Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_pilon, 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: 6772376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 32
Found at i:8217 original size:22 final size:21
Alignment explanation
Indices: 8192--8234 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
8182 TAAAAAATTT
*
8192 CCTAAAACATTATTTATTTTTA
1 CCTAAAACATTAATT-TTTTTA
8214 CCTAAAACATTAATTTTTTTA
1 CCTAAAACATTAATTTTTTTA
8235 ACATTTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (21 bp):
CCTAAAACATTAATTTTTTTA
Found at i:8262 original size:27 final size:27
Alignment explanation
Indices: 8232--8294 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
8222 ATTAATTTTT
*
8232 TTAACATTTCTGGTAAAGTGTTGAATA
1 TTAACATTTCTGGTAAAGTGTCGAATA
8259 TTAACATTTCTGGTAAAGTGTCGAATA
1 TTAACATTTCTGGTAAAGTGTCGAATA
8286 TTAACATTT
1 TTAACATTT
8295 TCGATAGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (27 bp):
TTAACATTTCTGGTAAAGTGTCGAATA
Found at i:9704 original size:32 final size:33
Alignment explanation
Indices: 9657--9732 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 33
9647 ACTTTTTTGA
*
9657 AAAATA-AAAAAATTATT-GAAATTTAAAATAT
1 AAAATATAAAAAATTATTAGAAATTTAAAACAT
* *
9688 AAAATATAAAAAATTATTAAGATATTTAATACAT
1 AAAATATAAAAAATTATT-AGAAATTTAAAACAT
*
9722 TAAATATAAAA
1 AAAATATAAAA
9733 TTACTAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 6 0.16
32 11 0.29
34 21 0.55
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (33 bp):
AAAATATAAAAAATTATTAGAAATTTAAAACAT
Found at i:10619 original size:32 final size:33
Alignment explanation
Indices: 10547--10619 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 33
10537 ACCTTTTTCT
*
10547 CTTCTCT-CTTAATTATCTCCATGACTCTCTTA
1 CTTCTCTCCTTAATTATCTCCAGGACTCTCTTA
*
10579 CTTCTCTCCTT-ATTATCTCCAGGCCTCTCTTA
1 CTTCTCTCCTTAATTATCTCCAGGACTCTCTTA
10611 CTTCTCTCC
1 CTTCTCTCC
10620 CTAAAATCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 35 0.92
33 3 0.08
ACGTcount: A:0.14, C:0.37, G:0.04, T:0.45
Consensus pattern (33 bp):
CTTCTCTCCTTAATTATCTCCAGGACTCTCTTA
Found at i:17084 original size:23 final size:23
Alignment explanation
Indices: 17058--17102 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
17048 TATATCATTA
*
17058 ATTTA-ATTCTTTTTTTAGTATAG
1 ATTTATATTCTATTTTT-GTATAG
*
17081 ATTTATTTTCTATTTTTGTATA
1 ATTTATATTCTATTTTTGTATA
17103 CCCTTTTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.64
Consensus pattern (23 bp):
ATTTATATTCTATTTTTGTATAG
Found at i:19180 original size:17 final size:18
Alignment explanation
Indices: 19135--19183 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
19125 TATTTCTGAG
*
19135 GGAATTGGAAACTGTGAA
1 GGAATTGGAATCTGTGAA
* * *
19153 TGAATTAGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
19170 GGAATTGGAATCTG
1 GGAATTGGAATCTG
19184 AAACCTGTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:21179 original size:8 final size:8
Alignment explanation
Indices: 21162--21197 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
21152 GTGCAGTGCT
*
21162 AAAAAATG
1 AAAAATTG
21170 AAAAATTG
1 AAAAATTG
21178 AAAAATTG
1 AAAAATTG
21186 AAAAATT-
1 AAAAATTG
21193 AAAAA
1 AAAAA
21198 GTTTAAGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
7 5 0.19
8 22 0.81
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (8 bp):
AAAAATTG
Found at i:23236 original size:19 final size:20
Alignment explanation
Indices: 23214--23251 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
23204 ACTACTATAT
*
23214 TACTTGCATCGA-TTGTGTA
1 TACTTGCATAGATTTGTGTA
23233 TACTTGCATAGATTTGTGT
1 TACTTGCATAGATTTGTGT
23252 GTTACAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.45
Consensus pattern (20 bp):
TACTTGCATAGATTTGTGTA
Found at i:28207 original size:31 final size:31
Alignment explanation
Indices: 28171--28230 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
28161 AACTTAAAAG
* *
28171 AGTTTTGTAATACTGAGATTTAAAAAATTTT
1 AGTTTTATAATACTGAAATTTAAAAAATTTT
*
28202 AGTTTTATAATACTGAAATTTAAATAATT
1 AGTTTTATAATACTGAAATTTAAAAAATT
28231 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (31 bp):
AGTTTTATAATACTGAAATTTAAAAAATTTT
Found at i:28745 original size:20 final size:20
Alignment explanation
Indices: 28697--28758 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
28687 AGCTTAAATC
*
28697 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
28717 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
28735 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
28754 AAAAT
1 AAAAT
28759 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:28755 original size:26 final size:24
Alignment explanation
Indices: 28726--28786 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 24
28716 TAAAATTTTA
*
28726 ATAATATATAAAATAATTTATATGAT
1 ATAATATATAAAATAATCTATA--AT
*
28752 ATAA-A-ATTAAAT-ATCTATAAT
1 ATAATATATAAAATAATCTATAAT
28773 ATAATAT-TAAAATA
1 ATAATATATAAAATA
28787 CTAATATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
21 6 0.21
22 6 0.21
23 6 0.21
24 6 0.21
25 1 0.03
26 4 0.14
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
ATAATATATAAAATAATCTATAAT
Found at i:28838 original size:63 final size:63
Alignment explanation
Indices: 28753--28909 Score: 239
Period size: 63 Copynumber: 2.5 Consensus size: 63
28743 TTATATGATA
*
28753 TAAAATTAAATATCTATAATATAATATTAAAATACTAATATTTAATTTATTTCAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAATACTAATATTTAATTTATTTAAAAATTAATAT
* *
28817 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAATACTAATATTTAATTTATTTAAAAATTAATAT
*
28880 TAAAAATTAAAATC-A-AATATAATA-TAAAAT
1 T-AAAATTAATATCTATAATATAATATTAAAAT
28910 TAAATATAAA
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
61 5 0.06
62 9 0.10
63 55 0.63
64 18 0.21
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (63 bp):
TAAAATTAATATCTATAATATAATATTAAAATACTAATATTTAATTTATTTAAAAATTAATAT
Found at i:28841 original size:26 final size:24
Alignment explanation
Indices: 28808--28880 Score: 87
Period size: 23 Copynumber: 3.0 Consensus size: 24
28798 TTTATTTCAA
28808 AATTAATATT-AAAATTAATATCTAT
1 AATTAATATTAAAAATTAATAT-T-T
28833 AATATAATATTAAAAAATTAATATTT
1 AAT-TAATATT-AAAAATTAATATTT
*
28859 AATTTAT-TTAAAAATTAATATT
1 AATTAATATTAAAAATTAATATT
28881 AAAAATTAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
23 13 0.30
24 2 0.05
25 6 0.14
26 11 0.25
27 1 0.02
28 11 0.25
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (24 bp):
AATTAATATTAAAAATTAATATTT
Found at i:28842 original size:14 final size:12
Alignment explanation
Indices: 28753--28912 Score: 89
Period size: 12 Copynumber: 12.8 Consensus size: 12
28743 TTATATGATA
28753 TAAAATTAAATAT
1 TAAAATT-AATAT
*
28766 CTATAATATAATAT
1 -TAAAAT-TAATAT
28780 TAAAATACTAATAT
1 TAAAAT--TAATAT
* *
28794 T-TAATTTAT-T
1 TAAAATTAATAT
28804 TCAAAATTAATAT
1 T-AAAATTAATAT
28817 TAAAATTAATAT
1 TAAAATTAATAT
*
28829 CTATAATATAATAT
1 -TAAAAT-TAATAT
28843 TAAAAAATTAATAT
1 T--AAAATTAATAT
* *
28857 T-TAATTTAT-T
1 TAAAATTAATAT
28867 TAAAAATTAATAT
1 T-AAAATTAATAT
*
28880 TAAAAATTAA-AA
1 T-AAAATTAATAT
*
28892 TCAAATATAATA-
1 TAAAAT-TAATAT
28904 TAAAATTAA
1 TAAAATTAA
28913 ATATAAAACT
Statistics
Matches: 116, Mismatches: 16, Indels: 31
0.71 0.10 0.19
Matches are distributed among these distances:
10 4 0.03
11 16 0.14
12 33 0.28
13 28 0.24
14 30 0.26
15 5 0.04
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATTAATAT
Found at i:33707 original size:28 final size:30
Alignment explanation
Indices: 33671--33727 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
33661 TTTTTAATAG
33671 AAATAAATTAATTTAAAAATTTTA-AATTT
1 AAATAAATTAATTTAAAAATTTTATAATTT
* * *
33700 AAAT-AATTATTTTATAATTTTTATAATT
1 AAATAAATTAATTTAAAAATTTTATAATT
33728 AAGAAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
AAATAAATTAATTTAAAAATTTTATAATTT
Found at i:35724 original size:48 final size:48
Alignment explanation
Indices: 35667--35972 Score: 423
Period size: 48 Copynumber: 6.4 Consensus size: 48
35657 ACTTCCAACC
* *
35667 CCAGCACCACCAGGCAAGGCCCCAACTCCACCGTATAAGCCACCGTCT
1 CCAGCACCACCAGTCAAGGCCCCAACACCACCGTATAAGCCACCGTCT
* ** * * *
35715 CCAGTACCACCAGTCAACCCCCCTACACCACCATATAAGCCACCATCT
1 CCAGCACCACCAGTCAAGGCCCCAACACCACCGTATAAGCCACCGTCT
* * ** * * *
35763 CCAGTACCCCCAACCAAGGCCCCAACTCCACCATATAAGCCCCCGTCT
1 CCAGCACCACCAGTCAAGGCCCCAACACCACCGTATAAGCCACCGTCT
35811 CCAGCACCACCAGTCAAGGCCCCAACACCACCGTATAAGCCACCGTCT
1 CCAGCACCACCAGTCAAGGCCCCAACACCACCGTATAAGCCACCGTCT
* *
35859 CCTGCACCACCAGTCAAGGCCCCAAAACCACCGTATAAGCCACCGTCT
1 CCAGCACCACCAGTCAAGGCCCCAACACCACCGTATAAGCCACCGTCT
* * *
35907 CCTGCACCACCAGTCAAGGCCCCAACTCCGCCGTATAAGCCACCGTCT
1 CCAGCACCACCAGTCAAGGCCCCAACACCACCGTATAAGCCACCGTCT
*
35955 CCTGCACCACCAGTCAAG
1 CCAGCACCACCAGTCAAG
35973 CCTCCTACCA
Statistics
Matches: 229, Mismatches: 29, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 229 1.00
ACGTcount: A:0.28, C:0.46, G:0.13, T:0.12
Consensus pattern (48 bp):
CCAGCACCACCAGTCAAGGCCCCAACACCACCGTATAAGCCACCGTCT
Found at i:35868 original size:144 final size:143
Alignment explanation
Indices: 35667--36011 Score: 440
Period size: 144 Copynumber: 2.4 Consensus size: 143
35657 ACTTCCAACC
* * *
35667 CCAGCACCACCAGGCAAGGCCCCAACTCCACCGTATAAGCCACCGTCTCCAGTACCACCAGTCAA
1 CCAGCACCACCAGTCAAGGCCCCAAC-CCACCGTATAAGCCACCGTCTCCTGCACCACCAGTCAA
* * * *
35732 CCCCCCTACACCACCATATAAGCCACCATCTCCAGTACCCCCAACCAAGGCCCCAACTCCACCAT
65 CCCCCCAAAACCACCATATAAGCCACCATCTCCAGCACCACCAACCAAGGCCCCAACTCCACCAT
*
35797 ATAAGCCCCCGTCT
130 ATAAGCCACCGTCT
35811 CCAGCACCACCAGTCAAGGCCCCAACACCACCGTATAAGCCACCGTCTCCTGCACCACCAGTCAA
1 CCAGCACCACCAGTCAAGGCCCCAAC-CCACCGTATAAGCCACCGTCTCCTGCACCACCAGTCAA
** * * * ** * *
35876 GGCCCCAAAACCACCGTATAAGCCACCGTCTCCTGCACCACCAGTCAAGGCCCCAACTCCGCCGT
65 CCCCCCAAAACCACCATATAAGCCACCATCTCCAGCACCACCAACCAAGGCCCCAACTCCACCAT
35941 ATAAGCCACCGTCT
130 ATAAGCCACCGTCT
* * * * * *
35955 CCTGCACCACCAGTCAA-GCCTCCTACCATACCATATAAGCCTCCGACTCCTGCACCA
1 CCAGCACCACCAGTCAAGGCC-CCAACC-CACCGTATAAGCCACCGTCTCCTGCACCA
36012 GCACCAGCAC
Statistics
Matches: 175, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
143 4 0.02
144 171 0.98
ACGTcount: A:0.28, C:0.46, G:0.13, T:0.13
Consensus pattern (143 bp):
CCAGCACCACCAGTCAAGGCCCCAACCCACCGTATAAGCCACCGTCTCCTGCACCACCAGTCAAC
CCCCCAAAACCACCATATAAGCCACCATCTCCAGCACCACCAACCAAGGCCCCAACTCCACCATA
TAAGCCACCGTCT
Found at i:35992 original size:48 final size:47
Alignment explanation
Indices: 35670--36011 Score: 389
Period size: 48 Copynumber: 7.1 Consensus size: 47
35660 TCCAACCCCA
* * *
35670 GCACCACCAGGCAAGGCCCCAACTCCACCGTATAAGCCACCGTCTCCA
1 GCACCACCAGTCAAGGCCCCAAC-CCACCATATAAGCCACCGTCTCCT
* ** * * *
35718 GTACCACCAGTCAACCCCCCTACACCACCATATAAGCCACCATCTCCA
1 GCACCACCAGTCAAGGCCCCAAC-CCACCATATAAGCCACCGTCTCCT
* * ** * *
35766 GTACCCCCAACCAAGGCCCCAACTCCACCATATAAGCCCCCGTCTCCA
1 GCACCACCAGTCAAGGCCCCAAC-CCACCATATAAGCCACCGTCTCCT
*
35814 GCACCACCAGTCAAGGCCCCAACACCACCGTATAAGCCACCGTCTCCT
1 GCACCACCAGTCAAGGCCCCAAC-CCACCATATAAGCCACCGTCTCCT
* *
35862 GCACCACCAGTCAAGGCCCCAAAACCACCGTATAAGCCACCGTCTCCT
1 GCACCACCAGTCAAGGCCCC-AACCCACCATATAAGCCACCGTCTCCT
* *
35910 GCACCACCAGTCAAGGCCCCAACTCCGCCGTATAAGCCACCGTCTCCT
1 GCACCACCAGTCAAGGCCCCAAC-CCACCATATAAGCCACCGTCTCCT
* * * *
35958 GCACCACCAGTCAA-GCCTCCTACCATACCATATAAGCCTCCGACTCCT
1 GCACCACCAGTCAAGGCC-CCAACC-CACCATATAAGCCACCGTCTCCT
36006 GCACCA
1 GCACCA
36012 GCACCAGCAC
Statistics
Matches: 256, Mismatches: 34, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
47 6 0.02
48 248 0.97
49 2 0.01
ACGTcount: A:0.27, C:0.46, G:0.13, T:0.13
Consensus pattern (47 bp):
GCACCACCAGTCAAGGCCCCAACCCACCATATAAGCCACCGTCTCCT
Found at i:36794 original size:21 final size:20
Alignment explanation
Indices: 36768--36811 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
36758 TTTTACTTTA
36768 ATTATTATTAATATTTTAATT
1 ATTATTATTAATA-TTTAATT
*
36789 ATTATTATTATTATTTAATT
1 ATTATTATTAATATTTAATT
36809 ATT
1 ATT
36812 TAAATGATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTATTATTAATATTTAATT
Found at i:36800 original size:18 final size:18
Alignment explanation
Indices: 36746--36811 Score: 78
Period size: 18 Copynumber: 3.5 Consensus size: 18
36736 ATTATACTAC
* *
36746 TTAATTATTTATTTTTACT
1 TTAATTA-TTATTATTATT
*
36765 TTAATTATTATTAATATT
1 TTAATTATTATTATTATT
36783 TTAATTATTATTATTATTAT
1 TTAATTATTATTATTA-T-T
36803 TTAATTATT
1 TTAATTATT
36812 TAAATGATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
18 23 0.56
19 8 0.20
20 10 0.24
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTAATTATTATTATTATT
Found at i:36892 original size:37 final size:37
Alignment explanation
Indices: 36843--36932 Score: 139
Period size: 37 Copynumber: 2.5 Consensus size: 37
36833 ATATAATTAT
*
36843 ATATTT-T-TATTAATATAATTATACATTTATCCTTA
1 ATATTTATATATTAATATAATTATACACTTATCCTTA
* *
36878 ATATTTATATATTAATATAATTATATACTTATCTTTA
1 ATATTTATATATTAATATAATTATACACTTATCCTTA
36915 ATATTTATATATTAATAT
1 ATATTTATATATTAATAT
36933 TATATTAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
35 6 0.12
36 1 0.02
37 43 0.86
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (37 bp):
ATATTTATATATTAATATAATTATACACTTATCCTTA
Found at i:36949 original size:37 final size:36
Alignment explanation
Indices: 36843--36956 Score: 121
Period size: 37 Copynumber: 3.2 Consensus size: 36
36833 ATATAATTAT
* * *
36843 ATATTT-T-TATTAATATAATTATACATTTATCCTTA
1 ATATTTATATATTAATATAATTATATACTGAT-CTTA
*
36878 ATATTTATATATTAATATAATTATATACTTATCTTTA
1 ATATTTATATATTAATATAATTATATACTGATC-TTA
36915 ATATTTATATATTAATATTATATTA-ATA-TGATCTTA
1 ATATTTATATATTAATA-TA-ATTATATACTGATCTTA
36951 AT-TTTA
1 ATATTTA
36957 ATTAATTTAA
Statistics
Matches: 71, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
35 10 0.14
36 7 0.10
37 45 0.63
38 5 0.07
39 4 0.06
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.54
Consensus pattern (36 bp):
ATATTTATATATTAATATAATTATATACTGATCTTA
Found at i:37244 original size:21 final size:21
Alignment explanation
Indices: 37220--37338 Score: 109
Period size: 21 Copynumber: 5.8 Consensus size: 21
37210 GCGAATTTGG
*
37220 AAAATCACAACGCGATAATAC
1 AAAATCGCAACGCGATAATAC
37241 AAAATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATAATAC
* *
37262 AAAATCGCAACGCGATACTGC
1 AAAATCGCAACGCGATAATAC
*** *
37283 -CTTTCGCAACGCGATACTTAC
1 AAAATCGCAACGCGATA-ATAC
**
37304 --TTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATAATAC
* *
37323 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
37339 TTTCAAAGCG
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 28 0.34
21 52 0.63
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.20
Consensus pattern (21 bp):
AAAATCGCAACGCGATAATAC
Found at i:37291 original size:20 final size:20
Alignment explanation
Indices: 37266--37318 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
37256 TAATACAAAA
*
37266 TCGCAACGCGATACTGCCTT
1 TCGCAACGCGATACTGACTT
*
37286 TCGCAACGCGATACTTACTT
1 TCGCAACGCGATACTGACTT
37306 TCGCAACGCGATA
1 TCGCAACGCGATA
37319 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:38726 original size:18 final size:18
Alignment explanation
Indices: 38705--38752 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
38695 TCCACTTCGG
38705 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
* *
38723 GAGCTATCACCTTACCCA
1 GAGCCATCACCTCACCCA
38741 GAGCCATCACCT
1 GAGCCATCACCT
38753 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:39231 original size:20 final size:20
Alignment explanation
Indices: 39206--39251 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
39196 TAGTTTACTT
39206 TCGCAACACGAAAATGGCTA
1 TCGCAACACGAAAATGGCTA
** *
39226 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGGCTA
39246 TCGCAA
1 TCGCAA
39252 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGGCTA
Found at i:39260 original size:19 final size:20
Alignment explanation
Indices: 39217--39260 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
39207 CGCAACACGA
39217 AAATGGCTATCGCAATGCGG
1 AAATGGCTATCGCAATGCGG
39237 AAATGGCTATCGCAATGC-G
1 AAATGGCTATCGCAATGCGG
39256 AAATG
1 AAATG
39261 AAAATCGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.20
Consensus pattern (20 bp):
AAATGGCTATCGCAATGCGG
Found at i:39267 original size:19 final size:19
Alignment explanation
Indices: 39225--39305 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
39215 GAAAATGGCT
***
39225 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
39245 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
39264 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
39278 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
39297 ATCGCAATG
1 ATCGCAATG
39306 TAATTTGTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 24 0.48
20 10 0.20
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:39383 original size:33 final size:33
Alignment explanation
Indices: 39315--39395 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
39305 GTAATTTGTG
* ***
39315 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATAGCCA
*
39348 TTTCGCATTGCTATTTTGTCGTTGCGATAGCCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATAGCCA
*
39381 TTTCCGCGTTGCGAT
1 TTT-CGCATTGCGAT
39396 AGTCATTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 31 0.77
34 9 0.22
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.44
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATAGCCA
Found at i:39390 original size:20 final size:20
Alignment explanation
Indices: 39367--39414 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
39357 GCTATTTTGT
39367 CGTTGCGATAGCCATTTCCG
1 CGTTGCGATAGCCATTTCCG
* *
39387 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGCCATTTCCG
39407 CGTTGCGA
1 CGTTGCGA
39415 AAGTAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTCCG
Found at i:39425 original size:20 final size:20
Alignment explanation
Indices: 39385--39440 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
39375 TAGCCATTTC
* * *
39385 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
39405 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
39425 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
39441 ACTATTATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:39815 original size:21 final size:21
Alignment explanation
Indices: 39782--39842 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
39772 GACTCACCTG
39782 TCATCCCTCAAGAGTCCCCT-
1 TCATCCCTCAAGAGTCCCCTA
** *
39802 TCAATCGTTCAAGAGGCCCCTA
1 TC-ATCCCTCAAGAGTCCCCTA
39824 TCATCCCTCAAGAGTCCCC
1 TCATCCCTCAAGAGTCCCC
39843 CCCCACCGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.23, C:0.41, G:0.13, T:0.23
Consensus pattern (21 bp):
TCATCCCTCAAGAGTCCCCTA
Found at i:39890 original size:42 final size:42
Alignment explanation
Indices: 39782--39870 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
39772 GACTCACCTG
** * * *
39782 TCATCCCTCAAGAGTCCCCTTCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTA
*
39824 TCATCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTA
39866 TCATC
1 TCATC
39871 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTA
Found at i:41467 original size:34 final size:33
Alignment explanation
Indices: 41420--41484 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
41410 AAAACAGACT
* **
41420 ATCGCAACACGAAACTGACTATCGCAACGAGAGA
1 ATCGCAACACGAAA-TAAAAATCGCAACGAGAGA
**
41454 ATCGCAATGCGAAATAAAAATCGCAACGAGA
1 ATCGCAACACGAAATAAAAATCGCAACGAGA
41485 AAATTGCGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
33 14 0.54
34 12 0.46
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAACACGAAATAAAAATCGCAACGAGAGA
Found at i:41513 original size:20 final size:20
Alignment explanation
Indices: 41488--41534 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
41478 AACGAGAAAA
* *
41488 TTGCGATAGCTATTTTCGCG
1 TTGCGATAGCCATTTTCACG
41508 TTGCGATAGCCATTTTCACG
1 TTGCGATAGCCATTTTCACG
41528 TTGCGAT
1 TTGCGAT
41535 TTCCCCGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCACG
Found at i:41780 original size:20 final size:20
Alignment explanation
Indices: 41757--41830 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
41747 ATTGCGATTT
*
41757 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
41777 TCAGAATCGAGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
41797 TCAAAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
41817 TCAGTATCGCGTTG
1 TCAGAATCGCGTTG
41831 TGATTTTGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:41867 original size:20 final size:20
Alignment explanation
Indices: 41768--41875 Score: 85
Period size: 20 Copynumber: 5.3 Consensus size: 20
41758 CAGAATCTCG
*
41768 TTGCGAAAGTCAGAATCG-A
1 TTGCGAAAGTCAGTATCGCA
** *
41787 GTTGCGAAAGTCAAAATCGCG
1 -TTGCGAAAGTCAGTATCGCA
*
41808 TTGCGAAAGTCAGTATCGCG
1 TTGCGAAAGTCAGTATCGCA
* ** *
41828 TTGTGATTTTGT-ATTATCGCA
1 TTGCGA--AAGTCAGTATCGCA
*
41849 TTGCGATAGTCAGTATCGCA
1 TTGCGAAAGTCAGTATCGCA
41869 TTGCGAA
1 TTGCGAA
41876 TTGGGAAAAT
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.04
20 54 0.76
21 12 0.17
22 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (20 bp):
TTGCGAAAGTCAGTATCGCA
Found at i:41888 original size:41 final size:41
Alignment explanation
Indices: 41768--41889 Score: 104
Period size: 41 Copynumber: 3.0 Consensus size: 41
41758 CAGAATCTCG
* * ** *
41768 TTGCGAAAGTCAGAATCG-AGTTGCGAA-AGTCAAAATCGCG
1 TTGCGAAAGTCAGTATCGCA-TTGCGAATTGGGAAAATCGCA
* * * * * **
41808 TTGCGAAAGTCAGTATCGCGTTGTGATTTTGTATTATCGCA
1 TTGCGAAAGTCAGTATCGCATTGCGAATTGGGAAAATCGCA
*
41849 TTGCGATAGTCAGTATCGCATTGCGAATTGGGAAAATCGCA
1 TTGCGAAAGTCAGTATCGCATTGCGAATTGGGAAAATCGCA
41890 ACGCGAAATT
Statistics
Matches: 61, Mismatches: 19, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
40 22 0.36
41 39 0.64
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (41 bp):
TTGCGAAAGTCAGTATCGCATTGCGAATTGGGAAAATCGCA
Found at i:41889 original size:21 final size:20
Alignment explanation
Indices: 41863--41916 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
41853 GATAGTCAGT
41863 ATCGCATTGCGAATTGGGAAA
1 ATCGCATTGCGAATT-GGAAA
** *
41884 ATCGCAACGCGAAATTGTAAA
1 ATCGCATTGCG-AATTGGAAA
41905 ATCGCATTGCGA
1 ATCGCATTGCGA
41917 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.81
22 4 0.15
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (20 bp):
ATCGCATTGCGAATTGGAAA
Found at i:41929 original size:20 final size:20
Alignment explanation
Indices: 41768--41936 Score: 60
Period size: 20 Copynumber: 8.3 Consensus size: 20
41758 CAGAATCTCG
* *
41768 TTGCGAAAGTCAGAATCG-A
1 TTGCGATAGTCATAATCGCA
* * *
41787 GTTGCGAAAGTCAAAATCGCG
1 -TTGCGATAGTCATAATCGCA
* *
41808 TTGCGAAAGTCAGT-ATCGCG
1 TTGCGATAGTCA-TAATCGCA
* * *
41828 TTGTGATTTTGT-ATTATCGCA
1 TTGCGA--TAGTCATAATCGCA
41849 TTGCGATAGTCAGT-ATCGCA
1 TTGCGATAGTCA-TAATCGCA
* ** *
41869 TTGCGAATTGGGAAAATCGCA
1 TTGCG-ATAGTCATAATCGCA
** * *
41890 ACGCGAAATTGT-AAAATCGCA
1 TTGCG--ATAGTCATAATCGCA
*
41911 TTGCGATAGTCATAATCGCG
1 TTGCGATAGTCATAATCGCA
41931 TTGCGA
1 TTGCGA
41937 ATCTGAAAAC
Statistics
Matches: 117, Mismatches: 21, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
19 7 0.06
20 66 0.56
21 37 0.32
22 7 0.06
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:44089 original size:30 final size:30
Alignment explanation
Indices: 44055--44117 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
44045 ATTCAAACTC
* *
44055 AAAAGATAATATTAAAAATCGAACTCAAAA
1 AAAAGATAATATTAAAAACCAAACTCAAAA
*
44085 AAAAGATAATATTAAAAGCCAAACTCAAAA
1 AAAAGATAATATTAAAAACCAAACTCAAAA
44115 AAA
1 AAA
44118 CTCGAATTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.65, C:0.11, G:0.06, T:0.17
Consensus pattern (30 bp):
AAAAGATAATATTAAAAACCAAACTCAAAA
Found at i:47067 original size:11 final size:11
Alignment explanation
Indices: 47051--47113 Score: 69
Period size: 11 Copynumber: 5.9 Consensus size: 11
47041 GTATTATAGA
47051 ATTTTTAATAT
1 ATTTTTAATAT
47062 ATTTTTAA-A-
1 ATTTTTAATAT
47071 ATTTTATAAT-T
1 ATTTT-TAATAT
***
47082 ATCAATAATAT
1 ATTTTTAATAT
47093 ATTTTTAATAT
1 ATTTTTAATAT
47104 ATTTTTAATA
1 ATTTTTAATA
47114 ATGTAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.19
11 29 0.69
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:47727 original size:38 final size:38
Alignment explanation
Indices: 47680--47753 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
47670 AAAATTTAGC
47680 GAAACCAAAATCAACCAGAACCAAAATTAACCTGAAGT
1 GAAACCAAAATCAACCAGAACCAAAATTAACCTGAAGT
* * * *
47718 GAAATCAAAATTAACCCGAACTAAAATTAACCTGAA
1 GAAACCAAAATCAACCAGAACCAAAATTAACCTGAA
47754 CAAAATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.53, C:0.22, G:0.09, T:0.16
Consensus pattern (38 bp):
GAAACCAAAATCAACCAGAACCAAAATTAACCTGAAGT
Found at i:47744 original size:22 final size:22
Alignment explanation
Indices: 47701--47744 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
47691 CAACCAGAAC
* * *
47701 CAAAATTAACCTGAAGTGAAAT
1 CAAAATTAACCCGAACTAAAAT
47723 CAAAATTAACCCGAACTAAAAT
1 CAAAATTAACCCGAACTAAAAT
47745 TAACCTGAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.20
Consensus pattern (22 bp):
CAAAATTAACCCGAACTAAAAT
Found at i:47760 original size:15 final size:15
Alignment explanation
Indices: 47723--47760 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
47713 GAAGTGAAAT
47723 CAAAATTAACCCGAA
1 CAAAATTAACCCGAA
*
47738 CTAAAATTAACCTGAA
1 C-AAAATTAACCCGAA
47754 CAAAATT
1 CAAAATT
47761 TTATCCGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.53, C:0.21, G:0.05, T:0.21
Consensus pattern (15 bp):
CAAAATTAACCCGAA
Found at i:47892 original size:18 final size:19
Alignment explanation
Indices: 47853--47908 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
47843 TAATAAACTA
*
47853 ATTTA-AATAAAATTGATA-
1 ATTTATAATAAAA-TAATAG
* *
47871 ATTTATTA-AAAATATTAG
1 ATTTATAATAAAATAATAG
47889 ATTTATAATAAAATAATAG
1 ATTTATAATAAAATAATAG
47908 A
1 A
47909 AAATTTAAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 3 0.10
18 16 0.53
19 11 0.37
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
ATTTATAATAAAATAATAG
Found at i:51265 original size:20 final size:21
Alignment explanation
Indices: 51240--51332 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
51230 TTTTCCCAAT
*
51240 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
51260 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
51281 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
51301 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
51322 TCGCAATGCGA
1 TCGCAATGCGA
51333 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:51347 original size:41 final size:41
Alignment explanation
Indices: 51240--51332 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
51230 TTTTCCCAAT
51240 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
51281 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
51322 TCGCAATGCGA
1 TCGCAATGCGA
51333 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:51411 original size:20 final size:20
Alignment explanation
Indices: 51363--51415 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
51353 TAATACAAAA
* *
51363 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
51383 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
51403 TCGCAACGCGATT
1 TCGCAACGCGATT
51416 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:51977 original size:19 final size:19
Alignment explanation
Indices: 51932--51979 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
51922 TTCGAGAATG
*
51932 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGCGGAAAC
*
51951 AACTATCGCAACGC-GAAACC
1 AA-AATCGCAACGCGGAAA-C
51971 AAAATCGCA
1 AAAATCGCA
51980 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGGAAAC
Found at i:51997 original size:19 final size:19
Alignment explanation
Indices: 51975--52159 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
51965 GAAACCAAAA
*
51975 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
51994 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
52013 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
52032 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
52052 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* ***
52068 T-G-GTCGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
*
52085 TCACGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
52099 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
52118 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
52138 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
52158 TC
1 TC
52160 AACCAAAAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 3 0.02
17 2 0.01
19 60 0.44
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:52052 original size:39 final size:38
Alignment explanation
Indices: 51975--52159 Score: 156
Period size: 33 Copynumber: 5.1 Consensus size: 38
51965 GAAACCAAAA
*
51975 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
52013 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * ***
52052 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGCCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * **
52085 TCACGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
52118 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
52158 TC
1 TC
52160 AACCAAAAGA
Statistics
Matches: 120, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
31 3 0.03
33 35 0.29
34 9 0.08
35 1 0.01
36 3 0.03
38 21 0.17
39 30 0.25
40 18 0.15
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:52136 original size:20 final size:20
Alignment explanation
Indices: 52102--52159 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
52092 GCGATTCTCT
**
52102 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
52122 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
52142 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
52160 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:54207 original size:42 final size:42
Alignment explanation
Indices: 54148--54270 Score: 131
Period size: 42 Copynumber: 2.9 Consensus size: 42
54138 GCCCGACTCG
* * *
54148 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
54190 CCTATCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
54232 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
54271 CCCGATTCAC
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 64 0.94
43 4 0.06
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:54225 original size:21 final size:21
Alignment explanation
Indices: 54201--54270 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
54191 CTATCATTCC
54201 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* * ** *
54222 TCAAGAGGCCACTGTCATCGT
1 TCAAGAGTCCCCTCCCACCGT
* *
54243 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTCCCACCGT
54264 TCAAGAG
1 TCAAGAG
54271 CCCGATTCAC
Statistics
Matches: 35, Mismatches: 13, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:55509 original size:13 final size:15
Alignment explanation
Indices: 55483--55519 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
55473 GATTGTTTAA
55483 TTGATTTGTAAAAAG
1 TTGATTTGTAAAAAG
55498 -TGATTTGT-AAAAG
1 TTGATTTGTAAAAAG
55511 TTGATTTGT
1 TTGATTTGT
55520 TTAATTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (15 bp):
TTGATTTGTAAAAAG
Found at i:55670 original size:19 final size:19
Alignment explanation
Indices: 55646--55704 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
55636 GAAATTAGCG
55646 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
55665 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
55679 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
55698 TTGCGAT
1 TTGCGAT
55705 AGTAATTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 5 0.16
16 7 0.23
17 7 0.23
19 12 0.39
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:55670 original size:33 final size:34
Alignment explanation
Indices: 55627--55703 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
55617 AAAAGTACTA
* *
55627 TCGCAATGCGAAAT-TAGCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCAATTTTCATT
* **
55660 TCGCATTGCG-ATTCTCTCGTTGCAATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCAATTTTCATT
55693 TCGCATTGCGA
1 TCGCATTGCGA
55704 TAGTAATTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (34 bp):
TCGCATTGCGAAATCTAGCGTTGCAATTTTCATT
Found at i:58217 original size:24 final size:24
Alignment explanation
Indices: 58183--58236 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
58173 CTGAAACATC
*
58183 ATCAAAATCCGTGTATTGACCAAT-
1 ATCAAAATCCGGGTATTGACC-ATG
*
58207 ATCAAAGTCCGGGTATTGACCATG
1 ATCAAAATCCGGGTATTGACCATG
58231 ATCAAA
1 ATCAAA
58237 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCATG
Found at i:60681 original size:23 final size:23
Alignment explanation
Indices: 60650--60699 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
60640 ATAGGTAAAA
*
60650 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
**
60673 ATATAATGTAATAGGTAGTTCTT
1 ATATAATGTAATAGGTAGCGCTT
60696 ATAT
1 ATAT
60700 TGTAAAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:61379 original size:391 final size:391
Alignment explanation
Indices: 60394--61448 Score: 1673
Period size: 391 Copynumber: 2.7 Consensus size: 391
60384 ATATTATTAT
60394 TAAATTAAAAACAAT-AA-ATATA-TACATATTTATTATTATCTTTGGTTAATATTGTTAAATTT
1 TAAATT-AAAACAATAAACATATATTACATA-TTATTATTATCTTTGGTTAATATTGTTAAATTT
*
60456 AAATTCTAAA-ATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTA
64 AAATTCGAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTA
* *
60520 TTAAATTAATATTGTAGATGGAAAACATGAAACACTATT-AAAAAAAATTGAAACATAAATTACA
129 TTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAATTGAAACATAAACTACA
* *
60584 TAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACAATTTCAATATAATAGGTAAA
194 TAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTAT-G--AA---C-A-CT--T---T---
*
60649 AATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTTCTTATATTGTAAAGTATCTAT
243 CA-AT-A--TAATAGGTAGCGCTTATATAATGTAATAGGTAGTTCTTATATTGTAAAGTATCTAT
60714 CCTTTTTATAAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTCTGAG
304 CCTTTTTATAAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTCTGAG
60779 TGAGTTTTAAGATATTAATTTAG
369 TGAGTTTTAAGATATTAATTTAG
60802 TAAATTAAAACAATAAACATATATTACATATTATTATTATCTTTGGTTAATATTGTTAAATTTAA
1 TAAATTAAAACAATAAACATATATTACATATTATTATTATCTTTGGTTAATATTGTTAAATTTAA
*
60867 ATTCGAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAACTTATT
66 ATTCGAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATT
60932 AAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAATTGAAACATAAACTACATA
131 AAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAATTGAAACATAAACTACATA
60997 ACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAGCGC
196 ACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAGCGC
*
61062 TTATATAATGTAATATGTAGTGT-TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCAT
261 TTATATAATGTAATAGGTAGT-TCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCAT
61126 ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTT-TGAGTGAGTTTTAAGATATTAATT
325 AC-TTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTCTGAGTGAGTTTTAAGATATTAATT
61190 TAG
389 TAG
61193 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1 TAAATT-AAAACAATAAAC--ATATATTACATA-TTATTATTATCTTTGGTTAATATTGTTAAAT
*
61258 TTAAATTC-TAA-ATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
62 TTAAATTCGAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
* *
61321 TATT-AATT-ATATTGTAGGTGGAAAACATGAAACACTATTAACAAAAAATTGAAACATAAATTA
127 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAATTGAAACATAAACTA
*
61384 CATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTA
192 CATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTA
61449 AAAATATGAT
Statistics
Matches: 623, Mismatches: 13, Indels: 39
0.92 0.02 0.06
Matches are distributed among these distances:
391 226 0.36
392 54 0.09
393 56 0.09
394 16 0.03
395 40 0.06
398 1 0.00
401 1 0.00
403 1 0.00
404 1 0.00
405 1 0.00
407 8 0.01
408 10 0.02
409 47 0.08
410 98 0.16
411 63 0.10
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.38
Consensus pattern (391 bp):
TAAATTAAAACAATAAACATATATTACATATTATTATTATCTTTGGTTAATATTGTTAAATTTAA
ATTCGAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATT
AAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAATTGAAACATAAACTACATA
ACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAGCGC
TTATATAATGTAATAGGTAGTTCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATA
CTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTCTGAGTGAGTTTTAAGATATTAATTTA
G
Found at i:61522 original size:23 final size:23
Alignment explanation
Indices: 61452--61524 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
61442 ATAGGTAAAA
* * *
61452 ATATGATGTAATATGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
*
61475 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
**
61498 ATATAATGTAATAGGTATTGCTT
1 ATATAATGTAATAGGTAGCGCTT
61521 ATAT
1 ATAT
61525 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:62047 original size:23 final size:23
Alignment explanation
Indices: 61993--62047 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
61983 ACTTATAAAA
*
61993 TATGTTAATATAAGCGCTACCTAT
1 TATGTT-ATATAAGCGCTACCTAG
**
62017 TACATTATATAAGCGCTACCTAG
1 TATGTTATATAAGCGCTACCTAG
62040 TATGTTAT
1 TATGTTAT
62048 TGTACTTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (23 bp):
TATGTTATATAAGCGCTACCTAG
Found at i:62616 original size:20 final size:20
Alignment explanation
Indices: 62591--62630 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
62581 CATTAAATGA
*
62591 TAAACGAACATAAACGAACG
1 TAAACGAACACAAACGAACG
62611 TAAACGAACACAAACGAACG
1 TAAACGAACACAAACGAACG
62631 AACATAAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.23, G:0.15, T:0.07
Consensus pattern (20 bp):
TAAACGAACACAAACGAACG
Found at i:62632 original size:14 final size:14
Alignment explanation
Indices: 62613--62643 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
62603 AACGAACGTA
62613 AACGAACACAAACG
1 AACGAACACAAACG
*
62627 AACGAACATAAACG
1 AACGAACACAAACG
62641 AAC
1 AAC
62644 ATAATAAATA
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:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:62647 original size:10 final size:10
Alignment explanation
Indices: 62590--62629 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
62580 TCATTAAATG
62590 ATAAACGAAC
1 ATAAACGAAC
62600 ATAAACGAAC
1 ATAAACGAAC
*
62610 GTAAACGAAC
1 ATAAACGAAC
*
62620 ACAAACGAAC
1 ATAAACGAAC
62630 GAACATAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:62944 original size:10 final size:10
Alignment explanation
Indices: 62929--62953 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
62919 ACTTGCTCTC
62929 TGAACATAAA
1 TGAACATAAA
62939 TGAACATAAA
1 TGAACATAAA
62949 TGAAC
1 TGAAC
62954 GAACATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (10 bp):
TGAACATAAA
Found at i:75078 original size:36 final size:36
Alignment explanation
Indices: 75031--75169 Score: 260
Period size: 36 Copynumber: 3.9 Consensus size: 36
75021 ACGGTGCTGG
75031 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
75067 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
75103 ACATTGATACACGAATATACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
75139 ACATTGATACACGAATGTATCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
75170 ATACTCAACT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 100 1.00
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:79761 original size:36 final size:36
Alignment explanation
Indices: 79643--79781 Score: 194
Period size: 36 Copynumber: 3.9 Consensus size: 36
79633 GAACAAAAGA
*
79643 AAGCATC-GCACTT-CGATTCAAATAGAACGGAAGG
1 AAGCATCGGCACTTCCGATTCAAATCGAACGGAAGG
* * * *
79677 AGGCATCGGCACTTCCGATTCAAATTGAA-TGAAGT
1 AAGCATCGGCACTTCCGATTCAAATCGAACGGAAGG
*
79712 AGGCATCGGCACTTCCGATTCAAATCGAACGGAAGG
1 AAGCATCGGCACTTCCGATTCAAATCGAACGGAAGG
*
79748 AAGCATCGGCACTTCCGATTCTAATCGAACGGAA
1 AAGCATCGGCACTTCCGATTCAAATCGAACGGAA
79782 AGATGTCGCA
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
34 6 0.06
35 38 0.41
36 49 0.53
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (36 bp):
AAGCATCGGCACTTCCGATTCAAATCGAACGGAAGG
Found at i:82327 original size:15 final size:15
Alignment explanation
Indices: 82304--82333 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
82294 TTACCCGATG
82304 TTTTCAACCTGACCT
1 TTTTCAACCTGACCT
*
82319 TTTTTAACCTGACCT
1 TTTTCAACCTGACCT
82334 AAAATTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.30, G:0.07, T:0.43
Consensus pattern (15 bp):
TTTTCAACCTGACCT
Found at i:82566 original size:14 final size:13
Alignment explanation
Indices: 82517--82592 Score: 66
Period size: 13 Copynumber: 5.7 Consensus size: 13
82507 AATTACATTA
82517 AAAATATATATTATAT
1 AAAAT-TAT-TTA-AT
82533 AAAATTATTTAAT
1 AAAATTATTTAAT
82546 AAAATTATTTAAT
1 AAAATTATTTAAT
* *
82559 GCAAATTATATAA-
1 -AAAATTATTTAAT
*
82572 AACATTA-TTAAT
1 AAAATTATTTAAT
*
82584 AATATTATT
1 AAAATTATT
82593 GCATTGAACA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
11 3 0.06
12 11 0.22
13 16 0.31
14 13 0.25
15 3 0.06
16 5 0.10
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (13 bp):
AAAATTATTTAAT
Found at i:83339 original size:20 final size:18
Alignment explanation
Indices: 83301--83339 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
83291 TGATTTTAAA
*
83301 AAATTAATTCTGTAAAAT
1 AAATTAATTCTGAAAAAT
83319 AAATTATATTCTTGAAAAAT
1 AAATTA-ATTC-TGAAAAAT
83339 A
1 A
83340 TTTTCTAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (18 bp):
AAATTAATTCTGAAAAAT
Found at i:83451 original size:16 final size:16
Alignment explanation
Indices: 83432--83468 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
83422 TTAATGTTAC
*
83432 CTATAATTTATGTAAA
1 CTATAATTTATATAAA
*
83448 CTATTATTTATATAAA
1 CTATAATTTATATAAA
83464 CTATA
1 CTATA
83469 TGAATTTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (16 bp):
CTATAATTTATATAAA
Found at i:83603 original size:2 final size:2
Alignment explanation
Indices: 83598--83684 Score: 85
Period size: 2 Copynumber: 45.0 Consensus size: 2
83588 TTTATATAGT
83598 TA TA TA TA TA -A TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
83638 TA TA TA TT TA TG TA T- TA TG T- TA TA TA TA GTT TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
83678 CTA TA TA
1 -TA TA TA
83685 GTTTATTCAT
Statistics
Matches: 71, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
1 5 0.07
2 63 0.89
3 3 0.04
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:83926 original size:14 final size:14
Alignment explanation
Indices: 83862--83926 Score: 69
Period size: 14 Copynumber: 4.7 Consensus size: 14
83852 TAGTTTATAG
83862 TTTAGGGTTTA-GA
1 TTTAGGGTTTATGA
*
83875 TTTAGGGTTCATGA
1 TTTAGGGTTTATGA
* * *
83889 TCTAGGGTTTAGGT
1 TTTAGGGTTTATGA
**
83903 TTTATAGTTTATGA
1 TTTAGGGTTTATGA
83917 TTTAGGGTTT
1 TTTAGGGTTT
83927 TTATAAACTA
Statistics
Matches: 39, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
13 10 0.26
14 29 0.74
ACGTcount: A:0.20, C:0.03, G:0.28, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTATGA
Found at i:83986 original size:47 final size:50
Alignment explanation
Indices: 83905--84010 Score: 114
Period size: 45 Copynumber: 2.1 Consensus size: 50
83895 GTTTAGGTTT
* *
83905 TATAGTTTATGATTTAGGGTTTTTATAAACTATATA-CT-T-ATTATTTA
1 TATAGTTTATGATATAGGGTTTCTATAAACTATATATCTATAATTATTTA
*
83952 TATAGTTT-TG-TATAGTGTTTCTATAAACTATATATATCTATAGATTATTTA
1 TATAGTTTATGATATAGGGTTTCTATAAAC--TATATATCTATA-ATTATTTA
84003 TATCAGTT
1 TAT-AGTT
84011 ATACATACAT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
45 15 0.31
46 2 0.04
47 14 0.29
48 2 0.04
49 1 0.02
51 11 0.22
52 4 0.08
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (50 bp):
TATAGTTTATGATATAGGGTTTCTATAAACTATATATCTATAATTATTTA
Found at i:83987 original size:2 final size:2
Alignment explanation
Indices: 83980--84099 Score: 53
Period size: 2 Copynumber: 63.0 Consensus size: 2
83970 TTCTATAAAC
* * * * *
83980 TA TA TA TA TC TA TA GA T- TA TT TA TA TCA GT- TA TA CA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A -TA TA TA TA TA TA TA
* * *
84022 TA TA TA CTA TA T- TA -A TA TA -A TT TA TA -A TT TA TA AA CTA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
84062 TA TA TG TA TA TA TA TA TA TA TA T- TA T- TA -A TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
84100 GTTTATCATT
Statistics
Matches: 86, Mismatches: 18, Indels: 28
0.65 0.14 0.21
Matches are distributed among these distances:
1 10 0.12
2 71 0.83
3 4 0.05
4 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:84110 original size:21 final size:21
Alignment explanation
Indices: 84069--84110 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
84059 ATATATATGT
*
84069 ATATATATATATATATTATTA
1 ATATATATATATATATCATTA
*
84090 ATATAT-TATAGTTTATCATTA
1 ATATATATATA-TATATCATTA
84111 TACTTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
ATATATATATATATATCATTA
Found at i:84221 original size:18 final size:19
Alignment explanation
Indices: 84188--84223 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
84178 TATATAGCTT
*
84188 ATATAATTATTAGTTTATA
1 ATATAAATATTAGTTTATA
84207 ATATAAATA-TAGTTTAT
1 ATATAAATATTAGTTTAT
84224 TATTTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (19 bp):
ATATAAATATTAGTTTATA
Found at i:84230 original size:26 final size:24
Alignment explanation
Indices: 84194--84241 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
84184 GCTTATATAA
84194 TTATTAGTTTATAATATAAATATAGT
1 TTATTAGTTTAT-ATA-AAATATAGT
*
84220 TTATTATTTTATATAAAATATA
1 TTATTAGTTTATATAAAATATA
84242 TATAGTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 3 0.14
26 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
TTATTAGTTTATATAAAATATAGT
Found at i:84250 original size:24 final size:26
Alignment explanation
Indices: 84195--84250 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 26
84185 CTTATATAAT
* *
84195 TATTAGTTTATAATATAAATATAGTT
1 TATTATTTTATAATATAAATATAGTA
84221 TATTATTTTAT-ATA-AAATATA-TA
1 TATTATTTTATAATATAAATATAGTA
84244 TAGTTAT
1 TA-TTAT
84251 ATATAAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 3 0.11
24 11 0.41
25 3 0.11
26 10 0.37
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (26 bp):
TATTATTTTATAATATAAATATAGTA
Found at i:85828 original size:2 final size:2
Alignment explanation
Indices: 85821--85855 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
85811 ACAATTTATC
85821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
85856 TGACAAATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:100160 original size:49 final size:49
Alignment explanation
Indices: 100107--100207 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
100097 ATATCCAAAG
100107 ACTCAGCTTTAATAATAATTTTATAATCCGACCGATTTAACAATCGATA
1 ACTCAGCTTTAATAATAATTTTATAATCCGACCGATTTAACAATCGATA
100156 ACTCAGCTTTAATAATAATTTTATAATCCGACCGATTTAACAATCGATA
1 ACTCAGCTTTAATAATAATTTTATAATCCGACCGATTTAACAATCGATA
100205 ACT
1 ACT
100208 AATTAACTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.35
Consensus pattern (49 bp):
ACTCAGCTTTAATAATAATTTTATAATCCGACCGATTTAACAATCGATA
Found at i:102850 original size:102 final size:100
Alignment explanation
Indices: 102676--102877 Score: 386
Period size: 102 Copynumber: 2.0 Consensus size: 100
102666 AGCACGAATC
102676 ATGTGCTTTCATCCTGAACATAACAAATTTGCATAAAACTCAAAGTAAACTGAATTATCTTGAGT
1 ATGTGCTTTCATCCTGAACATAACAAATTTGCATAAAACTCAAAGTAAACTGAATTATCTTGAGT
102741 AAACTTTGAAACTGAGAAAAGATTCTTATTTATGT
66 AAACTTTGAAACTGAGAAAAGATTCTTATTTATGT
102776 ATGTGCTTTCATCCTGAACATAACAAACATTTGCATAAAACTCAAAGTAAACTGAATTATCTTGA
1 ATGTGCTTTCATCCTGAACATAAC-AA-ATTTGCATAAAACTCAAAGTAAACTGAATTATCTTGA
102841 GTAAACTTTGAAACTGAGAAAAGATTCTTATTTATGT
64 GTAAACTTTGAAACTGAGAAAAGATTCTTATTTATGT
102878 TTGGAACATA
Statistics
Matches: 100, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
100 24 0.24
101 2 0.02
102 74 0.74
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (100 bp):
ATGTGCTTTCATCCTGAACATAACAAATTTGCATAAAACTCAAAGTAAACTGAATTATCTTGAGT
AAACTTTGAAACTGAGAAAAGATTCTTATTTATGT
Found at i:103086 original size:110 final size:105
Alignment explanation
Indices: 102878--103092 Score: 369
Period size: 110 Copynumber: 2.0 Consensus size: 105
102868 TTATTTATGT
102878 TTGGAACATATAGCGTATGATCAAGAAAAAGGTCTCGAAGAAGTTTGAAAACATTTCGACCATAG
1 TTGGAACATATAGCGTATGATCAAGAAAAAGGTCTCGAAGAAGTTTGAAAACATTTCGACCATAG
102943 AGTAATACAACAGTGGAACCATCCCCTAAATGAACTTTAC
66 AGTAATACAACAGTGGAACCATCCCCTAAATGAACTTTAC
102983 TTGGAACATATAGCGTATGATCAAG-AAAAGGTCTCTAGAAGAAGTTTGAAAAACATTTCGACCA
1 TTGGAACATATAGCGTATGATCAAGAAAAAGGTCTC--GAAGAAGTTTG-AAAACATTTCGACC-
103047 ATATGAGTAATTACAACAGTGGAACCATCCCCTAAATGAACTTTAC
62 ATA-GAGTAA-TACAACAGTGGAACCATCCCCTAAATGAACTTTAC
103093 CACTACCAGT
Statistics
Matches: 104, Mismatches: 0, Indels: 7
0.94 0.00 0.06
Matches are distributed among these distances:
104 10 0.10
105 25 0.24
106 11 0.11
107 14 0.13
108 3 0.03
109 6 0.06
110 35 0.34
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (105 bp):
TTGGAACATATAGCGTATGATCAAGAAAAAGGTCTCGAAGAAGTTTGAAAACATTTCGACCATAG
AGTAATACAACAGTGGAACCATCCCCTAAATGAACTTTAC
Found at i:103527 original size:37 final size:37
Alignment explanation
Indices: 103474--103578 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
103464 CCTTTTCGTC
* *
103474 CTACTAGGATTCAAACTCATAAAAATAGGATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
103511 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
103548 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
103579 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:104183 original size:11 final size:11
Alignment explanation
Indices: 104144--104199 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
104134 CTTTGCATTT
104144 TTATTATTACTA
1 TTATT-TTACTA
*
104156 TTATATTTATTA
1 TTAT-TTTACTA
104168 TTATTTTACTA
1 TTATTTTACTA
* *
104179 TTATTTTCCTT
1 TTATTTTACTA
*
104190 TTATTCTACT
1 TTATTTTACT
104200 TATTTATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
11 23 0.62
12 13 0.35
13 1 0.03
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATTTTACTA
Found at i:104879 original size:11 final size:11
Alignment explanation
Indices: 104811--104880 Score: 56
Period size: 11 Copynumber: 6.3 Consensus size: 11
104801 TACTTTGTTA
*
104811 TTATTATTTTG
1 TTATTATTTTT
104822 TTATTATTTTAT
1 TTATTATTTT-T
104834 TTATT-TTCTTT
1 TTATTATT-TTT
*
104845 TTCTT-TTTCTT
1 TTATTATTT-TT
*
104856 TT-TTATATATT
1 TTATTAT-TTTT
104867 TTATTATTTTT
1 TTATTATTTTT
104878 TTA
1 TTA
104881 CTTACTATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
10 3 0.06
11 34 0.69
12 12 0.24
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.77
Consensus pattern (11 bp):
TTATTATTTTT
Found at i:104893 original size:20 final size:19
Alignment explanation
Indices: 104870--104928 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 19
104860 ATATATTTTA
104870 TTATTTTTTTACTTACTATT
1 TTATTTTTTTACTTAC-ATT
*
104890 TTATCTTTGTTTTCTT-CATT
1 TTAT-TTT-TTTACTTACATT
**
104910 TTATCATTTTACTTA-ATT
1 TTATTTTTTTACTTACATT
104928 T
1 T
104929 GTTTTCTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 10 0.31
19 1 0.03
20 11 0.34
21 4 0.12
22 6 0.19
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.68
Consensus pattern (19 bp):
TTATTTTTTTACTTACATT
Found at i:104902 original size:23 final size:22
Alignment explanation
Indices: 104863--104914 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
104853 CTTTTTTATA
*
104863 TATTTTAT-TATTTTTTTACTTAC
1 TATTTTATCTATTGTTTT-CTT-C
104886 TATTTTATCT-TTGTTTTCTTC
1 TATTTTATCTATTGTTTTCTTC
104907 -ATTTTATC
1 TATTTTATC
104915 ATTTTACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 8 0.30
21 1 0.04
22 3 0.11
23 14 0.52
24 1 0.04
ACGTcount: A:0.17, C:0.12, G:0.02, T:0.69
Consensus pattern (22 bp):
TATTTTATCTATTGTTTTCTTC
Found at i:106057 original size:20 final size:21
Alignment explanation
Indices: 106024--106063 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
106014 ACCTTACTAA
106024 CTCTTTTCATTTTTTTTTCCT
1 CTCTTTTCATTTTTTTTTCCT
106045 CTCTTTT-ATTTTTTTTTCC
1 CTCTTTTCATTTTTTTTTCC
106064 ATCATCTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (21 bp):
CTCTTTTCATTTTTTTTTCCT
Found at i:108011 original size:44 final size:44
Alignment explanation
Indices: 107943--108030 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
107933 AAACATAAGA
107943 CTTGTCAACCTGCTGGAAGCTGTTCGGGGTCTAGAGGATTTAGT
1 CTTGTCAACCTGCTGGAAGCTGTTCGGGGTCTAGAGGATTTAGT
* *
107987 CTTGTCAACCTGCTGGAAGTTGTTCGGGGTCTTGAGGATTTAGT
1 CTTGTCAACCTGCTGGAAGCTGTTCGGGGTCTAGAGGATTTAGT
108031 TTGAATGTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.17, C:0.17, G:0.32, T:0.34
Consensus pattern (44 bp):
CTTGTCAACCTGCTGGAAGCTGTTCGGGGTCTAGAGGATTTAGT
Found at i:109381 original size:10 final size:10
Alignment explanation
Indices: 109368--109398 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
109358 GGAAAAAAAG
109368 AAAAGAAGAA
1 AAAAGAAGAA
109378 AAAAGAAGAA
1 AAAAGAAGAA
*
109388 AAAAAAAGAA
1 AAAAGAAGAA
109398 A
1 A
109399 GAACAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAGAAGAA
Found at i:109386 original size:13 final size:14
Alignment explanation
Indices: 109360--109420 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 14
109350 ACAAAAAGGG
109360 AAAAAAAGAAAAGAA
1 AAAAAAAG-AAAGAA
*
109375 GAAAAAAG-AAGAA
1 AAAAAAAGAAAGAA
109388 AAAAAAAGAAAGAA
1 AAAAAAAGAAAGAA
109402 CAAAAATCAA-AAAGAA
1 -AAAAA--AAGAAAGAA
109418 AAA
1 AAA
109421 GGGATAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
13 12 0.30
14 5 0.12
15 15 0.38
16 6 0.15
17 2 0.05
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.02
Consensus pattern (14 bp):
AAAAAAAGAAAGAA
Found at i:109396 original size:20 final size:19
Alignment explanation
Indices: 109362--109420 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
109352 AAAAAGGGAA
*
109362 AAAAAGAAAAGAAGAAAAAAG
1 AAAAA-AAAA-AAGAAAAAAC
*
109383 AAGAAAAAAAAAGAAAGAAC
1 AA-AAAAAAAAAGAAAAAAC
*
109403 AAAAATCAAAAAGAAAAA
1 AAAAA-AAAAAAGAAAAA
109421 GGGATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 3 0.09
20 20 0.62
21 6 0.19
22 3 0.09
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAAGAAAAAAC
Found at i:109419 original size:27 final size:28
Alignment explanation
Indices: 109360--109421 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
109350 ACAAAAAGGG
* *
109360 AAAAAAAGAAAAGAAGAAAAAAGAAGAA
1 AAAAAAAGAAAAGAACAAAAAACAAGAA
*
109388 AAAAAAAG-AAAGAACAAAAATCAA-AA
1 AAAAAAAGAAAAGAACAAAAAACAAGAA
*
109414 AGAAAAAG
1 AAAAAAAG
109422 GGATAAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 9 0.30
27 13 0.43
28 8 0.27
ACGTcount: A:0.81, C:0.03, G:0.15, T:0.02
Consensus pattern (28 bp):
AAAAAAAGAAAAGAACAAAAAACAAGAA
Found at i:111087 original size:106 final size:106
Alignment explanation
Indices: 110874--112352 Score: 2111
Period size: 106 Copynumber: 14.0 Consensus size: 106
110864 ATATCGTGCC
* * * * * * *
110874 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGACAAC-AACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
110938 AATTTCGGAGCCAATTTCAACTTCACAGGGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
110979 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
111044 AATTTTAGAACCAATTTCAACTTCACAGCGAGGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
111085 ACTCCAGATAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGTCAATAAACAACTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
111150 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
111191 ACTCCAAACAACGCAAGTTCAACTTCACAATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
111256 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
111297 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
111362 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
111403 ACTCCAGACAACGCAAGTTCAACTTAACAACTAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
111468 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
111509 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
111574 AATTTCAAAGCCAATTTTAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
111615 ACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGA-CGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
111679 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
111720 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
111785 AATTTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
111826 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
111891 AATTTTAGAGCCACTTTCAACTTCACAACG-AGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
111931 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** *
111996 AATTTCAGAGCCAATTTCAACTTCACAATGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** *
112037 ACTCAAGACAACGCAAGTTCAACTTCAAAACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
112102 AATTTCAAAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
112143 AC-CCAAGACAACACAAGCTCAAGTTCACGACGAAAGGG--CGACTGATTGTTAAC-AA-AA-TT
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACG-AAGGGACCG-CTGGTTGTCAACAAACAACTT
* *
112202 -TC--TTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
63 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * * * * *
112243 ACTCAAGACAATACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAGCAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** * *
112308 GGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
112349 ACTC
1 ACTC
112353 GGAACAATGC
Statistics
Matches: 1239, Mismatches: 119, Indels: 31
0.89 0.09 0.02
Matches are distributed among these distances:
99 4 0.00
100 69 0.06
101 4 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 247 0.20
106 900 0.73
107 5 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:111824 original size:317 final size:317
Alignment explanation
Indices: 110874--112352 Score: 2192
Period size: 317 Copynumber: 4.7 Consensus size: 317
110864 ATATCGTGCC
* * * * * *
110874 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGACAAC-AACAA-TTTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCT-
* ** *
110937 CAATTTCGGAGCCAATTTCAACTTCACAGGGAAGGATATTGGACTCCAGACAATGCAAGTTCAAC
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* *
111002 TTCACGACGAAGGGACGGCTGGTTGTCAATAAACAATTTCCCAATTTTAGAACCAATTTCAACTT
130 TTCACGACGAAGGGAC-GCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTT
* * * **
111067 CACAGCGAGGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTT
194 CACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTT
*
111132 GTCAATAAACAACTTTCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
259 GTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
111191 ACTCCAAACAACGCAAGTTCAACTTCACAATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
111256 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
111321 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGA-CGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
* * *
111386 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTAACAACTAAGGGACCGCTGGTTG
195 ACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTG
* * *
111451 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
260 TCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
111509 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* * * *
111574 AATTTCAAAGCCAATTTTAACTTCACAACAAAGGATATTGGACTCCAGATAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
111639 TCACGACGAAGGGACGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
131 TCACGACGAAGGGACGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
* *
111704 CAGTGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
196 CAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGT
*
111769 CAATAAACAACTTCCCAATTTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTGG
261 CAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
111826 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
111891 AATTTTAGAGCCACTTTCAACTTCACAACG-AGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
111955 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGA-CGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
** * *
112020 ACAATGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCAAAACGAAGGGACCGCTGGTTG
195 ACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTG
* * *
112085 TCAATAAACAACTTCCCAATTTCAAAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
260 TCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
112143 AC-CCAAGACAACACAAGCTCAAGTTCACGACGAAAGGG--CGACTGATTGTTAAC-AA-AA-TT
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACG-AAGGGACCG-CTGGTTGTCAACAAACAACTT
* * * **
112202 -TC--TTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAATACAAGTTCA
63 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCA
* * ** ** *
112264 ACTTCACAACGAATGGACGGCTGGTTGTCAGCAAACAATTTCCCGGTTCCAGAGCCAATTTCAAC
128 ACTTCACGACGAAGGGAC-GCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAAC
*
112329 TTCAC-GACGGAGGATATTGGACTC
192 TTCACAG-CGAAGGATATTGGACTC
112353 GGAACAATGC
Statistics
Matches: 1069, Mismatches: 83, Indels: 25
0.91 0.07 0.02
Matches are distributed among these distances:
311 25 0.02
312 104 0.10
313 2 0.00
314 2 0.00
315 2 0.00
316 53 0.05
317 496 0.46
318 381 0.36
319 4 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (317 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGGGACGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
CAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGT
CAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:113104 original size:37 final size:37
Alignment explanation
Indices: 113041--113144 Score: 122
Period size: 37 Copynumber: 2.8 Consensus size: 37
113031 CCTTTTCGTC
113041 CTACTAGGATTAAAAACT-C-AAAAATAGGATAGAATT
1 CTACTAGGATT-AAAACTCCTAAAAATAGGATAGAATT
* * * *
113077 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTAAAACTCCTAAAAATAGGATAGAATT
* * *
113114 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTAAAACTCCTAAAAATAGGAT
113145 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
35 5 0.09
36 10 0.18
37 42 0.74
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTAAAACTCCTAAAAATAGGATAGAATT
Found at i:113789 original size:26 final size:26
Alignment explanation
Indices: 113742--113794 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
113732 CCTTTTCTAC
*
113742 TTATTTTTATTATATATGTATATTTT
1 TTATTTTTATTATATATATATATTTT
113768 TTATATTTTATTAT-TATATATATTTT
1 TTAT-TTTTATTATATATATATATTTT
113794 T
1 T
113795 ACTTTCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (26 bp):
TTATTTTTATTATATATATATATTTT
Found at i:113859 original size:2 final size:2
Alignment explanation
Indices: 113852--113876 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
113842 TATTATTTGT
113852 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
113877 GCGTATGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:117391 original size:2 final size:2
Alignment explanation
Indices: 117384--117409 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
117374 ACAAGTAACC
117384 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
117410 CAAATAGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118035 original size:16 final size:16
Alignment explanation
Indices: 118014--118047 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
118004 ATGAACAATA
118014 TTTCGGTGGTGTTAAT
1 TTTCGGTGGTGTTAAT
*
118030 TTTCGGTGGTGTTTAT
1 TTTCGGTGGTGTTAAT
118046 TT
1 TT
118048 ATGAATTACA
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:0.09, C:0.06, G:0.29, T:0.56
Consensus pattern (16 bp):
TTTCGGTGGTGTTAAT
Found at i:121883 original size:2 final size:2
Alignment explanation
Indices: 121876--121908 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
121866 TAATCAGATA
121876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
121909 CAAATAGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:123732 original size:16 final size:17
Alignment explanation
Indices: 123713--123744 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
123703 TGAAAAACAT
123713 AAAA-TTTGACTTTTTA
1 AAAATTTTGACTTTTTA
123729 AAAATTTTGACTTTTT
1 AAAATTTTGACTTTTT
123745 GGTCAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
AAAATTTTGACTTTTTA
Found at i:126424 original size:15 final size:15
Alignment explanation
Indices: 126404--126441 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
126394 ATATTTAGCT
*
126404 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
126419 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
126434 GGGCGGGC
1 GGGCGGGC
126442 ATTATCCGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.18, G:0.68, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:128084 original size:18 final size:18
Alignment explanation
Indices: 128061--128124 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
128051 TACTTCTATT
*
128061 TATATTTAGTATATAATA
1 TATATTTATTATATAATA
*
128079 TATATTTATTATTAAAATA
1 TATATTTATTA-TATAATA
*
128098 TATATTT-TTATATTAT-
1 TATATTTATTATATAATA
128114 TATATTTATTA
1 TATATTTATTA
128125 GGTATCATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 7 0.17
17 7 0.17
18 13 0.32
19 13 0.32
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TATATTTATTATATAATA
Found at i:128250 original size:2 final size:2
Alignment explanation
Indices: 128243--128281 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
128233 CTTTCTTCAT
128243 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
128282 TCTATTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:128465 original size:14 final size:15
Alignment explanation
Indices: 128435--128477 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
128425 TTTACTTATT
128435 TTATTTATCTCTATTTA
1 TTATTT-TCTCT-TTTA
128452 TTATTTT-TCTTTTA
1 TTATTTTCTCTTTTA
128466 -TATTTTCTCTTT
1 TTATTTTCTCTTT
128478 GATTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.24
14 9 0.36
15 3 0.12
16 1 0.04
17 6 0.24
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATTTTCTCTTTTA
Found at i:130273 original size:30 final size:31
Alignment explanation
Indices: 130224--130347 Score: 216
Period size: 31 Copynumber: 4.0 Consensus size: 31
130214 CCCGAAGGAC
*
130224 CAGTCCATA-GATCCCGAAGAACTTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
130255 CAGTCCATATGT-CCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
130285 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
130316 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
130347 C
1 C
130348 CCTCGACCCT
Statistics
Matches: 90, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
30 29 0.32
31 60 0.67
32 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:130319 original size:61 final size:62
Alignment explanation
Indices: 130224--130347 Score: 216
Period size: 61 Copynumber: 2.0 Consensus size: 62
130214 CCCGAAGGAC
*
130224 CAGTCCATAGATCCCGAAGAACTTAGGTAAACAGTCCATATGT-CCGAAGAACATAGGTAAA
1 CAGTCCATAGATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
130285 CAGTCCATATG-TCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
130347 C
1 C
130348 CCTCGACCCT
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
61 40 0.67
62 20 0.33
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (62 bp):
CAGTCCATAGATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:131138 original size:64 final size:64
Alignment explanation
Indices: 131005--131161 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 64
130995 CAATGAATGT
* ** *
131005 ATGCATCGATGCACTA-TTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCACTACTT-ATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAAAGAG
* * *
131069 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATG-TTGTATTATTAAAGAG
* *
131132 AGTGCATCGATGCACTTCTTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
131162 ACACCTTCAA
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
63 2 0.02
64 71 0.88
65 8 0.10
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAAAGAG
Found at i:132740 original size:18 final size:19
Alignment explanation
Indices: 132708--132743 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
132698 CAGTTTTGAC
132708 CCGACCCGTTTGACCCGAT
1 CCGACCCGTTTGACCCGAT
132727 CCGACCCG-TTGACCCGA
1 CCGACCCGTTTGACCCGA
132744 CCCGTTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.17, C:0.44, G:0.22, T:0.17
Consensus pattern (19 bp):
CCGACCCGTTTGACCCGAT
Found at i:135455 original size:43 final size:43
Alignment explanation
Indices: 135364--135697 Score: 436
Period size: 43 Copynumber: 7.7 Consensus size: 43
135354 GTATTTCAGC
* * * * * * *
135364 TCCTCTGCTATGTGCAAGAGTAAGTCCTTACCGTTAT-CGCATGC
1 TCCTTTGCTGTGTGCAAGGGTAAG-CCTTACAGTT-TCCCCAGGT
*
135408 TCCTTTGCTGTGTGCAAGGGTCAGCCTTACAGTTTCCCCAGGT
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
*
135451 TCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
* *
135494 TCATTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGT
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
*
135537 TCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
* *
135580 TCCTTTGCTGTGTACAAGGGTAAGCCTTACAGTTTCCCCATGT
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
* * *
135623 TCCTTTGCTGTGTGCAAGGGTAAGACCTTATAGTTTCCCCATGC
1 TCCTTTGCTGTGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGGT
* * * *
135667 TCTTTTTCTATGTGGAAGGGTAAGACCTTAC
1 TCCTTTGCTGTGTGCAAGGGTAAG-CCTTAC
135698 CGATTTTGCA
Statistics
Matches: 261, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
42 1 0.00
43 197 0.75
44 63 0.24
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.34
Consensus pattern (43 bp):
TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
Found at i:136674 original size:19 final size:19
Alignment explanation
Indices: 136648--136690 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
136638 ACATTTTATC
*
136648 TAATTTTTAATATAAATGTT
1 TAATTTTCAATATAAAT-TT
136668 TAATTTTCAATATAAATTT
1 TAATTTTCAATATAAATTT
136687 TAAT
1 TAAT
136691 AAGATTTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TAATTTTCAATATAAATTT
Found at i:141637 original size:35 final size:35
Alignment explanation
Indices: 141579--141647 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
141569 GGCAACCAAC
141579 TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTTT
1 TTTGAAAAATGATTTTCAAAGTTTGGTAAA-GTTTT
141615 TTTGAAAAATG-TTTTCAAAGTTTGGTAAAGTTT
1 TTTGAAAAATGATTTTCAAAGTTTGGTAAAGTTT
141648 GATAAATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 4 0.12
35 18 0.55
36 11 0.33
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.46
Consensus pattern (35 bp):
TTTGAAAAATGATTTTCAAAGTTTGGTAAAGTTTT
Found at i:146551 original size:14 final size:14
Alignment explanation
Indices: 146532--146564 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
146522 ATAAGATACA
146532 CCAAATTTAAGCAC
1 CCAAATTTAAGCAC
*
146546 CCAAATTTAAGCAG
1 CCAAATTTAAGCAC
146560 CCAAA
1 CCAAA
146565 ATTCAATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.27, G:0.09, T:0.18
Consensus pattern (14 bp):
CCAAATTTAAGCAC
Found at i:147735 original size:13 final size:13
Alignment explanation
Indices: 147714--147752 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
147704 GTCATAAATC
147714 TATGACGCGCATT
1 TATGACGCGCATT
*
147727 TATGGCGCGCATT
1 TATGACGCGCATT
*
147740 TATGACGTGCATT
1 TATGACGCGCATT
147753 GCACGTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.33
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:147821 original size:96 final size:97
Alignment explanation
Indices: 147685--147899 Score: 238
Period size: 96 Copynumber: 2.2 Consensus size: 97
147675 CATAAATCTC
* * * * * * *
147685 AGATGACACACAATTGTGTGTCATAAATCTATGACGCGCATTTATGGCGCGCATTTATGACGTGC
1 AGATGACACACATTTGTGTGTCACAAATCTATGACACGCATTTATGACGCACATTTACGACGTAC
** *
147750 ATTGCACGTCATTAAAGCCCCCGTCA-TAAATGA
66 ATTGCACGTCATTAAAGAACACGTCATTAAA--A
* ** *
147783 AGATGACACACATTTGTGTG-C-CAAATTTATGACACGCATTTATGACTTACATTTACGACTTAC
1 AGATGACACACATTTGTGTGTCACAAATCTATGACACGCATTTATGACGCACATTTACGACGTAC
* *
147846 ATTGCATGTCATTGAAGAACACGTCATTAAAA
66 ATTGCACGTCATTAAAGAACACGTCATTAAAA
*
147878 AGATGACACACATTCGTGTGTC
1 AGATGACACACATTTGTGTGTC
147900 GTGATTGTAT
Statistics
Matches: 98, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
95 20 0.20
96 54 0.55
97 5 0.05
98 19 0.19
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (97 bp):
AGATGACACACATTTGTGTGTCACAAATCTATGACACGCATTTATGACGCACATTTACGACGTAC
ATTGCACGTCATTAAAGAACACGTCATTAAAA
Found at i:147835 original size:13 final size:13
Alignment explanation
Indices: 147819--147848 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
147809 TTATGACACG
*
147819 CATTTATGACTTA
1 CATTTACGACTTA
147832 CATTTACGACTTA
1 CATTTACGACTTA
147845 CATT
1 CATT
147849 GCATGTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (13 bp):
CATTTACGACTTA
Done.