Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold168
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: 938898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 20427 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:3884 original size:20 final size:19
Alignment explanation
Indices: 3858--3929 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
3848 AATTACAAAA
3858 CAAAATTCAAAATAATTTT
1 CAAAATTCAAAATAATTTT
*
3877 CAAGAATTTAAAATAATTTT
1 CAA-AATTCAAAATAATTTT
*
3897 TAAAATTCAAAAT-ATTTAT
1 CAAAATTCAAAATAATTT-T
*
3916 AAAAATTTCAAAAT
1 CAAAA-TTCAAAAT
3930 TTATATTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
18 4 0.09
19 17 0.37
20 25 0.54
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (19 bp):
CAAAATTCAAAATAATTTT
Found at i:3937 original size:24 final size:25
Alignment explanation
Indices: 3908--3960 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
3898 AAAATTCAAA
* *
3908 ATATTTATAAAAATTTC-AAAATTT
1 ATATTTATAAAAAATTCTAAAAATT
*
3932 ATATTTTTAAAAAATTCTAAAAATT
1 ATATTTATAAAAAATTCTAAAAATT
3957 ATAT
1 ATAT
3961 AAAAAGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATTTATAAAAAATTCTAAAAATT
Found at i:3954 original size:26 final size:27
Alignment explanation
Indices: 3911--3961 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
3901 ATTCAAAATA
*
3911 TTTATAAAAATTTCAAAATT-TATATT
1 TTTATAAAAATTTAAAAATTATATATT
3937 TTTA-AAAAATTCTAAAAATTATATA
1 TTTATAAAAATT-TAAAAATTATATA
3962 AAAAGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 11 0.50
27 4 0.18
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (27 bp):
TTTATAAAAATTTAAAAATTATATATT
Found at i:3984 original size:45 final size:44
Alignment explanation
Indices: 3891--3983 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
3881 AATTTAAAAT
*
3891 AATTTTT--AAAATTCAAAATATTTATAAAAATTTCAAAATTTA
1 AATTTTTAAAAAATTCAAAATATTTATAAAAAGTTCAAAATTTA
*
3933 TATTTTTAAAAAATTCTAAAA-ATTATATAAAAAGTT-AAAATTTA
1 AATTTTTAAAAAATTC-AAAATATT-TATAAAAAGTTCAAAATTTA
3977 AATTTTT
1 AATTTTT
3984 TTTCTAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
42 6 0.14
44 24 0.55
45 14 0.32
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (44 bp):
AATTTTTAAAAAATTCAAAATATTTATAAAAAGTTCAAAATTTA
Found at i:5183 original size:43 final size:43
Alignment explanation
Indices: 5135--5230 Score: 122
Period size: 43 Copynumber: 2.2 Consensus size: 43
5125 ACCACCACTA
* * *
5135 ATTTGCAGATATAAACTGTCACTGGGTTGTGA-ATGTACAACAT
1 ATTTGCAGATAAAAACTGCCACTGGGTTG-GAGATGCACAACAT
* *
5178 ATTTGCAGATAAAAATTGCCACTGGGTTGGAGATGCGCAACAT
1 ATTTGCAGATAAAAACTGCCACTGGGTTGGAGATGCACAACAT
*
5221 ATTTGTAGAT
1 ATTTGCAGAT
5231 GAACTGACAC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 2 0.04
43 44 0.96
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (43 bp):
ATTTGCAGATAAAAACTGCCACTGGGTTGGAGATGCACAACAT
Found at i:7174 original size:42 final size:42
Alignment explanation
Indices: 7117--7216 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
7107 GCTCTTGGTA
*
7117 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
* * *
7159 TCGCACACTTCGTGCCCATTATTCAACATCGTCATTTTAGTT
1 TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
* *
7201 TCACACATTTAGTGCC
1 TCGCACACTTAGTGCC
7217 GTTCATATAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.24, C:0.28, G:0.11, T:0.37
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
Found at i:10884 original size:30 final size:30
Alignment explanation
Indices: 10850--10948 Score: 128
Period size: 30 Copynumber: 3.3 Consensus size: 30
10840 ATGTGTGTAT
** *
10850 GGAGCTGAATTAAAGCATGCATGTGTTTAG
1 GGAGCTGAATTGGAGCATGCATGTATTTAG
* * *
10880 GGAGCTAAATGGGGGCATGCATGTATTTAG
1 GGAGCTGAATTGGAGCATGCATGTATTTAG
*
10910 GGAGCTGAA-TGGAGCATGCATGAATTTAG
1 GGAGCTGAATTGGAGCATGCATGTATTTAG
10939 GGAGCTGAAT
1 GGAGCTGAAT
10949 GAGGATGCTA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 26 0.45
30 32 0.55
ACGTcount: A:0.29, C:0.10, G:0.34, T:0.26
Consensus pattern (30 bp):
GGAGCTGAATTGGAGCATGCATGTATTTAG
Found at i:10936 original size:29 final size:29
Alignment explanation
Indices: 10863--10949 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
10853 GCTGAATTAA
* *
10863 AGCATGCATGTGTTTAGGGAGCTAAATGGG
1 AGCATGCATGTATTTAGGGAGCTGAAT-GG
*
10893 GGCATGCATGTATTTAGGGAGCTGAATGG
1 AGCATGCATGTATTTAGGGAGCTGAATGG
*
10922 AGCATGCATGAATTTAGGGAGCTGAATG
1 AGCATGCATGTATTTAGGGAGCTGAATG
10950 AGGATGCTAG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
29 28 0.54
30 24 0.46
ACGTcount: A:0.28, C:0.10, G:0.36, T:0.26
Consensus pattern (29 bp):
AGCATGCATGTATTTAGGGAGCTGAATGG
Found at i:13026 original size:2 final size:2
Alignment explanation
Indices: 13019--13065 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
13009 ATATGGTAAA
* *
13019 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AT AA AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13061 AG AG A
1 AG AG A
13066 TAAAAATTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.53, C:0.00, G:0.45, T:0.02
Consensus pattern (2 bp):
AG
Found at i:15508 original size:17 final size:17
Alignment explanation
Indices: 15473--15505 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15463 TCAAGATAAG
*
15473 TATTAAATTTAATTTAA
1 TATTAAATTTAATTAAA
15490 TATTAAATTT-ATTAAA
1 TATTAAATTTAATTAAA
15506 ATAATATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAAATTTAATTAAA
Found at i:21793 original size:29 final size:29
Alignment explanation
Indices: 21759--21831 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
21749 ATGTATTAGT
* *
21759 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
21788 TTAGGACATATTTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
21817 TTAGGACATATTTAA
1 TTAGGACATATTTAA
21832 TAATATCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:27527 original size:10 final size:10
Alignment explanation
Indices: 27511--27570 Score: 68
Period size: 10 Copynumber: 5.9 Consensus size: 10
27501 ACCGTATACA
27511 ATTTTTTTCTT
1 ATTTTTTT-TT
*
27522 -TTTTTTTTCA
1 ATTTTTTTT-T
*
27532 ATTTTTTTTG
1 ATTTTTTTTT
*
27542 ATTTTTTTTG
1 ATTTTTTTTT
27552 ATTTTTTTTT
1 ATTTTTTTTT
27562 ATTTTTTTT
1 ATTTTTTTT
27571 CAAATTTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
9 1 0.02
10 35 0.80
11 8 0.18
ACGTcount: A:0.10, C:0.03, G:0.03, T:0.83
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:27581 original size:20 final size:21
Alignment explanation
Indices: 27509--27582 Score: 89
Period size: 20 Copynumber: 3.5 Consensus size: 21
27499 AGACCGTATA
*
27509 CAATTTTTTTCT-TTTTTTTTT
1 CAATTTTTTT-TGATTTTTTTT
27530 CAATTTTTTTTGATTTTTTTT
1 CAATTTTTTTTGATTTTTTTT
* *
27551 -GATTTTTTTTTATTTTTTTT
1 CAATTTTTTTTGATTTTTTTT
27571 CAAATTTTTTTT
1 C-AATTTTTTTT
27583 TCACGAGTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
20 19 0.41
21 18 0.39
22 9 0.20
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (21 bp):
CAATTTTTTTTGATTTTTTTT
Found at i:29076 original size:13 final size:13
Alignment explanation
Indices: 29058--29083 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29048 CCTCCCTCTT
29058 CGACCAAATGATA
1 CGACCAAATGATA
29071 CGACCAAATGATA
1 CGACCAAATGATA
29084 GCTTGTCCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (13 bp):
CGACCAAATGATA
Found at i:31635 original size:16 final size:15
Alignment explanation
Indices: 31610--31639 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
31600 GTAAGCACTA
31610 ATTTGATAGGTGAAC
1 ATTTGATAGGTGAAC
31625 ATTTAGATAGGTGAA
1 ATTT-GATAGGTGAA
31640 ACTGAGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (15 bp):
ATTTGATAGGTGAAC
Found at i:32456 original size:6 final size:6
Alignment explanation
Indices: 32445--32478 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
32435 AAAATTTTAA
32445 AAAATC AAAATC AAAATC AAAATC AAAAT- AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
32479 TTAAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATC
Found at i:32533 original size:22 final size:24
Alignment explanation
Indices: 32491--32535 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
32481 AAAATTTAAA
*
32491 ATATTTATAAAAATTCCAAAATTT
1 ATATTTATAAAAATTCAAAAATTT
32515 ATATTT-TAAAAATT-AAAAATT
1 ATATTTATAAAAATTCAAAAATT
32536 CTAAAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 8 0.40
24 6 0.30
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATTTATAAAAATTCAAAAATTT
Found at i:37661 original size:17 final size:18
Alignment explanation
Indices: 37641--37675 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
37631 CGAATTATCT
37641 GAATTAAAGTATT-AATC
1 GAATTAAAGTATTGAATC
37658 GAATTAAAGTATTGAATC
1 GAATTAAAGTATTGAATC
37676 ACTACATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (18 bp):
GAATTAAAGTATTGAATC
Found at i:39315 original size:237 final size:239
Alignment explanation
Indices: 38898--39368 Score: 811
Period size: 237 Copynumber: 2.0 Consensus size: 239
38888 AAATACAAAC
38898 ATTAAGACACAACATCTTATTGCACTCTCTCTTTTCCACCACAACACACTCCTTAAACTTTTTTA
1 ATTAAGACACAACATCTTATTGCACTCTCTCTTTTCCACCACAACACACTCCTTAAACTTTTTTA
* * *
38963 ATCTAACTGGAGATTGTCTCACATATCTAATAGTCCCCTAACACATTCAACAGATTTATTCATTT
66 ATCTAACTAGAGATTGTCTCACATATCTAATAGCCCCCGAACACATTCAACAGATTTATTCATTT
* *
39028 CCTTTAAGTCTTCAACAACAATTAAATTCACAATTTGTGTCATGCATCTCATATGAAGATATTTA
131 CCTTTAAGTCTTCAACAACAATCAAATTCACAATGTGTGTCATGCATCTCATATGAAGATATTTA
39093 CCATTTTGAACAAAACCCCCTCGAGGGTTAAATTTTTTTCTCAT
196 CCATTTTGAACAAAACCCCCTCGAGGGTTAAATTTTTTTCTCAT
* *
39137 ATTAAGACACAACATCTTCTTGCACTCTCTCTTTT-C-CCACAACACACTCTTTAAACTTTTTTA
1 ATTAAGACACAACATCTTATTGCACTCTCTCTTTTCCACCACAACACACTCCTTAAACTTTTTTA
* * *
39200 ATCTAACTAGAGATTGTCTCACATGTGTAATAGCCCCCGAACACTTTCAACAGATTTATTCATTT
66 ATCTAACTAGAGATTGTCTCACATATCTAATAGCCCCCGAACACATTCAACAGATTTATTCATTT
*
39265 CCTTTAAGTCTTCAACACCAATCAAATTCACAATGTGTGTCATGCATCTCATATGAAGATATTTA
131 CCTTTAAGTCTTCAACAACAATCAAATTCACAATGTGTGTCATGCATCTCATATGAAGATATTTA
* *
39330 CCATTTTGAACTAAACCCCCTCGAGGGTTAATTTTTTTT
196 CCATTTTGAACAAAACCCCCTCGAGGGTTAAATTTTTTT
39369 TCTTAAATAA
Statistics
Matches: 219, Mismatches: 13, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
237 184 0.84
238 1 0.00
239 34 0.16
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (239 bp):
ATTAAGACACAACATCTTATTGCACTCTCTCTTTTCCACCACAACACACTCCTTAAACTTTTTTA
ATCTAACTAGAGATTGTCTCACATATCTAATAGCCCCCGAACACATTCAACAGATTTATTCATTT
CCTTTAAGTCTTCAACAACAATCAAATTCACAATGTGTGTCATGCATCTCATATGAAGATATTTA
CCATTTTGAACAAAACCCCCTCGAGGGTTAAATTTTTTTCTCAT
Found at i:41333 original size:25 final size:25
Alignment explanation
Indices: 41305--41354 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
41295 TACCCTATAC
41305 ATGCCATGATAACCAAAATTAGTTT
1 ATGCCATGATAACCAAAATTAGTTT
*
41330 ATGCCATTATAACCAAAATTAGTTT
1 ATGCCATGATAACCAAAATTAGTTT
41355 TCTATATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (25 bp):
ATGCCATGATAACCAAAATTAGTTT
Found at i:42011 original size:24 final size:24
Alignment explanation
Indices: 41906--42044 Score: 93
Period size: 25 Copynumber: 5.7 Consensus size: 24
41896 TGTAAACGAT
* * *
41906 AAGCTCTTTCGAGCCATATAACGAG
1 AAGCTCATGCGAGCCATA-AACGGG
* *** *
41931 AAGCTCATGTGAGTTGTATAACGAG
1 AAGCTCATGCGAGCCATA-AACGGG
* *
41956 AAGCTCATGCAAGCCA-AATATCAGG
1 AAGCTCATGCGAGCCATAA-A-CGGG
41981 AAGCTCATGCGAGCCATAAACGGG
1 AAGCTCATGCGAGCCATAAACGGG
*** *
42005 AAGCTCAAAAGAGCCA-AATTCGGG
1 AAGCTCATGCGAGCCATAA-ACGGG
42029 AAGCTCATGCGAGCCA
1 AAGCTCATGCGAGCCA
42045 ATATCAGGAA
Statistics
Matches: 88, Mismatches: 22, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
23 3 0.03
24 35 0.40
25 48 0.55
26 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.18
Consensus pattern (24 bp):
AAGCTCATGCGAGCCATAAACGGG
Found at i:42045 original size:24 final size:24
Alignment explanation
Indices: 41955--42045 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
41945 TGTATAACGA
* *
41955 GAAGCTCATGCAAGCCAAATATCAG
1 GAAGCTCATGCGAGCCAAAT-TCGG
*
41980 GAAGCTCATGCGAGCCATAA-ACGG
1 GAAGCTCATGCGAGCCA-AATTCGG
***
42004 GAAGCTCAAAAGAGCCAAATTCGG
1 GAAGCTCATGCGAGCCAAATTCGG
42028 GAAGCTCATGCGAGCCAA
1 GAAGCTCATGCGAGCCAA
42046 TATCAGGAAG
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
23 2 0.04
24 34 0.63
25 16 0.30
26 2 0.04
ACGTcount: A:0.37, C:0.24, G:0.25, T:0.13
Consensus pattern (24 bp):
GAAGCTCATGCGAGCCAAATTCGG
Found at i:42054 original size:24 final size:24
Alignment explanation
Indices: 41955--42057 Score: 102
Period size: 24 Copynumber: 4.2 Consensus size: 24
41945 TGTATAACGA
*
41955 GAAGCTCATGCAAGCCAAATATCAG
1 GAAGCTCATGCGAGCC-AATATCAG
* *
41980 GAAGCTCATGCGAGCC-ATAAACGG
1 GAAGCTCATGCGAGCCAAT-ATCAG
*** *
42004 GAAGCTCAAAAGAGCCAA-ATTCGG
1 GAAGCTCATGCGAGCCAATA-TCAG
42028 GAAGCTCATGCGAGCCAATATCAG
1 GAAGCTCATGCGAGCCAATATCAG
42052 GAAGCT
1 GAAGCT
42058 TCGAAGAGCC
Statistics
Matches: 63, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
23 3 0.05
24 43 0.68
25 17 0.27
ACGTcount: A:0.37, C:0.23, G:0.25, T:0.15
Consensus pattern (24 bp):
GAAGCTCATGCGAGCCAATATCAG
Found at i:42065 original size:48 final size:49
Alignment explanation
Indices: 41967--42085 Score: 136
Period size: 48 Copynumber: 2.4 Consensus size: 49
41957 AGCTCATGCA
*
41967 AGCCAAATATCAGGAAGCTCATGCGAGCCATAAACGGGAAGCTCAAAAG
1 AGCCAAATATCAGGAAGCTCATGCGAGCCATAAACAGGAAGCTCAAAAG
* * *
42016 AGCCAAAT-TCGGGAAGCTCATGCGAGCCA-ATATCAGGAAGCTTC-GAAG
1 AGCCAAATATCAGGAAGCTCATGCGAGCCATA-AACAGGAAGC-TCAAAAG
* * *
42064 AGCCATATATTAGGATGCTCAT
1 AGCCAAATATCAGGAAGCTCAT
42086 AAGAGTTAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
47 1 0.02
48 38 0.64
49 20 0.34
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (49 bp):
AGCCAAATATCAGGAAGCTCATGCGAGCCATAAACAGGAAGCTCAAAAG
Found at i:49710 original size:25 final size:24
Alignment explanation
Indices: 49683--49772 Score: 74
Period size: 25 Copynumber: 3.7 Consensus size: 24
49673 AAGCTCTTCT
* *
49683 GAGCCATATAACAGGAAGCTTATGT
1 GAGCCATATAAC-GGAAGCTCATGC
**
49708 GAGCTGTATAACGAGAAGCTCATGC
1 GAGCCATATAACG-GAAGCTCATGC
* * * *
49733 AAGCCAAATATCAGGAAGATCATGC
1 GAGCCATATAAC-GGAAGCTCATGC
49758 GAGCCATA-AACGGAA
1 GAGCCATATAACGGAA
49773 AGCTGAAGAG
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
23 4 0.08
24 3 0.06
25 42 0.84
26 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (24 bp):
GAGCCATATAACGGAAGCTCATGC
Found at i:49810 original size:24 final size:24
Alignment explanation
Indices: 49723--49812 Score: 76
Period size: 24 Copynumber: 3.7 Consensus size: 24
49713 GTATAACGAG
*
49723 AAGCTCATGCAAGCCAAATATCAGG
1 AAGCTCATGCAAGCCAAAT-TCAGA
* * * *
49748 AAGATCATGCGAGCCATAA-ACGGA
1 AAGCTCATGCAAGCCA-AATTCAGA
* *
49772 AAGCTGAAG-AGAGCCAAATTCAGA
1 AAGCTCATGCA-AGCCAAATTCAGA
49796 AAGCTCATGCAAGCCAA
1 AAGCTCATGCAAGCCAA
49813 TAGTTGGAAG
Statistics
Matches: 48, Mismatches: 13, Indels: 9
0.69 0.19 0.13
Matches are distributed among these distances:
23 2 0.04
24 29 0.60
25 15 0.31
26 2 0.04
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.13
Consensus pattern (24 bp):
AAGCTCATGCAAGCCAAATTCAGA
Found at i:51198 original size:25 final size:25
Alignment explanation
Indices: 51145--51207 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
51135 TCGAAAGAAC
*
51145 ATCCCATTA-TTAGCTCTCATGAGT
1 ATCCCATTATTTGGCTCTCATGAGT
51169 ATCCCGA-TATTTGGCTCTCATGAGCT
1 ATCCC-ATTATTTGGCTCTCATGAG-T
51195 -TCCCATTATTTGG
1 ATCCCATTATTTGG
51208 TTCTTGCGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
24 8 0.24
25 25 0.74
26 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (25 bp):
ATCCCATTATTTGGCTCTCATGAGT
Found at i:54136 original size:93 final size:93
Alignment explanation
Indices: 53977--54162 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
53967 GATGGATTAT
53977 CTTCAAAACATAGAACATGGGATGCTACTCTATTTTACTCCATTTTCAGTTCCAAATTAAGAAAC
1 CTTCAAAACATAGAACATGGGATGCTACTCTATTTTACTCCATTTTCAGTTCCAAATTAAGAAAC
54042 GAGCAAATAGTTAATTAATACAACAATG
66 GAGCAAATAGTTAATTAATACAACAATG
*
54070 CTTCAAAACATAGAACATGGGATGCTACTCTATTTTACTCCCTTTTCAGTTCCAAATTAAGAAAC
1 CTTCAAAACATAGAACATGGGATGCTACTCTATTTTACTCCATTTTCAGTTCCAAATTAAGAAAC
54135 GAGCAAATAGTTAATTAATACAACAATG
66 GAGCAAATAGTTAATTAATACAACAATG
54163 TCATCGCTGC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (93 bp):
CTTCAAAACATAGAACATGGGATGCTACTCTATTTTACTCCATTTTCAGTTCCAAATTAAGAAAC
GAGCAAATAGTTAATTAATACAACAATG
Found at i:56663 original size:25 final size:25
Alignment explanation
Indices: 56609--56655 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
56599 AAATCTACTC
56609 TAAAAAGAAAAGAGAAAGCCTAAAT
1 TAAAAAGAAAAGAGAAAGCCTAAAT
56634 TAAAAATGAAAAGA-AAA-CCTAA
1 TAAAAA-GAAAAGAGAAAGCCTAA
56656 CCTTAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.24
25 9 0.43
26 7 0.33
ACGTcount: A:0.66, C:0.09, G:0.13, T:0.13
Consensus pattern (25 bp):
TAAAAAGAAAAGAGAAAGCCTAAAT
Found at i:57603 original size:19 final size:19
Alignment explanation
Indices: 57579--57619 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
57569 TATAAAATAT
*
57579 AAAATTAAAAACCCAATTA
1 AAAATTAAAAACCAAATTA
*
57598 AAAATTTAAAACCAAATTA
1 AAAATTAAAAACCAAATTA
57617 AAA
1 AAA
57620 GGCCTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAATTAAAAACCAAATTA
Found at i:57872 original size:30 final size:28
Alignment explanation
Indices: 57838--57916 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 28
57828 AGAATCAGTC
* *
57838 TGGGCCTGAGCCCTATACAGTAGCAGTGTG
1 TGGGCCT-AGCCCAATACAGTA-CAGAGTG
* *
57868 TGGGCCATAGCACAATACAATTACAGAGTG
1 TGGGCC-TAGCCCAATAC-AGTACAGAGTG
57898 TGGGCCTTAGCCCAATACA
1 TGGGCC-TAGCCCAATACA
57917 TTAACCAGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
29 1 0.02
30 36 0.88
31 4 0.10
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.22
Consensus pattern (28 bp):
TGGGCCTAGCCCAATACAGTACAGAGTG
Found at i:58056 original size:26 final size:26
Alignment explanation
Indices: 58026--58128 Score: 109
Period size: 26 Copynumber: 4.0 Consensus size: 26
58016 GCCAACACAC
*
58026 CAATATCGCAATAAAGCTGCCAGTAT
1 CAATATCGCAACAAAGCTGCCAGTAT
* *
58052 CAATAAT-GCAGCAAAGCTGCCAGTAA
1 CAAT-ATCGCAACAAAGCTGCCAGTAT
* * *
58078 CAGTATCGCAGCAGAGCTGCCAGTAT
1 CAATATCGCAACAAAGCTGCCAGTAT
* * *
58104 CAGTATCACAACAGAGCTGCCAGTA
1 CAATATCGCAACAAAGCTGCCAGTA
58129 ACAGTATTTG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
25 2 0.03
26 63 0.94
27 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (26 bp):
CAATATCGCAACAAAGCTGCCAGTAT
Found at i:58133 original size:26 final size:26
Alignment explanation
Indices: 58066--58135 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
58056 AATGCAGCAA
* *
58066 AGCTGCCAGTAACAGTATCGCAGCAG
1 AGCTGCCAGTAACAGTATCACAACAG
*
58092 AGCTGCCAGTATCAGTATCACAACAG
1 AGCTGCCAGTAACAGTATCACAACAG
58118 AGCTGCCAGTAACAGTAT
1 AGCTGCCAGTAACAGTAT
58136 TTGTGGCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (26 bp):
AGCTGCCAGTAACAGTATCACAACAG
Found at i:58358 original size:27 final size:27
Alignment explanation
Indices: 58328--58714 Score: 417
Period size: 27 Copynumber: 14.4 Consensus size: 27
58318 GATATAGTGG
* * *
58328 TAATTTTACCCTTCGGGGGCATTTTGA
1 TAATTTTACCCTTCGAGGGTATTTCGA
* *
58355 TAATTTTA-CCTATTGAGGGTATTTCGG
1 TAATTTTACCCT-TCGAGGGTATTTCGA
* * *
58382 TAATTTTATCCTTCGGGGGCATTTCGA
1 TAATTTTACCCTTCGAGGGTATTTCGA
* * *
58409 TAATTTTACCCTTTGGGGGTATTTTGA
1 TAATTTTACCCTTCGAGGGTATTTCGA
*
58436 TAATTTTACCCTTCGAGGGTATTTCAA
1 TAATTTTACCCTTCGAGGGTATTTCGA
** * **
58463 TAATTTTTTCCATCGAGGGTATTTTAA
1 TAATTTTACCCTTCGAGGGTATTTCGA
* *
58490 TAATTTTACTCTT-TAGGGGTATTTC-A
1 TAATTTTACCCTTCGA-GGGTATTTCGA
*
58516 GTAATTTTACCCTTTGAGGGTATTTCGA
1 -TAATTTTACCCTTCGAGGGTATTTCGA
58544 TAATTTTA-CCTTCGAGGGTATTTCGA
1 TAATTTTACCCTTCGAGGGTATTTCGA
*
58570 TAATTTTACCCTTTGAGGGTATTTC-A
1 TAATTTTACCCTTCGAGGGTATTTCGA
* *
58596 GTAATTTTACCCTTCGAGAGTATTTCGG
1 -TAATTTTACCCTTCGAGGGTATTTCGA
* * * *
58624 TAATTTTACTCATCGAGGGTATTTTGG
1 TAATTTTACCCTTCGAGGGTATTTCGA
* * *
58651 TAATTTTACCCATCGAAGGTATTTTGA
1 TAATTTTACCCTTCGAGGGTATTTCGA
*
58678 TAATTTTACCCTTCGAGGGTATTTCAA
1 TAATTTTACCCTTCGAGGGTATTTCGA
58705 TAA-TTTACCC
1 TAATTTTACCC
58715 ACGAATCGAA
Statistics
Matches: 306, Mismatches: 45, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
26 38 0.12
27 263 0.86
28 5 0.02
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.43
Consensus pattern (27 bp):
TAATTTTACCCTTCGAGGGTATTTCGA
Found at i:61380 original size:90 final size:90
Alignment explanation
Indices: 61218--61482 Score: 267
Period size: 90 Copynumber: 3.0 Consensus size: 90
61208 CTCAGTTTAA
* * * * * *
61218 AAATTCGGTGAATAT-ATCAAGTCTACCTCACTAGGACCACCCAAAGC-CTGAGATATGAATTCA
1 AAATTTGGTGAAT-TCATCAAGTCTATCTCAATAGGACCACCCAAA-CTCTGGGCTATGAACTCA
* * **
61281 TTAAGAACATTTAGTGGCTCATCCTAT
64 TTAAAAACATCTAGAAGCTCATCCTAT
* * *
61308 AAATTTGGT-AAGTTCATCAAGTTTGTCTCAATAGGAACC-CCCGAAA-TCTGGGTTATGAACTC
1 AAATTTGGTGAA-TTCATCAAGTCTATCTCAATAGG-ACCACCC-AAACTCTGGGCTATGAACTC
*
61370 ATTAAAAACATCTAGAAGTTCATCCTAT
63 ATTAAAAACATCTAGAAGCTCATCCTAT
* * *
61398 AAATTTGGTGAATTTATCAAGTCTATCTTAATAGGACCATCCAAACTCTGGGCTATGAACTCATT
1 AAATTTGGTGAATTCATCAAGTCTATCTCAATAGGACCACCCAAACTCTGGGCTATGAACTCATT
*
61463 AAAAGCA-C-AG-AGCTCATCCT
66 AAAAACATCTAGAAGCTCATCCT
61483 TATACATCAT
Statistics
Matches: 146, Mismatches: 21, Indels: 19
0.78 0.11 0.10
Matches are distributed among these distances:
87 9 0.06
88 2 0.01
89 10 0.07
90 117 0.80
91 8 0.05
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.29
Consensus pattern (90 bp):
AAATTTGGTGAATTCATCAAGTCTATCTCAATAGGACCACCCAAACTCTGGGCTATGAACTCATT
AAAAACATCTAGAAGCTCATCCTAT
Found at i:63232 original size:63 final size:63
Alignment explanation
Indices: 63154--63280 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
63144 CTAAATTAAC
63154 AATTTCGGTTATAAAAGAAGTAAGGAAGCCAGGACCAAAACTAGTTACAGCTTTTTGTCTTTT
1 AATTTCGGTTATAAAAGAAGTAAGGAAGCCAGGACCAAAACTAGTTACAGCTTTTTGTCTTTT
* *
63217 AATTTCGGTTATAAAAGAAGTAAGGAAGGCAGGACCAAAACTAGTTGCAGCTTTTTGTCTTTT
1 AATTTCGGTTATAAAAGAAGTAAGGAAGCCAGGACCAAAACTAGTTACAGCTTTTTGTCTTTT
63280 A
1 A
63281 CTCCTCCTAG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (63 bp):
AATTTCGGTTATAAAAGAAGTAAGGAAGCCAGGACCAAAACTAGTTACAGCTTTTTGTCTTTT
Found at i:65225 original size:18 final size:18
Alignment explanation
Indices: 65183--65226 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
65173 TATGAGTTAT
65183 AAATTAC-ATAATATATA
1 AAATTACAATAATATATA
*
65200 AAAATACAATAATATA-A
1 AAATTACAATAATATATA
65217 AACATTACAA
1 AA-ATTACAA
65227 ACTAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATTACAATAATATATA
Found at i:70182 original size:50 final size:50
Alignment explanation
Indices: 70083--70182 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
70073 TTTTTTGAAT
* * * ** * *
70083 TTTTTTAGAATTAAGATTAAATTGATATTATTTGTAAACTTTTAGGGTTA
1 TTTTTTAAAATTAAGATTAAATTGATATAATATGTAAAAATTAAAGGTTA
*
70133 TTTTTTAAAATTATGATTAAATTGATATAATATGTAAAAATTAAAGGTTA
1 TTTTTTAAAATTAAGATTAAATTGATATAATATGTAAAAATTAAAGGTTA
70183 AATTTATTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (50 bp):
TTTTTTAAAATTAAGATTAAATTGATATAATATGTAAAAATTAAAGGTTA
Found at i:75852 original size:62 final size:64
Alignment explanation
Indices: 75739--75861 Score: 160
Period size: 62 Copynumber: 2.0 Consensus size: 64
75729 ATCACTTTAA
* * * * *
75739 TATTAAACTAATATAATATAATATTTATCAAGATAAATATTAGATTAAATTTAATACTAAATCT
1 TATTAAAATAATAGAATATAATATCTATCAAGATAAACATTAAATTAAATTTAATACTAAATCT
* * *
75803 TATTAAAATAATAGAATAT-TTATCTA-CAAGATAAGCATTAAATTAAATTTAATATTAAA
1 TATTAAAATAATAGAATATAATATCTATCAAGATAAACATTAAATTAAATTTAATACTAAA
75862 GATAATCATT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 29 0.57
63 5 0.10
64 17 0.33
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (64 bp):
TATTAAAATAATAGAATATAATATCTATCAAGATAAACATTAAATTAAATTTAATACTAAATCT
Found at i:77218 original size:12 final size:12
Alignment explanation
Indices: 77197--77254 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 12
77187 ACGTCACAAG
77197 CGAATTAATTCA
1 CGAATTAATTCA
*
77209 CGAATGAATTCA
1 CGAATTAATTCA
77221 -GAATTAATTCA
1 CGAATTAATTCA
** *
77232 CGAACGAATTTA
1 CGAATTAATTCA
77244 -GAATTAATTCA
1 CGAATTAATTCA
77255 TCTTGGATCT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
11 18 0.49
12 19 0.51
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (12 bp):
CGAATTAATTCA
Found at i:77228 original size:23 final size:23
Alignment explanation
Indices: 77198--77254 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
77188 CGTCACAAGC
*
77198 GAATTAATTCACGAATGAATTCA
1 GAATTAATTCACGAACGAATTCA
*
77221 GAATTAATTCACGAACGAATTTA
1 GAATTAATTCACGAACGAATTCA
77244 GAATTAATTCA
1 GAATTAATTCA
77255 TCTTGGATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (23 bp):
GAATTAATTCACGAACGAATTCA
Found at i:79074 original size:9 final size:9
Alignment explanation
Indices: 79060--79117 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
79050 TTTGGTTAAA
*
79060 AATTAACTG
1 AATTAACCG
79069 AATTAACCG
1 AATTAACCG
* *
79078 AATTCACTG
1 AATTAACCG
*
79087 AATTACCCG
1 AATTAACCG
79096 AATTAACCG
1 AATTAACCG
79105 AATTAACCG
1 AATTAACCG
79114 AATT
1 AATT
79118 GAATCACTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:79086 original size:18 final size:18
Alignment explanation
Indices: 79060--79117 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
79050 TTTGGTTAAA
79060 AATTAACTGAATTAACCG
1 AATTAACTGAATTAACCG
* *
79078 AATTCACTGAATTACCCG
1 AATTAACTGAATTAACCG
*
79096 AATTAACCGAATTAACCG
1 AATTAACTGAATTAACCG
79114 AATT
1 AATT
79118 GAATCACTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (18 bp):
AATTAACTGAATTAACCG
Found at i:84467 original size:37 final size:37
Alignment explanation
Indices: 84424--84504 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
84414 TGAGCTTTAT
* * *
84424 TTCAGTATATCTGTAG-ATTTTACTCATTTGAGCTCCA
1 TTCAGTATAACAGTAGAATTTT-CTCATTTGAGCTACA
* *
84461 TTCAGTATAACAGTAGAATTTTCTCGTTTGAGCTACT
1 TTCAGTATAACAGTAGAATTTTCTCATTTGAGCTACA
84498 TTCAGTA
1 TTCAGTA
84505 GAATCATTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
37 33 0.87
38 5 0.13
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (37 bp):
TTCAGTATAACAGTAGAATTTTCTCATTTGAGCTACA
Found at i:84596 original size:40 final size:40
Alignment explanation
Indices: 84501--84753 Score: 235
Period size: 40 Copynumber: 6.3 Consensus size: 40
84491 AGCTACTTTC
* * * *
84501 AGTAGAATCATTAGGTATGGCTTGATAA--AGCATAC-TTTC
1 AGTAGATTCAATAGGTATGGCTCGA-AAGCA-CATACATTTT
* ** * *
84540 AGTAGAATCAGCAGGTAAGGCTCGATAGCACATACATTTT
1 AGTAGATTCAATAGGTATGGCTCGAAAGCACATACATTTT
* **
84580 AGTGGGATT-GGTAGGTATGGCTCGAAAGCACATACATTTT
1 AGT-AGATTCAATAGGTATGGCTCGAAAGCACATACATTTT
* *
84620 AGTAGATTCAATAGGTATGGCTCGAAAGCACATACGTTTC
1 AGTAGATTCAATAGGTATGGCTCGAAAGCACATACATTTT
* * * * * *
84660 AGTAAATTCAACAGATATCGCTCGAAAGCACATACGTTTC
1 AGTAGATTCAATAGGTATGGCTCGAAAGCACATACATTTT
* * * *
84700 AGTAGATTCAGTAGGTATGACTCGAAAGCACATACGTTTC
1 AGTAGATTCAATAGGTATGGCTCGAAAGCACATACATTTT
84740 AGTAGATTCAATAG
1 AGTAGATTCAATAG
84754 ATATCACTCG
Statistics
Matches: 181, Mismatches: 28, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
38 1 0.01
39 30 0.17
40 147 0.81
41 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (40 bp):
AGTAGATTCAATAGGTATGGCTCGAAAGCACATACATTTT
Found at i:88468 original size:167 final size:167
Alignment explanation
Indices: 88192--88534 Score: 677
Period size: 167 Copynumber: 2.0 Consensus size: 167
88182 TTGTTTAAGG
88192 TGGAAAAATGGTTTGGGAGAAGGTAGTTGAATGCCACACCAAAGGCTGGTGATAAGTTCAGAAAC
1 TGGAAAAATGGTTTGGGAGAAGGTAGTTGAATGCCACACCAAAGGCTGGTGATAAGTTCAGAAAC
88257 AAGTTCGGGTTGACGCACTAGCACCCTAGATAAGTCACTCGAGACTCGTACGAAATTGGAGAGGA
66 AAGTTCGGGTTGACGCACTAGCACCCTAGATAAGTCACTCGAGACTCGTACGAAATTGGAGAGGA
88322 AGTTAACCTCACAGAAACAAAGTTTCATTTAACAAAT
131 AGTTAACCTCACAGAAACAAAGTTTCATTTAACAAAT
88359 TGGAAAAATGGTTTGGGAGAAGGTAGTTGAATGCCACACCAAAGGCTGGTGATAAGTTCAGAAAC
1 TGGAAAAATGGTTTGGGAGAAGGTAGTTGAATGCCACACCAAAGGCTGGTGATAAGTTCAGAAAC
88424 AAGTTCGGGTTGACGCACTAGCACCCTAGATAAGTCACTCGAGACTCGTACGAAATTGGAGAGGA
66 AAGTTCGGGTTGACGCACTAGCACCCTAGATAAGTCACTCGAGACTCGTACGAAATTGGAGAGGA
88489 AGTTAACCTCACAGAAACAAAGTTTCATTTAACAAAT
131 AGTTAACCTCACAGAAACAAAGTTTCATTTAACAAAT
88526 TGGCAAAAA
1 TGG-AAAAA
88535 GTCTCTCAAA
Statistics
Matches: 175, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
167 170 0.97
168 5 0.03
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.22
Consensus pattern (167 bp):
TGGAAAAATGGTTTGGGAGAAGGTAGTTGAATGCCACACCAAAGGCTGGTGATAAGTTCAGAAAC
AAGTTCGGGTTGACGCACTAGCACCCTAGATAAGTCACTCGAGACTCGTACGAAATTGGAGAGGA
AGTTAACCTCACAGAAACAAAGTTTCATTTAACAAAT
Found at i:89263 original size:19 final size:19
Alignment explanation
Indices: 89236--89274 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
89226 TGATTTAAGC
89236 AACTAAATTAACTAAGATG
1 AACTAAATTAACTAAGATG
* *
89255 AACTTAATTAACTACGATG
1 AACTAAATTAACTAAGATG
89274 A
1 A
89275 GTAATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (19 bp):
AACTAAATTAACTAAGATG
Found at i:89301 original size:35 final size:35
Alignment explanation
Indices: 89255--89328 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
89245 AACTAAGATG
*
89255 AACTTAATTAACTACGATGAGTAATTTATTCAAGC
1 AACTTAATTAACTAAGATGAGTAATTTATTCAAGC
*
89290 AACTTAATTAACTAAGATGAGTAATTTATTCCAGC
1 AACTTAATTAACTAAGATGAGTAATTTATTCAAGC
89325 AACT
1 AACT
89329 AAATACTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.34
Consensus pattern (35 bp):
AACTTAATTAACTAAGATGAGTAATTTATTCAAGC
Found at i:89389 original size:21 final size:20
Alignment explanation
Indices: 89364--89402 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
89354 ATGGTTTGAA
*
89364 GTTAAGCTAAATGAGCTTGGG
1 GTTAA-CTAAACGAGCTTGGG
*
89385 GTTAACTAGACGAGCTTG
1 GTTAACTAAACGAGCTTG
89403 AAGAAGCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (20 bp):
GTTAACTAAACGAGCTTGGG
Found at i:89850 original size:25 final size:24
Alignment explanation
Indices: 89822--89889 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 24
89812 GTTATATAGT
*
89822 TCTTGCGAGCTTCCTGATAATTGGC
1 TCTT-CGAGCTTCCTGATAACTGGC
*
89847 TCTTCAGAGCTTCCCGATAACTGGC
1 TCTTC-GAGCTTCCTGATAACTGGC
*
89872 TCTTATGAGCTTCCTGAT
1 TCTT-CGAGCTTCCTGAT
89890 CAATGAATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.03
25 36 0.97
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (24 bp):
TCTTCGAGCTTCCTGATAACTGGC
Found at i:93240 original size:37 final size:37
Alignment explanation
Indices: 93197--93432 Score: 184
Period size: 37 Copynumber: 6.3 Consensus size: 37
93187 CATACATTTC
*
93197 GTATAATCAGTAGATATCGCTCGTTTAAGCCCATTCA
1 GTATAATCAGTAGATATCGCTCGTTTAAGCACATTCA
* * * *
93234 GTATAATCAGTGGATATCGCTCGTTTGAGAAACTTTCA
1 GTATAATCAGTAGATATCGCTCGTTTAAG-CACATTCA
* *** * * *
93272 GTATAATCAGTAGACATTTATCTTTTAAGCACGTTTA
1 GTATAATCAGTAGATATCGCTCGTTTAAGCACATTCA
* * ** * * *
93309 GTATATTTAGTAGATATTTCTCATTTGAGCCCATTCA
1 GTATAATCAGTAGATATCGCTCGTTTAAGCACATTCA
* * * * *
93346 GTATAATCAATGGATATCGCTTGTTTGAGCAACTTTCA
1 GTATAATCAGTAGATATCGCTCGTTTAAGC-ACATTCA
* * * * *
93384 GTATAATCAGTAGACATTGCTCTTTTAAGCACGTTTA
1 GTATAATCAGTAGATATCGCTCGTTTAAGCACATTCA
*
93421 GTATATTCAGTA
1 GTATAATCAGTA
93433 TTCCATTTTT
Statistics
Matches: 153, Mismatches: 44, Indels: 4
0.76 0.22 0.02
Matches are distributed among these distances:
37 98 0.64
38 55 0.36
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (37 bp):
GTATAATCAGTAGATATCGCTCGTTTAAGCACATTCA
Found at i:93312 original size:75 final size:76
Alignment explanation
Indices: 93161--93313 Score: 168
Period size: 75 Copynumber: 2.0 Consensus size: 76
93151 TCATTTCGCG
* * * *
93161 TAATTAGTGGATAATGCTCGTTCGAGCATACATTTCGTATAATCAGTAGATATCGCTCGTTTAAG
1 TAATCAGTGGATAATGCTCGTTCGAGCAAACATTTCGTATAATCAGTAGACATCGATCGTTTAAG
*
93226 CCCATTCAGTA
66 CACATTCAGTA
* ** *
93237 TAATCAGTGGAT-ATCGCTCGTTTGAG-AAAC-TTTCAGTATAATCAGTAGACATTTATCTTTTA
1 TAATCAGTGGATAAT-GCTCGTTCGAGCAAACATTTC-GTATAATCAGTAGACATCGATCGTTTA
* *
93299 AGCACGTTTAGTA
64 AGCACATTCAGTA
93312 TA
1 TA
93314 TTTAGTAGAT
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
74 4 0.06
75 39 0.61
76 21 0.33
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (76 bp):
TAATCAGTGGATAATGCTCGTTCGAGCAAACATTTCGTATAATCAGTAGACATCGATCGTTTAAG
CACATTCAGTA
Found at i:93394 original size:112 final size:112
Alignment explanation
Indices: 93197--93432 Score: 373
Period size: 112 Copynumber: 2.1 Consensus size: 112
93187 CATACATTTC
* * *
93197 GTATAATCAGTAGATATCGCTCGTTTAAGCCCATTCAGTATAATCAGTGGATATCGCTCGTTTGA
1 GTATATTCAGTAGATATCGCTCATTTAAGCCCATTCAGTATAATCAATGGATATCGCTCGTTTGA
*
93262 GAAACTTTCAGTATAATCAGTAGACATTTATCTTTTAAGCACGTTTA
66 GAAACTTTCAGTATAATCAGTAGACATTGATCTTTTAAGCACGTTTA
* ** * *
93309 GTATATTTAGTAGATATTTCTCATTTGAGCCCATTCAGTATAATCAATGGATATCGCTTGTTTGA
1 GTATATTCAGTAGATATCGCTCATTTAAGCCCATTCAGTATAATCAATGGATATCGCTCGTTTGA
* *
93374 GCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTAAGCACGTTTA
66 GAAACTTTCAGTATAATCAGTAGACATTGATCTTTTAAGCACGTTTA
93421 GTATATTCAGTA
1 GTATATTCAGTA
93433 TTCCATTTTT
Statistics
Matches: 112, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (112 bp):
GTATATTCAGTAGATATCGCTCATTTAAGCCCATTCAGTATAATCAATGGATATCGCTCGTTTGA
GAAACTTTCAGTATAATCAGTAGACATTGATCTTTTAAGCACGTTTA
Found at i:97595 original size:20 final size:19
Alignment explanation
Indices: 97570--97608 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
97560 CCGGCCCGAT
*
97570 TTTTAATAAACACAAAAATA
1 TTTTAA-AAACAAAAAAATA
*
97590 TTTTAAAAATAAAAAAATA
1 TTTTAAAAACAAAAAAATA
97609 AAAAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
TTTTAAAAACAAAAAAATA
Found at i:103295 original size:42 final size:42
Alignment explanation
Indices: 103247--103329 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
103237 ATTTGCAATG
*
103247 TTATACATTAATTTTAATTTGGTCTATTTGTATATATCAAAA
1 TTATACATTAATTTTAATTTGGTCTATTTATATATATCAAAA
*
103289 TTATACATTAATTTTAATTTGGTTTATTTATATATATCAAA
1 TTATACATTAATTTTAATTTGGTCTATTTATATATATCAAA
103330 CTTTAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (42 bp):
TTATACATTAATTTTAATTTGGTCTATTTATATATATCAAAA
Found at i:105992 original size:4 final size:4
Alignment explanation
Indices: 105983--106009 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
105973 CCTAACTTTA
105983 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
106010 TGTAGCCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:106143 original size:19 final size:18
Alignment explanation
Indices: 106119--106164 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
106109 ATAACTTTTG
106119 ATTTTTGATTCAAGTTAAT
1 ATTTTTGATTCAA-TTAAT
*
106138 ATTTTT--TTCAATTGAT
1 ATTTTTGATTCAATTAAT
*
106154 ATTATTGATTC
1 ATTTTTGATTC
106165 TTGCAAGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 9 0.39
17 5 0.22
18 3 0.13
19 6 0.26
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.57
Consensus pattern (18 bp):
ATTTTTGATTCAATTAAT
Found at i:107732 original size:33 final size:33
Alignment explanation
Indices: 107673--107735 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
107663 ACGGCTACTG
* *
107673 GGAGATGGCGGAGATTTTTGCTTAGGAGGGTTA
1 GGAGATGGCGGAGATTGTTGCGTAGGAGGGTTA
*
107706 GGAGATGGCGGTA-ATTGTTGGGTAGGAGGG
1 GGAGATGGCGG-AGATTGTTGCGTAGGAGGG
107736 GTATGAGACG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 25 0.96
34 1 0.04
ACGTcount: A:0.21, C:0.05, G:0.48, T:0.27
Consensus pattern (33 bp):
GGAGATGGCGGAGATTGTTGCGTAGGAGGGTTA
Found at i:107942 original size:30 final size:30
Alignment explanation
Indices: 107908--107983 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
107898 GTTATTTCTG
*
107908 GTGGTGGTGGTGGTGAAAGTTTTTCTCCTA
1 GTGGTGGCGGTGGTGAAAGTTTTTCTCCTA
* * *
107938 GTGGTGGCGGTGGTGAATGTTTTTCTTCTT
1 GTGGTGGCGGTGGTGAAAGTTTTTCTCCTA
*
107968 GTGGTGGCGATGGTGA
1 GTGGTGGCGGTGGTGA
107984 CGTTTTAGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.11, C:0.09, G:0.41, T:0.39
Consensus pattern (30 bp):
GTGGTGGCGGTGGTGAAAGTTTTTCTCCTA
Found at i:108970 original size:134 final size:135
Alignment explanation
Indices: 108808--109077 Score: 533
Period size: 134 Copynumber: 2.0 Consensus size: 135
108798 TCACTTATGT
108808 TTATTTTTAAAATAATAATAAAATCAAAATTTTATTTTAAATAAAACTAAAATTAATTTTTAGAA
1 TTATTTTTAAAATAATAATAAAATCAAAATTTTATTTTAAATAAAACTAAAATTAATTTTTAGAA
108873 AATCAGTTTTAAATAAAAATAAGGCTTTTTTTTATCTAAATAATACAAGAAACAAAATAATCTAC
66 AATCAGTTTTAAATAAAAATAAGGCTTTTTTTTATCTAAATAATACAAGAAACAAAATAATCTAC
108938 GAAAA
131 GAAAA
108943 TTATTTTT-AAATAATAATAAAATCAAAATTTTATTTTAAATAAAACTAAAATTAATTTTTAGAA
1 TTATTTTTAAAATAATAATAAAATCAAAATTTTATTTTAAATAAAACTAAAATTAATTTTTAGAA
109007 AATCAGTTTTAAATAAAAATAAGGCTTTTTTTTATCTAAATAATACAAGAAACAAAATAATCTAC
66 AATCAGTTTTAAATAAAAATAAGGCTTTTTTTTATCTAAATAATACAAGAAACAAAATAATCTAC
109072 GAAAA
131 GAAAA
109077 T
1 T
109078 GGTATCCTAC
Statistics
Matches: 135, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
134 127 0.94
135 8 0.06
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.37
Consensus pattern (135 bp):
TTATTTTTAAAATAATAATAAAATCAAAATTTTATTTTAAATAAAACTAAAATTAATTTTTAGAA
AATCAGTTTTAAATAAAAATAAGGCTTTTTTTTATCTAAATAATACAAGAAACAAAATAATCTAC
GAAAA
Found at i:108992 original size:29 final size:28
Alignment explanation
Indices: 108939--108994 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
108929 ATAATCTACG
108939 AAAATTATTTTTAAATAATAATAAAATC
1 AAAATTATTTTTAAATAATAATAAAATC
*
108967 AAAATTTTATTTTAAATAA-AACTAAAAT
1 AAAATTAT-TTTTAAATAATAA-TAAAAT
108995 TAATTTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (28 bp):
AAAATTATTTTTAAATAATAATAAAATC
Found at i:117647 original size:26 final size:27
Alignment explanation
Indices: 117596--117652 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
117586 AAAGGTTGTT
*
117596 AAATGACCGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTAGAAGGGTA
*
117623 AAATGA-CGAAAATACCCTAG-GGGGTA
1 AAATGACCG-AAATACCCTAGAAGGGTA
117649 AAAT
1 AAAT
117653 TACCATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.18
Consensus pattern (27 bp):
AAATGACCGAAATACCCTAGAAGGGTA
Found at i:117792 original size:33 final size:33
Alignment explanation
Indices: 117744--117822 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
117734 CTGATACTGA
* *
117744 GCATGACATCTTGCATTCACA-TATGTTACTATG
1 GCATGTCATCCTGCATTCA-AGTATGTTACTATG
117777 GCATGTCATCCTGCATTCAAGTATGTTACTATG
1 GCATGTCATCCTGCATTCAAGTATGTTACTATG
117810 GCATGTCATCCTG
1 GCATGTCATCCTG
117823 TATGGGGTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 1 0.02
33 42 0.98
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (33 bp):
GCATGTCATCCTGCATTCAAGTATGTTACTATG
Found at i:119278 original size:14 final size:14
Alignment explanation
Indices: 119261--119304 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
119251 ATATTGTAAC
119261 GGTCAGATTCCAAT
1 GGTCAGATTCCAAT
* **
119275 GGTCATATTGTAAT
1 GGTCAGATTCCAAT
*
119289 GGTTAGATTCCAAT
1 GGTCAGATTCCAAT
119303 GG
1 GG
119305 CCATATTGTA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (14 bp):
GGTCAGATTCCAAT
Found at i:119282 original size:28 final size:28
Alignment explanation
Indices: 119249--119344 Score: 113
Period size: 28 Copynumber: 3.5 Consensus size: 28
119239 CATTCAACGA
119249 CCATATTGTAACGGTCAGATTCCAATGG
1 CCATATTGTAACGGTCAGATTCCAATGG
* * *
119277 TCATATTGTAATGGTTAGATTCCAATGG
1 CCATATTGTAACGGTCAGATTCCAATGG
** * **
119305 CCATATTGTAACAATTAGATTCCAA-CA
1 CCATATTGTAACGGTCAGATTCCAATGG
119332 CCATATTGTAACG
1 CCATATTGTAACG
119345 ATCAAATTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
27 12 0.21
28 46 0.79
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (28 bp):
CCATATTGTAACGGTCAGATTCCAATGG
Found at i:128802 original size:15 final size:16
Alignment explanation
Indices: 128777--128807 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
128767 CTTTCGGGTC
128777 ATTACAATTTATTTAA
1 ATTACAATTTATTTAA
128793 ATTA-AATTTATTTAA
1 ATTACAATTTATTTAA
128808 TAAATCCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTACAATTTATTTAA
Found at i:139173 original size:15 final size:15
Alignment explanation
Indices: 139153--139185 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
139143 TATTAAATAC
139153 TATTATTGTTTA-TAT
1 TATTATT-TTTATTAT
139168 TATTATTTTTATTAT
1 TATTATTTTTATTAT
139183 TAT
1 TAT
139186 ATTATGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TATTATTTTTATTAT
Found at i:140693 original size:3 final size:3
Alignment explanation
Indices: 140685--140714 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
140675 ATTATATTCC
140685 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
140715 TGAATTATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:145981 original size:50 final size:50
Alignment explanation
Indices: 145898--146138 Score: 329
Period size: 50 Copynumber: 4.8 Consensus size: 50
145888 ATTTGGGTAA
* * *
145898 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGCCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
145948 AGAGGTCCCATGTAAGACCATGTCTGGGGCATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
145998 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCGAGATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* ** * * *
146048 AGATGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * *
146098 AGAACATCCCATGTAAGACCATGTCTCGGACATGGCTTTGG
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGG
146139 AATGTTATGA
Statistics
Matches: 168, Mismatches: 22, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
50 137 0.82
51 31 0.18
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:153073 original size:50 final size:50
Alignment explanation
Indices: 152998--153182 Score: 203
Period size: 50 Copynumber: 3.7 Consensus size: 50
152988 AAAGAGATCC
*
152998 CATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAAAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAAAGGTCT
* **
153048 CATGTAAGACCATGTCTGAGACATGG-AGTTGGCACCGAGATGAGTGGT-T
1 CATGTAAGACCATGTCTGGGACATGGCA-TTGGCACCGAGATGAAAGGTCT
** * * * ** *
153097 CCCCGTAAGACCAAGTCTGGGACATGGCATGGGCACCGACATGAGAACATCC
1 -CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA-AAGGTCT
* *
153149 CATGTAAGACCATGTCTCGGACATGGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
153183 TGTTATGATC
Statistics
Matches: 109, Mismatches: 21, Indels: 9
0.78 0.15 0.06
Matches are distributed among these distances:
49 2 0.02
50 77 0.71
51 30 0.28
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAAAGGTCT
Found at i:155279 original size:26 final size:26
Alignment explanation
Indices: 155248--155308 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
155238 AGCCATATCG
*
155248 GGAAGCTCACAAAGAGCCAATTAACA
1 GGAAGCTCACAAAGAGCCAATGAACA
* * * *
155274 GGAAGCTTACGAAGAGCCTATGATCA
1 GGAAGCTCACAAAGAGCCAATGAACA
155300 GGAAGCTCA
1 GGAAGCTCA
155309 TAAGAGTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCAATGAACA
Found at i:158264 original size:20 final size:20
Alignment explanation
Indices: 158236--158282 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
158226 ACCACTTCAC
*
158236 TTACATACTTACCATTCCAT
1 TTACTTACTTACCATTCCAT
* * *
158256 TTTCTTACTTTCCGTTCCAT
1 TTACTTACTTACCATTCCAT
158276 TTACTTA
1 TTACTTA
158283 GCATAAGCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.28, G:0.02, T:0.49
Consensus pattern (20 bp):
TTACTTACTTACCATTCCAT
Found at i:164899 original size:27 final size:30
Alignment explanation
Indices: 164840--164906 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 30
164830 AAGCGATGGT
164840 GATCTTATTTTACTAGAAGTTGATGTGATAA
1 GATCTTATTTTACTAGAAG-TGATGTGATAA
164871 GATCTTATTTTACTAGAA-TG-TG-GATAA
1 GATCTTATTTTACTAGAAGTGATGTGATAA
164898 GATCTTATT
1 GATCTTATT
164907 CTGGCAATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
27 14 0.39
28 2 0.06
29 2 0.06
31 18 0.50
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.43
Consensus pattern (30 bp):
GATCTTATTTTACTAGAAGTGATGTGATAA
Found at i:176799 original size:19 final size:19
Alignment explanation
Indices: 176772--176809 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
176762 GAAGTCTTCA
*
176772 AGATTAGTATTAATCAGAC
1 AGATCAGTATTAATCAGAC
176791 AGATCAGTATTAATCAGAC
1 AGATCAGTATTAATCAGAC
176810 GCATTAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (19 bp):
AGATCAGTATTAATCAGAC
Found at i:180024 original size:13 final size:13
Alignment explanation
Indices: 180001--180037 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
179991 TTTAAATATA
180001 TATAA-TTTATTT
1 TATAATTTTATTT
*
180013 TATATTTTTATTT
1 TATAATTTTATTT
180026 TATAATTTTATT
1 TATAATTTTATT
180038 AACTGAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TATAATTTTATTT
Found at i:180405 original size:3 final size:3
Alignment explanation
Indices: 180397--180426 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
180387 TAATCGATTG
180397 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
180427 GATGATGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:186328 original size:15 final size:16
Alignment explanation
Indices: 186299--186328 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
186289 CAAACATGCT
186299 TTAACACATTATCAAA
1 TTAACACATTATCAAA
186315 TTAACACA-TATCAA
1 TTAACACATTATCAA
186329 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:187478 original size:25 final size:25
Alignment explanation
Indices: 187449--187558 Score: 116
Period size: 25 Copynumber: 4.4 Consensus size: 25
187439 TACGAGCTAT
*
187449 GAATCGGTATGCTCTCACAAGATGTA
1 GAATCGGTAAGCTCTCACAAGATG-A
** **
187475 -AATCGGTAAGCTCAT-ATGAGCCGA
1 GAATCGGTAAGCTC-TCACAAGATGA
*
187499 GAATCGGTAAGCTCTCACTAGATGA
1 GAATCGGTAAGCTCTCACAAGATGA
* *
187524 TAATCGGTAAGCTCTCACAAGCTGA
1 GAATCGGTAAGCTCTCACAAGATGA
187549 GAATCGGTAA
1 GAATCGGTAA
187559 TCCCTAATGA
Statistics
Matches: 68, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
24 2 0.03
25 65 0.96
26 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (25 bp):
GAATCGGTAAGCTCTCACAAGATGA
Found at i:187551 original size:50 final size:50
Alignment explanation
Indices: 187449--187558 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 50
187439 TACGAGCTAT
* **
187449 GAATCGGTATGCTCTCACAAGATGTAAATCGGTAAGCTCATATGAGCCGA
1 GAATCGGTAAGCTCTCACAAGATGTAAATCGGTAAGCTCATACAAGCCGA
* *
187499 GAATCGGTAAGCTCTCACTAGATG-ATAATCGGTAAGCTC-TCACAAGCTGA
1 GAATCGGTAAGCTCTCACAAGATGTA-AATCGGTAAGCTCAT-ACAAGCCGA
187549 GAATCGGTAA
1 GAATCGGTAA
187559 TCCCTAATGA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
49 2 0.04
50 51 0.96
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (50 bp):
GAATCGGTAAGCTCTCACAAGATGTAAATCGGTAAGCTCATACAAGCCGA
Found at i:189406 original size:11 final size:11
Alignment explanation
Indices: 189390--189414 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
189380 TTAAAACCTC
189390 TTAAGGAAAGT
1 TTAAGGAAAGT
189401 TTAAGGAAAGT
1 TTAAGGAAAGT
189412 TTA
1 TTA
189415 GAAACCTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (11 bp):
TTAAGGAAAGT
Found at i:191393 original size:14 final size:14
Alignment explanation
Indices: 191374--191428 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
191364 CTGAACCTTG
*
191374 AGGTTTAGGGTTCT
1 AGGTTTAGGGTTCA
*
191388 AGGTTTAAGGTTCA
1 AGGTTTAGGGTTCA
*
191402 AGGTTT-GAGTTCA
1 AGGTTTAGGGTTCA
*
191415 AGGTTCAGGGTTCA
1 AGGTTTAGGGTTCA
191429 TGGTAAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 10 0.29
14 24 0.71
ACGTcount: A:0.22, C:0.09, G:0.33, T:0.36
Consensus pattern (14 bp):
AGGTTTAGGGTTCA
Found at i:191418 original size:27 final size:28
Alignment explanation
Indices: 191374--191428 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
191364 CTGAACCTTG
* * *
191374 AGGTTTAGGGTTCTAGGTTTAAGGTTCA
1 AGGTTTAGAGTTCAAGGTTCAAGGTTCA
*
191402 AGGTTT-GAGTTCAAGGTTCAGGGTTCA
1 AGGTTTAGAGTTCAAGGTTCAAGGTTCA
191429 TGGTAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.22, C:0.09, G:0.33, T:0.36
Consensus pattern (28 bp):
AGGTTTAGAGTTCAAGGTTCAAGGTTCA
Found at i:192956 original size:34 final size:33
Alignment explanation
Indices: 192851--192960 Score: 132
Period size: 34 Copynumber: 3.3 Consensus size: 33
192841 TTTAGTGTTC
* *
192851 TTTTTTAAAAATTAATTAAATTAGGGTTTAGGG
1 TTTTTAAAAAATTAATTAAATTAGGGTTTAGTG
* * *
192884 GTTTTAAATAAATTAAATAAATTAGGGTTTAGTA
1 TTTTTAAA-AAATTAATTAAATTAGGGTTTAGTG
*
192918 TTTTTAAGAAAATTAATTAAATTAAGGTTT-GTTG
1 TTTTTAA-AAAATTAATTAAATTAGGGTTTAG-TG
192952 TTTTTAAAA
1 TTTTTAAAA
192961 TAATATTGTA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
33 9 0.14
34 55 0.85
35 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (33 bp):
TTTTTAAAAAATTAATTAAATTAGGGTTTAGTG
Found at i:193171 original size:126 final size:126
Alignment explanation
Indices: 193022--193290 Score: 398
Period size: 126 Copynumber: 2.1 Consensus size: 126
193012 ATTTTTTGTT
* * *
193022 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTCAGAATACGATTT-TGAACAAATAGTGTGAAA
1 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTCAGAAGACG-TTTCTGAACAAATAGTGTCAAA
* *
193086 AATGCTTCAAGCAAGATGCACTGTTAGCAAAATT-ACTGAAAAAAGCTCCCATGTAGATACTC
65 AATGCTTCAAGCAAGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCCACGTAGATACTC
* *
193148 TTTTTCTATAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTCAGAAGACGTTTCTGAACAAATAGTGTCAAAA
* * *
193213 ATGCTTCAAGCAAGATGCACTGTCAGCAAAATTGATGAAAAAAGTTCTCACGTTGATACTC
66 ATGCTTCAAGCAAGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCACGTAGATACTC
**
193274 GATTTCTATAGTAGTTC
1 TTTTTCTATAGTAGTTC
193291 ATGTTTGGCC
Statistics
Matches: 129, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
125 3 0.02
126 125 0.97
127 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (126 bp):
TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTCAGAAGACGTTTCTGAACAAATAGTGTCAAAA
ATGCTTCAAGCAAGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCACGTAGATACTC
Found at i:196408 original size:24 final size:23
Alignment explanation
Indices: 196352--196408 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 23
196342 AAGAACTTAT
196352 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAATA
196375 ATTTACTATT-AAAATATTAAAAATA
1 ATTT--TATTAAAAATA-TAAAAATA
196400 ACTTTTATT
1 A-TTTTATT
196409 TTATTAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 4 0.13
24 10 0.33
25 13 0.43
26 3 0.10
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAATA
Found at i:196858 original size:18 final size:18
Alignment explanation
Indices: 196835--196870 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
196825 AAAAGAAAAT
*
196835 ATATAAGGGTTAGGATAC
1 ATATAAGGGATAGGATAC
196853 ATATAAGGGATAGGATAC
1 ATATAAGGGATAGGATAC
196871 GCACCTACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.28, T:0.25
Consensus pattern (18 bp):
ATATAAGGGATAGGATAC
Found at i:198666 original size:30 final size:30
Alignment explanation
Indices: 198622--198682 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
198612 ATTAAAGAGG
* *
198622 GCTTTGAGATATTTAAGGAGAAATTTGAGA
1 GCTTTAAGAAATTTAAGGAGAAATTTGAGA
*
198652 GCTTTAAGAAATTTAGGGAGAAATTTGAGA
1 GCTTTAAGAAATTTAAGGAGAAATTTGAGA
198682 G
1 G
198683 TTTTTTTTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.31
Consensus pattern (30 bp):
GCTTTAAGAAATTTAAGGAGAAATTTGAGA
Found at i:205958 original size:51 final size:51
Alignment explanation
Indices: 205834--205969 Score: 170
Period size: 50 Copynumber: 2.7 Consensus size: 51
205824 AGTGAAAAAG
*
205834 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
* * * * *
205885 A-GATCGCATGTGTAGTACTATGTGTAGGCTACTGCGTGTATCC-G-ATGGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CCGGAATGAT
*
205934 AATGGTCACATGTGTAGTACTATGTACAGGCTACTA
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
205970 TGTGAACCAA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
49 4 0.06
50 36 0.51
51 31 0.44
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
Found at i:208090 original size:74 final size:74
Alignment explanation
Indices: 207977--208125 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
207967 CTTGGTGTTG
207977 AAACAACTCATTTACTTGAAAGATTATATGGCTAGTATGTGATGAACTCACCTCTTGATATGGTT
1 AAACAACTCATTTACTTGAAAGATTATATGGCTAGTATGTGATGAACTCACCTCTTGATATGGTT
208042 GTGGTGACA
66 GTGGTGACA
208051 AAACAACTCATTTACTTGAAAGATTATATGGCTAGTATGTGATGAACTCACCTCTTGATATGGTT
1 AAACAACTCATTTACTTGAAAGATTATATGGCTAGTATGTGATGAACTCACCTCTTGATATGGTT
208116 GTGGTGACA
66 GTGGTGACA
208125 A
1 A
208126 GATTAAGTGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (74 bp):
AAACAACTCATTTACTTGAAAGATTATATGGCTAGTATGTGATGAACTCACCTCTTGATATGGTT
GTGGTGACA
Found at i:224161 original size:28 final size:28
Alignment explanation
Indices: 224125--224184 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
224115 GGGGGGAAGT
* *
224125 AAAAGTTTTGCGTGAAAGCAAAAGGAAA
1 AAAACTTTTGCGAGAAAGCAAAAGGAAA
* *
224153 AAAACTTTTGGGAGAAAGTAAAAGGAAA
1 AAAACTTTTGCGAGAAAGCAAAAGGAAA
224181 AAAA
1 AAAA
224185 AATTTGTGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.55, C:0.05, G:0.23, T:0.17
Consensus pattern (28 bp):
AAAACTTTTGCGAGAAAGCAAAAGGAAA
Found at i:224238 original size:83 final size:85
Alignment explanation
Indices: 224093--224247 Score: 199
Period size: 83 Copynumber: 1.8 Consensus size: 85
224083 ACATAAATTC
* * * * *
224093 AAAAAAAATGTTTTTGGAGTTTGGGGGGAAGTAAAAGTTTTGCGTGAAAGCAAAAGGAAAAAAAC
1 AAAAAAAATATTTGTGGAGTTTGGAGGGAAGTAAAAGTTTTGCGAGAAAACAAAAGGAAAAAAAC
224158 TTTTGGGAGAAAGTAAAAGG
66 TTTTGGGAGAAAGTAAAAGG
* * *
224178 AAAAAAAA-ATTTGTGG-GTTTGGAGGGAAGTAACAGTTTTGGGGAGAAAATAAAAGG-AAAAAA
1 AAAAAAAATATTTGTGGAGTTTGGAGGGAAGTAAAAGTTTT-GCGAGAAAACAAAAGGAAAAAAA
*
224240 GTTTTGGG
65 CTTTTGGG
224248 GGAACTAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
83 34 0.57
84 18 0.30
85 8 0.13
ACGTcount: A:0.43, C:0.03, G:0.30, T:0.24
Consensus pattern (85 bp):
AAAAAAAATATTTGTGGAGTTTGGAGGGAAGTAAAAGTTTTGCGAGAAAACAAAAGGAAAAAAAC
TTTTGGGAGAAAGTAAAAGG
Found at i:224385 original size:30 final size:29
Alignment explanation
Indices: 224325--224385 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
224315 AAGGGAAAGT
* *
224325 AAAAGTTTTGGGGAGAAAGTAAAAGAAAA
1 AAAAGTCTTGGGGAGAAAATAAAAGAAAA
*
224354 AAAAGTCTTGGGGAGAAAATAAAAGGAAA
1 AAAAGTCTTGGGGAGAAAATAAAAGAAAA
224383 AAA
1 AAA
224386 GTTTTGAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.57, C:0.02, G:0.26, T:0.15
Consensus pattern (29 bp):
AAAAGTCTTGGGGAGAAAATAAAAGAAAA
Found at i:225979 original size:20 final size:21
Alignment explanation
Indices: 225956--226006 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
225946 ACGGGTTTAC
* *
225956 ACTTCGGTGCCATTGTTTG-T
1 ACTTCGGTGCCACTATTTGCT
*
225976 ACTTCAGTGCCACTATTTGCT
1 ACTTCGGTGCCACTATTTGCT
225997 -CTTCGGTGCC
1 ACTTCGGTGCC
226007 TTGGAGTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.39
Consensus pattern (21 bp):
ACTTCGGTGCCACTATTTGCT
Found at i:238243 original size:19 final size:20
Alignment explanation
Indices: 238205--238244 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
238195 CATATCAATG
* *
238205 ACATATGTTATGAAATAAAT
1 ACATATGTTAAGAAAAAAAT
238225 ACATAT-TTAAGAAAAAAAT
1 ACATATGTTAAGAAAAAAAT
238244 A
1 A
238245 TTGAAGTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (20 bp):
ACATATGTTAAGAAAAAAAT
Found at i:238636 original size:2 final size:2
Alignment explanation
Indices: 238629--238656 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
238619 AGTATACTCC
238629 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
238657 GGGAGATCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:241841 original size:38 final size:38
Alignment explanation
Indices: 241720--241866 Score: 136
Period size: 38 Copynumber: 3.8 Consensus size: 38
241710 TAAAGACATG
* * * **
241720 TATTAAAGATG-TCTAAAATAGGACATATTTAAAACATA
1 TATTAAAGATGTTC-AAATTATGACATAATTAAAACCCA
* * *
241758 TATTTAAA-ATGTCCTAAACTATGACATAATTAAAAACCCT
1 TA-TTAAAGATGTTC-AAATTATGACATAATT-AAAACCCA
* *
241798 TATTAAAGATGTTCAGATTATGACATAATTAAAACTCA
1 TATTAAAGATGTTCAAATTATGACATAATTAAAACCCA
* *
241836 TATTAATGATGTTCAAATTGTGACATAATTA
1 TATTAAAGATGTTCAAATTATGACATAATTA
241867 TAGACTTAAA
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
38 39 0.43
39 39 0.43
40 12 0.13
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.35
Consensus pattern (38 bp):
TATTAAAGATGTTCAAATTATGACATAATTAAAACCCA
Found at i:247690 original size:43 final size:43
Alignment explanation
Indices: 247560--247811 Score: 321
Period size: 42 Copynumber: 5.9 Consensus size: 43
247550 GCTATATAAT
* * *
247560 ATGACCTTTAGCGGCGCTTCTAT-AAAAACGCCACTAAAGAAC
1 ATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAAC
* * *
247602 ATGACATTTAGCGGCGCTTCTAT-AAAAACGCCGCTAAAGAAC
1 ATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAAC
*
247644 ATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAGC
1 ATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAAC
* *
247687 ATGACC-TTAGCGGTGCTTTTATCACAAACGCCGCTAAAGAGC
1 ATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAAC
* * * *
247729 ATGACCTTTAACGGTGCTTTTATCACAAACACCTCTAAAGAAC
1 ATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAAC
* * * *
247772 ATGATCTTTAGTGGCACTTTTTATCACAAATGCCGCTAAA
1 ATGACCTTTAGCGGCGC-TTTTATCACAAACGCCGCTAAA
247812 AATGTCGTTC
Statistics
Matches: 188, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
42 102 0.54
43 67 0.36
44 19 0.10
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAAC
Found at i:247721 original size:85 final size:85
Alignment explanation
Indices: 247560--247811 Score: 319
Period size: 85 Copynumber: 3.0 Consensus size: 85
247550 GCTATATAAT
* * *
247560 ATGACCTTTAGCGGCGCTTCTAT-AAAAACGCCACTAAAGAACATGACATTTAGCGGCGCTTCTA
1 ATGACCTTTAGCGGCGCTTTTATCACAAACGCCACTAAAGAACATGAC-TTTAGCGGCGCTTTTA
*
247624 T-AAAAACGCCGCTAAAGAAC
65 TCACAAACGCCGCTAAAGAAC
* * * *
247644 ATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAGCATGACCTTAGCGGTGCTTTTAT
1 ATGACCTTTAGCGGCGCTTTTATCACAAACGCCACTAAAGAACATGACTTTAGCGGCGCTTTTAT
*
247709 CACAAACGCCGCTAAAGAGC
66 CACAAACGCCGCTAAAGAAC
* * * * * *
247729 ATGACCTTTAACGGTGCTTTTATCACAAACACCTCTAAAGAACATGATCTTTAGTGGCACTTTTT
1 ATGACCTTTAGCGGCGCTTTTATCACAAACGCCACTAAAGAACATGA-CTTTAGCGGCGC-TTTT
*
247794 ATCACAAATGCCGCTAAA
64 ATCACAAACGCCGCTAAA
247812 AATGTCGTTC
Statistics
Matches: 145, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
84 36 0.25
85 80 0.55
86 8 0.06
87 21 0.14
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (85 bp):
ATGACCTTTAGCGGCGCTTTTATCACAAACGCCACTAAAGAACATGACTTTAGCGGCGCTTTTAT
CACAAACGCCGCTAAAGAAC
Found at i:253081 original size:7 final size:7
Alignment explanation
Indices: 252942--253156 Score: 100
Period size: 7 Copynumber: 30.7 Consensus size: 7
252932 CCATATCAAT
252942 CTAAACC
1 CTAAACC
*
252949 ATAAACC
1 CTAAACC
* *
252956 TTAAGCCC
1 CTAA-ACC
*
252964 CTAACCC
1 CTAAACC
252971 CTAAACC
1 CTAAACC
* *
252978 AT-AACTA
1 CTAAAC-C
252985 CTAAA-C
1 CTAAACC
252991 CTAAAACC
1 CT-AAACC
*
252999 TTAAACC
1 CTAAACC
*
253006 TTAAACC
1 CTAAACC
253013 CTAAACC
1 CTAAACC
*
253020 ATAAA-C
1 CTAAACC
*
253026 CTACACC
1 CTAAACC
*
253033 CTAAATC
1 CTAAACC
* *
253040 GTAAACA
1 CTAAACC
*
253047 CTAAACT
1 CTAAACC
* *
253054 CTTAACA
1 CTAAACC
253061 CTAAACC
1 CTAAACC
253068 CTAAACC
1 CTAAACC
253075 CTAAACC
1 CTAAACC
*
253082 TTAAACC
1 CTAAACC
*
253089 CCAAA--
1 CTAAACC
*
253094 CTAGAAAC
1 CTA-AACC
**
253102 CTTCACC
1 CTAAACC
*
253109 CTAAACT
1 CTAAACC
253116 CTAAACC
1 CTAAACC
*
253123 CT-TACC
1 CTAAACC
253129 CTTAAACC
1 C-TAAACC
* *
253137 GTAATAGC
1 CTAA-ACC
*
253145 CTAACCC
1 CTAAACC
253152 CTAAA
1 CTAAA
253157 ACCATGAACA
Statistics
Matches: 152, Mismatches: 44, Indels: 24
0.69 0.20 0.11
Matches are distributed among these distances:
5 2 0.01
6 15 0.10
7 116 0.76
8 19 0.12
ACGTcount: A:0.42, C:0.35, G:0.02, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:253089 original size:21 final size:21
Alignment explanation
Indices: 252942--253122 Score: 120
Period size: 21 Copynumber: 8.7 Consensus size: 21
252932 CCATATCAAT
* *
252942 CTAAACCATAAACCTTAAGCCC
1 CTAAACCCTAAACCTTAA-ACC
* * *
252964 CTAACCCCTAAACCAT-AACTA
1 CTAAACCCTAAACCTTAAAC-C
252985 CTAAA-CCTAAAACCTTAAACC
1 CTAAACCCT-AAACCTTAAACC
* *
253006 TTAAACCCTAAACCATAAA-C
1 CTAAACCCTAAACCTTAAACC
* * * *
253026 CTACACCCTAAATCGTAAACA
1 CTAAACCCTAAACCTTAAACC
* *
253047 CTAAACTCTTAACAC-TAAACC
1 CTAAACCCTAAAC-CTTAAACC
253068 CTAAACCCTAAACCTTAAACC
1 CTAAACCCTAAACCTTAAACC
* *** *
253089 CCAAACTAGAAACCTT-CACC
1 CTAAACCCTAAACCTTAAACC
*
253109 CTAAACTCTAAACC
1 CTAAACCCTAAACC
253123 CTTACCCTTA
Statistics
Matches: 122, Mismatches: 30, Indels: 16
0.73 0.18 0.10
Matches are distributed among these distances:
20 35 0.29
21 67 0.55
22 20 0.16
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.19
Consensus pattern (21 bp):
CTAAACCCTAAACCTTAAACC
Found at i:253325 original size:21 final size:20
Alignment explanation
Indices: 253301--253339 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
253291 CCATAGACAT
253301 TAAACCTTAAATATAAAATCC
1 TAAACCTTAAA-ATAAAATCC
253322 TAAACCTTAAAATAAAAT
1 TAAACCTTAAAATAAAAT
253340 GATTTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAACCTTAAAATAAAATCC
Found at i:253480 original size:40 final size:40
Alignment explanation
Indices: 253423--253612 Score: 236
Period size: 40 Copynumber: 4.8 Consensus size: 40
253413 TAATTTTTTT
*
253423 GCGGCATTTTTCAAAAAGCGCCGCTAATGATCGACCTATA
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
* * *
253463 GTGGCATTTTTCAAAAAGCGACGCTAATGCTCGACCTACA
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
* * * * * *
253503 GTGGCATTTTTCACAAATCTCCGTTAATGCTCGATCTATA
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
* * * * *
253543 GCGGCGTTTTTCAAAAAGTGCTGCTAACGCTCGATCTATA
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
*
253583 GCGGCATTTTTCAAAAAACGCCGCTAATGC
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGC
253613 CACTACAGCT
Statistics
Matches: 125, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 125 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (40 bp):
GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
Found at i:253724 original size:40 final size:40
Alignment explanation
Indices: 253657--253766 Score: 175
Period size: 40 Copynumber: 2.8 Consensus size: 40
253647 ATTTTTTTTT
*
253657 GCAGCGTTTTTCAAAAAGTGCCGCTAATGCTCGATCTATA
1 GCAGCGTTTTTCAAAAAGTGCCACTAATGCTCGATCTATA
* * *
253697 GCGGCGTCTTTCAAAAAGTGCCACTAATGTTCGATCTATA
1 GCAGCGTTTTTCAAAAAGTGCCACTAATGCTCGATCTATA
*
253737 GCAGCTTTTTTCAAAAAGTGCCACTAATGC
1 GCAGCGTTTTTCAAAAAGTGCCACTAATGC
253767 CACTAAAGCT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (40 bp):
GCAGCGTTTTTCAAAAAGTGCCACTAATGCTCGATCTATA
Found at i:253874 original size:152 final size:153
Alignment explanation
Indices: 253527--253892 Score: 518
Period size: 154 Copynumber: 2.4 Consensus size: 153
253517 AAATCTCCGT
** * *
253527 TAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGTGCTGCTAACGCTCGATCTATAGCGGCATTT
1 TAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGTGCCACTAATGCTCGATCTATAGCAGCATTT
* * *
253592 TTCAAAAAACGCCGCTAATGCCACTACAGCTCAACATAAAATGGCGTTGTGCTTAATTTTTTTTT
66 TTCAAAAAACGCCACTAATGCCACTAAAGCTCAACATAAAACGGCGTTGTGCTTAA-TTTTTTTT
* * **
253657 GCAGCGTTTTTCAAAAAGTGCCGC
130 GCAGAGTTTTGCAAAAAGCACCGC
* * *
253681 TAATGCTCGATCTATAGCGGCGTCTTTCAAAAAGTGCCACTAATGTTCGATCTATAGCAGCTTTT
1 TAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGTGCCACTAATGCTCGATCTATAGCAGCATTT
** * *
253746 TTCAAAAAGTGCCACTAATGCCACTAAAGCTTAACATAAAACGGTGTTGTGCTTAA-TTTTTTTG
66 TTCAAAAAACGCCACTAATGCCACTAAAGCTCAACATAAAACGGCGTTGTGCTTAATTTTTTTTG
*
253810 CGGAGTTTTGCAAAAAGCACCGC
131 CAGAGTTTTGCAAAAAGCACCGC
* * *
253833 TAATTCTCGATCTATAGCGGCATTTTTCAAAAAGAGCCACTAATGCTCGATCTATAGCAG
1 TAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGTGCCACTAATGCTCGATCTATAGCAG
253893 TGTTTTTATC
Statistics
Matches: 188, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
152 81 0.43
154 107 0.57
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (153 bp):
TAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGTGCCACTAATGCTCGATCTATAGCAGCATTT
TTCAAAAAACGCCACTAATGCCACTAAAGCTCAACATAAAACGGCGTTGTGCTTAATTTTTTTTG
CAGAGTTTTGCAAAAAGCACCGC
Found at i:253876 original size:40 final size:40
Alignment explanation
Indices: 253815--253890 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
253805 TTTTGCGGAG
* *
253815 TTTTGCAAAAAGCACCGCTAATTCTCGATCTATAGCGGCA
1 TTTTGCAAAAAGCACCACTAATGCTCGATCTATAGCGGCA
*
253855 TTTTTCAAAAAG-AGCCACTAATGCTCGATCTATAGC
1 TTTTGCAAAAAGCA-CCACTAATGCTCGATCTATAGC
253891 AGTGTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 1 0.03
40 31 0.97
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (40 bp):
TTTTGCAAAAAGCACCACTAATGCTCGATCTATAGCGGCA
Found at i:253899 original size:40 final size:40
Alignment explanation
Indices: 253814--253899 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
253804 TTTTTGCGGA
* * * *
253814 GTTTTGCAAAAAGCACCGCTAATTCTCGATCTATAGCGGC
1 GTTTTTCAAAAAGCACCACTAATGCTCGATCTATAGCAGC
* *
253854 ATTTTTCAAAAAG-AGCCACTAATGCTCGATCTATAGCAGT
1 GTTTTTCAAAAAGCA-CCACTAATGCTCGATCTATAGCAGC
253894 GTTTTT
1 GTTTTT
253900 ATCCAAATAC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 1 0.03
40 37 0.97
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (40 bp):
GTTTTTCAAAAAGCACCACTAATGCTCGATCTATAGCAGC
Found at i:254396 original size:25 final size:25
Alignment explanation
Indices: 254368--254415 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
254358 AAAGCACGCC
254368 ATATCAGGAAGCTCACAAAGAGCCT
1 ATATCAGGAAGCTCACAAAGAGCCT
* *
254393 ATATCAGGACGCTCATAAAGAGC
1 ATATCAGGAAGCTCACAAAGAGC
254416 TGCAGTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.17
Consensus pattern (25 bp):
ATATCAGGAAGCTCACAAAGAGCCT
Found at i:264322 original size:21 final size:22
Alignment explanation
Indices: 264268--264323 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
264258 GATTTCACAA
264268 CTCCCTTCAAATGGCTCTAATC
1 CTCCCTTCAAATGGCTCTAATC
264290 CTCCCTTCAAATGGCTCTAATC
1 CTCCCTTCAAATGGCTCTAATC
*
264312 TTCCC-TCAAATG
1 CTCCCTTCAAATG
264324 AAAATCAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 7 0.21
22 26 0.79
ACGTcount: A:0.23, C:0.36, G:0.09, T:0.32
Consensus pattern (22 bp):
CTCCCTTCAAATGGCTCTAATC
Found at i:270583 original size:192 final size:192
Alignment explanation
Indices: 270256--270613 Score: 490
Period size: 192 Copynumber: 1.9 Consensus size: 192
270246 AATACGGTCG
*
270256 TGTAAATATTTACAATATTTTACAATTAGGTCCAACACGACCATAGTTAGTTACACAGTCTGTCG
1 TGTAAATATTTACAATATTTTACAATTAGGTCCAACACGACCATAGTTAGTTACACAGCCTGTCG
*** * *
270321 AAATGGTCATATGACTCTGCATACACAATCTTAGCTCCCATACACAGTTAGGCTACATGGCTGTG
66 AAACAATCATATGACTCTGCATACACAATCTCAGCTCCCATACACAGTTAGGCTACATAGCTGTG
*
270386 TGTTTTAATCCCACATAGCCTCAGCCTATCACATGGTCTTTTAACAAATGTGCACACAGTCA
131 TGTTTTAATCCCACACAGCCTCAGCCTATCACATGGTCTTTTAACAAATGTGCACACAGTCA
*
270448 TGTAAATATTTACAA-AGTTTTACAATTAGGTCCAACAC-AGCCATAGTTAGTTACACGGCCTG-
1 TGTAAATATTTACAATA-TTTTACAATTAGGTCCAACACGA-CCATAGTTAGTTACACAGCCTGT
* * * * ** *
270510 CAGACACAATCATTTGACTTTGCATATACGGTCTCAG-TGCCCATACACAGTTGGGCTACATAGC
64 C-GAAACAATCATATGACTCTGCATACACAATCTCAGCT-CCCATACACAGTTAGGCTACATAGC
* * *
270574 TGTGTGTTTTAATCCCACACGGCCTCTGCCTGTCACATGG
127 TGTGTGTTTTAATCCCACACAGCCTCAGCCTATCACATGG
270614 CTTGGCCACA
Statistics
Matches: 144, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
191 4 0.03
192 140 0.97
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (192 bp):
TGTAAATATTTACAATATTTTACAATTAGGTCCAACACGACCATAGTTAGTTACACAGCCTGTCG
AAACAATCATATGACTCTGCATACACAATCTCAGCTCCCATACACAGTTAGGCTACATAGCTGTG
TGTTTTAATCCCACACAGCCTCAGCCTATCACATGGTCTTTTAACAAATGTGCACACAGTCA
Found at i:271459 original size:13 final size:13
Alignment explanation
Indices: 271441--271466 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
271431 TTAAGTTATA
271441 TGTGTGAAAATTT
1 TGTGTGAAAATTT
271454 TGTGTGAAAATTT
1 TGTGTGAAAATTT
271467 GATAGTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:279828 original size:17 final size:15
Alignment explanation
Indices: 279808--279850 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 15
279798 TTCCAATTAG
279808 CAGTTCATAACATATAA
1 CAGTTCATAA-A-ATAA
279825 CAGTTCATGCAAAATAA
1 CAGTTCAT--AAAATAA
279842 CAGTTCATA
1 CAGTTCATA
279851 CCCCATCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
17 20 0.83
18 1 0.04
19 2 0.08
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (15 bp):
CAGTTCATAAAATAA
Found at i:280359 original size:21 final size:19
Alignment explanation
Indices: 280335--280373 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
280325 TTTTATGTTA
280335 TATTTAAATTATAAAATTATT
1 TATTTAAA-TAT-AAATTATT
*
280356 TATTTAGATATAAATTAT
1 TATTTAAATATAAATTAT
280374 GTTAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 3 0.18
21 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TATTTAAATATAAATTATT
Found at i:281857 original size:23 final size:21
Alignment explanation
Indices: 281813--281891 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
281803 TTATCAGCTT
* **
281813 TGCCG-ATCAGGCACTTTATG
1 TGCCGTATCAGGCACCTCGTG
281833 TGCCGTATTTCAGGCACCTCGTG
1 TGCCGTA--TCAGGCACCTCGTG
*
281856 TGTCGTATCAGGCACCTCGTG
1 TGCCGTATCAGGCACCTCGTG
** *
281877 TATCGTTTCAGGCAC
1 TGCCGTATCAGGCAC
281892 TTATGTGTCG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
20 5 0.10
21 28 0.56
23 17 0.34
ACGTcount: A:0.16, C:0.28, G:0.25, T:0.30
Consensus pattern (21 bp):
TGCCGTATCAGGCACCTCGTG
Found at i:281868 original size:21 final size:21
Alignment explanation
Indices: 281842--281904 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
281832 GTGCCGTATT
281842 TCAGGCACCTCGTGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
* *
281863 TCAGGCACCTCGTGTATCGTT
1 TCAGGCACCTCGTGTGTCGTA
**
281884 TCAGGCA-CTTATGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
281904 T
1 T
281905 ATTGATCAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 10 0.28
21 26 0.72
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
TCAGGCACCTCGTGTGTCGTA
Found at i:289105 original size:23 final size:20
Alignment explanation
Indices: 289078--289138 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
289068 GCTTTGTCGA
289078 TCAGGCACTTTATGTGTCATATT
1 TCAGGCAC-TTATGTGTC--ATT
** *
289101 TCAGGCACCTCGTGTGTCGTT
1 TCAGGCA-CTTATGTGTCATT
289122 TCAGGCACTTATGTGTC
1 TCAGGCACTTATGTGTC
289139 GTATATTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 8 0.25
21 9 0.28
23 14 0.44
24 1 0.03
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
TCAGGCACTTATGTGTCATT
Found at i:290262 original size:17 final size:17
Alignment explanation
Indices: 290242--290283 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
290232 AATAGGGCTT
290242 GCAATTAAGCAAAGCTC
1 GCAATTAAGCAAAGCTC
*
290259 GCAATTAAGCAGAGCTC
1 GCAATTAAGCAAAGCTC
290276 GCACATTA
1 GCA-ATTA
290284 TAACATAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (17 bp):
GCAATTAAGCAAAGCTC
Found at i:290538 original size:18 final size:18
Alignment explanation
Indices: 290485--290575 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
290475 AGCTCACAAT
* *
290485 ATACAATTTAGCAAATTA
1 ATACAATTCACCAAATTA
* ** *
290503 ATGCAATTTGCCATATTA
1 ATACAATTCACCAAATTA
*
290521 ATACAAATCACCAAATTA
1 ATACAATTCACCAAATTA
*
290539 ACACAATTCACCATAA-TA
1 ATACAATTCACCA-AATTA
* *
290557 ATATAATTCACCAAGTTA
1 ATACAATTCACCAAATTA
290575 A
1 A
290576 CATGGTTCAC
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
17 1 0.02
18 54 0.95
19 2 0.04
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.30
Consensus pattern (18 bp):
ATACAATTCACCAAATTA
Found at i:292756 original size:28 final size:27
Alignment explanation
Indices: 292689--292756 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 27
292679 TGTATTTCTG
292689 AGACTGTATCTGATATGGGCCAAGGCCC
1 AGACTGTATCT-ATATGGGCCAAGGCCC
*
292717 AAACTG-ATTCTATGATGGG-CACAGGCCC
1 AGACTGTA-TCTAT-ATGGGCCA-AGGCCC
292745 AGACTGTATCTA
1 AGACTGTATCTA
292757 ACTGAATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 5 0.15
28 28 0.82
29 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.24
Consensus pattern (27 bp):
AGACTGTATCTATATGGGCCAAGGCCC
Found at i:293464 original size:20 final size:20
Alignment explanation
Indices: 293428--293466 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
293418 CGGCGCTGAT
293428 TCTGTAAGTGTTCTAAAAAA
1 TCTGTAAGTGTTCTAAAAAA
*
293448 TCTGATAAGT-TTTTAAAAA
1 TCTG-TAAGTGTTCTAAAAA
293467 TATGAGTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (20 bp):
TCTGTAAGTGTTCTAAAAAA
Found at i:295086 original size:28 final size:28
Alignment explanation
Indices: 295055--295173 Score: 168
Period size: 28 Copynumber: 4.2 Consensus size: 28
295045 CAGTAATAGT
295055 ACAGTGTGGGCCTTAGCCCAATACAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
* * *
295083 ACAGTTTGGGCCTTAGCTCAATAAAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
295111 ACAGTGTGGGCCTTAGCCCAATACAG-A
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
* * *
295138 ATTAGTGTGGGCATTAGCCAAATACAGTA
1 A-CAGTGTGGGCCTTAGCCCAATACAGTA
295167 ACAGTGT
1 ACAGTGT
295174 AGTGCAATAA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
27 2 0.03
28 75 0.95
29 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCCAATACAGTA
Done.