Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001356.1 Hibiscus syriacus cultivar Beakdansim tig00002641_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: 126339
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:185 original size:23 final size:23
Alignment explanation
Indices: 154--209 Score: 94
Period size: 24 Copynumber: 2.4 Consensus size: 23
144 TTCTTGTAAG
*
154 TTTGTGAAATTTGTATTCTTCTC
1 TTTGGGAAATTTGTATTCTTCTC
177 TTTGGGAAAATTTGTATTCTTCTC
1 TTTGGG-AAATTTGTATTCTTCTC
201 TTTGGGAAA
1 TTTGGGAAA
210 GAGCGTTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 8 0.26
24 23 0.74
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (23 bp):
TTTGGGAAATTTGTATTCTTCTC
Found at i:191 original size:24 final size:24
Alignment explanation
Indices: 160--209 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
150 TAAGTTTGTG
160 AAATTTGTATTCTTCTCTTTGGGA
1 AAATTTGTATTCTTCTCTTTGGGA
184 AAATTTGTATTCTTCTCTTTGGGA
1 AAATTTGTATTCTTCTCTTTGGGA
208 AA
1 AA
210 GAGCGTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (24 bp):
AAATTTGTATTCTTCTCTTTGGGA
Found at i:8308 original size:65 final size:64
Alignment explanation
Indices: 8185--8317 Score: 189
Period size: 65 Copynumber: 2.1 Consensus size: 64
8175 TCCCATTTCG
* * *
8185 AATGCATTTTATGCGCCGATGCACAGCCATACATCGATGCACTCTGGATTTTATTGAAACATCA
1 AATGCATTTTATGCACCGATGCACAACCATACATCGATGCACTCTGGATTGTATTGAAACATCA
8249 AATGCATTTTATGCACCGATGCACAAACCATACATCGATGCACTCCT-GACTTGT-TTGAAACAT
1 AATGCATTTTATGCACCGATGCAC-AACCATACATCGATGCACT-CTGGA-TTGTATTGAAACAT
*
8312 CG
63 CA
8314 AATG
1 AATG
8318 TAATTAGTGT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
64 23 0.37
65 34 0.55
66 5 0.08
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (64 bp):
AATGCATTTTATGCACCGATGCACAACCATACATCGATGCACTCTGGATTGTATTGAAACATCA
Found at i:8332 original size:65 final size:64
Alignment explanation
Indices: 8185--8337 Score: 177
Period size: 65 Copynumber: 2.4 Consensus size: 64
8175 TCCCATTTCG
* * * *
8185 AATGCATTTTATGCGCCGATGCACAGCCATACATCGATGCACTCTGGATTTTATTGAAACATCA
1 AATGCATATTATGCACCGATGCACAACCATACATCGATGCACTCTGGATTGTATTGAAACATCA
*
8249 AATGCATTTTATGCACCGATGCACAAACCATACATCGATGCACTCCT-GACTTGT-TTGAAACAT
1 AATGCATATTATGCACCGATGCAC-AACCATACATCGATGCACT-CTGGA-TTGTATTGAAACAT
*
8312 CG
63 CA
* *
8314 AATGTA-ATTAGTGTACCGATGCAC
1 AATGCATATTA-TGCACCGATGCAC
8338 GAAGTCTTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
64 26 0.33
65 47 0.60
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (64 bp):
AATGCATATTATGCACCGATGCACAACCATACATCGATGCACTCTGGATTGTATTGAAACATCA
Found at i:35779 original size:12 final size:12
Alignment explanation
Indices: 35751--35791 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
35741 GAAAGAAGGT
35751 AAGAAACAAGAT-
1 AAGAAA-AAGATA
*
35763 TAGAAAAAGATA
1 AAGAAAAAGATA
35775 AAG-AAAAGATA
1 AAGAAAAAGATA
35786 AAGAAA
1 AAGAAA
35792 TTAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.71, C:0.02, G:0.17, T:0.10
Consensus pattern (12 bp):
AAGAAAAAGATA
Found at i:40082 original size:21 final size:20
Alignment explanation
Indices: 40056--40102 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
40046 TTCGTTTGCA
40056 TTTTTTTGAAATTTTTGCTTT
1 TTTTTTTG-AATTTTTGCTTT
**
40077 TTTTTTTGCCTTTTTG-TTT
1 TTTTTTTGAATTTTTGCTTT
40096 TTTTTTT
1 TTTTTTT
40103 TTTGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.42
20 6 0.25
21 8 0.33
ACGTcount: A:0.06, C:0.06, G:0.09, T:0.79
Consensus pattern (20 bp):
TTTTTTTGAATTTTTGCTTT
Found at i:42744 original size:6 final size:6
Alignment explanation
Indices: 42730--42776 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
42720 ATAATTTAAA
*
42730 TTTAAT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT
42777 CTTAACTTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:43450 original size:18 final size:18
Alignment explanation
Indices: 43398--43451 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
43388 ATTGCCATCA
* *
43398 AATTAAAATATATAATTT
1 AATTAAATTATTTAATTT
*
43416 AATTAAATTATTAAATTT
1 AATTAAATTATTTAATTT
*
43434 -ATTTAATTATCTTAATTT
1 AATTAAATTAT-TTAATTT
43452 TTTCATACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 9 0.30
18 21 0.70
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTAAATTATTTAATTT
Found at i:48407 original size:2 final size:2
Alignment explanation
Indices: 48400--48434 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
48390 CAGGCGCCGT
48400 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
48435 GAGTATAATA
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:48896 original size:20 final size:20
Alignment explanation
Indices: 48867--48904 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
48857 TTTTAAAGGG
48867 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
48887 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
48905 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:53359 original size:64 final size:65
Alignment explanation
Indices: 53209--53368 Score: 225
Period size: 64 Copynumber: 2.5 Consensus size: 65
53199 TTGTTGAAGG
* *
53209 TGCATCGATGCATAAGGAGTGCATCGATGCACTCATTTAAATTAATGAACATCAAATGCCATTGA
1 TGCATCGATGCATAAGGAGTGCATCGATGCACTCATTTAAAATAATAAACATCAAATGCCATTGA
* * * *
53274 TGCATCGATGCATAAGGAGTGCATCGATGCACAT-GTTTAAAAT-ATAAACATCGAATGCCTTTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCAC-TCATTTAAAATAATAAACATCAAATGCCATTG
53337 A
65 A
* *
53338 TGCACCGATGCATAAGTAGTGCATCGATGCA
1 TGCATCGATGCATAAGGAGTGCATCGATGCA
53369 TACCTTCATT
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
64 46 0.53
65 39 0.45
66 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCACTCATTTAAAATAATAAACATCAAATGCCATTGA
Found at i:53900 original size:22 final size:22
Alignment explanation
Indices: 53875--53977 Score: 170
Period size: 22 Copynumber: 4.7 Consensus size: 22
53865 GGGTATATTA
53875 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
53897 GTCCTTCGGGACATATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
53919 GTCCTTCGGGACGTATCTAGTG
1 GTCCTTCGGGACGTATCCAGTG
53941 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
**
53963 GTGTTTCGGGACGTA
1 GTCCTTCGGGACGTA
53978 GTGGTCATTC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 75 1.00
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:72729 original size:22 final size:21
Alignment explanation
Indices: 72671--72739 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
72661 TAGTCCTTTG
*
72671 GGACGTATCCAGTGGTCCTTCA
1 GGACATAT-CAGTGGTCCTTCA
* *
72693 GGAC--GT-AGTGCTCCTTCA
1 GGACATATCAGTGGTCCTTCA
72711 GGACATATACAGTGGTCCTTCA
1 GGACATAT-CAGTGGTCCTTCA
72733 GGACATA
1 GGACATA
72740 GAAGTCCTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 15 0.38
20 2 0.05
22 22 0.56
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (21 bp):
GGACATATCAGTGGTCCTTCA
Found at i:72748 original size:18 final size:18
Alignment explanation
Indices: 72685--72754 Score: 52
Period size: 18 Copynumber: 3.7 Consensus size: 18
72675 GTATCCAGTG
* *
72685 GTCCTTCAGGACGTAG-T
1 GTCCTTCAGGACATAGAA
*
72702 GCTCCTTCAGGACATATACA
1 G-TCCTTCAGGACATAGA-A
72722 GTGGTCCTTCAGGACATAGAA
1 ---GTCCTTCAGGACATAGAA
*
72743 GTCCTTCGGGAC
1 GTCCTTCAGGAC
72755 GAATACTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
17 1 0.02
18 24 0.57
21 1 0.02
22 15 0.36
23 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (18 bp):
GTCCTTCAGGACATAGAA
Found at i:72748 original size:40 final size:39
Alignment explanation
Indices: 72662--72754 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 39
72652 AGGGTATATT
* * * *
72662 AGTCCTTTGGGACGTATCCAGTGGTCCTTCAGGACGTAG
1 AGTCCTTCGGGACATATACAGTGGTCCTTCAGGACATAG
* *
72701 TGCTCCTTCAGGACATATACAGTGGTCCTTCAGGACATAG
1 AG-TCCTTCGGGACATATACAGTGGTCCTTCAGGACATAG
72741 AAGTCCTTCGGGAC
1 -AGTCCTTCGGGAC
72755 GAATACTGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.02
40 42 0.95
41 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.27
Consensus pattern (39 bp):
AGTCCTTCGGGACATATACAGTGGTCCTTCAGGACATAG
Found at i:75849 original size:23 final size:23
Alignment explanation
Indices: 75802--75866 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
75792 TGCATCCCTT
*
75802 TGAATGTGCATCGAT--ACACCA
1 TGAATGTGCACCGATGCACACCA
*
75823 TGAA-GTTGCACCGATGCACACCT
1 TGAATG-TGCACCGATGCACACCA
*
75846 TGAATGTGCATCGATGCACAC
1 TGAATGTGCACCGATGCACAC
75867 TGCCATGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.03
21 12 0.32
23 23 0.62
24 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (23 bp):
TGAATGTGCACCGATGCACACCA
Found at i:78248 original size:13 final size:12
Alignment explanation
Indices: 78215--78249 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
78205 TAAGGGGGAG
78215 TAATTTCAAAAT
1 TAATTTCAAAAT
78227 TAATTTCAAAAT
1 TAATTTCAAAAT
78239 TAATTTTCAAA
1 TAA-TTTCAAA
78250 GAAAATCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATTTCAAAAT
Found at i:78576 original size:20 final size:20
Alignment explanation
Indices: 78547--78584 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
78537 TTTCAAAGGG
78547 ATGCACCGATGCACCAATCT
1 ATGCACCGATGCACCAATCT
*
78567 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
78585 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCT
Found at i:78746 original size:64 final size:64
Alignment explanation
Indices: 78595--78753 Score: 194
Period size: 65 Copynumber: 2.5 Consensus size: 64
78585 GAATAAATTG
* * * * * *
78595 AACATCGAATGCAATTAATGCACCGATGCACTCTCCATGCATCGATGCACTCAGGTTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATACATCGATGCACTCAGGTTTT-ATGAA
* ** *
78660 AACATCGAATGCATTTTATGCATCGATGCACACACCATACATCGATGTACTTGGGCTTTT-TTAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATACATCGATGCACTCAGG-TTTTATGAA
*
78724 AATATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTTATGCATCGATGCA
78754 TGCTTAGTGC
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
64 32 0.39
65 46 0.56
66 4 0.05
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACACACCATACATCGATGCACTCAGGTTTTATGAA
Found at i:81360 original size:40 final size:40
Alignment explanation
Indices: 81305--81444 Score: 244
Period size: 40 Copynumber: 3.5 Consensus size: 40
81295 AAGTTAGGGA
* *
81305 CCATATTGTAAACGTACTAATGACAGTGTAATGGAGGGGG
1 CCATATTGCAAACGTACTAATGACAGTGCAATGGAGGGGG
81345 CCATATTGCAAACGTACTAATGACAGTGCAATGGAGGGGG
1 CCATATTGCAAACGTACTAATGACAGTGCAATGGAGGGGG
81385 CCATATTGCAAACGTACTAATGACAGTGCAATGGAGGGGG
1 CCATATTGCAAACGTACTAATGACAGTGCAATGGAGGGGG
* *
81425 ACATATTGCAAACGGACTAA
1 CCATATTGCAAACGTACTAA
81445 ATGTTTGAGG
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 96 1.00
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.21
Consensus pattern (40 bp):
CCATATTGCAAACGTACTAATGACAGTGCAATGGAGGGGG
Found at i:84672 original size:24 final size:24
Alignment explanation
Indices: 84645--84716 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
84635 AAACGGAGAT
* *
84645 ATCATAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
84669 ATCAGATATCAGAACGGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
84693 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
84717 GTAATGTATC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:84716 original size:12 final size:12
Alignment explanation
Indices: 84657--84716 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
84647 CATAAATCAA
84657 AACAGAATTCAG
1 AACAGAATTCAG
*
84669 ATCAG-ATATCAG
1 AACAGAAT-TCAG
* *
84681 AACGGAATCCAG
1 AACAGAATTCAG
* *
84693 ATCAGAAATCAG
1 AACAGAATTCAG
84705 AACAGAATTCAG
1 AACAGAATTCAG
84717 GTAATGTATC
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
11 2 0.06
12 32 0.89
13 2 0.06
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.17
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:84727 original size:48 final size:47
Alignment explanation
Indices: 84645--84753 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 47
84635 AAACGGAGAT
* * * *
84645 ATCATAAATCAAAACAGAATTCAGATCAGATATCAGAACGGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCA
* * * *
84692 GATCAGAAATCAGAACAGAATTCAGGTAATG-TATCATAATAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGATAA-GATATCAGAACAGAATCCA
84740 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
84754 TAAAATATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
47 1 0.02
48 49 0.96
49 1 0.02
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.21
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCA
Found at i:89722 original size:24 final size:24
Alignment explanation
Indices: 89695--89766 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
89685 AAACGGAGAT
*
89695 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
89719 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
89743 ACCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
89767 GTAATGTATC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.15
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:89724 original size:12 final size:12
Alignment explanation
Indices: 89697--89766 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
89687 ACGGAGATAT
* *
89697 CAGAAATCAAAA
1 CAGAATTCAGAA
*
89709 CAGAATTCAGAT
1 CAGAATTCAGAA
89721 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
89733 CAGAATCCAGAC
1 CAGAATTCAGAA
*
89745 CAGAAATCAGAA
1 CAGAATTCAGAA
89757 CAGAATTCAG
1 CAGAATTCAG
89767 GTAATGTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.50, C:0.20, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:89803 original size:48 final size:48
Alignment explanation
Indices: 89697--89791 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
89687 ACGGAGATAT
* * *
89697 CAGAAATCAAAACAGAATTCAGATCAGATATCAGAACAGAATCCAGAC
1 CAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCAAGAC
* *
89745 CAGAAATCAGAACAGAATTCAGGTAATG-TATCAGAATAGAATTCAAG
1 CAGAAATCAGAACAGAATTCAGATAA-GATATCAGAACAGAA-TCAAG
89792 TCGGAAATCA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
48 35 0.88
49 5 0.12
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (48 bp):
CAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCAAGAC
Found at i:93890 original size:226 final size:226
Alignment explanation
Indices: 93535--93947 Score: 551
Period size: 226 Copynumber: 1.8 Consensus size: 226
93525 GGGGCTTTGG
* *
93535 AAATCCAACGATTACATAATCGGTTAATTATTGGAAACATTACCAAGCATAATAACATATTAGGT
1 AAATCCAACGATAACATAATCGGTTAATTACTGGAAACATTACCAAGCATAATAACATATTAGGT
** * * * ** * *
93600 AGTCCTTATATAACGTAAATAGGTAGCACCTTTTTAAGCTGATAGGGTTTTGGAAATTCGACGAT
66 AGTCCTTATATAACGTAAATAAATAACACATTTTAAAGCTGATAGGGCCTTAGAAATCCGACGAT
* * * * * *
93665 AACAAATTAGGTTAATTACTTAATTTGTTATTAGAATTATCAACATATTAGGTAACGCCTAAAAT
131 AAAAAAATAGGTTAATTACTTAATTTATTATCAGAATCATCAACATATTAGGCAACGCCTAAAAT
93730 GTTACCAAAGTTTAAGCTGATAGAGCCTTAA
196 GTTACCAAAGTTTAAGCTGATAGAGCCTTAA
* * * * *
93761 AAATCCGACGATAACATACTCGGTTAATTACTGGAAATATTATCAAGCATACTAACATATTAGGT
1 AAATCCAACGATAACATAATCGGTTAATTACTGGAAACATTACCAAGCATAATAACATATTAGGT
* * *
93826 AG-CGCTTATGTAACGT-AATAAATAACACATTATTAAATCTGATGGGGCCTTAGAAATCCGACG
66 AGTC-CTTATATAACGTAAATAAATAACACATT-TTAAAGCTGATAGGGCCTTAGAAATCCGACG
* *
93889 ATAAAAAAATAGTTTAATTACTTAATTTATTATCAGTATCATCAACATATTAGGCAACG
129 ATAAAAAAATAGGTTAATTACTTAATTTATTATCAGAATCATCAACATATTAGGCAACG
93948 TACTCTATTG
Statistics
Matches: 158, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
225 12 0.08
226 146 0.92
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (226 bp):
AAATCCAACGATAACATAATCGGTTAATTACTGGAAACATTACCAAGCATAATAACATATTAGGT
AGTCCTTATATAACGTAAATAAATAACACATTTTAAAGCTGATAGGGCCTTAGAAATCCGACGAT
AAAAAAATAGGTTAATTACTTAATTTATTATCAGAATCATCAACATATTAGGCAACGCCTAAAAT
GTTACCAAAGTTTAAGCTGATAGAGCCTTAA
Found at i:97709 original size:30 final size:30
Alignment explanation
Indices: 97673--97744 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
97663 TACCCAAATC
97673 TCGATACTTTTGTGTCAGGTGTCGATACTT
1 TCGATACTTTTGTGTCAGGTGTCGATACTT
97703 TCGATACTTTTGTGTCAGGTGTCGATACTT
1 TCGATACTTTTGTGTCAGGTGTCGATACTT
97733 TCGATACGTTTT
1 TCGATAC-TTTT
97745 CATTTTTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 37 0.90
31 4 0.10
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (30 bp):
TCGATACTTTTGTGTCAGGTGTCGATACTT
Found at i:98207 original size:173 final size:174
Alignment explanation
Indices: 97852--98210 Score: 528
Period size: 173 Copynumber: 2.1 Consensus size: 174
97842 TACTGAAACT
*
97852 AATTTTGTCATATTTTTACCTCTTATATTATTATATATCGCTACATGTTTATAAAGTATCGATAC
1 AATTTTGTCATATTTTTACCTCTTATATTATTATATATCGATACATGTTTATAAAGTATCGATAC
* * * ** *
97917 TTTATAGGCGCCATTATTGTAATTCTTTTAAATTCCTAAAGTATTGATAATATCTTGCATATACT
66 TTTATAGGCGCCATTATTGCAATTATTTTAAATTCATAAAGTATCAATAATATCTTACATATACT
*
97982 TATTAAAGTATCGATACATTCAACATATTCGGTAGTACTTTACC
131 TATTAAAGTATCGATACATTCAACATATTCAGTAGTACTTTACC
** * * *
98026 GGTTTTGTCATATTTTTACTTCTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATAC
1 AATTTTGTCATATTTTTACCTCTTATATTATTATATATCGATACATGTTTATAAAGTATCGATAC
*
98091 TTTATAGGCG-CATTATTGCAATTATTTTAAATTCATAAAGTATCAATATTAT-TATACATATAC
66 TTTATAGGCGCCATTATTGCAATTATTTTAAATTCATAAAGTATCAATAATATCT-TACATATAC
*
98154 TTATTAAAGTATCGATACCTTCAACATA-TCTAGTAGATA-TTTACC
130 TTATTAAAGTATCGATACATTCAACATATTC-AGTAG-TACTTTACC
98199 AATTTTGTCATA
1 AATTTTGTCATA
98211 ATGAAACCGG
Statistics
Matches: 165, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
172 3 0.02
173 91 0.55
174 71 0.43
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (174 bp):
AATTTTGTCATATTTTTACCTCTTATATTATTATATATCGATACATGTTTATAAAGTATCGATAC
TTTATAGGCGCCATTATTGCAATTATTTTAAATTCATAAAGTATCAATAATATCTTACATATACT
TATTAAAGTATCGATACATTCAACATATTCAGTAGTACTTTACC
Found at i:98420 original size:193 final size:193
Alignment explanation
Indices: 98023--98455 Score: 620
Period size: 193 Copynumber: 2.2 Consensus size: 193
98013 GTAGTACTTT
* *
98023 ACCGGTTTTGTCATATTTTTA-CTTCTTATATTGTTATGTATCGATACATGTTTATAAAGTATCG
1 ACCGATTTTGTCATATTTTTATC-TGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCG
* *
98087 ATACTTTATAGGCGCATTATTGCAATTATTTTAAATTCATAAAGTATCAATATTATTATACATAT
65 ATACTTTATAGGCGCATTATTGCAATTATTTTAAATTCATAAAGTATCAATAATATGATACATAT
* *
98152 ACTTATTAAAGTATCGATACCTTCAACATATCTAGTAGATATTTACCAATTTTGTCATAATGAA
130 ACTTATTAAAGTATCGATACCTTCAACATATCCAGTAGAGATTTACCAATTTTGTCATAATGAA
*
98216 ACCGGTTTTGTCATATTTTTATCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGA
1 ACCGATTTTGTCATATTTTTATCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGA
* * ** * *
98281 TACTTTATAGGCGCTATTATTGCAATTCTTTTAAATTCCTAAAGTATTTATAATATGATACTTTT
66 TACTTTATAGGCGC-ATTATTGCAATTATTTTAAATTCATAAAGTATCAATAATATGATACATAT
* * * * ** *
98346 ACTTATTACAA-TATCGATACCTTTAACATATCCGGTAGCGCTTTACCGGTTTTGTCAT-TTGAA
130 ACTTATTA-AAGTATCGATACCTTCAACATATCCAGTAGAGATTTACCAATTTTGTCATAATGAA
* *
98409 CCCGATTTTGTCATATTTTTATCTGATATATTGTTATGTATCGATAC
1 ACCGATTTTGTCATATTTTTATCTGTTATATTGTTATGTATCGATAC
98456 TTATTTGAAT
Statistics
Matches: 216, Mismatches: 21, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
193 124 0.57
194 90 0.42
195 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (193 bp):
ACCGATTTTGTCATATTTTTATCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGA
TACTTTATAGGCGCATTATTGCAATTATTTTAAATTCATAAAGTATCAATAATATGATACATATA
CTTATTAAAGTATCGATACCTTCAACATATCCAGTAGAGATTTACCAATTTTGTCATAATGAA
Found at i:106422 original size:19 final size:19
Alignment explanation
Indices: 106398--106436 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
106388 ATAAATTTAG
*
106398 TTTTTATATTAATTCTAAT
1 TTTTTATATTAATTATAAT
106417 TTTTTATATTAATTATAAT
1 TTTTTATATTAATTATAAT
106436 T
1 T
106437 CTTATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTATATTAATTATAAT
Found at i:107092 original size:15 final size:15
Alignment explanation
Indices: 107072--107117 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
107062 AAGCATCATT
107072 GCATCAATTCAGCAA
1 GCATCAATTCAGCAA
**
107087 GCATCAATTCAGCTT
1 GCATCAATTCAGCAA
107102 GCATCAATTCAGCAA
1 GCATCAATTCAGCAA
107117 G
1 G
107118 TATCCTACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (15 bp):
GCATCAATTCAGCAA
Found at i:107239 original size:20 final size:20
Alignment explanation
Indices: 107214--107254 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
107204 AACCCTTACA
107214 AATATCAAACAGAAACAAGC
1 AATATCAAACAGAAACAAGC
107234 AATATCAAACAGAAACAAGC
1 AATATCAAACAGAAACAAGC
107254 A
1 A
107255 CCAAGTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.61, C:0.20, G:0.10, T:0.10
Consensus pattern (20 bp):
AATATCAAACAGAAACAAGC
Found at i:110014 original size:5 final size:5
Alignment explanation
Indices: 110006--110057 Score: 50
Period size: 5 Copynumber: 9.2 Consensus size: 5
109996 CAGACCCGTT
110006 GACCC GACCC GACCC GTTTACCC GACCC GTTGACCC GACCC GACCC GACCC
1 GACCC GACCC GACCC G---ACCC GACCC ---GACCC GACCC GACCC GACCC
110057 G
1 G
110058 TTGACCGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
5 31 0.76
8 10 0.24
ACGTcount: A:0.17, C:0.52, G:0.21, T:0.10
Consensus pattern (5 bp):
GACCC
Found at i:110014 original size:13 final size:13
Alignment explanation
Indices: 110011--110063 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
110001 CCGTTGACCC
110011 GACCCGACCCGTT
1 GACCCGACCCGTT
*
110024 TACCCGACCCGTT
1 GACCCGACCCGTT
110037 GACCCGACCC---
1 GACCCGACCCGTT
110047 GACCCGACCCGTT
1 GACCCGACCCGTT
110060 GACC
1 GACC
110064 GTTGACCGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 10 0.29
13 25 0.71
ACGTcount: A:0.17, C:0.49, G:0.21, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:110063 original size:18 final size:18
Alignment explanation
Indices: 109989--110063 Score: 84
Period size: 18 Copynumber: 4.2 Consensus size: 18
109979 ACCGGTCACA
*
109989 ACCCGACCAGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
110007 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
110025 ACCCGACCCGTTGACCC---G
1 ACCCGACCC---GACCCGTTG
110043 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
110061 ACC
1 ACC
110064 GTTGACCGGA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
15 5 0.10
18 38 0.79
21 5 0.10
ACGTcount: A:0.19, C:0.49, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:112629 original size:24 final size:24
Alignment explanation
Indices: 112533--112641 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
112523 GAATATTTTA
* *
112533 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
112557 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
112581 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
112605 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
* *
112629 TTTGATTTCTGAT
1 TCTGATATCTGAT
112642 ATCTCCGTTT
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
23 1 0.02
24 64 0.97
25 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:114792 original size:5 final size:5
Alignment explanation
Indices: 114784--114840 Score: 51
Period size: 5 Copynumber: 10.2 Consensus size: 5
114774 CAGACCCGTT
*
114784 GACCC GACCT GACCC GTTTACCC GACCC GTTGACCC GACCC GACCC GACCC
1 GACCC GACCC GACCC G---ACCC GACCC G---ACCC GACCC GACCC GACCC
114835 GACCC G
1 GACCC G
114841 TTGACCCGAC
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
5 34 0.77
8 10 0.23
ACGTcount: A:0.18, C:0.51, G:0.21, T:0.11
Consensus pattern (5 bp):
GACCC
Found at i:114792 original size:13 final size:13
Alignment explanation
Indices: 114789--114859 Score: 88
Period size: 13 Copynumber: 5.3 Consensus size: 13
114779 CCGTTGACCC
*
114789 GACCTGACCCGTT
1 GACCCGACCCGTT
*
114802 TACCCGACCCGTT
1 GACCCGACCCGTT
**
114815 GACCCGACCCGACCC
1 GACCCGACCCG--TT
114830 GACCCGACCCGTT
1 GACCCGACCCGTT
114843 GACCCGACCCGTT
1 GACCCGACCCGTT
114856 GACC
1 GACC
114860 GTTGACCGGA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
13 38 0.78
15 11 0.22
ACGTcount: A:0.17, C:0.48, G:0.21, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:114852 original size:18 final size:18
Alignment explanation
Indices: 114767--114853 Score: 84
Period size: 18 Copynumber: 4.6 Consensus size: 18
114757 ACCGGTCACA
*
114767 ACCCGACCAGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
114785 ACCCGACCTGACCCGTTT
1 ACCCGACCCGACCCGTTG
**
114803 ACCCGACCCGTTGACCCGACCCG
1 ACCCGACCC---GACCCG--TTG
114826 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
114844 ACCCGACCCG
1 ACCCGACCCG
114854 TTGACCGTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
18 35 0.62
20 6 0.11
21 6 0.11
23 9 0.16
ACGTcount: A:0.18, C:0.49, G:0.21, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:114853 original size:5 final size:5
Alignment explanation
Indices: 114815--114840 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
114805 CCGACCCGTT
114815 GACCC GACCC GACCC GACCC GACCC G
1 GACCC GACCC GACCC GACCC GACCC G
114841 TTGACCCGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.58, G:0.23, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:117417 original size:24 final size:24
Alignment explanation
Indices: 117321--117429 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
117311 GAATATTTTA
* *
117321 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
117345 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
117369 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
117393 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
* *
117417 TTTGATTTCTGAT
1 TCTGATATCTGAT
117430 ATCTCCGTTT
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
23 1 0.02
24 64 0.97
25 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:118798 original size:13 final size:13
Alignment explanation
Indices: 118780--118804 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
118770 ATACGGGTTT
118780 GTTTGGGTTTTGG
1 GTTTGGGTTTTGG
118793 GTTTGGGTTTTG
1 GTTTGGGTTTTG
118805 ACCCGCGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.44, T:0.56
Consensus pattern (13 bp):
GTTTGGGTTTTGG
Found at i:118943 original size:60 final size:59
Alignment explanation
Indices: 118853--118992 Score: 201
Period size: 60 Copynumber: 2.3 Consensus size: 59
118843 TTGTCTCCTA
*
118853 ATTTTAAATTTGTTCAATTTAGTTCAAATTTAATGATGT-AATATATTAATGTAAGCTTCAT
1 ATTTCAAATTTGTTCAA-TTAGTTCAAATTTAAT-AT-TAAATATATTAATGTAAGCTTCAT
* * *
118914 ATTTCAAATTTCTTCAATTAGTTCAAATTTAATATTACAATTTATTAATTTAAGCTTCAT
1 ATTTCAAATTTGTTCAATTAGTTCAAATTTAATATTA-AATATATTAATGTAAGCTTCAT
118974 ATTTCAAATTTGTTCAATT
1 ATTTCAAATTTGTTCAATT
118993 GATCCTTATA
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
58 1 0.01
59 2 0.03
60 54 0.75
61 15 0.21
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (59 bp):
ATTTCAAATTTGTTCAATTAGTTCAAATTTAATATTAAATATATTAATGTAAGCTTCAT
Found at i:119087 original size:30 final size:30
Alignment explanation
Indices: 119051--119190 Score: 171
Period size: 30 Copynumber: 4.6 Consensus size: 30
119041 TAATAAATTA
119051 ATATATAT-GTCATATATACTAATGAACTAT
1 ATATATATAGT-ATATATACTAATGAACTAT
*
119081 ATATATATAGT-TTTATTACTAATGAACTAT
1 ATATATATAGTATATA-TACTAATGAACTAT
*
119111 ATATATGTATAGTTTATAT-CTAAT-AACTAT
1 ATATA--TATAGTATATATACTAATGAACTAT
*
119141 ATAATGTATAGTTATATATACTAATGAACTAT
1 AT-ATATATAG-TATATATACTAATGAACTAT
119173 ATATATATAGTATATATA
1 ATATATATAGTATATATA
119191 TCTTATATTT
Statistics
Matches: 96, Mismatches: 5, Indels: 18
0.81 0.04 0.15
Matches are distributed among these distances:
29 8 0.08
30 49 0.51
31 21 0.22
32 15 0.16
33 3 0.03
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (30 bp):
ATATATATAGTATATATACTAATGAACTAT
Found at i:119188 original size:15 final size:15
Alignment explanation
Indices: 119108--119191 Score: 50
Period size: 15 Copynumber: 5.6 Consensus size: 15
119098 ACTAATGAAC
*
119108 TATATATATGTATAG
1 TATATATATATATAG
* * *
119123 TTTATATCTA-ATAAC
1 TATATATATATAT-AG
*
119138 TATATA-ATGTATAG
1 TATATATATATATAG
119152 T-TATATATACTA-ATG
1 TATATATATA-TATA-G
*
119167 AACTATATATATATAG
1 TA-TATATATATATAG
119183 TATATATAT
1 TATATATAT
119192 CTTATATTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 16
0.65 0.14 0.21
Matches are distributed among these distances:
13 4 0.08
14 8 0.16
15 25 0.50
16 4 0.08
17 9 0.18
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (15 bp):
TATATATATATATAG
Found at i:119189 original size:47 final size:47
Alignment explanation
Indices: 119138--119230 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 47
119128 ATCTAATAAC
119138 TATATA-AT-GTATAGTTAT-ATATACTAATGAACTATAT-ATATATAG
1 TATATATATCGTATA-TTATAATATACTAAT-AACTATATAATATATAG
* *
119183 TATATATATCTTATATTTTAATATACTAATAACTATATAATATATAG
1 TATATATATCGTATATTATAATATACTAATAACTATATAATATATAG
119230 T
1 T
119231 TTGTATATAC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
45 6 0.14
46 13 0.31
47 23 0.55
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.45
Consensus pattern (47 bp):
TATATATATCGTATATTATAATATACTAATAACTATATAATATATAG
Found at i:119193 original size:62 final size:61
Alignment explanation
Indices: 119051--119193 Score: 188
Period size: 62 Copynumber: 2.3 Consensus size: 61
119041 TAATAAATTA
*
119051 ATATATAT-GTCATATATA-CTAATGAACTATATATATATAGTTTTATTACTAATGAACTAT
1 ATATATATAGT-ATATATATCTAATGAACTATATATATATAGTTATATTACTAATGAACTAT
*
119111 ATATATGTATAGT-T-TATATCTAAT-AACTATATAATGTATAGTTATATATACTAATGAACTAT
1 ATATA--TATAGTATATATATCTAATGAACTATAT-ATATATAGTTATAT-TACTAATGAACTAT
119173 ATATATATAGTATATATATCT
1 ATATATATAGTATATATATCT
119194 TATATTTTAA
Statistics
Matches: 73, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
60 23 0.32
61 19 0.26
62 29 0.40
63 2 0.03
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (61 bp):
ATATATATAGTATATATATCTAATGAACTATATATATATAGTTATATTACTAATGAACTAT
Found at i:119238 original size:49 final size:49
Alignment explanation
Indices: 119152--119258 Score: 139
Period size: 47 Copynumber: 2.2 Consensus size: 49
119142 TAATGTATAG
* *
119152 TTATATATACTAATGAACTATATATATATAGTATATATATCTTATA-TT
1 TTATATATACTAATGAACTATATATATATAGTATATATACCATATACTT
*
119200 TTA-ATATACTAAT-AACTATATAATATATAGTTTGTATATACCATATACTT
1 TTATATATACTAATGAACTATAT-ATATATAG--TATATATACCATATACTT
119250 TTATATATA
1 TTATATATA
119259 GTTTTTATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
46 8 0.16
47 18 0.35
48 3 0.06
49 12 0.24
50 5 0.10
51 5 0.10
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (49 bp):
TTATATATACTAATGAACTATATATATATAGTATATATACCATATACTT
Found at i:119266 original size:13 final size:13
Alignment explanation
Indices: 119248--119274 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
119238 TACCATATAC
119248 TTTTATATATAGT
1 TTTTATATATAGT
119261 TTTTATATATAGT
1 TTTTATATATAGT
119274 T
1 T
119275 CATATGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TTTTATATATAGT
Found at i:119300 original size:16 final size:15
Alignment explanation
Indices: 119276--119322 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
119266 TATATAGTTC
*
119276 ATATGTAAACTATAGT
1 ATATATAAACTATA-T
119292 ATATATAAACTATAT
1 ATATATAAACTATAT
* *
119307 ATGTATATACTATAT
1 ATATATAAACTATAT
119322 A
1 A
119323 AATCGTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (15 bp):
ATATATAAACTATAT
Found at i:119497 original size:16 final size:16
Alignment explanation
Indices: 119465--119498 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
119455 TTTTTACATA
*
119465 TAGTTCATATGTAAAC
1 TAGTTCATATATAAAC
*
119481 TAGTTCATATATCAAC
1 TAGTTCATATATAAAC
119497 TA
1 TA
119499 TATAATTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (16 bp):
TAGTTCATATATAAAC
Found at i:119543 original size:30 final size:33
Alignment explanation
Indices: 119489--119552 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 33
119479 ACTAGTTCAT
119489 ATATCAACTATATAATTATATAGTTTATACATA
1 ATATCAACTATATAATTATATAGTTTATACATA
*
119522 ATATCAACTATA-AA-T-TATAGTTTATATATA
1 ATATCAACTATATAATTATATAGTTTATACATA
119552 A
1 A
119553 ACTATAGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 15 0.50
31 1 0.03
32 2 0.07
33 12 0.40
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (33 bp):
ATATCAACTATATAATTATATAGTTTATACATA
Found at i:119553 original size:18 final size:18
Alignment explanation
Indices: 119530--119567 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
119520 TAATATCAAC
*
119530 TATAAATTATAGTTTATA
1 TATAAACTATAGTTTATA
119548 TATAAACTATAGTTTATA
1 TATAAACTATAGTTTATA
119566 TA
1 TA
119568 GTTTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (18 bp):
TATAAACTATAGTTTATA
Found at i:119608 original size:2 final size:2
Alignment explanation
Indices: 119596--119842 Score: 94
Period size: 2 Copynumber: 124.0 Consensus size: 2
119586 TGTAAATTAC
* *
119596 TA TA TA GTA TA TA TA GTT TA TA TA TA TA -A TA TA TA GTA TA AA
1 TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
119638 TA TA AA CTA TA GA T- TA TA -A TG TA GTA TA TA CTA TA TA AA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* * * * * *
119679 -A TT TA TA TT TCA TA TG TA AA CTA TA TA T- TA GT- TT TA TA CA
1 TA TA TA TA TA T-A TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA
* * *
119719 T- TG TA TA TA TA GTT TA TGA T- TA -A TA TA TA TA -A TA TA TA GTT
1 TA TA TA TA TA TA -TA TA T-A TA TA TA TA TA TA TA TA TA TA TA -TA
*
119760 TA TA TA TA GTA TA TA -A TA -A TA TA -A TA TA -A CTA TA TA GTT
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
*
119799 TA TA T- TA TA GA TA TA TA TA TA TA TA TA TA TA 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
119839 TA TA
1 TA TA
119843 GTTTAGTTTT
Statistics
Matches: 182, Mismatches: 32, Indels: 62
0.66 0.12 0.22
Matches are distributed among these distances:
1 16 0.09
2 145 0.80
3 21 0.12
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:119621 original size:20 final size:20
Alignment explanation
Indices: 119555--119844 Score: 76
Period size: 20 Copynumber: 14.3 Consensus size: 20
119545 ATATATAAAC
* *
119555 TATAGTTTATATAGTTTTTA
1 TATAGTATATATAGTTTATA
* * **
119575 TATAATTCATATGTAAATTACTA
1 TAT-AGT-ATATATAGTTTA-TA
119598 TATAGTATATATAGTTTATA
1 TATAGTATATATAGTTTATA
119618 TATA-TAATATATAG--TATA
1 TATAGT-ATATATAGTTTATA
* * *
119636 AATA-TAAACTATAGATTATA
1 TATAGTATA-TATAGTTTATA
* *
119656 -AT-GTAGTATATACTATATA
1 TATAGTA-TATATAGTTTATA
* *
119675 AATA--ATTTATA-TTTCATA
1 TATAGTATATATAGTTT-ATA
* *
119693 TGTAAACTATATATTAGTTTTATA
1 --TATAGTATATA-TAG-TTTATA
* *
119717 CATTGTATATATAGTTTATGATTAA
1 TATAGTATATATAG-TT-T-A-T-A
*
119742 TATATATAATATATAGTTTATA
1 TATA-GT-ATATATAGTTTATA
* *
119764 TATAGTATATAATAATATA-A
1 TATAGTATAT-ATAGTTTATA
119784 TATA--ACTATATAGTTTATA
1 TATAGTA-TATATAGTTTATA
119803 TTATAG-ATATATA---TATA
1 -TATAGTATATATAGTTTATA
119820 TATA-TATATATA-TTATATA
1 TATAGTATATATAGTT-TATA
119839 TATAGT
1 TATAGT
119845 TTAGTTTTCA
Statistics
Matches: 202, Mismatches: 33, Indels: 70
0.66 0.11 0.23
Matches are distributed among these distances:
16 11 0.05
17 8 0.04
18 28 0.14
19 26 0.13
20 46 0.23
21 25 0.12
22 26 0.13
23 9 0.04
24 5 0.02
25 7 0.03
26 3 0.01
27 8 0.04
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (20 bp):
TATAGTATATATAGTTTATA
Found at i:119753 original size:27 final size:28
Alignment explanation
Indices: 119723--119847 Score: 91
Period size: 27 Copynumber: 4.4 Consensus size: 28
119713 TATACATTGT
119723 ATATATAGTTTATGAT-TAATATAT-ATA
1 ATATATAGTTTAT-ATATAATATATAATA
*
119750 ATATATAGTTTATATATAGTATATAATA
1 ATATATAGTTTATATATAATATATAATA
* * *
119778 ATATA-A-TATAACTATATAGTTTATATTATA
1 ATATATAGT-TTA-TATATA--ATATATAATA
* *
119808 GATATATA-TATATATAT-ATATATATTA
1 -ATATATAGTTTATATATAATATATAATA
119835 TATATATAGTTTA
1 -ATATATAGTTTA
119848 GTTTTCAATT
Statistics
Matches: 78, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
26 3 0.04
27 37 0.47
28 17 0.22
30 13 0.17
31 6 0.08
32 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.48
Consensus pattern (28 bp):
ATATATAGTTTATATATAATATATAATA
Found at i:120257 original size:207 final size:211
Alignment explanation
Indices: 119945--120655 Score: 1064
Period size: 215 Copynumber: 3.4 Consensus size: 211
119935 TTGATCCCTT
* * *
119945 TGTGTTTTTTAA-TTATTTAAAACTTATTTGTAATTTCGTATTTGTTCAATTTAGTCCTTAAAAT
1 TGTGTTGTTTAATTTATTT-AAATTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAAT
*
120009 TATATTTGCATAT-AAATTGGCCCATACTTATTACTTATTTATA-TTTTAATTAGCCCATAACTT
65 TATATTTGCATATGAAATTGGCTCATACTTATTACTTATTTATATTTTTAATTAGCCCATAACTT
*
120072 TTTAAAGGGTATAATTTAGTACTTTTTTGTA-TAATTTAAACTCACAATTTAAAATTATTTCGAT
130 TTTAAAGGGTATAATTTAGTACTTTTTTGTATTAATTTAACCTCACAATTTAAAATTATTTCGAT
120136 TTGA-CCCTCATCAATG
195 TTGATCCCTCATCAATG
*
120152 TGTGTTGTTTAATTTATTTAAATTTATTTTTAATTTCATA-TTGTTCAATTTAGTCCTTAAAATT
1 TGTGTTGTTTAATTTATTTAAATTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATT
*
120216 ATATTTGCATCTGAAA-TGGTCTCATACTTATTACTTATTTATATTTTTTAATTAGCCCATAACT
66 ATATTTGCATATGAAATTGG-CTCATACTTATTACTTATTTATA-TTTTTAATTAGCCCATAACT
* * *
120280 TTTTAAATGGTTTAATTTAGTACTTTTTTGTATTAATCTAGACCTCACAATTTAAAATTATTTCG
129 TTTTAAAGGGTATAATTTAGTACTTTTTTGTATTAATTTA-ACCTCACAATTTAAAATTATTTCG
120345 ATTTGATCCCTCATCAATG
193 ATTTGATCCCTCATCAATG
* *
120364 TGT-CTGTTTAATTTTTATTAAATTTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAA
1 TGTGTTGTTTAATTTAT-TTAAA---TTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAA
*
120428 AATTATATTTGCATATGAAATTAGCTCATACTTATTACTTATTTATATTTTTAATT-GACCCATA
62 AATTATATTTGCATATGAAATTGGCTCATACTTATTACTTATTTATATTTTTAATTAG-CCCATA
*
120492 ACTTTTTAAATGGGTAAAATTTAGTAC-TTTTTGTATTAATTTCAACCTCACAATTTAAAATTAT
126 ACTTTTTAAA-GGGTATAATTTAGTACTTTTTTGTATTAATTT-AACCTCACAATTTAAAATTAT
120556 TTCGATTTGATCCCTCATCAATG
189 TTCGATTTGATCCCTCATCAATG
* * * * *
120579 TGTGTTGTTTAATTTATTTAATTTTAATTTGTAATTTTATATTTATTCAATTTAGTTCTTAAATT
1 TGTGTTGTTTAATTTATTTAAATTT-ATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAAT
*
120644 TATATTTTCATA
65 TATATTTGCATA
120656 AAATTGAACC
Statistics
Matches: 458, Mismatches: 27, Indels: 32
0.89 0.05 0.06
Matches are distributed among these distances:
206 38 0.08
207 54 0.12
208 6 0.01
209 49 0.11
210 6 0.01
211 40 0.09
212 23 0.05
213 46 0.10
214 1 0.00
215 106 0.23
216 87 0.19
217 2 0.00
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.50
Consensus pattern (211 bp):
TGTGTTGTTTAATTTATTTAAATTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATT
ATATTTGCATATGAAATTGGCTCATACTTATTACTTATTTATATTTTTAATTAGCCCATAACTTT
TTAAAGGGTATAATTTAGTACTTTTTTGTATTAATTTAACCTCACAATTTAAAATTATTTCGATT
TGATCCCTCATCAATG
Found at i:120606 original size:15 final size:15
Alignment explanation
Indices: 120586--120631 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 15
120576 ATGTGTGTTG
120586 TTTAATTTATTTAAT
1 TTTAATTTATTTAAT
*
120601 TTTAA-TT-TGTAAT
1 TTTAATTTATTTAAT
*
120614 TTTATATTTATTCAAT
1 TTTA-ATTTATTTAAT
120630 TT
1 TT
120632 AGTTCTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 9 0.36
14 3 0.12
15 7 0.28
16 6 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTAATTTATTTAAT
Found at i:121641 original size:2 final size:2
Alignment explanation
Indices: 121636--121670 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
121626 GTGTATCAGC
121636 AT 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 AT A
121671 AGAGCAAGTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.