Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3329
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: 1261902
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 1 of 4
Found at i:3469 original size:29 final size:28
Alignment explanation
Indices: 3426--3485 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
3416 TACGAGCTGT
* * *
3426 ATGCACTCAACAAAATCATCATAGCAGC
1 ATGCACTCAACAAAAACATAACAGCAGC
*
3454 ATGCACTTTAACAAAAACATAACAGCAGC
1 ATGCAC-TCAACAAAAACATAACAGCAGC
3483 ATG
1 ATG
3486 GTTGGCCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.45, C:0.25, G:0.12, T:0.18
Consensus pattern (28 bp):
ATGCACTCAACAAAAACATAACAGCAGC
Found at i:4661 original size:18 final size:18
Alignment explanation
Indices: 4615--4662 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
4605 TATAAGAATA
*
4615 TTAATTATTA-ATA-ATT
1 TTAATTATAATATATATT
4631 TT-ATTA-AATTATATATT
1 TTAATTATAA-TATATATT
4648 TTAATTATAATATAT
1 TTAATTATAATATAT
4663 TTAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 5 0.19
17 5 0.19
18 9 0.35
19 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATAATATATATT
Found at i:4673 original size:18 final size:16
Alignment explanation
Indices: 4615--4664 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
4605 TATAAGAATA
4615 TTAATTATTAATA-ATT
1 TTAATTA-TAATATATT
*
4631 TT-ATTAAATTATATATT
1 TTAATT--ATAATATATT
4648 TTAATTATAATATATT
1 TTAATTATAATATATT
4664 T
1 T
4665 AATAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 3 0.11
16 16 0.57
17 6 0.21
18 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATTATAATATATT
Found at i:4781 original size:15 final size:15
Alignment explanation
Indices: 4761--4792 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4751 TTATTAAATT
*
4761 ATATATTTAATTATA
1 ATATATTTAATAATA
4776 ATATATTTAATAATA
1 ATATATTTAATAATA
4791 AT
1 AT
4793 TATGTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATTTAATAATA
Found at i:5027 original size:45 final size:43
Alignment explanation
Indices: 4927--5036 Score: 111
Period size: 45 Copynumber: 2.6 Consensus size: 43
4917 TTTTCCATTA
4927 TGCTATTACACCTCTATTCCA-T---TTAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTAACCAAACACAAGAT
* * * ***
4966 TACTATTACGCATCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATT-AACCAAACACAAGA-T
*
5011 TGCTATTACACCTCTATTCTATTACA
1 TGCTATTACACCTCTATTCCATTACA
5037 CCTCTAATCC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
39 18 0.33
40 1 0.02
43 2 0.04
44 11 0.20
45 23 0.42
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.35
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATTACATTAACCAAACACAAGAT
Found at i:5052 original size:16 final size:16
Alignment explanation
Indices: 5017--5068 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
5007 GATTTGCTAT
* * *
5017 TACACCTCTATTCTAT
1 TACACCTCTAATCCAA
5033 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
5049 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
5065 TACA
1 TACA
5069 GCGAACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:29245 original size:74 final size:75
Alignment explanation
Indices: 29123--29264 Score: 232
Period size: 74 Copynumber: 1.9 Consensus size: 75
29113 ATCGAGTCAC
* * *
29123 TTATATGTTAAATTATGTTGACGTGATTTTTTTCTTGGTATAATAGTAAAATTAACCTGCCAATA
1 TTATAAGTTAAATCATGTTGACGTGATTTTTTTCTTGGTATAATAGTAAAATTAACCTACCAATA
29188 TTTGCTTATT
66 TTTGCTTATT
* *
29198 TTATAAGTTAAATCATGTTGATGTGATTTTTTT-TTGGTATAATAGTAAAATTAACTTACCAATA
1 TTATAAGTTAAATCATGTTGACGTGATTTTTTTCTTGGTATAATAGTAAAATTAACCTACCAATA
29262 TTT
66 TTT
29265 ATAATTTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
74 32 0.52
75 30 0.48
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.48
Consensus pattern (75 bp):
TTATAAGTTAAATCATGTTGACGTGATTTTTTTCTTGGTATAATAGTAAAATTAACCTACCAATA
TTTGCTTATT
Found at i:34183 original size:12 final size:12
Alignment explanation
Indices: 34166--34190 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34156 CTTGAAATGC
34166 CTTCTCTTCACT
1 CTTCTCTTCACT
34178 CTTCTCTTCACT
1 CTTCTCTTCACT
34190 C
1 C
34191 CTTTCTGCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (12 bp):
CTTCTCTTCACT
Found at i:57619 original size:11 final size:11
Alignment explanation
Indices: 57603--57627 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
57593 AACAAAGAAC
57603 CTATTTATAGG
1 CTATTTATAGG
57614 CTATTTATAGG
1 CTATTTATAGG
57625 CTA
1 CTA
57628 AATTCTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (11 bp):
CTATTTATAGG
Found at i:62046 original size:36 final size:36
Alignment explanation
Indices: 61999--62072 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
61989 ATTGTCACAT
61999 TGGCTTGATTCTAAGGTATGTTCTTCTACTCATTAA
1 TGGCTTGATTCTAAGGTATGTTCTTCTACTCATTAA
*
62035 TGGCTTTATTCTAAGGTATGTTCTTCTACTCATTAA
1 TGGCTTGATTCTAAGGTATGTTCTTCTACTCATTAA
62071 TG
1 TG
62073 AGTATTGATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (36 bp):
TGGCTTGATTCTAAGGTATGTTCTTCTACTCATTAA
Found at i:62202 original size:31 final size:31
Alignment explanation
Indices: 62164--62226 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
62154 AACAAACCAA
62164 TGACTTAAATAAAAACTTTCAAATAGTTCAG
1 TGACTTAAATAAAAACTTTCAAATAGTTCAG
*
62195 TGACTTAAATGAAAACTTTCAAATAGTTCAG
1 TGACTTAAATAAAAACTTTCAAATAGTTCAG
62226 T
1 T
62227 AACTATTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAGTTCAG
Found at i:62279 original size:15 final size:15
Alignment explanation
Indices: 62261--62292 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
62251 TAAGTGACCA
62261 AAACTTAAACTTATT
1 AAACTTAAACTTATT
62276 AAACTTAAACTTATT
1 AAACTTAAACTTATT
62291 AA
1 AA
62293 TAGTTTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (15 bp):
AAACTTAAACTTATT
Found at i:65027 original size:28 final size:28
Alignment explanation
Indices: 64986--65061 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
64976 CATCAATTCA
*
64986 TAAATGTCAACTTGTGTGAGCAAATCCT
1 TAAATGTCAGCTTGTGTGAGCAAATCCT
* *
65014 TAAATGTCAGCTTGTATGAACAAATCCT
1 TAAATGTCAGCTTGTGTGAGCAAATCCT
* * *
65042 TAAAAGCCAGCTTATGTGAG
1 TAAATGTCAGCTTGTGTGAG
65062 TAATGTTAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (28 bp):
TAAATGTCAGCTTGTGTGAGCAAATCCT
Found at i:69528 original size:29 final size:30
Alignment explanation
Indices: 69470--69526 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
69460 TCCGAGCCTT
*
69470 GGGCAAAAATGTAATTATGTAAAAGTTTAG
1 GGGCAAAAATGTAATTATGAAAAAGTTTAG
* *
69500 GGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGCAAAAATGTAATTATGAAAAAGTT
69527 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.32
Consensus pattern (30 bp):
GGGCAAAAATGTAATTATGAAAAAGTTTAG
Found at i:69756 original size:13 final size:13
Alignment explanation
Indices: 69738--69769 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
69728 TTTCCAGCAA
69738 TTATGAATTTATT
1 TTATGAATTTATT
69751 TTATGAATTTATT
1 TTATGAATTTATT
*
69764 TGATGA
1 TTATGA
69770 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:69939 original size:50 final size:50
Alignment explanation
Indices: 69864--70056 Score: 296
Period size: 50 Copynumber: 3.8 Consensus size: 50
69854 ATTTGGGTAA
69864 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
69914 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
69964 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
70014 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
70057 TGTTATTATC
Statistics
Matches: 129, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 95 0.74
51 34 0.26
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:77065 original size:29 final size:30
Alignment explanation
Indices: 77006--77063 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
76996 TCCGAGCCTT
*
77006 GGGGAAAAAATGTAATTATGTAAAAGTTTA
1 GGGGAAAAAATGTAATTATGAAAAAGTTTA
* * *
77036 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAAATGTAATTATGAAAAAGTT
77064 AGAGTTGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGAAAAAATGTAATTATGAAAAAGTTTA
Found at i:77293 original size:13 final size:13
Alignment explanation
Indices: 77275--77306 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
77265 TTTCCAGCAA
77275 TTATGAATTTATT
1 TTATGAATTTATT
77288 TTATGAATTTATT
1 TTATGAATTTATT
*
77301 TGATGA
1 TTATGA
77307 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:77481 original size:50 final size:50
Alignment explanation
Indices: 77401--77689 Score: 451
Period size: 50 Copynumber: 5.8 Consensus size: 50
77391 ATTTGGGTAA
*
77401 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
77451 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT-
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
77500 -GA-GT-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
77547 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
77597 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
77647 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
77690 TGTTATTATC
Statistics
Matches: 220, Mismatches: 14, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
46 42 0.19
47 2 0.01
48 4 0.02
49 2 0.01
50 136 0.62
51 34 0.15
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:77572 original size:96 final size:99
Alignment explanation
Indices: 77401--77689 Score: 449
Period size: 96 Copynumber: 2.9 Consensus size: 99
77391 ATTTGGGTAA
*
77401 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAA
77466 GACCATGTCTGGGACATGGCATTGGCACCGAGAT
66 GACCATGTCTGGGACATGGCATTGGCACCGAGAT
77500 -GA-GT-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAA
*
77562 GACCATGTCTGGGACATGGCGTTGGCACCGAGAT
66 GACCATGTCTGGGACATGGCATTGGCACCGAGAT
* * * * * **
77596 GAGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATGAGAACATCCCATGT
1 -AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG-AGGTCCCATGT
*
77661 AAGACCATGTCTGGGACATGGCTTTGGCA
64 AAGACCATGTCTGGGACATGGCATTGGCA
77690 TGTTATTATC
Statistics
Matches: 175, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
96 91 0.52
97 1 0.01
98 4 0.02
99 2 0.01
100 40 0.23
101 37 0.21
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (99 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAA
GACCATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:79197 original size:23 final size:22
Alignment explanation
Indices: 79161--79229 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 22
79151 GGACTCACCA
79161 CAGCTCGTATGAGCTTACCGTTT
1 CAGCTC-TATGAGCTTACCGTTT
79184 CAGCTCTATGGAGCTTACCGTTT
1 CAGCTCTAT-GAGCTTACCGTTT
*
79207 CAGCTCAATAGAGCTTACCGTTT
1 CAGCTCTAT-GAGCTTACCGTTT
79230 ATTAGCTCGG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
22 3 0.07
23 40 0.93
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.33
Consensus pattern (22 bp):
CAGCTCTATGAGCTTACCGTTT
Found at i:80747 original size:23 final size:24
Alignment explanation
Indices: 80720--80764 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
80710 GAAAAATATT
*
80720 AAATAT-ATATTTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
80743 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
80765 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:80875 original size:9 final size:9
Alignment explanation
Indices: 80861--80888 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
80851 TTTTGTTACA
80861 ACAATTAAT
1 ACAATTAAT
80870 ACAATTAAT
1 ACAATTAAT
80879 ACAATTAAT
1 ACAATTAAT
80888 A
1 A
80889 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:80910 original size:68 final size:68
Alignment explanation
Indices: 80831--81031 Score: 307
Period size: 59 Copynumber: 3.1 Consensus size: 68
80821 TCAAGTTTGT
*
80831 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
80896 AAA
66 AAA
80899 TTTACTAATCAAATGTTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
80955 AAA
66 AAA
80958 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
81021 AAT
66 AAA
81024 TTTACTAA
1 TTTACTAA
81032 CAATTAATTT
Statistics
Matches: 122, Mismatches: 2, Indels: 20
0.85 0.01 0.14
Matches are distributed among these distances:
59 56 0.46
60 1 0.01
62 2 0.02
65 2 0.02
66 27 0.22
67 2 0.02
68 32 0.26
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:81041 original size:16 final size:16
Alignment explanation
Indices: 81020--81062 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
81010 AATAATTTGA
*
81020 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
81036 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
81052 TAGTTTTAATA
1 TAATTTTAATA
81063 TTATTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:93775 original size:59 final size:56
Alignment explanation
Indices: 93680--93798 Score: 157
Period size: 59 Copynumber: 2.1 Consensus size: 56
93670 AGAAATGTCA
* * * *
93680 TAACCTTTTGGTGGCTAATTGCATTTTATTATAATCACCACCATTCATTTGCAAAATGT
1 TAACCTTTTGGTAGCTAAGTGCATTGTATTACAAT---CACCATTCATTTGCAAAATGT
* *
93739 TAACCTTTTGGTAGCTAAGTGCATTGTATTGCAATCACCATTCATTTGCAAAATTT
1 TAACCTTTTGGTAGCTAAGTGCATTGTATTACAATCACCATTCATTTGCAAAATGT
93795 TAAC
1 TAAC
93799 ACAGTATTGG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
56 24 0.44
59 30 0.56
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (56 bp):
TAACCTTTTGGTAGCTAAGTGCATTGTATTACAATCACCATTCATTTGCAAAATGT
Found at i:97095 original size:15 final size:15
Alignment explanation
Indices: 97077--97106 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
97067 TAGCGTGAGA
97077 TAAAAAATAAGTAGC
1 TAAAAAATAAGTAGC
97092 TAAAAAATAAGTAGC
1 TAAAAAATAAGTAGC
97107 GTGAGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (15 bp):
TAAAAAATAAGTAGC
Found at i:97116 original size:21 final size:21
Alignment explanation
Indices: 97066--97124 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
97056 TAATGATACT
97066 GTAGCGTGAGATAAAAAATAA
1 GTAGCGTGAGATAAAAAATAA
97087 GTAGC------TAAAAAATAA
1 GTAGCGTGAGATAAAAAATAA
97102 GTAGCGTGAGATAAAAAATAA
1 GTAGCGTGAGATAAAAAATAA
97123 GT
1 GT
97125 TAAATCACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
15 15 0.47
21 17 0.53
ACGTcount: A:0.53, C:0.05, G:0.22, T:0.20
Consensus pattern (21 bp):
GTAGCGTGAGATAAAAAATAA
Found at i:106660 original size:20 final size:20
Alignment explanation
Indices: 106622--106662 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
106612 TAAAAATATG
**
106622 AATAAAAACTCTTGTAAATA
1 AATAAAAACTCTTCAAAATA
*
106642 AATAAAACCTCTTCAAAATA
1 AATAAAAACTCTTCAAAATA
106662 A
1 A
106663 GCAAAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.27
Consensus pattern (20 bp):
AATAAAAACTCTTCAAAATA
Found at i:107354 original size:19 final size:18
Alignment explanation
Indices: 107325--107360 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
107315 AAATTAACAT
107325 AATTTTTTTTACAATAAA
1 AATTTTTTTTACAATAAA
*
107343 AATTTATTTTTATAATAA
1 AATTT-TTTTTACAATAA
107361 TGTCAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTTTTTTACAATAAA
Found at i:117615 original size:6 final size:6
Alignment explanation
Indices: 117607--117638 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
117597 AAATAAAGGT
*
117607 AAAGCT AAAGCA AAAGCA AAAGCA AAAGCA AA
1 AAAGCA AAAGCA AAAGCA AAAGCA AAAGCA AA
117639 CCACGCCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.66, C:0.16, G:0.16, T:0.03
Consensus pattern (6 bp):
AAAGCA
Found at i:125595 original size:30 final size:32
Alignment explanation
Indices: 125537--125597 Score: 81
Period size: 30 Copynumber: 1.9 Consensus size: 32
125527 AAAAAAAAGT
125537 AAAAATCTAACCTTTTCCATATGAAAGAGAAAC
1 AAAAATCTAACC-TTTCCATATGAAAGAGAAAC
* *
125570 AAAAATCTAA-C-TTCTATATGGAAGAGAA
1 AAAAATCTAACCTTTCCATATGAAAGAGAA
125598 GCAATGGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 15 0.58
32 1 0.04
33 10 0.38
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.25
Consensus pattern (32 bp):
AAAAATCTAACCTTTCCATATGAAAGAGAAAC
Found at i:129622 original size:21 final size:22
Alignment explanation
Indices: 129592--129632 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
129582 ACAATGGATT
* *
129592 GCTCTTGATGTTGTAACACCCA
1 GCTCTTGATGTCGCAACACCCA
129614 GCTC-TGATGTCGCAACACC
1 GCTCTTGATGTCGCAACACC
129633 ACCTCTAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.27
Consensus pattern (22 bp):
GCTCTTGATGTCGCAACACCCA
Found at i:153649 original size:25 final size:25
Alignment explanation
Indices: 153620--153670 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
153610 TTTAATCCTT
153620 TTTCCATTCCTAAGTTTTTAAACCA
1 TTTCCATTCCTAAGTTTTTAAACCA
153645 TTTCCATTCCTAAGTTTTTAAACCA
1 TTTCCATTCCTAAGTTTTTAAACCA
153670 T
1 T
153671 CATTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.45
Consensus pattern (25 bp):
TTTCCATTCCTAAGTTTTTAAACCA
Found at i:154017 original size:7 final size:7
Alignment explanation
Indices: 154005--154036 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
153995 ACATGACATT
154005 AACCCTA
1 AACCCTA
154012 AACCCTA
1 AACCCTA
154019 AACCCTA
1 AACCCTA
154026 AACCCTA
1 AACCCTA
154033 AACC
1 AACC
154037 GTCCACTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.44, G:0.00, T:0.12
Consensus pattern (7 bp):
AACCCTA
Found at i:163844 original size:4 final size:4
Alignment explanation
Indices: 163837--163865 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
163827 GGTATATATA
163837 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
163866 TCTTTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:174128 original size:19 final size:19
Alignment explanation
Indices: 174106--174148 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
174096 GCATATTAGC
174106 CACTATGTAT-TCATATAAT
1 CACTATGTATGT-ATATAAT
174125 CACTATGTATGTATATAAT
1 CACTATGTATGTATATAAT
174144 CACTA
1 CACTA
174149 GTTAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (19 bp):
CACTATGTATGTATATAAT
Found at i:175703 original size:61 final size:61
Alignment explanation
Indices: 175638--175766 Score: 258
Period size: 61 Copynumber: 2.1 Consensus size: 61
175628 ACTAAAAAAT
175638 TAAAATAAATGTTATACTTAAATAACACTAAGATAATAGCAACTTAGCAAGCAAATGACTC
1 TAAAATAAATGTTATACTTAAATAACACTAAGATAATAGCAACTTAGCAAGCAAATGACTC
175699 TAAAATAAATGTTATACTTAAATAACACTAAGATAATAGCAACTTAGCAAGCAAATGACTC
1 TAAAATAAATGTTATACTTAAATAACACTAAGATAATAGCAACTTAGCAAGCAAATGACTC
175760 TAAAATA
1 TAAAATA
175767 GTAGCAAAAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.50, C:0.14, G:0.09, T:0.26
Consensus pattern (61 bp):
TAAAATAAATGTTATACTTAAATAACACTAAGATAATAGCAACTTAGCAAGCAAATGACTC
Found at i:192700 original size:14 final size:14
Alignment explanation
Indices: 192683--192712 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
192673 TTAATTATTT
*
192683 AATTTTTAATTGGA
1 AATTATTAATTGGA
192697 AATTATTAATTGGA
1 AATTATTAATTGGA
192711 AA
1 AA
192713 AGAACCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
AATTATTAATTGGA
Found at i:200965 original size:17 final size:17
Alignment explanation
Indices: 200921--200966 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
200911 ACCTTGTACT
200921 TTTATTTATTAA-AAAA
1 TTTATTTATTAATAAAA
* *
200937 TATATTTATTAATACAA
1 TTTATTTATTAATAAAA
*
200954 TTTATTTTTTAAT
1 TTTATTTATTAAT
200967 TGCACCTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTATTTATTAATAAAA
Found at i:204143 original size:10 final size:9
Alignment explanation
Indices: 204124--204164 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
204114 TCCCCCACAA
204124 TTTTTTATT
1 TTTTTTATT
204133 TTTTATTATT
1 TTTT-TTATT
204143 TTTTTATATT
1 TTTTT-TATT
*
204153 TTTTTCATT
1 TTTTTTATT
204162 TTT
1 TTT
204165 ACATTTACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 11 0.38
10 18 0.62
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTATT
Found at i:204147 original size:18 final size:19
Alignment explanation
Indices: 204124--204164 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
204114 TCCCCCACAA
204124 TTTTTTAT-TTTTTATT-AT
1 TTTTTTATATTTTT-TTCAT
204142 TTTTTTATATTTTTTTCAT
1 TTTTTTATATTTTTTTCAT
204161 TTTT
1 TTTT
204165 ACATTTACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTTATATTTTTTTCAT
Found at i:205877 original size:35 final size:35
Alignment explanation
Indices: 205831--205901 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
205821 ATGTATAAGG
205831 ATTAGGTTTTAATAGTAGAAATAGATGCAATTTTT
1 ATTAGGTTTTAATAGTAGAAATAGATGCAATTTTT
205866 ATTAGGTTTTAATAGTAGAAATAGATGCAATTTTT
1 ATTAGGTTTTAATAGTAGAAATAGATGCAATTTTT
205901 A
1 A
205902 ACATAAGGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (35 bp):
ATTAGGTTTTAATAGTAGAAATAGATGCAATTTTT
Found at i:211033 original size:24 final size:24
Alignment explanation
Indices: 211005--211057 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
210995 ATTAGTAAGT
* *
211005 TAAATAAACTATGCTAATAAATGC
1 TAAATAAACTATACTAATAAATAC
* *
211029 TAAATATATTATACTAATAAATAC
1 TAAATAAACTATACTAATAAATAC
211053 TAAAT
1 TAAAT
211058 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (24 bp):
TAAATAAACTATACTAATAAATAC
Found at i:211904 original size:60 final size:60
Alignment explanation
Indices: 211792--211905 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
211782 TGGGCTATAA
* * * *
211792 GAGTATTCTCTAGTCAATATGGGATCAAAATTAACTTTTTAGTGAAGAAGTAAATTATGG
1 GAGTATTCTCTAGTCAATATGAGATCAAAATTAACTTTTCAATGAAAAAGTAAATTATGG
*
211852 GAGTATT-TCCTAGTCAATATGAGATTAAAATTAA-TTTTCAATGAAAATAGTAAA
1 GAGTATTCT-CTAGTCAATATGAGATCAAAATTAACTTTTCAATGAAAA-AGTAAA
211906 GAAGTGAGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 11 0.23
60 36 0.77
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (60 bp):
GAGTATTCTCTAGTCAATATGAGATCAAAATTAACTTTTCAATGAAAAAGTAAATTATGG
Found at i:212001 original size:69 final size:65
Alignment explanation
Indices: 211874--212027 Score: 152
Period size: 69 Copynumber: 2.3 Consensus size: 65
211864 GTCAATATGA
* *
211874 GATTAAAATTAA-TTTTCAATGAAAATAGTAAAGAAGTGAGTTATGGTAATATTCTCTAGTCGAT
1 GATTAAAATTAACTTTTTAATAAAAATAGTAAAGAAGTGAGTTATGGTAATATTCTCTAGTC-A-
211938 GTAC
64 --AC
* * * ** *
211942 TATTAAAATTAACTTTTTAATAAAAATAGTGGAA-AAGTTAGTTATGAG-CGTATTTTCTAGTCA
1 GATTAAAATTAACTTTTTAATAAAAATAGT-AAAGAAGTGAGTTATG-GTAATATTCTCTAGTCA
*
212005 AG
64 AC
212007 GATTAAAATTAACTTTTTAAT
1 GATTAAAATTAACTTTTTAAT
212028 TTCTTAAATT
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
65 21 0.29
68 12 0.16
69 37 0.51
70 3 0.04
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (65 bp):
GATTAAAATTAACTTTTTAATAAAAATAGTAAAGAAGTGAGTTATGGTAATATTCTCTAGTCAAC
Found at i:215096 original size:23 final size:22
Alignment explanation
Indices: 215042--215097 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
215032 GCATCAAATT
*
215042 TTAATTATAAATTTTTTATAAA
1 TTAATTATAAATTTATTATAAA
* **
215064 TTAAAGTATAAATTTATTATGTA
1 TT-AATTATAAATTTATTATAAA
215087 TTAATTTATAA
1 TTAA-TTATAA
215098 TTTCATATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TTAATTATAAATTTATTATAAA
Found at i:224198 original size:30 final size:30
Alignment explanation
Indices: 224164--224221 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
224154 TTTTTGATTA
*
224164 TTTTTAATAGTACAGAGACAAAATTGATCT
1 TTTTTAATAATACAGAGACAAAATTGATCT
* * *
224194 TTTTTAATAATATAGAGACTAATTTGAT
1 TTTTTAATAATACAGAGACAAAATTGAT
224222 ACAATCCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (30 bp):
TTTTTAATAATACAGAGACAAAATTGATCT
Found at i:233179 original size:34 final size:34
Alignment explanation
Indices: 233141--233205 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
233131 AATTTTTAAT
*
233141 TTAATATAGGGACTAAATTGA-TCAATTTGATTCA
1 TTAATATAAGGACTAAATTGATTC-ATTTGATTCA
*
233175 TTAATATAAGGACTGAATTGATTCATTTGAT
1 TTAATATAAGGACTAAATTGATTCATTTGAT
233206 AATAGTGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (34 bp):
TTAATATAAGGACTAAATTGATTCATTTGATTCA
Found at i:236017 original size:30 final size:29
Alignment explanation
Indices: 235983--236115 Score: 99
Period size: 30 Copynumber: 4.4 Consensus size: 29
235973 TTTAGGGATC
*
235983 TAATTAAAATTTTCAAAAACTTTAAGGGTT
1 TAATTAAAATTTTCAAAAA-TTTAAGGGCT
** ***
236013 TAATTAATTTTTTTTTAAATTTGAAGGGCT
1 TAATTAAAATTTTCAAAAATTT-AAGGGCT
* * *
236043 TAA-TAAGAA-TTTCTAAAATTTACAAGTCT
1 TAATTAA-AATTTTCAAAAATTTA-AGGGCT
*
236072 TAATTAAAATTTTCAAAAATTTTAGGAGGCT
1 TAATTAAAATTTTCAAAAA-TTTAAG-GGCT
*
236103 TAATGAAAATTTT
1 TAATTAAAATTTT
236116 AATTAAATCC
Statistics
Matches: 79, Mismatches: 17, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
28 1 0.01
29 25 0.32
30 34 0.43
31 19 0.24
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.43
Consensus pattern (29 bp):
TAATTAAAATTTTCAAAAATTTAAGGGCT
Found at i:238090 original size:14 final size:13
Alignment explanation
Indices: 238055--238104 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
238045 GGAAAATAAG
*
238055 AGAAAA-AAGAAA
1 AGAAAAGAAGGAA
238067 AGAAAAGAAGGAA
1 AGAAAAGAAGGAA
238080 AGAAAATGAAGGAA
1 AGAAAA-GAAGGAA
*
238094 ATAAAAAGAAG
1 A-GAAAAGAAG
238105 AGATTCAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 6 0.18
13 11 0.33
14 12 0.36
15 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (13 bp):
AGAAAAGAAGGAA
Found at i:247317 original size:3 final size:3
Alignment explanation
Indices: 247309--247358 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
247299 TTAGGAGCTG
247309 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
247357 TA
1 TA
247359 CTCTTGAGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:254876 original size:21 final size:20
Alignment explanation
Indices: 254848--254886 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
254838 CCCGTTCGGA
254848 GAAAGAAAA-TCTGGGTTCTT
1 GAAAGAAAATTC-GGGTTCTT
254868 GAAAGGAAAATTCGGGTTC
1 GAAA-GAAAATTCGGGTTC
254887 GAATGAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 11 0.65
22 2 0.12
ACGTcount: A:0.36, C:0.10, G:0.28, T:0.26
Consensus pattern (20 bp):
GAAAGAAAATTCGGGTTCTT
Found at i:258774 original size:17 final size:17
Alignment explanation
Indices: 258752--258791 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
258742 ATGTGTGCTT
*
258752 TTTTTAATATATTTTAG
1 TTTTTAATATATTATAG
* *
258769 TTTTTAATTTATTATAT
1 TTTTTAATATATTATAG
258786 TTTTTA
1 TTTTTA
258792 TTGAATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTTAATATATTATAG
Found at i:262301 original size:28 final size:28
Alignment explanation
Indices: 262232--262301 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
262222 TAGGGACATG
* * * *
262232 ATCAAATTAGTCCCTCTACTATTAAATGG
1 ATCAAA-TAGTCCCTATACTATAAAAAGA
* *
262261 ATCAATTCAGTCCCTATCCTATAAAAAGA
1 ATCAAAT-AGTCCCTATACTATAAAAAGA
262290 ATCAAATAGTCC
1 ATCAAATAGTCC
262302 ATTTTCCAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
28 6 0.18
29 27 0.82
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (28 bp):
ATCAAATAGTCCCTATACTATAAAAAGA
Found at i:262786 original size:40 final size:40
Alignment explanation
Indices: 262723--262807 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
262713 TAGCTTGAAT
* * *
262723 ATCAACACTTCAATATTTGATATGTAAGGAATTATCAAAA
1 ATCAACACTTCAATATTTGATATGCAAGAAATTAACAAAA
*
262763 ATCAACATTTCAATAATTT-ATATGCAAGAAATTAACAAAA
1 ATCAACACTTCAAT-ATTTGATATGCAAGAAATTAACAAAA
262803 ATCAA
1 ATCAA
262808 TCTTACAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (40 bp):
ATCAACACTTCAATATTTGATATGCAAGAAATTAACAAAA
Found at i:263041 original size:86 final size:85
Alignment explanation
Indices: 262828--263159 Score: 375
Period size: 86 Copynumber: 3.9 Consensus size: 85
262818 GTTAATGTGA
* ** * * * *
262828 AACAAATTAGCAAAAATCAACT-ATTCATAGTTCATATATTTACCGACAA-TAGGGCTAAATCTT
1 AACAAATTAGCAAAAATCAA-TGGTTCA-AGTTCATGCATTTACCAACAACCA-GACTAAATTTT
* *
262891 CAATTTCTATAACGATTTATATGC
63 CAATTT-TATAACAACTTATATGC
* * *
262915 AACAAATTA-CAAAAATCAATGGTTCAAGTTCATGTATTTACCATA-AATCAGACTAATTTTTCA
1 AACAAATTAGCAAAAATCAATGGTTCAAGTTCATGCATTTACCA-ACAACCAGACTAAATTTTCA
262978 ATATTTATAACAACTTATATGC
65 AT-TTTATAACAACTTATATGC
* *
263000 AACAAATTAGCAAAAATAAATGGTTCCAGTTCATGCATTTACCAACAACCAGACTAAATTTTCAA
1 AACAAATTAGCAAAAATCAATGGTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCAA
*
263065 TTTTTATAACAACTTATGTGC
66 -TTTTATAACAACTTATATGC
* ** * * *
263086 AACAAATTAGAAAAAATCAACAGTTCAAGTTCGTGCATTCACCAACAACCAGACCAAATTTTCAA
1 AACAAATTAGCAAAAATCAATGGTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCAA
263151 CTTTTATAA
66 -TTTTATAA
263160 AGTAGAAGGA
Statistics
Matches: 214, Mismatches: 24, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
85 55 0.26
86 149 0.70
87 10 0.05
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (85 bp):
AACAAATTAGCAAAAATCAATGGTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCAA
TTTTATAACAACTTATATGC
Found at i:266919 original size:207 final size:203
Alignment explanation
Indices: 266513--267041 Score: 602
Period size: 207 Copynumber: 2.6 Consensus size: 203
266503 AAGGTGAAAC
* * * *
266513 AAGTTAACAAACCAAGTTTACATGACA-GTATCATCTCACCATTCTAGCTTAACCCGAATCA-TT
1 AAGTTAACAAACCAAG-TTACATGGCATG-ATCATCTAACCATTGTAGCTTAACTCGAAT-AGTT
* * *
266576 ACATTTAATCCGACCCA-ATATCATACCCCATTCACCGGTTATATGCAACTATTCAAGTTAAACT
63 ACATTTAATCC-AACCAGAT-TCATACCCCATTCAACGATTATATGCAACTATTCAAGTTAAACT
* * * *
266640 CTAGTGTGTCTAATGAATATGACACGTTACATTATATTTTAAAATAATACCACATCATTAAATTA
126 CTAGTGTGGCCAATGAATAAGACACGTTACATTATATTTTAAAATAATACCAAATCATTAAATTA
266705 AGCTCAACTCATA
191 AGCTCAACTCATA
* *
266718 AAGTTAACAAACCAAGTTACATGGTATGATCATCTAACCATTGTAGCTTATTAACTCGAATTGTT
1 AAGTTAACAAACCAAGTTACATGGCATGATCATCTAACCATTGTAGC---TTAACTCGAATAGTT
* *
266783 ACATTTAATCTAACCAGATCTCATACCCCATTCAACGATTACATGCAACTATTCAAGTTAAAACT
63 ACATTTAATCCAACCAGAT-TCATACCCCATTCAACGATTATATGCAACTATTCAAGTT-AAACT
* * ** **
266848 CTAGTG-GGCCAAGTGAATAAGACACGTTACATTATATTTTAAACTAATGCCAAATTGTTTTATT
126 CTAGTGTGGCCAA-TGAATAAGACACGTTACATTATATTTTAAAATAATACCAAATCATTAAATT
*
266912 -TGCTCAACTCATA
190 AAGCTCAACTCATA
* * *** *
266925 AAGTTGACAAGCCAAGTTACATGGCATGATCATCTGGTCATTGTAGCTTAACTCGAGTAGTTACA
1 AAGTTAACAAACCAAGTTACATGGCATGATCATCTAACCATTGTAGCTTAACTCGAATAGTTACA
* * * * * *
266990 TTTGACCCGACCCGATTCATACTCCATTC-ACTGATTATATGCAACCATTCAA
66 TTTAATCCAACCAGATTCATACCCCATTCAAC-GATTATATGCAACTATTCAA
267042 ATAAATATGG
Statistics
Matches: 276, Mismatches: 39, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
202 2 0.01
203 30 0.11
204 52 0.19
205 17 0.06
206 4 0.01
207 117 0.42
208 54 0.20
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.32
Consensus pattern (203 bp):
AAGTTAACAAACCAAGTTACATGGCATGATCATCTAACCATTGTAGCTTAACTCGAATAGTTACA
TTTAATCCAACCAGATTCATACCCCATTCAACGATTATATGCAACTATTCAAGTTAAACTCTAGT
GTGGCCAATGAATAAGACACGTTACATTATATTTTAAAATAATACCAAATCATTAAATTAAGCTC
AACTCATA
Found at i:267191 original size:182 final size:181
Alignment explanation
Indices: 266868--267343 Score: 711
Period size: 182 Copynumber: 2.6 Consensus size: 181
266858 AAGTGAATAA
*
266868 GACACGTTACATTATATTTTAAACTAATGCCAAATTGTTTTATTTGCTCAACTCATAAAGTTGAC
1 GACACGTTACATTATATTTTAAACTAATGCCACA-TGTTTTATTTGCTCAACTCATAAAGTTGAC
*
266933 AAGCCAAGTTACATGGCATGATCATCTGGTCATTGTAGCTTAACTCGAGTAGTTACATTTGACCC
65 AAACCAAGTTACATGGCATGATCATCTGGTCATTGTAGCTTAACTCGAGTAGTTACATTTGACCC
*
266998 GACCCGATTCATACTCCATTCACTGATTATATGCAACCATTCAAAT-AAATAT
130 GACCCGATTCATACTCCATTCACTGATTACATGCAACCATTCAAATGAAA-AT
* *
267050 GGCGCGTTACATTATATTTTAAACTAATGCCACACTGTTTTATTTGCTCAACTCATAAAGTTGAC
1 GACACGTTACATTATATTTTAAACTAATGCCACA-TGTTTTATTTGCTCAACTCATAAAGTTGAC
* * *
267115 AAACCAAGTTATATGGCATGATCATCTGGTCATTGTAGCTTAACTCGAGTAGTTACATTTGATCT
65 AAACCAAGTTACATGGCATGATCATCTGGTCATTGTAGCTTAACTCGAGTAGTTACATTTGACCC
** * * *
267180 GACTTGATTCATTCTCCATTCACTGATTACATGCAACTATTCAAGTGAAAAT
130 GACCCGATTCATACTCCATTCACTGATTACATGCAACCATTCAAATGAAAAT
* * * *
267232 GACACGTTACATTATATTTTAAACTAATGCTACATCATTTAATTAAGCTCAACTCATAAAGTTGA
1 GACACGTTACATTATATTTTAAACTAATGCCACAT-GTTTTATT-TGCTCAACTCATAAAGTTGA
*** *
267297 CAAACCAAGTTACATGGCATGATCATCTAACCATTGTAGCGTAACTC
64 CAAACCAAGTTACATGGCATGATCATCTGGTCATTGTAGCTTAACTC
267344 AAATGTATAC
Statistics
Matches: 266, Mismatches: 25, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
181 1 0.00
182 201 0.76
183 64 0.24
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (181 bp):
GACACGTTACATTATATTTTAAACTAATGCCACATGTTTTATTTGCTCAACTCATAAAGTTGACA
AACCAAGTTACATGGCATGATCATCTGGTCATTGTAGCTTAACTCGAGTAGTTACATTTGACCCG
ACCCGATTCATACTCCATTCACTGATTACATGCAACCATTCAAATGAAAAT
Found at i:273380 original size:31 final size:30
Alignment explanation
Indices: 273313--273381 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
273303 ATGATAACGT
**
273313 AAGTGACTAAAATATAACATTTCAAACATA
1 AAGTGACTAAAATATAACATGGCAAACATA
*
273343 AA-TGACTAAAATATAACCTGAGGCAAACA-A
1 AAGTGACTAAAATATAACAT--GGCAAACATA
273373 AAGTGACTA
1 AAGTGACTA
273382 TTTTGGTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 16 0.48
30 5 0.15
31 12 0.36
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.22
Consensus pattern (30 bp):
AAGTGACTAAAATATAACATGGCAAACATA
Found at i:274194 original size:21 final size:21
Alignment explanation
Indices: 274168--274214 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
274158 CGTGCTAATC
274168 GTCTTTGTTATTTCGAGTTTT
1 GTCTTTGTTATTTCGAGTTTT
274189 GTCTTTGTTATTTCGAGTTTT
1 GTCTTTGTTATTTCGAGTTTT
274210 GTCTT
1 GTCTT
274215 ATGCTTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.09, C:0.11, G:0.19, T:0.62
Consensus pattern (21 bp):
GTCTTTGTTATTTCGAGTTTT
Found at i:279536 original size:30 final size:31
Alignment explanation
Indices: 279470--279536 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
279460 AGAATCAATA
*
279470 AAAATTTTCAAAATTTTTGAGGAGTCAAATT
1 AAAATTTTCAAAATTTTTAAGGAGTCAAATT
* *
279501 AAAATTTTTAAAATTATTTAAGG-GTGAAA-T
1 AAAATTTTCAAAATT-TTTAAGGAGTCAAATT
279531 AAAATT
1 AAAATT
279537 ATCGAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.22
31 19 0.59
32 6 0.19
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (31 bp):
AAAATTTTCAAAATTTTTAAGGAGTCAAATT
Found at i:281823 original size:11 final size:11
Alignment explanation
Indices: 281776--281805 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
281766 AAAACAAAAA
281776 TTTAAAAAGTAT
1 TTTAAAAA-TAT
281788 TTTAAAAATAT
1 TTTAAAAATAT
281799 TTTAAAA
1 TTTAAAA
281806 TAAAAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (11 bp):
TTTAAAAATAT
Found at i:281840 original size:29 final size:30
Alignment explanation
Indices: 281753--281841 Score: 101
Period size: 29 Copynumber: 3.0 Consensus size: 30
281743 ACCAAAAATT
**
281753 TATTTTAAAAATTAAAACAAAAATTTAAAAAG
1 TATTTTAAAAA-TAATTC-AAAATTTAAAAAG
* * *
281785 TATTTTAAAAATATTTTAAAA-TAAAAAAG
1 TATTTTAAAAATAATTCAAAATTTAAAAAG
281814 TATTTTAAAAA-AATTCAAAATTTAAAAA
1 TATTTTAAAAATAATTCAAAATTTAAAAA
281842 TTAAAAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
28 7 0.15
29 24 0.50
30 4 0.08
31 2 0.04
32 11 0.23
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (30 bp):
TATTTTAAAAATAATTCAAAATTTAAAAAG
Found at i:281860 original size:23 final size:24
Alignment explanation
Indices: 281834--281882 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
281824 AAATTCAAAA
*
281834 TTTAAAAATTAAAAA-AAAAGTAT
1 TTTAAAAATTAAAAATAAAAATAT
*
281857 TTTAAAATTTAAAAATAAAAATAT
1 TTTAAAAATTAAAAATAAAAATAT
281881 TT
1 TT
281883 ATTATATTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
TTTAAAAATTAAAAATAAAAATAT
Found at i:284468 original size:6 final size:6
Alignment explanation
Indices: 284459--284487 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
284449 GATCATGATC
284459 ATGTAT ATGTAT ATGTAT ATGTAT ATGTA
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTA
284488 GGTACACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (6 bp):
ATGTAT
Found at i:284700 original size:2 final size:2
Alignment explanation
Indices: 284693--284717 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
284683 GCATCATTTA
284693 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
284718 GTTTGGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:285159 original size:60 final size:61
Alignment explanation
Indices: 285048--285161 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 61
285038 AACTAATACA
* * * * *
285048 AAATAATATCTAAATATTAAATCGGTAAAAATAAAGTTTAGGAATTGTAATATCTAAGTAT
1 AAATAATACCTAAATATTAAATAGGTAAAAATAAACTTAAGGAATTATAATATCTAAGTAT
* *
285109 AAATGATACCTAAATATT-AATAGGTAAAAATAAACTTAAATG-ATTATAATATC
1 AAATAATACCTAAATATTAAATAGGTAAAAATAAACTT-AAGGAATTATAATATC
285162 GGATACATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
60 27 0.60
61 18 0.40
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (61 bp):
AAATAATACCTAAATATTAAATAGGTAAAAATAAACTTAAGGAATTATAATATCTAAGTAT
Found at i:291887 original size:75 final size:75
Alignment explanation
Indices: 291797--291947 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
291787 CCAAATTTTA
291797 TTTGCATAATAGTCCTTCAACATCTGTGATATTTCATATACCGCACAGATTTTGAAGATTCAATT
1 TTTGCATAATAGTCCTTCAACATCTGTGATATTTCATATACCGCACAGATTTTGAAGATTCAATT
291862 CTCTTATTGC
66 CTCTTATTGC
291872 TTTGCATAATAGTCCTTCAACATCTGTGATATTTCATATACCGCACAGATTTTGAAGATTCAATT
1 TTTGCATAATAGTCCTTCAACATCTGTGATATTTCATATACCGCACAGATTTTGAAGATTCAATT
291937 CTCTTATTGC
66 CTCTTATTGC
291947 T
1 T
291948 GGTTTGTTGA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (75 bp):
TTTGCATAATAGTCCTTCAACATCTGTGATATTTCATATACCGCACAGATTTTGAAGATTCAATT
CTCTTATTGC
Found at i:299574 original size:20 final size:20
Alignment explanation
Indices: 299544--299601 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
299534 TTTTTCGAAA
*
299544 AAATTATTTTTACATATATT
1 AAATAATTTTTACATATATT
*
299564 -AATAAATTTTT--ATATTTT
1 AAAT-AATTTTTACATATATT
*
299582 AAATTATTTTTACATATATT
1 AAATAATTTTTACATATATT
299602 GCAATGATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
18 12 0.40
19 6 0.20
20 12 0.40
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
AAATAATTTTTACATATATT
Found at i:299988 original size:20 final size:20
Alignment explanation
Indices: 299963--300005 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
299953 TTCAATCAAA
299963 CAGACCCTGAGAAAGAGAGG
1 CAGACCCTGAGAAAGAGAGG
299983 CAGACCCTGAGAAAGAGAGG
1 CAGACCCTGAGAAAGAGAGG
300003 CAG
1 CAG
300006 GAGGGGCTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.21, G:0.35, T:0.05
Consensus pattern (20 bp):
CAGACCCTGAGAAAGAGAGG
Found at i:300211 original size:29 final size:29
Alignment explanation
Indices: 300178--300236 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
300168 TAGACTTTGG
*
300178 ATCAATTACGGATCTGTTTACATAAATGC
1 ATCAATTACGGATCTGTCTACATAAATGC
300207 ATCAATTACGGATCTGTCTACATAAATGC
1 ATCAATTACGGATCTGTCTACATAAATGC
300236 A
1 A
300237 ACGAACTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.32
Consensus pattern (29 bp):
ATCAATTACGGATCTGTCTACATAAATGC
Found at i:312728 original size:180 final size:183
Alignment explanation
Indices: 312385--312728 Score: 414
Period size: 180 Copynumber: 1.9 Consensus size: 183
312375 CTAGATTAGT
* * *
312385 ATGCATTGATTTTTACACCTTATGTTAAGCTTGACTTTGGGCTCGAAATGAGGTATAATGGCACC
1 ATGCATTGATTTTTACACCTTATCTTAAGCTTGACTTTGGACTCGAAATGAAGTATAATGGCACC
* * *
312450 CATTGGTTCTCTTTCTCTTACTTGATTCATATGTCCTTGTGTCATCTCTTTCTCCATCTTTATCA
66 CATTGGTTCTCTTTCTCTTACTTAATTCATATGACCTCGTGTCATCTCTTTCTCCATCTTTATCA
* * *
312515 TTTTATGTGAACTTGGTAAGATAATACAAGTGGGTGGAGCTTTAGATTTTATC
131 TATGATGTGAACTTGGCAAGATAATACAAGTGGGTGGAGCTTTAGATTTTATC
* * * * * **
312568 ATGCATTGATTTTTTCACCTTATCTTCAGCTTTTACTTTGGACTTGAAATGAATTATTCTGGCA-
1 ATGCATTGATTTTTACACCTTATCTTAAGC-TTGACTTTGGACTCGAAATGAAGTATAATGGCAC
*
312632 CCAGTTGGTTCT-TTT-TC-T-CTTAATTC-TCATGACCTCCG-GTCATCTCTTTCTCCATGTTT
65 CCA-TTGGTTCTCTTTCTCTTACTTAATTCAT-ATGACCT-CGTGTCATCTCTTTCTCCATCTTT
** **
312691 ATCATATGATGTGATTTTGGCAAGATAATGGAAGTGGG
127 ATCATATGATGTGAACTTGGCAAGATAATACAAGTGGG
312729 AAGAGTCTTA
Statistics
Matches: 136, Mismatches: 21, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
179 1 0.01
180 64 0.47
181 2 0.01
182 2 0.01
183 33 0.24
184 34 0.25
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (183 bp):
ATGCATTGATTTTTACACCTTATCTTAAGCTTGACTTTGGACTCGAAATGAAGTATAATGGCACC
CATTGGTTCTCTTTCTCTTACTTAATTCATATGACCTCGTGTCATCTCTTTCTCCATCTTTATCA
TATGATGTGAACTTGGCAAGATAATACAAGTGGGTGGAGCTTTAGATTTTATC
Found at i:314589 original size:26 final size:26
Alignment explanation
Indices: 314560--314629 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
314550 CCATTTTTTT
* *
314560 AATAAACACCAAAAAATTATTTTAAA
1 AATAAAAACCAAAAAAATATTTTAAA
**
314586 AATAAAAATTAAAAAAATATTTTAAA
1 AATAAAAACCAAAAAAATATTTTAAA
*
314612 AATAAAAA-TAAAAAAATA
1 AATAAAAACCAAAAAAATA
314630 AATATTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 10 0.25
26 30 0.75
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (26 bp):
AATAAAAACCAAAAAAATATTTTAAA
Found at i:314628 original size:25 final size:26
Alignment explanation
Indices: 314570--314629 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
314560 AATAAACACC
*
314570 AAAAAATTATTTTAAAAATAAAAATT
1 AAAAAAATATTTTAAAAATAAAAATT
314596 AAAAAAATATTTTAAAAATAAAAA-T
1 AAAAAAATATTTTAAAAATAAAAATT
314621 AAAAAAATA
1 AAAAAAATA
314630 AATATTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 10 0.30
26 23 0.70
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (26 bp):
AAAAAAATATTTTAAAAATAAAAATT
Found at i:316039 original size:26 final size:27
Alignment explanation
Indices: 315998--316060 Score: 96
Period size: 26 Copynumber: 2.4 Consensus size: 27
315988 TAAACACCAA
*
315998 ATTTT-AAAA-AATAAAATAAAAAA-T
1 ATTTTAAAAATAAAAAAATAAAAAAGT
316022 ATTTTAAAAATAAAAAAATAAAAAAGT
1 ATTTTAAAAATAAAAAAATAAAAAAGT
316049 ATTTTAAAAATA
1 ATTTTAAAAATA
316061 TTTTAAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
24 5 0.14
25 4 0.11
26 13 0.37
27 13 0.37
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (27 bp):
ATTTTAAAAATAAAAAAATAAAAAAGT
Found at i:316046 original size:38 final size:38
Alignment explanation
Indices: 316002--316100 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 38
315992 CACCAAATTT
316002 TAAAAAATAAAATAAAAAATATTTTAAAAATAAAAAAA
1 TAAAAAATAAAATAAAAAATATTTTAAAAATAAAAAAA
** * *
316040 TAAAAAAGT-ATTTTAAAAATATTTTAAAACTAAAAAAA
1 TAAAAAA-TAAAATAAAAAATATTTTAAAAATAAAAAAA
316078 TAAAAAATAAAAGATAAAAAATA
1 TAAAAAAT-AAA-ATAAAAAATA
316101 AATATATTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
37 1 0.02
38 39 0.78
39 2 0.04
40 8 0.16
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25
Consensus pattern (38 bp):
TAAAAAATAAAATAAAAAATATTTTAAAAATAAAAAAA
Found at i:316082 original size:7 final size:7
Alignment explanation
Indices: 316072--316102 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
316062 TTTAAAACTA
316072 AAAAAAT
1 AAAAAAT
316079 AAAAAAT
1 AAAAAAT
*
316086 AAAAGAT
1 AAAAAAT
316093 AAAAAAT
1 AAAAAAT
316100 AAA
1 AAA
316103 TATATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:321897 original size:48 final size:48
Alignment explanation
Indices: 321841--321939 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
321831 ACCGGCAAGA
* * *
321841 TTAGTTGAACTAATTGGATTAGAAATGTCACCATGGTTAACTCAAATT
1 TTAGTTGAACTAATCGAATTAGAAATATCACCATGGTTAACTCAAATT
321889 TTAGTTGAACTAATCGAATTAGAAATATCACCATGGTTAACTCAAATT
1 TTAGTTGAACTAATCGAATTAGAAATATCACCATGGTTAACTCAAATT
321937 TTA
1 TTA
321940 ATGGTACCTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (48 bp):
TTAGTTGAACTAATCGAATTAGAAATATCACCATGGTTAACTCAAATT
Found at i:324160 original size:26 final size:26
Alignment explanation
Indices: 324124--324175 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
324114 TCATGTTTCC
324124 TTGATTTCTCTAGATATTCTTTTATA
1 TTGATTTCTCTAGATATTCTTTTATA
324150 TTGATTTCTCTAGATATTCTTTTATA
1 TTGATTTCTCTAGATATTCTTTTATA
324176 CAGTTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.58
Consensus pattern (26 bp):
TTGATTTCTCTAGATATTCTTTTATA
Found at i:327058 original size:14 final size:15
Alignment explanation
Indices: 327036--327066 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
327026 TGTAATAATG
327036 TAACTAAAATAAATT
1 TAACTAAAATAAATT
327051 TAAC-AAAATAAATT
1 TAACTAAAATAAATT
327065 TA
1 TA
327067 TTAGTGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (15 bp):
TAACTAAAATAAATT
Found at i:328280 original size:209 final size:210
Alignment explanation
Indices: 327913--328331 Score: 743
Period size: 209 Copynumber: 2.0 Consensus size: 210
327903 CATCTCATAC
327913 AAGTAGTAGTATACATCTATTACAAAATCGTTCGATAAATGCAGGAAAGATTACCCGGACACACT
1 AAGTAGTAGTATACATCTATTACAAAATCGTTCGATAAATGCAGGAAAGATTACCCGGACACACT
* *
327978 CGAACTCAGAGTATGGATTCTTACCCTATTATGCCTAAAATCGGACCGAGAAGCAATAGTCCGAG
66 CGAACTCAGAGTATGGATTCTTACCCCATTATGCCTAAAATCGGACAGAGAAGCAATAGTCCGAG
* *
328043 CGCTTACTCGAACAAGATACCTGCTAGAACTACTACAACAAAGGTACTAAATGCTTCGAGGAACC
131 CGCTTACTCGAACAAGATACCCGCTAGAACTACTACAACAAAGGTACTAAATGCTTCGAGAAACC
*
328108 C-AAAATAAACACTG
196 CGAAAATAAAAACTG
*
328122 AAGTAGTGGTATACATCTATTACAAAATCGTTCGATAAATGCAGGAAAGATTACCCGGACACACT
1 AAGTAGTAGTATACATCTATTACAAAATCGTTCGATAAATGCAGGAAAGATTACCCGGACACACT
*
328187 CGAACTCGGAGTATGGATTCTTACCCCATTATGCCTAAAATCGGACAGAGAAGCAATAGTCCGAG
66 CGAACTCAGAGTATGGATTCTTACCCCATTATGCCTAAAATCGGACAGAGAAGCAATAGTCCGAG
*
328252 CGCTTACTC-ATACACGATACCCGCTAGAACTACTACAACAAAGGTACTAAATGCTTCGAGAAAC
131 CGCTTACTCGA-ACAAGATACCCGCTAGAACTACTACAACAAAGGTACTAAATGCTTCGAGAAAC
328316 CCGAAAATAAAAACTG
195 CCGAAAATAAAAACTG
328332 GCATAATATA
Statistics
Matches: 200, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
208 1 0.00
209 187 0.94
210 12 0.06
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (210 bp):
AAGTAGTAGTATACATCTATTACAAAATCGTTCGATAAATGCAGGAAAGATTACCCGGACACACT
CGAACTCAGAGTATGGATTCTTACCCCATTATGCCTAAAATCGGACAGAGAAGCAATAGTCCGAG
CGCTTACTCGAACAAGATACCCGCTAGAACTACTACAACAAAGGTACTAAATGCTTCGAGAAACC
CGAAAATAAAAACTG
Found at i:330151 original size:4 final size:4
Alignment explanation
Indices: 330142--330195 Score: 54
Period size: 4 Copynumber: 13.5 Consensus size: 4
330132 CTAAGAAATA
* * * * *
330142 TATG TATG TATG CATG CATG CATG CATG TGTG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
330190 CATG TA
1 TATG TA
330196 AAGTAATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (4 bp):
TATG
Found at i:330182 original size:12 final size:12
Alignment explanation
Indices: 330143--330195 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
330133 TAAGAAATAT
330143 ATGTATGTATGC
1 ATGTATGTATGC
* *
330155 ATGCATGCATGC
1 ATGTATGTATGC
* *
330167 ATGTGTGTATGT
1 ATGTATGTATGC
330179 ATGTATGTATGC
1 ATGTATGTATGC
330191 ATGTA
1 ATGTA
330196 AAGTAATTGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.25, C:0.09, G:0.26, T:0.40
Consensus pattern (12 bp):
ATGTATGTATGC
Found at i:330981 original size:23 final size:23
Alignment explanation
Indices: 330938--330985 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
330928 TGGCTTCAAA
* *
330938 TTCAATTTGGTACTTGAGTTTTT
1 TTCAATTTGATACTAGAGTTTTT
330961 TTCAATTTGATACTCAG-GTTTTT
1 TTCAATTTGATACT-AGAGTTTTT
330984 TT
1 TT
330986 ACTAATTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.19, C:0.10, G:0.15, T:0.56
Consensus pattern (23 bp):
TTCAATTTGATACTAGAGTTTTT
Found at i:343633 original size:31 final size:31
Alignment explanation
Indices: 343589--343648 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
343579 TTTTAAGCTA
*
343589 AATTTGACCTTTAACCTTCTAAATAAAGTCG
1 AATTTGACCTTTAACCTTCTAAAAAAAGTCG
** *
343620 AATTTGAGTTTTAACCTTTTAAAAAAAGT
1 AATTTGACCTTTAACCTTCTAAAAAAAGT
343649 TGAACTGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (31 bp):
AATTTGACCTTTAACCTTCTAAAAAAAGTCG
Found at i:345280 original size:15 final size:16
Alignment explanation
Indices: 345262--345304 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
345252 TATATTAAAA
345262 TTTAAATTTATTT-AT
1 TTTAAATTTATTTAAT
*
345277 TTTAAATATATTTAAAT
1 TTTAAATTTATTT-AAT
345294 TTTAATATTTA
1 TTTAA-ATTTA
345305 AGGCCTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 12 0.52
17 7 0.30
18 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAAATTTATTTAAT
Found at i:346476 original size:32 final size:32
Alignment explanation
Indices: 346431--346491 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
346421 ATACCATTTT
346431 ATTTTCAAGAATTTAATTTATCAATTTTTTTTAG
1 ATTTTCAAGAATTTAATTT-T-AATTTTTTTTAG
346465 ATTTT-AA-AATTTAATTTTAATTTTTTT
1 ATTTTCAAGAATTTAATTTTAATTTTTTT
346492 ATTAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 9 0.33
31 1 0.04
32 10 0.37
33 2 0.07
34 5 0.19
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (32 bp):
ATTTTCAAGAATTTAATTTTAATTTTTTTTAG
Found at i:348851 original size:222 final size:221
Alignment explanation
Indices: 348452--349076 Score: 895
Period size: 222 Copynumber: 2.8 Consensus size: 221
348442 TTTCCAGAAC
* * * * * *
348452 AGCAAACACGATATCTTGTTAAGAACTAATATCGGACATAATAATATTCACACACAAAAAAACAC
1 AGCAAACACGACATCTTGTTAAGAACTAATATCAGACACAACAAGATTCACACA-AAAATAACA-
* * * * * *
348517 CGGAATATCAACAACGGATAGG-AGCAACATTTGACCCTCAGAACCTTGATGCATAAAACCGA--
64 -GGCATATCGACAACGGAT-GGAAGCAGCATTTGACTCTCAGAACCTCGATGCATAAAATCGATT
* * *
348579 --ACGGACTAAACGA-TTCTTTGCTTTCACATGATGCTAGAGAAATGAAAGTACCATACACAATA
127 CTAAGGACTAAACGAGTT-TTTGCTTTCACACGA-GCTAGAGAAACGAAAGTACCATACACAATA
348641 AGTACGATGAAGGTTCGGTTTAACGATGAGGG
190 AGTACGATGAAGGTTCGGTTTAACGATGAGGG
*
348673 AGCAAACACGACATCTTGTTAAGAACTAATATCAGACACACCAAGATTCACACAAAAATAACAGG
1 AGCAAACACGACATCTTGTTAAGAACTAATATCAGACACAACAAGATTCACACAAAAATAACAGG
* * *
348738 CATGTGGACAACGGATGGAAGCAGCATTTGACTCTCAGAACCTCAATGCATAAAATCGATTCTAA
66 CATATCGACAACGGATGGAAGCAGCATTTGACTCTCAGAACCTCGATGCATAAAATCGATTCTAA
348803 GGACTAAACGAGTTTTTGCTTTCACACGACGCTAGAGAAACGAAAGTACCATACACAATAAGTAC
131 GGACTAAACGAGTTTTTGCTTTCACACGA-GCTAGAGAAACGAAAGTACCATACACAATAAGTAC
*
348868 GATGGAGGTTCGGTTTAACGATGAGGG
195 GATGAAGGTTCGGTTTAACGATGAGGG
* *
348895 AGCAAACACGACATCTTGTTAAGAACTAATATCAGGCACAACAAGATTCACACAAAAATAACTGG
1 AGCAAACACGACATCTTGTTAAGAACTAATATCAGACACAACAAGATTCACACAAAAATAACAGG
* * *
348960 CATATCGACAGCGGATGGAAGCAGCATTTGACTCTCAGAACCTCGATGCATGAAATTGATTCTAA
66 CATATCGACAACGGATGGAAGCAGCATTTGACTCTCAGAACCTCGATGCATAAAATCGATTCTAA
*
349025 GGACTAAACAAGTCTTTT-CTTTCACACGAGCTAGAGAAACGAAAGTACCATA
131 GGACTAAACGAGT-TTTTGCTTTCACACGAGCTAGAGAAACGAAAGTACCATA
349077 TACGATATAT
Statistics
Matches: 366, Mismatches: 31, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
217 2 0.01
218 49 0.13
220 8 0.02
221 71 0.19
222 230 0.63
223 6 0.02
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (221 bp):
AGCAAACACGACATCTTGTTAAGAACTAATATCAGACACAACAAGATTCACACAAAAATAACAGG
CATATCGACAACGGATGGAAGCAGCATTTGACTCTCAGAACCTCGATGCATAAAATCGATTCTAA
GGACTAAACGAGTTTTTGCTTTCACACGAGCTAGAGAAACGAAAGTACCATACACAATAAGTACG
ATGAAGGTTCGGTTTAACGATGAGGG
Found at i:349648 original size:18 final size:18
Alignment explanation
Indices: 349625--349663 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
349615 TTTCAACAGT
*
349625 AAAATAGGACGTTTGATG
1 AAAATAAGACGTTTGATG
349643 AAAATAAGACGTTTGATG
1 AAAATAAGACGTTTGATG
349661 AAA
1 AAA
349664 TTTTTAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.23, T:0.26
Consensus pattern (18 bp):
AAAATAAGACGTTTGATG
Found at i:352549 original size:29 final size:29
Alignment explanation
Indices: 352508--352564 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
352498 ATCATTTCTC
*
352508 CCTTGAAGTTTTTAGAAAATTTTAATTAAG
1 CCTTCAAGTTTTTA-AAAATTTTAATTAAG
352538 CCTTCAAGTTTTTAAAAATTTTAATTA
1 CCTTCAAGTTTTTAAAAATTTTAATTA
352565 GACCACTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (29 bp):
CCTTCAAGTTTTTAAAAATTTTAATTAAG
Found at i:352580 original size:30 final size:29
Alignment explanation
Indices: 352513--352585 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 29
352503 TTCTCCCTTG
*
352513 AAGTTTTTAGAAAATTTTAATTAAGCCTTC
1 AAGTTTTTA-AAAATTTTAATTAAGCCCTC
352543 AAGTTTTTAAAAATTTTAATT-AGACCACTC
1 AAGTTTTTAAAAATTTTAATTAAG-CC-CTC
*
352573 AATTTTTTAAAAA
1 AAGTTTTTAAAAA
352586 GAATTTCTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 14 0.36
30 23 0.59
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (29 bp):
AAGTTTTTAAAAATTTTAATTAAGCCCTC
Found at i:355063 original size:30 final size:28
Alignment explanation
Indices: 355029--355103 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 28
355019 TATTCTAAGA
355029 GTTTAATGAAATTTCAAGAAAAA-CTGAAGG
1 GTTTAATGAAATTTCAA-AAAAATC-G-AGG
*
355059 GTTTAATTAAATTTTTCAAAAAAATCGAGG
1 GTTTAATGAAA--TTTCAAAAAAATCGAGG
355089 GTTTAATGAGAATTT
1 GTTTAATGA-AATTT
355104 ATAATAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
29 3 0.08
30 21 0.54
31 8 0.21
32 7 0.18
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (28 bp):
GTTTAATGAAATTTCAAAAAAATCGAGG
Found at i:355904 original size:4 final size:4
Alignment explanation
Indices: 355897--355943 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
355887 AAGTTGCATG
355897 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
355944 TTGATGATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:356513 original size:29 final size:29
Alignment explanation
Indices: 356464--356529 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
356454 GTTTTAAGAA
*
356464 GTTTAATTAAAATTTTCAAAATTTT-GAGG
1 GTTTAATTAAAATTCTCAAAATTTTGGA-G
356493 GTTTAATTAAAATATCT-AAAATTTTGGAG
1 GTTTAATTAAAAT-TCTCAAAATTTTGGAG
356522 GTTTAATT
1 GTTTAATT
356530 TTTTAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 30 0.88
30 4 0.12
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45
Consensus pattern (29 bp):
GTTTAATTAAAATTCTCAAAATTTTGGAG
Found at i:356890 original size:18 final size:17
Alignment explanation
Indices: 356856--356901 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
356846 TCAAATTTAA
356856 TATTTTTAAAAATATAT
1 TATTTTTAAAAATATAT
*
356873 TATTTTCT-AAAACA-A-
1 TATTTT-TAAAAATATAT
356888 TATTTTTAAAAATA
1 TATTTTTAAAAATA
356902 GATAAACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 1 0.04
15 11 0.44
16 1 0.04
17 11 0.44
18 1 0.04
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTTTTAAAAATATAT
Found at i:373009 original size:10 final size:9
Alignment explanation
Indices: 372991--373029 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
372981 AACAATTTAA
372991 TTTTTTTTC
1 TTTTTTTTC
373000 TTTTTATTTC
1 TTTTT-TTTC
*
373010 TTTATTTTC
1 TTTTTTTTC
*
373019 CTTTTTTTC
1 TTTTTTTTC
373028 TT
1 TT
373030 CCCTTTTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:376359 original size:18 final size:18
Alignment explanation
Indices: 376327--376391 Score: 85
Period size: 18 Copynumber: 3.4 Consensus size: 18
376317 TTATAACTAT
*
376327 TTATATATATCTTTATATC
1 TTAT-TATATATTTATATC
376346 TTATTATATATTTATATC
1 TTATTATATATTTATATC
376364 TTATTATATATCTATATATC
1 TTATTATATAT-T-TATATC
*
376384 TTTTTATA
1 TTATTATA
376392 AACATATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
18 24 0.57
19 5 0.12
20 13 0.31
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATATATTTATATC
Found at i:376570 original size:30 final size:30
Alignment explanation
Indices: 376498--376570 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
376488 TACGTCTATT
* *
376498 TTCTTTTATATATACATATACATACTTACA
1 TTCTTTTATTTTTACATATACATACTTACA
* *
376528 TTGTTTTA-TTTTACGATATACATACTTATA
1 TTCTTTTATTTTTAC-ATATACATACTTACA
376558 -TCTTTTATTTTTA
1 TTCTTTTATTTTTA
376571 TGTAATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 10 0.28
30 26 0.72
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (30 bp):
TTCTTTTATTTTTACATATACATACTTACA
Found at i:381095 original size:15 final size:15
Alignment explanation
Indices: 381075--381110 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
381065 TCTCATGAAT
381075 TCAAAAAAATAAAAA
1 TCAAAAAAATAAAAA
* *
381090 TCAAAAAAATCAAAG
1 TCAAAAAAATAAAAA
381105 TCAAAA
1 TCAAAA
381111 TAGGAAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.72, C:0.11, G:0.03, T:0.14
Consensus pattern (15 bp):
TCAAAAAAATAAAAA
Found at i:383380 original size:88 final size:88
Alignment explanation
Indices: 383231--384277 Score: 1798
Period size: 88 Copynumber: 11.9 Consensus size: 88
383221 CAATGAAGTT
*
383231 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
383296 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
383319 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
383384 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
*
383407 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATTGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
383472 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
383495 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
383560 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
*
383583 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATTGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
*
383648 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
* * *
383671 AAAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
383736 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
383759 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
383824 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
*
383847 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATTGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
383912 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
383935 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
384000 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
*
384023 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATTGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
*
384088 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
* * * *
384111 AAAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
*
384176 TGT-AGTGGAGCTGGTTAAAGA-A
66 TGTGA-TGGAGCTGGTTGAAGACA
** * * * * * * **
384198 GCAGATCTTACCTTCCTGCATTAACAGCAAAGCGGATC-AA-AAACAAAGCCTTGCCTCCATCGG
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTTTCGG
*
384261 TTG-CATTGGAGCTGGTT
65 TTGTGA-TGGAGCTGGTT
384278 AAAGGTTACA
Statistics
Matches: 920, Mismatches: 36, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
85 6 0.01
86 30 0.03
87 32 0.03
88 852 0.93
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (88 bp):
AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
TGTGATGGAGCTGGTTGAAGACA
Found at i:385921 original size:18 final size:18
Alignment explanation
Indices: 385889--385953 Score: 85
Period size: 18 Copynumber: 3.4 Consensus size: 18
385879 TTATAACTAT
*
385889 TTATATATATCTTTATATC
1 TTAT-TATATATTTATATC
385908 TTATTATATATTTATATC
1 TTATTATATATTTATATC
385926 TTATTATATATCTATATATC
1 TTATTATATAT-T-TATATC
*
385946 TTTTTATA
1 TTATTATA
385954 AACATATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
18 24 0.57
19 5 0.12
20 13 0.31
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATATATTTATATC
Found at i:386132 original size:30 final size:30
Alignment explanation
Indices: 386060--386132 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
386050 TACGTCTATT
* *
386060 TTCTTTTATATATACATATACATACTTACA
1 TTCTTTTATTTTTACATATACATACTTACA
* *
386090 TTGTTTTA-TTTTACGATATACATACTTATA
1 TTCTTTTATTTTTAC-ATATACATACTTACA
386120 -TCTTTTATTTTTA
1 TTCTTTTATTTTTA
386133 TGTAATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 10 0.28
30 26 0.72
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (30 bp):
TTCTTTTATTTTTACATATACATACTTACA
Found at i:388427 original size:5 final size:5
Alignment explanation
Indices: 388417--388444 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
388407 AATTGGAATT
388417 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
388445 GTTTTTCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:389757 original size:31 final size:30
Alignment explanation
Indices: 389678--389790 Score: 75
Period size: 31 Copynumber: 3.6 Consensus size: 30
389668 AGGGATCTTC
*
389678 GCCTCTCAAAAATTTTGAAAAATTTTC-ATTATA
1 GCCT-TCAAAAGTTTT-AAAAA-TTTCAATTA-A
* ** *
389711 TCCTTTGAAATTTTTAAAAATTTCAATTAA
1 GCCTTCAAAAGTTTTAAAAATTTCAATTAA
* * * *
389741 GCCTCTCAAAAGTTTTAAGAATTTTACTTGA
1 GCCT-TCAAAAGTTTTAAAAATTTCAATTAA
* *
389772 GTCTTCAAAAGTTTCAAAA
1 GCCTTCAAAAGTTTTAAAA
389791 TTTTGAAAAT
Statistics
Matches: 63, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
30 21 0.33
31 31 0.49
32 8 0.13
33 3 0.05
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (30 bp):
GCCTTCAAAAGTTTTAAAAATTTCAATTAA
Found at i:408362 original size:31 final size:30
Alignment explanation
Indices: 408327--408384 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
408317 ATATGATTGC
408327 TGAACTATTCAAAAGTTTTCATCTAAGTTGT
1 TGAACTATTCAAAAGTTTT-ATCTAAGTTGT
* *
408358 TGAACTATTCGAAAGTTTTATTTAAGT
1 TGAACTATTCAAAAGTTTTATCTAAGT
408385 CATTGAGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (30 bp):
TGAACTATTCAAAAGTTTTATCTAAGTTGT
Found at i:408396 original size:30 final size:31
Alignment explanation
Indices: 408327--408396 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
408317 ATATGATTGC
**
408327 TGAACTATTCAAAAGTTTTCATCTAAGTTGT
1 TGAACTATTCAAAAGTTTTCATCTAAGTCAT
* *
408358 TGAACTATTCGAAAGTTTT-ATTTAAGTCAT
1 TGAACTATTCAAAAGTTTTCATCTAAGTCAT
*
408388 TGAGCTATT
1 TGAACTATT
408397 AAGGTTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (31 bp):
TGAACTATTCAAAAGTTTTCATCTAAGTCAT
Found at i:416945 original size:193 final size:191
Alignment explanation
Indices: 416460--417000 Score: 785
Period size: 194 Copynumber: 2.8 Consensus size: 191
416450 TTTTACCAAT
* * * * * * * * *
416460 GGGTGCTCTAGCCATCAGAAACATTTCATTATAAAAGCATATAAGTCACGGATTCATATCGCCAC
1 GGGTGCACTAGACATAAAAAACATTTCATTATAAAAGCATAAAAGTCACGAATTCACACCGCTAC
* * ** * **
416525 TCGTAAAGACATTGGTTTTTGAGTTCTAAACCCTCTTTTCTAGAGGGTGTTACTGCGGTATAGCA
66 TTGTAAAGATATTGGTTTCCGAATTCTAAACATTCTTTTCTAGAGGGTGTTACT-CGGTA-AGCA
*
416590 ACGTGCTTCATTCATTCAAGTTCACAGTATGCAGCAGAACATGAATATGGCTTCAATCAAAAG
129 ATGTGCTTCATTCATTCAAGTTCACAGTATGCAGCAGAACATGAATATGGCTTCAATCAAAAG
* * *
416653 GGGTTGCACTATACATAAAAAACATTTCATTATAAAAGCATAATAGTTACGAATTCACACCGCTA
1 GGG-TGCACTAGACATAAAAAACATTTCATTATAAAAGCATAAAAGTCACGAATTCACACCGCTA
416718 CTTGTAAAGATATTGGTTTCCGAATTCTAAACATTCTTTTCTAGAGGGTGTTACGTCGGTACAGC
65 CTTGTAAAGATATTGGTTTCCGAATTCTAAACATTCTTTTCTAGAGGGTGTTAC-TCGGTA-AGC
**
416783 AATGTGCTTCATTCATTCAAGTTCGTAGTATGCAGCAGAACATGAATATGGCTTCAATCAAAAG
128 AATGTGCTTCATTCATTCAAGTTCACAGTATGCAGCAGAACATGAATATGGCTTCAATCAAAAG
*
416847 GGGTGCACTAGACATAAAAAACATTTCATTATAAATGCATAAAAGTCACGAATTCACACCGCTAC
1 GGGTGCACTAGACATAAAAAACATTTCATTATAAAAGCATAAAAGTCACGAATTCACACCGCTAC
* * *
416912 TTGTAAAGATATTGGTTTCCGAATTCTAAACATTCCTTTCTAGAGGGTGTTACATCGGTTAAACG
66 TTGTAAAGATATTGGTTTCCGAATTCTAAACATTCTTTTCTAGAGGGTGTTAC-TCGG-TAAGCA
416977 ATGTGCTTCATTCATTCAAGTTCA
129 ATGTGCTTCATTCATTCAAGTTCA
417001 TAATTGCTTT
Statistics
Matches: 313, Mismatches: 32, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
193 142 0.45
194 170 0.54
195 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (191 bp):
GGGTGCACTAGACATAAAAAACATTTCATTATAAAAGCATAAAAGTCACGAATTCACACCGCTAC
TTGTAAAGATATTGGTTTCCGAATTCTAAACATTCTTTTCTAGAGGGTGTTACTCGGTAAGCAAT
GTGCTTCATTCATTCAAGTTCACAGTATGCAGCAGAACATGAATATGGCTTCAATCAAAAG
Found at i:417193 original size:155 final size:154
Alignment explanation
Indices: 416890--417168 Score: 350
Period size: 155 Copynumber: 1.8 Consensus size: 154
416880 AATGCATAAA
** * *
416890 AGTCACGAATTCACACCGCTACTTGTAAAGATATTGGTTTCCGAATTCTAAACATTCCTTTCTAG
1 AGTCACGAATTCACACCGCTACTCATAAAGACATTGGGTTCCGAATTCTAAACATTCCTTTCTAG
* * ***
416955 AGGGTGTTACATCGGTTAAACGATGTGCTTCATTCATTCAAGTTCATAATTGCTTTAGACATCGA
66 ACGGTGTTACATCGGATAAACGATGTGCTTCATTCATTCAAGTTCATAATTGCAGCAGACATCGA
* *
417020 AAACATTTCAGTATAAAAGCATATG
131 AAACACTGCAG-ATAAAAGCATATG
* * *
417045 AGTCACGAATTCACATCGCTACTCATAAAGACATTGGGTTCC-AGGTTCTAAACATTCTTTTCTA
1 AGTCACGAATTCACACCGCTACTCATAAAGACATTGGGTTCCGA-ATTCTAAACATTCCTTTCTA
*
417109 GACGGTGTTACGTCGGCATACAACG-T-T-CTTCATTCATTCAAGTTCATAATATGCAGCAGA
65 GACGGTGTTACATCGG-ATA-AACGATGTGCTTCATTCATTCAAGTTCATAAT-TGCAGCAGA
417169 ACATGAATAT
Statistics
Matches: 107, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
154 24 0.22
155 76 0.71
156 3 0.03
157 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (154 bp):
AGTCACGAATTCACACCGCTACTCATAAAGACATTGGGTTCCGAATTCTAAACATTCCTTTCTAG
ACGGTGTTACATCGGATAAACGATGTGCTTCATTCATTCAAGTTCATAATTGCAGCAGACATCGA
AAACACTGCAGATAAAAGCATATG
Found at i:417348 original size:191 final size:192
Alignment explanation
Indices: 417005--417705 Score: 900
Period size: 191 Copynumber: 3.7 Consensus size: 192
416995 AGTTCATAAT
* * *
417005 TGCTTTAGACATCGAAAACATTTCAGTATAAAAGCATATGAGTCACGAATTCACATCGCTACTCA
1 TGCTCTAGACATCGAAAACATTTCATTATAAAAGCATATGAGTCACGAATTCACATCGCTACTCG
* * * *
417070 TAAAGACATTGGGTTCCAGGTTCTAAACATTCTTTTCTAGACGGTGTTACGTCGGCATA-CAACG
66 TAAAGACATCGGTTTCCAGGTTCTAAACATTCTTTTCTAGAGGGTGTTACGTCGGTATAGCAACG
* *
417134 T-TCTTCATTCATTCAAGTTCATAATATGCAGCAGAACATGAATATGACTGCAATCAAAAGGG
131 TGT-TTCATTCATTCAAGTTCATAATATGCAGCAGAACATGAATATGGCTTCAATCAAAAGGG
*
417196 TGCTCTAGACA-CTGAAAACATTTCATTATAAAAGCATATGCGTCACGAATTCACATAC-CTACT
1 TGCTCTAGACATC-GAAAACATTTCATTATAAAAGCATATGAGTCACGAATTCACAT-CGCTACT
* * ** * *
417259 CGTAAAGACATCGTTTTCCGGGTTCTAAACATTCTTTAATATAGGGTGTTACGCCGGTATA-CAA
64 CGTAAAGACATCGGTTTCCAGGTTCTAAACATTCTTTTCTAGAGGGTGTTACGTCGGTATAGCAA
* *
417323 TGTGTTTCATTCATTCAAATTCATAATATGCAGCAGAACATGAATATGGCTTCAATCAAAAGGGG
129 CGTGTTTCATTCATTCAAGTTCATAATATGCAGCAGAACATGAATATGGCTTCAATCAAAA-GGG
* * * *
417388 TGCTCTAGACATCGAAAACATTTCATTATAAATGCATAT--GTCGC-AGATTCACATCTCTGCTC
1 TGCTCTAGACATCGAAAACATTTCATTATAAAAGCATATGAGTCACGA-ATTCACATCGCTACTC
* * * *
417450 GTAAAGACATTGATTTCTC-GGTTCTAAACATTCTTTTCTAGAAGGTGTTACGTCTGTATAGCAA
65 GTAAAGACATCGGTTTC-CAGGTTCTAAACATTCTTTTCTAGAGGGTGTTACGTCGGTATAGCAA
* * ** * * *
417514 CATGCTTCATTCATTCAAGTTCATAATATGCAGTTGAACATGAATATGGTTTCGATCAAAAGGA
129 CGTGTTTCATTCATTCAAGTTCATAATATGCAGCAGAACATGAATATGGCTTCAATCAAAAGGG
* * ** *
417578 TGCTCTAGACATCAAAAACATGTCATTATAAAAGCATACAAGTCATGAATTCACA-CTGCTACTC
1 TGCTCTAGACATCGAAAACATTTCATTATAAAAGCATATGAGTCACGAATTCACATC-GCTACTC
* * *
417642 GTAAAGACATCGGTTTCTAGGTTCTAAACATTCTTTTCTAGAGAGTGTTATGTCGGTATAGCAA
65 GTAAAGACATCGGTTTCCAGGTTCTAAACATTCTTTTCTAGAGGGTGTTACGTCGGTATAGCAA
417706 TGTGCTTTGC
Statistics
Matches: 443, Mismatches: 53, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
189 2 0.00
190 105 0.24
191 222 0.50
192 112 0.25
193 2 0.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (192 bp):
TGCTCTAGACATCGAAAACATTTCATTATAAAAGCATATGAGTCACGAATTCACATCGCTACTCG
TAAAGACATCGGTTTCCAGGTTCTAAACATTCTTTTCTAGAGGGTGTTACGTCGGTATAGCAACG
TGTTTCATTCATTCAAGTTCATAATATGCAGCAGAACATGAATATGGCTTCAATCAAAAGGG
Found at i:420677 original size:31 final size:31
Alignment explanation
Indices: 420619--420677 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
420609 GTTGTAATGG
* *
420619 TCAATTTGGTACTAAGTATTTGTTTTGGGTT
1 TCAATTTGGTACTAAGTATTGGCTTTGGGTT
420650 TCAATTTGGTACTTAAGT-TTGGCTTTGG
1 TCAATTTGGTAC-TAAGTATTGGCTTTGG
420678 TTAAGGGTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.19, C:0.08, G:0.24, T:0.49
Consensus pattern (31 bp):
TCAATTTGGTACTAAGTATTGGCTTTGGGTT
Found at i:421261 original size:34 final size:35
Alignment explanation
Indices: 421206--421271 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
421196 CAAACACCAG
*
421206 AAAATATTTTCCAGTAAATCATTTTACAGAAACGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAACGT
* *
421241 AAAACATTTTCCCG-AAATCATTTTACGGAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAA
421272 ATATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAACGT
Found at i:427130 original size:22 final size:22
Alignment explanation
Indices: 427087--427131 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
427077 CCGATTTTTC
* **
427087 TATTTTTTTATTGTTTAATATA
1 TATTTATTTATTACTTAATATA
*
427109 TATTTATTTATTACTTATTATA
1 TATTTATTTATTACTTAATATA
427131 T
1 T
427132 CTCGCCACTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTTATTTATTACTTAATATA
Found at i:427285 original size:30 final size:31
Alignment explanation
Indices: 427243--427302 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
427233 TTTAAGTTTA
* *
427243 TTAATATTTTAT-ATATATTTATAATTTAATT
1 TTAATATTTTATAATA-AATTATAATATAATT
427274 TTAAT-TTTTATAATAAATTATAATATAAT
1 TTAATATTTTATAATAAATTATAATATAAT
427303 ATATACGTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
TTAATATTTTATAATAAATTATAATATAATT
Found at i:433550 original size:13 final size:12
Alignment explanation
Indices: 433532--433572 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
433522 GCTTTGTGGG
433532 AAAAAAATATAGA
1 AAAAAAATATA-A
433545 AAAAAAATATAA
1 AAAAAAATATAA
*
433557 AAATAAAAGATAA
1 AAA-AAAATATAA
433570 AAA
1 AAA
433573 GGAGATTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 4 0.15
13 22 0.85
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (12 bp):
AAAAAAATATAA
Found at i:440499 original size:167 final size:167
Alignment explanation
Indices: 440208--440628 Score: 637
Period size: 167 Copynumber: 2.5 Consensus size: 167
440198 CTGTTACATA
**
440208 CGATTTTAGTGAAACAAACTTGTGTCATGTTTGTATGTTGTGTTTGCAACCTTTGTTTCATGGTC
1 CGATTTTAGCAAAACAAACTTGTGTCATGTTTGTATGTTGTGTTTG----CTTTGTTTCATGGT-
* *
440273 CTT-TTCCTCATTCTAATTATCTAGTGTTTATGGAGAAATTTTGTAAGTTCACAATAGCTGCTGT
61 CTTATTCCTCGTTCTAATTAACTAGTGTTTATGGAGAAATTTTGTAAGTTCACAATAGCTGCTGT
* *
440337 TAAAACCCTTGAAGACATCTCGAAAACATTGGCTGTTGCACT
126 TAAAACCATCGAAGACATCTCGAAAACATTGGCTGTTGCACT
* * * *
440379 CGGTTTTAGCAAAACAAACTTGTATCATGTATGCATGTTGTGTTTGCTTTGTTTCATGGTCTTAT
1 CGATTTTAGCAAAACAAACTTGTGTCATGTTTGTATGTTGTGTTTGCTTTGTTTCATGGTCTTAT
* *
440444 TCCTTGTTCTAATTAACTAGTGTTTATGGAGAAATTTTGTAAGTTCACAATAGCTGCTGTTAGAA
66 TCCTCGTTCTAATTAACTAGTGTTTATGGAGAAATTTTGTAAGTTCACAATAGCTGCTGTTAAAA
*
440509 CCATCGAAGACATCTCGAAAACATTGGCTGTTGCATT
131 CCATCGAAGACATCTCGAAAACATTGGCTGTTGCACT
* * * *
440546 TGATTTTAGCAAAATAAACTTGTGTCATGTTTGTATATTGTGTTTGCTTTGTTTCATGGTTTTAT
1 CGATTTTAGCAAAACAAACTTGTGTCATGTTTGTATGTTGTGTTTGCTTTGTTTCATGGTCTTAT
440611 TCCTCGTTCTAATTAACT
66 TCCTCGTTCTAATTAACT
440629 TTGGTCCATT
Statistics
Matches: 227, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
166 3 0.01
167 184 0.81
171 40 0.18
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (167 bp):
CGATTTTAGCAAAACAAACTTGTGTCATGTTTGTATGTTGTGTTTGCTTTGTTTCATGGTCTTAT
TCCTCGTTCTAATTAACTAGTGTTTATGGAGAAATTTTGTAAGTTCACAATAGCTGCTGTTAAAA
CCATCGAAGACATCTCGAAAACATTGGCTGTTGCACT
Found at i:441781 original size:15 final size:16
Alignment explanation
Indices: 441761--441790 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
441751 AGTTTGAGGT
441761 TTTTTTTTAT-TTTTA
1 TTTTTTTTATATTTTA
441776 TTTTTTTTATATTTT
1 TTTTTTTTATATTTT
441791 GGGTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTTTATATTTTA
Found at i:442322 original size:29 final size:29
Alignment explanation
Indices: 442268--442323 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
442258 AAAATTATTA
*
442268 ATAGTTGAATGACCATTTTGTAATTTTTT
1 ATAGTTGAATGACCATTTAGTAATTTTTT
**
442297 ATAGTTGGGTGACCA-TTAGTATATTTT
1 ATAGTTGAATGACCATTTAGTA-ATTTT
442324 GCCTTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (29 bp):
ATAGTTGAATGACCATTTAGTAATTTTTT
Found at i:444006 original size:20 final size:19
Alignment explanation
Indices: 443964--444007 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
443954 TTATAAATTT
* *
443964 TTATTTTTGATTTTTTAAA
1 TTATTTTTGAATTTTAAAA
443983 -TATTTTTGTAATTTTAAAA
1 TTATTTTTG-AATTTTAAAA
444002 TTATTT
1 TTATTT
444008 ATTAACGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TTATTTTTGAATTTTAAAA
Found at i:445117 original size:32 final size:32
Alignment explanation
Indices: 445080--445144 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
445070 TGTCTTAAAG
445080 TATATTATCTCTATCTTATCAAATATATATTA
1 TATATTATCTCTATCTTATCAAATATATATTA
445112 TATATTATCTCTATCTTATCAAATATATATTA
1 TATATTATCTCTATCTTATCAAATATATATTA
445144 T
1 T
445145 CTCTATTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTATCTCTATCTTATCAAATATATATTA
Done.