Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 47 of 333
Found at i:13472477 original size:5 final size:5
Alignment explanation
Indices: 13472467--13472502 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
13472457 TACATTGTAA
*
13472467 AAATT AAATT AATTAT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAAT-T AAATT AAATT AAATT AAATT
13472503 CTGAGACACG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AAATT
Found at i:13475897 original size:10 final size:10
Alignment explanation
Indices: 13475882--13475907 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
13475872 GTATACGAAT
13475882 CTGTTGAAAG
1 CTGTTGAAAG
13475892 CTGTTGAAAG
1 CTGTTGAAAG
13475902 CTGTTG
1 CTGTTG
13475908 TGATATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.35
Consensus pattern (10 bp):
CTGTTGAAAG
Found at i:13479347 original size:15 final size:16
Alignment explanation
Indices: 13479327--13479356 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13479317 GACCTAAGAG
13479327 CACA-TTCATGTAATC
1 CACATTTCATGTAATC
13479342 CACATTTCATGTAAT
1 CACATTTCATGTAAT
13479357 ACAGCGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (16 bp):
CACATTTCATGTAATC
Found at i:13486851 original size:63 final size:62
Alignment explanation
Indices: 13486781--13486995 Score: 161
Period size: 63 Copynumber: 3.3 Consensus size: 62
13486771 ACTGTTCATA
*
13486781 ATCGTAAATCAATGAACTTAAATTGTGATCGTAAATCAACAAGTTTTAATAATACCAATTGTG
1 ATCGTAAATCAATGAACTTAAATTGTGATCGTAAATAAACAAG-TTTAATAATACCAATTGTG
* ** * *
13486844 ATCGTAAATCAGTGAACTATTTGAATGGAGTT-TGGATCGTAAATTGACGAA--CTAAAAATA--
1 ATCGTAAATCAATGAAC---TT-AA---A-TTGT-GATCGTAAATAAAC-AAGTTTAATAATACC
13486904 AATTGTTCATG
56 AATTG----TG
* *
13486915 ATCGTAAATCAATGAACTTAAGTTGTGATCGTAAATAAACAAGCTTTAATAATACCAATCGTG
1 ATCGTAAATCAATGAACTTAAATTGTGATCGTAAATAAACAAG-TTTAATAATACCAATTGTG
* *
13486978 TTCGTAAATCAGTGAACT
1 ATCGTAAATCAATGAACT
13486996 ATTTGAATAG
Statistics
Matches: 118, Mismatches: 14, Indels: 40
0.69 0.08 0.23
Matches are distributed among these distances:
62 2 0.02
63 48 0.41
64 1 0.01
65 7 0.06
66 2 0.02
67 13 0.11
68 2 0.02
69 7 0.06
70 2 0.02
71 32 0.27
72 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.32
Consensus pattern (62 bp):
ATCGTAAATCAATGAACTTAAATTGTGATCGTAAATAAACAAGTTTAATAATACCAATTGTG
Found at i:13487129 original size:134 final size:134
Alignment explanation
Indices: 13486538--13487122 Score: 710
Period size: 134 Copynumber: 4.4 Consensus size: 134
13486528 AAACTGTTCA
* * * **
13486538 TGATTGTAAATCAACAAGCTTTAATAATACCAGTTGTAATCATAAATCAGTGAACCGTTTGAAT-
1 TGATCGTAAATCAACAAGCTTTAATAATACCAGTTGTGATCGTAAATCAGTGAACTATTTGAATA
* * ** * *
13486602 GAGGTTGTGATTGTAAATCAGTAAACTCAAAATAAATTGTTCATGATTGTAAATCAACGAACTTA
66 GA-GTTGCGATCGTAAATCAGCGAACTCAAAATAAATTGTTCATGATCGTAAATCAATGAACTTA
13486667 AGCTG
130 AGCTG
* * ** * *
13486672 TGATCGTAAATCAGA-AAGCTTTAGTAATACTAGCCGTGATCATAAATCAGTGAACTTTTTGAAT
1 TGATCGTAAATCA-ACAAGCTTTAATAATACCAGTTGTGATCGTAAATCAGTGAACTATTTGAAT
* * * * *
13486736 AAAGTTGCAATTGTAAATCAGCGAACTCAAAATAAACTGTTCATAATCGTAAATCAATGAACTTA
65 AGAGTTGCGATCGTAAATCAGCGAACTCAAAATAAATTGTTCATGATCGTAAATCAATGAACTTA
**
13486801 AATTG
130 AGCTG
* * *
13486806 TGATCGTAAATCAACAAGTTTTAATAATACCAATTGTGATCGTAAATCAGTGAACTATTTGAATG
1 TGATCGTAAATCAACAAGCTTTAATAATACCAGTTGTGATCGTAAATCAGTGAACTATTTGAATA
* *
13486871 GAGTTTG-GATCGTAAAT-TGACGAACTAAAAATAAATTGTTCATGATCGTAAATCAATGAACTT
66 GAG-TTGCGATCGTAAATCAG-CGAACTCAAAATAAATTGTTCATGATCGTAAATCAATGAACTT
*
13486934 AAGTTG
129 AAGCTG
* * * *
13486940 TGATCGTAAATAAACAAGCTTTAATAATACCAATCGTGTTCGTAAATCAGTGAACTATTTGAATA
1 TGATCGTAAATCAACAAGCTTTAATAATACCAGTTGTGATCGTAAATCAGTGAACTATTTGAATA
* * * * *
13487005 GAGTTGCGACCATAAATCAGTGAACTTAAAATGAATTGTTCATGATCGTAAATCAATGAACTTAA
66 GAGTTGCGATCGTAAATCAGCGAACTCAAAATAAATTGTTCATGATCGTAAATCAATGAACTTAA
*
13487070 GCTA
131 GCTG
* * * *
13487074 TGATTGCAAATCAGCAAGCTTTAATAATACCAGTTGTGATTGTAAATCA
1 TGATCGTAAATCAACAAGCTTTAATAATACCAGTTGTGATCGTAAATCA
13487123 ACGAACTCAA
Statistics
Matches: 387, Mismatches: 57, Indels: 14
0.84 0.12 0.03
Matches are distributed among these distances:
133 5 0.01
134 376 0.97
135 6 0.02
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (134 bp):
TGATCGTAAATCAACAAGCTTTAATAATACCAGTTGTGATCGTAAATCAGTGAACTATTTGAATA
GAGTTGCGATCGTAAATCAGCGAACTCAAAATAAATTGTTCATGATCGTAAATCAATGAACTTAA
GCTG
Found at i:13487158 original size:233 final size:233
Alignment explanation
Indices: 13486890--13487334 Score: 584
Period size: 233 Copynumber: 1.9 Consensus size: 233
13486880 TCGTAAATTG
* * * * **
13486890 ACGAACTAAAAATAAATTGTTCATGATCGTAAATCAATGAACTTAAGTTGTGATCGTAAATAAAC
1 ACGAACTAAAAATAAACTATTCATGATCATAAATCAATGAACTTAAATTGTGATAATAAATAAAC
* * **
13486955 AAGCTTTAATAATACCAATCGTGTTCGTAAATCAGTGAACTATTTGAATAGAGTTGCGACCATAA
66 AAGCTTTAATAATACCAATCGGGATCGTAAATCAACGAACTATTTGAATAGAGTTGCGACCATAA
** * * * **
13487020 ATCAGTGAACTTAAAATGAATTGTTCATGATCGTAAATCAATGAACTTAAGCTATGATTGCAAAT
131 ATCAGCAAACTCAAAATGAACTATTCATGATCGTAAATCAATGAACTTAAGCTATGATCACAAAT
*
13487085 CAGCAAGCTTTAATAATACCAGTTGTGATTGTAAATCA
196 CAACAAGCTTTAATAATACCAGTTGTGATTGTAAATCA
* * * *
13487123 ACGAACTCAAAATGAACTATTCATGATCATAAATCATTGAACTTAAATTGTGATAATAAATCAAC
1 ACGAACTAAAAATAAACTATTCATGATCATAAATCAATGAACTTAAATTGTGATAATAAATAAAC
* * * * * *
13487188 AAGTTTTAATAATACCAGTCGGGATCGTAAATCAACGAACTGTTTGAATGGAGTTGCGATCGTAA
66 AAGCTTTAATAATACCAATCGGGATCGTAAATCAACGAACTATTTGAATAGAGTTGCGACCATAA
* * * * * *
13487253 ATTAGCAAACTCAAAATGAACTATTTATGATCGTAAATCACTGAACTTAAGTTGTGATCATAAAT
131 ATCAGCAAACTCAAAATGAACTATTCATGATCGTAAATCAATGAACTTAAGCTATGATCACAAAT
13487318 CAACAAGCTTTAATAAT
196 CAACAAGCTTTAATAAT
13487335 TCCAATCGTG
Statistics
Matches: 178, Mismatches: 34, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
233 178 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (233 bp):
ACGAACTAAAAATAAACTATTCATGATCATAAATCAATGAACTTAAATTGTGATAATAAATAAAC
AAGCTTTAATAATACCAATCGGGATCGTAAATCAACGAACTATTTGAATAGAGTTGCGACCATAA
ATCAGCAAACTCAAAATGAACTATTCATGATCGTAAATCAATGAACTTAAGCTATGATCACAAAT
CAACAAGCTTTAATAATACCAGTTGTGATTGTAAATCA
Found at i:13487184 original size:99 final size:99
Alignment explanation
Indices: 13487017--13487228 Score: 262
Period size: 99 Copynumber: 2.1 Consensus size: 99
13487007 GTTGCGACCA
** * * * * * **
13487017 TAAATCAGTGAACTTAAAATGAATTGTTCATGATCGTAAATCAATGAACTTAAGCTATGATTGCA
1 TAAATCAACGAACTCAAAATGAACTATTCATGATCATAAATCAATGAACTTAAACTATGATAACA
* * * *
13487082 AATCAGCAAGCTTTAATAATACCAGTTGTGATTG
66 AATCAACAAGCTTTAATAATACCAGTCGGGATCG
* * * *
13487116 TAAATCAACGAACTCAAAATGAACTATTCATGATCATAAATCATTGAACTTAAATTGTGATAATA
1 TAAATCAACGAACTCAAAATGAACTATTCATGATCATAAATCAATGAACTTAAACTATGATAACA
*
13487181 AATCAACAAGTTTTAATAATACCAGTCGGGATCG
66 AATCAACAAGCTTTAATAATACCAGTCGGGATCG
13487215 TAAATCAACGAACT
1 TAAATCAACGAACT
13487229 GTTTGAATGG
Statistics
Matches: 95, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
99 95 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (99 bp):
TAAATCAACGAACTCAAAATGAACTATTCATGATCATAAATCAATGAACTTAAACTATGATAACA
AATCAACAAGCTTTAATAATACCAGTCGGGATCG
Found at i:13487273 original size:134 final size:134
Alignment explanation
Indices: 13487126--13487368 Score: 378
Period size: 134 Copynumber: 1.8 Consensus size: 134
13487116 TAAATCAACG
*
13487126 AACTCAAAATGAACTATTCATGATCATAAATCATTGAACTTAAATTGTGATAATAAATCAACAAG
1 AACTCAAAATGAACTATTCATGATCATAAATCACTGAACTTAAATTGTGATAATAAATCAACAAG
* * *
13487191 TTTTAATAATACCAGTCGGGATCGTAAATCAACGAACTGTTTGAATGGAGTTGCGATCGTAAATT
66 CTTTAATAATACCAATCGGGATCATAAATCAACGAACTGTTTGAATGGAGTTGCGATCGTAAATT
13487256 AGCA
131 AGCA
* * * *
13487260 AACTCAAAATGAACTATTTATGATCGTAAATCACTGAACTTAAGTTGTGATCATAAATCAACAAG
1 AACTCAAAATGAACTATTCATGATCATAAATCACTGAACTTAAATTGTGATAATAAATCAACAAG
* * * *
13487325 CTTTAATAATTCCAATCGTGATCATAAATCATCGATCTGTTTGA
66 CTTTAATAATACCAATCGGGATCATAAATCAACGAACTGTTTGA
13487369 TGTATTCCAA
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
134 97 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (134 bp):
AACTCAAAATGAACTATTCATGATCATAAATCACTGAACTTAAATTGTGATAATAAATCAACAAG
CTTTAATAATACCAATCGGGATCATAAATCAACGAACTGTTTGAATGGAGTTGCGATCGTAAATT
AGCA
Found at i:13488111 original size:16 final size:16
Alignment explanation
Indices: 13488090--13488120 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
13488080 CCAAACCTAC
13488090 AAAAAATAGATTTCTA
1 AAAAAATAGATTTCTA
13488106 AAAAAATAGATTTCT
1 AAAAAATAGATTTCT
13488121 TTTGAGCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (16 bp):
AAAAAATAGATTTCTA
Found at i:13493077 original size:21 final size:21
Alignment explanation
Indices: 13493036--13493090 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
13493026 ATACTAAATT
*
13493036 TATAAATAAAATGTATGATAA
1 TATAAATAAAATGAATGATAA
*
13493057 TATAAATAATAT-AATGAATAA
1 TATAAATAAAATGAATG-ATAA
13493078 TATATACATAAAA
1 TATA-A-ATAAAA
13493091 GTTATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 3 0.11
21 19 0.68
22 1 0.04
23 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (21 bp):
TATAAATAAAATGAATGATAA
Found at i:13500603 original size:22 final size:25
Alignment explanation
Indices: 13500577--13500630 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
13500567 TTATAAATTC
13500577 AATTTAAAAG-ATA-TAAT-ACAAT
1 AATTTAAAAGCATATTAATAACAAT
*
13500599 AATTT-CAAGCATATTTAATAACAAT
1 AATTTAAAAGCATA-TTAATAACAAT
13500624 AATTTAA
1 AATTTAA
13500631 TCATCAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
24 4 0.16
25 10 0.40
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (25 bp):
AATTTAAAAGCATATTAATAACAAT
Found at i:13505290 original size:18 final size:18
Alignment explanation
Indices: 13505247--13505290 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
13505237 TTCTATATAG
*
13505247 TTTATAATTTTTTACTCT
1 TTTATAATTTTTTACTAT
*
13505265 TTTATAATTTTTTCCTAAT
1 TTTATAATTTTTTACT-AT
13505284 TTT-TAAT
1 TTTATAAT
13505291 AAATTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTATAATTTTTTACTAT
Found at i:13512929 original size:13 final size:14
Alignment explanation
Indices: 13512891--13512931 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
13512881 TGTGGGGTAG
*
13512891 GATTCTGTATATCT
1 GATTCTGCATATCT
*
13512905 G-TTCTGCTTATCT
1 GATTCTGCATATCT
13512918 GATTCTG-ATATCT
1 GATTCTGCATATCT
13512931 G
1 G
13512932 TATTTGTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (14 bp):
GATTCTGCATATCT
Found at i:13519914 original size:3 final size:3
Alignment explanation
Indices: 13519901--13519993 Score: 57
Period size: 3 Copynumber: 31.3 Consensus size: 3
13519891 AAGGAATACT
* * * * * *
13519901 ATA ACA ATA ATA AT- GTA ATT ATA ATA ATA ATA TTA ATA ATA TTA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
13519948 ATC AT- ATC ATA ATA ATA AGTA GATA A-A ATA ATG ATA ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA A-TA -ATA ATA ATA ATA ATA ATA ATA ATA
13519993 A
1 A
13519994 CAGGGATAAA
Statistics
Matches: 68, Mismatches: 17, Indels: 10
0.72 0.18 0.11
Matches are distributed among these distances:
2 5 0.07
3 58 0.85
4 4 0.06
5 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:13526084 original size:13 final size:14
Alignment explanation
Indices: 13526066--13526094 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13526056 TTTATTAAAT
13526066 AATATA-ATTTTAA
1 AATATATATTTTAA
13526079 AATATATATTTTAA
1 AATATATATTTTAA
13526093 AA
1 AA
13526095 ATACAGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATATATATTTTAA
Found at i:13526085 original size:15 final size:15
Alignment explanation
Indices: 13526062--13526094 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
13526052 TTAATTTATT
13526062 AAATAATATAATTTTA
1 AAATAATAT-ATTTTA
13526078 AAAT-ATATATTTTA
1 AAATAATATATTTTA
13526092 AAA
1 AAA
13526095 ATACAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 4 0.24
16 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATAATATATTTTA
Found at i:13526095 original size:15 final size:14
Alignment explanation
Indices: 13526060--13526097 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
13526050 TTTTAATTTA
13526060 TTAAATAATATAATT
1 TTAAA-AATATAATT
13526075 TT-AAAATATATATT
1 TTAAAAATATA-ATT
13526089 TTAAAAATA
1 TTAAAAATA
13526098 CAGATTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 7 0.33
15 8 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAAAATATAATT
Found at i:13541453 original size:32 final size:32
Alignment explanation
Indices: 13541394--13541470 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
13541384 CAAGGCTCCC
13541394 CATTTTTGAAAATATTCTTTTTATTTTATTTT
1 CATTTTTGAAAATATTCTTTTTATTTTATTTT
13541426 CATTTTT-AAAATATT-TTTTTATTTTTTATTTT
1 CATTTTTGAAAATATTCTTTTTA--TTTTATTTT
**
13541458 TTTTTTTGAAAAT
1 CATTTTTGAAAAT
13541471 TGAAAATACG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 6 0.15
31 8 0.20
32 21 0.52
33 5 0.12
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.68
Consensus pattern (32 bp):
CATTTTTGAAAATATTCTTTTTATTTTATTTT
Found at i:13541459 original size:17 final size:17
Alignment explanation
Indices: 13541411--13541462 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
13541401 GAAAATATTC
*
13541411 TTTTTATTTTATTTTCAT
1 TTTTTATTTT-TTTTTAT
* *
13541429 TTTTAAAATATTTTTTTAT
1 TTTT--TATTTTTTTTTAT
13541448 TTTTTATTTTTTTTT
1 TTTTTATTTTTTTTT
13541463 TTGAAAATTG
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
17 9 0.33
18 4 0.15
19 10 0.37
20 4 0.15
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTATTTTTTTTTAT
Found at i:13541752 original size:13 final size:13
Alignment explanation
Indices: 13541734--13541758 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13541724 TAGTATTATT
13541734 ATTATTAAAATAA
1 ATTATTAAAATAA
13541747 ATTATTAAAATA
1 ATTATTAAAATA
13541759 GTCACTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTATTAAAATAA
Found at i:13544484 original size:18 final size:17
Alignment explanation
Indices: 13544463--13544519 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
13544453 TTTTTGAGTA
13544463 TTTTATATATTTTATAAT
1 TTTTATATATTTT-TAAT
* *
13544481 TTTTAATAAATTTTGAAT
1 TTTT-ATATATTTTTAAT
*
13544499 TTATATATATTTTTTAAT
1 TTTTATATA-TTTTTAAT
13544517 TTT
1 TTT
13544520 AATTTATGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
17 4 0.13
18 19 0.61
19 8 0.26
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTATATATTTTTAAT
Found at i:13544513 original size:19 final size:17
Alignment explanation
Indices: 13544444--13544520 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 17
13544434 AATATATTTC
13544444 TTTTATA-ATTTTTTGAGTA
1 TTTTATATATTTTTT-A--A
*
13544463 TTTTATATATTTTATAA
1 TTTTATATATTTTTTAA
* *
13544480 TTTT-TAATAAATTTTGAA
1 TTTTAT-AT-ATTTTTTAA
13544498 TTTATATATATTTTTTAA
1 TTT-TATATATTTTTTAA
13544516 TTTTA
1 TTTTA
13544521 ATTTATGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
16 1 0.02
17 9 0.19
18 19 0.40
19 11 0.23
20 7 0.15
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
TTTTATATATTTTTTAA
Found at i:13545775 original size:124 final size:124
Alignment explanation
Indices: 13545555--13545802 Score: 460
Period size: 124 Copynumber: 2.0 Consensus size: 124
13545545 GAAGTTTCAG
13545555 AACAAGTTACAGTGGAACCGGCTGCACCCAGAGTCAATTCAAAATGTTAAGCCCAGCTGAGGGAG
1 AACAAGTTACAGTGGAACCGGCTGCACCCAGAGTCAATTCAAAATGTTAAGCCCAGCTGAGGGAG
13545620 GTTTTAATGATCTCATAAGCCGTCCAATTGATATCTTGGAAGATGAAAAGGTTCCTGTT
66 GTTTTAATGATCTCATAAGCCGTCCAATTGATATCTTGGAAGATGAAAAGGTTCCTGTT
* * *
13545679 AACAAGTTACAGTGGAACCGGCTGCACCTAGAGTTAATTCAAAATGTTGAGCCCAGCTGAGGGAG
1 AACAAGTTACAGTGGAACCGGCTGCACCCAGAGTCAATTCAAAATGTTAAGCCCAGCTGAGGGAG
*
13545744 GTTTTAATGATCTCATAAGCCGTCCAATTGATATCTTGGAAGATGAAAATGTTCCTGTT
66 GTTTTAATGATCTCATAAGCCGTCCAATTGATATCTTGGAAGATGAAAAGGTTCCTGTT
13545803 CTTCCAAAGT
Statistics
Matches: 120, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 120 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (124 bp):
AACAAGTTACAGTGGAACCGGCTGCACCCAGAGTCAATTCAAAATGTTAAGCCCAGCTGAGGGAG
GTTTTAATGATCTCATAAGCCGTCCAATTGATATCTTGGAAGATGAAAAGGTTCCTGTT
Found at i:13562707 original size:104 final size:105
Alignment explanation
Indices: 13562461--13562728 Score: 441
Period size: 104 Copynumber: 2.6 Consensus size: 105
13562451 TTGTATATAA
** *
13562461 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
13562525 TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
13562566 AAGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
13562631 TGAAATGTG-AAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
** *
13562670 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGCGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
13562729 ATAACGGTTA
Statistics
Matches: 152, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
104 84 0.55
105 67 0.44
106 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (105 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:13579870 original size:23 final size:22
Alignment explanation
Indices: 13579832--13579874 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
13579822 AAATATAATT
13579832 ATTTTTATAATATTTTAAATAC
1 ATTTTTATAATATTTTAAATAC
*
13579854 ATTTTATATAATTTTTTAAAT
1 ATTTT-TATAATATTTTAAAT
13579875 TTAAATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTTATAATATTTTAAATAC
Found at i:13590093 original size:2 final size:2
Alignment explanation
Indices: 13590086--13590125 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
13590076 TGCTATAGTG
13590086 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13590126 TACAAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13595162 original size:2 final size:2
Alignment explanation
Indices: 13595157--13595197 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
13595147 ATACTTACAA
*
13595157 AC AC AC AC AC AC AC AC AC AC AA AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
13595198 TATATATACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:13595761 original size:21 final size:21
Alignment explanation
Indices: 13595700--13595761 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
13595690 AGAGTTGAAC
* * *
13595700 AGAAGCTCATAGGAGCTGAAT
1 AGAAGCTCAAAAGAGCTAAAT
* * *
13595721 AGAAACCCATAAAG-GTTAAAT
1 AGAAGCTCA-AAAGAGCTAAAT
13595742 AGAAGCTCAAAAGAGCTAAA
1 AGAAGCTCAAAAGAGCTAAA
13595762 CGAAAAGCCA
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
20 4 0.13
21 24 0.80
22 2 0.07
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.16
Consensus pattern (21 bp):
AGAAGCTCAAAAGAGCTAAAT
Found at i:13597879 original size:162 final size:162
Alignment explanation
Indices: 13597678--13598006 Score: 500
Period size: 162 Copynumber: 2.0 Consensus size: 162
13597668 TCAACACAGT
* ** * *
13597678 TAAAC-TTTACTTACTTGTCTAAAACCACATTTTTCAAACATATAAATATAATTTCACAATATTA
1 TAAACATTTACTTACTTATCTAAAACCACAAATTTCAAACATAAAAATATAAATTCACAATATTA
*
13597742 TACTTGATTTAATTTCAATAAATTCAATTAAACATAAAATAAGTGTCTACAAAATAATTTTCATA
66 TACTCGATTTAATTTCAATAAATTCAATTAAACATAAAATAAGTGTCTACAAAA-AATTTTCATA
*
13597807 ATCTTTCAACCGTTTCAATATTTTAAGTTTGTA
130 ATCTTTCAACCGTTTCAATATTTTAAGCTTGTA
* *
13597840 TCAACATTTACTTTCTTATCT-AAACCACAAATTTCAAACATAAAAATATAAATTCACAATATTA
1 TAAACATTTACTTACTTATCTAAAACCACAAATTTCAAACATAAAAATATAAATTCACAATATTA
* * *
13597904 TACTCGATTTAATTTCAGTAAATTCAATTAAACATAAAATAATTGTCTACAAAAGATTTTCATAA
66 TACTCGATTTAATTTCAATAAATTCAATTAAACATAAAATAAGTGTCTACAAAAAATTTTCATAA
* **
13597969 TCTTTCAGCCGTTTTGATATTTTAAGCTTGTA
131 TCTTTCAACCGTTTCAATATTTTAAGCTTGTA
13598001 TAAACA
1 TAAACA
13598007 CTTATTAACT
Statistics
Matches: 150, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
161 43 0.29
162 94 0.63
163 13 0.09
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (162 bp):
TAAACATTTACTTACTTATCTAAAACCACAAATTTCAAACATAAAAATATAAATTCACAATATTA
TACTCGATTTAATTTCAATAAATTCAATTAAACATAAAATAAGTGTCTACAAAAAATTTTCATAA
TCTTTCAACCGTTTCAATATTTTAAGCTTGTA
Found at i:13601054 original size:22 final size:23
Alignment explanation
Indices: 13601007--13601056 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
13600997 ATATTTTTAC
*
13601007 TTTATAAATTAGTTTTTAATTAT
1 TTTATAAATTAGTTTTGAATTAT
*
13601030 TTTATAATTTATGTTTTGAATT-T
1 TTTATAAATTA-GTTTTGAATTAT
13601053 TTTA
1 TTTA
13601057 AATATACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (23 bp):
TTTATAAATTAGTTTTGAATTAT
Found at i:13601507 original size:25 final size:25
Alignment explanation
Indices: 13601479--13601531 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
13601469 CCTTACTCAA
*
13601479 ACAACACTTGGGATAACAAGTTAGG
1 ACAACACTTGGGACAACAAGTTAGG
* * *
13601504 ACAACAGTTGGGACAATATGTTAGG
1 ACAACACTTGGGACAACAAGTTAGG
13601529 ACA
1 ACA
13601532 GTTAAAGCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.21
Consensus pattern (25 bp):
ACAACACTTGGGACAACAAGTTAGG
Found at i:13602434 original size:27 final size:27
Alignment explanation
Indices: 13602405--13602633 Score: 192
Period size: 27 Copynumber: 8.5 Consensus size: 27
13602395 GAATACTTTA
* * *
13602405 GTTTACCAAATCACCAAAATACCCCTA
1 GTTTACAAAATTACCAAAATACCCCTG
** *
13602432 GTTTGTAAAATTACCAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCCTG
*
13602459 GTTTACAAAATTACCAAAATACCCCCG
1 GTTTACAAAATTACCAAAATACCCCTG
** *
13602486 GTTTGTAAAATTA-CAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCCTG
*
13602512 GTTTACAAAATTACCAAAATACCACTG
1 GTTTACAAAATTACCAAAATACCCCTG
** * * *
13602539 GTTTGTAAAATTACCGAAATACCCTTA
1 GTTTACAAAATTACCAAAATACCCCTG
** **
13602566 GTTTGTAAAATTACTGAAATA-CCCTCG
1 GTTTACAAAATTACCAAAATACCCCT-G
* ** * *
13602593 ATTTGTAAAATTACCAAAGTACCCCTA
1 GTTTACAAAATTACCAAAATACCCCTG
* *
13602620 ATTTACAGAATTAC
1 GTTTACAAAATTAC
13602634 TGTTTTACCC
Statistics
Matches: 164, Mismatches: 35, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
26 25 0.15
27 135 0.82
28 4 0.02
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (27 bp):
GTTTACAAAATTACCAAAATACCCCTG
Found at i:13602477 original size:54 final size:54
Alignment explanation
Indices: 13602405--13602616 Score: 284
Period size: 54 Copynumber: 3.9 Consensus size: 54
13602395 GAATACTTTA
* * *
13602405 GTTTACCAAATCACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
*
13602459 GTTTACAAAATTACCAAAATACCCCCGGTTTGTAAAATTA-CAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
* * *
13602512 GTTTACAAAATTACCAAAATACCACTGGTTTGTAAAATTACCGAAATACCCTTA
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
** ** * *
13602566 GTTTGTAAAATTACTGAAATA-CCCTCGATTTGTAAAATTACCAAAGTACCC
1 GTTTACAAAATTACCAAAATACCCCT-GGTTTGTAAAATTACCAAAATACCC
13602617 CTAATTTACA
Statistics
Matches: 140, Mismatches: 16, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
53 54 0.39
54 86 0.61
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.29
Consensus pattern (54 bp):
GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
Found at i:13602531 original size:80 final size:79
Alignment explanation
Indices: 13602419--13602616 Score: 243
Period size: 80 Copynumber: 2.5 Consensus size: 79
13602409 ACCAAATCAC
* *
13602419 CAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCC
1 CAAAATACCCTTGGTTTGTAAAATTACCAAAATACCC-TGGTTTACAAAATTACCAAAATACCCC
*
13602484 CGGTTTGTAAAATTA
65 CAGTTTGTAAAATTA
** ** * *
13602499 CAAAATACCCTTGGTTTACAAAATTACCAAAATACCACTGGTTTGTAAAATTACCGAAATACCCT
1 CAAAATACCCTTGGTTTGTAAAATTACCAAAATACC-CTGGTTTACAAAATTACCAAAATACCCC
*
13602564 TAGTTTGTAAAATTA
65 CAGTTTGTAAAATTA
* * * *
13602579 CTGAAATACCCTCGATTTGTAAAATTACCAAAGTACCC
1 C-AAAATACCCTTGGTTTGTAAAATTACCAAAATACCC
13602617 CTAATTTACA
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
80 70 0.70
81 30 0.30
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (79 bp):
CAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTGGTTTACAAAATTACCAAAATACCCCC
AGTTTGTAAAATTA
Found at i:13602598 original size:107 final size:108
Alignment explanation
Indices: 13602405--13602616 Score: 300
Period size: 107 Copynumber: 2.0 Consensus size: 108
13602395 GAATACTTTA
* * *
13602405 GTTTACCAAATCACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAAT
1 GTTTACAAAATCACCAAAATACCACTAGTTTGTAAAATTACCAAAATACCCTTAGTTTACAAAAT
*
13602470 TACCAAAATACCCCCGGTTTGTAAAATTA-CAAAATACCCTTG
66 TACCAAAATACCCCCGATTTGTAAAATTACCAAAATACCCTTG
* * * **
13602512 GTTTACAAAATTACCAAAATACCACTGGTTTGTAAAATTACCGAAATACCCTTAGTTTGTAAAAT
1 GTTTACAAAATCACCAAAATACCACTAGTTTGTAAAATTACCAAAATACCCTTAGTTTACAAAAT
** * *
13602577 TACTGAAATACCCTCGATTTGTAAAATTACCAAAGTACCC
66 TACCAAAATACCCCCGATTTGTAAAATTACCAAAATACCC
13602617 CTAATTTACA
Statistics
Matches: 91, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
107 82 0.90
108 9 0.10
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.29
Consensus pattern (108 bp):
GTTTACAAAATCACCAAAATACCACTAGTTTGTAAAATTACCAAAATACCCTTAGTTTACAAAAT
TACCAAAATACCCCCGATTTGTAAAATTACCAAAATACCCTTG
Found at i:13602978 original size:27 final size:27
Alignment explanation
Indices: 13602655--13602970 Score: 438
Period size: 27 Copynumber: 11.7 Consensus size: 27
13602645 CAATTGACAA
*
13602655 AATTATTGAAATACTCC-TGTAGGGTAG
1 AATTACTGAAATAC-CCTTGTAGGGTAG
*
13602682 AATTACCGAAATA-CCTCTGTAGGGTAG
1 AATTACTGAAATACCCT-TGTAGGGTAG
*
13602709 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
*
13602736 AATTATTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
* *
13602763 AATTACCGGAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
*
13602790 AAATACTGAAATACCCATTGTAGGGTAG
1 AATTACTGAAATACCC-TTGTAGGGTAG
* *
13602818 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
* *
13602845 AATTAATGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
*
13602872 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
*
13602899 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
* *
13602926 AATTACTAAAATACCCTTGTAAGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
* *
13602953 AATTACCGAGATACCCTT
1 AATTACTGAAATACCCTT
13602971 TTGGGGTAAA
Statistics
Matches: 261, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
25 2 0.01
27 231 0.89
28 28 0.11
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Consensus pattern (27 bp):
AATTACTGAAATACCCTTGTAGGGTAG
Found at i:13603227 original size:25 final size:25
Alignment explanation
Indices: 13603189--13603258 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
13603179 AGGAAGTGCT
*
13603189 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
13603214 AATAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
13603239 AAAAGGGCTTTACCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
13603259 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:13604379 original size:14 final size:14
Alignment explanation
Indices: 13604360--13604389 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
13604350 TTGAATAAAA
13604360 TTATGGATCTATTG
1 TTATGGATCTATTG
13604374 TTATGGATCTATTG
1 TTATGGATCTATTG
13604388 TT
1 TT
13604390 GAATAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (14 bp):
TTATGGATCTATTG
Found at i:13615129 original size:26 final size:26
Alignment explanation
Indices: 13615100--13615152 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
13615090 TTTACAGTTT
13615100 TACCCCTAAGAGTTAAATT-ACCGAAA
1 TACCCCT-AGAGTTAAATTGACCGAAA
* *
13615126 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGTTAAATTGACCGAAA
13615152 T
1 T
13615153 GCATGTTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (26 bp):
TACCCCTAGAGTTAAATTGACCGAAA
Found at i:13621403 original size:15 final size:15
Alignment explanation
Indices: 13621380--13621422 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
13621370 GTTATCGTGA
*
13621380 TATTACTGTATCTGT
1 TATTTCTGTATCTGT
13621395 TATTTCTGTATCTG-
1 TATTTCTGTATCTGT
*
13621409 TATTT-TGTTTCTGT
1 TATTTCTGTATCTGT
13621423 GATTGGGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 7 0.28
14 5 0.20
15 13 0.52
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.60
Consensus pattern (15 bp):
TATTTCTGTATCTGT
Found at i:13624077 original size:18 final size:19
Alignment explanation
Indices: 13624054--13624105 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
13624044 TTGAAATGGC
13624054 ATGATATGTGAAATAG-AA
1 ATGATATGTGAAATAGAAA
* *
13624072 ATGATATAGTG-GATTGAAA
1 ATGATAT-GTGAAATAGAAA
*
13624091 ATGAAATGTGAAATA
1 ATGATATGTGAAATA
13624106 TGTTGTGAGC
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (19 bp):
ATGATATGTGAAATAGAAA
Found at i:13629462 original size:22 final size:23
Alignment explanation
Indices: 13629431--13629474 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
13629421 TTAAGTCCTC
* *
13629431 AAATTTTCATTTTG-ATTTTTTA
1 AAATTATCATTTAGTATTTTTTA
13629453 AAATTATCATTTAGTATTTTTT
1 AAATTATCATTTAGTATTTTTT
13629475 TATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (23 bp):
AAATTATCATTTAGTATTTTTTA
Found at i:13629503 original size:18 final size:18
Alignment explanation
Indices: 13629471--13629514 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
13629461 ATTTAGTATT
*
13629471 TTTTTATATATTTTTAAGA
1 TTTTTA-ATAATTTTAAGA
* *
13629490 TTTTTAATAATTTTTAGT
1 TTTTTAATAATTTTAAGA
13629508 TTTTTAA
1 TTTTTAA
13629515 GATTATTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTTAATAATTTTAAGA
Found at i:13629512 original size:19 final size:20
Alignment explanation
Indices: 13629462--13629534 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
13629452 AAAATTATCA
*
13629462 TTTAGTATTTTTTTATATATT
1 TTTAGT-TTTTTTAATATATT
*
13629483 TTTAAG-ATTTTTAATA-ATT
1 TTT-AGTTTTTTTAATATATT
*
13629502 TTTAG-TTTTTTAAGATTATT
1 TTTAGTTTTTTTAATA-TATT
* *
13629522 TTGAATTTTTTTA
1 TTTAGTTTTTTTA
13629535 GAGGGATCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 10 0.24
19 6 0.14
20 14 0.33
21 10 0.24
22 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTAGTTTTTTTAATATATT
Found at i:13631063 original size:39 final size:39
Alignment explanation
Indices: 13631020--13631102 Score: 157
Period size: 39 Copynumber: 2.1 Consensus size: 39
13631010 TTCTCTTCTC
*
13631020 AAATAGAAAATGGCACAATTGTTATTCTGGAAGTTGTGT
1 AAATAGAAAATGGCACAATCGTTATTCTGGAAGTTGTGT
13631059 AAATAGAAAATGGCACAATCGTTATTCTGGAAGTTGTGT
1 AAATAGAAAATGGCACAATCGTTATTCTGGAAGTTGTGT
13631098 AAATA
1 AAATA
13631103 ATCTCTCTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (39 bp):
AAATAGAAAATGGCACAATCGTTATTCTGGAAGTTGTGT
Found at i:13633337 original size:19 final size:21
Alignment explanation
Indices: 13633298--13633340 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13633288 GGAAACTTAT
13633298 AAGGTTAGACTTCTAGAAAAA
1 AAGGTTAGACTTCTAGAAAAA
*
13633319 AAGGTTATACTT-T-GAAAAA
1 AAGGTTAGACTTCTAGAAAAA
13633338 AAG
1 AAG
13633341 TAATGATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 1 0.05
21 11 0.52
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (21 bp):
AAGGTTAGACTTCTAGAAAAA
Found at i:13634689 original size:18 final size:19
Alignment explanation
Indices: 13634658--13634700 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
13634648 ATGCAAAACC
*
13634658 ATCCAAAAAACACAA-TAA
1 ATCCAAAAAACACAAGAAA
**
13634676 ATCCAAAATCCACAAGAAA
1 ATCCAAAAAACACAAGAAA
13634695 ATCCAA
1 ATCCAA
13634701 GTCCAAAACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.60, C:0.26, G:0.02, T:0.12
Consensus pattern (19 bp):
ATCCAAAAAACACAAGAAA
Found at i:13641097 original size:19 final size:18
Alignment explanation
Indices: 13641064--13641102 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
13641054 AATAAATCCA
*
13641064 AAGTCCAAAAGAAAGTCC
1 AAGTCCAAAACAAAGTCC
13641082 AAGTCCAAAACCAAAGTCC
1 AAGTCCAAAA-CAAAGTCC
13641101 AA
1 AA
13641103 AGCAACTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.51, C:0.26, G:0.13, T:0.10
Consensus pattern (18 bp):
AAGTCCAAAACAAAGTCC
Found at i:13641702 original size:59 final size:59
Alignment explanation
Indices: 13641610--13641735 Score: 207
Period size: 59 Copynumber: 2.1 Consensus size: 59
13641600 ATGCATATGA
* *
13641610 TATGGCATACAGAACATAATTTCAGTAAGCATGCTTTACATACGGATAGGAATCAGAAG
1 TATGGCATACAGAACATAATTTCAGTAAGCATGCTTTACATACGAATAAGAATCAGAAG
* * *
13641669 TATGGCATATAGAACATAATTTCAGTAAGCATGCTTTACATGCGAATAAGAATTAGAAG
1 TATGGCATACAGAACATAATTTCAGTAAGCATGCTTTACATACGAATAAGAATCAGAAG
13641728 TATGGCAT
1 TATGGCAT
13641736 GTTTATCATG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (59 bp):
TATGGCATACAGAACATAATTTCAGTAAGCATGCTTTACATACGAATAAGAATCAGAAG
Found at i:13642308 original size:21 final size:21
Alignment explanation
Indices: 13642284--13642323 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13642274 AATACTCGTG
13642284 TTAATACA-GATTAATAAATAA
1 TTAATACATGATTAA-AAATAA
*
13642305 TTAATCCATGATTAAAAAT
1 TTAATACATGATTAAAAAT
13642324 TATTGTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (21 bp):
TTAATACATGATTAAAAATAA
Found at i:13644896 original size:6 final size:6
Alignment explanation
Indices: 13644885--13644945 Score: 68
Period size: 6 Copynumber: 9.8 Consensus size: 6
13644875 GGTTTTCTCA
* * * *
13644885 AAATGG AAATGG AAATGG AAATGA AAATGA AAATGA AAATGA AAATGAG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATG-G
13644934 AAATGAG AAATG
1 AAATG-G AAATG
13644946 AATTTATTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
6 40 0.77
7 12 0.23
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.16
Consensus pattern (6 bp):
AAATGG
Found at i:13644902 original size:12 final size:12
Alignment explanation
Indices: 13644884--13644947 Score: 83
Period size: 12 Copynumber: 5.2 Consensus size: 12
13644874 TGGTTTTCTC
13644884 AAAATGGAAATG
1 AAAATGGAAATG
*
13644896 GAAATGGAAATG
1 AAAATGGAAATG
*
13644908 AAAATGAAAATG
1 AAAATGGAAATG
*
13644920 AAAATGAAAATG
1 AAAATGGAAATG
13644932 AGAAATGAGAAATG
1 A-AAATG-GAAATG
13644946 AA
1 AA
13644948 TTTATTTAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
12 34 0.74
13 6 0.13
14 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:13644912 original size:18 final size:18
Alignment explanation
Indices: 13644885--13644947 Score: 81
Period size: 18 Copynumber: 3.4 Consensus size: 18
13644875 GGTTTTCTCA
*
13644885 AAATGGAAATGGAAATGG
1 AAATGAAAATGGAAATGG
* *
13644903 AAATGAAAATGAAAATGA
1 AAATGAAAATGGAAATGG
13644921 AAATGAAAATGAGAAATGAG
1 AAATGAAAATG-GAAATG-G
13644941 AAATGAA
1 AAATGAA
13644948 TTTATTTAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
18 26 0.68
19 5 0.13
20 7 0.18
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (18 bp):
AAATGAAAATGGAAATGG
Found at i:13657371 original size:25 final size:25
Alignment explanation
Indices: 13657343--13657416 Score: 112
Period size: 25 Copynumber: 3.0 Consensus size: 25
13657333 AAAGGGAAAA
**
13657343 TCCTAATCTAATTCCTAATTTAAAG
1 TCCTAATAAAATTCCTAATTTAAAG
* *
13657368 TCCTAGTAGAATTCCTAATTTAAAG
1 TCCTAATAAAATTCCTAATTTAAAG
13657393 TCCTAATAAAATTCCTAATTTAAA
1 TCCTAATAAAATTCCTAATTTAAA
13657417 TTTTATAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.38
Consensus pattern (25 bp):
TCCTAATAAAATTCCTAATTTAAAG
Found at i:13657398 original size:13 final size:13
Alignment explanation
Indices: 13657355--13657416 Score: 58
Period size: 12 Copynumber: 4.9 Consensus size: 13
13657345 CTAATCTAAT
13657355 TCCTAATTTAAAG
1 TCCTAATTTAAAG
* *
13657368 TCCT-A-GTAGAAT
1 TCCTAATTTA-AAG
13657380 TCCTAATTTAAAG
1 TCCTAATTTAAAG
* *
13657393 TCCTAA-TAAAAT
1 TCCTAATTTAAAG
13657405 TCCTAATTTAAA
1 TCCTAATTTAAA
13657417 TTTTATAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
11 2 0.05
12 17 0.45
13 17 0.45
14 2 0.05
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (13 bp):
TCCTAATTTAAAG
Found at i:13657475 original size:28 final size:27
Alignment explanation
Indices: 13657422--13657476 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
13657412 TTAAATTTTA
*
13657422 TAAAAAAATTAGTAAAACTAAGACTCT
1 TAAAAAAATTAGTAAAACTAAAACTCT
* **
13657449 TAAAGAAATTAAGTAAATGTAAAACTCT
1 TAAAAAAATT-AGTAAAACTAAAACTCT
13657477 AATTCCTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (27 bp):
TAAAAAAATTAGTAAAACTAAAACTCT
Found at i:13667019 original size:8 final size:8
Alignment explanation
Indices: 13667004--13667039 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
13666994 TTAAAGCGAT
13667004 AAATGCCG
1 AAATGCCG
*
13667012 AAAAGCCG
1 AAATGCCG
13667020 AAATGCCG
1 AAATGCCG
13667028 AAATGCCG
1 AAATGCCG
13667036 AAAT
1 AAAT
13667040 TCTGGCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.11
Consensus pattern (8 bp):
AAATGCCG
Found at i:13667575 original size:20 final size:20
Alignment explanation
Indices: 13667552--13667589 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
13667542 TAAACATGGT
13667552 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
13667572 ATGTATGATATGCACATG
1 ATGTATGATATGCACATG
13667590 GTGTATTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:13667670 original size:23 final size:23
Alignment explanation
Indices: 13667640--13667712 Score: 128
Period size: 23 Copynumber: 3.1 Consensus size: 23
13667630 AGGAAGTGCA
13667640 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
13667663 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
13667686 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
13667710 AAA
1 AAA
13667713 AGAGGCTAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
23 26 0.54
24 22 0.46
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:13667695 original size:24 final size:24
Alignment explanation
Indices: 13667639--13667719 Score: 137
Period size: 24 Copynumber: 3.4 Consensus size: 24
13667629 GAGGAAGTGC
13667639 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
13667663 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
13667686 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
13667710 AAAAGAGGCT
1 AAAAG-GGCT
13667720 AGACCTCTAG
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
23 23 0.43
24 27 0.50
25 4 0.07
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:13667965 original size:31 final size:31
Alignment explanation
Indices: 13667927--13667990 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
13667917 CATTTACAGT
13667927 AAAGGCTTCGACCCAGTAATATGAAATATGA
1 AAAGGCTTCGACCCAGTAATATGAAATATGA
* **
13667958 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGACCCAGTAATATGAAATATGA
13667989 AA
1 AA
13667991 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGACCCAGTAATATGAAATATGA
Found at i:13670349 original size:42 final size:42
Alignment explanation
Indices: 13670296--13670380 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
13670286 AGAGGTCGTG
13670296 GGCAATGGTAACGGACGGGGACGTGGGGCAACTGGCAGAGGT
1 GGCAATGGTAACGGACGGGGACGTGGGGCAACTGGCAGAGGT
*
13670338 GGCAATGGTAACGGACGGGGACGTGGGGCACCTGGCAGAGGT
1 GGCAATGGTAACGGACGGGGACGTGGGGCAACTGGCAGAGGT
13670380 G
1 G
13670381 CTGGACATGC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.18, G:0.48, T:0.12
Consensus pattern (42 bp):
GGCAATGGTAACGGACGGGGACGTGGGGCAACTGGCAGAGGT
Found at i:13678058 original size:6 final size:6
Alignment explanation
Indices: 13678042--13678093 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
13678032 CCAGAGTGAA
* *
13678042 AAAAAT AAAAAAT AAAAAC AAAAAT AAAAAT AACAAT AAATAATT AAAAAT
1 AAAAAT -AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA-AA-T AAAAAT
13678093 A
1 A
13678094 TTCACTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
6 25 0.64
7 10 0.26
8 4 0.10
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:13682558 original size:22 final size:23
Alignment explanation
Indices: 13682505--13682558 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
13682495 CAAAAGTGGC
13682505 TACTCTCAAAACTTTGCAAATAA
1 TACTCTCAAAACTTTGCAAATAA
13682528 TACTCTCAAAACTTTGCAAATAA
1 TACTCTCAAAACTTTGCAAATAA
13682551 T-CTCTCAA
1 TACTCTCAA
13682559 GTGGGAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 7 0.23
23 24 0.77
ACGTcount: A:0.41, C:0.24, G:0.04, T:0.31
Consensus pattern (23 bp):
TACTCTCAAAACTTTGCAAATAA
Found at i:13683555 original size:9 final size:9
Alignment explanation
Indices: 13683541--13683566 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
13683531 ATGGACCATT
13683541 TTGTAAAAG
1 TTGTAAAAG
13683550 TTGTAAAAG
1 TTGTAAAAG
13683559 TTGTAAAA
1 TTGTAAAA
13683567 ATGGCATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (9 bp):
TTGTAAAAG
Found at i:13687183 original size:16 final size:16
Alignment explanation
Indices: 13687162--13687192 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13687152 GATATTTTAA
13687162 TATATTATATTAATAT
1 TATATTATATTAATAT
*
13687178 TATATTATGTTAATA
1 TATATTATATTAATA
13687193 AAATAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTATATTAATAT
Found at i:13687289 original size:12 final size:12
Alignment explanation
Indices: 13687272--13687302 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
13687262 GAAGCAGGGG
13687272 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
13687284 AGAAAAAGGGAA
1 AGAAAAAGAGAA
13687296 AGAAAAA
1 AGAAAAA
13687303 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:13690564 original size:16 final size:16
Alignment explanation
Indices: 13690523--13690579 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
13690513 TAAGTATAAA
*
13690523 ATTTCACTTCCCACTT
1 ATTTCACTTACCACTT
*
13690539 ACTTT-GCTTACCACTT
1 A-TTTCACTTACCACTT
* *
13690555 ATTTCTCTTAGCACTT
1 ATTTCACTTACCACTT
13690571 ATTTCACTT
1 ATTTCACTT
13690580 GGTCACTTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 3 0.09
16 28 0.82
17 3 0.09
ACGTcount: A:0.19, C:0.30, G:0.04, T:0.47
Consensus pattern (16 bp):
ATTTCACTTACCACTT
Found at i:13692596 original size:46 final size:45
Alignment explanation
Indices: 13692537--13692661 Score: 142
Period size: 46 Copynumber: 2.7 Consensus size: 45
13692527 CTCTTAGCCG
* *
13692537 ATGCATGTTCCAGACATGTCTTACACTGGCTTATGTCTCGAGGCCA
1 ATGCATGTCCCAGACATGTCTTACACTGGCTT-TGTCTCAAGGCCA
* * * **
13692583 ATGCATGTCCCAGACATGTCTTACACTTGCACTTGTCTCAATGCTG
1 ATGCATGTCCCAGACATGTCTTACACTGGC-TTTGTCTCAAGGCCA
*
13692629 ATGCCATGTCTCAGACATGGTCTTACACTGGCT
1 ATG-CATGTCCCAGACAT-GTCTTACACTGGCT
13692662 CTCATAATGT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
46 40 0.61
47 14 0.21
48 12 0.18
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (45 bp):
ATGCATGTCCCAGACATGTCTTACACTGGCTTTGTCTCAAGGCCA
Found at i:13698680 original size:17 final size:17
Alignment explanation
Indices: 13698658--13698692 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
13698648 AATCATACAG
13698658 TAGAACTCAGTCCTTAA
1 TAGAACTCAGTCCTTAA
13698675 TAGAACTCAGTCCTTAA
1 TAGAACTCAGTCCTTAA
13698692 T
1 T
13698693 CATAGCCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (17 bp):
TAGAACTCAGTCCTTAA
Found at i:13700427 original size:46 final size:46
Alignment explanation
Indices: 13700360--13700456 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 46
13700350 TCACATTGTG
13700360 ATATGAATTTTTGTTCAAAGACATAGCAATGCTCCACTAAAGCCCA
1 ATATGAATTTTTGTTCAAAGACATAGCAATGCTCCACTAAAGCCCA
13700406 ATATGAATTTTTGTTCAAAGACATAGCAATGCTCCACTAAAGCCCA
1 ATATGAATTTTTGTTCAAAGACATAGCAATGCTCCACTAAAGCCCA
*
13700452 CTATG
1 ATATG
13700457 GCTAGATCAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (46 bp):
ATATGAATTTTTGTTCAAAGACATAGCAATGCTCCACTAAAGCCCA
Found at i:13703939 original size:60 final size:61
Alignment explanation
Indices: 13703861--13704000 Score: 210
Period size: 60 Copynumber: 2.3 Consensus size: 61
13703851 CCCTCAATAC
* * *
13703861 TTACATATTTTATTAATTTGATCCTAATTCTAAGTAATTCAATAAATTTAA-TCTTCACAT
1 TTACAAATTTTATCAATTTGATCCTAATTCTAAATAATTCAATAAATTTAACTCTTCACAT
* * *
13703921 TTATAAATTTTATCAATTTGATCCTACTTCTAAATAATTTAATAAATTTAACTCTTCACAT
1 TTACAAATTTTATCAATTTGATCCTAATTCTAAATAATTCAATAAATTTAACTCTTCACAT
*
13703982 TTACAAATTCTATCAATTT
1 TTACAAATTTTATCAATTT
13704001 AATATTCAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
60 45 0.63
61 26 0.37
ACGTcount: A:0.37, C:0.14, G:0.02, T:0.46
Consensus pattern (61 bp):
TTACAAATTTTATCAATTTGATCCTAATTCTAAATAATTCAATAAATTTAACTCTTCACAT
Found at i:13703960 original size:30 final size:30
Alignment explanation
Indices: 13703875--13703969 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
13703865 ATATTTTATT
* * *
13703875 AATTTGATCCTAATTCTAAGTAATTCAATA
1 AATTTGATCCTACTTCTAAATAATTTAATA
* * * * *
13703905 AATTTAATCTTCACATT-TATA-AATTTTATC
1 AATTTGATCCT-AC-TTCTAAATAATTTAATA
13703935 AATTTGATCCTACTTCTAAATAATTTAATA
1 AATTTGATCCTACTTCTAAATAATTTAATA
13703965 AATTT
1 AATTT
13703970 AACTCTTCAC
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
28 2 0.04
29 5 0.10
30 36 0.75
31 3 0.06
32 2 0.04
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (30 bp):
AATTTGATCCTACTTCTAAATAATTTAATA
Found at i:13704857 original size:16 final size:17
Alignment explanation
Indices: 13704825--13704862 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
13704815 ACCGCACTTA
13704825 ATTTATTTATTAATTTT
1 ATTTATTTATTAATTTT
13704842 ATTT-TTTA-TAATTTT
1 ATTTATTTATTAATTTT
*
13704857 TTTTAT
1 ATTTAT
13704863 AAATGCATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 10 0.53
16 5 0.26
17 4 0.21
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTAATTTT
Found at i:13710634 original size:13 final size:13
Alignment explanation
Indices: 13710616--13710641 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13710606 AAGAAATCGA
13710616 ACATGGGCGTGTC
1 ACATGGGCGTGTC
13710629 ACATGGGCGTGTC
1 ACATGGGCGTGTC
13710642 CCTGTCAAGC
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:0.15, C:0.23, G:0.38, T:0.23
Consensus pattern (13 bp):
ACATGGGCGTGTC
Found at i:13720901 original size:157 final size:157
Alignment explanation
Indices: 13720610--13720924 Score: 612
Period size: 157 Copynumber: 2.0 Consensus size: 157
13720600 GTAACACCCC
*
13720610 TAACTTGTAACCGTCGCAGGAATAGGTTAAAAGGTATTACTAGACTTATAACTCAGTTCAGAACA
1 TAACCTGTAACCGTCGCAGGAATAGGTTAAAAGGTATTACTAGACTTATAACTCAGTTCAGAACA
13720675 ATCATTTATCCGATAACATCTTATCTCAATCAATATCATTCAATCACACTCAATATGTACTTAAA
66 ATCATTTATCCGATAACATCTTATCTCAATCAATATCATTCAATCACACTCAATATGTACTTAAA
13720740 TCAAGCATACAAGGCTCTAATCATGCA
131 TCAAGCATACAAGGCTCTAATCATGCA
13720767 TAACCTGTAACCGTCGCAGGAATAGGTTAAAAGGTATTACTAGACTTATAACTCAGTTCAGAACA
1 TAACCTGTAACCGTCGCAGGAATAGGTTAAAAGGTATTACTAGACTTATAACTCAGTTCAGAACA
*
13720832 ATCATTTATCCGATAACATCTTTTCTCAATCAATATCATTCAATCACACTCAATATGTACTTAAA
66 ATCATTTATCCGATAACATCTTATCTCAATCAATATCATTCAATCACACTCAATATGTACTTAAA
13720897 TCAAGCATACAAGGCTCTAATCATGCA
131 TCAAGCATACAAGGCTCTAATCATGCA
13720924 T
1 T
13720925 TCGGGACTAA
Statistics
Matches: 156, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 156 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.30
Consensus pattern (157 bp):
TAACCTGTAACCGTCGCAGGAATAGGTTAAAAGGTATTACTAGACTTATAACTCAGTTCAGAACA
ATCATTTATCCGATAACATCTTATCTCAATCAATATCATTCAATCACACTCAATATGTACTTAAA
TCAAGCATACAAGGCTCTAATCATGCA
Found at i:13722088 original size:46 final size:46
Alignment explanation
Indices: 13722026--13722138 Score: 176
Period size: 46 Copynumber: 2.5 Consensus size: 46
13722016 AAAAATACAA
* *
13722026 TCACATAT-CCATATGTCTCATATAGCTCATTTCATCATAATTCAT
1 TCACATATAACATATGTCTCACATAGCTCATTTCATCATAATTCAT
* *
13722071 TCACATATAACATATGTCTCACATGGCTCATTTGATCATAATTCAT
1 TCACATATAACATATGTCTCACATAGCTCATTTCATCATAATTCAT
13722117 TCACATATAACATATGT-TCACA
1 TCACATATAACATATGTCTCACA
13722139 AATGTACATA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 13 0.21
46 50 0.79
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (46 bp):
TCACATATAACATATGTCTCACATAGCTCATTTCATCATAATTCAT
Found at i:13722363 original size:43 final size:42
Alignment explanation
Indices: 13722302--13722465 Score: 152
Period size: 43 Copynumber: 3.8 Consensus size: 42
13722292 CAACGCCAAC
* *
13722302 GTCCCAAACGTGGTCTTACATGTAATCAAATATCGATGCCATT
1 GTCCCAAACATGGTCTTACACGTAATCAAATATCGATGCCA-T
* * *
13722345 GTCCCAAACAAGGTCTTACACGAAATCAAATA-CGATGTCGAT
1 GTCCCAAACATGGTCTTACACGTAATCAAATATCGATG-CCAT
* * *
13722387 GTCCCAAACATGGCCTTACACGTAAATCTCAA-ATCGATGCCAAC
1 GTCCCAAACATGGTCTTACACGT-AATC-AAATATCGATGCC-AT
** * * *
13722431 GTCCCAGGCGTGGTCTTACACGAAATCACATATCG
1 GTCCCAAACATGGTCTTACACGTAATCAAATATCG
13722466 GAATCCTATG
Statistics
Matches: 97, Mismatches: 18, Indels: 12
0.76 0.14 0.09
Matches are distributed among these distances:
42 27 0.28
43 44 0.45
44 26 0.27
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (42 bp):
GTCCCAAACATGGTCTTACACGTAATCAAATATCGATGCCAT
Found at i:13731688 original size:18 final size:18
Alignment explanation
Indices: 13731661--13731753 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
13731651 TACGACCGTT
13731661 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
13731679 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
**
13731697 TATAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
**
13731715 TACGACACTATTCACGTA
1 TACGGTACTATTCACGTA
*
13731733 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
13731751 TAC
1 TAC
13731754 AGTAGTTGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:13736675 original size:8 final size:8
Alignment explanation
Indices: 13736662--13736693 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
13736652 TCTAATTATA
13736662 TATATATT
1 TATATATT
13736670 TATATATT
1 TATATATT
13736678 TATATA--
1 TATATATT
13736684 TATATATT
1 TATATATT
13736692 TA
1 TA
13736694 CCTAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.27
8 16 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATATATT
Found at i:13738777 original size:24 final size:22
Alignment explanation
Indices: 13738750--13738798 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
13738740 ATGGATAAAA
13738750 TTATATTAAATAATAAGATTTTTT
1 TTATATTAAATAA-AAG-TTTTTT
* * *
13738774 TTATTTTTAATAACAGTTTTTT
1 TTATATTAAATAAAAGTTTTTT
13738796 TTA
1 TTA
13738799 AGAAATAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 9 0.41
23 2 0.09
24 11 0.50
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (22 bp):
TTATATTAAATAAAAGTTTTTT
Found at i:13739358 original size:19 final size:19
Alignment explanation
Indices: 13739330--13739373 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
13739320 CTCCTTACCA
*
13739330 ACCACCAACCACCAATCAC
1 ACCACAAACCACCAATCAC
* *
13739349 ACCACAAACCACCATTCAT
1 ACCACAAACCACCAATCAC
13739368 ACCACA
1 ACCACA
13739374 CAAATACATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.48, G:0.00, T:0.09
Consensus pattern (19 bp):
ACCACAAACCACCAATCAC
Found at i:13740059 original size:24 final size:24
Alignment explanation
Indices: 13740027--13740074 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
13740017 ATTTCGTGTT
13740027 TTCAAGCTAGTTTCTCTATTCTAA
1 TTCAAGCTAGTTTCTCTATTCTAA
13740051 TTCAAGCTAGTTTCTCTATTCTAA
1 TTCAAGCTAGTTTCTCTATTCTAA
13740075 CATGTCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (24 bp):
TTCAAGCTAGTTTCTCTATTCTAA
Found at i:13742727 original size:9 final size:8
Alignment explanation
Indices: 13742700--13742724 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
13742690 GTTTATATAT
13742700 ATTTTAAA
1 ATTTTAAA
13742708 ATTTTAAA
1 ATTTTAAA
13742716 ATTTTAAA
1 ATTTTAAA
13742724 A
1 A
13742725 ATTAATTATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTTAAA
Found at i:13745571 original size:27 final size:27
Alignment explanation
Indices: 13745541--13745594 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
13745531 AAAATAATAG
13745541 ACTATACACCTTTAA-AATTTAGATTCT
1 ACTATACACCTTTAAGAA-TTAGATTCT
13745568 ACTATACACCTTTAAGAATTAGATTCT
1 ACTATACACCTTTAAGAATTAGATTCT
13745595 TTGTCCATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.39
Consensus pattern (27 bp):
ACTATACACCTTTAAGAATTAGATTCT
Found at i:13748354 original size:12 final size:12
Alignment explanation
Indices: 13748337--13748370 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
13748327 CCAGCCCGTC
13748337 TATATTAATTTT
1 TATATTAATTTT
13748349 TATATT-ATTTT
1 TATATTAATTTT
13748360 TATA-TAATTTT
1 TATATTAATTTT
13748371 AAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 14 0.67
12 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:13754940 original size:64 final size:63
Alignment explanation
Indices: 13754837--13755027 Score: 301
Period size: 64 Copynumber: 3.0 Consensus size: 63
13754827 TCATTCATAA
* *
13754837 CACATTTAGTTAGGAACATTTGGTTCATTTTGATTATGGCATCCAAATTATTTGACATAAGCAT
1 CACATTTAGTTAGGAGCATTTGGTTCATTTTGATCATGGCATCC-AATTATTTGACATAAGCAT
13754901 CACATTTAGTTAGGAGCATTTGGTTCATTTTGATCATGGCATCCTAATTATTTGACATAAGCAT
1 CACATTTAGTTAGGAGCATTTGGTTCATTTTGATCATGGCATCC-AATTATTTGACATAAGCAT
* * ** *
13754965 CACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAACATCCAATTATTTGGCATAAGCAT
1 CACATTTAGTTAGGAGCATTTGGTTCATTTTGATCATGGCATCCAATTATTTGACATAAGCAT
13755028 ATAAAATGAA
Statistics
Matches: 119, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
63 18 0.15
64 101 0.85
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (63 bp):
CACATTTAGTTAGGAGCATTTGGTTCATTTTGATCATGGCATCCAATTATTTGACATAAGCAT
Found at i:13755604 original size:180 final size:180
Alignment explanation
Indices: 13755085--13756245 Score: 1524
Period size: 180 Copynumber: 6.5 Consensus size: 180
13755075 CATGAGTAAA
* * *
13755085 AATTGAAGATCTTATCCCCCTGAAGTTGCAGCGGAGTAGATCTTCGCAGATGGTGAATCTTATCT
1 AATTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCT
* * * *
13755150 CCATGTATCGGTAATGGAGCAGATTTTACCACTAA-CCTCATCTCTCTGAGGTAGCAAGAGAGCA
66 CCATGTATCAGCAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
* * * *
13755214 GGTTGAAGAGTGAGTCTTATCTTCTTGAGGTAGCAAGGAAGCAGACTGAG
131 GGTTGAAGAATAAGTCTTATCTTCCTGAGGTAGCAAGGAAACAGACTGAG
* * *** * * * * *
13755264 AATTGAAGATTTTATCTCTCT-AAACAGTAGCGGAGCAAATC--GA-AAATGGTGAATCTTATTT
1 AATTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCT
* * * *
13755325 CCATGTATCGGCAATGGAGTAGATTTTACCACTAA-CCTTATTTCTCTGAGGTAGCAAGAGAGCA
66 CCATGTATCAGCAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
* * *
13755389 GGTTGAGGAATGAGTCTTATCTTCTTGAGGTAGCAAGGAAACAGACTGAG
131 GGTTGAAGAATAAGTCTTATCTTCCTGAGGTAGCAAGGAAACAGACTGAG
* * * *
13755439 AATTAAAGATCTTATCTCCCTAAAGTTACAGCGGAGCAGATCTTTACAGATGGTGAATCTTATCT
1 AATTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCT
13755504 CCATGTATCAGCAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
66 CCATGTATCAGCAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
*
13755569 GGTTGAAGAATAAGTCTTATCTTCCTGAAGTAGCAAGGAAACAGACTGA-
131 GGTTGAAGAATAAGTCTTATCTTCCTGAGGTAGCAAGGAAACAGACTGAG
* * * *
13755618 AGATTGAAAATTTTATCTCCCTG-AGATTGCAGCGGAGCAGATCTTCGCTGATGGTGAATCTTAT
1 A-ATTGAAGATCTTATCTCCCTGAAG-TTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTAT
* * * *
13755682 CTCCATGTATC-GACAATGAAGCAGATTTTACCACCAAGCCTTATCTCACTGAGGGAGTAAGAGA
64 CTCCATGTATCAG-CAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGA
* * * *
13755746 ACAGGTTGAAGAATGAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGACTGAG
128 GCAGGTTGAAGAATAAGTCTTATCTTCCTGAGGTAGCAAGGAAACAGACTGAG
* *
13755799 AATTAAAGATCTTATCTCCCTGAAGTTGCAGCGGAGTAGATCTTCACAGATGGTGAATCTTATCT
1 AATTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCT
* * *
13755864 CCATGTATCGGCAATGGAGAAGATTTTACCATCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
66 CCATGTATCAGCAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
*
13755929 GATTGAAGAATAAGTCTTATCTTCCTGAGGTAGCAAGGAAACAGACTGAG
131 GGTTGAAGAATAAGTCTTATCTTCCTGAGGTAGCAAGGAAACAGACTGAG
* * * * * * *
13755979 AATTGAAGATTTTATATCCCTG-AGATTGCAGAGGAACAGATCTTCGCAGATTGTGAATCTTATT
1 AATTGAAGATCTTATCTCCCTGAAG-TTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATC
* * *
13756043 TCCATGTATCAGCAATGGAGCAGATTTTACCTCC-AGCCTCATCTCTCTGAAGTAGCAAGAGAGC
65 TCCATGTATCAGCAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGC
* * *
13756107 AGGTTGAAGAATAAGTATTGTCTTCCTGAGGTAGCAAGGAAGCAGACTGATG
130 AGGTTGAAGAATAAGTCTTATCTTCCTGAGGTAGCAAGGAAACAGACTGA-G
* * * ** * *
13756159 -GTTGAGGATCTTATCTCCCTGAAGTGGCAATGGAGCAGA--TTGA-AAATGGTGAATCTTATCT
1 AATTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCT
*
13756220 CCATGTATCAGCAATAGAGCAGATTT
66 CCATGTATCAGCAATGGAGCAGATTT
13756246 AACCTATCAA
Statistics
Matches: 861, Mismatches: 107, Indels: 31
0.86 0.11 0.03
Matches are distributed among these distances:
175 141 0.16
176 54 0.06
177 2 0.00
178 15 0.02
179 174 0.20
180 471 0.55
181 4 0.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (180 bp):
AATTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCACAGATGGTGAATCTTATCT
CCATGTATCAGCAATGGAGCAGATTTTACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
GGTTGAAGAATAAGTCTTATCTTCCTGAGGTAGCAAGGAAACAGACTGAG
Found at i:13765164 original size:14 final size:15
Alignment explanation
Indices: 13765145--13765177 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
13765135 TTTTATCCAC
13765145 TTATATTGTTAT-AA
1 TTATATTGTTATAAA
13765159 TTATATTGTTATAAA
1 TTATATTGTTATAAA
13765174 TTAT
1 TTAT
13765178 TAGACAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
TTATATTGTTATAAA
Found at i:13770012 original size:42 final size:42
Alignment explanation
Indices: 13769949--13770054 Score: 153
Period size: 42 Copynumber: 2.5 Consensus size: 42
13769939 ACAGCTTAAC
* * *
13769949 TATGGTCTTACACGA-ACTCTCATATTGATTCTATATCCTAGA
1 TATGGTCTTACAC-ATAGTCTCATATTGATTCCATATCCCAGA
13769991 TACT-GTCTTACACATAGTCTCATATTGATTCCATATCCCAGA
1 TA-TGGTCTTACACATAGTCTCATATTGATTCCATATCCCAGA
13770033 TATGGTCTTACACATAGTCTCA
1 TATGGTCTTACACATAGTCTCA
13770055 GTAACCCAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
41 2 0.03
42 55 0.95
43 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (42 bp):
TATGGTCTTACACATAGTCTCATATTGATTCCATATCCCAGA
Found at i:13774203 original size:22 final size:22
Alignment explanation
Indices: 13774175--13774218 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
13774165 CTTTAGCTAT
13774175 TTTTTATTTTTAATACAATTTA
1 TTTTTATTTTTAATACAATTTA
* *
13774197 TTTTTATTTTTATTATAATTTA
1 TTTTTATTTTTAATACAATTTA
13774219 CTAACTTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTATTTTTAATACAATTTA
Found at i:13777396 original size:20 final size:20
Alignment explanation
Indices: 13777373--13777424 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
13777363 TGTGTTCGGA
*
13777373 CACACTAGCGTGTGGGATAC
1 CACACGAGCGTGTGGGATAC
* *
13777393 CACACGGGCGTGTGGTATAC
1 CACACGAGCGTGTGGGATAC
*
13777413 CACACGGGCGTG
1 CACACGAGCGTG
13777425 AGAGAAACAA
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:0.27, G:0.35, T:0.17
Consensus pattern (20 bp):
CACACGAGCGTGTGGGATAC
Found at i:13778117 original size:26 final size:28
Alignment explanation
Indices: 13778080--13778131 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 28
13778070 GATACTTTAG
13778080 ATTTTTATTTTT-ATT-TT-ATTATTAT
1 ATTTTTATTTTTCATTCTTAATTATTAT
*
13778105 ATTTTTTTCTTTTCATTCTTAATTATT
1 ATTTTTAT-TTTTCATTCTTAATTATT
13778132 TCTTTGGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 7 0.32
26 4 0.18
27 3 0.14
28 2 0.09
29 6 0.27
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (28 bp):
ATTTTTATTTTTCATTCTTAATTATTAT
Found at i:13779831 original size:7 final size:6
Alignment explanation
Indices: 13779793--13779885 Score: 91
Period size: 6 Copynumber: 15.5 Consensus size: 6
13779783 TTGAGTCTGA
* *
13779793 TTATTT TTATGT TTATGT TTATTT TTATTT TTATCTT TTATCTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTAT-TT TTAT-TT TTATTT
* * * * *
13779843 TTATTT ATACTT TTA-CT TT-TTT TTATTT TTCTTT TTATGT TTA
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTA
13779886 GTTTGTTTTC
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
5 6 0.08
6 55 0.74
7 13 0.18
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.75
Consensus pattern (6 bp):
TTATTT
Found at i:13779922 original size:12 final size:11
Alignment explanation
Indices: 13779793--13779923 Score: 66
Period size: 12 Copynumber: 10.9 Consensus size: 11
13779783 TTGAGTCTGA
13779793 TTATTTTTATGT
1 TTATTTTTAT-T
*
13779805 TTATGTTTATTT
1 TTATTTTTA-TT
13779817 TTATTTTTATCTT
1 TTATTTTTA--TT
13779830 TTATCTTTTATTT
1 TTAT-TTTTA-TT
*
13779843 TTATTTATACTT
1 TTATTTTTA-TT
*
13779855 TTACTTTT-TT
1 TTATTTTTATT
*
13779865 TTATTTTTCTTT
1 TTATTTTT-ATT
* *
13779877 TTATGTTTAGT
1 TTATTTTTATT
*
13779888 TTGTTTTCCTATT
1 TTATTTT--TATT
**
13779901 TTAAACTTTATT
1 TT-ATTTTTATT
13779913 TTAATTTTTAT
1 TT-ATTTTTAT
13779924 GGTTGTTTCT
Statistics
Matches: 91, Mismatches: 20, Indels: 16
0.72 0.16 0.13
Matches are distributed among these distances:
10 9 0.10
11 6 0.07
12 51 0.56
13 18 0.20
14 7 0.08
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.73
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:13796701 original size:28 final size:28
Alignment explanation
Indices: 13796670--13796726 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
13796660 TAAATGTCTG
* *
13796670 AAGTACTTAATGACTCAAAAAGATTTGA
1 AAGTACTTAATGAATAAAAAAGATTTGA
*
13796698 AAGTACTTGATGAATAAAAAAGATTTGA
1 AAGTACTTAATGAATAAAAAAGATTTGA
13796726 A
1 A
13796727 CCTACGGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (28 bp):
AAGTACTTAATGAATAAAAAAGATTTGA
Found at i:13801792 original size:20 final size:20
Alignment explanation
Indices: 13801767--13801807 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
13801757 CAAAAAGTTT
13801767 AAGAACTAAATTGTGAATTA
1 AAGAACTAAATTGTGAATTA
13801787 AAGAACTAAATTGTGAATTA
1 AAGAACTAAATTGTGAATTA
13801807 A
1 A
13801808 TTGTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (20 bp):
AAGAACTAAATTGTGAATTA
Found at i:13805333 original size:33 final size:33
Alignment explanation
Indices: 13805291--13805357 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
13805281 AGTTATGCTC
13805291 TCATATAATTCTCCTCCTTGGAATTTGTTTTTA
1 TCATATAATTCTCCTCCTTGGAATTTGTTTTTA
13805324 TCATATAATTCTCCTCCTTGGAATTTGTTTTTA
1 TCATATAATTCTCCTCCTTGGAATTTGTTTTTA
13805357 T
1 T
13805358 AAGTTGCTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.52
Consensus pattern (33 bp):
TCATATAATTCTCCTCCTTGGAATTTGTTTTTA
Found at i:13808212 original size:37 final size:37
Alignment explanation
Indices: 13808171--13808246 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
13808161 TATAGTTCAA
13808171 CTAAAACTACATAAAAGAACAATGAAGATAACTGCGT
1 CTAAAACTACATAAAAGAACAATGAAGATAACTGCGT
13808208 CTAAAACTACATAAAAGAACAATGAAGATAACTGCGT
1 CTAAAACTACATAAAAGAACAATGAAGATAACTGCGT
13808245 CT
1 CT
13808247 GATGTCAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (37 bp):
CTAAAACTACATAAAAGAACAATGAAGATAACTGCGT
Found at i:13811943 original size:46 final size:46
Alignment explanation
Indices: 13811880--13811976 Score: 158
Period size: 46 Copynumber: 2.1 Consensus size: 46
13811870 TTTACATGCG
*
13811880 AAGATCTCATTACAAATTAACACATTGACATGCTTAACATGAGAAT
1 AAGATCTCATTACAAATTAACACAGTGACATGCTTAACATGAGAAT
* * *
13811926 CAGATCTCATTATAAATTAACACAGTGACATGCTTAACATGCGAAT
1 AAGATCTCATTACAAATTAACACAGTGACATGCTTAACATGAGAAT
13811972 AAGAT
1 AAGAT
13811977 TAATAACAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (46 bp):
AAGATCTCATTACAAATTAACACAGTGACATGCTTAACATGAGAAT
Found at i:13812259 original size:19 final size:19
Alignment explanation
Indices: 13812221--13812259 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13812211 GTTAAACAAA
*
13812221 TATTTAATATTATCACATT
1 TATTTAATATTAACACATT
13812240 TATTTAATTATTAACA-ATT
1 TATTTAA-TATTAACACATT
13812259 T
1 T
13812260 CACACATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTAATATTAACACATT
Found at i:13816874 original size:20 final size:20
Alignment explanation
Indices: 13816846--13816885 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
13816836 CTCTAATTAG
*
13816846 AATCTCTAAAAATCAGCTAT
1 AATCCCTAAAAATCAGCTAT
* *
13816866 AATCCCTAAAGATTAGCTAT
1 AATCCCTAAAAATCAGCTAT
13816886 TGAATGCTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (20 bp):
AATCCCTAAAAATCAGCTAT
Found at i:13831537 original size:51 final size:51
Alignment explanation
Indices: 13831477--13831580 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
13831467 CTGATGAGTT
* *
13831477 TAATAGATTGTGCAAGTCAGAAGGGATTATGAGACACTTGACAGTTCGTCA
1 TAATAGATTGTGCAAGTCAGAAGGGATCATGAGACACTTGACAGTTCATCA
13831528 TAATAGATTGTGCAAGTCAGAAGGGATCATGAGACACTTGACAGTTCATCA
1 TAATAGATTGTGCAAGTCAGAAGGGATCATGAGACACTTGACAGTTCATCA
13831579 TA
1 TA
13831581 CTCCACAGCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (51 bp):
TAATAGATTGTGCAAGTCAGAAGGGATCATGAGACACTTGACAGTTCATCA
Found at i:13837276 original size:15 final size:15
Alignment explanation
Indices: 13837256--13837300 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
13837246 ATAAAAGAAT
13837256 ATTTAACTATAAAAA
1 ATTTAACTATAAAAA
*
13837271 ATTTAA--A-ATAAA
1 ATTTAACTATAAAAA
13837283 ATTTAACTATAAAAA
1 ATTTAACTATAAAAA
13837298 ATT
1 ATT
13837301 AAAATAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 10 0.40
13 1 0.04
14 1 0.04
15 13 0.52
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (15 bp):
ATTTAACTATAAAAA
Found at i:13837303 original size:26 final size:27
Alignment explanation
Indices: 13837247--13837308 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
13837237 ATCATTGTTA
* *
13837247 TAAAAGAATATTTAACTATAAAAAATT
1 TAAAATAAAATTTAACTATAAAAAATT
13837274 TAAAATAAAATTTAACTATAAAAAA-T
1 TAAAATAAAATTTAACTATAAAAAATT
13837300 TAAAATAAA
1 TAAAATAAA
13837309 TTATAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (27 bp):
TAAAATAAAATTTAACTATAAAAAATT
Found at i:13842220 original size:20 final size:20
Alignment explanation
Indices: 13842195--13842234 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
13842185 ATGGAAGGGA
13842195 AAAAAAAAGTGTTCAGCTTT
1 AAAAAAAAGTGTTCAGCTTT
13842215 AAAAAAAAGTGTTCAGCTTT
1 AAAAAAAAGTGTTCAGCTTT
13842235 CTTCTGTCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (20 bp):
AAAAAAAAGTGTTCAGCTTT
Found at i:13844831 original size:46 final size:46
Alignment explanation
Indices: 13844780--13844871 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
13844770 ATCATGATAT
*
13844780 TTTTAGTGGATTGAC-CTTATGACCAAATAATTTGCAATTAATAGAC
1 TTTTAGTGGATTGACTC-CATGACCAAATAATTTGCAATTAATAGAC
*
13844826 TTTTAGTGGATTGACTCCGTGACCAAATAATTTGCAATTAATAGAC
1 TTTTAGTGGATTGACTCCATGACCAAATAATTTGCAATTAATAGAC
13844872 GAAGCATTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 42 0.98
47 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (46 bp):
TTTTAGTGGATTGACTCCATGACCAAATAATTTGCAATTAATAGAC
Found at i:13846623 original size:3 final size:3
Alignment explanation
Indices: 13846609--13846662 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
13846599 GACAATAAAG
*
13846609 AAT AAT AGT AAT AAT AAT AAT -AT AGAT AAT AAT -AT ATAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT
13846653 AAT AAT AAT A
1 AAT AAT AAT A
13846663 GTTAGAGATA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 6 0.14
3 32 0.73
4 6 0.14
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:13846889 original size:15 final size:16
Alignment explanation
Indices: 13846871--13846905 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
13846861 AAATATAAGT
13846871 ATAAAT-ATGATAATA
1 ATAAATAATGATAATA
13846886 AT-AATAATGATAATA
1 ATAAATAATGATAATA
13846901 ATAAA
1 ATAAA
13846906 AGTAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.17
15 13 0.72
16 2 0.11
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
ATAAATAATGATAATA
Found at i:13847303 original size:17 final size:17
Alignment explanation
Indices: 13847245--13847307 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
13847235 AAAATAATAT
13847245 TAAAATATATATACGAGTAA
1 TAAAA-ATATATAC-A-TAA
* * * *
13847265 TAAAAAATGTATCCGTAT
1 T-AAAAATATATACATAA
13847283 TAAAAATATATACATAA
1 TAAAAATATATACATAA
13847300 TAAAAATA
1 TAAAAATA
13847308 CAATATTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 20 0.59
18 3 0.09
20 7 0.21
21 4 0.12
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (17 bp):
TAAAAATATATACATAA
Found at i:13847644 original size:15 final size:14
Alignment explanation
Indices: 13847619--13847654 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
13847609 TAATAATACT
13847619 ATATAATATATATA
1 ATATAATATATATA
13847633 ATATACATATATATA
1 ATATA-ATATATATA
13847648 AGTATAA
1 A-TATAA
13847655 CAAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 11 0.55
16 4 0.20
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (14 bp):
ATATAATATATATA
Found at i:13848355 original size:21 final size:20
Alignment explanation
Indices: 13848331--13848382 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
13848321 AGCAAATTCG
13848331 AAAATAAAATAAAAAGGAAAA
1 AAAATAAAATAAAAA-GAAAA
* *
13848352 AAAAT--AATAAATAGAAAG
1 AAAATAAAATAAAAAGAAAA
13848370 AAAATAATAATAA
1 AAAATAA-AATAA
13848383 TGTAATATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 9 0.35
19 7 0.27
21 10 0.38
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (20 bp):
AAAATAAAATAAAAAGAAAA
Found at i:13848368 original size:18 final size:17
Alignment explanation
Indices: 13848330--13848379 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
13848320 AAGCAAATTC
*
13848330 GAAAATAAAATAA-AAAG
1 GAAAA-AAAATAATAAAA
13848347 GAAAAAAAATAATAAATA
1 GAAAAAAAATAATAAA-A
*
13848365 GAAAGAAAATAATAA
1 GAAAAAAAATAATAA
13848380 TAATGTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 7 0.24
17 8 0.28
18 14 0.48
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (17 bp):
GAAAAAAAATAATAAAA
Found at i:13850181 original size:21 final size:21
Alignment explanation
Indices: 13850151--13850196 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
13850141 TCAGAAGTAA
*
13850151 TAATACGACACACATGGTGCC
1 TAATACGACACACATAGTGCC
* *
13850172 TAATATGACACATATAGTGCC
1 TAATACGACACACATAGTGCC
13850193 TAAT
1 TAAT
13850197 CAACTCGAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (21 bp):
TAATACGACACACATAGTGCC
Found at i:13851188 original size:19 final size:19
Alignment explanation
Indices: 13851138--13851219 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 19
13851128 TTCTTTTCTC
* *
13851138 CTTTCTTTCTTTCCTATTT
1 CTTTGTTTCTTTTCTATTT
* * *
13851157 C-GT-TTTCTATTCTGTTT
1 CTTTGTTTCTTTTCTATTT
*
13851174 CTTTGTTTCTTTTCTATCT
1 CTTTGTTTCTTTTCTATTT
*
13851193 -TTTATTTCTTTT-TATTT
1 CTTTGTTTCTTTTCTATTT
13851210 CATTTGTTTC
1 C-TTTGTTTC
13851220 ATTTGTTTAT
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
17 16 0.33
18 13 0.27
19 19 0.40
ACGTcount: A:0.07, C:0.18, G:0.05, T:0.70
Consensus pattern (19 bp):
CTTTGTTTCTTTTCTATTT
Found at i:13851395 original size:21 final size:22
Alignment explanation
Indices: 13851360--13851400 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
13851350 ATTTTACATA
*
13851360 ATAATATAATATAATATATTTT
1 ATAATATAAAATAATATATTTT
13851382 ATAAT-TAAAATAATATATT
1 ATAATATAAAATAATATATT
13851401 AATATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAATATAAAATAATATATTTT
Found at i:13851419 original size:29 final size:31
Alignment explanation
Indices: 13851359--13851420 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
13851349 AATTTTACAT
* *
13851359 AATAATATAATATAATATATTTTATAATTAA
1 AATAATATAATATAATATATTTTAAAAATAA
13851390 AATAATAT-AT-TAATATA-TTTAAAACATAA
1 AATAATATAATATAATATATTTTAAAA-ATAA
13851419 AA
1 AA
13851421 ATCTAAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 6 0.21
29 12 0.43
30 2 0.07
31 8 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (31 bp):
AATAATATAATATAATATATTTTAAAAATAA
Found at i:13851865 original size:15 final size:16
Alignment explanation
Indices: 13851839--13851868 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13851829 TTGGTAACTT
13851839 TGAAATTTATTATTTA
1 TGAAATTTATTATTTA
13851855 TGAAA-TTATTATTT
1 TGAAATTTATTATTT
13851869 TTAAAGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
TGAAATTTATTATTTA
Found at i:13851960 original size:21 final size:21
Alignment explanation
Indices: 13851896--13851962 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
13851886 GATTTAACAT
*
13851896 ATTTGAAATTTAAGATTTTGAATTA
1 ATTT-AAATTT-AGA-TTTGGA-TA
*
13851921 ATTTAAATTTATTATTTGGATA
1 ATTTAAATTTA-GATTTGGATA
13851943 ATTTAAATTTAGATTTGGAT
1 ATTTAAATTTAGATTTGGAT
13851963 TGTAACTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 8 0.21
22 13 0.34
23 6 0.16
24 7 0.18
25 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (21 bp):
ATTTAAATTTAGATTTGGATA
Found at i:13863125 original size:37 final size:37
Alignment explanation
Indices: 13863074--13863152 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
13863064 TAGAATGATA
* *
13863074 ACAACCTAAATCTCTCTGAGTT-ACCTGATTTAAGATC
1 ACAACCTAAATCTCTCTAAGTTAACAT-ATTTAAGATC
*
13863111 GCAACCTAAATCTCTCTAAGTTAACATATTTAAGATC
1 ACAACCTAAATCTCTCTAAGTTAACATATTTAAGATC
13863148 ACAAC
1 ACAAC
13863153 TCCCAAACAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 34 0.92
38 3 0.08
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (37 bp):
ACAACCTAAATCTCTCTAAGTTAACATATTTAAGATC
Done.