Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 96 of 295
Found at i:28516229 original size:21 final size:21
Alignment explanation
Indices: 28516206--28516260 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
28516196 TAATTACTTA
*
28516206 TTTAGCTTTTTTAAAAATTAAT
1 TTTAG-TTTTTTAAAAATTAAC
* *
28516228 TTTA-TTTTTTTAGAATTAAC
1 TTTAGTTTTTTAAAAATTAAC
28516248 TTTAGATTTTTTA
1 TTTAG-TTTTTTA
28516261 GTAAAAGGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 17 0.63
22 10 0.37
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTAGTTTTTTAAAAATTAAC
Found at i:28516261 original size:21 final size:21
Alignment explanation
Indices: 28516206--28516261 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
28516196 TAATTACTTA
* * *
28516206 TTTAGCTTTTTTAAAAATTAAT
1 TTTAGATTTTTT-AGAATTAAC
*
28516228 TTTA-TTTTTTTAGAATTAAC
1 TTTAGATTTTTTAGAATTAAC
28516248 TTTAGATTTTTTAG
1 TTTAGATTTTTTAG
28516262 TAAAAGGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 11 0.38
21 14 0.48
22 4 0.14
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (21 bp):
TTTAGATTTTTTAGAATTAAC
Found at i:28516972 original size:21 final size:21
Alignment explanation
Indices: 28516943--28516985 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
28516933 GGTTCGCTGT
*
28516943 ATTGAATTAGAGGTGTATTGG
1 ATTGAATTAGAGGTGTAATGG
*
28516964 ATTGGATTAGAGGTGTAATGG
1 ATTGAATTAGAGGTGTAATGG
28516985 A
1 A
28516986 ATAGAGGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.35, T:0.35
Consensus pattern (21 bp):
ATTGAATTAGAGGTGTAATGG
Found at i:28516990 original size:16 final size:16
Alignment explanation
Indices: 28516966--28516998 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28516956 TGTATTGGAT
*
28516966 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
28516982 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
28516998 T
1 T
28516999 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:28517043 original size:45 final size:44
Alignment explanation
Indices: 28516977--28517071 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
28516967 GGATTAGAGG
* *
28516977 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
28517022 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
28517066 TGTAAT
1 TGTAAT
28517072 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:28517254 original size:18 final size:17
Alignment explanation
Indices: 28517233--28517267 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28517223 TTATTATTTA
*
28517233 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28517251 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28517268 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28517261 original size:28 final size:27
Alignment explanation
Indices: 28517191--28517263 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
28517181 TTTATTATCA
*
28517191 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
28517219 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
28517246 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
28517264 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:28522586 original size:69 final size:70
Alignment explanation
Indices: 28522456--28522586 Score: 151
Period size: 69 Copynumber: 1.9 Consensus size: 70
28522446 GTTTTATTAG
* ** *
28522456 TTTTTTTACAATTTAGGCCCCTAAATTCTATTTAAATTTTGATTCAATCCTTTTTATATTTATTC
1 TTTTATTACAATTTAGGCCCCTAAATTCTATTTAAATTTCAATTCAATCCTTTTTACATTTATTC
28522521 ATTTA
66 ATTTA
* * * *
28522526 TTTTATTATAATTTAGG-CTCTAAATT-TCATTTTAATTTCAATTTAATCCTTTATT-CATTTA
1 TTTTATTACAATTTAGGCCCCTAAATTCT-ATTTAAATTTCAATTCAATCCTTT-TTACATTTA
28522587 ATTTCAACCT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
68 1 0.02
69 33 0.65
70 17 0.33
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.55
Consensus pattern (70 bp):
TTTTATTACAATTTAGGCCCCTAAATTCTATTTAAATTTCAATTCAATCCTTTTTACATTTATTC
ATTTA
Found at i:28522642 original size:4 final size:4
Alignment explanation
Indices: 28522633--28522680 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
28522623 TCTGTTCTGT
* ** * *
28522633 TTTA TTTA TTTA TTTA TTTA TGTA TTCG TTCA TTTA TTTA TTTC TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
28522681 ATGTTTTTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:28526498 original size:19 final size:20
Alignment explanation
Indices: 28526455--28526500 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
28526445 TTGCATTCAT
28526455 TTTTCATTCATCAGCATTACA
1 TTTTCA-TCATCAGCATTACA
28526476 -TTTCATCAT-ATGCATTA-A
1 TTTTCATCATCA-GCATTACA
28526494 TTTTCAT
1 TTTTCAT
28526501 AAAAAGGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.09
19 16 0.70
20 5 0.22
ACGTcount: A:0.28, C:0.20, G:0.04, T:0.48
Consensus pattern (20 bp):
TTTTCATCATCAGCATTACA
Found at i:28529300 original size:21 final size:22
Alignment explanation
Indices: 28529267--28529307 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28529257 TTCATTTATG
*
28529267 TTTCATTGGCACATA-ATCATA
1 TTTCATTGCCACATACATCATA
*
28529288 TTTCATTTCCACATACATCA
1 TTTCATTGCCACATACATCA
28529308 CAATACATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (22 bp):
TTTCATTGCCACATACATCATA
Found at i:28529709 original size:28 final size:28
Alignment explanation
Indices: 28529678--28529747 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
28529668 GAATTATTCG
28529678 ATATTTCGCACACTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGTCATTCTCA
* * *
28529706 ATATCTCACACGCTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGTCATTCTCA
* *
28529734 AAATTTCGTACACT
1 ATATTTCGCACACT
28529748 GAGAGCCATA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGTCATTCTCA
Found at i:28536934 original size:40 final size:35
Alignment explanation
Indices: 28536847--28537143 Score: 281
Period size: 35 Copynumber: 8.5 Consensus size: 35
28536837 GGCAAAGTGC
28536847 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
* * * **
28536882 GAAATGTAGGTATGGTATTAACCATATTGAGTTGT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
28536917 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
* * * ** *
28536952 GAAACGTAGGTATGGTATTAACCATACTGAACTAT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
** * * * *
28536987 GAAACGTAGGTATGGCGTCGTCCATACTGAGCTAT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
* * * * *
28537022 GATACGTAGGTATGGCATCGTCCATACTGAGTTAT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
** * * ** **
28537057 GAAATATAGCTATGGTCTTTTCCATACCGAG-CAT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
* * **
28537091 GAAAAGTAGGTATGGTGTTTTCCATACCGAGTTGT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
28537126 GAAACGTAGGTATGGTAT
1 GAAACGTAGGTATGGTAT
28537144 TTCAATGAGG
Statistics
Matches: 218, Mismatches: 43, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
34 29 0.13
35 189 0.87
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (35 bp):
GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
Found at i:28536961 original size:70 final size:70
Alignment explanation
Indices: 28536847--28537143 Score: 317
Period size: 70 Copynumber: 4.3 Consensus size: 70
28536837 GGCAAAGTGC
* * *
28536847 GAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAATGTAGGTATGGTATTAACCATATTGA
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATTAACCATACTGA
*
28536912 GTTGT
66 GTTAT
*
28536917 GAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAACGTAGGTATGGTATTAACCATACTGA
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATTAACCATACTGA
**
28536982 ACTAT
66 GTTAT
** * * * * * ***
28536987 GAAACGTAGGTATGGCGTCGTCCATACTGAGCTATGATACGTAGGTATGGCATCGTCCATACTGA
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATTAACCATACTGA
28537052 GTTAT
66 GTTAT
** * * ** * * * ** *
28537057 GAAATATAGCTATGGTCTTTTCCATACCGAG-CATGAAAAGTAGGTATGGTGTTTTCCATACCGA
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATTAACCATACTGA
*
28537121 GTTGT
66 GTTAT
28537126 GAAACGTAGGTATGGTAT
1 GAAACGTAGGTATGGTAT
28537144 TTCAATGAGG
Statistics
Matches: 188, Mismatches: 39, Indels: 1
0.82 0.17 0.00
Matches are distributed among these distances:
69 43 0.23
70 145 0.77
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (70 bp):
GAAACGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATTAACCATACTGA
GTTAT
Found at i:28537029 original size:105 final size:105
Alignment explanation
Indices: 28536847--28537143 Score: 335
Period size: 105 Copynumber: 2.8 Consensus size: 105
28536837 GGCAAAGTGC
* * * * * * *
28536847 GAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAATGTAGGTATGGTATTAACCATATTGA
1 GAAACGTAGGTATGGTATTATCCATACCGAGCTATGAAAAGTAGGTATGGTGTTATCCATACTGA
*
28536912 GTTGTGAAACGTAGGTATGGTATCATCCATACCGAGTTGT
66 GTTGTGAAACGTAGGTATGGTATCATCCATACCGAGTTAT
* * * * * **
28536952 GAAACGTAGGTATGGTATTAACCATACTGAACTATGAAACGTAGGTATGGCGTCGTCCATACTGA
1 GAAACGTAGGTATGGTATTATCCATACCGAGCTATGAAAAGTAGGTATGGTGTTATCCATACTGA
* * * * * *
28537017 GCTATGATACGTAGGTATGGCATCGTCCATACTGAGTTAT
66 GTTGTGAAACGTAGGTATGGTATCATCCATACCGAGTTAT
** * * * * *
28537057 GAAATATAGCTATGGTCTTTTCCATACCGAGC-ATGAAAAGTAGGTATGGTGTTTTCCATACCGA
1 GAAACGTAGGTATGGTATTATCCATACCGAGCTATGAAAAGTAGGTATGGTGTTATCCATACTGA
28537121 GTTGTGAAACGTAGGTATGGTAT
66 GTTGTGAAACGTAGGTATGGTAT
28537144 TTCAATGAGG
Statistics
Matches: 155, Mismatches: 37, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
104 46 0.30
105 109 0.70
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (105 bp):
GAAACGTAGGTATGGTATTATCCATACCGAGCTATGAAAAGTAGGTATGGTGTTATCCATACTGA
GTTGTGAAACGTAGGTATGGTATCATCCATACCGAGTTAT
Found at i:28544207 original size:30 final size:30
Alignment explanation
Indices: 28544142--28544216 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
28544132 GACAAATTTT
* **
28544142 GCAGCAACTACAACTACAGCAACTGTGACA
1 GCAGCAACAACAACTACAGCAACTACGACA
* *
28544172 ACAGCAACAACGACTACAGCAACTACGACA
1 GCAGCAACAACAACTACAGCAACTACGACA
*
28544202 GCAGCAAGAACAACT
1 GCAGCAACAACAACT
28544217 GTGTCGTCAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.44, C:0.31, G:0.16, T:0.09
Consensus pattern (30 bp):
GCAGCAACAACAACTACAGCAACTACGACA
Found at i:28544208 original size:15 final size:15
Alignment explanation
Indices: 28544143--28544200 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 15
28544133 ACAAATTTTG
*
28544143 CAGCAACTACAACTA
1 CAGCAACTACGACTA
** *
28544158 CAGCAACTGTGACAA
1 CAGCAACTACGACTA
*
28544173 CAGCAACAACGACTA
1 CAGCAACTACGACTA
28544188 CAGCAACTACGAC
1 CAGCAACTACGAC
28544201 AGCAGCAAGA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.43, C:0.33, G:0.14, T:0.10
Consensus pattern (15 bp):
CAGCAACTACGACTA
Found at i:28549063 original size:14 final size:14
Alignment explanation
Indices: 28549044--28549074 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28549034 AACATTTTAA
*
28549044 TGGAATGTAATTTT
1 TGGAATGTAATTGT
28549058 TGGAATGTAATTGT
1 TGGAATGTAATTGT
28549072 TGG
1 TGG
28549075 GGGAAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (14 bp):
TGGAATGTAATTGT
Found at i:28551079 original size:11 final size:11
Alignment explanation
Indices: 28551063--28551087 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28551053 GTATAAATGT
28551063 AATATCCCTAA
1 AATATCCCTAA
28551074 AATATCCCTAA
1 AATATCCCTAA
28551085 AAT
1 AAT
28551088 TGATATCTAA
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:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (11 bp):
AATATCCCTAA
Found at i:28554239 original size:71 final size:71
Alignment explanation
Indices: 28554176--28554329 Score: 260
Period size: 71 Copynumber: 2.2 Consensus size: 71
28554166 TTTTTCTTAC
28554176 TTTACAATT-TACTCCCCTTTTCAACTACTTTGATATACCGACTTAATTTTCATTCATAATA-TT
1 TTTACAATTATACTCCCCTTTTCAACTACTTTGATATACCGACTTAATTTTCATTCATAATATTT
28554239 TGCACA
66 TGCACA
*
28554245 TTTACAATTCATACTCCCCTTTTCAACTACTTTGATATACCGATTTAATTTTCATTCATAATA-T
1 TTTACAATT-ATACTCCCCTTTTCAACTACTTTGATATACCGACTTAATTTTCATTCATAATATT
28554309 TTGCACA
65 TTGCACA
28554316 TTTACAATTCATAC
1 TTTACAATT-ATAC
28554330 AACTAATTTA
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
69 9 0.11
71 73 0.89
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.44
Consensus pattern (71 bp):
TTTACAATTATACTCCCCTTTTCAACTACTTTGATATACCGACTTAATTTTCATTCATAATATTT
TGCACA
Found at i:28557290 original size:15 final size:15
Alignment explanation
Indices: 28557266--28557301 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
28557256 CTTCATACAT
*
28557266 ATTTTTTTTTGCATC
1 ATTTTATTTTGCATC
*
28557281 ATTTTATTTTGTATC
1 ATTTTATTTTGCATC
28557296 ATTTTA
1 ATTTTA
28557302 ATTATCGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (15 bp):
ATTTTATTTTGCATC
Found at i:28562086 original size:14 final size:13
Alignment explanation
Indices: 28562068--28562110 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
28562058 AAAAAAAATC
28562068 AAAATAAAAAAAG
1 AAAATAAAAAAAG
28562081 AGAAATAAAAAGAA-
1 A-AAATAAAAA-AAG
*
28562095 AAAATCAAAAAAG
1 AAAATAAAAAAAG
28562108 AAA
1 AAA
28562111 GAAAGAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 2 0.08
13 12 0.46
14 10 0.38
15 2 0.08
ACGTcount: A:0.81, C:0.02, G:0.09, T:0.07
Consensus pattern (13 bp):
AAAATAAAAAAAG
Found at i:28562123 original size:23 final size:24
Alignment explanation
Indices: 28562089--28562133 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
28562079 AGAGAAATAA
28562089 AAAGAAAAAATCAA-AAAAGAAAG
1 AAAGAAAAAATCAATAAAAGAAAG
*
28562112 AAAGAAAGAATCAATAAAAGAA
1 AAAGAAAAAATCAATAAAAGAA
28562134 GTTGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (24 bp):
AAAGAAAAAATCAATAAAAGAAAG
Found at i:28563383 original size:67 final size:64
Alignment explanation
Indices: 28563223--28563407 Score: 244
Period size: 64 Copynumber: 2.8 Consensus size: 64
28563213 TCATTCATAA
* *
28563223 CACATCTAGTTAGGAGCATTTGATTCATTGCGATCATAGCATCCTAATTAATTGACATCAACAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATCAACAT
* * * *
28563287 CACATCTAGTTAGGAGCATTTGATTCATTTTGATCGTAGCATCCTAATTATTTGACATCGCTCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACAT--C-AAC
28563352 AT
63 AT
* * * * *
28563354 CTCATTTAGTTAGAAGCATTGGATTCATTTCAATCATAGCATCCTAATTATTTG
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTG
28563408 GCACAAACAT
Statistics
Matches: 105, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
64 54 0.51
66 1 0.01
67 50 0.48
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATCAACAT
Found at i:28563891 original size:43 final size:45
Alignment explanation
Indices: 28563813--28563905 Score: 111
Period size: 43 Copynumber: 2.1 Consensus size: 45
28563803 AGCCTCAAGC
* * * *
28563813 CTTATCTCTCTGATGTAGCAATAGAGCAAGTTGAAGATTG-AG-T
1 CTTATCTCTCTGAGGTAGCAAGAAAGCAAGCTGAAGATTGAAGAT
*
28563856 CTTATCTTTCTGAGGTAGCAAGAAAGC-AGACTGAAGATTGAAGAT
1 CTTATCTCTCTGAGGTAGCAAGAAAGCAAG-CTGAAGATTGAAGAT
28563901 CTTAT
1 CTTAT
28563906 TTCCCTAAGC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 2 0.05
43 32 0.76
44 2 0.05
45 6 0.14
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (45 bp):
CTTATCTCTCTGAGGTAGCAAGAAAGCAAGCTGAAGATTGAAGAT
Found at i:28564085 original size:176 final size:174
Alignment explanation
Indices: 28563758--28564154 Score: 510
Period size: 176 Copynumber: 2.3 Consensus size: 174
28563748 TGAAGATTGG
* * *
28563758 AAGA-GGCAAATCTTATCTCTATGTATCGACAATGAAGCAGATTTAAGCCTCAAGCCTTATCTCT
1 AAGATGGCAAATCTTATCTCTATGTATCGGCAATGGAGCAGATTTAAGCCACAAGCCTTATCTCT
* * * * *
28563822 CTGATGTAGCAATAGAGCAAGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGAC
66 CTGAGGTAACAAGAGAGCAAGTTGAAGATTGAGTCTTATCTTCCTGAGGAAGCAAGAAAGCAGAC
*
28563887 TGAAGATTGAAGATCTTATTTCCCTAAGCAGTAGCGGAGCAGATCA
131 TGAAGATTGAAGATCTTATTTCCCTAAGCAGTAGCAGAGC--ATCA
* * * * * * *
28563933 AAGATGGCGAGTCTTATCTCCATGTATCGGTAATGGAGTAGATTTTAGCCACTAGCCTTATCTCT
1 AAGATGGCAAATCTTATCTCTATGTATCGGCAATGGAGCAGATTTAAGCCACAAGCCTTATCTCT
* ** *
28563998 CTGAGGTAACAAGAGAGCAGGTTGGCGATTGTAGTCTTATCTTCCTGAGGAAGCAAGGAAGCAGA
66 CTGAGGTAACAAGAGAGCAAGTTGAAGATTG-AGTCTTATCTTCCTGAGGAAGCAAGAAAGCAGA
* * * *
28564063 CTGAAGATTGAAGATC-TATTTCCTTAAGTAGTTGTAGAGCATCA
130 CTGAAGATTGAAGATCTTATTTCCCTAAGCAGTAGCAGAGCATCA
* * *
28564107 ATGATGGCAAATCTTATTTCTATGTATTGGCAATGGAGCAGATTTAAG
1 AAGATGGCAAATCTTATCTCTATGTATCGGCAATGGAGCAGATTTAAG
28564155 TCCCCAAGAT
Statistics
Matches: 187, Mismatches: 33, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
174 43 0.23
175 4 0.02
176 94 0.50
177 46 0.25
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (174 bp):
AAGATGGCAAATCTTATCTCTATGTATCGGCAATGGAGCAGATTTAAGCCACAAGCCTTATCTCT
CTGAGGTAACAAGAGAGCAAGTTGAAGATTGAGTCTTATCTTCCTGAGGAAGCAAGAAAGCAGAC
TGAAGATTGAAGATCTTATTTCCCTAAGCAGTAGCAGAGCATCA
Found at i:28564263 original size:264 final size:266
Alignment explanation
Indices: 28563934--28564429 Score: 657
Period size: 264 Copynumber: 1.9 Consensus size: 266
28563924 AGCAGATCAA
* *
28563934 AGATGGCGAGTCTTATCTCCATGTATCGGTAATGGAGTAGATTTTAGCCACTAGCCTTATCTCTC
1 AGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGTAGATTTTAGCCACTAGCCTTATCTCTC
* * ***
28563999 TGAGGTAACAAGAGAGCAGGTTGGCGATTGTAGTCTTATCTTCCT-GAG-GAAGCAAGGAAGCAG
66 TGAGGTAACAAGAAAGCAGGCTAAAGATTG-AGTCTTATCTTCCTAGAGTG-A-CAAGGAAGCAG
* * *
28564062 ACTGAAGATTGAAGAT-CTATTTCCTTA-AGTAGTTGTA-GAGC-ATCAATGATGGCAAATCTTA
128 ACTGAAGATTGAAGATACTATTTCCCTAGAGCAGTTG-AGGAGCAATCAAGGATGGCAAATCTTA
* * * * *
28564123 TTTCTATGTATTGGCAATGGAGCAGATTTAAGTCCCCAAGATTTATTTCCCTAAAGTTGCAGCAG
192 TCTCCATGTATTAGCAATGGAGCAAATTTAAGTCACCAAGATTTATTTCCCTAAAGTTGCAGCAG
28564188 AGCAATTTGC
257 AGCAATTTGC
*
28564198 AGATGGTGAATCTTATCTCCATGTATCGGCAATGGAGTAGA-TTTAGACCA-TCAGCCTTATCTC
1 AGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGTAGATTTTAG-CCACT-AGCCTTATCTC
* * * *
28564261 TCTGAGGTAGCAAGAAAGCAGGCTAAAGTTTGGGTCTTATCTTCCTATAGTGACAAGGAAGCAGA
64 TCTGAGGTAACAAGAAAGCAGGCTAAAGATTGAGTCTTATCTTCCTAGAGTGACAAGGAAGCAGA
* ** *
28564326 CTGAAGATTGAAGATATTATTTCCCTAGAGCAGTTGAGGAGCAGATTGAGGATGGCGAATCTTAT
129 CTGAAGATTGAAGATACTATTTCCCTAGAGCAGTTGAGGAGCA-ATCAAGGATGGCAAATCTTAT
28564391 CTCCATGTATTAGCAATGGAGCAAATTTAAGTCACCAAG
193 CTCCATGTATTAGCAATGGAGCAAATTTAAGTCACCAAG
28564430 CCTATTTCCT
Statistics
Matches: 199, Mismatches: 24, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
263 46 0.23
264 90 0.45
265 12 0.06
267 51 0.26
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (266 bp):
AGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGTAGATTTTAGCCACTAGCCTTATCTCTC
TGAGGTAACAAGAAAGCAGGCTAAAGATTGAGTCTTATCTTCCTAGAGTGACAAGGAAGCAGACT
GAAGATTGAAGATACTATTTCCCTAGAGCAGTTGAGGAGCAATCAAGGATGGCAAATCTTATCTC
CATGTATTAGCAATGGAGCAAATTTAAGTCACCAAGATTTATTTCCCTAAAGTTGCAGCAGAGCA
ATTTGC
Found at i:28569547 original size:26 final size:26
Alignment explanation
Indices: 28569518--28569625 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28569508 TGGTACAAAT
*
28569518 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
28569544 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28569570 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28569596 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28569622 TGAT
1 TGAT
28569626 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:28571052 original size:28 final size:26
Alignment explanation
Indices: 28571021--28571085 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
28571011 AATTACTTGA
* **
28571021 ATACCCCTATGTACGAAAAATTACTGTT
1 ATACCCCTAGGT--GAAAAATTACCATT
*
28571049 ATACCCCTAGGTGCAAAATTACCATT
1 ATACCCCTAGGTGAAAAATTACCATT
28571075 ATACCCCTAGG
1 ATACCCCTAGG
28571086 GTTACTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 22 0.67
28 11 0.33
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (26 bp):
ATACCCCTAGGTGAAAAATTACCATT
Found at i:28571272 original size:54 final size:53
Alignment explanation
Indices: 28571190--28571329 Score: 199
Period size: 54 Copynumber: 2.6 Consensus size: 53
28571180 GGAAGCGTCC
28571190 TGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTATTA
1 TGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTATTA
* * *
28571244 TGGTGGTTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTATTA
* * *
28571298 TGGTGGCTCTGCCACAATATTTGTATCTGGTG
1 TGGTGGCTATGCCACATTATCTG-ATCTGGTG
28571330 ACTTCGTCAC
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
53 6 0.08
54 71 0.92
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (53 bp):
TGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATATATCTATTA
Found at i:28571325 original size:32 final size:27
Alignment explanation
Indices: 28571189--28571329 Score: 164
Period size: 27 Copynumber: 5.2 Consensus size: 27
28571179 AGGAAGCGTC
*
28571189 CTGGTGGCTATGCCACA-ATTATCTGAT
1 CTGGTGGCTCTGCCACATA-TATCTGAT
28571216 CTGGTGGCTCTGCCACATATATCT-ATT
1 CTGGTGGCTCTGCCACATATATCTGA-T
* * *
28571243 ATGGTGGTTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTGCCAC-ATATATCTGAT
*
28571270 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACATATATCTGAT
*
28571297 CTGGTGGCTCTGCCACA-ATATTTGTAT
1 CTGGTGGCTCTGCCACATATATCTG-AT
28571324 CTGGTG
1 CTGGTG
28571330 ACTTCGTCAC
Statistics
Matches: 98, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
26 9 0.09
27 85 0.87
28 4 0.04
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATATATCTGAT
Found at i:28575459 original size:12 final size:14
Alignment explanation
Indices: 28575442--28575478 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
28575432 TCAAGGACTT
28575442 ATTTAATCAC-C-A
1 ATTTAATCACTCTA
*
28575454 ATTTAATCTCTCTA
1 ATTTAATCACTCTA
28575468 ATTTAATCACT
1 ATTTAATCACT
28575479 TTACAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 9 0.43
13 1 0.05
14 11 0.52
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTTAATCACTCTA
Found at i:28575595 original size:27 final size:29
Alignment explanation
Indices: 28575539--28575605 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
28575529 ATACTTAATA
*
28575539 ATTTATCTAATTTACTTACTAAATATTTTT
1 ATTT-TCTAATTTAATTACTAAATATTTTT
*
28575569 A-TTTCTAATTTAATTA-TTAATATTTTT
1 ATTTTCTAATTTAATTACTAAATATTTTT
28575596 ATTTTCTAAT
1 ATTTTCTAAT
28575606 CCCGCACTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 11 0.32
28 20 0.59
29 2 0.06
30 1 0.03
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (29 bp):
ATTTTCTAATTTAATTACTAAATATTTTT
Found at i:28576747 original size:35 final size:35
Alignment explanation
Indices: 28576659--28576761 Score: 93
Period size: 35 Copynumber: 3.0 Consensus size: 35
28576649 ATGTTTTATT
* * * ** *
28576659 TAAAATTTAAATATTTTCAAATTTTCATAATCATTT
1 TAAAAATTATATATTTTGAAATTTTC-TAAAAATTA
* * *
28576695 TAAAAATAATTTTTTTTGAAATTTTCTAAAAATTA
1 TAAAAATTATATATTTTGAAATTTTCTAAAAATTA
*
28576730 TAAAAATTATATATTTTG--ATTTTTTAAAAATT
1 TAAAAATTATATATTTTGAAATTTTCTAAAAATT
28576762 TCAATTCTTA
Statistics
Matches: 54, Mismatches: 13, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
33 13 0.24
35 21 0.39
36 20 0.37
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (35 bp):
TAAAAATTATATATTTTGAAATTTTCTAAAAATTA
Found at i:28576844 original size:9 final size:9
Alignment explanation
Indices: 28576832--28576883 Score: 54
Period size: 9 Copynumber: 5.6 Consensus size: 9
28576822 AACTTTTTCT
28576832 ATTTTTTGA
1 ATTTTTTGA
28576841 A-TTTTTGA
1 ATTTTTTGA
28576849 TTCATTTTTTTGA
1 ---A-TTTTTTGA
28576862 ATTTTTTGA
1 ATTTTTTGA
28576871 ATTTTTT-A
1 ATTTTTTGA
28576879 ATTTT
1 ATTTT
28576884 AAAAAAATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
8 13 0.34
9 16 0.42
10 1 0.03
11 1 0.03
13 7 0.18
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.69
Consensus pattern (9 bp):
ATTTTTTGA
Found at i:28577795 original size:14 final size:15
Alignment explanation
Indices: 28577771--28577803 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
28577761 ATAAAACAAA
*
28577771 AAATAAAATATTTAT
1 AAATAAAATATTAAT
28577786 AAAT-AAATATTAAT
1 AAATAAAATATTAAT
28577800 AAAT
1 AAAT
28577804 TTATTTAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATAAAATATTAAT
Found at i:28580434 original size:21 final size:21
Alignment explanation
Indices: 28580408--28580448 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28580398 ATCTGCTCAA
* *
28580408 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
28580429 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
28580449 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:28587036 original size:2 final size:2
Alignment explanation
Indices: 28587029--28587053 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28587019 TAAATATTCT
28587029 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 T
28587054 TTTAAGTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:28604047 original size:23 final size:24
Alignment explanation
Indices: 28604006--28604050 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
28603996 TTGCCCTTAG
28604006 TGTAGTTGTTTCGTTATTAATGCT
1 TGTAGTTGTTTCGTTATTAATGCT
*
28604030 TGTAGTT-TTTTGTTATTAATG
1 TGTAGTTGTTTCGTTATTAATG
28604051 GGGATTTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.18, C:0.04, G:0.20, T:0.58
Consensus pattern (24 bp):
TGTAGTTGTTTCGTTATTAATGCT
Found at i:28612812 original size:66 final size:66
Alignment explanation
Indices: 28612706--28612838 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
28612696 GCTACCGTAA
28612706 AACTCAAACTACAGTGACGACATATACCAATAAATTAGGTTGTGATTTAGGATGTCGCTCGCAAC
1 AACTCAAACTACAGTGACGACATATACCAATAAATTAGGTTGTGATTTAGGATGTCGCTCGCAAC
28612771 T
66 T
28612772 AACTCAAACTACAGTGACGACATATACCAATAAATTAGGTTGTGATTTAGGATGTCGCTCGCAAC
1 AACTCAAACTACAGTGACGACATATACCAATAAATTAGGTTGTGATTTAGGATGTCGCTCGCAAC
28612837 T
66 T
28612838 A
1 A
28612839 GTTCCATTAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (66 bp):
AACTCAAACTACAGTGACGACATATACCAATAAATTAGGTTGTGATTTAGGATGTCGCTCGCAAC
T
Found at i:28613732 original size:30 final size:30
Alignment explanation
Indices: 28613698--28613779 Score: 155
Period size: 30 Copynumber: 2.7 Consensus size: 30
28613688 AAAACCCTAG
28613698 CCACCTTGCCTCCCACTTGCACCTACTCCA
1 CCACCTTGCCTCCCACTTGCACCTACTCCA
*
28613728 CCACCTTGCCTCCCATTTGCACCTACTCCA
1 CCACCTTGCCTCCCACTTGCACCTACTCCA
28613758 CCACCTTGCCTCCCACTTGCAC
1 CCACCTTGCCTCCCACTTGCAC
28613780 TTACACCATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.16, C:0.52, G:0.07, T:0.24
Consensus pattern (30 bp):
CCACCTTGCCTCCCACTTGCACCTACTCCA
Found at i:28614305 original size:12 final size:11
Alignment explanation
Indices: 28614282--28614363 Score: 62
Period size: 12 Copynumber: 7.4 Consensus size: 11
28614272 TGTTTTATTT
28614282 TTATTTTT-TA
1 TTATTTTTATA
28614292 TTATTTTTACTA
1 TTATTTTTA-TA
28614304 TTA--TTTATA
1 TTATTTTTATA
* *
28614313 TTATTATTATT
1 TTATTTTTATA
* *
28614324 TCTCATGTATATA
1 T-T-ATTTTTATA
28614337 TTATTATTTATA
1 TTATT-TTTATA
*
28614349 TTATTATTATA
1 TTATTTTTATA
28614360 TTAT
1 TTAT
28614364 ATATACCCTC
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
9 5 0.09
10 12 0.21
11 16 0.29
12 17 0.30
13 6 0.11
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (11 bp):
TTATTTTTATA
Found at i:28614308 original size:3 final size:3
Alignment explanation
Indices: 28614276--28614363 Score: 53
Period size: 3 Copynumber: 29.3 Consensus size: 3
28614266 GAGCTTTGTT
* * *
28614276 TTA TTT TTA TT- TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
28614319 TTA TT- TCTCA TGTA TATA TTA TTA TT- TATA TTA TTA TTA -TA TTA
1 TTA TTA T-T-A T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
28614363 T
1 T
28614364 ATATACCCTC
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
2 9 0.13
3 50 0.74
4 7 0.10
5 2 0.03
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28619288 original size:4 final size:4
Alignment explanation
Indices: 28619281--28619312 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
28619271 CCTAAAAAAA
28619281 AAAG AAAG AAAG AAAG AAAG AAAG AGAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG A-AAG AAA
28619313 AAGGAGAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:28620892 original size:87 final size:87
Alignment explanation
Indices: 28620793--28621458 Score: 870
Period size: 87 Copynumber: 7.8 Consensus size: 87
28620783 AGAATATTTG
* *
28620793 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGTGATGAACCTTAAACCCCTAAGCAGTAGGGTAA
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAGCCTTAAACCCCTAAGCAGTAGGGTAA
* * *
28620858 TAGGTTGAATTTATAGATCTTA
66 CAGGTTAAATTTACAGATCTTA
* * * * * *
28620880 ACCCCATAAGCAGTAGGGAAACAGATCGAAAGCAACGAGCCTT-AACTCCCTAAGTAGTAGCGTA
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAGCCTTAAAC-CCCTAAGCAGTAGGGTA
*
28620944 ACAGGCTAAATTTACAGATCTTA
65 ACAGGTTAAATTTACAGATCTTA
** * *
28620967 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGGGCCTTAAACCCTTAAGCAGTAGGGTAA
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAGCCTTAAACCCCTAAGCAGTAGGGTAA
*
28621032 CAGGTTGAATTTACAGATCTTA
66 CAGGTTAAATTTACAGATCTTA
* * *
28621054 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATG-GCCTTAACCCCCTAAGTAGTAGGGTAG
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAGCCTTAAACCCCTAAGCAGTAGGGTAA
* * *
28621118 TAGGCTAAATTTACAAATCTTA
66 CAGGTTAAATTTACAGATCTTA
** *
28621140 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGGGCCTTAAACCCCTAAGCAGTAGGGTAA
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAGCCTTAAACCCCTAAGCAGTAGGGTAA
*
28621205 CAGGTTGAATTTACAGATCTTA
66 CAGGTTAAATTTACAGATCTTA
* *
28621227 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATG-GCCTTAACCCCCTAA-CAGTAGGGTAG
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAGCCTTAAACCCCTAAGCAGTAGGGTAA
*
28621290 CAGGCTAAATTTACAGATCTTA
66 CAGGTTAAATTTACAGATCTTA
* * * * *
28621312 ACCCCCTAAGCAGTAGGGAAATAGATCAAAGACGATAAGCCTTAAACCCCTAAGTAGTAGGGTAA
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAGCCTTAAACCCCTAAGCAGTAGGGTAA
28621377 CAGGTTAAATTTACAG------
66 CAGGTTAAATTTACAGATCTTA
* * * ** *
28621393 A--CCCTAAACAGTAAGGAAACAGATCGAAGGTGACAAGCCTTAAACCCCTAAGCAGTAGGGAAA
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAGCCTTAAACCCCTAAGCAGTAGGGTAA
28621456 CAG
66 CAG
28621459 ATCAAAGGTG
Statistics
Matches: 508, Mismatches: 66, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
79 56 0.11
81 1 0.00
85 63 0.12
86 107 0.21
87 278 0.55
88 3 0.01
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (87 bp):
ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAGCCTTAAACCCCTAAGCAGTAGGGTAA
CAGGTTAAATTTACAGATCTTA
Found at i:28620894 original size:43 final size:43
Alignment explanation
Indices: 28620793--28621544 Score: 344
Period size: 43 Copynumber: 17.6 Consensus size: 43
28620783 AGAATATTTG
* * * * * *
28620793 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGTGA-TGAACCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAA-TTTACAG-ATCTTA
* * * *
28620837 AACCCCTAAGCAGTAGGGTAATAGGTTGAATTTATAGATCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAATTTACAGATCTTA
* * * *** *
28620880 ACCCCATAAGCAGTAGGGAAACAGATCGAAAGCA-ACGAGCCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAATTTACA-GA-TCTTA
* * * * * *
28620924 ACTCCCTAAGTAGTAGCGTAACAGGCTAAATTTACAGATCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAATTTACAGATCTTA
* * * * ** **
28620967 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGGGCCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAA-TTTACAGATCTTA
* * *
28621011 AACCCTTAAGCAGTAGGGTAACAGGTTGAATTTACAGATCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAATTTACAGATCTTA
* * **
28621054 ACCCCCTAAGCAGTAGGGAAACAGATCGAA--GGC-GATGGCCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAATTTACAGAT---CTTA
* * ** * * *
28621097 ACCCCCTAAGTAGTAGGGTAGTAGGCTAAATTTACAAATCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAATTTACAGATCTTA
* * * * ** **
28621140 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGGGCCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAA-TTTACAGATCTTA
* *
28621184 AACCCCTAAGCAGTAGGGTAACAGGTTGAATTTACAGATCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAATTTACAGATCTTA
* * **
28621227 ACCCCCTAAGCAGTAGGGAAACAGATCGAA--GGC-GATGGCCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAATTTACAGAT---CTTA
* * * *
28621270 ACCCCCTAA-CAGTAGGGTAGCAGGCTAAATTTACAGATCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAATTTACAGATCTTA
* * * **
28621312 ACCCCCTAAGCAGTAGGGAAATA-GATCAA-AGAC-GATAAGCCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAATTTACAGAT----CTTA
* * * *
28621356 AACCCCTAAGTAGTAGGGTAACAGGTTAAATTTACAG------
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAATTTACAGATCTTA
* * * * * * *
28621393 A--CCCTAAACAGTAAGGAAACAGATCGAAGGTGACA-AGCCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAA-TTTACAGA-TCTTA
* * ** * * *
28621435 AACCCCTAAGCAGTAGGGAAACAGATCAAAGGTGACA-AGCCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAA-TTTACAGA-TCTTA
* * * *
28621479 A-CCCCTAAACAGTAGGGTAACAGGCTAAATTTACAGATCTTA
1 ACCCCCTAAGCAGTAGGGAAACAGGTTGAATTTACAGATCTTA
*
28621521 ACACCCTAAGCAGTAGGGAAACAG
1 ACCCCCTAAGCAGTAGGGAAACAG
28621545 ATCGAAGACG
Statistics
Matches: 518, Mismatches: 152, Indels: 77
0.69 0.20 0.10
Matches are distributed among these distances:
35 20 0.04
36 4 0.01
37 1 0.00
40 9 0.02
41 4 0.01
42 42 0.08
43 243 0.47
44 181 0.35
45 9 0.02
46 4 0.01
47 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (43 bp):
ACCCCCTAAGCAGTAGGGAAACAGGTTGAATTTACAGATCTTA
Found at i:28621172 original size:173 final size:173
Alignment explanation
Indices: 28620793--28621393 Score: 979
Period size: 173 Copynumber: 3.5 Consensus size: 173
28620783 AGAATATTTG
* *
28620793 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGTGATGAACCTTAAACCCCTAAGCAGTAGGGTAA
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCCTTAAACCCCTAAGCAGTAGGGTAA
* * * * * *
28620858 TAGGTTGAATTTATAGATCTTAACCCCATAAGCAGTAGGGAAACAGATCGAAAGCAACGAGCCTT
66 CAGGTTGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATG-GCCTT
* * *
28620923 AACTCCCTAAGTAGTAGCGTAACAGGCTAAATTTACAGATCTTA
130 AACCCCCTAAGTAGTAGGGTAGCAGGCTAAATTTACAGATCTTA
* *
28620967 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGGGCCTTAAACCCTTAAGCAGTAGGGTAA
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCCTTAAACCCCTAAGCAGTAGGGTAA
28621032 CAGGTTGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGCCTTA
66 CAGGTTGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGCCTTA
* *
28621097 ACCCCCTAAGTAGTAGGGTAGTAGGCTAAATTTACAAATCTTA
131 ACCCCCTAAGTAGTAGGGTAGCAGGCTAAATTTACAGATCTTA
*
28621140 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGGGCCTTAAACCCCTAAGCAGTAGGGTAA
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCCTTAAACCCCTAAGCAGTAGGGTAA
28621205 CAGGTTGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGCCTTA
66 CAGGTTGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGCCTTA
*
28621270 ACCCCCTAA-CAGTAGGGTAGCAGGCTAAATTTACAGATCTTA
131 ACCCCCTAAGTAGTAGGGTAGCAGGCTAAATTTACAGATCTTA
* * * * *
28621312 ACCCCCTAAGCAGTAGGGAAATAGATCAAAGACGATAAGCCTTAAACCCCTAAGTAGTAGGGTAA
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCCTTAAACCCCTAAGCAGTAGGGTAA
*
28621377 CAGGTTAAATTTACAGA
66 CAGGTTGAATTTACAGA
28621394 CCCTAAACAG
Statistics
Matches: 401, Mismatches: 26, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
172 105 0.26
173 182 0.45
174 114 0.28
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (173 bp):
ACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCCTTAAACCCCTAAGCAGTAGGGTAA
CAGGTTGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGCCTTA
ACCCCCTAAGTAGTAGGGTAGCAGGCTAAATTTACAGATCTTA
Found at i:28622144 original size:30 final size:30
Alignment explanation
Indices: 28622105--28622190 Score: 145
Period size: 30 Copynumber: 2.9 Consensus size: 30
28622095 AAAAACCTAG
* *
28622105 CCACTTTGCCTCCTACTTGCACCTACTCCA
1 CCACCTTGCCTCCCACTTGCACCTACTCCA
28622135 CCACCTTGCCTCCCACTTGCACCTACTCCA
1 CCACCTTGCCTCCCACTTGCACCTACTCCA
*
28622165 CCACCTTGTCTCCCACTTGCACCTAC
1 CCACCTTGCCTCCCACTTGCACCTAC
28622191 ACCATCAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.16, C:0.50, G:0.07, T:0.27
Consensus pattern (30 bp):
CCACCTTGCCTCCCACTTGCACCTACTCCA
Found at i:28622713 original size:9 final size:9
Alignment explanation
Indices: 28622690--28622768 Score: 63
Period size: 9 Copynumber: 8.6 Consensus size: 9
28622680 GAGCTTTGTT
28622690 TTATTTTTA
1 TTATTTTTA
28622699 TT-TTTTTA
1 TTATTTTTA
28622707 TTATTTTTA
1 TTATTTTTA
*
28622716 CTATTATTTA
1 TTATT-TTTA
*
28622726 -TATTATTA
1 TTATTTTTA
*
28622734 TTATTTCTCA
1 TTATTT-TTA
*
28622744 TGTATATATTA
1 T-TAT-TTTTA
*
28622755 TTATTTATA
1 TTATTTTTA
28622764 TTATT
1 TTATT
28622769 ATATTATATA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
8 11 0.20
9 28 0.50
10 10 0.18
11 6 0.11
12 1 0.02
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (9 bp):
TTATTTTTA
Found at i:28622714 original size:12 final size:12
Alignment explanation
Indices: 28622688--28622770 Score: 64
Period size: 12 Copynumber: 7.0 Consensus size: 12
28622678 GAGAGCTTTG
*
28622688 TTTTATTTTTAT
1 TTTTATTATTAT
28622700 TTTT-TTATTAT
1 TTTTATTATTAT
*
28622711 TTTTACTATTAT
1 TTTTATTATTAT
*
28622723 TTATATTATTAT
1 TTTTATTATTAT
* *
28622735 TATTTCTCATGTA-
1 T-TTTATTAT-TAT
*
28622748 -TATATTATTAT
1 TTTTATTATTAT
*
28622759 TTATATTATTAT
1 TTTTATTATTAT
28622771 ATTATATATA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
10 2 0.04
11 15 0.27
12 32 0.57
13 5 0.09
14 2 0.04
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:28622856 original size:3 final size:3
Alignment explanation
Indices: 28622850--28622904 Score: 60
Period size: 3 Copynumber: 18.0 Consensus size: 3
28622840 TTCTGACTAC
*
28622850 TAT TAT TAT TAT TA- TAT ATAT GTAT TAT TGT T-T GTAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT -TAT TAT TAT TAT
28622896 TAT TAT TAT
1 TAT TAT TAT
28622905 CACCCCTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 3 0.07
3 36 0.78
4 7 0.15
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:28624649 original size:61 final size:61
Alignment explanation
Indices: 28624582--28624718 Score: 158
Period size: 60 Copynumber: 2.3 Consensus size: 61
28624572 CAGTGTTAAC
* *
28624582 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAG-CCCCTTAC-AGTATC-AGAGTATAT
1 TGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGTCCCATTACAAG--TCGAGA-TATAT
* * * *
28624643 TGGGCC-TAGCCCATATCAGTATCAATTTGGGCCGTAGTCCTATTACAAGTCGAGATATAT
1 TGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGTCCCATTACAAGTCGAGATATAT
28624703 TGGGCCTTAG-CCATAT
1 TGGGCCTTAGCCCATAT
28624719 TAACACAGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
60 46 0.70
61 18 0.27
62 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (61 bp):
TGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGTCCCATTACAAGTCGAGATATAT
Found at i:28625860 original size:39 final size:39
Alignment explanation
Indices: 28625813--28625890 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
28625803 TATCCACCAC
28625813 TTCATCATGCTGCTAAGAAGAGCTTCGGTCCCCCACTTA
1 TTCATCATGCTGCTAAGAAGAGCTTCGGTCCCCCACTTA
28625852 TTCATCATGCTGCTAAGAAGAGCTTCGGTCCCCCACTTA
1 TTCATCATGCTGCTAAGAAGAGCTTCGGTCCCCCACTTA
28625891 AACAACAAAA
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:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (39 bp):
TTCATCATGCTGCTAAGAAGAGCTTCGGTCCCCCACTTA
Found at i:28626629 original size:15 final size:15
Alignment explanation
Indices: 28626594--28626622 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28626584 TTTCCCTATC
28626594 TAATAATAATAATTA
1 TAATAATAATAATTA
28626609 TAATAATAATAATT
1 TAATAATAATAATT
28626623 TTCATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:28626690 original size:19 final size:18
Alignment explanation
Indices: 28626653--28626696 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
28626643 ATACATGCAG
28626653 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
28626670 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
28626689 TACTAATT
1 TAATAATT
28626697 AAAATTTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:28646288 original size:44 final size:41
Alignment explanation
Indices: 28646225--28646344 Score: 134
Period size: 44 Copynumber: 2.8 Consensus size: 41
28646215 TATGTGTTTC
* *
28646225 TGTGTAAGAACACGTCTGGGACGTTGGCATCGACTTACGATTT
1 TGTGTAAGACCATGTCTGGGACGTTGGCATCGA-TT-CGATTT
* *
28646268 ATGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTT
1 -TGTGTAAGACCATGTCTGGGACGTTGGCATCG-ATTCGATTT
* *
28646311 TGTGTAAGACCTTGTTTGGGACAG-TGGCATCGAT
1 TGTGTAAGACCATGTCTGGGAC-GTTGGCATCGAT
28646345 ATTTGATTAC
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
41 2 0.03
42 28 0.42
43 5 0.07
44 31 0.46
45 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (41 bp):
TGTGTAAGACCATGTCTGGGACGTTGGCATCGATTCGATTT
Found at i:28646331 original size:42 final size:43
Alignment explanation
Indices: 28646225--28646383 Score: 153
Period size: 43 Copynumber: 3.7 Consensus size: 43
28646215 TATGTGTTTC
* * * *
28646225 TGTGTAAGAACACGTCTGGGACGTTGGCATCG-ACTTACGATTTA
1 TGTGTAAGACCATGTCTGGGACATTGGCATCGTA-TT-TGATTTA
28646269 TGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTT-
1 TGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTTA
* * *
28646311 TGTGTAAGACCTTGTTTGGGACAGTGGCATCGATATTTGA-TTA
1 TGTGTAAGACCATGTCTGGGACATTGGCATCG-TATTTGATTTA
** ** * *
28646354 CATGTAAGACCACATCTGAGACGTTGGCAT
1 TGTGTAAGACCATGTCTGGGACATTGGCAT
28646384 TGTACGAGCT
Statistics
Matches: 96, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
42 31 0.32
43 33 0.34
44 31 0.32
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (43 bp):
TGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTTA
Found at i:28646349 original size:43 final size:43
Alignment explanation
Indices: 28646225--28646365 Score: 146
Period size: 42 Copynumber: 3.3 Consensus size: 43
28646215 TATGTGTTTC
* * *
28646225 TGTGTAAGAACACGTCTGGGAC-GTTGGCATCG-ACTTACGATTTA
1 TGTGTAAGACCATGTCTGGGACAG-TGGCATCGTA-TT-TGATTTA
*
28646269 TGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTT-
1 TGTGTAAGACCATGTCTGGGACAGTGGCATCGTATTTGATTTA
* *
28646311 TGTGTAAGACCTTGTTTGGGACAGTGGCATCGATATTTGA-TTA
1 TGTGTAAGACCATGTCTGGGACAGTGGCATCG-TATTTGATTTA
**
28646354 CATGTAAGACCA
1 TGTGTAAGACCA
28646366 CATCTGAGAC
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
42 31 0.37
43 21 0.25
44 30 0.36
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (43 bp):
TGTGTAAGACCATGTCTGGGACAGTGGCATCGTATTTGATTTA
Found at i:28649498 original size:33 final size:33
Alignment explanation
Indices: 28649461--28649534 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 33
28649451 CCTGCCATGA
* *
28649461 TCTTACACTCATAATGCCATAACCCAGTTATGG
1 TCTTACACTCAGAATGCCATAACCCAGGTATGG
* * **
28649494 TCTTATCA-TCAGGATGCCATAGCTTAGGTATGG
1 TCTTA-CACTCAGAATGCCATAACCCAGGTATGG
28649527 TCTTACAC
1 TCTTACAC
28649535 ATATACATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
32 2 0.06
33 29 0.88
34 2 0.06
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (33 bp):
TCTTACACTCAGAATGCCATAACCCAGGTATGG
Found at i:28649636 original size:105 final size:101
Alignment explanation
Indices: 28649475--28649671 Score: 234
Period size: 105 Copynumber: 1.9 Consensus size: 101
28649465 ACACTCATAA
** ** *
28649475 TGCCATAACCCAGTTATGGTCTTATCATCAGGATGCCATAGCTTAGGTATGGTCTTACACATATA
1 TGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGGTCTT--ACAT-T-
* *
28649540 CATATAATACCATGGTCCAATCATGGTCTTACGTTTATGG
62 CAAACAATACCATGGTCCAATCATGGTCTTACGTTTATGG
* * *
28649580 TGCCATAACCC-GATTATGGTCTTTTCATTAAAATGCCATAGCCCAGCTATGTTCTTACATTCAA
1 TGCCATAACCCAG-TTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGGTCTTACATTCAA
* *
28649644 ACATTGCCATGGTCCAATCATGGTCTTA
65 ACAATACCATGGTCCAATCATGGTCTTA
28649672 TCCATCAATT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
101 27 0.34
102 1 0.01
103 4 0.05
104 1 0.01
105 46 0.58
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (101 bp):
TGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGGTCTTACATTCAAA
CAATACCATGGTCCAATCATGGTCTTACGTTTATGG
Found at i:28652327 original size:18 final size:18
Alignment explanation
Indices: 28652304--28652339 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28652294 TTTCATCATG
*
28652304 TTAATTAGGTTAATTAAT
1 TTAATTAGGTTAACTAAT
*
28652322 TTAATTAGTTTAACTAAT
1 TTAATTAGGTTAACTAAT
28652340 ATTTTAATTT
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:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (18 bp):
TTAATTAGGTTAACTAAT
Found at i:28652819 original size:84 final size:84
Alignment explanation
Indices: 28652664--28652819 Score: 206
Period size: 84 Copynumber: 1.9 Consensus size: 84
28652654 TTCAATTGGG
* * * *
28652664 TACTTGAACTTTCAAAATGCATCAAAAAGGCCCTCATACTTTAAGAAAAAAACAATAAAGCCCTA
1 TACTTGAACTTTCAAAATGCATAAAAAAAGCCCTCAAACTTTAACAAAAAAACAATAAAGCCCTA
*
28652729 TTTTTTTCACTTAATTTGT
66 TGTTTTTCACTTAATTTGT
* ** * *
28652748 TACTTGAACTTTCAAAGTGCATAAAAAAAGCCCTCAAACTTTTTCAAAAAAATCAATTAAGCTCT
1 TACTTGAACTTTCAAAATGCATAAAAAAAGCCCTCAAACTTTAACAAAAAAA-CAATAAAGCCCT
28652813 -TGTTTTT
65 ATGTTTTT
28652820 TTTTTTGCAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
84 51 0.84
85 10 0.16
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (84 bp):
TACTTGAACTTTCAAAATGCATAAAAAAAGCCCTCAAACTTTAACAAAAAAACAATAAAGCCCTA
TGTTTTTCACTTAATTTGT
Found at i:28655398 original size:21 final size:21
Alignment explanation
Indices: 28655372--28655416 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
28655362 ACAGTCTATT
28655372 ACACGG-TCGTGTAACCCTTCC
1 ACACGGCT-GTGTAACCCTTCC
28655393 ACACGGCTGTGTAACCCTTCC
1 ACACGGCTGTGTAACCCTTCC
28655414 ACA
1 ACA
28655417 TGATTTGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.22
Consensus pattern (21 bp):
ACACGGCTGTGTAACCCTTCC
Found at i:28660719 original size:24 final size:24
Alignment explanation
Indices: 28660692--28660739 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28660682 CTATGCTGTC
28660692 TAAGATTCAACTCCTTCTAAGTCA
1 TAAGATTCAACTCCTTCTAAGTCA
28660716 TAAGATTCAACTCCTTCTAAGTCA
1 TAAGATTCAACTCCTTCTAAGTCA
28660740 GGAGGTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.33
Consensus pattern (24 bp):
TAAGATTCAACTCCTTCTAAGTCA
Found at i:28667345 original size:26 final size:26
Alignment explanation
Indices: 28667309--28667364 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
28667299 TGAAATTCCA
*
28667309 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACACATT
28667335 ATCATGGAACATTTACCTAACACATT
1 ATCATGGAACATTTACCTAACACATT
28667361 ATCA
1 ATCA
28667365 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACACATT
Found at i:28672437 original size:38 final size:38
Alignment explanation
Indices: 28672330--28672488 Score: 228
Period size: 38 Copynumber: 4.1 Consensus size: 38
28672320 ATATTCGATG
* *
28672330 TATATCCGGGTTAAATCCCGCAGGCTTCGTGTTGGTGT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* *
28672368 TATATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAA
1 TATATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAT
*
28672408 AATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* * *
28672446 TATATCCGGGATAAATCCCGCAGGCCTAGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
28672484 TATAT
1 TATAT
28672489 TGGGGCCTTC
Statistics
Matches: 108, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
38 70 0.65
39 10 0.09
40 28 0.26
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
Found at i:28672610 original size:43 final size:43
Alignment explanation
Indices: 28672486--28672597 Score: 188
Period size: 43 Copynumber: 2.6 Consensus size: 43
28672476 GCTGGTATTA
* * *
28672486 TATTGGGGCCTTCGTGCCTAGTAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
28672529 TATTCGGGCCTTCGTGTCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
28672572 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
28672598 GTAATGCCGG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.11, C:0.24, G:0.34, T:0.31
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:28689000 original size:43 final size:43
Alignment explanation
Indices: 28688951--28689060 Score: 132
Period size: 43 Copynumber: 2.6 Consensus size: 43
28688941 CTGGAATTTC
** ** *
28688951 GCCTGCTAGGATTGAAGCCTGATATCATTTCACC-AGCATTATA
1 GCCTGCTAGGACCGAAGCCCAATATCATCTCACCGA-CATTATA
* *
28688994 GCCTGCTAGGCCCGAAGCCCAATATTATCTCACCGACATTATA
1 GCCTGCTAGGACCGAAGCCCAATATCATCTCACCGACATTATA
*
28689037 GCCTGCTAGGCCCGAAGCCCAATA
1 GCCTGCTAGGACCGAAGCCCAATA
28689061 ATATTATTCA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 58 0.98
44 1 0.02
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (43 bp):
GCCTGCTAGGACCGAAGCCCAATATCATCTCACCGACATTATA
Found at i:28691013 original size:14 final size:15
Alignment explanation
Indices: 28690984--28691013 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28690974 CAAAATTTAG
28690984 ACATGATACTTTCAC
1 ACATGATACTTTCAC
28690999 ACATGATAC-TTCAC
1 ACATGATACTTTCAC
28691013 A
1 A
28691014 TATAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
ACATGATACTTTCAC
Found at i:28691526 original size:15 final size:15
Alignment explanation
Indices: 28691506--28691534 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28691496 AATTTGTGAA
28691506 AAAATAAAATAAAAG
1 AAAATAAAATAAAAG
28691521 AAAATAAAATAAAA
1 AAAATAAAATAAAA
28691535 AATATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (15 bp):
AAAATAAAATAAAAG
Found at i:28692690 original size:30 final size:30
Alignment explanation
Indices: 28692656--28692733 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
28692646 TAAATTTTAT
28692656 TAAAAATTAGAAAAAAAATTATAAAA-ACCA
1 TAAAAATTAGAAAAAAAATTATAAAATA-CA
*
28692686 TAAAAATT-GTAAAAAAAATTATAAAATATA
1 TAAAAATTAG-AAAAAAAATTATAAAATACA
*
28692716 TAGAAAAATAGAAAAAAA
1 TA-AAAATTAGAAAAAAA
28692734 TGAAATTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 1 0.02
30 27 0.64
31 13 0.31
32 1 0.02
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.22
Consensus pattern (30 bp):
TAAAAATTAGAAAAAAAATTATAAAATACA
Found at i:28693310 original size:88 final size:87
Alignment explanation
Indices: 28693154--28693424 Score: 375
Period size: 89 Copynumber: 3.1 Consensus size: 87
28693144 TCAAAGGATT
* * * *
28693154 TTTTTGATGCATTTTGATAGTTCAAGTACCCAATTGAGTGAAAAAAAAGTAGGGGCTTAATAGCT
1 TTTTTGATACATTTTGAAAGTTCAAGTA-CCAATTGAGTGCAAAAAAAGTAGGGGCTTAATTGCT
*
28693219 TTTTTTGAAAAAGTTTGAGGGTC
65 TTTTTTGAAAAAGTTTGAGGGCC
*
28693242 TTTTTGATACATTTTGAAAGTTCAAGTACCAAATTGAGTGCAAAAAAAG-GGGGGCTTAATTGCT
1 TTTTTGATACATTTTGAAAGTTCAAGTACC-AATTGAGTGCAAAAAAAGTAGGGGCTTAATTGC-
* *
28693306 TTTTTTTTTAAAAAGTTTGAGAGCC
64 -TTTTTTTGAAAAAGTTTGAGGGCC
*
28693331 TTTTTGATACATTTTGAAAGTTCAAGTATCCAATTGAGTGCATAAAAAGAGTAGGGACTTAATTG
1 TTTTTGATACATTTTGAAAGTTCAAGTA-CCAATTGAGTGCA-AAAAA-AGTAGGGGCTTAATTG
*
28693396 CTTGTTTTGAAAAAGTTTGA-GGCC
63 CTTTTTTTGAAAAAGTTTGAGGGCC
28693420 TTTTT
1 TTTTT
28693425 TACTTTAAAA
Statistics
Matches: 163, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
87 14 0.09
88 43 0.26
89 68 0.42
90 24 0.15
91 2 0.01
92 12 0.07
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.38
Consensus pattern (87 bp):
TTTTTGATACATTTTGAAAGTTCAAGTACCAATTGAGTGCAAAAAAAGTAGGGGCTTAATTGCTT
TTTTTGAAAAAGTTTGAGGGCC
Found at i:28696296 original size:13 final size:13
Alignment explanation
Indices: 28696278--28696305 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28696268 GCCTGCATAT
28696278 CAACAAATTCAAC
1 CAACAAATTCAAC
28696291 CAACAAATTCAAC
1 CAACAAATTCAAC
28696304 CA
1 CA
28696306 TTTTTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.14
Consensus pattern (13 bp):
CAACAAATTCAAC
Found at i:28706324 original size:49 final size:49
Alignment explanation
Indices: 28706252--28706349 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
28706242 ATAAAACATA
28706252 AGTCTTTAATAGTAATGCTTAAAAGGAAAGATAAATGTTTTATCGAGCT
1 AGTCTTTAATAGTAATGCTTAAAAGGAAAGATAAATGTTTTATCGAGCT
28706301 AGTCTTTAATAGTAATGCTTAAAAGGAAAGATAAATGTTTTATCGAGCT
1 AGTCTTTAATAGTAATGCTTAAAAGGAAAGATAAATGTTTTATCGAGCT
28706350 CCCGCGACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (49 bp):
AGTCTTTAATAGTAATGCTTAAAAGGAAAGATAAATGTTTTATCGAGCT
Found at i:28708982 original size:19 final size:19
Alignment explanation
Indices: 28708960--28709002 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
28708950 TTCTCAAGCT
*
28708960 CAATTTTCAATCTTAGGTC
1 CAATTTTCAATCTCAGGTC
*
28708979 CAATTTTCAATCTCGGGTC
1 CAATTTTCAATCTCAGGTC
28708998 CAATT
1 CAATT
28709003 ATTGTAACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.40
Consensus pattern (19 bp):
CAATTTTCAATCTCAGGTC
Found at i:28712212 original size:27 final size:27
Alignment explanation
Indices: 28712164--28712216 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28712154 GCGAGGCTGC
*
28712164 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGATA
*
28712191 CAGATATTGTGGC-AGAGCCACCAGAT
1 CAGATATTGTGACGA-AGCCACCAGAT
28712217 GTGGCAGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (27 bp):
CAGATATTGTGACGAAGCCACCAGATA
Found at i:28712219 original size:18 final size:18
Alignment explanation
Indices: 28712198--28712252 Score: 110
Period size: 18 Copynumber: 3.1 Consensus size: 18
28712188 ATACAGATAT
28712198 TGTGGCAGAGCCACCAGA
1 TGTGGCAGAGCCACCAGA
28712216 TGTGGCAGAGCCACCAGA
1 TGTGGCAGAGCCACCAGA
28712234 TGTGGCAGAGCCACCAGA
1 TGTGGCAGAGCCACCAGA
28712252 T
1 T
28712253 CAGATAATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.33, T:0.13
Consensus pattern (18 bp):
TGTGGCAGAGCCACCAGA
Found at i:28712264 original size:27 final size:27
Alignment explanation
Indices: 28712234--28712331 Score: 146
Period size: 27 Copynumber: 3.6 Consensus size: 27
28712224 AGCCACCAGA
28712234 TGTGGCAGAGCCACCAGATCAGATAAT
1 TGTGGCAGAGCCACCAGATCAGATAAT
*
28712261 TGTGGCATAGCCACCAGGA-CAGAT-AT
1 TGTGGCAGAGCCACCA-GATCAGATAAT
28712287 ATGTGGCAGAGCCACCAGATCAGATAAT
1 -TGTGGCAGAGCCACCAGATCAGATAAT
*
28712315 TGTGGCATAGCCACCAG
1 TGTGGCAGAGCCACCAG
28712332 GACGCTTCCT
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.06
27 56 0.88
28 4 0.06
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (27 bp):
TGTGGCAGAGCCACCAGATCAGATAAT
Found at i:28713956 original size:26 final size:26
Alignment explanation
Indices: 28713925--28714032 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28713915 TGAAATGCCC
*
28713925 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
28713951 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
28713977 ATCATGGAATATTTACCTAATCTATT
1 ATCATGGAACATTTACCTAACCCATT
28714003 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28714029 ATCA
1 ATCA
28714033 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28718037 original size:21 final size:20
Alignment explanation
Indices: 28718013--28718056 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 20
28718003 TCACCAGATA
28718013 CAGATATTGTAGCAGAGCCAC
1 CAGATA-TGTAGCAGAGCCAC
*
28718034 CAG--ATGTGGCAGAGCCAC
1 CAGATATGTAGCAGAGCCAC
28718052 CAGAT
1 CAGAT
28718057 CAGATAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
18 16 0.80
19 1 0.05
21 3 0.15
ACGTcount: A:0.32, C:0.25, G:0.27, T:0.16
Consensus pattern (20 bp):
CAGATATGTAGCAGAGCCAC
Found at i:28718076 original size:27 final size:27
Alignment explanation
Indices: 28718038--28718135 Score: 119
Period size: 27 Copynumber: 3.6 Consensus size: 27
28718028 AGCCACCAGA
*
28718038 TGTGGCAGAGCCACCAGATCAGATAAT
1 TGTGGCATAGCCACCAGATCAGATAAT
* *
28718065 TGTCGCATAGCCATCAGGA-CAGAT-AT
1 TGTGGCATAGCCACCA-GATCAGATAAT
*
28718091 ATGTGGCAGAGCCACCAGATCAGATAAT
1 -TGTGGCATAGCCACCAGATCAGATAAT
*
28718119 TGTGGCATAGTCACCAG
1 TGTGGCATAGCCACCAG
28718136 GACGCTTCCT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
26 4 0.07
27 51 0.86
28 4 0.07
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (27 bp):
TGTGGCATAGCCACCAGATCAGATAAT
Found at i:28719763 original size:26 final size:26
Alignment explanation
Indices: 28719732--28719839 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28719722 TGAAATGCCC
* *
28719732 ATCATGGAGCATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
28719758 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28719784 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
28719810 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28719836 ATCA
1 ATCA
28719840 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28723837 original size:21 final size:20
Alignment explanation
Indices: 28723813--28723856 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 20
28723803 TCACCAGATA
28723813 CAGATATTGTGGCAGAGCCAC
1 CAGATA-TGTGGCAGAGCCAC
28723834 CAG--ATGTGGCAGAGCCAC
1 CAGATATGTGGCAGAGCCAC
28723852 CAGAT
1 CAGAT
28723857 CAGATAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 17 0.81
19 1 0.05
21 3 0.14
ACGTcount: A:0.30, C:0.25, G:0.30, T:0.16
Consensus pattern (20 bp):
CAGATATGTGGCAGAGCCAC
Found at i:28723841 original size:18 final size:18
Alignment explanation
Indices: 28723820--28723856 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28723810 ATACAGATAT
28723820 TGTGGCAGAGCCACCAGA
1 TGTGGCAGAGCCACCAGA
28723838 TGTGGCAGAGCCACCAGA
1 TGTGGCAGAGCCACCAGA
28723856 T
1 T
28723857 CAGATAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.32, T:0.14
Consensus pattern (18 bp):
TGTGGCAGAGCCACCAGA
Found at i:28725501 original size:26 final size:26
Alignment explanation
Indices: 28725470--28725576 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28725460 TGAAATGCCC
*
28725470 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
28725496 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28725522 ATCAT-GAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
28725547 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28725573 ATCA
1 ATCA
28725577 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
25 23 0.31
26 52 0.69
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28725546 original size:51 final size:52
Alignment explanation
Indices: 28725470--28725576 Score: 189
Period size: 51 Copynumber: 2.1 Consensus size: 52
28725460 TGAAATGCCC
28725470 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
* *
28725522 ATCAT-GAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
28725573 ATCA
1 ATCA
28725577 ATTTGTACCA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
51 48 0.91
52 5 0.09
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (52 bp):
ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
Found at i:28729568 original size:18 final size:18
Alignment explanation
Indices: 28729545--28729597 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
28729535 ATACAGATAT
28729545 TGTGGTAGAGCCACCAGA
1 TGTGGTAGAGCCACCAGA
*
28729563 TGTGGTAGAGCCACCAAA
1 TGTGGTAGAGCCACCAGA
*
28729581 TGTGGCAGAGCCACCAG
1 TGTGGTAGAGCCACCAG
28729598 GACAGATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.32, T:0.15
Consensus pattern (18 bp):
TGTGGTAGAGCCACCAGA
Found at i:28729610 original size:27 final size:26
Alignment explanation
Indices: 28729579--28729650 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 26
28729569 AGAGCCACCA
28729579 AATGTGGCAGAGCCACCAGGA-CAGAT
1 AATGTGGCAGAGCCACCA-GATCAGAT
28729605 ATATGTGGCAGAGCCACCAGATCAGAT
1 A-ATGTGGCAGAGCCACCAGATCAGAT
*
28729632 AATTGTGGCATAGCCACCA
1 AA-TGTGGCAGAGCCACCA
28729651 AGACGCTTCC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 4 0.10
27 38 0.90
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (26 bp):
AATGTGGCAGAGCCACCAGATCAGAT
Found at i:28731280 original size:26 final size:26
Alignment explanation
Indices: 28731249--28731356 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28731239 TGAAATGCCC
*
28731249 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
28731275 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28731301 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
28731327 ATCATGGAACATTTACATAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28731353 ATCA
1 ATCA
28731357 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28736688 original size:19 final size:19
Alignment explanation
Indices: 28736664--28736701 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28736654 TCTTTAATTG
*
28736664 AGAGAAAAGATGAGTAAAA
1 AGAGAAAAGAAGAGTAAAA
*
28736683 AGAGAAGAGAAGAGTAAAA
1 AGAGAAAAGAAGAGTAAAA
28736702 GAAGATAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.29, T:0.08
Consensus pattern (19 bp):
AGAGAAAAGAAGAGTAAAA
Found at i:28739271 original size:42 final size:43
Alignment explanation
Indices: 28739159--28739464 Score: 209
Period size: 42 Copynumber: 7.1 Consensus size: 43
28739149 ATGTTGTACA
* * * * * *
28739159 ATGCCATTTCCCGGATATGGTCTTACATGTAATCTTAT-ATCG
1 ATGCCATGTCCCAGACATGGTCTTACACGAAATCTCATAATCG
*
28739201 AAGCCAATAG-CCCAG-CTATGGTCTTACACGAAATCTCATAAT-G
1 ATGCC-AT-GTCCCAGAC-ATGGTCTTACACGAAATCTCATAATCG
* * * *
28739244 ATGCCATGTCCTAGACATGGTCTTACACGTAATATCAT-ACCG
1 ATGCCATGTCCCAGACATGGTCTTACACGAAATCTCATAATCG
* * *
28739286 ATGCTAATAG-CCCAG-CTATGGTCTTACACGAAATCTCGT-ATCA
1 ATGC-CAT-GTCCCAGAC-ATGGTCTTACACGAAATCTCATAATCG
* * * *
28739329 ATGCCATGTCCCAGACACGGTCTTACATGAAATATCAT-ATCA
1 ATGCCATGTCCCAGACATGGTCTTACACGAAATCTCATAATCG
* * * *
28739371 AAGACATGTCCCAGACATGGTCTTACATGAAGTCTCATAACGGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACGAAATCTCATAA---T--CG
* * * *
28739419 ATGCCATGTCCGAGACATGGTCTTATACGAGACCTCAT-ATCG
1 ATGCCATGTCCCAGACATGGTCTTACACGAAATCTCATAATCG
28739461 ATGC
1 ATGC
28739465 TAATGTTATA
Statistics
Matches: 208, Mismatches: 38, Indels: 36
0.74 0.13 0.13
Matches are distributed among these distances:
41 3 0.01
42 104 0.50
43 64 0.31
44 4 0.02
46 1 0.00
47 1 0.00
48 31 0.15
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (43 bp):
ATGCCATGTCCCAGACATGGTCTTACACGAAATCTCATAATCG
Found at i:28739302 original size:85 final size:85
Alignment explanation
Indices: 28739157--28739409 Score: 280
Period size: 85 Copynumber: 3.0 Consensus size: 85
28739147 ATATGTTGTA
* * * * * *
28739157 CAATGCCATTTCCCGGATATGGTCTTACATGTAATCTTATATCGAAGCCAATAGCCCAGCTATGG
1 CAATGCCATGTCCCAGACATGGTCTTACATGTAATATCATACCGAAGCCAATAGCCCAGCTATGG
28739222 TCTTACACGAAATCTCATAAT
66 TCTTACACGAAATCTCAT-AT
* * * * *
28739243 -GATGCCATGTCCTAGACATGGTCTTACACGTAATATCATACCGATGCTAATAGCCCAGCTATGG
1 CAATGCCATGTCCCAGACATGGTCTTACATGTAATATCATACCGAAGCCAATAGCCCAGCTATGG
*
28739307 TCTTACACGAAATCTCGTAT
66 TCTTACACGAAATCTCATAT
* * * * *
28739327 CAATGCCATGTCCCAGACACGGTCTTACATGAAATATCATATCAAAGAC-AT-GTCCCAGAC-AT
1 CAATGCCATGTCCCAGACATGGTCTTACATGTAATATCATACCGAAGCCAATAG-CCCAG-CTAT
* *
28739389 GGTCTTACATGAAGTCTCATA
64 GGTCTTACACGAAATCTCATA
28739410 ACGGTGCCGA
Statistics
Matches: 139, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
83 1 0.01
84 29 0.21
85 109 0.78
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (85 bp):
CAATGCCATGTCCCAGACATGGTCTTACATGTAATATCATACCGAAGCCAATAGCCCAGCTATGG
TCTTACACGAAATCTCATAT
Found at i:28740671 original size:13 final size:13
Alignment explanation
Indices: 28740655--28740691 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
28740645 CAAACAAAAT
*
28740655 TTTCATGAAATCA
1 TTTCATAAAATCA
28740668 TTTCATAAAATCA
1 TTTCATAAAATCA
28740681 TTTCATAAAAT
1 TTTCATAAAAT
28740692 TATAGACCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.41
Consensus pattern (13 bp):
TTTCATAAAATCA
Found at i:28741598 original size:16 final size:17
Alignment explanation
Indices: 28741579--28741611 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28741569 AATATTTTCA
28741579 TTATTA-CTTATTAATT
1 TTATTATCTTATTAATT
*
28741595 TTATTATCTTGTTAATT
1 TTATTATCTTATTAATT
28741612 AATCATTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TTATTATCTTATTAATT
Found at i:28741726 original size:24 final size:24
Alignment explanation
Indices: 28741696--28741746 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
28741686 TGTTAAAACG
28741696 TTTGGTTCTTTTCAAAACTCAAGT
1 TTTGGTTCTTTTCAAAACTCAAGT
*
28741720 TTTGGTTCTTTTGAAAACTCAAGT
1 TTTGGTTCTTTTCAAAACTCAAGT
28741744 TTT
1 TTT
28741747 CCTAAAGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (24 bp):
TTTGGTTCTTTTCAAAACTCAAGT
Found at i:28742952 original size:28 final size:28
Alignment explanation
Indices: 28742894--28742965 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
28742884 TGTCCAACCA
* *
28742894 AAACACACCAGTATTATATAATCCTCTC
1 AAACACACCAGAATAATATAATCCTCTC
*
28742922 AAACACACTAGAATAATATAATCCATC-C
1 AAACACACCAGAATAATATAATCC-TCTC
*
28742950 AAAATACACCAGAATA
1 -AAACACACCAGAATA
28742966 GCACAGAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 22 0.59
29 15 0.41
ACGTcount: A:0.49, C:0.25, G:0.04, T:0.22
Consensus pattern (28 bp):
AAACACACCAGAATAATATAATCCTCTC
Found at i:28743142 original size:17 final size:17
Alignment explanation
Indices: 28743102--28743143 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
28743092 ACTTTTTTTT
*
28743102 ATTTCAATTTAATTTTC
1 ATTTCAATTTAATTTCC
*
28743119 ATATCAATTTCAA-TTCC
1 ATTTCAATTT-AATTTCC
28743136 ATTTCAAT
1 ATTTCAAT
28743144 ATACAATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTCAATTTAATTTCC
Found at i:28744420 original size:17 final size:17
Alignment explanation
Indices: 28744400--28744433 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28744390 ATACACTAAT
28744400 ATAAT-ATCAATTAAATA
1 ATAATAATCAA-TAAATA
28744417 ATAATAATCAATAAATA
1 ATAATAATCAATAAATA
28744434 TCTTTTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAATAATCAATAAATA
Found at i:28750716 original size:28 final size:28
Alignment explanation
Indices: 28750684--28750767 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
28750674 AACAAACCAG
* *
28750684 TATAATCCTCCAAAACACACCAGTATTA
1 TATAATCCTCCAAAACACACCAGAATAA
*
28750712 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
*
28750740 TATAATCCATCCAAAACACACCATAATA
1 TATAATCC-TCCAAAACACACCAGAATA
28750768 GCACAGAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 33 0.66
29 17 0.34
ACGTcount: A:0.46, C:0.30, G:0.02, T:0.21
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:28750739 original size:23 final size:23
Alignment explanation
Indices: 28750670--28750740 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 23
28750660 AAATGTCCAA
* *
28750670 CCAAAACAAACCAGTATAATCCT
1 CCAAAACACACCAGAATAATCCT
28750693 CCAAAACACACCAGTATTATATAATCCT
1 CCAAAACACACCAG----A-ATAATCCT
*
28750721 CCCAAACACACCAGAATAAT
1 CCAAAACACACCAGAATAAT
28750741 ATAATCCATC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 18 0.45
24 1 0.03
28 21 0.52
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.18
Consensus pattern (23 bp):
CCAAAACACACCAGAATAATCCT
Found at i:28751887 original size:8 final size:8
Alignment explanation
Indices: 28751853--28751904 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
28751843 TAGTGATGTG
*
28751853 AATAATAA
1 AATATTAA
*
28751861 AGTATATAA
1 AATAT-TAA
28751870 AATA-TAA
1 AATATTAA
28751877 AATATTAA
1 AATATTAA
*
28751885 AATATCAA
1 AATATTAA
*
28751893 AATATTAG
1 AATATTAA
28751901 AATA
1 AATA
28751905 ATAATTAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.19
8 23 0.64
9 6 0.17
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:28751894 original size:16 final size:15
Alignment explanation
Indices: 28751857--28751904 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
28751847 GATGTGAATA
*
28751857 ATAAAGTATATAAAAT
1 ATAAAATAT-TAAAAT
28751873 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
28751888 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
28751904 A
1 A
28751905 ATAATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:28752069 original size:20 final size:20
Alignment explanation
Indices: 28752012--28752071 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
28752002 AATACTACAT
28752012 AAATATGTACAT-ATATAAA
1 AAATATGTACATAATATAAA
** *
28752031 AAATAAATACGTGATAATATTAA
1 AAATATGTAC---ATAATATAAA
28752054 AAATATGTACATAATATA
1 AAATATGTACATAATATA
28752072 GTGTAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 2 0.06
23 14 0.45
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATATGTACATAATATAAA
Found at i:28752110 original size:22 final size:23
Alignment explanation
Indices: 28752049--28752119 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 23
28752039 ACGTGATAAT
*
28752049 ATTAAAAATATGTACATAATATA
1 ATTAAAAATATATACATAATATA
* *
28752072 GTGTAAAAAATACATACATAATATA
1 AT-T-AAAAATATATACATAATATA
*
28752097 ATT-AAAATATATACATAAGATA
1 ATTAAAAATATATACATAATATA
28752119 A
1 A
28752120 CATGTAGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 18 0.45
23 1 0.03
24 2 0.05
25 19 0.47
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (23 bp):
ATTAAAAATATATACATAATATA
Found at i:28752171 original size:25 final size:24
Alignment explanation
Indices: 28752135--28752266 Score: 101
Period size: 23 Copynumber: 5.6 Consensus size: 24
28752125 AGAAAAAAAT
*
28752135 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATT-AAG
* *
28752160 ATATATACATAAAATAGTA-TAAT
1 ATATATACATAATATAGTATTAAG
* * *
28752183 ATATATACGTAATATAGAATTTAG
1 ATATATACATAATATAGTATTAAG
* * *
28752207 A-ATATACCTAATATATTA-AAAG
1 ATATATACATAATATAGTATTAAG
* * *
28752229 AATATATATAAAATATAATATTAAG
1 -ATATATACATAATATAGTATTAAG
*
28752254 AAATATA-ATAATA
1 ATATATACATAATA
28752267 ACAAAAAAAA
Statistics
Matches: 83, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
22 2 0.02
23 38 0.46
24 23 0.28
25 20 0.24
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (24 bp):
ATATATACATAATATAGTATTAAG
Found at i:28752774 original size:30 final size:30
Alignment explanation
Indices: 28752738--28752806 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
28752728 TAGGTACAAG
28752738 TGGTGGTGGAGCAAATGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAATGTGGCTAGTGGAGT
*
28752768 TGGTGGTGGAGCAATTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAATGTGGCTAGTGGAGT
28752798 TGGTGGTGG
1 TGGTGGTGG
28752807 CAAAGGCTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.16, C:0.06, G:0.49, T:0.29
Consensus pattern (30 bp):
TGGTGGTGGAGCAAATGTGGCTAGTGGAGT
Found at i:28753600 original size:88 final size:86
Alignment explanation
Indices: 28753460--28753757 Score: 291
Period size: 88 Copynumber: 3.4 Consensus size: 86
28753450 GTGATCCTGA
* * * *
28753460 GCTCAACTCATTTCTCGCAATATGAATTGACTCTTTAAAACTAGACA-T-TAAAAACATAAATTT
1 GCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTAAAAC-A-AAATTGTAAAAACATAAATTT
* *
28753523 AAAATAGCTCAGCACGTGAGCCAAG
63 AAAATACCTCAG-ACGTGACCCAAG
* *
28753548 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAAAATTTGT-AAAACA-GATTTTGA
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAAAA-TTGTAAAAACATAAATTT-A
* *
28753611 AAATACCTCGGTATGTGACCCAAG
64 AAATACCTCAG-ACGTGACCCAAG
* * * * * * *
28753635 GCTCAACTCATTTCTCGTAATATGAGTTGATTCTTGAAAAGTATAAATTGAAAAAACATTAATTA
1 GCTCAACTCACTTCTCGCAATATGAGTTGATT-TTTAAAA-CA-AAATTGTAAAAACATAAATTT
* *
28753700 AAAATACCTCAG-CGTGCCCCGAG
63 AAAATACCTCAGACGTGACCCAAG
*
28753723 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
28753758 TTGAAAAACA
Statistics
Matches: 174, Mismatches: 27, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
85 2 0.01
86 5 0.03
87 68 0.39
88 72 0.41
89 4 0.02
90 20 0.11
91 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (86 bp):
GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAAAATTGTAAAAACATAAATTTAAA
ATACCTCAGACGTGACCCAAG
Found at i:28753812 original size:77 final size:76
Alignment explanation
Indices: 28753686--28754236 Score: 546
Period size: 77 Copynumber: 7.3 Consensus size: 76
28753676 TATAAATTGA
** * *
28753686 AAAAACATTAATTAAAAATACCTCAGC--GTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
28753749 TTGATTTTTTTG
66 TTGA-TTTTTTG
* *
28753761 AAAAACATAAATTGAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
28753826 TTGATTTTTTG
66 TTGATTTTTTG
** * * * *
28753837 ATGAACAGAAATT-AAAATTACCTCAAC-TAGT--CCTGAGGCTCAACTCACCTCTCACAACATG
1 AAAAACAGAAATTGAAAA-TACCTCAGCGT-GTGACCCGAGGCTCAACTCACCTCTCGCAATATG
28753898 AGTTGATTTTTTG
64 AGTTGATTTTTTG
* *
28753911 AAAAACAGAAGTTGAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
28753976 TTGATTTTTTTG
66 TTGA-TTTTTTG
* * *
28753988 ACAAACAGAAATTGAAAACACCTCAGCATGT-----GAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
28754048 TTGA-TTTTTG
66 TTGATTTTTTG
* * * **
28754058 AAAAACATAAATTGAGCAGAAAATGAAAATACCTCAACG-G-GTCTTGAGGCTCAACTCACCTCT
1 ------A-AAA---A-CAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCT
28754121 CGCAATATGAGTTGATTTTTT-
55 CGCAATATGAGTTGATTTTTTG
* ** * * **
28754142 --TATGATAAATTGAAAATACCTCA--ATGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
28754203 TTGATTTTTTG
66 TTGATTTTTTG
28754214 AATTAAAACAGAAATTGAAAATA
1 -A--AAAACAGAAATTGAAAATA
28754237 GAAATGGAAA
Statistics
Matches: 403, Mismatches: 39, Indels: 66
0.79 0.08 0.13
Matches are distributed among these distances:
70 7 0.02
71 60 0.15
72 33 0.08
74 59 0.15
75 35 0.09
76 60 0.15
77 90 0.22
80 2 0.00
81 19 0.05
84 33 0.08
85 5 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (76 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTG
Found at i:28753967 original size:150 final size:150
Alignment explanation
Indices: 28753720--28754234 Score: 613
Period size: 150 Copynumber: 3.4 Consensus size: 150
28753710 AGCGTGCCCC
*
28753720 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACATAAATTGAAAACACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAACACCTC
28753785 AGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATGAACAGAAATT
65 AGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATGAACAGAAATT
28753850 -AAAATTACCTCAACTAGTCCT
130 GAAAA-TACCTCAACTAGTCCT
* * *
28753871 GAGGCTCAACTCACCTCTCACAACATGAGTTGATTTTTTGAAAAACAGAAGTTGAAAACACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAACACCTCA
**
28753936 GCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAATT
66 GCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGATGAACAGAAATT
* * *
28754001 GAAAACACCTCAGC-A-T-GT
130 GAAAATACCTCAACTAGTCCT
*
28754019 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACATAAATTGAGCAGAAAATG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG------A-AAA---A-CAGAAATTG
* * * ** *
28754083 AAAATACCTCAACG-G-GTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTATG
55 AAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATG
* *
28754146 ---ATAAATTGAAAATACCTCAA-T-GTGACTT
120 AACAGAAATTGAAAATACCTCAACTAGT--CCT
28754174 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAATTAAAACAGAAATTGAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-A--AAAACAGAAATTGAAAA
28754235 TAGAAATGGA
Statistics
Matches: 317, Mismatches: 27, Indels: 43
0.82 0.07 0.11
Matches are distributed among these distances:
147 6 0.02
148 44 0.14
149 2 0.01
150 75 0.24
151 57 0.18
152 26 0.08
153 1 0.00
154 3 0.01
155 41 0.13
156 41 0.13
157 2 0.01
158 19 0.06
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (150 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAACACCTCA
GCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATGAACAGAAATTG
AAAATACCTCAACTAGTCCT
Found at i:28754197 original size:71 final size:71
Alignment explanation
Indices: 28754081--28754212 Score: 237
Period size: 71 Copynumber: 1.9 Consensus size: 71
28754071 GAGCAGAAAA
*
28754081 TGAAAATACCTCAACGGGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTATG
1 TGAAAATACCTCAACGGGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTATG
28754146 ATAAAT
66 ATAAAT
* *
28754152 TGAAAATACCTCAATGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 TGAAAATACCTCAACGGGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
28754213 GAATTAAAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (71 bp):
TGAAAATACCTCAACGGGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTATG
ATAAAT
Found at i:28754296 original size:159 final size:155
Alignment explanation
Indices: 28753947--28754301 Score: 434
Period size: 159 Copynumber: 2.3 Consensus size: 155
28753937 CGTGTGACCC
* ** * *
28753947 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAACACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTT----ATGATAAATTGAAAATACCTC
* *
28754012 -A-G-CA-TGTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGA
62 AATGTGACT-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGA
** * *
28754073 GCAGAAAATGAAAATACCTCAACGGGTCTT
126 AAAGAAAATGAAAACACCTCAACGCGTCTT
*
28754103 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTATGATAAATTGAAAATACCTCAATG
1 GAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTATGATAAATTGAAAATACCTCAATG
28754168 TGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAATTAAAACAGAAATTGAA
66 TGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-A--AAAACAGAAATTGAA
*
28754233 AATAGAAATGGAAAACACCTC-A-GCGTCTT
127 AAGA-AAAT-GAAAACACCTCAACGCGTCTT
* *
28754262 GAGGTTCAACTGACCTCTCGCAATATGAGCTGATTTTTTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTT
28754302 GAAACACATA
Statistics
Matches: 175, Mismatches: 14, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
152 17 0.10
153 1 0.01
154 1 0.01
155 35 0.20
156 47 0.27
157 1 0.01
159 58 0.33
160 5 0.03
161 10 0.06
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (155 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTATGATAAATTGAAAATACCTCAATG
TGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAGA
AAATGAAAACACCTCAACGCGTCTT
Found at i:28754455 original size:75 final size:75
Alignment explanation
Indices: 28754330--28754632 Score: 344
Period size: 77 Copynumber: 4.0 Consensus size: 75
28754320 AAAAGAAATT
* ** * * *
28754330 AAAAACAGAATTTGAAAGGACCTCGACGTGTGGCCCGAGACTCAACTCACCTCTCCCAATATGAG
1 AAAAACAGAAATTGAAAATACCTC-A-GTGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
*
28754395 TTGATTCTTTTG
64 TTGATTTTTTTG
28754407 AAAAACAGAAATTGAAAATACCTCAGTGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGTGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
28754472 GATTTTTTTG
66 GATTTTTTTG
* * * * * *
28754482 ATACAAATAGAATTTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGAG
1 A-A-AAACAGAAATTGAAAATACCTCAGTGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
28754547 TTGA--TTTTTG
64 TTGATTTTTTTG
* * * * ** ** *
28754557 ACAACCAAAAATTGAAATTACCTCA--ACGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGTGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
28754620 GATTTTTTTG
66 GATTTTTTTG
28754630 AAA
1 AAA
28754633 CATAAATTAA
Statistics
Matches: 196, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
71 35 0.18
73 25 0.13
75 54 0.28
76 2 0.01
77 80 0.41
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (75 bp):
AAAAACAGAAATTGAAAATACCTCAGTGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTTTG
Found at i:28754533 original size:77 final size:77
Alignment explanation
Indices: 28754370--28754712 Score: 362
Period size: 77 Copynumber: 4.4 Consensus size: 77
28754360 TGGCCCGAGA
* * *
28754370 CTCAACTCACCTCTCCCAATATGAGTTGATTCTTTTG-AA-AAACAGAAATTGAAAATACCTCAG
1 CTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGAAACAAATAGAAATTGAAAATACCTCAG
* *
28754433 TGTGTCCCGAGG
66 CGTGTCCTGAGG
* * * *
28754445 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGATACAAATAGAATTTGAAAATATCTCAG
1 CTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGAAACAAATAGAAATTGAAAATACCTCAG
28754510 CGTGTCCTGAGG
66 CGTGTCCTGAGG
* *
28754522 CTCAACTCACCTCTCACAATATGAGTTGA--TTTTTGACAAC-CA-A-AAATTGAAATTACCTCA
1 CTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGA-AACAAATAGAAATTGAAAATACCTCA
* *
28754582 AC--GTCTTGAGG
65 GCGTGTCCTGAGG
* *
28754593 CTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAACATAAATTAAAAAAACGAAAATTGA
1 CTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGAAAC--AAA-T------A-G-AAATTGA
*
28754658 AAATACCTCAGCATGTCCTGAGG
55 AAATACCTCAGCGTGTCCTGAGG
*
28754681 CTCAACTCACTTCTCACAATATGAGTTGATTT
1 CTCAACTCACCTCTCACAATATGAGTTGATTT
28754713 GAAAAGCAGA
Statistics
Matches: 224, Mismatches: 23, Indels: 29
0.81 0.08 0.11
Matches are distributed among these distances:
71 35 0.16
72 3 0.01
73 22 0.10
74 1 0.00
75 44 0.20
76 3 0.01
77 59 0.26
83 1 0.00
86 17 0.08
88 39 0.17
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (77 bp):
CTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGAAACAAATAGAAATTGAAAATACCTCAG
CGTGTCCTGAGG
Found at i:28754703 original size:415 final size:407
Alignment explanation
Indices: 28753908--28754991 Score: 1158
Period size: 415 Copynumber: 2.6 Consensus size: 407
28753898 AGTTGATTTT
* *
28753908 TTGAAAAACAGAAGTTGAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAACACCTCA-CGTGTGGCCCGAGGCTCAACTCACCTCTCGCAATAT
* * *
28753973 GAGTTGATTTTTTTGACAAACAGAAATTGAAAACACCTCAGCATGT---GAGGCTCAACTCACCT
65 GAGTTGA-TTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCT
*** * * *
28754035 CTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAGCAGAAAATGAAAATACCTCAACGGGT
129 CTCGCAATATGAGTTGATTTTT-TTGAAC--AAA-T----AG-AATTGAAAATACCTCAGCGTGT
* ** **
28754100 CTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT--TTATGATAAATTGAAAATACCT
185 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACCATAAATTGAAAATACCT
*
28754163 CAATGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAATTAAAACAGAAA
250 CAACGT-ACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT--ATTAAAACAGAAA
* * * * * *
28754228 TTGAAAATAGAAATGGAAAACACCTCAGCGTCTTGAGGTTCAACTGACCTCTCGCAATATGAGCT
312 TTAAAAAAAGAAATGGAAAACACCTCAGCGTCCTGAGGCTCAACTCACCTCTCACAATATGAGCT
*
28754293 GATTTTTTTGAAACA-CATAAATT-AAAAAAAAGAAA
377 GA----TTTGAAA-AGCAGAAATTGAAAAAAAA-AAA
* ** * *
28754328 TT-AAAAACAGAATTTGAAAGGACCTCGACGTGTGGCCCGAGACTCAACTCACCTCTCCCAATAT
1 TTGAAAAACAGAAATTGAAAACACCTC-ACGTGTGGCCCGAGGCTCAACTCACCTCTCGCAATAT
*
28754392 GAGTTGATTCTTTTGAAAAACAGAAATTGAAAATACCTCAGTGTGTCCCGAGGCTCAACTCACCT
65 GAGTTGATT-TTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCT
*
28754457 CTCGCAATATGAGTTGATTTTTTTGATACAAATAGAATTTGAAAATATCTCAGCGTGTCCTGAGG
129 CTCGCAATATGAGTTGATTTTTTTGA-ACAAATAGAA-TTGAAAATACCTCAGCGTGTCCTGAGG
* * * *
28754522 CTCAACTCACCTCTCACAATATGAGTTGATTTTTGACAACCAAAAATTGAAATTACCTCAACGT-
192 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACCATAAATTGAAAATACCTCAACGTA
* * *
28754586 CTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTT-TTGAAACATAAATTAAAAAAAC
257 CTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTATTAAAACAGAAATTAAAAAAA-
* * * *
28754649 GAAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACTTCTCACAATATGAGTTGATTTG
321 G-AAATGGAAAACACCTCAGC--GTCCTGAGGCTCAACTCACCTCTCACAATATGAGCTGATTTG
* * ***
28754714 AAAAGCAGAATTTGTAAGGCAAAAA
383 AAAAGCAGAAATTGAAAAAAAAAAA
* *
28754739 TTGAAAAACAGAAATTGAAAATACCTCA-GCGT-GCCCTGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAACACCTCACGTGTGGCCC-GAGGCTCAACTCACCTCTCGCAATAT
* * * *
28754802 GAGTTGATTTTGAAAAACATAAATTAAAAACAGAAATTAAAAATACCTCGGCGTGCCCCGAGGCT
65 GAGTTGATTTT--------T---TGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCT
* *
28754867 CAGCTCACCTCTCGCAATATGAGTTGA--TTTTTGAA-AAGCATA-AATTGAAATTACCTCAGCG
119 CAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAACAA--ATAGAATTGAAAATACCTCAGCG
*
28754928 TGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGCATAAATTGAAAA
182 TGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAACCATAAATTGAAAA
28754992 AATGGAAATT
Statistics
Matches: 569, Mismatches: 64, Indels: 65
0.82 0.09 0.09
Matches are distributed among these distances:
409 6 0.01
410 37 0.07
411 36 0.06
412 26 0.05
413 17 0.03
414 7 0.01
415 124 0.22
416 55 0.10
417 45 0.08
418 12 0.02
419 94 0.17
420 69 0.12
421 1 0.00
422 40 0.07
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (407 bp):
TTGAAAAACAGAAATTGAAAACACCTCACGTGTGGCCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCT
CGCAATATGAGTTGATTTTTTTGAACAAATAGAATTGAAAATACCTCAGCGTGTCCTGAGGCTCA
ACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACCATAAATTGAAAATACCTCAACGTACTTG
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTATTAAAACAGAAATTAAAAAAAGAAAT
GGAAAACACCTCAGCGTCCTGAGGCTCAACTCACCTCTCACAATATGAGCTGATTTGAAAAGCAG
AAATTGAAAAAAAAAAA
Found at i:28754839 original size:99 final size:98
Alignment explanation
Indices: 28754643--28754916 Score: 288
Period size: 99 Copynumber: 2.9 Consensus size: 98
28754633 CATAAATTAA
* * * *
28754643 AAAAACGAAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACTTCTCACAATATGAGTT
1 AAAAACG-AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* * * **
28754708 GA-TTTGAAAAGCAGAATTTGTAAGGCAAAAATT
65 GATTTTGAAAAGCATAAATTGAAAAACAAAAATT
28754741 GAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 -AAAAAC-GAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
*
28754806 TGATTTTGAAAAACATAAATT-AAAAAC-------
64 TGATTTTGAAAAGCATAAATTGAAAAACAAAAATT
* * * *
28754833 ----A-GAAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCTCGCAATATGAGTTG
1 AAAAACGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
28754893 ATTTTTGAAAAGCATAAATTGAAA
66 A-TTTTGAAAAGCATAAATTGAAA
28754917 TTACCTCAGC
Statistics
Matches: 156, Mismatches: 15, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
85 56 0.36
86 17 0.11
87 4 0.03
99 64 0.41
100 15 0.10
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (98 bp):
AAAAACGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTGAAAAGCATAAATTGAAAAACAAAAATT
Found at i:28754844 original size:14 final size:13
Alignment explanation
Indices: 28754814--28754844 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28754804 GTTGATTTTG
*
28754814 AAAAACATAAATT
1 AAAAACAGAAATT
28754827 AAAAACAGAAATT
1 AAAAACAGAAATT
28754840 AAAAA
1 AAAAA
28754845 TACCTCGGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.16
Consensus pattern (13 bp):
AAAAACAGAAATT
Found at i:28754885 original size:85 final size:87
Alignment explanation
Indices: 28754736--28754916 Score: 303
Period size: 85 Copynumber: 2.1 Consensus size: 87
28754726 TGTAAGGCAA
* *
28754736 AAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATA
1 AAATTGAAAAACAGAAATTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATA
28754801 TGAGTTGA-TTTTGAAAAACAT
66 TGAGTTGATTTTTGAAAAACAT
* *
28754822 AAATT-AAAAACAGAAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCTCGCAATA
1 AAATTGAAAAACAGAAATTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATA
*
28754886 TGAGTTGATTTTTGAAAAGCAT
66 TGAGTTGATTTTTGAAAAACAT
28754908 AAATTGAAA
1 AAATTGAAA
28754917 TTACCTCAGC
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
85 63 0.72
86 22 0.25
87 3 0.03
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (87 bp):
AAATTGAAAAACAGAAATTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATA
TGAGTTGATTTTTGAAAAACAT
Found at i:28754891 original size:184 final size:186
Alignment explanation
Indices: 28754565--28754906 Score: 485
Period size: 184 Copynumber: 1.8 Consensus size: 186
28754555 TGACAACCAA
* * * ***
28754565 AAATTGAAATTACCTCAACGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTG
1 AAATTGAAAATACCTCAACGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
* * * *
28754630 AAACATAAATTAAAAAAACGAAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACTTCT
66 AAACATAAATTAAAAAAACGAAAATTAAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCT
28754695 CACAATATGAGTTGA-TTTGAAAAGCAGAATTTGTAAGGCAAAAATTGAAAAACAG
131 CACAATATGAGTTGATTTTGAAAAGCAGAATTTGTAAGGCAAAAATTGAAAAACAG
*
28754750 AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTG
1 AAATTGAAAATACCTCAACGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
* * * *
28754814 AAAAACATAAATTAAAAACA-G-AAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCT
64 AAAAACATAAATTAAAAAAACGAAAATTAAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCT
*
28754877 CTCGCAATATGAGTTGATTTTTGAAAAGCA
129 CTCACAATATGAGTTGA-TTTTGAAAAGCA
28754907 TAAATTGAAA
Statistics
Matches: 137, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
184 51 0.37
185 20 0.15
186 32 0.23
187 34 0.25
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (186 bp):
AAATTGAAAATACCTCAACGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
AAACATAAATTAAAAAAACGAAAATTAAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCT
CACAATATGAGTTGATTTTGAAAAGCAGAATTTGTAAGGCAAAAATTGAAAAACAG
Found at i:28754954 original size:73 final size:74
Alignment explanation
Indices: 28754835--28754991 Score: 253
Period size: 73 Copynumber: 2.1 Consensus size: 74
28754825 TTAAAAACAG
* * *
28754835 AAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCTCGCAATATGAGTTGA-TTTTT
1 AAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
28754899 GAAAAGCAT
66 GAAAAGCAT
* * *
28754908 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
28754973 GAAAAGCAT
66 GAAAAGCAT
28754982 AAATTGAAAA
1 AAATTGAAAA
28754992 AATGGAAATT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
73 53 0.70
74 23 0.30
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (74 bp):
AAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
GAAAAGCAT
Found at i:28762066 original size:24 final size:24
Alignment explanation
Indices: 28762039--28762094 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
28762029 TAGTGATGTG
28762039 AATAATAAAGTATAT-AAAATA-TAA
1 AATAATAAA--ATATCAAAATATTAA
* *
28762063 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
28762087 AATAATAA
1 AATAATAA
28762095 TAATTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 6 0.22
24 17 0.63
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Done.