Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008990.1 Hibiscus syriacus cultivar Beakdansim tig00112357_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: 317955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:11664 original size:25 final size:23
Alignment explanation
Indices: 11619--11693 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 23
11609 GAAAATAAAA
* *
11619 AATA-AAAAAAATTAAATTAAGTT
1 AATATAAAAATATTTAA-TAAGTT
11642 AATAGTAAAATATATTTAATAAGTT
1 AATA-TAAAA-ATATTTAATAAGTT
*
11667 AATATAAAAATATTT--TAATTT
1 AATATAAAAATATTTAATAAGTT
11688 AATATA
1 AATATA
11694 TATAAATTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 11 0.24
23 10 0.22
24 5 0.11
25 14 0.30
26 6 0.13
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
AATATAAAAATATTTAATAAGTT
Found at i:11985 original size:39 final size:39
Alignment explanation
Indices: 11942--12025 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 39
11932 AAAAATTAAC
11942 TTAGAAAGTTAAT-GTG-AAATAATTTAAGAAATTAAGAAT
1 TTAGAAAGTT-ATGGTGTAAA-AATTTAAGAAATTAAGAAT
* * * *
11981 TTAGAATGTTATGGTGTCAAAATTTAAGAAATTAGGATT
1 TTAGAAAGTTATGGTGTAAAAATTTAAGAAATTAAGAAT
12020 TTAGAA
1 TTAGAA
12026 TGCTAGAGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
38 2 0.05
39 35 0.90
40 2 0.05
ACGTcount: A:0.45, C:0.01, G:0.18, T:0.36
Consensus pattern (39 bp):
TTAGAAAGTTATGGTGTAAAAATTTAAGAAATTAAGAAT
Found at i:27527 original size:29 final size:31
Alignment explanation
Indices: 27494--27563 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 31
27484 GTTGTATTAT
27494 TTATACCACTT-AACTTTTAATTTT-A-TCAA
1 TTATACCACTTGAAC-TTTAATTTTCATTCAA
**
27523 TTATAGTA-TTGAACTTTAATTTTCATTTCAA
1 TTATACCACTTGAACTTTAATTTTCA-TTCAA
27554 TTATACCACT
1 TTATACCACT
27564 AGGCATTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
28 11 0.34
29 10 0.31
31 10 0.31
32 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.03, T:0.49
Consensus pattern (31 bp):
TTATACCACTTGAACTTTAATTTTCATTCAA
Found at i:27872 original size:21 final size:22
Alignment explanation
Indices: 27846--27887 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
27836 ATGCACATGG
*
27846 TCGGAT-AAAAATCGATCCGGA
1 TCGGATAAAAAACCGATCCGGA
27867 TCGGATAAAAAACCGATCCGG
1 TCGGATAAAAAACCGATCCGG
27888 TTTTTTCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (22 bp):
TCGGATAAAAAACCGATCCGGA
Found at i:29557 original size:19 final size:19
Alignment explanation
Indices: 29533--29575 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
29523 AACGAAAAAT
* * *
29533 GATGTGGTTGATGTTTGTC
1 GATGTGATTGACGGTTGTC
29552 GATGTGATTGACGGTTGTC
1 GATGTGATTGACGGTTGTC
29571 GATGT
1 GATGT
29576 AGACACCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.07, G:0.37, T:0.42
Consensus pattern (19 bp):
GATGTGATTGACGGTTGTC
Found at i:32561 original size:16 final size:16
Alignment explanation
Indices: 32542--32598 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
32532 AAACAATCTA
* *
32542 AACCGAAATTAACCCG
1 AACCGAAAATAACTCG
*
32558 AACCGAAAACAACTCG
1 AACCGAAAATAACTCG
* *
32574 AACCAAAAATAACTTG
1 AACCGAAAATAACTCG
32590 AACCGAAAA
1 AACCGAAAA
32599 GCAACCCAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.53, C:0.26, G:0.11, T:0.11
Consensus pattern (16 bp):
AACCGAAAATAACTCG
Found at i:33073 original size:15 final size:15
Alignment explanation
Indices: 33053--33110 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
33043 TCTAGATCTG
33053 AAATGACAC-GACCCA
1 AAATGAC-CTGACCCA
33068 AAATGACCTGACCC-
1 AAATGACCTGACCCA
*
33082 -AA--ACCTGACCCG
1 AAATGACCTGACCCA
33094 AAATGACCTGACCCA
1 AAATGACCTGACCCA
33109 AA
1 AA
33111 CCTGATCCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
11 9 0.24
13 4 0.11
14 1 0.03
15 23 0.62
ACGTcount: A:0.41, C:0.34, G:0.14, T:0.10
Consensus pattern (15 bp):
AAATGACCTGACCCA
Found at i:33089 original size:11 final size:11
Alignment explanation
Indices: 33073--33115 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 11
33063 ACCCAAAATG
33073 ACCTGACCCAA
1 ACCTGACCCAA
33084 ACCTGACCCGAAA
1 ACCTGACCC--AA
33097 TGACCTGACCCAA
1 --ACCTGACCCAA
33110 ACCTGA
1 ACCTGA
33116 TCCGAATGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 15 0.54
13 4 0.14
15 9 0.32
ACGTcount: A:0.35, C:0.40, G:0.14, T:0.12
Consensus pattern (11 bp):
ACCTGACCCAA
Found at i:33120 original size:26 final size:26
Alignment explanation
Indices: 33062--33126 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
33052 GAAATGACAC
*
33062 GACCCAAAATGACCTGACCCAAACCT
1 GACCCGAAATGACCTGACCCAAACCT
33088 GACCCGAAATGACCTGACCCAAACCT
1 GACCCGAAATGACCTGACCCAAACCT
*
33114 GATCCG-AATGACC
1 GACCCGAAATGACC
33127 CGTGTGTCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
25 7 0.19
26 30 0.81
ACGTcount: A:0.35, C:0.37, G:0.15, T:0.12
Consensus pattern (26 bp):
GACCCGAAATGACCTGACCCAAACCT
Found at i:54295 original size:11 final size:11
Alignment explanation
Indices: 54279--54309 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
54269 GTGGTTGCAT
54279 TGGTTGATTTG
1 TGGTTGATTTG
*
54290 TGGTTGATTTT
1 TGGTTGATTTG
54301 TGGTTGATT
1 TGGTTGATT
54310 AGTGTTGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.32, T:0.58
Consensus pattern (11 bp):
TGGTTGATTTG
Found at i:56069 original size:90 final size:91
Alignment explanation
Indices: 55967--56150 Score: 325
Period size: 90 Copynumber: 2.0 Consensus size: 91
55957 GTTAAGAGTT
* *
55967 TGACAATGGGGTACTAAAATAAAACAAAAACTAGACATTCGGTATATTTTTGAAAAA-AATAAAA
1 TGACAATGGGGTACTAAAATAAAACAAAAACTAAACATTAGGTATATTTTTGAAAAACAATAAAA
56031 GTTTAGATACTAAAACGGACCAAAAC
66 GTTTAGATACTAAAACGGACCAAAAC
* *
56057 TGACAATGGGGTACTAAAATAAAACAAAAACTAAACATTAGGTATATTTTTGAAAAACATTGAAA
1 TGACAATGGGGTACTAAAATAAAACAAAAACTAAACATTAGGTATATTTTTGAAAAACAATAAAA
56122 GTTTAGATACTAAAACGGACCAAAAC
66 GTTTAGATACTAAAACGGACCAAAAC
56148 TGA
1 TGA
56151 TAGTTTAGAT
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
90 55 0.62
91 34 0.38
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (91 bp):
TGACAATGGGGTACTAAAATAAAACAAAAACTAAACATTAGGTATATTTTTGAAAAACAATAAAA
GTTTAGATACTAAAACGGACCAAAAC
Found at i:58433 original size:27 final size:27
Alignment explanation
Indices: 58403--58470 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
58393 CTGTAGGAAT
*
58403 TATAGAGATGATTTGTTACCATTCCTA
1 TATAGATATGATTTGTTACCATTCCTA
*
58430 TATAGATATGATTTGTTACTATTCCTA
1 TATAGATATGATTTGTTACCATTCCTA
*
58457 TAGAGATATGATTT
1 TATAGATATGATTT
58471 TGTAAATAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (27 bp):
TATAGATATGATTTGTTACCATTCCTA
Found at i:62208 original size:27 final size:27
Alignment explanation
Indices: 62166--62233 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
62156 GTGTAGGAAT
62166 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
62191 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
62218 TATAGAGATATGATTT
1 TATAGAGATATGATTT
62234 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:66293 original size:4 final size:4
Alignment explanation
Indices: 66284--66313 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
66274 CTCAAATCAC
66284 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
66314 TACAAATTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:67845 original size:20 final size:20
Alignment explanation
Indices: 67822--67863 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
67812 TAAAGAAAGT
67822 ATTTTGAGAGTAAAATATTG
1 ATTTTGAGAGTAAAATATTG
*
67842 ATTTTGGGAGTAAAATATTG
1 ATTTTGAGAGTAAAATATTG
67862 AT
1 AT
67864 AAGAATATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTTTGAGAGTAAAATATTG
Found at i:68407 original size:157 final size:154
Alignment explanation
Indices: 68052--68400 Score: 470
Period size: 157 Copynumber: 2.2 Consensus size: 154
68042 GTGGTTCATT
* * *
68052 TTTGGTAAAAACGGACTTAAAAT-AAGGATGAATTGAAGAAATAAAAAAATTATGAAAAATTGAG
1 TTTGGTAAAAACAGACTTAAAATAAAAGATGAATTGAAGAAATAAGAAAATTATGAAAAATTGAG
* * *
68116 GACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGGGAATTGAAAGTACATATGTATTCTACA
66 GACTAAATTGAAAAATAAAAAATTTGTTAGCAAAAAGGGAATTAAAAATACATATGTATTCTACA
68181 ATGTTTAGGAGCATATAGTTAAAA
131 ATGTTTAGGAGCATATAGTTAAAA
* *
68205 TTTGGTAAAAA-ATTGATTTAAAATAAATGATGAATTGAAGAAATAAGAAAATTATGAAAAATTG
1 TTTGGTAAAAACA--GACTTAAAATAAAAGATGAATTGAAGAAATAAGAAAATTATGAAAAATTG
* * *
68269 AGAGACTAGATTGAAAAATAGAAAAA-TTGTTAGCAAAAAGATGAATTAAAAATATATATGTATT
64 AG-GACTAAATTGAAAAATA-AAAAATTTGTTAGCAAAAAG-GGAATTAAAAATACATATGTATT
* * *
68333 CTACGATGGTTTAGGAGCATGTAGTTTAAA
126 CTACAAT-GTTTAGGAGCATATAGTTAAAA
* * *
68363 TTTGGGAAAAACAGACTTAACATAAAAAATGAATTGAA
1 TTTGGTAAAAACAGACTTAAAATAAAAGATGAATTGAA
68401 AGAATAATGA
Statistics
Matches: 170, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
153 11 0.06
154 9 0.05
155 39 0.23
156 29 0.17
157 51 0.30
158 30 0.18
159 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.29
Consensus pattern (154 bp):
TTTGGTAAAAACAGACTTAAAATAAAAGATGAATTGAAGAAATAAGAAAATTATGAAAAATTGAG
GACTAAATTGAAAAATAAAAAATTTGTTAGCAAAAAGGGAATTAAAAATACATATGTATTCTACA
ATGTTTAGGAGCATATAGTTAAAA
Found at i:71449 original size:17 final size:17
Alignment explanation
Indices: 71427--71460 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
71417 GTATTCCCGT
71427 ATCGCTTTCCGTTCAAA
1 ATCGCTTTCCGTTCAAA
71444 ATCGCTTTCCGTTCAAA
1 ATCGCTTTCCGTTCAAA
71461 GCTGTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (17 bp):
ATCGCTTTCCGTTCAAA
Found at i:76130 original size:20 final size:20
Alignment explanation
Indices: 76105--76146 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
76095 AAAAATGATT
76105 TAATATTATCGAGTTGAATA
1 TAATATTATCGAGTTGAATA
76125 TAATATTATCGAGTTGAATA
1 TAATATTATCGAGTTGAATA
76145 TA
1 TA
76147 GGTAAATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.40
Consensus pattern (20 bp):
TAATATTATCGAGTTGAATA
Found at i:76995 original size:21 final size:22
Alignment explanation
Indices: 76960--77013 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
76950 AAACCCTAAA
*
76960 TTAAGATTT-TAGGTT-TAGGGT
1 TTAAGATTTATAGGTTAT-GGGG
76981 TTAAGATTTAT-GGTTATGGGG
1 TTAAGATTTATAGGTTATGGGG
*
77002 TTATGATTTATA
1 TTAAGATTTATA
77014 TTTAGAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (22 bp):
TTAAGATTTATAGGTTATGGGG
Found at i:77467 original size:11 final size:11
Alignment explanation
Indices: 77436--77468 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
77426 TTATTTATTA
77436 AATATAAAAAT
1 AATATAAAAAT
77447 AAT-TAAAAAT
1 AATATAAAAAT
*
77457 AATATATAAAT
1 AATATAAAAAT
77468 A
1 A
77469 TAGTAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:84031 original size:6 final size:7
Alignment explanation
Indices: 84009--84045 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
83999 GTTAAAGAAA
84009 GTCAACG
1 GTCAACG
*
84016 GTTAACG
1 GTCAACG
84023 GTC-ACG
1 GTCAACG
84029 GTCAACG
1 GTCAACG
84036 GTCAACG
1 GTCAACG
84043 GTC
1 GTC
84046 GGGTCGGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:84035 original size:13 final size:14
Alignment explanation
Indices: 84009--84045 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
83999 GTTAAAGAAA
*
84009 GTCAACGGTTAACG
1 GTCAACGGTCAACG
84023 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
84036 GTCAACGGTC
1 GTCAACGGTC
84046 GGGTCGGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.19
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:84063 original size:17 final size:17
Alignment explanation
Indices: 84035--84092 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
84025 CACGGTCAAC
*
84035 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
84052 GTTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
84069 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
84086 GGTCAAC
1 GGTCAAC
84093 CCGGTTCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.17, C:0.24, G:0.40, T:0.19
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:84110 original size:19 final size:19
Alignment explanation
Indices: 84086--84156 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
84076 AGTCGGGTCG
*
84086 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
84105 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
84124 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
84144 GGTCAAACCGGTT
1 GGTCAAACCGGTT
84157 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 32 0.67
20 16 0.33
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:84124 original size:10 final size:10
Alignment explanation
Indices: 84088--84156 Score: 72
Period size: 9 Copynumber: 7.1 Consensus size: 10
84078 TCGGGTCGGG
*
84088 TCAACCCGGT
1 TCAAACCGGT
*
84098 TCAGACCGG-
1 TCAAACCGGT
84107 TCAAACCGGT
1 TCAAACCGGT
*
84117 TCAGACCGG-
1 TCAAACCGGT
84126 TCAAACCGGT
1 TCAAACCGGT
*
84136 TCAAAACTGG-
1 TC-AAACCGGT
84146 TCAAACCGGT
1 TCAAACCGGT
84156 T
1 T
84157 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 22 0.46
10 20 0.42
11 6 0.12
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:91335 original size:7 final size:7
Alignment explanation
Indices: 91323--91359 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
91313 GTCAAAGAAA
91323 GTCAACG
1 GTCAACG
91330 GTCAACG
1 GTCAACG
91337 GTC-ACG
1 GTCAACG
91343 GTCAACG
1 GTCAACG
91350 GTCAACG
1 GTCAACG
91357 GTC
1 GTC
91360 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:91345 original size:13 final size:14
Alignment explanation
Indices: 91323--91359 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
91313 GTCAAAGAAA
91323 GTCAACGGTCAACG
1 GTCAACGGTCAACG
91337 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
91350 GTCAACGGTC
1 GTCAACGGTC
91360 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:91371 original size:17 final size:17
Alignment explanation
Indices: 91349--91389 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
91339 CACGGTCAAC
*
91349 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
91366 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
91383 GGTCAAC
1 GGTCAAC
91390 CCGGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:99716 original size:30 final size:32
Alignment explanation
Indices: 99658--99717 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
99648 TAATTAAAAA
99658 ATTAATTTGAAAGTTAGAGTGATTAAATTATG
1 ATTAATTTGAAAGTTAGAGTGATTAAATTATG
99690 ATTAATTTGAAA-TTA-AGT-AGTTAAATTA
1 ATTAATTTGAAAGTTAGAGTGA-TTAAATTA
99718 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 1 0.04
30 11 0.41
31 3 0.11
32 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.15, T:0.42
Consensus pattern (32 bp):
ATTAATTTGAAAGTTAGAGTGATTAAATTATG
Found at i:100442 original size:20 final size:20
Alignment explanation
Indices: 100417--100510 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
100407 AATTGGAAAA
*
100417 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
100437 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
100458 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
100478 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
100498 TTCGCAACGCGAT
1 ATCGCAACGCGAT
100511 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:101103 original size:19 final size:19
Alignment explanation
Indices: 101067--101108 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
101057 ACGAGAGAAT
*
101067 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
* *
101086 CGCAACGCGAAACCAAAAT
1 CGCAACGCGAAACAAAAAA
101105 CGCA
1 CGCA
101109 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.29, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:101126 original size:19 final size:19
Alignment explanation
Indices: 101104--101195 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
101094 GAAACCAAAA
*
101104 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
101123 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
101137 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
101156 TAGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
101175 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
101195 T
1 T
101196 TAACCAAAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 26 0.46
20 16 0.28
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:101195 original size:39 final size:33
Alignment explanation
Indices: 101109--101171 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
101099 CAAAATCGCA
*
101109 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTAGCGTTGCGATTCTCTCG
**
101142 TTGCGATAGTCATTTAGCGTTGCGATTCTC
1 TTGCGATTTTCATTTAGCGTTGCGATTCTC
101172 ATTATCTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTAGCGTTGCGATTCTCTCG
Found at i:102741 original size:63 final size:63
Alignment explanation
Indices: 102642--102772 Score: 253
Period size: 63 Copynumber: 2.1 Consensus size: 63
102632 GTTACGTGAT
*
102642 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGATACTCTACGCGATAACGATGGTGCATGGCGTGTG
102705 GAGGTCAATGCCTTGCGTGAGGAGATCGATACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGATACTCTACGCGATAACGATGGTGCATGGCGTGTG
102768 GAGGT
1 GAGGT
102773 ATCTACTTTA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.24
Consensus pattern (63 bp):
GAGGTCAATGCCTTGCGTGAGGAGATCGATACTCTACGCGATAACGATGGTGCATGGCGTGTG
Found at i:103422 original size:21 final size:21
Alignment explanation
Indices: 103398--103464 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
103388 TCATTCCTCG
103398 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
103419 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
103440 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
103461 AGAG
1 AGAG
103465 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:103422 original size:42 final size:42
Alignment explanation
Indices: 103346--103464 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
103336 GACTCGCCTG
* * * * * * *
103346 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
103388 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
103430 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
103465 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:104845 original size:13 final size:14
Alignment explanation
Indices: 104814--104849 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
104804 TGATTGTTAA
104814 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
104828 GTGATTTGT-AAAG
1 TTGATTTGTAAAAG
104841 TTGATTTGT
1 TTGATTTGT
104850 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:104858 original size:13 final size:14
Alignment explanation
Indices: 104803--104850 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
104793 TTGCTTATTT
104803 TTGA-TTGTT-AA-
1 TTGATTTGTTAAAG
*
104814 TTGATTTGTAAAAG
1 TTGATTTGTTAAAG
*
104828 GTGATTTG-TAAAG
1 TTGATTTGTTAAAG
104841 TTGATTTGTT
1 TTGATTTGTT
104851 TAATTGATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
11 4 0.14
12 4 0.14
13 13 0.45
14 8 0.28
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (14 bp):
TTGATTTGTTAAAG
Found at i:104992 original size:14 final size:14
Alignment explanation
Indices: 104973--105029 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
104963 GCGAAATGAA
104973 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
104987 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
105006 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
105020 AAACGCAACG
1 AATCGCAACG
105030 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.25, T:0.07
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:105000 original size:33 final size:33
Alignment explanation
Indices: 104955--105044 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
104945 CAAAAGTACT
*
104955 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
104988 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
105021 AACGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
105045 GTTACGATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:105014 original size:19 final size:19
Alignment explanation
Indices: 104955--105015 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
104945 CAAAAGTACT
*
104955 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
104974 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
104988 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
105007 ATCGCAACG
1 ATCGCAACG
105016 AGAGAAACGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:105127 original size:32 final size:33
Alignment explanation
Indices: 105044--105136 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
105034 ATTAAATTCG
*
105044 CGTTACGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
105077 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
105110 CGTTGCGA-TTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
105137 AGTAATTTCC
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 19 0.33
33 39 0.67
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:107409 original size:12 final size:12
Alignment explanation
Indices: 107392--107416 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
107382 TCTTCGGGGA
107392 CTTTTTCTTCTT
1 CTTTTTCTTCTT
107404 CTTTTTCTTCTT
1 CTTTTTCTTCTT
107416 C
1 C
107417 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:108717 original size:20 final size:20
Alignment explanation
Indices: 108692--108749 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
108682 ATTCATTTGA
108692 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
108712 CTATCGCAACGCGAAAATTG
1 CTATCGCAACGCGAAAATGG
*
108732 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
108750 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:108792 original size:14 final size:14
Alignment explanation
Indices: 108773--108826 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
108763 GAAAATCGCA
108773 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
108787 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
108804 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
108820 TTGCGAT
1 TTGCGAT
108827 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:108792 original size:33 final size:33
Alignment explanation
Indices: 108755--108825 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
108745 AAAATCGCAA
108755 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
108788 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
108821 TGCGA
1 TGCGA
108826 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:108826 original size:33 final size:33
Alignment explanation
Indices: 108768--108845 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
108758 GAAATGAAAA
***
108768 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
108801 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
108834 TCGCGTTGCGAT
1 TCGCATTGCGAT
108846 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:108952 original size:14 final size:14
Alignment explanation
Indices: 108933--108969 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
108923 CATCAATTAA
108933 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
108947 ACAAATCATCTTTT
1 ACAAATCAACATTT
108961 ACAAATCAA
1 ACAAATCAA
108970 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:110873 original size:18 final size:18
Alignment explanation
Indices: 110778--110915 Score: 103
Period size: 18 Copynumber: 7.9 Consensus size: 18
110768 ACGAAACTTA
110778 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
110796 ACTATCGCAACGCGGAAATGG
1 A-AATCGCAACGC-GAAAT-G
** **
110817 CTATCGCAATACGAAATG
1 AAATCGCAACGCGAAATG
* *
110835 AAAATCTCAA--CGACA--
1 -AAATCGCAACGCGAAATG
*
110850 AAATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
110868 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
110886 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
110900 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
110916 CACAAATCGC
Statistics
Matches: 97, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
14 17 0.18
16 12 0.12
17 4 0.04
18 28 0.29
19 21 0.22
20 14 0.14
21 1 0.01
ACGTcount: A:0.44, C:0.23, G:0.20, T:0.13
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:110903 original size:50 final size:51
Alignment explanation
Indices: 110799--110915 Score: 155
Period size: 50 Copynumber: 2.3 Consensus size: 51
110789 CGAAATGACT
** * *
110799 ATCGCAACGCGGAAATGGCTATCGCAATACGAAATGAAAATCTCAACGACAAA
1 ATCGCAACGC-GAAAT-GAAATCGCAACACGAAATGAAAATCGCAACGACAAA
* *
110852 ATCGCAATGCGAAATGAAATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACACGAAATGAAAATCGCAACGACAAA
110902 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
110916 CACAAATCGC
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
50 28 0.49
51 15 0.26
52 5 0.09
53 9 0.16
ACGTcount: A:0.44, C:0.23, G:0.20, T:0.13
Consensus pattern (51 bp):
ATCGCAACGCGAAATGAAATCGCAACACGAAATGAAAATCGCAACGACAAA
Found at i:110923 original size:51 final size:51
Alignment explanation
Indices: 110819--110926 Score: 146
Period size: 50 Copynumber: 2.1 Consensus size: 51
110809 GGAAATGGCT
* * * **
110819 ATCGCAATACGAAATGAAAATCTCAACGACAAAATCGCAATGCGAAATGAA
1 ATCGCAACACGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAAACAA
*
110870 ATCGCAACGCGAAATG-AAATCGCAACGACAAAATCGCAACGCGAAACACAA
1 ATCGCAACACGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAA-ACAA
110921 ATCGCA
1 ATCGCA
110927 TTGCGATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
50 28 0.56
51 22 0.44
ACGTcount: A:0.47, C:0.24, G:0.17, T:0.12
Consensus pattern (51 bp):
ATCGCAACACGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAAACAA
Found at i:110963 original size:14 final size:14
Alignment explanation
Indices: 110944--111001 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
110934 TTTCATTTCG
110944 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
110958 CGTTGCGATTTTATTT
1 CGTTGCGA-TTT-TGT
110974 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
110990 CGTTGCGATTTT
1 CGTTGCGATTTT
111002 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 8 0.21
17 3 0.08
18 6 0.16
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:110982 original size:32 final size:33
Alignment explanation
Indices: 110927--111017 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
110917 ACAAATCGCA
*
110927 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
110960 TTGCGATTTT-ATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
110992 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
111018 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:111036 original size:20 final size:19
Alignment explanation
Indices: 111002--111056 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
110992 TTGCGATTTT
*
111002 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
111021 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
111041 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
111057 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:111564 original size:18 final size:18
Alignment explanation
Indices: 111538--111582 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
111528 GTCGATCAGA
*
111538 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
111556 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
111574 TGATGGCTC
1 TGATGGCTC
111583 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:112947 original size:20 final size:20
Alignment explanation
Indices: 112899--112957 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
112889 AATAGTTTCT
** *
112899 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
112919 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
112939 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
112958 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:113247 original size:22 final size:22
Alignment explanation
Indices: 113220--113263 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
113210 GATGGAGATA
113220 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
113242 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
113264 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:113565 original size:20 final size:20
Alignment explanation
Indices: 113451--113564 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
113441 GATTATGTAT
113451 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
113471 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
113491 TATCGCGTTGCGAAAATAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
113511 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
113532 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
113552 TATCGCATTGCGA
1 TATCGCGTTGCGA
113565 TTTTCCCAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.79
21 12 0.15
22 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:113583 original size:21 final size:21
Alignment explanation
Indices: 113554--113646 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
113544 ATAGTCAGTA
113554 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
113575 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
113595 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
113616 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
113636 TCGCATTGCGA
1 TCGCATTGCGA
113647 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:113584 original size:41 final size:41
Alignment explanation
Indices: 113554--113646 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
113544 ATAGTCAGTA
* *
113554 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* *
113595 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
113636 TCGCATTGCGA
1 TCGCATTGCGA
113647 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:116512 original size:16 final size:16
Alignment explanation
Indices: 116491--116529 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
116481 AAAAAAAACT
116491 TAACCGGGTATTCGGG
1 TAACCGGGTATTCGGG
116507 TAACCGGGTATTCGGG
1 TAACCGGGTATTCGGG
*
116523 TACCCGG
1 TAACCGG
116530 AAAATCAAAT
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:0.18, C:0.23, G:0.36, T:0.23
Consensus pattern (16 bp):
TAACCGGGTATTCGGG
Found at i:120939 original size:23 final size:23
Alignment explanation
Indices: 120913--120960 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
120903 ATAAAGTACA
*
120913 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
120936 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
120959 AT
1 AT
120961 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:121404 original size:23 final size:22
Alignment explanation
Indices: 121342--121413 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
121332 ACACTTTACA
*
121342 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
121365 ATATAACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
* *
121387 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
121410 ATAT
1 ATAT
121414 GTTTACCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
22 20 0.47
23 23 0.53
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.35
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:121868 original size:39 final size:39
Alignment explanation
Indices: 121814--121900 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
121804 TCAAGTTGTA
*
121814 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
121853 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
121892 GATTTTGAT
1 GATTTTGAT
121901 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:122454 original size:25 final size:25
Alignment explanation
Indices: 122426--122476 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
122416 TTAATCCAAA
*
122426 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
122451 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
122476 T
1 T
122477 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:122770 original size:21 final size:22
Alignment explanation
Indices: 122745--122796 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
122735 ACACTTTACA
*
122745 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
122768 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
122791 ATATAA
1 ATATAA
122797 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:122781 original size:23 final size:23
Alignment explanation
Indices: 122755--122817 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
122745 ATATAACCAC
122755 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
122778 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
122801 TACCTATTACATCATAT
1 TACCTATTACATTATAT
122818 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:123194 original size:21 final size:22
Alignment explanation
Indices: 123169--123220 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
123159 ACACTTTACA
*
123169 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
123192 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
123215 ATATAA
1 ATATAA
123221 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:123205 original size:23 final size:23
Alignment explanation
Indices: 123179--123241 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
123169 ATATAACCAC
123179 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
123202 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
123225 TACCTATTACATCATAT
1 TACCTATTACATTATAT
123242 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:126037 original size:199 final size:198
Alignment explanation
Indices: 125312--127042 Score: 3060
Period size: 199 Copynumber: 8.8 Consensus size: 198
125302 CTGCACCCAG
*
125312 CTATGTTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
1 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
125377 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
66 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
125442 TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACAC
131 TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACAC
125507 AAA
196 AAA
* *
125510 CTATATTAGTGTCGACACATTATTTAGACAAATCCTCTCATAAAACCGGTATAATTGTACCGGTT
1 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
125575 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
66 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
*
125640 TATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAAAAATATCGACAC
131 TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACAC
125705 AAA
196 AAA
*
125708 CTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTT
1 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
125773 AGATTGAAAAATTACAT-TTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
66 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
* *
125837 TATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGGAAAAAATATCGACA
131 TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAAAAAAATATCGACA
125902 CAAA
195 CAAA
125906 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
1 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
125971 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
66 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
*
126036 TATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAAAAAATATCGACA
131 TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAAAAAAATATCGACA
126101 CAAA
195 CAAA
*
126105 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGGTATAATTGTACCGGTT
1 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
126170 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
66 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
*
126235 TATATGGATCGACACTTTATGGGTGCACCCTATTTTCCATTCATTCTGGGAAAAAAATATCGACA
131 TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAAAAAAATATCGACA
126300 CAAA
195 CAAA
126304 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
1 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
*
126369 AGATTG-AAAATTACATATT--ATTATAC-TTT-GGTTCGATGCTTTTGGGATCGACACTTTTTA
66 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
126429 TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACAC
131 TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACAC
126494 AAA
196 AAA
*
126497 CTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTT
1 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
*
126562 AGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGATCGACACTTTTT
66 AGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGATCGACACTTTTT
* **
126627 ATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGAC
130 ATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAATATCGAC
126692 ACAAA
194 ACAAA
126697 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAA-TGTACCGGTT
1 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
126761 AGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
66 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
126825 TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACAC
131 TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACAC
126890 AAA
196 AAA
126893 CTATATTAGTGT-----CA-TA--T---C-----CTCTCATAAAACCGGTATAATTGTACCGGTT
1 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
* * *
126942 AGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATTGACACTTTTT
66 AGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGATCGACAC-TTTT
127007 TATATATGGATCGACACTTTATGGGTGCACCCTGTT
129 TATATATGGATCGACACTTTATGGGTGCACCCTGTT
127043 GGCCATATTG
Statistics
Matches: 1492, Mismatches: 28, Indels: 40
0.96 0.02 0.03
Matches are distributed among these distances:
180 20 0.01
181 16 0.01
182 28 0.02
183 21 0.01
184 40 0.03
185 1 0.00
188 1 0.00
190 2 0.00
191 2 0.00
193 91 0.06
194 89 0.06
195 3 0.00
196 45 0.03
197 172 0.12
198 418 0.28
199 471 0.32
200 72 0.05
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (198 bp):
CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGACAC
AAA
Found at i:126049 original size:396 final size:396
Alignment explanation
Indices: 125312--127042 Score: 3067
Period size: 396 Copynumber: 4.4 Consensus size: 396
125302 CTGCACCCAG
* *
125312 CTATGTTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
1 CTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTT
125377 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
66 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
125442 TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAAAAAAATATCGACA
131 TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGGAAAAAAATATCGACA
* *
125506 CAAACTATATTAGTGTCGACACATTATTTAGACAAATCCTCTCATAAAACCGGTATAATTGTACC
196 CAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACC
125571 GGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTT
261 GGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTT
*
125636 TTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAAAAATATCG
325 TTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCG
125701 ACACAAA
390 ACACAAA
125708 CTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTT
1 CTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTT
125773 AGATTGAAAAATTACAT-TTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
66 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
* *
125837 TATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGGAAAAAATATCGACA
131 TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGGAAAAAAATATCGACA
125902 CAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACC
196 CAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACC
125967 GGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTT
261 GGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTT
*
126032 TTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAAAAAATATC
325 TTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAAAAAAATATC
126097 GACACAAA
389 GACACAAA
* *
126105 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGGTATAATTGTACCGGTT
1 CTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTT
126170 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
66 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
*
126235 TATATGGATCGACACTTTATGGGTGCACCCTATTTTCCATTCATTCTGGGAAAAAAATATCGACA
131 TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGGAAAAAAATATCGACA
126300 CAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACC
196 CAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACC
*
126365 GGTTAGATTGAAAATTACATATT--ATTATAC-TTT-GGTTCGATGCTTTTGGGATCGACACTTT
261 GGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTT
126426 TTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGA
326 TTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGA
126491 CACAAA
391 CACAAA
126497 CTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTT
1 CTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTT
*
126562 AGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGATCGACACTTTTT
66 AGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGATCGACACTTTTT
* ** *
126627 ATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGAC
130 ATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGGAAAAAAATATCGAC
126692 ACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAA-TGTAC
195 ACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTAC
126756 CGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTT
260 CGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTT
126821 TTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCG
325 TTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCG
126886 ACACAAA
390 ACACAAA
126893 CTATATTA--GT-G----------T---CATATCCTCTCATAAAACCGGTATAATTGTACCGGTT
1 CTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTT
* * *
126942 AGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATTGACACTTTTT
66 AGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGATCGACAC-TTTT
127007 TATATATGGATCGACACTTTATGGGTGCACCCTGTT
129 TATATATGGATCGACACTTTATGGGTGCACCCTGTT
127043 GGCCATATTG
Statistics
Matches: 1301, Mismatches: 25, Indels: 33
0.96 0.02 0.02
Matches are distributed among these distances:
380 95 0.07
381 39 0.03
383 1 0.00
392 148 0.11
393 224 0.17
394 12 0.01
395 103 0.08
396 381 0.29
397 114 0.09
398 184 0.14
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (396 bp):
CTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTT
AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGGAAAAAAATATCGACA
CAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACC
GGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTT
TTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCGA
CACAAA
Found at i:127207 original size:19 final size:19
Alignment explanation
Indices: 127161--127209 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
127151 TTATATTCAC
*
127161 ATACAAAAATATAAATAGT
1 ATACAAAATTATAAATAGT
**
127180 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATAGT
127199 ATACAAAATTA
1 ATACAAAATTA
127210 ACTCGACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATAGT
Found at i:129031 original size:33 final size:33
Alignment explanation
Indices: 128994--129059 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
128984 CATCTTAATA
*
128994 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
129027 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
129060 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:131375 original size:17 final size:18
Alignment explanation
Indices: 131353--131395 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
131343 ATATATCCGG
131353 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
131370 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
131390 TATCAT
1 TATCAT
131396 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:131413 original size:20 final size:19
Alignment explanation
Indices: 131358--131404 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
131348 TCCGGTATCA
131358 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
131377 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
131398 TTTTACC
1 TTTTACC
131405 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:131552 original size:20 final size:20
Alignment explanation
Indices: 131526--131571 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
131516 CACTTTTAAA
131526 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
131545 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
131566 TTTACC
1 TTTACC
131572 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:139858 original size:254 final size:253
Alignment explanation
Indices: 139409--139916 Score: 691
Period size: 254 Copynumber: 2.0 Consensus size: 253
139399 CGTCTAGACG
* * *
139409 CTTGAATTCGATTTGTTTGTCCTTTGAGTCCGACACTTGGATTCAATTTCTGGACTCTGATGAAA
1 CTTGAATTCGATTTGTTTGTCCGTTGAATCCGACACTTAGATTCAATTTCTGGAC-CTGATGAAA
* *
139474 CCACTTTAGCATTCATGTATGTTGTTAGGATTGATCAAATTTTCCATCTATAGTTAGCTATCAAA
65 CCACTTTAGCATTCATGTATGTTGTTAGGATTGATCAAATTTTCCACCTATAGTTAGCTAGCAAA
*
139539 CTGGTTTTTGAACATCTTAAGACGATACACATATAAGTGATTGTATTCACTCGATTTTACGAGGC
130 CTGGTTTTTGAACATCATAAGACGATACACATATAAGTGATTGTATTCACTCGATTTTACGAGGC
* * *
139604 TGATTATATATTGAAATGGTTTGATGCT-ACTAGAGACATTGTTTTGAGAGTGGTTGACA
195 TGATAATATATTGAAATGGTTTGATG-TAACTAGAGACATCGTTTTGAGAATGGTTGACA
* ** *
139663 CTTGAATTCGATTTGTTTGTCCGTTGAATCCGACACTTAGTTTGGATTTCTGGA-CTGATGGAAC
1 CTTGAATTCGATTTGTTTGTCCGTTGAATCCGACACTTAGATTCAATTTCTGGACCTGATGAAAC
* * * * *
139727 CACTTTGGCATTCTTGTATGTTTGTTAGGATTGATCAGA-TTTCCGCCTATTGTTAGCTAGCAAA
66 CACTTTAGCATTCATGTATG-TTGTTAGGATTGATCAAATTTTCCACCTATAGTTAGCTAGCAAA
* * * * * *
139791 CTGGTTTTTTAACATCATCAGACATTGTTGCACATCTAAGTGTTTGTATTCACTCGA-TTTACGA
130 CTGGTTTTTGAACATCATAAGAC---GATACACATATAAGTGATTGTATTCACTCGATTTTACGA
* * *
139855 GGCTGATAATATATTGAAGTGTTTTGATGTAACTAGAGGCATCGTTTTGAGAATGGTTGACA
192 GGCTGATAATATATTGAAATGGTTTGATGTAACTAGAGACATCGTTTTGAGAATGGTTGACA
139917 TTGTAGACAT
Statistics
Matches: 222, Mismatches: 27, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
252 68 0.31
253 18 0.08
254 109 0.49
255 27 0.12
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (253 bp):
CTTGAATTCGATTTGTTTGTCCGTTGAATCCGACACTTAGATTCAATTTCTGGACCTGATGAAAC
CACTTTAGCATTCATGTATGTTGTTAGGATTGATCAAATTTTCCACCTATAGTTAGCTAGCAAAC
TGGTTTTTGAACATCATAAGACGATACACATATAAGTGATTGTATTCACTCGATTTTACGAGGCT
GATAATATATTGAAATGGTTTGATGTAACTAGAGACATCGTTTTGAGAATGGTTGACA
Found at i:142813 original size:63 final size:64
Alignment explanation
Indices: 142705--142836 Score: 248
Period size: 63 Copynumber: 2.1 Consensus size: 64
142695 TAAAAAACAA
*
142705 ACCATTAATGAGTATCGTTAAAAAAACCTCTTTTAAACCTAATAAATAGTAAGAGTACTTAACT
1 ACCATTAATGAGTATCGTTAAAAAAACATCTTTTAAACCTAATAAATAGTAAGAGTACTTAACT
142769 ACCATTAATGAGTATCGTT-AAAAAACATCTTTTAAACCTAATAAATAGTAAGAGTACTTAACT
1 ACCATTAATGAGTATCGTTAAAAAAACATCTTTTAAACCTAATAAATAGTAAGAGTACTTAACT
142832 ACCAT
1 ACCAT
142837 AAATCAAGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
63 48 0.72
64 19 0.28
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (64 bp):
ACCATTAATGAGTATCGTTAAAAAAACATCTTTTAAACCTAATAAATAGTAAGAGTACTTAACT
Found at i:144841 original size:59 final size:58
Alignment explanation
Indices: 144778--144945 Score: 171
Period size: 59 Copynumber: 2.8 Consensus size: 58
144768 AGAGATGTGA
* * *
144778 TTAGAAT-ATACAT-ATAATTTAGGATTAAATTGAAATGTTCAAAAAGTTTGGGGATTAAT
1 TTAGAATGATA-ATAATAGTTTAGGATGAAATTGAAATGTT--AAAAGTTTGAGGATTAAT
* * * *
144837 TTAGAATGA-AGATCATAGTTTGGGGATGAAAATGAAATGTTAAAAGTCTGAGGATTAAT
1 TTAGAATGATA-ATAATAGTTT-AGGATGAAATTGAAATGTTAAAAGTTTGAGGATTAAT
* *
144896 TTAAAATGATAGTAATAGTTTAGGGATGAAATTGAAATGTTTAAAAGTTT
1 TTAGAATGATAATAATAGTTTA-GGATGAAATTGAAATG-TTAAAAGTTT
144946 AGGTACTAAT
Statistics
Matches: 90, Mismatches: 13, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
59 57 0.63
60 17 0.19
61 16 0.18
ACGTcount: A:0.42, C:0.02, G:0.21, T:0.35
Consensus pattern (58 bp):
TTAGAATGATAATAATAGTTTAGGATGAAATTGAAATGTTAAAAGTTTGAGGATTAAT
Found at i:144983 original size:60 final size:57
Alignment explanation
Indices: 144798--144983 Score: 158
Period size: 59 Copynumber: 3.1 Consensus size: 57
144788 CATATAATTT
* * * *
144798 AGGATTAAATTGAAATGTTCAAAAAGTTTGGGGATTAATTTAGAATGAAGATCATAGTTTG
1 AGGATGAAATTGAAATGTT-TAAAAGTTT-AGGATTAATTTA-AATG-AGATCATAGTTTA
* * * * *
144859 GGGATGAAAATGAAATG-TTAAAAGTCTGAGGATTAATTTAAAATGATAGTAATAGTTTA
1 AGGATGAAATTGAAATGTTTAAAAGT-TTAGGATTAATTT-AAATGAGA-TCATAGTTTA
* * * *
144918 GGGATGAAATTGAAATGTTTAAAAGTTTAGGTACTAATTTGAAATGAGGATCATAGATCA
1 AGGATGAAATTGAAATGTTTAAAAGTTTAGG-ATTAATTT-AAATGA-GATCATAGTTTA
144978 AGGATG
1 AGGATG
144984 TGTGATGCAA
Statistics
Matches: 101, Mismatches: 18, Indels: 13
0.77 0.14 0.10
Matches are distributed among these distances:
58 2 0.02
59 48 0.48
60 36 0.36
61 15 0.15
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (57 bp):
AGGATGAAATTGAAATGTTTAAAAGTTTAGGATTAATTTAAATGAGATCATAGTTTA
Found at i:145800 original size:16 final size:18
Alignment explanation
Indices: 145761--145801 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
145751 ATTTAATAAT
145761 AATTATTATAGTAAATTA
1 AATTATTATAGTAAATTA
*
145779 AA-TATT-TAGT-ACTTA
1 AATTATTATAGTAAATTA
145794 AATTATTA
1 AATTATTA
145802 ATTTTGACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 6 0.30
16 8 0.40
17 4 0.20
18 2 0.10
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (18 bp):
AATTATTATAGTAAATTA
Found at i:146174 original size:2 final size:2
Alignment explanation
Indices: 146167--146223 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
146157 AAAAATAAAT
146167 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
146209 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
146224 TAGATCGAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:146494 original size:15 final size:15
Alignment explanation
Indices: 146474--146504 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
146464 TAAAATTAAT
*
146474 AAATATAGTTTACTA
1 AAATATAATTTACTA
146489 AAATATAATTTACTA
1 AAATATAATTTACTA
146504 A
1 A
146505 CATCATGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (15 bp):
AAATATAATTTACTA
Found at i:151629 original size:20 final size:22
Alignment explanation
Indices: 151585--151630 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
151575 TAAGCCGTCT
* *
151585 TATGATTATGTTTTTTTATTAA
1 TATGATTATGTTTTTTAAATAA
151607 TATGATTATG-TTTTTAAAT-A
1 TATGATTATGTTTTTTAAATAA
151627 TATG
1 TATG
151631 TATCTGAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 7 0.32
22 10 0.45
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (22 bp):
TATGATTATGTTTTTTAAATAA
Found at i:154425 original size:19 final size:19
Alignment explanation
Indices: 154391--154454 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
154381 TAAAATAAAT
154391 TTTATTTTCTATCAATATAA
1 TTTATTTT-TATCAATATAA
* *
154411 TTTATTTTAATCAAT-T-T
1 TTTATTTTTATCAATATAA
*
154428 TTTATATTTTATAAATATAA
1 TTTAT-TTTTATCAATATAA
154448 TTTATTT
1 TTTATTT
154455 AATTGAGTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
17 5 0.14
18 9 0.25
19 9 0.25
20 13 0.36
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATTTTTATCAATATAA
Found at i:155375 original size:60 final size:60
Alignment explanation
Indices: 155262--155375 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
155252 AATAATTGAG
* * *
155262 TGATCATTTTGTAATTTCTAATAGTTAAAAGACTTAACAAAATAACATTTTATAGTCAGA
1 TGATCATTTTATAATTTCTAATAGTTAAAAGACTTAACAAAAGAACATCTTATAGTCAGA
* * * * * *
155322 TGATTATTTTATAATTTTTAATAGTTTAAGGACTTAATAAAAGAATATCTTATA
1 TGATCATTTTATAATTTCTAATAGTTAAAAGACTTAACAAAAGAACATCTTATA
155376 ATTAGAAACC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (60 bp):
TGATCATTTTATAATTTCTAATAGTTAAAAGACTTAACAAAAGAACATCTTATAGTCAGA
Found at i:158954 original size:36 final size:36
Alignment explanation
Indices: 158914--158986 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
158904 TTGTAAACAC
158914 CCTAAATTTTAAGCTAATGGCTAGACTAATCAGGAA
1 CCTAAATTTTAAGCTAATGGCTAGACTAATCAGGAA
*
158950 CCTAAATTTTAAGCTAATGGCTAGACTAATCCGGAA
1 CCTAAATTTTAAGCTAATGGCTAGACTAATCAGGAA
158986 C
1 C
158987 GAACGCATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (36 bp):
CCTAAATTTTAAGCTAATGGCTAGACTAATCAGGAA
Found at i:161614 original size:28 final size:28
Alignment explanation
Indices: 161582--161675 Score: 179
Period size: 28 Copynumber: 3.4 Consensus size: 28
161572 GAGCTCAATG
161582 CACTCACTATAAAGGATCGAGGATATAC
1 CACTCACTATAAAGGATCGAGGATATAC
161610 CACTCACTATAAAGGATCGAGGATATAC
1 CACTCACTATAAAGGATCGAGGATATAC
161638 CACTCACTATAAAGGATCGAGGATATAC
1 CACTCACTATAAAGGATCGAGGATATAC
*
161666 CACTAACTAT
1 CACTCACTAT
161676 TTTTCTCCCT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.22
Consensus pattern (28 bp):
CACTCACTATAAAGGATCGAGGATATAC
Found at i:164931 original size:15 final size:15
Alignment explanation
Indices: 164913--164953 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
164903 CTCGAGTTCT
164913 TCATGATCGTCGTCG
1 TCATGATCGTCGTCG
164928 TCATCG-TCGTCGTCG
1 TCAT-GATCGTCGTCG
*
164943 TCATCATCGTC
1 TCATGATCGTC
164954 CGATGATGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 22 0.96
16 1 0.04
ACGTcount: A:0.12, C:0.32, G:0.22, T:0.34
Consensus pattern (15 bp):
TCATGATCGTCGTCG
Found at i:166347 original size:24 final size:24
Alignment explanation
Indices: 166295--166348 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
166285 AGATTCGTTT
* *
166295 GTTTAAGTTCATTCATTTGTATTT
1 GTTTATGTTCATTCATTTGTATTC
* * *
166319 TTTTATGTTCGTTCATTTGTGTTC
1 GTTTATGTTCATTCATTTGTATTC
166343 GTTTAT
1 GTTTAT
166349 CATTTTAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.61
Consensus pattern (24 bp):
GTTTATGTTCATTCATTTGTATTC
Found at i:169807 original size:3 final size:3
Alignment explanation
Indices: 169792--169825 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
169782 TCTTTGTTAC
*
169792 TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
169826 TACTATTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:170825 original size:6 final size:6
Alignment explanation
Indices: 170814--170861 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
170804 AAAAGAAATG
* * *
170814 AAATAA AAATAA AAATAT AAATAA ATAAT-A AAATAA GAATAA TAATAA
1 AAATAA AAATAA AAATAA AAATAA A-AATAA AAATAA AAATAA AAATAA
170862 CGGTCTCCGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 3 0.08
6 30 0.83
7 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (6 bp):
AAATAA
Found at i:171787 original size:34 final size:32
Alignment explanation
Indices: 171740--171824 Score: 82
Period size: 34 Copynumber: 2.6 Consensus size: 32
171730 AAAAATTATT
* *
171740 ATATATATATATATATTATTATGAG-TTATCTTA
1 ATATAT-TTTATATATTATTAT-AGTTTAACTTA
* * *
171773 ACATATTTTTTATATTTCATTATAGTTTAAGTTA
1 ATATATTTTATATA-TT-ATTATAGTTTAACTTA
171807 ATATATTTTATATATTAT
1 ATATATTTTATATATTAT
171825 AGTATTAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
32 8 0.19
33 11 0.26
34 23 0.55
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (32 bp):
ATATATTTTATATATTATTATAGTTTAACTTA
Found at i:173621 original size:31 final size:32
Alignment explanation
Indices: 173561--173622 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
173551 TGGCTAAGGG
* *
173561 ACTAAAATTGAACGGATTCGATAATGTTAGGA
1 ACTAAAATCGAACGGATTCGATAACGTTAGGA
173593 ACTAAAATCGAACGGA-TCGATAACGTTAGG
1 ACTAAAATCGAACGGATTCGATAACGTTAGG
173623 GATTATTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (32 bp):
ACTAAAATCGAACGGATTCGATAACGTTAGGA
Found at i:174512 original size:5 final size:5
Alignment explanation
Indices: 174475--174503 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
174465 GAATAAACTA
174475 GAAGT GAAGT GAAGT GAAGT GAAGT GAAG
1 GAAGT GAAGT GAAGT GAAGT GAAGT GAAG
174504 AAAGTAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.17
Consensus pattern (5 bp):
GAAGT
Found at i:175964 original size:21 final size:21
Alignment explanation
Indices: 175938--175985 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
175928 TTAACAAGAC
*
175938 AGTTCACTGTGTTGACGTGTT
1 AGTTCACTGTGTTGACGTGGT
175959 AGTTCACTGTGTTGACGTGGT
1 AGTTCACTGTGTTGACGTGGT
175980 AGTTCA
1 AGTTCA
175986 TCTGCCACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.29, T:0.40
Consensus pattern (21 bp):
AGTTCACTGTGTTGACGTGGT
Found at i:183747 original size:29 final size:31
Alignment explanation
Indices: 183712--183769 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
183702 TTCATTTAAG
*
183712 TACCTAAA-GTAT-TTTTTGGTCAAAATAAA
1 TACCTAAACGTATCTTTTTAGTCAAAATAAA
*
183741 TACCTAAACTTATCTTTTTAGTCAAAATA
1 TACCTAAACGTATCTTTTTAGTCAAAATA
183770 GGTGGCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
30 3 0.12
31 14 0.56
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (31 bp):
TACCTAAACGTATCTTTTTAGTCAAAATAAA
Found at i:183928 original size:27 final size:27
Alignment explanation
Indices: 183887--183949 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
183877 TGAAAAATTG
* *
183887 AATACTTTAGGTACCAATTTTGACCAA
1 AATACTTTAGATACCAATTTTGACAAA
*
183914 AATACTTTAGATACCTATTTTGACAAA
1 AATACTTTAGATACCAATTTTGACAAA
183941 AATACTTTA
1 AATACTTTA
183950 AATATTCCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (27 bp):
AATACTTTAGATACCAATTTTGACAAA
Found at i:188889 original size:38 final size:39
Alignment explanation
Indices: 188847--188920 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
188837 TTTGAAAAAC
* *
188847 ATATAATATATA-A-TTTTAGAAAATGGTTTTTGAAAGTA
1 ATATAATATATATATTTTTAAAAAACGG-TTTTGAAAGTA
188885 ATATAATATATATATTTTTAAAAAACGGTTTTGAAA
1 ATATAATATATATATTTTTAAAAAACGGTTTTGAAA
188921 AAAAAACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
38 12 0.38
39 9 0.28
40 11 0.34
ACGTcount: A:0.46, C:0.01, G:0.11, T:0.42
Consensus pattern (39 bp):
ATATAATATATATATTTTTAAAAAACGGTTTTGAAAGTA
Found at i:189558 original size:31 final size:30
Alignment explanation
Indices: 189514--189572 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
189504 AGATGCTAAA
* * *
189514 TTTAGTGATCATTTTGTAATCATTTAAAAAG
1 TTTAATGACCATTTTGTAAT-ATTCAAAAAG
189545 TTTAATGACCATTTTGTAATATTCAAAA
1 TTTAATGACCATTTTGTAATATTCAAAA
189573 TTTACTGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.44
Consensus pattern (30 bp):
TTTAATGACCATTTTGTAATATTCAAAAAG
Found at i:192923 original size:207 final size:209
Alignment explanation
Indices: 192552--193083 Score: 750
Period size: 207 Copynumber: 2.5 Consensus size: 209
192542 AAATAAGTTG
* *
192552 GATTCAAGCTAAA-TGATAGTCAAGTTAAGACTTTTCCTCAATCCCAAACAGAAAATTGCAGATT
1 GATTCAAG-AAAATTGATAGTCAAGTTAAGACTTTTCCTCAA-CCCAAACAGAAAAATGCAGATT
* *
192616 CCCCAGAATTTTGCATGCATCCAAAAGAAGAAAACAACAAACAAATTGAAAATCAGAAACACACA
64 CCCCAGAATTTTGCATGCATTCAAAAGAAGAAAACAACAAACAAATTGAAAACCAGAAACACACA
* *
192681 CAAGCATGGGACTAAAACTTATAAGCTAATAACTTTGCTCATGTAAAAGAAAACAACACAACTAA
129 CAAGCATGGGACTAAAACTTATAAGCTAATAACTTTCCTCATGCAAAAGAAAACAACACAACTAA
192746 ATCAGCAAAATATTGT
194 ATCAGCAAAATATTGT
* * *
192762 GGTTCAAGAAAATTGATAGTCAAGTTAAGACTTTCCCTCAA-ACAAACA-AAAAATGCAGATTCC
1 GATTCAAGAAAATTGATAGTCAAGTTAAGACTTTTCCTCAACCCAAACAGAAAAATGCAGATTCC
*
192825 CCAGAATTTTGCATGCATTCAAAAGAAGAAAACAACCAACAAATTGAAAACCA-ACAACACACAC
66 CCAGAATTTTGCATGCATTCAAAAGAAGAAAACAACAAACAAATTGAAAACCAGA-AACACACAC
* * * *
192889 AAGCATGGGACTTAAACTTATAA-ATCAATAACTTTCCTCGTGCAACAGAAAACAACACAACTAA
130 AAGCATGGGACTAAAACTTATAAGCT-AATAACTTTCCTCATGCAAAAGAAAACAACACAACTAA
*
192953 ATCAGCAACATATTGT
194 ATCAGCAAAATATTGT
** * * *
192969 GATTCAAGCTAATTGATATTCAAGTTAAAACTTTTCCTCAATCCCAAACAGAAAAATGCAGATTT
1 GATTCAAGAAAATTGATAGTCAAGTTAAGACTTTTCCTCAA-CCCAAACAGAAAAATGCAGATTC
* *** * *
193034 CCCAGATTTTTTTGTGCATTCAAAAGAAGAAAACAACTAACCAATTGAAA
65 CCCAGAATTTTGCATGCATTCAAAAGAAGAAAACAACAAACAAATTGAAA
193084 GTGCATCAAA
Statistics
Matches: 287, Mismatches: 29, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
206 2 0.01
207 179 0.62
208 6 0.02
209 9 0.03
210 91 0.32
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (209 bp):
GATTCAAGAAAATTGATAGTCAAGTTAAGACTTTTCCTCAACCCAAACAGAAAAATGCAGATTCC
CCAGAATTTTGCATGCATTCAAAAGAAGAAAACAACAAACAAATTGAAAACCAGAAACACACACA
AGCATGGGACTAAAACTTATAAGCTAATAACTTTCCTCATGCAAAAGAAAACAACACAACTAAAT
CAGCAAAATATTGT
Found at i:199168 original size:23 final size:23
Alignment explanation
Indices: 199142--199185 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
199132 TTAAATCGAA
* * *
199142 GTCAATTTATATTTATGTTATGT
1 GTCAAATTAAATTTATATTATGT
199165 GTCAAATTAAATTTATATTAT
1 GTCAAATTAAATTTATATTAT
199186 AATTGAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (23 bp):
GTCAAATTAAATTTATATTATGT
Found at i:203836 original size:21 final size:20
Alignment explanation
Indices: 203809--203907 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
203799 AATCAGTTTC
203809 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
203830 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
203851 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
203871 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
203892 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
203908 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:203898 original size:20 final size:20
Alignment explanation
Indices: 203874--204067 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
203864 CGATTTTCCA
* ** *
203874 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
203894 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
203914 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
203934 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
203954 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
203974 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
203994 ATATCGCAACGCGTATCTGT
1 AAATCGCAACGCGTATCCGT
* * *
204014 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
204034 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
204055 AAATCGCAACGCG
1 AAATCGCAACGCG
204068 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:203958 original size:60 final size:60
Alignment explanation
Indices: 203874--204067 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
203864 CGATTTTCCA
* ** * *
203874 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
203934 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * **
203994 ATATCGCAACGCGTATCTGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
204055 AAATCGCAACGCG
1 AAATCGCAACGCG
204068 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:204488 original size:33 final size:33
Alignment explanation
Indices: 204449--204519 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
204439 TTCACTTAAA
*
204449 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
204482 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
204515 TTTCA
1 TTTCA
204520 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.25, G:0.15, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:204625 original size:21 final size:20
Alignment explanation
Indices: 204599--204702 Score: 87
Period size: 21 Copynumber: 5.5 Consensus size: 20
204589 TGCAGAAGAG
204599 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
204620 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
204640 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
204661 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
204675 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
204694 TCGCAACGA
1 TCGCAACGA
204703 CAGAATCGCA
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 10 0.15
20 16 0.25
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.11
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:204643 original size:20 final size:21
Alignment explanation
Indices: 204597--204675 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
204587 TTTGCAGAAG
*
204597 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
204619 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
204638 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
204660 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
204676 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:204656 original size:41 final size:41
Alignment explanation
Indices: 204598--204675 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
204588 TTGCAGAAGA
* *
204598 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAATGACT
204639 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAAT
204676 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.27, T:0.12
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAATGACT
Found at i:204691 original size:33 final size:33
Alignment explanation
Indices: 204651--204720 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
204641 CGCAACGAGA
*
204651 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGACAGAATCGCAACGC
*
204684 GAAATGAAAATCGCAACGACAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGACAGAATCGCAACGC
204717 GAAA
1 GAAA
204721 CCAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.47, C:0.21, G:0.24, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGACAGAATCGCAACGC
Found at i:204727 original size:33 final size:33
Alignment explanation
Indices: 204657--204731 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
204647 GAGAGAAATG
* * **
204657 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
204690 AAAATCGCAACGACAGAATCGCAACGCGAAACC
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
204723 AAAATCGCA
1 AAAATCGCA
204732 TTGCGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.47, C:0.25, G:0.21, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGACAGAATCGCAACGCGAAACC
Found at i:204730 original size:19 final size:18
Alignment explanation
Indices: 204673--204731 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
204663 GCAACGAGAG
*
204673 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-CAA
*
204692 AATCGCAA--CG--ACAG
1 AATCGCAACGCGAAACAA
204706 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-CAA
204725 AATCGCA
1 AATCGCA
204732 TTGCGATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 9 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.53
ACGTcount: A:0.46, C:0.27, G:0.19, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAACAA
Found at i:204749 original size:19 final size:19
Alignment explanation
Indices: 204727--204824 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
204717 GAAACCAAAA
*
204727 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
204746 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
204760 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
204779 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
204793 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
204812 TCGCGTTGCGATT
1 TCGCGTTGCGATT
204825 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:204768 original size:14 final size:14
Alignment explanation
Indices: 204749--204838 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
204739 TTTCATTTCG
204749 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
204763 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
204782 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
204796 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
204813 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
204829 CGTTGCGATT
1 CGTTGCGATT
204839 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:204774 original size:33 final size:33
Alignment explanation
Indices: 204732--204846 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
204722 CAAAATCGCA
204732 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
204765 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
204798 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
204831 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
204847 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:206862 original size:184 final size:184
Alignment explanation
Indices: 206547--206922 Score: 691
Period size: 184 Copynumber: 2.0 Consensus size: 184
206537 TTGCTTAGTA
* *
206547 AATTTATTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTATTCGGTTGCTACCAATTCTGCTAAACTATGTATTCTATAACACTGTGAAATAGTATTTG
206612 TCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGT
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGT
206677 ATTCTTTAACACTGTG-AATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
131 ATTCTTTAACACTGTGAAATAGTATTTGTC-TTGTTTTGTCTTTTGGTTGAAAGT
* *
206731 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTATAACACTGTGAAATAGTATTTG
1 AATTTATTCGGTTGCTACCAATTCTGCTAAACTATGTATTCTATAACACTGTGAAATAGTATTTG
206796 TCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGT
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGT
206861 ATTCTTTAACACTGTGAAATAGTATTTGTCTTGTTTTGTCTTTTGGTTGAAAGT
131 ATTCTTTAACACTGTGAAATAGTATTTGTCTTGTTTTGTCTTTTGGTTGAAAGT
206915 AAATTTAT
1 -AATTTAT
206923 CCATTCAAGT
Statistics
Matches: 185, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
184 166 0.90
185 19 0.10
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (184 bp):
AATTTATTCGGTTGCTACCAATTCTGCTAAACTATGTATTCTATAACACTGTGAAATAGTATTTG
TCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGT
ATTCTTTAACACTGTGAAATAGTATTTGTCTTGTTTTGTCTTTTGGTTGAAAGT
Found at i:206939 original size:93 final size:93
Alignment explanation
Indices: 206543--206920 Score: 699
Period size: 93 Copynumber: 4.1 Consensus size: 93
206533 TAGATTGCTT
* *
206543 AGTAAATTTATTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
206608 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
206636 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
206700 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
206728 AGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
206792 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
206820 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
206885 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
206912 AGTAAATTT
1 AGTAAATTT
206921 ATCCATTCAA
Statistics
Matches: 277, Mismatches: 6, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
91 51 0.18
92 106 0.38
93 120 0.43
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:207004 original size:19 final size:19
Alignment explanation
Indices: 206964--207091 Score: 107
Period size: 19 Copynumber: 7.3 Consensus size: 19
206954 TAGTTTACTT
* *
206964 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
206984 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
207003 TCGCAACGCGAAA-TGAAA
1 TCGCAACGCGAAACCAAAA
*
207021 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
207035 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* *
207054 TCGCAA--CG--A-TAAGA
1 TCGCAACGCGAAACCAAAA
207068 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
207087 TCGCA
1 TCGCA
207092 TTGCGATTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
14 18 0.21
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.13
19 35 0.41
20 13 0.15
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:207060 original size:33 final size:32
Alignment explanation
Indices: 207000--207091 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 32
206990 CGCGAAACCA
**
207000 AAATCGCAACGCGAAA-TGAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
207031 AGAATCGCAACGCGAAACCAAAATCGCAACGAT
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
207064 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
207092 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
31 1 0.02
32 16 0.29
33 38 0.69
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:207109 original size:19 final size:19
Alignment explanation
Indices: 207087--207221 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
207077 GAAACCAAAA
*
207087 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
207106 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
207122 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
207139 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
207155 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
207172 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
207191 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
207211 TCGTGTTGCGA
1 TCGCGTTGCGA
207222 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Done.