Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002194.1 Hibiscus syriacus cultivar Beakdansim tig00004471_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: 85261
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:143 original size:3 final size:3
Alignment explanation
Indices: 135--161 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
125 AAAGCCTGAA
135 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
162 GGGACAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4941 original size:13 final size:14
Alignment explanation
Indices: 4916--4943 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4906 ATGGTACTTG
4916 TTTAACTTTTTTTA
1 TTTAACTTTTTTTA
4930 TTTAACTTTTTTTA
1 TTTAACTTTTTTTA
4944 ATTTTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTAACTTTTTTTA
Found at i:5919 original size:22 final size:22
Alignment explanation
Indices: 5876--5920 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5866 AAAATAATAT
* *
5876 AAAAAACGTTATTATTAATTAA
1 AAAAAACGATATTATGAATTAA
* *
5898 AAAAAATGATATTATGATTTAA
1 AAAAAACGATATTATGAATTAA
5920 A
1 A
5921 TATATTAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (22 bp):
AAAAAACGATATTATGAATTAA
Found at i:6005 original size:71 final size:71
Alignment explanation
Indices: 5915--6106 Score: 271
Period size: 71 Copynumber: 2.7 Consensus size: 71
5905 GATATTATGA
* * **
5915 TTTAAATATATTAAATTTTTT-GAACAAAAAATAGTGCTATTATAAAAAAAATTGAAAGTGGAGA
1 TTTAAATATA--ATATTTTTTATAACAAAAGTTAGTGCTATTATAAAAAAAATTGAAAGTGGAGA
5979 CATGAGAT
64 CATGAGAT
* * *
5987 TTTAAATATAGTATTTTTTATTAACAAAAGTTAGTGCTATTA-ATAAAAACTTGAAAGTGGAGAC
1 TTTAAATATAATATTTTTTA-TAACAAAAGTTAGTGCTATTATAAAAAAAATTGAAAGTGGAGAC
6051 ATGAGAT
65 ATGAGAT
*
6058 TTTAAATATAATATTTTTTATAACAAAAGTTAGTGCTTTTATAAAAAAA
1 TTTAAATATAATATTTTTTATAACAAAAGTTAGTGCTATTATAAAAAAA
6107 TAAAAATTAA
Statistics
Matches: 107, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
70 27 0.25
71 52 0.49
72 28 0.26
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (71 bp):
TTTAAATATAATATTTTTTATAACAAAAGTTAGTGCTATTATAAAAAAAATTGAAAGTGGAGACA
TGAGAT
Found at i:6137 original size:18 final size:17
Alignment explanation
Indices: 6103--6141 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
6093 CTTTTATAAA
6103 AAAATAAAAATTAAATT
1 AAAATAAAAATTAAATT
6120 AAAATAATATAATT-AATT
1 AAAATAA-A-AATTAAATT
6138 AAAA
1 AAAA
6142 ACGTGGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATAAAAATTAAATT
Found at i:7559 original size:123 final size:123
Alignment explanation
Indices: 7421--8000 Score: 941
Period size: 123 Copynumber: 4.7 Consensus size: 123
7411 GAATCAATCT
* * * *
7421 AAGGTTGAACGAGTTCTTCTTCA-GATTAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTC-TCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
* *
7485 TGAACTTCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCGA
65 CGAACTTCTTCTGGAAATGTTGATGTTGATCTAGCTCCTTCTGTGATAGAATCAAGCGA
7544 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAC
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAC
* * *
7609 GAACTTCTTCTGGAAATGTTGATGTTAATCTATCTCCTTCTGTTATAGAATCAAGCGA
66 GAACTTCTTCTGGAAATGTTGATGTTGATCTAGCTCCTTCTGTGATAGAATCAAGCGA
* *
7667 AAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAC
* * *
7732 GAACTTCTTCTGGAAATGTTGATGTTGATCTGGCTCCTTATATGATAGAATCAAGCGA
66 GAACTTCTTCTGGAAATGTTGATGTTGATCTAGCTCCTTCTGTGATAGAATCAAGCGA
* * *
7790 AAGGTTGAACAAGTTTTTCTTCATGT-T-AACTTTTTCTTCCTTTTCAGATGAGTTCTTCTCATT
1 AAGGTTGAACAAGTTCTTC-TCAT-TATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
7853 ACGAACTTCTTCTGGAAATGTTGATGTTGATCTAGCTCCTTCTGTGATAGAATCAAGCGA
64 ACGAACTTCTTCTGGAAATGTTGATGTTGATCTAGCTCCTTCTGTGATAGAATCAAGCGA
* *
7913 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTTATTAC
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAC
7978 GAACTTCTTCTGGAAATGTTGAT
66 GAACTTCTTCTGGAAATGTTGAT
8001 CCATCGAGTG
Statistics
Matches: 424, Mismatches: 28, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
121 1 0.00
122 8 0.02
123 409 0.96
124 5 0.01
125 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAC
GAACTTCTTCTGGAAATGTTGATGTTGATCTAGCTCCTTCTGTGATAGAATCAAGCGA
Found at i:8501 original size:21 final size:23
Alignment explanation
Indices: 8472--8517 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
8462 TTATAAAATA
*
8472 TTTATAAAAGAAT-AAATTGAAT
1 TTTATAAAAGAATAAAATGGAAT
8494 TTTA-AAAAGAATAAAATGGAAT
1 TTTATAAAAGAATAAAATGGAAT
8516 TT
1 TT
8518 GGGAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (23 bp):
TTTATAAAAGAATAAAATGGAAT
Found at i:16257 original size:15 final size:15
Alignment explanation
Indices: 16237--16268 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
16227 TATAATGAAT
16237 AATGAATGTATGCAA
1 AATGAATGTATGCAA
16252 AATGAATGTATGCAA
1 AATGAATGTATGCAA
16267 AA
1 AA
16269 GATGTTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:20059 original size:71 final size:72
Alignment explanation
Indices: 19921--20114 Score: 291
Period size: 71 Copynumber: 2.7 Consensus size: 72
19911 GAGATTATGA
* ** * * *
19921 TTTAAATATATTAAATTTTATGAACAAAAATTAGTGCTATTATAAAAAAAATTGAAAGTGGAAAC
1 TTTAAATATAATATTTTTTATTAACAAAAGTTAGTGCTATTATAAAAAAACTTGAAAGTGGAAAC
19986 ATGAGAT
66 ATGAGAT
* *
19993 TTTAAATATAGTATTTTTTATTAACAAAAGTTAGTGCTATTA-AAAAAAACTTGAAAGTGGAGAC
1 TTTAAATATAATATTTTTTATTAACAAAAGTTAGTGCTATTATAAAAAAACTTGAAAGTGGAAAC
20057 ATGAGAT
66 ATGAGAT
* *
20064 TTTAAATATAATATTTTTTATTACCAAAAGTTAGTGCTTTTATAAAAAAAC
1 TTTAAATATAATATTTTTTATTAACAAAAGTTAGTGCTATTATAAAAAAAC
20115 AAAAATTAAA
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
71 66 0.59
72 45 0.41
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (72 bp):
TTTAAATATAATATTTTTTATTAACAAAAGTTAGTGCTATTATAAAAAAACTTGAAAGTGGAAAC
ATGAGAT
Found at i:23520 original size:28 final size:29
Alignment explanation
Indices: 23480--23537 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
23470 CTTAATTAAG
*
23480 TTTTTCGAAAT-AAAATCGAACATATAAT
1 TTTTTCGAAATAAAAATCCAACATATAAT
* * *
23508 TTTTTTGACATAAAAATCCAAGATATAAT
1 TTTTTCGAAATAAAAATCCAACATATAAT
23537 T
1 T
23538 AAAACTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (29 bp):
TTTTTCGAAATAAAAATCCAACATATAAT
Found at i:23645 original size:2 final size:2
Alignment explanation
Indices: 23638--23697 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
23628 ATGGTGAGTG
23638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23680 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
23698 TACAGATTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25185 original size:21 final size:23
Alignment explanation
Indices: 25140--25197 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
25130 AAGATTAAAA
25140 AAAAAAG-ATGAAAAGTAACCACC
1 AAAAAAGAAT-AAAAGTAACCACC
*
25163 AAAAATGAATAAAAG-AACC-CC
1 AAAAAAGAATAAAAGTAACCACC
*
25184 AAAAAAGGATAAAA
1 AAAAAAGAATAAAA
25198 AAGTTCACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 14 0.45
22 4 0.13
23 11 0.35
24 2 0.06
ACGTcount: A:0.66, C:0.14, G:0.12, T:0.09
Consensus pattern (23 bp):
AAAAAAGAATAAAAGTAACCACC
Found at i:35678 original size:7 final size:7
Alignment explanation
Indices: 35668--35697 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
35658 TGTTATTCTT
35668 TATAGTA
1 TATAGTA
35675 TATAGTA
1 TATAGTA
35682 TATAGTA
1 TATAGTA
35689 TATATGTA
1 TATA-GTA
35697 T
1 T
35698 TATATTACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (7 bp):
TATAGTA
Found at i:36930 original size:13 final size:14
Alignment explanation
Indices: 36914--36942 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
36904 TTTTATAGTC
36914 TATTTTTATTT-TT
1 TATTTTTATTTATT
36927 TATTTTTATTTATT
1 TATTTTTATTTATT
36941 TA
1 TA
36943 ATAGTACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTTATTTATT
Found at i:37046 original size:5 final size:5
Alignment explanation
Indices: 37038--37162 Score: 80
Period size: 5 Copynumber: 25.6 Consensus size: 5
37028 CTTTTTCCTT
* * * * * * *
37038 TTTTG TTTTA TTTAA TTTTG TTTTA -TTAA TTTAA TTTT- TTCTA -TTCA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* *
37085 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT- TATGTA TTTTA -TGTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA
* * * *
37134 ATTTG TTTGA TTTTT TCTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA T-TTTA TTTTA TTT
37163 ATGTTAATAT
Statistics
Matches: 90, Mismatches: 23, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
4 12 0.13
5 73 0.81
6 5 0.06
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:37071 original size:19 final size:18
Alignment explanation
Indices: 37047--37101 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
37037 TTTTTGTTTT
37047 ATTTAATTTTGTTTTATTA
1 ATTTAATTTT-TTTTATTA
* *
37066 ATTTAATTTTTTCTATTC
1 ATTTAATTTTTTTTATTA
*
37084 ATTTTATTTTATTTTATT
1 ATTTAATTTT-TTTTATT
37102 TTATTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTAATTTTTTTTATTA
Found at i:37149 original size:35 final size:34
Alignment explanation
Indices: 37084--37170 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 34
37074 TTTTCTATTC
* *
37084 ATTTTATTTTATTTTATTTTATTTTATTTTTATGT
1 ATTTTA-TTTATTTTAATTTATTTGATTTTTATGT
* * * *
37119 ATTTTATGTATTTTAATTTGTTTGATTTTTTCTTT
1 ATTTTATTTATTTTAATTTATTTGA-TTTTTATGT
*
37154 ATTTTATTTATGTTAAT
1 ATTTTATTTATTTTAAT
37171 ATTTTCCATT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 15 0.35
35 28 0.65
ACGTcount: A:0.21, C:0.01, G:0.06, T:0.72
Consensus pattern (34 bp):
ATTTTATTTATTTTAATTTATTTGATTTTTATGT
Found at i:37158 original size:9 final size:9
Alignment explanation
Indices: 37044--37164 Score: 65
Period size: 9 Copynumber: 13.6 Consensus size: 9
37034 CCTTTTTTGT
*
37044 TTTATTTAA
1 TTTATTTTA
*
37053 TTTTGTTTTA
1 -TTTATTTTA
* *
37063 TTAATTTAA
1 TTTATTTTA
37072 TTT-TTTCTA
1 TTTATTT-TA
*
37081 TTCATTTTA
1 TTTATTTTA
37090 TTTTATTTTA
1 -TTTATTTTA
37100 TTTTATTTTA
1 -TTTATTTTA
37110 --T-TTTTA
1 TTTATTTTA
*
37116 TGTATTTTA
1 TTTATTTTA
*
37125 TGTATTTTAA
1 TTTATTTT-A
* *
37135 TTTGTTTGA
1 TTTATTTTA
*
37144 -TT-TTTTC
1 TTTATTTTA
37151 TTTATTTTA
1 TTTATTTTA
37160 TTTAT
1 TTTAT
37165 GTTAATATTT
Statistics
Matches: 87, Mismatches: 15, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
6 5 0.06
7 4 0.05
8 8 0.09
9 36 0.41
10 34 0.39
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (9 bp):
TTTATTTTA
Found at i:43933 original size:6 final size:6
Alignment explanation
Indices: 43922--43975 Score: 54
Period size: 6 Copynumber: 8.0 Consensus size: 6
43912 GTCCTAAGTT
43922 GAAAAA GAAAAA GAAAAGAGA GAAAAA GAAAAA GAAAAAAA GAAAAA GAGAAAA
1 GAAAAA GAAAAA G-AAA-A-A GAAAAA GAAAAA G--AAAAA GAAAAA GA-AAAA
43976 ACATTTAGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
6 22 0.52
7 8 0.19
8 10 0.24
9 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:43948 original size:21 final size:20
Alignment explanation
Indices: 43922--43975 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
43912 GTCCTAAGTT
*
43922 GAAAAAGAAAAAGAAAAGAGA
1 GAAAAAGAAAAAGAAAA-AAA
43943 GAAAAAGAAAAAGAAAAAAA
1 GAAAAAGAAAAAGAAAAAAA
43963 GAAAAAGAGAAAA
1 GAAAAAGA-AAAA
43976 ACATTTAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (20 bp):
GAAAAAGAAAAAGAAAAAAA
Found at i:43961 original size:14 final size:14
Alignment explanation
Indices: 43923--43976 Score: 83
Period size: 14 Copynumber: 3.9 Consensus size: 14
43913 TCCTAAGTTG
43923 AAAA-AGAAAAAGA
1 AAAAGAGAAAAAGA
43936 AAAGAGAGAAAAAGA
1 AAA-AGAGAAAAAGA
*
43951 AAAAGAAAAAAAGA
1 AAAAGAGAAAAAGA
43965 AAAAGAGAAAAA
1 AAAAGAGAAAAA
43977 CATTTAGGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 3 0.08
14 22 0.59
15 12 0.32
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAGAAAAAGA
Found at i:44030 original size:6 final size:6
Alignment explanation
Indices: 44014--44071 Score: 57
Period size: 6 Copynumber: 9.3 Consensus size: 6
44004 CCCTAAATTG
*
44014 AAAGAAA AAAGAA AAAG-A AAAGAAA AAGAGAAA AAATAA AAAGAA AAAG-A
1 AAAG-AA AAAGAA AAAGAA AAAG-AA AA-AG-AA AAAGAA AAAGAA AAAGAA
44064 AAAGAA AA
1 AAAGAA AA
44072 TAAGGTGGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
5 10 0.22
6 20 0.44
7 8 0.18
8 7 0.16
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:44034 original size:11 final size:11
Alignment explanation
Indices: 44020--44071 Score: 72
Period size: 11 Copynumber: 4.8 Consensus size: 11
44010 ATTGAAAGAA
44020 AAAAGAAAAAG
1 AAAAGAAAAAG
44031 AAAAGAAAAAG
1 AAAAGAAAAAG
*
44042 AGAAA-AAATA-
1 A-AAAGAAAAAG
44052 AAAAGAAAAAG
1 AAAAGAAAAAG
44063 AAAAGAAAA
1 AAAAGAAAA
44072 TAAGGTGGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
9 3 0.08
10 5 0.14
11 25 0.69
12 3 0.08
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:44046 original size:26 final size:27
Alignment explanation
Indices: 44016--44066 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
44006 CTAAATTGAA
44016 AGAAAAAAGAAAAAG-AAAAGAAAAAG
1 AGAAAAAAGAAAAAGAAAAAGAAAAAG
*
44042 AGAAAAAATAAAAAGAAAAAGAAAA
1 AGAAAAAAGAAAAAGAAAAAGAAAA
44067 GAAAATAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (27 bp):
AGAAAAAAGAAAAAGAAAAAGAAAAAG
Found at i:44054 original size:15 final size:14
Alignment explanation
Indices: 44014--44066 Score: 58
Period size: 13 Copynumber: 4.0 Consensus size: 14
44004 CCCTAAATTG
*
44014 AAAGAAAAA-AGAA
1 AAAGAAAAAGAAAA
44027 AAAG-AAAAGAAAA
1 AAAGAAAAAGAAAA
* *
44040 AGAGAAAAA-ATAA
1 AAAGAAAAAGAAAA
44053 AAAGAAAAAGAAAA
1 AAAGAAAAAGAAAA
44067 GAAAATAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 4 0.12
13 21 0.66
14 7 0.22
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (14 bp):
AAAGAAAAAGAAAA
Found at i:44836 original size:11 final size:11
Alignment explanation
Indices: 44822--44846 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44812 ATATGCACAA
44822 CATTTTAGTTG
1 CATTTTAGTTG
44833 CATTTTAGTTG
1 CATTTTAGTTG
44844 CAT
1 CAT
44847 GTAGGTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.52
Consensus pattern (11 bp):
CATTTTAGTTG
Found at i:72250 original size:18 final size:18
Alignment explanation
Indices: 72206--72265 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
72196 ATAATACTAC
72206 TAATAATAATTATAATTTTA
1 TAATAATAATTATAA--TTA
** *
72226 TTGTAATAATTATGATTA
1 TAATAATAATTATAATTA
*
72244 TAATAATAATTATTATTA
1 TAATAATAATTATAATTA
72262 TAAT
1 TAAT
72266 GTAATAGTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 22 0.65
20 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TAATAATAATTATAATTA
Found at i:72517 original size:55 final size:55
Alignment explanation
Indices: 72458--72671 Score: 252
Period size: 55 Copynumber: 3.9 Consensus size: 55
72448 TTTCGGAAAA
* * * *
72458 CATGTCTGCTCCCTATTCTTTCAGAGAGTATAGGACTTGATCAATCTTCAACAAT
1 CATGTCTGCTCCCTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
* * * * *
72513 CATGTATGCTCCCTATTTC-TTCAGAGAGTATGAGACTCGAATAATCTTTAATAAT
1 CATGTCTGCTCCCTA-TTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
* * * * *
72568 CGTGTCCT-CTCTCTATTCGTTCAAAGAGTATAAGACTCGAACAGTCTTGAACAAT
1 CATGT-CTGCTCCCTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
* *
72623 CATGTCCGCTCTCTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTC
1 CATGTCTGCTCCCTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTC
72672 TTCTTATGGA
Statistics
Matches: 133, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
54 4 0.03
55 125 0.94
56 4 0.03
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (55 bp):
CATGTCTGCTCCCTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
Found at i:72648 original size:110 final size:110
Alignment explanation
Indices: 72470--72670 Score: 278
Period size: 110 Copynumber: 1.8 Consensus size: 110
72460 TGTCTGCTCC
* * * * * *
72470 CTATTCTTTCAGAGAGTATAGGACTTGATCAATCTTCAACAATCATGTATGCTCCCTATTTCTTC
1 CTATTCGTTCAAAGAGTATAAGACTCGAACAATCTTCAACAATCATGTACGCTCCCTATTTCTTC
* *
72535 AGAGAGTATGAGACTCGAATAATCTTTAATAATCGTGTCCTCTCT
66 AGAGAGTATAAGACTCGAACAATCTTTAATAATCGTGTCCTCTCT
* * * *
72580 CTATTCGTTCAAAGAGTATAAGACTCGAACAGTCTTGAACAATCATGTCCGCTCTCTA-TTCGTT
1 CTATTCGTTCAAAGAGTATAAGACTCGAACAATCTTCAACAATCATGTACGCTCCCTATTTC-TT
72644 CAGAGAGTATAAGACTCGAACAATCTT
65 CAGAGAGTATAAGACTCGAACAATCTT
72671 CTTCTTATGG
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
109 3 0.04
110 75 0.96
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (110 bp):
CTATTCGTTCAAAGAGTATAAGACTCGAACAATCTTCAACAATCATGTACGCTCCCTATTTCTTC
AGAGAGTATAAGACTCGAACAATCTTTAATAATCGTGTCCTCTCT
Found at i:72744 original size:54 final size:54
Alignment explanation
Indices: 72686--73039 Score: 469
Period size: 54 Copynumber: 6.6 Consensus size: 54
72676 TATGGATTCA
* *
72686 CTCCCTCTTTCTCTAGGGAGTATGAAACTCGGACATCTTCTTCAAACGGGTTTG
1 CTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCG
*
72740 CTCCCTCTTTCTCTAGGGAGTATGGAACTCAGACATCTTCTTCAAACGGGTTCG
1 CTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCG
* * * * ** *
72794 CTCCCTCTTGCTCTAAGGAGTATGGAACTTGAACATCTTCTTCTTACGGGTTTG
1 CTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCG
* *
72848 CTCCCTCTTTATCTAGGGAGTATGAAACTCGGACATCTTCTTCAAACGGGTTCG
1 CTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCG
* * * *
72902 TTCCCTCTTTCTCCAGGGAGTATGGAACCCGGATATCTTCTTCAAACGGGTTCG
1 CTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCG
* * * * *
72956 CTCCCTCTTTCT-TCAGGGAGTATAGAACTCGAACGTCTTCTTCAAACGAGATCG
1 CTCCCTCTTTCTCT-AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCG
* *
73010 CTCCTTCTTTC-CTTAAGGAGTATGGAACTC
1 CTCCCTCTTTCTC-TAGGGAGTATGGAACTC
73040 AAATAATCTT
Statistics
Matches: 259, Mismatches: 38, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
54 258 1.00
55 1 0.00
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.33
Consensus pattern (54 bp):
CTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCG
Found at i:72856 original size:162 final size:162
Alignment explanation
Indices: 72648--72998 Score: 517
Period size: 162 Copynumber: 2.2 Consensus size: 162
72638 TTCGTTCAGA
* *
72648 GAGTATA-AGACTCGAACAATCTTCTTCTTATGGATTCACTCCCTCTTTCTCTAGGGAGTATGAA
1 GAGTATAGA-ACTCGAAC-ATCTTCTTCTTACGGATTCACTCCCTCTTTATCTAGGGAGTATGAA
* * *
72712 ACTCGGACATCTTCTTCAAACGGGTTTGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAGACATC
64 ACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCCAGGGAGTATGGAACCCAGACATC
72777 TTCTTCAAACGGGTTCGCTCCCTCTTGC-TCTAAG
129 TTCTTCAAACGGGTTCGCTCCCTCTTGCTTC-AAG
* * * **
72811 GAGTATGGAACTTGAACATCTTCTTCTTACGGGTTTGCTCCCTCTTTATCTAGGGAGTATGAAAC
1 GAGTATAGAACTCGAACATCTTCTTCTTACGGATTCACTCCCTCTTTATCTAGGGAGTATGAAAC
* * *
72876 TCGGACATCTTCTTCAAACGGGTTCGTTCCCTCTTTCTCCAGGGAGTATGGAACCCGGATATCTT
66 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCCAGGGAGTATGGAACCCAGACATCTT
* *
72941 CTTCAAACGGGTTCGCTCCCTCTTTCTTCAGG
131 CTTCAAACGGGTTCGCTCCCTCTTGCTTCAAG
*
72973 GAGTATAGAACTCGAACGTCTTCTTC
1 GAGTATAGAACTCGAACATCTTCTTC
72999 AAACGAGATC
Statistics
Matches: 168, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
162 152 0.90
163 15 0.09
164 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (162 bp):
GAGTATAGAACTCGAACATCTTCTTCTTACGGATTCACTCCCTCTTTATCTAGGGAGTATGAAAC
TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCCAGGGAGTATGGAACCCAGACATCTT
CTTCAAACGGGTTCGCTCCCTCTTGCTTCAAG
Found at i:74777 original size:125 final size:124
Alignment explanation
Indices: 74550--74819 Score: 355
Period size: 125 Copynumber: 2.2 Consensus size: 124
74540 CCTTCACTAG
* * * *
74550 TGCCGCAACATCATCTTATACCGGTACGGGCCTTCAAAATGCCCAAACACCTCAAATTGTAAGGC
1 TGCCCCAACATTATCTTA-ACTGGTACGAGCCTTCAAAATGCCCAAACACCTCAAATTGTAAGGC
* * * *
74615 TCATTCTCAAGGCATTCTTGGTCTGTATCTTGTCATCTCAACATGATGTGGGTTCAGTCA
65 TCATTCTCAAGGCATCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTACAGACA
* **
74675 TGCCCCAACATTATCTTAACTGGTACGAGCCTTCAAAATGCCCCCATTACCTCAAATTGTAAGGC
1 TGCCCCAACATTATCTTAACTGGTACGAGCCTTCAAAATG-CCCAAACACCTCAAATTGTAAGGC
* * * *
74740 TCATTCTTC-ATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGGTGTGGGTACAGACG
65 TCATTC-TCAAGGCATCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTACAGACA
*
74800 TGCCCCAACA-TATCATAACT
1 TGCCCCAACATTATCTTAACT
74820 TGAATGTTCT
Statistics
Matches: 127, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
124 29 0.23
125 96 0.76
126 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (124 bp):
TGCCCCAACATTATCTTAACTGGTACGAGCCTTCAAAATGCCCAAACACCTCAAATTGTAAGGCT
CATTCTCAAGGCATCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTACAGACA
Found at i:76085 original size:14 final size:13
Alignment explanation
Indices: 76066--76109 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
76056 TCATTTCCAA
76066 TTTTCTTTTCTTT
1 TTTTCTTTTCTTT
76079 GTTTTCTATTT-TTT
1 -TTTTCT-TTTCTTT
76093 TTTTCTTCTTCTTT
1 TTTTCTT-TTCTTT
76107 TTT
1 TTT
76110 CTACATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 8 0.30
14 15 0.56
15 3 0.11
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (13 bp):
TTTTCTTTTCTTT
Found at i:78747 original size:41 final size:42
Alignment explanation
Indices: 78700--78830 Score: 160
Period size: 41 Copynumber: 3.1 Consensus size: 42
78690 TTCTTACCTA
78700 TCTTCATGTCTTTATGAAGGGTCTTCATGTCTTTATGAAT-G
1 TCTTCATGTCTTTATGAAGGGTCTTCATGTCTTTATGAATGG
*
78741 TCTTCATGTCTTTATGAATGGTCTTCATGTCTTTATGAATGG
1 TCTTCATGTCTTTATGAAGGGTCTTCATGTCTTTATGAATGG
** * * *
78783 TCTTC-TCGTCCTTGGTGAATGGTTTTC-TCGTCTTTATGAACGG
1 TCTTCAT-GT-CTTTATGAAGGGTCTTCAT-GTCTTTATGAATGG
78826 TCTTC
1 TCTTC
78831 TCATCCTTGG
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
41 40 0.49
42 9 0.11
43 32 0.40
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.47
Consensus pattern (42 bp):
TCTTCATGTCTTTATGAAGGGTCTTCATGTCTTTATGAATGG
Found at i:78768 original size:62 final size:64
Alignment explanation
Indices: 78700--78830 Score: 171
Period size: 62 Copynumber: 2.1 Consensus size: 64
78690 TTCTTACCTA
* *
78700 TCTTCATGTCTTTATGAAGGGTCTTCAT-GT-CTTTATGAAT-GTCTTCAT-GTCTTTATGAATG
1 TCTTCATGTCTTTATGAAGGGTCTTC-TCGTCCTTGATGAATGGTCTTC-TCGTCTTTATGAACG
78761 G
64 G
* * *
78762 TCTTCATGTCTTTATGAATGGTCTTCTCGTCCTTGGTGAATGGTTTTCTCGTCTTTATGAACGG
1 TCTTCATGTCTTTATGAAGGGTCTTCTCGTCCTTGATGAATGGTCTTCTCGTCTTTATGAACGG
78826 TCTTC
1 TCTTC
78831 TCATCCTTGG
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
61 1 0.02
62 27 0.45
63 9 0.15
64 23 0.38
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.47
Consensus pattern (64 bp):
TCTTCATGTCTTTATGAAGGGTCTTCTCGTCCTTGATGAATGGTCTTCTCGTCTTTATGAACGG
Found at i:78816 original size:43 final size:43
Alignment explanation
Indices: 78714--78841 Score: 156
Period size: 43 Copynumber: 3.0 Consensus size: 43
78704 CATGTCTTTA
* **
78714 TGAAGGGTCTTCATGTCTTTATGAAT-GTCTTCAT-GT-CTTTA
1 TGAATGGTCTTCATGTCTTTATGAATGGTCTTC-TCGTCCTTGG
78755 TGAATGGTCTTCATGTCTTTATGAATGGTCTTCTCGTCCTTGG
1 TGAATGGTCTTCATGTCTTTATGAATGGTCTTCTCGTCCTTGG
* * *
78798 TGAATGGTTTTC-TCGTCTTTATGAACGGTCTTCTCATCCTTGG
1 TGAATGGTCTTCAT-GTCTTTATGAATGGTCTTCTCGTCCTTGG
78841 T
1 T
78842 ATGACTGTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
41 26 0.34
42 9 0.12
43 42 0.55
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (43 bp):
TGAATGGTCTTCATGTCTTTATGAATGGTCTTCTCGTCCTTGG
Found at i:78832 original size:21 final size:21
Alignment explanation
Indices: 78700--78830 Score: 169
Period size: 21 Copynumber: 6.2 Consensus size: 21
78690 TTCTTACCTA
*
78700 TCTTCATGTCTTTATGAAGGG
1 TCTTCATGTCTTTATGAATGG
78721 TCTTCATGTCTTTATGAAT-G
1 TCTTCATGTCTTTATGAATGG
78741 TCTTCATGTCTTTATGAATGG
1 TCTTCATGTCTTTATGAATGG
78762 TCTTCATGTCTTTATGAATGG
1 TCTTCATGTCTTTATGAATGG
**
78783 TCTTC-TCGTCCTTGGTGAATGG
1 TCTTCAT-GT-CTTTATGAATGG
* *
78805 TTTTC-TCGTCTTTATGAACGG
1 TCTTCAT-GTCTTTATGAATGG
78826 TCTTC
1 TCTTC
78831 TCATCCTTGG
Statistics
Matches: 99, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
20 21 0.21
21 60 0.61
22 18 0.18
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.47
Consensus pattern (21 bp):
TCTTCATGTCTTTATGAATGG
Found at i:83113 original size:14 final size:14
Alignment explanation
Indices: 83089--83141 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 14
83079 TTCTTTTTCC
83089 TTTTAATTAATTTTG
1 TTTT-ATTAATTTTG
*
83104 TTTTATTAATTTTAT
1 TTTTATTAATTTT-G
83119 TATTCTATTAATTTTG
1 T-TT-TATTAATTTTG
83135 TTTTATT
1 TTTTATT
83142 TCACTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 13 0.39
15 7 0.21
16 3 0.09
17 10 0.30
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (14 bp):
TTTTATTAATTTTG
Found at i:83151 original size:11 final size:9
Alignment explanation
Indices: 83135--83192 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 9
83125 ATTAATTTTG
83135 TTTTATTTCA
1 TTTTATTT-A
83145 CTTTTATTTA
1 -TTTTATTTA
83155 TTTTA-TTA
1 TTTTATTTA
83163 TTTTAATTTA
1 TTTT-ATTTA
*
83173 TTTGA-TT-
1 TTTTATTTA
83180 TTTTATTTTA
1 TTTTA-TTTA
83190 TTT
1 TTT
83193 ATGTTAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
7 4 0.10
8 9 0.22
9 9 0.22
10 10 0.25
11 8 0.20
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:83183 original size:17 final size:18
Alignment explanation
Indices: 83146--83192 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
83136 TTTATTTCAC
*
83146 TTTT-ATTTATTTTATTA
1 TTTTAATTTATTTGATTA
83163 TTTTAATTTATTTGATT-
1 TTTTAATTTATTTGATTA
*
83180 TTTTATTTTATTT
1 TTTTAATTTATTT
83193 ATGTTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTAATTTATTTGATTA
Found at i:83187 original size:30 final size:29
Alignment explanation
Indices: 83151--83227 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
83141 TTCACTTTTA
**
83151 TTTATTTTATTATTTTAAT-TTATTTGATTT
1 TTTATTTTATTATTTTAATATT-TTCCA-TT
*
83181 TTTATTTTATTTATGTTAATATTTTCCATT
1 TTTATTTTA-TTATTTTAATATTTTCCATT
*
83211 TTTCTTTTATTATTTTA
1 TTTATTTTATTATTTTA
83228 TTTTTGTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 7 0.17
30 19 0.47
31 12 0.30
32 2 0.05
ACGTcount: A:0.22, C:0.04, G:0.03, T:0.71
Consensus pattern (29 bp):
TTTATTTTATTATTTTAATATTTTCCATT
Found at i:83189 original size:39 final size:39
Alignment explanation
Indices: 83099--83205 Score: 108
Period size: 42 Copynumber: 2.7 Consensus size: 39
83089 TTTTAATTAA
* * * *
83099 TTTTGTTTTATTAATTTTATTATTCTATTAATTTTGTTT
1 TTTTATTTTATTTATTTTATTATTTTATTAATTTTGATT
*
83138 TATTTCACTTTTATTTATTTTATTATTTTAATTTA-TTTGATT
1 T-TTT-A-TTTTATTTATTTTATTATTTT-ATTAATTTTGATT
* *
83180 TTTTATTTTATTTATGTTAATATTTT
1 TTTTATTTTATTTATTTTATTATTTT
83206 CCATTTTTCT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 20 0.35
40 4 0.07
41 3 0.05
42 26 0.46
43 4 0.07
ACGTcount: A:0.22, C:0.03, G:0.04, T:0.71
Consensus pattern (39 bp):
TTTTATTTTATTTATTTTATTATTTTATTAATTTTGATT
Found at i:83205 original size:22 final size:22
Alignment explanation
Indices: 83147--83205 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
83137 TTATTTCACT
*
83147 TTTATTT-ATTTTATTATTTTAA
1 TTTATTTAATATT-TTATTTTAA
* *
83169 TTTATTTGATTTTTTATTTT-A
1 TTTATTTAATATTTTATTTTAA
83190 TTTATGTTAATATTTT
1 TTTAT-TTAATATTTT
83206 CCATTTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 6 0.18
22 22 0.67
23 5 0.15
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (22 bp):
TTTATTTAATATTTTATTTTAA
Found at i:85078 original size:22 final size:22
Alignment explanation
Indices: 85010--85091 Score: 78
Period size: 22 Copynumber: 3.7 Consensus size: 22
85000 TGAGTTAACT
*
85010 CGTTGACTTTGACTAAGTCA-AC
1 CGTTGACTTTGACT-TGTCAGAC
** *
85032 CGTTGACTTTGACCGGT-ATGCC
1 CGTTGACTTTGACTTGTCA-GAC
85054 CGTTGACTTTGACTTGTCAGAC
1 CGTTGACTTTGACTTGTCAGAC
*
85076 CGTTGATTGTTGACTT
1 CGTTGACT-TTGACTT
85092 TGACAAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.02
21 2 0.04
22 38 0.78
23 8 0.16
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (22 bp):
CGTTGACTTTGACTTGTCAGAC
Done.