Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001678.1 Hibiscus syriacus cultivar Beakdansim tig00003355_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: 107383
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:297 original size:19 final size:20
Alignment explanation
Indices: 273--318 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
263 TTTAATTTTC
*
273 AATTGATAGAGACAA-TTGT
1 AATTGATAGAGACAATTTAT
**
292 AATTGATTTAGACAATTTAT
1 AATTGATAGAGACAATTTAT
312 AATTGAT
1 AATTGAT
319 TTTAAAGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.39
Consensus pattern (20 bp):
AATTGATAGAGACAATTTAT
Found at i:316 original size:20 final size:19
Alignment explanation
Indices: 282--320 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
272 CAATTGATAG
*
282 AGACAATTGTAATTGATTT
1 AGACAATTATAATTGATTT
301 AGACAATTTATAATTGATTT
1 AGACAA-TTATAATTGATTT
321 TAAAGCTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (19 bp):
AGACAATTATAATTGATTT
Found at i:2007 original size:16 final size:17
Alignment explanation
Indices: 1986--2035 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
1976 TAGTTAATTT
1986 TATTTAAAAAATAA-AA
1 TATTTAAAAAATAATAA
*
2002 TATTTAAAATTATAATAA
1 TATTTAAAA-AATAATAA
*
2020 GATTTAAAAATATAAT
1 TATTTAAAAA-ATAAT
2036 TGTAAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 9 0.32
17 4 0.14
18 15 0.54
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
TATTTAAAAAATAATAA
Found at i:5076 original size:2 final size:2
Alignment explanation
Indices: 5069--5100 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5059 GATATGTTTA
5069 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
5101 TGAATTCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11732 original size:2 final size:2
Alignment explanation
Indices: 11719--11748 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11709 CGACAAAGTC
*
11719 AT AT AT AC 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
11749 TGAATCAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11958 original size:11 final size:11
Alignment explanation
Indices: 11942--11966 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11932 TATAGATAAG
11942 CATGTTTTCTT
1 CATGTTTTCTT
11953 CATGTTTTCTT
1 CATGTTTTCTT
11964 CAT
1 CAT
11967 ATTGATAAAG
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:0.12, C:0.20, G:0.08, T:0.60
Consensus pattern (11 bp):
CATGTTTTCTT
Found at i:13435 original size:17 final size:17
Alignment explanation
Indices: 13413--13446 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
13403 GTAAGCTGCA
13413 CAAATATTTTTTAATTG
1 CAAATATTTTTTAATTG
13430 CAAATATTTTTTAATTG
1 CAAATATTTTTTAATTG
13447 GTACAATCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
CAAATATTTTTTAATTG
Found at i:14819 original size:94 final size:95
Alignment explanation
Indices: 14653--14849 Score: 342
Period size: 94 Copynumber: 2.1 Consensus size: 95
14643 AGTGCTTGAA
*
14653 CCTATAACCTCTAAGAACAACAACGACTATTTTAATCACTGTGATAAGTTAGTTCGTGCTAATCC
1 CCTATAACCTCTAAG-A-AACAACGACTATTTTAATCACTGTGATAAGTTAGTTCATGCTAATCC
*
14718 TTTTCCTTTAATTGGCATAATTTGATCCCTCT
64 TTCTCCTTTAATTGGCATAATTTGATCCCTCT
*
14750 CCTATAACCTCTAAG-AACAACGACTCTTTTAATCACTGTGATAAGTTAGTTCATGCTAATCCTT
1 CCTATAACCTCTAAGAAACAACGACTATTTTAATCACTGTGATAAGTTAGTTCATGCTAATCCTT
14814 CTCCTTTAATTGGCATAATTTGATCCCTCT
66 CTCCTTTAATTGGCATAATTTGATCCCTCT
14844 CCTATA
1 CCTATA
14850 TAATATCATC
Statistics
Matches: 97, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
94 82 0.85
97 15 0.15
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (95 bp):
CCTATAACCTCTAAGAAACAACGACTATTTTAATCACTGTGATAAGTTAGTTCATGCTAATCCTT
CTCCTTTAATTGGCATAATTTGATCCCTCT
Found at i:25339 original size:13 final size:14
Alignment explanation
Indices: 25321--25352 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
25311 TTAGTGAGAC
25321 ATAATAATAATA-T
1 ATAATAATAATACT
25334 ATAATAATAATACT
1 ATAATAATAATACT
25348 ATAAT
1 ATAAT
25353 GAGATGGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATAATAATACT
Found at i:25573 original size:23 final size:24
Alignment explanation
Indices: 25539--25607 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 24
25529 CACCACAGCT
*
25539 CGTATAAATACACCGAAGTGCCA-
1 CGTAGAAATACACCGAAGTGCCAG
*
25562 CGTAGAATTACACCGAAGTG-CAG
1 CGTAGAAATACACCGAAGTGCCAG
*
25585 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
25608 TATAAAATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
22 2 0.05
23 36 0.90
24 2 0.05
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (24 bp):
CGTAGAAATACACCGAAGTGCCAG
Found at i:27632 original size:19 final size:19
Alignment explanation
Indices: 27605--27643 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
27595 GATAAAAGGA
27605 AAAAAATATAAACCATATG
1 AAAAAATATAAACCATATG
* * *
27624 AAAAGATATGAGCCATATG
1 AAAAAATATAAACCATATG
27643 A
1 A
27644 TATGATCTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (19 bp):
AAAAAATATAAACCATATG
Found at i:28174 original size:6 final size:6
Alignment explanation
Indices: 28165--28190 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28155 TAATGAAATG
28165 ATATGT ATATGT ATATGT ATATGT AT
1 ATATGT ATATGT ATATGT ATATGT AT
28191 GTATTTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:46748 original size:22 final size:23
Alignment explanation
Indices: 46723--46773 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
46713 TGAAAATAAT
46723 TTTTATGTT-ATTTTATAAATGC
1 TTTTATGTTAATTTTATAAATGC
* * * *
46745 TTTTATTTTAATTTTCTTAATGG
1 TTTTATGTTAATTTTATAAATGC
46768 TTTTAT
1 TTTTAT
46774 ATGGTTGCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.65
Consensus pattern (23 bp):
TTTTATGTTAATTTTATAAATGC
Found at i:50252 original size:3 final size:3
Alignment explanation
Indices: 50237--50288 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
50227 CGGGTTTTAA
*
50237 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
50285 ATT A
1 ATT A
50289 CCCTACCCAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:50359 original size:20 final size:20
Alignment explanation
Indices: 50334--50378 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
50324 CCACTCAACT
50334 TTCCACCATTCCATGTTTTA
1 TTCCACCATTCCATGTTTTA
*
50354 TTCCACCATTCCATGTTTTC
1 TTCCACCATTCCATGTTTTA
50374 TTCCA
1 TTCCA
50379 TGTTTTATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.33, G:0.04, T:0.44
Consensus pattern (20 bp):
TTCCACCATTCCATGTTTTA
Found at i:53898 original size:12 final size:12
Alignment explanation
Indices: 53881--53917 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
53871 GAGTAAAAAG
53881 AAAAAACAAGAA
1 AAAAAACAAGAA
53893 AAAAAACAA-AA
1 AAAAAACAAGAA
*
53904 AAGAAA-AAGAA
1 AAAAAACAAGAA
53915 AAA
1 AAA
53918 GCAAGCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
10 2 0.09
11 11 0.50
12 9 0.41
ACGTcount: A:0.86, C:0.05, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAACAAGAA
Found at i:53907 original size:16 final size:16
Alignment explanation
Indices: 53856--53917 Score: 63
Period size: 16 Copynumber: 3.7 Consensus size: 16
53846 AAGGAGAATA
*
53856 AAAAAGAGAAACAAAGAG
1 AAAAAGA-AAA-AAAAAG
*
53874 TAAAAAGAAAAAACAAG
1 -AAAAAGAAAAAAAAAG
53891 AAAAA-AAACAAAAAAG
1 AAAAAGAAA-AAAAAAG
53907 AAAAAGAAAAA
1 AAAAAGAAAAA
53918 GCAAGCAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 3 0.08
16 18 0.47
17 7 0.18
18 3 0.08
19 7 0.18
ACGTcount: A:0.81, C:0.05, G:0.13, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAAAAAAG
Found at i:53927 original size:16 final size:15
Alignment explanation
Indices: 53876--53927 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
53866 ACAAAGAGTA
53876 AAAAGAAAAAACAAG
1 AAAAGAAAAAACAAG
* *
53891 AAAAAAAACAAAAAAG
1 AAAAGAAA-AAACAAG
*
53907 AAAAAGAAAAAGCAAG
1 -AAAAGAAAAAACAAG
53923 CAAAA
1 -AAAA
53928 AGGGACGATA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 7 0.24
16 15 0.52
17 7 0.24
ACGTcount: A:0.81, C:0.08, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAACAAG
Found at i:55331 original size:120 final size:120
Alignment explanation
Indices: 55168--55926 Score: 851
Period size: 120 Copynumber: 6.3 Consensus size: 120
55158 AAAACAATTC
* ** *
55168 TTGGATTTCAACTTCATGACGAAGGATATTTAATTCGATGCTCAACTTCACGACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCAT
* * ** * * *
55233 CCACGATTTCAACTTCATGATGAATAATATCGTGTCTATCGGAAACATCCTTATA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATCAGAAACATCCTTAGA
** * **
55288 TTGGATTTCAACTTCACGATAAAGGATATCCAATTTGAGGCTCAACTTCACGACGAATAGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCAT
* * **
55353 CCACAATTTCAACTTCACGACGAATGATATCGTGTCCATCACCAACATCCTTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATCAGAAACATCCTTAGA
* * *
55408 TTGGATTTTAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCAT
* * *
55473 CCATGATTTCAACTTCACGACGAAGGATATCGTGTCAATCAGCAACATCCTTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATCAGAAACATCCTTAGA
* *
55528 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCATGACGAAGGGGCTAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCAT
* *
55593 CCACAATTTCAACTTCACGACGAAGGATATCGTGTCCATCA-ATAACATCCTGAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATCAGA-AACATCCTTAGA
* * * *
55648 TTGTATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCAT
* * * * * * * * **
55713 CCACGATTTCAACTACACAACGAAGGATATCATGCCCA-CAAGCAGCAATGC-AATCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATC-AGAAAC-ATCCTTA-GA
* * * * * * * *
55769 TTGGGTTTCAACTTCATGACGAAGGATATCCAATTCAAAGCTCAACATCACAACGAATGAGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCAT
* * * * * * *
55834 TCATGATTTCAACTTCACGGCGAAGGATATCGTGCCCA-CAAGTAGCAATACAACTCGAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATC-AGAAAC-AT-C--CT-TAGA
* *
55894 TTGGATTTCAACTTCACGATGAATGATATCCAA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAA
55927 CCCGACATGA
Statistics
Matches: 550, Mismatches: 79, Indels: 15
0.85 0.12 0.02
Matches are distributed among these distances:
119 1 0.00
120 416 0.76
121 102 0.19
124 1 0.00
125 29 0.05
126 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (120 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATCAGAAACATCCTTAGA
Found at i:56073 original size:40 final size:41
Alignment explanation
Indices: 56029--56213 Score: 153
Period size: 40 Copynumber: 4.4 Consensus size: 41
56019 TGGCATGTCG
* *
56029 TCCTCACCACGTAGGAACTGTGTCATCACC-TGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCACCATGACCAGATC
* * * * *
56069 TCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAGCA-G
1 TCCTCATCACGTAGGAACCGTGTCATCACC--ATGACCAG-ATC
* * *
56112 TCCTCATCACGTAGGAACCGTGTTATCACCCTTAGACGACCTG-TC
1 TCCTCATCACGTAGGAACCGTGTCATCA-CC----ATGACCAGATC
* *
56157 ATCCTCATCACGTAGGAACCGTGTCATCACC-CGACCTGATC
1 -TCCTCATCACGTAGGAACCGTGTCATCACCATGACCAGATC
56198 TCCTCATCACGTAGGA
1 TCCTCATCACGTAGGA
56214 GTCGTGCCAA
Statistics
Matches: 119, Mismatches: 16, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
40 48 0.40
41 2 0.02
43 30 0.25
44 3 0.03
45 2 0.02
46 34 0.29
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.22
Consensus pattern (41 bp):
TCCTCATCACGTAGGAACCGTGTCATCACCATGACCAGATC
Found at i:56170 original size:46 final size:45
Alignment explanation
Indices: 55941--56188 Score: 187
Period size: 46 Copynumber: 5.7 Consensus size: 45
55931 ACATGATCTC
* * * * * *
55941 CCTCATCACGTAGGAGCC-TGTCA-AACTCTAGATAATCAGTCGT
1 CCTCATCACGTAGGAACCGTGTCATCACCCTAGATGACCAGTCAT
* * * * * *
55984 CCTCATCACGTAGGAACCATGTTATCATCCTTAAATG-GCATGTCGT
1 CCTCATCACGTAGGAACCGTGTCATCA-CCCTAGATGACCA-GTCAT
* *
56030 CCTCACCACGTAGGAACTGTGTCATCA-CC----TGACCAGATC-T
1 CCTCATCACGTAGGAACCGTGTCATCACCCTAGATGACCAG-TCAT
* * *
56070 CCTCATCACGTAGGAGCCGTGTCA--ACCCCAGATAACCAG-CAGT
1 CCTCATCACGTAGGAACCGTGTCATCACCCTAGATGACCAGTCA-T
* * *
56113 CCTCATCACGTAGGAACCGTGTTATCACCCTTAGACGACCTGTCAT
1 CCTCATCACGTAGGAACCGTGTCATCACCC-TAGATGACCAGTCAT
56159 CCTCATCACGTAGGAACCGTGTCATCACCC
1 CCTCATCACGTAGGAACCGTGTCATCACCC
56189 GACCTGATCT
Statistics
Matches: 163, Mismatches: 25, Indels: 31
0.74 0.11 0.14
Matches are distributed among these distances:
38 1 0.01
39 2 0.01
40 25 0.15
41 5 0.03
43 46 0.28
44 5 0.03
45 7 0.04
46 70 0.43
47 2 0.01
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (45 bp):
CCTCATCACGTAGGAACCGTGTCATCACCCTAGATGACCAGTCAT
Found at i:56171 original size:129 final size:129
Alignment explanation
Indices: 55926--56226 Score: 401
Period size: 129 Copynumber: 2.3 Consensus size: 129
55916 ATGATATCCA
* * *
55926 ACCCGA-CATGATCTCCCTCATCACGTAGGAGCC-TGTCAAACTCTAGATAATCAGTCGTCCTCA
1 ACCCGACCA-GATCT-CCTCATCACGTAGGAGCCGTGTC-AACCCCAGATAACCAGTCGTCCTCA
* * * * *
55989 TCACGTAGGAACCATGTTATCATCCTTAAATGGCATGTCGTCCTCACCACGTAGGAACTGTGTCA
63 TCACGTAGGAACCATGTTATCACCCTTAAACGACATGTCATCCTCACCACGTAGGAACCGTGTCA
56054 TC
128 TC
*
56056 ACCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAG-CAGTCCTCATC
1 ACCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAGTC-GTCCTCATC
* * * *
56120 ACGTAGGAACCGTGTTATCACCCTTAGACGACCTGTCATCCTCATCACGTAGGAACCGTGTCATC
65 ACGTAGGAACCATGTTATCACCCTTAAACGACATGTCATCCTCACCACGTAGGAACCGTGTCATC
* * *
56185 ACCCGACCTGATCTCCTCATCACGTAGGAGTCGTGCCAACCC
1 ACCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCC
56227 TTAGATGACC
Statistics
Matches: 151, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
128 1 0.01
129 134 0.89
130 14 0.09
131 2 0.01
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.23
Consensus pattern (129 bp):
ACCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAGTCGTCCTCATCA
CGTAGGAACCATGTTATCACCCTTAAACGACATGTCATCCTCACCACGTAGGAACCGTGTCATC
Found at i:56182 original size:25 final size:25
Alignment explanation
Indices: 56112--56184 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 25
56102 TAACCAGCAG
*
56112 TCCTCATCACGTAGGAACCGTGTTA
1 TCCTCATCACGTAGGAACCGTGTCA
* * *
56137 TCAC-CCTTA-G-ACG-ACC-TGTCA
1 TC-CTCATCACGTAGGAACCGTGTCA
56158 TCCTCATCACGTAGGAACCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCA
56183 TC
1 TC
56185 ACCCGACCTG
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
20 1 0.03
21 9 0.26
22 4 0.11
23 4 0.11
24 4 0.11
25 12 0.34
26 1 0.03
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (25 bp):
TCCTCATCACGTAGGAACCGTGTCA
Found at i:56895 original size:146 final size:146
Alignment explanation
Indices: 56627--56914 Score: 342
Period size: 146 Copynumber: 2.0 Consensus size: 146
56617 TTCGTCGGTG
* * * *
56627 ATCGGGATCTCCAATCAACGTTCTGAACGCTGAAAATTTGCGCAAGGCCAACACGAACAACATAC
1 ATCGGGATCTACAATCAACGTTCCGAACGCTGAAAAGTTGCACAAGGCCAACACGAACAACATAC
* * ** * * *
56692 TAAAAAATCAGGACGATAAGACAGTGGACGACGGTGGATTGGAGAAAATAAATCCGAACGGTTTT
66 TAAAAAATCAGGACGAGAAGACAGTGGACGACGGCGGATCAGAGAAAAGAAAGCCGAACAGTTTT
*
56757 TGGCCTTTTTACAATA
131 TGGCCTTCTTACAATA
* * * *
56773 ATCGGGATCTACGATCAACGTTCCGAACGGTGAAAAGTTGTACAAGGCCAACACGGACAACATAC
1 ATCGGGATCTACAATCAACGTTCCGAACGCTGAAAAGTTGCACAAGGCCAACACGAACAACATAC
* ** * ** * * *
56838 TGAAAAATCAGGACGAGCGGACGGTGGACGGTGGCGGATCAGATAATAGAAAGCCGAATAGTTTT
66 TAAAAAATCAGGACGAGAAGACAGTGGACGACGGCGGATCAGAGAAAAGAAAGCCGAACAGTTTT
*
56903 TTGCCTTCTTAC
131 TGGCCTTCTTAC
56915 TACAAACGAA
Statistics
Matches: 116, Mismatches: 26, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
146 116 1.00
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.21
Consensus pattern (146 bp):
ATCGGGATCTACAATCAACGTTCCGAACGCTGAAAAGTTGCACAAGGCCAACACGAACAACATAC
TAAAAAATCAGGACGAGAAGACAGTGGACGACGGCGGATCAGAGAAAAGAAAGCCGAACAGTTTT
TGGCCTTCTTACAATA
Found at i:57179 original size:29 final size:28
Alignment explanation
Indices: 57147--57213 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
57137 CCTGAATCTC
*
57147 TGTGTTTTTCTGATTTT-GACACTTTAGTT
1 TGTGTTTTT-T-ATTTTAGACACTTAAGTT
*
57176 TGTGTTATTTTATTTTAGTCACTTAAGTT
1 TGTGTT-TTTTATTTTAGACACTTAAGTT
*
57205 TCTGTTTTT
1 TGTGTTTTT
57214 GTTATTTACG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 8 0.24
29 22 0.67
30 3 0.09
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.61
Consensus pattern (28 bp):
TGTGTTTTTTATTTTAGACACTTAAGTT
Found at i:57221 original size:29 final size:29
Alignment explanation
Indices: 57166--57270 Score: 79
Period size: 30 Copynumber: 3.6 Consensus size: 29
57156 CTGATTTTGA
* * *
57166 CACTTTAGTTTGTGTTATT-TTATTTTAGT
1 CACTTAAGTTTCTGTTTTTGTTA-TTTAGT
57195 CACTTAAGTTTCTGTTTTTGTTATTTACGT
1 CACTTAAGTTTCTGTTTTTGTTATTTA-GT
* ** *
57225 C-CATTAAATTTCTGTTTAAGTTGTTTTAGT
1 CAC-TTAAGTTTCTGTTTTTGTT-ATTTAGT
**
57255 CTTTTAAGTTTCTGTT
1 CACTTAAGTTTCTGTT
57271 CTTACCATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
29 21 0.34
30 37 0.60
31 4 0.06
ACGTcount: A:0.18, C:0.10, G:0.13, T:0.58
Consensus pattern (29 bp):
CACTTAAGTTTCTGTTTTTGTTATTTAGT
Found at i:57950 original size:180 final size:180
Alignment explanation
Indices: 57648--57996 Score: 680
Period size: 180 Copynumber: 1.9 Consensus size: 180
57638 CAATTTTTTT
*
57648 CAAATTAATCTAAAACCCTAAATTTTCTAAAATTAAAAGTCGTAACTATTTTTAAAACAATAAAT
1 CAAATTAATCTAAAACCCTAAATTTTCTAAAATTAAAAATCGTAACTATTTTTAAAACAATAAAT
57713 AATTGTTCCACCTAAAAACGGTTATGACAAATTGTACATTTTCTATTTTCACCATATAGTTCATT
66 AATTGTTCCACCTAAAAACGGTTATGACAAATTGTACATTTTCTATTTTCACCATATAGTTCATT
57778 TTCTTTTGATTTTCTAATCTTTGAAGATTCCTAATTTTCCATTTTTTCCC
131 TTCTTTTGATTTTCTAATCTTTGAAGATTCCTAATTTTCCATTTTTTCCC
*
57828 CAAATTAATCTAAAACCCTAAATTTTCTAAAATTAAAAATCGTAACTGTTTTTAAAACAATAAAT
1 CAAATTAATCTAAAACCCTAAATTTTCTAAAATTAAAAATCGTAACTATTTTTAAAACAATAAAT
57893 AATTGTTCCACCTAAAAACGGTTATGACAAATTGTACATTTTCTATTTTCACCATATAGTTCATT
66 AATTGTTCCACCTAAAAACGGTTATGACAAATTGTACATTTTCTATTTTCACCATATAGTTCATT
57958 TTCTTTTGATTTTCTAATCTTTGAAGATTCCTAATTTTC
131 TTCTTTTGATTTTCTAATCTTTGAAGATTCCTAATTTTC
57997 TTATGAACAT
Statistics
Matches: 167, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 167 1.00
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (180 bp):
CAAATTAATCTAAAACCCTAAATTTTCTAAAATTAAAAATCGTAACTATTTTTAAAACAATAAAT
AATTGTTCCACCTAAAAACGGTTATGACAAATTGTACATTTTCTATTTTCACCATATAGTTCATT
TTCTTTTGATTTTCTAATCTTTGAAGATTCCTAATTTTCCATTTTTTCCC
Found at i:59948 original size:6 final size:6
Alignment explanation
Indices: 59937--59974 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
59927 TTTTAACCTC
*
59937 TTTTAT TTTTAT TTTTAT TTTTAT TTTT-T ATTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
59975 CTGTTCGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:62323 original size:96 final size:91
Alignment explanation
Indices: 62220--62390 Score: 234
Period size: 96 Copynumber: 1.8 Consensus size: 91
62210 AAAAACAATG
* * *
62220 GTTAAATTTAATTCAAAATTAAATGAATGAATAAGAGGAATGAGAAAAGATGGTAAAAAACTAAG
1 GTTAAATTTAATTCAAAAATAAATGAATGAATAAGA-GAA--ACAAAAAAT-GTAAAAAACTAA-
*
62285 CATTTTATGAAATTATAAATATAAAAAGTTT
61 AATTTTATGAAATTATAAATATAAAAAGTTT
* * *
62316 GTTAAATTTAATTCAAAAATGAATGAATTAATAAGAGAAACAAAAAATGTCAAAAACTAAAATTT
1 GTTAAATTTAATTCAAAAATAAATGAATGAATAAGAGAAACAAAAAATGTAAAAAACTAAAATTT
62381 TATGAAATTA
66 TATGAAATTA
62391 CAAAAATTAG
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
91 14 0.21
92 11 0.16
93 7 0.10
95 3 0.04
96 33 0.49
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.30
Consensus pattern (91 bp):
GTTAAATTTAATTCAAAAATAAATGAATGAATAAGAGAAACAAAAAATGTAAAAAACTAAAATTT
TATGAAATTATAAATATAAAAAGTTT
Found at i:62423 original size:28 final size:29
Alignment explanation
Indices: 62392--62458 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
62382 ATGAAATTAC
* *
62392 AAAAATTAGGA-CCCTAATTATAAATATA
1 AAAAATTAGGAGCCCTAATTACAAATACA
* *
62420 AAAAATTAAGAGTCCTAATTACAAATACA
1 AAAAATTAGGAGCCCTAATTACAAATACA
*
62449 AAAAAATAGG
1 AAAAATTAGG
62459 GGCCTGAGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 10 0.31
29 22 0.69
ACGTcount: A:0.57, C:0.10, G:0.09, T:0.24
Consensus pattern (29 bp):
AAAAATTAGGAGCCCTAATTACAAATACA
Found at i:64526 original size:17 final size:17
Alignment explanation
Indices: 64504--64542 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
64494 CCCTAAAAAA
*
64504 AAATAAACA-AAATGAAT
1 AAATAAA-ATAAATAAAT
64521 AAATAAAATAAATAAAT
1 AAATAAAATAAATAAAT
64538 AAATA
1 AAATA
64543 CAATGTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
AAATAAAATAAATAAAT
Found at i:64537 original size:13 final size:13
Alignment explanation
Indices: 64499--64540 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
64489 TTGGACCCTA
* *
64499 AAAAAAAATAAAC
1 AAAATAAATAAAT
*
64512 AAAATGAATAAAT
1 AAAATAAATAAAT
64525 AAAATAAATAAAT
1 AAAATAAATAAAT
64538 AAA
1 AAA
64541 TACAATGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:64635 original size:36 final size:36
Alignment explanation
Indices: 64570--64762 Score: 252
Period size: 36 Copynumber: 5.3 Consensus size: 36
64560 TATTTTTTAA
64570 AAAACTA-ATATTATATATATTTTCAAAAAATGTTTTC
1 AAAACTATATATTATATATA-TTTC-AAAAATGTTTTC
64607 AAAACTATATATTATATATATTTCAAAAATGTTTTC
1 AAAACTATATATTATATATATTTCAAAAATGTTTTC
64643 AAAACTATATATTATATATATTTTCAAAAATGTTTTC
1 AAAACTATATATTATATATA-TTTCAAAAATGTTTTC
** *
64680 AAAAC--TATATTATATAT-TTTCAAAAACAATTCTC
1 AAAACTATATATTATATATATTTCAAAAA-TGTTTTC
*
64714 AAAACTATATATTATATAT-TTTCAAAAAAATGATTTC
1 AAAACTATATATTATATATATTTC--AAAAATGTTTTC
*
64751 AACACTATATAT
1 AAAACTATATAT
64763 ATACGTTATA
Statistics
Matches: 141, Mismatches: 8, Indels: 14
0.87 0.05 0.09
Matches are distributed among these distances:
33 9 0.06
34 9 0.06
35 12 0.09
36 48 0.34
37 46 0.33
38 17 0.12
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (36 bp):
AAAACTATATATTATATATATTTCAAAAATGTTTTC
Found at i:64730 original size:71 final size:72
Alignment explanation
Indices: 64570--64765 Score: 269
Period size: 71 Copynumber: 2.8 Consensus size: 72
64560 TATTTTTTAA
64570 AAAACTA-ATATTATATATATTTTCAAAAAATGTTTTCAAAACTATATATTATATATATTTCAAA
1 AAAACTATATATTATATATATTTTCAAAAAATGTTTTCAAAAC--TATATTATATATATTTCAAA
** *
64634 AATGTTTTC
64 AAAATTCTC
64643 AAAACTATATATTATATATATTTTC-AAAAATGTTTTCAAAACTATATTATATAT-TTTCAAAAA
1 AAAACTATATATTATATATATTTTCAAAAAATGTTTTCAAAACTATATTATATATATTTCAAAAA
64706 CAATTCTC
66 -AATTCTC
* *
64714 AAAACTATATA-T-TATATATTTTCAAAAAAATGATTTCAACACTATA-TATATA
1 AAAACTATATATTATATATATTTTC-AAAAAATGTTTTCAAAACTATATTATATA
64766 CGTTATATGT
Statistics
Matches: 114, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
69 11 0.10
70 16 0.14
71 46 0.40
73 24 0.21
74 17 0.15
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (72 bp):
AAAACTATATATTATATATATTTTCAAAAAATGTTTTCAAAACTATATTATATATATTTCAAAAA
AATTCTC
Found at i:66040 original size:15 final size:15
Alignment explanation
Indices: 66020--66049 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
66010 TGGCGCCCAA
66020 AGCTGAGAAGAAGCC
1 AGCTGAGAAGAAGCC
66035 AGCTGAGAAGAAGCC
1 AGCTGAGAAGAAGCC
66050 GGCCGAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.33, T:0.07
Consensus pattern (15 bp):
AGCTGAGAAGAAGCC
Found at i:68128 original size:20 final size:20
Alignment explanation
Indices: 68089--68163 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 20
68079 AATTACTCAA
* **
68089 CTAATTATTTTATTTTTCAC
1 CTAATTATTTTCTTAATCAC
68109 CTAATTATTTTCTTAATCAC
1 CTAATTATTTTCTTAATCAC
*** *
68129 CCGTTCTATTTTTTTAATCAC
1 CTAAT-TATTTTCTTAATCAC
**
68150 CTAACAATTTTCTT
1 CTAATTATTTTCTT
68164 TTTCAAAATC
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.25, C:0.20, G:0.01, T:0.53
Consensus pattern (20 bp):
CTAATTATTTTCTTAATCAC
Found at i:88452 original size:3 final size:3
Alignment explanation
Indices: 88444--88480 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
88434 CCATTTTAAA
88444 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
88481 ACAAATAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:89896 original size:20 final size:20
Alignment explanation
Indices: 89873--89921 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 20
89863 ATTTTATTTC
89873 ATATAAATATATTTAATTAA
1 ATATAAATATATTTAATTAA
89893 ATAT--ATATA--TAATTAA
1 ATATAAATATATTTAATTAA
89909 ATA-AAA-ATATTTA
1 ATATAAATATATTTA
89922 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
16 13 0.52
17 1 0.04
18 7 0.28
20 4 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATAAATATATTTAATTAA
Found at i:89900 original size:16 final size:16
Alignment explanation
Indices: 89876--89911 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
89866 TTATTTCATA
89876 TAAATATAT-T-TAAT
1 TAAATATATATATAAT
89890 TAAATATATATATAAT
1 TAAATATATATATAAT
89906 TAAATA
1 TAAATA
89912 AAAATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATATATATATAAT
Found at i:98171 original size:55 final size:55
Alignment explanation
Indices: 98079--98247 Score: 232
Period size: 55 Copynumber: 3.1 Consensus size: 55
98069 TCAATGATTG
* * * * *
98079 AGAACATCTGGGCAGAAGCCACAGAAAAGAATGAATGTGTTATCAAATGTTTTAT
1 AGAACATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
* *
98134 AGAACATTTGTGCAGAAGCCACAGGAAAGGATAAATGTGTTGTCAAATGTTTTAC
1 AGAACATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
* * * *
98189 GGAACATCTGTGCAGAAGCCATAGGAAAGGATGAATGTATTGTCAAATGCTTTAC
1 AGAACATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
98244 -GAAC
1 AGAAC
98248 CAGTGATTAT
Statistics
Matches: 101, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
54 4 0.04
55 97 0.96
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (55 bp):
AGAACATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
Found at i:98637 original size:22 final size:22
Alignment explanation
Indices: 98612--98712 Score: 141
Period size: 22 Copynumber: 4.6 Consensus size: 22
98602 ACATCTACAT
98612 TCTTCAAAGATGATAGATTCAT-
1 TCTTCAAAGATGATAGATTC-TC
* *
98634 TCTTCAAAGATGATATATCCTC
1 TCTTCAAAGATGATAGATTCTC
*
98656 TCTTCAAAGATGATAGGTTCTC
1 TCTTCAAAGATGATAGATTCTC
*
98678 TCTTCAAAGATGATATATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
98700 TTTTCAAAGATGA
1 TCTTCAAAGATGA
98713 AAGCTTTATT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
21 1 0.01
22 69 0.99
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:98682 original size:44 final size:44
Alignment explanation
Indices: 98612--98712 Score: 159
Period size: 44 Copynumber: 2.3 Consensus size: 44
98602 ACATCTACAT
98612 TCTTCAAAGATGATAGATTCATTCTTCAAAGATGATATATCCTC
1 TCTTCAAAGATGATAGATTCATTCTTCAAAGATGATATATCCTC
* *
98656 TCTTCAAAGATGATAGGTTC-TCTCTTCAAAGATGATATATTCTC
1 TCTTCAAAGATGATAGATTCAT-TCTTCAAAGATGATATATCCTC
*
98700 TTTTCAAAGATGA
1 TCTTCAAAGATGA
98713 AAGCTTTATT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
43 1 0.02
44 52 0.98
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.38
Consensus pattern (44 bp):
TCTTCAAAGATGATAGATTCATTCTTCAAAGATGATATATCCTC
Found at i:99574 original size:116 final size:116
Alignment explanation
Indices: 99370--100054 Score: 1102
Period size: 116 Copynumber: 5.9 Consensus size: 116
99360 CTATTTTCCA
* *
99370 CATCTGTAAGACCTACAGTGTAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAATGCAG
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAG
*
99435 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTAAAGCCTCCGGGT
66 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
* * *
99486 CATCTGTAAGACCTATAGTGCAAGATGATAAGACCCCAGGGCCATCCATAAGTCCTACAGTGCAG
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAG
99551 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
66 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
* * *
99602 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGTCATCCATAAGACCTACAGTACAT
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAG
*
99667 GATG-TTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCTGGGT
66 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
99717 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAG
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAG
*
99782 GATGTTTTCAAAAAGCATTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
66 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
* * * * *
99833 CATCTGTAAGACCTATAGTGCAAGATGATAAGACATCAGGGTCATCCATAAGACCTATACTGCAG
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAG
* **
99898 GATGTTTTCAAAAAGCCTTCGGGAGTTTTTTGATATTTAAAGCCTTTGGGT
66 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
* ** *
99949 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGTGTTATCCATAAGACCTACTGTGCAG
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAG
* *
100014 GATGTTTTCAAAAAAAAAGCCTTCGGAAGCTTTTTAATATT
66 GATGTTTTC----AAAAAGCCTTCGGGAGCTTTTTGATATT
100055 CAAGACCTAA
Statistics
Matches: 527, Mismatches: 37, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
115 111 0.21
116 391 0.74
120 25 0.05
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (116 bp):
CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAG
GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
Found at i:99751 original size:22 final size:21
Alignment explanation
Indices: 99723--99781 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
99713 GGGTCATCTG
99723 TAAGACCTACAGTGCAAGATGA
1 TAAGACCTACAGTGC-AGATGA
* * *
99745 TAAGACCT-CAGGGC-CATCCA
1 TAAGACCTACAGTGCAGAT-GA
99765 TAAGACCTACAGTGCAG
1 TAAGACCTACAGTGCAG
99782 GATGTTTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 2 0.07
20 9 0.31
21 10 0.34
22 8 0.28
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (21 bp):
TAAGACCTACAGTGCAGATGA
Found at i:99776 original size:231 final size:232
Alignment explanation
Indices: 99370--100054 Score: 1120
Period size: 231 Copynumber: 2.9 Consensus size: 232
99360 CTATTTTCCA
* *
99370 CATCTGTAAGACCTACAGTGTAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAATGCAG
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGTCATCCATAAGACCTACAATGCAG
* *
99435 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTAAAGCCTCCGGGTCATCTGTAAGACCT
66 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCTGGGTCATCTGTAAGACCT
* * *
99500 ATAGTGCAAGATGATAAGACCCCAGGGCCATCCATAAGTCCTACAGTGCAGGATGTTTTCAAAAA
131 ACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAA
99565 GCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
196 GCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
* * *
99602 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGTCATCCATAAGACCTACAGTACAT
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGTCATCCATAAGACCTACAATGCAG
99667 GATG-TTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCTGGGTCATCTGTAAGACCT
66 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCTGGGTCATCTGTAAGACCT
99731 ACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAA
131 ACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAA
*
99796 GCATTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
196 GCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
* * * *
99833 CATCTGTAAGACCTATAGTGCAAGATGATAAGACATCAGGGTCATCCATAAGACCTATACTGCAG
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGTCATCCATAAGACCTACAATGCAG
* *
99898 GATGTTTTCAAAAAGCCTTCGGGAGTTTTTTGATATTTAAAGCCTTTGGGTCATCTGTAAGACCT
66 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCTGGGTCATCTGTAAGACCT
* ** *
99963 ACAGTGCAAGATGATAAGACCTCAGTGTTATCCATAAGACCTACTGTGCAGGATGTTTTCAAAAA
131 ACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAGGATGTTTTC----A
* *
100028 AAAAGCCTTCGGAAGCTTTTTAATATT
192 AAAAGCCTTCGGGAGCTTTTTGATATT
100055 CAAGACCTAA
Statistics
Matches: 422, Mismatches: 26, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
231 219 0.52
232 178 0.42
236 25 0.06
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (232 bp):
CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGTCATCCATAAGACCTACAATGCAG
GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCTGGGTCATCTGTAAGACCT
ACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAA
GCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
Found at i:100005 original size:347 final size:349
Alignment explanation
Indices: 99370--100054 Score: 1149
Period size: 347 Copynumber: 2.0 Consensus size: 349
99360 CTATTTTCCA
*
99370 CATCTGTAAGACCTACAGTGTAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAATGCAG
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAATGCAG
* *
99435 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTAAAGCCTCCGGGTCATCTGTAAGACCT
66 GATGTTTTCAAAAAGCATTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGTCATCTGTAAGACCT
* * *
99500 ATAGTGCAAGATGATAAGACCCCAGGGCCATCCATAAGTCCTACAGTGCAGGATGTTTTCAAAAA
131 ATAGTGCAAGATGATAAGACACCAGGGCCATCCATAAGACCTACACTGCAGGATGTTTTCAAAAA
99565 GCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGA
196 GCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGA
* *
99630 TAAGACCTCAGGGTCATCCATAAGACCTACAGTACATGATG-TTTC-AAAAAGCCTTCGGGAGCT
261 TAAGACCTCAGGGTCATCCATAAGACCTACAGTACAGGATGTTTTCAAAAAAGCCTTCGGAAGCT
*
99693 TTTTGATATTTAAAGCCTCTGGGT
326 TTTTAATATTTAAAGCCTCTGGGT
*
99717 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAG
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAATGCAG
99782 GATGTTTTCAAAAAGCATTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGTCATCTGTAAGACCT
66 GATGTTTTCAAAAAGCATTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGTCATCTGTAAGACCT
* * *
99847 ATAGTGCAAGATGATAAGACATCAGGGTCATCCATAAGACCTATACTGCAGGATGTTTTCAAAAA
131 ATAGTGCAAGATGATAAGACACCAGGGCCATCCATAAGACCTACACTGCAGGATGTTTTCAAAAA
* **
99912 GCCTTCGGGAGTTTTTTGATATTTAAAGCCTTTGGGTCATCTGTAAGACCTACAGTGCAAGATGA
196 GCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGA
* * * *
99977 TAAGACCTCAGTGTTATCCATAAGACCTACTGTGCAGGATGTTTTCAAAAAAAAAGCCTTCGGAA
261 TAAGACCTCAGGGTCATCCATAAGACCTACAGTACAGGATGTTTTC---AAAAAAGCCTTCGGAA
100042 GCTTTTTAATATT
323 GCTTTTTAATATT
100055 CAAGACCTAA
Statistics
Matches: 313, Mismatches: 20, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
347 283 0.90
348 4 0.01
352 26 0.08
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (349 bp):
CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAATGCAG
GATGTTTTCAAAAAGCATTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGTCATCTGTAAGACCT
ATAGTGCAAGATGATAAGACACCAGGGCCATCCATAAGACCTACACTGCAGGATGTTTTCAAAAA
GCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGA
TAAGACCTCAGGGTCATCCATAAGACCTACAGTACAGGATGTTTTCAAAAAAGCCTTCGGAAGCT
TTTTAATATTTAAAGCCTCTGGGT
Found at i:100107 original size:78 final size:78
Alignment explanation
Indices: 100008--100181 Score: 276
Period size: 78 Copynumber: 2.2 Consensus size: 78
99998 AAGACCTACT
* *
100008 GTGCAGGATGTTTTCAAAAAAAAAGCCTTCGGAAGCTTTTTAATATTCAAGACCTAAGGGTCATC
1 GTGCAGGATGTTTTCAAAAAAAAAGCCTTAGGAAGCTTTTTAATATTCAAGACCTAAGGGCCATC
100073 TATAAAAACTCCA
66 TATAAAAACTCCA
** *
100086 GTGCAGGATGTTTTCAAAAAAAAAGCCTTAGGGTGCTTTTTAATATTCAAGACCTCAGGGCCATC
1 GTGCAGGATGTTTTCAAAAAAAAAGCCTTAGGAAGCTTTTTAATATTCAAGACCTAAGGGCCATC
* *
100151 TGTAAGAACTCCA
66 TATAAAAACTCCA
*
100164 GTGCATGATGTTTTCAAA
1 GTGCAGGATGTTTTCAAA
100182 TGAGATTTTA
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 88 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (78 bp):
GTGCAGGATGTTTTCAAAAAAAAAGCCTTAGGAAGCTTTTTAATATTCAAGACCTAAGGGCCATC
TATAAAAACTCCA
Found at i:100443 original size:3 final size:3
Alignment explanation
Indices: 100435--100490 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
100425 CCATTTTAAA
*
100435 ATT ATT ATT ATT ATA ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
100481 ATT ATT ATT A
1 ATT ATT ATT A
100491 ACAAATAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 4 0.08
3 45 0.92
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:100465 original size:23 final size:23
Alignment explanation
Indices: 100435--100490 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
100425 CCATTTTAAA
100435 ATTATTATTATTATAATTATTAT
1 ATTATTATTATTATAATTATTAT
*
100458 ATTATTATTATTATTATTATTAT
1 ATTATTATTATTATAATTATTAT
100481 ATTATTATTA
1 ATTATTATTA
100491 ACAAATAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTATTATTATTATAATTATTAT
Found at i:103397 original size:27 final size:26
Alignment explanation
Indices: 103359--103417 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
103349 GAATGGTAGA
* * *
103359 AGAAGAATCTGGTTGTGGAACAAGAGG
1 AGAAGAAGCTGGTTGAGAAACAA-AGG
*
103386 AGAAGAAGCTGGTTGAGAAACAATGG
1 AGAAGAAGCTGGTTGAGAAACAAAGG
103412 AGAAGA
1 AGAAGA
103418 GTCTAACTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.42, C:0.07, G:0.36, T:0.15
Consensus pattern (26 bp):
AGAAGAAGCTGGTTGAGAAACAAAGG
Found at i:104314 original size:14 final size:15
Alignment explanation
Indices: 104288--104316 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
104278 AATCATATGA
104288 TGATTATTTTATCAT
1 TGATTATTTTATCAT
104303 TGATTA-TTTATCAT
1 TGATTATTTTATCAT
104317 ATTTATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (15 bp):
TGATTATTTTATCAT
Done.