Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 344 of 352
Found at i:110152164 original size:32 final size:31
Alignment explanation
Indices: 110152117--110152185 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
110152107 TATTTTTCTA
* *
110152117 TTTTTTTTAATTTTTAAAGG-ACTTAATATTT
1 TTTTTTTTAACTTTT-AAGGAACTTAAAATTT
110152148 TTTTCTTTTAACTTTTAAGGAACTTAAAATTT
1 TTTT-TTTTAACTTTTAAGGAACTTAAAATTT
*
110152180 TATTTT
1 TTTTTT
110152186 ATTATTTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 10 0.30
32 23 0.70
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (31 bp):
TTTTTTTTAACTTTTAAGGAACTTAAAATTT
Found at i:110155213 original size:20 final size:20
Alignment explanation
Indices: 110155176--110155213 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
110155166 GTAAAACTAG
*
110155176 TATGAAAATATAAGATTAAA
1 TATGAAAATATAAAATTAAA
110155196 TATGAAAA-ATTAAAATTA
1 TATGAAAATA-TAAAATTA
110155214 GTCTCGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (20 bp):
TATGAAAATATAAAATTAAA
Found at i:110155695 original size:37 final size:36
Alignment explanation
Indices: 110155653--110155734 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 36
110155643 TTTTGTTTTT
110155653 AAACACGAGAACTTTGAAACAC-AATAATAATTTTTG-A
1 AAACACGAGAACTTTGAAACACGAA-AAT--TTTTTGAA
**
110155690 AAACACGAAGATTTTTGAAACACGAAAATTTTTTGAA
1 AAACACG-AGAACTTTGAAACACGAAAATTTTTTGAA
110155727 AAACACGA
1 AAACACGA
110155735 AAACACGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
36 7 0.17
37 15 0.38
38 16 0.40
39 2 0.05
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.26
Consensus pattern (36 bp):
AAACACGAGAACTTTGAAACACGAAAATTTTTTGAA
Found at i:110155705 original size:18 final size:18
Alignment explanation
Indices: 110155681--110155737 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
110155671 ACACAATAAT
110155681 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
110155699 GATTTTTG-AAACACGAA
1 AATTTTTGAAAACACGAA
110155716 AATTTTTTGAAAAACACGAA
1 AA-TTTTTG-AAAACACGAA
110155736 AA
1 AA
110155738 CACGAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 10 0.29
18 13 0.38
20 11 0.32
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:110155776 original size:18 final size:18
Alignment explanation
Indices: 110155749--110155814 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 18
110155739 ACGAAATTTT
* *
110155749 TTTTTTAAAACACGGGAA
1 TTTTTGAAAACACGAGAA
*
110155767 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAGAA
* **
110155785 TTTTT-TATTCACGAGAA
1 TTTTTGAAAACACGAGAA
110155802 TTTTTG-AAACACG
1 TTTTTGAAAACACG
110155815 GATTTTTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
17 18 0.47
18 20 0.53
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (18 bp):
TTTTTGAAAACACGAGAA
Found at i:110155814 original size:17 final size:17
Alignment explanation
Indices: 110155750--110155814 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
110155740 CGAAATTTTT
* *
110155750 TTTTTAAAACACGGGAA
1 TTTTTGAAACACGAGAA
*
110155767 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAGAA
* **
110155785 TTTTTTATTCACGAGAA
1 TTTTTGAAACACGAGAA
110155802 TTTTTGAAACACG
1 TTTTTGAAACACG
110155815 GATTTTTTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
17 23 0.62
18 14 0.38
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (17 bp):
TTTTTGAAACACGAGAA
Found at i:110155899 original size:17 final size:18
Alignment explanation
Indices: 110155877--110155924 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
110155867 TATTATTATT
110155877 ATTTTGAAACACGTG-AA
1 ATTTTGAAACACGTGAAA
110155894 ATTTTGAAGACA--TGAAA
1 ATTTTGAA-ACACGTGAAA
110155911 ATTTTTGAAACACG
1 A-TTTTGAAACACG
110155925 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.08
17 14 0.54
18 10 0.38
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (18 bp):
ATTTTGAAACACGTGAAA
Found at i:110156529 original size:14 final size:14
Alignment explanation
Indices: 110156505--110156568 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 14
110156495 TAGTTTTTTT
*
110156505 TTTCTTTTTTCTTTC
1 TTTC-TTTTTCCTTC
*
110156520 TTTCTTTTTCCCAT-
1 TTTCTTTTT-CCTTC
110156534 TTTCTTCTTTCCTTC
1 TTTCTT-TTTCCTTC
110156549 -TTCTTTTT-CTTCC
1 TTTCTTTTTCCTT-C
110156562 TTTCTTT
1 TTTCTTT
110156569 CTCCCCGATC
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
12 3 0.07
13 4 0.10
14 25 0.61
15 9 0.22
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTCTTTTTCCTTC
Found at i:110156570 original size:29 final size:29
Alignment explanation
Indices: 110156505--110156570 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 29
110156495 TAGTTTTTTT
*
110156505 TTTCTTT-TTTCTTTCTTTCTTTTTCCCA
1 TTTCTTTCTTTCCTTCTTTCTTTTTCCCA
110156533 TTT-TCTTCTTTCCTTC-TTCTTTTTCTTCC-
1 TTTCT-TTCTTTCCTTCTTTCTTTTTC--CCA
110156562 TTTCTTTCT
1 TTTCTTTCT
110156571 CCCCGATCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
27 1 0.03
28 14 0.44
29 14 0.44
30 3 0.09
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (29 bp):
TTTCTTTCTTTCCTTCTTTCTTTTTCCCA
Found at i:110157132 original size:30 final size:30
Alignment explanation
Indices: 110157092--110157193 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 30
110157082 ATTTAGGATT
*
110157092 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * * *
110157122 TAAGTGAAATTTAAAAAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
110157152 AAAATGAAATTTAGGAA-AAA-TTTAGGGGTC
1 AAAATGAAATTTA--AAGAAAGTTTAGGGGTC
*
110157182 AAAATGCAATTT
1 AAAATGAAATTT
110157194 TTTTTTTTGA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
30 56 0.92
31 3 0.05
32 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:110157672 original size:54 final size:54
Alignment explanation
Indices: 110157451--110158361 Score: 1506
Period size: 54 Copynumber: 17.0 Consensus size: 54
110157441 CACGTGAGCC
* * *
110157451 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCTA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT--AA
* * *
110157506 AAGGCTCGACTTACCTCTCGCAATATGAGTTGATTTTTGAAAAATAG--A--AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* *
110157556 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTT-GATTTTTGAAAAACAGAAATTAA
110157611 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
110157665 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
110157719 AAGGCTCAACTCA-C-CTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* *
110157770 AAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAATCAGAAATT-A
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
110157823 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTG-AAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
110157875 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATCAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
110157929 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
110157983 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
110158037 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATCAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* *
110158091 AAGGCTCAACTCACCTCTCGTAATATGAGTTGGTTTTTG-AAAA-AGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
110158143 AAGTCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
110158197 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATCAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* * *
110158251 AAGGCTCAACTCACCTCTCGTAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
110158305 AAGTCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-AA
110158360 AA
1 AA
110158362 TACCTCAACG
Statistics
Matches: 805, Mismatches: 36, Indels: 30
0.92 0.04 0.03
Matches are distributed among these distances:
50 30 0.04
51 53 0.07
52 108 0.13
53 69 0.09
54 466 0.58
55 73 0.09
56 6 0.01
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (54 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
Found at i:110158158 original size:214 final size:215
Alignment explanation
Indices: 110157451--110158361 Score: 1495
Period size: 214 Copynumber: 4.3 Consensus size: 215
110157441 CACGTGAGCC
* * * *
110157451 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCTAAAGGCTCGAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATT--AAAAGGCTCAAC
* *
110157516 TTACCTCTCGCAATATGAGTTGATTTTTGAAAAATAG--A--AAAAGGCTCAACTCACCTCTCGC
64 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGC
* *
110157577 AATATGAGTTGGTTTTTTGAAAAATAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTT
129 AATATGAGTT-GATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTT
*
110157642 GATTTTTGAAAAACAGAAATTAA
193 GATTTTTGAAAATCAGAAATTAA
110157665 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTAAAAGGCTCAACT
*
110157730 CA-C-CTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTAAAAGGCTCAACTCACCTCTCACA
65 CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCA
*
110157792 ATATGAGTTGATTTTTGAAAATCAGAAATT-AAAGGCTCAACTCACCTCTCGCAATATGAGTTGA
130 ATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGA
110157856 -TTTTGAAAA-CAGAAATTAA
195 TTTTTGAAAATCAGAAATTAA
110157875 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATCAGAAATTAAAAGGCTCAACT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-CAGAAATTAAAAGGCTCAACT
*
110157940 CACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAAGGCTCAACTCACCTCTCGCA
65 CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCA
110158005 ATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGA
130 ATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGA
110158070 TTTTTGAAAATCAGAAATTAA
195 TTTTTGAAAATCAGAAATTAA
* * *
110158091 AAGGCTCAACTCACCTCTCGTAATATGAGTTGGTTTTTGAAAA-AGAAATTAAAAGTCTCAACTC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTAAAAGGCTCAACTC
110158155 ACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAA
66 ACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAA
* * *
110158220 TATGAGTTGATTTTTGAAAATCAGAAATTAAAAGGCTCAACTCACCTCTCGTAATATGAGTTGGT
131 TATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
110158285 TTTTGAAAAAT-AGAAATTAA
196 TTTTG-AAAATCAGAAATTAA
*
110158305 AAGTCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATT-AAAA
110158362 TACCTCAACG
Statistics
Matches: 658, Mismatches: 23, Indels: 29
0.93 0.03 0.04
Matches are distributed among these distances:
209 4 0.01
210 78 0.12
211 33 0.05
212 59 0.09
213 93 0.14
214 300 0.46
215 29 0.04
216 58 0.09
217 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (215 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTAAAAGGCTCAACTC
ACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAA
TATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTGAAAATCAGAAATTAA
Found at i:110158539 original size:72 final size:72
Alignment explanation
Indices: 110158309--110158917 Score: 1010
Period size: 72 Copynumber: 8.5 Consensus size: 72
110158299 AATTAAAAGT
** * *
110158309 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAACGTG
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAAATTACCTCAACGTG
110158374 TCTTGAGG
65 TCTTGAGG
*
110158382 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTCAACGTG
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACCTCAACGTG
110158447 TCTTGAGG
65 TCTTGAGG
*
110158455 CTCAACTCATTTCTCGCAATATGAGTTAAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
110158520 CTTGAGG
66 CTTGAGG
* * *
110158527 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATTGAAAATACCTCAATGTG
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACCTCAACGTG
110158592 TCTTGAGG
65 TCTTGAGG
* *
110158600 CTCAACTCA-TT-TCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCATGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
*
110158663 CCTGAGG
66 CTTGAGG
*
110158670 CTCAACTCATTTCTCGCAATATGAGTTGAA-TTTGAAAACAAAAATTGAAATTACCTCAACGTGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
110158734 CTTGAGG
66 CTTGAGG
* *
110158741 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCATGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
*
110158806 CCTGAGG
66 CTTGAGG
*
110158813 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
110158878 CTTGAGG
66 CTTGAGG
110158885 CTCAACTCATTTCTCGCAATATGAGTTG-ATTTT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTT
110158918 CCTTGGAAAG
Statistics
Matches: 504, Mismatches: 27, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
70 36 0.07
71 100 0.20
72 226 0.45
73 142 0.28
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (72 bp):
CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
CTTGAGG
Found at i:110158758 original size:143 final size:145
Alignment explanation
Indices: 110158309--110158917 Score: 1032
Period size: 143 Copynumber: 4.2 Consensus size: 145
110158299 AATTAAAAGT
** * * *
110158309 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAACGTG
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAAATTACCTCAACATG
* *
110158374 TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACC
65 TCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATTGAAAATACC
110158439 TCAACGTGTCTTGAGG
130 TCAACGTGTCTTGAGG
* *
110158455 CTCAACTCATTTCTCGCAATATGAGTTAAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACATGT
*
110158520 CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATTGAAAATACCT
66 CCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATTGAAAATACCT
*
110158585 CAATGTGTCTTGAGG
131 CAACGTGTCTTGAGG
*
110158600 CTCAACTCA-TT-TCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCATGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACATGT
*
110158663 CCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA-TTTGAAAA-CAAAAATTGAAATTACCT
66 CCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATTGAAAATACCT
110158726 CAACGTGTCTTGAGG
131 CAACGTGTCTTGAGG
*
110158741 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCATGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACATGT
*
110158806 CCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAAAAATTGAAATTACCT
66 CCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATTGAAAATACCT
110158870 CAACGTGTCTTGAGG
131 CAACGTGTCTTGAGG
110158885 CTCAACTCATTTCTCGCAATATGAGTTG-ATTTT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTT
110158918 CCTTGGAAAG
Statistics
Matches: 447, Mismatches: 13, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
141 40 0.09
142 10 0.02
143 179 0.40
144 71 0.16
145 116 0.26
146 31 0.07
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (145 bp):
CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACATGT
CCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATTGAAAATACCT
CAACGTGTCTTGAGG
Found at i:110163787 original size:24 final size:24
Alignment explanation
Indices: 110163759--110163804 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
110163749 CGGCCCAAAG
*
110163759 TTCTTGCAAT-TCTTCTTTCTTTCC
1 TTCTTCCAATGTCTTC-TTCTTTCC
*
110163783 TTCTTCCACTGTCTTCTTCTTT
1 TTCTTCCAATGTCTTCTTCTTT
110163805 GGCGCATGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.07, C:0.30, G:0.04, T:0.59
Consensus pattern (24 bp):
TTCTTCCAATGTCTTCTTCTTTCC
Found at i:110170709 original size:27 final size:28
Alignment explanation
Indices: 110170678--110170731 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
110170668 AAGATTTTTG
110170678 AAACACGAAA-ATTTTTTGAAAACACGA
1 AAACACGAAATATTTTTTGAAAACACGA
* *
110170705 AAACACGAAATTTTTTTTTAAAACACG
1 AAACACGAAATATTTTTTGAAAACACG
110170732 GGAATTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.28
Consensus pattern (28 bp):
AAACACGAAATATTTTTTGAAAACACGA
Found at i:110170745 original size:18 final size:18
Alignment explanation
Indices: 110170718--110170783 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 18
110170708 CACGAAATTT
* *
110170718 TTTTTTAAAACACGGGAA
1 TTTTTGAAAACACGAGAA
*
110170736 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAGAA
* **
110170754 TTTTT-TATTCACGAGAA
1 TTTTTGAAAACACGAGAA
110170771 TTTTTG-AAACACG
1 TTTTTGAAAACACG
110170784 GATTTTTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
17 18 0.47
18 20 0.53
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (18 bp):
TTTTTGAAAACACGAGAA
Found at i:110170759 original size:19 final size:18
Alignment explanation
Indices: 110170652--110170707 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 18
110170642 ACACAATAAT
110170652 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
110170670 GATTTTTG-AAACACGAA
1 AATTTTTGAAAACACGAA
110170687 AATTTTTTGAAAACACGAA
1 AA-TTTTTGAAAACACGAA
110170706 AA
1 AA
110170708 CACGAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 10 0.29
18 13 0.38
19 11 0.32
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:110170783 original size:17 final size:17
Alignment explanation
Indices: 110170719--110170783 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
110170709 ACGAAATTTT
* *
110170719 TTTTTAAAACACGGGAA
1 TTTTTGAAACACGAGAA
*
110170736 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAGAA
* **
110170754 TTTTTTATTCACGAGAA
1 TTTTTGAAACACGAGAA
110170771 TTTTTGAAACACG
1 TTTTTGAAACACG
110170784 GATTTTTTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
17 23 0.62
18 14 0.38
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (17 bp):
TTTTTGAAACACGAGAA
Found at i:110170868 original size:17 final size:18
Alignment explanation
Indices: 110170846--110170893 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
110170836 TATTATTATT
110170846 ATTTTGAAACACGTG-AA
1 ATTTTGAAACACGTGAAA
110170863 ATTTTGAAGACA--TGAAA
1 ATTTTGAA-ACACGTGAAA
110170880 ATTTTTGAAACACG
1 A-TTTTGAAACACG
110170894 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.08
17 14 0.54
18 10 0.38
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (18 bp):
ATTTTGAAACACGTGAAA
Found at i:110171040 original size:20 final size:20
Alignment explanation
Indices: 110171011--110171048 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
110171001 GGGATTCTAA
110171011 TAAAACACGAGAATTTTTAT
1 TAAAACACGAGAATTTTTAT
* *
110171031 TAAAATACGAGGATTTTT
1 TAAAACACGAGAATTTTT
110171049 GAATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (20 bp):
TAAAACACGAGAATTTTTAT
Found at i:110171537 original size:29 final size:29
Alignment explanation
Indices: 110171476--110171530 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
110171466 TTTAGTTTTT
* *
110171476 CTTTTCTTTTTTCTTTCTTTCTTTTTCCC
1 CTTTTCTTCTTTCCTTCTTTCTTTTTCCC
110171505 CTTTTCTTCTTTCCTTC-TTCTTTTTC
1 CTTTTCTTCTTTCCTTCTTTCTTTTTC
110171531 TTCCTTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (29 bp):
CTTTTCTTCTTTCCTTCTTTCTTTTTCCC
Found at i:110171543 original size:29 final size:29
Alignment explanation
Indices: 110171478--110171543 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
110171468 TAGTTTTTCT
*
110171478 TTTCTTT-TTTCTTTCTTTCTTTTTCCCC
1 TTTCTTTCTTTCCTTCTTTCTTTTTCCCC
*
110171506 TTT-TCTTCTTTCCTTC-TTCTTTTTCTTCC
1 TTTCT-TTCTTTCCTTCTTTCTTTTTC-CCC
110171535 TTTCTTTCT
1 TTTCTTTCT
110171544 CCCCGATCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
27 1 0.03
28 14 0.44
29 16 0.50
30 1 0.03
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (29 bp):
TTTCTTTCTTTCCTTCTTTCTTTTTCCCC
Found at i:110172105 original size:30 final size:29
Alignment explanation
Indices: 110172065--110172166 Score: 123
Period size: 30 Copynumber: 3.4 Consensus size: 29
110172055 ATTTAGGATT
110172065 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAA-GAAAGTTTAGGGGTC
* * * *
110172095 TAAGTGAAATTTAAAAAAAGTTTAAGGGTC
1 AAAATGAAATTT-AAGAAAGTTTAGGGGTC
*
110172125 AAAATGAAATTTAAGAAAAATTTAGGGGTC
1 AAAATGAAATTTAAG-AAAGTTTAGGGGTC
*
110172155 AAAATGCAATTT
1 AAAATGAAATTT
110172167 TTTTTTTGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 2 0.03
30 56 0.93
31 2 0.03
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.29
Consensus pattern (29 bp):
AAAATGAAATTTAAGAAAGTTTAGGGGTC
Found at i:110172506 original size:25 final size:25
Alignment explanation
Indices: 110172458--110172506 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
110172448 CATAATTGAA
* * *
110172458 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
110172483 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
110172507 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:110176951 original size:34 final size:34
Alignment explanation
Indices: 110176908--110176975 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
110176898 GTGTAGTTAG
110176908 ATTGCCAATAATTCTTCAACTTTTTAGATTTATT
1 ATTGCCAATAATTCTTCAACTTTTTAGATTTATT
110176942 ATTGCCAATAATTCTTCAACTTTTTAGATTTATT
1 ATTGCCAATAATTCTTCAACTTTTTAGATTTATT
110176976 CTTCTTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (34 bp):
ATTGCCAATAATTCTTCAACTTTTTAGATTTATT
Found at i:110180176 original size:127 final size:127
Alignment explanation
Indices: 110179873--110180157 Score: 534
Period size: 127 Copynumber: 2.2 Consensus size: 127
110179863 ATTTTTTTTC
* * **
110179873 TTTTTGAAGTGTTGAAAAGAAATATTCCCATCTAACCATGGGGGCAAGGCTTTTGTATTAACAAA
1 TTTTTGGAGGGTTGAAAATTAATATTCCCATCTAACCATGGGGGCAAGGCTTTTGTATTAACAAA
110179938 TAATAATTTTTCCATTTAATCAAAGGCTAACGTTAGAAGTGTTAAGTTGAATGTTTTAAATT
66 TAATAATTTTTCCATTTAATCAAAGGCTAACGTTAGAAGTGTTAAGTTGAATGTTTTAAATT
110180000 TTTTTGGAGGGTTGAAAATTAATATTCCCATCTAACCATGGGGGCAAGGCTTTTGTATTAACAAA
1 TTTTTGGAGGGTTGAAAATTAATATTCCCATCTAACCATGGGGGCAAGGCTTTTGTATTAACAAA
110180065 TAATAATTTTTCCATTTAATCAAAGGCTAACGTTAGAAGTGTTAAGTTGAATGTTTTAAATT
66 TAATAATTTTTCCATTTAATCAAAGGCTAACGTTAGAAGTGTTAAGTTGAATGTTTTAAATT
110180127 TTTTTGGAGGGTTGAAAATTAATATTCCCAT
1 TTTTTGGAGGGTTGAAAATTAATATTCCCAT
110180158 TTAGCTAGGA
Statistics
Matches: 154, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 154 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (127 bp):
TTTTTGGAGGGTTGAAAATTAATATTCCCATCTAACCATGGGGGCAAGGCTTTTGTATTAACAAA
TAATAATTTTTCCATTTAATCAAAGGCTAACGTTAGAAGTGTTAAGTTGAATGTTTTAAATT
Found at i:110182329 original size:15 final size:15
Alignment explanation
Indices: 110182309--110182416 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
110182299 TTTATGGAAA
110182309 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
110182324 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
110182338 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
110182354 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
110182368 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
110182384 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
110182398 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
110182414 ATC
1 ATC
110182417 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:110182346 original size:30 final size:30
Alignment explanation
Indices: 110182303--110182426 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
110182293 TCCATATTTA
* *
110182303 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
110182333 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
110182363 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
110182393 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
110182424 TGG
1 TGG
110182427 CATAATAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 80 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:110187028 original size:30 final size:30
Alignment explanation
Indices: 110186992--110187066 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
110186982 ATGGAAAATA
110186992 AAAGATATGGGTATCAAATAATAGAAAGTC
1 AAAGATATGGGTATCAAATAATAGAAAGTC
* *
110187022 AAAGATATGGGTATCAAATATTGGAAAGTC
1 AAAGATATGGGTATCAAATAATAGAAAGTC
110187052 AAAGATATGGGTATC
1 AAAGATATGGGTATC
110187067 GAGATATTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
AAAGATATGGGTATCAAATAATAGAAAGTC
Found at i:110187038 original size:15 final size:15
Alignment explanation
Indices: 110186992--110187066 Score: 55
Period size: 15 Copynumber: 5.0 Consensus size: 15
110186982 ATGGAAAATA
110186992 AAAGATATGGGTATC
1 AAAGATATGGGTATC
* * **
110187007 AAATA-ATAGAAAGTC
1 AAAGATATGGGTA-TC
110187022 AAAGATATGGGTATC
1 AAAGATATGGGTATC
* **
110187037 AAATAT-TGGAAAGTC
1 AAAGATATGGGTA-TC
110187052 AAAGATATGGGTATC
1 AAAGATATGGGTATC
110187067 GAGATATTGG
Statistics
Matches: 42, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
14 8 0.19
15 26 0.62
16 8 0.19
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (15 bp):
AAAGATATGGGTATC
Found at i:110189182 original size:17 final size:17
Alignment explanation
Indices: 110189162--110189195 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
110189152 AGGTTTAGGT
110189162 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
*
110189179 TTAAAATTTTTAATTAA
1 TTAAAAATTTTAATTAA
110189196 AAATCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:110189249 original size:18 final size:20
Alignment explanation
Indices: 110189212--110189249 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
110189202 ATTTTCGTCT
110189212 CATTTAGAAATCTAAGTTGG
1 CATTTAGAAATCTAAGTTGG
110189232 CATTTA-AAATCT-AGTTGG
1 CATTTAGAAATCTAAGTTGG
110189250 ACTGTCACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (20 bp):
CATTTAGAAATCTAAGTTGG
Found at i:110189536 original size:17 final size:18
Alignment explanation
Indices: 110189494--110189536 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
110189484 ATATTAAAAA
110189494 TATAA-TTTTATCATTTT
1 TATAATTTTTATCATTTT
* *
110189511 AATAGTTTTTAT-ATTTT
1 TATAATTTTTATCATTTT
110189528 TATAATTTT
1 TATAATTTT
110189537 AACGGATTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TATAATTTTTATCATTTT
Found at i:110191913 original size:11 final size:11
Alignment explanation
Indices: 110191897--110191922 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
110191887 GTTCAATATG
110191897 GAAACAAAAAA
1 GAAACAAAAAA
110191908 GAAACAAAAAA
1 GAAACAAAAAA
110191919 GAAA
1 GAAA
110191923 TGCTGTATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.08, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAACAAAAAA
Found at i:110193746 original size:26 final size:26
Alignment explanation
Indices: 110193717--110193768 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
110193707 TCCTAATAAT
110193717 CCCTTCAGTAGTGAAGTTAGGAGTGC
1 CCCTTCAGTAGTGAAGTTAGGAGTGC
110193743 CCCTTCAGTAGTGAAGTTAGGAGTGC
1 CCCTTCAGTAGTGAAGTTAGGAGTGC
110193769 TGGCAAGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (26 bp):
CCCTTCAGTAGTGAAGTTAGGAGTGC
Found at i:110195263 original size:2 final size:2
Alignment explanation
Indices: 110195256--110195280 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
110195246 GACAGGTTAT
110195256 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 T
110195281 TCATAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:110195326 original size:28 final size:29
Alignment explanation
Indices: 110195281--110195339 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 29
110195271 ATATATATAT
110195281 TCATAAAAAAAAGAGAGTGACTAAGTTAA
1 TCATAAAAAAAAGAGAGTGACTAAGTTAA
110195310 TCATAAAAAAAA-AGAGTGACTAAGTTAA
1 TCATAAAAAAAAGAGAGTGACTAAGTTAA
110195338 TC
1 TC
110195340 CTTTAAAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.22
Consensus pattern (29 bp):
TCATAAAAAAAAGAGAGTGACTAAGTTAA
Found at i:110195388 original size:49 final size:50
Alignment explanation
Indices: 110195344--110195447 Score: 176
Period size: 49 Copynumber: 2.1 Consensus size: 50
110195334 TTAATCCTTT
*
110195344 AAAGCAGAGATGGTAAGTGAAAAAGTATTAATAAACAATATAAT-CTGCA
1 AAAGAAGAGATGGTAAGTGAAAAAGTATTAATAAACAATATAATCCTGCA
*
110195393 AAAGAAGAGATGGTATGTGAAAAAGTATTAATAAACAATATAAT-CTGCA
1 AAAGAAGAGATGGTAAGTGAAAAAGTATTAATAAACAATATAATCCTGCA
110195442 AAAGAA
1 AAAGAA
110195448 TATTCTCCAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.22
Consensus pattern (50 bp):
AAAGAAGAGATGGTAAGTGAAAAAGTATTAATAAACAATATAATCCTGCA
Found at i:110197832 original size:13 final size:13
Alignment explanation
Indices: 110197814--110197839 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
110197804 GGACTAGTCA
110197814 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
110197827 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
110197840 GTTTTCAAAA
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:110199592 original size:16 final size:17
Alignment explanation
Indices: 110199545--110199598 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
110199535 ATTTGAACGT
110199545 AAAA-TAACT-TAAACC
1 AAAATTAACTCTAAACC
*
110199560 ACAAATTAACTCGAAACC
1 A-AAATTAACTCTAAACC
*
110199578 AAAATTTA-TCTAAACC
1 AAAATTAACTCTAAACC
110199594 GAAAA
1 -AAAA
110199599 AACTTGACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 1 0.03
16 10 0.31
17 15 0.47
18 6 0.19
ACGTcount: A:0.56, C:0.20, G:0.04, T:0.20
Consensus pattern (17 bp):
AAAATTAACTCTAAACC
Found at i:110205163 original size:224 final size:218
Alignment explanation
Indices: 110204728--110205170 Score: 647
Period size: 224 Copynumber: 2.0 Consensus size: 218
110204718 GATATCAGAT
* * **
110204728 AATTCCTAACCTAGTTAGATTGAAAAAAAATGTCATTTTTTAAACAACCAACCATGTCATTAGAA
1 AATTCCCAACCTAGTTAGATTGAAAAAAAATGTCATTTTTAAAACAACCAACCACCTCATTAGAA
*
110204793 TCATTTTTAAGATTTTCCGCTTCGACGCAGGATAATCTGCTAGTCAGTTCCTCGATTTGTGTCTT
66 TCATTTTTAAGATTTTCCGCTTCGACGCAGGATAATCTGCTAGTCAGTTCCTCGATATGTGTCTT
* *
110204858 TAGTTTATCCCTTTCTCTTGAAATGTACAGAAGTTGATCTTTAAGATTCTGCAAAGAATGAAATA
131 TAGTTCATCCCTTTCTCTTGAAATGTACAGAAGTTGATCTTTAAGAATCTGCAAAGAATGAAATA
110204923 AACTTTTCAGTCTCTAAGAAATA
196 AACTTTTCAGTCTCTAAGAAATA
*
110204946 AATTCCCAACCTAGTTAGATTGCTAGCAAGAAAAGA-GTCATTTTTAAAAATAACCAACCACCTC
1 AATTCCCAACCTAGTTAGATTG--A--AA-AAAA-ATGTCATTTTT-AAAACAACCAACCACCTC
* ** * * *
110205010 ATTAGAATCGTTTTTAAGATTTTCCTTTTCGAGGCAGGATAATTTGCTGGTCAGTTCCTCGATAT
59 ATTAGAATCATTTTTAAGATTTTCCGCTTCGACGCAGGATAATCTGCTAGTCAGTTCCTCGATAT
* *
110205075 GTGTCTTTAGTTCATCCCTTTCTGTTGAAATGTCCAGAAGTTGAT-TTTGAAGAATCTGCAAAGA
124 GTGTCTTTAGTTCATCCCTTTCTCTTGAAATGTACAGAAGTTGATCTTT-AAGAATCTGCAAAGA
*
110205139 ATGAATTAAACTTTTCAGTCTCTAAGAAATA
188 ATGAAATAAACTTTTCAGTCTCTAAGAAATA
110205170 A
1 A
110205171 TTACCAGTTC
Statistics
Matches: 200, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
218 21 0.10
220 1 0.00
222 2 0.01
223 16 0.08
224 160 0.80
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (218 bp):
AATTCCCAACCTAGTTAGATTGAAAAAAAATGTCATTTTTAAAACAACCAACCACCTCATTAGAA
TCATTTTTAAGATTTTCCGCTTCGACGCAGGATAATCTGCTAGTCAGTTCCTCGATATGTGTCTT
TAGTTCATCCCTTTCTCTTGAAATGTACAGAAGTTGATCTTTAAGAATCTGCAAAGAATGAAATA
AACTTTTCAGTCTCTAAGAAATA
Found at i:110210418 original size:20 final size:20
Alignment explanation
Indices: 110210393--110210443 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
110210383 AGAAAAGGAA
110210393 AAATGCATGCAAAAATGAAG
1 AAATGCATGCAAAAATGAAG
110210413 AAATGCATGCAAAAATGAAG
1 AAATGCATGCAAAAATGAAG
* *
110210433 ACACGCATGCA
1 AAATGCATGCA
110210444 CACATTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.51, C:0.16, G:0.20, T:0.14
Consensus pattern (20 bp):
AAATGCATGCAAAAATGAAG
Found at i:110218650 original size:12 final size:12
Alignment explanation
Indices: 110218637--110218668 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
110218627 AGACAGCACT
110218637 TTTTTCTTTT-C
1 TTTTTCTTTTGC
110218648 -TTTTCTTTTGC
1 TTTTTCTTTTGC
110218659 TTTTTCTTTT
1 TTTTTCTTTT
110218669 ACCTAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.47
11 1 0.05
12 9 0.47
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTTGC
Found at i:110241753 original size:40 final size:40
Alignment explanation
Indices: 110241707--110241884 Score: 250
Period size: 40 Copynumber: 4.4 Consensus size: 40
110241697 TCCAATTTCT
110241707 AGCACAAAGCCTGCGGGATTTAACCCGAATATCTATTACC
1 AGCACAAAGCCTGCGGGATTTAACCCGAATATCTATTACC
* *
110241747 AGCACAAAGCCTGTGGGATTTAACCCGGATATCTATTACC
1 AGCACAAAGCCTGCGGGATTTAACCCGAATATCTATTACC
* * *
110241787 AGCACAAAACCTGCGGGATTTAACCCGGCGGATATCTATTATC
1 AGCACAAAGCCTGCGGGATTTAA-CC--CGAATATCTATTACC
* * *
110241830 AGCAC-AAGCCTACGGGATTTAACCCCAATATCTATTGCC
1 AGCACAAAGCCTGCGGGATTTAACCCGAATATCTATTACC
110241869 AGCACAAAGCCTGCGG
1 AGCACAAAGCCTGCGG
110241885 ACTATAAGTC
Statistics
Matches: 122, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
39 16 0.13
40 68 0.56
41 4 0.03
42 15 0.12
43 19 0.16
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (40 bp):
AGCACAAAGCCTGCGGGATTTAACCCGAATATCTATTACC
Found at i:110241864 original size:82 final size:80
Alignment explanation
Indices: 110241707--110241884 Score: 250
Period size: 82 Copynumber: 2.2 Consensus size: 80
110241697 TCCAATTTCT
**
110241707 AGCACAAAGCCTGCGGGATTTAACCCGAATATCTATTACCAGCACAAAGCCTGTGGGATTTAACC
1 AGCACAAAGCCTGCGGGATTTAACCCGAATATCTATTACCAGCACAAAGCCTACGGGATTTAACC
**
110241772 CGGATATCTATTACC
66 CCAATATCTATTACC
* * *
110241787 AGCACAAAACCTGCGGGATTTAACCCGGCGGATATCTATTATCAGCAC-AAGCCTACGGGATTTA
1 AGCACAAAGCCTGCGGGATTTAA-CC--CGAATATCTATTACCAGCACAAAGCCTACGGGATTTA
*
110241851 ACCCCAATATCTATTGCC
63 ACCCCAATATCTATTACC
110241869 AGCACAAAGCCTGCGG
1 AGCACAAAGCCTGCGG
110241885 ACTATAAGTC
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
80 22 0.26
81 2 0.02
82 44 0.51
83 18 0.21
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (80 bp):
AGCACAAAGCCTGCGGGATTTAACCCGAATATCTATTACCAGCACAAAGCCTACGGGATTTAACC
CCAATATCTATTACC
Found at i:110248088 original size:37 final size:37
Alignment explanation
Indices: 110248038--110248113 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
110248028 TAAGCTTTAT
110248038 AACCCTTCCTCAAATATCTCTGAGCAGACATCGAATA
1 AACCCTTCCTCAAATATCTCTGAGCAGACATCGAATA
110248075 AACCCTTCCTCAAATATCTCTGAGCAGACATCGAATA
1 AACCCTTCCTCAAATATCTCTGAGCAGACATCGAATA
110248112 AA
1 AA
110248114 TCACACTAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.24
Consensus pattern (37 bp):
AACCCTTCCTCAAATATCTCTGAGCAGACATCGAATA
Found at i:110265010 original size:11 final size:11
Alignment explanation
Indices: 110264976--110265009 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
110264966 TTCTCTGATC
110264976 TTCTTTATTTT
1 TTCTTTATTTT
*
110264987 CTCTTTATTTT
1 TTCTTTATTTT
110264998 TTCTTT-TTTT
1 TTCTTTATTTT
110265008 TT
1 TT
110265010 TGCCTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (11 bp):
TTCTTTATTTT
Found at i:110265858 original size:234 final size:229
Alignment explanation
Indices: 110265393--110265902 Score: 779
Period size: 234 Copynumber: 2.2 Consensus size: 229
110265383 TTGTGTTCGG
* * * * *
110265393 TGAAATTAGATGAATTTGAGGCAGTATAATCTTTTGTTTTAATCGAATCTTTTGTTTGCATGATC
1 TGAAATTAGATGACTTTGAGGCAATTTAATCTCTTGTTTTAATCGAATCTTGTGTTTGCATGATC
*
110265458 ATATAATCGAGTTTTGTTTGTCAAAGTTTTCCCCCCTTATTTGATAAGTTTGATGTTCTATTATT
66 ATATAATCGAGTTTTGTTTGTCAAAGTTTTCCCCCCTTATTTGATAAATTTGATGTTCTATTATT
* * * *
110265523 GGAAAAATATGATTAGGAAAATGAAAGATGAATAATTTTAGAAAATTCTTTAATTCCGTTGTTTC
131 GGAAAAAAATGATTAGGAAAATGAAAGATGAATAATTGTAGAAAATTCTTTAACTACGTTGTTTC
110265588 ATGCTGATCACCGCTTTAAATTAGAAGTGCTAGA
196 ATGCTGATCACCGCTTTAAATTAGAAGTGCTAGA
* * *
110265622 TGAAATTAGATGACTTTGAGGCAATTTAATCTCTTGTTTTGATCTAATGTTGTGTTTGCATGATC
1 TGAAATTAGATGACTTTGAGGCAATTTAATCTCTTGTTTTAATCGAATCTTGTGTTTGCATGATC
* **
110265687 ATATAATCGAGTTTTGTTTGTCAATGTTCTTTTTCCCCTTATTTGATAAATTTG-TGGTTCTATT
66 ATATAATCGAGTTTTGTTTGTCAAAG-T-TTTCCCCCCTTATTTGATAAATTTGAT-GTTCTATT
*
110265751 ATTGGAAAAAAAATTGATTAGGAAAATGAAAAGATTAATAATTGTAGAAAATTCTTTAACTACGT
128 ATTGG-AAAAAAA-TGATTAGGAAAATG-AAAGATGAATAATTGTAGAAAATTCTTTAACTACGT
* *
110265816 TGTTTCATGCTGATCACTGCTTTAAATTAGTAGTGCTAGA
190 TGTTTCATGCTGATCACCGCTTTAAATTAGAAGTGCTAGA
*
110265856 TGAAATTAGATGACTTTGAGGCAATTTAATCTCTTATTTTAATCGAA
1 TGAAATTAGATGACTTTGAGGCAATTTAATCTCTTGTTTTAATCGAA
110265903 CCCAAGTTTT
Statistics
Matches: 253, Mismatches: 22, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
229 82 0.32
230 2 0.01
231 35 0.14
232 6 0.02
233 14 0.06
234 114 0.45
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (229 bp):
TGAAATTAGATGACTTTGAGGCAATTTAATCTCTTGTTTTAATCGAATCTTGTGTTTGCATGATC
ATATAATCGAGTTTTGTTTGTCAAAGTTTTCCCCCCTTATTTGATAAATTTGATGTTCTATTATT
GGAAAAAAATGATTAGGAAAATGAAAGATGAATAATTGTAGAAAATTCTTTAACTACGTTGTTTC
ATGCTGATCACCGCTTTAAATTAGAAGTGCTAGA
Found at i:110266352 original size:229 final size:234
Alignment explanation
Indices: 110265927--110266439 Score: 625
Period size: 229 Copynumber: 2.2 Consensus size: 234
110265917 GTCAAGTGAA
* * * * * *
110265927 TTTTTTCCTTATTTAATAATTTTGCTGTTAAATTATTAATGAAAAATTT-ATCAGTAAAAAGAGA
1 TTTTTTTCTTAGTTGATAATTTTGCTGTTAAATTATTGATG-AAAATTTGATCAGGAAAAAGAAA
* *
110265991 AGATGAATAATTGTTGAAATTTTTTTAGTTATGTTGTTTCATGTGGATCACTGCTTTAAACTCGT
65 AGATGAATAATTGTTGAAATTTCTTTAGTTATATTGTTTCATGTGGATCACTGCTTTAAACTCGT
* ** * * *
110266056 AGTGTTTTATGAAATTAAGTGACTTTGAGGTGATTTAATCTATTGTTTTAACTGAATCTTGTGTT
130 AGTGCTAGATGAAATTAAGTGACTTTGAGGAGATTAAATCTATTGTTTTAACTGAATCTTCTGTT
* * *
110266121 TGCATGATCAAATAATCAAGTT-TTATTTGTAAAGTT-CT
195 TGCATGATCAAATAATCAAGTTCTTATCTGCAAAGTTAAT
* * *
110266159 TTTTTTT-TT-GTTGATAATTTTGATGTTAAATTATTGATGAAAATTTGATCAGGGAGAAGAAAA
1 TTTTTTTCTTAGTTGATAATTTTGCTGTTAAATTATTGATGAAAATTTGATCAGGAAAAAGAAAA
* * *
110266222 GATTAATAGTTGTTGAGAA-TTCTTT-GTTATATTGTTTCATGTTGG-TCACTGCTTTAAACTTG
66 GATGAATAATTGTTGA-AATTTCTTTAGTTATATTGTTTCATG-TGGATCACTGCTTTAAACTCG
*
110266284 TAGTGCTAGATGAAATT-AGATGACTTTGAGGCAG-TTAAATCTCTTGTTTTAATCT-AATCTTC
129 TAGTGCTAGATGAAATTAAG-TGACTTTGAGG-AGATTAAATCTATTGTTTTAA-CTGAATCTTC
* * *
110266346 TGTTTGCATGATCATATAATCAAGTTCTTGTCTGCCAAGTTAAT
191 TGTTTGCATGATCAAATAATCAAGTTCTTATCTGCAAAGTTAAT
* * *
110266390 TTTTTTTCTTATTTTATAATTTTGCTGTTAAATTATTGATGAAAAATTGA
1 TTTTTTTCTTAGTTGATAATTTTGCTGTTAAATTATTGATGAAAATTTGA
110266440 GCAAGAGTGA
Statistics
Matches: 240, Mismatches: 31, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
228 2 0.01
229 110 0.46
230 73 0.30
231 12 0.05
232 8 0.03
233 35 0.15
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (234 bp):
TTTTTTTCTTAGTTGATAATTTTGCTGTTAAATTATTGATGAAAATTTGATCAGGAAAAAGAAAA
GATGAATAATTGTTGAAATTTCTTTAGTTATATTGTTTCATGTGGATCACTGCTTTAAACTCGTA
GTGCTAGATGAAATTAAGTGACTTTGAGGAGATTAAATCTATTGTTTTAACTGAATCTTCTGTTT
GCATGATCAAATAATCAAGTTCTTATCTGCAAAGTTAAT
Found at i:110266538 original size:85 final size:86
Alignment explanation
Indices: 110266436--110266608 Score: 339
Period size: 85 Copynumber: 2.0 Consensus size: 86
110266426 TGATGAAAAA
110266436 TTGAGCAAGAGTGAATCGTATAAGGATATTAATTTACTTATGCTTGAATATGTATA-TTTTGTAT
1 TTGAGCAAGAGTGAATCGTATAAGGATATTAATTTACTTATGCTTGAATATGTATATTTTTGTAT
110266500 TTGTTGTCAAATTGTGTTTAT
66 TTGTTGTCAAATTGTGTTTAT
110266521 TTGAGCAAGAGTGAATCGTATAAGGATATTAATTTACTTATGCTTGAATATGTATATTTTTGTAT
1 TTGAGCAAGAGTGAATCGTATAAGGATATTAATTTACTTATGCTTGAATATGTATATTTTTGTAT
110266586 TTGTTGTCAAATTGTGTTTAT
66 TTGTTGTCAAATTGTGTTTAT
110266607 TT
1 TT
110266609 TCAGGTATGG
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 56 0.64
86 31 0.36
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (86 bp):
TTGAGCAAGAGTGAATCGTATAAGGATATTAATTTACTTATGCTTGAATATGTATATTTTTGTAT
TTGTTGTCAAATTGTGTTTAT
Found at i:110271361 original size:21 final size:21
Alignment explanation
Indices: 110271337--110271379 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
110271327 GAATATTGGA
110271337 TGGTTTTATATATTCTGGTTT
1 TGGTTTTATATATTCTGGTTT
110271358 TGGTTTTATATATTCTGGTTT
1 TGGTTTTATATATTCTGGTTT
110271379 T
1 T
110271380 ATATTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.05, G:0.19, T:0.63
Consensus pattern (21 bp):
TGGTTTTATATATTCTGGTTT
Found at i:110271434 original size:17 final size:17
Alignment explanation
Indices: 110271408--110271441 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
110271398 TTGCTCTAAA
110271408 TATGTAGTCAAATTATG
1 TATGTAGTCAAATTATG
*
110271425 TATGTGGTCAAATTATG
1 TATGTAGTCAAATTATG
110271442 GTGCCAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (17 bp):
TATGTAGTCAAATTATG
Found at i:110280346 original size:32 final size:32
Alignment explanation
Indices: 110280309--110280372 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
110280299 AATAAAAGTA
110280309 TACTTACTTTATAAAAGGAAATATCTTTTGAT
1 TACTTACTTTATAAAAGGAAATATCTTTTGAT
110280341 TACTTACTTTATAAAAGGAAATATCTTTTGAT
1 TACTTACTTTATAAAAGGAAATATCTTTTGAT
110280373 GATTTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (32 bp):
TACTTACTTTATAAAAGGAAATATCTTTTGAT
Found at i:110286226 original size:21 final size:21
Alignment explanation
Indices: 110286196--110286235 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
110286186 ATTTCTAAAC
110286196 AATAACAATAAAATAATAACA
1 AATAACAATAAAATAATAACA
*
110286217 AATAATAATAAAATAATAA
1 AATAACAATAAAATAATAA
110286236 GAAAATAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (21 bp):
AATAACAATAAAATAATAACA
Found at i:110286230 original size:11 final size:11
Alignment explanation
Indices: 110286196--110286242 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
110286186 ATTTCTAAAC
*
110286196 AATAACAATAA
1 AATAATAATAA
*
110286207 AATAATAA-CA
1 AATAATAATAA
110286217 AATAATAATAA
1 AATAATAATAA
*
110286228 AATAATAAGAA
1 AATAATAATAA
110286239 AATA
1 AATA
110286243 GTAGGAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 9 0.29
11 22 0.71
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (11 bp):
AATAATAATAA
Found at i:110305969 original size:58 final size:58
Alignment explanation
Indices: 110305842--110305972 Score: 140
Period size: 58 Copynumber: 2.3 Consensus size: 58
110305832 TTTAGGCCCA
* * * * * *
110305842 AATGTGGTAATAATTGCCAAGTGCAAGTGCTAACTTTGACAAAAAAAGTCCAGGCCTC
1 AATGTGGGAACAATTGCCAAGTGCAAGGGCTAACTTAGACAAAAAAAATCCAAGCCTC
* * * *
110305900 AATTTGCGAACAATTGCCAAGTTC-AGGGACTAACTTAGACAAAAAAAATTCAAGCAC-C
1 AATGTGGGAACAATTGCCAAGTGCAAGGG-CTAACTTAGACAAAAAAAATCCAAGC-CTC
110305958 AATGTGGGAACAATT
1 AATGTGGGAACAATT
110305973 ATTAAGTCCA
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
57 3 0.05
58 55 0.93
59 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (58 bp):
AATGTGGGAACAATTGCCAAGTGCAAGGGCTAACTTAGACAAAAAAAATCCAAGCCTC
Found at i:110306911 original size:22 final size:22
Alignment explanation
Indices: 110306883--110306926 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
110306873 TGCCCCCTTT
110306883 ACTAAAAAAATAAGCAAATTAG
1 ACTAAAAAAATAAGCAAATTAG
*
110306905 ACTAAAAAAATGAGCAAATTAG
1 ACTAAAAAAATAAGCAAATTAG
110306927 TCCTATACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
ACTAAAAAAATAAGCAAATTAG
Found at i:110315402 original size:24 final size:24
Alignment explanation
Indices: 110315362--110315407 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
110315352 TTATATTCTT
* *
110315362 GTTAATTTAATTCTTATTCTTTTA
1 GTTAATTTAACTCTTATCCTTTTA
110315386 GTTAA-TTAACTCTTTATCCTTT
1 GTTAATTTAACTC-TTATCCTTT
110315408 GAAATAGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.24, C:0.13, G:0.04, T:0.59
Consensus pattern (24 bp):
GTTAATTTAACTCTTATCCTTTTA
Found at i:110321125 original size:3 final size:3
Alignment explanation
Indices: 110321117--110321141 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
110321107 AAATTTAGCT
110321117 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
110321142 AGACCAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:110321852 original size:3 final size:3
Alignment explanation
Indices: 110321844--110321873 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
110321834 TTCCCTTAAA
110321844 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
110321874 TGGAAATACA
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:110322050 original size:14 final size:14
Alignment explanation
Indices: 110322019--110322085 Score: 71
Period size: 14 Copynumber: 4.7 Consensus size: 14
110322009 GTTTGCAGGT
* *
110322019 AAAATGTTTTCCGA
1 AAAATGATTTCTGA
*
110322033 AAAATGATTTCTGG
1 AAAATGATTTCTGA
* *
110322047 AAAATAATTTCTTGG
1 AAAATGATTTC-TGA
*
110322062 AAAATAATTTCTGA
1 AAAATGATTTCTGA
110322076 AAAATGATTT
1 AAAATGATTT
110322086 ACTTTTCTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 32 0.70
15 14 0.30
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCTGA
Found at i:110322062 original size:15 final size:15
Alignment explanation
Indices: 110322033--110322073 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
110322023 TGTTTTCCGA
*
110322033 AAAATGATTTC-TGG
1 AAAATAATTTCTTGG
110322047 AAAATAATTTCTTGG
1 AAAATAATTTCTTGG
110322062 AAAATAATTTCT
1 AAAATAATTTCT
110322074 GAAAAATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (15 bp):
AAAATAATTTCTTGG
Found at i:110323396 original size:129 final size:129
Alignment explanation
Indices: 110323166--110323404 Score: 442
Period size: 129 Copynumber: 1.9 Consensus size: 129
110323156 CATTTTACAT
110323166 AAAAAGCAAGCAATTTTACCCGTGTTCCTGAAAATGTTTTCCGTAGGTAAAATGTTTTCAGGTTA
1 AAAAAGCAAGCAATTTTACCCGTGTTCCTGAAAATGTTTTCCGTAGGTAAAATGTTTTCAGGTTA
*
110323231 CCAAATAACATAAAACCAGGAAAACATTTTCCGGAAAATGTTTTCCTGGTTGCCAAACGGAGCC
66 CCAAACAACATAAAACCAGGAAAACATTTTCCGGAAAATGTTTTCCTGGTTGCCAAACGGAGCC
*
110323295 AAAAAGCAGGCAATTTTACCCGTGTTCCTGAAAATGTTTTCCGTAGGTAAAATGTTTTCAGGTTA
1 AAAAAGCAAGCAATTTTACCCGTGTTCCTGAAAATGTTTTCCGTAGGTAAAATGTTTTCAGGTTA
* *
110323360 CCAAACAACGTAAAATCAGGAAAACATTTTCCGGAAAATGTTTTC
66 CCAAACAACATAAAACCAGGAAAACATTTTCCGGAAAATGTTTTC
110323405 AGGTTACCAA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 106 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (129 bp):
AAAAAGCAAGCAATTTTACCCGTGTTCCTGAAAATGTTTTCCGTAGGTAAAATGTTTTCAGGTTA
CCAAACAACATAAAACCAGGAAAACATTTTCCGGAAAATGTTTTCCTGGTTGCCAAACGGAGCC
Found at i:110323405 original size:51 final size:51
Alignment explanation
Indices: 110323343--110323455 Score: 172
Period size: 51 Copynumber: 2.2 Consensus size: 51
110323333 TTCCGTAGGT
*
110323343 AAAATGTTTTCAGGTTACCAAACAACGTAAAATCAGGAAAACATTTTCCGG
1 AAAATGTTTTCAGGTTACCAAACAACGTAAAACCAGGAAAACATTTTCCGG
* ** * *
110323394 AAAATGTTTTCAGGTTACCAATCAATTTCAAACCAGGAAAATATTTTCCGG
1 AAAATGTTTTCAGGTTACCAAACAACGTAAAACCAGGAAAACATTTTCCGG
110323445 AAAATGTTTTC
1 AAAATGTTTTC
110323456 CTGGTTGCCA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (51 bp):
AAAATGTTTTCAGGTTACCAAACAACGTAAAACCAGGAAAACATTTTCCGG
Found at i:110324275 original size:21 final size:19
Alignment explanation
Indices: 110324237--110324274 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
110324227 TGTGAAGTTC
110324237 ATTGATGAATATTTATATA
1 ATTGATGAATATTTATATA
*
110324256 ATTGATGAATATTTTTATA
1 ATTGATGAATATTTATATA
110324275 TTTAAAGTTT
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:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (19 bp):
ATTGATGAATATTTATATA
Found at i:110329895 original size:18 final size:18
Alignment explanation
Indices: 110329874--110329908 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
110329864 TTTATTGTTT
*
110329874 TTAAATATTTTTTAAATA
1 TTAAATATTTTTGAAATA
110329892 TTAAATATTTTTGAAAT
1 TTAAATATTTTTGAAAT
110329909 CTATACGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTAAATATTTTTGAAATA
Found at i:110331658 original size:3 final size:3
Alignment explanation
Indices: 110331640--110332204 Score: 143
Period size: 3 Copynumber: 187.0 Consensus size: 3
110331630 AATTAAAATA
* * * *
110331640 AAT AAT AAC AAA AAT AAT AAT AGT AAC AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * **
110331688 AAT AAT AAT AAT AAT AAT AAGCC AA- AGT AGAA AAT AAT AAT -AT GTT
1 AAT AAT AAT AAT AAT AAT AA--T AAT AAT A-AT AAT AAT AAT AAT AAT
* * * * * * * * *
110331734 AAC AAG AGT AAT AAT CAT ATAT ATT AAT AAT AA- AGT GAT GGCAT -GT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT --AAT AAT
* * * *
110331780 CAAT AAG GAT AAT AAT AAT AAAT AAT AATT AAT AAT ACT AA- ATT AAT
1 -AAT AAT AAT AAT AAT AAT -AAT AAT AA-T AAT AAT AAT AAT AAT AAT
* * * * *
110331827 AAT AA- AGT AAT AAG CA- AAT AA- ACAC AA- AAA AAT AA- AAT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT A-AT
* * * * *
110331869 AAT -AT AAT AAT AAC AA- AAT GAA- ATT AATT AGT -TT AAT ACT AA-
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA-T AAT AAT AAT AAT AAT
* * * * *
110331911 GAT AAT AAT AAT AGT AAT AGAG AGT AAC AAT ACATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-A-T AAT AAT AAT AAT
** * * * *
110331959 -AT GTT AAT AAC AAT AAT AAT AAT ATAT AAA AAGGG AAT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AA--T AAT AAT AAT AAT
* * * * *
110332006 -AT AGT AAA AAT AAT AAT -GT ATT AAT AAT AAT GAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
110332051 GAGAT AAT AAT AAT AAT ATT AAT AAA AAT AGACGT AA- AAGA AAT AGT
1 -A-AT AAT AAT AAT AAT AAT AAT AAT AAT A-A--T AAT AA-T AAT AAT
* * **
110332098 AAT AAT AGT AAT AAT AAT AGT AAT AAT -AT AAAT AAT AAT ATAT GTT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT A-AT AAT
*** * * *
110332144 TGC AA- AAT AAC GAT AGT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
110332190 GGA- AAT AAT AAT AAT
1 -AAT AAT AAT AAT AAT
110332205 GGCATTAGAA
Statistics
Matches: 403, Mismatches: 107, Indels: 104
0.66 0.17 0.17
Matches are distributed among these distances:
2 35 0.09
3 319 0.79
4 36 0.09
5 11 0.03
6 2 0.00
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:110332051 original size:28 final size:28
Alignment explanation
Indices: 110331912--110332077 Score: 104
Period size: 28 Copynumber: 5.6 Consensus size: 28
110331902 TAATACTAAG
* * *
110331912 ATAATAATAATAGTAATA-GAGAGTAACA
1 ATAATAATAATAATAAAATGAGA-TAATA
* *
110331940 ATACATTAATAATAATAATATGTTA-ATAACA
1 ATA-A-TAATAATAATAAAATG--AGATAATA
* *
110331971 ATAATAATAATATATAAAAAGGGAATAATA
1 ATAATAATAATA-ATAAAATGAG-ATAATA
* * *
110332001 ATAGTATAGTAAAAATAATAATGTA-TTAATA
1 ATA--ATAATAATAATAA-AATG-AGATAATA
*
110332032 ATAATGATAATAATAAAATGAGATAATA
1 ATAATAATAATAATAAAATGAGATAATA
*
110332060 ATAATAATATTAATAAAA
1 ATAATAATAATAATAAAA
110332078 ATAGACGTAA
Statistics
Matches: 109, Mismatches: 16, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
27 1 0.01
28 28 0.26
29 19 0.17
30 28 0.26
31 21 0.19
32 11 0.10
33 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (28 bp):
ATAATAATAATAATAAAATGAGATAATA
Found at i:110333938 original size:10 final size:10
Alignment explanation
Indices: 110333923--110333947 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
110333913 AAGCTATTAT
110333923 AAAAAATAAA
1 AAAAAATAAA
110333933 AAAAAATAAA
1 AAAAAATAAA
110333943 AAAAA
1 AAAAA
110333948 GTGTTCTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:110334114 original size:18 final size:18
Alignment explanation
Indices: 110334091--110334125 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
110334081 ATAATTATTA
*
110334091 TTTTTTTAATTTAGTCTT
1 TTTTTTTAATTGAGTCTT
110334109 TTTTTTTAATTGAGTCT
1 TTTTTTTAATTGAGTCT
110334126 ATAATTCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.09, T:0.69
Consensus pattern (18 bp):
TTTTTTTAATTGAGTCTT
Found at i:110334646 original size:23 final size:22
Alignment explanation
Indices: 110334577--110334646 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
110334567 TTTATTGACT
*
110334577 TGTTCGTGAACATGTACAATTATA
1 TGTTCGTGAACATGTTC-ATTA-A
**
110334601 TGTTTATGAACATGTTCATTTAA
1 TGTTCGTGAACATGTTCA-TTAA
*
110334624 TGTTCGTGAACATATTCGATTAA
1 TGTTCGTGAACATGTTC-ATTAA
110334647 GTTAAATGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (22 bp):
TGTTCGTGAACATGTTCATTAA
Found at i:110335705 original size:16 final size:16
Alignment explanation
Indices: 110335684--110335715 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
110335674 CAAGTAAATG
110335684 TCTCTAAAATAGTAAC
1 TCTCTAAAATAGTAAC
110335700 TCTCTAAAATAGTAAC
1 TCTCTAAAATAGTAAC
110335716 AAAATTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (16 bp):
TCTCTAAAATAGTAAC
Found at i:110335820 original size:20 final size:21
Alignment explanation
Indices: 110335785--110335824 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
110335775 AAATTGATAG
110335785 CAAAATAGTGAAAAAAAACAA
1 CAAAATAGTGAAAAAAAACAA
110335806 CAAAATAGT-AAAAAAAACA
1 CAAAATAGTGAAAAAAAACA
110335825 GTAAGAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.72, C:0.10, G:0.07, T:0.10
Consensus pattern (21 bp):
CAAAATAGTGAAAAAAAACAA
Found at i:110343651 original size:62 final size:62
Alignment explanation
Indices: 110343554--110343676 Score: 183
Period size: 62 Copynumber: 2.0 Consensus size: 62
110343544 TTACTGCCAC
* * *
110343554 ACGGCCTGGACACACGCCTATGTCCTTGGCTGTGTGGTTTTATACCATAAACAGTGAGTTAT
1 ACGGCCTGGACACACGCCTATGTCCCTAGCCGTGTGGTTTTATACCATAAACAGTGAGTTAT
* * * *
110343616 ACGGCCTGGGCACACTCCTGTGTCCCTAGCCGTGTGGTTTTATTCCATAAACAGTGAGTTA
1 ACGGCCTGGACACACGCCTATGTCCCTAGCCGTGTGGTTTTATACCATAAACAGTGAGTTA
110343677 CACGATCATT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.30
Consensus pattern (62 bp):
ACGGCCTGGACACACGCCTATGTCCCTAGCCGTGTGGTTTTATACCATAAACAGTGAGTTAT
Found at i:110351888 original size:30 final size:30
Alignment explanation
Indices: 110351852--110351950 Score: 180
Period size: 30 Copynumber: 3.3 Consensus size: 30
110351842 CTAGCCTTTG
110351852 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
110351882 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
110351912 CCACTACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
110351942 CCACCACCA
1 CCACCACCA
110351951 CTTGTACCTA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.26, C:0.51, G:0.06, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:110352510 original size:25 final size:24
Alignment explanation
Indices: 110352429--110352635 Score: 90
Period size: 23 Copynumber: 8.6 Consensus size: 24
110352419 CTTTTTTTGT
*
110352429 TATTAT-TATAT-TTCTTAATATTA
1 TATTATGTATATATTC-TAATACTA
* ** *
110352452 TATTATATATATATTCTTTTA-AA
1 TATTATGTATATATTCTAATACTA
* *
110352475 TATTA-G-GTATATTCTAAATTCTA
1 TATTATGTATATATTCT-AATACTA
110352498 TATTATGTATATATAT-T-ATACTA
1 TATTATGTATATAT-TCTAATACTA
* *
110352521 TTTTATGTATATATCTTTAATACTA
1 TATTATGTATATAT-TCTAATACTA
* * **
110352546 TATTATTTATATATATATTTACATGTTA
1 TATTA--TGTATATAT-TCTA-ATACTA
* *
110352574 TCTTATGTATATATTTTAAT--TA
1 TATTATGTATATATTCTAATACTA
* * * *
110352596 TATTATGTATGTATTTTTTACACTA
1 TATTATGTATATA-TTCTAATACTA
*
110352621 TATTATGTACATATT
1 TATTATGTATATATT
110352636 TTTAATATTA
Statistics
Matches: 143, Mismatches: 26, Indels: 29
0.72 0.13 0.15
Matches are distributed among these distances:
21 8 0.06
22 14 0.10
23 42 0.29
24 14 0.10
25 36 0.25
26 9 0.06
27 12 0.08
28 8 0.06
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (24 bp):
TATTATGTATATATTCTAATACTA
Found at i:110352596 original size:22 final size:22
Alignment explanation
Indices: 110352571--110352678 Score: 71
Period size: 22 Copynumber: 4.9 Consensus size: 22
110352561 TATTTACATG
*
110352571 TTATCTTATGTATATATTTTAA
1 TTATATTATGTATATATTTTAA
*
110352593 TTATATTATGTATGTATTTTTTACA
1 TTATATTATGTA--TATATTTTA-A
* *
110352618 CTATATTATGTACATATTTTTAA
1 TTATATTATGTATATA-TTTTAA
* * *
110352641 -TATTATCACGTATTTATTTT--
1 TTA-TATTATGTATATATTTTAA
*
110352661 TTATA-TATGTACATATTT
1 TTATATTATGTATATATTT
110352679 ATGTAGTATT
Statistics
Matches: 67, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
19 9 0.13
20 2 0.03
21 2 0.03
22 17 0.25
23 12 0.18
24 13 0.19
25 12 0.18
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (22 bp):
TTATATTATGTATATATTTTAA
Found at i:110352636 original size:25 final size:25
Alignment explanation
Indices: 110352495--110352638 Score: 109
Period size: 25 Copynumber: 5.8 Consensus size: 25
110352485 ATTCTAAATT
* *
110352495 CTATATTATGTATATA--TATTATA
1 CTATATTATGTATATATTTTTTACA
* * * *
110352518 CTATTTTATGTATATATCTTTAATA
1 CTATATTATGTATATATTTTTTACA
* *
110352543 CTATATTATTTATATATATATTTACA
1 CTATATTATGTATATAT-TTTTTACA
* *
110352569 TGTTATCTTATGTATATA--TTTTA-A
1 --CTATATTATGTATATATTTTTTACA
* *
110352593 TTATATTATGTATGTATTTTTTACA
1 CTATATTATGTATATATTTTTTACA
*
110352618 CTATATTATGTACATATTTTT
1 CTATATTATGTATATATTTTT
110352639 AATATTATCA
Statistics
Matches: 95, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
22 14 0.15
23 15 0.16
24 6 0.06
25 43 0.45
26 4 0.04
28 13 0.14
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (25 bp):
CTATATTATGTATATATTTTTTACA
Found at i:110352645 original size:20 final size:20
Alignment explanation
Indices: 110352620--110352678 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 20
110352610 TTTTTACACT
110352620 ATATTATGTACATATTTTTA
1 ATATTATGTACATATTTTTA
** *
110352640 ATATTATCACGTATTTATTTTTT
1 ATATTAT---GTACATATTTTTA
110352663 ATA-TATGTACATATTT
1 ATATTATGTACATATTT
110352679 ATGTAGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 3 0.10
23 13 0.42
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
ATATTATGTACATATTTTTA
Found at i:110360972 original size:4 final size:4
Alignment explanation
Indices: 110360963--110360987 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
110360953 AAAAAATGTA
110360963 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
110360988 GAATGTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:110361084 original size:15 final size:15
Alignment explanation
Indices: 110361060--110361105 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
110361050 ATATAAATAG
*
110361060 AAATAAAAATATAAT
1 AAATAGAAATATAAT
110361075 AAATAGAAATATAAT
1 AAATAGAAATATAAT
110361090 AATAGTAGAAATATAA
1 AA-A-TAGAAATATAA
110361106 ATAGGTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:110361093 original size:23 final size:25
Alignment explanation
Indices: 110361035--110361096 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 25
110361025 AAATAGTAAT
*
110361035 GAAA-ATAATATTAGTATATAAATA
1 GAAATATAATAATAGTATATAAATA
110361059 GAAATA-AA-AATA-TA-ATAAATA
1 GAAATATAATAATAGTATATAAATA
110361080 GAAATATAATAATAGTA
1 GAAATATAATAATAGTA
110361097 GAAATATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 13 0.39
22 4 0.12
23 7 0.21
24 8 0.24
25 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (25 bp):
GAAATATAATAATAGTATATAAATA
Found at i:110361131 original size:15 final size:14
Alignment explanation
Indices: 110361052--110361138 Score: 52
Period size: 15 Copynumber: 6.0 Consensus size: 14
110361042 ATATTAGTAT
*
110361052 ATAAATAGAAATA-
1 ATAAATAAAAATAG
*
110361065 AAAATATAATAAATAG
1 ATAA-ATAA-AAATAG
*
110361081 A-AATATAATAATAG
1 ATAA-ATAAAAATAG
* *
110361095 TAGAAATATAAATAG
1 -ATAAATAAAAATAG
*
110361110 GTAAATAAAAATTAG
1 ATAAATAAAAA-TAG
*
110361125 ATAAATAATAATAG
1 ATAAATAAAAATAG
110361139 TATTAGAATA
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
13 3 0.05
14 19 0.33
15 33 0.57
16 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.26
Consensus pattern (14 bp):
ATAAATAAAAATAG
Found at i:110361701 original size:5 final size:5
Alignment explanation
Indices: 110361693--110361720 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
110361683 ATAATTTAAT
110361693 AATAA AATAA AATAA AATAA AATAA AAT
1 AATAA AATAA AATAA AATAA AATAA AAT
110361721 CATATCTTCC
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:110362110 original size:26 final size:26
Alignment explanation
Indices: 110362074--110362157 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
110362064 TGATACAAAT
*
110362074 TGATAATAGGTTAGGTAAATATTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
110362100 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
110362126 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
110362152 TGATAA
1 TGATAA
110362158 GAATTTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:110363642 original size:28 final size:26
Alignment explanation
Indices: 110363600--110363674 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
110363590 AAAAGTAGCT
* *
110363600 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGGA
* *
110363628 AAATTACTGTTATACCCCTAGGTGTA
1 AAATTACTGTTATACCCCTAGATGGA
*
110363654 AAATTACCGTTATACCCCTAG
1 AAATTACTGTTATACCCCTAG
110363675 GGTTAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 23 0.55
27 1 0.02
28 18 0.43
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGGA
Found at i:110363819 original size:27 final size:27
Alignment explanation
Indices: 110363778--110363890 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 27
110363768 GAGGAAGCGT
*
110363778 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
110363805 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
110363832 TCTGGTGGCACTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
110363860 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
110363886 TCTGG
1 TCTGG
110363891 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.07
27 54 0.74
28 14 0.19
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:110363883 original size:54 final size:54
Alignment explanation
Indices: 110363776--110363890 Score: 162
Period size: 54 Copynumber: 2.1 Consensus size: 54
110363766 TGGAGGAAGC
*
110363776 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * *
110363830 GTTCTGGTGGC-ACTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTA-TGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
110363884 GTTCTGG
1 GTTCTGG
110363891 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
53 1 0.02
54 36 0.65
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:110368782 original size:2 final size:2
Alignment explanation
Indices: 110368777--110368809 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
110368767 TTCACACATG
110368777 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 A
110368810 AAATGAGACT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:110369150 original size:43 final size:43
Alignment explanation
Indices: 110369090--110369174 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
110369080 AATCAAATTT
*
110369090 TTTTATTGAAGTTATTCTACTTATAAGCTTTCACATATAACCA
1 TTTTATTGAAGTTATTCTACTTATAAGCTTTCACACATAACCA
*
110369133 TTTTATTGAAGTTATTCTACTTATAAGCTTTCAGACATAACC
1 TTTTATTGAAGTTATTCTACTTATAAGCTTTCACACATAACC
110369175 GTGCTTCTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (43 bp):
TTTTATTGAAGTTATTCTACTTATAAGCTTTCACACATAACCA
Found at i:110369193 original size:35 final size:35
Alignment explanation
Indices: 110369147--110369218 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
110369137 ATTGAAGTTA
110369147 TTCTACTTATAAGCTTTCAGACATAACCGTGCTTC
1 TTCTACTTATAAGCTTTCAGACATAACCGTGCTTC
* *
110369182 TTCTACTTATAAGCTTTCAGATATAACGGTGCTTC
1 TTCTACTTATAAGCTTTCAGACATAACCGTGCTTC
110369217 TT
1 TT
110369219 TAGATATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.40
Consensus pattern (35 bp):
TTCTACTTATAAGCTTTCAGACATAACCGTGCTTC
Found at i:110370680 original size:30 final size:30
Alignment explanation
Indices: 110370636--110370748 Score: 117
Period size: 30 Copynumber: 3.9 Consensus size: 30
110370626 TTTAACGAAC
* *
110370636 TTGCTCACATAAGCTGACTTTATATTAGAA
1 TTGCTCACACAAGCTGACTTTATAATAGAA
*
110370666 TTGTTCACACAAGCTGACTTTATAATAGAA
1 TTGCTCACACAAGCTGACTTTATAATAGAA
** *
110370696 TTGCTCACACAAATTGAC-TT-T-GT-GAA
1 TTGCTCACACAAGCTGACTTTATAATAGAA
* * *
110370722 TTGCTCACATAAGTTGACTTTGTAATA
1 TTGCTCACACAAGCTGACTTTATAATA
110370749 TTTCCATACA
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
26 19 0.28
27 3 0.04
28 2 0.03
29 3 0.04
30 42 0.61
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (30 bp):
TTGCTCACACAAGCTGACTTTATAATAGAA
Found at i:110370722 original size:26 final size:26
Alignment explanation
Indices: 110370693--110370744 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
110370683 CTTTATAATA
110370693 GAATTGCTCACACAAATTGACTTTGT
1 GAATTGCTCACACAAATTGACTTTGT
* *
110370719 GAATTGCTCACATAAGTTGACTTTGT
1 GAATTGCTCACACAAATTGACTTTGT
110370745 AATATTTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (26 bp):
GAATTGCTCACACAAATTGACTTTGT
Found at i:110373276 original size:28 final size:28
Alignment explanation
Indices: 110373224--110373278 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
110373214 TAAAATTATA
**
110373224 AATAATATTGGTAATCCCCCCAAAAAAT
1 AATAATATTGGTAATCCCCAAAAAAAAT
110373252 AATAATATTGGTAATCCCCAAAAAAAA
1 AATAATATTGGTAATCCCCAAAAAAAA
110373279 CAAGCTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.24
Consensus pattern (28 bp):
AATAATATTGGTAATCCCCAAAAAAAAT
Found at i:110379518 original size:21 final size:21
Alignment explanation
Indices: 110379492--110379532 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
110379482 AGACGAGCGA
* *
110379492 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
110379513 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
110379533 TTGAGCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:110384181 original size:23 final size:23
Alignment explanation
Indices: 110384151--110384200 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
110384141 AATTTCAATA
110384151 AAAATCATTAAATAATAATAATG
1 AAAATCATTAAATAATAATAATG
110384174 AAAATCATTAAATAATAATAATG
1 AAAATCATTAAATAATAATAATG
110384197 AAAA
1 AAAA
110384201 CATAAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (23 bp):
AAAATCATTAAATAATAATAATG
Found at i:110385481 original size:11 final size:11
Alignment explanation
Indices: 110385465--110385489 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
110385455 CGGTTTTCTT
110385465 TATATCTTTAA
1 TATATCTTTAA
110385476 TATATCTTTAA
1 TATATCTTTAA
110385487 TAT
1 TAT
110385490 TTTTCAAAAA
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATCTTTAA
Found at i:110386892 original size:3 final size:3
Alignment explanation
Indices: 110386884--110386921 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
110386874 ATTTATCTCA
110386884 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
110386922 AGAATAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:110388056 original size:13 final size:14
Alignment explanation
Indices: 110388040--110388081 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
110388030 TTTCAATTTT
110388040 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
110388053 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
110388068 ATTTTAAATAATAT
1 ATTTT-AATAATAT
110388082 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:110388066 original size:16 final size:16
Alignment explanation
Indices: 110388044--110388080 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
110388034 AATTTTATTT
110388044 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
110388061 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
110388076 TAATA
1 TAATA
110388081 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:110391544 original size:17 final size:18
Alignment explanation
Indices: 110391531--110391655 Score: 100
Period size: 19 Copynumber: 6.9 Consensus size: 18
110391521 TAATCTTCAA
110391531 TGATATGCAATCTTAGATG
1 TGATATGCAATCTTAGA-G
110391550 TGATATGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
110391567 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
110391586 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
110391602 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
*
110391621 TGAT-TGCAATCTTAGATA
1 TGATATGCAATCTTAGA-G
*
110391639 TGATATACAATCTTAGA
1 TGATATGCAATCTTAGA
110391656 AGATATGATT
Statistics
Matches: 91, Mismatches: 5, Indels: 20
0.78 0.04 0.17
Matches are distributed among these distances:
15 2 0.02
16 3 0.03
17 24 0.26
18 28 0.31
19 30 0.33
20 4 0.04
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (18 bp):
TGATATGCAATCTTAGAG
Found at i:110391600 original size:35 final size:35
Alignment explanation
Indices: 110391538--110391655 Score: 200
Period size: 35 Copynumber: 3.3 Consensus size: 35
110391528 CAATGATATG
*
110391538 CAATCTTAGATGTGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
110391574 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
110391609 CAATCTTAGATATGATTGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATTGCAATCTTAGATATG--ATA
110391646 CAATCTTAGA
1 CAATCTTAGA
110391656 AGATATGATT
Statistics
Matches: 79, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
35 51 0.65
36 15 0.19
37 13 0.16
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:110392157 original size:17 final size:16
Alignment explanation
Indices: 110392137--110392195 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 16
110392127 CCAATATATT
110392137 TTATATTTTTTATATAA
1 TTAT-TTTTTTATATAA
*
110392154 TTATTATTCTTATA-AA
1 TTATT-TTTTTATATAA
110392170 -TATTTTTTTATTATATA
1 TTATTTTTTTA-TATA-A
110392187 TTATATTTT
1 TTAT-TTTT
110392196 AAATTTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 5 0.15
15 6 0.18
16 4 0.12
17 12 0.35
18 3 0.09
19 4 0.12
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTTTTTATATAA
Found at i:110392196 original size:17 final size:17
Alignment explanation
Indices: 110392131--110392196 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 17
110392121 TCTAAACCAA
*
110392131 TATATTTTATATTTT-T
1 TATATATTATATTTTAT
110392147 TATATAATTATTATTCTTA-
1 TATAT-ATTA-TATT-TTAT
*
110392166 TAAATATT-T-TTTTAT
1 TATATATTATATTTTAT
110392181 TATATATTATATTTTA
1 TATATATTATATTTTA
110392197 AATTTATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
14 3 0.08
15 9 0.22
16 7 0.17
17 8 0.20
18 7 0.17
19 6 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATATTATATTTTAT
Found at i:110398135 original size:7 final size:7
Alignment explanation
Indices: 110398123--110398169 Score: 62
Period size: 7 Copynumber: 6.7 Consensus size: 7
110398113 TTCTATTTTA
110398123 AAAAAAG
1 AAAAAAG
110398130 AAAAAAG
1 AAAAAAG
110398137 -AAAAAG
1 AAAAAAG
110398143 AAAAATA-
1 AAAAA-AG
110398150 AAAAAGAG
1 AAAAA-AG
110398158 AAAAAAG
1 AAAAAAG
110398165 AAAAA
1 AAAAA
110398170 TGGTAAGGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
6 6 0.17
7 24 0.67
8 6 0.17
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:110398142 original size:13 final size:13
Alignment explanation
Indices: 110398124--110398169 Score: 65
Period size: 13 Copynumber: 3.4 Consensus size: 13
110398114 TCTATTTTAA
110398124 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
*
110398137 AAAAAGAAAAATAA
1 AAAAAGAAAAA-AG
110398151 AAAAGAGAAAAAAG
1 AAAA-AGAAAAAAG
110398165 AAAAA
1 AAAAA
110398170 TGGTAAGGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 12 0.41
14 10 0.34
15 7 0.24
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:110399869 original size:205 final size:205
Alignment explanation
Indices: 110399114--110399865 Score: 1173
Period size: 205 Copynumber: 3.7 Consensus size: 205
110399104 GATCTGGCTA
*
110399114 AAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGAT
1 AAGC-AGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGAT
* * * * *
110399179 TTGGCTTTCATGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCATCCCTGTATTGTCAGAGA
65 TTGGCTTTCACGTATTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTAGTGTCAGAGA
* * *
110399244 ACAAATCAAAGTCTGGCATCTCCATTTCGACAGAGAGTAGATACATAGCAGATCT-AGCCTTCAG
130 ACAAATCAAAGTCTGGCATCTCCACTTCAATAGAGAGTAGATACATAGCAGATCTCA-CCTTCAG
*
110399308 ATGTTTATACTG
194 ATGTTTATGCTG
* * *
110399320 AAACAGATCTAAGCTGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATT
1 AAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATT
* * *
110399385 TGGCTTTCACGTATTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTATGTAGTGTCAGAGAA
66 TGGCTTTCACGTATTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTAGTGTCAGAGAA
*
110399450 CAAATCAAAGTCTGGCATCTCTACTTCAATAGAGAGTAGATACATAGCAGATCTCACCTTCAGAT
131 CAAATCAAAGTCTGGCATCTCCACTTCAATAGAGAGTAGATACATAGCAGATCTCACCTTCAGAT
110399515 GTTTATGCTG
196 GTTTATGCTG
* *
110399525 AAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAACAAATCGAAGATATAGCTGATT
1 AAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATT
* ** *
110399590 TGGCTTTCATGTATTTACGATGAAGCAAATCTAAGATGATTTTTCGTCTCTGTAGTGTCAGAGAA
66 TGGCTTTCACGTATTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTAGTGTCAGAGAA
* * * *
110399655 CAAATCGAAGTCTGGCATCTCCACTTCAATGGAGAGCAGATACATGGCAGATCTCACCTTCAGAT
131 CAAATCAAAGTCTGGCATCTCCACTTCAATAGAGAGTAGATACATAGCAGATCTCACCTTCAGAT
110399720 GTTTATGCTG
196 GTTTATGCTG
*
110399730 AAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATT
1 AAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATT
** * * * *
110399795 TGGCTTTCACGTGCTTACGTTAAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGGGAA
66 TGGCTTTCACGTATTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTAGTGTCAGAGAA
110399860 CAAATC
131 CAAATC
110399866 GAAGAAGTTA
Statistics
Matches: 502, Mismatches: 43, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
205 498 0.99
206 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (205 bp):
AAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATT
TGGCTTTCACGTATTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTAGTGTCAGAGAA
CAAATCAAAGTCTGGCATCTCCACTTCAATAGAGAGTAGATACATAGCAGATCTCACCTTCAGAT
GTTTATGCTG
Found at i:110400276 original size:17 final size:17
Alignment explanation
Indices: 110400238--110400355 Score: 155
Period size: 17 Copynumber: 6.6 Consensus size: 17
110400228 TAATGATATG
*
110400238 CAATCTTAGATGTGATATA
1 CAATCTTAGATATG--ATA
110400257 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
110400274 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
110400292 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
110400309 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
110400327 CAATCTTAGATATGATATA
1 CAATCTTAGATATG--ATA
110400346 CAATCTTAGA
1 CAATCTTAGA
110400356 AGTTATGATT
Statistics
Matches: 90, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
17 34 0.38
18 31 0.34
19 24 0.27
20 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:110400302 original size:35 final size:35
Alignment explanation
Indices: 110400238--110400355 Score: 191
Period size: 35 Copynumber: 3.3 Consensus size: 35
110400228 TAATGATATG
* *
110400238 CAATCTTAGATGTGATATACAATCTTAGATATGATA
1 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
110400274 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
110400309 CAATCTTAGATATGATTGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATTGCAATCTTAGATATG--ATA
110400346 CAATCTTAGA
1 CAATCTTAGA
110400356 AGTTATGATT
Statistics
Matches: 78, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
35 50 0.64
36 15 0.19
37 13 0.17
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:110400850 original size:17 final size:17
Alignment explanation
Indices: 110400830--110400895 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
110400820 TTCTAAACCA
*
110400830 ATATATTTTATATTTTT
1 ATATATATTATATTTTT
*
110400847 ATATA-ATTATTATTCTT
1 ATATATATTA-TATTTTT
*
110400864 ATAAATA-TAT-TTTTT
1 ATATATATTATATTTTT
110400879 ATTATATATTATATTTT
1 A-TATATATTATATTTT
110400896 AAATTTATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
15 5 0.13
16 9 0.23
17 20 0.51
18 5 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATATATTATATTTTT
Found at i:110400871 original size:38 final size:37
Alignment explanation
Indices: 110400795--110400881 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 37
110400785 ATTCTTTTAC
* *
110400795 ATATTTGATA-TTTTATATATTATTTTTCTAAACCAAT
1 ATATTTTATATTTTTATATATTATTATTCTAAA-CAAT
*
110400832 ATATTTTATATTTTTATATAATTATTATTCTTATA-AAT
1 ATATTTTATATTTTTATAT-ATTATTATTC-TAAACAAT
*
110400870 ATATTTTTTATT
1 ATATTTTATATT
110400882 ATATATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
37 9 0.21
38 22 0.51
39 9 0.21
40 3 0.07
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (37 bp):
ATATTTTATATTTTTATATATTATTATTCTAAACAAT
Found at i:110400920 original size:26 final size:26
Alignment explanation
Indices: 110400872--110400921 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
110400862 TTATAAATAT
* * * *
110400872 ATTTTTTATTATATATTATATTTTAA
1 ATTTATTATTAAATATCACATTTTAA
110400898 ATTTATTATTAAATATCACATTTT
1 ATTTATTATTAAATATCACATTTT
110400922 TTATATGCTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTATTATTAAATATCACATTTTAA
Found at i:110405972 original size:23 final size:23
Alignment explanation
Indices: 110405944--110405995 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
110405934 TAGATCTTTC
*
110405944 CTAAATATTATCACTAGATAATT
1 CTAAATATTATCACTAAATAATT
110405967 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
110405990 CAAAAT
1 CTAAAT
110405996 TTAAAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:110409186 original size:15 final size:15
Alignment explanation
Indices: 110409166--110409201 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
110409156 ATAAGCCCTC
110409166 AAATTAAAAAAATAA
1 AAATTAAAAAAATAA
110409181 AAATTAAAAAAATAA
1 AAATTAAAAAAATAA
110409196 AAATTA
1 AAATTA
110409202 TAATTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
AAATTAAAAAAATAA
Found at i:110409212 original size:23 final size:22
Alignment explanation
Indices: 110409181--110409231 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
110409171 AAAAAAATAA
110409181 AAATT-AAAAAAATAAAAATTAT
1 AAATTAAAAAAAAT-AAAATTAT
*
110409203 AATTTAAAAAAAATAAAATTAT
1 AAATTAAAAAAAATAAAATTAT
110409225 AAATTAA
1 AAATTAA
110409232 TACATGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATTAAAAAAAATAAAATTAT
Found at i:110413508 original size:26 final size:26
Alignment explanation
Indices: 110413449--110413513 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
110413439 AGCGAGTCGT
*
110413449 ATCAGGAAGCTCACAAAGAGCCAATT
1 ATCAGGAAGCTCACAAAGAGCCAATG
* * * *
110413475 AACGGGAAGCTCACGAAGAGCCTATG
1 ATCAGGAAGCTCACAAAGAGCCAATG
110413501 ATCAGGAAGCTCA
1 ATCAGGAAGCTCA
110413514 TAAGGGCTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.14
Consensus pattern (26 bp):
ATCAGGAAGCTCACAAAGAGCCAATG
Found at i:110413609 original size:25 final size:24
Alignment explanation
Indices: 110413579--110413640 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
110413569 CGAAGAGCAT
*
110413579 TAACGGGAAGCTCGCAAGAACCATA
1 TAACGGGAAGCTCACAAGAACCA-A
* *
110413604 TAACGGGAAGCTCACAAGAGCTAA
1 TAACGGGAAGCTCACAAGAACCAA
*
110413628 TAACGGGACGCTC
1 TAACGGGAAGCTC
110413641 TTTTGAGCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.37, C:0.24, G:0.26, T:0.13
Consensus pattern (24 bp):
TAACGGGAAGCTCACAAGAACCAA
Found at i:110413635 original size:24 final size:23
Alignment explanation
Indices: 110413571--110413640 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 23
110413561 GGATGCTTCG
* *
110413571 AAGAGCATTAACGGGAAGCTCGC
1 AAGAGCAATAACGGGAAGCTCAC
*
110413594 AAGAACCATATAACGGGAAGCTCAC
1 AAG-AGCA-ATAACGGGAAGCTCAC
*
110413619 AAGAGCTAATAACGGGACGCTC
1 AAGAGC-AATAACGGGAAGCTC
110413641 TTTTGAGCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 3 0.08
24 18 0.46
25 18 0.46
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.13
Consensus pattern (23 bp):
AAGAGCAATAACGGGAAGCTCAC
Found at i:110418165 original size:31 final size:31
Alignment explanation
Indices: 110418130--110418191 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
110418120 TTTACAATTC
*
110418130 CTCAATTATTTGGATTAGATTGAAAAACAAT
1 CTCAATTATTTGGATTAGATTCAAAAACAAT
110418161 CTCAATTATTTGGATTAGATTCAAAAACAAT
1 CTCAATTATTTGGATTAGATTCAAAAACAAT
110418192 TGACACTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.35
Consensus pattern (31 bp):
CTCAATTATTTGGATTAGATTCAAAAACAAT
Done.