Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, 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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 19 of 84
Found at i:3632855 original size:21 final size:22
Alignment explanation
Indices: 3632813--3632855 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
3632803 TAATATAATT
**
3632813 AATATATAATATATGATATTAA
1 AATATATAATATAAAATATTAA
*
3632835 AATA-ATAATATAAAATTTTAA
1 AATATATAATATAAAATATTAA
3632856 TAGCACTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AATATATAATATAAAATATTAA
Found at i:3634762 original size:42 final size:42
Alignment explanation
Indices: 3634707--3634830 Score: 214
Period size: 42 Copynumber: 3.0 Consensus size: 42
3634697 TGGAGCCAAG
*
3634707 GGTGGA-CTCAGTGATGGAGGGCTTGATGGAACCAATGTTGGT
1 GGTGGACCT-AGTGATGGAGGGCTCGATGGAACCAATGTTGGT
*
3634749 GGTGGACCTAGTGATGGAAGGCTCGATGGAACCAATGTTGGT
1 GGTGGACCTAGTGATGGAGGGCTCGATGGAACCAATGTTGGT
3634791 GGTGGACCTAGTGATGGAGGGCTCGATGGAACCAATGTTG
1 GGTGGACCTAGTGATGGAGGGCTCGATGGAACCAATGTTG
3634831 ATCTCTGCAC
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
42 76 0.97
43 2 0.03
ACGTcount: A:0.23, C:0.14, G:0.40, T:0.24
Consensus pattern (42 bp):
GGTGGACCTAGTGATGGAGGGCTCGATGGAACCAATGTTGGT
Found at i:3649765 original size:45 final size:45
Alignment explanation
Indices: 3649701--3649811 Score: 123
Period size: 45 Copynumber: 2.5 Consensus size: 45
3649691 TCGAACCAAG
* * * *
3649701 GGTGGACTTAGCGATGGAGGGCTTGATGGAAACAATGTTGATCTC
1 GGTGGACTTGGTGATGGAGGGCTTGATAGAAACAATGTTGAACTC
* * * * **
3649746 GGTGGACTTGGTGATGGAGGGGTTGTTATATATGATGTTGAACTC
1 GGTGGACTTGGTGATGGAGGGCTTGATAGAAACAATGTTGAACTC
*
3649791 GGTGGACTTGGTGGTGGAGGG
1 GGTGGACTTGGTGATGGAGGG
3649812 GGTGGACTTG
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.20, C:0.09, G:0.41, T:0.30
Consensus pattern (45 bp):
GGTGGACTTGGTGATGGAGGGCTTGATAGAAACAATGTTGAACTC
Found at i:3649808 original size:12 final size:12
Alignment explanation
Indices: 3649791--3649850 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 12
3649781 TGTTGAACTC
3649791 GGTGGACTTGGT
1 GGTGGACTTGGT
*
3649803 GGTGGA---GGG
1 GGTGGACTTGGT
3649812 GGTGGACTTGGT
1 GGTGGACTTGGT
*
3649824 GGTGGA---GGG
1 GGTGGACTTGGT
3649833 GGTGGACTTGGT
1 GGTGGACTTGGT
*
3649845 GATGGA
1 GGTGGA
3649851 GGGCTTGATA
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
9 16 0.43
12 21 0.57
ACGTcount: A:0.12, C:0.05, G:0.58, T:0.25
Consensus pattern (12 bp):
GGTGGACTTGGT
Found at i:3649817 original size:21 final size:21
Alignment explanation
Indices: 3649791--3649853 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
3649781 TGTTGAACTC
3649791 GGTGGACTTGGTGGTGGAGGG
1 GGTGGACTTGGTGGTGGAGGG
3649812 GGTGGACTTGGTGGTGGAGGG
1 GGTGGACTTGGTGGTGGAGGG
*
3649833 GGTGGACTTGGTGATGGAGGG
1 GGTGGACTTGGTGGTGGAGGG
3649854 CTTGATAGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.11, C:0.05, G:0.60, T:0.24
Consensus pattern (21 bp):
GGTGGACTTGGTGGTGGAGGG
Found at i:3649946 original size:45 final size:47
Alignment explanation
Indices: 3649895--3649990 Score: 144
Period size: 48 Copynumber: 2.1 Consensus size: 47
3649885 TTATGAAGGA
*
3649895 TGAACTCGGTGGAC-T-TGGTGATGGAGGGCTTGATAGATA-CAATGT
1 TGAACTCGGTGGACTTGTGGTGATGGAGGGCCTGATAGA-ACCAATGT
3649940 TGAACTCGGTGGACTTGGTGGTGATGGAGGGCCTGATAGAACCAATGT
1 TGAACTCGGTGGACTT-GTGGTGATGGAGGGCCTGATAGAACCAATGT
3649988 TGA
1 TGA
3649991 TCTCTGCACC
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
45 14 0.30
46 1 0.02
47 1 0.02
48 30 0.65
ACGTcount: A:0.24, C:0.12, G:0.36, T:0.27
Consensus pattern (47 bp):
TGAACTCGGTGGACTTGTGGTGATGGAGGGCCTGATAGAACCAATGT
Found at i:3666694 original size:16 final size:17
Alignment explanation
Indices: 3666664--3666697 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3666654 GCGAATTCTT
3666664 TTTTTCATTTGTTTTTG
1 TTTTTCATTTGTTTTTG
*
3666681 TTTTTC-TTTTTTTTTG
1 TTTTTCATTTGTTTTTG
3666697 T
1 T
3666698 GGTAATTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.03, C:0.06, G:0.09, T:0.82
Consensus pattern (17 bp):
TTTTTCATTTGTTTTTG
Found at i:3668242 original size:14 final size:14
Alignment explanation
Indices: 3668223--3668252 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3668213 TCAATAGTGA
*
3668223 AGTAATTTTGTTTT
1 AGTAATTTTCTTTT
3668237 AGTAATTTTCTTTT
1 AGTAATTTTCTTTT
3668251 AG
1 AG
3668253 ATAAGCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.60
Consensus pattern (14 bp):
AGTAATTTTCTTTT
Found at i:3675147 original size:2 final size:2
Alignment explanation
Indices: 3675140--3675190 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
3675130 CCTCGGGCAA
3675140 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3675182 TC TC TC TC T
1 TC TC TC TC T
3675191 TTGTTTTTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3675648 original size:3 final size:3
Alignment explanation
Indices: 3675640--3675664 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3675630 TTAAGGGCCA
3675640 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3675665 TTGCAGGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3676475 original size:37 final size:37
Alignment explanation
Indices: 3676434--3676537 Score: 95
Period size: 38 Copynumber: 2.8 Consensus size: 37
3676424 TTAATAATAA
*
3676434 TTATATATAAATATAATAAAAATAAAAATA-ATATATT
1 TTATATATAAATATAATATAAATAAAAATATATA-ATT
* ** * * *
3676471 TTATATTTTTATATCGATTTAAATAATAATATATAATT
1 TTATATATAAATAT-AATATAAATAAAAATATATAATT
3676509 TT-TATATAAAATATAATATAAATACAAAA
1 TTATATAT-AAATATAATATAAATA-AAAA
3676538 ATTTTAATAT
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
37 23 0.46
38 24 0.48
39 3 0.06
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (37 bp):
TTATATATAAATATAATATAAATAAAAATATATAATT
Found at i:3677035 original size:26 final size:27
Alignment explanation
Indices: 3677006--3677088 Score: 84
Period size: 26 Copynumber: 3.1 Consensus size: 27
3676996 TTTGGGATTA
3677006 TTTTATTT-TTAAAATAATTTTTATAT
1 TTTTATTTATTAAAATAATTTTTATAT
*
3677032 TTTTATTATATTTAAA-AATTTTTAT-T
1 TTTTATT-TATTAAAATAATTTTTATAT
*
3677058 TTTTAATTTATATGGAAATAATTTTT-TAT
1 TTTT-ATTTAT-T-AAAATAATTTTTATAT
3677087 TT
1 TT
3677089 CAAATAAAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
26 15 0.31
27 14 0.29
28 9 0.19
29 10 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
TTTTATTTATTAAAATAATTTTTATAT
Found at i:3677045 original size:29 final size:29
Alignment explanation
Indices: 3677008--3677088 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
3676998 TGGGATTATT
*
3677008 TTATTTTTAAAATAATTTTTATATTTTT-A
1 TTATATTT-AAATAATTTTTATATTTTTAA
3677037 TTATATTTAAA-AATTTTTAT-TTTTTAA
1 TTATATTTAAATAATTTTTATATTTTTAA
**
3677064 TTTATATGGAAATAATTTTT-TATTT
1 -TTATATTTAAATAATTTTTATATTT
3677089 CAAATAAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
26 5 0.11
27 10 0.22
28 13 0.29
29 17 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (29 bp):
TTATATTTAAATAATTTTTATATTTTTAA
Found at i:3677061 original size:27 final size:29
Alignment explanation
Indices: 3677017--3677088 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
3677007 TTTATTTTTA
**
3677017 AAATAATTTTTATATTTTT-A-TTATATTT
1 AAATAATTTTTAT-TTTTTAATTTATATGG
3677045 AAA-AATTTTTATTTTTTAATTTATATGG
1 AAATAATTTTTATTTTTTAATTTATATGG
3677073 AAATAATTTTTTATTT
1 AAATAA-TTTTTATTT
3677089 CAAATAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 5 0.13
27 10 0.26
28 12 0.32
29 2 0.05
30 9 0.24
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (29 bp):
AAATAATTTTTATTTTTTAATTTATATGG
Found at i:3680151 original size:17 final size:16
Alignment explanation
Indices: 3680079--3680153 Score: 55
Period size: 16 Copynumber: 4.4 Consensus size: 16
3680069 GTTTTAAGAT
3680079 TTAAATTTTAAATTTA
1 TTAAATTTTAAATTTA
* *
3680095 TTAAATATT--ATTTT
1 TTAAATTTTAAATTTA
*
3680109 TTAAATAATTATATGAATTAA
1 TTAAAT--TT-TA--AATTTA
3680130 TTAAATTTTAAATTTTA
1 TTAAATTTTAAA-TTTA
3680147 TTAAATT
1 TTAAATT
3680154 AAATATGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
14 10 0.22
16 11 0.24
17 11 0.24
18 2 0.04
19 2 0.04
21 9 0.20
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (16 bp):
TTAAATTTTAAATTTA
Found at i:3693568 original size:19 final size:19
Alignment explanation
Indices: 3693546--3693583 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3693536 TTATAAACAT
*
3693546 ATTTA-TATTATATTAATAA
1 ATTTATTATT-TAATAATAA
3693565 ATTTATTATTTAATAATAA
1 ATTTATTATTTAATAATAA
3693584 TTAGAAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTATTATTTAATAATAA
Found at i:3695049 original size:15 final size:15
Alignment explanation
Indices: 3695026--3695072 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
3695016 TTACCTTGTT
*
3695026 AATTCGAATAATTTTA
1 AATT-GAATTATTTTA
*
3695042 AATTGAATTATTTAA
1 AATTGAATTATTTTA
*
3695057 AATTAAATTATTTTA
1 AATTGAATTATTTTA
3695072 A
1 A
3695073 TTCTCTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 23 0.85
16 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (15 bp):
AATTGAATTATTTTA
Found at i:3695386 original size:22 final size:23
Alignment explanation
Indices: 3695341--3695387 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
3695331 AATTTTTTAA
* * *
3695341 AAAATTATTATTATTAATTGATT
1 AAAATTAATATTAATAATTAATT
3695364 AAAATTAAT-TTAATAATTAATT
1 AAAATTAATATTAATAATTAATT
3695386 AA
1 AA
3695388 TTAATCAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATTAATATTAATAATTAATT
Found at i:3696028 original size:11 final size:12
Alignment explanation
Indices: 3696007--3696034 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3695997 GCACAATTTC
3696007 TTTTTCTTTTTT
1 TTTTTCTTTTTT
3696019 TTTTTCTTTTTT
1 TTTTTCTTTTTT
3696031 TTTT
1 TTTT
3696035 GGGGTGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:3697086 original size:16 final size:17
Alignment explanation
Indices: 3697065--3697102 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3697055 CAATTATATA
* *
3697065 AATTTTAAGAAA-AGAT
1 AATTTTAACAAATAAAT
3697081 AATTTTAACAAATAAAT
1 AATTTTAACAAATAAAT
3697098 AATTT
1 AATTT
3697103 ATTATATCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (17 bp):
AATTTTAACAAATAAAT
Found at i:3705471 original size:52 final size:51
Alignment explanation
Indices: 3705390--3705529 Score: 138
Period size: 52 Copynumber: 2.7 Consensus size: 51
3705380 AAAAAATTTT
*
3705390 AAGATAAAGAAGATTCTTAATAGGTAAGTTTGATATGCAAGAGAAGAATTCTAA
1 AAGA-AAA-AAGATTTTTAATAGGTAAGTTT-ATATGCAAGAGAAGAATTCTAA
* * * * *
3705444 AAGAAAAAAGATTTTTAATAAGCAAGTTTA-ACTTACAGGAGAATAATTCTAA
1 AAGAAAAAAGATTTTTAATAGGTAAGTTTATA--TGCAAGAGAAGAATTCTAA
* * * *
3705496 GAGGAGAGAGATTTTTAATAGGTAAGTTTATATG
1 AAGAAAAAAGATTTTTAATAGGTAAGTTTATATG
3705530 GTTATAAATA
Statistics
Matches: 70, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
50 1 0.01
51 2 0.03
52 59 0.84
53 4 0.06
54 4 0.06
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (51 bp):
AAGAAAAAAGATTTTTAATAGGTAAGTTTATATGCAAGAGAAGAATTCTAA
Found at i:3721378 original size:16 final size:17
Alignment explanation
Indices: 3721334--3721384 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
3721324 TCAGTTTGAA
3721334 AAAATT-TTAAAAATATT
1 AAAATTATT-AAAATATT
* *
3721351 ATAATCATTAAAAT-TT
1 AAAATTATTAAAATATT
3721367 AAAATTATTAAATATATT
1 AAAATTATTAAA-ATATT
3721385 TTTAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 12 0.44
17 11 0.41
18 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATTATTAAAATATT
Found at i:3722740 original size:30 final size:31
Alignment explanation
Indices: 3722706--3722795 Score: 87
Period size: 30 Copynumber: 2.9 Consensus size: 31
3722696 TAATTATGAG
*
3722706 TTTTAAAAAAATATAAAATAT-ATTTCATA-T
1 TTTTAAAAAAATATAAAATATAATAT-ATAGT
* ** * *
3722736 TTTTATATTAATATTAATTATAATATATAGT
1 TTTTAAAAAAATATAAAATATAATATATAGT
3722767 TTTTAAATAAAATATAAAATA-AATATATA
1 TTTTAAA-AAAATATAAAATATAATATATA
3722796 AATTATTAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
30 19 0.41
31 18 0.39
32 9 0.20
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (31 bp):
TTTTAAAAAAATATAAAATATAATATATAGT
Found at i:3722988 original size:24 final size:25
Alignment explanation
Indices: 3722960--3723006 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
3722950 ATTATAATTA
*
3722960 TAAAATTTATATAATATA-AATACC
1 TAAAATTTATATAAAATATAATACC
3722984 TAAAATTTATATAAAATATAATA
1 TAAAATTTATATAAAATATAATA
3723007 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAAATTTATATAAAATATAATACC
Found at i:3723026 original size:33 final size:32
Alignment explanation
Indices: 3722968--3723054 Score: 90
Period size: 33 Copynumber: 2.8 Consensus size: 32
3722958 TATAAAATTT
*
3722968 ATATAATATAAATA-CCTAAAATTTATATAAA
1 ATATAATATAAATATACTAAAATTTATATAAA
***
3722999 ATATAATATAAATATAC-AAATATTTTATATTTT
1 ATATAATATAAATATACTAAA-A-TTTATATAAA
*
3723032 ATATAATACAAATATA-TAAAATT
1 ATATAATATAAATATACTAAAATT
3723055 CTCGAATCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
31 19 0.40
32 3 0.06
33 25 0.53
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (32 bp):
ATATAATATAAATATACTAAAATTTATATAAA
Found at i:3723163 original size:221 final size:218
Alignment explanation
Indices: 3722768--3723168 Score: 544
Period size: 221 Copynumber: 1.8 Consensus size: 218
3722758 ATATATAGTT
* *
3722768 TTTAAATAAAATATAAAATAAATATATAAATTATTAATATTTTATATGATACAAATAAATAAAAT
1 TTTAAATAAAATATAAAATAAATATACAAATTATTAATATTTTATATAATACAAATAAATAAAAT
* * *
3722833 TTTTAAATCTACCTCAAATAATAATAAAAGTAAATCTTGCATTTGCAACCTTGAATCCTGATCTT
66 TCTCAAATCTACCTCAAATAATAATAAAAG-AAATCTTGCATTTGCAACCTGGAATCCTGATCTT
* * *
3722898 GCCTCTTTGTCCTTTCCCTTTCACTTTTTCATTATTTTTAAATAAATAAATTATTATAATTATAA
130 G-C-CTTTGTCCTTTCACTTTCACTTTCTCATAATTTTTAAATAAATAAATTATTATAATTATAA
3722963 AATTTATATAATATAAATACCTAAAA
193 AATTTATATAATATAAATACCTAAAA
* * * *
3722989 TTTATATAAAATATAATATAAATATACAAA-TATTTTATATTTTATATAATACAAATATATAAAA
1 TTTAAATAAAATATAAAATAAATATACAAATTA-TTAATATTTTATATAATACAAATAAATAAAA
* * * *
3723053 TTCTCGAATCTATCC-CACATAATAA-AAAA-AAATCTTGCATTTGTAACCTGGAATCTTAGATC
65 TTCTCAAATCTA-CCTCAAATAATAATAAAAGAAATCTTGCATTTGCAACCTGGAATCCT-GATC
3723115 TTG-CTTTGTACCATTTCAC-TTCACTTTCTCATAATTTTTAAATAAATAAATTAT
128 TTGCCTTTGT-CC-TTTCACTTTCACTTTCTCATAATTTTTAAATAAATAAATTAT
3723169 CGTGTTATGT
Statistics
Matches: 159, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
216 6 0.04
217 35 0.22
218 30 0.19
219 7 0.04
220 6 0.04
221 73 0.46
222 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (218 bp):
TTTAAATAAAATATAAAATAAATATACAAATTATTAATATTTTATATAATACAAATAAATAAAAT
TCTCAAATCTACCTCAAATAATAATAAAAGAAATCTTGCATTTGCAACCTGGAATCCTGATCTTG
CCTTTGTCCTTTCACTTTCACTTTCTCATAATTTTTAAATAAATAAATTATTATAATTATAAAAT
TTATATAATATAAATACCTAAAA
Found at i:3735721 original size:16 final size:16
Alignment explanation
Indices: 3735675--3735726 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
3735665 TTAAAAAAAT
*
3735675 TAATTTTATATTTAAA
1 TAATATTATATTTAAA
*
3735691 TAATAAATT-TA-TTAAT
1 TAAT--ATTATATTTAAA
3735707 TAATATTATATTTAAA
1 TAATATTATATTTAAA
3735723 TAAT
1 TAAT
3735727 TATTTAACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
14 3 0.10
15 2 0.07
16 20 0.69
17 2 0.07
18 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATATTATATTTAAA
Found at i:3740384 original size:62 final size:61
Alignment explanation
Indices: 3740301--3740421 Score: 172
Period size: 62 Copynumber: 2.0 Consensus size: 61
3740291 CTATACTAAA
* * * *
3740301 ATATTTAATATGATATCTAAATTTTAAAATTTTTTAATATAATTTTTAAATTAATAAATAAT
1 ATATTTAATATCATATCTAAATTTTAAAAATTTTTAATATAATTCTTAAAAT-ATAAATAAT
*
3740363 ATATTTAATGTCATA-CTTAAATTTTAAAAATTTTTAATATAATTCTTAAAATATAAATA
1 ATATTTAATATCATATC-TAAATTTTAAAAATTTTTAATATAATTCTTAAAATATAAATA
3740422 TGTGAAATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 8 0.15
62 45 0.85
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (61 bp):
ATATTTAATATCATATCTAAATTTTAAAAATTTTTAATATAATTCTTAAAATATAAATAAT
Found at i:3740410 original size:29 final size:29
Alignment explanation
Indices: 3740298--3740412 Score: 106
Period size: 29 Copynumber: 3.8 Consensus size: 29
3740288 ATTCTATACT
* *
3740298 AAAATATTTAATATGATATC-TAAATTTTA
1 AAAATTTTTAATATAAT-TCTTAAATTTTA
* * *
3740327 AAATTTTTTAATATAATTTTTAAATTAATA
1 AAAATTTTTAATATAATTCTTAAATT-TTA
* * *
3740357 AATAATATATTTAATGTCATACTTAAATTTTA
1 AA-AAT-T-TTTAATATAATTCTTAAATTTTA
3740389 AAAATTTTTAATATAATTCTTAAA
1 AAAATTTTTAATATAATTCTTAAA
3740413 ATATAAATAT
Statistics
Matches: 67, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
28 1 0.01
29 35 0.52
30 5 0.07
31 5 0.07
32 5 0.07
33 16 0.24
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (29 bp):
AAAATTTTTAATATAATTCTTAAATTTTA
Found at i:3744983 original size:30 final size:29
Alignment explanation
Indices: 3744947--3745068 Score: 147
Period size: 30 Copynumber: 4.2 Consensus size: 29
3744937 CAGTTAAGAC
3744947 TTTAATTAATTAAAAATAAATATTTAAAAA
1 TTTAATTAATT-AAAATAAATATTTAAAAA
* * *
3744977 TTTAATTAAATAAAA-AAATATTTAAGAG
1 TTTAATTAATTAAAATAAATATTTAAAAA
* *
3745005 TTTAATTAATTAAAAATAAATATTTGATAA
1 TTTAATTAATT-AAAATAAATATTTAAAAA
* **
3745035 TTTAATTAATTATAATAAATAGATAAAAA
1 TTTAATTAATTAAAATAAATATTTAAAAA
3745064 TTTAA
1 TTTAA
3745069 AAAATTATTT
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
28 21 0.27
29 26 0.33
30 31 0.40
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (29 bp):
TTTAATTAATTAAAATAAATATTTAAAAA
Found at i:3745854 original size:81 final size:81
Alignment explanation
Indices: 3745712--3745876 Score: 197
Period size: 81 Copynumber: 2.0 Consensus size: 81
3745702 ACAAGTTAAA
* * * ** * ** *
3745712 TATTGATCAATGAAATTAGGAATCTGACATTTTACTAACAAGTTGGATGATTATGATAAATTGAT
1 TATTGATCAATGAAATTAAGAATCTGACATTTTACTAACAAATTGAACAACTACAACAAATTGAT
*
3745777 AATTTGATGAAAAATG
66 AATTTAATGAAAAATG
*
3745793 TATTGATCAATGAAATTAAGAATCT-AGCATTTTACTAATAAATTGAACAACTACAACAAATTGA
1 TATTGATCAATGAAATTAAGAATCTGA-CATTTTACTAACAAATTGAACAACTACAACAAATTGA
* *
3745857 TAATTTAATGAGAAGTG
65 TAATTTAATGAAAAATG
3745874 TAT
1 TAT
3745877 AAAATATATT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
80 1 0.01
81 69 0.99
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.35
Consensus pattern (81 bp):
TATTGATCAATGAAATTAAGAATCTGACATTTTACTAACAAATTGAACAACTACAACAAATTGAT
AATTTAATGAAAAATG
Found at i:3751810 original size:2 final size:2
Alignment explanation
Indices: 3751803--3751827 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3751793 CAACTAATCC
3751803 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
3751828 ATAGTATAAA
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:3755809 original size:15 final size:15
Alignment explanation
Indices: 3755789--3755822 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3755779 GTTTCCACCT
*
3755789 ATGGAAGATCCTGCC
1 ATGGAAGATCCAGCC
*
3755804 ATGGAAGTTCCAGCC
1 ATGGAAGATCCAGCC
3755819 ATGG
1 ATGG
3755823 CAAAGACCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (15 bp):
ATGGAAGATCCAGCC
Found at i:3765560 original size:3 final size:3
Alignment explanation
Indices: 3765552--3765589 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3765542 GTATCAAAGC
3765552 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3765590 GATGATGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3786326 original size:23 final size:23
Alignment explanation
Indices: 3786291--3786336 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3786281 TAATCAAGTA
3786291 TTTTAATTCATATTTTTA-ATAT
1 TTTTAATTCATATTTTTATATAT
*
3786313 TTTTAAATTTATATTTTTATATAT
1 TTTT-AATTCATATTTTTATATAT
3786337 AAATGATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 13 0.62
24 4 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTAATTCATATTTTTATATAT
Found at i:3795710 original size:16 final size:18
Alignment explanation
Indices: 3795689--3795721 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3795679 AGCTAGCAAT
3795689 ATATTA-AAAAA-AAAAC
1 ATATTATAAAAAGAAAAC
3795705 ATATTATAAAAAGAAAA
1 ATATTATAAAAAGAAAA
3795722 GCGAAGGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
ATATTATAAAAAGAAAAC
Found at i:3798081 original size:12 final size:13
Alignment explanation
Indices: 3798060--3798098 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
3798050 CTTTGTTTAT
3798060 ATACATATATA-A
1 ATACATATATATA
*
3798072 ATATATATATATA
1 ATACATATATATA
3798085 A-ACATATATATA
1 ATACATATATATA
3798097 AT
1 AT
3798099 GATTAGGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 21 0.91
13 2 0.09
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (13 bp):
ATACATATATATA
Found at i:3798081 original size:14 final size:14
Alignment explanation
Indices: 3798058--3798096 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
3798048 GACTTTGTTT
*
3798058 ATATACATATATAA
1 ATATATATATATAA
3798072 ATATATATATATAA
1 ATATATATATATAA
*
3798086 ACATATATATA
1 ATATATATATA
3798097 ATGATTAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATATATATATAA
Found at i:3798095 original size:16 final size:16
Alignment explanation
Indices: 3798057--3798096 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3798047 TGACTTTGTT
*
3798057 TATATACATATATAAA
1 TATATATATATATAAA
3798073 TATATATATATA-AACA
1 TATATATATATATAA-A
3798089 TATATATA
1 TATATATA
3798097 ATGATTAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (16 bp):
TATATATATATATAAA
Found at i:3803386 original size:22 final size:22
Alignment explanation
Indices: 3803345--3803402 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
3803335 TATATTAATA
*
3803345 TATT-AAA-TATAAATATTTTT
1 TATTAAAATTATAAATAATTTT
*
3803365 TATTAAAATTATATATAATTTT
1 TATTAAAATTATAAATAATTTT
* *
3803387 TGTTAAAATTTTAAAT
1 TATTAAAATTATAAAT
3803403 TATATTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 4 0.13
21 3 0.10
22 24 0.77
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TATTAAAATTATAAATAATTTT
Found at i:3820343 original size:13 final size:13
Alignment explanation
Indices: 3820314--3820353 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
3820304 AATTGTAAGG
3820314 ATTTTTA-TTC-T
1 ATTTTTATTTCAT
3820325 -TTTTTATTTCAT
1 ATTTTTATTTCAT
3820337 ATTTTTATTTCAT
1 ATTTTTATTTCAT
3820350 ATTT
1 ATTT
3820354 ATCATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.23
11 3 0.12
12 1 0.04
13 16 0.62
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTATTTCAT
Found at i:3820837 original size:63 final size:63
Alignment explanation
Indices: 3820717--3820868 Score: 167
Period size: 55 Copynumber: 2.5 Consensus size: 63
3820707 CACTGCAATC
* * **
3820717 AATCCAGCCTCACATCCAATCAACTTTTTCACCAATTCACTAATTCCCTGTAAACAATTTCAT
1 AATCCAGCCTCACATCCAATCAACTTTTCCACCAATTCACTAATACAATGTAAACAATTTCAT
* *
3820780 AATCTAGCCTCACATCCAATCAACTTTTCCACCAATTC-C-----C--TGTAAACAATTTCAC
1 AATCCAGCCTCACATCCAATCAACTTTTCCACCAATTCACTAATACAATGTAAACAATTTCAT
* **
3820835 AATCCAGCCTTATGTCCAATCAACTTTTCCACCA
1 AATCCAGCCTCACATCCAATCAACTTTTCCACCA
3820869 CCAATTCCCC
Statistics
Matches: 82, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
55 44 0.54
57 1 0.01
62 1 0.01
63 36 0.44
ACGTcount: A:0.32, C:0.34, G:0.04, T:0.30
Consensus pattern (63 bp):
AATCCAGCCTCACATCCAATCAACTTTTCCACCAATTCACTAATACAATGTAAACAATTTCAT
Found at i:3820844 original size:55 final size:55
Alignment explanation
Indices: 3820758--3820868 Score: 177
Period size: 55 Copynumber: 2.0 Consensus size: 55
3820748 CCAATTCACT
* *
3820758 AATTCCCTGTAAACAATTTCATAATCTAGCCTCACATCCAATCAACTTTTCCACC
1 AATTCCCTGTAAACAATTTCACAATCCAGCCTCACATCCAATCAACTTTTCCACC
* **
3820813 AATTCCCTGTAAACAATTTCACAATCCAGCCTTATGTCCAATCAACTTTTCCACC
1 AATTCCCTGTAAACAATTTCACAATCCAGCCTCACATCCAATCAACTTTTCCACC
3820868 A
1 A
3820869 CCAATTCCCC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (55 bp):
AATTCCCTGTAAACAATTTCACAATCCAGCCTCACATCCAATCAACTTTTCCACC
Found at i:3822175 original size:60 final size:59
Alignment explanation
Indices: 3822111--3822354 Score: 307
Period size: 60 Copynumber: 4.1 Consensus size: 59
3822101 TTTGCAATGA
* *
3822111 TTCTTCTAAAATAAAATTTTTTAAAAAATAT-TTTTAAGAAAAAATTGAAAGTATCAATTT
1 TTCTT-TAAAATAAAA-TTTTAAAAAAATATATTTTAAGAAAAAGTTGAAAGTATCAATTT
* *
3822171 TTCTTGAAAATAAAATTTTAAAAAATATATATTTGTGAGAAAAAGTTGAAAGTATCAA-TT
1 TTCTTTAAAATAAAATTTTAAAAAA-ATATATTT-TAAGAAAAAGTTGAAAGTATCAATTT
* * *
3822231 TTCTTTGAAAATAAAATTGTTAAAAAAA-ACATTTCTAAGAAAAAGTTGGAAGTACCAATTT
1 TTCTTT-AAAATAAAATT-TTAAAAAAATATATTT-TAAGAAAAAGTTGAAAGTATCAATTT
* * *
3822292 TTCTTAAAAATAAAA-CTTAAAAAAATATATTTTGAGAAAAAGTTGAAAGTATCAATTT
1 TTCTTTAAAATAAAATTTTAAAAAAATATATTTTAAGAAAAAGTTGAAAGTATCAATTT
3822350 TTCTT
1 TTCTT
3822355 GTATAAAAAC
Statistics
Matches: 161, Mismatches: 16, Indels: 16
0.83 0.08 0.08
Matches are distributed among these distances:
58 46 0.29
59 18 0.11
60 49 0.30
61 40 0.25
62 8 0.05
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (59 bp):
TTCTTTAAAATAAAATTTTAAAAAAATATATTTTAAGAAAAAGTTGAAAGTATCAATTT
Found at i:3822214 original size:61 final size:59
Alignment explanation
Indices: 3822118--3822355 Score: 313
Period size: 58 Copynumber: 4.0 Consensus size: 59
3822108 TGATTCTTCT
* *
3822118 AAAATAAAATTTTTTAAAAAATAT-TTTTAAGAAAAAATTGAAAGTATCAATTTTTCTTG
1 AAAATAAAA-TTTTAAAAAAATATATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTG
*
3822177 AAAATAAAATTTTAAAAAATATATATTTGTGAGAAAAAGTTGAAAGTATCAA-TTTTCTTTG
1 AAAATAAAATTTTAAAAAA-ATATATTT-TAAGAAAAAGTTGAAAGTATCAATTTTTC-TTG
* * * *
3822238 AAAATAAAATTGTTAAAAAAA-ACATTTCTAAGAAAAAGTTGGAAGTACCAATTTTTCTTA
1 AAAATAAAATT-TTAAAAAAATATATTT-TAAGAAAAAGTTGAAAGTATCAATTTTTCTTG
* *
3822298 AAAATAAAA-CTTAAAAAAATATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAAATAAAATTTTAAAAAAATATATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTG
3822356 TATAAAAACA
Statistics
Matches: 157, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
58 46 0.29
59 18 0.11
60 44 0.28
61 41 0.26
62 8 0.05
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (59 bp):
AAAATAAAATTTTAAAAAAATATATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTG
Found at i:3822292 original size:121 final size:117
Alignment explanation
Indices: 3822118--3822350 Score: 349
Period size: 121 Copynumber: 2.0 Consensus size: 117
3822108 TGATTCTTCT
** * * * *
3822118 AAAATAAAATTTTTTAAAAAATATTTTTAAGAAAAAATTGAAAGTATCAATTTTTCTTGAAAATA
1 AAAATAAAATTTTAAAAAAAACATTTCTAAGAAAAAATTGAAAGTACCAATTTTTCTTAAAAATA
*
3822183 AAATTTTAAAAAATATATATTTGTGAGAAAAAGTTGAAAGTATCAATTTTCTTTG
66 AAA-CTTAAAAAA-ATATATTT-TGAGAAAAAGTTGAAAGTATCAATTTTCTTTG
* *
3822238 AAAATAAAATTGTTAAAAAAAACATTTCTAAGAAAAAGTTGGAAGTACCAATTTTTCTTAAAAAT
1 AAAATAAAATT-TTAAAAAAAACATTTCTAAGAAAAAATTGAAAGTACCAATTTTTCTTAAAAAT
3822303 AAAACTTAAAAAAATATATTTTGAGAAAAAGTTGAAAGTATCAATTTT
65 AAAACTTAAAAAAATATATTTTGAGAAAAAGTTGAAAGTATCAATTTT
3822351 TCTTGTATAA
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
118 27 0.26
119 8 0.08
120 19 0.18
121 49 0.48
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (117 bp):
AAAATAAAATTTTAAAAAAAACATTTCTAAGAAAAAATTGAAAGTACCAATTTTTCTTAAAAATA
AAACTTAAAAAAATATATTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTG
Found at i:3826199 original size:11 final size:11
Alignment explanation
Indices: 3826183--3826239 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
3826173 AACAATGGAT
*
3826183 AAAAAAAGGTG
1 AAAAAAAAGTG
*
3826194 AAAAAAAAGAG
1 AAAAAAAAGTG
3826205 AAAAAAAAG-G
1 AAAAAAAAGTG
* *
3826215 AAAATAGA-TG
1 AAAAAAAAGTG
3826225 -AAAAAAA-TG
1 AAAAAAAAGTG
3826234 AAAAAA
1 AAAAAA
3826240 TAAAATAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 7 0.18
10 13 0.34
11 18 0.47
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (11 bp):
AAAAAAAAGTG
Found at i:3826227 original size:31 final size:31
Alignment explanation
Indices: 3826184--3826263 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
3826174 ACAATGGATA
* *
3826184 AAAAAAGGTGAAAAAAAAGAGAAAAA-AAAGG
1 AAAAAAGATGAAAAAAAAGA-AAAAATAAAAG
* * *
3826215 AAAATAGATGAAAAAAATGAAAAAATAAAAT
1 AAAAAAGATGAAAAAAAAGAAAAAATAAAAG
3826246 AAAAAAGATGAAAAAAAA
1 AAAAAAGATGAAAAAAAA
3826264 AGGAAGACTC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 5 0.12
31 36 0.88
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (31 bp):
AAAAAAGATGAAAAAAAAGAAAAAATAAAAG
Found at i:3827123 original size:79 final size:79
Alignment explanation
Indices: 3826941--3827134 Score: 289
Period size: 79 Copynumber: 2.5 Consensus size: 79
3826931 GAGAAATCTG
* * * *
3826941 TGAATAGTGATCAAGTGATAAAAATAGTATAGATCAACAGACAAAATTTGTTCTGAAATAGTTAC
1 TGAATGGTGATCAAGTGATAAAAATAGTATAGATCAACAGACAAAATTTGTTATGAAACAATTAC
*
3827006 TATTGAAAAGCCTG
66 TATTGAAAAGCCTA
** *
3827020 TGAATGGTGATCAAACGATAAAAATAGTATAGATCAACAGACAGAATTTGTTATGAAACAATTAC
1 TGAATGGTGATCAAGTGATAAAAATAGTATAGATCAACAGACAAAATTTGTTATGAAACAATTAC
3827085 TATTGAAAAGCCTA
66 TATTGAAAAGCCTA
* * *
3827099 TGAATGGTGATCAAGTGATGAAAATAATAAAGATCA
1 TGAATGGTGATCAAGTGATAAAAATAGTATAGATCA
3827135 GTTGATGAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 102 1.00
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (79 bp):
TGAATGGTGATCAAGTGATAAAAATAGTATAGATCAACAGACAAAATTTGTTATGAAACAATTAC
TATTGAAAAGCCTA
Found at i:3827581 original size:58 final size:58
Alignment explanation
Indices: 3827495--3827771 Score: 195
Period size: 58 Copynumber: 4.7 Consensus size: 58
3827485 TCTTTGAGTG
* * *
3827495 TCAAATGAAAATTTTTAAATTTCAAATGAGAATCTTTGAGGTGTGAAAC-CTAAAATTTA
1 TCAAATGTAAATCTTTAAA-TTCAAATGAGAATCTTTGAGATGTGAAACTC-AAAATTTA
** * * * * * * * *
3827554 TTGAATGTAAATTTTTGAACTCAAATGAAAATCTTTGA-ATCCTCAAA-TGAGAATCTTTGA
1 TCAAATGTAAATCTTTAAATTCAAATGAGAATCTTTGAGAT-GTGAAACTCA-AA-ATTT-A
* * * * *
3827614 GTTCAAAT-AAGAATCGTTGAATTTTAAAATGAGAATCTTTGAGGTGTGAAACTCAAAATTTA
1 --TCAAATGTA-AATC-TTTAA-ATTCAAATGAGAATCTTTGAGATGTGAAACTCAAAATTTA
* * * * *
3827676 TCGAATGTGAATCTTCAAACTCAAATGAGAATCTTTGAAATGTGAAA-TCCAAAATTTA
1 TCAAATGTAAATCTTTAAATTCAAATGAGAATCTTTGAGATGTGAAACT-CAAAATTTA
*
3827734 TCAAATGTAAATCTTCAAATTCAAATGAGAATCTTTGA
1 TCAAATGTAAATCTTTAAATTCAAATGAGAATCTTTGA
3827772 ATTTCAAATG
Statistics
Matches: 166, Mismatches: 38, Indels: 29
0.71 0.16 0.12
Matches are distributed among these distances:
57 3 0.02
58 91 0.55
59 22 0.13
60 10 0.06
61 1 0.01
62 8 0.05
63 6 0.04
64 22 0.13
65 3 0.02
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (58 bp):
TCAAATGTAAATCTTTAAATTCAAATGAGAATCTTTGAGATGTGAAACTCAAAATTTA
Found at i:3827601 original size:22 final size:21
Alignment explanation
Indices: 3827557--3827655 Score: 78
Period size: 22 Copynumber: 4.7 Consensus size: 21
3827547 AAATTTATTG
* *
3827557 AATGTAAATTTTTGAA-CTCA
1 AATGAAAATCTTTGAATCTCA
3827577 AATGAAAATCTTTGAATCCTCA
1 AATGAAAATCTTTGAAT-CTCA
* *
3827599 AATGAGAATCTTTGAGT-TCA
1 AATGAAAATCTTTGAATCTCA
* * *
3827619 AAT-AAGAATCGTTGAATTTTAA
1 AATGAA-AATCTTTGAA-TCTCA
*
3827641 AATGAGAATCTTTGA
1 AATGAAAATCTTTGA
3827656 GGTGTGAAAC
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.02
20 28 0.44
21 1 0.02
22 32 0.51
23 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (21 bp):
AATGAAAATCTTTGAATCTCA
Found at i:3827614 original size:122 final size:122
Alignment explanation
Indices: 3827451--3827714 Score: 345
Period size: 122 Copynumber: 2.1 Consensus size: 122
3827441 CTGATTTTTT
* * * *
3827451 AAATGAAAATCTTTAAAGAATCTTCAATTGAGAATCTTTGAGTGTCAAATGAA-AAT-TTTTAAA
1 AAATGAAAATCTTT---GAATCCTCAAATGAGAATCTTTGAGT-TCAAAT-AAGAATCGTTGAAA
* * * **
3827514 TTTCAAATGAGAATCTTTGAGGTGTGAAAC-CTAAAATTTATTGAATGTAAATTTTTGAACTC
61 TTTAAAATGAGAATCTTTGAGGTGTGAAACTC-AAAATTTATCGAATGTAAATCTTCAAACTC
*
3827576 AAATGAAAATCTTTGAATCCTCAAATGAGAATCTTTGAGTTCAAATAAGAATCGTTGAATTTTAA
1 AAATGAAAATCTTTGAATCCTCAAATGAGAATCTTTGAGTTCAAATAAGAATCGTTGAAATTTAA
*
3827641 AATGAGAATCTTTGAGGTGTGAAACTCAAAATTTATCGAATGTGAATCTTCAAACTC
66 AATGAGAATCTTTGAGGTGTGAAACTCAAAATTTATCGAATGTAAATCTTCAAACTC
*
3827698 AAATGAGAATCTTTGAA
1 AAATGAAAATCTTTGAA
3827715 ATGTGAAATC
Statistics
Matches: 124, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
120 2 0.02
121 9 0.07
122 98 0.79
123 1 0.01
125 14 0.11
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (122 bp):
AAATGAAAATCTTTGAATCCTCAAATGAGAATCTTTGAGTTCAAATAAGAATCGTTGAAATTTAA
AATGAGAATCTTTGAGGTGTGAAACTCAAAATTTATCGAATGTAAATCTTCAAACTC
Found at i:3827766 original size:20 final size:20
Alignment explanation
Indices: 3827734--3827809 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
3827724 CCAAAATTTA
3827734 TCAAATGTA-AATCTTCAAAT
1 TCAAATG-AGAATCTTCAAAT
* *
3827754 TCAAATGAGAATCTTTGAATT
1 TCAAATGAGAATC-TTCAAAT
* *
3827775 TCAAATGAGAATTTTCGAACT
1 TCAAATGAGAATCTTC-AAAT
3827796 T-AAATGAGAATCTT
1 TCAAATGAGAATCTT
3827810 TGAGTATCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.02
20 25 0.53
21 21 0.45
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (20 bp):
TCAAATGAGAATCTTCAAAT
Found at i:3827772 original size:58 final size:58
Alignment explanation
Indices: 3827640--3827772 Score: 205
Period size: 58 Copynumber: 2.3 Consensus size: 58
3827630 TTGAATTTTA
** * *
3827640 AAATGAGAATCTTTGAGGTGTGAAACTCAAAATTTATCGAATGTGAATCTTCAAACTC
1 AAATGAGAATCTTTGAAATGTGAAACTCAAAATTTATCAAATGTAAATCTTCAAACTC
*
3827698 AAATGAGAATCTTTGAAATGTGAAA-TCCAAAATTTATCAAATGTAAATCTTCAAATTC
1 AAATGAGAATCTTTGAAATGTGAAACT-CAAAATTTATCAAATGTAAATCTTCAAACTC
3827756 AAATGAGAATCTTTGAA
1 AAATGAGAATCTTTGAA
3827773 TTTCAAATGA
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
57 1 0.01
58 68 0.99
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (58 bp):
AAATGAGAATCTTTGAAATGTGAAACTCAAAATTTATCAAATGTAAATCTTCAAACTC
Found at i:3827779 original size:21 final size:21
Alignment explanation
Indices: 3827753--3827854 Score: 127
Period size: 21 Copynumber: 4.9 Consensus size: 21
3827743 AATCTTCAAA
3827753 TTCAAATGAGAATCTTTGAAT
1 TTCAAATGAGAATCTTTGAAT
*
3827774 TTCAAATGAGAAT-TTTCGAAC
1 TTCAAATGAGAATCTTT-GAAT
*
3827795 TT-AAATGAGAATCTTTGAGT
1 TTCAAATGAGAATCTTTGAAT
* * *
3827815 ATCAAATGATAATTTTTGAAT
1 TTCAAATGAGAATCTTTGAAT
*
3827836 TTCAAATGAGAATTTTTGA
1 TTCAAATGAGAATCTTTGA
3827855 GGTGTGAAAC
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
20 16 0.23
21 53 0.77
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (21 bp):
TTCAAATGAGAATCTTTGAAT
Found at i:3827801 original size:41 final size:42
Alignment explanation
Indices: 3827732--3827854 Score: 144
Period size: 41 Copynumber: 3.0 Consensus size: 42
3827722 ATCCAAAATT
* *
3827732 TATCAAATGTA-AATCTTC-AAATTCAAATGAGAATCTTTGAA
1 TATCAAATG-AGAATTTTCGAACTTCAAATGAGAATCTTTGAA
* *
3827773 TTTCAAATGAGAATTTTCGAACTT-AAATGAGAATCTTTGAG
1 TATCAAATGAGAATTTTCGAACTTCAAATGAGAATCTTTGAA
* * * *
3827814 TATCAAATGATAATTTTTGAATTTCAAATGAGAATTTTTGA
1 TATCAAATGAGAATTTTCGAACTTCAAATGAGAATCTTTGA
3827855 GGTGTGAAAC
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
40 1 0.01
41 50 0.71
42 19 0.27
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (42 bp):
TATCAAATGAGAATTTTCGAACTTCAAATGAGAATCTTTGAA
Found at i:3827846 original size:199 final size:198
Alignment explanation
Indices: 3827495--3828152 Score: 629
Period size: 201 Copynumber: 3.3 Consensus size: 198
3827485 TCTTTGAGTG
* * * * * * * **
3827495 TCAAATGAAAAT-TTTTAAATTTCAAATGAGAATCTTTGAGGTGTGAAACCTAAAATTTATTGAA
1 TCAAATGAGAATCTTTGAAATGTCAAATCAAAATCTTTAAGGTGAGAAACCTAAAA-TTATCAAA
** * *
3827559 TGTA-AATTTTTGAACTCAAATGAA-AATCTTTGAATCCTCAAATGAGAATCTTTGAGTTCAAAT
65 TG-AGAATTTTCAAATTCAAAT-AAGAATCTTTGAAT-CTTAAATGAGAATCTTTGAGTTCAAAT
* * *
3827622 AAGAATCGTTGAATTTTAAAATGAGAATCTTTGAGGTGTGAAACTCAAAATTTATCGAATGTGAA
127 GAGAATCTTTGAA-TTTCAAATGAGAATCTTTGAGGTGTGAAAC-CAAAATTTATCGAATGTGAA
3827687 TCTTCAAAC
190 TCTTCAAAC
* * * * *
3827696 TCAAATGAGAATCTTTGAAATGTGAAATCCAAAAT-TTATCAA-ATGTA-AATCTTCAAA-T-TC
1 TCAAATGAGAATCTTTGAAATGTCAAAT-CAAAATCTT-T-AAGGTG-AGAAACCTAAAATTATC
* * *
3827756 AAATGAGAATCTTTGAATTTCAAATGAGAAT-TTTCGAA-CTTAAATGAGAATCTTTGAGTATCA
62 AAATGAGAAT-TTTCAAATTCAAATAAGAATCTTT-GAATCTTAAATGAGAATCTTTGAGT-TCA
* * * * *
3827819 AATGATAATTTTTGAATTTCAAATGAGAATTTTTGAGGTGTGAAACCTAAAATTTGTCGAATGTA
124 AATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACC-AAAATTTATCGAATGTG
3827884 AATCTTCAAAC
188 AATCTTCAAAC
* * * * *
3827895 TCAAATTAGTATCTTTG-AATTTCAAATGAGAATCTTTAAGGTGAGAAACCTAAAATTTATCAAA
1 TCAAATGAGAATCTTTGAAATGTCAAATCAAAATCTTTAAGGTGAGAAACCTAAAA-TTATCAAA
* * * *
3827959 TGTGAATTTTCAAATTCAAATAAGAATCTTTGAATTTTAAATAAGAATCTTTAAGTGTCAAATGA
65 TGAGAATTTTCAAATTCAAATAAGAATCTTTGAATCTTAAATGAGAATCTTTGAGT-TCAAATGA
* * * *
3828024 GAATCTTTGAATCCTCAAATGAGAATCTTTGAGATGAGAAACCCAAAATTTATCGAATGTGAATT
129 GAATCTTTGAAT-TTCAAATGAGAATCTTTGAGGTGTGAAA-CCAAAATTTATCGAATGTGAATC
* *
3828089 TTCGAAT
192 TTCAAAC
* * * * *
3828096 TCAAATGAGAATTTTTG-AATTTCAAATGAGAATCTTTGAGGTGAGAAACCTAAAATT
1 TCAAATGAGAATCTTTGAAATGTCAAATCAAAATCTTTAAGGTGAGAAACCTAAAATT
3828153 TGTCGAATAT
Statistics
Matches: 375, Mismatches: 61, Indels: 43
0.78 0.13 0.09
Matches are distributed among these distances:
196 3 0.01
197 14 0.04
198 11 0.03
199 111 0.30
200 79 0.21
201 126 0.34
202 16 0.04
203 14 0.04
204 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (198 bp):
TCAAATGAGAATCTTTGAAATGTCAAATCAAAATCTTTAAGGTGAGAAACCTAAAATTATCAAAT
GAGAATTTTCAAATTCAAATAAGAATCTTTGAATCTTAAATGAGAATCTTTGAGTTCAAATGAGA
ATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCAAAATTTATCGAATGTGAATCTTCA
AAC
Found at i:3827919 original size:79 final size:79
Alignment explanation
Indices: 3827829--3828013 Score: 262
Period size: 79 Copynumber: 2.3 Consensus size: 79
3827819 AATGATAATT
* * * * *
3827829 TTTGAATTTCAAATGAGAATTTTTGAGGTGTGAAACCTAAAATTTGTCGAATGTAAATCTTCAAA
1 TTTGAATTTCAAATGAGAATCTTTAAGGTGAGAAACCTAAAATTTATCAAATGTAAATCTTCAAA
* *
3827894 CTCAAATTAGTATC
66 CTCAAATAAGAATC
* *
3827908 TTTGAATTTCAAATGAGAATCTTTAAGGTGAGAAACCTAAAATTTATCAAATGTGAATTTTCAAA
1 TTTGAATTTCAAATGAGAATCTTTAAGGTGAGAAACCTAAAATTTATCAAATGTAAATCTTCAAA
*
3827973 TTCAAATAAGAATC
66 CTCAAATAAGAATC
* *
3827987 TTTGAATTTTAAATAAGAATCTTTAAG
1 TTTGAATTTCAAATGAGAATCTTTAAG
3828014 TGTCAAATGA
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 94 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (79 bp):
TTTGAATTTCAAATGAGAATCTTTAAGGTGAGAAACCTAAAATTTATCAAATGTAAATCTTCAAA
CTCAAATAAGAATC
Found at i:3828044 original size:22 final size:21
Alignment explanation
Indices: 3827974--3828055 Score: 94
Period size: 21 Copynumber: 3.9 Consensus size: 21
3827964 ATTTTCAAAT
*
3827974 TCAAATAAGAATCTTTGAATT
1 TCAAATAAGAATCTTTGAATC
* *
3827995 TTAAATAAGAATCTTT-AAGTG
1 TCAAATAAGAATCTTTGAA-TC
*
3828016 TCAAATGAGAATCTTTGAATCC
1 TCAAATAAGAATCTTTGAAT-C
*
3828038 TCAAATGAGAATCTTTGA
1 TCAAATAAGAATCTTTGA
3828056 GATGAGAAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.04
21 31 0.58
22 20 0.38
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (21 bp):
TCAAATAAGAATCTTTGAATC
Found at i:3828052 original size:122 final size:121
Alignment explanation
Indices: 3827895--3828132 Score: 359
Period size: 122 Copynumber: 2.0 Consensus size: 121
3827885 ATCTTCAAAC
* * * * *
3827895 TCAAATTAGTATCTTTGAATTTCAAATGAGAATCTTTAAGGTGAGAAACCTAAAATTTATCAAAT
1 TCAAATGAGAATCTTTGAATCTCAAATGAGAATCTTTAAGATGAGAAACCCAAAATTTATCAAAT
*
3827960 GTGAATTTTCAAATTCAAATAAGAATCTTTGAATTTTAAATAAGAATCTTTAAGTG
66 GTGAATTTTCAAATTCAAATAAGAATCTTTGAATTTCAAATAAGAATCTTTAAGTG
* *
3828016 TCAAATGAGAATCTTTGAATCCTCAAATGAGAATCTTTGAGATGAGAAACCCAAAATTTATCGAA
1 TCAAATGAGAATCTTTGAAT-CTCAAATGAGAATCTTTAAGATGAGAAACCCAAAATTTATCAAA
* * * *
3828081 TGTGAATTTTCGAATTCAAATGAGAATTTTTGAATTTCAAATGAGAATCTTT
65 TGTGAATTTTCAAATTCAAATAAGAATCTTTGAATTTCAAATAAGAATCTTT
3828133 GAGGTGAGAA
Statistics
Matches: 104, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
121 18 0.17
122 86 0.83
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (121 bp):
TCAAATGAGAATCTTTGAATCTCAAATGAGAATCTTTAAGATGAGAAACCCAAAATTTATCAAAT
GTGAATTTTCAAATTCAAATAAGAATCTTTGAATTTCAAATAAGAATCTTTAAGTG
Found at i:3828074 original size:79 final size:78
Alignment explanation
Indices: 3827997--3828153 Score: 199
Period size: 79 Copynumber: 2.0 Consensus size: 78
3827987 TTTGAATTTT
3827997 AAATAAGAATCTTT-AAGTGTCAAATGAGAATCTTTGAATCCTCAAATGAGAATCTTTGAGATGA
1 AAATAAGAAT-TTTCAA-T-TCAAATGAGAATCTTTGAAT-CTCAAATGAGAATCTTTGAGATGA
3828061 GAAACCCAAAATTTATC
62 GAAACCCAAAATTTATC
* ** * * *
3828078 GAATGTGAATTTTCGAATTCAAATGAGAATTTTTGAATTTCAAATGAGAATCTTTGAGGTGAGAA
1 AAATAAGAATTTTC-AATTCAAATGAGAATCTTTGAATCTCAAATGAGAATCTTTGAGATGAGAA
*
3828143 ACCTAAAATTT
65 ACCCAAAATTT
3828154 GTCGAATATA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
79 35 0.52
80 22 0.33
81 8 0.12
82 2 0.03
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (78 bp):
AAATAAGAATTTTCAATTCAAATGAGAATCTTTGAATCTCAAATGAGAATCTTTGAGATGAGAAA
CCCAAAATTTATC
Found at i:3828107 original size:20 final size:21
Alignment explanation
Indices: 3828079--3828128 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
3828069 AAATTTATCG
*
3828079 AATGTGAATTTTCGAA-TTCA
1 AATGAGAATTTTCGAATTTCA
*
3828099 AATGAGAATTTTTGAATTTCA
1 AATGAGAATTTTCGAATTTCA
3828120 AATGAGAAT
1 AATGAGAAT
3828129 CTTTGAGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (21 bp):
AATGAGAATTTTCGAATTTCA
Found at i:3828119 original size:21 final size:20
Alignment explanation
Indices: 3828079--3828134 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
3828069 AAATTTATCG
* *
3828079 AATGTGAATTTTCGAATTCA
1 AATGAGAATTTTTGAATTCA
3828099 AATGAGAATTTTTGAATTTCA
1 AATGAGAATTTTTGAA-TTCA
*
3828120 AATGAGAATCTTTGA
1 AATGAGAATTTTTGA
3828135 GGTGAGAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (20 bp):
AATGAGAATTTTTGAATTCA
Found at i:3828159 original size:79 final size:78
Alignment explanation
Indices: 3828016--3828190 Score: 244
Period size: 79 Copynumber: 2.2 Consensus size: 78
3828006 TCTTTAAGTG
3828016 TCAAATGAGAATCTTTGAATCCTCAAATGAGAATCTTTGAGATGAGAAACCCAAAATTTATCGAA
1 TCAAATGAGAATCTTTGAATCCTCAAATGAGAATCTTTGAGATGAGAAACCCAAAATTTATCGAA
* *
3828081 TGTGAATTTTCGAAT
66 TAT--ATCTTCGAAT
* * * * *
3828096 TCAAATGAGAATTTTTGAAT-TTCAAATGAGAATCTTTGAGGTGAGAAACCTAAAATTTGTCGAA
1 TCAAATGAGAATCTTTGAATCCTCAAATGAGAATCTTTGAGATGAGAAACCCAAAATTTATCGAA
*
3828160 TATATCTTGGAAT
66 TATATCTTCGAAT
*
3828173 TCAAATAAGAATCTTTGA
1 TCAAATGAGAATCTTTGA
3828191 GATGTAAAAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
77 24 0.28
79 42 0.49
80 19 0.22
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (78 bp):
TCAAATGAGAATCTTTGAATCCTCAAATGAGAATCTTTGAGATGAGAAACCCAAAATTTATCGAA
TATATCTTCGAAT
Found at i:3828361 original size:41 final size:42
Alignment explanation
Indices: 3828298--3828379 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 42
3828288 TCAACTTTTG
*
3828298 GATGCGAATCTCTAAATTTTTTG-TGAAAACCTTTGAACTTA
1 GATGCGAAACTCTAAATTTTTTGATGAAAACCTTTGAACTTA
* **
3828339 GATGTGAAACTCTAAGA-TTTTTGAATGTGAACCTTTGAACT
1 GATGCGAAACTCTAA-ATTTTTTG-ATGAAAACCTTTGAACT
3828380 CGAACAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
41 19 0.56
42 1 0.03
43 14 0.41
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (42 bp):
GATGCGAAACTCTAAATTTTTTGATGAAAACCTTTGAACTTA
Found at i:3828954 original size:13 final size:13
Alignment explanation
Indices: 3828936--3828966 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3828926 GATTTTTATT
3828936 TATTTTTATTTCA
1 TATTTTTATTTCA
*
3828949 TATTTTTATTTCG
1 TATTTTTATTTCA
3828962 TATTT
1 TATTT
3828967 ATCATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.71
Consensus pattern (13 bp):
TATTTTTATTTCA
Found at i:3830740 original size:15 final size:16
Alignment explanation
Indices: 3830714--3830755 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
3830704 AAGTATCAAT
3830714 TTTTCTTAAAAAT-AAA
1 TTTTC-TAAAAATAAAA
3830730 TTTTCTAAAAATAAAA
1 TTTTCTAAAAATAAAA
*
3830746 ATTTCTAAAA
1 TTTTCTAAAA
3830756 GTATTTTGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTTCTAAAAATAAAA
Found at i:3830811 original size:72 final size:74
Alignment explanation
Indices: 3830663--3830820 Score: 200
Period size: 72 Copynumber: 2.2 Consensus size: 74
3830653 TGATTCTTCT
* *
3830663 AAAATAAAATTTTCAGAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATA
1 AAAATAAAAATTTCAGAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTTTTCTTAAAAATA
*
3830728 AATTTTCTA
66 AATTGTCTA
* * *
3830737 AAAATAAAAATTTC-TAAAAGTA-TTTTGAGGAAAAATTGAAAGTATCAA-TTTTCTTTGAAAAT
1 AAAATAAAAATTTCAGAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTTTTC-TTAAAAAT
3830799 AAAATTGT-TA
65 -AAATTGTCTA
*
3830809 AAAA-AAACATTT
1 AAAATAAAAATTT
3830821 ATGAGGAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
71 12 0.16
72 38 0.51
73 12 0.16
74 13 0.17
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.36
Consensus pattern (74 bp):
AAAATAAAAATTTCAGAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTTTTCTTAAAAATA
AATTGTCTA
Found at i:3830840 original size:60 final size:59
Alignment explanation
Indices: 3830758--3830912 Score: 197
Period size: 60 Copynumber: 2.6 Consensus size: 59
3830748 TTCTAAAAGT
* *
3830758 ATTTTGAGGAAAAATTGAAAGTATCAA-TTTTCTTTGAAAATAAAATTGTT-AAAAAAAAC
1 ATTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAAATT-TTCAAAAAAAAC
* * *
3830817 ATTTATGAGGAAAAGTTGGAAGTACCAATTTTTCTTAAAAATAAAATTTTCAAAAAAAAT
1 ATTT-TGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAAAAC
* *
3830877 ATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTT
1 A-TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT
3830913 CTATAAAAAC
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
59 6 0.07
60 69 0.83
61 8 0.10
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (59 bp):
ATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAAAAC
Found at i:3835115 original size:21 final size:21
Alignment explanation
Indices: 3835065--3835115 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
3835055 TTTTTCAACG
3835065 TCAATATTAATCTATTAATAA
1 TCAATATTAATCTATTAATAA
*
3835086 --AATATTAATCTCTTAA-AA
1 TCAATATTAATCTATTAATAA
3835104 TCAATAATTAAT
1 TCAAT-ATTAAT
3835116 ATTAATTGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.08
19 15 0.58
20 3 0.12
21 6 0.23
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (21 bp):
TCAATATTAATCTATTAATAA
Found at i:3837828 original size:15 final size:15
Alignment explanation
Indices: 3837808--3837850 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
3837798 TTTAAGGTAA
3837808 AAATTTATAATTATT
1 AAATTTATAATTATT
*
3837823 AAATTTATAAATATT
1 AAATTTATAATTATT
3837838 AAATTTATTAATT
1 AAATTTA-TAATT
3837851 TATATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATTTATAATTATT
Found at i:3837842 original size:23 final size:23
Alignment explanation
Indices: 3837808--3837854 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
3837798 TTTAAGGTAA
3837808 AAATTTATAA-TTATTAAATTTAT
1 AAATTTATAATTTATT-AATTTAT
3837831 AAATATTA-AATTTATTAATTTAT
1 AAAT-TTATAATTTATTAATTTAT
3837854 A
1 A
3837855 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTTATAATTTATTAATTTAT
Found at i:3840416 original size:31 final size:31
Alignment explanation
Indices: 3840370--3840434 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
3840360 TGGTATATTG
*
3840370 TTATTATTATATTTATAATTTT-AGAACAAAT
1 TTATCATTATATTTATAATTTTGA-AACAAAT
*
3840401 TTATCATTATTTTTATAATTTTGAAACAAAT
1 TTATCATTATATTTATAATTTTGAAACAAAT
3840432 TTA
1 TTA
3840435 GTCAAGATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (31 bp):
TTATCATTATATTTATAATTTTGAAACAAAT
Found at i:3840610 original size:18 final size:18
Alignment explanation
Indices: 3840589--3840623 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3840579 ATATTATGAT
3840589 AAAAGAAAAATTAAAATA
1 AAAAGAAAAATTAAAATA
* *
3840607 AAAATAAAATTTAAAAT
1 AAAAGAAAAATTAAAAT
3840624 TATGTGACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAAGAAAAATTAAAATA
Found at i:3845426 original size:20 final size:20
Alignment explanation
Indices: 3845397--3845440 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
3845387 TTGTATCATA
3845397 TTTTGAATTAATAGA-TTTATT
1 TTTTGAATT-A-AGATTTTATT
3845418 TTTTG-ATTAAGATTTTATT
1 TTTTGAATTAAGATTTTATT
3845437 TTTT
1 TTTT
3845441 TTAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.14
19 11 0.50
20 3 0.14
21 5 0.23
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (20 bp):
TTTTGAATTAAGATTTTATT
Found at i:3854591 original size:18 final size:19
Alignment explanation
Indices: 3854553--3854591 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3854543 TTTGAAATTT
*
3854553 ATCCAATTTATCAAATCAA
1 ATCCAATTAATCAAATCAA
*
3854572 ATCCAATTAAT-AATTCAA
1 ATCCAATTAATCAAATCAA
3854590 AT
1 AT
3854592 ATATAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (19 bp):
ATCCAATTAATCAAATCAA
Found at i:3855013 original size:27 final size:27
Alignment explanation
Indices: 3854961--3855013 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
3854951 ACTAAATTTG
* *
3854961 ATAAAGATCTAATTTGAACATATTAAA
1 ATAAAGAACTAATTTCAACATATTAAA
*
3854988 ATAAAGAGACTAATTTCATCAT-TTAA
1 ATAAAGA-ACTAATTTCAACATATTAA
3855014 CTAAAGTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34
Consensus pattern (27 bp):
ATAAAGAACTAATTTCAACATATTAAA
Found at i:3856561 original size:25 final size:25
Alignment explanation
Indices: 3856495--3856561 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
3856485 TCACTGTTCT
*
3856495 TTTCTTTTTTTTCTTTTTTAAATCTC
1 TTTCTTTTTTTT-TTTTCTAAATCTC
* * **
3856521 TTTCTGTTGTAGTTTTCTAAATC-C
1 TTTCTTTTTTTTTTTTCTAAATCTC
3856545 ATTTCTTTTTTTTTTTT
1 -TTTCTTTTTTTTTTTT
3856562 TGCTTGTTCA
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
24 1 0.03
25 22 0.71
26 8 0.26
ACGTcount: A:0.12, C:0.13, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTCTTTTTTTTTTTTCTAAATCTC
Found at i:3868480 original size:18 final size:19
Alignment explanation
Indices: 3868441--3868489 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
3868431 ACCAAAGTTT
* *
3868441 AAATATTA-TTATCTGATT
1 AAATATTATTTATCAGATA
3868459 AAATATTATTTAT-AGATA
1 AAATATTATTTATCAGATA
3868477 AAATTATTATTTA
1 AAA-TATTATTTA
3868490 AATATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
AAATATTATTTATCAGATA
Found at i:3868497 original size:29 final size:29
Alignment explanation
Indices: 3868457--3868515 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
3868447 TATTATCTGA
3868457 TTAAATATTATTTATAGATAAAATTATTAT
1 TTAAATATTATTTATAGATAAAATT-TTAT
* *
3868487 TTAAATA-TATTTATGGATTAAATTTTAT
1 TTAAATATTATTTATAGATAAAATTTTAT
3868515 T
1 T
3868516 AAGACTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 5 0.19
29 15 0.56
30 7 0.26
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (29 bp):
TTAAATATTATTTATAGATAAAATTTTAT
Found at i:3868507 original size:17 final size:16
Alignment explanation
Indices: 3868439--3868509 Score: 51
Period size: 18 Copynumber: 4.4 Consensus size: 16
3868429 ATACCAAAGT
*
3868439 TTAAATATTATTATCTGA
1 TTAAATA-TATT-TATGA
3868457 TTAAATATTATTTATAGA
1 TTAAATA-TATTTAT-GA
*
3868475 TAAAAT-TA-TTAT--
1 TTAAATATATTTATGA
3868487 TTAAATATATTTATGGA
1 TTAAATATATTTAT-GA
3868504 TTAAAT
1 TTAAAT
3868510 TTTATTAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
12 5 0.11
13 2 0.05
14 4 0.09
15 4 0.09
16 2 0.05
17 8 0.18
18 19 0.43
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (16 bp):
TTAAATATATTTATGA
Found at i:3870274 original size:29 final size:30
Alignment explanation
Indices: 3870241--3870297 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
3870231 TTTTTTATTA
3870241 TTTTGTAACTTAAATAGGT-TTTTACATAT
1 TTTTGTAACTTAAATAGGTCTTTTACATAT
* *
3870270 TTTTGTAACTTGAGTAGGTCTTTTACAT
1 TTTTGTAACTTAAATAGGTCTTTTACAT
3870298 TAATTATTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (30 bp):
TTTTGTAACTTAAATAGGTCTTTTACATAT
Found at i:3871993 original size:25 final size:25
Alignment explanation
Indices: 3871947--3871994 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3871937 TTTTTACCAA
* *
3871947 TATATATTTTTAAATATTTTTAATT
1 TATATATATTTAAATATATTTAATT
3871972 TATATATATTTAAAGTA-ATTTAA
1 TATATATATTTAAA-TATATTTAA
3871995 AAAATCTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TATATATATTTAAATATATTTAATT
Found at i:3890618 original size:2 final size:2
Alignment explanation
Indices: 3890611--3890642 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3890601 AAATTCCATG
3890611 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
3890643 GCATCAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3891189 original size:2 final size:2
Alignment explanation
Indices: 3891182--3891208 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3891172 GGGTGATGTG
3891182 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
3891209 AACAATCCCC
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:3892660 original size:2 final size:2
Alignment explanation
Indices: 3892653--3892685 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3892643 TGGATACTTT
3892653 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3892686 GACAATGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3893026 original size:2 final size:2
Alignment explanation
Indices: 3893019--3893043 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3893009 TAAAAAGGCC
3893019 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3893044 TCTAAGATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3918633 original size:14 final size:14
Alignment explanation
Indices: 3918616--3918655 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
3918606 CTATCTTTTG
3918616 TTTATAATCTATAA
1 TTTATAATCTATAA
3918630 TTTATAAT-T-T-A
1 TTTATAATCTATAA
*
3918641 TTTTTAATCTATAA
1 TTTATAATCTATAA
3918655 T
1 T
3918656 CTATGTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
11 8 0.36
12 2 0.09
13 2 0.09
14 10 0.45
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATAATCTATAA
Found at i:3920198 original size:2 final size:2
Alignment explanation
Indices: 3920191--3920242 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
3920181 GTGCTATCCT
3920191 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3920232 TT TA TA TA TA T
1 TA TA TA TA TA T
3920243 CATTGCAAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:3926501 original size:14 final size:14
Alignment explanation
Indices: 3926467--3926494 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3926457 CTCCAACTAG
3926467 CTAAAAGTTAATTA
1 CTAAAAGTTAATTA
3926481 CTAAAAGTTAATTA
1 CTAAAAGTTAATTA
3926495 AGTAAAGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
CTAAAAGTTAATTA
Found at i:3927840 original size:7 final size:7
Alignment explanation
Indices: 3927828--3927855 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3927818 AATATTTAAC
3927828 AAATTTA
1 AAATTTA
3927835 AAATTTA
1 AAATTTA
3927842 AAATTTA
1 AAATTTA
3927849 AAATTTA
1 AAATTTA
3927856 CACCTACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAATTTA
Found at i:3929825 original size:2 final size:2
Alignment explanation
Indices: 3929818--3929847 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3929808 TGATAAAAAC
3929818 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
3929848 AATCATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3930028 original size:2 final size:2
Alignment explanation
Indices: 3930021--3930045 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3930011 AAGCTGACTT
3930021 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3930046 CTGTGTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3935219 original size:60 final size:60
Alignment explanation
Indices: 3935126--3935245 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
3935116 TTCACACCAT
3935126 TTCCTTACAACCAAACAATATAAACACTTCACAATTTTCACATGTCACTATAAATTCTAA
1 TTCCTTACAACCAAACAATATAAACACTTCACAATTTTCACATGTCACTATAAATTCTAA
3935186 TTCCTTACAACCAAACAATATAAACACTTCACAATTTTCACATGTCACTATAAATTCTAA
1 TTCCTTACAACCAAACAATATAAACACTTCACAATTTTCACATGTCACTATAAATTCTAA
3935246 CTTTCTTTTG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.42, C:0.25, G:0.02, T:0.32
Consensus pattern (60 bp):
TTCCTTACAACCAAACAATATAAACACTTCACAATTTTCACATGTCACTATAAATTCTAA
Found at i:3935238 original size:30 final size:30
Alignment explanation
Indices: 3935144--3935239 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 30
3935134 AACCAAACAA
3935144 TATAAACACTTCACAATTTTCACATGTCAC
1 TATAAACACTTCACAATTTTCACATGTCAC
* ** *
3935174 TAT-AA-A-TTC-TAATTCCTTACAACCA-AACAA
1 TATAAACACTTCACAATT--TT-C-A-CATGTCAC
3935204 TATAAACACTTCACAATTTTCACATGTCAC
1 TATAAACACTTCACAATTTTCACATGTCAC
3935234 TATAAA
1 TATAAA
3935240 TTCTAACTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 20
0.63 0.11 0.26
Matches are distributed among these distances:
26 4 0.08
27 3 0.06
28 3 0.06
29 5 0.10
30 18 0.38
31 5 0.10
32 3 0.06
33 3 0.06
34 4 0.08
ACGTcount: A:0.42, C:0.24, G:0.02, T:0.32
Consensus pattern (30 bp):
TATAAACACTTCACAATTTTCACATGTCAC
Found at i:3938324 original size:26 final size:26
Alignment explanation
Indices: 3938295--3938346 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3938285 CAGTCTTGAG
3938295 TCTCTTTGACATTTACTCTAAGTTTT
1 TCTCTTTGACATTTACTCTAAGTTTT
3938321 TCTCTTTGACATTTACTCTAAGTTTT
1 TCTCTTTGACATTTACTCTAAGTTTT
3938347 ATAATAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.08, T:0.54
Consensus pattern (26 bp):
TCTCTTTGACATTTACTCTAAGTTTT
Found at i:3944778 original size:14 final size:15
Alignment explanation
Indices: 3944749--3944778 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3944739 TTATTTTTCT
3944749 TTTTTTTTAAATAAA
1 TTTTTTTTAAATAAA
3944764 TTTTTTTTAAA-AAA
1 TTTTTTTTAAATAAA
3944778 T
1 T
3944779 AGAATAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTTTTAAATAAA
Found at i:3944975 original size:30 final size:30
Alignment explanation
Indices: 3944941--3945017 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
3944931 TATTTTGCTC
*
3944941 TCAAATAAATTTTTAACTTTTAATTTGTAT
1 TCAAATAAACTTTTAACTTTTAATTTGTAT
* *
3944971 TCAAATAAGCTTTTATCTTTTAATTTGTAT
1 TCAAATAAACTTTTAACTTTTAATTTGTAT
* *
3945001 TTAAATAAACCTTTAAC
1 TCAAATAAACTTTTAAC
3945018 ATAAATCAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.49
Consensus pattern (30 bp):
TCAAATAAACTTTTAACTTTTAATTTGTAT
Found at i:3945175 original size:14 final size:14
Alignment explanation
Indices: 3945156--3945187 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3945146 TATTTTAACT
3945156 TATTGTAAGATAAA
1 TATTGTAAGATAAA
3945170 TATTGTAAGATAAA
1 TATTGTAAGATAAA
3945184 TATT
1 TATT
3945188 AATTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (14 bp):
TATTGTAAGATAAA
Found at i:3945213 original size:20 final size:20
Alignment explanation
Indices: 3945180--3945218 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3945170 TATTGTAAGA
3945180 TAAATATTAATTTTTCAAAT
1 TAAATATTAATTTTTCAAAT
* *
3945200 TAAATTTTAGTTTTTCAAA
1 TAAATATTAATTTTTCAAA
3945219 GAACAACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (20 bp):
TAAATATTAATTTTTCAAAT
Found at i:3952976 original size:24 final size:23
Alignment explanation
Indices: 3952949--3953011 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
3952939 TTATTAATAA
*
3952949 TTTATAAAA-TAAATATATAATATT
1 TTTA-AAAATTAAATAAATAA-ATT
3952973 TTTAAAAATTAAATAAATAAA--
1 TTTAAAAATTAAATAAATAAATT
3952994 TTTAAAAA-TAAA-AAATAA
1 TTTAAAAATTAAATAAATAA
3953012 CATCATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 6 0.16
20 4 0.11
21 8 0.22
23 5 0.14
24 14 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TTTAAAAATTAAATAAATAAATT
Found at i:3952991 original size:32 final size:32
Alignment explanation
Indices: 3952932--3952994 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
3952922 ATTTTTATAT
* *
3952932 TATAATATTATTAATAATTTATAAAATAAATA
1 TATAATATTATTAAAAATTAATAAAATAAATA
*
3952964 TATAATATTTTTAAAAATTAA-ATAAATAAAT
1 TATAATATTATTAAAAATTAATA-AAATAAAT
3952995 TTAAAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
TATAATATTATTAAAAATTAATAAAATAAATA
Found at i:3953020 original size:21 final size:21
Alignment explanation
Indices: 3952975--3953021 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
3952965 ATAATATTTT
*
3952975 TAAAAATTAAATAAATAAATT
1 TAAAAATTAAATAAATAAATA
3952996 TAAAAA-TAAA-AAATAACATCA
1 TAAAAATTAAATAAATAA-AT-A
3953017 TAAAA
1 TAAAA
3953022 TTTTTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.26
20 6 0.26
21 11 0.48
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAAAATTAAATAAATAAATA
Found at i:3953223 original size:35 final size:35
Alignment explanation
Indices: 3953182--3953251 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
3953172 AAAAAAATAC
*
3953182 TTATAAA-TTTTAATTTTAAA-AAATAAATTATAAAA
1 TTATAAACTTTT-A-TTTAAAGAAATAAAGTATAAAA
3953217 TTATAAACTTTTATTTAAAGAAATAAAGTATAAAA
1 TTATAAACTTTTATTTAAAGAAATAAAGTATAAAA
3953252 GAGAATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 6 0.19
35 22 0.69
36 4 0.12
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (35 bp):
TTATAAACTTTTATTTAAAGAAATAAAGTATAAAA
Found at i:3953260 original size:17 final size:16
Alignment explanation
Indices: 3953233--3953276 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
3953223 ACTTTTATTT
3953233 AAAGAAATAAAGTATA
1 AAAGAAATAAAGTATA
*
3953249 AAAGAGAATAAATTATA
1 AAAGA-AATAAAGTATA
3953266 ATAA-AAATAAA
1 A-AAGAAATAAA
3953277 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 11 0.44
17 12 0.48
18 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (16 bp):
AAAGAAATAAAGTATA
Found at i:3954170 original size:30 final size:29
Alignment explanation
Indices: 3954131--3954222 Score: 71
Period size: 30 Copynumber: 3.1 Consensus size: 29
3954121 TAGGTTAAAA
*
3954131 AAATATTTAATATTTATTTTACATTCAAAT
1 AAATTTTTAAT-TTTATTTTACATTCAAAT
* *
3954161 AAATTTTTAACCTTTATTTTGC--TCAAAAAT
1 AAATTTTTAA-TTTTATTTTACATTC--AAAT
* * *
3954191 AAATTTTTTAATTTTAATTTATATCCAAAT
1 AAA-TTTTTAATTTTATTTTACATTCAAAT
3954221 AA
1 AA
3954223 GCTTTTGTCT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
28 2 0.04
30 38 0.79
31 7 0.15
32 1 0.02
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (29 bp):
AAATTTTTAATTTTATTTTACATTCAAAT
Found at i:3954407 original size:17 final size:16
Alignment explanation
Indices: 3954380--3954418 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
3954370 AAATTTATGA
*
3954380 AATTTTTTAATATTTT
1 AATTTTTTAATATTAT
3954396 AATTTATTTAATATTAT
1 AATTT-TTTAATATTAT
3954413 AATTTT
1 AATTTT
3954419 ATACCCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
AATTTTTTAATATTAT
Found at i:3956179 original size:20 final size:21
Alignment explanation
Indices: 3956133--3956183 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3956123 TTAAATAATT
**
3956133 TATAAAA-TAAAATTATTGGG
1 TATAAAATTAAAATTATTCAG
*
3956153 TAAAAAATTAAAATTATTCAG
1 TATAAAATTAAAATTATTCAG
3956174 -ATAAAATTAA
1 TATAAAATTAA
3956184 TATTTCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33
Consensus pattern (21 bp):
TATAAAATTAAAATTATTCAG
Found at i:3959151 original size:2 final size:2
Alignment explanation
Indices: 3959144--3959172 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3959134 TATTCCTATT
3959144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3959173 TAATATTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3967863 original size:16 final size:16
Alignment explanation
Indices: 3967842--3967876 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3967832 TATATATAAA
* *
3967842 TAATTTTAATAATTTT
1 TAATTTTAAAAATATT
3967858 TAATTTTAAAAATATT
1 TAATTTTAAAAATATT
3967874 TAA
1 TAA
3967877 AATATATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TAATTTTAAAAATATT
Found at i:3967870 original size:28 final size:28
Alignment explanation
Indices: 3967837--3967937 Score: 80
Period size: 30 Copynumber: 3.4 Consensus size: 28
3967827 TTTGATATAT
3967837 ATAAATAATTTTAATAATTTTTAATTTTA
1 ATAAAT-ATTTTAATAATTTTTAATTTTA
* * *
3967866 A-AAATATTTAAAATATATTATAAATTTTA
1 ATAAATATTT-TAATA-ATTTTTAATTTTA
*
3967895 ATATAATATTTTAATAACTTTATT-ATTATA
1 ATA-AATATTTTAATAA-TTT-TTAATTTTA
*
3967925 ATAATTAATTTTA
1 ATAAAT-ATTTTA
3967938 TCATTACTGC
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
27 4 0.07
28 8 0.14
29 16 0.28
30 21 0.37
31 8 0.14
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
ATAAATATTTTAATAATTTTTAATTTTA
Found at i:3975555 original size:2 final size:2
Alignment explanation
Indices: 3975548--3975604 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
3975538 GTTGATAACC
3975548 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3975590 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
3975605 GTGTTGTTGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3980070 original size:3 final size:3
Alignment explanation
Indices: 3980062--3980100 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3980052 ACTAAAACCA
3980062 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3980101 GGTGAGAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3982342 original size:13 final size:14
Alignment explanation
Indices: 3982324--3982356 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3982314 GAATTTTAAT
3982324 TATTTTA-AAATAA
1 TATTTTATAAATAA
*
3982337 TATTTTATTAATAA
1 TATTTTATAAATAA
3982351 TATTTT
1 TATTTT
3982357 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTTTATAAATAA
Found at i:3982349 original size:14 final size:14
Alignment explanation
Indices: 3982332--3982361 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3982322 ATTATTTTAA
3982332 AATAATATTTTATT
1 AATAATATTTTATT
*
3982346 AATAATATTTTTTT
1 AATAATATTTTATT
3982360 AA
1 AA
3982362 AAAAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATAATATTTTATT
Found at i:3983155 original size:20 final size:21
Alignment explanation
Indices: 3983122--3983160 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3983112 AATGAATATC
*
3983122 AAAATTTTAATTTTTATAATT
1 AAAATTTTAATTTTAATAATT
*
3983143 AAAA-TTTACTTTTAATAA
1 AAAATTTTAATTTTAATAA
3983161 CTTTAAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAATTTTAATTTTAATAATT
Found at i:3983842 original size:20 final size:22
Alignment explanation
Indices: 3983799--3983851 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
3983789 TTATTTTGAA
*
3983799 TAATATATATTTTTAAAATTTT
1 TAATATATATTTTTAAAATGTT
*
3983821 TAATAT-TA-TTTTAATATGTT
1 TAATATATATTTTTAAAATGTT
*
3983841 TAA-ATACATTT
1 TAATATATATTT
3983852 AAATATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 2 0.08
20 14 0.54
21 4 0.15
22 6 0.23
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TAATATATATTTTTAAAATGTT
Found at i:3983846 original size:21 final size:22
Alignment explanation
Indices: 3983800--3983846 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
3983790 TATTTTGAAT
*
3983800 AATATATATTTTTAAAATTTTT
1 AATATATATTTTTAAAATTTTA
*
3983822 AATAT-TA-TTTTAATATGTTTA
1 AATATATATTTTTAAAAT-TTTA
3983843 AATA
1 AATA
3983847 CATTTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
AATATATATTTTTAAAATTTTA
Found at i:3986183 original size:2 final size:2
Alignment explanation
Indices: 3986176--3986201 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3986166 CTGTTTTCGA
3986176 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
3986202 CTTTTGAAAA
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:3992432 original size:2 final size:2
Alignment explanation
Indices: 3992417--3992460 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
3992407 TTTCTTAAAG
3992417 AT AT -T AT A- 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
3992457 AT AT
1 AT AT
3992461 TGAGCATTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.