Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 27 of 259
Found at i:7568988 original size:28 final size:26
Alignment explanation
Indices: 7568947--7569000 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
7568937 AAAAATTTTA
*
7568947 AATATTAAATATTAATAAAAATATATTT
1 AATATTAAAGATTAA-AAAAATA-ATTT
*
7568975 AATATTTAAGATTAAAAAAATAATTT
1 AATATTAAAGATTAAAAAAATAATTT
7569001 CAAAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 7 0.29
28 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
AATATTAAAGATTAAAAAAATAATTT
Found at i:7569010 original size:28 final size:28
Alignment explanation
Indices: 7568943--7569008 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
7568933 ATTTAAAAAT
* *
7568943 TTTAAATATTAAATATTAATAAAAATATA
1 TTTAAA-ATTTAAGATTAATAAAAATATA
*
7568972 TTTAATATTTAAGATTAA-AAAAATA-A
1 TTTAAAATTTAAGATTAATAAAAATATA
7568998 TTTCAAAATTT
1 TTT-AAAATTT
7569009 TATTTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 4 0.12
27 13 0.41
28 10 0.31
29 5 0.16
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (28 bp):
TTTAAAATTTAAGATTAATAAAAATATA
Found at i:7569053 original size:36 final size:33
Alignment explanation
Indices: 7568976--7569247 Score: 169
Period size: 34 Copynumber: 7.9 Consensus size: 33
7568966 AATATATTTA
* * * *
7568976 ATATTTAAGATTAAAAAAATAATTTCAAAATTTT
1 ATATTTAAAATTTAAAAAATAATTT-AAAAATAT
*
7569010 ATTTTTAAAATTTATAAGAAATAATTTCAAAAATAT
1 ATATTTAAAATTTA-AA-AAATAATTT-AAAAATAT
* * **
7569046 ATATTT-AAA-TTAAATATATATTTTTGAAAT-T
1 ATATTTAAAATTTAAA-AAATAATTTAAAAATAT
*** * *
7569077 AT-TTTATTTTGTTTAAAAATATATTTTTAAAA-AT
1 ATATTTA--AAATTTAAAAA-ATAATTTAAAAATAT
7569111 ATATTTAAAATTTAGAAAAATATATTTAAAAAATAT
1 ATATTTAAAATTTA-AAAAATA-ATTT-AAAAATAT
* *
7569147 ATTTTTAAAATTTATAAGACATAATTTAAAAATAT
1 ATATTTAAAATTTA-AA-AAATAATTTAAAAATAT
* *
7569182 AATACTCAAAATTTAAAAAATAATTTAAAAATA-
1 -ATATTTAAAATTTAAAAAATAATTTAAAAATAT
*
7569215 ATATTTAAAAATTTTAAAATATATATTATAAAA
1 ATATTT-AAAA-TTTAAAAAATA-ATT-TAAAA
7569248 CATTTCAAAT
Statistics
Matches: 188, Mismatches: 31, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
30 3 0.02
31 3 0.02
32 8 0.04
33 21 0.11
34 65 0.35
35 26 0.14
36 58 0.31
37 4 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (33 bp):
ATATTTAAAATTTAAAAAATAATTTAAAAATAT
Found at i:7569058 original size:69 final size:69
Alignment explanation
Indices: 7568976--7569213 Score: 199
Period size: 69 Copynumber: 3.5 Consensus size: 69
7568966 AATATATTTA
* *
7568976 ATAT-TTAAGATTAAAAAAATA-ATTTCAAAATTTTATTTTTAAAATTTATAAGAAATAATTTCA
1 ATATATTAAAATTAAAAAAATATATTTAAAAATTTTATTTTTAAAATTTATAAGAAATAATTT-A
7569039 AAAAT
65 AAAAT
* * * * * * *
7569044 ATATATTTAAATTAAATATATATTTTTGAAATTATTTTA-TTTT---GTTTA-AA-AATATATTT
1 ATATATTAAAATTAAAAAAATATATTT-AAA-AATTTTATTTTTAAAATTTATAAGAA-ATA-AT
7569103 TTAAAAAT
62 TTAAAAAT
* * * *
7569111 ATAT-TTAAAATTTAGAAAAATATATTTAAAAAATATATTTTTAAAATTTATAAGACATAATTTA
1 ATATATTAAAA-TTAAAAAAATATATTTAAAAATTTTATTTTTAAAATTTATAAGAAATAATTTA
7569175 AAAAT
65 AAAAT
* *
7569180 ATAATACTCAAAATTTAAAAAATA-ATTTAAAAAT
1 AT-ATA-TTAAAATTAAAAAAATATATTTAAAAAT
7569214 AATATTTAAA
Statistics
Matches: 130, Mismatches: 24, Indels: 30
0.71 0.13 0.16
Matches are distributed among these distances:
65 4 0.03
66 14 0.11
67 27 0.21
68 11 0.08
69 28 0.22
70 19 0.15
71 16 0.12
72 11 0.08
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (69 bp):
ATATATTAAAATTAAAAAAATATATTTAAAAATTTTATTTTTAAAATTTATAAGAAATAATTTAA
AAAT
Found at i:7569107 original size:14 final size:14
Alignment explanation
Indices: 7569088--7569156 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 14
7569078 TTTTATTTTG
7569088 TTTAAAAATATATT
1 TTTAAAAATATATT
7569102 TTTAAAAATATATTT
1 TTTAAAAATATA-TT
7569117 AAAATTTAGAAAA-ATATAT
1 ----TTTA-AAAATATAT-T
*
7569136 TTAAAAAATATATT
1 TTTAAAAATATATT
7569150 TTTAAAA
1 TTTAAAA
7569157 TTTATAAGAC
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
14 23 0.51
15 9 0.20
18 1 0.02
19 8 0.18
20 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (14 bp):
TTTAAAAATATATT
Found at i:7569144 original size:13 final size:14
Alignment explanation
Indices: 7569120--7569150 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
7569110 TATATTTAAA
7569120 ATTTAGAAAAATAT
1 ATTTAGAAAAATAT
7569134 ATTTA-AAAAATAT
1 ATTTAGAAAAATAT
7569147 ATTT
1 ATTT
7569151 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
ATTTAGAAAAATAT
Found at i:7569156 original size:13 final size:13
Alignment explanation
Indices: 7569092--7569157 Score: 50
Period size: 13 Copynumber: 5.4 Consensus size: 13
7569082 ATTTTGTTTA
7569092 AAAATATATTTTT
1 AAAATATATTTTT
*
7569105 AAAA-ATATATTT
1 AAAATATATTTTT
***
7569117 -AAA-AT-TTAGA
1 AAAATATATTTTT
**
7569127 AAAATATATTTAA
1 AAAATATATTTTT
7569140 AAAATATATTTTT
1 AAAATATATTTTT
7569153 AAAAT
1 AAAAT
7569158 TTATAAGACA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
10 1 0.02
11 8 0.20
12 9 0.22
13 23 0.56
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
AAAATATATTTTT
Found at i:7569162 original size:15 final size:15
Alignment explanation
Indices: 7569091--7569156 Score: 53
Period size: 15 Copynumber: 4.2 Consensus size: 15
7569081 TATTTTGTTT
*
7569091 AAAAATATATTTTTA
1 AAAAATATATATTTA
*
7569106 AAAATATATTTAAAATTTA
1 AAAA-ATA--T-ATATTTA
*
7569125 GAAAA-ATATATTTA
1 AAAAATATATATTTA
*
7569139 AAAAATATATTTTTA
1 AAAAATATATATTTA
7569154 AAA
1 AAA
7569157 TTTATAAGAC
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
14 10 0.25
15 16 0.40
16 3 0.08
17 1 0.03
18 2 0.05
19 8 0.20
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
AAAAATATATATTTA
Found at i:7569220 original size:13 final size:14
Alignment explanation
Indices: 7569191--7569226 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
7569181 TAATACTCAA
7569191 AATTT-AAAA-AAT
1 AATTTAAAAATAAT
7569203 AATTTAAAAATAAT
1 AATTTAAAAATAAT
7569217 -ATTTAAAAAT
1 AATTTAAAAAT
7569227 TTTAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.23
13 14 0.64
14 3 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATTTAAAAATAAT
Found at i:7569233 original size:21 final size:22
Alignment explanation
Indices: 7569203--7569269 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 22
7569193 TTTAAAAAAT
7569203 AATTTAAAAATA-ATATTTAAA
1 AATTTAAAAATACATATTTAAA
* *
7569224 AATTTTAAAATATATATTATAAA
1 AATTTAAAAATACATATT-TAAA
*
7569247 ACATTTCAAATATACAT-TTTAAA
1 A-ATTT-AAAAATACATATTTAAA
7569270 TTTTTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 11 0.29
22 5 0.13
23 9 0.24
24 6 0.16
25 7 0.18
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTTAAAAATACATATTTAAA
Found at i:7569233 original size:22 final size:24
Alignment explanation
Indices: 7569205--7569269 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
7569195 TAAAAAATAA
7569205 TTTAAAAATA-ATATTTAAAA-AT
1 TTTAAAAATACATATTTAAAACAT
*
7569227 TTT-AAAATATATATTATAAAACAT
1 TTTAAAAATACATATT-TAAAACAT
* *
7569251 TTCAAATATACAT-TTTAAA
1 TTTAAAAATACATATTTAAA
7569270 TTTTTTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 6 0.17
22 8 0.22
23 9 0.25
24 6 0.17
25 7 0.19
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.42
Consensus pattern (24 bp):
TTTAAAAATACATATTTAAAACAT
Found at i:7569381 original size:19 final size:18
Alignment explanation
Indices: 7569325--7569394 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 18
7569315 ATAAAATAAT
*
7569325 AAAAAATATAAAACTTAAA
1 AAAAAAGATAAAACTT-AA
* * *
7569344 AAAAGAAAAAAAAATTTAA
1 AAAA-AAGATAAAACTTAA
*
7569363 AGAAAAAGATAAAAGTTAA
1 A-AAAAAGATAAAACTTAA
7569382 TAAAAAAG-TAAAA
1 -AAAAAAGATAAAA
7569395 AAAGAAGAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
18 5 0.12
19 24 0.57
20 13 0.31
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.17
Consensus pattern (18 bp):
AAAAAAGATAAAACTTAA
Found at i:7569508 original size:13 final size:13
Alignment explanation
Indices: 7569492--7569544 Score: 81
Period size: 13 Copynumber: 4.2 Consensus size: 13
7569482 TTATAATATA
7569492 TATTTTTAATTTT
1 TATTTTTAATTTT
*
7569505 TATTTTAAATTTT
1 TATTTTTAATTTT
7569518 TATTTTT-ATTTT
1 TATTTTTAATTTT
*
7569530 TATTTTTATTTTT
1 TATTTTTAATTTT
7569543 TA
1 TA
7569545 ATATATATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
12 12 0.33
13 24 0.67
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTTTTAATTTT
Found at i:7569509 original size:6 final size:6
Alignment explanation
Indices: 7569492--7569542 Score: 75
Period size: 6 Copynumber: 8.2 Consensus size: 6
7569482 TTATAATATA
*
7569492 TATTTT TAATTTT TATTTT AAATTTT TATTTT TATTTT TATTTT TATTTT
1 TATTTT T-ATTTT TATTTT -TATTTT TATTTT TATTTT TATTTT TATTTT
7569542 T
1 T
7569543 TAATATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 30 0.73
7 11 0.27
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:7569811 original size:18 final size:18
Alignment explanation
Indices: 7569785--7569838 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
7569775 AATTTGAAAG
*
7569785 TTTAAAATATTTAAATAT
1 TTTATAATATTTAAATAT
* *
7569803 TTTATAATATTAAAAAAT
1 TTTATAATATTTAAATAT
*
7569821 ATT-TAATATTT-AATAT
1 TTTATAATATTTAAATAT
7569837 TT
1 TT
7569839 AAAAAATAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 5 0.17
17 7 0.24
18 17 0.59
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTATAATATTTAAATAT
Found at i:7569828 original size:27 final size:26
Alignment explanation
Indices: 7569788--7569846 Score: 84
Period size: 25 Copynumber: 2.2 Consensus size: 26
7569778 TTGAAAGTTT
*
7569788 AAAATATTTAAATATTTTATAATATTAA
1 AAAATATTTAAATATTTAAT-AT-TTAA
7569816 AAAATATTT-AATATTTAATATTTAA
1 AAAATATTTAAATATTTAATATTTAA
7569841 AAAATA
1 AAAATA
7569847 ATATTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 10 0.33
26 2 0.07
27 9 0.30
28 9 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAATATTTAAATATTTAATATTTAA
Found at i:7569837 original size:14 final size:14
Alignment explanation
Indices: 7569818--7569859 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
7569808 AATATTAAAA
*
7569818 AATATTTAATATTT
1 AATATTTAAAATTT
**
7569832 AATATTTAAAAAAT
1 AATATTTAAAATTT
7569846 AATATTTAAAATTT
1 AATATTTAAAATTT
7569860 TAAAAAATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTAAAATTT
Found at i:7569859 original size:21 final size:21
Alignment explanation
Indices: 7569824--7569878 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
7569814 AAAAAATATT
*
7569824 TAATATTTAATATTTAAAAAA
1 TAATATTTAAAATTTAAAAAA
7569845 TAATATTTAAAATTTTAAAAAA
1 TAATATTTAAAA-TTTAAAAAA
*
7569867 TAAT-TTCAAAAT
1 TAATATTTAAAAT
7569879 ATATATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 1 0.03
21 17 0.55
22 13 0.42
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATATTTAAAATTTAAAAAA
Found at i:7569885 original size:48 final size:48
Alignment explanation
Indices: 7569798--7569890 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 48
7569788 AAAATATTTA
* * *
7569798 AATATTTTATAATATTAAAAAATATTTAATATTTAATATTTAAAAAAT
1 AATATTTTAAAATATTAAAAAATATTTAAAATATAATATTTAAAAAAT
*
7569846 AATA-TTTAAAATTTTAAAAAATAATTTCAAAATAT-ATATTTAAAA
1 AATATTTTAAAATATTAAAAAAT-ATTT-AAAATATAATATTTAAAA
7569891 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 16 0.41
48 18 0.46
49 5 0.13
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (48 bp):
AATATTTTAAAATATTAAAAAATATTTAAAATATAATATTTAAAAAAT
Found at i:7569891 original size:13 final size:13
Alignment explanation
Indices: 7569858--7569938 Score: 50
Period size: 13 Copynumber: 6.6 Consensus size: 13
7569848 TATTTAAAAT
*
7569858 TTTAAAAAATA-A
1 TTTAAAATATATA
7569870 TTTCAAAATATATA
1 TTT-AAAATATATA
7569884 TTTAAAAT-T-TA
1 TTTAAAATATATA
**
7569895 -AAAAAATATATA
1 TTTAAAATATATA
7569907 -TTAATAA-A-ATA
1 TTTAA-AATATATA
*
7569918 TTTCAAATATATA
1 TTTAAAATATATA
*
7569931 TTTTAAAT
1 TTTAAAAT
7569939 TTTTTAAAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
10 5 0.09
11 8 0.15
12 13 0.24
13 24 0.44
14 4 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (13 bp):
TTTAAAATATATA
Found at i:7569982 original size:8 final size:8
Alignment explanation
Indices: 7569971--7570016 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
7569961 AGAAAGAAAG
7569971 AAAAGTAAA
1 AAAAGT-AA
*
7569980 AAAAGTAC
1 AAAAGTAA
7569988 AAAAGTCAA
1 AAAAGT-AA
*
7569997 AAAAATAA
1 AAAAGTAA
7570005 AAAAGTAA
1 AAAAGTAA
7570013 AAAA
1 AAAA
7570017 AAAAAAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
8 20 0.62
9 12 0.38
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (8 bp):
AAAAGTAA
Found at i:7569983 original size:9 final size:9
Alignment explanation
Indices: 7569958--7570017 Score: 56
Period size: 9 Copynumber: 6.9 Consensus size: 9
7569948 TTAATAATAA
*
7569958 TAAAGAAAG
1 TAAAAAAAG
7569967 -AAAGAAAAG
1 TAAA-AAAAG
7569976 TAAAAAAAG
1 TAAAAAAAG
*
7569985 T-ACAAAAG
1 TAAAAAAAG
7569993 TCAAAAAAA-
1 T-AAAAAAAG
7570002 T-AAAAAAG
1 TAAAAAAAG
7570010 TAAAAAAA
1 TAAAAAAA
7570018 AAAAAGAAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
7 6 0.14
8 11 0.26
9 17 0.40
10 8 0.19
ACGTcount: A:0.75, C:0.03, G:0.12, T:0.10
Consensus pattern (9 bp):
TAAAAAAAG
Found at i:7569993 original size:17 final size:16
Alignment explanation
Indices: 7569971--7570022 Score: 70
Period size: 17 Copynumber: 3.2 Consensus size: 16
7569961 AGAAAGAAAG
*
7569971 AAAAGTAAAAAAAGTAC
1 AAAAGTAAAAAAA-TAA
7569988 AAAAGTCAAAAAAATAA
1 AAAAGT-AAAAAAATAA
7570005 AAAAGTAAAAAAA-AA
1 AAAAGTAAAAAAATAA
7570020 AAA
1 AAA
7570023 GAAACTGACA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
15 5 0.15
16 7 0.21
17 14 0.42
18 7 0.21
ACGTcount: A:0.79, C:0.04, G:0.08, T:0.10
Consensus pattern (16 bp):
AAAAGTAAAAAAATAA
Found at i:7579556 original size:12 final size:12
Alignment explanation
Indices: 7579521--7579556 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
7579511 AGGCTCGTAG
7579521 AAGGTTCTTTTT
1 AAGGTTCTTTTT
*
7579533 AAGAGTTGTTTTT
1 AAG-GTTCTTTTT
7579546 AAGGTTCTTTT
1 AAGGTTCTTTT
7579557 ATCATTTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (12 bp):
AAGGTTCTTTTT
Found at i:7591251 original size:17 final size:17
Alignment explanation
Indices: 7591229--7591281 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
7591219 AACGGGCTAT
7591229 CACACGACCGTGTGACA
1 CACACGACCGTGTGACA
*
7591246 CACACGGCC-TAGTG---
1 CACACGACCGT-GTGACA
7591260 -ACACGACCGTGTGACA
1 CACACGACCGTGTGACA
7591276 CACACG
1 CACACG
7591282 GCCTAGTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
13 10 0.36
14 1 0.04
16 1 0.04
17 16 0.57
ACGTcount: A:0.28, C:0.36, G:0.25, T:0.11
Consensus pattern (17 bp):
CACACGACCGTGTGACA
Found at i:7591264 original size:30 final size:30
Alignment explanation
Indices: 7591230--7591297 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
7591220 ACGGGCTATC
7591230 ACACGACCGTGTGACACACACGGCCTAGTG
1 ACACGACCGTGTGACACACACGGCCTAGTG
7591260 ACACGACCGTGTGACACACACGGCCTAGTG
1 ACACGACCGTGTGACACACACGGCCTAGTG
7591290 ACACGACC
1 ACACGACC
7591298 ATTTGTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.28, C:0.35, G:0.25, T:0.12
Consensus pattern (30 bp):
ACACGACCGTGTGACACACACGGCCTAGTG
Found at i:7591290 original size:17 final size:17
Alignment explanation
Indices: 7591240--7591293 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
7591230 ACACGACCGT
7591240 GTGACACACACGGCCTA
1 GTGACACACACGGCCTA
7591257 GTGACACGAC-C-G--T-
1 GTGACAC-ACACGGCCTA
7591270 GTGACACACACGGCCTA
1 GTGACACACACGGCCTA
7591287 GTGACAC
1 GTGACAC
7591294 GACCATTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
12 2 0.06
13 8 0.26
14 2 0.06
16 2 0.06
17 15 0.48
18 2 0.06
ACGTcount: A:0.28, C:0.33, G:0.26, T:0.13
Consensus pattern (17 bp):
GTGACACACACGGCCTA
Found at i:7595811 original size:46 final size:46
Alignment explanation
Indices: 7595744--7596044 Score: 404
Period size: 46 Copynumber: 6.7 Consensus size: 46
7595734 TGGCAACCTG
7595744 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
*
7595790 TGTGTAAGACTATGGTTGAAAGATACCATGGCAACC-----TG---
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
*
7595828 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
*
7595874 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* *
7595920 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* ** * *
7595966 AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAA
* * * *
7596012 TGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
7596045 TCACGTCAAA
Statistics
Matches: 229, Mismatches: 17, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
38 35 0.15
41 2 0.01
43 1 0.00
45 1 0.00
46 190 0.83
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
Found at i:7595830 original size:84 final size:84
Alignment explanation
Indices: 7595698--7596000 Score: 462
Period size: 84 Copynumber: 3.5 Consensus size: 84
7595688 GTGCTCTCTA
*
7595698 ATATGAAATGTTTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGTTGA
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGTTGA
7595763 AAGATACCATGGCAACCTG
66 AAGATACCATGGCAACCTG
*
7595782 ATATGAAATGTGTAAGACTATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGTTGA
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGTTGA
7595847 AAGATACCATGGCAACCTG
66 AAGATACCATGGCAACCTG
*
7595866 ATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGATGTGTAAGACC
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----T--G-TGTGTAAGACC
*
7595931 ATGGTTGAAAGATACCATGGCAACGTG
58 ATGGTTGAAAGATACCATGGCAACCTG
* * **
7595958 ACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
7596001 ATGACAGAAA
Statistics
Matches: 201, Mismatches: 10, Indels: 8
0.92 0.05 0.04
Matches are distributed among these distances:
84 124 0.62
89 1 0.00
91 1 0.00
92 75 0.37
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (84 bp):
ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGTTGA
AAGATACCATGGCAACCTG
Found at i:7596350 original size:23 final size:25
Alignment explanation
Indices: 7596305--7596351 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
7596295 AATAAATATA
*
7596305 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
7596330 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
7596352 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:7601706 original size:93 final size:93
Alignment explanation
Indices: 7601547--7601717 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
7601537 GCCCATAAGT
* * *
7601547 GAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCATGAGTGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
7601612 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
7601640 GAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
7601704 ACGAGTTCGGATGC
65 ACGAGCTCGGATGC
7601718 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:7601714 original size:46 final size:45
Alignment explanation
Indices: 7601539--7601713 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 45
7601529 TGTAACCCGC
*
7601539 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCAT
* * *
7601585 CCATGAGTGAACTTGGACTCAACTCAACGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--T
* *** *
7601631 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCAT
*
7601678 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
7601714 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 65 0.61
47 31 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:7601733 original size:46 final size:46
Alignment explanation
Indices: 7601544--7601733 Score: 128
Period size: 46 Copynumber: 4.1 Consensus size: 46
7601534 CCCGCCCATA
* * *
7601544 AGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTC--GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGCTC-GGATGCTCAACCATCC-T
*
7601589 GAGTGAACTTGGACTCAACTCAACGAGCTCGGATGC-CTAGTTA-CATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTC-A---ACCATC-CT
* * * * * *
7601639 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGCTCAACCATCCT
*
7601683 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAACCATCCT
7601729 AGTGA
1 AGTGA
7601734 CATGTCACTT
Statistics
Matches: 114, Mismatches: 14, Indels: 32
0.71 0.09 0.20
Matches are distributed among these distances:
44 9 0.08
45 3 0.03
46 62 0.54
47 29 0.25
49 4 0.04
50 6 0.05
51 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAACCATCCT
Found at i:7611585 original size:13 final size:14
Alignment explanation
Indices: 7611567--7611598 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
7611557 ATCGTCCATC
7611567 TCTTTTTAT-TTAT
1 TCTTTTTATATTAT
7611580 TCTTTTTATATTAT
1 TCTTTTTATATTAT
7611594 TCTTT
1 TCTTT
7611599 AATTATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (14 bp):
TCTTTTTATATTAT
Found at i:7625298 original size:29 final size:30
Alignment explanation
Indices: 7625251--7625351 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 30
7625241 TTTACAAATT
*
7625251 TGCTCAAATGAAG-GTCAAACC-CTTCAAAA
1 TGCTTAAAT-AAGAGTCAAACCTCTTCAAAA
* * * *
7625280 TGGTTAAATATGAGTCAAACCTTTTTAAAA
1 TGCTTAAATAAGAGTCAAACCTCTTCAAAA
* * * *
7625310 TGCTTAAATAAGGGTCAAACATTTTCGAAAG
1 TGCTTAAATAAGAGTCAAACCTCTTC-AAAA
7625341 TGCTTAAATAA
1 TGCTTAAATAA
7625352 AGGATTCTCA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
28 2 0.03
29 15 0.26
30 27 0.47
31 14 0.24
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (30 bp):
TGCTTAAATAAGAGTCAAACCTCTTCAAAA
Found at i:7625317 original size:30 final size:31
Alignment explanation
Indices: 7625276--7625351 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
7625266 CAAACCCTTC
* * * *
7625276 AAAATGGTTAAATATGAGTCAAACCTTTT-T
1 AAAATGCTTAAATAAGAGTCAAACATTTTCG
*
7625306 AAAATGCTTAAATAAGGGTCAAACATTTTCG
1 AAAATGCTTAAATAAGAGTCAAACATTTTCG
*
7625337 AAAGTGCTTAAATAA
1 AAAATGCTTAAATAA
7625352 AGGATTCTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 25 0.64
31 14 0.36
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (31 bp):
AAAATGCTTAAATAAGAGTCAAACATTTTCG
Found at i:7626056 original size:29 final size:29
Alignment explanation
Indices: 7625995--7626057 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
7625985 GTTTAATGTG
* * * *
7625995 CAATTATATACATGAACTTTGATTTTATA
1 CAATTATAAACATGAAATTTGATCTGATA
* *
7626024 CAATTTTAAACATGAAATTTGATCTGATC
1 CAATTATAAACATGAAATTTGATCTGATA
7626053 CAATT
1 CAATT
7626058 CTTTTAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (29 bp):
CAATTATAAACATGAAATTTGATCTGATA
Found at i:7627922 original size:18 final size:18
Alignment explanation
Indices: 7627894--7627939 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
7627884 AGTGAAATTT
* *
7627894 ATATGAAAATCCCTGAATG
1 ATAT-AAAATCCCAGAAGG
*
7627913 ATTTAAAATCCCAGAAGG
1 ATATAAAATCCCAGAAGG
7627931 ATATAAAAT
1 ATATAAAAT
7627940 TTTTCGGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (18 bp):
ATATAAAATCCCAGAAGG
Found at i:7630381 original size:18 final size:18
Alignment explanation
Indices: 7630360--7630399 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
7630350 GAAATATTTA
*
7630360 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
7630378 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
7630396 TTTT
1 TTTT
7630400 AAAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:7630430 original size:12 final size:12
Alignment explanation
Indices: 7630400--7630432 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
7630390 ATATATTTTT
7630400 AAAATT-ATATA
1 AAAATTAATATA
7630411 AAAA-TAATATA
1 AAAATTAATATA
7630422 AAAATTAATAT
1 AAAATTAATAT
7630433 GGGCGGGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:7638091 original size:12 final size:12
Alignment explanation
Indices: 7638061--7638102 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
7638051 TCACAGAGTT
*
7638061 ACACGGATGAGG
1 ACACGGGTGAGG
7638073 ACACGGGTGAGG
1 ACACGGGTGAGG
*
7638085 GCACGGGCTGA-G
1 ACACGGG-TGAGG
7638097 ACACGG
1 ACACGG
7638103 TAATGTGTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 23 0.88
13 3 0.12
ACGTcount: A:0.26, C:0.21, G:0.45, T:0.07
Consensus pattern (12 bp):
ACACGGGTGAGG
Found at i:7644400 original size:18 final size:18
Alignment explanation
Indices: 7644387--7644421 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
7644377 GTGGAGGGGA
7644387 AGGGGGAGGAGGAGGAGG
1 AGGGGGAGGAGGAGGAGG
*
7644405 AGGGGGAGGTGGAGGAG
1 AGGGGGAGGAGGAGGAG
7644422 CTGGAGGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.71, T:0.03
Consensus pattern (18 bp):
AGGGGGAGGAGGAGGAGG
Found at i:7644434 original size:24 final size:24
Alignment explanation
Indices: 7644374--7644435 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
7644364 GGTGGCGGCA
* *
7644374 CAGGTGGAGGGGAAGGGGGAGGAG
1 CAGGAGGAGGGGGAGGGGGAGGAG
* *
7644398 GAGGAGGAGGGGGAGGTGGAGGAG
1 CAGGAGGAGGGGGAGGGGGAGGAG
*
7644422 CTGGAGGAGGGGGA
1 CAGGAGGAGGGGGA
7644436 AGTATGTCGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.68, T:0.05
Consensus pattern (24 bp):
CAGGAGGAGGGGGAGGGGGAGGAG
Found at i:7647902 original size:37 final size:37
Alignment explanation
Indices: 7647852--7647928 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
7647842 ACTTCACTGG
*
7647852 TTATGTTTCCTTGCTATGTGAAACCTTTTCCATCATT
1 TTATGTCTCCTTGCTATGTGAAACCTTTTCCATCATT
*
7647889 TTATGTCTCCTTGCTATGTGAAACCTTTTTCATCATT
1 TTATGTCTCCTTGCTATGTGAAACCTTTTCCATCATT
7647926 TTA
1 TTA
7647929 ACTTTCGGAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.49
Consensus pattern (37 bp):
TTATGTCTCCTTGCTATGTGAAACCTTTTCCATCATT
Found at i:7649520 original size:14 final size:14
Alignment explanation
Indices: 7649501--7649531 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
7649491 ACCTATGCAA
7649501 TTTGGTTAATTTGG
1 TTTGGTTAATTTGG
*
7649515 TTTGGTTAGTTTGG
1 TTTGGTTAATTTGG
7649529 TTT
1 TTT
7649532 TAATGTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.00, G:0.29, T:0.61
Consensus pattern (14 bp):
TTTGGTTAATTTGG
Found at i:7650987 original size:17 final size:17
Alignment explanation
Indices: 7650965--7651008 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
7650955 GATTTCTAAA
7650965 TCTTTTTAGTTATTTCT
1 TCTTTTTAGTTATTTCT
* *
7650982 TCTTTTTTGTTCTTTCT
1 TCTTTTTAGTTATTTCT
* *
7650999 ACATTTTAGT
1 TCTTTTTAGT
7651009 AAGTATTCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.07, T:0.68
Consensus pattern (17 bp):
TCTTTTTAGTTATTTCT
Found at i:7654341 original size:198 final size:198
Alignment explanation
Indices: 7654003--7654383 Score: 744
Period size: 198 Copynumber: 1.9 Consensus size: 198
7653993 TTATTAGAAG
*
7654003 CACCTAATTGGTTACTAAAAAATTCCCCACCATTGTCACTCCGAAGTACTTCTATTCTCACACCA
1 CACCTAATTGGTGACTAAAAAATTCCCCACCATTGTCACTCCGAAGTACTTCTATTCTCACACCA
7654068 AATTGTGTTTTCACCATAGCATAAATAGACTAAAACACATTTTTAACTTCAGACTTATTTTTTAA
66 AATTGTGTTTTCACCATAGCATAAATAGACTAAAACACATTTTTAACTTCAGACTTATTTTTTAA
*
7654133 TAAAAACACCCAGCAAATGTGAGTATGATCATCAATAAATGTCACAAACCAACATTTGGTTAATA
131 TAAAAACACCCAACAAATGTGAGTATGATCATCAATAAATGTCACAAACCAACATTTGGTTAATA
7654198 AAA
196 AAA
7654201 CACCTAATTGGTGACTAAAAAATTCCCCACCATTGTCACTCCGAAGTACTTCTATTCTCACACCA
1 CACCTAATTGGTGACTAAAAAATTCCCCACCATTGTCACTCCGAAGTACTTCTATTCTCACACCA
7654266 AATTGTGTTTTCACCATAGCATAAATAGACTAAAACACATTTTTAACTTCAGACTTATTTTTTAA
66 AATTGTGTTTTCACCATAGCATAAATAGACTAAAACACATTTTTAACTTCAGACTTATTTTTTAA
7654331 TAAAAACACCCAACAAATGTGAGTATGATCATCAATAAATGTCACAAACCAAC
131 TAAAAACACCCAACAAATGTGAGTATGATCATCAATAAATGTCACAAACCAAC
7654384 GTTTTCTTGA
Statistics
Matches: 181, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
198 181 1.00
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (198 bp):
CACCTAATTGGTGACTAAAAAATTCCCCACCATTGTCACTCCGAAGTACTTCTATTCTCACACCA
AATTGTGTTTTCACCATAGCATAAATAGACTAAAACACATTTTTAACTTCAGACTTATTTTTTAA
TAAAAACACCCAACAAATGTGAGTATGATCATCAATAAATGTCACAAACCAACATTTGGTTAATA
AAA
Found at i:7656136 original size:20 final size:19
Alignment explanation
Indices: 7656113--7656177 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
7656103 AAGCTCAAAC
7656113 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
7656133 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
7656153 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
7656173 GAGCT
1 GAGCT
7656178 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:7665534 original size:18 final size:19
Alignment explanation
Indices: 7665511--7665553 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
7665501 GCTTATTAGG
7665511 TATTTTTA-ATTTTTATAT
1 TATTTTTATATTTTTATAT
* *
7665529 TA-TTTTATATTTTTTTTT
1 TATTTTTATATTTTTATAT
7665547 TATTTTT
1 TATTTTT
7665554 TTATACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 12 0.57
19 4 0.19
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (19 bp):
TATTTTTATATTTTTATAT
Found at i:7665553 original size:10 final size:10
Alignment explanation
Indices: 7665520--7665558 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
7665510 GTATTTTTAA
7665520 TTTTTATATT
1 TTTTTATATT
*
7665530 ATTTTATATTT
1 TTTTTATA-TT
*
7665541 TTTTTTTATT
1 TTTTTATATT
7665551 TTTTTATA
1 TTTTTATA
7665559 CAATATTGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTATATT
Found at i:7668800 original size:6 final size:6
Alignment explanation
Indices: 7668789--7668949 Score: 50
Period size: 6 Copynumber: 27.0 Consensus size: 6
7668779 AAGAAAAGCT
* * *
7668789 ATAATA ATAATA GTAATT ATAATA A-AAGTA ATAATA ATAA-A TATAACA
1 ATAATA ATAATA ATAATA ATAATA ATAA-TA ATAATA ATAATA -ATAATA
* * * * * * *
7668837 ATAGTA ATATTA GTGATA A-AA-A ATAATA GCT-ATA AAAACA A-ACATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA -ATAATA ATAATA ATA-ATA
** * * * *
7668883 ATAACC ATGACA ATAAAGA ATAATA GTAATA ATAATA ATAATGA A-AATA
1 ATAATA ATAATA AT-AATA ATAATA ATAATA ATAATA ATAAT-A ATAATA
*
7668932 A-AAGTA ATATTA ATAATA
1 ATAA-TA ATAATA ATAATA
7668950 TATTATATTA
Statistics
Matches: 113, Mismatches: 28, Indels: 28
0.67 0.17 0.17
Matches are distributed among these distances:
4 2 0.02
5 11 0.10
6 88 0.78
7 12 0.11
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (6 bp):
ATAATA
Found at i:7668812 original size:15 final size:15
Alignment explanation
Indices: 7668789--7668829 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
7668779 AAGAAAAGCT
*
7668789 ATAATAATAATAGTA
1 ATAATAATAAAAGTA
*
7668804 ATTATAATAAAAGTA
1 ATAATAATAAAAGTA
7668819 ATAATAATAAA
1 ATAATAATAAA
7668830 TATAACAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (15 bp):
ATAATAATAAAAGTA
Found at i:7668820 original size:24 final size:24
Alignment explanation
Indices: 7668793--7668850 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
7668783 AAAGCTATAA
* *
7668793 TAATAATAGTAATTATAATAAAAG
1 TAATAATAGTAAATATAACAAAAG
* *
7668817 TAATAATAATAAATATAACAATAG
1 TAATAATAGTAAATATAACAAAAG
*
7668841 TAATATTAGT
1 TAATAATAGT
7668851 GATAAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (24 bp):
TAATAATAGTAAATATAACAAAAG
Found at i:7669569 original size:3 final size:3
Alignment explanation
Indices: 7669555--7669760 Score: 127
Period size: 3 Copynumber: 68.7 Consensus size: 3
7669545 AAACATACAC
* * *
7669555 TAA TAT TAA TAA TAA TAA TAA TAC TAGA -AA TAA TAA TAA CTAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA -TAA TAA
* ** * * *
7669601 TAA TAA TACA TTAA GAA TAA TAA T-A TGT TAA TAA AAA TAG TAG TAA
1 TAA TAA TA-A -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *** *
7669647 TGAA -AA TAA TAC TAA CGG TAA TAA TAA TAA TAC TAA TAA TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
7669692 TAA TAA TAA TAGA -AA TAA -AA TAA TAA TAA CAT TAT TAA TAT TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
7669736 TAA TAT TAA -AA AAA TAA TAA GAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
7669761 TTTAATAAAG
Statistics
Matches: 155, Mismatches: 36, Indels: 24
0.72 0.17 0.11
Matches are distributed among these distances:
2 10 0.06
3 136 0.88
4 7 0.05
5 2 0.01
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:7671611 original size:15 final size:15
Alignment explanation
Indices: 7671591--7671621 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7671581 ATGAGGCGGC
7671591 ATATATAAATATTAT
1 ATATATAAATATTAT
*
7671606 ATATATAATTATTAT
1 ATATATAAATATTAT
7671621 A
1 A
7671622 ATTATTAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATAAATATTAT
Found at i:7671628 original size:3 final size:3
Alignment explanation
Indices: 7671600--7671685 Score: 93
Period size: 3 Copynumber: 27.7 Consensus size: 3
7671590 CATATATAAA
* * * *
7671600 TAT TA- TAT ATAT AAT TAT TAT AAT TAT TAAC CAT TAT TAT GGTAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT --TAT TAT
7671648 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
7671686 AATAAAGTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
2 2 0.03
3 61 0.87
4 4 0.06
5 3 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:7672987 original size:17 final size:17
Alignment explanation
Indices: 7672961--7673013 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
7672951 TTGGAAGGAT
7672961 ATTG-AATGG-ATTGTAA
1 ATTGAAATGGAATTG-AA
7672977 ATTGAAATGGAATTGAA
1 ATTGAAATGGAATTGAA
* * *
7672994 ATTGATATGAAAATGAA
1 ATTGAAATGGAATTGAA
7673011 ATT
1 ATT
7673014 AAAAAAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 4 0.12
17 24 0.75
18 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (17 bp):
ATTGAAATGGAATTGAA
Found at i:7676845 original size:14 final size:15
Alignment explanation
Indices: 7676828--7676862 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
7676818 ATTTAAGTTA
7676828 ATTATTTTAGTAT-T
1 ATTATTTTAGTATCT
7676842 ATTATTTTAGTATCT
1 ATTATTTTAGTATCT
7676857 ATTATT
1 ATTATT
7676863 AATGTCATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (15 bp):
ATTATTTTAGTATCT
Found at i:7677873 original size:24 final size:25
Alignment explanation
Indices: 7677845--7677909 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
7677835 TTTATATATA
7677845 TATTATTATGTATATATACTC-TAGC
1 TATTATTATGTATATATACTCTTA-C
* *
7677870 -ATTACTAAT-TATATATATTCTTAC
1 TATTA-TTATGTATATATACTCTTAC
7677894 TATT-TTATGTATATAT
1 TATTATTATGTATATAT
7677910 TTCAAATACT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
23 3 0.09
24 22 0.67
25 8 0.24
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (25 bp):
TATTATTATGTATATATACTCTTAC
Found at i:7680392 original size:58 final size:58
Alignment explanation
Indices: 7680330--7680479 Score: 144
Period size: 58 Copynumber: 2.6 Consensus size: 58
7680320 AGGACTATGC
** * * *
7680330 AAATTGAGAATGTAGCAAAATGTGTTACCATTCAA-AGTCGAACTGTTCAAAATTAGAA
1 AAATTGAGAATGTAGCAAAA-GTGCCACCATTCAATAGTCGAACTATTCAAAATAACAA
* * * * * *
7680388 AAATTTATAAATG-AGCAATAGATGCCACCATT-AATAGTTGAACTATTCAAGATAACAC
1 AAATTGA-GAATGTAGCAAAAG-TGCCACCATTCAATAGTCGAACTATTCAAAATAACAA
7680446 AAATTGAGAATGTAGCAAAAGGTGCCACCATTCA
1 AAATTGAGAATGTAGCAAAA-GTGCCACCATTCA
7680480 CGGTTAAACT
Statistics
Matches: 72, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
57 7 0.10
58 59 0.82
59 6 0.08
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (58 bp):
AAATTGAGAATGTAGCAAAAGTGCCACCATTCAATAGTCGAACTATTCAAAATAACAA
Found at i:7684616 original size:5 final size:5
Alignment explanation
Indices: 7684606--7684632 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
7684596 TGATACAAAA
7684606 TATAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TA
7684633 CGTTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:7685826 original size:3 final size:3
Alignment explanation
Indices: 7685820--7685850 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
7685810 ACAATTTTCC
*
7685820 CTT CTT CTT CTT TTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
7685851 CTCCGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:7686223 original size:13 final size:13
Alignment explanation
Indices: 7686179--7686239 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
7686169 AGGAAAGAAG
7686179 TTTAAAAGTTAAAAT
1 TTTAAAA-TT-AAAT
* *
7686194 TGTTATAA-TAAAA
1 T-TTAAAATTAAAT
7686207 TTTAAAATTAAAT
1 TTTAAAATTAAAT
* *
7686220 TTTAAAAATAAAG
1 TTTAAAATTAAAT
7686233 TTTAAAA
1 TTTAAAA
7686240 CAATTTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 5 0.13
13 26 0.68
14 1 0.03
15 1 0.03
16 5 0.13
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (13 bp):
TTTAAAATTAAAT
Found at i:7686227 original size:14 final size:13
Alignment explanation
Indices: 7686200--7686239 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
7686190 AAATTGTTAT
*
7686200 AATAAAATTTAAA
1 AATAAAGTTTAAA
* *
7686213 ATTAAATTTTAAA
1 AATAAAGTTTAAA
7686226 AATAAAGTTTAAA
1 AATAAAGTTTAAA
7686239 A
1 A
7686240 CAATTTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (13 bp):
AATAAAGTTTAAA
Found at i:7686614 original size:16 final size:16
Alignment explanation
Indices: 7686593--7686627 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
7686583 TATGGTTATG
* *
7686593 AAATAAATATTAAGAT
1 AAATAAAGATAAAGAT
7686609 AAATAAAGATAAAGAT
1 AAATAAAGATAAAGAT
7686625 AAA
1 AAA
7686628 GATAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (16 bp):
AAATAAAGATAAAGAT
Found at i:7686620 original size:22 final size:22
Alignment explanation
Indices: 7686595--7686637 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
7686585 TGGTTATGAA
* *
7686595 ATAAATATTAAGATAAATAAAG
1 ATAAAGATAAAGATAAATAAAG
*
7686617 ATAAAGATAAAGATAATTAAA
1 ATAAAGATAAAGATAAATAAA
7686638 TAATATTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (22 bp):
ATAAAGATAAAGATAAATAAAG
Found at i:7686675 original size:21 final size:21
Alignment explanation
Indices: 7686636--7686685 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
7686626 AAGATAATTA
* *
7686636 AATAATATTTATTTTTATGAT
1 AATAATATTTATCTCTATGAT
*
7686657 AATAGTATTTATCTCTATGA-
1 AATAATATTTATCTCTATGAT
*
7686677 AAAAATATT
1 AATAATATT
7686686 AAAAATAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (21 bp):
AATAATATTTATCTCTATGAT
Found at i:7688959 original size:17 final size:18
Alignment explanation
Indices: 7688924--7688966 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
7688914 AACATATATA
*
7688924 TAAAGTGTATAATAAAAT
1 TAAAATGTATAATAAAAT
7688942 TAAAATGTATAA-AAAAT
1 TAAAATGTATAATAAAAT
7688959 TCAAAATG
1 T-AAAATG
7688967 AAGTTTTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (18 bp):
TAAAATGTATAATAAAAT
Found at i:7690779 original size:26 final size:24
Alignment explanation
Indices: 7690742--7690789 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
7690732 TTAAAAAAAA
*
7690742 TTAAAAATATAATAAATCAAATATAT
1 TTAAAAACATAA-AAAT-AAATATAT
7690768 TTAAAAACATAAAAATAAATAT
1 TTAAAAACATAAAAATAAATAT
7690790 TAAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 4 0.19
26 11 0.52
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
TTAAAAACATAAAAATAAATATAT
Found at i:7690801 original size:22 final size:22
Alignment explanation
Indices: 7690760--7690818 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
7690750 ATAATAAATC
* *
7690760 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
7690780 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
* *
7690802 AAAT-GATACTAAAACAA
1 AAATAAATATTAAAACAA
7690819 TTCTTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.21
21 17 0.52
22 9 0.27
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:7691330 original size:15 final size:15
Alignment explanation
Indices: 7691307--7691340 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
7691297 AACAATTTTT
7691307 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
* *
7691322 AAAAGAAAATAAAAG
1 AAAAAAAAAAAAAAG
7691337 AAAA
1 AAAA
7691341 CAAATCTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:7697116 original size:112 final size:112
Alignment explanation
Indices: 7696874--7697099 Score: 452
Period size: 112 Copynumber: 2.0 Consensus size: 112
7696864 ATCCAATCAG
7696874 AACAGAACTCTTCAATATTTGGAAACAAAATAGGTTTGAGTAGAAAAAAGAAAAAAATATTTAAA
1 AACAGAACTCTTCAATATTTGGAAACAAAATAGGTTTGAGTAGAAAAAAGAAAAAAATATTTAAA
7696939 ATATGGGTTGGCCTAACTTGTTTTGCAAGTTTCTGATAACAAAAAGA
66 ATATGGGTTGGCCTAACTTGTTTTGCAAGTTTCTGATAACAAAAAGA
7696986 AACAGAACTCTTCAATATTTGGAAACAAAATAGGTTTGAGTAGAAAAAAGAAAAAAATATTTAAA
1 AACAGAACTCTTCAATATTTGGAAACAAAATAGGTTTGAGTAGAAAAAAGAAAAAAATATTTAAA
7697051 ATATGGGTTGGCCTAACTTGTTTTGCAAGTTTCTGATAACAAAAAGA
66 ATATGGGTTGGCCTAACTTGTTTTGCAAGTTTCTGATAACAAAAAGA
7697098 AA
1 AA
7697100 TGATCTCTTT
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 114 1.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (112 bp):
AACAGAACTCTTCAATATTTGGAAACAAAATAGGTTTGAGTAGAAAAAAGAAAAAAATATTTAAA
ATATGGGTTGGCCTAACTTGTTTTGCAAGTTTCTGATAACAAAAAGA
Found at i:7698842 original size:43 final size:44
Alignment explanation
Indices: 7698760--7698842 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 44
7698750 TGTAAATTAA
* *
7698760 ATTATAATTATTTTTAAATGTGTAATAATCACTACTTCTAATGC
1 ATTATAATTATTTTTAAATGTATAATAATCACGACTTCTAATGC
* * *
7698804 ATTATAATT-TTTTTAAATGTATAGTTATCACGATTTCTA
1 ATTATAATTATTTTTAAATGTATAATAATCACGACTTCTA
7698843 TTTTGCTTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 25 0.74
44 9 0.26
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (44 bp):
ATTATAATTATTTTTAAATGTATAATAATCACGACTTCTAATGC
Found at i:7707679 original size:18 final size:18
Alignment explanation
Indices: 7707656--7707691 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
7707646 GAACTTAAAC
7707656 CTACAGCTAGGTTTTGGT
1 CTACAGCTAGGTTTTGGT
7707674 CTACAGCTAGGTTTTGGT
1 CTACAGCTAGGTTTTGGT
7707692 AGACTTAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (18 bp):
CTACAGCTAGGTTTTGGT
Found at i:7708078 original size:26 final size:26
Alignment explanation
Indices: 7707979--7708085 Score: 124
Period size: 26 Copynumber: 4.1 Consensus size: 26
7707969 ATTCTTGTGA
* * * *
7707979 ACTCATGCTTGGAATAGTGCTTGTGG
1 ACTCATACATGGAATAGTCCTTGCGG
* * *
7708005 ACTCATACATGGAATAATCCTCGTGG
1 ACTCATACATGGAATAGTCCTTGCGG
*
7708031 AATCATACATGGAATAGTCCTTGCGG
1 ACTCATACATGGAATAGTCCTTGCGG
* *
7708057 ACTCATACAGGGAATAGTCCTTGCAG
1 ACTCATACATGGAATAGTCCTTGCGG
7708083 ACT
1 ACT
7708086 TTTGCTTAAA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 69 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (26 bp):
ACTCATACATGGAATAGTCCTTGCGG
Found at i:7713432 original size:39 final size:39
Alignment explanation
Indices: 7713389--7713465 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
7713379 CACAGAAGGG
7713389 TTAAGAACCTTACCTGCTTGCTAGTTTCCCTACTTTTTA
1 TTAAGAACCTTACCTGCTTGCTAGTTTCCCTACTTTTTA
* *
7713428 TTAAGAACCTTACCTGTTTGCTAGTTTTCCTACTTTTT
1 TTAAGAACCTTACCTGCTTGCTAGTTTCCCTACTTTTT
7713466 TTTATCTCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.47
Consensus pattern (39 bp):
TTAAGAACCTTACCTGCTTGCTAGTTTCCCTACTTTTTA
Found at i:7717702 original size:12 final size:12
Alignment explanation
Indices: 7717685--7717709 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7717675 CATAAGACTT
7717685 CCAACTTTGAAG
1 CCAACTTTGAAG
7717697 CCAACTTTGAAG
1 CCAACTTTGAAG
7717709 C
1 C
7717710 ATATGGAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (12 bp):
CCAACTTTGAAG
Found at i:7734148 original size:18 final size:18
Alignment explanation
Indices: 7734125--7734164 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
7734115 TTTACCTACA
7734125 CGTTTAAAACAATAAACG
1 CGTTTAAAACAATAAACG
7734143 CGTTTAAAACAATAAACG
1 CGTTTAAAACAATAAACG
7734161 CGTT
1 CGTT
7734165 AAGTTTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.25
Consensus pattern (18 bp):
CGTTTAAAACAATAAACG
Found at i:7741319 original size:20 final size:20
Alignment explanation
Indices: 7741296--7741371 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
7741286 TAAATTTTAA
* *
7741296 TTCATTCATATAACCAGTAG
1 TTCATCCATATAAACAGTAG
* *
7741316 TTCATCCGTATAAATAGTAG
1 TTCATCCATATAAACAGTAG
* *
7741336 TTCAT-CAGTA-ATAAGAGTAA
1 TTCATCCA-TATA-AACAGTAG
7741356 TTCATCCATATAAACA
1 TTCATCCATATAAACA
7741372 CATATATTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
19 2 0.05
20 39 0.89
21 3 0.07
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (20 bp):
TTCATCCATATAAACAGTAG
Found at i:7741598 original size:23 final size:23
Alignment explanation
Indices: 7741545--7741599 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
7741535 GATAAACAGT
7741545 TGAGCTG-AACGGTAAGCTCATA
1 TGAGCTGAAACGGTAAGCTCATA
* *
7741567 CGAGTTGAAACGGTAAGCTCCA-A
1 TGAGCTGAAACGGTAAGCT-CATA
7741590 TGAGCTGAAA
1 TGAGCTGAAA
7741600 AATAATAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 5 0.19
23 20 0.74
24 2 0.07
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (23 bp):
TGAGCTGAAACGGTAAGCTCATA
Found at i:7741897 original size:35 final size:36
Alignment explanation
Indices: 7741835--7741905 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
7741825 AGTACATACA
* *
7741835 TTTAAATATTCAATTTGCACACCTAATGCATATTAT
1 TTTAAATACTCAATTCGCACACCTAATGCATATTAT
*
7741871 TTTAAATACTC-ATTCGCATACCTAATGCATATTAT
1 TTTAAATACTCAATTCGCACACCTAATGCATATTAT
7741906 CATACCGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 22 0.69
36 10 0.31
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (36 bp):
TTTAAATACTCAATTCGCACACCTAATGCATATTAT
Found at i:7746246 original size:8 final size:8
Alignment explanation
Indices: 7746233--7746267 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
7746223 CATATCTCAT
7746233 ACATTTAA
1 ACATTTAA
7746241 ACATTTAA
1 ACATTTAA
7746249 ACATTTAA
1 ACATTTAA
*
7746257 ACATTCAA
1 ACATTTAA
7746265 ACA
1 ACA
7746268 CATACATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (8 bp):
ACATTTAA
Found at i:7747225 original size:17 final size:17
Alignment explanation
Indices: 7747203--7747237 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
7747193 AAATACGGAA
7747203 AATAAGCACAGTAAGCT
1 AATAAGCACAGTAAGCT
**
7747220 AATAAGCTTAGTAAGCT
1 AATAAGCACAGTAAGCT
7747237 A
1 A
7747238 GTATGACTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (17 bp):
AATAAGCACAGTAAGCT
Found at i:7747758 original size:20 final size:19
Alignment explanation
Indices: 7747735--7747832 Score: 79
Period size: 20 Copynumber: 4.9 Consensus size: 19
7747725 AATACATTCA
* *
7747735 TATAACCAGTAGTTCATCTG
1 TATAA-CAGTAATTCATCAG
* **
7747755 TATAAATAGTAGCTCATCAG
1 TAT-AACAGTAATTCATCAG
* *
7747775 TAATAATAGTAATTCATCCG
1 T-ATAACAGTAATTCATCAG
*
7747795 TATTAACAGTAATTCATCAA
1 TA-TAACAGTAATTCATCAG
7747815 TATTAACAGTAATTCATC
1 TA-TAACAGTAATTCATC
7747833 CATATAAACA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 61 0.92
21 4 0.06
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (19 bp):
TATAACAGTAATTCATCAG
Found at i:7747791 original size:40 final size:40
Alignment explanation
Indices: 7747736--7747842 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 40
7747726 ATACATTCAT
* * * * *
7747736 ATAACCAGTAGTTCATCTGTATAAATAGTAGCTCATCAGTA
1 ATAA-CAGTAATTCATCCGTATAAACAGTAACTCATCAATA
* * *
7747777 ATAATAGTAATTCATCCGTATTAACAGTAATTCATCAATA
1 ATAACAGTAATTCATCCGTATAAACAGTAACTCATCAATA
* *
7747817 TTAACAGTAATTCATCCATATAAACA
1 ATAACAGTAATTCATCCGTATAAACA
7747843 CATATCTTAT
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
40 50 0.93
41 4 0.07
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (40 bp):
ATAACAGTAATTCATCCGTATAAACAGTAACTCATCAATA
Found at i:7747837 original size:20 final size:20
Alignment explanation
Indices: 7747782--7747842 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
7747772 CAGTAATAAT
*
7747782 AGTAATTCATCCGTATTAAC
1 AGTAATTCATCCATATTAAC
*
7747802 AGTAATTCATCAATATTAAC
1 AGTAATTCATCCATATTAAC
*
7747822 AGTAATTCATCCATATAAAC
1 AGTAATTCATCCATATTAAC
7747842 A
1 A
7747843 CATATCTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (20 bp):
AGTAATTCATCCATATTAAC
Found at i:7748055 original size:23 final size:23
Alignment explanation
Indices: 7748009--7748065 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
7747999 CTGAGTTGAT
* *
7748009 AAACAGTAAGCTCTATTGAGCTG
1 AAACAGTAAGCTCTATCGAACTG
* *
7748032 AAACTGTAAGCTTTATCGAACTG
1 AAACAGTAAGCTCTATCGAACTG
*
7748055 -AACAATAAGCT
1 AAACAGTAAGCT
7748066 TATAAGAGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.26
Consensus pattern (23 bp):
AAACAGTAAGCTCTATCGAACTG
Found at i:7761392 original size:21 final size:21
Alignment explanation
Indices: 7761368--7761432 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
7761358 AAATCTAACT
7761368 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
*** *
7761389 GAAGC-CCGGAG-GCT-AACT
1 GAAGCACATAAGTGCTAAACG
7761407 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
7761428 GAAGC
1 GAAGC
7761433 CCGAAAGCTA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 6 0.18
21 13 0.39
ACGTcount: A:0.38, C:0.22, G:0.28, T:0.12
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACG
Found at i:7761405 original size:39 final size:39
Alignment explanation
Indices: 7761350--7761450 Score: 175
Period size: 39 Copynumber: 2.6 Consensus size: 39
7761340 ATCGTGATCT
*
7761350 GAAGCCCGAAATCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAAGCTAACTGAAGCACATAAGTGCTAAACG
* *
7761389 GAAGCCCGGAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAAGCTAACTGAAGCACATAAGTGCTAAACG
7761428 GAAGCCCGAAAGCTAACTGAAGC
1 GAAGCCCGAAAGCTAACTGAAGC
7761451 TCATCAGAGC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.39, C:0.24, G:0.25, T:0.13
Consensus pattern (39 bp):
GAAGCCCGAAAGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:7774859 original size:37 final size:37
Alignment explanation
Indices: 7774808--7774904 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 37
7774798 ATCATTCAGA
*
7774808 ATAACGGTAAGATTTGCTC-AGTTAAGCTCCATTTAGT
1 ATAACGATAAGATTTGCTCGA-TTAAGCTCCATTTAGT
* * *
7774845 ATAACGATATGATTTGCTCGATTGAGCTTCATTTAGT
1 ATAACGATAAGATTTGCTCGATTAAGCTCCATTTAGT
* *
7774882 ATAACAATAGGATTTGGCTCGAT
1 ATAACGATAAGATTT-GCTCGAT
7774905 AGAGCGTACT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
37 44 0.85
38 8 0.15
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (37 bp):
ATAACGATAAGATTTGCTCGATTAAGCTCCATTTAGT
Found at i:7780350 original size:8 final size:8
Alignment explanation
Indices: 7780339--7780382 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
7780329 TTTAAGAAAT
7780339 TAATATAA
1 TAATATAA
*
7780347 TAATATAT
1 TAATATAA
7780355 TAATATAA
1 TAATATAA
7780363 T-ATA-ATA
1 TAATATA-A
7780370 TAATATAA
1 TAATATAA
7780378 TAATA
1 TAATA
7780383 AAACAAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
6 1 0.03
7 5 0.16
8 24 0.77
9 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TAATATAA
Found at i:7780363 original size:5 final size:5
Alignment explanation
Indices: 7780339--7780379 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
7780329 TTTAAGAAAT
7780339 TAATA TAATA -ATATA TTAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TA-ATA -TAATA TAATA TAATA TAATA TAATA
7780380 ATAAAACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 1 0.03
5 28 0.85
6 3 0.09
7 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:7781573 original size:25 final size:25
Alignment explanation
Indices: 7781538--7781594 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
7781528 CTGTACTGGA
*
7781538 AATTGATTGTTATTGATTGATATAT
1 AATTGAATGTTATTGATTGATATAT
7781563 AATTGAATGTTATTGATTGATATAT
1 AATTGAATGTTATTGATTGATATAT
7781588 AATTGAA
1 AATTGAA
7781595 CTGAATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (25 bp):
AATTGAATGTTATTGATTGATATAT
Found at i:7785715 original size:30 final size:30
Alignment explanation
Indices: 7785679--7785741 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
7785669 ACTTAACAAG
7785679 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
7785709 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
7785739 CAA
1 CAA
7785742 TAAAATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:7794526 original size:23 final size:23
Alignment explanation
Indices: 7794500--7794593 Score: 125
Period size: 23 Copynumber: 4.1 Consensus size: 23
7794490 AAGTTAGAAG
7794500 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
7794523 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
* *
7794546 AGTGAAGAGACTTGAAGATCAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
7794569 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
7794592 AG
1 AG
7794594 ATACACACAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.48, C:0.05, G:0.24, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:7799033 original size:23 final size:23
Alignment explanation
Indices: 7799007--7799100 Score: 125
Period size: 23 Copynumber: 4.1 Consensus size: 23
7798997 AAGTTAGAAG
7799007 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
7799030 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
* *
7799053 AGTGAAGAGACTTGAAGATCAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
7799076 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
7799099 AG
1 AG
7799101 ATACACACAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.48, C:0.05, G:0.24, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:7800829 original size:36 final size:36
Alignment explanation
Indices: 7800782--7800896 Score: 140
Period size: 45 Copynumber: 2.9 Consensus size: 36
7800772 CTCAATTTAA
7800782 TCATGCATGTGTTCTATTCATTGAAAAGAAATTGAT
1 TCATGCATGTGTTCTATTCATTGAAAAGAAATTGAT
7800818 TCATGCATGTGTTCTATTCATTCTAGTCATTGAAAAGAAATTGAT
1 TCATGCATGTGTTC---T-A---T--TCATTGAAAAGAAATTGAT
*
7800863 TCATGCATGTGTTGTATTCATTGAAAAGAAATTG
1 TCATGCATGTGTTCTATTCATTGAAAAGAAATTG
7800897 GTATAAGTAT
Statistics
Matches: 69, Mismatches: 1, Indels: 18
0.78 0.01 0.20
Matches are distributed among these distances:
36 31 0.45
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 1 0.01
45 32 0.46
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.39
Consensus pattern (36 bp):
TCATGCATGTGTTCTATTCATTGAAAAGAAATTGAT
Found at i:7800848 original size:45 final size:45
Alignment explanation
Indices: 7800793--7800884 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
7800783 CATGCATGTG
*
7800793 TTCTATTCATTGAAAAGAAATTGATTCATGCATGTGTTCTATTCA
1 TTCTAGTCATTGAAAAGAAATTGATTCATGCATGTGTTCTATTCA
*
7800838 TTCTAGTCATTGAAAAGAAATTGATTCATGCATGTGTTGTATTCA
1 TTCTAGTCATTGAAAAGAAATTGATTCATGCATGTGTTCTATTCA
7800883 TT
1 TT
7800885 GAAAAGAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (45 bp):
TTCTAGTCATTGAAAAGAAATTGATTCATGCATGTGTTCTATTCA
Found at i:7801529 original size:21 final size:22
Alignment explanation
Indices: 7801505--7801551 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
7801495 ATTTGAATAG
7801505 TTCAAGCCATTGGCTTTTGTC-
1 TTCAAGCCATTGGCTTTTGTCA
7801526 TTCAAGCCATTGGCTTTTGTCA
1 TTCAAGCCATTGGCTTTTGTCA
7801548 TTCA
1 TTCA
7801552 TCTTTTAGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (22 bp):
TTCAAGCCATTGGCTTTTGTCA
Found at i:7806240 original size:13 final size:13
Alignment explanation
Indices: 7806222--7806246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7806212 GAAGTAAACG
7806222 TACACGGGCGTGC
1 TACACGGGCGTGC
7806235 TACACGGGCGTG
1 TACACGGGCGTG
7806247 TCCCTGCCGA
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:0.16, C:0.28, G:0.40, T:0.16
Consensus pattern (13 bp):
TACACGGGCGTGC
Found at i:7807768 original size:17 final size:18
Alignment explanation
Indices: 7807746--7807784 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
7807736 TGCATACACA
7807746 AATTAATTCAG-CACATT
1 AATTAATTCAGACACATT
*
7807763 AATTAATTTAGACACATT
1 AATTAATTCAGACACATT
7807781 AATT
1 AATT
7807785 TCCGGCTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AATTAATTCAGACACATT
Found at i:7812866 original size:18 final size:17
Alignment explanation
Indices: 7812829--7812867 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
7812819 TGCACACACA
7812829 AATTAATTCAACACATT
1 AATTAATTCAACACATT
* *
7812846 AATTAATTTAGACATATT
1 AATTAATTCA-ACACATT
7812864 AATT
1 AATT
7812868 TTCGGCTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (17 bp):
AATTAATTCAACACATT
Found at i:7813768 original size:20 final size:19
Alignment explanation
Indices: 7813727--7813769 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
7813717 CAATATTAAT
*
7813727 AATAATTAATAATTATAGA
1 AATAATTAATAATTAAAGA
* *
7813746 AATAATTTAATATTTAAATA
1 AATAA-TTAATAATTAAAGA
7813766 AATA
1 AATA
7813770 TCTATTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AATAATTAATAATTAAAGA
Found at i:7817352 original size:43 final size:43
Alignment explanation
Indices: 7817265--7817353 Score: 101
Period size: 43 Copynumber: 2.1 Consensus size: 43
7817255 ATATAACACA
* * *
7817265 AAACAAAACAAATAAAGAAAAAGAGAATAAAAAAATAAGCAAG
1 AAACAAAACAAAGAAAGAAAAAGAGAATAAAAAAAGAAGAAAG
* *
7817308 AAACAAAACAAAGAAAGGAAAAGGGAGAA-AGAAAAAGAA-AAAG
1 AAACAAAACAAAGAAA-GAAAA-AGAGAATAAAAAAAGAAGAAAG
7817351 AAA
1 AAA
7817354 AATTAGGGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
43 21 0.54
44 13 0.33
45 5 0.13
ACGTcount: A:0.74, C:0.06, G:0.17, T:0.03
Consensus pattern (43 bp):
AAACAAAACAAAGAAAGAAAAAGAGAATAAAAAAAGAAGAAAG
Found at i:7825207 original size:20 final size:20
Alignment explanation
Indices: 7825182--7825227 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
7825172 ATTGGGTCTT
7825182 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
7825202 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
7825221 GCCCATA
1 GCCCATA
7825228 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:7825236 original size:19 final size:20
Alignment explanation
Indices: 7825194--7825237 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
7825184 CCATATTAAC
** *
7825194 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
7825214 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
7825233 ACAGT
1 ACAGT
7825238 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:7834622 original size:16 final size:16
Alignment explanation
Indices: 7834601--7834631 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
7834591 ATCCCAATTA
7834601 TTAAAAATATTTTTAT
1 TTAAAAATATTTTTAT
7834617 TTAAAAATATTTTTA
1 TTAAAAATATTTTTA
7834632 AAAATATTAT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAAAATATTTTTAT
Found at i:7835311 original size:22 final size:23
Alignment explanation
Indices: 7835271--7835313 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
7835261 ATGTAATATT
*
7835271 TTTTTTAAAAATACCATTAAAAA
1 TTTTTTAAAAATACAATTAAAAA
*
7835294 TTTTTT-AAAATAGAATTAAA
1 TTTTTTAAAAATACAATTAAA
7835314 TACACAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (23 bp):
TTTTTTAAAAATACAATTAAAAA
Found at i:7841308 original size:3 final size:3
Alignment explanation
Indices: 7841290--7841335 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
7841280 TCATAATACA
7841290 ATT ATT -TT ACTT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
7841334 AT
1 AT
7841336 AAGAGTGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:7841322 original size:17 final size:18
Alignment explanation
Indices: 7841290--7841332 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
7841280 TCATAATACA
*
7841290 ATTATTTTACTTATTATT
1 ATTATTATACTTATTATT
7841308 ATTATTATA-TTATTATT
1 ATTATTATACTTATTATT
7841325 ATTATTAT
1 ATTATTAT
7841333 TATAAGAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTATTATACTTATTATT
Found at i:7842350 original size:6 final size:6
Alignment explanation
Indices: 7842339--7842386 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
7842329 ATATATACAC
*
7842339 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ACGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
7842387 CAGTTTATGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (6 bp):
ATGTAT
Found at i:7845987 original size:17 final size:17
Alignment explanation
Indices: 7845962--7845996 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
7845952 TTCGATTTGG
*
7845962 TTAAATCAATTTTGATT
1 TTAAATCAATTTTAATT
*
7845979 TTAAGTCAATTTTAATT
1 TTAAATCAATTTTAATT
7845996 T
1 T
7845997 AGTTAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (17 bp):
TTAAATCAATTTTAATT
Found at i:7846627 original size:48 final size:48
Alignment explanation
Indices: 7846562--7846664 Score: 170
Period size: 48 Copynumber: 2.1 Consensus size: 48
7846552 GTGGCTGAGT
*
7846562 TGGTGGTATAGGTGCTGTTGGTTCATATGGGAGACTAGGAGCCATGAC
1 TGGTGGTATAGGAGCTGTTGGTTCATATGGGAGACTAGGAGCCATGAC
* * *
7846610 TGGTGGTGTAGGAGCTGTTGGTTCATGTGGGGGACTAGGAGCCATGAC
1 TGGTGGTATAGGAGCTGTTGGTTCATATGGGAGACTAGGAGCCATGAC
7846658 TGGTGGT
1 TGGTGGT
7846665 TCATATGGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.17, C:0.12, G:0.42, T:0.29
Consensus pattern (48 bp):
TGGTGGTATAGGAGCTGTTGGTTCATATGGGAGACTAGGAGCCATGAC
Found at i:7846678 original size:33 final size:33
Alignment explanation
Indices: 7846628--7846697 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
7846618 TAGGAGCTGT
* * *
7846628 TGGTTCATGTGGGGGACTAGGAGCCATGACTGG
1 TGGTTCATATGGAGGACTAGGAACCATGACTGG
*
7846661 TGGTTCATATGGAGGACTAGGAACCTTGACTGG
1 TGGTTCATATGGAGGACTAGGAACCATGACTGG
7846694 TGGT
1 TGGT
7846698 GGAGCTGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.20, C:0.14, G:0.39, T:0.27
Consensus pattern (33 bp):
TGGTTCATATGGAGGACTAGGAACCATGACTGG
Found at i:7850608 original size:16 final size:16
Alignment explanation
Indices: 7850587--7850620 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
7850577 AATATGATTC
*
7850587 TGTGTATTGTGATATA
1 TGTGTAATGTGATATA
7850603 TGTGTAATGTGATATA
1 TGTGTAATGTGATATA
7850619 TG
1 TG
7850621 CCTAAACGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (16 bp):
TGTGTAATGTGATATA
Found at i:7852649 original size:17 final size:18
Alignment explanation
Indices: 7852629--7852663 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
7852619 CTAATTGCTA
7852629 TAAGTGTAT-AATATATT
1 TAAGTGTATAAATATATT
7852646 TAAGTGTATAAATATATT
1 TAAGTGTATAAATATATT
7852664 GACTTGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (18 bp):
TAAGTGTATAAATATATT
Found at i:7854161 original size:15 final size:15
Alignment explanation
Indices: 7854134--7854167 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
7854124 GTAAAACTGG
7854134 TGGTATAGATTTTGT
1 TGGTATAGATTTTGT
7854149 TGGTA-AGAGTTTTGT
1 TGGTATAGA-TTTTGT
7854164 TGGT
1 TGGT
7854168 TTTGATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (15 bp):
TGGTATAGATTTTGT
Found at i:7854199 original size:18 final size:19
Alignment explanation
Indices: 7854162--7854199 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
7854152 TAAGAGTTTT
*
7854162 GTTGGTTTTGATTTTATGG
1 GTTGGTTTAGATTTTATGG
*
7854181 GTTGGTTTAG-TTTTGTGG
1 GTTGGTTTAGATTTTATGG
7854199 G
1 G
7854200 GAATATTGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.08, C:0.00, G:0.37, T:0.55
Consensus pattern (19 bp):
GTTGGTTTAGATTTTATGG
Found at i:7855611 original size:17 final size:17
Alignment explanation
Indices: 7855576--7855609 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
7855566 TATATTTTAG
*
7855576 ATTAATTTTTATTTAAA
1 ATTAATTTTTATTAAAA
7855593 ATTAATTTTT-TTAAAA
1 ATTAATTTTTATTAAAA
7855609 A
1 A
7855610 ATATAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTAATTTTTATTAAAA
Found at i:7861642 original size:10 final size:9
Alignment explanation
Indices: 7861589--7861649 Score: 65
Period size: 9 Copynumber: 7.0 Consensus size: 9
7861579 ATATCAAAAA
7861589 TATAATTTT
1 TATAATTTT
*
7861598 AATAA-TTT
1 TATAATTTT
7861606 TA-AATTTT
1 TATAATTTT
* *
7861614 TAAAAAGTTT
1 T-ATAATTTT
7861624 TATAATTTT
1 TATAATTTT
7861633 TATAATTTT
1 TATAATTTT
7861642 T-TAATTTT
1 TATAATTTT
7861650 GAAAAATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
7 2 0.05
8 15 0.34
9 21 0.48
10 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (9 bp):
TATAATTTT
Done.