Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001697.1 Hibiscus syriacus cultivar Beakdansim tig00003390_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: 121491
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2308 original size:29 final size:30
Alignment explanation
Indices: 2265--2325 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
2255 AATTTTGACC
2265 AGTGACTAAAATGTAAGTTTTG-AAAGTTT
1 AGTGACTAAAATGTAAGTTTTGAAAAGTTT
* * *
2294 AGTGGCTAAAGTGTAATTTTTGAAAAGTTT
1 AGTGACTAAAATGTAAGTTTTGAAAAGTTT
2324 AG
1 AG
2326 GACCCAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (30 bp):
AGTGACTAAAATGTAAGTTTTGAAAAGTTT
Found at i:7844 original size:23 final size:23
Alignment explanation
Indices: 7810--7876 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
7800 ACAATTATGT
7810 GGCA-TTTCGGTGCAAACCTATTC
1 GGCACTTT-GGTGCAAACCTATTC
* *
7833 GGCACTTTGGTGCAAACCTTTTT
1 GGCACTTTGGTGCAAACCTATTC
* * *
7856 GGCACTTCGATGCAAATCTAT
1 GGCACTTTGGTGCAAACCTAT
7877 GTGGTCCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 34 0.92
24 3 0.08
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (23 bp):
GGCACTTTGGTGCAAACCTATTC
Found at i:8751 original size:22 final size:20
Alignment explanation
Indices: 8705--8757 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
8695 ACTTCCTTTT
*
8705 AAATTTTTATATATTTTAGA
1 AAATTTTTTTATATTTTAGA
* *
8725 TAATTTTTTTATTTTTTATTGA
1 AAATTTTTTTATATTTTA--GA
8747 AAATTTATTTT
1 AAATTT-TTTT
8758 CGTCCCTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 15 0.58
22 7 0.27
23 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (20 bp):
AAATTTTTTTATATTTTAGA
Found at i:9675 original size:16 final size:16
Alignment explanation
Indices: 9656--9695 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
9646 TGCCTTAAGT
*
9656 AGAGGATGCCACCGGA
1 AGAGGATGCCACCAGA
9672 AGAGGATGCCACCAGA
1 AGAGGATGCCACCAGA
9688 AGAGGATG
1 AGAGGATG
9696 TCTTTTGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.20, G:0.38, T:0.07
Consensus pattern (16 bp):
AGAGGATGCCACCAGA
Found at i:11228 original size:3 final size:3
Alignment explanation
Indices: 11220--11284 Score: 51
Period size: 3 Copynumber: 21.7 Consensus size: 3
11210 ATATTCTGGG
* * * * *
11220 CAT CAT CAT CACT C-T GAT CAT CAC CAT CAT CAT CAC CAC CAC CAT
1 CAT CAT CAT CA-T CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
* *
11265 CAC CAT CAC CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CA
11285 CCCTCATCTA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 1 0.02
3 47 0.94
4 2 0.04
ACGTcount: A:0.32, C:0.43, G:0.02, T:0.23
Consensus pattern (3 bp):
CAT
Found at i:11247 original size:6 final size:6
Alignment explanation
Indices: 11238--11286 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
11228 TCACTCTGAT
* * *
11238 CATCAC CATCAT CATCAC CACCAC CATCAC CATCAC CATCAT CATCAC
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC
11286 C
1 C
11287 CTCATCTACA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.33, C:0.49, G:0.00, T:0.18
Consensus pattern (6 bp):
CATCAC
Found at i:11292 original size:12 final size:12
Alignment explanation
Indices: 11220--11284 Score: 69
Period size: 12 Copynumber: 5.4 Consensus size: 12
11210 ATATTCTGGG
11220 CATCATCATCAC
1 CATCATCATCAC
*
11232 TC-TGATCATCAC
1 -CATCATCATCAC
11244 CATCATCATCAC
1 CATCATCATCAC
* *
11256 CACCACCATCAC
1 CATCATCATCAC
* *
11268 CATCACCATCAT
1 CATCATCATCAC
11280 CATCA
1 CATCA
11285 CCCTCATCTA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
11 1 0.02
12 43 0.96
13 1 0.02
ACGTcount: A:0.32, C:0.43, G:0.02, T:0.23
Consensus pattern (12 bp):
CATCATCATCAC
Found at i:13250 original size:4 final size:4
Alignment explanation
Indices: 13241--13336 Score: 70
Period size: 4 Copynumber: 23.0 Consensus size: 4
13231 ATATTCCTTC
* *
13241 AAAT AAAT AAAT AAAT AAATT CAAAA AAATT AAAT AAAT GAATTT AAATT
1 AAAT AAAT AAAT AAAT AAA-T -AAAT AAA-T AAAT AAAT -AA-AT AAA-T
** **
13291 AAAT AAAT CCA- AAAT AAAT AAAT AAAT TCA- AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
13337 CAAACAAAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
3 2 0.03
4 54 0.75
5 12 0.17
6 4 0.06
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:13276 original size:19 final size:19
Alignment explanation
Indices: 13252--13348 Score: 94
Period size: 19 Copynumber: 5.1 Consensus size: 19
13242 AATAAATAAA
13252 TAAATAAATTCAAAAAAAT
1 TAAATAAATTCAAAAAAAT
* **
13271 TAAATAAA-TGAATTTAAAT
1 TAAATAAATTCAA-AAAAAT
*
13290 TAAATAAATCCAAAATAAA-
1 TAAATAAATTCAAAA-AAAT
13309 TAAATAAATTCAAAATAAA-
1 TAAATAAATTCAAAA-AAAT
13328 TAAATAAA-TCAAACAAAAT
1 TAAATAAATTCAAA-AAAAT
13347 TA
1 TA
13349 TTGAAGAAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
18 11 0.17
19 49 0.75
20 5 0.08
ACGTcount: A:0.66, C:0.06, G:0.01, T:0.27
Consensus pattern (19 bp):
TAAATAAATTCAAAAAAAT
Found at i:13278 original size:23 final size:22
Alignment explanation
Indices: 13238--13298 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
13228 TTCATATTCC
*
13238 TTCAAATAAATAAATAAATAAA
1 TTCAAAAAAATAAATAAATAAA
*
13260 TTCAAAAAAATTAAATAAATGAA
1 TTCAAAAAAA-TAAATAAATAAA
* *
13283 TTTAAATTAAATAAAT
1 TTCAAA-AAAATAAAT
13299 CCAAAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 9 0.27
23 21 0.64
24 3 0.09
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (22 bp):
TTCAAAAAAATAAATAAATAAA
Found at i:13309 original size:34 final size:35
Alignment explanation
Indices: 13266--13332 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
13256 TAAATTCAAA
* * *
13266 AAAATTAAATAAATGAATTTAAATTAAATAAATCC
1 AAAATTAAATAAATAAATTCAAAATAAATAAATCC
13301 AAAA-TAAATAAATAAATTCAAAATAAATAAAT
1 AAAATTAAATAAATAAATTCAAAATAAATAAAT
13333 AAATCAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 25 0.86
35 4 0.14
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.28
Consensus pattern (35 bp):
AAAATTAAATAAATAAATTCAAAATAAATAAATCC
Found at i:13363 original size:57 final size:54
Alignment explanation
Indices: 13241--13364 Score: 133
Period size: 57 Copynumber: 2.2 Consensus size: 54
13231 ATATTCCTTC
* *** *
13241 AAATAAATAAATAAATAAATTCAAAAAAATTAAATAAATGAATTTAAATTAAAT
1 AAATAAATAAATAAATAAATTCAAAAAAATTAAATAAATCAAACAAAATTAAAG
13295 AAATCCAAAATAAATAAATAAATTCAAAATAAA-TAAATAAATCAAACAAAATTATTGAAG
1 AAAT---AAATAAATAAATAAATTCAAAA-AAATTAAATAAATCAAACAAAATTA---AAG
13355 AAATAAATAA
1 AAATAAATAA
13365 GTTATTCAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
54 4 0.07
57 45 0.78
58 3 0.05
60 6 0.10
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (54 bp):
AAATAAATAAATAAATAAATTCAAAAAAATTAAATAAATCAAACAAAATTAAAG
Found at i:15261 original size:17 final size:17
Alignment explanation
Indices: 15239--15271 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
15229 TGTTTTGCAT
15239 TTAAAGTAAATCTTTAC
1 TTAAAGTAAATCTTTAC
15256 TTAAAGTAAATCTTTA
1 TTAAAGTAAATCTTTA
15272 ACATTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (17 bp):
TTAAAGTAAATCTTTAC
Found at i:15446 original size:2 final size:2
Alignment explanation
Indices: 15379--15427 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
15369 ATATCACAAC
15379 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
15421 TA TA TA T
1 TA TA TA T
15428 TAAACATAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21116 original size:98 final size:97
Alignment explanation
Indices: 20947--21141 Score: 372
Period size: 98 Copynumber: 2.0 Consensus size: 97
20937 TGCCGCAGCA
20947 GCCAGAGAGCTGCCTTTTCCTTTATAACTCAACAATGAGAACCAGTAACAGATGTGACAGTGATG
1 GCCAGAGAGCTGCCTTTTCCTTTATAACTCAACAATGAGAACCAGTAACAGATGTGACAGTGATG
21012 GAAAAAACTTGGGATGATGATGGAGGATTGTCT
66 GAAAAAACTT-GGATGATGATGGAGGATTGTCT
21045 GCCAGAGAGCTGCCTTTTCCTTTATAACTCAACAATGAGAACCAGTAACAGATGTGACAGTGATG
1 GCCAGAGAGCTGCCTTTTCCTTTATAACTCAACAATGAGAACCAGTAACAGATGTGACAGTGATG
*
21110 GAAAAAACTTGGCTGATGATGGAGGATTGTCT
66 GAAAAAACTTGGATGATGATGGAGGATTGTCT
21142 AATTATATTA
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
97 21 0.22
98 75 0.78
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (97 bp):
GCCAGAGAGCTGCCTTTTCCTTTATAACTCAACAATGAGAACCAGTAACAGATGTGACAGTGATG
GAAAAAACTTGGATGATGATGGAGGATTGTCT
Found at i:22050 original size:24 final size:22
Alignment explanation
Indices: 22024--22068 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
22014 TAAGAATTTT
22024 TATT-TTTATATTATTAAAATA
1 TATTATTTATATTATTAAAATA
22045 TATTATTTA-ATTATTAAAAATA
1 TATTATTTATATTATT-AAAATA
22067 TA
1 TA
22069 AAAAATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATTTATATTATTAAAATA
Found at i:22077 original size:40 final size:40
Alignment explanation
Indices: 22033--22139 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
22023 TTATTTTTAT
22033 ATTATTAAAATATATTATTTAATTATTAAAAATATAAAAA
1 ATTATTAAAATATATTATTTAATTATTAAAAATATAAAAA
* * ** **
22073 ATTATAAAAATATATTAATTTAA-GATTTTAAATATAATTA
1 ATTATTAAAATATATT-ATTTAATTATTAAAAATATAAAAA
*
22113 ATAATTATAAATATATTA-TTAATTATT
1 ATTATTA-AAATATATTATTTAATTATT
22140 TTAATTATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
39 4 0.07
40 36 0.65
41 15 0.27
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (40 bp):
ATTATTAAAATATATTATTTAATTATTAAAAATATAAAAA
Found at i:22130 original size:18 final size:18
Alignment explanation
Indices: 22036--22138 Score: 64
Period size: 20 Copynumber: 5.3 Consensus size: 18
22026 TTTTTATATT
*
22036 ATTA-AAATATATTATTTA
1 ATTATAAATATATTA-ATA
* * *
22054 ATTATTAAAAATATAAAAA
1 ATTA-TAAATATATTAATA
22073 ATTATAAAAATATATTAATTTAA
1 ATTAT--AAATATATTAA--T-A
*
22096 GATTTTAAATATAATTAATA
1 -ATTATAAATAT-ATTAATA
*
22116 ATTATAAATATATTATTA
1 ATTATAAATATATTAATA
22134 ATTAT
1 ATTAT
22139 TTTAATTATT
Statistics
Matches: 66, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
18 16 0.24
19 15 0.23
20 18 0.27
21 1 0.02
22 6 0.09
23 6 0.09
24 4 0.06
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (18 bp):
ATTATAAATATATTAATA
Found at i:24022 original size:66 final size:66
Alignment explanation
Indices: 23936--24162 Score: 252
Period size: 66 Copynumber: 3.5 Consensus size: 66
23926 GGAGGTGAAG
* * *
23936 GAAGTGTAGATGGAGGTGGAAGTTGTGTAGATGAAGATTGTTGTGGGGAAGTGGATGAAGATGAG
1 GAAGTGTAGATGGAGATGGAAGTCGTGAAGATGAAGATTGTTGTGGGGAAGTGGATGAAGATGAG
24001 T
66 T
* * * **
24002 GTAGTGTTGATGGAGATGGAAGTCGTGAAGATGGAA-ATAGTTGT---GAAGACG--GAA-ATAG
1 GAAGTGTAGATGGAGATGGAAGTCGTGAAGAT-GAAGATTGTTGTGGGGAAGTGGATGAAGAT-G
24060 AGGT
64 A-GT
* * *
24064 GAAGTGTAGATGGAGGTGGAAGTTGTGAAGATGAAGATTGTTGTGGGGAAGTGGATGGAGATGAG
1 GAAGTGTAGATGGAGATGGAAGTCGTGAAGATGAAGATTGTTGTGGGGAAGTGGATGAAGATGAG
24129 T
66 T
* * *
24130 GCAGTGTTGATGGAGATGGAAGTCGTGGAGATG
1 GAAGTGTAGATGGAGATGGAAGTCGTGAAGATG
24163 GAATTAATGG
Statistics
Matches: 130, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
60 2 0.02
61 8 0.06
62 37 0.28
63 5 0.04
65 5 0.04
66 64 0.49
67 7 0.05
68 2 0.02
ACGTcount: A:0.30, C:0.02, G:0.43, T:0.26
Consensus pattern (66 bp):
GAAGTGTAGATGGAGATGGAAGTCGTGAAGATGAAGATTGTTGTGGGGAAGTGGATGAAGATGAG
T
Found at i:24065 original size:18 final size:18
Alignment explanation
Indices: 24026--24067 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
24016 GATGGAAGTC
* **
24026 GTGAAGATGGAAATAGTT
1 GTGAAGACGGAAATAGAG
24044 GTGAAGACGGAAATAGAG
1 GTGAAGACGGAAATAGAG
24062 GTGAAG
1 GTGAAG
24068 TGTAGATGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.38, T:0.19
Consensus pattern (18 bp):
GTGAAGACGGAAATAGAG
Found at i:25006 original size:3 final size:3
Alignment explanation
Indices: 24995--25035 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
24985 ACCCATTTTT
24995 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25036 AAAAATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:26649 original size:118 final size:117
Alignment explanation
Indices: 26525--26752 Score: 275
Period size: 117 Copynumber: 1.9 Consensus size: 117
26515 TTTAATCCTA
* * * * *
26525 TTTTAA-TATTTATTTCTTTTCCAATAT-TAAG-AAAGGGCAGTCTTAAAATAACTGGATGTCCA
1 TTTTAATTATTTATTT-TTTT--AATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-CA
* *
26587 TTTTCTGATATTTTTAAATAAATAAATATCTTATTTTATAAAT-TATATATTAATTG
62 TTTTCTGATATTTCTAAATAAATAAATATCTTA-TTTAAAAATATATATATTAATTG
* ** *
26643 TTTTAATTATTTATTTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCATTTT
1 TTTTAATTATTTATTTTTTTAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATTTT
*
26708 CTGATATTTCTAAATAAATAAATATTTTATTTAAAAATATATATA
66 CTGATATTTCTAAATAAATAAATATCTTATTTAAAAATATATATA
26753 AATCAATATA
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
116 13 0.14
117 42 0.45
118 30 0.32
119 9 0.10
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (117 bp):
TTTTAATTATTTATTTTTTTAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATTTT
CTGATATTTCTAAATAAATAAATATCTTATTTAAAAATATATATATTAATTG
Found at i:28805 original size:8 final size:7
Alignment explanation
Indices: 28781--28822 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
28771 TTTTCATACA
28781 TGCA-TT
1 TGCATTT
28787 TGCATTT
1 TGCATTT
28794 TGCATCTT
1 TGCAT-TT
28802 TGCATTT
1 TGCATTT
* *
28809 TTCATTG
1 TGCATTT
28816 TGCATTT
1 TGCATTT
28823 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:28805 original size:15 final size:14
Alignment explanation
Indices: 28781--28822 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
28771 TTTTCATACA
28781 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
28794 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
28809 TTCATTGTGCATTT
1 TGCATTTTGCATTT
28823 ATACTCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:31419 original size:20 final size:20
Alignment explanation
Indices: 31380--31421 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
31370 AAAGAGCGAG
***
31380 AGATGAGTGACATCTTAAAT
1 AGATGAGTGACATAGAAAAT
31400 AGATGAGTGACATAGAAAAT
1 AGATGAGTGACATAGAAAAT
31420 AG
1 AG
31422 GAAGGCCATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.24
Consensus pattern (20 bp):
AGATGAGTGACATAGAAAAT
Found at i:33158 original size:115 final size:115
Alignment explanation
Indices: 32956--33757 Score: 1372
Period size: 115 Copynumber: 7.0 Consensus size: 115
32946 AAGTGACATG
32956 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * *
33021 TGGTTTGATATGAACCCTAAAAACCAATCATTGGATTTGAAATATGAATG
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
33071 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
33136 TGATTTGGTATGAACCCCAAAAACCAATCATTAGATTTAAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
33186 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
33251 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTAAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
* *
33301 TTCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
33366 TGATTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
33416 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
33481 TTGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
33531 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
33596 TGGTTTGGTATGAACCCTAAAAACCAATCATTAGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
* * * *
33646 TGCTCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * *
33711 TGGTTCGGTAGGAACCAC-AGAACCAATCATTGGAATTAAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAA
33758 CTGCATGATC
Statistics
Matches: 653, Mismatches: 34, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
114 25 0.04
115 628 0.96
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (115 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
Found at i:35748 original size:40 final size:40
Alignment explanation
Indices: 35693--35770 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
35683 AGCAGAAGCC
35693 ACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCCA
1 ACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCCA
35733 ACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATC
1 ACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATC
35771 TGAGCTGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (40 bp):
ACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCCA
Found at i:35853 original size:54 final size:54
Alignment explanation
Indices: 35733--35875 Score: 159
Period size: 54 Copynumber: 2.7 Consensus size: 54
35723 TTTACATCCA
* * *
35733 ACAGAAAAGGATGAATGTGTTGTCAAGTGTTTT----ACATCTGAGCTGAAACC
1 ACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAACC
* * * * *
35783 ACATGAGATGAAGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAGCC
1 ACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAACC
* * *
35837 ACAGGAAAGGATGAATGCGCTGTCAAATATTTTACGAAC
1 ACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
35876 CTGCTATTTT
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
50 27 0.36
54 47 0.64
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.26
Consensus pattern (54 bp):
ACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAACC
Found at i:36997 original size:114 final size:113
Alignment explanation
Indices: 36667--37234 Score: 861
Period size: 113 Copynumber: 5.0 Consensus size: 113
36657 TAGCAAAGAT
36667 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
36732 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
36780 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
36845 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
36893 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
* *
36958 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGT
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * ** * *
37007 TTGAATTCATCATTTGATGGATCAG-TATCCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATA
1 TCAAATCCATCATTTGATGGATCAGCT-TTTCCA--GAAAAAGTTCATAATGAGAAGAACTCATC
* *
37071 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
63 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
* * * * * * *
37122 TCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * ** *
37187 AGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
37235 ATGACTCTAT
Statistics
Matches: 425, Mismatches: 23, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
113 216 0.51
114 114 0.27
115 93 0.22
116 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:37338 original size:120 final size:121
Alignment explanation
Indices: 37149--37377 Score: 315
Period size: 120 Copynumber: 1.9 Consensus size: 121
37139 TGGATCAACT
* *
37149 TTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAGAGTTCACAATGAGAAGAACTCATCT--AGAAAGAAGAAGAAGTTCACAATGAGA
*
37214 AGAGCTTGTTCGACCTTTTGC-ATGACT-CTATCACAGAAGGAGATATATCATCATCAGCA
64 AGAGCTTGTTCAACC-TTTGCTA-GACTAC-ATCACAGAAGGAGATATATCATCATCAGCA
* *
37273 TTTCCAGA-AGAAGTTTACAATTAGAAGAACTCATCT-G-AAGAAGAAGAAGTTCACAATGAGAA
1 TTTCCAGAGAG-AGTTCACAATGAGAAGAACTCATCTAGAAAGAAGAAGAAGTTCACAATGAGAA
*
37335 GAGCTTGTTCAACCTTTGCTAGATTACATCACAGAAGGAGATA
65 GAGCTTGTTCAACCTTTGCTAGACTACATCACAGAAGGAGATA
37378 AATTGTCATC
Statistics
Matches: 96, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
119 24 0.25
120 39 0.41
121 1 0.01
123 2 0.02
124 30 0.31
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.25
Consensus pattern (121 bp):
TTTCCAGAGAGAGTTCACAATGAGAAGAACTCATCTAGAAAGAAGAAGAAGTTCACAATGAGAAG
AGCTTGTTCAACCTTTGCTAGACTACATCACAGAAGGAGATATATCATCATCAGCA
Found at i:37583 original size:3 final size:3
Alignment explanation
Indices: 37577--37609 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
37567 CCCATTTTAT
37577 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
37610 AAAAATAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:38797 original size:15 final size:15
Alignment explanation
Indices: 38777--38805 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38767 TTAGAATCTT
38777 TAATTTTAATAATTA
1 TAATTTTAATAATTA
38792 TAATTTTAATAATT
1 TAATTTTAATAATT
38806 TATTAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTTTAATAATTA
Found at i:39237 original size:20 final size:20
Alignment explanation
Indices: 39212--39254 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
39202 TTATTTTATA
39212 AATTATATATTAATTGTTTT
1 AATTATATATTAATTGTTTT
* * *
39232 AATTATTTATTTATTTTTTT
1 AATTATATATTAATTGTTTT
39252 AAT
1 AAT
39255 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTATATATTAATTGTTTT
Found at i:45841 original size:21 final size:21
Alignment explanation
Indices: 45812--45887 Score: 116
Period size: 21 Copynumber: 3.6 Consensus size: 21
45802 GGAGCGTGTA
*
45812 TGCATCGATGCATGGTGATGG
1 TGCACCGATGCATGGTGATGG
45833 TGCACCGATGCATGGTGATGG
1 TGCACCGATGCATGGTGATGG
*
45854 TGCACCGATGCATGGTGATTG
1 TGCACCGATGCATGGTGATGG
* *
45875 TGCATCGGTGCAT
1 TGCACCGATGCAT
45888 TGAGTGTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.18, C:0.18, G:0.36, T:0.28
Consensus pattern (21 bp):
TGCACCGATGCATGGTGATGG
Found at i:51382 original size:20 final size:20
Alignment explanation
Indices: 51359--51399 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
51349 CTGTTCATGG
51359 AGTATCGATACTTTAAGAAT
1 AGTATCGATACTTTAAGAAT
*
51379 AGTATCGGTACTTTAAGAAT
1 AGTATCGATACTTTAAGAAT
51399 A
1 A
51400 ATATAAGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (20 bp):
AGTATCGATACTTTAAGAAT
Found at i:51409 original size:20 final size:20
Alignment explanation
Indices: 51367--51410 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
51357 GGAGTATCGA
* **
51367 TACTTTAAGAATAGTATCGG
1 TACTTTAAGAATAATATAAG
51387 TACTTTAAGAATAATATAAG
1 TACTTTAAGAATAATATAAG
51407 TACT
1 TACT
51411 ACGTACTCAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (20 bp):
TACTTTAAGAATAATATAAG
Found at i:51770 original size:18 final size:18
Alignment explanation
Indices: 51728--51771 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
51718 AAGAGATTTA
51728 AAGAATTTAAAAAGTTTG
1 AAGAATTTAAAAAGTTTG
* * *
51746 AATAATTTAAGAATTTTG
1 AAGAATTTAAAAAGTTTG
*
51764 TAGAATTT
1 AAGAATTT
51772 TTTAGATTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (18 bp):
AAGAATTTAAAAAGTTTG
Found at i:52342 original size:17 final size:17
Alignment explanation
Indices: 52322--52354 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
52312 AATATATTCT
52322 AAAAATAAATAAAATTA
1 AAAAATAAATAAAATTA
52339 AAAAATAAATAAAATT
1 AAAAATAAATAAAATT
52355 TACAATAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATAAATAAAATTA
Found at i:60874 original size:42 final size:42
Alignment explanation
Indices: 60709--61103 Score: 303
Period size: 43 Copynumber: 9.6 Consensus size: 42
60699 TGAGAACAAA
* * * * *
60709 AAACGCCGTAATAGGTAAAGATCTATCGCGGCGTTTTCGGAAC
1 AAACGCCGCAAAAGGT-CAGATCTATAGCGGCGTTTTTGGAAC
* * * * **
60752 AAACGTCGCGAAAGGTCGATATCTATAACAACGTTTTTGGAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
* * * * *
60795 AAACGCCGCAAAAGTTAGAGATCTATAGCGACATTTTTAGAAC
1 AAACGCCGCAAAAGGT-CAGATCTATAGCGGCGTTTTTGGAAC
* * * *
60838 AAACGCCGCAAAAGGTCATATCTATAGCAGTGTTTTTAGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* *
60880 AAACACCGCAAAAGGTCAGATCTATAGTGGC-TTTTT-----
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* * *
60916 ------TGCAAAAGGTCAGATCTATAGTGGC-TTTTTGGATAG
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
*
60952 AAACGCCGCAAAAGGTCAGTTCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
* * * *
60995 AAACGCCGCAAAAGATCAAATCTATAGCGGCATTTTTGGTAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* * * * * *
61037 AATCGCTGTAAAAGGTCAGATCTATGGCGGTGTTTTTAGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
**
61080 AAACTTCGCAAAAGGTCAGATCTA
1 AAACGCCGCAAAAGGTCAGATCTA
61104 GCACTCCGTT
Statistics
Matches: 279, Mismatches: 57, Indels: 32
0.76 0.15 0.09
Matches are distributed among these distances:
30 29 0.10
41 5 0.02
42 100 0.36
43 145 0.52
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:60889 original size:85 final size:85
Alignment explanation
Indices: 60748--60906 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 85
60738 GGCGTTTTCG
* * * * * *
60748 GAACAAACGTCGCGAAAGGTCGATATCTATAACAACGTTTTTGGAACAAACGCCGCAAAAGTTAG
1 GAACAAACGCCGCAAAAGGTCGATATCTATAACAACGTTTTTAGAACAAACACCGCAAAAGGT-C
60813 AGATCTATAGCGACATTTTTA
65 AGATCTATAGCGACATTTTTA
* **
60834 GAACAAACGCCGCAAAAGGTC-ATATCTATAGCAGTGTTTTTAGAACAAACACCGCAAAAGGTCA
1 GAACAAACGCCGCAAAAGGTCGATATCTATAACAACGTTTTTAGAACAAACACCGCAAAAGGTCA
60898 GATCTATAG
66 GATCTATAG
60907 TGGCTTTTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 10 0.16
85 35 0.55
86 19 0.30
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (85 bp):
GAACAAACGCCGCAAAAGGTCGATATCTATAACAACGTTTTTAGAACAAACACCGCAAAAGGTCA
GATCTATAGCGACATTTTTA
Found at i:60923 original size:30 final size:30
Alignment explanation
Indices: 60887--60945 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
60877 AACAAACACC
60887 GCAAAAGGTCAGATCTATAGTGGCTTTTTT
1 GCAAAAGGTCAGATCTATAGTGGCTTTTTT
60917 GCAAAAGGTCAGATCTATAGTGGCTTTTT
1 GCAAAAGGTCAGATCTATAGTGGCTTTTT
60946 GGATAGAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.36
Consensus pattern (30 bp):
GCAAAAGGTCAGATCTATAGTGGCTTTTTT
Found at i:60962 original size:72 final size:72
Alignment explanation
Indices: 60845--60989 Score: 186
Period size: 72 Copynumber: 2.0 Consensus size: 72
60835 AACAAACGCC
* *
60845 GCAAAAGGTCATATCTATAGCAGTGTTTTTAGAACAAACACCGCAAAAGGTCAGATCTATAGTGG
1 GCAAAAGGTCAGATCTATAGCAGTGTTTTTAGAACAAACACCGCAAAAGGTCAGATCTATAGCGG
*
60910 CTTTTTT
66 CGTTTTT
* * * * *
60917 GCAAAAGGTCAGATCTATAG-TG-GCTTTTTGGATAGAAACGCCGCAAAAGGTCAGTTCTATAGC
1 GCAAAAGGTCAGATCTATAGCAGTG-TTTTTAGA-ACAAACACCGCAAAAGGTCAGATCTATAGC
60980 GGCGTTTTT
64 GGCGTTTTT
60989 G
1 G
60990 GATACAAACG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
70 1 0.02
71 8 0.13
72 54 0.86
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (72 bp):
GCAAAAGGTCAGATCTATAGCAGTGTTTTTAGAACAAACACCGCAAAAGGTCAGATCTATAGCGG
CGTTTTT
Found at i:61061 original size:85 final size:85
Alignment explanation
Indices: 60917--61103 Score: 241
Period size: 85 Copynumber: 2.2 Consensus size: 85
60907 TGGCTTTTTT
* * *
60917 GCAAAAGGTCAGATCTATAGTGGCTTTTTGGATAGAAACGCCGCAAAAGGTCAGTTCTATAGCGG
1 GCAAAAGGTCAGATCTATAGCGGCTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTATAGCGG
*
60982 CGTTTTTGGATACAAACGCC
66 CGTTTTTAGATACAAACGCC
* * * * * *
61002 GCAAAAGATCAAATCTATAGCGGCATTTTTGG-TACAATCGCTGTAAAAGGTCAGATCTATGGCG
1 GCAAAAGGTCAGATCTATAGCGGC-TTTTTGGATACAAACGCCGCAAAAGGTCAGATCTATAGCG
* **
61066 GTGTTTTTAGATACAAACTTC
65 GCGTTTTTAGATACAAACGCC
61087 GCAAAAGGTCAGATCTA
1 GCAAAAGGTCAGATCTA
61104 GCACTCCGTT
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
85 79 0.92
86 7 0.08
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (85 bp):
GCAAAAGGTCAGATCTATAGCGGCTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTATAGCGG
CGTTTTTAGATACAAACGCC
Found at i:61073 original size:157 final size:156
Alignment explanation
Indices: 60785--61066 Score: 359
Period size: 157 Copynumber: 1.8 Consensus size: 156
60775 TATAACAACG
* *
60785 TTTTTGGAACAAACGCCGCAAAAGTTAGAGATCTATAGCGACATTTTTAGAACAAACGCCGCAAA
1 TTTTTGGAACAAACGCCGCAAAAGGTACAGATCTATAGCGACATTTTTAGAACAAACGCCGCAAA
* * ** *
60850 AGGTCATATCTATAGCAGTGTTTTTAGAACAAACACCGCAAAAGGTCAGATCTATAGTGGCTTTT
66 AGATCAAATCTATAGCAGCATTTTTAGAACAAACACCGCAAAAGGTCAGATCTATAGCGGCTTTT
60915 TTGCAAAAGGTCAGATCTATAGTGGC
131 TTGCAAAAGGTCAGATCTATAGTGGC
* * * * *
60941 TTTTTGGATAGAAACGCCGCAAAAGGT-CAGTTCTATAGCGGCGTTTTTGGATACAAACGCCGCA
1 TTTTTGGA-ACAAACGCCGCAAAAGGTACAGATCTATAGCGACATTTTTAGA-ACAAACGCCGCA
* * * * * * * *
61005 AAAGATCAAATCTATAGCGGCATTTTTGGTACAATCGCTGTAAAAGGTCAGATCTATGGCGG
64 AAAGATCAAATCTATAGCAGCATTTTTAGAACAAACACCGCAAAAGGTCAGATCTATAGCGG
61067 TGTTTTTAGA
Statistics
Matches: 104, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
156 27 0.26
157 77 0.74
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (156 bp):
TTTTTGGAACAAACGCCGCAAAAGGTACAGATCTATAGCGACATTTTTAGAACAAACGCCGCAAA
AGATCAAATCTATAGCAGCATTTTTAGAACAAACACCGCAAAAGGTCAGATCTATAGCGGCTTTT
TTGCAAAAGGTCAGATCTATAGTGGC
Found at i:65049 original size:41 final size:41
Alignment explanation
Indices: 65004--65287 Score: 309
Period size: 41 Copynumber: 6.9 Consensus size: 41
64994 TTATAAATAC
* * * * * *
65004 AAACGCCACTAAACTACGAGTCTATAGTGGCGTATGTATAT
1 AAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAA
* * *
65045 AAACGCCACTAAAGTACAATTATATAGCGGCGTTTATATAA
1 AAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAA
* * *
65086 AAACGCCACCAAAGTACCAGTGTATAGCGGCGTTTGTATAT
1 AAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAA
* *
65127 AAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTATAAACA
1 AAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATA-A
* **
65169 CAAACGCCACTAAAGTACAATTGTATAGCAACGTTTGTAT-A
1 -AAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAA
* * * * *
65210 AAACACCACTAAAGTACGAGTCTATAGCAGCGTTTGTACAA
1 AAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAA
* * * *
65251 AAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGT
1 AAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGT
65288 TGAAAAAACA
Statistics
Matches: 205, Mismatches: 35, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
40 33 0.16
41 138 0.67
43 34 0.17
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (41 bp):
AAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAA
Found at i:65118 original size:82 final size:82
Alignment explanation
Indices: 64987--65287 Score: 343
Period size: 82 Copynumber: 3.6 Consensus size: 82
64977 TTATAAATTT
* * * * * *
64987 GCGGCGTTTATAAATACAAACGCCACTAAACTACGAGTCTATAGTGGCGTATGTATATAAACGCC
1 GCGGCGTTTAT--ATAAAAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATATAAACGCC
*
65052 ACTAAAGTACAATTATATA
64 ACTAAAGTACAAGTATATA
* *
65071 GCGGCGTTTATATAAAAACGCCACCAAAGTACCAGTGTATAGCGGCGTTTGTATATAAACGCCAC
1 GCGGCGTTTATATAAAAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATATAAACGCCAC
*
65136 TAAAGTACAAGTGTATA
66 TAAAGTACAAGTATATA
* * ** *
65153 GCGGCGTTTATAAACACAAACGCCACTAAAGTACAATTGTATAGCAACGTTTGTATA-AAACACC
1 GCGGCGTTTATATA-A-AAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATATAAACGCC
* *
65217 ACTAAAGTACGAGTCTATA
64 ACTAAAGTACAAGTATATA
* * * * * * *
65236 GCAGCGTTTGTACAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGT
1 GCGGCGTTTATATAAAAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGT
65288 TGAAAAAACA
Statistics
Matches: 188, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
81 31 0.16
82 76 0.40
83 35 0.19
84 46 0.24
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (82 bp):
GCGGCGTTTATATAAAAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATATAAACGCCAC
TAAAGTACAAGTATATA
Found at i:65266 original size:124 final size:125
Alignment explanation
Indices: 65045--65285 Score: 340
Period size: 124 Copynumber: 1.9 Consensus size: 125
65035 GTATGTATAT
** * *
65045 AAACGCCACTAAAGTACAATTATATAGCGGCGTTTATATAAAAACGCCACCAAAGTACCAGTGTA
1 AAACGCCACTAAAGTACAATTATATAGCAACGTTTATATAAAAACACCACCAAAGTACCAGTCTA
* * * * *
65110 TAGCGGCGTTTGTATATAAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTATAAACAC
66 TAGCAGCGTTTGTACAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTATAAACAC
* * * *
65170 AAACGCCACTAAAGTACAATTGTATAGCAACGTTTGTAT-AAAACACCACTAAAGTACGAGTCTA
1 AAACGCCACTAAAGTACAATTATATAGCAACGTTTATATAAAAACACCACCAAAGTACCAGTCTA
* *
65234 TAGCAGCGTTTGTACAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTT
66 TAGCAGCGTTTGTACAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTT
65286 GTTGAAAAAA
Statistics
Matches: 101, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
124 66 0.65
125 35 0.35
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (125 bp):
AAACGCCACTAAAGTACAATTATATAGCAACGTTTATATAAAAACACCACCAAAGTACCAGTCTA
TAGCAGCGTTTGTACAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTATAAACAC
Found at i:65294 original size:41 final size:40
Alignment explanation
Indices: 65004--65371 Score: 269
Period size: 41 Copynumber: 9.0 Consensus size: 40
64994 TTATAAATAC
* * * * *
65004 AAACGCCACTAAACTACGAGTCTATAGTGGCGTATGTATAT
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGT-TAA
* * *
65045 AAACGCCACTAAAGTACAATTATATAGCGGCGTTTATATAA
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGT-TAA
* * * *
65086 AAACGCCACCAAAGTACCAGTGTATAGCGGCGTTTGTATAT
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGT-TAA
* * *
65127 AAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTATAAACA
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGT-TA-A
* * **
65169 CAAACGCCACTAAAGTACAATTGTATAGCAACGTTTG-TATA
1 -AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTTA-A
* * * *
65210 AAACACCACTAAAGTACGAGTCTATAGCAGCGTTTGTACAA
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGT-TAA
* * *
65251 AAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTTGAAA
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTT--AA
* * * *
65293 AAACACCACTATAAAT-GAA-CCTATTA-CGGCGTTTGTATAA
1 AAACGCCACTA-AAGTACAAGTCTA-TAGCGGCGTTTGT-TAA
* * * * *
65333 AAACACCGCTAAAGTACTACTCTATAGCGGCCTTT-TTAA
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTTAA
65372 GAAAAACGCT
Statistics
Matches: 266, Mismatches: 49, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
39 6 0.02
40 47 0.18
41 162 0.61
42 16 0.06
43 35 0.13
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.26
Consensus pattern (40 bp):
AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTTAA
Found at i:67361 original size:24 final size:24
Alignment explanation
Indices: 67333--67379 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
67323 CCATAAGAAA
*
67333 CGTGCCACAAGAGCAGAGAAAAAG
1 CGTGCCACAAAAGCAGAGAAAAAG
67357 CGTGCCACAAAAGCAGAGAAAAA
1 CGTGCCACAAAAGCAGAGAAAAA
67380 TATGCAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.49, C:0.21, G:0.26, T:0.04
Consensus pattern (24 bp):
CGTGCCACAAAAGCAGAGAAAAAG
Found at i:67736 original size:19 final size:19
Alignment explanation
Indices: 67698--67736 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
67688 CTATTATATC
*
67698 ATATTTAAATTAATATTTA
1 ATATTTAAATTAATAGTTA
* *
67717 ATATTTTAATTAATGGTTA
1 ATATTTAAATTAATAGTTA
67736 A
1 A
67737 CTTAATAAAA
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:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
ATATTTAAATTAATAGTTA
Found at i:67768 original size:21 final size:21
Alignment explanation
Indices: 67744--67811 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
67734 TAACTTAATA
67744 AAAATATTTAAATAATAATTT
1 AAAATATTTAAATAATAATTT
*
67765 AAAAT-TTTAATTAA-AATCTT
1 AAAATATTTAAATAATAAT-TT
* * *
67785 TAAAGATTTAAA-ATTAATTT
1 AAAATATTTAAATAATAATTT
67805 CAAAATA
1 -AAAATA
67812 ATATATTCTA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
19 3 0.08
20 16 0.44
21 17 0.47
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (21 bp):
AAAATATTTAAATAATAATTT
Found at i:70086 original size:2 final size:2
Alignment explanation
Indices: 70081--70140 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
70071 AATTACCTTG
70081 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
70123 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
70141 CCTGAACTTT
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:72290 original size:18 final size:18
Alignment explanation
Indices: 72267--72314 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
72257 AACTTTATTA
*
72267 TTTCTCATTGAACTTTGT
1 TTTCTCTTTGAACTTTGT
72285 TTTCTCTTTGAACTTTGT
1 TTTCTCTTTGAACTTTGT
72303 TTTCTCTTTGAA
1 TTTCTCTTTGAA
72315 TTTTATGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.58
Consensus pattern (18 bp):
TTTCTCTTTGAACTTTGT
Found at i:72342 original size:100 final size:100
Alignment explanation
Indices: 72218--72420 Score: 352
Period size: 100 Copynumber: 2.0 Consensus size: 100
72208 GCAATACAAC
**
72218 TATGGTTTAATGTTTACATTCTCTAAATCATTAAAGGTAAACTTTATTATTTCTCATTGAACTTT
1 TATGGTTTAATACTTACATTCTCTAAATCATTAAAGGTAAACTTTATTATTTCTCATTGAACTTT
* * * *
72283 GTTTTCTCTTTGAACTTTGTTTTCTCTTTGAATTT
66 GTTTTCTCATTCAACTTTGCTTTCTCTTTGAACTT
72318 TATGGTTTAATACTTACATTCTCTAAATCATTAAAGGTAAACTTTATTATTTCTCATTGAACTTT
1 TATGGTTTAATACTTACATTCTCTAAATCATTAAAGGTAAACTTTATTATTTCTCATTGAACTTT
72383 GTTTTCTCATTCAACTTTGCTTTCTCTTTGAACTT
66 GTTTTCTCATTCAACTTTGCTTTCTCTTTGAACTT
72418 TAT
1 TAT
72421 TTACTAATAT
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.25, C:0.15, G:0.09, T:0.51
Consensus pattern (100 bp):
TATGGTTTAATACTTACATTCTCTAAATCATTAAAGGTAAACTTTATTATTTCTCATTGAACTTT
GTTTTCTCATTCAACTTTGCTTTCTCTTTGAACTT
Found at i:72390 original size:18 final size:18
Alignment explanation
Indices: 72367--72418 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
72357 AACTTTATTA
*
72367 TTTCTCATTGAACTTTGT
1 TTTCTCATTGAACTTTGC
*
72385 TTTCTCATTCAACTTTGC
1 TTTCTCATTGAACTTTGC
*
72403 TTTCTCTTTGAACTTT
1 TTTCTCATTGAACTTT
72419 ATTTACTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.15, C:0.21, G:0.08, T:0.56
Consensus pattern (18 bp):
TTTCTCATTGAACTTTGC
Found at i:72507 original size:27 final size:27
Alignment explanation
Indices: 72477--72558 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 27
72467 ATGAAGTGAC
72477 ATTTTATATATTATTAAATATAAAAAT
1 ATTTTATATATTATTAAATATAAAAAT
* * * *
72504 ATTTTA-AAATAAATT-TA-ATAAAAGT
1 ATTTTATATAT-TATTAAATATAAAAAT
* *
72529 ATTTTAT-TATTATTAAATTTAAAAAG
1 ATTTTATATATTATTAAATATAAAAAT
72555 ATTT
1 ATTT
72559 AAAATGATCA
Statistics
Matches: 41, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
24 3 0.07
25 16 0.39
26 13 0.32
27 9 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
ATTTTATATATTATTAAATATAAAAAT
Found at i:77620 original size:49 final size:51
Alignment explanation
Indices: 77526--77631 Score: 180
Period size: 49 Copynumber: 2.1 Consensus size: 51
77516 GGATTGAAAG
77526 TAATCAAACGCTGTAAGAGGGGGGGGGGGGCGAACCAAAACTTTGTAAGCTTT
1 TAATCAAACGCTGTAAGA--GGGGGGGGGGCGAACCAAAACTTTGTAAGCTTT
77579 TAATCAAACGCTGTAAGA-GGGGGGGGG-GAACCAAAACTTTGTAAGCTTT
1 TAATCAAACGCTGTAAGAGGGGGGGGGGCGAACCAAAACTTTGTAAGCTTT
77628 TAAT
1 TAAT
77632 GAGAAACCAA
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
49 26 0.49
50 9 0.17
53 18 0.34
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (51 bp):
TAATCAAACGCTGTAAGAGGGGGGGGGGCGAACCAAAACTTTGTAAGCTTT
Found at i:78720 original size:14 final size:15
Alignment explanation
Indices: 78685--78717 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
78675 TCGAAATACA
78685 GAAATCAGATATCAG
1 GAAATCAGATATCAG
78700 GAAATCA-ATATTCAG
1 GAAATCAGATA-TCAG
78715 GAA
1 GAA
78718 TCACGTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (15 bp):
GAAATCAGATATCAG
Found at i:79504 original size:29 final size:31
Alignment explanation
Indices: 79456--79523 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 31
79446 CAGTTTACAT
79456 AAATAGCACCCCTTTTTAAAA-TAATAACCA
1 AAATAGCACCCCTTTTTAAAATTAATAACCA
*
79486 AAATAGCA-CCCTTTTTAAAATTAATTACCA
1 AAATAGCACCCCTTTTTAAAATTAATAACCA
79516 AAATAGCA
1 AAATAGCA
79524 TATTTTGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 12 0.33
30 24 0.67
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.28
Consensus pattern (31 bp):
AAATAGCACCCCTTTTTAAAATTAATAACCA
Found at i:79603 original size:29 final size:29
Alignment explanation
Indices: 79581--79637 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
79571 AATAGTATCC
79581 ATTTCGAATTAATTCCCAGAATAGCACCA
1 ATTTCGAATTAATTCCCAGAATAGCACCA
** *
79610 AAATCGAATTAATTCCCAGAATATCACC
1 ATTTCGAATTAATTCCCAGAATAGCACC
79638 GGTGAACGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.26
Consensus pattern (29 bp):
ATTTCGAATTAATTCCCAGAATAGCACCA
Found at i:79709 original size:19 final size:19
Alignment explanation
Indices: 79687--79723 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
79677 TGGGCCGGAC
* *
79687 CGGTTCAGACCGGTCAAAT
1 CGGTTCAAACCGATCAAAT
79706 CGGTTCAAACCGATCAAA
1 CGGTTCAAACCGATCAAA
79724 ACATGTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (19 bp):
CGGTTCAAACCGATCAAAT
Found at i:85150 original size:17 final size:18
Alignment explanation
Indices: 85128--85161 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
85118 ATAGAACATT
85128 AAATATA-ATACAAAACA
1 AAATATATATACAAAACA
*
85145 AAATATATATCCAAAAC
1 AAATATATATACAAAAC
85162 GACAGCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.21
Consensus pattern (18 bp):
AAATATATATACAAAACA
Found at i:86443 original size:29 final size:30
Alignment explanation
Indices: 86390--86456 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 30
86380 CATTTTACAT
*
86390 AAATAGCACCCCTTTTTAAAATAATAACCA
1 AAATAGCACCCCTTTTCAAAATAATAACCA
* *
86420 AAATAGCA-CCCTTTTCAAATTAATTACCA
1 AAATAGCACCCCTTTTCAAAATAATAACCA
86449 AAATAGCA
1 AAATAGCA
86457 TATTTCGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 26 0.76
30 8 0.24
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.27
Consensus pattern (30 bp):
AAATAGCACCCCTTTTCAAAATAATAACCA
Found at i:89936 original size:2 final size:2
Alignment explanation
Indices: 89931--89974 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
89921 AATTACCTTG
89931 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
89973 AT
1 AT
89975 CCTGAACTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92133 original size:18 final size:18
Alignment explanation
Indices: 92110--92157 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
92100 AACTTTATTA
*
92110 TTTCTCATTGAACTTTGT
1 TTTCTCTTTGAACTTTGT
92128 TTTCTCTTTGAACTTTGT
1 TTTCTCTTTGAACTTTGT
92146 TTTCTCTTTGAA
1 TTTCTCTTTGAA
92158 TTTTATGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.58
Consensus pattern (18 bp):
TTTCTCTTTGAACTTTGT
Found at i:92185 original size:100 final size:100
Alignment explanation
Indices: 92061--92263 Score: 352
Period size: 100 Copynumber: 2.0 Consensus size: 100
92051 GCAATACAAC
**
92061 TATGGTTTAATGTTTACATTCTCTAAATCATTAAAGGTAAACTTTATTATTTCTCATTGAACTTT
1 TATGGTTTAATACTTACATTCTCTAAATCATTAAAGGTAAACTTTATTATTTCTCATTGAACTTT
* * * *
92126 GTTTTCTCTTTGAACTTTGTTTTCTCTTTGAATTT
66 GTTTTCTCATTCAACTTTGCTTTCTCTTTGAACTT
92161 TATGGTTTAATACTTACATTCTCTAAATCATTAAAGGTAAACTTTATTATTTCTCATTGAACTTT
1 TATGGTTTAATACTTACATTCTCTAAATCATTAAAGGTAAACTTTATTATTTCTCATTGAACTTT
92226 GTTTTCTCATTCAACTTTGCTTTCTCTTTGAACTT
66 GTTTTCTCATTCAACTTTGCTTTCTCTTTGAACTT
92261 TAT
1 TAT
92264 TTACTAATAT
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.25, C:0.15, G:0.09, T:0.51
Consensus pattern (100 bp):
TATGGTTTAATACTTACATTCTCTAAATCATTAAAGGTAAACTTTATTATTTCTCATTGAACTTT
GTTTTCTCATTCAACTTTGCTTTCTCTTTGAACTT
Found at i:92233 original size:18 final size:18
Alignment explanation
Indices: 92210--92261 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
92200 AACTTTATTA
*
92210 TTTCTCATTGAACTTTGT
1 TTTCTCATTGAACTTTGC
*
92228 TTTCTCATTCAACTTTGC
1 TTTCTCATTGAACTTTGC
*
92246 TTTCTCTTTGAACTTT
1 TTTCTCATTGAACTTT
92262 ATTTACTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.15, C:0.21, G:0.08, T:0.56
Consensus pattern (18 bp):
TTTCTCATTGAACTTTGC
Found at i:92350 original size:27 final size:27
Alignment explanation
Indices: 92320--92401 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 27
92310 ATGAAGTGAC
92320 ATTTTATATATTATTAAATATAAAAAT
1 ATTTTATATATTATTAAATATAAAAAT
* * * *
92347 ATTTTA-AAATAAATT-TA-ATAAAAGT
1 ATTTTATATAT-TATTAAATATAAAAAT
* *
92372 ATTTTAT-TATTATTAAATTTAAAAAG
1 ATTTTATATATTATTAAATATAAAAAT
92398 ATTT
1 ATTT
92402 AAAATGATCA
Statistics
Matches: 41, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
24 3 0.07
25 16 0.39
26 13 0.32
27 9 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
ATTTTATATATTATTAAATATAAAAAT
Found at i:94288 original size:91 final size:91
Alignment explanation
Indices: 94133--94314 Score: 346
Period size: 91 Copynumber: 2.0 Consensus size: 91
94123 ATTCATTTAG
94133 ATCTTTGCAGGCACATCTAGAGAAAGGAGATAAAGGTTTGTTAATTTACTTGGACATCGAGTACC
1 ATCTTTGCAGGCACATCTAGAGAAAGGAGATAAAGGTTTGTTAATTTACTTGGACATCGAGTACC
* *
94198 CGATTTTGTTCGGGTTGACTAATGCT
66 CGATGTTATTCGGGTTGACTAATGCT
94224 ATCTTTGCAGGCACATCTAGAGAAAGGAGATAAAGGTTTGTTAATTTACTTGGACATCGAGTACC
1 ATCTTTGCAGGCACATCTAGAGAAAGGAGATAAAGGTTTGTTAATTTACTTGGACATCGAGTACC
94289 CGATGTTATTCGGGTTGACTAATGCT
66 CGATGTTATTCGGGTTGACTAATGCT
94315 CCTGTGGGGC
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (91 bp):
ATCTTTGCAGGCACATCTAGAGAAAGGAGATAAAGGTTTGTTAATTTACTTGGACATCGAGTACC
CGATGTTATTCGGGTTGACTAATGCT
Found at i:97530 original size:48 final size:50
Alignment explanation
Indices: 97474--97569 Score: 178
Period size: 50 Copynumber: 2.0 Consensus size: 50
97464 ATTGAAAGTA
97474 ATCAAACGCTGTAAGA-GGGGGGGGGGG-ACCAAAACTTTGTAAGCTTGT
1 ATCAAACGCTGTAAGAGGGGGGGGGGGGAACCAAAACTTTGTAAGCTTGT
97522 ATCAAACGCTGTAAGAGGGGGGGGGGGGAACCAAAACTTTGTAAGCTT
1 ATCAAACGCTGTAAGAGGGGGGGGGGGGAACCAAAACTTTGTAAGCTT
97570 TTAATGAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 16 0.35
49 11 0.24
50 19 0.41
ACGTcount: A:0.30, C:0.15, G:0.35, T:0.20
Consensus pattern (50 bp):
ATCAAACGCTGTAAGAGGGGGGGGGGGGAACCAAAACTTTGTAAGCTTGT
Found at i:98955 original size:61 final size:61
Alignment explanation
Indices: 98834--98955 Score: 163
Period size: 61 Copynumber: 2.0 Consensus size: 61
98824 GTAGTGCTAA
* * * * *
98834 ACCTGCACTAAGCTTACGCCATAGTGCTAATCCGGATATGACATATAAGGTTGTGCCCACC
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCGGACATGACACATAAGGTCGTACCCACC
* * * *
98895 ACCTACACTAAGCTTACGCTATAGTGCTAATTCGGACATGATACATAAGGTCGTATCCACC
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCGGACATGACACATAAGGTCGTACCCACC
98956 TTCCCGCACT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (61 bp):
ACCTACACTAAGCTTACGCCATAGTGCTAATCCGGACATGACACATAAGGTCGTACCCACC
Found at i:100457 original size:30 final size:31
Alignment explanation
Indices: 100423--100491 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 31
100413 CCATTTGTAA
*
100423 TTTTCCAAA-ATTACATTTTGGTC-CCTAAAC
1 TTTTCCAAAGATTACACTTTGGTCACC-AAAC
* *
100453 TTTT-CAAAGCTTATACTTTGGTCACCAAAC
1 TTTTCCAAAGATTACACTTTGGTCACCAAAC
*
100483 TTTACCAAA
1 TTTTCCAAA
100492 TGTATAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 4 0.12
30 22 0.69
31 6 0.19
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (31 bp):
TTTTCCAAAGATTACACTTTGGTCACCAAAC
Found at i:103380 original size:12 final size:12
Alignment explanation
Indices: 103350--103393 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
103340 CATTTTCCAC
103350 TTTCATATTCAT
1 TTTCATATTCAT
**
103362 TCACATATTCAT
1 TTTCATATTCAT
103374 TTTCATATTCCAT
1 TTTCATATT-CAT
*
103387 GTTCATA
1 TTTCATA
103394 ATAAATACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.27, C:0.20, G:0.02, T:0.50
Consensus pattern (12 bp):
TTTCATATTCAT
Found at i:103511 original size:19 final size:19
Alignment explanation
Indices: 103418--103512 Score: 75
Period size: 19 Copynumber: 5.0 Consensus size: 19
103408 ATTTCAGAAT
* *
103418 TTATTTTCTAAA-CCATAAC
1 TTATTTTC-AAATTCATAGC
* * *
103437 TTATTTACAGATTCATAAC
1 TTATTTTCAAATTCATAGC
* * *
103456 TTATTGTCAGACTCATAGC
1 TTATTTTCAAATTCATAGC
* * *
103475 TTACTGTCAAAATCATAGC
1 TTATTTTCAAATTCATAGC
103494 TTATTTTCAAATTCATAGC
1 TTATTTTCAAATTCATAGC
103513 CCAATGCATA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
18 2 0.03
19 60 0.97
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (19 bp):
TTATTTTCAAATTCATAGC
Found at i:105189 original size:20 final size:20
Alignment explanation
Indices: 105151--105189 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
105141 TCTAAAATAG
* *
105151 TCAAATTTAACATTCTAACA
1 TCAAATTCAACATTATAACA
*
105171 TCAAATTCAATATTATAAC
1 TCAAATTCAACATTATAAC
105190 TTTCAATTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (20 bp):
TCAAATTCAACATTATAACA
Found at i:108175 original size:15 final size:14
Alignment explanation
Indices: 108153--108205 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
108143 ATATTTGCTC
108153 TTTAATTTCTACTA
1 TTTAATTTCTACTA
* *
108167 TTTATATTTCTTCCA
1 TTTA-ATTTCTACTA
**
108182 TTTAATTTCTGTTA
1 TTTAATTTCTACTA
108196 TTCTAATTTC
1 TT-TAATTTC
108206 AGCCTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
14 13 0.41
15 19 0.59
ACGTcount: A:0.23, C:0.15, G:0.02, T:0.60
Consensus pattern (14 bp):
TTTAATTTCTACTA
Found at i:109802 original size:64 final size:63
Alignment explanation
Indices: 109729--109913 Score: 214
Period size: 64 Copynumber: 2.9 Consensus size: 63
109719 GACCGTTGGA
* *
109729 CCCTTAGTGCATCGGTGCACTAAGAGTGCATCGATGCATAAAATGCATTCGATGTTTCCA-AATA
1 CCCTGAGTGCATCGATGCA-T-AGAGTGCATCGATGCATAAAATGCATTCGATGTTTCCATAA-A
109793 G
63 G
* * *
109794 -CCTGAGTGCATTGATGCAT-GTCTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA
1 CCCTGAGTGCATCGATGCATAG---AGTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAA
109857 G
63 G
* *
109858 CCCTGAGTGCATCGATGCATGGTATGTACATCGATGCATAAAATGCATTCGATGTT
1 CCCTGAGTGCATCGATGCATAG-A-GTGCATCGATGCATAAAATGCATTCGATGTT
109914 CAATTTATTC
Statistics
Matches: 105, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
61 1 0.01
63 1 0.01
64 53 0.50
65 49 0.47
66 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (63 bp):
CCCTGAGTGCATCGATGCATAGAGTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAG
Found at i:109895 original size:65 final size:64
Alignment explanation
Indices: 109757--109913 Score: 228
Period size: 65 Copynumber: 2.4 Consensus size: 64
109747 ACTAAGAGTG
* * *
109757 CATCGATGCATAAAATGCATTCGATGTTTCCAAATAGCCTGAGTGCATTGATGCATGTCTAGTG
1 CATCGATGCATAAAATGCATTCGATGTTTCCAAATAGCCTGAGTGCATCGATGCATGTATAGTA
* *
109821 CATCGATGCATCAAATGCATTCGATGTTTTCATAA-AGCCCTGAGTGCATCGATGCATGGTAT-G
1 CATCGATGCATAAAATGCATTCGATGTTTCCA-AATAG-CCTGAGTGCATCGATGCAT-GTATAG
109884 TA
63 TA
109886 CATCGATGCATAAAATGCATTCGATGTT
1 CATCGATGCATAAAATGCATTCGATGTT
109914 CAATTTATTC
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
64 32 0.38
65 49 0.58
66 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (64 bp):
CATCGATGCATAAAATGCATTCGATGTTTCCAAATAGCCTGAGTGCATCGATGCATGTATAGTA
Found at i:109955 original size:65 final size:63
Alignment explanation
Indices: 109754--109961 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 63
109744 TGCACTAAGA
* * ** *
109754 GTGCATCGATGCATAAAATGCATTCGATGTTTCCAAATAGCCTGAGTGCATTGATGCATGTCTA
1 GTGCATCGATGCATAAAATGCATTCGATGTTT-CAATTAGCCTGAGTGCATCGATGCATGGATC
* *
109818 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAGCCCTGAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAT-TAG-CCTGAGTGCATCGATGCATGG-A
109882 T-
62 TC
* *
109883 GTACATCGATGCATAAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAA-TTA-GCC-TGAGTGCATCGATGCATGGAT
109946 C
63 C
*
109947 GGTGCATCGGTGCAT
1 -GTGCATCGATGCAT
109962 CACTTTGAAA
Statistics
Matches: 122, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
63 6 0.05
64 51 0.42
65 64 0.52
66 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAATTAGCCTGAGTGCATCGATGCATGGATC
Found at i:110566 original size:2 final size:2
Alignment explanation
Indices: 110559--110587 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
110549 CAACCAAACC
110559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
110588 AAGTTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:111028 original size:21 final size:21
Alignment explanation
Indices: 111004--111047 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
110994 CCGAAGGAGG
*
111004 AGGAGGAACACGAGAAGAGCT
1 AGGAGGAACACGAGAAGAACT
* * *
111025 AGGAGTAGCACGTGAAGAACT
1 AGGAGGAACACGAGAAGAACT
111046 AG
1 AG
111048 CTCCCGAAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.14, G:0.36, T:0.09
Consensus pattern (21 bp):
AGGAGGAACACGAGAAGAACT
Found at i:112618 original size:23 final size:22
Alignment explanation
Indices: 112588--112668 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
112578 GCATGACCTT
*
112588 GTGCATCGATGCTCATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
112610 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
112632 GTGAATCGATGCACATACAAGG
1 GTGCATCGATGCACATTCAAGG
112654 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
112669 TGTTAAGTGC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
21 14 0.30
22 5 0.11
23 27 0.59
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:118528 original size:45 final size:46
Alignment explanation
Indices: 118462--118568 Score: 146
Period size: 45 Copynumber: 2.3 Consensus size: 46
118452 GGTGCACTAA
*
118462 GAGTGCATCGATGTATAAAATGCATTCGATG-TTTCAAAATAG-CCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAA-AGCCCT
* * *
118507 GAGTGCGTCGATGCATCAAATGCATTCGATGTTTTCATAAAGCCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAAGCCCT
*
118553 GAGTGTATCGATGCAT
1 GAGTGCATCGATGCAT
118569 GGTATGTGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 30 0.56
46 24 0.44
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (46 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAAGCCCT
Found at i:120523 original size:21 final size:21
Alignment explanation
Indices: 120494--120614 Score: 147
Period size: 21 Copynumber: 5.7 Consensus size: 21
120484 AAGGTGTCAA
120494 AGTGCATCCATGCACTCCTAC
1 AGTGCATCCATGCACTCCTAC
*
120515 AGTGTATCCATGCACTCCTAC
1 AGTGCATCCATGCACTCCTAC
* * *
120536 AGTGCATTCATGCACCCCTGC
1 AGTGCATCCATGCACTCCTAC
120557 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCA-CT-CCTAC
*
120579 TAGTGCATCGATGCAC-CCTAC
1 -AGTGCATCCATGCACTCCTAC
*
120600 TGTGCATCCATGCAC
1 AGTGCATCCATGCAC
120615 CAAGGCTGCA
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
20 15 0.18
21 52 0.61
22 3 0.04
23 15 0.18
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCACTCCTAC
Done.