Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 32 of 135
Found at i:12895717 original size:24 final size:23
Alignment explanation
Indices: 12895675--12895719 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
12895665 CGATATTAAT
* *
12895675 ATAAAAAATAGATTAAATTGTGA
1 ATAAAAAATACACTAAATTGTGA
12895698 ATAAAAAATACACTATAATTGT
1 ATAAAAAATACACTA-AATTGT
12895720 AAATGTATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (23 bp):
ATAAAAAATACACTAAATTGTGA
Found at i:12903276 original size:46 final size:46
Alignment explanation
Indices: 12903203--12903378 Score: 273
Period size: 46 Copynumber: 3.8 Consensus size: 46
12903193 AGTGTGGAAC
* *
12903203 GTAGGTATGGTATTTCAGTAAATAAAACTATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* * *
12903249 GTAGGTATGATATTTCAATAAAGAAAACCATACTGAGTTGTGAGAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* *
12903295 GTAGGTATGGTATTTCAGTAACGAAAATCATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
*
12903341 GTA-GTATGGTATTTCAGTGAAGAAAACCATACTGAGTT
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
12903379 ATAGCATTGT
Statistics
Matches: 117, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
45 32 0.27
46 85 0.73
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.31
Consensus pattern (46 bp):
GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
Found at i:12906846 original size:51 final size:51
Alignment explanation
Indices: 12906768--12906877 Score: 193
Period size: 51 Copynumber: 2.2 Consensus size: 51
12906758 ATCACATTTC
*
12906768 TCACTTGTCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
1 TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
* *
12906819 TCACTTGTTACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTACCACTTA
1 TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
12906870 TCACTTGT
1 TCACTTGT
12906878 GACTGATTAG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (51 bp):
TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
Found at i:12908054 original size:42 final size:42
Alignment explanation
Indices: 12908001--12908100 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
12907991 CTATACGAAT
* ** * *
12908001 GGCACTAAGTGTGTGAAATTAAAATGACAATGTTGAATAAAG
1 GGCACTAAGTGTGCGAAACAAAAATAACAATGTCGAATAAAG
* *
12908043 GGCACTAAGTGTGCGAAACAAAAATAACGATGTCGAATAACG
1 GGCACTAAGTGTGCGAAACAAAAATAACAATGTCGAATAAAG
12908085 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
12908101 TACCAAGATC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAACAAAAATAACAATGTCGAATAAAG
Found at i:12909263 original size:40 final size:40
Alignment explanation
Indices: 12909210--12909293 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
12909200 AATTTGTTAC
* * * * *
12909210 TTCAGTAATTTCACAGTTCAA-TGCATTACACATAACAATA
1 TTCAATAACTTCACAATTCAAGT-CAGTACACAGAACAATA
*
12909250 TTCAATAACTTCACAATTCAAGTCAGTACTCAGAACAATA
1 TTCAATAACTTCACAATTCAAGTCAGTACACAGAACAATA
12909290 TTCA
1 TTCA
12909294 GTATTCCATA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
40 36 0.97
41 1 0.03
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (40 bp):
TTCAATAACTTCACAATTCAAGTCAGTACACAGAACAATA
Found at i:12909890 original size:5 final size:5
Alignment explanation
Indices: 12909880--12909921 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
12909870 TTCTTTAGTT
12909880 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
12909922 CTTATTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:12910911 original size:21 final size:21
Alignment explanation
Indices: 12910871--12910967 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 21
12910861 ATACGCCAAT
*
12910871 AGAAGCTCG-AA-AGCTGAAC
1 AGAAGCTCGTAAGAGTTGAAC
*
12910890 AGAAGCTCATAAGAGTTGAAC
1 AGAAGCTCGTAAGAGTTGAAC
* *
12910911 AGAAGCTCGTAAGAGTTTAAA
1 AGAAGCTCGTAAGAGTTGAAC
* *
12910932 AGAAGCTCGTAAGAGCTGAGC
1 AGAAGCTCGTAAGAGTTGAAC
*
12910953 AGAAGCTCGAAAGAG
1 AGAAGCTCGTAAGAG
12910968 CTAAACCGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
19 8 0.12
20 2 0.03
21 56 0.85
ACGTcount: A:0.41, C:0.15, G:0.28, T:0.15
Consensus pattern (21 bp):
AGAAGCTCGTAAGAGTTGAAC
Found at i:12932375 original size:14 final size:14
Alignment explanation
Indices: 12932313--12932376 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 14
12932303 ATTTTTCTAG
12932313 AATTTTTATATAAA
1 AATTTTTATATAAA
* *
12932327 AATTTCTATTCTTTAAA
1 AA-TT-T-TTATATAAA
*
12932344 TAATTTTTATTATTAA
1 -AATTTTTA-TATAAA
12932360 AATTTTTATATAAA
1 AATTTTTATATAAA
12932374 AAT
1 AAT
12932377 ATAAAAATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
14 10 0.26
15 12 0.31
16 6 0.15
17 9 0.23
18 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTTTTATATAAA
Found at i:12934922 original size:6 final size:6
Alignment explanation
Indices: 12934911--12934936 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12934901 GACTTTATAG
12934911 AGGGGC AGGGGC AGGGGC AGGGGC AG
1 AGGGGC AGGGGC AGGGGC AGGGGC AG
12934937 CGACAGGGCA
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:0.19, C:0.15, G:0.65, T:0.00
Consensus pattern (6 bp):
AGGGGC
Found at i:12935883 original size:80 final size:78
Alignment explanation
Indices: 12935785--12935938 Score: 281
Period size: 80 Copynumber: 1.9 Consensus size: 78
12935775 TAACATCCTT
12935785 GTTCCCATTTCCCTCATTTGCAATATATATATATATATATATATATTTTATAAATCAACTTTGCT
1 GTTCCCATTTCCCTCATTTGCAATATATATATATATATATATATA--TTATAAATCAACTTTGCT
12935850 TTCTGAACACAGAGC
64 TTCTGAACACAGAGC
12935865 GTTCCCATTTCCCTCATTTGCAATATATATATATATATATATATATTATAAATCAACTTTGCTTT
1 GTTCCCATTTCCCTCATTTGCAATATATATATATATATATATATATTATAAATCAACTTTGCTTT
*
12935930 CTGACCACA
66 CTGAACACA
12935939 AAGTTCTAAA
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
78 28 0.38
80 45 0.62
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (78 bp):
GTTCCCATTTCCCTCATTTGCAATATATATATATATATATATATATTATAAATCAACTTTGCTTT
CTGAACACAGAGC
Found at i:12935908 original size:78 final size:80
Alignment explanation
Indices: 12935785--12935938 Score: 276
Period size: 78 Copynumber: 1.9 Consensus size: 80
12935775 TAACATCCTT
*
12935785 GTTCCCATTTCCCTCATTTGCAATATATATATATATATATATATATTTTATAAATCAACTTTGCT
1 GTTCCCATTTCCCTCATTTGCAATATATATATATATATATATATATATTATAAATCAACTTTGCT
12935850 TTCTGAACACAGAGC
66 TTCTGAACACAGAGC
12935865 GTTCCCATTTCCCTCATTTGC-A-ATATATATATATATATATATATATTATAAATCAACTTTGCT
1 GTTCCCATTTCCCTCATTTGCAATATATATATATATATATATATATATTATAAATCAACTTTGCT
*
12935928 TTCTGACCACA
66 TTCTGAACACA
12935939 AAGTTCTAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
78 50 0.69
79 1 0.01
80 21 0.29
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (80 bp):
GTTCCCATTTCCCTCATTTGCAATATATATATATATATATATATATATTATAAATCAACTTTGCT
TTCTGAACACAGAGC
Found at i:12937090 original size:16 final size:16
Alignment explanation
Indices: 12937043--12937090 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
12937033 TATCAAGTTA
12937043 ATAATTTAATATAA-AT
1 ATAA-TTAATATAATAT
*
12937059 ATAATTATTACTTAATAT
1 ATAATTAATA--TAATAT
12937077 ATAATTAATATAAT
1 ATAATTAATATAAT
12937091 CATGTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 5 0.19
16 8 0.30
17 3 0.11
18 11 0.41
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAATATAATAT
Found at i:12944032 original size:113 final size:114
Alignment explanation
Indices: 12943832--12944059 Score: 440
Period size: 113 Copynumber: 2.0 Consensus size: 114
12943822 AGTGGAACCG
12943832 CAACTATCAAAAGCTTACTTAATTTCGTGCTTTGTCTAAATATAGGGTTAAAAATTACTTAAATT
1 CAACTATC-AAAGCTTACTTAATTTCGTGCTTTGTCTAAATATAGGGTTAAAAATTACTTAAATT
12943897 TTATTACACTGTGTGTACCAAAATATTTTATATTAAAAATATATTTATAA
65 TTATTACACTGTGTGTACCAAAATATTTTATATTAAAAATATATTTATAA
12943947 CAACTATC-AAGCTTACTTAATTTCGTGCTTTGTCTAAATATAGGGTTAAAAATTACTTAAATTT
1 CAACTATCAAAGCTTACTTAATTTCGTGCTTTGTCTAAATATAGGGTTAAAAATTACTTAAATTT
12944011 TATTACACTGTGTGTACCAAAATATTTTATATTAAAAATATATTTATAA
66 TATTACACTGTGTGTACCAAAATATTTTATATTAAAAATATATTTATAA
12944060 AATTATTTTT
Statistics
Matches: 113, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
113 105 0.93
115 8 0.07
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (114 bp):
CAACTATCAAAGCTTACTTAATTTCGTGCTTTGTCTAAATATAGGGTTAAAAATTACTTAAATTT
TATTACACTGTGTGTACCAAAATATTTTATATTAAAAATATATTTATAA
Found at i:12951225 original size:10 final size:9
Alignment explanation
Indices: 12951210--12951252 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 9
12951200 TTAAATTTTA
12951210 TAAAAATATT
1 TAAAAA-ATT
12951220 TAAAAAATT
1 TAAAAAATT
12951229 T--AAAATT
1 TAAAAAATT
12951236 TAAAAAAATT
1 T-AAAAAATT
12951246 TAAAAAA
1 TAAAAAA
12951253 AAAGAATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 7 0.23
9 10 0.33
10 13 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAAAAATT
Found at i:12951238 original size:16 final size:17
Alignment explanation
Indices: 12951217--12951250 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12951207 TTATAAAAAT
12951217 ATTT-AAAAAATTTAAA
1 ATTTAAAAAAATTTAAA
12951233 ATTTAAAAAAATTTAAA
1 ATTTAAAAAAATTTAAA
12951250 A
1 A
12951251 AAAAAGAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAAAAATTTAAA
Found at i:12951254 original size:28 final size:28
Alignment explanation
Indices: 12951197--12951252 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
12951187 GCTAATGATT
*
12951197 AATTTAAATTTTATAAAAATATTTAAAA
1 AATTTAAAATTTATAAAAATATTTAAAA
12951225 AATTTAAAATTTA-AAAAA-ATTTAAAA
1 AATTTAAAATTTATAAAAATATTTAAAA
12951251 AA
1 AA
12951253 AAAGAATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 10 0.37
27 5 0.19
28 12 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
AATTTAAAATTTATAAAAATATTTAAAA
Found at i:12960133 original size:1 final size:1
Alignment explanation
Indices: 12960129--12960190 Score: 61
Period size: 1 Copynumber: 62.0 Consensus size: 1
12960119 TTTTCCTTCG
**** ** *
12960129 TTTTTTTTTTTTTTTTTTTTTTTTTAAAATTTTCCTTTGTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12960191 CAAAATTTGC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.06, C:0.03, G:0.02, T:0.89
Consensus pattern (1 bp):
T
Found at i:12960181 original size:38 final size:39
Alignment explanation
Indices: 12960119--12960198 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 39
12960109 TCAATTATGT
*
12960119 TTTTCCTTCGTTTTTTTTTTTTTTTTTTTTTTTTTAAAA
1 TTTTCCTTCGTTTTTTTTTTTTTTTTTTTTTTTTCAAAA
*
12960158 TTTTCCTTTG-TTTTTTTTTTTTTTTTTTTTTTTCAAAA
1 TTTTCCTTCGTTTTTTTTTTTTTTTTTTTTTTTTCAAAA
12960196 TTT
1 TTT
12960199 GCTCGATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 30 0.77
39 9 0.23
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (39 bp):
TTTTCCTTCGTTTTTTTTTTTTTTTTTTTTTTTTCAAAA
Found at i:12962212 original size:6 final size:6
Alignment explanation
Indices: 12962203--12962227 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12962193 TAAAAGTAAA
12962203 AAAATT AAAATT AAAATT AAAATT A
1 AAAATT AAAATT AAAATT AAAATT A
12962228 CCTCTGCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:12964684 original size:30 final size:30
Alignment explanation
Indices: 12964650--12964709 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
12964640 TGATAATTTT
*
12964650 AATAACAATTAGTTTTAATTTT-ATTAAAAA
1 AATAA-AATTAATTTTAATTTTAATTAAAAA
**
12964680 AATAATTTTAATTTTAATTTTAATTAAAAA
1 AATAAAATTAATTTTAATTTTAATTAAAAA
12964710 CGGGCCGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
AATAAAATTAATTTTAATTTTAATTAAAAA
Found at i:12965057 original size:83 final size:83
Alignment explanation
Indices: 12964909--12965061 Score: 188
Period size: 83 Copynumber: 1.8 Consensus size: 83
12964899 GATAAAATGA
* * * *
12964909 AATTTTAATTTTTAATAATTTATATTTTATTATTTTTAAATGATTAAATTAAAATTTTATAATTT
1 AATTTTAACTTTTAATAATTTAAATTTTATTATTTTTAAATGACTAAAATAAAATTTTATAATTT
12964974 TAAAGAAGGTTAAAGTAT
66 TAAAGAAGGTTAAAGTAT
* *
12964992 AATTTT-ACTTTTACTAATTTAAAATTTTAATT-TTTTTAAA-GAACTAAAATAATAATTTT-TC
1 AATTTTAACTTTTAATAATTT-AAATTTT-ATTATTTTTAAATG-ACTAAAATAA-AATTTTATA
12965053 ATTTTAAAG
62 ATTTTAAAG
12965062 GGTCGAAGCA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
82 13 0.22
83 38 0.63
84 9 0.15
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (83 bp):
AATTTTAACTTTTAATAATTTAAATTTTATTATTTTTAAATGACTAAAATAAAATTTTATAATTT
TAAAGAAGGTTAAAGTAT
Found at i:12982942 original size:25 final size:26
Alignment explanation
Indices: 12982893--12982944 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
12982883 TTTAAAATAC
* * *
12982893 TTTTAAAATATTTTTTATTTTTTTAT
1 TTTTAAAATAATTTTTATATGTTTAT
12982919 TTTTAAAATAATTTTTA-ATGTTTAT
1 TTTTAAAATAATTTTTATATGTTTAT
12982944 T
1 T
12982945 AAAAAATGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTTAAAATAATTTTTATATGTTTAT
Found at i:12983381 original size:24 final size:24
Alignment explanation
Indices: 12983353--12983408 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
12983343 CATTCGATCA
12983353 AATCGAGTGGAAAACTTTCAAGAT
1 AATCGAGTGGAAAACTTTCAAGAT
*
12983377 AATCGAGTGGAAAATTTTCAAGAT
1 AATCGAGTGGAAAACTTTCAAGAT
12983401 AATCGAGT
1 AATCGAGT
12983409 TGACAAATCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (24 bp):
AATCGAGTGGAAAACTTTCAAGAT
Found at i:12983748 original size:18 final size:18
Alignment explanation
Indices: 12983725--12983763 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12983715 ACATCAATTT
12983725 ATTATTCAAATTATTAGA
1 ATTATTCAAATTATTAGA
* * *
12983743 ATTATTTAAGTTATTCGA
1 ATTATTCAAATTATTAGA
12983761 ATT
1 ATT
12983764 GTAAAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (18 bp):
ATTATTCAAATTATTAGA
Found at i:12986262 original size:22 final size:23
Alignment explanation
Indices: 12986237--12986284 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
12986227 ACAATAATTA
12986237 TTTTGTA-AAATAAATAAGATAT
1 TTTTGTACAAATAAATAAGATAT
* *
12986259 TTTTTTACAAATAAATGAGATAT
1 TTTTGTACAAATAAATAAGATAT
12986282 TTT
1 TTT
12986285 GACTTTATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (23 bp):
TTTTGTACAAATAAATAAGATAT
Found at i:12991783 original size:21 final size:20
Alignment explanation
Indices: 12991752--12991804 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
12991742 CTTGAATTTT
*
12991752 ATTTATTTTTTCA-TATTCAC
1 ATTTATTTTTTTATTATT-AC
*
12991772 ATTTATTTTTTTATTATTTC
1 ATTTATTTTTTTATTATTAC
12991792 ATTATATTTTTTT
1 ATT-TATTTTTTT
12991805 GACCCCTGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTATTTTTTTATTATTAC
Found at i:12992341 original size:20 final size:21
Alignment explanation
Indices: 12992316--12992372 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
12992306 TAAATGCTAC
12992316 TTATTCACAATTTTT-AATAA
1 TTATTCACAATTTTTAAATAA
*
12992336 TTATTCGCAATTTTTTTAAATAA
1 TTATTCACAA--TTTTTAAATAA
*
12992359 AT-TTCACAATTTTT
1 TTATTCACAATTTTT
12992373 GATGATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 14 0.45
22 11 0.35
23 6 0.19
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.53
Consensus pattern (21 bp):
TTATTCACAATTTTTAAATAA
Found at i:12992354 original size:22 final size:22
Alignment explanation
Indices: 12992319--12992372 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
12992309 ATGCTACTTA
*
12992319 TTCACAA--TTTTT-AATAATT
1 TTCACAATTTTTTTAAATAAAT
*
12992338 ATTCGCAATTTTTTTAAATAAAT
1 -TTCACAATTTTTTTAAATAAAT
12992361 TTCACAATTTTT
1 TTCACAATTTTT
12992373 GATGATCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 6 0.21
22 16 0.57
23 6 0.21
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (22 bp):
TTCACAATTTTTTTAAATAAAT
Found at i:12992479 original size:18 final size:19
Alignment explanation
Indices: 12992436--12992480 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
12992426 ACAATTTAAA
12992436 AATATTTTTAACAATATTT
1 AATATTTTTAACAATATTT
*
12992455 -ATTTTTTTAA-AAGT-TTT
1 AATATTTTTAACAA-TATTT
12992472 AATATTTTT
1 AATATTTTT
12992481 TTAATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
AATATTTTTAACAATATTT
Found at i:12992493 original size:12 final size:11
Alignment explanation
Indices: 12992468--12992516 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
12992458 TTTTTAAAAG
12992468 TTTTAATATTT
1 TTTTAATATTT
12992479 TTTTAATATTT
1 TTTTAATATTT
12992490 TTTT-ATATATT
1 TTTTAATAT-TT
* *
12992501 TTTAAATATTA
1 TTTTAATATTT
12992512 TTTTA
1 TTTTA
12992517 TGATTTTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 4 0.12
11 25 0.76
12 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTAATATTT
Found at i:12998450 original size:17 final size:17
Alignment explanation
Indices: 12998430--12998466 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
12998420 ATTACATATT
12998430 TTTAG-ATTTTTTAAGAA
1 TTTAGAATTTTTTAA-AA
12998447 TTTAGAATTTTTTAAAA
1 TTTAGAATTTTTTAAAA
12998464 TTT
1 TTT
12998467 TATCTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (17 bp):
TTTAGAATTTTTTAAAA
Found at i:12998468 original size:18 final size:18
Alignment explanation
Indices: 12998429--12998468 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12998419 TATTACATAT
12998429 TTTTAGATTTTTTAAGAA
1 TTTTAGATTTTTTAAGAA
12998447 -TTTAGAATTTTTTAA-AA
1 TTTTAG-ATTTTTTAAGAA
12998464 TTTTA
1 TTTTA
12998469 TCTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (18 bp):
TTTTAGATTTTTTAAGAA
Found at i:12998499 original size:32 final size:31
Alignment explanation
Indices: 12998447--12998533 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 31
12998437 TTTTTAAGAA
*
12998447 TTTAGAATTTTTTAAAATTTTAT-CTTTTAT-T
1 TTTAGAATTTTTT-ATATTTTATACTTTT-TCT
*
12998478 TTATAGAATTTTTATATATTTTTTACTTTTTCT
1 TT-TAGAATTTTT-TATATTTTATACTTTTTCT
* *
12998511 TTTTGAATTATTTATATTTTATA
1 TTTAGAATTTTTTATATTTTATA
12998534 TAATTTTTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
31 12 0.26
32 26 0.55
33 9 0.19
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (31 bp):
TTTAGAATTTTTTATATTTTATACTTTTTCT
Found at i:13002063 original size:2 final size:2
Alignment explanation
Indices: 13002056--13002082 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13002046 TTCTCATGTG
13002056 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
13002083 CAAAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13007560 original size:16 final size:17
Alignment explanation
Indices: 13007528--13007560 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
13007518 TCTCTAAGAA
13007528 ATTTGAATATCAAAATAT
1 ATTTGAATA-CAAAATAT
13007546 ATTTGAATA-AAAATA
1 ATTTGAATACAAAATA
13007561 AAAGCATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (17 bp):
ATTTGAATACAAAATAT
Found at i:13017944 original size:21 final size:21
Alignment explanation
Indices: 13017919--13017959 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13017909 GTATCCATAT
13017919 CCAGGATAACTCGGCATGTAG
1 CCAGGATAACTCGGCATGTAG
* *
13017940 CCAGGGTAACTTGGCATGTA
1 CCAGGATAACTCGGCATGTA
13017960 TCCATATCCA
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:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (21 bp):
CCAGGATAACTCGGCATGTAG
Found at i:13019497 original size:4 final size:4
Alignment explanation
Indices: 13019488--13019521 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
13019478 TGCTGATGAC
13019488 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
13019522 TTCATGGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:13020648 original size:20 final size:19
Alignment explanation
Indices: 13020612--13020687 Score: 82
Period size: 19 Copynumber: 3.8 Consensus size: 19
13020602 CTTTATATAT
13020612 TTTTTAAGAATATTTTTGAAA
1 TTTTTAA-AATA-TTTTGAAA
*
13020633 TTTTTATAAATATTTT-TAA
1 TTTTTA-AAATATTTTGAAA
*
13020652 TTTTAAAAAATATTTTGAAA
1 TTTT-TAAAATATTTTGAAA
13020672 TTTTTAAAATTATTTT
1 TTTTTAAAA-TATTTT
13020688 ATATTTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
19 19 0.40
20 17 0.36
21 10 0.21
22 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
TTTTTAAAATATTTTGAAA
Found at i:13020693 original size:19 final size:18
Alignment explanation
Indices: 13020607--13020695 Score: 63
Period size: 19 Copynumber: 4.5 Consensus size: 18
13020597 ACTTTCTTTA
13020607 TATATTTTTTAAGAATATTTT
1 TATA-TTTTTAA-AATA-TTT
*
13020628 TGAAATTTTTATAAATATTT
1 T-ATATTTTTA-AAATATTT
*
13020648 T-TAATTTTAAAAAATATTT
1 TAT-ATTTT-TAAAATATTT
*
13020667 TGAAATTTTTAAAATTATTT
1 T-ATATTTTTAAAA-TATTT
13020687 TATATTTTT
1 TATATTTTT
13020696 TTGTTGAGAG
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
19 25 0.45
20 16 0.29
21 11 0.20
22 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TATATTTTTAAAATATTT
Found at i:13029077 original size:19 final size:18
Alignment explanation
Indices: 13029053--13029109 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
13029043 TTTAAAAATA
13029053 TTTATTTTTACAAATTATT
1 TTTA-TTTTACAAATTATT
*
13029072 TTTATTTT-C--ATCATT
1 TTTATTTTACAAATTATT
*
13029087 TTTACTTTTACAAAATATT
1 TTTA-TTTTACAAATTATT
13029106 TTTA
1 TTTA
13029110 GTAGGAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 9 0.29
16 4 0.13
17 2 0.06
18 4 0.13
19 12 0.39
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTATTTTACAAATTATT
Found at i:13034748 original size:2 final size:2
Alignment explanation
Indices: 13034741--13034767 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13034731 GCTCTCCCCA
13034741 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
13034768 TTCAGTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:13055324 original size:39 final size:39
Alignment explanation
Indices: 13055281--13055361 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
13055271 AGCAAAACAA
* * *
13055281 TAATGGAAAGGAATCAAAGGATTGAGAATCAAATAAATG
1 TAATGGAAAGAAATCAAAAGATTGAGAATAAAATAAATG
*
13055320 TAATGGAAAGAAATCAAAAGATTGAGAATAAAATCAATG
1 TAATGGAAAGAAATCAAAAGATTGAGAATAAAATAAATG
13055359 TAA
1 TAA
13055362 ACAAGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (39 bp):
TAATGGAAAGAAATCAAAAGATTGAGAATAAAATAAATG
Found at i:13055355 original size:20 final size:20
Alignment explanation
Indices: 13055292--13055356 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
13055282 AATGGAAAGG
* *
13055292 AATCAAAGGATTGAGAATCA
1 AATCAAAAGATTGAGAATAA
* *
13055312 AAT-AAATGTAATG-GAA-AGA
1 AATCAAAAG-ATTGAGAATA-A
13055331 AATCAAAAGATTGAGAATAA
1 AATCAAAAGATTGAGAATAA
13055351 AATCAA
1 AATCAA
13055357 TGTAAACAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
19 14 0.40
20 20 0.57
21 1 0.03
ACGTcount: A:0.57, C:0.06, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCAAAAGATTGAGAATAA
Found at i:13060754 original size:19 final size:19
Alignment explanation
Indices: 13060730--13060786 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
13060720 ATTATGTTTT
13060730 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
13060749 TATATTATATTATATTATA
1 TATATTATATTATATTATA
13060768 TATA-TATA-TATA-TATA
1 TATATTATATTATATTATA
13060784 TAT
1 TAT
13060787 TTTCTAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.19
17 4 0.11
18 9 0.24
19 17 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:13060764 original size:10 final size:10
Alignment explanation
Indices: 13060702--13060787 Score: 72
Period size: 10 Copynumber: 8.4 Consensus size: 10
13060692 AAAAAAATAT
13060702 TATTATATTA
1 TATTATATTA
*
13060712 TAGTAATGATTA
1 TA-TTAT-ATTA
*
13060724 TGTT-T-TTA
1 TATTATATTA
13060732 TATTATATTA
1 TATTATATTA
13060742 TTATTA-A-TA
1 -TATTATATTA
13060751 TATTATATTA
1 TATTATATTA
13060761 TATTATATATA
1 TATTATAT-TA
13060772 TATATATATATA
1 TAT-TATAT-TA
13060784 TATT
1 TATT
13060788 TTCTAAATTC
Statistics
Matches: 63, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
8 11 0.17
9 4 0.06
10 17 0.27
11 15 0.24
12 16 0.25
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (10 bp):
TATTATATTA
Found at i:13060769 original size:2 final size:2
Alignment explanation
Indices: 13060730--13060786 Score: 58
Period size: 2 Copynumber: 32.5 Consensus size: 2
13060720 ATTATGTTTT
13060730 TA TA T- TA TA T- TA T- TA T- TA -A TA TA T- TA TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13060764 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
13060787 TTTCTAAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
1 8 0.17
2 39 0.83
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:13060777 original size:8 final size:8
Alignment explanation
Indices: 13060730--13060786 Score: 58
Period size: 7 Copynumber: 8.1 Consensus size: 8
13060720 ATTATGTTTT
13060730 TATAT-TA
1 TATATATA
13060737 TAT-TAT-
1 TATATATA
13060743 TAT-TA-A
1 TATATATA
13060749 TATAT-TA
1 TATATATA
13060756 TAT-TATA
1 TATATATA
13060763 T-TATATA
1 TATATATA
13060770 TATATATA
1 TATATATA
13060778 TATATATA
1 TATATATA
13060786 T
1 T
13060787 TTTCTAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
6 11 0.26
7 17 0.40
8 15 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TATATATA
Found at i:13067653 original size:14 final size:14
Alignment explanation
Indices: 13067630--13067660 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13067620 TGTCGCGTTC
*
13067630 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
13067644 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
13067658 TTA
1 TTA
13067661 AAAAAATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:13073204 original size:18 final size:18
Alignment explanation
Indices: 13073167--13073205 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
13073157 CGATAGTGAC
* * *
13073167 TAATTTAAAAAATTATAT
1 TAATTAAAAAAACTAAAT
13073185 TAATTAAAAAAACTAAAT
1 TAATTAAAAAAACTAAAT
13073203 TAA
1 TAA
13073206 CAAAAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATTAAAAAAACTAAAT
Found at i:13115565 original size:274 final size:275
Alignment explanation
Indices: 13115066--13115614 Score: 1091
Period size: 274 Copynumber: 2.0 Consensus size: 275
13115056 TTCAAAAAAT
13115066 GTATTAAAATTTTAATAAATAATTATAATAATATTAAAGTTGTATAAGAAAAATTGAAATCCTGC
1 GTATTAAAATTTTAATAAATAATTATAATAATATTAAAGTTGTATAAGAAAAATTGAAATCCTGC
13115131 TTGTGGCTAAAAGTTTGGGCTGTCACCTGCAGGTGCACGTGTGATTCCATTCCTAGTGTTAATGT
66 TTGTGGCTAAAAGTTTGGGCTGTCACCTGCAGGTGCACGTGTGATTCCATTCCTAGTGTTAATGT
13115196 CCCTTCACTACTCTGTTGGTGCTTTGGTTCAGTGGTGAAGAAGGGAATTGATGCTTCTTCATTGT
131 CCCTTCACTACTCTGTTGGTGCTTTGGTTCAGTGGTGAAGAAGGGAATTGATGCTTCTTCATTGT
13115261 TGGTATTTAGAAGGAGCTCCTTCTATTCTGTATAAAGGAATGCAAAACTCTTGTTTTGGTGTTTT
196 TGGTATTTAGAAGGAGCTCCTTCTATTCTGTATAAAGGAATGCAAAACTCTTGTTTTGGTGTTTT
13115326 GTATTGTTGGGTTTG
261 GTATTGTTGGGTTTG
13115341 GTATTAAAA-TTTAATAAATAATTATAATAATATTAAAGTTGTATAAGAAAAATTGAAATCCTGC
1 GTATTAAAATTTTAATAAATAATTATAATAATATTAAAGTTGTATAAGAAAAATTGAAATCCTGC
13115405 TTGTGGCTAAAAGTTTGGGCTGTCACCTGCAGGTGCACGTGTGATTCCATTCCTAGTGTTAATGT
66 TTGTGGCTAAAAGTTTGGGCTGTCACCTGCAGGTGCACGTGTGATTCCATTCCTAGTGTTAATGT
13115470 CCCTTCACTACTCTGTTGGTGCTTTGGTTCAGTGGTGAAGAAGGGAATTGATGCTTCTTCATTGT
131 CCCTTCACTACTCTGTTGGTGCTTTGGTTCAGTGGTGAAGAAGGGAATTGATGCTTCTTCATTGT
13115535 TGGTATTTAGAAGGAGCTCCTTCTATTCTGTATAAAGGAATGCAAAACTCTTGTTTTGGTGTTTT
196 TGGTATTTAGAAGGAGCTCCTTCTATTCTGTATAAAGGAATGCAAAACTCTTGTTTTGGTGTTTT
13115600 GTATTGTTGGGTTTG
261 GTATTGTTGGGTTTG
13115615 TTAGTAGAAG
Statistics
Matches: 274, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
274 265 0.97
275 9 0.03
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (275 bp):
GTATTAAAATTTTAATAAATAATTATAATAATATTAAAGTTGTATAAGAAAAATTGAAATCCTGC
TTGTGGCTAAAAGTTTGGGCTGTCACCTGCAGGTGCACGTGTGATTCCATTCCTAGTGTTAATGT
CCCTTCACTACTCTGTTGGTGCTTTGGTTCAGTGGTGAAGAAGGGAATTGATGCTTCTTCATTGT
TGGTATTTAGAAGGAGCTCCTTCTATTCTGTATAAAGGAATGCAAAACTCTTGTTTTGGTGTTTT
GTATTGTTGGGTTTG
Found at i:13116413 original size:247 final size:246
Alignment explanation
Indices: 13116027--13116674 Score: 824
Period size: 247 Copynumber: 2.7 Consensus size: 246
13116017 TATTATTATT
* *** *
13116027 ATTATTATCGATCACTAAAAA-ATATATATATTTGACCATGGTAATTAAAATTATCTACAACAAA
1 ATTATTATCTATCACTAAAAATA-ATATATATTTGACCACAATAATTAAAATCATCTACAACAAA
* *
13116091 ATATATAAGGATATTTTAGTTGGCCGTTAAAACCGTTATCACTCTCACTCACTATAATAAACGCA
65 ATATATAAGGATATTTTAGTTGGCCGTTAAAACCGTTATCACTCTCACTCACTAAAATAAACACA
* * * *
13116156 TATCTTGATCGATAAATTGTTTGAATAAATTCACAATTATATTTTAATTGATCATTAAAATAAAT
130 TATCTTGATCGATAAATTGTTTAAATAAATTCACAATTATATTTTAATTAACCATTAAAACAAAT
* *
13116221 TAGATTTACAATATAAATGCATAACGATATTTTAACAACCATTAAAATCATC
195 TAGATTTACAAGATAAATGCATAACGACATTTTAACAACCATTAAAATCATC
* *
13116273 ATTATTATCTATCACTAAAAATAATATATATTTGGCCACAATAATTAAAATCATCTATAACAAAA
1 ATTATTATCTATCACTAAAAATAATATATATTTGACCACAATAATTAAAATCATCTACAACAAAA
* *
13116338 TATAGTAAGGATATTTTAGTTGGCCGTTAAAACCTTTATTACTCTCACTCACTAAAATAAACACA
66 TATA-TAAGGATATTTTAGTTGGCCGTTAAAACCGTTATCACTCTCACTCACTAAAATAAACACA
* *
13116403 TATTTTGATCGATAAATTGTTTAAATAAATTCACAATTATATTTTAATTAACCGTTAAAACAAAT
130 TATCTTGATCGATAAATTGTTTAAATAAATTCACAATTATATTTTAATTAACCATTAAAACAAAT
* * * *
13116468 TAGATTTATAAGATAAATGCATAATGACATTTTAACAATCATTAAAATCATT
195 TAGATTTACAAGATAAATGCATAACGACATTTTAACAACCATTAAAATCATC
13116520 ATTATTATCTATCACTAAAAATAATATATA--T-----C------T---A-CA---AC-A-AA-A
1 ATTATTATCTATCACTAAAAATAATATATATTTGACCACAATAATTAAAATCATCTACAACAAAA
* * * *
13116562 TATATAAGAATATTTTAGTTGACCGTTAAAACCGTTATTACTATCTA-TCACTAAAATAAACACA
66 TATATAAGGATATTTTAGTTGGCCGTTAAAACCGTTATCACTCTC-ACTCACTAAAATAAACACA
* * *
13116626 TATTTTTATCGATAAATTGTTTAAATAAGTTCACAATTATATTTTAATT
130 TATCTTGATCGATAAATTGTTTAAATAAATTCACAATTATATTTTAATT
13116675 GAAAATGCAT
Statistics
Matches: 369, Mismatches: 30, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
223 101 0.27
224 6 0.02
225 2 0.01
226 1 0.00
227 1 0.00
230 2 0.01
231 1 0.00
234 1 0.00
240 1 0.00
245 1 0.00
246 60 0.16
247 192 0.52
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (246 bp):
ATTATTATCTATCACTAAAAATAATATATATTTGACCACAATAATTAAAATCATCTACAACAAAA
TATATAAGGATATTTTAGTTGGCCGTTAAAACCGTTATCACTCTCACTCACTAAAATAAACACAT
ATCTTGATCGATAAATTGTTTAAATAAATTCACAATTATATTTTAATTAACCATTAAAACAAATT
AGATTTACAAGATAAATGCATAACGACATTTTAACAACCATTAAAATCATC
Found at i:13121586 original size:22 final size:19
Alignment explanation
Indices: 13121535--13121587 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 19
13121525 TACCATGTTT
*
13121535 ATTAAAATATTTATTTTTA
1 ATTAAAATATTGATTTTTA
13121554 ATTAATCAATATTGATTTTATA
1 ATTAA--AATATTGATTTT-TA
13121576 ATCATAAAATAT
1 AT--TAAAATAT
13121588 ATATAACTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 5 0.18
21 11 0.39
22 9 0.32
24 3 0.11
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTAAAATATTGATTTTTA
Found at i:13124725 original size:2 final size:2
Alignment explanation
Indices: 13124718--13124747 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13124708 CAAATGATGC
13124718 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13124748 CCATAGATAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13129165 original size:17 final size:17
Alignment explanation
Indices: 13129143--13129183 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
13129133 TTGGGTTAGA
*
13129143 GAAACTTGAACCTACCC
1 GAAACTCGAACCTACCC
13129160 GAAACTCGAACCTACCC
1 GAAACTCGAACCTACCC
13129177 GAAACTC
1 GAAACTC
13129184 CACTGCTTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.37, G:0.12, T:0.15
Consensus pattern (17 bp):
GAAACTCGAACCTACCC
Found at i:13131405 original size:103 final size:103
Alignment explanation
Indices: 13131226--13131435 Score: 420
Period size: 103 Copynumber: 2.0 Consensus size: 103
13131216 CGATGTTCCT
13131226 AAGAATGAGAAGATATCATGAAGCAAATGGGTAATAATAAATAAGGAAATGAGAGTTTGCTTAAA
1 AAGAATGAGAAGATATCATGAAGCAAATGGGTAATAATAAATAAGGAAATGAGAGTTTGCTTAAA
13131291 CTTGAGAATTGGAGCCATGAAAGATATAAAGAAATACA
66 CTTGAGAATTGGAGCCATGAAAGATATAAAGAAATACA
13131329 AAGAATGAGAAGATATCATGAAGCAAATGGGTAATAATAAATAAGGAAATGAGAGTTTGCTTAAA
1 AAGAATGAGAAGATATCATGAAGCAAATGGGTAATAATAAATAAGGAAATGAGAGTTTGCTTAAA
13131394 CTTGAGAATTGGAGCCATGAAAGATATAAAGAAATACA
66 CTTGAGAATTGGAGCCATGAAAGATATAAAGAAATACA
13131432 AAGA
1 AAGA
13131436 GACAGATCCT
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.49, C:0.07, G:0.22, T:0.22
Consensus pattern (103 bp):
AAGAATGAGAAGATATCATGAAGCAAATGGGTAATAATAAATAAGGAAATGAGAGTTTGCTTAAA
CTTGAGAATTGGAGCCATGAAAGATATAAAGAAATACA
Found at i:13135453 original size:29 final size:29
Alignment explanation
Indices: 13135398--13135453 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
13135388 ATAATACAAA
* **
13135398 AATATTTACCAAACTAATATATGTTTTAC
1 AATACTTACCAAACTAATATAAATTTTAC
* *
13135427 AATACTTACCAAATTAGTATAAATTTT
1 AATACTTACCAAACTAATATAAATTTT
13135454 GTTGGAGGAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (29 bp):
AATACTTACCAAACTAATATAAATTTTAC
Found at i:13138578 original size:51 final size:51
Alignment explanation
Indices: 13138501--13138617 Score: 198
Period size: 51 Copynumber: 2.3 Consensus size: 51
13138491 CGGATCACAT
* *
13138501 TTATCACTTGTCACTTGTCACCGATCAGTTAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACCGATCAGATAAGTGCAGCTAAAGCTACCAC
* *
13138552 TTATCACTTGTTACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACCGATCAGATAAGTGCAGCTAAAGCTACCAC
13138603 TTATCACTTGTCACT
1 TTATCACTTGTCACT
13138618 GATCAGAAGT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACCGATCAGATAAGTGCAGCTAAAGCTACCAC
Found at i:13150283 original size:16 final size:16
Alignment explanation
Indices: 13150262--13150292 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13150252 TCAATGAAAG
13150262 ATTTAGATAGCTTAGA
1 ATTTAGATAGCTTAGA
*
13150278 ATTTAGATAGTTTAG
1 ATTTAGATAGCTTAG
13150293 GCAGAGCCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.19, T:0.42
Consensus pattern (16 bp):
ATTTAGATAGCTTAGA
Found at i:13166932 original size:42 final size:42
Alignment explanation
Indices: 13166869--13166948 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
13166859 TATTTTCGTC
13166869 CACACGGCCAGAGACACGGGCGTGT-GTCTCAGCCGTGTATGA
1 CACACGGCCAGAGACACGGGCGTGTAGTCT-AGCCGTGTATGA
* * *
13166911 CACACGGCCTG-GCACATGGGCGTGTAGTCTGGCCGTGT
1 CACACGGCCAGAG-ACACGGGCGTGTAGTCTAGCCGTGT
13166949 GTCCCCTGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 1 0.03
42 28 0.85
43 4 0.12
ACGTcount: A:0.17, C:0.29, G:0.35, T:0.19
Consensus pattern (42 bp):
CACACGGCCAGAGACACGGGCGTGTAGTCTAGCCGTGTATGA
Found at i:13171477 original size:32 final size:32
Alignment explanation
Indices: 13171427--13171487 Score: 90
Period size: 30 Copynumber: 1.9 Consensus size: 32
13171417 TATATCATAA
13171427 ATTATAAAAAAAAATTCTAACTA-TACATTTT
1 ATTATAAAAAAAAATTCTAACTACTACATTTT
13171458 ATTA-AAAAAAAAACTTTCTAACTACTACAT
1 ATTATAAAAAAAAA--TTCTAACTACTACAT
13171488 ATAATCAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 9 0.33
31 4 0.15
32 9 0.33
33 5 0.19
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (32 bp):
ATTATAAAAAAAAATTCTAACTACTACATTTT
Found at i:13176275 original size:27 final size:27
Alignment explanation
Indices: 13176245--13176306 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
13176235 ATTAACAATT
13176245 AATTAATTTTTTAAAATTTAAAAAAAA
1 AATTAATTTTTTAAAATTTAAAAAAAA
* * * **
13176272 AATTAATTTTTTTAATTTTACAAAATT
1 AATTAATTTTTTAAAATTTAAAAAAAA
13176299 AATTAATT
1 AATTAATT
13176307 ACTTATGCGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
AATTAATTTTTTAAAATTTAAAAAAAA
Found at i:13189945 original size:2 final size:2
Alignment explanation
Indices: 13189938--13189975 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
13189928 GGGCATTGCG
13189938 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
13189976 ATATATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:13189980 original size:2 final size:2
Alignment explanation
Indices: 13189975--13190006 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13189965 TCTCTCTCTC
13189975 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13190007 CACGTTGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13190672 original size:60 final size:60
Alignment explanation
Indices: 13190579--13190701 Score: 237
Period size: 60 Copynumber: 2.0 Consensus size: 60
13190569 CCGGCAGTCA
*
13190579 TGGGATTTAAAGGAGGGACAAAGTTCCGCACCTCCCACCGTGGAACTGCAGCATATCAAC
1 TGGGATTTAAAGGAGGCACAAAGTTCCGCACCTCCCACCGTGGAACTGCAGCATATCAAC
13190639 TGGGATTTAAAGGAGGCACAAAGTTCCGCACCTCCCACCGTGGAACTGCAGCATATCAAC
1 TGGGATTTAAAGGAGGCACAAAGTTCCGCACCTCCCACCGTGGAACTGCAGCATATCAAC
13190699 TGG
1 TGG
13190702 TGTGTTTTAG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (60 bp):
TGGGATTTAAAGGAGGCACAAAGTTCCGCACCTCCCACCGTGGAACTGCAGCATATCAAC
Found at i:13190893 original size:4 final size:4
Alignment explanation
Indices: 13190884--13190908 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
13190874 TGTGAGTATC
13190884 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
13190909 ATCCGAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:13196552 original size:13 final size:13
Alignment explanation
Indices: 13196531--13196591 Score: 86
Period size: 13 Copynumber: 4.7 Consensus size: 13
13196521 ACATTCAAAT
*
13196531 TTTTCAAAAGCAC
1 TTTTCAAAAACAC
*
13196544 TTCTCAAAAACAC
1 TTTTCAAAAACAC
* *
13196557 TTTTCCACAACAC
1 TTTTCAAAAACAC
13196570 TTTTCAAAAACAC
1 TTTTCAAAAACAC
13196583 TTTTCAAAA
1 TTTTCAAAA
13196592 GCAATGAAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.41, C:0.26, G:0.02, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAACAC
Found at i:13198621 original size:24 final size:25
Alignment explanation
Indices: 13198569--13198626 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
13198559 TTTTAATAAT
* *
13198569 ATTATTTTT-AAAATTTAAACTTAC
1 ATTATTTTTAAAAATATAAACATAC
13198593 ATTATTTTTAAAAATATAAA-ATAC
1 ATTATTTTTAAAAATATAAACATAC
* *
13198617 CTTATCTTTA
1 ATTATTTTTA
13198627 GAGTCAACCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTATTTTTAAAAATATAAACATAC
Found at i:13199107 original size:2 final size:2
Alignment explanation
Indices: 13199100--13199129 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13199090 AAATACATCA
13199100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13199130 TTAGTTTTCT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13199584 original size:5 final size:5
Alignment explanation
Indices: 13199574--13199606 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
13199564 AAGTCCTTGA
*
13199574 GATGT GATGT GATGT GATGT GATGT GAAGT GAT
1 GATGT GATGT GATGT GATGT GATGT GATGT GAT
13199607 TAATCCTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.36
Consensus pattern (5 bp):
GATGT
Found at i:13199954 original size:29 final size:29
Alignment explanation
Indices: 13199905--13199967 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
13199895 AGATGCACCA
13199905 AAGTGCAATAACTAAACAGAATGACA-TCG
1 AAGTGCAATAACTAAACAGAATGACACT-G
* *
13199934 AAGTGCAATATC-ATAATAGAATGACACTG
1 AAGTGCAATAACTA-AACAGAATGACACTG
13199963 AAGTG
1 AAGTG
13199968 TTTTAGCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 28 0.93
30 1 0.03
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.21
Consensus pattern (29 bp):
AAGTGCAATAACTAAACAGAATGACACTG
Found at i:13202787 original size:31 final size:31
Alignment explanation
Indices: 13202721--13202801 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
13202711 TTTTAATAGT
* * *
13202721 AGAGTGACTAAAACTAACAACTTAATTGATG
1 AGAGTGACTAAAATTAACAACTTAATTAATA
* *
13202752 AGAGTGACTAAAATTGATAACTT-ATCTAATA
1 AGAGTGACTAAAATTAACAACTTAAT-TAATA
*
13202783 AGAGTAACTAAAA-TAACAA
1 AGAGTGACTAAAATTAACAA
13202802 ATTTTTTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 6 0.15
31 35 0.85
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (31 bp):
AGAGTGACTAAAATTAACAACTTAATTAATA
Found at i:13203579 original size:3 final size:3
Alignment explanation
Indices: 13203571--13203634 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
13203561 TAGTTCAGCT
13203571 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
13203619 GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA G
13203635 GTGGTGCCGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:13204047 original size:37 final size:37
Alignment explanation
Indices: 13203921--13204058 Score: 111
Period size: 37 Copynumber: 3.7 Consensus size: 37
13203911 AACTAATATT
* **
13203921 ATTATTATGGTTAGTTATTAGGATTAGTAAAAACCCTA
1 ATTATTATTGTTAGTTATTATTATTAGT-AAAACCCTA
* *** * *
13203959 ATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTA-CATT
1 ATTATTATTGTTAGTTA-T-T-ATTATTAG-TAAAACCCTA
*
13203998 A-TATTATTGTTAGTTATTATTTTTAGTAAAACCCTA
1 ATTATTATTGTTAGTTATTATTATTAGTAAAACCCTA
*
13204034 ATTATTATTGTTAGTTAGTATTATT
1 ATTATTATTGTTAGTTATTATTATT
13204059 TTAGGTAAAA
Statistics
Matches: 76, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
35 2 0.03
36 10 0.13
37 29 0.38
38 17 0.22
39 11 0.14
40 6 0.08
41 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.51
Consensus pattern (37 bp):
ATTATTATTGTTAGTTATTATTATTAGTAAAACCCTA
Found at i:13204079 original size:76 final size:78
Alignment explanation
Indices: 13203875--13204093 Score: 216
Period size: 76 Copynumber: 2.8 Consensus size: 78
13203865 GTTTAGTTAT
* * *
13203875 TAATAATTATTGTTACTTAGTATTATTGTTA-GAAAAAACTAATATTATTATTATGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGGTAAAAA--AATATTATTA-T-T-GTTAGTTAT
**
13203939 TAGGATTAGTAAAAACCC
61 TATTATTAGTAAAAACCC
* * *** * * *
13203957 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTACATTA-TATTATTGTTAGTTATTATTT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGGTAAAAAAATATTATTATTGTTAGTTATTATTA
13204020 TTAGT-AAAACCC
66 TTAGTAAAAACCC
* *
13204032 TAATTATTATTGTTAGTTAGTATTATT-TTAGGTAAAAAAACATTATTATTATTA-TTATTATT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGGTAAAAAAATATTATTATTGTTAGTTATTATT
13204094 GTGTTAGTTA
Statistics
Matches: 112, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
75 34 0.30
76 40 0.36
77 1 0.01
78 1 0.01
79 5 0.04
80 3 0.03
81 17 0.15
82 11 0.10
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.50
Consensus pattern (78 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTAGGTAAAAAAATATTATTATTGTTAGTTATTATTA
TTAGTAAAAACCC
Found at i:13209439 original size:154 final size:153
Alignment explanation
Indices: 13209158--13209659 Score: 714
Period size: 154 Copynumber: 3.3 Consensus size: 153
13209148 ACTTCAAAAC
* *
13209158 AAATTTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCATATTTTTTCCCCTAGATTTTATTACTT
1 AAATTTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTT-CCCGA-ATTTTATTACTT
* * * *
13209223 TCAAAAAATTTACTATTTTCTAATTTTATTATTTTACATTATTTTAGTATATTATGTTTGAAATG
64 TCAAAAAATATACTATTTTTTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATG
* * * * *
13209288 TATTAATTAATTTTATTTTTTAAAT
129 TATTAATTTAGTGTGTTTTTTATAT
*
13209313 AAATTTAGTAAAAAACCCTTATTTCGACCCTTTGTTCGTATTTATTTCCCGAATTTTATTACTTT
1 AAATTTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTT-TTTCCCGAATTTTATTACTTT
*
13209378 CAAAAAATATACTATTTTTTAATTTTCTAATTTTACATTATTTTAGTACATTATGTTTGAAATGT
65 CAAAAAATATACTATTTTTTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGT
*
13209443 ATTAATTTAGTGTGCTTTTTATAT
130 ATTAATTTAGTGTGTTTTTTATAT
*
13209467 AAATTTAGTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGTATTTTATTACTT
1 AAATTTAGT-AAAAAACCCTTATTTCGGCCCTTTGTTCGTA-TTTTTTCCCGAATTTTATTACTT
*
13209532 TC-AAAAA-ATA-TA----TT-ATTTTCTTATCTTACATTATTTTAGTACATTATGTTTGAAATG
64 TCAAAAAATATACTATTTTTTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATG
13209589 TATTAATTTAGTGTGTGTTTTTATAT
129 TATTAATTTAGTGTGT-TTTTTATAT
** * *
13209615 AAATTTAGTAAAAAACTTTTATTTTGGCCATTTGTTCGTATTTTT
1 AAATTTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTT
13209660 CTTATTTTCA
Statistics
Matches: 320, Mismatches: 23, Indels: 17
0.89 0.06 0.05
Matches are distributed among these distances:
146 5 0.02
147 83 0.26
148 20 0.06
152 2 0.01
153 3 0.01
154 105 0.33
155 96 0.30
156 6 0.02
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (153 bp):
AAATTTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGAATTTTATTACTTTC
AAAAAATATACTATTTTTTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTA
TTAATTTAGTGTGTTTTTTATAT
Found at i:13209649 original size:147 final size:149
Alignment explanation
Indices: 13209158--13209659 Score: 679
Period size: 155 Copynumber: 3.3 Consensus size: 149
13209148 ACTTCAAAAC
* *
13209158 AAATTTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCATA-TTTTTTCCCCTAGATTTTATTACT
1 AAATTTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGT--ATTTTATTACT
* *
13209222 TTCAAAAAATTTACTATTTTCTAATTTTATTATTTTACATTATTTTAGTATATTATGTTTGAAAT
64 TTCAAAAAA--TACTA--TT-TAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAAT
* * * * *
13209287 GTATTAATTAATTTTATTTTTTAAAT
124 GTATTAATTTAGTGTGTTTTTTATAT
* * *
13209313 AAATTTAGTAAAAAACCCTTATTTCGACCCTTTGTTCGTATTTATTTCCCGAATTTTATTACTTT
1 AAATTTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGTATTTTATTACTTT
*
13209378 CAAAAAATATACTATTTTTTAATTTTCTAATTTTACATTATTTTAGTACATTATGTTTGAAATGT
66 C-AAAAA-ATACTA---TTTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGT
*
13209443 ATTAATTTAGTGTGCTTTTTATAT
126 ATTAATTTAGTGTGTTTTTTATAT
13209467 AAATTTAGTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGTATTTTATTACTT
1 AAATTTAGT-AAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGTATTTTATTACTT
*
13209532 TCAAAAAATA-TA-TT-ATTTTCTTATCTTACATTATTTTAGTACATTATGTTTGAAATGTATTA
65 TCAAAAAATACTATTTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTA
13209594 ATTTAGTGTGTGTTTTTATAT
130 ATTTAGTGTGT-TTTTTATAT
** * *
13209615 AAATTTAGTAAAAAACTTTTATTTTGGCCATTTGTTCGTATTTTT
1 AAATTTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTT
13209660 CTTATTTTCA
Statistics
Matches: 317, Mismatches: 24, Indels: 20
0.88 0.07 0.06
Matches are distributed among these distances:
147 88 0.28
148 20 0.06
152 2 0.01
153 3 0.01
154 94 0.30
155 101 0.32
156 9 0.03
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (149 bp):
AAATTTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGTATTTTATTACTTT
CAAAAAATACTATTTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAA
TTTAGTGTGTTTTTTATAT
Found at i:13210071 original size:13 final size:13
Alignment explanation
Indices: 13210047--13210075 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
13210037 TTCTTTCTTT
13210047 TTCTTTCTTCTCC
1 TTCTTTCTTCTCC
13210060 TTCTTTCTTCTCC
1 TTCTTTCTTCTCC
13210073 TTC
1 TTC
13210076 AGCCGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
TTCTTTCTTCTCC
Found at i:13210154 original size:27 final size:27
Alignment explanation
Indices: 13210105--13210166 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
13210095 ATATAAGAGG
* * *
13210105 CTGGTGCCGCCTGTGGCAGTGGCACCT
1 CTGGTGCCGCCTCTGCCACTGGCACCT
*
13210132 TTGGTGCCGCCTCTGCCACTGGCACCT
1 CTGGTGCCGCCTCTGCCACTGGCACCT
13210159 CTGGTGCC
1 CTGGTGCC
13210167 TCCTGTGGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.06, C:0.37, G:0.32, T:0.24
Consensus pattern (27 bp):
CTGGTGCCGCCTCTGCCACTGGCACCT
Found at i:13211777 original size:22 final size:22
Alignment explanation
Indices: 13211729--13211777 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
13211719 CATGTTTAAT
*
13211729 TTTTTTTTCATTATTAAAAATA
1 TTTTTTTTCATTACTAAAAATA
* *
13211751 CTTTTTTTCATTACCT-AACATA
1 TTTTTTTTCATTA-CTAAAAATA
13211773 TTTTT
1 TTTTT
13211778 CAATTTTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTTTTTCATTACTAAAAATA
Found at i:13213415 original size:125 final size:122
Alignment explanation
Indices: 13213192--13213442 Score: 439
Period size: 125 Copynumber: 2.0 Consensus size: 122
13213182 AACCCCCAAT
13213192 AGTAAAGACATACCCTGTGAGAGATCTTTTATCAAGGTCTCCAACAAAATCAGAATCAACATACT
1 AGTAAAGACATACCCTGTGAGAGATCTTTTATCAAGGTCTCCAACAAAATCAGAATCAACATACT
*
13213257 CAATGACTCCATCTCTAGTTCTTCCAAACTGTAAGAAAATATCAGTAGTACATCGTA
66 CAATGACTCCATCTCTAGTTCTTCCAAACTGTAAGAAAATATCAGTAATACATCGTA
*
13213314 AGTAAAGACATACCCTGTGAGAGATCTTCTTTTATCAATGTCTCCAACAAAATCAGAATCAACAT
1 AGTAAAGACATACCCTGTGAGAGA---TCTTTTATCAAGGTCTCCAACAAAATCAGAATCAACAT
* *
13213379 ACTCAATGACTCCATCTCTAGTTCTTCCAAATTGTAAGAAAATATCAGTAATATATCGTA
63 ACTCAATGACTCCATCTCTAGTTCTTCCAAACTGTAAGAAAATATCAGTAATACATCGTA
13213439 AGTA
1 AGTA
13213443 TCTGAAAATC
Statistics
Matches: 122, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
122 24 0.20
125 98 0.80
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (122 bp):
AGTAAAGACATACCCTGTGAGAGATCTTTTATCAAGGTCTCCAACAAAATCAGAATCAACATACT
CAATGACTCCATCTCTAGTTCTTCCAAACTGTAAGAAAATATCAGTAATACATCGTA
Found at i:13225869 original size:9 final size:9
Alignment explanation
Indices: 13225855--13225908 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
13225845 ATTCACATCC
13225855 TTCTCTCAA
1 TTCTCTCAA
13225864 TTCTCTCAAA
1 TTCTCTC-AA
13225874 TTCTCTCAAA
1 TTCTCTC-AA
* *
13225884 CTGTCTCAA
1 TTCTCTCAA
*
13225893 GTCTCTCAA
1 TTCTCTCAA
*
13225902 CTCTCTC
1 TTCTCTC
13225909 GTTTTTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
9 22 0.56
10 17 0.44
ACGTcount: A:0.22, C:0.35, G:0.04, T:0.39
Consensus pattern (9 bp):
TTCTCTCAA
Found at i:13225890 original size:12 final size:10
Alignment explanation
Indices: 13225855--13225901 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
13225845 ATTCACATCC
13225855 TTCTCTC-AA
1 TTCTCTCAAA
13225864 TTCTCTCAAA
1 TTCTCTCAAA
13225874 TTCTCTCAAA
1 TTCTCTCAAA
* *
13225884 CTGTCTC-AA
1 TTCTCTCAAA
*
13225893 GTCTCTCAA
1 TTCTCTCAA
13225902 CTCTCTCGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 14 0.44
10 18 0.56
ACGTcount: A:0.26, C:0.32, G:0.04, T:0.38
Consensus pattern (10 bp):
TTCTCTCAAA
Found at i:13229006 original size:13 final size:14
Alignment explanation
Indices: 13228968--13229006 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
13228958 TTTATTTAGT
*
13228968 AAATATGTATTTTTA
1 AAATATATA-TTTTA
13228983 AAATATATATTTTA
1 AAATATATATTTTA
13228997 AAAT-TATATT
1 AAATATATATT
13229007 ATTTATGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (14 bp):
AAATATATATTTTA
Found at i:13231824 original size:20 final size:20
Alignment explanation
Indices: 13231786--13231824 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13231776 TATTACTCAC
*
13231786 TTTATCATTTTAAATATTTT
1 TTTATCATTTTAAAGATTTT
13231806 TTTATCA-TTTATAAGATTT
1 TTTATCATTTTA-AAGATTT
13231825 ATCACATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTATCATTTTAAAGATTTT
Found at i:13238143 original size:6 final size:6
Alignment explanation
Indices: 13238134--13238166 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
13238124 ATGATATGAT
13238134 TATTAA TATTAA TATTAA TATTAA TATTAA TAT
1 TATTAA TATTAA TATTAA TATTAA TATTAA TAT
13238167 ATTATTATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATTAA
Found at i:13249847 original size:21 final size:21
Alignment explanation
Indices: 13249771--13249856 Score: 68
Period size: 21 Copynumber: 4.1 Consensus size: 21
13249761 TTTTGATATA
* **
13249771 TTTTATAATTTTTACGAATTT
1 TTTTATAACTTTTAATAATTT
* *
13249792 TTTAGAAAAC-TTTAAT-ATTT
1 TTT-TATAACTTTTAATAATTT
**
13249812 TTTTATTAAAGTTTAATAATTT
1 TTTTA-TAACTTTTAATAATTT
*
13249834 TTTTATAACTTTTATTAATTT
1 TTTTATAACTTTTAATAATTT
13249855 TT
1 TT
13249857 ATTTTTTTAT
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
19 1 0.02
20 9 0.18
21 28 0.56
22 12 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTTATAACTTTTAATAATTT
Found at i:13250031 original size:23 final size:23
Alignment explanation
Indices: 13249988--13250032 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
13249978 ACCCAAGTAA
* *
13249988 TTAAAAAAAACTTAATTACTTTT
1 TTAAAAAAAAATTAATAACTTTT
*
13250011 TTAAAAAAAAATTGATAACTTT
1 TTAAAAAAAAATTAATAACTTT
13250033 ATTGCCGTAT
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:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (23 bp):
TTAAAAAAAAATTAATAACTTTT
Found at i:13268679 original size:23 final size:22
Alignment explanation
Indices: 13268635--13268683 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
13268625 AATAAAGTAT
13268635 TTGAGAGAATTGATGAATAGGA
1 TTGAGAGAATTGATGAATAGGA
13268657 TTGAGAGAATTAAGA-GAATAGGA
1 TTGAGAGAATT--GATGAATAGGA
13268680 TTGA
1 TTGA
13268684 ATGAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 11 0.44
23 12 0.48
24 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTGATGAATAGGA
Found at i:13268776 original size:19 final size:18
Alignment explanation
Indices: 13268728--13268776 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
13268718 AAATTAACCA
13268728 TTGGAAAAATAAGTAATCG
1 TTGGAAAAA-AAGTAATCG
*
13268747 TT-GAAAGAAAAGGTTATCG
1 TTGGAAA-AAAA-GTAATCG
13268766 TTGGAAAAAAA
1 TTGGAAAAAAA
13268777 AAAGGTTGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 6 0.23
19 16 0.62
20 4 0.15
ACGTcount: A:0.49, C:0.04, G:0.22, T:0.24
Consensus pattern (18 bp):
TTGGAAAAAAAGTAATCG
Found at i:13272010 original size:15 final size:16
Alignment explanation
Indices: 13271985--13272018 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
13271975 TGAGAAGTTT
13271985 TTTTTTGTTAAAAAGG
1 TTTTTTGTTAAAAAGG
*
13272001 TTTTTT-TTAAGAAGG
1 TTTTTTGTTAAAAAGG
13272016 TTT
1 TTT
13272019 GGAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (16 bp):
TTTTTTGTTAAAAAGG
Found at i:13272923 original size:264 final size:266
Alignment explanation
Indices: 13272440--13272972 Score: 1034
Period size: 264 Copynumber: 2.0 Consensus size: 266
13272430 TTTATTATTA
13272440 TATGTATATATATATATAAATGTTTCTTTTGTATGTATTTATACCTTAAAAATTAATATTTCTTG
1 TATGTATATATATATATAAATGTTTCTTTTGTATGTATTTATACCTTAAAAATTAATATTTCTTG
13272505 TATATTTTTTTAAATACATGTTTTATTAATTTTGATACTATTTAATTATTTTAAATTTATATATT
66 TATATTTTTTTAAATACATGTTTTATTAATTTTGATACTATTTAATTATTTTAAATTTATATATT
13272570 TTCTTGGGTACATGTATATTTTTTTTTGTTTATTTCAATCATCTGTTTATTAATTTAGGTTTACA
131 TTCTTGGGTACATGTATATTTTTTTTTGTTTATTTCAATCATCTGTTTATTAATTTAGGTTTACA
13272635 TATTTTTATCTTGTCCATTTATTTAATATTCTGCAGGCCATTA-TTTATTTATTTGTTCATATAT
196 TATTTTTATCTTGTCCATTTATTTAATATTCTGCAGGCCATTATTTTATTTATTTGTTCATATAT
13272699 TTGTAT
261 TTGTAT
13272705 TATGTATATATA-ATATAAATGTTTCTTTTGTATGTATTTATACCTTAAAAATTAATATTTCTTG
1 TATGTATATATATATATAAATGTTTCTTTTGTATGTATTTATACCTTAAAAATTAATATTTCTTG
13272769 TATATTTTTTTAAATACATGTTTTATTAATTTTGATACTATTTAATTATTTTAAATTTATATATT
66 TATATTTTTTTAAATACATGTTTTATTAATTTTGATACTATTTAATTATTTTAAATTTATATATT
13272834 TTCTTGGGTACATGTATATTTTTTTTTGTTTATTTCAATCATCTGTTTATTAATTTAGGTTTACA
131 TTCTTGGGTACATGTATATTTTTTTTTGTTTATTTCAATCATCTGTTTATTAATTTAGGTTTACA
* *
13272899 TATTTTTATCTTGTCCATTTATTTAATATTTTGCAGGCCATTATTTTATTTATTTGTTCGTATAT
196 TATTTTTATCTTGTCCATTTATTTAATATTCTGCAGGCCATTATTTTATTTATTTGTTCATATAT
13272964 TTGTAT
261 TTGTAT
13272970 TAT
1 TAT
13272973 TTCTATGCTA
Statistics
Matches: 265, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
264 224 0.85
265 41 0.15
ACGTcount: A:0.28, C:0.07, G:0.08, T:0.57
Consensus pattern (266 bp):
TATGTATATATATATATAAATGTTTCTTTTGTATGTATTTATACCTTAAAAATTAATATTTCTTG
TATATTTTTTTAAATACATGTTTTATTAATTTTGATACTATTTAATTATTTTAAATTTATATATT
TTCTTGGGTACATGTATATTTTTTTTTGTTTATTTCAATCATCTGTTTATTAATTTAGGTTTACA
TATTTTTATCTTGTCCATTTATTTAATATTCTGCAGGCCATTATTTTATTTATTTGTTCATATAT
TTGTAT
Found at i:13273301 original size:98 final size:98
Alignment explanation
Indices: 13273178--13273372 Score: 318
Period size: 98 Copynumber: 2.0 Consensus size: 98
13273168 AAAAATCATG
* *
13273178 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTAGGTGTGGTTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTAGGTGTGATTTCTT
*
13273243 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
66 AAATCTTGGATAAGTGGATGTTCCTTTAAAGTA
* * * *
13273276 AAGGAAATATTTCGATTTTGAGATTCTAAAGGGATCGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTAGGTGTGATTTCTT
*
13273341 AAATCTTGGATGAGTGGATGTTCCTTTAAAGT
66 AAATCTTGGATAAGTGGATGTTCCTTTAAAGT
13273373 TTTATTGTAT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTAGGTGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCCTTTAAAGTA
Found at i:13273792 original size:7 final size:7
Alignment explanation
Indices: 13273780--13273810 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
13273770 AAGAGGAAGA
13273780 AATAAAG
1 AATAAAG
13273787 AATAAAG
1 AATAAAG
13273794 AATAAAG
1 AATAAAG
13273801 AATAAAG
1 AATAAAG
13273808 AAT
1 AAT
13273811 TTGAGAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (7 bp):
AATAAAG
Found at i:13275302 original size:134 final size:134
Alignment explanation
Indices: 13275056--13275369 Score: 396
Period size: 134 Copynumber: 2.3 Consensus size: 134
13275046 AACTGTTCAT
* * * * * *
13275056 GATCGTAAATCAACAAGTTTTAATAATATCAGTCGTGATCATAATTCTGCAAACCGTTTGAATGA
1 GATCATAAATCAACAAGTTTTAATAATACCAGTCGTGATCGTAAATCAGCAAACCGTTTGAATAA
* * * * *
13275121 AGTTGTGGTCGTAAATCAGTAAACTCAAAATAAATTGTTCATGATCGTAAATCAATGAACTTAAG
66 AGTTGCGATCGTAAATCAGTAAACTCAAAATAAACTGTTCATAATCGTAAATCAATGAACTTAAA
13275186 TTGC
131 TTGC
* * * * **
13275190 GATCTTAAATCAAAAAGCTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTTTTTGAATAA
1 GATCATAAATCAACAAGTTTTAATAATACCAGTCGTGATCGTAAATCAGCAAACCGTTTGAATAA
* * * *
13275255 AGTTGCGATTGTAAATTAG-AGAACTCAAAATGAACTGTTCATAATCGTAAATCAGTGAACTTAA
66 AGTTGCGATCGTAAATCAGTA-AACTCAAAATAAACTGTTCATAATCGTAAATCAATGAACTTAA
*
13275319 ATTGT
130 ATTGC
* *
13275324 GATCATAAATCAACAAGTTTTAATAATACCAGTTGTGATTGTAAAT
1 GATCATAAATCAACAAGTTTTAATAATACCAGTCGTGATCGTAAAT
13275370 TGACGAACTA
Statistics
Matches: 153, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
133 1 0.01
134 152 0.99
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (134 bp):
GATCATAAATCAACAAGTTTTAATAATACCAGTCGTGATCGTAAATCAGCAAACCGTTTGAATAA
AGTTGCGATCGTAAATCAGTAAACTCAAAATAAACTGTTCATAATCGTAAATCAATGAACTTAAA
TTGC
Found at i:13275401 original size:99 final size:99
Alignment explanation
Indices: 13275255--13275477 Score: 313
Period size: 99 Copynumber: 2.3 Consensus size: 99
13275245 TTTTGAATAA
* * * *
13275255 AGTTGCGATTGTAAATTAGAGAACTCAAAATGAACTGTTCATAATCGTAAATCAGTGAACTTAAA
1 AGTTGTGATTGTAAATTAGAGAACTAAAAATAAACTGTTCATAATCGTAAATCAATGAACTTAAA
*
13275320 TTGTGATCATAAATCAACAAGTTTTAATAATACC
66 TTGTGATCATAAATCAACAAGCTTTAATAATACC
* * *
13275354 AGTTGTGATTGTAAATT-GACGAACTAAAAATAAATTGTTCGTGATCGTAAATCAATGAACTTAA
1 AGTTGTGATTGTAAATTAGA-GAACTAAAAATAAACTGTTCATAATCGTAAATCAATGAACTTAA
* *
13275418 GTTGTGATTATAAATCAACAAGCTTTAATAATACC
65 ATTGTGATCATAAATCAACAAGCTTTAATAATACC
* * *
13275453 AGTCGTGATTGTAAATCAGTGAACT
1 AGTTGTGATTGTAAATTAGAGAACT
13275478 GTTTGAATGG
Statistics
Matches: 109, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
98 2 0.02
99 106 0.97
100 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (99 bp):
AGTTGTGATTGTAAATTAGAGAACTAAAAATAAACTGTTCATAATCGTAAATCAATGAACTTAAA
TTGTGATCATAAATCAACAAGCTTTAATAATACC
Found at i:13275435 original size:233 final size:232
Alignment explanation
Indices: 13275142--13275586 Score: 651
Period size: 233 Copynumber: 1.9 Consensus size: 232
13275132 TAAATCAGTA
*
13275142 AACTCAAAATAAATTGTTCATGATCGTAAATCAATGAACTTAAGTTGCGATCTTAAATCAAAAAG
1 AACTAAAAATAAATTGTTCATGATCGTAAATCAATGAACTTAAGTTGCGATCTTAAATCAAAAAG
* ** *
13275207 CTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTTTTTGAATAAAGTTGCGATTGTAAATT
66 CTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTGAATAAAGTTGCGACCGTAAATC
* * *
13275272 AGAGAACTCAAAATGAACTGTTCATAATCGTAAATCAGTGAACTTAAATTGTGATCA-TAAATCA
131 AGAGAACTCAAAATGAACTATTCATAATCGTAAATCAATGAACTT-AAGTGTGAT-ATTAAATCA
*
13275336 ACAAGTTTTAATAATACCAGTTGTGATTGTAAATTGACG
194 ACAAGCTTTAATAATACCAGTTGTGATTGTAAATTGACG
* * *
13275375 AACTAAAAATAAATTGTTCGTGATCGTAAATCAATGAACTTAAGTTGTGAT-TATAAATCAACAA
1 AACTAAAAATAAATTGTTCATGATCGTAAATCAATGAACTTAAGTTGCGATCT-TAAATCAAAAA
* * ** *
13275439 GCTTTAATAATACCAGTCGTGATTGTAAATCAGTGAACTGTTTGAATGGAGTTGTGACCGTAAAT
65 GCTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTGAATAAAGTTGCGACCGTAAAT
* * * * *
13275504 CAGTGAACTCAAAATGAATTATTCATGATCGTAAATCAATTAACTTAAGTGTGATATTAAATTAA
130 CAGAGAACTCAAAATGAACTATTCATAATCGTAAATCAATGAACTTAAGTGTGATATTAAATCAA
13275569 CAAGCTTTAATAATACCA
195 CAAGCTTTAATAATACCA
13275587 TTCATAATCA
Statistics
Matches: 188, Mismatches: 22, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
231 1 0.01
232 33 0.18
233 154 0.82
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (232 bp):
AACTAAAAATAAATTGTTCATGATCGTAAATCAATGAACTTAAGTTGCGATCTTAAATCAAAAAG
CTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTGAATAAAGTTGCGACCGTAAATC
AGAGAACTCAAAATGAACTATTCATAATCGTAAATCAATGAACTTAAGTGTGATATTAAATCAAC
AAGCTTTAATAATACCAGTTGTGATTGTAAATTGACG
Found at i:13275533 original size:134 final size:134
Alignment explanation
Indices: 13275374--13276003 Score: 710
Period size: 134 Copynumber: 4.7 Consensus size: 134
13275364 GTAAATTGAC
* * * * * *
13275374 GAACTAAAAATAAATTGTTCGTGATCGTAAATCAATGAACTTAAGTTGTGATTATAAATCAACAA
1 GAACTCAAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAGTTGTGATTATAAATCAGCAA
* ** *
13275439 GCTTTAATAATACCAGTCGTGATTGTAAATCAGTGAACTGTTTGAATGGAGTTGTGACCGTAAAT
66 GCTTTAATAATACCAGTCGTGATTGTAAATCAGCGAACTGTTTGAATGGAGTTGCAATCGTAAAT
13275504 CAGT
131 CAGT
* * * * *
13275508 GAACTCAAAATGAATTATTCATGATCGTAAATCAATTAACTTAAG-TGTGA-TATTAAATTAACA
1 GAACTCAAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAGTTGTGATTA-TAAATCAGCA
* * * ** *
13275571 AGCTTTAATAATACCATTCATAATCATAAATCAGCGAACTGTTTGAATGGAGTTGCAATTGTAAA
65 AGCTTTAATAATACCAGTCGTGATTGTAAATCAGCGAACTGTTTGAATGGAGTTGCAATCGTAAA
*
13275636 TC-GA
130 TCAGT
* * * * ** *
13275640 CAAGCTCAAAATTAACTGTTAATGGTCGTAAATCAATAAACTTAAGTTGTGATCGTAAATCAGTA
1 GAA-CTCAAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAGTTGTGATTATAAATCAGCA
* * * * * *
13275705 AGCTTTAATAATACTAGTTGTGATTGTAAATCAGTGAACTTTTTGAATGGAGTTGCGATTGTAAA
65 AGCTTTAATAATACCAGTCGTGATTGTAAATCAGCGAACTGTTTGAATGGAGTTGCAATCGTAAA
** *
13275770 TTGGC
130 TCAGT
* * * * *
13275775 GAACTCAAAATGAACTGTTTATGATCATAAATTAATAAACCTAAGCTGTGA-TAGTAAATCAGCA
1 GAACTCAAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAGTTGTGATTA-TAAATCAGCA
* * * * * *
13275839 AGCTTTAATAATTCTAGTCGTGATTGTAAATCAGCGAATTGTTTGAATGGAGATGCAATCATGAA
65 AGCTTTAATAATACCAGTCGTGATTGTAAATCAGCGAACTGTTTGAATGGAGTTGCAATCGTAAA
13275904 TCAGT
130 TCAGT
* * * *
13275909 GAACTCATAATGAACTGGTCATGATCGTAAATCAATGAACTTAAGTTGTGATTGTAAATCAGCAA
1 GAACTCAAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAGTTGTGATTATAAATCAGCAA
* *
13275974 GCTTTAATAATACCAGTTGTGATCGTAAAT
66 GCTTTAATAATACCAGTCGTGATTGTAAAT
13276004 ACCCGAACTC
Statistics
Matches: 411, Mismatches: 78, Indels: 14
0.82 0.16 0.03
Matches are distributed among these distances:
132 5 0.01
133 107 0.26
134 295 0.72
135 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (134 bp):
GAACTCAAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAGTTGTGATTATAAATCAGCAA
GCTTTAATAATACCAGTCGTGATTGTAAATCAGCGAACTGTTTGAATGGAGTTGCAATCGTAAAT
CAGT
Found at i:13275734 original size:366 final size:367
Alignment explanation
Indices: 13275061--13275735 Score: 949
Period size: 366 Copynumber: 1.8 Consensus size: 367
13275051 TTCATGATCG
* * * *
13275061 TAAATCAACAAGTTTTAATAATATCAGTCGTGATCATAATTCTGCAAACCGTTTGAATGAAGTTG
1 TAAATCAACAAGCTTTAATAATACCAGTCGTGATCATAAATCAGCAAACCGTTTGAATGAAGTTG
** *
13275126 TGGTCGTAAATCAGTAAACTCAAAATAAATTGTTCATGATCGTAAATCAATGAACTTAAGTTGCG
66 TGACCGTAAATCAGTAAACTCAAAATAAATTATTCATGATCGTAAATCAATGAACTTAAGTTGCG
* * * * *
13275191 ATCTTAAATCAAAAAGCTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTTTTTGAATAAA
131 ATATTAAATCAAAAAGCTTTAATAATACCAGTCATAATCATAAATCAGCGAACTGTTTGAATAAA
* * * * *
13275256 GTTGCGATTGTAAATTAGAGAACTCAAAATGAACTGTTCATAATCGTAAATCAGTGAACTTAAAT
196 GTTGCAATTGTAAATTAGACAACTCAAAATGAACTGTTAATAATCGTAAATCAATAAACTTAAAT
*
13275321 TGTGATCATAAATCAACAAGTTTTAATAATACCAGTTGTGATTGTAAATTGACGAACTAAAAATA
261 TGTGATCATAAATCAACAAGCTTTAATAATACCAGTTGTGATTGTAAATTGACGAACTAAAAATA
13275386 AATTGTTCGTGATCGTAAATCAATGAACTTAAGTTGTGATTA
326 AATTGTTCGTGATCGTAAATCAATGAACTTAAGTTGTGATTA
** ** * *
13275428 TAAATCAACAAGCTTTAATAATACCAGTCGTGATTGTAAATCAGTGAACTGTTTGAATGGAGTTG
1 TAAATCAACAAGCTTTAATAATACCAGTCGTGATCATAAATCAGCAAACCGTTTGAATGAAGTTG
* * * *
13275493 TGACCGTAAATCAGTGAACTCAAAATGAATTATTCATGATCGTAAATCAATTAACTTAAG-TGTG
66 TGACCGTAAATCAGTAAACTCAAAATAAATTATTCATGATCGTAAATCAATGAACTTAAGTTGCG
* * * **
13275557 ATATTAAATTAACAAGCTTTAATAATACCATTCATAATCATAAATCAGCGAACTGTTTGAATGGA
131 ATATTAAATCAAAAAGCTTTAATAATACCAGTCATAATCATAAATCAGCGAACTGTTTGAATAAA
* * ** *
13275622 GTTGCAATTGTAAA-TCGACAAGCTCAAAATTAACTGTTAATGGTCGTAAATCAATAAACTTAAG
196 GTTGCAATTGTAAATTAGACAA-CTCAAAATGAACTGTTAATAATCGTAAATCAATAAACTTAAA
* ** *
13275686 TTGTGATCGTAAATCAGTAAGCTTTAATAATACTAGTTGTGATTGTAAAT
260 TTGTGATCATAAATCAACAAGCTTTAATAATACCAGTTGTGATTGTAAAT
13275736 CAGTGAACTT
Statistics
Matches: 265, Mismatches: 42, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
365 5 0.02
366 151 0.57
367 109 0.41
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (367 bp):
TAAATCAACAAGCTTTAATAATACCAGTCGTGATCATAAATCAGCAAACCGTTTGAATGAAGTTG
TGACCGTAAATCAGTAAACTCAAAATAAATTATTCATGATCGTAAATCAATGAACTTAAGTTGCG
ATATTAAATCAAAAAGCTTTAATAATACCAGTCATAATCATAAATCAGCGAACTGTTTGAATAAA
GTTGCAATTGTAAATTAGACAACTCAAAATGAACTGTTAATAATCGTAAATCAATAAACTTAAAT
TGTGATCATAAATCAACAAGCTTTAATAATACCAGTTGTGATTGTAAATTGACGAACTAAAAATA
AATTGTTCGTGATCGTAAATCAATGAACTTAAGTTGTGATTA
Found at i:13275959 original size:268 final size:267
Alignment explanation
Indices: 13275395--13276003 Score: 797
Period size: 268 Copynumber: 2.3 Consensus size: 267
13275385 AAATTGTTCG
* * *
13275395 TGATCGTAAATCAATGAACTTAAGTTGTGATTATAAATCAACAAGCTTTAATAATACCAGTCGTG
1 TGATCGTAAATCAATGAACTTAAGTTGTGATTGTAAATCAGCAAGCTTTAATAATACCAGTTGTG
* * *
13275460 ATTGTAAATCAGTGAACTGTTTGAATGGAGTTGTGACCGTAAATCAGTGAACTCAAAATGAATTA
66 ATTGTAAATCAGTGAACTGTTTGAATGGAGTTGCGACCGTAAATCAGCGAACTCAAAATGAACTA
* * * * * *
13275525 TTCATGATCGTAAATCAATTAACTTAAGTGTGATATTAAATTAACAAGCTTTAATAATACCATTC
131 TTCATGATCATAAATCAATAAACCTAAGTGTGATAGTAAATCAACAAGCTTTAATAATACCAGTC
* ** *
13275590 ATAATCATAAATCAGCGAACTGTTTGAATGGAGTTGCAATTGTAAATCGACAAGCTCAAAATTAA
196 ATAATCATAAATCAGCGAACTGTTTGAATGGAGATGCAATCATAAATCGACAAGCTCAAAATGAA
*
13275655 CTGTTAA
261 CTGGTAA
* * * * *
13275662 TGGTCGTAAATCAATAAACTTAAGTTGTGATCGTAAATCAGTAAGCTTTAATAATACTAGTTGTG
1 TGATCGTAAATCAATGAACTTAAGTTGTGATTGTAAATCAGCAAGCTTTAATAATACCAGTTGTG
* ** ** *
13275727 ATTGTAAATCAGTGAACTTTTTGAATGGAGTTGCGATTGTAAATTGGCGAACTCAAAATGAACTG
66 ATTGTAAATCAGTGAACTGTTTGAATGGAGTTGCGACCGTAAATCAGCGAACTCAAAATGAACTA
* * * * *
13275792 TTTATGATCATAAATTAATAAACCTAAGCTGTGATAGTAAATCAGCAAGCTTTAATAATTCTAGT
131 TTCATGATCATAAATCAATAAACCTAAG-TGTGATAGTAAATCAACAAGCTTTAATAATACCAGT
* * ** * * ** *
13275857 CGTGATTGTAAATCAGCGAATTGTTTGAATGGAGATGCAATCATGAATCAGTGAA-CTCATAATG
195 CATAATCATAAATCAGCGAACTGTTTGAATGGAGATGCAATCATAAATC-GACAAGCTCAAAATG
*
13275921 AACTGGTCA
259 AACTGGTAA
13275930 TGATCGTAAATCAATGAACTTAAGTTGTGATTGTAAATCAGCAAGCTTTAATAATACCAGTTGTG
1 TGATCGTAAATCAATGAACTTAAGTTGTGATTGTAAATCAGCAAGCTTTAATAATACCAGTTGTG
*
13275995 ATCGTAAAT
66 ATTGTAAAT
13276004 ACCCGAACTC
Statistics
Matches: 291, Mismatches: 49, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
267 136 0.47
268 152 0.52
269 3 0.01
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (267 bp):
TGATCGTAAATCAATGAACTTAAGTTGTGATTGTAAATCAGCAAGCTTTAATAATACCAGTTGTG
ATTGTAAATCAGTGAACTGTTTGAATGGAGTTGCGACCGTAAATCAGCGAACTCAAAATGAACTA
TTCATGATCATAAATCAATAAACCTAAGTGTGATAGTAAATCAACAAGCTTTAATAATACCAGTC
ATAATCATAAATCAGCGAACTGTTTGAATGGAGATGCAATCATAAATCGACAAGCTCAAAATGAA
CTGGTAA
Found at i:13286476 original size:196 final size:193
Alignment explanation
Indices: 13286136--13286544 Score: 649
Period size: 196 Copynumber: 2.1 Consensus size: 193
13286126 AATTCAATAC
* *
13286136 ATACATTCGGCTAACATATATGTAATTCATTAAATTTCATTCAACTTACAAAACTCAGCATATAT
1 ATACATTCGGCTAACATATATGGAATTCATTAAATTTCATTCAACTTACAAAACCCAGC--A-AT
* * *
13286201 ATATATTCGGCTAAATATATATAGAATTTATGCAATTTATTTTATCTTATAAGACTCAAATATAC
63 ATATATTCAGCTAAATATATATAGAATTTATGCAATTTATTTTAACTTATAAAACTCAAATATAC
*
13286266 ATTGACTAACACATATATATATATACAATTCATATATTTTATTTTAACTTATAAAATTCAAAACA
128 ATTGACTAACAC----ATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACA
13286331 TATAT
189 TATAT
*
13286336 ATACATTTGGCTAACATATATGGAATTCATTAAATTTCATTCAACTTACAAAACCCAGC-ATATA
1 ATACATTCGGCTAACATATATGGAATTCATTAAATTTCATTCAACTTACAAAACCCAGCAATATA
* * * *
13286400 TATTCAGCTAAATATATATCGAATTTCTGGAATTTATTTTAACTTATAAAACTTAAATATACATT
66 TATTCAGCTAAATATATATAGAATTTATGCAATTTATTTTAACTTATAAAACTCAAATATACATT
13286465 GACTAACACATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACATATAT
131 GACTAACACATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACATATAT
13286528 ATACATTCGGCTAACAT
1 ATACATTCGGCTAACAT
13286545 TTTTATACAA
Statistics
Matches: 197, Mismatches: 12, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
192 69 0.35
196 72 0.37
200 56 0.28
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.38
Consensus pattern (193 bp):
ATACATTCGGCTAACATATATGGAATTCATTAAATTTCATTCAACTTACAAAACCCAGCAATATA
TATTCAGCTAAATATATATAGAATTTATGCAATTTATTTTAACTTATAAAACTCAAATATACATT
GACTAACACATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACATATAT
Found at i:13287540 original size:13 final size:13
Alignment explanation
Indices: 13287522--13287546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13287512 ACAAACGATA
13287522 AAATTTTCACACG
1 AAATTTTCACACG
13287535 AAATTTTCACAC
1 AAATTTTCACAC
13287547 AAGTAAATTC
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:13296793 original size:84 final size:84
Alignment explanation
Indices: 13296648--13296953 Score: 290
Period size: 84 Copynumber: 3.6 Consensus size: 84
13296638 TCATTGTAAC
* * * *
13296648 AGGCTTAGTAGTGGTAGGA-AGCAGACTGGTTGCAAGAATCTGAGTGGTTGCATGCTAGTTTAGG
1 AGGCTTAGTAGTGGTAGGAGA-CAAACTGGTTGCAAGAATTTGAGTGGTTGCTTGCTGGTTTAGG
* *
13296712 GTCTTAATTATTGATGCATG
65 GCCTTAATTGTTGATGCATG
* * * * *
13296732 AGGCTTAGTAGTGGTAGGAGACAAACTGGTTGTAGGAGTTTGGGTGGTTGCTTACTGGTTTAGGG
1 AGGCTTAGTAGTGGTAGGAGACAAACTGGTTGCAAGAATTTGAGTGGTTGCTTGCTGGTTTAGGG
* * *
13296797 CCTTAGTGGTTGATGCAAG
66 CCTTAATTGTTGATGCATG
* * * * **** ** * * *
13296816 AAGCTTAATGGTGGTAGGAGGCCGGTTGGTTTTAGGAGTTTGAGTGATTGCTTGCTGGTTTAGGG
1 AGGCTTAGTAGTGGTAGGAGACAAACTGGTTGCAAGAATTTGAGTGGTTGCTTGCTGGTTTAGGG
* * *
13296881 CCTCAATTGTTGCTACATG
66 CCTTAATTGTTGATGCATG
* * **
13296900 AGGCTTAGTGGTGGTAGGAGGCAATTTGGTTGCAAGAATTTGAGTGGTTGCTTG
1 AGGCTTAGTAGTGGTAGGAGACAAACTGGTTGCAAGAATTTGAGTGGTTGCTTG
13296954 TTGGCTTGTT
Statistics
Matches: 179, Mismatches: 42, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
84 178 0.99
85 1 0.01
ACGTcount: A:0.21, C:0.10, G:0.36, T:0.33
Consensus pattern (84 bp):
AGGCTTAGTAGTGGTAGGAGACAAACTGGTTGCAAGAATTTGAGTGGTTGCTTGCTGGTTTAGGG
CCTTAATTGTTGATGCATG
Found at i:13298027 original size:20 final size:20
Alignment explanation
Indices: 13298002--13298040 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
13297992 AAGTAGTGTT
13298002 TAAGACTAGTGCCAATTGCG
1 TAAGACTAGTGCCAATTGCG
13298022 TAAGACTAGTGCCAATTGC
1 TAAGACTAGTGCCAATTGC
13298041 TTTAGGCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (20 bp):
TAAGACTAGTGCCAATTGCG
Found at i:13299215 original size:13 final size:13
Alignment explanation
Indices: 13299197--13299227 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13299187 TAAAATTATA
*
13299197 AAAAAATATTTTT
1 AAAAAATATCTTT
13299210 AAAAAATATCTTT
1 AAAAAATATCTTT
13299223 AAAAA
1 AAAAA
13299228 CTTTTATAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAAAATATCTTT
Found at i:13299372 original size:37 final size:37
Alignment explanation
Indices: 13299308--13299423 Score: 151
Period size: 37 Copynumber: 3.1 Consensus size: 37
13299298 TTACAAAACT
* * * * *
13299308 TTTGTAGAGAATCTTCACTCTTAATCTCCGTCTTTTC
1 TTTGCAGAGAATCTTTACTGTTGATCTCCATCTTTTC
*
13299345 TTTGCAGATAATCTTTACTGTTGATCTCCATCTTTTC
1 TTTGCAGAGAATCTTTACTGTTGATCTCCATCTTTTC
* * *
13299382 TTTGCATAGAATCTTTATTGTTGATCTCCATTTTTTC
1 TTTGCAGAGAATCTTTACTGTTGATCTCCATCTTTTC
13299419 TTTGC
1 TTTGC
13299424 TTGTCTTGGC
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50
Consensus pattern (37 bp):
TTTGCAGAGAATCTTTACTGTTGATCTCCATCTTTTC
Found at i:13299511 original size:37 final size:37
Alignment explanation
Indices: 13299425--13299511 Score: 95
Period size: 37 Copynumber: 2.4 Consensus size: 37
13299415 TTTCTTTGCT
* *
13299425 TGTCTTGGCTTTGCAAGGAACCACCTCAGTTCATTTC
1 TGTCTTTGCTTTGCAAGGAACCACCTCAGTTCATCTC
* * * * *
13299462 TATCTTTACTTTGCAAGGAATCACCCTTA-TTTATCTC
1 TGTCTTTGCTTTGCAAGGAACCA-CCTCAGTTCATCTC
13299499 TGTCTTTGCTTTG
1 TGTCTTTGCTTTG
13299512 TTGCAAAACA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
37 36 0.90
38 4 0.10
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (37 bp):
TGTCTTTGCTTTGCAAGGAACCACCTCAGTTCATCTC
Found at i:13305671 original size:13 final size:13
Alignment explanation
Indices: 13305602--13305661 Score: 84
Period size: 13 Copynumber: 4.5 Consensus size: 13
13305592 TCATACATCT
13305602 ATTTCCATATAACC
1 ATTT-CATATAACC
*
13305616 AATTCATATAACC
1 ATTTCATATAACC
* *
13305629 ATTTCATGTAATC
1 ATTTCATATAACC
13305642 ATTTCATATAACC
1 ATTTCATATAACC
13305655 ATTTCAT
1 ATTTCAT
13305662 TCACACATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
13 37 0.93
14 3 0.08
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.40
Consensus pattern (13 bp):
ATTTCATATAACC
Found at i:13305671 original size:39 final size:41
Alignment explanation
Indices: 13305602--13305686 Score: 104
Period size: 39 Copynumber: 2.1 Consensus size: 41
13305592 TCATACATCT
*
13305602 ATTTCCATATAACCAATTCATATAACCATTT-CATGTAATC
1 ATTTCCATATAACCAATTCATATAACCATTTACACGTAATC
* *
13305642 ATTT-CATATAACCATTTCAT-TCACACATTTAACACGTAATC
1 ATTTCCATATAACCAATTCATATAAC-CATTT-ACACGTAATC
13305683 ATTT
1 ATTT
13305687 TGTATATCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
38 3 0.08
39 20 0.51
40 4 0.10
41 12 0.31
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.39
Consensus pattern (41 bp):
ATTTCCATATAACCAATTCATATAACCATTTACACGTAATC
Found at i:13307652 original size:25 final size:25
Alignment explanation
Indices: 13307620--13307667 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
13307610 ACAAATTGTA
*
13307620 ATTTAT-AAATATTTAATAATTTACT
1 ATTTATAAAATA-TGAATAATTTACT
13307645 ATTTATAAAATATGAATAATTTA
1 ATTTATAAAATATGAATAATTTA
13307668 ATACCATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
ATTTATAAAATATGAATAATTTACT
Found at i:13319097 original size:32 final size:32
Alignment explanation
Indices: 13319044--13319106 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
13319034 AAATTATAAC
* * *
13319044 TATTCAAGTGATATTACTTGAATAGTTATGTT
1 TATTCAAGAGATATTAATTGAATAATTATGTT
*
13319076 TATTTAAGAGATATTAATTGAATAATTATGT
1 TATTCAAGAGATATTAATTGAATAATTATGT
13319107 CTCTTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (32 bp):
TATTCAAGAGATATTAATTGAATAATTATGTT
Found at i:13322666 original size:22 final size:22
Alignment explanation
Indices: 13322636--13322677 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
13322626 AACAGTTCAA
13322636 TATTAAAAAAATAAAA-AAAAGG
1 TATT-AAAAAATAAAATAAAAGG
*
13322658 TATTTAAAAATAAAATAAAA
1 TATTAAAAAATAAAATAAAA
13322678 TAATACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (22 bp):
TATTAAAAAATAAAATAAAAGG
Found at i:13326260 original size:23 final size:23
Alignment explanation
Indices: 13326232--13326279 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
13326222 TTCTTGATTA
13326232 ATGGCTC-CCCGAAGCTTCCCGAT
1 ATGGCTCGCCCGAA-CTTCCCGAT
**
13326255 ATGGCTCGCTTGAACTTCCCGAT
1 ATGGCTCGCCCGAACTTCCCGAT
13326278 AT
1 AT
13326280 ATGGCTATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.19, C:0.33, G:0.21, T:0.27
Consensus pattern (23 bp):
ATGGCTCGCCCGAACTTCCCGAT
Found at i:13326308 original size:25 final size:24
Alignment explanation
Indices: 13326244--13326308 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
13326234 GGCTCCCCGA
* *
13326244 AGCTTCCCGAT-ATGGCTCGCTTG
1 AGCTTCCCGATAATGGCTAGCTGG
* *
13326267 AACTTCCCGATATATGGCTATCTGG
1 AGCTTCCCGATA-ATGGCTAGCTGG
13326292 AGCTTCCCGATTAATGG
1 AGCTTCCCGA-TAATGG
13326309 TTTTTTGGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 10 0.29
25 22 0.65
26 2 0.06
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (24 bp):
AGCTTCCCGATAATGGCTAGCTGG
Found at i:13326416 original size:25 final size:25
Alignment explanation
Indices: 13326365--13326428 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
13326355 AGCTCTTATG
**
13326365 AGCTTCCCGTTATACAGCTAGGGTA
1 AGCTTCCCGTTATACAGCTAGCATA
13326390 AGCTTCCCGTTATACAGCTCA-CATA
1 AGCTTCCCGTTATACAGCT-AGCATA
13326415 AGC-TCCCTGTTATA
1 AGCTTCCC-GTTATA
13326429 TGGCTCGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 4 0.11
25 30 0.86
26 1 0.03
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (25 bp):
AGCTTCCCGTTATACAGCTAGCATA
Found at i:13327271 original size:19 final size:21
Alignment explanation
Indices: 13327237--13327282 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 21
13327227 ATGCATAAGA
13327237 CTTGGATTTGGCTTGGTTTAAATGT
1 CTTGGA-TTGGCTT-G--TAAATGT
13327262 CTTGGATTGGCTTGTAAATGT
1 CTTGGATTGGCTTGTAAATGT
13327283 GATAAAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
23 1 0.05
24 7 0.33
25 6 0.29
ACGTcount: A:0.17, C:0.09, G:0.28, T:0.46
Consensus pattern (21 bp):
CTTGGATTGGCTTGTAAATGT
Found at i:13341406 original size:43 final size:42
Alignment explanation
Indices: 13341341--13341444 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 42
13341331 AAAAAAACAT
* *
13341341 AATAAAAT--AAAAT-AAAAGATATAAATTTAGAAAATAAAA
1 AATAAAATAAAAAATAAAAATATATAAATATAGAAAATAAAA
*
13341380 GAT-AAATAAAGAAACTAAAAATATATAAATATAGAAAATAAAA
1 AATAAAATAAA-AAA-TAAAAATATATAAATATAGAAAATAAAA
13341423 AATAAAATAAAAAATAAAAATA
1 AATAAAATAAAAAATAAAAATA
13341445 GGGCTTGGGA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
38 4 0.07
39 2 0.04
40 1 0.02
41 3 0.05
42 9 0.16
43 29 0.53
44 7 0.13
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (42 bp):
AATAAAATAAAAAATAAAAATATATAAATATAGAAAATAAAA
Found at i:13341426 original size:7 final size:7
Alignment explanation
Indices: 13341383--13341442 Score: 52
Period size: 7 Copynumber: 8.3 Consensus size: 7
13341373 AATAAAAGAT
13341383 AAATAAA
1 AAATAAA
13341390 GAAACTAAA
1 -AAA-TAAA
13341399 AATATATAA
1 AA-ATA-AA
* *
13341408 ATATAGA
1 AAATAAA
13341415 AAATAAA
1 AAATAAA
13341422 AAAT--A
1 AAATAAA
13341427 AAATAAA
1 AAATAAA
13341434 AAATAAA
1 AAATAAA
13341441 AA
1 AA
13341443 TAGGGCTTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
5 5 0.12
7 20 0.47
8 10 0.23
9 8 0.19
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (7 bp):
AAATAAA
Found at i:13349413 original size:22 final size:22
Alignment explanation
Indices: 13349385--13349428 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
13349375 GAAAGCCGTG
13349385 TTTGTAACTTTGGGGCACAAAT
1 TTTGTAACTTTGGGGCACAAAT
13349407 TTTGTAACTTTGGGGCACAAAT
1 TTTGTAACTTTGGGGCACAAAT
13349429 GAAGCGTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (22 bp):
TTTGTAACTTTGGGGCACAAAT
Found at i:13350881 original size:14 final size:13
Alignment explanation
Indices: 13350851--13350896 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
13350841 AAATTATTAA
13350851 TTAAGTTTAATAAT
1 TTAA-TTTAATAAT
*
13350865 TTAATTTAATAGCT
1 TTAATTTAATA-AT
13350879 TTAATTTAA-AAT
1 TTAATTTAATAAT
13350891 TTAATT
1 TTAATT
13350897 ATAAAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 7 0.24
13 8 0.28
14 14 0.48
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (13 bp):
TTAATTTAATAAT
Found at i:13350903 original size:13 final size:12
Alignment explanation
Indices: 13350851--13350903 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 12
13350841 AAATTATTAA
13350851 TTAAGTTTAATAAT
1 TTAA-TTTAA-AAT
*
13350865 TTAATTTAATAGCT
1 TTAATTTAA-A-AT
13350879 TTAATTTAAAAT
1 TTAATTTAAAAT
13350891 TTAATTATAAAAT
1 TTAATT-TAAAAT
13350904 AATCAAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 7 0.20
13 14 0.40
14 14 0.40
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (12 bp):
TTAATTTAAAAT
Done.