Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007042.1 Hibiscus syriacus cultivar Beakdansim tig00018258_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: 71805
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:3141 original size:57 final size:57
Alignment explanation
Indices: 3063--3229 Score: 235
Period size: 57 Copynumber: 2.9 Consensus size: 57
3053 TCACTCGTCA
* * *
3063 CCATCTATACATCAATCCATCTTTCACTTCTAATCGACCAACCATCTCCACTTCTATT
1 CCATCTA-CCATCAATCCATCTTTCACTTCTATTCCACCAACCATCTCCACTTCTATT
* * *
3121 CCATTTACCATCAATCCATCTTTCACTTCTATTCCATCAACCATCTCTACTTCTATT
1 CCATCTACCATCAATCCATCTTTCACTTCTATTCCACCAACCATCTCCACTTCTATT
* * **
3178 CCATCTACCATCAATCCACCTTTCGCTTCTATTCCACCAATTATCTCCACTT
1 CCATCTACCATCAATCCATCTTTCACTTCTATTCCACCAACCATCTCCACTT
3230 TAAAAGTTAC
Statistics
Matches: 96, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
57 90 0.94
58 6 0.06
ACGTcount: A:0.25, C:0.37, G:0.01, T:0.37
Consensus pattern (57 bp):
CCATCTACCATCAATCCATCTTTCACTTCTATTCCACCAACCATCTCCACTTCTATT
Found at i:3149 original size:33 final size:33
Alignment explanation
Indices: 3111--3213 Score: 107
Period size: 33 Copynumber: 3.4 Consensus size: 33
3101 CAACCATCTC
3111 CACTTCTATTCCATTTACCATCAATCCATCTTT
1 CACTTCTATTCCATTTACCATCAATCCATCTTT
*
3144 CACTTC---T--A-TT-CCATCAA-CCATCTCT
1 CACTTCTATTCCATTTACCATCAATCCATCTTT
* *
3169 -ACTTCTATTCCATCTACCATCAATCCACCTTT
1 CACTTCTATTCCATTTACCATCAATCCATCTTT
*
3201 CGCTTCTATTCCA
1 CACTTCTATTCCA
3214 CCAATTATCT
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
24 5 0.09
25 7 0.12
26 7 0.12
27 3 0.05
28 1 0.02
29 1 0.02
30 2 0.04
31 7 0.12
32 6 0.11
33 17 0.30
ACGTcount: A:0.23, C:0.37, G:0.01, T:0.39
Consensus pattern (33 bp):
CACTTCTATTCCATTTACCATCAATCCATCTTT
Found at i:3175 original size:24 final size:25
Alignment explanation
Indices: 3128--3189 Score: 90
Period size: 24 Copynumber: 2.5 Consensus size: 25
3118 ATTCCATTTA
*
3128 CCATCAATCCATCTTTCACTTCTATT
1 CCATCAA-CCATCTCTCACTTCTATT
3154 CCATCAACCATCTCT-ACTTCTATT
1 CCATCAACCATCTCTCACTTCTATT
*
3178 CCATCTACCATC
1 CCATCAACCATC
3190 AATCCACCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 20 0.59
25 7 0.21
26 7 0.21
ACGTcount: A:0.24, C:0.39, G:0.00, T:0.37
Consensus pattern (25 bp):
CCATCAACCATCTCTCACTTCTATT
Found at i:6390 original size:15 final size:15
Alignment explanation
Indices: 6370--6422 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
6360 AATTTTTTTC
6370 AAATAATCAT-ATATA
1 AAATAAT-ATAATATA
6385 AAATAAATATAATATA
1 AAAT-AATATAATATA
* *
6401 ATATAATATAATAAA
1 AAATAATATAATATA
6416 AAATAAT
1 AAATAAT
6423 TTTATCTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 22 0.67
16 11 0.33
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAATATAATATA
Found at i:6397 original size:21 final size:21
Alignment explanation
Indices: 6372--6411 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6362 TTTTTTTCAA
6372 ATAATCAT-ATATAAAATAAAT
1 ATAAT-ATAATATAAAATAAAT
*
6393 ATAATATAATATAATATAA
1 ATAATATAATATAAAATAA
6412 TAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAATATAATATAAAATAAAT
Found at i:6398 original size:5 final size:5
Alignment explanation
Indices: 6380--6413 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
6370 AAATAATCAT
*
6380 ATATA AAATAA ATATA ATATA ATATA ATATA ATA
1 ATATA ATAT-A ATATA ATATA ATATA ATATA ATA
6414 AAAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
ATATA
Found at i:6421 original size:10 final size:10
Alignment explanation
Indices: 6380--6422 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
6370 AAATAATCAT
6380 ATATAAAATAA
1 ATATAAAAT-A
*
6391 ATATAATATA
1 ATATAAAATA
*
6401 ATATAATATA
1 ATATAAAATA
*
6411 ATAAAAAATA
1 ATATAAAATA
6421 AT
1 AT
6423 TTTATCTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
ATATAAAATA
Found at i:8982 original size:19 final size:19
Alignment explanation
Indices: 8937--8973 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
8927 TATAAATTTT
*
8937 AAATTTTAAAATATATTCA
1 AAATTTTCAAATATATTCA
8956 AAATTTTCAAA-ATATTCA
1 AAATTTTCAAATATATTCA
8974 CTAATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATTTTCAAATATATTCA
Found at i:9182 original size:13 final size:13
Alignment explanation
Indices: 9157--9200 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
9147 TTTATATAAA
*
9157 CAATTAATTAAAT
1 CAATTAATCAAAT
**
9170 CAATTTCTCAAAT
1 CAATTAATCAAAT
*
9183 CAACTAATCAAAT
1 CAATTAATCAAAT
9196 CAATT
1 CAATT
9201 GGTTAAATAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (13 bp):
CAATTAATCAAAT
Found at i:9208 original size:26 final size:26
Alignment explanation
Indices: 9153--9214 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
9143 CACTTTTATA
* * *
9153 TAAA-CAATTAATTAAATCAATTTCT
1 TAAATCAACTAATCAAATCAATTGCT
* *
9178 CAAATCAACTAATCAAATCAATTGGT
1 TAAATCAACTAATCAAATCAATTGCT
*
9204 TAAATAAACTA
1 TAAATCAACTA
9215 CTAGAATCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 3 0.10
26 26 0.90
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32
Consensus pattern (26 bp):
TAAATCAACTAATCAAATCAATTGCT
Found at i:12115 original size:133 final size:132
Alignment explanation
Indices: 11876--12286 Score: 555
Period size: 133 Copynumber: 3.1 Consensus size: 132
11866 GTAAATTCAA
* *
11876 TATTTGGTTTGTATT-TAATTTGAATGTTGTAATTGATGTTTGTTTCTAATTAGTGTTATTGGTG
1 TATTTGCTTTGT-TTCTAATTTGAATGTTGTAATTGATGTTTGTTTCTAATTAGTGTTATTAGTG
* * *
11940 TTTTTATATAATTTGAATGTTCAAATTAGACCATTTTTATTTTTACATGTAATTGAACTAATTGG
65 TTTGTATATAATTTGAATGTTCTAATTAGACTA-TTTTATTTTTACATGTAATTGAACTAATTGG
12005 TGGT
129 TGGT
*
12009 TATTTGCTTTGTTTCTACTTTGAATGTTGTAATTGATGTTTGTTTCTAATTAGTGTTACTT-GTG
1 TATTTGCTTTGTTTCTAATTTGAATGTTGTAATTGATGTTTGTTTCTAATTAGTGTTA-TTAGTG
* * * *
12073 TTTGTATATAACTTGAATGTTTTAATTATACTACTTTGATTTTTACATGTAATTGAACT-A---G
65 TTTGTATATAATTTGAATGTTCTAATTAGACTA-TTTTATTTTTACATGTAATTGAACTAATTGG
12134 TGGT
129 TGGT
* * *
12138 TGTTTGCTTTGTTTCTAATTTGAATGTTGTAATTGATGTTTATTTCTAATTAGAGTTATTAGTGT
1 TATTTGCTTTGTTTCTAATTTGAATGTTGTAATTGATGTTTGTTTCTAATTAGTGTTATTAGTGT
* * * * * *
12203 ATGTGTCTAATTTGAAAGTTCTAATTAGACTATTTTATTTTTACATATAATTGGACTAATTGGTG
66 TTGTATATAATTTGAATGTTCTAATTAGACTATTTTATTTTTACATGTAATTGAACTAATTGGTG
12268 GT
131 GT
* *
12270 TGTTTACTTTGTTTCTA
1 TATTTGCTTTGTTTCTA
12287 TTTTAAATTT
Statistics
Matches: 246, Mismatches: 25, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
128 24 0.10
129 89 0.36
132 24 0.10
133 107 0.43
134 2 0.01
ACGTcount: A:0.24, C:0.06, G:0.17, T:0.53
Consensus pattern (132 bp):
TATTTGCTTTGTTTCTAATTTGAATGTTGTAATTGATGTTTGTTTCTAATTAGTGTTATTAGTGT
TTGTATATAATTTGAATGTTCTAATTAGACTATTTTATTTTTACATGTAATTGAACTAATTGGTG
GT
Found at i:13299 original size:29 final size:30
Alignment explanation
Indices: 13267--13337 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
13257 ATGGATTTGG
* *
13267 TTAGGGACTAAAATAAAAAATTT-AGAAGT
1 TTAGGGACCAAAATAAAAAATTTGAAAAGT
* * *
13296 TTAGTGACCAAAATATAAACTTTGGAAAAGT
1 TTAGGGACCAAAATAAAAAATTT-GAAAAGT
13327 TTAGGGACCAA
1 TTAGGGACCAA
13338 TATGATAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.27
Consensus pattern (30 bp):
TTAGGGACCAAAATAAAAAATTTGAAAAGT
Found at i:15003 original size:30 final size:30
Alignment explanation
Indices: 14969--15030 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
14959 AAGGCATACT
14969 ATGTGAGTGCATTTATTATGTACATATATA
1 ATGTGAGTGCATTTATTATGTACATATATA
14999 ATGTGAGTGCATTTATTATGTACATATATA
1 ATGTGAGTGCATTTATTATGTACATATATA
15029 AT
1 AT
15031 ATGAAGACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (30 bp):
ATGTGAGTGCATTTATTATGTACATATATA
Found at i:15419 original size:53 final size:53
Alignment explanation
Indices: 15356--15466 Score: 186
Period size: 53 Copynumber: 2.1 Consensus size: 53
15346 TTTTGTGTAC
*
15356 TTTCGGCACTATTTGTGCACCCATGGTATTCATAATGAGTTTGTGAATTACCA
1 TTTCGGCACTATGTGTGCACCCATGGTATTCATAATGAGTTTGTGAATTACCA
* * *
15409 TTTCGGCACTATGTGTGCATCTATGGTATTCATAATGAGTTTTTGAATTACCA
1 TTTCGGCACTATGTGTGCACCCATGGTATTCATAATGAGTTTGTGAATTACCA
15462 TTTCG
1 TTTCG
15467 TTACCTTAGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (53 bp):
TTTCGGCACTATGTGTGCACCCATGGTATTCATAATGAGTTTGTGAATTACCA
Found at i:16554 original size:41 final size:41
Alignment explanation
Indices: 16504--16585 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
16494 AAAATAGTAG
* * *
16504 GCACACATGTTCATAACTTTCTAAATAGAACATGTCCAAAA
1 GCACACATGTTCATAACTTCCTAAACAAAACATGTCCAAAA
*
16545 GCACCCATGTTCATAACTTCCTAAACAAAACATGTCCAAAA
1 GCACACATGTTCATAACTTCCTAAACAAAACATGTCCAAAA
16586 CAGTAGGCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (41 bp):
GCACACATGTTCATAACTTCCTAAACAAAACATGTCCAAAA
Found at i:19107 original size:20 final size:20
Alignment explanation
Indices: 19078--19116 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19068 AATACTTAAC
19078 AATATATATTTAAATAACAA
1 AATATATATTTAAATAACAA
* *
19098 AATATTTATTTAAGTAACA
1 AATATATATTTAAATAACA
19117 TAAAAACGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (20 bp):
AATATATATTTAAATAACAA
Found at i:20300 original size:25 final size:22
Alignment explanation
Indices: 20253--20305 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
20243 TAATAATAAT
20253 AACAATAATAATTAAATATATA
1 AACAATAATAATTAAATATATA
20275 AACATATAA-AATATAAATATAAATA
1 AACA-ATAATAAT-TAAATAT--ATA
20300 AACAAT
1 AACAAT
20306 GACTAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 7 0.26
23 11 0.41
24 2 0.07
25 7 0.26
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (22 bp):
AACAATAATAATTAAATATATA
Found at i:23204 original size:344 final size:344
Alignment explanation
Indices: 22577--23265 Score: 1360
Period size: 344 Copynumber: 2.0 Consensus size: 344
22567 GACAGATATA
22577 TCAAGCCTCTCACTCATACAAGATTGTGGAGTGAAGGAGAGACAAGAATGTTCCAGCTCAACTCC
1 TCAAGCCTCTCACTCATACAAGATTGTGGAGTGAAGGAGAGACAAGAATGTTCCAGCTCAACTCC
22642 AAAGCCATCCATATCATATTTTGTGCTCTTGGACCAGATGAATATGGAAGAGTTTCATCTTGTAC
66 AAAGCCATCCATATCATATTTTGTGCTCTTGGACCAGATGAATATGGAAGAGTTTCATCTTGTAC
22707 AACCGCCAAAGAAATATGGGATAAACTACAAGTCACTCATGAAGGCACCGACGAGGTAAAAGAAT
131 AACCGCCAAAGAAATATGGGATAAACTACAAGTCACTCATGAAGGCACCGACGAGGTAAAAGAAT
22772 TTAAAATTAGTCTTCTAACACATAGCTATGAAAATTTCAGGATGAAACCAAATGAAGATATCAAA
196 TTAAAATTAGTCTTCTAACACATAGCTATGAAAATTTCAGGATGAAACCAAATGAAGATATCAAA
22837 GCTATGACGGATAGATTCTCAACGATTGTCAATGGTTTCAAATCATATGGAGAGATCATTCCAAA
261 GCTATGACGGATAGATTCTCAACGATTGTCAATGGTTTCAAATCATATGGAGAGATCATTCCAAA
22902 TGAAAAGCTTGTGAGGAAG
326 TGAAAAGCTTGTGAGGAAG
22921 TCAAGCCTCTCACTCATACAAGATTGTGGAGTGAAGGAGAGACAAGAATGTTCCAGCTCAACTCC
1 TCAAGCCTCTCACTCATACAAGATTGTGGAGTGAAGGAGAGACAAGAATGTTCCAGCTCAACTCC
*
22986 AAAGCCATTCATATCATATTTTGTGCTCTTGGACCAGATGAATATGGAAGAGTTTCATCTTGTAC
66 AAAGCCATCCATATCATATTTTGTGCTCTTGGACCAGATGAATATGGAAGAGTTTCATCTTGTAC
*
23051 AACCGCCAAAGAAATATGGGATAAACTACAAGTCACTTATGAAGGCACCGACGAGGTAAAAGAAT
131 AACCGCCAAAGAAATATGGGATAAACTACAAGTCACTCATGAAGGCACCGACGAGGTAAAAGAAT
23116 TTAAAATTAGTCTTCTAACACATAGCTATGAAAATTTCAGGATGAAACCAAATGAAGATATCAAA
196 TTAAAATTAGTCTTCTAACACATAGCTATGAAAATTTCAGGATGAAACCAAATGAAGATATCAAA
23181 GCTATGACGGATAGATTCTCAACGATTGTCAATGGTTTCAAATCATATGGAGAGATCATTCCAAA
261 GCTATGACGGATAGATTCTCAACGATTGTCAATGGTTTCAAATCATATGGAGAGATCATTCCAAA
23246 TGAAAAGCTTGTGAGGAAG
326 TGAAAAGCTTGTGAGGAAG
23265 T
1 T
23266 TAGTTTACTC
Statistics
Matches: 343, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
344 343 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (344 bp):
TCAAGCCTCTCACTCATACAAGATTGTGGAGTGAAGGAGAGACAAGAATGTTCCAGCTCAACTCC
AAAGCCATCCATATCATATTTTGTGCTCTTGGACCAGATGAATATGGAAGAGTTTCATCTTGTAC
AACCGCCAAAGAAATATGGGATAAACTACAAGTCACTCATGAAGGCACCGACGAGGTAAAAGAAT
TTAAAATTAGTCTTCTAACACATAGCTATGAAAATTTCAGGATGAAACCAAATGAAGATATCAAA
GCTATGACGGATAGATTCTCAACGATTGTCAATGGTTTCAAATCATATGGAGAGATCATTCCAAA
TGAAAAGCTTGTGAGGAAG
Found at i:25565 original size:18 final size:18
Alignment explanation
Indices: 25542--25598 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
25532 TCATAACTCT
25542 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
25560 ACCCGACTCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
25578 ACCCGACCCAATCCGTTG
1 ACCCGACCCGACCCGTTG
25596 ACC
1 ACC
25599 GTTGACCGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.19, C:0.47, G:0.19, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:25945 original size:20 final size:20
Alignment explanation
Indices: 25920--25966 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
25910 CCTGATTCGA
25920 TCCGTTTATCGTAATTAAGC
1 TCCGTTTATCGTAATTAAGC
25940 TCCGTTTATCGTAATTAAGC
1 TCCGTTTATCGTAATTAAGC
*
25960 TCTGTTT
1 TCCGTTT
25967 TTTTTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (20 bp):
TCCGTTTATCGTAATTAAGC
Found at i:26948 original size:26 final size:26
Alignment explanation
Indices: 26900--26949 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
26890 AATGACTTAA
*
26900 GAATATCACCAAGCTCAGGAATGATT
1 GAATATCACCAAGCTCAGAAATGATT
* * *
26926 GAATATCATCGAGCTCTGAAATGA
1 GAATATCACCAAGCTCAGAAATGA
26950 ATAGAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (26 bp):
GAATATCACCAAGCTCAGAAATGATT
Found at i:27970 original size:12 final size:12
Alignment explanation
Indices: 27954--28007 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
27944 CATTGCCTGA
*
27954 ATTCTGTTCTGG
1 ATTCTGATCTGG
*
27966 TTTCTGATCTGG
1 ATTCTGATCTGG
*
27978 ATTCTGCTCT-G
1 ATTCTGATCTGG
*
27989 ATATCTGATCTGA
1 AT-TCTGATCTGG
28002 ATTCTG
1 ATTCTG
28008 TTTTGATTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 3 0.09
12 29 0.85
13 2 0.06
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.46
Consensus pattern (12 bp):
ATTCTGATCTGG
Found at i:27981 original size:24 final size:24
Alignment explanation
Indices: 27950--28021 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
27940 GATACATTGC
*
27950 CTGAATTCTGTTCTGGTTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* * *
27974 CTGGATTCTGCTCTGATATCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
*
27998 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
28022 ATCTCCGTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.15, C:0.17, G:0.19, T:0.49
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:32649 original size:24 final size:24
Alignment explanation
Indices: 32622--32681 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
32612 GATACATTAC
* *
32622 CTGAATTCTGATCTGGATTTTGTT
1 CTGAATTCTGATCTGAATTCTGTT
*
32646 CTGATATT-TTATCTGAATTCTGTT
1 CTGA-ATTCTGATCTGAATTCTGTT
* *
32670 TTGATTTCTGAT
1 CTGAATTCTGAT
32682 ATCTATGTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
23 2 0.07
24 23 0.82
25 3 0.11
ACGTcount: A:0.18, C:0.12, G:0.17, T:0.53
Consensus pattern (24 bp):
CTGAATTCTGATCTGAATTCTGTT
Found at i:34775 original size:41 final size:41
Alignment explanation
Indices: 34730--34811 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
34720 TCACAACTCA
* * *
34730 ACCCGACCTGTTAACCCGACCCGACCCATTGACCTGACCCG
1 ACCCGACCCGTTAACCCAACCCGACCCATTGACCCGACCCG
* * * *
34771 ACCCGACCCGTTGATCCAACCCGATCCGTTGACCCGACCCG
1 ACCCGACCCGTTAACCCAACCCGACCCATTGACCCGACCCG
34812 TTGACCGGCG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.21, C:0.46, G:0.18, T:0.15
Consensus pattern (41 bp):
ACCCGACCCGTTAACCCAACCCGACCCATTGACCCGACCCG
Found at i:34792 original size:23 final size:23
Alignment explanation
Indices: 34741--34794 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
34731 CCCGACCTGT
34741 TAACCCGACCCGACCCATTGACC
1 TAACCCGACCCGACCCATTGACC
* *
34764 TGACCCGACCCGACCCGTTGATCC
1 TAACCCGACCCGACCCATTGA-CC
34788 -AACCCGA
1 TAACCCGA
34795 TCCGTTGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 25 0.93
24 2 0.07
ACGTcount: A:0.24, C:0.46, G:0.17, T:0.13
Consensus pattern (23 bp):
TAACCCGACCCGACCCATTGACC
Found at i:34810 original size:18 final size:18
Alignment explanation
Indices: 34764--34811 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
34754 CCCATTGACC
34764 TGACCCGACCCGACCCGT
1 TGACCCGACCCGACCCGT
* * *
34782 TGATCCAACCCGATCCGT
1 TGACCCGACCCGACCCGT
34800 TGACCCGACCCG
1 TGACCCGACCCG
34812 TTGACCGGCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.19, C:0.46, G:0.21, T:0.15
Consensus pattern (18 bp):
TGACCCGACCCGACCCGT
Found at i:39419 original size:18 final size:18
Alignment explanation
Indices: 39396--39445 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
39386 GATCACAACT
**
39396 CGACCCGACCTGTTGACC
1 CGACCCGACCCATTGACC
39414 CGACCCGACCCATTGACC
1 CGACCCGACCCATTGACC
39432 CGACCCGACCCATT
1 CGACCCGACCCATT
39446 AATCCAACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.20, C:0.48, G:0.18, T:0.14
Consensus pattern (18 bp):
CGACCCGACCCATTGACC
Found at i:39455 original size:18 final size:18
Alignment explanation
Indices: 39411--39457 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
39401 CGACCTGTTG
* *
39411 ACCCGACCCGACCCATTG
1 ACCCAACCCGACCCATTA
*
39429 ACCCGACCCGACCCATTA
1 ACCCAACCCGACCCATTA
*
39447 ATCCAACCCGA
1 ACCCAACCCGA
39458 TCTGTTGACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.28, C:0.49, G:0.13, T:0.11
Consensus pattern (18 bp):
ACCCAACCCGACCCATTA
Found at i:44342 original size:10 final size:9
Alignment explanation
Indices: 44307--44405 Score: 81
Period size: 10 Copynumber: 10.3 Consensus size: 9
44297 GATGCTGGAA
*
44307 ACCGGTTTA
1 ACCGGTTTG
*
44316 ACCGGTTTTCA
1 ACCGG-TTT-G
44327 ACCGGTTCTG
1 ACCGGTT-TG
44337 ACCGGTTTG
1 ACCGGTTTG
*
44346 ACCGGTTTCA
1 ACCGGTTT-G
*
44356 ACCGGTTCG
1 ACCGGTTTG
44365 AACCGGTTTG
1 -ACCGGTTTG
*
44375 ACCGGTCTG
1 ACCGGTTTG
*
44384 AATCGGTTTG
1 -ACCGGTTTG
*
44394 ACCGGTCTG
1 ACCGGTTTG
44403 ACC
1 ACC
44406 CGACCCGACC
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
9 33 0.45
10 34 0.46
11 7 0.09
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:44351 original size:19 final size:19
Alignment explanation
Indices: 44308--44405 Score: 78
Period size: 19 Copynumber: 5.1 Consensus size: 19
44298 ATGCTGGAAA
* * *
44308 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
44328 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
44347 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
44367 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
44386 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
44404 CC
1 CC
44406 CGACCCGACC
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
18 5 0.07
19 39 0.58
20 15 0.22
21 8 0.12
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:44369 original size:29 final size:30
Alignment explanation
Indices: 44306--44405 Score: 118
Period size: 29 Copynumber: 3.4 Consensus size: 30
44296 GGATGCTGGA
*
44306 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
44337 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
* * *
44365 AACCGGTTTGACCGGTCTGAATCGGTT-TG
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
44394 -ACCGGTCTGACC
1 AACCGGTTTGACC
44406 CGACCCGACC
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
28 12 0.19
29 37 0.60
30 13 0.21
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:44412 original size:5 final size:5
Alignment explanation
Indices: 44402--44459 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
44392 TGACCGGTCT
* *
44402 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
44451 GACCC GACC
1 GACCC GACC
44460 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:44428 original size:22 final size:22
Alignment explanation
Indices: 44402--44466 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
44392 TGACCGGTCT
44402 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
44424 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
44446 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
44467 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:44468 original size:7 final size:7
Alignment explanation
Indices: 44456--44486 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
44446 GACCCGACCC
44456 GACCGTT
1 GACCGTT
44463 GACCGTT
1 GACCGTT
44470 GACCGTT
1 GACCGTT
44477 GACCGTT
1 GACCGTT
44484 GAC
1 GAC
44487 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:51662 original size:9 final size:9
Alignment explanation
Indices: 51648--51741 Score: 71
Period size: 10 Copynumber: 9.8 Consensus size: 9
51638 GGATGCTGGA
51648 AACCGGTTT
1 AACCGGTTT
51657 AACCGGTTTT
1 AACCGG-TTT
51667 CAACCGGTTCT
1 -AACCGGTT-T
*
51678 GACCGGTTT
1 AACCGGTTT
*
51687 GACCGGTTT
1 AACCGGTTT
*
51696 CAACCGGTTCA
1 -AACCGGTT-T
51707 AACCGGTTT
1 AACCGGTTT
* *
51716 GACCGGTCTG
1 AACCGGT-TT
*
51726 AATCGGTTT
1 AACCGGTTT
*
51735 GACCGGT
1 AACCGGT
51742 CTGACCCGAC
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
9 28 0.41
10 33 0.49
11 7 0.10
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:51693 original size:19 final size:19
Alignment explanation
Indices: 51650--51747 Score: 76
Period size: 19 Copynumber: 5.1 Consensus size: 19
51640 ATGCTGGAAA
* * *
51650 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
51670 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
* **
51689 CCGGTTTCAACCGGTTCAAA
1 CCGGTTT-GACCGGTTCTGA
51709 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
51728 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
51746 CC
1 CC
51748 CGACCCGACC
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.08
19 36 0.56
20 15 0.23
21 8 0.12
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:51711 original size:29 final size:29
Alignment explanation
Indices: 51647--51722 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
51637 TGGATGCTGG
*
51647 AAACCGGTTTAACCGGTTTTCAACCGGTTC
1 AAACCGGTTTGACCGG-TTTCAACCGGTTC
**
51677 TGACCGGTTTGACCGGTTTCAACCGGTTC
1 AAACCGGTTTGACCGGTTTCAACCGGTTC
51706 AAACCGGTTTGACCGGT
1 AAACCGGTTTGACCGGT
51723 CTGAATCGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 28 0.68
30 13 0.32
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (29 bp):
AAACCGGTTTGACCGGTTTCAACCGGTTC
Found at i:51746 original size:9 final size:9
Alignment explanation
Indices: 51669--51747 Score: 50
Period size: 9 Copynumber: 8.3 Consensus size: 9
51659 CCGGTTTTCA
51669 ACCGGTTCTG
1 ACCGG-TCTG
*
51679 ACCGGTTTG
1 ACCGGTCTG
* *
51688 ACCGGTTTCA
1 ACCGGTCT-G
**
51698 ACCGGTTCAA
1 ACCGG-TCTG
*
51708 ACCGGTTTG
1 ACCGGTCTG
51717 ACCGGTCTG
1 ACCGGTCTG
* *
51726 AATCGGTTTG
1 -ACCGGTCTG
51736 ACCGGTCTG
1 ACCGGTCTG
51745 ACC
1 ACC
51748 CGACCCGACC
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
9 30 0.56
10 23 0.43
11 1 0.02
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:51754 original size:5 final size:5
Alignment explanation
Indices: 51744--51801 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
51734 TGACCGGTCT
* *
51744 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
51793 GACCC GACC
1 GACCC GACC
51802 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:51770 original size:22 final size:22
Alignment explanation
Indices: 51744--51808 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
51734 TGACCGGTCT
51744 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
51766 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
51788 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
51809 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:51810 original size:7 final size:7
Alignment explanation
Indices: 51798--51828 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
51788 GACCCGACCC
51798 GACCGTT
1 GACCGTT
51805 GACCGTT
1 GACCGTT
51812 GACCGTT
1 GACCGTT
51819 GACCGTT
1 GACCGTT
51826 GAC
1 GAC
51829 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:56568 original size:23 final size:23
Alignment explanation
Indices: 56542--56593 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
56532 GATTAGATAA
56542 TGACGGGTTAGACAATGAAAAAC
1 TGACGGGTTAGACAATGAAAAAC
56565 TGACGGGTTAGACAATGAAAAAC
1 TGACGGGTTAGACAATGAAAAAC
56588 TGACGG
1 TGACGG
56594 TAGGATCTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.29, T:0.17
Consensus pattern (23 bp):
TGACGGGTTAGACAATGAAAAAC
Found at i:58944 original size:46 final size:44
Alignment explanation
Indices: 58869--58983 Score: 124
Period size: 46 Copynumber: 2.5 Consensus size: 44
58859 ATCAAAAAGC
* * * **
58869 ACCCGAAGGCTTTTTGAAAACATCTTGCACTGCATGTCTTATGGATG
1 ACCCGAAGG--TTTTG-AAACATCATGCACTGAAGGTCTTACAGATG
58916 ACCCCGAAGGTTTTGAAAGCATCATGCACTGAAGGTCTTACAGATG
1 A-CCCGAAGGTTTTGAAA-CATCATGCACTGAAGGTCTTACAGATG
58962 ACCCGAA-GTCTTTGAAACATCA
1 ACCCGAAGGT-TTTGAAACATCA
58984 AAAAGCTCCC
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
44 7 0.12
45 16 0.27
46 28 0.47
47 1 0.02
48 8 0.13
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (44 bp):
ACCCGAAGGTTTTGAAACATCATGCACTGAAGGTCTTACAGATG
Found at i:59021 original size:75 final size:74
Alignment explanation
Indices: 58918--59059 Score: 180
Period size: 75 Copynumber: 1.9 Consensus size: 74
58908 TATGGATGAC
*
58918 CCCGAAGGTTTTGAAAGCATCATGCACTGAAGGTCTTACAGATGACCCGAA-GTCTTTG-AAACA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT-TTTGAAAACA
58981 TCAAAAAGCT
65 TCAAAAAGCT
* * * ** *
58991 CCCGAAGGCTTCTTGAAAATATCCTGCACTGCAGGTCTTATGGATGACCTGAAGGTTTTGAAAAC
1 CCCGAAGG-TT-TTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAAC
59056 ATCA
64 ATCA
59060 TGCACAGAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
73 8 0.14
74 2 0.03
75 38 0.66
76 10 0.17
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (74 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACAT
CAAAAAGCT
Found at i:60330 original size:117 final size:117
Alignment explanation
Indices: 60108--60409 Score: 412
Period size: 117 Copynumber: 2.6 Consensus size: 117
60098 TTTTATATAT
* * * **
60108 TTCCCC-GAAACATACACACACCTGGACACCAGTAAGGACTTACCCTAAGCACGA-AGCTGAGGA
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCAC-ACAGCAAAGGA
** *
60171 GCCTGCAGTAATAACGTCTTCATCCAGTCGCTTCCATAACTACAATGTGTAGG
65 GCCTGCAGTAATAACGTCCCCATCCAGTCACTTCCATAACTACAATGTGTAGG
* ** *
60224 TTCCTCATTACCATACACCCACCTGCACACCAGTAAGGACTTACCCCAAGCACACAGCAAAGGAG
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAG
* *
60289 CCTGCAGTAATAACTTCCCCATCCAGTCAC-TCCAATCACTACAATGTGTAGG
66 CCTGCAGTAATAACGTCCCCATCCAGTCACTTCC-ATAACTACAATGTGTAGG
* * *
60341 TTCCCCAGAACCATACACCCACATGCACACCAGTAAGGACTTACCCTGAGCACACAACAAAGGAG
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAG
60406 CCTG
66 CCTG
60410 AAATACTTCC
Statistics
Matches: 162, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
116 9 0.06
117 153 0.94
ACGTcount: A:0.32, C:0.33, G:0.16, T:0.19
Consensus pattern (117 bp):
TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAG
CCTGCAGTAATAACGTCCCCATCCAGTCACTTCCATAACTACAATGTGTAGG
Found at i:61405 original size:30 final size:28
Alignment explanation
Indices: 61324--61444 Score: 116
Period size: 29 Copynumber: 4.1 Consensus size: 28
61314 CATTTTATAG
* *
61324 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCA-CCTTTTTAAATTAATTCCCA
* * *
61353 AAATAACACATTTTTGAATTAAATTCCCA
1 AAATAGCACCTTTTTAAATT-AATTCCCA
61382 AAATAGCACCTTTTTCAAATTAAATTCCCA
1 AAATAGCACCTTTTT-AAATT-AATTCCCA
* * **
61412 GAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCA-CCTTTTTAAATTAATTCCCA
61441 AAAT
1 AAAT
61445 GTCACTCGGT
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
28 9 0.12
29 38 0.50
30 24 0.32
31 5 0.07
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.31
Consensus pattern (28 bp):
AAATAGCACCTTTTTAAATTAATTCCCA
Found at i:61483 original size:17 final size:18
Alignment explanation
Indices: 61461--61497 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
61451 CGGTCAACGA
*
61461 TCAAC-GGTCGGGTTGGG
1 TCAACGGGTCGGGTCGGG
61478 TCAACGGGTCGGGTCGGG
1 TCAACGGGTCGGGTCGGG
61496 TC
1 TC
61498 TGGTCAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.11, C:0.22, G:0.46, T:0.22
Consensus pattern (18 bp):
TCAACGGGTCGGGTCGGG
Found at i:66667 original size:115 final size:116
Alignment explanation
Indices: 66489--66793 Score: 402
Period size: 115 Copynumber: 2.6 Consensus size: 116
66479 TTTTATATAT
* **
66489 TTCCCC-GAAACATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACGA-AGCTGAGGA
1 TTCCCCAGAACCATACACCCA-CTGCACACCAGTAAGGACTTACCCTAAGCAC-ACAGCAAAGGA
* * *
66552 GCCTGCAGTAATAACGTCTCCATCCAGTCGCTTCC-ATAACTACAATGTGTAGG
64 GCCTGCAATAATAACGTCCCCATCCAGTCAC-TCCAATAACTACAATGTGTAGG
* * *
66605 TTCCCCAGTACCATACACCCA-TGTACACCAATAAGGACTTACCCTAAGCACACAGCAAAGGAGC
1 TTCCCCAGAACCATACACCCACTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGC
* * *
66669 CTGCAATAATAACTTCCCCATCCAGTCACTCCAATCACTATAATGTGTAGG
66 CTGCAATAATAACGTCCCCATCCAGTCACTCCAATAACTACAATGTGTAGG
* * *
66720 TTCCCCAGAACCATACACCCACCTGGACACCTGTAAGGACTTACCCTGAGCACACAGCAAAGGAG
1 TTCCCCAGAACCATACACCCA-CTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAG
*
66785 CCTGAAATA
65 CCTGCAATA
66794 CTTCCCTCAA
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
114 4 0.02
115 98 0.59
116 6 0.04
117 58 0.35
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.19
Consensus pattern (116 bp):
TTCCCCAGAACCATACACCCACTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGC
CTGCAATAATAACGTCCCCATCCAGTCACTCCAATAACTACAATGTGTAGG
Found at i:67770 original size:29 final size:29
Alignment explanation
Indices: 67738--67864 Score: 170
Period size: 29 Copynumber: 4.4 Consensus size: 29
67728 TTTTTAAAAT
*
67738 AATTACCAAAATAGTACCTTTTCGAATTA
1 AATTCCCAAAATAGTACCTTTTCGAATTA
*
67767 AATTCCCAAAATAGCA-CTTTTCGAATTA
1 AATTCCCAAAATAGTACCTTTTCGAATTA
*
67795 AATTCCCAAAATAGTACATTTTCGAATTA
1 AATTCCCAAAATAGTACCTTTTCGAATTA
* *
67824 AATTCCCAGAATA-TCACCCATTTCGAATT-
1 AATTCCCAAAATAGT-A-CCTTTTCGAATTA
67853 AATTCCCAAAAT
1 AATTCCCAAAAT
67865 GTCACCCGGT
Statistics
Matches: 87, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
28 28 0.32
29 49 0.56
30 10 0.11
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.32
Consensus pattern (29 bp):
AATTCCCAAAATAGTACCTTTTCGAATTA
Found at i:67808 original size:57 final size:57
Alignment explanation
Indices: 67737--67864 Score: 186
Period size: 57 Copynumber: 2.2 Consensus size: 57
67727 CTTTTTAAAA
* * *
67737 TAATTACCAAAATAGTACCTTTTCGAATTAAATTCCCAAAATAGCA-CTTTTCGAAT
1 TAATTCCCAAAATAGTACATTTTCGAATTAAATTCCCAAAATAGCACCATTTCGAAT
* *
67793 TAAATTCCCAAAATAGTACATTTTCGAATTAAATTCCCAGAATATCACCCATTTCGAAT
1 T-AATTCCCAAAATAGTACATTTTCGAATTAAATTCCCAAAATAGCA-CCATTTCGAAT
67852 TAATTCCCAAAAT
1 TAATTCCCAAAAT
67865 GTCACCCGGT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
56 1 0.02
57 41 0.64
58 12 0.19
59 10 0.16
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (57 bp):
TAATTCCCAAAATAGTACATTTTCGAATTAAATTCCCAAAATAGCACCATTTCGAAT
Found at i:67901 original size:17 final size:18
Alignment explanation
Indices: 67879--67963 Score: 76
Period size: 18 Copynumber: 4.9 Consensus size: 18
67869 CCCGGTCAAC
67879 GGTCAAC-GGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
67896 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
67914 GGT---CGGTTCAATGGGTCG
1 GGTCAACGGGTC---GGGTCG
67932 GGT---CGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
67947 GTTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
67964 AAAACCGGTC
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
15 13 0.22
17 7 0.12
18 38 0.66
ACGTcount: A:0.09, C:0.21, G:0.48, T:0.21
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:67956 original size:23 final size:23
Alignment explanation
Indices: 67886--67963 Score: 102
Period size: 23 Copynumber: 3.2 Consensus size: 23
67876 AACGGTCAAC
*
67886 GGTCGGGTCGGGTCAACGGGTCG
1 GGTCGGGTCGGTTCAACGGGTCG
67909 GGTCGGGTCGGTTCAATGGGTCGGGTCG
1 GGTCGGGTCGGTTCAA-----CGGGTCG
67937 GGTCGGGTCGGTTCAACGGGTCG
1 GGTCGGGTCGGTTCAACGGGTCG
67960 GGTC
1 GGTC
67964 AAAACCGGTC
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
23 26 0.53
28 23 0.47
ACGTcount: A:0.08, C:0.21, G:0.50, T:0.22
Consensus pattern (23 bp):
GGTCGGGTCGGTTCAACGGGTCG
Found at i:67963 original size:5 final size:5
Alignment explanation
Indices: 67886--67947 Score: 61
Period size: 5 Copynumber: 11.2 Consensus size: 5
67876 AACGGTCAAC
*
67886 GGTCG GGTCG GGTCAACG GGTCG GGTCG GGTCG GTTCAATG GGTCG GGTCG
1 GGTCG GGTCG GGT---CG GGTCG GGTCG GGTCG GGTC---G GGTCG GGTCG
67937 GGTCG GGTCG G
1 GGTCG GGTCG G
67948 TTCAACGGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
5 40 0.82
8 9 0.18
ACGTcount: A:0.06, C:0.19, G:0.53, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:67973 original size:28 final size:28
Alignment explanation
Indices: 67914--67973 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
67904 GGTCGGGTCG
* **** *
67914 GGTCGGTTCAATGGGTCGGGTCGGGTCG
1 GGTCGGTTCAACGGGTCGGGTCAAAACC
67942 GGTCGGTTCAACGGGTCGGGTCAAAACC
1 GGTCGGTTCAACGGGTCGGGTCAAAACC
67970 GGTC
1 GGTC
67974 AAACCAGTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.13, C:0.22, G:0.43, T:0.22
Consensus pattern (28 bp):
GGTCGGTTCAACGGGTCGGGTCAAAACC
Found at i:68618 original size:22 final size:22
Alignment explanation
Indices: 68580--68632 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
68570 GTTACAATCT
68580 ATCTTTG-AGAGAAAATCTATC
1 ATCTTTGAAGAGAAAATCTATC
*
68601 ATCTTTGAAGAGAGAATCTATC
1 ATCTTTGAAGAGAAAATCTATC
68623 A--TTTGAAGAG
1 ATCTTTGAAGAG
68633 TGTAGATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 9 0.30
21 7 0.23
22 14 0.47
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (22 bp):
ATCTTTGAAGAGAAAATCTATC
Found at i:70072 original size:73 final size:74
Alignment explanation
Indices: 69926--70149 Score: 247
Period size: 73 Copynumber: 3.0 Consensus size: 74
69916 CTTCAACAGC
* * * * * * *
69926 CTGATACAGACGTTCAAAATGCACCAACATTCCTGA-TTCTGATTAAAAGGGCTTTCAGCATGTC
1 CTGATACAAACGTTCAAAATGCATCAATATTCC-AACTTCTGATTGAAATGGCTTTCAGCATGCC
*
69990 CCAACATTTG
65 CCAGCATTTG
* * *** * *
70000 CTGATACACATGTTCAAAATG-AGTCAATATTTTTA-TTTTGATTGAAATGGCTTTCAGTATGCC
1 CTGATACAAACGTTCAAAATGCA-TCAATATTCCAACTTCTGATTGAAATGGCTTTCAGCATGCC
*
70063 CCAGTATTTG
65 CCAGCATTTG
*
70073 CTGATACAAACGTTCAAAATGCATTAATATTCCAACTTCTGATTGAAATGGGCTTTCAGCATGCC
1 CTGATACAAACGTTCAAAATGCATCAATATTCCAACTTCTGATTGAAAT-GGCTTTCAGCATGCC
70138 CCAGCATTTG
65 CCAGCATTTG
70148 CT
1 CT
70150 TCTTGTTGAT
Statistics
Matches: 123, Mismatches: 23, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
73 60 0.49
74 38 0.31
75 25 0.20
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (74 bp):
CTGATACAAACGTTCAAAATGCATCAATATTCCAACTTCTGATTGAAATGGCTTTCAGCATGCCC
CAGCATTTG
Done.