Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 15 of 150
Found at i:4069346 original size:24 final size:23
Alignment explanation
Indices: 4069303--4069347 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
4069293 TTGGTGTGAC
*
4069303 TTAAAAAAACGTAAATTTAAAAG
1 TTAAAAAAACGTAAAATTAAAAG
4069326 TTAAAAAAA-GTGAAAAATTAAA
1 TTAAAAAAACGT--AAAATTAAA
4069348 CCGAGGACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 9 0.47
24 8 0.42
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.24
Consensus pattern (23 bp):
TTAAAAAAACGTAAAATTAAAAG
Found at i:4073277 original size:98 final size:95
Alignment explanation
Indices: 4073175--4073363 Score: 243
Period size: 95 Copynumber: 2.0 Consensus size: 95
4073165 ATTCATCCAT
* ** * *
4073175 TGATCTCTAATTTGATCCCTCAAACTATTTTTCATAATTTTCATTGTAAAAAAACTACTCTTTCC
1 TGATCTCCAATTCAATCCCTC-AACTATTCTTCATAATTTTAATTG--AAAAAACTACTCTTTCC
*
4073240 ACATTTGATGTAACAACTAGCAAAGTCAACCAC
63 ACATTTGATGTAACAACTAGCAAAATCAACCAC
* * * * *
4073273 TGATCTCCAATTCAATTCCTCAATTATTCTTCATGATTTTAATTGCAAAAAGTACTCTTTCCACA
1 TGATCTCCAATTCAATCCCTCAACTATTCTTCATAATTTTAATTGAAAAAACTACTCTTTCCACA
*
4073338 TTTGTTGTAACAACTAGCAAAATCAA
66 TTTGATGTAACAACTAGCAAAATCAA
4073364 TGCAAGCTAG
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
95 42 0.53
97 20 0.25
98 17 0.22
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (95 bp):
TGATCTCCAATTCAATCCCTCAACTATTCTTCATAATTTTAATTGAAAAAACTACTCTTTCCACA
TTTGATGTAACAACTAGCAAAATCAACCAC
Found at i:4077580 original size:44 final size:44
Alignment explanation
Indices: 4077486--4077581 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 44
4077476 AAGATATACA
* * * *
4077486 GTATAAGACCATAGATAAAAGATGTTATAACAGCCAAGTATAGT
1 GTATAAGACCATAGATAAAAGACGTCATAACAGCCAAGTACAAT
* * ** **
4077530 GAATAAGGCCATAGATAAAAGACGTCATGGCAGCTTAGTACAAT
1 GTATAAGACCATAGATAAAAGACGTCATAACAGCCAAGTACAAT
4077574 GTATAAGA
1 GTATAAGA
4077582 TATACGGTAT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (44 bp):
GTATAAGACCATAGATAAAAGACGTCATAACAGCCAAGTACAAT
Found at i:4078523 original size:11 final size:12
Alignment explanation
Indices: 4078501--4078544 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
4078491 AACAAATCCG
4078501 CTCTCAAATTTC
1 CTCTCAAATTTC
4078513 CTCTC-AATTTC
1 CTCTCAAATTTC
4078524 CT-TCCAAATTT-
1 CTCT-CAAATTTC
4078535 CTCTCAAATT
1 CTCTCAAATT
4078545 CATATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 17 0.59
12 11 0.38
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:4081120 original size:29 final size:29
Alignment explanation
Indices: 4081059--4081132 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
4081049 CCTTAACGTA
** *
4081059 AAACCCTAAACAATAAACCTAAAAAACCC
1 AAACCCTAAACCCTAAACCTAAAAAACAC
* * *
4081088 AAACCCTAAACCCTAAACTTAAAAATCAT
1 AAACCCTAAACCCTAAACCTAAAAAACAC
4081117 AAACCCT-AACCCTAAA
1 AAACCCTAAACCCTAAA
4081133 AACCCTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 9 0.23
29 30 0.77
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (29 bp):
AAACCCTAAACCCTAAACCTAAAAAACAC
Found at i:4081136 original size:44 final size:44
Alignment explanation
Indices: 4081088--4081292 Score: 261
Period size: 44 Copynumber: 4.6 Consensus size: 44
4081078 TAAAAAACCC
* *
4081088 AAACCCTAAACCCTAAACTTAAAAA-TCATAAACCCTAACCCTAA
1 AAACCCTAAACCCTAAACTTAAAAACT-ACAAACCCTAAACCTAA
* *
4081132 AAACCCTAAAACCTTAAA-TTAAAAACTACAAACTCTAAACCTAA
1 AAACCCT-AAACCCTAAACTTAAAAACTACAAACCCTAAACCTAA
* *
4081176 AAACACTAAACCCTAAACTTAAAAACTACAAATCCTAAACCTAA
1 AAACCCTAAACCCTAAACTTAAAAACTACAAACCCTAAACCTAA
* * * *
4081220 AAACCCTAAACCCTTAACTTAAAAACCATAAACCCTAAACTTAA
1 AAACCCTAAACCCTAAACTTAAAAACTACAAACCCTAAACCTAA
**
4081264 AAATTCTAAACCCTAAACTTAAAACACTA
1 AAACCCTAAACCCTAAACTTAAAA-ACTA
4081293 AACCTTAAAA
Statistics
Matches: 139, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
43 9 0.06
44 117 0.84
45 13 0.09
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (44 bp):
AAACCCTAAACCCTAAACTTAAAAACTACAAACCCTAAACCTAA
Found at i:4081229 original size:15 final size:15
Alignment explanation
Indices: 4081117--4081231 Score: 53
Period size: 15 Copynumber: 7.8 Consensus size: 15
4081107 TAAAAATCAT
*
4081117 AAACCCTAACCCTAA
1 AAACCCTAAACCTAA
*
4081132 AAACCCTAAAACCT-T
1 AAACCCT-AAACCTAA
* * *
4081147 AAA--TTAAAAACTAC
1 AAACCCT-AAACCTAA
*
4081161 AAACTCTAAACCTAA
1 AAACCCTAAACCTAA
*
4081176 AAACACTAAACCCT--
1 AAACCCTAAA-CCTAA
* * *
4081190 AAA-CTTAAAAACTAC
1 AAACCCT-AAACCTAA
*
4081205 AAATCCTAAACCTAA
1 AAACCCTAAACCTAA
4081220 AAACCCTAAACC
1 AAACCCTAAACC
4081232 CTTAACTTAA
Statistics
Matches: 75, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
13 10 0.13
14 9 0.12
15 45 0.60
16 11 0.15
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (15 bp):
AAACCCTAAACCTAA
Found at i:4081303 original size:22 final size:20
Alignment explanation
Indices: 4081093--4081301 Score: 168
Period size: 22 Copynumber: 9.6 Consensus size: 20
4081083 AACCCAAACC
4081093 CTAAACCCTAAACTTAAAAA
1 CTAAACCCTAAACTTAAAAA
* *
4081113 TCATAAACCCTAACCCTAAAAA
1 -C-TAAACCCTAAACTTAAAAA
*
4081135 CCCTAAAACCTTAAA-TTAAAAA
1 --CT-AAACCCTAAACTTAAAAA
* *
4081157 CTACAAACTCTAAACCTAAAAACA
1 CT--AAACCCTAAA-CTTAAAA-A
4081181 CTAAACCCTAAACTTAAAAA
1 CTAAACCCTAAACTTAAAAA
* *
4081201 CTACAAATCCTAAACCTAAAAA
1 CT--AAACCCTAAACTTAAAAA
*
4081223 CCCTAAACCCTTAACTTAAAAA
1 --CTAAACCCTAAACTTAAAAA
4081245 CCATAAACCCTAAACTTAAAAA
1 -C-TAAACCCTAAACTTAAAAA
4081267 TTCTAAACCCTAAACTTAAAACA
1 --CTAAACCCTAAACTTAAAA-A
*
4081290 CTAAACCTTAAA
1 CTAAACCCTAAA
4081302 ACCTTAACTT
Statistics
Matches: 154, Mismatches: 20, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
20 5 0.03
21 28 0.18
22 100 0.65
23 16 0.10
24 5 0.03
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (20 bp):
CTAAACCCTAAACTTAAAAA
Found at i:4081303 original size:29 final size:29
Alignment explanation
Indices: 4081270--4081329 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
4081260 TTAAAAATTC
*
4081270 TAAACCCTAAACTT-AAAACACTAAACCT
1 TAAAACCTAAACTTCAAAACACTAAACCT
* * *
4081298 TAAAACCTTAACTTCAAAACCCTAACCCT
1 TAAAACCTAAACTTCAAAACACTAAACCT
4081327 TAA
1 TAA
4081330 GTTAAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (29 bp):
TAAAACCTAAACTTCAAAACACTAAACCT
Found at i:4081323 original size:14 final size:14
Alignment explanation
Indices: 4081271--4081322 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
4081261 TAAAAATTCT
4081271 AAACCCTAAACTTA
1 AAACCCTAAACTTA
*
4081285 AAACACTAAACCTTA
1 AAACCCTAAA-CTTA
*
4081300 AAA-CCTTAACTTCA
1 AAACCCTAAACTT-A
4081314 AAACCCTAA
1 AAACCCTAA
4081323 CCCTTAAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 3 0.10
14 17 0.55
15 11 0.35
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (14 bp):
AAACCCTAAACTTA
Found at i:4084948 original size:250 final size:250
Alignment explanation
Indices: 4084506--4085069 Score: 878
Period size: 250 Copynumber: 2.3 Consensus size: 250
4084496 CCCAAACATG
4084506 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
4084571 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCAAAATTATTTCTTCCAGGACCAACT
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCAAAATTATTTCTTCCAGGACCAACT
* * * *
4084636 GTAGGAAAAGCGCGTCCACGAGGGCGCAATTTCAAAAATTCTTCTCAAATAGCATTCTGCTTGAA
131 GTAGCAAAAGCGCATCCACGAGGGCGCAATTTCAAAAATTCTTCGCAAATAGCATCCTGCTTGAA
*
4084701 GTGTTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATAATTTTTTCAGGAC
196 GTGTTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATAATTTTTCCAGGAC
* *
4084756 CTACTGTAGCAAAAGCGCGTCCACGTGAGCACGATTTCACAAATTCTTCTCATAAAGCATCCTGG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
* * **
4084821 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCTTGGACCAACT
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCAAAATTATTTCTTCCAGGACCAACT
* * **
4084886 GTAGCAAAAGCGCATCCA-GTAGGGCGCGATTTCATAAATTCTTCGCATGTAGCATCCTGCTTGA
131 GTAGCAAAAGCGCATCCACG-AGGGCGCAATTTCAAAAATTCTTCGCAAATAGCATCCTGCTTGA
* * * *
4084950 AGTGTTTTTTATATTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGAC
195 AGTGTTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATAATTTTTCCAGGAC
* * * * * * *
4085006 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTGCAAAAATCCTTCTGATAAATCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTG
4085070 CTTTGATTTT
Statistics
Matches: 285, Mismatches: 28, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
249 1 0.00
250 284 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (250 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCAAAATTATTTCTTCCAGGACCAACT
GTAGCAAAAGCGCATCCACGAGGGCGCAATTTCAAAAATTCTTCGCAAATAGCATCCTGCTTGAA
GTGTTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATAATTTTTCCAGGAC
Found at i:4085072 original size:125 final size:125
Alignment explanation
Indices: 4084506--4085072 Score: 728
Period size: 125 Copynumber: 4.5 Consensus size: 125
4084496 CCCAAACATG
* *
4084506 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAAAAATTCTTCTCATAAAGCATCCTGC
* *
4084571 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCAAAATTATTTCTTCCAGGAC
66 TTGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGAC
* * * * *
4084631 CAACTGTAGGAAAAGCGCGTCCACGAGGGCGCAATTTCAAAAATTCTTCTCA-AATAGCATTCTG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAAAAATTCTTCTCATAA-AGCATCCTG
* * * *
4084695 CTTGAAGTGTTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATAATTT-TTTCAGGAC
65 CTTGAAGCG-ATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGAC
* * * *
4084756 CTACTGTAGCAAAAGCGCGTCCACGTGAGCACGATTTCACAAATTCTTCTCATAAAGCATCCTGG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAAAAATTCTTCTCATAAAGCATCCTGC
* * **
4084821 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCTTGGAC
66 TTGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGAC
* * * * **
4084881 CAACTGTAGCAAAAGCGCATCCA-GTAGGGCGCGATTTCATAAATTCTTCGCATGTAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGT-GGGCGCGATTTCAAAAATTCTTCTCATAAAGCATCCTG
* * * * *
4084945 CTTGAAGTGTTTTTTATATTATTTGCTCAGAAACGTCAAGTCGAAATTATTT-TTCCAGGAC
65 CTTGAAGCG-ATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGAC
* * * * * *
4085006 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTGCAAAAATCCTTCTGATAAATCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAAAAATTCTTCTCATAAAGCATCCTGC
4085071 TT
66 TT
4085073 TGATTTTATC
Statistics
Matches: 377, Mismatches: 58, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
124 43 0.11
125 252 0.67
126 82 0.22
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAAAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGAC
Found at i:4092060 original size:27 final size:28
Alignment explanation
Indices: 4092001--4092060 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
4091991 AAACCAAAAG
*
4092001 CAAACAGTCCAGAGAGTCCTAAAAATTA
1 CAAACAGTCCAAAGAGTCCTAAAAATTA
*
4092029 CAAACAGTCCAAAGAGTCC-CAAAATTA
1 CAAACAGTCCAAAGAGTCCTAAAAATTA
4092056 CAAAC
1 CAAAC
4092061 TCTCAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 12 0.40
28 18 0.60
ACGTcount: A:0.48, C:0.25, G:0.12, T:0.15
Consensus pattern (28 bp):
CAAACAGTCCAAAGAGTCCTAAAAATTA
Found at i:4100591 original size:34 final size:31
Alignment explanation
Indices: 4100541--4100615 Score: 82
Period size: 34 Copynumber: 2.4 Consensus size: 31
4100531 GTTTTAATTT
* *
4100541 GATTCATTCTTATTATATTATAATATATACATTA
1 GATTCATT-TTATTATAATA-AACATA-ACATTA
4100575 GATTCATTTTATTTATAATAAACATAACATTA
1 GATTCATTTTA-TTATAATAAACATAACATTA
4100607 -ATTC-TTTTA
1 GATTCATTTTA
4100616 ACCCATGACC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 5 0.13
31 4 0.11
32 6 0.16
33 8 0.21
34 15 0.39
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (31 bp):
GATTCATTTTATTATAATAAACATAACATTA
Found at i:4110709 original size:2 final size:2
Alignment explanation
Indices: 4110704--4110743 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
4110694 AAAAAAAATG
*
4110704 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4110744 TTTTATATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4116419 original size:5 final size:5
Alignment explanation
Indices: 4116405--4116444 Score: 71
Period size: 5 Copynumber: 7.8 Consensus size: 5
4116395 TTCAAATGGG
4116405 TTTTC TTTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
4116445 TCCTTTTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:4123006 original size:31 final size:31
Alignment explanation
Indices: 4122971--4123032 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
4122961 ATTTGCTACA
* * * * *
4122971 TGAATTTAGTTTTAATGTTTAATTTGGTATT
1 TGAATTTAATTTCAATATTCAATTTGATATT
4123002 TGAATTTAATTTCAATATTCAATTTGATATT
1 TGAATTTAATTTCAATATTCAATTTGATATT
4123033 CAGATCAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.55
Consensus pattern (31 bp):
TGAATTTAATTTCAATATTCAATTTGATATT
Found at i:4123248 original size:31 final size:32
Alignment explanation
Indices: 4123204--4123269 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
4123194 TCAAATTAAA
* * *
4123204 AAAACTTATATACCAAAGTGAACATTGAAACT
1 AAAACTTACATACCAAAGTAAACATTAAAACT
*
4123236 AAAA-TTACATACCAAATTAAACATTAAAACT
1 AAAACTTACATACCAAAGTAAACATTAAAACT
4123267 AAA
1 AAA
4123270 TTTAAGTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.24
Consensus pattern (32 bp):
AAAACTTACATACCAAAGTAAACATTAAAACT
Found at i:4123766 original size:29 final size:29
Alignment explanation
Indices: 4123675--4123768 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
4123665 TAATTAGGAC
* *
4123675 AAAAAAACTAAAGTATCAAATTGAACATTAA
1 AAAAAAACTCAAGTATCAAATTGAA-A-AAA
*** * ** *
4123706 AGCTAAACTCAAGTACTTAAATTG-GGACA
1 AAAAAAACTCAAGTA-TCAAATTGAAAAAA
4123735 AAAAAAACTCAAGTATCAAATTGAAAAAA
1 AAAAAAACTCAAGTATCAAATTGAAAAAA
4123764 AAAAA
1 AAAAA
4123769 TTTCAGGTAC
Statistics
Matches: 45, Mismatches: 16, Indels: 6
0.67 0.24 0.09
Matches are distributed among these distances:
28 7 0.16
29 20 0.44
31 11 0.24
32 7 0.16
ACGTcount: A:0.59, C:0.12, G:0.10, T:0.20
Consensus pattern (29 bp):
AAAAAAACTCAAGTATCAAATTGAAAAAA
Found at i:4131966 original size:5 final size:6
Alignment explanation
Indices: 4131951--4131975 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4131941 GGAAGAGAGA
4131951 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
4131976 GATTAGAGTG
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:4134983 original size:37 final size:37
Alignment explanation
Indices: 4134929--4135038 Score: 115
Period size: 37 Copynumber: 3.0 Consensus size: 37
4134919 TTATTCTAAA
*
4134929 ATTAATATTATTTTAATAGTTTAATATTTAATTTAAT
1 ATTAATATTATCTTAATAGTTTAATATTTAATTTAAT
*
4134966 -TTAATACTTATCTTAATAGTATT-TTA-TTAATTTAAT
1 ATTAATA-TTATCTTAATAGT-TTAATATTTAATTTAAT
4135002 ATTAAAGTGATTATCTTAATA--TTAA-ATTTAATTTAAT
1 ATT-AA-T-ATTATCTTAATAGTTTAATATTTAATTTAAT
4135039 GTTTATCTAG
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
36 19 0.31
37 26 0.42
38 4 0.06
39 12 0.19
40 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.54
Consensus pattern (37 bp):
ATTAATATTATCTTAATAGTTTAATATTTAATTTAAT
Found at i:4135030 original size:68 final size:67
Alignment explanation
Indices: 4134949--4135145 Score: 189
Period size: 62 Copynumber: 3.0 Consensus size: 67
4134939 TTTTAATAGT
* *
4134949 TTAATATTTAATTTAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTGATT
1 TTAATATTAAATTTAATTTAATATTTATCTTAATA-TATTTTATTAATTTAATATTAAAGTGATT
4135014 ATC
65 ATC
* * *
4135017 TTAATATTAAATTTAATTTAATGTTTATCTAGTAAATAAACTTTCTATT-ATTT--TAAT-AA--
1 TTAATATTAAATTTAATTTAATATTTATCT--T-AATATA-TTT-TATTAATTTAATATTAAAGT
4135076 GA-T-TC
61 GATTATC
* *
4135081 --AATATTAAATTTAATTTAATATTTATCTTGATAATTATTATATTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTTAATTTAATATTTATCTTAAT-A-TATTTTATTAATTTAATATTAAAGTGAT
4135144 TA
64 TA
4135146 AGTTTACTCG
Statistics
Matches: 104, Mismatches: 10, Indels: 31
0.72 0.07 0.21
Matches are distributed among these distances:
59 6 0.06
60 8 0.08
61 1 0.01
62 30 0.29
63 2 0.02
64 2 0.02
65 3 0.03
66 3 0.03
68 29 0.28
69 3 0.03
70 2 0.02
71 11 0.11
72 4 0.04
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (67 bp):
TTAATATTAAATTTAATTTAATATTTATCTTAATATATTTTATTAATTTAATATTAAAGTGATTA
TC
Found at i:4136570 original size:27 final size:27
Alignment explanation
Indices: 4136498--4136573 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 27
4136488 TTGTGGTGGC
* *
4136498 GGTATAACACCAGTAGGTATGGCAAGAT
1 GGTAT-ACGCCAGTAGGTCTGGCAAGAT
** * **
4136526 GGT-TACGCCAACAAGTCTGGTGAGAT
1 GGTATACGCCAGTAGGTCTGGCAAGAT
4136552 GGTATACGCCAGTAGGTCTGGC
1 GGTATACGCCAGTAGGTCTGGC
4136574 GAGTTAGTAT
Statistics
Matches: 36, Mismatches: 11, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
26 18 0.50
27 15 0.42
28 3 0.08
ACGTcount: A:0.28, C:0.18, G:0.32, T:0.22
Consensus pattern (27 bp):
GGTATACGCCAGTAGGTCTGGCAAGAT
Found at i:4144955 original size:26 final size:26
Alignment explanation
Indices: 4144917--4144976 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
4144907 GAAGCTCTGG
4144917 AGAGCCATCAATCAAGAAGCTCACAA
1 AGAGCCATCAATCAAGAAGCTCACAA
* * ** **
4144943 AGAGCCTTTAATCGGGAAGCTCATGA
1 AGAGCCATCAATCAAGAAGCTCACAA
4144969 AGAGCCAT
1 AGAGCCAT
4144977 ATATCGGGAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (26 bp):
AGAGCCATCAATCAAGAAGCTCACAA
Found at i:4153076 original size:24 final size:24
Alignment explanation
Indices: 4153045--4153090 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
4153035 AAATGCAGCT
4153045 TGATTAATTTGATTTAATTCAACC
1 TGATTAATTTGATTTAATTCAACC
4153069 TGATTAATTTGATTTAATTCAA
1 TGATTAATTTGATTTAATTCAA
4153091 GTTTTAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (24 bp):
TGATTAATTTGATTTAATTCAACC
Found at i:4156505 original size:16 final size:16
Alignment explanation
Indices: 4156460--4156519 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
4156450 TAAAAGAAAT
4156460 AAAGAAAGACAAAAGCAA
1 AAAGAAAGA-AAAAG-AA
* *
4156478 AACGAAACAAAAAGAA
1 AAAGAAAGAAAAAGAA
*
4156494 AGAA-AAAGAAAAAGAG
1 A-AAGAAAGAAAAAGAA
4156510 AAAGAAAGAA
1 AAAGAAAGAA
4156520 GAACATACAG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 2 0.06
16 20 0.57
17 6 0.17
18 7 0.20
ACGTcount: A:0.75, C:0.07, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAAAAGAA
Found at i:4156952 original size:19 final size:20
Alignment explanation
Indices: 4156928--4156968 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
4156918 GAATTTAGGC
*
4156928 AAATATTGAATA-AAAATTG
1 AAATATTCAATATAAAATTG
*
4156947 AAATATTCAATATGAAATTG
1 AAATATTCAATATAAAATTG
4156967 AA
1 AA
4156969 TTGTGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (20 bp):
AAATATTCAATATAAAATTG
Found at i:4161527 original size:42 final size:41
Alignment explanation
Indices: 4161419--4161546 Score: 166
Period size: 42 Copynumber: 3.0 Consensus size: 41
4161409 TTCCAACAAG
* * * *
4161419 AAGAACCAAACCAAGCTTGTTAAACCATCAAATGTATCCACC
1 AAGAACCAAACCAAGCTCGTTAAATCAT-GAATGTATCAACC
* *
4161461 AAGAACCAAACCAAGCTGGTTAAATCAGTGAATGTATCGACC
1 AAGAACCAAACCAAGCTCGTTAAATCA-TGAATGTATCAACC
*
4161503 AAGAACCAAACCAAGCTCGTTAAATCATTGGATGTATCAACC
1 AAGAACCAAACCAAGCTCGTTAAATCA-TGAATGTATCAACC
4161545 AA
1 AA
4161547 AACGTCGAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 76 0.99
43 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (41 bp):
AAGAACCAAACCAAGCTCGTTAAATCATGAATGTATCAACC
Found at i:4162550 original size:4 final size:4
Alignment explanation
Indices: 4162541--4162566 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4162531 GGGGAAGAAA
4162541 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
4162567 AGATTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:4166419 original size:23 final size:25
Alignment explanation
Indices: 4166393--4166441 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
4166383 TTTACTCTCC
*
4166393 AAAATACCCAACAAAAG-A-TTAAT
1 AAAACACCCAACAAAAGCACTTAAT
*
4166416 AAAACACTCAACAAAAGCACTTAAT
1 AAAACACCCAACAAAAGCACTTAAT
4166441 A
1 A
4166442 TGCACATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
24 1 0.05
25 6 0.27
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.16
Consensus pattern (25 bp):
AAAACACCCAACAAAAGCACTTAAT
Found at i:4182004 original size:19 final size:19
Alignment explanation
Indices: 4181950--4182004 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
4181940 TGAACTAGAA
4181950 TCAATAATTAAGTTT-AGGG
1 TCAATAATTAA-TTTAAGGG
*
4181969 TCAATAATATAAATTAAGGG
1 TCAATAAT-TAATTTAAGGG
4181989 -CAATAATGTAATTTAA
1 TCAATAAT-TAATTTAA
4182005 TAGTATAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 24 0.77
20 7 0.23
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (19 bp):
TCAATAATTAATTTAAGGG
Found at i:4188393 original size:2 final size:2
Alignment explanation
Indices: 4188386--4188411 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4188376 TCATCTCATA
4188386 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4188412 TTTTTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4195482 original size:12 final size:12
Alignment explanation
Indices: 4195465--4195490 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4195455 AAAGTATCAA
4195465 AAATAATAAAAT
1 AAATAATAAAAT
4195477 AAATAATAAAAT
1 AAATAATAAAAT
4195489 AA
1 AA
4195491 CGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATAATAAAAT
Found at i:4196499 original size:30 final size:30
Alignment explanation
Indices: 4196463--4196521 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
4196453 TTCGAATTTT
4196463 ATAACCGAAATATACTACATTATATTACTG
1 ATAACCGAAATATACTACATTATATTACTG
4196493 ATAACCGAAATATACTACATTATATTACT
1 ATAACCGAAATATACTACATTATATTACT
4196522 ATTTTTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (30 bp):
ATAACCGAAATATACTACATTATATTACTG
Found at i:4199422 original size:3 final size:3
Alignment explanation
Indices: 4199414--4199438 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4199404 CCAAGAAAAG
4199414 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
4199439 AAGGGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:4215827 original size:21 final size:21
Alignment explanation
Indices: 4215786--4215828 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4215776 AATAAAGTAC
*
4215786 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
4215807 ATTATATATTATAATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
4215828 A
1 A
4215829 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:4215870 original size:17 final size:18
Alignment explanation
Indices: 4215845--4215890 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
4215835 TATAAGAATA
*
4215845 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
4215862 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
4215880 ATTAAATTATA
1 ATTAAATTATA
4215891 TTTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:4215993 original size:59 final size:57
Alignment explanation
Indices: 4215811--4215994 Score: 187
Period size: 64 Copynumber: 3.1 Consensus size: 57
4215801 TATAGTATTA
4215811 TATATTATAATTTTAGTAAATTCATATAAGAATAATTATATTAAGAATTTTATTAAAT
1 TATATTAT-ATTTTAGTAAATTCATATAAGAATAATTATATTAAGAATTTTATTAAAT
* * * * *
4215869 TATA-TAT-TTTTATTAAATT-ATATTTAATAATAATTATTTTAAATTATATTTTA-TAGTATT
1 TATATTATATTTTAGTAAATTCATA--TAAGAATAATTATATT-AA-GA-ATTTTATTA--AAT
*
4215929 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAAT
1 -TATATTAT-ATTTTAGTAAATTCATATAAGAATAATT-ATATTAAGAATTTTATTAAAT
4215989 TATATT
1 TATATT
4215995 TAATAATAAC
Statistics
Matches: 101, Mismatches: 11, Indels: 27
0.73 0.08 0.19
Matches are distributed among these distances:
54 3 0.03
55 11 0.11
56 14 0.14
57 5 0.05
58 7 0.07
59 12 0.12
60 4 0.04
61 10 0.10
62 6 0.06
63 11 0.11
64 15 0.15
65 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (57 bp):
TATATTATATTTTAGTAAATTCATATAAGAATAATTATATTAAGAATTTTATTAAAT
Found at i:4216055 original size:119 final size:118
Alignment explanation
Indices: 4215793--4216028 Score: 315
Period size: 119 Copynumber: 2.0 Consensus size: 118
4215783 TACATTATAT
*
4215793 ATTAT-TTTTATAGTATTATATATTATAATTTTAGTAAATTCATATAAGAATAATTATATTAAGA
1 ATTATATTTTATAGTATAATATATTATAATTTTAGTAAATTCATATAAGAATAATTATATTAAGA
** * * * *
4215857 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
66 ATTTTATTAAATTATATATTAATAATAAACTATAGTTAATAATAATGA-TTTAA
* * *
4215911 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATAATATATTATAATTTTAGTAAATTCATATAAGAATAATT-ATATTAAG
4215976 AATTTTATTAAATTATAT-TTAATAAT-AACTAT-GTTAA-AAT-ATGA-TTAA
65 AATTTTATTAAATTATATATTAATAATAAACTATAGTTAATAATAATGATTTAA
4216024 ATTAT
1 ATTAT
4216029 TTATTATTTA
Statistics
Matches: 108, Mismatches: 8, Indels: 9
0.86 0.06 0.07
Matches are distributed among these distances:
113 9 0.08
115 3 0.03
116 3 0.03
117 4 0.04
118 10 0.09
119 53 0.49
120 26 0.24
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (118 bp):
ATTATATTTTATAGTATAATATATTATAATTTTAGTAAATTCATATAAGAATAATTATATTAAGA
ATTTTATTAAATTATATATTAATAATAAACTATAGTTAATAATAATGATTTAA
Found at i:4218844 original size:23 final size:23
Alignment explanation
Indices: 4218818--4218864 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
4218808 ATTTTGCTTA
*
4218818 AATTAACA-AAATATTGAATAATT
1 AATTAA-ATAAATATTGAAAAATT
*
4218841 AATTAAATTAATATTGAAAAATT
1 AATTAAATAAATATTGAAAAATT
4218864 A
1 A
4218865 GAATAACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (23 bp):
AATTAAATAAATATTGAAAAATT
Found at i:4218875 original size:23 final size:23
Alignment explanation
Indices: 4218827--4218875 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
4218817 AAATTAACAA
* * *
4218827 AATATTGAATAATTAATTAAATT
1 AATATTGAAAAATTAAATAAACT
4218850 AATATTGAAAAATTAGAAT-AACT
1 AATATTGAAAAATTA-AATAAACT
4218873 AAT
1 AAT
4218876 TAACTGAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (23 bp):
AATATTGAAAAATTAAATAAACT
Found at i:4229854 original size:23 final size:22
Alignment explanation
Indices: 4229827--4229869 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
4229817 GACCTAAATT
4229827 TTAAACTATGAAAAGTAAAAAAA
1 TTAAACTATGAAAA-TAAAAAAA
* *
4229850 TTAAATTATTAAAATAAAAA
1 TTAAACTATGAAAATAAAAA
4229870 TATAGAGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (22 bp):
TTAAACTATGAAAATAAAAAAA
Found at i:4230486 original size:15 final size:14
Alignment explanation
Indices: 4230466--4230518 Score: 72
Period size: 15 Copynumber: 3.7 Consensus size: 14
4230456 GTCGGTGAGT
4230466 GAAGGAGAAGAAATA
1 GAAGGAGAAGAAA-A
4230481 GAAGGAGAAGAAAA
1 GAAGGAGAAGAAAA
*
4230495 GAA-GAGAAGAAGGA
1 GAAGGAGAAGAA-AA
4230509 GAAGGAGAAG
1 GAAGGAGAAG
4230519 GAGAGGGCGG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
13 8 0.23
14 8 0.23
15 19 0.54
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.02
Consensus pattern (14 bp):
GAAGGAGAAGAAAA
Found at i:4230564 original size:13 final size:13
Alignment explanation
Indices: 4230540--4230573 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
4230530 AAGGGAAGGT
4230540 AAAAAAGA-AAGA
1 AAAAAAGAGAAGA
4230552 AAAAAAGAGAAGA
1 AAAAAAGAGAAGA
*
4230565 GAAAAAGAG
1 AAAAAAGAG
4230574 CGAGGGAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAAAGAGAAGA
Found at i:4234908 original size:27 final size:27
Alignment explanation
Indices: 4234868--4234937 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
4234858 ACTAGGTATA
4234868 CCGCCTATCAGATAGGGGTCACTGGTG
1 CCGCCTATCAGATAGGGGTCACTGGTG
** *
4234895 TTGCCTACCAGATAGGGGTCACTGGTG
1 CCGCCTATCAGATAGGGGTCACTGGTG
4234922 CCGCCTATCAGATAGG
1 CCGCCTATCAGATAGG
4234938 CACCACACCC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.20, C:0.26, G:0.31, T:0.23
Consensus pattern (27 bp):
CCGCCTATCAGATAGGGGTCACTGGTG
Found at i:4237844 original size:26 final size:26
Alignment explanation
Indices: 4237813--4237863 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
4237803 ATTAGACATT
4237813 GAAAAATATGAAAAACGTTGTGTCAC
1 GAAAAATATGAAAAACGTTGTGTCAC
4237839 GAAAAATATGAAAAACGTTGTGTCA
1 GAAAAATATGAAAAACGTTGTGTCA
4237864 TTGTGATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.24
Consensus pattern (26 bp):
GAAAAATATGAAAAACGTTGTGTCAC
Found at i:4251670 original size:10 final size:10
Alignment explanation
Indices: 4251655--4251683 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
4251645 TAAATTCTTA
4251655 AAAGATAAAT
1 AAAGATAAAT
4251665 AAAGATAAAT
1 AAAGATAAAT
4251675 AAAGATAAA
1 AAAGATAAA
4251684 AGCTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:4253713 original size:7 final size:7
Alignment explanation
Indices: 4253694--4253744 Score: 70
Period size: 7 Copynumber: 7.3 Consensus size: 7
4253684 ATCCAAACAA
4253694 AATAAAGT
1 AATAAA-T
4253702 AATAAAT
1 AATAAAT
4253709 AAT-AA-
1 AATAAAT
4253714 AATAAAAT
1 AAT-AAAT
4253722 AATAAAT
1 AATAAAT
4253729 AATAAAT
1 AATAAAT
4253736 AATAAAT
1 AATAAAT
4253743 AA
1 AA
4253745 AGAAAAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 3 0.08
6 2 0.05
7 26 0.65
8 9 0.22
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (7 bp):
AATAAAT
Found at i:4253717 original size:20 final size:20
Alignment explanation
Indices: 4253692--4253734 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
4253682 ATATCCAAAC
*
4253692 AAAATAAAGTAATAAATAAT
1 AAAATAAAATAATAAATAAT
4253712 AAAATAAAATAATAAATAAT
1 AAAATAAAATAATAAATAAT
4253732 AAA
1 AAA
4253735 TAATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAATAAAATAATAAATAAT
Found at i:4253753 original size:14 final size:14
Alignment explanation
Indices: 4253692--4253755 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
4253682 ATATCCAAAC
4253692 AAAATAAAGTAATAA
1 AAAATAAA-TAATAA
*
4253707 ATAAT-AA-AATAA
1 AAAATAAATAATAA
4253719 AATAATAAATAATAA
1 AA-AATAAATAATAA
*
4253734 ATAATAAATAA-AGA
1 AAAATAAATAATA-A
4253748 AAAATAAA
1 AAAATAAA
4253756 AATTGGGTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
12 6 0.15
13 4 0.10
14 21 0.51
15 10 0.24
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (14 bp):
AAAATAAATAATAA
Found at i:4257438 original size:10 final size:10
Alignment explanation
Indices: 4257423--4257447 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4257413 TTCTTAAAAG
4257423 ATAAATAAAT
1 ATAAATAAAT
4257433 ATAAATAAAT
1 ATAAATAAAT
4257443 ATAAA
1 ATAAA
4257448 AGCTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAAATAAAT
Found at i:4260920 original size:17 final size:19
Alignment explanation
Indices: 4260887--4260922 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
4260877 TTTTCTGAAT
4260887 TTTTTATATATATTTTTTA
1 TTTTTATATATATTTTTTA
4260906 TTTTTA-ATA-ATTTTTTA
1 TTTTTATATATATTTTTTA
4260923 AGATTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 3 0.18
19 6 0.35
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTATATATATTTTTTA
Found at i:4266537 original size:2 final size:2
Alignment explanation
Indices: 4266530--4266555 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4266520 GGTTTAATTA
4266530 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4266556 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4269133 original size:3 final size:3
Alignment explanation
Indices: 4269120--4269162 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
4269110 CGCAAGTATG
4269120 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4269163 AAAAGTATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:4269837 original size:13 final size:13
Alignment explanation
Indices: 4269819--4269844 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4269809 ACCGGTTCAC
4269819 CTTAGAAACTTTG
1 CTTAGAAACTTTG
4269832 CTTAGAAACTTTG
1 CTTAGAAACTTTG
4269845 TACTCTCAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
CTTAGAAACTTTG
Found at i:4270755 original size:44 final size:44
Alignment explanation
Indices: 4270672--4270807 Score: 123
Period size: 44 Copynumber: 3.1 Consensus size: 44
4270662 GGCTTCAATG
** * * *
4270672 TACTCCACTGTAACCTCAGGGAGGTAAAATCTGTCATCTTCGATC
1 TACTCCACTACAACCTCAGGGAGATAAGATCTAT-ATCTTCGATC
** * *
4270717 TACTCCACTACTGCCT-AGGGAGATAAGATCTATAATCTTCAATT
1 TACTCCACTACAACCTCAGGGAGATAAGATCTAT-ATCTTCGATC
* * * *
4270761 TGC-CCCCTACAACTTCAGGGAGATAAGATTTATATCTTCGATC
1 TACTCCACTACAACCTCAGGGAGATAAGATCTATATCTTCGATC
4270804 TACT
1 TACT
4270808 TCACGCTAAT
Statistics
Matches: 70, Mismatches: 19, Indels: 5
0.74 0.20 0.05
Matches are distributed among these distances:
43 18 0.26
44 40 0.57
45 12 0.17
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (44 bp):
TACTCCACTACAACCTCAGGGAGATAAGATCTATATCTTCGATC
Found at i:4270849 original size:44 final size:44
Alignment explanation
Indices: 4270793--4270878 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
4270783 ATAAGATTTA
* *
4270793 TATCTTCGATCTACTTCACGCTAATACATGAAGACAAGATCTGC
1 TATCTTCAATCTACTTCACGCCAATACATGAAGACAAGATCTGC
4270837 TATCTTCAATCTACTTCACGCCAATACATGAAGACAAGATCT
1 TATCTTCAATCTACTTCACGCCAATACATGAAGACAAGATCT
4270879 ACTTCCCCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.29
Consensus pattern (44 bp):
TATCTTCAATCTACTTCACGCCAATACATGAAGACAAGATCTGC
Found at i:4270991 original size:89 final size:89
Alignment explanation
Indices: 4270874--4271087 Score: 347
Period size: 89 Copynumber: 2.4 Consensus size: 89
4270864 ATGAAGACAA
*
4270874 GATCTACTTCCCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTAATTCACACCAATAC
1 GATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTAATTCACACCAATAC
4270939 ATGAAGACAAGATCTGCTTTCTTC
66 ATGAAGACAAGATCTGCTTTCTTC
* * * *
4270963 GATCTGCTTCACCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACACCAGTAC
1 GATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTAATTCACACCAATAC
4271028 ATGAAGACAAGATCTGCTTTCTTC
66 ATGAAGACAAGATCTGCTTTCTTC
* * * *
4271052 GATCTACTTCGCCACCAATATGGGAATATAAGATCT
1 GATCTACTTCACCACCAGTATGGGAAGACAAGATCT
4271088 ACTGCTACTC
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 115 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (89 bp):
GATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTAATTCACACCAATAC
ATGAAGACAAGATCTGCTTTCTTC
Found at i:4270994 original size:45 final size:45
Alignment explanation
Indices: 4270874--4271087 Score: 245
Period size: 44 Copynumber: 4.8 Consensus size: 45
4270864 ATGAAGACAA
* * *
4270874 GATCTACTTCCCCACCAGTATGGGAAGACAAGATCTGCTATCTTT
1 GATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTTTCTTC
* * ***
4270919 GATCTAATTCA-CACCAATACATGAAGACAAGATCTGCTTTCTTC
1 GATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTTTCTTC
* *
4270963 GATCTGCTTCACCACCAGTATGGGAAGACAAGATCTG-TTATCTTT
1 GATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTT-TCTTC
***
4271008 GATCTACTTCA-CACCAGTACATGAAGACAAGATCTGCTTTCTTC
1 GATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTTTCTTC
* * * *
4271052 GATCTACTTCGCCACCAATATGGGAATATAAGATCT
1 GATCTACTTCACCACCAGTATGGGAAGACAAGATCT
4271088 ACTGCTACTC
Statistics
Matches: 138, Mismatches: 27, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
44 74 0.54
45 64 0.46
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (45 bp):
GATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTTTCTTC
Found at i:4282707 original size:2 final size:2
Alignment explanation
Indices: 4282700--4282751 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
4282690 AATATAAGAG
4282700 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4282742 TA TA TA -A TA T
1 TA TA TA TA TA T
4282752 TGTATGAGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4286033 original size:22 final size:21
Alignment explanation
Indices: 4285996--4286039 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
4285986 AATGCCACCT
4285996 CATACTCCTCCTTACCTCTTC
1 CATACTCCTCCTTACCTCTTC
4286017 CATATCTCCTTCC-TACCTCTTC
1 CATA-CTCC-TCCTTACCTCTTC
4286039 C
1 C
4286040 CTTGTTGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 14 0.67
23 3 0.14
ACGTcount: A:0.14, C:0.48, G:0.00, T:0.39
Consensus pattern (21 bp):
CATACTCCTCCTTACCTCTTC
Found at i:4291067 original size:31 final size:32
Alignment explanation
Indices: 4291004--4291087 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 32
4290994 AAGACAAACA
* * *
4291004 TTTCAAAGTTCTCAAATAAGGACCGAAGC-TT
1 TTTCAAAGTGCTCAAATAAGAACCAAAGCTTT
* *
4291035 TTTCAAAGTGCTCAAATAAGAATCAAATCTTT
1 TTTCAAAGTGCTCAAATAAGAACCAAAGCTTT
* *
4291067 TTTGAAAGGGCTCAAATAAGA
1 TTTCAAAGTGCTCAAATAAGA
4291088 GCTTCTCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 24 0.53
32 21 0.47
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (32 bp):
TTTCAAAGTGCTCAAATAAGAACCAAAGCTTT
Found at i:4291560 original size:43 final size:41
Alignment explanation
Indices: 4291505--4291592 Score: 124
Period size: 43 Copynumber: 2.1 Consensus size: 41
4291495 TAAAAATATT
*
4291505 AAAAAATATATTTTTATACTTTTTT-AATCATTTTAATTTTTAA
1 AAAAAATATATTTTTA-ACTTTTTTGAAT--TTTTAAATTTTAA
*
4291548 AAAAAATATATTTTTAATTTTTTTGAATTTTTAAATTTTAA
1 AAAAAATATATTTTTAACTTTTTTGAATTTTTAAATTTTAA
4291589 AAAA
1 AAAA
4291593 TACTTAATTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 16 0.38
42 7 0.17
43 19 0.45
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (41 bp):
AAAAAATATATTTTTAACTTTTTTGAATTTTTAAATTTTAA
Found at i:4293144 original size:17 final size:19
Alignment explanation
Indices: 4293103--4293147 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
4293093 TGTTGCTATT
4293103 ATTTTGTTGTTATTGTATA
1 ATTTTGTTGTTATTGTATA
*
4293122 ACTTTTGTT-TTATTGT-TC
1 A-TTTTGTTGTTATTGTATA
4293140 ATTTTGTT
1 ATTTTGTT
4293148 ACTATTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.29
18 2 0.08
19 8 0.33
20 7 0.29
ACGTcount: A:0.16, C:0.04, G:0.13, T:0.67
Consensus pattern (19 bp):
ATTTTGTTGTTATTGTATA
Found at i:4293266 original size:20 final size:20
Alignment explanation
Indices: 4293241--4293291 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
4293231 TTTATTAAGA
*
4293241 AATATTTATTTTAATATTTT
1 AATATTTATTTTAATATGTT
4293261 AATATTTA-TTT-ATATGTT
1 AATATTTATTTTAATATGTT
*
4293279 -ATATATATTTTAA
1 AATATTTATTTTAA
4293292 AAATAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.22
18 9 0.33
19 4 0.15
20 8 0.30
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
AATATTTATTTTAATATGTT
Found at i:4298035 original size:21 final size:20
Alignment explanation
Indices: 4298005--4298043 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4297995 TGTTGATGTA
*
4298005 TGTTACATTTTTTGCCCAAGT
1 TGTTACATTTATT-CCCAAGT
*
4298026 TGTTATATTTATTCCCAA
1 TGTTACATTTATTCCCAA
4298044 AATAATTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (20 bp):
TGTTACATTTATTCCCAAGT
Found at i:4298410 original size:27 final size:27
Alignment explanation
Indices: 4298372--4298469 Score: 142
Period size: 27 Copynumber: 3.6 Consensus size: 27
4298362 GTGGAGGGTA
*
4298372 TCCCATGGGCGGCACCAAAGGTGCCTT
1 TCCCATAGGCGGCACCAAAGGTGCCTT
* * *
4298399 TCCCATAGGCGGCACCGATGGTGCCAT
1 TCCCATAGGCGGCACCAAAGGTGCCTT
* *
4298426 TCCCATAGGCGACACCGAAGGTGCCTT
1 TCCCATAGGCGGCACCAAAGGTGCCTT
4298453 TCCCATAGGCGGCACCA
1 TCCCATAGGCGGCACCA
4298470 CTTGTGTCAT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (27 bp):
TCCCATAGGCGGCACCAAAGGTGCCTT
Found at i:4298804 original size:43 final size:40
Alignment explanation
Indices: 4298744--4298860 Score: 119
Period size: 40 Copynumber: 2.8 Consensus size: 40
4298734 TAGATGTTAC
*
4298744 TTAGTATTATTGTTAGTAAAAAAACTAGTATTATTATTATGG
1 TTAGTATTATTTTTAGT-AAAAAACTA-TATTATTATTATGG
** * *
4298786 TTAGTTATTATTTTTAGTAAAACCCTA-ATTATTATTGTTTG
1 TTAG-TATTATTTTTAGTAAAAAACTATATTATTATT-ATGG
* *
4298827 TTAGTATTATTTTGAGTATAAAACTATTATTATT
1 TTAGTATTATTTTTAGTAAAAAACTA-TATTATT
4298861 GCTATTGTGT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
40 27 0.44
41 6 0.10
42 17 0.27
43 12 0.19
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.50
Consensus pattern (40 bp):
TTAGTATTATTTTTAGTAAAAAACTATATTATTATTATGG
Found at i:4298808 original size:40 final size:40
Alignment explanation
Indices: 4298764--4298879 Score: 94
Period size: 40 Copynumber: 2.8 Consensus size: 40
4298754 TGTTAGTAAA
*
4298764 AAAACTAGTATTATTATTATGGTTAGTTATTATTTTTAG-T
1 AAAACTA-TATTATTATTATGGTTAGTTATTATTTTGAGAT
* *
4298804 AAAACCCTA-ATTATTATTGTTTGTTAG-TATTATTTTGAGTAT
1 AAAA--CTATATTATTATT-ATGGTTAGTTATTATTTTGAG-AT
**
4298846 AAAACTATTATTATTGCTATTGTGTTAGTTATTA
1 AAAACTA-TATTATTATTA-TG-GTTAGTTATTA
4298880 GGGTTAGTGG
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
40 27 0.46
41 6 0.10
42 16 0.27
43 5 0.08
44 5 0.08
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (40 bp):
AAAACTATATTATTATTATGGTTAGTTATTATTTTGAGAT
Found at i:4298873 original size:43 final size:41
Alignment explanation
Indices: 4298744--4298879 Score: 106
Period size: 43 Copynumber: 3.2 Consensus size: 41
4298734 TAGATGTTAC
* *
4298744 TTAG-TATTATTGTTAGTAAAAAAACTAGTATTA-T-TATTATGG
1 TTAGTTATTATT-TTAGT--AAAAACTATTATTATTGTATTGT-G
*
4298786 TTAGTTATTATTTTTAGTAAAACCCTAATTATTATTG--TT-TG
1 TTAGTTATTA-TTTTAGTAAAA-ACT-ATTATTATTGTATTGTG
4298827 TTAG-TATTATTTTGAGTATAAAACTATTATTATTGCTATTGTG
1 TTAGTTATTATTTT-AGTA-AAAACTATTATTATTG-TATTGTG
4298870 TTAGTTATTA
1 TTAGTTATTA
4298880 GGGTTAGTGG
Statistics
Matches: 78, Mismatches: 3, Indels: 24
0.74 0.03 0.23
Matches are distributed among these distances:
39 14 0.18
40 11 0.14
41 12 0.15
42 9 0.12
43 24 0.31
44 8 0.10
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.51
Consensus pattern (41 bp):
TTAGTTATTATTTTAGTAAAAACTATTATTATTGTATTGTG
Found at i:4299918 original size:35 final size:35
Alignment explanation
Indices: 4299872--4299942 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
4299862 CAACAAGGAA
*
4299872 TCCATGTGTGAGGAACGAATTGGGGTGAAAAAGGT
1 TCCATGTGTGAGGAACGAATTGGGATGAAAAAGGT
4299907 TCCATGTGTGAGGAACGAATTGGGATGAAAAAGGT
1 TCCATGTGTGAGGAACGAATTGGGATGAAAAAGGT
4299942 T
1 T
4299943 GCGAAATTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.32, C:0.08, G:0.35, T:0.24
Consensus pattern (35 bp):
TCCATGTGTGAGGAACGAATTGGGATGAAAAAGGT
Found at i:4308617 original size:158 final size:153
Alignment explanation
Indices: 4308198--4308617 Score: 413
Period size: 158 Copynumber: 2.7 Consensus size: 153
4308188 GCATGTTGAA
* * *
4308198 AAAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTTGTATTTTTTTCT-TCGCATTTTATT
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCTATTTCTTCGTATTTTTTTCTCT-GCATTTTATT
* *
4308262 ATTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTAAGTGCATTATGTTTGAA
65 ATTTTAAAAAATATCATAATTTCTAATTTTATAATTTTATATTATTTAAGTACATTATGTTTGAA
* *
4308327 ATTTATTAATTTAGTGTGTTTTTT
130 ATTTATTAATTTAGTCTGATTTTT
* * * * * * * * *
4308351 AAATTAATTTAGTGGAAAAAAACCCTTATTTCTGTCCT-TTGC-TCGTATTATTTTC-CCGAATT
1 AAA-AAATTTAGT---AAAACACTCTTACTTC-G-GCTATTTCTTCGTATTTTTTTCTCTGCATT
* * ** *
4308413 TTATTATTTTCAATAAAAAAT-ATTATTTTCGT-ATTTTATTGTTTTATATTATTTCAGTACATT
60 TTATTATTTT-AA-AAAATATCA-TAATTTC-TAATTTTATAATTTTATATTATTTAAGTACATT
* *
4308476 TTGTTTGAAATATTTGTATTAA-TTATTTCTGAATTTTT
121 ATGTTTG-AA-A-TT-TATTAATTTA-GTCTG-ATTTTT
4308514 AAAAAATTTAGTAAAACACTCTTACTTCGGCTATTTCTTCGTATTTTTTTCTCTGCATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCTATTTCTTCGTATTTTTTTCTCTGCATTTTATTA
* *
4308579 CTTTAAAAAATATCATAATTTCTAATTTTATAAATTTAT
66 TTTTAAAAAATATCATAATTTCTAATTTTATAATTTTAT
4308618 TAATTTGGTC
Statistics
Matches: 207, Mismatches: 38, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
153 3 0.01
154 7 0.03
156 14 0.07
157 30 0.14
158 76 0.37
159 32 0.15
160 15 0.07
161 5 0.02
162 17 0.08
163 8 0.04
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.51
Consensus pattern (153 bp):
AAAAAATTTAGTAAAACACTCTTACTTCGGCTATTTCTTCGTATTTTTTTCTCTGCATTTTATTA
TTTTAAAAAATATCATAATTTCTAATTTTATAATTTTATATTATTTAAGTACATTATGTTTGAAA
TTTATTAATTTAGTCTGATTTTT
Found at i:4308838 original size:286 final size:285
Alignment explanation
Indices: 4308325--4308902 Score: 1021
Period size: 286 Copynumber: 2.0 Consensus size: 285
4308315 ATTATGTTTG
** * * *
4308325 AAATTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGGAAAAAAACCCTTATTTCTGTCCTT
1 AAATTTATTAATTTAGTCCGTTTTTTAAATTAATTTAGTGAAAAAAAACCCTTATTCCTGCCCTT
* *
4308390 TGCTCGTATTATTTTCCCGAATTTTATTATTTTCAATAAAAAATATTATTTTCGTATTTTATTGT
66 TGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATTAT
4308455 TTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAA
131 TTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAA
*
4308520 TTTAGTAAAACACTCTTACTTCGGCTATTTCTTCGTATTTTTTTCTCTGCATTTTATTACTTTAA
196 TTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCTGCATTTTATTACTTTAA
4308585 AAAATATCATAATTTCTAATTTTAT
261 AAAATATCATAATTTCTAATTTTAT
* *
4308610 AAATTTATTAATTTGGTCCGTTTTTTAAATTATTTTAGTGTAAAAAAAACCCTTATTCCTGCCCT
1 AAATTTATTAATTTAGTCCGTTTTTTAAATTAATTTAGTG-AAAAAAAACCCTTATTCCTGCCCT
4308675 TTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATTA
65 TTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATTA
*
4308740 TTTTATATTATTTTAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAA
130 TTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAA
* *
4308805 ATTTAGTAAAACACTCTTATTTCGGCCATTTCTTCGTATTTTTTTCTCTTCATTTTATTACTTTA
195 ATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCTGCATTTTATTACTTTA
4308870 AAAAATATCATAATTTCTAATTTTAT
260 AAAAATATCATAATTTCTAATTTTAT
*
4308896 AATTTTA
1 AAATTTA
4308903 CTTTATTTCA
Statistics
Matches: 278, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
285 36 0.13
286 242 0.87
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (285 bp):
AAATTTATTAATTTAGTCCGTTTTTTAAATTAATTTAGTGAAAAAAAACCCTTATTCCTGCCCTT
TGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATTAT
TTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAA
TTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCTGCATTTTATTACTTTAA
AAAATATCATAATTTCTAATTTTAT
Found at i:4309324 original size:47 final size:48
Alignment explanation
Indices: 4309272--4309382 Score: 113
Period size: 47 Copynumber: 2.4 Consensus size: 48
4309262 AAATTACCTT
*
4309272 TTTTCTTTCTTTTTCC-TCCCTCCCCTCTTCTTCTTCTTCT-CTTCTCC
1 TTTTCTTTCTCTTTCCTTCCCTCCCCTCTTCTTCTTCTTCTCCTT-TCC
* * ** * *
4309319 TTTTCTTT-TCTTTCCTTTCCTTCTTTTTTTTTCTTCTTCTCCTTTCC
1 TTTTCTTTCTCTTTCCTTCCCTCCCCTCTTCTTCTTCTTCTCCTTTCC
*
4309366 TTTTCTTTC-CTCTCCTT
1 TTTTCTTTCTCTTTCCTT
4309383 TCCTTTTCTT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
46 6 0.11
47 44 0.83
48 3 0.06
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (48 bp):
TTTTCTTTCTCTTTCCTTCCCTCCCCTCTTCTTCTTCTTCTCCTTTCC
Found at i:4309336 original size:10 final size:10
Alignment explanation
Indices: 4309311--4309404 Score: 72
Period size: 10 Copynumber: 9.6 Consensus size: 10
4309301 CTTCTTCTTC
4309311 TCTTCTCCTTT
1 TCTT-TCCTTT
*
4309322 TCTTTTCTTT
1 TCTTTCCTTT
*
4309332 CCTTTCCTTCT
1 TCTTTCCTT-T
4309343 T-TTT--TTT
1 TCTTTCCTTT
4309350 TC-TT-CTTCT
1 TCTTTCCTT-T
*
4309359 CCTTTCCTTT
1 TCTTTCCTTT
*
4309369 TCTTTCCTCT
1 TCTTTCCTTT
*
4309379 CCTTTCCTTT
1 TCTTTCCTTT
*
4309389 TCTTTCTTTT
1 TCTTTCCTTT
4309399 TCTTTC
1 TCTTTC
4309405 TTTCCCTCTC
Statistics
Matches: 66, Mismatches: 11, Indels: 13
0.73 0.12 0.14
Matches are distributed among these distances:
7 4 0.06
8 4 0.06
9 2 0.03
10 48 0.73
11 8 0.12
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TCTTTCCTTT
Found at i:4309347 original size:20 final size:20
Alignment explanation
Indices: 4309316--4309404 Score: 90
Period size: 20 Copynumber: 4.3 Consensus size: 20
4309306 TCTTCTCTTC
*
4309316 TCCTTTTCTTTTCTTTCCTT
1 TCCTTTCCTTTTCTTTCCTT
* *
4309336 TCC-TTCTTTTTTTTTCTTCTT
1 TCCTTTCCTTTTCTTTC--CTT
*
4309357 CTCCTTTCCTTTTCTTTCCTC
1 -TCCTTTCCTTTTCTTTCCTT
*
4309378 TCCTTTCCTTTTCTTTCTTT
1 TCCTTTCCTTTTCTTTCCTT
*
4309398 TTCTTTC
1 TCCTTTC
4309405 TTTCCCTCTC
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
19 10 0.18
20 27 0.48
21 5 0.09
22 3 0.05
23 11 0.20
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TCCTTTCCTTTTCTTTCCTT
Found at i:4309357 original size:42 final size:43
Alignment explanation
Indices: 4309311--4309401 Score: 130
Period size: 42 Copynumber: 2.1 Consensus size: 43
4309301 CTTCTTCTTC
* * * *
4309311 TCTTCTCCTTTTCTTTTCTTTCCTTTCC-TTCTTTTTTTTTCT
1 TCTTCTCCTTTCCTTTTCTTTCCTCTCCTTTCCTTTTCTTTCT
4309353 TCTTCTCCTTTCCTTTTCTTTCCTCTCCTTTCCTTTTCTTTCT
1 TCTTCTCCTTTCCTTTTCTTTCCTCTCCTTTCCTTTTCTTTCT
*
4309396 TTTTCT
1 TCTTCT
4309402 TTCTTTCCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 26 0.60
43 17 0.40
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (43 bp):
TCTTCTCCTTTCCTTTTCTTTCCTCTCCTTTCCTTTTCTTTCT
Found at i:4309383 original size:47 final size:48
Alignment explanation
Indices: 4309297--4309402 Score: 144
Period size: 47 Copynumber: 2.2 Consensus size: 48
4309287 CTCCCTCCCC
* * *
4309297 TCTTCTTCTTCTTCTCTTCTCCTTTTCTTTTCTTTCCTTTCC-TTCTT
1 TCTTTTTCTTCTTCTCTTCTCCTTTTCTTTCCTCTCCTTTCCTTTCTT
*
4309344 TTTTTTTCTTCTTCTCCTT-TCCTTTTCTTTCCTCTCCTTTCCTTTTCTT
1 TCTTTTTCTTCTTCT-CTTCTCCTTTTCTTTCCTCTCCTTTCC-TTTCTT
4309393 TCTTTTTCTT
1 TCTTTTTCTT
4309403 TCTTTCCCTC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
47 34 0.67
48 3 0.06
49 14 0.27
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (48 bp):
TCTTTTTCTTCTTCTCTTCTCCTTTTCTTTCCTCTCCTTTCCTTTCTT
Found at i:4309417 original size:30 final size:30
Alignment explanation
Indices: 4309354--4309422 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
4309344 TTTTTTTCTT
*
4309354 CTTCTCCTTTCCTTTTCTTTCCTCTCCTTTC
1 CTTCT-CTTTCCTTTTCTTTCCTCTCCTCTC
* * *
4309385 CTTTTCTTTCTTTTTCTTT-CTTTCCCTCTC
1 CTTCTCTTTCCTTTTCTTTCCTCT-CCTCTC
4309415 CTTCTCTT
1 CTTCTCTT
4309423 CCCCCCACCC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 3 0.09
30 25 0.78
31 4 0.12
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (30 bp):
CTTCTCTTTCCTTTTCTTTCCTCTCCTCTC
Found at i:4309491 original size:27 final size:27
Alignment explanation
Indices: 4309461--4309528 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
4309451 TATATGGGCA
*
4309461 GTGCCGCCCATGGGAATGGCACAACCG
1 GTGCCGCCCATGGGAAAGGCACAACCG
* ***
4309488 GTGCCGCCTATGGGAAAGGCACATTTG
1 GTGCCGCCCATGGGAAAGGCACAACCG
4309515 GTGCCGCCCATGGG
1 GTGCCGCCCATGGG
4309529 CTACCCTCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.19, C:0.29, G:0.35, T:0.16
Consensus pattern (27 bp):
GTGCCGCCCATGGGAAAGGCACAACCG
Found at i:4309683 original size:22 final size:22
Alignment explanation
Indices: 4309658--4309700 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4309648 TAAAAATTTC
4309658 TCCACATCATAACATCATCTCT
1 TCCACATCATAACATCATCTCT
*
4309680 TCCATATCATAACATCATCTC
1 TCCACATCATAACATCATCTC
4309701 ACATGTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (22 bp):
TCCACATCATAACATCATCTCT
Found at i:4311036 original size:29 final size:29
Alignment explanation
Indices: 4310997--4311064 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
4310987 GAGTTTCCCG
* *
4310997 TGTAT-AATTG-CATCAAATTAAAGTTCA
1 TGTATAAATTGACATCAAATCAAAATTCA
*
4311024 TGTATACAATTGCACATTAAATCAAAATTCA
1 TGTATA-AATTG-ACATCAAATCAAAATTCA
4311055 TGTATAAATT
1 TGTATAAATT
4311065 TGAGATTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 5 0.15
29 5 0.15
30 4 0.12
31 20 0.59
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.37
Consensus pattern (29 bp):
TGTATAAATTGACATCAAATCAAAATTCA
Found at i:4313569 original size:12 final size:12
Alignment explanation
Indices: 4313552--4313584 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4313542 TGGCCCGCCC
4313552 ATATTAATTTTT
1 ATATTAATTTTT
4313564 ATATT-ATTTTT
1 ATATTAATTTTT
4313575 ATA-TAATTTT
1 ATATTAATTTT
4313585 AAAAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:4313606 original size:18 final size:18
Alignment explanation
Indices: 4313585--4313624 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
4313575 ATATAATTTT
*
4313585 AAAAATA-TATAATACATC
1 AAAAATACTA-AAAACATC
4313603 AAAAATACTAAAAACATC
1 AAAAATACTAAAAACATC
4313621 AAAA
1 AAAA
4313625 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATACTAAAAACATC
Found at i:4313751 original size:30 final size:30
Alignment explanation
Indices: 4313707--4313769 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
4313697 ACTTAACAAG
*
4313707 CAAATGCTTCTAAAATAATAACAAAATTAA
1 CAAATGCTTCTAAAAAAATAACAAAATTAA
* * *
4313737 CAAATGTTTTTAAAAAAATAACAAAATTGA
1 CAAATGCTTCTAAAAAAATAACAAAATTAA
4313767 CAA
1 CAA
4313770 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (30 bp):
CAAATGCTTCTAAAAAAATAACAAAATTAA
Found at i:4320559 original size:6 final size:6
Alignment explanation
Indices: 4320548--4320582 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
4320538 TAGGTTTCTA
*
4320548 GAAATG GAAATG GAAATG AAAATG GAAATG GAAAT
1 GAAATG GAAATG GAAATG GAAATG GAAATG GAAAT
4320583 TTGTAATCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (6 bp):
GAAATG
Found at i:4325116 original size:20 final size:20
Alignment explanation
Indices: 4325088--4325126 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4325078 TGTTAAATGA
4325088 ACAAATTTGACAACGAAGAT
1 ACAAATTTGACAACGAAGAT
* *
4325108 ACAACTTTGACAAGGAAGA
1 ACAAATTTGACAACGAAGA
4325127 CTCAGCATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (20 bp):
ACAAATTTGACAACGAAGAT
Found at i:4325245 original size:69 final size:69
Alignment explanation
Indices: 4325134--4325318 Score: 223
Period size: 69 Copynumber: 2.7 Consensus size: 69
4325124 AGACTCAGCA
* *
4325134 TCTTTAAAATGTGTTCATTTACGTTCGATTTAAATGCTTAATGTGCTGTTGCAAAGGGCTGATTT
1 TCTTTAAAATGTGTTCATTTACATTCCATTTAAATGCTTAATGTGCTGTTGCAAAGGGCTGATTT
4325199 GTAT-
66 GT-TG
* * * ***
4325203 TCTTTAAAATGTGTTCATTTACATTCCATTTAAGTTCTTAATGTGTTGTTGTGTAGGGCTGATTT
1 TCTTTAAAATGTGTTCATTTACATTCCATTTAAATGCTTAATGTGCTGTTGCAAAGGGCTGATTT
4325268 GTTG
66 GTTG
* * *
4325272 TC-TTAAAACTGTGTTCTTTTACGTT-AATTTTAAATGCTTAATGTGCT
1 TCTTTAAAA-TGTGTTCATTTACATTCCA-TTTAAATGCTTAATGTGCT
4325319 TTCCAAAAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
68 8 0.08
69 91 0.92
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.47
Consensus pattern (69 bp):
TCTTTAAAATGTGTTCATTTACATTCCATTTAAATGCTTAATGTGCTGTTGCAAAGGGCTGATTT
GTTG
Found at i:4329662 original size:10 final size:10
Alignment explanation
Indices: 4329647--4329679 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
4329637 AATTGAACCC
4329647 TTTTCTTTTT
1 TTTTCTTTTT
4329657 TTTTCTTTTT
1 TTTTCTTTTT
*
4329667 TCTTCTTTTT
1 TTTTCTTTTT
4329677 TTT
1 TTT
4329680 CTACTGCTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:4329896 original size:27 final size:28
Alignment explanation
Indices: 4329848--4329908 Score: 97
Period size: 27 Copynumber: 2.2 Consensus size: 28
4329838 TTTTCTTAGG
*
4329848 GGGCTGCTATTTTTTTATTTGGGCTGCT
1 GGGCTGCTAGTTTTTTATTTGGGCTGCT
4329876 GGGCTGCT-GTTTTTTATTTGGGCTGCT
1 GGGCTGCTAGTTTTTTATTTGGGCTGCT
*
4329903 AGGCTG
1 GGGCTG
4329909 ATGTGGGTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.07, C:0.15, G:0.33, T:0.46
Consensus pattern (28 bp):
GGGCTGCTAGTTTTTTATTTGGGCTGCT
Found at i:4329979 original size:11 final size:11
Alignment explanation
Indices: 4329963--4330055 Score: 71
Period size: 11 Copynumber: 8.1 Consensus size: 11
4329953 GTTAAAAAAA
4329963 TTTCTTTCTTT
1 TTTCTTTCTTT
4329974 TTTCTTTTTCTTT
1 TTTC--TTTCTTT
*
4329987 TTT-TTTCCCTT
1 TTTCTTT-CTTT
4329998 TTTCTTTCTTT
1 TTTCTTTCTTT
* *
4330009 TTCCTCCTTCTTC
1 TT--TCTTTCTTT
4330022 TTTCTTTCTTT
1 TTTCTTTCTTT
* * *
4330033 CTTCTTCCCTT
1 TTTCTTTCTTT
*
4330044 TTTCTTCCTTT
1 TTTCTTTCTTT
4330055 T
1 T
4330056 CCGTTCAGCC
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
10 3 0.05
11 40 0.62
12 3 0.05
13 19 0.29
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTCTTTCTTT
Found at i:4329998 original size:18 final size:18
Alignment explanation
Indices: 4329963--4330012 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
4329953 GTTAAAAAAA
4329963 TTTCTTTCTTTTTT--CTT
1 TTTCTTT-TTTTTTCCCTT
4329980 TTTCTTTTTTTTTCCCTT
1 TTTCTTTTTTTTTCCCTT
*
4329998 TTTCTTTCTTTTTCC
1 TTTCTTTTTTTTTCC
4330013 TCCTTCTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 6 0.20
17 7 0.23
18 17 0.57
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTCTTTTTTTTTCCCTT
Found at i:4330029 original size:28 final size:28
Alignment explanation
Indices: 4329964--4330040 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
4329954 TTAAAAAAAT
* ** *
4329964 TTCTTTCTTT-TTTCTTTTTCTTTTTTT
1 TTCTTTCTTTCTTTCTTTTTCCTCCTTC
*
4329991 TTCCCTT-TTTCTTTCTTTTTCCTCCTTC
1 TT-CTTTCTTTCTTTCTTTTTCCTCCTTC
*
4330019 TTCTTTCTTTCTTTCTTCTTCC
1 TTCTTTCTTTCTTTCTTTTTCC
4330041 CTTTTTCTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (28 bp):
TTCTTTCTTTCTTTCTTTTTCCTCCTTC
Found at i:4330037 original size:7 final size:7
Alignment explanation
Indices: 4329964--4330038 Score: 57
Period size: 7 Copynumber: 10.7 Consensus size: 7
4329954 TTAAAAAAAT
4329964 TTCTTTC
1 TTCTTTC
*
4329971 TTTTTTC
1 TTCTTTC
4329978 TT-TTTC
1 TTCTTTC
* *
4329984 TTTTTTT
1 TTCTTTC
4329991 TTCCCTTT-
1 TT--CTTTC
4329999 TTCTTTC
1 TTCTTTC
4330006 TT-TTTC
1 TTCTTTC
* *
4330012 CTCCTTC
1 TTCTTTC
4330019 TTCTTTC
1 TTCTTTC
4330026 TTTCTTTC
1 -TTCTTTC
4330034 TTCTT
1 TTCTT
4330039 CCCTTTTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
6 15 0.27
7 28 0.51
8 9 0.16
9 3 0.05
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (7 bp):
TTCTTTC
Found at i:4330038 original size:35 final size:34
Alignment explanation
Indices: 4329963--4330053 Score: 85
Period size: 35 Copynumber: 2.6 Consensus size: 34
4329953 GTTAAAAAAA
* ** *
4329963 TTTCTTTCTTTTTTCTTTTTCTTTTTTTTTCCCTT
1 TTTCTTTCTTTTTCCTCCTTCTTTTTCTTT-CCTT
4329998 TTTCTTTCTTTTTCCTCCTTCTTCTTTCTTT-CTT
1 TTTCTTTCTTTTTCCTCCTTCTT-TTTCTTTCCTT
* *
4330032 TCTTCTTCCCTTTTTCTTCCTT
1 T-TTCTT-TCTTTTTCCTCCTT
4330054 TTCCGTTCAG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
34 4 0.09
35 25 0.53
36 18 0.38
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (34 bp):
TTTCTTTCTTTTTCCTCCTTCTTTTTCTTTCCTT
Found at i:4330548 original size:30 final size:30
Alignment explanation
Indices: 4330505--4330672 Score: 223
Period size: 30 Copynumber: 5.6 Consensus size: 30
4330495 CAAAACTTTT
*
4330505 GGGGTTGAAATGTAATTTTGAGAAAGTTTA
1 GGGGTTAAAATGTAATTTTGAGAAAGTTTA
*
4330535 GAGGTTAAAATGTAATTTTGAGAAAGTTTA
1 GGGGTTAAAATGTAATTTTGAGAAAGTTTA
*
4330565 GAGGTTAAAATGTAATTTTGAGAAAGTTTA
1 GGGGTTAAAATGTAATTTTGAGAAAGTTTA
* * *
4330595 GGGGTTGAAATGCAA-TTTCA-AAATGTTTA
1 GGGGTTAAAATGTAATTTTGAGAAA-GTTTA
* *
4330624 GGGGTTTAAATGTAATTTTGAAAAAGTTTA
1 GGGGTTAAAATGTAATTTTGAGAAAGTTTA
* *
4330654 GGGGTCAAAATGCAATTTT
1 GGGGTTAAAATGTAATTTT
4330673 TTTAAAACAC
Statistics
Matches: 123, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.02
29 22 0.18
30 95 0.77
31 3 0.02
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
GGGGTTAAAATGTAATTTTGAGAAAGTTTA
Found at i:4330581 original size:60 final size:60
Alignment explanation
Indices: 4330507--4330672 Score: 228
Period size: 59 Copynumber: 2.8 Consensus size: 60
4330497 AAACTTTTGG
* * * *
4330507 GGTTGAAATGTAATTTTGAGAAAGTTTAGAGGTTAAAATGTAATTTTGAGAAA-GTTTAGA
1 GGTTAAAATGTAATTTTGAGAAAGTTTAGGGGTTAAAATGCAATTTTCA-AAATGTTTAGA
* *
4330567 GGTTAAAATGTAATTTTGAGAAAGTTTAGGGGTTGAAATGCAA-TTTCAAAATGTTTAGG
1 GGTTAAAATGTAATTTTGAGAAAGTTTAGGGGTTAAAATGCAATTTTCAAAATGTTTAGA
* * *
4330626 GGTTTAAATGTAATTTTGAAAAAGTTTAGGGGTCAAAATGCAATTTT
1 GGTTAAAATGTAATTTTGAGAAAGTTTAGGGGTTAAAATGCAATTTT
4330673 TTTAAAACAC
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
58 3 0.03
59 49 0.52
60 42 0.45
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (60 bp):
GGTTAAAATGTAATTTTGAGAAAGTTTAGGGGTTAAAATGCAATTTTCAAAATGTTTAGA
Found at i:4331099 original size:76 final size:76
Alignment explanation
Indices: 4330808--4331270 Score: 565
Period size: 78 Copynumber: 6.0 Consensus size: 76
4330798 TTTCTTTTTA
* * * * * * *
4330808 TTTGAAAATCAGAAATCG-ATAATAGCTCAGCGTGCGACCCAAGGCTCAACTCACCTCTCGCAAT
1 TTTGAAAAACAGAAATTGAAAAATACCTCGGCATGTGACCCAAGGCTCAACTCACCTCTCGCAAT
4330872 ATGAGTTGATT
66 ATGAGTTGATT
* *
4330883 TTTGAAAAACAGAAATTGAAAAGAATACATCGGCATGCGACCCAAGGCTCAACTCACCTCTCGCA
1 TTTGAAAAACAGAAATTG-AAA-AATACCTCGGCATGTGACCCAAGGCTCAACTCACCTCTCGCA
4330948 ATATGAGTTGATT
64 ATATGAGTTGATT
* * *
4330961 TTTGAAAAA-AGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACTTCTCGC
1 TTTGAAAAACAGAAA-TT-GAA-AAATACCTCGGCATGTGACCCAAGGCTCAACTCACCTCTCGC
4331025 AATATGAGTTGATT
63 AATATGAGTTGATT
* * *
4331039 TTTGAAAAATA-ACAATTGAAAAATACCTCGGCGTATGACCCAAGGCTCAACTCACCTCTCGCAA
1 TTTGAAAAACAGA-AATTGAAAAATACCTCGGCATGTGACCCAAGGCTCAACTCACCTCTCGCAA
4331103 TATGAGTTGATT
65 TATGAGTTGATT
* * ** *
4331115 TTTGAAAAACAGAAATTGAAAAATACCTCAGCTTGTGACCTGAGGCTCAACTCACCTCTCGCATT
1 TTTGAAAAACAGAAATTGAAAAATACCTCGGCATGTGACCCAAGGCTCAACTCACCTCTCGCAAT
4331180 ATGAGTTGATTTT
66 ATGAGTTGA--TT
* * ** * * * * *
4331193 TTTGAAAAATAGAAATTG-AAAATACCTCAGTGTGCGGCCCAAGGCTCAACTTACCTCTCGTATT
1 TTTGAAAAACAGAAATTGAAAAATACCTCGGCATGTGACCCAAGGCTCAACTCACCTCTCGCAAT
4331257 ATGAGTTGATT
66 ATGAGTTGATT
4331268 TTT
1 TTT
4331271 TTTTTTGAAA
Statistics
Matches: 344, Mismatches: 33, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
75 21 0.06
76 117 0.34
77 56 0.16
78 146 0.42
79 4 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (76 bp):
TTTGAAAAACAGAAATTGAAAAATACCTCGGCATGTGACCCAAGGCTCAACTCACCTCTCGCAAT
ATGAGTTGATT
Found at i:4332160 original size:10 final size:9
Alignment explanation
Indices: 4332147--4332207 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
4332137 TTCATCTTGA
4332147 TTTTTCTTTCT
1 TTTTTC-TT-T
4332158 TTTTTCTTT
1 TTTTTCTTT
*
4332167 TTTTCCTTT
1 TTTTTCTTT
4332176 TTTTTGC-TT
1 TTTTT-CTTT
*
4332185 TTTTCCTTT
1 TTTTTCTTT
4332194 TTTTT-TTGT
1 TTTTTCTT-T
4332203 TTTTT
1 TTTTT
4332208 TAGGCATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 3 0.07
9 31 0.72
10 3 0.07
11 6 0.14
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:4332163 original size:11 final size:10
Alignment explanation
Indices: 4332147--4332208 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 10
4332137 TTCATCTTGA
4332147 TTTTTCTTTCT
1 TTTTTCTTT-T
4332158 TTTTTC-TTT
1 TTTTTCTTTT
*
4332167 TTTTCCTTTT
1 TTTTTCTTTT
*
4332177 TTTTGCTTTT
1 TTTTTCTTTT
**
4332187 TTCCT-TTTT
1 TTTTTCTTTT
*
4332196 TTTTTGTTTT
1 TTTTTCTTTT
4332206 TTT
1 TTT
4332209 AGGCATAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
9 13 0.31
10 23 0.55
11 6 0.14
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:4332171 original size:19 final size:18
Alignment explanation
Indices: 4332147--4332199 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
4332137 TTCATCTTGA
4332147 TTTTTCTTTCTTTTTTCTT
1 TTTTTCTTT-TTTTTTCTT
*
4332166 TTTTTCCTTTTTTTTGCTT
1 TTTTT-CTTTTTTTTTCTT
*
4332185 TTTTCCTTTTTTTTT
1 TTTTTCTTTTTTTTT
4332200 TGTTTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.30
19 17 0.57
20 4 0.13
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTCTTTTTTTTTCTT
Found at i:4332176 original size:26 final size:27
Alignment explanation
Indices: 4332147--4332197 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
4332137 TTCATCTTGA
4332147 TTTTTCTTT-CTTTTTT-CTTTTTTTCC
1 TTTTT-TTTGCTTTTTTCCTTTTTTTCC
4332173 TTTTTTTTGCTTTTTTCCTTTTTTT
1 TTTTTTTTGCTTTTTTCCTTTTTTT
4332198 TTTGTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 3 0.13
26 12 0.52
27 8 0.35
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (27 bp):
TTTTTTTTGCTTTTTTCCTTTTTTTCC
Found at i:4332178 original size:18 final size:18
Alignment explanation
Indices: 4332147--4332198 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
4332137 TTCATCTTGA
*
4332147 TTTTT-CTTTCTTTTTTCTT
1 TTTTTCCTTT-TTTTTGC-T
4332166 TTTTTCCTTTTTTTTGCT
1 TTTTTCCTTTTTTTTGCT
4332184 TTTTTCCTTTTTTTT
1 TTTTTCCTTTTTTTT
4332199 TTGTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 16 0.52
19 11 0.35
20 4 0.13
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTCCTTTTTTTTGCT
Found at i:4332205 original size:18 final size:17
Alignment explanation
Indices: 4332147--4332206 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 17
4332137 TTCATCTTGA
*
4332147 TTTTTCTTTCTTTTTTCTT
1 TTTTTCCTT-TTTTTT-TT
*
4332166 TTTTTCCTTTTTTTTGCT
1 TTTTTCCTTTTTTTT-TT
4332184 TTTTTCCTTTTTTTTTT
1 TTTTTCCTTTTTTTTTT
4332201 GTTTTT
1 -TTTTT
4332207 TTAGGCATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 1 0.03
18 27 0.75
19 8 0.22
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (17 bp):
TTTTTCCTTTTTTTTTT
Found at i:4332205 original size:19 final size:19
Alignment explanation
Indices: 4332147--4332207 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
4332137 TTCATCTTGA
4332147 TTTTT-CTTTCTTTTTTCT-T
1 TTTTTCCTTT-TTTTTT-TGT
4332166 TTTTTCC--TTTTTTTTGCT
1 TTTTTCCTTTTTTTTTTG-T
4332184 TTTTTCCTTTTTTTTTTGT
1 TTTTTCCTTTTTTTTTTGT
4332203 TTTTT
1 TTTTT
4332208 TAGGCATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.03
17 6 0.16
18 9 0.24
19 11 0.30
20 10 0.27
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (19 bp):
TTTTTCCTTTTTTTTTTGT
Found at i:4339649 original size:17 final size:18
Alignment explanation
Indices: 4339608--4339649 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
4339598 ACAACTTTTT
4339608 CTTTTTTTGAAAACACAA
1 CTTTTTTTGAAAACACAA
***
4339626 AAATTTTTG-AAACACAA
1 CTTTTTTTGAAAACACAA
4339643 CTTTTTT
1 CTTTTTT
4339650 AAGAAGTACC
Statistics
Matches: 18, Mismatches: 6, Indels: 1
0.72 0.24 0.04
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (18 bp):
CTTTTTTTGAAAACACAA
Found at i:4340129 original size:8 final size:8
Alignment explanation
Indices: 4340116--4340153 Score: 58
Period size: 8 Copynumber: 4.5 Consensus size: 8
4340106 AATTGAACCC
4340116 TTTTCTTT
1 TTTTCTTT
4340124 TTTTCTTT
1 TTTTCTTT
4340132 TTTTCTTTT
1 TTTTC-TTT
4340141 TTCTTCTTT
1 TT-TTCTTT
4340150 TTTT
1 TTTT
4340154 TTCTGCTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 15 0.54
9 10 0.36
10 3 0.11
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTCTTT
Found at i:4340140 original size:15 final size:15
Alignment explanation
Indices: 4340115--4340155 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
4340105 AAATTGAACC
4340115 CTTTTCTTTTTTTCTT
1 CTTTTC-TTTTTTCTT
*
4340131 TTTTTCTTTTTTCTT
1 CTTTTCTTTTTTCTT
4340146 CTTTT-TTTTT
1 CTTTTCTTTTT
4340156 CTGCTGCTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 13 0.57
16 5 0.22
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
CTTTTCTTTTTTCTT
Found at i:4340382 original size:27 final size:28
Alignment explanation
Indices: 4340334--4340394 Score: 106
Period size: 27 Copynumber: 2.2 Consensus size: 28
4340324 TTTTTTTAGG
4340334 GGGCTGCTGTTTTTTTATTTGGGCTGCT
1 GGGCTGCTGTTTTTTTATTTGGGCTGCT
4340362 GGGCTGCTG-TTTTTTATTTGGGCTGCT
1 GGGCTGCTGTTTTTTTATTTGGGCTGCT
*
4340389 AGGCTG
1 GGGCTG
4340395 ATGTGGGTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 23 0.72
28 9 0.28
ACGTcount: A:0.05, C:0.15, G:0.34, T:0.46
Consensus pattern (28 bp):
GGGCTGCTGTTTTTTTATTTGGGCTGCT
Found at i:4340459 original size:4 final size:4
Alignment explanation
Indices: 4340450--4340519 Score: 50
Period size: 4 Copynumber: 19.8 Consensus size: 4
4340440 TTAAAAAAAG
* *
4340450 TTCT TTCT TT-T TTCT TT-T TTCT TT-T TT-T TCCC TT-T TTCT TTC-
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
*
4340492 TT-T TTCC TTC- TTC- TTCT TTCT TTCT TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
4340520 ATCTTCCCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
3 23 0.43
4 31 0.57
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:4340466 original size:11 final size:11
Alignment explanation
Indices: 4340450--4340542 Score: 60
Period size: 11 Copynumber: 8.1 Consensus size: 11
4340440 TTAAAAAAAG
4340450 TTCTTTCTTTT
1 TTCTTTCTTTT
*
4340461 TTCTTTTTTCTT
1 TTCTTTCTT-TT
* *
4340473 TTTTTTCCCTTT
1 TTCTTT-CTTTT
4340485 TTCTTTCTTTT
1 TTCTTTCTTTT
* *
4340496 TCCTTCTTCTTCT
1 TTC-T-TTCTTTT
*
4340509 TTCTTTCTTTC
1 TTCTTTCTTTT
* * *
4340520 ATCTTCCCTTT
1 TTCTTTCTTTT
*
4340531 TTCTTCCTTTT
1 TTCTTTCTTTT
4340542 T
1 T
4340543 CGTTCAGCCC
Statistics
Matches: 61, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
11 36 0.59
12 16 0.26
13 9 0.15
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (11 bp):
TTCTTTCTTTT
Found at i:4340494 original size:10 final size:10
Alignment explanation
Indices: 4340450--4340514 Score: 59
Period size: 10 Copynumber: 7.0 Consensus size: 10
4340440 TTAAAAAAAG
4340450 TTCTTTCTTT
1 TTCTTTCTTT
*
4340460 TT-TCT-TTT
1 TTCTTTCTTT
4340468 TTCTTT-TTT
1 TTCTTTCTTT
*
4340477 TTC--CCTTT
1 TTCTTTCTTT
4340485 TTCTTTCTTT
1 TTCTTTCTTT
* *
4340495 TTCCTTCTTC
1 TTCTTTCTTT
4340505 TTCTTTCTTT
1 TTCTTTCTTT
4340515 CTTTCATCTT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
8 11 0.26
9 10 0.23
10 22 0.51
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:4340500 original size:17 final size:17
Alignment explanation
Indices: 4340450--4340510 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
4340440 TTAAAAAAAG
*
4340450 TTCTTTCTTTTTTCTTTT
1 TTCTTTC-TTTTTCCTTT
4340468 TTCTTT-TTTTTCCCTTT
1 TTCTTTCTTTTT-CCTTT
*
4340485 TTCTTTCTTTTTCCTTC
1 TTCTTTCTTTTTCCTTT
4340502 TTC-TTCTTT
1 TTCTTTCTTT
4340511 CTTTCTTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
16 11 0.28
17 17 0.44
18 11 0.28
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCTTTCTTTTTCCTTT
Found at i:4340646 original size:20 final size:21
Alignment explanation
Indices: 4340616--4340655 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
4340606 AGCTCTCCTC
*
4340616 TTCTCTTCTCTTTTTCTTTTT
1 TTCTCTTCTCTTTCTCTTTTT
4340637 TTCT-TTCTCTTTCTCTTTT
1 TTCTCTTCTCTTTCTCTTTT
4340656 GTTTTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (21 bp):
TTCTCTTCTCTTTCTCTTTTT
Found at i:4340991 original size:30 final size:30
Alignment explanation
Indices: 4340957--4341086 Score: 140
Period size: 30 Copynumber: 4.4 Consensus size: 30
4340947 CAAAACTTTT
* *
4340957 GGGGTCGAAACGTAATTTTTAGAAAGTTTA
1 GGGGTCGAAATGTAATTTTGAGAAAGTTTA
*
4340987 GGGGTC-AAATTGTAATTTTGAGAAATTTTA
1 GGGGTCGAAA-TGTAATTTTGAGAAAGTTTA
* *
4341017 AGGGTTGAAATGTAA-TTTGA-AAATGTTTA
1 GGGGTCGAAATGTAATTTTGAGAAA-GTTTA
** *
4341046 GGGGTTTAAATGTAATTTTGAAAAAGTTTA
1 GGGGTCGAAATGTAATTTTGAGAAAGTTTA
*
4341076 GGGGTCAAAAT
1 GGGGTCGAAAT
4341087 ACAATTTTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
28 3 0.04
29 25 0.29
30 51 0.60
31 6 0.07
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
GGGGTCGAAATGTAATTTTGAGAAAGTTTA
Found at i:4341093 original size:59 final size:59
Alignment explanation
Indices: 4340982--4341093 Score: 136
Period size: 59 Copynumber: 1.9 Consensus size: 59
4340972 TTTTTAGAAA
* * ** **
4340982 GTTTAGGGGTCAAATTGTAATTTTGAGAAATTTTAAGGGTTGAAATGTAATTTGAAAAT
1 GTTTAGGGGTCAAATTGTAATTTTGAAAAAGTTTAAGGGTCAAAATACAATTTGAAAAT
* *
4341041 GTTTAGGGGTTTAAA-TGTAATTTTGAAAAAGTTTAGGGGTCAAAATACAATTT
1 GTTTAGGGG-TCAAATTGTAATTTTGAAAAAGTTTAAGGGTCAAAATACAATTT
4341094 TTTTAAAACA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
59 40 0.91
60 4 0.09
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (59 bp):
GTTTAGGGGTCAAATTGTAATTTTGAAAAAGTTTAAGGGTCAAAATACAATTTGAAAAT
Found at i:4346815 original size:10 final size:10
Alignment explanation
Indices: 4346800--4346861 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
4346790 TTTGAACCAT
*
4346800 TACCAATTCG
1 TACCAATTCA
*
4346810 TACCAAATACCA
1 TACC-AAT-TCA
*
4346822 TACCATTTCA
1 TACCAATTCA
4346832 TACCAATTCCA
1 TACCAATT-CA
* *
4346843 TACCATTTCG
1 TACCAATTCA
4346853 TACCAATTC
1 TACCAATTC
4346862 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:4346845 original size:21 final size:21
Alignment explanation
Indices: 4346800--4346862 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
4346790 TTTGAACCAT
* *
4346800 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
4346822 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
4346843 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
4346863 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:4348834 original size:32 final size:33
Alignment explanation
Indices: 4348793--4348854 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
4348783 TGCAATAGAT
*
4348793 TTGCGACGT-GCTGTATCATACAGCTAATAGGC
1 TTGCAACGTGGCTGTATCATACAGCTAATAGGC
* *
4348825 TTGCAACGTGGCTGTGTTATACAGCTAATA
1 TTGCAACGTGGCTGTATCATACAGCTAATA
4348855 TTCGTCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (33 bp):
TTGCAACGTGGCTGTATCATACAGCTAATAGGC
Found at i:4352457 original size:25 final size:26
Alignment explanation
Indices: 4352428--4352476 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
4352418 TTCCTCTAAC
4352428 GTTTTCTTCTTCTTTC-TTTCTTTCT
1 GTTTTCTTCTTCTTTCATTTCTTTCT
* *
4352453 GTTTTGTTTTTCTTTCATTTCTTT
1 GTTTTCTTCTTCTTTCATTTCTTT
4352477 TCATTTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.02, C:0.18, G:0.06, T:0.73
Consensus pattern (26 bp):
GTTTTCTTCTTCTTTCATTTCTTTCT
Done.