Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005779.1 Hibiscus syriacus cultivar Beakdansim tig00013533_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: 318131
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3221 original size:20 final size:21
Alignment explanation
Indices: 3192--3230 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3182 CATTTCTTTA
3192 TTTTCATTTCATT-CTTATTT
1 TTTTCATTTCATTACTTATTT
*
3212 TTTTCCTTTCATTACTTAT
1 TTTTCATTTCATTACTTAT
3231 ATTATTACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTCATTTCATTACTTATTT
Found at i:3534 original size:13 final size:12
Alignment explanation
Indices: 3487--3534 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 12
3477 ATTAGAGTGC
*
3487 AAAAAGAAGAGA
1 AAAAAGAAAAGA
3499 AAAATCAGAAAAGA
1 AAAA--AGAAAAGA
3513 ATAAAAGAAAAGA
1 A-AAAAGAAAAGA
3526 AAAAGAGAA
1 AAAA-AGAA
3535 GTTCAAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 7 0.23
13 13 0.42
14 8 0.26
15 3 0.10
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:7738 original size:18 final size:19
Alignment explanation
Indices: 7715--7765 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
7705 GCCATCTCTA
7715 TCATTCTT-TATTTTCATT
1 TCATTCTTATATTTTCATT
* *
7733 TCATTCTTATTTTTTCCTT
1 TCATTCTTATATTTTCATT
7752 TCATTACTTATATT
1 TCATT-CTTATATT
7766 ATTACCCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 8 0.29
19 13 0.46
20 7 0.25
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (19 bp):
TCATTCTTATATTTTCATT
Found at i:12268 original size:22 final size:20
Alignment explanation
Indices: 12222--12259 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
12212 CATTTCTTTA
*
12222 TTTTCATTTCATT-CTTATT
1 TTTTCCTTTCATTACTTATT
12241 TTTTCCTTTCATTACTTAT
1 TTTTCCTTTCATTACTTAT
12260 ATTATTTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTCCTTTCATTACTTATT
Found at i:16073 original size:16 final size:16
Alignment explanation
Indices: 16036--16073 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
16026 CATTGTGACC
16036 TTTCATGAATGATGCT
1 TTTCATGAATGATGCT
*
16052 TCTCATGAA-GATGCCT
1 TTTCATGAATGATG-CT
16068 TTTCAT
1 TTTCAT
16074 CTAGAAGCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (16 bp):
TTTCATGAATGATGCT
Found at i:17135 original size:13 final size:13
Alignment explanation
Indices: 17099--17146 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
17089 ATTGGAGTGT
*
17099 AAAAAGAAGAGAA
1 AAAAAGAAAAGAA
*
17112 AAATCAGAAAAGAA
1 AAA-AAGAAAAGAA
*
17126 GAAAAGAAAAGAA
1 AAAAAGAAAAGAA
17139 AAAAAGAA
1 AAAAAGAA
17147 GTTTAAAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:26093 original size:36 final size:36
Alignment explanation
Indices: 26046--26149 Score: 138
Period size: 36 Copynumber: 2.9 Consensus size: 36
26036 ATACAATCTA
*
26046 TCCATCACCATTATCATGACTATATCATCACCATAG
1 TCCATCACCATTATCACGACTATATCATCACCATAG
* * *
26082 TCCATCACCATTATCACGCCTATATGATCACCATAT
1 TCCATCACCATTATCACGACTATATCATCACCATAG
* * *
26118 TCCATCACCA-TATCACGCCCATATTATCACCA
1 TCCATCACCATTATCACGACTATATCATCACCA
26150 ACTTATAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 20 0.32
36 42 0.68
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGACTATATCATCACCATAG
Found at i:33181 original size:19 final size:20
Alignment explanation
Indices: 33140--33190 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
33130 GAAACCCCTT
*
33140 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
33160 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
33179 TGAAGATACATG
1 TGAAAATACATG
33191 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:37380 original size:19 final size:20
Alignment explanation
Indices: 37339--37389 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
37329 GAAACCCCTT
*
37339 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
37359 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
37378 TGAAGATACATG
1 TGAAAATACATG
37390 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:39146 original size:13 final size:13
Alignment explanation
Indices: 39128--39171 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
39118 TTTCATTCTT
39128 ATTCTTTCCTTTC
1 ATTCTTTCCTTTC
*
39141 ATTCTTATTC-TT-
1 ATTCTT-TCCTTTC
39153 ATTCTTTCCTTTC
1 ATTCTTTCCTTTC
39166 ATTCTT
1 ATTCTT
39172 GTGAGCCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 2 0.08
12 8 0.31
13 14 0.54
14 2 0.08
ACGTcount: A:0.11, C:0.25, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTCTTTCCTTTC
Found at i:39153 original size:25 final size:25
Alignment explanation
Indices: 39122--39171 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
39112 CTTTCCTTTC
39122 ATTCTTATTCTTTCCTTTCATTCTT
1 ATTCTTATTCTTTCCTTTCATTCTT
39147 ATTCTTATTCTTTCCTTTCATTCTT
1 ATTCTTATTCTTTCCTTTCATTCTT
39172 GTGAGCCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTCTTATTCTTTCCTTTCATTCTT
Found at i:39171 original size:19 final size:19
Alignment explanation
Indices: 39112--39152 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
39102 TCTCAAAGTC
39112 CTTTCCTTTCATTCTTATT
1 CTTTCCTTTCATTCTTATT
39131 CTTTCCTTTCATTCTTATT
1 CTTTCCTTTCATTCTTATT
39150 CTT
1 CTT
39153 ATTCTTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.10, C:0.27, G:0.00, T:0.63
Consensus pattern (19 bp):
CTTTCCTTTCATTCTTATT
Found at i:59937 original size:23 final size:24
Alignment explanation
Indices: 59911--59969 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
59901 AAAATCTGCA
59911 AAGAAAATAAAAGCACT-AAAAAG
1 AAGAAAATAAAAGCACTCAAAAAG
* * *
59934 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCAAAAAG
59958 AAGAAAAATAAA
1 AAG-AAAATAAA
59970 GAAAGAAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 15 0.52
24 8 0.28
25 6 0.21
ACGTcount: A:0.66, C:0.08, G:0.15, T:0.10
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCAAAAAG
Found at i:69160 original size:23 final size:24
Alignment explanation
Indices: 69118--69175 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 24
69108 TTTCTTTCTT
69118 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
69142 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
69165 TTTCTTGCTTT
1 TTTCTT-CTTT
69176 CTTTCACTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.09, C:0.17, G:0.12, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:72619 original size:14 final size:15
Alignment explanation
Indices: 72602--72630 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
72592 GAACATTCAG
72602 AAAAGAAGA-AGAAA
1 AAAAGAAGAGAGAAA
72616 AAAAGAAGAGAGAAA
1 AAAAGAAGAGAGAAA
72631 GCAAGCCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAGAGAAA
Found at i:75241 original size:13 final size:12
Alignment explanation
Indices: 75222--75307 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
75212 AAATAGGCGT
75222 GATATGGTGATG
1 GATATGGTGATG
75234 GAATATGGTGAT-
1 G-ATATGGTGATG
*
75246 GATATAGGCG-T-
1 GATAT-GGTGATG
75257 GATAATGGTGATG
1 GAT-ATGGTGATG
75270 GACTATGGTGAT-
1 GA-TATGGTGATG
*
75282 GATATAGGCG-T-
1 GATAT-GGTGATG
75293 GATAATGGTGATG
1 GAT-ATGGTGATG
75306 GA
1 GA
75308 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:75277 original size:36 final size:36
Alignment explanation
Indices: 75204--75308 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
75194 ATTTATAAGT
* * *
75204 TGGTGATAAAATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
75239 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
75275 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
75309 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:82990 original size:14 final size:14
Alignment explanation
Indices: 82971--83000 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
82961 TTTCTTACTA
*
82971 TTTCATTTTTTTTC
1 TTTCATCTTTTTTC
82985 TTTCATCTTTTTTC
1 TTTCATCTTTTTTC
82999 TT
1 TT
83001 ATTTCATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCATCTTTTTTC
Found at i:85844 original size:18 final size:19
Alignment explanation
Indices: 85821--85868 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
85811 TTCGGCCAAG
**
85821 ATGTATCTTC-TTTAAATC
1 ATGTATCTTCATCAAAATC
*
85839 ATGTATTTTCATCAAAATC
1 ATGTATCTTCATCAAAATC
*
85858 ATGTATTTTCA
1 ATGTATCTTCA
85869 AAAGGGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (19 bp):
ATGTATCTTCATCAAAATC
Found at i:86562 original size:154 final size:155
Alignment explanation
Indices: 86377--86687 Score: 615
Period size: 155 Copynumber: 2.0 Consensus size: 155
86367 TTGAAGGAGA
86377 TTTATTCAACACTTCTGCAGCCCATCTTTTATAACTATTCTATCCA-TTCAATTCTTTCCATTTC
1 TTTATTCAACACTTCTGCAGCCCATCTTTTATAACTATTCTATCCATTTCAATTCTTTCCATTTC
86441 TATTTCCTTTCTTTATTATTCATTTATTTAACCAATAATTCTTCTTTTGTGCAGATTGATTTCCA
66 TATTTCCTTTCTTTATTATTCATTTATTTAACCAATAATTCTTCTTTTGTGCAGATTGATTTCCA
86506 ATTCAAGGTGTAGCATTTGGTGTTT
131 ATTCAAGGTGTAGCATTTGGTGTTT
86531 TTTATTCAACACTTCTGCAGCCCATCTTTTATAACTATTCTATCCATTTCAATTCTTTCCATTTC
1 TTTATTCAACACTTCTGCAGCCCATCTTTTATAACTATTCTATCCATTTCAATTCTTTCCATTTC
86596 TATTTCCTTTCTTTATTATTCATTTATTTAACCAATAATTCTTCTTTTGTGCAGATTGATTTCCA
66 TATTTCCTTTCTTTATTATTCATTTATTTAACCAATAATTCTTCTTTTGTGCAGATTGATTTCCA
86661 ATTCAAGGTGTAGCATTTGGTGTTT
131 ATTCAAGGTGTAGCATTTGGTGTTT
86686 TT
1 TT
86688 CCTAGATCGG
Statistics
Matches: 156, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
154 46 0.29
155 110 0.71
ACGTcount: A:0.23, C:0.20, G:0.08, T:0.49
Consensus pattern (155 bp):
TTTATTCAACACTTCTGCAGCCCATCTTTTATAACTATTCTATCCATTTCAATTCTTTCCATTTC
TATTTCCTTTCTTTATTATTCATTTATTTAACCAATAATTCTTCTTTTGTGCAGATTGATTTCCA
ATTCAAGGTGTAGCATTTGGTGTTT
Found at i:88439 original size:13 final size:11
Alignment explanation
Indices: 88398--88482 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
88388 ACAATCTGTC
88398 CATCACCATTAT
1 CATCACCA-TAT
*
88410 CA-CGCCTATAT
1 CATCACC-ATAT
88421 CATCACCATAGT
1 CATCACCATA-T
88433 CCATCACCATTAT
1 -CATCACCA-TAT
*
88446 CA-CGCCTATAT
1 CATCACC-ATAT
88457 CATCACCATATT
1 CATCACCATA-T
88469 CCATCACCATAT
1 -CATCACCATAT
88481 CA
1 CA
88483 CGCCTATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:88442 original size:36 final size:36
Alignment explanation
Indices: 88395--88499 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
88385 GATACAATCT
88395 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
88431 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
88467 TTCCATCACCA-TATCACGCCTATTTTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
88500 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:95754 original size:13 final size:14
Alignment explanation
Indices: 95736--95764 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
95726 TTTCTTACTA
95736 TTTCAT-TTTTTTC
1 TTTCATCTTTTTTC
95749 TTTCATCTTTTTTC
1 TTTCATCTTTTTTC
95763 TT
1 TT
95765 ATTTCATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCATCTTTTTTC
Found at i:99224 original size:18 final size:17
Alignment explanation
Indices: 99183--99224 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
99173 GCAAAGGAAA
99183 AAGAAACACTCAAAAAG
1 AAGAAACACTCAAAAAG
*
99200 ATTGAAAGCACTCAAAAAG
1 A-AGAAA-CACTCAAAAAG
99219 AAGAAA
1 AAGAAA
99225 AAAGAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 8 0.38
19 12 0.57
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.10
Consensus pattern (17 bp):
AAGAAACACTCAAAAAG
Found at i:102002 original size:11 final size:13
Alignment explanation
Indices: 101970--101999 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
101960 TGGCCAAAGA
101970 TGAAAAGGTATGT
1 TGAAAAGGTATGT
101983 TGAAAAGGTATG-
1 TGAAAAGGTATGT
101995 TGAAA
1 TGAAA
102000 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:106564 original size:13 final size:14
Alignment explanation
Indices: 106546--106574 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
106536 TTTCTTACTA
106546 TTTCAT-TTTTTTC
1 TTTCATCTTTTTTC
106559 TTTCATCTTTTTTC
1 TTTCATCTTTTTTC
106573 TT
1 TT
106575 ATTTCATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCATCTTTTTTC
Found at i:110276 original size:17 final size:17
Alignment explanation
Indices: 110251--110302 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
110241 ACAAAGTGCT
*
110251 ACAACAAAAAAAAAGCA
1 ACAAGAAAAAAAAAGCA
*
110268 ACAAGAAAAAATAAAACA
1 ACAAGAAAAAA-AAAGCA
*
110286 AAAGAGAAAAGAAAAAG
1 ACA-AGAAAA-AAAAAG
110303 ACTCCTACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 10 0.36
18 7 0.25
19 9 0.32
20 2 0.07
ACGTcount: A:0.77, C:0.10, G:0.12, T:0.02
Consensus pattern (17 bp):
ACAAGAAAAAAAAAGCA
Found at i:110359 original size:14 final size:15
Alignment explanation
Indices: 110325--110371 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
110315 AATTTGGAGT
110325 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
110340 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
110354 TCAAAAGTAAAAGAAAA
1 GCAAAAG--AAAGAAAA
110371 G
1 G
110372 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.04
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:110531 original size:14 final size:14
Alignment explanation
Indices: 110512--110541 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
110502 TTTCTTACTA
*
110512 TTTCATTTTTTTTC
1 TTTCATCTTTTTTC
110526 TTTCATCTTTTTTC
1 TTTCATCTTTTTTC
110540 TT
1 TT
110542 ATTTCATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCATCTTTTTTC
Found at i:115876 original size:13 final size:11
Alignment explanation
Indices: 115835--115919 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
115825 ACAATCTGTC
115835 CATCACCATTAT
1 CATCACCA-TAT
*
115847 CA-CGCCTATAT
1 CATCACC-ATAT
115858 CATCACCATAGT
1 CATCACCATA-T
115870 CCATCACCATTAT
1 -CATCACCA-TAT
*
115883 CA-CGCCTATAT
1 CATCACC-ATAT
115894 CATCACCATATT
1 CATCACCATA-T
115906 CCATCACCATAT
1 -CATCACCATAT
115918 CA
1 CA
115920 CGCCTATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:115879 original size:36 final size:36
Alignment explanation
Indices: 115832--115936 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
115822 GATACAATCT
115832 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
115868 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
115904 TTCCATCACCA-TATCACGCCTATTTTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
115937 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:120422 original size:13 final size:13
Alignment explanation
Indices: 120400--120429 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
120390 ACTAAACACC
120400 TTTC-ACATACCT
1 TTTCAACATACCT
120412 TTTCAACATACCT
1 TTTCAACATACCT
120425 TTTCA
1 TTTCA
120430 TCTTTGGCCA
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:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:122980 original size:18 final size:17
Alignment explanation
Indices: 122959--123000 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
122949 TTCTTTCTTT
122959 TTTCTTCTTTTTGAGTG
1 TTTCTTCTTTTTGAGTG
*
122976 CTTTCAATCTTTTTGAGTG
1 -TTTC-TTCTTTTTGAGTG
122995 TTTCTT
1 TTTCTT
123001 TTTCCTTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 8 0.38
19 12 0.57
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.62
Consensus pattern (17 bp):
TTTCTTCTTTTTGAGTG
Found at i:126095 original size:22 final size:22
Alignment explanation
Indices: 126070--126112 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
126060 CAATTCATTT
126070 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
126092 ATCTTATTTTTATCTTGTTTT
1 ATCTTATTTTTATCTTGTTTT
126113 CAGCACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:128374 original size:22 final size:22
Alignment explanation
Indices: 128349--128391 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
128339 CAATTCATTT
128349 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
128371 ATCTTATTTTTATCTTGTTTT
1 ATCTTATTTTTATCTTGTTTT
128392 CAGCACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:133524 original size:23 final size:24
Alignment explanation
Indices: 133493--133537 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
133483 GCCATCTCTA
*
133493 TCTTTTTATTTA-TTTCATTACAT
1 TCTTATTATTTATTTTCATTACAT
133516 TCTTATTATTTATTTTCATTAC
1 TCTTATTATTTATTTTCATTAC
133538 TTATATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.22, C:0.13, G:0.00, T:0.64
Consensus pattern (24 bp):
TCTTATTATTTATTTTCATTACAT
Found at i:135451 original size:13 final size:11
Alignment explanation
Indices: 135410--135498 Score: 67
Period size: 11 Copynumber: 7.6 Consensus size: 11
135400 ACAATCTGTC
135410 CATCACCATTAT
1 CATCACCA-TAT
*
135422 CA-CGCCTATAT
1 CATCACC-ATAT
135433 CATCACCATAGT
1 CATCACCATA-T
135445 CCATCACCATTAT
1 -CATCACCA-TAT
*
135458 CA-CGCCTATAT
1 CATCACC-ATAT
135469 CATCACCATATT
1 CATCACCATA-T
135481 CCATCACCATAT
1 -CATCACCATAT
135493 CA-CACC
1 CATCACC
135499 TATTTTATCG
Statistics
Matches: 64, Mismatches: 4, Indels: 20
0.73 0.05 0.23
Matches are distributed among these distances:
10 4 0.06
11 24 0.38
12 15 0.23
13 19 0.30
14 2 0.03
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.27
Consensus pattern (11 bp):
CATCACCATAT
Found at i:135454 original size:36 final size:36
Alignment explanation
Indices: 135407--135501 Score: 165
Period size: 36 Copynumber: 2.7 Consensus size: 36
135397 GATACAATCT
135407 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
135443 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
135479 TTCCATCACCA-TATCACACCTAT
1 GTCCATCACCATTATCACGCCTAT
135502 TTTATCGCCA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
35 11 0.19
36 46 0.81
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:158535 original size:13 final size:13
Alignment explanation
Indices: 158517--158541 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
158507 AAGAAAATCT
158517 AAAGAAAGCAAAC
1 AAAGAAAGCAAAC
158530 AAAGAAAGCAAA
1 AAAGAAAGCAAA
158542 ATGCAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.12, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAGAAAGCAAAC
Found at i:164993 original size:24 final size:21
Alignment explanation
Indices: 164959--165001 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
164949 TCCACAAGAC
*
164959 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
164981 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
165002 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:167227 original size:24 final size:21
Alignment explanation
Indices: 167193--167235 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
167183 TCCACAAGAC
*
167193 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
167215 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
167236 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:172068 original size:17 final size:18
Alignment explanation
Indices: 172036--172070 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
172026 AATTTTGATG
*
172036 AATGGATATTCATCTTTT
1 AATGGATATACATCTTTT
172054 AATGGA-ATACATCTTTT
1 AATGGATATACATCTTTT
172071 GGCCGAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
AATGGATATACATCTTTT
Found at i:178031 original size:24 final size:25
Alignment explanation
Indices: 177985--178039 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
177975 ACAGTTATGC
177985 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTTCAAAAAGATGTGAT
* *
178009 CACTTGAAGTGTC-ACAAGTTGTGAT
1 CACTTGAAGT-TCAAAAAGATGTGAT
178034 CA-TTGA
1 CACTTGA
178040 GGCTCCAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (25 bp):
CACTTGAAGTTCAAAAAGATGTGAT
Found at i:180883 original size:13 final size:13
Alignment explanation
Indices: 180865--180889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
180855 AAGAAAATAT
180865 AAAGAAAGAAAAC
1 AAAGAAAGAAAAC
180878 AAAGAAAGAAAA
1 AAAGAAAGAAAA
180890 ATGCAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAAC
Found at i:182594 original size:26 final size:26
Alignment explanation
Indices: 182562--182612 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
182552 TTCTTCCATA
182562 TTTTATTACTTATTTACTCATTTATT
1 TTTTATTACTTATTTACTCATTTATT
182588 TTTTATTACTTATTTACTCATTTAT
1 TTTTATTACTTATTTACTCATTTAT
182613 GCTTTATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTATTACTTATTTACTCATTTATT
Found at i:182618 original size:26 final size:26
Alignment explanation
Indices: 182563--182619 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
182553 TCTTCCATAT
**
182563 TTTATTACTTATTTACTCATTTATTT
1 TTTATTACTTATTTACTCATTTATGC
182589 TTTATTACTTATTTACTCATTTATGC
1 TTTATTACTTATTTACTCATTTATGC
182615 TTTAT
1 TTTAT
182620 ATGTGTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.23, C:0.12, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTATTACTTATTTACTCATTTATGC
Found at i:185195 original size:33 final size:34
Alignment explanation
Indices: 185146--185232 Score: 104
Period size: 33 Copynumber: 2.5 Consensus size: 34
185136 ATTGGTGGTT
*
185146 ATATAGGCGTGAAATGGTGATCGAAGATGGTAAG
1 ATATAGGCGTGAAATGGTAATCGAAGATGGTAAG
* * *
185180 ATATAGG-GTGCAATGGTAATGGAAGATGGTGATG
1 ATATAGGCGTGAAATGGTAATCGAAGATGGT-AAG
*
185214 GTATAGGCGTGAAAATGGT
1 ATATAGGCGTG-AAATGGT
185233 GATATTTAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
33 20 0.45
34 15 0.34
35 3 0.07
36 6 0.14
ACGTcount: A:0.33, C:0.05, G:0.37, T:0.25
Consensus pattern (34 bp):
ATATAGGCGTGAAATGGTAATCGAAGATGGTAAG
Found at i:188582 original size:2 final size:2
Alignment explanation
Indices: 188575--188624 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
188565 ACTATAGGTA
188575 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
188617 AT AT AT AT
1 AT AT AT AT
188625 GAAAATAACT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:191571 original size:26 final size:26
Alignment explanation
Indices: 191521--191584 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
191511 CTTGGCTTGC
191521 TTTTCTCTTTT-TGAAATCTTTTTCT
1 TTTTCTCTTTTCTGAAATCTTTTTCT
191546 TTTTCTTCTTTTCTG-AAT-TTTCTTCT
1 TTTTC-TCTTTTCTGAAATCTTT-TTCT
*
191572 TTTTGTCTTTTCT
1 TTTTCTCTTTTCT
191585 TTCTTTTTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 16 0.46
26 17 0.49
27 2 0.06
ACGTcount: A:0.08, C:0.17, G:0.05, T:0.70
Consensus pattern (26 bp):
TTTTCTCTTTTCTGAAATCTTTTTCT
Found at i:191588 original size:17 final size:15
Alignment explanation
Indices: 191537--191593 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
191527 CTTTTTGAAA
*
191537 TCTTTTTCTTTTTCT
1 TCTTTTTGTTTTTCT
*
191552 TCTTTTCTGAATTTTCT
1 TCTTTT-TG-TTTTTCT
191569 TCTTTTTGTCTTTTCTT
1 TCTTTTTGT-TTTTC-T
191586 TCTTTTTG
1 TCTTTTTG
191594 CACTCCAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 6 0.17
16 8 0.23
17 21 0.60
ACGTcount: A:0.04, C:0.18, G:0.05, T:0.74
Consensus pattern (15 bp):
TCTTTTTGTTTTTCT
Found at i:204565 original size:58 final size:58
Alignment explanation
Indices: 204496--204625 Score: 215
Period size: 58 Copynumber: 2.2 Consensus size: 58
204486 TCCCTTCAAA
* *
204496 TTGGCGCCAAATGGGATAGGAGATGATGCTTGGCCGAATAGTTAAATGGCTCTTCATC
1 TTGGCGCCAAATGGGAGAGGAGATGATGATTGGCCGAATAGTTAAATGGCTCTTCATC
* *
204554 TTGGCGCCAAATGGGAGAGGAGATGATGATTGGCCGAATGGTTAAATGGCTCTTTATC
1 TTGGCGCCAAATGGGAGAGGAGATGATGATTGGCCGAATAGTTAAATGGCTCTTCATC
204612 TTGGCGCCTAAATG
1 TTGGCGCC-AAATG
204626 AACCCACATG
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 62 0.93
59 5 0.07
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (58 bp):
TTGGCGCCAAATGGGAGAGGAGATGATGATTGGCCGAATAGTTAAATGGCTCTTCATC
Found at i:208477 original size:25 final size:26
Alignment explanation
Indices: 208441--208505 Score: 105
Period size: 25 Copynumber: 2.5 Consensus size: 26
208431 CTAGAACACT
* *
208441 CATGTGCTTTGCATATGATCAG-CCC
1 CATGTGCCTTGCATATGACCAGCCCC
208466 CATGTGCCTTGCATATGACCAGCCCC
1 CATGTGCCTTGCATATGACCAGCCCC
208492 CATGTGCCTTGCAT
1 CATGTGCCTTGCAT
208506 GTGGGTTCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
25 20 0.54
26 17 0.46
ACGTcount: A:0.18, C:0.32, G:0.20, T:0.29
Consensus pattern (26 bp):
CATGTGCCTTGCATATGACCAGCCCC
Found at i:211065 original size:25 final size:26
Alignment explanation
Indices: 211027--211093 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
211017 CCCTATAACA
* * *
211027 CCCATGTGCTTTGCATATGATCA-AT
1 CCCATGTGCCTTGCATATGACCAGAC
* *
211052 CCCATGTGCCTTGCAAATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAGAC
211078 CCCATGTGCCTTGCAT
1 CCCATGTGCCTTGCAT
211094 GTGGGTTCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
25 20 0.57
26 15 0.43
ACGTcount: A:0.21, C:0.33, G:0.18, T:0.28
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGAC
Found at i:212567 original size:19 final size:21
Alignment explanation
Indices: 212524--212575 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
212514 GAAACCCCTT
212524 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
212545 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
212564 TGAAGATACATG
1 TGAAAATACATG
212576 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:216352 original size:27 final size:26
Alignment explanation
Indices: 216289--216352 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
216279 CTTTTTGAAC
* *
216289 TTCTTTTTTTCTTTTCTTTTCTTCTT
1 TTCTTTTTTTATCTTCTTTTCTTCTT
*
216315 TTCTGATTTTTATCTTCTTTT-TGTCTT
1 TTCT-TTTTTTATCTTCTTTTCT-TCTT
216342 TTCTTTCTTTT
1 TTCTTT-TTTT
216353 TGCACTCCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
26 6 0.19
27 25 0.81
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (26 bp):
TTCTTTTTTTATCTTCTTTTCTTCTT
Found at i:217102 original size:19 final size:21
Alignment explanation
Indices: 217059--217110 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
217049 GAAACCCCTT
217059 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
217080 TGAAAATACATTA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
217099 TGAAGATACATG
1 TGAAAATACATG
217111 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:220213 original size:27 final size:28
Alignment explanation
Indices: 220161--220225 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
220151 AAATAAAATC
*
220161 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTGAAGCACTCAAAAAGA
* *
220189 A-AGAAAGAAATT-CAGCATTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTCAAAAAGA
220216 AGAAAAGAAA
1 AGAAAAGAAA
220226 AGAAAGAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.62, C:0.11, G:0.17, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTCAAAAAGA
Found at i:226288 original size:15 final size:15
Alignment explanation
Indices: 226253--226281 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
226243 GTGCTTCAAC
226253 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
226267 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
226282 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:228219 original size:36 final size:36
Alignment explanation
Indices: 228171--228275 Score: 142
Period size: 35 Copynumber: 2.9 Consensus size: 36
228161 ACTACCTAAA
228171 CATCACCATCTTCCATCACCATTTTCATGCCTATAAT
1 CATCACCATCTTCCATCACCA-TTTCATGCCTATAAT
* *
228208 -ATCACCATCTTCCATTACCATTGCATGCCTAT-AT
1 CATCACCATCTTCCATCACCATTTCATGCCTATAAT
* * *
228242 CATTACCATCTTCTATCACCATTTCACGCCTATA
1 CATCACCATCTTCCATCACCATTTCATGCCTATA
228276 TAACTACCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
34 2 0.03
35 38 0.64
36 19 0.32
ACGTcount: A:0.27, C:0.34, G:0.04, T:0.35
Consensus pattern (36 bp):
CATCACCATCTTCCATCACCATTTCATGCCTATAAT
Found at i:229909 original size:13 final size:13
Alignment explanation
Indices: 229891--229948 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
229881 ACTATCTGTT
229891 CATCACCATCTTC
1 CATCACCATCTTC
*
229904 CATCACCAT-TTT
1 CATCACCATCTTC
* **
229916 CA-CACC-TATAA
1 CATCACCATCTTC
229927 CATCACCATCTTC
1 CATCACCATCTTC
229940 CATCACCAT
1 CATCACCAT
229949 TGCACGCCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
10 1 0.03
11 7 0.19
12 8 0.22
13 20 0.56
ACGTcount: A:0.29, C:0.41, G:0.00, T:0.29
Consensus pattern (13 bp):
CATCACCATCTTC
Found at i:230008 original size:35 final size:35
Alignment explanation
Indices: 229890--230043 Score: 200
Period size: 35 Copynumber: 4.3 Consensus size: 35
229880 TACTATCTGT
229890 TCATCACCATCTTCCATCACCATTTTCACACCTATA
1 TCATCACCATCTTCCATCACCA-TTTCACACCTATA
* * *
229926 ACATCACCATCTTCCATCACCATTGCACGCCTATATTA
1 TCATCACCATCTTCCATCACCATTTCACACC--TA-TA
* **
229964 TCATCACCATCTTCTATCACCATTTCACGTCTATA
1 TCATCACCATCTTCCATCACCATTTCACACCTATA
* *
229999 TCATCACCATCTTCTATCACCATTTCATACCTATA
1 TCATCACCATCTTCCATCACCATTTCACACCTATA
230034 TCATCACCAT
1 TCATCACCAT
230044 TCCCTTATCA
Statistics
Matches: 105, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
35 51 0.49
36 23 0.22
37 2 0.02
38 29 0.28
ACGTcount: A:0.28, C:0.36, G:0.02, T:0.34
Consensus pattern (35 bp):
TCATCACCATCTTCCATCACCATTTCACACCTATA
Found at i:230032 original size:73 final size:74
Alignment explanation
Indices: 229890--230039 Score: 212
Period size: 73 Copynumber: 2.0 Consensus size: 74
229880 TACTATCTGT
*
229890 TCATCACCATCTTCCATCACCATTTTCACACCTATAACATCACCATCTTCCATCACCATTGCACG
1 TCATCACCATCTTCCATCACCATTTTCACACCTATAACATCACCATCTTCCATCACCATTGCACA
*
229955 CCTATATTA
66 CCTATATCA
* ** * * * *
229964 TCATCACCATCTTCTATCACCA-TTTCACGTCTATATCATCACCATCTTCTATCACCATTTCATA
1 TCATCACCATCTTCCATCACCATTTTCACACCTATAACATCACCATCTTCCATCACCATTGCACA
230028 CCTATATCA
66 CCTATATCA
230037 TCA
1 TCA
230040 CCATTCCCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
73 46 0.69
74 21 0.31
ACGTcount: A:0.28, C:0.36, G:0.02, T:0.34
Consensus pattern (74 bp):
TCATCACCATCTTCCATCACCATTTTCACACCTATAACATCACCATCTTCCATCACCATTGCACA
CCTATATCA
Found at i:230582 original size:17 final size:16
Alignment explanation
Indices: 230552--230585 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
230542 TGAAATGAAA
*
230552 AAATAAGAATGAAATG
1 AAATAAGAAAGAAATG
230568 AAATAAAGAAAGAAATG
1 AAAT-AAGAAAGAAATG
230585 A
1 A
230586 TAGAGATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.15
Consensus pattern (16 bp):
AAATAAGAAAGAAATG
Found at i:232477 original size:69 final size:69
Alignment explanation
Indices: 232366--232521 Score: 294
Period size: 69 Copynumber: 2.3 Consensus size: 69
232356 TCCTTATAAG
*
232366 TCACGCCCTTTGGATGAAAAATCATTTCCCTTTGGTTTTCAATAGGCACGACTCTTGATTCTTGA
1 TCACGTCCTTTGGATGAAAAATCATTTCCCTTTGGTTTTCAATAGGCACGACTCTTGATTCTTGA
232431 TGGA
66 TGGA
*
232435 TCACGTCCTTTGGATGAAAAATCATTTCCCTTTGGTTTTCAATAGGCATGACTCTTGATTCTTGA
1 TCACGTCCTTTGGATGAAAAATCATTTCCCTTTGGTTTTCAATAGGCACGACTCTTGATTCTTGA
232500 TGGA
66 TGGA
232504 TCACGTCCTTTGGATGAA
1 TCACGTCCTTTGGATGAA
232522 GAGTTACCAT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 85 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (69 bp):
TCACGTCCTTTGGATGAAAAATCATTTCCCTTTGGTTTTCAATAGGCACGACTCTTGATTCTTGA
TGGA
Found at i:235037 original size:11 final size:11
Alignment explanation
Indices: 235023--235059 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
235013 TCAAAAAAAC
235023 AAAAAAAGGCA
1 AAAAAAAGGCA
235034 AAAAAAAGGCA
1 AAAAAAAGGCA
235045 AAAAAAAGGCA
1 AAAAAAAGGCA
235056 AAAA
1 AAAA
235060 GAAAAGTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAAGGCA
Found at i:235071 original size:22 final size:21
Alignment explanation
Indices: 235015--235059 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
235005 ATTTTTTTTC
235015 AAAAAAA--CAAAAAAAGGCA
1 AAAAAAAGGCAAAAAAAGGCA
235034 AAAAAAAGGCAAAAAAAAGGCA
1 AAAAAAAGGC-AAAAAAAGGCA
235056 AAAA
1 AAAA
235060 GAAAAGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.30
21 1 0.04
22 15 0.65
ACGTcount: A:0.78, C:0.09, G:0.13, T:0.00
Consensus pattern (21 bp):
AAAAAAAGGCAAAAAAAGGCA
Found at i:239307 original size:11 final size:11
Alignment explanation
Indices: 239291--239337 Score: 71
Period size: 10 Copynumber: 4.5 Consensus size: 11
239281 CTATTTTTTT
239291 CAAAAAAAAGG
1 CAAAAAAAAGG
239302 C-AAAAAAAGG
1 CAAAAAAAAGG
239312 C-AAAAAAAGG
1 CAAAAAAAAGG
*
239322 CAAAAAAAAGC
1 CAAAAAAAAGG
239333 CAAAA
1 CAAAA
239338 TTTCAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
10 20 0.59
11 14 0.41
ACGTcount: A:0.72, C:0.13, G:0.15, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGG
Found at i:239308 original size:10 final size:10
Alignment explanation
Indices: 239293--239329 Score: 74
Period size: 10 Copynumber: 3.7 Consensus size: 10
239283 ATTTTTTTCA
239293 AAAAAAAGGC
1 AAAAAAAGGC
239303 AAAAAAAGGC
1 AAAAAAAGGC
239313 AAAAAAAGGC
1 AAAAAAAGGC
239323 AAAAAAA
1 AAAAAAA
239330 AGCCAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAAAGGC
Found at i:243333 original size:11 final size:12
Alignment explanation
Indices: 243319--243366 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
243309 TCAAAAAAAC
243319 AAAAAAAGGC--
1 AAAAAAAGGCAA
243329 AAAAAAAGGCAA
1 AAAAAAAGGCAA
* *
243341 AAAAAAAAGCTA
1 AAAAAAAGGCAA
*
243353 AAAAAAAGCCAA
1 AAAAAAAGGCAA
243365 AA
1 AA
243367 TTTCAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 10 0.32
12 21 0.68
ACGTcount: A:0.75, C:0.10, G:0.12, T:0.02
Consensus pattern (12 bp):
AAAAAAAGGCAA
Found at i:243366 original size:10 final size:10
Alignment explanation
Indices: 243310--243345 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
243300 ATTTTTTTTT
243310 CAAAAAAA--
1 CAAAAAAAGG
243318 CAAAAAAAGG
1 CAAAAAAAGG
243328 CAAAAAAAGG
1 CAAAAAAAGG
243338 CAAAAAAA
1 CAAAAAAA
243346 AAAGCTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
10 18 0.69
ACGTcount: A:0.78, C:0.11, G:0.11, T:0.00
Consensus pattern (10 bp):
CAAAAAAAGG
Found at i:243366 original size:23 final size:22
Alignment explanation
Indices: 243319--243366 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
243309 TCAAAAAAAC
* *
243319 AAAAAAAGGCAAAAAAAGGCAA
1 AAAAAAAAGCAAAAAAAAGCAA
*
243341 AAAAAAAAGCTAAAAAAAAGCCA
1 AAAAAAAAGC-AAAAAAAAGCAA
243364 AAA
1 AAA
243367 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.75, C:0.10, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAAAGCAAAAAAAAGCAA
Found at i:255023 original size:12 final size:13
Alignment explanation
Indices: 255006--255035 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
254996 TCAAAAAAAC
255006 AAAAAAAGG-AAA
1 AAAAAAAGGCAAA
255018 AAAAAAAGGCAAA
1 AAAAAAAGGCAAA
255031 AAAAA
1 AAAAA
255036 GACAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAAGGCAAA
Found at i:255043 original size:12 final size:11
Alignment explanation
Indices: 254998--255046 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
254988 TATTTTTTTC
254998 AAAAAA-ACAA
1 AAAAAAGACAA
* *
255008 AAAAAGGAAAA
1 AAAAAAGACAA
*
255019 AAAAAAGGCAA
1 AAAAAAGACAA
255030 AAAAAAGACAA
1 AAAAAAGACAA
255041 AAAAAA
1 AAAAAA
255047 CACCAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 5 0.16
11 27 0.84
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAGACAA
Found at i:261571 original size:13 final size:13
Alignment explanation
Indices: 261553--261578 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
261543 AACACCTTTT
261553 ACATACCTTTTCA
1 ACATACCTTTTCA
261566 ACATACCTTTTCA
1 ACATACCTTTTCA
261579 TCTTTCGCCA
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:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Found at i:267851 original size:21 final size:22
Alignment explanation
Indices: 267827--267878 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
267817 TTGGAGTGCA
267827 AAAAGAAAAGAC-AAAAAGAAG
1 AAAAGAAAAGACAAAAAAGAAG
* **
267848 AAAAAAAAATTCAAAAAAGAAG
1 AAAAGAAAAGACAAAAAAGAAG
267870 AAAAGAAAA
1 AAAAGAAAA
267879 AGAAGTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (22 bp):
AAAAGAAAAGACAAAAAAGAAG
Found at i:272054 original size:20 final size:20
Alignment explanation
Indices: 272027--272078 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
272017 TTCATCTTGA
272027 AAAAAAAAGAATTCCGAAAATT
1 AAAAAAAA-AA-TCCGAAAATT
*
272049 AAAAAAAAAATCTGAAAATT
1 AAAAAAAAAATCCGAAAATT
272069 AAAAAGAAAA
1 AAAAA-AAAA
272079 GAAAAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 14 0.50
21 6 0.21
22 8 0.29
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.15
Consensus pattern (20 bp):
AAAAAAAAAATCCGAAAATT
Found at i:275998 original size:13 final size:13
Alignment explanation
Indices: 275980--276004 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
275970 TGGCCAAAGA
275980 TGAAAAGGTATGT
1 TGAAAAGGTATGT
275993 TGAAAAGGTATG
1 TGAAAAGGTATG
276005 CGAAAGGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:291483 original size:18 final size:18
Alignment explanation
Indices: 291462--291501 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
291452 TTTTTTAAAA
*
291462 TTTTGGCTTTTTTTTGTT
1 TTTTGGCCTTTTTTTGTT
*
291480 TTTTTGCCTTTTTTTGTT
1 TTTTGGCCTTTTTTTGTT
291498 TTTT
1 TTTT
291502 TTTTGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.80
Consensus pattern (18 bp):
TTTTGGCCTTTTTTTGTT
Found at i:291503 original size:12 final size:11
Alignment explanation
Indices: 291488--291517 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
291478 TTTTTTTGCC
291488 TTTTTTTGTTT
1 TTTTTTTGTTT
291499 TTTTTTTGTTT
1 TTTTTTTGTTT
291510 TTTTTTTG
1 TTTTTTTG
291518 AAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:291514 original size:10 final size:10
Alignment explanation
Indices: 291469--291515 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
291459 AAATTTTGGC
291469 TTTTTTTTG-
1 TTTTTTTTGT
*
291478 -TTTTTTTGC
1 TTTTTTTTGT
*
291487 CTTTTTTTGTT
1 TTTTTTTTG-T
291498 TTTTTTTTGT
1 TTTTTTTTGT
291508 TTTTTTTT
1 TTTTTTTT
291516 TGAAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 8 0.24
10 17 0.52
11 8 0.24
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:294677 original size:36 final size:36
Alignment explanation
Indices: 294598--294709 Score: 138
Period size: 36 Copynumber: 3.2 Consensus size: 36
294588 AATGGAAGGA
* * * *
294598 TGATGTTATTGGCGTGAT-ATTGTGATGGAATAT-G
1 TGATGATATAGGCGTGATAATGGAGATGGAATATGG
* * *
294632 TGATAATATAGGCGTGATAATGGCGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGAGATGGAATATGG
*
294668 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGAGATGGAATATGG
294704 TGATGA
1 TGATGA
294710 AAATAGTATC
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
34 15 0.22
35 12 0.18
36 40 0.60
ACGTcount: A:0.29, C:0.04, G:0.34, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGAGATGGAATATGG
Found at i:299022 original size:33 final size:33
Alignment explanation
Indices: 298980--299048 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
298970 GTTGATGAAT
*
298980 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
299013 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
299046 GAA
1 GAA
299049 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:299053 original size:13 final size:12
Alignment explanation
Indices: 299034--299130 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
299024 TTATTGGCGT
299034 GATATGGTGATG
1 GATATGGTGATG
299046 GAATATGGTGAT-
1 G-ATATGGTGATG
*
299058 GATATAGGCG-T-
1 GATAT-GGTGATG
299069 GATAATGGTGATG
1 GAT-ATGGTGATG
299082 GACTATGGTGAT-
1 GA-TATGGTGATG
*
299094 GATATAGGCG-T-
1 GATAT-GGTGATG
*
299105 GATAATGGAGATG
1 GAT-ATGGTGATG
299118 GATTATGGTGATG
1 GA-TATGGTGATG
299131 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:299089 original size:36 final size:36
Alignment explanation
Indices: 299019--299131 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
299009 AATGGAAGGA
* *
299019 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
299054 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
299090 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
299126 TGATGA
1 TGATGA
299132 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:302694 original size:13 final size:13
Alignment explanation
Indices: 302672--302701 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
302662 ACTAAACACC
302672 TTTC-ACATACCT
1 TTTCAACATACCT
302684 TTTCAACATACCT
1 TTTCAACATACCT
302697 TTTCA
1 TTTCA
302702 TCTTTGGCCA
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:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:305075 original size:13 final size:14
Alignment explanation
Indices: 305055--305093 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
305045 GGAAAAAAAG
305055 GAAAAAAAGAATCA
1 GAAAAAAAGAATCA
305069 GAAAAAAAGAATCA
1 GAAAAAAAGAATCA
305083 GAAAAAAAGAA
1 GAAAAAAAGAA
305094 AAGAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.05
Consensus pattern (14 bp):
GAAAAAAAGAATCA
Found at i:305079 original size:8 final size:9
Alignment explanation
Indices: 305038--305063 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
305028 TTGGAGTGCA
305038 AAAAAAAGG
1 AAAAAAAGG
305047 AAAAAAAGG
1 AAAAAAAGG
305056 AAAAAAAG
1 AAAAAAAG
305064 AATCAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:308495 original size:13 final size:13
Alignment explanation
Indices: 308473--308502 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
308463 ACTAAACACC
308473 TTTC-ACATACCT
1 TTTCAACATACCT
308485 TTTCAACATACCT
1 TTTCAACATACCT
308498 TTTCA
1 TTTCA
308503 TTTTGGCCAA
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:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:315052 original size:22 final size:18
Alignment explanation
Indices: 315006--315049 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
314996 GTCTCCTTCA
315006 AGCTAGCTTGAGTTGTGG
1 AGCTAGCTTGAGTTGTGG
315024 AGCTAGCTTGAGTTGTGG
1 AGCTAGCTTGAGTTGTGG
315042 AGCTAGCT
1 AGCTAGCT
315050 AGCAAACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (18 bp):
AGCTAGCTTGAGTTGTGG
Done.