Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 14 of 25
Found at i:1966271 original size:26 final size:27
Alignment explanation
Indices: 1966241--1966292 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1966231 TTTTCTTTCC
* *
1966241 TCTTTCT-TTTCCTATGTTTCTCTTTA
1 TCTTTCTATTCCCTATATTTCTCTTTA
*
1966267 TCTTTCTATTCCCTTTATTTCTCTTT
1 TCTTTCTATTCCCTATATTTCTCTTT
1966293 TTTTTTCTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.08, C:0.25, G:0.02, T:0.65
Consensus pattern (27 bp):
TCTTTCTATTCCCTATATTTCTCTTTA
Found at i:1967842 original size:8 final size:8
Alignment explanation
Indices: 1967829--1967862 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1967819 GCTTAATAAA
1967829 AAATTATT
1 AAATTATT
1967837 AAATTATT
1 AAATTATT
1967845 AAA-TATT
1 AAATTATT
*
1967852 AAATTTTT
1 AAATTATT
1967860 AAA
1 AAA
1967863 AATGATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
AAATTATT
Found at i:1967853 original size:15 final size:15
Alignment explanation
Indices: 1967833--1967862 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1967823 AATAAAAAAT
1967833 TATTAAATTATTAAA
1 TATTAAATTATTAAA
*
1967848 TATTAAATTTTTAAA
1 TATTAAATTATTAAA
1967863 AATGATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAAATTATTAAA
Found at i:1968909 original size:2 final size:2
Alignment explanation
Indices: 1968904--1968949 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
1968894 AAAATTTGAA
* * *
1968904 AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1968946 AT AT
1 AT AT
1968950 CTTCTGAAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1970048 original size:14 final size:14
Alignment explanation
Indices: 1970026--1970058 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1970016 TAAAATACAA
*
1970026 GATAACTATTTTAT
1 GATATCTATTTTAT
1970040 GATATCTATTTTAT
1 GATATCTATTTTAT
1970054 GATAT
1 GATAT
1970059 GATTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (14 bp):
GATATCTATTTTAT
Found at i:1971978 original size:16 final size:16
Alignment explanation
Indices: 1971928--1971981 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
1971918 TGTTTTAAAT
*
1971928 TTTTAAATTTAGATAA
1 TTTTAAATTTAAATAA
* * *
1971944 TTTTGATTTTGAATAA
1 TTTTAAATTTAAATAA
*
1971960 TTTTAAATTTAAATCA
1 TTTTAAATTTAAATAA
1971976 TTTTAA
1 TTTTAA
1971982 GTTTTGATCA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.54
Consensus pattern (16 bp):
TTTTAAATTTAAATAA
Found at i:1972022 original size:5 final size:5
Alignment explanation
Indices: 1972012--1972078 Score: 55
Period size: 5 Copynumber: 13.0 Consensus size: 5
1972002 ATATTTAAAA
* * *
1972012 TAATT TAATT TAATT TAATC AAATT TAATAT TCAAAT TAA-T TAATTT
1 TAATT TAATT TAATT TAATT TAATT TAAT-T T-AATT TAATT TAA-TT
* *
1972059 TAAAT TAATT AAATT TAATT
1 TAATT TAATT TAATT TAATT
1972079 CTCAAATTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
4 4 0.08
5 35 0.71
6 8 0.16
7 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (5 bp):
TAATT
Found at i:1972053 original size:37 final size:37
Alignment explanation
Indices: 1971998--1972086 Score: 110
Period size: 37 Copynumber: 2.4 Consensus size: 37
1971988 ATCAATCGAG
* * *
1971998 TTTAATATTTAAAATAATTTAA-TTTAATTTAATCAAA
1 TTTAATATTCAAATTAA-TTAATTTTAAATTAATCAAA
*
1972035 TTTAATATTCAAATTAATTAATTTTAAATTAATTAAA
1 TTTAATATTCAAATTAATTAATTTTAAATTAATCAAA
1972072 TTTAAT-TCTCAAATT
1 TTTAATAT-TCAAATT
1972087 TATCAAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
36 5 0.11
37 41 0.89
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (37 bp):
TTTAATATTCAAATTAATTAATTTTAAATTAATCAAA
Found at i:1972094 original size:22 final size:21
Alignment explanation
Indices: 1972013--1972096 Score: 65
Period size: 22 Copynumber: 4.2 Consensus size: 21
1972003 TATTTAAAAT
*
1972013 AATTTAATTT-AATTTAATCA
1 AATTTAATTTCAAATTAATCA
1972033 AATTTAATATTCAAA-T--T--
1 AATTTAAT-TTCAAATTAATCA
* *
1972050 AA-TTAATTTTAAATTAATTA
1 AATTTAATTTCAAATTAATCA
*
1972070 AATTTAATTCTCAAATTTATCA
1 AATTTAATT-TCAAATTAATCA
1972092 AATTT
1 AATTT
1972097 GATATTTTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
15 5 0.10
16 6 0.12
17 2 0.04
18 1 0.02
19 1 0.02
20 10 0.20
21 9 0.18
22 16 0.32
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTTAATTTCAAATTAATCA
Found at i:1972835 original size:30 final size:30
Alignment explanation
Indices: 1972795--1972858 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
1972785 AATAACAATA
*
1972795 ACATTCATTATATCCATAACCGTTATAAAT
1 ACATTCATTATATCCATAACCATTATAAAT
*
1972825 ACATTTATTATATCCATAACCATTATAAAT
1 ACATTCATTATATCCATAACCATTATAAAT
1972855 ACAT
1 ACAT
1972859 CGTGATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.38
Consensus pattern (30 bp):
ACATTCATTATATCCATAACCATTATAAAT
Found at i:1981948 original size:2 final size:2
Alignment explanation
Indices: 1981889--1981929 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1981879 CAGTGAGATC
*
1981889 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1981930 ACTTGCCTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1982272 original size:15 final size:15
Alignment explanation
Indices: 1982252--1982281 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1982242 ACAACTTCAT
1982252 TTATATTTTTTAAAA
1 TTATATTTTTTAAAA
1982267 TTATATTTTTTAAAA
1 TTATATTTTTTAAAA
1982282 ATAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATTTTTTAAAA
Found at i:1983283 original size:22 final size:22
Alignment explanation
Indices: 1983258--1983303 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1983248 TTTTATTTTA
1983258 AAATTTGATTCATT-TTTAAAAT
1 AAATTT-ATTCATTATTTAAAAT
**
1983280 AAATTTATTTTTTATTTAAAAT
1 AAATTTATTCATTATTTAAAAT
1983302 AA
1 AA
1983304 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
AAATTTATTCATTATTTAAAAT
Found at i:1983846 original size:26 final size:25
Alignment explanation
Indices: 1983811--1983871 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
1983801 GATTTAATTT
1983811 TAATTAAATTTAAATATAATATTTTA
1 TAATTAAATTTAAAT-TAATATTTTA
* * *
1983837 TAATTCAATTTAAATTATTATTTATT
1 TAATTAAATTTAAATTAATATTT-TA
1983863 TAATTAAAT
1 TAATTAAAT
1983872 AATATTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 7 0.23
26 23 0.77
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TAATTAAATTTAAATTAATATTTTA
Found at i:1983881 original size:21 final size:21
Alignment explanation
Indices: 1983826--1983888 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 21
1983816 AAATTTAAAT
*
1983826 ATAATATTTTATAATTCAATTTAA
1 ATAATATTTT-T-ATTTAA-TTAA
1983850 AT--TATTATTTATTTAATTAA
1 ATAATATT-TTTATTTAATTAA
1983870 ATAATATTTTTATTTAATT
1 ATAATATTTTTATTTAATT
1983889 TTAATTATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
20 6 0.17
21 16 0.46
22 9 0.26
23 2 0.06
24 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATAATATTTTTATTTAATTAA
Found at i:1983991 original size:6 final size:6
Alignment explanation
Indices: 1983974--1984002 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1983964 ATCCTCGAGC
1983974 AAATTT -AATTT AAATTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT
1984003 TTAAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:1986014 original size:2 final size:2
Alignment explanation
Indices: 1986007--1986039 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1985997 TTGTCTGCAC
1986007 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
1986040 TGTAAGATGA
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:1989912 original size:2 final size:2
Alignment explanation
Indices: 1989905--1989934 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1989895 ATGAAAAACA
1989905 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1989935 TTATTGACTT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1992022 original size:21 final size:21
Alignment explanation
Indices: 1991978--1992025 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1991968 CTCAAGCAAC
*
1991978 CATTTTC--CCTTTTTTCTTT
1 CATTTTCTTCCTTATTTCTTT
1991997 C-TTTTCTTCCTTATTTCTTT
1 CATTTTCTTCCTTATTTCTTT
1992017 CATTTTCTT
1 CATTTTCTT
1992026 TCTCCCCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 5 0.20
19 1 0.04
20 12 0.48
21 7 0.28
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (21 bp):
CATTTTCTTCCTTATTTCTTT
Found at i:1995350 original size:19 final size:18
Alignment explanation
Indices: 1995319--1995363 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
1995309 GCACATATGA
* *
1995319 AATTAATAAATAATAAAT
1 AATTAAAAAATAAAAAAT
1995337 AATATAAAAAATAAAAAAT
1 AAT-TAAAAAATAAAAAAT
1995356 AATTAAAA
1 AATTAAAA
1995364 GAAAGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AATTAAAAAATAAAAAAT
Found at i:1996901 original size:18 final size:17
Alignment explanation
Indices: 1996875--1996912 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
1996865 TTATTGTTTG
*
1996875 ATATAAATATAGTTTTA
1 ATATAAATATAATTTTA
1996892 ATATATAATATAATTTTA
1 ATATA-AATATAATTTTA
1996910 ATA
1 ATA
1996913 ATTTTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATAAATATAATTTTA
Found at i:1996932 original size:27 final size:26
Alignment explanation
Indices: 1996865--1996957 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 26
1996855 CTTTATAAAT
* *
1996865 TTATTGTTTGATATAAATATAGTTTTAA
1 TTATTATTTAATATAAATAT--TTTTAA
* * * *
1996893 TATATAATATAATTTTAATAATTTTTAA
1 T-TATTATTTAATATAAAT-ATTTTTAA
1996921 TTATTATTTAATATAAATATTTTTAAA
1 TTATTATTTAATATAAATATTTTT-AA
*
1996948 TTTTTATTTA
1 TTATTATTTA
1996958 TTATTATATT
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
26 6 0.12
27 24 0.47
28 8 0.16
29 11 0.22
30 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (26 bp):
TTATTATTTAATATAAATATTTTTAA
Found at i:1996953 original size:34 final size:38
Alignment explanation
Indices: 1996888--1996962 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 38
1996878 TAAATATAGT
1996888 TTTAATATATAATATAATTTTAATAATTTTTAATTATTA
1 TTTAATATATAATAT-ATTTTAATAATTTTTAATTATTA
*
1996927 TTTAATATA-AATAT-TTTT-A-AATTTTTATTTATTA
1 TTTAATATATAATATATTTTAATAATTTTTAATTATTA
1996961 TT
1 TT
1996963 ATATTTATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
34 16 0.46
35 1 0.03
36 4 0.11
38 5 0.14
39 9 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (38 bp):
TTTAATATATAATATATTTTAATAATTTTTAATTATTA
Found at i:1996966 original size:26 final size:27
Alignment explanation
Indices: 1996913--1996990 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
1996903 AATTTTAATA
*
1996913 ATTTTT-AATTATTATTTAATATAAAT
1 ATTTTTAAATTTTTATTTAATATAAAT
* *
1996939 ATTTTTAAATTTTTATTTATTAT-TAT
1 ATTTTTAAATTTTTATTTAATATAAAT
* *
1996965 ATTTATACATTTTTTAATTTAATATA
1 ATTTTTA-AATTTTT-ATTTAATATA
1996991 TTTATAGTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
26 14 0.33
27 20 0.48
28 8 0.19
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (27 bp):
ATTTTTAAATTTTTATTTAATATAAAT
Found at i:1996977 original size:34 final size:34
Alignment explanation
Indices: 1996912--1996984 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
1996902 TAATTTTAAT
*
1996912 AATTTTTAATTATTATTTAATATAAATATTTTTA
1 AATTTTTAATTATTATTTAATATAAACATTTTTA
* * * *
1996946 AATTTTTATTTATTA-TTATATTTATACATTTTTT
1 AATTTTTAATTATTATTTA-ATATAAACATTTTTA
1996980 AATTT
1 AATTT
1996985 AATATATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 3 0.09
34 30 0.91
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (34 bp):
AATTTTTAATTATTATTTAATATAAACATTTTTA
Found at i:1999448 original size:24 final size:25
Alignment explanation
Indices: 1999413--1999461 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
1999403 AAATTAGTTG
1999413 TATTATTATATA-AAAGTA-ATTTTA
1 TATTATTATATATAAA-TATATTTTA
1999437 TATTA-TATTATATAAATATATTTTA
1 TATTATTA-TATATAAATATATTTTA
1999462 ATATAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
23 2 0.09
24 11 0.50
25 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TATTATTATATATAAATATATTTTA
Found at i:1999472 original size:16 final size:17
Alignment explanation
Indices: 1999446--1999487 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1999436 ATATTATATT
*
1999446 ATATAAATATA-TTTTA
1 ATATAAATATACTTATA
1999462 ATATAAATATACTTATA
1 ATATAAATATACTTATA
*
1999479 CTATAAATA
1 ATATAAATA
1999488 AAATATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAAATATACTTATA
Found at i:1999485 original size:17 final size:16
Alignment explanation
Indices: 1999435--1999500 Score: 62
Period size: 16 Copynumber: 4.0 Consensus size: 16
1999425 AAAGTAATTT
1999435 TATATTATATTATATAAA
1 TATATTATA--ATATAAA
*
1999453 TATATTTTAATATAAA
1 TATATTATAATATAAA
*
1999469 TATACTTATACTATAAA
1 TATA-TTATAATATAAA
* *
1999486 TAAAATATAAT-TAAA
1 TATATTATAATATAAA
1999501 AATAAAATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
15 4 0.10
16 16 0.39
17 13 0.32
18 8 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TATATTATAATATAAA
Found at i:2001908 original size:16 final size:15
Alignment explanation
Indices: 2001889--2001930 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2001879 AATATTGATA
2001889 TAAAAATAATATTTTT
1 TAAAAATAA-ATTTTT
*
2001905 TAAATATAAATTTTT
1 TAAAAATAAATTTTT
*
2001920 TATAAA-AAATT
1 TAAAAATAAATT
2001931 AAATATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 5 0.22
15 10 0.43
16 8 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAAATAAATTTTT
Found at i:2001919 original size:15 final size:16
Alignment explanation
Indices: 2001889--2001926 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2001879 AATATTGATA
2001889 TAAAAATAATATTTTT
1 TAAAAATAATATTTTT
*
2001905 TAAATATAA-ATTTTT
1 TAAAAATAATATTTTT
2001920 TATAAAA
1 TA-AAAA
2001927 AATTAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAAAATAATATTTTT
Found at i:2003380 original size:17 final size:16
Alignment explanation
Indices: 2003358--2003396 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2003348 ATTAATTTAT
*
2003358 ATATAATTATTATTAAA
1 ATATAATTATTAAT-AA
*
2003375 ATATAATTTTTAATAA
1 ATATAATTATTAATAA
2003391 ATATAA
1 ATATAA
2003397 ATTTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATAATTATTAATAA
Found at i:2003394 original size:16 final size:17
Alignment explanation
Indices: 2003358--2003404 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
2003348 ATTAATTTAT
* *
2003358 ATATAATTATTATTAAA
1 ATATAATTTTTAATAAA
2003375 ATATAATTTTTAAT-AA
1 ATATAATTTTTAATAAA
*
2003391 ATATAAATTTTAAT
1 ATATAATTTTTAAT
2003405 TTTAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATAATTTTTAATAAA
Found at i:2003669 original size:2 final size:2
Alignment explanation
Indices: 2003662--2003702 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2003652 TACCGTATTT
2003662 TA TA TA TA TA TA TA TA TA TA TA -A T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2003702 T
1 T
2003703 TGCATTGGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2005141 original size:14 final size:14
Alignment explanation
Indices: 2005122--2005151 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2005112 GATAAAATAC
2005122 TTTTTTATATAAAA
1 TTTTTTATATAAAA
*
2005136 TTTTTTATATTAAA
1 TTTTTTATATAAAA
2005150 TT
1 TT
2005152 AATTATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTTATATAAAA
Found at i:2005255 original size:3 final size:3
Alignment explanation
Indices: 2005240--2005280 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
2005230 CTTTTTCTTA
2005240 TAT TAT TACT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2005281 TTGTAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2012381 original size:17 final size:15
Alignment explanation
Indices: 2012359--2012405 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
2012349 AAAAATATAT
2012359 AAATATTAATATTAAAA
1 AAATATTAA-A-TAAAA
2012376 AAATATTAAAT-AAA
1 AAATATTAAATAAAA
*
2012390 AAAT-TTTAATAAAA
1 AAATATTAAATAAAA
2012404 AA
1 AA
2012406 TAAAATTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.18
14 12 0.43
15 1 0.04
16 1 0.04
17 9 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATATTAAATAAAA
Found at i:2012405 original size:13 final size:14
Alignment explanation
Indices: 2012359--2012407 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
2012349 AAAAATATAT
2012359 AAATATTAATATTAAAA
1 AAATATTAA-A-T-AAA
2012376 AAATATTAAATAAA
1 AAATATTAAATAAA
*
2012390 AAAT-TTTAATAAA
1 AAATATTAAATAAA
2012403 AAATA
1 AAATA
2012408 AAATTTGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 12 0.40
14 7 0.23
15 1 0.03
16 1 0.03
17 9 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATTAAATAAA
Found at i:2014209 original size:15 final size:17
Alignment explanation
Indices: 2014156--2014224 Score: 61
Period size: 17 Copynumber: 4.0 Consensus size: 17
2014146 AGTTCACACG
2014156 AATATTTAATTATTTTAT
1 AATA-TTAATTATTTTAT
* * *
2014174 AAATATAAATAATAATTAT
1 -AATATTAATTAT-TTTAT
2014193 AA-ATT-ATTATTTTAT
1 AATATTAATTATTTTAT
*
2014208 AATTTTAATTATTTTAT
1 AATATTAATTATTTTAT
2014225 CATCAATATT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
15 6 0.15
16 6 0.15
17 12 0.30
18 8 0.20
19 8 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATATTAATTATTTTAT
Found at i:2014258 original size:17 final size:17
Alignment explanation
Indices: 2014238--2014298 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
2014228 CAATATTTAT
2014238 TTAATAAATTATAAATA
1 TTAATAAATTATAAATA
*
2014255 TTAATTAAATTTATAATTA
1 TTAA-TAAA-TTATAAATA
2014274 -TAATAAA-TATAATATAA
1 TTAATAAATTATAA-AT-A
2014291 TTAA-AAAT
1 TTAATAAAT
2014299 ATTTTTACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
15 5 0.14
16 1 0.03
17 12 0.33
18 10 0.28
19 8 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATAAATTATAAATA
Found at i:2014295 original size:15 final size:16
Alignment explanation
Indices: 2014242--2014295 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 16
2014232 ATTTATTTAA
2014242 TAAATTATAAATATTAAT
1 TAAATTAT-AATA-TAAT
2014260 TAAATTTATAATTATAA-
1 TAAA-TTATAA-TATAAT
2014277 TAAA-TATAATATAAT
1 TAAATTATAATATAAT
2014292 TAAA
1 TAAA
2014296 AATATTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.15
15 9 0.27
17 4 0.12
18 9 0.27
19 6 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTATAATATAAT
Found at i:2014999 original size:3 final size:3
Alignment explanation
Indices: 2014991--2015018 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2014981 CACCTATCAA
2014991 AAC AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC A
2015019 GATTGAGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:2020872 original size:2 final size:2
Alignment explanation
Indices: 2020865--2020899 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2020855 TTCAAATCTG
2020865 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 A
2020900 ATTCATCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2026728 original size:5 final size:5
Alignment explanation
Indices: 2026713--2026742 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2026703 TTTTTCCTTG
2026713 CTTCT -TTCT CTTCT CTTCT CTTCT CTTCT C
1 CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT C
2026743 CTCTTTGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CTTCT
Found at i:2026738 original size:15 final size:14
Alignment explanation
Indices: 2026713--2026748 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
2026703 TTTTTCCTTG
2026713 CTTCTTTCTCTTCT
1 CTTCTTTCTCTTCT
2026727 CTTCTCTTCTCTTCT
1 CTTCT-TTCTCTTCT
*
2026742 CCTCTTT
1 CTTCTTT
2026749 GGTCTCATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (14 bp):
CTTCTTTCTCTTCT
Found at i:2026887 original size:3 final size:3
Alignment explanation
Indices: 2026879--2026912 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2026869 AAGACTCACA
2026879 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2026913 GATATAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2029033 original size:13 final size:13
Alignment explanation
Indices: 2029015--2029039 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2029005 TATTTATATT
2029015 TAAATATAAATAC
1 TAAATATAAATAC
2029028 TAAATATAAATA
1 TAAATATAAATA
2029040 TATAAAATAA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAATATAAATAC
Found at i:2032224 original size:17 final size:15
Alignment explanation
Indices: 2032202--2032238 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
2032192 AATTTTTCTA
2032202 TTTTTAATTTTAGTAAT
1 TTTTTAATTTT--TAAT
2032219 TTTTTAATTTTTAAT
1 TTTTTAATTTTTAAT
2032234 TTTTT
1 TTTTT
2032239 TAAAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTTTAATTTTTAAT
Found at i:2036358 original size:27 final size:27
Alignment explanation
Indices: 2036328--2036379 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2036318 TAAAAAAAAT
* *
2036328 AAATTTAAAAATTTTATTTTAATTTTA
1 AAATTTAAAAATTGTAATTTAATTTTA
*
2036355 AAATTTTAAAATTGTAATTTAATTT
1 AAATTTAAAAATTGTAATTTAATTT
2036380 AATTTATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
AAATTTAAAAATTGTAATTTAATTTTA
Found at i:2036556 original size:34 final size:32
Alignment explanation
Indices: 2036517--2036592 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
2036507 ATCAAACTTA
* *
2036517 TAATAATTTTTATTTAATCTATATAAATATTAA-T
1 TAATAATTTTTATTTAA-AT-TATAAAT-TAAACT
* *
2036551 TAATAATATATATTTAAATTATAAATTAAACT
1 TAATAATTTTTATTTAAATTATAAATTAAACT
2036583 TAATAATTTT
1 TAATAATTTT
2036593 AAATATAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 3 0.09
32 16 0.46
33 1 0.03
34 15 0.43
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
TAATAATTTTTATTTAAATTATAAATTAAACT
Found at i:2036988 original size:2 final size:2
Alignment explanation
Indices: 2036983--2037022 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
2036973 TAATTAAAAA
* *
2036983 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT -T GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2037023 GAGCATGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2037684 original size:3 final size:3
Alignment explanation
Indices: 2037676--2037721 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2037666 CATAAAATAG
2037676 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2037722 AGGATTATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2037742 original size:19 final size:19
Alignment explanation
Indices: 2037688--2037736 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
2037678 TATTATTATT
**
2037688 ATTATTATTATTATT-ATT
1 ATTATTATTATTATTAAGG
2037706 ATTATTATTATTATTAAGG
1 ATTATTATTATTATTAAGG
*
2037725 ATTATTCTTATT
1 ATTATTATTATT
2037737 TATAAGCACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (19 bp):
ATTATTATTATTATTAAGG
Found at i:2038610 original size:16 final size:15
Alignment explanation
Indices: 2038589--2038628 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
2038579 TTTTTAATAC
*
2038589 ATTAAATAAAATAATT
1 ATTAAATAAAATAA-A
*
2038605 ATTAAATATAATAAA
1 ATTAAATAAAATAAA
2038620 ATTAAATAA
1 ATTAAATAA
2038629 TAGCTTAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTAAATAAAATAAA
Found at i:2039790 original size:15 final size:17
Alignment explanation
Indices: 2039756--2039798 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
2039746 AGTAGTAGCC
2039756 AATATTAAATATTATTT
1 AATATTAAATATTATTT
2039773 AATATTAAATA-T-TTT
1 AATATTAAATATTATTT
*
2039788 AATATTTAATA
1 AATATTAAATA
2039799 AAATATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 13 0.52
16 1 0.04
17 11 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATATTAAATATTATTT
Found at i:2040480 original size:17 final size:18
Alignment explanation
Indices: 2040440--2040481 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2040430 TAAAATTTAA
*
2040440 AAAAATATTTATATTTTT
1 AAAAATATTAATATTTTT
*
2040458 -ATAATATTAAT-TTTTT
1 AAAAATATTAATATTTTT
2040474 AAAAATAT
1 AAAAATAT
2040482 ATTCTAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AAAAATATTAATATTTTT
Found at i:2040976 original size:2 final size:2
Alignment explanation
Indices: 2040969--2040998 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2040959 CCCAAAAAGC
2040969 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2040999 TAATTTAGAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2041252 original size:18 final size:19
Alignment explanation
Indices: 2041231--2041318 Score: 51
Period size: 20 Copynumber: 4.7 Consensus size: 19
2041221 TGTATATTTT
2041231 TTATTAATTATATATA-AA
1 TTATTAATTATATATATAA
* *
2041249 TTATGGAA-TATATA-AAAA
1 TTAT-TAATTATATATATAA
* *
2041267 AT-TTAATTATAAATATAA
1 TTATTAATTATATATATAA
*
2041285 TT-TATATATTAAATATATAA
1 TTAT-TA-ATTATATATATAA
*
2041305 TAATTACATTATAT
1 TTATTA-ATTATAT
2041319 TTTTTATTAA
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
16 2 0.04
17 7 0.13
18 18 0.35
19 4 0.08
20 20 0.38
21 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (19 bp):
TTATTAATTATATATATAA
Found at i:2041707 original size:11 final size:11
Alignment explanation
Indices: 2041687--2041747 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
2041677 ATTAAATTTG
*
2041687 ATAATTTTTAA
1 ATAATATTTAA
2041698 ATAATATTTAA
1 ATAATATTTAA
*
2041709 ATAA-ATATAAA
1 ATAATAT-TTAA
2041720 ATAATA--TAA
1 ATAATATTTAA
2041729 AT-ATATTTAA
1 ATAATATTTAA
2041739 ATATATATT
1 ATA-ATATT
2041748 ATATATATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
8 3 0.07
9 4 0.10
10 7 0.17
11 21 0.51
12 6 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATAATATTTAA
Found at i:2041739 original size:10 final size:10
Alignment explanation
Indices: 2041693--2041755 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
2041683 TTTGATAATT
2041693 TTTAAATAATA
1 TTTAAAT-ATA
*
2041704 TTTAAATAAA
1 TTTAAATATA
*
2041714 TATAAA-ATAA
1 TTTAAATAT-A
*
2041724 TATAAATATA
1 TTTAAATATA
2041734 TTTAAATATA
1 TTTAAATATA
*
2041744 TATTATATATA
1 T-TTAAATATA
2041755 T
1 T
2041756 ATATATGTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 1 0.02
10 25 0.57
11 18 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTAAATATA
Found at i:2041744 original size:2 final size:2
Alignment explanation
Indices: 2041723--2041778 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
2041713 ATATAAAATA
* * * *
2041723 AT AT AA AT AT AT TT AA AT AT AT AT -T AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2041764 AT AT CT GT AT AT AT A
1 AT AT AT AT AT AT AT A
2041779 AAATAAATTA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2042248 original size:7 final size:7
Alignment explanation
Indices: 2042238--2042310 Score: 52
Period size: 7 Copynumber: 10.9 Consensus size: 7
2042228 AAAAAAATTA
2042238 TAAATAT
1 TAAATAT
2042245 TAAA-ATT
1 TAAATA-T
2042252 TAAATAT
1 TAAATAT
2042259 TAAATTTAT
1 TAAA--TAT
2042268 TAAATAT
1 TAAATAT
2042275 T--A-AT
1 TAAATAT
*
2042279 TAATTAT
1 TAAATAT
2042286 ATAAAT-T
1 -TAAATAT
2042293 TAAAT-T
1 TAAATAT
2042299 TAAAT-T
1 TAAATAT
2042305 TAAATA
1 TAAATA
2042311 AAAATTTAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
4 3 0.05
5 1 0.02
6 18 0.33
7 21 0.38
8 5 0.09
9 7 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAAATAT
Found at i:2042271 original size:47 final size:46
Alignment explanation
Indices: 2042220--2042309 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 46
2042210 AGTTTTTAAT
2042220 TTAAAAATAAAAAAATTATA-AATATTAAAATTTAAATATTAAATTTA
1 TTAAAAATAAAAAAATTATATAA-ATTAAAATTTAAAT-TTAAATTTA
* * ** *
2042267 TTAAATATTAATTAATTATATAAATTTAAATTTAAATTTAAAT
1 TTAAAAATAAAAAAATTATATAAATTAAAATTTAAATTTAAAT
2042310 AAAAATTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
46 6 0.16
47 29 0.78
48 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (46 bp):
TTAAAAATAAAAAAATTATATAAATTAAAATTTAAATTTAAATTTA
Found at i:2042298 original size:6 final size:6
Alignment explanation
Indices: 2042287--2042324 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
2042277 ATTAATTATA
* *
2042287 TAAATT TAAATT TAAATT TAAATA AAAATT T-AATT TAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAA
2042325 TTCAAGTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:2042435 original size:16 final size:17
Alignment explanation
Indices: 2042414--2042445 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2042404 AATAATATTT
2042414 AAAAAATT-AATTCAAA
1 AAAAAATTCAATTCAAA
2042430 AAAAAATTCAATTCAA
1 AAAAAATTCAATTCAA
2042446 TCAATTTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAAAATTCAATTCAAA
Found at i:2042646 original size:15 final size:16
Alignment explanation
Indices: 2042615--2042647 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2042605 TTCTTACTAT
*
2042615 ATTTAATAATTATTTA
1 ATTTAATAATTACTTA
2042631 ATTTAA-AATTACTTA
1 ATTTAATAATTACTTA
2042646 AT
1 AT
2042648 ATTTAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTAATAATTACTTA
Found at i:2042837 original size:3 final size:3
Alignment explanation
Indices: 2042823--2042853 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2042813 TGGCTGTTTC
*
2042823 ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2042854 GCTAAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2046841 original size:4 final size:4
Alignment explanation
Indices: 2046832--2046856 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2046822 ACACCACCAA
2046832 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
2046857 TACACACACA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2046896 original size:2 final size:2
Alignment explanation
Indices: 2046889--2046918 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2046879 TTTGTACATG
2046889 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
2046919 ATGAAGCAGG
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:2049560 original size:16 final size:17
Alignment explanation
Indices: 2049534--2049565 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2049524 TCACATATTC
2049534 TTTATATATTATATTAT
1 TTTATATATTATATTAT
2049551 TTTATA-ATTATATTA
1 TTTATATATTATATTA
2049566 AAAATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATATATTATATTAT
Found at i:2054368 original size:6 final size:6
Alignment explanation
Indices: 2054357--2054389 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2054347 ATAACTTTAG
2054357 TTTTTC TTTTTC TTTTTC TTTTT- TTTTT- TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
2054390 GGTTATTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (6 bp):
TTTTTC
Found at i:2057501 original size:2 final size:2
Alignment explanation
Indices: 2057494--2057523 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2057484 AAACAACATA
2057494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2057524 TAAAACAATG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2064317 original size:2 final size:2
Alignment explanation
Indices: 2064310--2064337 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2064300 CAAATCACAA
2064310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2064338 TATCCCATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2070843 original size:29 final size:30
Alignment explanation
Indices: 2070788--2070845 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 30
2070778 AGCTTAATTC
2070788 TCATGTTTGACCTTTAAATTCAATTATTTG
1 TCATGTTTGACCTTTAAATTCAATTATTTG
2070818 TCATGTTTGACC-TTAAATTCAATTATTT
1 TCATGTTTGACCTTTAAATTCAATTATTT
2070846 ATATTTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.50
Consensus pattern (30 bp):
TCATGTTTGACCTTTAAATTCAATTATTTG
Found at i:2072549 original size:2 final size:2
Alignment explanation
Indices: 2072542--2072603 Score: 79
Period size: 2 Copynumber: 30.0 Consensus size: 2
2072532 TTACCAAATC
* *
2072542 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC ACT CAT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T -AT AT
*
2072586 AT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2072604 CAACATACTA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 50 0.96
3 1 0.02
4 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2073212 original size:2 final size:2
Alignment explanation
Indices: 2073205--2073243 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
2073195 CAGACAGTTA
2073205 AT AT AT AT -T AT GAT AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2073244 GAGCAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2076030 original size:15 final size:14
Alignment explanation
Indices: 2076006--2076035 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2075996 CACGATTATG
2076006 ATATAATACATAAT
1 ATATAATACATAAT
2076020 ATATGAATACATAAT
1 ATAT-AATACATAAT
2076035 A
1 A
2076036 AATATTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (14 bp):
ATATAATACATAAT
Found at i:2077105 original size:3 final size:3
Alignment explanation
Indices: 2077097--2077130 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2077087 ATATATTAAC
*
2077097 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2077131 TTGTCATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2078739 original size:2 final size:2
Alignment explanation
Indices: 2078732--2078759 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2078722 GTTAAGGTTT
2078732 TA 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 TA
2078760 AAGAAAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2082573 original size:17 final size:17
Alignment explanation
Indices: 2082551--2082584 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2082541 AATTATTGTG
2082551 ATAATTTATTGATGAAT
1 ATAATTTATTGATGAAT
2082568 ATAATTTATTGATGAAT
1 ATAATTTATTGATGAAT
2082585 TACAAGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
ATAATTTATTGATGAAT
Found at i:2087161 original size:2 final size:2
Alignment explanation
Indices: 2087154--2087191 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2087144 ATTATAATTT
*
2087154 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2087192 AAGAAACTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2090680 original size:29 final size:29
Alignment explanation
Indices: 2090630--2090730 Score: 86
Period size: 29 Copynumber: 3.4 Consensus size: 29
2090620 TAAAAAATAA
*
2090630 TTAAAAATAATATAAATATAATATTAAATTT
1 TTAAAAAT--TATTAATATAATATTAAATTT
2090661 TTAAAAATTATTAATATAATTATT-AATTT
1 TTAAAAATTATTAATATAA-TATTAAATTT
*
2090690 ATTAAAATTTA-T-ATA-AATA-TATAATATT
1 -TTAAAAATTATTAATATAATATTA-AAT-TT
*
2090718 TTAAAAATAATTA
1 TTAAAAATTATTA
2090731 TAATATATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
25 1 0.02
26 2 0.03
27 13 0.22
28 6 0.10
29 16 0.27
30 13 0.22
31 8 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTAAAAATTATTAATATAATATTAAATTT
Found at i:2090695 original size:30 final size:30
Alignment explanation
Indices: 2090629--2090710 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 30
2090619 TTAAAAAATA
*
2090629 ATTAAAAATAATATAAATATAATATTAAATTT
1 ATTAAAAAT--TATTAATATAATATTAAATTT
2090661 -TTAAAAATTATTAATATAATTATT-AATTT
1 ATTAAAAATTATTAATATAA-TATTAAATTT
*
2090690 ATTAAAATTTATATAAATATA
1 ATTAAAAATTAT-T-AATATA
2090711 TAATATTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
29 15 0.34
30 14 0.32
31 9 0.20
32 6 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
ATTAAAAATTATTAATATAATATTAAATTT
Found at i:2090739 original size:29 final size:30
Alignment explanation
Indices: 2090630--2090742 Score: 103
Period size: 30 Copynumber: 3.8 Consensus size: 30
2090620 TAAAAAATAA
2090630 TTAAAAATAATATAAATATAATATTAA-ATTT
1 TTAAAAATAATAT-AATATAATATTAATA-TT
*
2090661 TTAAAAATTAT-TAATATAATTATTAAT-TT
1 TTAAAAATAATATAATATAA-TATTAATATT
* *
2090690 ATTAAAATTTATATAA-AT-ATA-TAATATT
1 -TTAAAAATAATATAATATAATATTAATATT
2090718 TTAAAAATAATTATAATATATATAT
1 TTAAAAATAA-TATAATATA-ATAT
2090743 ATATATATAT
Statistics
Matches: 68, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
27 12 0.18
28 9 0.13
29 12 0.18
30 19 0.28
31 16 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TTAAAAATAATATAATATAATATTAATATT
Found at i:2090740 original size:2 final size:2
Alignment explanation
Indices: 2090729--2090759 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2090719 TAAAAATAAT
2090729 TA TA -A 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 TA TA TA
2090760 AAATTTGGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2091088 original size:29 final size:29
Alignment explanation
Indices: 2091034--2091093 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
2091024 TTGAATTATT
*** *
2091034 ATTTAATTAATAAAAATATTTTTATTTAA
1 ATTTAATTAATAAAAATATAAATATTAAA
2091063 ATTTAATT-ATAAAATATATAAATATTAAA
1 ATTTAATTAATAAAA-ATATAAATATTAAA
2091092 AT
1 AT
2091094 AAAAATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTTAATTAATAAAAATATAAATATTAAA
Found at i:2092074 original size:20 final size:20
Alignment explanation
Indices: 2091978--2092068 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
2091968 AATAATGGTG
* * *
2091978 AGCTTGAAAAGGATTATGATA
1 AGCTT-AAAAAGATAATGAAA
* * *
2091999 AGCTTAAAAGGATAATGGAG
1 AGCTTAAAAAGATAATGAAA
*
2092019 AG-TGTAAAAAGACAATGAAA
1 AGCT-TAAAAAGATAATGAAA
*
2092039 AGCTTAAAAAGATAATGACA
1 AGCTTAAAAAGATAATGAAA
2092059 AGCTTAAAAA
1 AGCTTAAAAA
2092069 ATTAATAGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 51 0.88
21 6 0.10
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (20 bp):
AGCTTAAAAAGATAATGAAA
Found at i:2094377 original size:17 final size:17
Alignment explanation
Indices: 2094352--2094384 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2094342 GTTCAAGTTA
2094352 TTTCAAGTTCGAATCAT
1 TTTCAAGTTCGAATCAT
*
2094369 TTTCGAGTTCGAATCA
1 TTTCAAGTTCGAATCA
2094385 ATCAGTTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (17 bp):
TTTCAAGTTCGAATCAT
Found at i:2096019 original size:31 final size:30
Alignment explanation
Indices: 2095984--2096041 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
2095974 ATCAATTCCG
2095984 TCGGAAATAA-TTATTATCGATGAAAATTCGA
1 TCGGAAA-AACTT-TTATCGATGAAAATTCGA
*
2096015 TCGGAAAAACTTTTTTCGATGAAAATT
1 TCGGAAAAACTTTTATCGATGAAAATT
2096042 TTAAGTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (30 bp):
TCGGAAAAACTTTTATCGATGAAAATTCGA
Found at i:2098827 original size:2 final size:2
Alignment explanation
Indices: 2098820--2098887 Score: 84
Period size: 2 Copynumber: 34.0 Consensus size: 2
2098810 TTTCTTTTAA
* * *
2098820 AT AT AT AT AT AT AT AT AT AT AT GCT AT TT GT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
*
2098862 AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2098888 TTATGCTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
1 1 0.02
2 56 0.97
3 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2104678 original size:18 final size:18
Alignment explanation
Indices: 2104655--2104691 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2104645 ATATTAATCT
2104655 AATACTAATAGAATAGAA
1 AATACTAATAGAATAGAA
*
2104673 AATACTAATATAATAGAA
1 AATACTAATAGAATAGAA
2104691 A
1 A
2104692 GAAAAGAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.24
Consensus pattern (18 bp):
AATACTAATAGAATAGAA
Found at i:2104688 original size:23 final size:23
Alignment explanation
Indices: 2104653--2104696 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
2104643 TAATATTAAT
2104653 CTAATACTAATAGAATAGAAAATA
1 CTAATACTAATAGAA-AGAAAATA
2104677 CTAATA-TAATAGAAAGAAAA
1 CTAATACTAATAGAAAGAAAA
2104697 GAACTGTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 8 0.40
24 6 0.30
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.23
Consensus pattern (23 bp):
CTAATACTAATAGAAAGAAAATA
Found at i:2108846 original size:3 final size:3
Alignment explanation
Indices: 2108838--2108867 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2108828 TGCAGCTTTA
2108838 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2108868 ATATAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:2109502 original size:17 final size:17
Alignment explanation
Indices: 2109452--2109504 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
2109442 TATATATTTC
2109452 AAATTTATAT-AATAT-
1 AAATTTATATAAATATA
*
2109467 AAA-TTAT-TAACGTATTA
1 AAATTTATATAA-ATA-TA
2109484 AAATTTATATAAATATA
1 AAATTTATATAAATATA
2109501 AAAT
1 AAAT
2109505 ATAAAATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 1 0.03
14 5 0.17
15 5 0.17
16 1 0.03
17 9 0.30
18 6 0.20
19 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
AAATTTATATAAATATA
Found at i:2110017 original size:20 final size:20
Alignment explanation
Indices: 2109994--2110038 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2109984 GTTTAGTTTA
* *
2109994 ATTTTAGTAAATTTAATTTG
1 ATTTTAATAAATTTAATTCG
**
2110014 ATTTTAATTTATTTAATTCG
1 ATTTTAATAAATTTAATTCG
2110034 ATTTT
1 ATTTT
2110039 TAATTTATAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (20 bp):
ATTTTAATAAATTTAATTCG
Found at i:2110041 original size:21 final size:20
Alignment explanation
Indices: 2110004--2110046 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
2109994 ATTTTAGTAA
*
2110004 ATTTAATTTGATTTTAATTT
1 ATTTAATTCGATTTTAATTT
2110024 ATTTAATTCGATTTTTAATTT
1 ATTTAATTCGA-TTTTAATTT
2110045 AT
1 AT
2110047 AGATTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (20 bp):
ATTTAATTCGATTTTAATTT
Found at i:2110225 original size:3 final size:3
Alignment explanation
Indices: 2110211--2110264 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
2110201 TTCCTTAGGA
2110211 ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
2110258 ATC ATT A
1 ATT ATT A
2110265 CAAATTTATA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2110359 original size:2 final size:2
Alignment explanation
Indices: 2110352--2110399 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2110342 TAGGGGTTTT
2110352 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
2110394 TA TA TA
1 TA TA TA
2110400 AAGTCAGCTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2110586 original size:18 final size:20
Alignment explanation
Indices: 2110555--2110594 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
2110545 TAATCTAATT
2110555 TTGAATTTATGATTTTG-AA
1 TTGAATTTATGATTTTGTAA
*
2110574 TTGATTTTA-GATTTTGTAA
1 TTGAATTTATGATTTTGTAA
2110593 TT
1 TT
2110595 TAATGATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (20 bp):
TTGAATTTATGATTTTGTAA
Found at i:2111117 original size:16 final size:16
Alignment explanation
Indices: 2111080--2111177 Score: 60
Period size: 16 Copynumber: 6.2 Consensus size: 16
2111070 TTATTTAAAA
*
2111080 ATATTAAAATT-TTAT
1 ATATTAAAATTAATAT
*
2111095 ATATTAATATTAATAT
1 ATATTAAAATTAATAT
* *
2111111 ATTTTAAAATTAAATTT
1 ATATTAAAATT-AATAT
* * * *
2111128 AAATAAAAAATAATTT
1 ATATTAAAATTAATAT
*
2111144 TTATT-AAATTAA-AT
1 ATATTAAAATTAATAT
2111158 AATAATTAAAATTAAT-T
1 -AT-ATTAAAATTAATAT
2111175 ATA
1 ATA
2111178 ACAATAATTC
Statistics
Matches: 62, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
14 1 0.02
15 18 0.29
16 24 0.39
17 19 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTAAAATTAATAT
Found at i:2111171 original size:22 final size:22
Alignment explanation
Indices: 2111118--2111186 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
2111108 TATATTTTAA
*
2111118 AATTAAATTTAAA-TAAAAAAT
1 AATTAAAATTAAATTAAAAAAT
*** *
2111139 AATTTTTATTAAATTAAATAAT
1 AATTAAAATTAAATTAAAAAAT
*
2111161 AATTAAAATT-AATTATAACAAT
1 AATTAAAATTAAATTA-AAAAAT
2111183 AATT
1 AATT
2111187 CGGGTCAAGT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
21 14 0.38
22 23 0.62
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTAAAATTAAATTAAAAAAT
Found at i:2111175 original size:26 final size:27
Alignment explanation
Indices: 2111118--2111175 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
2111108 TATATTTTAA
**
2111118 AATTAAATTTAAATAAAAAATAATTTT
1 AATTAAATTTAAATAAAAAATAAAATT
* * *
2111145 TATTAAA-TTAAATAATAATTAAAATT
1 AATTAAATTTAAATAAAAAATAAAATT
2111171 AATTA
1 AATTA
2111176 TAACAATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AATTAAATTTAAATAAAAAATAAAATT
Found at i:2112506 original size:25 final size:27
Alignment explanation
Indices: 2112464--2112515 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
2112454 ATTTTAAAAA
2112464 AATTTAAAATTAAAAAT-AT-TTTTAT
1 AATTTAAAATTAAAAATAATATTTTAT
*
2112489 AATTT-AATTTAAATAATAATATTTTAT
1 AATTTAAAATTAAA-AATAATATTTTAT
2112516 TAATAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 7 0.30
25 8 0.35
26 2 0.09
27 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
AATTTAAAATTAAAAATAATATTTTAT
Found at i:2112739 original size:34 final size:34
Alignment explanation
Indices: 2112684--2112900 Score: 242
Period size: 34 Copynumber: 6.4 Consensus size: 34
2112674 AATTAACAAG
*
2112684 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
2112717 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
2112751 TGTTGACTAAATGAGAT-ATTTGGTAGCTTACCAT
1 TGTTGATTAAATG-GGTGATTTGGTAGCTTACCAT
* **
2112785 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
2112819 TATTGATTAAATGGGTGATTTGATGGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * * *
2112853 TGTTGACTAAAT-GGTAGATTTGATAGGTTGCCAT
1 TGTTGATTAAATGGGT-GATTTGGTAGCTTACCAT
*
2112887 TATTGATTAAATGG
1 TGTTGATTAAATGG
2112901 TGTTTTTTAC
Statistics
Matches: 155, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
33 15 0.10
34 137 0.88
35 3 0.02
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
Found at i:2112887 original size:102 final size:101
Alignment explanation
Indices: 2112684--2112900 Score: 301
Period size: 102 Copynumber: 2.1 Consensus size: 101
2112674 AATTAACAAG
** * * * * *
2112684 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGATGGCTTACC
* *
2112749 ATTGTTGACTAAATGAGATATTTGGTAGCTTACCAT
66 ATTGTTGACTAAATGAGAGATTTGATAGCTTACCAT
2112785 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGATGGCTTAC
1 TGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGATGGCTTAC
* *
2112850 CATTGTTGACTAAATG-GTAGATTTGATAGGTTGCCAT
65 CATTGTTGACTAAATGAG-AGATTTGATAGCTTACCAT
*
2112887 TATTGATTAAATGG
1 TGTTGATTAAATGG
2112901 TGTTTTTTAC
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
101 15 0.15
102 87 0.85
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGATGGCTTACC
ATTGTTGACTAAATGAGAGATTTGATAGCTTACCAT
Found at i:2117339 original size:34 final size:34
Alignment explanation
Indices: 2117282--2117500 Score: 271
Period size: 34 Copynumber: 6.5 Consensus size: 34
2117272 AAGTGGGAGA
*
2117282 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2117315 ATTGTTGATTAAATGGGTGATTTGGTGGTTTTCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2117349 ATTGTTGACTAAATGGGAGATTTGGTAGCTTATC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
2117383 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2117417 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * **
2117451 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGTC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
2117485 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2117501 TGGTTTTTAC
Statistics
Matches: 159, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
33 17 0.11
34 141 0.89
35 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.42
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:2117425 original size:102 final size:101
Alignment explanation
Indices: 2117282--2117500 Score: 348
Period size: 102 Copynumber: 2.2 Consensus size: 101
2117272 AAGTGGGAGA
** * * * *
2117282 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTT
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
2117347 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTATC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTATC
2117383 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
2117448 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGTC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTATC
2117485 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2117501 TGGTTTTTAC
Statistics
Matches: 108, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 92 0.85
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.42
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTATC
Found at i:2118239 original size:12 final size:12
Alignment explanation
Indices: 2118206--2118244 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
2118196 TTTGTTAATT
2118206 TTTATAATTATA
1 TTTATAATTATA
*
2118218 -TTATATTTATA
1 TTTATAATTATA
2118229 TTTATAATTATA
1 TTTATAATTATA
2118241 TTTA
1 TTTA
2118245 AAATATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATAATTATA
Found at i:2118329 original size:17 final size:17
Alignment explanation
Indices: 2118213--2118331 Score: 72
Period size: 17 Copynumber: 6.9 Consensus size: 17
2118203 ATTTTTATAA
2118213 TTATATTATA-TTTATAT
1 TTATATTATATTTTAT-T
2118230 TTATAATTATATTTAAAATATT
1 TTAT-ATTATATTT----TATT
* *
2118252 ATATATT-TATTTAAATT
1 TTATATTATATTT-TATT
2118269 TTA-A-TATTATTTTA-T
1 TTATATTA-TATTTTATT
**
2118284 TTA-ATTCATATCAT-TT
1 TTATATT-ATATTTTATT
2118300 TTATATTATATTTTATT
1 TTATATTATATTTTATT
2118317 TTATATTATATTTTA
1 TTATATTATATTTTA
2118332 ATATTTTAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 26
0.70 0.07 0.23
Matches are distributed among these distances:
15 6 0.07
16 16 0.20
17 36 0.44
18 6 0.07
19 2 0.02
20 5 0.06
21 3 0.04
22 4 0.05
23 3 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATATTATATTTTATT
Found at i:2119491 original size:2 final size:2
Alignment explanation
Indices: 2119484--2119515 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2119474 CCTTATAAAC
2119484 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2119516 TGCATATTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2119795 original size:6 final size:7
Alignment explanation
Indices: 2119705--2119801 Score: 59
Period size: 6 Copynumber: 14.6 Consensus size: 7
2119695 TATGTTAAAA
2119705 ATAATAT
1 ATAATAT
2119712 A-AATAT
1 ATAATAT
2119718 ATCAATAT
1 AT-AATAT
*
2119726 -TTATAT
1 ATAATAT
*
2119732 ATAACAT
1 ATAATAT
2119739 A-AAT-T
1 ATAATAT
2119744 ATTAATAT
1 A-TAATAT
2119752 ATTAA-AT
1 A-TAATAT
*
2119759 -TTATAT
1 ATAATAT
2119765 A-AATAT
1 ATAATAT
2119771 ATAATATT
1 ATAATA-T
*
2119779 TTAA-AT
1 ATAATAT
2119785 ATAAT-T
1 ATAATAT
2119791 ATAATAT
1 ATAATAT
2119798 ATAA
1 ATAA
2119802 AAATATATGA
Statistics
Matches: 70, Mismatches: 8, Indels: 24
0.69 0.08 0.24
Matches are distributed among these distances:
5 4 0.06
6 29 0.41
7 22 0.31
8 15 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (7 bp):
ATAATAT
Found at i:2404322 original size:18 final size:18
Alignment explanation
Indices: 2404309--2404372 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
2404299 AAAATATTTT
*
2404309 TTAATATTTTAATATATA
1 TTAATATATTAATATATA
*
2404327 TTAATATATTAAAATA-A
1 TTAATATATTAATATATA
*
2404344 TT-ATATTATTTAATATTAAA
1 TTAATA-TA-TTAATA-TATA
2404364 TTAA-ATATT
1 TTAATATATT
2404373 TCAATTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
16 3 0.08
17 5 0.13
18 21 0.55
19 4 0.11
20 4 0.11
21 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTAATATATTAATATATA
Found at i:2404786 original size:32 final size:33
Alignment explanation
Indices: 2404719--2404799 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 33
2404709 TAACAATAGC
*
2404719 AATA-ATATGATACTAAATATATAAATATGTCAA
1 AATATATATAATA-TAAATATATAAATATGTCAA
* * *
2404752 AATATATATAATATAAAT-TATTAATGTGTTAA
1 AATATATATAATATAAATATATAAATATGTCAA
*
2404784 AATTTATATAAATATA
1 AATATATAT-AATATA
2404800 TAACATTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 19 0.46
33 15 0.37
34 7 0.17
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (33 bp):
AATATATATAATATAAATATATAAATATGTCAA
Found at i:2404986 original size:18 final size:17
Alignment explanation
Indices: 2404965--2404998 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2404955 TATAAGAATT
2404965 TTAAATTATTTATTTTTG
1 TTAAATT-TTTATTTTTG
*
2404983 TTAACTTTTTATTTTT
1 TTAAATTTTTATTTTT
2404999 TGTTTCATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TTAAATTTTTATTTTTG
Found at i:2408189 original size:18 final size:17
Alignment explanation
Indices: 2408142--2408190 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 17
2408132 TATCATTTCT
*
2408142 AATTATATAAATTTTTATA
1 AATTA-ATAAA-TTTTAAA
2408161 AATTAATTAAATTTTAAA
1 AATTAA-TAAATTTTAAA
2408179 AATTTAATAAAT
1 AA-TTAATAAAT
2408191 AATAATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAATAAATTTTAAA
Found at i:2408238 original size:19 final size:20
Alignment explanation
Indices: 2408214--2408258 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2408204 TTATTATTTT
2408214 TTAATTAAAAAAAATTTA-A
1 TTAATTAAAAAAAATTTATA
**
2408233 TTAATT-TTAAAAATTTATA
1 TTAATTAAAAAAAATTTATA
2408252 TTAATTA
1 TTAATTA
2408259 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAATTAAAAAAAATTTATA
Found at i:2408277 original size:23 final size:23
Alignment explanation
Indices: 2408202--2408278 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
2408192 ATAATATATT
*
2408202 AATT-ATTATTTTTTAATTAAAAAA
1 AATTAATTATTTTTTAA--AATAAA
* * **
2408226 AATTTAATTAATTTTAAAAATTTA
1 AA-TTAATTATTTTTTAAAATAAA
*
2408250 TATTAATTATTTTTTAAAATAAA
1 AATTAATTATTTTTTAAAATAAA
2408273 AATTAA
1 AATTAA
2408279 ATTAAAAATA
Statistics
Matches: 40, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
23 22 0.55
24 6 0.15
25 2 0.05
26 10 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTAATTATTTTTTAAAATAAA
Found at i:2408284 original size:41 final size:44
Alignment explanation
Indices: 2408239--2408322 Score: 104
Period size: 44 Copynumber: 1.9 Consensus size: 44
2408229 TTAATTAATT
2408239 TTAAAAAT-TTATATTA-ATTATTTTT-TAAAA-TAAAAATTAAA
1 TTAAAAATATT-TATTATATTATTTTTATAAAATTAAAAATTAAA
2408280 TTAAAAATAGTTTATTATTATTATTTTTAATAAAATTAAAAAT
1 TTAAAAATA-TTTATTA-TATTATTTTT-ATAAAATTAAAAAT
2408323 AATATTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
41 8 0.22
42 5 0.14
43 2 0.06
44 9 0.25
46 5 0.14
47 7 0.19
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (44 bp):
TTAAAAATATTTATTATATTATTTTTATAAAATTAAAAATTAAA
Found at i:2408418 original size:35 final size:38
Alignment explanation
Indices: 2408366--2408445 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 38
2408356 CAAATTAAAA
2408366 TATTAATTATATATTTTT-ATAAAAATAAAAA-G-TATT
1 TATTAATTATATATTTTTAAT-AAAATAAAAATGATATT
2408402 TATT-ATTAT-TATTTTTTAATAAAATAAAAATGATATT
1 TATTAATTATATA-TTTTTAATAAAATAAAAATGATATT
2408439 TAATTAA
1 T-ATTAA
2408446 ATTTTAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
34 2 0.05
35 20 0.53
36 7 0.18
37 5 0.13
38 3 0.08
39 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (38 bp):
TATTAATTATATATTTTTAATAAAATAAAAATGATATT
Found at i:2409295 original size:61 final size:65
Alignment explanation
Indices: 2409177--2409309 Score: 168
Period size: 67 Copynumber: 2.1 Consensus size: 65
2409167 CAATTATAAA
* *
2409177 AATAATACATATACAATATTAATTAATTTTAATAAAAATAAATTTGTATAATTTATAA-AT-AAA
1 AATAATACATACACAATATTAATTAATTTTAATAAAAATAAA--T-TATAATGTATAATATCAAA
2409240 AAG
63 AAG
*
2409243 TAATAATACATGCACAATATTAATTAATTTTAATAAAAAT-AA-TAT-ATGTATAATATCAAAAA
1 -AATAATACATACACAATATTAATTAATTTTAATAAAAATAAATTATAATGTATAATATCAAAAA
2409305 G
65 G
2409306 AATA
1 AATA
2409310 TGATTTTCAG
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
61 7 0.11
62 9 0.15
63 6 0.10
66 2 0.03
67 37 0.61
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.36
Consensus pattern (65 bp):
AATAATACATACACAATATTAATTAATTTTAATAAAAATAAATTATAATGTATAATATCAAAAAG
Found at i:2418985 original size:40 final size:40
Alignment explanation
Indices: 2418941--2419021 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
2418931 GGAATACAGT
2418941 TCATAGGTATTTTAATTGTTACTATAATCCAATAAAATGC
1 TCATAGGTATTTTAATTGTTACTATAATCCAATAAAATGC
2418981 TCATAGGTATTTTAATTGTTACTATAATCCAATAAAATGC
1 TCATAGGTATTTTAATTGTTACTATAATCCAATAAAATGC
2419021 T
1 T
2419022 TATGAATCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (40 bp):
TCATAGGTATTTTAATTGTTACTATAATCCAATAAAATGC
Done.