Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015144.1 Kokia drynarioides strain JFW-HI SEQ_130188, whole genome shotgun sequence
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: 220396
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 446 characters in sequence are not A, C, G, or T
Found at i:19735 original size:22 final size:22
Alignment explanation
Indices: 19710--19752 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
19700 AGCCTCCCGA
19710 CGAAATGCTCGAATCCTTCCGT
1 CGAAATGCTCGAATCCTTCCGT
19732 CGAAATGCTCGAATCCTTCCG
1 CGAAATGCTCGAATCCTTCCG
19753 GAAGGATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.26
Consensus pattern (22 bp):
CGAAATGCTCGAATCCTTCCGT
Found at i:22258 original size:21 final size:21
Alignment explanation
Indices: 22219--22258 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
22209 ACATTAAATT
*
22219 AAATTAAATTAATCCTTTTGG
1 AAATTAAATTAATCATTTTGG
* *
22240 AAATTAATTTATTCATTTT
1 AAATTAAATTAATCATTTT
22259 ATAGTTTGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
AAATTAAATTAATCATTTTGG
Found at i:23253 original size:29 final size:30
Alignment explanation
Indices: 23209--23279 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
23199 ATTAATAAAA
*
23209 ATAAAATTATACTTTAA-CTTTCT-AAAATT
1 ATAAAATTATAATTTAATCTTT-TAAAAATT
*
23238 ATAAAATTTTAATTTAATCTTTTAAAAATT
1 ATAAAATTATAATTTAATCTTTTAAAAATT
*
23268 ATAAAAATATAA
1 ATAAAATTATAA
23280 ACTATTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 16 0.44
30 20 0.56
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.44
Consensus pattern (30 bp):
ATAAAATTATAATTTAATCTTTTAAAAATT
Found at i:24063 original size:12 final size:12
Alignment explanation
Indices: 24046--24085 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
24036 ATTTTGATGC
24046 TGTTATTTTTGT
1 TGTTATTTTTGT
*
24058 TGTTATTTTTGC
1 TGTTATTTTTGT
*
24070 TGCTATTTTTGT
1 TGTTATTTTTGT
24082 TGTT
1 TGTT
24086 TTTGTTATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.07, C:0.05, G:0.17, T:0.70
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:24070 original size:24 final size:25
Alignment explanation
Indices: 24034--24085 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
24024 GTTTTTTTAA
*
24034 TTATTTTGATGCTGTTATTTTTGTTG
1 TTATTTT-ATGCTGCTATTTTTGTTG
24060 TTATTTT-TGCTGCTATTTTTGTTG
1 TTATTTTATGCTGCTATTTTTGTTG
24084 TT
1 TT
24086 TTTGTTATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.72
26 7 0.28
ACGTcount: A:0.10, C:0.06, G:0.17, T:0.67
Consensus pattern (25 bp):
TTATTTTATGCTGCTATTTTTGTTG
Found at i:24088 original size:33 final size:32
Alignment explanation
Indices: 24046--24130 Score: 84
Period size: 33 Copynumber: 2.7 Consensus size: 32
24036 ATTTTGATGC
*
24046 TGTTATTTTTGTTGTTATTTTTGCTGCTATTTT
1 TGTTGTTTTTGTTGTTATTTTTGCTG-TATTTT
* * *
24079 TGTTGTTTTTGTTATT-GTTTTGCTGTTTTTT
1 TGTTGTTTTTGTTGTTATTTTTGCTGTATTTT
* * *
24110 TATTG-TTTGGATGTTATTTTT
1 TGTTGTTTTTGTTGTTATTTTT
24131 ATGCGTTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
30 7 0.17
31 13 0.31
32 8 0.19
33 14 0.33
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.71
Consensus pattern (32 bp):
TGTTGTTTTTGTTGTTATTTTTGCTGTATTTT
Found at i:24093 original size:30 final size:31
Alignment explanation
Indices: 24048--24117 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
24038 TTTGATGCTG
24048 TTATT-TTTGTTGTTA-T-TTTTGCTGCTATTT
1 TTATTGTTT-TTGTTATTGTTTTGCTG-TATTT
* *
24078 TTGTTGTTTTTGTTATTGTTTTGCTGTTTTT
1 TTATTGTTTTTGTTATTGTTTTGCTGTATTT
24109 TTATTGTTT
1 TTATTGTTT
24118 GGATGTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 10 0.29
31 16 0.47
32 8 0.24
ACGTcount: A:0.07, C:0.04, G:0.16, T:0.73
Consensus pattern (31 bp):
TTATTGTTTTTGTTATTGTTTTGCTGTATTT
Found at i:24112 original size:19 final size:19
Alignment explanation
Indices: 24076--24132 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
24066 TTGCTGCTAT
*
24076 TTTTGTTGTTTTTGTTATTG
1 TTTTGATGTTTTT-TTATTG
*
24096 TTTTGCTGTTTTTTTATTG
1 TTTTGATGTTTTTTTATTG
*
24115 TTTGGATGTTATTTTTAT
1 TTTTGATGTT-TTTTTAT
24133 GCGTTTTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.09, C:0.02, G:0.18, T:0.72
Consensus pattern (19 bp):
TTTTGATGTTTTTTTATTG
Found at i:24151 original size:11 final size:11
Alignment explanation
Indices: 24137--24182 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
24127 TTTTATGCGT
*
24137 TTTTACTATTA
1 TTTTAATATTA
* *
24148 TTTTACTATTT
1 TTTTAATATTA
24159 TTTTAATATTA
1 TTTTAATATTA
*
24170 TTTGAATATTA
1 TTTTAATATTA
24181 TT
1 TT
24183 GAACTTATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (11 bp):
TTTTAATATTA
Found at i:44881 original size:46 final size:46
Alignment explanation
Indices: 44823--44910 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
44813 AAGGGAAATA
* *
44823 AAAACCTAATATAATAAGGAAAATAACTAAAACAAAAACTCTTAAT
1 AAAACCTAATATAATAAAGAAAATAAATAAAACAAAAACTCTTAAT
* * * *
44869 AAAACCTGATATAATAAAGAAATTAAATAAATCTAAAACTCT
1 AAAACCTAATATAATAAAGAAAATAAATAAAACAAAAACTCT
44911 AAATGCAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.59, C:0.12, G:0.05, T:0.24
Consensus pattern (46 bp):
AAAACCTAATATAATAAAGAAAATAAATAAAACAAAAACTCTTAAT
Found at i:62354 original size:6 final size:6
Alignment explanation
Indices: 62343--62367 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
62333 TATTGATACA
62343 CACACG CACACG CACACG CACACG C
1 CACACG CACACG CACACG CACACG C
62368 TTCTTCCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CACACG
Found at i:65752 original size:18 final size:18
Alignment explanation
Indices: 65710--65752 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
65700 TACTTCATGC
* *
65710 TATTTTTTTAACTTTTTA
1 TATTTTTTTAAATCTTTA
*
65728 TAATTTTTTAAATCTTTA
1 TATTTTTTTAAATCTTTA
65746 T-TTTTTT
1 TATTTTTT
65753 ATTTTCGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTTTTTTAAATCTTTA
Found at i:67528 original size:90 final size:86
Alignment explanation
Indices: 67377--67552 Score: 307
Period size: 90 Copynumber: 2.0 Consensus size: 86
67367 TGTACATAAA
*
67377 GTCGAACATGTTATATCCTTATGGCTTAGCAACCCTTTCTTTTATTATGCCATGTCGTCTTTGAT
1 GTCGAACATGTTATATCCTTATGGCTTAGCAACCCTTTCTTTTATTATGCCATGTCATCTTTGAT
67442 AATCGCGAGCCGTGTAATTTT
66 AATCGCGAGCCGTGTAATTTT
67463 GTCGAACATGTTATATCCTTATGGCTTGCTTAGCAACCCTTTCTTTTATTATGCCATGTCATCTT
1 GTCGAACATGTTATATCCTTAT-G---GCTTAGCAACCCTTTCTTTTATTATGCCATGTCATCTT
67528 TGATAATCGCGAGCCGTGTAATTTT
62 TGATAATCGCGAGCCGTGTAATTTT
67553 ATGTTGTTCT
Statistics
Matches: 85, Mismatches: 1, Indels: 4
0.94 0.01 0.04
Matches are distributed among these distances:
86 22 0.26
87 1 0.01
90 62 0.73
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (86 bp):
GTCGAACATGTTATATCCTTATGGCTTAGCAACCCTTTCTTTTATTATGCCATGTCATCTTTGAT
AATCGCGAGCCGTGTAATTTT
Found at i:75470 original size:16 final size:16
Alignment explanation
Indices: 75449--75479 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
75439 AATTAAATAA
*
75449 TAATAAAAAACTAAAT
1 TAATAAAAAAATAAAT
75465 TAATAAAAAAATAAA
1 TAATAAAAAAATAAA
75480 ACATTTAGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
TAATAAAAAAATAAAT
Found at i:78569 original size:34 final size:34
Alignment explanation
Indices: 78526--78592 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
78516 TCATCTCCTA
**
78526 AAAAGTCATAC-AAAGTCATTTTGGTTACTTTAGC
1 AAAAGTCATACTAAA-TCATTAGGGTTACTTTAGC
78560 AAAAGTCATACTAAATCATTAGGGTTACTTTAG
1 AAAAGTCATACTAAATCATTAGGGTTACTTTAG
78593 ATAAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.90
35 3 0.10
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34
Consensus pattern (34 bp):
AAAAGTCATACTAAATCATTAGGGTTACTTTAGC
Found at i:82158 original size:21 final size:21
Alignment explanation
Indices: 82132--82174 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
82122 TCTGTTAAAA
*
82132 GCTCTATCAGAAATCTAACAT
1 GCTCTAACAGAAATCTAACAT
82153 GCTCTAACAGAAATCTAACAT
1 GCTCTAACAGAAATCTAACAT
82174 G
1 G
82175 ATATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.26
Consensus pattern (21 bp):
GCTCTAACAGAAATCTAACAT
Found at i:88025 original size:34 final size:34
Alignment explanation
Indices: 87987--88051 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
87977 GCACACGGTA
*
87987 TCTCACTCGCTAAATATCTGTGACACATGGACTT
1 TCTCACTCACTAAATATCTGTGACACATGGACTT
88021 TCTCACTCACTAAATATCTGTGACACATGGA
1 TCTCACTCACTAAATATCTGTGACACATGGA
88052 TTTTGTCCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (34 bp):
TCTCACTCACTAAATATCTGTGACACATGGACTT
Found at i:90279 original size:14 final size:14
Alignment explanation
Indices: 90262--90288 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
90252 AATAATAACA
90262 GTTAAATTCATTTG
1 GTTAAATTCATTTG
90276 GTTAAATTCATTT
1 GTTAAATTCATTT
90289 ATTAATCCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (14 bp):
GTTAAATTCATTTG
Found at i:96540 original size:20 final size:20
Alignment explanation
Indices: 96517--96601 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
96507 AATAAAAATC
*
96517 AATAAAAATTATTAAATTTT
1 AATAAAAATTATAAAATTTT
*
96537 AATAAAAATATAGAAAATATTT
1 AATAAAAAT-TATAAAAT-TTT
* * **
96559 AAGAAATATTA-AAAATTAG
1 AATAAAAATTATAAAATTTT
96578 AA-AAAAATTATAAAATTTT
1 AATAAAAATTATAAAATTTT
96597 -ATAAA
1 AATAAA
96602 GTCGTAAGAA
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.15
19 12 0.23
20 14 0.27
21 8 0.15
22 10 0.19
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (20 bp):
AATAAAAATTATAAAATTTT
Found at i:96889 original size:14 final size:16
Alignment explanation
Indices: 96860--96892 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
96850 CCTAAAAAAT
96860 AAAATATTATTCTAAA
1 AAAATATTATTCTAAA
96876 AAAATATT-TT-TAAA
1 AAAATATTATTCTAAA
96890 AAA
1 AAA
96893 TTAATTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 2 0.12
16 8 0.47
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATATTATTCTAAA
Found at i:98126 original size:22 final size:22
Alignment explanation
Indices: 98101--98154 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
98091 TATATATTTT
98101 AACCCAAACCCAATACCAACCA
1 AACCCAAACCCAATACCAACCA
* * *
98123 AACCTAAATCCAATACCATCCA
1 AACCCAAACCCAATACCAACCA
*
98145 AA-TCAAACCC
1 AACCCAAACCC
98155 TAAACCCAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.48, C:0.41, G:0.00, T:0.11
Consensus pattern (22 bp):
AACCCAAACCCAATACCAACCA
Found at i:99622 original size:21 final size:21
Alignment explanation
Indices: 99598--99700 Score: 82
Period size: 22 Copynumber: 4.8 Consensus size: 21
99588 ATTATATTGT
99598 TGTTTTGGTGCTGTTTTTTGC
1 TGTTTTGGTGCTGTTTTTTGC
* *
99619 TGTTTTGGTTTCTATTTTTTGC
1 TGTTTTGG-TGCTGTTTTTTGC
* * * **
99641 TATTTTGATGTTGTGTTTTTAT
1 TGTTTTGGTGCTGT-TTTTTGC
* *
99663 TGTTTTAGTG-TTTTTTTTGC
1 TGTTTTGGTGCTGTTTTTTGC
*
99683 TGTTTTGATTGCTGTTTT
1 TGTTTTG-GTGCTGTTTT
99701 GGTGCTACCT
Statistics
Matches: 60, Mismatches: 18, Indels: 7
0.71 0.21 0.08
Matches are distributed among these distances:
20 11 0.18
21 15 0.25
22 34 0.57
ACGTcount: A:0.06, C:0.06, G:0.21, T:0.67
Consensus pattern (21 bp):
TGTTTTGGTGCTGTTTTTTGC
Found at i:99758 original size:24 final size:24
Alignment explanation
Indices: 99731--99799 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 24
99721 TTTGGTGTTG
*
99731 TTTTTATTCTTATTTTTGTTGCTA
1 TTTTTATTATTATTTTTGTTGCTA
** *
99755 TTTTT-TCTATTATTTTTAATGCTG
1 TTTTTAT-TATTATTTTTGTTGCTA
* * *
99779 TTTTGATTGTTATTTTGGTTG
1 TTTTTATTATTATTTTTGTTG
99800 TTTGGATGTT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
23 1 0.03
24 32 0.94
25 1 0.03
ACGTcount: A:0.13, C:0.06, G:0.13, T:0.68
Consensus pattern (24 bp):
TTTTTATTATTATTTTTGTTGCTA
Found at i:99765 original size:21 final size:20
Alignment explanation
Indices: 99710--99765 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 20
99700 TGGTGCTACC
*
99710 TTTTTTACTATTTTGGTGTTG
1 TTTTTTTCTATTTT-GTGTTG
99731 TTTTTATTCTTATTTT-TGTTG
1 TTTTT-TTC-TATTTTGTGTTG
99752 CTATTTTTTCTATT
1 -T-TTTTTTCTATT
99766 ATTTTTAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
21 14 0.47
22 6 0.20
23 10 0.33
ACGTcount: A:0.11, C:0.07, G:0.11, T:0.71
Consensus pattern (20 bp):
TTTTTTTCTATTTTGTGTTG
Found at i:101119 original size:6 final size:6
Alignment explanation
Indices: 101108--101164 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
101098 TATATATTTT
* *
101108 AACCCA AACCCA AACCCA AACCC- AA-CCA AACCTA AATCCA ATA-CC-
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA A-ACCCA
101153 -ACCCA AACCCA A
1 AACCCA AACCCA A
101165 CCCTAAGCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
3 1 0.02
4 4 0.10
5 4 0.10
6 32 0.76
7 1 0.02
ACGTcount: A:0.49, C:0.46, G:0.00, T:0.05
Consensus pattern (6 bp):
AACCCA
Found at i:101137 original size:22 final size:22
Alignment explanation
Indices: 101111--101164 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
101101 ATATTTTAAC
101111 CCAAACCCAAACCCAA-ACCCAA
1 CCAAACCCAAACCCAATA-CCAA
* * *
101133 CCAAACCTAAATCCAATACCAC
1 CCAAACCCAAACCCAATACCAA
101155 CCAAACCCAA
1 CCAAACCCAA
101165 CCCTAAGCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.48, C:0.46, G:0.00, T:0.06
Consensus pattern (22 bp):
CCAAACCCAAACCCAATACCAA
Found at i:101138 original size:16 final size:16
Alignment explanation
Indices: 101117--101166 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
101107 TAACCCAAAC
101117 CCAAACCCAAACCCAA
1 CCAAACCCAAACCCAA
* *
101133 CCAAACCTAAATCCAATA
1 CCAAACCCAAA-CCCA-A
101151 CC--ACCCAAACCCAA
1 CCAAACCCAAACCCAA
101165 CC
1 CC
101167 CTAAGCTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 3 0.11
15 3 0.11
16 16 0.57
17 3 0.11
18 3 0.11
ACGTcount: A:0.46, C:0.48, G:0.00, T:0.06
Consensus pattern (16 bp):
CCAAACCCAAACCCAA
Found at i:101479 original size:17 final size:18
Alignment explanation
Indices: 101432--101479 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
101422 TATTAAGTCA
101432 TTATATATTT-TATACATT
1 TTATATATTTAT-TACATT
*
101450 TTA-ATAATTATTA-ATT
1 TTATATATTTATTACATT
101466 TTATATATTTATTA
1 TTATATATTTATTA
101480 TACATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 6 0.23
17 16 0.62
18 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATATTTATTACATT
Found at i:102101 original size:15 final size:16
Alignment explanation
Indices: 102074--102108 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
102064 TATAATTTTT
102074 TAAAAGTATTTTTAAA
1 TAAAAGTATTTTTAAA
102090 TAAAAG-ATTTTTAAA
1 TAAAAGTATTTTTAAA
102105 -AAAA
1 TAAAA
102109 ATATCCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 9 0.47
16 6 0.32
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (16 bp):
TAAAAGTATTTTTAAA
Found at i:103833 original size:21 final size:20
Alignment explanation
Indices: 103809--103851 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
103799 ACACGATTCC
103809 AAACAACAAAACAAAAAATAA
1 AAACAACAAAA-AAAAAATAA
* *
103830 AAACAACACAATAAAAATAA
1 AAACAACAAAAAAAAAATAA
103850 AA
1 AA
103852 TAAATAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.79, C:0.14, G:0.00, T:0.07
Consensus pattern (20 bp):
AAACAACAAAAAAAAAATAA
Found at i:104972 original size:22 final size:23
Alignment explanation
Indices: 104947--104995 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
104937 GAATTTAGTT
104947 TTTA-TATTTTTATTTTCAAAAA
1 TTTAGTATTTTTATTTTCAAAAA
* * *
104969 TTTAGTTTTTTTATTTTTAAAAT
1 TTTAGTATTTTTATTTTCAAAAA
104992 TTTA
1 TTTA
104996 AAATTCAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTAGTATTTTTATTTTCAAAAA
Found at i:106205 original size:25 final size:25
Alignment explanation
Indices: 106171--106221 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
106161 GTATGTTATA
106171 TAGGTAGAGATGTTCATGGGTCAGG
1 TAGGTAGAGATGTTCATGGGTCAGG
*
106196 TAGGTAGAGATGTTCATGGGTTAGG
1 TAGGTAGAGATGTTCATGGGTCAGG
106221 T
1 T
106222 CGAGTCAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.06, G:0.39, T:0.31
Consensus pattern (25 bp):
TAGGTAGAGATGTTCATGGGTCAGG
Found at i:108123 original size:23 final size:25
Alignment explanation
Indices: 108097--108142 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
108087 CCAATTAGGG
108097 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
108120 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
108143 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:108559 original size:15 final size:15
Alignment explanation
Indices: 108522--108560 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
108512 TTATGTGTGC
*
108522 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
108537 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
108551 TTAATTCTTG
1 TTAATTCTTG
108561 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:111362 original size:10 final size:10
Alignment explanation
Indices: 111347--111380 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
111337 CATGTTTTTA
111347 AAAAAAATTG
1 AAAAAAATTG
*
111357 AAAAAAATTA
1 AAAAAAATTG
111367 AAAAAAATTG
1 AAAAAAATTG
111377 AAAA
1 AAAA
111381 GTTCAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:112376 original size:13 final size:12
Alignment explanation
Indices: 112357--112416 Score: 61
Period size: 11 Copynumber: 4.9 Consensus size: 12
112347 TTATTGTTTA
112357 GAAAAAAAAAAT
1 GAAAAAAAAAAT
*
112369 G-AAAAAAAAGT
1 GAAAAAAAAAAT
*
112380 CGAAAAGAAAAATT
1 -GAAAA-AAAAAAT
112394 GAAAAAAAAAA-
1 GAAAAAAAAAAT
112405 GAAAAAGAAAAA
1 GAAAAA-AAAAA
112417 AAAGAGACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
11 15 0.37
12 12 0.29
13 8 0.20
14 6 0.15
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (12 bp):
GAAAAAAAAAAT
Found at i:112404 original size:19 final size:17
Alignment explanation
Indices: 112382--112429 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 17
112372 AAAAAAGTCG
112382 AAAAGAAAAATTGAAAAAA
1 AAAAGAAAAA--GAAAAAA
112401 AAAAGAAAAAGAAAAAA
1 AAAAGAAAAAGAAAAAA
*
112418 AAGAGACAAAAG
1 AAAAGA-AAAAG
112430 TGTGTTTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 12 0.44
18 5 0.19
19 10 0.37
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (17 bp):
AAAAGAAAAAGAAAAAA
Found at i:112410 original size:25 final size:25
Alignment explanation
Indices: 112356--112416 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
112346 TTTATTGTTT
*
112356 AGAAAAA-AAAAATGAAAAAAAAGT
1 AGAAAAAGAAAAATGAAAAAAAAGA
*
112380 CG-AAAAGAAAAATTGAAAAAAAA-A
1 AGAAAAAGAAAAA-TGAAAAAAAAGA
112404 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
112417 AAAGAGACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 4 0.13
24 7 0.23
25 20 0.65
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.07
Consensus pattern (25 bp):
AGAAAAAGAAAAATGAAAAAAAAGA
Found at i:123756 original size:25 final size:26
Alignment explanation
Indices: 123714--123766 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
123704 GAAAATAAAG
* *
123714 GTGAGAAATATGTGATTATGTAT-AT
1 GTGAGAAAAATGTGATTATATATGAT
123739 GTGATGAAAAATGT-ATTATATATGAT
1 GTGA-GAAAAATGTGATTATATATGAT
123765 GT
1 GT
123767 ATAAGTTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.40
Consensus pattern (26 bp):
GTGAGAAAAATGTGATTATATATGAT
Found at i:123972 original size:41 final size:40
Alignment explanation
Indices: 123924--124023 Score: 107
Period size: 38 Copynumber: 2.5 Consensus size: 40
123914 TCGACCTTGA
** *
123924 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
123964 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGTTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
124002 GTCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
124024 GTTTATTGCT
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
37 11 0.24
38 17 0.37
39 4 0.09
40 3 0.07
41 11 0.24
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:126208 original size:20 final size:20
Alignment explanation
Indices: 126185--126234 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
126175 GTTCTTTTAG
*
126185 ATTTTTTTATCGT-ACTAAT
1 ATTTTTTTATAGTGACTAAT
* *
126204 AATTTTTTATAGTGATTAAT
1 ATTTTTTTATAGTGACTAAT
126224 ATTTTTTTATA
1 ATTTTTTTATA
126235 TATAAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (20 bp):
ATTTTTTTATAGTGACTAAT
Found at i:127679 original size:29 final size:29
Alignment explanation
Indices: 127637--127695 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
127627 ATTCTTGAAA
127637 AAAGAGATCATTTGTTGATATGGAATGCC
1 AAAGAGATCATTTGTTGATATGGAATGCC
127666 AAAGAGATCATTTGTTGATATGGAATGCC
1 AAAGAGATCATTTGTTGATATGGAATGCC
127695 A
1 A
127696 GAAAGGATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.31
Consensus pattern (29 bp):
AAAGAGATCATTTGTTGATATGGAATGCC
Found at i:127713 original size:29 final size:29
Alignment explanation
Indices: 127637--127714 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
127627 ATTCTTGAAA
* *
127637 AAAGAGATCATTTGTTGATATGGAATGCC
1 AAAGAGATCATATGCTGATATGGAATGCC
* *
127666 AAAGAGATCATTTGTTGATATGGAATGCC
1 AAAGAGATCATATGCTGATATGGAATGCC
127695 AGAA-AGGATCATAT-CTGATA
1 A-AAGA-GATCATATGCTGATA
127715 ATGCTTTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 36 0.80
30 9 0.20
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.29
Consensus pattern (29 bp):
AAAGAGATCATATGCTGATATGGAATGCC
Found at i:129269 original size:78 final size:77
Alignment explanation
Indices: 129064--129501 Score: 327
Period size: 78 Copynumber: 5.7 Consensus size: 77
129054 ATTGAAGATT
* * * * * *
129064 CCAATCTCTTACCCCAAGCCTGGGGTAGATTGAAGTTATCCGATCTTTTACCTCGAGCTTGAAGT
1 CCAATCTCTTACCCCGAGCCTGGGGAAGATTGAAGTCATCCGATCTTTTACCCCGAGCTTG-GGC
129129 AGATCACCATCAG
65 AGATCACCATCAG
** * *
129142 CCAATCTCTTA-CTTGAGCCTGGGGAAGATTAAAGCCATCCGATCTTTTACCCCGAGCTTAGGGC
1 CCAATCTCTTACCCCGAGCCTGGGGAAGATTGAAGTCATCCGATCTTTTACCCCGAGCTT-GGGC
* *
129206 AAATCAACATCAG
65 AGATCACCATCAG
* * * * ** *
129219 TCAATCTTTTACCCCGAGCCTGAGGCAGATTGAAGTCATCTAATCTTTTACCCCGAGCCTGGGGC
1 CCAATCTCTTACCCCGAGCCTGGGGAAGATTGAAGTCATCCGATCTTTTACCCCGAG-CTTGGGC
*
129284 AGATCACCATCAA
65 AGATCACCATCAG
* * * ** * * *
129297 CCAATCTCTTACGCCGAGCCT-GGGATAGATTGCAA-CCATCCGATCTCTTACTTCGATCATAGA
1 CCAATCTCTTACCCCGAGCCTGGGGA-AGATTG-AAGTCATCCGATCTTTTACCCCGAGC-TTGG
*
129360 GCAGATCA-CAGTCAT
63 GCAGATCACCA-TCAG
* * * * * * * * * *
129375 CCGATCTTTTACCTCGAGCCT-AGGCAGA-TCACCA-TCAGCCAATCTCTTACCCCGAACTTGGG
1 CCAATCTCTTACCCCGAGCCTGGGGAAGATTGA--AGTCATCCGATCTTTTACCCCGAGCTT-GG
129437 GCA-ATCACCATCAG
63 GCAGATCACCATCAG
* * * *
129451 CCAATCTCTTACCCCGAG-CTTGGGATAGATTGCAGCCATCCGATCTCTTAC
1 CCAATCTCTTACCCCGAGCCTGGGGA-AGATTGAAGTCATCCGATCTTTTAC
129502 TTCGATCATG
Statistics
Matches: 278, Mismatches: 67, Indels: 31
0.74 0.18 0.08
Matches are distributed among these distances:
75 3 0.01
76 27 0.10
77 109 0.39
78 135 0.49
79 4 0.01
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (77 bp):
CCAATCTCTTACCCCGAGCCTGGGGAAGATTGAAGTCATCCGATCTTTTACCCCGAGCTTGGGCA
GATCACCATCAG
Found at i:129376 original size:39 final size:39
Alignment explanation
Indices: 129333--129583 Score: 165
Period size: 38 Copynumber: 6.5 Consensus size: 39
129323 AGATTGCAAC
* * *
129333 CATCCGATCTCTTACTTCGATCATAGAGCAGATCACAGT
1 CATCCGATCTCTTACCTCGAGCATAGGGCAGATCACAGT
* *
129372 CATCCGATCTTTTACCTCGAGCCTA-GGCAGATCACCA-T
1 CATCCGATCTCTTACCTCGAGCATAGGGCAGATCA-CAGT
* * * * * *
129410 CAGCCAATCTCTTACCCCGAACTTGGGGCA-ATCACCA-T
1 CATCCGATCTCTTACCTCGAGCATAGGGCAGATCA-CAGT
* * * * * ** *
129448 CAGCCAATCTCTTACCCCGAGC-TTGGGATAGATTGCAGC
1 CATCCGATCTCTTACCTCGAGCATAGGG-CAGATCACAGT
* * *
129487 CATCCGATCTCTTACTTCGATCATGGGGCAGATCACAGT
1 CATCCGATCTCTTACCTCGAGCATAGGGCAGATCACAGT
* * *
129526 CATCCGATCTTTTACCTCGAGCCTA-GGCAGATTACCA-T
1 CATCCGATCTCTTACCTCGAGCATAGGGCAGATCA-CAGT
* * *
129564 CAGCCAATCTTTTACCTCGA
1 CATCCGATCTCTTACCTCGA
129584 ACTTGGGGCA
Statistics
Matches: 169, Mismatches: 36, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
37 4 0.02
38 86 0.51
39 75 0.44
40 4 0.02
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (39 bp):
CATCCGATCTCTTACCTCGAGCATAGGGCAGATCACAGT
Found at i:129476 original size:154 final size:155
Alignment explanation
Indices: 129106--129596 Score: 584
Period size: 154 Copynumber: 3.2 Consensus size: 155
129096 AAGTTATCCG
* * ** * ** *
129106 ATCTTTTACCTCGAGCTTGAAGTAGATCACCATCAGCCAATCTCTTA-CTTGAGCCTGGGGA-AG
1 ATCTTTTACCCCGAACTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAG-CTTGGGATAG
* * ** * * * *
129169 ATT-AAAGCCATCCGATCTTTTACCCCGAGCTTAGGGCAAATCAACA-TCAGT-CAATCTTTTAC
65 ATTGCAA-CCATCCGATCTCTTACTTCGATCATAGGGCAGATC-ACAGTCA-TCCGATCTTTTAC
* * * *
129231 CCCGAGCCTGAGGCAGATTGA--AGTCATCTA
127 CTCGAGCCT-AGGCAGA-TCACCA-TCAGCCA
* * * * *
129261 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAACCAATCTCTTACGCCGAGCCTGGGATAGA
1 ATCTTTTACCCCGAACTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGATAGA
*
129326 TTGCAACCATCCGATCTCTTACTTCGATCATAGAGCAGATCACAGTCATCCGATCTTTTACCTCG
66 TTGCAACCATCCGATCTCTTACTTCGATCATAGGGCAGATCACAGTCATCCGATCTTTTACCTCG
129391 AGCCTAGGCAGATCACCATCAGCCA
131 AGCCTAGGCAGATCACCATCAGCCA
*
129416 ATCTCTTACCCCGAACTTGGGGCA-ATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGATAGA
1 ATCTTTTACCCCGAACTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGATAGA
* *
129480 TTGCAGCCATCCGATCTCTTACTTCGATCATGGGGCAGATCACAGTCATCCGATCTTTTACCTCG
66 TTGCAACCATCCGATCTCTTACTTCGATCATAGGGCAGATCACAGTCATCCGATCTTTTACCTCG
*
129545 AGCCTAGGCAGATTACCATCAGCCA
131 AGCCTAGGCAGATCACCATCAGCCA
*
129570 ATCTTTTACCTCGAACTTGGGGCAGAT
1 ATCTTTTACCCCGAACTTGGGGCAGAT
129597 AGAAGCTATT
Statistics
Matches: 292, Mismatches: 36, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
154 147 0.50
155 85 0.29
156 58 0.20
157 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (155 bp):
ATCTTTTACCCCGAACTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGATAGA
TTGCAACCATCCGATCTCTTACTTCGATCATAGGGCAGATCACAGTCATCCGATCTTTTACCTCG
AGCCTAGGCAGATCACCATCAGCCA
Found at i:129517 original size:116 final size:117
Alignment explanation
Indices: 129183--129674 Score: 345
Period size: 116 Copynumber: 4.2 Consensus size: 117
129173 AAGCCATCCG
* * * * * * *
129183 ATCTTTTACCCCGAGCTT-AGGGCAAATCAACATCAGTCAATCTTTTACCCCGAGCCTGAGG-CA
1 ATCTCTTACCCCGAGCTTGA-GGCAGATCACCATCAGCCAATCTCTTACCCCGAACTTG-GGACA
* * ** * * * * *
129246 GATTGAAGTCATCTAATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAACCA
64 GATAGAAGCCATCCGATCTCTTACCTCGAGCATGAGGCAGATCACCATCAGCCA
* * * ** * * * * ** * * *
129300 ATCTCTTACGCCGAGCCTG-GGATAGATTGCAACCATCCGATCTCTTACTTCGATCAT-AGAGCA
1 ATCTCTTACCCCGAGCTTGAGG-CAGATCACCATCAGCCAATCTCTTACCCCGAACTTGGGA-CA
* * * *
129363 GATCA-CAGTCATCCGATCTTTTACCTCGAGCCT-AGGCAGATCACCATCAGCCA
64 GAT-AGAAGCCATCCGATCTCTTACCTCGAGCATGAGGCAGATCACCATCAGCCA
* * * *
129416 ATCTCTTACCCCGAACTTGGGGCA-ATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGATAGA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCCGAACTTGGGACAGA
* * * * * * *
129480 TTGCAGCCATCCGATCTCTTACTTCGATCATGGGGCAGATCA-CAGTCATCCG
66 TAGAAGCCATCCGATCTCTTACCTCGAGCATGAGGCAGATCACCA-TCAGCCA
* * * * * * *
129532 ATCTTTTACCTCGAGCCT-AGGCAGATTACCATCAGCCAATCTTTTACCTCGAACTTGGGGCAGA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCCGAACTTGGGACAGA
* * * * * *
129596 TAGAAGCTATTCGATCTTTTACCTCGAGCCTGAGGCAGATTACCATCAGCTA
66 TAGAAGCCATCCGATCTCTTACCTCGAGCATGAGGCAGATCACCATCAGCCA
129648 ATCTCTTACCCCGAGCTTGAGGCAGAT
1 ATCTCTTACCCCGAGCTTGAGGCAGAT
129675 TGCAACCATT
Statistics
Matches: 284, Mismatches: 78, Indels: 26
0.73 0.20 0.07
Matches are distributed among these distances:
115 56 0.20
116 152 0.54
117 76 0.27
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (117 bp):
ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCCGAACTTGGGACAGA
TAGAAGCCATCCGATCTCTTACCTCGAGCATGAGGCAGATCACCATCAGCCA
Found at i:129633 original size:39 final size:38
Alignment explanation
Indices: 129103--129700 Score: 135
Period size: 39 Copynumber: 15.4 Consensus size: 38
129093 TTGAAGTTAT
* * * * *
129103 CCGATCTTTTACCTCGAGCTTGAAGTAGATCACCATCAG
1 CCGATCTTTTACCTCGAGCCTGAGGCAGAT-ACAAGCAG
* * * * * *
129142 CCAATCTCTTA-CTTGAGCCTGGGGAAGATTA-AAGCCAT
1 CCGATCTTTTACCTCGAGCCTGAGGCAGA-TACAAG-CAG
* * * *
129180 CCGATCTTTTACCCCGAG-CTTAGGGCAAAT-CAACATCAG
1 CCGATCTTTTACCTCGAGCCTGA-GGCAGATAC-A-AGCAG
* * * ** *
129219 TCAATCTTTTACCCCGAGCCTGAGGCAGATTGAAGTCAT
1 CCGATCTTTTACCTCGAGCCTGAGGCAGATACAAG-CAG
** * * * * *
129258 CTAATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAA
1 CCGATCTTTTACCTCGAGCCTGAGGCAGAT-ACAAGCAG
* * * * * *
129297 CCAATCTCTTACGC-CGAGCCTG-GGATAGATTGCAACCAT
1 CCGATCTTTTAC-CTCGAGCCTGAGG-CAGA-TACAAGCAG
* * * * *
129336 CCGATCTCTTACTTCGATCAT-AGAGCAGAT-CACAGTCAT
1 CCGATCTTTTACCTCGAGCCTGAG-GCAGATACA-AG-CAG
* *
129375 CCGATCTTTTACCTCGAGCCT-AGGCAGATCACCATCAG
1 CCGATCTTTTACCTCGAGCCTGAGGCAGAT-ACAAGCAG
* * * * * * * *
129413 CCAATCTCTTACCCCGAACTTGGGGCA-ATCACCATCAG
1 CCGATCTTTTACCTCGAGCCTGAGGCAGAT-ACAAGCAG
* * * * * * *
129451 CCAATCTCTTACCCCGAGCTTG-GGATAGATTGC-AGCCAT
1 CCGATCTTTTACCTCGAGCCTGAGG-CAGA-TACAAG-CAG
* * * * * *
129490 CCGATCTCTTACTTCGATCATGGGGCAGAT-CACAGTCAT
1 CCGATCTTTTACCTCGAGCCTGAGGCAGATACA-AG-CAG
* *
129529 CCGATCTTTTACCTCGAGCCT-AGGCAGATTACCATCAG
1 CCGATCTTTTACCTCGAGCCTGAGGCAGA-TACAAGCAG
* * * * * *
129567 CCAATCTTTTACCTCGAACTTGGGGCAGATAGAAGCTAT
1 CCGATCTTTTACCTCGAGCCTGAGGCAGATACAAGC-AG
* * *
129606 TCGATCTTTTACCTCGAGCCTGAGGCAGATTACCATCAG
1 CCGATCTTTTACCTCGAGCCTGAGGCAGA-TACAAGCAG
** * * * * * *
129645 CTAATCTCTTACCCCGAGCTTGAGGCAGATTGCAACCAT
1 CCGATCTTTTACCTCGAGCCTGAGGCAGA-TACAAGCAG
*
129684 TCGATCTTTTACCTCGA
1 CCGATCTTTTACCTCGA
129701 TCATTAGGCA
Statistics
Matches: 412, Mismatches: 113, Indels: 68
0.69 0.19 0.11
Matches are distributed among these distances:
37 6 0.01
38 121 0.29
39 268 0.65
40 17 0.04
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (38 bp):
CCGATCTTTTACCTCGAGCCTGAGGCAGATACAAGCAG
Found at i:129672 original size:78 final size:77
Alignment explanation
Indices: 129376--129738 Score: 304
Period size: 78 Copynumber: 4.7 Consensus size: 77
129366 CACAGTCATC
* *
129376 CGATCTTTTACCTCGAGCCTAGGCAGATCACCATCAGCCAATCTCTTACCCCGAACTTGGGGCA-
1 CGATCTTTTACCTCGAGCCTAGGCAGATTACCATCAGCCAATCTCTTACCCCGAACTTGAGGCAG
* * **
129440 ATCA-CCATCAGC
66 AT-AGCAACCATT
* * * * * * * * * * ** * * *
129452 CAATCTCTTACCCCGAGCTTGGGATAGATT-GCAGCCATCCGATCTCTTACTTCGATCATGGGGC
1 CGATCTTTTACCTCGAGCCTAGG-CAGATTACCA-TCAGCCAATCTCTTACCCCGAACTTGAGGC
** *
129516 AGATCA-CAGTCATC
64 AGAT-AGCAACCATT
* * *
129530 CGATCTTTTACCTCGAGCCTAGGCAGATTACCATCAGCCAATCTTTTACCTCGAACTTGGGGCAG
1 CGATCTTTTACCTCGAGCCTAGGCAGATTACCATCAGCCAATCTCTTACCCCGAACTTGAGGCAG
*
129595 ATAG-AAGCTATT
66 ATAGCAA-CCATT
* *
129607 CGATCTTTTACCTCGAGCCTGAGGCAGATTACCATCAGCTAATCTCTTACCCCGAGCTTGAGGCA
1 CGATCTTTTACCTCGAGCCT-AGGCAGATTACCATCAGCCAATCTCTTACCCCGAACTTGAGGCA
*
129672 GATTGCAACCATT
65 GATAGCAACCATT
* * * * *
129685 CGATCTTTTACCTCGATCATTAGGCAGATCATCGTCAGCCAATCTCTTACCCCG
1 CGATCTTTTACCTCGAGC-CTAGGCAGATTACCATCAGCCAATCTCTTACCCCG
129739 CGATAGGGGC
Statistics
Matches: 229, Mismatches: 49, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
76 22 0.10
77 82 0.36
78 122 0.53
79 3 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (77 bp):
CGATCTTTTACCTCGAGCCTAGGCAGATTACCATCAGCCAATCTCTTACCCCGAACTTGAGGCAG
ATAGCAACCATT
Found at i:129710 original size:39 final size:38
Alignment explanation
Indices: 129323--129713 Score: 165
Period size: 39 Copynumber: 10.1 Consensus size: 38
129313 AGCCTGGGAT
* * * * *
129323 AGATTGCAACCATCCGATCTCTTACTTCGATCATAGAGC
1 AGATTACAACCATCCGATCTTTTACCTCGAGCTTAG-GC
* ** *
129362 AGATCACAGTCATCCGATCTTTTACCTCGAGCCTAGGC
1 AGATTACAACCATCCGATCTTTTACCTCGAGCTTAGGC
* * * * * * * * *
129400 AGATCACCATCAGCCAATCTCTTACCCCGAACTTGGGGC
1 AGATTACAACCATCCGATCTTTTACCTCGAGCTT-AGGC
* * * * * * * * *
129439 A-ATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGAT
1 AGATTACAACCATCCGATCTTTTACCTCGAGCTTAGG-C
* * * * * **
129477 AGATTGCAGCCATCCGATCTCTTACTTCGATCATGGGGC
1 AGATTACAACCATCCGATCTTTTACCTCGAGC-TTAGGC
* ** *
129516 AGATCACAGTCATCCGATCTTTTACCTCGAGCCTAGGC
1 AGATTACAACCATCCGATCTTTTACCTCGAGCTTAGGC
* * * * * *
129554 AGATTACCATCAGCCAATCTTTTACCTCGAACTTGGGGC
1 AGATTACAACCATCCGATCTTTTACCTCGAGCTT-AGGC
* * * *
129593 AGA-TAGAAGCTATTCGATCTTTTACCTCGAGCCTGAGGC
1 AGATTACAA-CCATCCGATCTTTTACCTCGAG-CTTAGGC
* * * ** * *
129632 AGATTACCATCAGCTAATCTCTTACCCCGAGCTTGAGGC
1 AGATTACAACCATCCGATCTTTTACCTCGAGCTT-AGGC
* * *
129671 AGATTGCAACCATTCGATCTTTTACCTCGATCATTAGGC
1 AGATTACAACCATCCGATCTTTTACCTCGAGC-TTAGGC
129710 AGAT
1 AGAT
129714 CATCGTCAGC
Statistics
Matches: 263, Mismatches: 79, Indels: 20
0.73 0.22 0.06
Matches are distributed among these distances:
37 3 0.01
38 95 0.36
39 154 0.59
40 11 0.04
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (38 bp):
AGATTACAACCATCCGATCTTTTACCTCGAGCTTAGGC
Found at i:130155 original size:124 final size:124
Alignment explanation
Indices: 129943--130202 Score: 414
Period size: 124 Copynumber: 2.1 Consensus size: 124
129933 TCCCGGTGAA
* * *
129943 ATACAGAGAAGTAAACCAATTCAATGAAACGAAGCTCAATGTGAGTGAAACTTCCAAACCTCATC
1 ATACAGAGAAGTAAACCAATTCAATGAAACGAAACTCAATATGAGTGAAACTTCCAAACCCCATC
*
130008 TTCTTGATGAGATACAAAGAAGTGGGTCGAAGCAATAAAGTGGTCATCTTCTTGATGAG
66 TTCCTGATGAGATACAAAGAAGTGGGTCGAAGCAATAAAGTGGTCATCTTCTTGATGAG
* * * *
130067 ATACAGAGAAGTAGACCAATTTAATGAAGCGAAACTCAATATGAGTGAAACTTTCAAACCCCATC
1 ATACAGAGAAGTAAACCAATTCAATGAAACGAAACTCAATATGAGTGAAACTTCCAAACCCCATC
*
130132 TTCCTGATGAGATATAGAA-AAGTGGGTCGAAGCAATAAAGTGGTCATCTTCTTGATGAG
66 TTCCTGATGAGATACA-AAGAAGTGGGTCGAAGCAATAAAGTGGTCATCTTCTTGATGAG
*
130191 ATGCAGAGAAGT
1 ATACAGAGAAGT
130203 GAACTAAATT
Statistics
Matches: 125, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
124 123 0.98
125 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (124 bp):
ATACAGAGAAGTAAACCAATTCAATGAAACGAAACTCAATATGAGTGAAACTTCCAAACCCCATC
TTCCTGATGAGATACAAAGAAGTGGGTCGAAGCAATAAAGTGGTCATCTTCTTGATGAG
Found at i:130902 original size:2 final size:2
Alignment explanation
Indices: 130895--130920 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
130885 ATATGTTTGT
130895 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
130921 CATTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:131596 original size:30 final size:30
Alignment explanation
Indices: 131555--131772 Score: 203
Period size: 30 Copynumber: 7.3 Consensus size: 30
131545 AGCAACCCCC
*
131555 AAACTTTTCCAAAATCACATTTTAA-CCTCT
1 AAACTTTTCCAAAATTACATTTTAACCCT-T
* * * *
131585 AAACTTCTCCAAAATTATATTTTGACCCAT
1 AAACTTTTCCAAAATTACATTTTAACCCTT
* *
131615 GAACTTTTCCAAAATTACATTTTAGCCCTT
1 AAACTTTTCCAAAATTACATTTTAACCCTT
* * *
131645 AAA-ATTTCCAAATTTTCATTTTAA-CCTCT
1 AAACTTTTCCAAAATTACATTTTAACCCT-T
* *
131674 AAACTTCTCTAAAATTACATTTT-ACTCC-T
1 AAACTTTTCCAAAATTACATTTTAAC-CCTT
*
131703 AAACTTTTCCAAAATTATATTTTAACCCTT
1 AAACTTTTCCAAAATTACATTTTAACCCTT
*** * *
131733 AAACTTAAACAAAATTACACTTTGACCCTT
1 AAACTTTTCCAAAATTACATTTTAACCCTT
131763 AAACCTTTTC
1 AAA-CTTTTC
131773 AACCTCGTAT
Statistics
Matches: 147, Mismatches: 33, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
28 3 0.02
29 45 0.31
30 92 0.63
31 7 0.05
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (30 bp):
AAACTTTTCCAAAATTACATTTTAACCCTT
Found at i:131676 original size:29 final size:29
Alignment explanation
Indices: 131572--131670 Score: 67
Period size: 29 Copynumber: 3.3 Consensus size: 29
131562 TCCAAAATCA
* *
131572 CATTTTAACCTC-TAAACTTCTCCAAAATTAT
1 CATTTTAACC-CATAAAATT-TCC-AAATTTT
* ** * *
131603 -ATTTTGACCCATGAACTTTTCCAAAATTA
1 CATTTTAACCCAT-AAAATTTCCAAATTTT
* *
131632 CATTTTAGCCCTTAAAATTTCCAAATTTT
1 CATTTTAACCCATAAAATTTCCAAATTTT
131661 CATTTTAACC
1 CATTTTAACC
131671 TCTAAACTTC
Statistics
Matches: 51, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
29 26 0.51
30 21 0.41
31 4 0.08
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.40
Consensus pattern (29 bp):
CATTTTAACCCATAAAATTTCCAAATTTT
Found at i:131688 original size:59 final size:59
Alignment explanation
Indices: 131555--131738 Score: 182
Period size: 59 Copynumber: 3.1 Consensus size: 59
131545 AGCAACCCCC
* * * *
131555 AAACTTTTCCAAAATCACATTTTAAC-CTCTAAAC-TTCTCCAAAATTATATTTTGACCCAT
1 AAACTTCTCCAAAATTACATTTT-ACTC-CTAAACATT-TCCAAAATTATATTTTAACCCTT
* * *
131615 GAACTTTTCCAAAATTACATTTTAGC-CCTTAAA-ATTTCC-AAATTTTCATTTTAA-CCTCT
1 AAACTTCTCCAAAATTACATTTTA-CTCC-TAAACATTTCCAAAATTAT-ATTTTAACCCT-T
* *
131674 AAACTTCTCTAAAATTACATTTTACTCCTAAACTTTTCCAAAATTATATTTTAACCCTT
1 AAACTTCTCCAAAATTACATTTTACTCCTAAACATTTCCAAAATTATATTTTAACCCTT
131733 AAACTT
1 AAACTT
131739 AAACAAAATT
Statistics
Matches: 105, Mismatches: 10, Indels: 19
0.78 0.07 0.14
Matches are distributed among these distances:
58 13 0.12
59 54 0.51
60 38 0.36
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (59 bp):
AAACTTCTCCAAAATTACATTTTACTCCTAAACATTTCCAAAATTATATTTTAACCCTT
Found at i:131747 original size:59 final size:57
Alignment explanation
Indices: 131564--131772 Score: 172
Period size: 59 Copynumber: 3.5 Consensus size: 57
131554 CAAACTTTTC
* * * * * **
131564 CAAAATCACATTTTAACCTCTAAACTTCTCCAAAATTATATTTTGACCCATGAACTTTTC
1 CAAAATTACATTTT-ACC-CTAAACTTTTCCAAAATTATATTTTAACCCTTAAAC-TTAA
* * **
131624 CAAAATTACATTTTAGCCCTTAAA-ATTTCC-AAATTTTCATTTTAA-CCTCTAAACTTCT
1 CAAAATTACATTTTA-CCC-TAAACTTTTCCAAAATTAT-ATTTTAACCCT-TAAACTTAA
131682 CTAAAATTACATTTTACTCCTAAACTTTTCCAAAATTATATTTTAACCCTTAAACTTAAA
1 C-AAAATTACATTTTAC-CCTAAACTTTTCCAAAATTATATTTTAACCCTTAAACTT-AA
*
131742 CAAAATTACACTTTGACCCTTAAACCTTTTC
1 CAAAATTACA-TTTTACCC-TAAA-CTTTTC
131773 AACCTCGTAT
Statistics
Matches: 122, Mismatches: 14, Indels: 25
0.76 0.09 0.16
Matches are distributed among these distances:
58 16 0.13
59 62 0.51
60 38 0.31
61 6 0.05
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (57 bp):
CAAAATTACATTTTACCCTAAACTTTTCCAAAATTATATTTTAACCCTTAAACTTAA
Found at i:137130 original size:29 final size:28
Alignment explanation
Indices: 137098--137212 Score: 95
Period size: 29 Copynumber: 4.0 Consensus size: 28
137088 AAACTCCGTG
* * *
137098 TCAAAATATGATTTTGGAGAAGTTTGAGT
1 TCAAAACATAATTTTGGAGAAGTTT-AGA
*
137127 TCAAAACATAATTTTGGCGAAGTTTAGAA
1 TCAAAACATAATTTTGGAGAAGTTTAG-A
* * * * * *
137156 ACAAAACGTGATTTTGAATAAGTTTAGGG
1 TCAAAACATAATTTTGGAGAAGTTTA-GA
* *
137185 TCAAAATATAATTTTAGAGAAGTTTAGA
1 TCAAAACATAATTTTGGAGAAGTTTAGA
137213 GGTTAAAATG
Statistics
Matches: 65, Mismatches: 19, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
28 3 0.05
29 61 0.94
30 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (28 bp):
TCAAAACATAATTTTGGAGAAGTTTAGA
Found at i:137161 original size:58 final size:58
Alignment explanation
Indices: 137099--137212 Score: 140
Period size: 58 Copynumber: 2.0 Consensus size: 58
137089 AACTCCGTGT
* * * * *
137099 CAAAATATGATTTTGGAGAAGTTT-GAGTTCAAAACATAATTTTGGCGAAGTTTAGAAA
1 CAAAACATGATTTTGAAGAAGTTTAG-GGTCAAAACATAATTTTAGAGAAGTTTAGAAA
* * *
137157 CAAAACGTGATTTTGAATAAGTTTAGGGTCAAAATATAATTTTAGAGAAGTTTAGA
1 CAAAACATGATTTTGAAGAAGTTTAGGGTCAAAACATAATTTTAGAGAAGTTTAGA
137213 GGTTAAAATG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
58 46 0.98
59 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.33
Consensus pattern (58 bp):
CAAAACATGATTTTGAAGAAGTTTAGGGTCAAAACATAATTTTAGAGAAGTTTAGAAA
Found at i:137239 original size:31 final size:30
Alignment explanation
Indices: 137166--137411 Score: 219
Period size: 30 Copynumber: 8.2 Consensus size: 30
137156 ACAAAACGTG
* *
137166 ATTTT-GAATAAGTTTAG-GGTCAAAATATA
1 ATTTTAGAA-AAGTTTAGAGGTTAAAATGTA
*
137195 ATTTTAGAGAAGTTTAGAGGTTAAAATGTA
1 ATTTTAGAAAAGTTTAGAGGTTAAAATGTA
* * *
137225 ATTTTTAAAAAAGTTTAGGGGTTAAGATGTA
1 A-TTTTAGAAAAGTTTAGAGGTTAAAATGTA
* * *
137256 ATTTTTAAAAAAGTTTAGGGGTCAAAATGTA
1 A-TTTTAGAAAAGTTTAGAGGTTAAAATGTA
* * * * * *
137287 ATTTTGGACAAGTTTATATGTCAAAATATA
1 ATTTTAGAAAAGTTTAGAGGTTAAAATGTA
* ** * *
137317 ATTTTGGTGAAGTTTAG-GGGTCAAATGTA
1 ATTTTAGAAAAGTTTAGAGGTTAAAATGTA
* * *
137346 ATTTTGGAAAATTTTAAAGGTTAAAATGTA
1 ATTTTAGAAAAGTTTAGAGGTTAAAATGTA
* *
137376 ATTTTGGAAAAGTTTAGGGGTTAAAATGTA
1 ATTTTAGAAAAGTTTAGAGGTTAAAATGTA
137406 ATTTTA
1 ATTTTA
137412 AAGAAGCTTA
Statistics
Matches: 179, Mismatches: 34, Indels: 7
0.81 0.15 0.03
Matches are distributed among these distances:
29 33 0.18
30 91 0.51
31 55 0.31
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.39
Consensus pattern (30 bp):
ATTTTAGAAAAGTTTAGAGGTTAAAATGTA
Found at i:137432 original size:30 final size:30
Alignment explanation
Indices: 137157--137432 Score: 200
Period size: 30 Copynumber: 9.2 Consensus size: 30
137147 AGTTTAGAAA
* * * *
137157 CAAAACGTGATTTTGAATAAGTTTAG-GGT
1 CAAAATGTAATTTTAAAGAAGTTTAGAGGT
* *
137186 CAAAATATAATTTTAGAGAAGTTTAGAGGT
1 CAAAATGTAATTTTAAAGAAGTTTAGAGGT
* * *
137216 TAAAATGTAATTTTTAAAAAAGTTTAGGGGT
1 CAAAATGTAA-TTTTAAAGAAGTTTAGAGGT
* * * *
137247 TAAGATGTAATTTTTAAAAAAGTTTAGGGGT
1 CAAAATGTAA-TTTTAAAGAAGTTTAGAGGT
** * * *
137278 CAAAATGTAATTTTGGACAAGTTTATATGT
1 CAAAATGTAATTTTAAAGAAGTTTAGAGGT
* *** *
137308 CAAAATATAATTTTGGTGAAGTTTAGGGGT
1 CAAAATGTAATTTTAAAGAAGTTTAGAGGT
* * *
137338 C-AAATGTAATTTTGGAA-AATTTTAAAGGT
1 CAAAATGTAATTTT-AAAGAAGTTTAGAGGT
* * *
137367 TAAAATGTAATTTTGGAA-AAGTTTAGGGGT
1 CAAAATGTAATTTT-AAAGAAGTTTAGAGGT
* * *
137397 TAAAATGTAATTTTAAAGAAGCTTAAAGGT
1 CAAAATGTAATTTTAAAGAAGTTTAGAGGT
137427 CAAAAT
1 CAAAAT
137433 ATGATTTCTT
Statistics
Matches: 201, Mismatches: 41, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
29 42 0.21
30 104 0.52
31 55 0.27
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (30 bp):
CAAAATGTAATTTTAAAGAAGTTTAGAGGT
Found at i:137432 original size:60 final size:59
Alignment explanation
Indices: 137166--137439 Score: 237
Period size: 60 Copynumber: 4.6 Consensus size: 59
137156 ACAAAACGTG
* * * *
137166 ATTTTGAATAAGTTT-AGGGTCAAAATATAATTTTAGAGAAGTTTAGAGGTTAAAATGTA
1 ATTTT-AAAAAGTTTAAAGGTCAAAATATAATTTTAGAAAAGTTTAGGGGTTAAAATGTA
** * * * * *
137225 ATTTTTAAAAAAGTTTAGGGGTTAAGATGTAATTTTTAAAAAAGTTTAGGGGTCAAAATGTA
1 A-TTTT-AAAAAGTTTAAAGGTCAAAATATAA-TTTTAGAAAAGTTTAGGGGTTAAAATGTA
* * * * * ** *
137287 ATTTTGGACAAGTTTATATGTCAAAATATAATTTTGGTGAAGTTTAGGGG-TCAAATGTA
1 ATTTT-AAAAAGTTTAAAGGTCAAAATATAATTTTAGAAAAGTTTAGGGGTTAAAATGTA
* * * * *
137346 ATTTTGGAAAATTTTAAAGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATGTA
1 ATTTT-AAAAAGTTTAAAGGTCAAAATATAATTTTAGAAAAGTTTAGGGGTTAAAATGTA
* *
137406 ATTTTAAAGAAGCTTAAAGGTCAAAATATGATTT
1 ATTTTAAA-AAGTTTAAAGGTCAAAATATAATTT
137440 CTTGAAAGTC
Statistics
Matches: 170, Mismatches: 40, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
59 52 0.31
60 60 0.35
61 32 0.19
62 26 0.15
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (59 bp):
ATTTTAAAAAGTTTAAAGGTCAAAATATAATTTTAGAAAAGTTTAGGGGTTAAAATGTA
Found at i:140810 original size:2 final size:2
Alignment explanation
Indices: 140803--140831 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
140793 ACAGCAATAA
140803 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
140832 GAATAGAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:142272 original size:20 final size:22
Alignment explanation
Indices: 142233--142273 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
142223 AAATAAAATA
*
142233 AAAATAATAATTATAATACGAT
1 AAAATAATAATTAAAATACGAT
142255 AAAAT-ATAA-TAAAATACGA
1 AAAATAATAATTAAAATACGA
142274 ATATTGGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 4 0.22
22 5 0.28
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (22 bp):
AAAATAATAATTAAAATACGAT
Found at i:142805 original size:29 final size:25
Alignment explanation
Indices: 142773--142830 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 25
142763 TTTTAACATT
142773 TATTTACAATTAATTATTATTTATTTATA
1 TATTTA-AA-TAA-TATTA-TTATTTATA
142802 TATTTAAATAATATTATTATTTATA
1 TATTTAAATAATATTATTATTTATA
142827 -ATTT
1 TATTT
142831 TTTTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.14
25 9 0.31
26 5 0.17
27 3 0.10
28 2 0.07
29 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TATTTAAATAATATTATTATTTATA
Found at i:156339 original size:11 final size:11
Alignment explanation
Indices: 156314--156362 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
156304 TTTGTTGTTG
*
156314 TTATTTTGCTG
1 TTATTTTGCTA
*
156325 TTATTTTGTTA
1 TTATTTTGCTA
*
156336 TTATATTGCTA
1 TTATTTTGCTA
* *
156347 CTATTTTGATA
1 TTATTTTGCTA
156358 TTATT
1 TTATT
156363 ATATGGATAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.20, C:0.06, G:0.10, T:0.63
Consensus pattern (11 bp):
TTATTTTGCTA
Found at i:156339 original size:22 final size:22
Alignment explanation
Indices: 156308--156362 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
156298 TTGTTGTTTG
* **
156308 TTGTTGTTATTTTGCTGTTATT
1 TTGTTATTATTTTGCTACTATT
*
156330 TTGTTATTATATTGCTACTATT
1 TTGTTATTATTTTGCTACTATT
*
156352 TTGATATTATT
1 TTGTTATTATT
156363 ATATGGATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.05, G:0.13, T:0.64
Consensus pattern (22 bp):
TTGTTATTATTTTGCTACTATT
Found at i:166143 original size:29 final size:31
Alignment explanation
Indices: 166111--166171 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
166101 TACAAAACGA
*
166111 TCGTTGAACTATTC-AAA-TTTTTGTTTAAG
1 TCGTTGAACTATTCTAAAGTTTTTATTTAAG
*
166140 TCGTTGAATTATTCTAAAGTTTTTATTTAAG
1 TCGTTGAACTATTCTAAAGTTTTTATTTAAG
166171 T
1 T
166172 TATTGTGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 13 0.46
30 3 0.11
31 12 0.43
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.51
Consensus pattern (31 bp):
TCGTTGAACTATTCTAAAGTTTTTATTTAAG
Found at i:167424 original size:26 final size:26
Alignment explanation
Indices: 167378--167431 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
167368 TATAATATAA
* *
167378 TTTTTATAATTTATATGAAATTAATT
1 TTTTTAAAATTTATATGAAATGAATT
*
167404 TTTTTAAAATTTGAT-TTAAATGAATT
1 TTTTTAAAATTT-ATATGAAATGAATT
167430 TT
1 TT
167432 ACTCGTGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (26 bp):
TTTTTAAAATTTATATGAAATGAATT
Found at i:169197 original size:20 final size:20
Alignment explanation
Indices: 169148--169198 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
169138 TTTTTTTAAG
169148 TTTTAAATTTGTATTTTTTA
1 TTTTAAATTTGTATTTTTTA
*
169168 TTTCAAAAATTTGTATTTTTT-
1 TTT--TAAATTTGTATTTTTTA
169189 TTATTAAATT
1 TT-TTAAATT
169199 ACTTCAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 8 0.31
21 2 0.08
22 16 0.62
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTTAAATTTGTATTTTTTA
Found at i:170124 original size:17 final size:18
Alignment explanation
Indices: 170102--170136 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
170092 TGCTTCAAAC
170102 TTTTTTAAATT-TTAAAT
1 TTTTTTAAATTATTAAAT
*
170119 TTTTTTAACTTATTAAAT
1 TTTTTTAAATTATTAAAT
170137 ACTTCATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTTAAATTATTAAAT
Found at i:175220 original size:21 final size:22
Alignment explanation
Indices: 175178--175220 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
175168 TTCACAAAAA
* *
175178 AAAATGCCTTAACCATTCTAAC
1 AAAATGCCTTAACCAATATAAC
175200 AAAAT-CCTTAACCAATATAAC
1 AAAATGCCTTAACCAATATAAC
175221 TGCTCACCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.47, C:0.26, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAATGCCTTAACCAATATAAC
Found at i:178989 original size:87 final size:86
Alignment explanation
Indices: 178796--179094 Score: 268
Period size: 88 Copynumber: 3.4 Consensus size: 86
178786 GGATGCCCGG
* * * * * *
178796 GGGTAAAATGATAATTTTT-GAAGGTTTGGGGGTAAAACAGTAATTTTTGGACACTCGGGGGTGA
1 GGGTAAAATGGTAATTTTTGGAA-GTTCGAGGGCAAAATAGTAATTTTTGGACACTC-GGGGTAA
* * * *
178860 AAATGGTAAATTTTAGATGTTCGA
64 AAAT-GTAATTTTTGGAAGTTTGA
* * * * *
178884 GGGTAAAATGAT-AGTTTTGGACACTTCGAGGGC-AAATGGTAATTTTTGGACACTCGGTGGCAA
1 GGGTAAAATGGTAATTTTTGGA-AGTTCGAGGGCAAAATAGTAATTTTTGGACACTCGG-GGTAA
178947 AAATGTAATTTTTGGAAGTTTGA
64 AAATGTAATTTTTGGAAGTTTGA
* * * * * *
178970 GGGTAAAATGGTAATTTTTGGAAGTT-TAGGAGCAAAATAGTAATTTTTAGAAAATTTAGGGTTA
1 GGGTAAAATGGTAATTTTTGGAAGTTCGAGG-GCAAAATAGTAATTTTT-GGACA-CTCGGGGTA
179034 AAAATG-ATATTTTTGGAAGTTT-A
63 AAAATGTA-ATTTTTGGAAGTTTGA
*
179057 GGAGTAAAATGGTAATTTTTGGAAGTTCGAGGGAAAAA
1 GG-GTAAAATGGTAATTTTTGGAAGTTCGAGGGCAAAA
179095 ATGATAATTT
Statistics
Matches: 174, Mismatches: 26, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
85 3 0.02
86 33 0.19
87 57 0.33
88 74 0.43
89 7 0.04
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.33
Consensus pattern (86 bp):
GGGTAAAATGGTAATTTTTGGAAGTTCGAGGGCAAAATAGTAATTTTTGGACACTCGGGGTAAAA
ATGTAATTTTTGGAAGTTTGA
Found at i:178992 original size:29 final size:28
Alignment explanation
Indices: 178796--179310 Score: 237
Period size: 29 Copynumber: 17.6 Consensus size: 28
178786 GGATGCCCGG
*
178796 GGGTAAAATGATAATTTTT-GAAGGTTTGG
1 GGGTAAAATG-TAATTTTTGGAA-GTTTGA
* * * *
178825 GGGTAAAACAGTAATTTTTGGACA-CTCGG
1 GGGTAAAA-TGTAATTTTTGGA-AGTTTGA
* * * *
178854 GGGTGAAAATGGTAAATTTTAGATGTTCGA
1 GGGT-AAAAT-GTAATTTTTGGAAGTTTGA
* * *
178884 GGGTAAAATG-ATAGTTTTGGACACTTCGA
1 GGGTAAAATGTA-ATTTTTGGA-AGTTTGA
* * ** *
178913 GGG-CAAATGGTAATTTTTGGACACTCGGT
1 GGGTAAAAT-GTAATTTTTGGA-AGTTTGA
**
178942 GGCAAAAATGTAATTTTTGGAAGTTTGA
1 GGGTAAAATGTAATTTTTGGAAGTTTGA
178970 GGGTAAAATGGTAATTTTTGGAAGTTT-A
1 GGGTAAAAT-GTAATTTTTGGAAGTTTGA
* * *
178998 GGAGCAAAATAGTAATTTTTAGAAAATTT-A
1 GG-GTAAAAT-GTAATTTTT-GGAAGTTTGA
179028 GGGTTAAAAATG-ATATTTTTGGAAGTTT-A
1 GGG-T-AAAATGTA-ATTTTTGGAAGTTTGA
*
179057 GGAGTAAAATGGTAATTTTTGGAAGTTCGA
1 GG-GTAAAAT-GTAATTTTTGGAAGTTTGA
* *
179087 GGGAAAAAATGATAA-TTTTAGAAGTTT-A
1 GGG-TAAAATG-TAATTTTTGGAAGTTTGA
* *
179115 GGGGTAAAATGTAATTTTTGAAAATTTAGA
1 -GGGTAAAATGTAATTTTTGGAAGTTT-GA
** *
179145 GGCAAAAATGTAA-TTTTGTAAAGTTTGA
1 GGGTAAAATGTAATTTTTG-GAAGTTTGA
* * *
179173 AGTTAAAAATGTATTTTTTGTGAAGTTT-A
1 GGGT-AAAATGTAATTTTTG-GAAGTTTGA
* * *
179202 GGGGTCAAAATATGA-TTTTGGAAAAGTTTAA
1 -GGGT-AAAATGTAATTTTTGG--AAGTTTGA
* * * *
179233 GGGTCAAAATATGATTTTTGGAAAATTTAA
1 GGGT-AAAATGTAATTTTTGG-AAGTTTGA
* *
179263 GGGTTAAAATATAATTTTTGGAAAGTTTTA
1 GGG-TAAAATGTAATTTTTGG-AAGTTTGA
* *
179293 GGTTAAAATGTGATTTTT
1 GGGTAAAATGTAATTTTT
179311 AAAAAAATTA
Statistics
Matches: 388, Mismatches: 62, Indels: 72
0.74 0.12 0.14
Matches are distributed among these distances:
27 4 0.01
28 55 0.14
29 181 0.47
30 134 0.35
31 14 0.04
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (28 bp):
GGGTAAAATGTAATTTTTGGAAGTTTGA
Found at i:179046 original size:30 final size:28
Alignment explanation
Indices: 178946--179315 Score: 161
Period size: 30 Copynumber: 12.7 Consensus size: 28
178936 CTCGGTGGCA
* *
178946 AAAATG-TAATTTTTGGAAGTTTGAGGGT
1 AAAATGATAATTTTTGAAAATTT-AGGGT
* * * *
178974 AAAATGGTAATTTTTGGAAGTTTAGGAGC
1 AAAATGATAATTTTTGAAAATTTAGG-GT
179003 AAAAT-AGTAATTTTTAGAAAATTTAGGGTT
1 AAAATGA-TAATTTTT-GAAAATTTAGGG-T
* *
179033 AAAAATGAT-ATTTTTGGAAGTTTAGGAGT
1 -AAAATGATAATTTTTGAAAATTTAGG-GT
* * * * *
179062 AAAATGGTAATTTTTGGAAGTTCGAGGGAA
1 AAAATGATAATTTTTGAAAATT-TAGGG-T
* *
179092 AAAATGATAATTTTAG-AAGTTTAGGGGT
1 AAAATGATAATTTTTGAAAATTTA-GGGT
*
179120 AAAATG-TAATTTTTGAAAATTTAGAGGCA
1 AAAATGATAATTTTTGAAAATTTAG-GG-T
* * *
179149 AAAATG-TAA-TTTTGTAAAGTTTGAAGTT
1 AAAATGATAATTTTTG-AAAATTT-AGGGT
* * *
179177 AAAAATG-TATTTTTTGTGAAGTTTAGGGGT
1 -AAAATGATAATTTTTG-AAAATTTA-GGGT
* *
179207 CAAAAT-ATGATTTTGGAAAAGTTTAAGGGT
1 -AAAATGATAATTTTTGAAAA-TTT-AGGGT
*
179237 CAAAAT-ATGATTTTTGGAAAATTTAAGGGTT
1 -AAAATGATAATTTTT-GAAAATTT-AGGG-T
* *
179268 AAAAT-ATAATTTTTGGAAAGTTTTAGGTT
1 AAAATGATAATTTTT-GAAA-ATTTAGGGT
* *
179297 AAAATG-TGATTTTTAAAAA
1 AAAATGATAATTTTTGAAAA
179316 AATTAAAGGT
Statistics
Matches: 277, Mismatches: 38, Indels: 55
0.75 0.10 0.15
Matches are distributed among these distances:
27 9 0.03
28 39 0.14
29 103 0.37
30 109 0.39
31 16 0.06
32 1 0.00
ACGTcount: A:0.39, C:0.01, G:0.22, T:0.38
Consensus pattern (28 bp):
AAAATGATAATTTTTGAAAATTTAGGGT
Found at i:179106 original size:88 final size:87
Alignment explanation
Indices: 178945--179161 Score: 250
Period size: 88 Copynumber: 2.5 Consensus size: 87
178935 ACTCGGTGGC
* *
178945 AAAAATGTAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGTTTAGGAGCAAAATAG
1 AAAAATGTAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGTTGAGGAGAAAAATAG
*
179010 TAATTTTTAGAAAATTTAGGGTT
66 TAATTTTTAG-AAATTTAGGGGT
179033 AAAAATG-ATATTTTTGGAAGTTT-AGGAGTAAAATGGTAATTTTTGGAAGTTCGAGG-GAAAAA
1 AAAAATGTA-ATTTTTGGAAGTTTGAGG-GTAAAATGGTAATTTTTGGAAGTT-GAGGAGAAAAA
*
179095 -ATGATAA-TTTTAGAAGTTTAGGGGT
63 TA-G-TAATTTTTAGAAATTTAGGGGT
* * **
179120 -AAAATGTAATTTTTGAAAATTTAGAGGCAAAAAT-GTAATTTT
1 AAAAATGTAATTTTTGGAAGTTT-GAGGGTAAAATGGTAATTTT
179162 GTAAAGTTTG
Statistics
Matches: 113, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
86 26 0.23
87 21 0.19
88 60 0.53
89 6 0.05
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.36
Consensus pattern (87 bp):
AAAAATGTAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGTTGAGGAGAAAAATAG
TAATTTTTAGAAATTTAGGGGT
Found at i:179242 original size:60 final size:60
Alignment explanation
Indices: 178946--179380 Score: 195
Period size: 59 Copynumber: 7.4 Consensus size: 60
178936 CTCGGTGGCA
* * * * *
178946 AAAATGT-AATTTTTGG-AAGTTTGAGGGT-AAAATGGTAATTTTTGG-AAGTTT-AGGAGC
1 AAAATGTGATTTTTTGGAAAATTTAAGGGTCAAAAT-ATAATTTTTGGAAAGTTTAAGG-TC
* * * *
179003 AAAATAGT-AATTTTTAGAAAATTT-AGGGTTAAAA-ATGATATTTTTGG-AAGTTTAGGAGT-
1 AAAAT-GTGATTTTTTGGAAAATTTAAGGGTCAAAATAT-A-ATTTTTGGAAAGTTTAAG-GTC
* * ** ** * *
179062 AAAATG-GTAATTTTTGG-AAGTTCGAGGGAAAAAATGATAA-TTTTAG-AAGTTTAGGGGT-
1 AAAATGTG-ATTTTTTGGAAAATTTAAGGGTCAAAAT-ATAATTTTTGGAAAGTTTA-AGGTC
* * * * *
179120 AAAATGT-AATTTTT-GAAAATTT-AGAGG-CAAAAATGTAA-TTTTGTAAAGTTTGAAGTTA
1 AAAATGTGATTTTTTGGAAAATTTAAG-GGTC-AAAATATAATTTTTGGAAAGTTT-AAGGTC
* * *
179178 AAAATGT-ATTTTTTGTG-AAGTTTAGGGGTCAAAATATGA-TTTTGGAAAAGTTTAAGGGTC
1 AAAATGTGATTTTTTG-GAAAATTTAAGGGTCAAAATATAATTTTTGG-AAAGTTTAA-GGTC
* * * *
179238 AAAATATGA-TTTTTGGAAAATTTAAGGGTTAAAATATAATTTTTGGAAAGTTTTAGGTT
1 AAAATGTGATTTTTTGGAAAATTTAAGGGTCAAAATATAATTTTTGGAAAGTTTAAGGTC
** * * * * **
179297 AAAATGTGA-TTTTTAAAAAAATTAAAGGTCAAAATATAATTTCTAGAAAGTTTGGGGGTC
1 AAAATGTGATTTTTTGGAAAATTTAAGGGTCAAAATATAATTTTTGGAAAGTTT-AAGGTC
179357 AAAACT-TGA-TTTTTGGAAAATTTA
1 AAAA-TGTGATTTTTTGGAAAATTTA
179381 GAGACCTTTT
Statistics
Matches: 299, Mismatches: 48, Indels: 59
0.74 0.12 0.15
Matches are distributed among these distances:
56 10 0.03
57 32 0.11
58 55 0.18
59 117 0.39
60 74 0.25
61 11 0.04
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (60 bp):
AAAATGTGATTTTTTGGAAAATTTAAGGGTCAAAATATAATTTTTGGAAAGTTTAAGGTC
Found at i:180443 original size:18 final size:18
Alignment explanation
Indices: 180414--180458 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
180404 TTTTTATTAA
*
180414 TATTATTTAATATTA-ATCT
1 TATTA-TTAATAGTATAT-T
180433 TATTATTAATAGTATATT
1 TATTATTAATAGTATATT
180451 TATTATTA
1 TATTATTA
180459 TCGTTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
TATTATTAATAGTATATT
Found at i:181148 original size:23 final size:24
Alignment explanation
Indices: 181103--181148 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
181093 ATTTTGAACT
* *
181103 TTTAAATTAAATTTTAAAATTAAG
1 TTTAAAATAAATTTCAAAATTAAG
*
181127 TTTAAAAT-AATTTCAAATTTAA
1 TTTAAAATAAATTTCAAAATTAA
181149 ACTAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TTTAAAATAAATTTCAAAATTAAG
Found at i:181162 original size:6 final size:6
Alignment explanation
Indices: 181103--181218 Score: 73
Period size: 6 Copynumber: 20.0 Consensus size: 6
181093 ATTTTGAACT
* * *
181103 TTTAAA -TTAAA TTTTAAA ATTAAG TTTAAA -AT-AA TTTCAAA TTTAAA
1 TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
* ** ** **
181150 -CTAAA TTTAAA TTTAAA -ACAAA TTTAAA TTTAAA AATAAA AATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
181196 TTTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
181219 ATCGAAAGTT
Statistics
Matches: 84, Mismatches: 18, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
4 2 0.02
5 18 0.21
6 54 0.64
7 10 0.12
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:181166 original size:34 final size:35
Alignment explanation
Indices: 181117--181201 Score: 102
Period size: 35 Copynumber: 2.5 Consensus size: 35
181107 AATTAAATTT
* * *
181117 TAAAATTAAGTTTAAAA-TAATTTCAAATTT-AAAC
1 TAAAATTAAATTTAAAACAAATTT-AAATTTAAAAA
*
181151 TAAATTTAAATTTAAAACAAATTTAAATTTAAAAA
1 TAAAATTAAATTTAAAACAAATTTAAATTTAAAAA
*
181186 TAAAAATAAATTTAAA
1 TAAAATTAAATTTAAA
181202 TTTAAAATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
34 21 0.49
35 22 0.51
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (35 bp):
TAAAATTAAATTTAAAACAAATTTAAATTTAAAAA
Found at i:181208 original size:23 final size:23
Alignment explanation
Indices: 181151--181212 Score: 88
Period size: 24 Copynumber: 2.7 Consensus size: 23
181141 AAATTTAAAC
* *
181151 TAAATTTAAATTTAAAACAAATT
1 TAAATTTAAAATAAAAACAAATT
*
181174 TAAATTTAAAAATAAAAATAAATT
1 TAAATTT-AAAATAAAAACAAATT
181198 TAAATTTAAAATAAA
1 TAAATTTAAAATAAA
181213 TTTAAAATCG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 15 0.43
24 20 0.57
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAATTTAAAATAAAAACAAATT
Found at i:181210 original size:17 final size:17
Alignment explanation
Indices: 181117--181220 Score: 95
Period size: 17 Copynumber: 6.1 Consensus size: 17
181107 AATTAAATTT
* *
181117 TAAAATTAAGTTTAAAA
1 TAAATTTAAATTTAAAA
*
181134 T-AATTTCAAATTTAAAC
1 TAAATTT-AAATTTAAAA
181151 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
181168 CAAATTTAAATTTAAAAA
1 TAAATTTAAATTT-AAAA
** *
181186 TAAAAATAAATTTAAATT
1 TAAATTTAAATTTAAA-A
*
181204 TAAA-ATAAATTTAAAA
1 TAAATTTAAATTTAAAA
181220 T
1 T
181221 CGAAAGTTTG
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
16 5 0.07
17 45 0.62
18 23 0.32
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:185963 original size:17 final size:16
Alignment explanation
Indices: 185946--185985 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
185936 ATAATATTAT
185946 TTTAATAAATTTAATA
1 TTTAATAAATTTAATA
*
185962 TTAAATTAAATTTAATA
1 TTTAA-TAAATTTAATA
185979 TTTAATA
1 TTTAATA
185986 TTTATCTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAATAAATTTAATA
Found at i:188788 original size:31 final size:31
Alignment explanation
Indices: 188753--188814 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
188743 AGCCTGCGTC
188753 TTTATAATTTTTAAAGGATAAAAT-TAATTTT
1 TTTATAATTTTTAAA-GATAAAATGTAATTTT
* * *
188784 TTTATCATTTTTGAAGATAAAGTGTAATTTT
1 TTTATAATTTTTAAAGATAAAATGTAATTTT
188815 ATCATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (31 bp):
TTTATAATTTTTAAAGATAAAATGTAATTTT
Found at i:190159 original size:6 final size:6
Alignment explanation
Indices: 190148--190177 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
190138 TGGTAATGTA
190148 AAAAAT AAAAAT AAAAAT AAAAAT ATAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT A-AAAA
190178 AACACCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:190650 original size:3 final size:3
Alignment explanation
Indices: 190642--190672 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
190632 TGTTAAGCCC
*
190642 ATT ATT ATT ATT ATT CTT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
190673 ATGGACCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:191223 original size:24 final size:26
Alignment explanation
Indices: 191185--191232 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
191175 TTTTACTATT
191185 ATTTATATTTAATTG-TTTATTTTGGC
1 ATTTATATTTAATTGATTT-TTTTGGC
191211 ATTTA-ATTT-ATTGATTTTTTTG
1 ATTTATATTTAATTGATTTTTTTG
191233 TTTATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 9 0.43
25 7 0.33
26 5 0.24
ACGTcount: A:0.23, C:0.02, G:0.10, T:0.65
Consensus pattern (26 bp):
ATTTATATTTAATTGATTTTTTTGGC
Found at i:191397 original size:96 final size:94
Alignment explanation
Indices: 191181--191443 Score: 228
Period size: 101 Copynumber: 2.7 Consensus size: 94
191171 TCTTTTTTAC
* ** *
191181 TATTATTTATATTTAATTGTTTATTTTGGCATTTAATTTATTGATTTTTTTGTTTATTTATTTAT
1 TATTCTTTATATTTGTTTATTTATTTT-GCATTTAATTT-TT-ATTTTTTTGTTTATTTATTTAT
*
191246 TTTTCATTTATTTTCATGCTTAATCCCAATTATTTT
63 TGTTCATTTATTTTCATGC-TAAT--C-ATTATTTT
* *
191282 TATTGTTTATATTTGTTTATTTATTTTAGCATTTAATTTTTATTTTTATTGTTTATTTATCTTGT
1 TATTCTTTATATTTGTTTATTTATTTT-GCATTTAATTTTTATTTTT-TTGTTTATTTAT-TTAT
* *
191347 TGTT-ATTTATTTTCATGC-CAT-TTTATTGTT
63 TGTTCATTTATTTTCATGCTAATCATTATT-TT
* * * * *
191377 ATCTTCTTTATTATTT-TTTATTTAATTTGCATTTATTGTTATTATTTTATTTGCTTGTTTATTT
1 -TATTCTTTA-TATTTGTTTATTTATTTTGCATTTAAT-TT-TTATTTT-TTTGTTTATTTATTT
191441 ATT
61 ATT
191444 TATTTATCAT
Statistics
Matches: 138, Mismatches: 16, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
94 5 0.04
95 10 0.07
96 24 0.17
97 22 0.16
98 3 0.02
99 6 0.04
100 28 0.20
101 40 0.29
ACGTcount: A:0.21, C:0.06, G:0.07, T:0.67
Consensus pattern (94 bp):
TATTCTTTATATTTGTTTATTTATTTTGCATTTAATTTTTATTTTTTTGTTTATTTATTTATTGT
TCATTTATTTTCATGCTAATCATTATTTT
Found at i:191423 original size:24 final size:22
Alignment explanation
Indices: 191387--191449 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 22
191377 ATCTTCTTTA
191387 TTATTTTTTATTTAATTTGCAT
1 TTATTTTTTATTTAATTTGCAT
* *
191409 TTATTGTTATTATTTTATTTGCTTGT
1 TTATT-TT-TTATTTAATTTGC--AT
191435 TTATTTATTTATTTA
1 TTATTT-TTTATTTA
191450 TCATTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 5 0.15
23 2 0.06
24 12 0.36
25 7 0.21
26 7 0.21
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (22 bp):
TTATTTTTTATTTAATTTGCAT
Found at i:193425 original size:4 final size:4
Alignment explanation
Indices: 193416--193480 Score: 55
Period size: 4 Copynumber: 16.2 Consensus size: 4
193406 AAATTTAATG
* *
193416 ATAA ATAA ATAA ATAA ACAA ATAA GAT-A ATAACA ATAA ATAA A-AA TTAA
1 ATAA ATAA ATAA ATAA ATAA ATAA -ATAA AT-A-A ATAA ATAA ATAA ATAA
*
193465 ATAA AAAA AT-A ATAA A
1 ATAA ATAA ATAA ATAA A
193481 AGAGATAACA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
3 7 0.14
4 36 0.73
5 3 0.06
6 3 0.06
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:193510 original size:17 final size:16
Alignment explanation
Indices: 193470--193512 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
193460 ATTAAATAAA
*
193470 AAAATAATAAAAGAGAT
1 AAAATAA-AAAAGACAT
193487 AACAATAAAAAAGACATT
1 AA-AATAAAAAAGACA-T
193505 AAAATAAA
1 AAAATAAA
193513 TAACAAGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.72, C:0.05, G:0.07, T:0.16
Consensus pattern (16 bp):
AAAATAAAAAAGACAT
Found at i:193643 original size:16 final size:16
Alignment explanation
Indices: 193608--193650 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
193598 ATTAGGCATG
*
193608 AAAATAAAT-GACAAA
1 AAAATAAATAAACAAA
*
193623 TAAATAAATAAACAAA
1 AAAATAAATAAACAAA
*
193639 AAAATCAATAAA
1 AAAATAAATAAA
193651 TTAAATGCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (16 bp):
AAAATAAATAAACAAA
Found at i:199497 original size:13 final size:14
Alignment explanation
Indices: 199471--199500 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
199461 AAAACATGAC
199471 TAAAAACTAGAAAT
1 TAAAAACTAGAAAT
199485 TAAAAACTA-AAAT
1 TAAAAACTAGAAAT
199498 TAA
1 TAA
199501 GTGTGGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.23
Consensus pattern (14 bp):
TAAAAACTAGAAAT
Found at i:202560 original size:37 final size:33
Alignment explanation
Indices: 202513--202583 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 33
202503 CGAAAAATAA
202513 TTCGAATTTCGATTTATTCGAATCGAGTTGAACTTTT
1 TTCGAATTTCGA---ATTCGAATCGAGTTGAA-TTTT
*
202550 TTCGAATTTCGAGTTCGAATCGAGTTGAATTTT
1 TTCGAATTTCGAATTCGAATCGAGTTGAATTTT
202583 T
1 T
202584 GAATTCAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
33 5 0.15
34 16 0.48
37 12 0.36
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (33 bp):
TTCGAATTTCGAATTCGAATCGAGTTGAATTTT
Found at i:202606 original size:18 final size:18
Alignment explanation
Indices: 202585--202622 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
202575 TGAATTTTTG
202585 AATTCAAAT-AACTCGAAT
1 AATTCAAATAAAC-CGAAT
*
202603 AATTCGAATAAACCGAAT
1 AATTCAAATAAACCGAAT
202621 AA
1 AA
202623 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.24
Consensus pattern (18 bp):
AATTCAAATAAACCGAAT
Found at i:202960 original size:5 final size:5
Alignment explanation
Indices: 202950--202980 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
202940 AAACAAATAT
*
202950 ATTCG ATTCG ATTCG ATTCA ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
202981 ATTCTATCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:209251 original size:30 final size:30
Alignment explanation
Indices: 209217--209274 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
209207 TTATTAAAGG
* *
209217 TAAAATTATACTTTGATCTCTTAAAAATGA
1 TAAAATTATAATTTAATCTCTTAAAAATGA
*
209247 TAAAATTATAATTTAATCTTTTAAAAAT
1 TAAAATTATAATTTAATCTCTTAAAAAT
209275 TGTACTTTTA
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:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (30 bp):
TAAAATTATAATTTAATCTCTTAAAAATGA
Found at i:209273 original size:22 final size:23
Alignment explanation
Indices: 209248--209307 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
209238 TAAAAATGAT
*
209248 AAAATTATAATTTAATCT-TT-TA
1 AAAATTATAATTTAA-CTATTGCA
* * *
209270 AAAATTGTACTTTTACTATTGCA
1 AAAATTATAATTTAACTATTGCA
209293 AAAATTATAATTTAA
1 AAAATTATAATTTAA
209308 ATTTGATCCC
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 2 0.07
22 14 0.48
23 13 0.45
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (23 bp):
AAAATTATAATTTAACTATTGCA
Found at i:211698 original size:30 final size:30
Alignment explanation
Indices: 211653--211880 Score: 277
Period size: 30 Copynumber: 7.8 Consensus size: 30
211643 AGAGGTCCTC
*
211653 AAACTTCTTAAAAATTACATTTTGACCCTT
1 AAACTTCTCAAAAATTACATTTTGACCCTT
* *
211683 AAATTTCTCAAAAATTACATTTTGACCGTT
1 AAACTTCTCAAAAATTACATTTTGACCCTT
211713 AAACTTCTCAAAAATTACATTTT-ACCCTT
1 AAACTTCTCAAAAATTACATTTTGACCCTT
* *
211742 AAACTTCTCAAAAATTACATGTTGACCCCT
1 AAACTTCTCAAAAATTACATTTTGACCCTT
* * *
211772 AAAATTCTTAAAAATTACATTTTAACCCTT
1 AAACTTCTCAAAAATTACATTTTGACCCTT
* * *
211802 AAACTTCACAAAAAATACATTTTGACCC-C
1 AAACTTCTCAAAAATTACATTTTGACCCTT
* * * *
211831 AAACTTCTCCAAAAGTCCATTTT--CCCCT
1 AAACTTCTCAAAAATTACATTTTGACCCTT
*
211859 AAATTTC-CAAAAATTACATTTT
1 AAACTTCTCAAAAATTACATTTT
211881 CAACCTCAAA
Statistics
Matches: 169, Mismatches: 27, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
27 15 0.09
28 6 0.04
29 46 0.27
30 102 0.60
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
AAACTTCTCAAAAATTACATTTTGACCCTT
Found at i:211758 original size:59 final size:59
Alignment explanation
Indices: 211653--211880 Score: 275
Period size: 59 Copynumber: 3.9 Consensus size: 59
211643 AGAGGTCCTC
* * * *
211653 AAACTTCTTAAAAATTACATTTTGACCCTTAAATTTCTCAAAAATTACATTTTGACCGTT
1 AAACTTCTCAAAAATTACATTTTAACCCTTAAACTTCTCAAAAATTACATTTTGACC-CT
*
211713 AAACTTCTCAAAAATTACATTTT-ACCCTTAAACTTCTCAAAAATTACATGTTGACCCCT
1 AAACTTCTCAAAAATTACATTTTAACCCTTAAACTTCTCAAAAATTACATTTTGA-CCCT
* * * * *
211772 AAAATTCTTAAAAATTACATTTTAACCCTTAAACTTCACAAAAAATACATTTTGACCCC
1 AAACTTCTCAAAAATTACATTTTAACCCTTAAACTTCTCAAAAATTACATTTTGACCCT
* * * * *
211831 AAACTTCTCCAAAAGTCCATTTT--CCCCTAAATTTC-CAAAAATTACATTTT
1 AAACTTCTCAAAAATTACATTTTAACCCTTAAACTTCTCAAAAATTACATTTT
211881 CAACCTCAAA
Statistics
Matches: 148, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
56 14 0.09
57 10 0.07
59 72 0.49
60 52 0.35
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.36
Consensus pattern (59 bp):
AAACTTCTCAAAAATTACATTTTAACCCTTAAACTTCTCAAAAATTACATTTTGACCCT
Found at i:211804 original size:89 final size:88
Alignment explanation
Indices: 211652--211885 Score: 294
Period size: 89 Copynumber: 2.6 Consensus size: 88
211642 AAGAGGTCCT
* * * *
211652 CAAACTTCTTAAAAATTACATTTTGACCCTTAAATTTCTCAAAAATTACATTTTGACCGTTAAAC
1 CAAACTTCTCAAAAATTACA-TTTGACCCCTAAATTTCTCAAAAATTACATTTTAACCCTTAAAC
* *
211717 TTCTCAAAAATTACATTTT-ACCC
65 TTCACAAAAAATACATTTTGACCC
* * *
211740 TTAAACTTCTCAAAAATTACATGTTGACCCCTAAAATTCTTAAAAATTACATTTTAACCCTTAAA
1 -CAAACTTCTCAAAAATTACAT-TTGACCCCTAAATTTCTCAAAAATTACATTTTAACCCTTAAA
211805 CTTCACAAAAAATACATTTTGACCC
64 CTTCACAAAAAATACATTTTGACCC
* * * *
211830 CAAACTTCTCCAAAAGTCCATTT-TCCCCTAAATTTC-CAAAAATTACATTTTCAACC
1 CAAACTTCTCAAAAATTACATTTGACCCCTAAATTTCTCAAAAATTACATTTT-AACC
211886 TCAAATTTTC
Statistics
Matches: 126, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
86 14 0.11
87 15 0.12
88 3 0.02
89 90 0.71
90 4 0.03
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (88 bp):
CAAACTTCTCAAAAATTACATTTGACCCCTAAATTTCTCAAAAATTACATTTTAACCCTTAAACT
TCACAAAAAATACATTTTGACCC
Found at i:211900 original size:29 final size:28
Alignment explanation
Indices: 211662--211929 Score: 157
Period size: 30 Copynumber: 9.2 Consensus size: 28
211652 CAAACTTCTT
*
211662 AAAAATTACATTTTGACCCTTAAATTTCTC
1 AAAAATTACATTTT-AACCTTAAATTT-TC
* *
211692 AAAAATTACATTTTGACCGTTAAACTTCTC
1 AAAAATTACATTTTAACC-TTAAA-TTTTC
* *
211722 AAAAATTACATTTTACCCTTAAACTTCTC
1 AAAAATTACATTTTAACCTTAAA-TTTTC
* * *
211751 AAAAATTACATGTTGACCCCTAAAATTCTT-
1 AAAAATTACAT-TTTA-ACCTTAAATT-TTC
**
211781 AAAAATTACATTTTAACCCTTAAACTTCAC
1 AAAAATTACATTTTAA-CCTTAAA-TTTTC
* * ** *
211811 AAAAAATACATTTTGACCCCAAACTTCTC
1 AAAAATTACATTTTAACCTTAAA-TTTTC
* * * * * *
211840 CAAAAGTCCATTTT-CCCCTAAATTTCC
1 AAAAATTACATTTTAACCTTAAATTTTC
*
211867 AAAAATTACATTTTCAACCTCAAATTTTCC
1 AAAAATTACATTTT-AACCTTAAATTTT-C
* *
211897 AAAAGTT-CGATTTTAATCC-CAAATTTTC
1 AAAAATTAC-ATTTTAA-CCTTAAATTTTC
211925 AAAAA
1 AAAAA
211930 ATTTCAATTT
Statistics
Matches: 191, Mismatches: 34, Indels: 28
0.75 0.13 0.11
Matches are distributed among these distances:
27 14 0.07
28 11 0.06
29 73 0.38
30 83 0.43
31 10 0.05
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAAATTACATTTTAACCTTAAATTTTC
Found at i:211910 original size:30 final size:29
Alignment explanation
Indices: 211838--211929 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
211828 CCCAAACTTC
* *
211838 TCCAAAAGTCCATTTTC-CCCT-AAA-TT
1 TCCAAAAGTTCATTTTCAACCTCAAATTT
*
211864 TCCAAAAATTACATTTTCAACCTCAAATTT
1 TCCAAAAGTT-CATTTTCAACCTCAAATTT
211894 TCCAAAAGTTCGATTTT-AATCC-CAAATTT
1 TCCAAAAGTTC-ATTTTCAA-CCTCAAATTT
*
211923 TCAAAAA
1 TCCAAAA
211930 ATTTCAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
26 8 0.15
27 7 0.13
28 3 0.05
29 19 0.35
30 18 0.33
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (29 bp):
TCCAAAAGTTCATTTTCAACCTCAAATTT
Found at i:211946 original size:30 final size:30
Alignment explanation
Indices: 211853--211952 Score: 82
Period size: 30 Copynumber: 3.3 Consensus size: 30
211843 AAGTCCATTT
*
211853 TCCCCTAAATTTCCAAAAA-TT-ACATTTTCAA
1 TCCCC-AAATTTTCAAAAAGTTCA-ATTTT-AA
* * *
211884 -CCTCAAATTTTCCAAAAGTTCGATTTTAA
1 TCCCCAAATTTTCAAAAAGTTCAATTTTAA
* *
211913 T-CCCAAATTTTCAAAAAATTTCAATTTTGA
1 TCCCCAAATTTTC-AAAAAGTTCAATTTTAA
211943 TCCCCAAATT
1 TCCCCAAATT
211953 CCTCGAAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
29 23 0.42
30 24 0.44
31 8 0.15
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
TCCCCAAATTTTCAAAAAGTTCAATTTTAA
Found at i:213883 original size:65 final size:65
Alignment explanation
Indices: 213779--213903 Score: 250
Period size: 65 Copynumber: 1.9 Consensus size: 65
213769 AGAATATACT
213779 GCATTGATTCGTTGTCCAAAAATTCAAGTCAACAAGGCATACTCAAAAGATGCATGTGTCCCAAC
1 GCATTGATTCGTTGTCCAAAAATTCAAGTCAACAAGGCATACTCAAAAGATGCATGTGTCCCAAC
213844 GCATTGATTCGTTGTCCAAAAATTCAAGTCAACAAGGCATACTCAAAAGATGCATGTGTC
1 GCATTGATTCGTTGTCCAAAAATTCAAGTCAACAAGGCATACTCAAAAGATGCATGTGTC
213904 TCATCCTTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (65 bp):
GCATTGATTCGTTGTCCAAAAATTCAAGTCAACAAGGCATACTCAAAAGATGCATGTGTCCCAAC
Done.