Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003905.1 Hibiscus syriacus cultivar Beakdansim tig00008441_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: 51410
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2633 original size:44 final size:44
Alignment explanation
Indices: 2552--2637 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
2542 TAAGAAAAGT
* * *
2552 AACTGAGCTTTGATGTGTTAGAACATGATAAAAAGAAACACCCTG
1 AACTGAACTTTGATGAGTTAGAACATAATAAAAAGAAA-ACCCTG
* *
2597 AACTGAACTTTGAT-AGTTAGAACATAATATACAGAAAACCC
1 AACTGAACTTTGATGAGTTAGAACATAATAAAAAGAAAACCC
2638 AGAAATTCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 4 0.11
44 19 0.53
45 13 0.36
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (44 bp):
AACTGAACTTTGATGAGTTAGAACATAATAAAAAGAAAACCCTG
Found at i:4716 original size:31 final size:31
Alignment explanation
Indices: 4680--4738 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
4670 AACTTAAAAG
* *
4680 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
4711 AGTTTTACAATATTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
4739 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:4789 original size:22 final size:22
Alignment explanation
Indices: 4763--4805 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4753 TAATAAATTA
4763 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
4785 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
4806 CTAATAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:4814 original size:22 final size:22
Alignment explanation
Indices: 4765--4813 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
4755 ATAAATTATT
**
4765 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
4787 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
4810 TAAA
1 TAAA
4814 TGATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:4858 original size:80 final size:78
Alignment explanation
Indices: 4768--5420 Score: 509
Period size: 80 Copynumber: 7.8 Consensus size: 78
4758 AATTATTTAA
*
4768 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATGATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
4833 CCATACAACTACAAT
66 CCATACAA-TA-AAT
* * *
4848 AATAAATCAATCAATATTTTAAAATAAATCAATTAATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
*
4913 TCATACTAATAAATTATTT
66 CCATAC-AAT-AA--A--T
4932 AAAATAAATCAATCCATATTTTAAAATAAATCAA-TCTATACTAATAAATTATTTAAAATAAATC
1 --AATAAATCAATCCATATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAATAAATC
* *
4996 AATTCATACAACTGTAAT
63 AATCCATACAA-T-AAAT
*
5014 AATAAATCAATACATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATC-AT
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
* **
5078 CTATA-TTTAAA-
66 CCATACAATAAAT
* * * * * *
5089 AATTCAATCTATACTAATAAATTATTTAAATAAATC-ATCCATATTTTAAAATAATTAATCAATG
1 AA-TAAATCAAT-C-CAT--ATT-TTAAAATAAATCAATTCATA--CT--AAT-A--AAT---T-
* *
5153 TTTTAAAATAAATTAATCCATACAATAATTATTT
49 ATTTAAAATAAATCAATCCATACAATAA--A--T
* * * * * *
5187 AAAATAAATCAATCCATA--CT--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATTCATACT-AATAAAT---TA-TTTAAAATA
*
5247 AATCAATCTATACTAATAAATTATTT
59 AATCAATCCATAC-AAT-AA--A--T
5273 AAAATAAATCAATCCATATTTTAAAATAAATCAA-TCTATACTAATAAATTATTTAAAATAAATC
1 --AATAAATCAATCCATATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAATAAATC
*
5337 AATTCATACAACTATAAT
63 AATCCATACAA-TA-AAT
*
5355 AATAAATCAATACATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
5420 C
66 C
5421 TATATTTTAA
Statistics
Matches: 472, Mismatches: 51, Indels: 100
0.76 0.08 0.16
Matches are distributed among these distances:
75 2 0.00
76 9 0.02
77 1 0.00
78 2 0.00
79 5 0.01
80 196 0.42
81 18 0.04
82 4 0.01
84 32 0.07
85 10 0.02
86 116 0.25
87 9 0.02
88 2 0.00
90 26 0.06
91 16 0.03
92 7 0.01
93 3 0.01
95 2 0.00
97 2 0.00
98 1 0.00
99 7 0.01
100 2 0.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (78 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAATAAAT
Found at i:4877 original size:18 final size:18
Alignment explanation
Indices: 4851--4966 Score: 54
Period size: 18 Copynumber: 6.7 Consensus size: 18
4841 CTACAATAAT
*
4851 AAATCAATCAATATTTTA
1 AAATAAATCAATATTTTA
**
4869 AAATAAATCAAT-TAATA
1 AAATAAATCAATATTTTA
4886 CAAATAAAT---TA-TTTA
1 -AAATAAATCAATATTTTA
**
4901 AAATAAATCAAT-TCATA
1 AAATAAATCAATATTTTA
*
4918 CTAATAAAT---TA-TTTA
1 -AAATAAATCAATATTTTA
4933 AAATAAATCAATCCATATTTTA
1 AAATAAATC-A---ATATTTTA
4955 AAATAAATCAAT
1 AAATAAATCAAT
4967 CTATACTAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 32
0.62 0.10 0.28
Matches are distributed among these distances:
14 15 0.21
15 6 0.08
17 6 0.08
18 28 0.39
21 3 0.04
22 13 0.18
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATAAATCAATATTTTA
Found at i:4901 original size:32 final size:32
Alignment explanation
Indices: 4865--4944 Score: 142
Period size: 32 Copynumber: 2.5 Consensus size: 32
4855 CAATCAATAT
4865 TTTAAAATAAATCAATTAATACAAATAAATTA
1 TTTAAAATAAATCAATTAATACAAATAAATTA
* *
4897 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTAATACAAATAAATTA
4929 TTTAAAATAAATCAAT
1 TTTAAAATAAATCAAT
4945 CCATATTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATTAATACAAATAAATTA
Found at i:4904 original size:14 final size:14
Alignment explanation
Indices: 4887--4940 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
4877 CAATTAATAC
4887 AAATAAATTATTTA
1 AAATAAATTATTTA
*
4901 AAATAAATCAATTCATA
1 AAATAAAT-TATT--TA
*
4918 CTAATAAATTATTTA
1 -AAATAAATTATTTA
4933 AAATAAAT
1 AAATAAAT
4941 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 5 0.16
17 5 0.16
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:4941 original size:166 final size:165
Alignment explanation
Indices: 4753--5720 Score: 900
Period size: 166 Copynumber: 6.0 Consensus size: 165
4743 ACAACTACAA
*
4753 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATGAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAA-TCATACTAATAAATTAT
*
4818 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCAATATTTTAAAATAAATCAATTA
65 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCAATATTTTAAAATAAATCAATTC
*
4883 ATACAAATAAATTATTTAAAATAAATCAATTCATAC
130 ATACTAATAAATTATTTAAAATAAATCAATTCATAC
4919 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATC-ATACTAATAAATTAT
* **
4984 TTAAAATAAATCAATTCATACAACTGTAATAATAAATCAAT-ACATATTTTAAAATAAATCAATT
65 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCA-ATATTTTAAAATAAATCAATT
*
5048 CATACTAATAAATTATTTAAAATAAATC-A-TCTATATT
129 CATACTAATAAATTATTTAAAATAAATCAATTC-ATA-C
* * * * **
5085 TAA-AAATTCAATCTATACT-AATAAAT---TA-TTT-AAATAAATC-ATCCATA-TTTTAAA--
1 TAATAAATT--ATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-CATACTAATAAATT
* *** * **
5139 A--T--AATTAATCAATGTTTTA-AAATA-AATTAATCCATACAAT-AATTA-TTTAAAATAAAT
63 ATTTAAAATAAATCAAT-CCATACAACTACAA-TAATAAAT-CAATCAA-TATTTTAAAATAAAT
* * *
5196 CAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTT
124 CAATTCATACTAATAAATTATTTAAAATAAATCAATTCATA--C
* * * * *
5240 TAAAATAAATCAATCTATACT-AATAAAT---TA-TTTAAAATAAATCAATC---C--AT--A-T
1 T--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCATACTAATAAATT
* * * ** *
5292 -TTTAAAATAAATCAATCTATACTAA-TA-AATTATTTAAAATAAATCAAT-TCATACAACTATA
63 ATTTAAAATAAATCAATCCATAC-AACTACAA-TA-AT-AAATCAATCAATATTTTA-AAATA-A
** *
5353 AT-AATAAAT-C-AATACA-TATTTTAAAATAAATCAATTCATAC
122 ATCAATTCATACTAATAAATTA-TTTAAAATAAATCAATTCATAC
* * * *
5394 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAATTCGATCTATGCTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATC-ATACTAATAAATTAT
* ** *
5459 TTAAAATAAATCAATCCAT---ATTTTAA-AATAAATTAATCAATATTTTAAAATAAATCAA-TC
65 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCAATATTTTAAAATAAATCAATTC
*
5519 TATACAAATAAATTATTTAAAATAAATCAA-TCTATAC
130 -ATACTAATAAATTATTTAAAATAAATCAATTC-ATAC
*
5556 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-CATACTAATAAATTAT
*
5621 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
65 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCAATATTTTAAAATAAATCAATTC
*
5686 ATACTAATAAATTATTTAAAATAAATCAATCCATA
130 ATACTAATAAATTATTTAAAATAAATCAATTCATA
5721 TTTTATAATA
Statistics
Matches: 668, Mismatches: 68, Indels: 132
0.77 0.08 0.15
Matches are distributed among these distances:
151 6 0.01
152 16 0.02
153 64 0.10
154 17 0.03
155 12 0.02
156 57 0.09
157 34 0.05
158 27 0.04
159 13 0.02
160 25 0.04
161 17 0.03
162 109 0.16
163 5 0.01
164 5 0.01
165 17 0.03
166 235 0.35
167 9 0.01
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (165 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCATACTAATAAATTATT
TAAAATAAATCAATCCATACAACTACAATAATAAATCAATCAATATTTTAAAATAAATCAATTCA
TACTAATAAATTATTTAAAATAAATCAATTCATAC
Found at i:4955 original size:134 final size:134
Alignment explanation
Indices: 4817--5720 Score: 461
Period size: 134 Copynumber: 6.8 Consensus size: 134
4807 TAATAAATGA
* * *
4817 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCAATATTTTAAAATAAATCAATT
1 TTTAAAATAAATCAATCAATACAATTAAAATAATAAATCAATCAATATTTTAAAATAAATCAATT
4882 AATACAAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCC
66 AATACAAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCC
4947 ATAT
131 ATAT
* * * * ** * *
4951 TTTAAAATAAATCAATCTATACTAA-TAAATTATTTAAAATAAATCAAT-TCATACAACTGTAAT
1 TTTAAAATAAATCAATCAATAC-AATTAAAATA-AT-AAATCAATCAATATTTTA-AAAT-AAAT
* *
5014 -AATAAAT-C-AATACA-TATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAAT
61 CAATTAATACAAATAAATTA-TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAAT
*
5075 C-ATCTATAT
125 CAATCCATAT
* * * ** *
5084 TTAAAAATTCAATCTATACTAATA-AATT-ATTTAAATAAATC-ATCCATATTTT---A-AAAT-
1 TTTAAAA-TAAATCAAT-C-AATACAATTAAAAT-AATAAATCAATCAATATTTTAAAATAAATC
* * *
5141 AATTAAT-C-AAT---GT-TTTAAAATAAATTAATCCATAC-AAT-AATTATTTAAAATAAATCA
62 AATTAATACAAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCA
5198 ATCCATACT
127 ATCCATA-T
** * * ** **
5207 AATAAATTATTTAAAATAAATCAATCCATATTTTAA-AATAAATCAATC--TATACT--AATAAA
1 TTTAAA--A--T-AAATCAATCAATACA-ATTAAAATAATAAATCAATCAATATTTTAAAATAAA
* * * * *
5267 TTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAA-TCTATACTAATAAATTATTTAAAA
60 TCAATTAATACAAATAAAT---TA-TTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAA
* *
5331 TAAATCAATTCATACA
120 TAAATCAATCCATA-T
** * * ** * * *
5347 ACTATAAT-AATAAATCAATACATATTTTAA-AATAAATCAATTC-ATA--CT--AATAAATTAT
1 TTTAAAATAAATCAATCAATACA-ATTAAAATAATAAATCAA-TCAATATTTTAAAATAAATCAA
* * * * * *
5405 TTAAAATAAATCAATCTATATTTTAAAATAATTCGA-TCTATGCTAATAAATTATTTAAAATAAA
64 TTAATACAAAT-AA-AT-TA-TTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAATAAA
5469 TCAATCCATAT
124 TCAATCCATAT
* ** * *
5480 TTTAAAATAAATTAATCAATA-TTTTAAAATAAATCAATCTATACAAATAAATTATTTAAAATAA
1 TTTAAAATAAATCAATCAATACAATTAAAAT-AATAAATCAAT-C-AAT--A-T-TTTAAAATAA
* * ** * ** * *
5544 ATCAATCT-ATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATAT
59 ATCAAT-TAATACAAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAA
**
5606 ATACTAATAAAT-T
123 AT-C-AATCCATAT
* * * *
5619 ATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAT
1 -TTTAAAATAAATCAATCAATACAATTAAAATAATAAATCAATCAATATTTTAAAATAAATCAAT
* * *
5684 TCATACTAATAAATTATTTAAAATAAATCAATCCATA
65 TAATACAAATAAATTATTTAAAATAAATCAATTCATA
5721 TTTTATAATA
Statistics
Matches: 609, Mismatches: 97, Indels: 128
0.73 0.12 0.15
Matches are distributed among these distances:
121 18 0.03
122 9 0.01
123 24 0.04
125 9 0.01
126 13 0.02
127 28 0.05
128 5 0.01
130 3 0.00
132 9 0.01
133 28 0.05
134 267 0.44
135 14 0.02
136 31 0.05
137 4 0.01
138 28 0.05
139 14 0.02
140 78 0.13
141 8 0.01
142 2 0.00
143 2 0.00
144 14 0.02
145 1 0.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (134 bp):
TTTAAAATAAATCAATCAATACAATTAAAATAATAAATCAATCAATATTTTAAAATAAATCAATT
AATACAAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCC
ATAT
Found at i:4980 original size:22 final size:22
Alignment explanation
Indices: 4931--4979 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
4921 ATAAATTATT
**
4931 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
4953 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
4976 TAAA
1 TAAA
4980 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:5018 original size:26 final size:24
Alignment explanation
Indices: 4985--5052 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 24
4975 ATAAATTATT
4985 TAAAATAAATCAATTCATACAACTG
1 TAAAATAAATCAATTCATAC-ACTG
* * *
5010 TAATAATAAATCAATACAT--ATTT
1 TAA-AATAAATCAATTCATACACTG
5033 TAAAATAAATCAATTCATAC
1 TAAAATAAATCAATTCATAC
5053 TAATAAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
22 14 0.39
23 5 0.14
25 3 0.08
26 14 0.39
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.32
Consensus pattern (24 bp):
TAAAATAAATCAATTCATACACTG
Found at i:5142 original size:21 final size:21
Alignment explanation
Indices: 5116--5174 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
5106 TAAATTATTT
*
5116 AAATAAATCATCCATATTTTA
1 AAATAAATAATCCATATTTTA
* * *
5137 AAATAATTAATCAATGTTTTA
1 AAATAAATAATCCATATTTTA
5158 AAATAAATTAATCCATA
1 AAATAAA-TAATCCATA
5175 CAATAATTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATAAATAATCCATATTTTA
Found at i:5220 original size:32 final size:32
Alignment explanation
Indices: 5154--5720 Score: 287
Period size: 32 Copynumber: 19.7 Consensus size: 32
5144 TAATCAATGT
*
5154 TTTAAAATAAATTAATCCATAC-AAT-AATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
5184 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
5216 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
5238 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
5270 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
5292 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
5324 TTTAAAATAAATCAATTCATAC-AACT--A-TA
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* * **
5353 ---ATAATAAATCAATACATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
5379 -------TAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
5404 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* * * *
5426 TTTAAAATAATTCGATCTATGCTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
5458 TTTAAAATAAATCAATCCATATTTTAAAATAAATTAATCAATA
1 TTTAAAATAAATCAATCCATA--CT--AAT--A--AAT---TA
* *
5501 TTTTAAAATAAATCAATCTATACAAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
*
5534 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
5566 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
**
5588 TTTAAAATAAATCAATATATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
5620 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
5650 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
5668 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
5700 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
5721 TTTTATAATA
Statistics
Matches: 423, Mismatches: 30, Indels: 166
0.68 0.05 0.27
Matches are distributed among these distances:
20 1 0.00
22 86 0.20
23 11 0.03
24 6 0.01
25 3 0.01
26 45 0.11
27 5 0.01
28 14 0.03
29 2 0.00
30 27 0.06
31 13 0.03
32 171 0.40
33 2 0.00
34 1 0.00
36 6 0.01
38 2 0.00
40 6 0.01
43 2 0.00
44 20 0.05
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:5263 original size:54 final size:54
Alignment explanation
Indices: 5184--5344 Score: 304
Period size: 54 Copynumber: 3.0 Consensus size: 54
5174 ACAATAATTA
*
5184 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
5238 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
5292 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATA
5345 CAACTATAAT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 105 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (54 bp):
TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:5267 original size:22 final size:22
Alignment explanation
Indices: 5218--5266 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5208 ATAAATTATT
**
5218 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
5240 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
5263 TAAA
1 TAAA
5267 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:5321 original size:22 final size:22
Alignment explanation
Indices: 5272--5320 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5262 ATAAATTATT
**
5272 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
5294 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
5317 TAAA
1 TAAA
5321 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:5321 original size:40 final size:40
Alignment explanation
Indices: 5275--5401 Score: 102
Period size: 40 Copynumber: 3.2 Consensus size: 40
5265 AATTATTTAA
*
5275 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACT
1 AATAAATCAATACATATTTTAAAATAAATCAATCTATACT
* * * * ** *
5315 AATAAATTATTTA-A-A-ATAAATCAATTCATACAA-CTATAAT
1 AATAAATCA-ATACATATTTTAA--AATAAAT-CAATCTATACT
5355 AATAAATCAATACATATTTTAAAATAAATCAAT-TCATACT
1 AATAAATCAATACATATTTTAAAATAAATCAATCT-ATACT
5395 AATAAAT
1 AATAAAT
5402 TATTTAAAAT
Statistics
Matches: 63, Mismatches: 15, Indels: 18
0.66 0.16 0.19
Matches are distributed among these distances:
38 3 0.05
39 7 0.11
40 45 0.71
41 5 0.08
42 3 0.05
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (40 bp):
AATAAATCAATACATATTTTAAAATAAATCAATCTATACT
Found at i:5401 original size:22 final size:23
Alignment explanation
Indices: 5326--5400 Score: 80
Period size: 22 Copynumber: 3.2 Consensus size: 23
5316 ATAAATTATT
*
5326 TAAAATAAATCAATTCATACAACTA
1 TAAAATAAATCAATTCATACTA--A
* **
5351 TAATAATAAATCAATACATA-TTT
1 TAA-AATAAATCAATTCATACTAA
5374 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATTCATACTAA
5397 TAAA
1 TAAA
5401 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAAATAAATCAATTCATACTAA
Found at i:5419 original size:54 final size:54
Alignment explanation
Indices: 5355--5640 Score: 350
Period size: 54 Copynumber: 5.3 Consensus size: 54
5345 CAACTATAAT
*
5355 AATAAATCAATACATATTTTAAAATAAATCAAT-TCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCT-ATACTAATAAATTATTTAA
* * * *
5409 AATAAATCAATCTATATTTTAAAATAATTCGATCTATGCTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
* ** * *
5463 AATAAATCAATCCATATTTTAAAATAAATTAATCAATATTTTAAAATAAATCAATCT-A
1 AATAAATCAATCCATATTTTAAAATAAATCAATC--TATACT--AATAAAT-TATTTAA
* * *
5521 TACAAATAAAT---TA-TTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
*
5571 AATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
5625 AATAAATCAATCCATA
1 AATAAATCAATCCATA
5641 CAACTACAAT
Statistics
Matches: 196, Mismatches: 25, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
49 3 0.02
50 16 0.08
52 4 0.02
53 2 0.01
54 145 0.74
55 3 0.02
56 4 0.02
58 16 0.08
59 3 0.02
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
Found at i:5430 original size:22 final size:22
Alignment explanation
Indices: 5404--5445 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5394 TAATAAATTA
5404 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCTATAT
* *
5426 TTTAAAATAATTCGATCTAT
1 TTTAAAATAAATCAATCTAT
5446 GCTAATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (22 bp):
TTTAAAATAAATCAATCTATAT
Found at i:5484 original size:22 final size:22
Alignment explanation
Indices: 5458--5518 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
5448 TAATAAATTA
*
5458 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCAATAT
*
5480 TTTAAAATAAATTAATCAATAT
1 TTTAAAATAAATCAATCAATAT
5502 TTTAAAATAAATCAATC
1 TTTAAAATAAATCAATC
5519 TATACAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATCAATAT
Found at i:5541 original size:14 final size:14
Alignment explanation
Indices: 5524--5577 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
5514 CAATCTATAC
5524 AAATAAATTATTTA
1 AAATAAATTATTTA
*
5538 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
5555 CTAATAAATTATTTA
1 -AAATAAATTATTTA
5570 AAATAAAT
1 AAATAAAT
5578 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:5562 original size:162 final size:165
Alignment explanation
Indices: 5372--5720 Score: 530
Period size: 162 Copynumber: 2.1 Consensus size: 165
5362 CAATACATAT
*
5372 TTTAAAATAAATCAAT-TCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAA
1 TTTAAAATAAATCAATCTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
* * * * * ** *
5436 TTCGATCTATGCTAATAAATTATTTAAAATAAATCAATCCAT-ATTTTAA-AATAAATTAATCAA
66 ATCAATATATACTAATAAATTATTTAAAATAAATCAATCCATAACTACAATAATAAATCAATCAA
5499 TATTTTAAAATAAATCAA-TCTATACAAATAAATTA
131 TATTTTAAAATAAATCAATTC-ATACAAATAAATTA
5534 TTTAAAATAAATCAATCT-ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
1 TTTAAAATAAATCAATCTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
5598 ATCAATATATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATC
66 ATCAATATATACTAATAAATTATTTAAAATAAATCAATCCAT--AACTACAATAATAAATCAATC
* *
5663 CATATTTTAAAATAAATCAATTCATACTAATAAATTA
129 AATATTTTAAAATAAATCAATTCATACAAATAAATTA
5700 TTTAAAATAAATCAATC-CATA
1 TTTAAAATAAATCAATCTCATA
5721 TTTTATAATA
Statistics
Matches: 169, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
162 99 0.59
163 1 0.01
165 4 0.02
166 63 0.37
167 2 0.01
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (165 bp):
TTTAAAATAAATCAATCTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
ATCAATATATACTAATAAATTATTTAAAATAAATCAATCCATAACTACAATAATAAATCAATCAA
TATTTTAAAATAAATCAATTCATACAAATAAATTA
Found at i:5773 original size:12 final size:15
Alignment explanation
Indices: 5719--5868 Score: 237
Period size: 15 Copynumber: 10.0 Consensus size: 15
5709 AATCAATCCA
*
5719 TATTTTATAATAATT
1 TATTTTATAATAAAT
*
5734 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
5749 TATTTTATAATAAAT
1 TATTTTATAATAAAT
5764 TATTTTATAATAAAT
1 TATTTTATAATAAAT
*
5779 TATTTTATAATAAAA
1 TATTTTATAATAAAT
*
5794 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
*
5809 TGTTTTATAATAAAT
1 TATTTTATAATAAAT
5824 TATTTTATAATAAAT
1 TATTTTATAATAAAT
*
5839 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
*
5854 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
5869 AACATTATTA
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 125 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
TATTTTATAATAAAT
Found at i:6139 original size:2 final size:2
Alignment explanation
Indices: 6123--6197 Score: 52
Period size: 2 Copynumber: 40.0 Consensus size: 2
6113 TAATAAAATG
* * * *
6123 TA TA AA TA T- TA TA TA TA TA TA TA TG TA TA TA TA TA AA AA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
6163 TA TT TA -A TA -A AA TA TA TA AA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6198 ACTGTTTGAA
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
1 5 0.09
2 52 0.91
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (2 bp):
TA
Found at i:6858 original size:24 final size:24
Alignment explanation
Indices: 6826--6881 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
6816 TAGAAGTTCG
6826 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
6850 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
6874 ATTGAAGC
1 ATTGAAGC
6882 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:10180 original size:27 final size:27
Alignment explanation
Indices: 10109--10201 Score: 140
Period size: 25 Copynumber: 3.6 Consensus size: 27
10099 TCTATTTACA
*
10109 AAATCATATCTCTATAGGAATGATAAC
1 AAATCATATCTCTATAGGAATGGTAAC
10136 AAAT--TATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
*
10161 AAATCATAACTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
10188 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
10202 ATTCCTACAC
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
25 32 0.52
27 29 0.48
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:13933 original size:27 final size:28
Alignment explanation
Indices: 13903--13988 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 28
13893 AAATCTATTT
*
13903 ACAAAACCATA-TCCTTTAGGAATGATA
1 ACAAAACCATATTCCTATAGGAATGATA
* * *
13930 AC-AAATCATATTTCTATAGGAATGGTA
1 ACAAAACCATATTCCTATAGGAATGATA
* * *
13957 AC-AAATCATGACT-CTATAGGAATGGTA
1 ACAAAACCAT-ATTCCTATAGGAATGATA
13984 ACAAA
1 ACAAA
13989 TCATCTCTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
26 7 0.14
27 40 0.78
28 4 0.08
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (28 bp):
ACAAAACCATATTCCTATAGGAATGATA
Found at i:13989 original size:27 final size:26
Alignment explanation
Indices: 13919--13999 Score: 119
Period size: 27 Copynumber: 3.1 Consensus size: 26
13909 CCATATCCTT
* *
13919 TAGGAATGATAACAAATCATATTTCTA
1 TAGGAATGGTAACAAATCATA-CTCTA
13946 TAGGAATGGTAACAAATCATGACTCTA
1 TAGGAATGGTAACAAATCAT-ACTCTA
13973 TAGGAATGGTAACAAATCAT-CTCTA
1 TAGGAATGGTAACAAATCATACTCTA
13998 TA
1 TA
14000 ATTCCTACAC
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.14
27 43 0.84
28 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.30
Consensus pattern (26 bp):
TAGGAATGGTAACAAATCATACTCTA
Found at i:16067 original size:21 final size:21
Alignment explanation
Indices: 16043--16098 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
16033 GTAATATTTT
16043 TTTTATAAAAGTTA-ATGATCA
1 TTTTATAAAAGTTAGA-GATCA
* *
16064 TTTTATAACAGTATAGAGATTA
1 TTTTATAAAAGT-TAGAGATCA
*
16086 TTTTATAATAGTT
1 TTTTATAAAAGTT
16099 TGCTGAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 12 0.40
22 17 0.57
23 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (21 bp):
TTTTATAAAAGTTAGAGATCA
Found at i:17433 original size:30 final size:29
Alignment explanation
Indices: 17399--17455 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
17389 ATGTGTTTTT
*
17399 TAAATATAAATCTATTTAATTCATAATTTA
1 TAAATATAAATCTATCTAATT-ATAATTTA
*
17429 TAAATATAAATTTATCTAATTATAATT
1 TAAATATAAATCTATCTAATTATAATT
17456 ATTTAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (29 bp):
TAAATATAAATCTATCTAATTATAATTTA
Found at i:29843 original size:8 final size:8
Alignment explanation
Indices: 29829--29867 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
29819 ATGAAGTACA
29829 GTATATAT
1 GTATATAT
*
29837 ATATATAT
1 GTATATAT
*
29845 GTATGTAT
1 GTATATAT
*
29853 GTATGTAT
1 GTATATAT
29861 GTATATA
1 GTATATA
29868 GGATTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (8 bp):
GTATATAT
Found at i:30562 original size:15 final size:14
Alignment explanation
Indices: 30533--30559 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30523 AATAAACGAG
30533 TATGAACATAAAAT
1 TATGAACATAAAAT
30547 TATGAACATAAAA
1 TATGAACATAAAA
30560 ATTTTATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.26
Consensus pattern (14 bp):
TATGAACATAAAAT
Found at i:32486 original size:54 final size:53
Alignment explanation
Indices: 32425--32532 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 53
32415 GGTGAGACTT
*
32425 AATTTCATTTAACTTTAAAATCGATAATGTCTTAAAAAATAATTAAACTAAAAA
1 AATTTCATTTAACTTTAAAATCGAAAATGTCTT-AAAAATAATTAAACTAAAAA
32479 AATTTCATTTAACTTTAAAATCGAAAATGTCTTAAAAATAATTAAACTAAAAA
1 AATTTCATTTAACTTTAAAATCGAAAATGTCTTAAAAATAATTAAACTAAAAA
32532 A
1 A
32533 TTTTTAGAGG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 21 0.40
54 32 0.60
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (53 bp):
AATTTCATTTAACTTTAAAATCGAAAATGTCTTAAAAATAATTAAACTAAAAA
Found at i:34373 original size:42 final size:42
Alignment explanation
Indices: 34313--34395 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
34303 CCCGAAATCG
* * * *
34313 CGTGTTTGTTTCATGTAATTCGTTTTTCGGAAAATGTTTTCT
1 CGTGTTTGTTTCACGTAATTCATTTTCCAGAAAATGTTTTCT
*
34355 CGTGTTTGTTTTACGTAATTCATTTTCCAGAAAATGTTTTC
1 CGTGTTTGTTTCACGTAATTCATTTTCCAGAAAATGTTTTC
34396 CAGAGTTTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.19, C:0.13, G:0.17, T:0.51
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCATTTTCCAGAAAATGTTTTCT
Found at i:34404 original size:42 final size:42
Alignment explanation
Indices: 34316--34404 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
34306 GAAATCGCGT
* * * * *
34316 GTTTGTTTCATGTAATTCGTTTTTCGGAAAATGTTTTCTCGT
1 GTTTGTTTCACGTAATTCATTTTCCAGAAAATGTTTTCTCGA
*
34358 GTTTGTTTTACGTAATTCATTTTCCAGAAAATGTTTTC-CAGA
1 GTTTGTTTCACGTAATTCATTTTCCAGAAAATGTTTTCTC-GA
34400 GTTTG
1 GTTTG
34405 GTTGGAGGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
41 1 0.03
42 39 0.98
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.49
Consensus pattern (42 bp):
GTTTGTTTCACGTAATTCATTTTCCAGAAAATGTTTTCTCGA
Found at i:34658 original size:21 final size:20
Alignment explanation
Indices: 34619--34670 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
34609 AATTATTAAA
*
34619 ATATTTAAAAT-ATATTTATT
1 ATATTTATAATAATATTTA-T
34639 GATATTTATAATAATA-TTAT
1 -ATATTTATAATAATATTTAT
*
34659 ATATTTTTAATA
1 ATATTTATAATA
34671 TTTTAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 11 0.39
20 1 0.04
21 13 0.46
22 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
ATATTTATAATAATATTTAT
Found at i:34695 original size:23 final size:23
Alignment explanation
Indices: 34668--34720 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
34658 TATATTTTTA
34668 ATATTTTAATAAAATAATCA-ATT
1 ATATTTTAATAAAATAA-CATATT
* * *
34691 ATATTATAATAATATAAGATATT
1 ATATTTTAATAAAATAACATATT
34714 ATATTTT
1 ATATTTT
34721 TGTTTTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATTTTAATAAAATAACATATT
Found at i:34840 original size:23 final size:23
Alignment explanation
Indices: 34814--34858 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
34804 AATAATAGTT
34814 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
34837 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
34859 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:34991 original size:27 final size:28
Alignment explanation
Indices: 34961--35016 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 28
34951 ATTATAAAAA
34961 TAATA-TTTAATAATAAATAA-ATT-ATTT
1 TAATATTTTAA-AAT-AATAATATTAATTT
34988 TAATATTTTAAAATAATAATATTAATTT
1 TAATATTTTAAAATAATAATATTAATTT
35016 T
1 T
35017 TATGATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 5 0.19
27 11 0.42
28 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TAATATTTTAAAATAATAATATTAATTT
Found at i:35012 original size:22 final size:22
Alignment explanation
Indices: 34975--35033 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
34965 ATTTAATAAT
* *
34975 AAATAAATTATTTTAATATTTTA
1 AAATAAATAATATTAAT-TTTTA
34998 AAAT-AATAATATTAATTTTTA
1 AAATAAATAATATTAATTTTTA
**
35019 TGATAAATAATATTA
1 AAATAAATAATATTA
35034 TTTATTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 7 0.23
22 20 0.65
23 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATAAATAATATTAATTTTTA
Found at i:35238 original size:15 final size:15
Alignment explanation
Indices: 35203--35284 Score: 82
Period size: 15 Copynumber: 5.5 Consensus size: 15
35193 TTCCATAAAT
**
35203 GTAATTCATTTTTCA
1 GTAATTCAAATTTCA
35218 -TAATTCAAATTTCA
1 GTAATTCAAATTTCA
*
35232 GTAATTC-ATTTTCCA
1 GTAATTCAAATTT-CA
35247 GTAATTCAAA-TTCTA
1 GTAATTCAAATTTC-A
35262 GTAATTCAAA-TTCTA
1 GTAATTCAAATTTC-A
35277 GTAATTCA
1 GTAATTCA
35285 TTTTCCAGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
14 17 0.29
15 41 0.69
16 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (15 bp):
GTAATTCAAATTTCA
Found at i:35254 original size:30 final size:30
Alignment explanation
Indices: 35203--35284 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
35193 TTCCATAAAT
*
35203 GTAATTCATTTTTCA-TAATTCAAATT-TCA
1 GTAATTCATTTTCCAGTAATTCAAATTCT-A
35232 GTAATTCATTTTCCAGTAATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCTA
** *
35262 GTAATTCAAATTCTAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
35285 TTTTCCAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
29 14 0.30
30 32 0.68
31 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCTA
Found at i:40338 original size:2 final size:2
Alignment explanation
Indices: 40331--40408 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
40321 GGTTATTACT
40331 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40373 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40409 AAGGGTATAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40664 original size:31 final size:30
Alignment explanation
Indices: 40625--40683 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 30
40615 TAAGGTAAAA
40625 TATGTTTAAT-ATTTAAATTATT-AATTTTGG
1 TATGTTTAATCA-TTAAATT-TTCAATTTTGG
40655 TATGTTTTAATCATTAAATTTTCAATTTT
1 TATG-TTTAATCATTAAATTTTCAATTTT
40684 TTTAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 6 0.23
31 19 0.73
32 1 0.04
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (30 bp):
TATGTTTAATCATTAAATTTTCAATTTTGG
Found at i:41152 original size:20 final size:20
Alignment explanation
Indices: 41129--41167 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
41119 AATATCTAAA
41129 TTTTATTTTTATTTTTCAAC
1 TTTTATTTTTATTTTTCAAC
41149 TTTTATTTTTATTTTTCAA
1 TTTTATTTTTATTTTTCAA
41168 AACTATGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATTTTTATTTTTCAAC
Found at i:41360 original size:35 final size:33
Alignment explanation
Indices: 41298--41363 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 33
41288 ATCTAAACGT
41298 TAAATTTTGAACAGTACTAAATAAAATAAAAAC
1 TAAATTTTGAACAGTACTAAATAAAATAAAAAC
*
41331 TAAAGTTTTTAACAGTA-TAATACTAAAATAAAA
1 TAAA-TTTTGAACAGTACTAA-A-TAAAATAAAA
41364 TAAAAACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.24
34 12 0.41
35 10 0.34
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.30
Consensus pattern (33 bp):
TAAATTTTGAACAGTACTAAATAAAATAAAAAC
Found at i:44783 original size:2 final size:2
Alignment explanation
Indices: 44776--44808 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
44766 ATAATACTTC
44776 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 T
44809 TTCAATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47192 original size:2 final size:2
Alignment explanation
Indices: 47187--47236 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
47177 AGAATTTATC
47187 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
47229 AT AT AT AT
1 AT AT AT AT
47237 GATAAATTAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51312 original size:12 final size:12
Alignment explanation
Indices: 51283--51404 Score: 145
Period size: 12 Copynumber: 10.2 Consensus size: 12
51273 AATCAAAGTA
51283 ATGTATGTACGT
1 ATGTATGTACGT
* *
51295 ATGTACGTATGT
1 ATGTATGTACGT
* * *
51307 ACGTACGTATGT
1 ATGTATGTACGT
*
51319 ACGTATGTACGT
1 ATGTATGTACGT
**
51331 ACATATGTACGT
1 ATGTATGTACGT
* *
51343 ATGTACGTACAT
1 ATGTATGTACGT
*
51355 ATGTATGTATGT
1 ATGTATGTACGT
51367 ATGTATGTACGT
1 ATGTATGTACGT
51379 ATGTATGTACGT
1 ATGTATGTACGT
51391 ATGTATGTACGT
1 ATGTATGTACGT
51403 AT
1 AT
51405 CCGTAT
Statistics
Matches: 96, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 96 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (12 bp):
ATGTATGTACGT
Found at i:51312 original size:20 final size:20
Alignment explanation
Indices: 51283--51404 Score: 163
Period size: 20 Copynumber: 6.1 Consensus size: 20
51273 AATCAAAGTA
*
51283 ATGTATGTACGTATGTACGT
1 ATGTACGTACGTATGTACGT
51303 ATGTACGTACGTATGTACGT
1 ATGTACGTACGTATGTACGT
*
51323 ATGTACGTACATATGTACGT
1 ATGTACGTACGTATGTACGT
* *
51343 ATGTACGTACATATGTATGT
1 ATGTACGTACGTATGTACGT
* * * *
51363 ATGTATGTATGTACGTATGT
1 ATGTACGTACGTATGTACGT
*
51383 ATGTACGTATGTATGTACGT
1 ATGTACGTACGTATGTACGT
51403 AT
1 AT
51405 CCGTAT
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 92 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (20 bp):
ATGTACGTACGTATGTACGT
Found at i:51404 original size:8 final size:8
Alignment explanation
Indices: 51285--51395 Score: 105
Period size: 8 Copynumber: 13.9 Consensus size: 8
51275 TCAAAGTAAT
51285 GTATGTAC
1 GTATGTAC
51293 GTATGTAC
1 GTATGTAC
51301 GTATGTAC
1 GTATGTAC
* *
51309 GTACGTAT
1 GTATGTAC
* *
51317 GTACGTAT
1 GTATGTAC
*
51325 GTACGTAC
1 GTATGTAC
*
51333 ATATGTAC
1 GTATGTAC
51341 GTATGTAC
1 GTATGTAC
** *
51349 GTACATAT
1 GTATGTAC
*
51357 GTATGTAT
1 GTATGTAC
*
51365 GTATGTAT
1 GTATGTAC
* *
51373 GTACGTAT
1 GTATGTAC
51381 GTATGTAC
1 GTATGTAC
51389 GTATGTA
1 GTATGTA
51396 TGTACGTATC
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 89 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (8 bp):
GTATGTAC
Done.