Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, whole genome shotgun sequence
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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 47 of 138
Found at i:10118177 original size:18 final size:17
Alignment explanation
Indices: 10118156--10118205 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
10118146 GCAAAATCCA
10118156 AAAATTCACAAAAATTTC
1 AAAATT-ACAAAAATTTC
*
10118174 AAAATTTACAAAGATTTC
1 AAAA-TTACAAAAATTTC
*
10118192 AAGATTACAAAAAT
1 AAAATTACAAAAAT
10118206 CTAAAGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.32
18 17 0.61
19 2 0.07
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.28
Consensus pattern (17 bp):
AAAATTACAAAAATTTC
Found at i:10118502 original size:45 final size:44
Alignment explanation
Indices: 10118453--10118648 Score: 147
Period size: 45 Copynumber: 4.5 Consensus size: 44
10118443 CATCCAAGGT
10118453 TTCAAAGATTCACATTTGAAATATTTTAGAAATTCACATATAAAA
1 TTCAAAGATTCACATTTGAAA-ATTTTAGAAATTCACATATAAAA
* ** * *
10118498 TTCAAAGGATTTCAC--TTGAAAGTTTTAGGGATTCATATCTAAAA
1 TTCAAA-GA-TTCACATTTGAAAATTTTAGAAATTCACATATAAAA
** * *
10118542 TTCAAAGATTCTTATTTGAAAAATTTTA-AGGA-TC-C--A-AAAT
1 TTCAAAGATTCACATTTG-AAAATTTTAGA-AATTCACATATAAAA
* * **
10118582 TTCAAAAATTCATATTTGAAAATTTTTAGAAATTCACATCGAAAA
1 TTCAAAGATTCACATTTGAAAA-TTTTAGAAATTCACATATAAAA
* *
10118627 TTCAAATATTCTCATTTGAAAA
1 TTCAAAGATTCACATTTGAAAA
10118649 GTTCAAAAAT
Statistics
Matches: 118, Mismatches: 20, Indels: 26
0.72 0.12 0.16
Matches are distributed among these distances:
39 4 0.03
40 25 0.21
41 3 0.03
42 4 0.03
43 2 0.02
44 29 0.25
45 44 0.37
46 2 0.02
47 5 0.04
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (44 bp):
TTCAAAGATTCACATTTGAAAATTTTAGAAATTCACATATAAAA
Found at i:10118654 original size:23 final size:22
Alignment explanation
Indices: 10118577--10118666 Score: 76
Period size: 23 Copynumber: 4.0 Consensus size: 22
10118567 TTAAGGATCC
10118577 AAAATTTCAAAAATTCAT-ATTTG
1 AAAA-TTCAAAAATTC-TCATTTG
* * * *
10118600 AAAATTTTTAGAAATTCACA-TCG
1 AAAA--TTCAAAAATTCTCATTTG
*
10118623 AAAATTCAAATATTCTCATTTG
1 AAAATTCAAAAATTCTCATTTG
10118645 AAAAGTTCAAAAATTCTCATTT
1 AAAA-TTCAAAAATTCTCATTT
10118667 TAAACTTTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
21 10 0.19
22 6 0.11
23 26 0.49
24 11 0.21
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (22 bp):
AAAATTCAAAAATTCTCATTTG
Found at i:10118741 original size:66 final size:66
Alignment explanation
Indices: 10118582--10118780 Score: 190
Period size: 66 Copynumber: 3.0 Consensus size: 66
10118572 GATCCAAAAT
* * * * *
10118582 TTCAAAAATTCAT-ATTTGAAAATTTTTAGA-AATTCACATCGAAAATTCAAATATTCTCATTTG
1 TTCAAAAATTC-TCATTTG-AAACTTTTAGAGAA-TCATATCCAAAATTCAAAGATTCACATTTG
10118645 AAAAG
63 -AAAG
* *
10118650 TTCAAAAATTCTCATTTTAAACTTTTAGATAATC-TCATCCAAAATT-ATAAGATTCACATTTGA
1 TTCAAAAATTCTCATTTGAAACTTTTAGAGAATCAT-ATCCAAAATTCA-AAGATTCACATTTGA
10118713 AAG
64 AAG
* ** * * **
10118716 TTCAAAGATTCTTGTTTGGAACTTTTAGAGATTCATATCCAAAATTCAAAGATTTGCATTTGAAA
1 TTCAAAAATTCTCATTTGAAACTTTTAGAGAATCATATCCAAAATTCAAAGATTCACATTTGAAA
10118781 AGTTTACATT
Statistics
Matches: 110, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
66 57 0.52
67 36 0.33
68 17 0.15
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (66 bp):
TTCAAAAATTCTCATTTGAAACTTTTAGAGAATCATATCCAAAATTCAAAGATTCACATTTGAAA
G
Found at i:10119573 original size:15 final size:15
Alignment explanation
Indices: 10119553--10119591 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
10119543 GCCTCATCAA
10119553 TTTTCTTTCTTTTTC
1 TTTTCTTTCTTTTTC
* *
10119568 TTTTCTTTTTTTTTT
1 TTTTCTTTCTTTTTC
10119583 TTTGTCTTT
1 TTT-TCTTT
10119592 TGTCATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:10119577 original size:21 final size:21
Alignment explanation
Indices: 10119553--10119592 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
10119543 GCCTCATCAA
*
10119553 TTTTCTTTCTTTT-TCTTTTC
1 TTTTTTTTCTTTTGTCTTTTC
*
10119573 TTTTTTTTTTTTTGTCTTTT
1 TTTTTTTTCTTTTGTCTTTT
10119593 GTCATATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (21 bp):
TTTTTTTTCTTTTGTCTTTTC
Found at i:10124235 original size:220 final size:216
Alignment explanation
Indices: 10123822--10124474 Score: 805
Period size: 220 Copynumber: 3.0 Consensus size: 216
10123812 TGTGTTGTGC
* * * * * *
10123822 TAATGTCAATGAACAGATTCTTCCATTTATCCTTTTTTTATTTGAGTGCTTAAACTTCCTTTTCA
1 TAATGTCAATGAATAGATTCTTCCATTCATCCATTTTTTGTTTGAGTGCTTGAACTTCCTTTTTA
* * *
10123887 AGGCTTTTGTTTGCAAGCTTCAATTCTTTAGACTTCATTTTCAAGCAAATATAGGATTTTACTAG
66 AGCCTTTTGTTTGCAAG-TTCAATTC-TTAGACTTCATTTTCAAGC-TA-ATAGGA-TTTGCTAG
* * *
10123952 GCTTTCCATAGATGTATTAAGATTCTTTTTGTTAAAATTGTTTTGTGGCAATCACTTCTTGTTAT
126 GCTTTCCATTGATGTATTAAGATT-TTTTTGTTAAAATTATTTTGTGGCAATCACTCCTTGTTAT
* *
10124017 AAATCTGATGATGTAAATGTATTATGT
190 AAATTTGATGATGTAAATGCATTATGT
* * *
10124044 TAATATCAATGAATAGCTTCTTCCATTCATCCATTTTTTGTTTGAGTGCTTGTACTTCCTTTTTA
1 TAATGTCAATGAATAGATTCTTCCATTCATCCATTTTTTGTTTGAGTGCTTGAACTTCCTTTTTA
* * *
10124109 AGCCTTTTGTTTGCAAGTTCCAATTCTCAAACTTC-CTTTCAAGCTAATAGGGGATTTCGCTAGG
66 AGCCTTTTGTTTGCAAGTT-CAATTCTTAGACTTCATTTTCAAGCTAATA--GGATTT-GCTAGG
** *
10124173 CTTTTTATTGATGTATTAAGATTGTTTTTGTTAAAATTATTTTGTAGCAATCACTCCTTGTTATA
127 CTTTCCATTGATGTATTAAGATT-TTTTTGTTAAAATTATTTTGTGGCAATCACTCCTTGTTATA
*
10124238 AATTTGATGATGTTAATGCATTATGT
191 AATTTGATGATGTAAATGCATTATGT
* * * * * *
10124264 TAATGTCAATGAATAAATTTTTCCATTCATCCCTTTTTTGTTTGAGTGTTTGAACTTTCTTTCTA
1 TAATGTCAATGAATAGATTCTTCCATTCATCCATTTTTTGTTTGAGTGCTTGAACTTCCTTTTTA
* * * *
10124329 AGCCTTTTGTTTGCAACCTTCAATTACTTAGACTTCTTTTTCAGGCTAATATG--TTG---GGCT
66 AGCCTTTTGTTTGCAA-GTTCAATT-CTTAGACTTCATTTTCAAGCTAATAGGATTTGCTAGGCT
* * *
10124389 TTCCATTGATGTATTAAGATTTTTTTGGTTAAAATTATTTTATGGCAATCAATCTTTGTTATAAA
129 TTCCATTGATGTATTAAGATTTTTTT-GTTAAAATTATTTTGTGGCAATCACTCCTTGTTATAAA
10124454 TTTGATGATGTAAATGCATTA
193 TTTGATGATGTAAATGCATTA
10124475 AAACATAGTA
Statistics
Matches: 376, Mismatches: 47, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
213 5 0.01
214 77 0.20
217 1 0.00
218 5 0.01
219 4 0.01
220 175 0.47
221 19 0.05
222 90 0.24
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (216 bp):
TAATGTCAATGAATAGATTCTTCCATTCATCCATTTTTTGTTTGAGTGCTTGAACTTCCTTTTTA
AGCCTTTTGTTTGCAAGTTCAATTCTTAGACTTCATTTTCAAGCTAATAGGATTTGCTAGGCTTT
CCATTGATGTATTAAGATTTTTTTGTTAAAATTATTTTGTGGCAATCACTCCTTGTTATAAATTT
GATGATGTAAATGCATTATGT
Found at i:10125659 original size:17 final size:19
Alignment explanation
Indices: 10125618--10125660 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
10125608 GCAACCATGC
10125618 AATCATGCAAATATCATAA
1 AATCATGCAAATATCATAA
*
10125637 ATATCATGCTAATAT-A-AA
1 A-ATCATGCAAATATCATAA
10125655 AATCAT
1 AATCAT
10125661 ACCATAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 3 0.14
19 2 0.09
20 12 0.55
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (19 bp):
AATCATGCAAATATCATAA
Found at i:10125852 original size:41 final size:41
Alignment explanation
Indices: 10125771--10125859 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
10125761 ATGAAAAAAT
10125771 ATAT-ATAATAAATCATGCAATTAAATTAAATCTATACAAA
1 ATATCATAATAAATCATGCAATTAAATTAAATCTATACAAA
*
10125811 ATATCATAAGTAAATCATGCAA-TAAATTAAAT-TCATGCAAA
1 ATATCATAA-TAAATCATGCAATTAAATTAAATCT-ATACAAA
10125852 ATATCATA
1 ATATCATA
10125860 CAAATATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
40 5 0.11
41 28 0.62
42 12 0.27
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (41 bp):
ATATCATAATAAATCATGCAATTAAATTAAATCTATACAAA
Found at i:10126194 original size:6 final size:6
Alignment explanation
Indices: 10126185--10126259 Score: 64
Period size: 6 Copynumber: 12.2 Consensus size: 6
10126175 ACTAAAAAAC
* *
10126185 AATAAA AATAAA AATAAA AATAAA AATGAAGCTA AA-AAA AATTAA ACT-AA
1 AATAAA AATAAA AATAAA AATAAA AAT-AA---A AATAAA AATAAA AATAAA
* *
10126235 AATAAA AATACA TATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
10126260 TTGTGGGCTT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
5 7 0.12
6 42 0.75
7 2 0.04
8 2 0.04
10 3 0.05
ACGTcount: A:0.75, C:0.04, G:0.03, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:10128507 original size:14 final size:14
Alignment explanation
Indices: 10128489--10128521 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10128479 TTTATATATA
10128489 TTAAAT-AATATTT
1 TTAAATAAATATTT
10128502 TGTAAATAAATATTT
1 T-TAAATAAATATTT
10128517 TTAAA
1 TTAAA
10128522 AAACTTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 9 0.50
15 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
TTAAATAAATATTT
Found at i:10139226 original size:20 final size:20
Alignment explanation
Indices: 10139188--10139230 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
10139178 TTTTCATTCA
10139188 TCAAATCATCAAATTTCTTTT
1 TCAAATCA-CAAATTTCTTTT
10139209 TCAAATCA-AAATTTTCTTTT
1 TCAAATCACAAA-TTTCTTTT
10139229 TC
1 TC
10139231 TAAGAATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 10 0.48
21 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TCAAATCACAAATTTCTTTT
Found at i:10143059 original size:21 final size:19
Alignment explanation
Indices: 10143035--10143077 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
10143025 AGATAATATA
10143035 AAATAAGATGAAAATACAATG
1 AAATAAGATG-AAATACAA-G
**
10143056 AAATGTGATGAAATACAAG
1 AAATAAGATGAAATACAAG
10143075 AAA
1 AAA
10143078 GAAACTAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 8 0.40
21 8 0.40
ACGTcount: A:0.60, C:0.05, G:0.16, T:0.19
Consensus pattern (19 bp):
AAATAAGATGAAATACAAG
Found at i:10144244 original size:2 final size:2
Alignment explanation
Indices: 10144237--10144264 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10144227 ATTAAAATTA
10144237 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10144265 TGGATTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10153315 original size:14 final size:14
Alignment explanation
Indices: 10153296--10153329 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
10153286 TCGTTCAAAC
10153296 CAAACAAACCAGAA
1 CAAACAAACCAGAA
10153310 CAAACAAACCAGAA
1 CAAACAAACCAGAA
*
10153324 CCAACA
1 CAAACA
10153330 TTCCACGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.62, C:0.32, G:0.06, T:0.00
Consensus pattern (14 bp):
CAAACAAACCAGAA
Found at i:10154567 original size:11 final size:11
Alignment explanation
Indices: 10154551--10154591 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
10154541 CAATGATATG
10154551 ATATAAAAATA
1 ATATAAAAATA
*
10154562 ATATAATTAAAAA
1 ATATAA--AAATA
10154575 ATATAAAAATA
1 ATATAAAAATA
10154586 ATATAA
1 ATATAA
10154592 TTTAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:10154578 original size:24 final size:24
Alignment explanation
Indices: 10154551--10154618 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
10154541 CAATGATATG
10154551 ATATAAAAATAATATAATTAAAAA
1 ATATAAAAATAATATAATTAAAAA
*
10154575 ATATAAAAATAATATAATT-TAAA
1 ATATAAAAATAATATAATTAAAAA
* * *
10154598 TTTTAAAAA-AATATAAATAAA
1 ATATAAAAATAATATAATTAAA
10154619 TTTAATAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
22 8 0.21
23 11 0.29
24 19 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
ATATAAAAATAATATAATTAAAAA
Found at i:10154620 original size:21 final size:20
Alignment explanation
Indices: 10154569--10154636 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
10154559 ATAATATAAT
*
10154569 TAAA-AAATATAAAAATAATA
1 TAAATAAATTTAAAAA-AATA
*
10154589 TAATTTAAATTTTAAAAAAATA
1 TAA-ATAAA-TTTAAAAAAATA
*
10154611 TAAATAAATTTAATAAAATCA
1 TAAATAAATTTAAAAAAAT-A
10154632 TAAAT
1 TAAAT
10154637 TTTTATTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 13 0.32
21 10 0.25
22 10 0.25
23 7 0.17
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAATAAATTTAAAAAAATA
Found at i:10154708 original size:16 final size:17
Alignment explanation
Indices: 10154687--10154727 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
10154677 TTATTTTTGT
10154687 ATAAAATATTATATA-A
1 ATAAAATATTATATATA
*
10154703 ATAAAATATTTTATATA
1 ATAAAATATTATATATA
*
10154720 ATATAATA
1 ATAAAATA
10154728 ATACGAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAAAATATTATATATA
Found at i:10154959 original size:24 final size:23
Alignment explanation
Indices: 10154904--10154959 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
10154894 AATAAAAAAT
*
10154904 AAATAAATTTTATCATTTTAATT
1 AAATAAATTTTATCATTTTAATC
*
10154927 AAATAAAATTTTAT-ATTTATTATAC
1 AAAT-AAATTTTATCATTT-TAAT-C
10154952 AAATAAAT
1 AAATAAAT
10154960 CTTCAACCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 8 0.29
24 16 0.57
25 4 0.14
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATAAATTTTATCATTTTAATC
Found at i:10155016 original size:30 final size:30
Alignment explanation
Indices: 10154935--10155035 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
10154925 TTAAATAAAA
* * *
10154935 TTTTATATTTATTATACAAATAAATCTTCAAC
1 TTTTA-ATTTA-TATTCAAATAAAACTTTAAC
* *
10154967 CTTTAATTTATGCTT-AAATAAAACTTTAAC
1 TTTTAATTTAT-ATTCAAATAAAACTTTAAC
* * *
10154997 TTTTCATTTATATTCAAATAAACCTTTAAT
1 TTTTAATTTATATTCAAATAAAACTTTAAC
10155027 TTTTAATTT
1 TTTTAATTT
10155036 TTAATTTTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 2 0.04
30 44 0.79
31 6 0.11
32 4 0.07
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.50
Consensus pattern (30 bp):
TTTTAATTTATATTCAAATAAAACTTTAAC
Found at i:10155033 original size:7 final size:7
Alignment explanation
Indices: 10155021--10155048 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
10155011 CAAATAAACC
10155021 TTTAATT
1 TTTAATT
10155028 TTTAATT
1 TTTAATT
10155035 TTTAATT
1 TTTAATT
10155042 TTTAATT
1 TTTAATT
10155049 AAATATCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTAATT
Found at i:10168551 original size:7 final size:7
Alignment explanation
Indices: 10168539--10168674 Score: 76
Period size: 7 Copynumber: 20.6 Consensus size: 7
10168529 ATAGAGGTGA
10168539 TTTAGGG
1 TTTAGGG
10168546 TTTA-GG
1 TTTAGGG
10168552 -TTAGGG
1 TTTAGGG
*
10168558 TTTATGGT
1 TTTA-GGG
10168566 TTTAGGG
1 TTTAGGG
*
10168573 TTT-GGA
1 TTTAGGG
*
10168579 ATTAGGG
1 TTTAGGG
*
10168586 TTT-TGG
1 TTTAGGG
10168592 TTTAGGG
1 TTTAGGG
* **
10168599 TCTAATG
1 TTTAGGG
10168606 -TTAGGG
1 TTTAGGG
10168612 -TTAGGG
1 TTTAGGG
10168618 -TTA-GG
1 TTTAGGG
*
10168623 TTTTGGG
1 TTTAGGG
10168630 TTTAGGG
1 TTTAGGG
*
10168637 TTTA-TG
1 TTTAGGG
*
10168643 ATTAGGG
1 TTTAGGG
*
10168650 TTTGGGG
1 TTTAGGG
*
10168657 TTT-GATG
1 TTTAG-GG
10168664 TTTAGGG
1 TTTAGGG
10168671 TTTA
1 TTTA
10168675 TGATTAAGGT
Statistics
Matches: 96, Mismatches: 23, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
5 5 0.05
6 32 0.33
7 52 0.54
8 7 0.07
ACGTcount: A:0.15, C:0.01, G:0.38, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:10168596 original size:13 final size:14
Alignment explanation
Indices: 10168537--10168599 Score: 62
Period size: 13 Copynumber: 4.7 Consensus size: 14
10168527 ATATAGAGGT
*
10168537 GATTTAGGGTTTAG
1 GATTTAGGGTTTTG
10168551 G--TTAGGGTTTATG
1 GATTTAGGGTTT-TG
*
10168564 GTTTTAGGG-TTTG
1 GATTTAGGGTTTTG
*
10168577 GAATTAGGGTTTTG
1 GATTTAGGGTTTTG
10168591 G-TTTAGGGT
1 GATTTAGGGT
10168600 CTAATGTTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
12 9 0.22
13 18 0.44
14 8 0.20
15 6 0.15
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.46
Consensus pattern (14 bp):
GATTTAGGGTTTTG
Found at i:10168647 original size:13 final size:13
Alignment explanation
Indices: 10168539--10168652 Score: 58
Period size: 13 Copynumber: 8.8 Consensus size: 13
10168529 ATAGAGGTGA
10168539 TTTAGGGTTTA-G
1 TTTAGGGTTTATG
*
10168551 GTTAGGGTTTATGG
1 TTTAGGGTTTAT-G
*
10168565 TTTTAGGGTTT-GG
1 -TTTAGGGTTTATG
*
10168578 AATTAGGGTTT-TGG
1 -TTTAGGGTTTAT-G
*
10168592 TTTAGGGTCTAATG
1 TTTAGGGT-TTATG
*
10168606 -TTAGGG-TTAGG
1 TTTAGGGTTTATG
* * **
10168617 GTTAGGTTTTGGG
1 TTTAGGGTTTATG
10168630 TTTAGGGTTTATG
1 TTTAGGGTTTATG
*
10168643 ATTAGGGTTT
1 TTTAGGGTTT
10168653 GGGGTTTGAT
Statistics
Matches: 77, Mismatches: 17, Indels: 15
0.71 0.16 0.14
Matches are distributed among these distances:
11 3 0.04
12 15 0.19
13 45 0.58
14 4 0.05
15 10 0.13
ACGTcount: A:0.16, C:0.01, G:0.37, T:0.46
Consensus pattern (13 bp):
TTTAGGGTTTATG
Found at i:10168667 original size:34 final size:34
Alignment explanation
Indices: 10168629--10168696 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
10168619 TAGGTTTTGG
*
10168629 GTTTAGGGTTTATGATTAGGGTTTGGGGTTTGAT
1 GTTTAGGGTTTATGATTAAGGTTTGGGGTTTGAT
10168663 GTTTAGGGTTTATGATTAAGGTTTGGGGTTTGAT
1 GTTTAGGGTTTATGATTAAGGTTTGGGGTTTGAT
10168697 TTAAAGTTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.47
Consensus pattern (34 bp):
GTTTAGGGTTTATGATTAAGGTTTGGGGTTTGAT
Found at i:10168691 original size:20 final size:19
Alignment explanation
Indices: 10168628--10168693 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
10168618 TTAGGTTTTG
10168628 GGTTTAGGGTTTATGATTA
1 GGTTTAGGGTTTATGATTA
*
10168647 GGGTTT-GGGGTT-TGA-T-
1 -GGTTTAGGGTTTATGATTA
10168663 -GTTTAGGGTTTATGATTAA
1 GGTTTAGGGTTTATGATT-A
*
10168682 GGTTTGGGGTTT
1 GGTTTAGGGTTT
10168694 GATTTAAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
14 4 0.11
15 5 0.14
16 3 0.08
17 2 0.05
18 3 0.08
19 5 0.14
20 15 0.41
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.47
Consensus pattern (19 bp):
GGTTTAGGGTTTATGATTA
Found at i:10168750 original size:12 final size:13
Alignment explanation
Indices: 10168735--10168844 Score: 55
Period size: 13 Copynumber: 8.4 Consensus size: 13
10168725 CAGTTTTAAA
10168735 GTTT-GATTTAGG
1 GTTTAGATTTAGG
*
10168747 GTTTAGTTTTAGG
1 GTTTAGATTTAGG
* *
10168760 GTTCA-AGTTTAAG
1 GTTTAGA-TTTAGG
* *
10168773 GTTTAGGTTTTATG
1 GTTTA-GATTTAGG
* * *
10168787 GTTTGCGATTAAGT
1 GTTT-AGATTTAGG
* *
10168801 TTTTA-ATTTGGG
1 GTTTAGATTTAGG
*
10168813 GTTTGGGATTTAGG
1 GTTT-AGATTTAGG
*
10168827 GTTTTGATTTAGG
1 GTTTAGATTTAGG
10168840 GTTTA
1 GTTTA
10168845 AAAATTGGGG
Statistics
Matches: 69, Mismatches: 22, Indels: 13
0.66 0.21 0.12
Matches are distributed among these distances:
12 11 0.16
13 32 0.46
14 26 0.38
ACGTcount: A:0.18, C:0.02, G:0.30, T:0.50
Consensus pattern (13 bp):
GTTTAGATTTAGG
Found at i:10169967 original size:14 final size:15
Alignment explanation
Indices: 10169948--10169980 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
10169938 GCTTTTCAAA
*
10169948 TTTTTTTCTCT-TTT
1 TTTTTTTCACTATTT
10169962 TTTTTTTCACTATTT
1 TTTTTTTCACTATTT
10169977 TTTT
1 TTTT
10169981 CACACCACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTTCACTATTT
Found at i:10171269 original size:50 final size:50
Alignment explanation
Indices: 10171143--10171269 Score: 175
Period size: 50 Copynumber: 2.5 Consensus size: 50
10171133 TGAAAAACTT
* * **
10171143 TAAACAAAGGCTTTGAAACTTTAAAAATGTAAACTTTTGAAAAACTCCTT
1 TAAACAAAGGCTATGAAACTTTAAAATTGTAAACTTTTGAAAAACTCCAC
* * *
10171193 TAAATACAA-GATATGAAACTTTAAAATTGTAAACTTTTGAAAAATTCCAC
1 TAAACA-AAGGCTATGAAACTTTAAAATTGTAAACTTTTGAAAAACTCCAC
10171243 TAAACAAAGGCTATGAAACTTTAAAAT
1 TAAACAAAGGCTATGAAACTTTAAAAT
10171270 CCCAATTTGG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
49 2 0.03
50 62 0.94
51 2 0.03
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (50 bp):
TAAACAAAGGCTATGAAACTTTAAAATTGTAAACTTTTGAAAAACTCCAC
Found at i:10171392 original size:9 final size:9
Alignment explanation
Indices: 10171355--10171385 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
10171345 GAAAGGTTAG
10171355 AAAACTTTA
1 AAAACTTTA
10171364 AAAACTTTA
1 AAAACTTTA
10171373 AAAACTTTA
1 AAAACTTTA
10171382 AAAA
1 AAAA
10171386 TCTTAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAACTTTA
Found at i:10171461 original size:49 final size:49
Alignment explanation
Indices: 10171374--10171639 Score: 295
Period size: 49 Copynumber: 5.4 Consensus size: 49
10171364 AAAACTTTAA
* * * ***
10171374 AAACTTTAAAAATCTTAAATTCTGAAAAGGCTTATATAAAGATAATTTAAG
1 AAACTTTAAAAATC-T-CATTTTAAAAAGGCTTATATAAAGATAGGCTAAG
*
10171425 AAACTTTAAAAATCTCATTTTAAAAAGGCTTATATAAAGTTAGGCTAAG
1 AAACTTTAAAAATCTCATTTTAAAAAGGCTTATATAAAGATAGGCTAAG
* * * *
10171474 AAACTTTAAAAATCTCATTTT-GAAAGGCTTCTATAAAGATGGGCTAGG
1 AAACTTTAAAAATCTCATTTTAAAAAGGCTTATATAAAGATAGGCTAAG
* * * * * *
10171522 AAACTTTCAAAATCTCAGTTGAAAAAAGCTCATATAAAAATAGGCTAAG
1 AAACTTTAAAAATCTCATTTTAAAAAGGCTTATATAAAGATAGGCTAAG
* * *
10171571 AAGCTTTAAAAATCTCATTTTGAAATA-G-TTCCTATAAAGATAGGCTAAG
1 AAACTTTAAAAATCTCATTTT-AAAAAGGCTT-ATATAAAGATAGGCTAAG
10171620 AAACTTTAAAAATCTCATTT
1 AAACTTTAAAAATCTCATTT
10171640 CGGAAAAGGG
Statistics
Matches: 181, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
48 41 0.23
49 121 0.67
50 5 0.03
51 14 0.08
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (49 bp):
AAACTTTAAAAATCTCATTTTAAAAAGGCTTATATAAAGATAGGCTAAG
Found at i:10171511 original size:97 final size:97
Alignment explanation
Indices: 10171374--10171682 Score: 334
Period size: 97 Copynumber: 3.1 Consensus size: 97
10171364 AAAACTTTAA
* * * ***
10171374 AAACTTTAAAAATCTTAAATTCTGAAAAGGCTTATATAAAGATAATTTAAGAAACTTTAAAAATC
1 AAACTTTAAAAATC-T-CATTTTG-AAAGGCTTCTATAAAGATAGGCTAAGAAACTTTAAAAATC
* * * **
10171439 TCATTTTAAAAAGGCTTATATAAAGTTAGGCTAAG
63 TCATTTGAAAAAAGCTCATATAAAAATAGGCTAAG
* * *
10171474 AAACTTTAAAAATCTCATTTTGAAAGGCTTCTATAAAGATGGGCTAGGAAACTTTCAAAATCTCA
1 AAACTTTAAAAATCTCATTTTGAAAGGCTTCTATAAAGATAGGCTAAGAAACTTTAAAAATCTCA
*
10171539 GTTGAAAAAAGCTCATATAAAAATAGGCTAAG
66 TTTGAAAAAAGCTCATATAAAAATAGGCTAAG
* *
10171571 AAGCTTTAAAAATCTCATTTTGAAATAG-TTCCTATAAAGATAGGCTAAGAAACTTTAAAAATCT
1 AAACTTTAAAAATCTCATTTTGAAA-GGCTT-CTATAAAGATAGGCTAAGAAACTTTAAAAATCT
** * *
10171635 CATTTCGGAAAAGGGTTCCTATAAAAATAGGCTAA-
64 CATTT--GAAAAAAGCTCATATAAAAATAGGCTAAG
*
10171670 AGAACTTAAAAAA
1 A-AACTTTAAAAA
10171683 AAATCTCCAT
Statistics
Matches: 177, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
97 88 0.50
98 40 0.23
99 2 0.01
100 47 0.27
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (97 bp):
AAACTTTAAAAATCTCATTTTGAAAGGCTTCTATAAAGATAGGCTAAGAAACTTTAAAAATCTCA
TTTGAAAAAAGCTCATATAAAAATAGGCTAAG
Found at i:10172346 original size:14 final size:14
Alignment explanation
Indices: 10172327--10172367 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
10172317 ATTTTCATTT
10172327 ATTTTTCCATTTTC
1 ATTTTTCCATTTTC
*
10172341 ATTTTTTCATTTTC
1 ATTTTTCCATTTTC
*
10172355 CTTTTTCCATTTT
1 ATTTTTCCATTTT
10172368 TTTGGTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTTCCATTTTC
Found at i:10172388 original size:21 final size:20
Alignment explanation
Indices: 10172364--10172421 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
10172354 CCTTTTTCCA
*
10172364 TTTTTTTGGTTTTTTTGTGTC
1 TTTTTTT-GTTTTTTTGTGCC
*
10172385 TTTTTGCTT-TTTTTTTTTGCC
1 TTTTT--TTGTTTTTTTGTGCC
10172406 TTTTTTTTGTTTTTTT
1 -TTTTTTTGTTTTTTT
10172422 AAAAAACAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
20 2 0.06
21 22 0.71
22 5 0.16
23 2 0.06
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.81
Consensus pattern (20 bp):
TTTTTTTGTTTTTTTGTGCC
Found at i:10172401 original size:13 final size:14
Alignment explanation
Indices: 10172385--10172413 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10172375 TTTTTGTGTC
10172385 TTTTTG-CTTTTTT
1 TTTTTGCCTTTTTT
10172398 TTTTTGCCTTTTTT
1 TTTTTGCCTTTTTT
10172412 TT
1 TT
10172414 GTTTTTTTAA
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:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (14 bp):
TTTTTGCCTTTTTT
Found at i:10173174 original size:106 final size:108
Alignment explanation
Indices: 10172983--10173177 Score: 261
Period size: 106 Copynumber: 1.8 Consensus size: 108
10172973 CAAATATCAT
* * *
10172983 CACCAAGAGAGTTTTAATGAAAGGTTGAATTTCACCACTAAGAAAAAGTTGTAAGAAAAGGTCAG
1 CACCAAGAGAGTTTTAATGAAAAGTAGAATTTCACCACTAAGAAAAAGTTGTAAGAAAAGGTCAA
*
10173048 ATTTTGCCATCGAGGAAATTTTAACAAATAGACTAGATTTTAA
66 ATTTTGCCATCGAGAAAATTTTAACAAATAGACTAGATTTTAA
* * * * *
10173091 CACCGAGAGAGTTTTAATGAAAAGTA-AGATTTCACCA-T-TGAGAGAGTTTTAAGAAAAGGTCA
1 CACCAAGAGAGTTTTAATGAAAAGTAGA-ATTTCACCACTAAGAAAAAGTTGTAAGAAAAGGTCA
* *
10173153 AATTTTGTCATTGAGAAAATTTTAA
65 AATTTTGCCATCGAGAAAATTTTAA
10173178 TGAAATTCAA
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
106 41 0.55
107 2 0.03
108 32 0.43
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (108 bp):
CACCAAGAGAGTTTTAATGAAAAGTAGAATTTCACCACTAAGAAAAAGTTGTAAGAAAAGGTCAA
ATTTTGCCATCGAGAAAATTTTAACAAATAGACTAGATTTTAA
Found at i:10173778 original size:22 final size:22
Alignment explanation
Indices: 10173752--10173798 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
10173742 TCTCAATTTC
10173752 TCTTTCTTTTGTTTTGTTT-TTT
1 TCTTT-TTTTGTTTTGTTTGTTT
* *
10173774 TCTTTTTTTTTTTTTTTTGTTT
1 TCTTTTTTTGTTTTGTTTGTTT
10173796 TCT
1 TCT
10173799 CCATCTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (22 bp):
TCTTTTTTTGTTTTGTTTGTTT
Found at i:10174710 original size:14 final size:14
Alignment explanation
Indices: 10174691--10174720 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10174681 CATTTTTAAT
*
10174691 ATACAACATGCAAC
1 ATACAAAATGCAAC
10174705 ATACAAAATGCAAC
1 ATACAAAATGCAAC
10174719 AT
1 AT
10174721 GTGTTTTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.23, G:0.07, T:0.17
Consensus pattern (14 bp):
ATACAAAATGCAAC
Found at i:10175861 original size:16 final size:17
Alignment explanation
Indices: 10175830--10175871 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
10175820 TCTTTAGTTC
*
10175830 TTGTTTTTCATTTCTTCA
1 TTGTTCTTC-TTTCTTCA
*
10175848 TT-TTCTTCTTTCTTTA
1 TTGTTCTTCTTTCTTCA
10175864 TTGTTCTT
1 TTGTTCTT
10175872 TCCTTTTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 9 0.43
17 10 0.48
18 2 0.10
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.71
Consensus pattern (17 bp):
TTGTTCTTCTTTCTTCA
Found at i:10179904 original size:19 final size:19
Alignment explanation
Indices: 10179882--10179959 Score: 106
Period size: 19 Copynumber: 4.2 Consensus size: 19
10179872 GTAAAAGTTA
10179882 AAACCCTAGGTGAAACCCT
1 AAACCCTAGGTGAAACCCT
* *
10179901 AAA-CCTAGGT-AAAACTT
1 AAACCCTAGGTGAAACCCT
*
10179918 AAAACCCTAGGTAAAACCCT
1 -AAACCCTAGGTGAAACCCT
10179938 AAACCCTAGGTGAAACCCT
1 AAACCCTAGGTGAAACCCT
10179957 AAA
1 AAA
10179960 TCTACCCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
17 5 0.10
18 10 0.20
19 31 0.61
20 5 0.10
ACGTcount: A:0.44, C:0.27, G:0.13, T:0.17
Consensus pattern (19 bp):
AAACCCTAGGTGAAACCCT
Found at i:10179914 original size:37 final size:37
Alignment explanation
Indices: 10179861--10179953 Score: 132
Period size: 37 Copynumber: 2.5 Consensus size: 37
10179851 TCATGCATTG
* * *
10179861 CTAAACCCATGGTAAAAGTTAAAACCCTAGGTGAAACC
1 CTAAACCTA-GGTAAAACTTAAAACCCTAGGTAAAACC
10179899 CTAAACCTAGGTAAAACTTAAAACCCTAGGTAAAACC
1 CTAAACCTAGGTAAAACTTAAAACCCTAGGTAAAACC
*
10179936 CTAAACCCTAGGTGAAAC
1 CTAAA-CCTAGGTAAAAC
10179954 CCTAAATCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
37 31 0.62
38 19 0.38
ACGTcount: A:0.43, C:0.25, G:0.14, T:0.18
Consensus pattern (37 bp):
CTAAACCTAGGTAAAACTTAAAACCCTAGGTAAAACC
Found at i:10183639 original size:16 final size:16
Alignment explanation
Indices: 10183618--10183655 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
10183608 GAAGTGACTC
10183618 GAAAAAA-AGAGGGAAA
1 GAAAAAAGAGAGGG-AA
*
10183634 GAAAAAAGAGAGTGAA
1 GAAAAAAGAGAGGGAA
10183650 GAAAAA
1 GAAAAA
10183656 TGAAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (16 bp):
GAAAAAAGAGAGGGAA
Found at i:10184514 original size:37 final size:36
Alignment explanation
Indices: 10184465--10184557 Score: 111
Period size: 37 Copynumber: 2.6 Consensus size: 36
10184455 AAAAATTTTG
*
10184465 TGAAAA-CAAAAAAAGAAAAA-CCTAAAAGCCTAAAA-
1 TGAAAAGCAAAAAAA-AAAAAGCCAAAAAGCC-AAAAT
*
10184500 TGAAAAAGCCAAAAAAAAAAAGTCCAAAAAGCCAAAAT
1 TG-AAAAGCAAAAAAAAAAAAG-CCAAAAAGCCAAAAT
10184538 TGAAAAGCAAAAAAAAAAAA
1 TGAAAAGCAAAAAAAAAAAA
10184558 AAAGAAGAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
35 2 0.04
36 9 0.18
37 28 0.56
38 11 0.22
ACGTcount: A:0.70, C:0.13, G:0.10, T:0.08
Consensus pattern (36 bp):
TGAAAAGCAAAAAAAAAAAAGCCAAAAAGCCAAAAT
Found at i:10184916 original size:14 final size:14
Alignment explanation
Indices: 10184894--10184981 Score: 54
Period size: 14 Copynumber: 5.9 Consensus size: 14
10184884 GAGAAAAGGA
10184894 AAAGAAAAAAAAAAG
1 AAAG-AAAAAAAAAG
*
10184909 AATGAAAAAAAAAAGG
1 AAAG-AAAAAAAAA-G
*
10184925 TGAAGAAAAAAAAAAGG
1 -AAAG-AAAAAAAAA-G
**
10184942 AAA-AAAATGAAAG
1 AAAGAAAAAAAAAG
*
10184955 AAAGAAAAAGAAA-
1 AAAGAAAAAAAAAG
10184968 AAAGAAGAAAAAAA
1 AAAGAA-AAAAAAA
10184982 ATCAATCAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
13 10 0.16
14 21 0.34
15 13 0.21
16 3 0.05
17 14 0.23
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:10184918 original size:17 final size:16
Alignment explanation
Indices: 10184892--10184982 Score: 71
Period size: 17 Copynumber: 5.6 Consensus size: 16
10184882 TAGAGAAAAG
10184892 GAAAAGAAAAAAAA-AA
1 GAAAA-AAAAAAAAGAA
**
10184908 GAATGAAAAAAAAAAGGT
1 GAA--AAAAAAAAAAGAA
10184926 GAAGAAAAAAAAAAG--
1 GAA-AAAAAAAAAAGAA
**
10184941 GAAAAAAATGAAAGAAA
1 GAAAAAAAAAAAAG-AA
*
10184958 GAAAAAGAAAAAAGAA
1 GAAAAAAAAAAAAGAA
10184974 GAAAAAAAA
1 GAAAAAAAA
10184983 TCAATCAATG
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
14 9 0.15
15 3 0.05
16 13 0.21
17 31 0.51
18 5 0.08
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (16 bp):
GAAAAAAAAAAAAGAA
Found at i:10187096 original size:40 final size:40
Alignment explanation
Indices: 10187045--10187223 Score: 132
Period size: 40 Copynumber: 4.4 Consensus size: 40
10187035 CCTCTGGGCC
* *
10187045 AAATCTTTTGAATGATTTTTAAGAACTCTAGGCAAAATTTT
1 AAAT-TTTTGAATGATTTTCAAGAACTCTAGGCAAAATCTT
* *
10187086 AGATTTTTGAATGATTTTCAA-AAC-CTTCGGACAAAATCTT
1 AAATTTTTGAATGATTTTCAAGAACTC-TAGG-CAAAATCTT
* * * * *
10187126 AAAATTTTGAATGATTCTCAAGACCTTTGGGCAAAATCTT
1 AAATTTTTGAATGATTTTCAAGAACTCTAGGCAAAATCTT
* * * * *
10187166 ATATTTTTAAAT-AATTTCAAAATACCTCT-GAGCAAAATTTT
1 AAATTTTTGAATGATTTTCAAGA-A-CTCTAG-GCAAAATCTT
* *
10187207 GAATTTTTAAATGATTT
1 AAATTTTTGAATGATTT
10187224 CCAAATACCT
Statistics
Matches: 108, Mismatches: 22, Indels: 15
0.74 0.15 0.10
Matches are distributed among these distances:
38 1 0.01
39 13 0.12
40 61 0.56
41 30 0.28
42 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (40 bp):
AAATTTTTGAATGATTTTCAAGAACTCTAGGCAAAATCTT
Found at i:10187253 original size:41 final size:41
Alignment explanation
Indices: 10187168--10187265 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 41
10187158 AAAATCTTAT
* ** * **
10187168 ATTTTTAAATAATTTCAAAATACCTCTGAGCAAAATTTTGA
1 ATTTTTAAATGATTTCAAAATACCTCCAAGCAAAATATCAA
*
10187209 ATTTTTAAATGATTTCCAAATACCTCCAAGCAAAATATCAA
1 ATTTTTAAATGATTTCAAAATACCTCCAAGCAAAATATCAA
*
10187250 ATTTCTAAATGATTTC
1 ATTTTTAAATGATTTC
10187266 TAATAAAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (41 bp):
ATTTTTAAATGATTTCAAAATACCTCCAAGCAAAATATCAA
Found at i:10187359 original size:39 final size:41
Alignment explanation
Indices: 10187316--10187393 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
10187306 AGGTAAAATC
* *
10187316 TTAAAATTTTCAAGGA-TT-TCAAGACCTCTGGGCAAAACT
1 TTAAAATTTTAAAGGATTTCTCAAGAACTCTGGGCAAAACT
* * *
10187355 TTAAATTTTTAAATGATTTCTCAAGAACTTTGGGCAAAA
1 TTAAAATTTTAAAGGATTTCTCAAGAACTCTGGGCAAAA
10187394 ATTCGAATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 13 0.41
40 2 0.06
41 17 0.53
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (41 bp):
TTAAAATTTTAAAGGATTTCTCAAGAACTCTGGGCAAAACT
Found at i:10187688 original size:46 final size:46
Alignment explanation
Indices: 10187599--10187697 Score: 112
Period size: 46 Copynumber: 2.2 Consensus size: 46
10187589 TATCTCCTAT
* * * *
10187599 TTTATTTTCTAAAGTTATTGAACTTTTTTTCAAAAGAGCTTTTAAA
1 TTTATTTTCAAAAGTTAGTGAACCTTTGTTCAAAAGAGCTTTTAAA
*
10187645 TTTATTTTCAAAAGTT-GTGCAACCTTTGTT-AAAAGAAGTTTTTAAA
1 TTTATTTTCAAAAGTTAGTG-AACCTTTGTTCAAAAG-AGCTTTTAAA
*
10187691 TTCATTT
1 TTTATTT
10187698 CCAAGTGGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 7 0.16
46 38 0.84
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.48
Consensus pattern (46 bp):
TTTATTTTCAAAAGTTAGTGAACCTTTGTTCAAAAGAGCTTTTAAA
Found at i:10187738 original size:6 final size:6
Alignment explanation
Indices: 10187727--10187776 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
10187717 AAATAGTCTA
10187727 AAAAAC AAAAAC AAAAAC AAATGAA- AAAAA- AAAAAC -AAAAC AAAAA-
1 AAAAAC AAAAAC AAAAAC AAA--AAC AAAAAC AAAAAC AAAAAC AAAAAC
10187773 AAAA
1 AAAA
10187777 CTCTCTCGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
5 16 0.40
6 19 0.47
7 3 0.08
8 2 0.05
ACGTcount: A:0.86, C:0.10, G:0.02, T:0.02
Consensus pattern (6 bp):
AAAAAC
Found at i:10187759 original size:23 final size:24
Alignment explanation
Indices: 10187726--10187777 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
10187716 TAAATAGTCT
10187726 AAAAAAC-AAAAACAAAAACAAATG
1 AAAAAACAAAAAAC-AAAACAAATG
10187750 AAAAAA-AAAAAACAAAACAAA--
1 AAAAAACAAAAAACAAAACAAATG
10187771 AAAAAAC
1 AAAAAAC
10187778 TCTCTCGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 6 0.23
23 8 0.31
24 12 0.46
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.02
Consensus pattern (24 bp):
AAAAAACAAAAAACAAAACAAATG
Found at i:10187760 original size:18 final size:18
Alignment explanation
Indices: 10187728--10187776 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
10187718 AATAGTCTAA
*
10187728 AAAAC-AAAAACAAAAAC
1 AAAACAAAAAAAAAAAAC
**
10187745 AAATGAAAAAAAAAAAAC
1 AAAACAAAAAAAAAAAAC
10187763 AAAACAAAAAAAAA
1 AAAACAAAAAAAAA
10187777 CTCTCTCGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.86, C:0.10, G:0.02, T:0.02
Consensus pattern (18 bp):
AAAACAAAAAAAAAAAAC
Found at i:10187760 original size:24 final size:23
Alignment explanation
Indices: 10187726--10187770 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
10187716 TAAATAGTCT
*
10187726 AAAAAACAAAAACAAAAACAAATG
1 AAAAAAAAAAAAC-AAAACAAATG
10187750 AAAAAAAAAAAACAAAACAAA
1 AAAAAAAAAAAACAAAACAAA
10187771 AAAAAACTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAAAACAAAACAAATG
Found at i:10190389 original size:18 final size:19
Alignment explanation
Indices: 10190335--10190405 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
10190325 AAAACCCTAA
*
10190335 AAGTGAAACCCTAAACCCC
1 AAGTGAAACCCTAAACCCT
* *
10190354 AAGTTAAACCCAAAACCCT
1 AAGTGAAACCCTAAACCCT
10190373 -AGCTGAAA-CCTAAACCCT
1 AAG-TGAAACCCTAAACCCT
10190391 AAGTGAAACCCTAAA
1 AAGTGAAACCCTAAA
10190406 TCTACCCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
18 16 0.36
19 28 0.64
ACGTcount: A:0.45, C:0.31, G:0.10, T:0.14
Consensus pattern (19 bp):
AAGTGAAACCCTAAACCCT
Found at i:10192297 original size:37 final size:37
Alignment explanation
Indices: 10192247--10192432 Score: 201
Period size: 37 Copynumber: 5.0 Consensus size: 37
10192237 TGACACTACC
* *
10192247 ATTAAAATGTGCATGAAATGGAATGCATATACTATGT
1 ATTAAGATGTGCATGAAATGGAATGCATATACTATCT
* * * * *
10192284 ATTAAGATATGCATGAAATAGAATGTAGATAATATCT
1 ATTAAGATGTGCATGAAATGGAATGCATATACTATCT
* * *
10192321 ATTAAGATGTGCATGAGATGGAATGCATGTACTATATT
1 ATTAAGATGTGCATGAAATGGAATGCATATACTAT-CT
* * * *
10192359 ATTAAGATGTGTATAAAATGGAATACACATACTATCT
1 ATTAAGATGTGCATGAAATGGAATGCATATACTATCT
* * * *
10192396 ATTAATATGTGCATGAAATGTAGTGCATGTACTATCT
1 ATTAAGATGTGCATGAAATGGAATGCATATACTATCT
10192433 TAGTTATTTT
Statistics
Matches: 118, Mismatches: 30, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
37 88 0.75
38 30 0.25
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (37 bp):
ATTAAGATGTGCATGAAATGGAATGCATATACTATCT
Found at i:10192408 original size:75 final size:74
Alignment explanation
Indices: 10192247--10192430 Score: 224
Period size: 75 Copynumber: 2.5 Consensus size: 74
10192237 TGACACTACC
* * ** *
10192247 ATTAAAATGTGCATGAAATGGAATGCATATACTATGTATTAAGATATGCATGAAATAGAATGTAG
1 ATTAAAATGTGCATGAAATGGAATGCATGTACTATGTATTAAGATATGCATAAAATAGAATACAC
10192312 ATAATATCT
66 ATAATATCT
* * * * * *
10192321 ATTAAGATGTGCATGAGATGGAATGCATGTACTATATTATTAAGATGTGTATAAAATGGAATACA
1 ATTAAAATGTGCATGAAATGGAATGCATGTACTAT-GTATTAAGATATGCATAAAATAGAATACA
*
10192386 CATACTATCT
65 CATAATATCT
* * *
10192396 ATTAATATGTGCATGAAATGTAGTGCATGTACTAT
1 ATTAAAATGTGCATGAAATGGAATGCATGTACTAT
10192431 CTTAGTTATT
Statistics
Matches: 93, Mismatches: 16, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
74 32 0.34
75 61 0.66
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (74 bp):
ATTAAAATGTGCATGAAATGGAATGCATGTACTATGTATTAAGATATGCATAAAATAGAATACAC
ATAATATCT
Found at i:10195149 original size:3 final size:3
Alignment explanation
Indices: 10195143--10195246 Score: 81
Period size: 3 Copynumber: 35.7 Consensus size: 3
10195133 CCATACTACT
* * *
10195143 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GT- ATT AGA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * ** *
10195189 ATA CT- ATA CT- ATA ATA CTA GTA ATA ATA ACG ATA ATA ATA ACAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
10195233 ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
10195247 TGAAATCAAC
Statistics
Matches: 78, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
2 5 0.06
3 71 0.91
4 2 0.03
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10195901 original size:55 final size:55
Alignment explanation
Indices: 10195772--10195912 Score: 142
Period size: 55 Copynumber: 2.6 Consensus size: 55
10195762 GACAGAGCCA
* *
10195772 AGATCAAATGATCATGATT-AACTACAAGTCTGAAAAGATGATCTAAACTAAGTCG
1 AGATCAAATGATCAAGATTGAACTACAAGTCTGAAAAGA-GATCTAAACCAAGTCG
*** * * *
10195827 AGATTGGATGATCAAGATTGAACTACAGGTTTGGAAAGCA-ATCTAAACCAAGTCG
1 AGATCAAATGATCAAGATTGAACTACAAGTCTGAAAAG-AGATCTAAACCAAGTCG
* * * *
10195882 AGATCAAATGACCAGGATTGAATTGCAAGTC
1 AGATCAAATGATCAAGATTGAACTACAAGTC
10195913 ACAATGATAA
Statistics
Matches: 67, Mismatches: 17, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
55 51 0.76
56 15 0.22
57 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (55 bp):
AGATCAAATGATCAAGATTGAACTACAAGTCTGAAAAGAGATCTAAACCAAGTCG
Found at i:10196714 original size:41 final size:42
Alignment explanation
Indices: 10196668--10196747 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
10196658 TTTTTGGGCT
* **
10196668 CAAGTTGCCCTTTTGGGTTTTCAA-ATAAACTTTTTTTTGTG
1 CAAGTTACCCTTTCAGGTTTTCAATATAAACTTTTTTTTGTG
* *
10196709 CAAGTTACCCTTTCAGGTTTTCAATTTATACTTTTTTTT
1 CAAGTTACCCTTTCAGGTTTTCAATATAAACTTTTTTTT
10196748 TTTGCTCAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 21 0.64
42 12 0.36
ACGTcount: A:0.20, C:0.16, G:0.12, T:0.51
Consensus pattern (42 bp):
CAAGTTACCCTTTCAGGTTTTCAATATAAACTTTTTTTTGTG
Found at i:10200028 original size:50 final size:50
Alignment explanation
Indices: 10199970--10200071 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
10199960 TGAGACTCAA
* *
10199970 TAAATTTATTCTCTTACTCAATTAATATCATTAAATCCACTGGCAAAGTG
1 TAAATTTATTCTCTTACTCAATTAATATCATTAAATCCACAGACAAAGTG
10200020 TAAATTTATTCTCTTACTCAATTAATATCATTAAATCCACAGACAAAGTG
1 TAAATTTATTCTCTTACTCAATTAATATCATTAAATCCACAGACAAAGTG
10200070 TA
1 TA
10200072 TTCTTTATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (50 bp):
TAAATTTATTCTCTTACTCAATTAATATCATTAAATCCACAGACAAAGTG
Found at i:10202669 original size:20 final size:20
Alignment explanation
Indices: 10202641--10202688 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 20
10202631 GCTTGAGCCT
*
10202641 CATTTTTTTTTCCTTTTAGG
1 CATTCTTTTTTCCTTTTAGG
10202661 CATTC-TTTTTCCTTTTAGG
1 CATTCTTTTTTCCTTTTAGG
10202680 CATTCTTTT
1 CATTCTTTT
10202689 AGTAGTAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.10, C:0.19, G:0.08, T:0.62
Consensus pattern (20 bp):
CATTCTTTTTTCCTTTTAGG
Found at i:10202671 original size:19 final size:19
Alignment explanation
Indices: 10202647--10202688 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
10202637 GCCTCATTTT
10202647 TTTTTCCTTTTAGGCATTC
1 TTTTTCCTTTTAGGCATTC
10202666 TTTTTCCTTTTAGGCATTC
1 TTTTTCCTTTTAGGCATTC
10202685 TTTT
1 TTTT
10202689 AGTAGTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.10, C:0.19, G:0.10, T:0.62
Consensus pattern (19 bp):
TTTTTCCTTTTAGGCATTC
Found at i:10207350 original size:13 final size:13
Alignment explanation
Indices: 10207332--10207426 Score: 60
Period size: 13 Copynumber: 7.6 Consensus size: 13
10207322 TAAGTTACTC
10207332 AATAAAAATAAAT
1 AATAAAAATAAAT
*
10207345 AATAAAAATCAAT
1 AATAAAAATAAAT
* *
10207358 AAAATAAAATACAT
1 AATA-AAAATAAAT
*
10207372 AA-AAAACTAAA-
1 AATAAAAATAAAT
*
10207383 AAT-AAAATCAA-
1 AATAAAAATAAAT
*
10207394 AATCAAAAT--AT
1 AATAAAAATAAAT
10207405 AA-AATAAATAAAT
1 AATAA-AAATAAAT
10207418 AAATAAAAA
1 -AATAAAAA
10207427 CATGTAATCG
Statistics
Matches: 64, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
10 2 0.03
11 17 0.27
12 11 0.17
13 18 0.28
14 14 0.22
15 2 0.03
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (13 bp):
AATAAAAATAAAT
Found at i:10207360 original size:23 final size:23
Alignment explanation
Indices: 10207330--10207420 Score: 75
Period size: 23 Copynumber: 3.9 Consensus size: 23
10207320 AATAAGTTAC
10207330 TCAATAAAAATAAATAATAAAAA
1 TCAATAAAAATAAATAATAAAAA
10207353 TCAAT-AAAATAAAATACATAAAAA
1 TCAATAAAAAT-AAATA-ATAAAAA
* *
10207377 --ACTAAAAAT-AA-AATCAAAA
1 TCAATAAAAATAAATAATAAAAA
10207396 TCAAAATATAAAATAAATAAATAAA
1 TC--AATA-AAAATAAAT-AATAAA
10207421 TAAAAACATG
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
19 6 0.11
20 1 0.02
21 2 0.04
22 7 0.13
23 18 0.34
24 12 0.23
25 2 0.04
27 5 0.09
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.21
Consensus pattern (23 bp):
TCAATAAAAATAAATAATAAAAA
Found at i:10207416 original size:42 final size:45
Alignment explanation
Indices: 10207332--10207426 Score: 126
Period size: 42 Copynumber: 2.2 Consensus size: 45
10207322 TAAGTTACTC
*
10207332 AATAAAAATAAATAATAAAAATCAATAAAATAAAATACATAAA-A
1 AATAAAAATAAATAATAAAAATCAATAAAATAAAATAAATAAATA
* *
10207376 AACTAAAAAT-AA-AATCAAAATCAA-AATATAAAATAAATAAATA
1 AA-TAAAAATAAATAATAAAAATCAATAAAATAAAATAAATAAATA
10207419 AATAAAAA
1 AATAAAAA
10207427 CATGTAATCG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
42 21 0.46
43 14 0.30
44 4 0.09
45 7 0.15
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (45 bp):
AATAAAAATAAATAATAAAAATCAATAAAATAAAATAAATAAATA
Found at i:10208226 original size:3 final size:3
Alignment explanation
Indices: 10208218--10208417 Score: 116
Period size: 3 Copynumber: 68.3 Consensus size: 3
10208208 AAAATAAAAC
* * * * *
10208218 AAT AAT AAT AAT AAT AAT AAT TAT AAC GAT AAT AA- CAT AAT -AT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
10208264 AAT AAT -AT AAT -GT AAT -AT AAT AAT AAT -GT AGCAT ACCAT ACT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A--AT A--AT AAT AAT
* * *
10208308 CAT AAT AAT AAT AAT AAT AAT ATAC AAT AAT AAT AGT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
10208353 -AT AAT -AT ACT -AT AAT ATT GAT AAT AAT AAC AAT AAT GAT AACA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
10208396 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
10208418 GAAATTGACT
Statistics
Matches: 149, Mismatches: 33, Indels: 30
0.70 0.16 0.14
Matches are distributed among these distances:
2 17 0.11
3 122 0.82
4 4 0.03
5 6 0.04
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:10208273 original size:5 final size:5
Alignment explanation
Indices: 10208249--10208369 Score: 62
Period size: 5 Copynumber: 22.4 Consensus size: 5
10208239 TATAACGATA
* * * * ** **
10208249 ATAAC ATAAT ATTAT AATAAT ATAAT GTAAT ATAAT AATAAT GTAGC ATACC
1 ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT
* *
10208301 ATACT ATCAT AATAAT AATAAT AATAAT ATACAAT AATAAT AGTAAT ATAAT
1 ATAAT ATAAT -ATAAT -ATAAT -ATAAT AT--AAT -ATAAT A-TAAT ATAAT
*
10208353 ATAAT ATACT ATAAT AT
1 ATAAT ATAAT ATAAT AT
10208370 TGATAATAAT
Statistics
Matches: 93, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
5 55 0.59
6 33 0.35
7 3 0.03
8 2 0.02
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:10208415 original size:22 final size:22
Alignment explanation
Indices: 10208311--10208415 Score: 85
Period size: 22 Copynumber: 4.9 Consensus size: 22
10208301 ATACTATCAT
10208311 AATAATAATAATAATAATATAC-
1 AATAATAATAATAATAATA-ACA
* *
10208333 AATAATAATAGTAAT-ATAATA
1 AATAATAATAATAATAATAACA
* * * *
10208354 TAAT-ATACT-ATAATATTGA-T
1 -AATAATAATAATAATAATAACA
* *
10208374 AATAATAACAATAATGATAACA
1 AATAATAATAATAATAATAACA
10208396 AATAATAATAATAATAATAA
1 AATAATAATAATAATAATAA
10208416 TAGAAATTGA
Statistics
Matches: 62, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
19 3 0.05
20 8 0.13
21 16 0.26
22 35 0.56
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (22 bp):
AATAATAATAATAATAATAACA
Found at i:10208626 original size:11 final size:11
Alignment explanation
Indices: 10208612--10208636 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10208602 TTTTTTTCAA
10208612 TTTTTTAATTT
1 TTTTTTAATTT
10208623 TTTTTTAATTT
1 TTTTTTAATTT
10208634 TTT
1 TTT
10208637 CTCTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTAATTT
Found at i:10209426 original size:17 final size:18
Alignment explanation
Indices: 10209406--10209439 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10209396 CAAAAGTCAT
10209406 TCTTA-CTTAAAATATTA
1 TCTTATCTTAAAATATTA
*
10209423 TCTTATTTTAAAATATT
1 TCTTATCTTAAAATATT
10209440 TTCCTTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (18 bp):
TCTTATCTTAAAATATTA
Found at i:10209726 original size:6 final size:6
Alignment explanation
Indices: 10209717--10209886 Score: 52
Period size: 6 Copynumber: 26.7 Consensus size: 6
10209707 TTTAGATTAA
* * * * * * *
10209717 GGTTAG GGTTAA GGTTTG GGTTTG GGTTTG TGTTTG GGTTTTG GGTTTAG
1 GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG GG-TTAG GG-TTAG
* * * * * * * *
10209767 GGTTTAG GTTTAG GTTTAG AGTTTAA GGTTTG GTTTAG GATTTAG GATTAG
1 GG-TTAG GGTTAG GGTTAG -GGTTAG GGTTAG GGTTAG G-GTTAG GGTTAG
* * * * * * *
10209818 GTTTAG GGTTTG TGTTTG GGTTTTG GGTTTAG GGTTTAG GTTTAG GTTTAG
1 GGTTAG GGTTAG GGTTAG GG-TTAG GG-TTAG GG-TTAG GGTTAG GGTTAG
10209869 GGTTTAG GGTTTAG GGTT
1 GG-TTAG GG-TTAG GGTT
10209887 TGTTTTAGGA
Statistics
Matches: 137, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
6 77 0.56
7 60 0.44
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48
Consensus pattern (6 bp):
GGTTAG
Found at i:10209761 original size:7 final size:6
Alignment explanation
Indices: 10209729--10210069 Score: 121
Period size: 7 Copynumber: 52.8 Consensus size: 6
10209719 TTAGGGTTAA
* * *
10209729 GGTTTG GGTTTG GGTTTG TGTTTG GGTTTTG GGTTTAG GGTTTA GGTTTA
1 GGTTTG GGTTTG GGTTTG GGTTTG GG-TTTG GGTTT-G GGTTTG GGTTTG
* * * * * *
10209779 GGTTTAG AGTTTAA GGTTT- GGTTTAG GATTTA GGATTA GGTTTAG GGTTTG
1 GGTTT-G GGTTT-G GGTTTG GGTTT-G GGTTTG GGTTTG GGTTT-G GGTTTG
* * *
10209830 TGTTTG GGTTTTG GGTTTAG GGTTTA GGTTTA GGTTTAG GGTTTAG GGTTTAG
1 GGTTTG GG-TTTG GGTTT-G GGTTTG GGTTTG GGTTT-G GGTTT-G GGTTT-G
* * * * * * * *
10209883 GGTTT- GTTTTAG GATTTA CGATTA GGTTTAA GGTTTG GGTTTAG GGTTTA
1 GGTTTG GGTTT-G GGTTTG GGTTTG GGTTT-G GGTTTG GGTTT-G GGTTTG
* * * * * * *
10209933 AGTTTAG GATTTAG GGTTTG GTTTTG TTGTTTA GGTTAG GGTTTG GGATTGAG
1 GGTTT-G GGTTT-G GGTTTG GGTTTG -GGTTTG GGTTTG GGTTTG GG-TT-TG
* * * *
10209986 GGTTTT GATTTGG GGTTTG GGTTTTAG AGTTTT GGTTTAG GG-TTG GGATTTGG
1 GGTTTG GGTTT-G GGTTTG GG-TTT-G GGTTTG GGTTT-G GGTTTG GG-TTT-G
* *
10210039 GGTTTT GGTTTGG GGTTTG GGATTTT GGTTT
1 GGTTTG GGTTT-G GGTTTG GG-TTTG GGTTT
10210070 TACATGAGAA
Statistics
Matches: 256, Mismatches: 53, Indels: 52
0.71 0.15 0.14
Matches are distributed among these distances:
5 12 0.05
6 116 0.45
7 120 0.47
8 8 0.03
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.49
Consensus pattern (6 bp):
GGTTTG
Found at i:10209764 original size:13 final size:13
Alignment explanation
Indices: 10209729--10210066 Score: 76
Period size: 13 Copynumber: 26.1 Consensus size: 13
10209719 TTAGGGTTAA
10209729 GGTTTGGG-TTTG
1 GGTTTGGGTTTTG
*
10209741 GGTTTGTG-TTTG
1 GGTTTGGGTTTTG
*
10209753 GGTTTTGGGTTTAG
1 GG-TTTGGGTTTTG
* *
10209767 GGTTTAGG-TTTA
1 GGTTTGGGTTTTG
* **
10209779 GGTTTAGAGTTTAA
1 GGTTT-GGGTTTTG
*
10209793 GGTTT-GGTTTAG
1 GGTTTGGGTTTTG
* * * *
10209805 GATTTAGG-ATTA
1 GGTTTGGGTTTTG
10209817 GGTTTAGGG-TTTG
1 GGTTT-GGGTTTTG
*
10209830 TGTTTGGGTTTTG
1 GGTTTGGGTTTTG
*
10209843 GGTTTAGGG-TTTA
1 GGTTT-GGGTTTTG
* *
10209856 GGTTTAGGTTTAG
1 GGTTTGGGTTTTG
*
10209869 GGTTTAGGGTTTAG
1 GGTTT-GGGTTTTG
10209883 GGTTT--GTTTTAG
1 GGTTTGGGTTTT-G
* ** * *
10209895 GATTTACG-ATTA
1 GGTTTGGGTTTTG
*
10209907 GGTTTAAGG-TTTG
1 GGTTT-GGGTTTTG
*
10209920 GGTTTAGGG-TTTA
1 GGTTT-GGGTTTTG
* * *
10209933 AGTTTAGGATTTAG
1 GGTTT-GGGTTTTG
10209947 GGTTT-GGTTTTG
1 GGTTTGGGTTTTG
* * *
10209959 TTGTTTAGG-TTAG
1 -GGTTTGGGTTTTG
**
10209972 GGTTTGGGATTGAG
1 GGTTTGGG-TTTTG
* * *
10209986 GGTTTTGATTTGG
1 GGTTTGGGTTTTG
10209999 GGTTTGGGTTTTAG
1 GGTTTGGGTTTT-G
* * *
10210013 AGTTTTGGTTTAG
1 GGTTTGGGTTTTG
*
10210026 GG-TTGGGATTTGG
1 GGTTTGGG-TTTTG
* *
10210039 GGTTTTGGTTTGG
1 GGTTTGGGTTTTG
10210052 GGTTTGGGATTTTG
1 GGTTTGGG-TTTTG
10210066 G
1 G
10210067 TTTTACATGA
Statistics
Matches: 239, Mismatches: 64, Indels: 44
0.69 0.18 0.13
Matches are distributed among these distances:
11 4 0.02
12 63 0.26
13 107 0.45
14 65 0.27
ACGTcount: A:0.12, C:0.00, G:0.39, T:0.49
Consensus pattern (13 bp):
GGTTTGGGTTTTG
Found at i:10209777 original size:26 final size:26
Alignment explanation
Indices: 10209731--10210059 Score: 160
Period size: 26 Copynumber: 12.2 Consensus size: 26
10209721 AGGGTTAAGG
10209731 TTTGGGTTT-GGGTTT-GTGTTTGGGT
1 TTTGGGTTTAGGGTTTAG-GTTTGGGT
*
10209756 TTTGGGTTTAGGGTTTAGGTTTAGGT
1 TTTGGGTTTAGGGTTTAGGTTTGGGT
* * *
10209782 TTAGAGTTTAAGGTTTGGTTTAGGATTTAGG-
1 TTTGGGTTT-A-G---GGTTTAGG-TTTGGGT
* *
10209813 ATTAGGTTTAGGGTTT-GTGTTTGGGT
1 TTTGGGTTTAGGGTTTAG-GTTTGGGT
*
10209839 TTTGGGTTTAGGGTTTAGGTTTAGGT
1 TTTGGGTTTAGGGTTTAGGTTTGGGT
*
10209865 TTAGGGTTTAGGGTTTAGGGTTT--GT
1 TTTGGGTTTAGGGTTTA-GGTTTGGGT
*
10209890 TTTAGGATTTACGATTAGGTTTAAGGTTTGGGT
1 TTT-GGGTTTA-G----GGTTT-AGGTTTGGGT
* *
10209923 TTAGGGTTTA-AGTTTAGGATTTAGGG-
1 TTTGGGTTTAGGGTTTAGG-TTT-GGGT
* * *
10209949 TTT-GGTTTTGTTGTTTAGGTTAGGG-
1 TTTGGGTTTAG-GGTTTAGGTTTGGGT
* * * *
10209974 TTTGGGATTGAGGGTTTTGATTTGGGG
1 TTTGGG-TTTAGGGTTTAGGTTTGGGT
* *
10210001 TTTGGGTTTTAGAGTTTTGGTTTAGGG-
1 TTTGGG-TTTAGGGTTTAGGTTT-GGGT
* * *
10210028 -TTGGGATTTGGGGTTTTGGTTTGGGG
1 TTTGGG-TTTAGGGTTTAGGTTTGGGT
10210054 TTTGGG
1 TTTGGG
10210060 ATTTTGGTTT
Statistics
Matches: 239, Mismatches: 34, Indels: 60
0.72 0.10 0.18
Matches are distributed among these distances:
25 36 0.15
26 111 0.46
27 46 0.19
28 4 0.02
29 1 0.00
30 1 0.00
31 23 0.10
32 13 0.05
33 4 0.02
ACGTcount: A:0.12, C:0.00, G:0.39, T:0.49
Consensus pattern (26 bp):
TTTGGGTTTAGGGTTTAGGTTTGGGT
Found at i:10209802 original size:12 final size:13
Alignment explanation
Indices: 10209713--10209956 Score: 108
Period size: 13 Copynumber: 19.2 Consensus size: 13
10209703 TTGGTTTAGA
*
10209713 TTAAGG-TTAGGG
1 TTAAGGTTTAGGT
*
10209725 TTAAGGTTTGGGT
1 TTAAGGTTTAGGT
*
10209738 TT-GGGTTT-GTGT
1 TTAAGGTTTAG-GT
* *
10209750 TT-GGGTTTTGGGT
1 TTAAGG-TTTAGGT
*
10209763 TTAGGGTTTAGGT
1 TTAAGGTTTAGGT
10209776 TT-AGGTTTAGAGT
1 TTAAGGTTTAG-GT
10209789 TTAAGGTTT-GGT
1 TTAAGGTTTAGGT
*
10209801 TT-AGGATTTAGGA
1 TTAAGG-TTTAGGT
10209814 TT-AGGTTTAGGGT
1 TTAAGGTTTA-GGT
*
10209827 TT--GTGTTTGGGT
1 TTAAG-GTTTAGGT
**
10209839 TTTGGGTTTAGGGT
1 TTAAGGTTTA-GGT
10209853 TT-AGGTTTAGGT
1 TTAAGGTTTAGGT
*
10209865 TTAGGGTTTAGGGT
1 TTAAGGTTTA-GGT
*
10209879 TTAGGGTTT--GT
1 TTAAGGTTTAGGT
* * *
10209890 TTTAGGATTTACGA
1 TTAAGG-TTTAGGT
10209904 TT-AGGTTTAAGGT
1 TTAAGGTTT-AGGT
*
10209917 TT-GGGTTTAGGGT
1 TTAAGGTTTA-GGT
10209930 TTAA-GTTTAGGAT
1 TTAAGGTTTAGG-T
*
10209943 TTAGGGTTT-GGT
1 TTAAGGTTTAGGT
10209955 TT
1 TT
10209957 TGTTGTTTAG
Statistics
Matches: 189, Mismatches: 19, Indels: 48
0.74 0.07 0.19
Matches are distributed among these distances:
11 10 0.05
12 59 0.31
13 85 0.45
14 35 0.19
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.48
Consensus pattern (13 bp):
TTAAGGTTTAGGT
Found at i:10209828 original size:45 final size:45
Alignment explanation
Indices: 10209719--10209956 Score: 227
Period size: 45 Copynumber: 5.3 Consensus size: 45
10209709 TAGATTAAGG
* * * * *
10209719 TTAGGGTTAAGGTTT-GGGTTTGGGTTT-GTGTTTGGGTTTTGGGT
1 TTAGGATT-AGGTTTAGGGTTTGGGTTTAGGGTTTAGGTTTAGGAT
* * *
10209763 TTAGGGTTTAGGTTTA-GGTTTAGAGTTTAAGGTTT-GGTTTAGGAT
1 TTA-GGATTAGGTTTAGGGTTT-GGGTTTAGGGTTTAGGTTTAGGAT
* * *
10209808 TTAGGATTAGGTTTAGGGTTTGTGTTT-GGGTTTTGGGTTTAGGGT
1 TTAGGATTAGGTTTAGGGTTTGGGTTTAGGG-TTTAGGTTTAGGAT
* *
10209853 TTAGGTTTAGGTTTAGGGTTTAGGGTTTAGGGTTT-GTTTTAGGAT
1 TTAGGATTAGGTTTAGGGTTT-GGGTTTAGGGTTTAGGTTTAGGAT
* * *
10209898 TTACGATTAGGTTTAAGGTTTGGGTTTAGGGTTTAAGTTTAGGAT
1 TTAGGATTAGGTTTAGGGTTTGGGTTTAGGGTTTAGGTTTAGGAT
* *
10209943 TTAGGGTTTGGTTT
1 TTAGGATTAGGTTT
10209957 TGTTGTTTAG
Statistics
Matches: 162, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
43 2 0.01
44 46 0.28
45 99 0.61
46 12 0.07
47 3 0.02
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (45 bp):
TTAGGATTAGGTTTAGGGTTTGGGTTTAGGGTTTAGGTTTAGGAT
Found at i:10210003 original size:27 final size:27
Alignment explanation
Indices: 10209971--10210062 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 27
10209961 GTTTAGGTTA
*
10209971 GGGTTTGGGATTGAGGGTTTTGATTTG
1 GGGTTTGGGATTGAGGGTTTTGGTTTG
* * * *
10209998 GGGTTTGGGTTTTAGAGTTTTGGTTTA
1 GGGTTTGGGATTGAGGGTTTTGGTTTG
10210025 GGG-TTGGGATTTG-GGGTTTTGGTTTG
1 GGGTTTGGGA-TTGAGGGTTTTGGTTTG
10210051 GGGTTTGGGATT
1 GGGTTTGGGATT
10210063 TTGGTTTTAC
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
26 21 0.39
27 33 0.61
ACGTcount: A:0.09, C:0.00, G:0.45, T:0.47
Consensus pattern (27 bp):
GGGTTTGGGATTGAGGGTTTTGGTTTG
Found at i:10210042 original size:20 final size:20
Alignment explanation
Indices: 10210019--10210059 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
10210009 TTAGAGTTTT
10210019 GGTTTAGGGTTGGGATTTGG
1 GGTTTAGGGTTGGGATTTGG
* * *
10210039 GGTTTTGGTTTGGGGTTTGG
1 GGTTTAGGGTTGGGATTTGG
10210059 G
1 G
10210060 ATTTTGGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.00, G:0.51, T:0.44
Consensus pattern (20 bp):
GGTTTAGGGTTGGGATTTGG
Found at i:10210064 original size:20 final size:20
Alignment explanation
Indices: 10210028--10210069 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
10210018 TGGTTTAGGG
*
10210028 TTGGGATTTGGGGTTTTGGT
1 TTGGGATTTGGGATTTTGGT
*
10210048 TTGGGGTTTGGGATTTTGGT
1 TTGGGATTTGGGATTTTGGT
10210068 TT
1 TT
10210070 TACATGAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.00, G:0.43, T:0.52
Consensus pattern (20 bp):
TTGGGATTTGGGATTTTGGT
Found at i:10212212 original size:10 final size:10
Alignment explanation
Indices: 10212197--10212245 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
10212187 GATTTTAACC
*
10212197 AAATTTGACA
1 AAATTTGACT
10212207 AAATTTGACT
1 AAATTTGACT
**
10212217 TTATTTGACT
1 AAATTTGACT
*
10212227 AAATTTGACC
1 AAATTTGACT
10212237 AAATTTGAC
1 AAATTTGAC
10212246 CCTAAGGTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (10 bp):
AAATTTGACT
Found at i:10217571 original size:2 final size:2
Alignment explanation
Indices: 10217564--10217595 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
10217554 ATTTCCATCT
*
10217564 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10217596 CTTATCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:10218984 original size:23 final size:23
Alignment explanation
Indices: 10218935--10218984 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
10218925 TTAAGATTTT
*
10218935 TTTATTTTATTTTATTATATATA
1 TTTATTTTATTTTATTATATAGA
10218958 TTTA-TTTATTTTTATTA-ATAGA
1 TTTATTTTA-TTTTATTATATAGA
10218980 GTTTA
1 -TTTA
10218985 ATATATAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (23 bp):
TTTATTTTATTTTATTATATAGA
Found at i:10219412 original size:14 final size:13
Alignment explanation
Indices: 10219385--10219423 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
10219375 AGGATTTTAT
10219385 ACTAGAAGAAAGAA
1 ACTAGAA-AAAGAA
10219399 ACATAGAAAAAGAA
1 AC-TAGAAAAAGAA
10219413 ACTAGGAAAAA
1 ACTA-GAAAAA
10219424 ATCGTAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 16 0.70
15 5 0.22
ACGTcount: A:0.67, C:0.08, G:0.18, T:0.08
Consensus pattern (13 bp):
ACTAGAAAAAGAA
Found at i:10221469 original size:51 final size:52
Alignment explanation
Indices: 10221408--10221510 Score: 147
Period size: 51 Copynumber: 2.0 Consensus size: 52
10221398 TGGATAAGAA
* * * *
10221408 AACTTTCAGAAGATAAATTTTAAAAG-GAAAGAGATTCTTAATA-GCAAGTTT
1 AACTTGCAGAAGAAAAATTCTAAAAGAAAAAG-GATTCTTAATAGGCAAGTTT
10221459 AACTTGCAGAAGAAAAATTCTAAAAGAAAAAGGATTCTTAATAGGCAAGTTT
1 AACTTGCAGAAGAAAAATTCTAAAAGAAAAAGGATTCTTAATAGGCAAGTTT
10221511 GTATGCTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
51 34 0.74
52 12 0.26
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.28
Consensus pattern (52 bp):
AACTTGCAGAAGAAAAATTCTAAAAGAAAAAGGATTCTTAATAGGCAAGTTT
Found at i:10221753 original size:35 final size:35
Alignment explanation
Indices: 10221687--10221757 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
10221677 TCCATATAGG
* * *
10221687 TATGATGAATGGGTACATATGGGTATGTGTTTGTT
1 TATGATGAAAGGGTACACATGGGTATATGTTTGTT
* * *
10221722 TATGTTGAAAGGGTGCACATGGGTTTATGTTTGTT
1 TATGATGAAAGGGTACACATGGGTATATGTTTGTT
10221757 T
1 T
10221758 GGTTTGAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.21, C:0.04, G:0.31, T:0.44
Consensus pattern (35 bp):
TATGATGAAAGGGTACACATGGGTATATGTTTGTT
Found at i:10222278 original size:14 final size:15
Alignment explanation
Indices: 10222248--10222280 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
10222238 ATTAGTCTTA
10222248 TTTCTTTTCAGTTTT
1 TTTCTTTTCAGTTTT
10222263 TTTCTTTT-A-TTTT
1 TTTCTTTTCAGTTTT
10222276 TTTCT
1 TTTCT
10222281 AGTGACAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 1 0.06
15 8 0.44
ACGTcount: A:0.06, C:0.12, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTCTTTTCAGTTTT
Found at i:10223037 original size:145 final size:143
Alignment explanation
Indices: 10222702--10223103 Score: 460
Period size: 143 Copynumber: 2.8 Consensus size: 143
10222692 TTAAAATACC
* * * * *
10222702 AAAAATCATGAAAAATTATAAAATTGAA-ATCTAGTAAGTTTCATGAAAA-TCAAAGCTCGACAA
1 AAAAATCATGAAATATTATGAAATT-AAGATCTTGAAAGTTTCATGAAAATTC-AAGCTCGAAAA
** * * * *
10222765 CATCAAATTATAAAAATACCTTTGTAGAGGTATTTTAGTAATTTCATA-TTTTAGTAATTGTTAT
64 GGTCAAATTATAAAAATACCTTTATAG-GGTATTTTGGTAATTTCACACTTTGAGTAATTGTTAT
10222829 GATTTCAAATGCACCA
128 GATTTCAAATGCACCA
* *
10222845 AAAAATCATGAAATATTATGAAATTAAGAT-GTGAAAAGTTTCATGAAAATTCAAGCTCGAGAAG
1 AAAAATCATGAAATATTATGAAATTAAGATCTTG-AAAGTTTCATGAAAATTCAAGCTCGAAAAG
* * *
10222909 GTCAAATTATAAAAATACCCTTATAAGGGTATTTTGGTAATTTTACACTTCTCGGGGT-ATTGTT
65 GTCAAATTATAAAAATACCTTTAT-AGGGTATTTTGGTAATTTCACACTT-T--GAGTAATTGTT
* *
10222973 GTGATTTCAAATGGA-CA
126 ATGATTTCAAATGCACCA
*
10222990 AAAAATCATGAAATATTATGAAATTAAGATCTTGAAAGTTTCATGAAAATGT-GAGCTC-ACAAA
1 AAAAATCATGAAATATTATGAAATTAAGATCTTGAAAGTTTCATGAAAAT-TCAAGCTCGA-AAA
* **
10223053 GGACAAATTACGAAAATACCTTTATAGGGTATTTTGGTAATTTCACACTTT
64 GGTCAAATTATAAAAATACCTTTATAGGGTATTTTGGTAATTTCACACTTT
10223104 TCCTAATACA
Statistics
Matches: 223, Mismatches: 25, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
142 3 0.01
143 88 0.39
144 31 0.14
145 77 0.35
146 22 0.10
147 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (143 bp):
AAAAATCATGAAATATTATGAAATTAAGATCTTGAAAGTTTCATGAAAATTCAAGCTCGAAAAGG
TCAAATTATAAAAATACCTTTATAGGGTATTTTGGTAATTTCACACTTTGAGTAATTGTTATGAT
TTCAAATGCACCA
Found at i:10225813 original size:13 final size:13
Alignment explanation
Indices: 10225795--10225823 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
10225785 AACTACCTAG
10225795 CATTTGAATGTAC
1 CATTTGAATGTAC
10225808 CATTTGAATGTAC
1 CATTTGAATGTAC
10225821 CAT
1 CAT
10225824 GACAAAGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTTGAATGTAC
Found at i:10228255 original size:26 final size:27
Alignment explanation
Indices: 10228203--10228255 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 27
10228193 AATACTTTAA
10228203 TTAAAAAATCATATTAGTTTAAATTTTT
1 TTAAAAAATCATATTA-TTTAAATTTTT
10228231 TTAATAAAATCA-ATT-TTT-AATTTTT
1 TTAA-AAAATCATATTATTTAAATTTTT
10228256 AAAAATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 7 0.29
26 3 0.12
28 7 0.29
29 7 0.29
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (27 bp):
TTAAAAAATCATATTATTTAAATTTTT
Found at i:10228557 original size:19 final size:17
Alignment explanation
Indices: 10228519--10228557 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
10228509 TATTAGGAAA
*
10228519 ATTTTAAAAAAATTATT
1 ATTTTAAAAAAATTAAT
10228536 ATTTTAAAAAAAATATAAT
1 ATTTT-AAAAAAAT-TAAT
10228555 ATT
1 ATT
10228558 GATAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 8 0.42
19 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTTAAAAAAATTAAT
Found at i:10228667 original size:16 final size:15
Alignment explanation
Indices: 10228646--10228675 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
10228636 AAATATTATT
10228646 TTAAAAAATTAAAATA
1 TTAAAAAA-TAAAATA
10228662 TTAAAAAATAAAAT
1 TTAAAAAATAAAAT
10228676 TAATATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TTAAAAAATAAAATA
Found at i:10230466 original size:31 final size:32
Alignment explanation
Indices: 10230398--10230468 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
10230388 TAATGTCCCA
*
10230398 TAAATATTTTCTACATCTATTTTTTAATTAAT
1 TAAATATTTTCAACATCTATTTTTTAATTAAT
*
10230430 T-AATATTTTCAAC-TCT-TATTTTT-ATTATTT
1 TAAATATTTTCAACATCTAT-TTTTTAATTA-AT
10230460 TAAATATTT
1 TAAATATTT
10230469 ATATGAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
29 5 0.15
30 10 0.29
31 18 0.53
32 1 0.03
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (32 bp):
TAAATATTTTCAACATCTATTTTTTAATTAAT
Found at i:10234135 original size:281 final size:274
Alignment explanation
Indices: 10233629--10234185 Score: 737
Period size: 281 Copynumber: 2.0 Consensus size: 274
10233619 GAATTAGTTG
* * ** *
10233629 CCAATGGTTGCTACCCCATGTTGTTCTGGAATTGTTGTTTATATAGGCCAACAATCCAACTTGAG
1 CCAATGGTTACTACCCCATGTTGTGCTGGAATTGTTGTTTATATAGGCCAACAATCCAACTCAAA
* * *
10233694 AAGAGTTTGAGTTGGAAACAAAATCTTAATTGAAAGTGATCTGTTATCTTTATGACTCAATTCTT
66 AAGAGTTTGAGTTGGAAACAAAATCTTAATCGAAAGTGATCTATTATCTTTATGACTCAATTCCT
* *
10233759 TAAAGGTAATTCAATTGTAATCCATCCAACAGAATTTGATCACAAATATTTTCAAAAAGTGTTGC
131 T-AAGGTAATTCAATTGTAA--CATCCAACAGAATTTGATCACAAAGATTTTCAAAAAGTGCTGC
* *
10233824 AATCTTATTCAACTTTCTTTCTTTTTTTTTTTTTTTCAAACTTTCAAATACAAATAATGAAAATC
193 AATCTTATTCAACTTTCTTTC---ATATTTTTTTTTCAAACTTTCAAATACAAATAATGAAAATC
10233889 AAAGGAAAAAAAGAAATGCA
255 AAAGGAAAAAAAGAAATGCA
*
10233909 CCAATGGTTACTACCCCCTGTTGTGCTGGAATTGTTGTTTATATAGGCCAACAATCCAACTCAAA
1 CCAATGGTTACTACCCCATGTTGTGCTGGAATTGTTGTTTATATAGGCCAACAATCCAACTCAAA
* * *
10233974 AAGAGTTTTGAGTTGGAAAGAAAATCTTAATCGAAAGTGATCTATTATCTTTATGATTTAATTCC
66 AAGAG-TTTGAGTTGGAAACAAAATCTTAATCGAAAGTGATCTATTATCTTTATGACTCAATTCC
* * *
10234039 TT-AGGTAATTCAATTGT-A-A-CCAA-TGGATTTGATCACAAAACCAACCAGATTTTCACAAAG
130 TTAAGGTAATTCAATTGTAACATCCAACAGAATTTGAT--C---A-CAA--AGATTTTCAAAAAG
* *
10234099 TGCTGCAATCTTATTCGACTTTCTTTCATATTTTTTTTTCAAAGTTTCAAATACAAATAATGAAA
187 TGCTGCAATCTTATTCAACTTTCTTTCATATTTTTTTTTCAAACTTTCAAATACAAATAATGAAA
* *
10234164 ATCAAATGAAGAAAAGAAATGC
252 ATCAAAGGAAAAAAAGAAATGC
10234186 TCAACAAATT
Statistics
Matches: 245, Mismatches: 23, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
273 8 0.03
274 4 0.02
275 2 0.01
278 57 0.23
279 18 0.07
280 64 0.26
281 92 0.38
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Consensus pattern (274 bp):
CCAATGGTTACTACCCCATGTTGTGCTGGAATTGTTGTTTATATAGGCCAACAATCCAACTCAAA
AAGAGTTTGAGTTGGAAACAAAATCTTAATCGAAAGTGATCTATTATCTTTATGACTCAATTCCT
TAAGGTAATTCAATTGTAACATCCAACAGAATTTGATCACAAAGATTTTCAAAAAGTGCTGCAAT
CTTATTCAACTTTCTTTCATATTTTTTTTTCAAACTTTCAAATACAAATAATGAAAATCAAAGGA
AAAAAAGAAATGCA
Found at i:10234506 original size:22 final size:22
Alignment explanation
Indices: 10234444--10234510 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
10234434 CAATTAAAAT
*
10234444 AAAATTCGTAATTTAAAATT-A
1 AAAATTCATAATTTAAAATTCA
* *
10234465 AAGAATTCATGACTTAAAATTCA
1 AA-AATTCATAATTTAAAATTCA
*
10234488 AAAATTCATAATTTGAAATTCA
1 AAAATTCATAATTTAAAATTCA
10234510 A
1 A
10234511 GGATTCGCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 2 0.05
22 33 0.87
23 3 0.08
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (22 bp):
AAAATTCATAATTTAAAATTCA
Found at i:10234645 original size:18 final size:18
Alignment explanation
Indices: 10234597--10234749 Score: 68
Period size: 18 Copynumber: 8.7 Consensus size: 18
10234587 AAAGAACTAC
* * *
10234597 AAGATTCTCAAAAATTCA
1 AAGATTCACAAGAATTTA
*
10234615 AAGATTCATAAGAATTTA
1 AAGATTCACAAGAATTTA
*
10234633 AAGATTCACAAGATTTCTA
1 AAGATTCACAAGAATT-TA
* * *
10234652 AGGTTTGCA-AA-ATTTTA
1 AAGATT-CACAAGAATTTA
** *
10234669 AAGATTTGCAAGAATTAA
1 AAGATTCACAAGAATTTA
* * * *
10234687 AAG-GTCATAGGATTTTA
1 AAGATTCACAAGAATTTA
* *
10234704 ACA-ATTCGCAAGAATTGA
1 A-AGATTCACAAGAATTTA
10234722 AA-ATTCACAAGAA--TA
1 AAGATTCACAAGAATTTA
*
10234737 AATATTCACAAGA
1 AAGATTCACAAGA
10234750 TTTTTAGATT
Statistics
Matches: 99, Mismatches: 29, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
15 3 0.03
16 10 0.10
17 27 0.27
18 49 0.49
19 8 0.08
20 2 0.02
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.29
Consensus pattern (18 bp):
AAGATTCACAAGAATTTA
Found at i:10234732 original size:17 final size:15
Alignment explanation
Indices: 10234706--10234749 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
10234696 GGATTTTAAC
*
10234706 AATTCGCAAGAATTGAA
1 AATTCACAAGAA-T-AA
10234723 AATTCACAAGAATAA
1 AATTCACAAGAATAA
10234738 ATATTCACAAGA
1 A-ATTCACAAGA
10234750 TTTTTAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 3 0.12
16 11 0.44
17 11 0.44
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.23
Consensus pattern (15 bp):
AATTCACAAGAATAA
Found at i:10234882 original size:21 final size:21
Alignment explanation
Indices: 10234829--10234885 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
10234819 AATTGTAATT
*
10234829 TTTAAAAATCCACATCCAAAA
1 TTTAAAAATTCACATCCAAAA
** * * *
10234850 TTTCTAAGTTCACGTCTAAAA
1 TTTAAAAATTCACATCCAAAA
10234871 TTTAAAAATTCACAT
1 TTTAAAAATTCACAT
10234886 TTGAAATATT
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (21 bp):
TTTAAAAATTCACATCCAAAA
Found at i:10242921 original size:57 final size:56
Alignment explanation
Indices: 10242857--10242964 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 56
10242847 AATTTAGTAT
*
10242857 GATTGAAAATTTTATTATTTTATAAAAAAAACATTAAAT-CTTCTAATAGTTTAATGG
1 GATTGAAAATTTTATTATTTTAT-AAAAAAACATTAAATATTTC-AATAGTTTAATGG
*
10242914 GATTGAAAATTTTATTATTTTATAAAAAATCATTAAATATTTCAATAGTTT
1 GATTGAAAATTTTATTATTTTATAAAAAAACATTAAATATTTCAATAGTTT
10242965 GGTAAGAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
56 22 0.46
57 26 0.54
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (56 bp):
GATTGAAAATTTTATTATTTTATAAAAAAACATTAAATATTTCAATAGTTTAATGG
Found at i:10247708 original size:17 final size:17
Alignment explanation
Indices: 10247686--10247733 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
10247676 GATTTTAAAG
*
10247686 ATTATTACGGTAATTTA
1 ATTATTAAGGTAATTTA
*
10247703 ATTATTAAGGTAATTTT
1 ATTATTAAGGTAATTTA
10247720 ATTATTAAGGTAAT
1 ATTATTAAGGTAAT
10247734 CTTTTGCCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (17 bp):
ATTATTAAGGTAATTTA
Found at i:10250933 original size:62 final size:61
Alignment explanation
Indices: 10250855--10250994 Score: 151
Period size: 62 Copynumber: 2.3 Consensus size: 61
10250845 ATACCCTTAC
** * * * * *
10250855 ATCATAATTACAAAAATGTTCCTTA-T-CCTATAATTGGCTAAAATTTTTATAATGTCCCTTT-T
1 ATCATAATTATGAAAAT-TTCCCTACTACCT-TAATTGACCAAAATTGTTATAATAT--CTTTCT
*
10250917 ATCATAATTATGAAAATTTCCCTACTACCTTGATTGACCAAAATTGTTATAATATCTTTCT
1 ATCATAATTATGAAAATTTCCCTACTACCTTAATTGACCAAAATTGTTATAATATCTTTCT
10250978 ATCATAATTATGAAAAT
1 ATCATAATTATGAAAAT
10250995 ATCCTCCTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
60 4 0.06
61 24 0.36
62 36 0.54
63 3 0.04
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.41
Consensus pattern (61 bp):
ATCATAATTATGAAAATTTCCCTACTACCTTAATTGACCAAAATTGTTATAATATCTTTCT
Found at i:10251659 original size:10 final size:10
Alignment explanation
Indices: 10251612--10251659 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
10251602 GATGGGATAT
*
10251612 AAAAAGGAAA
1 AAAAAGAAAA
10251622 AAAAAGAAAA
1 AAAAAGAAAA
10251632 AATTAAATGAAAA
1 AA--AAA-GAAAA
*
10251645 TAAAAGAAAA
1 AAAAAGAAAA
10251655 AAAAA
1 AAAAA
10251660 TCATGAGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 20 0.62
11 3 0.09
12 3 0.09
13 6 0.19
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.08
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:10251665 original size:24 final size:22
Alignment explanation
Indices: 10251613--10251656 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
10251603 ATGGGATATA
*
10251613 AAAAGGAAAAAAAAGAAAAAAT
1 AAAATGAAAAAAAAGAAAAAAT
*
10251635 TAAATGAAAATAAAAGAAAAAA
1 AAAATGAAAA-AAAAGAAAAAA
10251657 AAATCATGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (22 bp):
AAAATGAAAAAAAAGAAAAAAT
Found at i:10253608 original size:11 final size:11
Alignment explanation
Indices: 10253592--10253621 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
10253582 ATCATAGCTC
10253592 TCTTCTTTTTT
1 TCTTCTTTTTT
*
10253603 TCTTCTCTTTT
1 TCTTCTTTTTT
10253614 TCTTCTTT
1 TCTTCTTT
10253622 CTCTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TCTTCTTTTTT
Found at i:10253625 original size:15 final size:13
Alignment explanation
Indices: 10253595--10253631 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 13
10253585 ATAGCTCTCT
10253595 TCTTTTTTTCTTC
1 TCTTTTTTTCTTC
10253608 TCTTTTTCTTCTTTC
1 TCTTTTT-TTC-TTC
10253623 TCTTTTTTT
1 TCTTTTTTT
10253632 TTTTGAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.32
14 5 0.23
15 10 0.45
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TCTTTTTTTCTTC
Found at i:10256166 original size:21 final size:21
Alignment explanation
Indices: 10256140--10256193 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
10256130 GGATAGAAAT
10256140 GATCAATCCTCTAAGGGGAGG
1 GATCAATCCTCTAAGGGGAGG
10256161 GATCAATCCTCTAAGGGGAGG
1 GATCAATCCTCTAAGGGGAGG
10256182 GATCAATCCTCT
1 GATCAATCCTCT
10256194 TCCTTACCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (21 bp):
GATCAATCCTCTAAGGGGAGG
Found at i:10262708 original size:10 final size:10
Alignment explanation
Indices: 10262656--10262710 Score: 65
Period size: 10 Copynumber: 5.2 Consensus size: 10
10262646 CGCAGCTCCT
10262656 TTATTTCTTTC
1 TTATTT-TTTC
*
10262667 TTCTATTTTTTT
1 -T-TATTTTTTC
*
10262679 TTATTTTTCC
1 TTATTTTTTC
10262689 TTATTTTTTC
1 TTATTTTTTC
10262699 TTATTTTTTC
1 TTATTTTTTC
10262709 TT
1 TT
10262711 TCAAAATGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 28 0.74
11 1 0.03
12 4 0.11
13 5 0.13
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (10 bp):
TTATTTTTTC
Found at i:10264639 original size:20 final size:20
Alignment explanation
Indices: 10264611--10264649 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10264601 CTTGTAAATT
* *
10264611 CATTTTTGAAAATGCATTTG
1 CATTCTTGAAAATCCATTTG
10264631 CATTCTTGAAAATCCATTT
1 CATTCTTGAAAATCCATTT
10264650 TCAAGAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (20 bp):
CATTCTTGAAAATCCATTTG
Found at i:10265903 original size:22 final size:21
Alignment explanation
Indices: 10265869--10265930 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
10265859 AATAATATTT
10265869 TTAAAAAATTAATTTTAAAAA
1 TTAAAAAATTAATTTTAAAAA
*
10265890 TTAAATAACTTAATTTTAAAAA
1 TTAAA-AAATTAATTTTAAAAA
*
10265912 TATATTTAAAATTAATTTT
1 T-TA--AAAAATTAATTTT
10265931 TTAAATAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 5 0.15
22 16 0.47
23 2 0.06
24 10 0.29
25 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAAAAATTAATTTTAAAAA
Found at i:10280723 original size:6 final size:6
Alignment explanation
Indices: 10280712--10280764 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
10280702 TATTATTTTT
10280712 AATATA AATATA AATATA AA-ATTA AATA-A ATATATA AATAT- -ATATA
1 AATATA AATATA AATATA AATA-TA AATATA A-ATATA AATATA AATATA
10280758 AAT-TA AA
1 AATATA AA
10280765 AATTAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
4 4 0.10
5 7 0.17
6 27 0.66
7 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:10280737 original size:18 final size:18
Alignment explanation
Indices: 10280716--10280771 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
10280706 ATTTTTAATA
10280716 TAAATATAAATATAAAAT
1 TAAATATAAATATAAAAT
10280734 T-AA-ATAAATATATAAA-
1 TAAATATAAATATA-AAAT
*
10280750 TATATATAAAT-TAAAAAT
1 TAAATATAAATAT-AAAAT
10280768 TAAA
1 TAAA
10280772 AAATAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
16 10 0.32
17 10 0.32
18 11 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAATATAAATATAAAAT
Found at i:10293803 original size:38 final size:38
Alignment explanation
Indices: 10293761--10293837 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
10293751 TTGAGTTGTG
*
10293761 TTGGATTAGGATGCATAAATTGAGGGAGAGTTTTGCCA
1 TTGGATTAGGATGCACAAATTGAGGGAGAGTTTTGCCA
*
10293799 TTGGATTAGGATGCACAAATTGAGGGGGAGTTTTGCCA
1 TTGGATTAGGATGCACAAATTGAGGGAGAGTTTTGCCA
10293837 T
1 T
10293838 GCATTAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.27, C:0.09, G:0.32, T:0.31
Consensus pattern (38 bp):
TTGGATTAGGATGCACAAATTGAGGGAGAGTTTTGCCA
Found at i:10295952 original size:105 final size:105
Alignment explanation
Indices: 10295763--10295959 Score: 304
Period size: 105 Copynumber: 1.9 Consensus size: 105
10295753 TTGTGACTTT
* * * *
10295763 CTAACCATTTTGATTGTCTGACTTTGTGCATTTGCATGTCATGCATCATTTTTATTGTCATATGT
1 CTAACCAATTTGATTGTCTAACTTTGTGCATTTGCATGTCATGCATCATTTTCATTATCATATGT
* *
10295828 AACATTGTGCATTTACATCACTTTCATTTCATCTATAAAA
66 AACATTATGCATCTACATCACTTTCATTTCATCTATAAAA
* *
10295868 CTAACCAATTTGTTTGTTTAACTTTGTGCATTTGCATGTCATGCATCATTTTCATTATCATATGT
1 CTAACCAATTTGATTGTCTAACTTTGTGCATTTGCATGTCATGCATCATTTTCATTATCATATGT
* *
10295933 AACATTATGTATCTGCATCACTTTCAT
66 AACATTATGCATCTACATCACTTTCAT
10295960 ATTAGATTTC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 82 1.00
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.45
Consensus pattern (105 bp):
CTAACCAATTTGATTGTCTAACTTTGTGCATTTGCATGTCATGCATCATTTTCATTATCATATGT
AACATTATGCATCTACATCACTTTCATTTCATCTATAAAA
Found at i:10298424 original size:22 final size:23
Alignment explanation
Indices: 10298391--10298436 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
10298381 TTTCAAGGAT
* *
10298391 AGAACGCAAAAAAACAAAGAAAA
1 AGAACGCAAAAAAAAAAAAAAAA
10298414 AGAA-GCAAAAAAAAAAAAAAAA
1 AGAACGCAAAAAAAAAAAAAAAA
10298436 A
1 A
10298437 CAAAGAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (23 bp):
AGAACGCAAAAAAAAAAAAAAAA
Found at i:10298427 original size:26 final size:25
Alignment explanation
Indices: 10298399--10298448 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
10298389 ATAGAACGCA
* *
10298399 AAAAAACAAAGAA-AAAGAAGCAAAA
1 AAAAAAAAAAAAACAAAGAAG-AAAA
10298424 AAAAAAAAAAAAACAAAGAAGAAAA
1 AAAAAAAAAAAAACAAAGAAGAAAA
10298449 GAGGAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAAAAACAAAGAAGAAAA
Found at i:10298848 original size:15 final size:15
Alignment explanation
Indices: 10298828--10298869 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
10298818 TAAAATAAAG
10298828 AAAAAAGAAAA-GAGA
1 AAAAAAGAAAATGA-A
10298843 AAAAAAGAAAATGAA
1 AAAAAAGAAAATGAA
10298858 AAAAAATGAAAA
1 AAAAAA-GAAAA
10298870 ATAGAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (15 bp):
AAAAAAGAAAATGAA
Found at i:10299874 original size:21 final size:21
Alignment explanation
Indices: 10299848--10299904 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
10299838 ATGAAGTTTT
* *
10299848 AAATGAGAATTTTTTAGTCTC
1 AAATGAGAATCTTTGAGTCTC
*
10299869 AAATGAGAATCTTTGAGTTTC
1 AAATGAGAATCTTTGAGTCTC
* *
10299890 AAATAAGAAACTTTG
1 AAATGAGAATCTTTG
10299905 GGATGTGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.37
Consensus pattern (21 bp):
AAATGAGAATCTTTGAGTCTC
Found at i:10300154 original size:22 final size:22
Alignment explanation
Indices: 10300122--10300177 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
10300112 TAAATGTTGG
* *
10300122 ATGCGAGTCTTGAAATTTGTAA
1 ATGCGAATCTTGAAATTTGCAA
*
10300144 ATGCGAATCTTGCAATTTGCAA
1 ATGCGAATCTTGAAATTTGCAA
10300166 ATGCGAATCTTG
1 ATGCGAATCTTG
10300178 GGATCTTGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (22 bp):
ATGCGAATCTTGAAATTTGCAA
Found at i:10300420 original size:41 final size:41
Alignment explanation
Indices: 10300365--10300693 Score: 424
Period size: 41 Copynumber: 7.9 Consensus size: 41
10300355 GATTGTCAAT
* *
10300365 GAGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAT
1 GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* * *
10300406 GAGCATTTTATTTTTCAAAGTTGTGGTGCCTCTATTTAAAG
1 GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* * *
10300447 GAGCATTTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTTTAGAA
1 GAGCAATTTA-TTTTTCAAAGTTGTGGTGCCTCTG--TTTAGAG
* *
10300491 GAGCAATTTATTTTTCAAACGTTGTGGTGCCTCTATTTAGAT
1 GAGCAATTTATTTTTCAAA-GTTGTGGTGCCTCTGTTTAGAG
* * * * *
10300533 GAGCAATTTATATTTCAAAGTTGTGATGCCTTTATTTAAAG
1 GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* * * *
10300574 GAGTAATTTATTTTTCAAAGTTATGGTACCTTTGTTTAGAG
1 GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
*
10300615 GAGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* *
10300656 GAACAATTTATTTTTCAAAGTTGTAGTGCCTCTGTTTA
1 GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTA
10300694 AAGGTGCCTC
Statistics
Matches: 253, Mismatches: 31, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
41 171 0.68
42 46 0.18
43 8 0.03
44 28 0.11
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (41 bp):
GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
Found at i:10300749 original size:59 final size:57
Alignment explanation
Indices: 10300639--10300752 Score: 183
Period size: 59 Copynumber: 2.0 Consensus size: 57
10300629 TCAAAGTTGT
10300639 GGTGCCTCTGTTTAGAGGAACAATTTATTTTTCAAAGTTGTAGTGCCTCTGTTTAAA
1 GGTGCCTCTGTTTAGAGGAACAATTTATTTTTCAAAGTTGTAGTGCCTCTGTTTAAA
* * *
10300696 GGTGCCTCTGTTTAGAGGGAGCATTTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTA
1 GGTGCCTCTGTTTAGA-GGAACAATTTATTTTTC-AAAGTTGTAGTGCCTCTGTTTA
10300753 GAGGAGCAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
57 16 0.31
58 15 0.29
59 21 0.40
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (57 bp):
GGTGCCTCTGTTTAGAGGAACAATTTATTTTTCAAAGTTGTAGTGCCTCTGTTTAAA
Done.