Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 15 of 105
Found at i:3002450 original size:17 final size:18
Alignment explanation
Indices: 3002410--3002451 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
3002400 GGACTAGGTA
3002410 GGGTGGCTGTCTGATGGTT
1 GGGTGGCTGTCTGATGG-T
*
3002429 AGGGTGGCTGTCTGGTGG-
1 -GGGTGGCTGTCTGATGGT
3002447 GGGTG
1 GGGTG
3002452 AGCAGAGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
20 16 0.76
ACGTcount: A:0.05, C:0.10, G:0.55, T:0.31
Consensus pattern (18 bp):
GGGTGGCTGTCTGATGGT
Found at i:3003197 original size:13 final size:12
Alignment explanation
Indices: 3003179--3003226 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
3003169 TCGACCGAGT
3003179 AAATAAAAACAAA
1 AAATAAAAA-AAA
3003192 AAATAAAAAAAA
1 AAATAAAAAAAA
*
3003204 AACTAAACTAAAAA
1 AAATAAA--AAAAA
*
3003218 TAATAAAAA
1 AAATAAAAA
3003227 TGCTTTGGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 11 0.37
13 9 0.30
14 10 0.33
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (12 bp):
AAATAAAAAAAA
Found at i:3008946 original size:17 final size:17
Alignment explanation
Indices: 3008909--3008947 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3008899 TATTAATTAA
* *
3008909 AAAAATATAAAAAATAC
1 AAAAATACAAAAAAAAC
*
3008926 AAAAATACAAAAAAAAT
1 AAAAATACAAAAAAAAC
3008943 AAAAA
1 AAAAA
3008948 AAGGGTCGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (17 bp):
AAAAATACAAAAAAAAC
Found at i:3008949 original size:9 final size:9
Alignment explanation
Indices: 3008907--3008949 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
3008897 TTTATTAATT
3008907 AAAAAAATA
1 AAAAAAATA
*
3008916 TAAAAAATA
1 AAAAAAATA
* *
3008925 CAAAAATACA
1 -AAAAAAATA
3008935 AAAAAAATA
1 AAAAAAATA
3008944 AAAAAA
1 AAAAAA
3008950 GGGTCGGAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
9 21 0.78
10 6 0.22
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAATA
Found at i:3010069 original size:21 final size:21
Alignment explanation
Indices: 3010027--3010070 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3010017 TTTTATTTTC
* **
3010027 TTTAAATATTATTTTTGTTAT
1 TTTAAATATTATTATTAATAT
*
3010048 TTTAAATTTTATTATTAATAT
1 TTTAAATATTATTATTAATAT
3010069 TT
1 TT
3010071 ATACATGTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTAAATATTATTATTAATAT
Found at i:3010214 original size:10 final size:10
Alignment explanation
Indices: 3010201--3010235 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3010191 TAAATCTTTT
*
3010201 AAAATAACAA
1 AAAATAAGAA
3010211 AAAATAAGAA
1 AAAATAAGAA
*
3010221 AAAACAAGAA
1 AAAATAAGAA
3010231 AAAAT
1 AAAAT
3010236 TTTTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.80, C:0.06, G:0.06, T:0.09
Consensus pattern (10 bp):
AAAATAAGAA
Found at i:3010967 original size:5 final size:5
Alignment explanation
Indices: 3010957--3011037 Score: 62
Period size: 5 Copynumber: 15.8 Consensus size: 5
3010947 TTATCTAAAG
3010957 AAAAT AAAATAT AAAAT AAAAT AAAAT AAAAAT AAAAAT AAAA- AATAA-
1 AAAAT -AAA-AT AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAAT AA-AAT
* *
3011005 AAAAT AAAGA- AGAA- AAATT AAAAT AAAAT AAAA
1 AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAA
3011038 AATTAAACAA
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
4 7 0.11
5 38 0.58
6 18 0.28
7 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:3010972 original size:7 final size:7
Alignment explanation
Indices: 3010957--3011095 Score: 68
Period size: 7 Copynumber: 18.1 Consensus size: 7
3010947 TTATCTAAAG
3010957 AAAATAA
1 AAAATAA
*
3010964 AATATAA
1 AAAATAA
3010971 AATAA-AA
1 AA-AATAA
3010978 TAAAAT-A
1 -AAAATAA
3010985 AAAAT-A
1 AAAATAA
3010991 AAAATAA
1 AAAATAA
3010998 AAAATAA
1 AAAATAA
3011005 AAAATAA
1 AAAATAA
* *
3011012 AGAAGAA
1 AAAATAA
*
3011019 AAATTAAAA
1 AAA--ATAA
3011028 TAAAATAA
1 -AAAATAA
3011036 AAAATTAA
1 AAAA-TAA
*
3011044 ACAATTCTAA
1 A-AA--ATAA
3011054 TAATAATAA
1 -AA-AATAA
3011063 TAATAATAA
1 -AA-AATAA
*
3011072 TAAATAA
1 AAAATAA
3011079 ATAAATAA
1 A-AAATAA
3011087 ATAAATAA
1 A-AAATAA
3011095 A
1 A
3011096 TAACGAAAAA
Statistics
Matches: 107, Mismatches: 11, Indels: 27
0.74 0.08 0.19
Matches are distributed among these distances:
6 11 0.10
7 44 0.41
8 26 0.24
9 17 0.16
10 7 0.07
11 2 0.02
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (7 bp):
AAAATAA
Found at i:3010974 original size:12 final size:11
Alignment explanation
Indices: 3010957--3011038 Score: 80
Period size: 11 Copynumber: 7.4 Consensus size: 11
3010947 TTATCTAAAG
3010957 AAAATAAAATA
1 AAAATAAAATA
3010968 TAAAATAAAAT-
1 -AAAATAAAATA
3010979 AAAATAAAAATA
1 AAAAT-AAAATA
3010991 AAAATAAAA-A
1 AAAATAAAATA
*
3011001 ATAA-AAAATA
1 AAAATAAAATA
* *
3011011 AAGAAGAAAAATT
1 AA-AA-TAAAATA
3011024 AAAATAAAATA
1 AAAATAAAATA
3011035 AAAA
1 AAAA
3011039 ATTAAACAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
9 4 0.07
10 11 0.19
11 20 0.34
12 17 0.29
13 7 0.12
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:3010990 original size:6 final size:6
Alignment explanation
Indices: 3010957--3011038 Score: 82
Period size: 6 Copynumber: 13.7 Consensus size: 6
3010947 TTATCTAAAG
3010957 AAAAT- AAAATA TAAAAT- AAAAT- AAAATA AAAATA AAAATAA AAAATAA
1 AAAATA AAAATA -AAAATA AAAATA AAAATA AAAATA AAAAT-A AAAAT-A
* *
3011005 AAAATA AAGAAGA AAAATT AAAAT- AAAATA AAAA
1 AAAATA AA-AATA AAAATA AAAATA AAAATA AAAA
3011039 ATTAAACAAT
Statistics
Matches: 68, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
5 20 0.29
6 25 0.37
7 23 0.34
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:3011039 original size:12 final size:12
Alignment explanation
Indices: 3010957--3011095 Score: 81
Period size: 12 Copynumber: 11.1 Consensus size: 12
3010947 TTATCTAAAG
*
3010957 AAAATAAAATAT
1 AAAATAAAATAA
3010969 AAAATAAAATAA
1 AAAATAAAATAA
*
3010981 AATA-AAAATAA
1 AAAATAAAATAA
*
3010992 AAATAAAAAATAA
1 AAA-ATAAAATAA
3011005 AAAATAAAGA-AGA
1 AAAATAAA-ATA-A
3011018 AAAATTAAAATAA
1 AAAA-TAAAATAA
3011031 AATAA-AAAATTAA
1 AA-AATAAAA-TAA
* **
3011044 ACAATTCTAATAA
1 A-AAATAAAATAA
3011057 TAATAATAATAATAA
1 -AA-AATAA-AATAA
*
3011072 TAAAT-AAATAA
1 AAAATAAAATAA
3011083 ATAAAT-AAATAA
1 A-AAATAAAATAA
3011095 A
1 A
3011096 TAACGAAAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 28
0.72 0.09 0.20
Matches are distributed among these distances:
11 14 0.14
12 36 0.36
13 32 0.32
14 14 0.14
15 5 0.05
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:3011079 original size:4 final size:4
Alignment explanation
Indices: 3011070--3011098 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3011060 TAATAATAAT
3011070 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
3011099 CGAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:3011922 original size:26 final size:23
Alignment explanation
Indices: 3011885--3011996 Score: 91
Period size: 26 Copynumber: 4.6 Consensus size: 23
3011875 CCTAATCTTA
*
3011885 ATAAAAAATTAATCAAAATAAAAAG
1 ATAAATAATTAAT-AAAA-AAAAAG
*
3011910 ATAAATATATTAATAGATAAAAAAAA
1 ATAAATA-ATTAATA-A-AAAAAAAG
* *
3011936 ATAATTAAATAAATAAAAAAAAAG
1 ATAAAT-AATTAATAAAAAAAAAG
*
3011960 ATAAATAA-TAATAAAAAATAAAA
1 ATAAATAATTAATAAAAAA-AAAG
* *
3011983 ATAGATAAATAATA
1 ATAAATAATTAATA
3011997 TAAATATTAA
Statistics
Matches: 72, Mismatches: 9, Indels: 13
0.77 0.10 0.14
Matches are distributed among these distances:
22 9 0.12
23 12 0.17
24 17 0.24
25 8 0.11
26 23 0.32
27 3 0.04
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (23 bp):
ATAAATAATTAATAAAAAAAAAG
Found at i:3011958 original size:23 final size:22
Alignment explanation
Indices: 3011900--3012074 Score: 101
Period size: 23 Copynumber: 7.8 Consensus size: 22
3011890 AAATTAATCA
* *
3011900 AAATAAAAAGATAAATATATTAAT
1 AAATAAAAA-AAAAATA-ATAAAT
*
3011924 AGAT-AAAAAAAAATAATTAAAT
1 AAATAAAAAAAAAATAA-TAAAT
3011946 AAATAAAAAAAAAGATAA-ATAAT
1 AAATAAAAAAAAA-ATAATA-AAT
* *
3011969 -AATAAAAAATAAA-AATAGAT
1 AAATAAAAAAAAAATAATAAAT
* * * *
3011989 AAATAATATAAATATTAATAGAT
1 AAATAA-AAAAAAAATAATAAAT
*
3012012 AAA-AAAATAAAAAATATATTAAT
1 AAATAAAA-AAAAAATA-ATAAAT
* * *
3012035 AAATAGACAAATAATAA-AAAT
1 AAATAAAAAAAAAATAATAAAT
3012056 AAAATAAAAATAAAAATAA
1 -AAATAAAAA-AAAAATAA
3012075 AAGCCTCTTG
Statistics
Matches: 116, Mismatches: 22, Indels: 27
0.70 0.13 0.16
Matches are distributed among these distances:
20 4 0.03
21 12 0.10
22 45 0.39
23 46 0.40
24 9 0.08
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (22 bp):
AAATAAAAAAAAAATAATAAAT
Found at i:3011958 original size:27 final size:28
Alignment explanation
Indices: 3011928--3012076 Score: 92
Period size: 29 Copynumber: 5.2 Consensus size: 28
3011918 ATTAATAGAT
3011928 AAAAAAAAATAAT-TAAATAAATAAAAA
1 AAAAAAAAATAATATAAATAAATAAAAA
*
3011955 AAAAGATAAATAATAATAAA-AAATAAAAA
1 AAAA-AAAAATAAT-ATAAATAAATAAAAA
* * *
3011984 TAGATAAATAATATAAATATTAATAGATAAAAA
1 -A-A-AAA-AAAAT-AATATAAATAAATAAAAA
* *
3012017 AATAAAAAAT-ATATTAATAAATAGACAAA
1 AAAAAAAAATAATATAAATAAATA-A-AAA
* * *
3012046 TAATAAAAATAAAAT-AA-AAATAAAAA
1 AAAAAAAAATAATATAAATAAATAAAAA
*
3012072 TAAAA
1 AAAAA
3012077 GCCTCTTGGG
Statistics
Matches: 97, Mismatches: 13, Indels: 25
0.72 0.10 0.19
Matches are distributed among these distances:
26 7 0.07
27 17 0.18
28 14 0.14
29 25 0.26
30 10 0.10
31 3 0.03
32 10 0.10
33 11 0.11
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (28 bp):
AAAAAAAAATAATATAAATAAATAAAAA
Found at i:3011999 original size:5 final size:4
Alignment explanation
Indices: 3011900--3012063 Score: 78
Period size: 4 Copynumber: 41.8 Consensus size: 4
3011890 AAATTAATCA
* * * *
3011900 AAAT AAA- AAGAT AAAT ATAT TAAT AGAT AAA- AAA- AAAT AATT AAAT
1 AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
3011946 AAAT AAA- AAAA AAGAT AAAT -AAT -AAT AAA- AAAT -AA- AAAT AGAT
1 AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
3011989 AAAT AATAT AAAT ATTAAT AGAT AAAA AAAT AAA- AAAT ATAT TAAT AAAT
1 AAAT AA-AT AAAT A--AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
3012039 AGAC AAAT AATAA AAAT AAAAT AAA
1 AAAT AAAT AA-AT AAAT -AAAT AAA
3012064 AATAAAAATA
Statistics
Matches: 120, Mismatches: 25, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
3 27 0.22
4 73 0.61
5 16 0.13
6 4 0.03
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:3012051 original size:84 final size:80
Alignment explanation
Indices: 3011884--3012074 Score: 192
Period size: 84 Copynumber: 2.4 Consensus size: 80
3011874 TCCTAATCTT
** * * * *
3011884 AATAAAAAATTAATCAAAATAAAAA-GATA-AATATATTAATAGATAAAAAAAAATAATTAAATA
1 AATAAAAAAAAAATAAAAATAAAAATAATATAA-ATATTAATAGATAAAAAAAAAAAAATAAATA
3011947 AATAAAAAAAAAGATA
65 AATAAAAAAAAAGATA
3011963 AATAATAATAAAAAATAAAAATAGATAAATAATATAAATATTAATAGATAAAAAAATAAAAAATA
1 AATAA-AA-AAAAAATAAAAATA-A-AAATAATATAAATATTAATAGATAAAAAAA-AAAAAATA
* * * *
3012028 TATTAATAAATAGACAA-AT-
61 AATAAATAAA-AAAAAAGATA
*
3012047 AATAAAAATAAAATAAAAATAAAAATAA
1 AATAAAAAAAAAATAAAAATAAAAATAA
3012075 AAGCCTCTTG
Statistics
Matches: 93, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
79 5 0.05
80 8 0.09
81 12 0.13
82 14 0.15
83 5 0.05
84 27 0.29
85 18 0.19
86 4 0.04
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (80 bp):
AATAAAAAAAAAATAAAAATAAAAATAATATAAATATTAATAGATAAAAAAAAAAAAATAAATAA
ATAAAAAAAAAGATA
Found at i:3012061 original size:11 final size:12
Alignment explanation
Indices: 3012047--3012076 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
3012037 ATAGACAAAT
3012047 AATAAAAAT-AA
1 AATAAAAATAAA
3012058 AATAAAAATAAA
1 AATAAAAATAAA
3012070 AATAAAA
1 AATAAAA
3012077 GCCTCTTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
AATAAAAATAAA
Found at i:3012064 original size:5 final size:6
Alignment explanation
Indices: 3012047--3012076 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3012037 ATAGACAAAT
3012047 AATAAA AAT-AA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA AATAAA A
3012077 GCCTCTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:3012465 original size:39 final size:40
Alignment explanation
Indices: 3012339--3012901 Score: 366
Period size: 42 Copynumber: 13.2 Consensus size: 40
3012329 AATAGACAAA
* * *
3012339 GCTCCTTTAAACAGAGGCTCCACGA-TCTTGAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACT-TTGAAAATAAATG
* *
3012379 GCTCCCCCTAATCAGAGGCTCAATGACTTTGAAAAATAAATG
1 GCT-CCTCTAATCAGAGGCTCAACGACTTTG-AAAATAAATG
* * * *
3012421 GCTCCTCTGATCAGAGGCTCCATGAC-TTCAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAATAAATG
3012460 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAATAAATG
* **
3012500 GCTCATCTAATCAGA-GCTCAACGACTTTGAAAATGAACAAA
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAT-AA-ATG
* **
3012541 GCTCCTCTAATAAGAGGCTCAACGACGTTTGAAAATGAATAAA
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAT-AA-ATG
* * *
3012584 GCTCCTCTAATCCAAAGGGCCTCAACGACTTTTAAAAAAATAAATAAA
1 GCTCCTCTAAT-CAGA-GG-CTCAACGAC-TTT--GAAAATAAAT--G
* * *
3012632 GCTCCTCTAATAAGAGGGTCAACGGACTTTTGGAAAAAATAAATAAA
1 GCTCCTCTAATCAGAGGCTCAAC-GAC-TTT-G--AAAATAAAT--G
* *
3012679 GCTCCTCTAAACAGAGGCGACCAA--ACTTTGAAAAGTAAATTG
1 GCTCCTCTAATCAGAGGC--TCAACGACTTTGAAAA-TAAA-TG
* * * *
3012721 GCTCCTCTAAACAGAGGCCTTAACGACTTTAGAAATTAAATT
1 GCTCCTCTAATCAGAGG-CTCAACGACTTT-GAAAATAAATG
*
3012763 GCTCCTCTAAAT-AGAGGCTCCAACGACTTTGGAGAAAAAAAATG
1 GCTCCTCT-AATCAGAGGCT-CAACGACTTT---GAAAATAAATG
* * *
3012807 AAAGATCCTCTAAACAGAGGCTCAACGACTTTTGAAAAATACAAATT
1 ---GCTCCTCTAATCAGAGGCTCAACGAC-TTTG-AAAAT--AAATG
* * * *
3012854 GCTCCACTAAAT-AGAGGCAACCACGACTTTGAAAAATAAATT
1 GCTCCTCT-AATCAGAGGC-TCAACGACTTTG-AAAATAAATG
3012896 GCTCCT
1 GCTCCT
3012902 TAACAATCAT
Statistics
Matches: 430, Mismatches: 53, Indels: 78
0.77 0.09 0.14
Matches are distributed among these distances:
39 52 0.12
40 33 0.08
41 58 0.13
42 78 0.18
43 42 0.10
44 40 0.09
45 22 0.05
46 33 0.08
47 52 0.12
48 17 0.04
49 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (40 bp):
GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAATAAATG
Found at i:3012634 original size:48 final size:47
Alignment explanation
Indices: 3012529--3012688 Score: 181
Period size: 47 Copynumber: 3.5 Consensus size: 47
3012519 AACGACTTTG
* * * *
3012529 AAAATGAACAAAGCTCCTCTAATAAGAGGCTCAAC-GACGTTTG---
1 AAAATAAATAAAGCTCCTCTAATAAGAGGGTCAACGGACTTTTGAAA
*
3012572 AAAATGAATAAAGCTCCTCTAATCCAA-AGGGCCTCAAC-GACTTTT-AAA
1 AAAATAAATAAAGCTCCTCTAAT--AAGAGGG--TCAACGGACTTTTGAAA
*
3012620 AAAATAAATAAAGCTCCTCTAATAAGAGGGTCAACGGACTTTTGGAA
1 AAAATAAATAAAGCTCCTCTAATAAGAGGGTCAACGGACTTTTGAAA
3012667 AAAATAAATAAAGCTCCTCTAA
1 AAAATAAATAAAGCTCCTCTAA
3012689 ACAGAGGCGA
Statistics
Matches: 102, Mismatches: 5, Indels: 16
0.83 0.04 0.13
Matches are distributed among these distances:
43 22 0.22
44 3 0.03
45 7 0.07
46 20 0.20
47 28 0.27
48 22 0.22
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (47 bp):
AAAATAAATAAAGCTCCTCTAATAAGAGGGTCAACGGACTTTTGAAA
Found at i:3012642 original size:91 final size:82
Alignment explanation
Indices: 3012291--3012844 Score: 280
Period size: 81 Copynumber: 6.5 Consensus size: 82
3012281 TTTTTTTATC
* * * *
3012291 AAAGCTCTTCTAAGT-AGAGGCTCTAA-GACTTTGAAAAAAATAGACAAAGCTCCTTTAAACAGA
1 AAAGCTCCTCTAA-TAAGAGGCTC-AACGACTTTG---AAAATA-ATAAAGCTCCTCTAATCAGA
* *
3012354 GGCTCCACGA-TCTTGAAAATAAAT
60 -GCTCAACGACT-TTAAAAATAAAT
* * * * *
3012378 --GGCTCCCCCTAATCAGAGGCTCAATGACTTTG-AAA-AATAAATGGCTCCTCTGATCAGAGGC
1 AAAGCT-CCTCTAATAAGAGGCTCAACGACTTTGAAAATAATAAA--GCTCCTCTAATCAGA-GC
* * *
3012439 TCCATGAC-TTCAAAATAAAT
62 TCAACGACTTTAAAAATAAAT
* * ** *
3012459 --GGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAATAA-ATGGCTCATCTAATCAGAGCTCAA
1 AAAGCTCCTCTAATAAGAGGCTCAACGACTTTGAAAATAATAAAGCTCCTCTAATCAGAGCTCAA
* * *
3012521 CGACTTTGAAAATGAAC
66 CGACTTTAAAAATAAAT
*
3012538 AAAGCTCCTCTAATAAGAGGCTCAACGACGTTTGAAAATGAATAAAGCTCCTCTAATCCAAAGGG
1 AAAGCTCCTCTAATAAGAGGCTCAACGAC-TTTGAAAAT-AATAAAGCTCCTCTAAT-C--AGAG
3012603 CCTCAACGACTTTTAAAAAAATAAAT
61 -CTCAACGAC-TTT--AAAAATAAAT
* *
3012629 AAAGCTCCTCTAATAAGAGGGTCAACGGACTTTTGGAAAAAATAAATAAAGCTCCTCTAAACAGA
1 AAAGCTCCTCTAATAAGAGGCTCAAC-GAC-TTT-G--AAAAT-AATAAAGCTCCTCTAATCAGA
* *
3012694 GGCGACCAA--ACTTTGAAAAGTAAAT
60 -GC--TCAACGACTTT-AAAAATAAAT
** * * **
3012719 -TGGCTCCTCTAA-ACAGAGGCCTTAACGACTTTAGAAATTAA-ATTGCTCCTCTAAAT-AGAGG
1 AAAGCTCCTCTAATA-AGAGG-CTCAACGACTTT-GAAAATAATAAAGCTCCTCT-AATCAGA-G
*
3012780 CTCCAACGACTTTGGAGAAAAAAAAT
61 CT-CAACGACTTT--A-AAAATAAAT
*
3012806 GAAAGATCCTCTAA-ACAGAGGCTCAACGACTTTTGAAAA
1 -AAAGCTCCTCTAATA-AGAGGCTCAACGAC-TTTGAAAA
3012845 ATACAAATTG
Statistics
Matches: 374, Mismatches: 54, Indels: 77
0.74 0.11 0.15
Matches are distributed among these distances:
78 8 0.02
79 22 0.06
80 29 0.08
81 45 0.12
82 35 0.09
83 5 0.01
84 26 0.07
85 16 0.04
86 26 0.07
87 10 0.03
88 26 0.07
89 40 0.11
90 13 0.03
91 35 0.09
92 11 0.03
93 2 0.01
94 4 0.01
95 21 0.06
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (82 bp):
AAAGCTCCTCTAATAAGAGGCTCAACGACTTTGAAAATAATAAAGCTCCTCTAATCAGAGCTCAA
CGACTTTAAAAATAAAT
Found at i:3012687 original size:47 final size:45
Alignment explanation
Indices: 3012491--3012845 Score: 203
Period size: 43 Copynumber: 8.0 Consensus size: 45
3012481 ACGACTTTGA
* * *
3012491 AAATAAATGGCTCATCTAATCAGA-GCTCAACGAC-TTTG--AAAAT
1 AAATAAA--GCTCCTCTAATAAGAGGGTCAACGACTTTTGAAAAAAT
* * * *
3012534 GAACAAAGCTCCTCTAATAAGAGGCTCAACGACGTTTG--AAAAT
1 AAATAAAGCTCCTCTAATAAGAGGGTCAACGACTTTTGAAAAAAT
* *
3012577 GAATAAAGCTCCTCTAATCCAA-AGGGCCTCAACGACTTTTAAAAAAAT
1 AAATAAAGCTCCTCTAAT--AAGAGGG--TCAACGACTTTTGAAAAAAT
3012625 AAATAAAGCTCCTCTAATAAGAGGGTCAACGGACTTTTGGAAAAAAT
1 AAATAAAGCTCCTCTAATAAGAGGGTCAAC-GACTTTT-GAAAAAAT
* *
3012672 AAATAAAGCTCCTCTAA-ACAGAGGCGACCAA--AC-TTTG-AAAAGT
1 AAATAAAGCTCCTCTAATA-AGAGG-G-TCAACGACTTTTGAAAAAAT
** * * * *
3012715 AAAT-TGGCTCCTCTAA-ACAGAGGCCTTAACGAC-TTT-AGAAATT
1 AAATAAAGCTCCTCTAATA-AGAGG-GTCAACGACTTTTGAAAAAAT
* * *
3012758 AAAT--TGCTCCTCTAA-ATAGAGGCTCCAACGACTTTGGAGAAAAA-
1 AAATAAAGCTCCTCTAATA-AGAGGGT-CAACGACTTTTGA-AAAAAT
* *
3012802 AAATGAAAGATCCTCTAA-ACAGAGGCTCAACGACTTTTGAAAAA
1 AAAT-AAAGCTCCTCTAATA-AGAGGGTCAACGACTTTTGAAAAA
3012846 TACAAATTGC
Statistics
Matches: 259, Mismatches: 29, Indels: 46
0.78 0.09 0.14
Matches are distributed among these distances:
41 17 0.07
42 50 0.19
43 55 0.21
44 9 0.03
45 17 0.07
46 35 0.14
47 50 0.19
48 23 0.09
49 3 0.01
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (45 bp):
AAATAAAGCTCCTCTAATAAGAGGGTCAACGACTTTTGAAAAAAT
Found at i:3018669 original size:59 final size:58
Alignment explanation
Indices: 3018542--3018700 Score: 246
Period size: 59 Copynumber: 2.7 Consensus size: 58
3018532 TTGTGTAGGA
* ** *
3018542 AAAATTGATACTTTCAACTTTTCCCAAAAAATATATTTTTTGGAAAGCTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCTC-AAAAATAT-TTTTTTAAAAAGCTTATTTTCAAGG
3018602 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAAAAAGCTTATTTTCAAGG
1 AAAATTGATACTTTCAAC-TTTTCTCAAAAATATTTTTTTAAAAAGCTTATTTTCAAGG
3018661 AAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTC-TCAAAAATATTTTTTT
3018701 TTGAATTTAT
Statistics
Matches: 93, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
58 5 0.05
59 56 0.60
60 26 0.28
61 6 0.06
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCTCAAAAATATTTTTTTAAAAAGCTTATTTTCAAGG
Found at i:3018751 original size:6 final size:5
Alignment explanation
Indices: 3018729--3018786 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
3018719 AATAAAGTAC
*
3018729 TAAAA TAAAA TAAAA TGAAAA TGAAAA TAAAA AATAAA TAAAAA TAAAA
1 TAAAA TAAAA TAAAA T-AAAA T-AAAA TAAAA TA-AAA T-AAAA TAAAA
*
3018778 TAAGA TAAA
1 TAAAA TAAA
3018787 TATTAAACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
5 27 0.59
6 18 0.39
7 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:3018757 original size:17 final size:16
Alignment explanation
Indices: 3018729--3018786 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
3018719 AATAAAGTAC
3018729 TAAAAT-AAAATAAAA
1 TAAAATAAAAATAAAA
*
3018744 TGAAAATGAAAATAAAA
1 T-AAAATAAAAATAAAA
*
3018761 AATAAATAAAAATAAAA
1 TA-AAATAAAAATAAAA
*
3018778 TAAGATAAA
1 TAAAATAAA
3018787 TATTAAACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 1 0.03
16 12 0.33
17 23 0.64
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (16 bp):
TAAAATAAAAATAAAA
Found at i:3018779 original size:11 final size:11
Alignment explanation
Indices: 3018729--3018780 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
3018719 AATAAAGTAC
3018729 TAAAAT-AAAA
1 TAAAATAAAAA
*
3018739 TAAAATGAAAA
1 TAAAATAAAAA
3018750 TGAAAATAAAAA
1 T-AAAATAAAAA
3018762 -ATAAATAAAAA
1 TA-AAATAAAAA
3018773 TAAAATAA
1 TAAAATAA
3018781 GATAAATATT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
10 7 0.19
11 20 0.54
12 10 0.27
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:3018808 original size:3 final size:3
Alignment explanation
Indices: 3018800--3018853 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
3018790 TAAACAATTC
*
3018800 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3018848 TAA TAA
1 TAA TAA
3018854 ATAAATAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3018864 original size:15 final size:15
Alignment explanation
Indices: 3018753--3018865 Score: 51
Period size: 15 Copynumber: 7.4 Consensus size: 15
3018743 ATGAAAATGA
*
3018753 AAATAAAAAATAAAT
1 AAATAATAAATAAAT
3018768 AAA-AATAAAATAAGAT
1 AAATAAT-AAATAA-AT
* * *
3018784 AAATATTAAACAATT
1 AAATAATAAATAAAT
*
3018799 CTAATAAT-AAT-AAT
1 -AAATAATAAATAAAT
3018813 -AATAAT-AAT-AAT
1 AAATAATAAATAAAT
3018825 -AATAATAATAATAGTAAT
1 AAATAAT-A-AATA--AAT
3018843 AATAATAATAAATAAAT
1 -A-AATAATAAATAAAT
3018860 AAATAA
1 AAATAA
3018866 CGAAAAAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 26
0.69 0.07 0.23
Matches are distributed among these distances:
12 18 0.23
14 4 0.05
15 20 0.26
16 16 0.21
17 5 0.06
18 3 0.04
19 4 0.05
20 1 0.01
21 6 0.08
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
AAATAATAAATAAAT
Found at i:3019724 original size:24 final size:24
Alignment explanation
Indices: 3019665--3019773 Score: 62
Period size: 25 Copynumber: 4.4 Consensus size: 24
3019655 AATAGATAAC
*
3019665 AAAAAAAATAATTAGATAAATAAAA
1 AAAAAAAATAAATAGAT-AATAAAA
* * *
3019690 GAAATAGATAAATA-ATAATAAAA
1 AAAAAAAATAAATAGATAATAAAA
*
3019713 AATAAAAAATAAA-AGCA-GATAAATA
1 AA-AAAAAATAAATAG-ATAATAAA-A
* * * *
3019738 ATATAAATATTAATAGATAAAAAAA
1 A-AAAAAAATAAATAGATAATAAAA
3019763 TAAAAAAAATA
1 -AAAAAAAATA
3019774 TTAATAAATA
Statistics
Matches: 60, Mismatches: 16, Indels: 16
0.65 0.17 0.17
Matches are distributed among these distances:
23 9 0.15
24 15 0.25
25 28 0.47
26 8 0.13
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (24 bp):
AAAAAAAATAAATAGATAATAAAA
Found at i:3019743 original size:5 final size:4
Alignment explanation
Indices: 3019634--3019802 Score: 50
Period size: 4 Copynumber: 41.8 Consensus size: 4
3019624 AAATTAATCA
* * * * * *
3019634 AAAT AAA- AAGAT AAAT ATAT TAAT AGAT AACA- AAAA AAAT AATT AGAT
1 AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT
* *
3019682 AAAT AAAAG AAAT AGAT AAAT -AAT -AAT AAA- AAAT AAA- AAAT AAA-
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
3019726 AGCAGAT AAAT AATAT AAAT ATTAAT AGAT AAAA AAAT AAA- AAA- AATAT
1 A--A-AT AAAT AA-AT AAAT A--AAT AAAT AAAT AAAT AAAT AAAT AA-AT
* * * *
3019775 TAAT AAAT AGAC AAAT AATAA AAAT AAA
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAA
3019803 AATAAAAGCC
Statistics
Matches: 120, Mismatches: 27, Indels: 36
0.66 0.15 0.20
Matches are distributed among these distances:
3 21 0.17
4 77 0.64
5 16 0.13
6 5 0.04
7 1 0.01
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:3019764 original size:27 final size:27
Alignment explanation
Indices: 3019733--3019800 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
3019723 AAAAGCAGAT
* *
3019733 AAATAATATAAATATTAATAGATAAAA
1 AAATAATAAAAATATTAATAAATAAAA
* * *
3019760 AAATAAAAAAAATATTAATAAATAGAC
1 AAATAATAAAAATATTAATAAATAAAA
3019787 AAATAATAAAAATA
1 AAATAATAAAAATA
3019801 AAAATAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (27 bp):
AAATAATAAAAATATTAATAAATAAAA
Found at i:3019971 original size:26 final size:27
Alignment explanation
Indices: 3019919--3019972 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
3019909 GGGTGTCTAC
** *
3019919 AATAATAAAAAAAAATTTTTCTTATAA
1 AATAATAAAAAAAAATTTAACTAATAA
*
3019946 AATAATAAATAAAAA-TTAACTAATAA
1 AATAATAAAAAAAAATTTAACTAATAA
3019972 A
1 A
3019973 TTAAGAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (27 bp):
AATAATAAAAAAAAATTTAACTAATAA
Found at i:3023423 original size:144 final size:144
Alignment explanation
Indices: 3023163--3023847 Score: 993
Period size: 144 Copynumber: 4.7 Consensus size: 144
3023153 CACCGGCCTT
* * * *
3023163 ATCCCTTCTTCTATTGCTAATTTATCAAAATTGCAA-TTTCTGTCACTTGATTCAAATATTCTAG
1 ATCCCTTCTTCTATTGGTAATTTATCAAAATTGCAAGATT-TGTCCCTTGATTCAAATCTTCTAG
* * *
3023227 AAGGTCCTATACCAAAAGAACTTGGGAATTTAAATACAATAACTCAATTATCCCTCTTTGGAAAC
65 AAGGTCCTATACCAAAAGAAATTGGGAATTTAAATGCACTAACTCAATTATCCCTCTTTGGAAAC
*
3023292 AAATTGAATGGTTTA
130 AAATTGAATGGTTCA
**
3023307 ATCCCTTCTTCTATTATTAATTTATCAAAATTGCAAGATTTGTCCCTTGATTCAAATCTTCTAGA
1 ATCCCTTCTTCTATTGGTAATTTATCAAAATTGCAAGATTTGTCCCTTGATTCAAATCTTCTAGA
3023372 AGGTCCTATACCAAAAGAAATTGGGAATTTAAATGCACTAACTCAATTATCCCTCTTTGGAAACA
66 AGGTCCTATACCAAAAGAAATTGGGAATTTAAATGCACTAACTCAATTATCCCTCTTTGGAAACA
3023437 AATT-AAGTGGTTCA
131 AATTGAA-TGGTTCA
3023451 ATCCCTTCTTCTATTGGTAATTTATCAAAATTGCAAGATTTGTCCCTTGATTCAAATCTTCTAGA
1 ATCCCTTCTTCTATTGGTAATTTATCAAAATTGCAAGATTTGTCCCTTGATTCAAATCTTCTAGA
* * *
3023516 AGGTCCTATACCAAAAGAAATTGGGAATTTAAATGCATTAAGTCAATTATCCCTCTTTAGAAACA
66 AGGTCCTATACCAAAAGAAATTGGGAATTTAAATGCACTAACTCAATTATCCCTCTTTGGAAACA
*
3023581 AATTGAGTGGTTCA
131 AATTGAATGGTTCA
* * * * *
3023595 ATCCCTTCTTCTATTGGTAATTTATCAAGATTACAATATCTGTCCCTCGATTCAAATCTTCTAGA
1 ATCCCTTCTTCTATTGGTAATTTATCAAAATTGCAAGATTTGTCCCTTGATTCAAATCTTCTAGA
* * * *
3023660 AGGTCCTATACCAAAAGAAATTGGAAATTTAAATGCAGTAACTCAATTATCCCTGTCTGGAAACA
66 AGGTCCTATACCAAAAGAAATTGGGAATTTAAATGCACTAACTCAATTATCCCTCTTTGGAAACA
*
3023725 AATTGAGTGGTTCA
131 AATTGAATGGTTCA
* * * *
3023739 ATCCCTTCTTCTATTGGGAATTGCAATTTATCAAAATTGCAATATCTGTTCCTTTATTCAAATCT
1 ATCCCTTCTTCTATT-GG---T--AATTTATCAAAATTGCAAGATTTGTCCCTTGATTCAAATCT
*
3023804 TCTAGGA-GTCCTATACCAAAAGAAA-TGGGAATTTAGAA-GCACTA
60 TCTAGAAGGTCCTATACCAAAAGAAATTGGGAATTTA-AATGCACTA
3023848 TATCTATTAG
Statistics
Matches: 497, Mismatches: 34, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
143 2 0.00
144 413 0.83
145 5 0.01
148 15 0.03
149 20 0.04
150 42 0.08
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (144 bp):
ATCCCTTCTTCTATTGGTAATTTATCAAAATTGCAAGATTTGTCCCTTGATTCAAATCTTCTAGA
AGGTCCTATACCAAAAGAAATTGGGAATTTAAATGCACTAACTCAATTATCCCTCTTTGGAAACA
AATTGAATGGTTCA
Found at i:3024034 original size:73 final size:70
Alignment explanation
Indices: 3023896--3024043 Score: 181
Period size: 73 Copynumber: 2.1 Consensus size: 70
3023886 TATACCTTCA
* *
3023896 CAAATTGGAGTTGCTTAAATTTGCGGGGATTGTACCTAAGCAACAATAATTTAAAGGGTACATCC
1 CAAATTGGAGTTGCTTAAATTTGCGGGGATTGGACCTAAGCAACAATAATTTAAAGGGAACATCC
3023961 CTCCT
66 CTCCT
* * ** *
3023966 CAAATTGGGAGTTGCTTAAATTTGCGGGCTG-TTGGGATCTAAGCAGCAATAATTTAGGGGGAAG
1 CAAATT-GGAGTTGCTTAAATTTGCGGG--GATT-GGACCTAAGCAACAATAATTTAAAGGGAAC
*
3024030 ATCCCTGCT
62 ATCCCTCCT
3024039 CAAAT
1 CAAAT
3024044 AGGCAAGTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
70 6 0.09
71 21 0.32
72 2 0.03
73 37 0.56
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (70 bp):
CAAATTGGAGTTGCTTAAATTTGCGGGGATTGGACCTAAGCAACAATAATTTAAAGGGAACATCC
CTCCT
Found at i:3026281 original size:24 final size:24
Alignment explanation
Indices: 3026248--3026298 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3026238 TTGATGGCTC
* * *
3026248 AATCCGTTCCATTCTAGGTCAATT
1 AATCCCTTCCATGCGAGGTCAATT
3026272 AATCCCTTCCATGCGAGGTCAATT
1 AATCCCTTCCATGCGAGGTCAATT
3026296 AAT
1 AAT
3026299 GAATTTAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (24 bp):
AATCCCTTCCATGCGAGGTCAATT
Found at i:3027009 original size:49 final size:49
Alignment explanation
Indices: 3026955--3027048 Score: 154
Period size: 49 Copynumber: 1.9 Consensus size: 49
3026945 ACCTTATAAA
*
3026955 ATTAGAAAAGATTGAGA-TGGTTCACATAACTATGATGATTATTATGTTT
1 ATTAGAAAAGATTGAGAGT-GTTCACATAACTATAATGATTATTATGTTT
*
3027004 ATTAGAAAAGATTGAGAGTGTTCACATAACTATAATGATTGTTAT
1 ATTAGAAAAGATTGAGAGTGTTCACATAACTATAATGATTATTAT
3027049 ATTTGTAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
49 41 0.98
50 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.37
Consensus pattern (49 bp):
ATTAGAAAAGATTGAGAGTGTTCACATAACTATAATGATTATTATGTTT
Found at i:3033098 original size:13 final size:16
Alignment explanation
Indices: 3033062--3033101 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3033052 TGATAAACCA
*
3033062 ATGATAATGATGATTT
1 ATGATGATGATGATTT
3033078 ATGATGATGATGATTT
1 ATGATGATGATGATTT
*
3033094 GTGATGAT
1 ATGATGAT
3033102 TTTTAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (16 bp):
ATGATGATGATGATTT
Found at i:3033579 original size:16 final size:17
Alignment explanation
Indices: 3033553--3033585 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3033543 AAAGATATGA
*
3033553 ATTTTACTTGATAAATT
1 ATTTTACTTGAAAAATT
3033570 ATTTTA-TTGAAAAATT
1 ATTTTACTTGAAAAATT
3033586 TTAGAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (17 bp):
ATTTTACTTGAAAAATT
Found at i:3046343 original size:3 final size:3
Alignment explanation
Indices: 3046335--3046361 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3046325 TGCCCACACC
3046335 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
3046362 AAGAACTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3056541 original size:144 final size:144
Alignment explanation
Indices: 3056293--3056597 Score: 565
Period size: 144 Copynumber: 2.1 Consensus size: 144
3056283 AAATCAAATC
3056293 AGTGGTTCAATCCCTTCTTCTATTGGTAATTTATCAAAATTGCAATATCTGTTCCTCGATTCAAA
1 AGTGGTTCAATCCCTTCTTCTATTGGTAATTTATCAAAATTGCAATATCTGTTCCTCGATTCAAA
3056358 TCTTCTAGAAGGTCCTATACCAAAAGAAATTGGGAATTTAGAAGCACTATATCAATTAGACACCT
66 TCTTCTAGAAGGTCCTATACCAAAAGAAATTGGGAATTTAGAAGCACTATATCAATTAGACACCT
3056423 CTGAAAACAAATTG
131 CTGAAAACAAATTG
**
3056437 AGTGGTTCAATCCCTTCTTCTATTGGTAATTTATCAAAATTGCAATATCTGTTCCTTTATTCAAA
1 AGTGGTTCAATCCCTTCTTCTATTGGTAATTTATCAAAATTGCAATATCTGTTCCTCGATTCAAA
3056502 TCTTCTAGAAGGTCCTATACCAAAAGAAATTGGGAATTTAGAAGCACTATATCAATTAGACACCT
66 TCTTCTAGAAGGTCCTATACCAAAAGAAATTGGGAATTTAGAAGCACTATATCAATTAGACACCT
3056567 CTGAAAACAAATTG
131 CTGAAAACAAATTG
* * *
3056581 AGCGGTTCTATACCTTC
1 AGTGGTTCAATCCCTTC
3056598 ACAAATTGGG
Statistics
Matches: 156, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 156 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (144 bp):
AGTGGTTCAATCCCTTCTTCTATTGGTAATTTATCAAAATTGCAATATCTGTTCCTCGATTCAAA
TCTTCTAGAAGGTCCTATACCAAAAGAAATTGGGAATTTAGAAGCACTATATCAATTAGACACCT
CTGAAAACAAATTG
Found at i:3060708 original size:13 final size:14
Alignment explanation
Indices: 3060690--3060727 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3060680 TCAATTTATA
3060690 AAAAAATAAAAG-T
1 AAAAAATAAAAGAT
*
3060703 AAAAAATAAATGAT
1 AAAAAATAAAAGAT
*
3060717 TAAAAATAAAA
1 AAAAAATAAAA
3060728 ATGTGATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (14 bp):
AAAAAATAAAAGAT
Found at i:3061072 original size:18 final size:18
Alignment explanation
Indices: 3061030--3061075 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3061020 TGCCTCAACA
3061030 TAATTGATTAATTACTAG
1 TAATTGATTAATTACTAG
* *
3061048 TAA-TGATTGAATTTC-AT
1 TAATTGATT-AATTACTAG
3061065 TAATTGATTAA
1 TAATTGATTAA
3061076 AATTAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (18 bp):
TAATTGATTAATTACTAG
Found at i:3063952 original size:21 final size:20
Alignment explanation
Indices: 3063922--3063960 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3063912 TAAAAAAATT
3063922 TTTATTTTATTTTACTTTAA
1 TTTATTTTATTTTACTTTAA
*
3063942 TTTATTTTTATTTTTCTTT
1 TTTA-TTTTATTTTACTTT
3063961 TTTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTATTTTATTTTACTTTAA
Found at i:3064082 original size:25 final size:22
Alignment explanation
Indices: 3064047--3064094 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 22
3064037 AAAAAATTTC
3064047 TTACCTAGAAATTTTATAAAAAT
1 TTACCTAGAAA-TTTATAAAAAT
*
3064070 TTACCATATGAAATTTCTAAAAAT
1 TTACC-TA-GAAATTTATAAAAAT
3064094 T
1 T
3064095 CTATCATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 13 0.59
25 4 0.18
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (22 bp):
TTACCTAGAAATTTATAAAAAT
Found at i:3064131 original size:212 final size:210
Alignment explanation
Indices: 3063781--3064167 Score: 469
Period size: 212 Copynumber: 1.8 Consensus size: 210
3063771 AACTATTTTC
* * * * * *
3063781 TTGAAATTTCATTTAAATTCTTTTACCATTTGAGACAATTTTAAAGAAATTTCTCACTTAGAGAT
1 TTGAAATTTCATTTAAATTATTCTACCATTTGAGACAAATTTAAAAAAATTTCTCACCTAGAAAT
* * * * * * *
3063846 TTATTAGAAAATTTATCGTTTGAAATTTTTAATATTCTCATCCTTAGATAATTGTCAAATATTTT
66 TTATTAGAAAATTTACCATATGAAATTTTAAAAATTCTCATCATTAGATAATTATCAAATA-TTT
* * * *
3063911 TTAAAAAAATTTTTATTTTATTTTACTTTA-ATTTATTTTTATTTTTCTTTTTTTGTTTGAAAAT
130 TCAAAAAAAATTTTATTTTATTTTA-TATATATAT-TTTTTATTTTTCTTTTTTTGTTTGAAAAT
3063975 AAATATTAATTATTGTTA
193 AAATATTAATTATTGTTA
* *
3063993 TTGAAACTTT-ATTTAAATTATTCTACCATTTGTGACAAATTTAGAAAAAATTTCTTACCTAGAA
1 TTGAAA-TTTCATTTAAATTATTCTACCATTTGAGACAAATTTA-AAAAAATTTCTCACCTAGAA
* **
3064057 ATTT-TATA-AAAATTTACCATATGAAATTTCTAAAAATTCT-ATCATTAGATAATTATTATTTA
64 ATTTAT-TAGAAAATTTACCATATGAAATTT-TAAAAATTCTCATCATTAGATAATTATCAAATA
*
3064119 TTTTCAAAAAAAATTTTATTTTGTTTTATATATATATTTTTTATTTTTC
127 TTTTCAAAAAAAATTTTATTTTATTTTATATATATATTTTTTATTTTTC
3064168 CTAAAATGTA
Statistics
Matches: 147, Mismatches: 23, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
210 15 0.10
211 28 0.19
212 71 0.48
213 33 0.22
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.51
Consensus pattern (210 bp):
TTGAAATTTCATTTAAATTATTCTACCATTTGAGACAAATTTAAAAAAATTTCTCACCTAGAAAT
TTATTAGAAAATTTACCATATGAAATTTTAAAAATTCTCATCATTAGATAATTATCAAATATTTT
CAAAAAAAATTTTATTTTATTTTATATATATATTTTTTATTTTTCTTTTTTTGTTTGAAAATAAA
TATTAATTATTGTTA
Found at i:3064533 original size:19 final size:21
Alignment explanation
Indices: 3064509--3064559 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 21
3064499 TTTCTCTTAC
3064509 TTTCTCTCTCTTTT-TC-TCT
1 TTTCTCTCTCTTTTATCTTCT
3064528 TTTCTCTCT-TTTTATCTTCT
1 TTTCTCTCTCTTTTATCTTCT
3064548 TTTCTTCTCTCT
1 TTTC-TCTCTCT
3064560 CTACCACCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.14
19 11 0.39
20 7 0.25
21 5 0.18
22 1 0.04
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTCTCTCTCTTTTATCTTCT
Found at i:3064535 original size:17 final size:18
Alignment explanation
Indices: 3064508--3064545 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
3064498 ATTTCTCTTA
*
3064508 CTTTCTCTCTCTTTTTCT
1 CTTTCTCTCTCTTTTTAT
3064526 CTTT-TCTCTCTTTTTAT
1 CTTTCTCTCTCTTTTTAT
3064543 CTT
1 CTT
3064546 CTTTTCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (18 bp):
CTTTCTCTCTCTTTTTAT
Found at i:3065195 original size:16 final size:15
Alignment explanation
Indices: 3065158--3065196 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
3065148 ATCAACACAT
3065158 TTTTTTTGTTTTTTG
1 TTTTTTTGTTTTTTG
3065173 TTCTTTTTGTTTTTTG
1 TT-TTTTTGTTTTTTG
3065189 CTTTTTTT
1 -TTTTTTT
3065197 TTAAGCATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 18 0.82
17 2 0.09
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (15 bp):
TTTTTTTGTTTTTTG
Found at i:3065365 original size:87 final size:86
Alignment explanation
Indices: 3065243--3065828 Score: 443
Period size: 87 Copynumber: 6.8 Consensus size: 86
3065233 TAAAGGCTTT
* * * *
3065243 ACAACTTTTGAAAAATAAATAAAGCTCATTTAAATAAAGGCTCAACAACTTTG-AAAATAAATAA
1 ACAAC-TTTGAAAAAAAAATAAAGCTCCTCTAAATAGAGGCTCAACAACTTTGAAAAATAAATAA
*
3065307 AGCTCCTCTAAGTAGAGGCTCA
65 AGCTCCTCTAAGCAGAGGCTCA
* * * * *
3065329 ACGACTTTGAAAAAAACCAATAAAGCTCTTAC-AAATAGAGACTTAACGA-TGTTGAAAAATAAA
1 ACAACTTTGAAAAAAA--AATAAAGCTCCT-CTAAATAGAGGCTCAACAACT-TTGAAAAATAAA
* * * *
3065392 TAAGGCTCCCCTAAACAGAGGTTCA
62 TAAAGCTCCTCTAAGCAGAGGCTCA
** * * * *
3065417 ATGACTTT-AGATAATAAATAAGGCTCCTCTAAGTAGAGGCTCTAA-AACTTTGAAAAATAAAAT
1 ACAACTTTGA-AAAAAAAATAAAGCTCCTCTAAATAGAGGCTC-AACAACTTTGAAAAAT-AAAT
*
3065480 AAGGCTCCTCTAAGCAGAGGCTCA
63 AAAGCTCCTCTAAGCAGAGGCTCA
* * * * * * * * * *
3065504 ACAACTATGGACAATAAATAAGGCTCCTCTAAGTAGAGGCTCAATAACTTTGGACAACAAAT-AA
1 ACAACTTTGAAAAAAAAATAAAGCTCCTCTAAATAGAGGCTCAACAACTTTGAAAAATAAATAAA
* *
3065568 GACTCTTCTAAGCAGAAGCTCA
66 G-CTCCTCTAAGCAGAGGCTCA
** * ** * * * *
3065590 ATGACTTTGAAAATTAAAAT-AAGACTCCTCTAAGCAGAGGTTCAATAACTTTGGATAATAAATA
1 ACAACTTTGAAAA-AAAAATAAAG-CTCCTCTAAATAGAGGCTCAACAACTTTGAAAAATAAATA
* *
3065654 AGGCTCCTCTAAGTAGAGGCTCA
64 AAGCTCCTCTAAGCAGAGGCTCA
* * * * **
3065677 ACAACTTTGAAAAATAAATAAAACTCCTCTAAACAGAGGCTTAACATTTTTGAAAAATAAATAAA
1 ACAACTTTGAAAAAAAAATAAAGCTCCTCTAAATAGAGGCTCAACAACTTTGAAAAATAAATAAA
** *
3065742 GCTTTTCTAAACAGAGGCTCA
66 GCTCCTCTAAGCAGAGGCTCA
* * ** * * * *
3065763 ATAACTTTAAAAAAATAAAT-AAGACTTTTCTAAACAGA-GCTTAACGACTTTGAAAAGTAAATA
1 ACAACTTTGAAAAAA-AAATAAAG-CTCCTCTAAATAGAGGCTCAACAACTTTGAAAAATAAATA
3065826 AAG
64 AAG
3065829 TTCTTGACAA
Statistics
Matches: 401, Mismatches: 80, Indels: 38
0.77 0.15 0.07
Matches are distributed among these distances:
85 13 0.03
86 160 0.40
87 187 0.47
88 41 0.10
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (86 bp):
ACAACTTTGAAAAAAAAATAAAGCTCCTCTAAATAGAGGCTCAACAACTTTGAAAAATAAATAAA
GCTCCTCTAAGCAGAGGCTCA
Found at i:3065368 original size:45 final size:42
Alignment explanation
Indices: 3065249--3065833 Score: 207
Period size: 43 Copynumber: 13.5 Consensus size: 42
3065239 CTTTACAACT
* * * *
3065249 TTTGAAAAATAAATAAAGCTCATTTAAATAAAGGCTCAACAAC
1 TTTGAAAAAAAAATAAAGCTC-TTCAAATAGAGGCTCAACGAC
* * *
3065292 TTTG-AAAATAAATAAAGCTCCTCTAAGTAGAGGCTCAACGAC
1 TTTGAAAAAAAAATAAAGCTCTTC-AAATAGAGGCTCAACGAC
* *
3065334 TTTGAAAAAAACCAATAAAGCTCTTACAAATAGAGACTTAACGA-
1 TTTGAAAAAAA--AATAAAGCTCTT-CAAATAGAGGCTCAACGAC
* * ** * * *
3065378 TGTTGAAAAATAAATAAGGCTCCCCTAAACAGAGGTTCAATGAC
1 T-TTGAAAAAAAAATAAAGCTCTTC-AAATAGAGGCTCAACGAC
* * * * * *
3065422 TTT-AGATAATAAATAAGGCTCCTCTAAGTAGAGGCTCTAA-AAC
1 TTTGA-AAAAAAAATAAAGCTCTTC-AAATAGAGGCTC-AACGAC
* * ** *
3065465 TTTGAAAAATAAAATAAGGCTCCTCTAAGCAGAGGCTCAACAAC
1 TTTGAAAAA-AAAATAAAGCTCTTC-AAATAGAGGCTCAACGAC
* * * * * * * **
3065509 TATGGACAATAAATAAGGCTCCTCTAAGTAGAGGCTCAATAAC
1 TTTGAAAAAAAAATAAAGCTCTTC-AAATAGAGGCTCAACGAC
* * * ** * *
3065552 TTTGGACAACAAAT-AAGACTCTTCTAAGCAGAAGCTCAATGAC
1 TTTGAAAAAAAAATAAAG-CTCTTC-AAATAGAGGCTCAACGAC
* * ** * **
3065595 TTTGAAAATTAAAAT-AAGACTCCTCTAAGCAGAGGTTCAATAAC
1 TTTGAAAA-AAAAATAAAG-CTCTTC-AAATAGAGGCTCAACGAC
* * * * * * *
3065639 TTTGGATAATAAATAAGGCTCCTCTAAGTAGAGGCTCAACAAC
1 TTTGAAAAAAAAATAAAGCTCTTC-AAATAGAGGCTCAACGAC
* * * * * *
3065682 TTTGAAAAATAAATAAAACTCCTCTAAACAGAGGCTTAAC-ATT
1 TTTGAAAAAAAAATAAAGCTCTTC-AAATAGAGGCTCAACGA-C
* * * **
3065725 TTTGAAAAATAAATAAAGCTTTTCTAAACAGAGGCTCAATAAC
1 TTTGAAAAAAAAATAAAGCTCTTC-AAATAGAGGCTCAACGAC
* * * *
3065768 TTTAAAAAAATAAAT-AAGACTTTTCTAAACAGA-GCTTAACGAC
1 TTTGAAAAAA-AAATAAAG-CTCTTC-AAATAGAGGCTCAACGAC
** *
3065811 TTTGAAAAGTAAATAAAGTTCTT
1 TTTGAAAAAAAAATAAAGCTCTT
3065834 GACAATCATG
Statistics
Matches: 440, Mismatches: 81, Indels: 43
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.00
42 47 0.11
43 261 0.59
44 96 0.22
45 34 0.08
46 1 0.00
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.26
Consensus pattern (42 bp):
TTTGAAAAAAAAATAAAGCTCTTCAAATAGAGGCTCAACGAC
Found at i:3065433 original size:43 final size:42
Alignment explanation
Indices: 3065384--3065826 Score: 386
Period size: 43 Copynumber: 10.3 Consensus size: 42
3065374 ACGATGTTGA
* * * *
3065384 AAAATAAATAAGGCTCCCCTAAACAGAGGTTCAATGACTTTAG
1 AAAATAAATAAGGCTCCTCTAAGCAGAGGCTCAATAACTTT-G
* *
3065427 ATAATAAATAAGGCTCCTCTAAGTAGAGGCTCTAA-AACTTTG
1 AAAATAAATAAGGCTCCTCTAAGCAGAGGCTC-AATAACTTTG
* *
3065469 AAAAATAAAATAAGGCTCCTCTAAGCAGAGGCTCAACAACTATGG
1 -AAAAT-AAATAAGGCTCCTCTAAGCAGAGGCTCAATAACT-TTG
* *
3065514 ACAATAAATAAGGCTCCTCTAAGTAGAGGCTCAATAACTTTGG
1 AAAATAAATAAGGCTCCTCTAAGCAGAGGCTCAATAACTTT-G
* * * * * *
3065557 ACAACAAATAAGACTCTTCTAAGCAGAAGCTCAATGACTTTG
1 AAAATAAATAAGGCTCCTCTAAGCAGAGGCTCAATAACTTTG
* *
3065599 AAAATTAAAATAAGACTCCTCTAAGCAGAGGTTCAATAACTTTGG
1 AAAA-T-AAATAAGGCTCCTCTAAGCAGAGGCTCAATAACTTT-G
* * *
3065644 ATAATAAATAAGGCTCCTCTAAGTAGAGGCTCAACAACTTTG
1 AAAATAAATAAGGCTCCTCTAAGCAGAGGCTCAATAACTTTG
** * * * **
3065686 AAAAATAAATAAAACTCCTCTAAACAGAGGCTTAACATTTTTG
1 -AAAATAAATAAGGCTCCTCTAAGCAGAGGCTCAATAACTTTG
* ** * *
3065729 AAAAATAAATAAAGCTTTTCTAAACAGAGGCTCAATAACTTTAAA
1 -AAAATAAATAAGGCTCCTCTAAGCAGAGGCTCAATAACTTT--G
* ** * * **
3065774 AAAATAAATAAGACTTTTCTAAACAGA-GCTTAACGACTTTG
1 AAAATAAATAAGGCTCCTCTAAGCAGAGGCTCAATAACTTTG
3065815 AAAAGTAAATAA
1 AAAA-TAAATAA
3065827 AGTTCTTGAC
Statistics
Matches: 335, Mismatches: 52, Indels: 27
0.81 0.13 0.07
Matches are distributed among these distances:
41 4 0.01
42 14 0.04
43 217 0.65
44 94 0.28
45 6 0.02
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.25
Consensus pattern (42 bp):
AAAATAAATAAGGCTCCTCTAAGCAGAGGCTCAATAACTTTG
Found at i:3065548 original size:130 final size:129
Alignment explanation
Indices: 3065243--3065827 Score: 500
Period size: 130 Copynumber: 4.5 Consensus size: 129
3065233 TAAAGGCTTT
* * * * *
3065243 ACAACTTTTGAAAAATAAATAAAGCTCATTTAAATAAAGGCTCAACAACTTTGAAAATAAATAAA
1 ACAAC-TTTGGAAAATAAATAAGGCTCCTCTAAATAGAGGCTCAACAACTTTGAAAATAAATAAA
* * * * * *
3065308 GCTCCTCTAAGTAGAGGCTCAACGACTTTGAAAAA-AACCAATAAAGCTCTTAC-AAATAGAGAC
65 ACTCCTCTAAGCAGAGGCTCAACAACTTTGAAAAATAA--AATAAAGCTCCT-CTAAACAGAGGC
*
3065371 TTA
127 TCA
* * * * * ** *
3065374 ACGA-TGTTGAAAAATAAATAAGGCTCCCCTAAACAGAGGTTCAATGACTTTAGATAATAAATAA
1 ACAACT-TTGGAAAATAAATAAGGCTCCTCTAAATAGAGGCTCAACAACTTT-GAAAATAAATAA
** * * *
3065438 GGCTCCTCTAAGTAGAGGCTCTAA-AACTTTGAAAAATAAAATAAGGCTCCTCTAAGCAGAGGCT
64 AACTCCTCTAAGCAGAGGCTC-AACAACTTTGAAAAATAAAATAAAGCTCCTCTAAACAGAGGCT
3065502 CA
128 CA
* * * * * * *
3065504 ACAACTATGGACAATAAATAAGGCTCCTCTAAGTAGAGGCTCAATAACTTTGGACAACAAATAAG
1 ACAACTTTGGAAAATAAATAAGGCTCCTCTAAATAGAGGCTCAACAACTTT-GAAAATAAATAAA
* * ** * * *
3065569 ACTCTTCTAAGCAGAAGCTCAATGACTTTGAAAATTAAAAT-AAGACTCCTCTAAGCAGAGGTTC
65 ACTCCTCTAAGCAGAGGCTCAACAACTTTGAAAAATAAAATAAAG-CTCCTCTAAACAGAGGCTC
3065633 A
129 A
* * *
3065634 ATAACTTTGGATAATAAATAAGGCTCCTCTAAGTAGAGGCTCAACAACTTTGAAAAATAAATAAA
1 ACAACTTTGGAAAATAAATAAGGCTCCTCTAAATAGAGGCTCAACAACTTTG-AAAATAAATAAA
* * ** **
3065699 ACTCCTCTAAACAGAGGCTTAACATTTTTGAAAAAT-AAATAAAGCTTTTCTAAACAGAGGCTCA
65 ACTCCTCTAAGCAGAGGCTCAACAACTTTGAAAAATAAAATAAAGCTCCTCTAAACAGAGGCTCA
* ** * ** * * *
3065763 ATAACTTTAAAAAAATAAATAAGACTTTTCTAAACAGA-GCTTAACGACTTTGAAAAGTAAATAA
1 ACAACTTT-GGAAAATAAATAAGGCTCCTCTAAATAGAGGCTCAACAACTTTGAAAA-TAAATAA
3065827 A
64 A
3065828 GTTCTTGACA
Statistics
Matches: 373, Mismatches: 69, Indels: 26
0.80 0.15 0.06
Matches are distributed among these distances:
128 4 0.01
129 55 0.15
130 264 0.71
131 46 0.12
132 4 0.01
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (129 bp):
ACAACTTTGGAAAATAAATAAGGCTCCTCTAAATAGAGGCTCAACAACTTTGAAAATAAATAAAA
CTCCTCTAAGCAGAGGCTCAACAACTTTGAAAAATAAAATAAAGCTCCTCTAAACAGAGGCTCA
Found at i:3066627 original size:65 final size:65
Alignment explanation
Indices: 3066545--3066669 Score: 196
Period size: 65 Copynumber: 1.9 Consensus size: 65
3066535 CTCAACATTA
* *
3066545 GCAATTTCAAAATAAATTTCGTACATTGATCCACATTATTTTCATAATTTGATCACAACTTACTC
1 GCAATTTCAAAATAAATTTCGTACACTAATCCACATTATTTTCATAATTTGATCACAACTTACTC
* * * *
3066610 GCAATTTTAAAATAAATTTCGTTCACTAATCCACATTATTTTCATTATTTGCTCACAACT
1 GCAATTTCAAAATAAATTTCGTACACTAATCCACATTATTTTCATAATTTGATCACAACT
3066670 CACAGGCTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (65 bp):
GCAATTTCAAAATAAATTTCGTACACTAATCCACATTATTTTCATAATTTGATCACAACTTACTC
Found at i:3067375 original size:19 final size:18
Alignment explanation
Indices: 3067333--3067376 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
3067323 TTGAATTTCA
*
3067333 TTTTTTTTCATTTTTTTT
1 TTTTTTTTCATTTTCTTT
*
3067351 TCTTTTTTTCCTCTTTCTTT
1 T-TTTTTTTCAT-TTTCTTT
3067371 TTTTTT
1 TTTTTT
3067377 CCTTTTCCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 14 0.64
20 7 0.32
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTTTCATTTTCTTT
Found at i:3067377 original size:10 final size:10
Alignment explanation
Indices: 3067328--3067413 Score: 50
Period size: 10 Copynumber: 8.4 Consensus size: 10
3067318 TTCTTTTGAA
*
3067328 TTTCATTTTT
1 TTTCTTTTTT
3067338 TTTCATTTTTT
1 TTTC-TTTTTT
3067349 TTTCTTTTTT
1 TTTCTTTTTT
*
3067359 TCCTCTTTCTTT
1 T-TTCTTT-TTT
*
3067371 TTT-TTTCCTT
1 TTTCTTT-TTT
* ***
3067381 TTCCCCCTTT
1 TTTCTTTTTT
*
3067391 TTTCCTTTTT
1 TTTCTTTTTT
3067401 TTT-TTTTTT
1 TTTCTTTTTT
3067410 TTTC
1 TTTC
3067414 ATTCATTATT
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
9 8 0.14
10 31 0.53
11 15 0.26
12 4 0.07
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:3090534 original size:144 final size:144
Alignment explanation
Indices: 3090322--3090705 Score: 644
Period size: 144 Copynumber: 2.7 Consensus size: 144
3090312 ATAGTGCTTC
* * * *
3090322 TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATAAAGGAACAGATATTGTA
1 TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAAATATTGCA
3090387 ATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAAAGAGGGATAAT
66 ATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAAAGAGGGATAAT
*
3090452 TGAGTTAATGCATT
131 TGAATTAATGCATT
*
3090466 TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAAATCTTGCA
1 TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAAATATTGCA
*
3090531 ATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCATTCAATTTGTTTCCAAAGAGGGATAAT
66 ATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAAAGAGGGATAAT
* *
3090596 TGAATTATTGTATT
131 TGAATTAATGCATT
* * *
3090610 TAAATTCCCAAGTTCTTTTGGTATAGGACCTTCTAGAATATTTGAATCAAGTGACAGAA-ATTGC
1 TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACA-AATATTGC
3090674 AATTTTGATAAATTACCAATAGAAGAAGGGAT
65 AATTTTGATAAATTACCAATAGAAGAAGGGAT
3090706 AAGGCCAGTG
Statistics
Matches: 226, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
144 224 0.99
145 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (144 bp):
TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAAATATTGCA
ATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAAAGAGGGATAAT
TGAATTAATGCATT
Found at i:3100068 original size:13 final size:13
Alignment explanation
Indices: 3100033--3100086 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
3100023 AAATTGTAGA
3100033 TTTTT-ATTTTTC
1 TTTTTGATTTTTC
**
3100045 TTTTTCTTTTTTC
1 TTTTTGATTTTTC
3100058 TTTTTGATTTTAT-
1 TTTTTGATTTT-TC
*
3100071 TTTTTGGTTTTTC
1 TTTTTGATTTTTC
3100084 TTT
1 TTT
3100087 GCCAATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 6 0.17
13 28 0.80
14 1 0.03
ACGTcount: A:0.06, C:0.07, G:0.06, T:0.81
Consensus pattern (13 bp):
TTTTTGATTTTTC
Found at i:3104904 original size:72 final size:72
Alignment explanation
Indices: 3104764--3104909 Score: 195
Period size: 72 Copynumber: 2.0 Consensus size: 72
3104754 CTTGCCGATC
* *
3104764 TGAGGAGGGATGTACCCCTCTAAATGATTGCTGCTTAGGTCCAAATAGGATAAACTTAAGCAACT
1 TGAGGAGGGATGTACCCCTCTAAATGATTGCTGCTTAGGTCCAAATAGCACAAACTTAAGCAACT
3104829 CCCAATT
66 CCCAATT
* * * * * * *
3104836 TGAGGAGGGATGTATCCCTCTAAATTATTGTTGCTTAGGTCC-AATCGCCACAAATTTACGCAAT
1 TGAGGAGGGATGTACCCCTCTAAATGATTGCTGCTTAGGTCCAAATAG-CACAAACTTAAGCAAC
3104900 TCCCAATT
65 TCCCAATT
3104908 TG
1 TG
3104910 TGAAGGTATG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
71 4 0.06
72 60 0.94
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (72 bp):
TGAGGAGGGATGTACCCCTCTAAATGATTGCTGCTTAGGTCCAAATAGCACAAACTTAAGCAACT
CCCAATT
Found at i:3112654 original size:3 final size:3
Alignment explanation
Indices: 3112646--3112683 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3112636 AAACACCATT
3112646 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3112684 TAATTTTTTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3112942 original size:23 final size:24
Alignment explanation
Indices: 3112910--3112956 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
3112900 TGAAAAAATG
*
3112910 GGATTCGAATCCCATAAGA-TCTA
1 GGATTCGAATCCCAAAAGACTCTA
*
3112933 GGATTTGAATCCCAAAAGACTCTA
1 GGATTCGAATCCCAAAAGACTCTA
3112957 TAAATAGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (24 bp):
GGATTCGAATCCCAAAAGACTCTA
Found at i:3113713 original size:17 final size:17
Alignment explanation
Indices: 3113677--3113731 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
3113667 AAATAAACTT
3113677 TAAAAAGTAAAATAAT-A
1 TAAAAA-TAAAATAATAA
*
3113694 TAAAAATAAATTAATAA
1 TAAAAATAAAATAATAA
* * *
3113711 TAACACTAAAGTAATAA
1 TAAAAATAAAATAATAA
3113728 -AAAA
1 TAAAA
3113732 TGAAAGAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
16 11 0.34
17 21 0.66
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (17 bp):
TAAAAATAAAATAATAA
Found at i:3114080 original size:196 final size:193
Alignment explanation
Indices: 3113717--3114080 Score: 470
Period size: 195 Copynumber: 1.9 Consensus size: 193
3113707 ATAATAACAC
* *
3113717 TAAAGTAATAAAAAATGAAAGAAAAGGAAATTTTTATCCAATGATGAGATTTAAAGATATTTCGA
1 TAAAGTAATAAAAAATGAAAGAAAAAGAAAATTTTATCCAATGATGAGATTTAAAGATATTTCGA
* * * ** *
3113782 GTAGTGATGCTTACGAAATCTCTAGGTAAGAAGTTTTTTTTAAATACTACCAGTGTATTGGAGTA
66 GTAGTGATGCTTAAGAAATCTCTAAGTAAGAAGTTTTTTTAAAATACTACCAACGTATTGGAATA
3113847 TTTATAAAAAAAATTTCAATACAATAAAATTTTCTTTTCTTGATAAAAAATAAAATTAATTAATT
131 TTTAT-AAAAAAATTTCAATACAATAAAA-TTTCTTTTCTTGATAAAAAATAAAATTAATTAATT
*
3113912 TAAA-TAATAATATAAAT-AAAGAAAAAGAAAATTTTATCCAATGATGGGATTCTAAA-AGTATT
1 TAAAGTAATAA-A-AAATGAAAGAAAAAGAAAATTTTATCCAATGATGAGATT-TAAAGA-TATT
* *
3113974 TCGAGTA-TAGATGCTTTAAGAAATCTCTAAGTGAGAAGATTTTTTGTAAAATATTACCAACGTA
62 TCGAGTAGT-GATGC-TTAAGAAATCTCTAAGTAAGAAG-TTTTTT-TAAAATACTACCAACGTA
* *
3114038 TTGGAATATTTAT-AAAAAATCTTCAATATAATTAAA-TTCTTTT
123 TTGGAATATTTATAAAAAAAT-TTCAATACAATAAAATTTCTTTT
3114081 TTCTTCAAAA
Statistics
Matches: 147, Mismatches: 13, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
194 6 0.04
195 38 0.26
196 31 0.21
197 27 0.18
198 19 0.13
199 26 0.18
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.36
Consensus pattern (193 bp):
TAAAGTAATAAAAAATGAAAGAAAAAGAAAATTTTATCCAATGATGAGATTTAAAGATATTTCGA
GTAGTGATGCTTAAGAAATCTCTAAGTAAGAAGTTTTTTTAAAATACTACCAACGTATTGGAATA
TTTATAAAAAAATTTCAATACAATAAAATTTCTTTTCTTGATAAAAAATAAAATTAATTAATT
Found at i:3126129 original size:142 final size:140
Alignment explanation
Indices: 3125861--3126707 Score: 953
Period size: 142 Copynumber: 6.0 Consensus size: 140
3125851 AGATGAAAAT
* * * * *
3125861 TTTTTAAAGTTGTTGAGCCTCTGCTGAAAGGAGCTTTTTTA-A-GAGAATTTTAAAGTTGTTGCG
1 TTTTTAAAGTTATTGAGCCTCTACTGAGAGGAGCTTTTTCAGATGAG-ATTTTAAAGTTGTTGAG
*
3125924 TCTCTGCTGAGAGAAGC-TTTTCAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCT
65 CCTCTGCTGAGAGAAGCTTTTTCAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCT
3125988 TTTTCAAGAGA
130 TTTTCAAGAGA
* *
3125999 TTTTTAAAGTTATTGAGCCTCTACTGAAAGGAGCTTTTTCAGATGAGATTCTTAAATTTGTTGAG
1 TTTTTAAAGTTATTGAGCCTCTACTGAGAGGAGCTTTTTCAGATGAGATT-TTAAAGTTGTTGAG
* * *
3126064 CCTCTGCTGAGATAAGCTTTTTCCAGATGAGATTTTAAAGTTGTTGAACCTCTGCTGAGATGAGC
65 CCTCTGCTGAGAGAAGCTTTTT-CAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC
*
3126129 TATTTCAAGAGA
129 TTTTTCAAGAGA
* * * *
3126141 TTTTTAAAGTTGTTAAGCCTCTGCTGAGAGGAGCCATTTTCA-A-GAGATTTTTAAAGTTGTTGA
1 TTTTTAAAGTTATTGAGCCTCTACTGAGAGGAG-CTTTTTCAGATGAGA-TTTTAAAGTTGTTGA
* * *
3126204 GTCTCTGCTGAGAGAAGCCATTTTCATGATATGAGATTTTAAAGTTGTTAAGCCTCTGCTGAGAG
64 GCCTCTGCTGAGAGAAG-CTTTTTCA-G--ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAG
3126269 GAGCTTTTTCCAAAATGAGA
125 GAGCTTTTT-C--AA-GAGA
* * * * *
3126289 -TTTTAAAGTTATTGAGCCTTTAGTGAGAGGAACTTTTTCATATGAGATTTTAAAGTTGTTAAGC
1 TTTTTAAAGTTATTGAGCCTCTACTGAGAGGAGCTTTTTCAGATGAGATTTTAAAGTTGTTGAGC
* * **
3126353 CTCTGCTGAGAAAAGCTTTTTTA-A-GAGAATTTTAAAGTTGTTGAGCCTCTATTGAGAGGAG-T
66 CTCTGCTGAGAGAAGCTTTTTCAGATGAG-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCT
3126415 TTTTCCAAGATGAGA
130 TTTT-C-A-A-GAGA
* * *
3126430 TTTTTAAAGTTATTGTGCCTCTACTGAGAGGAGCTTTTCCAGATGA-AGTTTTAAAGTTATTGAG
1 TTTTTAAAGTTATTGAGCCTCTACTGAGAGGAGCTTTTTCAGATGAGA-TTTTAAAGTTGTTGAG
* * *
3126494 CCTCTGCTGAGAGAAACTTTTTCAGATGAAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAAGAGC
65 CCTCTGCTGAGAGAAGCTTTTTCAGATG-AGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC
*
3126559 TTTTCCAAGATAAGA
129 TTTTTCAAG---AGA
* * * * * * *
3126574 ATTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGCCTTTCCAAGATAAGAATTTTAAAGTTGTTGA
1 TTTTTAAAGTTATTGAGCCTCTACTGAGAGGAGCTTTTTC-AGATGAG-ATTTTAAAGTTGTTGA
* ** *
3126639 GCCTCTGCTGATATG-AGCTTTTTCA-AAAAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG
64 GCCTCTGCTGAGA-GAAGCTTTTTCAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG
*
3126702 CCTTTT
128 CTTTTT
3126708 AAACTTTCAA
Statistics
Matches: 608, Mismatches: 69, Indels: 58
0.83 0.09 0.08
Matches are distributed among these distances:
138 38 0.06
139 4 0.01
140 32 0.05
141 55 0.09
142 195 0.32
143 9 0.01
144 147 0.24
145 12 0.02
146 48 0.08
147 60 0.10
148 8 0.01
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (140 bp):
TTTTTAAAGTTATTGAGCCTCTACTGAGAGGAGCTTTTTCAGATGAGATTTTAAAGTTGTTGAGC
CTCTGCTGAGAGAAGCTTTTTCAGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTT
TTTCAAGAGA
Found at i:3126307 original size:49 final size:47
Alignment explanation
Indices: 3125862--3126707 Score: 903
Period size: 46 Copynumber: 17.8 Consensus size: 47
3125852 GATGAAAATT
* *
3125862 TTTTAAAGTTGTTGAGCCTCTGCTGAAAGGAGCTTTTTTA-A-GAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAGATGAG-A
* * *
3125908 TTTTAAAGTTGTTGCGTCTCTGCTGAGAGAAGC-TTTTCAGATGAGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAGATGAGA
3125954 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCA-A-GAGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAGATGAGA
* * *
3125999 TTTTTAAAGTTATTGAGCCTCTACTGAAAGGAGCTTTTTCAGATGAGA
1 -TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAGATGAGA
* **
3126047 TTCTTAAATTTGTTGAGCCTCTGCTGAGATAAGCTTTTTCCAGATGAGA
1 TT-TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT-CAGATGAGA
* * *
3126096 TTTTAAAGTTGTTGAACCTCTGCTGAGATGAGCTATTTCA-A-GAGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAGATGAGA
* *
3126141 TTTTTAAAGTTGTTAAGCCTCTGCTGAGAGGAGCCATTTTCA-A-GAGA
1 -TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAGATGAGA
* * *
3126188 TTTTTAAAGTTGTTGAGTCTCTGCTGAGAGAAGCCATTTTCATGATATGAGA
1 -TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCA-G--ATGAGA
* *
3126240 TTTTAAAGTTGTTAAGCCTCTGCTGAGAGGAGCTTTTTCCAAAATGAGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT-C-AGATGAGA
* * * *
3126289 TTTTAAAGTTATTGAGCCTTTAG-TGAGAGGAACTTTTTCATATGAGA
1 TTTTAAAGTTGTTGAGCCTCT-GCTGAGAGGAGCTTTTTCAGATGAGA
* ** *
3126336 TTTTAAAGTTGTTAAGCCTCTGCTGAGAAAAGCTTTTTTA-A-GAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAGATGAG-A
**
3126382 TTTTAAAGTTGTTGAGCCTCTATTGAGAGGAG-TTTTTCCAAGATGAGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT-C-AGATGAGA
* * * *
3126430 TTTTTAAAGTTATTGTGCCTCTACTGAGAGGAGCTTTTCCAGATGA-A
1 -TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAGATGAGA
* * * *
3126477 GTTTTAAAGTTATTGAGCCTCTGCTGAGAGAAACTTTTTCAGATGAAAA
1 -TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAGATG-AGA
* * *
3126526 TTTTAAAGTTGTTGAGCCTCTGCTGAGAAGAGCTTTTCCAAGATAAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC-AGATGAG-A
* * * *
3126575 TTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGCCTTTCCAAGATAAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC-AGATGAG-A
* * ** *
3126624 TTTTAAAGTTGTTGAGCCTCTGCTGATATGAGCTTTTTCA-AAAAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAGATGAGA
*
3126670 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT
3126708 AAACTTTCAA
Statistics
Matches: 691, Mismatches: 79, Indels: 60
0.83 0.10 0.07
Matches are distributed among these distances:
45 21 0.03
46 195 0.28
47 146 0.21
48 112 0.16
49 171 0.25
50 10 0.01
51 31 0.04
52 5 0.01
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (47 bp):
TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAGATGAGA
Found at i:3126896 original size:3 final size:3
Alignment explanation
Indices: 3126888--3126931 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3126878 AAACACCATT
3126888 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3126932 TATTTAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3138776 original size:20 final size:20
Alignment explanation
Indices: 3138739--3138777 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3138729 TGTATCTGAA
* *
3138739 TTTTAATATTTTTTTTGTTG
1 TTTTAATATTTATATTGTTG
*
3138759 TTTTGATATTTATATTGTT
1 TTTTAATATTTATATTGTT
3138778 ATTAATTCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72
Consensus pattern (20 bp):
TTTTAATATTTATATTGTTG
Found at i:3148646 original size:2 final size:2
Alignment explanation
Indices: 3148639--3148671 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3148629 TTAAGCTTCA
3148639 AT AT AT 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 AT AT AT A
3148672 AAGCTTAAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3149061 original size:13 final size:13
Alignment explanation
Indices: 3149043--3149067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3149033 TCATTCTTAA
3149043 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
3149056 AAAAAAAAAAAA
1 AAAAAAAAAAAA
3149068 AAGAAAGACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.00, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:3149061 original size:15 final size:15
Alignment explanation
Indices: 3149041--3149073 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3149031 TCTCATTCTT
3149041 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
3149056 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
3149071 AAA
1 AAA
3149074 GACTTTACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:3154937 original size:17 final size:17
Alignment explanation
Indices: 3154908--3154941 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3154898 GGTGAGATGT
3154908 TTATAATTTATAATTTA
1 TTATAATTTATAATTTA
3154925 TTAT-ATTTAATAATTTA
1 TTATAATTT-ATAATTTA
3154942 AAATATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATAATTTATAATTTA
Found at i:3157059 original size:8 final size:9
Alignment explanation
Indices: 3157046--3157090 Score: 53
Period size: 8 Copynumber: 5.4 Consensus size: 9
3157036 AATAATATTT
3157046 AACAAA-AA
1 AACAAACAA
3157054 AACAAA-AA
1 AACAAACAA
3157062 AA-AAACAA
1 AACAAACAA
3157070 AACAAACAA
1 AACAAACAA
*
3157079 AA-AAATAA
1 AACAAACAA
3157087 AACA
1 AACA
3157091 GAAATAAGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
7 3 0.09
8 21 0.64
9 9 0.27
ACGTcount: A:0.84, C:0.13, G:0.00, T:0.02
Consensus pattern (9 bp):
AACAAACAA
Found at i:3157070 original size:19 final size:20
Alignment explanation
Indices: 3157046--3157083 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3157036 AATAATATTT
3157046 AACAAAA-AAACAAAAAAAA
1 AACAAAACAAACAAAAAAAA
3157065 AACAAAACAAACAAAAAAA
1 AACAAAACAAACAAAAAAA
3157084 TAAAACAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (20 bp):
AACAAAACAAACAAAAAAAA
Found at i:3157073 original size:16 final size:17
Alignment explanation
Indices: 3157052--3157090 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3157042 ATTTAACAAA
3157052 AAAACAAA-AAAAAAAC
1 AAAACAAACAAAAAAAC
*
3157068 AAAACAAACAAAAAAAT
1 AAAACAAACAAAAAAAC
3157085 AAAACA
1 AAAACA
3157091 GAAATAAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.03
Consensus pattern (17 bp):
AAAACAAACAAAAAAAC
Found at i:3158064 original size:38 final size:38
Alignment explanation
Indices: 3158022--3158101 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
3158012 AATCAAACCG
* * ** *
3158022 GCCCGAACCGTCGATCCGATTGTCGAACCGGTCGGATC
1 GCCCGAACCGTAGATCCAACCGTCGAACCGGTCAGATC
3158060 GCCCGAACCGTAGATCCAACCGTCGAACCGGTCAGATC
1 GCCCGAACCGTAGATCCAACCGTCGAACCGGTCAGATC
3158098 GCCC
1 GCCC
3158102 AGATCAGCGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (38 bp):
GCCCGAACCGTAGATCCAACCGTCGAACCGGTCAGATC
Found at i:3158606 original size:16 final size:16
Alignment explanation
Indices: 3158584--3158683 Score: 89
Period size: 16 Copynumber: 6.2 Consensus size: 16
3158574 AAAACTCCTA
3158584 AAAATCCAAAATCCCT
1 AAAATCCAAAATCCCT
* *
3158600 TAAATCC-AAACCCCAT
1 AAAATCCAAAATCCC-T
*
3158616 AAAATTCAAAATCCCT
1 AAAATCCAAAATCCCT
* *
3158632 AAAATCCAAAACCCCC
1 AAAATCCAAAATCCCT
3158648 AAAAGTCCAAAAT-CCT
1 AAAA-TCCAAAATCCCT
* *
3158664 CGAAATCCAAAGT-CCT
1 -AAAATCCAAAATCCCT
3158680 AAAA
1 AAAA
3158684 AATCCTAAGG
Statistics
Matches: 67, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
15 9 0.13
16 42 0.63
17 16 0.24
ACGTcount: A:0.49, C:0.31, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAATCCAAAATCCCT
Found at i:3158674 original size:33 final size:33
Alignment explanation
Indices: 3158574--3158662 Score: 110
Period size: 32 Copynumber: 2.7 Consensus size: 33
3158564 ATAGGTTTCT
* * *
3158574 AAAACTCCTAAAAATCCAAAATCCCTTAAATCC
1 AAAACCCCCAAAAATCCAAAATCCCTAAAATCC
*
3158607 -AAA-CCCCATAAAATTCAAAATCCCTAAAATCC
1 AAAACCCCCA-AAAATCCAAAATCCCTAAAATCC
*
3158639 AAAACCCCCAAAAGTCCAAAATCC
1 AAAACCCCCAAAAATCCAAAATCC
3158663 TCGAAATCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
31 3 0.06
32 24 0.51
33 15 0.32
34 5 0.11
ACGTcount: A:0.49, C:0.33, G:0.01, T:0.17
Consensus pattern (33 bp):
AAAACCCCCAAAAATCCAAAATCCCTAAAATCC
Found at i:3161461 original size:32 final size:30
Alignment explanation
Indices: 3161410--3161484 Score: 80
Period size: 32 Copynumber: 2.5 Consensus size: 30
3161400 GGGTAGATCG
* * * *
3161410 AAATTTTTCGTTCCTGAACTCTGAAGCTGGAA
1 AAATTTTTTGTTTCAGAACTCT-AACCT-GAA
*
3161442 AAATTTTTTGTTTCAGAACTCTCACCTGAA
1 AAATTTTTTGTTTCAGAACTCTAACCTGAA
3161472 AAATTTTTT-TTTC
1 AAATTTTTTGTTTC
3161485 TCCTTCTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 4 0.11
30 12 0.32
31 3 0.08
32 19 0.50
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (30 bp):
AAATTTTTTGTTTCAGAACTCTAACCTGAA
Found at i:3161697 original size:8 final size:8
Alignment explanation
Indices: 3161684--3161752 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
3161674 ACTCCTTCAC
3161684 TTTTTTCT
1 TTTTTTCT
*
3161692 TTTTTTTT
1 TTTTTTCT
3161700 GTTTGTTTACT
1 -TTT-TTT-CT
* *
3161711 TGTTTTGT
1 TTTTTTCT
3161719 TTTTTTC-
1 TTTTTTCT
* *
3161726 TGTTTTAT
1 TTTTTTCT
3161734 TTTTTTCT
1 TTTTTTCT
*
3161742 TTTTTTGT
1 TTTTTTCT
3161750 TTT
1 TTT
3161753 GTTTTGTTAA
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
7 5 0.11
8 29 0.63
9 6 0.13
10 5 0.11
11 1 0.02
ACGTcount: A:0.03, C:0.06, G:0.09, T:0.83
Consensus pattern (8 bp):
TTTTTTCT
Found at i:3161729 original size:23 final size:21
Alignment explanation
Indices: 3161691--3161752 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 21
3161681 CACTTTTTTC
3161691 TTTTTTTTTGTTTG-TTTACTTG
1 TTTTTTTTT-TTTGTTTTA-TTG
3161713 TTTTGTTTTTTTCTGTTTTATT-
1 TTTT-TTTTTTT-TGTTTTATTG
3161735 TTTTTCTTTTTTTGTTTT
1 TTTTT-TTTTTTTGTTTT
3161753 GTTTTGTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
21 7 0.19
22 16 0.44
23 9 0.25
24 4 0.11
ACGTcount: A:0.03, C:0.05, G:0.10, T:0.82
Consensus pattern (21 bp):
TTTTTTTTTTTTGTTTTATTG
Found at i:3161731 original size:15 final size:16
Alignment explanation
Indices: 3161696--3161752 Score: 71
Period size: 15 Copynumber: 3.6 Consensus size: 16
3161686 TTTTCTTTTT
*
3161696 TTTTGTTTGTTTACTTG
1 TTTTGTTT-TTTTCTTG
3161713 TTTTGTTTTTTTC-TG
1 TTTTGTTTTTTTCTTG
* *
3161728 TTTTATTTTTTTCTTT
1 TTTTGTTTTTTTCTTG
3161744 TTTTGTTTT
1 TTTTGTTTT
3161753 GTTTTGTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 14 0.40
16 13 0.37
17 8 0.23
ACGTcount: A:0.04, C:0.05, G:0.11, T:0.81
Consensus pattern (16 bp):
TTTTGTTTTTTTCTTG
Found at i:3161750 original size:36 final size:35
Alignment explanation
Indices: 3161684--3161757 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
3161674 ACTCCTTCAC
*
3161684 TTTTTTCTTTTTTTTTGTTTGTTTACTTGTTTTGT
1 TTTTTTCTTTTTTTTTGTTTCTTTACTTGTTTTGT
**
3161719 TTTTTTCTGTTTTATTTT-TTTCTTTTTTTGTTTTGT
1 TTTTTTCT-TTTT-TTTTGTTTCTTTACTTGTTTTGT
3161755 TTT
1 TTT
3161758 GTTAAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 8 0.24
36 22 0.65
37 4 0.12
ACGTcount: A:0.03, C:0.05, G:0.09, T:0.82
Consensus pattern (35 bp):
TTTTTTCTTTTTTTTTGTTTCTTTACTTGTTTTGT
Found at i:3161758 original size:5 final size:5
Alignment explanation
Indices: 3161710--3161760 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
3161700 GTTTGTTTAC
* * *
3161710 TTGTT TTGTT TT-TT TCTGTT TTATT TTTTT CTTTTT TTGTT TTGTT TTGTT
1 TTGTT TTGTT TTGTT T-TGTT TTGTT TTGTT -TTGTT TTGTT TTGTT TTGTT
3161761 AAATATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 3 0.08
5 29 0.73
6 8 0.20
ACGTcount: A:0.02, C:0.04, G:0.12, T:0.82
Consensus pattern (5 bp):
TTGTT
Found at i:3166181 original size:15 final size:15
Alignment explanation
Indices: 3166161--3166190 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3166151 AAACTTGTGT
3166161 ATAATAAAATTTTTA
1 ATAATAAAATTTTTA
*
3166176 ATAATAATATTTTTA
1 ATAATAAAATTTTTA
3166191 CAATTAAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAATAAAATTTTTA
Found at i:3166715 original size:18 final size:19
Alignment explanation
Indices: 3166683--3166729 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
3166673 AAATACTTTA
3166683 AATAAAAAATTTAAA-GTAAC
1 AATAAAAAA-TTAAATG-AAC
*
3166703 AATAAAAAA-TAAATGAAT
1 AATAAAAAATTAAATGAAC
3166721 AATAAAAAA
1 AATAAAAAA
3166730 GATAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 15 0.60
19 1 0.04
20 9 0.36
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (19 bp):
AATAAAAAATTAAATGAAC
Found at i:3166884 original size:32 final size:31
Alignment explanation
Indices: 3166844--3166906 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
3166834 AAATAGTAAT
*
3166844 AAAAGTTATTGTAATTATAATTGAAAAGAAAA
1 AAAAGTTATTGTAACTATAATTGAAAA-AAAA
* *
3166876 AAAAGTTATTGTAACTGTGATTGAAAAAAAA
1 AAAAGTTATTGTAACTATAATTGAAAAAAAA
3166907 TCATTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.54, C:0.02, G:0.14, T:0.30
Consensus pattern (31 bp):
AAAAGTTATTGTAACTATAATTGAAAAAAAA
Found at i:3168536 original size:64 final size:65
Alignment explanation
Indices: 3168469--3169126 Score: 381
Period size: 64 Copynumber: 10.3 Consensus size: 65
3168459 CATTTCTGAT
* * * * *
3168469 CAAAAATGCCTTGAATAATCCCCTCAATAAATTTTTAT-AACGGATTATTGAAGATATTTTTGGT
1 CAAAAACGCCTTCAATAATCCCCTCAATAAATTTTTATGAATGGATTATTGAAGGTATTTTTGGA
* * * ** *
3168533 CAAATACACCTTCAATAATCCCCTCAACAAAATTTTT-TGTTTGGATTATTAAAGGTATTTTTGG
1 CAAAAACGCCTTCAATAATCCCCTCAA-TAAATTTTTATGAATGGATTATTGAAGGTATTTTTGG
3168597 A
65 A
** ** ** **
3168598 CAAAAACGCCTTCAATAAT-CCCT-TTTAAA-TTTTATGAGGGGATTATTGAAGG-CGTTTTAAA
1 CAAAAACGCCTTCAATAATCCCCTCAATAAATTTTTATGAATGGATTATTGAAGGTATTTTTGGA
* * * * ** * * * * *
3168659 CTAAAAACGCCTTTAATAATCCCTTCAACAAAATTTTATGTTTAGATTATTAAAAGCATTTTTAG
1 C-AAAAACGCCTTCAATAATCCCCTCAATAAATTTTTATGAATGGATTATTGAAGGTATTTTTGG
*
3168724 C
65 A
** * *
3168725 CAAAAACGCACTT-AATAAT---CTCTTTCAAATTTTT-TCAATGGATTATTGAAAATGT-TTTT
1 CAAAAACGC-CTTCAATAATCCCCTCAAT-AAATTTTTATGAATGGATTATTG--AAGGTATTTT
**
3168784 TTTA
62 TGGA
** *
3168788 TCAAAAATACCTTCAATAATTCCCTCAATAAATTTTTATGAA-GGATTATTGAAGGTATTTTT-G
1 -CAAAAACGCCTTCAATAATCCCCTCAATAAATTTTTATGAATGGATTATTGAAGGTATTTTTGG
3168851 A
65 A
** * * *
3168852 CCAAAAATACTTTCAATAATCCCCTCAATAAATTTTTATGAA-AGATTATTGAAGGTGTTTTT-G
1 -CAAAAACGCCTTCAATAATCCCCTCAATAAATTTTTATGAATGGATTATTGAAGGTATTTTTGG
3168915 A
65 A
* * * * * * **
3168916 CTAAAAACACATTCAATAATCCCCTCAACAAA-ATTTA-AAAGGGATTATTGAAGGCGTTTTTGG
1 C-AAAAACGCCTTCAATAATCCCCTCAATAAATTTTTATGAATGGATTATTGAAGGTATTTTTGG
3168979 A
65 A
* *** * * *
3168980 CAAAAATGCCTTCAATAATCTGTTC--CAAATTTTT-TCAA-GAGATTATTGAAGGCATTTTTGG
1 CAAAAACGCCTTCAATAATCCCCTCAATAAATTTTTATGAATG-GATTATTGAAGGTATTTTTGG
3169041 -
65 A
* * * * * ** * ** *
3169041 CTAAAAACACCTTTAATAATTCCCTTAATAAAATTTTTTTGTTTAGATTATTGAAGGCGTTTTTT
1 C-AAAAACGCCTTCAATAATCCCCTCAAT-AAATTTTTATGAATGGATTATTGAAGGTATTTTTG
*
3169106 GC
64 GA
* *
3169108 CAAAAATGCTTTCAATAAT
1 CAAAAACGCCTTCAATAAT
3169127 TTCTTTCAAT
Statistics
Matches: 461, Mismatches: 101, Indels: 62
0.74 0.16 0.10
Matches are distributed among these distances:
61 16 0.03
62 88 0.19
63 59 0.13
64 141 0.31
65 89 0.19
66 60 0.13
67 8 0.02
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (65 bp):
CAAAAACGCCTTCAATAATCCCCTCAATAAATTTTTATGAATGGATTATTGAAGGTATTTTTGGA
Found at i:3168677 original size:127 final size:127
Alignment explanation
Indices: 3168538--3169149 Score: 490
Period size: 128 Copynumber: 4.8 Consensus size: 127
3168528 TTGGTCAAAT
* *
3168538 ACACCTTCAATAATCCCCTCAACAAAATTTTTTGTTTGGATTATTAAAGGTATTTTTGGACAAAA
1 ACACCTTCAATAATCCCCTCAACAAAATTTTTTGTTTGGATTATTGAAGGCATTTTTGGACAAAA
* * * * * **
3168603 ACGCCTTCAATAATCCCTTTTAAATTTTATGAGGGGATTATTGAAGGCGTTTTAAACTAAAA
66 ATGCCTTCAATAATCCCTTTCAAATTTTATCAAGAGATTATTGAAGGCGTTTTTGACTAAAA
* * * * * * * * *
3168665 ACGCCTTTAATAATCCCTTCAACAAAATTTTATGTTTAGATTATTAAAAGCATTTTTAGCCAAAA
1 ACACCTTCAATAATCCCCTCAACAAAATTTTTTGTTTGGATTATTGAAGGCATTTTTGGACAAAA
* * * * ** *
3168730 ACGCACTT-AATAATCTCTTTCAAATTTTTTCAATG-GATTATTGAAAATGTTTTTTTTA-TCAA
66 ATGC-CTTCAATAATCCCTTTCAAATTTTATCAA-GAGATTATTG--AAGGCGTTTTTGACT-AA
3168792 AA
126 AA
* * * ** *
3168794 ATACCTTCAATAATTCCCTCAA-TAAATTTTTATG-AAGGATTATTGAAGGTATTTTT-GACCAA
1 ACACCTTCAATAATCCCCTCAACAAAATTTTT-TGTTTGGATTATTGAAGGCATTTTTGGA-CAA
* * * * *
3168856 AAATACTTTCAATAATCCC-CTCAATAAATTTTTATGAA-AGATTATTGAAGGTGTTTTTGACTA
64 AAATGCCTTCAATAATCCCTTTC---AAA-TTTTATCAAGAGATTATTGAAGGCGTTTTTGACTA
3168919 AAA
125 AAA
* *** *
3168922 ACACATTCAATAATCCCCTCAACAAAATTTAAAAG---GGATTATTGAAGGCGTTTTTGGACAAA
1 ACACCTTCAATAATCCCCTCAACAAAATTT-TTTGTTTGGATTATTGAAGGCATTTTTGGACAAA
** * * * *
3168984 AATGCCTTCAATAATCTGTTCCAAATTTTTTCAAGAGATTATTGAAGGCATTTTTGGCTAAAA
65 AATGCCTTCAATAATCCCTTTCAAATTTTATCAAGAGATTATTGAAGGCGTTTTTGACTAAAA
* * * * * * * *
3169047 ACACCTTTAATAATTCCCTTAATAAAATTTTTTTGTTTAGATTATTGAAGGCGTTTTTTGCCAAA
1 ACACCTTCAATAATCCCCTCAACAAAA-TTTTTTGTTTGGATTATTGAAGGCATTTTTGGACAAA
* ** * *
3169112 AATGCTTTCAATAATTTCTTTCAATTTTTTTCAAGAGA
65 AATGCCTTCAATAATCCCTTTCAAATTTTATCAAGAGA
3169150 CTTCAATAAT
Statistics
Matches: 383, Mismatches: 79, Indels: 45
0.76 0.16 0.09
Matches are distributed among these distances:
124 7 0.02
125 51 0.13
126 3 0.01
127 129 0.34
128 136 0.36
129 39 0.10
130 11 0.03
131 7 0.02
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (127 bp):
ACACCTTCAATAATCCCCTCAACAAAATTTTTTGTTTGGATTATTGAAGGCATTTTTGGACAAAA
ATGCCTTCAATAATCCCTTTCAAATTTTATCAAGAGATTATTGAAGGCGTTTTTGACTAAAA
Found at i:3169077 original size:320 final size:319
Alignment explanation
Indices: 3168467--3169079 Score: 695
Period size: 320 Copynumber: 1.9 Consensus size: 319
3168457 GGCATTTCTG
* * *
3168467 ATCAAAAATGCCTTGAATAATCCCCTCAATAAATTTTTATAACGGATTATTGAAGATATTTTTGG
1 ATCAAAAATACCTTCAATAATCCCCTCAATAAATTTTTATAACGGATTATTGAAGATATTTTTGA
* * ***
3168532 TCAAATACACCTTCAATAATCCCCTCAACAAAATTTTTTGTTTGGATTATTAAAGGTATTTTTGG
66 CCAAAAACACCTTCAATAATCCCCTCAACAAAATTTTTTGTAAAGATTATTAAAGGTATTTTTGG
* * *** * * *
3168597 ACAAAAACGCCTTCAATAATCCCTTTTAAATTTTATGAGGGGATTATTGAAGGCGTTTTAAACTA
131 ACAAAAACACATTCAATAATCCCTAACAAAATTTATAAAGGGATTATTGAAGGCGTTTTAAACTA
* ****
3168662 AAAACGCCTTTAATAATCCCTTCAACAAAATTTTATGTTTAGATTATTAAAAGCATTTTTAGCCA
196 AAAACGCCTTCAATAATCCCTTC-ACAAAATTTTATCAAGAGATTATTAAAAGCATTTTTAGCCA
* * *
3168727 AAAACGCACTTAATAATCTCTTTCAAATTTTTTCAATGGATTATTGAAAATGTTTTTTTT
260 AAAACACACTTAATAATCCCTTTAAAATTTTTTCAATGGATTATTGAAAATGTTTTTTTT
* *
3168787 ATCAAAAATACCTTCAATAATTCCCTCAATAAATTTTTATGAA-GGATTATTGAAGGTATTTTTG
1 ATCAAAAATACCTTCAATAATCCCCTCAATAAATTTTTAT-AACGGATTATTGAAGATATTTTTG
* * * * *
3168851 ACCAAAAATACTTTCAATAATCCCCTCAA-TAAATTTTTATG-AAAGATTATTGAAGGTGTTTTT
65 ACCAAAAACACCTTCAATAATCCCCTCAACAAAATTTTT-TGTAAAGATTATTAAAGGTATTTTT
3168914 -GACTAAAAACACATTCAATAATCCCCTCAACAAAATTTA-AAAGGGATTATTGAAGGCGTTTTT
129 GGAC-AAAAACACATTCAATAAT-CCCT-AACAAAATTTATAAAGGGATTATTGAAGGCG-TTTT
** * ** * * *
3168977 GGAC-AAAAATGCCTTCAATAATCTGTTC-C-AAATTTTTTCAAGAGATTATTGAAGGCATTTTT
190 AAACTAAAAACGCCTTCAATAATCCCTTCACAAAATTTTATCAAGAGATTATTAAAAGCATTTTT
* *
3169039 GGCTAAAAACAC-CTTTAATAATTCCCTTAATAAAATTTTTT
255 AGCCAAAAACACAC-TTAATAA-TCCCTT--TAAAATTTTTT
3169080 TGTTTAGATT
Statistics
Matches: 242, Mismatches: 41, Indels: 20
0.80 0.14 0.07
Matches are distributed among these distances:
316 1 0.00
317 42 0.17
318 9 0.04
319 41 0.17
320 134 0.55
321 15 0.06
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (319 bp):
ATCAAAAATACCTTCAATAATCCCCTCAATAAATTTTTATAACGGATTATTGAAGATATTTTTGA
CCAAAAACACCTTCAATAATCCCCTCAACAAAATTTTTTGTAAAGATTATTAAAGGTATTTTTGG
ACAAAAACACATTCAATAATCCCTAACAAAATTTATAAAGGGATTATTGAAGGCGTTTTAAACTA
AAAACGCCTTCAATAATCCCTTCACAAAATTTTATCAAGAGATTATTAAAAGCATTTTTAGCCAA
AAACACACTTAATAATCCCTTTAAAATTTTTTCAATGGATTATTGAAAATGTTTTTTTT
Found at i:3169092 original size:255 final size:252
Alignment explanation
Indices: 3168497--3169126 Score: 629
Period size: 255 Copynumber: 2.5 Consensus size: 252
3168487 TCCCCTCAAT
* * * * *
3168497 AAATTTTTAT-AACGGATTATTGAAGATATTTTTGGTCAAATACACCTTCAATAATCCCCTCAAC
1 AAATTTTT-TCAATGGATTATTGAAG-GATTTTTGGTCAAAAACACCTTCAATAATTCCCTCAAT
* * * * **
3168561 AAAA-TTTTTTGTTTGGATTATTAAAGGTATTTTTGGA-CAAAAACGCCTTCAATAATCCCTTTT
64 AAAATTTTTTTGTTTAGATTATTGAAGGTATTTTT-GACCAAAAATGCTTTCAATAATCCCTAAT
** * * * *
3168624 AAATTTTATGAGGGGATTATTGAAGGCGTTTTAAACTAAAAACGCCTTTAATAATCCCTTCAACA
128 AAATTTTATGAGAAGATTATTGAAGGCGTTTTAAACTAAAAACACATTCAATAATCCCCTCAACA
* * * *
3168689 AAATTTTATGTTTAGATTATTAAAAGCATTTTTAGCCAAAAACGCACTTAATAATCTCTTTC
193 AAATTTAAAG--TAGATTATTAAAAGCATTTTTAGACAAAAACGCACTTAATAATCTCTTCC
** ** *
3168751 AAATTTTTTCAATGGATTATTGAAAATGTTTTTTTTATCAAAAATACCTTCAATAATTCCCTCAA
1 AAATTTTTTCAATGGATTATTG--AA-GGATTTTTGGTCAAAAACACCTTCAATAATTCCCTCAA
* * *
3168816 T-AAATTTTTATG--AAGGATTATTGAAGGTATTTTTGACCAAAAATACTTTCAATAATCCCCTC
63 TAAAATTTTTTTGTTTA-GATTATTGAAGGTATTTTTGACCAAAAATGCTTTCAATAAT-CCCT-
* **
3168878 AATAAATTTTTATGA-AAGATTATTGAAGGTGTTTTTGACTAAAAACACATTCAATAATCCCCTC
125 AATAAA-TTTTATGAGAAGATTATTGAAGGCGTTTTAAACTAAAAACACATTCAATAATCCCCTC
* * * * * * *
3168942 AACAAAATTTAAAAG-GGATTATTGAAGGCGTTTTTGGACAAAAATGC-CTTCAATAATCTGTTC
189 AACAAAATTT-AAAGTAGATTATTAAAAGCATTTTTAGACAAAAACGCACTT-AATAATCTCTTC
3169005 C
252 C
* *
3169006 AAATTTTTTCAA-GAGATTATTGAAGGCATTTTTGG-CTAAAAACACCTTTAATAATTCCCTTAA
1 AAATTTTTTCAATG-GATTATTGAAGG-ATTTTTGGTC-AAAAACACCTTCAATAATTCCCTCAA
3169069 TAAAATTTTTTTGTTTAGATTATTGAAGGCGT-TTTTTG-CCAAAAATGCTTTCAATAAT
63 TAAAATTTTTTTGTTTAGATTATTGAA-G-GTATTTTTGACCAAAAATGCTTTCAATAAT
3169127 TTCTTTCAAT
Statistics
Matches: 309, Mismatches: 47, Indels: 39
0.78 0.12 0.10
Matches are distributed among these distances:
252 2 0.01
253 32 0.10
254 35 0.11
255 122 0.39
256 51 0.17
257 57 0.18
258 10 0.03
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (252 bp):
AAATTTTTTCAATGGATTATTGAAGGATTTTTGGTCAAAAACACCTTCAATAATTCCCTCAATAA
AATTTTTTTGTTTAGATTATTGAAGGTATTTTTGACCAAAAATGCTTTCAATAATCCCTAATAAA
TTTTATGAGAAGATTATTGAAGGCGTTTTAAACTAAAAACACATTCAATAATCCCCTCAACAAAA
TTTAAAGTAGATTATTAAAAGCATTTTTAGACAAAAACGCACTTAATAATCTCTTCC
Found at i:3169147 original size:128 final size:128
Alignment explanation
Indices: 3168511--3169149 Score: 507
Period size: 127 Copynumber: 5.0 Consensus size: 128
3168501 TTTTATAACG
** * * *
3168511 GATTATTGAAGATATTTTTG-GTCAAATACACCTTCAATAATCCCCTCAACAAAATTTTT-TGTT
1 GATTATTGAAGGCATTTTTGACT-AAAAACACCTTCAATAATTCCCTCAACAAAATTTTTATGTT
* * ** * * * * * * * *
3168574 TGGATTATTAAAGGTATTTTTGGACAAAAACGCCTTCAATAATCCCTTTTAAATTTTATGAGGG
65 TAGATTATTGAAGGCGTTTTTGGCCAAAAATGCCTTCAATAATCTCTTTCAAATTTTTTCAAGA
* ** * *
3168638 GATTATTGAAGGCGTTTTAAACTAAAAACGCCTTTAATAA-TCCCTTCAACAAAA-TTTTATGTT
1 GATTATTGAAGGCATTTTTGACTAAAAACACCTTCAATAATTCCC-TCAACAAAATTTTTATGTT
* * * * *
3168701 TAGATTATTAAAAGCATTTTTAGCCAAAAACGCACTT-AATAATCTCTTTCAAATTTTTTCAATG
65 TAGATTATTGAAGGCGTTTTTGGCCAAAAATGC-CTTCAATAATCTCTTTCAAATTTTTTCAA-G
3168765 -
128 A
* ** * * *
3168765 GATTATTGAAAATGTTTTTTTTA-TCAAAAATACCTTCAATAATTCCCTCAA-TAAATTTTTATG
1 GATTATTG--AAGGCATTTTTGACT-AAAAACACCTTCAATAATTCCCTCAACAAAATTTTTATG
* ** * * * **
3168828 --AAGGATTATTGAAGGTATTTTTGACCAAAAATACTTTCAATAATC-CCCTCAATAAATTTTTA
63 TTTA-GATTATTGAAGGCGTTTTTGGCCAAAAATGCCTTCAATAATCTCTTTC---AAATTTTT-
*
3168890 TGAA-A
123 TCAAGA
** * * ** *
3168895 GATTATTGAAGGTGTTTTTGACTAAAAACACATTCAATAATCCCCTCAACAAAATTTAAAAG---
1 GATTATTGAAGGCATTTTTGACTAAAAACACCTTCAATAATTCCCTCAACAAAATTTTTATGTTT
* * * *
3168957 GGATTATTGAAGGCGTTTTTGGACAAAAATGCCTTCAATAATCTGTTCCAAATTTTTTCAAGA
66 AGATTATTGAAGGCGTTTTTGGCCAAAAATGCCTTCAATAATCTCTTTCAAATTTTTTCAAGA
* * * * *
3169020 GATTATTGAAGGCATTTTTGGCTAAAAACACCTTTAATAATTCCCTTAATAAAATTTTTTTGTTT
1 GATTATTGAAGGCATTTTTGACTAAAAACACCTTCAATAATTCCCTCAACAAAATTTTTATGTTT
* * * *
3169085 AGATTATTGAAGGCGTTTTTTGCCAAAAATGCTTTCAATAATTTCTTTCAATTTTTTTCAAGA
66 AGATTATTGAAGGCGTTTTTGGCCAAAAATGCCTTCAATAATCTCTTTCAAATTTTTTCAAGA
3169148 GA
1 GA
3169150 CTTCAATAAT
Statistics
Matches: 405, Mismatches: 83, Indels: 47
0.76 0.16 0.09
Matches are distributed among these distances:
124 3 0.01
125 59 0.15
126 7 0.02
127 140 0.35
128 131 0.32
129 42 0.10
130 20 0.05
131 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (128 bp):
GATTATTGAAGGCATTTTTGACTAAAAACACCTTCAATAATTCCCTCAACAAAATTTTTATGTTT
AGATTATTGAAGGCGTTTTTGGCCAAAAATGCCTTCAATAATCTCTTTCAAATTTTTTCAAGA
Found at i:3169405 original size:64 final size:64
Alignment explanation
Indices: 3169169--3169417 Score: 175
Period size: 64 Copynumber: 3.9 Consensus size: 64
3169159 TCCCCTCAAT
* ** * * * *
3169169 AAAATTTTATGAA-GGATTATTGAAGGTGTTTTTTTGCCAAAAATGCCTTTAATAAATTAC-CTC
1 AAAATTTTTTGAATGGATTATTGAAGG-CATTTTTGGCCAAAAACGCCTTCAAT-AATTTCTCTC
3169232 AAC
64 --C
** * ** ** ***
3169235 AAAATTTTTTGTTTGAATTATTGAAGATATTTTTGGATAAAAACATTTTCAATAATCTTCT-T-C
1 AAAATTTTTTGAATGGATTATTGAAGGCATTTTTGGCCAAAAACGCCTTCAATAAT-TTCTCTCC
* * * * *** *
3169298 AAAATTTTTT-TATAGATTATTGAAAGCGTTTTTTTATCGAAAACGCCTTCAATAATTTCTCTCC
1 AAAATTTTTTGAATGGATTATTGAAGGC-ATTTTTGGCCAAAAACGCCTTCAATAATTTCTCTCC
*
3169362 AAAATTTTTTGAATGGATTATTGAAGGCATTTTTGGCCAAAAACGCCTACAATAAT
1 AAAATTTTTTGAATGGATTATTGAAGGCATTTTTGGCCAAAAACGCCTTCAATAAT
3169418 CCTATTCAGT
Statistics
Matches: 136, Mismatches: 40, Indels: 16
0.71 0.21 0.08
Matches are distributed among these distances:
62 15 0.11
63 31 0.23
64 33 0.24
65 17 0.12
66 29 0.21
67 11 0.08
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (64 bp):
AAAATTTTTTGAATGGATTATTGAAGGCATTTTTGGCCAAAAACGCCTTCAATAATTTCTCTCC
Found at i:3169920 original size:303 final size:301
Alignment explanation
Indices: 3169368--3169930 Score: 672
Period size: 303 Copynumber: 1.9 Consensus size: 301
3169358 CTCCAAAATT
* *
3169368 TTTTGAATGGATTATTGAAGGCATTTTTGGCCAAAAACGCCTACAATAATCCTATTCAGTTTGTT
1 TTTTGAATGGATTATTGAAGGCATTTTTGGCCAAAAACACCTACAATAATCCTATTCAGTTTGTA
* * *
3169433 AGCCAATAGTTTTTTTTTTATTTGAGCCTATACCGACGATTACGTTAATAACCGTCAGTATATAA
66 AGCCAATAGTTTTTTTTTTATAT-AGCCTATACCGACGATTACGTTAATAACCATCAATATATAA
* * * * *
3169498 CATATTTAGACTAACAAATAATCATATACTATCAGAAAAAGTTTATTTATACTGATGATTAAATA
130 CATATTTAGACTAACAAATAATCATACACTATCAAAAAAAGTTCATTTATACTAACGATTAAATA
* * *
3169563 AAGTGTTGATATAAGTATGGTATATTCTGACAGTATTAAAAAACTGTCAGTAAAAGTCTCTTTTA
195 AAGTGTTGATATAAGTATAGAATATTCTGACAGTATTAAAAAACTGTCAGTAAAAATCTCTTTTA
3169628 CTAACAAAATTAAACCATCAGTAAATAATCCATATAAAAAAA
260 CTAACAAAATTAAACCATCAGTAAATAATCCATATAAAAAAA
* * * ** * *
3169670 TTTTGTATGGATTATTGAATGCGTTTTTGGCCAAAAACACCTTTAATAAT-TTCATTCAATTTTT
1 TTTTGAATGGATTATTGAAGGCATTTTTGGCCAAAAACACCTACAATAATCCT-ATTC-A--GTT
* * * * *
3169734 TGTAAGTCAATAGTTTTTTTGTTT-TAT-GCTTATACTGACGGTTATGTTAATAACCATCAATAT
62 TGTAAGCCAATAGTTTTTTT-TTTATATAGCCTATACCGACGATTACGTTAATAACCATCAATAT
* * * ** * * *
3169797 ATAACATATTTATATTGACGGATAGTCATACA-TCGTCAAAAAAAGTTCATTTATACTAACGGTT
126 ATAACATATTTAGACTAACAAATAATCATACACT-ATCAAAAAAAGTTCATTTATACTAACGATT
* *
3169861 AAATAAAGTGTT-AGTATAAGTATAGAATATTCTGA-TGATATT-AAAAATTCGTCAGTAAAAAT
190 AAATAAAGTGTTGA-TATAAGTATAGAATATTCTGACAG-TATTAAAAAACT-GTCAGTAAAAAT
3169923 CTCTTTTA
252 CTCTTTTA
3169931 TTGATGAAAT
Statistics
Matches: 217, Mismatches: 35, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
301 1 0.00
302 57 0.26
303 134 0.62
305 22 0.10
306 3 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (301 bp):
TTTTGAATGGATTATTGAAGGCATTTTTGGCCAAAAACACCTACAATAATCCTATTCAGTTTGTA
AGCCAATAGTTTTTTTTTTATATAGCCTATACCGACGATTACGTTAATAACCATCAATATATAAC
ATATTTAGACTAACAAATAATCATACACTATCAAAAAAAGTTCATTTATACTAACGATTAAATAA
AGTGTTGATATAAGTATAGAATATTCTGACAGTATTAAAAAACTGTCAGTAAAAATCTCTTTTAC
TAACAAAATTAAACCATCAGTAAATAATCCATATAAAAAAA
Found at i:3171587 original size:3 final size:3
Alignment explanation
Indices: 3171579--3171608 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3171569 TTAATGTAAT
3171579 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
3171609 GGGATCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:3174138 original size:3 final size:3
Alignment explanation
Indices: 3174132--3174161 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3174122 AAAATTGTTT
*
3174132 TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3174162 AAAACATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:3175993 original size:3 final size:3
Alignment explanation
Indices: 3175985--3176009 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3175975 GAGATGGTTT
3175985 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
3176010 ACCTCATCAC
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:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:3178439 original size:23 final size:24
Alignment explanation
Indices: 3178408--3178456 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
3178398 AGATTTTTTA
3178408 TTAAATAATATA-AATT-AT-TATT
1 TTAAATAAT-TAGAATTAATATATT
3178430 TTAAATTAATTAGAATTAATATATT
1 TTAAA-TAATTAGAATTAATATATT
3178455 TT
1 TT
3178457 TATTGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 7 0.30
23 8 0.35
24 2 0.09
25 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TTAAATAATTAGAATTAATATATT
Found at i:3179595 original size:29 final size:29
Alignment explanation
Indices: 3179553--3179610 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3179543 CATATGGTAC
3179553 AAATTAATTTAAGTCAAGAAAAAGAAATA
1 AAATTAATTTAAGTCAAGAAAAAGAAATA
3179582 AAATTAATTTAAGTCAAGAAAAAGAAATA
1 AAATTAATTTAAGTCAAGAAAAAGAAATA
3179611 TTTGGTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.24
Consensus pattern (29 bp):
AAATTAATTTAAGTCAAGAAAAAGAAATA
Found at i:3181933 original size:32 final size:32
Alignment explanation
Indices: 3181880--3181954 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
3181870 CAATTGAAAT
* *
3181880 CAAATGAAATC-CACTTGCATTAATACTTTAC
1 CAAATGAAATCAAACTTGCATTAATACTTTAA
*
3181911 CAAATGAAATCAAACTTGCATTAATATTTTAA
1 CAAATGAAATCAAACTTGCATTAATACTTTAA
3181943 CAAATGAAATCA
1 CAAATGAAATCA
3181955 TATTTAATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 11 0.28
32 29 0.73
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (32 bp):
CAAATGAAATCAAACTTGCATTAATACTTTAA
Found at i:3184692 original size:2 final size:2
Alignment explanation
Indices: 3184666--3184752 Score: 57
Period size: 2 Copynumber: 43.0 Consensus size: 2
3184656 TCTCTAAGAG
* * * * * *
3184666 TA TA TG TA TA TA CA TA TG TA CA TA TA TA TA CA TA TA TA TA CTG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * * * *
3184709 TG TA CA TA TA TA TG TA TA TA TA TG TA CA TA TG 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
3184751 TA
1 TA
3184753 CGCACAAAAT
Statistics
Matches: 62, Mismatches: 22, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
2 61 0.98
3 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (2 bp):
TA
Found at i:3184737 original size:39 final size:39
Alignment explanation
Indices: 3184670--3184744 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
3184660 TAAGAGTATA
*
3184670 TGTATATACATATGTACATATATATACATATATATACTG
1 TGTACATACATATGTACATATATATACATATATATACTG
* * * *
3184709 TGTACATATATATGTATATATATGTACATATGTATA
1 TGTACATACATATGTACATATATATACATATATATA
3184745 TATATATACG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (39 bp):
TGTACATACATATGTACATATATATACATATATATACTG
Found at i:3185194 original size:2 final size:2
Alignment explanation
Indices: 3185177--3185213 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3185167 AACTAATGTC
* *
3185177 AT AT AA AT AA 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 AT AT AT AT AT A
3185214 CACACACACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3190605 original size:75 final size:75
Alignment explanation
Indices: 3190534--3190672 Score: 224
Period size: 75 Copynumber: 1.9 Consensus size: 75
3190524 TTAAGAATTT
* * *
3190534 TAAAATTAAAATTAATTTTTTTTCATCTATTTATTATTATCTTAATATAATTTTACATGAAAAAG
1 TAAAATTAAAATTAACTTTTTTTCATCTATTTATTATTATCATAATATAATTTTACATAAAAAAG
3190599 AAAAGAATCC
66 AAAAGAATCC
* * *
3190609 TAAAATTAAAATTAACTTTTTTTCATCTATTTGTTCTTATCATAATATATTTTTACATAAAAAA
1 TAAAATTAAAATTAACTTTTTTTCATCTATTTATTATTATCATAATATAATTTTACATAAAAAA
3190673 TATTTATTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 58 1.00
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (75 bp):
TAAAATTAAAATTAACTTTTTTTCATCTATTTATTATTATCATAATATAATTTTACATAAAAAAG
AAAAGAATCC
Found at i:3190783 original size:20 final size:20
Alignment explanation
Indices: 3190760--3190804 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3190750 TTAAACTTAT
*
3190760 TTATTTAATTT-TTTTAGATA
1 TTATTT-ATTTATTTTACATA
*
3190780 TTATATATTTATTTTACATA
1 TTATTTATTTATTTTACATA
3190800 TTATT
1 TTATT
3190805 AATAGTAGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
TTATTTATTTATTTTACATA
Found at i:3192361 original size:6 final size:6
Alignment explanation
Indices: 3192350--3192380 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3192340 GTTTTATGGT
*
3192350 ATGAAG ATGAAG ATGAAG ATGAAA ATGAAG A
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG A
3192381 CTACTACTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.16
Consensus pattern (6 bp):
ATGAAG
Found at i:3193100 original size:3 final size:3
Alignment explanation
Indices: 3193092--3193118 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3193082 TAAAACACAC
3193092 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
3193119 TAGAGAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3197363 original size:12 final size:12
Alignment explanation
Indices: 3197343--3197375 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3197333 CCCATGACTC
*
3197343 TCATTGTTGTCT
1 TCATGGTTGTCT
3197355 TCATGGTTGTCT
1 TCATGGTTGTCT
3197367 TCATGGTTG
1 TCATGGTTG
3197376 AGTCCGGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.15, G:0.24, T:0.52
Consensus pattern (12 bp):
TCATGGTTGTCT
Found at i:3199109 original size:16 final size:16
Alignment explanation
Indices: 3199084--3199119 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3199074 TATAATTACG
3199084 ATTAAAAAAATTTTAA
1 ATTAAAAAAATTTTAA
* *
3199100 ATTAATAAAATTTTAT
1 ATTAAAAAAATTTTAA
3199116 ATTA
1 ATTA
3199120 TATTTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTAAAAAAATTTTAA
Found at i:3207349 original size:30 final size:30
Alignment explanation
Indices: 3207315--3207371 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
3207305 ATTGCAATCA
3207315 ATTAAAATCTTAAATATTTATTTTTATTAC
1 ATTAAAATCTTAAATATTTATTTTTATTAC
* *
3207345 ATTAAAATTTTCAATATTTATTTTTAT
1 ATTAAAATCTTAAATATTTATTTTTAT
3207372 CTAATTGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTAAAATCTTAAATATTTATTTTTATTAC
Found at i:3213773 original size:28 final size:27
Alignment explanation
Indices: 3213721--3213774 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 27
3213711 TTTATAAAAT
*
3213721 ATTATATATATAATCAATTGAATAATCA
1 ATTATATATATAATAAATT-AATAATCA
3213749 ATTATATATCATAATTAAATT-ATAAT
1 ATTATATAT-ATAA-TAAATTAATAAT
3213775 TACTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 14 0.61
29 4 0.17
30 5 0.22
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (27 bp):
ATTATATATATAATAAATTAATAATCA
Found at i:3214365 original size:4 final size:4
Alignment explanation
Indices: 3214356--3214381 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3214346 TAAAGAAGCA
3214356 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
3214382 CAGCAGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3222843 original size:22 final size:22
Alignment explanation
Indices: 3222814--3222856 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3222804 AATTTTTTAA
3222814 AAATAAAATA-ATAAAATTTTT
1 AAATAAAATAGATAAAATTTTT
*
3222835 AAATCAAAATAGATAATATTTT
1 AAAT-AAAATAGATAAAATTTT
3222857 ATCAGTTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
AAATAAAATAGATAAAATTTTT
Found at i:3223393 original size:13 final size:14
Alignment explanation
Indices: 3223375--3223407 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3223365 CCACCTTTGT
3223375 AAAAAGAAAA-AAA
1 AAAAAGAAAACAAA
*
3223388 AAAAAGAAAACAGA
1 AAAAAGAAAACAAA
3223402 AAAAAG
1 AAAAAG
3223408 TAATGCCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAACAAA
Found at i:3224496 original size:139 final size:139
Alignment explanation
Indices: 3224246--3224526 Score: 526
Period size: 139 Copynumber: 2.0 Consensus size: 139
3224236 AAAATCATAA
*
3224246 TTGGGTTTTGAGTAAGACCCAAGAGAAAGCCTGTGGACACTCATTGATCCATTGGTTGAATTTGG
1 TTGGGTTTTGAATAAGACCCAAGAGAAAGCCTGTGGACACTCATTGATCCATTGGTTGAATTTGG
3224311 GCCTAATTGTTAAGCCTTCACAACAATAAATTTGATCATTAGCAGTTTGCACATCTATTGTGACA
66 GCCTAATTGTTAAGCCTTCACAACAATAAATTTGATCATTAGCAGTTTGCACATCTATTGTGACA
3224376 TAAAATTTT
131 TAAAATTTT
*
3224385 TTGGGTTTTGAATAGGACCCAAGAGAAAGCCTGTGGACACTCATTGATCCATTGGTTGAATTTGG
1 TTGGGTTTTGAATAAGACCCAAGAGAAAGCCTGTGGACACTCATTGATCCATTGGTTGAATTTGG
* *
3224450 GCCTATTTGTTAAGCTTTCACAACAATAAATTTGATCATTAGCAGTTTGCACATCTATTGTGACA
66 GCCTAATTGTTAAGCCTTCACAACAATAAATTTGATCATTAGCAGTTTGCACATCTATTGTGACA
3224515 TAAAATTTT
131 TAAAATTTT
3224524 TTG
1 TTG
3224527 CTACAAAACA
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 138 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (139 bp):
TTGGGTTTTGAATAAGACCCAAGAGAAAGCCTGTGGACACTCATTGATCCATTGGTTGAATTTGG
GCCTAATTGTTAAGCCTTCACAACAATAAATTTGATCATTAGCAGTTTGCACATCTATTGTGACA
TAAAATTTT
Found at i:3227747 original size:23 final size:21
Alignment explanation
Indices: 3227721--3227772 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
3227711 AATGTTATTT
*
3227721 AATTAATAAATAAATAATTATCA
1 AATTAATAAATAAAT-A-TATAA
*
3227744 AATT-TTGAAATAAATATATAA
1 AATTAAT-AAATAAATATATAA
3227765 AATTAATA
1 AATTAATA
3227773 TTTTTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
AATTAATAAATAAATATATAA
Found at i:3235063 original size:24 final size:26
Alignment explanation
Indices: 3235030--3235079 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
3235020 GTTTTGTCAA
3235030 TTTTAAATTATATTTTT-T-ATATTT
1 TTTTAAATTATATTTTTGTCATATTT
* *
3235054 TTTTATATTATGTTTTTGTCATATTT
1 TTTTAAATTATATTTTTGTCATATTT
3235080 AAAATTATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
25 1 0.05
26 6 0.27
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (26 bp):
TTTTAAATTATATTTTTGTCATATTT
Found at i:3235257 original size:2 final size:2
Alignment explanation
Indices: 3235250--3235278 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3235240 CTAATCAATG
3235250 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
3235279 TAGTGTTCAA
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:3238511 original size:35 final size:35
Alignment explanation
Indices: 3238465--3238534 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
3238455 TTCCTGAAGG
*
3238465 GAGTGGTTGTAAATAATAGGTCTTCAATATGGCTT
1 GAGTGGTTGTAAATAATAGGTCTTCAAAATGGCTT
* *
3238500 GAGTGGTTGTAACTAATAGGTCTTGAAAATGGCTT
1 GAGTGGTTGTAAATAATAGGTCTTCAAAATGGCTT
3238535 CCCTTGCTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.36
Consensus pattern (35 bp):
GAGTGGTTGTAAATAATAGGTCTTCAAAATGGCTT
Found at i:3241550 original size:5 final size:6
Alignment explanation
Indices: 3241533--3241557 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3241523 TTTCAGCCGC
3241533 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
3241558 AACCCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:3242649 original size:271 final size:271
Alignment explanation
Indices: 3242166--3242692 Score: 1018
Period size: 271 Copynumber: 1.9 Consensus size: 271
3242156 GTTATGACAA
*
3242166 AATGCGATTCAAGATCTGTTAGTACAACAAGGATTGGATCAGGCATTAAAAAATAGTGAGCTTGA
1 AATGCGATTCAAGATCTGTTAGTACAACAAGGATTGGATCAGGCATTAAAAAATAGTAAGCTTGA
3242231 GGGAATGTTTGATGCTAATTGGAATAGGATTTAGAATAAAGCTGTTAGTACTATTAGATTGGCGC
66 GGGAATGTTTGATGCTAATTGGAATAGGATTTAGAATAAAGCTGTTAGTACTATTAGATTGGCGC
*
3242296 TAGCTCTAGAGGTAAAATACAGTGTGTTGATTGAGAGTACTCCGAAGAGTTTGTGAGATAAACTT
131 TAGCTCCAGAGGTAAAATACAGTGTGTTGATTGAGAGTACTCCGAAGAGTTTGTGAGATAAACTT
* *
3242361 GAAGGTATTTATGCTTCGAAGTCGTTGACTAATAGATTATGTTTTAAGATGGATCTGTATTCTCT
196 GAAGGTATTTATGCTTCGAAGTCGTTGACTAATAGATTATATTTGAAGATGGATCTGTATTCTCT
3242426 GAAGATGGAAG
261 GAAGATGGAAG
3242437 AATGCGATTCAAGATCTGTTAGTACAACAAGGATTGGATCAGGCATTAAAAAATAGTAAGCTTGA
1 AATGCGATTCAAGATCTGTTAGTACAACAAGGATTGGATCAGGCATTAAAAAATAGTAAGCTTGA
3242502 GGGAATGTTTGATGCTAATTGGAATAGGATTTAGAATAAAGCTGTTAGTACTATTAGATTGGCGC
66 GGGAATGTTTGATGCTAATTGGAATAGGATTTAGAATAAAGCTGTTAGTACTATTAGATTGGCGC
3242567 TAGCTCCAGAGGTAAAATACAGTGTGTTGATTGAGAGTACTCCGAAGAGTTTGTGAGATAAACTT
131 TAGCTCCAGAGGTAAAATACAGTGTGTTGATTGAGAGTACTCCGAAGAGTTTGTGAGATAAACTT
3242632 GAAGGTATTTATGCTTCGAAGTCGTTGACTAATAGATTATATTTGAAGATGGATCTGTATT
196 GAAGGTATTTATGCTTCGAAGTCGTTGACTAATAGATTATATTTGAAGATGGATCTGTATT
3242693 GGGAAGAAGG
Statistics
Matches: 252, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
271 252 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (271 bp):
AATGCGATTCAAGATCTGTTAGTACAACAAGGATTGGATCAGGCATTAAAAAATAGTAAGCTTGA
GGGAATGTTTGATGCTAATTGGAATAGGATTTAGAATAAAGCTGTTAGTACTATTAGATTGGCGC
TAGCTCCAGAGGTAAAATACAGTGTGTTGATTGAGAGTACTCCGAAGAGTTTGTGAGATAAACTT
GAAGGTATTTATGCTTCGAAGTCGTTGACTAATAGATTATATTTGAAGATGGATCTGTATTCTCT
GAAGATGGAAG
Done.