Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001838.1 Hibiscus syriacus cultivar Beakdansim tig00003721_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3924084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 18
Found at i:3720623 original size:18 final size:18
Alignment explanation
Indices: 3720618--3720686 Score: 120
Period size: 18 Copynumber: 3.8 Consensus size: 18
3720608 GTCAACGGGT
*
3720618 CGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCGGGTAAA
3720636 CGGGTCGGGTCGGGTAAA
1 CGGGTCGGGTCGGGTAAA
*
3720654 TGGGTCGGGTCGGGTAAA
1 CGGGTCGGGTCGGGTAAA
3720672 CGGGTCGGGTCGGGT
1 CGGGTCGGGTCGGGT
3720687 TGTGACCGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.12, C:0.17, G:0.52, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCGGGTAAA
Found at i:3720634 original size:23 final size:23
Alignment explanation
Indices: 3720581--3720650 Score: 95
Period size: 23 Copynumber: 2.9 Consensus size: 23
3720571 GACGGTCAAC
*
3720581 GGTCAACGGGTCGAGTCAACGGGTCG
1 GGTCAACGGGTCGGGT---CGGGTCG
*
3720607 AGTCAACGGGTCGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCGGGTCG
3720630 GGTCAACGGGTCGGGTCGGGT
1 GGTCAACGGGTCGGGTCGGGT
3720651 AAATGGGTCG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
23 27 0.66
26 14 0.34
ACGTcount: A:0.14, C:0.21, G:0.47, T:0.17
Consensus pattern (23 bp):
GGTCAACGGGTCGGGTCGGGTCG
Found at i:3720643 original size:13 final size:13
Alignment explanation
Indices: 3720581--3720646 Score: 93
Period size: 13 Copynumber: 5.3 Consensus size: 13
3720571 GACGGTCAAC
3720581 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
3720594 AGTCAACGGGTCG
1 GGTCAACGGGTCG
*
3720607 AGTCAACGGGTCG
1 GGTCAACGGGTCG
3720620 GGT---CGGGTCG
1 GGTCAACGGGTCG
3720630 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3720643 GGTC
1 GGTC
3720647 GGGTAAATGG
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
10 10 0.21
13 38 0.79
ACGTcount: A:0.15, C:0.23, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3724427 original size:18 final size:18
Alignment explanation
Indices: 3724404--3724438 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3724394 TTCCATCCGG
*
3724404 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
3724422 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
3724439 GTCCTTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:3725600 original size:18 final size:18
Alignment explanation
Indices: 3725577--3725650 Score: 86
Period size: 18 Copynumber: 4.4 Consensus size: 18
3725567 GTCGAGTCAA
3725577 CGGGTCGAGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
*
3725595 CGGGTCGGGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
3725613 CGGGT--A---AACGGGT
1 CGGGTCGAGTCAACGGGT
* *
3725626 CGGGTCGGGTAAACGGGT
1 CGGGTCGAGTCAACGGGT
3725644 CGGGTCG
1 CGGGTCG
3725651 GGTTGTGACC
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
13 12 0.25
18 36 0.75
ACGTcount: A:0.15, C:0.20, G:0.49, T:0.16
Consensus pattern (18 bp):
CGGGTCGAGTCAACGGGT
Found at i:3725611 original size:13 final size:13
Alignment explanation
Indices: 3725558--3725631 Score: 76
Period size: 13 Copynumber: 5.3 Consensus size: 13
3725548 GACGGTCAAC
3725558 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
3725571 AGTCAACGGGTCG
1 GGTCAACGGGTCG
*
3725584 AGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
3725602 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
3725615 GGTAAACGGGTCG
1 GGTCAACGGGTCG
3725628 GGTC
1 GGTC
3725632 GGGTAAACGG
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 40 0.77
18 12 0.23
ACGTcount: A:0.18, C:0.22, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3725646 original size:31 final size:31
Alignment explanation
Indices: 3725564--3725648 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
3725554 CAACGGTCAA
* * *
3725564 CGGGTCGAGTCAACGGGTCGAGTCAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTAAACGGGT
3725595 CGGGTCGGGTCAACGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTAAACGGGT
*
3725626 CGGGTCGGGTAAACGGGTCGGGT
1 CGGGTCGGGTCAACGGGTCGGGT
3725649 CGGGTTGTGA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.16, C:0.20, G:0.47, T:0.16
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCGGGTAAACGGGT
Found at i:3725651 original size:18 final size:18
Alignment explanation
Indices: 3725608--3725653 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
3725598 GTCGGGTCAA
3725608 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
3725626 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
3725644 CGGGTCGGGT
1 CGGGTCGGGT
3725654 TGTGACCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.13, C:0.17, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:3729044 original size:18 final size:17
Alignment explanation
Indices: 3729021--3729054 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3729011 AAATAAAAGT
3729021 TCAGTGTATACATGAGAG
1 TCAGTG-ATACATGAGAG
*
3729039 TCAGTGGTACATGAGA
1 TCAGTGATACATGAGA
3729055 TGAAGTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.26
Consensus pattern (17 bp):
TCAGTGATACATGAGAG
Found at i:3729479 original size:17 final size:17
Alignment explanation
Indices: 3729459--3729499 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
3729449 AACAATATAG
*
3729459 TAAAAGATATAATACAA
1 TAAAAGATATAAAACAA
3729476 TAAACA-ATATAAAACAA
1 TAAA-AGATATAAAACAA
3729493 TAAAAGA
1 TAAAAGA
3729500 ATTAGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 19 0.90
18 1 0.05
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (17 bp):
TAAAAGATATAAAACAA
Found at i:3739088 original size:20 final size:20
Alignment explanation
Indices: 3739063--3739101 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3739053 TTCATTCTAA
3739063 TTCATCCAATATCGATACTT
1 TTCATCCAATATCGATACTT
*
3739083 TTCATCCAGTATCGATACT
1 TTCATCCAATATCGATACT
3739102 CAAACCCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (20 bp):
TTCATCCAATATCGATACTT
Found at i:3741832 original size:10 final size:11
Alignment explanation
Indices: 3741804--3741831 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3741794 AAAAAAGACA
3741804 AAAAAAATTAG
1 AAAAAAATTAG
3741815 AAAAAAATTAG
1 AAAAAAATTAG
3741826 AAAAAA
1 AAAAAA
3741832 TGAGTTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (11 bp):
AAAAAAATTAG
Found at i:3747370 original size:78 final size:78
Alignment explanation
Indices: 3747287--3747448 Score: 306
Period size: 78 Copynumber: 2.1 Consensus size: 78
3747277 AGGATTCAGA
3747287 ATTTAATATAAATATTAAATTCATCAAAATAATTATCCTACTAATATTCAAATTAAATAATATCT
1 ATTTAATATAAATATTAAATTCATCAAAATAATTATCCTACTAATATTCAAATTAAATAATATCT
* *
3747352 TTTAATTTGTAAT
66 ATTAATTTATAAT
3747365 ATTTAATATAAATATTAAATTCATCAAAATAATTATCCTACTAATATTCAAATTAAATAATATCT
1 ATTTAATATAAATATTAAATTCATCAAAATAATTATCCTACTAATATTCAAATTAAATAATATCT
3747430 ATTAATTTATAAT
66 ATTAATTTATAAT
3747443 ATTTAA
1 ATTTAA
3747449 AAAAACTATA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 82 1.00
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.43
Consensus pattern (78 bp):
ATTTAATATAAATATTAAATTCATCAAAATAATTATCCTACTAATATTCAAATTAAATAATATCT
ATTAATTTATAAT
Found at i:3752163 original size:26 final size:25
Alignment explanation
Indices: 3752127--3752179 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
3752117 TATTTTAATC
3752127 ATATAAATAAA-AATAAATCGAATCAA
1 ATATAAATAAATAATAAATC-AAT-AA
*
3752153 ATATAATTAAATAATAAATCAATAA
1 ATATAAATAAATAATAAATCAATAA
3752178 AT
1 AT
3752180 CTTACATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 4 0.16
26 13 0.52
27 8 0.32
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (25 bp):
ATATAAATAAATAATAAATCAATAA
Found at i:3755076 original size:32 final size:32
Alignment explanation
Indices: 3755039--3755204 Score: 132
Period size: 30 Copynumber: 5.4 Consensus size: 32
3755029 AATTATTATT
*
3755039 TTTTATTTTCATCTTAACTTATTAAATATATA
1 TTTTATTTTTATCTTAACTTATTAAATATATA
* ** *
3755071 TTTTATTTTTGTCCAAACCTATT-AA-ATATA
1 TTTTATTTTTATCTTAACTTATTAAATATATA
* ** *
3755101 TTTTATTTTTGTCTCGACCTATTAAATATATA
1 TTTTATTTTTATCTTAACTTATTAAATATATA
*
3755133 TTTT-TTTTTATTTTAA-TGTA--AATATATATA
1 TTTTATTTTTATCTTAACT-TATTAA-ATATATA
** * *
3755163 TTTTACCTTTATCTTCACTTA-AAAATATAT-
1 TTTTATTTTTATCTTAACTTATTAAATATATA
3755193 TTTTATTTTTAT
1 TTTTATTTTTAT
3755205 TTTTTTAAAA
Statistics
Matches: 108, Mismatches: 19, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
29 2 0.02
30 46 0.43
31 30 0.28
32 30 0.28
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (32 bp):
TTTTATTTTTATCTTAACTTATTAAATATATA
Found at i:3756654 original size:57 final size:56
Alignment explanation
Indices: 3756582--3756691 Score: 143
Period size: 56 Copynumber: 1.9 Consensus size: 56
3756572 ATGCACACAC
3756582 CATGCATCGAAGCACT-GGGA-ATTTTATGAAAACATCAAATGCATTTGATGCATCAGT
1 CATGCATCGAAGCACTCGGGATA-TTT-TG-AAACATCAAATGCATTTGATGCATCAGT
* * * *
3756639 CATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTGATGCATC
1 CATGCATCGAAGCACTCGGGATATTTTGAAACATCAAATGCATTTGATGCATC
3756692 GATGCACTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
56 24 0.51
57 17 0.36
58 5 0.11
59 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (56 bp):
CATGCATCGAAGCACTCGGGATATTTTGAAACATCAAATGCATTTGATGCATCAGT
Found at i:3762484 original size:21 final size:21
Alignment explanation
Indices: 3762419--3762513 Score: 86
Period size: 23 Copynumber: 4.4 Consensus size: 21
3762409 TTGTGCTTAA
*
3762419 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-TG
*
3762439 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
* *
3762461 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAATG
* *
3762482 TGCACCGATGCACGCCTTGAATG
1 TGCATCGAT--ACACCTTGAATG
3762505 TGCATCGAT
1 TGCATCGAT
3762514 GCATCTATCG
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 17 0.28
22 13 0.22
23 19 0.32
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:3762507 original size:23 final size:23
Alignment explanation
Indices: 3762438--3762516 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 23
3762428 ACACCTAACA
*
3762438 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
3762460 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
3762481 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
3762504 GTGCATCGATGCA
1 GTGCATCGATGCA
3762517 TCTATCGGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.33
22 10 0.22
23 20 0.43
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.24
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:3762509 original size:44 final size:42
Alignment explanation
Indices: 3762419--3762513 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 42
3762409 TTGTGCTTAA
* *
3762419 TGCATCGATACACCTAACAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACCTAACAGTGCACCGATGCAGCCTTGAATG
*
3762461 TGCATCGATACACCATGAA-GGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACC-T-AACAGTGCACCGATGCA-GCCTTGAATG
3762505 TGCATCGAT
1 TGCATCGAT
3762514 GCATCTATCG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
42 14 0.30
43 13 0.28
44 20 0.43
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (42 bp):
TGCATCGATACACCTAACAGTGCACCGATGCAGCCTTGAATG
Found at i:3763860 original size:26 final size:26
Alignment explanation
Indices: 3763831--3763892 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
3763821 TGGACATCAT
*
3763831 AAACATTGTTCCTTCAAAACATGTTG
1 AAACATTGATCCTTCAAAACATGTTG
3763857 AAACATTGATCCTTCAAAACATGTTG
1 AAACATTGATCCTTCAAAACATGTTG
3763883 AAACATTGAT
1 AAACATTGAT
3763893 TTATGGATGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (26 bp):
AAACATTGATCCTTCAAAACATGTTG
Found at i:3765281 original size:65 final size:63
Alignment explanation
Indices: 3765164--3765365 Score: 230
Period size: 65 Copynumber: 3.1 Consensus size: 63
3765154 AGTGATTCAC
** * *
3765164 CGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATAGAATGCATTTCATGC
1 CGATGCA-CAA-CCATGCATCGATGCACTCA-GG-ATATTTTGAAACATCGAATGCATTTGATGC
3765227 AT
62 AT
*
3765229 CGATGCACACACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGCA
1 CGATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCATTTGATGCA
3765293 T
63 T
* * * *
3765294 CGATGCATCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCAT
1 CGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTGATGCAT
3765358 CGATGCAC
1 CGATGCAC
3765366 TCTTATTGCA
Statistics
Matches: 120, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 50 0.42
65 59 0.49
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
CGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTGATGCAT
Found at i:3766478 original size:20 final size:20
Alignment explanation
Indices: 3766453--3766490 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3766443 ACGTTTTTAG
3766453 TTTTTGCGTTGCGAATTTCA
1 TTTTTGCGTTGCGAATTTCA
*
3766473 TTTTTGTGTTGCGAATTT
1 TTTTTGCGTTGCGAATTT
3766491 AAGTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.11, G:0.21, T:0.55
Consensus pattern (20 bp):
TTTTTGCGTTGCGAATTTCA
Found at i:3768038 original size:42 final size:42
Alignment explanation
Indices: 3767991--3768089 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
3767981 CCCCTCACTT
* * *
3767991 CGAGAGCCATCACCTGATCAAGCCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCAAGCCGATTATACACCTCAACAC
* *
3768033 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCAACAT
1 CGAGAGCCATCACCTGATCAAGCCGATTATACACCTCAACAC
3768075 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
3768090 ATTCCATCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.17
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCAAGCCGATTATACACCTCAACAC
Found at i:3768233 original size:21 final size:21
Alignment explanation
Indices: 3768204--3768253 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3768194 GTTAGGGGAG
* *
3768204 TTACATGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
* *
3768225 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
3768246 TTACGTGA
1 TTACGTGA
3768254 CGATAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:3768319 original size:42 final size:43
Alignment explanation
Indices: 3768273--3768365 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 43
3768263 TACATGGCGT
**
3768273 GATGAGGTACGGT-CTTTACATGGTGAGGTAGCTGTTTTACGC
1 GATGAGGTACGGTGCTTTACATGGTGAGGTAGCTACTTTACGC
** * * * *
3768315 GATGA-AAATGGTGCTTTACGTGGTGAGGTATCTACTTTACGT
1 GATGAGGTACGGTGCTTTACATGGTGAGGTAGCTACTTTACGC
3768357 GATGAGGTA
1 GATGAGGTA
3768366 GCCGCTCTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
41 4 0.10
42 34 0.87
43 1 0.03
ACGTcount: A:0.23, C:0.12, G:0.32, T:0.33
Consensus pattern (43 bp):
GATGAGGTACGGTGCTTTACATGGTGAGGTAGCTACTTTACGC
Found at i:3768703 original size:21 final size:21
Alignment explanation
Indices: 3768674--3768745 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
3768664 ATTCACTTGT
*
3768674 CATCATTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
3768695 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* *
3768716 CATCGTTCAAGAAGCCCCTTC
1 CATCGTTCAAGAGGCCCCTCC
3768737 CATCGTTCA
1 CATCGTTCA
3768746 GGATCCACCT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.22, C:0.40, G:0.15, T:0.22
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:3768765 original size:42 final size:42
Alignment explanation
Indices: 3768679--3768766 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
3768669 CTTGTCATCA
* *
3768679 TTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTCCCATCG
1 TTCAAGAAGCCCCTCCCATCGTTCAAGAGGCCCCTCCCACCG
* * *
3768721 TTCAAGAAGCCCCTTCCATCGTTCAGGA-TCCACCTCCCACCG
1 TTCAAGAAGCCCCTCCCATCGTTCAAGAGGCC-CCTCCCACCG
3768763 TTCA
1 TTCA
3768767 GGATCCACAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 2 0.05
42 38 0.95
ACGTcount: A:0.20, C:0.42, G:0.16, T:0.22
Consensus pattern (42 bp):
TTCAAGAAGCCCCTCCCATCGTTCAAGAGGCCCCTCCCACCG
Found at i:3770396 original size:20 final size:20
Alignment explanation
Indices: 3770379--3770417 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3770369 CGATTTTCGT
3770379 GTTGCGAATTTGACTTTCAC
1 GTTGCGAATTTGACTTTCAC
* *
3770399 GTTGCAAATTTGACATTCA
1 GTTGCGAATTTGACTTTCA
3770418 ATTCAAGGCA
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:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTCAC
Found at i:3770644 original size:18 final size:18
Alignment explanation
Indices: 3770621--3770656 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3770611 AAGCCGGTTG
*
3770621 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
3770639 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
3770657 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:3773125 original size:12 final size:12
Alignment explanation
Indices: 3773104--3773137 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3773094 GGTTGTGGGT
*
3773104 TTTGAGATTGTG
1 TTTGATATTGTG
3773116 TTTGATATTGTG
1 TTTGATATTGTG
*
3773128 TTTGGTATTG
1 TTTGATATTG
3773138 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:3773947 original size:20 final size:20
Alignment explanation
Indices: 3773922--3773986 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
3773912 AAATAAAAGT
3773922 TGTTGCAAAATTAAAATTCG
1 TGTTGCAAAATTAAAATTCG
*
3773942 TGTTGC-GAATTCGAAAATT-G
1 TGTTGCAAAATT--AAAATTCG
* *
3773962 AGTTGCGAAAA-CAAAATTCG
1 TGTTGC-AAAATTAAAATTCG
3773982 TGTTG
1 TGTTG
3773987 TGAATTAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
19 10 0.29
20 17 0.49
21 6 0.17
22 2 0.06
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (20 bp):
TGTTGCAAAATTAAAATTCG
Found at i:3774007 original size:40 final size:39
Alignment explanation
Indices: 3773916--3774011 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 39
3773906 TTGCGAAAAT
* * *
3773916 AAAAGTTGTTGCAAAATTAAAATTCGTGTTGCGAATTCG
1 AAAATTTGTTGCAAAATCAAAATTCGTGTTGCGAATTAG
* *
3773955 AAAATTGAGTTGCGAAAA-CAAAATTCGTGTTGTGAATTAG
1 AAAATT-TGTTGC-AAAATCAAAATTCGTGTTGCGAATTAG
3773995 AAAATCTTGTTGCAAAA
1 AAAAT-TTGTTGCAAAA
3774012 AGGAAACTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
39 9 0.19
40 34 0.71
41 5 0.10
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (39 bp):
AAAATTTGTTGCAAAATCAAAATTCGTGTTGCGAATTAG
Found at i:3774112 original size:20 final size:21
Alignment explanation
Indices: 3774084--3774132 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
3774074 AAAATTCCGT
*
3774084 GTTGAGAATTTGG-AAATCGC
1 GTTGTGAATTTGGAAAATCGC
3774104 GTTGTGAATTTGGAAAATCGC
1 GTTGTGAATTTGGAAAATCGC
3774125 GTTGTGAA
1 GTTGTGAA
3774133 AAAGTAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.29, C:0.08, G:0.31, T:0.33
Consensus pattern (21 bp):
GTTGTGAATTTGGAAAATCGC
Found at i:3774206 original size:20 final size:20
Alignment explanation
Indices: 3774183--3774223 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3774173 TTTGGAAACT
3774183 GTGTTACGAAATTAGAGTTC
1 GTGTTACGAAATTAGAGTTC
* *
3774203 GTGTTGCGAATTTAGAGTTC
1 GTGTTACGAAATTAGAGTTC
3774223 G
1 G
3774224 CGTTGCGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.37
Consensus pattern (20 bp):
GTGTTACGAAATTAGAGTTC
Found at i:3774228 original size:20 final size:20
Alignment explanation
Indices: 3774189--3774235 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
3774179 AACTGTGTTA
* *
3774189 CGAAATTAGAGTTCGTGTTG
1 CGAATTTAGAGTTCGCGTTG
3774209 CGAATTTAGAGTTCGCGTTG
1 CGAATTTAGAGTTCGCGTTG
3774229 CGAATTT
1 CGAATTT
3774236 GTTAGTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (20 bp):
CGAATTTAGAGTTCGCGTTG
Found at i:3778484 original size:35 final size:33
Alignment explanation
Indices: 3778399--3778485 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 33
3778389 AATATAATTT
*
3778399 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATA-AACAAAATTACAATAAGAATTAAATGG
3778433 TAAAAGATAAAC-AAATTACAATAACTGATATTAAATGG
1 T--AA-ATAAACAAAATTACAATAA--GA-ATTAAATGG
3778471 T-AATAAACAAAATTA
1 TAAATAAACAAAATTA
3778486 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
34 7 0.16
35 18 0.40
36 5 0.11
37 5 0.11
38 10 0.22
ACGTcount: A:0.57, C:0.09, G:0.08, T:0.25
Consensus pattern (33 bp):
TAAATAAACAAAATTACAATAAGAATTAAATGG
Found at i:3779102 original size:18 final size:18
Alignment explanation
Indices: 3779079--3779129 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
3779069 AAGGTGGCGA
*
3779079 CATCATATATGGTTGAGG
1 CATCATAAATGGTTGAGG
*
3779097 CATCATAAATGGTTGCGG
1 CATCATAAATGGTTGAGG
3779115 CATCATAAATGGTTG
1 CATCATAAATGGTTG
3779130 TGGTGGCTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (18 bp):
CATCATAAATGGTTGAGG
Found at i:3780845 original size:18 final size:19
Alignment explanation
Indices: 3780822--3780858 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3780812 TAGTGAAACA
3780822 TTAAATAAAGTAAA-ATAT
1 TTAAATAAAGTAAATATAT
*
3780840 TTAAATAAATTAAATATAT
1 TTAAATAAAGTAAATATAT
3780859 AATATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TTAAATAAAGTAAATATAT
Found at i:3784979 original size:51 final size:54
Alignment explanation
Indices: 3784880--3784981 Score: 138
Period size: 55 Copynumber: 1.9 Consensus size: 54
3784870 AACAATTATA
* * *
3784880 TTTCATATGAATAAAGAAAGTATCCTTACAAATTTTCTCTCTTCCATAAGTGGAC
1 TTTCATATAAACAAAGAAAGTATCCTTAC-AAGTTTCTCTCTTCCATAAGTGGAC
*
3784935 TTTCATATAAACAAAGAAAGTATCCTTGC-AGTTT-T-TCTTCCATAAGT
1 TTTCATATAAACAAAGAAAGTATCCTTACAAGTTTCTCTCTTCCATAAGT
3784982 CTACTTCACC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 12 0.28
52 1 0.02
53 4 0.09
55 26 0.60
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (54 bp):
TTTCATATAAACAAAGAAAGTATCCTTACAAGTTTCTCTCTTCCATAAGTGGAC
Found at i:3796913 original size:3 final size:3
Alignment explanation
Indices: 3796905--3796950 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3796895 GATTTTTATT
3796905 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3796951 GTTGAAACCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3800045 original size:18 final size:18
Alignment explanation
Indices: 3800018--3800055 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3800008 AAAAGCTCCT
*
3800018 TTCTTTCTTCATCTTCTC
1 TTCTTCCTTCATCTTCTC
*
3800036 TTCTTCCTTCATTTTCTC
1 TTCTTCCTTCATCTTCTC
3800054 TT
1 TT
3800056 AACTCAAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (18 bp):
TTCTTCCTTCATCTTCTC
Found at i:3804769 original size:9 final size:9
Alignment explanation
Indices: 3804745--3804775 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
3804735 AATATAAATC
3804745 AAAATAAAA
1 AAAATAAAA
3804754 AAGAATAAAA
1 AA-AATAAAA
3804764 AAAATAAAA
1 AAAATAAAA
3804773 AAA
1 AAA
3804776 TTTACATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (9 bp):
AAAATAAAA
Found at i:3810426 original size:24 final size:25
Alignment explanation
Indices: 3810399--3810448 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
3810389 GTGCTACAAT
* *
3810399 AAAAAAACAACAAG-AAAGAAGAAG
1 AAAAAAACAAAAAGAAAAGAAAAAG
3810423 AAAAAAACAAAAAGAAAAGAAAAAG
1 AAAAAAACAAAAAGAAAAGAAAAAG
3810448 A
1 A
3810449 CTTCTACATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (25 bp):
AAAAAAACAAAAAGAAAAGAAAAAG
Found at i:3810532 original size:24 final size:24
Alignment explanation
Indices: 3810477--3810525 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
3810467 AGTGCAAAAG
* *
3810477 AAAGAAAAGAAAAAGAAGAATCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
*
3810501 AAAGCAAAGAAAAAG-TGAAGCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
3810524 AA
1 AA
3810526 TTGCAAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.04
Consensus pattern (24 bp):
AAAGCAAAGAAAAAGAAGAAGCAA
Found at i:3828197 original size:20 final size:19
Alignment explanation
Indices: 3828108--3828207 Score: 67
Period size: 20 Copynumber: 4.8 Consensus size: 19
3828098 AGGGTGTCAA
*
3828108 AGTGCATCCATGCACTCCTGC
1 AGTGCATCGATGCA--CCTGC
*
3828129 AGTGCATCG-TGCACACTTGT
1 AGTGCATCGATGCAC-C-TGC
* *
3828149 AGTGGATCGATGTACCTGCCAC
1 AGTGCATCGATGCACCTG---C
3828171 TAGTGCATCGATGCACCATGC
1 -AGTGCATCGATGCACC-TGC
*
3828192 AGTGCATCCATGCACC
1 AGTGCATCGATGCACC
3828208 CCATTTCGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
18 1 0.02
19 3 0.05
20 30 0.48
21 13 0.21
23 14 0.22
24 2 0.03
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCACCTGC
Found at i:3830794 original size:21 final size:21
Alignment explanation
Indices: 3830770--3830809 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3830760 ATATTTAATG
3830770 AAAAAGATAACAATTGTTAAC
1 AAAAAGATAACAATTGTTAAC
* *
3830791 AAAATGATATCAATTGTTA
1 AAAAAGATAACAATTGTTA
3830810 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATAACAATTGTTAAC
Found at i:3831380 original size:21 final size:21
Alignment explanation
Indices: 3831346--3831385 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3831336 AAAAAATTGG
*
3831346 TAACAATTGATATCATTTTGT
1 TAACAATTCATATCATTTTGT
* *
3831367 TAACAATTCTTATCTTTTT
1 TAACAATTCATATCATTTT
3831386 CATTAAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (21 bp):
TAACAATTCATATCATTTTGT
Found at i:3834286 original size:21 final size:21
Alignment explanation
Indices: 3834247--3834286 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3834237 AAACAATTGG
*
3834247 TAACAATTGATGTCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
3834268 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
3834287 CATTAAACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:3834598 original size:20 final size:20
Alignment explanation
Indices: 3834509--3834609 Score: 89
Period size: 20 Copynumber: 4.8 Consensus size: 20
3834499 AGGGTGTCAA
*
3834509 AGTGCATCCATGCACTCCTGC
1 AGTGCATCGATGCAC-CCTGC
3834530 AGTGCATCG-TGCACACCTGC
1 AGTGCATCGATGCAC-CCTGC
* *
3834550 AGTGGATCGATGTA-CCTGCCAC
1 AGTGCATCGATGCACCCTG---C
*
3834572 TAGTGCATCGATGCACCATGC
1 -AGTGCATCGATGCACCCTGC
*
3834593 AGTGCATCCATGCACCC
1 AGTGCATCGATGCACCC
3834610 CATTTTGAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 4 0.06
20 33 0.51
21 12 0.18
22 1 0.02
23 12 0.18
24 3 0.05
ACGTcount: A:0.22, C:0.34, G:0.23, T:0.22
Consensus pattern (20 bp):
AGTGCATCGATGCACCCTGC
Found at i:3846722 original size:21 final size:21
Alignment explanation
Indices: 3846696--3846735 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3846686 CACCCTTTGA
*
3846696 AGGGGAACCGATTCCCCCCGC
1 AGGGGAACCGATACCCCCCGC
*
3846717 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
3846736 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.28, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCGC
Found at i:3851134 original size:31 final size:31
Alignment explanation
Indices: 3851096--3851158 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
3851086 CATGCATCTA
*
3851096 ATCTTTATTATGTTTAGTAGCGTCCATTTTT
1 ATCTTTATTATATTTAGTAGCGTCCATTTTT
*
3851127 ATCTTTATTATATTTAGTAGTGTCCATTTTT
1 ATCTTTATTATATTTAGTAGCGTCCATTTTT
3851158 A
1 A
3851159 GTCTGTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (31 bp):
ATCTTTATTATATTTAGTAGCGTCCATTTTT
Found at i:3851549 original size:55 final size:55
Alignment explanation
Indices: 3851485--3851595 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
3851475 TTGATAATTC
3851485 AAACCTTTTTTCTTTTAATGAAATTGAACCTGAAAAATCATTCCTTAGCACATGT
1 AAACCTTTTTTCTTTTAATGAAATTGAACCTGAAAAATCATTCCTTAGCACATGT
*
3851540 AAACCTTTTTTCTTTTAATGAAATTGAATCTGAAAAATCATTCCTTAGCACATGT
1 AAACCTTTTTTCTTTTAATGAAATTGAACCTGAAAAATCATTCCTTAGCACATGT
3851595 A
1 A
3851596 TAAACATATA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (55 bp):
AAACCTTTTTTCTTTTAATGAAATTGAACCTGAAAAATCATTCCTTAGCACATGT
Found at i:3852522 original size:51 final size:51
Alignment explanation
Indices: 3852438--3852557 Score: 197
Period size: 51 Copynumber: 2.4 Consensus size: 51
3852428 TCCTTTTTGC
* * *
3852438 AAAGGGATCGAT-CATTTTTCTAGAAAATGCAAGGGATCAATCCTTTTCTT
1 AAAGGGATCGATCCTTTTTTCTAGAAAATGCAAGGAATCAATCCTTCTCTT
*
3852488 AAAGGGATTGATCCTTTTTTCTAGAAAATGCAAGGAATCAATCCTTCTCTT
1 AAAGGGATCGATCCTTTTTTCTAGAAAATGCAAGGAATCAATCCTTCTCTT
3852539 AAAGGGATCGATCCTTTTT
1 AAAGGGATCGATCCTTTTT
3852558 ATGAAAAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
50 11 0.17
51 53 0.83
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (51 bp):
AAAGGGATCGATCCTTTTTTCTAGAAAATGCAAGGAATCAATCCTTCTCTT
Found at i:3853470 original size:15 final size:16
Alignment explanation
Indices: 3853452--3853486 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3853442 AATTTTCAAA
3853452 TCAAAAATTTC-TTTT
1 TCAAAAATTTCATTTT
*
3853467 TCAAAATTTTCATTTT
1 TCAAAAATTTCATTTT
3853483 TCAA
1 TCAA
3853487 TTTTGAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (16 bp):
TCAAAAATTTCATTTT
Found at i:3853978 original size:11 final size:11
Alignment explanation
Indices: 3853946--3853994 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
3853936 TTGAAGGCTA
3853946 TTCTTACTTC-C
1 TTCTT-CTTCTC
3853957 TTCTT-TT-TC
1 TTCTTCTTCTC
*
3853966 TTGTTCTTCTC
1 TTCTTCTTCTC
3853977 TTCTTCTTC-C
1 TTCTTCTTCTC
3853987 TTCTTCTT
1 TTCTTCTT
3853995 TTGGAGTCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 7 0.21
10 11 0.33
11 15 0.45
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.65
Consensus pattern (11 bp):
TTCTTCTTCTC
Found at i:3855724 original size:19 final size:19
Alignment explanation
Indices: 3855702--3855769 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 19
3855692 CTATATTTAA
3855702 AAATTATTTAAAATTAAAT
1 AAATTATTTAAAATTAAAT
*
3855721 AAA-TAGTTTAAAAAT-AAT
1 AAATTA-TTTAAAATTAAAT
*
3855739 --ATTATTTTAAA-TAAAT
1 AAATTATTTAAAATTAAAT
*
3855755 AAATAATTTAAAATT
1 AAATTATTTAAAATT
3855770 TAAACCTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
15 1 0.03
16 10 0.26
17 2 0.05
18 14 0.36
19 12 0.31
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (19 bp):
AAATTATTTAAAATTAAAT
Found at i:3855837 original size:23 final size:23
Alignment explanation
Indices: 3855777--3855838 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
3855767 ATTTAAACCT
*
3855777 TAAATAAATATTTTTATAATATTA
1 TAAATATA-ATTTTTATAATATTA
* *
3855801 TAAATATACTTTTTATAATTATTT
1 TAAATATAATTTTTATAA-TATTA
*
3855825 TATATA-AATTTTTA
1 TAAATATAATTTTTA
3855839 AAAAATATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TAAATATAATTTTTATAATATTA
Found at i:3855837 original size:24 final size:23
Alignment explanation
Indices: 3855777--3855837 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
3855767 ATTTAAACCT
3855777 TAAATAAATATTTTTATAATATTA
1 TAAATAAAT-TTTTTATAATATTA
* * *
3855801 TAAATATACTTTTTATAATTATTT
1 TAAATAAATTTTTTATAA-TATTA
*
3855825 TATATAAATTTTT
1 TAAATAAATTTTT
3855838 AAAAAATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TAAATAAATTTTTTATAATATTA
Found at i:3865758 original size:20 final size:22
Alignment explanation
Indices: 3865721--3865760 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3865711 GTGCTATAAT
*
3865721 TTTTTTATAGTATAAATTATGA
1 TTTTTTATAGAATAAATTATGA
3865743 TTTTTTATA-AAT-AATTAT
1 TTTTTTATAGAATAAATTAT
3865761 AATTGGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TTTTTTATAGAATAAATTATGA
Found at i:3868058 original size:35 final size:35
Alignment explanation
Indices: 3868019--3868114 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 35
3868009 AACACAATCA
* * *
3868019 TCAATTACATTCTAAACCCCAAATTCCAAAATAGT
1 TCAATTACATACTAAACCCCAAATTCCAAAACACT
* * *
3868054 TCAATTACATCCTAAACCTCAAATTCTAAAACACT
1 TCAATTACATACTAAACCCCAAATTCCAAAACACT
* **
3868089 TTAATTACATACCCAACCCCAAATTC
1 TCAATTACATACTAAACCCCAAATTC
3868115 ATAATCCATT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.42, C:0.29, G:0.01, T:0.28
Consensus pattern (35 bp):
TCAATTACATACTAAACCCCAAATTCCAAAACACT
Found at i:3868871 original size:148 final size:148
Alignment explanation
Indices: 3868601--3868897 Score: 540
Period size: 148 Copynumber: 2.0 Consensus size: 148
3868591 AAACTATTTA
* * *
3868601 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
**
3868666 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAATTTTCGAGTCAACT
66 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAACT
3868731 ATTTTATAAACTGAATTG
131 ATTTTATAAACTGAATTG
*
3868749 AATTATAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
3868814 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAACT
66 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAACT
3868879 ATTTTATAAACTGAATTG
131 ATTTTATAAACTGAATTG
3868897 A
1 A
3868898 GCATTTAGGT
Statistics
Matches: 143, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
148 143 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (148 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAACT
ATTTTATAAACTGAATTG
Found at i:3869113 original size:35 final size:34
Alignment explanation
Indices: 3869058--3869153 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 34
3869048 AAGGGATTAT
* * *
3869058 GAATTTGGGGTTGAGCATGTAATTGAAGTATTTTG
1 GAATTT-GGGTTTAGAATGTAATTGAAGCATTTTG
3869093 GAATTTGAGGTTTAGAATGTAATTGAAGCATTTTG
1 GAATTTG-GGTTTAGAATGTAATTGAAGCATTTTG
* *
3869128 GATTTTGGGATGTAGAATGTAATTGA
1 GAATTTGGG-TTTAGAATGTAATTGA
3869154 TGATTGTGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
34 3 0.06
35 51 0.94
ACGTcount: A:0.29, C:0.02, G:0.29, T:0.40
Consensus pattern (34 bp):
GAATTTGGGTTTAGAATGTAATTGAAGCATTTTG
Found at i:3871865 original size:2 final size:2
Alignment explanation
Indices: 3871858--3871888 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3871848 TAAACTTTAT
3871858 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3871889 TATATACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3873532 original size:2 final size:2
Alignment explanation
Indices: 3873525--3873556 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3873515 TGATAAACCA
3873525 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
3873557 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3873561 original size:2 final size:2
Alignment explanation
Indices: 3873556--3873604 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3873546 TCTCTCTCTC
3873556 TA TA 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 TA TA
3873598 TA TA TA T
1 TA TA TA T
3873605 TAAAATAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3877426 original size:11 final size:11
Alignment explanation
Indices: 3877410--3877434 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3877400 AAATTTATTT
3877410 TTAAAAAAATA
1 TTAAAAAAATA
3877421 TTAAAAAAATA
1 TTAAAAAAATA
3877432 TTA
1 TTA
3877435 TATTTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TTAAAAAAATA
Found at i:3879464 original size:31 final size:29
Alignment explanation
Indices: 3879428--3879503 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
3879418 TACAAACAGG
*
3879428 AATTTAAGGGAATAAAATTGGAAAAAATAGA
1 AATTTAAGGGAATAAAA-TAG-AAAAATAGA
* * *
3879459 CATTTAAAGGACTAAAATAGAAAAATAGA
1 AATTTAAGGGAATAAAATAGAAAAATAGA
* *
3879488 AACTTAAGGGATTAAA
1 AATTTAAGGGAATAAA
3879504 TAGTGAATAC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 21 0.57
30 2 0.05
31 14 0.38
ACGTcount: A:0.57, C:0.04, G:0.17, T:0.22
Consensus pattern (29 bp):
AATTTAAGGGAATAAAATAGAAAAATAGA
Found at i:3879494 original size:29 final size:29
Alignment explanation
Indices: 3879450--3879563 Score: 97
Period size: 29 Copynumber: 3.9 Consensus size: 29
3879440 TAAAATTGGA
* *
3879450 AAAAATAGACATTTAAAGGACTAAAATAG
1 AAAAATAGAAACTTAAAGGACTAAAATAG
* *
3879479 AAAAATAGAAACTTAAGGGA-TTAAATAG
1 AAAAATAGAAACTTAAAGGACTAAAATAG
** *
3879507 -TGAATACAAACATTTAAAGGACTAAAATAG
1 AAAAATAGAAAC--TTAAAGGACTAAAATAG
* * *
3879537 CAAAAACAAAAACTTAAGGGACTAAAA
1 -AAAAATAGAAACTTAAAGGACTAAAA
3879564 CAACAAAAAC
Statistics
Matches: 66, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
27 8 0.12
28 7 0.11
29 24 0.36
30 20 0.30
32 7 0.11
ACGTcount: A:0.58, C:0.09, G:0.14, T:0.19
Consensus pattern (29 bp):
AAAAATAGAAACTTAAAGGACTAAAATAG
Found at i:3879546 original size:30 final size:30
Alignment explanation
Indices: 3879392--3879592 Score: 124
Period size: 30 Copynumber: 6.7 Consensus size: 30
3879382 GAATGGGAAC
* * *
3879392 AACAAAAACTTAAAGGACCAAAATA-CTACA
1 AACAAAAATTTAAAGGACTAAAATAGC-AAA
** * * * *
3879422 AACAGGAATTTAAGGGAATAAAATTGGAAA
1 AACAAAAATTTAAAGGACTAAAATAGCAAA
*
3879452 AA-ATAGACATTTAAAGGACTAAAATAG-AAA
1 AACA-A-AAATTTAAAGGACTAAAATAGCAAA
* * * * * **
3879482 AATAGAAACTTAAGGGA-TTAAATAGTGAA
1 AACAAAAATTTAAAGGACTAAAATAGCAAA
* *
3879511 TACAAACATTTAAAGGACTAAAATAGCAAA
1 AACAAAAATTTAAAGGACTAAAATAGCAAA
* * * *
3879541 AACAAAAACTTAAGGGACTAAAACAACAAA
1 AACAAAAATTTAAAGGACTAAAATAGCAAA
3879571 AACAAAAATTTTAAA-GACTAAA
1 AACAAAAA-TTTAAAGGACTAAA
3879593 CTGATATTGA
Statistics
Matches: 126, Mismatches: 38, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
28 7 0.06
29 23 0.18
30 75 0.60
31 21 0.17
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.18
Consensus pattern (30 bp):
AACAAAAATTTAAAGGACTAAAATAGCAAA
Found at i:3880501 original size:15 final size:16
Alignment explanation
Indices: 3880475--3880504 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3880465 GTTGATTGGT
3880475 TCTTTTTATTTTTCTA
1 TCTTTTTATTTTTCTA
3880491 TCTTTTT-TTTTTCT
1 TCTTTTTATTTTTCT
3880505 TTTGCTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (16 bp):
TCTTTTTATTTTTCTA
Found at i:3881153 original size:3 final size:3
Alignment explanation
Indices: 3881145--3881204 Score: 81
Period size: 3 Copynumber: 20.7 Consensus size: 3
3881135 AATAATTTAT
*
3881145 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA T-A TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
3881190 TAA T-A TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TA
3881205 TTTTTTCGAG
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 6 0.12
3 42 0.82
4 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3881168 original size:18 final size:17
Alignment explanation
Indices: 3881135--3881204 Score: 97
Period size: 18 Copynumber: 4.1 Consensus size: 17
3881125 AAACTGTAAC
* *
3881135 AATAATTTATTAATAAT
1 AATAATATAATAATAAT
3881152 AATAATTATAATAATAAT
1 AATAA-TATAATAATAAT
3881170 AATAATATAATAATAAAT
1 AATAATATAATAAT-AAT
3881188 AATAATATAAT-ATAAT
1 AATAATATAATAATAAT
3881204 A
1 A
3881205 TTTTTTCGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
16 4 0.08
17 16 0.33
18 29 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATAATATAATAATAAT
Found at i:3881672 original size:131 final size:130
Alignment explanation
Indices: 3881370--3882014 Score: 659
Period size: 131 Copynumber: 4.9 Consensus size: 130
3881360 ACACGACTCA
* * * ** * * * *
3881370 TACGTGATGAAGAGGACTAGTCGTCTAAGGGTGACACAGCTCCTACGTGATGATGAGATCTTGTC
1 TACGTGATGAGGACGACTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTC
* ** * * * * * *
3881435 GGTGGATGACA-TATCTCATACGTGATGAAGA-GTTTTGGCCTTCTTTAGGAAGGGGTGATAACA
66 GG-GGATAACACGGT-TCCTACGTGATGAGGATG-ATAGGCCATCTTT----AGGGATGATAACA
*
3881498 CGATTCC
124 CGGTTCC
* * * *
3881505 TACGCGATGAGGACGACTAGTTATCTAGGGGTGACACGGCTCCTACGTGTTGAGGAGGTCTGGTC
1 TACGTGATGAGGACGACTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTC
* * *
3881570 GGTGGATAACACGGTTCCTATGTGATGAGGATGATAGGCTATTTTTAGGGATGATAACACGGTTC
66 GG-GGATAACACGGTTCCTACGTGATGAGGATGATAGGCCATCTTTAGGGATGATAACACGGTTC
3881635 C
130 C
* *
3881636 TACGTGATGAGGATGGA-TGGTTATCTAAGGGTGACACGGCTCCTACGTGATGATGAGGTCTGGT
1 TACGTGATGAGGA-CGACTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGT
** * * *
3881700 CAGGGGATAACACAATTCCTACGTGATGAGTATGGTAGGCCATCTTTAGGGATGATAACATGGTT
65 C-GGGGATAACACGGTTCCTACGTGATGAGGATGATAGGCCATCTTTAGGGATGATAACACGGTT
*
3881765 TC
129 CC
* * * * * * *
3881767 AACATGATGAGGACAACTGGTTATCTAAGGGTGACATGGCTCCTACGTAATAAAGAGGTCTGGTC
1 TACGTGATGAGGACGACTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTC
* ** * *
3881832 GGGGGATGACACGGTTCCTACGTGATGAGGATGATATACCACCTTTAGGGATGATAACACTGTTC
66 -GGGGATAACACGGTTCCTACGTGATGAGGATGATAGGCCATCTTTAGGGATGATAACACGGTTC
3881897 C
130 C
* * * * *
3881898 TACGTGATGATGAC-AGTTGGTTATCTGAGGGTGACACGACTCCTACGTGATGAGGAGGTCTGTT
1 TACGTGATGAGGACGA-CTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGT
* * *
3881962 CGGAGGATGACACGGTTCCTACGTGATGAGGACGATAGGCCATCTTTAAGGAT
65 CGG-GGATAACACGGTTCCTACGTGATGAGGATGATAGGCCATCTTTAGGGAT
3882015 AATGGTTTCA
Statistics
Matches: 428, Mismatches: 75, Indels: 18
0.82 0.14 0.03
Matches are distributed among these distances:
130 4 0.01
131 333 0.78
132 4 0.01
135 85 0.20
136 2 0.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (130 bp):
TACGTGATGAGGACGACTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTC
GGGGATAACACGGTTCCTACGTGATGAGGATGATAGGCCATCTTTAGGGATGATAACACGGTTCC
Found at i:3882209 original size:68 final size:63
Alignment explanation
Indices: 3882112--3882271 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 63
3882102 CAAAGGTAAT
* *
3882112 AAAACTTGTTTCAAGAGAAACAAACTCAAAGATGGGTTGT-TTCAAGAGAA-ACTGTCTCAAGAG
1 AAAATTTGTTTTAAGAGAAACAAACTCAAAG-T---TTGTCTT-AA-AGAAGACTGTCTCAAGAG
3882175 AGAC
60 AGAC
* ** *
3882179 AAAATTTTGTTTTAAGAGAAATAATTTCAAAGTTTGTCTTAAAGAAGACTGTCTCAAGTGAGAC
1 AAAA-TTTGTTTTAAGAGAAACAAACTCAAAGTTTGTCTTAAAGAAGACTGTCTCAAGAGAGAC
* * *
3882243 AAAATTTGTTTTGAGAAAAACAATCTCAA
1 AAAATTTGTTTTAAGAGAAACAAACTCAA
3882272 GTGAGATCAA
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
63 25 0.31
64 26 0.32
65 2 0.03
67 5 0.06
68 22 0.28
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (63 bp):
AAAATTTGTTTTAAGAGAAACAAACTCAAAGTTTGTCTTAAAGAAGACTGTCTCAAGAGAGAC
Found at i:3883829 original size:4 final size:4
Alignment explanation
Indices: 3883803--3883845 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
3883793 AGCTTTATTG
* * * *
3883803 TATA CATA TACA TACA TACA TATA TATA TATA TATA TATA TAT
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TAT
3883846 TCTGGGTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:3883845 original size:6 final size:6
Alignment explanation
Indices: 3883803--3883845 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
3883793 AGCTTTATTG
* * * *
3883803 TATACA TATACA TACATA CATATA TATATA TATATA TATATA T
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA T
3883846 TCTGGGTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (6 bp):
TATATA
Found at i:3888361 original size:30 final size:30
Alignment explanation
Indices: 3888260--3888390 Score: 117
Period size: 30 Copynumber: 4.4 Consensus size: 30
3888250 AAACAAATAT
*
3888260 TTAAAGGACTAAAATAG-AAAAATAGAAAC
1 TTAAGGGACTAAAATAGAAAAAATAGAAAC
** * * * *
3888289 TTAAGGGAC-AAAATAGTGAATACAGACAT
1 TTAAGGGACTAAAATAGAAAAAATAGAAAC
3888318 TTATA-GGACTAAAATAGAAAAAATAGAAAC
1 TTA-AGGGACTAAAATAGAAAAAATAGAAAC
* *
3888348 TTAAGGGATTAAAATA-ACAAAAATAGAAAT
1 TTAAGGGACTAAAATAGA-AAAAATAGAAAC
**
3888378 TTAAAAGACTAAA
1 TTAAGGGACTAAA
3888391 CTGGTATTAA
Statistics
Matches: 80, Mismatches: 17, Indels: 9
0.75 0.16 0.08
Matches are distributed among these distances:
28 7 0.09
29 24 0.30
30 49 0.61
ACGTcount: A:0.58, C:0.07, G:0.15, T:0.21
Consensus pattern (30 bp):
TTAAGGGACTAAAATAGAAAAAATAGAAAC
Found at i:3889005 original size:22 final size:22
Alignment explanation
Indices: 3888977--3889026 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
3888967 GCCCTACACC
3888977 GACGGCACCTATGGTGGCCCAT
1 GACGGCACCTATGGTGGCCCAT
3888999 GACGGCACCTATGGTGGCCCAT
1 GACGGCACCTATGGTGGCCCAT
3889021 GACGGC
1 GACGGC
3889027 GTACGGTGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.18, C:0.32, G:0.34, T:0.16
Consensus pattern (22 bp):
GACGGCACCTATGGTGGCCCAT
Found at i:3889927 original size:3 final size:3
Alignment explanation
Indices: 3889919--3889995 Score: 79
Period size: 3 Copynumber: 26.3 Consensus size: 3
3889909 GTAAAAAATG
* * * * *
3889919 TAA TAA TAA T-T TAA TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3889966 T-A TAA TAA TAA TAA TAA TAAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA T
3889996 TTTTTTCGAG
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 5 0.08
3 58 0.88
4 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:3896832 original size:18 final size:15
Alignment explanation
Indices: 3896796--3896861 Score: 105
Period size: 15 Copynumber: 4.4 Consensus size: 15
3896786 GTCACCTTAT
3896796 CCACCATCTTATTCA
1 CCACCATCTTATTCA
3896811 CCACCATCTTATTCA
1 CCACCATCTTATTCA
*
3896826 CCACCACCTTATTCA
1 CCACCATCTTATTCA
* *
3896841 TCACCATCTTATTTA
1 CCACCATCTTATTCA
3896856 CCACCA
1 CCACCA
3896862 AAGAAGGAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.27, C:0.41, G:0.00, T:0.32
Consensus pattern (15 bp):
CCACCATCTTATTCA
Found at i:3896863 original size:129 final size:130
Alignment explanation
Indices: 3896683--3896987 Score: 427
Period size: 129 Copynumber: 2.3 Consensus size: 130
3896673 CATCCTTTCT
* * * *
3896683 CACCGCCTTATTTA-CACACACCTTATTCATCAACATCTTATTCACCCCCAAAGAAGGAAAAACA
1 CACCACCTTATTCACCAC-CACCTTATTCATCACCATCTTATTCACCACCAAAGAAGGAAAAACA
* *
3896747 CGAATACAAATCACCAAAGTATGAGAAACCCAAAGAGAAGTCACCTTAT-CCACCATCTTATTCA
65 CGAATACAAATCACCAAAGTACGAGAAACCCAAAGAGAAGTCACCTTATCCCACCATCCTATTCA
3896811 C
130 C
* *
3896812 CACCATCTTATTCACCACCACCTTATTCATCACCATCTTATTTACCACCAAAGAAGGAAAAACAC
1 CACCACCTTATTCACCACCACCTTATTCATCACCATCTTATTCACCACCAAAGAAGGAAAAACAC
* *
3896877 GAATACAAATCGCCAAAGTACGAGAAACCCAAATAGAAGTCACCTTATCCACCACCATCCTATTC
66 GAATACAAATCACCAAAGTACGAGAAACCCAAAGAGAAGTCACCTTAT-C-CCACCATCCTATTC
3896942 AC
129 AC
* ** *
3896944 CACCACCTTATTCATCACCGTCTTATTCA-CACACACCTTATTCA
1 CACCACCTTATTCACCACCACCTTATTCATCAC-CATCTTATTCA
3896988 TCACTGTCGA
Statistics
Matches: 155, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
129 100 0.65
130 3 0.02
131 3 0.02
132 49 0.32
ACGTcount: A:0.37, C:0.32, G:0.07, T:0.23
Consensus pattern (130 bp):
CACCACCTTATTCACCACCACCTTATTCATCACCATCTTATTCACCACCAAAGAAGGAAAAACAC
GAATACAAATCACCAAAGTACGAGAAACCCAAAGAGAAGTCACCTTATCCCACCATCCTATTCAC
Found at i:3896946 original size:15 final size:15
Alignment explanation
Indices: 3896926--3896973 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
3896916 TCACCTTATC
3896926 CACCACCATCCTATT
1 CACCACCATCCTATT
3896941 CACCACCA-CCTTATT
1 CACCACCATCC-TATT
* * *
3896956 CATCACCGTCTTATT
1 CACCACCATCCTATT
3896971 CAC
1 CAC
3896974 ACACACCTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 2 0.07
15 24 0.89
16 1 0.04
ACGTcount: A:0.25, C:0.44, G:0.02, T:0.29
Consensus pattern (15 bp):
CACCACCATCCTATT
Found at i:3896983 original size:15 final size:15
Alignment explanation
Indices: 3896937--3896987 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
3896927 ACCACCATCC
3896937 TATTCAC-CACCACCT
1 TATTCACACA-CACCT
**
3896952 TATTCATCAC-CGTCT
1 TATTCA-CACACACCT
3896967 TATTCACACACACCT
1 TATTCACACACACCT
3896982 TATTCA
1 TATTCA
3896988 TCACTGTCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 3 0.10
15 24 0.83
16 1 0.03
17 1 0.03
ACGTcount: A:0.27, C:0.37, G:0.02, T:0.33
Consensus pattern (15 bp):
TATTCACACACACCT
Found at i:3896985 original size:30 final size:30
Alignment explanation
Indices: 3896917--3896991 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
3896907 AAATAGAAGT
* *
3896917 CACCTTATCCACCACCATCCTATTCACCAC
1 CACCTTATTCATCACCATCCTATTCACCAC
* *
3896947 CACCTTATTCATCACCGTCTTATTCA-CAC
1 CACCTTATTCATCACCATCCTATTCACCAC
3896976 ACACCTTATTCATCAC
1 -CACCTTATTCATCAC
3896992 TGTCGACACC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 3 0.08
30 37 0.93
ACGTcount: A:0.27, C:0.43, G:0.01, T:0.29
Consensus pattern (30 bp):
CACCTTATTCATCACCATCCTATTCACCAC
Found at i:3898538 original size:20 final size:20
Alignment explanation
Indices: 3898502--3898540 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3898492 AAACCATTAA
* *
3898502 GGGGGAATCGGTTCCCTATT
1 GGGGGAATCGATACCCTATT
3898522 GGGGGAATCGATACCCTAT
1 GGGGGAATCGATACCCTAT
3898541 GAGTAAACTG
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:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATACCCTATT
Found at i:3898570 original size:75 final size:75
Alignment explanation
Indices: 3898447--3898593 Score: 222
Period size: 75 Copynumber: 2.0 Consensus size: 75
3898437 CGTTACACAG
* * * *
3898447 GGGGGAATCGGTACCCTCCGAGTAATCTGTTATTTCTTGGAGCCAAAACCATTAAGGGGGAATCG
1 GGGGGAATCGATACCCTACGAGTAAACTGTTATTTCTCGGAGCCAAAACCATTAAGGGGGAATCG
*
3898512 GTTCCCTATT
66 GTACCCTATT
* * *
3898522 GGGGGAATCGATACCCTATGAGTAAACTGTTATTTCTCGGAGCCAAAACCTTTCAGGGGGAATCG
1 GGGGGAATCGATACCCTACGAGTAAACTGTTATTTCTCGGAGCCAAAACCATTAAGGGGGAATCG
3898587 GTACCCT
66 GTACCCT
3898594 CTGAGTAAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (75 bp):
GGGGGAATCGATACCCTACGAGTAAACTGTTATTTCTCGGAGCCAAAACCATTAAGGGGGAATCG
GTACCCTATT
Found at i:3898758 original size:19 final size:20
Alignment explanation
Indices: 3898734--3898771 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3898724 AATTTAATCG
*
3898734 AATATATAAT-TTAAAATTT
1 AATATAAAATCTTAAAATTT
3898753 AATATAAAATCTTAAAATT
1 AATATAAAATCTTAAAATT
3898772 CATTACACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTT
Found at i:3900636 original size:13 final size:13
Alignment explanation
Indices: 3900620--3900653 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3900610 AATGGGTAAT
*
3900620 TTTGAAAACTAGG
1 TTTGAAAACAAGG
3900633 TTTGAAAACAAGG
1 TTTGAAAACAAGG
3900646 TTTGAAAA
1 TTTGAAAA
3900654 TCAATATACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (13 bp):
TTTGAAAACAAGG
Found at i:3901176 original size:23 final size:23
Alignment explanation
Indices: 3901148--3901193 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
3901138 TTCCCATTTA
* *
3901148 AAGGGGAAATCGGTTCC-CCTGC
1 AAGGGGGAATCGATTCCTCCTGC
*
3901170 AAGGGGGTATCGATTCCTCCTGC
1 AAGGGGGAATCGATTCCTCCTGC
3901193 A
1 A
3901194 CTAAAATTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (23 bp):
AAGGGGGAATCGATTCCTCCTGC
Found at i:3909506 original size:42 final size:41
Alignment explanation
Indices: 3909414--3909515 Score: 134
Period size: 42 Copynumber: 2.5 Consensus size: 41
3909404 CCCGAAGGTC
* * *
3909414 TTATGGATGGCCCGAAGGATTTAACATCTTGCTCGAAAGAA
1 TTATAGATGGCCCGAAGGATTTAAAATCATGCTCGAAAGAA
* *
3909455 TTATAGATGGCTCGAAGGATTTAAGAATCATGCTCGAAAGAC
1 TTATAGATGGCCCGAAGGATTTAA-AATCATGCTCGAAAGAA
3909497 TTACT-GATGGCCCGAAGGA
1 TTA-TAGATGGCCCGAAGGA
3909516 CTTACTCATA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 22 0.42
42 30 0.57
43 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (41 bp):
TTATAGATGGCCCGAAGGATTTAAAATCATGCTCGAAAGAA
Found at i:3909620 original size:39 final size:39
Alignment explanation
Indices: 3909577--3910183 Score: 449
Period size: 39 Copynumber: 15.7 Consensus size: 39
3909567 TGTTTCATGC
* * *
3909577 GAAACTATCTCAAGCGAGACAAAATATTATATTTCGAGG
1 GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGG
* *
3909616 GAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGATG
1 GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGG
* * * *
3909655 GAAACTATCTCAGGCGAGATAAAATATTTTGTTTCGAGC
1 GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGG
*
3909694 GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCAAGG
1 GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGG
*
3909733 GAAA-TAATCTCAAGCGAGATAAAATCTTTTGTTTCGAGG
1 GAAACT-ATCTCAAGCGAGATAAAATCTTATGTTTCGAGG
*
3909772 GAAACTATCTCAAGCGAGACAAAATCTTATGTTTCGAGG
1 GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGG
*
3909811 GAAACTATCTCAAGCGAGATAAAATATTA--TTT--A--
1 GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGG
* * ** * * * *
3909844 AAAACAATCTTGAGTGAAATGAAATGTCTTA--TTTCGAGTA
1 GAAACTATCTCAAGCGAGAT-AAA-ATCTTATGTTTCGAG-G
* ** * * * *
3909884 AAAACCGTATCAAGCGAGA-CAAATC-T-TGTTT-TAAG
1 GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGG
* * ** * * * *
3909919 AAAAATAATCTTGAGTGAAAT-AAATCTTCTTGTTTCGAGTA
1 GAAACT-ATCTCAAGCGAGATAAAATCTT-ATGTTTCGAG-G
* * * * * *
3909960 AAAACCATCTCAAGCGAGAT-AAATCTTGTTTTTTTTGAGA
1 GAAACTATCTCAAGCGAGATAAAATC-T-TATGTTTCGAGG
* * ** * * * *
3910000 AAAACGATCTTGAGTGAAAT-AAATCTTCTTGTTTCGAGT
1 GAAACTATCTCAAGCGAGATAAAATCTT-ATGTTTCGAGG
* * * *
3910039 AAAATCTGTCTCAAGTGAGA-CAAATCTTATGTTTCGAGG
1 GAAA-CTATCTCAAGCGAGATAAAATCTTATGTTTCGAGG
*
3910078 GAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGG
1 GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGG
* *
3910117 GAAACTATCTCAAACGAGATAAAATCTGT-TGTTTCAAGG
1 GAAACTATCTCAAGCGAGATAAAATCT-TATGTTTCGAGG
* *
3910156 GAAACTATCTCAAGAGAGATAAATTCTT
1 GAAACTATCTCAAGCGAGATAAAATCTT
3910184 CTTTAAAAAC
Statistics
Matches: 458, Mismatches: 85, Indels: 51
0.77 0.14 0.09
Matches are distributed among these distances:
33 14 0.03
34 3 0.01
35 12 0.03
36 14 0.03
37 10 0.02
38 18 0.04
39 305 0.67
40 68 0.15
41 13 0.03
42 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (39 bp):
GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGG
Found at i:3909934 original size:76 final size:77
Alignment explanation
Indices: 3909843--3910066 Score: 299
Period size: 80 Copynumber: 2.9 Consensus size: 77
3909833 AATATTATTT
* * *
3909843 AAAAACAATCTTGAGTGAAATGAAAT-GTCTTATTTCGAGTAAAAACCGTATCAAGCGAGACAAA
1 AAAAACAATCTTGAGTGAAAT-AAATCTTCTTGTTTCGAGTAAAAACCGTCTCAAGCGAGACAAA
3909907 TCTTG-TTTTAAG
65 TCTTGTTTTTAAG
* * *
3909919 AAAAATAATCTTGAGTGAAATAAATCTTCTTGTTTCGAGTAAAAACCATCTCAAGCGAGATAAAT
1 AAAAACAATCTTGAGTGAAATAAATCTTCTTGTTTCGAGTAAAAACCGTCTCAAGCGAGACAAAT
*
3909984 CTTGTTTTTTTTGAG
66 CTTG---TTTTTAAG
* * * *
3909999 AAAAACGATCTTGAGTGAAATAAATCTTCTTGTTTCGAGTAAAATCTGTCTCAAGTGAGACAAAT
1 AAAAACAATCTTGAGTGAAATAAATCTTCTTGTTTCGAGTAAAAACCGTCTCAAGCGAGACAAAT
3910064 CTT
66 CTT
3910067 ATGTTTCGAG
Statistics
Matches: 129, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
75 4 0.03
76 58 0.45
80 67 0.52
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (77 bp):
AAAAACAATCTTGAGTGAAATAAATCTTCTTGTTTCGAGTAAAAACCGTCTCAAGCGAGACAAAT
CTTGTTTTTAAG
Found at i:3917534 original size:15 final size:15
Alignment explanation
Indices: 3917443--3917534 Score: 78
Period size: 15 Copynumber: 6.1 Consensus size: 15
3917433 AAAGAGAAAT
*
3917443 CACCTTATACACCAC
1 CACCTTATTCACCAC
**
3917458 CATTTTATTCACCAC
1 CACCTTATTCACCAC
* *
3917473 AACCTTATTCATCAC
1 CACCTTATTCACCAC
*
3917488 CGCCTTATTCA-CAC
1 CACCTTATTCACCAC
* **
3917502 ACACCTTATTTAAAAC
1 -CACCTTATTCACCAC
*
3917518 CATCTTATTCACCAC
1 CACCTTATTCACCAC
3917533 CA
1 CA
3917535 AAATATGAGA
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
14 3 0.05
15 54 0.92
16 2 0.03
ACGTcount: A:0.32, C:0.37, G:0.01, T:0.30
Consensus pattern (15 bp):
CACCTTATTCACCAC
Found at i:3919162 original size:3 final size:3
Alignment explanation
Indices: 3919147--3919185 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
3919137 AACCCGCCCT
*
3919147 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3919186 AATTAGTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Done.