Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005932.1 Hibiscus syriacus cultivar Beakdansim tig00013922_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: 123337
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:61 original size:17 final size:18
Alignment explanation
Indices: 34--68 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
24 CTCAAAGTTA
34 TACATTATTTTAAATAAT
1 TACATTATTTTAAATAAT
*
52 TACA-TATTTTATATAAT
1 TACATTATTTTAAATAAT
69 ATATCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
TACATTATTTTAAATAAT
Found at i:7155 original size:42 final size:43
Alignment explanation
Indices: 7109--7199 Score: 130
Period size: 42 Copynumber: 2.1 Consensus size: 43
7099 AATAGTATTT
*
7109 TTATATCTCTATTTTTATTGAATACAAATAATATTTTTT-TAA
1 TTATATCTCTATTTTGATTGAATACAAATAATATTTTTTATAA
* * *
7151 TTATATCTCTATTTTGATTGATTATAAATGATATTTTTTATAA
1 TTATATCTCTATTTTGATTGAATACAAATAATATTTTTTATAA
*
7194 ATATAT
1 TTATAT
7200 TATTAAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 35 0.81
43 8 0.19
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.55
Consensus pattern (43 bp):
TTATATCTCTATTTTGATTGAATACAAATAATATTTTTTATAA
Found at i:13340 original size:20 final size:20
Alignment explanation
Indices: 13304--13342 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13294 TTTACTTTTA
*
13304 AATTTTATATACTTTAAACC
1 AATTTTATAAACTTTAAACC
13324 AATTTATATAAAC-TTAAAC
1 AATTT-TATAAACTTTAAAC
13343 TGTTGATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTTATAAACTTTAAACC
Found at i:13754 original size:31 final size:31
Alignment explanation
Indices: 13716--13784 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 31
13706 ATTATAAAAA
*
13716 AAAAATATTAAA-TCATTATTTGAATATATTT
1 AAAAATATTAAACTC-TTATTTGAAAATATTT
13747 AAAAATATTAAACTCTTATTTGAAAATATTT
1 AAAAATATTAAACTCTTATTTGAAAATATTT
13778 AAAAATA
1 AAAAATA
13785 ATAAGTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (31 bp):
AAAAATATTAAACTCTTATTTGAAAATATTT
Found at i:13856 original size:16 final size:16
Alignment explanation
Indices: 13835--13868 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13825 CGGAAACGAC
13835 TATTTAAAGATTAAAT
1 TATTTAAAGATTAAAT
* *
13851 TATTTAAATATTTAAT
1 TATTTAAAGATTAAAT
13867 TA
1 TA
13869 ATACATTAAC
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TATTTAAAGATTAAAT
Found at i:16225 original size:20 final size:19
Alignment explanation
Indices: 16186--16223 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
16176 GTCTCATAAT
16186 TTTAATTCATCCCCTTAAA
1 TTTAATTCATCCCCTTAAA
16205 TTTAAGTTCA-CCCCTTAAA
1 TTTAA-TTCATCCCCTTAAA
16224 ATAAAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (19 bp):
TTTAATTCATCCCCTTAAA
Found at i:20338 original size:23 final size:23
Alignment explanation
Indices: 20304--20372 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
20294 CACCACAGCT
*
20304 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
20327 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
20350 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
20373 TATAAGGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:20486 original size:20 final size:20
Alignment explanation
Indices: 20463--20513 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
20453 GACCTCACAC
20463 ATGTTCCGAAGAATACATAT
1 ATGTTCCGAAGAATACATAT
20483 ATGTTCCGAAGAATACATAT
1 ATGTTCCGAAGAATACATAT
*
20503 ATGTCCCGAAG
1 ATGTTCCGAAG
20514 GACCGCGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (20 bp):
ATGTTCCGAAGAATACATAT
Found at i:21809 original size:18 final size:18
Alignment explanation
Indices: 21786--21820 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
21776 TGCATCGATG
21786 CTTATGCATCGATGCATC
1 CTTATGCATCGATGCATC
21804 CTTATGCATCGATGCAT
1 CTTATGCATCGATGCAT
21821 AAATTGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (18 bp):
CTTATGCATCGATGCATC
Found at i:26112 original size:26 final size:26
Alignment explanation
Indices: 26057--26112 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
26047 ATTTGAGTTG
* * *
26057 TATTTTGTGGATTGACTCTCCGTATG
1 TATTTTGTAGATTGACTCTCCCTATA
*
26083 TATTTTGTAGATTGACTTTCCCCT-TA
1 TATTTTGTAGATTGACTCT-CCCTATA
26109 TATT
1 TATT
26113 ATGTCGTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (26 bp):
TATTTTGTAGATTGACTCTCCCTATA
Found at i:26540 original size:15 final size:15
Alignment explanation
Indices: 26520--26555 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
26510 GAATATATCA
26520 ATATTTTAAAATAAT
1 ATATTTTAAAATAAT
*
26535 ATATTTTATAATAAT
1 ATATTTTAAAATAAT
26550 ATATTT
1 ATATTT
26556 ATAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTTAAAATAAT
Found at i:26568 original size:14 final size:14
Alignment explanation
Indices: 26519--26560 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
26509 CGAATATATC
*
26519 AATAT-TTTAAAAT
1 AATATATTTATAAT
26532 AATATATTTTATAAT
1 AATATA-TTTATAAT
26547 AATATATTTATAAT
1 AATATATTTATAAT
26561 TATTTATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 5 0.19
14 8 0.31
15 13 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATATATTTATAAT
Found at i:27021 original size:13 final size:13
Alignment explanation
Indices: 26977--27021 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
26967 TATTTTCTAT
26977 ATTAATTATAATC
1 ATTAATTATAATC
*
26990 CTTATATTATAAATC
1 ATTA-ATTAT-AATC
27005 -TTAATTATAATC
1 ATTAATTATAATC
27017 ATTAA
1 ATTAA
27022 ATTAATCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 8 0.29
15 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTAATTATAATC
Found at i:29273 original size:122 final size:122
Alignment explanation
Indices: 29056--29300 Score: 481
Period size: 122 Copynumber: 2.0 Consensus size: 122
29046 TTGACACTTA
29056 TCACTTAACGATAAATTTAATGCTCTTTATCGCTAAGACGCCTAAAAGTATAATATTGTAAACAT
1 TCACTTAACGATAAATTTAATGCTCTTTATCGCTAAGACGCCTAAAAGTATAATATTGTAAACAT
29121 TAGACACCTGGATTGACCAAAAAAATTACACACCTAAATAGAAAAAACGACATAATT
66 TAGACACCTGGATTGACCAAAAAAATTACACACCTAAATAGAAAAAACGACATAATT
*
29178 TCACTTAACGATAAATTTAATGCTCTTTATGGCTAAGACGCCTAAAAGTATAATATTGTAAACAT
1 TCACTTAACGATAAATTTAATGCTCTTTATCGCTAAGACGCCTAAAAGTATAATATTGTAAACAT
29243 TAGACACCTGGATTGACCAAAAAAATTACACACCTAAATAGAAAAAACGACATAATT
66 TAGACACCTGGATTGACCAAAAAAATTACACACCTAAATAGAAAAAACGACATAATT
29300 T
1 T
29301 GAACACTTAT
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 122 1.00
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (122 bp):
TCACTTAACGATAAATTTAATGCTCTTTATCGCTAAGACGCCTAAAAGTATAATATTGTAAACAT
TAGACACCTGGATTGACCAAAAAAATTACACACCTAAATAGAAAAAACGACATAATT
Found at i:48159 original size:6 final size:6
Alignment explanation
Indices: 48148--48172 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
48138 GAAGACACAT
48148 ATTACC ATTACC ATTACC ATTACC A
1 ATTACC ATTACC ATTACC ATTACC A
48173 CGACCACGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTACC
Found at i:48178 original size:6 final size:6
Alignment explanation
Indices: 48169--48199 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
48159 CATTACCATT
48169 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
48200 GCCGAGACGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:53396 original size:26 final size:26
Alignment explanation
Indices: 53359--53418 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
53349 CAGTTCACAG
* *
53359 TTTTCCCTTGTAGCGAGCGGCTTTCC
1 TTTTCCCCTGTAGCGAACGGCTTTCC
53385 TTTTCCCCTGTAGCGAACGGCTTTCC
1 TTTTCCCCTGTAGCGAACGGCTTTCC
53411 TTTTCCCC
1 TTTTCCCC
53419 ATTTCCTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.08, C:0.35, G:0.18, T:0.38
Consensus pattern (26 bp):
TTTTCCCCTGTAGCGAACGGCTTTCC
Found at i:57139 original size:23 final size:23
Alignment explanation
Indices: 57113--57157 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
57103 CACCACAGCT
*
57113 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
57136 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
57158 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:57392 original size:147 final size:149
Alignment explanation
Indices: 57125--57437 Score: 535
Period size: 147 Copynumber: 2.1 Consensus size: 149
57115 TATAATTGCA
57125 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
**
57189 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTT
*
57254 CCACAG-A-ATATATATATC
130 CCAAAGAATATATATATATC
*
57272 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
*
57337 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTT
57401 CCAAAGAATATATATATATC
130 CCAAAGAATATATATATATC
57421 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
57438 CCCTCGACTC
Statistics
Matches: 157, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
146 1 0.01
147 126 0.80
148 2 0.01
149 28 0.18
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTC
CAAAGAATATATATATATC
Found at i:57991 original size:2 final size:2
Alignment explanation
Indices: 57984--58031 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
57974 TCTCTTAGAC
57984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58026 AT AT AT
1 AT AT AT
58032 TCACATGTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58228 original size:2 final size:2
Alignment explanation
Indices: 58221--58246 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58211 CTAATATTTC
58221 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
58247 ATCTAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58394 original size:18 final size:18
Alignment explanation
Indices: 58373--58407 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
58363 TCCCATCTAG
58373 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
58391 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
58408 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:58997 original size:64 final size:63
Alignment explanation
Indices: 58899--59059 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
58889 TAATGAAGGT
* *
58899 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
58962 GG
62 GC
*
58964 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
59028 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
59060 CCTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:62639 original size:149 final size:149
Alignment explanation
Indices: 62361--62662 Score: 536
Period size: 149 Copynumber: 2.0 Consensus size: 149
62351 CGAAGTGTCA
62361 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACAACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACAACATAGAATTCCTTAAGAAT
** *
62426 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATATA
62491 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
* *
62510 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACAACATAGAATTCCTTAAGAAT
*
62575 CATATACATATGCTAGGGATC-A-TATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATATA
62638 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
62657 CGTAGA
1 CGTAGA
62663 CCCTCGACTC
Statistics
Matches: 147, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
147 62 0.42
148 1 0.01
149 84 0.57
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACAACATAGAATTCCTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATATA
TATATATCCCGAAGGACCG
Found at i:63216 original size:2 final size:2
Alignment explanation
Indices: 63209--63234 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63199 TCTCTTAGAC
63209 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
63235 TCACATGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63589 original size:18 final size:18
Alignment explanation
Indices: 63568--63602 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
63558 TCCCATCTAG
63568 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
63586 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
63603 AATCTCCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:64192 original size:64 final size:68
Alignment explanation
Indices: 64082--64218 Score: 212
Period size: 64 Copynumber: 2.1 Consensus size: 68
64072 AATTTCATCT
64082 TTTAATGAAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTT
1 TTTAATGAAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTT
*
64146 GTA
66 CTA
*
64149 TTTAATG-AGG-ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTT
1 TTTAATGAAGGTATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATGTTT
64210 TCTA
65 TCTA
64214 TTTAA
1 TTTAA
64219 ATTCATGCAT
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
63 1 0.02
64 30 0.45
65 25 0.38
66 3 0.05
67 7 0.11
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (68 bp):
TTTAATGAAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTT
CTA
Found at i:64227 original size:64 final size:64
Alignment explanation
Indices: 64094--64236 Score: 193
Period size: 64 Copynumber: 2.2 Consensus size: 64
64084 TAATGAAGGT
* *
64094 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGAGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-AGC
*
64159 ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA-AT
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTTAATA-
*
64221 TC
63 GC
64223 ATGCATCGATGCAC
1 ATGCATCGATGCAC
64237 CTTAAACAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
63 2 0.03
64 44 0.62
65 25 0.35
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATAGC
Found at i:65492 original size:13 final size:13
Alignment explanation
Indices: 65470--65499 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
65460 TCTTTGGGAA
65470 TGAA-AGTAATTT
1 TGAATAGTAATTT
65482 TGAATAGTAATTT
1 TGAATAGTAATTT
65495 TGAAT
1 TGAAT
65500 GTTTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (13 bp):
TGAATAGTAATTT
Found at i:66895 original size:23 final size:22
Alignment explanation
Indices: 66857--66900 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
66847 GTGTCAAGAA
* *
66857 GCAGAAAAAATGTGTCGTAAAG
1 GCAGAAAAAATATGTCATAAAG
66879 GCAGAAAAAATCATGTCATAAA
1 GCAGAAAAAAT-ATGTCATAAA
66901 TACATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.50, C:0.11, G:0.20, T:0.18
Consensus pattern (22 bp):
GCAGAAAAAATATGTCATAAAG
Found at i:70765 original size:18 final size:18
Alignment explanation
Indices: 70728--70765 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
70718 ATCTTGCCCG
*
70728 TCTTCTCTTCTGGTCAGT
1 TCTTCTCTTCTGATCAGT
70746 TCTTCTCTTCCTGATC-GT
1 TCTTCTCTT-CTGATCAGT
70764 TC
1 TC
70766 CCTTTCTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.05, C:0.32, G:0.13, T:0.50
Consensus pattern (18 bp):
TCTTCTCTTCTGATCAGT
Found at i:71148 original size:3 final size:3
Alignment explanation
Indices: 71140--71205 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
71130 TTGGTTAGAG
71140 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
71188 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
71206 ACTGCTTATT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:75204 original size:30 final size:30
Alignment explanation
Indices: 75168--75224 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
75158 AAGCTACGCG
75168 TATTAAACATATGGTTAATGTATTTAGTTA
1 TATTAAACATATGGTTAATGTATTTAGTTA
75198 TATTAAACATATGGTTAATGTATTTAG
1 TATTAAACATATGGTTAATGTATTTAG
75225 GATCCAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.46
Consensus pattern (30 bp):
TATTAAACATATGGTTAATGTATTTAGTTA
Found at i:78011 original size:30 final size:30
Alignment explanation
Indices: 77971--78052 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
77961 GGGAGCAGGC
*
77971 GGTGGGGTAGCTGGAGGAGGAGTTGCGGGT
1 GGTGGAGTAGCTGGAGGAGGAGTTGCGGGT
78001 GGTGGAGTAGCTGGAGGAGGAGTTGCGGGT
1 GGTGGAGTAGCTGGAGGAGGAGTTGCGGGT
* *
78031 GGTGGAGTAGCGGGAGGGGGAG
1 GGTGGAGTAGCTGGAGGAGGAG
78053 ATGTTGGCGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.16, C:0.06, G:0.61, T:0.17
Consensus pattern (30 bp):
GGTGGAGTAGCTGGAGGAGGAGTTGCGGGT
Found at i:78022 original size:15 final size:15
Alignment explanation
Indices: 77977--78052 Score: 71
Period size: 15 Copynumber: 5.1 Consensus size: 15
77967 AGGCGGTGGG
*
77977 GTAGCTGGAGGAGGA
1 GTAGCGGGAGGAGGA
* * *
77992 GTTGCGGGTGGTGGA
1 GTAGCGGGAGGAGGA
*
78007 GTAGCTGGAGGAGGA
1 GTAGCGGGAGGAGGA
* * *
78022 GTTGCGGGTGGTGGA
1 GTAGCGGGAGGAGGA
*
78037 GTAGCGGGAGGGGGA
1 GTAGCGGGAGGAGGA
78052 G
1 G
78053 ATGTTGGCGG
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.17, C:0.07, G:0.59, T:0.17
Consensus pattern (15 bp):
GTAGCGGGAGGAGGA
Found at i:78089 original size:60 final size:60
Alignment explanation
Indices: 78016--78143 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
78006 AGTAGCTGGA
* * * * * * *
78016 GGAGGAGTTGCGGGTGGTGGAGTAGCGGGAGGGGGAGATG-TTGGCGGAGGAGAGGC-AGGT
1 GGAGGGGTGGCGGGAGGTGGAGAAGCGGGAGGAGGAG-TGACTGGAGGAGGAGA-GCTAGGT
* *
78076 GGTGGGGTGGCGGGAGGTGGAGAAGCGGGTGGAGGAGTGACTGGAGGAGGAGAGCTAGGT
1 GGAGGGGTGGCGGGAGGTGGAGAAGCGGGAGGAGGAGTGACTGGAGGAGGAGAGCTAGGT
78136 GGAGGGGT
1 GGAGGGGT
78144 TGAAACTGGG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
59 4 0.07
60 52 0.93
ACGTcount: A:0.19, C:0.06, G:0.61, T:0.14
Consensus pattern (60 bp):
GGAGGGGTGGCGGGAGGTGGAGAAGCGGGAGGAGGAGTGACTGGAGGAGGAGAGCTAGGT
Found at i:78098 original size:30 final size:29
Alignment explanation
Indices: 78061--78143 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 29
78051 AGATGTTGGC
* *
78061 GGAGGAGAGGCAGGTGGTGGGGTGGCGGGA
1 GGAGGAGA-GCAGGTGGAGGGGTGACGGGA
* * * *
78091 GGTGGAGAAGCGGGTGGAGGAGTGACTGGA
1 GGAGGAG-AGCAGGTGGAGGGGTGACGGGA
78121 GGAGGAGAGCTAGGTGGAGGGGT
1 GGAGGAGAGC-AGGTGGAGGGGT
78144 TGAAACTGGG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
29 3 0.07
30 38 0.90
31 1 0.02
ACGTcount: A:0.20, C:0.06, G:0.61, T:0.12
Consensus pattern (29 bp):
GGAGGAGAGCAGGTGGAGGGGTGACGGGA
Found at i:78110 original size:45 final size:45
Alignment explanation
Indices: 77989--78112 Score: 122
Period size: 45 Copynumber: 2.8 Consensus size: 45
77979 AGCTGGAGGA
* * * ** *
77989 GGAGTTGCGGGTGGTGGAGTAGCTGGAGGAGGAGTTGCGGGTGGT
1 GGAGTAGCGGGAGGTGGAGAAGCTGGAGGAGGAGAGGCAGGTGGT
* * * *
78034 GGAGTAGCGGGAGGGGGAGATGTTGGCGGAGGAGAGGCAGGTGGT
1 GGAGTAGCGGGAGGTGGAGAAGCTGGAGGAGGAGAGGCAGGTGGT
* * * *
78079 GGGGTGGCGGGAGGTGGAGAAGCGGGTGGAGGAG
1 GGAGTAGCGGGAGGTGGAGAAGCTGGAGGAGGAG
78113 TGACTGGAGG
Statistics
Matches: 62, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.17, C:0.06, G:0.61, T:0.15
Consensus pattern (45 bp):
GGAGTAGCGGGAGGTGGAGAAGCTGGAGGAGGAGAGGCAGGTGGT
Found at i:85449 original size:176 final size:176
Alignment explanation
Indices: 85155--85506 Score: 695
Period size: 176 Copynumber: 2.0 Consensus size: 176
85145 TTGGAGCCTA
85155 GAAAACCAATTCCTAGACAGGTTTAATGTTGCTTTCCTGCCTTTTGGGTGTTCATCGTAATGACC
1 GAAAACCAATTCCTAGACAGGTTTAATGTTGCTTTCCTGCCTTTTGGGTGTTCATCGTAATGACC
85220 TTTGTGCAATTATTTGTATGTGGCTCTGCATTCTTATTACTACTGGCTCATAGTTTTTCTCTCAT
66 TTTGTGCAATTATTTGTATGTGGCTCTGCATTCTTATTACTACTGGCTCATAGTTTTTCTCTCAT
85285 GCTCGAGAAATGTTTTACACACTCATATACGTGTGTGTGCACTTTT
131 GCTCGAGAAATGTTTTACACACTCATATACGTGTGTGTGCACTTTT
*
85331 GAAAACCAATTCCTAGACAGGTTTAATGTTGTTTTCCTGCCTTTTGGGTGTTCATCGTAATGACC
1 GAAAACCAATTCCTAGACAGGTTTAATGTTGCTTTCCTGCCTTTTGGGTGTTCATCGTAATGACC
85396 TTTGTGCAATTATTTGTATGTGGCTCTGCATTCTTATTACTACTGGCTCATAGTTTTTCTCTCAT
66 TTTGTGCAATTATTTGTATGTGGCTCTGCATTCTTATTACTACTGGCTCATAGTTTTTCTCTCAT
85461 GCTCGAGAAATGTTTTACACACTCATATACGTGTGTGTGCACTTTT
131 GCTCGAGAAATGTTTTACACACTCATATACGTGTGTGTGCACTTTT
85507 TTTTTTATTT
Statistics
Matches: 175, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 175 1.00
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (176 bp):
GAAAACCAATTCCTAGACAGGTTTAATGTTGCTTTCCTGCCTTTTGGGTGTTCATCGTAATGACC
TTTGTGCAATTATTTGTATGTGGCTCTGCATTCTTATTACTACTGGCTCATAGTTTTTCTCTCAT
GCTCGAGAAATGTTTTACACACTCATATACGTGTGTGTGCACTTTT
Found at i:86136 original size:11 final size:11
Alignment explanation
Indices: 86101--86142 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
86091 ACGGAAACAG
86101 ATTATTAAAAAA
1 ATTA-TAAAAAA
*
86113 AATATAAAAAA
1 ATTATAAAAAA
*
86124 ATTATACAAAA
1 ATTATAAAAAA
86135 ATT-TAAAA
1 ATTATAAAA
86143 TTTTCAACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 4 0.15
11 19 0.73
12 3 0.12
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (11 bp):
ATTATAAAAAA
Found at i:98344 original size:29 final size:29
Alignment explanation
Indices: 98310--98393 Score: 159
Period size: 29 Copynumber: 2.9 Consensus size: 29
98300 CCTAAATTAA
98310 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
98339 TTTGATGCCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
98368 TTTGATGTCATTGCTTACATCAATTT
1 TTTGATGTCATTGCTTACATCAATTT
98394 GGTTAGGTGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.48
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:106589 original size:24 final size:24
Alignment explanation
Indices: 106562--106609 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
106552 TAAAAAAAAA
106562 AGTCTTAATTTTTTTTAATTTTTT
1 AGTCTTAATTTTTTTTAATTTTTT
*
106586 AGTCTTAATTTTTTTTTATTTTTT
1 AGTCTTAATTTTTTTTAATTTTTT
106610 TCGTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (24 bp):
AGTCTTAATTTTTTTTAATTTTTT
Found at i:110019 original size:2 final size:2
Alignment explanation
Indices: 109979--110009 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
109969 TAGAATAAAT
*
109979 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
110010 GAAAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:111930 original size:50 final size:50
Alignment explanation
Indices: 111825--111930 Score: 158
Period size: 50 Copynumber: 2.1 Consensus size: 50
111815 TATTCAAATA
* * *
111825 GAGTTATTCGAATCAACTCGAATTGTCAATTCGGTTTTCGAGTTCGAGTC
1 GAGTTGTTCGAATCAACTCAAATTGTCAATTCGATTTTCGAGTTCGAGTC
* * *
111875 GAGTTGTTTGAATCTACTCAAATTGTCAGTTCGATTTTCGAGTTCGAGTC
1 GAGTTGTTCGAATCAACTCAAATTGTCAATTCGATTTTCGAGTTCGAGTC
111925 GAGTTG
1 GAGTTG
111931 AAGTTTTGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.38
Consensus pattern (50 bp):
GAGTTGTTCGAATCAACTCAAATTGTCAATTCGATTTTCGAGTTCGAGTC
Found at i:112462 original size:19 final size:21
Alignment explanation
Indices: 112419--112468 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
112409 ATACTTTGAA
112419 TTATAATATTATGATTATATT
1 TTATAATATTATGATTATATT
* *
112440 TTATAATTTTA-GATTGT-TT
1 TTATAATATTATGATTATATT
112459 TTAT-ATATTA
1 TTATAATATTA
112469 AATAAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 5 0.19
19 6 0.23
20 5 0.19
21 10 0.38
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (21 bp):
TTATAATATTATGATTATATT
Found at i:114232 original size:2 final size:2
Alignment explanation
Indices: 114225--114250 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
114215 CATCTTCTTA
114225 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
114251 TTGGGTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114656 original size:27 final size:26
Alignment explanation
Indices: 114618--114694 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 26
114608 TCATTTAAAT
114618 TTATTATTATTATTAAA-T-TTATTA
1 TTATTATTATTATTAAATTATTATTA
114642 TTATTATTATTATTAAA-TATTATTA
1 TTATTATTATTATTAAATTATTATTA
*
114667 TTAGTATATTATTATTAAATAATTATTA
1 TTA-T-TATTATTATTAAATTATTATTA
114695 CAAGCCCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
24 18 0.38
25 9 0.19
26 1 0.02
27 13 0.27
28 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTATTATTATTATTAAATTATTATTA
Found at i:114694 original size:3 final size:3
Alignment explanation
Indices: 114618--114683 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
114608 TCATTTAAAT
* *
114618 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
114664 TTA TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
114684 AATAATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
2 3 0.06
3 48 0.89
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:115494 original size:13 final size:13
Alignment explanation
Indices: 115476--115504 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
115466 ACCACCGTTA
115476 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
115489 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
115502 CGG
1 CGG
115505 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:117041 original size:7 final size:7
Alignment explanation
Indices: 117029--117080 Score: 59
Period size: 7 Copynumber: 6.9 Consensus size: 7
117019 CTTTCAAATT
117029 TTTATTA
1 TTTATTA
117036 TTTATTA
1 TTTATTA
*
117043 TTTTTATA
1 TTTAT-TA
117051 TATTATTA
1 T-TTATTA
117059 TTTATTA
1 TTTATTA
117066 TTTTATTTA
1 -TTTA-TTA
117075 TTTATT
1 TTTATT
117081 TTATTCAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 19 0.49
8 14 0.36
9 6 0.15
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTATTA
Found at i:117047 original size:16 final size:16
Alignment explanation
Indices: 117026--117082 Score: 62
Period size: 16 Copynumber: 3.3 Consensus size: 16
117016 TTTCTTTCAA
117026 ATTTTTATTATTTATT
1 ATTTTTATTATTTATT
117042 ATTTTTA-TATATTATT
1 ATTTTTATTAT-TTATT
117058 ATTTATTATTTTATTTATTT
1 ATTT-TTA--TTATTTA-TT
117078 ATTTT
1 ATTTT
117083 ATTCAAGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.09
16 16 0.46
17 3 0.09
19 4 0.11
20 9 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTATTATTTATT
Found at i:117049 original size:13 final size:14
Alignment explanation
Indices: 117033--117085 Score: 69
Period size: 13 Copynumber: 4.1 Consensus size: 14
117023 CAAATTTTTA
117033 TTATTTATTATT-T
1 TTATTTATTATTAT
*
117046 TTATATATTATTAT
1 TTATTTATTATTAT
117060 TTA-TTATT-TTAT
1 TTATTTATTATTAT
117072 TTATTTATT-TTAT
1 TTATTTATTATTAT
117085 T
1 T
117086 CAAGAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
12 7 0.19
13 25 0.69
14 4 0.11
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTATTATTAT
Found at i:117056 original size:20 final size:20
Alignment explanation
Indices: 117026--117085 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
117016 TTTCTTTCAA
117026 ATTTT-TATTATTTATTATT
1 ATTTTATATTATTTATTATT
117045 -TTTATATATTA-TTATTTATT
1 ATTT-TATATTATTTA-TTATT
117065 ATTTTAT-TTATTTATT-TT
1 ATTTTATATTATTTATTATT
117083 ATT
1 ATT
117086 CAAGAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
18 8 0.22
19 9 0.25
20 16 0.44
21 3 0.08
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
ATTTTATATTATTTATTATT
Found at i:117079 original size:23 final size:22
Alignment explanation
Indices: 117029--117080 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
117019 CTTTCAAATT
117029 TTTATTATTTATTATTTTTATA
1 TTTATTATTTATTATTTTTATA
*
117051 TATTATTATTTATTATTTTATTTA
1 T-TTATTATTTATTATTTT-TATA
117075 TTTATT
1 TTTATT
117081 TTATTCAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 1 0.04
23 22 0.81
24 4 0.15
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTATTATTTATTATTTTTATA
Found at i:121330 original size:2 final size:2
Alignment explanation
Indices: 121323--121348 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
121313 TTATCCCTTA
121323 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
121349 CCTTTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.