Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008458.1 Hibiscus syriacus cultivar Beakdansim tig00111271_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: 111851
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4973 original size:20 final size:21
Alignment explanation
Indices: 4948--5000 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
4938 GTGAGTTTTG
4948 GATCGATCCTTTG-CAAAAAC
1 GATCGATCCTTTGCCAAAAAC
* ** *
4968 GATCGATCTTTTGCCTTAAAG
1 GATCGATCCTTTGCCAAAAAC
4989 GATCGATCCTTT
1 GATCGATCCTTT
5001 TGAGCAAGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (21 bp):
GATCGATCCTTTGCCAAAAAC
Found at i:27170 original size:11 final size:11
Alignment explanation
Indices: 27154--27189 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
27144 AAAAACAAAA
*
27154 GAAGTGCAAGT
1 GAAGTGCAAGC
27165 GAAGTGCAAGC
1 GAAGTGCAAGC
27176 GAAGTGCAAGC
1 GAAGTGCAAGC
27187 GAA
1 GAA
27190 ATAAAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.39, C:0.14, G:0.36, T:0.11
Consensus pattern (11 bp):
GAAGTGCAAGC
Found at i:28611 original size:24 final size:21
Alignment explanation
Indices: 28577--28619 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
28567 TCCACAAGAC
*
28577 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
28599 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
28620 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:30518 original size:22 final size:22
Alignment explanation
Indices: 30490--30547 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
30480 GCAAGAAGAC
30490 CCATGTGCATTCATTTAGGCTG
1 CCATGTGCATTCATTTAGGCTG
* *
30512 CCATGTGCATTTATATAGGCTG
1 CCATGTGCATTCATTTAGGCTG
30534 CCATGTGCA-TCATT
1 CCATGTGCATTCATT
30548 CAAGCATGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 3 0.09
22 29 0.91
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (22 bp):
CCATGTGCATTCATTTAGGCTG
Found at i:43226 original size:31 final size:31
Alignment explanation
Indices: 43184--43245 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
43174 TGAATTAAAG
43184 AAACAAATGAATTTTTATTTTATGTTCACAT
1 AAACAAATGAATTTTTATTTTATGTTCACAT
* *
43215 AAACGAATGAATTTTTATTTTATTTTCACAT
1 AAACAAATGAATTTTTATTTTATGTTCACAT
43246 TAGAAATTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (31 bp):
AAACAAATGAATTTTTATTTTATGTTCACAT
Found at i:47392 original size:32 final size:32
Alignment explanation
Indices: 47301--47419 Score: 120
Period size: 32 Copynumber: 3.8 Consensus size: 32
47291 CCTAAGGTGG
* *
47301 CCTTGGGTAGGCTCTAAGTCCCCAAGGCATTT
1 CCTTGGGTAGGCTCTAAGTCCCCAAGGTACTT
** *
47333 CCTTGGGTAATCTCTAAGGCCCCAAGGTACTT
1 CCTTGGGTAGGCTCTAAGTCCCCAAGGTACTT
* * *
47365 CCTTGGATAGGCTCTTAGTCCCTAAGGTAC-T
1 CCTTGGGTAGGCTCTAAGTCCCCAAGGTACTT
*
47396 CCTTTGG--GGCTCTTAAG-CCCCAAG
1 CCTTGGGTAGGCTC-TAAGTCCCCAAG
47420 ATAATCCCTT
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
29 11 0.15
30 3 0.04
31 6 0.08
32 51 0.72
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.29
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTAAGTCCCCAAGGTACTT
Found at i:48038 original size:19 final size:20
Alignment explanation
Indices: 48011--48048 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
48001 AATGATTTTC
48011 TAAACTTGTATT-TTATTTA
1 TAAACTTGTATTATTATTTA
* *
48030 TAAATTTGTTTTATTATTT
1 TAAACTTGTATTATTATTT
48049 TACACGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (20 bp):
TAAACTTGTATTATTATTTA
Found at i:52932 original size:13 final size:14
Alignment explanation
Indices: 52916--52944 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
52906 TTTGATTCAA
52916 AAATTAATT-AATT
1 AAATTAATTGAATT
52929 AAATTAATTGAATT
1 AAATTAATTGAATT
52943 AA
1 AA
52945 CTAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
AAATTAATTGAATT
Found at i:53536 original size:24 final size:24
Alignment explanation
Indices: 53466--53537 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 24
53456 ATTAGAAATT
* *
53466 ATATTTTGAAAATTATTA-ATTAAT
1 ATATTTT-AAGATTATTATATTAAA
* *
53490 ATATTTTAAGAATCTT-TATTAAA
1 ATATTTTAAGATTATTATATTAAA
53513 ATATTATT-AGATTATTATATTAAA
1 ATATT-TTAAGATTATTATATTAAA
53537 A
1 A
53538 CTAAATAGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
23 22 0.56
24 17 0.44
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (24 bp):
ATATTTTAAGATTATTATATTAAA
Found at i:53762 original size:24 final size:24
Alignment explanation
Indices: 53719--53773 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
53709 TATTATATTC
53719 TATTATTAGAAATATTAATAAAT-A
1 TATT-TTAGAAATATTAATAAATAA
*
53743 TATTTTA-AAATATTTGAATAATTAA
1 TATTTTAGAAATA-TT-AATAAATAA
53768 TATTTT
1 TATTTT
53774 GATTAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 5 0.19
23 5 0.19
24 10 0.37
25 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TATTTTAGAAATATTAATAAATAA
Found at i:53791 original size:25 final size:24
Alignment explanation
Indices: 53759--53807 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
53749 AAAATATTTG
*
53759 AATAATT-AATATTTTGATTAAAAT
1 AATAATTAAATATTAT-ATTAAAAT
53783 AATATATTAAATATTATATTAAAAT
1 AATA-ATTAAATATTATATTAAAAT
53808 TAAATACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 11 0.50
26 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
AATAATTAAATATTATATTAAAAT
Found at i:54984 original size:17 final size:17
Alignment explanation
Indices: 54944--54985 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
54934 AGGTAAAGAG
*
54944 CTTCTCCTGAAATGAGT
1 CTTCTCTTGAAATGAGT
54961 CTTCTCTTGAAATGAGT
1 CTTCTCTTGAAATGAGT
54978 CTTCTCTT
1 CTTCTCTT
54986 TATGTAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (17 bp):
CTTCTCTTGAAATGAGT
Found at i:66866 original size:19 final size:18
Alignment explanation
Indices: 66829--66879 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
66819 TATTTTCACT
* *
66829 ATTTTATTTTTGAATATA
1 ATTTTATTTTTTAAAATA
66847 AGTTTTATTTTTTAAAATA
1 A-TTTTATTTTTTAAAATA
*
66866 ATTATATTCTTTTA
1 ATTTTATT-TTTTA
66880 GAACCAATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (18 bp):
ATTTTATTTTTTAAAATA
Found at i:67786 original size:3 final size:3
Alignment explanation
Indices: 67778--67839 Score: 72
Period size: 3 Copynumber: 19.3 Consensus size: 3
67768 CGGGTCTTTT
67778 TTA TTA TTA TT- TATA TATA TTTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA T-TA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA
67826 TTTA TTA TTA TTA T
1 -TTA TTA TTA TTA T
67840 GTTTATTAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 1 0.02
3 40 0.74
4 12 0.22
5 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:67798 original size:10 final size:10
Alignment explanation
Indices: 67777--67837 Score: 99
Period size: 10 Copynumber: 6.2 Consensus size: 10
67767 CCGGGTCTTT
67777 TTTATTATTA
1 TTTATTATTA
67787 TTTA-TATATA
1 TTTATTAT-TA
67797 TTTATTATTA
1 TTTATTATTA
67807 TTTATTATTA
1 TTTATTATTA
67817 -TTATTATTA
1 TTTATTATTA
67826 TTTATTATTA
1 TTTATTATTA
67836 TT
1 TT
67838 ATGTTTATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
9 12 0.25
10 33 0.69
11 3 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATTATTA
Found at i:67846 original size:19 final size:19
Alignment explanation
Indices: 67778--67839 Score: 99
Period size: 19 Copynumber: 3.2 Consensus size: 19
67768 CGGGTCTTTT
67778 TTATTATTATTTA-TATATA
1 TTATTATTATTTATTAT-TA
67797 TTTATTATTATTTATTATTA
1 -TTATTATTATTTATTATTA
67817 TTATTATTATTTATTATTA
1 TTATTATTATTTATTATTA
67836 TTAT
1 TTAT
67840 GTTTATTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
19 23 0.56
20 15 0.37
21 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTATTATTTATTATTA
Found at i:67851 original size:16 final size:15
Alignment explanation
Indices: 67781--67847 Score: 84
Period size: 16 Copynumber: 4.4 Consensus size: 15
67771 GTCTTTTTTA
67781 TTATTATTTATATATAT
1 TTATTA-TTAT-TATAT
67798 TTATTATTATT-TA-
1 TTATTATTATTATAT
67811 TTATTATTATTATTAT
1 TTATTATTATTA-TAT
*
67827 TTATTATTATTATGT
1 TTATTATTATTATAT
67842 TTATTA
1 TTATTA
67848 ATTACATATT
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
13 11 0.24
14 2 0.04
15 11 0.24
16 16 0.35
17 6 0.13
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (15 bp):
TTATTATTATTATAT
Found at i:67851 original size:19 final size:17
Alignment explanation
Indices: 67778--67851 Score: 80
Period size: 19 Copynumber: 4.2 Consensus size: 17
67768 CGGGTCTTTT
67778 TTATTATTATTTATATATA
1 TTATTATTATTTAT-TA-A
67797 TTTATTATTATTTATTATTA
1 -TTATTATTATTTATTA--A
67817 TTATTATTATTTATT-A
1 TTATTATTATTTATTAA
*
67833 TTATTA-TGTTTATTAA
1 TTATTATTATTTATTAA
67849 TTA
1 TTA
67852 CATATTACAA
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
15 7 0.14
16 11 0.22
19 17 0.33
20 16 0.31
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (17 bp):
TTATTATTATTTATTAA
Found at i:70994 original size:18 final size:19
Alignment explanation
Indices: 70973--71011 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
70963 AAGGAATTAA
70973 ATAAAATAAA-ATTAAAAT
1 ATAAAATAAAGATTAAAAT
70991 ATAAAATAAAGGATTAAAAT
1 ATAAAATAAA-GATTAAAAT
71011 A
1 A
71012 AAAGATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
20 9 0.47
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (19 bp):
ATAAAATAAAGATTAAAAT
Found at i:71012 original size:18 final size:18
Alignment explanation
Indices: 70961--71014 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
70951 TTACTGAAAT
70961 TAAAGGAATT-AAATAAAA
1 TAAAGG-ATTAAAATAAAA
70979 TAAA--ATTAAAATATAAAA
1 TAAAGGATT-AAA-ATAAAA
70997 TAAAGGATTAAAATAAAA
1 TAAAGGATTAAAATAAAA
71015 GATATCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 3 0.10
17 2 0.06
18 20 0.65
19 3 0.10
20 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (18 bp):
TAAAGGATTAAAATAAAA
Found at i:72195 original size:3 final size:3
Alignment explanation
Indices: 72187--72218 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
72177 TAAACACACT
72187 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
72219 TTTATAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:72225 original size:9 final size:9
Alignment explanation
Indices: 72213--72239 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
72203 AATAATAATA
72213 ATAATATTT
1 ATAATATTT
72222 ATAATATTT
1 ATAATATTT
72231 ATAATATTT
1 ATAATATTT
72240 TTTTAAGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATAATATTT
Found at i:72225 original size:18 final size:18
Alignment explanation
Indices: 72187--72239 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
72177 TAAACACACT
* *
72187 TAATAATAATAATAATAA
1 TAATAATAATAATATTTA
72205 TAATAATAATAATATTTA
1 TAATAATAATAATATTTA
* *
72223 TAATATTTATAATATTT
1 TAATAATAATAATATTT
72240 TTTTAAGCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATAATAATAATATTTA
Found at i:72686 original size:16 final size:17
Alignment explanation
Indices: 72637--72686 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
72627 TATGAACTTA
72637 TTCTCTCTCATTGGATGAG
1 TTCT-TCTCATT-GATGAG
72656 TTCTTCGT--TTGATGAG
1 TTCTTC-TCATTGATGAG
72672 TTCTTCTCATT-ATGA
1 TTCTTCTCATTGATGA
72687 ACTCTTCACT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 1 0.04
16 16 0.57
17 4 0.14
18 2 0.07
19 5 0.18
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.48
Consensus pattern (17 bp):
TTCTTCTCATTGATGAG
Found at i:72910 original size:136 final size:136
Alignment explanation
Indices: 72666--72974 Score: 510
Period size: 136 Copynumber: 2.3 Consensus size: 136
72656 TTCTTCGTTT
* * ** *
72666 GATGAGTTCTTCTCATTATGAACTCTTCACTGGAAATGTTGATCCCTCAAGCGAGGTGTCACTGA
1 GATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGA
*
72731 TTCAAAATGTTGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCT
66 TTCAAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCT
72796 CTGTCG
131 CTGTCG
* *
72802 GATGAGTTCTTCTCATTATGAACTCTCCATTAGAAATACTGATCCTTCAAGCAAGGTGTCACTGA
1 GATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGA
*
72867 TTCAAAATGTCGTGAATCTAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCT
66 TTCAAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCT
72932 CTGTCG
131 CTGTCG
* * *
72938 AATGAGTTCTTCTTATTATGAACTCTCAATTGGAAAT
1 GATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
72975 GCTGGTTCAC
Statistics
Matches: 160, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
136 160 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (136 bp):
GATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGA
TTCAAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCT
CTGTCG
Found at i:73870 original size:12 final size:11
Alignment explanation
Indices: 73853--73913 Score: 70
Period size: 12 Copynumber: 5.3 Consensus size: 11
73843 TCTCTTTTTA
73853 TTTTTTCATTT
1 TTTTTTCATTT
73864 CTTTTTTCATTT
1 -TTTTTTCATTT
*
73876 TTTTTT-TTTT
1 TTTTTTCATTT
73886 TTTTTTCATTT
1 TTTTTTCATTT
73897 TTCATTTTCATCTT
1 TT--TTTTCAT-TT
73911 TTT
1 TTT
73914 ATTTGTTCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 9 0.21
11 11 0.26
12 12 0.28
13 7 0.16
14 4 0.09
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:73904 original size:21 final size:21
Alignment explanation
Indices: 73865--73904 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
73855 TTTTCATTTC
**
73865 TTTTTTCATTTTTTTTTTTTT
1 TTTTTTCATTTTTCATTTTTT
73886 TTTTTTCATTTTTCATTTT
1 TTTTTTCATTTTTCATTTT
73905 CATCTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTTTTCATTTTTCATTTTTT
Found at i:85350 original size:2 final size:2
Alignment explanation
Indices: 85286--85341 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
85276 TGTAATAATA
85286 AT AT AT AT AT A- AT AT -T AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
85325 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
85342 CAAATATATC
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 48 0.94
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:86458 original size:18 final size:19
Alignment explanation
Indices: 86437--86475 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
86427 AAGGAATTAA
86437 ATAAAATAAA-ATTAAAAT
1 ATAAAATAAAGATTAAAAT
86455 ATAAAATAAAGGATTAAAAT
1 ATAAAATAAA-GATTAAAAT
86475 A
1 A
86476 AAAGATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
20 9 0.47
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (19 bp):
ATAAAATAAAGATTAAAAT
Found at i:86476 original size:18 final size:18
Alignment explanation
Indices: 86425--86478 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
86415 TTACTGAAAT
86425 TAAAGGAATT-AAATAAAA
1 TAAAGG-ATTAAAATAAAA
86443 TAAA--ATTAAAATATAAAA
1 TAAAGGATT-AAA-ATAAAA
86461 TAAAGGATTAAAATAAAA
1 TAAAGGATTAAAATAAAA
86479 GATATCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 3 0.10
17 2 0.06
18 20 0.65
19 3 0.10
20 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (18 bp):
TAAAGGATTAAAATAAAA
Found at i:88481 original size:20 final size:20
Alignment explanation
Indices: 88434--88650 Score: 132
Period size: 20 Copynumber: 10.2 Consensus size: 20
88424 AATGACCAAC
* *
88434 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
88453 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * **
88473 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
* * **
88493 AAGATCGCAACACGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
88514 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
*
88535 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
*
88555 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--TAG
*
88577 AATCGCGAGAATCGCAACGCGATTAAG
1 -A-----A-AATCGCAACGCGATTTAG
**
88604 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
88625 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
88646 AAAAT
1 AAAAT
88651 GAGTAAATTC
Statistics
Matches: 154, Mismatches: 28, Indels: 31
0.72 0.13 0.15
Matches are distributed among these distances:
19 18 0.12
20 73 0.47
21 14 0.09
22 28 0.18
23 1 0.01
26 1 0.01
27 3 0.02
28 1 0.01
29 15 0.10
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:88562 original size:62 final size:62
Alignment explanation
Indices: 88434--88619 Score: 182
Period size: 62 Copynumber: 2.9 Consensus size: 62
88424 AATGACCAAC
* * * *
88434 AAAATCGCAACGCGAT-AT-CAA-AACCGCAACGCGATTTAGAAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACGCGATCATCCAAGAATCGCAACGCGATTAAGAAAATCGCAACG-CGATAAAG
* * * **
88493 AAGATCGCAACACGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATCATCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATAAAG
*
88555 AAAATCGCAACGCGATTCCAAGAATCGCGAGAATCGCAACGCGATTAAGAAAATCGCAACGCGAT
1 AAAATCGCAACGCGA-T-C----ATC-CAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGAT
88620 CTTCCAAGAA
Statistics
Matches: 103, Mismatches: 13, Indels: 12
0.80 0.10 0.09
Matches are distributed among these distances:
59 14 0.14
60 1 0.01
61 5 0.05
62 42 0.41
63 1 0.01
64 1 0.01
68 2 0.02
69 37 0.36
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (62 bp):
AAAATCGCAACGCGATCATCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATAAAG
Found at i:88609 original size:49 final size:50
Alignment explanation
Indices: 88537--88633 Score: 169
Period size: 49 Copynumber: 1.9 Consensus size: 50
88527 CGATTAAGAA
*
88537 AATCGCAACGCGATTCAGAAAATCGCAACGCGA-TTCCAAGAATCGCGAG
1 AATCGCAACGCGATTAAGAAAATCGCAACGCGACTTCCAAGAATCGCGAG
88586 AATCGCAACGCGATTAAGAAAATCGCAACGCGATCTTCCAAGAATCGC
1 AATCGCAACGCGATTAAGAAAATCGCAACGCGA-CTTCCAAGAATCGC
88634 AACGCGATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 32 0.71
51 13 0.29
ACGTcount: A:0.37, C:0.27, G:0.21, T:0.15
Consensus pattern (50 bp):
AATCGCAACGCGATTAAGAAAATCGCAACGCGACTTCCAAGAATCGCGAG
Found at i:88647 original size:69 final size:68
Alignment explanation
Indices: 88515--88647 Score: 207
Period size: 69 Copynumber: 1.9 Consensus size: 68
88505 CGATCTTCCA
88515 AGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGAAT
1 AGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATT-CAAGAAT
88580 CGCG
65 CGCG
*
88584 AGAATCGCAACGCGATTAAGAAAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATT-AAGA
1 AGAATCGCAACGCGATTAAGAAAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTCAAGA
88647 A
63 A
88648 AATGAGTAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
69 40 0.67
71 18 0.30
72 2 0.03
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (68 bp):
AGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAAGAATC
GCG
Found at i:88767 original size:6 final size:6
Alignment explanation
Indices: 88758--88808 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
88748 CATTACCATT
88758 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
88806 ACC
1 ACC
88809 CGAGACGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:89323 original size:6 final size:6
Alignment explanation
Indices: 89312--89435 Score: 241
Period size: 6 Copynumber: 20.8 Consensus size: 6
89302 TCGGGTCGTG
89312 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC G-GGTC GTGGTC
1 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
89359 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
1 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
89407 GTGGTC GTGGTC GTGGTC GTGGTC GTGGT
1 GTGGTC GTGGTC GTGGTC GTGGTC GTGGT
89436 AATACGTGTC
Statistics
Matches: 117, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.04
6 112 0.96
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GTGGTC
Found at i:89587 original size:20 final size:20
Alignment explanation
Indices: 89539--89805 Score: 291
Period size: 20 Copynumber: 13.1 Consensus size: 20
89529 TCATTTTCTT
89539 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
89559 AAGATCGCGTTGCGATTCTTGG
1 -A-ATCGCGTTGCGATTCTTGG
*
89581 AATCGCGTTGCGATT-TTCTG
1 AATCGCGTTGCGATTCTT-GG
89601 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
89621 AATCGCGTTGCGATTTTCTT--
1 AATCGCGTTGCGA--TTCTTGG
89641 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
*
89661 AAGATCGCGTTGCGATT-TTCTG
1 -A-ATCGCGTTGCGATTCTT-GG
*
89683 AATCGCGTTGCGATT-TTCTG
1 AATCGCGTTGCGATTCTT-GG
*
89703 AATCGCGTTGCGATT-TTCTG
1 AATCGCGTTGCGATTCTT-GG
89723 AATCGCGTTGCGATT-TCT-G
1 AATCGCGTTGCGATTCT-TGG
89742 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
*
89762 AAGATCGCGTTGCGATT-TTATG
1 -A-ATCGCGTTGCGATTCTT-GG
*
89784 AATCGCATTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
89804 AA
1 AA
89806 GATCGTTGCG
Statistics
Matches: 223, Mismatches: 6, Indels: 35
0.84 0.02 0.13
Matches are distributed among these distances:
18 5 0.02
19 19 0.09
20 130 0.58
21 15 0.07
22 54 0.24
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTTGG
Found at i:89606 original size:40 final size:39
Alignment explanation
Indices: 89539--89879 Score: 323
Period size: 40 Copynumber: 8.4 Consensus size: 39
89529 TCATTTTCTT
*
89539 AATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGATT-TTGG
89581 AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT-TTGG
*
89621 AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT-TTGG
*
89661 AAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTG
1 -A-ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTT-GG
89703 AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTCT-G
1 AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTT-TGG
* *
89742 AATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATTTTATG
1 AATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGATTTT-GG
* * *** * **
89784 AATCGCATTGCGATTCTT-GGAAGATCGTTGCGATCTTCT
1 AATCGCGTTGCGATT-TTCTGAATCGCGTTGCGATTTTGG
** * * * *
89823 TTTCAACGTTGCGCTTTTCTAAATCGCGTTGCGGTTTT-G
1 AATC-GCGTTGCGATTTTCTGAATCGCGTTGCGATTTTGG
89862 ATATCGCGTTGCGATTTT
1 A-ATCGCGTTGCGATTTT
89880 GTTGGTCATT
Statistics
Matches: 257, Mismatches: 29, Indels: 29
0.82 0.09 0.09
Matches are distributed among these distances:
39 32 0.12
40 131 0.51
41 24 0.09
42 70 0.27
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.38
Consensus pattern (39 bp):
AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTGG
Found at i:89707 original size:102 final size:101
Alignment explanation
Indices: 89531--89798 Score: 450
Period size: 102 Copynumber: 2.6 Consensus size: 101
89521 GAATTTACTC
*
89531 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCGATT
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTTGAATCGCGTTGCGATT
89596 TTCTGAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
65 TTCTGAATCGCGTTGCGATT-TTCGGAATCGCGTTGCG
89633 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTT-TGAATCGCGTTGCGATT
*
89698 TTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCG
65 TTCTGAATCGCGTTGCGATTTTCGGAATCGCGTTGCG
* *
89735 A-TTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATGAATCGCATTGCGATT
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTT-TGAATCGCGTTGCGATT
89799 CTTGGAAGAT
Statistics
Matches: 159, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
101 64 0.40
102 95 0.60
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (101 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTTGAATCGCGTTGCGATTT
TCTGAATCGCGTTGCGATTTTCGGAATCGCGTTGCG
Found at i:89814 original size:20 final size:20
Alignment explanation
Indices: 89747--89817 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
89737 TTCTGAATCG
89747 CGTTGCGATTCTTGGAAGAT
1 CGTTGCGATTCTTGGAAGAT
*
89767 CGCGTTGCGATT-TT--ATGAAT
1 --CGTTGCGATTCTTGGAAG-AT
89787 CGCATTGCGATTCTTGGAAGAT
1 CG--TTGCGATTCTTGGAAGAT
89809 CGTTGCGAT
1 CGTTGCGAT
89818 CTTCTTTTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 17 0.41
21 4 0.10
22 14 0.34
23 2 0.05
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (20 bp):
CGTTGCGATTCTTGGAAGAT
Found at i:89852 original size:20 final size:19
Alignment explanation
Indices: 89829--89880 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
89819 TTCTTTTCAA
* *
89829 CGTTGCGCTTTTCTAAATCG
1 CGTTGCGATTTT-GAAATCG
* *
89849 CGTTGCGGTTTTGATATCG
1 CGTTGCGATTTTGAAATCG
89868 CGTTGCGATTTTG
1 CGTTGCGATTTTG
89881 TTGGTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.12, C:0.19, G:0.27, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTGAAATCG
Found at i:90565 original size:25 final size:25
Alignment explanation
Indices: 90537--90587 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
90527 AATACTGGTT
90537 AAATT-GTAGAAT-TTTTAAATATAAA
1 AAATTAGTA-AATATTTTAAAT-TAAA
*
90562 AAATTATTAAATATTTTAAATTAAA
1 AAATTAGTAAATATTTTAAATTAAA
90587 A
1 A
90588 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (25 bp):
AAATTAGTAAATATTTTAAATTAAA
Found at i:95675 original size:19 final size:19
Alignment explanation
Indices: 95632--95730 Score: 58
Period size: 19 Copynumber: 5.1 Consensus size: 19
95622 ATATTTACAA
*
95632 AATATAATTAAATTAAAAT
1 AATATAATAAAATTAAAAT
* * *
95651 ATTATAATAAAATTGATAT
1 AATATAATAAAATTAAAAT
* *
95670 AATATACATGAAAACTAACATT
1 AATATA-AT-AAAATTAA-AAT
*
95692 AAGATAATATAAATATAAAAT
1 AATATAATA-AAAT-TAAAAT
* *
95713 CATGT--TAAAATTAAAAT
1 AATATAATAAAATTAAAAT
95730 A
1 A
95731 TTAATATTTA
Statistics
Matches: 59, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
17 6 0.10
18 4 0.07
19 22 0.37
20 3 0.05
21 15 0.25
22 9 0.15
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (19 bp):
AATATAATAAAATTAAAAT
Found at i:102520 original size:11 final size:11
Alignment explanation
Indices: 102500--102542 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
102490 TGCTGGAAAC
102500 AAGATAAAAAA
1 AAGATAAAAAA
* *
102511 AAGATTAAAAT
1 AAGATAAAAAA
102522 AAGATAAAGAAA
1 AAGATAAA-AAA
102534 AACGATAAA
1 AA-GATAAA
102543 GGAATTGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 16 0.62
12 4 0.15
13 6 0.23
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.14
Consensus pattern (11 bp):
AAGATAAAAAA
Found at i:106797 original size:13 final size:12
Alignment explanation
Indices: 106774--106807 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
106764 AAATTTGGTT
106774 TTTTGTTTTTTTG
1 TTTT-TTTTTTTG
106787 TCTTTTTTTTTTG
1 T-TTTTTTTTTTG
106800 TTTTTTTT
1 TTTTTTTT
106808 AAATAGCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 10 0.50
14 3 0.15
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:107767 original size:19 final size:19
Alignment explanation
Indices: 107743--107784 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
107733 ATTGAAAATT
107743 CGTAATATTTACAAAATCC
1 CGTAATATTTACAAAATCC
*
107762 CGTAATATTTACAAAATCT
1 CGTAATATTTACAAAATCC
107781 CGTA
1 CGTA
107785 TTAATCCCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.33
Consensus pattern (19 bp):
CGTAATATTTACAAAATCC
Found at i:111831 original size:20 final size:19
Alignment explanation
Indices: 111798--111835 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
111788 TCTGTTAGGT
111798 ATTAGATAAGATCAGTTTTA
1 ATTAGATAAGATCA-TTTTA
111818 ATTAGAT-AGAATCATTTT
1 ATTAGATAAG-ATCATTTT
111836 TTTATTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (19 bp):
ATTAGATAAGATCATTTTA
Done.