Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015368.1 Kokia drynarioides strain JFW-HI SEQ_130415, 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: 216984
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 546 characters in sequence are not A, C, G, or T
Found at i:89 original size:17 final size:17
Alignment explanation
Indices: 64--98 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54 TTTACATATT
*
64 TTAAGTTACTTACTTGG
1 TTAAATTACTTACTTGG
*
81 TTAAATTACTTAGTTGG
1 TTAAATTACTTACTTGG
98 T
1 T
99 CGCCCATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49
Consensus pattern (17 bp):
TTAAATTACTTACTTGG
Found at i:1917 original size:25 final size:24
Alignment explanation
Indices: 1879--1947 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 24
1869 ATGCTTTTAT
*
1879 TAAAAATAAAAAAATTGTAAAAAA
1 TAAAAATAAAAAAATTATAAAAAA
*
1903 TAAAAATCAATAAAATTATATAAAATTA
1 TAAAAAT-AAAAAAATTATA-AAAA--A
* *
1931 TAAAATTATAAAAATTA
1 TAAAAATAAAAAAATTA
1948 AAATTTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 7 0.19
25 10 0.28
26 4 0.11
27 8 0.22
28 7 0.19
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (24 bp):
TAAAAATAAAAAAATTATAAAAAA
Found at i:1993 original size:30 final size:31
Alignment explanation
Indices: 1928--2041 Score: 91
Period size: 30 Copynumber: 3.9 Consensus size: 31
1918 TTATATAAAA
* *
1928 TTATAAAATTAT--AAAAA-T-TAAAATTTA
1 TTATAAAATTATAAAAAAATTATAAAAATTG
*
1955 TT-TGAAATTATAAAAAAATTATAAAAATTG
1 TTATAAAATTATAAAAAAATTATAAAAATTG
* *
1985 TTA-AAAATTATAAAAAAAATTGT--AAATTT
1 TTATAAAATTAT-AAAAAAATTATAAAAATTG
**
2014 TTATAAAGATCGTAAAAAAATTATAAAA
1 TTATAAA-ATTATAAAAAAATTATAAAA
2042 TATATAGAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
26 8 0.12
27 2 0.03
28 5 0.07
29 9 0.13
30 29 0.43
31 13 0.19
32 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (31 bp):
TTATAAAATTATAAAAAAATTATAAAAATTG
Found at i:2001 original size:10 final size:9
Alignment explanation
Indices: 1879--2000 Score: 78
Period size: 9 Copynumber: 13.7 Consensus size: 9
1869 ATGCTTTTAT
1879 TAAAAA-TA
1 TAAAAATTA
* *
1887 AAAAAATTG
1 TAAAAATTA
1896 TAAAAA--A
1 TAAAAATTA
*
1903 TAAAAATCA
1 TAAAAATTA
1912 -ATAAAATTA
1 TA-AAAATTA
1921 TATAAAATTA
1 TA-AAAATTA
1931 T-AAAATTA
1 TAAAAATTA
1939 TAAAAA-T-
1 TAAAAATTA
*
1946 TAAAATTTA
1 TAAAAATTA
**
1955 TTTGAAATTA
1 -TAAAAATTA
1965 TAAAAAAATTA
1 T--AAAAATTA
*
1976 TAAAAATTGT
1 TAAAAATT-A
1986 TAAAAATTA
1 TAAAAATTA
1995 TAAAAA
1 TAAAAA
2001 AAATTGTAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 23
0.71 0.10 0.18
Matches are distributed among these distances:
7 11 0.12
8 16 0.18
9 31 0.35
10 24 0.27
11 7 0.08
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (9 bp):
TAAAAATTA
Found at i:2002 original size:11 final size:10
Alignment explanation
Indices: 1914--2001 Score: 55
Period size: 10 Copynumber: 9.4 Consensus size: 10
1904 AAAAATCAAT
*
1914 AAAATTATAT
1 AAAATTATAA
1924 AAAATTAT--
1 AAAATTATAA
1932 AAAATTAT-A
1 AAAATTATAA
1941 AAAA-T-T-A
1 AAAATTATAA
* **
1948 AAATTTATTT
1 AAAATTATAA
*
1958 GAAATTATAAA
1 AAAATTAT-AA
1969 AAAATTAT-A
1 AAAATTATAA
* *
1978 AAAATTGTTA
1 AAAATTATAA
1988 AAAATTATAA
1 AAAATTATAA
1998 AAAA
1 AAAA
2002 AATTGTAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
7 5 0.08
8 10 0.16
9 13 0.21
10 27 0.44
11 7 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (10 bp):
AAAATTATAA
Found at i:2115 original size:62 final size:59
Alignment explanation
Indices: 1964--2120 Score: 160
Period size: 61 Copynumber: 2.6 Consensus size: 59
1954 ATTTGAAATT
*
1964 ATAAAAAAATTATAAAAATTGTTAAAAATTATAAAAAAAATTGTAAATTTTTATAAAGATC
1 ATAAAAAAATTATAAAAA-TG-TAAAAAATATAAAAAAAATTGTAAATTTTTATAAAGATC
* * *
2025 GTAAAAAAATTAT-AAAATATATAGAAATATGGAAAAAAAATCATG-AAA-TTTTATAAAG-TC
1 ATAAAAAAATTATAAAAATGTA-AAAAATAT--AAAAAAAAT--TGTAAATTTTTATAAAGATC
*
2085 ATAAGAAAATTATACAAAATGTAAATAAATATAAAA
1 ATAAAAAAATTATA-AAAATGTAAA-AAATATAAAA
2121 TTCATAAAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
58 2 0.03
59 7 0.09
60 21 0.26
61 32 0.40
62 16 0.20
63 2 0.03
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.30
Consensus pattern (59 bp):
ATAAAAAAATTATAAAAATGTAAAAAATATAAAAAAAATTGTAAATTTTTATAAAGATC
Found at i:2316 original size:20 final size:20
Alignment explanation
Indices: 2291--2335 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2281 TCAAAGGGTC
*
2291 TTTTTGATATATTTTATAAT-
1 TTTTTGATAAATTTTA-AATA
*
2311 TTTTTGGTAAATTTTAAATA
1 TTTTTGATAAATTTTAAATA
2331 TTTTT
1 TTTTT
2336 TATTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (20 bp):
TTTTTGATAAATTTTAAATA
Found at i:2342 original size:21 final size:20
Alignment explanation
Indices: 2301--2355 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
2291 TTTTTGATAT
* *
2301 ATTTTATAATTTTTTGGTAA
1 ATTTTAAAATTTTTTAGTAA
*
2321 ATTTTAAATATTTTTTATTAA
1 ATTTTAAA-ATTTTTTAGTAA
*
2342 AATTTAATAATTTT
1 ATTTTAA-AATTTT
2356 CTAACTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 7 0.24
21 21 0.72
22 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
ATTTTAAAATTTTTTAGTAA
Found at i:3251 original size:24 final size:24
Alignment explanation
Indices: 3224--3271 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3214 TAACTCTCCA
3224 TGTTACAAAGAAAAACAAAACTAC
1 TGTTACAAAGAAAAACAAAACTAC
3248 TGTTACAAAGAAAAACAAAACTAC
1 TGTTACAAAGAAAAACAAAACTAC
3272 AAAATGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.58, C:0.17, G:0.08, T:0.17
Consensus pattern (24 bp):
TGTTACAAAGAAAAACAAAACTAC
Found at i:5049 original size:6 final size:6
Alignment explanation
Indices: 5040--5089 Score: 73
Period size: 6 Copynumber: 8.2 Consensus size: 6
5030 GAATGAAAAT
* *
5040 GGAAAA GGAAGAA GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGGAGA
1 GGAAGA GGAAG-A GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA
5089 G
1 G
5090 ATCATAGCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 35 0.85
7 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GGAAGA
Found at i:6173 original size:18 final size:18
Alignment explanation
Indices: 6150--6187 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6140 TAACATAATT
*
6150 TTATTCG-GTTTATTTGAA
1 TTATTCGAG-TTATTTAAA
6168 TTATTCGAGTTATTTAAA
1 TTATTCGAGTTATTTAAA
6186 TT
1 TT
6188 CGAAAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.55
Consensus pattern (18 bp):
TTATTCGAGTTATTTAAA
Found at i:20966 original size:31 final size:31
Alignment explanation
Indices: 20931--20994 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
20921 GTAACCAAAT
* *
20931 TTGACAATTTTTCTTAATTTTGTACTTAAAC
1 TTGACAATTTTTCTTAAATTGGTACTTAAAC
* *
20962 TTGACACTTTTTCTTAAATTGGTATTTAAAC
1 TTGACAATTTTTCTTAAATTGGTACTTAAAC
20993 TT
1 TT
20995 TTTGGGAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.52
Consensus pattern (31 bp):
TTGACAATTTTTCTTAAATTGGTACTTAAAC
Found at i:23875 original size:21 final size:21
Alignment explanation
Indices: 23836--23875 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
23826 CAGTGCAGAC
*
23836 TTCTACCGATACTTGGTAAAG
1 TTCTACCGATACTAGGTAAAG
23857 TTCTACCGATA-TAGTGTAA
1 TTCTACCGATACTAG-GTAA
23876 CTTTTACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
TTCTACCGATACTAGGTAAAG
Found at i:33111 original size:14 final size:15
Alignment explanation
Indices: 33085--33118 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
33075 AATTTTCAAT
33085 TTCATCATCTTCTTC
1 TTCATCATCTTCTTC
33100 TTCATC-TCTTCTTC
1 TTCATCATCTTCTTC
*
33114 ATCAT
1 TTCAT
33119 TTTAATTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.15, C:0.32, G:0.00, T:0.53
Consensus pattern (15 bp):
TTCATCATCTTCTTC
Found at i:34095 original size:31 final size:29
Alignment explanation
Indices: 34060--34136 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 29
34050 ATTAAAATTA
34060 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTT-AAAAAAATAAT
*
34091 TTTAATAATTTTATATTTTAAAAAATAAT
1 TTTAATAATTTTATATTTAAAAAAATAAT
* *
34120 TTAAAT-TTTTTATATTT
1 TTTAATAATTTTATATTT
34137 TAATAAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 10 0.23
29 15 0.35
30 5 0.12
31 13 0.30
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTAATAATTTTATATTTAAAAAAATAAT
Found at i:34133 original size:28 final size:29
Alignment explanation
Indices: 34053--34144 Score: 107
Period size: 28 Copynumber: 3.2 Consensus size: 29
34043 ATTGGAAATT
* *
34053 AAAATTATTT-AATAATTTTATTATTTCAAA
1 AAAATAATTTAAATAATTTTA-TATTT-TAA
*
34083 AAAATAATTTTAATAATTTTATATTTTAA
1 AAAATAATTTAAATAATTTTATATTTTAA
*
34112 AAAATAATTTAAAT-TTTTTATATTTTAA
1 AAAATAATTTAAATAATTTTATATTTTAA
*
34140 TAAAT
1 AAAAT
34145 TTAAAATCAT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 17 0.30
29 15 0.27
30 14 0.25
31 10 0.18
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
AAAATAATTTAAATAATTTTATATTTTAA
Found at i:35874 original size:23 final size:22
Alignment explanation
Indices: 35839--35959 Score: 100
Period size: 23 Copynumber: 5.3 Consensus size: 22
35829 AGCACTTAAT
*
35839 AGTAAGCGCACACAGTGCAATCC
1 AGTAAGCACACACAGTGCAAT-C
*
35862 AGTAAGCATACACAGTGCAATC
1 AGTAAGCACACACAGTGCAATC
* * * *
35884 AGTAGGCGCACATAGCGCAAATC
1 AGTAAGCACACACAGTGC-AATC
* *
35907 AGTAGGCACACA-AGGTGCGAAAC
1 AGTAAGCACACACA-GTGC-AATC
* *
35930 AGTAAGCACACAAAGTGCGAAAC
1 AGTAAGCACACACAGTGC-AATC
35953 AGTAAGC
1 AGTAAGC
35960 GCGCTAACGT
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
22 15 0.18
23 67 0.81
24 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (22 bp):
AGTAAGCACACACAGTGCAATC
Found at i:36440 original size:11 final size:11
Alignment explanation
Indices: 36413--36443 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
36403 TCAGACTCTA
36413 ATGATTTTTCT
1 ATGATTTTTCT
36424 AT-ATTTTTCT
1 ATGATTTTTCT
36434 ATGATTTTTC
1 ATGATTTTTC
36444 AAATTCAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (11 bp):
ATGATTTTTCT
Found at i:43093 original size:22 final size:23
Alignment explanation
Indices: 43068--43111 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
43058 ACAGTAAACA
*
43068 CACACAGTAC-AATCAGTAGGCG
1 CACACAGCACAAATCAGTAGGCG
* *
43090 CACATAGCGCAAATCAGTAGGC
1 CACACAGCACAAATCAGTAGGC
43112 ATACAAGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (23 bp):
CACACAGCACAAATCAGTAGGCG
Found at i:46964 original size:22 final size:22
Alignment explanation
Indices: 46934--47104 Score: 180
Period size: 22 Copynumber: 7.5 Consensus size: 22
46924 ATGCTAGCAC
* * *
46934 GCTTACTGTTTAGTACTATGTAT
1 GCTT-CTGTTTAGCACTGTGTGT
*
46957 GCTTCTGTTCAGCACTGTGTGT
1 GCTTCTGTTTAGCACTGTGTGT
46979 GCTTCTGTTTAGCACTGTGTGT
1 GCTTCTGTTTAGCACTGTGTGT
* *
47001 TCTTCTGTTACCCAGCACTGTGTGT
1 GCTTCTGTT---TAGCACTGTGTGT
*
47026 GCTTCTGTTCAGCACTGTGTGT
1 GCTTCTGTTTAGCACTGTGTGT
*
47048 GCTTCTGTTACCCAGCACTGTGTGT
1 GCTTCTGTT---TAGCACTGTGTGT
* * *
47073 GCTTCTGTTCAACACTGTGTCT
1 GCTTCTGTTTAGCACTGTGTGT
47095 GCTTCTGTTT
1 GCTTCTGTTT
47105 CCCCAGTACT
Statistics
Matches: 131, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
22 85 0.65
23 4 0.03
25 42 0.32
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.43
Consensus pattern (22 bp):
GCTTCTGTTTAGCACTGTGTGT
Found at i:47022 original size:25 final size:22
Alignment explanation
Indices: 46956--47103 Score: 206
Period size: 22 Copynumber: 6.5 Consensus size: 22
46946 GTACTATGTA
46956 TGCTTCTGTTCAGCACTGTGTG
1 TGCTTCTGTTCAGCACTGTGTG
*
46978 TGCTTCTGTTTAGCACTGTGTG
1 TGCTTCTGTTCAGCACTGTGTG
*
47000 TTCTTCTGTTACCCAGCACTGTGTG
1 TGCTTCTGTT---CAGCACTGTGTG
47025 TGCTTCTGTTCAGCACTGTGTG
1 TGCTTCTGTTCAGCACTGTGTG
47047 TGCTTCTGTTACCCAGCACTGTGTG
1 TGCTTCTGTT---CAGCACTGTGTG
* *
47072 TGCTTCTGTTCAACACTGTGTC
1 TGCTTCTGTTCAGCACTGTGTG
47094 TGCTTCTGTT
1 TGCTTCTGTT
47104 TCCCCAGTAC
Statistics
Matches: 114, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
22 72 0.63
25 42 0.37
ACGTcount: A:0.10, C:0.24, G:0.24, T:0.42
Consensus pattern (22 bp):
TGCTTCTGTTCAGCACTGTGTG
Found at i:47028 original size:47 final size:47
Alignment explanation
Indices: 46966--47103 Score: 240
Period size: 47 Copynumber: 2.9 Consensus size: 47
46956 TGCTTCTGTT
* *
46966 CAGCACTGTGTGTGCTTCTGTTTAGCACTGTGTGTTCTTCTGTTACC
1 CAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGTTACC
47013 CAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGTTACC
1 CAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGTTACC
* *
47060 CAGCACTGTGTGTGCTTCTGTTCAACACTGTGTCTGCTTCTGTT
1 CAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGTT
47104 TCCCCAGTAC
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 87 1.00
ACGTcount: A:0.11, C:0.25, G:0.24, T:0.41
Consensus pattern (47 bp):
CAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGTTACC
Found at i:47089 original size:69 final size:67
Alignment explanation
Indices: 46956--47103 Score: 208
Period size: 69 Copynumber: 2.1 Consensus size: 67
46946 GTACTATGTA
* * *
46956 TGCTTCTGTTCAGCACTGTGTGTGCTTCTGTTTAGCACTGTGTGTTCTTCTGTTACCCAGCACTG
1 TGCTTCTGTTCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGTT--CCAACACTG
*
47021 TGTG
64 TGTC
47025 TGCTTCTGTTCAGCACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGCTTCTGTT-CAACACT
1 TGCTTCTGTTCAGCACTGTGTGTGCTTCTGTT---CAGCACTGTGTGTGCTTCTGTTCCAACACT
47089 GTGTC
63 GTGTC
47094 TGCTTCTGTT
1 TGCTTCTGTT
47104 TCCCCAGTAC
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
69 52 0.72
72 20 0.28
ACGTcount: A:0.10, C:0.24, G:0.24, T:0.42
Consensus pattern (67 bp):
TGCTTCTGTTCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGTTCCAACACTGTG
TC
Found at i:47127 original size:47 final size:47
Alignment explanation
Indices: 46966--47128 Score: 157
Period size: 47 Copynumber: 3.5 Consensus size: 47
46956 TGCTTCTGTT
* * * * * * *
46966 CAGCACTGTGTGTGCTTCTGTTTAGCACTGTGTGTTCTTCTGTTACC
1 CAGCACTGTATGTACCTCTGTTCAACACTGTGTCTGCTTCTGTTACC
* * * * *
47013 CAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGTTACC
1 CAGCACTGTATGTACCTCTGTTCAACACTGTGTCTGCTTCTGTTACC
* * * *
47060 CAGCACTGTGTGTGCTTCTGTTCAACACTGTGTCTGCTTCTGTTTCCC
1 CAGCACTGTATGTACCTCTGTTCAACACTGTGTCTGCTTCTG-TTACC
*
47108 CAGTACT-TATGTACCTCTGTT
1 CAGCACTGTATGTACCTCTGTT
47129 AAGTACTTCG
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
47 96 0.91
48 10 0.09
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (47 bp):
CAGCACTGTATGTACCTCTGTTCAACACTGTGTCTGCTTCTGTTACC
Found at i:47620 original size:13 final size:13
Alignment explanation
Indices: 47598--47627 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
47588 AGACACCGAG
47598 TTTT-AAAGAAAA
1 TTTTCAAAGAAAA
47610 TTTTCAAAGAAAA
1 TTTTCAAAGAAAA
47623 TTTTC
1 TTTTC
47628 TGTTACTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (13 bp):
TTTTCAAAGAAAA
Found at i:51143 original size:24 final size:24
Alignment explanation
Indices: 51097--51149 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
51087 GCCTGAGCCA
51097 AAGA-AAG-AAGAAGAAAACAAGG
1 AAGAGAAGAAAGAAGAAAACAAGG
*
51119 ATGAGAAGAAAGAAGAAAA-AGAGG
1 AAGAGAAGAAAGAAGAAAACA-AGG
51143 AAGAGAA
1 AAGAGAA
51150 ACCTGCTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 3 0.12
23 4 0.15
24 19 0.73
ACGTcount: A:0.66, C:0.02, G:0.30, T:0.02
Consensus pattern (24 bp):
AAGAGAAGAAAGAAGAAAACAAGG
Found at i:57859 original size:2 final size:2
Alignment explanation
Indices: 57852--57877 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57842 TCTAGCCTTT
57852 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
57878 CATAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64102 original size:4 final size:4
Alignment explanation
Indices: 64088--64122 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
64078 ACGGCTGAAC
*
64088 AAAG AAAAG AAAG AAAG AAAG AAAG GAAG AAAG AA
1 AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
64123 GAATAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:64136 original size:16 final size:15
Alignment explanation
Indices: 64089--64137 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
64079 CGGCTGAACA
64089 AAGAAAAGAAAGAAAG
1 AAGAAAAGAAA-AAAG
* *
64105 AAAGAAAGGAAGAAAG
1 -AAGAAAAGAAAAAAG
64121 AAGAATAAGAAAAAAG
1 AAGAA-AAGAAAAAAG
64137 A
1 A
64138 GAATGAGAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 5 0.19
16 13 0.48
17 9 0.33
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (15 bp):
AAGAAAAGAAAAAAG
Found at i:64186 original size:13 final size:12
Alignment explanation
Indices: 64158--64182 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
64148 AAGGTAGTGT
64158 ATTTATTTTTAA
1 ATTTATTTTTAA
64170 ATTTATTTTTAA
1 ATTTATTTTTAA
64182 A
1 A
64183 ATTTTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATTTTTAA
Found at i:65007 original size:30 final size:30
Alignment explanation
Indices: 64973--65067 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
64963 AAATTGTACA
64973 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATTTATTTTGTACCATTTTAGT
** * * * *
65003 AAAT-AAT-GGTGTGTGGATACCATTTTGGT
1 AAATAAATATTTATTTTG-TACCATTTTAGT
* *
65032 ATATAAATATTTATTTTGTATCATTTTAGT
1 AAATAAATATTTATTTTGTACCATTTTAGT
65062 AAATAA
1 AAATAA
65068 TTCATTTTGG
Statistics
Matches: 47, Mismatches: 15, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
28 4 0.09
29 17 0.36
30 22 0.47
31 4 0.09
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (30 bp):
AAATAAATATTTATTTTGTACCATTTTAGT
Found at i:66214 original size:43 final size:43
Alignment explanation
Indices: 66130--66214 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
66120 ATTAACATGT
* * *
66130 TAAATTATATTATTTGACTCATGTTAATATGGTTACGTGTTAC
1 TAAATTATATTATTTGACTCATATTAATATGCTTACATGTTAC
*
66173 TAAATTATATTACTTT-ACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTA-TTTGACTCATATTAATATGCTT-ACATGTTA
66215 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 2 0.06
43 31 0.86
44 3 0.08
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (43 bp):
TAAATTATATTATTTGACTCATATTAATATGCTTACATGTTAC
Found at i:68413 original size:26 final size:28
Alignment explanation
Indices: 68357--68413 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
68347 TTTCAATAAA
* *
68357 TAAAATACGAATTTAAAAATATATCATAC
1 TAAAATAC-AATTTAAAAATATAACACAC
68386 TAAAATA-AATTTAAAAATA-AACACAC
1 TAAAATACAATTTAAAAATATAACACAC
68412 TA
1 TA
68414 CCTTTCTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.27
27 12 0.46
29 7 0.27
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.28
Consensus pattern (28 bp):
TAAAATACAATTTAAAAATATAACACAC
Found at i:71394 original size:21 final size:21
Alignment explanation
Indices: 71364--71412 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
71354 AAAAAATAAC
71364 AAATCA-ATCCTAAATTTAAA
1 AAATCATATCCTAAATTTAAA
71384 AAATCATATCCTAAATTTAAA
1 AAATCATATCCTAAATTTAAA
71405 AAATCATA
1 AAATCATA
71413 CACCCAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATCATATCCTAAATTTAAA
Found at i:77175 original size:2 final size:2
Alignment explanation
Indices: 77170--77219 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
77160 ATATAAAAGC
77170 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
77212 GA GA GA GA
1 GA GA GA GA
77220 AAAAGACGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:78912 original size:4 final size:4
Alignment explanation
Indices: 78903--78927 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
78893 TATCAAAGTC
78903 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
78928 TTAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:90566 original size:18 final size:18
Alignment explanation
Indices: 90524--90558 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
90514 AAACAAATTT
90524 TTAATTAAATAAATTTAA
1 TTAATTAAATAAATTTAA
90542 TTAATTAAA-AAATTTAA
1 TTAATTAAATAAATTTAA
90559 ATTGATTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAATTAAATAAATTTAA
Found at i:91468 original size:20 final size:20
Alignment explanation
Indices: 91443--91483 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
91433 TTGGGATTTA
*
91443 GGGTTTATTGGCCCGTTCTT
1 GGGTTTATTGACCCGTTCTT
91463 GGGTTTATTGACCCGTTCTT
1 GGGTTTATTGACCCGTTCTT
91483 G
1 G
91484 ATATTTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.07, C:0.20, G:0.29, T:0.44
Consensus pattern (20 bp):
GGGTTTATTGACCCGTTCTT
Found at i:97333 original size:15 final size:15
Alignment explanation
Indices: 97266--97337 Score: 64
Period size: 14 Copynumber: 5.0 Consensus size: 15
97256 TAAGATAAAT
*
97266 TTAAAATATTTTTTAA
1 TTAAAATA-TTATTAA
*
97282 TT-AAAT-TTATAAA
1 TTAAAATATTATTAA
*
97295 TTAAAATAATAGTT--
1 TTAAAATATTA-TTAA
97309 TTAAAA-ATTATTAA
1 TTAAAATATTATTAA
97323 TTAAAATATTATTAA
1 TTAAAATATTATTAA
97338 ATATTTAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
12 2 0.04
13 10 0.22
14 16 0.36
15 14 0.31
16 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (15 bp):
TTAAAATATTATTAA
Found at i:97360 original size:12 final size:12
Alignment explanation
Indices: 97312--97360 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 12
97302 AATAGTTTTA
*
97312 AAAATTATTAATT
1 AAAA-TATTTATT
97325 AAAATA-TTATT
1 AAAATATTTATT
97336 -AAATATTTAATT
1 AAAATATTT-ATT
97348 AAAATATTTATT
1 AAAATATTTATT
97360 A
1 A
97361 CTAATAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.16
11 6 0.19
12 9 0.28
13 12 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AAAATATTTATT
Found at i:97370 original size:23 final size:23
Alignment explanation
Indices: 97321--97370 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
97311 AAAAATTATT
* *
97321 AATTAAAATATTATTAAATATTT
1 AATTAAAATATTATTAAATAATA
*
97344 AATTAAAATATTTATT-ACTAATA
1 AATTAAAATA-TTATTAAATAATA
97367 AATT
1 AATT
97371 TTATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTAAAATATTATTAAATAATA
Found at i:98618 original size:36 final size:37
Alignment explanation
Indices: 98577--98648 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
98567 GAAAAAAATG
98577 AATGTGA-ATAGATTCTT-TTTAAGCAAACAAAAGAGC
1 AATGTGATATAGATT-TTCTTTAAGCAAACAAAAGAGC
* * *
98613 AATGTGATTTGGGTTTTCTTTAAGCAAACAAAAGAG
1 AATGTGATATAGATTTTCTTTAAGCAAACAAAAGAG
98649 ATAATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 9 0.29
37 22 0.71
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (37 bp):
AATGTGATATAGATTTTCTTTAAGCAAACAAAAGAGC
Found at i:98642 original size:37 final size:37
Alignment explanation
Indices: 98594--98710 Score: 128
Period size: 38 Copynumber: 3.1 Consensus size: 37
98584 ATAGATTCTT
* * *
98594 TTTAAGCAAACAAAAGAGCAATGTGATTTGGGTTTTC
1 TTTAAGCAAACAAAAGAGTAATGTAAATTGGGTTTTC
* * *
98631 TTTAAGCAAACAAAAGAGATAATTTTAACTGGGTTTT-
1 TTTAAGCAAACAAAAGAG-TAATGTAAATTGGGTTTTC
*
98668 TTTAAGCAAAAAAAAAGAGGTAATGTAAATTGGGTTGTTC
1 TTTAAGC-AAACAAAAGA-GTAATGTAAATTGGGTT-TTC
98708 TTT
1 TTT
98711 TTCTCGAGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
37 25 0.38
38 35 0.53
39 3 0.05
40 3 0.05
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (37 bp):
TTTAAGCAAACAAAAGAGTAATGTAAATTGGGTTTTC
Found at i:105690 original size:103 final size:103
Alignment explanation
Indices: 105519--105719 Score: 312
Period size: 103 Copynumber: 2.0 Consensus size: 103
105509 AGACCTAGAT
** * * *
105519 TGAATATTTAAAATTGTCATTTCGATATCCCTAGCTTCAAGCTTGATTTTTTGATCCGATTTCAA
1 TGAATATTTAAAATTACCATTTCGATATACCTAGCTTCAAGCTCGATTTTTGGATCCGATTTCAA
105584 ACCAATCTTCATAAAAAGTCTCCCACTTAAACCTAAAC
66 ACCAATCTTCATAAAAAGTCTCCCACTTAAACCTAAAC
* * *
105622 TGAATATTTAAAATTACCGTTTCGATTTACCTAGCTTCAGGCTCGATTTTTGGATCCGATTTCAA
1 TGAATATTTAAAATTACCATTTCGATATACCTAGCTTCAAGCTCGATTTTTGGATCCGATTTCAA
* *
105687 ACCAATCTTCATAACAAGTCTCCCACTTCAACC
66 ACCAATCTTCATAAAAAGTCTCCCACTTAAACC
105720 AATAAATTAG
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 88 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (103 bp):
TGAATATTTAAAATTACCATTTCGATATACCTAGCTTCAAGCTCGATTTTTGGATCCGATTTCAA
ACCAATCTTCATAAAAAGTCTCCCACTTAAACCTAAAC
Found at i:107537 original size:50 final size:50
Alignment explanation
Indices: 107483--107585 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 50
107473 CTTTTTTTTT
107483 TTTTTTTTTTAAAGTTTACGTGTCTGCTTTTAACAAGTAAAAAAATTAA-A
1 TTTTTTTTTT-AAGTTTACGTGTCTGCTTTTAACAAGTAAAAAAATTAATA
* *
107533 TTTTTTTTTTTAGTTTACGTGTCTGCTTTTAACAAGTAAAGAAATTAATA
1 TTTTTTTTTTAAGTTTACGTGTCTGCTTTTAACAAGTAAAAAAATTAATA
107583 TTT
1 TTT
107586 AATATTTATA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
49 36 0.72
50 14 0.28
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.50
Consensus pattern (50 bp):
TTTTTTTTTTAAGTTTACGTGTCTGCTTTTAACAAGTAAAAAAATTAATA
Found at i:109656 original size:2 final size:2
Alignment explanation
Indices: 109649--109673 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
109639 GATTAATGTA
109649 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
109674 ATTGTGATGG
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:120333 original size:17 final size:17
Alignment explanation
Indices: 120311--120345 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
120301 CCACTCACAC
120311 TTAGATTTCTGCTTCCA
1 TTAGATTTCTGCTTCCA
120328 TTAGATTTCTGCTTCCA
1 TTAGATTTCTGCTTCCA
120345 T
1 T
120346 AATAGTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.11, T:0.49
Consensus pattern (17 bp):
TTAGATTTCTGCTTCCA
Found at i:122157 original size:23 final size:23
Alignment explanation
Indices: 122088--122211 Score: 106
Period size: 23 Copynumber: 5.3 Consensus size: 23
122078 ACACTAGCGC
* *
122088 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
*
122111 GCTCTTTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
* * *
122136 GCTGTCTGATTAGCATTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
** *
122159 GCTCTCTGATTAGTGCTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
122182 ACTCTTTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
122205 GCTCTCT
1 GCTCTCT
122212 ATTGCCCAGC
Statistics
Matches: 79, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
23 61 0.77
25 15 0.19
26 3 0.04
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.46
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:127449 original size:29 final size:29
Alignment explanation
Indices: 127137--127449 Score: 301
Period size: 29 Copynumber: 10.8 Consensus size: 29
127127 TTTCGGAGAA
* * **
127137 TTTAGGATTAATATGTAATTTTATAAAAG
1 TTTAGGGTTAAAATGTAATTTTGGAAAAG
* *
127166 TTTAAGGGTAAAAATGTAATTTAGG-AAAG
1 TTT-AGGGTTAAAATGTAATTTTGGAAAAG
* * * *
127195 TTTAGGGTCAAAATATGATTTTTGAAAAG
1 TTTAGGGTTAAAATGTAATTTTGGAAAAG
* * * * *
127224 TTTGGGGTCAAAGTGTGATTTTGGGAAAG
1 TTTAGGGTTAAAATGTAATTTTGGAAAAG
* *
127253 TTTTGGGTT-AAATGTAAGTTTGGAAAAG
1 TTTAGGGTTAAAATGTAATTTTGGAAAAG
* *
127281 TTTAAAGGTTAAAATGTAATTTTAGAAAAG
1 TTT-AGGGTTAAAATGTAATTTTGGAAAAG
*
127311 TTTAGGGTT-AAATGTAATTTTAGAAAAG
1 TTTAGGGTTAAAATGTAATTTTGGAAAAG
* *
127339 TTTAGGGGTTAAAATGCAATTTTAGAAAAG
1 TTTA-GGGTTAAAATGTAATTTTGGAAAAG
*
127369 TTTAAGGGTTAAAATGCAATTTTGGAAAA-
1 TTT-AGGGTTAAAATGTAATTTTGGAAAAG
* * *
127398 TTTTGAGGTTAAATTGTAATTTTGGAAAGG
1 TTTAG-GGTTAAAATGTAATTTTGGAAAAG
* *
127428 CTTGGGGTTAAAATGTAATTTT
1 TTTAGGGTTAAAATGTAATTTT
127450 TAAATAAAAT
Statistics
Matches: 239, Mismatches: 36, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
28 58 0.24
29 98 0.41
30 82 0.34
31 1 0.00
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.38
Consensus pattern (29 bp):
TTTAGGGTTAAAATGTAATTTTGGAAAAG
Found at i:127464 original size:88 final size:88
Alignment explanation
Indices: 127137--127449 Score: 224
Period size: 88 Copynumber: 3.6 Consensus size: 88
127127 TTTCGGAGAA
* * * * * * * * *
127137 TTTAGGATTAATATGTAATTTTATAAAAGTTTAAGGGTAAAAATGTAA-TTTAGGAAAG-TTTAG
1 TTTAGGGTTAA-ATGTAATTTTAGAAAAGCTTAGGGGTTAAAATGCAATTTTAGAAAAGAATAAG
* *** *
127200 GGTCAAAATATGATTTTTGAAAAG
65 GGTTAAAATGCAATTTTAGAAAAG
* * * * * ** * * * ** *
127224 TTTGGGGTCAAAGTGTGATTTTGGGAAAG-TTTTGGGTT-AAATGTAAGTTTGGAAAAGTTTAAA
1 TTTAGGGTTAAA-TGTAATTTTAGAAAAGCTTAGGGGTTAAAATGCAATTTTAGAAAAGAATAAG
*
127287 GGTTAAAATGTAATTTTAGAAAAG
65 GGTTAAAATGCAATTTTAGAAAAG
* **
127311 TTTAGGGTTAAATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGCAATTTTAGAAAAGTTTAAGG
1 TTTAGGGTTAAATGTAATTTTAGAAAAGCTTAGGGGTTAAAATGCAATTTTAGAAAAGAATAAGG
*
127376 GTTAAAATGCAATTTTGGAAAA-
66 GTTAAAATGCAATTTTAGAAAAG
* * * *
127398 TTTTGAGGTTAAATTGTAATTTTGGAAAGGCTT-GGGGTTAAAATGTAATTTT
1 TTTAG-GGTTAAA-TGTAATTTTAGAAAAGCTTAGGGGTTAAAATGCAATTTT
127450 TAAATAAAAT
Statistics
Matches: 183, Mismatches: 36, Indels: 13
0.79 0.16 0.06
Matches are distributed among these distances:
85 8 0.04
86 28 0.15
87 64 0.35
88 67 0.37
89 16 0.09
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.38
Consensus pattern (88 bp):
TTTAGGGTTAAATGTAATTTTAGAAAAGCTTAGGGGTTAAAATGCAATTTTAGAAAAGAATAAGG
GTTAAAATGCAATTTTAGAAAAG
Found at i:130048 original size:19 final size:19
Alignment explanation
Indices: 130021--130059 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
130011 TTTTATTGGT
*
130021 TATATTTTA-ATATTTCAAA
1 TATAGTTTATATA-TTCAAA
130040 TATAGTTTATATATTCAAA
1 TATAGTTTATATATTCAAA
130059 T
1 T
130060 TAATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (19 bp):
TATAGTTTATATATTCAAA
Found at i:130070 original size:18 final size:20
Alignment explanation
Indices: 130024--130070 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
130014 TATTGGTTAT
*
130024 ATTTTAATATTTCAAATATA
1 ATTTTTATATTTCAAATATA
* *
130044 GTTTATATA-TTCAAAT-TA
1 ATTTTTATATTTCAAATATA
130062 ATTTTTATA
1 ATTTTTATA
130071 AAAAAAACTA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 6 0.27
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTTTATATTTCAAATATA
Found at i:132643 original size:20 final size:20
Alignment explanation
Indices: 132614--132653 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
132604 GATATGCTAA
*
132614 ATTTTTTTTTGAATTTCAAG
1 ATTTTATTTTGAATTTCAAG
**
132634 ATTTTATTTTTTATTTCAAG
1 ATTTTATTTTGAATTTCAAG
132654 TGCACAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (20 bp):
ATTTTATTTTGAATTTCAAG
Found at i:133797 original size:57 final size:56
Alignment explanation
Indices: 133653--133797 Score: 132
Period size: 57 Copynumber: 2.6 Consensus size: 56
133643 AATACGAATA
** * * * *
133653 AAAAATATTTTTTTAGTGTTTGTC-ATCAATGGCTTACACCACTTTTTTCAAATTT
1 AAAAATATTTTTTGGGTGTTTGCCAAACAATGGCCTACACCACTTTTTCCAAATTT
* * * ** *
133708 AAAATTATTTTTTTGGATATTTGCCACCCAATGGCCTACACCA-TCTTTTCCAGATTT
1 AAAAATA-TTTTTTGGGTGTTTGCCAAACAATGGCCTACACCACT-TTTTCCAAATTT
*
133765 AAAAATATTTTTGTGGGTGTTTGGCAAACAATG
1 AAAAATATTTTT-TGGGTGTTTGCCAAACAATG
133798 ATCGACACCC
Statistics
Matches: 69, Mismatches: 17, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
55 6 0.09
56 18 0.26
57 45 0.65
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (56 bp):
AAAAATATTTTTTGGGTGTTTGCCAAACAATGGCCTACACCACTTTTTCCAAATTT
Found at i:134350 original size:59 final size:58
Alignment explanation
Indices: 134288--134546 Score: 175
Period size: 56 Copynumber: 4.4 Consensus size: 58
134278 CATTGGGTGC
* *
134288 CAAACACCCAAAAAATTATTTTTTTATTCGTATTTTTTTGGGTGTCGACCATTGCTTGC
1 CAAACACCCAAAAAAATATTTTTTTATTCGTA-TTTTTTGGGTGTCGACCATTGCTTGA
** * * * ***** * * * **
134347 CAAACATTCAAAAAAATA-TTTTTAAATCTGGAAAAGGT-GATGTAGGCCATTGGGTGA
1 CAAACACCCAAAAAAATATTTTTTTATTC-GTATTTTTTGGGTGTCGACCATTGCTTGA
* *
134404 CAAACACCC-AAAAAATATTTTTTTATTCGTA-TTTTTGGGTGTCAACCATGGCTTGA
1 CAAACACCCAAAAAAATATTTTTTTATTCGTATTTTTTGGGTGTCGACCATTGCTTGA
** * * * * * *
134460 CAAACACAAAAAAAAAAACTAATTTTTTATTCGTATTTTTTTTGGGTGACGGCTATTGATTGG
1 CAAACAC--CCAAAAAAA-TATTTTTTTATTCGTA--TTTTTTGGGTGTCGACCATTGCTTGA
*
134523 CAAACACTCAAAAAAATATTTTTT
1 CAAACACCCAAAAAAATATTTTTT
134547 AATGTAAAAA
Statistics
Matches: 144, Mismatches: 46, Indels: 19
0.69 0.22 0.09
Matches are distributed among these distances:
55 1 0.01
56 29 0.20
57 28 0.19
58 9 0.06
59 23 0.16
60 22 0.15
61 7 0.05
63 25 0.17
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (58 bp):
CAAACACCCAAAAAAATATTTTTTTATTCGTATTTTTTGGGTGTCGACCATTGCTTGA
Found at i:134476 original size:116 final size:115
Alignment explanation
Indices: 134240--134486 Score: 324
Period size: 116 Copynumber: 2.1 Consensus size: 115
134230 CCCAACACTC
*
134240 AAAAAAATATTTTTAAATCTGAGAAAAGTAGTGTTAGCCATTGGGTGCCAAACACCCAAAAAATT
1 AAAAAAATATTTTTAAATCTGAGAAAAGTAGTGTTAGCCATTGGGTGACAAACACCCAAAAAATT
* * * ***
134305 ATTTTTTTATTCGTATTTTTTTGGGTGTCGACCATTGCTTGCCAAACATTC
66 ATTTTTTTATTCGTA-TTTTTTGGGTGTCAACCATGGCTTGCAAAACAAAA
134356 AAAAAAATATTTTTAAATCTG-GAAAAG--GTGATGTAGGCCATTGGGTGACAAACACCCAAAAA
1 AAAAAAATATTTTTAAATCTGAGAAAAGTAGTG-T-TA-GCCATTGGGTGACAAACACCCAAAAA
134418 A-TATTTTTTTATTCGTA-TTTTTGGGTGTCAACCATGGCTTGACAAACACAAAA
63 ATTATTTTTTTATTCGTATTTTTTGGGTGTCAACCATGGCTTG-CAAA-ACAAAA
134471 AAAAAAACTAATTTTT
1 AAAAAAA-T-ATTTTT
134487 TATTCGTATT
Statistics
Matches: 117, Mismatches: 7, Indels: 13
0.85 0.05 0.09
Matches are distributed among these distances:
113 25 0.21
114 4 0.03
115 34 0.29
116 48 0.41
117 6 0.05
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (115 bp):
AAAAAAATATTTTTAAATCTGAGAAAAGTAGTGTTAGCCATTGGGTGACAAACACCCAAAAAATT
ATTTTTTTATTCGTATTTTTTGGGTGTCAACCATGGCTTGCAAAACAAAA
Found at i:136859 original size:19 final size:21
Alignment explanation
Indices: 136835--136879 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
136825 CCCACTCATA
*
136835 TTATT-ATTTTTAAT-TATAT
1 TTATTAATTTTTAATATATAG
*
136854 TTATTAATTTTTTATATATAG
1 TTATTAATTTTTAATATATAG
136875 TTATT
1 TTATT
136880 TTAACAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 8 0.36
21 9 0.41
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATTAATTTTTAATATATAG
Found at i:137919 original size:31 final size:28
Alignment explanation
Indices: 137830--137929 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 28
137820 TCAAAATTTT
* * *
137830 ATGTATAATTTGAACCACGATCAAAGTTC
1 ATGTATAAATTGAACTA-AATCAAAGTTC
*
137859 ATGTATATAATTGAACTAAATTAAAGTTC
1 ATGTATA-AATTGAACTAAATCAAAGTTC
*
137888 ATGTATCAAATT-ATACATTTAATCAAAGTTC
1 ATGTAT-AAATTGA-AC--TAAATCAAAGTTC
137919 ATGTATAAATT
1 ATGTATAAATT
137930 TATGATTTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.02
29 28 0.47
30 14 0.23
31 17 0.28
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (28 bp):
ATGTATAAATTGAACTAAATCAAAGTTC
Found at i:138204 original size:20 final size:22
Alignment explanation
Indices: 138172--138220 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
138162 CAAAAATCCT
138172 GGTTCAA-TCGATT-TTTACTC
1 GGTTCAACTCGATTGTTTACTC
* *
138192 GGTTCAACT-GATTGTTTAGTT
1 GGTTCAACTCGATTGTTTACTC
138213 GGTTCAAC
1 GGTTCAAC
138221 CAATTCATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (22 bp):
GGTTCAACTCGATTGTTTACTC
Found at i:145464 original size:25 final size:25
Alignment explanation
Indices: 145387--145465 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 25
145377 ACAATATAGG
145387 AAAAAGGAAAGGCTCAAATGCGTACA
1 AAAAAGG-AAGGCTCAAATGCGTACA
* *
145413 AAAATA--AA-GCTC-AGTTC-TACTAAA
1 AAAA-AGGAAGGCTCAAATGCGTAC---A
145437 AAAAAGGAAGGCTCAAATGCGTACA
1 AAAAAGGAAGGCTCAAATGCGTACA
145462 AAAA
1 AAAA
145466 TAAAGCTCAG
Statistics
Matches: 40, Mismatches: 4, Indels: 19
0.63 0.06 0.30
Matches are distributed among these distances:
21 3 0.08
22 3 0.08
23 5 0.12
24 7 0.17
25 7 0.17
26 8 0.20
27 4 0.10
28 3 0.08
ACGTcount: A:0.52, C:0.15, G:0.18, T:0.15
Consensus pattern (25 bp):
AAAAAGGAAGGCTCAAATGCGTACA
Found at i:145482 original size:22 final size:22
Alignment explanation
Indices: 145405--145498 Score: 100
Period size: 22 Copynumber: 4.0 Consensus size: 22
145395 AAGGCTCAAA
145405 TGCGTACAAAAATAAAGCTCAG
1 TGCGTACAAAAATAAAGCTCAG
* * *
145427 TTC-TACTAAAAAAAAGGAAGGCTCAAA
1 TGCGTAC--AAAAATA--AA-GCTC-AG
145454 TGCGTACAAAAATAAAGCTCAG
1 TGCGTACAAAAATAAAGCTCAG
145476 TGCGTACAAAAATAAAGCTCAG
1 TGCGTACAAAAATAAAGCTCAG
145498 T
1 T
145499 TCTACTAACG
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
21 3 0.05
22 26 0.44
23 10 0.17
24 2 0.03
25 2 0.03
26 10 0.17
27 3 0.05
28 3 0.05
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (22 bp):
TGCGTACAAAAATAAAGCTCAG
Found at i:145487 original size:49 final size:50
Alignment explanation
Indices: 145387--145492 Score: 171
Period size: 49 Copynumber: 2.1 Consensus size: 50
145377 ACAATATAGG
*
145387 AAAAAGGAAAGGCTCAAATGCGTACAAAAATAAAGCTCAGTTCTACTAAA
1 AAAAAGGAAAGGCTCAAATGCGTACAAAAATAAAGCTCAGTGCTACTAAA
145437 AAAAAGG-AAGGCTCAAATGCGTACAAAAATAAAGCTCAGTGCGTAC-AAA
1 AAAAAGGAAAGGCTCAAATGCGTACAAAAATAAAGCTCAGTGC-TACTAAA
145486 AATAAAG
1 AA-AAAG
145493 CTCAGTTCTA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
49 39 0.74
50 14 0.26
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.16
Consensus pattern (50 bp):
AAAAAGGAAAGGCTCAAATGCGTACAAAAATAAAGCTCAGTGCTACTAAA
Found at i:147798 original size:12 final size:12
Alignment explanation
Indices: 147783--147829 Score: 62
Period size: 11 Copynumber: 4.0 Consensus size: 12
147773 TTTAATTTAT
147783 TTTAAATTTAAA
1 TTTAAATTTAAA
147795 TTT-AATTTAAA
1 TTTAAATTTAAA
147806 TTTAAATTT-AA
1 TTTAAATTTAAA
*
147817 TTTCAAAATTAAA
1 TTT-AAATTTAAA
147830 AGTCCAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
11 16 0.52
12 13 0.42
13 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:147798 original size:17 final size:17
Alignment explanation
Indices: 147776--147829 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
147766 CCCCTTTTTT
147776 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
147793 AATTTAATTTAAATTTA
1 AATTTATTTTAAATTTA
* *
147810 AATTTAATTTCAAAATTA
1 AATTT-ATTTTAAATTTA
147828 AA
1 AA
147830 AGTCCAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 21 0.66
18 11 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:147830 original size:6 final size:6
Alignment explanation
Indices: 147783--147829 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
147773 TTTAATTTAT
*
147783 TTTAAA TTTAAA TTT-AA TTTAAA TTTAAA TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
147830 AGTCCAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 10 0.27
6 23 0.62
7 4 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:147857 original size:14 final size:15
Alignment explanation
Indices: 147820--147858 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
147810 AATTTAATTT
147820 CAAAATTA-AAAGTC
1 CAAAATTACAAAGTC
*
147834 CAAAAATACAAAGTC
1 CAAAATTACAAAGTC
147849 C-AAATTACAA
1 CAAAATTACAA
147859 TCTTGGGCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.59, C:0.18, G:0.05, T:0.18
Consensus pattern (15 bp):
CAAAATTACAAAGTC
Found at i:148567 original size:10 final size:9
Alignment explanation
Indices: 148499--148573 Score: 51
Period size: 9 Copynumber: 7.8 Consensus size: 9
148489 AAATGTTTTA
148499 AATAGATATT
1 AATA-ATATT
**
148509 AATAATGCT
1 AATAATATT
*
148518 AATAATAAT
1 AATAATATT
* *
148527 AACAATAAT
1 AATAATATT
148536 AATGAATTTATT
1 AAT-AA--TATT
*
148548 AATGATATT
1 AATAATATT
148557 AAATAATATT
1 -AATAATATT
148567 AATAATA
1 AATAATA
148574 AATTATTAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
9 31 0.60
10 14 0.27
11 1 0.02
12 6 0.12
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (9 bp):
AATAATATT
Found at i:149586 original size:29 final size:29
Alignment explanation
Indices: 149544--149852 Score: 245
Period size: 29 Copynumber: 10.5 Consensus size: 29
149534 CTAAATTTTT
*
149544 CAAAAATTTCATTTTTACCCCCGAACTTC
1 CAAAAATTCCATTTTTACCCCCGAACTTC
* *
149573 CAAAAATTCCATTTTTAACCCCCAAACCTC
1 CAAAAATTCCATTTTT-ACCCCCGAACTTC
*
149603 CAAAAATTCCATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCCCGAACTTC
* *
149632 CAAAAATTCCATTTTTGA-TCCCGAAAGTTC
1 CAAAAATTCCATTTTT-ACCCCCG-AACTTC
* * *
149662 CAAAAATTCCATTTTAACCCTCAAACTTC
1 CAAAAATTCCATTTTTACCCCCGAACTTC
* * * * **
149691 CAAAGATGCCATTTTGACCTCTAAACTTC
1 CAAAAATTCCATTTTTACCCCCGAACTTC
* *
149720 CAAAAATTCCATTTTTACCCTCGAACCTC
1 CAAAAATTCCATTTTTACCCCCGAACTTC
* * *
149749 C-AAAATCTCTATTTTCGA-CCTCGAAAC-TC
1 CAAAAAT-TCCATTTT-TACCCCCG-AACTTC
*
149778 TC-AAAATTACCA-TTTTACCCTCGAA-TATC
1 -CAAAAATT-CCATTTTTACCCCCGAACT-TC
* *
149807 TAAAAATTCCATTTTTATCCCCGAACTTTC
1 CAAAAATTCCATTTTTACCCCCGAAC-TTC
**
149837 TTAAAATTACCATTTT
1 CAAAAATT-CCATTTT
149853 GCCCCGAGAA
Statistics
Matches: 227, Mismatches: 36, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
28 11 0.05
29 137 0.60
30 71 0.31
31 8 0.04
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCCGAACTTC
Found at i:149693 original size:88 final size:85
Alignment explanation
Indices: 149544--149852 Score: 297
Period size: 88 Copynumber: 3.5 Consensus size: 85
149534 CTAAATTTTT
* *
149544 CAAAAATTTCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCCCCAAACCTCCAAAAA
1 CAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATTCCA-TTTTAACCCTCAAA-CTCCAAAAA
149609 TTCCATTTTTACCCTCGAACTTC
63 TTCCATTTTTACCCTCGAACTTC
* * *
149632 CAAAAATTCCATTTTTGATCCCGAAAGTTCCAAAAATTCCATTTTAACCCTCAAACTTCCAAAGA
1 CAAAAATTCCATTTTT-ACCCCG-AACTTCCAAAAATTCCATTTTAACCCTCAAAC-TCCAAAAA
* * *
149697 TGCCATTTTGA-CCTCTAAACTTC
63 TTCCATTTTTACCCTC-GAACTTC
* * *
149720 CAAAAATTCCATTTTTACCCTCGAACCTCC-AAAATCTCTATTTTCGA-CCTCGAAACTCTC-AA
1 CAAAAATTCCATTTTTACCC-CGAACTTCCAAAAAT-TCCATTTT-AACCCTC-AAACTC-CAAA
149782 AATTACCA-TTTTACCCTCGAA-TATC
61 AATT-CCATTTTTACCCTCGAACT-TC
* **
149807 TAAAAATTCCATTTTTATCCCCGAACTTTCTTAAAATTACCATTTT
1 CAAAAATTCCATTTTTA-CCCCGAAC-TTCCAAAAATT-CCATTTT
149853 GCCCCGAGAA
Statistics
Matches: 184, Mismatches: 21, Indels: 31
0.78 0.09 0.13
Matches are distributed among these distances:
86 6 0.03
87 59 0.32
88 91 0.49
89 28 0.15
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (85 bp):
CAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTAACCCTCAAACTCCAAAAATTC
CATTTTTACCCTCGAACTTC
Found at i:149821 original size:58 final size:59
Alignment explanation
Indices: 149544--149822 Score: 320
Period size: 59 Copynumber: 4.8 Consensus size: 59
149534 CTAAATTTTT
* * * * * *
149544 CAAAAATTTCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCCCCAAACCTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC
*
149603 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGATCC-CGAAAGTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA-CCTCGAAACTTC
* * * * *
149662 CAAAAATTCCATTTTAACCCTCAAACTTCCAAAGATGCCA-TTTTGACCTCTAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC
* * *
149720 CAAAAATTCCATTTTTACCCTCGAACCTCC-AAAATCTCTATTTTCGACCTCGAAAC-TC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAAT-TCCATTTTTGACCTCGAAACTTC
*
149778 TC-AAAATTACCA-TTTTACCCTCGAA-TATCTAAAAATTCCATTTTT
1 -CAAAAATT-CCATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTT
149823 ATCCCCGAAC
Statistics
Matches: 188, Mismatches: 24, Indels: 17
0.82 0.10 0.07
Matches are distributed among these distances:
57 6 0.03
58 72 0.38
59 108 0.57
60 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (59 bp):
CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC
Found at i:161923 original size:86 final size:86
Alignment explanation
Indices: 161820--162021 Score: 359
Period size: 86 Copynumber: 2.3 Consensus size: 86
161810 TGGTTAGCTC
*
161820 CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGA
1 CCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGA
161885 AACAAACGACGCGGTCATCTT
66 AACAAACGACGCGGTCATCTT
*
161906 CCTGATGAGATATTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGA
1 CCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGA
*
161971 AACAAATGACGCGGTCATCTT
66 AACAAACGACGCGGTCATCTT
* *
161992 CCTGATGAGATACTGAGAAGAAGTCCAAAT
1 CCTGATGAGATACTGAGAAGTAGACCAAAT
162022 CAAACCCACG
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 110 1.00
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (86 bp):
CCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGA
AACAAACGACGCGGTCATCTT
Found at i:161925 original size:49 final size:48
Alignment explanation
Indices: 161853--162011 Score: 142
Period size: 49 Copynumber: 3.5 Consensus size: 48
161843 ACCAAATTCG
*
161853 TCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAACGACGCGGTCA
1 TCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAA-GACGCGGTCA
** * * * *
161902 TCTTCCTGATGAGATATTGAGAA---G--T-AGACCAA-A----TTCG
1 TCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAAGACGCGGTCA
*
161939 TCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAATGACGCGGTCA
1 TCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAA-GACGCGGTCA
*
161988 TCTTCCTGATGAGATACTGAGAAG
1 TCTTCCTGATGAGATACAGAGAAG
162012 AAGTCCAAAT
Statistics
Matches: 82, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
37 22 0.27
40 1 0.01
41 1 0.01
42 1 0.01
43 10 0.12
44 1 0.01
45 1 0.01
46 1 0.01
49 44 0.54
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.23
Consensus pattern (48 bp):
TCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAAGACGCGGTCA
Found at i:162217 original size:292 final size:294
Alignment explanation
Indices: 161687--162217 Score: 827
Period size: 292 Copynumber: 1.8 Consensus size: 294
161677 AACAATGATA
* * *
161687 CGGTCATCTTCCTGATGAGATACTGAGAAGTAAACCAAATCAATGAAACGAGGCTCGATGTGAGC
1 CGGTCATCTTCCTGATGAGATACTGAGAAGTAAACCAAATCAA-GAAACCACGCTCAATGTGAGC
* * * * *
161752 AAATCTTCGAACTCCAGCCTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAG
65 AAATCTTCGAACCCCAGCCTCCTGATGAGACACCGAGAAGCAGGTCGAAGAAATAAAATGGTTAA
* * * * *
161817 CTCCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGAT
130 CTCCCTGATGAGATACTGAGAAGTGAACAAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAC
* * *
161882 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATATTGAGAAGTAGACCAAATTCGTCTTCCTG
195 TGAAACAAACGACGCAGTCATCTTCCTGATAAGATACTGAGAAGTAGACCAAATTCGTCTTCCTG
161947 ATGAGGTACAGAGAAGCGGATTGAAACAAATGACG
260 ATGAGGTACAGAGAAGCGGATTGAAACAAATGACG
* *
161982 CGGTCATCTTCCTGATGAGATACTGAGAAG-AAGTCCAAATC-A-AACCCACGCTCAATGTGAGC
1 CGGTCATCTTCCTGATGAGATACTGAGAAGTAA-ACCAAATCAAGAAACCACGCTCAATGTGAGC
*
162044 AAATCTTCGAACCCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGAAATAAAA-GGTTA
65 AAATCTTCGAA-CCCCAGCCTCCTGATGAGACACCGAGAAGCAGGTCGAAGAAATAAAATGGTTA
*
162108 ACTTCCTGATGAGATACTGAGAAGTGAACAAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
129 ACTCCCTGATGAGATACTGAGAAGTGAACAAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
162173 CTGAAACAAACGACGCAGTCATCTTCCTGATAAGATACTGAGAAG
194 CTGAAACAAACGACGCAGTCATCTTCCTGATAAGATACTGAGAAG
162218 AAGGCCAAGT
Statistics
Matches: 214, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
292 132 0.62
293 42 0.20
294 3 0.01
295 37 0.17
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (294 bp):
CGGTCATCTTCCTGATGAGATACTGAGAAGTAAACCAAATCAAGAAACCACGCTCAATGTGAGCA
AATCTTCGAACCCCAGCCTCCTGATGAGACACCGAGAAGCAGGTCGAAGAAATAAAATGGTTAAC
TCCCTGATGAGATACTGAGAAGTGAACAAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAACT
GAAACAAACGACGCAGTCATCTTCCTGATAAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGA
TGAGGTACAGAGAAGCGGATTGAAACAAATGACG
Found at i:162563 original size:11 final size:11
Alignment explanation
Indices: 162546--162598 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
162536 GGGCCCCTTT
*
162546 TTTAATTT-AT
1 TTTAATTTAAA
*
162556 TTTAAATTTAGA
1 TTT-AATTTAAA
*
162568 TTTATTTTAAA
1 TTTAATTTAAA
162579 TTTAAATTTAAA
1 TTT-AATTTAAA
162591 TTTAATTT
1 TTTAATTT
162599 CAAAATTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
10 3 0.09
11 19 0.54
12 13 0.37
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:162572 original size:17 final size:16
Alignment explanation
Indices: 162546--162598 Score: 69
Period size: 17 Copynumber: 3.5 Consensus size: 16
162536 GGGCCCCTTT
162546 TTTAATTTATTTTAAA
1 TTTAATTTATTTTAAA
162562 TTTAGATTTATTTTAAA
1 TTTA-ATTTATTTTAAA
162579 TTTAA---A-TTTAAA
1 TTTAATTTATTTTAAA
162591 TTTAATTT
1 TTTAATTT
162599 CAAAATTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 11 0.33
13 1 0.03
16 5 0.15
17 16 0.48
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTAATTTATTTTAAA
Found at i:162609 original size:6 final size:6
Alignment explanation
Indices: 162556--162608 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
162546 TTTAATTTAT
* *
162556 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA TTTAAA TTT-AA TTTCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
*
162603 ATTAAA
1 TTTAAA
162609 AGTCCAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
5 8 0.21
6 27 0.69
7 4 0.10
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:163337 original size:33 final size:33
Alignment explanation
Indices: 163300--163364 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
163290 AATAATGCTA
*
163300 ATAAT-AATAACAATAATAATGAATTTATTAATG
1 ATAATAAATAACAATAATAAT-AAATTATTAATG
* *
163333 ATAATAAATAATATTAATAATAAATTATTAAT
1 ATAATAAATAACAATAATAATAAATTATTAAT
163365 AAAAAAAACG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 15 0.54
34 13 0.46
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (33 bp):
ATAATAAATAACAATAATAATAAATTATTAATG
Found at i:163354 original size:16 final size:14
Alignment explanation
Indices: 163333--163366 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
163323 TTTATTAATG
163333 ATAATAAATAATATTA
1 ATAATAAAT--TATTA
163349 ATAATAAATTATTA
1 ATAATAAATTATTA
163363 ATAA
1 ATAA
163367 AAAAAACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
16 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATAAATTATTA
Found at i:164401 original size:29 final size:29
Alignment explanation
Indices: 164359--164635 Score: 226
Period size: 29 Copynumber: 9.6 Consensus size: 29
164349 TAAACTATCC
164359 AAAAATTCCATTTTTACCCCCGAACTTCT
1 AAAAATTCCATTTTTACCCCCGAACTTCT
* **
164388 AAAAATTCCATTTTAACCCCAAAACTTCCT
1 AAAAATTCCATTTTTACCCCCGAACTT-CT
164418 -AAAATTCCATTTTTACCCCCGAACTTCT
1 AAAAATTCCATTTTTACCCCCGAACTTCT
* ** * *
164446 AAAAATTCCATTTTGA-CATCGAAACCTCC
1 AAAAATTCCATTTTTACCCCCG-AACTTCT
** *
164475 AAAAATTCCATTTTTAACCCCAAAACCTC-
1 AAAAATTCCATTTTT-ACCCCCGAACTTCT
* **
164504 CAAAATTCCATTTTTACCCTTGAACTTCT
1 AAAAATTCCATTTTTACCCCCGAACTTCT
* *
164533 AAAAATTCCATTTTTACCCTCGAACCTC-
1 AAAAATTCCATTTTTACCCCCGAACTTCT
* * * * *
164561 CAAAATCTCCATTTTCGA-CCTCTAAATTCT
1 AAAAAT-TCCATTTT-TACCCCCGAACTTCT
* *
164591 TAAAATTACC-CTTTTACCCCCGAA-TGTCT
1 AAAAATT-CCATTTTTACCCCCGAACT-TCT
*
164620 AAAAATTTCATTTTTA
1 AAAAATTCCATTTTTA
164636 ACCTTTAACT
Statistics
Matches: 198, Mismatches: 37, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
28 22 0.11
29 158 0.80
30 17 0.09
31 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCCCGAACTTCT
Found at i:164450 original size:58 final size:58
Alignment explanation
Indices: 164346--164668 Score: 266
Period size: 58 Copynumber: 5.5 Consensus size: 58
164336 TCTTGAAGGT
*
164346 CCCTAAACTATCCAAAAATTCCATTTTTACCCCCGAACTTCTAAAAATTCCATTTTAAC
1 CCCTAAACT-TCCTAAAATTCCATTTTTACCCCCGAACTTCTAAAAATTCCATTTTAAC
* *
164405 CCCAAAACTTCCTAAAATTCCATTTTTACCCCCGAACTTCTAAAAATTCCATTTTGAC
1 CCCTAAACTTCCTAAAATTCCATTTTTACCCCCGAACTTCTAAAAATTCCATTTTAAC
** * * * ** * * *
164463 ATCGAAACCTCCAAAAATTCCATTTTTAACCCCAAAACCTC-CAAAATTCCATTTTTAC
1 CCCTAAACTTCCTAAAATTCCATTTTT-ACCCCCGAACTTCTAAAAATTCCATTTTAAC
* * * * * *
164521 CCTTGAACTT-CTAAAAATTCCATTTTTACCCTCGAACCTC-CAAAATCTCCATTTTCGAC
1 CCCTAAACTTCCT-AAAATTCCATTTTTACCCCCGAACTTCTAAAAAT-TCCATTTT-AAC
* * * *
164580 CTCTAAA-TTCTTAAAATTACC-CTTTTACCCCCGAA-TGTCTAAAAATTTCATTTTTAA-
1 CCCTAAACTTCCTAAAATT-CCATTTTTACCCCCGAACT-TCTAAAAATTCCA-TTTTAAC
* * *
164637 CCTTTAACTTTCCCAAAATTACCA-TTTTACCC
1 CCCTAAAC-TTCCTAAAATT-CCATTTTTACCC
164669 TGAGAATAAA
Statistics
Matches: 213, Mismatches: 39, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
57 21 0.10
58 136 0.64
59 56 0.26
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (58 bp):
CCCTAAACTTCCTAAAATTCCATTTTTACCCCCGAACTTCTAAAAATTCCATTTTAAC
Found at i:164509 original size:87 final size:88
Alignment explanation
Indices: 164359--164633 Score: 303
Period size: 87 Copynumber: 3.2 Consensus size: 88
164349 TAAACTATCC
* ** * * *
164359 AAAAATTCCATTTTTACCCCCGAACTTCTAAAAATTCCA-TTTTAACCCCAAAACTTCCTAAAAT
1 AAAAATTCCATTTTGACCATCGAACCTCCAAAAATTCCATTTTTAACCCCAAAACCTCCTAAAAT
164423 TCCATTTTTACCCCCGAACTTCT
66 TCCATTTTTACCCCCGAACTTCT
164446 AAAAATTCCATTTTGA-CATCGAAACCTCCAAAAATTCCATTTTTAACCCCAAAACCTCC-AAAA
1 AAAAATTCCATTTTGACCATCG-AACCTCCAAAAATTCCATTTTTAACCCCAAAACCTCCTAAAA
**
164509 TTCCATTTTTACCCTTGAACTTCT
65 TTCCATTTTTACCCCCGAACTTCT
* * ** * * * *
164533 AAAAATTCCATTTTTACCCTCGAACCTCC-AAAATCTCCATTTTCGACCTCTAAA-TTCTTAAAA
1 AAAAATTCCATTTTGACCATCGAACCTCCAAAAAT-TCCATTTTTAACCCCAAAACCTCCTAAAA
*
164596 TTACC-CTTTTACCCCCGAA-TGTCT
65 TT-CCATTTTTACCCCCGAACT-TCT
*
164620 AAAAATTTCATTTT
1 AAAAATTCCATTTT
164634 TAACCTTTAA
Statistics
Matches: 161, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
86 11 0.07
87 126 0.78
88 24 0.15
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.34
Consensus pattern (88 bp):
AAAAATTCCATTTTGACCATCGAACCTCCAAAAATTCCATTTTTAACCCCAAAACCTCCTAAAAT
TCCATTTTTACCCCCGAACTTCT
Found at i:166735 original size:42 final size:42
Alignment explanation
Indices: 166688--166770 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
166678 ACCTATTTCG
*
166688 TTGGAACTTTATTCTATTCCAACCAACAAAACGTAATGTCTA
1 TTGGAACTTTATTCTATTCCAACCAACAAAACCTAATGTCTA
166730 TTGGAACTTTATTCTATTCCAACCAACAAAACCTAATGTCT
1 TTGGAACTTTATTCTATTCCAACCAACAAAACCTAATGTCT
166771 GTGGTGCTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (42 bp):
TTGGAACTTTATTCTATTCCAACCAACAAAACCTAATGTCTA
Found at i:167566 original size:90 final size:90
Alignment explanation
Indices: 167407--167593 Score: 227
Period size: 90 Copynumber: 2.1 Consensus size: 90
167397 TATAAAATGT
* * * * * ** * *
167407 CCTCAAATTTTTTCAAAAAAGCAATTAAGTCCTTCCTTTTTTTTGCACTCAATTGAGCACTTGAG
1 CCTCAAACTTCTTCAAAAAAGCAATTAAGCCCCTACTTTTTTTCCCACTCAATTGAGCACTTAAA
*
167472 CTTTCAAAATGCAT-AAAAAAAG-C
66 CTTTCAAAATACATAAAAAAAAGAC
*
167495 CCTCAAACTTCTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTCCCCACTCAATTG-GATACTT
1 CCTCAAACTTCTTC-AAAAAAGCAATTAAGCCCCTACTTTTTTT-CCCACTCAATTGAG-CACTT
167559 AAACTTTCAAAATACATAAAAAAAAGAC
63 AAACTTTCAAAATACATAAAAAAAAGAC
167587 CCTCAAA
1 CCTCAAA
167594 ATTAAAAAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
88 12 0.14
89 27 0.33
90 28 0.34
91 8 0.10
92 8 0.10
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (90 bp):
CCTCAAACTTCTTCAAAAAAGCAATTAAGCCCCTACTTTTTTTCCCACTCAATTGAGCACTTAAA
CTTTCAAAATACATAAAAAAAAGAC
Found at i:167602 original size:89 final size:87
Alignment explanation
Indices: 167421--167604 Score: 201
Period size: 89 Copynumber: 2.1 Consensus size: 87
167411 AAATTTTTTC
* * * ** * * *
167421 AAAAAAGCAATTAAGTCCTTCCTTTTTTTTGCACTCAATTGAGCACTTGAGCTTTCAAAATGCAT
1 AAAAAAGCAATTAAGCCCCTACTTTTTTTCCCACTCAATTGAGCACTTAAACTTTCAAAATACAT
* *
167486 AAAAAAAGCCCTCAAACTTCTTCA
66 AAAAAAAGCCCTCAAA--TATTAA
*
167510 AAAAAAGCAATTAAGCCCCTACTTTTTTTCCCCACTCAATTG-GATACTTAAACTTTCAAAATAC
1 AAAAAAGCAATTAAGCCCCTACTTTTTTT-CCCACTCAATTGAG-CACTTAAACTTTCAAAATAC
167574 ATAAAAAAAAGACCCTCAAA-ATTAA
64 AT-AAAAAAAG-CCCTCAAATATTAA
167599 AAAAAA
1 AAAAAA
167605 AATAAAAAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
89 36 0.45
90 28 0.35
91 8 0.10
92 8 0.10
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (87 bp):
AAAAAAGCAATTAAGCCCCTACTTTTTTTCCCACTCAATTGAGCACTTAAACTTTCAAAATACAT
AAAAAAAGCCCTCAAATATTAA
Found at i:167718 original size:65 final size:65
Alignment explanation
Indices: 167649--167770 Score: 149
Period size: 65 Copynumber: 1.9 Consensus size: 65
167639 TAGAAAAAAG
*** * *
167649 TTATAAAAAAAATAAATTTTAGAAAAATTATTAATTTTTAATA-AAAT-ATAAAAAATTCAAATT
1 TTATAAAAAAAATAAAAAATA-AAAAATTATAAAATTTT-ATAGAAATCATAAAAAATTCAAATT
167712 TT
64 TT
* *
167714 TTATAAAAATAGTAAAAAATAAAAAATTATAAAATTTTATAGAAATCATAAAAAATT
1 TTATAAAAAAAATAAAAAATAAAAAATTATAAAATTTTATAGAAATCATAAAAAATT
167771 ATAAAATGCA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
63 3 0.06
64 19 0.40
65 26 0.54
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (65 bp):
TTATAAAAAAAATAAAAAATAAAAAATTATAAAATTTTATAGAAATCATAAAAAATTCAAATTTT
Found at i:167752 original size:36 final size:36
Alignment explanation
Indices: 167689--167769 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 36
167679 TTAATTTTTA
* **
167689 ATAAAATATAAAAAATTCAAATTTTTTATAAAAAT-
1 ATAAAAAATAAAAAATTCAAAAATTTTATAAAAATC
*
167724 AGTAAAAAATAAAAAATT-ATAAAATTTTATAGAAATC
1 A-TAAAAAATAAAAAATTCA-AAAATTTTATAAAAATC
167761 ATAAAAAAT
1 ATAAAAAAT
167770 TATAAAATGC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
35 2 0.05
36 36 0.92
37 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (36 bp):
ATAAAAAATAAAAAATTCAAAAATTTTATAAAAATC
Found at i:168087 original size:20 final size:20
Alignment explanation
Indices: 168045--168092 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
168035 TTACAATTTT
* **
168045 TTTTATATATTTTTCTTCTAA
1 TTTTA-ATATTTTTATTAAAA
168066 TTTTAATATTTTTATTAAAA
1 TTTTAATATTTTTATTAAAA
168086 -TTTAATA
1 TTTTAATA
168093 ACATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.29
20 12 0.50
21 5 0.21
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTAATATTTTTATTAAAA
Found at i:171061 original size:2 final size:2
Alignment explanation
Indices: 171054--171083 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
171044 TCGAAAAAGT
171054 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
171084 AAGTTAGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:182248 original size:44 final size:45
Alignment explanation
Indices: 182197--182285 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 45
182187 GATGATGATG
* *
182197 AAGGGAGAATTGAAAGCAAATTA-AAGAAAAAAAAAAAAAAAAAA
1 AAGGGAGAATGGAAAGCAAACTATAAGAAAAAAAAAAAAAAAAAA
* * * * *
182241 AAGGGAGACTGGAAAGGAAACTATTAGAAAGAAAATAAAAAAAAA
1 AAGGGAGAATGGAAAGCAAACTATAAGAAAAAAAAAAAAAAAAAA
182286 TTCAAATCCA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 19 0.51
45 18 0.49
ACGTcount: A:0.67, C:0.03, G:0.19, T:0.10
Consensus pattern (45 bp):
AAGGGAGAATGGAAAGCAAACTATAAGAAAAAAAAAAAAAAAAAA
Found at i:186384 original size:6 final size:6
Alignment explanation
Indices: 186369--186399 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
186359 GGTGGGTGGG
*
186369 GGGAGT GGGAGA GGGAGA GGGAGA GGGAGA G
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA G
186400 AGAAGGGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.68, T:0.03
Consensus pattern (6 bp):
GGGAGA
Found at i:190094 original size:19 final size:19
Alignment explanation
Indices: 190070--190107 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
190060 TGCGCTGAGA
190070 ATGTATTATTATATGCAGT
1 ATGTATTATTATATGCAGT
190089 ATGTATTATTATATGCAGT
1 ATGTATTATTATATGCAGT
190108 TTTGGTGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (19 bp):
ATGTATTATTATATGCAGT
Found at i:203867 original size:2 final size:2
Alignment explanation
Indices: 203860--203892 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
203850 AATTGTTCTT
203860 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
203893 TTGAAAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:207816 original size:36 final size:36
Alignment explanation
Indices: 207721--207800 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
207711 AAGAATGTTG
* * *
207721 AATGTCCAGCTATTTCATCATCTCTGATGGCTCTTA
1 AATGTCTAGCAATTTCATCATCTCTGATGGCCCTTA
* * *
207757 AATGTCTAGCAATCTCATCATCTCTGTTGGCCCTTG
1 AATGTCTAGCAATTTCATCATCTCTGATGGCCCTTA
207793 AATGTCTA
1 AATGTCTA
207801 CTTGTTTCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (36 bp):
AATGTCTAGCAATTTCATCATCTCTGATGGCCCTTA
Found at i:210400 original size:18 final size:18
Alignment explanation
Indices: 210354--210407 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
210344 ACTTTAATTT
*
210354 TAATTATTATTTTTTCAA
1 TAATAATTATTTTTTCAA
* *
210372 TATATATTTATTTTTTCGA
1 TA-ATAATTATTTTTTCAA
*
210391 TAATAATTATTTCTTCA
1 TAATAATTATTTTTTCA
210408 CATTTTCACA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.59
Consensus pattern (18 bp):
TAATAATTATTTTTTCAA
Done.