTTATAT
Found at i:3651407 original size:19 final size:21
Alignment explanation
Indices: 3651374--3651417 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
3651364 CTAGAACAAA
3651374 AAAAAGATATTAATA-AAAT-
1 AAAAAGATATTAATAGAAATG
3651393 AAAAAG-TATTAAATAGAAATG
1 AAAAAGATATT-AATAGAAATG
3651414 AAAA
1 AAAA
3651418 TAAAATGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 10 0.45
20 4 0.18
21 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (21 bp):
AAAAAGATATTAATAGAAATG
Found at i:3652000 original size:27 final size:27
Alignment explanation
Indices: 3651947--3652002 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
3651937 CTATTTTCGA
* *
3651947 CTCTATTACACATCAATCTGTTCAGTT
1 CTCTATTACACATCAAGCGGTTCAGTT
*
3651974 CTCTATTACACATCAAGCGGTTGAGTT
1 CTCTATTACACATCAAGCGGTTCAGTT
3652001 CT
1 CT
3652003 TGGACTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (27 bp):
CTCTATTACACATCAAGCGGTTCAGTT
Found at i:3665058 original size:28 final size:28
Alignment explanation
Indices: 3664994--3665076 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
3664984 TTCGTATAAT
* *
3664994 AAAAGCACAGTGGTTTAACAGAATT-TC
1 AAAAGCACAGTAGTTTAGCAGAATTATC
*
3665021 AAAAGCACAGTAGCTTAGCAGAATTATC
1 AAAAGCACAGTAGTTTAGCAGAATTATC
*
3665049 AAAAGCACAGTAGTTTAGTAGAATTATC
1 AAAAGCACAGTAGTTTAGCAGAATTATC
3665077 TCCAGACTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 22 0.44
28 28 0.56
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (28 bp):
AAAAGCACAGTAGTTTAGCAGAATTATC
Found at i:3680355 original size:18 final size:20
Alignment explanation
Indices: 3680329--3680374 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
3680319 GGCAACAAAA
*
3680329 ATATGTATGGATG-AT-AAT
1 ATATATATGGATGTATGAAT
* *
3680347 ATATATATGTATGTATGTAT
1 ATATATATGGATGTATGAAT
3680367 ATATATAT
1 ATATATAT
3680375 ATATATGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 11 0.48
19 2 0.09
20 10 0.43
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (20 bp):
ATATATATGGATGTATGAAT
Found at i:3680355 original size:22 final size:24
Alignment explanation
Indices: 3680329--3680378 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 24
3680319 GGCAACAAAA
3680329 ATATGTATGGATG-ATA-ATATAT
1 ATATGTATGGATGTATATATATAT
*
3680351 ATATGTATGTATGTATATATATAT
1 ATATGTATGGATGTATATATATAT
3680375 ATAT
1 ATAT
3680379 ATGTATAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 12 0.48
23 3 0.12
24 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (24 bp):
ATATGTATGGATGTATATATATAT
Found at i:3680359 original size:26 final size:26
Alignment explanation
Indices: 3680330--3680384 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
3680320 GCAACAAAAA
3680330 TATGTATGGATGATA-ATATATATATG
1 TATGTATGGAT-ATATATATATATATG
*
3680356 TATGTATGTATATATATATATATATG
1 TATGTATGGATATATATATATATATG
3680382 TAT
1 TAT
3680385 AAGCATTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (26 bp):
TATGTATGGATATATATATATATATG
Found at i:3680381 original size:18 final size:18
Alignment explanation
Indices: 3680346--3680385 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3680336 TGGATGATAA
* *
3680346 TATATATATGTATGTATG
1 TATATATATATATATATG
3680364 TATATATATATATATATG
1 TATATATATATATATATG
3680382 TATA
1 TATA
3680386 AGCATTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (18 bp):
TATATATATATATATATG
Found at i:3681878 original size:17 final size:17
Alignment explanation
Indices: 3681856--3681890 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3681846 TTCAGTTGTT
3681856 TTATTTCTGTTACCAGG
1 TTATTTCTGTTACCAGG
3681873 TTATTTCTGTTACCAGG
1 TTATTTCTGTTACCAGG
3681890 T
1 T
3681891 ACTGGTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (17 bp):
TTATTTCTGTTACCAGG
Found at i:3684708 original size:23 final size:23
Alignment explanation
Indices: 3684681--3684730 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
3684671 TAAGGTTAAA
*
3684681 AACTTAGTCATTAAAATTATTTC
1 AACTTAGTCATTAAAACTATTTC
*
3684704 AACTTAGTCATTAAGACTATTTC
1 AACTTAGTCATTAAAACTATTTC
3684727 AACT
1 AACT
3684731 ATTTCCGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (23 bp):
AACTTAGTCATTAAAACTATTTC
Found at i:3684917 original size:29 final size:29
Alignment explanation
Indices: 3684884--3684941 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
3684874 CAACAGACTA
3684884 AGAAAATATTTTAGACGTTTAAAATTAAG
1 AGAAAATATTTTAGACGTTTAAAATTAAG
* * *
3684913 AGAAAATATTTTGGATGTTTAAGATTAAG
1 AGAAAATATTTTAGACGTTTAAAATTAAG
3684942 TTAGATGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.36
Consensus pattern (29 bp):
AGAAAATATTTTAGACGTTTAAAATTAAG
Found at i:3684959 original size:35 final size:35
Alignment explanation
Indices: 3684916--3684982 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
3684906 AATTAAGAGA
* *
3684916 AAATATTTTGGATGTTTAAGATTAAGTTAGATGAG
1 AAATATTTTGAACGTTTAAGATTAAGTTAGATGAG
*
3684951 AAATATTTTGAACGTTTAAGATTATGTTAGAT
1 AAATATTTTGAACGTTTAAGATTAAGTTAGAT
3684983 AAGGTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.37, C:0.01, G:0.19, T:0.42
Consensus pattern (35 bp):
AAATATTTTGAACGTTTAAGATTAAGTTAGATGAG
Found at i:3685124 original size:88 final size:89
Alignment explanation
Indices: 3684964--3685134 Score: 209
Period size: 88 Copynumber: 1.9 Consensus size: 89
3684954 TATTTTGAAC
* * * * ** *
3684964 GTTTAAGATTATGTTAGATAAGGTTAAAAACTTAGTCATTAAAATTATTTCAACTATCGTTGGTT
1 GTTTAAGATTAAGTCAGATAAGATTAAAAACTTAGTCATTAAAACTATTTCAACTATCACTGGCT
*
3685029 GAAAAGAAAGA-AAAATTTTAGAT
66 GAAAAGAAAAATAAAATTTTAGAT
** * *
3685052 GTTTAAGATTAAGTCAGATAAGATTAATGACTTAGTCATTAAACCTATTTCAATTATCACTGGCT
1 GTTTAAGATTAAGTCAGATAAGATTAAAAACTTAGTCATTAAAACTATTTCAACTATCACTGGCT
**
3685117 GCGAAGAAAAATAAAATT
66 GAAAAGAAAAATAAAATT
3685135 AAGTTACAAA
Statistics
Matches: 68, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
88 62 0.91
89 6 0.09
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (89 bp):
GTTTAAGATTAAGTCAGATAAGATTAAAAACTTAGTCATTAAAACTATTTCAACTATCACTGGCT
GAAAAGAAAAATAAAATTTTAGAT
Found at i:3700639 original size:16 final size:18
Alignment explanation
Indices: 3700608--3700642 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3700598 ATCTAAAAAT
3700608 TATTAATTTAGTACATTA
1 TATTAATTTAGTACATTA
3700626 TATTAATTT-G-ACATTA
1 TATTAATTTAGTACATTA
3700642 T
1 T
3700643 TCATCCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 1 0.06
18 9 0.53
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (18 bp):
TATTAATTTAGTACATTA
Found at i:3724279 original size:16 final size:16
Alignment explanation
Indices: 3724260--3724292 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3724250 CATATATATA
3724260 TATATATTTATTTATT
1 TATATATTTATTTATT
3724276 TATATATTTATTTATT
1 TATATATTTATTTATT
3724292 T
1 T
3724293 TCCAAGCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATATATTTATTTATT
Found at i:3724283 original size:8 final size:8
Alignment explanation
Indices: 3724252--3724292 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
3724242 AGGCTATACA
*
3724252 TATATATA
1 TATATATT
3724260 TATATATT
1 TATATATT
*
3724268 TATTTATT
1 TATATATT
3724276 TATATATT
1 TATATATT
*
3724284 TATTTATT
1 TATATATT
3724292 T
1 T
3724293 TCCAAGCATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATATATT
Found at i:3725919 original size:2 final size:2
Alignment explanation
Indices: 3725912--3725936 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3725902 ACAGAAAAGT
3725912 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3725937 TAAACATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3726828 original size:84 final size:81
Alignment explanation
Indices: 3726664--3726836 Score: 193
Period size: 84 Copynumber: 2.1 Consensus size: 81
3726654 CTGAACTCGA
* * * * *** *
3726664 TAATGGTGTTCAACTTGAACAAACTGATGTTACTCGTGGTGAGGTGTTAGATGATTTGACTGATA
1 TAATGATGTTCAACTCGAACAAACTGATGATACTCGTGGTGAGGTGTTAGATAATGCAACTAATA
*
3726729 AGGAGCATCAGCTTGG
66 AGGAGCACCAGCTTGG
*
3726745 TAATGATGTTCAACTCGAACAAACTGATAATGATATTCGTGGTGAGGTGTTAGATAATGCAACTA
1 TAATGATGTTCAACTCGAACAAACTG---ATGATACTCGTGGTGAGGTGTTAGATAATGCAACTA
*** *
3726810 ATTTTGAGCACCATCTTGG
63 ATAAGGAGCACCAGCTTGG
3726829 TAATGATG
1 TAATGATG
3726837 GAACAAAGGC
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 24 0.32
84 51 0.68
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (81 bp):
TAATGATGTTCAACTCGAACAAACTGATGATACTCGTGGTGAGGTGTTAGATAATGCAACTAATA
AGGAGCACCAGCTTGG
Found at i:3730149 original size:34 final size:35
Alignment explanation
Indices: 3730111--3730179 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
3730101 AATCACAATC
*
3730111 ATCAAAATTTCCCTTCAAGGGTGAAAAC-AATGGA
1 ATCAAAATTTCCCTTCAAGGGCGAAAACAAATGGA
3730145 ATCAAAATTTCCCTTCAAGGGCGAAAACAAATGGA
1 ATCAAAATTTCCCTTCAAGGGCGAAAACAAATGGA
3730180 GAACGGGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 27 0.82
35 6 0.18
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (35 bp):
ATCAAAATTTCCCTTCAAGGGCGAAAACAAATGGA
Found at i:3734532 original size:23 final size:21
Alignment explanation
Indices: 3734486--3734535 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
3734476 ATATAAAAGC
**
3734486 AAAAT-TCAAAATATATATTG
1 AAAATGTCAAAATATATATAA
3734506 AAAATGTCAAAATAATTATATAA
1 AAAATGTCAAAAT-A-TATATAA
3734529 AAAATGT
1 AAAATGT
3734536 ACTTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 7 0.28
22 1 0.04
23 12 0.48
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (21 bp):
AAAATGTCAAAATATATATAA
Found at i:3741586 original size:15 final size:15
Alignment explanation
Indices: 3741566--3741595 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3741556 ACAGTAAAAC
3741566 CTCTATAAATTAATA
1 CTCTATAAATTAATA
3741581 CTCTATAAATTAATA
1 CTCTATAAATTAATA
3741596 ACCTCGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
CTCTATAAATTAATA
Found at i:3751518 original size:18 final size:18
Alignment explanation
Indices: 3751481--3751520 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3751471 TGTGTGAATA
* * *
3751481 TATATATATATTTGTTTG
1 TATATATATATATATATG
3751499 TATATATATATATATATG
1 TATATATATATATATATG
3751517 TATA
1 TATA
3751521 CACATATACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TATATATATATATATATG
Found at i:3760441 original size:17 final size:19
Alignment explanation
Indices: 3760416--3760453 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
3760406 CTCTACGGAG
3760416 AAGAAAAG-AAATGAA-AC
1 AAGAAAAGAAAATGAATAC
*
3760433 AAGACAAGAAAATGAATAC
1 AAGAAAAGAAAATGAATAC
3760452 AA
1 AA
3760454 CTAATGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 7 0.39
19 4 0.22
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (19 bp):
AAGAAAAGAAAATGAATAC
Found at i:3767901 original size:6 final size:6
Alignment explanation
Indices: 3767890--3767931 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
3767880 AGTAGGAGGT
* *
3767890 CGTGAC CGTGAC CGTGAC CTTGAC CGTGAC CTTGAC CGTGAC
1 CGTGAC CGTGAC CGTGAC CGTGAC CGTGAC CGTGAC CGTGAC
3767932 ATAGACCTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (6 bp):
CGTGAC
Found at i:3767938 original size:12 final size:12
Alignment explanation
Indices: 3767890--3767931 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
3767880 AGTAGGAGGT
*
3767890 CGTGACCGTGAC
1 CGTGACCTTGAC
3767902 CGTGACCTTGAC
1 CGTGACCTTGAC
3767914 CGTGACCTTGAC
1 CGTGACCTTGAC
3767926 CGTGAC
1 CGTGAC
3767932 ATAGACCTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (12 bp):
CGTGACCTTGAC
Found at i:3790255 original size:19 final size:20
Alignment explanation
Indices: 3790231--3790268 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3790221 ACAATTATAC
*
3790231 AAAAAG-TATTTAGAGGGAA
1 AAAAAGATATTTAAAGGGAA
3790250 AAAAAGATATTTAAAGGGA
1 AAAAAGATATTTAAAGGGA
3790269 GTAAAGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (20 bp):
AAAAAGATATTTAAAGGGAA
Found at i:3792136 original size:28 final size:28
Alignment explanation
Indices: 3792086--3792180 Score: 127
Period size: 29 Copynumber: 3.3 Consensus size: 28
3792076 ACATTACAAC
* *
3792086 AAAATATGTTTTTCTTGTTTAAATTAAGA
1 AAAACATGTTTTT-TTATTTAAATTAAGA
* *
3792115 GAAACATGTTTTTTTATCTAAATTAAGA
1 AAAACATGTTTTTTTATTTAAATTAAGA
3792143 TAAAACATGTTTTTTTATTTAAATTAAGA
1 -AAAACATGTTTTTTTATTTAAATTAAGA
*
3792172 CAAACATGT
1 AAAACATGT
3792181 AAAAGTTACA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
28 21 0.36
29 37 0.64
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.44
Consensus pattern (28 bp):
AAAACATGTTTTTTTATTTAAATTAAGA
Found at i:3798136 original size:94 final size:91
Alignment explanation
Indices: 3798031--3798210 Score: 254
Period size: 94 Copynumber: 1.9 Consensus size: 91
3798021 AAAGTGATGG
* * *
3798031 AAAATTTTCATTTACATTAATAAAATATTTCATGAAATATTCTAATTCCATAATATTTTGGT-TC
1 AAAATTTTCATTTACATTAATAAAATATTTCATGAAATATTCCAATTCCAT--TACTTT-ATATC
*
3798095 AAAATCATCAAAATTGAAAGTATAATTGC
63 AAAATCAACAAAATTGAAAGTATAATTGC
* *
3798124 AAAATTTGTCATTTATATTACTAAAATATTTCATGAAATATTCCAATTCCATTACTTTATATCAA
1 AAAATTT-TCATTTACATTAATAAAATATTTCATGAAATATTCCAATTCCATTACTTTATATCAA
*
3798189 TATCAACAAAATTGAAAGTATA
65 AATCAACAAAATTGAAAGTATA
3798211 GTGATAAAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
91 1 0.01
92 29 0.37
93 7 0.09
94 41 0.53
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (91 bp):
AAAATTTTCATTTACATTAATAAAATATTTCATGAAATATTCCAATTCCATTACTTTATATCAAA
ATCAACAAAATTGAAAGTATAATTGC
Found at i:3807206 original size:12 final size:12
Alignment explanation
Indices: 3807189--3807222 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
3807179 TTAAGATGTA
3807189 AAATTTTTAATT
1 AAATTTTTAATT
3807201 AAATTTTTATAATT
1 AAA-TTTT-TAATT
3807215 AAATTTTT
1 AAATTTTT
3807223 TTAATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.20
13 8 0.40
14 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
AAATTTTTAATT
Found at i:3807215 original size:14 final size:13
Alignment explanation
Indices: 3807187--3807223 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
3807177 TTTTAAGATG
*
3807187 TAAAATTTTTAAT
1 TAAATTTTTTAAT
3807200 TAAATTTTTATAAT
1 TAAATTTTT-TAAT
3807214 TAAATTTTTT
1 TAAATTTTTT
3807224 TAATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATTTTTTAAT
Found at i:3807227 original size:14 final size:14
Alignment explanation
Indices: 3807192--3807227 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3807182 AGATGTAAAA
3807192 TTTTTAATTAAATT
1 TTTTTAATTAAATT
*
3807206 TTTATAATTAAATT
1 TTTTTAATTAAATT
3807220 TTTTTAAT
1 TTTTTAAT
3807228 ATTTTTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTAATTAAATT
Found at i:3807411 original size:22 final size:22
Alignment explanation
Indices: 3807386--3807444 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 22
3807376 CAATATATAC
*
3807386 ATTTGGAAAATAATTGA-ATCTT
1 ATTTGGAAAATAATTGATAT-GT
*
3807408 ATTT-TAAAAGTAA-T-ATATGT
1 ATTTGGAAAA-TAATTGATATGT
3807428 ATTTGGAAAATAATTGA
1 ATTTGGAAAATAATTGA
3807445 GACGTCTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
20 9 0.31
21 12 0.41
22 8 0.28
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.41
Consensus pattern (22 bp):
ATTTGGAAAATAATTGATATGT
Found at i:3807414 original size:42 final size:42
Alignment explanation
Indices: 3807364--3807444 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
3807354 ATTGTTAATA
3807364 TTATTTTAAAAGCAATATATACATTTGGAAAATAATTGAATC
1 TTATTTTAAAAGCAATATATACATTTGGAAAATAATTGAATC
* **
3807406 TTATTTTAAAAGTAATATATGTATTTGGAAAATAATTGA
1 TTATTTTAAAAGCAATATATACATTTGGAAAATAATTGA
3807445 GACGTCTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.41
Consensus pattern (42 bp):
TTATTTTAAAAGCAATATATACATTTGGAAAATAATTGAATC
Found at i:3807547 original size:91 final size:88
Alignment explanation
Indices: 3807387--3807553 Score: 194
Period size: 91 Copynumber: 1.9 Consensus size: 88
3807377 AATATATACA
* * * *
3807387 TTTGGAAAATAATTGAATCTTATTTTAAAAGTAATATATGTATTTGGAAAATAATTGAGACGTCT
1 TTTGGAAAATAATTGAATCTTATTATAAAAGTAATATATGCATTTGGAAAAGAATTGAGACGTCG
*
3807452 TATATACTTAAGTATACATGCAT
66 TATATAATTAAGTATACATGCAT
* * *
3807475 TTTGGAAAATAATTGAGA-CTTCTTATACAATTAAGTATACATGCATTTGGAAAAGAATTGA-AT
1 TTTGGAAAATAATTGA-ATCTTATTATAAAAGTAA-TAT--ATGCATTTGGAAAAGAATTGAGA-
*
3807538 CTTCGTATATAATTAA
61 CGTCGTATATAATTAA
3807554 AAATGTTGAT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
88 28 0.43
89 4 0.06
90 1 0.02
91 32 0.49
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (88 bp):
TTTGGAAAATAATTGAATCTTATTATAAAAGTAATATATGCATTTGGAAAAGAATTGAGACGTCG
TATATAATTAAGTATACATGCAT
Found at i:3807552 original size:45 final size:45
Alignment explanation
Indices: 3807385--3807553 Score: 188
Period size: 46 Copynumber: 3.8 Consensus size: 45
3807375 GCAATATATA
* *
3807385 CATTTGGAAAATAATTGA-A--TCTTATTTTAA--AAGTAATATATG
1 CATTTGGAAAATAATTGAGACTTCTTA-TATAATTAAGT-ATACATG
* * *
3807427 TATTTGGAAAATAATTGAGACGTCTTATATACTTAAGTATACATG
1 CATTTGGAAAATAATTGAGACTTCTTATATAATTAAGTATACATG
*
3807472 CATTTTGGAAAATAATTGAGACTTCTTATACAATTAAGTATACATG
1 CA-TTTGGAAAATAATTGAGACTTCTTATATAATTAAGTATACATG
* *
3807518 CATTTGGAAAAGAATTGA-ATCTTCGTATATAATTAA
1 CATTTGGAAAATAATTGAGA-CTTCTTATATAATTAA
3807554 AAATGTTGAT
Statistics
Matches: 109, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
42 17 0.16
43 1 0.01
44 4 0.04
45 41 0.38
46 46 0.42
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (45 bp):
CATTTGGAAAATAATTGAGACTTCTTATATAATTAAGTATACATG
Found at i:3815028 original size:13 final size:13
Alignment explanation
Indices: 3815012--3815067 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
3815002 AAGTTTAATA
*
3815012 TATTTATATTTTT
1 TATTAATATTTTT
* *
3815025 TATTATTAATTTT
1 TATTAATATTTTT
3815038 TATATAATATTATTT
1 TAT-TAATATT-TTT
3815053 T-TTAATATATTTT
1 TATTAATAT-TTTT
3815066 TA
1 TA
3815068 ATATCATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 23 0.68
14 7 0.21
15 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTAATATTTTT
Found at i:3815047 original size:27 final size:29
Alignment explanation
Indices: 3815017--3815085 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 29
3815007 TAATATATTT
3815017 ATATTTTTTATTATTA-ATTTTT-ATATA
1 ATATTTTTTATTATTATATTTTTAATATA
* *
3815044 ATATTATTTT-TTAATATATTTTTAATATC
1 ATATT-TTTTATTATTATATTTTTAATATA
*
3815073 ATA-TATTTATTAT
1 ATATTTTTTATTAT
3815086 GATGAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
27 13 0.38
28 14 0.41
29 7 0.21
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (29 bp):
ATATTTTTTATTATTATATTTTTAATATA
Found at i:3815054 original size:17 final size:18
Alignment explanation
Indices: 3815028--3815061 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3815018 TATTTTTTAT
3815028 TATTAATTTTT-ATATAA
1 TATTAATTTTTAATATAA
*
3815045 TATTATTTTTTAATATA
1 TATTAATTTTTAATATA
3815062 TTTTTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTAATTTTTAATATAA
Found at i:3815066 original size:29 final size:29
Alignment explanation
Indices: 3814986--3815080 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 29
3814976 AAAATTATTC
* * * *
3814986 ATATTTATTAAAATATAAGTTTAATATATTT
1 ATATTTTTTAATAT-TAATTTTAATATA-AT
* *
3815017 ATATTTTTTATTATTAATTTTTATATAAT
1 ATATTTTTTAATATTAATTTTAATATAAT
* *
3815046 ATTATTTTTTAATA-TATTTTTAATATCAT
1 A-TATTTTTTAATATTAATTTTAATATAAT
3815075 ATATTT
1 ATATTT
3815081 ATTATGATGA
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
28 5 0.09
29 15 0.28
30 22 0.42
31 11 0.21
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (29 bp):
ATATTTTTTAATATTAATTTTAATATAAT
Found at i:3816609 original size:31 final size:30
Alignment explanation
Indices: 3816555--3816631 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 30
3816545 AAAAAAATTT
*
3816555 AAATAAGTTCTTATACTTTTATTTT-AAGTC
1 AAATAAGTTTTTATACTTTTATTTTGAA-TC
*
3816585 AAATAAGTTTTTATATTTTTTATTTTGAATC
1 AAATAAGTTTTTATA-CTTTTATTTTGAATC
3816616 AAATAAGTCTTTTATA
1 AAATAAGT-TTTTATA
3816632 ATTAATAGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 14 0.33
31 19 0.45
32 9 0.21
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (30 bp):
AAATAAGTTTTTATACTTTTATTTTGAATC
Found at i:3822959 original size:23 final size:23
Alignment explanation
Indices: 3822933--3822976 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3822923 TAAATTCTTA
3822933 TTTTTTA-TTATATTTAATTAAT
1 TTTTTTATTTATATTTAATTAAT
*
3822955 TTTTTTATTTTTATTTAATTAA
1 TTTTTTATTTATATTTAATTAA
3822977 ATTTAGGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTTTATTTATATTTAATTAAT
Found at i:3822962 original size:19 final size:20
Alignment explanation
Indices: 3822934--3822974 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
3822924 AAATTCTTAT
3822934 TTTTTATTATATTTAATTAA
1 TTTTTATTATATTTAATTAA
* *
3822954 TTTTT-TTATTTTTATTTAA
1 TTTTTATTATATTTAATTAA
3822973 TT
1 TT
3822975 AAATTTAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTATTATATTTAATTAA
Found at i:3823401 original size:19 final size:20
Alignment explanation
Indices: 3823377--3823416 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3823367 AGGAATCCTC
3823377 TTATATGTT-TTTAAATAAT
1 TTATATGTTGTTTAAATAAT
* *
3823396 TTATATTTTGTTTATATAAT
1 TTATATGTTGTTTAAATAAT
3823416 T
1 T
3823417 CTTAAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TTATATGTTGTTTAAATAAT
Found at i:3824008 original size:32 final size:30
Alignment explanation
Indices: 3823965--3824032 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 30
3823955 CTCTTTTTGG
*
3823965 CATTTTCTGGGTTTTGATTCTCTTTTTCTTTT
1 CATTTTCTGGGTTTTAATTCT-TTTTT-TTTT
* *
3823997 CATTTTGTGGGTTTTAATTGTTTTTTTTTT
1 CATTTTCTGGGTTTTAATTCTTTTTTTTTT
3824027 C-TTTTC
1 CATTTTC
3824033 ATTTATGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 4 0.12
30 5 0.16
31 5 0.16
32 18 0.56
ACGTcount: A:0.07, C:0.12, G:0.13, T:0.68
Consensus pattern (30 bp):
CATTTTCTGGGTTTTAATTCTTTTTTTTTT
Found at i:3837641 original size:7 final size:7
Alignment explanation
Indices: 3837625--3837656 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
3837615 AAAGCTTAAT
*
3837625 TAAACTC
1 TAAACCC
3837632 TAAACCC
1 TAAACCC
3837639 TAAACCC
1 TAAACCC
3837646 TAAACCC
1 TAAACCC
3837653 TAAA
1 TAAA
3837657 AAAAGAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:3837724 original size:22 final size:22
Alignment explanation
Indices: 3837676--3837725 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3837666 CTAAGTTAAA
*
3837676 ATAAAAAATAAAAAATTTATTT
1 ATAAAAAATAAAAAATTAATTT
*
3837698 ATAAATAATAAAAAATTAATATT
1 ATAAAAAATAAAAAATTAAT-TT
3837721 -TAAAA
1 ATAAAA
3837726 TTTTTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
ATAAAAAATAAAAAATTAATTT
Found at i:3837785 original size:15 final size:15
Alignment explanation
Indices: 3837767--3837814 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
3837757 AATTATAAAG
3837767 TAAAATATTAATTTT
1 TAAAATATTAATTTT
*
3837782 TAAAAATATTAATGTT
1 T-AAAATATTAATTTT
** *
3837798 TAACTTATTAAATTT
1 TAAAATATTAATTTT
3837813 TA
1 TA
3837815 TTACTATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (15 bp):
TAAAATATTAATTTT
Found at i:3837789 original size:16 final size:16
Alignment explanation
Indices: 3837768--3837800 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3837758 ATTATAAAGT
*
3837768 AAAATATTAATTTTTA
1 AAAATATTAATGTTTA
3837784 AAAATATTAATGTTTA
1 AAAATATTAATGTTTA
3837800 A
1 A
3837801 CTTATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AAAATATTAATGTTTA
Found at i:3840812 original size:18 final size:18
Alignment explanation
Indices: 3840762--3840846 Score: 59
Period size: 18 Copynumber: 4.7 Consensus size: 18
3840752 AGGGATCAGT
* *
3840762 GAGGAAGAAGGAGAGCAA
1 GAGGAAGGAGGAGAGGAA
* *
3840780 GAGGAAGGCA-CAGAGGGA
1 GAGGAAGG-AGGAGAGGAA
*
3840798 GAGGAAGGAGGAGAGGAT
1 GAGGAAGGAGGAGAGGAA
* *
3840816 GAGGATTGCA-GAGATGGAA
1 GAGGA-AGGAGGAGA-GGAA
3840835 -AGGAAGGAGGAG
1 GAGGAAGGAGGAG
3840847 TTGAAGCATC
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
17 3 0.06
18 41 0.82
19 6 0.12
ACGTcount: A:0.41, C:0.05, G:0.49, T:0.05
Consensus pattern (18 bp):
GAGGAAGGAGGAGAGGAA
Found at i:3840820 original size:36 final size:36
Alignment explanation
Indices: 3840762--3840846 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 36
3840752 AGGGATCAGT
*
3840762 GAGGAAGAAGGAGAGCAAGAGGAAGGCACAGAGGGA
1 GAGGAAGGAGGAGAGCAAGAGGAAGGCACAGAGGGA
* * ** * *
3840798 GAGGAAGGAGGAGAGGATGAGGATTGCAGAGATGGA
1 GAGGAAGGAGGAGAGCAAGAGGAAGGCACAGAGGGA
*
3840834 AAGGAAGGAGGAG
1 GAGGAAGGAGGAG
3840847 TTGAAGCATC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.41, C:0.05, G:0.49, T:0.05
Consensus pattern (36 bp):
GAGGAAGGAGGAGAGCAAGAGGAAGGCACAGAGGGA
Found at i:3853200 original size:2 final size:2
Alignment explanation
Indices: 3853193--3853218 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3853183 TGATTTCACA
3853193 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
3853219 CCTCGTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3854383 original size:31 final size:29
Alignment explanation
Indices: 3854306--3854379 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
3854296 CATTAAAGTG
* * *
3854306 TAACAAAATGTTTTTAAATATGATGTGTAA
1 TAACAATAT-TTTTTTAATATGGTGTGTAA
*
3854336 TAATAATATTTTTTTAATATGGTGTGTAA
1 TAACAATATTTTTTTAATATGGTGTGTAA
3854365 TAACAATATTTTTTT
1 TAACAATATTTTTTT
3854380 TTAACATGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 32 0.82
30 7 0.18
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.49
Consensus pattern (29 bp):
TAACAATATTTTTTTAATATGGTGTGTAA
Found at i:3854395 original size:31 final size:29
Alignment explanation
Indices: 3854306--3854388 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
3854296 CATTAAAGTG
* * * *
3854306 TAACAAAATGTTTTTAAATATGATGTGTAA
1 TAACAATAT-TTTTTTAACATGGTGTGTAA
* *
3854336 TAATAATATTTTTTTAATATGGTGTGTAA
1 TAACAATATTTTTTTAACATGGTGTGTAA
3854365 TAACAATATTTTTTTTTAACATGG
1 TAACAATA--TTTTTTTAACATGG
3854389 GATGTAACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 25 0.56
30 7 0.16
31 13 0.29
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (29 bp):
TAACAATATTTTTTTAACATGGTGTGTAA
Found at i:3854431 original size:27 final size:26
Alignment explanation
Indices: 3854374--3854424 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
3854364 ATAACAATAT
*
3854374 TTTTTTTTAACATGGGATGTAACAAC
1 TTTTTTTTAACATGCGATGTAACAAC
3854400 TTTTTTTTAACTATGACG-TGTAACA
1 TTTTTTTTAAC-ATG-CGATGTAACA
3854425 TGTTTTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 11 0.50
27 10 0.45
28 1 0.05
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (26 bp):
TTTTTTTTAACATGCGATGTAACAAC
Found at i:3865684 original size:15 final size:15
Alignment explanation
Indices: 3865648--3865697 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
3865638 TCCTATAATC
* *
3865648 ACATTACTTACAATT
1 ACATTATTTGCAATT
3865663 ACATTATTTGCAATT
1 ACATTATTTGCAATT
* *
3865678 ACATTATTTGAAATC
1 ACATTATTTGCAATT
3865693 ACATT
1 ACATT
3865698 GCATTATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (15 bp):
ACATTATTTGCAATT
Found at i:3868309 original size:17 final size:16
Alignment explanation
Indices: 3868290--3868327 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3868280 ATTTGAGCTT
3868290 TTTTTTTTCTTCTTCT-
1 TTTTTTTTCTT-TTCTC
*
3868306 TTTTGTTTCTTTTCTC
1 TTTTTTTTCTTTTCTC
3868322 TTTTTT
1 TTTTTT
3868328 CCTTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTTTTTCTTTTCTC
Found at i:3868314 original size:16 final size:15
Alignment explanation
Indices: 3868289--3868338 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
3868279 TATTTGAGCT
*
3868289 TTTTTTTTTCTTCTTC
1 TTTTTGTTTCTT-TTC
3868305 TTTTTGTTTCTTTTC
1 TTTTTGTTTCTTTTC
*
3868320 TCTTTT-TTCCTTTT-
1 T-TTTTGTTTCTTTTC
3868334 TTTTT
1 TTTTT
3868339 TCCCAAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 4 0.13
14 1 0.03
15 11 0.35
16 15 0.48
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (15 bp):
TTTTTGTTTCTTTTC
Found at i:3868403 original size:21 final size:21
Alignment explanation
Indices: 3868362--3868404 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3868352 CTACCTATCT
*
3868362 CTTCTTTGAGCTTGTCCCAAG
1 CTTCTTTGAGCTTGTCACAAG
*
3868383 CTTCTTT-AGCTATTTCACAAG
1 CTTCTTTGAGCT-TGTCACAAG
3868404 C
1 C
3868405 CTAAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.19, C:0.28, G:0.14, T:0.40
Consensus pattern (21 bp):
CTTCTTTGAGCTTGTCACAAG
Found at i:3882198 original size:20 final size:19
Alignment explanation
Indices: 3882173--3882226 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
3882163 TCATGTATAC
3882173 ATGTTTAAACACGATTAAAT
1 ATGTTTAAACACGATT-AAT
* *
3882193 ATGTTTATACAC-ATTTAT
1 ATGTTTAAACACGATTAAT
*
3882211 ACGTTTAAAACACGAT
1 ATGTTT-AAACACGAT
3882227 AACATGATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.25
19 8 0.29
20 13 0.46
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (19 bp):
ATGTTTAAACACGATTAAT
Found at i:3890606 original size:15 final size:16
Alignment explanation
Indices: 3890578--3890628 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
3890568 ATTAATATTA
*
3890578 TTAATTATATAAAATT
1 TTAATTATAAAAAATT
3890594 TTAA-TATAAAAAA-T
1 TTAATTATAAAAAATT
* *
3890608 ATAATTAATAAAACATT
1 TTAATT-ATAAAAAATT
3890625 TTAA
1 TTAA
3890629 CACTTTACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
14 4 0.14
15 9 0.32
16 11 0.39
17 4 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAATTATAAAAAATT
Found at i:3892425 original size:2 final size:2
Alignment explanation
Indices: 3892418--3892455 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3892408 AAGCAACGAG
3892418 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3892456 AAATTGTTAT
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):
TA
Found at i:3893920 original size:15 final size:15
Alignment explanation
Indices: 3893884--3893933 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
3893874 CAGTTCTGAT
*
3893884 TACTTTCTTTTTCTC
1 TACTTTCTTCTTCTC
** *
3893899 TGTTTTCTTGTTCTC
1 TACTTTCTTCTTCTC
*
3893914 TACTTTCTTCTTCTT
1 TACTTTCTTCTTCTC
3893929 TACTT
1 TACTT
3893934 AACCTTGTGA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.06, C:0.24, G:0.04, T:0.66
Consensus pattern (15 bp):
TACTTTCTTCTTCTC
Found at i:3894886 original size:28 final size:29
Alignment explanation
Indices: 3894843--3894898 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
3894833 CTGTTCTATT
*
3894843 TTTCCTTCTCATTGTTTCCTCTTCTCTAC
1 TTTCCTTCTCACTGTTTCCTCTTCTCTAC
3894872 TTTCCTT-TCACTGTTTCCTCTTCTCTA
1 TTTCCTTCTCACTGTTTCCTCTTCTCTA
3894899 ATTTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.07, C:0.34, G:0.04, T:0.55
Consensus pattern (29 bp):
TTTCCTTCTCACTGTTTCCTCTTCTCTAC
Found at i:3895434 original size:28 final size:31
Alignment explanation
Indices: 3895384--3895447 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 31
3895374 CATTGCTTTT
* *
3895384 TCTTCTCTACTTTCTTCTTCTCACTGTTTCC
1 TCTTCTCTACTTTCTACTTCTCACTATTTCC
3895415 TCTTCTCTAC-TT-TAC-TCTCACTATTTCC
1 TCTTCTCTACTTTCTACTTCTCACTATTTCC
3895443 TCTTC
1 TCTTC
3895448 GTGCTTTCGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 17 0.55
29 2 0.06
30 2 0.06
31 10 0.32
ACGTcount: A:0.09, C:0.36, G:0.02, T:0.53
Consensus pattern (31 bp):
TCTTCTCTACTTTCTACTTCTCACTATTTCC
Found at i:3895469 original size:15 final size:15
Alignment explanation
Indices: 3895438--3895483 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
3895428 ACTCTCACTA
*
3895438 TTTCCTCTTC-GTGC
1 TTTCCTCTTCTTTGC
* *
3895452 TTTCGTTTTCTTTGC
1 TTTCCTCTTCTTTGC
3895467 TTTCCTCTTCTTTGC
1 TTTCCTCTTCTTTGC
3895482 TT
1 TT
3895484 AACCTTGCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.00, C:0.28, G:0.11, T:0.61
Consensus pattern (15 bp):
TTTCCTCTTCTTTGC
Found at i:3895917 original size:76 final size:77
Alignment explanation
Indices: 3895796--3895952 Score: 244
Period size: 76 Copynumber: 2.0 Consensus size: 77
3895786 TGCTTTCTTC
*
3895796 TTCTCTAGCTAACCTTTGATTATATTATGTGCACAAACTAATTAAAAAGAGTCTGCTTTCCTCTT
1 TTCTCTAGCTAACCTTTG----TATTATGTGCACAAACTAATTAAAAAGAGTATGCTTTCCTCTT
* *
3895861 TTGTGTTTAACCCTTA
62 CTCTGTTTAACCCTTA
3895877 TTCTCTAGCTAACCTTTG-ATTATGTGCACAAACTAATTAAAAAGAGTATGCTTTCCTCTTCTCT
1 TTCTCTAGCTAACCTTTGTATTATGTGCACAAACTAATTAAAAAGAGTATGCTTTCCTCTTCTCT
3895941 GTTTAACCCTTA
66 GTTTAACCCTTA
3895953 ACCTTCGGTT
Statistics
Matches: 73, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
76 55 0.75
81 18 0.25
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (77 bp):
TTCTCTAGCTAACCTTTGTATTATGTGCACAAACTAATTAAAAAGAGTATGCTTTCCTCTTCTCT
GTTTAACCCTTA
Found at i:3897119 original size:22 final size:22
Alignment explanation
Indices: 3897092--3897135 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3897082 TGCTGCAAAC
3897092 TTTGGTTCTTCTGCTGCGCTAT
1 TTTGGTTCTTCTGCTGCGCTAT
3897114 TTTGGTTCTTCTGCTGCGCTAT
1 TTTGGTTCTTCTGCTGCGCTAT
3897136 CAGTTCACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.05, C:0.23, G:0.23, T:0.50
Consensus pattern (22 bp):
TTTGGTTCTTCTGCTGCGCTAT
Found at i:3898452 original size:22 final size:22
Alignment explanation
Indices: 3898422--3898479 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
3898412 ATAAAAAAAA
3898422 TAAATTAAATTTTTATTTTAAAT
1 TAAA-TAAATTTTTATTTTAAAT
3898445 TAAATAAATTTTTATTTTAAAT
1 TAAATAAATTTTTATTTTAAAT
3898467 TAAATAAATTTTT
1 TAAATAAATTTTT
3898480 TTTACTAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 31 0.89
23 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAAATAAATTTTTATTTTAAAT
Found at i:3907169 original size:2 final size:2
Alignment explanation
Indices: 3907162--3907188 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3907152 TCAGCTATTC
3907162 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3907189 AATTTTAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3923956 original size:67 final size:67
Alignment explanation
Indices: 3923848--3923976 Score: 213
Period size: 67 Copynumber: 1.9 Consensus size: 67
3923838 AACAAGTAGG
* * *
3923848 AATGTCAATAAATACGGATATCTAATTCAATTATATAAAATTAGAATATTTTATAATTGAATACA
1 AATGTCAATAAATACGAATATCTAATTCAACTACATAAAATTAGAATATTTTATAATTGAATACA
3923913 AT
66 AT
* *
3923915 AATGTCAATGAATACGAATATTTAATTCAACTACATAAAATTAGAATATTTTATAATTGAAT
1 AATGTCAATAAATACGAATATCTAATTCAACTACATAAAATTAGAATATTTTATAATTGAAT
3923977 TTGAAACGGG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (67 bp):
AATGTCAATAAATACGAATATCTAATTCAACTACATAAAATTAGAATATTTTATAATTGAATACA
AT
Found at i:3924393 original size:16 final size:16
Alignment explanation
Indices: 3924374--3924410 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3924364 ATTTTATATT
3924374 TTATAAAAATTA-TAG
1 TTATAAAAATTATTAG
3924389 CTTAT-AAAATTATTAG
1 -TTATAAAAATTATTAG
3924405 TTATAA
1 TTATAA
3924411 TAATACTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (16 bp):
TTATAAAAATTATTAG
Found at i:3925155 original size:26 final size:25
Alignment explanation
Indices: 3925106--3925155 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3925096 TAAATTTTAA
3925106 AAATATCTAAATAATTATAAAATTT
1 AAATATCTAAATAATTATAAAATTT
*
3925131 AAATATCT-TATAATTTAATAAAATT
1 AAATATCTAAATAA-TT-ATAAAATT
3925156 CGAGTACCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 10 0.45
26 8 0.36
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
AAATATCTAAATAATTATAAAATTT
Found at i:3930020 original size:24 final size:25
Alignment explanation
Indices: 3929970--3930024 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
3929960 AATTTTTTTT
3929970 AAAAA-AATTTAATTTTGAAAATAA
1 AAAAATAATTTAATTTTGAAAATAA
* * *
3929994 AAAAATAATTT-ATTTTGTATATTA
1 AAAAATAATTTAATTTTGAAAATAA
3930018 AAAAATA
1 AAAAATA
3930025 GTTGTTGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
AAAAATAATTTAATTTTGAAAATAA
Found at i:3934196 original size:2 final size:2
Alignment explanation
Indices: 3934191--3934240 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3934181 TTGGATATAT
3934191 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3934233 GA GA GA GA
1 GA GA GA GA
3934241 TTTTGTGTGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3935050 original size:18 final size:18
Alignment explanation
Indices: 3935027--3935065 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3935017 CTGCTGCTGA
*
3935027 TATATATTTTTCGTTATT
1 TATATATTTTTCATTATT
3935045 TATATATTTTTCATTATT
1 TATATATTTTTCATTATT
3935063 TAT
1 TAT
3935066 GTAATTTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (18 bp):
TATATATTTTTCATTATT
Found at i:3951829 original size:5 final size:5
Alignment explanation
Indices: 3951819--3951956 Score: 65
Period size: 5 Copynumber: 28.4 Consensus size: 5
3951809 CTATTATAAT
* * *
3951819 TAAAA TAAAA T-ATA TAATA TAAAA -ATCAA -AAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA
* * ** * * *
3951867 TATAA -AAAT TAAAA T-TTA TATAA TATAAG TAAAA TAAAT TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA
* * * **
3951916 T-ATA TAATA TAAAA -AATA TATTA TAAAA TAAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA TA
3951957 TATAAGATTA
Statistics
Matches: 102, Mismatches: 22, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
4 16 0.16
5 78 0.76
6 8 0.08
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.29
Consensus pattern (5 bp):
TAAAA
Found at i:3951864 original size:24 final size:24
Alignment explanation
Indices: 3951820--3951991 Score: 88
Period size: 26 Copynumber: 7.0 Consensus size: 24
3951810 TATTATAATT
*
3951820 AAAATAAAATATATAATATAAAAATCAA
1 AAAATAAAATA-A-AATA-AAATAT-AA
3951848 AAAATAAAATAAAATAAAATATAA
1 AAAATAAAATAAAATAAAATATAA
* ** *
3951872 AAATTAAAAT-TTATATAATATAA
1 AAAATAAAATAAAATAAAATATAA
*
3951895 GTAAAATAAATTAAAATAAAATATATA
1 --AAAATAAAATAAAATAAAATATA-A
* *
3951922 ATATAA-AAAATATATTATAAA-AT-A
1 A-A-AATAAAATAAAATA-AAATATAA
* *
3951946 AAAATAAAAT-ATATAAGAT-TATA
1 AAAATAAAATAAAATAAAATATA-A
*
3951969 ATAAT-AAATAAAAATAAAATATA
1 AAAATAAAAT-AAAATAAAATATA
3951992 TAACATTAAA
Statistics
Matches: 110, Mismatches: 20, Indels: 31
0.68 0.12 0.19
Matches are distributed among these distances:
21 3 0.03
22 8 0.07
23 21 0.19
24 20 0.18
25 16 0.15
26 24 0.22
27 7 0.06
28 11 0.10
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (24 bp):
AAAATAAAATAAAATAAAATATAA
Found at i:3951925 original size:33 final size:33
Alignment explanation
Indices: 3951823--3952059 Score: 134
Period size: 33 Copynumber: 6.9 Consensus size: 33
3951813 TATAATTAAA
*
3951823 ATAA-AATATATAATATAAAAATCAAAA-A-ATAAA
1 ATAATAATA-ATAA-ATAAAAAT-AAAATATATAAT
3951856 ATAA-AATAA-AATATAAAAATTAAAATTTATATAAT
1 ATAATAATAATAA-ATAAAAA-TAAAA--TATATAAT
*
3951891 ATAAGTAA-AATAAATTAAAATAAAATATATAAT
1 ATAA-TAATAATAAATAAAAATAAAATATATAAT
* *
3951924 ATAAAAAATATATTATAAAATAAAAATAAAATATATAAG
1 AT----AATA-ATAAT-AAATAAAAATAAAATATATAAT
* *
3951963 ATTATAATAATAAATAAAAATAAAATATATAAC
1 ATAATAATAATAAATAAAAATAAAATATATAAT
* ** *
3951996 ATTAAAAATATATATTTAAGAAATAATATTATATAA-
1 A-TAATAATA-ATAAATAA-AAATAA-AATATATAAT
*
3952032 A-AATTAATAATAAA-AAATAT-AAATATAT
1 ATAA-TAATAATAAATAAAAATAAAATATAT
3952060 TAAACTTGTA
Statistics
Matches: 166, Mismatches: 18, Indels: 43
0.73 0.08 0.19
Matches are distributed among these distances:
30 6 0.04
31 15 0.09
32 5 0.03
33 42 0.25
34 16 0.10
35 26 0.16
36 17 0.10
37 15 0.09
38 2 0.01
39 22 0.13
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (33 bp):
ATAATAATAATAAATAAAAATAAAATATATAAT
Found at i:3951936 original size:49 final size:49
Alignment explanation
Indices: 3951847--3951956 Score: 134
Period size: 49 Copynumber: 2.2 Consensus size: 49
3951837 ATAAAAATCA
** *
3951847 AAAAATAAAATAAAATAAAATATAAAAATTAAAATTTATATAATATAAGT
1 AAAAATAAAATAAAATAAAATATAAAAATTAAAAAATATATAATA-AAAT
* * *
3951897 -AAAATAAATTAAAATAAAATAT-ATAATATAAAAAATATATTATAAAAT
1 AAAAATAAAATAAAATAAAATATAAAAAT-TAAAAAATATATAATAAAAT
3951945 AAAAATAAAATA
1 AAAAATAAAATA
3951957 TATAAGATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
48 7 0.14
49 44 0.86
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (49 bp):
AAAAATAAAATAAAATAAAATATAAAAATTAAAAAATATATAATAAAAT
Found at i:3951940 original size:54 final size:49
Alignment explanation
Indices: 3951825--3951961 Score: 125
Period size: 54 Copynumber: 2.7 Consensus size: 49
3951815 TAATTAAAAT
* *
3951825 AAAATATATAATATAA-AAATCAAA-AAATAAAATAAAATAAAATATAA
1 AAAATATATTATATAATAAATAAAATAAATAAAATAAAATAAAATATAA
* *
3951872 AAATTAAAATTTATATAATATAAGTAAAATAAATTAAAATAAAATATATAATATAA
1 AAAAT-ATA-TTATATAATA-AA-TAAAATAAA-TAAAATAAAATA-A-AATATAA
* *
3951928 AAAATATATTATAAAATAAAAATAAAATATATAA
1 AAAATATATTATATAAT--AAATAAAATAAATAA
3951962 GATTATAATA
Statistics
Matches: 71, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
47 4 0.06
48 2 0.03
49 7 0.10
50 1 0.01
51 2 0.03
52 4 0.06
53 6 0.08
54 28 0.39
55 5 0.07
56 12 0.17
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (49 bp):
AAAATATATTATATAATAAATAAAATAAATAAAATAAAATAAAATATAA
Found at i:3951959 original size:72 final size:74
Alignment explanation
Indices: 3951868--3952008 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 74
3951858 AAAATAAAAT
* * *
3951868 ATAAAAATTAAAATTTATATAATATAAGTAA-AATAAATTAAAATAAAATATATAATATAAAAAA
1 ATAAAAATTAAAA-TTATATAAGATAA-TAATAATAAATAAAAATAAAATATATAACATAAAAAA
3951932 TATATTATAAA
64 TATATTATAAA
* *
3951943 ATAAAAA-TAAAA-TATATAAGATTATAATAATAAATAAAAATAAAATATATAACATTAAAAATA
1 ATAAAAATTAAAATTATATAAGATAATAATAATAAATAAAAATAAAATATATAACATAAAAAATA
3952006 TAT
66 TAT
3952009 ATTTAAGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
71 3 0.05
72 45 0.75
74 5 0.08
75 7 0.12
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (74 bp):
ATAAAAATTAAAATTATATAAGATAATAATAATAAATAAAAATAAAATATATAACATAAAAAATA
TATTATAAA
Found at i:3951987 original size:87 final size:88
Alignment explanation
Indices: 3951816--3952054 Score: 235
Period size: 87 Copynumber: 2.7 Consensus size: 88
3951806 ATACTATTAT
**
3951816 AATTAAAATAAAATATATAATAT-AAAAATCAA-AAAATAAAATAAAATAAAATATAAAAATTAA
1 AATTAAAATAAAATATATAATATAAAAAAT-AATATTATAAAATAAAATAAAATATAAAAATTAA
* * *
3951879 AATTTATATAATATAAGTAAAATA
65 AATTAATATAATAAAAATAAAATA
*
3951903 AATTAAAATAAAATATATAATATAAAAAAT-ATATTATAAAATAAAAATAAAATATATAAGATTA
1 AATTAAAATAAAATATATAATATAAAAAATAATATTATAAAAT-AAAATAAAATATA-AAAATTA
*
3951967 TAA-TAATA-AATAAAAATAAAATA
64 AAATTAATATAATAAAAATAAAATA
* * * * * *
3951990 TA-TAACATTAAAA-ATATATATTTAAGAAATAATATTATATAA-AAATTAATAATA-AAAAATA
1 AATTAA-AATAAAATATATA-ATATAAAAAATAATATTATAAAATAAAATAA-AATATAAAAAT-
3952051 TAAA
62 TAAA
3952055 TATATTAAAC
Statistics
Matches: 128, Mismatches: 15, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
85 4 0.03
86 19 0.15
87 64 0.50
88 33 0.26
89 8 0.06
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (88 bp):
AATTAAAATAAAATATATAATATAAAAAATAATATTATAAAATAAAATAAAATATAAAAATTAAA
ATTAATATAATAAAAATAAAATA
Found at i:3952030 original size:72 final size:72
Alignment explanation
Indices: 3951868--3952056 Score: 188
Period size: 72 Copynumber: 2.6 Consensus size: 72
3951858 AAAATAAAAT
* * * *
3951868 ATAAAAATTAAAATTTATATAATATAAGTAA-AATAAATTAAAATAAAATATATAATATAAAAAA
1 ATAAAAA-TAAAATATA-AAAAT-TAA-TAATAATAAATAAAAATAAAATATATAACATAAAAAA
3951932 TATATTATAAA
62 TATATTATAAA
*
3951943 ATAAAAATAAAATATATAAGATT-ATAATAATAAATAAAAATAAAATATATAACATTAAAAATAT
1 ATAAAAATAAAATATA-AAAATTAATAATAATAAATAAAAATAAAATATATAACA-TAAAAA-AT
*
3952007 ATATT-TAAG
63 ATATTATAAA
* ** * *
3952016 A-AATAATATTATATAAAAATTAATAATAAAAAATATAAATA
1 ATAAAAATAAAATATAAAAATTAATAATAATAAATAAAAATA
3952057 TATTAAACTT
Statistics
Matches: 98, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
71 8 0.08
72 53 0.54
73 11 0.11
74 19 0.19
75 7 0.07
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.32
Consensus pattern (72 bp):
ATAAAAATAAAATATAAAAATTAATAATAATAAATAAAAATAAAATATATAACATAAAAAATATA
TTATAAA
Found at i:3956821 original size:2 final size:2
Alignment explanation
Indices: 3956816--3956840 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3956806 ACACACACAC
3956816 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3956841 ATCAGCTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3957837 original size:2 final size:2
Alignment explanation
Indices: 3957830--3957859 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3957820 TTTCATTGAA
3957830 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
3957860 GCAGGTCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3961943 original size:33 final size:33
Alignment explanation
Indices: 3961883--3961968 Score: 82
Period size: 33 Copynumber: 2.6 Consensus size: 33
3961873 TTTAATGTCA
* * * * * *
3961883 TATATTTTATTTTCATCTCTTATTATAATCTTC
1 TATATTTTGTTTTTATTTTTTAATATAATATTC
*
3961916 TATATTTTGTTTTTATTTTTTAATATAATATTT
1 TATATTTTGTTTTTATTTTTTAATATAATATTC
* *
3961949 TATATTATGTACTTTATTTT
1 TATATTTTGT-TTTTATTTT
3961969 AATTTCTTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
33 35 0.81
34 8 0.19
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (33 bp):
TATATTTTGTTTTTATTTTTTAATATAATATTC
Found at i:3962037 original size:31 final size:33
Alignment explanation
Indices: 3961993--3962059 Score: 95
Period size: 31 Copynumber: 2.1 Consensus size: 33
3961983 ATATTATATA
3961993 AATTTTAATTTCTTATATT-T-TATTTCATTTT
1 AATTTTAATTTCTTATATTATATATTTCATTTT
*
3962024 AATTTCTAA-TTCTTATATTATATATTTTATTTT
1 AATTT-TAATTTCTTATATTATATATTTCATTTT
3962057 AAT
1 AAT
3962060 ATTTTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 15 0.47
32 4 0.12
33 13 0.41
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (33 bp):
AATTTTAATTTCTTATATTATATATTTCATTTT
Found at i:3964348 original size:6 final size:6
Alignment explanation
Indices: 3964339--3964374 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
3964329 TCGTTCGCAT
3964339 TAATGA TAATGA TAATGA TAATGA TAATGA TAATGA
1 TAATGA TAATGA TAATGA TAATGA TAATGA TAATGA
3964375 CGATGTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
TAATGA
Found at i:3968417 original size:3 final size:3
Alignment explanation
Indices: 3968409--3968440 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3968399 TCCTCCGCTA
3968409 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
3968441 TGTCTGTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:3975364 original size:2 final size:2
Alignment explanation
Indices: 3975357--3975390 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3975347 TAAAGAATTA
*
3975357 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3975391 TCGTTTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3976427 original size:16 final size:16
Alignment explanation
Indices: 3976406--3976436 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3976396 AAGATTAGGA
*
3976406 AAAAAAATTAAAAATG
1 AAAAAAATGAAAAATG
3976422 AAAAAAATGAAAAAT
1 AAAAAAATGAAAAAT
3976437 ATAACATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (16 bp):
AAAAAAATGAAAAATG
Found at i:3989526 original size:55 final size:54
Alignment explanation
Indices: 3989397--3989527 Score: 124
Period size: 55 Copynumber: 2.3 Consensus size: 54
3989387 TATAATTAAA
* *
3989397 TAAAATATATAATATAGAAATAAAAATTAAAATAAAATAAAATATAAAAAATAATATT
1 TAAAAAATATAA-ATA-AAA-ACAAATTAAAATAAAATAAAATATAAAAAAT-ATATT
* * *
3989455 TATATAATATAGATAAAAACAAATTAAAATAAAAATATAAATATAAAAAAT-TA-T
1 TAAAAAATATAAATAAAAACAAATTAAAAT-AAAATA-AAATATAAAAAATATATT
3989509 TAAAGAAATGA-AAATAAAA
1 TAAA-AAAT-ATAAATAAAA
3989528 TATAAAAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
54 4 0.07
55 23 0.38
56 10 0.16
57 16 0.26
58 8 0.13
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (54 bp):
TAAAAAATATAAATAAAAACAAATTAAAATAAAATAAAATATAAAAAATATATT
Found at i:3989534 original size:32 final size:33
Alignment explanation
Indices: 3989481--3989563 Score: 116
Period size: 32 Copynumber: 2.5 Consensus size: 33
3989471 AAACAAATTA
*
3989481 AAATAAAAATATAAATATAAAAAATTATTA-AAG
1 AAATAAAAATA-AAATATAAAAAATTATAATAAG
* *
3989514 AAATGAAAATAAAATAT-AAAAATTATAATAAT
1 AAATAAAAATAAAATATAAAAAATTATAATAAG
3989546 AAATAAAAATAAAATATA
1 AAATAAAAATAAAATATA
3989564 TTGACATTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
31 10 0.23
32 24 0.55
33 10 0.23
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (33 bp):
AAATAAAAATAAAATATAAAAAATTATAATAAG
Found at i:3989638 original size:115 final size:114
Alignment explanation
Indices: 3989519--3989862 Score: 604
Period size: 113 Copynumber: 3.0 Consensus size: 114
3989509 TAAAGAAATG
3989519 AAAATAAAATATAAAAATTATAATAATAAATAAAAATAAAATATATTGACATTAAAAATATATTT
1 AAAATAAAATATAAAAATTATAATAATAAATAAAAATAAAATATA-TGACATTAAAAATATATTT
3989584 AA-AATATGATATTATATAAAAATTAATAATATAAAATATAAATATATTAA
65 AAGAA-ATGATATTATATAAAAATTAATAATATAAAATATAAATATATTAA
* *
3989634 AAAATAAAATATAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTA
1 AAAATAAAATATAAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTA
3989699 AGAAATGATATTATATAAAAATTAATAATAT-AAATATAAATATATT-A
66 AGAAATGATATTATATAAAAATTAATAATATAAAATATAAATATATTAA
3989746 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAA-ATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
*
3989811 AAGAAATGATATTATATAAAAATTAATAATAAAAAAATATAAATATATTAA
65 AAGAAATGATATTATATAAAAATTAATAAT-ATAAAATATAAATATATTAA
3989862 A
1 A
3989863 CTTATATTTT
Statistics
Matches: 219, Mismatches: 5, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
112 16 0.07
113 92 0.42
114 48 0.22
115 61 0.28
116 2 0.01
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (114 bp):
AAAATAAAATATAAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTA
AGAAATGATATTATATAAAAATTAATAATATAAAATATAAATATATTAA
Found at i:3989670 original size:50 final size:49
Alignment explanation
Indices: 3989607--3989792 Score: 153
Period size: 50 Copynumber: 3.5 Consensus size: 49
3989597 ATATAAAAAT
3989607 TAAT-AATATAAAATATAAATATATTAAAAAATAAAATATAAATATTATAA
1 TAATAAATA-AAAATA-AAATATATTAAAAAATAAAATATAAATATTATAA
*
3989657 TAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGA-AATGATATTATATAA
1 TAATAAATAAAAATAAAATATAT--TA--AAAAATA-A---AATATAA--ATA-T-TATAA
* *
3989717 AAATTAATAATATAAATATAAATATATT-AAAAATAAAATATAAAATATTATAA
1 TAA-T-A-AATAAAAATA-AAATATATTAAAAAATAAAATAT-AAATATTATAA
3989770 TAATAAATAAAAATAAAATATAT
1 TAATAAATAAAAATAAAATATAT
3989793 GACATTAAAA
Statistics
Matches: 111, Mismatches: 6, Indels: 39
0.71 0.04 0.25
Matches are distributed among these distances:
49 16 0.14
50 19 0.17
51 7 0.06
52 1 0.01
53 14 0.13
54 2 0.02
55 6 0.05
56 2 0.02
57 5 0.05
58 4 0.04
59 8 0.07
60 7 0.06
61 1 0.01
62 2 0.02
63 9 0.08
64 8 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (49 bp):
TAATAAATAAAAATAAAATATATTAAAAAATAAAATATAAATATTATAA
Done.