Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011807.1 Kokia drynarioides strain JFW-HI SEQ_126802, 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: 282844
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 242 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:261 original size:24 final size:23
Alignment explanation
Indices: 225--273 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
215 CAATTTAAAA
225 TTCATATCACTTTCAATTCCAAT
1 TTCATATCACTTTCAATTCCAAT
* *
248 TTCACTATCACTTTCACTTTCAAT
1 TTCA-TATCACTTTCAATTCCAAT
272 TT
1 TT
274 TGATCACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (23 bp):
TTCATATCACTTTCAATTCCAAT
Found at i:3962 original size:21 final size:21
Alignment explanation
Indices: 3936--3989 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3926 CGACCTAAGA
*
3936 ACACGGGCGTGTGGGATGACC
1 ACACGGGCATGTGGGATGACC
*
3957 ACACGGGCATGTGGTATGACC
1 ACACGGGCATGTGGGATGACC
*
3978 ACACGGCCATGT
1 ACACGGGCATGT
3990 ATGAGCCGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.26, G:0.35, T:0.17
Consensus pattern (21 bp):
ACACGGGCATGTGGGATGACC
Found at i:12691 original size:17 final size:18
Alignment explanation
Indices: 12652--12693 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
12642 TCTTAATAGC
12652 TAAATAACTCAATATTCTA
1 TAAA-AACTCAATATTCTA
* *
12671 TAAAAACTC-ATTTTCTT
1 TAAAAACTCAATATTCTA
12688 TAAAAA
1 TAAAAA
12694 AATAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 12 0.57
18 5 0.24
19 4 0.19
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAACTCAATATTCTA
Found at i:12712 original size:18 final size:20
Alignment explanation
Indices: 12691--12742 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
12681 TTTTCTTTAA
12691 AAAAAT-AAAATTTATT-AT
1 AAAAATAAAAATTTATTGAT
* *
12709 AAAAATGAAAA-TGATTGAT
1 AAAAATAAAAATTTATTGAT
*
12728 CAAAATAAAAATTTA
1 AAAAATAAAAATTTA
12743 CTGAAATTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 10 0.37
19 15 0.56
20 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (20 bp):
AAAAATAAAAATTTATTGAT
Found at i:13816 original size:22 final size:22
Alignment explanation
Indices: 13785--13831 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
13775 NNNNNNNNTT
*
13785 AAACTTTCAAAATGCATAAAAA
1 AAACTCTCAAAATGCATAAAAA
* **
13807 AAACTCTCAAACTTTATAAAAA
1 AAACTCTCAAAATGCATAAAAA
13829 AAA
1 AAA
13832 ATTAAGTCCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.60, C:0.15, G:0.02, T:0.23
Consensus pattern (22 bp):
AAACTCTCAAAATGCATAAAAA
Found at i:13965 original size:19 final size:19
Alignment explanation
Indices: 13924--13976 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
13914 GTCAAATATC
* *
13924 AAAAATTTATTAAAATTGG
1 AAAAATTTATAAAAATCGG
* *
13943 AAAATTTTATAAAAATCGTA
1 AAAAATTTATAAAAATCG-G
*
13963 AAAAAATTATAAAA
1 AAAAATTTATAAAA
13977 TATATAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (19 bp):
AAAAATTTATAAAAATCGG
Found at i:13972 original size:20 final size:19
Alignment explanation
Indices: 13949--13997 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
13939 TTGGAAAATT
*
13949 TTATAAAAATCGTAAAAAAA
1 TTATAAAAAT-ATAAAAAAA
13969 TTATAAAATATATAAAAAAA
1 TTATAAAA-ATATAAAAAAA
*
13989 ATATAAAAA
1 TTATAAAAA
13998 ATTATAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 23 0.88
21 2 0.08
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
TTATAAAAATATAAAAAAA
Found at i:13977 original size:30 final size:30
Alignment explanation
Indices: 13943--14032 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
13933 TTAAAATTGG
*
13943 AAAATTTTATAAAAATCGTAAAAAAATTAT
1 AAAATTTTATAAAAATCATAAAAAAATTAT
* **
13973 AAAA-TATATAAAAAAAATATAAAAAATTAT
1 AAAATTTTATAAAAATCATA-AAAAAATTAT
** * *
14003 AAGTTTTTAT-AAAGTCATAAGAAAATTAT
1 AAAATTTTATAAAAATCATAAAAAAATTAT
14032 A
1 A
14033 CAAAATGTAA
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
29 21 0.45
30 22 0.47
31 4 0.09
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAATTTTATAAAAATCATAAAAAAATTAT
Found at i:15112 original size:12 final size:11
Alignment explanation
Indices: 15095--15146 Score: 61
Period size: 12 Copynumber: 4.5 Consensus size: 11
15085 TTTATACATT
15095 TAAAATTAATAA
1 TAAAA-TAATAA
*
15107 TAAAAT-ATAT
1 TAAAATAATAA
15117 TCAAAATAATAA
1 T-AAAATAATAA
15129 TAATAATAATAA
1 TAA-AATAATAA
15141 TAAAAT
1 TAAAAT
15147 TTACTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
10 4 0.11
11 11 0.31
12 20 0.57
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:32010 original size:182 final size:182
Alignment explanation
Indices: 31703--32066 Score: 701
Period size: 182 Copynumber: 2.0 Consensus size: 182
31693 AAAGTCATCG
31703 CAAATAGGTTGATTTTCTCAAACTTGAAAATTGGCAGTTTCGGTGCATGAAATTTAATAAATTTC
1 CAAATAGGTTGATTTTCTCAAACTTGAAAATTGGCAGTTTCGGTGCATGAAATTTAATAAATTTC
31768 AACCAATCCATGCATGTATCAGTTGTTGCAGTAAATTTGTTACAGCAAATATATAATAGACTTAC
66 AACCAATCCATGCATGTATCAGTTGTTGCAGTAAATTTGTTACAGCAAATATATAATAGACTTAC
31833 TTGCAAGCAAAGTTACTAAACTTTGTTGCAAATAAAGTTTTATTATTAACCC
131 TTGCAAGCAAAGTTACTAAACTTTGTTGCAAATAAAGTTTTATTATTAACCC
* *
31885 CAAATAGGTTGATTTTCTCATACTTGAAAATTGGCAGTTTCGGTGCATGCAATTTAATAAATTTC
1 CAAATAGGTTGATTTTCTCAAACTTGAAAATTGGCAGTTTCGGTGCATGAAATTTAATAAATTTC
*
31950 ACCCAATCCATGCATGTATCAGTTGTTGCAGTAAATTTGTTACAGCAAATATATAATAGACTTAC
66 AACCAATCCATGCATGTATCAGTTGTTGCAGTAAATTTGTTACAGCAAATATATAATAGACTTAC
32015 TTGCAAGCAAAGTTACTAAACTTTGTTGCAAATAAAGTTTTATTATTAACCC
131 TTGCAAGCAAAGTTACTAAACTTTGTTGCAAATAAAGTTTTATTATTAACCC
32067 TAATCTTAAC
Statistics
Matches: 179, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
182 179 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (182 bp):
CAAATAGGTTGATTTTCTCAAACTTGAAAATTGGCAGTTTCGGTGCATGAAATTTAATAAATTTC
AACCAATCCATGCATGTATCAGTTGTTGCAGTAAATTTGTTACAGCAAATATATAATAGACTTAC
TTGCAAGCAAAGTTACTAAACTTTGTTGCAAATAAAGTTTTATTATTAACCC
Found at i:37374 original size:14 final size:15
Alignment explanation
Indices: 37347--37379 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
37337 GGCATATACA
37347 TTTATATTTATTTAT
1 TTTATATTTATTTAT
37362 TTTATATTT-TTTAT
1 TTTATATTTATTTAT
37376 TTTA
1 TTTA
37380 ATGAGTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATATTTATTTAT
Found at i:37529 original size:13 final size:12
Alignment explanation
Indices: 37510--37539 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
37500 CAAAAAAACC
*
37510 TAAAAAACGAAA
1 TAAAAAAAGAAA
37522 TAAAAAAAGAAA
1 TAAAAAAAGAAA
37534 TAAAAA
1 TAAAAA
37540 CATAAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (12 bp):
TAAAAAAAGAAA
Found at i:38210 original size:30 final size:28
Alignment explanation
Indices: 38180--38280 Score: 105
Period size: 30 Copynumber: 3.5 Consensus size: 28
38170 CCTCTAAACT
38180 TTCCAAAAATTTAGATTTGACCCTCGAAC
1 TTCCAAAAATTTAGATTTGACCC-CGAAC
* *
38209 TTTCCAAATA-TTATGTTTTGACCCCTGAAC
1 -TTCCAAAAATTTA-GATTTGACCCC-GAAC
* * *
38239 TTCCAAAAAATTCAAATTTGACCCCAAAC
1 TTCC-AAAAATTTAGATTTGACCCCGAAC
38268 TTCCAAAAATTTA
1 TTCCAAAAATTTA
38281 AAATTTTTCA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
28 8 0.14
29 15 0.25
30 34 0.58
31 2 0.03
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.33
Consensus pattern (28 bp):
TTCCAAAAATTTAGATTTGACCCCGAAC
Found at i:38268 original size:29 final size:30
Alignment explanation
Indices: 38225--38286 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
38215 AATATTATGT
* *
38225 TTTGACCCCTGAACTTCCAAAAAATTCAAA
1 TTTGACCCCTAAACTTCCAAAAAATTAAAA
*
38255 TTTGACCCC-AAACTTCCAAAAATTTAAAA
1 TTTGACCCCTAAACTTCCAAAAAATTAAAA
38284 TTT
1 TTT
38287 TTCAAATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (30 bp):
TTTGACCCCTAAACTTCCAAAAAATTAAAA
Found at i:41288 original size:16 final size:16
Alignment explanation
Indices: 41263--41305 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
41253 TATGCATACA
41263 TGCA-TTCATTAGCAT
1 TGCATTTCATTAGCAT
41278 TGCATTTCATTAGCAT
1 TGCATTTCATTAGCAT
41294 TGCATTTCATTA
1 TGCATTTCATTA
41306 CATACATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.44
Consensus pattern (16 bp):
TGCATTTCATTAGCAT
Found at i:42109 original size:16 final size:16
Alignment explanation
Indices: 42073--42121 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
42063 AAAACAGGTC
*
42073 AAAA-AAAGAGGAAAA
1 AAAAGAAAGAAGAAAA
42088 AGAAAGAAAGAAGAAAA
1 A-AAAGAAAGAAGAAAA
*
42105 AAAAGAAAAAAGAAAA
1 AAAAGAAAGAAGAAAA
42121 A
1 A
42122 GAAAAGGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 1 0.03
16 18 0.60
17 11 0.37
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAGAAAGAAGAAAA
Found at i:43099 original size:17 final size:15
Alignment explanation
Indices: 43077--43137 Score: 54
Period size: 16 Copynumber: 4.0 Consensus size: 15
43067 GAGAGAGAGA
*
43077 AAAAAAATGAAAAAGGG
1 AAAAAAA-GAAAAA-AG
43094 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
**
43109 -AAAAAA-AAGGAAG
1 AAAAAAAGAAAAAAG
43122 AAGAAAAAGAAAAAAG
1 AA-AAAAAGAAAAAAG
43138 GAGAGGTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
13 5 0.14
14 7 0.19
15 6 0.17
16 11 0.31
17 7 0.19
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:43113 original size:16 final size:16
Alignment explanation
Indices: 43074--43129 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
43064 GAAGAGAGAG
43074 AGAAAAAAAATGAAAAA
1 AGAAAAAAAA-GAAAAA
* *
43091 GGGAAAAAAAGAAAAA
1 AGAAAAAAAAGAAAAA
* *
43107 AGAAAAAAAAGGAAGA
1 AGAAAAAAAAGAAAAA
43123 AGAAAAA
1 AGAAAAA
43130 GAAAAAAGGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 25 0.76
17 8 0.24
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (16 bp):
AGAAAAAAAAGAAAAA
Found at i:44189 original size:49 final size:49
Alignment explanation
Indices: 43973--44261 Score: 183
Period size: 49 Copynumber: 6.0 Consensus size: 49
43963 CTAAAGACTT
* ** * *
43973 AAAGAGAAAGATTGAGGTCGCAAC-AGCGAATCTCGTACCCT-AGGAATGTG
1 AAAG-GAAAGATTGAGGCCGCAACGA-CGAATCTTATACCTTAAAG-ATGTG
* * * * * * *
44023 AAGGGAAAGATTAAGGTCGCAACGATGAATCTTGTACCCTAGAGATGTG
1 AAAGGAAAGATTGAGGCCGCAACGACGAATCTTATACCTTAAAGATGTG
* * * * *
44072 -AAGGAAAGGA-TGAGGCTGCAATGGCGAACCATATACCTTAGAA-A--T-
1 AAAGGAAA-GATTGAGGCCGCAACGACGAATCTTATACCTTA-AAGATGTG
* *
44117 AAA-AAACCAGATTGAAGCCGCAACGACGAATCTTGA-ACCTTAAAGATGTG
1 AAAGGAA--AGATTGAGGCCGCAACGACGAATCTT-ATACCTTAAAGATGTG
* * *
44167 -AAGGAAAAGGTTGAGGCCGCAACGACGAACCTTATA-CTATATAGATGTG
1 AAAGG-AAAGATTGAGGCCGCAACGACGAATCTTATACCT-TAAAGATGTG
44216 AAAGGAAAGATTGAGGCCGCAACTG-CGAATCTTATACCTT-AAGATG
1 AAAGGAAAGATTGAGGCCGCAAC-GACGAATCTTATACCTTAAAGATG
44262 AAGCAGACTG
Statistics
Matches: 186, Mismatches: 33, Indels: 42
0.71 0.13 0.16
Matches are distributed among these distances:
45 2 0.01
46 7 0.04
47 24 0.13
48 36 0.19
49 103 0.55
50 12 0.06
51 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.20
Consensus pattern (49 bp):
AAAGGAAAGATTGAGGCCGCAACGACGAATCTTATACCTTAAAGATGTG
Found at i:44709 original size:123 final size:123
Alignment explanation
Indices: 44488--44982 Score: 658
Period size: 123 Copynumber: 4.0 Consensus size: 123
44478 GGGTCAGAGA
* * * *
44488 TCAAAACAATGAAGCAGTCATCTTTCTGATGAGATACAAAGAAGT-GAACCAAATCAATGAAGCA
1 TCAAAACAATGAAGCGGTCATCTTCCTGATGAGATACAAAGAAGTAG-ACCAAAACAATGAAGCG
*
44552 AAGCTCAATGCAAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGG
65 AAGCTCAATGCGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGG
* * * * *
44611 TCAAAACAATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCAACGAAACGA
1 TCAAAACAATGAAGCGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGCGA
* * * * *
44676 AGATCAATGCGAGTGAAACTTCAAACCCTATCTTCCTGATGAGATACATAGAAATGAG
66 AGCTCAATGCGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGG
* * * *
44734 TCAAAA-ACATGAGGTGGTCATATTCCTGATGAGATACAGAGAAGTAGACCAAAACAATGAAGCG
1 TCAAAACA-ATGAAGCGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGCG
* * * *
44798 AAGCTCAATACGAGTGAAACTTCAAACCCCATCTTCTTAATGAGATACAGAAAAGTGGG
65 AAGCTCAATGCGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGG
* * *
44857 TTAAAACAATGAAGTGTTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAACAATTG-AGCG
1 TCAAAACAATGAAGCGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAACAA-TGAAGCG
* * *
44921 AAG--CAATGCGAATGAAACTTCAAACCCCATCTTCTTGATGAGATGCAGAGAAGTGGG
65 AAGCTCAATGCGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGG
*
44978 CCAAA
1 TCAAA
44983 TAAGTAAACA
Statistics
Matches: 328, Mismatches: 40, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
121 52 0.16
122 1 0.00
123 271 0.83
124 4 0.01
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (123 bp):
TCAAAACAATGAAGCGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGCGA
AGCTCAATGCGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGG
Found at i:45638 original size:21 final size:21
Alignment explanation
Indices: 45614--45688 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 21
45604 AAAGTCCAAA
45614 TTACAAACCCAATTGATCCAT
1 TTACAAACCCAATTGATCCAT
* * *
45635 TTACATAAAACCAATTAAAAAGTCCAAA
1 TTAC--AAACCCAATT---GA-TCC-AT
45663 TTACAAACCCAATTGATCCAT
1 TTACAAACCCAATTGATCCAT
45684 TTACA
1 TTACA
45689 TAAAACCAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
21 10 0.24
22 3 0.07
23 10 0.24
26 10 0.24
27 3 0.07
28 5 0.12
ACGTcount: A:0.45, C:0.24, G:0.04, T:0.27
Consensus pattern (21 bp):
TTACAAACCCAATTGATCCAT
Found at i:45649 original size:23 final size:23
Alignment explanation
Indices: 45622--45699 Score: 70
Period size: 23 Copynumber: 3.3 Consensus size: 23
45612 AATTACAAAC
45622 CCAATTGATCCATTTACATAAAA
1 CCAATTGATCCATTTACATAAAA
* * *
45645 CCAATTAAAAAGTCCAAATTAC--AAAC
1 CCAATT---GA-TCC-ATTTACATAAAA
45671 CCAATTGATCCATTTACATAAAA
1 CCAATTGATCCATTTACATAAAA
45694 CCAATT
1 CCAATT
45700 AAAATACCCA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
21 5 0.12
22 3 0.07
23 16 0.38
26 10 0.24
27 3 0.07
28 5 0.12
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.27
Consensus pattern (23 bp):
CCAATTGATCCATTTACATAAAA
Found at i:45657 original size:49 final size:49
Alignment explanation
Indices: 45604--45703 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
45594 AAAGAAGAAG
45604 AAAGTCCAAATTACAAACCCAATTGATCCATTTACATAAAACCAATTAA
1 AAAGTCCAAATTACAAACCCAATTGATCCATTTACATAAAACCAATTAA
45653 AAAGTCCAAATTACAAACCCAATTGATCCATTTACATAAAACCAATTAA
1 AAAGTCCAAATTACAAACCCAATTGATCCATTTACATAAAACCAATTAA
45702 AA
1 AA
45704 TACCCAAGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.24
Consensus pattern (49 bp):
AAAGTCCAAATTACAAACCCAATTGATCCATTTACATAAAACCAATTAA
Found at i:46232 original size:14 final size:13
Alignment explanation
Indices: 46212--46261 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
46202 GCAAAAAACC
*
46212 TAAAAAAACGAAA
1 TAAAAAAAAGAAA
46225 TAAAAAAAAGAAA
1 TAAAAAAAAGAAA
46238 TAAAACATAAA-AAA
1 TAAAA-A-AAAGAAA
*
46252 AAAAAAAAAG
1 TAAAAAAAAG
46262 GCTTCGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 3 0.09
13 18 0.56
14 8 0.25
15 3 0.09
ACGTcount: A:0.82, C:0.04, G:0.06, T:0.08
Consensus pattern (13 bp):
TAAAAAAAAGAAA
Found at i:46894 original size:27 final size:25
Alignment explanation
Indices: 46860--46911 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
46850 TACTTTTGAC
46860 CCCTAAAC-TTCTCAAAAATAGATTTAA
1 CCCTAAACTTTC-CAAAAA-A-ATTTAA
46887 CCCTAAACTTTCCAAAAAAATTTAA
1 CCCTAAACTTTCCAAAAAAATTTAA
46912 TTTTGGCCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 6 0.25
26 1 0.04
27 14 0.58
28 3 0.12
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.29
Consensus pattern (25 bp):
CCCTAAACTTTCCAAAAAAATTTAA
Found at i:58686 original size:28 final size:29
Alignment explanation
Indices: 58632--58694 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
58622 AAAATGTGAT
* *
58632 TTTTGGATACCCGAGAGGCAAAATGGTTA
1 TTTTGGACACCCGAGAGGCAAAATGGTAA
*
58661 TTTTGGACACTCGAG-GGCAAAATGGTAA
1 TTTTGGACACCCGAGAGGCAAAATGGTAA
58689 TTTTGG
1 TTTTGG
58695 GAAAGTTCGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 18 0.58
29 13 0.42
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.30
Consensus pattern (29 bp):
TTTTGGACACCCGAGAGGCAAAATGGTAA
Found at i:58808 original size:29 final size:29
Alignment explanation
Indices: 58776--58870 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 29
58766 TAAAAAATTA
*
58776 AATTTTTGGAAGTTTGGGGGTAAAATGGT
1 AATTTTTGGAAGTTCGGGGGTAAAATGGT
* *
58805 AA-TTTTGAGAAGAATCGGGGTTAAAAATGG-
1 AATTTTTG-GAAG-TTCGGGGGT-AAAATGGT
* *
58835 AATTTTTGGAAGTTCGAGGGTAAAATTGT
1 AATTTTTGGAAGTTCGGGGGTAAAATGGT
*
58864 ATTTTTT
1 AATTTTT
58871 TTTTGAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
28 11 0.21
29 18 0.34
30 12 0.23
31 12 0.23
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.38
Consensus pattern (29 bp):
AATTTTTGGAAGTTCGGGGGTAAAATGGT
Found at i:58812 original size:58 final size:57
Alignment explanation
Indices: 58750--59108 Score: 269
Period size: 59 Copynumber: 6.1 Consensus size: 57
58740 TGGTAATTTC
* **
58750 TTTGAAAAAATCGGGATAAAAAATTAAATTTTTGGAAGTTTGGGGGTAAAATGGTAAT
1 TTTGAAAAAATCGGG-TCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAATGGTAAT
* * * * * *
58808 TTTGAGAAGAATCGGGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATTGTATTTTTTT
1 TTTGA-AAAAATC-GGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAATGGTA-----AT
* * * * * *
58872 TTTGAAAAAATTGGGGTCAAAAATGGAA-TTTTAGAGGTTCGAGAGTAAAATGGTAATTT
1 TTTGAAAAAA-TCGGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAATGGTAA--T
* * * *
58931 TTTGAAAAAAATCGAGGTTAAAAATGGTATTTTAGGAAGTTTGTGGGTAAAATGGTAATT
1 TTTG-AAAAAATCG-GGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAATGGTAA-T
* * * * *
58991 TTTG-GAAAATTGATGTCAAAAATGGAATTTTGGGAAGTTT-GGGGTAAAATAGTAAT
1 TTTGAAAAAATCG-GGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAATGGTAAT
* **
59047 TTTTAGAAAAATCAAAGTCAAAAATGGAA-TTTTGGAAAGTTTGGGGGTAAAAAT-GTAAT
1 TTTGA-AAAAATC-GGGTCAAAAATGGAATTTTTGG-AAGTTTGGGGGT-AAAATGGTAAT
59106 TTT
1 TTT
59109 TAGAAAGTTT
Statistics
Matches: 243, Mismatches: 39, Indels: 37
0.76 0.12 0.12
Matches are distributed among these distances:
56 4 0.02
57 18 0.07
58 59 0.24
59 60 0.25
60 32 0.13
61 22 0.09
62 23 0.09
63 18 0.07
64 7 0.03
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (57 bp):
TTTGAAAAAATCGGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAATGGTAAT
Found at i:58991 original size:29 final size:29
Alignment explanation
Indices: 58951--59049 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 29
58941 ATCGAGGTTA
58951 AAAATGGT-ATTTTAGGAAGTTTGTGGGT
1 AAAATGGTAATTTTAGGAAGTTTGTGGGT
* ** ***
58979 AAAATGGTAATTTTTGGAAAATTGATGTCA
1 AAAATGGTAATTTTAGGAAGTTTG-TGGGT
*
59009 AAAATGG-AATTTTGGGAAGTTTG-GGGT
1 AAAATGGTAATTTTAGGAAGTTTGTGGGT
*
59036 AAAATAGTAATTTT
1 AAAATGGTAATTTT
59050 TAGAAAAATC
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
27 7 0.13
28 14 0.25
29 25 0.45
30 9 0.16
ACGTcount: A:0.35, C:0.01, G:0.26, T:0.37
Consensus pattern (29 bp):
AAAATGGTAATTTTAGGAAGTTTGTGGGT
Found at i:59098 original size:29 final size:27
Alignment explanation
Indices: 59066--59153 Score: 88
Period size: 29 Copynumber: 3.1 Consensus size: 27
59056 AATCAAAGTC
59066 AAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAAAT-GAATTTTGGAAAGTTT-GGGGT
*
59095 AAAAATGTAATTTTTAGAAAGTTTGGGGT
1 AAAAATG-AA-TTTTGGAAAGTTTGGGGT
* *
59124 TAATAT-AATTTTGGAGAAGTTTAGGGGT
1 AAAAATGAATTTTGGA-AAGTTT-GGGGT
59152 AA
1 AA
59154 TAAAACCAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
26 6 0.12
27 8 0.16
28 7 0.14
29 17 0.34
30 12 0.24
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.35
Consensus pattern (27 bp):
AAAAATGAATTTTGGAAAGTTTGGGGT
Found at i:59117 original size:30 final size:29
Alignment explanation
Indices: 59066--59122 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
59056 AATCAAAGTC
*
59066 AAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAAATGGAATTTTAGAAAGTTTGGGGGT
*
59095 AAAAATGTAATTTTTAGAAAGTTTGGGG
1 AAAAATGGAA-TTTTAGAAAGTTTGGGG
59123 TTAATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (29 bp):
AAAAATGGAATTTTAGAAAGTTTGGGGGT
Found at i:59143 original size:27 final size:28
Alignment explanation
Indices: 59074--59155 Score: 73
Period size: 27 Copynumber: 3.0 Consensus size: 28
59064 TCAAAAATGG
* * *
59074 AATTTTGGA-AAGTTTGGGGGTAAAAATGT
1 AATTTTGGAGAAGTTTAGGGGT--TAATAT
*
59103 AATTTT-TAGAAAGTTT-GGGGTTAATAT
1 AATTTTGGAG-AAGTTTAGGGGTTAATAT
59130 AATTTTGGAGAAGTTTAGGGG-TAATA
1 AATTTTGGAGAAGTTTAGGGGTTAATA
59156 AAACCAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
27 21 0.47
28 7 0.16
29 11 0.24
30 6 0.13
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (28 bp):
AATTTTGGAGAAGTTTAGGGGTTAATAT
Found at i:59910 original size:83 final size:82
Alignment explanation
Indices: 59797--59961 Score: 312
Period size: 83 Copynumber: 2.0 Consensus size: 82
59787 ATCCTTTCCT
*
59797 TTCACTTTTAAAAGAGTGATCTGGGTACGGATCTTGAAAGATCCAACCTAGAGCTTCATAAAAAA
1 TTCACTTTTAAAAAAGTGATCTGGGTACGGATCTTGAAAGATCCAACCTAGAGCTTCATAAAAAA
59862 AAAACCTTTTTTGAACA
66 AAAACCTTTTTTGAACA
59879 NTTCACTTTTAAAAAAGTGATCTGGGTACGGATCTTGAAAGATCCAACCTAGAGCTTCATAAAAA
1 -TTCACTTTTAAAAAAGTGATCTGGGTACGGATCTTGAAAGATCCAACCTAGAGCTTCATAAAAA
59944 AAAAACCTTTTTTGAACA
65 AAAAACCTTTTTTGAACA
59962 AAGAACCAAA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (82 bp):
TTCACTTTTAAAAAAGTGATCTGGGTACGGATCTTGAAAGATCCAACCTAGAGCTTCATAAAAAA
AAAACCTTTTTTGAACA
Found at i:61305 original size:6 final size:6
Alignment explanation
Indices: 61286--61349 Score: 59
Period size: 6 Copynumber: 11.5 Consensus size: 6
61276 TAATAAACTC
**
61286 AAATTT -AA-TT AAATTT AAATTT AAGA--T AAATTT AAATTT AAAAAT
1 AAATTT AAATTT AAATTT AAATTT AA-ATTT AAATTT AAATTT AAATTT
61331 AAATTT AAA--T AAATTT AAA
1 AAATTT AAATTT AAATTT AAA
61350 CCCAACTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
4 7 0.15
5 7 0.15
6 32 0.68
7 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (6 bp):
AAATTT
Found at i:61317 original size:17 final size:16
Alignment explanation
Indices: 61286--61349 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
61276 TAATAAACTC
*
61286 AAATTTAATTAAATTT
1 AAATTTAAATAAATTT
61302 AAATTTAAGATAAATTT
1 AAATTTAA-ATAAATTT
61319 AAATTT-AA-AAA--T
1 AAATTTAAATAAATTT
61331 AAATTTAAATAAATTT
1 AAATTTAAATAAATTT
61347 AAA
1 AAA
61350 CCCAACTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
12 7 0.17
13 2 0.05
14 6 0.14
15 1 0.02
16 13 0.31
17 13 0.31
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
AAATTTAAATAAATTT
Found at i:61334 original size:18 final size:17
Alignment explanation
Indices: 61286--61340 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
61276 TAATAAACTC
*
61286 AAATTT-AATTAAATTT
1 AAATTTAAAATAAATTT
*
61302 AAATTTAAGATAAATTT
1 AAATTTAAAATAAATTT
61319 AAATTTAAAAATAAATTT
1 AAATTT-AAAATAAATTT
61337 AAAT
1 AAAT
61341 AAATTTAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 6 0.18
17 14 0.41
18 14 0.41
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAATTTAAAATAAATTT
Found at i:61954 original size:49 final size:50
Alignment explanation
Indices: 61800--62172 Score: 275
Period size: 49 Copynumber: 7.5 Consensus size: 50
61790 GTATCAGGTT
* * **
61800 TGCCATTGCGACATAAACC-TTCCTCATT-GTGTCTTCACGGTACTGGATCC
1 TGCCATTGCGACTTAAACCTTTCC-C-TTCATGTCTTCGTGGTACTGGATCC
* * * * * * *
61850 TGCCATTGTGGCTTAGATCTTTTCCCTTCATGTCTTTGAGGTACTAGG-TTC
1 TGCCATTGCGACTTA-AACCTTTCCCTTCATGTCTTCGTGGTACT-GGATCC
* *
61901 -GCCATTGCAACTTAAACCTTTCCCTT-GTGTCTTCGTGGTACTGGATCC
1 TGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATCC
* * * * * *
61949 TGCCATTGCGGCTTAGATCTTTTCCCTTCATGTCTTTGAGGTACTAGG-TTC
1 TGCCATTGCGACTTA-AACCTTTCCCTTCATGTCTTCGTGGTACT-GGATCC
*
62000 -GCCATTGCGACTTAAACCTTTCCCTT-GTGTCTTCGTGGTACTGGAT-C
1 TGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATCC
* * * * **
62047 TGCCGTTGCGGCTTAGATCTTTATCTTCATGTCTTCGTGGTACTGGATCC
1 TGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATCC
** * * * * * *
62097 -GCTGTTGCGGCTTAGATCTTTCCCTTCATGTCTTTTGAGGTACTAGG-TTC
1 TGCCATTGCGACTTAAACCTTTCCCTTCATGTC-TTCGTGGTACT-GGATCC
*
62147 -GCCATTGCGACTTAAACCCTTCCCTT
1 TGCCATTGCGACTTAAACCTTTCCCTT
62173 TGCGTCTTTG
Statistics
Matches: 256, Mismatches: 52, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
47 5 0.02
48 49 0.19
49 80 0.31
50 80 0.31
51 34 0.13
52 8 0.03
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (50 bp):
TGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATCC
Found at i:61964 original size:99 final size:99
Alignment explanation
Indices: 61784--62090 Score: 462
Period size: 99 Copynumber: 3.1 Consensus size: 99
61774 CTTTTCTGCT
* * **
61784 TTTGAGGTA-TCAGGTTTGCCATTGCGACATAAACC-TTCCTCATTGTGTCTTCACGGTACTGGA
1 TTTGAGGTACT-AGGTTCGCCATTGCGACTTAAACCTTTCC-C-TTGTGTCTTCGTGGTACTGGA
*
61847 TCCTGCCATTGTGGCTTAGATCTTTTCCCTTCATGTC
63 TCCTGCCATTGCGGCTTAGATCTTTTCCCTTCATGTC
*
61884 TTTGAGGTACTAGGTTCGCCATTGCAACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGATCC
1 TTTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGATCC
61949 TGCCATTGCGGCTTAGATCTTTTCCCTTCATGTC
66 TGCCATTGCGGCTTAGATCTTTTCCCTTCATGTC
61983 TTTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGAT-C
1 TTTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGATCC
*
62047 TGCCGTTGCGGCTTAGATCTTTAT--CTTCATGTC
66 TGCCATTGCGGCTTAGATCTTT-TCCCTTCATGTC
* *
62080 TTCGTGGTACT
1 TTTGAGGTACT
62091 GGATCCGCTG
Statistics
Matches: 194, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
97 18 0.09
98 22 0.11
99 118 0.61
100 31 0.16
101 5 0.03
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.39
Consensus pattern (99 bp):
TTTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGATCC
TGCCATTGCGGCTTAGATCTTTTCCCTTCATGTC
Found at i:62117 original size:147 final size:149
Alignment explanation
Indices: 61928--62216 Score: 458
Period size: 148 Copynumber: 2.0 Consensus size: 149
61918 CTTTCCCTTG
61928 TGTCTTCGTGGTACTGGATCCTGCCATTGCGGCTTAGATCTTTTCCCTTCATGTC-TTTGAGGTA
1 TGTCTTCGTGGTACTGGATCCTGCCATTGCGGCTTAGATC-TTTCCCTTCATGTCTTTTGAGGTA
* * * * *
61992 CTAGGTTCGCCATTGCGACTTAAACCTTTCCC-TTGTGTCTTCGTGGTACTGGATCTGCCGTTGC
65 CTAGGTTCGCCATTGCGACTTAAACCCTTCCCTTTGCGTCTTCGCGGTACTAGATCCGCCGTTGC
62056 GGCTTAGATCTTTATCTTCA
130 GGCTTAGATCTTTATCTTCA
**
62076 TGTCTTCGTGGTACTGGATCC-GCTGTTGCGGCTTAGATCTTTCCCTTCATGTCTTTTGAGGTAC
1 TGTCTTCGTGGTACTGGATCCTGCCATTGCGGCTTAGATCTTTCCCTTCATGTCTTTTGAGGTAC
* * *
62140 TAGGTTCGCCATTGCGACTTAAACCCTTCCCTTTGCGTCTTTGCGGTACTAGATCCGTCGTTGTG
66 TAGGTTCGCCATTGCGACTTAAACCCTTCCCTTTGCGTCTTCGCGGTACTAGATCCGCCGTTGCG
62205 GCTTAGATCTTT
131 GCTTAGATCTTT
62217 CTGTTTATGT
Statistics
Matches: 129, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
146 14 0.11
147 56 0.43
148 59 0.46
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.39
Consensus pattern (149 bp):
TGTCTTCGTGGTACTGGATCCTGCCATTGCGGCTTAGATCTTTCCCTTCATGTCTTTTGAGGTAC
TAGGTTCGCCATTGCGACTTAAACCCTTCCCTTTGCGTCTTCGCGGTACTAGATCCGCCGTTGCG
GCTTAGATCTTTATCTTCA
Found at i:67720 original size:29 final size:29
Alignment explanation
Indices: 67678--67736 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
67668 ATCGTCGCTG
67678 AAGAAAATAAAATTATCAGCACTGATGTT
1 AAGAAAATAAAATTATCAGCACTGATGTT
67707 AAGAAAATAAAATTATCAGCACTGATGTT
1 AAGAAAATAAAATTATCAGCACTGATGTT
67736 A
1 A
67737 TTAATCAGAC
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:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (29 bp):
AAGAAAATAAAATTATCAGCACTGATGTT
Found at i:73681 original size:29 final size:28
Alignment explanation
Indices: 73649--73709 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
73639 AAAATGTGAT
* * *
73649 TTTTGGATAGTCGAGAGGTAAAATGGTAA
1 TTTTGGACACTCG-GAGGCAAAATGGTAA
*
73678 TTTTGGACACTCGGGGGCAAAATGGTAA
1 TTTTGGACACTCGGAGGCAAAATGGTAA
73706 TTTT
1 TTTT
73710 TTGAAAGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.30, C:0.08, G:0.30, T:0.33
Consensus pattern (28 bp):
TTTTGGACACTCGGAGGCAAAATGGTAA
Found at i:73765 original size:28 final size:27
Alignment explanation
Indices: 73663--73766 Score: 75
Period size: 28 Copynumber: 3.7 Consensus size: 27
73653 GGATAGTCGA
* * *
73663 GAGGTAAAATGGTAATTTTGGACACTC
1 GAGGTAAAATGATAATTTTAGACATTC
* * * * *
73690 GGGGGCAAAATGGTAATTTTTTGAAAGTTC
1 -GAGGTAAAATGATAA-TTTTAGACA-TTC
*
73720 GGGGTTAAAATGA-AATTTTAGACATTC
1 GAGG-TAAAATGATAATTTTAGACATTC
73747 GAGGATAAAATGATAATTTT
1 GAGG-TAAAATGATAATTTT
73767 TTGGAAAAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
27 14 0.23
28 26 0.43
29 13 0.21
30 8 0.13
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.33
Consensus pattern (27 bp):
GAGGTAAAATGATAATTTTAGACATTC
Found at i:73827 original size:29 final size:29
Alignment explanation
Indices: 73794--74061 Score: 162
Period size: 29 Copynumber: 9.4 Consensus size: 29
73784 TCAAAAATGA
73794 AATTTTTGGAAGTTTAGGGGTAAAATGGT
1 AATTTTTGGAAGTTTAGGGGTAAAATGGT
* ** *
73823 AATTTTGGGAAGAATCGGGGTTAAAATGG-
1 AATTTTTGGAAGTTTAGGGG-TAAAATGGT
*
73852 AATTTTTGGAAGTCTAGGGGTAAAATGGT
1 AATTTTTGGAAGTTTAGGGGTAAAATGGT
** ** * ** *
73881 TTTTTTTTAAAATCGA-GGTTAAAATGG-
1 AATTTTTGGAAGTTTAGGGGTAAAATGGT
* *
73908 AA-TTTTAGAGGTTTAGGGGTAAAATGGT
1 AATTTTTGGAAGTTTAGGGGTAAAATGGT
* ** *
73936 AATTTTTGAAAAAATTA-GGGTCAAAAAT-GA
1 AATTTTTG-GAAGTTTAGGGGT--AAAATGGT
73966 AATTTTTGGAAGTTTAGGGGT-AAA--GT
1 AATTTTTGGAAGTTTAGGGGTAAAATGGT
*** * *
73992 AATTTTTTGGAAAAATCGAGGTCAAAAATGG-
1 AA-TTTTTGGAAGTTTAGGGGT--AAAATGGT
* *
74023 AATTTTTAGAAGATT-GGGGTAAAATGGT
1 AATTTTTGGAAGTTTAGGGGTAAAATGGT
74051 AATTTTTGGAA
1 AATTTTTGGAA
74062 AAATTGGGTT
Statistics
Matches: 179, Mismatches: 44, Indels: 33
0.70 0.17 0.13
Matches are distributed among these distances:
26 10 0.06
27 34 0.19
28 30 0.17
29 59 0.33
30 38 0.21
31 7 0.04
32 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (29 bp):
AATTTTTGGAAGTTTAGGGGTAAAATGGT
Found at i:73859 original size:58 final size:58
Alignment explanation
Indices: 73691--74157 Score: 341
Period size: 58 Copynumber: 8.1 Consensus size: 58
73681 TGGACACTCG
* * ** * * *
73691 GGGGCAAAATGGTAATTTTTTGAAAGTTCGGGGTTAAAAT-GAAATTTTAGACA--TTC
1 GGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTTAAAATGGAATTTTTGGA-AGTTTA
* * * * * *
73747 GAGGATAAAATGATAATTTTTTGGAAAAAAATCAGGATCAAAAATGAAATTTTTGGAAGTTTA
1 G-GGGTAAAATGGTAA-TTTTTGG--AAAAATCGGGGT-TAAAATGGAATTTTTGGAAGTTTA
* * *
73810 GGGGTAAAATGGTAATTTTGGGAAGAATCGGGGTTAAAATGGAATTTTTGGAAGTCTA
1 GGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTTAAAATGGAATTTTTGGAAGTTTA
*** * * *
73868 GGGGTAAAATGGT--TTTTTTTTAAAATCGAGGTTAAAATGGAA-TTTTAGAGGTTTA
1 GGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTTAAAATGGAATTTTTGGAAGTTTA
* ** * *
73923 GGGGTAAAATGGTAATTTTTGAAAAAATTAGGGTCAAAAATGAAATTTTTGGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGAAAAATCGGGGT-TAAAATGGAATTTTTGGAAGTTTA
* * * *
73982 GGGGT-AAA--GTAATTTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTAGAAGATT-
1 GGGGTAAAATGGTAA-TTTTTGGAAAAATCGGGGT-TAAAATGGAATTTTTGGAAGTTTA
* *
74038 GGGGTAAAATGGTAATTTTTGGAAAAAT-TGGGTTCAAAAATGGAA-TTTTGTAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTT--AAAATGGAATTTTTG-GAAGTTTA
* ** * * ** *
74097 GGGGTAAAAAT-G-AATTTTTAGAAAGTTCAGGGTCAAAATATAATTTTTGGACAATTTA
1 GGGGT-AAAATGGTAATTTTTGGAAAAATCGGGGTTAAAATGGAATTTTTGGA-AGTTTA
74155 GGG
1 GGG
74158 ACCTTCAGGG
Statistics
Matches: 324, Mismatches: 63, Indels: 46
0.75 0.15 0.11
Matches are distributed among these distances:
55 23 0.07
56 33 0.10
57 78 0.24
58 103 0.32
59 39 0.12
60 13 0.04
61 12 0.04
62 20 0.06
63 3 0.01
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTTAAAATGGAATTTTTGGAAGTTTA
Found at i:74066 original size:115 final size:115
Alignment explanation
Indices: 73759--74115 Score: 420
Period size: 115 Copynumber: 3.1 Consensus size: 115
73749 GGATAAAATG
* *
73759 ATAATTTTTTGGAAAAAAATC-AGGATCAAAAATGAAATTTTTGGAAGTTTAGGGGTAAAATGGT
1 ATAATTTTTTGG--AAAAATCGAGG-TCAAAAATGGAATTTTTAGAAGTTTAGGGGTAAAATGGT
* * * * *
73823 AATTTTGGGAAGAATCGGGGT-TAAAATGGAATTTTTGGAAGTCTAGGGGTAAA
63 AATTTTTGGAAAAAT-TGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAA
** *** * *
73876 ATGGTTTTTTTTTAAAATCGAGGT-TAAAATGGAA-TTTTAGAGGTTTAGGGGTAAAATGGTAAT
1 ATAATTTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTAGAAGTTTAGGGGTAAAATGGTAAT
* *
73939 TTTTGAAAAAATTAGGGTCAAAAATGAAATTTTTGGAAGTTTAGGGGTAAA
66 TTTTGGAAAAATT-GGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAA
* *
73990 GTAATTTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTAGAAGATT-GGGGTAAAATGGTAAT
1 ATAATTTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTAGAAGTTTAGGGGTAAAATGGTAAT
*
74054 TTTTGGAAAAATTGGGTTCAAAAATGGAA-TTTTGTAAAGTTTAGGGGTAAAA
66 TTTTGGAAAAATTGGG-TCAAAAATGGAATTTTTG-GAAGTTTAGGGGT-AAA
74106 ATGAATTTTT
1 AT-AATTTTT
74116 AGAAAGTTCA
Statistics
Matches: 202, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
113 40 0.20
114 63 0.31
115 67 0.33
116 17 0.08
117 15 0.07
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (115 bp):
ATAATTTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTAGAAGTTTAGGGGTAAAATGGTAAT
TTTTGGAAAAATTGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAA
Found at i:74087 original size:29 final size:28
Alignment explanation
Indices: 73996--74087 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
73986 TAAAGTAATT
*
73996 TTTTGGAAAAATCGAGGTCAAAAATGGAA
1 TTTTGGAAAAATTG-GGTCAAAAATGGAA
* *
74025 TTTT-TAGAAGATTGGGGT--AAAATGGTAA
1 TTTTGGA-AAAATT-GGGTCAAAAATGG-AA
74053 TTTTTGGAAAAATTGGGTTCAAAAATGGAA
1 -TTTTGGAAAAATTGGG-TCAAAAATGGAA
74083 TTTTG
1 TTTTG
74088 TAAAGTTTAG
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
27 7 0.14
28 6 0.12
29 26 0.52
30 4 0.08
31 7 0.14
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (28 bp):
TTTTGGAAAAATTGGGTCAAAAATGGAA
Found at i:74105 original size:29 final size:28
Alignment explanation
Indices: 74015--74114 Score: 98
Period size: 29 Copynumber: 3.5 Consensus size: 28
74005 AATCGAGGTC
74015 AAAAATGGAATTTT-TAGAAGATTGGGGT
1 AAAAATGGAATTTTGTA-AAGATTGGGGT
* * *
74043 -AAAATGGTAATTTTTGGAAAAATTGGGTT
1 AAAAATGG-AA-TTTTGTAAAGATTGGGGT
*
74072 CAAAAATGGAATTTTGTAAAGTTTAGGGGT
1 -AAAAATGGAATTTTGTAAAGATT-GGGGT
74102 AAAAAT-GAATTTT
1 AAAAATGGAATTTT
74115 TAGAAAGTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
27 7 0.12
28 9 0.15
29 29 0.49
30 7 0.12
31 7 0.12
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.35
Consensus pattern (28 bp):
AAAAATGGAATTTTGTAAAGATTGGGGT
Found at i:74129 original size:28 final size:30
Alignment explanation
Indices: 74071--74145 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
74061 AAAATTGGGT
*
74071 TCAAAAATGGAA-TTTTGTAAAGTTTAGGGG
1 TCAAAAAT-GAATTTTTGTAAAGTTCAGGGG
74101 T-AAAAATGAATTTTTAG-AAAGTTCA-GGG
1 TCAAAAATGAATTTTT-GTAAAGTTCAGGGG
74129 TCAAAATAT-AATTTTTG
1 TCAAAA-ATGAATTTTTG
74146 GACAATTTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
28 8 0.20
29 28 0.70
30 4 0.10
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (30 bp):
TCAAAAATGAATTTTTGTAAAGTTCAGGGG
Found at i:76195 original size:6 final size:6
Alignment explanation
Indices: 76173--76268 Score: 58
Period size: 6 Copynumber: 16.5 Consensus size: 6
76163 TTTTTTAATC
* **
76173 AATTCA AATTT- AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTAA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A
** * * **
76219 AAGATA AATTTA AA-TT- GATGATA AATTTA AATTTA AAAATA AATTTA
1 AATTTA AATTTA AATTTA AAT-TTA AATTTA AATTTA AATTTA AATTTA
76266 AAT
1 AAT
76269 CAATTTAAAC
Statistics
Matches: 66, Mismatches: 17, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
4 3 0.05
5 9 0.14
6 48 0.73
7 6 0.09
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:76210 original size:17 final size:19
Alignment explanation
Indices: 76188--76268 Score: 82
Period size: 17 Copynumber: 4.5 Consensus size: 19
76178 AAATTTAATT
76188 AAATTTAAATTT-AAAG-C
1 AAATTTAAATTTAAAAGAC
*
76205 AAATTTAAATTTAAAAGAT
1 AAATTTAAATTTAAAAGAC
* * *
76224 AAATTTAAA-TT-GATGAT
1 AAATTTAAATTTAAAAGAC
*
76241 AAATTTAAATTTAAAA-AT
1 AAATTTAAATTTAAAAGAC
76259 AAATTTAAAT
1 AAATTTAAAT
76269 CAATTTAAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
17 25 0.45
18 20 0.36
19 10 0.18
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (19 bp):
AAATTTAAATTTAAAAGAC
Found at i:76230 original size:36 final size:36
Alignment explanation
Indices: 76187--76268 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
76177 CAAATTTAAT
76187 TAAATTTAAATTTAAAG-CAAATTTAAATTTAAAAGA
1 TAAATTTAAATTTAAAGACAAATTTAAATTTAAAA-A
* * *
76223 TAAATTTAAA-TTGATGATAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAAGACAAATTTAAATTTAAAAA
76258 TAAATTTAAAT
1 TAAATTTAAAT
76269 CAATTTAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
35 15 0.37
36 26 0.63
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (36 bp):
TAAATTTAAATTTAAAGACAAATTTAAATTTAAAAA
Found at i:79459 original size:17 final size:16
Alignment explanation
Indices: 79417--79447 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
79407 TTATATTTTT
*
79417 TTATAAATTTTATATA
1 TTATAAACTTTATATA
79433 TTATAAACTTTATAT
1 TTATAAACTTTATAT
79448 TATTTTAGAC
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:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATAAACTTTATATA
Found at i:79865 original size:17 final size:17
Alignment explanation
Indices: 79845--79932 Score: 88
Period size: 17 Copynumber: 5.0 Consensus size: 17
79835 TTCATTTTGG
79845 GTTTAAATTTAATTTAA
1 GTTTAAATTTAATTTAA
**
79862 GTTTAAACTTTTCTTTTAAA
1 GTTTAAA--TTTAATTT-AA
*
79882 GTTTAAATTTAAATTAA
1 GTTTAAATTTAATTTAA
*
79899 GTTTAAATTTAAATTGAA
1 GTTTAAATTT-AATTTAA
*
79917 -TTTAAATTGAATTTAA
1 GTTTAAATTTAATTTAA
79933 AGGTCCAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
16 6 0.10
17 27 0.47
18 10 0.17
19 6 0.10
20 9 0.16
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (17 bp):
GTTTAAATTTAATTTAA
Found at i:79866 original size:11 final size:11
Alignment explanation
Indices: 79846--79933 Score: 59
Period size: 11 Copynumber: 7.5 Consensus size: 11
79836 TCATTTTGGG
79846 TTTAAATTTAA
1 TTTAAATTTAA
*
79857 TTTAAGTTTAAA
1 TTTAAATTT-AA
***
79869 CTTTTCTTTTAAA
1 -TTTAAATTT-AA
79882 GTTTAAATTTAA
1 -TTTAAATTTAA
* *
79894 ATTAAGTTTAAA
1 TTTAAATTT-AA
*
79906 TTTAAATTGAA
1 TTTAAATTTAA
*
79917 TTTAAATTGAA
1 TTTAAATTTAA
79928 TTTAAA
1 TTTAAA
79934 GGTCCAATTC
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
11 34 0.56
12 12 0.20
13 15 0.25
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:79894 original size:6 final size:6
Alignment explanation
Indices: 79846--79933 Score: 67
Period size: 6 Copynumber: 15.0 Consensus size: 6
79836 TCATTTTGGG
* ***
79846 TTTAAA TTT-AA TTTAAG TTTAAA CTTTTCT TTTAAA GTTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA -TTTAAA TTTAAA
* * *
79895 -TTAAG TTTAAA TTTAAA -TTGAA TTTAAA -TTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
79934 GGTCCAATTC
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
5 17 0.27
6 36 0.58
7 9 0.15
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:80605 original size:3 final size:3
Alignment explanation
Indices: 80597--80680 Score: 62
Period size: 3 Copynumber: 27.0 Consensus size: 3
80587 ATACTGTTAT
** * ** *
80597 TAA TAA TAA CCA TAA TTAA TAA TAA TAA TAA TAA CTAT TTT TAA -AT
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
*
80643 TAA TAA TAG TAA TAA TAA TAA TTAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA T-AA TAA TAA
80681 AAAATAAAAC
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
2 1 0.02
3 52 0.81
4 11 0.17
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:80685 original size:10 final size:10
Alignment explanation
Indices: 80608--80687 Score: 63
Period size: 10 Copynumber: 7.8 Consensus size: 10
80598 AATAATAACC
*
80608 ATAATTAATA
1 ATAAATAATA
80618 AT-AATAATA
1 ATAAATAATA
* * *
80627 ATAACTATTT
1 ATAAATAATA
*
80637 TTAAATTAATA
1 ATAAA-TAATA
80648 ATAGTAATAATA
1 ATA--AATAATA
*
80660 ATAATTAATA
1 ATAAATAATA
80670 ATAAATAATA
1 ATAAATAATA
*
80680 AAAAATAA
1 ATAAATAA
80688 AACCAAAAGT
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
9 8 0.15
10 31 0.57
11 5 0.09
12 8 0.15
13 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (10 bp):
ATAAATAATA
Found at i:81012 original size:24 final size:24
Alignment explanation
Indices: 80967--81013 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
80957 AGAAAGAAAG
* *
80967 GGTTTTCAAAGAAAAATCAAAATT
1 GGTTTTAAAAGAAAAAGCAAAATT
* *
80991 GGTTTTAAAATAAAAAGGAAAAT
1 GGTTTTAAAAGAAAAAGCAAAAT
81014 CAAAGAAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (24 bp):
GGTTTTAAAAGAAAAAGCAAAATT
Found at i:81784 original size:30 final size:29
Alignment explanation
Indices: 81718--81979 Score: 184
Period size: 30 Copynumber: 9.0 Consensus size: 29
81708 CCTTAGAGGC
* * *
81718 CCCTAAACTATCCAAAAATT--ATTTTGA
1 CCCTAAACTTTCTAAAAATTACATTTTTA
81745 CCACTAAACTTTCTAAAAATTACATTTTTA
1 CC-CTAAACTTTCTAAAAATTACATTTTTA
*
81775 CCCTCAAACTTCCTAAAAATTACATTTTTA
1 CCCT-AAACTTTCTAAAAATTACATTTTTA
* *
81805 CCCCCCAAAC-TACTTAAAAATTACATTTTTA
1 --CCCTAAACTTTC-TAAAAATTACATTTTTA
* *
81836 CCCT-TACTCTTCTTAAAAATTACA-TTTTC
1 CCCTAAACT-TTC-TAAAAATTACATTTTTA
*
81865 CCCT-TACTTTC-AAAAATTACATTTTTA
1 CCCTAAACTTTCTAAAAATTACATTTTTA
* * *
81892 CCCTTAAACTTTC-CAAAATTCCATTTTAA
1 CCC-TAAACTTTCTAAAAATTACATTTTTA
* ** * * *
81921 ACCTTGATTTTACCAAAAAATAC-TATTTTA
1 CCCTAAACTTT-CTAAAAATTACAT-TTTTA
*
81951 CCCTCGAACTTTC-AAAAATTACATTTTTA
1 CCCT-AAACTTTCTAAAAATTACATTTTTA
81980 ACTTCGATTT
Statistics
Matches: 190, Mismatches: 28, Indels: 32
0.76 0.11 0.13
Matches are distributed among these distances:
26 10 0.05
27 9 0.05
28 27 0.14
29 53 0.28
30 63 0.33
31 25 0.13
32 3 0.02
ACGTcount: A:0.36, C:0.24, G:0.01, T:0.39
Consensus pattern (29 bp):
CCCTAAACTTTCTAAAAATTACATTTTTA
Found at i:81823 original size:31 final size:31
Alignment explanation
Indices: 81757--81838 Score: 130
Period size: 31 Copynumber: 2.7 Consensus size: 31
81747 ACTAAACTTT
* *
81757 CTAAAAATTACATTTTTA-CCCTCAAACTTC
1 CTAAAAATTACATTTTTACCCCCCAAACTAC
81787 CTAAAAATTACATTTTTACCCCCCAAACTAC
1 CTAAAAATTACATTTTTACCCCCCAAACTAC
*
81818 TTAAAAATTACATTTTTACCC
1 CTAAAAATTACATTTTTACCC
81839 TTACTCTTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 18 0.38
31 30 0.62
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (31 bp):
CTAAAAATTACATTTTTACCCCCCAAACTAC
Found at i:81826 original size:61 final size:56
Alignment explanation
Indices: 81758--81918 Score: 175
Period size: 61 Copynumber: 2.8 Consensus size: 56
81748 CTAAACTTTC
*
81758 TAAAAATTACATTTTTACCCTCAAACTTCCTAAAAATTACATTTTTACCCCCCAAACTACT
1 TAAAAATTACATTTTTACCCTTAAACTTCCTAAAAATTACATTTTT---CCCCAAACT--T
** * **
81819 TAAAAATTACATTTTTACCCTTACTCTTCTTAAAAATTACA-TTTTCCCCTTACTT
1 TAAAAATTACATTTTTACCCTTAAACTTCCTAAAAATTACATTTTTCCCCAAACTT
*
81874 TCAAAAATTACATTTTTACCCTTAAACTTTCC--AAAATTCCATTTT
1 T-AAAAATTACATTTTTACCCTTAAAC-TTCCTAAAAATTACATTTT
81919 AAACCTTGAT
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
55 10 0.11
56 26 0.30
57 10 0.11
60 4 0.05
61 37 0.43
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (56 bp):
TAAAAATTACATTTTTACCCTTAAACTTCCTAAAAATTACATTTTTCCCCAAACTT
Found at i:81916 original size:29 final size:29
Alignment explanation
Indices: 81749--81979 Score: 186
Period size: 30 Copynumber: 7.9 Consensus size: 29
81739 TTTTGACCAC
81749 TAAACTTTCTAAAAATTACATTTTTACCCT
1 TAAACTTTC-AAAAATTACATTTTTACCCT
* * *
81779 CAAACTTCCTAAAAATTACATTTTTACCCCC
1 TAAACTTTC-AAAAATTACATTTTTA-CCCT
*
81810 CAAACTACTT-AAAAATTACATTTTTACCCT
1 TAAACT--TTCAAAAATTACATTTTTACCCT
** * *
81840 TACTCTTCTTAAAAATTACA-TTTTCCCCT
1 TAAACTT-TCAAAAATTACATTTTTACCCT
81869 T--ACTTTCAAAAATTACATTTTTACCCT
1 TAAACTTTCAAAAATTACATTTTTACCCT
* * * *
81896 TAAACTTTCCAAAATTCCATTTTAAACCT
1 TAAACTTTCAAAAATTACATTTTTACCCT
* * *
81925 T-GATTTTACCAAAAAATAC-TATTTTACCCT
1 TAAACTTT--CAAAAATTACAT-TTTTACCCT
**
81955 CGAACTTTCAAAAATTACATTTTTA
1 TAAACTTTCAAAAATTACATTTTTA
81980 ACTTCGATTT
Statistics
Matches: 161, Mismatches: 27, Indels: 27
0.75 0.13 0.13
Matches are distributed among these distances:
26 11 0.07
27 12 0.07
28 5 0.03
29 48 0.30
30 55 0.34
31 29 0.18
33 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.01, T:0.40
Consensus pattern (29 bp):
TAAACTTTCAAAAATTACATTTTTACCCT
Found at i:81953 original size:59 final size:59
Alignment explanation
Indices: 81875--82130 Score: 256
Period size: 59 Copynumber: 4.4 Consensus size: 59
81865 CCCTTACTTT
* * *
81875 CAAAAATTA-CATTTTTACCCTTAAACTTTCCAAAATTCCATTTTAAACCTTGATTTTAC
1 CAAAAATTACCA-TTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTTGATTTCAC
* * * * *
81934 CAAAAAATACTATTTTACCCTCGAACTTTCAAAAATTACATTTTTAA-CTTCGATTTCAC
1 CAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTT-GATTTCAC
* * * *
81993 CAAAAATTACCATTTTACCC-CTAAAATATCCAAAATTCCATTTTTGACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCTC-AAACTTTCCAAAATTCCATTTTTAACCTTGATTTCAC
* * * * *
82052 TAAAAATTACCATTTTACCCTCGAAC-TTCTCAAAATTTCATTTTTGA-CTCAGATTTC-C
1 CAAAAATTACCATTTTACCCTCAAACTTTC-CAAAATTCCATTTTTAACCT-TGATTTCAC
*
82110 C-AAAATTACCATTTTGCCCTC
1 CAAAAATTACCATTTTACCCTC
82131 GAGTGTCTAA
Statistics
Matches: 165, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
57 19 0.12
58 9 0.05
59 133 0.81
60 4 0.02
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.38
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTTGATTTCAC
Found at i:82026 original size:118 final size:117
Alignment explanation
Indices: 81875--82124 Score: 328
Period size: 118 Copynumber: 2.1 Consensus size: 117
81865 CCCTTACTTT
* * * * *
81875 CAAAAATTA-CATTTTTACCCTTAAACTTTCCAAAATTCCATTTTAAACCTTGATTTTACCAAAA
1 CAAAAATTACCA-TTTTACCCCTAAAATATCCAAAATTCCATTTTAAACCTCGATTTCACCAAAA
*
81939 AATACTATTTTACCCTCGAACTT-TCAAAAATTACATTTTTAACTTC-GATTTCAC
65 AATACCATTTTACCCTCGAACTTCTC-AAAATTACATTTTTAAC-TCAGATTTC-C
** *
81993 CAAAAATTACCATTTTACCCCTAAAATATCCAAAATTCCATTTTTGACCTCGATTTCACTAAAAA
1 CAAAAATTACCATTTTACCCCTAAAATATCCAAAATTCCATTTTAAACCTCGATTTCACCAAAAA
* * *
82058 TTACCATTTTACCCTCGAACTTCTCAAAATTTCATTTTTGACTCAGATTTCC
66 ATACCATTTTACCCTCGAACTTCTCAAAATTACATTTTTAACTCAGATTTCC
82110 C-AAAATTACCATTTT
1 CAAAAATTACCATTTT
82125 GCCCTCGAGT
Statistics
Matches: 117, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
116 14 0.12
117 4 0.03
118 95 0.81
119 4 0.03
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (117 bp):
CAAAAATTACCATTTTACCCCTAAAATATCCAAAATTCCATTTTAAACCTCGATTTCACCAAAAA
ATACCATTTTACCCTCGAACTTCTCAAAATTACATTTTTAACTCAGATTTCC
Found at i:82074 original size:30 final size:29
Alignment explanation
Indices: 81906--82157 Score: 98
Period size: 28 Copynumber: 8.7 Consensus size: 29
81896 TAAACTTTCC
* * *
81906 AAAATT-CCATTTTAAACCTTGATTTTACCA
1 AAAATTACCATTTT-ACCCTCGATTTCA-CA
* *
81936 AAAAATACTATTTTACCCTCGAACTTT--CA
1 AAAATTACCATTTTACCCTCG-A-TTTCACA
* *
81965 AAAATTA-CATTTTTAACTTCGATTTCACCA
1 AAAATTACCA-TTTTACCCTCGATTTCA-CA
** *
81995 AAAATTACCATTTTACCCCTAAAATATC-C-
1 AAAATTACCATTTTA-CCCT-CGATTTCACA
82024 AAAATT-CCATTTTTGA-CCTCGATTTCACTA
1 AAAATTACCA-TTTT-ACCCTCGATTTCAC-A
* *
82054 AAAATTACCATTTTACCCTCGAACTTCTC-
1 AAAATTACCATTTTACCCTCG-ATTTCACA
* *** *
82083 AAAATT-TCATTTTTGACTCAGATTTC-CC
1 AAAATTACCATTTTACCCTC-GATTTCACA
* * *
82111 AAAATTACCATTTTGCCCTCGAGTGT--CT
1 AAAATTACCATTTTACCCTCGA-TTTCACA
*
82139 AAAATTACCATTTTGCCCT
1 AAAATTACCATTTTACCCT
82158 AAGTACCCAA
Statistics
Matches: 171, Mismatches: 29, Indels: 46
0.70 0.12 0.19
Matches are distributed among these distances:
27 8 0.05
28 50 0.29
29 46 0.27
30 41 0.24
31 19 0.11
32 7 0.04
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.37
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGATTTCACA
Found at i:82170 original size:28 final size:28
Alignment explanation
Indices: 82107--82179 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 28
82097 GACTCAGATT
*
82107 TCCC-AAAATTACCATTTTGCCCTCGAG
1 TCCCAAAAATTACCATTTTGCCCTCAAG
** *
82134 TGTCTAAAATTACCATTTTGCCCT-AAG
1 TCCCAAAAATTACCATTTTGCCCTCAAG
*
82161 TACCCAAAAATCA-CATTTT
1 T-CCCAAAAATTACCATTTT
82180 CAACTTCGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
27 11 0.30
28 26 0.70
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.33
Consensus pattern (28 bp):
TCCCAAAAATTACCATTTTGCCCTCAAG
Found at i:94419 original size:146 final size:146
Alignment explanation
Indices: 94250--94565 Score: 542
Period size: 146 Copynumber: 2.2 Consensus size: 146
94240 TAAAAAGGTT
*
94250 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTATAAAGAAGCGG
1 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGCGG
* * * * *
94315 ATTGAAACAAGTGAGGCAGTCATCTTCTTGATGAGATACAGAGAAGTATATCAACTCAATACGAA
66 ATTGAAACAAGTGAGGCAGTCATCTTCCTGATGAGACACAAAGAAGTATACCAACTCAATACAAA
94380 CAAATCTTCGAACCCC
131 CAAATCTTCGAACCCC
*
94396 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGG
1 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGCGG
*
94461 ATTGAAACAAGTGAGGCAGTCATCTTCCTGATGAGACACAAAGAAGTATACCAACTCAATGCAAA
66 ATTGAAACAAGTGAGGCAGTCATCTTCCTGATGAGACACAAAGAAGTATACCAACTCAATACAAA
94526 CAAATCTTCGAACCCC
131 CAAATCTTCGAACCCC
* *
94542 AGCTTCCTCATGAGATACTAAGAA
1 AGCTTCCTGATGAGATACTGAGAA
94566 TCAGGGCGAA
Statistics
Matches: 160, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
146 160 1.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.23
Consensus pattern (146 bp):
AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGCGG
ATTGAAACAAGTGAGGCAGTCATCTTCCTGATGAGACACAAAGAAGTATACCAACTCAATACAAA
CAAATCTTCGAACCCC
Found at i:95059 original size:17 final size:17
Alignment explanation
Indices: 95039--95123 Score: 64
Period size: 17 Copynumber: 4.8 Consensus size: 17
95029 TTCATTTTGG
95039 GTTTAAATTTAATTTAA
1 GTTTAAATTTAATTTAA
**
95056 GTTTAAACTTTTCTTTTAAA
1 GTTTAAA--TTTAATTT-AA
* *
95076 GTTCAAATTTAAATTAA
1 GTTTAAATTTAATTTAA
* *
95093 GTTTAATTTTAAATTGAA
1 GTTTAAATTT-AATTTAA
*
95111 -TTTAAATTGAATT
1 GTTTAAATTTAATT
95124 AAAAGGTCTA
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
16 4 0.08
17 24 0.46
18 10 0.19
19 6 0.12
20 8 0.15
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.51
Consensus pattern (17 bp):
GTTTAAATTTAATTTAA
Found at i:95838 original size:3 final size:3
Alignment explanation
Indices: 95832--95880 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
95822 ATATTGTTAT
*
95832 TAA TAA TAA CAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
95878 TAA
1 TAA
95881 CTATTTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:95852 original size:31 final size:29
Alignment explanation
Indices: 95817--95910 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 29
95807 TAATGCTTAA
95817 TAATAATATTGTTATTAATAATAACAATAAT
1 TAATAATATT-TTATTAATAATAA-AATAAT
* *
95848 TAATAATA--ATAATAATAATAATAATAA-
1 TAATAATATTTTATTAATAATAA-AATAAT
95875 TAATAACTATTTT-TTAATTAAT-AAA-AAT
1 TAATAA-TATTTTATTAA-TAATAAAATAAT
95903 TAATAATA
1 TAATAATA
95911 AATAAATAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
27 10 0.19
28 26 0.49
29 4 0.08
30 5 0.09
31 8 0.15
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (29 bp):
TAATAATATTTTATTAATAATAAAATAAT
Found at i:96231 original size:23 final size:23
Alignment explanation
Indices: 96188--96242 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
96178 ACAAAAAGTT
*
96188 TTTTAAAAGAAAGAAAGAAAAGA
1 TTTTAAAAGAAAGAAAAAAAAGA
* *
96211 TTTTCAAAGAAA-AATAAAAAATGG
1 TTTTAAAAGAAAGAA-AAAAAA-GA
96235 TTTTAAAA
1 TTTTAAAA
96243 TAAAAAGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 2 0.08
23 16 0.62
24 8 0.31
ACGTcount: A:0.60, C:0.02, G:0.13, T:0.25
Consensus pattern (23 bp):
TTTTAAAAGAAAGAAAAAAAAGA
Found at i:97187 original size:86 final size:86
Alignment explanation
Indices: 97074--97376 Score: 396
Period size: 86 Copynumber: 3.5 Consensus size: 86
97064 GAACTTCTTG
* * *
97074 AAAATTA-CATTTTTACCCTTAAACTTTCAAAAATTACATTTTTATCCTCGAACTTTCCAAAACT
1 AAAATTATCA-TTTTACCCTCAAACTTTCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATT
*
97138 CCATTTTGACC-CTAATTTCACC
65 CCATTTTGACCTC-GATTTCACC
* * * * *
97160 AAAATTACCATTTTACCCTCGAACTTTCAAAAATTAAATTTTTACCCTCGAAATTTCTAAAATTC
1 AAAATTATCATTTTACCCTCAAACTTTCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTC
97225 CATTTTGACCTCGATTTCACC
66 CATTTTGACCTCGATTTCACC
* ** * *
97246 AAAATTATCATTTTACCCCCAAACTTTCACCAATTACATTTTTACCCTTGAACTTTCCAAAGTTC
1 AAAATTATCATTTTACCCTCAAACTTTCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTC
97311 CACTTTTGACCTCGATTTCACC
66 CA-TTTTGACCTCGATTTCACC
* *
97333 AAAAATTATTATTTTACCCTCAAACTTTCCAAAATT-CTATTTTT
1 -AAAATTATCATTTTACCCTCAAACTTTCAAAAATTAC-ATTTTT
97377 GACACCGATT
Statistics
Matches: 189, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
86 130 0.69
87 23 0.12
88 36 0.19
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (86 bp):
AAAATTATCATTTTACCCTCAAACTTTCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTC
CATTTTGACCTCGATTTCACC
Found at i:97299 original size:29 final size:29
Alignment explanation
Indices: 97005--97447 Score: 202
Period size: 29 Copynumber: 15.2 Consensus size: 29
96995 TTAATCCCTA
* * *
97005 AACTTTCTA-AAAATACATTTTTACCCCCA
1 AACTTTC-ACAAATTACATTTTTACCCTCG
*
97034 AAC-TTCATGAAAATTACATTTTTTACCCTCG
1 AACTTTCA--CAAATTACA-TTTTTACCCTCG
* **
97065 AACTTCTTGA-AAATTACATTTTTACCCTTA
1 AAC-T-TTCACAAATTACATTTTTACCCTCG
* *
97095 AACTTTCAAAAATTACATTTTTATCCTCG
1 AACTTTCACAAATTACATTTTTACCCTCG
* * *
97124 AACTTTC-CAAAACTCCATTTTGACCCT--
1 AACTTTCAC-AAATTACATTTTTACCCTCG
97151 AA-TTTCACCAAAATTACCA-TTTTACCCTCG
1 AACTTTCA-C-AAATTA-CATTTTTACCCTCG
* *
97181 AACTTTCAAAAATTAAATTTTTACCCTCG
1 AACTTTCACAAATTACATTTTTACCCTCG
* * *
97210 AAATTTCTA-AAATTCCATTTTGA-CCTCG
1 AACTTTC-ACAAATTACATTTTTACCCTCG
* *
97238 -A-TTTCACCAAAATTATCA-TTTTACCCCCA
1 AACTTTCA-C-AAATTA-CATTTTTACCCTCG
* *
97267 AACTTTCACCAATTACATTTTTACCCTTG
1 AACTTTCACAAATTACATTTTTACCCTCG
* *
97296 AACTTTC-CAAAGTTCCACTTTTGA-CCTCG
1 AACTTTCACAAA-TTACA-TTTTTACCCTCG
* *
97325 -A-TTTCACCAAAAATTA-TTATTTTACCCTCA
1 AACTTTCA-C--AAATTACAT-TTTTACCCTCG
*
97355 AACTTTC-CAAAATT-CTATTTTTGACAC-CG
1 AACTTTCAC-AAATTAC-ATTTTT-ACCCTCG
97384 -A-TTTCACCAAAAATTACA-TTTTACCCTCG
1 AACTTTCA-C--AAATTACATTTTTACCCTCG
*
97413 AACTTCTCA-AAATTTCATTTTTGACCC-C-
1 AACTT-TCACAAATTACATTTTT-ACCCTCG
97441 AACTTTC
1 AACTTTC
97448 CTAAAATTAC
Statistics
Matches: 321, Mismatches: 45, Indels: 98
0.69 0.10 0.21
Matches are distributed among these distances:
25 1 0.00
26 8 0.02
27 14 0.04
28 58 0.18
29 139 0.43
30 53 0.17
31 38 0.12
32 7 0.02
34 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.38
Consensus pattern (29 bp):
AACTTTCACAAATTACATTTTTACCCTCG
Found at i:97348 original size:59 final size:58
Alignment explanation
Indices: 97277--97471 Score: 200
Period size: 59 Copynumber: 3.3 Consensus size: 58
97267 AACTTTCACC
* *
97277 AATTACATTTTTACCCTTGAACTTTCCAAAGTTCCACTTTTGAC-CTCGATTTCACCAAA
1 AATTACA-TTTTACCCTCGAACTTTCCAAAATTCCACTTTTGACAC-CGATTTCACCAAA
* * * *
97336 AATTATTATTTTACCCTCAAACTTTCCAAAATTCTATTTTTGACACCGATTTCACCAAA
1 AATTA-CATTTTACCCTCGAACTTTCCAAAATTCCACTTTTGACACCGATTTCACCAAA
* * * * *
97395 AATTACATTTTACCCTCGAAC-TTCTCAAAATTTCATTTTTGACCCCAACTTT--CCTAA
1 AATTACATTTTACCCTCGAACTTTC-CAAAATTCCACTTTTGACACCGA-TTTCACCAAA
*
97452 AATTACCATTTTGCCCTCGA
1 AATTA-CATTTTACCCTCGA
97472 GTGTTTAAAA
Statistics
Matches: 117, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
57 12 0.10
58 46 0.39
59 57 0.49
60 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.38
Consensus pattern (58 bp):
AATTACATTTTACCCTCGAACTTTCCAAAATTCCACTTTTGACACCGATTTCACCAAA
Found at i:97462 original size:58 final size:55
Alignment explanation
Indices: 97043--97471 Score: 225
Period size: 58 Copynumber: 7.4 Consensus size: 55
97033 AAACTTCATG
* * *
97043 AAAATTACATTTTTTACCCTCGAACTTCTTGAAAATTACATTTTT-ACCCTTAAACTTT-CA
1 AAAATTACA--TTTTACCCTCGAAC-T-TTCAAAATTTCATTTTTGACCC--CAA-TTTCCA
* * * * *
97103 AAAATTACATTTTTATCCTCGAACTTTCCAAAACTCCA-TTTTGACCCTAATTTCACC
1 AAAATTACA-TTTTACCCTCGAACTTT-CAAAATTTCATTTTTGACCCCAATTTC-CA
** *
97160 AAAATTACCATTTTACCCTCGAACTTTCAAAAATTAAATTTTT-ACCCTCGAAATTT-CT
1 AAAATTA-CATTTTACCCTCGAACTTTC-AAAATTTCATTTTTGACCC-C--AATTTCCA
*
97218 AAAATTCCATTTTGA-CCTCG-A-TTTCACCAAAATTATCA-TTTT-ACCCCCAAACTTT-CA
1 AAAATTACATTTT-ACCCTCGAACTTT---CAAAATT-TCATTTTTGA-CCCC-AA-TTTCCA
** * * * * * *
97275 CCAATTACATTTTTACCCTTGAACTTTCCAAAGTTCCACTTTTGACCTCGATTTCACCA
1 AAAATTACA-TTTTACCCTCGAACTTT-CAAAATTTCATTTTTGACCCCAATTT--CCA
* * * *
97334 AAAATTATTATTTTACCCTCAAACTTTCCAAAA-TTCTATTTTTGACACCGATTTCACCA
1 AAAATTA-CATTTTACCCTCGAACTTT-CAAAATTTC-ATTTTTGACCCCAATTT--CCA
*
97393 AAAATTACATTTTACCCTCGAACTTCTCAAAATTTCATTTTTGACCCCAACTTTCCT
1 AAAATTACATTTTACCCTCGAACTT-TCAAAATTTCATTTTTGACCCCAA-TTTCCA
*
97450 AAAATTACCATTTTGCCCTCGA
1 AAAATTA-CATTTTACCCTCGA
97472 GTGTTTAAAA
Statistics
Matches: 297, Mismatches: 40, Indels: 66
0.74 0.10 0.16
Matches are distributed among these distances:
55 6 0.02
56 10 0.03
57 86 0.29
58 101 0.34
59 76 0.26
60 18 0.06
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (55 bp):
AAAATTACATTTTACCCTCGAACTTTCAAAATTTCATTTTTGACCCCAATTTCCA
Found at i:108230 original size:18 final size:19
Alignment explanation
Indices: 108209--108248 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
108199 ATTTTAAATT
*
108209 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
108227 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTGAA
108246 TTT
1 TTT
108249 ACTGGCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:108955 original size:361 final size:360
Alignment explanation
Indices: 108497--109211 Score: 1065
Period size: 361 Copynumber: 2.0 Consensus size: 360
108487 TTTCAAATCA
**
108497 AATCGTGTTTTGCTCACCTTTAATAATAACCACAAGTTGAACCAAGTATACTATTAAGCCTAATT
1 AATCGTGTTTTGCTCACCCCTAATAATAACCACAAGTTGAACCAAGTATACTATTAAGCCTAATT
*
108562 AAATCAAGTTATTTTATTAAAATAGGTTGTCCTTATACTTTTATTAAAATTTTAAAATTCTAATT
66 AAATCAAGTTATTTTACTAAAATAGGTTGTCCTTATACTTTTATTAAAATTTTAAAATTCTAATT
* *
108627 TAGACTTTAATACTAAAAAATATC-AATTTTTTTTCAAATTTATCGAATTAGGCCAATTTTTGGA
131 TAGACTTTAATACCAAAAAATACCGAA-TTTTTTTCAAATTTATCGAATTAGGCCAATTTTTGGA
* * * * **
108691 ATAATTACGAGAATAGGTTGATTTAAGGAAAACACTTTCAACTGGAAACGTTTTCAAGTAATATG
195 ATAATTACAAGAATAGGCTGATTTAAGAAAAACACTTCCAACTAAAAACGTTTTCAAGTAATATG
* * * * *
108756 CAGAAAAACGCTTCCAGCTAGAAGCACTTTCCGCGGGTCACCAGTAAAACATTTCTAGTTGGAAG
260 CAGAAAAACG-TTCCAGCTAGAAGCACTTTCCGCAGGACACCAGTAAAACATTTCCAGCTAGAAG
*
108821 CATTTTTAGGTAATCGCATGTAAATGCTTCCAACTAG
324 CATTTTTAGGTAATCGCATGTAAACGCTTCCAACTAG
* * *
108858 AATCGTGTTTTGCTCACCCCTAATAATAACCACGAGTTGAACCAAGTATACTATTCAGTCTAATT
1 AATCGTGTTTTGCTCACCCCTAATAATAACCACAAGTTGAACCAAGTATACTATTAAGCCTAATT
*
108923 AAATCGAA-TTATTTTACTAAAATAGGTTGTCCTTATACTTTTGTTAAAATTTTAAAATTCTAAT
66 AAATC-AAGTTATTTTACTAAAATAGGTTGTCCTTATACTTTTATTAAAATTTTAAAATTCTAAT
* * * *
108987 TTAGACTTTAATACCCAAAAATGCCGAATTTTTTTCAAATTTATCGAATTAGGTCGATTTTTGGA
130 TTAGACTTTAATACCAAAAAATACCGAATTTTTTTCAAATTTATCGAATTAGGCCAATTTTTGGA
* *
109052 ATAATTATAAGAATAGGCTGATTTAAGAAAAACACTTCCAACTAAAAACGTTTTCAAGTGATATG
195 ATAATTACAAGAATAGGCTGATTTAAGAAAAACACTTCCAACTAAAAACGTTTTCAAGTAATATG
* * * * * * *
109117 CAGAAAAACGTTCCAGCTGGAAGCACTTTTCGCATGACATCGGTAAGACGTTTCCAGCTAGAAGC
260 CAGAAAAACGTTCCAGCTAGAAGCACTTTCCGCAGGACACCAGTAAAACATTTCCAGCTAGAAGC
* *
109182 ATTTTTAGGTAGTTGCATGTAAACGCTTCC
325 ATTTTTAGGTAATCGCATGTAAACGCTTCC
109212 TACTTTAAGG
Statistics
Matches: 316, Mismatches: 36, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
360 70 0.22
361 242 0.77
362 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (360 bp):
AATCGTGTTTTGCTCACCCCTAATAATAACCACAAGTTGAACCAAGTATACTATTAAGCCTAATT
AAATCAAGTTATTTTACTAAAATAGGTTGTCCTTATACTTTTATTAAAATTTTAAAATTCTAATT
TAGACTTTAATACCAAAAAATACCGAATTTTTTTCAAATTTATCGAATTAGGCCAATTTTTGGAA
TAATTACAAGAATAGGCTGATTTAAGAAAAACACTTCCAACTAAAAACGTTTTCAAGTAATATGC
AGAAAAACGTTCCAGCTAGAAGCACTTTCCGCAGGACACCAGTAAAACATTTCCAGCTAGAAGCA
TTTTTAGGTAATCGCATGTAAACGCTTCCAACTAG
Found at i:113485 original size:36 final size:35
Alignment explanation
Indices: 113445--113513 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
113435 AATTATATTT
*
113445 TTAAAAGATTAAATTAATTTTTATCATTTTAAAAAG
1 TTAAAAGA-TAAATTAATTTTTATCAATTTAAAAAG
* * * *
113481 TTAAAATATAATTTTATTTTTATTAATTTAAAA
1 TTAAAAGATAAATTAATTTTTATCAATTTAAAA
113514 TTTTATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 21 0.75
36 7 0.25
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (35 bp):
TTAAAAGATAAATTAATTTTTATCAATTTAAAAAG
Found at i:114503 original size:27 final size:27
Alignment explanation
Indices: 114472--114524 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
114462 AAAAAATATC
114472 AATAAATCAAAATTAAAATTACATTTG
1 AATAAATCAAAATTAAAATTACATTTG
114499 AATAAATCAAAATTAAAATTACATTT
1 AATAAATCAAAATTAAAATTACATTT
114525 CAATCACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.34
Consensus pattern (27 bp):
AATAAATCAAAATTAAAATTACATTTG
Found at i:119590 original size:15 final size:16
Alignment explanation
Indices: 119550--119592 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
119540 ATGTCTATCG
*
119550 AAATCATATATTTAGA
1 AAATAATATATTTAGA
*
119566 ACATAGATATATTTA-A
1 AAATA-ATATATTTAGA
119582 AAATAATATAT
1 AAATAATATAT
119593 AATAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 6 0.26
16 8 0.35
17 9 0.39
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (16 bp):
AAATAATATATTTAGA
Found at i:119610 original size:19 final size:18
Alignment explanation
Indices: 119586--119680 Score: 62
Period size: 18 Copynumber: 5.5 Consensus size: 18
119576 ATTTAAAAAT
119586 AATATATAATAAATAATTA
1 AATATATAAT-AATAATTA
* *
119605 AATATAAAATTAA-AATTG
1 AATATATAA-TAATAATTA
* *
119623 ATTA-ATAATAATACATAA
1 AATATATAATAATA-ATTA
119641 AATATAT-ATAAT-ATTA
1 AATATATAATAATAATTA
119657 AA-ATA-AA-AATAGATTA
1 AATATATAATAATA-ATTA
119673 AAT-TATAA
1 AATATATAA
119681 ATAAAACAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
14 3 0.05
15 4 0.07
16 16 0.27
17 6 0.10
18 17 0.29
19 12 0.20
20 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (18 bp):
AATATATAATAATAATTA
Found at i:119682 original size:22 final size:22
Alignment explanation
Indices: 119582--119686 Score: 65
Period size: 22 Copynumber: 4.7 Consensus size: 22
119572 ATATATTTAA
* *
119582 AAATAATATATAATAAATA-ATT
1 AAATTATAAATAA-AAATAGATT
* *
119604 AAA-TATAAAATTAAAATTGATT
1 AAATTAT-AAATAAAAATAGATT
* * *
119626 -AATAATAATACATAAAATATATAT
1 AAATTATAA-ATA-AAAATAGAT-T
119650 AATATTA-AAATAAAAATAGATT
1 AA-ATTATAAATAAAAATAGATT
119672 AAATTATAAATAAAA
1 AAATTATAAATAAAA
119687 CAAAATTTAA
Statistics
Matches: 62, Mismatches: 12, Indels: 18
0.67 0.13 0.20
Matches are distributed among these distances:
21 14 0.23
22 24 0.39
23 15 0.24
24 3 0.05
25 3 0.05
26 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATTATAAATAAAAATAGATT
Found at i:119686 original size:21 final size:21
Alignment explanation
Indices: 119588--119686 Score: 62
Period size: 23 Copynumber: 4.5 Consensus size: 21
119578 TTAAAAATAA
119588 TATATAAT-AAATA-ATTAAA-
1 TATA-AATAAAATAGATTAAAT
*
119607 TATAAAATTAAAATTGATTAATAAT
1 TAT-AAA-TAAAATAGATT-A-AAT
* * *
119632 AATACATAAAATATATATAATAT
1 TATAAATAAAATAGAT-TAA-AT
119655 TA-AAATAAAAATAGATTAAAT
1 TATAAAT-AAAATAGATTAAAT
119676 TATAAATAAAA
1 TATAAATAAAA
119687 CAAAATTTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
19 5 0.08
20 2 0.03
21 12 0.20
22 14 0.23
23 21 0.34
24 5 0.08
25 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (21 bp):
TATAAATAAAATAGATTAAAT
Found at i:122455 original size:18 final size:18
Alignment explanation
Indices: 122432--122473 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
122422 ATTCAAAGTG
122432 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
122450 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
122468 TAATTA
1 TAATTA
122474 TAAACTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:123476 original size:23 final size:23
Alignment explanation
Indices: 123450--123502 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
123440 TTTATTTAAC
123450 TTAATTAAACATGTTCATGAACA
1 TTAATTAAACATGTTCATGAACA
*** *
123473 TTAAACGAACATGTTCATTAACA
1 TTAATTAAACATGTTCATGAACA
123496 TATAATT
1 T-TAATT
123503 GTTCGTTAAG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (23 bp):
TTAATTAAACATGTTCATGAACA
Found at i:128662 original size:33 final size:35
Alignment explanation
Indices: 128617--128688 Score: 112
Period size: 33 Copynumber: 2.1 Consensus size: 35
128607 TAATATAAAT
*
128617 ATAAGTAGTCCCTTAAC-AAACTTTCAAGCA-AAC
1 ATAAGTAATCCCTTAACAAAACTTTCAAGCATAAC
*
128650 ATAAGTAATCCCTTAACAAAACTTTCAAGTATAAC
1 ATAAGTAATCCCTTAACAAAACTTTCAAGCATAAC
128685 ATAA
1 ATAA
128689 TAGAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 16 0.46
34 12 0.34
35 7 0.20
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.26
Consensus pattern (35 bp):
ATAAGTAATCCCTTAACAAAACTTTCAAGCATAAC
Found at i:133135 original size:23 final size:23
Alignment explanation
Indices: 133102--133148 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
133092 GGATGGATGA
*
133102 TATGATATCTTTAGTATGCTTTT
1 TATGATATCTTTAATATGCTTTT
*
133125 TATGATGTCTTTAATATGCTTTT
1 TATGATATCTTTAATATGCTTTT
133148 T
1 T
133149 GTCTCAGCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.09, G:0.13, T:0.57
Consensus pattern (23 bp):
TATGATATCTTTAATATGCTTTT
Found at i:134138 original size:11 final size:11
Alignment explanation
Indices: 134124--134155 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
134114 TGAATTCTAA
134124 ATAATAATTAT
1 ATAATAATTAT
134135 ATAATAATTAT
1 ATAATAATTAT
*
134146 GTAATAATTA
1 ATAATAATTA
134156 AAATTCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
ATAATAATTAT
Found at i:136495 original size:42 final size:42
Alignment explanation
Indices: 136449--136529 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
136439 CACCAATATT
* * ** *
136449 ACCTCCATATCCACCCCTTAAACCACTTCCAACACTACCTCC
1 ACCTCCACACCCACCCAGTAAACCACCTCCAACACTACCTCC
* *
136491 ACCTCCACCCCCACCCAGTAAACCACCTCCAGCACTACC
1 ACCTCCACACCCACCCAGTAAACCACCTCCAACACTACC
136530 AGCAGCACCA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.28, C:0.53, G:0.02, T:0.16
Consensus pattern (42 bp):
ACCTCCACACCCACCCAGTAAACCACCTCCAACACTACCTCC
Found at i:136596 original size:24 final size:24
Alignment explanation
Indices: 136569--136627 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
136559 CGGTAGCACT
*
136569 ACCTC-CAACACTGCTTCCACCTCC
1 ACCTCTCAA-ACTGCCTCCACCTCC
* *
136593 ACCTCTTAAACTGCCTCCAGCTCC
1 ACCTCTCAAACTGCCTCCACCTCC
*
136617 ACCTCTTAAAC
1 ACCTCTCAAAC
136628 CACCTCCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 29 0.94
25 2 0.06
ACGTcount: A:0.24, C:0.47, G:0.05, T:0.24
Consensus pattern (24 bp):
ACCTCTCAAACTGCCTCCACCTCC
Found at i:136633 original size:24 final size:24
Alignment explanation
Indices: 136584--136634 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
136574 CAACACTGCT
**
136584 TCCACCTCCACCTCTTAAACTGCC
1 TCCACCTCCACCTCTTAAACCACC
*
136608 TCCAGCTCCACCTCTTAAACCACC
1 TCCACCTCCACCTCTTAAACCACC
136632 TCC
1 TCC
136635 TAAGCCTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.51, G:0.04, T:0.24
Consensus pattern (24 bp):
TCCACCTCCACCTCTTAAACCACC
Found at i:146451 original size:17 final size:18
Alignment explanation
Indices: 146429--146468 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
146419 ACATGACCTA
146429 TTGACC-AACCCAACCCG
1 TTGACCTAACCCAACCCG
* *
146446 TTGACCTAACTCGACCCG
1 TTGACCTAACCCAACCCG
146464 TTGAC
1 TTGAC
146469 TTGGCTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.25, C:0.40, G:0.15, T:0.20
Consensus pattern (18 bp):
TTGACCTAACCCAACCCG
Found at i:156944 original size:17 final size:17
Alignment explanation
Indices: 156922--156955 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
156912 TCCCTATAGG
156922 TTAGTATTTGGAAAAGC
1 TTAGTATTTGGAAAAGC
156939 TTAGTATTTGGAAAAGC
1 TTAGTATTTGGAAAAGC
156956 CTATCATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (17 bp):
TTAGTATTTGGAAAAGC
Found at i:158489 original size:15 final size:16
Alignment explanation
Indices: 158449--158494 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
158439 GTAAAAACTC
158449 ATCTTTTAATTT-TTA
1 ATCTTTTAATTTATTA
*
158464 ATTTATTTAATTTATTA
1 ATCT-TTTAATTTATTA
158481 A-CTTTTAATTTATT
1 ATCTTTTAATTTATT
158495 TTAAATTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 14 0.52
16 9 0.33
17 4 0.15
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (16 bp):
ATCTTTTAATTTATTA
Found at i:159162 original size:18 final size:18
Alignment explanation
Indices: 159139--159189 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
159129 TGGTCTTGAT
159139 GAAGAAAAAGATCCTAAA
1 GAAGAAAAAGATCCTAAA
* * * *
159157 GAAGAAAAGGATCTTGAT
1 GAAGAAAAAGATCCTAAA
*
159175 GAAGAAGAAGATCCT
1 GAAGAAAAAGATCCT
159190 GAGGAAGATA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.51, C:0.10, G:0.24, T:0.16
Consensus pattern (18 bp):
GAAGAAAAAGATCCTAAA
Found at i:159196 original size:18 final size:17
Alignment explanation
Indices: 159139--159197 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
159129 TGGTCTTGAT
*
159139 GAAGAAAAAGATCCTAAA
1 GAAG-AAAAGATCCTGAA
* *
159157 GAAGAAAAGGATCTTGAT
1 GAAGAAAA-GATCCTGAA
*
159175 GAAGAAGAAGATCCTGAG
1 GAAGAA-AAGATCCTGAA
159193 GAAGA
1 GAAGA
159198 TACTGTGGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.12
18 28 0.82
19 2 0.06
ACGTcount: A:0.51, C:0.08, G:0.27, T:0.14
Consensus pattern (17 bp):
GAAGAAAAGATCCTGAA
Found at i:163970 original size:211 final size:205
Alignment explanation
Indices: 163568--163980 Score: 672
Period size: 211 Copynumber: 2.0 Consensus size: 205
163558 ATTTGGTGAC
*
163568 TGAAATTCCGCTCGTTTTTGGTGATTTTTATATTTTGAGTTCGTATTAGCTTAATCTAGCTAACT
1 TGAAATTCCGCTCGTTTTTGGTGATTTTTATATTTTGAGTCCGTATTAGCTTAATCTAGCTAACT
*
163633 CAAGGACCAATTTGTGAATCTGTCAAATGTTATAAAGTTTGCCATTGATGAATAAGTTTATTCTT
66 CAAGGACCAATTTGTGAATCTGTCAAAAGTTATAAAGTTTGCCATTGATGAATAAGTTTATTCTT
163698 GAAAGTTTATGAAATTTTTGGAAGCTTGGTTGTTAGATTGGTTGAATTTTGTAAAGTGATTTTTG
131 GAAA---TATG--A-TTTTGGAAGCTTGGTTGTTAGATTGGTTGAATTTTGTAAAGTGATTTTTG
163763 GTGATTTTTGGTTTAG
190 GTGATTTTTGGTTTAG
* *
163779 TGAAATTCTGCTCGTTTTTGGTGATTTTTATATTTTGAGTCCGTATTAGCTTAATCTAGCTAAGT
1 TGAAATTCCGCTCGTTTTTGGTGATTTTTATATTTTGAGTCCGTATTAGCTTAATCTAGCTAACT
* *
163844 CAAGGACCAATTTTTGAATCTGTCAAAAGTTATAAAGTTTTCCATTGATGAATAAGTTTATTCTT
66 CAAGGACCAATTTGTGAATCTGTCAAAAGTTATAAAGTTTGCCATTGATGAATAAGTTTATTCTT
163909 G-AA-A-G-TTTTGGAAGCTTGGTTGTTAGATTGGTTGAATTTTGTAAAGTGATTTTTGGTGATT
131 GAAATATGATTTTGGAAGCTTGGTTGTTAGATTGGTTGAATTTTGTAAAGTGATTTTTGGTGATT
*
163970 TTAGGGTTTAG
196 TT-TGGTTTAG
163981 GGACTAAAAT
Statistics
Matches: 194, Mismatches: 7, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
201 58 0.30
202 7 0.04
205 1 0.01
206 1 0.01
210 2 0.01
211 125 0.64
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.45
Consensus pattern (205 bp):
TGAAATTCCGCTCGTTTTTGGTGATTTTTATATTTTGAGTCCGTATTAGCTTAATCTAGCTAACT
CAAGGACCAATTTGTGAATCTGTCAAAAGTTATAAAGTTTGCCATTGATGAATAAGTTTATTCTT
GAAATATGATTTTGGAAGCTTGGTTGTTAGATTGGTTGAATTTTGTAAAGTGATTTTTGGTGATT
TTTGGTTTAG
Found at i:164454 original size:19 final size:19
Alignment explanation
Indices: 164426--164506 Score: 99
Period size: 19 Copynumber: 4.3 Consensus size: 19
164416 AAGGAATCTA
* *
164426 CAATATTGGCTTGGAAGAG
1 CAATAATGGCTCGGAAGAG
* *
164445 TAATAATGGCTCGAAAGAG
1 CAATAATGGCTCGGAAGAG
*
164464 CAATACTGGCTCGGAAGAG
1 CAATAATGGCTCGGAAGAG
* *
164483 CAATAATGGCTTGTAAGAG
1 CAATAATGGCTCGGAAGAG
164502 CAATA
1 CAATA
164507 CACTGTACTG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (19 bp):
CAATAATGGCTCGGAAGAG
Found at i:164480 original size:38 final size:38
Alignment explanation
Indices: 164426--164507 Score: 119
Period size: 38 Copynumber: 2.2 Consensus size: 38
164416 AAGGAATCTA
* * *
164426 CAATATTGGCTTGGAAGAGTAATAATGGCTCGAAAGAG
1 CAATACTGGCTCGGAAGAGCAATAATGGCTCGAAAGAG
* *
164464 CAATACTGGCTCGGAAGAGCAATAATGGCTTGTAAGAG
1 CAATACTGGCTCGGAAGAGCAATAATGGCTCGAAAGAG
164502 CAATAC
1 CAATAC
164508 ACTGTACTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.22
Consensus pattern (38 bp):
CAATACTGGCTCGGAAGAGCAATAATGGCTCGAAAGAG
Found at i:182776 original size:12 final size:12
Alignment explanation
Indices: 182759--182784 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
182749 TAGCCAATCT
182759 TCCTCTTCCTCC
1 TCCTCTTCCTCC
182771 TCCTCTTCCTCC
1 TCCTCTTCCTCC
182783 TC
1 TC
182785 ATTCTCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (12 bp):
TCCTCTTCCTCC
Found at i:184533 original size:209 final size:209
Alignment explanation
Indices: 184173--184590 Score: 827
Period size: 209 Copynumber: 2.0 Consensus size: 209
184163 TGATTTGAAT
184173 ACGTTTTGCTGATTCCCGATCCTTTTTGTTGTTTGGCATTTGTTGATTCTATTCTGAATTTGAAC
1 ACGTTTTGCTGATTCCCGATCCTTTTTGTTGTTTGGCATTTGTTGATTCTATTCTGAATTTGAAC
184238 TTTTGATTCTATTTTTTTATGCCTTGATTTTCACGTACTGCGTTTGTGCATTTACCTGTTTGATC
66 TTTTGATTCTATTTTTTTATGCCTTGATTTTCACGTACTGCGTTTGTGCATTTACCTGTTTGATC
184303 TGTCTTTGTTGGAATGAATCAATAAAAAGAAGGAAAGACAGAATAATTGGAATCATTGAATTTGT
131 TGTCTTTGTTGGAATGAATCAATAAAAAGAAGGAAAGACAGAATAATTGGAATCATTGAATTTGT
184368 TCATTACTGTTGCA
196 TCATTACTGTTGCA
184382 ACGTTTTGCTGATTCCCGATCCTTTTTGTTGTTTGGCATTTGTTGATTCTATTCTGAATTTGAAC
1 ACGTTTTGCTGATTCCCGATCCTTTTTGTTGTTTGGCATTTGTTGATTCTATTCTGAATTTGAAC
184447 TTTTGATTCTATTTTTTTATGCCTTGATTTTCACGTACTGCGTTTGTGCATTTACCTGTTTGATC
66 TTTTGATTCTATTTTTTTATGCCTTGATTTTCACGTACTGCGTTTGTGCATTTACCTGTTTGATC
*
184512 TGTCTTTGTTGGAATGAATCAATAAAATGAAGGAAAGACAGAATAATTGGAATCATTGAATTTGT
131 TGTCTTTGTTGGAATGAATCAATAAAAAGAAGGAAAGACAGAATAATTGGAATCATTGAATTTGT
184577 TCATTACTGTTGCA
196 TCATTACTGTTGCA
184591 TTCAAAGAAT
Statistics
Matches: 208, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 208 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (209 bp):
ACGTTTTGCTGATTCCCGATCCTTTTTGTTGTTTGGCATTTGTTGATTCTATTCTGAATTTGAAC
TTTTGATTCTATTTTTTTATGCCTTGATTTTCACGTACTGCGTTTGTGCATTTACCTGTTTGATC
TGTCTTTGTTGGAATGAATCAATAAAAAGAAGGAAAGACAGAATAATTGGAATCATTGAATTTGT
TCATTACTGTTGCA
Found at i:185082 original size:40 final size:41
Alignment explanation
Indices: 185038--185121 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
185028 GAATGAGACC
185038 AAAATCTTTAAAT-AAAAAAATATAATAGCTTAATTTCTCA
1 AAAATCTTTAAATAAAAAAAATATAATAGCTTAATTTCTCA
185078 AAAATCTTTAAATAAAAAAAATATAATAGCTTAATTTCTCA
1 AAAATCTTTAAATAAAAAAAATATAATAGCTTAATTTCTCA
185119 AAA
1 AAA
185122 TTGAAGAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 13 0.30
41 30 0.70
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (41 bp):
AAAATCTTTAAATAAAAAAAATATAATAGCTTAATTTCTCA
Found at i:185911 original size:16 final size:16
Alignment explanation
Indices: 185892--185934 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
185882 TTTTTATTAA
*
185892 ATTAAATTATAATCAT
1 ATTATATTATAATCAT
*
185908 ATTATATTCTAATCAT
1 ATTATATTATAATCAT
185924 A-TATATTATAA
1 ATTATATTATAA
185935 GGTTTAAGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATATTATAATCAT
Found at i:186764 original size:69 final size:69
Alignment explanation
Indices: 186591--186764 Score: 217
Period size: 69 Copynumber: 2.5 Consensus size: 69
186581 AGTGTCAATT
* * * **
186591 TTTTCATTATTTTCATTAAAAAGTTAATCTTAATCTCATATTTGACTAGAGACCTCTCTCATAAC
1 TTTTCATTATTTTCATTAAAAAATTAATTTTAATTTCATATTTGACTAGAGAAATCTCTCATAAC
*
186656 TTAC
66 TCAC
* * * *
186660 TTTTCACTATTTTCATTAAAGAATTTCATTTTAATTTCATA-TTGACTAGA-AAATACTCTTATA
1 TTTTCATTATTTTCATTAAA-AAATTAATTTTAATTTCATATTTGACTAGAGAAAT-CTCTCATA
186723 ACTCAC
64 ACTCAC
186729 TTCTTCATTATTTTCATTAAAAAATTAATTTTAATT
1 TT-TTCATTATTTTCATTAAAAAATTAATTTTAATT
186765 CTACATTAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
68 2 0.02
69 55 0.61
70 33 0.37
ACGTcount: A:0.34, C:0.16, G:0.04, T:0.47
Consensus pattern (69 bp):
TTTTCATTATTTTCATTAAAAAATTAATTTTAATTTCATATTTGACTAGAGAAATCTCTCATAAC
TCAC
Found at i:186789 original size:69 final size:69
Alignment explanation
Indices: 186591--186801 Score: 178
Period size: 69 Copynumber: 3.1 Consensus size: 69
186581 AGTGTCAATT
* * * * * * * *** *
186591 TTTTCATTATTTTCATTAAA-AAGTTAATCTTAATCTCATATTTGACTAGAGACCTCTCTCATAA
1 TTTTCACTATTTTCATTAAAGAAATTAATTTTAATTTCACA-TTAACTAGAAAAGACTCTTATAA
*
186655 CTTAC
65 CTCAC
* * * * *
186660 TTTTCACTATTTTCATTAAAGAATTTCATTTTAATTTCATATTGACTAGAAAATACTCTTATAAC
1 TTTTCACTATTTTCATTAAAGAAATTAATTTTAATTTCACATTAACTAGAAAAGACTCTTATAAC
186725 TCAC
66 TCAC
* * *
186729 TTCTTCATTATTTTCATTAAA-AAATTAATTTTAA-TTCTACATTAATTA-AAGAAGATTCTTAT
1 TT-TTCACTATTTTCATTAAAGAAATTAATTTTAATTTC-ACATTAACTAGAA-AAGACTCTTAT
186791 AACTCAC
63 AACTCAC
186798 TTTT
1 TTTT
186802 TTTTAATCTC
Statistics
Matches: 119, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
68 7 0.06
69 79 0.66
70 33 0.28
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.45
Consensus pattern (69 bp):
TTTTCACTATTTTCATTAAAGAAATTAATTTTAATTTCACATTAACTAGAAAAGACTCTTATAAC
TCAC
Found at i:187442 original size:347 final size:350
Alignment explanation
Indices: 187044--187681 Score: 838
Period size: 350 Copynumber: 1.8 Consensus size: 350
187034 CCTAACCCCA
* * * ** *
187044 TATCTCACATTTACCTTATAAATAAGTGATCATTTCTTCACTATTTTCATTAAAAATTTAATTTT
1 TATCTCACATTTACCTTATAAATAAGTGATAATTTATTAACTACGTTCATTAAAAAGTTAATTTT
* * *
187109 AACTCCA-GATTAATTA-TAGAACATTTTTATAGCTCACTTTCTCACT-TTTTCATT-AAAAATT
66 AACTCCATG-TTAACTAGT-GAACACTTTTAAAGCTCACTTTCTCACTATTTTCATTAAAAAATT
* * * ** *
187170 AATTTTAATCT-CCATTAACTAGAAAATACTCACATGGCCCATTTCTTTTTCTGTTTTCACTAAA
129 AATTTTAATCTAACATTAACTAGAAAATACTCACATAGCCCACTTCTTTCACTATTTTCACTAAA
* * *
187234 AATTAATTTTTAATCCCTTAAAATGTTAATTTTAAA-ATTAATTTTAATCCTATATTAATTAGAG
194 AAATAA-TTTTAAACCCTTAAAAAGTTAATTTTAAATATTAATTTTAATCCTATATTAATTAGAG
* *
187298 ATCACTCTCATGCTCACACTTATCCTATAAATAACTGGCAATTTCTTGAATACTCTGAAGTTAAT
258 AACACTCTCATGCTCACACTTACCCTATAAATAACTGGCAATTTCTTGAATACTCTGAAGTTAAT
187363 TTTAATCTCACTTTAACTAGAGAACATG
323 TTTAATCTCACTTTAACTAGAGAACATG
* * *
187391 TATCTCACATTTACTTTATAAGTAAGTGATAATTTATTAACTACGTTCATTAAAAAGTTGATTTT
1 TATCTCACATTTACCTTATAAATAAGTGATAATTTATTAACTACGTTCATTAAAAAGTTAATTTT
** * * * *
187456 AGTTCCATGTTGACTAGTGAATACTTTTAAAGTTCACTTTTTCACTATTTTCATTAAAAAATTAA
66 AACTCCATGTTAACTAGTGAACACTTTTAAAGCTCACTTTCTCACTATTTTCATTAAAAAATTAA
* * ***
187521 TTTTAATCTAACATTAATTAGAAAATACTCTCATATTTCACTTCTTTCACTATTTTCACTAAAAA
131 TTTTAATCTAACATTAACTAGAAAATACTCACATAGCCCACTTCTTTCACTATTTTCACTAAAAA
* ** * ** *
187586 ATAATTTTAAACTCTTAAAAAGTTTTTTTTAAATTTTAATTTTAATTTTATATTAGTTAGAGAAC
196 ATAATTTTAAACCCTTAAAAAGTTAATTTTAAATATTAATTTTAATCCTATATTAATTAGAGAAC
187651 ACTCTCATGCTCACACTTACCCTATAAATAA
261 ACTCTCATGCTCACACTTACCCTATAAATAA
187682 GTGTTTTTTT
Statistics
Matches: 244, Mismatches: 41, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
347 89 0.36
348 10 0.04
349 42 0.17
350 103 0.42
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (350 bp):
TATCTCACATTTACCTTATAAATAAGTGATAATTTATTAACTACGTTCATTAAAAAGTTAATTTT
AACTCCATGTTAACTAGTGAACACTTTTAAAGCTCACTTTCTCACTATTTTCATTAAAAAATTAA
TTTTAATCTAACATTAACTAGAAAATACTCACATAGCCCACTTCTTTCACTATTTTCACTAAAAA
ATAATTTTAAACCCTTAAAAAGTTAATTTTAAATATTAATTTTAATCCTATATTAATTAGAGAAC
ACTCTCATGCTCACACTTACCCTATAAATAACTGGCAATTTCTTGAATACTCTGAAGTTAATTTT
AATCTCACTTTAACTAGAGAACATG
Found at i:188432 original size:14 final size:15
Alignment explanation
Indices: 188413--188446 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
188403 TTAATTATAT
188413 TTTTTTTCTTGTC-C
1 TTTTTTTCTTGTCTC
*
188427 TTTTTTTTTTGTCTC
1 TTTTTTTCTTGTCTC
188442 TTTTT
1 TTTTT
188447 AAGAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (15 bp):
TTTTTTTCTTGTCTC
Found at i:188432 original size:15 final size:15
Alignment explanation
Indices: 188412--188446 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
188402 ATTAATTATA
188412 TTTTTTTTCTTGTC-C
1 TTTTTTTT-TTGTCTC
188427 TTTTTTTTTTGTCTC
1 TTTTTTTTTTGTCTC
188442 TTTTT
1 TTTTT
188447 AAGAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (15 bp):
TTTTTTTTTTGTCTC
Found at i:192678 original size:16 final size:17
Alignment explanation
Indices: 192639--192679 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
192629 ATAGTAAAAA
192639 TATAATTTTATGATTTT
1 TATAATTTTATGATTTT
*
192656 AAT-ATTTTAT-ATTTT
1 TATAATTTTATGATTTT
192671 TATAATTTT
1 TATAATTTT
192680 TAAAAGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 7 0.33
16 12 0.57
17 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
TATAATTTTATGATTTT
Found at i:205655 original size:18 final size:18
Alignment explanation
Indices: 205607--205655 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
205597 AACTTGTGAG
205607 CCCGACCCATTGACCCAA
1 CCCGACCCATTGACCCAA
** ** *
205625 TTCGACCTGTTGACCTAA
1 CCCGACCCATTGACCCAA
205643 CCCGACCCATTGA
1 CCCGACCCATTGA
205656 TCGACCCGAA
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.41, G:0.14, T:0.20
Consensus pattern (18 bp):
CCCGACCCATTGACCCAA
Found at i:211159 original size:21 final size:21
Alignment explanation
Indices: 211113--211159 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
211103 AAATAAAATT
*
211113 ATTTTATTTTATAAAAGATAT
1 ATTTTATTTTATAAAAGATAA
* *
211134 TTTTTATTTTA-AAAAGCTTAA
1 ATTTTATTTTATAAAAG-ATAA
211155 ATTTT
1 ATTTT
211160 TAAATAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
ATTTTATTTTATAAAAGATAA
Found at i:214425 original size:42 final size:42
Alignment explanation
Indices: 214366--214451 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
214356 TTCGAAAACA
214366 AAACCTGGCTTATCTCTAAACTTAAAATCGATGACTATACCC
1 AAACCTGGCTTATCTCTAAACTTAAAATCGATGACTATACCC
*
214408 AAACCTTGCTTATCTCTAAACTTAAAATCGATGACTATACCC
1 AAACCTGGCTTATCTCTAAACTTAAAATCGATGACTATACCC
214450 AA
1 AA
214452 TCATTCCTAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (42 bp):
AAACCTGGCTTATCTCTAAACTTAAAATCGATGACTATACCC
Found at i:215183 original size:19 final size:18
Alignment explanation
Indices: 215143--215191 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
215133 GATATAAATA
215143 AAAAAATAAAAATATTTT
1 AAAAAATAAAAATATTTT
* *
215161 -AAAAATATAAATTTGTTT
1 AAAAAATAAAAATAT-TTT
215179 AAAAAAGTAAAAA
1 AAAAAA-TAAAAA
215192 AATTCAGCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 12 0.48
18 3 0.12
19 5 0.20
20 5 0.20
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (18 bp):
AAAAAATAAAAATATTTT
Found at i:216870 original size:188 final size:187
Alignment explanation
Indices: 216526--216884 Score: 483
Period size: 188 Copynumber: 1.9 Consensus size: 187
216516 TGCAATCAAG
* * * * *
216526 TCACCTATTGTCAATTATGTAAACAACTATAATCCCAAATTAATTTATAATACTTCTGATTAAAT
1 TCACCTATTGCCAAGTATGCAAACAACTATAATCCCAAATTAATTTATAACACTTCTCATTAAAT
*
216591 TACCCATATTTCATCGTCATCATCCAGTATGCCTATATCAAACATATATCGACACTTCAACGCAT
66 TACCCATATTTCATCGTCATCATCCAGTATGCCTATATCAAACATATA-CGACACTTCAACACAT
216656 GCATAATTAGAAAACAGCCAAATTTTATAATACTGCACTACCAAACCAGCCAATCATT
130 GCATAATTAGAAAACAGCCAAATTTTATAATACTGCACTACCAAACCAGCCAATCATT
* * *
216714 TCACCTTTTGCCAAGTATGCAAACAACTATAATCCCAGATTAATTTATAACCCTT-TCATTAAAT
1 TCACCTATTGCCAAGTATGCAAACAACTATAATCCCAAATTAATTTATAACACTTCTCATTAAAT
* * * *
216778 TACCTATATTTCATTGTCATCAT-CTGCTTTGTCCGTATATCAAACATATA-GACACTTCAAGCA
66 TACCCATATTTCATCGTCATCATCCAG-TATG-CC-TATATCAAACATATACGACACTTCAA-CA
* * * *
216841 CATGCAT-ATGTAGCAAATAGCCCAATTTTATAATATTGCACTAC
127 CATGCATAAT-TAGAAAACAGCCAAATTTTATAATACTGCACTAC
216885 TAAAAAATGT
Statistics
Matches: 149, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
186 2 0.01
187 44 0.30
188 88 0.59
189 15 0.10
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (187 bp):
TCACCTATTGCCAAGTATGCAAACAACTATAATCCCAAATTAATTTATAACACTTCTCATTAAAT
TACCCATATTTCATCGTCATCATCCAGTATGCCTATATCAAACATATACGACACTTCAACACATG
CATAATTAGAAAACAGCCAAATTTTATAATACTGCACTACCAAACCAGCCAATCATT
Found at i:220781 original size:13 final size:14
Alignment explanation
Indices: 220751--220783 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
220741 TAAATTAGGT
*
220751 TTAATATATATTTT
1 TTAATATATATTTA
220765 TTAATAT-TATTTA
1 TTAATATATATTTA
220778 TTAATA
1 TTAATA
220784 AACGTGTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTAATATATATTTA
Found at i:224380 original size:29 final size:29
Alignment explanation
Indices: 224338--224395 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
224328 CCAAAGAGAA
224338 CAAATTACCCCCACACAAAGTTGCTAGAG
1 CAAATTACCCCCACACAAAGTTGCTAGAG
*
224367 CAAATTGCCCCCACACAAAGTTGCTAGAG
1 CAAATTACCCCCACACAAAGTTGCTAGAG
224396 GGTTAAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.31, G:0.16, T:0.17
Consensus pattern (29 bp):
CAAATTACCCCCACACAAAGTTGCTAGAG
Found at i:252276 original size:40 final size:40
Alignment explanation
Indices: 252187--252276 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
252177 CTATCACTTG
* * * * **
252187 GCTTGAATTGTAACATCGACTCATAGCTTTCTAAGTCGTA
1 GCTTGAATTTTAACATCAACTCATAGCTTGCTAAGCCACA
252227 GCTTGAATTTTAACA-CTAACTCATAGCTTGCTAAGCCACA
1 GCTTGAATTTTAACATC-AACTCATAGCTTGCTAAGCCACA
252267 GCTTGAATTT
1 GCTTGAATTT
252277 CTCCGCTATA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.02
40 42 0.98
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (40 bp):
GCTTGAATTTTAACATCAACTCATAGCTTGCTAAGCCACA
Found at i:255023 original size:80 final size:80
Alignment explanation
Indices: 254890--255046 Score: 233
Period size: 80 Copynumber: 2.0 Consensus size: 80
254880 ATCAACCAAA
** * ** * * *
254890 TCCGTCAATTCATGGCACCTGGTGCCTAGCGGATAAACCGTAATAAGTGAGCCCAGCTCTAGTTG
1 TCCGTCAATTCATGGCACCCAGTGCCTAGCAGATAAACCACAATAAATGAGCCCAACTATAGTTG
254955 GATTAACCAACGAAT
66 GATTAACCAACGAAT
*
254970 TCCGTCAATTCATGGCACCCAGTGCCTAGCAGATAAACCACGATAAATGAGCCCAACTATAGTTG
1 TCCGTCAATTCATGGCACCCAGTGCCTAGCAGATAAACCACAATAAATGAGCCCAACTATAGTTG
255035 GATTAACCAACG
66 GATTAACCAACG
255047 GTTTGTGCCC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (80 bp):
TCCGTCAATTCATGGCACCCAGTGCCTAGCAGATAAACCACAATAAATGAGCCCAACTATAGTTG
GATTAACCAACGAAT
Found at i:258135 original size:28 final size:29
Alignment explanation
Indices: 258103--258164 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
258093 TGGATTAGAG
*
258103 GAGCAATACTTT-GATTTCTGGCTCAA-AA
1 GAGCAATACTTTGGA-CTCTGGCTCAATAA
258131 GAGCAATACTTTGGACTCTGGCTCAATAA
1 GAGCAATACTTTGGACTCTGGCTCAATAA
258160 GAGCA
1 GAGCA
258165 TAACTCTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 22 0.71
29 9 0.29
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (29 bp):
GAGCAATACTTTGGACTCTGGCTCAATAA
Found at i:258196 original size:26 final size:25
Alignment explanation
Indices: 258166--258251 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 25
258156 ATAAGAGCAT
258166 AACTCTGTACAGGCTCGAATGAACTA
1 AACTCTGT-CAGGCTCGAATGAACTA
* * *
258192 AACTCTGTCTGGGCTTGAA-CAAGCTA
1 AACTCTGTC-AGGCTCGAATGAA-CTA
* *
258218 AACTCTGTCTGAGCTCGAATGAGCTA
1 AACTCTGTCAG-GCTCGAATGAACTA
258244 AACTCTGT
1 AACTCTGT
258252 TTGGGCTTGA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
25 4 0.08
26 44 0.90
27 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (25 bp):
AACTCTGTCAGGCTCGAATGAACTA
Done.