Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004087.1 Hibiscus syriacus cultivar Beakdansim tig00008942_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: 105519
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6663 original size:25 final size:27
Alignment explanation
Indices: 6635--6691 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
6625 TTAGTTAGAG
*
6635 ATTATGA-CTAATTTAATTTAA-AAA-A
1 ATTATGATATAATTT-ATTTAATAAAGA
*
6660 ATTACGATATAATTTATTTAATAAAGA
1 ATTATGATATAATTTATTTAATAAAGA
6687 ATTAT
1 ATTAT
6692 CTTAAGCAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 12 0.46
26 9 0.35
27 5 0.19
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (27 bp):
ATTATGATATAATTTATTTAATAAAGA
Found at i:7304 original size:12 final size:12
Alignment explanation
Indices: 7289--7319 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
7279 GTTATTTAAA
*
7289 CGGGTATCGGGC
1 CGGGTATCAGGC
7301 CGGGTATCAGGC
1 CGGGTATCAGGC
7313 CGGGTAT
1 CGGGTAT
7320 ATATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (12 bp):
CGGGTATCAGGC
Found at i:14062 original size:20 final size:20
Alignment explanation
Indices: 14039--14076 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
14029 CATGACATTT
*
14039 TTTTTATTATTTTAATAACA
1 TTTTTATTAATTTAATAACA
*
14059 TTTTTTTTAATTTAATAA
1 TTTTTATTAATTTAATAA
14077 ATAATTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTATTAATTTAATAACA
Found at i:14138 original size:32 final size:32
Alignment explanation
Indices: 14097--14157 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
14087 TAAAAAAAAT
*
14097 TAAACTTGAAAGTTATAATGATTAAATTAAGAG
1 TAAACTTGAAAGTTA-AATAATTAAATTAAGAG
* *
14130 TAAA-TTGAATGTTAAGTAATTAAATTAA
1 TAAACTTGAAAGTTAAATAATTAAATTAA
14158 AAAATTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 12 0.48
32 9 0.36
33 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (32 bp):
TAAACTTGAAAGTTAAATAATTAAATTAAGAG
Found at i:21157 original size:6 final size:6
Alignment explanation
Indices: 21146--21194 Score: 73
Period size: 6 Copynumber: 8.0 Consensus size: 6
21136 CGTTCAATTA
21146 GTAGCT GTAGCT GTAGCT GTAGCT GTAGCT GTAGCCT GTAAGCT -TAGCT
1 GTAGCT GTAGCT GTAGCT GTAGCT GTAGCT GTAG-CT GT-AGCT GTAGCT
21195 TAGAAAGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
5 4 0.10
6 29 0.71
7 6 0.15
8 2 0.05
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.33
Consensus pattern (6 bp):
GTAGCT
Found at i:22056 original size:21 final size:20
Alignment explanation
Indices: 22030--22148 Score: 114
Period size: 21 Copynumber: 5.8 Consensus size: 20
22020 ATCAGTTTCC
22030 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
22051 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
22072 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
22091 ACAAATTCGCATTGCGATTTTCC
1 A-AAA-TCGCAACGCGATTTT-G
* *
22114 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
22134 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
22149 ACACATAAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
19 1 0.01
20 19 0.23
21 59 0.71
22 3 0.04
23 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:22087 original size:42 final size:41
Alignment explanation
Indices: 22025--22148 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 41
22015 CGCAAATCAG
22025 TTTCCAAAATCGCAACGCGATTCTTGAAAATCGCAACGCGAT
1 TTTCCAAAATCGCAACGCGATT-TTGAAAATCGCAACGCGAT
* * ** **
22067 TCTT-GAAAATCGCAATGCGATAGT-ACAAATTCGCATTGCGAT
1 T-TTCCAAAATCGCAACGCGATTTTGA-AAA-TCGCAACGCGAT
* *
22109 TTTCCAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 TTTCCAAAATCGCAACGCGATTTTGAAAATCGCAACGCGA
22149 ACACATAAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
40 1 0.02
41 15 0.23
42 45 0.70
43 3 0.05
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (41 bp):
TTTCCAAAATCGCAACGCGATTTTGAAAATCGCAACGCGAT
Found at i:22139 original size:20 final size:20
Alignment explanation
Indices: 22030--22207 Score: 92
Period size: 20 Copynumber: 8.7 Consensus size: 20
22020 ATCAGTTTCC
* *
22030 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGAAT-ATG
* *
22051 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGAAT-ATG
*
22072 AAAATCGCAATGCG-ATA-G
1 AAAATCGCAACGCGAATATG
** * * *
22090 TACAAATTCGCATTGCGATTTTCC
1 -A-AAA-TCGCAACGCGAATAT-G
22114 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGAATATG
* *
22134 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAATATG
* **
22153 ATAAATCGCAACGCGTATCCG
1 A-AAATCGCAACGCGAATATG
* * **
22174 TAAATCGCAACGCGTATCCG
1 AAAATCGCAACGCGAATATG
*
22194 TAAATCGCAACGCG
1 AAAATCGCAACGCG
22208 TATGGGTAAA
Statistics
Matches: 130, Mismatches: 19, Indels: 17
0.78 0.11 0.10
Matches are distributed among these distances:
18 1 0.01
19 2 0.02
20 68 0.52
21 54 0.42
22 4 0.03
23 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATG
Found at i:22199 original size:60 final size:60
Alignment explanation
Indices: 22115--22308 Score: 262
Period size: 60 Copynumber: 3.2 Consensus size: 60
22105 CGATTTTCCA
* ** * *
22115 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* *** *
22175 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
22235 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
22296 AAATCGCAACGCG
1 AAATCGCAACGCG
22309 ATATTTAAAG
Statistics
Matches: 114, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 83 0.73
61 31 0.27
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:22208 original size:20 final size:20
Alignment explanation
Indices: 22115--22308 Score: 230
Period size: 20 Copynumber: 9.7 Consensus size: 20
22105 CGATTTTCCA
* ** *
22115 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
22135 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
22155 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
22175 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
22195 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
22215 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
22235 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
22255 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
22275 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
22296 AAATCGCAACGCG
1 AAATCGCAACGCG
22309 ATATTTAAAG
Statistics
Matches: 148, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.86
21 17 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:22728 original size:33 final size:33
Alignment explanation
Indices: 22689--22759 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
22679 TTCACTTAGA
* *
22689 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
22722 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
22755 TTTCA
1 TTTCA
22760 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:22865 original size:21 final size:20
Alignment explanation
Indices: 22839--22944 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
22829 TGCAGAAGAG
22839 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
22860 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
22880 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
22901 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
22915 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
22934 TCGCAACGAGA
1 TCGCAACGAGA
22945 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:22883 original size:20 final size:21
Alignment explanation
Indices: 22837--22915 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
22827 TTTGCAGAAG
*
22837 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
22859 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
22878 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
22900 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
22916 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:22896 original size:41 final size:38
Alignment explanation
Indices: 22832--22948 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
22822 TTCAATTTGC
* *
22832 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
22870 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
22911 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
22944 AGAAT
1 AGAAT
22949 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:22921 original size:14 final size:14
Alignment explanation
Indices: 22902--22955 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
22892 AAATGAAAAG
22902 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
22916 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
22935 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
22949 CGCAACG
1 CGCAACG
22956 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:22931 original size:33 final size:33
Alignment explanation
Indices: 22891--22960 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
22881 CGCAACGAGA
22891 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
22924 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
22957 GAAA
1 GAAA
22961 CCAAATCGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:22993 original size:19 final size:18
Alignment explanation
Indices: 22966--23083 Score: 80
Period size: 14 Copynumber: 7.1 Consensus size: 18
22956 CGAAACCAAA
*
22966 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
22985 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
*
22999 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
23018 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
* *
23032 TCTCGTTGCGATTGTCAT
1 TCGCGTTGCGATTTTCAT
23050 CTCGCGTTGCGA--TTC--
1 -TCGCGTTGCGATTTTCAT
*
23065 TCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
23083 T
1 T
23084 TCAACCAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 29
0.68 0.07 0.25
Matches are distributed among these distances:
14 30 0.39
16 8 0.10
17 8 0.10
18 1 0.01
19 30 0.39
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCAT
Found at i:23007 original size:14 final size:14
Alignment explanation
Indices: 22988--23077 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
22978 TTTCATTTCG
22988 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
23002 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
23021 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
23035 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
23052 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
23068 CGTTGCGATT
1 CGTTGCGATT
23078 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:23013 original size:33 final size:33
Alignment explanation
Indices: 22971--23085 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
22961 CCAAATCGCA
22971 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
23004 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
23037 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
23070 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
23086 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:24939 original size:93 final size:93
Alignment explanation
Indices: 24780--25251 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
24770 TAGATTGCTT
*
24780 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24845 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24873 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24938 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24966 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
25031 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
25059 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
25124 -TTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
25150 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
25215 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
25243 AGTAAATTT
1 AGTAAATTT
25252 ATCCATTCAA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
91 81 0.22
92 18 0.05
93 275 0.74
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:25335 original size:19 final size:19
Alignment explanation
Indices: 25295--25371 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
25285 TAGTTTACTT
* *
25295 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
25315 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
25334 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
25348 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
25367 TCGCA
1 TCGCA
25372 TTGCGATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
14 10 0.21
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 19 0.40
20 13 0.27
ACGTcount: A:0.45, C:0.30, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:25389 original size:19 final size:19
Alignment explanation
Indices: 25367--25501 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
25357 GAAACCAAAA
*
25367 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
25386 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
25402 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
25419 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
25435 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
25452 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
25471 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
25491 TCGTGTTGCGA
1 TCGCGTTGCGA
25502 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:25408 original size:14 final size:14
Alignment explanation
Indices: 25389--25445 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
25379 TTTCATTTCG
25389 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
25403 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
25420 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
25436 CGTTGCGATT
1 CGTTGCGATT
25446 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:25414 original size:33 final size:33
Alignment explanation
Indices: 25372--25464 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
25362 CAAAATCGCA
*
25372 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
25405 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
25438 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
25465 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:27443 original size:14 final size:14
Alignment explanation
Indices: 27424--27459 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
27414 ATTGTTTAAT
27424 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
27438 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
27452 TGATTTGT
1 TGATTTGT
27460 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:27588 original size:19 final size:19
Alignment explanation
Indices: 27564--27663 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
27554 AAAATTGACT
27564 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27583 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
27602 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
27616 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27635 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
27655 ATCGCAATG
1 ATCGCAATG
27664 GGAGAATCGC
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:27693 original size:53 final size:53
Alignment explanation
Indices: 27564--27680 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
27554 AAAATTGACT
27564 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
27616 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
27669 ATCGCAATGCGA
1 ATCGCAATGCGA
27681 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:27698 original size:19 final size:19
Alignment explanation
Indices: 27670--27818 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
27660 AATGGGAGAA
* *
27670 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
27689 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
27705 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
27722 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
27741 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
27757 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
27774 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
27790 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
27807 TCCGCATTGCGA
1 T-CGCATTGCGA
27819 AATGTAATGG
Statistics
Matches: 107, Mismatches: 7, Indels: 31
0.74 0.05 0.21
Matches are distributed among these distances:
14 18 0.17
16 21 0.20
17 19 0.18
18 2 0.02
19 41 0.38
20 6 0.06
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:27733 original size:52 final size:52
Alignment explanation
Indices: 27670--27786 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
27660 AATGGGAGAA
*
27670 TCGCAATGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* *
27722 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
27774 TCGCATTGCGATT
1 TCGCATTGCGATT
27787 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
Found at i:27764 original size:33 final size:33
Alignment explanation
Indices: 27727--27818 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
27717 TCATTTCGCA
27727 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
27760 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
27793 TTGCGATTTTCATTTCCGCATTGCGA
1 TTGCGATTTTCATTT-CGCATTGCGA
27819 AATGTAATGG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 48 0.83
34 10 0.17
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:27765 original size:14 final size:14
Alignment explanation
Indices: 27746--27800 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
27736 TCATTTCGCA
27746 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
27760 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
27777 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
27793 TTGCGATT
1 TTGCGATT
27801 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:27901 original size:19 final size:19
Alignment explanation
Indices: 27877--27974 Score: 125
Period size: 19 Copynumber: 5.4 Consensus size: 19
27867 AAAATTGACT
27877 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27896 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
27915 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
27929 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
27948 ATCGCAACACGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
27968 ATCGCAA
1 ATCGCAA
27975 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 37 0.54
20 16 0.23
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:28006 original size:53 final size:53
Alignment explanation
Indices: 27877--27993 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
27867 AAAATTGACT
**
27877 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACACGGAAATGAAAATCGCAACGAGAGA
27929 ATCGCAATGCGAAATGAAAATCGCAACACGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACACGGAAATGAAAATCGCAACGAGAGA
27982 ATCGCAATGCGA
1 ATCGCAATGCGA
27994 TTTTCATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 27 0.44
53 35 0.56
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAACACGGAAATGAAAATCGCAACGAGAGA
Found at i:30326 original size:12 final size:12
Alignment explanation
Indices: 30309--30333 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30299 TCTTCGGGGA
30309 CTTTTTCTTCTT
1 CTTTTTCTTCTT
30321 CTTTTTCTTCTT
1 CTTTTTCTTCTT
30333 C
1 C
30334 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:30542 original size:24 final size:24
Alignment explanation
Indices: 30508--30554 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
30498 CTGAAACATC
30508 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
30532 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
30555 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:31264 original size:20 final size:20
Alignment explanation
Indices: 31236--31485 Score: 259
Period size: 20 Copynumber: 12.5 Consensus size: 20
31226 AAATTTCAGT
* * *
31236 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
31256 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
31276 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
31296 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
31316 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
31336 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
31356 ATTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
31376 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
*
31396 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
31416 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
31436 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
31456 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
31476 GTTGCGATTT
1 GTTGCGATTT
31486 TGGAAAATCG
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:31502 original size:21 final size:21
Alignment explanation
Indices: 31472--31554 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
31462 ATTTTCATAT
*
31472 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
31493 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
31514 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
31535 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
31555 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:31545 original size:42 final size:43
Alignment explanation
Indices: 31452--31550 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
31442 ATTTATGTGT
* *
31452 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
31493 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
31535 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
31551 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:37696 original size:114 final size:114
Alignment explanation
Indices: 37496--37715 Score: 361
Period size: 114 Copynumber: 1.9 Consensus size: 114
37486 GTAACCCCTA
*
37496 GAATTAAATCAAATAACTCATGATATTAACAGTTTATCTCCTTTGTACAAAGCTGAAAATCAGTC
1 GAATTAAATCAAATAACTCATGATATTAACAGTTTATCCCCTTTGTACAAAGCTGAAAATCAGTC
*
37561 CTCAGCAGCCTATAAATACCAGTTGAAATCTTTCATATTTTTTCATCTG
66 CTCAGCAGCCTATAAATACCAGTTGAAATCTTTCACATTTTTTCATCTG
* * *
37610 GAATTAAATCAAATAACTTC-TGATATTAACAGTTTGTCCCCTTTTTACAAAGTTGAAAATCAGT
1 GAATTAAATCAAATAAC-TCATGATATTAACAGTTTATCCCCTTTGTACAAAGCTGAAAATCAGT
* *
37674 CCTTAGCAGCCTATAAATACCAGTTGAAATTTTTCACATTTT
65 CCTCAGCAGCCTATAAATACCAGTTGAAATCTTTCACATTTT
37716 CTATTTATTT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
114 96 0.98
115 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (114 bp):
GAATTAAATCAAATAACTCATGATATTAACAGTTTATCCCCTTTGTACAAAGCTGAAAATCAGTC
CTCAGCAGCCTATAAATACCAGTTGAAATCTTTCACATTTTTTCATCTG
Found at i:38857 original size:15 final size:15
Alignment explanation
Indices: 38839--38894 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
38829 TAACCGGTTT
38839 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
38854 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
38871 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
38886 CGATTTTAA
1 CGGTTTTAA
38895 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:38867 original size:17 final size:17
Alignment explanation
Indices: 38842--38892 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
38832 CCGGTTTCGG
38842 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
38859 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
38874 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
38891 TT
1 TT
38893 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:39310 original size:13 final size:13
Alignment explanation
Indices: 39289--39343 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
39279 AAGTTCGATA
*
39289 AATTCAAATACTT
1 AATTGAAATACTT
39302 AATTGAAATACTT
1 AATTGAAATACTT
* *
39315 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
39329 AATTGAAATACTT
1 AATTGAAATACTT
39342 AA
1 AA
39344 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:39425 original size:32 final size:33
Alignment explanation
Indices: 39329--39427 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
39319 AACTCAACAT
* * *
39329 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
39362 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
39395 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
39427 A
1 A
39428 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:39446 original size:21 final size:21
Alignment explanation
Indices: 39422--39461 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
39412 ACTTCAAGTT
39422 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
39443 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
39462 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:42488 original size:29 final size:29
Alignment explanation
Indices: 42446--42503 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
42436 ATGCCAATTA
42446 CAAATACACAATCCTGGTAAGAACACTGC
1 CAAATACACAATCCTGGTAAGAACACTGC
*
42475 CAAATACACAATCCTGGTAAGTACACTGC
1 CAAATACACAATCCTGGTAAGAACACTGC
42504 TACTGTGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.19
Consensus pattern (29 bp):
CAAATACACAATCCTGGTAAGAACACTGC
Found at i:54596 original size:294 final size:295
Alignment explanation
Indices: 54067--55210 Score: 2118
Period size: 295 Copynumber: 3.9 Consensus size: 295
54057 TTTTACTTAC
54067 CCCTAATCTCCTTAGATCCAAGTAGTGATGGGTATCGAACTTGGACCTTACATGTATTGATCCGA
1 CCCTAATCTCCTTAGATCCAAGTAGTGATGGGTATCGAACTTGGACCTTACATGTATTGATCCGA
54132 CCCTGTAAGATTGATTTTG-AAAAAAATGAAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGA
66 CCCTGTAAGATTGATTTTGAAAAAAAATGAAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGA
54196 TAAATTCAAGTTAGATCGTATTCGAATTAAAGAGAAAAATTCTTAGATCTAATACAAGATAGTAG
131 TAAATTCAAGTTAGATCGTATTCGAATTAAAGAGAAAAATTCTTAGATCTAATACAAGATAGTAG
54261 -ATTAATTTTTCTTTATCTATTTAAGAACGGACAATACGTAAATCCCAAAAATAGGCAATCTGTA
196 TA-TAATTTTTCTTTATCTATTTAAGAACGGACAATACGTAAATCCCAAAAATAGGCAATCTGTA
* *
54325 CATTTCTATGTAAATCTCATTTGGGCATTAGTTTTG
260 AATTTCTATGTAAATCTCATTTGGGCATTAGATTTG
54361 CCCTAATCTCCTTAGATCCAAGTAGTGATGGGTATCGAACTTGGACCTTACATGTATTGATCCGA
1 CCCTAATCTCCTTAGATCCAAGTAGTGATGGGTATCGAACTTGGACCTTACATGTATTGATCCGA
54426 CCCTGTAAGATTGATTTTG-AAAAAAATGAAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGA
66 CCCTGTAAGATTGATTTTGAAAAAAAATGAAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGA
54490 TAAATTCAAGTTAGATCGTATTCGAATTAAAGAGAAAAATTCTTAGATCTAATACAAGATAGTAG
131 TAAATTCAAGTTAGATCGTATTCGAATTAAAGAGAAAAATTCTTAGATCTAATACAAGATAGTAG
54555 TATAATTTTTCTTTATCTATTTAAGAACGGACAATACGTAAATCCCAAAAATAGGCAATCTGTAA
196 TATAATTTTTCTTTATCTATTTAAGAACGGACAATACGTAAATCCCAAAAATAGGCAATCTGTAA
54620 ATTTCTATGTAAATCTCATTTGGGCATTAGATTTG
261 ATTTCTATGTAAATCTCATTTGGGCATTAGATTTG
*
54655 CCCTAATCTCCTTAGATCCAAGTAGTGATGGGTATCGAACTTGGACCTTACATGTATTGATTCGA
1 CCCTAATCTCCTTAGATCCAAGTAGTGATGGGTATCGAACTTGGACCTTACATGTATTGATCCGA
*
54720 CCCTGTAAGATTGATTTTGAAAAAAAATGGAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGA
66 CCCTGTAAGATTGATTTTGAAAAAAAATGAAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGA
*
54785 TAAATTCAAGTTTGATCGTATTCGAATTAAAGAGAAAAATTCTTAGATCTAATACAAGATAGTAG
131 TAAATTCAAGTTAGATCGTATTCGAATTAAAGAGAAAAATTCTTAGATCTAATACAAGATAGTAG
* *
54850 TATATTTTTTCTTTATCTATTTAAGAACGGACAATACGTAAATCCCAAAAATAAGCAATCTGTAA
196 TATAATTTTTCTTTATCTATTTAAGAACGGACAATACGTAAATCCCAAAAATAGGCAATCTGTAA
54915 ATTTCTATGTAAATCTCATTTGGGCATTAGATTTG
261 ATTTCTATGTAAATCTCATTTGGGCATTAGATTTG
*
54950 CCCTAATCTCCTTAGATCTAAGTAGTGATGGGTATCGAACTTGGACCTTACATGTATTGATCCGA
1 CCCTAATCTCCTTAGATCCAAGTAGTGATGGGTATCGAACTTGGACCTTACATGTATTGATCCGA
* *
55015 CCCTATAAGATTGATTTTGAAAAAAAATGGAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGA
66 CCCTGTAAGATTGATTTTGAAAAAAAATGAAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGA
*
55080 TAAATTCAAGTTTGATCGTATTCGAATTAAAGAGAAAAATTCTTAGATCTAATACAAGATAGTAG
131 TAAATTCAAGTTAGATCGTATTCGAATTAAAGAGAAAAATTCTTAGATCTAATACAAGATAGTAG
* *
55145 TATAATTTTTCTTTATCTATTTAAGAACGGACAATATGTAAA-CCCAAAAAT-GGACAACCTGTA
196 TATAATTTTTCTTTATCTATTTAAGAACGGACAATACGTAAATCCCAAAAATAGG-CAATCTGTA
55208 AAT
260 AAT
55211 CTCATTTGAG
Statistics
Matches: 833, Mismatches: 14, Indels: 6
0.98 0.02 0.01
Matches are distributed among these distances:
293 1 0.00
294 393 0.47
295 439 0.53
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (295 bp):
CCCTAATCTCCTTAGATCCAAGTAGTGATGGGTATCGAACTTGGACCTTACATGTATTGATCCGA
CCCTGTAAGATTGATTTTGAAAAAAAATGAAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGA
TAAATTCAAGTTAGATCGTATTCGAATTAAAGAGAAAAATTCTTAGATCTAATACAAGATAGTAG
TATAATTTTTCTTTATCTATTTAAGAACGGACAATACGTAAATCCCAAAAATAGGCAATCTGTAA
ATTTCTATGTAAATCTCATTTGGGCATTAGATTTG
Found at i:54861 original size:589 final size:588
Alignment explanation
Indices: 54067--55210 Score: 2114
Period size: 589 Copynumber: 1.9 Consensus size: 588
54057 TTTTACTTAC
54067 CCCTAATCTCCTTAGATCCAAGTAGTGATGGGTATCGAACTTGGACCTTACATGTATTGATCCGA
1 CCCTAATCTCCTTAGATCCAAGTAGTGATGGGTATCGAACTTGGACCTTACATGTATTGATCCGA
54132 CCCTGTAAGATTGATTTTGAAAAAAATGAAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGAT
66 CCCTGTAAGATTGATTTTGAAAAAAATGAAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGAT
54197 AAATTCAAGTTAGATCGTATTCGAATTAAAGAGAAAAATTCTTAGATCTAATACAAGATAGTAGA
131 AAATTCAAGTTAGATCGTATTCGAATTAAAGAGAAAAATTCTTAGATCTAATACAAGATAGTAGA
* *
54262 TTAATTTTTCTTTATCTATTTAAGAACGGACAATACGTAAATCCCAAAAATAGGCAATCTGTACA
196 TTAATTTTTCTTTATCTATTTAAGAACGGACAATACGTAAATCCCAAAAATAAGCAATCTGTAAA
*
54327 TTTCTATGTAAATCTCATTTGGGCATTAGTTTTGCCCTAATCTCCTTAGATCCAAGTAGTGATGG
261 TTTCTATGTAAATCTCATTTGGGCATTAGATTTGCCCTAATCTCCTTAGATCCAAGTAGTGATGG
*
54392 GTATCGAACTTGGACCTTACATGTATTGATCCGACCCTGTAAGATTGATTTTG-AAAAAAATGAA
326 GTATCGAACTTGGACCTTACATGTATTGATCCGACCCTATAAGATTGATTTTGAAAAAAAATGAA
54456 ATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGATAAATTCAAGTTAGATCGTATTCGAATTAAA
391 ATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGATAAATTCAAGTTAGATCGTATTCGAATTAAA
54521 GAGAAAAATTCTTAGATCTAATACAAGATAGTAGTATAATTTTTCTTTATCTATTTAAGAACGGA
456 GAGAAAAATTCTTAGATCTAATACAAGATAGTAGTATAATTTTTCTTTATCTATTTAAGAACGGA
*
54586 CAATACGTAAATCCCAAAAATAGG-CAATCTGTAAATTTCTATGTAAATCTCATTTGGGCATTAG
521 CAATACGTAAA-CCCAAAAAT-GGACAACCTGTAAATTTCTATGTAAATCTCATTTGGGCATTAG
54650 ATTTG
584 ATTTG
*
54655 CCCTAATCTCCTTAGATCCAAGTAGTGATGGGTATCGAACTTGGACCTTACATGTATTGATTCGA
1 CCCTAATCTCCTTAGATCCAAGTAGTGATGGGTATCGAACTTGGACCTTACATGTATTGATCCGA
*
54720 CCCTGTAAGATTGATTTTGAAAAAAAATGGAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGA
66 CCCTGTAAGATTGATTTTG-AAAAAAATGAAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGA
*
54785 TAAATTCAAGTTTGATCGTATTCGAATTAAAGAGAAAAATTCTTAGATCTAATACAAGATAGTAG
130 TAAATTCAAGTTAGATCGTATTCGAATTAAAGAGAAAAATTCTTAGATCTAATACAAGATAGTAG
*
54850 -TATATTTTTTCTTTATCTATTTAAGAACGGACAATACGTAAATCCCAAAAATAAGCAATCTGTA
195 AT-TAATTTTTCTTTATCTATTTAAGAACGGACAATACGTAAATCCCAAAAATAAGCAATCTGTA
*
54914 AATTTCTATGTAAATCTCATTTGGGCATTAGATTTGCCCTAATCTCCTTAGATCTAAGTAGTGAT
259 AATTTCTATGTAAATCTCATTTGGGCATTAGATTTGCCCTAATCTCCTTAGATCCAAGTAGTGAT
54979 GGGTATCGAACTTGGACCTTACATGTATTGATCCGACCCTATAAGATTGATTTTGAAAAAAAATG
324 GGGTATCGAACTTGGACCTTACATGTATTGATCCGACCCTATAAGATTGATTTTGAAAAAAAATG
* *
55044 GAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGATAAATTCAAGTTTGATCGTATTCGAATTA
389 AAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGATAAATTCAAGTTAGATCGTATTCGAATTA
55109 AAGAGAAAAATTCTTAGATCTAATACAAGATAGTAGTATAATTTTTCTTTATCTATTTAAGAACG
454 AAGAGAAAAATTCTTAGATCTAATACAAGATAGTAGTATAATTTTTCTTTATCTATTTAAGAACG
*
55174 GACAATATGTAAACCCAAAAATGGACAACCTGTAAAT
519 GACAATACGTAAACCCAAAAATGGACAACCTGTAAAT
55211 CTCATTTGAG
Statistics
Matches: 539, Mismatches: 13, Indels: 7
0.96 0.02 0.01
Matches are distributed among these distances:
588 86 0.16
589 304 0.56
590 149 0.28
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (588 bp):
CCCTAATCTCCTTAGATCCAAGTAGTGATGGGTATCGAACTTGGACCTTACATGTATTGATCCGA
CCCTGTAAGATTGATTTTGAAAAAAATGAAATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGAT
AAATTCAAGTTAGATCGTATTCGAATTAAAGAGAAAAATTCTTAGATCTAATACAAGATAGTAGA
TTAATTTTTCTTTATCTATTTAAGAACGGACAATACGTAAATCCCAAAAATAAGCAATCTGTAAA
TTTCTATGTAAATCTCATTTGGGCATTAGATTTGCCCTAATCTCCTTAGATCCAAGTAGTGATGG
GTATCGAACTTGGACCTTACATGTATTGATCCGACCCTATAAGATTGATTTTGAAAAAAAATGAA
ATTCGAATCAGGTCAGATGGAGTTTTTTGAAAGATAAATTCAAGTTAGATCGTATTCGAATTAAA
GAGAAAAATTCTTAGATCTAATACAAGATAGTAGTATAATTTTTCTTTATCTATTTAAGAACGGA
CAATACGTAAACCCAAAAATGGACAACCTGTAAATTTCTATGTAAATCTCATTTGGGCATTAGAT
TTG
Found at i:57407 original size:11 final size:11
Alignment explanation
Indices: 57391--57423 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
57381 TTTTTATATA
57391 TTAATTTTAAT
1 TTAATTTTAAT
57402 TTAATTTT-AT
1 TTAATTTTAAT
57412 TATAATTTTAAT
1 T-TAATTTTAAT
57424 GATTGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 3 0.15
11 15 0.75
12 2 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTAATTTTAAT
Found at i:60732 original size:25 final size:25
Alignment explanation
Indices: 60677--60733 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
60667 TATATATATA
*
60677 TATATATGTCTTTATGACATGTTTG
1 TATATATGTCTTTATGACACGTTTG
*
60702 TTTATATG-CTTTTATGACACGATTT-
1 TATATATGTC-TTTATGACACG-TTTG
60727 TATATAT
1 TATATAT
60734 CGTTATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 1 0.04
25 23 0.85
26 3 0.11
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53
Consensus pattern (25 bp):
TATATATGTCTTTATGACACGTTTG
Found at i:63539 original size:14 final size:13
Alignment explanation
Indices: 63520--63567 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
63510 ATTAAATAAA
63520 TTAATATAATATTT
1 TTAATA-AATATTT
*
63534 TTAATAATATATAT
1 TTAATAA-ATATTT
* *
63548 TTCATAAATATTA
1 TTAATAAATATTT
63561 TTAATAA
1 TTAATAA
63568 TTATATTGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 11 0.39
14 17 0.61
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATAAATATTT
Found at i:75786 original size:36 final size:36
Alignment explanation
Indices: 75736--75811 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 36
75726 TTACCTATCA
* * * *
75736 ATTATCAACGCATTT-ATAAAAGTTATTGGATAAATT
1 ATTAACAAAGCATTTAAAAAAAG-TATTGAATAAATT
75772 ATTAACAAAGCATTTACAAAAAAGTATTGAATAAATT
1 ATTAACAAAGCATTTA-AAAAAAGTATTGAATAAATT
75809 ATT
1 ATT
75812 GGATTTTTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 13 0.38
37 15 0.44
38 6 0.18
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (36 bp):
ATTAACAAAGCATTTAAAAAAAGTATTGAATAAATT
Found at i:79799 original size:18 final size:18
Alignment explanation
Indices: 79758--79805 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
79748 GTTTTTATAA
*
79758 AAATAATTTATAAAAGAAT
1 AAATAAATT-TAAAAGAAT
* *
79777 TAATAAATTTAATAGAAT
1 AAATAAATTTAAAAGAAT
79795 AAATAATATTT
1 AAATAA-ATTT
79806 TTTTTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (18 bp):
AAATAAATTTAAAAGAAT
Found at i:81482 original size:181 final size:180
Alignment explanation
Indices: 81178--81534 Score: 633
Period size: 181 Copynumber: 2.0 Consensus size: 180
81168 TCTTAGCTGT
*
81178 ACGTTAACCTGCTGACTGAGATATGATAAAATTTGATCTCATAATCTTAAACGACTATCATATCT
1 ACGTTAACCTGCTGACTGAGATATAATAAAATTTGATCTCATAATCTTAAACGACTATCATATCT
* * *
81243 CAGTCGCATGTTAACGTTCAAGTTAGACGACTGTTAATTTTTTAATGGAAAATGATGAGTTTGGA
66 CAATCGCATGTTAACGTCCAAGTCAGACGACTGTTAATTTTTTAATGGAAAATGATGAGTTTGGA
*
81308 ACATAATGAATAGTCGGGTGATCATTTTGTAACTTTTAATAGTAGAGCCGG
131 ACATAATGAATAGTC-GGTGAACATTTTGTAACTTTTAATAGTAGAGCCGG
* *
81359 ACGTTAATCTGGTGACTGAGATATAATAAAATTTGATCTCATAATCTTAAACGACTATCATATCT
1 ACGTTAACCTGCTGACTGAGATATAATAAAATTTGATCTCATAATCTTAAACGACTATCATATCT
*
81424 CAATCGCATGTTAACGTCCAAGTCAGACGACTGTTAATTTTTTAATGGAAAATGATGAGTTTTGA
66 CAATCGCATGTTAACGTCCAAGTCAGACGACTGTTAATTTTTTAATGGAAAATGATGAGTTTGGA
81489 ACATAATGAATAGTCGGTGAACATTTTGTAACTTTTAATAGTAGAG
131 ACATAATGAATAGTCGGTGAACATTTTGTAACTTTTAATAGTAGAG
81535 GAACTCAACA
Statistics
Matches: 168, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
180 30 0.18
181 138 0.82
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (180 bp):
ACGTTAACCTGCTGACTGAGATATAATAAAATTTGATCTCATAATCTTAAACGACTATCATATCT
CAATCGCATGTTAACGTCCAAGTCAGACGACTGTTAATTTTTTAATGGAAAATGATGAGTTTGGA
ACATAATGAATAGTCGGTGAACATTTTGTAACTTTTAATAGTAGAGCCGG
Found at i:85287 original size:2 final size:2
Alignment explanation
Indices: 85282--85358 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
85272 ACACACACAC
85282 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
85324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
85359 TAAATTTATT
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 73 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:91379 original size:21 final size:21
Alignment explanation
Indices: 91355--91396 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
91345 AGTTTATTTT
91355 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
91376 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
91397 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:91444 original size:33 final size:33
Alignment explanation
Indices: 91391--91483 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
91381 TTTGTTTCAA
91391 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
91423 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
91456 TTATCAAACTTGGAAGTATTTAAGTATT
1 TTATCGAACTTGGAAGTTTTTAAGTATT
91484 CAATTATGTT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 11 0.19
33 47 0.81
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:91710 original size:15 final size:15
Alignment explanation
Indices: 91658--91710 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
91648 TTTAATAATA
* *
91658 TTAAAATCGATTTTT
1 TTAAAACCGGTTTTT
*
91673 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
91688 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
91705 TTAAAA
1 TTAAAA
91711 TCGAAACCGG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 17 0.57
17 13 0.43
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:91722 original size:21 final size:18
Alignment explanation
Indices: 91677--91710 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
91667 ATTTTTTTAT
91677 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
91694 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
91711 TCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:91830 original size:15 final size:17
Alignment explanation
Indices: 91804--91835 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
91794 TTCTATGGGA
91804 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
91820 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
91836 CGAATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:96322 original size:22 final size:22
Alignment explanation
Indices: 96291--96333 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
96281 ATTAAAAAAT
96291 ACTAACATTTATATAGCTATTA
1 ACTAACATTTATATAGCTATTA
*
96313 ACTAATATTTATATAGCTATT
1 ACTAACATTTATATAGCTATT
96334 TAATAAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.44
Consensus pattern (22 bp):
ACTAACATTTATATAGCTATTA
Done.