Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000179.1 Hibiscus syriacus cultivar Beakdansim tig00000314_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: 120636
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:5636 original size:25 final size:26
Alignment explanation
Indices: 5606--5664 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
5596 GTTCATATTT
*
5606 AAATAAATTAGATAT-GGTGATTATA
1 AAATAAATTAAATATCGGTGATTATA
*
5631 AAATAAATTAAATATCGTTGATTATA
1 AAATAAATTAAATATCGGTGATTATA
5657 AAATAAAT
1 AAATAAAT
5665 ACAAGGCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.36
Consensus pattern (26 bp):
AAATAAATTAAATATCGGTGATTATA
Found at i:6794 original size:20 final size:20
Alignment explanation
Indices: 6769--6853 Score: 93
Period size: 20 Copynumber: 4.2 Consensus size: 20
6759 AACTCTAATT
6769 TCGCAACACA-TGTTCCAAAA
1 TCGCAACACAGT-TTCCAAAA
*
6789 TTGCAACACAGTTTCCAAAA
1 TCGCAACACAGTTTCCAAAA
* * **
6809 TCGCAACGCGAATTT-GTAAA
1 TCGCAACAC-AGTTTCCAAAA
6829 TCGCAACACAGTTTCCAAAA
1 TCGCAACACAGTTTCCAAAA
6849 TCGCA
1 TCGCA
6854 TTGCGATAGT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.08
20 43 0.83
21 5 0.10
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (20 bp):
TCGCAACACAGTTTCCAAAA
Found at i:6908 original size:77 final size:77
Alignment explanation
Indices: 6816--7039 Score: 207
Period size: 77 Copynumber: 2.9 Consensus size: 77
6806 AAATCGCAAC
* * ** * *
6816 GCGAATTTGTAAATCGCAACAC-AGTTTCCAAAATCGCATTGCGATAGTACTGTTTACCTATATC
1 GCGAATTTGAAAATCGCAACACGAATTT-CAAAATCGCATTGCGATAACACTGTTTACATACATC
6880 GGTAATTACCGTT
65 GGTAATTACCGTT
**** * **
6893 GCGAATTTGAAAATCGCGTTGCGAATTTGAAAATCGTGTTGCGATAACACTGTTTACATACATCG
1 GCGAATTTGAAAATCGCAACACGAATTTCAAAATCGCATTGCGATAACACTGTTTACATACATCG
*
6958 GTAATTAGCGTT
66 GTAATTACCGTT
**** * * * * * *
6970 GCGAATTTGAAAATCGCGTTGCGATTTTTGAAAATCGCGTTGCGATAACACTGGTTACCTATATC
1 GCGAATTTGAAAATCGCAACACGA-ATTTCAAAATCGCATTGCGATAACACTGTTTACATACATC
7035 GGTAA
65 GGTAA
7040 ATTGCGTTGC
Statistics
Matches: 126, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
77 82 0.65
78 44 0.35
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (77 bp):
GCGAATTTGAAAATCGCAACACGAATTTCAAAATCGCATTGCGATAACACTGTTTACATACATCG
GTAATTACCGTT
Found at i:6914 original size:20 final size:20
Alignment explanation
Indices: 6889--6936 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
6879 CGGTAATTAC
6889 CGTTGCGAATTTGAAAATCG
1 CGTTGCGAATTTGAAAATCG
6909 CGTTGCGAATTTGAAAATCG
1 CGTTGCGAATTTGAAAATCG
*
6929 TGTTGCGA
1 CGTTGCGA
6937 TAACACTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (20 bp):
CGTTGCGAATTTGAAAATCG
Found at i:7001 original size:21 final size:21
Alignment explanation
Indices: 6965--7016 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
6955 TCGGTAATTA
6965 GCGTTGCGA-ATTTGAAAATC
1 GCGTTGCGATATTTGAAAATC
*
6985 GCGTTGCGATTTTTGAAAATC
1 GCGTTGCGATATTTGAAAATC
7006 GCGTTGCGATA
1 GCGTTGCGATA
7017 ACACTGGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 9 0.31
21 20 0.69
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (21 bp):
GCGTTGCGATATTTGAAAATC
Found at i:7047 original size:78 final size:77
Alignment explanation
Indices: 6845--7051 Score: 308
Period size: 77 Copynumber: 2.7 Consensus size: 77
6835 CACAGTTTCC
* ** *
6845 AAAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTACCGTTGCGAATTTGAAAATCGC
1 AAAATCGCGTTGCGATAACACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGC
6910 GTTGCGAATTTG
66 GTTGCGAATTTG
* * *
6922 AAAATCGTGTTGCGATAACACTGTTTACATACATCGGTAATTAGCGTTGCGAATTTGAAAATCGC
1 AAAATCGCGTTGCGATAACACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGC
*
6987 GTTGCGATTTTTG
66 GTTGCGA-ATTTG
*
7000 AAAATCGCGTTGCGATAACACTGGTTACCTATATCGGTAAATT-GCGTTGCGA
1 AAAATCGCGTTGCGATAACACTGTTTACCTATATCGGT-AATTAGCGTTGCGA
7052 TAGTACTGTT
Statistics
Matches: 116, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
77 65 0.56
78 47 0.41
79 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Consensus pattern (77 bp):
AAAATCGCGTTGCGATAACACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGC
GTTGCGAATTTG
Found at i:7051 original size:37 final size:37
Alignment explanation
Indices: 7001--7088 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
6991 CGATTTTTGA
* *
7001 AAATCGCGTTGCGATAACACTGGTTACCTATATCGGT
1 AAATTGCGTTGCGATAACACTGGTTACCTATATCGAT
** * *
7038 AAATTGCGTTGCGATAGTACTGTTTACTTATATCGAT
1 AAATTGCGTTGCGATAACACTGGTTACCTATATCGAT
7075 -AATTAGCGTTGCGA
1 AAATT-GCGTTGCGA
7089 ATTTGTAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
36 4 0.09
37 40 0.91
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (37 bp):
AAATTGCGTTGCGATAACACTGGTTACCTATATCGAT
Found at i:7105 original size:57 final size:56
Alignment explanation
Indices: 7036--7165 Score: 179
Period size: 57 Copynumber: 2.3 Consensus size: 56
7026 ACCTATATCG
* * *
7036 GTAAATTGCGTTGCGATAGTACTGTTTACTTATATCGATAATTAGCGTTGCGAATTT
1 GTAAATT-CGTTGCGATAGTACTATTTACCTATATCGATAATTAGCATTGCGAATTT
* *
7093 GTAAATATCGTTGCGATAGTACTATTTACCTATATCGGTAATTAGCATTGTGAATTT
1 GTAAAT-TCGTTGCGATAGTACTATTTACCTATATCGATAATTAGCATTGCGAATTT
*
7150 GAAAATCTCGTTGCGA
1 GTAAAT-TCGTTGCGA
7166 ATTTGTAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 64 0.98
58 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.38
Consensus pattern (56 bp):
GTAAATTCGTTGCGATAGTACTATTTACCTATATCGATAATTAGCATTGCGAATTT
Found at i:7169 original size:20 final size:20
Alignment explanation
Indices: 7144--7185 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
7134 TTAGCATTGT
*
7144 GAATTTGAAAATCTCGTTGC
1 GAATTTGAAAATCGCGTTGC
*
7164 GAATTTGTAAATCGCGTTGC
1 GAATTTGAAAATCGCGTTGC
7184 GA
1 GA
7186 TAGTACTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (20 bp):
GAATTTGAAAATCGCGTTGC
Found at i:7208 original size:77 final size:77
Alignment explanation
Indices: 7081--7239 Score: 264
Period size: 77 Copynumber: 2.1 Consensus size: 77
7071 CGATAATTAG
* *
7081 CGTTGCGAATTTGTAAATATCGTTGCGATAGTACTATTTACCTATATCGGTAATTAGCATTGTGA
1 CGTTGCGAATTTGTAAATAGCGTTGCGATAGTACTATTTACCTATATCGGTAATTAGCATTGCGA
*
7146 ATTTGAAAATCT
66 ATTTGAAAATCA
* * *
7158 CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGA
1 CGTTGCGAATTTGTAAATAGCGTTGCGATAGTACTATTTACCTATATCGGTAATTAGCATTGCGA
7223 ATTTGAAAATCA
66 ATTTGAAAATCA
7235 CGTTG
1 CGTTG
7240 TGATAGTATT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (77 bp):
CGTTGCGAATTTGTAAATAGCGTTGCGATAGTACTATTTACCTATATCGGTAATTAGCATTGCGA
ATTTGAAAATCA
Found at i:7246 original size:57 final size:57
Alignment explanation
Indices: 7158--7282 Score: 196
Period size: 57 Copynumber: 2.2 Consensus size: 57
7148 TTGAAAATCT
* * * *
7158 CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAG
1 CGTTGCGAATTTGAAAATCACGTTGCGATAGTACTGTTTACCTAAATCGGTAATCAG
* *
7215 CGTTGCGAATTTGAAAATCACGTTGTGATAGTATTGTTTACCTAAATCGGTAATCAG
1 CGTTGCGAATTTGAAAATCACGTTGCGATAGTACTGTTTACCTAAATCGGTAATCAG
7272 CGTTGCGAATT
1 CGTTGCGAATT
7283 ACATATTCAC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (57 bp):
CGTTGCGAATTTGAAAATCACGTTGCGATAGTACTGTTTACCTAAATCGGTAATCAG
Found at i:7282 original size:134 final size:135
Alignment explanation
Indices: 7035--7320 Score: 387
Period size: 134 Copynumber: 2.1 Consensus size: 135
7025 TACCTATATC
* * *
7035 GGTAAATTGCGTTGCGATAGTACTGTTTACTTATATCGATAATTAGCGTTGCGAATTTGTAAATA
1 GGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGATAATTAGCGTTGCGAATTTGAAAATA
* * * ** *
7100 TCGTTGCGATAGTACTATTTACCTATATCGGTAATTAGCATTGTGAATTTGAAAATCTCGTTGCG
66 TCGTTGCGATAGTACTATTTACCTAAATCGGTAATCAGCATTGCGAATTACAAAATCACGTTGCG
7165 AATTT
131 AATTT
*
7170 -GTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATC
1 GGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGATAATTAGCGTTGCGAATTTGAAAAT-
* * * * * *
7234 A-CGTTGTGATAGTATTGTTTACCTAAATCGGTAATCAGCGTTGCGAATTACATATTCACGTTGC
65 ATCGTTGCGATAGTACTATTTACCTAAATCGGTAATCAGCATTGCGAATTACAAAATCACGTTGC
7298 GAATTT
130 GAATTT
* *
7304 GGAAAATGGCGTTGCGA
1 GGTAAATCGCGTTGCGA
7321 AATTGGAGTT
Statistics
Matches: 131, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
134 116 0.89
135 15 0.11
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (135 bp):
GGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGATAATTAGCGTTGCGAATTTGAAAATA
TCGTTGCGATAGTACTATTTACCTAAATCGGTAATCAGCATTGCGAATTACAAAATCACGTTGCG
AATTT
Found at i:7293 original size:57 final size:57
Alignment explanation
Indices: 7158--7299 Score: 176
Period size: 57 Copynumber: 2.5 Consensus size: 57
7148 TTGAAAATCT
*** * * *
7158 CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAG
1 CGTTGCGAATTACAAAATCACGTTGCGATAGTACTGTTTACCTAAATCGGTAATCAG
** * *
7215 CGTTGCGAATTTGAAAATCACGTTGTGATAGTATTGTTTACCTAAATCGGTAATCAG
1 CGTTGCGAATTACAAAATCACGTTGCGATAGTACTGTTTACCTAAATCGGTAATCAG
* *
7272 CGTTGCGAATTACATATTCACGTTGCGA
1 CGTTGCGAATTACAAAATCACGTTGCGA
7300 ATTTGGAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 74 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (57 bp):
CGTTGCGAATTACAAAATCACGTTGCGATAGTACTGTTTACCTAAATCGGTAATCAG
Found at i:7318 original size:21 final size:20
Alignment explanation
Indices: 7292--7345 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
7282 TACATATTCA
*
7292 CGTTGCGAATTTGGAAAATGG
1 CGTTGCGAATTTGG-AAATCG
* **
7313 CGTTGCGAAATTGGAGTTCG
1 CGTTGCGAATTTGGAAATCG
7333 CGTTGCGAATTTG
1 CGTTGCGAATTTG
7346 TTGGTCATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.22, C:0.13, G:0.33, T:0.31
Consensus pattern (20 bp):
CGTTGCGAATTTGGAAATCG
Found at i:7798 original size:24 final size:23
Alignment explanation
Indices: 7771--7819 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
7761 ATTTGGTGTC
7771 CATGAACATGTT-AGTTTATATGTT
1 CATGAACATGTTCA-TTTA-ATGTT
7795 CATGAACATGTTCATTTAATGTT
1 CATGAACATGTTCATTTAATGTT
7818 CA
1 CA
7820 CGAATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.29
24 16 0.67
25 1 0.04
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (23 bp):
CATGAACATGTTCATTTAATGTT
Found at i:9073 original size:29 final size:29
Alignment explanation
Indices: 9031--9087 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
9021 TACGGTTTCG
* *
9031 TCCCCTAGAATTTTATAAGTTCAAGTTCT
1 TCCCCTAAAATTTTAAAAGTTCAAGTTCT
9060 TCCCCTAAAATTTTAAAAGTTCAAGTTC
1 TCCCCTAAAATTTTAAAAGTTCAAGTTC
9088 ACCCATTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.39
Consensus pattern (29 bp):
TCCCCTAAAATTTTAAAAGTTCAAGTTCT
Found at i:10622 original size:9 final size:8
Alignment explanation
Indices: 10592--10619 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
10582 ATTACAGGAT
10592 AAAATAAA
1 AAAATAAA
10600 AAAATAAA
1 AAAATAAA
10608 AAAATAAA
1 AAAATAAA
10616 AAAA
1 AAAA
10620 ATAGTATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:10717 original size:17 final size:18
Alignment explanation
Indices: 10695--10733 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
10685 CAATTCTTCC
* *
10695 AAATAAATTAGTAAAAT-
1 AAATAAATAAGGAAAATG
10712 AAATAAATAAGGAAAATG
1 AAATAAATAAGGAAAATG
10730 AAAT
1 AAAT
10734 TTAAAATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (18 bp):
AAATAAATAAGGAAAATG
Found at i:14602 original size:21 final size:21
Alignment explanation
Indices: 14573--14623 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
14563 ATGCTTGTAA
*
14573 ATTTCTATTGTAATTATGGAT
1 ATTTTTATTGTAATTATGGAT
14594 ATTTTTATTGTAATTATGGAT
1 ATTTTTATTGTAATTATGGAT
14615 ATTTTTATT
1 ATTTTTATT
14624 TTTAATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (21 bp):
ATTTTTATTGTAATTATGGAT
Found at i:15059 original size:4 final size:4
Alignment explanation
Indices: 15050--15083 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
15040 GATTTTGGTG
*
15050 TACA TACA TACA TACA AACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TA
15084 TATGGTAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:15315 original size:2 final size:2
Alignment explanation
Indices: 15308--15333 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15298 AAAGAAAATA
15308 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
15334 GAGTATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19455 original size:2 final size:2
Alignment explanation
Indices: 19448--19481 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19438 CCAATTTAAC
19448 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
19482 TATTATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22296 original size:23 final size:23
Alignment explanation
Indices: 22266--22312 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
22256 TCATTTCCTC
22266 ATTTTTTGTATACGAGGTTTGGA
1 ATTTTTTGTATACGAGGTTTGGA
*
22289 ATTTTTTGTATATGAGGTTTGGA
1 ATTTTTTGTATACGAGGTTTGGA
22312 A
1 A
22313 AACTGTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.02, G:0.26, T:0.49
Consensus pattern (23 bp):
ATTTTTTGTATACGAGGTTTGGA
Found at i:25816 original size:25 final size:25
Alignment explanation
Indices: 25788--25842 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
25778 GCACTTTTTA
25788 TATATGTG-ATAT-TAATATAAGTAAT
1 TATATG-GAATATGTAATATAAGT-AT
*
25813 TATA-GGAATATGTAATATAAGTGT
1 TATATGGAATATGTAATATAAGTAT
25837 TATATG
1 TATATG
25843 AATTGTGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 1 0.04
24 10 0.38
25 15 0.58
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (25 bp):
TATATGGAATATGTAATATAAGTAT
Found at i:26102 original size:21 final size:21
Alignment explanation
Indices: 26077--26126 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
26067 AGTGATATGA
26077 AATGTTATAAATGATAATGCC
1 AATGTTATAAATGATAATGCC
26098 AATGTTATAAATGATAATGCC
1 AATGTTATAAATGATAATGCC
*
26119 CATGTTAT
1 AATGTTAT
26127 GTAATATGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
AATGTTATAAATGATAATGCC
Found at i:27324 original size:21 final size:21
Alignment explanation
Indices: 27282--27334 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
27272 ATTCTGACTA
27282 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
27303 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
* *
27324 TTGCAATGCGA
1 TCGCATTGCGA
27335 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:27390 original size:20 final size:20
Alignment explanation
Indices: 27332--27407 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
27322 ATTTGCAATG
*
27332 CGAATACGTAAATCACAACA
1 CGAATACGTAAATCGCAACA
** *
27352 CGAATTTGGAAAATCGCAACA
1 CGAA-TACGTAAATCGCAACA
* * *
27373 CGATTACGTAAATTGCAACG
1 CGAATACGTAAATCGCAACA
27393 CGAATACGT-AATCGC
1 CGAATACGTAAATCGC
27408 GTTGCGAATT
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
19 5 0.12
20 23 0.53
21 15 0.35
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (20 bp):
CGAATACGTAAATCGCAACA
Found at i:27420 original size:20 final size:20
Alignment explanation
Indices: 27392--27448 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
27382 AAATTGCAAC
*
27392 GCGAA-TACGTAATCGCGTT
1 GCGAATTACGTAATCGCATT
27411 GCGAATTACGTAATCGCATT
1 GCGAATTACGTAATCGCATT
*
27431 GCGATTTA-GTAAATCGCA
1 GCGAATTACGT-AATCGCA
27449 ACGAGATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 7 0.21
20 27 0.79
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (20 bp):
GCGAATTACGTAATCGCATT
Found at i:30928 original size:19 final size:19
Alignment explanation
Indices: 30871--30990 Score: 108
Period size: 19 Copynumber: 6.5 Consensus size: 19
30861 CTTAATGTCT
30871 ATCGCAACGCGGAAATGAAA
1 ATCGCAACGC-GAAATGAAA
* *
30891 ATCACAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
30905 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
30924 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
**
30943 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGAAA
* *
30963 ATCGTAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
30982 ATCGCAACG
1 ATCGCAACG
30991 AGAGAATCAC
Statistics
Matches: 79, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 2 0.03
17 1 0.01
18 2 0.03
19 44 0.56
20 20 0.25
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:30975 original size:39 final size:38
Alignment explanation
Indices: 30871--30990 Score: 108
Period size: 39 Copynumber: 3.2 Consensus size: 38
30861 CTTAATGTCT
* *
30871 ATCGCAACGCGGAAATGAAAATCACAA--CG--A-GAGA
1 ATCGCAACGC-GAAATGAAAATCGCAACGCGAAATGAAA
*
30905 ATCGCAATGCGAAATGAAAATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAAA-TGAAA
** * *
30943 ATCGCAACGCGGAAATGACTATCGTAATGCGAAATGAAA
1 ATCGCAACGC-GAAATGAAAATCGCAACGCGAAATGAAA
30982 ATCGCAACG
1 ATCGCAACG
30991 AGAGAATCAC
Statistics
Matches: 70, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
33 15 0.21
34 9 0.13
35 2 0.03
37 1 0.01
38 12 0.17
39 31 0.44
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAA
Found at i:31015 original size:33 final size:33
Alignment explanation
Indices: 30968--31041 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
30958 TGACTATCGT
30968 AATGCGAAATGAAAATCGCAACGAGAGAATCAC
1 AATGCGAAATGAAAATCGCAACGAGAGAATCAC
* * * *
31001 AATGTGAAATGAAAATCGTAACGAGGGAATCGC
1 AATGCGAAATGAAAATCGCAACGAGAGAATCAC
*
31034 AACGCGAA
1 AATGCGAA
31042 TTTAGTTTCG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.14
Consensus pattern (33 bp):
AATGCGAAATGAAAATCGCAACGAGAGAATCAC
Found at i:31123 original size:19 final size:19
Alignment explanation
Indices: 31068--31126 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
31058 GATTTTGTCG
* *
31068 TTGCGATTTTTATTTTGCA
1 TTGCGATTTTCATTTCGCA
*
31087 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
31101 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
31120 TTGCGAT
1 TTGCGAT
31127 AGTTATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 6 0.19
16 6 0.19
17 6 0.19
19 13 0.42
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:31252 original size:14 final size:14
Alignment explanation
Indices: 31233--31269 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
31223 CATCAATTAA
31233 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
31247 ACAAATCATCTTTT
1 ACAAATCAACTTTT
31261 ACAAATCAA
1 ACAAATCAA
31270 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:32646 original size:21 final size:21
Alignment explanation
Indices: 32580--32646 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
32570 ATGAATCGGG
*
32580 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
32600 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
32622 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
32643 CTCT
1 CTCT
32647 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:32665 original size:42 final size:41
Alignment explanation
Indices: 32580--32702 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
32570 ATGAATCGGG
* * * *
32580 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
32622 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
32664 CTCTTAAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
32703 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:34700 original size:20 final size:19
Alignment explanation
Indices: 34631--34702 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
34621 CGATTCTCTC
*
34631 GTTGCGATTTTAATTTCTCT
1 GTTGCGATTTTCATTT-TCT
**
34651 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTC-T
34672 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTC-T
34692 GTTGCGATTTT
1 GTTGCGATTTT
34703 AAGTTTAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 30 0.68
21 14 0.32
ACGTcount: A:0.14, C:0.15, G:0.19, T:0.51
Consensus pattern (19 bp):
GTTGCGATTTTCATTTTCT
Found at i:35291 original size:20 final size:20
Alignment explanation
Indices: 35266--35448 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 20
35256 AATCGCATTA
*
35266 CGATTTACGGATACGCGTTG
1 CGATTTACGTATACGCGTTG
*
35286 CGATTTTACGTAT-TGTCGTTG
1 CGA-TTTACGTATACG-CGTTG
* * * *
35307 TGATTTATGGATACGCATTG
1 CGATTTACGTATACGCGTTG
* * *
35327 CAATTTACGTATTCTCGTTG
1 CGATTTACGTATACGCGTTG
* * **
35347 TGATTTACATATAAACGTTG
1 CGATTTACGTATACGCGTTG
* * *
35367 CGATTCACGTATTCTCGTTG
1 CGATTTACGTATACGCGTTG
*
35387 CGATTTACGGATACGCGTTG
1 CGATTTACGTATACGCGTTG
*
35407 CGATTTTACGTAT-TGTCGTTG
1 CGA-TTTACGTATACG-CGTTG
* *
35428 CGATTTACGGATACTCGTTG
1 CGATTTACGTATACGCGTTG
35448 C
1 C
35449 AATAGTCAGA
Statistics
Matches: 122, Mismatches: 35, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
20 90 0.74
21 32 0.26
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.39
Consensus pattern (20 bp):
CGATTTACGTATACGCGTTG
Found at i:35345 original size:40 final size:40
Alignment explanation
Indices: 35266--35451 Score: 219
Period size: 40 Copynumber: 4.6 Consensus size: 40
35256 AATCGCATTA
* *
35266 CGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTG
1 CGATTTACGGATACGCGTTGC-AATTTACGTATTCTCGTTG
* * *
35307 TGATTTATGGATACGCATTGCAATTTACGTATTCTCGTTG
1 CGATTTACGGATACGCGTTGCAATTTACGTATTCTCGTTG
* ** ** * *
35347 TGATTTACATATAAACGTTGCGATTCACGTATTCTCGTTG
1 CGATTTACGGATACGCGTTGCAATTTACGTATTCTCGTTG
* *
35387 CGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTG
1 CGATTTACGGATACGCGTTGC-AATTTACGTATTCTCGTTG
*
35428 CGATTTACGGATACTCGTTGCAAT
1 CGATTTACGGATACGCGTTGCAAT
35452 AGTCAGAATC
Statistics
Matches: 120, Mismatches: 24, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
40 67 0.56
41 53 0.44
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (40 bp):
CGATTTACGGATACGCGTTGCAATTTACGTATTCTCGTTG
Found at i:35467 original size:81 final size:80
Alignment explanation
Indices: 35302--35474 Score: 188
Period size: 81 Copynumber: 2.1 Consensus size: 80
35292 TACGTATTGT
* * * *
35302 CGTTGTGATTTATGGATACGCATTGCAATTTACGTATTCTCGTTGTGATTTACATATAAACGTTG
1 CGTTGCGATTTACGGATACGCATTGCAATTTACGTATTCTCGTTGCGATTTACAGATAAACGTTG
* * *
35367 CGATTCACGTATTCT
66 CAATTCACGTAATCG
* * * * **
35382 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACTCGTT
1 CGTTGCGATTTACGGATACGCATTGC-AATTTACGTATTCTCGTTGCGATTTACAGATAAACGTT
35447 GCAATAGTCA-G-AATCG
65 GCAAT--TCACGTAATCG
35463 CGTTGCGATTTA
1 CGTTGCGATTTA
35475 TATGTTCGCG
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
80 23 0.30
81 50 0.65
82 1 0.01
83 3 0.04
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (80 bp):
CGTTGCGATTTACGGATACGCATTGCAATTTACGTATTCTCGTTGCGATTTACAGATAAACGTTG
CAATTCACGTAATCG
Found at i:35483 original size:20 final size:21
Alignment explanation
Indices: 35460--35513 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
35450 ATAGTCAGAA
*
35460 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTTATAATAT
*
35480 TCGCGTTGCGATTTTTAATAT
1 TCGCGTTGCGATTTATAATAT
35501 TCGCGTTGCGATT
1 TCGCGTTGCGATT
35514 ATGTAAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.15, C:0.17, G:0.24, T:0.44
Consensus pattern (21 bp):
TCGCGTTGCGATTTATAATAT
Found at i:35525 original size:21 final size:20
Alignment explanation
Indices: 35458--35525 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
35448 CAATAGTCAG
*
35458 AATCGCGTTGCGATTTATAT
1 AATCGCGTTGCGATTTATAA
** *
35478 GTTCGCGTTGCGATTTTTAA
1 AATCGCGTTGCGATTTATAA
* *
35498 TATTCGCGTTGCGATTATGTAA
1 -AATCGCGTTGCGATT-TATAA
35520 AATCGC
1 AATCGC
35526 AACGCGAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 16 0.41
21 19 0.49
22 4 0.10
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (20 bp):
AATCGCGTTGCGATTTATAA
Found at i:35612 original size:20 final size:20
Alignment explanation
Indices: 35565--35616 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
35555 TCTTCATAAT
35565 CGCGTTGCGATTCTGGTAAC
1 CGCGTTGCGATTCTGGTAAC
* **
35585 TGATTTGCGATTCTGG-AGAC
1 CGCGTTGCGATTCTGGTA-AC
35605 CGCGTTGCGATT
1 CGCGTTGCGATT
35617 ATTATTTCGC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.15, C:0.21, G:0.31, T:0.33
Consensus pattern (20 bp):
CGCGTTGCGATTCTGGTAAC
Found at i:38761 original size:25 final size:25
Alignment explanation
Indices: 38733--38787 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
38723 GCACTTGTTA
38733 TATATGTG-ATAT-TAATATAAGTAAT
1 TATATG-GAATATGTAATATAAGT-AT
*
38758 TATA-GGAATATGTAATATAAGTGT
1 TATATGGAATATGTAATATAAGTAT
38782 TATATG
1 TATATG
38788 AATTGTGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 1 0.04
24 10 0.38
25 15 0.58
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (25 bp):
TATATGGAATATGTAATATAAGTAT
Found at i:39184 original size:31 final size:29
Alignment explanation
Indices: 39097--39203 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 29
39087 AGTCGAGGGT
* *
39097 TTACCTATGTTCTACGGATCATATTGACATAA
1 TTACCTATGTTCTAAGGAT-ATA-TGA-ATAG
* * *
39129 TTACCTATGTCTTTCAGGACATATGAATAG
1 TTACCTATGT-TCTAAGGATATATGAATAG
*
39159 TATACCTATGTTCTAAGGAATATATGAACAG
1 T-TACCTATGTTCTAAGG-ATATATGAATAG
*
39190 TTTACCTAGGTTCT
1 -TTACCTATGTTCT
39204 TTGGGACCTA
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
30 9 0.15
31 33 0.54
32 14 0.23
33 5 0.08
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (29 bp):
TTACCTATGTTCTAAGGATATATGAATAG
Found at i:40385 original size:104 final size:104
Alignment explanation
Indices: 40290--40479 Score: 281
Period size: 104 Copynumber: 1.8 Consensus size: 104
40280 GATGATCTTT
* *
40290 TTTGACACTAAAAATATATTTTGTGGCCATCAATATTGTCATAATAAGTATTTTTAGTGACCAAA
1 TTTGACACTAAAAATATATTTTGTGACCACCAATATTGTCATAATAAGTATTTTTAGTGACCAAA
*
40355 TGTTCGATACTATTATCAATAGAAACTGTGATAAATTTA
66 TATTCGATACTATTATCAATAGAAACTGTGATAAATTTA
* * * * * * *
40394 TTTGACACTAAAAGTTTATTTTGTGATCACCAATGTTGTCATAGTAAGTGTTTTTAGTGACCATA
1 TTTGACACTAAAAATATATTTTGTGACCACCAATATTGTCATAATAAGTATTTTTAGTGACCAAA
*
40459 TATTCGATACTATTAACAATA
66 TATTCGATACTATTATCAATA
40480 ACTCTGTCAC
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
104 75 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (104 bp):
TTTGACACTAAAAATATATTTTGTGACCACCAATATTGTCATAATAAGTATTTTTAGTGACCAAA
TATTCGATACTATTATCAATAGAAACTGTGATAAATTTA
Found at i:44618 original size:42 final size:40
Alignment explanation
Indices: 44571--44705 Score: 155
Period size: 42 Copynumber: 3.3 Consensus size: 40
44561 TTCACTTCAA
* * *
44571 TAGTGATAAAAAGTATTGTCGTCACAAATCACTAACTAAGAT
1 TAGTGACAAAAA--ATTATCGTCACAAATCACCAACTAAGAT
* *
44613 TAGTGA-AAATCAATTATCGTCATAAATCACCAACTAAGAT
1 TAGTGACAAA-AAATTATCGTCACAAATCACCAACTAAGAT
* *
44653 TAGTGACAAAAACAATTAACGTCACAAATCACCAACTAAGAC
1 TAGTGAC-AAAA-AATTATCGTCACAAATCACCAACTAAGAT
44695 TAGTGACAAAA
1 TAGTGACAAAA
44706 TTTTTCATCA
Statistics
Matches: 81, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
40 31 0.38
41 7 0.09
42 43 0.53
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.24
Consensus pattern (40 bp):
TAGTGACAAAAAATTATCGTCACAAATCACCAACTAAGAT
Found at i:44633 original size:40 final size:40
Alignment explanation
Indices: 44589--44705 Score: 162
Period size: 42 Copynumber: 2.9 Consensus size: 40
44579 AAAAGTATTG
* *
44589 TCGTCACAAATCACTAACTAAGATTAGTGAAAATCAATTA
1 TCGTCACAAATCACCAACTAAGATTAGTGAAAAACAATTA
*
44629 TCGTCATAAATCACCAACTAAGATTAGTGACAAAAACAATTA
1 TCGTCACAAATCACCAACTAAGATTAGTG--AAAAACAATTA
* *
44671 ACGTCACAAATCACCAACTAAGACTAGTGACAAAA
1 TCGTCACAAATCACCAACTAAGATTAGTGA-AAAA
44706 TTTTTCATCA
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
40 28 0.41
41 4 0.06
42 36 0.53
ACGTcount: A:0.47, C:0.21, G:0.10, T:0.22
Consensus pattern (40 bp):
TCGTCACAAATCACCAACTAAGATTAGTGAAAAACAATTA
Found at i:49229 original size:59 final size:59
Alignment explanation
Indices: 49130--49257 Score: 157
Period size: 59 Copynumber: 2.2 Consensus size: 59
49120 CAGCAGGCTA
* ** * *
49130 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACATAGTACAGATGGTGGACACGACCTTATGTGT
* ** * *
49189 CATATTCGGGATTGTACTTAAGGATACATAGTACAGATGGTGGACACGACTTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACATAGTACAGATGGTGGACACGACCTTATGTGT
*
49248 CATACTCGGG
1 CATATTCGGG
49258 TTAGCACTAC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACATAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:63294 original size:16 final size:16
Alignment explanation
Indices: 63269--63299 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63259 GTTTTATATT
*
63269 TTCGGGTCAATTTCGG
1 TTCGGATCAATTTCGG
63285 TTCGGATCAATTTCG
1 TTCGGATCAATTTCG
63300 ATTTAGAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (16 bp):
TTCGGATCAATTTCGG
Found at i:64721 original size:159 final size:155
Alignment explanation
Indices: 64501--64814 Score: 427
Period size: 159 Copynumber: 2.0 Consensus size: 155
64491 TAAAAGTTAC
64501 TTTCTAAAAACCATAAAATTATTAAAATTCTCAAAAAAAAAACACCTTAAATTCCAGAAAATCTC
1 TTTCTAAAAACCATAAAATTATTAAAATTCTC--AAAAAAAACACCTTAAATTCCAGAAAATCTC
* * *
64566 AAAAAACTCCTAAGTTTCTAAAAAATCTAAAAAAAACATAAACTCTAAATCGTACTAAAAAT-CA
64 AAAAAACTCCTAAATTCCTAAAAAATCCAAAAAAAACATAAACTCTAAATC--A-T---AATCCA
*
64630 TAAAAATCATAAGATTCATTTTTCGGGAGTTTA
123 TAAAAATCATAAGATTCATTTTTAGGGAGTTTA
* * * *
64663 TTTCTAAAAAACCATGAAATTATTAAAATTC-C-CAAAAAATACCTTAAATTCTAGAAAATCTCA
1 TTTCT-AAAAACCATAAAATTATTAAAATTCTCAAAAAAAACACCTTAAATTCCAGAAAATCTCA
* * *
64726 AAAAACTCCTAAATTCCTAAAAAATCCAAAAAAACCATAAATTCTAAATCATAATCCCTAAAAAT
65 AAAAACTCCTAAATTCCTAAAAAATCCAAAAAAAACATAAACTCTAAATCATAATCCATAAAAAT
64791 CATAAGATTCATTTTTAGGGAGTT
130 CATAAGATTCATTTTTAGGGAGTT
64815 CATAATTTGT
Statistics
Matches: 139, Mismatches: 11, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
153 3 0.02
154 31 0.22
156 1 0.01
157 1 0.01
159 73 0.53
162 6 0.04
163 24 0.17
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.29
Consensus pattern (155 bp):
TTTCTAAAAACCATAAAATTATTAAAATTCTCAAAAAAAACACCTTAAATTCCAGAAAATCTCAA
AAAACTCCTAAATTCCTAAAAAATCCAAAAAAAACATAAACTCTAAATCATAATCCATAAAAATC
ATAAGATTCATTTTTAGGGAGTTTA
Found at i:64727 original size:29 final size:27
Alignment explanation
Indices: 64694--64773 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 27
64684 ATTAAAATTC
*
64694 CCAAAAAATACCTTAAATTCTAGAAAAT
1 CCAAAAAATACC-TAAATTCTAAAAAAT
64722 CTCAAAAAACT-CCTAAATTCCTAAAAAAT
1 C-CAAAAAA-TACCTAAATT-CTAAAAAAT
64751 CCAAAAAA-ACCATAAATTCTAAA
1 CCAAAAAATACC-TAAATTCTAAA
64774 TCATAATCCC
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
27 7 0.15
28 20 0.43
29 18 0.39
30 1 0.02
ACGTcount: A:0.55, C:0.21, G:0.01, T:0.23
Consensus pattern (27 bp):
CCAAAAAATACCTAAATTCTAAAAAAT
Found at i:64728 original size:28 final size:26
Alignment explanation
Indices: 64668--64773 Score: 86
Period size: 29 Copynumber: 3.8 Consensus size: 26
64658 GTTTATTTCT
* * *
64668 AAAAAACCATGAAATTATTAAAATTCCC
1 AAAAAACCAT-AAATTCTAAAAAAT-CC
* *
64696 AAAAAATACCTTAAATTCTAGAAAATCTC
1 -AAAAA-ACCATAAATTCTAAAAAATC-C
*
64725 AAAAAACTCCTAAATTCCTAAAAAATCC
1 AAAAAAC-CATAAATT-CTAAAAAATCC
64753 AAAAAAACCATAAATTCTAAA
1 -AAAAAACCATAAATTCTAAA
64774 TCATAATCCC
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
27 7 0.11
28 21 0.33
29 32 0.50
30 4 0.06
ACGTcount: A:0.56, C:0.19, G:0.02, T:0.24
Consensus pattern (26 bp):
AAAAAACCATAAATTCTAAAAAATCC
Found at i:64912 original size:75 final size:74
Alignment explanation
Indices: 64819--64975 Score: 226
Period size: 74 Copynumber: 2.1 Consensus size: 74
64809 GGAGTTCATA
* **
64819 ATTTGTTGGTAATCCCTAAATTCAATT-TAAAAAATAAACCTTATGATTTTTAGGGATTACGCTT
1 ATTTTTTGGTAATCCCTAAATTC-ATTCTAAAAAATAAACCTTATG-TTTTTAGGGATTACAATT
64883 TAGAATTTATG
64 TAGAATTTATG
* * *
64894 ATTTTTTGGTAATCCCTAAATTCATTCTAAATAATGAATCTTATGTTTTTAGGGATTACAATTTA
1 ATTTTTTGGTAATCCCTAAATTCATTCTAAAAAATAAACCTTATGTTTTTAGGGATTACAATTTA
*
64959 GAGTTTATG
66 GAATTTATG
64968 ATTTTTTG
1 ATTTTTTG
64976 AGATTTTTAG
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
74 37 0.50
75 37 0.50
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (74 bp):
ATTTTTTGGTAATCCCTAAATTCATTCTAAAAAATAAACCTTATGTTTTTAGGGATTACAATTTA
GAATTTATG
Found at i:64966 original size:74 final size:75
Alignment explanation
Indices: 64810--64975 Score: 228
Period size: 75 Copynumber: 2.2 Consensus size: 75
64800 CATTTTTAGG
* * *
64810 GAGTTCATAATTTGTTGGTAATCCCTAAATTCAATTTAAAAAATAAACCTTATGATTTTTAGGGA
1 GAGTTTATGATTTTTTGGTAATCCCTAAATTCAATTTAAAAAATAAACCTTATGATTTTTAGGGA
**
64875 TTACGCTTTA
66 TTACAATTTA
* * * *
64885 GAATTTATGATTTTTTGGTAATCCCTAAATTC-ATTCTAAATAATGAATCTTATG-TTTTTAGGG
1 GAGTTTATGATTTTTTGGTAATCCCTAAATTCAATT-TAAAAAATAAACCTTATGATTTTTAGGG
64948 ATTACAATTTA
65 ATTACAATTTA
64959 GAGTTTATGATTTTTTG
1 GAGTTTATGATTTTTTG
64976 AGATTTTTAG
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
74 37 0.46
75 43 0.54
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (75 bp):
GAGTTTATGATTTTTTGGTAATCCCTAAATTCAATTTAAAAAATAAACCTTATGATTTTTAGGGA
TTACAATTTA
Found at i:65008 original size:29 final size:30
Alignment explanation
Indices: 64969--65044 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
64959 GAGTTTATGA
*
64969 TTTTTTGAGATTTTTAGAAATTT-AGGAGT
1 TTTTTTTAGATTTTTAGAAATTTAAGGAGT
* *
64998 TTTTTTTAGATTTTCT-GGAATTTAAGGTGT
1 TTTTTTTAGATTTT-TAGAAATTTAAGGAGT
*
65028 TTTTTTTGAGAATTTTA
1 TTTTTTT-AGATTTTTA
65045 ATTATTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 19 0.49
30 14 0.36
31 6 0.15
ACGTcount: A:0.24, C:0.01, G:0.18, T:0.57
Consensus pattern (30 bp):
TTTTTTTAGATTTTTAGAAATTTAAGGAGT
Found at i:66874 original size:373 final size:373
Alignment explanation
Indices: 66189--66937 Score: 1482
Period size: 373 Copynumber: 2.0 Consensus size: 373
66179 AATGGAAAAT
66189 ATGTGTTTCGGGCCTCCAACATTCAATCAGAGTCGAAATCAATATCGGGTTCACCTTAAAACCAC
1 ATGTGTTTCGGGCCTCCAACATTCAATCAGAGTCGAAATCAATATCGGGTTCACCTTAAAACCAC
66254 GTAGAAATGTGGTTGGATACAACCCAAATTGTTGTAGATATATAATAATCCACTGATGAGGATTT
66 GTAGAAATGTGGTTGGATACAACCCAAATTGTTGTAGATATATAATAATCCACTGATGAGGATTT
66319 CTAAGTGTCATTCCTCGTTATCGAATGCCTCGTTCTTCTTTCAGAGTGAGTTCGAAAGAAGAAAT
131 CTAAGTGTCATTCCTCGTTATCGAATGCCTCGTTCTTCTTTCAGAGTGAGTTCGAAAGAAGAAAT
66384 ATGAACAAAACAAGAAGTAACATTTCATATTGGGTAGACATTTTCAAGAATTCTTCAAAAAAATT
196 ATGAACAAAACAAGAAGTAACATTTCATATTGGGTAGACATTTTCAAGAATTCTTCAAAAAAATT
66449 ACAAAATTTCCTCAATTTTTTCTGAACAATAAACAATAAAAATCCTAAACCTC-AACTCCTATTT
261 ACAAAATTTCCTCAATTTTTTCTGAACAATAAACAATAAAAATCCTAAACCTCAAACTCCTATTT
66513 ATAACTCAATCCCAATGACTATAAAATACTATATTTTTTAAAAAATCTC
326 ATAACTCAATCCCAATGACTATAAAATACTATATTTTTT-AAAAATCTC
66562 ATGTGTTTCGGGCCTCCAACATTCAATCAGAGTCGAAATCAATATCGGGTTCACCTTAAAACCAC
1 ATGTGTTTCGGGCCTCCAACATTCAATCAGAGTCGAAATCAATATCGGGTTCACCTTAAAACCAC
66627 GTAGAAATGTGGTTGGATACAACCCAAATTGTTGTAGATATATAATAATCCACTGATGAGGATTT
66 GTAGAAATGTGGTTGGATACAACCCAAATTGTTGTAGATATATAATAATCCACTGATGAGGATTT
66692 CTAAGTGTCATTCCTCGTTATCGAATGCCTCGTTCTTCTTTCAGAGTGAGTTCGAAAGAAGAAAT
131 CTAAGTGTCATTCCTCGTTATCGAATGCCTCGTTCTTCTTTCAGAGTGAGTTCGAAAGAAGAAAT
66757 ATGAACAAAACAAGAAGTAACATTTCATATTGGGTAGACATTTTCAAGAATTCTTCAAAAAAATT
196 ATGAACAAAACAAGAAGTAACATTTCATATTGGGTAGACATTTTCAAGAATTCTTCAAAAAAATT
66822 ACAAAATTTCCTCAATTTTTTCTGAACAATAAACAATAAAAATCCTAAACCTCAAACTCCTATTT
261 ACAAAATTTCCTCAATTTTTTCTGAACAATAAACAATAAAAATCCTAAACCTCAAACTCCTATTT
66887 ATAACTCAATCCCAATGACTATAAAATACTATATTTTTTAAAAATCTC
326 ATAACTCAATCCCAATGACTATAAAATACTATATTTTTTAAAAATCTC
66935 ATG
1 ATG
66938 AAACTTATCA
Statistics
Matches: 375, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
373 325 0.87
374 50 0.13
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.31
Consensus pattern (373 bp):
ATGTGTTTCGGGCCTCCAACATTCAATCAGAGTCGAAATCAATATCGGGTTCACCTTAAAACCAC
GTAGAAATGTGGTTGGATACAACCCAAATTGTTGTAGATATATAATAATCCACTGATGAGGATTT
CTAAGTGTCATTCCTCGTTATCGAATGCCTCGTTCTTCTTTCAGAGTGAGTTCGAAAGAAGAAAT
ATGAACAAAACAAGAAGTAACATTTCATATTGGGTAGACATTTTCAAGAATTCTTCAAAAAAATT
ACAAAATTTCCTCAATTTTTTCTGAACAATAAACAATAAAAATCCTAAACCTCAAACTCCTATTT
ATAACTCAATCCCAATGACTATAAAATACTATATTTTTTAAAAATCTC
Found at i:68803 original size:20 final size:20
Alignment explanation
Indices: 68776--68831 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
68766 AATAGTATTG
68776 TATTGTATGAATAATATCGA
1 TATTGTATGAATAATATCGA
* *
68796 TGTTGTATGAATAGTATCGA
1 TATTGTATGAATAATATCGA
* *
68816 TATTGTGTGAACAATA
1 TATTGTATGAATAATA
68832 GTATCGATAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (20 bp):
TATTGTATGAATAATATCGA
Found at i:74217 original size:15 final size:15
Alignment explanation
Indices: 74197--74229 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
74187 TTTTTGTTAT
74197 ATTCTATCTAAATTA
1 ATTCTATCTAAATTA
*
74212 ATTCTATCTGAATTA
1 ATTCTATCTAAATTA
74227 ATT
1 ATT
74230 AATTAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTCTATCTAAATTA
Found at i:78656 original size:2 final size:2
Alignment explanation
Indices: 78649--78673 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
78639 TCGTTTATGC
78649 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
78674 CACGGGTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:89659 original size:2 final size:2
Alignment explanation
Indices: 89652--89697 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
89642 GAAGATGTGC
89652 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
89694 AT AT
1 AT AT
89698 CTGTGAAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:95100 original size:31 final size:32
Alignment explanation
Indices: 95054--95117 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
95044 AATCAATAAA
*
95054 ATAAATATTCTAAGGACTAAACTGAGTTAATT
1 ATAAATATTCTAAGGACTAAACTGAGTCAATT
* * *
95086 ATAAATGTT-TAAGGACTTAACTTAGTCAATT
1 ATAAATATTCTAAGGACTAAACTGAGTCAATT
95117 A
1 A
95118 AAACTTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (32 bp):
ATAAATATTCTAAGGACTAAACTGAGTCAATT
Found at i:96609 original size:16 final size:16
Alignment explanation
Indices: 96588--96618 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
96578 GTGATAATTT
*
96588 TTTATTATACTTATTG
1 TTTATTATAATTATTG
96604 TTTATTATAATTATT
1 TTTATTATAATTATT
96619 TCAAAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTATTATAATTATTG
Found at i:100058 original size:14 final size:14
Alignment explanation
Indices: 100041--100088 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
100031 AATGAAAAAT
100041 AATAAAAAAATTAC
1 AATAAAAAAATTAC
*
100055 AATAAAAAAGTT-C
1 AATAAAAAAATTAC
* *
100068 AAT-AAACAACTAC
1 AATAAAAAAATTAC
100081 AATAAAAA
1 AATAAAAA
100089 GTACTAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
12 5 0.19
13 8 0.30
14 14 0.52
ACGTcount: A:0.69, C:0.10, G:0.02, T:0.19
Consensus pattern (14 bp):
AATAAAAAAATTAC
Found at i:100063 original size:13 final size:13
Alignment explanation
Indices: 100045--100088 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
100035 AAAAATAATA
100045 AAAAAATTACAAT
1 AAAAAATTACAAT
100058 AAAAAAGTT-CAAT
1 AAAAAA-TTACAAT
* *
100071 AAACAACTACAAT
1 AAAAAATTACAAT
100084 AAAAA
1 AAAAA
100089 GTACTAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 1 0.04
13 23 0.88
14 2 0.08
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.18
Consensus pattern (13 bp):
AAAAAATTACAAT
Found at i:102348 original size:9 final size:9
Alignment explanation
Indices: 102334--102367 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
102324 TAAGTAAAAT
102334 ATTAAATAA
1 ATTAAATAA
102343 ATTAAAT-A
1 ATTAAATAA
*
102351 CTTAAATAA
1 ATTAAATAA
102360 ATTAAATA
1 ATTAAATA
102368 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:102366 original size:17 final size:17
Alignment explanation
Indices: 102330--102368 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
102320 TAATTAAGTA
102330 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
102346 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
102363 AAATAC
1 AAATAC
102369 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:103288 original size:86 final size:86
Alignment explanation
Indices: 103186--103381 Score: 320
Period size: 86 Copynumber: 2.3 Consensus size: 86
103176 TTTTGTAATC
* * *
103186 TGGATCATTGGATTGGTTCAGATCCGATGTGGTTGCACGATTTGACTTGGCTAAGGTTATGAATG
1 TGGACCATTGGATTGGTTCAGATCCGATGCGGTTGCACGATCTGACTTGGCTAAGGTTATGAATG
103251 AACCCTATTTTGCTTATAGTA
66 AACCCTATTTTGCTTATAGTA
* *
103272 TGGACTATTGGATTGGTTCATATCCGATGCGGTTGCACGATCTGACTTGGCTAAGGTTATGAATG
1 TGGACCATTGGATTGGTTCAGATCCGATGCGGTTGCACGATCTGACTTGGCTAAGGTTATGAATG
* *
103337 AACCCTATTTTGCTTGTAGTC
66 AACCCTATTTTGCTTATAGTA
*
103358 TGGACCGTTGGATTGGTTCAGATC
1 TGGACCATTGGATTGGTTCAGATC
103382 TTGCGGCAAG
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 100 1.00
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (86 bp):
TGGACCATTGGATTGGTTCAGATCCGATGCGGTTGCACGATCTGACTTGGCTAAGGTTATGAATG
AACCCTATTTTGCTTATAGTA
Found at i:104039 original size:13 final size:13
Alignment explanation
Indices: 104011--104066 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
104001 AGAGCATAAA
104011 AAATAATAA-AACT
1 AAATAA-AATAACT
*
104024 AAATAGAGATAA-T
1 AAATA-AAATAACT
104037 AAATAAAATAACT
1 AAATAAAATAACT
*
104050 AAATAAAGGTAACT
1 AAATAAA-ATAACT
104064 AAA
1 AAA
104067 GAGATGCATG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
12 5 0.14
13 20 0.56
14 11 0.31
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.21
Consensus pattern (13 bp):
AAATAAAATAACT
Found at i:104041 original size:26 final size:27
Alignment explanation
Indices: 104000--104054 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
103990 GAATATCAAT
104000 TAGAGCATAAAAAATAATAA-AACTAAA
1 TAGAGCATAAAAAATAA-AATAACTAAA
*
104027 TAGAG-ATAATAAATAAAATAACTAAA
1 TAGAGCATAAAAAATAAAATAACTAAA
104053 TA
1 TA
104055 AAGGTAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 2 0.08
26 19 0.73
27 5 0.19
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.22
Consensus pattern (27 bp):
TAGAGCATAAAAAATAAAATAACTAAA
Found at i:105072 original size:18 final size:20
Alignment explanation
Indices: 105049--105088 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
105039 GTTTAATTTA
105049 AAAG-TTAAGGAACT-AACT
1 AAAGTTTAAGGAACTAAACT
*
105067 AAAGTTTAAGGACCTAAACT
1 AAAGTTTAAGGAACTAAACT
105087 AA
1 AA
105089 GCTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 9 0.47
20 6 0.32
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (20 bp):
AAAGTTTAAGGAACTAAACT
Found at i:105425 original size:23 final size:22
Alignment explanation
Indices: 105378--105424 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
105368 ACAATTAAGG
* *
105378 AATTAATTTAATCCTAAATTAA
1 AATTAATTTAATCATAAAATAA
105400 AATTAATGTTAATCAATAAAATAA
1 AATTAAT-TTAATC-ATAAAATAA
105424 A
1 A
105425 TATTCTAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 6 0.29
24 8 0.38
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (22 bp):
AATTAATTTAATCATAAAATAA
Found at i:108399 original size:69 final size:68
Alignment explanation
Indices: 108309--108502 Score: 241
Period size: 69 Copynumber: 2.8 Consensus size: 68
108299 TATTGTATAG
* * * *
108309 ACTATTTTTCTAAATG-TTTTCCAAACTATATAATATATAATGTTTTTCAAATTGTTT-TTAAAA
1 ACTA-TTTTCAAAATGTTTTTCCAAACTATATAATATAT--TATTTTTCAAATTATTTCTCAAAA
108372 CTACAT
63 CTACAT
108378 ACTATTTTCAAAATGTTTTTCCAAAACTATATAATATATTATTTTTCAAATTATTTCTCAAAACT
1 ACTATTTTCAAAATGTTTTTCC-AAACTATATAATATATTATTTTTCAAATTATTTCTCAAAACT
*
108443 ATAT
65 ACAT
*
108447 ACTATTTTCAAAATGTTTTTTTTCAAAACTATATAATATATTA-TTTTCAAAATTAT
1 ACTATTTTCAAAATG---TTTTTCCAAACTATATAATATATTATTTTTC-AAATTAT
108503 ATACTAATTT
Statistics
Matches: 112, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
68 25 0.22
69 35 0.31
70 21 0.19
71 25 0.22
72 6 0.05
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (68 bp):
ACTATTTTCAAAATGTTTTTCCAAACTATATAATATATTATTTTTCAAATTATTTCTCAAAACTA
CAT
Found at i:108453 original size:32 final size:32
Alignment explanation
Indices: 108352--108481 Score: 99
Period size: 34 Copynumber: 3.9 Consensus size: 32
108342 TATATAATGT
*
108352 TTTTC-AAATTGTTTT-T-AAAACTACATACTA
1 TTTTCAAAATT-TTTTCTCAAAACTATATACTA
*
108382 TTTTCAAAATGTTTTTC-CAAAACTATATAATATATTA
1 TTTTCAAAAT-TTTTTCTCAAAAC----T-ATATACTA
*
108419 TTTTTC-AAATTATTTCTCAAAACTATATACTA
1 -TTTTCAAAATTTTTTCTCAAAACTATATACTA
*
108451 TTTTCAAAATGTTTTTTTTCAAAACTATATA
1 TTTTCAAAA--TTTTTTCTCAAAACTATATA
108482 ATATATTATT
Statistics
Matches: 80, Mismatches: 6, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
30 5 0.06
31 13 0.16
32 16 0.20
33 1 0.01
34 18 0.22
36 6 0.08
37 16 0.20
38 5 0.06
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (32 bp):
TTTTCAAAATTTTTTCTCAAAACTATATACTA
Found at i:108493 original size:71 final size:68
Alignment explanation
Indices: 108309--108502 Score: 241
Period size: 71 Copynumber: 2.8 Consensus size: 68
108299 TATTGTATAG
* * * * *
108309 ACTATTTTTCTAAATG--TTTTCCAAACTATATAATATATAATGTTTTTCAAATTGTTTTTAAAA
1 ACTA-TTTTCAAAATGTTTTTTCAAAACTATATAATATAT--TATTTTTCAAATTATTTTCAAAA
108372 CTACAT
63 CTACAT
*
108378 ACTATTTTCAAAATGTTTTTCCAAAACTATATAATATATTATTTTTCAAATTATTTCTCAAAACT
1 ACTATTTTCAAAATGTTTTTTCAAAACTATATAATATATTATTTTTCAAATTATTT-TCAAAACT
*
108443 ATAT
65 ACAT
108447 ACTATTTTCAAAATGTTTTTTTTCAAAACTATATAATATATTA-TTTTCAAAATTAT
1 ACTATTTTCAAAATG--TTTTTTCAAAACTATATAATATATTATTTTTC-AAATTAT
108503 ATACTAATTT
Statistics
Matches: 111, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
68 25 0.23
69 29 0.26
70 25 0.23
71 32 0.29
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (68 bp):
ACTATTTTCAAAATGTTTTTTCAAAACTATATAATATATTATTTTTCAAATTATTTTCAAAACTA
CAT
Found at i:108557 original size:20 final size:18
Alignment explanation
Indices: 108483--108564 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 18
108473 AACTATATAA
*
108483 TATATTATTTTCAAAATT
1 TATAATATTTTCAAAATT
* *
108501 ATATACTAATTTCAAAACTT
1 -TATAATATTTTCAAAA-TT
108521 ATATATAGTATTTT-AAAATT
1 -TATA-A-TATTTTCAAAATT
*
108541 GTATAATATTTTCTAAATT
1 -TATAATATTTTCAAAATT
108560 ATATA
1 -TATA
108565 CTATATATTG
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
18 6 0.12
19 24 0.46
20 13 0.25
21 4 0.08
22 5 0.10
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (18 bp):
TATAATATTTTCAAAATT
Found at i:111924 original size:31 final size:31
Alignment explanation
Indices: 111865--111951 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
111855 TTCGATAATA
* * *
111865 TAATAATTATTTTATAGT-ATTTAGATAAACT
1 TAATAAATATTTTATAATCTTTTA-ATAAACT
* *
111896 T-ATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAAT-ATTTTATAATCTTTTAATAAACT
*
111927 TAATAAATATTTTATAATTTTTTAA
1 TAATAAATATTTTATAATCTTTTAA
111952 ACTTTATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 4 0.09
31 33 0.72
32 9 0.20
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (31 bp):
TAATAAATATTTTATAATCTTTTAATAAACT
Found at i:112553 original size:31 final size:30
Alignment explanation
Indices: 112518--112604 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
112508 TCAATAAAGT
112518 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
112549 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
112580 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
112605 TATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:112580 original size:20 final size:20
Alignment explanation
Indices: 112513--112580 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
112503 TTTCGTCAAT
*
112513 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
112531 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
112552 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
112571 ATAA-ATTTAT
1 A-AAGATTTAT
112581 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:115125 original size:24 final size:25
Alignment explanation
Indices: 115089--115137 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
115079 AAGATTATTG
115089 TAAGAATTTAAGAGTT-TAAAATTA
1 TAAGAATTTAAGAGTTATAAAATTA
*
115113 TAAG-ATTTAAAGATTTATAAAATTA
1 TAAGAATTT-AAGAGTTATAAAATTA
115138 GATCATCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 10 0.45
25 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (25 bp):
TAAGAATTTAAGAGTTATAAAATTA
Found at i:116229 original size:60 final size:59
Alignment explanation
Indices: 116151--116284 Score: 187
Period size: 60 Copynumber: 2.2 Consensus size: 59
116141 TATAATCTTC
* * *
116151 TTTTAAATTGGTCCTTAAACTATTGAATATTCCAATTTCATCCTTAAACTATGACTCTCA
1 TTTTAAATTAGTCCTTAAACTATTGAACATTCCAATTTCATCCCTAAACTATGAC-CTCA
* * * *
116211 TTTTAAATTAGTCCTTAAACTTTTGAACATTTCAGTTTCATCCCTAAACTATGACCTTA
1 TTTTAAATTAGTCCTTAAACTATTGAACATTCCAATTTCATCCCTAAACTATGACCTCA
116270 TTTCTAAATTAGTCC
1 TTT-TAAATTAGTCC
116285 CCAAACATTA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 6 0.09
60 60 0.91
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.43
Consensus pattern (59 bp):
TTTTAAATTAGTCCTTAAACTATTGAACATTCCAATTTCATCCCTAAACTATGACCTCA
Found at i:116563 original size:61 final size:61
Alignment explanation
Indices: 116431--116569 Score: 169
Period size: 60 Copynumber: 2.3 Consensus size: 61
116421 GTATATACAT
* **
116431 ATAGTTT-GAGATGAAATTGGAATGTTCAAAAAGTTTGGGGACCAATTTAGAATGAATGTC
1 ATAGTTTGGGGATGAAATTGGAATGTTCAAAAAGTTTAAGGACCAATTTAGAATGAATGTC
** * *
116491 ATAGTTTGGGGATGAAATTGTTATGTTC-AAAAGTTTAAGGACTAATTTAGACT-AATAGTC
1 ATAGTTTGGGGATGAAATTGGAATGTTCAAAAAGTTTAAGGACCAATTTAGAATGAAT-GTC
116551 ATAGTTTAGGGGA-GAAATT
1 ATAGTTT-GGGGATGAAATT
116570 AGAAAATTTA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
59 3 0.04
60 44 0.64
61 22 0.32
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (61 bp):
ATAGTTTGGGGATGAAATTGGAATGTTCAAAAAGTTTAAGGACCAATTTAGAATGAATGTC
Found at i:116583 original size:60 final size:60
Alignment explanation
Indices: 116431--116600 Score: 161
Period size: 60 Copynumber: 2.8 Consensus size: 60
116421 GTATATACAT
* * **
116431 ATAGTTT-GAGATGAAATTGGAATGTTCAAAAAGTTTGGGGACCAATTTAGAATGAATGTC
1 ATAGTTTGGGGATGAAATTGAAATGTTC-AAAAGTTTAAGGACCAATTTAGAATGAATGTC
** * *
116491 ATAGTTTGGGGATGAAATTGTTATGTTCAAAAGTTTAAGGACTAATTTAGACT-AATAGTC
1 ATAGTTTGGGGATGAAATTGAAATGTTCAAAAGTTTAAGGACCAATTTAGAATGAAT-GTC
* *
116551 ATAGTTTAGGGGA-GAAATTAGAAAAT-TT-AAAAGTTTTAGGGACCGATTTA
1 ATAGTTT-GGGGATGAAATT-G-AAATGTTCAAAAG-TTTAAGGACCAATTTA
116601 AAATAAGAGT
Statistics
Matches: 92, Mismatches: 12, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
59 3 0.03
60 49 0.53
61 38 0.41
62 2 0.02
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.34
Consensus pattern (60 bp):
ATAGTTTGGGGATGAAATTGAAATGTTCAAAAGTTTAAGGACCAATTTAGAATGAATGTC
Found at i:117475 original size:42 final size:42
Alignment explanation
Indices: 117417--117639 Score: 394
Period size: 42 Copynumber: 5.3 Consensus size: 42
117407 CATATTCACA
117417 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* * *
117459 TTGCAATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
117501 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
117543 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAA-TTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
117584 TTGCGATAGTCCAAGTTCGCGTTGTGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
117626 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
117640 ATCGCAACGA
Statistics
Matches: 171, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
41 39 0.23
42 132 0.77
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
Found at i:118210 original size:21 final size:21
Alignment explanation
Indices: 118184--118314 Score: 174
Period size: 21 Copynumber: 6.2 Consensus size: 21
118174 TTCCTTGTTG
118184 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCAT
*
118205 TGCGATAGTCGAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCAT
*
118226 TACGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCAT
** *
118247 TGCGATAGT-TGACTATCGCAT
1 TGCGATAGTCCAAGT-TCGCAT
118268 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCAT
* * *
118289 TGCGATAGTCGAAGTTTGCGT
1 TGCGATAGTCCAAGTTCGCAT
118310 TGCGA
1 TGCGA
118315 ATCTGGAAAC
Statistics
Matches: 95, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
20 2 0.02
21 91 0.96
22 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (21 bp):
TGCGATAGTCCAAGTTCGCAT
Found at i:118313 original size:42 final size:42
Alignment explanation
Indices: 118184--118314 Score: 201
Period size: 42 Copynumber: 3.1 Consensus size: 42
118174 TTCCTTGTTG
118184 TGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCGCAT
* * *
118226 TACGATAGTCCAAGTTCGCATTGCGATAGTTG-ACTATCGCAT
1 TGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGT-TCGCAT
* *
118268 TGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTTGCGT
1 TGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCGCAT
118310 TGCGA
1 TGCGA
118315 ATCTGGAAAC
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
41 2 0.03
42 75 0.95
43 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (42 bp):
TGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCGCAT
Found at i:120187 original size:2 final size:2
Alignment explanation
Indices: 120143--120168 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
120133 GGACACTTAT
120143 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
120169 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.