Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 110 of 113
Found at i:21515290 original size:10 final size:10
Alignment explanation
Indices: 21515273--21515311 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
21515263 CTCTTCTTTC
21515273 CATTTTTTTT
1 CATTTTTTTT
21515283 C--TTTTTTT
1 CATTTTTTTT
21515291 CATTTTTTTT
1 CATTTTTTTT
21515301 CATTTTTTTT
1 CATTTTTTTT
21515311 C
1 C
21515312 TTTCACCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 8 0.30
10 19 0.70
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (10 bp):
CATTTTTTTT
Found at i:21515306 original size:18 final size:18
Alignment explanation
Indices: 21515273--21515308 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21515263 CTCTTCTTTC
*
21515273 CATTTTTTTTCTTTTTTT
1 CATTTTTTTTCATTTTTT
21515291 CATTTTTTTTCATTTTTT
1 CATTTTTTTTCATTTTTT
21515309 TTCTTTCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (18 bp):
CATTTTTTTTCATTTTTT
Found at i:21521521 original size:120 final size:118
Alignment explanation
Indices: 21521385--21521602 Score: 309
Period size: 120 Copynumber: 1.8 Consensus size: 118
21521375 TTTGTACAAA
* * *
21521385 AAAAATTGATAATTTCAATTTTTTCTTAAAATA-TTTTCTTGATAATATTTATTTTTTTA-AAAA
1 AAAAATTGATAATTTCAACTTTTTCTCAAAATACTTTTCTTGAT-A-ATTTA-TTTTTAAGAAAA
21521448 ATT-AGTAC-TTCTAACTTTTGCTCAAAATATATTTTTTTCTAAAATTCTAATTTCAAG
63 ATTGA-TACTTTC-AACTTTTGCTCAAAATAT-TTTTTTTCTAAAATTCTAATTTCAAG
*
21521505 AAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTCTTGATAATTTATTTTTAAGAAAAATT
1 AAAAATTGATAATTTCAACTTTTTCTCAAAATACTTTTCTTGATAATTTATTTTTAAGAAAAATT
*
21521570 GATACTTTCAACTTTTTCTCAAAATATTTTTTT
66 GATACTTTCAACTTTTGCTCAAAATATTTTTTT
21521603 AAAATTTTAT
Statistics
Matches: 89, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
118 12 0.13
119 32 0.36
120 35 0.39
121 10 0.11
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.50
Consensus pattern (118 bp):
AAAAATTGATAATTTCAACTTTTTCTCAAAATACTTTTCTTGATAATTTATTTTTAAGAAAAATT
GATACTTTCAACTTTTGCTCAAAATATTTTTTTTCTAAAATTCTAATTTCAAG
Found at i:21521602 original size:119 final size:120
Alignment explanation
Indices: 21521385--21521602 Score: 313
Period size: 119 Copynumber: 1.8 Consensus size: 120
21521375 TTTGTACAAA
* * *
21521385 AAAAATTGATAATTTCAATTTTTTCTTAAAATATTTTCTTGATAATATTTATTTTTTTAAAAAAT
1 AAAAATTGATAATTTCAACTTTTTCTCAAAATATTTTCTTGATAATATTTATTTTTTAAAAAAAT
21521450 TAGTACTTCTAACTTTTGCTCAAAATATATTTTTTTCTAAAATTCTAATTTCAAG
66 TAGTACTTCTAACTTTTGCTCAAAATATATTTTTTTCTAAAATTCTAATTTCAAG
*
21521505 AAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTCTTGAT-A-ATTTA-TTTTTAAGAAAA
1 AAAAATTGATAATTTCAACTTTTTCTCAAAATA-TTTTCTTGATAATATTTATTTTTTAA-AAAA
*
21521567 ATT-GATACTT-TCAACTTTTTCTCAAAATAT-TTTTTT
64 ATTAG-TACTTCT-AACTTTTGCTCAAAATATATTTTTT
21521603 AAAATTTTAT
Statistics
Matches: 89, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
118 14 0.16
119 34 0.38
120 31 0.35
121 10 0.11
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.50
Consensus pattern (120 bp):
AAAAATTGATAATTTCAACTTTTTCTCAAAATATTTTCTTGATAATATTTATTTTTTAAAAAAAT
TAGTACTTCTAACTTTTGCTCAAAATATATTTTTTTCTAAAATTCTAATTTCAAG
Found at i:21521629 original size:58 final size:58
Alignment explanation
Indices: 21521385--21521615 Score: 231
Period size: 58 Copynumber: 3.9 Consensus size: 58
21521375 TTTGTACAAA
* * * *
21521385 AAAAATTGATAATTTCAATTTTTTCTTAAAATA-TTTTCTTGATAATATTTATTTTTTTA-
1 AAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTCTTGA-AA-ATTTA-TTTTTAAG
* * * * * *
21521444 AAAAATT-AGTAC-TTCTAACTTTTGCTCAAAATATATTTTTTTCTAAAATTCTAATTTCAAG
1 AAAAATTGA-TACTTTC-AACTTTTTCTCAAAATA-CTTTTCTT-GAAAATT-TATTTTTAAG
*
21521505 AAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTCTTGATAATTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTCTTGAAAATTTATTTTTAAG
*
21521563 AAAAATTGATACTTTCAACTTTTTCTCAAAATA-TTTT-TTTAAAATTTTATTTT
1 AAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTCTTGAAAA-TTTATTTT
21521616 AAAAACATCA
Statistics
Matches: 144, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
56 5 0.03
57 12 0.08
58 45 0.31
59 28 0.19
60 13 0.09
61 36 0.25
62 5 0.03
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.50
Consensus pattern (58 bp):
AAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTCTTGAAAATTTATTTTTAAG
Found at i:21525888 original size:59 final size:58
Alignment explanation
Indices: 21525812--21526034 Score: 220
Period size: 58 Copynumber: 3.8 Consensus size: 58
21525802 ATTTGAAGAT
* * *
21525812 TTTTA-TTTTAAGGAAAATTAATACTTTCAACTTTTCCTTAAAATGTTTTTCTTAATAA
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAT-TTTTTCTTAATAA
* * * * *
21525870 TCTTATTTTTAAGGAAAATTTGGTTACTTTCAACTTTTCCTTCAAATATTTTTTTTTTGA-AA
1 TTTTATTTTTAA-GAAAAATT-GATACTTTCAACTTTTCC-TCAAA-A-TTTTTTCTTAATAA
* * **
21525932 TTTTAATTTCAAGAAAAATTGATACTTTCAAC-TTTCCTCAAAATACTTTCTTAATAA
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAATTTTTTCTTAATAA
* *
21525989 TTTTTATTTTTAAGAAAAATTTG-TACTTCCAACTTTTTCTCAAAAT
1 -TTTTATTTTTAAGAAAAA-TTGATACTTTCAACTTTTCCTCAAAAT
21526035 ATATTTTTTT
Statistics
Matches: 134, Mismatches: 21, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
56 7 0.05
57 3 0.02
58 34 0.25
59 25 0.19
60 17 0.13
61 23 0.17
62 15 0.11
63 9 0.07
64 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (58 bp):
TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAATTTTTTCTTAATAA
Found at i:21525996 original size:120 final size:120
Alignment explanation
Indices: 21525803--21526044 Score: 312
Period size: 120 Copynumber: 2.0 Consensus size: 120
21525793 CTTTAAAGCA
* * * * **
21525803 TTTGAAGATTTTTATTTTAAGGAAAATTAATACTTTCAACTTTTCCTTAAAATGTTTTTCTTAAT
1 TTTGAAGATTTTAATTTCAAGAAAAATTAATACTTTCAACTTTTCCTCAAAATGACTTTCTTAAT
* * *
21525868 AATCTTATTTTTAAGGAAAATTTGGTTACTTTCAACTTTTCCTTC-AAATATTTTTTT
66 AATCTTATTTTTAAGAAAAATTT-G-TACTTCCAACTTTTCC-TCAAAATATATTTTT
*
21525925 TTTGAA-ATTTTAATTTCAAGAAAAATTGATACTTTCAAC-TTTCCTCAAAAT-ACTTTCTTAAT
1 TTTGAAGATTTTAATTTCAAGAAAAATTAATACTTTCAACTTTTCCTCAAAATGACTTTCTTAAT
* *
21525987 AATTTTTATTTTTAAGAAAAATTTGTACTTCCAACTTTTTCTCAAAATATATTTTT
66 AA-TCTTATTTTTAAGAAAAATTTGTACTTCCAACTTTTCCTCAAAATATATTTTT
21526043 TT
1 TT
21526045 AAATTTATTT
Statistics
Matches: 106, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
117 2 0.02
118 27 0.25
119 12 0.11
120 30 0.28
121 29 0.27
122 6 0.06
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.50
Consensus pattern (120 bp):
TTTGAAGATTTTAATTTCAAGAAAAATTAATACTTTCAACTTTTCCTCAAAATGACTTTCTTAAT
AATCTTATTTTTAAGAAAAATTTGTACTTCCAACTTTTCCTCAAAATATATTTTT
Found at i:21526605 original size:13 final size:14
Alignment explanation
Indices: 21526589--21526629 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
21526579 AAAATTTTCT
21526589 AGAAAAT-AAAGAA
1 AGAAAATAAAAGAA
21526602 AG-AAATAAAAGAA
1 AGAAAATAAAAGAA
*
21526615 ATAAAATCAAAAGAA
1 AGAAAAT-AAAAGAA
21526630 TAATAATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.17
13 9 0.38
14 4 0.17
15 7 0.29
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (14 bp):
AGAAAATAAAAGAA
Found at i:21527003 original size:12 final size:12
Alignment explanation
Indices: 21526988--21527068 Score: 76
Period size: 12 Copynumber: 6.8 Consensus size: 12
21526978 ATCATAAAGG
21526988 AAAAAAATACT-
1 AAAAAAATACTA
21526999 AAAAAAATACTA
1 AAAAAAATACTA
* *
21527011 AGAAAAATATTA
1 AAAAAAATACTA
*
21527023 AATAAAATACTA
1 AAAAAAATACTA
* *
21527035 AATAAAATA-AA
1 AAAAAAATACTA
*
21527046 TAAAAAAATACCA
1 -AAAAAAATACTA
21527059 AAGAAAAATA
1 AA-AAAAATA
21527069 AAAAATGGCT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
11 12 0.21
12 38 0.66
13 8 0.14
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (12 bp):
AAAAAAATACTA
Found at i:21527029 original size:24 final size:23
Alignment explanation
Indices: 21526990--21527073 Score: 91
Period size: 24 Copynumber: 3.6 Consensus size: 23
21526980 CATAAAGGAA
*
21526990 AAAAATACTAAAAAAATACTAAG
1 AAAAATAATAAAAAAATACTAAG
*
21527013 AAAAATATTAAATAAAATACTAA-
1 AAAAATAATAAA-AAAATACTAAG
*
21527036 ATAAAATAAATAAAAAAATACCAAAG
1 A-AAAAT-AATAAAAAAATA-CTAAG
21527062 AAAAATAA-AAAA
1 AAAAATAATAAAA
21527074 TGGCTCAGTT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
23 16 0.30
24 23 0.43
25 13 0.25
26 1 0.02
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAAATAATAAAAAAATACTAAG
Found at i:21529079 original size:42 final size:41
Alignment explanation
Indices: 21528905--21529203 Score: 262
Period size: 42 Copynumber: 7.1 Consensus size: 41
21528895 AGTAAACAAA
* * *
21528905 GCTCCTCTAAACAGAGGTGA-AACAACTTTGAAAAAATAAATG
1 GCTCCTCTAAACAGAGG-CACCACAACTTTG-AAAAATAAATT
* * * * * * * *
21528947 GCTCATTTGAATATAGGCAACAGAACTTTGAAAAAATAAATAAA
1 GCTCCTCTAAACAGAGGCACCACAACTTTG-AAAAATAAAT--T
* * * *
21528991 AC-CCTTCTAATCAGAGGCTA-AACAACTTTGAAAAATAAAAT
1 GCTCC-TCTAAACAGAGGC-ACCACAACTTTGAAAAATAAATT
* * * *
21529032 GCTCCTCTAAATAAAGGCACTACAACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACAACTTT-GAAAAATAAATT
21529074 GCTCCTCTAAACAGAGGCACCACAACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACAACTTT-GAAAAATAAATT
* *
21529116 GCTCCTCTAAACAGAGGCACCATAACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
* * * *
21529157 GCTCCTCTAAATAGAGGCAACTATAACTTTGAAAAATAAAAT
1 GCTCCTCTAAACAGAGGC-ACCACAACTTTGAAAAATAAATT
21529199 GCTCC
1 GCTCC
21529204 GTAACAATCA
Statistics
Matches: 211, Mismatches: 37, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
40 1 0.00
41 48 0.23
42 134 0.64
43 10 0.05
44 17 0.08
45 1 0.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
Found at i:21529153 original size:83 final size:84
Alignment explanation
Indices: 21528996--21529203 Score: 289
Period size: 83 Copynumber: 2.5 Consensus size: 84
21528986 ATAAAACCCT
* * *
21528996 TCTAATCAGAGGCTAA--ACAACTTTGAAAAATAAAATGCTCCTCTAAATAAAGGCACTACAACT
1 TCTAAACAGAGGC-AACCACAACTTTGAAAAATAAAATGCTCCTCTAAACAAAGGCACCACAACT
21529059 TTGGAAAAGTAAATTGCTCC
65 TTGGAAAAGTAAATTGCTCC
* * *
21529079 TCTAAACAGAGGC-ACCACAACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCATAACT
1 TCTAAACAGAGGCAACCACAACTTT-GAAAAATAAAATGCTCCTCTAAACAAAGGCACCACAACT
21529143 TT-GAAAAGTAAATTGCTCC
65 TTGGAAAAGTAAATTGCTCC
* * *
21529162 TCTAAATAGAGGCAACTATAACTTTGAAAAATAAAATGCTCC
1 TCTAAACAGAGGCAACCACAACTTTGAAAAATAAAATGCTCC
21529204 GTAACAATCA
Statistics
Matches: 111, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
81 1 0.01
83 65 0.59
84 45 0.41
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (84 bp):
TCTAAACAGAGGCAACCACAACTTTGAAAAATAAAATGCTCCTCTAAACAAAGGCACCACAACTT
TGGAAAAGTAAATTGCTCC
Found at i:21529605 original size:79 final size:79
Alignment explanation
Indices: 21529522--21529721 Score: 258
Period size: 79 Copynumber: 2.5 Consensus size: 79
21529512 ACAGATCTTA
* *
21529522 GGGTTTCACACCAT-AAAGATTCTCATTCGAAACTCAAATATTCTCATTTAAGTTAAAAGATTCA
1 GGGTTTCACACC-TCAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTAAGTTAAAAGATTCA
* *
21529586 CATTCGACAAAGTTT
65 CATTCAAAAAAGTTT
* * * **
21529601 GGGTTTCACACCTCAAAGTTTCTCATTTGAATCTCAAAGATTCTCATTTGAGTTCGAAGATTCAC
1 GGGTTTCACACCTCAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTAAGTTAAAAGATTCAC
*
21529666 ATTCAAAAAATTTT
66 ATTCAAAAAAGTTT
* * * *
21529680 AGGTTTCACATCTCAAAGATTTTCATTTGAAATTCAAAGATT
1 GGGTTTCACACCTCAAAGATTCTCATTTGAAACTCAAAGATT
21529722 TTCAGTTTCT
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 1 0.01
79 103 0.99
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (79 bp):
GGGTTTCACACCTCAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTAAGTTAAAAGATTCAC
ATTCAAAAAAGTTT
Found at i:21529662 original size:20 final size:21
Alignment explanation
Indices: 21529612--21529668 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
21529602 GGTTTCACAC
*
21529612 CTCAAAGTTTCTCATTTGAAT
1 CTCAAAGATTCTCATTTGAAT
*
21529633 CTCAAAGATTCTCATTTGAGT
1 CTCAAAGATTCTCATTTGAAT
* *
21529654 -TCGAAGATTCACATT
1 CTCAAAGATTCTCATT
21529669 CAAAAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (21 bp):
CTCAAAGATTCTCATTTGAAT
Found at i:21530186 original size:56 final size:56
Alignment explanation
Indices: 21530037--21530189 Score: 209
Period size: 56 Copynumber: 2.7 Consensus size: 56
21530027 CTTATCAGTA
* * *
21530037 CAAATTTCATCCT-TCATCACTTGATCATCGTTCATGGCCTTCTCAGTATTTCAAAG
1 CAAATTTCATCCTCT-ATCACTTGATCATTGTTCATGGGCTTCTCAGTATTCCAAAG
* * * * *
21530093 CAAATTTCATGCTCCATCACTTAATTATTGTTCATGGGCTTCTCAGTATTCCATAG
1 CAAATTTCATCCTCTATCACTTGATCATTGTTCATGGGCTTCTCAGTATTCCAAAG
*
21530149 TAAATTTCATCCTCTATCACTTGATCATTGTTCATGGGCTT
1 CAAATTTCATCCTCTATCACTTGATCATTGTTCATGGGCTT
21530190 TTTAGCACCA
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
56 83 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (56 bp):
CAAATTTCATCCTCTATCACTTGATCATTGTTCATGGGCTTCTCAGTATTCCAAAG
Found at i:21530880 original size:18 final size:18
Alignment explanation
Indices: 21530854--21530895 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
21530844 TGAGTATCTA
*
21530854 TTTTCTCTTCTTTCCATT
1 TTTTTTCTTCTTTCCATT
* *
21530872 TTTTTTCTTTTTTTCATT
1 TTTTTTCTTCTTTCCATT
21530890 TTTTTT
1 TTTTTT
21530896 TCATTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTCTTCTTTCCATT
Found at i:21531821 original size:23 final size:23
Alignment explanation
Indices: 21531782--21531826 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
21531772 ATGAAATCCT
*
21531782 ATTGCCTAAAAAAAAATTCTAAC
1 ATTGCCTAAAAAAAAATCCTAAC
*
21531805 ATTGCTCT-AAAAGAAATCCTAA
1 ATTGC-CTAAAAAAAAATCCTAA
21531827 AATAACAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.49, C:0.18, G:0.07, T:0.27
Consensus pattern (23 bp):
ATTGCCTAAAAAAAAATCCTAAC
Found at i:21537111 original size:121 final size:121
Alignment explanation
Indices: 21536974--21537194 Score: 340
Period size: 122 Copynumber: 1.8 Consensus size: 121
21536964 TTTGTACAAA
* *
21536974 AAAAATTGATGATTTCAACTTTTCCTTAAAATA-TTTTCTTGATAATATTTATTTTTTAGAAAAA
1 AAAAATTGATGATTTCAACTTTTCCTCAAAATACTTTTCTTGATAATATTTATTTTTAAGAAAAA
21537038 TTAGTAC-TTCTAACTTTTGCTCAAAATATATTTTTTTTCTAAAATTTTAATTTCAAG
66 TTAGTACTTTC-AACTTTTGCTCAAAATAT-TTTTTTTTCTAAAATTTTAATTTCAAG
* *
21537095 AAAAATTGAT-ACTTTCAACTTTTTCTCAAAATACTTTTCTTGATAATTTTTATTTTTAAGAAAA
1 AAAAATTGATGA-TTTCAACTTTTCCTCAAAATACTTTTCTTGATAATATTTATTTTTAAGAAAA
* *
21537159 ATTGGTACTTTCAACTTTTTCTCAAAATATTTTTTT
65 ATTAGTACTTTCAACTTTTGCTCAAAATATTTTTTT
21537195 AAAAATTTAT
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
120 1 0.01
121 35 0.38
122 52 0.57
123 3 0.03
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.49
Consensus pattern (121 bp):
AAAAATTGATGATTTCAACTTTTCCTCAAAATACTTTTCTTGATAATATTTATTTTTAAGAAAAA
TTAGTACTTTCAACTTTTGCTCAAAATATTTTTTTTTCTAAAATTTTAATTTCAAG
Found at i:21537168 original size:60 final size:59
Alignment explanation
Indices: 21536986--21537191 Score: 243
Period size: 60 Copynumber: 3.4 Consensus size: 59
21536976 AAATTGATGA
* * * * *
21536986 TTTCAACTTTTCCTTAAAATATTTTCTTGATAATATTTATTTTTTAGAAAAATTAGTAC
1 TTTCAACTTTTTCTCAAAATATTTTCTTGATAATTTTTATTTTTAAGAAAAATTGGTAC
* * ** * * * *
21537045 -TTCTAACTTTTGCTCAAAATATATTTTTTTTCTAAAATTTTAATTTCAAGAAAAATTGATAC
1 TTTC-AACTTTTTCTC-AAA-ATATTTTCTTGAT-AATTTTTATTTTTAAGAAAAATTGGTAC
21537107 TTTCAACTTTTTCTCAAAATACTTTTCTTGATAATTTTTATTTTTAAGAAAAATTGGTAC
1 TTTCAACTTTTTCTCAAAATA-TTTTCTTGATAATTTTTATTTTTAAGAAAAATTGGTAC
21537167 TTTCAACTTTTTCTCAAAATATTTT
1 TTTCAACTTTTTCTCAAAATATTTT
21537192 TTTAAAAATT
Statistics
Matches: 121, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
58 3 0.02
59 13 0.11
60 51 0.42
61 20 0.17
62 31 0.26
63 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (59 bp):
TTTCAACTTTTTCTCAAAATATTTTCTTGATAATTTTTATTTTTAAGAAAAATTGGTAC
Found at i:21537870 original size:10 final size:10
Alignment explanation
Indices: 21537847--21537885 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
21537837 TTTCCGGAAC
21537847 CTTTT-TTTT
1 CTTTTGTTTT
21537856 GCTTTTGTTTT
1 -CTTTTGTTTT
21537867 CTTTTGTTTT
1 CTTTTGTTTT
21537877 CTTTTGTTT
1 CTTTTGTTT
21537886 CATGTCCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 24 0.86
11 4 0.14
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.79
Consensus pattern (10 bp):
CTTTTGTTTT
Found at i:21538038 original size:52 final size:52
Alignment explanation
Indices: 21537966--21538069 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 52
21537956 TTTCATCTGA
*
21537966 GATTGAGATTAAATCTTTGAATCCAATTCAAACTCTACCAGTCTCTAGATTC
1 GATTGAGATTAAATCTTTGAATCCAATTCAAACTCTACCAGTCCCTAGATTC
* * **
21538018 GATTGGGATTAAATCTTTGAATCTAATTCAAACTCTATTAGTCCCTAGATTC
1 GATTGAGATTAAATCTTTGAATCCAATTCAAACTCTACCAGTCCCTAGATTC
21538070 ACGACAAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (52 bp):
GATTGAGATTAAATCTTTGAATCCAATTCAAACTCTACCAGTCCCTAGATTC
Found at i:21539463 original size:7 final size:7
Alignment explanation
Indices: 21539447--21539477 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
21539437 TTTTTTTTTA
21539447 TTTTGA-
1 TTTTGAT
21539453 TTTTGAT
1 TTTTGAT
21539460 TTTTGAT
1 TTTTGAT
21539467 TTTTGAT
1 TTTTGAT
21539474 TTTT
1 TTTT
21539478 TATATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (7 bp):
TTTTGAT
Found at i:21539485 original size:15 final size:15
Alignment explanation
Indices: 21539452--21539495 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
21539442 TTTTATTTTG
*
21539452 ATTTTGATTTTTGAT
1 ATTTTGATTTTTTAT
21539467 -TTTTGATTTTTTAT
1 ATTTTGATTTTTTAT
* *
21539481 ATTTTTATATTTTAT
1 ATTTTGATTTTTTAT
21539496 TATAATTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (15 bp):
ATTTTGATTTTTTAT
Found at i:21541072 original size:4 final size:4
Alignment explanation
Indices: 21541063--21541092 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
21541053 AAGCTGATGT
*
21541063 AATA AATA AATA AATA AATA GATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
21541093 AGAATAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:21541099 original size:12 final size:13
Alignment explanation
Indices: 21541063--21541100 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
21541053 AAGCTGATGT
21541063 AATAAATA-AATA
1 AATAAATAGAATA
21541075 AATAAATAG-ATA
1 AATAAATAGAATA
21541087 AATAAA-AGAATA
1 AATAAATAGAATA
21541099 AA
1 AA
21541101 CTTCACGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 22 0.92
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (13 bp):
AATAAATAGAATA
Found at i:21545246 original size:20 final size:20
Alignment explanation
Indices: 21545210--21545247 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21545200 ACAAAATATT
*
21545210 AAATTATAAATATATTGATA
1 AAATTATAAATAAATTGATA
*
21545230 AAATTATAACTAAATTGA
1 AAATTATAAATAAATTGA
21545248 ATCATAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (20 bp):
AAATTATAAATAAATTGATA
Found at i:21546361 original size:17 final size:17
Alignment explanation
Indices: 21546328--21546367 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
21546318 ATAAAATATG
21546328 AAAAATTATTTAATTTTT
1 AAAAATTATTT-ATTTTT
21546346 AAAATATTATTT-TTTTT
1 AAAA-ATTATTTATTTTT
21546363 AAAAA
1 AAAAA
21546368 AAAAGGCGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.05
17 9 0.43
18 4 0.19
19 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAAAATTATTTATTTTT
Found at i:21546800 original size:2 final size:2
Alignment explanation
Indices: 21546795--21546819 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21546785 TCTCTCTCTC
21546795 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
21546820 TGTTTGACAA
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:21550173 original size:28 final size:28
Alignment explanation
Indices: 21550141--21550205 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
21550131 TAACTTGTTC
*
21550141 AATAAATAAACAACATACATATTGAATA
1 AATAAATAAACAACATACATATTAAATA
* * *
21550169 AATAAATAAGCAGCTTACATATTAAATA
1 AATAAATAAACAACATACATATTAAATA
21550197 AATAAATAA
1 AATAAATAA
21550206 TTTATATGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.60, C:0.09, G:0.05, T:0.26
Consensus pattern (28 bp):
AATAAATAAACAACATACATATTAAATA
Found at i:21550222 original size:28 final size:28
Alignment explanation
Indices: 21550191--21550248 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
21550181 GCTTACATAT
*
21550191 TAAATAAATAAATAATTTATATGTTAAA
1 TAAATAAATAAATAATTTACATGTTAAA
21550219 TAAATAAATAAATAATTTACATGTTAAA
1 TAAATAAATAAATAATTTACATGTTAAA
21550247 TA
1 TA
21550249 GCATAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (28 bp):
TAAATAAATAAATAATTTACATGTTAAA
Found at i:21550246 original size:24 final size:24
Alignment explanation
Indices: 21550079--21550248 Score: 92
Period size: 28 Copynumber: 6.8 Consensus size: 24
21550069 GAAACTTGTG
*
21550079 TAATTCACATGTTAAATAAAAATAAA
1 TAATTTACATGTTAAAT--AAATAAA
* * * *
21550105 AAATTTATATGTT--ATAATTAAT
1 TAATTTACATGTTAAATAAATAAA
* * *
21550127 TAATTAACTTGTTCAATAAATAAA
1 TAATTTACATGTTAAATAAATAAA
* ** * *
21550151 CAACATACATATTGAATAAATAAA
1 TAATTTACATGTTAAATAAATAAA
* *
21550175 TAAGCAGCTTACATATTAAATAAATAAA
1 T-A--A-TTTACATGTTAAATAAATAAA
*
21550203 TAATTTATATGTTAAATAAATAAATAAA
1 TAATTTACATG-T---TAAATAAATAAA
21550231 TAATTTACATGTTAAATA
1 TAATTTACATGTTAAATA
21550249 GCATAAAAAA
Statistics
Matches: 109, Mismatches: 25, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
22 14 0.13
24 37 0.34
25 3 0.03
26 10 0.09
27 3 0.03
28 42 0.39
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.36
Consensus pattern (24 bp):
TAATTTACATGTTAAATAAATAAA
Found at i:21552717 original size:4 final size:4
Alignment explanation
Indices: 21552708--21552758 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
21552698 AATATGTAAA
* * * *
21552708 TTAT TTAT TTAT TTAT CTAT TTA- TCAT GTAAA TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT
21552756 TTA
1 TTA
21552759 ACATGTAAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
3 2 0.05
4 34 0.89
5 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (4 bp):
TTAT
Found at i:21552729 original size:32 final size:32
Alignment explanation
Indices: 21552693--21552755 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
21552683 ATTTTTATGT
21552693 TATTTAAT-ATGTAAATTATTTATTTATTTATC
1 TATTT-ATCATGTAAATTATTTATTTATTTATC
21552725 TATTTATCATGTAAATTATTTATTTATTTAT
1 TATTTATCATGTAAATTATTTATTTATTTAT
21552756 TTAACATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 2 0.07
32 28 0.93
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (32 bp):
TATTTATCATGTAAATTATTTATTTATTTATC
Found at i:21552743 original size:28 final size:28
Alignment explanation
Indices: 21552686--21552805 Score: 118
Period size: 28 Copynumber: 4.1 Consensus size: 28
21552676 AACCCATATT
*
21552686 TTTATGTTATTTAATATGTAAATTATTTA
1 TTTAT-TTATTTAACATGTAAATTATTTA
*
21552715 TTTATTTATCTATTTATCATGTAAATTATTTA
1 TTTA--T-T-TATTTAACATGTAAATTATTTA
*
21552747 TTTATTTATTTAACATGTAAGTT-TCTTA
1 TTTATTTATTTAACATGTAAATTAT-TTA
***
21552775 TTTATTTA-TTAACATGTTTGTTATTTA
1 TTTATTTATTTAACATGTAAATTATTTA
21552802 TTTA
1 TTTA
21552806 AACATGCTAA
Statistics
Matches: 79, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
27 20 0.25
28 27 0.34
29 5 0.06
30 1 0.01
31 2 0.03
32 24 0.30
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (28 bp):
TTTATTTATTTAACATGTAAATTATTTA
Found at i:21552846 original size:19 final size:20
Alignment explanation
Indices: 21552746--21552846 Score: 71
Period size: 21 Copynumber: 4.7 Consensus size: 20
21552736 TAAATTATTT
21552746 ATTTATTTATTTAACATGTA
1 ATTTATTTATTTAACATGTA
21552766 AGTTTCTTATTTATTTATTAACATGT-
1 A---T-TTATTTA--T-TTAACATGTA
*
21552792 TTGTTATTTATTTAAACATGCTA
1 AT-TTATTTATTT-AACATG-TA
* *
21552815 AATTGTTTATTTAACATGTA
1 ATTTATTTATTTAACATGTA
21552835 ATTTATTT-TTTA
1 ATTTATTTATTTA
21552847 TTTAACATTG
Statistics
Matches: 64, Mismatches: 7, Indels: 21
0.70 0.08 0.23
Matches are distributed among these distances:
19 4 0.06
20 11 0.17
21 13 0.20
22 10 0.16
23 9 0.14
24 7 0.11
26 1 0.02
27 9 0.14
ACGTcount: A:0.31, C:0.06, G:0.07, T:0.56
Consensus pattern (20 bp):
ATTTATTTATTTAACATGTA
Found at i:21552850 original size:23 final size:23
Alignment explanation
Indices: 21552742--21552854 Score: 78
Period size: 23 Copynumber: 4.9 Consensus size: 23
21552732 CATGTAAATT
21552742 ATTTATTTATTTATTTAACATGTA
1 ATTTATTT-TTTATTTAACATGTA
21552766 AGTTTCTTATTTATTTA-TTAACATG--
1 A---T-TTATTT-TTTATTTAACATGTA
* *
21552791 -TTTGTTATTTATTTAAACATGCTA
1 ATTTATTTTTTATTT-AACATG-TA
*
21552815 A---ATTGTTTATTTAACATGTA
1 ATTTATTTTTTATTTAACATGTA
21552835 ATTTATTTTTTATTTAACAT
1 ATTTATTTTTTATTTAACAT
21552855 TGTACATTGT
Statistics
Matches: 71, Mismatches: 5, Indels: 27
0.69 0.05 0.26
Matches are distributed among these distances:
19 4 0.06
20 9 0.13
21 13 0.18
22 9 0.13
23 15 0.21
24 1 0.01
27 9 0.13
28 11 0.15
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (23 bp):
ATTTATTTTTTATTTAACATGTA
Found at i:21552975 original size:22 final size:22
Alignment explanation
Indices: 21552950--21553002 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
21552940 TCTAACATAT
* *
21552950 AAAAATAATTTTATTTTTTATA
1 AAAAATAATTTTATTTTGTAAA
*
21552972 AAAAAGAATTTTATTTTGTAAA
1 AAAAATAATTTTATTTTGTAAA
21552994 ATAAAATAA
1 A-AAAATAA
21553003 ATAAATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
AAAAATAATTTTATTTTGTAAA
Found at i:21553529 original size:21 final size:20
Alignment explanation
Indices: 21553505--21553550 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
21553495 TATATAAAAA
21553505 TTATGAATAAATTTATTAATT
1 TTATG-ATAAATTTATTAATT
21553526 TTATTGATAAATTTATTAATT
1 TTA-TGATAAATTTATTAATT
21553547 TTAT
1 TTAT
21553551 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 1 0.04
21 21 0.88
22 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
TTATGATAAATTTATTAATT
Found at i:21553551 original size:21 final size:21
Alignment explanation
Indices: 21553511--21553551 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
21553501 AAAATTATGA
21553511 ATAAATTTATTAATTTTATTG
1 ATAAATTTATTAATTTTATTG
21553532 ATAAATTTATTAATTTTATT
1 ATAAATTTATTAATTTTATT
21553552 AAAAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATAAATTTATTAATTTTATTG
Found at i:21553725 original size:22 final size:23
Alignment explanation
Indices: 21553697--21553743 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
21553687 TTTTTCAACC
21553697 TTTGGA-GTGTCCAACAAAAAAT
1 TTTGGAGGTGTCCAACAAAAAAT
* * *
21553719 TTTGGAGGTGTTCAACTAATAAT
1 TTTGGAGGTGTCCAACAAAAAAT
21553742 TT
1 TT
21553744 CTCTTCGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (23 bp):
TTTGGAGGTGTCCAACAAAAAAT
Found at i:21553755 original size:74 final size:74
Alignment explanation
Indices: 21553613--21553756 Score: 164
Period size: 74 Copynumber: 1.9 Consensus size: 74
21553603 AATATGTTTA
* * * ** * * * *
21553613 TTTTTGAATCTTTGGATTGTCCATTAAAAAATTTTGGTGGTATCCAATTGAAATTTTTCCTTCAA
1 TTTTTCAACCTTTGGAGTGTCCAACAAAAAATTTTGGAGGTATCCAACTAAAATTTCTCCTTCAA
21553678 ACTTTTATG
66 ACTTTTATG
* * *
21553687 TTTTTCAACCTTTGGAGTGTCCAACAAAAAATTTTGGAGGTGTTCAACTAATAATTTCT-CTTCG
1 TTTTTCAACCTTTGGAGTGTCCAACAAAAAATTTTGGAGGTATCCAACTAA-AATTTCTCCTTCA
21553751 AACTTT
65 AACTTT
21553757 CATATTTCTT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
74 51 0.89
75 6 0.11
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (74 bp):
TTTTTCAACCTTTGGAGTGTCCAACAAAAAATTTTGGAGGTATCCAACTAAAATTTCTCCTTCAA
ACTTTTATG
Found at i:21553953 original size:13 final size:12
Alignment explanation
Indices: 21553912--21553954 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
21553902 AAATATTAAT
*
21553912 AAACAAAAAAAA
1 AAACAAAAAAAG
*
21553924 AAAGAAAAAAAG
1 AAACAAAAAAAG
21553936 AAAACAAACAAAAG
1 -AAACAAA-AAAAG
21553950 AAACA
1 AAACA
21553955 GAATAAGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 10 0.38
13 11 0.42
14 5 0.19
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (12 bp):
AAACAAAAAAAG
Found at i:21555431 original size:16 final size:16
Alignment explanation
Indices: 21555407--21555467 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 16
21555397 TTTTAATTTT
*
21555407 CAAAATCCCTTAAATC
1 CAAAATCCCTAAAATC
* *
21555423 CAAACTCCCAAAAATC
1 CAAAATCCCTAAAATC
*
21555439 CAAAATCCCTGAAATC
1 CAAAATCCCTAAAATC
*
21555455 CAAAGT-CCTAAAA
1 CAAAATCCCTAAAA
21555468 ATCCTAATGA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
15 6 0.16
16 31 0.84
ACGTcount: A:0.48, C:0.31, G:0.03, T:0.18
Consensus pattern (16 bp):
CAAAATCCCTAAAATC
Found at i:21555446 original size:32 final size:32
Alignment explanation
Indices: 21555407--21555471 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
21555397 TTTTAATTTT
*
21555407 CAAAATCCCTTAAATCCAAACTCCCAAAAATC
1 CAAAATCCCTGAAATCCAAACTCCCAAAAATC
* *
21555439 CAAAATCCCTGAAATCCAAAGTCCTAAAAATC
1 CAAAATCCCTGAAATCCAAACTCCCAAAAATC
21555471 C
1 C
21555472 TAATGACACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.46, C:0.32, G:0.03, T:0.18
Consensus pattern (32 bp):
CAAAATCCCTGAAATCCAAACTCCCAAAAATC
Found at i:21563830 original size:29 final size:28
Alignment explanation
Indices: 21563794--21563848 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
21563784 AGGGAGACTG
21563794 TATTGA-TTATGCT-AAGAGATGTCATAAA
1 TATTGATTTATGCTGAA-AGAT-TCATAAA
21563822 TATTAGATTTATGCTGAAAGATTCATA
1 TATT-GATTTATGCTGAAAGATTCATA
21563849 CTCCGCTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 4 0.17
29 7 0.29
30 11 0.46
31 2 0.08
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (28 bp):
TATTGATTTATGCTGAAAGATTCATAAA
Found at i:21565625 original size:48 final size:49
Alignment explanation
Indices: 21565558--21565943 Score: 323
Period size: 49 Copynumber: 7.6 Consensus size: 49
21565548 TGAGATTTTC
* *
21565558 TTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAA-AGAGAATTT
1 TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAATAGAGAAATT
* *
21565606 TTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATATGAGAATTT
1 TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC-A-ATA-GAGAAATT
* *
21565658 TTAAAATTGTTGAGCCTCTGTTGAGAGGAGCTTTTTCATATGAGATTTTCAGATGAAATT
1 TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC-----A-A---T-AGA-GAAATT
* *
21565718 TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAG-AATT
1 TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAATA-GAGAAATT
* * * * * * * * *
21565767 TTAAAGTGGTGGAGCCTTTGTTGAGAGCAGCTTTTTTAAGAAAAAAATT
1 TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAATAGAGAAATT
* * *
21565816 TTAAAGTTATTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAG-AATT
1 TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAATA-GAGAAATT
* * * * * * *
21565865 TTAAAATGGTGGAGCCTCTGTTGAAATGAGCTTTTTC-A-AGAAAACATT
1 TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAATAGAGAA-ATT
* *
21565913 TTAAAGTTGTTGAACCTCTGCTGAGAAGAGC
1 TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC
21565944 CCTTTAAAAA
Statistics
Matches: 276, Mismatches: 44, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
46 2 0.01
47 2 0.01
48 66 0.24
49 109 0.39
50 4 0.01
51 3 0.01
52 42 0.15
54 1 0.00
55 1 0.00
56 3 0.01
59 3 0.01
60 40 0.14
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.35
Consensus pattern (49 bp):
TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAATAGAGAAATT
Found at i:21565735 original size:160 final size:158
Alignment explanation
Indices: 21565558--21565850 Score: 410
Period size: 160 Copynumber: 1.8 Consensus size: 158
21565548 TGAGATTTTC
* * *
21565558 TTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAA-A-GAGAATTTTTAAAGTTGTTGAGC
1 TTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTCCAAGATGAGAA-TTTTAAAGTGGTGGAGC
* * * * *
21565621 CTCTACTGAGAGGAGCTTTTTCAAGATATGAGAATTTTTAAAATTGTTGAGCCTCTGTTGAGAGG
65 CTCTACTGAGAGCAGCTTTTTCAAGA-A--AAAAATTTTAAAATTATTGAGCCTCTGCTGAGAGG
21565686 AGCTTTTTCATATGAGATTTTCAGATGAAATT
127 AGCTTTTTCATATGAGATTTTCAGATGAAATT
*
21565718 TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAATTTTAAAGTGGTGGAGCC
1 TTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTCCAAGATGAGAATTTTAAAGTGGTGGAGCC
* ** * *
21565783 TTTGTTGAGAGCAGCTTTTTTAAGAAAAAAATTTTAAAGTTATTGAGCCTCTGCTGAGAGGAGCT
66 TCTACTGAGAGCAGCTTTTTCAAGAAAAAAATTTTAAAATTATTGAGCCTCTGCTGAGAGGAGCT
21565848 TTT
131 TTT
21565851 CCAAGATGAG
Statistics
Matches: 117, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
158 37 0.32
160 38 0.32
161 37 0.32
162 5 0.04
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (158 bp):
TTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTCCAAGATGAGAATTTTAAAGTGGTGGAGCC
TCTACTGAGAGCAGCTTTTTCAAGAAAAAAATTTTAAAATTATTGAGCCTCTGCTGAGAGGAGCT
TTTTCATATGAGATTTTCAGATGAAATT
Found at i:21565887 original size:98 final size:97
Alignment explanation
Indices: 21565713--21565943 Score: 365
Period size: 98 Copynumber: 2.4 Consensus size: 97
21565703 TTTTCAGATG
*
21565713 AAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAATTTTAAAGTGGTG
1 AAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAATTTTAAAATGGTG
* * *
21565778 GAGCCTTTGTTGAGA-GCAGCTTTTTTAAGAAAA
66 GAGCCTCTGTTGAAATG-AGCTTTTTCAAG-AAA
*
21565811 AAATTTTAAAGTTATTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAATTTTAAAATGGTG
1 AAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAATTTTAAAATGGTG
21565876 GAGCCTCTGTTGAAATGAGCTTTTTCAAGAAA
66 GAGCCTCTGTTGAAATGAGCTTTTTCAAGAAA
* * *
21565908 ACATTTTAAAGTTGTTGAACCTCTGCTGAGAAGAGC
1 AAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC
21565944 CCTTTAAAAA
Statistics
Matches: 123, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
97 35 0.28
98 87 0.71
99 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.33
Consensus pattern (97 bp):
AAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAATTTTAAAATGGTG
GAGCCTCTGTTGAAATGAGCTTTTTCAAGAAA
Found at i:21566233 original size:12 final size:12
Alignment explanation
Indices: 21566217--21566249 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
21566207 ACTAACTACT
21566217 CGACCAGCCTCC
1 CGACCAGCCTCC
*
21566229 TGACCAGCCTCC
1 CGACCAGCCTCC
21566241 CGACCAGCC
1 CGACCAGCC
21566250 ACCCCACAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.55, G:0.18, T:0.09
Consensus pattern (12 bp):
CGACCAGCCTCC
Found at i:21566571 original size:13 final size:12
Alignment explanation
Indices: 21566549--21566578 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
21566539 TACACCAACC
21566549 AAAAAAAAATGA
1 AAAAAAAAATGA
21566561 AAAACAAAAATGA
1 AAAA-AAAAATGA
21566574 AAAAA
1 AAAAA
21566579 TAACACAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.83, C:0.03, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAAAAAATGA
Found at i:21567654 original size:16 final size:16
Alignment explanation
Indices: 21567635--21567688 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
21567625 AAAATCGCTT
*
21567635 AAATCCAAACTCCCAA
1 AAATCCAAAATCCCAA
* **
21567651 AAATTCAAAATCCCTG
1 AAATCCAAAATCCCAA
* *
21567667 AAATCCAAAGTCCTAA
1 AAATCCAAAATCCCAA
21567683 AAATCC
1 AAATCC
21567689 TAAGGACACG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.48, C:0.30, G:0.04, T:0.19
Consensus pattern (16 bp):
AAATCCAAAATCCCAA
Found at i:21567660 original size:32 final size:32
Alignment explanation
Indices: 21567622--21567686 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
21567612 ATTTTTAATT
* *
21567622 TTCAAAATCGCTTAAATCCAAACTCCCAAAAA
1 TTCAAAATCCCTGAAATCCAAACTCCCAAAAA
* *
21567654 TTCAAAATCCCTGAAATCCAAAGTCCTAAAAA
1 TTCAAAATCCCTGAAATCCAAACTCCCAAAAA
21567686 T
1 T
21567687 CCTAAGGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.46, C:0.26, G:0.05, T:0.23
Consensus pattern (32 bp):
TTCAAAATCCCTGAAATCCAAACTCCCAAAAA
Found at i:21569910 original size:5 final size:5
Alignment explanation
Indices: 21569900--21569953 Score: 60
Period size: 5 Copynumber: 11.0 Consensus size: 5
21569890 ATTATTATTA
*
21569900 TTTTC TTTTC TTTTC TTTT- TTTTC TTTT- TCTTTC TTTTC TCTTT- TCTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC TTTTC T-TTTC TTTTC
21569949 TTTTC
1 TTTTC
21569954 ATATTTGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
4 7 0.17
5 31 0.74
6 4 0.10
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:21569924 original size:19 final size:19
Alignment explanation
Indices: 21569900--21569937 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
21569890 ATTATTATTA
21569900 TTTTC-TTTTCTTTTCTTTT
1 TTTTCTTTTTC-TTTCTTTT
21569919 TTTTCTTTTTCTTTCTTTT
1 TTTTCTTTTTCTTTCTTTT
21569938 CTCTTTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTCTTTTTCTTTCTTTT
Found at i:21571406 original size:12 final size:12
Alignment explanation
Indices: 21571391--21571421 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21571381 CAAAATTAAA
21571391 AATAAAAAAATT
1 AATAAAAAAATT
*
21571403 AATAAAACAATT
1 AATAAAAAAATT
21571415 AATAAAA
1 AATAAAA
21571422 TTTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAAAAAAATT
Found at i:21571646 original size:24 final size:24
Alignment explanation
Indices: 21571617--21571664 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
21571607 ATTTTAAGAA
21571617 TTATTTCAATAAAAACGTTCTAAT
1 TTATTTCAATAAAAACGTTCTAAT
*
21571641 TTATTTCAATAAAAAGGTTCTAAT
1 TTATTTCAATAAAAACGTTCTAAT
21571665 AGCTTGTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (24 bp):
TTATTTCAATAAAAACGTTCTAAT
Found at i:21577281 original size:47 final size:47
Alignment explanation
Indices: 21577183--21577283 Score: 123
Period size: 47 Copynumber: 2.1 Consensus size: 47
21577173 ATATCTTCTC
* * * * * *
21577183 TTTTTAATTTCTAAATTTTTTACCATTTGGGCTTATTTAGAAAATAT
1 TTTTTTATTTCTAAATTTTTCACCATTTGGGCTTATCTACAAAAAAA
*
21577230 TTTTTTATTTCTAAATTTTTCACCATTTAGG-TCTATCTACAAAAAAA
1 TTTTTTATTTCTAAATTTTTCACCATTTGGGCT-TATCTACAAAAAAA
21577277 TTTTTTA
1 TTTTTTA
21577284 ATCTTTGAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
46 1 0.02
47 45 0.98
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52
Consensus pattern (47 bp):
TTTTTTATTTCTAAATTTTTCACCATTTGGGCTTATCTACAAAAAAA
Found at i:21577420 original size:26 final size:26
Alignment explanation
Indices: 21577364--21577420 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
21577354 GATAACTTTA
* * *
21577364 AAGAAAATTTTCATTTAGAGATTTTT
1 AAGAAAATTTCCATTTAGAAATTTCT
*
21577390 TAGAAAATTTACCATTT-GAAATTTCT
1 AAGAAAATTT-CCATTTAGAAATTTCT
21577416 AAGAA
1 AAGAA
21577421 TCTCATCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (26 bp):
AAGAAAATTTCCATTTAGAAATTTCT
Found at i:21578685 original size:14 final size:14
Alignment explanation
Indices: 21578668--21578697 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21578658 CATTATTTTT
21578668 TTTTCATTTTTGTA
1 TTTTCATTTTTGTA
*
21578682 TTTTCATTTTTTTA
1 TTTTCATTTTTGTA
21578696 TT
1 TT
21578698 AACAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTCATTTTTGTA
Found at i:21579118 original size:16 final size:17
Alignment explanation
Indices: 21579086--21579119 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21579076 AAGGTTGGGC
*
21579086 TAGAGATAAGGAAAGAG
1 TAGAGATAAGCAAAGAG
21579103 TAGAGATAA-CAAAGAG
1 TAGAGATAAGCAAAGAG
21579119 T
1 T
21579120 TGGGCAGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.29, T:0.15
Consensus pattern (17 bp):
TAGAGATAAGCAAAGAG
Found at i:21579323 original size:21 final size:21
Alignment explanation
Indices: 21579264--21579324 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
21579254 ATATTTATAA
21579264 AATATTTT-TTAACATAAATT
1 AATATTTTATTAACATAAATT
*
21579284 -ATATCTTAATTATACATAAATAT
1 AATAT-TTTATTA-ACATAAAT-T
21579307 AATATTTTATTAA-ATAAA
1 AATATTTTATTAACATAAA
21579325 ATATTACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 8 0.24
22 9 0.26
23 7 0.21
24 4 0.12
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATTTTATTAACATAAATT
Found at i:21581415 original size:2 final size:2
Alignment explanation
Indices: 21581410--21581442 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
21581400 TGAAAAAATA
*
21581410 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21581443 GTCATTCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:21583705 original size:1 final size:1
Alignment explanation
Indices: 21583699--21583723 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
21583689 TAACAAAGGG
21583699 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
21583724 GCATATTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:21584822 original size:4 final size:4
Alignment explanation
Indices: 21584813--21584885 Score: 59
Period size: 4 Copynumber: 18.8 Consensus size: 4
21584803 TAGTTTTAAT
21584813 TTTA TTTA TTTA TTTA TTTA TTTTA GGTTT- TTTA -TTA TTTA -TTA TTT-
1 TTTA TTTA TTTA TTTA TTTA -TTTA --TTTA TTTA TTTA TTTA TTTA TTTA
*
21584860 TTGT- TTTT TTTA TTT- TTTA TTTA TTT
1 TT-TA TTTA TTTA TTTA TTTA TTTA TTT
21584886 TTGGTTTCTT
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
3 15 0.25
4 37 0.63
5 4 0.07
6 3 0.05
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:21584826 original size:8 final size:8
Alignment explanation
Indices: 21584813--21584885 Score: 59
Period size: 7 Copynumber: 9.4 Consensus size: 8
21584803 TAGTTTTAAT
21584813 TTTATTTA
1 TTTATTTA
21584821 TTTATTTA
1 TTTATTTA
21584829 TTTATTTTA
1 TTTA-TTTA
21584838 GGTTT-TTTA
1 --TTTATTTA
21584847 -TTATTTA
1 TTTATTTA
21584854 -TTATTT-
1 TTTATTTA
*
21584860 TTGT-TTTT
1 TT-TATTTA
21584868 TTTATTT-
1 TTTATTTA
21584875 TTTATTTA
1 TTTATTTA
21584883 TTT
1 TTT
21584886 TTGGTTTCTT
Statistics
Matches: 56, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
6 2 0.04
7 22 0.39
8 21 0.38
9 8 0.14
11 3 0.05
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (8 bp):
TTTATTTA
Found at i:21584850 original size:25 final size:25
Alignment explanation
Indices: 21584817--21584892 Score: 100
Period size: 25 Copynumber: 3.0 Consensus size: 25
21584807 TTTAATTTTA
*
21584817 TTTATTTATTTATTTATTTTAGGTTT
1 TTTA-TTATTTATTTATTTTTGGTTT
*
21584843 TTTATTATTTA-TTATTTTTGTTTTT
1 TTTATTATTTATTTATTTTTG-GTTT
*
21584868 TTTATTTTTTATTTATTTTTGGTTT
1 TTTATTATTTATTTATTTTTGGTTT
21584893 CTTGGTTCGG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
24 8 0.18
25 23 0.52
26 13 0.30
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.78
Consensus pattern (25 bp):
TTTATTATTTATTTATTTTTGGTTT
Found at i:21584877 original size:33 final size:33
Alignment explanation
Indices: 21584799--21584885 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 33
21584789 AGATGATCCA
*
21584799 ATTTTAG-TTTTAATTTTATTTATTTATTTATTT
1 ATTTTAGTTTTTTA-TTTATTTATTTATTTATTT
* *
21584832 ATTTTAGGTTTTTTA-TTATTTATTATTTTTGTTT
1 ATTTTA-GTTTTTTATTTATTTATT-TATTTATTT
*
21584866 TTTTTA-TTTTTTATTTATTT
1 ATTTTAGTTTTTTATTTATTT
21584886 TTGGTTTCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
32 7 0.15
33 21 0.46
34 13 0.28
35 5 0.11
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.76
Consensus pattern (33 bp):
ATTTTAGTTTTTTATTTATTTATTTATTTATTT
Found at i:21585124 original size:24 final size:21
Alignment explanation
Indices: 21585097--21585140 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
21585087 AAACAGAGGG
21585097 AGAAACACAAAAAATAAGGTAAAC
1 AGAAA-AC-AAAAAT-AGGTAAAC
*
21585121 AGAAAGCAAAAATAGGTAAA
1 AGAAAACAAAAATAGGTAAA
21585141 AAAAACGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 6 0.32
23 1 0.05
24 5 0.26
ACGTcount: A:0.66, C:0.09, G:0.16, T:0.09
Consensus pattern (21 bp):
AGAAAACAAAAATAGGTAAAC
Found at i:21585770 original size:18 final size:19
Alignment explanation
Indices: 21585734--21585787 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
21585724 TCGTTTTTGG
*
21585734 TATTTTTTTAGTATTTTATT
1 TATTTATTTAGT-TTTTATT
21585754 TATTTATTTA-TTTTTATT
1 TATTTATTTAGTTTTTATT
* *
21585772 TGTTTTTTTAGTTTTT
1 TATTTATTTAGTTTTT
21585788 TTTTTTTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 15 0.50
19 6 0.20
20 9 0.30
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (19 bp):
TATTTATTTAGTTTTTATT
Found at i:21585779 original size:12 final size:12
Alignment explanation
Indices: 21585736--21585792 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
21585726 GTTTTTGGTA
*
21585736 TTTTTTTAGTAT
1 TTTTTTTAGTTT
* *
21585748 TTTATTTATTTAT
1 TTTTTTTAGTT-T
21585761 TTATTTTTA-TTT
1 TT-TTTTTAGTTT
21585773 GTTTTTTTAGTTT
1 -TTTTTTTAGTTT
21585786 TTTTTTT
1 TTTTTTT
21585793 TTGCATGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 22 0.59
13 10 0.27
14 5 0.14
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (12 bp):
TTTTTTTAGTTT
Found at i:21590109 original size:5 final size:6
Alignment explanation
Indices: 21590082--21590107 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
21590072 GAATGACATG
21590082 AAAGAA AAAGAA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AA
21590108 GACAAAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:21597790 original size:20 final size:20
Alignment explanation
Indices: 21597765--21597802 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21597755 TTGAGATTTC
*
21597765 TTGAATGAGAACCTTTGAGT
1 TTGAATGAAAACCTTTGAGT
*
21597785 TTGAATGAAAAGCTTTGA
1 TTGAATGAAAACCTTTGA
21597803 AATTTTGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (20 bp):
TTGAATGAAAACCTTTGAGT
Found at i:21598035 original size:41 final size:41
Alignment explanation
Indices: 21597968--21598317 Score: 418
Period size: 41 Copynumber: 8.5 Consensus size: 41
21597958 GATTGTTGAG
* *
21597968 GAGCCATTTATTTTTCAAAG-TTCGTTGCCTCTATTCAAAT
1 GAGCCATTTATTTTTCAAAGTTTCATTGCCTCTATTCAGAT
* * * * *
21598008 GAGCCATTTTTTTTTTAAAGTTTCGTTGCCTCTATTCAAAG
1 GAGCCATTTATTTTTCAAAGTTTCATTGCCTCTATTCAGAT
* ** * *
21598049 GAGCCATTTATTTTCCAAAGTTTTGTTACCTCTATTCAGAG
1 GAGCCATTTATTTTTCAAAGTTTCATTGCCTCTATTCAGAT
* * *
21598090 GAACCATTTATTTTCCAAAGTTTTATTGCCTCTATTCAGAT
1 GAGCCATTTATTTTTCAAAGTTTCATTGCCTCTATTCAGAT
* *
21598131 GAGCCATTTATTTTCCAAAG-TTCTGTTGCCTCTATTCAGAT
1 GAGCCATTTATTTTTCAAAGTTTC-ATTGCCTCTATTCAGAT
* * *
21598172 AAGCCATTTACTTTTCAAAG-TTCTATTGCCTTTATTCAGAT
1 GAGCCATTTATTTTTCAAAGTTTC-ATTGCCTCTATTCAGAT
*
21598213 GAGCCATTTATTTTTTCAAAGTTTCATTGCCTCTATTCAGAG
1 GAGCCATTTA-TTTTTCAAAGTTTCATTGCCTCTATTCAGAT
* *
21598255 GAGCCATTTATTTTCCAAAGTTTTATTGCCTCTATTCAGAT
1 GAGCCATTTATTTTTCAAAGTTTCATTGCCTCTATTCAGAT
* *
21598296 GAACAATTTATTTTTTCAAAGT
1 GAGCCATTTA-TTTTTCAAAGT
21598318 CATGTTTTTT
Statistics
Matches: 274, Mismatches: 31, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
40 20 0.07
41 207 0.76
42 44 0.16
43 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (41 bp):
GAGCCATTTATTTTTCAAAGTTTCATTGCCTCTATTCAGAT
Found at i:21598567 original size:4 final size:4
Alignment explanation
Indices: 21598551--21598630 Score: 60
Period size: 4 Copynumber: 19.5 Consensus size: 4
21598541 TAGTTTTAAT
*
21598551 TTTA TTT- TTTA TTTA TTTA TTTA TTTTA TTTTA TTTTA TGTTT TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA -TTTA T-TTA TTTA
*
21598598 -TT- TTTA TTT- TTATT TTTA TTTTA TTTA TTTA TT
1 TTTA TTTA TTTA TT-TA TTTA -TTTA TTTA TTTA TT
21598631 GGTTTCTTGG
Statistics
Matches: 65, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
3 9 0.14
4 33 0.51
5 23 0.35
ACGTcount: A:0.19, C:0.00, G:0.01, T:0.80
Consensus pattern (4 bp):
TTTA
Found at i:21598573 original size:19 final size:19
Alignment explanation
Indices: 21598551--21598630 Score: 78
Period size: 18 Copynumber: 4.3 Consensus size: 19
21598541 TAGTTTTAAT
21598551 TTTATTTTTTATTTATTTA
1 TTTATTTTTTATTTATTTA
*
21598570 TTTATTTTAT-TTTATTT-
1 TTTATTTTTTATTTATTTA
* *
21598587 TATGTTTTTTA-TT-TTTA
1 TTTATTTTTTATTTATTTA
*
21598604 TTTTTATTTTTATTTTATTTA
1 TTTAT-TTTTTA-TTTATTTA
21598625 TTTATT
1 TTTATT
21598631 GGTTTCTTGG
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
16 3 0.06
17 12 0.25
18 13 0.27
19 9 0.19
20 3 0.06
21 8 0.17
ACGTcount: A:0.19, C:0.00, G:0.01, T:0.80
Consensus pattern (19 bp):
TTTATTTTTTATTTATTTA
Found at i:21598580 original size:5 final size:5
Alignment explanation
Indices: 21598537--21598627 Score: 82
Period size: 5 Copynumber: 17.8 Consensus size: 5
21598527 GGATAGGCCA
*
21598537 ATTTT AGTTTT AATTTT ATTTT TTATTT A-TTT A-TTT ATTTT ATTTT
1 ATTTT A-TTTT -ATTTT ATTTT AT-TTT ATTTT ATTTT ATTTT ATTTT
*
21598583 ATTTT ATGTT -TTTT ATTTTT ATTTTT ATTTTT ATTTT A-TTT ATTT
1 ATTTT ATTTT ATTTT A-TTTT A-TTTT A-TTTT ATTTT ATTTT ATTT
21598628 ATTGGTTTCT
Statistics
Matches: 75, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
4 15 0.20
5 31 0.41
6 28 0.37
7 1 0.01
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:21599032 original size:31 final size:31
Alignment explanation
Indices: 21598989--21599047 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
21598979 ATTCTAACAA
21598989 AATTTTTCGGCACCAGTTGAATTTTTTGGCT
1 AATTTTTCGGCACCAGTTGAATTTTTTGGCT
*
21599020 AATTTTTTGGCACCAGTTGAATTTTTTG
1 AATTTTTCGGCACCAGTTGAATTTTTTG
21599048 ACAATATCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.47
Consensus pattern (31 bp):
AATTTTTCGGCACCAGTTGAATTTTTTGGCT
Found at i:21599044 original size:19 final size:19
Alignment explanation
Indices: 21598989--21599047 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
21598979 ATTCTAACAA
*
21598989 AATTTTTCGGCACCAGTTG
1 AATTTTTTGGCACCAGTTG
21599008 AATTTTTTGG---C---T-
1 AATTTTTTGGCACCAGTTG
21599020 AATTTTTTGGCACCAGTTG
1 AATTTTTTGGCACCAGTTG
21599039 AATTTTTTG
1 AATTTTTTG
21599048 ACAATATCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 14
0.68 0.02 0.30
Matches are distributed among these distances:
12 10 0.31
13 1 0.03
15 1 0.03
16 1 0.03
18 1 0.03
19 18 0.56
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.47
Consensus pattern (19 bp):
AATTTTTTGGCACCAGTTG
Found at i:21599514 original size:11 final size:12
Alignment explanation
Indices: 21599500--21599558 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 12
21599490 GTCGTTTTTG
21599500 GTATTTTTTTA-
1 GTATTTTTTTAT
21599511 GTATTTTATTTAT
1 GTATTTT-TTTAT
*
21599524 TTATTTATTTTTAT
1 GTA-TT-TTTTTAT
* *
21599538 GTGTTTTTTTAG
1 GTATTTTTTTAT
21599550 GT-TTTTTTT
1 GTATTTTTTT
21599559 CATTATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 14 0.35
12 12 0.30
13 4 0.10
14 8 0.20
15 2 0.05
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.75
Consensus pattern (12 bp):
GTATTTTTTTAT
Found at i:21599955 original size:188 final size:174
Alignment explanation
Indices: 21599619--21600121 Score: 497
Period size: 176 Copynumber: 2.8 Consensus size: 174
21599609 AATGTTATTT
* * *
21599619 ATCCAATTATGAAATT-TATAAAAATTTGAAATGGTAAATTTTTATAAAAT-TCTTAGGTGAGAA
1 ATCCAATGATGAAATTCT-TAAAAATTTCAAATGGTAAATTTTTA-AAAATCTC-TAGGTAAGAA
* *
21599682 ATTTTGTCTAAATTTGGTCCAAATGATGAAATAATTTAGAT-AAAGTTTCAATAACAATAATTAA
63 ATTTTCTCTAAATTT-GTCCAAATGGTGAAATAATTTAGATGAAAGTTTCAATAA-AATAATTAA
*
21599746 TATTTATTTTCAAACAAAAAAATGAAAAATA-TAT-AAAATTTATGGGAATTAAATACAA
126 TATTTATTTTCAAACAAAAAAA--AAAAATAGT-TGAAAATATAT--G-A-T-AAT---A
* **
21599804 ATTACTCAATGATGAGATTCTTAAAAATTTCAAATGGTAAATTCCTAAGAAATCTCTAGGTAAGA
1 A-T-C-CAATGATGAAATTCTTAAAAATTTCAAATGGTAAATTTTTAA-AAATCTCTAGGTAAGA
21599869 AATTTTCTCTAAATTTGTCCCAAATGGT-AGAATAATTTAGATGAAAGTTTCAATAAAAGTAATT
62 AATTTTCTCTAAATTTGT-CCAAATGGTGA-AATAATTTAGATGAAAGTTTCAATAAAA-TAATT
* *** *
21599933 -GTATTCT-TTTTCCAAA-AAAAAAAAATTTTAGTTGAAAATATATGATAATT
124 AATATT-TATTTT-CAAACAAAAAAAAAAAATAGTTGAAAATATATGATAATA
*
21599983 ATCCAATGATGAAATTCTTAGAAATTTCAAATGGTAAATTTTTAATAAATCTCTAGGTAAGAAAT
1 ATCCAATGATGAAATTCTTAAAAATTTCAAATGGTAAATTTTTAA-AAATCTCTAGGTAAGAAAT
* * *
21600048 TTTCTCTAAATTTGATCCTAATGGCGAAATAATTTAGGTGAAA-TTTCAATAAAAATAATT-ATC
65 TTTCTCTAAATTTG-TCCAAATGGTGAAATAATTTAGATGAAAGTTTCAAT-AAAATAATTAAT-
21600111 ATATTATTTTC
127 AT-TTATTTTC
21600122 TTTCCAAGAA
Statistics
Matches: 275, Mismatches: 23, Indels: 49
0.79 0.07 0.14
Matches are distributed among these distances:
175 13 0.05
176 101 0.37
177 8 0.03
178 1 0.00
179 1 0.00
182 3 0.01
183 1 0.00
184 1 0.00
185 2 0.01
186 6 0.02
187 14 0.05
188 98 0.36
189 26 0.09
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (174 bp):
ATCCAATGATGAAATTCTTAAAAATTTCAAATGGTAAATTTTTAAAAATCTCTAGGTAAGAAATT
TTCTCTAAATTTGTCCAAATGGTGAAATAATTTAGATGAAAGTTTCAATAAAATAATTAATATTT
ATTTTCAAACAAAAAAAAAAAATAGTTGAAAATATATGATAATA
Found at i:21603067 original size:22 final size:19
Alignment explanation
Indices: 21603017--21603069 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 19
21603007 TATATAATTA
21603017 ATTAAATAATT-AATTATT
1 ATTAAATAATTAAATTATT
**
21603035 ATTTTATAATTAAATTATGAT
1 ATTAAATAATTAAATTAT--T
21603056 CATTAAATAATTAA
1 -ATTAAATAATTAA
21603070 TTAATAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 9 0.33
19 6 0.22
21 1 0.04
22 11 0.41
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
ATTAAATAATTAAATTATT
Found at i:21603091 original size:40 final size:40
Alignment explanation
Indices: 21603017--21603092 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
21603007 TATATAATTA
* ** *
21603017 ATTAAATAATTAATTATTATTTTATAATTAAATTATGATC
1 ATTAAATAATTAATTAATAAATTAAAATTAAATTATGATC
21603057 ATTAAATAATTAATTAATAAATTAAAA-TATAATTAT
1 ATTAAATAATTAATTAATAAATTAAAATTA-AATTAT
21603093 ACAACCAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.06
40 29 0.94
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (40 bp):
ATTAAATAATTAATTAATAAATTAAAATTAAATTATGATC
Found at i:21605279 original size:18 final size:18
Alignment explanation
Indices: 21605242--21605281 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
21605232 TAGCTATACA
*
21605242 TAAATATAATATTTTTAT
1 TAAATATAATATTTTAAT
21605260 TAAAT-TAATATTTTAAAT
1 TAAATATAATATTTT-AAT
21605278 TAAA
1 TAAA
21605282 AAATTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAATATAATATTTTAAT
Found at i:21609555 original size:12 final size:12
Alignment explanation
Indices: 21609537--21609566 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21609527 TTTAAAAATG
21609537 ATTTAATAAAAA
1 ATTTAATAAAAA
*
21609549 TTTTAATAAAAA
1 ATTTAATAAAAA
21609561 ATTTAA
1 ATTTAA
21609567 ATTGATAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTTAATAAAAA
Found at i:21616136 original size:52 final size:50
Alignment explanation
Indices: 21616073--21616193 Score: 152
Period size: 51 Copynumber: 2.4 Consensus size: 50
21616063 TTATGAATCC
*
21616073 TCAAATGAGAATCTTTGAATTTTTTAGTTCTAAAATGAAAATATTTGAGTTT
1 TCAAATGAGAATCTTTGAA-TTTTTAGTTCTAAAATGAAAATATTTGA-ATT
* * * * * * *
21616125 TCAAATAAGAATCTTTGAATTTTTAGTTTTCAAATTAGAGTCTTTGAATT
1 TCAAATGAGAATCTTTGAATTTTTAGTTCTAAAATGAAAATATTTGAATT
21616175 TCAAATGAGAATCTTTGAA
1 TCAAATGAGAATCTTTGAA
21616194 ATGTGAAACT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
50 20 0.33
51 22 0.37
52 18 0.30
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.43
Consensus pattern (50 bp):
TCAAATGAGAATCTTTGAATTTTTAGTTCTAAAATGAAAATATTTGAATT
Found at i:21616152 original size:29 final size:29
Alignment explanation
Indices: 21616120--21616175 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
21616110 AAAATATTTG
21616120 AGTTTTCAAATAAGAATCTTTGAATTTTT
1 AGTTTTCAAATAAGAATCTTTGAATTTTT
* *
21616149 AGTTTTCAAATTAGAGTCTTTGAATTT
1 AGTTTTCAAATAAGAATCTTTGAATTT
21616176 CAAATGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.48
Consensus pattern (29 bp):
AGTTTTCAAATAAGAATCTTTGAATTTTT
Found at i:21616178 original size:21 final size:21
Alignment explanation
Indices: 21616152--21616193 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21616142 AATTTTTAGT
* *
21616152 TTTCAAATTAGAGTCTTTGAA
1 TTTCAAATGAGAATCTTTGAA
21616173 TTTCAAATGAGAATCTTTGAA
1 TTTCAAATGAGAATCTTTGAA
21616194 ATGTGAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (21 bp):
TTTCAAATGAGAATCTTTGAA
Found at i:21616425 original size:31 final size:30
Alignment explanation
Indices: 21616404--21616464 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
21616394 TTTTGTATAT
21616404 CTGAAATTTT-ACGAATCAAATTCTTATGAAA
1 CTGAAATTTTGA-GAATCAAATT-TTATGAAA
21616435 CTGAAATTTTGAGAATCAAATTTTAGTGAA
1 CTGAAATTTTGAGAATCAAATTTTA-TGAA
21616465 TTCTTGTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 3 0.11
31 24 0.86
32 1 0.04
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (30 bp):
CTGAAATTTTGAGAATCAAATTTTATGAAA
Found at i:21616670 original size:44 final size:43
Alignment explanation
Indices: 21616610--21617073 Score: 206
Period size: 43 Copynumber: 10.4 Consensus size: 43
21616600 CAAAGAGTCT
*
21616610 TTATTT-TTTTTCAAAGTCGTTAAGCTTTTGATTAGAGGAGCC
1 TTATTTATTTTTCAAAGTTGTTAAGCTTTTGATTAGAGGAGCC
* * * * *
21616652 TTATTTATTTTTCAAAAGTCGTTGAGCCTTTAATTAGATGAGCC
1 TTATTTATTTTTC-AAAGTTGTTAAGCTTTTGATTAGAGGAGCC
* * * * * **
21616696 TTTAATTAGATGAGCCTTTTATTTTTCAAAGTTATTAAGCCTCTAATTAGAAGAGTT
1 -TT-ATT---T-A------T--TTTTCAAAGTTGTTAAGCTTTTGATTAGAGGAGCC
* * *
21616753 TTATTTATTTTTTTTAAAGTTGTTAGGCCTCTT-ATTAGAGGAGCC
1 TTATTTA--TTTTTCAAAGTTGTTAAG-CTTTTGATTAGAGGAGCC
* * * *
21616798 TTATTTA-TTTTCTAAAGTCGTTGAGCTTCT-ATTTAGATGAGCC
1 TTATTTATTTTTC-AAAGTTGTTAAGCTTTTGA-TTAGAGGAGCC
* * * * *
21616841 TGATTTATTTTTCAAAGTTATTGAG-TCTTTGTTTATAGGAGCC
1 TTATTTATTTTTCAAAGTTGTTAAGCT-TTTGATTAGAGGAGCC
* * * * * * **
21616884 TTATTTATTTTTTAAAAGTTATTGAGCCTTTAATTAGATGAGTT
1 TTATTTA-TTTTTCAAAGTTGTTAAGCTTTTGATTAGAGGAGCC
*
21616928 TTATTTA-TTTTCTAAAGTTGTTAAG-TCTTTGTTTAGAGGAGCC
1 TTATTTATTTTTC-AAAGTTGTTAAGCT-TTTGATTAGAGGAGCC
** ** * * * *
21616971 TTGCTTATTTTTCAAAGTTGTCGAGCTTCTGTTTAGAGAAGGC
1 TTATTTATTTTTCAAAGTTGTTAAGCTTTTGATTAGAGGAGCC
* * * * *
21617014 TTCTTTATTTTTTCAAAGTTGTTAAGCCTCT-ACTTATAGGAGCT
1 TTATTTA-TTTTTCAAAGTTGTTAAGCTTTTGA-TTAGAGGAGCC
*
21617058 TTCTTTATTTTTCAAA
1 TTATTTATTTTTCAAA
21617074 TTCATTGAGC
Statistics
Matches: 323, Mismatches: 69, Indels: 59
0.72 0.15 0.13
Matches are distributed among these distances:
42 19 0.06
43 121 0.37
44 105 0.33
45 32 0.10
46 5 0.02
47 3 0.01
49 1 0.00
50 1 0.00
51 1 0.00
52 1 0.00
55 3 0.01
56 3 0.01
57 23 0.07
58 5 0.02
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.47
Consensus pattern (43 bp):
TTATTTATTTTTCAAAGTTGTTAAGCTTTTGATTAGAGGAGCC
Found at i:21616695 original size:16 final size:16
Alignment explanation
Indices: 21616674--21616714 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
21616664 CAAAAGTCGT
21616674 TGAGCCTTTAATTAGA
1 TGAGCCTTTAATTAGA
21616690 TGAGCCTTTAATTAGA
1 TGAGCCTTTAATTAGA
21616706 TGAGCCTTT
1 TGAGCCTTT
21616715 TATTTTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (16 bp):
TGAGCCTTTAATTAGA
Found at i:21616834 original size:43 final size:43
Alignment explanation
Indices: 21616701--21617112 Score: 268
Period size: 43 Copynumber: 9.5 Consensus size: 43
21616691 GAGCCTTTAA
* * * * *
21616701 TTAGATGAGCC-T-TTTATTTTTCAAAGTTATTAAGCCTCTAA
1 TTAGAGGAGCCTTATTTATTTTTCAAAGTTGTTGAGCTTCTAT
* ** * *
21616742 TTAGAAGAGTTTTATTTATTTTTTTTAAAGTTGTT-AGGCCTCT-T
1 TTAGAGGAGCCTTATTTA--TTTTTCAAAGTTGTTGA-GCTTCTAT
*
21616786 ATTAGAGGAGCCTTATTTA-TTTTCTAAAGTCGTTGAGCTTCTAT
1 -TTAGAGGAGCCTTATTTATTTTTC-AAAGTTGTTGAGCTTCTAT
* * * *
21616830 TTAGATGAGCCTGATTTATTTTTCAAAGTTATTGAGTCTT-TGT
1 TTAGAGGAGCCTTATTTATTTTTCAAAGTTGTTGAG-CTTCTAT
* * * *
21616873 TTATAGGAGCCTTATTTATTTTTTAAAAGTTATTGAGCCTT-TAA
1 TTAGAGGAGCCTTATTTA-TTTTTCAAAGTTGTTGAG-CTTCTAT
* ** * *
21616917 TTAGATGAGTTTTATTTA-TTTTCTAAAGTTGTTAAGTCTT-TGT
1 TTAGAGGAGCCTTATTTATTTTTC-AAAGTTGTTGAG-CTTCTAT
** * *
21616960 TTAGAGGAGCCTTGCTTATTTTTCAAAGTTGTCGAGCTTCTGT
1 TTAGAGGAGCCTTATTTATTTTTCAAAGTTGTTGAGCTTCTAT
* * * * * *
21617003 TTAGAGAAGGCTTCTTTATTTTTTCAAAGTTGTTAAGCCTCTAC
1 TTAGAGGAGCCTTATTTA-TTTTTCAAAGTTGTTGAGCTTCTAT
* * * * *
21617047 TTATAGGAGCTTTCTTTATTTTTCAAA-TTCATTGAGCCTCTAT
1 TTAGAGGAGCCTTATTTATTTTTCAAAGTT-GTTGAGCTTCTAT
* * *
21617090 TTGGATGAGCTTTATTTATTTTT
1 TTAGAGGAGCCTTATTTATTTTT
21617113 TTTAAAGGTT
Statistics
Matches: 293, Mismatches: 61, Indels: 32
0.76 0.16 0.08
Matches are distributed among these distances:
41 8 0.03
42 14 0.05
43 152 0.52
44 85 0.29
45 34 0.12
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.48
Consensus pattern (43 bp):
TTAGAGGAGCCTTATTTATTTTTCAAAGTTGTTGAGCTTCTAT
Found at i:21616941 original size:130 final size:127
Alignment explanation
Indices: 21616701--21617099 Score: 374
Period size: 130 Copynumber: 3.1 Consensus size: 127
21616691 GAGCCTTTAA
* * ** * **
21616701 TTAGATGAGCCT-TTTATTTTTCAAAGTTATTAAGCCTCTAATTAGAAGAGTTTTATTTATTTTT
1 TTAGATGAGCCTGTTTATTTTTCAAAGTTATTGAG-CTTTGTTTAGAGGAGCCTTATTTA-TTTT
* *
21616765 TTTAAAGTTGTTAGGCCTCTT-ATTAGAGGAGCCTTATTTATTTTCTAAAGTCGTTGAGCTTCTA
64 TTAAAAGTTGTTA-GCCT-TTAATTAGAGGAGCTTTATTTATTTTCTAAAGTCGTTGAGCTTCTA
21616829 T
127 T
*
21616830 TTAGATGAGCCTGATTTATTTTTCAAAGTTATTGAGTCTTTGTTTATAGGAGCCTTATTTATTTT
1 TTAGATGAGCCTG-TTTATTTTTCAAAGTTATTGAG-CTTTGTTTAGAGGAGCCTTATTTATTTT
* * * * * *
21616895 TTAAAAGTTATTGAGCCTTTAATTAGATGAGTTTTATTTATTTTCTAAAGTTGTTAAGTCTT-TG
64 TTAAAAGTTGTT-AGCCTTTAATTAGAGGAGCTTTATTTATTTTCTAAAGTCGTTGAG-CTTCTA
21616959 T
127 T
* * * * * * *
21616960 TTAGAGGAGCCTTGCTTATTTTTCAAAGTTGTCGAGCTTCTGTTTAGAGAAGGCTTCTTTATTTT
1 TTAGATGAGCC-TGTTTATTTTTCAAAGTTATTGAGCTT-TGTTTAGAGGAGCCTTATTTATTTT
* * * * * * * *
21617025 TTCAAAGTTGTTAAGCCTCTACTTATAGGAGCTTTCTTTATTTT-TCAAATTCATTGAGCCTCTA
64 TTAAAAGTTGTT-AGCCTTTAATTAGAGGAGCTTTATTTATTTTCT-AAAGTCGTTGAGCTTCTA
21617089 T
127 T
*
21617090 TTGGATGAGC
1 TTAGATGAGC
21617100 TTTATTTATT
Statistics
Matches: 219, Mismatches: 42, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
129 20 0.09
130 155 0.71
131 44 0.20
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (127 bp):
TTAGATGAGCCTGTTTATTTTTCAAAGTTATTGAGCTTTGTTTAGAGGAGCCTTATTTATTTTTT
AAAAGTTGTTAGCCTTTAATTAGAGGAGCTTTATTTATTTTCTAAAGTCGTTGAGCTTCTAT
Found at i:21617113 original size:87 final size:87
Alignment explanation
Indices: 21616692--21617113 Score: 358
Period size: 87 Copynumber: 4.9 Consensus size: 87
21616682 TAATTAGATG
* * * * * * *
21616692 AGCCTTTAATTAGATGAGCC-T-TTTATTTTTCAAAGTTATTAAGCCTCTAATTAGAAGAGTTTT
1 AGCCTCTATTTAGAGGAGCCTTATTTATTTTTCAAAGTTATTGAGCCTCTATTTAGATGAGCTTT
*
21616755 ATTTATTTTTTTTAAAGTTGTTA
66 ATTTA-TTTTTTCAAAGTTGTTA
* ** * *
21616778 GGCCTCT-TATTAGAGGAGCCTTATTTA-TTTTCTAAAGTCGTTGAGCTTCTATTTAGATGAGCC
1 AGCCTCTAT-TTAGAGGAGCCTTATTTATTTTTC-AAAGTTATTGAGCCTCTATTTAGATGAGCT
* * *
21616841 TGATTTA-TTTTTCAAAGTTATTG
64 TTATTTATTTTTTCAAAGTTGTTA
* * * * * * * *
21616864 AGTCTTTGTTTATAGGAGCCTTATTTATTTTTTAAAAGTTATTGAGCCTTTAATTAGATGAGTTT
1 AGCCTCTATTTAGAGGAGCCTTATTTA-TTTTTCAAAGTTATTGAGCCTCTATTTAGATGAGCTT
*
21616929 TATTTATTTTCT-AAAGTTGTTA
65 TATTTATTTTTTCAAAGTTGTTA
* * * ** * * * *
21616951 AGTCTTTGTTTAGAGGAGCCTTGCTTATTTTTCAAAGTTGTCGAGCTTCTGTTTAGA-GAAGGC-
1 AGCCTCTATTTAGAGGAGCCTTATTTATTTTTCAAAGTTATTGAGCCTCTATTTAGATG-A-GCT
*
21617014 TTCTTTATTTTTTCAAAGTTGTTA
64 TTATTTATTTTTTCAAAGTTGTTA
* * * * *
21617038 AGCCTCTACTTATAGGAGCTTTCTTTATTTTTCAAA-TTCATTGAGCCTCTATTTGGATGAGCTT
1 AGCCTCTATTTAGAGGAGCCTTATTTATTTTTCAAAGTT-ATTGAGCCTCTATTTAGATGAGCTT
21617102 TATTTATTTTTT
65 TATTTATTTTTT
21617114 TTAAAGGTTG
Statistics
Matches: 263, Mismatches: 59, Indels: 27
0.75 0.17 0.08
Matches are distributed among these distances:
85 1 0.00
86 88 0.33
87 133 0.51
88 41 0.16
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (87 bp):
AGCCTCTATTTAGAGGAGCCTTATTTATTTTTCAAAGTTATTGAGCCTCTATTTAGATGAGCTTT
ATTTATTTTTTCAAAGTTGTTA
Found at i:21618318 original size:22 final size:22
Alignment explanation
Indices: 21618285--21618334 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
21618275 GTTGAGCTAA
21618285 ATTTTTTGTATTTTATTCTT-GT
1 ATTTTTTGTA-TTTATTCTTAGT
*
21618307 ATTTTATT-TATTTATTTTTAGT
1 ATTTT-TTGTATTTATTCTTAGT
21618329 ATTTTT
1 ATTTTT
21618335 ATATGATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 9 0.36
22 14 0.56
23 2 0.08
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.74
Consensus pattern (22 bp):
ATTTTTTGTATTTATTCTTAGT
Found at i:21618324 original size:13 final size:13
Alignment explanation
Indices: 21618290--21618314 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21618280 GCTAAATTTT
21618290 TTGTATTTTATTC
1 TTGTATTTTATTC
21618303 TTGTATTTTATT
1 TTGTATTTTATT
21618315 TATTTATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (13 bp):
TTGTATTTTATTC
Found at i:21620261 original size:40 final size:40
Alignment explanation
Indices: 21620206--21620288 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
21620196 GCTCGTGTGT
21620206 AAACCTACAAATACCTCTATAGATCCTAATCATAAACTTA
1 AAACCTACAAATACCTCTATAGATCCTAATCATAAACTTA
*
21620246 AAACCTGCAAATACCTCTATAGATCCTAATCATAAACTTA
1 AAACCTACAAATACCTCTATAGATCCTAATCATAAACTTA
21620286 AAA
1 AAA
21620289 AAGCTAATGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.46, C:0.24, G:0.04, T:0.27
Consensus pattern (40 bp):
AAACCTACAAATACCTCTATAGATCCTAATCATAAACTTA
Found at i:21625397 original size:23 final size:22
Alignment explanation
Indices: 21625364--21625408 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
21625354 TTTTTTTCTT
21625364 CATTTTTTTTTTTTAAATTTAA
1 CATTTTTTTTTTTTAAATTTAA
*
21625386 CATTTTTATTTTTTTATATTTAA
1 CATTTTT-TTTTTTTAAATTTAA
21625409 AATTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (22 bp):
CATTTTTTTTTTTTAAATTTAA
Found at i:21625419 original size:28 final size:29
Alignment explanation
Indices: 21625365--21625429 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
21625355 TTTTTTCTTC
* * *
21625365 ATTTTTTT-TTTTTAAATTTAACATTTTT
1 ATTTTTTTATATTTAAAATTAACATTTTG
*
21625393 ATTTTTTTATATTTAAAATTAA-TTTTTG
1 ATTTTTTTATATTTAAAATTAACATTTTG
21625421 ATTTTTTTA
1 ATTTTTTTA
21625430 ACTTTTTGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 21 0.66
29 11 0.34
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (29 bp):
ATTTTTTTATATTTAAAATTAACATTTTG
Found at i:21632065 original size:6 final size:6
Alignment explanation
Indices: 21632054--21632088 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
21632044 TTATACATAC
* *
21632054 ATACAT ATACAT ATACAT ATATAT ATATAT ATACA
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACA
21632089 CACGCACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (6 bp):
ATACAT
Found at i:21632251 original size:4 final size:4
Alignment explanation
Indices: 21632242--21632280 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
21632232 GGCTACAATT
*
21632242 ATAC ATAC ATAC ATAC CTAC ATAC ATAC AT-C TATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC -ATAC ATA
21632281 TATATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 1 0.03
4 29 0.94
5 1 0.03
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:21632284 original size:8 final size:8
Alignment explanation
Indices: 21632241--21632297 Score: 51
Period size: 8 Copynumber: 7.1 Consensus size: 8
21632231 AGGCTACAAT
21632241 TATACATA
1 TATACATA
*
21632249 CATACATA
1 TATACATA
**
21632257 CCTACATA
1 TATACATA
* *
21632265 CATACATC
1 TATACATA
21632273 TATACATA
1 TATACATA
*
21632281 TATATATA
1 TATACATA
*
21632289 TATATATA
1 TATACATA
21632297 T
1 T
21632298 CCAAGCTTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 42 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.37
Consensus pattern (8 bp):
TATACATA
Found at i:21632465 original size:2 final size:2
Alignment explanation
Indices: 21632458--21632493 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
21632448 ATACATACAA
*
21632458 AT AT AT AT AT AT AT AT AA 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
21632494 CCAAGCTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21632571 original size:194 final size:195
Alignment explanation
Indices: 21632043--21632636 Score: 827
Period size: 203 Copynumber: 3.0 Consensus size: 195
21632033 TAAATAGAAT
* * * * * *** *
21632043 ATTATACATACATACATATACATATACATATATATATATATATACACACGCA-CCAAGCTTTCAG
1 ATTATACATACATACAAATATATATACATATATAAATATATATATATATATATCCAAGCTTTCAT
21632107 CATTGATCCAATAACATCACATCGTGTGAACAAACAAAAGCAAAGCCATTTGCTAACTAGTGATC
66 CATTGATCCAATAACATCACA--GTGTGAACAAACAAAAGCAAAGCCATTTGCTAACTAGTGATC
* *
21632172 AAATTCTAGAAAAAAAAAAGGAAAGAAAATAAAAAGATACAAGTTTTTGCTAGAATTTTAGGCTA
129 AAATTCTAGAAAAAAAAAAGGAAAGAAAATAAAAAGATACGAGTTTTTGCTAGAATTTTAGGCTT
21632237 CA
194 CA
* * *
21632239 ATTATACATACATACATACCTACATACATACATCTATACATATATATATATATATATATCCAAGC
1 ATTATACATACATACA-A---ATATATATACATATATA-A-ATATATATATATATATATCCAAGC
21632304 TTTCATCATTGATCCAATAACATCACGTAGTGTGAACAAACAAAAGCAAAGCCATTTGCTAACTA
60 TTTCATCATTGATCCAATAACATCAC--AGTGTGAACAAACAAAAGCAAAGCCATTTGCTAACTA
* *
21632369 GTGATCAAATTCTAGAAAAAAAAAA-TAAAGAAAATGAAAAGGA-ACGAGTTTTTGCTAGAATTT
123 GTGATCAAATTCTAGAAAAAAAAAAGGAAAGAAAAT-AAAAAGATACGAGTTTTTGCTAGAATTT
21632432 TAGGCTTC-
187 TAGGCTTCA
* *
21632440 ATATGTACATACATACAAATATATATATATATATAAATATATATATATATATATCCAAGCTTTCA
1 AT-TATACATACATACAAATATATATACATATATAAATATATATATATATATATCCAAGCTTTCA
* * *
21632505 TCATTGATCCAATAACTTCACAGTGTGAACAAGCAAAAGCAAAGCCATTTGGTAACTAGTGATCA
65 TCATTGATCCAATAACATCACAGTGTGAACAAACAAAAGCAAAGCCATTTGCTAACTAGTGATCA
* *
21632570 AATTCTAGAAAAAAAAAAGAGGAAAGAAAATAAAAAGATACGAGTGTTGGCTAGAATTTTAGGCT
130 AATTCTAG-AAAAAAAAA-AGGAAAGAAAATAAAAAGATACGAGTTTTTGCTAGAATTTTAGGCT
21632635 TC
193 TC
21632637 TTCGGTTTTT
Statistics
Matches: 355, Mismatches: 28, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
194 50 0.14
195 9 0.03
196 72 0.20
197 36 0.10
198 13 0.04
200 13 0.04
201 3 0.01
202 60 0.17
203 98 0.28
205 1 0.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (195 bp):
ATTATACATACATACAAATATATATACATATATAAATATATATATATATATATCCAAGCTTTCAT
CATTGATCCAATAACATCACAGTGTGAACAAACAAAAGCAAAGCCATTTGCTAACTAGTGATCAA
ATTCTAGAAAAAAAAAAGGAAAGAAAATAAAAAGATACGAGTTTTTGCTAGAATTTTAGGCTTCA
Found at i:21638754 original size:18 final size:18
Alignment explanation
Indices: 21638725--21638769 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
21638715 AATAAAAATT
*
21638725 ATTTTTTA-AGATCCAAA
1 ATTTTTTATAGATACAAA
*
21638742 ATTTTTTATAGATATAAA
1 ATTTTTTATAGATACAAA
*
21638760 ATTTTATATA
1 ATTTTTTATA
21638770 TTTTATATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (18 bp):
ATTTTTTATAGATACAAA
Found at i:21639698 original size:13 final size:14
Alignment explanation
Indices: 21639671--21639704 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
21639661 TAAATTTGAT
21639671 ATATTTTTAAGTAA
1 ATATTTTTAAGTAA
21639685 ATATTTTTAA-TAA
1 ATATTTTTAAGTAA
*
21639698 AAATTTT
1 ATATTTT
21639705 AACGACTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
ATATTTTTAAGTAA
Found at i:21639792 original size:13 final size:12
Alignment explanation
Indices: 21639769--21639848 Score: 71
Period size: 12 Copynumber: 6.8 Consensus size: 12
21639759 TTTTTATATA
21639769 TTATT-AATTTT
1 TTATTAAATTTT
21639780 TCTATTAAA--TT
1 T-TATTAAATTTT
*
21639791 TTATTAATATATTA
1 TTATTAA-AT-TTT
21639805 TT-TTAAATTTT
1 TTATTAAATTTT
*
21639816 TTATTAAAATTT
1 TTATTAAATTTT
21639828 TTATTAAATTATT
1 TTATTAAATT-TT
21639841 TT-TTAAAT
1 TTATTAAAT
21639849 AATTTCACAT
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
10 6 0.11
11 9 0.16
12 29 0.51
13 10 0.18
14 3 0.05
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTAAATTTT
Found at i:21639826 original size:36 final size:37
Alignment explanation
Indices: 21639751--21639848 Score: 106
Period size: 36 Copynumber: 2.8 Consensus size: 37
21639741 AATAATATTT
21639751 TTAATAATTTT-TT-ATATATTA--TT-AATTTTTCTA
1 TTAA-AATTTTATTAATATATTATTTTAAATTTTTCTA
21639784 TT-AAATTTTATTAATATATTATTTTAAATTTTT-TA
1 TTAAAATTTTATTAATATATTATTTTAAATTTTTCTA
21639819 TTAAAATTTTTATTAA-ATTATT-TTTTAAAT
1 TTAAAA-TTTTATTAATA-TATTATTTTAAAT
21639849 AATTTCACAT
Statistics
Matches: 57, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
31 6 0.11
32 3 0.05
33 10 0.18
35 6 0.11
36 19 0.33
37 13 0.23
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (37 bp):
TTAAAATTTTATTAATATATTATTTTAAATTTTTCTA
Found at i:21640139 original size:19 final size:18
Alignment explanation
Indices: 21640097--21640132 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
21640087 TTTATTTGGA
21640097 TAAATTAAATTAAATTTT
1 TAAATTAAATTAAATTTT
21640115 TAAATTAAAATT-AATTTT
1 TAAATT-AAATTAAATTTT
21640133 ATCAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAATTAAATTAAATTTT
Found at i:21643533 original size:24 final size:27
Alignment explanation
Indices: 21643496--21643558 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 27
21643486 ACGTAATATC
21643496 TTAATTATAAATTT-ATTTT-AT-TAA
1 TTAATTATAAATTTAATTTTAATATAA
21643520 TTAA-TATAATATTTAATTTTAATATAA
1 TTAATTATAA-ATTTAATTTTAATATAA
* *
21643547 TTATTTTTAAAT
1 TTAATTATAAAT
21643559 AATAATATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
23 5 0.16
24 8 0.25
25 5 0.16
26 2 0.06
27 8 0.25
28 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTAATTATAAATTTAATTTTAATATAA
Found at i:21643535 original size:16 final size:18
Alignment explanation
Indices: 21643516--21643552 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
21643506 ATTTATTTTA
21643516 TTAA-TTAATATAA-TAT
1 TTAATTTAATATAATTAT
21643532 TTAATTTTAATATAATTAT
1 TTAA-TTTAATATAATTAT
21643551 TT
1 TT
21643553 TTAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAATTTAATATAATTAT
Found at i:21644451 original size:36 final size:36
Alignment explanation
Indices: 21644409--21644507 Score: 94
Period size: 36 Copynumber: 2.7 Consensus size: 36
21644399 AAAAAATTCT
*
21644409 AAGAATTTCTAAATCGAGATCAAATTTCA-ACATTCC
1 AAGAATTTCTAAATCGAGATCAAATTTCATA-ATTAC
* * * *
21644445 ATGAA-TTCTTAAATTGAGATCATATCTCATAATTAC
1 AAGAATTTC-TAAATCGAGATCAAATTTCATAATTAC
**
21644481 AAGAATACCTAAATCTGAGATCAAATT
1 AAGAATTTCTAAATC-GAGATCAAATT
21644508 CTAAGAATTT
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
35 3 0.06
36 34 0.71
37 11 0.23
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.32
Consensus pattern (36 bp):
AAGAATTTCTAAATCGAGATCAAATTTCATAATTAC
Found at i:21645114 original size:20 final size:19
Alignment explanation
Indices: 21645091--21645129 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
21645081 AATATAAAAA
21645091 TTTATATATTTATAT-TATAT
1 TTTATA-ATTT-TATCTATAT
21645111 TTTATAATTTTATCTATAT
1 TTTATAATTTTATCTATAT
21645130 GAAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 9 0.50
20 6 0.33
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATAATTTTATCTATAT
Found at i:21648568 original size:12 final size:12
Alignment explanation
Indices: 21648546--21648584 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
21648536 AATATTATTT
21648546 TAATGTAAATATA
1 TAAT-TAAATATA
21648559 TAATTAAATATA
1 TAATTAAATATA
*
21648571 TAATTATATATA
1 TAATTAAATATA
21648583 TA
1 TA
21648585 CACAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (12 bp):
TAATTAAATATA
Found at i:21655944 original size:16 final size:15
Alignment explanation
Indices: 21655901--21655949 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
21655891 TAAAATAATT
21655901 AATAATTCAAATTAA
1 AATAATTCAAATTAA
* *
21655916 AATAATTTGAATTTAA
1 AATAA-TTCAAATTAA
*
21655932 AATGATTCAAATTAA
1 AATAATTCAAATTAA
21655947 AAT
1 AAT
21655950 TATCTAAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (15 bp):
AATAATTCAAATTAA
Found at i:21656658 original size:182 final size:179
Alignment explanation
Indices: 21656387--21656727 Score: 513
Period size: 181 Copynumber: 1.9 Consensus size: 179
21656377 TTTGAAACTC
* * * *
21656387 TTAAATTAAATTTAAATGATTATAATAAACTTTAAAGTCTATTGAAATTACATGTACATCAATTT
1 TTAAATTAAATTGAAATGATTAAAATAAACTTAAAAGTCTATTGAAATTACATGTAAATCAA--T
*
21656452 TTTTTAATATTTTAAGTGAAATTATTTTATTAAATTAACATAATAATTTAAAAGGATACGTATTG
64 TTTTTAATATTTTAAGTAAAATTATTTTATTAAA-TAACATAATAATTTAAAAGGATACGTATTG
*
21656517 ATTATTTAAACCCACTTATGCAACTTAAAAGTCAAAAGAATTTTTGACATCG
128 ATTATTTAAACCCACTTATGAAACTTAAAAGTCAAAAGAATTTTTGACATCG
*
21656569 TTAAATTAAATTCGAAATGGTTAAAATAAACTGTAAAAAGTCTATTGAAATTACATGTAAATCAA
1 TTAAATTAAATT-GAAATGATTAAAATAAACT-T-AAAAGTCTATTGAAATTACATGTAAATCAA
* * * *
21656634 -TTTTTATTATTTTAAGTAAAATTATTTTATTAAATAACATAATAATTTGAATGGATATGTATTG
63 TTTTTTAATATTTTAAGTAAAATTATTTTATTAAATAACATAATAATTTAAAAGGATACGTATTG
*
21656698 ATTATTTAAACCCATTTATGAAACTTAAAA
128 ATTATTTAAACCCACTTATGAAACTTAAAA
21656728 AGTTTTATTA
Statistics
Matches: 144, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
181 55 0.38
182 44 0.31
183 16 0.11
184 1 0.01
185 28 0.19
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (179 bp):
TTAAATTAAATTGAAATGATTAAAATAAACTTAAAAGTCTATTGAAATTACATGTAAATCAATTT
TTTAATATTTTAAGTAAAATTATTTTATTAAATAACATAATAATTTAAAAGGATACGTATTGATT
ATTTAAACCCACTTATGAAACTTAAAAGTCAAAAGAATTTTTGACATCG
Found at i:21657252 original size:87 final size:87
Alignment explanation
Indices: 21657121--21657282 Score: 229
Period size: 87 Copynumber: 1.9 Consensus size: 87
21657111 TATACTCTTG
** *
21657121 ATTATTTGGGTAAAATATTGAAATTTGTATATCGATGTCTTATAAAATATTAAAATTTATGTATT
1 ATTATTTGAATAAAATATTGAAATTTGTATATCGATATCTTATAAAATATTAAAATTTATGTATT
*
21657186 TATATCATATTTTATATTTTTA
66 CATATCATATTTTATATTTTTA
**
21657208 ATTATTTGAATAAAATATT-AATATTTGTATATTTATAT-TATATAAAATATTAAAATTTATGTA
1 ATTATTTGAATAAAATATTGAA-ATTTGTATATCGATATCT-TATAAAATATTAAAATTTATGTA
*
21657271 TTCATATTATAT
64 TTCATATCATAT
21657283 ATACAAAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
86 3 0.05
87 63 0.95
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (87 bp):
ATTATTTGAATAAAATATTGAAATTTGTATATCGATATCTTATAAAATATTAAAATTTATGTATT
CATATCATATTTTATATTTTTA
Found at i:21657285 original size:34 final size:32
Alignment explanation
Indices: 21657217--21657283 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
21657207 AATTATTTGA
* * *
21657217 ATAAAATATTAATATTTGTATATTTATATTAT
1 ATAAAATATTAAAATTTATATATTCATATTAT
*
21657249 ATAAAATATTAAAATTTATGTATTCATATTAT
1 ATAAAATATTAAAATTTATATATTCATATTAT
21657281 ATA
1 ATA
21657284 TACAAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (32 bp):
ATAAAATATTAAAATTTATATATTCATATTAT
Found at i:21662571 original size:16 final size:17
Alignment explanation
Indices: 21662531--21662580 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
21662521 GGTTTAACAA
*
21662531 TATAGTTTATAA-TATT
1 TATAATTTATAATTATT
21662547 T-TAATTTATAATTATT
1 TATAATTTATAATTATT
*
21662563 TATAA-TTATATTTATT
1 TATAATTTATAATTATT
21662579 TA
1 TA
21662581 AACAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 9 0.30
16 18 0.60
17 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TATAATTTATAATTATT
Found at i:21663145 original size:32 final size:32
Alignment explanation
Indices: 21663072--21663147 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
21663062 TTTTGTATAA
* * **
21663072 AATATAATATAAATATATAAATTTTAACATTT
1 AATATAATATAAATATATAAATTATAAAATCC
* *
21663104 TACATAATATAAATATATAAATTATAAAATCC
1 AATATAATATAAATATATAAATTATAAAATCC
*
21663136 AATAAAATATAA
1 AATATAATATAA
21663148 GTGATTTAGC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (32 bp):
AATATAATATAAATATATAAATTATAAAATCC
Found at i:21663355 original size:28 final size:28
Alignment explanation
Indices: 21663324--21663391 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
21663314 TATAAAAATC
* *
21663324 ATATAATAATTTAATAA-AAAAATATTTT
1 ATATAATAATTTAATAATAAAAAT-TATG
** * *
21663352 ATATTTTAATATATTAATAAAAATTATG
1 ATATAATAATTTAATAATAAAAATTATG
21663380 ATATAATAATTT
1 ATATAATAATTT
21663392 TCATAATTCA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
ATATAATAATTTAATAATAAAAATTATG
Done.