Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008041.1 Hibiscus syriacus cultivar Beakdansim tig00110528_pilon, 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: 4970990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 21
Found at i:3922764 original size:23 final size:23
Alignment explanation
Indices: 3922738--3922859 Score: 109
Period size: 23 Copynumber: 5.2 Consensus size: 23
3922728 AGGTTCAAAT
*
3922738 TCGAGTTTGAGTTCGAGCTTGAA
1 TCGAGTTCGAGTTCGAGCTTGAA
*
3922761 TCGAGTTCGAGTTTGAGCTTGAA
1 TCGAGTTCGAGTTCGAGCTTGAA
* * ** *
3922784 TCGAGCTCAAAATCGAGCTTCAA
1 TCGAGTTCGAGTTCGAGCTTGAA
* * *
3922807 TTGAGCTCGAGTCTCGAGCTTCAA
1 TCGAGTTCGAGT-TCGAGCTTGAA
* * *
3922831 TTGAGCTCGAGTCTCGAGCTTCAA
1 TCGAGTTCGAGT-TCGAGCTTGAA
3922855 TCGAG
1 TCGAG
3922860 CTCCTGAAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
23 46 0.54
24 39 0.46
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (23 bp):
TCGAGTTCGAGTTCGAGCTTGAA
Found at i:3922826 original size:24 final size:24
Alignment explanation
Indices: 3922796--3922862 Score: 125
Period size: 24 Copynumber: 2.8 Consensus size: 24
3922786 GAGCTCAAAA
3922796 TCGAGCTTCAATTGAGCTCGAGTC
1 TCGAGCTTCAATTGAGCTCGAGTC
3922820 TCGAGCTTCAATTGAGCTCGAGTC
1 TCGAGCTTCAATTGAGCTCGAGTC
*
3922844 TCGAGCTTCAATCGAGCTC
1 TCGAGCTTCAATTGAGCTC
3922863 CTGAAATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (24 bp):
TCGAGCTTCAATTGAGCTCGAGTC
Found at i:3923952 original size:24 final size:24
Alignment explanation
Indices: 3923925--3923970 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
3923915 TATTTTAATA
3923925 AAAATATTAATTATTAA-AATTTTT
1 AAAATA-TAATTATTAACAATTTTT
*
3923949 AAAATATATTTATTAACAATTT
1 AAAATATAATTATTAACAATTT
3923971 CAATAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATAATTATTAACAATTTTT
Found at i:3923978 original size:24 final size:23
Alignment explanation
Indices: 3923925--3923979 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
3923915 TATTTTAATA
* *
3923925 AAAATATTAATTATTAAAATTTTT
1 AAAATA-TATTTATTAAAATTTTC
3923949 AAAATATATTTATTAACAA-TTTC
1 AAAATATATTTATTAA-AATTTTC
3923972 AATAATAT
1 AA-AATAT
3923980 TATAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAATATATTTATTAAAATTTTC
Found at i:3924225 original size:27 final size:24
Alignment explanation
Indices: 3924193--3924247 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
3924183 AAAATATTTT
*
3924193 TAATATATTTAT-TTATAATTATAAA
1 TAATATATATATATTAT-ATTA-AAA
*
3924218 TAATATATATATATTATTTTAAAA
1 TAATATATATATATTATATTAAAA
3924242 TAATAT
1 TAATAT
3924248 TTTTAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 9 0.33
25 14 0.52
26 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATATATATATATTATATTAAAA
Found at i:3924279 original size:23 final size:22
Alignment explanation
Indices: 3924193--3924286 Score: 68
Period size: 20 Copynumber: 4.1 Consensus size: 22
3924183 AAAATATTTT
*
3924193 TAATATATTTATTTATAATTATAAA
1 TAATATA-TTAATTAT-ATTAT-AA
* *
3924218 TAATATATATATATTATTTTAAAA
1 TAATATAT-TA-ATTATATTATAA
3924242 TAATAT-TT--TTAATATTATAA
1 TAATATATTAATT-ATATTATAA
*
3924262 TAATATATTCAATTATATAATAA
1 TAATATATT-AATTATATTATAA
3924285 TA
1 TA
3924287 TTGTTATATT
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
19 2 0.04
20 13 0.23
21 2 0.04
22 1 0.02
23 11 0.20
24 11 0.20
25 12 0.21
26 4 0.07
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATATATTAATTATATTATAA
Found at i:3925547 original size:64 final size:63
Alignment explanation
Indices: 3925378--3925557 Score: 211
Period size: 64 Copynumber: 2.8 Consensus size: 63
3925368 GAATAAATTG
* * * * * *
3925378 AACATCGAATGCATTCCATGCATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTAGGCTATTATTAA
* *
3925442 AACATCGAATGCATTTCATGCATCGATGCACAAGC-AATGCACCGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACT-AGGCTATTATTA
3925505 A
63 A
* *
3925506 AACATCGAATGCATTTTATGCATCGATGCACACTTGGTGCACCGATGCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCACCGATGCACTA
3925558 AGTGTTCCAA
Statistics
Matches: 100, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 91 0.91
65 5 0.05
66 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTAGGCTATTATTAA
Found at i:3931349 original size:44 final size:44
Alignment explanation
Indices: 3931281--3931377 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
3931271 TTGTGCTTAA
* * *
3931281 TGCATCGATACACTTAACAGTGCACTGATGCATC-CCTTTGAATG
1 TGCATCGATACACTCAACAGTGCACCGATGCA-CGCCCTTGAATG
*
3931325 TGCATCGATACA-TCAACTGATGCACCGATGCACGCCCTTGAATG
1 TGCATCGATACACTCAACAG-TGCACCGATGCACGCCCTTGAATG
3931369 TGCATCGAT
1 TGCATCGAT
3931378 GTACAATAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
43 6 0.13
44 41 0.87
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (44 bp):
TGCATCGATACACTCAACAGTGCACCGATGCACGCCCTTGAATG
Found at i:3933252 original size:15 final size:15
Alignment explanation
Indices: 3933232--3933261 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3933222 CGCTTGAGAT
3933232 GAGAGCTCGTTACCC
1 GAGAGCTCGTTACCC
3933247 GAGAGCTCGTTACCC
1 GAGAGCTCGTTACCC
3933262 TCATCCTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.20
Consensus pattern (15 bp):
GAGAGCTCGTTACCC
Found at i:3934028 original size:20 final size:19
Alignment explanation
Indices: 3934003--3934040 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3933993 TTTTCAAAGG
3934003 CATGCACCGATGCATCCATC
1 CATGCACCGATGCA-CCATC
*
3934023 CATGCATCGATGCACCAT
1 CATGCACCGATGCACCAT
3934041 TGAATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.37, G:0.16, T:0.21
Consensus pattern (19 bp):
CATGCACCGATGCACCATC
Found at i:3934096 original size:64 final size:64
Alignment explanation
Indices: 3934024--3934148 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 64
3934014 GCATCCATCC
* *
3934024 ATGCATCGATGCACCATT-GAATAAATT-GAACATCGAATGCATTTCTTGCATCGATGCACTCTT
1 ATGCATCGATGCA-C-TTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTT
3934087 T
64 T
** **
3934088 ATGCATCGATGCACTTGGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCACTC
1 ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTC
3934149 AGGCTATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 2 0.04
63 6 0.11
64 45 0.85
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTTT
Found at i:3934138 original size:45 final size:45
Alignment explanation
Indices: 3934088--3934191 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
3934078 TGCACTCTTT
* * *
3934088 ATGCATCGATGCACT-TGGGTTTTATTAAAACATCGAATGCATTTC
1 ATGCATCGATGCACTCAGGCTATT-TTAAAACATCGAATGCATTTC
* *
3934133 ATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGCTATTTTAAAACATCGAATGCATTTC
*
3934178 ATGCATTGATGCAC
1 ATGCATCGATGCAC
3934192 ACTTGGTGCA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 47 0.90
46 5 0.10
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGCTATTTTAAAACATCGAATGCATTTC
Found at i:3940125 original size:33 final size:33
Alignment explanation
Indices: 3940088--3940200 Score: 93
Period size: 38 Copynumber: 3.2 Consensus size: 33
3940078 GGGGTTGGGT
*
3940088 CGGGTGAAATTCTAATTTTGCCGGATCGGGTCA
1 CGGGTGAAATTCTAATTTTGCCGGGTCGGGTCA
*** ** *
3940121 CGGGTGAAGGACTCCTTCTT-CTCGGGTCGGGGTCGGGT
1 CGGGTGAAATTCTAATT-TTGC-CGGGTC-GGGTC---A
3940159 CGGGTGAAATTCTAATTTTTGCCGGGTCGGGTCA
1 CGGGTGAAATTCTAA-TTTTGCCGGGTCGGGTCA
3940193 CGGGTGAA
1 CGGGTGAA
3940201 GGACCCCTTC
Statistics
Matches: 59, Mismatches: 13, Indels: 15
0.68 0.15 0.17
Matches are distributed among these distances:
33 13 0.22
34 15 0.25
35 5 0.08
37 5 0.08
38 18 0.31
39 3 0.05
ACGTcount: A:0.16, C:0.19, G:0.36, T:0.28
Consensus pattern (33 bp):
CGGGTGAAATTCTAATTTTGCCGGGTCGGGTCA
Found at i:3940153 original size:71 final size:72
Alignment explanation
Indices: 3940071--3940223 Score: 272
Period size: 72 Copynumber: 2.1 Consensus size: 72
3940061 AAATTGTCTA
* *
3940071 TCGGGTCGGGGTTGGGTCGGGTGAAATTCTAA-TTTTGCCGGATCGGGTCACGGGTGAAGGACTC
1 TCGGGTCGGGGTCGGGTCGGGTGAAATTCTAATTTTTGCCGGATCGGGTCACGGGTGAAGGACCC
3940135 CTTCTTC
66 CTTCTTC
*
3940142 TCGGGTCGGGGTCGGGTCGGGTGAAATTCTAATTTTTGCCGGGTCGGGTCACGGGTGAAGGACCC
1 TCGGGTCGGGGTCGGGTCGGGTGAAATTCTAATTTTTGCCGGATCGGGTCACGGGTGAAGGACCC
3940207 CTTCTTC
66 CTTCTTC
3940214 TCGGGTCGGG
1 TCGGGTCGGG
3940224 TCAGGTGGAC
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 31 0.40
72 47 0.60
ACGTcount: A:0.12, C:0.21, G:0.39, T:0.28
Consensus pattern (72 bp):
TCGGGTCGGGGTCGGGTCGGGTGAAATTCTAATTTTTGCCGGATCGGGTCACGGGTGAAGGACCC
CTTCTTC
Found at i:3940219 original size:34 final size:34
Alignment explanation
Indices: 3940113--3940226 Score: 104
Period size: 34 Copynumber: 3.2 Consensus size: 34
3940103 TTTTGCCGGA
3940113 TCGGGTCACGGGTGAAGGACTCCTTCTTCTCGGG
1 TCGGGTCACGGGTGAAGGACTCCTTCTTCTCGGG
* *** ** *
3940147 TCGGGGTCGGGTCGGGTGAAATTCTAATTTTTGC-CGGG
1 TC-GGGTC---ACGGGTGAAGGACTCCTTCTT-CTCGGG
*
3940185 TCGGGTCACGGGTGAAGGACCCCTTCTTCTCGGG
1 TCGGGTCACGGGTGAAGGACTCCTTCTTCTCGGG
3940219 TCGGGTCA
1 TCGGGTCA
3940227 GGTGGACCAA
Statistics
Matches: 59, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
33 1 0.02
34 27 0.46
35 5 0.08
37 5 0.08
38 20 0.34
39 1 0.02
ACGTcount: A:0.12, C:0.24, G:0.37, T:0.27
Consensus pattern (34 bp):
TCGGGTCACGGGTGAAGGACTCCTTCTTCTCGGG
Found at i:3954806 original size:111 final size:111
Alignment explanation
Indices: 3954669--3954890 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
3954659 ATTACAAAAA
3954669 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
3954734 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
*
3954780 TTAATTCTTAATCTAATAATCATGCATTAAATAAATTAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
3954845 AATTAAAATGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
3954891 ATGATTTTCA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
Found at i:3954995 original size:17 final size:18
Alignment explanation
Indices: 3954954--3954992 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3954944 ATTATATTAC
3954954 TAAAATA-TTAAATAAAG
1 TAAAATACTTAAATAAAG
*
3954971 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAG
3954989 TAAA
1 TAAA
3954993 TACATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAATACTTAAATAAAG
Found at i:3955225 original size:50 final size:51
Alignment explanation
Indices: 3955171--3955302 Score: 151
Period size: 51 Copynumber: 2.6 Consensus size: 51
3955161 AAATAACCAT
* * *
3955171 GTATAGCGCGGATCAGGGGGCGCACTATAC-CCACGTGGCGTCAAATCACC
1 GTATAGCGCGGATCAGGGGGCGCACTATACTCCACGTGACGCCAAATCAAC
* * * *
3955221 GTATATCGCGGGA-CAGGAGGCACGCTATACTCCACGTGACGCCAAATCAAC
1 GTATAGCGC-GGATCAGGGGGCGCACTATACTCCACGTGACGCCAAATCAAC
* * *
3955272 GTATAGCGCGGTTCAGGGCGCGCACTTTACT
1 GTATAGCGCGGATCAGGGGGCGCACTATACT
3955303 GCTAAGGGTG
Statistics
Matches: 65, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
50 24 0.37
51 41 0.63
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (51 bp):
GTATAGCGCGGATCAGGGGGCGCACTATACTCCACGTGACGCCAAATCAAC
Found at i:3957383 original size:30 final size:30
Alignment explanation
Indices: 3957322--3957384 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
3957312 TTCCAATTTC
* **
3957322 CATGAACATCTTTAAAAATAAATAAGTGAA
1 CATGAACACCTTTAAAAATAAATAAACGAA
*
3957352 CATGAACACCTTTAAAAATATATAAACGAA
1 CATGAACACCTTTAAAAATAAATAAACGAA
3957382 CAT
1 CAT
3957385 AAATACACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.52, C:0.14, G:0.08, T:0.25
Consensus pattern (30 bp):
CATGAACACCTTTAAAAATAAATAAACGAA
Found at i:3977509 original size:6 final size:6
Alignment explanation
Indices: 3977500--3977562 Score: 54
Period size: 6 Copynumber: 9.8 Consensus size: 6
3977490 AGTCAAATCG
* * * *
3977500 TTGACT TTGACT TTGACCA TTGATCC TTGACT TTGACT TTGACCA TTGATCG
1 TTGACT TTGACT TTGA-CT TTGA-CT TTGACT TTGACT TTGA-CT TTGA-CT
3977552 TTGACT TTGAC
1 TTGACT TTGAC
3977563 CAAAAAGTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
6 27 0.57
7 20 0.43
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (6 bp):
TTGACT
Found at i:3977530 original size:26 final size:26
Alignment explanation
Indices: 3977500--3977562 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
3977490 AGTCAAATCG
3977500 TTGACTTTGACTTTGACCATTGATCC
1 TTGACTTTGACTTTGACCATTGATCC
*
3977526 TTGACTTTGACTTTGACCATTGATCG
1 TTGACTTTGACTTTGACCATTGATCC
3977552 TTGACTTTGAC
1 TTGACTTTGAC
3977563 CAAAAAGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (26 bp):
TTGACTTTGACTTTGACCATTGATCC
Found at i:3983139 original size:27 final size:27
Alignment explanation
Indices: 3983082--3983141 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
3983072 GGAAAGGACT
3983082 AAAATACCCTTGAACTGTAAAATAACC
1 AAAATACCCTTGAACTGTAAAATAACC
*
3983109 AAAATACCCTAT-AA-TGTGAAATAACC
1 AAAATACCCT-TGAACTGTAAAATAACC
3983135 GAAAATA
1 -AAAATA
3983142 TCCCCAAGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 11 0.37
27 18 0.60
28 1 0.03
ACGTcount: A:0.52, C:0.18, G:0.08, T:0.22
Consensus pattern (27 bp):
AAAATACCCTTGAACTGTAAAATAACC
Found at i:3984399 original size:17 final size:17
Alignment explanation
Indices: 3984377--3984409 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3984367 GCTTGAGGGC
3984377 ACACCCCTCAGGTGGGA
1 ACACCCCTCAGGTGGGA
3984394 ACACCCCTCAGGTGGG
1 ACACCCCTCAGGTGGG
3984410 CACTTATGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.36, G:0.30, T:0.12
Consensus pattern (17 bp):
ACACCCCTCAGGTGGGA
Found at i:3986820 original size:19 final size:19
Alignment explanation
Indices: 3986798--3986854 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
3986788 AGAGAGAAAG
3986798 ACATGAGAAAGTAGTATCC
1 ACATGAGAAAGTAGTATCC
* * ***
3986817 ACATGTGAAAG-AGAGAAAG
1 ACATGAGAAAGTAG-TATCC
3986836 ACATGAGAAAGTAGTATCC
1 ACATGAGAAAGTAGTATCC
3986855 TCATCTTTTT
Statistics
Matches: 26, Mismatches: 10, Indels: 4
0.65 0.25 0.10
Matches are distributed among these distances:
18 2 0.08
19 22 0.85
20 2 0.08
ACGTcount: A:0.46, C:0.12, G:0.25, T:0.18
Consensus pattern (19 bp):
ACATGAGAAAGTAGTATCC
Found at i:3986825 original size:38 final size:38
Alignment explanation
Indices: 3986777--3986854 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
3986767 GTCGAGGAAG
*
3986777 CCACGTGTGAAAGAGAGAAAGACATGAGAAAGTAGTAT
1 CCACATGTGAAAGAGAGAAAGACATGAGAAAGTAGTAT
3986815 CCACATGTGAAAGAGAGAAAGACATGAGAAAGTAGTAT
1 CCACATGTGAAAGAGAGAAAGACATGAGAAAGTAGTAT
3986853 CC
1 CC
3986855 TCATCTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.45, C:0.13, G:0.27, T:0.15
Consensus pattern (38 bp):
CCACATGTGAAAGAGAGAAAGACATGAGAAAGTAGTAT
Found at i:3988136 original size:27 final size:24
Alignment explanation
Indices: 3988090--3988140 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 24
3988080 TACCCAATGC
*
3988090 ACTATTATATGATATTTTGATATA
1 ACTATTATATGATAATTTGATATA
3988114 ACTATATATATTGATACATTTGATATA
1 ACTAT-TATA-TGATA-ATTTGATATA
3988141 TAGATGATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 4 0.17
26 5 0.22
27 9 0.39
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (24 bp):
ACTATTATATGATAATTTGATATA
Found at i:3993051 original size:25 final size:25
Alignment explanation
Indices: 3993018--3993077 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
3993008 CTGGGAAAGC
3993018 AATTAATCCTAAGATCTTTAAATTAT
1 AATT-ATCCTAAGATCTTTAAATTAT
*
3993044 AATTATCCTAGGATCTTTAAATTAT
1 AATTATCCTAAGATCTTTAAATTAT
3993069 AATTATCCT
1 AATTATCCT
3993078 TGTTAAGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 29 0.88
26 4 0.12
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.43
Consensus pattern (25 bp):
AATTATCCTAAGATCTTTAAATTAT
Found at i:4005134 original size:409 final size:417
Alignment explanation
Indices: 4004309--4005153 Score: 1314
Period size: 427 Copynumber: 2.0 Consensus size: 417
4004299 TTTTGGATCA
* *
4004309 ATTTAG-AAGTTTGTTAAATTTAGGGGACCAAATTGAATAATGTAGGAAAATTGGATTTGAAATG
1 ATTTAGTAAGTTTGTTAAAGTTAGGGGACCAAATTGAATAATATAGGAAAATTGGATTTGAAATG
*
4004373 AAAATTGATTAGAAGTTGATGTGCAATGCTTAAATGGATGGTTGGCATGCTTGAATATATTATTA
66 AAAATTGATTAGAAGTTGATGTGCAATGCTTAAATGGATGGTTGGCAAGCTTGAATATATTATTA
4004438 GAACTTGAATTTCAAGTTAAAATGGAAAGGGACCATTTTGAATATTTTGGAAATATTGAGATGAA
131 GAACTTGAATTTCAAGTTAAAATGGAAAGGGACCATTTTGAATATTTTGGAAATATTGAGATGAA
* *
4004503 TTCTAAAAGATTCATTTTAGTAGTTGATTGTGAGATTGGAAATGGTTATGTGATATATTCTTTGA
196 TTCTAAAAGAATCATTTTAGTAGTTGATTGTGAGATTGGAAA----TACGTG------T-TTTGA
*
4004568 ATTAGATAATGGGAAAATTGAAGTTGTATTTTTGAAGTGTTAAGGTTGACATTGATGCTATGAAG
250 ATTAAATAATGGGAAAATTGAAGTTGTATTTTTGAAGTGTTAAGGTTGACATTGATGCTATGAAG
4004633 TGGAGTTAGTATCGAATAAGTCTCAAAAGAAATTTTTTAGAAATTTATTTCTTATTATGCACCTA
315 TGGAGTTAGTATCGAATAAGTCTCAAAAGAAATTTTTTAGAAATTTATTTCTTATTATGCACCTA
4004698 TATTAGTAAGATACTAACAAATACTTTGAAATGTATAT
380 TATTAGTAAGATACTAACAAATACTTTGAAATGTATAT
*
4004736 GTTTAGTAAGTTTGTTAAAGTTA-GGGACCAAATTGAATAATATAGGAAAATTGGATTTGAAATG
1 ATTTAGTAAGTTTGTTAAAGTTAGGGGACCAAATTGAATAATATAGGAAAATTGGATTTGAAATG
* *
4004800 GAAATTGATTAGAAGTTGATGTGCAATGCTTAAATGGATGGTTGTCAAGCTTGAATATATTATTA
66 AAAATTGATTAGAAGTTGATGTGCAATGCTTAAATGGATGGTTGGCAAGCTTGAATATATTATTA
* * *
4004865 TAACTTGAATTTCAAGTTAAAATGGAAA-GGACTATTTTGAATATTTTGGAAATATTGATATGAA
131 GAACTTGAATTTCAAGTTAAAATGGAAAGGGACCATTTTGAATATTTTGGAAATATTGAGATGAA
*
4004929 TTCTAAAAGAAATCATTTTAGTAGTTGTTTGTGAGATT-GAAA-ACG-G-TTTGAATTAAATAAT
196 TTCTAAAAG-AATCATTTTAGTAGTTGATTGTGAGATTGGAAATACGTGTTTTGAATTAAATAAT
* *
4004990 GGGTAAATTGAAGTT-TATTTTTGAAGTGTTAAGGTTGACATTGATGTTATGAAGTGGAGTTAGT
260 GGGAAAATTGAAGTTGTATTTTTGAAGTGTTAAGGTTGACATTGATGCTATGAAGTGGAGTTAGT
** ** **
4005054 ATCGAATAAGTCT-TGAA-ATTTTTTTTAGAAATTTATTTCTTATTATGTGCCTATATTAGTAAG
325 ATCGAATAAGTCTCAAAAGAAATTTTTTAGAAATTTATTTCTTATTATGCACCTATATTAGTAAG
*
4005117 ATACTAACAAGTACTTTGAAATGTATAT
390 ATACTAACAAATACTTTGAAATGTATAT
4005145 ATTTAGTAA
1 ATTTAGTAA
4005154 ATGATGTACA
Statistics
Matches: 393, Mismatches: 23, Indels: 22
0.90 0.05 0.05
Matches are distributed among these distances:
409 77 0.20
410 2 0.01
411 61 0.16
412 28 0.07
420 1 0.00
421 2 0.01
426 47 0.12
427 160 0.41
428 15 0.04
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.38
Consensus pattern (417 bp):
ATTTAGTAAGTTTGTTAAAGTTAGGGGACCAAATTGAATAATATAGGAAAATTGGATTTGAAATG
AAAATTGATTAGAAGTTGATGTGCAATGCTTAAATGGATGGTTGGCAAGCTTGAATATATTATTA
GAACTTGAATTTCAAGTTAAAATGGAAAGGGACCATTTTGAATATTTTGGAAATATTGAGATGAA
TTCTAAAAGAATCATTTTAGTAGTTGATTGTGAGATTGGAAATACGTGTTTTGAATTAAATAATG
GGAAAATTGAAGTTGTATTTTTGAAGTGTTAAGGTTGACATTGATGCTATGAAGTGGAGTTAGTA
TCGAATAAGTCTCAAAAGAAATTTTTTAGAAATTTATTTCTTATTATGCACCTATATTAGTAAGA
TACTAACAAATACTTTGAAATGTATAT
Found at i:4008338 original size:29 final size:28
Alignment explanation
Indices: 4008254--4008336 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
4008244 GCATTTGTGC
* *
4008254 CCTTTAATTGTTTAGTATTTTAACTTT-AGT
1 CCTTTAATT-TTCAATA-TTTAA-TTTCAGT
* *
4008284 TCTTTAATTTTCAACATTTACATTTCAGT
1 CCTTTAATTTTCAATATTTA-ATTTCAGT
4008313 CCTTTAATTTTCAATATTTAATTT
1 CCTTTAATTTTCAATATTTAATTT
4008337 TCTATATGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
28 11 0.24
29 26 0.58
30 8 0.18
ACGTcount: A:0.27, C:0.13, G:0.05, T:0.55
Consensus pattern (28 bp):
CCTTTAATTTTCAATATTTAATTTCAGT
Found at i:4008343 original size:14 final size:14
Alignment explanation
Indices: 4008286--4008343 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
4008276 ACTTTAGTTC
*
4008286 TTTAATTTTCAACA
1 TTTAATTTTCAATA
* *
4008300 TTTACA-TTTCAGTCC
1 TTTA-ATTTTCAAT-A
4008315 TTTAATTTTCAATA
1 TTTAATTTTCAATA
*
4008329 TTTAATTTTCTATA
1 TTTAATTTTCAATA
4008343 T
1 T
4008344 GATTTATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 24 0.69
15 11 0.31
ACGTcount: A:0.29, C:0.14, G:0.02, T:0.55
Consensus pattern (14 bp):
TTTAATTTTCAATA
Found at i:4013239 original size:13 final size:13
Alignment explanation
Indices: 4013223--4013247 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4013213 TTATCCCTTT
4013223 TTATTATTATTAA
1 TTATTATTATTAA
4013236 TTATTATTATTA
1 TTATTATTATTA
4013248 TTTTCAAATA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:4014659 original size:22 final size:22
Alignment explanation
Indices: 4014628--4015001 Score: 423
Period size: 22 Copynumber: 17.4 Consensus size: 22
4014618 CATTTAAATC
*
4014628 TATTTTAAAATATATATTGATT
1 TATTTTAAAATATAGATTGATT
*
4014650 TATTTGAAAATAT-GAATTGATT
1 TATTTTAAAATATAG-ATTGATT
4014672 TATTTTAAAATATAGATTGATT
1 TATTTTAAAATATAGATTGATT
***
4014694 TATTTTAAAATAT-GAAAAAATT
1 TATTTTAAAATATAG-ATTGATT
*
4014716 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATAGATTGATT
** *
4014738 TATTTTAAAATAT-GA-AAAAT
1 TATTTTAAAATATAGATTGATT
4014758 TATTTTAAAATAT-GATTGATT
1 TATTTTAAAATATAGATTGATT
*
4014779 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATAGATTGATT
4014801 TATTTTAAAATATA-A---ATT
1 TATTTTAAAATATAGATTGATT
4014819 TATTTTTAAAATAT-GAATTGATT
1 TA-TTTTAAAATATAG-ATTGATT
* ***
4014842 TATTTTAAAATATAAAAAAATT
1 TATTTTAAAATATAGATTGATT
*
4014864 TATTTTTAAATAT-GATTGATT
1 TATTTTAAAATATAGATTGATT
*
4014885 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATAGATTGATT
4014907 TATTTTAAAATATAGATTGATT
1 TATTTTAAAATATAGATTGATT
*
4014929 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATAGATTGATT
***
4014951 TATTTTAAAATAT-GAAAAATTT
1 TATTTTAAAATATAGATTGA-TT
*
4014973 TATTTTAAAATATGGATT-ATT
1 TATTTTAAAATATAGATTGATT
4014994 TATTTTAA
1 TATTTTAA
4015002 GAGAAAATAA
Statistics
Matches: 303, Mismatches: 33, Indels: 33
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.02
19 11 0.04
20 18 0.06
21 48 0.16
22 212 0.70
23 9 0.03
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (22 bp):
TATTTTAAAATATAGATTGATT
Found at i:4014678 original size:44 final size:44
Alignment explanation
Indices: 4014628--4015001 Score: 473
Period size: 44 Copynumber: 8.7 Consensus size: 44
4014618 CATTTAAATC
* *
4014628 TATTTTAAAATATATATTGATTTATTTGAAAATATGAATTGATT
1 TATTTTAAAATATAGATTGATTTATTTTAAAATATGAATTGATT
***
4014672 TATTTTAAAATATAGATTGATTTATTTTAAAATATGAAAAAATT
1 TATTTTAAAATATAGATTGATTTATTTTAAAATATGAATTGATT
* * *
4014716 TATTTTAAAATATGGATTGATTTATTTTAAAATATGAA--AAAT
1 TATTTTAAAATATAGATTGATTTATTTTAAAATATGAATTGATT
*
4014758 TATTTTAAAATAT-GATTGATTTATTTTAAAATATGGATTGATT
1 TATTTTAAAATATAGATTGATTTATTTTAAAATATGAATTGATT
4014801 TATTTTAAAATATA-A---ATTTATTTTTAAAATATGAATTGATT
1 TATTTTAAAATATAGATTGATTTA-TTTTAAAATATGAATTGATT
* *** *
4014842 TATTTTAAAATATAAAAAAATTTATTTTTAAATATG-ATTGATT
1 TATTTTAAAATATAGATTGATTTATTTTAAAATATGAATTGATT
*
4014885 TATTTTAAAATATGGATTGATTTATTTTAAAATAT-AGATTGATT
1 TATTTTAAAATATAGATTGATTTATTTTAAAATATGA-ATTGATT
* **
4014929 TATTTTAAAATATGGATTGATTTATTTTAAAATATGAA-AAATTT
1 TATTTTAAAATATAGATTGATTTATTTTAAAATATGAATTGA-TT
*
4014973 TATTTTAAAATATGGATT-ATTTATTTTAA
1 TATTTTAAAATATAGATTGATTTATTTTAA
4015002 GAGAAAATAA
Statistics
Matches: 298, Mismatches: 20, Indels: 25
0.87 0.06 0.07
Matches are distributed among these distances:
40 5 0.02
41 56 0.19
42 17 0.06
43 64 0.21
44 150 0.50
45 6 0.02
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (44 bp):
TATTTTAAAATATAGATTGATTTATTTTAAAATATGAATTGATT
Found at i:4015187 original size:20 final size:20
Alignment explanation
Indices: 4015164--4015321 Score: 178
Period size: 20 Copynumber: 7.9 Consensus size: 20
4015154 TGCGATTTTC
*
4015164 CAAATTCGTAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
4015184 CAAATTCGCAACGCGAATTTGT
1 CAAATTCGCAACGCGAA--AGT
*
4015206 -AAA-TCGCAACAC-ATAAGT
1 CAAATTCGCAACGCGA-AAGT
* *
4015224 CAAATTCGCAACGTGATAGT
1 CAAATTCGCAACGCGAAAGT
* *
4015244 TAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
4015264 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
* *
4015284 TAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
4015304 CAAATTCGCAACGCGAAA
1 CAAATTCGCAACGCGAAA
4015322 CACAATATTA
Statistics
Matches: 119, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
18 2 0.02
19 4 0.03
20 107 0.90
21 4 0.03
22 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:4015235 original size:40 final size:40
Alignment explanation
Indices: 4015165--4015319 Score: 217
Period size: 40 Copynumber: 3.9 Consensus size: 40
4015155 GCGATTTTCC
* * *
4015165 AAATTCGTAACGCGAAAGTCAAATTCGCAACGCGA-ATTTGT
1 AAATTCGCAACGCGATAGTCAAATTCGCAACGCGATA-GT-T
* *
4015206 AAA-TCGCAACAC-ATAAGTCAAATTCGCAACGTGATAGTT
1 AAATTCGCAACGCGAT-AGTCAAATTCGCAACGCGATAGTT
4015245 AAATTCGCAACGCGATAGTCAAATTCGCAACGCGATAGTT
1 AAATTCGCAACGCGATAGTCAAATTCGCAACGCGATAGTT
4015285 AAATTCGCAACGCGATAGTCAAATTCGCAACGCGA
1 AAATTCGCAACGCGATAGTCAAATTCGCAACGCGA
4015320 AACACAATAT
Statistics
Matches: 103, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
39 5 0.05
40 92 0.89
41 6 0.06
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (40 bp):
AAATTCGCAACGCGATAGTCAAATTCGCAACGCGATAGTT
Found at i:4015257 original size:60 final size:61
Alignment explanation
Indices: 4015164--4015320 Score: 205
Period size: 60 Copynumber: 2.6 Consensus size: 61
4015154 TGCGATTTTC
* * *
4015164 CAAATTCGTAACGCGAAAGTCAAATTCGCAACGCGAATTTGT-AAA-TCGCAACAC-ATAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAA-TAGTCAAATTCGCAACACGAT-AGT
* * *
4015224 CAAATTCGCAACGTGATAGTTAAATTCGCAACGCG-ATAGTCAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAATAGTCAAATTCGCAACACGATAGT
*
4015284 TAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAA
4015321 ACACAATATT
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
58 3 0.04
59 4 0.05
60 74 0.88
61 3 0.04
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (61 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAATAGTCAAATTCGCAACACGATAGT
Found at i:4015460 original size:22 final size:22
Alignment explanation
Indices: 4015435--4015485 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
4015425 CTACAGCGAC
4015435 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
4015457 ATCCGTCCCCATTTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
4015479 ATCCGTC
1 ATCCGTC
4015486 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:4015708 original size:13 final size:13
Alignment explanation
Indices: 4015690--4015721 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
4015680 AGTATTTGTC
4015690 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
4015703 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
4015716 TTTGTT
1 TTTGTT
4015722 GAAGAAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.16, T:0.78
Consensus pattern (13 bp):
TTTGTTTTGTCTT
Found at i:4015790 original size:19 final size:20
Alignment explanation
Indices: 4015750--4015792 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
4015740 AACACCAAAT
4015750 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
4015770 TCGCAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
4015789 TCGC
1 TCGC
4015793 GTTGCAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:4017968 original size:42 final size:42
Alignment explanation
Indices: 4017921--4018039 Score: 109
Period size: 42 Copynumber: 2.8 Consensus size: 42
4017911 GATGCACCTA
* * *
4017921 TCATCATTCAAGAGGCGCATCCTATCGTTCAAGAGGCCCCTC-
1 TCATCATTCAAGAGGCCCATCCCACCGTTCAAGAGGCCCC-CG
** *
4017963 TCATCA-TCAAAGAATCCCCTCCCACCGTTCAAGAGGCCCCCG
1 TCATCATTC-AAGAGGCCCATCCCACCGTTCAAGAGGCCCCCG
* * *
4018005 TCATCGTTCAAGAGGTCCC-GCCCGCCGTTCAAGAG
1 TCATCATTCAAGAGG-CCCATCCCACCGTTCAAGAG
4018040 CTCGATTCAT
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
41 3 0.05
42 54 0.87
43 5 0.08
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.20
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCATCCCACCGTTCAAGAGGCCCCCG
Found at i:4018002 original size:21 final size:21
Alignment explanation
Indices: 4017922--4018039 Score: 78
Period size: 21 Copynumber: 5.6 Consensus size: 21
4017912 ATGCACCTAT
* * *
4017922 CATCATTCAAGAGGCGCATCC
1 CATCGTTCAAGAGGCCCCTCC
* *
4017943 TATCGTTCAAGAGGCCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
* **
4017964 CATC-ATCAAAGAATCCCCTCC
1 CATCGTTC-AAGAGGCCCCTCC
* *
4017985 CACCGTTCAAGAGGCCCC-CGT
1 CATCGTTCAAGAGGCCCCTC-C
* *
4018006 CATCGTTCAAGAGGTCCCGCC
1 CATCGTTCAAGAGGCCCCTCC
**
4018027 CGCCGTTCAAGAG
1 CATCGTTCAAGAG
4018040 CTCGATTCAT
Statistics
Matches: 73, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
20 3 0.04
21 67 0.92
22 3 0.04
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.19
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:4019460 original size:14 final size:14
Alignment explanation
Indices: 4019441--4019480 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
4019431 TTTTGATTAA
4019441 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
4019455 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
4019469 TTGATTTGTAAA
1 TTGATTTGTAAA
4019481 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:4019491 original size:62 final size:63
Alignment explanation
Indices: 4019390--4019530 Score: 205
Period size: 66 Copynumber: 2.2 Consensus size: 63
4019380 TTTTACATTG
4019390 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA-TTTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTCTTGATTAATTGATTTGTA
** * *
4019451 AAAGTTGATTTGTTTAATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA-TTTTTT-CTTGATTAATTGATTTGT
4019516 A
63 A
4019517 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
4019531 GTTCCTAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
61 17 0.24
62 18 0.25
64 5 0.07
66 31 0.44
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (63 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTCTTGATTAATTGATTTGTA
Found at i:4019547 original size:66 final size:62
Alignment explanation
Indices: 4019390--4019547 Score: 140
Period size: 66 Copynumber: 2.5 Consensus size: 62
4019380 TTTTACATTG
* * ** *
4019390 AAAGTTGATTTGTTTAATTGATGA-GGAAATAAGAATTATTTTTTTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAACTAAAAATGTAAATAAGAATTATTTTTTTGATTAATTGATTTGTA
* ** ** *
4019451 AAAGTTGATTTGTTTAATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAACTAAAAATGTAAATAAGAATTA--TTTTT--TTGATTAATTGATTTGT
4019516 A
62 A
**
4019517 AAAGTTGATTTGTTGTTCCTAAAAAT-TAAAT
1 AAAGTTGATTTGTT-TAACTAAAAATGTAAAT
4019548 CTGCATTATG
Statistics
Matches: 77, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
61 19 0.25
62 13 0.17
64 5 0.06
66 36 0.47
67 4 0.05
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAACTAAAAATGTAAATAAGAATTATTTTTTTGATTAATTGATTTGTA
Found at i:4019673 original size:54 final size:54
Alignment explanation
Indices: 4019588--4019711 Score: 167
Period size: 54 Copynumber: 2.3 Consensus size: 54
4019578 GTTGAAGGTA
*** * **
4019588 CAAATTCGCAACGCGAAAGTCAAATTCGCAACGTTTATTTCGCGTTGCGATAGT
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAAATAAGCGTTGCGATAGT
* * *
4019642 CAAATTCGCAATGTGAAAGTCAAATTTGCAACGCGAAATAAGCGTTGCGATAGT
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAAATAAGCGTTGCGATAGT
4019696 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
4019712 TTTTCGGTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (54 bp):
CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAAATAAGCGTTGCGATAGT
Found at i:4019679 original size:20 final size:20
Alignment explanation
Indices: 4019634--4019679 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
4019624 ATTTCGCGTT
* *
4019634 GCGATAGTCAAATTCGCAAT
1 GCGAAAGTCAAATTCGCAAC
* *
4019654 GTGAAAGTCAAATTTGCAAC
1 GCGAAAGTCAAATTCGCAAC
4019674 GCGAAA
1 GCGAAA
4019680 TAAGCGTTGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:4019743 original size:20 final size:20
Alignment explanation
Indices: 4019720--4019792 Score: 77
Period size: 20 Copynumber: 4.0 Consensus size: 20
4019710 GATTTTCGGT
4019720 TTGCGAATTTGACTTTCGCA
1 TTGCGAATTTGACTTTCGCA
*
4019740 TTGCGAATTTGACTATCGCA
1 TTGCGAATTTGACTTTCGCA
* *
4019760 --ACG--CTT-A-TTTCGCA
1 TTGCGAATTTGACTTTCGCA
4019774 TTGCGAATTTGACTTTCGC
1 TTGCGAATTTGACTTTCGC
4019793 GTTGATCGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
14 6 0.15
15 1 0.02
16 4 0.10
18 4 0.10
19 1 0.02
20 25 0.61
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCA
Found at i:4020092 original size:18 final size:18
Alignment explanation
Indices: 4020069--4020103 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4020059 AAGCCGGTTG
*
4020069 TGATTGGGATTTTGATTA
1 TGATTGCGATTTTGATTA
4020087 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
4020104 TCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.26, T:0.51
Consensus pattern (18 bp):
TGATTGCGATTTTGATTA
Found at i:4023517 original size:19 final size:20
Alignment explanation
Indices: 4023342--4023538 Score: 129
Period size: 19 Copynumber: 10.0 Consensus size: 20
4023332 TTGTGAAATT
*
4023342 AAATTCGCGTTGCAAATTTG
1 AAATTCGCGTTGCGAATTTG
*
4023362 AAATTC-AGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
** *
4023381 ACTTTCGC-TTGTGAATTTG
1 AAATTCGCGTTGCGAATTTG
**
4023400 ACTTTCGC-TTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
** * *
4023419 ACTTTCGGGTTACGAATTTGG
1 AAATTCGCGTTGCGAATTT-G
* **
4023440 AAAATCGCAATGCG-ATTT-
1 AAATTCGCGTTGCGAATTTG
*
4023458 ACATATTCGCGTTGCGAAATTGG
1 A-A-ATTCGCGTTGCG-AATTTG
* * *
4023481 AAACT-GGGTTGCGAAATTG
1 AAATTCGCGTTGCGAATTTG
4023500 AAATTCGCGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
* *
4023520 AGA-CCGCGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
4023539 TTGGTCATTT
Statistics
Matches: 139, Mismatches: 29, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
18 1 0.01
19 74 0.53
20 49 0.35
21 10 0.07
22 4 0.03
23 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (20 bp):
AAATTCGCGTTGCGAATTTG
Found at i:4023850 original size:22 final size:22
Alignment explanation
Indices: 4023620--4023893 Score: 322
Period size: 22 Copynumber: 12.5 Consensus size: 22
4023610 TTATTTTCTC
**
4023620 TTATTTTAAAATATGGA-AAATT
1 TTATTTTAAAATATGGATTGA-T
*
4023642 TTGTTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
**
4023664 TTATTTTAAAATATGGAAATTTTT
1 TTATTTTAAAATATGG--ATTGAT
*
4023688 TTATTTTAAAATATGAATTGAT
1 TTATTTTAAAATATGGATTGAT
4023710 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
4023732 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
* *** *
4023754 TTATTTTAAAATATGAAAAAAA
1 TTATTTTAAAATATGGATTGAT
*
4023776 TTATTTTAAAATATGAATTGAT
1 TTATTTTAAAATATGGATTGAT
*
4023798 TTATTTTAAAATATGGA---AA
1 TTATTTTAAAATATGGATTGAT
** **
4023817 AAAAATTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
*
4023839 TTATTTTAAAATATAGATTGAT
1 TTATTTTAAAATATGGATTGAT
*
4023861 TTATTTTAAAATATGAATTGAT
1 TTATTTTAAAATATGGATTGAT
4023883 TTATTTTAAAA
1 TTATTTTAAAA
4023894 ACTTTATTAT
Statistics
Matches: 213, Mismatches: 33, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
19 14 0.07
22 179 0.84
23 1 0.00
24 19 0.09
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:4023875 original size:129 final size:130
Alignment explanation
Indices: 4023620--4023893 Score: 397
Period size: 129 Copynumber: 2.1 Consensus size: 130
4023610 TTATTTTCTC
* ** * *
4023620 TTATTTTAAAATATGGAAAATTTTGTTTTAAAATATGGATTGATTTATTTTAAAATATGGAAATT
1 TTATTTTAAAATATGAAAAAAATTATTTTAAAATATGAATTGATTTATTTTAAAATATGGAAA--
** ** * *
4023685 TTTTTATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAT
64 --TAAAAATTAAAATATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGAAT
4023750 TGAT
127 TGAT
4023754 TTATTTTAAAATATGAAAAAAATTATTTTAAAATATGAATTGATTTATTTTAAAATATGGAAA-A
1 TTATTTTAAAATATGAAAAAAATTATTTTAAAATATGAATTGATTTATTTTAAAATATGGAAATA
*
4023818 AAAATTAAAATATGGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGAATTGAT
66 AAAATTAAAATATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGAATTGAT
4023883 TTATTTTAAAA
1 TTATTTTAAAA
4023894 ACTTTATTAT
Statistics
Matches: 128, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
129 70 0.55
134 58 0.45
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (130 bp):
TTATTTTAAAATATGAAAAAAATTATTTTAAAATATGAATTGATTTATTTTAAAATATGGAAATA
AAAATTAAAATATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGAATTGAT
Found at i:4023974 original size:31 final size:31
Alignment explanation
Indices: 4023916--4023975 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
4023906 TAGTTGTATG
*
4023916 AATTATTTAAATTTCAGTATTATAAAACTAA
1 AATTATTTAAATTTCAGTATTACAAAACTAA
*
4023947 AATTATTTAAATTTCAGTATTGCAAAACT
1 AATTATTTAAATTTCAGTATTACAAAACT
4023976 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTACAAAACTAA
Found at i:4025941 original size:42 final size:42
Alignment explanation
Indices: 4025882--4025972 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
4025872 GTACCCTAAC
*
4025882 TATATTATATATGTTTAGGTTATAGTTTATATCATATATATG
1 TATATTATATATATTTAGGTTATAGTTTATATCATATATATG
4025924 TATATTATATATATTTAGGTTATAGTTTATATCATATATATG
1 TATATTATATATATTTAGGTTATAGTTTATATCATATATATG
*
4025966 CATATTA
1 TATATTA
4025973 AACAGACTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (42 bp):
TATATTATATATATTTAGGTTATAGTTTATATCATATATATG
Found at i:4028842 original size:15 final size:15
Alignment explanation
Indices: 4028822--4028854 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4028812 ATATTTAGCT
*
4028822 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
4028837 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
4028852 GGG
1 GGG
4028855 TGGGTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.15, G:0.70, T:0.09
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:4038815 original size:20 final size:23
Alignment explanation
Indices: 4038802--4038874 Score: 73
Period size: 21 Copynumber: 3.3 Consensus size: 23
4038792 GGGAATCGAT
4038802 CCCCCCTTGA-GGGAACCGATT-
1 CCCCCCTTGAGGGGAACCGATTA
* *
4038823 CCCCCTTTGAAGGGGAACCGATTC
1 CCCCCCTTG-AGGGGAACCGATTA
* *
4038847 CCCCCCAT-AGGGGAATCGA-TA
1 CCCCCCTTGAGGGGAACCGATTA
4038868 CCCCCCT
1 CCCCCCT
4038875 AGGGTTCTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
21 15 0.35
22 11 0.26
23 11 0.26
24 6 0.14
ACGTcount: A:0.21, C:0.40, G:0.22, T:0.18
Consensus pattern (23 bp):
CCCCCCTTGAGGGGAACCGATTA
Found at i:4038842 original size:23 final size:21
Alignment explanation
Indices: 4038790--4038851 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
4038780 GTTTGGTGCA
*
4038790 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
4038810 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
4038831 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
4038852 CATAGGGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:4038877 original size:20 final size:19
Alignment explanation
Indices: 4038792--4038878 Score: 57
Period size: 20 Copynumber: 4.1 Consensus size: 19
4038782 TTGGTGCAGA
* *
4038792 GGGAATCGATCCCCCCTTG
1 GGGAACCGATCCCCCCTAG
*
4038811 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAACCGA-TCCCCC-CT--AG
4038835 GGGAACCGATTCCCCCCCATAG
1 GGGAACCGA-T-CCCCCC-TAG
*
4038857 GGGAATCGATACCCCCCTAG
1 GGGAACCGAT-CCCCCCTAG
4038877 GG
1 GG
4038879 TTCTGATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
20 13 0.24
21 13 0.24
22 11 0.20
23 11 0.20
24 7 0.13
ACGTcount: A:0.22, C:0.34, G:0.26, T:0.17
Consensus pattern (19 bp):
GGGAACCGATCCCCCCTAG
Found at i:4045585 original size:16 final size:16
Alignment explanation
Indices: 4045564--4045600 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
4045554 TTGGTATGCG
4045564 TTTTACCAGAAATTCA
1 TTTTACCAGAAATTCA
*
4045580 TTTTACTAGAAATTCA
1 TTTTACCAGAAATTCA
4045596 TTTTA
1 TTTTA
4045601 AGCATTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (16 bp):
TTTTACCAGAAATTCA
Found at i:4047363 original size:13 final size:13
Alignment explanation
Indices: 4047345--4047371 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4047335 ATTTACTTTG
4047345 TATAATATATATA
1 TATAATATATATA
4047358 TATAATATATATA
1 TATAATATATATA
4047371 T
1 T
4047372 TTAAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATATATATA
Found at i:4048155 original size:76 final size:74
Alignment explanation
Indices: 4047978--4048262 Score: 237
Period size: 76 Copynumber: 3.8 Consensus size: 74
4047968 TGTTTTAAGG
* * ** * *
4047978 GAAATTGTCTCGAGTGATACGAAATTTGTTTAAAGGAAAACGATCTCGTGTGAGATAAAATTTTT
1 GAAATTGTCTCGAGTGAGACGAAATTTGTTTAAAAG-AAATTATCTCATGTGAGATAAAATTTTC
*
4048043 GTGTTCGAGA
65 GTTTTCGAGA
* * * * * *
4048053 GAAAATTATCTTGAATAAGATGAAATTTGTTTAAAAAGAAATTATCTCATGCGAGATAAAATTTT
1 G-AAATTGTCTCGAGTGAGACGAAATTTGTTT-AAAAGAAATTATCTCATGTGAGATAAAATTTT
*
4048118 GGTTTTCGAGA
64 CGTTTTCGAGA
* * * * * * *
4048129 GAAAGTTGTCTCGAGTGAGGCAAAATTTGTTTCAAGGAAACTTTTCTCACGTGAGATGAAATTTT
1 GAAA-TTGTCTCGAGTGAGACGAAATTTGTTTAAAAGAAA-TTATCTCATGTGAGATAAAATTTT
* **
4048194 CATTTTTAAGA
64 CGTTTTCGAGA
* * * * ** *
4048205 GAAATTTTCTTGAGTGAGATGAAATTTGTTTAAAAAAAACCCATCTCAAGTGAGATAA
1 GAAATTGTCTCGAGTGAGACGAAATTTGTTTAAAAGAAA-TTATCTCATGTGAGATAA
4048263 TTTTTTGCTT
Statistics
Matches: 163, Mismatches: 43, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
75 51 0.31
76 108 0.66
77 4 0.02
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (74 bp):
GAAATTGTCTCGAGTGAGACGAAATTTGTTTAAAAGAAATTATCTCATGTGAGATAAAATTTTCG
TTTTCGAGA
Found at i:4048230 original size:20 final size:20
Alignment explanation
Indices: 4048179--4048231 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
4048169 CTTTTCTCAC
*
4048179 GTGAGATGAAATTTTCATTT
1 GTGAGATGAAATTTTCATTA
* *
4048199 TTAAGA-GAAATTTTC-TTGA
1 GTGAGATGAAATTTTCATT-A
4048218 GTGAGATGAAATTT
1 GTGAGATGAAATTT
4048232 GTTTAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 2 0.08
19 13 0.50
20 11 0.42
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.42
Consensus pattern (20 bp):
GTGAGATGAAATTTTCATTA
Found at i:4049762 original size:3 final size:3
Alignment explanation
Indices: 4049754--4049830 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
4049744 TTCATTGTAT
4049754 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4049802 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4049831 CGTTGAACTT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4052814 original size:29 final size:30
Alignment explanation
Indices: 4052782--4052883 Score: 113
Period size: 29 Copynumber: 3.5 Consensus size: 30
4052772 TCTGTCACGA
* * *
4052782 TTCTGCATAAGATTAATTCCCC-TTCTTTT
1 TTCTGCATGAGATTAATTCCCCGTCCTATT
*
4052811 TTCTGCATGTGATTAATTCCCCGTCCTATT
1 TTCTGCATGAGATTAATTCCCCGTCCTATT
4052841 TT-TGCATGAGATT-ATATCCCCGTCCTA-T
1 TTCTGCATGAGATTAAT-TCCCCGTCCTATT
* *
4052869 ATCTGCATGGGATTA
1 TTCTGCATGAGATTA
4052884 TATCACTGTC
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.06
29 51 0.82
30 7 0.11
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.42
Consensus pattern (30 bp):
TTCTGCATGAGATTAATTCCCCGTCCTATT
Found at i:4052884 original size:29 final size:29
Alignment explanation
Indices: 4052812--4052897 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 29
4052802 CCTTCTTTTT
* *
4052812 TCTGCATGTGATTA-ATTCCCCGTCCTATT
1 TCTGCATGAGATTATA-TCCCCGTCCTATA
*
4052841 TTTGCATGAGATTATATCCCCGTCCTATA
1 TCTGCATGAGATTATATCCCCGTCCTATA
* * *
4052870 TCTGCATGGGATTATATCACTGTCCTAT
1 TCTGCATGAGATTATATCCCCGTCCTAT
4052898 TCCTGTTTGG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
29 48 0.98
30 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (29 bp):
TCTGCATGAGATTATATCCCCGTCCTATA
Found at i:4054913 original size:24 final size:24
Alignment explanation
Indices: 4054886--4054947 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
4054876 TACAAATGTT
*
4054886 ACTAATACGAGAGTGCATAAATGC
1 ACTAATACAAGAGTGCATAAATGC
4054910 ACTAATACAAGAGTGCATAAATGC
1 ACTAATACAAGAGTGCATAAATGC
4054934 ACTAATACAAGAGT
1 ACTAATACAAGAGT
4054948 TAACGAATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (24 bp):
ACTAATACAAGAGTGCATAAATGC
Found at i:4054956 original size:24 final size:24
Alignment explanation
Indices: 4054877--4054965 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 24
4054867 ATACAGGAGT
* * *
4054877 ACAAATGTTACTAATACGAGAGTGC
1 ACAAATG-CACTAATACAAGAGTGA
* *
4054902 ATAAATGCACTAATACAAGAGTGC
1 ACAAATGCACTAATACAAGAGTGA
* *
4054926 ATAAATGCACTAATACAAGAGTTA
1 ACAAATGCACTAATACAAGAGTGA
* *
4054950 ACGAATGTACTAATAC
1 ACAAATGCACTAATAC
4054966 GTGATCGCTC
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 50 0.89
25 6 0.11
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.24
Consensus pattern (24 bp):
ACAAATGCACTAATACAAGAGTGA
Found at i:4055885 original size:20 final size:20
Alignment explanation
Indices: 4055860--4055897 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4055850 AAAACGATCC
4055860 AAATTAACATTCTAACATCA
1 AAATTAACATTCTAACATCA
4055880 AAATTAACATTCTAACAT
1 AAATTAACATTCTAACAT
4055898 TCAACTCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATTAACATTCTAACATCA
Found at i:4059303 original size:65 final size:65
Alignment explanation
Indices: 4059131--4059332 Score: 186
Period size: 65 Copynumber: 3.1 Consensus size: 65
4059121 AGTGATTCAC
** ** *
4059131 CGATGCACCA-ATCCATGCATCGATGCAC-CATGAAATAAATTG-AACATTGAATGCATTTCATG
1 CGATGCACCATA-CCATGCATCGATGCACTCA-GAGTTTTA-TGAAACATCGAATGCATTTCATG
*
4059193 CAC
63 CAT
* *
4059196 CGATGCA-CATACTATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTGATGCA
1 CGATGCACCATACCATGCATCGATGCACTCAGAGTTTTATG-AAACATCGAATGCATTTCATGCA
4059260 T
65 T
* *
4059261 CGATGCACCA-GCCATGCATCGATGCACGT-AG-GCTATTT-TGAAACATCGAATGCATTTTATG
1 CGATGCACCATACCATGCATCGATGCAC-TCAGAG-T-TTTATGAAACATCGAATGCATTTCATG
4059322 CAT
63 CAT
*
4059325 TGATGCAC
1 CGATGCAC
4059333 TCTTAGTGCA
Statistics
Matches: 117, Mismatches: 12, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
63 2 0.02
64 52 0.44
65 57 0.49
66 6 0.05
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (65 bp):
CGATGCACCATACCATGCATCGATGCACTCAGAGTTTTATGAAACATCGAATGCATTTCATGCAT
Found at i:4059330 original size:64 final size:66
Alignment explanation
Indices: 4059173--4059332 Score: 188
Period size: 65 Copynumber: 2.5 Consensus size: 66
4059163 AAATAAATTG
* * *
4059173 AACATTGAATGCATTTCATGCACCGATGCA-CATACTATGCATCGATGCACTCAGAGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGAGTTTTATGA
4059237 A
66 A
* *
4059238 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACGT-AG-GCTATTT-
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCAC-TCAGAG-T-TTTA
4059299 TG-A
63 TGAA
* *
4059302 AACATCGAATGCATTTTATGCATTGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
4059333 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
64 31 0.37
65 47 0.56
66 6 0.07
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (66 bp):
AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGAGTTTTATGA
A
Found at i:4068175 original size:64 final size:62
Alignment explanation
Indices: 4067971--4068178 Score: 206
Period size: 65 Copynumber: 3.2 Consensus size: 62
4067961 TTTCAAAGTG
**
4067971 ATGCACCGATGCACCAATCCATGCATCGATGCACCATGGAATAAATTG-AACATCGAATGCATTT
1 ATGCACCGATGCACCAA-CCATGCATCGATGCACCAT-G--TATTTTGAAACATCGAATGCATTT
4068035 C
62 C
* * *
4068036 ATGCACCGATGCA-CATACTATGCATCGATGCACTCAAAGT-TTTATGAAAACATCGAATCCATT
1 ATGCACCGATGCACCA-ACCATGCATCGATGCAC-C-ATGTATTT-TG-AAACATCGAATGCATT
*
4068099 TG
61 TC
* * *
4068101 ATGCATCGATGCACCAGCCATGCATCGATGCACGCATGCTATTTTGAAACATCGAATGCATTTT
1 ATGCACCGATGCACCAACCATGCATCGATGCAC-CATG-TATTTTGAAACATCGAATGCATTTC
*
4068165 ATGCATCGATGCAC
1 ATGCACCGATGCAC
4068179 TCTTAGTGCA
Statistics
Matches: 121, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 49 0.40
65 62 0.51
66 6 0.05
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (62 bp):
ATGCACCGATGCACCAACCATGCATCGATGCACCATGTATTTTGAAACATCGAATGCATTTC
Found at i:4068994 original size:61 final size:60
Alignment explanation
Indices: 4068916--4069050 Score: 243
Period size: 61 Copynumber: 2.2 Consensus size: 60
4068906 TACACATTGT
4068916 TCCCATAATTTTCCATAATTACTGAATAGGTCTCTCAACTTTCACAAAATTACATAAGGG
1 TCCCATAATTTTCCATAATTACTGAATAGGTCTCTCAACTTTCACAAAATTACATAAGGG
4068976 TCCCTATAATTTTCCATAATTACTGAATAGGTCTCTCAACTTTCACAAAATTACATAAGGG
1 TCCC-ATAATTTTCCATAATTACTGAATAGGTCTCTCAACTTTCACAAAATTACATAAGGG
*
4069037 TCCCCATAACTTTC
1 T-CCCATAATTTTC
4069051 TAATATTTGT
Statistics
Matches: 72, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
60 4 0.06
61 65 0.90
62 3 0.04
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (60 bp):
TCCCATAATTTTCCATAATTACTGAATAGGTCTCTCAACTTTCACAAAATTACATAAGGG
Found at i:4068998 original size:30 final size:32
Alignment explanation
Indices: 4068916--4069050 Score: 90
Period size: 31 Copynumber: 4.4 Consensus size: 32
4068906 TACACATTGT
* *
4068916 TCCC-ATAATTTTC-CATAATTACTGAATAGG
1 TCCCTATAACTTTCACAAAATTACTGAATAGG
* * *
4068946 TCTCT-CAACTTTCACAAAATTACAT-AA-GGG
1 TCCCTATAACTTTCACAAAATTAC-TGAATAGG
* *
4068976 TCCCTATAATTTTC-CATAATTACTGAATAGG
1 TCCCTATAACTTTCACAAAATTACTGAATAGG
* * *
4069007 TCTCT-CAACTTTCACAAAATTACAT-AA-GGG
1 TCCCTATAACTTTCACAAAATTAC-TGAATAGG
*
4069037 TCCCCATAACTTTC
1 TCCCTATAACTTTC
4069051 TAATATTTGT
Statistics
Matches: 78, Mismatches: 18, Indels: 17
0.69 0.16 0.15
Matches are distributed among these distances:
29 1 0.01
30 36 0.46
31 39 0.50
32 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (32 bp):
TCCCTATAACTTTCACAAAATTACTGAATAGG
Found at i:4069048 original size:31 final size:31
Alignment explanation
Indices: 4068952--4069050 Score: 98
Period size: 31 Copynumber: 3.2 Consensus size: 31
4068942 TAGGTCTCTC
*
4068952 AACTTTCACAAAATTACATAAGGGTCCCTAT
1 AACTTTCACAAAATTACATAAGGGTCCCCAT
* * * *
4068983 AATTTTC-CATAATTAC-TGAATAGGT-CTC-T
1 AACTTTCACAAAATTACAT-AA-GGGTCCCCAT
4069012 CAACTTTCACAAAATTACATAAGGGTCCCCAT
1 -AACTTTCACAAAATTACATAAGGGTCCCCAT
4069044 AACTTTC
1 AACTTTC
4069051 TAATATTTGT
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
29 2 0.04
30 20 0.38
31 28 0.54
32 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.32
Consensus pattern (31 bp):
AACTTTCACAAAATTACATAAGGGTCCCCAT
Found at i:4069878 original size:131 final size:131
Alignment explanation
Indices: 4069723--4070080 Score: 459
Period size: 131 Copynumber: 2.7 Consensus size: 131
4069713 TAAGAATAGT
* * * *
4069723 AATATCCCTTCATTTTGGTTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTGTTCT
1 AATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCT
* * * * *
4069788 TGATTGGAAATAATTTGATATTA-CTGTTTTCTC-TCGAATCAATATTGACTTTTAAGACGGAAT
66 TGATTGGAAATAATTAGATATTATC-ATTTTCACAT-GAATCAATATTGAATTTTAAGACGAAAT
4069851 AAC
129 AAC
* * * *
4069854 GATATCTCTTCATTTCGATTGGAGTAATAAATGAGTGCTTTAAGGTATGAGAGCTCATTTATTCT
1 AATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCT
* * * * *
4069919 TGATTAGAAATCATTACATATTATCATTTTCACATGAATCTATATTGAATTTTAAGACGAAATAG
66 TGATTGGAAATAATTAGATATTATCATTTTCACATGAATCAATATTGAATTTTAAGACGAAATAA
*
4069984 T
131 C
* * * *
4069985 AATATCTCTTCATTTCGATTGGAGTAATAAATGATTGTTTTAAGGCATGAAATGTCATTTATTCT
1 AATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCT
* *
4070050 CGATTGGAAATAATTAGATATTATCCTTTTC
66 TGATTGGAAATAATTAGATATTATCATTTTC
4070081 TCTCCTAAAA
Statistics
Matches: 194, Mismatches: 31, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
131 192 0.99
132 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (131 bp):
AATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCT
TGATTGGAAATAATTAGATATTATCATTTTCACATGAATCAATATTGAATTTTAAGACGAAATAA
C
Found at i:4077883 original size:36 final size:37
Alignment explanation
Indices: 4077825--4077894 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 37
4077815 CTTGATATTT
*
4077825 TTGAGAGAAAATATCCTAAGTGAG-ATAAAATTTGTC
1 TTGAGAGAAAATATCCTAAGTGAGAAGAAAATTTGTC
* * * *
4077861 TTGAGAGAAATTGTCTTGAGTGAGAAGAAAATTT
1 TTGAGAGAAAATATCCTAAGTGAGAAGAAAATTT
4077895 TCAAAGAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 20 0.71
37 8 0.29
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (37 bp):
TTGAGAGAAAATATCCTAAGTGAGAAGAAAATTTGTC
Found at i:4078086 original size:72 final size:70
Alignment explanation
Indices: 4077830--4078207 Score: 408
Period size: 72 Copynumber: 5.4 Consensus size: 70
4077820 TATTTTTGAG
* * *
4077830 AGAAAATATC-CTAAGTGAGATAAAA-TTTGTCTT-GAGAGAAATTGTCTTGAGTGAGAAGAAAA
1 AGAAAATATCTC-AAGTGAAATAAAATTTTGT-TTCGAGAGAAACTGTCTCGAGTGAGAAGAAAA
4077892 TTTTCAA
64 TTTTCAA
* * * * * * *
4077899 AGAAAATATATCAAGTGAAATGAAA-TTTATTTCGAGATAAACTATTTCGAGTGAGATGAAAATT
1 AGAAAATATCTCAAGTGAAATAAAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGAAGAAAATT
4077963 TTCAA
66 TTCAA
* * ** *
4077968 GGAAAATATCTCCAGT-AAGATGGAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGAAGGAAAT
1 AGAAAATATCTCAAGTGAA-ATAAAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGAAGAAAAT
4078032 TTTCAA
65 TTTCAA
* * *
4078038 GGGAAAATATCTAAAGTGAAATAAAATTTTTGTTTCGAGAGAAACTGTCTCGAGTGAGATGAAAA
1 -AGAAAATATCTCAAGTGAAATAAAA-TTTTGTTTCGAGAGAAACTGTCTCGAGTGAGAAGAAAA
4078103 TTTTCAA
64 TTTTCAA
* * * * * *
4078110 TA-AAAATATCTCAAGTTAAATAAAAAGTTTAGTTTTGAGAGAAATTGTCTCGAGTGAGACGGAA
1 -AGAAAATATCTCAAGTGAAAT-AAAA-TTTTGTTTCGAGAGAAACTGTCTCGAGTGAGAAGAAA
4078174 ATTTTCAA
63 ATTTTCAA
*
4078182 GAGAAAATATTTCAAGTGAAATAAAA
1 -AGAAAATATCTCAAGTGAAATAAAA
4078208 ATATAAAATT
Statistics
Matches: 261, Mismatches: 39, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
68 4 0.02
69 72 0.28
70 39 0.15
71 35 0.13
72 94 0.36
73 17 0.07
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (70 bp):
AGAAAATATCTCAAGTGAAATAAAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGAAGAAAATT
TTCAA
Found at i:4078199 original size:144 final size:140
Alignment explanation
Indices: 4077832--4078207 Score: 472
Period size: 144 Copynumber: 2.7 Consensus size: 140
4077822 TTTTTGAGAG
* * * *
4077832 AAAATATC-CTAAGTGAGATAAAATTT-GTCTTGAGAGAAATTGTCTTGAGTGAGAAGAAAATTT
1 AAAATATCTC-AAGTAAGATAAAATTTAGTTTTGAGAGAAATTGTCTCGAGTGAGAAGGAAATTT
* * *
4077895 TCAA-AGAAAATATATCAAGTGAAATGAAATTTATTTCGAGATAAACTATTTCGAGTGAGATGAA
65 TCAAGAGAAAATATATCAAGTGAAATAAAATTTATTTCGAGAGAAACTATCTCGAGTGAGATGAA
*
4077959 AATTTTCAAGG
130 AATTTTCAAGA
* ** * * *
4077970 AAAATATCTCCAGTAAGATGGAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGAAGGAAATTTT
1 AAAATATCTCAAGTAAGATAAAATTTAGTTTTGAGAGAAATTGTCTCGAGTGAGAAGGAAATTTT
* * * * *
4078035 CAAGGGAAAATATCTAAAGTGAAATAAAATTTTTGTTTCGAGAGAAACTGTCTCGAGTGAGATGA
66 CAAGAGAAAATATATCAAGTGAAATAAAA--TTTATTTCGAGAGAAACTATCTCGAGTGAGATGA
*
4078100 AAATTTTCAATA
129 AAATTTTCAAGA
*
4078112 AAAATATCTCAAGTTAA-ATAAAAAGTTTAGTTTTGAGAGAAATTGTCTCGAGTGAGACGGAAAT
1 AAAATATCTCAAG-TAAGAT-AAAA-TTTAGTTTTGAGAGAAATTGTCTCGAGTGAGAAGGAAAT
*
4078176 TTTCAAGAGAAAATATTTCAAGTGAAATAAAA
63 TTTCAAGAGAAAATATATCAAGTGAAATAAAA
4078208 ATATAAAATT
Statistics
Matches: 201, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
138 20 0.10
139 37 0.18
140 21 0.10
142 54 0.27
143 5 0.02
144 64 0.32
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.30
Consensus pattern (140 bp):
AAAATATCTCAAGTAAGATAAAATTTAGTTTTGAGAGAAATTGTCTCGAGTGAGAAGGAAATTTT
CAAGAGAAAATATATCAAGTGAAATAAAATTTATTTCGAGAGAAACTATCTCGAGTGAGATGAAA
ATTTTCAAGA
Found at i:4078533 original size:45 final size:47
Alignment explanation
Indices: 4078445--4078543 Score: 114
Period size: 45 Copynumber: 2.1 Consensus size: 47
4078435 AAGAGGAGGA
* * *
4078445 AAAAAGTGATCTTAAGAAAGACAAAAATTTAAAGTATTCTCATGGGAG
1 AAAAA-TGATCTCAAGAAACACAAAAATTTAAAGTATTCTCATGAGAG
*
4078493 AAAAATGATCTCAAGAAACA-AAAAATTTGAA-TA-TCTTCATGAGAG
1 AAAAATGATCTCAAGAAACACAAAAATTTAAAGTATTC-TCATGAGAG
*
4078538 GAAAAT
1 AAAAAT
4078544 AATGAATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
44 2 0.04
45 15 0.33
46 10 0.22
47 13 0.29
48 5 0.11
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.24
Consensus pattern (47 bp):
AAAAATGATCTCAAGAAACACAAAAATTTAAAGTATTCTCATGAGAG
Found at i:4083053 original size:489 final size:483
Alignment explanation
Indices: 4082156--4083125 Score: 1336
Period size: 489 Copynumber: 2.0 Consensus size: 483
4082146 TCCAAACATT
* * * * *
4082156 GAACCTAAAATTCGTATCGATGCCAACTGGAAGAATCAATAATCTAGCTCGTAAGTACTGATACT
1 GAACCCAAAATTCGTATCGATACCAACTGGAAGAATCAATAATCAAGCCCGTAAGTACTAATACT
* * * * * *
4082221 CTAAGTAGAGTATTATTACCCTTATCATGATTTGGATAAGAAATCTTTCTAAGTTAAATATTTAA
66 CTAAGTAGAGTATGAGTACCCTCATCATAATTTCGATAAGAAATCCTTCTAAGTTAAATATTTAA
* * * * * *
4082286 AAAAAGGGTTTAGGGTTTCCAAACTTATGAAATAAGTCTATAAGAAAGAATACCTTAAATAAGTG
131 AAAAAGAGTTTAGGGTTTACAAACTTATAAAATAAGACTACAAGAAAGAACACCTTAAATAAGTG
*
4082351 TATACACAACTAGAAATGGAATAAACTAGGATGACATAAACTAGCCCTCTTTTGACGCTCGAGAA
196 TAAACACAACTAGAAATGGAATAAACTAGGATGACATAAACTAGCCCTCTTTTGACGCTCGAGAA
* * * * **
4082416 ATGACAGGACACCCGAGCTAATTTGGTAGGTGAAAACTATTGGTTCTCTAGAATTATCTAGTTAT
261 ATAACAGGACACCCGAGCTAATTTGGTAGGTGAAAACGATTGGTTCGCTAGAATTATCCAAATAT
* ** *** * *
4082481 GTCAGCTAGTGCTAAGGCACTTCAACTGCCAACTGGGTGTAGAAGCCCCAAGACTCGACAGAGTA
326 GTCAGCTAATGCTAAGGCACTTCAACTGCCAAAAGGGCACAAAAACCCCAAGACTCGACAGAGTA
* *
4082546 AGTTGGTCGGGTGTATGCTTTTGATGCAAAAATTTTAGAACTCACCTCAATACTTAAGGGTATTC
391 AGTTGGTCGGGTGTATGCTTTCGATGCAAAAA-TTTAGAACTCACCTCAATAC-CAAGGGTATTC
* *
4082611 TAGGTAGGCTAGGGTGTCATCCTGAGATAA
454 TAGGTAGGCTAAGGTGTCAACCTGAGATAA
* * * *
4082641 GAACCCAAAATTTGTATCGATACCAA-TGGAAGTATTAATACTCAAGCCCGTAAGTA-TAAATAC
1 GAACCCAAAATTCGTATCGATACCAACTGGAAGAATCAATAATCAAGCCCGTAAGTACT-AATAC
*
4082704 TCTAAGTAGAGTATGGGTACCCTCATCATAATTTCGATAAGAAATCCTTCTAAGTTAAATATTTG
65 TCTAAGTAGAGTATGAGTACCCTCATCATAATTTCGATAAGAAATCCTTCTAAGTTAAATATTT-
* **
4082769 GAGAAAAAAGAGTTTAGGGTTGTATAAACTTATAAAATAAGACTACAAGCGAGAACACCTTAAAT
129 -A-AAAAAAGAGTTTAGGGTT-TACAAACTTATAAAATAAGACTACAAGAAAGAACACCTTAAAT
4082834 AAGTGTAAACACAACTAGAAATGGAATAAACTAGGATGACATAAAACTAGCCCT-TATTTGACGC
191 AAGTGTAAACACAACTAGAAATGGAATAAACTAGGATGACAT-AAACTAGCCCTCT-TTTGACGC
* * *
4082898 TCGATAAATAACCAGGACACCCGAGCTAATTTGGTAGGTGAACACGGTTGGTTCGCTAGAATTAT
254 TCGAGAAATAA-CAGGACACCCGAGCTAATTTGGTAGGTGAAAACGATTGGTTCGCTAGAATTAT
* * *
4082963 CCAAATATGTCAGCTAATGCTAA-GTACTTCAATTGTCAAAAGGGCACAAAAACCCCAAGACTCG
318 CCAAATATGTCAGCTAATGCTAAGGCACTTCAACTGCCAAAAGGGCACAAAAACCCCAAGACTCG
* *
4083027 ACGGAGTAAGTTGGTCGGGTGTATGCTTTCGATGCAAAAATTTGGAACTCACCTCAATACCAAGG
383 ACAGAGTAAGTTGGTCGGGTGTATGCTTTCGATGCAAAAATTTAGAACTCACCTCAATACCAAGG
* *
4083092 GTATTCTTGGTAGGCTAAGGTGTTAACCTGAGAT
448 GTATTCTAGGTAGGCTAAGGTGTCAACCTGAGAT
4083126 GCAAAAAAAT
Statistics
Matches: 423, Mismatches: 54, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
483 1 0.00
484 86 0.20
485 23 0.05
486 1 0.00
487 51 0.12
488 96 0.23
489 97 0.23
490 68 0.16
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (483 bp):
GAACCCAAAATTCGTATCGATACCAACTGGAAGAATCAATAATCAAGCCCGTAAGTACTAATACT
CTAAGTAGAGTATGAGTACCCTCATCATAATTTCGATAAGAAATCCTTCTAAGTTAAATATTTAA
AAAAAGAGTTTAGGGTTTACAAACTTATAAAATAAGACTACAAGAAAGAACACCTTAAATAAGTG
TAAACACAACTAGAAATGGAATAAACTAGGATGACATAAACTAGCCCTCTTTTGACGCTCGAGAA
ATAACAGGACACCCGAGCTAATTTGGTAGGTGAAAACGATTGGTTCGCTAGAATTATCCAAATAT
GTCAGCTAATGCTAAGGCACTTCAACTGCCAAAAGGGCACAAAAACCCCAAGACTCGACAGAGTA
AGTTGGTCGGGTGTATGCTTTCGATGCAAAAATTTAGAACTCACCTCAATACCAAGGGTATTCTA
GGTAGGCTAAGGTGTCAACCTGAGATAA
Found at i:4083197 original size:16 final size:16
Alignment explanation
Indices: 4083176--4083214 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
4083166 CACGTACTAA
*
4083176 ATACTTCTGTATGCAC
1 ATACTTCTATATGCAC
4083192 ATACTTCTATATGCAC
1 ATACTTCTATATGCAC
4083208 ATACTTC
1 ATACTTC
4083215 AACTTGTCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (16 bp):
ATACTTCTATATGCAC
Found at i:4091015 original size:13 final size:13
Alignment explanation
Indices: 4090973--4091008 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
4090963 CTATGACGTG
4090973 CATTTATGACACA
1 CATTTATGACACA
4090986 CATTTATGACACA
1 CATTTATGACACA
4090999 CATTTATGAC
1 CATTTATGAC
4091009 GTTCATTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.33
Consensus pattern (13 bp):
CATTTATGACACA
Found at i:4091091 original size:84 final size:85
Alignment explanation
Indices: 4090987--4091151 Score: 221
Period size: 84 Copynumber: 2.0 Consensus size: 85
4090977 TATGACACAC
* * *
4090987 ATTTATGACACACATTTATGACGTT-CATTGA-GCGTCATTGAAGC-CCCGTCA-TAAATGAAGA
1 ATTTATGACACACATGTATGAC-TTACATT-ACGCGTCATTGAAGCACACGTCATTAAA-AAAGA
*
4091048 TGACACACATTTGTGTGTCATAA
63 TGACACACATTCGTGTGTCATAA
* *
4091071 ATTTATGACACGCATGTATGACTTACATTACGTGTCATTGAAGCACACGTCATTAAAAAAGATGA
1 ATTTATGACACACATGTATGACTTACATTACGCGTCATTGAAGCACACGTCATTAAAAAAGATGA
4091136 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
4091152 GTGATTGTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
83 3 0.04
84 36 0.51
85 28 0.39
86 4 0.06
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (85 bp):
ATTTATGACACACATGTATGACTTACATTACGCGTCATTGAAGCACACGTCATTAAAAAAGATGA
CACACATTCGTGTGTCATAA
Found at i:4091178 original size:2 final size:2
Alignment explanation
Indices: 4091171--4091205 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4091161 TTTTGTAAAT
4091171 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4091206 GTAGATTGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4092078 original size:54 final size:54
Alignment explanation
Indices: 4091992--4092097 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
4091982 TCCTATGTAT
* * *
4091992 GTACCGATGCACAAGCCATGCATCGATGCACTCTTGAATATTTTGAAACATCGA
1 GTACCGATGCACAAACCATGCATCGATACACTCCTGAATATTTTGAAACATCGA
** *
4092046 GTACCGATGCACAAACCATGCATCGATACACTCCTGGCTCTTTTGAAACATC
1 GTACCGATGCACAAACCATGCATCGATACACTCCTGAATATTTTGAAACATC
4092098 AAATGTAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (54 bp):
GTACCGATGCACAAACCATGCATCGATACACTCCTGAATATTTTGAAACATCGA
Found at i:4097920 original size:44 final size:43
Alignment explanation
Indices: 4097838--4097930 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 43
4097828 TTGTGCATAA
* * *
4097838 TGCATCGATACACTAGAGTGTGTACCGATGCATCCCTTGAATT
1 TGCATCGATACACCAGAGTGTGCACCGATGCATCCCTTGAATG
* *
4097881 TGCATCGATACACCATGAAG-GTGCATCGATGCATTCCTTGAATG
1 TGCATCGATACACCA-G-AGTGTGCACCGATGCATCCCTTGAATG
4097925 TGCATC
1 TGCATC
4097931 AATGCACTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 14 0.33
44 27 0.63
45 2 0.05
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (43 bp):
TGCATCGATACACCAGAGTGTGCACCGATGCATCCCTTGAATG
Found at i:4097927 original size:23 final size:22
Alignment explanation
Indices: 4097863--4097936 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 22
4097853 GAGTGTGTAC
*
4097863 CGATGCATCCCTTGAATTTGCAT
1 CGATGCAT-CCTTGAATGTGCAT
* * *
4097886 CGATACA-CCATGAAGGTGCAT
1 CGATGCATCCTTGAATGTGCAT
4097907 CGATGCATTCCTTGAATGTGCAT
1 CGATGCA-TCCTTGAATGTGCAT
*
4097930 CAATGCA
1 CGATGCA
4097937 CTATGTTGTG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 17 0.41
23 24 0.59
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (22 bp):
CGATGCATCCTTGAATGTGCAT
Found at i:4098446 original size:12 final size:13
Alignment explanation
Indices: 4098415--4098449 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
4098405 CTACATATTA
4098415 ATTTTCAAACATT
1 ATTTTCAAACATT
*
4098428 GTTTTCAAA-ATT
1 ATTTTCAAACATT
4098440 ATTTTCAAAC
1 ATTTTCAAAC
4098450 TTTGCCCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (13 bp):
ATTTTCAAACATT
Found at i:4100714 original size:66 final size:65
Alignment explanation
Indices: 4100589--4100725 Score: 159
Period size: 66 Copynumber: 2.1 Consensus size: 65
4100579 CACACCCATT
* * * *
4100589 TCGAATGCATTTTGTGTACCGATGCACAATCCATGCATCAATACACTCTTGAATATTTTGAAACG
1 TCGAATGCATTTTCTGTACCGATGCACAATCCAAGCATCAATACACTCCTGAATATTTTGAAACA
* * * ** *
4100654 TCGAATGCATTTTTCTGTACCGATGCACAGA-CCAAGCATCGATGCAGTCCTGGCTCTTTTGAAA
1 TCGAATGCA-TTTTCTGTACCGATGCACA-ATCCAAGCATCAATACACTCCTGAATATTTTGAAA
4100718 CA
64 CA
4100720 TCGAAT
1 TCGAAT
4100726 ATAATTAGTG
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
65 9 0.15
66 50 0.83
67 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTCTGTACCGATGCACAATCCAAGCATCAATACACTCCTGAATATTTTGAAACA
Found at i:4104032 original size:50 final size:50
Alignment explanation
Indices: 4103977--4104073 Score: 135
Period size: 50 Copynumber: 1.9 Consensus size: 50
4103967 CATGAAGAAA
4103977 TTGGCGCCAAGATGAACCAACACA-A-CACCATTCGGCCAAGGAAGATGACT
1 TTGGCGCCAAGATGAA-CAACA-ATATCACCATTCGGCCAAGGAAGATGACT
* * *
4104027 TTGGCGCCAAGATGAACAATAATATCACCATTCGGCCTAGGGAGATG
1 TTGGCGCCAAGATGAACAACAATATCACCATTCGGCCAAGGAAGATG
4104074 CATCTTCATC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
48 1 0.02
49 5 0.12
50 36 0.86
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.18
Consensus pattern (50 bp):
TTGGCGCCAAGATGAACAACAATATCACCATTCGGCCAAGGAAGATGACT
Found at i:4104556 original size:23 final size:22
Alignment explanation
Indices: 4104530--4104574 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
4104520 TTCCATACAA
*
4104530 CATCAACACCATCAATCATCTTC
1 CATCAACACCACCAA-CATCTTC
*
4104553 CATCAAGACCACCAACATCTTC
1 CATCAACACCACCAACATCTTC
4104575 ATTTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.36, C:0.40, G:0.02, T:0.22
Consensus pattern (22 bp):
CATCAACACCACCAACATCTTC
Found at i:4115833 original size:2 final size:2
Alignment explanation
Indices: 4115826--4115872 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4115816 GCCCAATGTG
4115826 TA TA TA TA TA 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 TA TA TA TA TA
4115868 TA TA T
1 TA TA T
4115873 GAGAATTAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4116020 original size:23 final size:23
Alignment explanation
Indices: 4115913--4116027 Score: 112
Period size: 23 Copynumber: 5.0 Consensus size: 23
4115903 AGTCGAGGGT
*
4115913 TCTATGTGGTC-CTTCGG-GACAA
1 TCTATGTGG-CACTTCGGTGAAAA
**
4115935 TCTATGTGGTC-CTTC-AAGACAAA
1 TCTATGTGG-CACTTCGGTGA-AAA
* *
4115958 CCTATTTGGCACTTCGGTGAAAA
1 TCTATGTGGCACTTCGGTGAAAA
*
4115981 CCTATGTGGCACTTCGGTGAAAA
1 TCTATGTGGCACTTCGGTGAAAA
*
4116004 TCTATGTGGCACTTCGGTGCAAA
1 TCTATGTGGCACTTCGGTGAAAA
4116027 T
1 T
4116028 TATATAAGCT
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
22 18 0.22
23 60 0.75
24 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (23 bp):
TCTATGTGGCACTTCGGTGAAAA
Found at i:4119564 original size:19 final size:19
Alignment explanation
Indices: 4119540--4119578 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
4119530 AGGAAATGAT
4119540 GAATATTTGAATTCTAAAG
1 GAATATTTGAATTCTAAAG
* *
4119559 GAATATTTGACTTCTCAAG
1 GAATATTTGAATTCTAAAG
4119578 G
1 G
4119579 GTTTAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (19 bp):
GAATATTTGAATTCTAAAG
Found at i:4120829 original size:22 final size:22
Alignment explanation
Indices: 4120802--4120845 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4120792 AGTCGAGGGT
4120802 TCTATGTCGTCCTTCAGGACAA
1 TCTATGTCGTCCTTCAGGACAA
* *
4120824 TCTATGTGGTCCTTCGGGACAA
1 TCTATGTCGTCCTTCAGGACAA
4120846 ACCTATTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (22 bp):
TCTATGTCGTCCTTCAGGACAA
Found at i:4120926 original size:69 final size:69
Alignment explanation
Indices: 4120813--4120991 Score: 177
Period size: 69 Copynumber: 2.6 Consensus size: 69
4120803 CTATGTCGTC
* * * *
4120813 CTTCAGGAC-AATCTATGTGGTC-CTTCGG-GACAAACCTATTTGGCATTTCGGTGAAAACCTAT
1 CTTCAGTACAAATCTATGTGG-CACTTCGGTG-CAAATCTATGTGGCACTTCGGTGAAAACCTAT
*
4120875 GTGGCA
64 GTGGAA
* * * *
4120881 CTTCAGTGCAAATCTATGTGGCACTTCGGTGCAAATCTATGTGGCACTTCGGTGCAAATCTTTGT
1 CTTCAGTACAAATCTATGTGGCACTTCGGTGCAAATCTATGTGGCACTTCGGTGAAAACCTATGT
4120946 GGAA
66 GGAA
** * * * *
4120950 CTTTGGTACAAATCTTTGTGGAACTTTGGTACAAAT-TATGTG
1 CTTCAGTACAAATCTATGTGGCACTTCGGTGCAAATCTATGTG
4120992 AGTTGTGGTG
Statistics
Matches: 92, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
68 14 0.15
69 77 0.84
70 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (69 bp):
CTTCAGTACAAATCTATGTGGCACTTCGGTGCAAATCTATGTGGCACTTCGGTGAAAACCTATGT
GGAA
Found at i:4120985 original size:23 final size:23
Alignment explanation
Indices: 4120822--4120991 Score: 146
Period size: 23 Copynumber: 7.4 Consensus size: 23
4120812 CCTTCAGGAC
** *
4120822 AATCTATGTGGTCCTTCGGGACA
1 AATCTATGTGGAACTTCGGTACA
* * * *
4120845 AACCTATTTGGCATTTCGGTGA-A
1 AATCTATGTGGAACTTCGGT-ACA
* * * *
4120868 AACCTATGTGGCACTTCAGTGCA
1 AATCTATGTGGAACTTCGGTACA
* *
4120891 AATCTATGTGGCACTTCGGTGCA
1 AATCTATGTGGAACTTCGGTACA
* *
4120914 AATCTATGTGGCACTTCGGTGCA
1 AATCTATGTGGAACTTCGGTACA
* *
4120937 AATCTTTGTGGAACTTTGGTACA
1 AATCTATGTGGAACTTCGGTACA
* *
4120960 AATCTTTGTGGAACTTTGGTACA
1 AATCTATGTGGAACTTCGGTACA
4120983 AAT-TATGTG
1 AATCTATGTG
4120992 AGTTGTGGTG
Statistics
Matches: 128, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
22 5 0.04
23 122 0.95
24 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (23 bp):
AATCTATGTGGAACTTCGGTACA
Found at i:4123431 original size:27 final size:27
Alignment explanation
Indices: 4123401--4123456 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
4123391 TAATTGGGTG
* * *
4123401 GGTTTGGGTTTTATTTTGGTTTGGTTT
1 GGTTTGGGTCTTATTTTGATTTAGTTT
4123428 GGTTTGGGTCTTATTTTGATTTAGTTT
1 GGTTTGGGTCTTATTTTGATTTAGTTT
4123455 GG
1 GG
4123457 GCTTGAGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.07, C:0.02, G:0.32, T:0.59
Consensus pattern (27 bp):
GGTTTGGGTCTTATTTTGATTTAGTTT
Found at i:4124010 original size:27 final size:27
Alignment explanation
Indices: 4123980--4124035 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
4123970 TAATTGGGTG
* * *
4123980 GGTTTGGGTTTTATTTTGGTTTGGTTT
1 GGTTTGGGTCTTATTTTGATTTAGTTT
4124007 GGTTTGGGTCTTATTTTGATTTAGTTT
1 GGTTTGGGTCTTATTTTGATTTAGTTT
4124034 GG
1 GG
4124036 GCTTGAGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.07, C:0.02, G:0.32, T:0.59
Consensus pattern (27 bp):
GGTTTGGGTCTTATTTTGATTTAGTTT
Found at i:4124482 original size:579 final size:574
Alignment explanation
Indices: 4123381--4124547 Score: 2122
Period size: 579 Copynumber: 2.0 Consensus size: 574
4123371 GGCCCAAGTC
4123381 AGATTTTAGGTAATTGGGTGGGTTTGGGTTTTATTTTGGTTTGGTTTGGTTTGGGTCTTATTTTG
1 AGATTTTAGGTAATTGGGTGGGTTTGGGTTTTATTTTGGTTTGGTTTGGTTTGGGTCTTATTTTG
4123446 ATTTAGTTTGGGCTTGAGGCCCGATTTGGTTTGGGGTAGAAAATGATGATTACAACCAATAAAAT
66 ATTTAGTTTGGGCTTGAGGCCCGATTTGGTTTGGGGTAGAAAATGATGATTACAACCAATAAAAT
4123511 ATGGCCTCACTTTATTATATAATCAATGATAAATAGGAGAAGAAGATGGAGTGATCGTCCCTACG
131 ATGGCCTCACTTTATTATATAATCAATGATAAATAGGAGAAGAAGATGGAGTGATCGTCCCTACG
4123576 TATGTAAATTTTTGTATATTTTAATTTTATATTTATTTTTACTTTTAAAAATTTATAACTTTTTC
196 TATGTAAATTTTTGTATATTTTAATTTTATATTTATTTTTACTTTTAAAAATTTATAACTTTTTC
4123641 TTCTCTTAAAATATCATAAGTTTACTCAACACATAAAATTTCACATTTGTCCTTCTATTATTAAT
261 TTCTCTTAAAATATCATAAGTTTACTCAACACATAAAATTTCACATTTGTCCTTCTATTATTAAT
*
4123706 TGCTTTTAAATAATTTGGGAGGATTACAAGATGGTTTTTGTTTAAAATCTTTCTTAGTCGTTAAT
326 TGCTTTAAAATAATTTGGGAGGATTACAAGATGGTTTTTGTTTAAAATCTTTCTTAGTCGTTAAT
4123771 AATTCACACTTAACAGACTCGATTGCTTTAATCCAATACATATAGGGAAAGAATATACTCTCTTT
391 AATTCACACTTAACAGACTCGATTGCTTTAATCCAATACATATAGGGAAAGAATATACTCTCTTT
* *
4123836 AACCACTACTATACTTAAATTCATTATTAATTTTCATTAGTTTAGTATAATAGTTCATTAATCAT
456 AACCACTAATATACTTAAATTCATTATTAAATTTCATTAGTTTAGTATAATAG----TT-ATCAT
4123901 TAAATTAATTAAAGTTATTAAATTATTTTTATTTAAAAAAGTAAGGAAAAATAGTATAT
516 TAAATTAATTAAAGTTATTAAATTATTTTTATTTAAAAAAGTAAGGAAAAATAGTATAT
4123960 AGATTTTAGGTAATTGGGTGGGTTTGGGTTTTATTTTGGTTTGGTTTGGTTTGGGTCTTATTTTG
1 AGATTTTAGGTAATTGGGTGGGTTTGGGTTTTATTTTGGTTTGGTTTGGTTTGGGTCTTATTTTG
4124025 ATTTAGTTTGGGCTTGAGGCCCGATTTGGTTTGGGGTAGAAAATGATGATTACAACCAATAAAAT
66 ATTTAGTTTGGGCTTGAGGCCCGATTTGGTTTGGGGTAGAAAATGATGATTACAACCAATAAAAT
4124090 ATGGCCTCACTTTATTATATAATCAATGATAAATAGGAGAAGAAGATGGAGTGATCGTCCCCTAC
131 ATGGCCTCACTTTATTATATAATCAATGATAAATAGGAGAAGAAGATGGAGTGATCGT-CCCTAC
4124155 GTATGTAAATTTTTTGTATATTTTAATTTTA-ATTTATTTTTACTTTTAAAAATTTATAACTTTT
195 GTATGTAAA-TTTTTGTATATTTTAATTTTATATTTATTTTTACTTTTAAAAATTTATAACTTTT
4124219 TCTTCTCTTAAAATATCATAAGTTTACTCAACACATAAAATTTCACATTTGTCCTTCTATTATTA
259 TCTTCTCTTAAAATATCATAAGTTTACTCAACACATAAAATTTCACATTTGTCCTTCTATTATTA
4124284 ATTGCTTTAAAATAATTTGGGAGGATTACAAGATGGTTTTTTGTTTAAAATCTTTCTTAGTCGTT
324 ATTGCTTTAAAATAATTTGGGAGGATTACAAGATGG-TTTTTGTTTAAAATCTTTCTTAGTCGTT
4124349 AATAATTCACACTTAACAGACTCGATTGCTTTAATCCAATACATATA-GGAAAGAATATACTCTC
388 AATAATTCACACTTAACAGACTCGATTGCTTTAATCCAATACATATAGGGAAAGAATATACTCTC
4124413 TTTAACCACTAATATTACTTAATAAATTCATTAATTATAATTTCATTAGTTTAGTATAATAGTTC
453 TTTAACCACTAATA-TAC-T--TAAATTCATT-ATTA-AATTTCATTAGTTTAGTATAATAG---
4124478 ATTAATCATTAAATTAATTAAAGTTATTAAATTATTTTTATTTAAAAAAGTAAGGAAAAATAGTA
509 -TT-ATCATTAAATTAATTAAAGTTATTAAATTATTTTTATTTAAAAAAGTAAGGAAAAATAGTA
4124543 TAT
572 TAT
4124546 AG
1 AG
4124548 TGTAAACAAA
Statistics
Matches: 576, Mismatches: 3, Indels: 11
0.98 0.01 0.02
Matches are distributed among these distances:
579 188 0.33
580 178 0.31
581 99 0.17
582 1 0.00
584 10 0.02
585 4 0.01
586 96 0.17
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.42
Consensus pattern (574 bp):
AGATTTTAGGTAATTGGGTGGGTTTGGGTTTTATTTTGGTTTGGTTTGGTTTGGGTCTTATTTTG
ATTTAGTTTGGGCTTGAGGCCCGATTTGGTTTGGGGTAGAAAATGATGATTACAACCAATAAAAT
ATGGCCTCACTTTATTATATAATCAATGATAAATAGGAGAAGAAGATGGAGTGATCGTCCCTACG
TATGTAAATTTTTGTATATTTTAATTTTATATTTATTTTTACTTTTAAAAATTTATAACTTTTTC
TTCTCTTAAAATATCATAAGTTTACTCAACACATAAAATTTCACATTTGTCCTTCTATTATTAAT
TGCTTTAAAATAATTTGGGAGGATTACAAGATGGTTTTTGTTTAAAATCTTTCTTAGTCGTTAAT
AATTCACACTTAACAGACTCGATTGCTTTAATCCAATACATATAGGGAAAGAATATACTCTCTTT
AACCACTAATATACTTAAATTCATTATTAAATTTCATTAGTTTAGTATAATAGTTATCATTAAAT
TAATTAAAGTTATTAAATTATTTTTATTTAAAAAAGTAAGGAAAAATAGTATAT
Found at i:4126210 original size:28 final size:28
Alignment explanation
Indices: 4126165--4126220 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
4126155 AGTTGATGGT
* *
4126165 AAAAAAAGAGTAGCAAGAAGAA-AAAAAG
1 AAAAAAAGAGAAGAAAGAA-AACAAAAAG
4126193 AAAAAAAGAGAAGAAAGAAAACAAAAAG
1 AAAAAAAGAGAAGAAAGAAAACAAAAAG
4126221 CAAATTGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.75, C:0.04, G:0.20, T:0.02
Consensus pattern (28 bp):
AAAAAAAGAGAAGAAAGAAAACAAAAAG
Found at i:4126446 original size:3 final size:3
Alignment explanation
Indices: 4126438--4126488 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
4126428 GTCCGCAATT
4126438 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
4126486 GAA
1 GAA
4126489 ATCAAGTAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4126551 original size:15 final size:15
Alignment explanation
Indices: 4126531--4126560 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4126521 CTACTTGGAG
4126531 TGATGAGGATGTCAT
1 TGATGAGGATGTCAT
4126546 TGATGAGGATGTCAT
1 TGATGAGGATGTCAT
4126561 CAATGACGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.33, T:0.33
Consensus pattern (15 bp):
TGATGAGGATGTCAT
Found at i:4126566 original size:15 final size:15
Alignment explanation
Indices: 4126533--4126566 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4126523 ACTTGGAGTG
**
4126533 ATGAGGATGTCATTG
1 ATGAGGATGTCATCA
4126548 ATGAGGATGTCATCA
1 ATGAGGATGTCATCA
4126563 ATGA
1 ATGA
4126567 CGAAGAGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (15 bp):
ATGAGGATGTCATCA
Found at i:4128695 original size:13 final size:13
Alignment explanation
Indices: 4128677--4128701 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4128667 GTGCTGAATA
4128677 TAAACGAACAAAG
1 TAAACGAACAAAG
4128690 TAAACGAACAAA
1 TAAACGAACAAA
4128702 CATAAATAAA
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:0.64, C:0.16, G:0.12, T:0.08
Consensus pattern (13 bp):
TAAACGAACAAAG
Found at i:4130825 original size:14 final size:16
Alignment explanation
Indices: 4130794--4130833 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
4130784 ACCAAGTTTA
*
4130794 TTATATATATATTATT
1 TTATATTTATATTATT
4130810 TTATATTTA-ATT-TT
1 TTATATTTATATTATT
4130824 TT-TATTTATA
1 TTATATTTATA
4130834 ATTCTCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 6 0.27
14 5 0.23
15 3 0.14
16 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATATTTATATTATT
Found at i:4130906 original size:39 final size:39
Alignment explanation
Indices: 4130863--4130945 Score: 116
Period size: 39 Copynumber: 2.1 Consensus size: 39
4130853 CGAACAATCA
*
4130863 AAATTCCTAATTTCTTAAATT-TTATCATCA-TAACATTTT
1 AAATTCCTAATTTCTTAAATTATT-TCA-CATTAACATTAT
*
4130902 AAATTCTTAATTTCTTAAATTATTTCACATTAACATTAT
1 AAATTCCTAATTTCTTAAATTATTTCACATTAACATTAT
4130941 AAATT
1 AAATT
4130946 ATTTTTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
38 2 0.05
39 36 0.90
40 2 0.05
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (39 bp):
AAATTCCTAATTTCTTAAATTATTTCACATTAACATTAT
Found at i:4133209 original size:27 final size:27
Alignment explanation
Indices: 4133152--4133209 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
4133142 GATTAGATTG
* * *
4133152 AAGTGTAAAATGACCAAAATTCCCCTG
1 AAGTGTAAAATGACCAAAAGTACCCTC
* *
4133179 AAGTGTAAAATGACCCAAAGTACCTTC
1 AAGTGTAAAATGACCAAAAGTACCCTC
4133206 AAGT
1 AAGT
4133210 CTTGGAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (27 bp):
AAGTGTAAAATGACCAAAAGTACCCTC
Found at i:4139774 original size:26 final size:27
Alignment explanation
Indices: 4139745--4139803 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
4139735 CAAGTCTAGG
*
4139745 AATGACTAAAT-ACCCTAAAGCT-CCAA
1 AATGACTAAATCAACCTAAAG-TACCAA
* *
4139771 AATGAATAAATCAACCTAGAGTACCAA
1 AATGACTAAATCAACCTAAAGTACCAA
4139798 AATGAC
1 AATGAC
4139804 CTAGAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.49, C:0.22, G:0.10, T:0.19
Consensus pattern (27 bp):
AATGACTAAATCAACCTAAAGTACCAA
Found at i:4145612 original size:172 final size:176
Alignment explanation
Indices: 4145324--4145674 Score: 665
Period size: 174 Copynumber: 2.0 Consensus size: 176
4145314 TCCCCAAACG
4145324 TTTGATGATGATAAACTCGTAGCCAAACTTTATAATTAATGTTTCGATATTAAGAACTGCTACCC
1 TTTGATGATGATAAACTCGTAGCCAAACTTTATAATTAATGTTTCGATATTAAGAACTGCTACCC
4145389 AAGTGGGATTGAAGAGCATATTTTGGTCCAAGTTACGATAAGGTGTTCTCCCCTT-AAGTT-TGC
66 AAGTGGGATTGAAGAGCATATTTTGGTCCAAGTTACGATAAGGTGTTCTCCCCTTAAAGTTCTGC
*
4145452 ACTGATGTACATAATTGAAGAATTTTTGAAATCATTCTTGTTCCAA
131 ACTGATGTACAGAATTGAAGAATTTTTGAAATCATTCTTGTTCCAA
4145498 TTTGATGATGATAAACTCGTAGCCAAAC-TTATAATTAATGTTTCGATATTAAGAACTGCTACCC
1 TTTGATGATGATAAACTCGTAGCCAAACTTTATAATTAATGTTTCGATATTAAGAACTGCTACCC
4145562 AAGT-GGATTGAAGAGCATATTTTGGTCCAAGTTACGATAAGGTGTTCTCCCCTTAAAGTTCTGC
66 AAGTGGGATTGAAGAGCATATTTTGGTCCAAGTTACGATAAGGTGTTCTCCCCTTAAAGTTCTGC
4145626 ACTGATGTACAGAATTGAAGAATTTTTGAAATCATTCTTGTTCCAA
131 ACTGATGTACAGAATTGAAGAATTTTTGAAATCATTCTTGTTCCAA
4145672 TTT
1 TTT
4145675 TACGAGTTTG
Statistics
Matches: 174, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
172 50 0.29
173 45 0.26
174 79 0.45
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (176 bp):
TTTGATGATGATAAACTCGTAGCCAAACTTTATAATTAATGTTTCGATATTAAGAACTGCTACCC
AAGTGGGATTGAAGAGCATATTTTGGTCCAAGTTACGATAAGGTGTTCTCCCCTTAAAGTTCTGC
ACTGATGTACAGAATTGAAGAATTTTTGAAATCATTCTTGTTCCAA
Found at i:4148964 original size:35 final size:35
Alignment explanation
Indices: 4148912--4148988 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
4148902 TGGAGTATGA
*
4148912 AGGTTCAGCTCAGTCAAAATAGTAATTCCTTATAT
1 AGGTTCAACTCAGTCAAAATAGTAATTCCTTATAT
*
4148947 AGGTTCAACTC-GCTCAAACTAGTAATTCCTTATAT
1 AGGTTCAACTCAG-TCAAAATAGTAATTCCTTATAT
4148982 AGGTTCA
1 AGGTTCA
4148989 GACCGATCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
34 1 0.03
35 38 0.97
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34
Consensus pattern (35 bp):
AGGTTCAACTCAGTCAAAATAGTAATTCCTTATAT
Found at i:4153899 original size:14 final size:14
Alignment explanation
Indices: 4153880--4153909 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4153870 TTGAGGCAGG
4153880 AAACATGTGAACAT
1 AAACATGTGAACAT
4153894 AAACATGTGAACAT
1 AAACATGTGAACAT
4153908 AA
1 AA
4153910 CAGCGAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (14 bp):
AAACATGTGAACAT
Found at i:4157037 original size:19 final size:19
Alignment explanation
Indices: 4157013--4157049 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4157003 ATGACCAACA
*
4157013 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
4157032 AAATCGTAACGCGATCTC
1 AAATCGCAACGCGATCTC
4157050 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:4157104 original size:20 final size:20
Alignment explanation
Indices: 4157079--4157117 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4157069 CCAGATTCGC
*
4157079 AACGCGATTTTGACTATCGT
1 AACGCGATTCTGACTATCGT
4157099 AACGCGATTCTGACTATCG
1 AACGCGATTCTGACTATCG
4157118 CAACACTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (20 bp):
AACGCGATTCTGACTATCGT
Found at i:4157290 original size:17 final size:17
Alignment explanation
Indices: 4157268--4157305 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
4157258 CGATATCCGT
4157268 TCCTATATCCAACGACA
1 TCCTATATCCAACGACA
4157285 TCCTATATCCAACGACA
1 TCCTATATCCAACGACA
4157302 TCCT
1 TCCT
4157306 TCCCCATCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.37, G:0.05, T:0.26
Consensus pattern (17 bp):
TCCTATATCCAACGACA
Found at i:4158227 original size:14 final size:14
Alignment explanation
Indices: 4158198--4158234 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4158188 AGAAAAAGAA
4158198 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
4158213 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
4158227 GAAGAAAA
1 GAAGAAAA
4158235 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:4160286 original size:18 final size:18
Alignment explanation
Indices: 4160263--4160297 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4160253 AGCAAAAGGC
*
4160263 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
4160281 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
4160298 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:4160493 original size:20 final size:20
Alignment explanation
Indices: 4160468--4160598 Score: 157
Period size: 20 Copynumber: 6.8 Consensus size: 20
4160458 TTACACATTC
*
4160468 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
4160488 ATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
4160507 A----A-AATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
*
4160522 ATTTGACTATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
*
4160542 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
4160562 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
4160582 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
4160599 AGAAAACCGC
Statistics
Matches: 94, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
14 9 0.10
15 3 0.03
19 3 0.03
20 79 0.84
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:4160524 original size:34 final size:36
Alignment explanation
Indices: 4160476--4160578 Score: 138
Period size: 34 Copynumber: 2.8 Consensus size: 36
4160466 TCATTTGAAT
*
4160476 ATCGCAACGCGAATTTGACTATCGCAACGCAAA-A-
1 ATCGCAACGTGAATTTGACTATCGCAACGCAAATAC
4160510 ATCGCAACGTGAATTTGACTATCGCAACGCAAATTTGAC
1 ATCGCAACGTGAATTTGACTATCGCAACGCAAA--T-AC
*
4160549 TATCGCAACGTGAATTTGATTATCGCAACG
1 -ATCGCAACGTGAATTTGACTATCGCAACG
4160579 GGAATTTGAC
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
34 32 0.52
38 1 0.02
40 28 0.46
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (36 bp):
ATCGCAACGTGAATTTGACTATCGCAACGCAAATAC
Found at i:4160554 original size:40 final size:40
Alignment explanation
Indices: 4160468--4160598 Score: 175
Period size: 40 Copynumber: 3.4 Consensus size: 40
4160458 TTACACATTC
* *
4160468 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGCAA
1 ATTTGACTATCGCAACGTGAATTTGACTATCGCAACGCAA
4160508 A----A--ATCGCAACGTGAATTTGACTATCGCAACGCAA
1 ATTTGACTATCGCAACGTGAATTTGACTATCGCAACGCAA
* **
4160542 ATTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGTGAATTTGACTATCGCAACGCAA
4160582 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
4160599 AGAAAACCGC
Statistics
Matches: 81, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
34 32 0.40
36 1 0.01
38 1 0.01
40 47 0.58
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (40 bp):
ATTTGACTATCGCAACGTGAATTTGACTATCGCAACGCAA
Found at i:4160644 original size:34 final size:33
Alignment explanation
Indices: 4160584--4160661 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 33
4160574 CAACGGGAAT
*
4160584 TTGACTATCGCAACGAGAAAACCGCAAAGCGTA
1 TTGACTATCGCAACGAGAAAACCGCAAAGCGAA
*
4160617 TTAGACTATCGCAACGCA-AAAATCGCAAAGCGAA
1 TT-GACTATCGCAACG-AGAAAACCGCAAAGCGAA
*
4160651 TTGACTTTCGC
1 TTGACTATCGC
4160662 GTTGCGATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
33 10 0.25
34 29 0.73
35 1 0.03
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (33 bp):
TTGACTATCGCAACGAGAAAACCGCAAAGCGAA
Done.