Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 50 of 226
Found at i:16649548 original size:25 final size:24
Alignment explanation
Indices: 16649519--16649566 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
16649509 TATAAAAAGA
* *
16649519 TTTATATTTCAATTTTAATTCTTTG
1 TTTATATTTAAAATTTAA-TCTTTG
16649544 TTTATATTTAAAATTTAATCTTT
1 TTTATATTTAAAATTTAATCTTT
16649567 ATATTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTATATTTAAAATTTAATCTTTG
Found at i:16651890 original size:54 final size:54
Alignment explanation
Indices: 16651827--16651996 Score: 161
Period size: 54 Copynumber: 3.2 Consensus size: 54
16651817 ATATAACGGA
16651827 CTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAAATTCGAGAATATATGATAG
1 CTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAAATTCGAGAATATATGATAG
* * * *** * * * * * * **
16651881 CTTGGAGGCAAACTCGCCACCTTGTAGACAAGCAAA----A-AAGATATAACGG
1 CTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAAATTCGAGAATATATGATAG
16651930 ACTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAAATTCGAGAATATATGATAG
1 -CTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAAATTCGAGAATATATGATAG
*
16651985 CTTGGAGGCAAA
1 CTTGAAGGCAAA
16651997 CTCGCCACCT
Statistics
Matches: 81, Mismatches: 29, Indels: 12
0.66 0.24 0.10
Matches are distributed among these distances:
49 8 0.10
50 27 0.33
54 38 0.47
55 8 0.10
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (54 bp):
CTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAAATTCGAGAATATATGATAG
Found at i:16651934 original size:104 final size:104
Alignment explanation
Indices: 16651812--16652020 Score: 418
Period size: 104 Copynumber: 2.0 Consensus size: 104
16651802 AAGGGAACCC
16651812 AAAAGATATAACGGACTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAAATTCGAGAATATATG
1 AAAAGATATAACGGACTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAAATTCGAGAATATATG
16651877 ATAGCTTGGAGGCAAACTCGCCACCTTGTAGACAAGCAA
66 ATAGCTTGGAGGCAAACTCGCCACCTTGTAGACAAGCAA
16651916 AAAAGATATAACGGACTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAAATTCGAGAATATATG
1 AAAAGATATAACGGACTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAAATTCGAGAATATATG
16651981 ATAGCTTGGAGGCAAACTCGCCACCTTGTAGACAAGCAA
66 ATAGCTTGGAGGCAAACTCGCCACCTTGTAGACAAGCAA
16652020 A
1 A
16652021 CTCAAGAAAT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 105 1.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (104 bp):
AAAAGATATAACGGACTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAAATTCGAGAATATATG
ATAGCTTGGAGGCAAACTCGCCACCTTGTAGACAAGCAA
Found at i:16651963 original size:50 final size:50
Alignment explanation
Indices: 16651812--16651966 Score: 132
Period size: 50 Copynumber: 3.0 Consensus size: 50
16651802 AAGGGAACCC
16651812 AAAAGATATAACGGACTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAA
1 AAAAGATATAACGGACTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAA
** * * * * * *** * * * *
16651862 ATTCGAGA-ATATATGATAGCTTGGAGGCAAACTCGCCACCTTGTAGACAAGCAA
1 A--AAAGATATA-ACG-GA-CTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAA
16651916 AAAAGATATAACGGACTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAA
1 AAAAGATATAACGGACTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAA
16651966 A
1 A
16651967 TTCGAGAATA
Statistics
Matches: 71, Mismatches: 28, Indels: 12
0.64 0.25 0.11
Matches are distributed among these distances:
50 27 0.38
51 4 0.06
52 10 0.14
53 4 0.06
54 26 0.37
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.22
Consensus pattern (50 bp):
AAAAGATATAACGGACTTGAAGGCAAAGTTGTTGCCCTATTGGCAAGCAA
Found at i:16652017 original size:54 final size:54
Alignment explanation
Indices: 16651855--16652020 Score: 162
Period size: 54 Copynumber: 3.1 Consensus size: 54
16651845 GCCCTATTGG
16651855 CAAGCAAATTCGAGAATATATGATAGCTTGGAGGCAAACTCGCCACCTTGTAGA
1 CAAGCAAATTCGAGAATATATGATAGCTTGGAGGCAAACTCGCCACCTTGTAGA
* * ** * * * *** * * * *
16651909 CAAGCAAA----A-AAGATATAACGGACTTGAAGGCAAAGTTGTTGCCCTATTGG
1 CAAGCAAATTCGAGAATATATGATAG-CTTGGAGGCAAACTCGCCACCTTGTAGA
16651959 CAAGCAAATTCGAGAATATATGATAGCTTGGAGGCAAACTCGCCACCTTGTAGA
1 CAAGCAAATTCGAGAATATATGATAGCTTGGAGGCAAACTCGCCACCTTGTAGA
16652013 CAAGCAAA
1 CAAGCAAA
16652021 CTCAAGAAAT
Statistics
Matches: 78, Mismatches: 28, Indels: 12
0.66 0.24 0.10
Matches are distributed among these distances:
49 8 0.10
50 27 0.35
54 35 0.45
55 8 0.10
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (54 bp):
CAAGCAAATTCGAGAATATATGATAGCTTGGAGGCAAACTCGCCACCTTGTAGA
Found at i:16652847 original size:9 final size:9
Alignment explanation
Indices: 16652833--16652863 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
16652823 GTTAAATGAA
16652833 TCGAGTTAT
1 TCGAGTTAT
*
16652842 TCGAGTTAA
1 TCGAGTTAT
16652851 TCGAGTTAT
1 TCGAGTTAT
16652860 TCGA
1 TCGA
16652864 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:16652933 original size:9 final size:9
Alignment explanation
Indices: 16652916--16652952 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
16652906 TAAGTTCTCG
16652916 AATTCGAAT
1 AATTCGAAT
*
16652925 AACTCGAAT
1 AATTCGAAT
*
16652934 AATTTGAAT
1 AATTCGAAT
16652943 AATTCGAAT
1 AATTCGAAT
16652952 A
1 A
16652953 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:16653199 original size:30 final size:31
Alignment explanation
Indices: 16653166--16653224 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
16653156 AACCTTTTAT
*
16653166 TTTTTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTTCCCTAAAACTTTTACTCCCTTCCCAC
*
16653195 TTTTTCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTTCCCTAAAACTTTTACTCCCTTCCCA
16653225 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 13 0.50
31 5 0.19
ACGTcount: A:0.20, C:0.36, G:0.00, T:0.44
Consensus pattern (31 bp):
TTTTTCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:16658288 original size:46 final size:46
Alignment explanation
Indices: 16658184--16658506 Score: 377
Period size: 46 Copynumber: 7.5 Consensus size: 46
16658174 GTATGATCAA
*
16658184 TTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTACCAC
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCAC
*
16658227 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCGC
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCAC
* *
16658273 TTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACAC
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCAC
16658319 TTATCACTTTGTCACTTGATCAGATAA--GTA--T-A-G----CAC
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCAC
* *
16658355 TTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCAC
* *
16658401 TTATCACTTTGTCTCTAGATCAGATAA--GT-G-T-A-G----CAC
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCAC
* *
16658437 TTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCAC
* *
16658483 TTATCACTTTATCTCTTGATCAGA
1 TTATCACTTTGTCACTTGATCAGA
16658507 AGTACTCAAA
Statistics
Matches: 242, Mismatches: 15, Indels: 43
0.81 0.05 0.14
Matches are distributed among these distances:
36 56 0.23
38 5 0.02
39 1 0.00
40 4 0.02
41 4 0.02
42 4 0.02
43 8 0.03
44 10 0.04
45 20 0.08
46 130 0.54
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (46 bp):
TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCAC
Found at i:16658357 original size:36 final size:36
Alignment explanation
Indices: 16658316--16658470 Score: 166
Period size: 36 Copynumber: 4.0 Consensus size: 36
16658306 CTAAGGCTAA
16658316 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
16658352 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG
* * *
16658394 CTACCACTTATCACTTTGTCTCTAGATCAGATAAGTGTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
16658434 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
16658470 C
1 C
16658471 TAAAGCTACC
Statistics
Matches: 101, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
36 63 0.62
38 3 0.03
40 3 0.03
42 3 0.03
44 2 0.02
46 27 0.27
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:16658409 original size:82 final size:82
Alignment explanation
Indices: 16658272--16658506 Score: 407
Period size: 82 Copynumber: 2.9 Consensus size: 82
16658262 AAGGCTACCG
* * * *
16658272 CTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTG
1 CTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTG
16658337 ATCAGATAAGTATAGCA
66 ATCAGATAAGTATAGCA
*
16658354 CTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTAG
1 CTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTG
*
16658419 ATCAGATAAGTGTAGCA
66 ATCAGATAAGTATAGCA
*
16658436 CTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCTTG
1 CTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTG
16658501 ATCAGA
66 ATCAGA
16658507 AGTACTCAAA
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 145 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (82 bp):
CTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTG
ATCAGATAAGTATAGCA
Found at i:16658484 original size:128 final size:133
Alignment explanation
Indices: 16658184--16658506 Score: 383
Period size: 128 Copynumber: 2.5 Consensus size: 133
16658174 GTATGATCAA
* * *
16658184 TTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGAT
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTATCACTTGAT
* * *
16658247 CAGATAAGTGTAGCTAAGGCTACCGCTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGG
66 CAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTCTCACTAGATCAGATAAG-GTAGCTAAGG
16658312 CTAACAC
130 ---ACAC
*
16658319 TTATCACTTTGTCACTTGATCAGATAA--GTA--T-AG----CACTTATCACTTTTTCACTTGAT
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTATCACTTGAT
* *
16658375 CAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTAGATCAGATAA-GT-G-T-A-G-
66 CAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTCTCACTAGATCAGATAAGGTAGCTAAGGA
16658434 CAC
131 CAC
* *
16658437 TTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCTTGA
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTATCACTTGA
16658502 TCAGA
65 TCAGA
16658507 AGTACTCAAA
Statistics
Matches: 165, Mismatches: 11, Indels: 31
0.80 0.05 0.15
Matches are distributed among these distances:
118 29 0.18
120 3 0.02
122 2 0.01
123 1 0.01
124 3 0.02
125 1 0.01
126 2 0.01
128 95 0.58
132 1 0.01
133 1 0.01
135 10 0.06
136 5 0.03
137 12 0.07
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (133 bp):
TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTATCACTTGAT
CAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTCTCACTAGATCAGATAAGGTAGCTAAGGA
CAC
Found at i:16662260 original size:10 final size:11
Alignment explanation
Indices: 16662243--16662267 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16662233 ATTAATTATT
16662243 TTTAAAAAATA
1 TTTAAAAAATA
16662254 TTTAAAAAATA
1 TTTAAAAAATA
16662265 TTT
1 TTT
16662268 TTTTAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TTTAAAAAATA
Found at i:16663633 original size:19 final size:19
Alignment explanation
Indices: 16663609--16663648 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
16663599 CCTAAAGCTG
16663609 AAAATGGATTTAGTTAACT
1 AAAATGGATTTAGTTAACT
16663628 AAAATGGATTTAGTTAACT
1 AAAATGGATTTAGTTAACT
16663647 AA
1 AA
16663649 GGTTTGAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (19 bp):
AAAATGGATTTAGTTAACT
Found at i:16664602 original size:14 final size:14
Alignment explanation
Indices: 16664583--16664611 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16664573 ATAACTCTTC
16664583 AAAGGGTAAAGATA
1 AAAGGGTAAAGATA
16664597 AAAGGGTAAAGATA
1 AAAGGGTAAAGATA
16664611 A
1 A
16664612 CTTATGTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.14
Consensus pattern (14 bp):
AAAGGGTAAAGATA
Found at i:16668488 original size:57 final size:57
Alignment explanation
Indices: 16668415--16668523 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 57
16668405 GATCCTATCC
*
16668415 TGATACAGCCCTCCCGAAGAATATGTGTGAAAA-AGATCTAGCCCGGATGGGTGATCT
1 TGATACAGCCCTCCCGAAGAATATGTG-GAAAATAGATCTAGCCCGGACGGGTGATCT
* * *
16668472 TGATATAGCCCTCCCGAAGAATATGTGGAAAATGGATTTAGCCCGGACGGGT
1 TGATACAGCCCTCCCGAAGAATATGTGGAAAATAGATCTAGCCCGGACGGGT
16668524 AATCCGAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
56 5 0.11
57 42 0.89
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (57 bp):
TGATACAGCCCTCCCGAAGAATATGTGGAAAATAGATCTAGCCCGGACGGGTGATCT
Found at i:16682081 original size:23 final size:22
Alignment explanation
Indices: 16682036--16682100 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
16682026 AAAATGATCC
*
16682036 TAATTATATAAAAAGTT-AAAAT
1 TAATT-TATAAAAAATTCAAAAT
*
16682058 TAATTTATAAAAATTTCAACAAT
1 TAATTTATAAAAAATTCAA-AAT
16682081 TAATTT-TAAAAAATTCAAAA
1 TAATTTATAAAAAATTCAAAA
16682101 AAATTATATC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
21 12 0.31
22 18 0.46
23 9 0.23
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (22 bp):
TAATTTATAAAAAATTCAAAAT
Found at i:16688150 original size:27 final size:27
Alignment explanation
Indices: 16688120--16688214 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
16688110 ATTATTTATA
* *
16688120 TATATTTGCATGACCTTGATTGTTACG
1 TATATTTGCATGAACTTGATTGTAACG
*
16688147 TATATTTGCACGAAC----TTGTAAC-
1 TATATTTGCATGAACTTGATTGTAACG
* *
16688169 -ATATTTGCATAAACTTGATTGTCACG
1 TATATTTGCATGAACTTGATTGTAACG
*
16688195 CATATTTGCATGAACTTGAT
1 TATATTTGCATGAACTTGAT
16688215 GGGCACGTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
21 12 0.22
23 6 0.11
25 6 0.11
27 31 0.56
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (27 bp):
TATATTTGCATGAACTTGATTGTAACG
Found at i:16688200 original size:48 final size:48
Alignment explanation
Indices: 16688121--16688212 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
16688111 TTATTTATAT
* * * *
16688121 ATATTTGCATGACCTTGATTGTTACGTATATTTGCACGAACTTGTAAC
1 ATATTTGCATAAACTTGATTGTCACGCATATTTGCACGAACTTGTAAC
*
16688169 ATATTTGCATAAACTTGATTGTCACGCATATTTGCATGAACTTG
1 ATATTTGCATAAACTTGATTGTCACGCATATTTGCACGAACTTG
16688213 ATGGGCACGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (48 bp):
ATATTTGCATAAACTTGATTGTCACGCATATTTGCACGAACTTGTAAC
Found at i:16688221 original size:27 final size:27
Alignment explanation
Indices: 16688168--16688221 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
16688158 GAACTTGTAA
* *
16688168 CATATTTGCATAAACTTGATTGTCACG
1 CATATTTGCATAAACTTGATGGGCACG
*
16688195 CATATTTGCATGAACTTGATGGGCACG
1 CATATTTGCATAAACTTGATGGGCACG
16688222 TATACTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (27 bp):
CATATTTGCATAAACTTGATGGGCACG
Found at i:16689003 original size:21 final size:22
Alignment explanation
Indices: 16688955--16689003 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
16688945 AATTAAATAA
*
16688955 AAAATTATGTGCAACTATTATG
1 AAAATTACGTGCAACTATTATG
16688977 AAAATTACGTGCAAC-ATTA-G
1 AAAATTACGTGCAACTATTATG
16688997 AACAATT
1 AA-AATT
16689004 TTTTACCGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 8 0.32
22 14 0.56
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (22 bp):
AAAATTACGTGCAACTATTATG
Found at i:16690745 original size:19 final size:20
Alignment explanation
Indices: 16690723--16690761 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16690713 CCCATTTTCG
16690723 TAATC-AACAAAAATATAAT
1 TAATCAAACAAAAATATAAT
*
16690742 TAATCAAACAAACATATAAT
1 TAATCAAACAAAAATATAAT
16690762 GTTCACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.26
Consensus pattern (20 bp):
TAATCAAACAAAAATATAAT
Found at i:16690802 original size:20 final size:20
Alignment explanation
Indices: 16690770--16690810 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
16690760 ATGTTCACTT
*
16690770 TTATATATTAAAATATACAA
1 TTATATATTAAAAAATACAA
16690790 TTAT-TATTAAAAAAATACAA
1 TTATATATT-AAAAAATACAA
16690810 T
1 T
16690811 AGTCAAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TTATATATTAAAAAATACAA
Found at i:16691191 original size:22 final size:22
Alignment explanation
Indices: 16691163--16691239 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
16691153 TTTCTTTTAA
16691163 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
** * *
16691185 TTAGGAGATAATATTTTGGTTTAA--
1 TTAGGAGAT--TA-GAT-GCTAAAGT
16691209 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
16691231 TTAGGAGAT
1 TTAGGAGAT
16691240 AATATTTTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 4 0.10
21 1 0.02
22 20 0.49
24 11 0.27
25 1 0.02
26 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (22 bp):
TTAGGAGATTAGATGCTAAAGT
Found at i:16691212 original size:46 final size:46
Alignment explanation
Indices: 16691158--16691253 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
16691148 TCTCTTTTCT
16691158 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
16691204 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
16691250 TTTA
1 TTTA
16691254 TATCTTTGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (46 bp):
TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
Found at i:16695780 original size:45 final size:46
Alignment explanation
Indices: 16695730--16695823 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
16695720 TCTCTTTTCT
16695730 TTTAATTAGGAGATTAGATGCT-AAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
16695775 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
16695821 TTT
1 TTT
16695824 CTATCTTTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 22 0.46
46 26 0.54
ACGTcount: A:0.33, C:0.02, G:0.23, T:0.41
Consensus pattern (46 bp):
TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
Found at i:16697899 original size:40 final size:41
Alignment explanation
Indices: 16697818--16697902 Score: 109
Period size: 40 Copynumber: 2.0 Consensus size: 41
16697808 CACACAACTG
16697818 TCCTTTGCATTTACCATTCTTGACATTACCAACCACCCTTTGC
1 TCCTTTGCATTTACCA-T-TTGACATTACCAACCACCCTTTGC
* * * *
16697861 TCCTTTGCCTTTACCA-TTGCCATTACCAACTACTCTTTGC
1 TCCTTTGCATTTACCATTTGACATTACCAACCACCCTTTGC
16697901 TC
1 TC
16697903 TCTCTCTCTC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
40 23 0.61
43 15 0.39
ACGTcount: A:0.19, C:0.35, G:0.07, T:0.39
Consensus pattern (41 bp):
TCCTTTGCATTTACCATTTGACATTACCAACCACCCTTTGC
Found at i:16699768 original size:20 final size:20
Alignment explanation
Indices: 16699730--16699768 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16699720 GACTCTTCAA
** *
16699730 ATGCATGGAAATTCTTGGAC
1 ATGCATGGAAAAACATGGAC
16699750 ATGCATGGAAAAACATGGA
1 ATGCATGGAAAAACATGGA
16699769 AAGAATTGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (20 bp):
ATGCATGGAAAAACATGGAC
Found at i:16700747 original size:121 final size:120
Alignment explanation
Indices: 16700557--16700801 Score: 386
Period size: 121 Copynumber: 2.0 Consensus size: 120
16700547 ATCTACTAAC
* * *
16700557 AAATTCGTTCTCAGACTTTTTTGATGAACTTCATTTTCTCTATCCATATTAAACTTTGAAAACAC
1 AAATTCGTTCTCAGACTTTCTTGATGAACCTCATTTTCTCTATCCATATTAAAATTTGAAAACAC
* *
16700622 CTCATCAATTTCAGTCTACAAAGAAT-TTGACTTAAAATTTGAGCTTTTCATCTTTT
66 CTCATCAATTTCAGCCTACAAAGAATGTGGA-TTAAAATTTGAGCTTTTCATC-TTT
16700678 AAATTCGTTC-CAAGACTTTCTTGATGAACCTCATTTTCTCTATCCATATTAAAATTTGAAAACA
1 AAATTCGTTCTC-AGACTTTCTTGATGAACCTCATTTTCTCTATCCATATTAAAATTTGAAAACA
* *
16700742 CCTCATCAATTTGAGCCTTCAAAGAATGTGGATTAAAATTTGAGCTTTTCATCTTT
65 CCTCATCAATTTCAGCCTACAAAGAATGTGGATTAAAATTTGAGCTTTTCATCTTT
16700798 AAAT
1 AAAT
16700802 ATTGTGTATA
Statistics
Matches: 115, Mismatches: 7, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
120 8 0.07
121 104 0.90
122 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (120 bp):
AAATTCGTTCTCAGACTTTCTTGATGAACCTCATTTTCTCTATCCATATTAAAATTTGAAAACAC
CTCATCAATTTCAGCCTACAAAGAATGTGGATTAAAATTTGAGCTTTTCATCTTT
Found at i:16708813 original size:30 final size:30
Alignment explanation
Indices: 16708779--16708835 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
16708769 GGTGGGATCG
*
16708779 GAAGGGAATAAAAGTTTTAGGGGAAAAGTC
1 GAAGGGAATAAAAATTTTAGGGGAAAAGTC
* *
16708809 GAAGGGAGTAAAAATTTTGGGGGAAAA
1 GAAGGGAATAAAAATTTTAGGGGAAAA
16708836 TAAAAAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.35, T:0.19
Consensus pattern (30 bp):
GAAGGGAATAAAAATTTTAGGGGAAAAGTC
Found at i:16709063 original size:9 final size:9
Alignment explanation
Indices: 16709049--16709084 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
16709039 TATAGTTTGA
16709049 TATTCGAAT
1 TATTCGAAT
16709058 TATTCGAAT
1 TATTCGAAT
*
16709067 TATT-GAGT
1 TATTCGAAT
16709075 TATTCGAAT
1 TATTCGAAT
16709084 T
1 T
16709085 TGAAAACTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (9 bp):
TATTCGAAT
Found at i:16712336 original size:15 final size:15
Alignment explanation
Indices: 16712316--16712381 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 15
16712306 ATAATAAAAC
16712316 AAAGAAATAAAAGAA
1 AAAGAAATAAAAGAA
16712331 AAAGAAAT---AGAA
1 AAAGAAATAAAAGAA
*
16712343 AAAGAAA-CAAAGAA
1 AAAGAAATAAAAGAA
* *
16712357 CAAACGAAACATGAAGAA
1 -AAA-GAAATA-AAAGAA
16712375 AAAGAAA
1 AAAGAAA
16712382 GAAAGGAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
12 11 0.26
14 4 0.10
15 11 0.26
16 8 0.19
17 3 0.07
18 5 0.12
ACGTcount: A:0.74, C:0.06, G:0.15, T:0.05
Consensus pattern (15 bp):
AAAGAAATAAAAGAA
Found at i:16712381 original size:16 final size:14
Alignment explanation
Indices: 16712325--16712386 Score: 56
Period size: 16 Copynumber: 4.3 Consensus size: 14
16712315 CAAAGAAATA
16712325 AAAGAAAAAG-AA-
1 AAAGAAAAAGAAAC
*
16712337 ATAGAAAAAGAAAC
1 AAAGAAAAAGAAAC
16712351 AAAGAACAAACGAAAC
1 AAAGAA-AAA-GAAAC
*
16712367 ATGAAGAAAAAGAAAG
1 A--AAGAAAAAGAAAC
16712383 AAAG
1 AAAG
16712387 GAGAAACTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
12 9 0.22
13 2 0.05
14 8 0.20
15 3 0.07
16 11 0.27
17 3 0.07
18 5 0.12
ACGTcount: A:0.73, C:0.06, G:0.18, T:0.03
Consensus pattern (14 bp):
AAAGAAAAAGAAAC
Found at i:16713321 original size:40 final size:38
Alignment explanation
Indices: 16713201--16713334 Score: 119
Period size: 37 Copynumber: 3.4 Consensus size: 38
16713191 ACTTCAAGTT
*
16713201 GATGAGACACTGGGTGTCAATTTATTACTTTGGATTAATTC
1 GATGAGACACTGGGTGTCAATTTATTACTTT--ATT-ATCC
* * * ** *
16713242 GATGAGGCACTAGGTGCCAATTTACTT-CGGT-TTAGCC
1 GATGAGACACTGGGTGTCAATTTA-TTACTTTATTATCC
*
16713279 GATGAGACATTGGGTGTCAATTTATTACTTTAAATTATCC
1 GATGAGACACTGGGTGTCAATTTATTACTTT--ATTATCC
*
16713319 GATGAGGCACTGGGTG
1 GATGAGACACTGGGTG
16713335 CCAAACTGGT
Statistics
Matches: 72, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
36 2 0.03
37 24 0.33
38 2 0.03
40 19 0.26
41 23 0.32
42 2 0.03
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (38 bp):
GATGAGACACTGGGTGTCAATTTATTACTTTATTATCC
Found at i:16719186 original size:30 final size:29
Alignment explanation
Indices: 16719148--16719243 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 29
16719138 TGAAATGAAG
16719148 ATGTTAATTACCTTATCTTCATTGTTTGC
1 ATGTTAATTACCTTATCTTCATTGTTTGC
*
16719177 ATGTGTAATT---TTATCTTTAACAATG-TT--
1 ATGT-TAATTACCTTATC-TT--CATTGTTTGC
16719204 ATAGTTAATTACCTTATCTTCATTGTTTGC
1 AT-GTTAATTACCTTATCTTCATTGTTTGC
*
16719234 AGGTGTAATT
1 ATGT-TAATT
16719244 TTATCTTTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 23
0.67 0.04 0.29
Matches are distributed among these distances:
27 16 0.31
28 6 0.12
29 10 0.19
30 20 0.38
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (29 bp):
ATGTTAATTACCTTATCTTCATTGTTTGC
Found at i:16719191 original size:27 final size:27
Alignment explanation
Indices: 16719160--16719250 Score: 73
Period size: 27 Copynumber: 3.3 Consensus size: 27
16719150 GTTAATTACC
16719160 TTATCTTCATTGTTTGCATGTGTAATT
1 TTATCTTCATTGTTTGCATGTGTAATT
*
16719187 TTATCTTTAACAATG-TT--ATAGT-TAATT
1 TTATC-TT--CATTGTTTGCAT-GTGTAATT
*
16719214 ACCTTATCTTCATTGTTTGCAGGTGTAATT
1 ---TTATCTTCATTGTTTGCATGTGTAATT
16719244 TTATCTT
1 TTATCTT
16719251 TAACAATGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 22
0.67 0.04 0.29
Matches are distributed among these distances:
27 23 0.46
28 6 0.12
29 6 0.12
30 15 0.30
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (27 bp):
TTATCTTCATTGTTTGCATGTGTAATT
Found at i:16719219 original size:57 final size:57
Alignment explanation
Indices: 16719150--16719263 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
16719140 AAATGAAGAT
*
16719150 GTTAATTACCTTATCTTCATTGTTTGCATGTGTAATTTTATCTTTAACAATGTTATA
1 GTTAATTACCTTATCTTCATTGTTTGCAGGTGTAATTTTATCTTTAACAATGTTATA
16719207 GTTAATTACCTTATCTTCATTGTTTGCAGGTGTAATTTTATCTTTAACAATGTTATA
1 GTTAATTACCTTATCTTCATTGTTTGCAGGTGTAATTTTATCTTTAACAATGTTATA
16719264 CAAAAAGTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.26, C:0.12, G:0.11, T:0.50
Consensus pattern (57 bp):
GTTAATTACCTTATCTTCATTGTTTGCAGGTGTAATTTTATCTTTAACAATGTTATA
Found at i:16721033 original size:43 final size:43
Alignment explanation
Indices: 16720971--16721154 Score: 160
Period size: 43 Copynumber: 4.3 Consensus size: 43
16720961 TCAATGGGTT
* * * *
16720971 ATGTTCTTTAGCGGTGTTTGTGGGGAAAACGCTGCTAAAAGTT
1 ATGTTCTTTAGCTGCGTTTGTGGGGAAAACGCCGCTAAAAGTC
*
16721014 ATGTTCTTTAGCTGCGTTTGTGGGGAAAGCGCCGCT-AAAGATC
1 ATGTTCTTTAGCTGCGTTTGTGGGGAAAACGCCGCTAAAAG-TC
* * * * * * *
16721057 ATATTCTATAGC-GACATTTGTGGGGAAAGCGTC-ATTAAAGATC
1 ATGTTCTTTAGCTG-CGTTTGTGGGGAAAACGCCGCTAAAAG-TC
* * *
16721100 ATGTTCTTTAGCTGTGTTTGT-GGGAAAAGTGCCGTTAAAAGTC
1 ATGTTCTTTAGCTGCGTTTGTGGGGAAAA-CGCCGCTAAAAGTC
*
16721143 ATGTTCTATAGC
1 ATGTTCTTTAGC
16721155 GACCTTTTAC
Statistics
Matches: 115, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
42 12 0.10
43 97 0.84
44 6 0.05
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (43 bp):
ATGTTCTTTAGCTGCGTTTGTGGGGAAAACGCCGCTAAAAGTC
Found at i:16723258 original size:7 final size:7
Alignment explanation
Indices: 16723246--16723270 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16723236 AGGACAGATT
16723246 TGGGAAG
1 TGGGAAG
16723253 TGGGAAG
1 TGGGAAG
16723260 TGGGAAG
1 TGGGAAG
16723267 TGGG
1 TGGG
16723271 TGGGGACGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.60, T:0.16
Consensus pattern (7 bp):
TGGGAAG
Found at i:16726481 original size:19 final size:20
Alignment explanation
Indices: 16726446--16726484 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
16726436 ACATGTATGA
16726446 TAATAATAAACATATGTATT
1 TAATAATAAACATATGTATT
16726466 TAATAATAAA-ATATGTATT
1 TAATAATAAACATATGTATT
16726485 GTTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Found at i:16726555 original size:14 final size:14
Alignment explanation
Indices: 16726536--16726575 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
16726526 TTAAAACAAT
*
16726536 AAAGTAAATAAAAG
1 AAAGTAAAGAAAAG
16726550 AAAGTAAAGAAAAG
1 AAAGTAAAGAAAAG
16726564 AAAGTAAAGAAA
1 AAAGTAAAGAAA
16726576 TAAAAACGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAGTAAAGAAAAG
Found at i:16727420 original size:13 final size:14
Alignment explanation
Indices: 16727399--16727438 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
16727389 ATTTGATTGG
16727399 AAAATGAATTAAA-
1 AAAATGAATTAAAT
*
16727412 AATATGAATTAAAT
1 AAAATGAATTAAAT
16727426 AAAAGTGAATTAA
1 AAAA-TGAATTAA
16727439 TTTATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 3 0.13
15 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (14 bp):
AAAATGAATTAAAT
Found at i:16727815 original size:23 final size:23
Alignment explanation
Indices: 16727777--16727862 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
16727767 GCTTTGCCGA
*
16727777 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTTATGTGTCGTATT
* *
16727800 TTAGGCACCTTGTGTGTCGTA--
1 TCAGGCACCTTATGTGTCGTATT
** *
16727821 TCAGGCACCTCGTGTG-C-CATT
1 TCAGGCACCTTATGTGTCGTATT
16727842 TCAGGCA-CTTATGTGTCGTAT
1 TCAGGCACCTTATGTGTCGTAT
16727863 ACTAATCAGG
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
19 1 0.02
20 7 0.14
21 22 0.44
22 2 0.04
23 18 0.36
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.37
Consensus pattern (23 bp):
TCAGGCACCTTATGTGTCGTATT
Found at i:16753308 original size:3 final size:3
Alignment explanation
Indices: 16753302--16753340 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
16753292 TGCAAAAAGT
16753302 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16753341 AGACGGAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16758718 original size:12 final size:12
Alignment explanation
Indices: 16758701--16758725 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16758691 TGCTTACCCC
16758701 TAAATCATGTGT
1 TAAATCATGTGT
16758713 TAAATCATGTGT
1 TAAATCATGTGT
16758725 T
1 T
16758726 TGCAGGGTGG
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TAAATCATGTGT
Found at i:16761781 original size:18 final size:19
Alignment explanation
Indices: 16761747--16761786 Score: 64
Period size: 18 Copynumber: 2.1 Consensus size: 19
16761737 ATTAAATATT
16761747 AAATATTTACTTTTAAATTA
1 AAATATTTAC-TTTAAATTA
16761767 AAATATTTA-TTTAAATTA
1 AAATATTTACTTTAAATTA
16761785 AA
1 AA
16761787 TTTAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 11 0.55
20 9 0.45
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATATTTACTTTAAATTA
Found at i:16761791 original size:24 final size:23
Alignment explanation
Indices: 16761735--16761792 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 23
16761725 GTTTAAATAA
16761735 TAATTAAATATT-AAATATTTACT
1 TAATTAAAT-TTAAAATATTTACT
*
16761758 T--TTAAA-TTAAAATATTTATT
1 TAATTAAATTTAAAATATTTACT
16761778 TAAATTAAATTTAAA
1 T-AATTAAATTTAAA
16761793 TAAATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
19 2 0.07
20 11 0.38
21 5 0.17
23 6 0.21
24 5 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATTAAATTTAAAATATTTACT
Found at i:16779024 original size:26 final size:26
Alignment explanation
Indices: 16778995--16779060 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
16778985 TTTTCAAAAA
16778995 TTATTACTTTTATAAAGTAGCACTAG
1 TTATTACTTTTATAAAGTAGCACTAG
* *
16779021 TTATTACATTGATAAAGTAGCACTAG
1 TTATTACTTTTATAAAGTAGCACTAG
*
16779047 -T-TTATTTTTATAAA
1 TTATTACTTTTATAAA
16779061 AAAAATCTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 10 0.29
25 1 0.03
26 24 0.69
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (26 bp):
TTATTACTTTTATAAAGTAGCACTAG
Found at i:16779132 original size:18 final size:18
Alignment explanation
Indices: 16779111--16779146 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16779101 TCCCCTTGAG
16779111 TAAAAAATTAAATTAAAT
1 TAAAAAATTAAATTAAAT
* *
16779129 TAAAAATTTTAATTAAAT
1 TAAAAAATTAAATTAAAT
16779147 CCCTCGTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAAAATTAAATTAAAT
Found at i:16779648 original size:19 final size:17
Alignment explanation
Indices: 16779620--16779684 Score: 51
Period size: 19 Copynumber: 3.6 Consensus size: 17
16779610 TAGTTTTATA
16779620 TTTTAT-TTTTTATAAT
1 TTTTATATTTTTATAAT
**
16779636 TTATTATCATTTTCCTAACT
1 TT-TTAT-ATTTTTATAA-T
*
16779656 TTTTATTATATTTATAATT
1 TTTTA-TATTTTTATAA-T
16779675 TTTTATATTT
1 TTTTATATTT
16779685 GCAAACATGT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
16 2 0.05
17 4 0.11
18 4 0.11
19 23 0.62
20 4 0.11
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATATTTTTATAAT
Found at i:16789325 original size:44 final size:45
Alignment explanation
Indices: 16789276--16789475 Score: 159
Period size: 45 Copynumber: 4.3 Consensus size: 45
16789266 GCAACCTTAG
* * **
16789276 GGAGATTAGATTC-GTATCTTCAATCTGCTCTGCTGTAACTTCAA
1 GGAGATAAGATTCACTATCTTCAATCTGCTCCACTGTAACTTCAA
* *
16789320 GGAGATAAGATTCACTATCTTCAATCTGCTCCACTGTAACTTTAG
1 GGAGATAAGATTCACTATCTTCAATCTGCTCCACTGTAACTTCAA
* * * * ** * *
16789365 GGAGATAAGATTGGTGACTTGCAGCTTTAATCTGTTCCACTACAACTTTAG
1 GGAGATAAGA-T--TCAC-T--ATCTTCAATCTGCTCCACTGTAACTTCAA
* ** * * *
16789416 GGAAATAAGATTTGCTATATTCAATCTGCTCCACTGTAACTTTAG
1 GGAGATAAGATTCACTATCTTCAATCTGCTCCACTGTAACTTCAA
16789461 GGAGATAAGATTCAC
1 GGAGATAAGATTCAC
16789476 CACGATGACT
Statistics
Matches: 125, Mismatches: 24, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
44 12 0.10
45 71 0.57
46 1 0.01
47 1 0.01
48 5 0.04
49 1 0.01
50 1 0.01
51 33 0.26
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (45 bp):
GGAGATAAGATTCACTATCTTCAATCTGCTCCACTGTAACTTCAA
Found at i:16789910 original size:262 final size:262
Alignment explanation
Indices: 16789438--16789933 Score: 848
Period size: 262 Copynumber: 1.9 Consensus size: 262
16789428 TGCTATATTC
*
16789438 AATCTGCTCCACTGTAACTTTAGGGAGATAAGATTCACCACGATGACTTCAATCCGTCCCACTGC
1 AATCTGATCCACTGTAACTTTAGGGAGATAAGATTCACCACGATGACTTCAATCCGTCCCACTGC
* *
16789503 AACTTCAGGGGTATAGGATTTGTGGTTTCACTAATCTGTTACACCATTCTCTAGGGAACATGACC
66 AACGTCAGGGGTATAGGATTTGTGGTTTCACTAATATGTTACACCATTCTCTAGGGAACATGACC
*
16789568 TGTAGAATCCATTTCATAGGCCTATATTTATGCCAAACGATTAGGATGTTATGATCAGAATGAAT
131 TGTAGAATCCATTTCATAGGCCTATATTTATGCCAAACAATTAGGATGTTATGATCAGAATGAAT
16789633 CAGATACTCCTAACTAGATGTGTATGAATGATATTTGCAACTTTAGGGAGATAAGATTTATGGCT
196 CAGATACTCCTAACTAGATGTGTATGAATGATATTTGCAACTTTAGGGAGATAAGATTTATGGCT
16789698 TT
261 TT
* * *
16789700 AATCTGATCCACTGTAACTTTAGTGAGATAAGATTCGCCACGATTACTTCAATCCGTCCCACTGC
1 AATCTGATCCACTGTAACTTTAGGGAGATAAGATTCACCACGATGACTTCAATCCGTCCCACTGC
* ** * *
16789765 AACGTCAGGGGTATAGGATTTGTGGTTTCACTGATATGTTACACTGTTCTTTGGGGAACATGACC
66 AACGTCAGGGGTATAGGATTTGTGGTTTCACTAATATGTTACACCATTCTCTAGGGAACATGACC
* *
16789830 TGTAGAATCCATTTCATGGGCCTATATTTATGCCAAGCAATTAGGATGTTATGATCAGAATGAAT
131 TGTAGAATCCATTTCATAGGCCTATATTTATGCCAAACAATTAGGATGTTATGATCAGAATGAAT
**
16789895 CAGATGTTCCTAACTAGATGTGTATGAATGATATTTGCA
196 CAGATACTCCTAACTAGATGTGTATGAATGATATTTGCA
16789934 TTAATGCAGA
Statistics
Matches: 218, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
262 218 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (262 bp):
AATCTGATCCACTGTAACTTTAGGGAGATAAGATTCACCACGATGACTTCAATCCGTCCCACTGC
AACGTCAGGGGTATAGGATTTGTGGTTTCACTAATATGTTACACCATTCTCTAGGGAACATGACC
TGTAGAATCCATTTCATAGGCCTATATTTATGCCAAACAATTAGGATGTTATGATCAGAATGAAT
CAGATACTCCTAACTAGATGTGTATGAATGATATTTGCAACTTTAGGGAGATAAGATTTATGGCT
TT
Found at i:16797364 original size:41 final size:41
Alignment explanation
Indices: 16797319--16797424 Score: 158
Period size: 41 Copynumber: 2.6 Consensus size: 41
16797309 ACCGACTTTT
* *
16797319 AGCCTACTAGACTTATAGTCTGAAATATTTCACTGGCATCA
1 AGCCTGCTAGACTTATAGTCTGAAATATTTCACCGGCATCA
* *
16797360 AGCCTGCTAGACTTATAGTCCGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACTTATAGTCTGAAATATTTCACCGGCATCA
* *
16797401 AGCCTGCTAGACATAAAGTCTGAA
1 AGCCTGCTAGACTTATAGTCTGAA
16797425 TCATCTCACT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATATTTCACCGGCATCA
Found at i:16798063 original size:76 final size:76
Alignment explanation
Indices: 16797920--16798064 Score: 166
Period size: 76 Copynumber: 1.9 Consensus size: 76
16797910 TTATATATAT
* * * * *
16797920 ATATTCGAATCTACCATATACATATATAATTACACACTTAAAATCAAAACATGAACTTATACTTG
1 ATATTCGAATCTAACATATACATATATAATTACACACTTAAAATCAAAACAAGAAATCATACATG
16797985 TATACTCATAC
66 TATACTCATAC
* * * * * * *
16797996 ATATTCGAATCTAATATATACATATCTAATTACATA-TTCAAACTCCATATAAGAAATCATACAT
1 ATATTCGAATCTAACATATACATATATAATTACACACTT-AAAATCAAAACAAGAAATCATACAT
16798060 GTATA
65 GTATA
16798065 TACATGCTTA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
75 2 0.04
76 54 0.96
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.34
Consensus pattern (76 bp):
ATATTCGAATCTAACATATACATATATAATTACACACTTAAAATCAAAACAAGAAATCATACATG
TATACTCATAC
Found at i:16800813 original size:17 final size:18
Alignment explanation
Indices: 16800786--16800824 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
16800776 TATATTGACA
16800786 AAAAAATTAAAATAATTT
1 AAAAAATTAAAATAATTT
*
16800804 AAAAAA-TAAAATACTTT
1 AAAAAATTAAAATAATTT
16800821 AAAA
1 AAAA
16800825 TTAACTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAATTAAAATAATTT
Found at i:16807010 original size:26 final size:27
Alignment explanation
Indices: 16806974--16807034 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
16806964 GGTCCTTGTA
16806974 TTTTTTT-CTTTT-TGTACAATTTAA-T
1 TTTTTTTCCTTTTATGT-CAATTTAACT
*
16806999 TTTTTTTCCTTTTATGTTAATTTAACT
1 TTTTTTTCCTTTTATGTCAATTTAACT
16807026 TTTTTTTCC
1 TTTTTTTCC
16807035 ATTCTCTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 7 0.22
26 12 0.38
27 13 0.41
ACGTcount: A:0.16, C:0.11, G:0.03, T:0.69
Consensus pattern (27 bp):
TTTTTTTCCTTTTATGTCAATTTAACT
Found at i:16810633 original size:30 final size:32
Alignment explanation
Indices: 16810599--16810659 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
16810589 TATTTCATGG
16810599 TTCTTTT-CAATT-ATATAATAA-TTTAGTAAA
1 TTCTTTTGCAATTGATAT-ATAATTTTAGTAAA
*
16810629 TTCTTTTGCCATTGATATATAATTTTAGTAA
1 TTCTTTTGCAATTGATATATAATTTTAGTAA
16810660 TATTTTTACC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 7 0.26
31 8 0.30
32 12 0.44
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (32 bp):
TTCTTTTGCAATTGATATATAATTTTAGTAAA
Found at i:16810729 original size:14 final size:14
Alignment explanation
Indices: 16810667--16810731 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
16810657 TAATATTTTT
*
16810667 ACCTCGAACCTTAA
1 ACCTCAAACCTTAA
* *
16810681 ACCTCAAATCTCAA
1 ACCTCAAACCTTAA
*
16810695 A-CT-AGAACGTTAA
1 ACCTCA-AACCTTAA
16810708 ATCC-CAAACCTTAA
1 A-CCTCAAACCTTAA
16810722 ACCTCAAACC
1 ACCTCAAACC
16810732 CCAAATTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
12 1 0.03
13 10 0.26
14 26 0.67
15 2 0.05
ACGTcount: A:0.42, C:0.34, G:0.05, T:0.20
Consensus pattern (14 bp):
ACCTCAAACCTTAA
Found at i:16810976 original size:28 final size:28
Alignment explanation
Indices: 16810916--16810979 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
16810906 CCTTGATTCG
*
16810916 AGTTTAGGGTTAAAGATTTAAAATTTAA
1 AGTTTAGGGTTAAAGATTTAAAATTCAA
* * * *
16810944 AGTTTGGGGTTCAAGATTTAGAGTTCAA
1 AGTTTAGGGTTAAAGATTTAAAATTCAA
*
16810972 GGTTTAGG
1 AGTTTAGG
16810980 AATGTGGGTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.38
Consensus pattern (28 bp):
AGTTTAGGGTTAAAGATTTAAAATTCAA
Found at i:16815410 original size:42 final size:41
Alignment explanation
Indices: 16815351--16815509 Score: 149
Period size: 42 Copynumber: 3.8 Consensus size: 41
16815341 ATAAGTGCTA
* * *
16815351 AACAGAAACCCGTAAGGGTTGAAC-GTAAGCTCATAGGAGCTG
1 AACAGAAACCCATAAGGGTT-AACTG-AAGCTCAAAAGAGCTG
* * *
16815393 AACAGAAACCCATAAGGGTTAATCTGAAGTTCAGAAGAGCTA
1 AACAGAAACCCATAAGGGTTAA-CTGAAGCTCAAAAGAGCTG
* * *
16815435 AACTGAAACCCATTAGGGTTAAATTGAAGCTCAAAAGAGCTG
1 AACAGAAACCCATAAGGGTT-AACTGAAGCTCAAAAGAGCTG
* * * *
16815477 AACTGAAACCCAAAAGGATTAAACTGAAACTCA
1 AACAGAAACCCATAAGGGTT-AACTGAAGCTCA
16815510 TATGAGTTAA
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.02
42 93 0.95
43 3 0.03
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.18
Consensus pattern (41 bp):
AACAGAAACCCATAAGGGTTAACTGAAGCTCAAAAGAGCTG
Found at i:16815501 original size:21 final size:21
Alignment explanation
Indices: 16815433--16815506 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
16815423 TCAGAAGAGC
** *
16815433 TAAACTGAAACCCATTAGGGT
1 TAAACTGAAACCCAAAAGGAT
* * * *
16815454 TAAATTGAAGCTCAAAA-GAGC
1 TAAACTGAAACCCAAAAGGA-T
*
16815475 TGAACTGAAACCCAAAAGGAT
1 TAAACTGAAACCCAAAAGGAT
16815496 TAAACTGAAAC
1 TAAACTGAAAC
16815507 TCATATGAGT
Statistics
Matches: 38, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
20 1 0.03
21 35 0.92
22 2 0.05
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.19
Consensus pattern (21 bp):
TAAACTGAAACCCAAAAGGAT
Found at i:16823192 original size:14 final size:14
Alignment explanation
Indices: 16823173--16823201 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16823163 AACGCCTCAA
16823173 TATATATATATATG
1 TATATATATATATG
16823187 TATATATATATATG
1 TATATATATATATG
16823201 T
1 T
16823202 TGAAGAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TATATATATATATG
Found at i:16823399 original size:104 final size:104
Alignment explanation
Indices: 16823211--16823398 Score: 256
Period size: 104 Copynumber: 1.8 Consensus size: 104
16823201 TTGAAGAACT
* *
16823211 AAGTAGTGGAGCCATAAAGAATGGCTCCACCAAAATAAAATATAATTTTTAAAATTTTTAGATTA
1 AAGTAGTGGAGCCATAAAGAATGGCTCCACCAAAATAAAATATAATTTTTAAAATATTTAGAATA
16823276 AAAAAAACACATTTAAAAAAGAAATTACATTGGTAATAA
66 AAAAAAACACATTTAAAAAAGAAATTACATTGGTAATAA
* ** *
16823315 AAGTGGTGGAGCCATTTAGAATGGCTCCACC-AAATAAAATATTATTTTTTTAAAA-ATTTA-AA
1 AAGTAGTGGAGCCATAAAGAATGGCTCCACCAAAATAAAATA-TA-ATTTTTAAAATATTTAGAA
* * *
16823377 TATAAAAAATATATTTAAAAAA
64 TAAAAAAAACACATTTAAAAAA
16823399 AATCTTAAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
103 30 0.41
104 34 0.47
105 9 0.12
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.30
Consensus pattern (104 bp):
AAGTAGTGGAGCCATAAAGAATGGCTCCACCAAAATAAAATATAATTTTTAAAATATTTAGAATA
AAAAAAACACATTTAAAAAAGAAATTACATTGGTAATAA
Found at i:16832331 original size:40 final size:40
Alignment explanation
Indices: 16832287--16832364 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
16832277 ATTCCTCTTT
16832287 AAACCATCCAAAATAGAGTTAAAGTCACTAGCAACAATAC
1 AAACCATCCAAAATAGAGTTAAAGTCACTAGCAACAATAC
* *
16832327 AAACCATCTAAAATTGAGTTAAAGTCACTAGCAACAAT
1 AAACCATCCAAAATAGAGTTAAAGTCACTAGCAACAAT
16832365 CCATGGCTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.21
Consensus pattern (40 bp):
AAACCATCCAAAATAGAGTTAAAGTCACTAGCAACAATAC
Found at i:16836313 original size:40 final size:40
Alignment explanation
Indices: 16836258--16836336 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
16836248 TGAGCCATGG
16836258 ATTGTTGCTAGTGACTTTAACTCCATTTTGAATGGTTTGT
1 ATTGTTGCTAGTGACTTTAACTCCATTTTGAATGGTTTGT
* *
16836298 ATTGTTGCTAGTGACTTTAACTCTATTTTGGATGGTTTG
1 ATTGTTGCTAGTGACTTTAACTCCATTTTGAATGGTTTG
16836337 AAGAGGAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.19, C:0.11, G:0.22, T:0.48
Consensus pattern (40 bp):
ATTGTTGCTAGTGACTTTAACTCCATTTTGAATGGTTTGT
Found at i:16836941 original size:115 final size:115
Alignment explanation
Indices: 16836739--16836992 Score: 352
Period size: 115 Copynumber: 2.2 Consensus size: 115
16836729 TTCGATAAAG
* * *
16836739 CGCCACTAATTATCGATATATAACGGCGTTTTTAGAAAAGCGCCGCAAAAAAATTAATCACAACG
1 CGCCACTAATTCTCGATATATAGCGGCATTTTTAGAAAAGCGCCGCAAAAAAATTAATCACAACG
* *
16836804 CCACCGTTTTGGATTGAGCTTTAGTGGCATTAGCAGCG-TTTGGGACAAAA
66 CCACCGTTTTGGATTAAGCTTTAGTGGCATTAGCAGCGCTTT-GGAAAAAA
*
16836854 CGCCACTAATTCTCGATATATAGCGGCATTTTTAGAAAAGCGCCGCAAAAAGATTAATCACAACG
1 CGCCACTAATTCTCGATATATAGCGGCATTTTTAGAAAAGCGCCGCAAAAAAATTAATCACAACG
* * **
16836919 CCATC-TTATTAGG-TTAAGCTTTAGTGGCATTAGCGGCGCTTTTTAAAAAA
66 CCACCGTT-TT-GGATTAAGCTTTAGTGGCATTAGCAGCGCTTTGGAAAAAA
* *
16836969 CGCCGCTAATTCTCGATCTATAGC
1 CGCCACTAATTCTCGATATATAGC
16836993 TTCGTTTTCG
Statistics
Matches: 124, Mismatches: 12, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
114 2 0.02
115 117 0.94
116 5 0.04
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (115 bp):
CGCCACTAATTCTCGATATATAGCGGCATTTTTAGAAAAGCGCCGCAAAAAAATTAATCACAACG
CCACCGTTTTGGATTAAGCTTTAGTGGCATTAGCAGCGCTTTGGAAAAAA
Found at i:16837050 original size:155 final size:150
Alignment explanation
Indices: 16836840--16837265 Score: 462
Period size: 140 Copynumber: 2.8 Consensus size: 150
16836830 GCATTAGCAG
* ** *
16836840 CGTTTGGGACAAAACGCCACTAATTCTCGATATATAGCGGCATTTTTAGAAAAGCGCCGCAAAAA
1 CGTTTGCGACAAAGTGCCACTAATTCTCGATATATAGCGGCGTTTTTAGAAAAGCGCCGCAAAAA
16836905 GATTAATCACAACGCCATCTTATTAGGTTAAGCTTTAGTGGCATTAGCGGCGCTTTTTAAAAAAC
66 -ATTAATCACAACG-CATCTT-TTA-GTT-AGCTTTAGTGGCATTAGCGGCGCTTTTTAAAAAAC
* * * **
16836970 GCCGCTAATTCTCGATCTATAGCTT
126 GCAGCTAATGCTCGATCTACAGCGA
* * *
16836995 CGTTTTCGACAAAGTGCCACTAATTCTCGATATATAGCGACGTTTTTAGAAAAGCGCAGCAAAAA
1 CGTTTGCGACAAAGTGCCACTAATTCTCGATATATAGCGGCGTTTTTAGAAAAGCGCCGC-AAAA
* * *
16837060 AATTAATCAC-A---A-C----A--TAGCTTTAGTGGCATTAGCGGCACTTTTTTAAAAGCGCAG
65 AATTAATCACAACGCATCTTTTAGTTAGCTTTAGTGGCATTAGCGGCGCTTTTTAAAAAACGCAG
16837114 CTAATGCTCGATCTACAGCGA
130 CTAATGCTCGATCTACAGCGA
* ** *
16837135 CGTTTGGGACAAAGTGCCACTAATTCTCGATATATAGCGGCGTTTTTAG-AAAGACGCCATAAAT
1 CGTTTGCGACAAAGTGCCACTAATTCTCGATATATAGCGGCGTTTTTAGAAAAG-CGCCGCAAAA
* *
16837199 AATTAATCACAACGCTGTCGTTTTAGATTGAGCTTTAGTGGCATTAGTGGCGCTTTTTTTAAAAA
65 AATTAATCACAACGC-ATC-TTTTAG-TT-AGCTTTAGTGGCATTAGCGGCGC--TTTTTAAAAA
16837264 AC
124 AC
16837266 ATCGTAAAGA
Statistics
Matches: 225, Mismatches: 27, Indels: 37
0.78 0.09 0.13
Matches are distributed among these distances:
139 17 0.08
140 102 0.45
141 1 0.00
144 1 0.00
145 1 0.00
149 1 0.00
150 2 0.01
153 1 0.00
154 22 0.10
155 62 0.28
156 15 0.07
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (150 bp):
CGTTTGCGACAAAGTGCCACTAATTCTCGATATATAGCGGCGTTTTTAGAAAAGCGCCGCAAAAA
ATTAATCACAACGCATCTTTTAGTTAGCTTTAGTGGCATTAGCGGCGCTTTTTAAAAAACGCAGC
TAATGCTCGATCTACAGCGA
Found at i:16837333 original size:21 final size:21
Alignment explanation
Indices: 16837292--16837339 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
16837282 ATTTTATTCT
* *
16837292 AGGTTTATTGTTTAGTATTTA
1 AGGTTTAATGTCTAGTATTTA
16837313 AGGTTTAATGTCTA-TAGTTTA
1 AGGTTTAATGTCTAGTA-TTTA
*
16837334 GGGTTT
1 AGGTTT
16837340 TTAGGGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.23, C:0.02, G:0.23, T:0.52
Consensus pattern (21 bp):
AGGTTTAATGTCTAGTATTTA
Found at i:16837627 original size:14 final size:14
Alignment explanation
Indices: 16837610--16837812 Score: 65
Period size: 14 Copynumber: 14.4 Consensus size: 14
16837600 TAGGATATAA
16837610 GTTTATGGTTTAGG
1 GTTTATGGTTTAGG
** *
16837624 GTTTAAAGTTTAAG
1 GTTTATGGTTTAGG
* *
16837638 GTTTATGATTTAGT
1 GTTTATGGTTTAGG
* *
16837652 G-TTAAGAGTTTAGT
1 GTTTATG-GTTTAGG
* * *
16837666 GTTTACGATTTAAG
1 GTTTATGGTTTAGG
* *
16837680 GTGTA-GGTTTATG
1 GTTTATGGTTTAGG
*
16837693 GTTTA-GTGTTTAGT
1 GTTTATG-GTTTAGG
* * *
16837707 GTTTAGGGGTTAGAA
1 GTTTATGGTTTAG-G
* * *
16837722 GCTTAAGATTTAAGG
1 GTTTATGGTTT-AGG
*
16837737 G-TTATAGGCTTAAGG
1 GTTTAT-GG-TTTAGG
* * *
16837752 GCTTATGATTTATG
1 GTTTATGGTTTAGG
*
16837766 GTTTAGGGTTTAGG
1 GTTTATGGTTTAGG
*
16837780 GTTTA-GTGTTTAGT
1 GTTTATG-GTTTAGG
**
16837794 GTTTGGGGTTTAGG
1 GTTTATGGTTTAGG
16837808 GTTTA
1 GTTTA
16837813 GCTAAAAACA
Statistics
Matches: 137, Mismatches: 41, Indels: 22
0.69 0.20 0.11
Matches are distributed among these distances:
13 16 0.12
14 93 0.68
15 20 0.15
16 8 0.06
ACGTcount: A:0.22, C:0.02, G:0.31, T:0.45
Consensus pattern (14 bp):
GTTTATGGTTTAGG
Found at i:16837634 original size:21 final size:20
Alignment explanation
Indices: 16837591--16837664 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
16837581 GTAGTATATA
16837591 TTTAAGGTTTAGGATATAAG
1 TTTAAGGTTTAGGATATAAG
* * *
16837611 TTTATGGTTTAGGGTTTAAAG
1 TTTAAGGTTTAGGATAT-AAG
* *
16837632 TTTAAGGTTTATGAT-TTAG
1 TTTAAGGTTTAGGATATAAG
16837651 TGTTAAGAGTTTAG
1 T-TTAAG-GTTTAG
16837665 TGTTTACGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.07
20 20 0.47
21 20 0.47
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (20 bp):
TTTAAGGTTTAGGATATAAG
Found at i:16837649 original size:28 final size:28
Alignment explanation
Indices: 16837610--16837711 Score: 77
Period size: 28 Copynumber: 3.7 Consensus size: 28
16837600 TAGGATATAA
*
16837610 GTTTATGGTTTAGGGTTTAAAGTTTAAG
1 GTTTATGATTTAGGGTTTAAAGTTTAAG
*
16837638 GTTTATGATTTAGTG-TTAAGAGTTT-AG
1 GTTTATGATTTAGGGTTTAA-AGTTTAAG
* * * * *
16837665 TGTTTACGATTTAAGGTGT-AGGTTTATG
1 -GTTTATGATTTAGGGTTTAAAGTTTAAG
*
16837693 GTTTAGTG-TTTAGTGTTTA
1 GTTTA-TGATTTAGGGTTTA
16837712 GGGGTTAGAA
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
27 22 0.39
28 33 0.59
29 1 0.02
ACGTcount: A:0.23, C:0.01, G:0.27, T:0.49
Consensus pattern (28 bp):
GTTTATGATTTAGGGTTTAAAGTTTAAG
Found at i:16837733 original size:22 final size:22
Alignment explanation
Indices: 16837708--16837750 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16837698 GTGTTTAGTG
*
16837708 TTTAGGGGTTAGAAGCTTAAGA
1 TTTAAGGGTTAGAAGCTTAAGA
* *
16837730 TTTAAGGGTTATAGGCTTAAG
1 TTTAAGGGTTAGAAGCTTAAG
16837751 GGCTTATGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
TTTAAGGGTTAGAAGCTTAAGA
Found at i:16837770 original size:7 final size:7
Alignment explanation
Indices: 16837760--16837813 Score: 72
Period size: 7 Copynumber: 7.7 Consensus size: 7
16837750 GGGCTTATGA
*
16837760 TTTATGG
1 TTTAGGG
16837767 TTTAGGG
1 TTTAGGG
16837774 TTTAGGG
1 TTTAGGG
*
16837781 TTTAGTG
1 TTTAGGG
*
16837788 TTTAGTG
1 TTTAGGG
*
16837795 TTTGGGG
1 TTTAGGG
16837802 TTTAGGG
1 TTTAGGG
16837809 TTTAG
1 TTTAG
16837814 CTAAAAACAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (7 bp):
TTTAGGG
Found at i:16837784 original size:21 final size:20
Alignment explanation
Indices: 16837610--16837813 Score: 86
Period size: 21 Copynumber: 9.6 Consensus size: 20
16837600 TAGGATATAA
**
16837610 GTTTATGGTTTAGGGTTTAAA
1 GTTTA-GGTTTAGGGTTTAGG
* * *
16837631 GTTTAAGGTTTATGATTTAGT
1 GTTT-AGGTTTAGGGTTTAGG
* * *
16837652 GTTAAGAGTTTAGTGTTTACG
1 GTTTAG-GTTTAGGGTTTAGG
* * *
16837673 ATTTAAGGTGTA-GGTTTATG
1 GTTT-AGGTTTAGGGTTTAGG
*
16837693 GTTTAGTGTTTAGTGTTTAGG
1 GTTTAG-GTTTAGGGTTTAGG
* * * *
16837714 GGTTAGAAGCTTAAGATTTAAGG
1 GTTTAG--GTTTAGGGTTT-AGG
* * *
16837737 GTTATAGGCTTAAGGGCTTATG
1 GTT-TAGG-TTTAGGGTTTAGG
*
16837759 ATTTATGGTTTAGGGTTTAGG
1 GTTTA-GGTTTAGGGTTTAGG
* *
16837780 GTTTAGTGTTTAGTGTTTGGG
1 GTTTAG-GTTTAGGGTTTAGG
16837801 GTTTAGGGTTTAG
1 GTTTA-GGTTTAG
16837814 CTAAAAACAT
Statistics
Matches: 132, Mismatches: 39, Indels: 24
0.68 0.20 0.12
Matches are distributed among these distances:
19 2 0.02
20 16 0.12
21 83 0.63
22 18 0.14
23 10 0.08
24 3 0.02
ACGTcount: A:0.22, C:0.02, G:0.31, T:0.45
Consensus pattern (20 bp):
GTTTAGGTTTAGGGTTTAGG
Found at i:16838537 original size:24 final size:23
Alignment explanation
Indices: 16838505--16838551 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
16838495 TCACGGACTC
16838505 TATTTTTGTTTCTATGTTTAATT
1 TATTTTTGTTTCTATGTTTAATT
16838528 TATTATTTGTTTCTATGTTTAATT
1 TATT-TTTGTTTCTATGTTTAATT
16838552 GTTAAGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.19, C:0.04, G:0.09, T:0.68
Consensus pattern (23 bp):
TATTTTTGTTTCTATGTTTAATT
Found at i:16840023 original size:28 final size:28
Alignment explanation
Indices: 16839978--16840051 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
16839968 TTTAATTGGT
16839978 TTAATGTGAATAAATTATCGATTTTTGAC
1 TTAAT-TGAATAAATTATCGATTTTTGAC
* * *
16840007 TTAATTGAATAATTTATCGTTTTTTGAT
1 TTAATTGAATAAATTATCGATTTTTGAC
16840035 TTAATTGAATAAATTAT
1 TTAATTGAATAAATTAT
16840052 GTTTGACTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 36 0.88
29 5 0.12
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.50
Consensus pattern (28 bp):
TTAATTGAATAAATTATCGATTTTTGAC
Found at i:16840064 original size:28 final size:28
Alignment explanation
Indices: 16839977--16840065 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
16839967 GTTTAATTGG
* *
16839977 TTTAATGTGAATAAATTATCGATTT-TTGA
1 TTTAAT-TGAATAAATTATCG-TTTACTAA
* * ** *
16840006 CTTAATTGAATAATTTATCGTTTTTTGA
1 TTTAATTGAATAAATTATCGTTTACTAA
16840034 TTTAATTGAATAAATTAT-GTTTGACTAA
1 TTTAATTGAATAAATTATCGTTT-ACTAA
16840062 TTTA
1 TTTA
16840066 TCGTTTTTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 7 0.14
28 39 0.76
29 5 0.10
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (28 bp):
TTTAATTGAATAAATTATCGTTTACTAA
Found at i:16840360 original size:9 final size:9
Alignment explanation
Indices: 16840346--16840380 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
16840336 AAAAATTATT
16840346 ATAACTTAC
1 ATAACTTAC
16840355 ATAACTTAC
1 ATAACTTAC
16840364 ATAACTTA-
1 ATAACTTAC
16840372 ATAACTTAC
1 ATAACTTAC
16840381 CTAATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:16840377 original size:17 final size:18
Alignment explanation
Indices: 16840346--16840380 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
16840336 AAAAATTATT
16840346 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
16840364 ATAACTTA-ATAACTTAC
1 ATAACTTACATAACTTAC
16840381 CTAATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAACTTACATAACTTAC
Found at i:16840504 original size:19 final size:21
Alignment explanation
Indices: 16840480--16840525 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
16840470 CTTATTTTAA
16840480 TATATTTTAAATTA-A-AACT
1 TATATTTTAAATTACATAACT
*
16840499 TATATTTTGAATTACATAACT
1 TATATTTTAAATTACATAACT
16840520 TA-ATTT
1 TATATTT
16840526 CTTCCCCGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 13 0.54
20 5 0.21
21 6 0.25
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (21 bp):
TATATTTTAAATTACATAACT
Found at i:16840705 original size:8 final size:9
Alignment explanation
Indices: 16840674--16840956 Score: 216
Period size: 9 Copynumber: 31.9 Consensus size: 9
16840664 AAATTAATAT
*
16840674 ATAATTTAC
1 ATAACTTAC
16840683 ATAACTTAC
1 ATAACTTAC
16840692 ATAACTTA-
1 ATAACTTAC
16840700 ATAACTTAC
1 ATAACTTAC
16840709 ATAA--TAC
1 ATAACTTAC
* *
16840716 ATAAATTAATAT
1 AT-AACT--TAC
*
16840728 ATAATTTATGC
1 ATAACTTA--C
*
16840739 AT--CTCAC
1 ATAACTTAC
16840746 ATAACTTAC
1 ATAACTTAC
16840755 ATAACTTA-
1 ATAACTTAC
16840763 ATAACTTAC
1 ATAACTTAC
16840772 ATAA--TAC
1 ATAACTTAC
* *
16840779 ATAA-ATAT
1 ATAACTTAC
* *
16840787 ATATCATATC
1 ATAACTTA-C
*
16840797 ACAACTTAC
1 ATAACTTAC
16840806 ATAACTTAC
1 ATAACTTAC
*
16840815 ATAATTTA-
1 ATAACTTAC
16840823 ATAACTTAC
1 ATAACTTAC
16840832 ATAACTTA-
1 ATAACTTAC
*
16840840 ATAACTCAC
1 ATAACTTAC
16840849 ATAACTTAC
1 ATAACTTAC
*
16840858 ATAATTTATAC
1 ATAA-CT-TAC
*
16840869 ATAATTTA-
1 ATAACTTAC
*
16840877 ATAACTTTC
1 ATAACTTAC
16840886 ATAACTTAC
1 ATAACTTAC
16840895 ATAACTTA-
1 ATAACTTAC
16840903 ATAACTTAC
1 ATAACTTAC
*
16840912 ATAATTTATAC
1 ATAA-CT-TAC
*
16840923 ATAATTTA-
1 ATAACTTAC
*
16840931 ATAACTTTC
1 ATAACTTAC
16840940 ATAACTTAC
1 ATAACTTAC
16840949 ATAACTTA
1 ATAACTTA
16840957 ATTATACTTG
Statistics
Matches: 226, Mismatches: 25, Indels: 46
0.76 0.08 0.15
Matches are distributed among these distances:
7 15 0.07
8 57 0.25
9 119 0.53
10 11 0.05
11 20 0.09
12 4 0.02
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.37
Consensus pattern (9 bp):
ATAACTTAC
Found at i:16840724 original size:24 final size:25
Alignment explanation
Indices: 16840674--16840958 Score: 87
Period size: 26 Copynumber: 11.1 Consensus size: 25
16840664 AAATTAATAT
* *
16840674 ATAATTTACATAACTTACATAACTTA
1 ATAACTTACATAAC-TACATAAATTA
16840700 ATAACTTACATAA-TACATAAATTAATA
1 ATAACTTACATAACTACATAAA-T--TA
* *
16840727 TATAATTTATGCAT--CTCACATAACTTA
1 -ATAACTTA--CATAACT-ACATAAATTA
16840754 CATAACTTA-ATAACTTACAT-AA-TA
1 -ATAACTTACATAAC-TACATAAATTA
* * * * *
16840778 CATAA-ATATATATCATATCACAACTTA
1 -ATAACTTACATAAC-TA-CATAAATTA
* *
16840805 CATAACTTACATAATTTA-ATAACTTA
1 -ATAACTTACATAA-CTACATAAATTA
*
16840831 CATAACTTA-ATAACTCACATAACTTA
1 -ATAACTTACATAACT-ACATAAATTA
*
16840857 CATAA-TT---T-A-TACATAATTTA
1 -ATAACTTACATAACTACATAAATTA
* *
16840877 ATAACTTTCATAACTTACATAACTTA
1 ATAACTTACATAAC-TACATAAATTA
* *
16840903 ATAACTTACATAATTTATACATAATTTA
1 ATAACTTACATAA---CTACATAAATTA
* *
16840931 ATAACTTTCATAACTTACATAACTTA
1 ATAACTTACATAAC-TACATAAATTA
16840957 AT
1 AT
16840959 TATACTTGTA
Statistics
Matches: 203, Mismatches: 26, Indels: 60
0.70 0.09 0.21
Matches are distributed among these distances:
19 4 0.02
20 11 0.05
21 1 0.00
22 1 0.00
23 4 0.02
24 24 0.12
25 11 0.05
26 81 0.40
27 19 0.09
28 36 0.18
29 2 0.01
30 9 0.04
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (25 bp):
ATAACTTACATAACTACATAAATTA
Found at i:16840955 original size:54 final size:54
Alignment explanation
Indices: 16840799--16840958 Score: 263
Period size: 54 Copynumber: 3.0 Consensus size: 54
16840789 ATCATATCAC
* * *
16840799 AACTTACATAA-CT-TACATAATTTAATAACTTACATAACTTA-ATAACTCACAT
1 AACTTACATAATTTATACATAATTTAATAACTTTCATAACTTACATAACTTA-AT
16840851 AACTTACATAATTTATACATAATTTAATAACTTTCATAACTTACATAACTTAAT
1 AACTTACATAATTTATACATAATTTAATAACTTTCATAACTTACATAACTTAAT
16840905 AACTTACATAATTTATACATAATTTAATAACTTTCATAACTTACATAACTTAAT
1 AACTTACATAATTTATACATAATTTAATAACTTTCATAACTTACATAACTTAAT
16840959 TATACTTGTA
Statistics
Matches: 102, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
52 11 0.11
53 1 0.01
54 83 0.81
55 7 0.07
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (54 bp):
AACTTACATAATTTATACATAATTTAATAACTTTCATAACTTACATAACTTAAT
Found at i:16847626 original size:45 final size:47
Alignment explanation
Indices: 16847572--16847683 Score: 129
Period size: 49 Copynumber: 2.4 Consensus size: 47
16847562 ATCCATATAA
* *
16847572 AACTACACTTCTTTTATTT-TATT-TTAGAATAAGGTTTTTCAATCT
1 AACTACACTTCTTCTATTTATATTATTAGAATAAGGTGTTTCAATCT
* * * *
16847617 TATTACACTTCATCTATTTGATGTTGATTAGAATAAGGTGTTTCAATCT
1 AACTACACTTCTTCTATTT-ATATT-ATTAGAATAAGGTGTTTCAATCT
*
16847666 AACTACACTCCTTCTATT
1 AACTACACTTCTTCTATT
16847684 AGAATATGGT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
45 15 0.28
47 3 0.06
49 35 0.66
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (47 bp):
AACTACACTTCTTCTATTTATATTATTAGAATAAGGTGTTTCAATCT
Found at i:16861946 original size:15 final size:15
Alignment explanation
Indices: 16861926--16861955 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16861916 GCAATGTATG
16861926 GAAAGAAAAAATATT
1 GAAAGAAAAAATATT
*
16861941 GAAAGAAAATATATT
1 GAAAGAAAAAATATT
16861956 TTTCTTTCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (15 bp):
GAAAGAAAAAATATT
Found at i:16863270 original size:21 final size:22
Alignment explanation
Indices: 16863243--16863310 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 22
16863233 CCATTTATAA
16863243 AAATTAATATTTTAATAAAAAT
1 AAATTAATATTTTAATAAAAAT
*
16863265 -AATTAATATAATTTAAAAATAAAT
1 AAATTAATAT--TTTAATAA-AAAT
16863289 AAATATTAATATTTTAACTAAA
1 -AA-ATTAATATTTTAA-TAAA
16863311 GGGGTATGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
21 9 0.24
23 7 0.19
24 4 0.11
25 6 0.16
26 3 0.08
27 8 0.22
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATTAATATTTTAATAAAAAT
Found at i:16873277 original size:15 final size:15
Alignment explanation
Indices: 16873257--16873313 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
16873247 TTATGGAAAG
*
16873257 TCAAATATATGGTTA
1 TCAAATATATGGATA
*
16873272 TCAAATA-ATGGAAA
1 TCAAATATATGGATA
* *
16873286 GTCAAAGATATGGGTA
1 -TCAAATATATGGATA
16873302 TCAAATAT-TGGA
1 TCAAATATATGGA
16873314 AAATCAAAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
14 8 0.24
15 20 0.61
16 5 0.15
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (15 bp):
TCAAATATATGGATA
Found at i:16873285 original size:30 final size:30
Alignment explanation
Indices: 16873249--16873332 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
16873239 ATCCGTATTT
* *
16873249 ATGGAAAGTCAAATATATGGTTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
16873279 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* * *
16873309 TTGGAAAATCAAAGAAATGGGTAT
1 ATGGAAAGTCAAAGATATGGGTAT
16873333 TGAGATATTG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.26
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:16873495 original size:2 final size:2
Alignment explanation
Indices: 16873488--16873534 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
16873478 AAGGCATTGT
16873488 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
16873530 TC TC T
1 TC TC T
16873535 TTGTAAATTC
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:16877998 original size:15 final size:15
Alignment explanation
Indices: 16877980--16878026 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
16877970 TAATAAAAAG
16877980 TCAAAGATATGGGTA
1 TCAAAGATATGGGTA
* **
16877995 TCAAATAT-TGGAAAA
1 TCAAAGATATGG-GTA
16878010 TCAAAGATATGGGTA
1 TCAAAGATATGGGTA
16878025 TC
1 TC
16878027 GAGATATTGG
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 3 0.12
15 18 0.75
16 3 0.12
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (15 bp):
TCAAAGATATGGGTA
Found at i:16878014 original size:30 final size:30
Alignment explanation
Indices: 16877945--16878036 Score: 105
Period size: 30 Copynumber: 3.0 Consensus size: 30
16877935 TGTATTTATA
* * * *
16877945 GAAAGTCAAATATATGGTTATCAAATAAT-
1 GAAAATCAAAGATATGGGTATCAAATATTG
*
16877974 AAAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAA-TCAAAGATATGGGTATCAAATATTG
*
16878005 GAAAATCAAAGATATGGGTATCGAGATATTG
1 GAAAATCAAAGATATGGGTATC-AAATATTG
16878036 G
1 G
16878037 CATAAGAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.06
30 38 0.72
31 12 0.23
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.27
Consensus pattern (30 bp):
GAAAATCAAAGATATGGGTATCAAATATTG
Found at i:16878188 original size:2 final size:2
Alignment explanation
Indices: 16878181--16878211 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16878171 AAGGCATTGT
16878181 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
16878212 TTGTAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16890983 original size:29 final size:30
Alignment explanation
Indices: 16890928--16890993 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 30
16890918 ATTTAATGTG
*
16890928 CAATTGTATACATAAATTTTGATTTTGA-A
1 CAATTTTATACATAAATTTTGATTTTGATA
*
16890957 CAATTTTATACATAAAATTTTGA-TTTGATC
1 CAATTTTATACAT-AAATTTTGATTTTGATA
16890987 CAATTTT
1 CAATTTT
16890994 TGTAAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (30 bp):
CAATTTTATACATAAATTTTGATTTTGATA
Found at i:16895895 original size:14 final size:14
Alignment explanation
Indices: 16895878--16895905 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16895868 ATGGTTCAGT
16895878 TAATATTTTTATAA
1 TAATATTTTTATAA
16895892 TAATATTTTTATAA
1 TAATATTTTTATAA
16895906 AAAAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATATTTTTATAA
Found at i:16904801 original size:26 final size:26
Alignment explanation
Indices: 16904765--16904816 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
16904755 TTTATATTAA
16904765 GTGCTTGGTTGCCCTTTTTTTTTCTT
1 GTGCTTGGTTGCCCTTTTTTTTTCTT
16904791 GTGCTTGGTTGCCCTTTTTTTTTCTT
1 GTGCTTGGTTGCCCTTTTTTTTTCTT
16904817 TGGCTGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.19, T:0.62
Consensus pattern (26 bp):
GTGCTTGGTTGCCCTTTTTTTTTCTT
Found at i:16904952 original size:15 final size:17
Alignment explanation
Indices: 16904927--16904960 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
16904917 TGGTTTCTCT
16904927 TTTGTCTTGA-GTATTC
1 TTTGTCTTGAGGTATTC
16904943 TTTG-CTTGAGGTATTC
1 TTTGTCTTGAGGTATTC
16904959 TT
1 TT
16904961 CACATGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.56
Consensus pattern (17 bp):
TTTGTCTTGAGGTATTC
Found at i:16913186 original size:19 final size:19
Alignment explanation
Indices: 16913162--16913199 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16913152 GAAAATAGAG
16913162 CGAAAGCAACTCAAAAGCA
1 CGAAAGCAACTCAAAAGCA
16913181 CGAAAGCAACTCAAAAGCA
1 CGAAAGCAACTCAAAAGCA
16913200 AAGGAGTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.26, G:0.16, T:0.05
Consensus pattern (19 bp):
CGAAAGCAACTCAAAAGCA
Found at i:16913845 original size:131 final size:131
Alignment explanation
Indices: 16913611--16913873 Score: 526
Period size: 131 Copynumber: 2.0 Consensus size: 131
16913601 GGTCATGAAC
16913611 TTTGATCCACAACTTGTGATAATAAAATGACTAATTGATGGATGTGCATAAAAGTTTTTTCTTTT
1 TTTGATCCACAACTTGTGATAATAAAATGACTAATTGATGGATGTGCATAAAAGTTTTTTCTTTT
16913676 CTCACCCAAAGATTTTTATAATTTTTATAAACCTATCATTTTTAATATTATAATATTATTCTTAA
66 CTCACCCAAAGATTTTTATAATTTTTATAAACCTATCATTTTTAATATTATAATATTATTCTTAA
16913741 A
131 A
16913742 TTTGATCCACAACTTGTGATAATAAAATGACTAATTGATGGATGTGCATAAAAGTTTTTTCTTTT
1 TTTGATCCACAACTTGTGATAATAAAATGACTAATTGATGGATGTGCATAAAAGTTTTTTCTTTT
16913807 CTCACCCAAAGATTTTTATAATTTTTATAAACCTATCATTTTTAATATTATAATATTATTCTTAA
66 CTCACCCAAAGATTTTTATAATTTTTATAAACCTATCATTTTTAATATTATAATATTATTCTTAA
16913872 A
131 A
16913873 T
1 T
16913874 AAATTATAAT
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 132 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.44
Consensus pattern (131 bp):
TTTGATCCACAACTTGTGATAATAAAATGACTAATTGATGGATGTGCATAAAAGTTTTTTCTTTT
CTCACCCAAAGATTTTTATAATTTTTATAAACCTATCATTTTTAATATTATAATATTATTCTTAA
A
Found at i:16921573 original size:24 final size:24
Alignment explanation
Indices: 16921520--16921573 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
16921510 AAAACAATAG
* *
16921520 AAAATATTAAAGGAACAACAGATTC
1 AAAA-ATTAAAGGAACAACAAAATC
16921545 AAAAATTAAAGGAACAA-AAAATC
1 AAAAATTAAAGGAACAACAAAATC
16921568 AGAAAA
1 A-AAAA
16921574 AAAAAATCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 5 0.19
24 17 0.65
25 4 0.15
ACGTcount: A:0.65, C:0.09, G:0.11, T:0.15
Consensus pattern (24 bp):
AAAAATTAAAGGAACAACAAAATC
Found at i:16924633 original size:18 final size:18
Alignment explanation
Indices: 16924612--16924647 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16924602 GATAATGCGG
16924612 CAAAATTCAATAAAAAAT
1 CAAAATTCAATAAAAAAT
* *
16924630 CAAATTTCAATAGAAAAT
1 CAAAATTCAATAAAAAAT
16924648 TCACTCAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.25
Consensus pattern (18 bp):
CAAAATTCAATAAAAAAT
Found at i:16928295 original size:56 final size:56
Alignment explanation
Indices: 16928229--16928337 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 56
16928219 GCATCCATTG
* * *
16928229 GATGATAAATCATCAC-TTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTAA
1 GATGATAAATCATCACTTTTTAATTTAAATAATGCTCATGAATAATT-AATTTGTAA
16928285 GATGATAAATCATCACTTTTTAATTTAAATAATGCTCATGAATAATTAATTTG
1 GATGATAAATCATCACTTTTTAATTTAAATAATGCTCATGAATAATTAATTTG
16928338 CAATCTATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
56 22 0.45
57 27 0.55
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.41
Consensus pattern (56 bp):
GATGATAAATCATCACTTTTTAATTTAAATAATGCTCATGAATAATTAATTTGTAA
Found at i:16934241 original size:39 final size:39
Alignment explanation
Indices: 16934187--16934264 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
16934177 TTGTTAGTGT
16934187 TCCATTTAATTCACAAACATCCGAATGAATTAAATCTAA
1 TCCATTTAATTCACAAACATCCGAATGAATTAAATCTAA
16934226 TCCATTTAATTCACAAACATCCGAATGAATTAAATCTAA
1 TCCATTTAATTCACAAACATCCGAATGAATTAAATCTAA
16934265 CACTTGTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (39 bp):
TCCATTTAATTCACAAACATCCGAATGAATTAAATCTAA
Found at i:16939113 original size:17 final size:16
Alignment explanation
Indices: 16939091--16939138 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
16939081 TAAATAATAG
*
16939091 ATAAATCAATTTTTTT
1 ATAAATCAATTATTTT
*
16939107 AATAAATTAATTATTTT
1 -ATAAATCAATTATTTT
**
16939124 ATAAAAAAATTATTT
1 ATAAATCAATTATTT
16939139 ATTTTTATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAAATCAATTATTTT
Found at i:16940537 original size:104 final size:104
Alignment explanation
Indices: 16940420--16940628 Score: 418
Period size: 104 Copynumber: 2.0 Consensus size: 104
16940410 TTTTTATAGT
16940420 TAAATAAGCCCTTAACTTATGGTTTTTACTCATAAAAGCCATTTATTTTAATATTAAAGTAAATA
1 TAAATAAGCCCTTAACTTATGGTTTTTACTCATAAAAGCCATTTATTTTAATATTAAAGTAAATA
16940485 TATTTTGAATTTCAAGCTCTTATCTTAATTTTTTGTTGA
66 TATTTTGAATTTCAAGCTCTTATCTTAATTTTTTGTTGA
16940524 TAAATAAGCCCTTAACTTATGGTTTTTACTCATAAAAGCCATTTATTTTAATATTAAAGTAAATA
1 TAAATAAGCCCTTAACTTATGGTTTTTACTCATAAAAGCCATTTATTTTAATATTAAAGTAAATA
16940589 TATTTTGAATTTCAAGCTCTTATCTTAATTTTTTGTTGA
66 TATTTTGAATTTCAAGCTCTTATCTTAATTTTTTGTTGA
16940628 T
1 T
16940629 GCAATAGAAA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 105 1.00
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.46
Consensus pattern (104 bp):
TAAATAAGCCCTTAACTTATGGTTTTTACTCATAAAAGCCATTTATTTTAATATTAAAGTAAATA
TATTTTGAATTTCAAGCTCTTATCTTAATTTTTTGTTGA
Found at i:16941563 original size:36 final size:36
Alignment explanation
Indices: 16941516--16941588 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
16941506 TTTTTTTAGT
*
16941516 GAAAGAGGGTAAATTGCAGTCTAACACTTAATACAA
1 GAAAGAGGGTAAATTACAGTCTAACACTTAATACAA
16941552 GAAAGAGGGTAAATTACAGTCTAACACTTAATACAA
1 GAAAGAGGGTAAATTACAGTCTAACACTTAATACAA
16941588 G
1 G
16941589 GACCTTCATG
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:0.45, C:0.14, G:0.19, T:0.22
Consensus pattern (36 bp):
GAAAGAGGGTAAATTACAGTCTAACACTTAATACAA
Found at i:16948511 original size:17 final size:16
Alignment explanation
Indices: 16948469--16948511 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
16948459 TTATTTTGAG
16948469 CTTTGAAAATTTTTAAA
1 CTTT-AAAATTTTTAAA
* *
16948486 ATTTCAAATTTCTTAAA
1 CTTTAAAATTT-TTAAA
16948503 CTTTAAAAT
1 CTTTAAAAT
16948512 GCATAAAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (16 bp):
CTTTAAAATTTTTAAA
Found at i:16952151 original size:11 final size:12
Alignment explanation
Indices: 16952125--16952157 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
16952115 CCAAATATTC
16952125 AAGAAGAAAAAGA
1 AAGAA-AAAAAGA
16952138 AAGAAAAAAA-A
1 AAGAAAAAAAGA
16952149 AAGAAAAAA
1 AAGAAAAAA
16952158 GTAGCAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 5 0.25
13 5 0.25
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAGA
Found at i:16953033 original size:43 final size:43
Alignment explanation
Indices: 16952913--16953033 Score: 161
Period size: 43 Copynumber: 2.8 Consensus size: 43
16952903 TAAATCAGAA
* *
16952913 CAATTATACTGGCACACATAGTGCATCATTGAATATACTGAAG
1 CAATTATACTGGCACACATAGTGCATCATTGGATATACCGAAG
* ** * * * *
16952956 CAATTATGCTAACACATACAGTGCATTATCGGATATACCGAAG
1 CAATTATACTGGCACACATAGTGCATCATTGGATATACCGAAG
16952999 CAATTATACTGGCACACATAGTGCATCATTGGATA
1 CAATTATACTGGCACACATAGTGCATCATTGGATA
16953034 AATAAAAGTA
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (43 bp):
CAATTATACTGGCACACATAGTGCATCATTGGATATACCGAAG
Found at i:16957941 original size:15 final size:16
Alignment explanation
Indices: 16957906--16957936 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16957896 CATTGGAAGC
16957906 AAATTAAAAATTTTTG
1 AAATTAAAAATTTTTG
16957922 AAATTAAAAATTTTT
1 AAATTAAAAATTTTT
16957937 TAATTTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AAATTAAAAATTTTTG
Found at i:16957990 original size:21 final size:19
Alignment explanation
Indices: 16957966--16958019 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
16957956 AATTAGTAAC
* *
16957966 AAATTAAAAAAAATCAATTTA
1 AAATTATAAAAAATC-A-TAA
*
16957987 AAATTTTAAAAAATCATAA
1 AAATTATAAAAAATCATAA
16958006 AAATTATAAAAAAT
1 AAATTATAAAAAAT
16958020 TTATTAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 15 0.52
20 1 0.03
21 13 0.45
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATTATAAAAAATCATAA
Found at i:16967847 original size:30 final size:30
Alignment explanation
Indices: 16967813--16967870 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
16967803 AAAACAAAAC
16967813 AAAAATCATTCATATCAAATAACCAATTAA
1 AAAAATCATTCATATCAAATAACCAATTAA
*
16967843 AAAAATCATTCATATCAAATAACTAATT
1 AAAAATCATTCATATCAAATAACCAATT
16967871 GAACTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (30 bp):
AAAAATCATTCATATCAAATAACCAATTAA
Found at i:16969545 original size:27 final size:26
Alignment explanation
Indices: 16969472--16969545 Score: 62
Period size: 27 Copynumber: 2.8 Consensus size: 26
16969462 TTTCCTCTCT
*
16969472 AAAAATGGCATAT-TCTCATAAATATA
1 AAAAATGGCATATATAT-ATAAATATA
* * *
16969498 AAAGAATGACCTA-AAATTATAAATATTA
1 AAA-AATGGCATATATA-TATAAATA-TA
16969526 AAAAATGGCATATATATATA
1 AAAAATGGCATATATATATA
16969546 TATAAATTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
26 3 0.08
27 25 0.69
28 8 0.22
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (26 bp):
AAAAATGGCATATATATATAAATATA
Found at i:16975487 original size:18 final size:18
Alignment explanation
Indices: 16975434--16975487 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
16975424 AGACCCAATG
* * *
16975434 TGAGTAGGAGGGTCAACA
1 TGAGCAGGAGAGTCAACT
*
16975452 TGAGCATGAGAGTCAACT
1 TGAGCAGGAGAGTCAACT
*
16975470 TGAGGAGGAGAGTCAACT
1 TGAGCAGGAGAGTCAACT
16975488 ATAGGCAAGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.35, T:0.19
Consensus pattern (18 bp):
TGAGCAGGAGAGTCAACT
Found at i:16981501 original size:35 final size:35
Alignment explanation
Indices: 16981460--16981533 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
16981450 TCACACAAAA
16981460 TATTTTTGGGCACATCCCCTTCAATTACAGATATT
1 TATTTTTGGGCACATCCCCTTCAATTACAGATATT
16981495 TATTTTTGGGCACATCCCCTTCAATTACAGATATT
1 TATTTTTGGGCACATCCCCTTCAATTACAGATATT
16981530 TATT
1 TATT
16981534 CGTGTATTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.42
Consensus pattern (35 bp):
TATTTTTGGGCACATCCCCTTCAATTACAGATATT
Found at i:16982040 original size:27 final size:27
Alignment explanation
Indices: 16982002--16982079 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
16981992 TAGTATTGGC
*
16982002 GCCTATCTCAGAAGCGCCAATGGTGGT
1 GCCTATCTCAGAGGCGCCAATGGTGGT
* **
16982029 GCCTATCTCAGAGGCGCCATTATTGGT
1 GCCTATCTCAGAGGCGCCAATGGTGGT
*
16982056 GCC-ATACTGAGAGGCGCCAATGGT
1 GCCTAT-CTCAGAGGCGCCAATGGT
16982080 CTGATTTTTC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 2 0.05
27 40 0.95
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (27 bp):
GCCTATCTCAGAGGCGCCAATGGTGGT
Found at i:16982559 original size:21 final size:21
Alignment explanation
Indices: 16982528--16982740 Score: 133
Period size: 21 Copynumber: 10.2 Consensus size: 21
16982518 AATTAATTAT
16982528 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
16982550 AAAAAATTACAATATTACAATATATC
1 AAAAAATTACAATATT-C---ATA-C
*** *
16982576 CCGACATTACAATATTCAT--
1 AAAAAATTACAATATTCATAC
*
16982595 AAAAAATTACAATATTCATAT
1 AAAAAATTACAATATTCATAC
16982616 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
* * *
16982637 --AAAA-TACTA-ATCCAAAAC
1 AAAAAATTACAATATTC-ATAC
* * * *
16982655 TATAAA-TACAA-ATTTAATTAT
1 AAAAAATTACAATA-TTCA-TAC
16982676 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
* *
16982698 --AACATTAGAATATTCATA-
1 AAAAAATTACAATATTCATAC
16982716 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
16982737 AAAA
1 AAAA
16982741 TTCTAATCTA
Statistics
Matches: 147, Mismatches: 26, Indels: 37
0.70 0.12 0.18
Matches are distributed among these distances:
17 3 0.02
18 7 0.05
19 33 0.22
20 27 0.18
21 40 0.27
22 11 0.07
23 8 0.05
24 1 0.01
25 4 0.03
26 13 0.09
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.31
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:16982605 original size:19 final size:19
Alignment explanation
Indices: 16982581--16982742 Score: 125
Period size: 19 Copynumber: 8.2 Consensus size: 19
16982571 ATATCCCGAC
16982581 ATTACAATATTCATAAAAA
1 ATTACAATATTCATAAAAA
16982600 ATTACAATATTCATATAAAAA
1 ATTACAATATTC--ATAAAAA
*
16982621 ATTACAATATTCATACAAA
1 ATTACAATATTCATAAAAA
* *
16982640 A-TACTA-ATCCA-AAACTATA
1 ATTACAATATTCATAAA--A-A
*
16982659 AATACAAATTTAATT-ATAAAATA
1 ATTAC-AA--T-ATTCATAAAA-A
* *
16982682 ATTACAATATTCATACAAC
1 ATTACAATATTCATAAAAA
*
16982701 ATTAGAATATTCATAAAAAA
1 ATTACAATATTCAT-AAAAA
*
16982721 ATTACAATATTCATACAAA
1 ATTACAATATTCATAAAAA
16982740 ATT
1 ATT
16982743 CTAATCTAAA
Statistics
Matches: 115, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
16 2 0.02
17 4 0.03
18 5 0.04
19 44 0.38
20 25 0.22
21 20 0.17
22 2 0.02
23 7 0.06
24 1 0.01
25 5 0.04
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (19 bp):
ATTACAATATTCATAAAAA
Found at i:16982785 original size:100 final size:101
Alignment explanation
Indices: 16982581--16982776 Score: 288
Period size: 100 Copynumber: 1.9 Consensus size: 101
16982571 ATATCCCGAC
16982581 ATTACAATATTCATAAAAAATTACAATATTCATATAAAAAATTACAATATTCATACAAAATACTA
1 ATTACAATATTCATAAAAAATTACAATATTCATATAAAAAATTACAATATTCATACAAAATACTA
* * *
16982646 ATCCAAAACTATAAATACAAATTTAATTATAAAATA
66 ATCCAAAACTATAAACACAAATATAATAATAAAATA
* * * *
16982682 ATTACAATATTCATACAACATTAGAATATTCATA-AAAAAATTACAATATTCATACAAAATTCTA
1 ATTACAATATTCATAAAAAATTACAATATTCATATAAAAAATTACAATATTCATACAAAATACTA
*
16982746 AT-CTAAACTATAAACACTAAATATAGATAAT
66 ATCCAAAACTATAAACAC-AAATATA-ATAAT
16982777 TTATAATTAA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
99 13 0.15
100 37 0.44
101 35 0.41
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.32
Consensus pattern (101 bp):
ATTACAATATTCATAAAAAATTACAATATTCATATAAAAAATTACAATATTCATACAAAATACTA
ATCCAAAACTATAAACACAAATATAATAATAAAATA
Found at i:16983548 original size:36 final size:36
Alignment explanation
Indices: 16983479--16983549 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
16983469 TTTAGAACAC
*
16983479 AAATGTGTGTTTAAAAATATTATATAATAAATAATG
1 AAATGTATGTTTAAAAATATTATATAATAAATAATG
*
16983515 AAATGTATGGTTTAAAACTAATTA-ATAAT-AATAAT
1 AAATGTAT-GTTTAAAAAT-ATTATATAATAAATAAT
16983550 AACATATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 13 0.42
37 14 0.45
38 4 0.13
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (36 bp):
AAATGTATGTTTAAAAATATTATATAATAAATAATG
Found at i:16984167 original size:19 final size:19
Alignment explanation
Indices: 16984143--16984180 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16984133 AAATTCCGAG
16984143 TTAATCAAGTGGACGAGTC
1 TTAATCAAGTGGACGAGTC
16984162 TTAATCAAGTGGACGAGTC
1 TTAATCAAGTGGACGAGTC
16984181 CTATTTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (19 bp):
TTAATCAAGTGGACGAGTC
Done.