Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 57 of 185
Found at i:16336124 original size:15 final size:15
Alignment explanation
Indices: 16336096--16336137 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
16336086 GTTTTGTCTC
* *
16336096 TTCTATTCTGTTTCTT
1 TTCT-TTCTTTTTCTA
16336112 TTCTTTCTTTTTCTA
1 TTCTTTCTTTTTCTA
16336127 TTCTTTCTTTT
1 TTCTTTCTTTT
16336138 GTTTTATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (15 bp):
TTCTTTCTTTTTCTA
Found at i:16336161 original size:5 final size:5
Alignment explanation
Indices: 16336147--16336224 Score: 74
Period size: 5 Copynumber: 15.6 Consensus size: 5
16336137 TGTTTTATGT
16336147 ATATA TATATA ATATA ATATA ATATA ATAT- AT-TA ATAATA ATATA ATATA
1 ATATA -ATATA ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA
* *
16336197 A-A-A ACATA ATCATTA CTATA ATATA ATA
1 ATATA ATATA AT-A-TA ATATA ATATA ATA
16336225 ATATTTTTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
3 3 0.05
4 6 0.10
5 39 0.63
6 11 0.18
7 3 0.05
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:16336177 original size:24 final size:25
Alignment explanation
Indices: 16336149--16336228 Score: 87
Period size: 24 Copynumber: 3.3 Consensus size: 25
16336139 TTTTATGTAT
16336149 ATATATATAAT-ATAATATAATATA
1 ATATATATAATAATAATATAATATA
16336173 ATATAT-TAATAATAATATAATATA
1 ATATATATAATAATAATATAATATA
* * * *
16336197 A-AAACATAATCATTACTATAATATA
1 ATATATATAAT-AATAATATAATATA
16336222 ATA-ATAT
1 ATATATAT
16336229 TTTTTTAACA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
23 6 0.13
24 24 0.51
25 16 0.34
26 1 0.02
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (25 bp):
ATATATATAATAATAATATAATATA
Found at i:16336187 original size:19 final size:19
Alignment explanation
Indices: 16336147--16336196 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 19
16336137 TGTTTTATGT
16336147 ATATATATATAATATAATATA
1 ATATA-ATAT-ATATAATATA
16336168 ATATAATATAT-TAATAATA
1 ATATAATATATATAAT-ATA
16336187 ATATAATATA
1 ATATAATATA
16336197 AAAACATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.14
19 15 0.54
20 4 0.14
21 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATAATATATATAATATA
Found at i:16338127 original size:13 final size:13
Alignment explanation
Indices: 16338109--16338136 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16338099 GATAAAAGAG
16338109 CATATAGAATACC
1 CATATAGAATACC
16338122 CATATAGAATACC
1 CATATAGAATACC
16338135 CA
1 CA
16338137 GAAGAGATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (13 bp):
CATATAGAATACC
Found at i:16340704 original size:50 final size:50
Alignment explanation
Indices: 16340580--16340828 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
16340570 GATAATAACA
* * ** * *
16340580 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
16340631 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
16340681 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
16340731 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
16340786 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
16340829 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:16340758 original size:100 final size:104
Alignment explanation
Indices: 16340579--16340828 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
16340569 TGATAATAAC
**
16340579 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
16340644 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
16340681 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
16340744 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
16340786 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
16340829 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:16340944 original size:13 final size:13
Alignment explanation
Indices: 16340923--16340954 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16340913 GCTTGGATCA
*
16340923 TCATCAAATAAAT
1 TCATAAAATAAAT
16340936 TCATAAAATAAAT
1 TCATAAAATAAAT
16340949 TCATAA
1 TCATAA
16340955 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:16341202 original size:30 final size:30
Alignment explanation
Indices: 16341166--16341223 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
16341156 CCTCGACTCT
*
16341166 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
16341196 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
16341224 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:16341809 original size:15 final size:15
Alignment explanation
Indices: 16341781--16341822 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
16341771 GTTTCGTCTC
* *
16341781 TTCTATTCTGTTTCTT
1 TTCT-TTCTTTTTCTA
16341797 TTCTTTCTTTTTCTA
1 TTCTTTCTTTTTCTA
16341812 TTCTTTCTTTT
1 TTCTTTCTTTT
16341823 GTTTTATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (15 bp):
TTCTTTCTTTTTCTA
Found at i:16341844 original size:5 final size:5
Alignment explanation
Indices: 16341831--16341902 Score: 62
Period size: 5 Copynumber: 14.4 Consensus size: 5
16341821 TTGTTTTATG
16341831 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
16341879 CATAA TCATTAC TATAA TATAA TA
1 TATAA T-A-TAA TATAA TATAA TA
16341903 ATATTTTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 34 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:16341856 original size:19 final size:19
Alignment explanation
Indices: 16341832--16341874 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
16341822 TGTTTTATGT
16341832 ATATATATAAT-ATAATATA
1 ATATAT-TAATAATAATATA
16341851 ATATATTAATAATAATATA
1 ATATATTAATAATAATATA
16341870 ATATA
1 ATATA
16341875 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAATAATAATATA
Found at i:16341884 original size:24 final size:25
Alignment explanation
Indices: 16341838--16341903 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
16341828 ATGTATATAT
* *
16341838 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
16341862 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
16341887 TTACTATAATATAATAA
1 ATAATATAATATAATAA
16341904 TATTTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.06
24 18 0.51
25 13 0.37
26 2 0.06
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:16344765 original size:28 final size:28
Alignment explanation
Indices: 16344725--16344780 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
16344715 GTGGAGAAAG
16344725 AAAATTAAAGAAGATGACATCTTTTTCT
1 AAAATTAAAGAAGATGACATCTTTTTCT
16344753 AAAATTAAAGAAGATGACATCTTTTTCT
1 AAAATTAAAGAAGATGACATCTTTTTCT
16344781 TTTCTTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (28 bp):
AAAATTAAAGAAGATGACATCTTTTTCT
Found at i:16349143 original size:30 final size:29
Alignment explanation
Indices: 16349066--16349143 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 29
16349056 ACGAACACAG
16349066 GGTATGATAG-GAAAATGTAAATGATTACAA
1 GGTATGATAGTGAAAA--TAAATGATTACAA
* * *
16349096 GGTATGAAAATGCAAATAAGAGTGATTAC-A
1 GGTATGATAGTGAAAATAA-A-TGATTACAA
16349126 GGTATGATAGTGAAAATA
1 GGTATGATAGTGAAAATA
16349144 TGAATATTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 3 0.08
30 25 0.64
31 11 0.28
ACGTcount: A:0.46, C:0.04, G:0.24, T:0.26
Consensus pattern (29 bp):
GGTATGATAGTGAAAATAAATGATTACAA
Found at i:16358950 original size:34 final size:34
Alignment explanation
Indices: 16358900--16359003 Score: 86
Period size: 34 Copynumber: 3.0 Consensus size: 34
16358890 AATTATTAAT
* * * *
16358900 AAAAAATTTATT--AAATTTTATATATTTTCTAA
1 AAAAAAATTATTAAAAATTTTAAAAATTTTATAA
*
16358932 AAAAAAATTATTAAAAATTATAAAAATTTTATAA
1 AAAAAAATTATTAAAAATTTTAAAAATTTTATAA
* * *
16358966 AACAATATTGTTATAAAATTTGTAAAAACTTTTTATAA
1 AAAAAAATTATTA-AAAATTT-TAAAAA--TTTTATAA
16359004 TTTCAAAATG
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
32 11 0.19
34 26 0.46
35 6 0.11
36 6 0.11
38 8 0.14
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (34 bp):
AAAAAAATTATTAAAAATTTTAAAAATTTTATAA
Found at i:16368008 original size:18 final size:18
Alignment explanation
Indices: 16367985--16368022 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
16367975 CGCTTCCGAT
16367985 CGTTGGTCTAACAGAAGC
1 CGTTGGTCTAACAGAAGC
16368003 CGTTGGTCTAACAGAAGC
1 CGTTGGTCTAACAGAAGC
16368021 CG
1 CG
16368023 CATATCTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (18 bp):
CGTTGGTCTAACAGAAGC
Found at i:16368902 original size:15 final size:15
Alignment explanation
Indices: 16368882--16368935 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
16368872 TATATAATAT
16368882 AATATATTAAATTAA
1 AATATATTAAATTAA
*
16368897 AATATA-TCAA-TAA
1 AATATATTAAATTAA
16368910 AATAT-TTAAATTAA
1 AATATATTAAATTAA
* *
16368924 ATTACATTAAAT
1 AATATATTAAAT
16368936 ATAATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
13 11 0.34
14 9 0.28
15 12 0.38
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATATTAAATTAA
Found at i:16368902 original size:27 final size:27
Alignment explanation
Indices: 16368871--16368924 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
16368861 CCGCCTATAT
*
16368871 ATATAT-AATATAATATATTAAATTAAA
1 ATATATCAATAAAATAT-TTAAATTAAA
16368898 ATATATCAATAAAATATTTAAATTAAA
1 ATATATCAATAAAATATTTAAATTAAA
16368925 TTACATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
ATATATCAATAAAATATTTAAATTAAA
Found at i:16368936 original size:28 final size:28
Alignment explanation
Indices: 16368877--16368941 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
16368867 ATATATATAT
* *
16368877 AATATAATATATTAAATTAAAATATATC
1 AATATAATATATTAAATTAAAATACATA
* *
16368905 AATAAAATAT-TTAAATTAAATTACATTA
1 AATATAATATATTAAATTAAAATACA-TA
16368933 AATATAATA
1 AATATAATA
16368942 AAAAAATTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (28 bp):
AATATAATATATTAAATTAAAATACATA
Found at i:16372864 original size:42 final size:43
Alignment explanation
Indices: 16372801--16372897 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 43
16372791 TGAGATTTAT
* * * *
16372801 GTGTAAGACCATGTCTGGGACATTGGCGTC-GTATATGATTAC
1 GTGTAAGACCATATCTAGGACAGTGGCATCAGTATATGATTAC
* * *
16372843 GTGTAAGACCCTATCTAGGACAGTGGCATCATTATTTGATTAC
1 GTGTAAGACCATATCTAGGACAGTGGCATCAGTATATGATTAC
*
16372886 ATGTAAGACCAT
1 GTGTAAGACCAT
16372898 GTCTGGGATG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 25 0.56
43 20 0.44
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (43 bp):
GTGTAAGACCATATCTAGGACAGTGGCATCAGTATATGATTAC
Found at i:16372913 original size:43 final size:43
Alignment explanation
Indices: 16372756--16372914 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 43
16372746 AATGTGACAT
* *
16372756 CGTGTAAGACCACGTCTGGGACGTTGGCCTCGATT-TGA-GATTTA
1 CGTGTAAGACCATGTCTGGGACGTTGGCATC-ATTAT-ATGA-TTA
* * * *
16372800 TGTGTAAGACCATGTCTGGGACATTGGCGTC-GTATATGATTA
1 CGTGTAAGACCATGTCTGGGACGTTGGCATCATTATATGATTA
* * * *
16372842 CGTGTAAGACCCTATCTAGGACAG-TGGCATCATTATTTGATTA
1 CGTGTAAGACCATGTCTGGGAC-GTTGGCATCATTATATGATTA
* *
16372885 CATGTAAGACCATGTCTGGGATGTTGGCAT
1 CGTGTAAGACCATGTCTGGGACGTTGGCAT
16372915 TGTACGAGCT
Statistics
Matches: 92, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
42 30 0.33
43 35 0.38
44 27 0.29
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACGTTGGCATCATTATATGATTA
Found at i:16373850 original size:13 final size:13
Alignment explanation
Indices: 16373832--16373859 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16373822 TATTTATTAG
16373832 TGATAATTAGTTA
1 TGATAATTAGTTA
16373845 TGATAATTAGTTA
1 TGATAATTAGTTA
16373858 TG
1 TG
16373860 TCTAGCCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (13 bp):
TGATAATTAGTTA
Found at i:16374792 original size:16 final size:16
Alignment explanation
Indices: 16374773--16374803 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16374763 AGAATTGCAA
16374773 AACAAAGAAGCAGCAG
1 AACAAAGAAGCAGCAG
16374789 AACAAAGAAGCAGCA
1 AACAAAGAAGCAGCA
16374804 AATATGGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.19, G:0.23, T:0.00
Consensus pattern (16 bp):
AACAAAGAAGCAGCAG
Found at i:16377292 original size:7 final size:7
Alignment explanation
Indices: 16377276--16377314 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
16377266 TTGAGTAATA
*
16377276 CATCATT
1 CATCAGT
16377283 CATCAGT
1 CATCAGT
16377290 CATCAGT
1 CATCAGT
16377297 CATCAGT
1 CATCAGT
16377304 CATCAG-
1 CATCAGT
16377310 CATCA
1 CATCA
16377315 ATCCATTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.28
Consensus pattern (7 bp):
CATCAGT
Found at i:16377515 original size:59 final size:59
Alignment explanation
Indices: 16377443--16377561 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
16377433 TCCTATGTGA
16377443 CTGTGTCGGACTGTCGGTATTCAATTGGCCATTGCACCTACTTGCTACCCATGGTGCCT
1 CTGTGTCGGACTGTCGGTATTCAATTGGCCATTGCACCTACTTGCTACCCATGGTGCCT
16377502 CTGTGTCGGACTGTCGGTATTCAATTGGCCATTGCACCTACTTGCTACCCATGGTGCCT
1 CTGTGTCGGACTGTCGGTATTCAATTGGCCATTGCACCTACTTGCTACCCATGGTGCCT
16377561 C
1 C
16377562 CTATCTGCGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.15, C:0.29, G:0.24, T:0.32
Consensus pattern (59 bp):
CTGTGTCGGACTGTCGGTATTCAATTGGCCATTGCACCTACTTGCTACCCATGGTGCCT
Found at i:16381824 original size:6 final size:6
Alignment explanation
Indices: 16381813--16381840 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
16381803 ACCATGAAAT
16381813 TCATTA TCATTA TCATTA TCATTA TCAT
1 TCATTA TCATTA TCATTA TCATTA TCAT
16381841 GGGCATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (6 bp):
TCATTA
Found at i:16384171 original size:14 final size:14
Alignment explanation
Indices: 16384142--16384170 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16384132 CCTCGTTTCA
16384142 TTATTTTTTTACTT
1 TTATTTTTTTACTT
16384156 TTATTTTTTTA-TT
1 TTATTTTTTTACTT
16384169 TT
1 TT
16384171 TTATACGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (14 bp):
TTATTTTTTTACTT
Found at i:16388963 original size:31 final size:32
Alignment explanation
Indices: 16388897--16388976 Score: 94
Period size: 31 Copynumber: 2.5 Consensus size: 32
16388887 CTAACTAACC
* * *
16388897 TAAAATATCCC-TATTAATTTTTTTATATTATT
1 TAAAATA-CCCTTATTAATTTATTTATACTACT
16388929 TAAAATACCCTTATTAA-TTATTTATACTACT
1 TAAAATACCCTTATTAATTTATTTATACTACT
16388960 TAAAATA-CCTCTATTAA
1 TAAAATACCCT-TATTAA
16388977 CTCTTAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 3 0.07
31 27 0.63
32 13 0.30
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (32 bp):
TAAAATACCCTTATTAATTTATTTATACTACT
Found at i:16397210 original size:31 final size:31
Alignment explanation
Indices: 16397172--16397231 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
16397162 CCGCCTCAAA
16397172 GACCTCTGAACCTTTAATATTTTCCTTGTGT
1 GACCTCTGAACCTTTAATATTTTCCTTGTGT
16397203 GACCTCTGAACCTTTAATATTTTCCTTGT
1 GACCTCTGAACCTTTAATATTTTCCTTGT
16397232 CAATATGATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (31 bp):
GACCTCTGAACCTTTAATATTTTCCTTGTGT
Found at i:16400620 original size:25 final size:26
Alignment explanation
Indices: 16400592--16400666 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 26
16400582 ATGAGCGTCT
*
16400592 CGATATATGGCTCTTTAGAACTTC-C
1 CGATATATGGCTCTCTAGAACTTCTC
*
16400617 CGAT-TAATGGCTCTCTAGAGCTTCTC
1 CGATAT-ATGGCTCTCTAGAACTTCTC
*
16400643 C-ATAT-TGGCT-TGCTTGAACTTCTC
1 CGATATATGGCTCT-CTAGAACTTCTC
16400667 AATTACGGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
23 1 0.02
24 16 0.38
25 22 0.52
26 3 0.07
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.37
Consensus pattern (26 bp):
CGATATATGGCTCTCTAGAACTTCTC
Found at i:16400687 original size:48 final size:50
Alignment explanation
Indices: 16400576--16400688 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 50
16400566 ACACACCACA
* * * *
16400576 GCTCTTATGAGCGTCTCGATATATGGCTCTTTAGAACTTCCCGATTAATG
1 GCTCTTATGAGCTTCTCCATATATGGCTCTTTAGAACTTCCCAATTAACG
*
16400626 GCTCTCTA-GAGCTTCTCCATAT-TGGCT-TGCTT-GAACTTCTCAATT-ACG
1 GCTCT-TATGAGCTTCTCCATATATGGCTCT--TTAGAACTTCCCAATTAACG
16400674 GCTCTTATGAGCTTC
1 GCTCTTATGAGCTTC
16400689 CCGTTATACA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
47 2 0.04
48 15 0.28
49 16 0.30
50 19 0.35
51 2 0.04
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (50 bp):
GCTCTTATGAGCTTCTCCATATATGGCTCTTTAGAACTTCCCAATTAACG
Found at i:16406370 original size:9 final size:9
Alignment explanation
Indices: 16406347--16406442 Score: 84
Period size: 9 Copynumber: 10.2 Consensus size: 9
16406337 TTAATTAATT
16406347 TTAATTTTAA
1 TTAA-TTTAA
*
16406357 TTAATTTGA
1 TTAATTTAA
16406366 TTAATTTAA
1 TTAATTTAA
* * *
16406375 TTTTACTTGA
1 -TTAATTTAA
16406385 TTAATTTAA
1 TTAATTTAA
*
16406394 TTAATTTGA
1 TTAATTTAA
*
16406403 TTAAATTAAA
1 TT-AATTTAA
*
16406413 TTAAATTAAA
1 TT-AATTTAA
*
16406423 TTAATTTGA
1 TTAATTTAA
16406432 TTAATTTAA
1 TTAATTTAA
16406441 TT
1 TT
16406443 TTACTTGATC
Statistics
Matches: 70, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
9 43 0.61
10 27 0.39
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (9 bp):
TTAATTTAA
Found at i:16406376 original size:5 final size:5
Alignment explanation
Indices: 16406337--16406443 Score: 57
Period size: 5 Copynumber: 22.4 Consensus size: 5
16406327 ATTGTTTGAC
* * * *
16406337 TTAA- TTAATT TTAATT TTAA- TTAAT TTGA- TTAAT TTAAT TTTAC TTGA-
1 TTAAT TTAA-T TTAA-T TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT
* * * * * *
16406385 TTAAT TTAA- TTAAT TTGA- TTAAA TTAAA TTAAA TTAAA TTAAT TTGA-
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT
16406432 TTAAT TTAAT TT
1 TTAAT TTAAT TT
16406444 TACTTGATCA
Statistics
Matches: 84, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
4 24 0.29
5 50 0.60
6 10 0.12
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (5 bp):
TTAAT
Found at i:16406440 original size:19 final size:18
Alignment explanation
Indices: 16406347--16406438 Score: 94
Period size: 19 Copynumber: 4.9 Consensus size: 18
16406337 TTAATTAATT
16406347 TTAATTTTAATTAATTTGA
1 TTAA-TTTAATTAATTTGA
* *
16406366 TTAATTTAATTTTACTTGA
1 TTAATTTAA-TTAATTTGA
16406385 TTAATTTAATTAATTTGA
1 TTAATTTAATTAATTTGA
* **
16406403 TTAAATTAAATTAAATTAAA
1 TT-AATTTAATT-AATTTGA
*
16406423 TTAATTTGATTAATTT
1 TTAATTTAATTAATTT
16406439 AATTTTACTT
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
18 18 0.30
19 35 0.58
20 7 0.12
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (18 bp):
TTAATTTAATTAATTTGA
Found at i:16409625 original size:29 final size:31
Alignment explanation
Indices: 16409569--16409635 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
16409559 ACCCTTAAAA
** * *
16409569 TATTTACACTATTGGTCCTTCAACTTTT-CG
1 TATTTACACTATTGACCCTTCAAATTTTGAG
16409599 TATTTACACT-TTGACCCTTCAAATTTTGAG
1 TATTTACACTATTGACCCTTCAAATTTTGAG
16409629 TATTTAC
1 TATTTAC
16409636 TCTTGGGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.46
Consensus pattern (31 bp):
TATTTACACTATTGACCCTTCAAATTTTGAG
Found at i:16411542 original size:31 final size:31
Alignment explanation
Indices: 16411504--16411566 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
16411494 GCACGGGTGC
16411504 TAGACTATATCTAACTAAATTTTGTTGATTA
1 TAGACTATATCTAACTAAATTTTGTTGATTA
16411535 TAGACTATATCTAACTAAATTTTGTTGATTA
1 TAGACTATATCTAACTAAATTTTGTTGATTA
16411566 T
1 T
16411567 CTGTATGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (31 bp):
TAGACTATATCTAACTAAATTTTGTTGATTA
Found at i:16418865 original size:36 final size:36
Alignment explanation
Indices: 16418820--16418895 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
16418810 TTTAGGGTCA
* * *
16418820 GTTTTAGGTGTAAGGGAGGAAAGTTCTAGATTTTAG
1 GTTTGAGGTGTAAGGGAGGAAACTTCTAGATTCTAG
16418856 GTTTGAGGTGTAAGGGAGGAAACTTCTAGATTCTAG
1 GTTTGAGGTGTAAGGGAGGAAACTTCTAGATTCTAG
16418892 GTTT
1 GTTT
16418896 CCTGTTAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.26, C:0.05, G:0.33, T:0.36
Consensus pattern (36 bp):
GTTTGAGGTGTAAGGGAGGAAACTTCTAGATTCTAG
Found at i:16434609 original size:18 final size:18
Alignment explanation
Indices: 16434586--16434622 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
16434576 CATAAATCCG
16434586 ACCTGTCCTAGATTAGCA
1 ACCTGTCCTAGATTAGCA
16434604 ACCTGTCCTAGATTAGCA
1 ACCTGTCCTAGATTAGCA
16434622 A
1 A
16434623 GAAAATTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (18 bp):
ACCTGTCCTAGATTAGCA
Found at i:16435539 original size:72 final size:71
Alignment explanation
Indices: 16435416--16435562 Score: 249
Period size: 72 Copynumber: 2.1 Consensus size: 71
16435406 CACTTTTTTG
* *
16435416 CTTTAGTTATTATTGTGATTATATCTGCTAATTGGGGTAAGTAAAGTTCAAACTTTGTAATATTC
1 CTTTAGTTATTATTGTGATTATATCTGCTAATTGGGGTAAGTAAAGGTCAAACCTTGTAATATTC
*
16435481 CACGAC
66 CACAAC
*
16435487 CTTTATGTTATTATTGTGATTATATCTGCTATTTGGGGTAAGTAAAGGTCAAACCTTGTAATATT
1 CTTTA-GTTATTATTGTGATTATATCTGCTAATTGGGGTAAGTAAAGGTCAAACCTTGTAATATT
16435552 CCACAAC
65 CCACAAC
16435559 CTTT
1 CTTT
16435563 TTGCATTGGT
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
71 5 0.07
72 66 0.93
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (71 bp):
CTTTAGTTATTATTGTGATTATATCTGCTAATTGGGGTAAGTAAAGGTCAAACCTTGTAATATTC
CACAAC
Found at i:16439288 original size:13 final size:13
Alignment explanation
Indices: 16439270--16439294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16439260 TATTTTAATA
16439270 TTATTTTGTGTGT
1 TTATTTTGTGTGT
16439283 TTATTTTGTGTG
1 TTATTTTGTGTG
16439295 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:16441187 original size:41 final size:41
Alignment explanation
Indices: 16441138--16441241 Score: 156
Period size: 41 Copynumber: 2.5 Consensus size: 41
16441128 GACTATAAGT
*
16441138 CTAGCAGGCTAAGTGCCGGTGAT-CGAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATACG-AATCAGGCTATAAAC
* * *
16441179 CTAGCAGGCTACGTGCCGGTGATATGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATACGAATCAGGCTATAAAC
16441220 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
16441242 ATATGTTAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 56 0.98
42 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATACGAATCAGGCTATAAAC
Found at i:16449589 original size:55 final size:55
Alignment explanation
Indices: 16449505--16449615 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
16449495 TCTCCGTGAA
16449505 CTTACTCGTAACCTCTCAAAATTTTTATGTGCTAAAAAATACCTAATGGATGTTC
1 CTTACTCGTAACCTCTCAAAATTTTTATGTGCTAAAAAATACCTAATGGATGTTC
16449560 CTTACTCGTAACCTCTCAAAATTTTTATGTGCTAAAAAATACCTAATGGATGTTC
1 CTTACTCGTAACCTCTCAAAATTTTTATGTGCTAAAAAATACCTAATGGATGTTC
16449615 C
1 C
16449616 GATTACTTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (55 bp):
CTTACTCGTAACCTCTCAAAATTTTTATGTGCTAAAAAATACCTAATGGATGTTC
Found at i:16459145 original size:44 final size:43
Alignment explanation
Indices: 16459097--16459381 Score: 140
Period size: 44 Copynumber: 6.6 Consensus size: 43
16459087 TCTTGTGTCT
*
16459097 GCTCCACTGCAACTTCAGGGAGATAAGATCTGACGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGAC-TTTCAATCC
* * * * * * *
16459141 GCTCCACCGCAACTT-TGGGGGATAGGATTATCGGC-TTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TCT-GACTTTCAATCC
* * * * * *
16459184 GTTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTG
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGAC-T-TTCAATC-C
* * * *
16459230 GC-CCACTGCAAC-TCAGGG-GAATAAGACCTG-CTTACTTAGTCT
1 GCTCCACTGCAACTTCAGGGAG-ATAAGATCTGACTT--TCAATCC
** * * *
16459272 GCTCTGCTGCAACTACAGGGAGATAAGA-CTTGA--TGCGATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATC-TGACTTTCAATCC
* * *
16459313 ACTCTACTGCAACTTCAGTGAGATAAGATCTGTTACTTT-AATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTG--ACTTTCAATCC
* *
16459357 GTTCCACTACAACTTCAGGGAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
16459382 GGATTATCGG
Statistics
Matches: 177, Mismatches: 44, Indels: 40
0.68 0.17 0.15
Matches are distributed among these distances:
41 29 0.16
42 6 0.03
43 45 0.25
44 76 0.43
45 20 0.11
46 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATCTGACTTTCAATCC
Found at i:16459155 original size:88 final size:87
Alignment explanation
Indices: 16459018--16459212 Score: 189
Period size: 87 Copynumber: 2.2 Consensus size: 87
16459008 TACTCTGCTA
* * * * * * *
16459018 CAACTTCAGAGAGATGAGACCTATCATTTTGATCCGCTCCGCTGTAACTTCAGGGAGATAGGATT
1 CAACTTCAGGGAGATAAGATCTATCATTTTAATCCGCTCCACCGCAACTT-AGGGAGATAGGATT
* ***
16459083 -T-GTTTCTTGTGTCTGCTCCACTG
65 ATCG--GCTTCAATCTGCTCCACTG
* * *
16459106 CAACTTCAGGGAGATAAGATCTGA-CGTTTTAATCCGCTCCACCGCAACTTTGGGGGATAGGATT
1 CAACTTCAGGGAGATAAGATCT-ATCATTTTAATCCGCTCCACCGCAACTTAGGGAGATAGGATT
*
16459170 ATCGGCTTCAATCTGTTCCACTG
65 ATCGGCTTCAATCTGCTCCACTG
*
16459193 CAACCTCAGGGAGATAAGAT
1 CAACTTCAGGGAGATAAGAT
16459213 TTGCCATCTT
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
87 45 0.51
88 41 0.47
89 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (87 bp):
CAACTTCAGGGAGATAAGATCTATCATTTTAATCCGCTCCACCGCAACTTAGGGAGATAGGATTA
TCGGCTTCAATCTGCTCCACTG
Found at i:16460560 original size:22 final size:23
Alignment explanation
Indices: 16460524--16460566 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
16460514 TTAGCCTCTC
*
16460524 CATTTTTACTCTTTCATTTTTTT
1 CATTTTTAATCTTTCATTTTTTT
16460547 CATTTTTAAT-TTTCATTTTT
1 CATTTTTAATCTTTCATTTTT
16460567 CATCATCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (23 bp):
CATTTTTAATCTTTCATTTTTTT
Found at i:16460572 original size:23 final size:23
Alignment explanation
Indices: 16460524--16460572 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
16460514 TTAGCCTCTC
* *
16460524 CATTTTTACTCTTTCATTTTTTT
1 CATTTTTAATCTTTCATTTTTAT
16460547 CATTTTTAAT-TTTCATTTTTCAT
1 CATTTTTAATCTTTCATTTTT-AT
16460570 CAT
1 CAT
16460573 CCTCCTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.65
Consensus pattern (23 bp):
CATTTTTAATCTTTCATTTTTAT
Found at i:16473134 original size:15 final size:15
Alignment explanation
Indices: 16473114--16473142 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16473104 TTTGATGCCG
16473114 GGTGGTTTCCATCCT
1 GGTGGTTTCCATCCT
16473129 GGTGGTTTCCATCC
1 GGTGGTTTCCATCC
16473143 GTTTTGGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.28, G:0.28, T:0.38
Consensus pattern (15 bp):
GGTGGTTTCCATCCT
Found at i:16475677 original size:17 final size:19
Alignment explanation
Indices: 16475641--16475683 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
16475631 AATATTTAAA
16475641 AATAAAGAGAGATGGAGAG
1 AATAAAGAGAGATGGAGAG
16475660 AATAAAGAGAGATGGAGAG
1 AATAAAGAGAGATGGAGAG
16475679 AATAA
1 AATAA
16475684 TATTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.33, T:0.12
Consensus pattern (19 bp):
AATAAAGAGAGATGGAGAG
Found at i:16475753 original size:11 final size:10
Alignment explanation
Indices: 16475691--16475725 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
16475681 TAATATTTAA
16475691 AAAAATGTTT
1 AAAAATGTTT
16475701 AAAAATGTTAT
1 AAAAATGTT-T
16475712 AAAAA-GTTT
1 AAAAATGTTT
16475721 AAAAA
1 AAAAA
16475726 AAGAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 6 0.25
10 12 0.50
11 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (10 bp):
AAAAATGTTT
Found at i:16480524 original size:2 final size:2
Alignment explanation
Indices: 16480517--16480559 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
16480507 CAAAAGTCAC
16480517 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
16480559 C
1 C
16480560 TCTCTCTCTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:16480564 original size:2 final size:2
Alignment explanation
Indices: 16480559--16480613 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
16480549 CACACACACA
16480559 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
16480601 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
16480614 CCTATATATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:16490150 original size:6 final size:6
Alignment explanation
Indices: 16490141--16490171 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
16490131 AACGAAATAC
16490141 ATGAAA ATGAAA ATGAAA ATGAAA ATGAAA A
1 ATGAAA ATGAAA ATGAAA ATGAAA ATGAAA A
16490172 ATAAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
ATGAAA
Found at i:16490177 original size:12 final size:13
Alignment explanation
Indices: 16490144--16490192 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
16490134 GAAATACATG
*
16490144 AAAATGAAAATG-
1 AAAATAAAAATGA
*
16490156 AAAATGAAAATGA
1 AAAATAAAAATGA
*
16490169 AAAATAAAAAATAA
1 AAAAT-AAAAATGA
16490183 AAAATAAAAA
1 AAAATAAAAA
16490193 ATTATTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 12 0.36
13 10 0.30
14 11 0.33
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (13 bp):
AAAATAAAAATGA
Found at i:16490178 original size:7 final size:7
Alignment explanation
Indices: 16490162--16490194 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
16490152 AATGAAAATG
*
16490162 AAAATGA
1 AAAATAA
16490169 AAAATAA
1 AAAATAA
16490176 AAAATAA
1 AAAATAA
16490183 AAAATAA
1 AAAATAA
16490190 AAAAT
1 AAAAT
16490195 TATTTTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:16491227 original size:5 final size:6
Alignment explanation
Indices: 16491198--16491241 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
16491188 CCATCCCCCT
*
16491198 TTTCCC TTTCCC TTTCCC TTTCCC TTCCCTC TTTCTCC TTTCCC
1 TTTCCC TTTCCC TTTCCC TTTCCC TTTCC-C TTTC-CC TTTCCC
16491242 CTTCTTTGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 24 0.71
7 9 0.26
8 1 0.03
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCCC
Found at i:16492846 original size:56 final size:56
Alignment explanation
Indices: 16492780--16492892 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
16492770 AATTATATTA
16492780 CATATGTTGTGTTTTGCTACATGGTTCTTTTTCTAGTTAGACATTCATGTTAAAAT
1 CATATGTTGTGTTTTGCTACATGGTTCTTTTTCTAGTTAGACATTCATGTTAAAAT
*
16492836 CATATGTTGTGTTTTGCTACTTGGTTCTTTTTCTAGTTAGACATTCATGTTAAAAT
1 CATATGTTGTGTTTTGCTACATGGTTCTTTTTCTAGTTAGACATTCATGTTAAAAT
16492892 C
1 C
16492893 TTTACTTATT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.49
Consensus pattern (56 bp):
CATATGTTGTGTTTTGCTACATGGTTCTTTTTCTAGTTAGACATTCATGTTAAAAT
Found at i:16493527 original size:32 final size:34
Alignment explanation
Indices: 16493491--16493562 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
16493481 AGTTTTTATT
* *
16493491 AAATATTTTTA-AGAAATTTG-CCAAACAATAGA
1 AAATATTTTTACACAAATTTGTCCAAACAACAGA
*
16493523 AAATA-TTTTACACAAATTTGTCCAAACACCAGA
1 AAATATTTTTACACAAATTTGTCCAAACAACAGA
16493556 AAATATT
1 AAATATT
16493563 AACTTTTCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 5 0.15
32 13 0.38
33 15 0.44
34 1 0.03
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.31
Consensus pattern (34 bp):
AAATATTTTTACACAAATTTGTCCAAACAACAGA
Found at i:16496981 original size:17 final size:17
Alignment explanation
Indices: 16496959--16496991 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16496949 AAACCGAGAA
16496959 AAGAAA-AAGAAAAAACC
1 AAGAAAGAA-AAAAAACC
16496976 AAGAAAGAAAAAAAAC
1 AAGAAAGAAAAAAAAC
16496992 TGCAAATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (17 bp):
AAGAAAGAAAAAAAACC
Found at i:16497894 original size:50 final size:50
Alignment explanation
Indices: 16497819--16498001 Score: 197
Period size: 50 Copynumber: 3.7 Consensus size: 50
16497809 TATAACTTTT
* * *
16497819 GGAAAGTAAGATTCGCCATTGTGGCTTTAACCTTTTTAACTGCAATGTCA
1 GGAAAGCAAGATTCACCATTGTGGCTTTAATCTTTTTAACTGCAATGTCA
* * * * ** * *
16497869 GGAAAGCATGATTCGCTATTGTGGCTTTAATCTGTTCCACTGCACTGCCTA
1 GGAAAGCAAGATTCACCATTGTGGCTTTAATCTTTTTAACTGCAATGTC-A
* ** * *
16497920 GG-AAGTAAGATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCG
1 GGAAAGCAAGATTCACCATTGTGGCTTTAATCTTTTTAACTGCAATGTCA
*
16497969 GGAAAGCAAGATTCACCGTTGTGGCTTTAATCT
1 GGAAAGCAAGATTCACCATTGTGGCTTTAATCT
16498002 GTTCCACTAC
Statistics
Matches: 108, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
49 2 0.02
50 103 0.95
51 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (50 bp):
GGAAAGCAAGATTCACCATTGTGGCTTTAATCTTTTTAACTGCAATGTCA
Found at i:16497995 original size:100 final size:100
Alignment explanation
Indices: 16497822--16498031 Score: 294
Period size: 100 Copynumber: 2.1 Consensus size: 100
16497812 AACTTTTGGA
* * * * *
16497822 AAGTAAGATTCGCCATTGTGGCTTTAACCTTTTTAACTGCAATGTCAGGAAAGCATGATTCGCTA
1 AAGTAAGATTCACCATTGTAGCTTTAACCTTTTTAACTGCAATGTCAGGAAAGCAAGATTCACCA
*
16497887 TTGTGGCTTTAATCTGTTCCACTGCACTGCCTAGG
66 TTGTGGCTTTAATCTGTTCCACTACACTGCCTAGG
** * * *
16497922 AAGTAAGATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGAAAGCAAGATTCACCG
1 AAGTAAGATTCACCATTGTAGCTTTAACCTTTTTAACTGCAATGTCAGGAAAGCAAGATTCACCA
* *
16497987 TTGTGGCTTTAATCTGTTCCACTACACTGCTTGGG
66 TTGTGGCTTTAATCTGTTCCACTACACTGCCTAGG
16498022 AAGATAAGAT
1 AAG-TAAGAT
16498032 CTGTAATTCT
Statistics
Matches: 96, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
100 90 0.94
101 6 0.06
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (100 bp):
AAGTAAGATTCACCATTGTAGCTTTAACCTTTTTAACTGCAATGTCAGGAAAGCAAGATTCACCA
TTGTGGCTTTAATCTGTTCCACTACACTGCCTAGG
Found at i:16498416 original size:219 final size:219
Alignment explanation
Indices: 16498023--16498426 Score: 673
Period size: 219 Copynumber: 1.8 Consensus size: 219
16498013 CTGCTTGGGA
* **
16498023 AGATAAGATCTGTAATTCTTCGCTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGAT
1 AGATAAGATCTGAAATTCTTCAATCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGAT
* * * *
16498088 CTACTCTACTGTAACTTCAGAGAGATTAGATCCTTTATTTTAATCCGCTCTACTGTAATCTCAGG
66 ATACTCTACTATAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCTACTGTAATCTCAGG
* * * *
16498153 GAAATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTCACCATTTTC
131 GAAATAGGACTACTAGCTTCAATATGCTCCACTGTAACCTCAGGGAGATAAGATTCACCATTTTC
16498218 GATTAGCTCCACTACTTCTTAGGG
196 GATTAGCTCCACTACTTCTTAGGG
*
16498242 AGATAAGATCTGAAATTCTTCAATCTATTCCACTGTAATCTTAGGGAGATAAGACCTGATGCGAT
1 AGATAAGATCTGAAATTCTTCAATCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGAT
*
16498307 ATACTCTACTATAATTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCTACTGTAATCTCAGG
66 ATACTCTACTATAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCTACTGTAATCTCAGG
* *
16498372 GAAATAGGACTACTGGCTTCGATATGCTCCACTGTAACCTCAGGGAGATAAGATT
131 GAAATAGGACTACTAGCTTCAATATGCTCCACTGTAACCTCAGGGAGATAAGATT
16498427 TAAAACCTTC
Statistics
Matches: 170, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
219 170 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (219 bp):
AGATAAGATCTGAAATTCTTCAATCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGAT
ATACTCTACTATAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCTACTGTAATCTCAGG
GAAATAGGACTACTAGCTTCAATATGCTCCACTGTAACCTCAGGGAGATAAGATTCACCATTTTC
GATTAGCTCCACTACTTCTTAGGG
Found at i:16498629 original size:129 final size:129
Alignment explanation
Indices: 16498440--16498691 Score: 441
Period size: 129 Copynumber: 2.0 Consensus size: 129
16498430 AACCTTCAAT
* *
16498440 CTATTCCACTGTTGACCAGTGATATAGGACTTATGGCTTAAATCTGCTTCCTTACACTTGAAGAT
1 CTATTCCACTGCTGACCAGGGATATAGGACTTATGGCTTAAATCTGCTTCCTTACACTTGAAGAT
*
16498505 AAGATTTGCCGTCTTCAATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAAC
66 AAGATTTGCCGTCTTCAATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAAC
* * *
16498569 CTATTCCACTGCTGATCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGAT
1 CTATTCCACTGCTGACCAGGGATATAGGACTTATGGCTTAAATCTGCTTCCTTACACTTGAAGAT
*
16498634 AAGATTTGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT
66 AAGATTTGCCGTCTTCAATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT
16498692 TCCAGATCTG
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 116 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (129 bp):
CTATTCCACTGCTGACCAGGGATATAGGACTTATGGCTTAAATCTGCTTCCTTACACTTGAAGAT
AAGATTTGCCGTCTTCAATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAAC
Found at i:16499924 original size:7 final size:7
Alignment explanation
Indices: 16499910--16499953 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
16499900 AGCCTCTCCA
16499910 TCATTTT
1 TCATTTT
*
16499917 TTATTTT
1 TCATTTT
16499924 TCATTTT
1 TCATTTT
16499931 CTC-TTTT
1 -TCATTTT
16499938 TCATTTT
1 TCATTTT
16499945 TCACTTTT
1 TCA-TTTT
16499953 T
1 T
16499954 TGACTCGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 2 0.06
7 23 0.72
8 7 0.22
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (7 bp):
TCATTTT
Found at i:16500816 original size:9 final size:9
Alignment explanation
Indices: 16500802--16500847 Score: 51
Period size: 8 Copynumber: 5.2 Consensus size: 9
16500792 TCCCCTTTTC
16500802 TTTTTCCTT
1 TTTTTCCTT
16500811 TTTTTCC-T
1 TTTTTCCTT
16500819 TTTTTCC-T
1 TTTTTCCTT
*
16500827 TCTTTCTCTT
1 TTTTTC-CTT
*
16500837 TTTTTCATT
1 TTTTTCCTT
16500846 TT
1 TT
16500848 CATTTTGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 14 0.44
9 12 0.38
10 6 0.19
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTCCTT
Found at i:16500824 original size:17 final size:17
Alignment explanation
Indices: 16500802--16500847 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
16500792 TCCCCTTTTC
*
16500802 TTTTTCCTTTTTTTCCT
1 TTTTTCCTTTTTCTCCT
*
16500819 TTTTTCCTTCTTTCTCTT
1 TTTTTCCTT-TTTCTCCT
*
16500837 TTTTTCATTTT
1 TTTTTCCTTTT
16500848 CATTTTGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCCTTTTTCTCCT
Found at i:16500918 original size:17 final size:18
Alignment explanation
Indices: 16500886--16500919 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16500876 TTTCTTCTTC
*
16500886 TTTGTTTTTGTTTTTGAT
1 TTTGCTTTTGTTTTTGAT
16500904 TTTGCTTTT-TTTTTGA
1 TTTGCTTTTGTTTTTGA
16500920 ATTGAATTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.06, C:0.03, G:0.15, T:0.76
Consensus pattern (18 bp):
TTTGCTTTTGTTTTTGAT
Found at i:16509207 original size:18 final size:17
Alignment explanation
Indices: 16509174--16509212 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
16509164 TTTTATAAAT
16509174 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
16509192 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
16509209 TGTG
1 TGTG
16509213 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:16509465 original size:23 final size:23
Alignment explanation
Indices: 16509438--16509536 Score: 155
Period size: 23 Copynumber: 4.3 Consensus size: 23
16509428 AATGTTATTG
*
16509438 ATCAGTGGCAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
16509461 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16509484 ATCAGTGGTAGCTAT-GGCTACAT
1 ATCAGTGGTAGCT-TCGGCTACAT
*
16509507 ATCAATGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16509530 ATCAGTG
1 ATCAGTG
16509537 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
22 1 0.01
23 67 0.97
24 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:16516833 original size:23 final size:23
Alignment explanation
Indices: 16516807--16516879 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
16516797 AGTGTTATTG
16516807 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
16516830 ATCAGTGGTAGCTACAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16516853 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16516876 ATCA
1 ATCA
16516880 ATGTGGCACT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:16538318 original size:19 final size:20
Alignment explanation
Indices: 16538277--16538318 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
16538267 ATTTCTATGT
* *
16538277 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
16538297 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
16538316 CAT
1 CAT
16538319 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:16549664 original size:216 final size:216
Alignment explanation
Indices: 16549290--16550095 Score: 1251
Period size: 216 Copynumber: 3.7 Consensus size: 216
16549280 TCGGTAGCCA
* * *
16549290 GCAAATCTTATCTCCCTGAAGTTGCAGTGGGGCAGATTGGAGCCGATAATCCTATCTCTCTGAAG
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCTCCCTGAAG
*
16549355 TTGCAGTGGAGTGGATTAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCT
66 TTGCAGTGGAGCGGATTAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCT
* *
16549420 AGTCTTATCTCCCTGAATTTGCAGTGGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGTTG
131 AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGTTG
16549485 CAGTGAGGCAGACTGAAGATG
196 CAGTGAGGCAGACTGAAGATG
* *
16549506 GCAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGGAGCCGATAATCCTATCTCCCTGAAG
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCTCCCTGAAG
* *
16549571 TTGCAGTGGAGTGGATTAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
66 TTGCAGTGGAGCGGATTAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCT
16549636 AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGTTG
131 AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGTTG
16549701 CAGTGAGGCAGACTGAAGATG
196 CAGTGAGGCAGACTGAAGATG
* *
16549722 GCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAAATTAGAGCCGATAATCCTATCTCCCTGAAG
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCTCCCTGAAG
* * *
16549787 TTGCAGTGGAGCGGATTAAAAC-CTTGGATCTTATCTCTCTAAAGTTACAGAGAGCAGATCGCAT
66 TTGCAGTGGAGCGGATTAAATCAC--AGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCAT
* * * * * * * *
16549851 TTGGTATTATCTCCTTAAAGTTGCAGTGAAGCAGACTAAGTAAGCAAGTCTTATCTTTCTGAAGT
129 CTAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGT
16549916 TGCAGTGAGGCAGACTGAAGATG
194 TGCAGTGAGGCAGACTGAAGATG
* * * *
16549939 GCAAATCTTATCTCCCTGAAGTTGTAGTGGCGCAGGTTAAAGCCGATAATCCTATCTCCCTGAAG
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCTCCCTGAAG
*** *
16550004 TTGCAGTGGAGCGGATTAAAATCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCA--
66 TTGCAGTGGAGCGGATT-AAATCACAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATC
* * *
16550067 -AGTCTTATCACCCTGAAGTTGCAGAGGAG
130 TAGTCTTATCTCCCTAAAGTTGCAGTGGAG
16550096 TAGATTGAAG
Statistics
Matches: 546, Mismatches: 40, Indels: 10
0.92 0.07 0.02
Matches are distributed among these distances:
214 22 0.04
215 1 0.00
216 291 0.53
217 228 0.42
218 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (216 bp):
GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCTCCCTGAAG
TTGCAGTGGAGCGGATTAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCT
AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGTTG
CAGTGAGGCAGACTGAAGATG
Found at i:16550039 original size:44 final size:43
Alignment explanation
Indices: 16549294--16550062 Score: 305
Period size: 44 Copynumber: 17.8 Consensus size: 43
16549284 TAGCCAGCAA
* ** **
16549294 ATCTTATCTCCCTGAAGTTGCAGTGGGGCAGATTGGAGCCGATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC--TAG
* * ** *
16549338 ATCCTATCTCTCTGAAGTTGCAGTGGAGTGGATT-AAATCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-TAG
* * * ***
16549381 ATCTTATCTCTCTGAAGTTACAG-AGAGCAGA-TCGCATCTAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTAG
* * * *
16549422 -TCTTATCTCCCTGAATTTGCAGTGGAGCAGACTAAGCAAGCAAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTAG
* * *
16549466 -TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGC-AA
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAAT--CTAG
* ** **
16549510 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGGAGCCGATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC--TAG
* ** *
16549554 ATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATT-AAATCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-TAG
* * ***
16549597 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCATCTAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTAG
* * * *
16549638 -TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGCAAGCAAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTAG
* * *
16549682 -TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGC-AA
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAAT--CTAG
* * * **
16549726 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAAATTAGAGCCGATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC--TAG
* * * *
16549770 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-TAG
* * * * *** *
16549814 ATCTTATCTCTCTAAAGTTACAG-AGAGCAGA-TCGCAT-TTG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTAG
* * * * * * * *
16549854 GTATTATCTCCTTAAAGTTGCAGTGAAGCAGACTAAGTAAGCAAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTAG
** * * *
16549899 -TCTTATCTTTCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGC-AA
1 ATCTTATCTCCCTGAAGTTGCAGTGGA-GCAGA-TTAAAAT--CTAG
* * * **
16549943 ATCTTATCTCCCTGAAGTTGTAGTGGCGCAGGTTAAAGCCGATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC--TAG
* * *
16549987 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCTTGG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-TAG
* *
16550031 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGAT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
16550063 CGCAAGTCTT
Statistics
Matches: 534, Mismatches: 141, Indels: 101
0.69 0.18 0.13
Matches are distributed among these distances:
40 59 0.11
41 26 0.05
42 28 0.05
43 71 0.13
44 257 0.48
45 87 0.16
46 6 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTAG
Found at i:16550375 original size:14 final size:14
Alignment explanation
Indices: 16550356--16550383 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16550346 TAAAAGACGG
16550356 TGGCCCAAAACAAA
1 TGGCCCAAAACAAA
16550370 TGGCCCAAAACAAA
1 TGGCCCAAAACAAA
16550384 ATCAAAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.29, G:0.14, T:0.07
Consensus pattern (14 bp):
TGGCCCAAAACAAA
Found at i:16562650 original size:31 final size:31
Alignment explanation
Indices: 16562612--16562686 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
16562602 GATATTAAAT
*
16562612 TTAATTTAATATTTATCTAGATAGTATTTTA
1 TTAATTTAATATTTATCTAGATAATATTTTA
*
16562643 TTAATTTAATATTTATCTTGATAATATTTTA
1 TTAATTTAATATTTATCTAGATAATATTTTA
16562674 TTAATTTAATATT
1 TTAATTTAATATT
16562687 AATGTGATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (31 bp):
TTAATTTAATATTTATCTAGATAATATTTTA
Found at i:16562655 original size:16 final size:16
Alignment explanation
Indices: 16562636--16562686 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
16562626 ATCTAGATAG
16562636 TATTTTATTAATTTAA
1 TATTTTATTAATTTAA
* *
16562652 TATTTATCTTGA--TAA
1 TATTT-TATTAATTTAA
16562667 TATTTTATTAATTTAA
1 TATTTTATTAATTTAA
16562683 TATT
1 TATT
16562687 AATGTGATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 4 0.14
15 8 0.29
16 12 0.43
17 4 0.14
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (16 bp):
TATTTTATTAATTTAA
Found at i:16572575 original size:9 final size:9
Alignment explanation
Indices: 16572563--16572600 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
16572553 CAAAAATTAT
*
16572563 ATATTAATA
1 ATATTAAAA
16572572 ATATTAAAAA
1 ATATT-AAAA
16572582 ATATTAAAA
1 ATATTAAAA
16572591 A-ATTAAAA
1 ATATTAAAA
16572599 AT
1 AT
16572601 TTTCATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 8 0.31
9 10 0.38
10 8 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
ATATTAAAA
Found at i:16572851 original size:21 final size:20
Alignment explanation
Indices: 16572800--16572851 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
16572790 CTTTAGACAT
* *
16572800 TTAATTATTTAATTTTTTAA
1 TTAAATATTTAATTTTTAAA
**
16572820 TTTTATAATTTAATTTTTAAAA
1 TTAAAT-ATTTAATTTTT-AAA
16572842 TTAAATATTT
1 TTAAATATTT
16572852 TAATCACTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
20 3 0.12
21 15 0.62
22 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAAATATTTAATTTTTAAA
Found at i:16575576 original size:53 final size:54
Alignment explanation
Indices: 16575513--16575702 Score: 256
Period size: 54 Copynumber: 3.5 Consensus size: 54
16575503 TATGATCATG
* * *
16575513 ACCTCTTACTTATGAGATTTTCGGAATATCGCGATTTG-TGATTTACGATCGCA
1 ACCTCCTACTTATGAGATTTTCAGAATCTCGCGATTTGCTGATTTACGATCGCA
* *
16575566 AACTCCTACTTATGAGATTTTCAGAATCTCACGATTTGCTGATTTACGATCGCA
1 ACCTCCTACTTATGAGATTTTCAGAATCTCGCGATTTGCTGATTTACGATCGCA
* * * * * *
16575620 ACCTCTTACTTATGAGATTTTCAAAATCTCGTGGTTTGTTGATTTACGATTGCA
1 ACCTCCTACTTATGAGATTTTCAGAATCTCGCGATTTGCTGATTTACGATCGCA
**
16575674 ACCTCCTACTTACAAGATTTTCAGAATCT
1 ACCTCCTACTTATGAGATTTTCAGAATCT
16575703 TACAGTTTAT
Statistics
Matches: 119, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
53 33 0.28
54 86 0.72
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (54 bp):
ACCTCCTACTTATGAGATTTTCAGAATCTCGCGATTTGCTGATTTACGATCGCA
Found at i:16575610 original size:107 final size:108
Alignment explanation
Indices: 16575445--16575702 Score: 297
Period size: 107 Copynumber: 2.4 Consensus size: 108
16575435 TGGATTCACG
* * * * ** * *
16575445 GATTTACGATCGCAACCT-CT-CATATACAAGATTTTCAGAATTTTACGGTTCACCGATTTATGA
1 GATTTACGATCGCAAACTCCTAC-T-TACAAGATTTTCAGAATCTCACGATTTGCTGATTTACGA
** **
16575508 TCATGACCTCTTACTTATGAGATTTTCGGAATATCGCGATTTG-T
64 TCACAACCTCTTACTTATGAGATTTTCAAAATATCGCGATTTGTT
**
16575552 GATTTACGATCGCAAACTCCTACTTATGAGATTTTCAGAATCTCACGATTTGCTGATTTACGATC
1 GATTTACGATCGCAAACTCCTACTTACAAGATTTTCAGAATCTCACGATTTGCTGATTTACGATC
* * * *
16575617 GCAACCTCTTACTTATGAGATTTTCAAAATCTCGTGGTTTGTT
66 ACAACCTCTTACTTATGAGATTTTCAAAATATCGCGATTTGTT
* *
16575660 GATTTACGATTGCAACCTCCTACTTACAAGATTTTCAGAATCT
1 GATTTACGATCGCAAACTCCTACTTACAAGATTTTCAGAATCT
16575703 TACAGTTTAT
Statistics
Matches: 126, Mismatches: 22, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
107 82 0.65
108 43 0.34
109 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (108 bp):
GATTTACGATCGCAAACTCCTACTTACAAGATTTTCAGAATCTCACGATTTGCTGATTTACGATC
ACAACCTCTTACTTATGAGATTTTCAAAATATCGCGATTTGTT
Found at i:16575632 original size:54 final size:54
Alignment explanation
Indices: 16575445--16575702 Score: 250
Period size: 54 Copynumber: 4.8 Consensus size: 54
16575435 TGGATTCACG
* ** * * * ** *
16575445 GATTTACGATCGCAACCTCTCA-TATACAAGATTTTCAGAATTTTACGGTTCACC
1 GATTTACGATCGCAACCTCTTACT-TATGAGATTTTCAGAATCTCACGATTTGCT
* *** * * *
16575499 GATTTATGATCATGACCTCTTACTTATGAGATTTTCGGAATATCGCGATTTG-T
1 GATTTACGATCGCAACCTCTTACTTATGAGATTTTCAGAATCTCACGATTTGCT
* *
16575552 GATTTACGATCGCAAACTCCTACTTATGAGATTTTCAGAATCTCACGATTTGCT
1 GATTTACGATCGCAACCTCTTACTTATGAGATTTTCAGAATCTCACGATTTGCT
* ** * *
16575606 GATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAATCTCGTGGTTTGTT
1 GATTTACGATCGCAACCTCTTACTTATGAGATTTTCAGAATCTCACGATTTGCT
* * **
16575660 GATTTACGATTGCAACCTCCTACTTACAAGATTTTCAGAATCT
1 GATTTACGATCGCAACCTCTTACTTATGAGATTTTCAGAATCT
16575703 TACAGTTTAT
Statistics
Matches: 166, Mismatches: 36, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
53 43 0.26
54 122 0.73
55 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (54 bp):
GATTTACGATCGCAACCTCTTACTTATGAGATTTTCAGAATCTCACGATTTGCT
Found at i:16575718 original size:54 final size:53
Alignment explanation
Indices: 16575445--16575755 Score: 220
Period size: 54 Copynumber: 5.8 Consensus size: 53
16575435 TGGATTCACG
* * * *
16575445 GATTTACGATCGCAACCT-CT-CATATACAAGATTTTCAGAATTTTACGGTTCACC
1 GATTTACGATCGCAACCTCCTAC-T-TACAAGATTTTCAGAATCTCAC-GTTTATC
* *** * ** * * * *
16575499 GATTTATGATCATGACCTCTTACTTATGAGATTTTCGGAATATCGCGATTTGT-
1 GATTTACGATCGCAACCTCCTACTTACAAGATTTTCAGAATCTCACG-TTTATC
* ** *
16575552 GATTTACGATCGCAAACTCCTACTTATGAGATTTTCAGAATCTCACGATTT-GC
1 GATTTACGATCGCAACCTCCTACTTACAAGATTTTCAGAATCTCACG-TTTATC
* ** * ** * *
16575605 TGATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAATCTCGTGGTTTGTT
1 -GATTTACGATCGCAACCTCCTACTTACAAGATTTTCAGAATCTC-ACGTTTATC
* *
16575660 GATTTACGATTGCAACCTCCTACTTACAAGATTTTCAGAATCTTACAGTTTATC
1 GATTTACGATCGCAACCTCCTACTTACAAGATTTTCAGAATCTCAC-GTTTATC
* *
16575714 GATTTACAATCGCAACCTACC-GCTTACAAGATTTT-AGAATCT
1 GATTTACGATCGCAACCT-CCTACTTACAAGATTTTCAGAATCT
16575756 TGTTGATGCC
Statistics
Matches: 204, Mismatches: 44, Indels: 19
0.76 0.16 0.07
Matches are distributed among these distances:
53 50 0.25
54 148 0.73
55 5 0.02
56 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (53 bp):
GATTTACGATCGCAACCTCCTACTTACAAGATTTTCAGAATCTCACGTTTATC
Found at i:16575746 original size:108 final size:107
Alignment explanation
Indices: 16575547--16575748 Score: 248
Period size: 108 Copynumber: 1.9 Consensus size: 107
16575537 AATATCGCGA
**
16575547 TTTGTGATTTACGATCGCAAACTCCTACTTATGAGATTTTCAGAATCTCACGATTTGCTGATTTA
1 TTTGTGATTTACGATCGCAAACTCCTACTTACAAGATTTTCAGAATCTCACGATTTGCTGATTTA
* * **
16575612 CGATCGCAACCTCTTACTTATGAGATTTTCAAAATCTCGTGG
66 CAATCGCAACCTCTCACTTACAAGATTTTCAAAATCTCGTGG
* * * *
16575654 TTTGTTGATTTACGATTGCAACCTCCTACTTACAAGATTTTCAGAATCTTAC-AGTTT-ATCGAT
1 TTTG-TGATTTACGATCGCAAACTCCTACTTACAAGATTTTCAGAATCTCACGA-TTTGCT-GAT
*
16575717 TTACAATCGCAACCTAC-CGCTTACAAGATTTT
63 TTACAATCGCAACCT-CTCACTTACAAGATTTT
16575749 AGAATCTTGT
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
107 6 0.08
108 73 0.91
109 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (107 bp):
TTTGTGATTTACGATCGCAAACTCCTACTTACAAGATTTTCAGAATCTCACGATTTGCTGATTTA
CAATCGCAACCTCTCACTTACAAGATTTTCAAAATCTCGTGG
Found at i:16576098 original size:24 final size:24
Alignment explanation
Indices: 16576071--16576371 Score: 221
Period size: 24 Copynumber: 12.5 Consensus size: 24
16576061 TACAGTTCGT
* *
16576071 ATAAATTTCTACTGCACAGCTAGC
1 ATAATTTTCTGCTGCACAGCTAGC
* * *
16576095 ATAATTTTCTGCTGTATAGCTCGC
1 ATAATTTTCTGCTGCACAGCTAGC
* * ** *
16576119 ATAAATTTTTTTCTATATAGCTAGC
1 AT-AATTTTCTGCTGCACAGCTAGC
* * * *
16576144 ATAATTTTCTGTTGTATAGCTTGC
1 ATAATTTTCTGCTGCACAGCTAGC
16576168 ATAATTTTCTGCTGCACAGCTAGC
1 ATAATTTTCTGCTGCACAGCTAGC
* **
16576192 ATAATTTTCTGTTGCACAATTCA-C
1 ATAATTTTCTGCTGCACAGCT-AGC
* * *
16576216 AT-ATTTTTTGTTGCAGAGCTAGC
1 ATAATTTTCTGCTGCACAGCTAGC
* * *
16576239 ATAATCTTCTACTCCACAGCTAGC
1 ATAATTTTCTGCTGCACAGCTAGC
* ** * *
16576263 ATAACTTTCTGCTATACAGTTCGC
1 ATAATTTTCTGCTGCACAGCTAGC
*
16576287 ATAATTTTCTACTGCACAGCTAGC
1 ATAATTTTCTGCTGCACAGCTAGC
* * * * * *
16576311 ATAATTTTTTGTTGTAGAGTTTGC
1 ATAATTTTCTGCTGCACAGCTAGC
*
16576335 ATAATTTT-TCGCTGCACAACTAGC
1 ATAATTTTCT-GCTGCACAGCTAGC
*
16576359 ATAATTTTTTGCT
1 ATAATTTTCTGCT
16576372 ACATAGCTTG
Statistics
Matches: 214, Mismatches: 57, Indels: 12
0.76 0.20 0.04
Matches are distributed among these distances:
22 1 0.00
23 18 0.08
24 173 0.81
25 22 0.10
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (24 bp):
ATAATTTTCTGCTGCACAGCTAGC
Found at i:16576123 original size:48 final size:48
Alignment explanation
Indices: 16576045--16576205 Score: 196
Period size: 48 Copynumber: 3.3 Consensus size: 48
16576035 TCACCAGTTC
* * * *
16576045 GCATAATTTTTTGTTGTACAGTTCGTATAAATTTCTACTGCACAGCTA
1 GCATAATTTTCTGTTGTATAGCTCGCATAAATTTCTACTGCACAGCTA
* * * ** *
16576093 GCATAATTTTCTGCTGTATAGCTCGCATAAATTTTTTTCTATATAGCTA
1 GCATAATTTTCTGTTGTATAGCTCGCATAAA-TTTCTACTGCACAGCTA
* * *
16576142 GCATAATTTTCTGTTGTATAGCTTGCATAATTTTCTGCTGCACAGCTA
1 GCATAATTTTCTGTTGTATAGCTCGCATAAATTTCTACTGCACAGCTA
16576190 GCATAATTTTCTGTTG
1 GCATAATTTTCTGTTG
16576206 CACAATTCAC
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
48 54 0.57
49 40 0.43
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (48 bp):
GCATAATTTTCTGTTGTATAGCTCGCATAAATTTCTACTGCACAGCTA
Found at i:16579605 original size:38 final size:39
Alignment explanation
Indices: 16579555--16579636 Score: 112
Period size: 38 Copynumber: 2.1 Consensus size: 39
16579545 CAATTTGACC
* *
16579555 TAATTTGATTCTTGTGCATAGTGTCATTATTTAGCCATA
1 TAATTTGATTCTTGTGCATAATATCATTATTTAGCCATA
* **
16579594 TAATTT-ATTCTTGTTCATAATATCATTATTTATTCATA
1 TAATTTGATTCTTGTGCATAATATCATTATTTAGCCATA
16579632 TAATT
1 TAATT
16579637 GACACCATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
38 32 0.84
39 6 0.16
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (39 bp):
TAATTTGATTCTTGTGCATAATATCATTATTTAGCCATA
Found at i:16584754 original size:13 final size:14
Alignment explanation
Indices: 16584738--16584779 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
16584728 TTTCAATTTT
16584738 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
16584751 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
16584766 ATTTTAAATAATAT
1 ATTTT-AATAATAT
16584780 TCTTCACATA
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:16584764 original size:16 final size:16
Alignment explanation
Indices: 16584742--16584778 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
16584732 AATTTTATTT
16584742 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
16584759 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
16584774 TAATA
1 TAATA
16584779 TTCTTCACAT
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:16595771 original size:24 final size:24
Alignment explanation
Indices: 16595739--16595789 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
16595729 TACCGAAGCT
*
16595739 ATTTAATAATCATCTTTTATAGAA
1 ATTTAATAATCATCTTTTATAAAA
16595763 ATTTAATAATCATCTTTTATAAAA
1 ATTTAATAATCATCTTTTATAAAA
16595787 ATT
1 ATT
16595790 ATAAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTTAATAATCATCTTTTATAAAA
Found at i:16596170 original size:9 final size:9
Alignment explanation
Indices: 16596153--16596258 Score: 65
Period size: 9 Copynumber: 11.4 Consensus size: 9
16596143 TTTTGATGTA
16596153 TTTTATAAT
1 TTTTATAAT
*
16596162 TTTTTTAAT
1 TTTTATAAT
*
16596171 TTTTAATAAA
1 TTTT-ATAAT
*
16596181 ATTTA-AAT
1 TTTTATAAT
*
16596189 ATTTTTTATAT
1 -TTTTATA-AT
*
16596200 TTTTATTAAAA
1 TTTTA-T-AAT
*
16596211 TTTAATAAT
1 TTTTATAAT
*
16596220 TTTTATAAC
1 TTTTATAAT
*
16596229 TTTTATTGAT
1 TTTTA-TAAT
16596239 TTTTAT--T
1 TTTTATAAT
16596246 TTTTATAAT
1 TTTTATAAT
16596255 TTTT
1 TTTT
16596259 TGCTACATGT
Statistics
Matches: 73, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
7 7 0.10
8 2 0.03
9 36 0.49
10 19 0.26
11 8 0.11
12 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:16596185 original size:28 final size:28
Alignment explanation
Indices: 16596154--16596233 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 28
16596144 TTTGATGTAT
16596154 TTTATAATTTTTTTAATTTTTAATAAAA
1 TTTATAATTTTTTTAATTTTTAATAAAA
*
16596182 TTTA-AATATTTTTTATATTTTTATTAAAA
1 TTTATAAT-TTTTTTA-ATTTTTAATAAAA
* *
16596211 TTTAATAATTTTTATAACTTTTA
1 TTT-ATAATTTTTTTAATTTTTA
16596234 TTGATTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
27 3 0.07
28 11 0.24
29 21 0.47
30 7 0.16
31 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTATAATTTTTTTAATTTTTAATAAAA
Found at i:16597446 original size:20 final size:20
Alignment explanation
Indices: 16597406--16597445 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
16597396 CCGAATATAA
*
16597406 TAAATATATTTTTTTAATTT
1 TAAAAATATTTTTTTAATTT
16597426 TAAAAATATTTTTTT-ATTT
1 TAAAAATATTTTTTTAATTT
16597445 T
1 T
16597446 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TAAAAATATTTTTTTAATTT
Found at i:16597467 original size:28 final size:28
Alignment explanation
Indices: 16597412--16597468 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
16597402 ATAATAAATA
**
16597412 TATTTTTTTAATTTTAAAAATATTTTTT
1 TATTTTTTTAATTTTAAAAATAAATTTT
* *
16597440 TATTTTTTTTATTTTTAAAATAAATTTT
1 TATTTTTTTAATTTTAAAAATAAATTTT
16597468 T
1 T
16597469 GGTGTTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (28 bp):
TATTTTTTTAATTTTAAAAATAAATTTT
Found at i:16597918 original size:7 final size:8
Alignment explanation
Indices: 16597901--16597927 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
16597891 TTTAAAATAC
16597901 TTTTTATT
1 TTTTTATT
16597909 TTTTTATT
1 TTTTTATT
16597917 TTTTTATT
1 TTTTTATT
16597925 TTT
1 TTT
16597928 AAAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTATT
Found at i:16598210 original size:20 final size:20
Alignment explanation
Indices: 16598194--16598232 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
16598184 ACCAAAAATT
16598194 TATTTTAAAAATAAAAAAAG
1 TATTTTAAAAATAAAAAAAG
*
16598214 TATTTTAAAATTAAAAAAA
1 TATTTTAAAAATAAAAAAA
16598233 TAAAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
TATTTTAAAAATAAAAAAAG
Found at i:16604615 original size:22 final size:23
Alignment explanation
Indices: 16604590--16604659 Score: 94
Period size: 22 Copynumber: 3.2 Consensus size: 23
16604580 AAAATCAATA
16604590 TCAATATCC-TTCAAAAATTCTC
1 TCAATATCCGTTCAAAAATTCTC
16604612 TCAAT-TCCGTTCAAAAATTCTC
1 TCAATATCCGTTCAAAAATTCTC
*
16604634 TCAA-ATTCCTTTC-AAAATTCTC
1 TCAATA-TCCGTTCAAAAATTCTC
16604656 TCAA
1 TCAA
16604660 ACTCTCAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
21 3 0.07
22 35 0.80
23 6 0.14
ACGTcount: A:0.34, C:0.27, G:0.01, T:0.37
Consensus pattern (23 bp):
TCAATATCCGTTCAAAAATTCTC
Found at i:16604660 original size:22 final size:23
Alignment explanation
Indices: 16604599--16604660 Score: 101
Period size: 22 Copynumber: 2.8 Consensus size: 23
16604589 ATCAATATCC
16604599 TTCAAAAATTCTCTC-AATTCCG
1 TTCAAAAATTCTCTCAAATTCCG
*
16604621 TTCAAAAATTCTCTCAAATTCCT
1 TTCAAAAATTCTCTCAAATTCCG
16604644 TTC-AAAATTCTCTCAAA
1 TTCAAAAATTCTCTCAAA
16604661 CTCTCAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 29 0.76
23 9 0.24
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (23 bp):
TTCAAAAATTCTCTCAAATTCCG
Found at i:16604666 original size:30 final size:30
Alignment explanation
Indices: 16604631--16604689 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
16604621 TTCAAAAATT
* *
16604631 CTCTCAAATTCCTTTCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
16604661 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
16604690 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:16604700 original size:21 final size:22
Alignment explanation
Indices: 16604661--16604702 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16604651 TTCTCTCAAA
16604661 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
16604683 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
16604703 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:16604808 original size:29 final size:29
Alignment explanation
Indices: 16604748--16604808 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
16604738 AATTTCATTA
* *
16604748 TTTTAAGAAAATTTTAAAATTTTTTATTT
1 TTTTAAGAAAATTTTAAAATTTTTAATAT
*
16604777 TTTTAA-AATAATTTTAATATTTTTAATAT
1 TTTTAAGAA-AATTTTAAAATTTTTAATAT
16604806 TTT
1 TTT
16604809 CAACAATGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTAAGAAAATTTTAAAATTTTTAATAT
Found at i:16604928 original size:14 final size:15
Alignment explanation
Indices: 16604899--16604932 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16604889 AAATTTTAAA
16604899 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
16604914 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
16604928 TTTTA
1 TTTTA
16604933 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:16609721 original size:3 final size:3
Alignment explanation
Indices: 16609713--16609767 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
16609703 CTTTCTTTTG
16609713 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16609761 TTA TTA T
1 TTA TTA T
16609768 ATAACATATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16609990 original size:27 final size:27
Alignment explanation
Indices: 16609957--16610011 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
16609947 ATTTACTTAG
16609957 CCAAGATCTAATTCATTACTAAACTAA
1 CCAAGATCTAATTCATTACTAAACTAA
16609984 CCAAGATCTAATTCATTACTAAACTAA
1 CCAAGATCTAATTCATTACTAAACTAA
16610011 C
1 C
16610012 TTGATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.24, G:0.04, T:0.29
Consensus pattern (27 bp):
CCAAGATCTAATTCATTACTAAACTAA
Found at i:16611582 original size:15 final size:14
Alignment explanation
Indices: 16611540--16611584 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
16611530 AATATGCCAA
16611540 ACTAATTTTTTCAAT
1 ACTAATTTTTT-AAT
*
16611555 ACTCATTTCTTTAAT
1 ACTAATTT-TTTAAT
16611570 ACTTAATTTTTTAAT
1 AC-TAATTTTTTAAT
16611585 TTATTGTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (14 bp):
ACTAATTTTTTAAT
Found at i:16618071 original size:35 final size:36
Alignment explanation
Indices: 16618010--16618091 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 36
16618000 AATCCCTTCA
* *
16618010 AAACACACCAATTGCTCACAAGAGCTAATCCAACCG
1 AAACACGCCAATTGCTCACAAAAGCTAATCCAACCG
* *
16618046 AAACACGCCAA-TGCTCATAAAAGCTAGTCCAACCG
1 AAACACGCCAATTGCTCACAAAAGCTAATCCAACCG
16618081 AAACACGCCAA
1 AAACACGCCAA
16618092 ACAGAGAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 32 0.76
36 10 0.24
ACGTcount: A:0.43, C:0.33, G:0.12, T:0.12
Consensus pattern (36 bp):
AAACACGCCAATTGCTCACAAAAGCTAATCCAACCG
Found at i:16618813 original size:20 final size:22
Alignment explanation
Indices: 16618788--16618830 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
16618778 AATACATGGT
16618788 ATTCATC-AT-AAAAATTCAAA
1 ATTCATCAATGAAAAATTCAAA
*
16618808 ATTCATCAATGAAAACTTCAAA
1 ATTCATCAATGAAAAATTCAAA
16618830 A
1 A
16618831 AATTTTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 2 0.10
22 11 0.55
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.28
Consensus pattern (22 bp):
ATTCATCAATGAAAAATTCAAA
Found at i:16619184 original size:23 final size:23
Alignment explanation
Indices: 16619140--16619184 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
16619130 TCAATTAGGG
* **
16619140 CTTAATTATCACTTAAGTCATTC
1 CTTAATTATCAATTAAACCATTC
*
16619163 CTTAATTATTAATTAAACCATT
1 CTTAATTATCAATTAAACCATT
16619185 TAATAACCTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.44
Consensus pattern (23 bp):
CTTAATTATCAATTAAACCATTC
Found at i:16626184 original size:18 final size:18
Alignment explanation
Indices: 16626153--16626195 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
16626143 TCGAGTTTGG
* * *
16626153 CCATGCACACTATGCGTT
1 CCATGCAAAATATGCATT
16626171 CCATGCAAAATATGCATT
1 CCATGCAAAATATGCATT
*
16626189 TCATGCA
1 CCATGCA
16626196 TTCCATGCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (18 bp):
CCATGCAAAATATGCATT
Found at i:16626194 original size:27 final size:27
Alignment explanation
Indices: 16626164--16626232 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
16626154 CATGCACACT
*
16626164 ATGCGTTCCATGCAAAATATGCATTTC
1 ATGCGTTCCATGCAAAACATGCATTTC
* *
16626191 ATGCATTCCATGCAACACATGCATTTC
1 ATGCGTTCCATGCAAAACATGCATTTC
**
16626218 ATGCGAACCATGCAA
1 ATGCGTTCCATGCAA
16626233 TGTGCTGCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (27 bp):
ATGCGTTCCATGCAAAACATGCATTTC
Found at i:16626211 original size:18 final size:18
Alignment explanation
Indices: 16626190--16626231 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
16626180 ATATGCATTT
16626190 CATGCATTCCATGC-AAC
1 CATGCATTCCATGCGAAC
*
16626207 ACATGCATTTCATGCGAAC
1 -CATGCATTCCATGCGAAC
16626226 CATGCA
1 CATGCA
16626232 ATGTGCTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (18 bp):
CATGCATTCCATGCGAAC
Found at i:16627596 original size:17 final size:17
Alignment explanation
Indices: 16627570--16627605 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
16627560 AATATTATTT
*
16627570 ATTAATTAAAATTTTCA
1 ATTAAATAAAATTTTCA
16627587 ATTAAATAAAATTTTCA
1 ATTAAATAAAATTTTCA
16627604 AT
1 AT
16627606 CTAATTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTAAATAAAATTTTCA
Found at i:16641127 original size:14 final size:14
Alignment explanation
Indices: 16641104--16641138 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
16641094 AAATTTGCCT
16641104 TTATTA-ATTATAG
1 TTATTACATTATAG
16641117 TTATTACATTATAG
1 TTATTACATTATAG
*
16641131 TTTTTACA
1 TTATTACA
16641139 AGCTTATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (14 bp):
TTATTACATTATAG
Found at i:16641294 original size:58 final size:58
Alignment explanation
Indices: 16641228--16641513 Score: 322
Period size: 58 Copynumber: 4.9 Consensus size: 58
16641218 TGAGTCCGCA
* * *
16641228 AGCTATTTTGAACTTAAGCAAATTTTCCAAAATAATCAGCTAGGAATATAAATCTGCG
1 AGCTGTTTTGAACTTAAACAAATTTTCCAAAATAATCAGCTGGGAATATAAATCTGCG
* * * * *
16641286 AGCTATTTTGAACTTAAGCATATTTTCTAAAATAATCAGTTGGGAATATAAATCTGCG
1 AGCTGTTTTGAACTTAAACAAATTTTCCAAAATAATCAGCTGGGAATATAAATCTGCG
* * * * * *
16641344 AGCTGTTTTAAACTTTAACAAATATTCAAAAAATCATTAGCTGGGAATATAAAT-TCGCG
1 AGCTGTTTTGAACTTAAACAAATTTTC-CAAAATAATCAGCTGGGAATATAAATCT-GCG
* * * * *
16641403 AGCTGTTCTGAGCTTAAACAAATTTTCCAAAATCATCAACTGGGAATATAAATCTGCA
1 AGCTGTTTTGAACTTAAACAAATTTTCCAAAATAATCAGCTGGGAATATAAATCTGCG
* * * * * *
16641461 AGTTGTTCTGAACTTAAACATATTTTCTAAAATAATCAGTTGAGAATATAAAT
1 AGCTGTTTTGAACTTAAACAAATTTTCCAAAATAATCAGCTGGGAATATAAAT
16641514 TCACAAGTTA
Statistics
Matches: 194, Mismatches: 31, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
58 146 0.75
59 48 0.25
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (58 bp):
AGCTGTTTTGAACTTAAACAAATTTTCCAAAATAATCAGCTGGGAATATAAATCTGCG
Found at i:16641475 original size:117 final size:117
Alignment explanation
Indices: 16641238--16641515 Score: 308
Period size: 117 Copynumber: 2.4 Consensus size: 117
16641228 AGCTATTTTG
* * * * *
16641238 AACTTAAGCAAATTTTCCAAAATAATCAGCTAGGAATATAAA-TCTGCGAGCTATTTTGAACTTA
1 AACTTAAACAAATATTCAAAAATAATCAGCTGGGAATATAAATTCTGCGAGCTATTCTGAACTTA
* * * ** * *
16641302 AGCATATTTTCTAAAATAATCAGTTGGGAATATAAATCTGCGAGCTGTTTTA
66 AACAAATTTTCCAAAATAATCAACTGGGAATATAAATCTGCAAGCTGTTCTA
* * * * *
16641354 AACTTTAACAAATATTCAAAAAATCATTAGCTGGGAATATAAATTC-GCGAGCTGTTCTGAGCTT
1 AACTTAAACAAATATTC-AAAAATAATCAGCTGGGAATATAAATTCTGCGAGCTATTCTGAACTT
* * *
16641418 AAACAAATTTTCCAAAATCATCAACTGGGAATATAAATCTGCAAGTTGTTCTG
65 AAACAAATTTTCCAAAATAATCAACTGGGAATATAAATCTGCAAGCTGTTCTA
* * * * *
16641471 AACTTAAACATATTTTCTAAAATAATCAGTTGAGAATATAAATTC
1 AACTTAAACAAATATTCAAAAATAATCAGCTGGGAATATAAATTC
16641516 ACAAGTTACT
Statistics
Matches: 132, Mismatches: 28, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
116 37 0.28
117 93 0.70
118 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (117 bp):
AACTTAAACAAATATTCAAAAATAATCAGCTGGGAATATAAATTCTGCGAGCTATTCTGAACTTA
AACAAATTTTCCAAAATAATCAACTGGGAATATAAATCTGCAAGCTGTTCTA
Found at i:16641694 original size:70 final size:70
Alignment explanation
Indices: 16641590--16642208 Score: 620
Period size: 70 Copynumber: 8.8 Consensus size: 70
16641580 ATTCTAGCGT
* * * * * * *
16641590 TATGAAATCAGCTAGCCTTGCAATTACAGTTGGGAGCTTTTAAGTCTCGCTAACAGTTTAAAGAC
1 TATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGCTAACTGTTTGAAGGC
* *
16641655 TACAA
66 TGCGA
* * * * * *
16641660 TATGAAATCAGCGAGCCTTGGAATTACAACTGGGAGTTTTTAACTATTGCTAACTGTTTGAAGGT
1 TATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGCTAACTGTTTGAAGGC
*
16641725 TGCAA
66 TGCGA
* * * * * *
16641730 TATGAAATCAGCGAGTCTTGAAATTACAGCTGAGAGCATTTAGCTCTCACTAATTGTTTGGAA-G
1 TATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGCTAACTGTTT-GAAGG
**
16641794 CCACGA
65 CTGCGA
* * * *
16641800 TATGAAATTAGCGAGCCTTGAAATTACAACTGGGAGCTTTTAACTCTTGCTAACTGTTTGAAGGT
1 TATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGCTAACTGTTTGAAGGC
16641865 TGCGA
66 TGCGA
* * *
16641870 TATGAAATCAGCGAGCCTTGAAATTATAGCTGAGAGCTTTTAACTCTCGCTAACTGTTTGGAGGC
1 TATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGCTAACTGTTTGAAGGC
* *
16641935 CGCAA
66 TGCGA
* * * ** *
16641940 TATGAAATCAACAAGCCTTGAAATTACAGTTAAGAGCTTTTAACT-T-GCTAACTGTTTGGAGG-
1 TATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGCTAACTGTTTGAAGGC
16642002 TCGCGA
66 T-GCGA
* * * *
16642008 TATGAAATTAGCGAGCCTTGAAATTACAACTGGGAGCTTTTAACTCTAGCTAACTATTT-AGAGG
1 TATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGCTAACTGTTTGA-AGG
*
16642072 CCGCGA
65 CTGCGA
* * * * * * *
16642078 TATGAAATCAGCGAGCCTTGAAATTATAGTTAGGAGCTTTTAACTATCACTTACCGTTTGTTTGG
1 TATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGC-TAAC---TGTTTGA
* *
16642143 AGGTTGCAA
62 AGGCTGCGA
* **
16642152 TATGAAA-CTAGCGAGCCTTGAAATTACAACTACGAGCTTTTAACTCTCGCTAACTGT
1 TATGAAATC-AGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGCTAACTGT
16642209 AACACCCCTA
Statistics
Matches: 449, Mismatches: 87, Indels: 26
0.80 0.15 0.05
Matches are distributed among these distances:
68 57 0.13
69 5 0.01
70 325 0.72
71 6 0.01
73 4 0.01
74 52 0.12
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (70 bp):
TATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGCTAACTGTTTGAAGGC
TGCGA
Found at i:16644909 original size:70 final size:70
Alignment explanation
Indices: 16644794--16644949 Score: 242
Period size: 70 Copynumber: 2.2 Consensus size: 70
16644784 GGCCGTTACA
* *
16644794 CTAACTGTTTAGAGGCCGCGATATGAAATCAACGAGCCTTAAAATTACAGCTGGGAGCTTTTGAA
1 CTAACTATTTAGAGGCCGCGATATGAAATCAACGAGCCTTAAAATTACAGCAGGGAGCTTTT-AA
*
16644859 -TCTTG
65 CTCTCG
* *
16644864 CTAACTATTTAGAGGTCGCGATATGAAATCAACGAGCCTTGAAATTACAGCAGGGAGCTTTTAAC
1 CTAACTATTTAGAGGCCGCGATATGAAATCAACGAGCCTTAAAATTACAGCAGGGAGCTTTTAAC
16644929 TCTCG
66 TCTCG
*
16644934 CTAACTATTTGGAGGC
1 CTAACTATTTAGAGGC
16644950 ACATCATGAT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
69 2 0.03
70 76 0.97
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (70 bp):
CTAACTATTTAGAGGCCGCGATATGAAATCAACGAGCCTTAAAATTACAGCAGGGAGCTTTTAAC
TCTCG
Found at i:16647924 original size:18 final size:18
Alignment explanation
Indices: 16647894--16647932 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16647884 GACCCACTAT
*
16647894 TTTTAATATATTTTAAAA
1 TTTTAATATATTTAAAAA
16647912 TTTT-ATATAATTTAAAAA
1 TTTTAATAT-ATTTAAAAA
16647930 TTT
1 TTT
16647933 ACGTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAATATATTTAAAAA
Found at i:16647925 original size:17 final size:17
Alignment explanation
Indices: 16647894--16647933 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
16647884 GACCCACTAT
*
16647894 TTTTAATATATTTTAAAA
1 TTTT-ATATAATTTAAAA
16647912 TTTTATATAATTTAAAA
1 TTTTATATAATTTAAAA
*
16647929 ATTTA
1 TTTTA
16647934 CGTTTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTATATAATTTAAAA
Found at i:16655734 original size:56 final size:56
Alignment explanation
Indices: 16655663--16655775 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
16655653 GGATTTTCCA
16655663 ACTCTTATTGCAATTTCATGGATTTCTTTGTCATCCGTTTTATCTGTTTAATGAAT
1 ACTCTTATTGCAATTTCATGGATTTCTTTGTCATCCGTTTTATCTGTTTAATGAAT
16655719 ACTCTTATTGCAATTTCATGGATTTCTTTGTCATCCGTTTTATCTGTTTAATGAAT
1 ACTCTTATTGCAATTTCATGGATTTCTTTGTCATCCGTTTTATCTGTTTAATGAAT
16655775 A
1 A
16655776 AATGTCTTGC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.50
Consensus pattern (56 bp):
ACTCTTATTGCAATTTCATGGATTTCTTTGTCATCCGTTTTATCTGTTTAATGAAT
Found at i:16660345 original size:10 final size:10
Alignment explanation
Indices: 16660332--16660372 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
16660322 TTAAGTTAAA
16660332 TTTAAAAT-T
1 TTTAAAATAT
*
16660341 TTT-TAAT-T
1 TTTAAAATAT
16660349 TTTAAAATAT
1 TTTAAAATAT
16660359 TTTAAAATAT
1 TTTAAAATAT
16660369 TTTA
1 TTTA
16660373 TTTTATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 7 0.25
9 6 0.21
10 15 0.54
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTAAAATAT
Done.