Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006368.1 Hibiscus syriacus cultivar Beakdansim tig00015309_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: 94924
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:875 original size:12 final size:12
Alignment explanation
Indices: 858--896 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
848 AACAATATAT
858 TTAAATATAATA
1 TTAAATATAATA
* *
870 TTAAATACATTA
1 TTAAATATAATA
882 -TAAATATAATA
1 TTAAATATAATA
893 TTAA
1 TTAA
897 TAAAAATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
TTAAATATAATA
Found at i:887 original size:23 final size:22
Alignment explanation
Indices: 851--896 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
841 ACATTAAAAC
*
851 AATATATTTAAATATAATATTA
1 AATACATTTAAATATAATATTA
873 AATACATTATAAATATAATATTA
1 AATACATT-TAAATATAATATTA
896 A
1 A
897 TAAAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AATACATTTAAATATAATATTA
Found at i:948 original size:20 final size:20
Alignment explanation
Indices: 923--974 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
913 GAAATTATTA
923 TTTAAATATGT-GTAATAATT
1 TTTAAATA-GTAGTAATAATT
*
943 TTTAAATAGTAATTAATAATT
1 TTTAAATAGT-AGTAATAATT
964 TTTAAATAGTA
1 TTTAAATAGTA
975 AATTAACATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 2 0.07
20 9 0.31
21 18 0.62
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (20 bp):
TTTAAATAGTAGTAATAATT
Found at i:961 original size:21 final size:22
Alignment explanation
Indices: 935--980 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
925 TAAATATGTG
935 TAATAATTTTTAAATAGT-AAT
1 TAATAATTTTTAAATAGTAAAT
956 TAATAATTTTTAAATAGTAAAT
1 TAATAATTTTTAAATAGTAAAT
978 TAA
1 TAA
981 CATGAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
TAATAATTTTTAAATAGTAAAT
Found at i:1919 original size:34 final size:34
Alignment explanation
Indices: 1876--1947 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
1866 GTTGAAACGA
*
1876 ATGTCTTCAATGTTTTGGGGTTATTTCAAAATTT
1 ATGTCTTCAATATTTTGGGGTTATTTCAAAATTT
*
1910 ATGTCTTCAATATTTTGGGGTTATTTCAAATTTT
1 ATGTCTTCAATATTTTGGGGTTATTTCAAAATTT
1944 ATGT
1 ATGT
1948 GTTTTCTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.24, C:0.08, G:0.17, T:0.51
Consensus pattern (34 bp):
ATGTCTTCAATATTTTGGGGTTATTTCAAAATTT
Found at i:7974 original size:26 final size:25
Alignment explanation
Indices: 7943--8022 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 25
7933 CCAATTTTTG
7943 ACATTCTATCTCTTTGAGACCTTG-A
1 ACATTCT-TCTCTTTGAGACCTTGAA
* *
7968 A-A-TATTCT-TTT-CGACCTTGAA
1 ACATTCTTCTCTTTGAGACCTTGAA
*
7989 ACATTCCCTCTCTTTGAGACCTTGAA
1 ACATT-CTTCTCTTTGAGACCTTGAA
8015 ACATTCTT
1 ACATTCTT
8023 TCCACCTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 7 0.16
21 5 0.12
22 4 0.09
23 3 0.07
24 4 0.09
25 6 0.14
26 14 0.33
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (25 bp):
ACATTCTTCTCTTTGAGACCTTGAA
Found at i:8669 original size:14 final size:14
Alignment explanation
Indices: 8650--8676 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8640 GAGAAAAGAA
8650 AAACAAAGTGAAAG
1 AAACAAAGTGAAAG
8664 AAACAAAGTGAAA
1 AAACAAAGTGAAA
8677 AAAAAGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.19, T:0.07
Consensus pattern (14 bp):
AAACAAAGTGAAAG
Found at i:9849 original size:4 final size:4
Alignment explanation
Indices: 9840--9889 Score: 70
Period size: 4 Copynumber: 13.2 Consensus size: 4
9830 GATCGAGAAA
*
9840 ACAT ACAT ACAT ACAT ACAT ACAT ATAT AC-- ACAT ACAT ACAT A-AT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
9885 ACAT A
1 ACAT A
9890 AAATTTGCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 3 0.07
4 36 0.88
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:10285 original size:36 final size:35
Alignment explanation
Indices: 10230--10367 Score: 170
Period size: 36 Copynumber: 3.9 Consensus size: 35
10220 TTTTGAGAAT
10230 TTTAAAACAAATTTTTGTCTCGCTTGAGACAATTTC
1 TTTAAAACAAA-TTTTGTCTCGCTTGAGACAATTTC
* *
10266 TTTCAAAGCAAATTTTGTCTCGCTTGAGACAGCTTTC
1 TTT-AAAACAAATTTTGTCTCGCTTGAGACA-ATTTC
* * *
10303 -TAAAAACAAATTTTGTCTCGTTTGAGACAAATTC
1 TTTAAAACAAATTTTGTCTCGCTTGAGACAATTTC
* *
10337 TCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 T-TTAAAACAAATTTTGTCTCGCTTGAGACA
10368 TTTTTCCTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
34 3 0.03
35 25 0.29
36 48 0.55
37 11 0.13
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (35 bp):
TTTAAAACAAATTTTGTCTCGCTTGAGACAATTTC
Found at i:10319 original size:71 final size:72
Alignment explanation
Indices: 10233--10367 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 72
10223 TGAGAATTTT
* * * *
10233 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCT-TTCAAAGCAAATTTTGTCTCGCTTGAGACA
1 AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTT-AAAACAAACTTCGTCTCGCTTGAGACA
10297 GCTTTCTA
65 GCTTTCTA
*
10305 AAAACAAA-TTTTGTCTCGTTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
10368 TTTTTCCTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
71 47 0.82
72 10 0.18
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (72 bp):
AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACAG
CTTTCTA
Found at i:10461 original size:105 final size:102
Alignment explanation
Indices: 10341--10579 Score: 288
Period size: 105 Copynumber: 2.3 Consensus size: 102
10331 AAATTCTCTT
* * *
10341 AAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* *
10405 TTAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 TT-AAACAAAATTAATCTCA-CTTGAGA---TCGTTTC-CTCA
* * *
10446 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* *
10511 TTAAACAAAGTTGATCTCACTTGAGATCGTTTCCTCA
66 TTAAACAAAATTAATCTCACTTGAGATCGTTTCCTCA
*
10548 AAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
10580 TCTAAAAACA
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
101 2 0.02
102 32 0.27
103 3 0.03
104 3 0.03
105 76 0.64
106 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (102 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TTAAACAAAATTAATCTCACTTGAGATCGTTTCCTCA
Found at i:10587 original size:36 final size:34
Alignment explanation
Indices: 10547--10644 Score: 108
Period size: 36 Copynumber: 2.8 Consensus size: 34
10537 TCGTTTCCTC
*
10547 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATATCT-T
** *
10583 AAAAACAAATTTTGTCTCATTTGAGACTATATCTT
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATATCTT
*
10618 -AAAGCAAATTTCGTCTCGCTTGAGACA
1 AAAAACAAATTT-GTCTCGCTTGAGACA
10645 TCATTTTCTC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
33 3 0.06
34 19 0.37
35 1 0.02
36 29 0.56
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (34 bp):
AAAAACAAATTTGTCTCGCTTGAGACAATATCTT
Found at i:10956 original size:29 final size:30
Alignment explanation
Indices: 10895--10955 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
10885 TTTGTAAAAC
*
10895 AATCTTTGAGATTGTTTCTTTTGAAACAAA
1 AATCTTTGAGATTGTTTCTTTGGAAACAAA
*
10925 AATCTTTGAGTTTGTTTCTTTGGAAACAAA
1 AATCTTTGAGATTGTTTCTTTGGAAACAAA
10955 A
1 A
10956 TTTTGTCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.43
Consensus pattern (30 bp):
AATCTTTGAGATTGTTTCTTTGGAAACAAA
Found at i:12020 original size:28 final size:28
Alignment explanation
Indices: 11983--12042 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
11973 AAAATATCAT
11983 CTTTGAGTTTATTT-TTCTTGAAACAAAG
1 CTTTGAGTTTATTTCTT-TTGAAACAAAG
* * *
12011 CTTTGGGTTTGTTTCTTTTGAAACAAAT
1 CTTTGAGTTTATTTCTTTTGAAACAAAG
12039 CTTT
1 CTTT
12043 AATTTGGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 26 0.93
29 2 0.07
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (28 bp):
CTTTGAGTTTATTTCTTTTGAAACAAAG
Found at i:12149 original size:40 final size:40
Alignment explanation
Indices: 12091--12281 Score: 152
Period size: 40 Copynumber: 4.5 Consensus size: 40
12081 CCAGCCGTCC
* * *
12091 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCT
* ** * *
12131 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCCAG---ACCAGATC-TCT
* * * * *
12174 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTCATC-CC--CAGA---CCAGATCTCT
12220 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCA-TCCCCAGACCAGATCTCT
12260 TCATCACGTATGAGCCGTGTCA
1 TCATCACGTATGAGCCGTGTCA
12282 CCCTAGATAA
Statistics
Matches: 119, Mismatches: 20, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
40 54 0.45
42 1 0.01
43 30 0.25
44 1 0.01
46 30 0.25
47 3 0.03
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (40 bp):
TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCT
Found at i:12239 original size:89 final size:83
Alignment explanation
Indices: 12081--12241 Score: 232
Period size: 83 Copynumber: 1.9 Consensus size: 83
12071 CTAAAGATGG
* *
12081 CCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGC
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
12146 CGTGTCAACCATAGATAA
66 CGTGTCAACCATAGATAA
* *
12164 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGAACTCTTCATCACGT
12229 ATGAGCCGTGTCA
60 ATGAGCCGTGTCA
12242 TTCCCCGACC
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
83 32 0.47
84 2 0.03
86 3 0.04
89 31 0.46
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (83 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
CGTGTCAACCATAGATAA
Found at i:12415 original size:91 final size:92
Alignment explanation
Indices: 12247--12457 Score: 255
Period size: 91 Copynumber: 2.3 Consensus size: 92
12237 TGTCATTCCC
* * *
12247 CGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTA
1 CGACCAGAACTCTTCATCACGTATGAGCCATGTCACCCTAGACAACCAGCCGTCCTCATCACGTA
* **
12312 GGAACCGTGTTATCACCCTTCCTAAAGA
66 GGAACCGAGTTATCACCCACCCT-AAGA
* * * * * **
12340 TGGCCAGAACTCTTCATCATGTATGAGCCATGTCATCC-A-CCAACCAGTTGTCCTCATCACGTA
1 CGACCAGAACTCTTCATCACGTATGAGCCATGTCACCCTAGACAACCAGCCGTCCTCATCACGTA
* *
12403 GGAACCGAGTTATCATCCACCCTTAGA
66 GGAACCGAGTTATCACCCACCCTAAGA
*
12430 CGACCAGACCTCTTCATCACGTATGAGC
1 CGACCAGAACTCTTCATCACGTATGAGC
12458 AGTGTCGTCC
Statistics
Matches: 99, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
90 27 0.27
91 39 0.39
92 1 0.01
93 32 0.32
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (92 bp):
CGACCAGAACTCTTCATCACGTATGAGCCATGTCACCCTAGACAACCAGCCGTCCTCATCACGTA
GGAACCGAGTTATCACCCACCCTAAGA
Found at i:16101 original size:18 final size:18
Alignment explanation
Indices: 16078--16113 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16068 TACTTCGTGA
*
16078 GAGTGGACAATGGTCAAC
1 GAGTGGACAATGATCAAC
16096 GAGTGGACAATGATCAAC
1 GAGTGGACAATGATCAAC
16114 CAGAATAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.17, G:0.31, T:0.17
Consensus pattern (18 bp):
GAGTGGACAATGATCAAC
Found at i:17721 original size:2 final size:2
Alignment explanation
Indices: 17714--17750 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17704 AAAACATGCA
17714 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
17751 CTTAACAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19307 original size:30 final size:30
Alignment explanation
Indices: 19272--19349 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
19262 GAAGTCGTTG
*
19272 GGAACACAATGCGTCTTTGG-AAAGTCGCC
1 GGAACACAATGCGTCTTCGGAAAAGTCGCC
* *
19301 GAGAACACAGTGTGTCTTCGGAAAAGTCGCC
1 G-GAACACAATGCGTCTTCGGAAAAGTCGCC
* *
19332 GGAAGACAATGCTTCTTC
1 GGAACACAATGCGTCTTC
19350 AACTAAAAGC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.73
31 10 0.25
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (30 bp):
GGAACACAATGCGTCTTCGGAAAAGTCGCC
Found at i:20932 original size:31 final size:31
Alignment explanation
Indices: 20892--20951 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
20882 CGTAAATGGG
* *
20892 TGAGTTAATGATATCTTCGAGCATCAACCCT
1 TGAGGTAATGATAACTTCGAGCATCAACCCT
20923 TGAGGTAATGATAACTTCGAGCATCAACC
1 TGAGGTAATGATAACTTCGAGCATCAACC
20952 GAAACAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (31 bp):
TGAGGTAATGATAACTTCGAGCATCAACCCT
Found at i:21202 original size:28 final size:28
Alignment explanation
Indices: 21170--21225 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
21160 GTTGTTTTGT
21170 TGAATCTCTCAACTATTAAAAGTTATAA
1 TGAATCTCTCAACTATTAAAAGTTATAA
**
21198 TGAATCTCTCGGCTATTAAAAGTTATAA
1 TGAATCTCTCAACTATTAAAAGTTATAA
21226 AATAATCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (28 bp):
TGAATCTCTCAACTATTAAAAGTTATAA
Found at i:23260 original size:18 final size:18
Alignment explanation
Indices: 23237--23272 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
23227 TACTTCGTGA
23237 GAGTGGACAATGATCAAC
1 GAGTGGACAATGATCAAC
23255 GAGTGGACAATGATCAAC
1 GAGTGGACAATGATCAAC
23273 CAGAATAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.17
Consensus pattern (18 bp):
GAGTGGACAATGATCAAC
Found at i:27475 original size:13 final size:13
Alignment explanation
Indices: 27457--27481 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27447 CAAGCTCACT
27457 ATCAACTATCATG
1 ATCAACTATCATG
27470 ATCAACTATCAT
1 ATCAACTATCAT
27482 TGAGGAACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
ATCAACTATCATG
Found at i:30019 original size:23 final size:22
Alignment explanation
Indices: 29993--30037 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
29983 TCCTCTATGG
*
29993 AGTTATACAGCGTAAAGACAACA
1 AGTT-TACAGCATAAAGACAACA
**
30016 AGTTTATGGCATAAAGACAACA
1 AGTTTACAGCATAAAGACAACA
30038 TAATTAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.20
Consensus pattern (22 bp):
AGTTTACAGCATAAAGACAACA
Found at i:33141 original size:24 final size:24
Alignment explanation
Indices: 33112--33161 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
33102 CGTTATATTA
33112 TACATGGTTAACAATGCAAAATAT
1 TACATGGTTAACAATGCAAAATAT
33136 TACATGGTTAACAATGCAAAATAT
1 TACATGGTTAACAATGCAAAATAT
33160 TA
1 TA
33162 GCTATTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (24 bp):
TACATGGTTAACAATGCAAAATAT
Found at i:40387 original size:134 final size:134
Alignment explanation
Indices: 40083--40484 Score: 750
Period size: 134 Copynumber: 3.0 Consensus size: 134
40073 CAAGCCAAAT
40083 AAATCGTTCAAAGAGGAGACAGAGTGAAAACCCGGCCGTTATGTAGCATCTGAGAACAAGAAAGC
1 AAATCGTTCAAAGAGGAGACAGAGTGAAAACCCGGCCGTTATGTAGCATCTGAGAACAAGAAAGC
*
40148 AGACATGCTTTGCTTTCCCTCCAATTCTGCCACCACGAACGGAATCTTTGCTTTACTCAGACAGA
66 AGACATGCTTTGCTTT-CCTCCAATTCTGCCACCACGAACGGAATCTTTGCTTTACTCGGACAGA
40213 ACACA
130 ACACA
*
40218 AAATCGTTCAAAGAGGAGACAGAGTGAAAAGCCGGCCGTTATGTAGCATCTGAGAACAAGAAAGC
1 AAATCGTTCAAAGAGGAGACAGAGTGAAAACCCGGCCGTTATGTAGCATCTGAGAACAAGAAAGC
* *
40283 AGACATGCTTTGCTTTCCTCCAATTCTGCCACCACGAACGGAATCTTTGCTTAACCCGGACAGAA
66 AGACATGCTTTGCTTTCCTCCAATTCTGCCACCACGAACGGAATCTTTGCTTTACTCGGACAGAA
40348 CACA
131 CACA
40352 AAATCGTTCAAAGAGGAGACAGAGTGAAAACCCGGCCGTTATGTAGCATCTGAGAACAAGAAAGC
1 AAATCGTTCAAAGAGGAGACAGAGTGAAAACCCGGCCGTTATGTAGCATCTGAGAACAAGAAAGC
*
40417 AGACATGCTTTGCTTTCCTCCAATTCTGCCACCACGAACGGAATCTTTGCTTTACTTGGACAGAA
66 AGACATGCTTTGCTTTCCTCCAATTCTGCCACCACGAACGGAATCTTTGCTTTACTCGGACAGAA
40482 CAC
131 CAC
40485 GAGCTGAATC
Statistics
Matches: 259, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
134 179 0.69
135 80 0.31
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (134 bp):
AAATCGTTCAAAGAGGAGACAGAGTGAAAACCCGGCCGTTATGTAGCATCTGAGAACAAGAAAGC
AGACATGCTTTGCTTTCCTCCAATTCTGCCACCACGAACGGAATCTTTGCTTTACTCGGACAGAA
CACA
Found at i:40718 original size:31 final size:31
Alignment explanation
Indices: 40681--40753 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
40671 TTTATATTTA
40681 GTACCTAAACTACTA-CTTTTATTTTATTATG
1 GTACCTAAACTACTATC-TTTATTTTATTATG
40712 GTACCTAAACTACTATCTTTATTTTATTATG
1 GTACCTAAACTACTATCTTTATTTTATTATG
40743 GTACCTAAACT
1 GTACCTAAACT
40754 TTATTTGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (31 bp):
GTACCTAAACTACTATCTTTATTTTATTATG
Found at i:41442 original size:23 final size:23
Alignment explanation
Indices: 41396--41442 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
41386 AATATATTTA
* *
41396 AAATATAATATTAAATACATTAT
1 AAATATAATATTAAATAAAATAT
41419 AAATATAATATT-AATAAAAATAT
1 AAATATAATATTAAAT-AAAATAT
41442 A
1 A
41443 TTCAATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATATAATATTAAATAAAATAT
Found at i:41486 original size:20 final size:20
Alignment explanation
Indices: 41461--41512 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
41451 GAAATTATTA
41461 TTTAAATATGT-GTAATAATT
1 TTTAAATA-GTAGTAATAATT
*
41481 TTTAAATAGTAATTAATAATT
1 TTTAAATAGT-AGTAATAATT
41502 TTTAAATAGTA
1 TTTAAATAGTA
41513 AATTAACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 2 0.07
20 9 0.31
21 18 0.62
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (20 bp):
TTTAAATAGTAGTAATAATT
Found at i:41499 original size:21 final size:22
Alignment explanation
Indices: 41473--41518 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
41463 TAAATATGTG
41473 TAATAATTTTTAAATAGT-AAT
1 TAATAATTTTTAAATAGTAAAT
41494 TAATAATTTTTAAATAGTAAAT
1 TAATAATTTTTAAATAGTAAAT
41516 TAA
1 TAA
41519 CATTAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
TAATAATTTTTAAATAGTAAAT
Found at i:42457 original size:34 final size:34
Alignment explanation
Indices: 42414--42519 Score: 194
Period size: 34 Copynumber: 3.1 Consensus size: 34
42404 GTTGAAACAA
* *
42414 ATGTCTTCAATGTTTTGGGGTTATTTCAAAATTT
1 ATGTCTTCAATGCTTTGGGGTTATTTCAAATTTT
42448 ATGTCTTCAATGCTTTGGGGTTATTTCAAATTTT
1 ATGTCTTCAATGCTTTGGGGTTATTTCAAATTTT
42482 ATGTCTTCAATGCTTTGGGGTTATTTCAAATTTT
1 ATGTCTTCAATGCTTTGGGGTTATTTCAAATTTT
42516 ATGT
1 ATGT
42520 GTTTTCTTTT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 70 1.00
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.50
Consensus pattern (34 bp):
ATGTCTTCAATGCTTTGGGGTTATTTCAAATTTT
Found at i:44234 original size:30 final size:30
Alignment explanation
Indices: 44199--44275 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
44189 TAAGTCGTTG
44199 GGAACACAATGCGTCTTTGG-AAAGTCGCC
1 GGAACACAATGCGTCTTTGGAAAAGTCGCC
* *
44228 GAGAACACAGTGTGTCTTTGGAAAAGTCGCC
1 G-GAACACAATGCGTCTTTGGAAAAGTCGCC
*
44259 GGAAGACAATGCGTCTT
1 GGAACACAATGCGTCTT
44276 CAACTAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.02
30 30 0.73
31 10 0.24
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.22
Consensus pattern (30 bp):
GGAACACAATGCGTCTTTGGAAAAGTCGCC
Found at i:44435 original size:28 final size:28
Alignment explanation
Indices: 44403--44458 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
44393 GTTGTTTTGT
44403 TGAATCTCTAAACTATTAAAAGTTATAA
1 TGAATCTCTAAACTATTAAAAGTTATAA
* **
44431 TGAATCTTTCGACTATTAAAAGTTATAA
1 TGAATCTCTAAACTATTAAAAGTTATAA
44459 AATAATCATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (28 bp):
TGAATCTCTAAACTATTAAAAGTTATAA
Found at i:46260 original size:47 final size:47
Alignment explanation
Indices: 46191--46291 Score: 202
Period size: 47 Copynumber: 2.1 Consensus size: 47
46181 TTTATCCCAT
46191 TACATATGGGAACAAGGGACAACCAACCAGTTATAGGTGCCTTGGAG
1 TACATATGGGAACAAGGGACAACCAACCAGTTATAGGTGCCTTGGAG
46238 TACATATGGGAACAAGGGACAACCAACCAGTTATAGGTGCCTTGGAG
1 TACATATGGGAACAAGGGACAACCAACCAGTTATAGGTGCCTTGGAG
46285 TACATAT
1 TACATAT
46292 ATCAAAGGTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.21
Consensus pattern (47 bp):
TACATATGGGAACAAGGGACAACCAACCAGTTATAGGTGCCTTGGAG
Found at i:48077 original size:18 final size:18
Alignment explanation
Indices: 48054--48089 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
48044 TACTTCGTGA
48054 GAGTGGACAATGATCAAC
1 GAGTGGACAATGATCAAC
48072 GAGTGGACAATGATCAAC
1 GAGTGGACAATGATCAAC
48090 CAGAATAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.17
Consensus pattern (18 bp):
GAGTGGACAATGATCAAC
Found at i:56084 original size:28 final size:28
Alignment explanation
Indices: 56052--56107 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
56042 GTTGTTTTGT
56052 TGAATCTCTAAACTATTAAAAGTTATAA
1 TGAATCTCTAAACTATTAAAAGTTATAA
* **
56080 TGAATCTTTCGACTATTAAAAGTTATAA
1 TGAATCTCTAAACTATTAAAAGTTATAA
56108 AATAATCATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (28 bp):
TGAATCTCTAAACTATTAAAAGTTATAA
Found at i:56596 original size:22 final size:22
Alignment explanation
Indices: 56568--56661 Score: 113
Period size: 22 Copynumber: 4.4 Consensus size: 22
56558 TTCCATTTCG
56568 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
56590 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
56609 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
56631 TGTTGCGATAGTATACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
56653 CGTTGCGAT
1 CGTTGCGAT
56662 TTTCCAAATT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
19 10 0.17
20 5 0.09
21 5 0.09
22 38 0.66
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:56623 original size:41 final size:41
Alignment explanation
Indices: 56548--56639 Score: 141
Period size: 41 Copynumber: 2.2 Consensus size: 41
56538 TTGCATTTTG
*
56548 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTCTACAGTTGT
56590 CGTTGCGATTTTCCAAATT-CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-AATTCCGTTGCGATAGTCTACAGTTGT
*
56631 TGTTGCGAT
1 CGTTGCGAT
56640 AGTATACAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 30 0.64
42 14 0.30
43 3 0.06
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAATTCCGTTGCGATAGTCTACAGTTGT
Found at i:57311 original size:6 final size:6
Alignment explanation
Indices: 57290--57332 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
57280 GTTCGTCTCG
57290 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
57333 AATACGTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:57455 original size:22 final size:22
Alignment explanation
Indices: 57430--57482 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
57420 AATTTGGAAA
57430 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
57452 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
57474 ATCGCAACG
1 ATCGCAACG
57483 CGAAATGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:57499 original size:20 final size:20
Alignment explanation
Indices: 57474--57539 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
57464 ACTGTAGACT
57474 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
57494 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
57515 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
57535 ATCGC
1 ATCGC
57540 GTTGCGATTT
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:57520 original size:21 final size:21
Alignment explanation
Indices: 57494--57608 Score: 72
Period size: 21 Copynumber: 5.6 Consensus size: 21
57484 GAAATGGAAA
57494 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
57515 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
***
57535 ATCGCGTTGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* * ** ** *
57556 ATCGTAGCGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
57576 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
57597 ATTGCAACGCGA
1 ATCGCAACGCGA
57609 AATTGCGATA
Statistics
Matches: 62, Mismatches: 30, Indels: 4
0.65 0.31 0.04
Matches are distributed among these distances:
20 25 0.40
21 37 0.60
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:57520 original size:41 final size:41
Alignment explanation
Indices: 57471--57611 Score: 228
Period size: 41 Copynumber: 3.4 Consensus size: 41
57461 ACAACTGTAG
57471 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
***
57512 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *
57553 ACTATCGTAGCGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
57594 ACTATTGCAACGCGAAAT
1 ACTATCGCAACGCGAAAT
57612 TGCGATAGTG
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:58142 original size:29 final size:29
Alignment explanation
Indices: 58100--58213 Score: 185
Period size: 29 Copynumber: 3.9 Consensus size: 29
58090 CAGTGACAGC
*
58100 ATAGGTCGCCATGCACGCCCGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGACGTCCTT
58129 ATAGGTCGCCATGCACGCCCGACGTCCTT
1 ATAGGTCGCCATGCACGCCCGACGTCCTT
*
58158 ATAGGTTGCCATGCACGCCCGACGTCC-T
1 ATAGGTCGCCATGCACGCCCGACGTCCTT
*
58186 ATAAGGTCGCCATGCACGCCCGGCGTCC
1 AT-AGGTCGCCATGCACGCCCGACGTCC
58214 AACATTCTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 3 0.04
29 77 0.96
ACGTcount: A:0.17, C:0.38, G:0.26, T:0.19
Consensus pattern (29 bp):
ATAGGTCGCCATGCACGCCCGACGTCCTT
Found at i:58432 original size:11 final size:11
Alignment explanation
Indices: 58394--58440 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
58384 CGTGAATTCA
58394 GCTGCATTATT
1 GCTGCATTATT
58405 G-TAGCACTTATT
1 GCT-GCA-TTATT
*
58417 GCTGCATTAGT
1 GCTGCATTATT
58428 GCTGCATTATT
1 GCTGCATTATT
58439 GC
1 GC
58441 AGTCCTTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 1 0.03
11 20 0.65
12 9 0.29
13 1 0.03
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (11 bp):
GCTGCATTATT
Found at i:58560 original size:15 final size:15
Alignment explanation
Indices: 58540--58576 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
58530 AGTGAAACAT
58540 AAAAGAGAGAAAGGG
1 AAAAGAGAGAAAGGG
* *
58555 AGAAGAGAGTAAGGG
1 AAAAGAGAGAAAGGG
58570 AAAAGAG
1 AAAAGAG
58577 GAAGAAGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.41, T:0.03
Consensus pattern (15 bp):
AAAAGAGAGAAAGGG
Found at i:58850 original size:18 final size:18
Alignment explanation
Indices: 58827--58881 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
58817 AATAATTATT
58827 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
58845 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
58857 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
58874 TAAATTAG
1 TAAATTAG
58882 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:59188 original size:22 final size:22
Alignment explanation
Indices: 59160--59240 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
59150 AATCATTTAT
*
59160 TAGTTTAAGTTATATTAAAAAA
1 TAGTTTAAGTTATATTAAAGAA
59182 TAGTTTATTAGTTACCGTTATATTAAAGAA
1 TAGTTTA--AG-T----T-ATATTAAAGAA
*
59212 TAGTTAAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
59234 TAGTTTA
1 TAGTTTA
59241 TTAGTTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
22 24 0.50
23 1 0.02
24 2 0.04
25 1 0.02
27 1 0.02
28 2 0.04
29 1 0.02
30 16 0.33
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.42
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:59202 original size:30 final size:30
Alignment explanation
Indices: 59147--59216 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
59137 AATTATAATC
59147 AAAAATCA-TTTATTAGTTTAAGTTATATTA
1 AAAAAT-AGTTTATTAGTTTAAGTTATATTA
*
59177 AAAAATAGTTTATTAG-TTACCGTTATATTA
1 AAAAATAGTTTATTAGTTTA-AGTTATATTA
*
59207 AAGAATAGTT
1 AAAAATAGTT
59217 AAAGTTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 4 0.11
30 32 0.89
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (30 bp):
AAAAATAGTTTATTAGTTTAAGTTATATTA
Found at i:61567 original size:21 final size:21
Alignment explanation
Indices: 61483--61567 Score: 54
Period size: 21 Copynumber: 4.2 Consensus size: 21
61473 TAATTTCATT
*
61483 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
* *
61504 ATTAAT-ATCAAATCATTAAAT-
1 ATTAATAATC--ATTACTAAATC
* * *
61525 ATTAATAATAATT--T-CATT
1 ATTAATAATCATTACTAAATC
*
61543 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
61564 ATTA
1 ATTA
61568 TTATAATTTC
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
17 2 0.04
18 12 0.26
20 6 0.13
21 17 0.36
22 10 0.21
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAATAATCATTACTAAATC
Found at i:61581 original size:60 final size:60
Alignment explanation
Indices: 61453--61567 Score: 221
Period size: 60 Copynumber: 1.9 Consensus size: 60
61443 AATCATTACT
61453 AAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
1 AAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
*
61513 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
1 AAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
61568 TTATAATTTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (60 bp):
AAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
Found at i:61670 original size:21 final size:22
Alignment explanation
Indices: 61640--61718 Score: 72
Period size: 24 Copynumber: 3.5 Consensus size: 22
61630 GTTCAAGTCG
61640 TAAATCATTACTATCAAATCAT
1 TAAATCATTACTATCAAATCAT
* * *
61662 TAAAT-ATTAATAACAAATTATTAT
1 TAAATCATTACTATC-AA--ATCAT
61686 TACTAATCATTACTATCAAATCAT
1 TA--AATCATTACTATCAAATCAT
61710 TAAAT-ATTA
1 TAAATCATTA
61719 ATAATAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
21 11 0.24
22 10 0.22
24 12 0.27
26 5 0.11
27 7 0.16
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATCATTACTATCAAATCAT
Found at i:61764 original size:108 final size:108
Alignment explanation
Indices: 61640--61857 Score: 382
Period size: 108 Copynumber: 2.0 Consensus size: 108
61630 GTTCAAGTCG
* *
61640 TAAATCATTACTATCAAATCATTAAATATTAATAACAAATTATTATTACTAATCATTACTATCAA
1 TAAATCATTAATATCAAATCATTAAATATTAATAACAAATTATTATTACTAATCATTACAATCAA
* * *
61705 ATCATTAAATATTAATAATAATTTCATTATTATTAATTATTAC
66 ATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
*
61748 TAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACAATCAA
1 TAAATCATTAATATCAAATCATTAAATATTAATAACAAATTATTATTACTAATCATTACAATCAA
61813 ATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
66 ATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
61856 TA
1 TA
61858 TCAAATCATT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 104 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (108 bp):
TAAATCATTAATATCAAATCATTAAATATTAATAACAAATTATTATTACTAATCATTACAATCAA
ATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
Found at i:61767 original size:60 final size:59
Alignment explanation
Indices: 61681--61820 Score: 201
Period size: 60 Copynumber: 2.3 Consensus size: 59
61671 ATAACAAATT
* * *
61681 ATTATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTATTA
1 ATTATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACTA
61740 ATTATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTA
1 ATTATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTA
*
61799 ATCATTACAATCAAATCATTAA
1 ATTATTAC--T-AAATCATTAA
61821 AAATTAATAA
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
59 25 0.34
60 37 0.51
61 1 0.01
62 10 0.14
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (59 bp):
ATTATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTA
Found at i:61787 original size:21 final size:21
Alignment explanation
Indices: 61703--61792 Score: 64
Period size: 21 Copynumber: 4.4 Consensus size: 21
61693 CATTACTATC
61703 AAATCATTAAATATTAATAAT
1 AAATCATTAAATATTAATAAT
* *
61724 AATTTCATT-ATTATTAAT--T
1 AA-ATCATTAAATATTAATAAT
* * **
61743 --ATTACTAAATCATTAATATC
1 AAATCATTAAAT-ATTAATAAT
61763 AAATCATTAAATATTAATAAT
1 AAATCATTAAATATTAATAAT
*
61784 AAATTATTA
1 AAATCATTA
61793 TTACTAATCA
Statistics
Matches: 50, Mismatches: 12, Indels: 14
0.66 0.16 0.18
Matches are distributed among these distances:
16 3 0.06
17 2 0.04
18 6 0.12
19 1 0.02
21 25 0.50
22 13 0.26
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATCATTAAATATTAATAAT
Found at i:61795 original size:49 final size:48
Alignment explanation
Indices: 61740--62033 Score: 361
Period size: 49 Copynumber: 6.4 Consensus size: 48
61730 ATTATTATTA
*
61740 ATTATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT
1 ATTATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAAATT
* * *
61789 ATTATTACTAATCATTACAATCAAATCATTAAAAATTAATAATAATTT
1 ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATT
* *
61837 CATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAAT-ATTT
1 -ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATT
*
61885 ATTATTACTAATCA-T--TAT-AAATCATTAAATATT-A-AATATATT
1 ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATT
*
61927 ATTA--ACTAATCATTACTATCAAATCATTAAATA-T--T-AT-AATC
1 ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATT
*
61968 ATTATTACTAATCATTACTATC-AATCATTAAATA-TAAT-ATAATTT
1 ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATT
62013 CATTATTACTAATCATTACTA
1 -ATTATTACTAATCATTACTA
62034 AATCATTACT
Statistics
Matches: 220, Mismatches: 12, Indels: 29
0.84 0.05 0.11
Matches are distributed among these distances:
40 8 0.04
41 10 0.05
42 22 0.10
43 34 0.15
44 19 0.09
45 2 0.01
46 21 0.10
47 14 0.06
48 39 0.18
49 51 0.23
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (48 bp):
ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATT
Found at i:61827 original size:87 final size:86
Alignment explanation
Indices: 61736--61999 Score: 251
Period size: 97 Copynumber: 3.0 Consensus size: 86
61726 TTTCATTATT
* *
61736 ATTAATTATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAAT
1 ATTAATTATTATTAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAAT
61801 CATTACAATCAAATCATTAAAAATTA
66 CATTAC-ATCAAATCATT--AAA--A
* *
61827 ATAATAATTTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAAT-ATTTATTATT
1 AT--TAA-TT-ATTATTA--AATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATT
*
61891 ACTAATCATT--AT-AAATCATTAAAT
60 ACTAATCATTACATCAAATCATTAAAA
*
61915 ATTAAATATATTATTAACTAATCATTACTATCAAATCATTAAATA-T--T-AT-AATCATTATTA
1 ATT-AAT-TATTATT-A--AATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTA
61975 CTAATCATTACTATC-AATCATTAAA
61 CTAATCATTAC-ATCAAATCATTAAA
62000 TATAATATAA
Statistics
Matches: 152, Mismatches: 8, Indels: 31
0.80 0.04 0.16
Matches are distributed among these distances:
83 20 0.13
84 1 0.01
86 21 0.14
87 31 0.20
88 2 0.01
90 3 0.02
91 2 0.01
92 8 0.05
93 5 0.03
94 2 0.01
95 6 0.04
96 19 0.12
97 32 0.21
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (86 bp):
ATTAATTATTATTAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAAT
CATTACATCAAATCATTAAAA
Found at i:61866 original size:27 final size:25
Alignment explanation
Indices: 61743--61868 Score: 56
Period size: 27 Copynumber: 5.2 Consensus size: 25
61733 ATTATTAATT
* *
61743 ATTACTAAATCATTAATATCAAATC
1 ATTATTAAATCATTACTATCAAATC
* *
61768 ---ATTAAAT-ATTAATAAT-AAATT
1 ATTATTAAATCATTACT-ATCAAATC
*
61789 ATTATTACTAATCATTACAATCAAATC
1 ATTATTA--AATCATTACTATCAAATC
* *
61816 ATTA--AAA--ATTAATAAT-AATTTC
1 ATTATTAAATCATTACT-ATCAA-ATC
61838 ATTATTACTAATCATTACTATCAAATC
1 ATTATTA--AATCATTACTATCAAATC
61865 ATTA
1 ATTA
61869 AAAATTAATA
Statistics
Matches: 74, Mismatches: 10, Indels: 32
0.64 0.09 0.28
Matches are distributed among these distances:
21 16 0.22
22 16 0.22
23 2 0.03
24 5 0.07
25 1 0.01
26 7 0.09
27 20 0.27
28 7 0.09
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTATTAAATCATTACTATCAAATC
Found at i:61989 original size:130 final size:134
Alignment explanation
Indices: 61735--62041 Score: 394
Period size: 130 Copynumber: 2.2 Consensus size: 134
61725 ATTTCATTAT
*
61735 TATTAATTATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAA
1 TATTTATTATTACT-AATCA-T--TAT-AAATCATTAAATATTAATAATAAATTATTA-TACTAA
61800 TCATTACAATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAAATC
60 TCATTACAATCAAATCATT-AAAATTAATAATAA-TTCATTATTACTAATCATTACTATC-AATC
61865 ATTAAAAATTAATAA
122 ATTAAAAA-TAAT-A
*
61880 TATTTATTATTACTAATCATTATAAATCATTAAATATT-A-AATATATTATTA-ACTAATCATTA
1 TATTTATTATTACTAATCATTATAAATCATTAAATATTAATAATAAATTATTATACTAATCATTA
* * *
61942 CTATCAAATCATT-AAA-T-ATTATAA-TCATTATTACTAATCATTACTATCAATCATTAAATAT
66 CAATCAAATCATTAAAATTAATAATAATTCATTATTACTAATCATTACTATCAATCATTAAAAAT
62003 AATA
131 AATA
62007 TAATTTCATTATTACTAATCATTACTAAATCATTA
1 T-ATTT-ATTATTACTAATCATTA-TAAATCATTA
62042 CTATCAAATC
Statistics
Matches: 154, Mismatches: 5, Indels: 21
0.86 0.03 0.12
Matches are distributed among these distances:
127 2 0.01
128 8 0.05
129 28 0.18
130 34 0.22
132 6 0.04
133 1 0.01
134 3 0.02
136 23 0.15
138 11 0.07
139 1 0.01
140 15 0.10
141 3 0.02
143 1 0.01
144 5 0.03
145 13 0.08
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (134 bp):
TATTTATTATTACTAATCATTATAAATCATTAAATATTAATAATAAATTATTATACTAATCATTA
CAATCAAATCATTAAAATTAATAATAATTCATTATTACTAATCATTACTATCAATCATTAAAAAT
AATA
Found at i:61997 original size:26 final size:25
Alignment explanation
Indices: 61961--62142 Score: 112
Period size: 26 Copynumber: 7.4 Consensus size: 25
61951 CATTAAATAT
61961 TATAATCATTATTACTAATCATTAC
1 TATAATCATTATTACTAATCATTAC
*
61986 TATCAATCATTAAATA-TAAT-A-TA-
1 TAT-AATCATT-ATTACTAATCATTAC
*
62009 -AT-TTCATTATTACTAATCATTAC
1 TATAATCATTATTACTAATCATTAC
* * *
62032 TA-AATCATTACTATCAAATCATTAT
1 TATAATCATTATTA-CTAATCATTAC
* * *
62057 TATTAAATTATTATTA-TAATGATTAT
1 TA-T-AATCATTATTACTAATCATTAC
* * *
62083 TATAATGATTATTATTAAATCATTAT
1 TATAATCATTATTACT-AATCATTAC
* * *
62109 TATAATGATTACTATCAAATCATTAC
1 TATAATCATTATTA-CTAATCATTAC
62135 TA-AATCAT
1 TATAATCAT
62143 CAAATCATTA
Statistics
Matches: 124, Mismatches: 18, Indels: 30
0.72 0.10 0.17
Matches are distributed among these distances:
19 3 0.02
20 9 0.07
21 1 0.01
22 4 0.03
24 21 0.17
25 22 0.18
26 52 0.42
27 3 0.02
28 9 0.07
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.45
Consensus pattern (25 bp):
TATAATCATTATTACTAATCATTAC
Found at i:62037 original size:86 final size:88
Alignment explanation
Indices: 61789--62058 Score: 310
Period size: 87 Copynumber: 3.1 Consensus size: 88
61779 ATAATAAATT
* *
61789 ATTATTACTAATCATTACAATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATT
1 ATTATTACTAATCATTACTATC-AATCATTAAATA-TAAT-ATAATTTCATTATTACTAATCATT
* *
61854 ACTATCAAATCATTAAAAATTAATAATATTT
63 AC-ATCAAATCATTAAATATT-AT-A-A-TC
*
61885 ATTATTACTAATCATTA-TA--AATCATTAAATAT--TA-AATAT-ATTATTAACTAATCATTAC
1 ATTATTACTAATCATTACTATCAATCATTAAATATAATATAATTTCATTATT-ACTAATCATTAC
61943 TATCAAATCATTAAATATTATAATC
65 -ATCAAATCATTAAATATTATAATC
61968 ATTATTACTAATCATTACTATCAATCATTAAATATAATATAATTTCATTATTACTAATCATTAC-
1 ATTATTACTAATCATTACTATCAATCATTAAATATAATATAATTTCATTATTACTAATCATTACA
* *
62032 T-AAATCATT-ACTATCA-AATC
66 TCAAATCATTAAATATTATAATC
62052 ATTATTA
1 ATTATTA
62059 TTAAATTATT
Statistics
Matches: 158, Mismatches: 8, Indels: 28
0.81 0.04 0.14
Matches are distributed among these distances:
83 18 0.11
84 14 0.09
85 6 0.04
86 29 0.18
87 35 0.22
88 3 0.02
89 17 0.11
90 6 0.04
91 1 0.01
92 11 0.07
95 1 0.01
96 17 0.11
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (88 bp):
ATTATTACTAATCATTACTATCAATCATTAAATATAATATAATTTCATTATTACTAATCATTACA
TCAAATCATTAAATATTATAATC
Found at i:62039 original size:44 final size:41
Alignment explanation
Indices: 61770--62041 Score: 236
Period size: 44 Copynumber: 6.2 Consensus size: 41
61760 ATCAAATCAT
*
61770 TAAAT-ATT-AATAATA-AATT-ATTATTACTAATCATTAC
1 TAAATCATTAAATATTATAATTCATTATTACTAATCATTAC
*
61807 AATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 --T-AAATCATT--AAA-T-ATTATAA-TTCATTATTACTAATCATTAC
* *
61856 TATCAAATCATTAAAAATTAATAATATTTATTATTACTAATCATTA-
1 --T-AAATCATTAAATATT-AT-A-ATTCATTATTACTAATCATTAC
61902 TAAATCATTAAATATTA-AATAT-ATTATTAACTAATCATTAC
1 TAAATCATTAAATATTATAAT-TCATTATT-ACTAATCATTAC
61943 TATCAAATCATTAAATATTATAA-TCATTATTACTAATCATTAC
1 --T-AAATCATTAAATATTATAATTCATTATTACTAATCATTAC
61986 TATCAATCATTAAATATAATATAATTTCATTATTACTAATCATTAC
1 TA--AATCATTAAATAT--TATAA-TTCATTATTACTAATCATTAC
62032 TAAATCATTA
1 TAAATCATTA
62042 CTATCAAATC
Statistics
Matches: 199, Mismatches: 7, Indels: 49
0.78 0.03 0.19
Matches are distributed among these distances:
39 9 0.05
40 18 0.09
41 4 0.02
42 14 0.07
43 28 0.14
44 38 0.19
45 5 0.03
46 26 0.13
47 25 0.13
48 3 0.02
49 29 0.15
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (41 bp):
TAAATCATTAAATATTATAATTCATTATTACTAATCATTAC
Found at i:62083 original size:12 final size:12
Alignment explanation
Indices: 62055--62119 Score: 87
Period size: 12 Copynumber: 5.3 Consensus size: 12
62045 TCAAATCATT
*
62055 ATTATTA-AATT
1 ATTATTATAATG
62066 ATTATTATAATG
1 ATTATTATAATG
62078 ATTATTATAATG
1 ATTATTATAATG
*
62090 ATTATTATTAAATC
1 ATTATTA-T-AATG
62104 ATTATTATAATG
1 ATTATTATAATG
62116 ATTA
1 ATTA
62120 CTATCAAATC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
11 7 0.15
12 29 0.60
13 2 0.04
14 10 0.21
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (12 bp):
ATTATTATAATG
Found at i:62167 original size:35 final size:35
Alignment explanation
Indices: 62125--62249 Score: 121
Period size: 35 Copynumber: 3.5 Consensus size: 35
62115 GATTACTATC
62125 AAATCATTACTAAATCATCAAATCATTAAATATTT
1 AAATCATTACTAAATCATCAAATCATTAAATATTT
* * * * *
62160 AAATCATTA-TCAAATCATTATTAT-AATGATTATTAT
1 AAATCATTACT-AAATCATCA-AATCATTAAATATT-T
*
62196 CATATCATTACTAAATCATCAAATCATTAAATA-TT
1 -AAATCATTACTAAATCATCAAATCATTAAATATTT
*
62231 AAATTCATTATTAAATCAT
1 AAA-TCATTACTAAATCAT
62250 TATAATGATT
Statistics
Matches: 70, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
34 3 0.04
35 39 0.56
36 6 0.09
37 21 0.30
38 1 0.01
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (35 bp):
AAATCATTACTAAATCATCAAATCATTAAATATTT
Found at i:62183 original size:72 final size:72
Alignment explanation
Indices: 62093--62273 Score: 298
Period size: 72 Copynumber: 2.6 Consensus size: 72
62083 TATAATGATT
*
62093 ATTATTAAATCATTATTATAATGATTACTATCAAATCATTACTAAATCATCAAATCATTAAATAT
1 ATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA-
62158 TTAAA-TC
65 TTAAATTC
* *
62165 ATTATCAAATCATTATTATAATGATTATTATCATATCATTACTAAATCATCAAATCATTAAATAT
1 ATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
62230 TAAATTC
66 TAAATTC
62237 ATTATTAAATC---ATTATAATGATTATTATCAAATCATT
1 ATTATTAAATCATTATTATAATGATTATTATCAAATCATT
62274 TTTATGGTTA
Statistics
Matches: 103, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
69 25 0.24
71 5 0.05
72 73 0.71
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.42
Consensus pattern (72 bp):
ATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
TAAATTC
Found at i:62205 original size:23 final size:24
Alignment explanation
Indices: 62165--62273 Score: 68
Period size: 26 Copynumber: 4.6 Consensus size: 24
62155 TATTTAAATC
*
62165 ATTATCAAATCATTATTATAATGATT
1 ATTATCAAATCATTA--CTAATGATT
*
62191 ATTATCATATCATTACT-A--A--
1 ATTATCAAATCATTACTAATGATT
* * * *
62210 ATCATCAAATCATTAAATATTAAATT
1 ATTATCAAATCATT-ACTAAT-GATT
*
62236 CATTATTAAATCATTA-TAATGATT
1 -ATTATCAAATCATTACTAATGATT
62260 ATTATCAAATCATT
1 ATTATCAAATCATT
62274 TTTATGGTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
19 12 0.19
20 2 0.03
21 1 0.02
23 14 0.22
24 5 0.08
25 3 0.05
26 15 0.23
27 12 0.19
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTATCAAATCATTACTAATGATT
Found at i:62251 original size:11 final size:11
Alignment explanation
Indices: 62012--62252 Score: 74
Period size: 11 Copynumber: 19.6 Consensus size: 11
62002 TAATATAATT
62012 TCATTATTACTAA
1 TCATTATTA--AA
*
62025 TCATTACTAAA
1 TCATTATTAAA
62036 TCATTACTATCAAA
1 TCATTA-T-T-AAA
62050 TCATTATTATTAAA
1 TC---ATTATTAAA
*
62064 TTATTATTATAA
1 TCATTATTA-AA
*
62076 TGATTATTATAATGA
1 TCATTA-T-TAA--A
*
62091 TTATTATTAAA
1 TCATTATTAAA
62102 TCATTATTATAA
1 TCATTATTA-AA
*
62114 TGATTACTATCAAA
1 TCATTA-T-T-AAA
*
62128 TCATTACTAAA
1 TCATTATTAAA
62139 TCATCAAATCATTAAA
1 TCAT----T-ATTAAA
62155 T-A-T-TTAAA
1 TCATTATTAAA
*
62163 TCATTATCAAA
1 TCATTATTAAA
62174 TCATTATTATAA
1 TCATTATTA-AA
*
62186 TGATTATTATCATA
1 TCATTATTA--A-A
*
62200 TCATTACTAAA
1 TCATTATTAAA
* * * *
62211 TCATCAAATCAT
1 TCAT-TATTAAA
* *
62223 TAAATATTAAA
1 TCATTATTAAA
62234 TTCATTATTAAA
1 -TCATTATTAAA
62246 TCATTAT
1 TCATTAT
62253 AATGATTATT
Statistics
Matches: 172, Mismatches: 28, Indels: 58
0.67 0.11 0.22
Matches are distributed among these distances:
8 6 0.03
9 1 0.01
10 2 0.01
11 58 0.34
12 40 0.23
13 16 0.09
14 28 0.16
15 10 0.06
16 7 0.04
17 4 0.02
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.44
Consensus pattern (11 bp):
TCATTATTAAA
Found at i:63646 original size:36 final size:36
Alignment explanation
Indices: 63546--63655 Score: 159
Period size: 36 Copynumber: 3.0 Consensus size: 36
63536 TACCCAATCT
*
63546 CCCCATGCAAGAACCGATCCTTGGTCGCCCCGAGTG
1 CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
***
63582 CCCCATGCATG-TTGGTCATCCTTGGTCGCCCCGAGTG
1 CCCCATGCATGAACCG--ATCCTTGGTCGCCCCGAGTG
63619 CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
1 CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
63655 C
1 C
63656 ATGGCACGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
35 1 0.02
36 31 0.48
37 31 0.48
38 1 0.02
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.21
Consensus pattern (36 bp):
CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
Found at i:68688 original size:18 final size:18
Alignment explanation
Indices: 68665--68700 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
68655 TACTTCGTGA
68665 GAGTGGACAATGATCAAC
1 GAGTGGACAATGATCAAC
68683 GAGTGGACAATGATCAAC
1 GAGTGGACAATGATCAAC
68701 CAGAATAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.17
Consensus pattern (18 bp):
GAGTGGACAATGATCAAC
Found at i:69693 original size:212 final size:214
Alignment explanation
Indices: 69308--69735 Score: 833
Period size: 212 Copynumber: 2.0 Consensus size: 214
69298 TGTTACAGAC
69308 CAGACTGAGGTCAGGGGAGAACTAATCTCATACAATACAGCTATGCTCAGGCAATAGTGCAGCTA
1 CAGACTGAGGTCAGGGGAGAACTAATCTCATACAATACAGCTATGCTCAGGCAATAGTGCAGCTA
69373 TGAACTGAAATTACTCGACAGAGTAAGGAAGGTGAGGGATTACTCGTACATGTAACAAAAGTGTG
66 TGAACTGAAATTACTCGACAGAGTAAGGAAGGTGAGGGATTACTCGTACATGTAACAAAAGTGTG
69438 ATCAAGTGACTCGTAGTTGACGGGCAAGAGACGAAAGGTGGGAGATTTGCATGACAGGGTTCCTG
131 ATCAAGTGACTCGTAGTTGACGGGCAAGAGACGAAAGGTGGGAGATTTGCATGACAGGGTTCCTG
69503 TGAATTCTGTCTAAATCAT
196 TGAATTCTGTCTAAATCAT
69522 CAGACTGAGGTCA-GGGAGAACTAATCTCATACAATACAGCTATGCTCAGGCAATAGTGCAGCTA
1 CAGACTGAGGTCAGGGGAGAACTAATCTCATACAATACAGCTATGCTCAGGCAATAGTGCAGCTA
69586 TGAACTGAAATTACTCGACAGAGTAAGG-AGGTGAGGGATTACTCGTACATGTAACAAAAGTGTG
66 TGAACTGAAATTACTCGACAGAGTAAGGAAGGTGAGGGATTACTCGTACATGTAACAAAAGTGTG
*
69650 ATCAAGTGACTCGTAGTTGACGGGCAAGAGACGAAAGGTGGGAGTTTTGCATGACAGGGTTCCTG
131 ATCAAGTGACTCGTAGTTGACGGGCAAGAGACGAAAGGTGGGAGATTTGCATGACAGGGTTCCTG
69715 TGAATTCTGTCTAAATCAT
196 TGAATTCTGTCTAAATCAT
69734 CA
1 CA
69736 CTATATTCAA
Statistics
Matches: 213, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
212 121 0.57
213 79 0.37
214 13 0.06
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (214 bp):
CAGACTGAGGTCAGGGGAGAACTAATCTCATACAATACAGCTATGCTCAGGCAATAGTGCAGCTA
TGAACTGAAATTACTCGACAGAGTAAGGAAGGTGAGGGATTACTCGTACATGTAACAAAAGTGTG
ATCAAGTGACTCGTAGTTGACGGGCAAGAGACGAAAGGTGGGAGATTTGCATGACAGGGTTCCTG
TGAATTCTGTCTAAATCAT
Found at i:80175 original size:134 final size:134
Alignment explanation
Indices: 79935--80201 Score: 498
Period size: 134 Copynumber: 2.0 Consensus size: 134
79925 CAAGCCAAAT
*
79935 AAATCGTTCAAAGAGGAGACAGAGTGAAAACCCGGCCGTTATGTAGCATCTGAGAACAAGAAAGC
1 AAATCGTTCAAAGAGGAGACAGAGTGAAAACCCGGCCGTTATGTAGCATCTGAGAACAAGAAAAC
* *
80000 ATACATGCTTTGCTTTCCTCCAATTCTGCCACCACGAACGGAATCTTTGCTTTACTCGGATAGAA
66 AGACATGCTTTGCTTTCCTCCAATTCTGCCACCACGAACGGAATCTTTGCTTTACTCGGACAGAA
80065 CACA
131 CACA
80069 AAATCGTTCAAAGAGGAGACAGAGTGAAAACCCGGCCGTTATGTAGCATCTGAGAACAAGAAAAC
1 AAATCGTTCAAAGAGGAGACAGAGTGAAAACCCGGCCGTTATGTAGCATCTGAGAACAAGAAAAC
*
80134 AGACATGCTTTGCTTTCCTCCAATTCTGCCACCACGAACGGAATCTTTGCTTTACTTGGACAGAA
66 AGACATGCTTTGCTTTCCTCCAATTCTGCCACCACGAACGGAATCTTTGCTTTACTCGGACAGAA
80199 CAC
131 CAC
80202 GAGCTGAATC
Statistics
Matches: 129, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
134 129 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (134 bp):
AAATCGTTCAAAGAGGAGACAGAGTGAAAACCCGGCCGTTATGTAGCATCTGAGAACAAGAAAAC
AGACATGCTTTGCTTTCCTCCAATTCTGCCACCACGAACGGAATCTTTGCTTTACTCGGACAGAA
CACA
Found at i:81214 original size:23 final size:23
Alignment explanation
Indices: 81168--81214 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
81158 AATATATTTA
* *
81168 AAATATAATATTAAATACATTAT
1 AAATATAATATTAAATAAAATAT
81191 AAATATAATATT-AATAAAAATAT
1 AAATATAATATTAAAT-AAAATAT
81214 A
1 A
81215 TTCAATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATATAATATTAAATAAAATAT
Found at i:81258 original size:20 final size:20
Alignment explanation
Indices: 81233--81283 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
81223 GAAATTATTA
81233 TTAAATATGT-GTAATAATTT
1 TTAAATA-GTAGTAATAATTT
*
81253 TTAAATAGTAATTAATAATTT
1 TTAAATAGT-AGTAATAATTT
81274 TTAAATAGTA
1 TTAAATAGTA
81284 AATTAACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 2 0.07
20 8 0.29
21 18 0.64
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (20 bp):
TTAAATAGTAGTAATAATTT
Found at i:81270 original size:21 final size:22
Alignment explanation
Indices: 81244--81289 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
81234 TAAATATGTG
81244 TAATAATTTTTAAATAGT-AAT
1 TAATAATTTTTAAATAGTAAAT
81265 TAATAATTTTTAAATAGTAAAT
1 TAATAATTTTTAAATAGTAAAT
81287 TAA
1 TAA
81290 CATGAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
TAATAATTTTTAAATAGTAAAT
Found at i:82233 original size:34 final size:34
Alignment explanation
Indices: 82187--82258 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
82177 GTTGAAACGA
*
82187 ATGTCTTTAATGTTTTGGGGTTATTTCAAAATTT
1 ATGTCTTCAATGTTTTGGGGTTATTTCAAAATTT
82221 ATGTCTTCAATGTTTTGGGGTTATTTCAAAATTT
1 ATGTCTTCAATGTTTTGGGGTTATTTCAAAATTT
82255 ATGT
1 ATGT
82259 GTTTTCTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.24, C:0.07, G:0.18, T:0.51
Consensus pattern (34 bp):
ATGTCTTCAATGTTTTGGGGTTATTTCAAAATTT
Found at i:83357 original size:18 final size:18
Alignment explanation
Indices: 83334--83369 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
83324 TACTTCGTGA
83334 GAGTGGACAATGATCAAC
1 GAGTGGACAATGATCAAC
83352 GAGTGGACAATGATCAAC
1 GAGTGGACAATGATCAAC
83370 CAGAATAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.17
Consensus pattern (18 bp):
GAGTGGACAATGATCAAC
Found at i:85150 original size:53 final size:53
Alignment explanation
Indices: 85088--85197 Score: 220
Period size: 53 Copynumber: 2.1 Consensus size: 53
85078 TACCCATGAA
85088 ACAACTATAAATTAAGAATAAAGACAAGGAAGAAGCTCTGCGGCGGAGGAGAG
1 ACAACTATAAATTAAGAATAAAGACAAGGAAGAAGCTCTGCGGCGGAGGAGAG
85141 ACAACTATAAATTAAGAATAAAGACAAGGAAGAAGCTCTGCGGCGGAGGAGAG
1 ACAACTATAAATTAAGAATAAAGACAAGGAAGAAGCTCTGCGGCGGAGGAGAG
85194 ACAA
1 ACAA
85198 GTGCAGAAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.46, C:0.14, G:0.27, T:0.13
Consensus pattern (53 bp):
ACAACTATAAATTAAGAATAAAGACAAGGAAGAAGCTCTGCGGCGGAGGAGAG
Found at i:88558 original size:24 final size:24
Alignment explanation
Indices: 88529--88578 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
88519 CGTTATATTA
88529 TACATGGTTAACAATGCAAAATAT
1 TACATGGTTAACAATGCAAAATAT
88553 TACATGGTTAACAATGCAAAATAT
1 TACATGGTTAACAATGCAAAATAT
88577 TA
1 TA
88579 GCTATTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (24 bp):
TACATGGTTAACAATGCAAAATAT
Done.