Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 21 of 250
Found at i:5917783 original size:16 final size:14
Alignment explanation
Indices: 5917764--5917806 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 14
5917754 TTCAAACTAC
5917764 TTTTTATTTTTTAA
1 TTTTTATTTTTTAA
5917778 TTTTTTAATTTTTTAA
1 -TTTTT-ATTTTTTAA
5917794 TTTTTATTTTTTA
1 TTTTTATTTTTTA
5917807 GCAGATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.30
15 10 0.37
16 9 0.33
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATTTTTTAA
Found at i:5924540 original size:20 final size:21
Alignment explanation
Indices: 5924512--5924550 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5924502 TAATTTTAAA
5924512 AAATCATTATTTTT-TTATCT
1 AAATCATTATTTTTATTATCT
*
5924532 AAATTATTATTTTTATTAT
1 AAATCATTATTTTTATTAT
5924551 TTTTTATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
AAATCATTATTTTTATTATCT
Found at i:5929453 original size:15 final size:15
Alignment explanation
Indices: 5929433--5929506 Score: 121
Period size: 15 Copynumber: 4.9 Consensus size: 15
5929423 CAATGGCGAA
5929433 AAATCAAAAGATGAC
1 AAATCAAAAGATGAC
5929448 AAATCAAAAGATGAC
1 AAATCAAAAGATGAC
*
5929463 AAATCAAAAGACGAC
1 AAATCAAAAGATGAC
5929478 AAATCAAAAGATGAC
1 AAATCAAAAGATGAC
* *
5929493 AAGTCAAAACATGA
1 AAATCAAAAGATGA
5929507 AGTCGGAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 55 1.00
ACGTcount: A:0.59, C:0.15, G:0.14, T:0.12
Consensus pattern (15 bp):
AAATCAAAAGATGAC
Found at i:5932320 original size:12 final size:12
Alignment explanation
Indices: 5932305--5932333 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5932295 AATTTAAATT
5932305 TTATTGTTAGGA
1 TTATTGTTAGGA
5932317 TTATTGTTAGGA
1 TTATTGTTAGGA
5932329 TTATT
1 TTATT
5932334 ATGATATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (12 bp):
TTATTGTTAGGA
Found at i:5934337 original size:20 final size:20
Alignment explanation
Indices: 5934287--5934339 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
5934277 AGTCTATTCC
*
5934287 TAATTAAAT-TATA-AAAGA
1 TAATTAAATATAAATAAAGA
*
5934305 TAAATACAA-ATAAATAAAGA
1 TAATTA-AATATAAATAAAGA
5934325 TAATTAAATATAAAT
1 TAATTAAATATAAAT
5934340 GAGGATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 5 0.18
19 7 0.25
20 16 0.57
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (20 bp):
TAATTAAATATAAATAAAGA
Found at i:5936026 original size:53 final size:53
Alignment explanation
Indices: 5935968--5936082 Score: 128
Period size: 53 Copynumber: 2.2 Consensus size: 53
5935958 AAATGTCTCT
* * *
5935968 TTTCATATGTCCATATCCATATAAAT-ATTTCATATAGA-CACTTCATA-TAATCA
1 TTTCATATATCCATATCCACAT-AATCAATTCATATA-ACCACTTCA-AGTAATCA
* * *
5936021 TTTCATATATCTATTTCCACATAATCAATTCATATAACCATTTCAAGTAATCA
1 TTTCATATATCCATATCCACATAATCAATTCATATAACCACTTCAAGTAATCA
5936074 TTTCATATA
1 TTTCATATA
5936083 ATCATTCTGT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
52 5 0.09
53 48 0.91
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41
Consensus pattern (53 bp):
TTTCATATATCCATATCCACATAATCAATTCATATAACCACTTCAAGTAATCA
Found at i:5936036 original size:13 final size:13
Alignment explanation
Indices: 5935985--5936150 Score: 119
Period size: 13 Copynumber: 12.7 Consensus size: 13
5935975 TGTCCATATC
5935985 CATATAAAT-ATTT
1 CATAT-AATCATTT
*
5935998 CATATAGA-CACTT
1 CATATA-ATCATTT
5936011 CATATAATCATTT
1 CATATAATCATTT
5936024 CATAT-ATCTATTT
1 CATATAATC-ATTT
* *
5936037 CCACATAATCAATT
1 -CATATAATCATTT
*
5936051 CATATAACCATTT
1 CATATAATCATTT
5936064 CA-AGTAATCATTT
1 CATA-TAATCATTT
5936077 CATATAATCA-TT
1 CATATAATCATTT
* *
5936089 CTGTATAA-CTATTC
1 C-ATATAATC-ATTT
* * *
5936103 CATCTAAACACTT
1 CATATAATCATTT
* *
5936116 CATATTACCATTT
1 CATATAATCATTT
*
5936129 CATGTAATCATTT
1 CATATAATCATTT
5936142 CATATAATC
1 CATATAATC
5936151 CTTCTGTATA
Statistics
Matches: 119, Mismatches: 22, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
12 10 0.08
13 95 0.80
14 11 0.09
15 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.40
Consensus pattern (13 bp):
CATATAATCATTT
Found at i:5936077 original size:40 final size:39
Alignment explanation
Indices: 5936009--5936086 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 39
5935999 ATATAGACAC
*
5936009 TTCATATAATCATTTCATATATCTATTTCCACATAATCAA
1 TTCATATAACCATTTCATATATCTATTT-CACATAATCAA
*
5936049 TTCATATAACCATTTCA-AGTAATC-ATTTCATATAATCA
1 TTCATATAACCATTTCATA-T-ATCTATTTCACATAATCA
5936087 TTCTGTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 10 0.29
40 21 0.62
41 3 0.09
ACGTcount: A:0.38, C:0.19, G:0.01, T:0.41
Consensus pattern (39 bp):
TTCATATAACCATTTCATATATCTATTTCACATAATCAA
Found at i:5936136 original size:65 final size:65
Alignment explanation
Indices: 5936009--5936196 Score: 238
Period size: 65 Copynumber: 2.9 Consensus size: 65
5935999 ATATAGACAC
* * * * *
5936009 TTCATATAATCATT-TCATATATCTATTTCCA-CATAATCAATTCATATAACCATTTCAAGTAAT
1 TTCATATAATCATTCT-GTATAACTA-TTCCATC-TAAACAATTCATATTACCATTTCATGTAAT
5936072 CAT
63 CAT
*
5936075 TTCATATAATCATTCTGTATAACTATTCCATCTAAACACTTCATATTACCATTTCATGTAATCAT
1 TTCATATAATCATTCTGTATAACTATTCCATCTAAACAATTCATATTACCATTTCATGTAATCAT
* * *
5936140 TTCATATAATCCTTCTGTATAACCATTCCATCTAAA-AATTTCATTTTACCATTTCAT
1 TTCATATAATCATTCTGTATAACTATTCCATCTAAACAA-TTCATATTACCATTTCAT
5936197 TTACACATTT
Statistics
Matches: 109, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
64 1 0.01
65 85 0.78
66 22 0.20
67 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (65 bp):
TTCATATAATCATTCTGTATAACTATTCCATCTAAACAATTCATATTACCATTTCATGTAATCAT
Found at i:5936779 original size:7 final size:7
Alignment explanation
Indices: 5936746--5936789 Score: 52
Period size: 7 Copynumber: 5.9 Consensus size: 7
5936736 AACTACTATA
5936746 TATCAAT
1 TATCAAT
5936753 TAATCCAAT
1 T-AT-CAAT
*
5936762 TCATCACT
1 T-ATCAAT
5936770 TATCAAT
1 TATCAAT
5936777 TATCAAT
1 TATCAAT
5936784 TATCAA
1 TATCAA
5936790 ACAAATGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 19 0.59
8 6 0.19
9 7 0.22
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (7 bp):
TATCAAT
Found at i:5940005 original size:27 final size:27
Alignment explanation
Indices: 5939975--5940029 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
5939965 CAATTTTGAG
5939975 ATGTTTTCCCCCATTGTTATGAACTAA
1 ATGTTTTCCCCCATTGTTATGAACTAA
*
5940002 ATGTTTTCCCCCATTTTTATGAACTAA
1 ATGTTTTCCCCCATTGTTATGAACTAA
5940029 A
1 A
5940030 ATCATTACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (27 bp):
ATGTTTTCCCCCATTGTTATGAACTAA
Found at i:5951334 original size:26 final size:24
Alignment explanation
Indices: 5951290--5951339 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
5951280 ATTTGTTTTA
*
5951290 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
5951314 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
5951340 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:5964162 original size:26 final size:26
Alignment explanation
Indices: 5964126--5964257 Score: 214
Period size: 26 Copynumber: 5.2 Consensus size: 26
5964116 TGAAATGCCC
5964126 ATCAT-GAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
5964151 ATCATGGAACATTTACCT-AACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
5964176 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
5964202 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
*
5964228 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
5964254 ATCA
1 ATCA
5964258 ATTTGTACCA
Statistics
Matches: 100, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
25 30 0.30
26 70 0.70
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:5964201 original size:51 final size:52
Alignment explanation
Indices: 5964126--5964257 Score: 232
Period size: 51 Copynumber: 2.6 Consensus size: 52
5964116 TGAAATGCCC
*
5964126 ATCAT-GAACATTTACCTAAACCATTATCATGGAACATTTACCTAA-CCATT
1 ATCATGGAACATTTACCTAACCCATTATCATGGAACATTTACCTAATCCATT
*
5964176 ATCATGGAACATTTACCTAACCCATTATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATTATCATGGAACATTTACCTAATCCATT
5964228 ATCATGGAACATTTACCTAACCCATTATCA
1 ATCATGGAACATTTACCTAACCCATTATCA
5964258 ATTTGTACCA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
50 5 0.06
51 38 0.49
52 35 0.45
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (52 bp):
ATCATGGAACATTTACCTAACCCATTATCATGGAACATTTACCTAATCCATT
Found at i:5971246 original size:26 final size:26
Alignment explanation
Indices: 5971215--5971322 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
5971205 TGAAATGCCC
*
5971215 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
5971241 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
5971267 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
5971293 ATTATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5971319 ATCA
1 ATCA
5971323 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:5977768 original size:67 final size:68
Alignment explanation
Indices: 5977660--5977793 Score: 234
Period size: 67 Copynumber: 2.0 Consensus size: 68
5977650 TATAGCATAT
* * *
5977660 TACATGTAATTGTTTGGTTAATCATGTCAATTTTAATAATAAAATTAGATGAA-TTTTTAGCATA
1 TACATGTAATTGCTTAGTTAATCATGTCAATTTTAATAATAAAATTAGATGAATTTTTTAACATA
5977724 AAG
66 AAG
5977727 TACATGTAATTGCTTAGTTAATCATGTCAATTTTAATAATAAAATTAGATGAATTTTTTAACATA
1 TACATGTAATTGCTTAGTTAATCATGTCAATTTTAATAATAAAATTAGATGAATTTTTTAACATA
5977792 AA
66 AA
5977794 ATATCAGTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
67 51 0.81
68 12 0.19
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (68 bp):
TACATGTAATTGCTTAGTTAATCATGTCAATTTTAATAATAAAATTAGATGAATTTTTTAACATA
AAG
Found at i:5983848 original size:24 final size:24
Alignment explanation
Indices: 5983821--5983880 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
5983811 ATTGTCACTA
5983821 TGAAATATCAAGTTCTTAGCTATT
1 TGAAATATCAAGTTCTTAGCTATT
5983845 TGAAATATCAAGTTCTTAGCTATT
1 TGAAATATCAAGTTCTTAGCTATT
*
5983869 TGAAGTAT-AAGT
1 TGAAATATCAAGT
5983881 GATGTATTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 4 0.11
24 31 0.89
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (24 bp):
TGAAATATCAAGTTCTTAGCTATT
Found at i:5990291 original size:20 final size:23
Alignment explanation
Indices: 5990266--5990314 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
5990256 ATATAAAATA
5990266 TTAAAATAA-ATA-AAT-ATTTT
1 TTAAAATAATATATAATGATTTT
*
5990286 TTAAAA-AATATATATTGATTTT
1 TTAAAATAATATATAATGATTTT
5990308 TTAAAAT
1 TTAAAAT
5990315 TATTTGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 2 0.08
20 9 0.38
21 2 0.08
22 11 0.46
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAAAATAATATATAATGATTTT
Found at i:5992967 original size:18 final size:19
Alignment explanation
Indices: 5992922--5992966 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
5992912 TTTACGAAAT
*
5992922 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
5992941 AATTCAAAAT-ATTTATAA
1 AATTCAAAATAATTTATAA
5992959 AATT-AAAA
1 AATTCAAAA
5992967 AAATCTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 4 0.16
18 11 0.44
19 10 0.40
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:5995459 original size:32 final size:32
Alignment explanation
Indices: 5995423--5995484 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
5995413 TTTGTATGTG
5995423 TATTTAAAATATTTCACATAT-AAACATAATGA
1 TATTTAAAATATTTCACATATGAAA-ATAATGA
*
5995455 TATTTAAAATATTTTACATATGAAAATAAT
1 TATTTAAAATATTTCACATATGAAAATAAT
5995485 AATTGTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (32 bp):
TATTTAAAATATTTCACATATGAAAATAATGA
Found at i:5995842 original size:95 final size:95
Alignment explanation
Indices: 5995673--5995844 Score: 210
Period size: 95 Copynumber: 1.8 Consensus size: 95
5995663 ATAATTATTA
* * ** *
5995673 ATTTATTTATATAAATAAAAGAGTTATTAATTTTAAATATCTTAAAATAATTATTTATATAATAT
1 ATTTATTTATATAAATAAAAGAGTTATTAATTTAAAATATATTAAAATAAAAATTTATATAACAT
*
5995738 ATATTTTTATTATATAATTACATATTTAAT
66 ATATATTTATTATATAATTACATATTTAAT
5995768 ATTTGATTT-TATAAATAAAAGAGTTATTAA-TTAAAATATGAATTAAAAATTAAAAATTTA-A-
1 ATTT-ATTTATATAAATAAAAGAGTTATTAATTTAAAATAT--ATT-AAAA-TAAAAATTTATAT
5995829 AACA-ATATATTTATTA
61 AACATATATATTTATTA
5995845 ATTAAAAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
94 8 0.12
95 36 0.55
96 9 0.14
97 5 0.08
98 8 0.12
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (95 bp):
ATTTATTTATATAAATAAAAGAGTTATTAATTTAAAATATATTAAAATAAAAATTTATATAACAT
ATATATTTATTATATAATTACATATTTAAT
Found at i:5997349 original size:108 final size:109
Alignment explanation
Indices: 5997151--5997353 Score: 311
Period size: 108 Copynumber: 1.9 Consensus size: 109
5997141 ATAAGGTCCT
* *
5997151 TCGGGGCGACACCTCAAGGAGGTTTAAGGTGTAAGACATAGCTCGACTTTGGCAACCAACAGAGT
1 TCGGGGCGACACCTCAAGGAGGTTTAAGGTGTAAGACATAGCTCGACTATGACAACCAACAGAGT
*
5997216 CCGCCAGGACATTAAACATGAGGTTATATTAAGCAAGACCATAG
66 CCACCAGGACATTAAACATGAGGTTATATTAAGCAAGACCATAG
* *
5997260 TCGGGG-GACACCTCAATGAGGTTTAAGGTGTCAA-ACATAGCTCGACTATGACAACCAACAGTG
1 TCGGGGCGACACCTCAAGGAGGTTTAAGGTGT-AAGACATAGCTCGACTATGACAACCAACAGAG
* * *
5997323 TCCACCAGGACCTTAAATATGGGGTTATATT
65 TCCACCAGGACATTAAACATGAGGTTATATT
5997354 GTTTAAGATC
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
108 77 0.91
109 8 0.09
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (109 bp):
TCGGGGCGACACCTCAAGGAGGTTTAAGGTGTAAGACATAGCTCGACTATGACAACCAACAGAGT
CCACCAGGACATTAAACATGAGGTTATATTAAGCAAGACCATAG
Found at i:5999141 original size:6 final size:6
Alignment explanation
Indices: 5999130--5999206 Score: 81
Period size: 6 Copynumber: 13.2 Consensus size: 6
5999120 ATGTTACAAG
* * *
5999130 GAAAAA GAAAAAA GGAAAA -AAAAG GAAAAA G-AAAA -AAAAT GAAAAA
1 GAAAAA G-AAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
5999176 TGAAAAA G-AAAA GAAAAA GAAAAA GAAAAA G
1 -GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G
5999207 CTGCAAATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
5 15 0.25
6 32 0.54
7 12 0.20
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:5999153 original size:17 final size:17
Alignment explanation
Indices: 5999131--5999193 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
5999121 TGTTACAAGG
5999131 AAAAAGAAAAAAGGAAA
1 AAAAAGAAAAAAGGAAA
*
5999148 AAAAAGGAAAAA-GAAA
1 AAAAAGAAAAAAGGAAA
* *
5999164 AAAAATGAAAAATGAAAA
1 AAAAA-GAAAAAAGGAAA
5999182 AGAAAAGAAAAA
1 A-AAAAGAAAAA
5999194 GAAAAAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
16 9 0.23
17 16 0.41
18 10 0.26
19 4 0.10
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAAAGGAAA
Found at i:5999155 original size:24 final size:23
Alignment explanation
Indices: 5999132--5999206 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 23
5999122 GTTACAAGGA
5999132 AAAAGAAAAAAGGAA-AAAAAAGGA
1 AAAAGAAAAAA--AATAAAAAAGGA
* *
5999156 AAAAGAAAAAAAATGAAAAATGA
1 AAAAGAAAAAAAATAAAAAAGGA
5999179 AAAAGAAAAGAAAA-AGAAAAA-GA
1 AAAAGAAAA-AAAATA-AAAAAGGA
5999202 AAAAG
1 AAAAG
5999207 CTGCAAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
22 2 0.04
23 23 0.51
24 20 0.44
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (23 bp):
AAAAGAAAAAAAATAAAAAAGGA
Found at i:6001906 original size:17 final size:19
Alignment explanation
Indices: 6001864--6001909 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
6001854 TAAATAGTTC
6001864 TTTAGATTTTATATAAATT
1 TTTAGATTTTATATAAATT
*
6001883 TTT--ATTTT-T-TAATTT
1 TTTAGATTTTATATAAATT
6001898 TTTAGATTTTAT
1 TTTAGATTTTAT
6001910 TCAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
15 8 0.35
16 1 0.04
17 10 0.43
18 1 0.04
19 3 0.13
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTAGATTTTATATAAATT
Found at i:6007789 original size:17 final size:18
Alignment explanation
Indices: 6007767--6007811 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
6007757 AGTTGTTGCT
6007767 GGTTTTGTTTTGTTTTG-
1 GGTTTTGTTTTGTTTTGA
* * *
6007784 GTTTTTTTTTTTTTTTGA
1 GGTTTTGTTTTGTTTTGA
6007802 GGTTTTGTTT
1 GGTTTTGTTT
6007812 AAGCATTAGC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.02, C:0.00, G:0.22, T:0.76
Consensus pattern (18 bp):
GGTTTTGTTTTGTTTTGA
Found at i:6022039 original size:7 final size:7
Alignment explanation
Indices: 6022029--6022053 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6022019 TCAATCCTAA
6022029 ATTCTCG
1 ATTCTCG
6022036 ATTCTCG
1 ATTCTCG
6022043 ATTCTCG
1 ATTCTCG
6022050 ATTC
1 ATTC
6022054 CCAAATCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.12, T:0.44
Consensus pattern (7 bp):
ATTCTCG
Found at i:6023488 original size:26 final size:28
Alignment explanation
Indices: 6023459--6023538 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
6023449 ATGATGCACA
*
6023459 AAAAAATTTAAAA-A-ATGATATATATG
1 AAAAAATTTAAAATAGATAATATATATG
*
6023485 AAAAATTTTAAAATAGATAATATATAT-
1 AAAAAATTTAAAATAGATAATATATATG
* * * *
6023512 ATAATAGTGTAAAATAAATAATATATA
1 A-AAAAATTTAAAATAGATAATATATA
6023539 AAAAACCTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 12 0.27
27 2 0.04
28 31 0.69
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (28 bp):
AAAAAATTTAAAATAGATAATATATATG
Found at i:6023880 original size:25 final size:25
Alignment explanation
Indices: 6023790--6023900 Score: 80
Period size: 26 Copynumber: 4.2 Consensus size: 25
6023780 AATAACGTAT
* * *
6023790 AAAAGCTTAAAATAAATAATATGTGGAA
1 AAAAACTTAAAATGAATAATATAT---A
*
6023818 AAAGAACTTTAAAATAAATAATATATA
1 AAA-AAC-TTAAAATGAATAATATATA
** **
6023845 AAAAGTTTTAACGTGAATAATATATA
1 AAAA-ACTTAAAATGAATAATATATA
6023871 AAAAACTTAAAATGAATAATA-ATA
1 AAAAACTTAAAATGAATAATATATA
6023895 ATAAAA
1 A-AAAA
6023901 TAGTTCTTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
24 4 0.06
25 17 0.25
26 21 0.31
27 4 0.06
28 3 0.04
29 2 0.03
30 17 0.25
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (25 bp):
AAAAACTTAAAATGAATAATATATA
Found at i:6028393 original size:20 final size:20
Alignment explanation
Indices: 6028356--6028393 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6028346 TGATGGGGAG
*
6028356 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
6028376 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
6028394 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:6030342 original size:46 final size:46
Alignment explanation
Indices: 6030290--6030471 Score: 240
Period size: 46 Copynumber: 4.0 Consensus size: 46
6030280 AGTGTGCTCT
* *
6030290 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
6030336 CTGATATGAAATGTGTAAGACCATGGTTGAAAGGTACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
** *
6030382 CTGATATGAAATGAACAAGATCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
6030428 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
6030472 TCATGTCAAA
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 1 0.01
46 119 0.99
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:6031284 original size:20 final size:20
Alignment explanation
Indices: 6031235--6031286 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
6031225 TGGGTAGGGG
** *
6031235 ACACGGGCGCATCCCGAAGC
1 ACACGGGCGTGTCCCCAAGC
6031255 ACACGGGCGTGTCCCCAAGC
1 ACACGGGCGTGTCCCCAAGC
6031275 ACACGGGCGTGT
1 ACACGGGCGTGT
6031287 GCTATGTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.21, C:0.37, G:0.33, T:0.10
Consensus pattern (20 bp):
ACACGGGCGTGTCCCCAAGC
Found at i:6035115 original size:68 final size:69
Alignment explanation
Indices: 6035040--6035174 Score: 175
Period size: 68 Copynumber: 2.0 Consensus size: 69
6035030 TACCAAAATA
* * *
6035040 TATAACTTTTATAAAATATAAGTACATAATTAG-ACC-AAAAATAATAAAAGTACCACATTAAAA
1 TATAACTTTTATAAAATATAAATAC-TAATTAGAACCAAAAAATAACAAAAATACCACATTAAAA
6035103 AAGTG
65 AAGTG
* * * *
6035108 TATAACTTTTATCAAATATAAATACTTATTTGAACCAAAAAAATAACAAAAATATCACATTAAAA
1 TATAACTTTTATAAAATATAAATACTAATTAGAACC-AAAAAATAACAAAAATACCACATTAAAA
6035173 AA
65 AA
6035175 TGTCAAACTC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
67 5 0.09
68 26 0.46
70 26 0.46
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (69 bp):
TATAACTTTTATAAAATATAAATACTAATTAGAACCAAAAAATAACAAAAATACCACATTAAAAA
AGTG
Found at i:6035729 original size:10 final size:10
Alignment explanation
Indices: 6035711--6035744 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
6035701 AATTTGTAAT
*
6035711 TTTTTTATAA
1 TTTTATATAA
6035721 TTTTATATAA
1 TTTTATATAA
6035731 TTTTATA-AA
1 TTTTATATAA
6035740 TTTTA
1 TTTTA
6035745 AATTGTTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTATATAA
Found at i:6045505 original size:26 final size:26
Alignment explanation
Indices: 6045469--6045520 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
6045459 GTGATGTAGG
6045469 AGTTTGATTGCATTTTACCTTCTCTA
1 AGTTTGATTGCATTTTACCTTCTCTA
6045495 AGTTTGATTGCATTTTACCTTCTCTA
1 AGTTTGATTGCATTTTACCTTCTCTA
6045521 CTTAGATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (26 bp):
AGTTTGATTGCATTTTACCTTCTCTA
Found at i:6047159 original size:17 final size:17
Alignment explanation
Indices: 6047105--6047160 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
6047095 TTCATAATTG
* *
6047105 TAATTATATTGTATTTA
1 TAATTATACTATATTTA
* * *
6047122 TAACTATACGATACTTA
1 TAATTATACTATATTTA
*
6047139 TAATTATACTATATTTG
1 TAATTATACTATATTTA
6047156 TAATT
1 TAATT
6047161 GCAAATCTTT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (17 bp):
TAATTATACTATATTTA
Found at i:6047836 original size:30 final size:30
Alignment explanation
Indices: 6047779--6047837 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
6047769 GTAGTAATTA
* *
6047779 GTACTTAAATTATACTTCATTACTTAAATG
1 GTACTTAAACTATACTACATTACTTAAATG
* *
6047809 GTACTTAAACTATACTACGTTATTTAAAT
1 GTACTTAAACTATACTACATTACTTAAAT
6047838 TATTCTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (30 bp):
GTACTTAAACTATACTACATTACTTAAATG
Found at i:6048373 original size:25 final size:24
Alignment explanation
Indices: 6048309--6048370 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
6048299 ATTGAAATAG
* *
6048309 TTTAATTT-ATTTACATTTTATTTT
1 TTTAATTTAATTTA-ATTCTATTCT
*
6048333 TTATAATTCAATTTAATTCTATTCT
1 TT-TAATTTAATTTAATTCTATTCT
6048358 TTTAATTTAATTT
1 TTTAATTTAATTT
6048371 TAACTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 12 0.38
25 15 0.47
26 5 0.16
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTAATTTAATTTAATTCTATTCT
Found at i:6052478 original size:40 final size:40
Alignment explanation
Indices: 6052413--6052621 Score: 220
Period size: 40 Copynumber: 5.2 Consensus size: 40
6052403 GGGCATGAAA
* * * ** *
6052413 GTGCATTCAGGCGTACCGAATTACAAACATCGGCACATAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
* * *
6052453 GTGCAATCAGGGGTACTGAAGTACAAATAGGGGCACATAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
* ** * * * *
6052493 GTGCAATTAGGACTACCAAAGTAAAAATAGGGGCATGTAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
* * * *
6052533 CTGTAATCAGGGGTACTGAAGTATAAACAGGGGCACGTAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
* *
6052573 GTGCAATTAGGGGTACCGAAGTACAAACAGGGACACGTAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
6052613 GTGCAATCA
1 GTGCAATCA
6052622 TACAATAAAT
Statistics
Matches: 137, Mismatches: 32, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 137 1.00
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (40 bp):
GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
Found at i:6052503 original size:20 final size:20
Alignment explanation
Indices: 6052444--6052503 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
6052434 TACAAACATC
*
6052444 GGCACATATGTGCAATCAGG
1 GGCACATATGTGCAATTAGG
* * * *
6052464 GGTAC-TGAAGTACAAATAGG
1 GGCACAT-ATGTGCAATTAGG
6052484 GGCACATATGTGCAATTAGG
1 GGCACATATGTGCAATTAGG
6052504 ACTACCAAAG
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (20 bp):
GGCACATATGTGCAATTAGG
Found at i:6052604 original size:20 final size:20
Alignment explanation
Indices: 6052540--6052604 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
6052530 TATCTGTAAT
* *
6052540 CAGGGGTACTGAAGTATAAA
1 CAGGGGTACCGAAGTACAAA
* * * *
6052560 CAGGGGCA-CGTATGTGCAAT
1 CAGGGGTACCG-AAGTACAAA
*
6052580 TAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
6052600 CAGGG
1 CAGGG
6052605 ACACGTATGT
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
19 1 0.03
20 28 0.90
21 2 0.06
ACGTcount: A:0.34, C:0.15, G:0.34, T:0.17
Consensus pattern (20 bp):
CAGGGGTACCGAAGTACAAA
Found at i:6059616 original size:40 final size:39
Alignment explanation
Indices: 6059572--6059776 Score: 153
Period size: 40 Copynumber: 5.1 Consensus size: 39
6059562 ATGTTTGTAT
*
6059572 AATCAAGAGTACCGAAGTACAAACATGGGAACATATGTGC
1 AATCAAGGGTACCGAAGTACAAACA-GGGAACATATGTGC
* * * ** *
6059612 AATC-AGTGGTACTGAAGTATAAACAGGGGCACGCATATGC
1 AATCAAG-GGTACCGAAGTACAAACA-GGGAACATATGTGC
* * * * * *
6059652 AATCAGGGGCACTGAAGTAGAAACA-GGAGCAGGTGTGTGC
1 AATCAAGGGTACCGAAGTACAAACAGGGAACA--TATGTGC
* *
6059692 AATCAAGGGAACCGAAGTACAAACAGGGACACGTATGTGC
1 AATCAAGGGTACCGAAGTACAAACAGGGA-ACATATGTGC
* * * * *
6059732 AACCAGGGGTATCGAAGTATAAATAGGGACACATATGTGC
1 AATCAAGGGTACCGAAGTACAAACAGGGA-ACATATGTGC
6059772 AATCA
1 AATCA
6059777 TACAATAATT
Statistics
Matches: 127, Mismatches: 32, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
38 3 0.02
39 2 0.02
40 117 0.92
41 4 0.03
42 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (39 bp):
AATCAAGGGTACCGAAGTACAAACAGGGAACATATGTGC
Found at i:6059656 original size:80 final size:78
Alignment explanation
Indices: 6059580--6059776 Score: 198
Period size: 80 Copynumber: 2.5 Consensus size: 78
6059570 ATAATCAAGA
* * * *
6059580 GTACCGAAGTACAAACATGGGAACATATGTGCAATCAGTGGTACTGAAGTATAAACAGGGGCACG
1 GTACCGAAGTACAAACA-GGGAACATATGTGCAATCAG-GGAACCGAAGTACAAACAGGGACACG
6059645 CATATGCAATCAGGG
64 CATATGCAATCAGGG
* * * * *
6059660 GCACTGAAGTAGAAACA-GGAGCAGGTGTGTGCAATCAAGGGAACCGAAGTACAAACAGGGACAC
1 GTACCGAAGTACAAACAGGGAACA--TATGTGCAATC-AGGGAACCGAAGTACAAACAGGGACAC
* * *
6059724 GTATGTGCAACCAGGG
63 GCATATGCAATCAGGG
* * *
6059740 GTATCGAAGTATAAATAGGGACACATATGTGCAATCA
1 GTACCGAAGTACAAACAGGGA-ACATATGTGCAATCA
6059777 TACAATAATT
Statistics
Matches: 93, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
78 5 0.05
79 1 0.01
80 80 0.86
81 5 0.05
82 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (78 bp):
GTACCGAAGTACAAACAGGGAACATATGTGCAATCAGGGAACCGAAGTACAAACAGGGACACGCA
TATGCAATCAGGG
Found at i:6059678 original size:20 final size:20
Alignment explanation
Indices: 6059622--6059678 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
6059612 AATCAGTGGT
*
6059622 ACTGAAGTATAAACAGGGGC
1 ACTGAAGTAGAAACAGGGGC
* *
6059642 AC-GCA-TATGCAATCAGGGGC
1 ACTGAAGTA-G-AAACAGGGGC
6059662 ACTGAAGTAGAAACAGG
1 ACTGAAGTAGAAACAGG
6059679 AGCAGGTGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
18 2 0.07
19 2 0.07
20 19 0.68
21 3 0.11
22 2 0.07
ACGTcount: A:0.39, C:0.18, G:0.30, T:0.14
Consensus pattern (20 bp):
ACTGAAGTAGAAACAGGGGC
Found at i:6061823 original size:18 final size:18
Alignment explanation
Indices: 6061785--6061828 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
6061775 TTTTTATTTT
6061785 TTAAATATTAATATAATTA
1 TTAAAT-TTAATATAATTA
*
6061804 TTTAATTTAATATTAA-TA
1 TTAAATTTAATA-TAATTA
6061822 TTAAATT
1 TTAAATT
6061829 ATTTTTAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTAAATTTAATATAATTA
Found at i:6065884 original size:33 final size:35
Alignment explanation
Indices: 6065847--6065917 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
6065837 ACTACTTTTT
* *
6065847 TGTCACTG-TACTGAGATGGGATAAGGCCCAA-AC
1 TGTCACTGATACTGAAAAGGGATAAGGCCCAAGAC
* *
6065880 TGTCACTGATACTGAAAAGGGCTTAGGCCCAAGAC
1 TGTCACTGATACTGAAAAGGGATAAGGCCCAAGAC
6065915 TGT
1 TGT
6065918 TCAACTGTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 8 0.25
34 19 0.59
35 5 0.16
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.23
Consensus pattern (35 bp):
TGTCACTGATACTGAAAAGGGATAAGGCCCAAGAC
Found at i:6082280 original size:37 final size:37
Alignment explanation
Indices: 6082212--6082304 Score: 100
Period size: 37 Copynumber: 2.4 Consensus size: 37
6082202 ATTCTAAAAA
*
6082212 TAATATTATTTTAATAGTTTAATATTAAATTTAAT-T
1 TAATATTATCTTAATAGTTTAATATTAAATTTAATAT
**
6082248 TAATACTTATCTTAATAGTTTTTTTATT-AATTTAATAT
1 TAATA-TTATCTTAATAG-TTTAATATTAAATTTAATAT
6082286 TAAAGTGATTATCTTAATA
1 T-AA-T-ATTATCTTAATA
6082305 TTAAATTTAG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
36 5 0.10
37 19 0.40
38 9 0.19
39 2 0.04
40 12 0.25
41 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (37 bp):
TAATATTATCTTAATAGTTTAATATTAAATTTAATAT
Found at i:6082469 original size:131 final size:126
Alignment explanation
Indices: 6082215--6082445 Score: 279
Period size: 131 Copynumber: 1.8 Consensus size: 126
6082205 CTAAAAATAA
* * ** * *
6082215 TATTATTTTAATAGTTTAATATTAAATTTAATTTAATACTTATCTTAATAGTTTTTTTATTAATT
1 TATTATTTTAATAGTTTAATATTAAATGTAATCTAATACTTATCTTAATAAATATTATATTAATT
* ** *
6082280 TAATATTAAAGTGATTATCTTAATATTAAATTTAGTTTAATGTTTATCTTGTAGATAAACATTT
66 TAATATTAAAGTGATTA---TAATATTAAATTTAGTTGAATGTTTATCTCCTACATAAACATTT
* *
6082344 TATTATTTTAATAAGTTTTAATATTAAATGTAATCTAATATTTATCTTGATAAATATTATATTAA
1 TATTATTTTAAT-AG-TTTAATATTAAATGTAATCTAATACTTATCTTAATAAATATTATATTAA
6082409 TTTAATATTAAAGTGATTA-AATA-T-AATTATAGTTGAA
64 TTTAATATTAAAGTGATTATAATATTAAATT-TAGTTGAA
6082446 CTTTCTAAAC
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
125 4 0.04
126 8 0.09
127 4 0.04
129 12 0.13
130 2 0.02
131 60 0.67
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.51
Consensus pattern (126 bp):
TATTATTTTAATAGTTTAATATTAAATGTAATCTAATACTTATCTTAATAAATATTATATTAATT
TAATATTAAAGTGATTATAATATTAAATTTAGTTGAATGTTTATCTCCTACATAAACATTT
Found at i:6093441 original size:17 final size:17
Alignment explanation
Indices: 6093409--6093442 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6093399 TTTTAAGCTT
*
6093409 TGTGGGCCATACGAGCC
1 TGTGGGCCACACGAGCC
*
6093426 TGTGGGCCACATGAGCC
1 TGTGGGCCACACGAGCC
6093443 GTAATATGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.29, G:0.35, T:0.18
Consensus pattern (17 bp):
TGTGGGCCACACGAGCC
Found at i:6095921 original size:17 final size:17
Alignment explanation
Indices: 6095879--6095925 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
6095869 TATCATTTAC
6095879 CATTTATCGGGCATTAT
1 CATTTATCGGGCATTAT
* *
6095896 TATTGATCGGGCACTT-T
1 CATTTATCGGGCA-TTAT
6095913 CATTTATCGGGCA
1 CATTTATCGGGCA
6095926 ATAACGAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 23 0.92
18 2 0.08
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (17 bp):
CATTTATCGGGCATTAT
Found at i:6105867 original size:40 final size:39
Alignment explanation
Indices: 6105791--6105885 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 39
6105781 CCATCTCCGA
* * *
6105791 CCAACCCAACACACC-ATGTGGGGATAGAATCGACCCAC
1 CCAACCCTACACACCAATATGGGGATAGAATCAACCCAC
* *
6105829 CCAACCCTACACACCAAGTATGGGGATATAATCAACCCAT
1 CCAACCCTACACACCAA-TATGGGGATAGAATCAACCCAC
6105869 CCAACCCTACACACCAA
1 CCAACCCTACACACCAA
6105886 AAGGTAACGT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
38 14 0.28
39 1 0.02
40 35 0.70
ACGTcount: A:0.37, C:0.38, G:0.13, T:0.13
Consensus pattern (39 bp):
CCAACCCTACACACCAATATGGGGATAGAATCAACCCAC
Found at i:6111589 original size:16 final size:16
Alignment explanation
Indices: 6111568--6111600 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6111558 TCCAATGATT
*
6111568 CCCTTAAATATCTCAG
1 CCCTTAAACATCTCAG
6111584 CCCTTAAACATCTCAG
1 CCCTTAAACATCTCAG
6111600 C
1 C
6111601 TCTATTCGAT
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:0.30, C:0.36, G:0.06, T:0.27
Consensus pattern (16 bp):
CCCTTAAACATCTCAG
Found at i:6122910 original size:3 final size:3
Alignment explanation
Indices: 6122902--6122937 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
6122892 TGGACAAACT
6122902 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6122938 CTTGTACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6124175 original size:24 final size:23
Alignment explanation
Indices: 6124108--6124175 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 23
6124098 TTTTAAATAT
* *
6124108 ATATAAAATATTGATAAATATCAA
1 ATATAAAATA-TAATAAATTTCAA
6124132 ATAATAAAAT-TAAATAAATTTCAA
1 AT-ATAAAATAT-AATAAATTTCAA
*
6124156 ATATAAAATAGTAATTAATT
1 ATATAAAATA-TAATAAATT
6124176 ATATAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 8 0.22
24 21 0.57
25 8 0.22
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (23 bp):
ATATAAAATATAATAAATTTCAA
Found at i:6130558 original size:19 final size:19
Alignment explanation
Indices: 6130534--6130573 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
6130524 TTTACTCACA
6130534 AACTATTCAAATTCAACTC
1 AACTATTCAAATTCAACTC
*
6130553 AACTATTCGAATTCAACTC
1 AACTATTCAAATTCAACTC
6130572 AA
1 AA
6130574 ATCATTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.30
Consensus pattern (19 bp):
AACTATTCAAATTCAACTC
Found at i:6131840 original size:3 final size:3
Alignment explanation
Indices: 6131834--6131859 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6131824 TATTAAAAAA
6131834 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
6131860 AATTGAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6133246 original size:42 final size:43
Alignment explanation
Indices: 6133187--6133273 Score: 167
Period size: 42 Copynumber: 2.0 Consensus size: 43
6133177 TATTTATCAC
6133187 TAGTTATTATTATTTTTTAATTCATTAATAAATTACCTAATTT
1 TAGTTATTATTATTTTTTAATTCATTAATAAATTACCTAATTT
6133230 TAGTTATTATT-TTTTTTAATTCATTAATAAATTACCTAATTT
1 TAGTTATTATTATTTTTTAATTCATTAATAAATTACCTAATTT
6133272 TA
1 TA
6133274 ATTTTAATTG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 33 0.75
43 11 0.25
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (43 bp):
TAGTTATTATTATTTTTTAATTCATTAATAAATTACCTAATTT
Found at i:6137933 original size:25 final size:26
Alignment explanation
Indices: 6137894--6137954 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 26
6137884 ATATAATTAG
6137894 AATATATATATTTAAAAAATTATAAA
1 AATATATATATTTAAAAAATTATAAA
* *
6137920 AATATAT-TATTTAATAAATTTTAAA
1 AATATATATATTTAAAAAATTATAAA
*
6137945 AATAAATATA
1 AATATATATA
6137955 GAAATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 22 0.71
26 9 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AATATATATATTTAAAAAATTATAAA
Found at i:6139420 original size:104 final size:104
Alignment explanation
Indices: 6139286--6139710 Score: 559
Period size: 104 Copynumber: 4.1 Consensus size: 104
6139276 GAATCTTAGT
* * * * *
6139286 AAAATCAACTATGAACGTAGGTTAGCGAGCTGTTAGGAGTTGCGGTATTAAATTAACGAACTCAA
1 AAAATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACTAACTCAA
* *
6139351 ATAATCGGAGGCTACAATCTTAAATCAGCTAGCCTTAAG
66 ATAATCGGAGGCTGCGATCTTAAATCAGCTAGCCTTAAG
* * * * * *
6139390 AAAATCAGCTATGAACGTAGGTCAGTGAGCTGTGAGGAGTTGCGATATTAAATTAGCTAACTCAA
1 AAAATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACTAACTCAA
*
6139455 ATAATCGGAGGCTGCGATCTTAAATCAGCTAGCCTT-TG
66 ATAATCGGAGGCTGCGATCTTAAATCAGCTAGCCTTAAG
* * *
6139493 TAACATCAACTGTGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACTAAATCA
1 -AAAATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACTAACTCA
* *
6139558 AACAATCGGAGGCTGCGATCTTAAATCACCTAG-CTTAA-
65 AATAATCGGAGGCTGCGATCTTAAATCAGCTAGCCTTAAG
* * * * * *
6139596 AACATTAACTATGAACGTAGGTCAGCGAGCTATTAAGAGTTACGATCTTAAATCAACCAACTCAA
1 AAAATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACTAACTCAA
* * *
6139661 ATAATCGAAGGCTGCGATCTTAAATTAGCTAGCCTTAAT
66 ATAATCGGAGGCTGCGATCTTAAATCAGCTAGCCTTAAG
*
6139700 AACATCAACTA
1 AAAATCAACTA
6139711 CAAGTTCAAA
Statistics
Matches: 283, Mismatches: 34, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
102 86 0.30
103 9 0.03
104 188 0.66
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (104 bp):
AAAATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACTAACTCAA
ATAATCGGAGGCTGCGATCTTAAATCAGCTAGCCTTAAG
Found at i:6139708 original size:206 final size:208
Alignment explanation
Indices: 6139280--6139710 Score: 596
Period size: 206 Copynumber: 2.1 Consensus size: 208
6139270 ATCAGTGAAT
* * * * *
6139280 CTTAGTAAAATCAACTATGAACGTAGGTTAGCGAGCTGTTAGGAGTTGCGGTATTAAATTAACGA
1 CTTAGTAACATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACGA
* * * *
6139345 ACTCAAATAATCGGAGGCTACAATCTTAAATCAGCTAGCCTTAAGAAAATCAGCTATGAACGTAG
66 AATCAAACAATCGGAGGCTACAATCTTAAATCACCTAGCCTTAAGAAAATCAACTATGAACGTAG
* * * * * * * *
6139410 GTCAGTGAGCTGTGAGGAGTTGCGATATTAAATTAGCTAACTCAAATAATCGGAGGCTGCGATCT
131 GTCAGCGAGCTATGAAGAGTTACGATATTAAATCAACCAACTCAAATAATCGAAGGCTGCGATCT
6139475 TAAATCAGCTAGC
196 TAAATCAGCTAGC
* * *
6139488 CTTTGTAACATCAACTGTGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACTA
1 CTTAGTAACATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACGA
* * * *
6139553 AATCAAACAATCGGAGGCTGCGATCTTAAATCACCTAG-CTTAA-AACATTAACTATGAACGTAG
66 AATCAAACAATCGGAGGCTACAATCTTAAATCACCTAGCCTTAAGAAAATCAACTATGAACGTAG
* *
6139616 GTCAGCGAGCTATTAAGAGTTACGATCTTAAATCAACCAACTCAAATAATCGAAGGCTGCGATCT
131 GTCAGCGAGCTATGAAGAGTTACGATATTAAATCAACCAACTCAAATAATCGAAGGCTGCGATCT
*
6139681 TAAATTAGCTAGC
196 TAAATCAGCTAGC
*
6139694 CTTAATAACATCAACTA
1 CTTAGTAACATCAACTA
6139711 CAAGTTCAAA
Statistics
Matches: 193, Mismatches: 30, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
206 98 0.51
207 5 0.03
208 90 0.47
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (208 bp):
CTTAGTAACATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACGA
AATCAAACAATCGGAGGCTACAATCTTAAATCACCTAGCCTTAAGAAAATCAACTATGAACGTAG
GTCAGCGAGCTATGAAGAGTTACGATATTAAATCAACCAACTCAAATAATCGAAGGCTGCGATCT
TAAATCAGCTAGC
Found at i:6141580 original size:31 final size:30
Alignment explanation
Indices: 6141545--6141617 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
6141535 ATAAAAGTGA
6141545 TATTTGAATTTCTCTATTT-TTCTTAGATTGG
1 TATTTGAATTTCTCT-TTTGTT-TTAGATTGG
*
6141576 TATTT-AAGGTTTTTCTTTTGTTTTAGATTGG
1 TATTTGAA--TTTCTCTTTTGTTTTAGATTGG
*
6141607 TACTTGAATTT
1 TATTTGAATTT
6141618 TTATTCATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
30 5 0.14
31 21 0.58
32 10 0.28
ACGTcount: A:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (30 bp):
TATTTGAATTTCTCTTTTGTTTTAGATTGG
Found at i:6141770 original size:15 final size:15
Alignment explanation
Indices: 6141752--6141780 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6141742 TAATTATCAT
6141752 AATTTAATTTTTTTA
1 AATTTAATTTTTTTA
6141767 AATTTAATTTTTTT
1 AATTTAATTTTTTT
6141781 GAAAAAAATC
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
AATTTAATTTTTTTA
Found at i:6148516 original size:6 final size:6
Alignment explanation
Indices: 6148505--6148575 Score: 92
Period size: 6 Copynumber: 11.7 Consensus size: 6
6148495 CCAATCTTTC
*
6148505 TTTTTA TTTTTA TTTTTA TTTTTA TTTATTA TTTTTC TTTTTA TTTATTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TTT-TTA
6148555 TTTATTA -TTTTA -TTTTA TTTT
1 TTT-TTA TTTTTA TTTTTA TTTT
6148576 AGTTAAATAT
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
5 8 0.13
6 36 0.60
7 16 0.27
ACGTcount: A:0.18, C:0.01, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:6148536 original size:19 final size:19
Alignment explanation
Indices: 6148505--6148569 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
6148495 CCAATCTTTC
6148505 TTTTTATTT-TTATTTTTA
1 TTTTTATTTATTATTTTTA
*
6148523 TTTTTATTTATTATTTTTC
1 TTTTTATTTATTATTTTTA
6148542 TTTTTATTTATTATTTATTA
1 TTTTTATTTATTATTT-TTA
6148562 -TTTTATTT
1 TTTTTATTT
6148570 TATTTTAGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
18 9 0.21
19 32 0.74
20 2 0.05
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTATTTATTATTTTTA
Found at i:6148555 original size:26 final size:25
Alignment explanation
Indices: 6148508--6148575 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
6148498 ATCTTTCTTT
6148508 TTATTTTTATTTTTATTTTTATTTA
1 TTATTTTTATTTTTATTTTTATTTA
*
6148533 TTATTTTTCTTTTTATTTATTATTTA
1 TTATTTTTATTTTTATTT-TTATTTA
6148559 TTA-TTTTA-TTTTATTTT
1 TTATTTTTATTTTTATTTT
6148576 AGTTAAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.03
24 8 0.20
25 21 0.52
26 10 0.25
ACGTcount: A:0.19, C:0.01, G:0.00, T:0.79
Consensus pattern (25 bp):
TTATTTTTATTTTTATTTTTATTTA
Found at i:6148707 original size:20 final size:20
Alignment explanation
Indices: 6148682--6148722 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
6148672 ATCCATGGTA
* *
6148682 CCAAACAGTTCTATTCCAGC
1 CCAAACAATCCTATTCCAGC
6148702 CCAAACAATCCTATTCCAGC
1 CCAAACAATCCTATTCCAGC
6148722 C
1 C
6148723 TAGAATCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.39, G:0.07, T:0.22
Consensus pattern (20 bp):
CCAAACAATCCTATTCCAGC
Found at i:6149706 original size:117 final size:118
Alignment explanation
Indices: 6149499--6149728 Score: 372
Period size: 117 Copynumber: 2.0 Consensus size: 118
6149489 TGTTTTCCAT
* * *
6149499 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGAGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGAGGAGGGTGCTTGGGTTGTCATT
6149564 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
**
6149617 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGG-GGAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGAGGAGGGTGCTTGGGTTGTCATT
****
6149681 CTACTTCGCGTCAAAAGGTTGTGTGACGTGTTGGGTAAAACTCCGCTA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTA
6149729 ACCGGAAATA
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
117 65 0.63
118 38 0.37
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGAGGAGGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:6150517 original size:26 final size:26
Alignment explanation
Indices: 6150457--6150517 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
6150447 ATTTTATTTT
6150457 ATTTATATTAGGATAATTAATATTAAG
1 ATTT-TATTAGGATAATTAATATTAAG
** * *
6150484 ATAATATTAGGATTATTTAAT-TTAGG
1 ATTTTATTAGGA-TAATTAATATTAAG
6150510 ATTTTATT
1 ATTTTATT
6150518 TTAATTATCT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.49
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:6153220 original size:45 final size:45
Alignment explanation
Indices: 6153138--6153267 Score: 134
Period size: 45 Copynumber: 2.9 Consensus size: 45
6153128 ACCAGGAGTG
* * * * * *
6153138 AGTAAGACCATAGCTGAAACATACTATGCCATAATGATGATAATA
1 AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAAAAATA
* * *
6153183 AGTAAGACCATAGCTGAAAGATGCTACGATATCATGATAAAAATG
1 AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAAAAATA
* * * * *
6153228 AGTAAGACAATAGTTGAAAGACGCTATGGCATAATGATAA
1 AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAA
6153268 GGGTGAGTAA
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (45 bp):
AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAAAAATA
Found at i:6154313 original size:17 final size:17
Alignment explanation
Indices: 6154291--6154334 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
6154281 TCTGATACCA
* *
6154291 ATGGCGGATACCTATCT
1 ATGGCGAATACCTATCC
6154308 ATGGCGAATACCTATCC
1 ATGGCGAATACCTATCC
6154325 ATGGCGAATA
1 ATGGCGAATA
6154335 GTTTTTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (17 bp):
ATGGCGAATACCTATCC
Found at i:6195586 original size:23 final size:23
Alignment explanation
Indices: 6195504--6195590 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
6195494 CCTGATCTGT
*
6195504 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
6195526 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
6195546 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
6195569 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
6195591 TCAGTAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:6197024 original size:16 final size:17
Alignment explanation
Indices: 6196989--6197024 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
6196979 CCTAATTCTC
6196989 CCTT-TTTCTTTTCTTT
1 CCTTCTTTCTTTTCTTT
6197005 -CTTCTTTC-TTTCTTT
1 CCTTCTTTCTTTTCTTT
6197020 CCTTC
1 CCTTC
6197025 CCCTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTTCTTTCTTTTCTTT
Found at i:6198958 original size:19 final size:19
Alignment explanation
Indices: 6198908--6198950 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
6198898 ACTTTATTTT
*
6198908 TAAATATGTAA-AAA-AAA
1 TAAATAAGTAATAAAGAAA
6198925 TAAATAAGTAATAAAGAAA
1 TAAATAAGTAATAAAGAAA
6198944 TAAATAA
1 TAAATAA
6198951 TTTGTAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.43
18 3 0.13
19 10 0.43
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (19 bp):
TAAATAAGTAATAAAGAAA
Found at i:6199380 original size:32 final size:31
Alignment explanation
Indices: 6199327--6199392 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
6199317 TACAATGACG
6199327 AAATAAAAGGATAAAAATAAAAA-AACAAAA
1 AAATAAAAGGATAAAAATAAAAAGAACAAAA
* * *
6199357 AAATGAAATAGGATCAAATTAAAAAGAACAAGA
1 AAAT-AAA-AGGATAAAAATAAAAAGAACAAAA
6199390 AAA
1 AAA
6199393 GCGGAAGGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 4 0.13
31 3 0.10
32 14 0.47
33 9 0.30
ACGTcount: A:0.73, C:0.05, G:0.11, T:0.12
Consensus pattern (31 bp):
AAATAAAAGGATAAAAATAAAAAGAACAAAA
Found at i:6201346 original size:29 final size:30
Alignment explanation
Indices: 6201284--6201357 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
6201274 ATGTTGGTGA
*
6201284 TATTTT-ATAGTTATTTAATTAGATTATTATT
1 TATTTTAATA-TT-TTTAATAAGATTATTATT
*
6201315 TA-TTTAATATTTTTAATAAGA-TATTTTAT
1 TATTTTAATATTTTTAATAAGATTATTAT-T
*
6201344 TATTTTATTATTTT
1 TATTTTAATATTTT
6201358 ATTTAGTCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 5 0.14
29 12 0.32
30 15 0.41
31 5 0.14
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (30 bp):
TATTTTAATATTTTTAATAAGATTATTATT
Found at i:6201349 original size:8 final size:8
Alignment explanation
Indices: 6201336--6201360 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6201326 TTTAATAAGA
6201336 TATTTTAT
1 TATTTTAT
6201344 TATTTTAT
1 TATTTTAT
6201352 TATTTTAT
1 TATTTTAT
6201360 T
1 T
6201361 TAGTCTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:6201821 original size:24 final size:21
Alignment explanation
Indices: 6201775--6201821 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
6201765 TTAATATGTT
6201775 AGTGAAGAGAAAATAAGAGAA
1 AGTGAAGAGAAAATAAGAGAA
*
6201796 AGTGATGAGAAATAGTATAGAGAA
1 AGTGAAGAGAAA-A-TA-AGAGAA
6201820 AG
1 AG
6201822 AACATAAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
22 1 0.05
23 2 0.09
24 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.30, T:0.15
Consensus pattern (21 bp):
AGTGAAGAGAAAATAAGAGAA
Found at i:6211683 original size:18 final size:16
Alignment explanation
Indices: 6211660--6211702 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
6211650 TGTCATTATT
*
6211660 CTTATTTTTTTCTCGTTG
1 CTTATTTTTTTCT--TTA
*
6211678 CTTATTTATTTCTTTA
1 CTTATTTTTTTCTTTA
6211694 CTTATTTTT
1 CTTATTTTT
6211703 ATACCTTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 10 0.45
18 12 0.55
ACGTcount: A:0.12, C:0.14, G:0.05, T:0.70
Consensus pattern (16 bp):
CTTATTTTTTTCTTTA
Found at i:6211779 original size:21 final size:21
Alignment explanation
Indices: 6211753--6211816 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
6211743 TTTTAATCAT
6211753 TTATTATTACTATTACTTTTA
1 TTATTATTACTATTACTTTTA
* * *
6211774 TTATTATTACTGTTTCTATTA
1 TTATTATTACTATTACTTTTA
* *
6211795 TTGTT-TTTCTATTACTATTTA
1 TTATTATTACTATTACT-TTTA
6211816 T
1 T
6211817 GTTATTGTTG
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 8 0.24
21 26 0.76
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.64
Consensus pattern (21 bp):
TTATTATTACTATTACTTTTA
Found at i:6211850 original size:3 final size:3
Alignment explanation
Indices: 6211837--6211972 Score: 86
Period size: 3 Copynumber: 45.7 Consensus size: 3
6211827 GCACTATTCT
*
6211837 TTA TT- TTA TTA TTA TTA TTA TTA TT- TTA TCA TTA CTT- TCTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA
* * * * * *
6211881 TTG TTA TTA TTA ATA -TA CTA TTA TTA TTC TTA TTAA CGTA TTA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A -TTA TTA TTA
* * * *
6211927 TTT TTA TTA TTA TTA TTT TCTA CT- TTA TTA TTA -TA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
6211971 TT
1 TT
6211973 GCTATCATCA
Statistics
Matches: 104, Mismatches: 18, Indels: 22
0.72 0.12 0.15
Matches are distributed among these distances:
2 10 0.10
3 87 0.84
4 6 0.06
5 1 0.01
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:6211862 original size:20 final size:20
Alignment explanation
Indices: 6211837--6211967 Score: 95
Period size: 23 Copynumber: 6.2 Consensus size: 20
6211827 GCACTATTCT
6211837 TTATTTTATTATTATTATTA
1 TTATTTTATTATTATTATTA
*
6211857 TTATTTTATCATTACTT-TCTA
1 TTATTTTATTATTA-TTAT-TA
*
6211878 TTATTGTTATTATTAATATACTA
1 TTATT-TTATTATT-AT-TATTA
* *
6211901 TTATTATTCTTATTAACGTATTA
1 TTATT-TTATTATT-A-TTATTA
* *
6211924 TTTTTTTTATTATTATTATTT
1 -TTATTTTATTATTATTATTA
*
6211945 TCTACTTTATTATTA-TATTA
1 T-TATTTTATTATTATTATTA
6211965 TTA
1 TTA
6211968 CTATTGCTAT
Statistics
Matches: 88, Mismatches: 14, Indels: 19
0.73 0.12 0.16
Matches are distributed among these distances:
19 2 0.02
20 20 0.23
21 24 0.27
22 9 0.10
23 29 0.33
24 4 0.05
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (20 bp):
TTATTTTATTATTATTATTA
Found at i:6212973 original size:35 final size:35
Alignment explanation
Indices: 6212934--6213004 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
6212924 AGGAGGGTGA
*
6212934 TGCTTTAAATTTTTGAGTGTTTTAAAAGTTTTTTT
1 TGCTTTAAATTTTTGAGTGTTCTAAAAGTTTTTTT
*
6212969 TGCTTTAAATTTTTGGGTGTTCTAAAAGTTTTTTT
1 TGCTTTAAATTTTTGAGTGTTCTAAAAGTTTTTTT
6213004 T
1 T
6213005 TAAGGTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.21, C:0.04, G:0.15, T:0.59
Consensus pattern (35 bp):
TGCTTTAAATTTTTGAGTGTTCTAAAAGTTTTTTT
Found at i:6217883 original size:21 final size:21
Alignment explanation
Indices: 6217859--6217903 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
6217849 GAGGGATCAA
*
6217859 ATGCTGGAGTCCCAGAAAAAC
1 ATGCTGGAGTCACAGAAAAAC
*
6217880 ATGCTGGAGTCACAGAACAAC
1 ATGCTGGAGTCACAGAAAAAC
6217901 ATG
1 ATG
6217904 ATGAGCCAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (21 bp):
ATGCTGGAGTCACAGAAAAAC
Found at i:6226765 original size:85 final size:85
Alignment explanation
Indices: 6225674--6226734 Score: 1468
Period size: 85 Copynumber: 12.5 Consensus size: 85
6225664 TCAGCAGGCT
* * *
6225674 TTAACTCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGTCGAGCAGTGGTG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGTAGTGGTG
** *
6225739 GAGCAGGTCGAAGACAGGCT
66 GAGCAGGTCGAAGACTTGCC
* * * * * * *** * * * *
6225759 TTAACCCCCTAATCAATAGGGTAACAAGAT-GAA-GTACAGATCTTATCTC-CCTAAGCAATAGT
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCC-GAGTAGTGGT
* ** **
6225821 GGAGCAGATTAAAGATACACGCC
65 GGAGCAGGTCGAAG--ACTTGCC
* * * *
6225844 TTAACTCCCTAAGCAGTAGGGCAATAGGCTAAAATTTACAGATATGGGCTCGCCGAGTAGTGGTG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGTAGTGGTG
6225909 GAGCAGGTCGAAGACTTGCC
66 GAGCAGGTCGAAGACTTGCC
* *
6225929 TTAACCCCCTAAGTAGTAAGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGTAGTGGTG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGTAGTGGTG
6225994 GAGCAGGTCGAAGACTTGCC
66 GAGCAGGTCGAAGACTTGCC
*
6226014 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTTGCCGAGTAGTGGTG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGTAGTGGTG
* * *
6226079 AAGCAGGTCGAAGACTCGTC
66 GAGCAGGTCGAAGACTTGCC
*
6226099 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGTCGAGTAGTGGTG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGTAGTGGTG
6226164 GAGCAGGTCGAAGACTTGCC
66 GAGCAGGTCGAAGACTTGCC
* * *
6226184 TTAACCCCTTAAGTAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGTAGTGGCG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGTAGTGGTG
*
6226249 GAGCAGGTCGAAGACTCGCC
66 GAGCAGGTCGAAGACTTGCC
* *
6226269 TTAACCCCCTAAGTAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGTGGTG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGTAGTGGTG
*
6226334 GAGCAAGTCGAAGACTTGCC
66 GAGCAGGTCGAAGACTTGCC
*
6226354 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAATAGTGGTG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGTAGTGGTG
*
6226419 GAGCAGGTCGAAGACTCGCC
66 GAGCAGGTCGAAGACTTGCC
*
6226439 TTAACCCCCTAAACAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGTAGTGGTG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGTAGTGGTG
6226504 GAGCAGGTCGAAGACTTGCC
66 GAGCAGGTCGAAGACTTGCC
* * ** *
6226524 TTAACCCCCTAAGTAGTAGGGTAACAGGCTAAAATTTACAGATCTAGGCTCGCCGAACAGTGGCG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGTAGTGGTG
*
6226589 GAGCAGGTCGAAGACTAGCC
66 GAGCAGGTCGAAGACTTGCC
* *** * * * * *
6226609 TTATCTTTACTAAGCAAGAATGG-AGCAGGCTAAAATTTACAGATCCT-GGCTCTCCGAGCAGTG
1 TTAAC-CCCCTAAGC-AGTAGGGTAACAGGCTAAAATTTACAGAT-CTGGGCTCGCCGAGTAGTG
*
6226672 GTGGAGCAGGTCGAAGACTCGCC
63 GTGGAGCAGGTCGAAGACTTGCC
*
6226695 TTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAA-TTACAG
1 TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAG
6226735 GTTTTAGCTT
Statistics
Matches: 863, Mismatches: 103, Indels: 21
0.87 0.10 0.02
Matches are distributed among these distances:
82 1 0.00
83 30 0.03
84 13 0.02
85 717 0.83
86 65 0.08
87 35 0.04
88 2 0.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (85 bp):
TTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGTAGTGGTG
GAGCAGGTCGAAGACTTGCC
Found at i:6227802 original size:22 final size:23
Alignment explanation
Indices: 6227777--6227835 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
6227767 CAACCAAATC
6227777 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
6227799 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
6227822 ACA-TCATCACATAT
1 A-ATTCAT-ACATAT
6227836 CTAAATCCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 6 0.19
23 18 0.58
24 7 0.23
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:6230609 original size:35 final size:34
Alignment explanation
Indices: 6230570--6230639 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 34
6230560 ATGAGGGTGA
*
6230570 TGCTTTAAATTTTTGAGTGTTTTAGAAATTTTTTT
1 TGCTTTAAATTTTTGAGTGTTCTA-AAATTTTTTT
* *
6230605 TGCTTTAAATTTTTGGGTGTTCTAAATTTTTTTT
1 TGCTTTAAATTTTTGAGTGTTCTAAAATTTTTTT
6230639 T
1 T
6230640 AAGGTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 10 0.31
35 22 0.69
ACGTcount: A:0.20, C:0.04, G:0.14, T:0.61
Consensus pattern (34 bp):
TGCTTTAAATTTTTGAGTGTTCTAAAATTTTTTT
Found at i:6233313 original size:130 final size:127
Alignment explanation
Indices: 6233154--6233464 Score: 387
Period size: 129 Copynumber: 2.4 Consensus size: 127
6233144 AAATTCGAGG
* * * * *
6233154 AATCGTGCCCTGTCGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAATGATCGAATATTCCTTTGG
1 AATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTC-AAATAATCGAATATTCCTTTAG
* *
6233219 AATTTCACACATGTTTTAAAAATTCTTTAAAACGAAGGGAACGTTCGAA-GTTTGGAAATTCG-G
65 AATTTCACACATGTTTTAAAAATTC--TAAAAC-AAGGCAACGTTC-AACGTTTGGAAATCCGAG
6233282 AA
126 AA
6233284 AATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTCAAATAATCGAATATTCCTTTAGA
1 AATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTCAAATAATCGAATATTCCTTTAGA
* ** * *
6233349 ATTTCACTCATGTTTTCTAAATTCTAAAACAAGGCAATGTTCAACGTTTGGGAATCCGAGAA
66 ATTTCACACATGTTTTAAAAATTCTAAAACAAGGCAACGTTCAACGTTTGGAAATCCGAGAA
* * * ** *
6233411 AA-CGTGCCCTA-CGTGCTGGGTTTCGATTTACCGTTTGACCAAACAATCGAATAT
1 AATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTCAAATAATCGAATAT
6233465 CATTTTAAAA
Statistics
Matches: 161, Mismatches: 18, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
125 39 0.24
126 30 0.19
127 11 0.07
129 42 0.26
130 39 0.24
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (127 bp):
AATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTCAAATAATCGAATATTCCTTTAGA
ATTTCACACATGTTTTAAAAATTCTAAAACAAGGCAACGTTCAACGTTTGGAAATCCGAGAA
Found at i:6241266 original size:17 final size:17
Alignment explanation
Indices: 6241244--6241280 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
6241234 TTAGAAAAAC
*
6241244 TATTCGCCATGGATAGG
1 TATTCGCCATAGATAGG
6241261 TATTCGCCATAGATAGG
1 TATTCGCCATAGATAGG
6241278 TAT
1 TAT
6241281 CCACCATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (17 bp):
TATTCGCCATAGATAGG
Found at i:6242361 original size:45 final size:45
Alignment explanation
Indices: 6242234--6242443 Score: 172
Period size: 45 Copynumber: 4.7 Consensus size: 45
6242224 CAAAGGATGT
* * *
6242234 CATAGTGTCTTTCAGCTATGGTCTTAGTC-TTATTTA-CTATGATGC
1 CATAGCGTCTTTCAGCTATGGTCTTACTCATT-TTTATC-ATGATAC
* * * *** *
6242279 CATAGCGTCTTTTAGCCATAGTCTTACTCACCCTTATCATTATAC
1 CATAGCGTCTTTCAGCTATGGTCTTACTCATTTTTATCATGATAC
* * *
6242324 CATAGCGTCTTTCAACTATTGTCTTACTCATTTTTATCATGATAT
1 CATAGCGTCTTTCAGCTATGGTCTTACTCATTTTTATCATGATAC
* * * * * * **
6242369 CGTAGCATCTTTCAGCTATGGTCTTACTTATTATCATCATTATGG
1 CATAGCGTCTTTCAGCTATGGTCTTACTCATTTTTATCATGATAC
** *
6242414 CATAGTATGTTTCAGCTATGGTCTTACTCA
1 CATAGCGTCTTTCAGCTATGGTCTTACTCA
6242444 CTCCTGGTGT
Statistics
Matches: 130, Mismatches: 33, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
45 129 0.99
46 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.42
Consensus pattern (45 bp):
CATAGCGTCTTTCAGCTATGGTCTTACTCATTTTTATCATGATAC
Found at i:6245063 original size:10 final size:10
Alignment explanation
Indices: 6245048--6245079 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
6245038 TAAATACATT
6245048 TAATTAAAGA
1 TAATTAAAGA
6245058 TAATTAAAGA
1 TAATTAAAGA
6245068 TAATTAAA-A
1 TAATTAAAGA
6245077 TAA
1 TAA
6245080 AATCCTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (10 bp):
TAATTAAAGA
Found at i:6248403 original size:29 final size:29
Alignment explanation
Indices: 6248362--6248426 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
6248352 AAACATTTGA
*
6248362 AAAATGAGGTTGAGAATTTGTTTAATAAG
1 AAAATCAGGTTGAGAATTTGTTTAATAAG
6248391 AAAATCAGGTTGAGAATTTGTTTAATAAG
1 AAAATCAGGTTGAGAATTTGTTTAATAAG
6248420 AAAATCA
1 AAAATCA
6248427 AAGTGTTTCG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.32
Consensus pattern (29 bp):
AAAATCAGGTTGAGAATTTGTTTAATAAG
Found at i:6251733 original size:20 final size:20
Alignment explanation
Indices: 6251697--6251736 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6251687 TAATTTTCCT
*
6251697 TTTCTTTCTTTTCTCGTTTC
1 TTTCTTTCTATTCTCGTTTC
6251717 TTTCTTTCCTATT-TCGTTTC
1 TTTCTTT-CTATTCTCGTTTC
6251737 ACTCTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.03, C:0.25, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTCTTTCTATTCTCGTTTC
Found at i:6253811 original size:11 final size:11
Alignment explanation
Indices: 6253791--6253833 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
6253781 TAGAATATAC
*
6253791 CCCATTCCTTG
1 CCCATACCTTG
6253802 CCCATACCTTG
1 CCCATACCTTG
*
6253813 CCCATACC-TA
1 CCCATACCTTG
6253823 CCCATACCTTG
1 CCCATACCTTG
6253834 GAAAGATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.19, C:0.47, G:0.07, T:0.28
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:6254411 original size:18 final size:18
Alignment explanation
Indices: 6254370--6254444 Score: 105
Period size: 18 Copynumber: 4.2 Consensus size: 18
6254360 ACCATTTATG
*
6254370 GTACTATTCACGTATTCA
1 GTACTATTCACGTATACA
** *
6254388 AAACTATTCACGTATACG
1 GTACTATTCACGTATACA
6254406 GTACTATTCACGTATACA
1 GTACTATTCACGTATACA
*
6254424 GTACTGTTCACGTATACA
1 GTACTATTCACGTATACA
6254442 GTA
1 GTA
6254445 GTTGGGATTG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.33
Consensus pattern (18 bp):
GTACTATTCACGTATACA
Found at i:6258510 original size:11 final size:11
Alignment explanation
Indices: 6258490--6258543 Score: 74
Period size: 11 Copynumber: 5.0 Consensus size: 11
6258480 TAGAATATAC
*
6258490 CCCATTCCTTG
1 CCCATACCTTG
6258501 CCCATACCTTG
1 CCCATACCTTG
*
6258512 CCCATACCTTT
1 CCCATACCTTG
*
6258523 CCCATACC-TA
1 CCCATACCTTG
6258533 CCCATACCTTG
1 CCCATACCTTG
6258544 GAAAGGTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
10 9 0.24
11 29 0.76
ACGTcount: A:0.19, C:0.46, G:0.06, T:0.30
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:6259734 original size:35 final size:35
Alignment explanation
Indices: 6259687--6259756 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
6259677 AGAAAAAAAA
* * *
6259687 ATTGCCTTAGACGTGTTTATCTCAACCTTTTAAAG
1 ATTGCCTCAGACGAGTTTATCCCAACCTTTTAAAG
6259722 ATTGCCTCAGACGAGTTTATCCCAACCTTTTAAAG
1 ATTGCCTCAGACGAGTTTATCCCAACCTTTTAAAG
6259757 GTTCCTTAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (35 bp):
ATTGCCTCAGACGAGTTTATCCCAACCTTTTAAAG
Found at i:6261194 original size:3 final size:3
Alignment explanation
Indices: 6261186--6261253 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
6261176 CTTATAACGT
6261186 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
6261234 TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TA
6261254 CGTTTCTATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:6264046 original size:43 final size:43
Alignment explanation
Indices: 6263983--6264078 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
6263973 AGAGGTCAAG
* * * * *
6263983 CGCCTGTGTAAAGAGGGGCACACGGTCGTGTGGCTGAGGCACA
1 CGCCCGTGTGAAGAGAGGCACACGGCCGTGTGACTGAGGCACA
* **
6264026 CGCTCGTGTGAAGAGAGGCACTTGGCCGTGTGACTGAGGCACA
1 CGCCCGTGTGAAGAGAGGCACACGGCCGTGTGACTGAGGCACA
*
6264069 TGCCCGTGTG
1 CGCCCGTGTG
6264079 GACCAAGAAC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.19, C:0.24, G:0.39, T:0.19
Consensus pattern (43 bp):
CGCCCGTGTGAAGAGAGGCACACGGCCGTGTGACTGAGGCACA
Found at i:6264218 original size:21 final size:21
Alignment explanation
Indices: 6264179--6264218 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6264169 TCTCATACGC
** *
6264179 CTGTGTGCCCATCAGACACGA
1 CTGTGTGCCCAAAACACACGA
6264200 CTGTGTGCCCAAAACACAC
1 CTGTGTGCCCAAAACACAC
6264219 ACCTATGTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.17
Consensus pattern (21 bp):
CTGTGTGCCCAAAACACACGA
Found at i:6264854 original size:18 final size:19
Alignment explanation
Indices: 6264831--6264866 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6264821 TTCAAAAATA
*
6264831 AAAAT-AAAGAAATAAAAC
1 AAAATAAAAAAAATAAAAC
6264849 AAAATAAAAAAAATAAAA
1 AAAATAAAAAAAATAAAA
6264867 ATCCATCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (19 bp):
AAAATAAAAAAAATAAAAC
Found at i:6264863 original size:9 final size:9
Alignment explanation
Indices: 6264830--6264867 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
6264820 CTTCAAAAAT
6264830 AAAAAT-AA
1 AAAAATAAA
*
6264838 AGAAATAAA
1 AAAAATAAA
6264847 ACAAAATAAA
1 A-AAAATAAA
6264857 AAAAATAAA
1 AAAAATAAA
6264866 AA
1 AA
6264868 TCCATCCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 5 0.19
9 13 0.50
10 8 0.31
ACGTcount: A:0.84, C:0.03, G:0.03, T:0.11
Consensus pattern (9 bp):
AAAAATAAA
Found at i:6266075 original size:40 final size:40
Alignment explanation
Indices: 6266020--6266106 Score: 174
Period size: 40 Copynumber: 2.2 Consensus size: 40
6266010 AGTATATGAA
6266020 CATAAAATAACAACATATGAGTATTTGCACAATTTCAATC
1 CATAAAATAACAACATATGAGTATTTGCACAATTTCAATC
6266060 CATAAAATAACAACATATGAGTATTTGCACAATTTCAATC
1 CATAAAATAACAACATATGAGTATTTGCACAATTTCAATC
6266100 CATAAAA
1 CATAAAA
6266107 CATTCCATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.29
Consensus pattern (40 bp):
CATAAAATAACAACATATGAGTATTTGCACAATTTCAATC
Found at i:6266449 original size:405 final size:405
Alignment explanation
Indices: 6265698--6266471 Score: 1404
Period size: 405 Copynumber: 1.9 Consensus size: 405
6265688 TTATCCAACC
6265698 AAAACATGCCACAATTGCAAATTAACATCACATATCATAAGCCTTACACAACTATAAGTTCAAAC
1 AAAACATGCCACAATTGCAAATTAACATCACATATCATAAGCCTTACACAACTATAAGTTCAAAC
**
6265763 ACAAATTAGCCAAATCATGTGGCTAAATATATACATCACAAAACATACTCCACAACAACTAGCCT
66 ACAAATTAGCCAAATCACATGGCTAAATATATACATCACAAAACATACTCCACAACAACTAGCCT
6265828 ATACATGCCATACTTCAAATATATATACATTTCCAAAAGTACCAAAAATGAGGTTCAATAGTGTG
131 ATACATGCCATACTTCAAATATATATACATTTCCAAAAGTACCAAAAATGAGGTTCAATAGTGTG
* *
6265893 GCGACAATCCTTGACGATCCTCGAGCTTGGTAGCTTCGATATCTACAAAAACAATTCAAACACAC
196 GCGACAATCCTTGACAATCCCCGAGCTTGGTAGCTTCGATATCTACAAAAACAATTCAAACACAC
6265958 ACACAAAGTAAGCTTTCAAAAAGCTTAGTAAGCTCGTACTCAAATCATCAATAGTATATGAACAT
261 ACACAAAGTAAGCTTTCAAAAAGCTTAGTAAGCTCGTACTCAAATCATCAATAGTATATGAACAT
6266023 AAAATAACAACATATGAGTATTTGCACAATTTCAATCCATAAAATAACAACATATGAGTATTTGC
326 AAAATAACAACATATGAGTATTTGCACAATTTCAATCCATAAAATAACAACATATGAGTATTTGC
6266088 ACAATTTCAATCCAT
391 ACAATTTCAATCCAT
* * * *
6266103 AAAACATTCCATAATTGTAAATTAACATCACATATCATAAGCCTTTCACAACTATAAGTTCAAAC
1 AAAACATGCCACAATTGCAAATTAACATCACATATCATAAGCCTTACACAACTATAAGTTCAAAC
*
6266168 ACAAATTAGCCAAATCACATGGCTAAATATATACATCACAAAACATACTCCACAACTACTAGCCT
66 ACAAATTAGCCAAATCACATGGCTAAATATATACATCACAAAACATACTCCACAACAACTAGCCT
*
6266233 ATACATGCCATACTTCAAATATATATACATTTCCAAAAGTACCAAAAATGAGGTTCGATAGTGTG
131 ATACATGCCATACTTCAAATATATATACATTTCCAAAAGTACCAAAAATGAGGTTCAATAGTGTG
** * *
6266298 GCGACAATCCTTGACAATCCCCGAGCTTGGTAGCTTCGATATCTGTAAAAATAATTCAAACATAC
196 GCGACAATCCTTGACAATCCCCGAGCTTGGTAGCTTCGATATCTACAAAAACAATTCAAACACAC
*
6266363 ACACAAAGTAAGCTTTCAAAAAGCTTAGTAAGCTCGTACTCAAATCATTAATAGTATATGAACAT
261 ACACAAAGTAAGCTTTCAAAAAGCTTAGTAAGCTCGTACTCAAATCATCAATAGTATATGAACAT
*
6266428 AAAATAACAACATATGAGTATTTGTACAATTTCAATCCATAAAA
326 AAAATAACAACATATGAGTATTTGCACAATTTCAATCCATAAAA
6266472 CCATATCAAC
Statistics
Matches: 353, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
405 353 1.00
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.26
Consensus pattern (405 bp):
AAAACATGCCACAATTGCAAATTAACATCACATATCATAAGCCTTACACAACTATAAGTTCAAAC
ACAAATTAGCCAAATCACATGGCTAAATATATACATCACAAAACATACTCCACAACAACTAGCCT
ATACATGCCATACTTCAAATATATATACATTTCCAAAAGTACCAAAAATGAGGTTCAATAGTGTG
GCGACAATCCTTGACAATCCCCGAGCTTGGTAGCTTCGATATCTACAAAAACAATTCAAACACAC
ACACAAAGTAAGCTTTCAAAAAGCTTAGTAAGCTCGTACTCAAATCATCAATAGTATATGAACAT
AAAATAACAACATATGAGTATTTGCACAATTTCAATCCATAAAATAACAACATATGAGTATTTGC
ACAATTTCAATCCAT
Found at i:6274046 original size:30 final size:29
Alignment explanation
Indices: 6274003--6274063 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
6273993 CAAGTAGCCG
6274003 AAGCTAGTTAAATCACACACTTAGTGCCA
1 AAGCTAGTTAAATCACACACTTAGTGCCA
*
6274032 AAGCTAGTTTAAATCTCACACTTAGTGCCA
1 AAGCTAG-TTAAATCACACACTTAGTGCCA
6274062 AA
1 AA
6274064 ACTTCTGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (29 bp):
AAGCTAGTTAAATCACACACTTAGTGCCA
Found at i:6276881 original size:6 final size:6
Alignment explanation
Indices: 6276870--6276894 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6276860 TCCTCCTTTT
6276870 TTTCTC TTTCTC TTTCTC TTTCTC T
1 TTTCTC TTTCTC TTTCTC TTTCTC T
6276895 CCTTTTATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCTC
Found at i:6276933 original size:11 final size:11
Alignment explanation
Indices: 6276913--6276956 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
6276903 ACTAGCTATT
6276913 TATT-ATAAAA
1 TATTAATAAAA
6276923 TATTAATAAAA
1 TATTAATAAAA
*
6276934 TATCTTATTAAAA
1 TA--TTAATAAAA
6276947 TATTAATAAA
1 TATTAATAAA
6276957 GTAATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 4 0.14
11 15 0.52
13 10 0.34
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
TATTAATAAAA
Found at i:6280371 original size:12 final size:13
Alignment explanation
Indices: 6280349--6280383 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
6280339 CAATTCAAAT
6280349 ATTATAATAAAAA
1 ATTATAATAAAAA
*
6280362 ATTA-AATAAATA
1 ATTATAATAAAAA
6280374 ATTATAATAA
1 ATTATAATAA
6280384 TTTTTTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATTATAATAAAAA
Found at i:6281977 original size:4 final size:4
Alignment explanation
Indices: 6281968--6281994 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
6281958 GGTATACAAT
6281968 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
6281995 TTCTTTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:6290079 original size:28 final size:28
Alignment explanation
Indices: 6290029--6290108 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 28
6290019 TGCATCTTCG
* * *
6290029 ATATCTCGTACACTAACTACCATACTCA
1 ATATCTCGCACACTAAGTGCCATACTCA
* * *
6290057 ATATCTCGCACACCAAGTGCCATTCTTA
1 ATATCTCGCACACTAAGTGCCATACTCA
* **
6290085 ATATTTTTCACACTAAGTGCCATA
1 ATATCTCGCACACTAAGTGCCATA
6290109 TACATATATA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (28 bp):
ATATCTCGCACACTAAGTGCCATACTCA
Found at i:6290166 original size:40 final size:40
Alignment explanation
Indices: 6290111--6290193 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
6290101 GTGCCATATA
*
6290111 CATATATAGCCGAAGCTATCTCC-AATCGCACACCAAGTGC
1 CATATATAGCCGAAGCTAT-TCCGAACCGCACACCAAGTGC
* *
6290151 CATATTTAGCCGAAGCTATTCCGAACCGCACACTAAGTGC
1 CATATATAGCCGAAGCTATTCCGAACCGCACACCAAGTGC
6290191 CAT
1 CAT
6290194 TTTTTTTAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
39 3 0.08
40 36 0.92
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (40 bp):
CATATATAGCCGAAGCTATTCCGAACCGCACACCAAGTGC
Found at i:6294804 original size:41 final size:41
Alignment explanation
Indices: 6294739--6294924 Score: 169
Period size: 41 Copynumber: 4.3 Consensus size: 41
6294729 ACATAAAATT
* * *
6294739 TGCTAGGC-ATAAAGCCTAGA-ATAATATACCGGTACAAAGCC
1 TGCTAGGCAAT-AAGCCT-GATATAATACACCGGCATAAAGCC
* *
6294780 TGCTAGGCAATAGGCCTGATATAATACATCGGCATAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCATAAAGCC
*
6294821 TGCTAGGTAATAAGCCTGATATAATACACCGGCATAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCATAAAGCC
** * *
6294862 TGATACAATACACCAGCATAGGGCCTGATACAATACACCGGCATAAAGCC
1 TG---C--TA-GGCA--ATA-AGCCTGATATAATACACCGGCATAAAGCC
6294912 TGCTAGGCAATAA
1 TGCTAGGCAATAA
6294925 AGCCCGAATA
Statistics
Matches: 118, Mismatches: 16, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
40 2 0.02
41 70 0.59
42 5 0.04
44 3 0.03
45 2 0.02
46 2 0.02
47 2 0.02
49 3 0.03
50 29 0.25
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (41 bp):
TGCTAGGCAATAAGCCTGATATAATACACCGGCATAAAGCC
Found at i:6294860 original size:25 final size:25
Alignment explanation
Indices: 6294832--6294913 Score: 128
Period size: 25 Copynumber: 3.3 Consensus size: 25
6294822 GCTAGGTAAT
*
6294832 AAGCCTGATATAATACACCGGCATA
1 AAGCCTGATACAATACACCGGCATA
*
6294857 AAGCCTGATACAATACACCAGCATA
1 AAGCCTGATACAATACACCGGCATA
**
6294882 GGGCCTGATACAATACACCGGCATA
1 AAGCCTGATACAATACACCGGCATA
6294907 AAGCCTG
1 AAGCCTG
6294914 CTAGGCAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.17
Consensus pattern (25 bp):
AAGCCTGATACAATACACCGGCATA
Found at i:6299255 original size:48 final size:45
Alignment explanation
Indices: 6299193--6299408 Score: 142
Period size: 46 Copynumber: 4.7 Consensus size: 45
6299183 CATATCCATA
* * *
6299193 CCGATGCCATGTCCCAGGCATTATCTTACACTGACACCTCTATACGT-G
1 CCGATGCCATGTCCCA-GAATGATCTTACACTGACACATC--T-CGTAG
*
6299241 CCGATGCCATGTCCCAGAATGGTCTTACACTGACACATCTCGTAG
1 CCGATGCCATGTCCCAGAATGATCTTACACTGACACATCTCGTAG
* *
6299286 CCGATG-CATGTCCCTA-ACATG-TCTTACACAGGCTTACATCTCG-AGG
1 CCGATGCCATGTCCC-AGA-ATGATCTTACACTGAC--ACATCTCGTA-G
** * * **
6299332 TTGATG-CATGTCCCAGACATG-TCTTACACTAGCTCTCATCTCAAAG
1 CCGATGCCATGTCCCAGA-ATGATCTTACACT-G-ACACATCTCGTAG
*
6299378 TCGATGCCATGTCCCAGACATG-TCTTACACT
1 CCGATGCCATGTCCCAGA-ATGATCTTACACT
6299409 AGCACACAAA
Statistics
Matches: 144, Mismatches: 13, Indels: 23
0.80 0.07 0.13
Matches are distributed among these distances:
44 22 0.15
45 14 0.10
46 46 0.32
47 45 0.31
48 17 0.12
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (45 bp):
CCGATGCCATGTCCCAGAATGATCTTACACTGACACATCTCGTAG
Found at i:6299406 original size:47 final size:46
Alignment explanation
Indices: 6299242--6299411 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
6299232 CTATACGTGC
* * * *
6299242 CGATGCCATGTCCCAGA-ATGGTCTTACACT-G-ACACATCTCGTAGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTCGAAGT
*
6299287 CGATGCATGTCCCTA-ACATGTCTTACAC-AGGCT-TACATCTCGAGGT
1 CGATGCATGTCCC-AGACATGTCTTACACTA-GCTCT-CATCTCGAAGT
* *
6299333 TGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAAAGT
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCGAAGT
6299379 CGATGCCATGTCCCAGACATGTCTTACACTAGC
1 CGATG-CATGTCCCAGACATGTCTTACACTAGC
6299412 ACACAAATAA
Statistics
Matches: 106, Mismatches: 9, Indels: 18
0.80 0.07 0.14
Matches are distributed among these distances:
44 18 0.17
45 10 0.09
46 49 0.46
47 29 0.27
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCGAAGT
Found at i:6300632 original size:18 final size:18
Alignment explanation
Indices: 6300609--6300646 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
6300599 CTATTGTGAG
6300609 AAATGTTTAGGACCAATT
1 AAATGTTTAGGACCAATT
6300627 AAATGTTTAGGACCAATT
1 AAATGTTTAGGACCAATT
6300645 AA
1 AA
6300647 TTCAGTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (18 bp):
AAATGTTTAGGACCAATT
Found at i:6302185 original size:44 final size:44
Alignment explanation
Indices: 6302122--6302209 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
6302112 ATGAAATAAA
*
6302122 GCTCTCATATACATCTAGATGACATGAGTTAAAATCGTGTCATC
1 GCTCTCATAGACATCTAGATGACATGAGTTAAAATCGTGTCATC
6302166 GCTCTCATAGACATCTAGATGACATGAGTTAAAATCGTGTCATC
1 GCTCTCATAGACATCTAGATGACATGAGTTAAAATCGTGTCATC
6302210 TCACCTATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (44 bp):
GCTCTCATAGACATCTAGATGACATGAGTTAAAATCGTGTCATC
Found at i:6306326 original size:20 final size:21
Alignment explanation
Indices: 6306274--6306326 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 21
6306264 ATATACAATA
*
6306274 TTCTATT-TCTTATTACTGCC
1 TTCTATTCTCTTTTTACTGCC
*
6306294 TT-TATTGCT-TTTTTCCTG-C
1 TTCTATT-CTCTTTTTACTGCC
6306313 TTCTATTCTCTTTT
1 TTCTATTCTCTTTT
6306327 AACTTTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
19 9 0.33
20 17 0.63
21 1 0.04
ACGTcount: A:0.09, C:0.23, G:0.06, T:0.62
Consensus pattern (21 bp):
TTCTATTCTCTTTTTACTGCC
Found at i:6317250 original size:19 final size:19
Alignment explanation
Indices: 6317226--6317263 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
6317216 ATTATCTATC
*
6317226 CAAATTTACTTTAATTATA
1 CAAATTTACCTTAATTATA
6317245 CAAATTTACCTTAATTATA
1 CAAATTTACCTTAATTATA
6317264 AAAAGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (19 bp):
CAAATTTACCTTAATTATA
Found at i:6319887 original size:20 final size:20
Alignment explanation
Indices: 6319864--6319910 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
6319854 TTTTTTATAA
6319864 TTTTTAATATTTT-CTAATAC
1 TTTTTAATATTTTCCTAA-AC
* *
6319884 TTTTT-TTATTTTCCTAAAT
1 TTTTTAATATTTTCCTAAAC
6319903 TTTTTAAT
1 TTTTTAAT
6319911 CAATTTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTAATATTTTCCTAAAC
Done.