Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008155.1 Hibiscus syriacus cultivar Beakdansim tig00110721_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: 962042
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:358748 original size:34 final size:34
Alignment explanation
Indices: 358695--358766 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 34
358685 CTTGTTTAAT
*
358695 TAAAAAAATATTTAAATTAAA-A-ATATAAA-ATA
1 TAAAAAAATATTAAAATTAAATACAT-TAAATATA
358727 TAAAAAAATATTAAGATATTAAATACATTAAATATA
1 TAAAAAAATATTAA-A-ATTAAATACATTAAATATA
358763 TAAA
1 TAAA
358767 TGCTACAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
32 13 0.38
33 1 0.03
34 6 0.18
35 5 0.15
36 9 0.26
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (34 bp):
TAAAAAAATATTAAAATTAAATACATTAAATATA
Found at i:358935 original size:2 final size:2
Alignment explanation
Indices: 358928--358960 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
358918 TAAGGTAAGT
*
358928 TA TA TA TA TA AA 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
358961 CATGTTTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:360683 original size:3 final size:3
Alignment explanation
Indices: 360675--360748 Score: 85
Period size: 3 Copynumber: 23.7 Consensus size: 3
360665 GTTTTATTTA
* *
360675 TAT TAT TAT TAT TAT ATAT TAT TATT TAT TAT ATAT TTT TAT TAT TAA
1 TAT TAT TAT TAT TAT -TAT TAT TA-T TAT TAT -TAT TAT TAT TAT TAT
* *
360723 TAT TAT TAT TAA GAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
360749 CAAACAGGCC
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
3 51 0.85
4 9 0.15
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:361193 original size:26 final size:26
Alignment explanation
Indices: 361119--361181 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
361109 CGGCTCACCT
* *
361119 GCAAAGAAAGAAAGCAGGAGACAGAGA
1 GCAAA-AAAAAAAGAAGGAGACAGAGA
361146 GCAAAAAAAAAAGAAGGGAGACAGAGA
1 GCAAAAAAAAAAGAA-GGAGACAGAGA
*
361173 GCAGAAAAA
1 GCAAAAAAA
361182 CGGAGAGGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 8 0.25
27 24 0.75
ACGTcount: A:0.60, C:0.10, G:0.30, T:0.00
Consensus pattern (26 bp):
GCAAAAAAAAAAGAAGGAGACAGAGA
Found at i:362718 original size:17 final size:20
Alignment explanation
Indices: 362695--362742 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 20
362685 TTACTTTTAT
362695 ATTATTTTATT-A-ATATT-
1 ATTATTTTATTCAGATATTA
*
362712 TTTATTTTATTCAGATATTA
1 ATTATTTTATTCAGATATTA
362732 ATTATTTTATT
1 ATTATTTTATT
362743 TGTCTGTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 10 0.38
18 1 0.04
19 5 0.19
20 10 0.38
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
ATTATTTTATTCAGATATTA
Found at i:364206 original size:8 final size:7
Alignment explanation
Indices: 364182--364223 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
364172 TTTTCATACA
364182 TGCA-TT
1 TGCATTT
364188 TGCATTT
1 TGCATTT
364195 TGCATCTT
1 TGCAT-TT
364203 TGCATTT
1 TGCATTT
* *
364210 TTCATTG
1 TGCATTT
364217 TGCATTT
1 TGCATTT
364224 ATACTTTTAT
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:364206 original size:15 final size:14
Alignment explanation
Indices: 364182--364223 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
364172 TTTTCATACA
364182 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
364195 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
364210 TTCATTGTGCATTT
1 TGCATTTTGCATTT
364224 ATACTTTTAT
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:365001 original size:104 final size:105
Alignment explanation
Indices: 364847--365054 Score: 400
Period size: 104 Copynumber: 2.0 Consensus size: 105
364837 GTTTTACCCA
364847 AAGAAAAAGGACATAGAAAAGGGTCAAAGGCTAGTCAAGAAGAAAAAGAATGTGCAGAGTTTTCA
1 AAGAAAAAGGACATAGAAAAGGGTCAAAGGCTAGTCAAGAAGAAAAAGAATGTGCAGAGTTTTCA
*
364912 ATTTCCTCCTTTCCACTTTTTAGGTGAAAAATCATATTCT
66 ATTTCCTCCTTTCCACTTTTCAGGTGAAAAATCATATTCT
364952 AAGAAAAA-GACATAGAAAAGGGTCAAAGGCTAGTCAAGAAGAAAAAGAATGTGCAGAGTTTTCA
1 AAGAAAAAGGACATAGAAAAGGGTCAAAGGCTAGTCAAGAAGAAAAAGAATGTGCAGAGTTTTCA
365016 ATTTCCTCCTTTCCACTTTTCAGGTGAAAAATCATATTC
66 ATTTCCTCCTTTCCACTTTTCAGGTGAAAAATCATATTC
365055 AAAATGCTCC
Statistics
Matches: 102, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
104 94 0.92
105 8 0.08
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (105 bp):
AAGAAAAAGGACATAGAAAAGGGTCAAAGGCTAGTCAAGAAGAAAAAGAATGTGCAGAGTTTTCA
ATTTCCTCCTTTCCACTTTTCAGGTGAAAAATCATATTCT
Found at i:367082 original size:26 final size:26
Alignment explanation
Indices: 367052--367104 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
367042 GTTTATACTC
367052 ATCCAGCAAAGAAAGAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAA
*
367078 ATCCAGCAAAGAAAGAAGAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAA
367104 A
1 A
367105 AAAAAGAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.68, C:0.11, G:0.17, T:0.04
Consensus pattern (26 bp):
ATCCAGCAAAGAAAGAAAAAAGAAAA
Found at i:371870 original size:22 final size:22
Alignment explanation
Indices: 371841--371895 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
371831 ACATCTACTC
*
371841 TTCAAAGATGATAGGTTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
371863 TTTAAAGATAATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
371885 TTCAAAGATGA
1 TTCAAAGATGA
371896 AAGCTTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:372640 original size:113 final size:113
Alignment explanation
Indices: 372332--372720 Score: 668
Period size: 113 Copynumber: 3.5 Consensus size: 113
372322 TTCCAGGTCG
* *
372332 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
372397 AACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAA
* *
372445 AGTTCATAAT--G-AGAACTCATCTGAATAAGGAAGAAGAAGTTCATAATGAGATGAGCTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
372507 AACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAA
372555 AGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
*
372620 AACCTTTTGCTCAAATCCATCACTCGATGGATCAACATTTCCAG-GTAA
66 AACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAG-AA
372668 AGTTCATAATGAGAAGAACTCATCT--A-AA-GAAGAAGAAGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAAGAAGTTCATAATGAGAAGA
372721 ACTCATAGAA
Statistics
Matches: 265, Mismatches: 7, Indels: 12
0.93 0.02 0.04
Matches are distributed among these distances:
109 25 0.09
110 107 0.40
111 2 0.01
112 2 0.01
113 129 0.49
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
AACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAA
Found at i:372714 original size:36 final size:39
Alignment explanation
Indices: 372667--372759 Score: 147
Period size: 39 Copynumber: 2.5 Consensus size: 39
372657 TTTCCAGGTA
*
372667 AAGTTCATAATGAGAAGAACTCAT-CTA-AA-GAAGAAG
1 AAGTTCATAATGAGAAGAACTCATACAAGAAGGAAGAAG
*
372703 AAGTTCATAATGAGAAGAACTCATAGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATACAAGAAGGAAGAAG
372742 AAGTTCATAATGAGAAGA
1 AAGTTCATAATGAGAAGA
372760 GCTTGTTCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
36 24 0.46
37 1 0.02
38 2 0.04
39 25 0.48
ACGTcount: A:0.51, C:0.09, G:0.23, T:0.18
Consensus pattern (39 bp):
AAGTTCATAATGAGAAGAACTCATACAAGAAGGAAGAAG
Found at i:372809 original size:260 final size:265
Alignment explanation
Indices: 372444--372984 Score: 911
Period size: 260 Copynumber: 2.1 Consensus size: 265
372434 TTTCCAGAGA
* * *
372444 AAGTTCATAAT--G-AGAACTCATCTGAATAAGGAAGAAGAAGTTCATAATGAGATGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCAGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
*
372506 TAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAG
66 CAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAG
*
372571 AACTCATCTGAATAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAAT
131 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAAT
**
372636 CCATCACTCGATGGATCAACATTTCCAGGTAAAGTTCATAATGAGAAGAACTCATCT-A-AA-GA
196 CCATCACTCGATGGATCAACATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAGAAGGA
372698 AGAAG
261 AGAAG
372703 AAGTTCATAATGAGAAGAACTCAT-AGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCAGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
372767 CAA-CTTTTGCTCAAATCCATCACTCGATGGATCAGA-TTTTCCAGAGAAAGTTCATAATGAGAA
66 CAACCTTTTGCTCAAATCCATCACTCGATGGATCA-ACTTTTCCAGAGAAAGTTCATAATGAGAA
372830 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAA
130 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAA
* * *
372895 TCCATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAATAACTCATCTGAAGAAG
195 TCCATCACTCGATGGATCAACATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCT-AAGAAG
372960 GAAGAAG
259 GAAGAAG
372967 AAGTTCATAATGAGAAGA
1 AAGTTCATAATGAGAAGA
372985 GCTTGTTCAA
Statistics
Matches: 264, Mismatches: 10, Indels: 11
0.93 0.04 0.04
Matches are distributed among these distances:
259 11 0.04
260 175 0.66
261 41 0.16
262 10 0.04
263 2 0.01
264 25 0.09
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (265 bp):
AAGTTCATAATGAGAAGAACTCATCAGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
CAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAG
AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAAT
CCATCACTCGATGGATCAACATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAGAAGGA
AGAAG
Found at i:372823 original size:147 final size:152
Alignment explanation
Indices: 372554--372871 Score: 533
Period size: 147 Copynumber: 2.1 Consensus size: 152
372544 TTTCCAGAGA
* *
372554 AAGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCAGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
372619 CAACCTTTTGCTCAAATCCATCACTCGATGGATCAACATTTCCAGGTAAAGTTCATAATGAGAAG
66 CAACCTTTTGCTCAAATCCATCACTCGATGGATCAACATTTCCAGGTAAAGTTCATAATGAGAAG
372684 AACTCATCT-A-AA-GAAGAAG
131 AACTCATCTAAGAAGGAAGAAG
372703 AAGTTCATAATGAGAAGAACTCAT-AGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCAGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
*
372767 CAA-CTTTTGCTCAAATCCATCACTCGATGGATCAGA-TTTTCCAGAG-AAAGTTCATAATGAGA
66 CAACCTTTTGCTCAAATCCATCACTCGATGGATCA-ACATTTCCAG-GTAAAGTTCATAATGAGA
372829 AGAACTCATCTGAAGAAGGAAGAAG
129 AGAACTCATCT-AAGAAGGAAGAAG
372854 AAGTTCATAATGAGAAGA
1 AAGTTCATAATGAGAAGA
372872 GCTTGTTCAA
Statistics
Matches: 160, Mismatches: 3, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
147 65 0.41
148 43 0.27
149 25 0.16
150 2 0.01
151 25 0.16
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (152 bp):
AAGTTCATAATGAGAAGAACTCATCAGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
CAACCTTTTGCTCAAATCCATCACTCGATGGATCAACATTTCCAGGTAAAGTTCATAATGAGAAG
AACTCATCTAAGAAGGAAGAAG
Found at i:372930 original size:113 final size:113
Alignment explanation
Indices: 372698--373174 Score: 715
Period size: 113 Copynumber: 4.3 Consensus size: 113
372688 CATCTAAAGA
* *
372698 AGAAGAAGTTCATAATGAGAAGAACTCAT-AGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
* *
372762 TTGTTCAA-CTTTTGCTCAAATCCATCACTCGATGGATCAGA-TTTTCC
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA-ACATTTCC
*
372809 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
*
372874 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCC
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCC
*
372922 AGAAAAAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
372987 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCC
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCC
* * * *
373035 AGAGAAAGTTCATAATGA-AAGAAATTATCT-------GAAGAAGAAGTTCATAATGAGAAGAGA
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
* *
373092 TTATTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTTCC
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCC
* *
373140 AGTGGAAAAGTTCATAATAAGAAGAACTCATCTGA
1 A--GAAAAAGTTCATAATGAGAAGAACTCATCTGA
373175 TGAGAGCAAT
Statistics
Matches: 339, Mismatches: 19, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
105 73 0.22
107 14 0.04
108 10 0.03
111 27 0.08
112 52 0.15
113 163 0.48
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (113 bp):
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCC
Found at i:373089 original size:17 final size:17
Alignment explanation
Indices: 373040--373089 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
373030 TTTCCAGAGA
373040 AAGTTCATAATGA-AAG
1 AAGTTCATAATGAGAAG
* *
373056 AAATT-AT-CTGAAGAAG
1 AAGTTCATAATG-AGAAG
373072 AAGTTCATAATGAGAAG
1 AAGTTCATAATGAGAAG
373089 A
1 A
373090 GATTATTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
14 2 0.08
15 3 0.12
16 11 0.42
17 8 0.31
18 2 0.08
ACGTcount: A:0.50, C:0.06, G:0.20, T:0.24
Consensus pattern (17 bp):
AAGTTCATAATGAGAAG
Found at i:373115 original size:218 final size:219
Alignment explanation
Indices: 372698--373174 Score: 719
Period size: 218 Copynumber: 2.2 Consensus size: 219
372688 CATCTAAAGA
* *
372698 AGAAGAAGTTCATAATGAGAAGAACTCAT-AGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
*
372762 TTGTTCAACTTTTGCTCAAATCCATCACTCGATGGATCAGATTTTCCAGAGAAAGTTCATAATGA
66 TTGTTCAACTTTTGCTCAAATCCATCACTCGATGGATCAGAATTTCCAGAGAAAGTTCATAATGA
* * *
372827 GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
131 GAAGAAATCATCT-----A-GAAGAAGAAGTTCATAATGAGAAGAGATTATTCAACCTTTTGCTC
*
372892 AAATCCATCACTTGATGGATCAACTTTTCC
190 AAATCCATCACTTGATGGATCAACATTTCC
*
372922 AGAAAAAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
*
372987 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA-ACATTTCCAGAGAAAGTTCATAAT
66 TTGTTCAA-CTTTTGCTCAAATCCATCACTCGATGGATCAGA-ATTTCCAGAGAAAGTTCATAAT
*
373051 GA-AAGAAATTATCT-GAAGAAGAAGTTCATAATGAGAAGAGATTATTCAACCTTTTGCTCAAAT
129 GAGAAGAAATCATCTAGAAGAAGAAGTTCATAATGAGAAGAGATTATTCAACCTTTTGCTCAAAT
*
373114 CCATCACTTGATGGATCAGCATTTCC
194 CCATCACTTGATGGATCAACATTTCC
* *
373140 AGTGGAAAAGTTCATAATAAGAAGAACTCATCTGA
1 A--GAAAAAGTTCATAATGAGAAGAACTCATCTGA
373175 TGAGAGCAAT
Statistics
Matches: 234, Mismatches: 14, Indels: 14
0.89 0.05 0.05
Matches are distributed among these distances:
218 72 0.31
220 29 0.12
224 27 0.12
225 53 0.23
226 53 0.23
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (219 bp):
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
TTGTTCAACTTTTGCTCAAATCCATCACTCGATGGATCAGAATTTCCAGAGAAAGTTCATAATGA
GAAGAAATCATCTAGAAGAAGAAGTTCATAATGAGAAGAGATTATTCAACCTTTTGCTCAAATCC
ATCACTTGATGGATCAACATTTCC
Found at i:373162 original size:105 final size:104
Alignment explanation
Indices: 372960--373159 Score: 337
Period size: 105 Copynumber: 1.9 Consensus size: 104
372950 TCTGAAGAAG
* *
372960 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAT
1 GAAGAAGAAGTTCATAATGAGAAGAGATTATTCAACCTTTTGCTCAAATCCATCACTTGATGGAT
373025 CAACATTTCCAGAGAAAGTTCATAATGAAAGAAATTATCT
66 CAACATTTCCAGAGAAAGTTCATAAT-AAAGAAATTATCT
373065 GAAGAAGAAGTTCATAATGAGAAGAGATTATTCAACCTTTTGCTCAAATCCATCACTTGATGGAT
1 GAAGAAGAAGTTCATAATGAGAAGAGATTATTCAACCTTTTGCTCAAATCCATCACTTGATGGAT
* *
373130 CAGCATTTCCAGTGGAAAAGTTCATAATAA
66 CAACATTTCCAG-AG-AAAGTTCATAATAA
373160 GAAGAACTCA
Statistics
Matches: 89, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
105 74 0.83
106 3 0.03
107 12 0.13
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (104 bp):
GAAGAAGAAGTTCATAATGAGAAGAGATTATTCAACCTTTTGCTCAAATCCATCACTTGATGGAT
CAACATTTCCAGAGAAAGTTCATAATAAAGAAATTATCT
Found at i:373543 original size:3 final size:3
Alignment explanation
Indices: 373529--373598 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
373519 GTTTTATTTA
* * *
373529 TAT TAC TAT TAT TAT TAT TAT TATT TAT ATAT TTT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT -TAT TAT TAT TAT TAT TAT
* *
373576 TAT TAT TAA GAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
373599 CAAACAGGCC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:374028 original size:24 final size:26
Alignment explanation
Indices: 373970--374029 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
373960 GCTCACCTAC
*
373970 AAAGAAAGAGAAGCAGAGACAGAGAG
1 AAAGAAAAAGAAGCAGAGACAGAGAG
* *
373996 CAAAAAAAAAGAAG-GGAGACAGAGAG
1 -AAAGAAAAAGAAGCAGAGACAGAGAG
374022 -AAGAAAAA
1 AAAGAAAAA
374030 CGGAGAGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 7 0.24
26 11 0.38
27 11 0.38
ACGTcount: A:0.63, C:0.07, G:0.30, T:0.00
Consensus pattern (26 bp):
AAAGAAAAAGAAGCAGAGACAGAGAG
Found at i:374831 original size:27 final size:28
Alignment explanation
Indices: 374801--374863 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
374791 TTACTAGTTT
374801 TTTTTATTTATAGTTTTA-ATTTCATTA
1 TTTTTATTTATAGTTTTATATTTCATTA
* * *
374828 TTTTTAATTATTGTTTTATATTTTATTA
1 TTTTTATTTATAGTTTTATATTTCATTA
*
374856 TTATTATT
1 TTTTTATT
374864 ATTAGTATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (28 bp):
TTTTTATTTATAGTTTTATATTTCATTA
Found at i:378843 original size:23 final size:23
Alignment explanation
Indices: 378817--378865 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
378807 TCAATCATAA
*
378817 TAACATAAAATGTAGCGC-TTATT
1 TAACATAAAAGGTAGCGCATT-TT
* *
378840 TAACGTAATAGGTAGCGCATTTT
1 TAACATAAAAGGTAGCGCATTTT
378863 TAA
1 TAA
378866 ATCTGATGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (23 bp):
TAACATAAAAGGTAGCGCATTTT
Found at i:379488 original size:179 final size:179
Alignment explanation
Indices: 379175--379663 Score: 784
Period size: 179 Copynumber: 2.7 Consensus size: 179
379165 TATTACCATG
*
379175 TACATTGTTAATTTACATATTACTTTAAAGTAATAAGTTTCAAAATTAT-AAGTATCGATACTTT
1 TACATTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCAAAATT-TCAAGTATCGATACTTT
* * * *
379239 ATATATGTATATCGAAACATTTTGCGTGCAAATTGTTTGAGAAGCATATTGTAATAAAAGTATTG
65 ATATATGTGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAGCATATTGGAATAAAAGTATCG
*
379304 ATACTTGGTATTTACGCCTATTATCAATATACAGATAGACTTTTACCGTT
130 ATACTTGGAATTTACGCCTATTATCAATATACAGATAGACTTTTACCGTT
* *
379354 TACATTATTAATTTACATATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGTATCGATATTTTA
1 TACATTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGTATCGATACTTTA
379419 TATATGTGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAGCATATTGGAATAAAAGTATCGA
66 TATATGTGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAGCATATTGGAATAAAAGTATCGA
** * * *
379484 TACTTGGAATTTGTGCCTATTATCATTATACCGGTAGACTTTTACCGTT
131 TACTTGGAATTTACGCCTATTATCAATATACAGATAGACTTTTACCGTT
* *
379533 TACATTGTTAATTTATC-TATTAATTTAAAGTAATAGGTTTCGAAATTTCAAGTATCGATACTTT
1 TACATTGTTAATTTA-CATATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGTATCGATACTTT
* * *
379597 ATATATGTGCATCAATATATTTTGCGTGCAAATTGTTTGAGAAGCATATTGGAATAAAAGTATCG
65 ATATATGTGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAGCATATTGGAATAAAAGTATCG
379662 AT
130 AT
379664 GCCTATATAA
Statistics
Matches: 288, Mismatches: 20, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
178 1 0.00
179 286 0.99
180 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (179 bp):
TACATTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGTATCGATACTTTA
TATATGTGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAGCATATTGGAATAAAAGTATCGA
TACTTGGAATTTACGCCTATTATCAATATACAGATAGACTTTTACCGTT
Found at i:379919 original size:197 final size:198
Alignment explanation
Indices: 379471--379955 Score: 733
Period size: 199 Copynumber: 2.4 Consensus size: 198
379461 GCATATTGGA
**
379471 ATAAAAGTATCGATACTTGGA-ATTTGTGCCTATTATCATTATACCGGTAGACTTTTACCGTTTA
1 ATAAAAGTATCGATACTT-GATATTTACGCCTATTATCATTATACCGGTAGACTTTTACCGTTTA
* * * * *
379535 CATTGTTAATTTATCTATTAATTTAAAGTAATAGGTTTCGAAATTTCAAGTATCGATACTTTATA
65 CATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGCATCAATACTTTATA
* * * * * *
379600 TATGTGCATCAATATATTTTGCGTGCAAATTGTTTGAGAAGCATATTGGAATAAAAGTATCGATG
130 CATGT-CATCAATACATTTTGCGTGCAAATTGATTGAGAAGCATACTGGAATAAAAGTATCCATA
379665 CCTAT
194 CCTAT
* **
379670 ATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTATACTAGTAGACTTTTACCGTTTAC
1 ATAAAAGTATCGATACTTGATATTTACGCCTATTATCATTATACCGGTAGACTTTTACCGTTTAC
379735 ATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGCATCAATACTTTATAC
66 ATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGCATCAATACTTTATAC
* *
379800 ATGT-ATCAATACATTTTGTGTGCAAATTGATTGAGAAGCATACTGGAATAAAAGTA-CCATACT
131 ATGTCATCAATACATTTTGCGTGCAAATTGATTGAGAAGCATACTGGAATAAAAGTATCCATACC
379863 TAT
196 TAT
*
379866 ATAAAGAGTATCAATACTTGATATTTACGCCTATTATCATTATACCGGTAGACTTTTACCGTTTA
1 ATAAA-AGTATCGATACTTGATATTTACGCCTATTATCATTATACCGGTAGACTTTTACCGTTTA
*
379931 AATTGTTTAATTTACCTATTACTTT
65 CATTG-TTAATTTACCTATTACTTT
379956 TGTTGAAAAC
Statistics
Matches: 260, Mismatches: 23, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
196 12 0.05
197 107 0.41
198 20 0.08
199 121 0.47
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (198 bp):
ATAAAAGTATCGATACTTGATATTTACGCCTATTATCATTATACCGGTAGACTTTTACCGTTTAC
ATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGCATCAATACTTTATAC
ATGTCATCAATACATTTTGCGTGCAAATTGATTGAGAAGCATACTGGAATAAAAGTATCCATACC
TAT
Found at i:385770 original size:23 final size:20
Alignment explanation
Indices: 385717--385776 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 20
385707 TTTTGGTGCA
385717 GAGGGAATCGA-TCCCCCTT
1 GAGGGAATCGATTCCCCCTT
385736 GAGGGAATCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCC-TT
*
385757 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAATCGATTCCCCC
385777 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 11 0.31
20 6 0.17
21 3 0.08
22 1 0.03
23 15 0.42
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.20
Consensus pattern (20 bp):
GAGGGAATCGATTCCCCCTT
Found at i:385785 original size:21 final size:21
Alignment explanation
Indices: 385759--385798 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
385749 CCCCCTTTGA
*
385759 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
385780 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
385799 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:390134 original size:45 final size:46
Alignment explanation
Indices: 390046--390136 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 46
390036 TTTGAAAAAC
* *
390046 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
390092 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
390137 TTCGATGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:390646 original size:21 final size:20
Alignment explanation
Indices: 390607--390652 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
390597 GTTTGACAAG
*
390607 CATACTGGAATAAAAGTATC
1 CATACAGGAATAAAAGTATC
*
390627 CATACAGGCATAAGAAGTATC
1 CATACAGGAATAA-AAGTATC
*
390648 GATAC
1 CATAC
390653 TTGGACATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (20 bp):
CATACAGGAATAAAAGTATC
Found at i:390704 original size:146 final size:146
Alignment explanation
Indices: 390440--390741 Score: 444
Period size: 146 Copynumber: 2.1 Consensus size: 146
390430 TGTTTTCAAC
* *
390440 ACGTACAAATTGTTTAAGAAGCATACTAGAATAAAAGTAATCATACCGGCATAAGAAGTATCAAT
1 ACGTACAAATTGTTTAACAAGCATACTAGAATAAAAGTAATCATACAGGCATAAGAAGTATCAAT
* * *
390505 AGTTGGACATTTTCATACTTTGCATACGTTGTTTCAAAATTATAAATATCAATACTTTAATAATG
66 ACTTGGACATTTTCATACTTTGCATACATTGTTTCAAAATTATAAATATCAATACTTAAATAATG
390570 TGTATCAATACATTTG
131 TGTATCAATACATTTG
* * *
390586 ACGTACAAATTGTTTGACAAGCATACTGGAATAAAAGT-ATCCATACAGGCATAAGAAGTATCGA
1 ACGTACAAATTGTTTAACAAGCATACTAGAATAAAAGTAAT-CATACAGGCATAAGAAGTATCAA
* * **
390650 TACTTGGACATTTTCATACTTTGCGTACATTTTTTTGAAATTATAAATATCAATACTTAAATAAT
65 TACTTGGACATTTTCATACTTTGCATACATTGTTTCAAAATTATAAATATCAATACTTAAATAAT
* * *
390715 GTGTATCGATGCTTTTG
130 GTGTATCAATACATTTG
*
390732 ACGTGCAAAT
1 ACGTACAAAT
390742 ATCGATACTT
Statistics
Matches: 139, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
145 2 0.01
146 137 0.99
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (146 bp):
ACGTACAAATTGTTTAACAAGCATACTAGAATAAAAGTAATCATACAGGCATAAGAAGTATCAAT
ACTTGGACATTTTCATACTTTGCATACATTGTTTCAAAATTATAAATATCAATACTTAAATAATG
TGTATCAATACATTTG
Found at i:391913 original size:20 final size:20
Alignment explanation
Indices: 391888--391926 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
391878 GCTCTTTACT
391888 GGTTTTGTCAAATTGAAATC
1 GGTTTTGTCAAATTGAAATC
*
391908 GGTTTTGTCAAATTTAAAT
1 GGTTTTGTCAAATTGAAAT
391927 ATATTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.44
Consensus pattern (20 bp):
GGTTTTGTCAAATTGAAATC
Found at i:392144 original size:198 final size:197
Alignment explanation
Indices: 391717--392318 Score: 774
Period size: 191 Copynumber: 3.1 Consensus size: 197
391707 GTGCTTTACT
* ** * *
391717 GATTTTTTCAAATTAAAACAGGTTATATTGTCATGTATCGATATATGTGTCTAAGGTATCAATAC
1 GATTTTTTCAAATTTAAACATATTATATTGTCATGTATCGATACATGTGTATAAGGTATCAATAC
* ** * * * *
391782 TTTATAGGCTTTATTATTGCAATTGTTTAAAATTCCTAAAATACCGATATTTTGGTAC----A--
66 TTTATAGCCACTATTATTGCAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACT
* *
391841 TATAAAAGTATTGATACAAATTTCAACCATTTCAGTAGCTCTTTACTGGTTTTGTCAAATTGAAA
131 TATAAAAGTATCGATACAAATTTCAACAATTTCAGTAGCTCTTTACTGGTTTTGTCAAATTGAAA
*
391906 TC
196 CC
* * *
391908 GGTTTTGTCAAATTTAAATATATTATATTGTCATGTATCGATACATGTGTATAAGGTATCAATAC
1 GATTTTTTCAAATTTAAACATATTATATTGTCATGTATCGATACATGTGTATAAGGTATCAATAC
* *
391973 TTTATAGCCACTATTATTGTAATTCTTTTAAATTCCTAAAGTCCCGATACTTTGGTACATATACT
66 TTTATAGCCACTATTATTGCAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACT
* * * * *
392038 TATAAAAAGTATCAATATAAATTTCAACAATTCCGGTAGTTCTTTACTGGTTTTGTCAAATTGAA
131 TAT-AAAAGTATCGATACAAATTTCAACAATTTCAGTAGCTCTTTACTGGTTTTGTCAAATTGAA
392103 ACC
195 ACC
* * * * *
392106 GATTTTTTCAAATTTCAACATATTATATTGTTATGTATCGATACATGTGTA-AA-ATATCGATAA
1 GATTTTTTCAAATTTAAACATATTATATTGTCATGTATCGATACATGTGTATAAGGTATCAATAC
* * * *
392169 TTTATAGCCGCTATTATTGCAATTCTTTTAAATTTCTACAGTGCCGATACTTTGGTACATATACT
66 TTTATAGCCACTATTATTGCAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACT
* *
392234 TATAAACGTATCGATACAAATTTCAACAATTTTTA-TAGCTCTTTACTGGTTTTGTCAAATTGAA
131 TATAAAAGTATCGATACAAATTTCAACAA-TTTCAGTAGCTCTTTACTGGTTTTGTCAAATTGAA
392298 ACC
195 ACC
*
392301 AATTTTATT-AAATTTAAA
1 GATTTT-TTCAAATTTAAA
392319 TCGATTTTGT
Statistics
Matches: 355, Mismatches: 47, Indels: 14
0.85 0.11 0.03
Matches are distributed among these distances:
191 106 0.30
195 68 0.19
196 74 0.21
197 5 0.01
198 102 0.29
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (197 bp):
GATTTTTTCAAATTTAAACATATTATATTGTCATGTATCGATACATGTGTATAAGGTATCAATAC
TTTATAGCCACTATTATTGCAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACT
TATAAAAGTATCGATACAAATTTCAACAATTTCAGTAGCTCTTTACTGGTTTTGTCAAATTGAAA
CC
Found at i:392325 original size:20 final size:21
Alignment explanation
Indices: 392302--392354 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
392292 ATTGAAACCA
392302 ATTTTATTAAATTT-AAATCG
1 ATTTTATTAAATTTCAAATCG
* * * *
392322 ATTTT-GTCAATTTCCAATTG
1 ATTTTATTAAATTTCAAATCG
392342 ATTTTATTAAATT
1 ATTTTATTAAATT
392355 CGTTATCTGT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 6 0.24
20 14 0.56
21 5 0.20
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.53
Consensus pattern (21 bp):
ATTTTATTAAATTTCAAATCG
Found at i:397041 original size:32 final size:31
Alignment explanation
Indices: 396910--397039 Score: 208
Period size: 31 Copynumber: 4.2 Consensus size: 31
396900 GCTCATATAA
396910 TAATCTGTCCATATGTCCCG-AAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAAG-ACATAGG
* *
396941 TAAACTGTCCATATTTCCCGAAAGACATAGG
1 TAATCTGTCCATATGTCCCGAAAGACATAGG
*
396972 TAATCTGTCCATATGTCCCAAAAGACATAGG
1 TAATCTGTCCATATGTCCCGAAAGACATAGG
397003 TAATCCTGTCCATATGTCCCGAAAGACATAGG
1 TAAT-CTGTCCATATGTCCCGAAAGACATAGG
397035 TAATC
1 TAATC
397040 CTCGACTCTT
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
31 58 0.64
32 33 0.36
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (31 bp):
TAATCTGTCCATATGTCCCGAAAGACATAGG
Found at i:398620 original size:3 final size:3
Alignment explanation
Indices: 398614--398657 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
398604 TATTATAGTA
*
398614 TAT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT TAAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT T
398658 TTTACATGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:400124 original size:22 final size:21
Alignment explanation
Indices: 400099--400139 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
400089 ATGTATGTAC
*
400099 ATGTTGTAAATGTTATTATTAT
1 ATGTTGTAAATATT-TTATTAT
400121 ATGTTGTAAATATTTTATT
1 ATGTTGTAAATATTTTATT
400140 TTACATCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (21 bp):
ATGTTGTAAATATTTTATTAT
Found at i:403756 original size:13 final size:13
Alignment explanation
Indices: 403715--403757 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
403705 GGATCAATAT
403715 TTTTGCATATGCA
1 TTTTGCATATGCA
*
403728 -TTTGTATATTTGCA
1 TTTTGCATA--TGCA
403742 TTTTGCATATGCA
1 TTTTGCATATGCA
403755 TTT
1 TTT
403758 CATTTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 7 0.28
13 7 0.28
14 4 0.16
15 7 0.28
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.53
Consensus pattern (13 bp):
TTTTGCATATGCA
Found at i:406653 original size:15 final size:15
Alignment explanation
Indices: 406633--406662 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
406623 CGTGAGGATT
406633 ATTTTTCTTTATTTA
1 ATTTTTCTTTATTTA
*
406648 ATTTTTTTTTATTTA
1 ATTTTTCTTTATTTA
406663 CTGTTTTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
ATTTTTCTTTATTTA
Found at i:409770 original size:45 final size:45
Alignment explanation
Indices: 409706--409807 Score: 186
Period size: 45 Copynumber: 2.3 Consensus size: 45
409696 CTAGAGCTTA
* *
409706 AGACTTTGCCAGGGCATCTTAAATATGTTTACTTAGGTAGTGGTG
1 AGACTTTACCAGGGCATCTTAAATATGTTTACTTAGGTAGTGATG
409751 AGACTTTACCAGGGCATCTTAAATATGTTTACTTAGGTAGTGATG
1 AGACTTTACCAGGGCATCTTAAATATGTTTACTTAGGTAGTGATG
409796 AGACTTTACCAG
1 AGACTTTACCAG
409808 TGATTATTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (45 bp):
AGACTTTACCAGGGCATCTTAAATATGTTTACTTAGGTAGTGATG
Found at i:413052 original size:19 final size:20
Alignment explanation
Indices: 413010--413058 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
413000 TTAACTTTTT
*
413010 CTTTTATCTTTCATTATTAA
1 CTTTTATCTTTCATTACTAA
*
413030 -TTTTCTCTTTCATT-CTAA
1 CTTTTATCTTTCATTACTAA
*
413048 CTTTTACCTTT
1 CTTTTATCTTT
413059 TTCTTTCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.61
Consensus pattern (20 bp):
CTTTTATCTTTCATTACTAA
Found at i:416794 original size:17 final size:16
Alignment explanation
Indices: 416763--416796 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
416753 CACGTGAGGA
416763 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
416779 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
416796 T
1 T
416797 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:421199 original size:44 final size:43
Alignment explanation
Indices: 421090--421213 Score: 146
Period size: 44 Copynumber: 2.9 Consensus size: 43
421080 CAAAATCCCT
421090 TGGCCAAGACTCATGAACAGATGAGCAGTGTCA--ACCCTAGA
1 TGGCCAAGACTCATGAACAGATGAGCAGTGTCATCACCCTAGA
** * * * *
421131 TAACCAAGACTTAT-CATAGTATGAGCAGTGTTATCACCCTTAGA
1 TGGCCAAGACTCATGAACAG-ATGAGCAGTGTCATCACCC-TAGA
*
421175 TGGCCAAGACTCATGAACAGATGAGCAATGTCATCACCC
1 TGGCCAAGACTCATGAACAGATGAGCAGTGTCATCACCC
421214 GACCATATTT
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
40 3 0.05
41 23 0.35
43 4 0.06
44 32 0.49
45 3 0.05
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (43 bp):
TGGCCAAGACTCATGAACAGATGAGCAGTGTCATCACCCTAGA
Found at i:421848 original size:10 final size:10
Alignment explanation
Indices: 421832--421882 Score: 63
Period size: 10 Copynumber: 5.2 Consensus size: 10
421822 GGGACAAAAA
421832 ATATATTA-T
1 ATATATTATT
421841 AGTATATTATT
1 A-TATATTATT
421852 AT-TATTATT
1 ATATATTATT
421861 ATATATTATT
1 ATATATTATT
421871 AT-TAATTATT
1 ATAT-ATTATT
421881 AT
1 AT
421883 TTTTACATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
9 11 0.29
10 25 0.66
11 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
ATATATTATT
Found at i:421853 original size:3 final size:3
Alignment explanation
Indices: 421845--421883 Score: 60
Period size: 3 Copynumber: 12.3 Consensus size: 3
421835 TATTATAGTA
421845 TAT TAT TAT TAT TAT TAT ATAT TAT TAT TAAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT T-AT TAT TAT T
421884 TTTACATGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:421859 original size:19 final size:18
Alignment explanation
Indices: 421835--421879 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 18
421825 ACAAAAAATA
421835 TATTATAGTATATTATTAT
1 TATTATA-TATATTATTAT
421854 TATTATTATATATTATTAT
1 TATTA-TATATATTATTAT
421873 TAATTAT
1 T-ATTAT
421880 TATTTTTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TATTATATATATTATTAT
Found at i:421867 original size:13 final size:13
Alignment explanation
Indices: 421845--421883 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
421835 TATTATAGTA
421845 TATTAT-TATTAT
1 TATTATATATTAT
421857 TATTATATATTAT
1 TATTATATATTAT
421870 TATTA-ATTATTAT
1 TATTATA-TATTAT
421883 T
1 T
421884 TTTACATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.28
13 18 0.72
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTATATATTAT
Found at i:423375 original size:22 final size:21
Alignment explanation
Indices: 423350--423390 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
423340 ATGTATGTAC
*
423350 ATGTTGTAAATGTTATTATTAT
1 ATGTTGTAAATATT-TTATTAT
423372 ATGTTGTAAATATTTTATT
1 ATGTTGTAAATATTTTATT
423391 TTACATCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (21 bp):
ATGTTGTAAATATTTTATTAT
Found at i:426289 original size:30 final size:32
Alignment explanation
Indices: 426243--426308 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
426233 CTTAATTAAG
426243 TTAATAAATAATTAAATAATAATA-AATATTT
1 TTAATAAATAATTAAATAATAATATAATATTT
* * *
426274 TTAATATAT-ATTAAATAATCATATAATCTTT
1 TTAATAAATAATTAAATAATAATATAATATTT
426305 TTAA
1 TTAA
426309 AATTTAATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (32 bp):
TTAATAAATAATTAAATAATAATATAATATTT
Found at i:427060 original size:24 final size:24
Alignment explanation
Indices: 427000--427060 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
426990 ATTTTTTAGG
* *
427000 AAAAAATAAAAAAAATCTAAATTT
1 AAAAATTAAAAAAAATCTAAATTC
* *
427024 AAATTATTCAAAAAAAT-TAAATATC
1 AAA-AATTAAAAAAAATCTAAAT-TC
427049 AAAAATTAAAAA
1 AAAAATTAAAAA
427061 TTAAAATATA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
24 15 0.52
25 14 0.48
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAAATTAAAAAAAATCTAAATTC
Found at i:427710 original size:15 final size:15
Alignment explanation
Indices: 427676--427718 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
427666 TATTAATTTA
*
427676 ATTTTTATTTTTAAT
1 ATTTTTATATTTAAT
*
427691 ATTTTTATATTTACT
1 ATTTTTATATTTAAT
*
427706 TTTTTCTATATTT
1 ATTTT-TATATTT
427719 GTATAGTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTTTTATATTTAAT
Found at i:428481 original size:2 final size:2
Alignment explanation
Indices: 428476--428506 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
428466 AGAATTTAAA
428476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
428507 GGAAAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:428520 original size:6 final size:6
Alignment explanation
Indices: 428511--428654 Score: 55
Period size: 6 Copynumber: 23.7 Consensus size: 6
428501 TATATAGGAA
* * *
428511 AAAAAT AAAATAAT AATAAAT AAATAAT AATAAAT ACAAAT AATAAT AATAAT
1 AAAAAT -AAA-AAT AA-AAAT AAA-AAT AA-AAAT AAAAAT AAAAAT AAAAAT
* * * * ** * ***
428564 AATAAT AATAAT AATAAT AATAAT AATGAT ATTAAAT AAACCC AAAAA-
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT
* *
428612 GAAAAT -AAAAT AAAAAT ATAAGAT -AAAAT -AAAAT -AAAAT AAAA
1 AAAAAT AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT AAAAAT AAAA
428655 CGGAAAAAAT
Statistics
Matches: 112, Mismatches: 16, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
5 23 0.21
6 58 0.52
7 26 0.23
8 5 0.04
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (6 bp):
AAAAAT
Found at i:428525 original size:3 final size:3
Alignment explanation
Indices: 428514--428590 Score: 104
Period size: 3 Copynumber: 25.0 Consensus size: 3
428504 ATAGGAAAAA
428514 AAT AA- AAT AAT AAT AAAT AAAT AAT AAT AAAT ACA- AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT -AAT AAT AAT -AAT A-AT AAT AAT AAT AAT
428561 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
428591 GATATTAAAT
Statistics
Matches: 69, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
2 3 0.04
3 55 0.80
4 11 0.16
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:428637 original size:13 final size:11
Alignment explanation
Indices: 428511--428654 Score: 69
Period size: 12 Copynumber: 12.4 Consensus size: 11
428501 TATATAGGAA
428511 AAAAATAAAAT
1 AAAAATAAAAT
*
428522 AATAAT-AAAT
1 AAAAATAAAAT
428532 AAATAATAATAAAT
1 AAA-AAT-A-AAAT
*
428546 ACAAATAATAAT
1 AAAAATAA-AAT
*
428558 AATAATAATAAT
1 AAAAATAA-AAT
*
428570 AATAATAATAAT
1 AAAAATAA-AAT
* *
428582 AATAATAATGAT
1 AAAAATAA-AAT
* **
428594 ATTAAATAAACCC
1 A-AAAATAAA-AT
*
428607 AAAAAGAAAAT
1 AAAAATAAAAT
428618 -AAAATAAAAAT
1 AAAAAT-AAAAT
*
428629 ATAAGATAAAAT
1 A-AAAATAAAAT
428641 -AAAATAAAAT
1 AAAAATAAAAT
428651 AAAA
1 AAAA
428655 CGGAAAAAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 22
0.72 0.12 0.15
Matches are distributed among these distances:
10 19 0.18
11 17 0.16
12 49 0.47
13 13 0.12
14 6 0.06
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:428662 original size:23 final size:23
Alignment explanation
Indices: 428613--428672 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 23
428603 ACCCAAAAAG
*
428613 AAAATAAAATAAAAATATAAG-AT
1 AAAATAAAAT-AAAATAAAAGAAT
428636 AAAATAAAATAAAATAAAACGGAA-
1 AAAATAAAATAAAATAAAA--GAAT
428660 AAAATAATAATAA
1 AAAATAA-AATAA
428673 GAAGTAAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 8 0.25
23 10 0.31
24 8 0.25
25 6 0.19
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (23 bp):
AAAATAAAATAAAATAAAAGAAT
Found at i:431272 original size:15 final size:15
Alignment explanation
Indices: 431252--431313 Score: 124
Period size: 15 Copynumber: 4.1 Consensus size: 15
431242 GTAGGACCAT
431252 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
431267 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
431282 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
431297 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
431312 TA
1 TA
431314 TTATACCCTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:431475 original size:12 final size:12
Alignment explanation
Indices: 431458--431507 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
431448 TATCGTGTTC
431458 TCATATCACATG
1 TCATATCACATG
*
431470 TCATATCACATA
1 TCATATCACATG
431482 TCATATCACATG
1 TCATATCACATG
*
431494 AACATAT-ACATG
1 -TCATATCACATG
431506 TC
1 TC
431508 TTATGCATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 1 0.03
12 27 0.82
13 5 0.15
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (12 bp):
TCATATCACATG
Found at i:431907 original size:64 final size:64
Alignment explanation
Indices: 431801--431977 Score: 239
Period size: 64 Copynumber: 2.8 Consensus size: 64
431791 TAATGAAGGT
* * * ** **
431801 ATGCATCGATGCACTACTGATGCATCGGTGCATCAAAGGCATTCGATGTAGT-ATTATTATTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-GTCATTATTAACGGG
* *
431865 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAACGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTGTCATTATTAACGGG
* *
431929 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTACATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT
431978 TTTGATTTTA
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
63 1 0.01
64 99 0.99
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTGTCATTATTAACGGG
Found at i:431978 original size:64 final size:62
Alignment explanation
Indices: 431801--432026 Score: 233
Period size: 64 Copynumber: 3.5 Consensus size: 62
431791 TAATGAAGGT
* * ** * **
431801 ATGCATCGATGCACTACTGATGCATCGGTGCATCAAAGGCATTCGATGTAGTATTATTATTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CAATTGCATTCGATGT-TTATTATTAACGGG
*
431865 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAACGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CAATTGCATTCGATGTTT-ATTATTAACGGG
* **
431929 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTACATTCGATGTTTTGATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCAC-AATTGCATTCGATG-TTT-ATTATTAACGGG
* *
431992 AGTGCATAGATGCACTA-TCAATGCATCGATGCACA
1 A-TGCATCGATGCACTACT-TATGCATCGATGCACA
432027 TTCAAACAAT
Statistics
Matches: 141, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
63 6 0.04
64 129 0.91
65 6 0.04
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (62 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAATTGCATTCGATGTTTATTATTAACGGG
Found at i:436662 original size:15 final size:15
Alignment explanation
Indices: 436642--436688 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
436632 GTAGGACCAT
436642 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
436657 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
436672 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
436687 TA
1 TA
436689 TTATACCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:436850 original size:12 final size:12
Alignment explanation
Indices: 436833--436882 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
436823 TATCGTGTTC
436833 TCATATCACATG
1 TCATATCACATG
*
436845 TCATATCACATA
1 TCATATCACATG
436857 TCATATCACATG
1 TCATATCACATG
*
436869 AACATAT-ACATG
1 -TCATATCACATG
436881 TC
1 TC
436883 TTATGCATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 1 0.03
12 27 0.82
13 5 0.15
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (12 bp):
TCATATCACATG
Found at i:437284 original size:64 final size:64
Alignment explanation
Indices: 437176--437400 Score: 233
Period size: 64 Copynumber: 3.5 Consensus size: 64
437166 TAATGAAGGT
* * * ** * **
437176 ATGCATCGATGCACTACTGATGCATCGGTGCATCAAAGGTATTCGATGTAGT-ATTATTATTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-GTCATTATTAACGGG
* *
437240 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAACGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTGTCATTATTAACGGG
* * * * **
437304 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTACATTCGATGTTTTGATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATG-TGTCATTATTAACGGG
*
437367 AGTGCATCGATGCACTA-TCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACT-TATGCATCGATGCAC
437401 ATTCAAACAA
Statistics
Matches: 140, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
63 4 0.03
64 130 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTGTCATTATTAACGGG
Found at i:439687 original size:22 final size:22
Alignment explanation
Indices: 439659--439714 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
439649 GGGTTTATTA
*
439659 GTCCTTCAGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
439681 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
439703 GTCTTTCGGGAC
1 GTCCTTCGGGAC
439715 AAATACTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.29
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:441982 original size:19 final size:20
Alignment explanation
Indices: 441960--441999 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
441950 ATATCCAGAA
*
441960 CCTG-AGGGGGTATCGATTC
1 CCTGTAGGGGGAATCGATTC
441979 CCTGTAGGGGGAATCGATTC
1 CCTGTAGGGGGAATCGATTC
441999 C
1 C
442000 TATTCAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.17, C:0.23, G:0.35, T:0.25
Consensus pattern (20 bp):
CCTGTAGGGGGAATCGATTC
Found at i:442014 original size:23 final size:21
Alignment explanation
Indices: 441984--442044 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 21
441974 GATTCCCTGT
441984 AGGGGGAATCGATTCCTATTCAA
1 AGGGGGAATCGATTCCTATT--A
* **
442007 AGGGGGAATCGGTTCCCCTTA
1 AGGGGGAATCGATTCCTATTA
*
442028 AGGGGGTATCGATTCCT
1 AGGGGGAATCGATTCCT
442045 CTTGCCAGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 15 0.47
23 17 0.53
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (21 bp):
AGGGGGAATCGATTCCTATTA
Found at i:445898 original size:22 final size:21
Alignment explanation
Indices: 445856--445895 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
445846 AAGACTGTTT
445856 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
445877 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
445896 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:447917 original size:19 final size:20
Alignment explanation
Indices: 447893--447933 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
447883 AAACCATTCA
447893 GGGGGAATCGGTACCC-CTG
1 GGGGGAATCGGTACCCTCTG
*
447912 GGGGGAATCGGTTCCCTCTG
1 GGGGGAATCGGTACCCTCTG
447932 GG
1 GG
447934 CAATCTGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.12, C:0.24, G:0.44, T:0.20
Consensus pattern (20 bp):
GGGGGAATCGGTACCCTCTG
Found at i:448284 original size:29 final size:28
Alignment explanation
Indices: 448226--448291 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
448216 AAAAATATCA
* *
448226 AAAAGAAAATGAAAAAAAGGACTAATTT
1 AAAAGAAAATGAAAAAAAGGACAAAATT
* **
448254 AAAAGAAAATGAAATTAGGGGACAAAATT
1 AAAAGAAAATGAAA-AAAAGGACAAAATT
448283 AAAAGAAAA
1 AAAAGAAAA
448292 ATCAAGGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 14 0.44
29 18 0.56
ACGTcount: A:0.65, C:0.03, G:0.17, T:0.15
Consensus pattern (28 bp):
AAAAGAAAATGAAAAAAAGGACAAAATT
Found at i:449364 original size:15 final size:14
Alignment explanation
Indices: 449309--449364 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 14
449299 TTTAAAACCC
449309 TAAAAA-ATATTTT
1 TAAAAATATATTTT
449322 TCAAAATAATATATTTT
1 T--AAA-AATATATTTT
* *
449339 CAAAAAAATATTTT
1 TAAAAATATATTTT
449353 TAAAAACTATAT
1 TAAAAA-TATAT
449365 ATTATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 1 0.03
14 14 0.41
15 10 0.29
16 2 0.06
17 7 0.21
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAAATATATTTT
Found at i:449384 original size:38 final size:36
Alignment explanation
Indices: 449330--449627 Score: 170
Period size: 38 Copynumber: 8.4 Consensus size: 36
449320 TTTCAAAATA
449330 ATATATTTTCAAAAAAATATTTTTAAAAACTATATATT
1 ATATATTTTC--AAAAATATTTTTAAAAACTATATATT
449368 ATATATATATTCAAAAA-ATGTTTTAAAAACTATATAATAT
1 ATATAT-T-TTCAAAAATAT-TTTTAAAAACTATAT-AT-T
* * * *
449408 ATATGTTTTCCAAAAT-GTTTTCAAAACTTATATATT
1 ATATATTTTCAAAAATATTTTTAAAAAC-TATATATT
*
449444 ATATGTTTTC-AAAA-A----T------TATATATT
1 ATATATTTTCAAAAATATTTTTAAAAACTATATATT
* * *
449468 ATATGTTTTCAAAAATGTTTTAAAAAAACTATATATT
1 ATATATTTTCAAAAATATTTT-TAAAAACTATATATT
* *
449505 ATATAAGTTTTCAAAAATGA-TTTTAAAACCCATATAATAT
1 ATAT-A-TTTTCAAAAAT-ATTTTTAAAAACTATAT-AT-T
* * *
449545 ATATATTTTCTAAAAT-GTTTTCAAAACTATATATT
1 ATATATTTTCAAAAATATTTTTAAAAACTATATATT
449580 ATATAGTTTTC--AAA-A-TTTTAAAAACT-TATTATAT
1 ATATA-TTTTCAAAAATATTTTTAAAAACTATA-TAT-T
*
449614 ACATATTTTCAAAA
1 ATATATTTTCAAAA
449628 TCCATTTGCA
Statistics
Matches: 210, Mismatches: 17, Indels: 69
0.71 0.06 0.23
Matches are distributed among these distances:
24 18 0.09
25 4 0.02
31 1 0.00
32 2 0.01
33 18 0.09
34 8 0.04
35 12 0.06
36 18 0.09
37 37 0.18
38 57 0.27
39 21 0.10
40 14 0.07
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.44
Consensus pattern (36 bp):
ATATATTTTCAAAAATATTTTTAAAAACTATATATT
Found at i:449454 original size:24 final size:24
Alignment explanation
Indices: 449422--449483 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
449412 GTTTTCCAAA
*
449422 ATGTTTTCAAAACTTATATATTAT
1 ATGTTTTCAAAAATTATATATTAT
449446 ATGTTTTCAAAAATTATATATTAT
1 ATGTTTTCAAAAATTATATATTAT
449470 ATGTTTTCAAAAAT
1 ATGTTTTCAAAAAT
449484 GTTTTAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.48
Consensus pattern (24 bp):
ATGTTTTCAAAAATTATATATTAT
Found at i:449641 original size:69 final size:72
Alignment explanation
Indices: 449492--449653 Score: 181
Period size: 69 Copynumber: 2.2 Consensus size: 72
449482 ATGTTTTAAA
* *
449492 AAAACTATATATTATATAAGTTTTCAAAAATGATTTTAAAACCCATATAATATATATATTTTCTA
1 AAAACTATATATTATAT-AGTTTTC-AAAA-GATTTTAAAACACATATAATATACATATTTTCTA
* *
449557 AAATGTTTTC
63 AAATATTTGC
* *
449567 AAAACTATATATTATATAGTTTTC-AAA-ATTTTAAAA-ACTTATTATATACATATTTTC-AAAA
1 AAAACTATATATTATATAGTTTTCAAAAGATTTTAAAACACATATAATATACATATTTTCTAAAA
449628 TCCATTTGC
66 T--ATTTGC
*
449637 -AAACTATATAATATATA
1 AAAACTATATATTATATA
449654 TATGTATATA
Statistics
Matches: 78, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
68 5 0.06
69 33 0.42
70 13 0.17
72 3 0.04
74 7 0.09
75 17 0.22
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (72 bp):
AAAACTATATATTATATAGTTTTCAAAAGATTTTAAAACACATATAATATACATATTTTCTAAAA
TATTTGC
Found at i:450579 original size:24 final size:23
Alignment explanation
Indices: 450552--450598 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
450542 AAATTATTAA
450552 AAAACAAAAAATATATTTATATAT
1 AAAA-AAAAAATATATTTATATAT
* *
450576 -AAAATATAATATATTTATATAT
1 AAAAAAAAAATATATTTATATAT
450598 A
1 A
450599 TTAAATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAAAAAAAATATATTTATATAT
Found at i:450677 original size:16 final size:16
Alignment explanation
Indices: 450656--450717 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
450646 TAAAATTAAT
450656 TATATTATAAAATATA
1 TATATTATAAAATATA
* *
450672 TATATTCTTTAAAATTTA
1 TATA-T-TATAAAATATA
* *
450690 TAAATTATTAAATATA
1 TATATTATAAAATATA
*
450706 TTTATTA-AAAAT
1 TATATTATAAAAT
450718 GGAAATTTAT
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
15 4 0.11
16 17 0.49
17 2 0.06
18 12 0.34
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATTATAAAATATA
Found at i:450703 original size:34 final size:35
Alignment explanation
Indices: 450645--450711 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
450635 TAATAAATTA
*
450645 TTAAAATTAATTATATTATAAAATATATATATTCT
1 TTAAAATTAATTAAATTATAAAATATATATATTCT
* * *
450680 TTAAAATTTA-TAAATTATTAAATATATTTATT
1 TTAAAATTAATTAAATTATAAAATATATATATT
450712 AAAAATGGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 19 0.68
35 9 0.32
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (35 bp):
TTAAAATTAATTAAATTATAAAATATATATATTCT
Found at i:451453 original size:29 final size:29
Alignment explanation
Indices: 451407--451494 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
451397 AGGGCACAGG
*
451407 ACAAGGTCGCCCAGCGTGCATGGCGACCT
1 ACAAGGTCGCCCGGCGTGCATGGCGACCT
* * * *
451436 ACCATGTTGCCTGGCGTGCATGGCGACCT
1 ACAAGGTCGCCCGGCGTGCATGGCGACCT
* *
451465 ACAAGGTCGCCCGGAGGGCATGGCGACCT
1 ACAAGGTCGCCCGGCGTGCATGGCGACCT
451494 A
1 A
451495 TGCTGGGAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.19, C:0.32, G:0.33, T:0.16
Consensus pattern (29 bp):
ACAAGGTCGCCCGGCGTGCATGGCGACCT
Found at i:454171 original size:6 final size:6
Alignment explanation
Indices: 454160--454190 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
454150 TTTTCCAAAA
*
454160 CCTAAC CCTAAC CCTAGC CCTAAC CCTAAC C
1 CCTAAC CCTAAC CCTAAC CCTAAC CCTAAC C
454191 TATTTCTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.29, C:0.52, G:0.03, T:0.16
Consensus pattern (6 bp):
CCTAAC
Found at i:460583 original size:24 final size:24
Alignment explanation
Indices: 460556--460635 Score: 83
Period size: 23 Copynumber: 3.3 Consensus size: 24
460546 AAATCAGAAG
460556 AAAAAAATCCTCAACATTCAAATA
1 AAAAAAATCCTCAACATTCAAATA
* * * *
460580 AAAAAAAACC-AAAAATT-AGAAGA
1 AAAAAAATCCTCAACATTCA-AATA
460603 AAAAAAATCCTCAACATTCAAATCA
1 AAAAAAATCCTCAACATTCAAAT-A
460628 TAAAAAAA
1 -AAAAAAA
460636 CCAAAAATCA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
22 1 0.02
23 17 0.40
24 16 0.37
25 2 0.05
26 7 0.16
ACGTcount: A:0.65, C:0.16, G:0.03, T:0.16
Consensus pattern (24 bp):
AAAAAAATCCTCAACATTCAAATA
Found at i:460601 original size:46 final size:46
Alignment explanation
Indices: 460530--460656 Score: 209
Period size: 47 Copynumber: 2.7 Consensus size: 46
460520 CTCTACATAT
460530 AATAAAAAAAAACCAAAAATCAGAAGAAAAAAATCCTCAACATTCA
1 AATAAAAAAAAACCAAAAATCAGAAGAAAAAAATCCTCAACATTCA
*
460576 AATAAAAAAAAACCAAAAATTAGAAGAAAAAAAATCCTCAACATTCA
1 AATAAAAAAAAACCAAAAATCAGAAG-AAAAAAATCCTCAACATTCA
* *
460623 AATCATAAAAAAACCAAAAATCAAAAGAAAAAAA
1 AAT-AAAAAAAAACCAAAAATCAGAAGAAAAAAA
460657 ATTATAGCGC
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
46 25 0.33
47 30 0.40
48 20 0.27
ACGTcount: A:0.69, C:0.15, G:0.04, T:0.13
Consensus pattern (46 bp):
AATAAAAAAAAACCAAAAATCAGAAGAAAAAAATCCTCAACATTCA
Found at i:460633 original size:48 final size:47
Alignment explanation
Indices: 460530--460658 Score: 215
Period size: 48 Copynumber: 2.7 Consensus size: 47
460520 CTCTACATAT
460530 AATAAAAAAAAACCAAAAATCAGAAG-AAAAAAATCCTCAACATTCA
1 AATAAAAAAAAACCAAAAATCAGAAGAAAAAAAATCCTCAACATTCA
*
460576 AATAAAAAAAAACCAAAAATTAGAAGAAAAAAAATCCTCAACATTCA
1 AATAAAAAAAAACCAAAAATCAGAAGAAAAAAAATCCTCAACATTCA
* *
460623 AATCATAAAAAAACCAAAAATCAAAAGAAAAAAAAT
1 AAT-AAAAAAAAACCAAAAATCAGAAGAAAAAAAAT
460659 TATAGCGCAG
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
46 25 0.32
47 23 0.30
48 29 0.38
ACGTcount: A:0.68, C:0.15, G:0.04, T:0.13
Consensus pattern (47 bp):
AATAAAAAAAAACCAAAAATCAGAAGAAAAAAAATCCTCAACATTCA
Found at i:463707 original size:3 final size:3
Alignment explanation
Indices: 463699--463752 Score: 99
Period size: 3 Copynumber: 17.7 Consensus size: 3
463689 ACCTAAAGAT
463699 TTA TTA TTA TTA 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 TTA TTA
463747 TATA TT
1 T-TA TT
463753 TTAAAATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:471415 original size:61 final size:62
Alignment explanation
Indices: 471348--471503 Score: 187
Period size: 61 Copynumber: 2.5 Consensus size: 62
471338 ATCCCTTGAC
* *
471348 GGTGCATCGATGCACTATCTATGCATCGATACA-TAAAT-CCTATTCGATGTTTGTA-TTAAGG
1 GGTGCATCGATGCACTATCTGTGCATCGATACACT-AATGCC-ATTCGATGTTTGTATTTAAAG
* * * *
471409 GGTGCATCGATGCACTA-CTGTGCATCGATACACTGATGGCATTCGATGTTTTTATTTAAAT
1 GGTGCATCGATGCACTATCTGTGCATCGATACACTAATGCCATTCGATGTTTGTATTTAAAG
*
471470 AGTGCATCGATGCACT-TCATGTGCATCGATACAC
1 GGTGCATCGATGCACTATC-TGTGCATCGATACAC
471504 CTTGAACAGT
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
60 29 0.35
61 39 0.47
62 15 0.18
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (62 bp):
GGTGCATCGATGCACTATCTGTGCATCGATACACTAATGCCATTCGATGTTTGTATTTAAAG
Found at i:477091 original size:42 final size:42
Alignment explanation
Indices: 477020--477487 Score: 346
Period size: 43 Copynumber: 11.0 Consensus size: 42
477010 AAGGTAATTA
* * *
477020 GCGGTGTTTGTATCCAAAAAGCCGTTATAGATCT-GACCTTTT
1 GCGGCGTTTGT-TCAAAAAAGCCGCTATAGATCTAGACCTTTT
* * * * *
477062 ACGGCGATTGTATCAAAAAAGCTGCTATAGATCTCGACTTTTT
1 GCGGCGTTTGT-TCAAAAAAGCCGCTATAGATCTAGACCTTTT
* *
477105 GCAGCGTTTGTTCCAAAAAAACCGCTATAGAT-TAGACCTTTT
1 GCGGCGTTTGTT-CAAAAAAGCCGCTATAGATCTAGACCTTTT
*
477147 GCGGCGTTTATTCCAAAAATA-CCGCTATAGATCTAGACCTTTT
1 GCGGCGTTTGTT-CAAAAA-AGCCGCTATAGATCTAGACCTTTT
* *
477190 GCGGCGTTTGTTCCAAAAACA-TCGCTATAGATC-AAACCTTTT
1 GCGGCGTTTGTT-CAAAAA-AGCCGCTATAGATCTAGACCTTTT
** * * *
477232 GTAGAGTTTGTTTCAAAAATGCCGCTATAGATCTAAACCTTTT
1 GCGGCGTTTG-TTCAAAAAAGCCGCTATAGATCTAGACCTTTT
* * * *
477275 GCGGCGTTTGTTCAAAAAGCGCCGCTATAGATATCA-TCCTTTA
1 GCGGCGTTTGTTCAAAAA-AGCCGCTATAGATCT-AGACCTTTT
* * * * * * *
477318 ACGGCATTTGTTCCAAAAACGTCGCTATCGATTTTGACCTTTT
1 GCGGCGTTTGTT-CAAAAAAGCCGCTATAGATCTAGACCTTTT
** *
477361 GCGGCGTTTGTTCAAAAAACGTTGCTATAGATATCA-ACCTTTT
1 GCGGCGTTTGTTCAAAAAA-GCCGCTATAGATCT-AGACCTTTT
* * * * *
477404 GTGGCGTTTGTTCCAAAAACA-CCGCTATCGATATCGATCTTTT
1 GCGGCGTTTGTT-CAAAAA-AGCCGCTATAGATCTAGACCTTTT
* * * * *
477447 GTGGCG-TT-CT-AAAAACGCCGCTATAGATCTTGACCTATT
1 GCGGCGTTTGTTCAAAAAAGCCGCTATAGATCTAGACCTTTT
477486 GC
1 GC
477488 AACGTTTTTT
Statistics
Matches: 348, Mismatches: 61, Indels: 37
0.78 0.14 0.08
Matches are distributed among these distances:
39 23 0.07
41 1 0.00
42 113 0.32
43 197 0.57
44 13 0.04
45 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (42 bp):
GCGGCGTTTGTTCAAAAAAGCCGCTATAGATCTAGACCTTTT
Found at i:477134 original size:85 final size:84
Alignment explanation
Indices: 477020--477379 Score: 295
Period size: 85 Copynumber: 4.2 Consensus size: 84
477010 AAGGTAATTA
* * *
477020 GCGGTGTTTGTATCC-AAAAAGCCGTTATAGATCTGACCTTTTACGGCGATTGTATCAAAAAAGC
1 GCGGCGTTTGT-TCCAAAAAAACCGCTATAGATCTGACCTTTTACGGCGATTGTATCAAAAAA-C
* * *
477084 TGCTATAGATCTCGACTTTTT
64 CGCTATAGATCTAGACCTTTT
* *
477105 GCAGCGTTTGTTCCAAAAAAACCGCTATAGAT-TAGACCTTTTGCGGCG-TT-TATTCCAAAAAT
1 GCGGCGTTTGTTCCAAAAAAACCGCTATAGATCT-GACCTTTTACGGCGATTGTA-T-CAAAAA-
477167 ACCGCTATAGATCTAGACCTTTT
62 ACCGCTATAGATCTAGACCTTTT
* * ** *** * * * *
477190 GCGGCGTTTGTTCCAAAAACATCGCTATAGATCAAACCTTTTGTAGAGTTTGTTTCAAAAATGCC
1 GCGGCGTTTGTTCCAAAAAAACCGCTATAGATCTGACCTTTTACGGCGATTGTATCAAAAA-ACC
*
477255 GCTATAGATCTAAACCTTTT
65 GCTATAGATCTAGACCTTTT
** * * * *
477275 GCGGCGTTTGTT-CAAAAAGCGCCGCTATAGATATCATCCTTTAACGGC-ATTTGT-TCCAAAAA
1 GCGGCGTTTGTTCCAAAAA-AACCGCTATAGATCTGA-CCTTTTACGGCGA-TTGTATCAAAAAA
* * *
477337 CGTCGCTATCGATTTTGACCTTTT
63 C--CGCTATAGATCTAGACCTTTT
477361 GCGGCGTTTGTT-CAAAAAA
1 GCGGCGTTTGTTCCAAAAAA
477380 CGTTGCTATA
Statistics
Matches: 225, Mismatches: 37, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
83 2 0.01
84 14 0.06
85 159 0.71
86 49 0.22
87 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (84 bp):
GCGGCGTTTGTTCCAAAAAAACCGCTATAGATCTGACCTTTTACGGCGATTGTATCAAAAAACCG
CTATAGATCTAGACCTTTT
Found at i:478047 original size:34 final size:34
Alignment explanation
Indices: 478004--478128 Score: 111
Period size: 34 Copynumber: 3.8 Consensus size: 34
477994 TTCGTCCTAC
*
478004 TAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
478038 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
478073 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * * *
478102 TATGATTTAAACTACTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
478129 CCACAAGCAC
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 38 0.52
35 4 0.05
37 8 0.11
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:478454 original size:2 final size:2
Alignment explanation
Indices: 478449--478489 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
478439 TTTACTTTAG
* *
478449 TA TA TA TA TA TA TA TA TA TT TA GA T- TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
478489 T
1 T
478490 TTTTTTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:478537 original size:20 final size:20
Alignment explanation
Indices: 478455--478554 Score: 75
Period size: 20 Copynumber: 5.0 Consensus size: 20
478445 TTAGTATATA
** *
478455 TATATATATATATTTAGATTA
1 TATATATATATA-TTATTTTT
478476 TATATATAATATATT-TTTTT
1 TATATAT-ATATATTATTTTT
* *
478496 T-TATCAGT-TTTATTA-ATTT
1 TATAT-A-TATATATTATTTTT
478515 TATATATATAT-TTACTTTTT
1 TATATATATATATTA-TTTTT
478535 TATATATATATATTATTTTT
1 TATATATATATATTATTTTT
478555 ACTTTTTTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
18 4 0.06
19 15 0.24
20 26 0.41
21 13 0.21
22 5 0.08
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TATATATATATATTATTTTT
Found at i:478595 original size:50 final size:49
Alignment explanation
Indices: 478513--478632 Score: 122
Period size: 50 Copynumber: 2.4 Consensus size: 49
478503 TTTTATTAAT
*
478513 TTTA-TATATATATTTACTTTTTTATATATATATATTATTTT-TACTTTTT-
1 TTTATTATTTATATTTA-TTTTTTATATATATAT-TT-TTTTCTACTTTTTC
* * *
478562 TATTATTATTT-TATTTATTTGTTTATTTCTATATTTTTTTCTTCTTTTTC
1 T-TTATTATTTATATTTATTT-TTTATATATATATTTTTTTCTACTTTTTC
*
478612 TTTATTTTTTATATTTATTTT
1 TTTATTATTTATATTTATTTT
478633 ACTTACTATT
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
48 4 0.07
49 22 0.37
50 30 0.50
51 4 0.07
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (49 bp):
TTTATTATTTATATTTATTTTTTATATATATATTTTTTTCTACTTTTTC
Found at i:478741 original size:14 final size:15
Alignment explanation
Indices: 478716--478744 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
478706 TATTTATTTC
478716 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
478731 TTACC-TTTTATCTA
1 TTACCTTTTTATCTA
478745 ACATGGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:480670 original size:18 final size:18
Alignment explanation
Indices: 480635--480685 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
480625 CTTCAAGTCT
480635 GATTCACATCC-C--CTG
1 GATTCACATCCACTTCTG
480650 GATTCACATCCACTTCTG
1 GATTCACATCCACTTCTG
480668 GATTCACATCCACTTCTG
1 GATTCACATCCACTTCTG
480686 AAAGACTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
15 11 0.33
16 1 0.03
18 21 0.64
ACGTcount: A:0.22, C:0.35, G:0.12, T:0.31
Consensus pattern (18 bp):
GATTCACATCCACTTCTG
Found at i:481211 original size:8 final size:8
Alignment explanation
Indices: 481198--481236 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
481188 GAACATTTCA
*
481198 TGCATTCT
1 TGCATTTT
481206 TGCA-TTT
1 TGCATTTT
481213 TGCATTTT
1 TGCATTTT
*
481221 TGCCTTTT
1 TGCATTTT
481229 TGCATTTT
1 TGCATTTT
481237 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:482345 original size:13 final size:13
Alignment explanation
Indices: 482327--482369 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
482317 CAATCAGAAT
482327 AAAAAAGGCAAAA
1 AAAAAAGGCAAAA
482340 AAAAAAGAAGCAAAA
1 AAAAAAG--GCAAAA
482355 AACAAAA-GCAAAA
1 AA-AAAAGGCAAAA
482368 AA
1 AA
482370 GAATAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 15 0.56
15 8 0.30
16 4 0.15
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGGCAAAA
Found at i:482354 original size:14 final size:13
Alignment explanation
Indices: 482327--482369 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
482317 CAATCAGAAT
*
482327 AAAAAAGGCAAAAA
1 AAAAAAAGC-AAAA
482341 AAAAAGAAGCAAAA
1 AAAAA-AAGCAAAA
*
482355 AACAAAAGCAAAA
1 AAAAAAAGCAAAA
482368 AA
1 AA
482370 GAATAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 10 0.38
14 13 0.50
15 3 0.12
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAGCAAAA
Found at i:483009 original size:22 final size:22
Alignment explanation
Indices: 482983--483026 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
482973 AGCTACCCCA
482983 TCAAACC-TTTAAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
483005 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
483027 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:483032 original size:23 final size:22
Alignment explanation
Indices: 482984--483032 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
482974 GCTACCCCAT
*
482984 CAAACCTTTAAGCATCAAATGT
1 CAAACCTTTAAGCATCAAATGA
483006 CAAACCATTT-AGCATCAAATGAA
1 CAAACC-TTTAAGCATCAAATG-A
483029 CAAA
1 CAAA
483033 AATGCCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.47, C:0.22, G:0.08, T:0.22
Consensus pattern (22 bp):
CAAACCTTTAAGCATCAAATGA
Found at i:483486 original size:18 final size:18
Alignment explanation
Indices: 483463--483498 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
483453 TCAACATCAA
* *
483463 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
483481 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
483499 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:484021 original size:36 final size:36
Alignment explanation
Indices: 483978--484127 Score: 255
Period size: 36 Copynumber: 4.1 Consensus size: 36
483968 ACTAGAAGAG
483978 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
484014 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
484050 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
484086 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
484122 TATTTG
1 T-TTTG
484128 AATATGTTTC
Statistics
Matches: 105, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
36 101 0.96
37 4 0.04
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:484021 original size:71 final size:73
Alignment explanation
Indices: 483936--484256 Score: 239
Period size: 72 Copynumber: 4.6 Consensus size: 73
483926 GTTTTTCTTA
* * * * * *
483936 AAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCACTAG-AA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
483998 TTTCCCTTG
65 TTTCCCTTG
* *
484007 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
484071 TTCCCTTG
66 TTCCCTTG
* * * *
484079 AAATAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA-------TAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACA-G
*
484134 TTT-CTTTG
65 TTTCCCTTG
* * ** * * * * *
484142 AAACAAATTTCGTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAAC-AAATTTCGTCTATCTTGAGACAG
*
484206 TTTCTCTTG
65 TTTCCCTTG
* * *
484215 AAAC-AATTTTCGTCTATC-TGAGACAG-TTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTTCACTAGAAACAAA
484257 ATCTTTGAAT
Statistics
Matches: 204, Mismatches: 30, Indels: 32
0.77 0.11 0.12
Matches are distributed among these distances:
63 40 0.20
64 10 0.05
65 3 0.01
70 8 0.04
71 29 0.14
72 100 0.49
73 14 0.07
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
TTCCCTTG
Found at i:484080 original size:72 final size:71
Alignment explanation
Indices: 483979--484256 Score: 308
Period size: 72 Copynumber: 4.0 Consensus size: 71
483969 CTAGAAGAGT
* *
483979 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
484044 AACAAA
66 AACAAA
*
484050 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
484115 AAACAAA
65 AAACAAA
* * * * **
484122 ------TAT-TTGA-ATATGTTT-CTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTG
1 TTTGTCTATCTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
484178 GAACTAAGT
65 AAAC-AA-A
* * *
484187 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AATTTTCGTCTATC-TGAGACAGTTTCCCTTG
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTG
484250 AAACAAA
65 AAACAAA
484257 ATCTTTGAAT
Statistics
Matches: 170, Mismatches: 23, Indels: 29
0.77 0.10 0.13
Matches are distributed among these distances:
63 40 0.24
64 10 0.06
65 3 0.02
71 7 0.04
72 96 0.56
73 14 0.08
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (71 bp):
TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
AACAAA
Found at i:484164 original size:135 final size:135
Alignment explanation
Indices: 483998--484318 Score: 414
Period size: 136 Copynumber: 2.4 Consensus size: 135
483988 CTTGAGACAG
*
483998 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAA-TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
*
484063 GAGACAGTTTCCCTTGAAATAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATATT
65 GAGACAGTTTCCCTTGAAA-AAATTTTCGTCTATC-TGAGACAGTTTCCCTTGAAACAAAATATT
*
484126 TGAATATG
128 TGAATATA
* * * * * *
484134 TTT-CTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTT-GTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * *
484198 TGAGACAGTTTCTCTTGAAACAATTTTCGTCTATCTGAGACAGTTTCCCTTGAAACAAAATCTTT
64 TGAGACAGTTTCCCTTGAAAAAATTTTCGTCTATCTGAGACAGTTTCCCTTGAAACAAAATATTT
*
484263 GAATTTA
129 GAATATA
* * * * *
484270 TTTCCCCTAAAACAAATTTGTCTCCTTTGAGACAATTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
484319 CAAATCTTCA
Statistics
Matches: 159, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
134 3 0.02
135 65 0.41
136 79 0.50
137 12 0.08
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (135 bp):
TTTCCCTTGAAACAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTG
AGACAGTTTCCCTTGAAAAAATTTTCGTCTATCTGAGACAGTTTCCCTTGAAACAAAATATTTGA
ATATA
Found at i:484215 original size:100 final size:100
Alignment explanation
Indices: 484033--484220 Score: 297
Period size: 100 Copynumber: 1.9 Consensus size: 100
484023 TCTTGAGACA
*
484033 GTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCT
1 GTTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCT
484098 TGAGACAGTTTCCCTTGAAACAAATATTTGAATAT
66 TGAGACAGTTTCCCTTGAAACAAATATTTGAATAT
* ** * *
484133 GTTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC
1 GTTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTC
*
484197 TTGAGACAGTTTCTCTTGAAACAA
65 TTGAGACAGTTTCCCTTGAAACAA
484221 TTTTCGTCTA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 34 0.43
100 46 0.57
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (100 bp):
GTTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCT
TGAGACAGTTTCCCTTGAAACAAATATTTGAATAT
Found at i:484244 original size:35 final size:36
Alignment explanation
Indices: 484133--484255 Score: 153
Period size: 35 Copynumber: 3.4 Consensus size: 36
484123 ATTTGAATAT
* *
484133 GTTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCTCTTGAAACAATTTTCGTCTCTCTTGAGACA
* *
484168 GTTTCTTTTGGAACTAAGTTTT-GTCTCTCTTGAGACA
1 GTTTCTCTTGAAAC-AA-TTTTCGTCTCTCTTGAGACA
*
484205 GTTTCTCTTGAAACAATTTTCGTCTATC-TGAGACA
1 GTTTCTCTTGAAACAATTTTCGTCTCTCTTGAGACA
*
484240 GTTTCCCTTGAAACAA
1 GTTTCTCTTGAAACAA
484256 AATCTTTGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
35 32 0.42
36 14 0.18
37 28 0.36
38 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.40
Consensus pattern (36 bp):
GTTTCTCTTGAAACAATTTTCGTCTCTCTTGAGACA
Found at i:484316 original size:64 final size:67
Alignment explanation
Indices: 484246--484369 Score: 182
Period size: 65 Copynumber: 1.9 Consensus size: 67
484236 GACAGTTTCC
** *
484246 CTTGAAACA-AAATCTTTGAATTTATTTCCCCTAAAACA-AA-TTTGTCTCCTTTGAGACAATTA
1 CTTGAAACACAAATCTTCAAATTTATTTCCCCTAAAACATAATTTTGTCTCCCTTGAGACAATTA
484308 CT
66 CT
* *
484310 CTTGAAACACAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTTTCCCTTGAGAC
1 CTTGAAACACAAATCTTCAAATTTATTTCCCCTAAAACATAATTTTGTCTCCCTTGAGAC
484370 CGTTTCTCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
64 9 0.17
65 26 0.50
66 2 0.04
67 15 0.29
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (67 bp):
CTTGAAACACAAATCTTCAAATTTATTTCCCCTAAAACATAATTTTGTCTCCCTTGAGACAATTA
CT
Found at i:485227 original size:105 final size:105
Alignment explanation
Indices: 484990--485650 Score: 870
Period size: 105 Copynumber: 6.3 Consensus size: 105
484980 GCCATCTGCG
* * * * * *
484990 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
485055 GGGACGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACGACTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
485099 ATTTCAACTTCACAATGATGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
485164 ACCG-CTGCTTGTCAACAACAACTTCTTAATTTCAGAGCCA
66 A-CGACTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
485204 ATTTCAACTTCACAACAAAGGATATGGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
485269 ACCG-CTGCTTGTCAACAACAACTTCCCAATCTCATAGCCA
66 A-CGACTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
485309 ATTTCAACTTCACAACGAAGGATATTGGACTCCATACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
485374 ACCG-CTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 A-CGACTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
485414 ATTTCAATTTCACAACGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
485479 ACGACTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACGACTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
485514 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * ** *
485579 ACGACTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACGACTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* * *
485620 ATTTCAACTTCACGACGGAGGATATTAGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
485651 TGGAACAATG
Statistics
Matches: 497, Mismatches: 47, Indels: 19
0.88 0.08 0.03
Matches are distributed among these distances:
100 82 0.16
101 3 0.01
102 3 0.01
103 4 0.01
104 5 0.01
105 294 0.59
106 81 0.16
107 5 0.01
109 20 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACGACTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:486229 original size:34 final size:34
Alignment explanation
Indices: 486186--486310 Score: 120
Period size: 34 Copynumber: 3.8 Consensus size: 34
486176 TTCGTCCTAC
486186 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
486220 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
486255 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * * *
486284 TATGATTTAAACTACTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
486311 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:486632 original size:25 final size:25
Alignment explanation
Indices: 486588--486656 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
486578 TCATGTAATA
* *
486588 TTTTTTACATTTTATGTA-TTTTCT
1 TTTTTTACATTTTATATATTTTTAT
486612 TTTTTTAC-TTTAGTATATATTTTTAT
1 TTTTTTACATTT--TATATATTTTTAT
* *
486638 TTTTTTAGATTATATATAT
1 TTTTTTACATTTTATATAT
486657 AATATATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 3 0.08
24 8 0.22
25 12 0.32
26 12 0.32
27 2 0.05
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.68
Consensus pattern (25 bp):
TTTTTTACATTTTATATATTTTTAT
Found at i:486755 original size:32 final size:33
Alignment explanation
Indices: 486681--486759 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 33
486671 TATTATCAGT
*
486681 TTTATTAATTTATATATATATATTACTTTTTTTA
1 TTTATTATTTTATATATATATATTAC-TTTTTTA
* *
486715 TTTTTTATTTTATATATATTATTTTAC-TTTTTA
1 TTTATTATTTTATATATA-TATATTACTTTTTTA
486748 -TTATTATTTTAT
1 TTTATTATTTTAT
486760 TTATTTGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
32 11 0.28
33 6 0.15
34 16 0.40
35 7 0.17
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (33 bp):
TTTATTATTTTATATATATATATTACTTTTTTA
Found at i:486760 original size:26 final size:27
Alignment explanation
Indices: 486697--486765 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
486687 AATTTATATA
*
486697 TATATATTACTTT-TTTTATTTTTTATTT
1 TATATA-TA-TTTATTTTACTTTTTATTT
486725 TATATATA-TTATTTTACTTTTTATTAT
1 TATATATATTTATTTTACTTTTTATT-T
*
486752 TAT-TTTATTTATTT
1 TATATATATTTATTT
486766 GTTTTATTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
25 2 0.06
26 16 0.44
27 12 0.33
28 6 0.17
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (27 bp):
TATATATATTTATTTTACTTTTTATTT
Found at i:486773 original size:36 final size:36
Alignment explanation
Indices: 486667--486774 Score: 103
Period size: 36 Copynumber: 2.9 Consensus size: 36
486657 AATATATTAT
* * *
486667 TTTTTATTATCAGTTTTATTAATTTATATATATATATTAC
1 TTTTTATTATTA-TTTTATTTATTTAT-T-T-TATTTTAC
* *
486707 TTTTT-TTATT-TTTTATTTTATATATATTATTTTAC
1 TTTTTATTATTATTTTA-TTTATTTATTTTATTTTAC
*
486742 TTTTTATTATTATTTTATTTATTTGTTTTATTT
1 TTTTTATTATTATTTTATTTATTTATTTTATTT
486775 CTATATTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
35 12 0.21
36 19 0.33
37 10 0.18
38 7 0.12
39 4 0.07
40 5 0.09
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (36 bp):
TTTTTATTATTATTTTATTTATTTATTTTATTTTAC
Found at i:486774 original size:18 final size:18
Alignment explanation
Indices: 486667--486758 Score: 75
Period size: 18 Copynumber: 4.9 Consensus size: 18
486657 AATATATTAT
*
486667 TTTTTATTATCAGTTTTA-
1 TTTTTATTATTA-TTTTAC
*
486685 TTAATTTATATATATATATTAC
1 TT--TTTAT-TAT-TATTTTAC
486707 TTTTT-TTATT-TTTTA-
1 TTTTTATTATTATTTTAC
486722 TTTTATATATATTATTTTAC
1 TTTT-TAT-TATTATTTTAC
486742 TTTTTATTATTATTTTA
1 TTTTTATTATTATTTTA
486759 TTTATTTGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 20
0.73 0.04 0.24
Matches are distributed among these distances:
15 4 0.07
16 5 0.08
17 2 0.03
18 19 0.31
19 9 0.15
20 12 0.20
21 7 0.11
22 3 0.05
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTTTATTATTATTTTAC
Found at i:486796 original size:9 final size:9
Alignment explanation
Indices: 486782--486807 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
486772 TTTCTATATT
486782 TTTTTCTTC
1 TTTTTCTTC
486791 TTTTTCTTC
1 TTTTTCTTC
486800 TTTTTCTT
1 TTTTTCTT
486808 TATTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:486932 original size:15 final size:15
Alignment explanation
Indices: 486914--486943 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
486904 TATTTATTTC
486914 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
486929 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
486944 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:497082 original size:70 final size:70
Alignment explanation
Indices: 497000--497182 Score: 348
Period size: 70 Copynumber: 2.6 Consensus size: 70
496990 TTTTTTTTAA
497000 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
1 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
497065 AGAAC
66 AGAAC
497070 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
1 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
497135 AGAAC
66 AGAAC
* *
497140 AAAACAATCACACATGGCTAAGAAACATATAAGAGCATCCCAA
1 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAA
497183 CTAACTTCTA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 111 1.00
ACGTcount: A:0.51, C:0.19, G:0.15, T:0.15
Consensus pattern (70 bp):
AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
AGAAC
Found at i:498474 original size:36 final size:37
Alignment explanation
Indices: 498433--498517 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 37
498423 TTCATATCAC
* *
498433 ATATATCACATA-ATATTCTCATATCTCATTTATA-AT
1 ATATATCACATACATATTCTCATAT-TCATATAGACAT
*
498469 ATATATCACATTACATATTCTTATATTCATATAGACAT
1 ATATATCACA-TACATATTCTCATATTCATATAGACAT
498507 ATAT-TCACATA
1 ATATATCACATA
498518 GATCACTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
36 12 0.28
37 14 0.33
38 17 0.40
ACGTcount: A:0.40, C:0.16, G:0.01, T:0.42
Consensus pattern (37 bp):
ATATATCACATACATATTCTCATATTCATATAGACAT
Found at i:503109 original size:21 final size:21
Alignment explanation
Indices: 503051--503124 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
503041 TGGAAGGGTA
503051 GTATCGATACCTGTTGAA-GA-G
1 GTATCGATACCTG-T-AAGGATG
*
503072 GTATCGATA-CTGTAAGGGGTG
1 GTATCGATACCTGTAA-GGATG
503093 GTATCGATACCTG-AAGGATG
1 GTATCGATACCTGTAAGGATG
*
503113 GTATTGATACCT
1 GTATCGATACCT
503125 TCAAACATCG
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 19 0.41
21 21 0.46
22 3 0.07
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (21 bp):
GTATCGATACCTGTAAGGATG
Found at i:503204 original size:53 final size:53
Alignment explanation
Indices: 503128--503236 Score: 130
Period size: 53 Copynumber: 2.1 Consensus size: 53
503118 GATACCTTCA
* * * * *
503128 AACATCGAATGCCATATTAGTATCGGTATC-TTGAAGAGGTTTGGATACCCTTG
1 AACATCGAATGACATATTAGTATCGGTACCATGGAA-AGGTATCGATACCCTTG
* * *
503181 AACATCGAATGATATTTTGGTATCGGTACCATGGAAAGGTATCGATACCCTTG
1 AACATCGAATGACATATTAGTATCGGTACCATGGAAAGGTATCGATACCCTTG
503234 AAC
1 AAC
503237 GGTAGTATTG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 43 0.91
54 4 0.09
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (53 bp):
AACATCGAATGACATATTAGTATCGGTACCATGGAAAGGTATCGATACCCTTG
Found at i:507241 original size:20 final size:21
Alignment explanation
Indices: 507197--507247 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
507187 TGTTGAAGAA
*
507197 GTATCGATACTGTAAGGGGTG
1 GTATCGATACTGTAAGGGATG
507218 GTATCGATACAT-TAA-GGATG
1 GTATCGATAC-TGTAAGGGATG
507238 GTATCGATAC
1 GTATCGATAC
507248 CTTGAAACGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 14 0.50
21 13 0.46
22 1 0.04
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (21 bp):
GTATCGATACTGTAAGGGATG
Found at i:507297 original size:53 final size:54
Alignment explanation
Indices: 507216--507360 Score: 154
Period size: 53 Copynumber: 2.7 Consensus size: 54
507206 CTGTAAGGGG
* * * *
507216 TGGTATCGATACATTAAGGATGGTATCGATA-CCTTGAAACGTCGAATG-TCATAT
1 TGGTATCGGTACCTTGAGGA-GGTATCGATACCCTTGAAACATCGAATGAT-ATAT
* *
507270 TGGTATCGGTACCTTGAGGAGGTATCGATACCCTTG-AACATTGAATGATATTT
1 TGGTATCGGTACCTTGAGGAGGTATCGATACCCTTGAAACATCGAATGATATAT
* * *
507323 TGGTATCGGTATCATG-GGAATGTATCGATACCCTTGAA
1 TGGTATCGGTACCTTGAGG-AGGTATCGATACCCTTGAA
507361 GGGTAGTATT
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
52 2 0.03
53 52 0.67
54 24 0.31
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (54 bp):
TGGTATCGGTACCTTGAGGAGGTATCGATACCCTTGAAACATCGAATGATATAT
Found at i:508018 original size:23 final size:23
Alignment explanation
Indices: 507989--508035 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
507979 AAAAGAATAC
507989 AAGTAAACTATGTGCCTAAGTGA
1 AAGTAAACTATGTGCCTAAGTGA
508012 AAGTAAACTATGTGCCTAAGTGA
1 AAGTAAACTATGTGCCTAAGTGA
508035 A
1 A
508036 TATGTGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (23 bp):
AAGTAAACTATGTGCCTAAGTGA
Found at i:516260 original size:2 final size:2
Alignment explanation
Indices: 516253--516304 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
516243 TCAATGAATT
516253 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
*
516295 T- TA TT TA TA T
1 TA TA TA TA TA T
516305 TATTTTAGAC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:517534 original size:53 final size:53
Alignment explanation
Indices: 517446--517577 Score: 203
Period size: 53 Copynumber: 2.5 Consensus size: 53
517436 CTAAAAATGG
* *
517446 GGGAGTAGAACTCGAATAATCTTCTGCTTATGGGTTCGCTCCCTCTTGCTTCA
1 GGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTGCTTCA
* *
517499 GGGAGTAAAACTCGAACAATCTTTTG-TCTACGGGTTCGCTCCCTCTTGCTTCA
1 GGGAGTAGAACTCGAACAATCTTCTGCT-TACGGGTTCGCTCCCTCTTGCTTCA
*
517552 GGGAGTTGAACTCGAACAATCTTCTG
1 GGGAGTAGAACTCGAACAATCTTCTG
517578 GTGTGATTCT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
52 1 0.01
53 70 0.99
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (53 bp):
GGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTGCTTCA
Done.