Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 8 of 199
Found at i:3048208 original size:30 final size:30
Alignment explanation
Indices: 3048173--3048230 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3048163 CCTCGACTCT
*
3048173 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
3048203 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
3048231 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:3068570 original size:14 final size:14
Alignment explanation
Indices: 3068551--3068584 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
3068541 ATTTTTTAAG
3068551 AAATTTCAAACGTA
1 AAATTTCAAACGTA
3068565 AAATTTCAAACGTA
1 AAATTTCAAACGTA
3068579 AAATTT
1 AAATTT
3068585 TTTTAAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (14 bp):
AAATTTCAAACGTA
Found at i:3089655 original size:31 final size:31
Alignment explanation
Indices: 3089620--3089685 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
3089610 AAAAACACTT
* *
3089620 AATAGTCTAGTCATTTAAATAAAAATTTTAG
1 AATAGTCTAGTCACTTAAATAAAAATTTTAA
* * *
3089651 AATAGTTTAGTGACTTAAATGAAAATTTTAA
1 AATAGTCTAGTCACTTAAATAAAAATTTTAA
3089682 AATA
1 AATA
3089686 ATTCAATTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.38
Consensus pattern (31 bp):
AATAGTCTAGTCACTTAAATAAAAATTTTAA
Found at i:3093494 original size:26 final size:26
Alignment explanation
Indices: 3093442--3093494 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3093432 AATTTATATA
* * *
3093442 TTTATAATTTTTGAATGATTAATTTT
1 TTTATAATTTTTGAAGGATCAAATTT
*
3093468 TTTATCATTTTTGAAGGATCAAATTT
1 TTTATAATTTTTGAAGGATCAAATTT
3093494 T
1 T
3093495 AATTTTATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (26 bp):
TTTATAATTTTTGAAGGATCAAATTT
Found at i:3096189 original size:5 final size:5
Alignment explanation
Indices: 3096179--3096206 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3096169 TTAAATTTAT
3096179 TATAA TATAA TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TAT
3096207 TATAACTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:3105689 original size:16 final size:18
Alignment explanation
Indices: 3105668--3105708 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
3105658 GTAAAAATCG
3105668 ATCTAAAACT-AAAA-TA
1 ATCTAAAACTCAAAATTA
3105684 ATCT-AAACTCAAAATTA
1 ATCTAAAACTCAAAATTA
*
3105701 ATTTAAAA
1 ATCTAAAA
3105709 AAAGTAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 8 0.38
17 5 0.24
18 3 0.14
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (18 bp):
ATCTAAAACTCAAAATTA
Found at i:3111100 original size:17 final size:18
Alignment explanation
Indices: 3111080--3111119 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3111070 TTTTATGTAA
*
3111080 AAAATTAT-TTTTTATAT
1 AAAATTATGTTATTATAT
*
3111097 AAAATTATGTTATTATTT
1 AAAATTATGTTATTATAT
3111115 AAAAT
1 AAAAT
3111120 AATATTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
AAAATTATGTTATTATAT
Found at i:3111100 original size:18 final size:19
Alignment explanation
Indices: 3111079--3111142 Score: 51
Period size: 22 Copynumber: 3.3 Consensus size: 19
3111069 ATTTTATGTA
*
3111079 AAAAATTAT-TTTTTATAT
1 AAAAATTATGTTATTATAT
*
3111097 -AAAATTATGTTATTATTT
1 AAAAATTATGTTATTATAT
* *
3111115 AAAATAATATTTGTTATTTTAT
1 -AAA-AAT-TATGTTATTATAT
3111137 AAAAAT
1 AAAAAT
3111143 AAATTGAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 8 0.22
18 7 0.19
20 5 0.14
21 6 0.17
22 10 0.28
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (19 bp):
AAAAATTATGTTATTATAT
Found at i:3111115 original size:22 final size:22
Alignment explanation
Indices: 3111095--3111145 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
3111085 TATTTTTTAT
3111095 ATAAAATTATGTTATTATTTAAA
1 ATAAAATT-TGTTATTATTTAAA
*
3111118 ATAATATTTGTTATT-TTATAAAA
1 ATAAAATTTGTTATTATT-T-AAA
3111141 ATAAA
1 ATAAA
3111146 TTGAGTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 2 0.08
22 8 0.33
23 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
ATAAAATTTGTTATTATTTAAA
Found at i:3122693 original size:14 final size:14
Alignment explanation
Indices: 3122671--3122703 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3122661 AAGGGATTGG
3122671 TTTTCTTTTTCCAT
1 TTTTCTTTTTCCAT
*
3122685 TTTTTTTTTTCCAT
1 TTTTCTTTTTCCAT
3122699 TTTTC
1 TTTTC
3122704 GGGTTTTCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTCCAT
Found at i:3125053 original size:23 final size:23
Alignment explanation
Indices: 3125008--3125053 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3124998 ATCAAACTAT
*
3125008 GATTAAAATATATAAATATATTA
1 GATTAAAATATATAAATACATTA
*
3125031 GATTAACAATAT-TAATTACATTA
1 GATTAA-AATATATAAATACATTA
3125054 TTATGATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (23 bp):
GATTAAAATATATAAATACATTA
Found at i:3127835 original size:18 final size:18
Alignment explanation
Indices: 3127812--3127849 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3127802 ATGATACCAA
3127812 TTGTGTCTGGATGAGCTT
1 TTGTGTCTGGATGAGCTT
3127830 TTGTGTCTGGATGAGCTT
1 TTGTGTCTGGATGAGCTT
3127848 TT
1 TT
3127850 ACTTCTTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.32, T:0.47
Consensus pattern (18 bp):
TTGTGTCTGGATGAGCTT
Found at i:3147029 original size:66 final size:60
Alignment explanation
Indices: 3146954--3147099 Score: 193
Period size: 60 Copynumber: 2.3 Consensus size: 60
3146944 ATAATGGAGC
3146954 TGGAGCTGGTGGAAATGATGCTTTGGGAGCTGGAGCTGGAGCTGGAGCCGCTGCAGCTAGTGGTT
1 TGGAGCTGGTGGAAATGATGCTTT-----C-GGAGCTGGAGCTGGAGCCGCTGCAGCTAGTGGTT
3147019 T
60 T
* * *
3147020 TGGAGCTGGTGGAAATAATGCTTTCGGAGCTGGAGCTGGAGCCGCTGGAGCTGGTGGTTT
1 TGGAGCTGGTGGAAATGATGCTTTCGGAGCTGGAGCTGGAGCCGCTGCAGCTAGTGGTTT
* *
3147080 TGGAGATGGTGGAGATGATG
1 TGGAGCTGGTGGAAATGATG
3147100 GTTTTGGCGG
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
60 50 0.68
61 1 0.01
66 23 0.31
ACGTcount: A:0.18, C:0.13, G:0.43, T:0.26
Consensus pattern (60 bp):
TGGAGCTGGTGGAAATGATGCTTTCGGAGCTGGAGCTGGAGCCGCTGCAGCTAGTGGTTT
Found at i:3147139 original size:21 final size:21
Alignment explanation
Indices: 3147114--3147154 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3147104 TGGCGGAGAC
*
3147114 GGTGGGGTCGACGGAGTTGAG
1 GGTGGGGTCGAAGGAGTTGAG
*
3147135 GGTGGGGTTGAAGGAGTTGA
1 GGTGGGGTCGAAGGAGTTGA
3147155 CGGAGGAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.56, T:0.22
Consensus pattern (21 bp):
GGTGGGGTCGAAGGAGTTGAG
Found at i:3156761 original size:21 final size:21
Alignment explanation
Indices: 3156735--3156779 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3156725 TTCATGTTAC
3156735 TTTTTTAAAATTTTTATGAAT
1 TTTTTTAAAATTTTTATGAAT
* * *
3156756 TTTTTTAATATTTTTTTGAGT
1 TTTTTTAAAATTTTTATGAAT
3156777 TTT
1 TTT
3156780 GAATATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (21 bp):
TTTTTTAAAATTTTTATGAAT
Found at i:3157196 original size:27 final size:25
Alignment explanation
Indices: 3157166--3157229 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
3157156 AAATATTTTA
* *
3157166 AAATAATAATAATTTTATATTTATATT
1 AAATAAAAATAA--TTATATTGATATT
*
3157193 AAATAAAAATCATTATATTGATATT
1 AAATAAAAATAATTATATTGATATT
3157218 AAATATAAAATA
1 AAATA-AAAATA
3157230 CTCTCCCACC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 17 0.53
26 5 0.16
27 10 0.31
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
AAATAAAAATAATTATATTGATATT
Found at i:3157211 original size:25 final size:26
Alignment explanation
Indices: 3157180--3157228 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
3157170 AATAATAATT
*
3157180 TTATATTTATATTAAATA-AAAATCA
1 TTATATTGATATTAAATATAAAATCA
3157205 TTATATTGATATTAAATATAAAAT
1 TTATATTGATATTAAATATAAAAT
3157229 ACTCTCCCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
TTATATTGATATTAAATATAAAATCA
Found at i:3188981 original size:8 final size:9
Alignment explanation
Indices: 3188958--3188986 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
3188948 AAAGAATGCA
3188958 TTAAAAATT
1 TTAAAAATT
3188967 TTAAAAATT
1 TTAAAAATT
3188976 TTAAAAATT
1 TTAAAAATT
3188985 TT
1 TT
3188987 GGACAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAAAAATT
Found at i:3192146 original size:12 final size:12
Alignment explanation
Indices: 3192086--3192162 Score: 51
Period size: 12 Copynumber: 6.6 Consensus size: 12
3192076 TTAATATAGT
3192086 TTTAATATTTAA
1 TTTAATATTTAA
*
3192098 TTTGATATTTAAA
1 TTTAATATTT-AA
3192111 TTT--T-TTT-A
1 TTTAATATTTAA
3192119 TCTT-A-ATTTAGTA
1 T-TTAATATTTA--A
3192132 TTTAA-ATTTAAA
1 TTTAATATTT-AA
3192144 TTTAATATTTAA
1 TTTAATATTTAA
3192156 TTTAATA
1 TTTAATA
3192163 CTCAAATTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 20
0.72 0.01 0.27
Matches are distributed among these distances:
8 2 0.04
9 2 0.04
10 6 0.11
11 1 0.02
12 26 0.48
13 16 0.30
14 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (12 bp):
TTTAATATTTAA
Found at i:3192147 original size:19 final size:18
Alignment explanation
Indices: 3192086--3192160 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 18
3192076 TTAATATAGT
*
3192086 TTTAATATTTAATTTGATA
1 TTTAATATTTAATTT-AAA
* *
3192105 TTTAAATTTTTTTATCTT-AA
1 TTT-AA-TATTTAAT-TTAAA
*
3192125 TTTAGTATTTAAATTTAAA
1 TTTAATATTT-AATTTAAA
3192144 TTTAATATTTAATTTAA
1 TTTAATATTTAATTTAA
3192161 TACTCAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
18 13 0.30
19 17 0.39
20 6 0.14
21 6 0.14
22 2 0.05
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTAATATTTAATTTAAA
Found at i:3193886 original size:215 final size:210
Alignment explanation
Indices: 3193626--3194052 Score: 737
Period size: 215 Copynumber: 2.0 Consensus size: 210
3193616 AATTGTTAGG
3193626 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTCATGTTTTCCCTT
1 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTCATGTTTTCCCTT
*
3193691 GGTATATAGCTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
66 GGTATATAACTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
* * *
3193756 GCGGGACAAACTTAAAAGGAAACGAGGAAAAAAAAAAGAGCAATCAATTTATGGTTGTTGTTACC
131 GCGGGACAAACTTAAAAAGAAAAGAGG--AAAAAAAAGAGCAATCAATCTAT-G--GTTGTTACC
3193821 GCATGACGATGTATCTAACC
191 GCATGACGATGTATCTAACC
* *
3193841 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCTTT
1 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTCATGTTTTCCCTT
3193906 GGTATATAACTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
66 GGTATATAACTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
* *
3193971 GCGGGACAAACTTAAAAAGAAAAGAGGAAAAAAGAGAGCAATCAATCTATGGTTGTTACGGCATG
131 GCGGGACAAACTTAAAAAGAAAAGAGGAAAAAAAAGAGCAATCAATCTATGGTTGTTACCGCATG
3194036 ACGATGTATCTAACC
196 ACGATGTATCTAACC
3194051 AT
1 AT
3194053 ATAACTAACA
Statistics
Matches: 204, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
210 30 0.15
212 1 0.00
213 21 0.10
215 152 0.75
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37
Consensus pattern (210 bp):
ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTCATGTTTTCCCTT
GGTATATAACTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
GCGGGACAAACTTAAAAAGAAAAGAGGAAAAAAAAGAGCAATCAATCTATGGTTGTTACCGCATG
ACGATGTATCTAACC
Found at i:3197410 original size:2 final size:2
Alignment explanation
Indices: 3197405--3197434 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3197395 ATGCACACAC
3197405 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3197435 GTGTCTCTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3204186 original size:2 final size:2
Alignment explanation
Indices: 3204181--3204211 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3204171 GTGTGTGTGA
*
3204181 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3204212 AGGATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3206485 original size:14 final size:14
Alignment explanation
Indices: 3206466--3206495 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3206456 AATTATAAGG
3206466 AATATTTTTTATAC
1 AATATTTTTTATAC
3206480 AATATTTTTTATAC
1 AATATTTTTTATAC
3206494 AA
1 AA
3206496 AAAAGTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (14 bp):
AATATTTTTTATAC
Found at i:3210338 original size:29 final size:30
Alignment explanation
Indices: 3210268--3210338 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 30
3210258 ACTTTTTTAA
*
3210268 AAAAATTAATGACCAAATTTAACTTAAAAAAG
1 AAAAA-TAAAGACCAAATTTAAC-TAAAAAAG
*
3210300 AAAGAATAAAGACC-AATTTAA-TAAAAAAT
1 AAA-AATAAAGACCAAATTTAACTAAAAAAG
3210329 AAAAACTAAA
1 AAAAA-TAAA
3210339 TCTATCTGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
28 2 0.06
29 14 0.40
31 7 0.20
32 10 0.29
33 2 0.06
ACGTcount: A:0.65, C:0.08, G:0.06, T:0.21
Consensus pattern (30 bp):
AAAAATAAAGACCAAATTTAACTAAAAAAG
Found at i:3232000 original size:30 final size:31
Alignment explanation
Indices: 3231966--3232031 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
3231956 AAATTTAAAT
* *
3231966 AAAAATATT-TGAAATTTATTA-AAAATTAGA
1 AAAAATATTATAAAATATA-TAGAAAATTAGA
*
3231996 AAAAA-ATTATAAAATATATAGAAAATTATA
1 AAAAATATTATAAAATATATAGAAAATTAGA
3232026 AAAAAT
1 AAAAAT
3232032 GTAAAGAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (31 bp):
AAAAATATTATAAAATATATAGAAAATTAGA
Found at i:3232009 original size:10 final size:10
Alignment explanation
Indices: 3231981--3232031 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
3231971 TATTTGAAAT
*
3231981 TTATTAAAAA
1 TTATAAAAAA
*
3231991 TTAGAAAAAAA
1 TTA-TAAAAAA
*
3232002 TTATAAAATA
1 TTATAAAAAA
*
3232012 -TATAGAAAA
1 TTATAAAAAA
3232021 TTATAAAAAA
1 TTATAAAAAA
3232031 T
1 T
3232032 GTAAAGAAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
9 7 0.22
10 17 0.53
11 8 0.25
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:3232275 original size:28 final size:29
Alignment explanation
Indices: 3232243--3232306 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 29
3232233 TATTTTGTAA
*
3232243 TTTTTATAAAAATTTACA-A-TTTTTATGT
1 TTTTTATAAAAATTTA-ATATTTTTTATAT
*
3232271 TTTTTATTAAAATTTAATATTTTTTATAT
1 TTTTTATAAAAATTTAATATTTTTTATAT
3232300 TTTTTAT
1 TTTTTAT
3232307 CACATGTCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 1 0.03
28 16 0.50
29 15 0.47
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (29 bp):
TTTTTATAAAAATTTAATATTTTTTATAT
Found at i:3236600 original size:30 final size:31
Alignment explanation
Indices: 3236564--3236623 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
3236554 ATTTATTCTT
* *
3236564 AGTTAAATTTAATT-TTAATATTTTGAAAAG
1 AGTTAAACTTAATTATTAATATTTTAAAAAG
*
3236594 AGTTAAACTTAATTATTAATTTTTTAAAAA
1 AGTTAAACTTAATTATTAATATTTTAAAAA
3236624 TAGTCAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (31 bp):
AGTTAAACTTAATTATTAATATTTTAAAAAG
Found at i:3236728 original size:6 final size:6
Alignment explanation
Indices: 3236717--3236743 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3236707 TTATATATAT
3236717 TTAAAA TTAAAA TTAAAA TTAAAA TTA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTA
3236744 TTTTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TTAAAA
Found at i:3241637 original size:18 final size:18
Alignment explanation
Indices: 3241616--3241650 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3241606 AATTTAATTT
3241616 TTAAAAAATTATAAAAAC
1 TTAAAAAATTATAAAAAC
**
3241634 TTAAACTATTATAAAAA
1 TTAAAAAATTATAAAAA
3241651 TATACAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAAAATTATAAAAAC
Found at i:3267777 original size:33 final size:34
Alignment explanation
Indices: 3267733--3267801 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 34
3267723 AATAAGAAAA
3267733 ATAAAGGTTTGATCCATTCTAAAAGTAATCTGCT
1 ATAAAGGTTTGATCCATTCTAAAAGTAATCTGCT
*
3267767 ATAAA-GTTTGATCCATTCTATAAGTAATCTGCT
1 ATAAAGGTTTGATCCATTCTAAAAGTAATCTGCT
3267800 AT
1 AT
3267802 CAACCTAGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 29 0.85
34 5 0.15
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (34 bp):
ATAAAGGTTTGATCCATTCTAAAAGTAATCTGCT
Found at i:3267789 original size:19 final size:19
Alignment explanation
Indices: 3267733--3267789 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
3267723 AATAAGAAAA
3267733 ATAAAGGTTTGATCCATTCT
1 ATAAA-GTTTGATCCATTCT
* *
3267753 A-AAAG--TAAT-C-TGCT
1 ATAAAGTTTGATCCATTCT
3267767 ATAAAGTTTGATCCATTCT
1 ATAAAGTTTGATCCATTCT
3267786 ATAA
1 ATAA
3267790 GTAATCTGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 11
0.65 0.09 0.26
Matches are distributed among these distances:
14 4 0.14
15 5 0.18
16 3 0.11
17 3 0.11
18 2 0.07
19 10 0.36
20 1 0.04
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
ATAAAGTTTGATCCATTCT
Found at i:3269322 original size:28 final size:28
Alignment explanation
Indices: 3269290--3269346 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3269280 ATTTTGAACA
3269290 TCACTTGAGTAGCTAACGGAATCAAACT
1 TCACTTGAGTAGCTAACGGAATCAAACT
3269318 TCACTTGAGTAGCTAACGGAATCAAACT
1 TCACTTGAGTAGCTAACGGAATCAAACT
3269346 T
1 T
3269347 ACATAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (28 bp):
TCACTTGAGTAGCTAACGGAATCAAACT
Found at i:3288233 original size:67 final size:67
Alignment explanation
Indices: 3288125--3288253 Score: 213
Period size: 67 Copynumber: 1.9 Consensus size: 67
3288115 TTTCCAATTC
* *
3288125 AGAGAGCACACTCCCACGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCTTA
1 AGAGAGCACACTCCCACAAACCTCATTTCTTACAGCCGGATTACCAGTCCAGGCTAAATCCCTTA
3288190 CA
66 CA
* * *
3288192 AGAGAGCACACTCTCGCAAACCTCATTTCTTATAGCCGGATTACCAGTCCAGGCTAAATCCC
1 AGAGAGCACACTCCCACAAACCTCATTTCTTACAGCCGGATTACCAGTCCAGGCTAAATCCC
3288254 CTGTAATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (67 bp):
AGAGAGCACACTCCCACAAACCTCATTTCTTACAGCCGGATTACCAGTCCAGGCTAAATCCCTTA
CA
Found at i:3292264 original size:17 final size:17
Alignment explanation
Indices: 3292242--3292274 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3292232 ATACAAAATA
3292242 AAAACTAAATGCTACAG
1 AAAACTAAATGCTACAG
*
3292259 AAAACTTAATGCTACA
1 AAAACTAAATGCTACA
3292275 AAATAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.21
Consensus pattern (17 bp):
AAAACTAAATGCTACAG
Found at i:3294474 original size:55 final size:55
Alignment explanation
Indices: 3294390--3294498 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
3294380 ATCTAAAGCA
*
3294390 CCAAGCAAAGGCTTAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAATT
1 CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAATT
*
3294445 CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAATGAAACACAAAGAAAT
1 CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAAT
3294499 ACATCACAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.17
Consensus pattern (55 bp):
CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAATT
Found at i:3296184 original size:14 final size:14
Alignment explanation
Indices: 3296167--3296214 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
3296157 CCCTGAATCA
3296167 CTAACCACAAACCC
1 CTAACCACAAACCC
*
3296181 CTAA-CATCTAACCC
1 CTAACCA-CAAACCC
*
3296195 CTAACCACAAACCT
1 CTAACCACAAACCC
3296209 CTAACC
1 CTAACC
3296215 CCTGACTACT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 2 0.07
14 25 0.86
15 2 0.07
ACGTcount: A:0.40, C:0.46, G:0.00, T:0.15
Consensus pattern (14 bp):
CTAACCACAAACCC
Found at i:3296228 original size:21 final size:21
Alignment explanation
Indices: 3296167--3296233 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
3296157 CCCTGAATCA
* * * *
3296167 CTAACCACAAACCCCTAACAT
1 CTAACCCCTAACCACTAACCT
*
3296188 CTAACCCCTAACCACAAACCT
1 CTAACCCCTAACCACTAACCT
* * *
3296209 CTAACCCCTGACTACTAACCC
1 CTAACCCCTAACCACTAACCT
3296230 CTAA
1 CTAA
3296234 ACCTTATTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.37, C:0.45, G:0.01, T:0.16
Consensus pattern (21 bp):
CTAACCCCTAACCACTAACCT
Found at i:3296426 original size:16 final size:16
Alignment explanation
Indices: 3296405--3296461 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
3296395 TTGGATTCGC
*
3296405 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
3296421 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
3296437 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
3296453 TGTAATGGA
1 TGTAATGGA
3296462 AAAGCTCTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:3296728 original size:18 final size:17
Alignment explanation
Indices: 3296707--3296741 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3296697 TTATTATTAA
*
3296707 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3296725 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3296742 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3296878 original size:16 final size:16
Alignment explanation
Indices: 3296841--3296882 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3296831 TTAATCATAT
*
3296841 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
3296857 TT-AAATATATTATAA
1 TTAAAATATATTATAA
3296872 TTAAAATATAT
1 TTAAAATATAT
3296883 AATTTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:3296880 original size:154 final size:156
Alignment explanation
Indices: 3296594--3296891 Score: 546
Period size: 154 Copynumber: 1.9 Consensus size: 156
3296584 TAGAATACCC
3296594 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-TA
*
3296659 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
65 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
3296724 TATATAATTTAATAAAATTCTTAATAA
130 TATATAATTTAATAAAATTCTTAATAA
* *
3296751 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-A-
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
3296814 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
3296879 ATATAATTTAATA
131 ATATAATTTAATA
3296892 TGAATTTACT
Statistics
Matches: 138, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
154 77 0.56
155 1 0.01
157 60 0.43
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAATAA
Found at i:3296889 original size:14 final size:15
Alignment explanation
Indices: 3296850--3296984 Score: 70
Period size: 15 Copynumber: 8.9 Consensus size: 15
3296840 TTTAAACATA
*
3296850 ATTATTATTAAATAT
1 ATTATAATTAAATAT
3296865 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
3296879 A-TATAATTTAATAT
1 ATTATAATTAAATAT
*
3296893 GAATTTACTCAAATCATAATAT
1 --A-TTA-T--AATTA-AATAT
* *
3296915 ATGATACTGTAAA-AT
1 ATTATAAT-TAAATAT
3296930 A-TA-AATTAACATA-
1 ATTATAATTAA-ATAT
*
3296943 ATTATTATTAAATAT
1 ATTATAATTAAATAT
3296958 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
3296972 A-TATAATTTAATA
1 ATTATAATTAAATA
3296985 AAATTCTTAA
Statistics
Matches: 92, Mismatches: 12, Indels: 33
0.67 0.09 0.24
Matches are distributed among these distances:
12 3 0.03
13 22 0.24
14 16 0.17
15 30 0.33
16 5 0.05
17 1 0.01
18 3 0.03
19 3 0.03
20 1 0.01
21 3 0.03
22 5 0.05
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:3296948 original size:154 final size:155
Alignment explanation
Indices: 3296633--3296948 Score: 401
Period size: 154 Copynumber: 2.0 Consensus size: 155
3296623 ATTGTTATTG
3296633 TTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATAATTTAATCATATTTAAACATAAT
1 TTATTTAAATTTTAATAAGATTA-TATTATCAATAATAAATAATTTAATCATATTTAAACATAAT
* *
3296698 TATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCATAAATT
65 TATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA-TAGCATAAATA
** * * *** **
3296763 TGTTTTGGTAAATTATTATTGTTATTG
129 TGTACTGGTAAAATATAATTAACATAA
3296790 TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAACATAATT
1 TTATTTAAATTTTAATAAGATTATATTATCAATAATAAATAATTTAATCATATTTAAACATAATT
* * *
3296853 ATTATTAAATATATTATAATTAAAATATATAATTTAATATGAA-T-TTACTCAA-ATCATAATAT
66 ATTATTAAATATATTATAATTAAAATATATAATTTAATA-AAATTCTTAAT-AATAGCATAA-AT
3296915 ATGATACT-GTAAAATATAAATTAACATAA
128 ATG-TACTGGTAAAATAT-AATTAACATAA
3296944 TTATT
1 TTATT
3296949 ATTAAATATA
Statistics
Matches: 140, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
152 6 0.04
153 16 0.11
154 92 0.66
155 3 0.02
157 23 0.16
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (155 bp):
TTATTTAAATTTTAATAAGATTATATTATCAATAATAAATAATTTAATCATATTTAAACATAATT
ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATAGCATAAATATG
TACTGGTAAAATATAATTAACATAA
Found at i:3296999 original size:44 final size:43
Alignment explanation
Indices: 3296910--3297000 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
3296900 CTCAAATCAT
* * *
3296910 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
* * *
3296953 AATATATTATAAT-TAAAATATATAATTTAATAAAATTCTTAATA
1 AATATATGATAATGTAAAATATA-AA-TTAACAAAATTATTAATA
3296997 AATA
1 AATA
3297001 AAATTCTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 9 0.22
43 13 0.32
44 18 0.45
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (43 bp):
AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
Found at i:3297025 original size:120 final size:119
Alignment explanation
Indices: 3296890--3297108 Score: 336
Period size: 120 Copynumber: 1.8 Consensus size: 119
3296880 TATAATTTAA
* * * *
3296890 TATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA-TT-AACATAATTATTATTA
1 TATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AAATTTCAA-ATAATTAATATCA
3296953 AATAT-ATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAAAATTCTTC
64 AATATGATT-TAATT-AAATATATAATTTAATAAAATTCTTAATAAATAAAATTCTTC
3297010 TATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATTTCAAATAATTAATATCAAA
1 TATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATTTCAAATAATTAATATCAAA
*
3297075 TATGATTTAATTAAATATATGATTTAATAAAATT
66 TATGATTTAATTAAATATATAATTTAATAAAATT
3297109 TAAAATTATT
Statistics
Matches: 91, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
119 24 0.26
120 62 0.68
121 5 0.05
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (119 bp):
TATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATTTCAAATAATTAATATCAAA
TATGATTTAATTAAATATATAATTTAATAAAATTCTTAATAAATAAAATTCTTC
Found at i:3297094 original size:17 final size:17
Alignment explanation
Indices: 3297074--3297107 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3297064 TTAATATCAA
*
3297074 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
3297091 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
3297108 TTAAAATTAT
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:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:3297250 original size:93 final size:92
Alignment explanation
Indices: 3297140--3297334 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
3297130 GATTATAGTT
* * *
3297140 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
3297203 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
3297233 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
3297298 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
3297325 TATGAATTTA
1 TATGAATTTA
3297335 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:3298939 original size:34 final size:34
Alignment explanation
Indices: 3298896--3298963 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
3298886 TCTGAAATTC
3298896 AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
1 AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
3298930 AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
1 AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
3298964 CTACATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (34 bp):
AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
Found at i:3299236 original size:78 final size:78
Alignment explanation
Indices: 3299107--3299263 Score: 215
Period size: 78 Copynumber: 2.0 Consensus size: 78
3299097 TATTAGTCAA
* * *
3299107 GGGGTTAACAAGGAGTGAATTTGCAATTGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAA
1 GGGGTTAACAAGGACTGAATTCGCAATGGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAA
* *
3299172 GGCAGCGACACTC
66 GACAGCAACACTC
** * * * *
3299185 GGGGTTAATGAGGACTGAATTCGCAATGGTGATTCTATCTTATTTGGCTTAGCTTCCTTTGGTAA
1 GGGGTTAACAAGGACTGAATTCGCAATGGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAA
3299250 GACAGCAACACTC
66 GACAGCAACACTC
3299263 G
1 G
3299264 AAACTTGCAT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
78 68 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (78 bp):
GGGGTTAACAAGGACTGAATTCGCAATGGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAA
GACAGCAACACTC
Found at i:3301181 original size:14 final size:14
Alignment explanation
Indices: 3301136--3301173 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
3301126 ATCCTAAATT
3301136 AACCATATATCCTA
1 AACCATATATCCTA
*
3301150 AACCATATACCCTA
1 AACCATATATCCTA
3301164 AACCATATAT
1 AACCATATAT
3301174 ATTAAACCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (14 bp):
AACCATATATCCTA
Found at i:3301706 original size:40 final size:40
Alignment explanation
Indices: 3301629--3301738 Score: 134
Period size: 40 Copynumber: 2.8 Consensus size: 40
3301619 TCTCAAAGAA
* ** * *
3301629 CGCCGCTAATTCTC-AT-TTTAGCGGCACTTTCCCTAAAG
1 CGCCGCTAATGCTCGATCTTTAGCGGCGTTTTACGTAAAG
* *
3301667 CGCCGCTAATGCTCTATCTTTAGTGGCGTTTTACGTAAAG
1 CGCCGCTAATGCTCGATCTTTAGCGGCGTTTTACGTAAAG
*
3301707 CGCCGCTAATGCTCGATTTTTAGCGGCGTTTT
1 CGCCGCTAATGCTCGATCTTTAGCGGCGTTTT
3301739 TTCTCCAAAC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 13 0.21
39 2 0.03
40 46 0.75
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (40 bp):
CGCCGCTAATGCTCGATCTTTAGCGGCGTTTTACGTAAAG
Found at i:3324034 original size:13 final size:15
Alignment explanation
Indices: 3324004--3324036 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
3323994 TTTATTGTTT
3324004 TAATAAATTTTAAAA
1 TAATAAATTTTAAAA
3324019 TAATAAA-TTT-AAA
1 TAATAAATTTTAAAA
3324032 TAATA
1 TAATA
3324037 TTATTTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 3 0.17
15 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATAAATTTTAAAA
Found at i:3324538 original size:32 final size:34
Alignment explanation
Indices: 3324502--3324573 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
3324492 GACTTTTATG
*
3324502 AAATATTTTTA-AGAAATCTA-CCAAACAACAGA
1 AAATATTTTTACACAAATCTATCCAAACAACAGA
* * *
3324534 AAATA-TTTTACACAGATTTATCCAAACACCAGA
1 AAATATTTTTACACAAATCTATCCAAACAACAGA
3324567 AAATATT
1 AAATATT
3324574 AACTTTTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
31 5 0.15
32 11 0.33
33 16 0.48
34 1 0.03
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (34 bp):
AAATATTTTTACACAAATCTATCCAAACAACAGA
Found at i:3345422 original size:17 final size:17
Alignment explanation
Indices: 3345387--3345425 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3345377 ATAAATGTTC
*
3345387 TATTGTTGGAATTTAAT
1 TATTGTTGGAATATAAT
3345404 TATTGTTGGAA-ATATAT
1 TATTGTTGGAATATA-AT
3345421 TATTG
1 TATTG
3345426 AATTTAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (17 bp):
TATTGTTGGAATATAAT
Found at i:3345637 original size:21 final size:21
Alignment explanation
Indices: 3345609--3345691 Score: 103
Period size: 21 Copynumber: 4.0 Consensus size: 21
3345599 CGGGTGGATA
3345609 AGCTCTTACGAGCTTCTGTTC
1 AGCTCTTACGAGCTTCTGTTC
*
3345630 AACTCTTACGAGCTTCTGTTC
1 AGCTCTTACGAGCTTCTGTTC
** * *
3345651 AGCTCTTTTGAGCTTTTTTTC
1 AGCTCTTACGAGCTTCTGTTC
**
3345672 AGCTCTTATAAGCTTCTGTT
1 AGCTCTTACGAGCTTCTGTT
3345692 AGTGTGTTCG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.45
Consensus pattern (21 bp):
AGCTCTTACGAGCTTCTGTTC
Found at i:3347626 original size:61 final size:61
Alignment explanation
Indices: 3347535--3347665 Score: 156
Period size: 61 Copynumber: 2.1 Consensus size: 61
3347525 ACATTTTATA
* * * * *
3347535 TATATATATGTGGTTCGAATATAGGTTACAAATTCATTGAGCTGAATTTAATGTTTTGAAC
1 TATATATATGAGGTTCGAATATAGATTACAAATTCATTGAGCTAAAGTTAATGTTATGAAC
* * * * *
3347596 TATACATATGAGGTTCGAATGTA-ATATACAAGTTCTTTGAGCTAAAGTTAATGTTATGAAT
1 TATATATATGAGGTTCGAATATAGAT-TACAAATTCATTGAGCTAAAGTTAATGTTATGAAC
3347657 TATATATAT
1 TATATATAT
3347666 TCATGTGGAT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 1 0.02
61 57 0.98
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (61 bp):
TATATATATGAGGTTCGAATATAGATTACAAATTCATTGAGCTAAAGTTAATGTTATGAAC
Found at i:3347873 original size:41 final size:41
Alignment explanation
Indices: 3347772--3347873 Score: 159
Period size: 41 Copynumber: 2.5 Consensus size: 41
3347762 GCTCTGTGTT
*
3347772 TAGCAGGCTTAATGCCAGTGAAATAATTCAAACTTTACGTC
1 TAGCAGGCTTAATGCCGGTGAAATAATTCAAACTTTACGTC
* * *
3347813 TAGCAGGCTTAATGCCGGTGAAATATTTTAGACTTTACGTC
1 TAGCAGGCTTAATGCCGGTGAAATAATTCAAACTTTACGTC
*
3347854 TAGCAGGCTTAATGTCGGTG
1 TAGCAGGCTTAATGCCGGTG
3347874 TTCTGAATCA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAATAATTCAAACTTTACGTC
Found at i:3347890 original size:41 final size:41
Alignment explanation
Indices: 3347772--3347916 Score: 143
Period size: 41 Copynumber: 3.5 Consensus size: 41
3347762 GCTCTGTGTT
* *
3347772 TAGCAGGCTTAATGCCAGTGAAATA-ATTCAAACTTTACGTC
1 TAGCAGGCTTAATGCCGGTGAAATATA-TCAGACTTTACGTC
* *
3347813 TAGCAGGCTTAATGCCGGTGAAATATTTTAGACTTTACGTC
1 TAGCAGGCTTAATGCCGGTGAAATATATCAGACTTTACGTC
* *** * * *
3347854 TAGCAGGCTTAATGTCGGTGTTCTGA-ATCAGGCTTTAAGCC
1 TAGCAGGCTTAATGCCGGTGAAAT-ATATCAGACTTTACGTC
3347895 TAGCAGGC-TACATGCCGGTGAA
1 TAGCAGGCTTA-ATGCCGGTGAA
3347917 TCATTTTAAA
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
40 2 0.02
41 82 0.96
42 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAATATATCAGACTTTACGTC
Found at i:3351260 original size:45 final size:45
Alignment explanation
Indices: 3351205--3351291 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
3351195 CAGATACTCG
* * *
3351205 GTGGATTCAGCACATAACAACCACCTTATTAATTAATAATGTCCA
1 GTGGAATCAGCACATAACAACCACCTTACTAATCAATAATGTCCA
* *
3351250 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATCATGT
1 GTGGAATCAGCACATAACAACCACCTTACTAATCAATAATGT
3351292 TCGGTTCACA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (45 bp):
GTGGAATCAGCACATAACAACCACCTTACTAATCAATAATGTCCA
Found at i:3351358 original size:51 final size:50
Alignment explanation
Indices: 3351293--3351436 Score: 191
Period size: 50 Copynumber: 2.9 Consensus size: 50
3351283 CAATCATGTT
* *
3351293 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGATCGAAAC-TATC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGA-CCAAACAT-TC
* * * *
3351344 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCAAACATTC
* *
3351394 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCA
3351437 TCACTTTCAC
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
50 43 0.53
51 38 0.47
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (50 bp):
CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCAAACATTC
Found at i:3351417 original size:50 final size:51
Alignment explanation
Indices: 3351293--3351428 Score: 186
Period size: 51 Copynumber: 2.7 Consensus size: 51
3351283 CAATCATGTT
* * *
3351293 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGATCGAAACTATC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGCGACCGAAACTATC
* * *
3351344 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATC-ATTC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGCGACCGAAACTA-TC
*
3351394 CGGTACACGTAGTAGCCTGCACATAGTACTACACA
1 CGGTACACATAGTAGCCTGCACATAGTACTACACA
3351429 CGTGACCATC
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
49 1 0.01
50 37 0.49
51 38 0.50
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (51 bp):
CGGTACACATAGTAGCCTGCACATAGTACTACACATGCGACCGAAACTATC
Found at i:3354628 original size:22 final size:23
Alignment explanation
Indices: 3354598--3354652 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
3354588 ACCTACTTTC
* *
3354598 TTACTGTAGTAATTTT-GGGGTA
1 TTACAGTAGTAATTTTCGGGATA
3354620 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
*
3354643 TTACATTAGT
1 TTACAGTAGT
3354653 CTTATTGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:3358280 original size:20 final size:20
Alignment explanation
Indices: 3358257--3358296 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3358247 ACTGTTTCTG
3358257 CTTAAATTGTACTTTTCCCT
1 CTTAAATTGTACTTTTCCCT
3358277 CTTAAATTGTACTTTTCCCT
1 CTTAAATTGTACTTTTCCCT
3358297 TTGAAAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.05, T:0.50
Consensus pattern (20 bp):
CTTAAATTGTACTTTTCCCT
Found at i:3373736 original size:25 final size:25
Alignment explanation
Indices: 3373694--3373743 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3373684 TAAGATTACT
*
3373694 TTAAAATAATATTATAAATTAATAA
1 TTAAAATAATATTATAAAATAATAA
*
3373719 TTAAAATTAA-ATTTTAAAATAATAA
1 TTAAAA-TAATATTATAAAATAATAA
3373744 AATTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TTAAAATAATATTATAAAATAATAA
Found at i:3376432 original size:29 final size:28
Alignment explanation
Indices: 3376384--3376440 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
3376374 ACAAACTTAA
3376384 TATTTTTTAAAATTCTAATTTATTTTTTT
1 TATTTTTTAAAATTCTAATTT-TTTTTTT
*
3376413 TATTTTTATGAAATTC-AATTTTTTTTTT
1 TATTTTT-TAAAATTCTAATTTTTTTTTT
3376441 GCTAATTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 7 0.27
29 12 0.46
30 7 0.27
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (28 bp):
TATTTTTTAAAATTCTAATTTTTTTTTT
Found at i:3378786 original size:5 final size:5
Alignment explanation
Indices: 3378776--3378802 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3378766 TTTTTTCTTG
3378776 GATTT GATTT GATTT GATTT GATTT GA
1 GATTT GATTT GATTT GATTT GATTT GA
3378803 CTGTGTCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (5 bp):
GATTT
Found at i:3388634 original size:76 final size:76
Alignment explanation
Indices: 3388508--3388736 Score: 458
Period size: 76 Copynumber: 3.0 Consensus size: 76
3388498 AATAGTGAAG
3388508 AAAGGCAAATTATAACATCTATTACTCTAATGGTAGGAGGAGAAAGAAGAAGAAGAAAGAGAAGG
1 AAAGGCAAATTATAACATCTATTACTCTAATGGTAGGAGGAGAAAGAAGAAGAAGAAAGAGAAGG
3388573 TACATTACCAT
66 TACATTACCAT
3388584 AAAGGCAAATTATAACATCTATTACTCTAATGGTAGGAGGAGAAAGAAGAAGAAGAAAGAGAAGG
1 AAAGGCAAATTATAACATCTATTACTCTAATGGTAGGAGGAGAAAGAAGAAGAAGAAAGAGAAGG
3388649 TACATTACCAT
66 TACATTACCAT
3388660 AAAGGCAAATTATAACATCTATTACTCTAATGGTAGGAGGAGAAAGAAGAAGAAGAAAGAGAAGG
1 AAAGGCAAATTATAACATCTATTACTCTAATGGTAGGAGGAGAAAGAAGAAGAAGAAAGAGAAGG
3388725 TACATTACCAT
66 TACATTACCAT
3388736 A
1 A
3388737 TATAGAACCA
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 153 1.00
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.20
Consensus pattern (76 bp):
AAAGGCAAATTATAACATCTATTACTCTAATGGTAGGAGGAGAAAGAAGAAGAAGAAAGAGAAGG
TACATTACCAT
Found at i:3401090 original size:2 final size:2
Alignment explanation
Indices: 3401085--3401138 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
3401075 TATATATCTT
3401085 AG AG AG AG AG AG AG AG 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 AG AG AG AG
*
3401127 AG AG AG AA AG AG
1 AG AG AG AG AG AG
3401139 TGAGGAGATT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3414635 original size:15 final size:15
Alignment explanation
Indices: 3414615--3414646 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3414605 AAACGCACCG
3414615 CCCATCCAAACTCAC
1 CCCATCCAAACTCAC
3414630 CCCATCCAAACTCAC
1 CCCATCCAAACTCAC
3414645 CC
1 CC
3414647 TAAGTGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.56, G:0.00, T:0.12
Consensus pattern (15 bp):
CCCATCCAAACTCAC
Found at i:3418395 original size:73 final size:74
Alignment explanation
Indices: 3418276--3418423 Score: 244
Period size: 73 Copynumber: 2.0 Consensus size: 74
3418266 ATTGATGAAA
*
3418276 AGCTTGGGGAAGTATCCTAGGTAGCGCATCATTTAAAAGCTCTTTTAC-TTAACCACTCGATTTT
1 AGCTTGGGGAAGTATCCTAGGTAGCGCATCATTTAAAAACTCTTTTACTTTAACCACTCGATTTT
3418340 TTATCTTAG
66 TTATCTTAG
* * *
3418349 AGCTTGGGGAAGTATCCTAGGTAGCTCATCATTTAAAAATTCTTTTACTTTTAACCACTCGGTTT
1 AGCTTGGGGAAGTATCCTAGGTAGCGCATCATTTAAAAACTCTTTTAC-TTTAACCACTCGATTT
3418414 TTTATCTTAG
65 TTTATCTTAG
3418424 TTGTTTGTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
73 45 0.65
75 24 0.35
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (74 bp):
AGCTTGGGGAAGTATCCTAGGTAGCGCATCATTTAAAAACTCTTTTACTTTAACCACTCGATTTT
TTATCTTAG
Found at i:3422037 original size:23 final size:24
Alignment explanation
Indices: 3421989--3422037 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
3421979 TAAACAACAA
*
3421989 AGAGAAAGAGTGAGTGAGAGAGAG
1 AGAGAAAGAGTGAGTGACAGAGAG
*
3422013 AGAGAAA-AGTG-GATGACAGATAG
1 AGAGAAAGAGTGAG-TGACAGAGAG
3422036 AG
1 AG
3422038 GGTGAGCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 1 0.05
23 14 0.64
24 7 0.32
ACGTcount: A:0.47, C:0.02, G:0.41, T:0.10
Consensus pattern (24 bp):
AGAGAAAGAGTGAGTGACAGAGAG
Found at i:3426207 original size:10 final size:11
Alignment explanation
Indices: 3426187--3426211 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3426177 CAATCGTCCA
3426187 TTTCTTTTTTT
1 TTTCTTTTTTT
3426198 TTTCTTTTTTT
1 TTTCTTTTTTT
3426209 TTT
1 TTT
3426212 TTGGTTTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:3426616 original size:21 final size:22
Alignment explanation
Indices: 3426576--3426624 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
3426566 AAATTCATAA
*
3426576 TTATTCAAATTAAAATTTATTT
1 TTATTTAAATTAAAATTTATTT
*
3426598 TTATTTAATTTAAAA-TTATTT
1 TTATTTAAATTAAAATTTATTT
3426619 TTATTT
1 TTATTT
3426625 TTATAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATTTAAATTAAAATTTATTT
Found at i:3426643 original size:25 final size:26
Alignment explanation
Indices: 3426591--3426643 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
3426581 CAAATTAAAA
* **
3426591 TTTATTTTTATTTAATTTAAAATTATT
1 TTTATTTTTA-TTAATATAAAAAAATT
3426618 TTTATTTTTA-TAATATAAAAAAATT
1 TTTATTTTTATTAATATAAAAAAATT
3426643 T
1 T
3426644 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 13 0.57
27 10 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTATTTTTATTAATATAAAAAAATT
Found at i:3429578 original size:39 final size:41
Alignment explanation
Indices: 3429483--3429579 Score: 117
Period size: 40 Copynumber: 2.4 Consensus size: 41
3429473 CGTTTGGACA
3429483 AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTCCAGG
1 AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTCCAGG
* * * **
3429524 -AAAGCGCTGCTAAAAA-TGAGCATTAGCGGCGTTTCTTGG
1 AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTCCAGG
* *
3429563 AAAAACACCGCAAAAAA
1 AAAAACGCCGCTAAAAA
3429580 CCTAAGCCCA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
39 20 0.43
40 26 0.57
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.18
Consensus pattern (41 bp):
AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTCCAGG
Found at i:3429579 original size:40 final size:40
Alignment explanation
Indices: 3429483--3429579 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 40
3429473 CGTTTGGACA
*
3429483 AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTCCAGG
1 AAAAACGCCGC-AAAAAATGAGCATTAGCGGCGCTTCCAGG
* * * * **
3429524 -AAAGCGCTGCTAAAAATGAGCATTAGCGGCGTTTCTTGG
1 AAAAACGCCGCAAAAAATGAGCATTAGCGGCGCTTCCAGG
*
3429563 AAAAACACCGCAAAAAA
1 AAAAACGCCGCAAAAAA
3429580 CCTAAGCCCA
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
39 24 0.55
40 20 0.45
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.18
Consensus pattern (40 bp):
AAAAACGCCGCAAAAAATGAGCATTAGCGGCGCTTCCAGG
Found at i:3429676 original size:41 final size:41
Alignment explanation
Indices: 3429619--3429768 Score: 194
Period size: 41 Copynumber: 3.7 Consensus size: 41
3429609 TTTCGGGGCA
* * *
3429619 TTAGCGGTGTTTTTGAAAAAGCGTCGCTAATGTTCAGGCTT
1 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCTT
* * * * *
3429660 TTAGCGTCGTTTTTGAAAAAGCGCCGCTATTACTCATGCTG
1 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCTT
* *
3429701 TTAGCGGCGTTTTT-AAAGAAGCGCCGCTAATGCTCTGACTT
1 TTAGCGGCGTTTTTGAAA-AAGCGCCGCTAATGCTCAGGCTT
3429742 TTAGCGGCGTTTTTGAAAAAGCGCCGC
1 TTAGCGGCGTTTTTGAAAAAGCGCCGC
3429769 AAAAACATTG
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
40 3 0.03
41 86 0.93
42 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCTT
Found at i:3430074 original size:14 final size:14
Alignment explanation
Indices: 3430057--3430084 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3430047 ATAGGGATTC
3430057 TGGTTTAAGGGTTA
1 TGGTTTAAGGGTTA
3430071 TGGTTTAAGGGTTA
1 TGGTTTAAGGGTTA
3430085 AGGGTTAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (14 bp):
TGGTTTAAGGGTTA
Found at i:3430188 original size:14 final size:14
Alignment explanation
Indices: 3430158--3430203 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
3430148 TAAATAAGGT
*
3430158 TTAGGGGTTAGTAG
1 TTAGGGGTTAGGAG
*
3430172 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGAG
* *
3430186 TTAGAGGTTAAGAG
1 TTAGGGGTTAGGAG
3430200 TTAG
1 TTAG
3430204 TGATTTAATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (14 bp):
TTAGGGGTTAGGAG
Found at i:3430202 original size:21 final size:21
Alignment explanation
Indices: 3430158--3430203 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3430148 TAAATAAGGT
* *
3430158 TTAGGGGTTAGTAGTTAGGGG
1 TTAGGGGTTAGTAGTTAAGAG
3430179 TTAGGGGTTAG-AGGTTAAGAG
1 TTAGGGGTTAGTA-GTTAAGAG
3430200 TTAG
1 TTAG
3430204 TGATTTAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (21 bp):
TTAGGGGTTAGTAGTTAAGAG
Found at i:3430739 original size:38 final size:39
Alignment explanation
Indices: 3430653--3430740 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 39
3430643 ATTTTCTTAA
*
3430653 CCGCTAAAAATAAGCATTAGCGGCGCTTTTCGAAAAACG
1 CCGCTAAAAATAAGCATTAGCGGCGCTTTTCAAAAAACG
* * * *
3430692 CCGCTAAAAATGAGCATTAGTGGTG-TTTTTAAAAAAGCG
1 CCGCTAAAAATAAGCATTAGCGGCGCTTTTCAAAAAA-CG
*
3430731 CCGCAAAAAA
1 CCGCTAAAAA
3430741 CCTAAGCCCA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 9 0.21
39 33 0.79
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (39 bp):
CCGCTAAAAATAAGCATTAGCGGCGCTTTTCAAAAAACG
Found at i:3430834 original size:40 final size:40
Alignment explanation
Indices: 3430779--3430854 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
3430769 GTTTTTGAGG
3430779 TTTTAGCGGCGTTTTTGAAAAAGCGCCACAAATGCTCTAT
1 TTTTAGCGGCGTTTTTGAAAAAGCGCCACAAATGCTCTAT
* * *
3430819 TTTTAGTGGCGTTTTTGAGAAAGCGCCACTAATGCT
1 TTTTAGCGGCGTTTTTGAAAAAGCGCCACAAATGCT
3430855 AATATTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTTGAAAAAGCGCCACAAATGCTCTAT
Found at i:3431660 original size:38 final size:38
Alignment explanation
Indices: 3431584--3431661 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
3431574 ACAAACTTTG
* * *
3431584 TCTGTTTTTTATATGTTTATCTCACAAATTTTCTTTTA
1 TCTGTTTTTTACATGTTTATCTCACAAAGTTTCGTTTA
*
3431622 TCTGTTTTTTACATGTTTATCTCACAAAGTTTGGTTTA
1 TCTGTTTTTTACATGTTTATCTCACAAAGTTTCGTTTA
3431660 TC
1 TC
3431662 AATTGTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.56
Consensus pattern (38 bp):
TCTGTTTTTTACATGTTTATCTCACAAAGTTTCGTTTA
Found at i:3437858 original size:43 final size:43
Alignment explanation
Indices: 3437768--3438008 Score: 360
Period size: 43 Copynumber: 5.6 Consensus size: 43
3437758 TGTTTTTTGT
* * *
3437768 GGCGTTTTTG-CAAGAAGCGTCGCTAAAGGT-TTGTTCTTTAGC
1 GGCGTTTGTGACAA-AAGCGCCGCTAAAGGTCATGTTCTTTAGC
* * *
3437810 GGCGTTTATGATAAAAGCGCCGCTAAAGGCCATGTTCTTTAGC
1 GGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGTTCTTTAGC
3437853 GGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGTTCTTTAGC
1 GGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGTTCTTTAGC
3437896 GGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGTTCTTTAGC
1 GGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGTTCTTTAGC
* * * *
3437939 GGCATTTGTGACAAAAGTGCCGCGAAAGGTCATATTCTTTAGC
1 GGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGTTCTTTAGC
*
3437982 GGCGTTTGTGATAAAAGCGCCGCTAAA
1 GGCGTTTGTGACAAAAGCGCCGCTAAA
3438009 TGCCTAAAAA
Statistics
Matches: 181, Mismatches: 16, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
42 23 0.13
43 158 0.87
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (43 bp):
GGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGTTCTTTAGC
Found at i:3439311 original size:22 final size:23
Alignment explanation
Indices: 3439258--3439313 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
3439248 GCCCGTTTTA
* * *
3439258 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
3439281 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
3439303 ATTAAAATTAA
1 ATTAAAATTAA
3439314 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:3439326 original size:16 final size:16
Alignment explanation
Indices: 3439289--3439328 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3439279 TTAATAAAAT
* *
3439289 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
3439305 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
3439321 TAAAATTA
1 TAAAATTA
3439329 TCAAATTATT
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:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:3439407 original size:59 final size:59
Alignment explanation
Indices: 3439339--3439508 Score: 322
Period size: 59 Copynumber: 2.9 Consensus size: 59
3439329 TCAAATTATT
*
3439339 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
3439398 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
3439457 AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
3439509 ACAAACTTGA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 109 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:3439615 original size:22 final size:24
Alignment explanation
Indices: 3439575--3439618 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
3439565 AAATAAACTT
*
3439575 AAAATGAAAAACTATTATATTTTA
1 AAAATGAAAAAATATTATATTTTA
3439599 AAAAT-AAAAAATA-TATATTT
1 AAAATGAAAAAATATTATATTT
3439619 AATATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAATGAAAAAATATTATATTTTA
Found at i:3445799 original size:22 final size:24
Alignment explanation
Indices: 3445749--3445799 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
3445739 TTGCAATACT
3445749 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
3445774 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
3445795 TTTAT
1 TTTAT
3445800 TTATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 4 0.17
24 6 0.25
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Found at i:3454170 original size:17 final size:17
Alignment explanation
Indices: 3454148--3454180 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3454138 GTGAGCAATC
3454148 ATCGCATTTTTTTTACT
1 ATCGCATTTTTTTTACT
3454165 ATCGCATTTTTTTTAC
1 ATCGCATTTTTTTTAC
3454181 CAACTGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.58
Consensus pattern (17 bp):
ATCGCATTTTTTTTACT
Found at i:3461438 original size:23 final size:23
Alignment explanation
Indices: 3461412--3461456 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3461402 AACTCAAATT
*
3461412 TTTTAAAATAAAGTTGTGGATTC
1 TTTTAAAATAAAATTGTGGATTC
* *
3461435 TTTTAAAGTAAAATTTTGGATT
1 TTTTAAAATAAAATTGTGGATT
3461457 TAAATTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (23 bp):
TTTTAAAATAAAATTGTGGATTC
Found at i:3461834 original size:16 final size:16
Alignment explanation
Indices: 3461788--3461836 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
3461778 GTCAACATTT
*
3461788 ATTTTTTTAATTTATA
1 ATTTTTTTAATTTTTA
** *
3461804 ATTTTTACAAGTTTTA
1 ATTTTTTTAATTTTTA
3461820 ATTTTTTTAATTTTTA
1 ATTTTTTTAATTTTTA
3461836 A
1 A
3461837 AAATAATAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
ATTTTTTTAATTTTTA
Found at i:3481564 original size:21 final size:21
Alignment explanation
Indices: 3481521--3481566 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3481511 ATACTTAATT
* *
3481521 TTAATTAATAATTTATATTTA
1 TTAATTAATAATTAAAATTTA
3481542 TTAATTAATAA-TAAAATTATA
1 TTAATTAATAATTAAAATT-TA
3481563 TTAA
1 TTAA
3481567 AATTTACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAATTAATAATTAAAATTTA
Found at i:3483523 original size:18 final size:18
Alignment explanation
Indices: 3483485--3483523 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3483475 ATCATCCATT
*
3483485 TCAATATATCATTATATA
1 TCAATATATCATTATACA
3483503 TCAATATATCA-TATACCA
1 TCAATATATCATTATA-CA
3483521 TCA
1 TCA
3483524 TTTTCATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (18 bp):
TCAATATATCATTATACA
Found at i:3488928 original size:20 final size:20
Alignment explanation
Indices: 3488892--3488929 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3488882 CGCCATCCCC
*
3488892 TTTTTATTTATATCATCATA
1 TTTTTATTTATACCATCATA
3488912 TTTTT-TTTATCACCATCA
1 TTTTTATTTAT-ACCATCA
3488930 ACGGTCCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.26, C:0.16, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTATTTATACCATCATA
Found at i:3493830 original size:357 final size:357
Alignment explanation
Indices: 3493175--3493891 Score: 1434
Period size: 357 Copynumber: 2.0 Consensus size: 357
3493165 CATTACAACT
3493175 GTTAAGTAATACCACATTTTACCTGTTCCCTTTACTACTTTGTACTACTTTTCTGGGGCTAATAT
1 GTTAAGTAATACCACATTTTACCTGTTCCCTTTACTACTTTGTACTACTTTTCTGGGGCTAATAT
3493240 GTTCATCCTGAGATTGGGATTTTTTCTCTTTCCTATAATATTAAATTTTCAGGAAGAAAACAAGC
66 GTTCATCCTGAGATTGGGATTTTTTCTCTTTCCTATAATATTAAATTTTCAGGAAGAAAACAAGC
3493305 AAATTTATGGGGTTTTGGCTCAGGATATCCAGAAGAATATACCAGACACAGGAACGTGGATGTTG
131 AAATTTATGGGGTTTTGGCTCAGGATATCCAGAAGAATATACCAGACACAGGAACGTGGATGTTG
3493370 TTATGAAAGGAACAACTGCACAGCACCCATTTTATATCCATCACACAAATCTGACAATGACATCG
196 TTATGAAAGGAACAACTGCACAGCACCCATTTTATATCCATCACACAAATCTGACAATGACATCG
3493435 ACCACAACATCATGCAACAACTTTTGCTCTTTTTATTTGTCAAGGAAAATCAAGGTGTGTGTGGA
261 ACCACAACATCATGCAACAACTTTTGCTCTTTTTATTTGTCAAGGAAAATCAAGGTGTGTGTGGA
3493500 TTGCCATGTTTGGTAAATGAATGTCATGTTCG
326 TTGCCATGTTTGGTAAATGAATGTCATGTTCG
3493532 GTTAAGTAATACCACATTTTACCTGTTCCCTTTACTACTTTGTACTACTTTTCTGGGGCTAATAT
1 GTTAAGTAATACCACATTTTACCTGTTCCCTTTACTACTTTGTACTACTTTTCTGGGGCTAATAT
3493597 GTTCATCCTGAGATTGGGATTTTTTCTCTTTCCTATAATATTAAATTTTCAGGAAGAAAACAAGC
66 GTTCATCCTGAGATTGGGATTTTTTCTCTTTCCTATAATATTAAATTTTCAGGAAGAAAACAAGC
3493662 AAATTTATGGGGTTTTGGCTCAGGATATCCAGAAGAATATACCAGACACAGGAACGTGGATGTTG
131 AAATTTATGGGGTTTTGGCTCAGGATATCCAGAAGAATATACCAGACACAGGAACGTGGATGTTG
3493727 TTATGAAAGGAACAACTGCACAGCACCCATTTTATATCCATCACACAAATCTGACAATGACATCG
196 TTATGAAAGGAACAACTGCACAGCACCCATTTTATATCCATCACACAAATCTGACAATGACATCG
3493792 ACCACAACATCATGCAACAACTTTTGCTCTTTTTATTTGTCAAGGAAAATCAAGGTGTGTGTGGA
261 ACCACAACATCATGCAACAACTTTTGCTCTTTTTATTTGTCAAGGAAAATCAAGGTGTGTGTGGA
3493857 TTGCCATGTTTGGTAAATGAATGTCATGTTCG
326 TTGCCATGTTTGGTAAATGAATGTCATGTTCG
3493889 GTT
1 GTT
3493892 GAACTTTACA
Statistics
Matches: 360, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
357 360 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (357 bp):
GTTAAGTAATACCACATTTTACCTGTTCCCTTTACTACTTTGTACTACTTTTCTGGGGCTAATAT
GTTCATCCTGAGATTGGGATTTTTTCTCTTTCCTATAATATTAAATTTTCAGGAAGAAAACAAGC
AAATTTATGGGGTTTTGGCTCAGGATATCCAGAAGAATATACCAGACACAGGAACGTGGATGTTG
TTATGAAAGGAACAACTGCACAGCACCCATTTTATATCCATCACACAAATCTGACAATGACATCG
ACCACAACATCATGCAACAACTTTTGCTCTTTTTATTTGTCAAGGAAAATCAAGGTGTGTGTGGA
TTGCCATGTTTGGTAAATGAATGTCATGTTCG
Found at i:3498525 original size:20 final size:20
Alignment explanation
Indices: 3498502--3498547 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3498492 TGTTAATATT
3498502 TTGTTA-TTAATTCAAATAGG
1 TTGTTACTTAATT-AAATAGG
**
3498522 TTGTTACTTGGTTAAATAGG
1 TTGTTACTTAATTAAATAGG
3498542 TTGTTA
1 TTGTTA
3498548 AGATTTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (20 bp):
TTGTTACTTAATTAAATAGG
Found at i:3500209 original size:13 final size:14
Alignment explanation
Indices: 3500177--3500210 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3500167 ACAATTACTT
*
3500177 TATTCAAAACAACG
1 TATTCAAAACAACA
3500191 TATTCAAAACAA-A
1 TATTCAAAACAACA
3500204 TATTCAA
1 TATTCAA
3500211 CATATTACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (14 bp):
TATTCAAAACAACA
Found at i:3500472 original size:21 final size:21
Alignment explanation
Indices: 3500448--3500489 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3500438 TCCAGCTTCT
* * *
3500448 GGCGGGGGTTGTGGTTGCTCC
1 GGCGGGGATTCTGGTTCCTCC
3500469 GGCGGGGATTCTGGTTCCTCC
1 GGCGGGGATTCTGGTTCCTCC
3500490 AGTAATGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.24, G:0.45, T:0.29
Consensus pattern (21 bp):
GGCGGGGATTCTGGTTCCTCC
Found at i:3505923 original size:2 final size:2
Alignment explanation
Indices: 3505916--3505944 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3505906 GTTCTTGTTT
3505916 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3505945 GATCATCTAT
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3509014 original size:23 final size:24
Alignment explanation
Indices: 3508969--3509014 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
3508959 TATAAAAAAT
* * *
3508969 AAATTATTTACTTAAATGTATTTG
1 AAATTATTTAATAAAATGAATTTG
3508993 AAATTATTTAATAAAAT-AATTT
1 AAATTATTTAATAAAATGAATTT
3509015 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTATTTAATAAAATGAATTTG
Found at i:3522930 original size:125 final size:124
Alignment explanation
Indices: 3522704--3522978 Score: 399
Period size: 125 Copynumber: 2.2 Consensus size: 124
3522694 TCTCAATTTC
* * * *
3522704 CAGGACCTATTGTAGCAAAAGCGCATCCACGAGAACGCAATTTCACAAATTCTTCTCAAATAGCA
1 CAGGACCTACTGTAGCAAAAGCGCATCCACGAGAACGCAATTTCACAAATTATTATCAAACAGCA
* * *
3522769 TCCTGTTAGAAGTGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTT
66 TCCTGCTAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTT-TTT
* * * *
3522829 CAGGACCTACTATAGCAAAAGCGCGTCCACGAG-GCTGCGATTTCACAAATTATTATCAAACAGC
1 CAGGACCTACTGTAGCAAAAGCGCATCCACGAGAAC-GCAATTTCACAAATTATTATCAAACAGC
* *
3522893 ATCTTGCTAGAAGCGATTTTATACTATTTGCTTAGAAACATCAACTCGAAATTATTTTTT
65 ATCCTGCTAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTT
*
3522953 CAGGACCTACTGTAGCAAAAGTGCAT
1 CAGGACCTACTGTAGCAAAAGCGCAT
3522979 AAACGTGGGC
Statistics
Matches: 133, Mismatches: 16, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
124 27 0.20
125 106 0.80
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (124 bp):
CAGGACCTACTGTAGCAAAAGCGCATCCACGAGAACGCAATTTCACAAATTATTATCAAACAGCA
TCCTGCTAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTT
Found at i:3524245 original size:10 final size:9
Alignment explanation
Indices: 3524206--3524398 Score: 61
Period size: 10 Copynumber: 20.0 Consensus size: 9
3524196 ACATGTGGCA
*
3524206 AAAAATGAT
1 AAAAATTAT
3524215 AAAAA--AT
1 AAAAATTAT
*
3524222 AAAAATCAAT
1 AAAAAT-TAT
*
3524232 AAAAGTTAT
1 AAAAATTAT
3524241 AAAAATTAT
1 AAAAATTAT
3524250 AAAAATTATT
1 AAAAATTA-T
**
3524260 AAATTTTAAT
1 AAAAATT-AT
*
3524270 AAAATAATAT
1 AAAA-ATTAT
*
3524280 AAAAAATATTT
1 -AAAAAT-TAT
**
3524291 AAATTTTATT
1 AAAAATTA-T
*
3524301 AAAAATTAG
1 AAAAATTAT
3524310 AAAATATTTTAT
1 AAAA-A--TTAT
3524322 AAAAATCGTA-
1 AAAAAT--TAT
3524332 AAAAATTA-
1 AAAAATTAT
*
3524340 CAAAATATAT
1 AAAAAT-TAT
* *
3524350 AGAAATATAGA
1 AAAAAT-TA-T
3524361 AATAAATTAT
1 AA-AAATTAT
* *
3524371 AAAAAATGT
1 AAAAATTAT
3524380 AAAGAATTAT
1 AAA-AATTAT
*
3524390 AAAAGTTAT
1 AAAAATTAT
3524399 CATACAGGAA
Statistics
Matches: 137, Mismatches: 28, Indels: 38
0.67 0.14 0.19
Matches are distributed among these distances:
7 7 0.05
8 7 0.05
9 44 0.32
10 54 0.39
11 14 0.10
12 11 0.08
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:3524251 original size:18 final size:19
Alignment explanation
Indices: 3524220--3524258 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3524210 ATGATAAAAA
*
3524220 ATAAAAATCAATAAAAGTT
1 ATAAAAATCAATAAAAATT
*
3524239 ATAAAAAT-TATAAAAATT
1 ATAAAAATCAATAAAAATT
3524257 AT
1 AT
3524259 TAAATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (19 bp):
ATAAAAATCAATAAAAATT
Found at i:3524283 original size:30 final size:30
Alignment explanation
Indices: 3524239--3524318 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
3524229 AATAAAAGTT
* *
3524239 ATAAAAATTATAAAAATTA-TTAAATTTTA
1 ATAAAAAATATAAAAAATATTTAAATTTTA
3524268 ATAAAATAATATAAAAAATATTTAAATTTT-
1 ATAAAA-AATATAAAAAATATTTAAATTTTA
* *
3524298 ATTAAAAAT-TAGAAAATATTT
1 ATAAAAAATATAAAAAATATTT
3524319 TATAAAAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
28 11 0.24
29 9 0.20
30 16 0.36
31 9 0.20
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (30 bp):
ATAAAAAATATAAAAAATATTTAAATTTTA
Found at i:3525162 original size:3 final size:3
Alignment explanation
Indices: 3525154--3525178 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3525144 GAACCACCCT
3525154 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
3525179 CAAGATTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3525243 original size:23 final size:23
Alignment explanation
Indices: 3525217--3525261 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3525207 TGAGGTTAAC
3525217 TTCTTTATTTTT-TTTTATATTCT
1 TTCTTTATTTTTCTTTT-TATTCT
*
3525240 TTCTTTGTTTTTCTTTTTATTC
1 TTCTTTATTTTTCTTTTTATTC
3525262 CTGATCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.78
Consensus pattern (23 bp):
TTCTTTATTTTTCTTTTTATTCT
Found at i:3534493 original size:14 final size:15
Alignment explanation
Indices: 3534474--3534502 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3534464 TACTTATTAA
3534474 TATAAAT-TTAACTT
1 TATAAATCTTAACTT
3534488 TATAAATCTTAACTT
1 TATAAATCTTAACTT
3534503 GTTTAGTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAAATCTTAACTT
Found at i:3544093 original size:26 final size:26
Alignment explanation
Indices: 3544064--3544114 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
3544054 TTTAAGCAGT
3544064 TAAAGTAAGTATTCACCCAATTTAAG
1 TAAAGTAAGTATTCACCCAATTTAAG
3544090 TAAAGTAAGTATTCACCCAATTTAA
1 TAAAGTAAGTATTCACCCAATTTAA
3544115 ATAAGTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (26 bp):
TAAAGTAAGTATTCACCCAATTTAAG
Found at i:3553231 original size:15 final size:16
Alignment explanation
Indices: 3553206--3553235 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3553196 GGCCCGTTCC
3553206 TATTATTTTAATTTAA
1 TATTATTTTAATTTAA
3553222 TATT-TTTTAATTTA
1 TATTATTTTAATTTA
3553236 TTAAACTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTATTTTAATTTAA
Found at i:3554039 original size:56 final size:56
Alignment explanation
Indices: 3553978--3554090 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
3553968 GAAAAAAAAG
3553978 TATGAGTCAGTTATACAAATGTTCACTTAATTATGTCCGCATTCTTATTTTATTAC
1 TATGAGTCAGTTATACAAATGTTCACTTAATTATGTCCGCATTCTTATTTTATTAC
3554034 TATGAGTCAGTTATACAAATGTTCACTTAATTATGTCCGCATTCTTATTTTATTAC
1 TATGAGTCAGTTATACAAATGTTCACTTAATTATGTCCGCATTCTTATTTTATTAC
3554090 T
1 T
3554091 CATTAAATTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.45
Consensus pattern (56 bp):
TATGAGTCAGTTATACAAATGTTCACTTAATTATGTCCGCATTCTTATTTTATTAC
Found at i:3560750 original size:33 final size:34
Alignment explanation
Indices: 3560707--3560775 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 34
3560697 TGGTAAGGCC
3560707 TCGTAATCACCCAATTAATCTTATTCATTTTTAT
1 TCGTAATCACCCAATTAATCTTATTCATTTTTAT
3560741 TCGT-ATCACCCAATTAATCTTATTCATTTTTAT
1 TCGTAATCACCCAATTAATCTTATTCATTTTTAT
3560774 TC
1 TC
3560776 ATGTCTGGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 31 0.89
34 4 0.11
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.48
Consensus pattern (34 bp):
TCGTAATCACCCAATTAATCTTATTCATTTTTAT
Found at i:3572364 original size:24 final size:24
Alignment explanation
Indices: 3572337--3572401 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
3572327 TTATCTTTTG
*
3572337 TTAAAGTTTGTTGAGTCATGTCCT
1 TTAAAGTTTGATGAGTCATGTCCT
* *
3572361 TTAAAGTTTGCTGAGTAATGTCCT
1 TTAAAGTTTGATGAGTCATGTCCT
3572385 TT-AAGTTTGATGAGTCA
1 TTAAAGTTTGATGAGTCA
3572402 GGTAAAACCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 13 0.35
24 24 0.65
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.43
Consensus pattern (24 bp):
TTAAAGTTTGATGAGTCATGTCCT
Found at i:3573607 original size:4 final size:4
Alignment explanation
Indices: 3573595--3573626 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
3573585 TGTTTTTTTT
3573595 TTTA CTTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTT
3573627 CTGTATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:3574093 original size:33 final size:33
Alignment explanation
Indices: 3574056--3574129 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
3574046 TGGTCCAACC
** ** *
3574056 ATGGTCTTATGTTTAATGTGCCATAACCCAGTT
1 ATGGTCTTATCATTAAAATGCCATAACCCAGCT
* *
3574089 ATGGTCTTTTCATTAAAATGCCATAGCCCAGCT
1 ATGGTCTTATCATTAAAATGCCATAACCCAGCT
3574122 ATGGTCTT
1 ATGGTCTT
3574130 GAGTGACAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (33 bp):
ATGGTCTTATCATTAAAATGCCATAACCCAGCT
Found at i:3575695 original size:13 final size:13
Alignment explanation
Indices: 3575677--3575702 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3575667 TTTTATTATA
3575677 AAATAATAGGGTG
1 AAATAATAGGGTG
3575690 AAATAATAGGGTG
1 AAATAATAGGGTG
3575703 TTGCCTGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (13 bp):
AAATAATAGGGTG
Found at i:3576802 original size:44 final size:47
Alignment explanation
Indices: 3576725--3576813 Score: 123
Period size: 44 Copynumber: 2.0 Consensus size: 47
3576715 TTTCTTGCAT
* *
3576725 TTTTATATTTTCTGAATATTTTTTATAAGTTTTA-AGTTATATACCGA
1 TTTTATATTTTCTGAATAATTTTTATAAATTTTATA-TTATATACCGA
3576772 TTTTAT-TTTT-TGAA-AATTTTTATAAATTTTATATTATATACC
1 TTTTATATTTTCTGAATAATTTTTATAAATTTTATATTATATACC
3576814 AATAAATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 24 0.62
45 5 0.13
46 4 0.10
47 6 0.15
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (47 bp):
TTTTATATTTTCTGAATAATTTTTATAAATTTTATATTATATACCGA
Found at i:3578845 original size:14 final size:15
Alignment explanation
Indices: 3578819--3578848 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3578809 TGTTAGTTTT
3578819 CTGGGGAAAAAAAAG
1 CTGGGGAAAAAAAAG
3578834 CTGGGGAAAAAAAAG
1 CTGGGGAAAAAAAAG
3578849 TAAAAGTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.33, T:0.07
Consensus pattern (15 bp):
CTGGGGAAAAAAAAG
Done.