Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 365 of 410
Found at i:112103442 original size:18 final size:21
Alignment explanation
Indices: 112103398--112103448 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 21
112103388 CATTATTTAT
112103398 TATTATATTTAAAATAAATTCA
1 TATT-TATTTAAAATAAATTCA
112103420 TATTTATTTAAAA-AAA-T-A
1 TATTTATTTAAAATAAATTCA
*
112103438 TATTTAATTAA
1 TATTTATTTAA
112103449 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 11 0.39
19 1 0.04
20 3 0.11
21 9 0.32
22 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTTATTTAAAATAAATTCA
Found at i:112103725 original size:2 final size:2
Alignment explanation
Indices: 112103718--112103769 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
112103708 TCTATACTTT
* *
112103718 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA AA T- TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
112103758 T- TA TA GA TA TA T
1 TA TA TA TA TA TA T
112103770 TGTAGATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:112104021 original size:14 final size:15
Alignment explanation
Indices: 112103994--112104024 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
112103984 TTAATTTAAT
112103994 TATAAAATATAAAAA
1 TATAAAATATAAAAA
112104009 TATAAAA-ATAAAAA
1 TATAAAATATAAAAA
112104023 TA
1 TA
112104025 GAAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
TATAAAATATAAAAA
Found at i:112104124 original size:13 final size:13
Alignment explanation
Indices: 112104108--112104142 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
112104098 GGCGAAAAGT
112104108 AAAAAA-AAAAAA
1 AAAAAAGAAAAAA
*
112104120 GAAAAAGAAAAAA
1 AAAAAAGAAAAAA
112104133 AAAAAAGAAA
1 AAAAAAGAAA
112104143 CTTGTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:112104130 original size:19 final size:20
Alignment explanation
Indices: 112104102--112104142 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
112104092 TAAATAGGCG
112104102 AAAAGTAAAAAAAAAAAAGA
1 AAAAGTAAAAAAAAAAAAGA
112104122 AAAAG-AAAAAAAAAAAAGA
1 AAAAGTAAAAAAAAAAAAGA
112104141 AA
1 AA
112104143 CTTGTCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.02
Consensus pattern (20 bp):
AAAAGTAAAAAAAAAAAAGA
Found at i:112108546 original size:19 final size:19
Alignment explanation
Indices: 112108507--112108546 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
112108497 TTGAATAAAC
**
112108507 AAATATTATAAAACATTTA
1 AAATATTATAAAACAAATA
112108526 AAATATTATAAAACAAATA
1 AAATATTATAAAACAAATA
112108545 AA
1 AA
112108547 GAAAAACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATATTATAAAACAAATA
Found at i:112108552 original size:14 final size:13
Alignment explanation
Indices: 112108535--112108564 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
112108525 AAAATATTAT
112108535 AAAACAAATAAAGA
1 AAAACAAATAAA-A
112108549 AAAACAAATAAAA
1 AAAACAAATAAAA
112108562 AAA
1 AAA
112108565 TGCGTTGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.83, C:0.07, G:0.03, T:0.07
Consensus pattern (13 bp):
AAAACAAATAAAA
Found at i:112109190 original size:22 final size:22
Alignment explanation
Indices: 112109165--112109209 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
112109155 AAAATTTAAA
112109165 AAAGAAAATATAAAGATATTTT
1 AAAGAAAATATAAAGATATTTT
* * * *
112109187 AAAGATATTATGAATATATTTT
1 AAAGAAAATATAAAGATATTTT
112109209 A
1 A
112109210 TAATTTTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (22 bp):
AAAGAAAATATAAAGATATTTT
Found at i:112111427 original size:21 final size:21
Alignment explanation
Indices: 112111368--112111428 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
112111358 GATTATATGA
* * *
112111368 ATTGGATTGAATATTGATTAT
1 ATTGAATTGATTATTGAATAT
112111389 ATTGAATTGATT-TATGAATAT
1 ATTGAATTGATTAT-TGAATAT
112111410 ATGTGAATTG-TTATTGAAT
1 AT-TGAATTGATTATTGAAT
112111429 TGAAATTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.03
21 25 0.74
22 8 0.24
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (21 bp):
ATTGAATTGATTATTGAATAT
Found at i:112112304 original size:45 final size:45
Alignment explanation
Indices: 112112240--112112339 Score: 155
Period size: 45 Copynumber: 2.2 Consensus size: 45
112112230 CTGTTACCGC
* * *
112112240 TACTGCTACTATTACCGATTCGGCACTGTGTGTGTCGAATATTGT
1 TACTGTTACTATTACCGATTCAGCACTGTGTGTGTCGAATACTGT
* *
112112285 TACTGTTACTATTACCGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTATTACCGATTCAGCACTGTGTGTGTCGAATACTGT
112112330 TACTGTTACT
1 TACTGTTACT
112112340 GTTATTGTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (45 bp):
TACTGTTACTATTACCGATTCAGCACTGTGTGTGTCGAATACTGT
Found at i:112112337 original size:51 final size:51
Alignment explanation
Indices: 112112228--112112343 Score: 136
Period size: 45 Copynumber: 2.4 Consensus size: 51
112112218 ATGTGCTAGT
* * * *
112112228 TACTGTTACCGCTACTGCTACTATTACCGATTCGGCACTGTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTACTATTACCGATTCAGCACTGTGTGTGTCGAA
* *
112112279 TA----T--TGTTACTGTTACTATTACCGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACTATTACCGATTCAGCACTGTGTGTGTCGAA
112112324 TACTGTTACTGTTACTGTTA
1 TACTGTTACTGTTACTGTTA
112112344 TTGTTCCGGA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
45 38 0.72
47 1 0.02
49 1 0.02
51 13 0.25
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.41
Consensus pattern (51 bp):
TACTGTTACTGTTACTGTTACTATTACCGATTCAGCACTGTGTGTGTCGAA
Found at i:112112545 original size:18 final size:18
Alignment explanation
Indices: 112112524--112112714 Score: 167
Period size: 18 Copynumber: 10.6 Consensus size: 18
112112514 TAACTGATTA
112112524 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
* *
112112542 TTACCGGATAATTGACTG
1 TTACTGAATAATTGACTG
*
112112560 TTACTGGAT-ATTAGACTG
1 TTACTGAATAATT-GACTG
* * *
112112578 TTACTGAATAACTGAATA
1 TTACTGAATAATTGACTG
* *
112112596 TTACTGAATAATTGATTA
1 TTACTGAATAATTGACTG
* *
112112614 TTACTGAATAACTGATTG
1 TTACTGAATAATTGACTG
*
112112632 TCACTGAATGAA-TGACTG
1 TTACTGAAT-AATTGACTG
* *
112112650 CTACTGAATAACTT-AATAG
1 TTACTGAATAA-TTGACT-G
*
112112669 TTACTGAAT-ATCTGA-TT
1 TTACTGAATAAT-TGACTG
112112686 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
*
112112704 TTACTGGATAA
1 TTACTGAATAA
112112715 CCGATCAATT
Statistics
Matches: 143, Mismatches: 20, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
17 18 0.13
18 110 0.77
19 15 0.10
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:112112600 original size:36 final size:36
Alignment explanation
Indices: 112112512--112112794 Score: 180
Period size: 36 Copynumber: 7.6 Consensus size: 36
112112502 AAAGGTATAA
* *
112112512 AATAACTGATTATTACTGAATAATTGACTGTTACCG
1 AATAACTGAATATTACTGAATAATTGACTGTTACTG
* * * * *
112112548 GATAATTGACTGTTACTGGAT-ATTAGACTGTTACTG
1 AATAACTGAATATTACTGAATAATT-GACTGTTACTG
* *
112112584 AATAACTGAATATTACTGAATAATTGATTATTACTG
1 AATAACTGAATATTACTGAATAATTGACTGTTACTG
* * * *
112112620 AATAACTGATTGTCACTGAATGAA-TGACTGCTACTG
1 AATAACTGAATATTACTGAAT-AATTGACTGTTACTG
* *
112112656 AATAACTTAATAGTTACTGAAT-ATCTGA-TTTTACTG
1 AATAACTGAATA-TTACTGAATAAT-TGACTGTTACTG
* * * *
112112692 AATAATTGACTGTTACTGGATAACCGATCAATTGA-TCGATACTG
1 AATAACTGAATATTACT-G---A---AT-AATTGACT-GTTACTG
** * * *
112112736 AATAACTGGTTATTATTGAATAATTGATTGTTACCG
1 AATAACTGAATATTACTGAATAATTGACTGTTACTG
* *
112112772 AATAACTGACTGTTACTGAATAA
1 AATAACTGAATATTACTGAATAA
112112795 ATAATTATTC
Statistics
Matches: 188, Mismatches: 42, Indels: 34
0.71 0.16 0.13
Matches are distributed among these distances:
35 9 0.05
36 132 0.70
37 19 0.10
39 1 0.01
40 1 0.01
42 2 0.01
43 5 0.03
44 19 0.10
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (36 bp):
AATAACTGAATATTACTGAATAATTGACTGTTACTG
Found at i:112112649 original size:72 final size:71
Alignment explanation
Indices: 112112512--112112794 Score: 237
Period size: 72 Copynumber: 3.8 Consensus size: 71
112112502 AAAGGTATAA
* * * * * * * *
112112512 AATAACTGATTATTACTGAATAATTGACTGTTACCGGATAATTGACTGTTACTGGATATTAGACT
1 AATAACTGAATATTACTGAATAATTGA-TTTTACTGAATAACTGACTGTCACTGAATAATAGACT
*
112112577 GTTACTG
65 GCTACTG
*
112112584 AATAACTGAATATTACTGAATAATTGATTATTACTGAATAACTGATTGTCACTGAATGAAT-GAC
1 AATAACTGAATATTACTGAATAATTGATT-TTACTGAATAACTGACTGTCACTGAAT-AATAGAC
112112648 TGCTACTG
64 TGCTACTG
* * * * **
112112656 AATAACTTAATAGTTACTGAAT-ATCTGATTTTACTGAATAATTGACTGTTACTGGATAACCGAT
1 AATAACTGAATA-TTACTGAATAAT-TGATTTTACTGAATAACTGACTGTCACTGAATAATAGA-
112112720 CAATTGATCGATACTG
63 C---TG--C--TACTG
** * * *
112112736 AATAACTGGTTATTATTGAATAATTGATTGTTACCGAATAACTGACTGTTACTGAATAA
1 AATAACTGAATATTACTGAATAATTGATT-TTACTGAATAACTGACTGTCACTGAATAA
112112795 ATAATTATTC
Statistics
Matches: 173, Mismatches: 23, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
71 3 0.02
72 95 0.55
73 17 0.10
76 2 0.01
78 1 0.01
79 13 0.08
80 42 0.24
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (71 bp):
AATAACTGAATATTACTGAATAATTGATTTTACTGAATAACTGACTGTCACTGAATAATAGACTG
CTACTG
Found at i:112112774 original size:18 final size:18
Alignment explanation
Indices: 112112753--112112794 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
112112743 GGTTATTATT
* *
112112753 GAATAATTGATTGTTACC
1 GAATAACTGACTGTTACC
*
112112771 GAATAACTGACTGTTACT
1 GAATAACTGACTGTTACC
112112789 GAATAA
1 GAATAA
112112795 ATAATTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (18 bp):
GAATAACTGACTGTTACC
Found at i:112115925 original size:40 final size:40
Alignment explanation
Indices: 112115831--112115975 Score: 202
Period size: 40 Copynumber: 3.6 Consensus size: 40
112115821 TACTCGAATG
*
112115831 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
112115872 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
112115912 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
*
112115952 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
112115976 CTTGTGCGAG
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 63 0.68
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:112118120 original size:6 final size:6
Alignment explanation
Indices: 112118094--112118154 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
112118084 ATATGCACAG
* * * * *
112118094 TCAGAT ACAGAT ACAGAT TCAGTT TCAGAT TCAGAT TTAGAT AACAGAT
1 TCAGAT TCAGAT TCAGAT TCAGAT TCAGAT TCAGAT TCAGAT -TCAGAT
112118143 TCA-ATT TCAGAT
1 TCAGA-T TCAGAT
112118155 ATTCAGAGTC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
5 1 0.02
6 38 0.86
7 5 0.11
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (6 bp):
TCAGAT
Found at i:112118143 original size:19 final size:19
Alignment explanation
Indices: 112118119--112118155 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
112118109 GATTCAGTTT
112118119 CAGATTCAGATTT-AGATAA
1 CAGATTCA-ATTTCAGATAA
112118138 CAGATTCAATTTCAGATA
1 CAGATTCAATTTCAGATA
112118156 TTCAGAGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (19 bp):
CAGATTCAATTTCAGATAA
Found at i:112121101 original size:38 final size:38
Alignment explanation
Indices: 112121035--112121126 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 38
112121025 ACCAATTCGG
*
112121035 CACCCAGTGCCTCATCGGATAGTTCGAAGCAAAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGCAAAGTTGA
* * * *
112121073 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAAAG-TGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGCAAAGTTGA
* *
112121110 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
112121127 AATCTATCCG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
37 16 0.36
38 26 0.58
39 3 0.07
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGCAAAGTTGA
Found at i:112124136 original size:14 final size:14
Alignment explanation
Indices: 112124119--112124145 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
112124109 TTTCAATCTT
112124119 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
112124133 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
112124146 TTGGTATATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:112129991 original size:104 final size:104
Alignment explanation
Indices: 112129795--112129991 Score: 245
Period size: 104 Copynumber: 1.9 Consensus size: 104
112129785 GTGTGGCTCG
* * ** *
112129795 AAATCGTAAACAGTGAGTCACACGGCTTGGACACACATTCGTGTCCTTGCCTGTGTGGCTCACAC
1 AAATCGTAAACACTGAGTCACACGGCTTGGACACACATCCGTGTCCTTGCCCATGTGACTCACAC
* * * *
112129860 TACTTGACACTCACTCATGTCATCTGGCCGTATGGGTCT
66 TACTGGACACACACCCATGTCACCTGGCCGTATGGGTCT
* *
112129899 AAATCGTATACACTGAGTCACACGGCTTGGACACACGTCCGTGTCCTTGCCCATGTGACTCACAC
1 AAATCGTAAACACTGAGTCACACGGCTTGGACACACATCCGTGTCCTTGCCCATGTGACTCACAC
* *
112129964 -AGCCTGGGCACACACCCGTGTC-CCTGGC
66 TA--CTGGACACACACCCATGTCACCTGGC
112129992 TCGTGTGGTC
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
103 1 0.01
104 63 0.81
105 14 0.18
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (104 bp):
AAATCGTAAACACTGAGTCACACGGCTTGGACACACATCCGTGTCCTTGCCCATGTGACTCACAC
TACTGGACACACACCCATGTCACCTGGCCGTATGGGTCT
Found at i:112131764 original size:6 final size:6
Alignment explanation
Indices: 112131753--112131798 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
112131743 GAGCAATCAG
*
112131753 CGTCAC CGTCAC CGTCAC CGTCAC CGTCAC CGTCAC CGTCGC CGTC
1 CGTCAC CGTCAC CGTCAC CGTCAC CGTCAC CGTCAC CGTCAC CGTC
112131799 TTCTTTTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.13, C:0.50, G:0.20, T:0.17
Consensus pattern (6 bp):
CGTCAC
Found at i:112144206 original size:10 final size:10
Alignment explanation
Indices: 112144176--112144217 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
112144166 CACGTATAAA
112144176 TTAAATTTTT
1 TTAAATTTTT
*
112144186 TT--ATTTCT
1 TTAAATTTTT
112144194 TTAAATTTTT
1 TTAAATTTTT
112144204 TTAAATATTTT
1 TTAAAT-TTTT
112144215 TTA
1 TTA
112144218 GTGTAACACC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 7 0.26
10 13 0.48
11 7 0.26
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (10 bp):
TTAAATTTTT
Found at i:112146405 original size:32 final size:32
Alignment explanation
Indices: 112146364--112146429 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
112146354 TTGCCTAACC
112146364 AAGAACCATAGAAACACTTAACATCAACATGA
1 AAGAACCATAGAAACACTTAACATCAACATGA
*
112146396 AAGAACCATAGAAACACTTAACATCATCATGA
1 AAGAACCATAGAAACACTTAACATCAACATGA
112146428 AA
1 AA
112146430 AGTAATCTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.53, C:0.21, G:0.09, T:0.17
Consensus pattern (32 bp):
AAGAACCATAGAAACACTTAACATCAACATGA
Found at i:112147651 original size:22 final size:22
Alignment explanation
Indices: 112147607--112147656 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
112147597 CCCATATGCT
*
112147607 CGTGTGCAACCCCTCACATGCC
1 CGTGTGCAACCCCTCACAGGCC
* * *
112147629 CGTGTGTAACCCTTCATAGGCC
1 CGTGTGCAACCCCTCACAGGCC
*
112147651 CCTGTG
1 CGTGTG
112147657 AAAATCGCTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.16, C:0.38, G:0.22, T:0.24
Consensus pattern (22 bp):
CGTGTGCAACCCCTCACAGGCC
Found at i:112156724 original size:18 final size:18
Alignment explanation
Indices: 112156672--112156760 Score: 101
Period size: 18 Copynumber: 5.1 Consensus size: 18
112156662 CAATCCCAAC
* *
112156672 TACTGTATATGTGAACAG
1 TACTGTATACGTGAATAG
*
112156690 TACTGTATACGTAAATAG
1 TACTGTATACGTGAATAG
*
112156708 TACTGTATACATGAATAG
1 TACTGTATACGTGAATAG
* **
112156726 TGCCATATACGTGAATAG
1 TACTGTATACGTGAATAG
112156744 T-C-GTATACGTGAATAG
1 TACTGTATACGTGAATAG
112156760 T
1 T
112156761 GCCGTAAATG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
16 14 0.23
17 1 0.02
18 46 0.75
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (18 bp):
TACTGTATACGTGAATAG
Found at i:112156757 original size:34 final size:36
Alignment explanation
Indices: 112156695--112156763 Score: 106
Period size: 34 Copynumber: 2.0 Consensus size: 36
112156685 AACAGTACTG
112156695 TATACGTAAATAGTACTGTATACATGAATAGTGCCA
1 TATACGTAAATAGTACTGTATACATGAATAGTGCCA
* *
112156731 TATACGTGAATAGT-C-GTATACGTGAATAGTGCC
1 TATACGTAAATAGTACTGTATACATGAATAGTGCC
112156764 GTAAATGGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 17 0.55
35 1 0.03
36 13 0.42
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.30
Consensus pattern (36 bp):
TATACGTAAATAGTACTGTATACATGAATAGTGCCA
Found at i:112157516 original size:40 final size:40
Alignment explanation
Indices: 112157461--112157605 Score: 236
Period size: 40 Copynumber: 3.6 Consensus size: 40
112157451 TATATATGTG
* *
112157461 GAAGGCAATCGTGCGGGTTATTATAACCGGGTTAAGTCTC
1 GAAGGCATTCGTGCGGGTTATTATAACCAGGTTAAGTCTC
112157501 GAAGGCATTCGTGCGGGTTATTATAACCAGGTTAAGTCTC
1 GAAGGCATTCGTGCGGGTTATTATAACCAGGTTAAGTCTC
* *
112157541 GAAGGCATTTGTGCGGGTTATTATAACCAGGTTAAGTCCC
1 GAAGGCATTCGTGCGGGTTATTATAACCAGGTTAAGTCTC
* *
112157581 GAAGGCATTCGTGCTGGTTGTTATA
1 GAAGGCATTCGTGCGGGTTATTATA
112157606 TCTGAGCCAA
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 98 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (40 bp):
GAAGGCATTCGTGCGGGTTATTATAACCAGGTTAAGTCTC
Found at i:112165669 original size:79 final size:79
Alignment explanation
Indices: 112165551--112165725 Score: 280
Period size: 79 Copynumber: 2.2 Consensus size: 79
112165541 TGGAACGTAA
*
112165551 TCGTGCGGGTTATTATAACAGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCGGGTT
1 TCGTGCGGGTTATTATAACACGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACC-GGTT
* *
112165616 ATGTCCCGAAAGCAT
65 AAGACCCGAAAGCAT
112165631 TCGTGCGGGTTATTATAAC-CGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCGGTTA
1 TCGTGCGGGTTATTATAACACGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCGGTTA
*
112165695 AGACCCGAAGGCAT
66 AGACCCGAAAGCAT
* *
112165709 TCGTGCTGGTTGTTATA
1 TCGTGCGGGTTATTATA
112165726 TCCGAGCCAA
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
78 31 0.35
79 39 0.44
80 19 0.21
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.30
Consensus pattern (79 bp):
TCGTGCGGGTTATTATAACACGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCGGTTA
AGACCCGAAAGCAT
Found at i:112165670 original size:39 final size:39
Alignment explanation
Indices: 112165551--112165725 Score: 278
Period size: 39 Copynumber: 4.4 Consensus size: 39
112165541 TGGAACGTAA
*
112165551 TCGTGCGGGTTATTATAACAGGGTTAAGTCCCGAAGGCAT
1 TCGTGCGGGTTATTATAAC-CGGTTAAGTCCCGAAGGCAT
* *
112165591 TCGTGCGGGTTATTATAACCGGGTTATGTCCCGAAAGCAT
1 TCGTGCGGGTTATTATAACC-GGTTAAGTCCCGAAGGCAT
112165631 TCGTGCGGGTTATTATAACCGGTTAAGTCCCGAAGGCAT
1 TCGTGCGGGTTATTATAACCGGTTAAGTCCCGAAGGCAT
*
112165670 TCGTGCGGGTTATTATAACCGGTTAAGACCCGAAGGCAT
1 TCGTGCGGGTTATTATAACCGGTTAAGTCCCGAAGGCAT
* *
112165709 TCGTGCTGGTTGTTATA
1 TCGTGCGGGTTATTATA
112165726 TCCGAGCCAA
Statistics
Matches: 126, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 70 0.56
40 56 0.44
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.30
Consensus pattern (39 bp):
TCGTGCGGGTTATTATAACCGGTTAAGTCCCGAAGGCAT
Found at i:112171322 original size:9 final size:9
Alignment explanation
Indices: 112171308--112171549 Score: 152
Period size: 9 Copynumber: 26.6 Consensus size: 9
112171298 TATTTAAGTA
112171308 TTATGTAAG
1 TTATGTAAG
*
112171317 TTATGTAAT
1 TTATGTAAG
*
112171326 TTATGATATG
1 TTATG-TAAG
* * *
112171336 ATATAT-AT
1 TTATGTAAG
*
112171344 TTATGTAAA
1 TTATGTAAG
*
112171353 TTATAT-A-
1 TTATGTAAG
*
112171360 TTATCTAAG
1 TTATGTAAG
*
112171369 TTATATAAG
1 TTATGTAAG
112171378 TTATGTAAG
1 TTATGTAAG
*
112171387 TTATGTAAA
1 TTATGTAAG
*
112171396 TTATGATATAAAA
1 TTATG---T-AAG
*
112171409 TATATTTAAG
1 T-TATGTAAG
112171419 TATTATGTAAG
1 --TTATGTAAG
112171430 TTATGTAAG
1 TTATGTAAG
* *
112171439 TTATAT-AT
1 TTATGTAAG
*
112171447 TTATCTAAG
1 TTATGTAAG
*
112171456 TTATATAAG
1 TTATGTAAG
*
112171465 TTATATAAG
1 TTATGTAAG
*
112171474 TTATGTATG
1 TTATGTAAG
*
112171483 TTATATAAG
1 TTATGTAAG
*
112171492 TTATGTATG
1 TTATGTAAG
*
112171501 -TATATAAG
1 TTATGTAAG
112171509 TTATGTAAG
1 TTATGTAAG
* *
112171518 TTATATATG
1 TTATGTAAG
*
112171527 TTATATAAG
1 TTATGTAAG
*
112171536 TTATGTAAA
1 TTATGTAAG
112171545 TTATG
1 TTATG
112171550 ATATCAAATA
Statistics
Matches: 183, Mismatches: 37, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
7 5 0.03
8 18 0.10
9 136 0.74
10 7 0.04
11 8 0.04
12 2 0.01
13 4 0.02
14 3 0.02
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:112171480 original size:44 final size:43
Alignment explanation
Indices: 112171344--112171533 Score: 192
Period size: 44 Copynumber: 4.4 Consensus size: 43
112171334 TGATATATAT
*
112171344 TTATGTAAATTATATATTATCTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATATTATCTAAGTTATATAAGTTATGTAAG
* * *
112171387 TTATGTAAATTATGATA-TA---AAATATATTTAAGTATTATGTAAG
1 TTATGTAAGTTAT-ATATTATCTAAGT-TATATAAG--TTATGTAAG
*
112171430 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATATAAG
1 TTATGTAAGTTATATA-TTATCTAAGTTATATAAGTTATGTAAG
* * *
112171474 TTATGTATGTTATATAAGTTATGTATG-TATATAAGTTATGTAAG
1 TTATGTAAGTTATAT-A-TTATCTAAGTTATATAAGTTATGTAAG
* *
112171518 TTATATATGTTATATA
1 TTATGTAAGTTATATA
112171534 AGTTATGTAA
Statistics
Matches: 125, Mismatches: 12, Indels: 20
0.80 0.08 0.13
Matches are distributed among these distances:
40 3 0.02
41 7 0.06
42 3 0.02
43 37 0.30
44 57 0.46
45 8 0.06
46 7 0.06
47 3 0.02
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (43 bp):
TTATGTAAGTTATATATTATCTAAGTTATATAAGTTATGTAAG
Found at i:112171492 original size:53 final size:53
Alignment explanation
Indices: 112171308--112171553 Score: 189
Period size: 53 Copynumber: 4.7 Consensus size: 53
112171298 TATTTAAGTA
* * * * * * *
112171308 TTATGTAAGTTATGTAATTTATGATATGATATATATTTATGTAAATTATAT-A-
1 TTATATAAGTTATGTAAGTTATG-TAAGTTATATATGTATATAAGTTATATAAG
* * * * * * *
112171360 TTATCTAAGTTATATAAGTTATGTAAGTTATGTA--AAT-TATGATATA-AAA
1 TTATATAAGTTATGTAAGTTATGTAAGTTATATATGTATATAAGTTATATAAG
* * *
112171409 TATATTTAAGTATTATGTAAGTTATGTAAGTTATATATTTATCTAAGTTATATAAG
1 T-TATATAAG--TTATGTAAGTTATGTAAGTTATATATGTATATAAGTTATATAAG
* * * *
112171465 TTATATAAGTTATGTATGTTATATAAGTTATGTATGTATATAAGTTATGTAAG
1 TTATATAAGTTATGTAAGTTATGTAAGTTATATATGTATATAAGTTATATAAG
* * *
112171518 TTATATATGTTATATAAGTTATGTAAATTATGATAT
1 TTATATAAGTTATGTAAGTTATGTAAGTTAT-ATAT
112171554 CAAATATTTT
Statistics
Matches: 154, Mismatches: 30, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
48 7 0.05
49 3 0.02
50 7 0.05
51 8 0.05
52 43 0.28
53 64 0.42
54 5 0.03
55 14 0.09
56 3 0.02
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.48
Consensus pattern (53 bp):
TTATATAAGTTATGTAAGTTATGTAAGTTATATATGTATATAAGTTATATAAG
Found at i:112171534 original size:44 final size:45
Alignment explanation
Indices: 112171421--112171548 Score: 179
Period size: 44 Copynumber: 2.9 Consensus size: 45
112171411 TATTTAAGTA
* * *
112171421 TTATGTAAGTTATGTAAGTTATAT-ATTTATCTAAGTTATATAAG
1 TTATGTAAGTTATGTATGTTATATAAGTTATGTAAGTTATATAAG
* *
112171465 TTATATAAGTTATGTATGTTATATAAGTTATGTATG-TATATAAG
1 TTATGTAAGTTATGTATGTTATATAAGTTATGTAAGTTATATAAG
* *
112171509 TTATGTAAGTTATATATGTTATATAAGTTATGTAAATTAT
1 TTATGTAAGTTATGTATGTTATATAAGTTATGTAAGTTAT
112171549 GATATCAAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
44 62 0.85
45 11 0.15
ACGTcount: A:0.37, C:0.01, G:0.14, T:0.48
Consensus pattern (45 bp):
TTATGTAAGTTATGTATGTTATATAAGTTATGTAAGTTATATAAG
Found at i:112171548 original size:18 final size:18
Alignment explanation
Indices: 112171308--112171549 Score: 179
Period size: 18 Copynumber: 13.3 Consensus size: 18
112171298 TATTTAAGTA
* *
112171308 TTATGTAAGTTATGTAAT
1 TTATGTAAGTTATATAAG
* * *
112171326 TTATGATATGATATAT-AT
1 TTATG-TAAGTTATATAAG
*
112171344 TTATGTAAATTATAT-A-
1 TTATGTAAGTTATATAAG
*
112171360 TTATCTAAGTTATATAAG
1 TTATGTAAGTTATATAAG
* *
112171378 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
* *
112171396 TTATGATATAAAATATATTTAAG
1 TTATG---T-AAGT-TATATAAG
*
112171419 TATTATGTAAGTTATGTAAG
1 --TTATGTAAGTTATATAAG
* * *
112171439 TTATAT-ATTTATCTAAG
1 TTATGTAAGTTATATAAG
*
112171456 TTATATAAGTTATATAAG
1 TTATGTAAGTTATATAAG
*
112171474 TTATGTATGTTATATAAG
1 TTATGTAAGTTATATAAG
*
112171492 TTATGTATG-TATATAAG
1 TTATGTAAGTTATATAAG
*
112171509 TTATGTAAGTTATATATG
1 TTATGTAAGTTATATAAG
* * *
112171527 TTATATAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
112171545 TTATG
1 TTATG
112171550 ATATCAAATA
Statistics
Matches: 182, Mismatches: 30, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
16 13 0.07
17 40 0.22
18 96 0.53
19 7 0.04
20 7 0.04
21 4 0.02
22 4 0.02
23 6 0.03
25 5 0.03
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (18 bp):
TTATGTAAGTTATATAAG
Found at i:112171739 original size:24 final size:24
Alignment explanation
Indices: 112171675--112171742 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
112171665 CTTAAACGGT
*
112171675 TAAAACAGACGATAATATTTGTGA
1 TAAAACGGACGATAATATTTGTGA
112171699 TAAAACGGA-GAATAATATTTGTGA
1 TAAAACGGACG-ATAATATTTGTGA
*
112171723 TAAAACGGACGAGAATATTT
1 TAAAACGGACGATAATATTT
112171743 CAATAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.03
24 38 0.95
25 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (24 bp):
TAAAACGGACGATAATATTTGTGA
Found at i:112172377 original size:11 final size:11
Alignment explanation
Indices: 112172361--112172398 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
112172351 ATGTTCCATG
112172361 ATGTTAGGTAA
1 ATGTTAGGTAA
*
112172372 ATGTTATG-ATA
1 ATGTTAGGTA-A
112172383 ATGTTAGGTAA
1 ATGTTAGGTAA
112172394 ATGTT
1 ATGTT
112172399 TCATGATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 1 0.04
11 21 0.91
12 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (11 bp):
ATGTTAGGTAA
Found at i:112172398 original size:43 final size:45
Alignment explanation
Indices: 112172318--112172433 Score: 155
Period size: 43 Copynumber: 2.5 Consensus size: 45
112172308 TTGATAATAG
112172318 GTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTCCATGAT
1 GTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTCCATGAT
*
112172363 GTTAGGTAAATGTT-ATGATAAT-GTTAGGTAAATGTTTCATGATAAT
1 GTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTCCATG---AT
112172409 GGGTTAGGTAAATGTTTCATGATAA
1 --GTTAGGTAAATG-TTCATGATAA
112172434 GAATTTCATG
Statistics
Matches: 63, Mismatches: 1, Indels: 9
0.86 0.01 0.12
Matches are distributed among these distances:
43 18 0.29
44 8 0.13
45 14 0.22
46 2 0.03
48 12 0.19
49 2 0.03
50 7 0.11
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (45 bp):
GTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTCCATGAT
Found at i:112172419 original size:26 final size:25
Alignment explanation
Indices: 112172309--112172433 Score: 167
Period size: 26 Copynumber: 5.2 Consensus size: 25
112172299 TGATACAAAT
112172309 TGATAATAGGTTAGGTAAATG-TTCA
1 TGATAAT-GGTTAGGTAAATGTTTCA
*
112172334 TGATAATGGTTAGGTAAATGTTCCA
1 TGATAATGGTTAGGTAAATGTTTCA
112172359 TG---AT-GTTAGGTAAATG-TT-A
1 TGATAATGGTTAGGTAAATGTTTCA
112172378 TGATAAT-GTTAGGTAAATGTTTCA
1 TGATAATGGTTAGGTAAATGTTTCA
112172402 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAAT-GGTTAGGTAAATGTTTCA
112172428 TGATAA
1 TGATAA
112172434 GAATTTCATG
Statistics
Matches: 90, Mismatches: 2, Indels: 15
0.84 0.02 0.14
Matches are distributed among these distances:
19 3 0.03
20 1 0.01
21 12 0.13
22 16 0.18
23 2 0.02
24 21 0.23
25 12 0.13
26 23 0.26
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (25 bp):
TGATAATGGTTAGGTAAATGTTTCA
Found at i:112175627 original size:12 final size:12
Alignment explanation
Indices: 112175610--112175640 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
112175600 ACTCGGGGAA
112175610 GAGGCCGTGGTC
1 GAGGCCGTGGTC
112175622 GAGGCCGTGGTC
1 GAGGCCGTGGTC
112175634 GAGGCCG
1 GAGGCCG
112175641 AGGTAGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.26, G:0.52, T:0.13
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:112180546 original size:26 final size:26
Alignment explanation
Indices: 112180489--112180621 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
112180479 TGATACAAAT
*
112180489 TGATAATAGGTTAGGTAAATG-TTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
112180514 TGATAATGTGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
112180540 TGATAATGGGTTAGGTAAATGTTT-A
1 TGATAATGGGTTAGGTAAATGTTTCA
*
112180565 TGATAAT-GTTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
112180590 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
112180616 TGATAA
1 TGATAA
112180622 GAATTTCATG
Statistics
Matches: 100, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
24 15 0.15
25 35 0.35
26 50 0.50
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.40
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:112180598 original size:50 final size:51
Alignment explanation
Indices: 112180489--112180621 Score: 232
Period size: 50 Copynumber: 2.6 Consensus size: 51
112180479 TGATACAAAT
* *
112180489 TGATAATAGGTTAGGTAAATGTTCATGATAATGTGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTATGATAATGTGTTAGGTAAATGTTTCA
112180540 TGATAATGGGTTAGGTAAATGTTTATGATAATGT-TTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTATGATAATGTGTTAGGTAAATGTTTCA
112180590 TGATAATGGGTTAGGTAAATGTTTCATGATAA
1 TGATAATGGGTTAGGTAAATGTTT-ATGATAA
112180622 GAATTTCATG
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
50 40 0.51
51 39 0.49
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.40
Consensus pattern (51 bp):
TGATAATGGGTTAGGTAAATGTTTATGATAATGTGTTAGGTAAATGTTTCA
Found at i:112184226 original size:499 final size:501
Alignment explanation
Indices: 112183283--112184235 Score: 1641
Period size: 499 Copynumber: 1.9 Consensus size: 501
112183273 TATTGTTGTA
112183283 ATTTTGATAAAAAGTAGTTATAACTTTTAAAGAAATTTAAAAATATTAAATATTAAAATAAAACA
1 ATTTTGATAAAAAGTAGTTATAACTTTTAAAGAAATTTAAAAATATTAAATATTAAAATAAAACA
* * *
112183348 TTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCAAAAAAGAATCGTAGTTTAATTTT
66 TTAGTAATACAAAAAAATAGTAATTTGAATATAATAATATAAAAAAAGAATCGTAGTTTAATTTT
* *
112183413 TATAAGTAAATTGGAAATAAATTAAGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAAT
131 TATAAGTAAATTGGAAATAAATTAA-GTTATATAAATATGC-ATA-CGATAGAACTTTTTTCAAG
112183478 TCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATAT
193 TCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATAT
112183543 CTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATAT
258 CTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATAT
* * *
112183608 TTAAAATAAGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTCTAATGGACAAACACGCTACACGG
323 TTAAAATAAGGTTGGAGAGAAGGCCAGCCATTGTTGTAATTCTAATGGACAAACAAGCTACACGG
112183673 TAATAAAATTAATTCATACCTATTCATACTTAACTTGAATAAAAAAATAATTAAGTTGAACCAAT
388 TAATAAAATTAATTCATACCTATTCATACTTAACTTGAATAAAAAAATAATTAAGTTGAACCAAT
112183738 TATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACT
453 TATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACT
*
112183787 ATTTTGATAAAAAGTAGTTATAACTTTTAAAGAAATTTAAAAATATTAAATATTAAAATCAAACA
1 ATTTTGATAAAAAGTAGTTATAACTTTTAAAGAAATTTAAAAATATTAAATATTAAAATAAAACA
*
112183852 TTAGTAATGCAAAAAAATAGTAATTTGAATATAATAATATAAAAAAAGAATCGTAGTTTAATTTT
66 TTAGTAATACAAAAAAATAGTAATTTGAATATAATAATATAAAAAAAGAATCGTAGTTTAATTTT
112183917 TATAAGTAAATTGGAAATAAA-T-A-TTCAATAGTAAATGA-GC-T-CGATAGAACTTTTTTCAA
131 TATAAGTAAATTGGAAATAAATTAAGTT--ATA-TAAAT-ATGCATACGATAGAACTTTTTTCAA
112183976 GTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATA
192 GTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATA
112184041 TCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATA
257 TCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATA
* * *
112184106 TTTAAAATAAGGTTGGAGAGAAGGCCATCCATTGTTGTAATTTTAATGGACAAGCAAGCTACACG
322 TTTAAAATAAGGTTGGAGAGAAGGCCAGCCATTGTTGTAATTCTAATGGACAAACAAGCTACACG
* * *
112184171 GTAATAAAATTAATTCATACTTATTCATACTTAAGC-TGAATCAAATAATAATTAAGTTGAACCA
387 GTAATAAAATTAATTCATACCTATTCATACTTAA-CTTGAATAAAAAAATAATTAAGTTGAACCA
112184235 A
451 A
112184236 ATATTTAAAA
Statistics
Matches: 428, Mismatches: 16, Indels: 15
0.93 0.03 0.03
Matches are distributed among these distances:
499 266 0.62
500 3 0.01
501 1 0.00
502 4 0.01
503 7 0.02
504 147 0.34
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (501 bp):
ATTTTGATAAAAAGTAGTTATAACTTTTAAAGAAATTTAAAAATATTAAATATTAAAATAAAACA
TTAGTAATACAAAAAAATAGTAATTTGAATATAATAATATAAAAAAAGAATCGTAGTTTAATTTT
TATAAGTAAATTGGAAATAAATTAAGTTATATAAATATGCATACGATAGAACTTTTTTCAAGTCT
TTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTT
GCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTA
AAATAAGGTTGGAGAGAAGGCCAGCCATTGTTGTAATTCTAATGGACAAACAAGCTACACGGTAA
TAAAATTAATTCATACCTATTCATACTTAACTTGAATAAAAAAATAATTAAGTTGAACCAATTAT
AAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACT
Found at i:112184394 original size:15 final size:15
Alignment explanation
Indices: 112184374--112184402 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
112184364 AGAATTTTGA
112184374 AATAAAACGTACCTT
1 AATAAAACGTACCTT
112184389 AATAAAACGTACCT
1 AATAAAACGTACCT
112184403 GGTCTACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (15 bp):
AATAAAACGTACCTT
Found at i:112185058 original size:14 final size:13
Alignment explanation
Indices: 112185039--112185068 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
112185029 CAATATAATT
112185039 TTACTTCATATATA
1 TTACTTCATATA-A
112185053 TTACTTCATATAA
1 TTACTTCATATAA
112185066 TTA
1 TTA
112185069 TTATAGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (13 bp):
TTACTTCATATAA
Found at i:112187241 original size:15 final size:15
Alignment explanation
Indices: 112187223--112187271 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
112187213 GGAAAAAATT
112187223 TTGGGGGAGAAGAAG
1 TTGGGGGAGAAGAAG
*
112187238 TT-GGGG-G-A-AAT
1 TTGGGGGAGAAGAAG
112187249 TTGGGGGAGAAGAAG
1 TTGGGGGAGAAGAAG
112187264 TTGGGGGA
1 TTGGGGGA
112187272 AATTTGGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
11 4 0.14
12 5 0.18
13 2 0.07
14 5 0.18
15 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.53, T:0.18
Consensus pattern (15 bp):
TTGGGGGAGAAGAAG
Found at i:112187253 original size:26 final size:26
Alignment explanation
Indices: 112187222--112187282 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
112187212 GGGAAAAAAT
112187222 TTTGGGGGAGAAGAAGTTGGGGGAAA
1 TTTGGGGGAGAAGAAGTTGGGGGAAA
112187248 TTTGGGGGAGAAGAAGTTGGGGGAAA
1 TTTGGGGGAGAAGAAGTTGGGGGAAA
112187274 TTTGGGGGA
1 TTTGGGGGA
112187283 AATCGGGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.28, C:0.00, G:0.51, T:0.21
Consensus pattern (26 bp):
TTTGGGGGAGAAGAAGTTGGGGGAAA
Found at i:112187254 original size:11 final size:11
Alignment explanation
Indices: 112187238--112187285 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 11
112187228 GGAGAAGAAG
112187238 TTGGGGGAAAT
1 TTGGGGGAAAT
*
112187249 TTGGGGGAGAAGAAG
1 TT-GGGG-G-A-AAT
112187264 TTGGGGGAAAT
1 TTGGGGGAAAT
112187275 TTGGGGGAAAT
1 TTGGGGGAAAT
112187286 CGGGGAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
11 15 0.48
12 5 0.16
13 2 0.06
14 5 0.16
15 4 0.13
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (11 bp):
TTGGGGGAAAT
Found at i:112187595 original size:28 final size:28
Alignment explanation
Indices: 112187563--112187620 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
112187553 AATCAAAACT
*
112187563 CTAT-ACCTTAAACCATTAAACTATATCC
1 CTATAACCTTAAACC-CTAAACTATATCC
* *
112187591 CTATAACCTTAATCCCTAAAGTATATCC
1 CTATAACCTTAAACCCTAAACTATATCC
112187619 CT
1 CT
112187621 TAAACCCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (28 bp):
CTATAACCTTAAACCCTAAACTATATCC
Found at i:112187621 original size:21 final size:21
Alignment explanation
Indices: 112187597--112187640 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
112187587 ATCCCTATAA
* *
112187597 CCTTAATCCCTAAAGTATATC
1 CCTTAAACCCTAAACTATATC
112187618 CCTTAAACCCTAAACTATATC
1 CCTTAAACCCTAAACTATATC
112187639 CC
1 CC
112187641 CTAACCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.34, G:0.02, T:0.30
Consensus pattern (21 bp):
CCTTAAACCCTAAACTATATC
Found at i:112187900 original size:21 final size:22
Alignment explanation
Indices: 112187869--112187912 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
112187859 ATTAACCCCT
*
112187869 AACCCCTAACCCTTAAATCATA
1 AACCCCTAACCCTTAAACCATA
112187891 AACCCC-AACCCTTAAACCATA
1 AACCCCTAACCCTTAAACCATA
112187912 A
1 A
112187913 TACATAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.18
Consensus pattern (22 bp):
AACCCCTAACCCTTAAACCATA
Found at i:112188068 original size:40 final size:40
Alignment explanation
Indices: 112187975--112188099 Score: 180
Period size: 41 Copynumber: 3.1 Consensus size: 40
112187965 CCTAAACTTA
*
112187975 TTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTATTT
1 TTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC-TATTT
*
112188016 TTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCTGTTT
1 TTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCTATTT
* *
112188056 TTAGCGGCGTTTTTCGTAAAA-CGCCGCTATTGCTCTATGTT
1 TTAGCGGCGTTTTAC-CAAAAGCGCCGCTATTGCTCTAT-TT
112188097 TTA
1 TTA
112188100 CAATTTGTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
40 34 0.44
41 43 0.56
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (40 bp):
TTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCTATTT
Found at i:112188140 original size:12 final size:12
Alignment explanation
Indices: 112188123--112188148 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
112188113 GTTTTTTGTT
112188123 AAAACGCCGCTA
1 AAAACGCCGCTA
112188135 AAAACGCCGCTA
1 AAAACGCCGCTA
112188147 AA
1 AA
112188149 GACCTGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:112188856 original size:2 final size:2
Alignment explanation
Indices: 112188849--112188881 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
112188839 TATTTTTAGT
112188849 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
112188882 TGTGCTATTT
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:112191489 original size:2 final size:2
Alignment explanation
Indices: 112191482--112191540 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
112191472 ATTGCTTTTG
112191482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
112191524 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
112191541 CTCCTTTAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:112193023 original size:13 final size:12
Alignment explanation
Indices: 112192982--112193025 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
112192972 ACCCAATACA
112192982 AACCCAAAACTT
1 AACCCAAAACTT
*
112192994 AGCCCAAAACTT
1 AACCCAAAACTT
*
112193006 AACCCAAAACACT
1 AACCCAAAAC-TT
112193019 AACCCAA
1 AACCCAA
112193026 CCCAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 20 0.71
13 8 0.29
ACGTcount: A:0.50, C:0.36, G:0.02, T:0.11
Consensus pattern (12 bp):
AACCCAAAACTT
Found at i:112193430 original size:12 final size:12
Alignment explanation
Indices: 112193409--112193444 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
112193399 TATATTAGAT
112193409 TATATCAAAAAAA
1 TATAT-AAAAAAA
*
112193422 TATTTAAAAAAA
1 TATATAAAAAAA
112193434 TATATAAAAAA
1 TATATAAAAAA
112193445 GCGTACCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (12 bp):
TATATAAAAAAA
Found at i:112194176 original size:22 final size:22
Alignment explanation
Indices: 112194151--112194192 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
112194141 TAACGTGCTA
* *
112194151 TTATTACTATTATTTTTATTTG
1 TTATTACCATTATTGTTATTTG
112194173 TTATTACCATTATTGTTATT
1 TTATTACCATTATTGTTATT
112194193 GTAATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.64
Consensus pattern (22 bp):
TTATTACCATTATTGTTATTTG
Found at i:112206102 original size:44 final size:44
Alignment explanation
Indices: 112206043--112206162 Score: 143
Period size: 44 Copynumber: 2.7 Consensus size: 44
112206033 CAAAAGCAGC
* * *
112206043 GAGCTTTAACCCCCTAAGCAGTAGGGTAACAAACTGAAGTTCAT
1 GAGCTTTAACACCCTAAGCAGTAGGGTAACAAACTGAAGATAAT
* * * * *
112206087 -AGATCTTATCACCCTAAGCAGTAGGGAAACAGATTGAAGATAAT
1 GAGCT-TTAACACCCTAAGCAGTAGGGTAACAAACTGAAGATAAT
*
112206131 GAGCTTTAACCCCCTAAGCAGTAGGGTAACAA
1 GAGCTTTAACACCCTAAGCAGTAGGGTAACAA
112206163 GCCAAATTTA
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
43 3 0.05
44 55 0.90
45 3 0.05
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (44 bp):
GAGCTTTAACACCCTAAGCAGTAGGGTAACAAACTGAAGATAAT
Found at i:112206543 original size:178 final size:178
Alignment explanation
Indices: 112206135--112206624 Score: 454
Period size: 178 Copynumber: 2.8 Consensus size: 178
112206125 GATAATGAGC
* * * *
112206135 TTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTA-CAGACCTTAACCCCCTAAGTAGTAGG
1 TTTAACCCCCTAAGCAGTAGGGTAACAAG-CAAAATAACCAGACTTTAACCCCCTAAGCAGTAGG
* * * * ** * * **
112206199 GTAATAGGCTGAAAATTACAGATCTTGTCTCCCTGAAGTTGCAGTGAAATAGATCGAATCCAGCG
65 GTAACAAGCTGAAAATTACAGATCTTATCGCCCTGAAGCAGCAGGGAAACAGATCGAAGACAGCG
* * * * *
112206264 AATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATTTACAGAT
130 AATCTTGCCCTCCTGAAGTTGCAGTGAAGCAGATTCAAGATCTACAAAT
* * * * * *
112206313 CTT-ACCCCCTAAGCAGTAGGGAAACAGATCAAAAGTAACGAG-CTTCAACCCCCTGAGCAGTAG
1 TTTAACCCCCTAAGCAGTAGGGTAACA-AGCAAAA-TAACCAGACTTTAACCCCCTAAGCAGTAG
* ** * * *
112206376 GGTAACAAGCTGGAGTTTATAGATCTTATCGCCCT-AAGCAGTAGGGAAGCAGATCAGAAGACAG
64 GGTAACAAGCTGAAAATTACAGATCTTATCGCCCTGAAGCAGCAGGGAAACAGATC-GAAGACAG
*
112206440 CGAATCTTGCCCTCCTGAAGTTGCAGTGAAGTAGATTCAA-A-CTACCAAAT
128 CGAATCTTGCCCTCCTGAAGTTGCAGTGAAGCAGATTCAAGATCTA-CAAAT
* * *
112206490 TTTAACCCCCTAAGCAGTAGGGTAACAAGCTAAATCCACCAGACTTTAACCCCCCAAGCAGTAGG
1 TTTAACCCCCTAAGCAGTAGGGTAACAAGCAAAAT-AACCAGACTTTAACCCCCTAAGCAGTAGG
* * * ** * ** * **
112206555 GTAATAGGCTGAAAATTACAAATCTCGTCTCCCTGAAGTTGCAGCGG-AACAGATCAAATCCAGC
65 GTAACAAGCTGAAAATTACAGATCTTATCGCCCTGAAGCAGCAG-GGAAACAGATCGAAGACAGC
112206619 GAATCT
129 GAATCT
112206625 GTCTTCTTGA
Statistics
Matches: 244, Mismatches: 58, Indels: 20
0.76 0.18 0.06
Matches are distributed among these distances:
176 3 0.01
177 56 0.23
178 168 0.69
179 15 0.06
180 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (178 bp):
TTTAACCCCCTAAGCAGTAGGGTAACAAGCAAAATAACCAGACTTTAACCCCCTAAGCAGTAGGG
TAACAAGCTGAAAATTACAGATCTTATCGCCCTGAAGCAGCAGGGAAACAGATCGAAGACAGCGA
ATCTTGCCCTCCTGAAGTTGCAGTGAAGCAGATTCAAGATCTACAAAT
Found at i:112210967 original size:20 final size:20
Alignment explanation
Indices: 112210929--112210976 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
112210919 TAAATTCTAA
* **
112210929 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
112210949 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
112210969 AAA-ATAAA
1 AAAGATAAA
112210977 ATCCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:112221966 original size:9 final size:9
Alignment explanation
Indices: 112221933--112221992 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
112221923 AAAATAATTC
*
112221933 TAATGATAG
1 TAATAATAG
* *
112221942 TAAAATATAC
1 TAATA-ATAG
112221952 TAATAATAG
1 TAATAATAG
112221961 TAATAATAG
1 TAATAATAG
*
112221970 CAATAATAG
1 TAATAATAG
112221979 T-A-AATAG
1 TAATAATAG
112221986 -AATAATA
1 TAATAATA
112221993 AATAATACTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
7 6 0.15
8 5 0.12
9 23 0.56
10 7 0.17
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (9 bp):
TAATAATAG
Found at i:112221996 original size:7 final size:8
Alignment explanation
Indices: 112221953--112221999 Score: 53
Period size: 9 Copynumber: 5.9 Consensus size: 8
112221943 AAAATATACT
112221953 AATAATAG
1 AATAATAG
112221961 TAATAATAG
1 -AATAATAG
112221970 CAATAATAG
1 -AATAATAG
*
112221979 TA-AATAG
1 AATAATAG
112221986 AATAATA-
1 AATAATAG
112221993 AATAATA
1 AATAATA
112222000 CTTAGAGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 13 0.38
8 5 0.15
9 16 0.47
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.28
Consensus pattern (8 bp):
AATAATAG
Found at i:112222353 original size:20 final size:21
Alignment explanation
Indices: 112222308--112222355 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
112222298 GCGATTAGTT
* *
112222308 ATATTTTTATGAATATTAATTT
1 ATATTTCTATGAATA-TAATTA
112222330 ATATTTCTATGAATA-AATTA
1 ATATTTCTATGAATATAATTA
112222350 ATATTT
1 ATATTT
112222356 GATTAATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.42
22 14 0.58
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (21 bp):
ATATTTCTATGAATATAATTA
Found at i:112224600 original size:5 final size:5
Alignment explanation
Indices: 112224590--112224617 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
112224580 TCAGTGAATA
112224590 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
112224618 GTTTCAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:112226349 original size:41 final size:40
Alignment explanation
Indices: 112226304--112226437 Score: 153
Period size: 41 Copynumber: 3.3 Consensus size: 40
112226294 CGGTTGCAAT
* * *
112226304 AAAACGCCGCAAAAAACAGAGCAATAGGGGCGTTTTTGATC
1 AAAACGCCGCTAAAAACTGAGCAATAGCGGCGTTTTTGA-C
* * *
112226345 AAAACGCCGCTAAAAACTGGGAAATAGCGGCGTTTTTGGCC
1 AAAACGCCGCTAAAAACTGAGCAATAGCGGCGTTTTT-GAC
* * *
112226386 CAAACGCCGCTAAAAACTGAACAATAGCGGCGCTTTTGGA-
1 AAAACGCCGCTAAAAACTGAGCAATAGCGGCG-TTTTTGAC
112226426 AAAACGCCGCTA
1 AAAACGCCGCTA
112226438 TAGGTCGGGG
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
40 11 0.14
41 62 0.79
42 5 0.06
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (40 bp):
AAAACGCCGCTAAAAACTGAGCAATAGCGGCGTTTTTGAC
Found at i:112226455 original size:41 final size:41
Alignment explanation
Indices: 112226410--112226599 Score: 283
Period size: 41 Copynumber: 4.6 Consensus size: 41
112226400 AACTGAACAA
* *
112226410 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGTCGGGGTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGTAGAGGTTT
* *
112226451 TAGCGGCGCTTCTT-TAAAAACGCTGCTATAGGTAGAGGTTT
1 TAGCGGCGCTT-TTGGAAAAACGCCGCTATAGGTAGAGGTTT
* * *
112226492 TAGCGGCGTTTTTGCAAAAACGCTGCTATAGGTAGAGGTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGTAGAGGTTT
* *
112226533 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGTATAGGTTG
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGTAGAGGTTT
112226574 TAGCGGCGCTTTTGGAAAAACGCCGC
1 TAGCGGCGCTTTTGGAAAAACGCCGC
112226600 AAAAAAGTAA
Statistics
Matches: 136, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
40 2 0.01
41 132 0.97
42 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (41 bp):
TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGTAGAGGTTT
Found at i:112226948 original size:18 final size:18
Alignment explanation
Indices: 112226922--112226971 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
112226912 TATATATATA
112226922 TATATATATATATTAAACT
1 TATA-ATATATATTAAACT
* **
112226941 TGTAATATATATTAAGTT
1 TATAATATATATTAAACT
112226959 TATAATATATATT
1 TATAATATATATT
112226972 TAGGGTGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (18 bp):
TATAATATATATTAAACT
Found at i:112226952 original size:2 final size:2
Alignment explanation
Indices: 112226906--112226934 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
112226896 TGTCCCTTGT
112226906 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 T
112226935 TAAACTTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:112231517 original size:18 final size:18
Alignment explanation
Indices: 112231491--112231535 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
112231481 CAAATTAATT
*
112231491 TTAAATATTTGGTTCAAC
1 TTAATTATTTGGTTCAAC
112231509 TTAATTATTTGGTTCAAC
1 TTAATTATTTGGTTCAAC
112231527 TTAATTATT
1 TTAATTATT
112231536 ATTTGATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (18 bp):
TTAATTATTTGGTTCAAC
Found at i:112231538 original size:21 final size:19
Alignment explanation
Indices: 112231491--112231551 Score: 81
Period size: 21 Copynumber: 3.2 Consensus size: 19
112231481 CAAATTAATT
112231491 TTAAA-TATTTGGTTCAAC
1 TTAAATTATTTGGTTCAAC
112231509 TT-AATTATTTGGTTCAAC
1 TTAAATTATTTGGTTCAAC
*
112231527 TTAATTATTATTTGATTCAAC
1 TTAA--ATTATTTGGTTCAAC
112231548 TTAA
1 TTAA
112231552 GTATGAAGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
17 2 0.05
18 17 0.45
19 1 0.03
21 18 0.47
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (19 bp):
TTAAATTATTTGGTTCAAC
Found at i:112232226 original size:371 final size:370
Alignment explanation
Indices: 112231603--112232513 Score: 1743
Period size: 371 Copynumber: 2.5 Consensus size: 370
112231593 CTTGTCCATT
*
112231603 AAAATTACAACAATAGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
1 AAAATTACAACAATAGCTGACATTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
112231668 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
66 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
*
112231733 GTAACAACGCCACGTATGATGAATCTTCAAAAATTCAAAAAAGACTTGAAAAAAGTTCTGTCGAG
131 GTAACAACGCCACGTATGATGAATCTTCAAAAATTC-AAAAAGACTTGAAAAAAGTTCTATCGAG
112231798 CTCATTTACTATTGAATATTTATATAACCTTAATTTATTTCCAATTTACTTATAAAAATTAAACT
195 CTCATTTACTATTGAATATTTATATAACCTTAATTTATTTCCAATTTACTTATAAAAATTAAACT
112231863 ACGATTCTTTTTTGATATTATTATATTCAAATTACTATTTTTTATATTAATAATGTTTTATTTTA
260 ACGATTCTTTTTTGATATTATTATATTCAAATTACTA-TTTTTATATTAATAATGTTTTATTTTA
112231928 ATATTTAATATTTTTAAATTTCTTTAAAAGTTATAACTACTTTTTATC
324 ATATTTAAT-TTTTTAAATTTCTTTAAAAGTTATAACTACTTTTTATC
112231976 AAAATTACAACAATAGCTGACATTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
1 AAAATTACAACAATAGCTGACATTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
112232041 ATAGGCTGGAAA-CTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
66 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
*
112232105 GTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
131 GTAACAACGCCACGTATGATGAATCTTCAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
112232170 TCATTTACTATTGAATATTTATATAACCTTAATTTATTTCCAATTTACTTATAAAAATTAAACTA
196 TCATTTACTATTGAATATTTATATAACCTTAATTTATTTCCAATTTACTTATAAAAATTAAACTA
112232235 CGATTCTTTTTTGATATTATTATATTCAAATTACTATTTTTATATTAATAATGTTTTATTTTAAT
261 CGATTCTTTTTTGATATTATTATATTCAAATTACTATTTTTATATTAATAATGTTTTATTTTAAT
112232300 ATTTAATTTTTTAAATTTCTTTAAAAGTTATAACTACTTTTTATC
326 ATTTAATTTTTTAAATTTCTTTAAAAGTTATAACTACTTTTTATC
112232345 AAAATTACAACAATAGCTGACATTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
1 AAAATTACAACAATAGCTGACATTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
*
112232410 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATAGATCCTCCCTAGGT
66 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
*
112232475 GTAACAACACCACGTATGATGAATCTTCAAAAATTCAAA
131 GTAACAACGCCACGTATGATGAATCTTCAAAAATTCAAA
112232514 TGTTTCAATT
Statistics
Matches: 531, Mismatches: 6, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
369 115 0.22
370 124 0.23
371 129 0.24
372 87 0.16
373 76 0.14
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (370 bp):
AAAATTACAACAATAGCTGACATTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
GTAACAACGCCACGTATGATGAATCTTCAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
TCATTTACTATTGAATATTTATATAACCTTAATTTATTTCCAATTTACTTATAAAAATTAAACTA
CGATTCTTTTTTGATATTATTATATTCAAATTACTATTTTTATATTAATAATGTTTTATTTTAAT
ATTTAATTTTTTAAATTTCTTTAAAAGTTATAACTACTTTTTATC
Found at i:112232311 original size:20 final size:21
Alignment explanation
Indices: 112232269--112232312 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
112232259 TTCAAATTAC
*
112232269 TATTTTTATATTAATAATGTTT
1 TATTTTAATATT-ATAATGTTT
*
112232291 TATTTTAATATT-TAATTTTT
1 TATTTTAATATTATAATGTTT
112232311 TA
1 TA
112232313 AATTTCTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
22 11 0.55
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TATTTTAATATTATAATGTTT
Found at i:112232628 original size:24 final size:24
Alignment explanation
Indices: 112232601--112232668 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
112232591 ATTATTATTG
*
112232601 AAATATTCTCGTCCGTTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
* *
112232625 AAATATTATTC-TCCATTTTATTAC
1 AAATATTA-TCGTCCGTTTTATCAC
112232649 AAATATTATCGTCCGTTTTA
1 AAATATTATCGTCCGTTTTA
112232669 CCATTTAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.05
24 34 0.89
25 2 0.05
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (24 bp):
AAATATTATCGTCCGTTTTATCAC
Found at i:112232891 original size:15 final size:15
Alignment explanation
Indices: 112232845--112232900 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
112232835 AACGACATGT
112232845 ATATTATTTAATTAAA
1 ATATTATTTAATT-AA
112232861 ATAGTT-TTT-A-TAA
1 ATA-TTATTTAATTAA
112232874 ATATTATTTAATTAA
1 ATATTATTTAATTAA
112232889 ATATTATTTAAT
1 ATATTATTTAAT
112232901 CCCACTACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.06
13 8 0.22
14 2 0.06
15 16 0.44
16 6 0.17
17 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTATTTAATTAA
Found at i:112233014 original size:9 final size:9
Alignment explanation
Indices: 112233002--112233254 Score: 179
Period size: 9 Copynumber: 27.6 Consensus size: 9
112232992 TATTTGATAT
*
112233002 CATAATTTA
1 CATAACTTA
112233011 CATAACTTA
1 CATAACTTA
* *
112233020 TATAACATA
1 CATAACTTA
*
112233029 TATAACTTA
1 CATAACTTA
112233038 CATAACTTA
1 CATAACTTA
* *
112233047 TATAACATA
1 CATAACTTA
112233056 CATAACTTA
1 CATAACTTA
112233065 CATAACTTA
1 CATAACTTA
* *
112233074 TATAACATA
1 CATAACTTA
112233083 CATAACTTA
1 CATAACTTA
*
112233092 TATAACTTA
1 CATAACTTA
*
112233101 TATAACTTA
1 CATAACTTA
* *
112233110 GATAA-ATA
1 CATAACTTA
*
112233118 TATAACTTA
1 CATAACTTA
112233127 CATAACTTA
1 CATAACTTA
112233136 CATAATGCTTA
1 CATAA--CTTA
* *
112233147 AATATATTTTATA
1 CATA-A--CT-TA
*
112233160 TCATAATTTA
1 -CATAACTTA
112233170 CATAACTTA
1 CATAACTTA
112233179 CATAACTTA
1 CATAACTTA
*
112233188 TATAACTTA
1 CATAACTTA
* *
112233197 GATAA-ATA
1 CATAACTTA
* *
112233205 TATAATTTA
1 CATAACTTA
*
112233214 CATAA-ATA
1 CATAACTTA
* * *
112233222 TATATCATA
1 CATAACTTA
*
112233231 TCATAAATTA
1 -CATAACTTA
112233241 CATAACTTA
1 CATAACTTA
112233250 CATAA
1 CATAA
112233255 TACTTAAATA
Statistics
Matches: 197, Mismatches: 38, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
8 17 0.09
9 155 0.79
10 7 0.04
11 9 0.05
12 3 0.02
13 3 0.02
14 3 0.02
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.38
Consensus pattern (9 bp):
CATAACTTA
Found at i:112233183 original size:114 final size:114
Alignment explanation
Indices: 112233054--112233278 Score: 310
Period size: 114 Copynumber: 2.0 Consensus size: 114
112233044 TTATATAACA
* * *
112233054 TACATAACTTACATAACTTATATAACATACATAACTTATATAACTTATATAACTTAGATA-AATA
1 TACATAACTTACATAACTTATATAACATACATAA-ATATATAACTTACATAA-ATAGATATAATA
* * * *
112233118 T-ATAACTTACATAACTTACATAATGCTTAAATATATTTTATATCATAATT
64 TCATAAATTACATAACTTACATAATACTTAAATATATATCATATCATAATT
* * * * *
112233168 TACATAACTTACATAACTTATATAACTTAGATAAATATATAATTTACATAAATATATATCATATC
1 TACATAACTTACATAACTTATATAACATACATAAATATATAACTTACATAAATAGATATAATATC
112233233 ATAAATTACATAACTTACATAATACTTAAATATATATCATATCATA
66 ATAAATTACATAACTTACATAATACTTAAATATATATCATATCATA
112233279 CATAACTAGT
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
112 5 0.05
113 18 0.19
114 74 0.76
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (114 bp):
TACATAACTTACATAACTTATATAACATACATAAATATATAACTTACATAAATAGATATAATATC
ATAAATTACATAACTTACATAATACTTAAATATATATCATATCATAATT
Found at i:112239044 original size:33 final size:31
Alignment explanation
Indices: 112238996--112239076 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
112238986 AGAATTAATA
* *
112238996 TTTTTGGTTGTATTTTTTATGTTAAATTTGTTG
1 TTTTTGGTTGCATTTTATATG--AAATTTGTTG
* *
112239029 TTTTTGGCTGCATTTTATATGATATTTGTTG
1 TTTTTGGTTGCATTTTATATGAAATTTGTTG
* *
112239060 TATTTGGTTGGATTTTA
1 TTTTTGGTTGCATTTTA
112239077 ATGCAGGAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 23 0.56
33 18 0.44
ACGTcount: A:0.16, C:0.02, G:0.20, T:0.62
Consensus pattern (31 bp):
TTTTTGGTTGCATTTTATATGAAATTTGTTG
Found at i:112239175 original size:43 final size:41
Alignment explanation
Indices: 112239128--112239399 Score: 294
Period size: 43 Copynumber: 6.3 Consensus size: 41
112239118 ATCTGCCAAA
* * *
112239128 TTTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAAGCCTTGACG
1 TTTAGCGGCGTTT-TACAAAAA-CGCCGCTAAAAGCCTAGACC
* * * *
112239171 TTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAAAGCCTTGACC
1 TTTAGCGGCG-TTTT-ACAAAAACGCCGCTAAAAGCCTAGACC
* *
112239214 TTTAGCGGCGCTTTACCCAAAAACGCCGCT-AAAGCCTTGACC
1 TTTAGCGGCGTTTTA--CAAAAACGCCGCTAAAAGCCTAGACC
*
112239256 TTTAGCGGCGCTTTACCCAAAAACGCCGCTAAAAAGCCTAGACC
1 TTTAGCGGCGTTTTA--CAAAAACGCCGCT-AAAAGCCTAGACC
* *
112239300 TTTAGCGGCGCTTTTCCCAAAAACGCCGCAAAAAGCCTAGACC
1 TTTAGCGGCG-TTTT-ACAAAAACGCCGCTAAAAGCCTAGACC
* *
112239343 TTTAGCGGCGCTTTTCCCAAAAATGCCGCTAAAAGCCTAGACC
1 TTTAGCGGCG-TTTT-ACAAAAACGCCGCTAAAAGCCTAGACC
112239386 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
112239400 TTTCCAATAA
Statistics
Matches: 206, Mismatches: 15, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
42 49 0.24
43 115 0.56
44 39 0.19
45 3 0.01
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.23
Consensus pattern (41 bp):
TTTAGCGGCGTTTTACAAAAACGCCGCTAAAAGCCTAGACC
Found at i:112239300 original size:86 final size:85
Alignment explanation
Indices: 112239145--112239395 Score: 385
Period size: 86 Copynumber: 2.9 Consensus size: 85
112239135 GCGTTTGTAA
* * * *
112239145 AAAAAGCGCCGCTAAAAGCCTTGACGTTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAAAGCCTT
1 AAAAA-CGCCGCT-AAAGCCTTGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAAGCCTA
112239210 GACCTTTAGCGGCGCTTTACCC
64 GACCTTTAGCGGCGCTTTACCC
*
112239232 AAAAACGCCGCTAAAGCCTTGACCTTTAGCGGCGCTTTACCCAAAAACGCCGCTAAAAAGCCTAG
1 AAAAACGCCGCTAAAGCCTTGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCT-AAAAGCCTAG
*
112239297 ACCTTTAGCGGCGCTTTTCCC
65 ACCTTTAGCGGCGCTTTACCC
* * *
112239318 AAAAACGCCGCAAAAAGCCTAGACCTTTAGCGGCGCTTTTCCCAAAAATGCCGCTAAAAGCCTAG
1 AAAAACGCCGC-TAAAGCCTTGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAAGCCTAG
112239383 ACCTTTAGCGGCG
65 ACCTTTAGCGGCG
112239396 TTTTTTTCCA
Statistics
Matches: 152, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
85 38 0.25
86 70 0.46
87 44 0.29
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (85 bp):
AAAAACGCCGCTAAAGCCTTGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAAGCCTAGA
CCTTTAGCGGCGCTTTACCC
Found at i:112239334 original size:129 final size:130
Alignment explanation
Indices: 112239145--112239395 Score: 398
Period size: 129 Copynumber: 1.9 Consensus size: 130
112239135 GCGTTTGTAA
* * * * * *
112239145 AAAAAGCGCCGCTAAAAGCCTTGACGTTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAAAGCCTT
1 AAAAAGCGCCGCTAAAAGCCTAGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCAAAAAGCCTA
*
112239210 GACCTTTAGCGGCGCTTTACCCAAAAACGCCGCT-AAAGCCTTGACCTTTAGCGGCGCTTTACCC
66 GACCTTTAGCGGCGCTTTACCCAAAAACGCCGCTAAAAGCCTAGACCTTTAGCGGCGCTTTACCC
112239274 AAAAA-CGCCGCTAAAAAGCCTAGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCAAAAAGCCT
1 AAAAAGCGCCGCT-AAAAGCCTAGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCAAAAAGCCT
* *
112239338 AGACCTTTAGCGGCGCTTTTCCCAAAAATGCCGCTAAAAGCCTAGACCTTTAGCGGCG
65 AGACCTTTAGCGGCGCTTTACCCAAAAACGCCGCTAAAAGCCTAGACCTTTAGCGGCG
112239396 TTTTTTTCCA
Statistics
Matches: 111, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
128 7 0.06
129 83 0.75
130 21 0.19
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (130 bp):
AAAAAGCGCCGCTAAAAGCCTAGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCAAAAAGCCTA
GACCTTTAGCGGCGCTTTACCCAAAAACGCCGCTAAAAGCCTAGACCTTTAGCGGCGCTTTACCC
Found at i:112240241 original size:33 final size:33
Alignment explanation
Indices: 112240204--112240271 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
112240194 GGTTAACTTA
112240204 AATATTGCTTTGTAATTTAGTCAGATTTGAACT
1 AATATTGCTTTGTAATTTAGTCAGATTTGAACT
112240237 AATATTGCTTTGTAATTTAGTCAGATTTGAACT
1 AATATTGCTTTGTAATTTAGTCAGATTTGAACT
112240270 AA
1 AA
112240272 GTTGATATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (33 bp):
AATATTGCTTTGTAATTTAGTCAGATTTGAACT
Found at i:112244791 original size:19 final size:19
Alignment explanation
Indices: 112244756--112244792 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
112244746 TCCTATTTTT
* *
112244756 ATATATTATTGTTATTAAC
1 ATATATTATTATCATTAAC
112244775 ATATATTATTATCATTAA
1 ATATATTATTATCATTAA
112244793 TGTATTGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (19 bp):
ATATATTATTATCATTAAC
Found at i:112244881 original size:22 final size:20
Alignment explanation
Indices: 112244850--112244893 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
112244840 TTTTTATTAA
*
112244850 TATTATTATTATAATCTTATTT
1 TATTACTATTATAAT-TT-TTT
112244872 TATTACTATTATAATTTTTT
1 TATTACTATTATAATTTTTT
112244892 TA
1 TA
112244894 AGTTATTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 2 0.10
22 14 0.67
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTACTATTATAATTTTTT
Found at i:112244995 original size:3 final size:3
Alignment explanation
Indices: 112244517--112244981 Score: 227
Period size: 3 Copynumber: 152.7 Consensus size: 3
112244507 CAATTTAATC
* * * *
112244517 TAT TAT TAT TACT TAT TAT T-T CAC TAT TAT TGT CTAG TA- TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * * * * * *
112244562 CAT TAT CAC TAT TAT TAC T-T TAC TAT TGT AACT TAAT GTAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T T-AT -TAT TAT TAT
112244609 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
112244657 TAT TA- TGT TAT TAC CAT TAC TAT TAT TAT TAT TAT TCT TAC TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
112244704 TAT TAT TAGCC TATT TAT TAT TCT TAT TAG TA- AAT TAT TAT T-T CCTAT
1 TAT TAT TA--T TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT --TAT
* * * * * *
112244752 TTT TAT ATAT TAT TGT TAT TAA CAT ATAT TAT TAT CAT TAAT GTAT TGT
1 TAT TAT -TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT T-AT -TAT TAT
* * * *
112244801 TAT TCT CTAT TAT TAT TAT TAC TAT CT-T TTT TAT GT-T TAT TTT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TAT
* * * * * *
112244847 TAA TAT TAT TAT TA- TAA TCT TAT T-T TAT TAC TAT TAT AAT T-T TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
112244892 TAAGT TAT TGT TAC TAT TAT TCT T-T TAC CAT T-T AAT ACAT TAT TAC
1 T-A-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
* *
112244938 TAT TTT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
112244982 CTAAAGTATT
Statistics
Matches: 341, Mismatches: 89, Indels: 64
0.69 0.18 0.13
Matches are distributed among these distances:
2 18 0.05
3 288 0.84
4 27 0.08
5 8 0.02
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:112245205 original size:3 final size:3
Alignment explanation
Indices: 112245184--112245387 Score: 89
Period size: 3 Copynumber: 68.7 Consensus size: 3
112245174 CAAACTTTAG
* **
112245184 ATT ATTT ATT ATT -TGT ATT ATT ACT ATT CATT ATT ACC ATT ATT ATT
1 ATT A-TT ATT ATT AT-T ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
* * * * * *
112245231 ACT ATT ATT TTT ACTT -TT ATT ACT ATT ACT A-T ATT GTT TTT ATT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * * * *
112245275 GTT ATT TTCT ATT ACT ATT ATC GTT ATT ATT AAT ACT AAT ATT AAT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
112245321 ATT -TT -TT ATT ATT ACT GTT ATT ATT ATC ATT AGT ATT ATT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** *
112245366 -TT GCT ACT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
112245388 CGTTTTCATT
Statistics
Matches: 148, Mismatches: 43, Indels: 20
0.70 0.20 0.09
Matches are distributed among these distances:
2 13 0.09
3 124 0.84
4 11 0.07
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:112245719 original size:25 final size:25
Alignment explanation
Indices: 112245685--112245734 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
112245675 TCCATATTTG
112245685 GAAATTCGAGGTAATCGTGCCCTAA
1 GAAATTCGAGGTAATCGTGCCCTAA
112245710 GAAATTCGAGGTAATCGTGCCCTAA
1 GAAATTCGAGGTAATCGTGCCCTAA
112245735 CTTACTGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (25 bp):
GAAATTCGAGGTAATCGTGCCCTAA
Found at i:112256855 original size:14 final size:14
Alignment explanation
Indices: 112256836--112256872 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
112256826 TTTCTCATTC
112256836 AATTCAATTTTCTA
1 AATTCAATTTTCTA
112256850 AATTCAATTTTCTA
1 AATTCAATTTTCTA
*
112256864 AATTGAATT
1 AATTCAATT
112256873 CAATAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.49
Consensus pattern (14 bp):
AATTCAATTTTCTA
Found at i:112262573 original size:2 final size:2
Alignment explanation
Indices: 112262566--112262601 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
112262556 TATGTATGTA
112262566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
112262602 TTAACTTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112267301 original size:13 final size:14
Alignment explanation
Indices: 112267285--112267320 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
112267275 CAATCTCATA
112267285 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
112267298 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
112267311 TCTC-ATTTCA
1 TCTCAATTTCA
112267321 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:112267310 original size:18 final size:19
Alignment explanation
Indices: 112267272--112267312 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
112267262 TGGTTCATGT
112267272 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
112267291 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
112267309 TTTC
1 TTTC
112267313 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:112267502 original size:39 final size:38
Alignment explanation
Indices: 112267435--112267569 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
112267425 ACCAATATGG
* * *
112267435 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
112267474 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
112267512 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
112267553 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
112267570 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:112267835 original size:18 final size:19
Alignment explanation
Indices: 112267809--112267847 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
112267799 TTTCAATTCA
112267809 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
112267828 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
112267846 AT
1 AT
112267848 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:112269175 original size:5 final size:5
Alignment explanation
Indices: 112269165--112269217 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
112269155 TTACTTATTT
* *
112269165 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
112269213 ATATA
1 ATATA
112269218 TATTTTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 30 0.73
6 7 0.17
7 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:112269181 original size:12 final size:12
Alignment explanation
Indices: 112269164--112269219 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
112269154 TTTACTTATT
112269164 TATATAATATAA
1 TATATAATATAA
112269176 TATATAATATAATA
1 TATATAATAT-A-A
112269190 TACTATAATATAA
1 TA-TATAATATAA
*
112269203 TA-ATAATTTAA
1 TATATAATATAA
112269214 TATATA
1 TATATA
112269220 TTTTAACACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:112273754 original size:13 final size:14
Alignment explanation
Indices: 112273738--112273773 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
112273728 CAATCTCATA
112273738 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
112273751 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
112273764 TCTC-ATTTCA
1 TCTCAATTTCA
112273774 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:112273763 original size:18 final size:19
Alignment explanation
Indices: 112273725--112273765 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
112273715 TGGTTCATGT
112273725 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
112273744 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
112273762 TTTC
1 TTTC
112273766 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:112273955 original size:39 final size:38
Alignment explanation
Indices: 112273888--112274022 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
112273878 ACCAATATGG
* * *
112273888 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
112273927 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
112273965 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
112274006 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
112274023 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:112274287 original size:18 final size:19
Alignment explanation
Indices: 112274261--112274299 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
112274251 TTTCAATTCA
112274261 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
112274280 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
112274298 AT
1 AT
112274300 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:112275625 original size:5 final size:5
Alignment explanation
Indices: 112275615--112275667 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
112275605 TTACTTATTT
* * *
112275615 ATATA ATATAA TATATA ATATA ATATA CTATA CTATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
112275663 ATATA
1 ATATA
112275668 TATTTTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 30 0.73
6 7 0.17
7 4 0.10
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:112275631 original size:12 final size:12
Alignment explanation
Indices: 112275614--112275669 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
112275604 TTTACTTATT
112275614 TATATAATATAA
1 TATATAATATAA
112275626 TATATAATATAA
1 TATATAATATAA
112275638 TATACTATACTATAA
1 TATA-TA-A-TATAA
*
112275653 TA-ATAATTTAA
1 TATATAATATAA
112275664 TATATA
1 TATATA
112275670 TTTTAACACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:112284956 original size:13 final size:13
Alignment explanation
Indices: 112284938--112284977 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
112284928 GCTCGACAGG
112284938 GACACGCCCGTGT
1 GACACGCCCGTGT
*
112284951 GACACGCCTGTGT
1 GACACGCCCGTGT
*
112284964 GACACTCCCGTGT
1 GACACGCCCGTGT
112284977 G
1 G
112284978 CAATTTCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.15, C:0.35, G:0.30, T:0.20
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:112288519 original size:3 final size:3
Alignment explanation
Indices: 112288511--112288538 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
112288501 AGCAAACACA
112288511 GGT GGT GGT GGT GGT GGT GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT G
112288539 TAAAACTCAT
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:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GGT
Found at i:112290582 original size:6 final size:7
Alignment explanation
Indices: 112290560--112290601 Score: 57
Period size: 7 Copynumber: 5.6 Consensus size: 7
112290550 CATTAAAAAT
112290560 AATTAAAA
1 AATT-AAA
112290568 AATTAAA
1 AATTAAA
112290575 AATTAAA
1 AATTAAA
112290582 AATTAAA
1 AATTAAA
112290589 ACATATAAA
1 A-AT-TAAA
112290598 AATT
1 AATT
112290602 TTATAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 19 0.59
8 8 0.25
9 5 0.16
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (7 bp):
AATTAAA
Found at i:112291053 original size:16 final size:16
Alignment explanation
Indices: 112291015--112291056 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
112291005 TCCTTTCTCC
*
112291015 TTCTTCCTTTTCCTTT
1 TTCTTTCTTTTCCTTT
*
112291031 TT-GTTCTTTTCCTTT
1 TTCTTTCTTTTCCTTT
112291046 TTCTTTCTTTT
1 TTCTTTCTTTT
112291057 ACATCTTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (16 bp):
TTCTTTCTTTTCCTTT
Found at i:112301395 original size:327 final size:327
Alignment explanation
Indices: 112300570--112301626 Score: 1509
Period size: 328 Copynumber: 3.2 Consensus size: 327
112300560 CCTAAACCCG
* * **
112300570 TTAGTTGCATTAAAGCTTAATATAATTAATTTCTTAATTTAAAAAGAAAGACTTTAAGTAATAAG
1 TTAGTTGCATAAAAACTTAGGATAATTAATTTCTTAATTTAAAAAGAAAGAC-TTAAGTAATAAG
* *
112300635 TAAATAATTTATTTAAAGTCAAGCCTAAAAAAGTTAATTCAAAATAAAGCAATTTGAATCGAATT
65 TAAATAATTTATTTAAAGTCGAGCCTAAAAAAATTAATTCAAAATAAAGCAATTTGAATCGAATT
*
112300700 ACTATTCTAATAATCATATTTAATCGACTCTAAGCATATATAATAACAACAGGGCTTTTCAATTA
130 ACTATTCTAATAATCATAATTAATCGACTCTAAGCATATATAATAACAACAGGGCTTTTCAATTA
* * * * *
112300765 CCATTTTAGTCATATAAGCCTCAGGTAAAAATTGTTGTTTATCAATATAAGTCACAGGCATAGAC
195 CCATTTGAGTCGTATAAGCCTCAGATAAAGATTGTTGTTTATCAATATAAGTCACAGGCATAGAA
* * *
112300830 TGTGAAATCACACTCGTAGAACCTTGTCGATTCTTATAAGTCGCACTTGGAAGCTCCCCCTGAAA
260 TGTGAAATCACACTCATAGAATCTTGTTGATTCTTATAAGTCGCACTTGGAAGCTCCCCCTGAAA
*
112300895 CCCA
325 -CTA
* * ** * *
112300899 TTAGCTGCATAAAAGCTTAATATAATGAATTTCTTAATTTAAAAAGAAAGAATTAAGTAATAAGT
1 TTAGTTGCATAAAAACTTAGGATAATTAATTTCTTAATTTAAAAAGAAAGACTTAAGTAATAAGT
* * * *
112300964 AAATAATTTATTTAAAGTCGAGCTTAAAAAAAATAATTCAAAATAAAACAATTTGTATCGAATTA
66 AAATAATTTATTTAAAGTCGAGCCTAAAAAAATTAATTCAAAATAAAGCAATTTGAATCGAATTA
*
112301029 CTATTCTAATAATCATAATTAATTGACTCTAAGCATATATAATAACAACAGGGCTTTTCAATTAC
131 CTATTCTAATAATCATAATTAATCGACTCTAAGCATATATAATAACAACAGGGCTTTTCAATTAC
* * * * *
112301094 CATTTGAGTCGTATAAGCCTTAGATAAAGATTGTTGTTTACCAATACAAGTTAAAGGCATAGAAT
196 CATTTGAGTCGTATAAGCCTCAGATAAAGATTGTTGTTTATCAATATAAGTCACAGGCATAGAAT
* *
112301159 GTGAAATCACACTCATAGAATTTTGTTGATTCTTATAAGTCGCACTTGGAAACTCCCCCTGAAAC
261 GTGAAATCACACTCATAGAATCTTGTTGATTCTTATAAGTCGCACTTGGAAGCTCCCCCTGAAAC
112301224 TA
326 TA
* *
112301226 TTAGTTGCATAAAAACTTGGGATGATTAATTTCTTAATTTAAAAAGAAAGACTTAAGTAATAAGT
1 TTAGTTGCATAAAAACTTAGGATAATTAATTTCTTAATTTAAAAAGAAAGACTTAAGTAATAAGT
* * **
112301291 AAATAATTTATTTAAAGTCGAGCCTAAAAAAATTAATTCAAGATAAAGCAATTTGAAACGACGTA
66 AAATAATTTATTTAAAGTCGAGCCTAAAAAAATTAATTCAAAATAAAGCAATTTGAATCGAATTA
* * * **
112301356 CTATTCTAATAATAATAATTAATCAACTGTAAGCATATATAATAACAACAGGATTTTTCAATTAC
131 CTATTCTAATAATCATAATTAATCGACTCTAAGCATATATAATAACAACAGGGCTTTTCAATTAC
* * * * *
112301421 CATTTGAATTGTATAAGTCTCGAGA-AAAGATTATTGTTCATCAATATAAGTCACAGGCAT---A
196 CATTTGAGTCGTATAAGCCTC-AGATAAAGATTGTTGTTTATCAATATAAGTCACAGGCATAGAA
** * *
112301482 ---GAACCCACA-TCCATAGAATCTTGTTGATTCTTATAAGTTGCACTTGGAAGCTCCCCATGAA
260 TGTGAAATCACACT-CATAGAATCTTGTTGATTCTTATAAGTCGCACTTGGAAGCTCCCCCTGAA
112301543 ACTA
324 ACTA
* * *
112301547 TTAGTTGCATAAAAACATAGGATAATTAATTTCTTAATTTAAAAAGAAAGACTTGAGTAATAAAT
1 TTAGTTGCATAAAAACTTAGGATAATTAATTTCTTAATTTAAAAAGAAAGACTTAAGTAATAAGT
112301612 AAATAATTTATTTAA
66 AAATAATTTATTTAA
112301627 GTAATAAACC
Statistics
Matches: 655, Mismatches: 71, Indels: 12
0.89 0.10 0.02
Matches are distributed among these distances:
320 1 0.00
321 132 0.20
324 1 0.00
327 221 0.34
328 252 0.38
329 48 0.07
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (327 bp):
TTAGTTGCATAAAAACTTAGGATAATTAATTTCTTAATTTAAAAAGAAAGACTTAAGTAATAAGT
AAATAATTTATTTAAAGTCGAGCCTAAAAAAATTAATTCAAAATAAAGCAATTTGAATCGAATTA
CTATTCTAATAATCATAATTAATCGACTCTAAGCATATATAATAACAACAGGGCTTTTCAATTAC
CATTTGAGTCGTATAAGCCTCAGATAAAGATTGTTGTTTATCAATATAAGTCACAGGCATAGAAT
GTGAAATCACACTCATAGAATCTTGTTGATTCTTATAAGTCGCACTTGGAAGCTCCCCCTGAAAC
TA
Found at i:112302325 original size:29 final size:28
Alignment explanation
Indices: 112302259--112302329 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
112302249 CTAGTATAAA
* * *
112302259 TTTTAAATTATTTTTATATTTACTTTTT
1 TTTTAAATTATTTTTATAATTAATTATT
* *
112302287 TTCTTGAATTATTTTTGTAATTAATTAATT
1 TT-TTAAATTATTTTTATAATTAATT-ATT
112302317 TTTTAAATTATTT
1 TTTTAAATTATTT
112302330 AAAAAACTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
28 2 0.06
29 29 0.83
30 4 0.11
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (28 bp):
TTTTAAATTATTTTTATAATTAATTATT
Found at i:112302656 original size:17 final size:19
Alignment explanation
Indices: 112302614--112302657 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
112302604 ATGAAATTTT
* *
112302614 AATTAGTATTATGAGATAA
1 AATTATTATTATCAGATAA
112302633 AATTATTATTATCAGA-AA
1 AATTATTATTATCAGATAA
112302651 AA-TATTA
1 AATTATTA
112302658 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (19 bp):
AATTATTATTATCAGATAA
Found at i:112306932 original size:17 final size:19
Alignment explanation
Indices: 112306890--112306933 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
112306880 ATGAAATTTT
* *
112306890 AATTAGTATTATGAGATAA
1 AATTATTATTATCAGATAA
112306909 AATTATTATTATCAGA-AA
1 AATTATTATTATCAGATAA
112306927 AA-TATTA
1 AATTATTA
112306934 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (19 bp):
AATTATTATTATCAGATAA
Found at i:112308776 original size:28 final size:28
Alignment explanation
Indices: 112308744--112308812 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
112308734 GCGTAGATCA
112308744 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
112308772 CGAAATTACCCCTAAAGAGTAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
112308800 CGATA-TACCCCTA
1 CGAAATTACCCCTA
112308813 GGGTTTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 8 0.21
28 31 0.79
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:112310856 original size:12 final size:12
Alignment explanation
Indices: 112310828--112310872 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
112310818 AAATAACAAT
112310828 ATATACATA-AA
1 ATATACATATAA
*
112310839 ATATACATATAC
1 ATATACATATAA
112310851 ATATACATATATA
1 ATATACATATA-A
112310864 TATATACAT
1 -ATATACAT
112310873 GACATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 9 0.31
12 12 0.41
14 8 0.28
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (12 bp):
ATATACATATAA
Found at i:112310869 original size:6 final size:6
Alignment explanation
Indices: 112310828--112310867 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
112310818 AAATAACAAT
* *
112310828 ATATAC ATA-AA ATATAC ATATAC ATATAC ATATAT ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
112310868 TACATGACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATAC
Found at i:112311449 original size:21 final size:20
Alignment explanation
Indices: 112311423--112311467 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
112311413 TAAAATGCAC
*
112311423 ATAATAATAATATATGTATAT
1 ATAATAATAAAATATG-ATAT
*
112311444 ATAATAGTAAAATATGATAT
1 ATAATAATAAAATATGATAT
112311464 ATAA
1 ATAA
112311468 AGTTAACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (20 bp):
ATAATAATAAAATATGATAT
Found at i:112311513 original size:20 final size:20
Alignment explanation
Indices: 112311490--112311554 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
112311480 ATAGAAATAC
112311490 ATAAAACAATAACGATAGTA
1 ATAAAACAATAACGATAGTA
*
112311510 ATAAAAC-AT--GGA-AGCTA
1 ATAAAACAATAACGATAG-TA
112311527 ATAAAACAATAACGATAGTA
1 ATAAAACAATAACGATAGTA
112311547 ATAAAACA
1 ATAAAACA
112311555 TGGAAGCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 2 0.05
17 11 0.29
18 2 0.05
19 2 0.05
20 19 0.50
21 2 0.05
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.18
Consensus pattern (20 bp):
ATAAAACAATAACGATAGTA
Found at i:112311530 original size:17 final size:17
Alignment explanation
Indices: 112311508--112311567 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
112311498 ATAACGATAG
112311508 TAATAAAACATGGAAGC
1 TAATAAAACATGGAAGC
*
112311525 TAATAAAACAATAACGATAG-
1 TAATAAAAC-AT--GGA-AGC
112311545 TAATAAAACATGGAAGC
1 TAATAAAACATGGAAGC
112311562 TAATAA
1 TAATAA
112311568 TATATATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
16 2 0.06
17 17 0.47
18 2 0.06
19 2 0.06
20 11 0.31
21 2 0.06
ACGTcount: A:0.57, C:0.10, G:0.13, T:0.20
Consensus pattern (17 bp):
TAATAAAACATGGAAGC
Found at i:112311531 original size:37 final size:37
Alignment explanation
Indices: 112311490--112311567 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
112311480 ATAGAAATAC
112311490 ATAAAACAATAACGATAGTAATAAAACATGGAAGCTA
1 ATAAAACAATAACGATAGTAATAAAACATGGAAGCTA
112311527 ATAAAACAATAACGATAGTAATAAAACATGGAAGCTA
1 ATAAAACAATAACGATAGTAATAAAACATGGAAGCTA
112311564 ATAA
1 ATAA
112311568 TATATATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (37 bp):
ATAAAACAATAACGATAGTAATAAAACATGGAAGCTA
Found at i:112311568 original size:20 final size:20
Alignment explanation
Indices: 112311508--112311569 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
112311498 ATAACGATAG
112311508 TAATAAAACATGGAAGCTAA
1 TAATAAAACATGGAAGCTAA
* * *
112311528 TAA-AACA-AT--AACGATAG
1 TAATAAAACATGGAA-GCTAA
112311545 TAATAAAACATGGAAGCTAA
1 TAATAAAACATGGAAGCTAA
112311565 TAATA
1 TAATA
112311570 TATATATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
16 2 0.06
17 6 0.19
18 5 0.16
19 5 0.16
20 11 0.35
21 2 0.06
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (20 bp):
TAATAAAACATGGAAGCTAA
Found at i:112311574 original size:2 final size:2
Alignment explanation
Indices: 112311567--112311603 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
112311557 GAAGCTAATA
112311567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
112311604 ATAAAAGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:112311737 original size:14 final size:14
Alignment explanation
Indices: 112311718--112311744 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
112311708 TTAATAATTG
112311718 ATACTAAAATAATA
1 ATACTAAAATAATA
112311732 ATACTAAAATAAT
1 ATACTAAAATAAT
112311745 TAGCTCAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
ATACTAAAATAATA
Found at i:112313766 original size:68 final size:67
Alignment explanation
Indices: 112313615--112313767 Score: 186
Period size: 68 Copynumber: 2.3 Consensus size: 67
112313605 GGTTTATTTG
* * * *
112313615 GAAAACAGGAATT-AAAAGGCTTAACTCCTCTCGCAATATGAGTTGATCTTTTTGAAAAATAGAA
1 GAAAACAGAAATTGAAAAAGCTCAACTCCTCTCGCAATATGAGTTGATCTTTTGGAAAAATAGAA
112313679 TT
66 TT
* *
112313681 TAAACACAGAGATTGAAAAAGCTCAACTCACTTCTCGCAATATGAGTTGAT-TTTTGGAAAACA-
1 GAAA-ACAGAAATTGAAAAAGCTCAACTC-C-TCTCGCAATATGAGTTGATCTTTTGGAAAA-AT
112313744 AGAATT
62 AGAATT
*
112313750 GCAAACAGAAATTGAAAA
1 GAAAACAGAAATTGAAAA
112313768 TACCTCATCA
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
66 3 0.04
67 7 0.10
68 25 0.34
69 18 0.25
70 20 0.27
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (67 bp):
GAAAACAGAAATTGAAAAAGCTCAACTCCTCTCGCAATATGAGTTGATCTTTTGGAAAAATAGAA
TT
Done.