Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold127
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: 4281254
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 21 of 26
Found at i:3311984 original size:17 final size:18
Alignment explanation
Indices: 3311957--3311996 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3311947 TAAATATAAT
**
3311957 AAAATTATTAACTTATTA
1 AAAATTATTAAAATATTA
3311975 AAAATT-TTAAAATATTA
1 AAAATTATTAAAATATTA
3311992 AAAAT
1 AAAAT
3311997 ATTTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTATTAAAATATTA
Found at i:3315707 original size:20 final size:20
Alignment explanation
Indices: 3315682--3315724 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
3315672 GTTAAACTAT
3315682 TTTGATAATACTTCCATATA
1 TTTGATAATACTTCCATATA
*
3315702 TTTGATAATACTTCCATGTA
1 TTTGATAATACTTCCATATA
3315722 TTT
1 TTT
3315725 TTAATAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (20 bp):
TTTGATAATACTTCCATATA
Found at i:3316053 original size:13 final size:13
Alignment explanation
Indices: 3316035--3316080 Score: 64
Period size: 11 Copynumber: 3.8 Consensus size: 13
3316025 TGTCACACAT
3316035 AAATATAATATAA
1 AAATATAATATAA
3316048 AAATATAAT-T-A
1 AAATATAATATAA
3316059 AAATAT--TATAA
1 AAATATAATATAA
3316070 AAATATAATAT
1 AAATATAATAT
3316081 GATATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 1 0.03
10 1 0.03
11 14 0.48
12 1 0.03
13 12 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:3316071 original size:22 final size:23
Alignment explanation
Indices: 3316034--3316078 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
3316024 ATGTCACACA
3316034 TAAATATAATATAAAAATATAAT
1 TAAATATAATATAAAAATATAAT
*
3316057 TAAA-ATATTATAAAAATATAAT
1 TAAATATAATATAAAAATATAAT
3316079 ATGATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAATATAATATAAAAATATAAT
Found at i:3316079 original size:27 final size:27
Alignment explanation
Indices: 3316049--3316138 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 27
3316039 ATAATATAAA
3316049 AATATAATTAAAATATTATAAAAATAT
1 AATATAATTAAAATATTATAAAAATAT
* * *
3316076 AATATGATATAAAA-ATAATACAAATAT
1 AATATAAT-TAAAATATTATAAAAATAT
* * *
3316103 AAGAATAACATATGAATATT-TAAAAATAT
1 AA-TATAA-TTA-AAATATTATAAAAATAT
3316132 -ATATAAT
1 AATATAAT
3316139 ATGAATTTTT
Statistics
Matches: 47, Mismatches: 11, Indels: 11
0.68 0.16 0.16
Matches are distributed among these distances:
27 24 0.51
28 11 0.23
29 10 0.21
30 2 0.04
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.33
Consensus pattern (27 bp):
AATATAATTAAAATATTATAAAAATAT
Found at i:3316248 original size:21 final size:19
Alignment explanation
Indices: 3316207--3316249 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3316197 GACATGATTA
*
3316207 AATATATAAATATGATACT
1 AATATATAAATATCATACT
3316226 AATATATAAATTATCATATCT
1 AATATATAAA-TATCATA-CT
3316247 AAT
1 AAT
3316250 TTTAATGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 6 0.29
21 5 0.24
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (19 bp):
AATATATAAATATCATACT
Found at i:3318115 original size:25 final size:26
Alignment explanation
Indices: 3318067--3318212 Score: 83
Period size: 25 Copynumber: 5.5 Consensus size: 26
3318057 AATAATTTTG
* *
3318067 TAATATTAA-AAAATATA-T-ATATA
1 TAATATAAATAAAATATATTAAAATA
3318090 TAATATAAATAAAATA-ATTAAAATA
1 TAATATAAATAAAATATATTAAAATA
*
3318115 TAATATGATAA-AAATATATCTTAAAATTTATA
1 TAATAT-A-AATAAA-ATATATT-AAA---ATA
*
3318147 TAATATAAATTATTAATATATTAAAATA
1 TAATATAAA-TA-AAATATATTAAAATA
*
3318175 T-ATA-AATATAAAATAT-TTTAAATA
1 TAATATAA-ATAAAATATATTAAAATA
3318199 TAATTATAATATAA
1 TAA-TATAA-ATAA
3318213 TAAAATAAAT
Statistics
Matches: 98, Mismatches: 7, Indels: 32
0.72 0.05 0.23
Matches are distributed among these distances:
23 9 0.09
24 15 0.15
25 16 0.16
26 10 0.10
27 16 0.16
28 6 0.06
29 3 0.03
30 2 0.02
31 4 0.04
32 16 0.16
33 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.40
Consensus pattern (26 bp):
TAATATAAATAAAATATATTAAAATA
Found at i:3318155 original size:16 final size:16
Alignment explanation
Indices: 3318136--3318201 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
3318126 AAATATATCT
3318136 TAAAAT-TTATATAATA
1 TAAAATATTATA-AATA
* *
3318152 TAAATTATTA-ATATA
1 TAAAATATTATAAATA
3318167 TTAAAATA-TATAAATA
1 -TAAAATATTATAAATA
*
3318183 TAAAATATTTTAAATA
1 TAAAATATTATAAATA
3318199 TAA
1 TAA
3318202 TTATAATATA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 12 0.29
16 26 0.63
17 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATATTATAAATA
Found at i:3318171 original size:32 final size:31
Alignment explanation
Indices: 3318083--3318191 Score: 97
Period size: 32 Copynumber: 3.6 Consensus size: 31
3318073 TAAAAAATAT
*
3318083 ATATATATAATAT-AAATA-AAATA-ATTAAA
1 ATATATA-AATATAAAATATTAATATATTAAA
* *
3318112 ATATA-ATATGATAAAA-A-T-ATATCTTAAA
1 ATATATAAAT-ATAAAATATTAATATATTAAA
* *
3318140 ATTTATATAATATAAATTATTAATATATTAAA
1 ATATATA-AATATAAAATATTAATATATTAAA
3318172 ATATATAAATATAAAATATT
1 ATATATAAATATAAAATATT
3318192 TTAAATATAA
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
27 5 0.08
28 13 0.21
29 14 0.22
30 3 0.05
31 13 0.21
32 15 0.24
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (31 bp):
ATATATAAATATAAAATATTAATATATTAAA
Found at i:3318214 original size:16 final size:16
Alignment explanation
Indices: 3318081--3318214 Score: 52
Period size: 16 Copynumber: 8.5 Consensus size: 16
3318071 ATTAAAAAAT
3318081 ATATATATATAA-TATA
1 ATATA-ATATAATTATA
* *
3318097 A-ATAAAATAATTAAA
1 ATATAATATAATTATA
* * *
3318112 ATATAATATGATAAAA
1 ATATAATATAATTATA
* *
3318128 ATATATCTTAAAATT-T-
1 ATATA--ATATAATTATA
3318144 ATATAATATAAATTATTA
1 ATATAATAT-AATTA-TA
* *
3318162 ATATATTAAAATATATAA
1 ATATAATATAAT-TAT-A
*
3318180 ATATAAAAT-ATT-T-
1 ATATAATATAATTATA
3318193 -TA-AATATAATTATA
1 ATATAATATAATTATA
3318207 ATATAATA
1 ATATAATA
3318215 AAATAAATAA
Statistics
Matches: 85, Mismatches: 18, Indels: 30
0.64 0.14 0.23
Matches are distributed among these distances:
11 4 0.05
12 5 0.06
13 1 0.01
14 7 0.08
15 14 0.16
16 27 0.32
17 7 0.08
18 20 0.24
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (16 bp):
ATATAATATAATTATA
Found at i:3318485 original size:24 final size:25
Alignment explanation
Indices: 3318456--3318517 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
3318446 AATAAAAATA
*
3318456 ATAAATATTAATTTAATATATT-TTT
1 ATAAATATTAATTTAAAAT-TTATTT
**
3318481 A-AAATAAAAATTTAAAATTTATTT
1 ATAAATATTAATTTAAAATTTATTT
3318505 ATAAATATATAAT
1 ATAAATAT-TAAT
3318518 ATTTTAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 2 0.07
24 18 0.62
25 6 0.21
26 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATAAATATTAATTTAAAATTTATTT
Found at i:3318528 original size:28 final size:27
Alignment explanation
Indices: 3318474--3318539 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
3318464 TAATTTAATA
*
3318474 TATTTTTAAA-ATAAAAATTTAAAATT
1 TATTTATAAATATAAAAATTTAAAATT
* *
3318500 TATTTATAAATATATAATATTTTAAATT
1 TATTTATAAATATA-AAAATTTAAAATT
*
3318528 TAATTATGAAAT
1 TATTTAT-AAAT
3318540 GAATATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 9 0.27
27 3 0.09
28 17 0.52
29 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
TATTTATAAATATAAAAATTTAAAATT
Found at i:3318597 original size:15 final size:14
Alignment explanation
Indices: 3318559--3318599 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
3318549 AATTATTAAA
3318559 TTAATATTTATTTT
1 TTAATATTTATTTT
* *
3318573 TTATTTTTTATCTTT
1 TTAATATTTAT-TTT
3318588 TTAATATTTATT
1 TTAATATTTATT
3318600 GGGGTCAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (14 bp):
TTAATATTTATTTT
Found at i:3323238 original size:53 final size:53
Alignment explanation
Indices: 3322963--3323226 Score: 307
Period size: 53 Copynumber: 5.0 Consensus size: 53
3322953 TGAGTTAGTG
* * ** * * * *
3322963 TCAGGGAGAATAATGACTTAGTGTTGCCTAGT-AAAGTAATGCCTTGGTGGTGG
1 TCAGGAAGAATTATGACTTAGTGTCACTTAGTGAAA-TAACGCCTTGGTGGCGA
* * * * *
3323016 TTAGGAAGAA-TAGTGACTTGGTGTCACTTAATGTAATAACACCTTTGGTGGCGA
1 TCAGGAAGAATTA-TGACTTAGTGTCACTTAGTGAAATAACGCC-TTGGTGGCGA
* * * * *
3323070 TCAGGGAGAATTGTGACTTGGTATCATTTAGTGAAATAACGCCTTGGTGGCGA
1 TCAGGAAGAATTATGACTTAGTGTCACTTAGTGAAATAACGCCTTGGTGGCGA
*
3323123 TCAGGAAGAATTATGACTTAGTGTCACTTAGTGAAATAACGCCTTGGTGGTGA
1 TCAGGAAGAATTATGACTTAGTGTCACTTAGTGAAATAACGCCTTGGTGGCGA
*
3323176 TCAGGAAGAATTATGACTTAGTGTCACTTAGTGAAATAACGCATTGGTGGC
1 TCAGGAAGAATTATGACTTAGTGTCACTTAGTGAAATAACGCCTTGGTGGC
3323227 AGGTAGAAAG
Statistics
Matches: 178, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
52 1 0.01
53 133 0.75
54 43 0.24
55 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (53 bp):
TCAGGAAGAATTATGACTTAGTGTCACTTAGTGAAATAACGCCTTGGTGGCGA
Found at i:3330557 original size:14 final size:15
Alignment explanation
Indices: 3330531--3330559 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3330521 GTTGGGTTTA
3330531 GTATTTGTTTATTAT
1 GTATTTGTTTATTAT
3330546 GTATTT-TTTATTAT
1 GTATTTGTTTATTAT
3330560 TTGCAATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (15 bp):
GTATTTGTTTATTAT
Found at i:3331462 original size:13 final size:14
Alignment explanation
Indices: 3331444--3331476 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3331434 GATAAAATAT
*
3331444 TAAATTTAAA-AGA
1 TAAATTTAAATAAA
3331457 TAAATTTAAATAAA
1 TAAATTTAAATAAA
3331471 TAAATT
1 TAAATT
3331477 ATTTAAAAAA
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:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
TAAATTTAAATAAA
Found at i:3331596 original size:18 final size:18
Alignment explanation
Indices: 3331575--3331630 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
3331565 TAGTTTTATT
3331575 TTTATATATAATATATAA
1 TTTATATATAATATATAA
*
3331593 TTTATATCAT-ATAAATAA
1 TTTATAT-ATAATATATAA
** *
3331611 TACATACATAATATTATAA
1 TTTATATATAATA-TATAA
3331630 T
1 T
3331631 AAAAAATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 2 0.07
18 21 0.70
19 7 0.23
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTATATATAATATATAA
Found at i:3338815 original size:15 final size:13
Alignment explanation
Indices: 3338780--3338845 Score: 57
Period size: 15 Copynumber: 4.9 Consensus size: 13
3338770 TAATATAAAT
3338780 TATTAAATATATTA
1 TATT-AATATATTA
*
3338794 AATTTAATCATATATA
1 TA-TTAAT-ATAT-TA
3338810 TATTAATATATTA
1 TATTAATATATTA
3338823 TATTAAT-TA--A
1 TATTAATATATTA
3338833 TATTAATTATATT
1 TATTAA-TATATT
3338846 TTAACGTGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
10 7 0.16
11 1 0.02
12 4 0.09
13 9 0.21
14 8 0.19
15 11 0.26
16 3 0.07
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
TATTAATATATTA
Found at i:3338849 original size:17 final size:15
Alignment explanation
Indices: 3338762--3338849 Score: 54
Period size: 15 Copynumber: 5.4 Consensus size: 15
3338752 TTTTTGTGAT
*
3338762 TTTTAATATAATATAAA
1 TTTTAATAT-AT-TATA
3338779 TTATTAAATATATTA-A
1 TT-TT-AATATATTATA
*
3338795 ATTTAATCATA-TATA
1 TTTTAAT-ATATTATA
*
3338810 TATTAATATATTATA
1 TTTTAATATATTATA
3338825 TTAATTAATATTAATTATA
1 TT--TTAATA-T-ATTATA
3338844 TTTTAA
1 TTTTAA
3338850 CGTGTCTTCT
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.14
15 16 0.28
16 2 0.03
17 14 0.24
18 5 0.09
19 13 0.22
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTTAATATATTATA
Found at i:3342145 original size:7 final size:7
Alignment explanation
Indices: 3342133--3342176 Score: 70
Period size: 7 Copynumber: 6.3 Consensus size: 7
3342123 GCTTATTGTA
3342133 ATACTAT
1 ATACTAT
3342140 ATACTAT
1 ATACTAT
3342147 ATACTAT
1 ATACTAT
*
3342154 ACACTAT
1 ATACTAT
*
3342161 ATACCAT
1 ATACTAT
3342168 ATACTAT
1 ATACTAT
3342175 AT
1 AT
3342177 TTCGGCCCGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (7 bp):
ATACTAT
Found at i:3343046 original size:12 final size:11
Alignment explanation
Indices: 3343004--3343046 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
3342994 CATTATTATA
3343004 ATATTAATTTT
1 ATATTAATTTT
3343015 ATATTAATATTT
1 ATATTAAT-TTT
3343027 ATA-T-ATTTT
1 ATATTAATTTT
3343036 ATTATTAATTT
1 A-TATTAATTT
3343047 AAAATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
9 4 0.14
10 4 0.14
11 10 0.36
12 10 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:3344591 original size:75 final size:75
Alignment explanation
Indices: 3344434--3344783 Score: 255
Period size: 75 Copynumber: 4.7 Consensus size: 75
3344424 TCTGGTGATT
* * * * ** * * *
3344434 AGGATTTAAGT-GACGAGCACAGGTTTGGCAGCCGGAGTGAATGTTATCTACCAAGATTCTATCA
1 AGGATTTATGTAG-CGAGCACAAGTCTGGCAGCCAGAGTGAATGTTGGCTACTAGGATTCTGTC-
*
3344498 TTT-T-AGCGATC
64 TTTCTGA-CGACC
** * *
3344509 AAAATTTATGTAGCGAGTACAAGTCTGGCAACCAGAGTGAATGTTGGCTACTAGGATTCTGTCTT
1 AGGATTTATGTAGCGAGCACAAGTCTGGCAGCCAGAGTGAATGTTGGCTACTAGGATTCTGTCTT
*
3344574 TCTGGCGACC
66 TCTGACGACC
* * * * * *
3344584 AGGATTTATGTGGCGAGGA-TAGATCTGGCAGTCAGAGT-AAGTGTTGGATA-TCAGGATTCCGT
1 AGGATTTATGTAGCGAGCACAAG-TCTGGCAGCCAGAGTGAA-TGTTGGCTACT-AGGATTCTGT
* *
3344646 CTTTTTGACGATC
63 CTTTCTGACGACC
* * * * * * * * * *
3344659 AAGATTTATGTGGCGAGCACAAATCTTGTAGTCAGAGTGAGTGTTGGCTACCAAGATT-TCATCT
1 AGGATTTATGTAGCGAGCACAAGTCTGGCAGCCAGAGTGAATGTTGGCTACTAGGATTCT-GTCT
3344723 TTCTGACGACC
65 TTCTGACGACC
* * * *
3344734 AGGATTTATGTAGCGAGCACAGGTCAGGCAGCGAGAGTGAGTGTTGGCTA
1 AGGATTTATGTAGCGAGCACAAGTCTGGCAGCCAGAGTGAATGTTGGCTA
3344784 GCAGGGTTGG
Statistics
Matches: 215, Mismatches: 50, Indels: 20
0.75 0.18 0.07
Matches are distributed among these distances:
74 8 0.04
75 204 0.95
76 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (75 bp):
AGGATTTATGTAGCGAGCACAAGTCTGGCAGCCAGAGTGAATGTTGGCTACTAGGATTCTGTCTT
TCTGACGACC
Found at i:3344764 original size:150 final size:150
Alignment explanation
Indices: 3344504--3344780 Score: 351
Period size: 150 Copynumber: 1.8 Consensus size: 150
3344494 ATCATTTTAG
* * * *
3344504 CGATCAAAATTTATGTAGCGAGTACAAGTCTGGCAACCAGAGTGAATGTTGGCTACTAGGATTCT
1 CGATCAAAATTTATGTAGCGAGCACAAATCTGGCAACCAGAGTGAATGTTGGCTACCAAGATTCT
* * * * * *
3344569 GTCTTTCTGGCGACCAGGATTTATGTGGCGAGGATAGATCTGGCAGTC-AGAGTAAGTGTTGGAT
66 ATCTTTCTGACGACCAGGATTTATGTAGCGAGCACAGATCAGGCAG-CGAGAGTAAGTGTTGGAT
3344633 ATCAGGATTCCGTCTTTTTGA
130 ATCAGGATTCCGTCTTTTTGA
* * * * ** *
3344654 CGATCAAGATTTATGTGGCGAGCACAAATCTTGTAGTCAGAGTGAGTGTTGGCTACCAAGATT-T
1 CGATCAAAATTTATGTAGCGAGCACAAATCTGGCAACCAGAGTGAATGTTGGCTACCAAGATTCT
* *
3344718 CATCTTTCTGACGACCAGGATTTATGTAGCGAGCACAGGTCAGGCAGCGAGAGTGAGTGTTGG
66 -ATCTTTCTGACGACCAGGATTTATGTAGCGAGCACAGATCAGGCAGCGAGAGTAAGTGTTGG
3344781 CTAGCAGGGT
Statistics
Matches: 106, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
149 2 0.02
150 104 0.98
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (150 bp):
CGATCAAAATTTATGTAGCGAGCACAAATCTGGCAACCAGAGTGAATGTTGGCTACCAAGATTCT
ATCTTTCTGACGACCAGGATTTATGTAGCGAGCACAGATCAGGCAGCGAGAGTAAGTGTTGGATA
TCAGGATTCCGTCTTTTTGA
Found at i:3344865 original size:88 final size:88
Alignment explanation
Indices: 3344701--3344869 Score: 239
Period size: 88 Copynumber: 1.9 Consensus size: 88
3344691 CAGAGTGAGT
* *
3344701 GTTGGCTACCAAGATTTCATCTTTCTGACGACCAGGATTTATGTAGCGAGCACAGGTCAGGCAGC
1 GTTGGCTACCAAGATTCCATCTTTCTGACGACCAGGATTTATGTAGCGAGCACAAGTCAGGCAGC
* *
3344766 GAGAGTGAGTGTTGGCTAGCAGG
66 GAGAATAAGTGTTGGCTAGCAGG
* * * * * *
3344789 GTTGGCTATCAAGATTCCATCTTTCTGACGACCAGGATTTATGTGGCGAGTATAAGTCTGGTAGC
1 GTTGGCTACCAAGATTCCATCTTTCTGACGACCAGGATTTATGTAGCGAGCACAAGTCAGGCAGC
*
3344854 TAGAATAAGTGTTGGC
66 GAGAATAAGTGTTGGC
3344870 AATCAAGGTA
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
88 70 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (88 bp):
GTTGGCTACCAAGATTCCATCTTTCTGACGACCAGGATTTATGTAGCGAGCACAAGTCAGGCAGC
GAGAATAAGTGTTGGCTAGCAGG
Found at i:3345429 original size:25 final size:26
Alignment explanation
Indices: 3345367--3345455 Score: 110
Period size: 26 Copynumber: 3.5 Consensus size: 26
3345357 ACAGTATTAA
* * *
3345367 TGCCATGGTGGCAATCAGGATC-GTAG
1 TGCCATGGTGGCTAGCAAGATCGGT-G
*
3345393 TGCCATCGTGGCTAGCAAGATCGGTG
1 TGCCATGGTGGCTAGCAAGATCGGTG
3345419 T-CCATGGTGGCTAGCAAGATCGGTG
1 TGCCATGGTGGCTAGCAAGATCGGTG
*
3345444 TGCAATGGTGGC
1 TGCCATGGTGGC
3345456 ATTGATACTA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
25 24 0.44
26 29 0.53
27 2 0.04
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (26 bp):
TGCCATGGTGGCTAGCAAGATCGGTG
Found at i:3345530 original size:78 final size:78
Alignment explanation
Indices: 3345421--3345803 Score: 383
Period size: 78 Copynumber: 4.9 Consensus size: 78
3345411 GATCGGTGTC
* * * * * * * *
3345421 CATGGTGGCTAGCAAGATCGGTGTGCAATGGTGGCATTGATACTATTGATGTCATGGTAGCGATC
1 CATGGTGGCTAGCAGGATCGGAGTGCCATGGTGGCACTGACAGTATTGATGCCATGGTGGCGATC
3345486 AAGG-TCGTAGTGA
66 -AGGATCGTAGTGA
* * * *
3345499 CATGGTGGCTAGCAGGATCAGAGTGCCATGGTGTCACTAACAGTATTGATGCCATGGTGACGATC
1 CATGGTGGCTAGCAGGATCGGAGTGCCATGGTGGCACTGACAGTATTGATGCCATGGTGGCGATC
** *
3345564 AGGATCGGGGTGC
66 AGGATCGTAGTGA
* * * * * * * * * * * *
3345577 CATGGTGACGAGCAGGATCGAATTGACTTGGTGTCACTGACAGTACTAATGTCGTGGTGGTGATC
1 CATGGTGGCTAGCAGGATCGGAGTGCCATGGTGGCACTGACAGTATTGATGCCATGGTGGCGATC
*
3345642 AGGATCATAGTGA
66 AGGATCGTAGTGA
* * * * ** * *
3345655 CATGGTGGCTAGCAAGATCGGAGTGACTTGGTGCCACTGACAAAATTGATGCCGTGGTGGCGATT
1 CATGGTGGCTAGCAGGATCGGAGTGCCATGGTGGCACTGACAGTATTGATGCCATGGTGGCGATC
*
3345720 AGGATCGTAGTGC
66 AGGATCGTAGTGA
* *
3345733 CATGGTGGCTAGCAGGATTGGAGTGCCATGGTGGCACTGACAGTAATGATGCCATGGTGGC-AGT
1 CATGGTGGCTAGCAGGATCGGAGTGCCATGGTGGCACTGACAGTATTGATGCCATGGTGGCGA-T
3345797 CAGGATC
65 CAGGATC
3345804 ATGGTGCCAT
Statistics
Matches: 245, Mismatches: 58, Indels: 4
0.80 0.19 0.01
Matches are distributed among these distances:
77 4 0.02
78 241 0.98
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (78 bp):
CATGGTGGCTAGCAGGATCGGAGTGCCATGGTGGCACTGACAGTATTGATGCCATGGTGGCGATC
AGGATCGTAGTGA
Found at i:3345835 original size:156 final size:156
Alignment explanation
Indices: 3345493--3345841 Score: 358
Period size: 156 Copynumber: 2.2 Consensus size: 156
3345483 ATCAAGGTCG
* * * * * * **
3345493 TAGTGACATGGTGGCTAGCAGGATCAGAGTGCCATGGTGTCACTAACAGTATTGATGCCATGGTG
1 TAGTGACATGATGGCGAGCAAGATCAGAGTGACTTGGTGCCACTAACAAAATTGATGCCATGGTG
* * * * *
3345558 ACGATCAGGATCGGGGTGCCATGGTGACGAGCAGGATCGAATTGACTTGGTGTCACTGACAGTAC
66 ACGATCAGGATCGGAGTGCCATGGTGACGAGCAGGATCGAAGTGACATGGTGGCACTGACAGTAA
* * *
3345623 TAATGTCGTGGTGGTGATCAGGATCA
131 TAATGCCATGGTGGAGATCAGGATCA
* * * * *
3345649 TAGTGACATGGTGGCTAGCAAGATCGGAGTGACTTGGTGCCACTGACAAAATTGATGCCGTGGTG
1 TAGTGACATGATGGCGAGCAAGATCAGAGTGACTTGGTGCCACTAACAAAATTGATGCCATGGTG
* * * * * * * *
3345714 GCGATTAGGATCGTAGTGCCATGGTGGCTAGCAGGATTGGAGTGCCATGGTGGCACTGACAGTAA
66 ACGATCAGGATCGGAGTGCCATGGTGACGAGCAGGATCGAAGTGACATGGTGGCACTGACAGTAA
*
3345779 TGATGCCATGGTGGCAG-TCAGGATCA
131 TAATGCCATGGTGG-AGATCAGGATCA
* * * * * *
3345805 TGGTGCCATGATGGGGAGTAGGCTCAGAGTGACTTGG
1 TAGTGACATGATGGCGAGCAAGATCAGAGTGACTTGG
3345842 AATCGAGACT
Statistics
Matches: 157, Mismatches: 35, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
156 156 0.99
157 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.24
Consensus pattern (156 bp):
TAGTGACATGATGGCGAGCAAGATCAGAGTGACTTGGTGCCACTAACAAAATTGATGCCATGGTG
ACGATCAGGATCGGAGTGCCATGGTGACGAGCAGGATCGAAGTGACATGGTGGCACTGACAGTAA
TAATGCCATGGTGGAGATCAGGATCA
Found at i:3347324 original size:75 final size:75
Alignment explanation
Indices: 3347134--3347324 Score: 188
Period size: 75 Copynumber: 2.5 Consensus size: 75
3347124 GACTGTTTGT
* * * * * *
3347134 CAGAGATT-CATCTTTCTGGTGACCAAGATTTAAGTGGCGAGTACAGGTTTGGCAGCCAGAGTGA
1 CAGA-ATTCCATCATTCTGGCGACCAAGATTTATGTGGCGAGTACAAGTCTGGCAACCAGAGTGA
3347198 ATATTGTCTAC
65 ATATTGTCTAC
* * * * * *
3347209 CAGAATTCTATCATTTTAGCGACCAGGATTTATATAGCGAGTACAAGTCTGGCAACCAGAGTGAA
1 CAGAATTCCATCATTCTGGCGACCAAGATTTATGTGGCGAGTACAAGTCTGGCAACCAGAGTGAA
*
3347274 TGTTGAT-TAC
66 TATTG-TCTAC
* * * * *
3347284 CAGGATTCCGTCCTTCTGGCGATCAAAATTTATGTGGCGAG
1 CAGAATTCCATCATTCTGGCGACCAAGATTTATGTGGCGAG
3347325 GATAGATCTG
Statistics
Matches: 90, Mismatches: 24, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
74 3 0.03
75 86 0.96
76 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (75 bp):
CAGAATTCCATCATTCTGGCGACCAAGATTTATGTGGCGAGTACAAGTCTGGCAACCAGAGTGAA
TATTGTCTAC
Found at i:3350441 original size:4 final size:4
Alignment explanation
Indices: 3350432--3350470 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
3350422 CAATGAAAAC
3350432 TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT
3350471 CAAAGGACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:3354483 original size:33 final size:31
Alignment explanation
Indices: 3354446--3354513 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 31
3354436 TTATCCACAT
3354446 ATTAAATATT-TTTAATTTT-TTAAAATATATAAA
1 ATTAAAT-TTATTT-ATTTTATTAAAAT-TA-AAA
3354479 ATTAAATTTATTTATTTTAATTAAAATTAAAA
1 ATTAAATTTATTTATTTT-ATTAAAATTAAAA
3354511 ATT
1 ATT
3354514 TATTAATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
32 13 0.41
33 12 0.38
34 7 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
ATTAAATTTATTTATTTTATTAAAATTAAAA
Found at i:3357119 original size:12 final size:12
Alignment explanation
Indices: 3357102--3357139 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3357092 ATATCACATC
3357102 ATATTTTATATT
1 ATATTTTATATT
3357114 ATATTTTA-ATT
1 ATATTTTATATT
3357125 AT-TTTTATAATT
1 ATATTTTAT-ATT
3357137 ATA
1 ATA
3357140 ATTAAAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.22
11 5 0.22
12 13 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATATTTTATATT
Found at i:3357331 original size:3 final size:3
Alignment explanation
Indices: 3357323--3357348 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3357313 CTTAAAAGAA
3357323 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3357349 CTTTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3359040 original size:23 final size:23
Alignment explanation
Indices: 3359014--3359060 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3359004 AATATGTCTG
* *
3359014 AAGTTTGAATTTTAACTATCGCA
1 AAGTTCGAATTTCAACTATCGCA
*
3359037 AAGTTCGAATTTCAACTATTGCA
1 AAGTTCGAATTTCAACTATCGCA
3359060 A
1 A
3359061 CTTTTCCTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (23 bp):
AAGTTCGAATTTCAACTATCGCA
Found at i:3360947 original size:24 final size:24
Alignment explanation
Indices: 3360895--3360959 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
3360885 CTTTATTTAA
* *
3360895 ATTTTATTTTATAATATTTTAATT
1 ATTTTATTTGATAATAATTTAATT
3360919 A-TTTATTTAGATAA-AATTTAATT
1 ATTTTATTT-GATAATAATTTAATT
3360942 ATTTTAATTT--TAATAATT
1 ATTTT-ATTTGATAATAATT
3360960 GACAAATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
22 3 0.09
23 20 0.57
24 8 0.23
25 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
ATTTTATTTGATAATAATTTAATT
Found at i:3361073 original size:16 final size:16
Alignment explanation
Indices: 3361052--3361093 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3361042 ACAACGTTAT
*
3361052 TGCTAGGTAACTTTGC
1 TGCTAGGTAACTTTAC
* *
3361068 TGCTAGGTAGCTTTAT
1 TGCTAGGTAACTTTAC
3361084 TGCTAGGTAA
1 TGCTAGGTAA
3361094 TGATGTTGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.38
Consensus pattern (16 bp):
TGCTAGGTAACTTTAC
Found at i:3361089 original size:32 final size:32
Alignment explanation
Indices: 3361048--3361124 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
3361038 GACAACAACG
*
3361048 TTATTGCTAGGTAACT-TTGCTGCTAGGTAGCT
1 TTATTGCTAGGTAA-TGATGCTGCTAGGTAGCT
* *
3361080 TTATTGCTAGGTAATGATGTTGCTTGGTAGCT
1 TTATTGCTAGGTAATGATGCTGCTAGGTAGCT
*
3361112 TTATCGCTAGGTA
1 TTATTGCTAGGTA
3361125 GAGTTGCCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 1 0.03
32 39 0.98
ACGTcount: A:0.19, C:0.13, G:0.26, T:0.42
Consensus pattern (32 bp):
TTATTGCTAGGTAATGATGCTGCTAGGTAGCT
Found at i:3361124 original size:16 final size:15
Alignment explanation
Indices: 3361052--3361125 Score: 51
Period size: 16 Copynumber: 4.7 Consensus size: 15
3361042 ACAACGTTAT
* *
3361052 TGCTAGGTAACTTTGC
1 TGCTAGGTAGCTTT-A
3361068 TGCTAGGTAGCTTTA
1 TGCTAGGTAGCTTTA
* *
3361083 TTGCTAGGTAATGATGT-
1 -TGCTAGGT-A-GCTTTA
*
3361100 TGCTTGGTAGCTTTA
1 TGCTAGGTAGCTTTA
3361115 TCGCTAGGTAG
1 T-GCTAGGTAG
3361126 AGTTGCCATA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
14 3 0.07
15 2 0.04
16 36 0.80
17 1 0.02
18 3 0.07
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.39
Consensus pattern (15 bp):
TGCTAGGTAGCTTTA
Found at i:3362513 original size:22 final size:22
Alignment explanation
Indices: 3362489--3362531 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
3362479 AAAATTTCAA
3362489 TTTT-TTATTTAATATTTATATAT
1 TTTTATTA-TTAA-ATTTATATAT
3362512 TTTTATTATTAAATTTATAT
1 TTTTATTATTAAATTTATAT
3362532 GAAAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 8 0.42
24 3 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTATTATTAAATTTATATAT
Found at i:3364854 original size:13 final size:14
Alignment explanation
Indices: 3364825--3364857 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3364815 GAAAATAAAA
3364825 AATTTAAAATGTTTT
1 AATTTAAAA-GTTTT
3364840 AATTTAAAA-TTTT
1 AATTTAAAAGTTTT
3364853 AATTT
1 AATTT
3364858 TTTCTTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
15 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
AATTTAAAAGTTTT
Found at i:3365282 original size:17 final size:17
Alignment explanation
Indices: 3365250--3365293 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
3365240 TTAATTATGA
3365250 AATATATAAA-TTTAAT
1 AATATATAAATTTTAAT
3365266 AATATATAAATTTTAAT
1 AATATATAAATTTTAAT
*
3365283 AATATAAAAAT
1 AATATATAAAT
3365294 AATATTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATATAAATTTTAAT
Found at i:3366653 original size:17 final size:17
Alignment explanation
Indices: 3366606--3366654 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
3366596 GTATATAATA
3366606 ATAAATATTCATAATTC
1 ATAAATATTCATAATTC
* * *
3366623 ATGAATGTTTATAACTT-
1 ATAAATATTCATAA-TTC
3366640 ATAAATATTCATAAT
1 ATAAATATTCATAAT
3366655 AACATTTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
16 1 0.04
17 22 0.88
18 2 0.08
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (17 bp):
ATAAATATTCATAATTC
Found at i:3368716 original size:28 final size:29
Alignment explanation
Indices: 3368685--3368747 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 29
3368675 TATTTTTTAT
3368685 TAATATTTATATATT-TTATAATTAAAAA
1 TAATATTTATATATTATTATAATTAAAAA
* * *
3368713 TAATA--AATATATTATTTTAATTTAAAA
1 TAATATTTATATATTATTATAATTAAAAA
*
3368740 TACTATTT
1 TAATATTT
3368748 TGAGATAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
26 7 0.26
27 15 0.56
28 5 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
TAATATTTATATATTATTATAATTAAAAA
Found at i:3373406 original size:13 final size:14
Alignment explanation
Indices: 3373370--3373407 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3373360 TAAAATTTGT
*
3373370 TAAATATAATTTTT
1 TAAATATAATTTTA
*
3373384 TTAATATAATTTTA
1 TAAATATAATTTTA
3373398 TAAAT-TAATT
1 TAAATATAATT
3373408 AAATTAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAAATATAATTTTA
Found at i:3378684 original size:44 final size:44
Alignment explanation
Indices: 3378596--3378691 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 44
3378586 TAACTACATA
* * *
3378596 TTTTGTGAAAATAAGGTGAAACTGTATGAAAGTGAGACCAAAAC
1 TTTTGTGAAAATAAGGTGAAAATATATGAAAGTAAGACCAAAAC
* * * * *
3378640 TTTTGTGAATATAAGGTGAAAATATGTGAGAGTAAGGCCCAAAC
1 TTTTGTGAAAATAAGGTGAAAATATATGAAAGTAAGACCAAAAC
3378684 TTTTGTGA
1 TTTTGTGA
3378692 GGCTTTCTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (44 bp):
TTTTGTGAAAATAAGGTGAAAATATATGAAAGTAAGACCAAAAC
Found at i:3379785 original size:23 final size:26
Alignment explanation
Indices: 3379730--3379785 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 26
3379720 TACTAATTAT
3379730 TTTTAATTTAATATTATAAAAATATA
1 TTTTAATTTAATATTATAAAAATATA
*
3379756 TTATAATTT-AT-TT-T-AAAATATAA
1 TTTTAATTTAATATTATAAAAATAT-A
3379779 TTTTAAT
1 TTTTAAT
3379786 ATATAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 7 0.26
23 8 0.30
24 2 0.07
25 2 0.07
26 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTAATTTAATATTATAAAAATATA
Found at i:3379942 original size:29 final size:31
Alignment explanation
Indices: 3379883--3379940 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3379873 GTGTATATAT
*
3379883 ATATATAATATATATTAAAAATATAAAAATA
1 ATATATAAAATATATTAAAAATATAAAAATA
3379914 ATATATAAAATAT-TTAAAGAA-ATAAAA
1 ATATATAAAATATATTAAA-AATATAAAA
3379941 TAGTAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (31 bp):
ATATATAAAATATATTAAAAATATAAAAATA
Found at i:3380250 original size:21 final size:21
Alignment explanation
Indices: 3380196--3380283 Score: 90
Period size: 22 Copynumber: 4.1 Consensus size: 21
3380186 TTTTTTTCTT
*
3380196 AAAATATTAAAAAA-AATATA
1 AAAATATTAAAAAATAAAATA
3380216 AAAATATTATAAAAATAAAATA
1 AAAATATTA-AAAAATAAAATA
* *
3380238 ATAATTTTAAAAAATAAAATA
1 AAAATATTAAAAAATAAAATA
* *
3380259 AAATAAAATAAAATAA-AAAATA
1 AAA-ATATTAAAA-AATAAAATA
3380281 AAA
1 AAA
3380284 CAAATATTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 9 0.16
21 19 0.33
22 27 0.47
23 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAATATTAAAAAATAAAATA
Found at i:3380283 original size:5 final size:5
Alignment explanation
Indices: 3380248--3380276 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3380238 ATAATTTTAA
3380248 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
3380277 AATAAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:3395913 original size:51 final size:51
Alignment explanation
Indices: 3395818--3395921 Score: 147
Period size: 51 Copynumber: 2.0 Consensus size: 51
3395808 TTTTTCAGTT
* * *
3395818 GGTTCTTTAGTGCAAGCGCGAGATTTATGAGATGTTTGGAGGTTAGAACTA
1 GGTTCTTTAGTGCAAACGCAAGATTTATGAGACGTTTGGAGGTTAGAACTA
* *
3395869 GGTTCTTTAGTGCAAACGCAAGGGTTTATGAGGCGTTTGG-GGTTAGAACTA
1 GGTTCTTTAGTGCAAACGCAA-GATTTATGAGACGTTTGGAGGTTAGAACTA
3395920 GG
1 GG
3395922 GCTTTGGGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 32 0.68
52 15 0.32
ACGTcount: A:0.24, C:0.11, G:0.34, T:0.32
Consensus pattern (51 bp):
GGTTCTTTAGTGCAAACGCAAGATTTATGAGACGTTTGGAGGTTAGAACTA
Found at i:3397699 original size:25 final size:24
Alignment explanation
Indices: 3397670--3397721 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
3397660 TATTATTAAT
3397670 AATAA-AATTATTTAATGAGAGCAAC
1 AATAATAATT-TTTAATGA-AGCAAC
* *
3397695 AATAATAATTTTTATTGAAGGAAC
1 AATAATAATTTTTAATGAAGCAAC
3397719 AAT
1 AAT
3397722 TTATAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 12 0.50
26 4 0.17
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.33
Consensus pattern (24 bp):
AATAATAATTTTTAATGAAGCAAC
Found at i:3399487 original size:21 final size:22
Alignment explanation
Indices: 3399460--3399516 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
3399450 ACTCGTAATT
3399460 ATTATTTTATAAAT-TTATTTA
1 ATTATTTTATAAATATTATTTA
* *
3399481 TTTATTTTAAATATATATTATTTA
1 ATTATTTT--ATAAATATTATTTA
3399505 ATTATTTATATA
1 ATTATTT-TATA
3399517 CGTAATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 7 0.24
23 8 0.28
24 13 0.45
25 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTATTTTATAAATATTATTTA
Found at i:3399840 original size:2 final size:2
Alignment explanation
Indices: 3399835--3399859 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3399825 CATACGTGTG
3399835 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3399860 TGCCATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3407269 original size:27 final size:27
Alignment explanation
Indices: 3407231--3407297 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
3407221 TTTATTTATC
3407231 GGGGATACTCCAATCTCATTCCTCCGA
1 GGGGATACTCCAATCTCATTCCTCCGA
*
3407258 GGGGATACTCCAATCTCATTCCTCTGA
1 GGGGATACTCCAATCTCATTCCTCCGA
*
3407285 AGGGATACTCCAA
1 GGGGATACTCCAA
3407298 CCCTGCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (27 bp):
GGGGATACTCCAATCTCATTCCTCCGA
Found at i:3421469 original size:2 final size:2
Alignment explanation
Indices: 3421462--3421500 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3421452 ATACTTGTTT
3421462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3421501 TGACATAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3424297 original size:2 final size:2
Alignment explanation
Indices: 3424290--3424346 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
3424280 ATGTACATAC
* * * * *
3424290 AT AT AT AT AC AT AT AT AT AC AT AT AT GT GT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
3424332 AT AC AT AT AC AT AT A
1 AT AT AT AT AT AT AT A
3424347 GTGACAAGCT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (2 bp):
AT
Found at i:3424334 original size:10 final size:10
Alignment explanation
Indices: 3424286--3424315 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
3424276 GCATATGTAC
3424286 ATACATATAT
1 ATACATATAT
3424296 ATACATATAT
1 ATACATATAT
3424306 ATACATATAT
1 ATACATATAT
3424316 GTGTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (10 bp):
ATACATATAT
Found at i:3424391 original size:6 final size:6
Alignment explanation
Indices: 3424382--3424519 Score: 80
Period size: 6 Copynumber: 23.2 Consensus size: 6
3424372 ACACACACAC
* * * * * * * *
3424382 ATATAT ATATAT ATGTAG ATATAT GTACAT ATACAT TTATAT CTAAAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * * *
3424430 ATATAT ATATAT ATATAT ACATAT ATTTAC ATCTAT A-ATAT ATATAA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * * * * * *
3424477 ATACAT ATGTAC ATACAT ATATGT GTATAT GTATAT ATGTAT A
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT A
3424520 CAAGTATACA
Statistics
Matches: 96, Mismatches: 35, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
5 4 0.04
6 92 0.96
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (6 bp):
ATATAT
Found at i:3424393 original size:8 final size:8
Alignment explanation
Indices: 3424382--3424519 Score: 80
Period size: 8 Copynumber: 17.4 Consensus size: 8
3424372 ACACACACAC
3424382 ATATATAT
1 ATATATAT
*
3424390 ATATATGT
1 ATATATAT
*
3424398 AGATATAT
1 ATATATAT
* *
3424406 GTACATAT
1 ATATATAT
* *
3424414 ACATTTAT
1 ATATATAT
* *
3424422 ATCTAAAT
1 ATATATAT
3424430 ATATATAT
1 ATATATAT
3424438 ATATATAT
1 ATATATAT
*
3424446 ATACATAT
1 ATATATAT
* *
3424454 ATTTACAT
1 ATATATAT
*
3424462 CTATA-AT
1 ATATATAT
*
3424469 ATATATAA
1 ATATATAT
*
3424477 ATACATAT
1 ATATATAT
* * *
3424485 GTACATAC
1 ATATATAT
*
3424493 ATATATGT
1 ATATATAT
* *
3424501 GTATATGT
1 ATATATAT
*
3424509 ATATATGT
1 ATATATAT
3424517 ATA
1 ATA
3424520 CAAGTATACA
Statistics
Matches: 95, Mismatches: 34, Indels: 2
0.73 0.26 0.02
Matches are distributed among these distances:
7 6 0.06
8 89 0.94
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (8 bp):
ATATATAT
Found at i:3424395 original size:10 final size:10
Alignment explanation
Indices: 3424382--3424519 Score: 80
Period size: 10 Copynumber: 13.9 Consensus size: 10
3424372 ACACACACAC
3424382 ATATATATAT
1 ATATATATAT
* *
3424392 ATATGTAGAT
1 ATATATATAT
* *
3424402 ATATGTACAT
1 ATATATATAT
* *
3424412 ATACATTTAT
1 ATATATATAT
* *
3424422 ATCTAAATAT
1 ATATATATAT
3424432 ATATATATAT
1 ATATATATAT
*
3424442 ATATATACAT
1 ATATATATAT
* *
3424452 ATATTTACAT
1 ATATATATAT
*
3424462 CTATA-ATAT
1 ATATATATAT
* *
3424471 ATATAAATAC
1 ATATATATAT
* *
3424481 ATATGTACAT
1 ATATATATAT
* *
3424491 ACATATATGT
1 ATATATATAT
* *
3424501 GTATATGTAT
1 ATATATATAT
*
3424511 ATATGTATA
1 ATATATATA
3424520 CAAGTATACA
Statistics
Matches: 92, Mismatches: 35, Indels: 2
0.71 0.27 0.02
Matches are distributed among these distances:
9 7 0.08
10 85 0.92
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (10 bp):
ATATATATAT
Found at i:3438087 original size:21 final size:21
Alignment explanation
Indices: 3438063--3438104 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3438053 AATCAAAGAT
*
3438063 CAGATACAAAGATCATTAACA
1 CAGATACAAAGAACATTAACA
3438084 CAGATACAAAGAACATTAACA
1 CAGATACAAAGAACATTAACA
3438105 ATCACCAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.19, G:0.10, T:0.17
Consensus pattern (21 bp):
CAGATACAAAGAACATTAACA
Found at i:3442526 original size:2 final size:2
Alignment explanation
Indices: 3442519--3442544 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3442509 TCAGTTCAGA
3442519 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3442545 TGTATCAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3452782 original size:3 final size:3
Alignment explanation
Indices: 3452774--3452800 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3452764 GAGAGAATGA
3452774 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3452801 TTCGATCGAA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3454761 original size:2 final size:2
Alignment explanation
Indices: 3454754--3454801 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
3454744 GACCTCCATG
3454754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3454796 AT AT AT
1 AT AT AT
3454802 TTGTGATACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3455057 original size:23 final size:23
Alignment explanation
Indices: 3455026--3455071 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
3455016 AAATAATTAA
3455026 AATATAATATGATATAAA-AAAT
1 AATATAATATGATATAAATAAAT
3455048 AATATGAATATGATATAAATAAAT
1 AATAT-AATATGATATAAATAAAT
3455072 GAATCTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.33
Consensus pattern (23 bp):
AATATAATATGATATAAATAAAT
Found at i:3455379 original size:10 final size:10
Alignment explanation
Indices: 3455364--3455528 Score: 67
Period size: 10 Copynumber: 17.3 Consensus size: 10
3455354 AATCTAATAC
3455364 AAATATATAT
1 AAATATATAT
*
3455374 AAATATGTCA-
1 AAATATAT-AT
*
3455384 AAATATACAT
1 AAATATATAT
*
3455394 AAAATAAATTATT
1 -AAATATA-TA-T
3455407 AATATATATAT
1 AA-ATATATAT
* *
3455418 AAATTTATAC
1 AAATATATAT
3455428 AAAT-T-TAT
1 AAATATATAT
*
3455436 -AATAT-TTT
1 AAATATATAT
3455444 AAATATATA-
1 AAATATATAT
3455453 AAA-A-ATA-
1 AAATATATAT
3455460 AAATA-A-A-
1 AAATATATAT
3455467 AAATA-AT-T
1 AAATATATAT
3455475 AAAATATAATAT
1 -AAATAT-ATAT
3455487 AAA-ATAATAT
1 AAATAT-ATAT
3455497 AAATATAATAT
1 AAATAT-ATAT
*
3455508 GAATATAT-T
1 AAATATATAT
3455517 AAAT-TATAT
1 AAATATATAT
3455526 AAA
1 AAA
3455529 AATAAACATA
Statistics
Matches: 124, Mismatches: 13, Indels: 37
0.71 0.07 0.21
Matches are distributed among these distances:
7 16 0.13
8 11 0.09
9 23 0.19
10 36 0.29
11 27 0.22
12 6 0.05
13 5 0.04
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (10 bp):
AAATATATAT
Found at i:3455467 original size:12 final size:12
Alignment explanation
Indices: 3455450--3455501 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
3455440 TTTTAAATAT
3455450 ATAAAAAATAAA
1 ATAAAAAATAAA
3455462 ATAAAAAAT-AA
1 ATAAAAAATAAA
* * *
3455473 TTAAAATATAAT
1 ATAAAAAATAAA
3455485 ATAAAATAATATAA
1 ATAAAA-AATA-AA
3455499 ATA
1 ATA
3455502 TAATATGAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 9 0.29
12 15 0.48
13 3 0.10
14 4 0.13
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:3455470 original size:23 final size:24
Alignment explanation
Indices: 3455444--3455497 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
3455434 ATAATATTTT
3455444 AAATATA-TAAAAAATAAAATAAA
1 AAATATATTAAAAAATAAAATAAA
* *
3455467 AAATA-ATTAAAATATAATATAAA
1 AAATATATTAAAAAATAAAATAAA
3455490 ATAATATA
1 A-AATATA
3455498 AATATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 1 0.04
23 20 0.77
24 4 0.15
25 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATATATTAAAAAATAAAATAAA
Found at i:3455480 original size:21 final size:22
Alignment explanation
Indices: 3455444--3455504 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
3455434 ATAATATTTT
*
3455444 AAATATATAAAAAATAAAATAAA
1 AAATA-ATATAAAATAAAATAAA
* *
3455467 AAATAAT-TAAAATATAATATA
1 AAATAATATAAAATAAAATAAA
3455488 AAATAATATAAATATAA
1 AAATAATATAAA-ATAA
3455505 TATGAATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 18 0.56
22 6 0.19
23 8 0.25
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATAATATAAAATAAAATAAA
Found at i:3455505 original size:21 final size:21
Alignment explanation
Indices: 3455454--3455533 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
3455444 AAATATATAA
* *
3455454 AAAATAAAATAAAAAATAATT
1 AAAATATAATATAAAATAATT
3455475 AAAATATAATATAAAATAA-T
1 AAAATATAATATAAAATAATT
*
3455495 ATAAATATAATAT-GAATATATT
1 A-AAATATAATATAAAATA-ATT
*
3455517 AAATTAT-ATA-AAAATAA
1 AAAATATAATATAAAATAA
3455534 ACATATAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.02
20 13 0.26
21 34 0.68
22 2 0.04
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (21 bp):
AAAATATAATATAAAATAATT
Found at i:3455506 original size:11 final size:11
Alignment explanation
Indices: 3455353--3455533 Score: 66
Period size: 11 Copynumber: 16.7 Consensus size: 11
3455343 AAAATAATTA
* *
3455353 AAATCTAATAC
1 AAATATAATAT
3455364 AAATAT-ATAT
1 AAATATAATAT
*
3455374 AAATAT-GTCA-
1 AAATATAAT-AT
3455384 AAATATACATA-
1 AAATATA-ATAT
3455395 AAATA-AATTAT
1 AAATATAA-TAT
*
3455406 TAATATATATAT
1 AAATATA-ATAT
* *
3455418 AAAT-TTATAC
1 AAATATAATAT
3455428 AAATTTATAATATTTT
1 AAA--TATAATA---T
3455444 AAATAT-ATA-
1 AAATATAATAT
* *
3455453 AAAAATAAAAT
1 AAATATAATAT
*
3455464 AAAAAATAAT-T
1 -AAATATAATAT
3455475 AAAATATAATAT
1 -AAATATAATAT
3455487 AAA-ATAATAT
1 AAATATAATAT
3455497 AAATATAATAT
1 AAATATAATAT
*
3455508 GAATAT-AT-T
1 AAATATAATAT
3455517 AAAT-T-ATAT
1 AAATATAATAT
*
3455526 AAAAATAA
1 AAATATAA
3455534 ACATATAAAA
Statistics
Matches: 132, Mismatches: 17, Indels: 42
0.69 0.09 0.22
Matches are distributed among these distances:
8 3 0.02
9 14 0.11
10 40 0.30
11 43 0.33
12 18 0.14
13 8 0.06
14 3 0.02
16 3 0.02
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (11 bp):
AAATATAATAT
Found at i:3456287 original size:22 final size:22
Alignment explanation
Indices: 3456261--3456339 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 22
3456251 TATGTATTTT
3456261 TATAATATTTAATTTTAAATTA
1 TATAATATTTAATTTTAAATTA
*
3456283 TATAAGTGTTTTAAATTTTAAATTTA
1 TATAA-T-ATTT-AATTTTAAA-TTA
* * *
3456309 TTTATTATTT-ATATTAAATTA
1 TATAATATTTAATTTTAAATTA
3456330 -AT-ATATTTAA
1 TATAATATTTAA
3456340 ATTAAATAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
19 5 0.11
20 2 0.04
21 3 0.07
22 12 0.27
23 1 0.02
24 6 0.13
25 10 0.22
26 6 0.13
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (22 bp):
TATAATATTTAATTTTAAATTA
Found at i:3456338 original size:19 final size:18
Alignment explanation
Indices: 3456314--3456351 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
3456304 ATTTATTTAT
*
3456314 TATTTATATTAAATTAATA
1 TATTTAAATTAAA-TAATA
3456333 TATTTAAATTAAATAATA
1 TATTTAAATTAAATAATA
3456351 T
1 T
3456352 TATCTGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTAAATTAAATAATA
Found at i:3457358 original size:17 final size:16
Alignment explanation
Indices: 3457338--3457375 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
3457328 TATATAATTT
3457338 ATTATTTTATTTGATAA
1 ATTATTTTATTTGAT-A
*
3457355 ATTATTTTATTTTATA
1 ATTATTTTATTTGATA
3457371 ATTAT
1 ATTAT
3457376 ATAAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
ATTATTTTATTTGATA
Found at i:3457363 original size:25 final size:25
Alignment explanation
Indices: 3457318--3457369 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 25
3457308 TTAGTAGTAA
*
3457318 TTTATTTGAGTATATAATTTATTAT
1 TTTATTTGAGTAAATAATTTATTAT
*
3457343 TTTATTTGA-TAAATTA-TT-TTAT
1 TTTATTTGAGTAAATAATTTATTAT
3457365 TTTAT
1 TTTAT
3457370 AATTATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.36
23 2 0.08
24 5 0.20
25 9 0.36
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (25 bp):
TTTATTTGAGTAAATAATTTATTAT
Found at i:3459918 original size:15 final size:13
Alignment explanation
Indices: 3459882--3459911 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3459872 TTTTATTTAT
3459882 GTACA-ATTGATA
1 GTACATATTGATA
3459894 GTACATATTGATA
1 GTACATATTGATA
3459907 GTACA
1 GTACA
3459912 CATATTGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
GTACATATTGATA
Found at i:3464448 original size:2 final size:2
Alignment explanation
Indices: 3464441--3464467 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3464431 AAGCACATAA
3464441 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3464468 AAACAACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3464922 original size:23 final size:22
Alignment explanation
Indices: 3464892--3464935 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3464882 AGAAAAAATA
*
3464892 AATTTTTTAAAATTTTTTTATT
1 AATTTTTTAAAATTATTTTATT
*
3464914 AATTATTTTTAAATTATTTTAT
1 AATT-TTTTAAAATTATTTTAT
3464936 AAAAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
AATTTTTTAAAATTATTTTATT
Found at i:3464948 original size:23 final size:23
Alignment explanation
Indices: 3464895--3464949 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
3464885 AAAAATAAAT
* **
3464895 TTTTTAAAATTTTTTTATTAATTA
1 TTTTT-AAATTATTTTATTAAAAA
3464919 TTTTTAAATTATTTTA-TAAAAA
1 TTTTTAAATTATTTTATTAAAAA
3464941 TTTATTAAA
1 TTT-TTAAA
3464950 AAAATAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.26
23 15 0.56
24 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTTAAATTATTTTATTAAAAA
Found at i:3466272 original size:2 final size:2
Alignment explanation
Indices: 3466265--3466293 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3466255 TGCAAGAGAA
3466265 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 A
3466294 AAACTACAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3472850 original size:23 final size:24
Alignment explanation
Indices: 3472820--3472868 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
3472810 TATATTTTTT
*
3472820 ATATATAA-ATTTTAAAATTATAA
1 ATATATAATATTTAAAAATTATAA
*
3472843 ATATATAATATTTAAAAATTTTAA
1 ATATATAATATTTAAAAATTATAA
3472867 AT
1 AT
3472869 GTTAAATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATATAATATTTAAAAATTATAA
Found at i:3473502 original size:19 final size:18
Alignment explanation
Indices: 3473475--3473545 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 18
3473465 AAATATGATA
* *
3473475 ATTTGTATATTTATATTTT
1 ATTTATATATTT-TATTAT
3473494 ATTTATATATTTTATTAT
1 ATTTATATATTTTATTAT
3473512 A-TTATAATTATTTTAAATTAT
1 ATTTAT-A-TATTTT--ATTAT
3473533 -TTTATAT-TTTTAT
1 ATTTATATATTTTAT
3473546 AAATTTTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
16 2 0.04
17 4 0.09
18 11 0.24
19 18 0.40
20 1 0.02
21 9 0.20
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (18 bp):
ATTTATATATTTTATTAT
Found at i:3473531 original size:21 final size:20
Alignment explanation
Indices: 3473507--3473550 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
3473497 TATATATTTT
3473507 ATTATATTATAATTATTT-TAA
1 ATTATATTAT-ATT-TTTATAA
*
3473528 ATTATTTTATATTTTTATAA
1 ATTATATTATATTTTTATAA
3473548 ATT
1 ATT
3473551 TTAATACGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 9 0.43
21 9 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTATATTATATTTTTATAA
Found at i:3473615 original size:17 final size:18
Alignment explanation
Indices: 3473581--3473616 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3473571 ATTATATAAA
*
3473581 ATTTAAAATATTTATTTT
1 ATTTAAAATATATATTTT
3473599 ATTTAAAAT-TATATTTT
1 ATTTAAAATATATATTTT
3473616 A
1 A
3473617 ATGATTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTAAAATATATATTTT
Found at i:3474136 original size:16 final size:15
Alignment explanation
Indices: 3474113--3474157 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
3474103 TTTTGTGATT
3474113 ATTTATTTATTTTTA
1 ATTTATTTATTTTTA
* *
3474128 ATATTATTTATGTTTG
1 AT-TTATTTATTTTTA
*
3474144 ATTTATATATTTTT
1 ATTTATTTATTTTT
3474158 TTAAATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (15 bp):
ATTTATTTATTTTTA
Found at i:3474277 original size:39 final size:38
Alignment explanation
Indices: 3474219--3474304 Score: 102
Period size: 39 Copynumber: 2.3 Consensus size: 38
3474209 AAATTAAATT
* *
3474219 ATTTAAA-AATTATTAATTGAGTGTTTTATCCATTCTAA
1 ATTTAAATTATTATTAATTGAATGTTTTATCCATT-TAA
* * **
3474257 TTTTAAATTATTATTTATTGAATGTTTTATTTATTTAA
1 ATTTAAATTATTATTAATTGAATGTTTTATCCATTTAA
3474295 ATTTAAATTA
1 ATTTAAATTA
3474305 ATTAAGCAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 18 0.45
39 22 0.55
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (38 bp):
ATTTAAATTATTATTAATTGAATGTTTTATCCATTTAA
Found at i:3477919 original size:34 final size:34
Alignment explanation
Indices: 3477881--3477946 Score: 82
Period size: 33 Copynumber: 1.9 Consensus size: 34
3477871 ATTAATTTAA
*
3477881 ATTTTT-TAAGTAATTTGTAAAAAAAAA-CAAAATT
1 ATTTTTATAAGTAA--TATAAAAAAAAAGCAAAATT
*
3477915 ATTTTTATAATTAATATAAAAAAAAAGCAAAA
1 ATTTTTATAAGTAATATAAAAAAAAAGCAAAA
3477947 CTGAAATTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 11 0.39
34 11 0.39
35 6 0.21
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.35
Consensus pattern (34 bp):
ATTTTTATAAGTAATATAAAAAAAAAGCAAAATT
Found at i:3478590 original size:17 final size:17
Alignment explanation
Indices: 3478547--3478579 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3478537 TTGATATATC
3478547 ATTTTAAAT-TTATTAA
1 ATTTTAAATATTATTAA
3478563 ATTTTAAATATTATTAA
1 ATTTTAAATATTATTAA
3478580 TTTATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTAAATATTATTAA
Found at i:3478808 original size:16 final size:16
Alignment explanation
Indices: 3478757--3478815 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
3478747 TTTATAAGTA
*
3478757 ATTATGTTTAATATTT
1 ATTATATTTAATATTT
* * *
3478773 ATCATATTT-ATGAGTA
1 ATTATATTTAAT-ATTT
3478789 ATTATATTTAATATTT
1 ATTATATTTAATATTT
*
3478805 ATTAAATTTAA
1 ATTATATTTAA
3478816 GATAATATCA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 2 0.06
16 29 0.88
17 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (16 bp):
ATTATATTTAATATTT
Found at i:3478814 original size:32 final size:32
Alignment explanation
Indices: 3478742--3478814 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
3478732 TTAATGATCG
*
3478742 TTAAATTTATAAGTAATTATGTTTAATATTTA
1 TTAAATTTATAAGTAATTATATTTAATATTTA
* * *
3478774 TCATATTTATGAGTAATTATATTTAATATTTA
1 TTAAATTTATAAGTAATTATATTTAATATTTA
3478806 TTAAATTTA
1 TTAAATTTA
3478815 AGATAATATC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (32 bp):
TTAAATTTATAAGTAATTATATTTAATATTTA
Found at i:3479035 original size:21 final size:21
Alignment explanation
Indices: 3478997--3479053 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
3478987 AACGGTGAAG
** * *
3478997 ATAAAATTAGTTAATATAGTA
1 ATAAAATTAAATATTATAATA
3479018 ATAAAATTAAATATTATAATA
1 ATAAAATTAAATATTATAATA
*
3479039 GTAAAATTAAA-ATTA
1 ATAAAATTAAATATTA
3479054 AAAGTAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
ATAAAATTAAATATTATAATA
Found at i:3479128 original size:18 final size:18
Alignment explanation
Indices: 3479091--3479129 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3479081 CTTAGCTGTG
* *
3479091 ATAGTGAGATAAGTGGTA
1 ATAGTGAGATAAATGATA
*
3479109 ATAGTGAGATAAATTATA
1 ATAGTGAGATAAATGATA
3479127 ATA
1 ATA
3479130 AGTAAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (18 bp):
ATAGTGAGATAAATGATA
Found at i:3479203 original size:19 final size:18
Alignment explanation
Indices: 3479181--3479230 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
3479171 GATATAATAG
3479181 AAATTATAAAATATTTGAA
1 AAATTATAAAATATTT-AA
3479200 AAATTA-ATAAATATTTAA
1 AAATTATA-AAATATTTAA
3479218 AAATTATTAAAAT
1 AAATTA-TAAAAT
3479231 CAAAATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.32
19 18 0.64
20 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATTATAAAATATTTAA
Found at i:3479221 original size:18 final size:19
Alignment explanation
Indices: 3479189--3479228 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
3479179 AGAAATTATA
3479189 AAATATTTGAAAAATTAAT
1 AAATATTTGAAAAATTAAT
*
3479208 AAATATTT-AAAAATTATT
1 AAATATTTGAAAAATTAAT
3479226 AAA
1 AAA
3479229 ATCAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AAATATTTGAAAAATTAAT
Found at i:3479344 original size:21 final size:21
Alignment explanation
Indices: 3479320--3479367 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3479310 AATAATTATA
3479320 TAAATAAT-TTTTAAATAGTTG
1 TAAATAATATTTTAAATA-TTG
*
3479341 TAAAT-TTATTTTAAATATTG
1 TAAATAATATTTTAAATATTG
*
3479361 TAGATAA
1 TAAATAA
3479368 ACAAAACGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (21 bp):
TAAATAATATTTTAAATATTG
Found at i:3479412 original size:15 final size:16
Alignment explanation
Indices: 3479389--3479421 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3479379 GACTAAAGAT
*
3479389 AAAATGAAAAA-AAAA
1 AAAAAGAAAAAGAAAA
3479404 AAAAAGAAAAAGAAAA
1 AAAAAGAAAAAGAAAA
3479420 AA
1 AA
3479422 CAAGGGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAAGAAAA
Found at i:3484953 original size:26 final size:25
Alignment explanation
Indices: 3484913--3484978 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 25
3484903 AATTTGAGTT
*
3484913 TAATTTTTTTATTATATA-ATATATA
1 TAATTTTTATATTATATATAT-TATA
*
3484938 TTATTTTTATATTTATATATATTATA
1 TAATTTTTATA-TTATATATATTATA
3484964 TAA--TTTATATTATAT
1 TAATTTTTATATTATAT
3484979 TAACTTCATC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 6 0.17
24 6 0.17
25 9 0.25
26 13 0.36
27 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TAATTTTTATATTATATATATTATA
Found at i:3484976 original size:5 final size:5
Alignment explanation
Indices: 3484922--3484980 Score: 52
Period size: 5 Copynumber: 12.0 Consensus size: 5
3484912 TTAATTTTTT
* * *
3484922 TATTA TATAA TA-TA TATTA TTTTTA TATT- TATATA TATTA TATAA T-TTA
1 TATTA TATTA TATTA TATTA -TATTA TATTA TAT-TA TATTA TATTA TATTA
3484971 TATTA TATTA
1 TATTA TATTA
3484981 ACTTCATCTG
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
4 9 0.21
5 27 0.63
6 7 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:3485176 original size:30 final size:30
Alignment explanation
Indices: 3485108--3485186 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
3485098 TAATAAATAT
* *
3485108 TAATAAAAATAATTTTTAATTTATTAATTAA
1 TAATAAAATTAATTTTTAATATATT-ATTAA
*
3485139 TAA-AAAATTAATATTTAATATATT-TTAAA
1 TAATAAAATTAATTTTTAATATATTATT-AA
*
3485168 TAATAAAATAAATTTTTAA
1 TAATAAAATTAATTTTTAA
3485187 ATTTAATTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.05
29 5 0.12
30 31 0.76
31 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TAATAAAATTAATTTTTAATATATTATTAA
Found at i:3485400 original size:16 final size:15
Alignment explanation
Indices: 3485375--3485404 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3485365 CGGCCAAAGG
3485375 TTTTTTTTTTTTTAA
1 TTTTTTTTTTTTTAA
3485390 TTTTATTTTTTTTTA
1 TTTT-TTTTTTTTTA
3485405 TAATTAACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTTTTTTTTAA
Found at i:3489296 original size:2 final size:2
Alignment explanation
Indices: 3489289--3489319 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3489279 AAAGAAAAGT
3489289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3489320 TTTGCTGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3491924 original size:32 final size:32
Alignment explanation
Indices: 3491869--3491932 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
3491859 AAAAATTGTA
3491869 AAATAATATTTCAATAATAATTA-TATTGATAT
1 AAATAATATTTCAATAATAATTATTATT-ATAT
* * *
3491901 AAATAATATTTTAATTATTATTATTATTATAT
1 AAATAATATTTCAATAATAATTATTATTATAT
3491933 TTTAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (32 bp):
AAATAATATTTCAATAATAATTATTATTATAT
Found at i:3492042 original size:15 final size:15
Alignment explanation
Indices: 3492013--3492067 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3492003 TATTTTAGCA
**
3492013 TTAAATATTGTTATT
1 TTAAATATTAATATT
*
3492028 TGAAATATTAATATT
1 TTAAATATTAATATT
* *
3492043 TTAAAAATAAATAGTT
1 TTAAATATTAATA-TT
3492059 TTAAATATT
1 TTAAATATT
3492068 TTAATAATTA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 22 0.71
16 9 0.29
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
TTAAATATTAATATT
Found at i:3492130 original size:29 final size:29
Alignment explanation
Indices: 3492097--3492154 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
3492087 TATTTATTGA
3492097 GTTATCCAAATATAAAAAAAATCTCTACC
1 GTTATCCAAATATAAAAAAAATCTCTACC
*
3492126 GTTATCCAAATATTAAAAAAATCTCTACC
1 GTTATCCAAATATAAAAAAAATCTCTACC
3492155 TTTCTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (29 bp):
GTTATCCAAATATAAAAAAAATCTCTACC
Found at i:3494584 original size:37 final size:37
Alignment explanation
Indices: 3494542--3494614 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
3494532 AGGGAACAAG
*
3494542 TTTAATTGAACAGTTGAAATTAGTAAACATTCTTTTC
1 TTTAATTGAACAGTCGAAATTAGTAAACATTCTTTTC
3494579 TTTAATTGAACAGTCGAAATTAGTAAACATTCTTTT
1 TTTAATTGAACAGTCGAAATTAGTAAACATTCTTTT
3494615 TCTTAAATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (37 bp):
TTTAATTGAACAGTCGAAATTAGTAAACATTCTTTTC
Found at i:3499056 original size:2 final size:2
Alignment explanation
Indices: 3499043--3499076 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3499033 ATATCAAGCA
*
3499043 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3499077 CTCATAACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3499521 original size:27 final size:26
Alignment explanation
Indices: 3499491--3499541 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
3499481 ACATGTAAAA
3499491 TAGATGGAGATACA-ATATCAACAAACC
1 TAGAT-GAGATACATA-ATCAACAAACC
*
3499518 TAGATGAGATTCATAATCAACAAA
1 TAGATGAGATACATAATCAACAAA
3499542 TCTGGAACGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (26 bp):
TAGATGAGATACATAATCAACAAACC
Found at i:3501538 original size:30 final size:30
Alignment explanation
Indices: 3501499--3501572 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
3501489 TTAATTTATA
*
3501499 TTAAAAATTTATTTAAGTATAAATTAAAA-G
1 TTAAAAATTTATTTAAGTACAAA-TAAAACG
* *
3501529 TTAATAATTTATTTAGGTACAAATAAAACG
1 TTAAAAATTTATTTAAGTACAAATAAAACG
* *
3501559 TTAAAGACTTATTT
1 TTAAAAATTTATTT
3501573 GGACACAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 5 0.14
30 32 0.86
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (30 bp):
TTAAAAATTTATTTAAGTACAAATAAAACG
Found at i:3502837 original size:2 final size:2
Alignment explanation
Indices: 3502832--3502879 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
3502822 TCAAATTAGC
*
3502832 AT AT AT CAT AT AT -T AT AT AT AT -T AT AT A- AT AA AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3502872 AT AT AT AT
1 AT AT AT AT
3502880 GTATGTATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 3 0.08
2 35 0.88
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3502851 original size:9 final size:9
Alignment explanation
Indices: 3502839--3502879 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
3502829 AGCATATATC
3502839 ATATATTAT
1 ATATATTAT
3502848 ATATATTAT
1 ATATATTAT
*
3502857 ATA-A-TAA
1 ATATATTAT
3502864 ATATATATAT
1 ATATAT-TAT
3502874 ATATAT
1 ATATAT
3502880 GTATGTATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
7 5 0.19
8 2 0.07
9 12 0.44
10 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
ATATATTAT
Found at i:3503420 original size:22 final size:21
Alignment explanation
Indices: 3503394--3503443 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
3503384 AAAATTAAAG
3503394 TAATTTGAAATAAATATTTATA
1 TAATTTGAAATAAA-ATTTATA
**
3503416 TAATTTTTCAATAAAATTTATA
1 TAA-TTTGAAATAAAATTTATA
*
3503438 TTATTT
1 TAATTT
3503444 AATTTGACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.12
22 12 0.50
23 9 0.38
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TAATTTGAAATAAAATTTATA
Found at i:3504365 original size:17 final size:17
Alignment explanation
Indices: 3504343--3504376 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3504333 ATATTGTCCC
3504343 CTTTTGACATACTGACA
1 CTTTTGACATACTGACA
*
3504360 CTTTTGACATAGTGACA
1 CTTTTGACATACTGACA
3504377 ATTTGATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (17 bp):
CTTTTGACATACTGACA
Found at i:3504565 original size:3 final size:3
Alignment explanation
Indices: 3504557--3504599 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3504547 CATAATTTTG
3504557 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3504600 TCTACTTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3504813 original size:2 final size:2
Alignment explanation
Indices: 3504806--3504833 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3504796 CGAATCAATC
3504806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3504834 GCTTAGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3506809 original size:13 final size:11
Alignment explanation
Indices: 3506779--3506812 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
3506769 GATACATGTT
3506779 TAAATATAATA
1 TAAATATAATA
3506790 TAAATATAATA
1 TAAATATAATA
3506801 TACAAATATAAT
1 T--AAATATAAT
3506813 TTTTTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
13 9 0.43
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAATATAATA
Found at i:3506934 original size:53 final size:54
Alignment explanation
Indices: 3506835--3506938 Score: 149
Period size: 53 Copynumber: 1.9 Consensus size: 54
3506825 TAAAAATTTT
* *
3506835 AAAAAAATTAAATAATATTTATATCAAAATATATATAAATAACCAACTCTTAAA
1 AAAAAAATTAAATAATACTTATATCAAAATATACATAAATAACCAACTCTTAAA
* *
3506889 AAAAAAATTAAACT-ATACTTATATC-AAATATACATAGATATCCAACTCTT
1 AAAAAAATTAAA-TAATACTTATATCAAAATATACATAAATAACCAACTCTT
3506939 GTCCTTGAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
53 22 0.49
54 22 0.49
55 1 0.02
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (54 bp):
AAAAAAATTAAATAATACTTATATCAAAATATACATAAATAACCAACTCTTAAA
Found at i:3511683 original size:35 final size:37
Alignment explanation
Indices: 3511625--3511700 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 37
3511615 GGGAACAAGT
* *
3511625 TTAATTGAACAGTTGAAATTAGTACACATTC-TTTTC
1 TTAATTGAACAGTCGAAATTAGTAAACATTCTTTTTC
3511661 TTAATTGAAC-GTCGAAATTAGTAAACATTCTTTTTC
1 TTAATTGAACAGTCGAAATTAGTAAACATTCTTTTTC
3511697 TTAA
1 TTAA
3511701 ATAGGATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 18 0.49
36 19 0.51
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (37 bp):
TTAATTGAACAGTCGAAATTAGTAAACATTCTTTTTC
Found at i:3516036 original size:2 final size:2
Alignment explanation
Indices: 3516029--3516062 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3516019 ATATCAAGCA
*
3516029 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3516063 CTCAAACCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3522005 original size:17 final size:17
Alignment explanation
Indices: 3521983--3522021 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
3521973 ATATTGTCCC
3521983 CTTTTGACATACTGACA
1 CTTTTGACATACTGACA
*
3522000 CTTTTGACATAGTGACA
1 CTTTTGACATACTGACA
*
3522017 ATTTT
1 CTTTT
3522022 ATTGAAGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (17 bp):
CTTTTGACATACTGACA
Found at i:3524052 original size:2 final size:2
Alignment explanation
Indices: 3524045--3524073 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3524035 AAAAGAAAGT
3524045 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
3524074 TTTGATGAGT
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:3526684 original size:32 final size:32
Alignment explanation
Indices: 3526629--3526692 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
3526619 AAAAATTGTA
3526629 AAATAATATTTCAATAATAATTA-TATTGATAT
1 AAATAATATTTCAATAATAATTATTATT-ATAT
* * *
3526661 AAATAATATTTTAATTATTATTATTATTATAT
1 AAATAATATTTCAATAATAATTATTATTATAT
3526693 TTTAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (32 bp):
AAATAATATTTCAATAATAATTATTATTATAT
Done.