Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000559.1 Hibiscus syriacus cultivar Beakdansim tig00001092_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: 117577
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3931 original size:31 final size:32
Alignment explanation
Indices: 3867--3935 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
3857 TTTCTTTATG
3867 TAAATTAAGGTATTTGGTTTTAATGAAAGTTT
1 TAAATTAAGGTATTTGGTTTTAATGAAAGTTT
3899 TAAATTAAGGTATTTGGTTTTAATG-AAGTTT
1 TAAATTAAGGTATTTGGTTTTAATGAAAGTTT
3930 TAAATT
1 TAAATT
3936 TCTCTGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 12 0.32
32 25 0.68
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (32 bp):
TAAATTAAGGTATTTGGTTTTAATGAAAGTTT
Found at i:11236 original size:3 final size:3
Alignment explanation
Indices: 11228--11264 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
11218 CATAAAACAT
11228 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATGA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA A
11265 CAGGAAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.88
4 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:13927 original size:2 final size:2
Alignment explanation
Indices: 13920--13958 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
13910 TGAAACATTC
13920 AT AT AT AT 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 AT AT AT AT A
13959 CTCATGAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19544 original size:2 final size:2
Alignment explanation
Indices: 19537--19561 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19527 GTCATTATTT
19537 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19562 TAAAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20324 original size:31 final size:31
Alignment explanation
Indices: 20283--20341 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
20273 CTTAAAAGAG
*
20283 TTTTACAATACTGAGATTTAAATAATTTTAA
1 TTTTACAATACTGAAATTTAAATAATTTTAA
*
20314 TTTTATAATACTGAAATTTAAATAATTT
1 TTTTACAATACTGAAATTTAAATAATTT
20342 ATACAACTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTTACAATACTGAAATTTAAATAATTTTAA
Found at i:20632 original size:28 final size:27
Alignment explanation
Indices: 20547--20632 Score: 68
Period size: 28 Copynumber: 3.1 Consensus size: 27
20537 ATGGCACAAC
20547 AACATTAATTATCATTAAACTATTATTA
1 AACATTAATTATCA-TAAACTATTATTA
* * * * *
20575 ATCAATAA--ATCATACACCTCTTTTTTTA
1 AACATTAATTATCATA-A--ACTATTATTA
20603 AACATTAATTATCATGAAACTATTATTA
1 AACATTAATTATCAT-AAACTATTATTA
20631 AA
1 AA
20633 TATGCAATTA
Statistics
Matches: 42, Mismatches: 10, Indels: 12
0.66 0.16 0.19
Matches are distributed among these distances:
25 2 0.05
26 5 0.12
28 28 0.67
30 6 0.14
31 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.41
Consensus pattern (27 bp):
AACATTAATTATCATAAACTATTATTA
Found at i:20964 original size:17 final size:17
Alignment explanation
Indices: 20933--20978 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
20923 AATATTATAT
20933 TTAAACTTAAA-TAAAAA
1 TTAAA-TTAAATTAAAAA
*
20950 TTAAATTAAATTAAATA
1 TTAAATTAAATTAAAAA
20967 -TAAATATAAATT
1 TTAAAT-TAAATT
20979 TTTAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAATTAAATTAAAAA
Found at i:21082 original size:14 final size:13
Alignment explanation
Indices: 21013--21118 Score: 76
Period size: 14 Copynumber: 8.1 Consensus size: 13
21003 TTATATGATA
*
21013 TAAAATTAAATAT
1 TAAAATTTAATAT
* *
21026 CTATAATATAATAT
1 -TAAAATTTAATAT
*
21040 TAAAAAATTAATAT
1 T-AAAATTTAATAT
*
21054 T-TAATTT-AT-T
1 TAAAATTTAATAT
21064 TAAAATTTTAATAT
1 TAAAA-TTTAATAT
21078 TAAAA-TTAATAT
1 TAAAATTTAATAT
* *
21090 CTATAATATAATAT
1 -TAAAATTTAATAT
21104 TAAAATTTTAATAT
1 TAAAA-TTTAATAT
21118 T
1 T
21119 TAATTTATTT
Statistics
Matches: 71, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
10 2 0.03
11 4 0.06
12 14 0.20
13 11 0.15
14 40 0.56
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAAATTTAATAT
Found at i:21096 original size:64 final size:65
Alignment explanation
Indices: 21013--21141 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 65
21003 TTATATGATA
**
21013 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAATTTTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
**
21078 TAAAATT-AATATCTATAATATAATATTAAAATTTTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
21142 CTATAATATA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
64 53 0.88
65 7 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (65 bp):
TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:21113 original size:40 final size:37
Alignment explanation
Indices: 21034--21118 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 37
21024 ATCTATAATA
*
21034 TAATATTAAAAAATTAATATTTAATTTATTTAAAATTT
1 TAATATT-AAAAATTAATATTTAATTAATTTAAAATTT
21072 TAATATT-AAAATTAATATCTATAATATAATATTAAAATTT
1 TAATATTAAAAATTAATAT-T-TAAT-TAAT-TTAAAATTT
21112 TAATATT
1 TAATATT
21119 TAATTTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
36 11 0.26
37 1 0.02
38 11 0.26
39 3 0.07
40 16 0.38
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (37 bp):
TAATATTAAAAATTAATATTTAATTAATTTAAAATTT
Found at i:21138 original size:24 final size:28
Alignment explanation
Indices: 21072--21159 Score: 98
Period size: 26 Copynumber: 3.4 Consensus size: 28
21062 TTTAAAATTT
21072 TAATATT--AAAATTAATATCTATAATA
1 TAATATTAAAAAATTAATATCTATAATA
**
21098 TAATATTAAAATTTTAATAT-T-TAAT-
1 TAATATTAAAAAATTAATATCTATAATA
*
21123 TTAT-TTAAAAAATTAATATCTATAATA
1 TAATATTAAAAAATTAATATCTATAATA
*
21150 TAAAATTAAA
1 TAATATTAAA
21160 TATAAAACCT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
24 13 0.27
25 4 0.08
26 15 0.31
27 3 0.06
28 14 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
TAATATTAAAAAATTAATATCTATAATA
Found at i:21162 original size:64 final size:64
Alignment explanation
Indices: 21013--21164 Score: 209
Period size: 64 Copynumber: 2.4 Consensus size: 64
21003 TTATATGATA
**
21013 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAATTTTAATAT
1 TAAAATTAAA-ATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
* **
21078 TAAAATTAATATCTATAATATAATATTAAAATTTTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAAATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
21142 CTATAATATAAAAT-TA-AATATAA
1 -TAAAAT-TAAAATCTATAATATAA
21165 AACCTCTTTG
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
64 57 0.73
65 16 0.21
66 5 0.06
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (64 bp):
TAAAATTAAAATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:25703 original size:19 final size:19
Alignment explanation
Indices: 25679--25716 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
25669 TTTAAGTCAA
25679 ATCAAAATCAATATAAACT
1 ATCAAAATCAATATAAACT
* *
25698 ATCAAATTCAGTATAAACT
1 ATCAAAATCAATATAAACT
25717 TTCGAATCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.29
Consensus pattern (19 bp):
ATCAAAATCAATATAAACT
Found at i:27175 original size:17 final size:16
Alignment explanation
Indices: 27149--27180 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
27139 TTGCCTGCTG
27149 GCCGCTGCCGCCGCCC
1 GCCGCTGCCGCCGCCC
27165 GCCGTCTGCCGCCGCC
1 GCCG-CTGCCGCCGCC
27181 GTCAGCCGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.59, G:0.31, T:0.09
Consensus pattern (16 bp):
GCCGCTGCCGCCGCCC
Found at i:27180 original size:20 final size:20
Alignment explanation
Indices: 27150--27197 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
27140 TGCCTGCTGG
* *
27150 CCGCTGCCGCCGCCCGCCGT
1 CCGCCGCCGCCGCCAGCCGT
* *
27170 CTGCCGCCGCCGTCAGCCGT
1 CCGCCGCCGCCGCCAGCCGT
27190 CCGCCGCC
1 CCGCCGCC
27198 ACACTCTGAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.02, C:0.58, G:0.29, T:0.10
Consensus pattern (20 bp):
CCGCCGCCGCCGCCAGCCGT
Found at i:35025 original size:23 final size:22
Alignment explanation
Indices: 34989--35032 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
34979 CATAATTATT
34989 TAAAAAATTAAATAAAAAATAC
1 TAAAAAATTAAATAAAAAATAC
*
35011 TAAAAATATTTAATAAAAAATA
1 TAAAAA-ATTAAATAAAAAATA
35033 TTTTTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAAAAATTAAATAAAAAATAC
Found at i:35239 original size:14 final size:14
Alignment explanation
Indices: 35222--35249 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35212 ATCATAACAA
35222 AATTATATAACTAT
1 AATTATATAACTAT
35236 AATTATATAACTAT
1 AATTATATAACTAT
35250 TTTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:36021 original size:134 final size:132
Alignment explanation
Indices: 35827--36078 Score: 335
Period size: 134 Copynumber: 1.9 Consensus size: 132
35817 TTTTGAGCTA
* * * * * *
35827 GATTTTAACTTCACGATGAAGGATATCATGCTTAAGTCATCTAAGATCGACTCAACTTCACGATG
1 GATTTCAACTTCACGACGAAAGATATCAAGCTCAAGTCATCCAAGATCGACTCAACTTCACGATG
** *
35892 AATGAGTCAAACCACAATTTAGT-TTAACTCAACAACGATGAGCTATTTTTCATCCTAGATTTCA
66 AATGAGTC-AACCACAACATA-TCTTAACTCAACAACGATCAGCTA-TTTTCATCCTAGATTTCA
35956 AGTCG
128 AGTCG
* * *
35961 GATTTCAACTTCACGACGAAAGATATCAAGCTCGAGTCATCCGAGATCGACTTAACTTCACGATG
1 GATTTCAACTTCACGACGAAAGATATCAAGCTCAAGTCATCCAAGATCGACTCAACTTCACGATG
* * *
36026 AATGAGTCATCCATAACATATCTTAACTCAACAACGATCAGTTATTTTCATCC
66 AATGAGTCAACCACAACATATCTTAACTCAACAACGATCAGCTATTTTCATCC
36079 AACTTAATTC
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
132 10 0.10
133 28 0.27
134 64 0.63
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (132 bp):
GATTTCAACTTCACGACGAAAGATATCAAGCTCAAGTCATCCAAGATCGACTCAACTTCACGATG
AATGAGTCAACCACAACATATCTTAACTCAACAACGATCAGCTATTTTCATCCTAGATTTCAAGT
CG
Found at i:37810 original size:36 final size:38
Alignment explanation
Indices: 37748--37821 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 38
37738 CTTTGGTAAA
*
37748 ATGTTTTATCAATTTTTTATT-CCTTTTTAAATTGCGT
1 ATGTTTTATCAATTTTTTATTACTTTTTTAAATTGCGT
*
37785 ATGTTTTATCAA-TTTTTATTACTTTTTTAATTTGCGT
1 ATGTTTTATCAATTTTTTATTACTTTTTTAAATTGCGT
37822 TTTAATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 8 0.24
37 26 0.76
ACGTcount: A:0.22, C:0.09, G:0.08, T:0.61
Consensus pattern (38 bp):
ATGTTTTATCAATTTTTTATTACTTTTTTAAATTGCGT
Found at i:43280 original size:2 final size:2
Alignment explanation
Indices: 43273--43301 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43263 TAACTATACT
43273 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43302 CTGGTTTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54687 original size:17 final size:17
Alignment explanation
Indices: 54599--54690 Score: 53
Period size: 17 Copynumber: 5.2 Consensus size: 17
54589 TAATGCAAAT
*
54599 AAATAAATAAAACAAGTA
1 AAATATATAAAA-AAGTA
*
54617 AAAGAATATAAAAACA-TA
1 AAA-TATATAAAAA-AGTA
* *
54635 AAATATAGGATAAATA-TAA
1 AAATATA-TA-AAAAAGT-A
* **
54654 AAATAAATAAATGAGTA
1 AAATATATAAAAAAGTA
54671 AAATATATAAAAAAGTA
1 AAATATATAAAAAAGTA
54688 AAA
1 AAA
54691 GCATATATAT
Statistics
Matches: 56, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
17 24 0.43
18 14 0.25
19 18 0.32
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.21
Consensus pattern (17 bp):
AAATATATAAAAAAGTA
Found at i:54698 original size:20 final size:20
Alignment explanation
Indices: 54673--54710 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54663 AATGAGTAAA
54673 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
54693 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
54711 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:54779 original size:2 final size:2
Alignment explanation
Indices: 54772--54812 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
54762 AAAATAGGAA
54772 AT AT AT AT AT 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 AT AT AT AT AT A
54813 ATAACACTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55323 original size:34 final size:34
Alignment explanation
Indices: 55280--55348 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
55270 GAATCCTAGC
55280 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
55314 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
55348 A
1 A
55349 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:56203 original size:109 final size:105
Alignment explanation
Indices: 55810--56999 Score: 1181
Period size: 105 Copynumber: 11.3 Consensus size: 105
55800 AATATTGTTC
* * * * *
55810 CGAGTCCAATATCCTCCG-CTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAA-TTGTTTGTTGA
1 CGAGTCCAATATCCTTCGTC-GTGAAGTTGAAATTGGCTCT-GAAATTGAAAAGTTG-TTGTTGA
** * * * * * * *
55873 CAGTCAGTCGCCCCTTTGCTATGAAGTTGAGCTTGTGCTGTCT
63 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
55916 CGAGTCTAATATCCTTCG-CTGTGAAGATGAAATTGACTCTG-AA-CG-AAA--TCTTGTTGACA
1 CGAGTCCAATATCCTTCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGTTGTTGACA
* *
55975 ATCAGCCGTCCCTTCGTTGTGAATTTGAACTTGTGTTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
56016 CGAGTCCAATATCCTTCG-C-TACGAAGTTGAAATTGGCTATGAAATTTGAAAA-ATGTTTGTTG
1 CGAGTCCAATATCCTTCGTCGT--GAAGTTGAAATTGGCTCTGAAA-TTGAAAAGTTG-TTGTTG
56078 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
62 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * ** *
56122 CGAGTGGCACGATATCCTCCGTCGTGGAGTTGAAA-TCGCGGATGAAACTGAAAAGTTGTTCGTT
1 CGAGT--C-CAATATCCTTCGTCGTGAAGTTGAAATTGGC-TCTGAAATTGAAAAGTTGTT-GTT
56186 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
61 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * *
56231 CGGGTAGCACGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAA-TTGTTTGTT
1 CGAGT--C-CAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATT-GAAAAGTTG-TTGTT
*
56295 GACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
61 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
56340 CGAGTCCAATATCCTTCG-CTGTGAAGTTGAGATTGGCTCCGAAATT-----G--CTTGTCGACA
1 CGAGTCCAATATCCTTCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGTTGTTGACA
** * * * *
56397 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * *
56438 TGGGTCCAATATCCTTCG-CTGTGAAGCTGAAATTGGCCCTGAAACTGGGAAA-TTATTGTTGAC
1 CGAGTCCAATATCCTTCGTC-GTGAAGTTGAAATTGGCTCTGAAA-TTGAAAAGTTGTTGTTGAC
56501 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * **
56543 CGAGTTCAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACA
1 CGAGTCCAATATCCTTCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGTTGTTGACA
* * * **
56607 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * **
56648 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAGATTGGGAAGTTGTTGTTGACAA
1 CGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGTTGTTGACAA
* * *
56713 GCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
56753 -GAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-AAGAAGTTGTTGTTGAC
1 CG-AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGAA-AAGTTGTTGTTGAC
* * * *
56816 AAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
64 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
56858 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTG-TTGTTGACA
**
56923 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTACGTTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
56964 CGAGTGCCACAATATCCTCCGTCGTGGAGTTGAAAT
1 CGAGT--C-CAATATCCTTCGTCGTGAAGTTGAAAT
57000 CGCGGATGGC
Statistics
Matches: 939, Mismatches: 106, Indels: 75
0.84 0.09 0.07
Matches are distributed among these distances:
98 83 0.09
99 1 0.00
100 75 0.08
101 3 0.00
102 3 0.00
103 2 0.00
104 10 0.01
105 376 0.40
106 171 0.18
107 1 0.00
108 13 0.01
109 191 0.20
110 9 0.01
111 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:57598 original size:33 final size:33
Alignment explanation
Indices: 57558--57654 Score: 88
Period size: 33 Copynumber: 2.8 Consensus size: 33
57548 GTTATCTTGA
57558 AAGAGATAGAATTTGTTTCAAGGGAAACGATCTC
1 AAGAGATA-AATTTGTTTCAAGGGAAACGATCTC
* * * *
57592 AA-AGATATATGTTGTTTCATGAGAAACGGTCTC
1 AAGAGATAAAT-TTGTTTCAAGGGAAACGATCTC
*
57625 AAGGGAGATAAAATTTTGTTTTAAGGGAAA
1 AA--GAGAT-AAA-TTTGTTTCAAGGGAAA
57655 TAAATTTGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
32 2 0.04
33 26 0.53
34 2 0.04
36 4 0.08
37 14 0.29
38 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (33 bp):
AAGAGATAAATTTGTTTCAAGGGAAACGATCTC
Found at i:57776 original size:36 final size:36
Alignment explanation
Indices: 57736--58016 Score: 175
Period size: 36 Copynumber: 8.0 Consensus size: 36
57726 TTCAAAGATT
* * *
57736 TTGTTTCAAGGGAACCTGTCTCAAGATAAACAAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAAA
* * *
57772 TTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAAC
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAAA
* * * * * ** *
57808 TTAGTTCCAAAAGAAACAGTCTCAAGGGAGACGGAAT
1 TT-GTTTCAAGAGAAACTGTCTCAAGAGAAACAAAAA
* * **
57845 TTGTTTCAA-AGAAAACATAT-TC------AA-ATATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAAACAAAAA
* * * *
57874 TTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAAT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAAA
* * * * * * *
57910 TTATTTCAAGGGAAATTGTCTCAAGATAGACGAAAT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAAA
* *
57946 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAAA
* *
57982 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAA
58017 CTCTTCTAGT
Statistics
Matches: 195, Mismatches: 38, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
28 2 0.01
29 16 0.08
30 2 0.01
35 3 0.02
36 143 0.73
37 29 0.15
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (36 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAAA
Found at i:57776 original size:65 final size:67
Alignment explanation
Indices: 57590--57786 Score: 175
Period size: 65 Copynumber: 2.9 Consensus size: 67
57580 GGAAACGATC
* * * * * * * *
57590 TCAAAGATATATGTTGTTTCATGAGAAACGGTCTCAAGGGAGATAAAATTTTGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGGAACTGTCTCAAGAGAAACAAAA-ATTGTTTTAAGGGAAA
57655 TAAAT
63 TAAAT
** * * * * * *
57660 TTGAAGATTTTGTGTTTCAAGAGTAATTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAA
1 TCAAAGATTTTGTGTTTCAAGAGGAACTGTCTCAAGAGAAACAAAAATTGTTTTAAGGGAAATAA
57725 AT
66 AT
* *
57727 TCAAAGA-TTT-TGTTTCAAG-GGAACCTGTCTCAAGATAAACAAAAATTGTTTTAAGAGAAA
1 TCAAAGATTTTGTGTTTCAAGAGGAA-CTGTCTCAAGAGAAACAAAAATTGTTTTAAGGGAAA
57787 CTGTCTCAAG
Statistics
Matches: 107, Mismatches: 19, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
64 3 0.03
65 38 0.36
66 3 0.03
67 25 0.23
68 29 0.27
69 3 0.03
70 6 0.06
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGGAACTGTCTCAAGAGAAACAAAAATTGTTTTAAGGGAAATAA
AT
Found at i:57849 original size:138 final size:137
Alignment explanation
Indices: 57688--57997 Score: 386
Period size: 138 Copynumber: 2.3 Consensus size: 137
57678 AAGAGTAATT
* * * *
57688 GTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGAACCT
1 GTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAACT
* * *
57753 GTCTCAAGATAAACAAAAATTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA
66 GTCTCAAGAGAAACAAAAATTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAA
57818 AAGAAACA
130 AAGAAACA
** * * * * *
57826 GTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTTAAGGGAAACT
1 GTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAACT
* * * * * * * * *
57891 GTCTCAAGAGAGACAAAATTTATTTCAAGGGAAATTGTCTCAAGATAGACGAAATTTGTTTCAAG
66 GTCTCAAGAGAAACAAAAATTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAA
*
57956 AGAAACT
131 AGAAACA
*
57963 GTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 GTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
57998 TGTCTCAAGA
Statistics
Matches: 143, Mismatches: 29, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
137 44 0.31
138 99 0.69
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
GTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAACT
GTCTCAAGAGAAACAAAAATTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAA
AGAAACA
Found at i:57896 original size:102 final size:102
Alignment explanation
Indices: 57772--57960 Score: 272
Period size: 102 Copynumber: 1.9 Consensus size: 102
57762 TAAACAAAAA
*
57772 TTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACAGTCTCAAGGGA
1 TTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACAGTCTCAAGAGA
*
57837 GACGGAATTTGTTTCAA-AGAAAACATATTCAAATATT
65 GACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
* * * ** ** *
57874 TTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAATTGTCTCAAGATAG
1 TTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACAGTCTCAAGAGAG
57939 ACGAAATTTGTTTCAAGAGAAA
66 ACGAAATTTGTTTCAAGAGAAA
57961 CTGTCTCAAG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
101 34 0.45
102 42 0.55
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (102 bp):
TTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACAGTCTCAAGAGAG
ACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
Found at i:57990 original size:72 final size:72
Alignment explanation
Indices: 57873--58012 Score: 235
Period size: 72 Copynumber: 1.9 Consensus size: 72
57863 ATTCAAATAT
* * * *
57873 TTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAATTGTCTCAAGATA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
57938 GACGAAA
66 GACGAAA
*
57945 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
58010 GAC
66 GAC
58013 AAAACTCTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (72 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
GACGAAA
Found at i:58038 original size:35 final size:36
Alignment explanation
Indices: 57881--58050 Score: 157
Period size: 36 Copynumber: 4.8 Consensus size: 36
57871 ATTTTGTTTT
* * **
57881 AAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTC
1 AAGGAAAACTGTCTCAAGAGAGACAAAATCTGCTTC
* * * * * *
57917 AAGGGAAATTGTCTCAAGATAGACGAAATTTGTTTC
1 AAGGAAAACTGTCTCAAGAGAGACAAAATCTGCTTC
* *
57953 AA-GAGAAACTGTCTCAAGAGAGACAAAATTTGTTTC
1 AAGGA-AAACTGTCTCAAGAGAGACAAAATCTGCTTC
*
57989 AAGGGAAACTGTCTCAAGAGAGACAAAA-CT-CTTC
1 AAGGAAAACTGTCTCAAGAGAGACAAAATCTGCTTC
* * *
58023 TAGTGAAAACGGTCTCAAGCGAGACAAA
1 AAG-GAAAACTGTCTCAAGAGAGACAAA
58051 TCTTGTTTTA
Statistics
Matches: 116, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
34 5 0.04
35 23 0.20
36 87 0.75
37 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (36 bp):
AAGGAAAACTGTCTCAAGAGAGACAAAATCTGCTTC
Found at i:58058 original size:71 final size:72
Alignment explanation
Indices: 57885--58058 Score: 219
Period size: 72 Copynumber: 2.4 Consensus size: 72
57875 TGTTTTAAGG
* * * ** *
57885 GAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAATTGTCTCAAGATAGACGAAATTTGT
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAACTGC
57950 TTCAAGA
66 TTCAAGA
57957 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAACT-C
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAACTGC
* *
58020 TTCTAGT
66 TTCAAGA
* *
58027 GAAAACGGTCTCAAGCGAGAC-AAATCTTGTTT
1 G-AAACTGTCTCAAGAGAGACAAAAT-TTGTTT
58059 TAAGAAAAAC
Statistics
Matches: 90, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
70 10 0.11
71 27 0.30
72 53 0.59
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (72 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAACTGC
TTCAAGA
Found at i:58523 original size:18 final size:18
Alignment explanation
Indices: 58496--58531 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
58486 TGTTGAATCC
* *
58496 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
58514 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
58532 TTGATGTTGA
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:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:58972 original size:22 final size:22
Alignment explanation
Indices: 58946--58994 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
58936 TTGTGTTTGG
* *
58946 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
58968 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
58990 TCAAA
1 TCAAA
58995 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:59001 original size:22 final size:22
Alignment explanation
Indices: 58958--59001 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
58948 AAAGGTTTGG
* * *
58958 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
58980 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
59002 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:59660 original size:8 final size:7
Alignment explanation
Indices: 59649--59717 Score: 57
Period size: 8 Copynumber: 8.9 Consensus size: 7
59639 ATTTTTGCTT
59649 TTTTTTCC
1 TTTTTT-C
59657 TTTTGTTC
1 TTTT-TTC
*
59665 TTGTTTC
1 TTTTTTC
59672 TCTTTTTC
1 T-TTTTTC
*
59680 TTTGTTTT
1 TTT-TTTC
59688 TTTTTTGC
1 TTTTTT-C
59696 TTTTTTGC
1 TTTTTT-C
59704 TTCTTTTC
1 TT-TTTTC
59712 TTTTTT
1 TTTTTT
59718 GTTCTTGATT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
7 13 0.25
8 33 0.63
9 6 0.12
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.78
Consensus pattern (7 bp):
TTTTTTC
Found at i:59714 original size:16 final size:16
Alignment explanation
Indices: 59641--59723 Score: 59
Period size: 16 Copynumber: 5.1 Consensus size: 16
59631 TCTTTTTGAT
59641 TTTTGCTTTTTT-TTCC
1 TTTTGCTTTTTTGTT-C
59657 TTTTG-TTCTTGTT-TCTC
1 TTTTGCTT-TT-TTGT-TC
* *
59674 TTTTTCTTTGTTT-TTT
1 TTTTGCTTT-TTTGTTC
59690 TTTTGCTTTTTTGCTTC
1 TTTTGCTTTTTTG-TTC
59707 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTTGTTC
59722 TT
1 TT
59724 GATTGGATCT
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
15 10 0.18
16 24 0.43
17 18 0.32
18 4 0.07
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.77
Consensus pattern (16 bp):
TTTTGCTTTTTTGTTC
Found at i:60896 original size:8 final size:8
Alignment explanation
Indices: 60880--60918 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
60870 AATGTAGATG
60880 AAAATGCA
1 AAAATGCA
*
60888 AAAAGGCA
1 AAAATGCA
60896 AAAATGC-
1 AAAATGCA
60903 AAAATGCA
1 AAAATGCA
*
60911 AGAATGCA
1 AAAATGCA
60919 CGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:60906 original size:15 final size:15
Alignment explanation
Indices: 60880--60918 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
60870 AATGTAGATG
60880 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
60896 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
60911 AGAATGCA
1 AAAATGCA
60919 CGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:61466 original size:18 final size:18
Alignment explanation
Indices: 61439--61478 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
61429 ATTAGTCTTT
61439 CAGAAATGGATGTGAATC
1 CAGAAATGGATGTGAATC
*
61457 CAGAAGTGGATGTGAATC
1 CAGAAATGGATGTGAATC
61475 CAGA
1 CAGA
61479 CTTGAAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (18 bp):
CAGAAATGGATGTGAATC
Found at i:63639 original size:21 final size:19
Alignment explanation
Indices: 63606--63646 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
63596 AAAATATAGG
63606 ATAAATATAAAATAGATAA
1 ATAAATATAAAATAGATAA
*
63625 ATAAATGAGTAAAATATATAA
1 ATAAAT-A-TAAAATAGATAA
63646 A
1 A
63647 AAAGTAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (19 bp):
ATAAATATAAAATAGATAA
Found at i:63652 original size:17 final size:17
Alignment explanation
Indices: 63561--63655 Score: 50
Period size: 18 Copynumber: 5.2 Consensus size: 17
63551 TAATGCAAAT
*
63561 AAATAAATAAAACAAGTA
1 AAATATATAAAA-AAGTA
*
63579 AAAGAATATAAAAACA-TA
1 AAA-TATATAAAAA-AGTA
* *
63597 AAATATAGGATAAATA-TA
1 AAATATA-TA-AAAAAGTA
*
63615 AAATAGATAAATAAATGAGTA
1 AAATATAT-AA-AAA--AGTA
63636 AAATATATAAAAAAGTA
1 AAATATATAAAAAAGTA
63653 AAA
1 AAA
63656 GCATATATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 19
0.68 0.10 0.22
Matches are distributed among these distances:
17 11 0.19
18 22 0.37
19 14 0.24
20 3 0.05
21 9 0.15
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.21
Consensus pattern (17 bp):
AAATATATAAAAAAGTA
Found at i:63753 original size:2 final size:2
Alignment explanation
Indices: 63740--63774 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
63730 AAAATAGGAA
*
63740 AT AT AT AA 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 AT AT A
63775 ATAACACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:64286 original size:34 final size:34
Alignment explanation
Indices: 64243--64311 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
64233 GAATCCTAGC
64243 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
64277 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
64311 A
1 A
64312 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:73188 original size:6 final size:6
Alignment explanation
Indices: 73167--73207 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
73157 AAAAAAGATT
*
73167 TATACGA TAAACA TATACA TATACA TATACA TATACA TATA
1 TATAC-A TATACA TATACA TATACA TATACA TATACA TATA
73208 TCAGGAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 28 0.88
7 4 0.12
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (6 bp):
TATACA
Found at i:76745 original size:316 final size:317
Alignment explanation
Indices: 76043--76924 Score: 1437
Period size: 316 Copynumber: 2.8 Consensus size: 317
76033 AGGGTGCTTT
76043 CACTTGGTCATTAAACTTTTAAAATTTGTATACAATCACTAAACTTTTAATTTACTTTTGTTATG
1 CACTTGGTCATTAAACTTTTAAAATTTGTATACAATCACTAAACTTTTAATTTACTTTTGTTATG
* ** * *
76108 GTCAATGCTATTAGCAGATGTTAAGAGATACCAACGTATTGCCTTAAAGTGCCCTTTCAAAAAAA
66 GTCACTGCTATTAGCAGATGTTAAGAGATACCAACGTAGCGTCTTAAAGTGCTCTTT---AAAAA
* *
76173 AAACGTTCAGATTCCAAATTTATAACCACCGAAAAGGCTAGACTTTCGGTGAAGAGAGCAATCGT
128 AAACGTTAAGATTCCAAATTTATAACCACCGAAAAGGCTAGATTTTCGGTGAAGAGAGCAATCGT
*
76238 CGATCAAATCCCAACGATCAGAATGATTTGTTTGGTCAGAATATTAATATAATTTGTATACAATA
193 CGATCAAATCCCAACGATCAGAATGATTCGTTTGGTCAGAATATTAATATAATTTGTATACAATA
*
76303 ACTAAACTTTTAATTTACTTTTGTTATGGTCACTGCTATTAGCAGATGTTAAGAGATATT
258 ACTAAACTTTTAATTTACTTTTGTTATGGTCACTGCTATTAGCAGATGTTAAGAGATATC
*
76363 CACTTGGTCATTAAACTTTTAAAATTTGTATAAAATCACTAAACTTTTAATTTACTTTTGTTATG
1 CACTTGGTCATTAAACTTTTAAAATTTGTATACAATCACTAAACTTTTAATTTACTTTTGTTATG
* * *
76428 GTCACTGCTATTAGCATATGTTAAGAGATACCAACGTGGCGTTTTAAAGTGCTCTTTAAAAAAAA
66 GTCACTGCTATTAGCAGATGTTAAGAGATACCAACGTAGCGTCTTAAAGTGCTCTTTAAAAAAAA
* *
76493 CGTTAAGATTCCAAATTTATAACCACCGAAAAGGCTGGATTTTGGGTGAAGAGAGCAATCGTCGA
131 CGTTAAGATTCCAAATTTATAACCACCGAAAAGGCTAGATTTTCGGTGAAGAGAGCAATCGTCGA
* *
76558 TCAAATCCCAACGATCAGAATGATTCGTTTGGTTAGAATATTAATATAATTTGTATACAATCACT
196 TCAAATCCCAACGATCAGAATGATTCGTTTGGTCAGAATATTAATATAATTTGTATACAATAACT
*
76623 -AACTTTTAATTTGCTTTTGTTATGGTCACTGCTATTAGCAGATGTTAAGAGATATC
261 AAACTTTTAATTTACTTTTGTTATGGTCACTGCTATTAGCAGATGTTAAGAGATATC
*
76679 CACTTGGTCATTAAACTTTTAAAATTTGTATACAATCACTAAACTTTTAATTTACTTTTATTATG
1 CACTTGGTCATTAAACTTTTAAAATTTGTATACAATCACTAAACTTTTAATTTACTTTTGTTATG
* * * * *
76744 GTCACTGCTATTAGCAGATGTTAATAGATACCAATGTAGCATCTTAAAGTGTTATTTAAAAAAAA
66 GTCACTGCTATTAGCAGATGTTAAGAGATACCAACGTAGCGTCTTAAAGTGCTCTTTAAAAAAAA
* ** *
76809 --TTAAGATTCCAAATTTATAACCACTGAAAAGGCTAGATTTTCGGTGAAGTTAGCAATCATCGA
131 CGTTAAGATTCCAAATTTATAACCACCGAAAAGGCTAGATTTTCGGTGAAGAGAGCAATCGTCGA
* * *
76872 TTAAATCCCAACGAACAGAATGATTCGTTTAGTCAGAATATTAATATAATTTG
196 TCAAATCCCAACGATCAGAATGATTCGTTTGGTCAGAATATTAATATAATTTG
76925 GTTTCAAGCT
Statistics
Matches: 524, Mismatches: 38, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
314 106 0.20
316 174 0.33
317 131 0.25
320 113 0.22
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (317 bp):
CACTTGGTCATTAAACTTTTAAAATTTGTATACAATCACTAAACTTTTAATTTACTTTTGTTATG
GTCACTGCTATTAGCAGATGTTAAGAGATACCAACGTAGCGTCTTAAAGTGCTCTTTAAAAAAAA
CGTTAAGATTCCAAATTTATAACCACCGAAAAGGCTAGATTTTCGGTGAAGAGAGCAATCGTCGA
TCAAATCCCAACGATCAGAATGATTCGTTTGGTCAGAATATTAATATAATTTGTATACAATAACT
AAACTTTTAATTTACTTTTGTTATGGTCACTGCTATTAGCAGATGTTAAGAGATATC
Found at i:79282 original size:2 final size:2
Alignment explanation
Indices: 79275--79317 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
79265 ATTTACTGGA
*
79275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
79317 A
1 A
79318 ACATTCAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:82170 original size:17 final size:18
Alignment explanation
Indices: 82144--82177 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
82134 AAAAAATAGC
*
82144 ATATTATAAAATTAAATA
1 ATATTATAAAAATAAATA
82162 ATATT-TAAAAATAAAT
1 ATATTATAAAAATAAAT
82178 TTATTTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATTATAAAAATAAATA
Found at i:84195 original size:23 final size:23
Alignment explanation
Indices: 84165--84215 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
84155 AAAAGTCTCG
84165 CCCACGACACCTTCTGATTGCCT
1 CCCACGACACCTTCTGATTGCCT
84188 CCCACGACACCTTCTGATTGCCT
1 CCCACGACACCTTCTGATTGCCT
*
84211 GCCAC
1 CCCAC
84216 TCATGCTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.18, C:0.45, G:0.14, T:0.24
Consensus pattern (23 bp):
CCCACGACACCTTCTGATTGCCT
Found at i:87209 original size:24 final size:23
Alignment explanation
Indices: 87174--87218 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
87164 AAATTATATA
*
87174 TTTTTTCTATTT-AGATATCTATT
1 TTTTTTCAATTTAAG-TATCTATT
87197 TTTTTGTCAATTTAAGTATCTA
1 TTTTT-TCAATTTAAGTATCTA
87219 ACATATCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.24, C:0.09, G:0.07, T:0.60
Consensus pattern (23 bp):
TTTTTTCAATTTAAGTATCTATT
Found at i:90465 original size:13 final size:13
Alignment explanation
Indices: 90447--90472 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
90437 TCCGATTCCT
90447 GCTTGCATTGATG
1 GCTTGCATTGATG
90460 GCTTGCATTGATG
1 GCTTGCATTGATG
90473 CTCATCAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.31, T:0.38
Consensus pattern (13 bp):
GCTTGCATTGATG
Found at i:90701 original size:21 final size:21
Alignment explanation
Indices: 90675--90717 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
90665 TACACCAACG
90675 TTCCATAAGTAAAATTGTCTT
1 TTCCATAAGTAAAATTGTCTT
90696 TTCCATAAGTAAAATTGTCTT
1 TTCCATAAGTAAAATTGTCTT
90717 T
1 T
90718 ATTATGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (21 bp):
TTCCATAAGTAAAATTGTCTT
Found at i:90888 original size:17 final size:17
Alignment explanation
Indices: 90868--90927 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
90858 TAAAAGAAAT
*
90868 ATTAAAAGTAATATCAA
1 ATTAAAAATAATATCAA
* *
90885 ATTAAAAAAAACATCAAA
1 ATTAAAAATAATATC-AA
*
90903 ATTAAAATTAATGATCAA
1 ATTAAAAATAAT-ATCAA
90921 TATTAAA
1 -ATTAAA
90928 TTTTGTGTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 12 0.35
18 13 0.38
19 9 0.26
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (17 bp):
ATTAAAAATAATATCAA
Found at i:90903 original size:29 final size:29
Alignment explanation
Indices: 90839--90903 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
90829 AATTTATTTG
* * *
90839 ATCAAAATTAATACTAAATTAAAAGAAAT
1 ATCAAAAGTAATACTAAATTAAAAAAAAC
*
90868 ATTAAAAGTAATA-TCAAATTAAAAAAAAC
1 ATCAAAAGTAATACT-AAATTAAAAAAAAC
90897 ATCAAAA
1 ATCAAAA
90904 TTAAAATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.65, C:0.08, G:0.03, T:0.25
Consensus pattern (29 bp):
ATCAAAAGTAATACTAAATTAAAAAAAAC
Found at i:90925 original size:19 final size:17
Alignment explanation
Indices: 90865--90927 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
90855 AATTAAAAGA
90865 AATATTAAAAGTAATATC
1 AATATTAAAA-TAATATC
* *
90883 AA-ATTAAAAAAAACATC
1 AATATT-AAAATAATATC
*
90900 AAAATTAAAATTAATGATC
1 AATATTAAAA-TAAT-ATC
90919 AATATTAAA
1 AATATTAAA
90928 TTTTGTGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
17 14 0.39
18 11 0.31
19 11 0.31
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (17 bp):
AATATTAAAATAATATC
Found at i:94650 original size:21 final size:21
Alignment explanation
Indices: 94626--94671 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
94616 AGTTGATGTT
94626 CGCTAAGCAGGCATATGTGTA
1 CGCTAAGCAGGCATATGTGTA
94647 CGCTAAGCAGGCATATGTGTA
1 CGCTAAGCAGGCATATGTGTA
94668 CGCT
1 CGCT
94672 CGTGTGCCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (21 bp):
CGCTAAGCAGGCATATGTGTA
Found at i:104776 original size:26 final size:25
Alignment explanation
Indices: 104726--104789 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 25
104716 ATTAATCTAT
*
104726 TAATTCTGATCGGTACTACAGAGGC
1 TAATTCTGATCGGTACTACAAAGGC
*
104751 TAATTCTGATCGAGTACTATAAAGGC
1 TAATTCTGATCG-GTACTACAAAGGC
104777 TAATTCTGATCGG
1 TAATTCTGATCGG
104790 GCATTGTGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 13 0.36
26 23 0.64
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (25 bp):
TAATTCTGATCGGTACTACAAAGGC
Found at i:110370 original size:16 final size:16
Alignment explanation
Indices: 110349--110382 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
110339 TAAATTTAAA
*
110349 ATTCAAAATATAAAAT
1 ATTCAAAAAATAAAAT
*
110365 ATTCAAAAAATCAAAT
1 ATTCAAAAAATAAAAT
110381 AT
1 AT
110383 AAAGATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
ATTCAAAAAATAAAAT
Done.