Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 56 of 206
Found at i:15808756 original size:80 final size:78
Alignment explanation
Indices: 15808568--15808760 Score: 183
Period size: 80 Copynumber: 2.4 Consensus size: 78
15808558 AGAGGTCAAT
* * * * * * *
15808568 AAATGATCCAATTACCCCATATGGTAAAATCACCGAATAACCCCATAGGGTAAAATGACCGAATT
1 AAATGA-CCAAATAACCCATAGGGTAAAATGACCGAATAACCCCACAGGGTAAAATAACCGAAAT
15808633 ACCCTCACAGGATA
65 ACCCTCACAGGATA
* * * * *
15808647 AAATGACCGAATTACCTCTACAGGATAAAATGATCGAA-ATACCCCACAGGGTAAAATAACCGAA
1 AAATGACCAAATAACC-C-ATAGGGTAAAATGACCGAATA-ACCCCACAGGGTAAAATAACCGAA
* *
15808711 ATATCCCT-ATAGGGTA
63 ATA-CCCTCACAGGATA
15808727 AAATGACCAAAATAATCCCATAGGGTAAAATGAC
1 AAATGACC-AAATAA-CCCATAGGGTAAAATGAC
15808761 TATTATGACC
Statistics
Matches: 89, Mismatches: 19, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
78 6 0.07
79 8 0.09
80 64 0.72
81 9 0.10
82 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (78 bp):
AAATGACCAAATAACCCATAGGGTAAAATGACCGAATAACCCCACAGGGTAAAATAACCGAAATA
CCCTCACAGGATA
Found at i:15809003 original size:26 final size:26
Alignment explanation
Indices: 15808967--15809047 Score: 110
Period size: 26 Copynumber: 3.1 Consensus size: 26
15808957 TTTGCCACAT
* *
15808967 ATACTGTTACTGGCAGCTTTGCTACG
1 ATACTGATACTGGCAGCTTTGCTGCG
*
15808993 ATACTGATACTGGCAGCTCTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
*
15809019 ATGCT-ATTACTGGCAGCTTTGCTGCG
1 ATACTGA-TACTGGCAGCTTTGCTGCG
15809045 ATA
1 ATA
15809048 TTGGTGTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
25 1 0.02
26 47 0.98
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTGCG
Found at i:15812771 original size:25 final size:26
Alignment explanation
Indices: 15812732--15812849 Score: 86
Period size: 25 Copynumber: 4.7 Consensus size: 26
15812722 ACGGACACAC
*
15812732 CACAACTCGTATGAGC-TCCCTGATT
1 CACAGCTCGTATGAGCATCCCTGATT
* *
15812757 TACAGCTCGTATGAGC-TCCCTAATTT
1 CACAGCTCGTATGAGCATCCCTGA-TT
* * * * *
15812783 GA-AGCTCTTATAAGCTTCCC-GAAT
1 CACAGCTCGTATGAGCATCCCTGATT
*
15812807 CACAGCTCGTGA-GAGCAT-ACTGATT
1 CACAGCTCGT-ATGAGCATCCCTGATT
*
15812832 CATAGCTCGTATGAGCAT
1 CACAGCTCGTATGAGCAT
15812850 ACATAAATAT
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
24 4 0.06
25 60 0.83
26 8 0.11
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (26 bp):
CACAGCTCGTATGAGCATCCCTGATT
Found at i:15822890 original size:31 final size:31
Alignment explanation
Indices: 15822855--15822913 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
15822845 ATAATCATTG
*
15822855 AATTATT-TAAAATATTTCATTAAAATCACTA
1 AATTATTCAAAAATATTT-ATTAAAATCACTA
*
15822886 AATTATTCAAAAATATTTATTTAAATCA
1 AATTATTCAAAAATATTTATTAAAATCA
15822914 TTGCCACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.42
Consensus pattern (31 bp):
AATTATTCAAAAATATTTATTAAAATCACTA
Found at i:15826805 original size:31 final size:32
Alignment explanation
Indices: 15826743--15826805 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
15826733 ATAGTAGCAA
*
15826743 AATTAATAACGAAACAAAAGTTATACAATATAC
1 AATTAATAAC-AAACAAAAATTATACAATATAC
*
15826776 AATTAATAAC-AACAAAATATTA-ACTATATA
1 AATTAATAACAAACAAAA-ATTATACAATATA
15826806 ATAGCGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 14 0.52
32 3 0.11
33 10 0.37
ACGTcount: A:0.59, C:0.11, G:0.03, T:0.27
Consensus pattern (32 bp):
AATTAATAACAAACAAAAATTATACAATATAC
Found at i:15827612 original size:25 final size:23
Alignment explanation
Indices: 15827563--15827613 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
15827553 TAAAAGCTGA
* * *
15827563 AAATAAATTAATAAAAAGTAGTT
1 AAATAAATTAAGAAAAAATAATT
15827586 AAATAAATCTGAAGAAAAAATAATT
1 AAATAAAT-T-AAGAAAAAATAATT
15827611 AAA
1 AAA
15827614 CTAAGCTCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 8 0.35
24 1 0.04
25 14 0.61
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (23 bp):
AAATAAATTAAGAAAAAATAATT
Found at i:15828503 original size:12 final size:12
Alignment explanation
Indices: 15828468--15828515 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
15828458 CTTGGTTTAT
15828468 GACTTGATGAAAAA
1 GACTTGATG--AAA
*
15828482 CACTTGATGAAA
1 GACTTGATGAAA
* *
15828494 GACTTAATGAAT
1 GACTTGATGAAA
15828506 GACTTGATGA
1 GACTTGATGA
15828516 TAAAATGAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 21 0.72
14 8 0.28
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (12 bp):
GACTTGATGAAA
Found at i:15843609 original size:20 final size:20
Alignment explanation
Indices: 15843584--15843624 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
15843574 CTTCGGTAGT
*
15843584 ACTTTGGACGACAATAGAAA
1 ACTTTGGACAACAATAGAAA
15843604 ACTTTGGACAACAATAGAAA
1 ACTTTGGACAACAATAGAAA
15843624 A
1 A
15843625 TTTATTCGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20
Consensus pattern (20 bp):
ACTTTGGACAACAATAGAAA
Found at i:15844325 original size:65 final size:65
Alignment explanation
Indices: 15844217--15844346 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
15844207 TTCTCATTGA
* * *
15844217 CATTAAATGATAGAAAGTAACGTGATCACGAGTCATTTGTCTAGGAAAAATGATTTAATTACTAT
1 CATTAAATAATAGAAAGTAACGTGATCACGAGTCATTTATCTAGGAAAAATGATGTAATTACTAT
*
15844282 CATTACATAATAGAAAGTAACGTGATCACGAGTCATTTATCTAGGAAAAATGATGTAATTACTAT
1 CATTAAATAATAGAAAGTAACGTGATCACGAGTCATTTATCTAGGAAAAATGATGTAATTACTAT
15844347 TTTTTAGTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (65 bp):
CATTAAATAATAGAAAGTAACGTGATCACGAGTCATTTATCTAGGAAAAATGATGTAATTACTAT
Found at i:15846645 original size:42 final size:42
Alignment explanation
Indices: 15846599--15846683 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
15846589 AAATACATAA
* * *
15846599 TCATACATGCAGATTCATAAATGCGAATTCATACATGCGGAT
1 TCATACATACAGATCCATAAATGCGAATTCATACATACGGAT
* * * *
15846641 TCATAGATATAGATCCATAAATGTGGATTCATACATACGGAT
1 TCATACATACAGATCCATAAATGCGAATTCATACATACGGAT
15846683 T
1 T
15846684 GATAGACACA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (42 bp):
TCATACATACAGATCCATAAATGCGAATTCATACATACGGAT
Found at i:15846673 original size:14 final size:14
Alignment explanation
Indices: 15846599--15846683 Score: 62
Period size: 14 Copynumber: 6.1 Consensus size: 14
15846589 AAATACATAA
* *
15846599 TCATACATGCAGAT
1 TCATAAATGCGGAT
*
15846613 TCATAAATGCGAAT
1 TCATAAATGCGGAT
*
15846627 TCATACATGCGGAT
1 TCATAAATGCGGAT
* ***
15846641 TCATAGATATAGAT
1 TCATAAATGCGGAT
* *
15846655 CCATAAATGTGGAT
1 TCATAAATGCGGAT
* *
15846669 TCATACATACGGAT
1 TCATAAATGCGGAT
15846683 T
1 T
15846684 GATAGACACA
Statistics
Matches: 54, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 54 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (14 bp):
TCATAAATGCGGAT
Found at i:15846689 original size:42 final size:42
Alignment explanation
Indices: 15846609--15846689 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
15846599 TCATACATGC
* *
15846609 AGATTCATAAATGCGAATTCATACATGCGGATTCATAGATAT
1 AGATCCATAAATGCGAATTCATACATACGGATTCATAGATAT
* * *
15846651 AGATCCATAAATGTGGATTCATACATACGGATTGATAGA
1 AGATCCATAAATGCGAATTCATACATACGGATTCATAGA
15846690 CACAGATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (42 bp):
AGATCCATAAATGCGAATTCATACATACGGATTCATAGATAT
Found at i:15847386 original size:54 final size:54
Alignment explanation
Indices: 15847265--15847392 Score: 139
Period size: 54 Copynumber: 2.4 Consensus size: 54
15847255 AGGTTACATG
* ** *
15847265 GCCGTGTCGTAGGCCGTGTGCCAGACCGTGTAACTCTCTAACTTGTGACACACG
1 GCCGTGTCGTAGGCCGTGTGCCAGACCGTGTAACTCACTAACTTGACACACACA
* * * * * *
15847319 GCCGTGTAGTAGGCTGTGTGCTAGACCGTGTAATTCAGTGACTTGACACACACA
1 GCCGTGTCGTAGGCCGTGTGCCAGACCGTGTAACTCACTAACTTGACACACACA
* * *
15847373 GCCTTGTCTTAGGCCATGTG
1 GCCGTGTCGTAGGCCGTGTG
15847393 AAAATTACAT
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.27
Consensus pattern (54 bp):
GCCGTGTCGTAGGCCGTGTGCCAGACCGTGTAACTCACTAACTTGACACACACA
Found at i:15849638 original size:2 final size:2
Alignment explanation
Indices: 15849631--15849675 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
15849621 GTAGTTTACC
15849631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15849673 AT A
1 AT A
15849676 CGTAACATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15854345 original size:49 final size:48
Alignment explanation
Indices: 15854286--15854421 Score: 148
Period size: 49 Copynumber: 2.8 Consensus size: 48
15854276 ACCAGTGGAC
* * *
15854286 GCCAACCTGGTTAACAACTAACATGTCCTACTAGTGGCCCA-ACATACAT
1 GCCAATCTGGTTAGCAACTAACATGTCCTACCAGTGGCCCACACAT-C-T
* * *
15854335 GCCAATCTGGTTAGCAACTAGCATGCCCTACCAGTGGTCCATCACATCT
1 GCCAATCTGGTTAGCAACTAACATGTCCTACCAGTGGCCCA-CACATCT
* * * *
15854384 GTCATTCTAGTTTGCAACTAACATGTCCTACCAGTGGC
1 GCCAATCTGGTTAGCAACTAACATGTCCTACCAGTGGC
15854422 TATTTATCTC
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
49 67 0.93
50 1 0.01
51 4 0.06
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (48 bp):
GCCAATCTGGTTAGCAACTAACATGTCCTACCAGTGGCCCACACATCT
Found at i:15857821 original size:33 final size:33
Alignment explanation
Indices: 15857762--15857844 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
15857752 TACATATATA
* * **
15857762 CATATATATTATAGAAAACATGACCCAAAAACG
1 CATATATATTATATATAACAAAACCCAAAAACG
* *
15857795 CATATATATTATATATAACAAAACCCATATACG
1 CATATATATTATATATAACAAAACCCAAAAACG
15857828 -ATTATATATTATATATA
1 CA-TATATATTATATATA
15857845 TACACATACC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 1 0.02
33 42 0.98
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.31
Consensus pattern (33 bp):
CATATATATTATATATAACAAAACCCAAAAACG
Found at i:15858500 original size:18 final size:18
Alignment explanation
Indices: 15858477--15858515 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
15858467 AAATGGAAAG
15858477 TTAGAAAAATGAATTATA
1 TTAGAAAAATGAATTATA
15858495 TTAGAAAAATGAATTATA
1 TTAGAAAAATGAATTATA
15858513 TTA
1 TTA
15858516 TTTCCAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (18 bp):
TTAGAAAAATGAATTATA
Found at i:15858866 original size:273 final size:276
Alignment explanation
Indices: 15858506--15859058 Score: 886
Period size: 273 Copynumber: 2.0 Consensus size: 276
15858496 TAGAAAAATG
* *
15858506 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTTAATGTCTTTTATATTTTGACCAAAATTAATTAA
* * *
15858571 TATAAATATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTTTATGAAACAAATT
66 TATAAATATTTACATGAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAAACAAATT
*
15858636 CATATATATTAATTATATT-TTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGA-TC
131 C--ATATATTAAATATATTGTTTT-CAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACT-
* *
15858699 GAAATTAA-T-ATA-AA-TGTTTATATTAATAAATTCGGTAAAATATATACGATTAATATTTCGT
192 GAAATTAATTAATATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTCGT
15858760 ATGAATCAAATTCATATATT
257 ATGAATCAAATTCATATATT
15858780 AATTATATTATTTCCAAAAGAATATTAATTTTAAT-TCTTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTTAATGTCTTTTATATTTTGACCAAAATTAATTAA
* * * * * *
15858844 TATAACTGTTTACATGAATAAATTCGGTAATATATATAGAGTTAATATTTTGTATGAATCAAATT
66 TATAAATATTTACATGAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAAACAAATT
15858909 CATATATTAAATATATTGTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAA
131 CATATATTAAATATATTGTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAA
*
15858974 TTAATTAATATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGA
196 TTAATTAATATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTCGTATGA
15859039 ATCAAATTCATATATT
261 ATCAAATTCATATATT
15859055 AATT
1 AATT
15859059 TTATCTATGT
Statistics
Matches: 258, Mismatches: 15, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
271 60 0.23
272 6 0.02
273 88 0.34
274 36 0.14
275 68 0.26
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (276 bp):
AATTATATTATTTCCAAAAGAATATTAATTTTAATGTCTTTTATATTTTGACCAAAATTAATTAA
TATAAATATTTACATGAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAAACAAATT
CATATATTAAATATATTGTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAA
TTAATTAATATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTCGTATGA
ATCAAATTCATATATT
Found at i:15859027 original size:138 final size:138
Alignment explanation
Indices: 15858506--15859058 Score: 855
Period size: 138 Copynumber: 4.0 Consensus size: 138
15858496 TAGAAAAATG
*
15858506 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *
15858571 TATAAATATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTTTATGAAACAAATT
66 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
15858636 CATATATATT
131 C--ATATATT
* *
15858646 AATTATATTTTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAA-T-A
1 AATTATATTATTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *
15858709 TA-AA-TGTTTATATTAATAAATTCGGTAAAATATATACGATTAATATTTCGTATGAATCAAATT
66 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
15858772 CATATATT
131 CATATATT
** *
15858780 AATTATATTATTTCCAAAAGAATATTAATTTTAAT-TCTTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * * * *
15858844 TATAACTGTTTACATGAATAAATTCGGTAATATATATAGAGTTAATATTTTGTATGAATCAAATT
66 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
15858909 CATATATT
131 CATATATT
* * * *
15858917 AAATATATTGTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
15858982 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
15859047 CATATATT
131 CATATATT
15859055 AATT
1 AATT
15859059 TTATCTATGT
Statistics
Matches: 374, Mismatches: 34, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
133 23 0.06
134 40 0.11
135 3 0.01
136 57 0.15
137 92 0.25
138 100 0.27
139 1 0.00
140 58 0.16
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (138 bp):
AATTATATTATTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:15860964 original size:45 final size:45
Alignment explanation
Indices: 15860905--15861025 Score: 154
Period size: 45 Copynumber: 2.7 Consensus size: 45
15860895 TATTTACCAT
* * *
15860905 GATGTCATATCATCTTTCAGCCATGGTCTTACTAAT-TTATATCAC
1 GATGTCATAGCATCTTTCAGCTATGGTCTTACTAATCCT-TATCAC
* * * * *
15860950 GATGCCATAGCATCTTTTAGCTATGGTCTTACTCATCCTTGTCAT
1 GATGTCATAGCATCTTTCAGCTATGGTCTTACTAATCCTTATCAC
15860995 GATGTCATAGCATCTTTCAGCTATGGTCTTA
1 GATGTCATAGCATCTTTCAGCTATGGTCTTA
15861026 TTCATTTCAA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 64 0.98
46 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (45 bp):
GATGTCATAGCATCTTTCAGCTATGGTCTTACTAATCCTTATCAC
Found at i:15861564 original size:26 final size:26
Alignment explanation
Indices: 15861532--15861585 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
15861522 TGTTTAGACT
15861532 TAGTTTTCTAGAAATATGCAAAATCC
1 TAGTTTTCTAGAAATATGCAAAATCC
15861558 TAGTTTTCTAGAAATATGCAAAATCC
1 TAGTTTTCTAGAAATATGCAAAATCC
15861584 TA
1 TA
15861586 AAAATGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (26 bp):
TAGTTTTCTAGAAATATGCAAAATCC
Found at i:15863241 original size:21 final size:22
Alignment explanation
Indices: 15863217--15863262 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
15863207 ATTGATTGTC
15863217 TTTCTATTTAAATCAATT-ATT
1 TTTCTATTTAAATCAATTCATT
* * *
15863238 TTTCTGTTTGAATCGATTCATT
1 TTTCTATTTAAATCAATTCATT
15863260 TTT
1 TTT
15863263 GTTTAAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.59
Consensus pattern (22 bp):
TTTCTATTTAAATCAATTCATT
Found at i:15863296 original size:20 final size:20
Alignment explanation
Indices: 15863223--15863297 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
15863213 TGTCTTTCTA
*
15863223 TTTAAATCAATT-ATTTTTCTG
1 TTTAAATCGATTCA-TTTT-TG
*
15863244 TTTGAATCGATTCATTTTTG
1 TTTAAATCGATTCATTTTTG
* *
15863264 TTTAAACCAATTC-TTTGTTG
1 TTTAAATCGATTCATTT-TTG
*
15863284 TTTAATTCGATTCA
1 TTTAAATCGATTCA
15863298 AACTCCAACA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.07
20 25 0.58
21 14 0.33
22 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.53
Consensus pattern (20 bp):
TTTAAATCGATTCATTTTTG
Found at i:15864426 original size:16 final size:16
Alignment explanation
Indices: 15864407--15864443 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
15864397 TACGTTTTGA
15864407 GGGTTCTTTGTTTTTC
1 GGGTTCTTTGTTTTTC
15864423 GGGTTCTTTGTTTTTC
1 GGGTTCTTTGTTTTTC
15864439 GGGTT
1 GGGTT
15864444 TTCGGGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.11, G:0.30, T:0.59
Consensus pattern (16 bp):
GGGTTCTTTGTTTTTC
Found at i:15866409 original size:16 final size:16
Alignment explanation
Indices: 15866390--15866426 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
15866380 TACGTTTTAA
15866390 GGGTTCTTTGTTTTTC
1 GGGTTCTTTGTTTTTC
15866406 GGGTTCTTTGTTTTTC
1 GGGTTCTTTGTTTTTC
15866422 GGGTT
1 GGGTT
15866427 TTCGGGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.11, G:0.30, T:0.59
Consensus pattern (16 bp):
GGGTTCTTTGTTTTTC
Found at i:15868256 original size:2 final size:2
Alignment explanation
Indices: 15868249--15868273 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15868239 TTTTTCTTGT
15868249 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15868274 GGTTTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15869535 original size:2 final size:2
Alignment explanation
Indices: 15869528--15869562 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15869518 TCGTTGGGTT
15869528 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
15869563 ACCACGAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:15872418 original size:7 final size:7
Alignment explanation
Indices: 15872417--15872455 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
15872407 TAAAAAGAAA
15872417 AAAAAAG
1 AAAAAAG
*
15872424 AAAAAAA
1 AAAAAAG
15872431 AAAGAAAG
1 AAA-AAAG
15872439 AAAAAAG
1 AAAAAAG
15872446 AAAAAAG
1 AAAAAAG
15872453 AAA
1 AAA
15872456 GAGAACAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:15872428 original size:11 final size:11
Alignment explanation
Indices: 15872408--15872457 Score: 75
Period size: 11 Copynumber: 4.6 Consensus size: 11
15872398 TTTAAACTTT
15872408 AAAAAG-AAAA
1 AAAAAGAAAAA
15872418 AAAAAGAAAAA
1 AAAAAGAAAAA
*
15872429 AAAAAGAAAGA
1 AAAAAGAAAAA
15872440 AAAAAGAAAAA
1 AAAAAGAAAAA
*
15872451 AGAAAGA
1 AAAAAGA
15872458 GAACAAATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
10 6 0.17
11 30 0.83
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:15874199 original size:43 final size:44
Alignment explanation
Indices: 15874139--15874225 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
15874129 AATCTGATTG
*
15874139 TTGTTTTATCTATTTTC-TGATTGATGCAAATATTGTTGATGTA
1 TTGTTTTATCTATTTTCTTGATTGATGCAAATATTCTTGATGTA
*
15874182 TTGTTTTATTCTA-TTTCTTGATTGATGCAAATTTTCTTGATGTA
1 TTGTTTTA-TCTATTTTCTTGATTGATGCAAATATTCTTGATGTA
15874226 GACTGATCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
43 12 0.30
44 28 0.70
ACGTcount: A:0.22, C:0.08, G:0.15, T:0.55
Consensus pattern (44 bp):
TTGTTTTATCTATTTTCTTGATTGATGCAAATATTCTTGATGTA
Found at i:15876389 original size:3 final size:3
Alignment explanation
Indices: 15876381--15876424 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
15876371 TTATAAATGT
*
15876381 ATC ATC ATC ATC ATC ATC AGC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
15876425 GTATGTAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:15877771 original size:2 final size:2
Alignment explanation
Indices: 15877760--15877792 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
15877750 ATCAGTGACA
15877760 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
15877793 GAAACTGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:15891859 original size:102 final size:101
Alignment explanation
Indices: 15891667--15891859 Score: 255
Period size: 102 Copynumber: 1.9 Consensus size: 101
15891657 AGTTGCTAGG
* * *
15891667 TCACGTGTGTAGTACTATGTGCAAGCTACTACATGTACCGGAATGATAGGTCGCATGTGCAGTAC
1 TCACGTATGTAGTACTATGTGCAAGCTACTACATGTACCGGAATGAAAGGTCACATGTGCAGTAC
*
15891732 CATGTGCAGGCTACCATGCGTACCGGATAGCTTCGA
66 CATGTGCAGGCTACCATGCGAACCGGATAGCTTCGA
* * *
15891768 TCACGTATGTAGTACTATGTGC-AGACTACTACGTGTATC-GAATGAAAATGGTCACATGTGTAG
1 TCACGTATGTAGTACTATGTGCAAG-CTACTACATGTACCGGAATG-AAA-GGTCACATGTGCAG
* * *
15891831 TACTATGTGCAGGCTACTATGTGAACCGG
63 TACCATGTGCAGGCTACCATGCGAACCGG
15891860 GTATCATTTA
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
100 7 0.09
101 35 0.44
102 37 0.47
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (101 bp):
TCACGTATGTAGTACTATGTGCAAGCTACTACATGTACCGGAATGAAAGGTCACATGTGCAGTAC
CATGTGCAGGCTACCATGCGAACCGGATAGCTTCGA
Found at i:15899538 original size:14 final size:14
Alignment explanation
Indices: 15899516--15899566 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
15899506 AAATTATTAT
* *
15899516 TTAATTAATTGAAA
1 TTAAATAATAGAAA
15899530 TTAAATAATAGAAA
1 TTAAATAATAGAAA
* *
15899544 TTCAA-AGTAGAAA
1 TTAAATAATAGAAA
15899557 TTAAACTAAT
1 TTAAA-TAAT
15899567 TAGTCATCAC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
13 11 0.38
14 16 0.55
15 2 0.07
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (14 bp):
TTAAATAATAGAAA
Found at i:15902596 original size:21 final size:22
Alignment explanation
Indices: 15902565--15902616 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
15902555 TTTCAAGCTT
*
15902565 CCAAGCTCCATAGTAAGTGATC
1 CCAAGCCCCATAGTAAGTGATC
15902587 CCAA-CCCCATAGTAAGTGATC
1 CCAAGCCCCATAGTAAGTGATC
*
15902608 TCAAGCCCC
1 CCAAGCCCC
15902617 GTTTTTAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.31, C:0.35, G:0.15, T:0.19
Consensus pattern (22 bp):
CCAAGCCCCATAGTAAGTGATC
Found at i:15903009 original size:29 final size:30
Alignment explanation
Indices: 15902950--15903009 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
15902940 TCCGAGCCTT
**
15902950 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGTAAAAACTTA
* *
15902980 GGGGCAAAATTGTAATTTTG-AAAAACTTA
1 GGGGCAAAAATGTAATTATGTAAAAACTTA
15903009 G
1 G
15903010 AGTCGAGGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGTAAAAACTTA
Found at i:15903237 original size:13 final size:13
Alignment explanation
Indices: 15903219--15903250 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
15903209 TTTCCAGCAA
15903219 TTATGAATTTATT
1 TTATGAATTTATT
15903232 TTATGAATTTATT
1 TTATGAATTTATT
*
15903245 TGATGA
1 TTATGA
15903251 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:15903465 original size:50 final size:50
Alignment explanation
Indices: 15903345--15903586 Score: 279
Period size: 50 Copynumber: 4.7 Consensus size: 50
15903335 ATTTGGGTAA
* * *
15903345 AGAGATCCCATATAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--AAGA-C--G
*
15903401 AGAGGTGCCC-TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGT-CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
15903451 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
15903501 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
15903551 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
15903587 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 17, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
49 3 0.02
50 90 0.54
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 35 0.21
57 3 0.02
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:15903538 original size:100 final size:103
Alignment explanation
Indices: 15903345--15903594 Score: 344
Period size: 100 Copynumber: 2.4 Consensus size: 103
15903335 ATTTGGGTAA
* *
15903345 AGAGATCCCATATAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTGCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* * *
15903410 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * *
15903451 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
*
15903513 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
15903551 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
15903595 GTTATTATCA
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
100 50 0.38
101 39 0.30
105 2 0.02
106 39 0.30
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:15909446 original size:41 final size:41
Alignment explanation
Indices: 15909389--15909574 Score: 320
Period size: 41 Copynumber: 4.5 Consensus size: 41
15909379 TTTAACATAT
* * *
15909389 TCACCGGCACTTAGCCTACTAGGCTTATAGCCTGATTCTA-A
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTC-AGA
15909430 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
15909471 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
15909512 TCACCGTCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
15909553 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
15909575 ACGTAAAGTC
Statistics
Matches: 139, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
40 1 0.01
41 138 0.99
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:15909598 original size:82 final size:81
Alignment explanation
Indices: 15909389--15909628 Score: 306
Period size: 82 Copynumber: 2.9 Consensus size: 81
15909379 TTTAACATAT
* * *
15909389 TCACCGGCACTTAGCCTACTAGGCTTATAGCCTGATTCTAATCACCGGCACTTAGCCTGCTAGGT
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTAT-ATCACCGGCACTTAGCCTGCTAGGT
15909454 TTATAACCTGATTCAGA
65 TTATAACCTGATTCAGA
* * *
15909471 TCACCGGCACTTAGCCTGCTAGGTTTATAA-CCTGATTCAGATCACCGTCACTTAGCCTGCTAGG
1 TCACCGGCACTTAGCCTGCTAGGCTTA-AAGCCTGATT-ATATCACCGGCACTTAGCCTGCTAGG
15909535 TTTATAACCTGATTCAGA
64 TTTATAACCTGATTCAGA
* * * * *
15909553 TCACCGGCACTTAGCCTGCTAGACGTAAAGTCTGAATTATTTCACCGGC-CTTAAGCCTGTTAGG
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTG-ATTATATCACCGGCACTT-AGCCTGCTAGG
15909617 TTT-TAAACCTGA
64 TTTAT-AACCTGA
15909629 AAATTTCAAT
Statistics
Matches: 138, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
81 6 0.04
82 128 0.93
83 4 0.03
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (81 bp):
TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTATATCACCGGCACTTAGCCTGCTAGGTT
TATAACCTGATTCAGA
Found at i:15909610 original size:123 final size:123
Alignment explanation
Indices: 15909389--15909628 Score: 301
Period size: 123 Copynumber: 2.0 Consensus size: 123
15909379 TTTAACATAT
* **
15909389 TCACCGGCACTTAGCCTACTAGGCTTATAGCCTGATTCTAATCACCGGCACTTAGCCTGCTAGGT
1 TCACCGGCACTTAGCCTACTAGGCTTATAACCTGATTCTAATCACCGGCACTTAGCCTGCTAGAC
*
15909454 TTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGG-TTTATAACCTGATTCAGA
66 GTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGGTTTTA-AACCTGATTCAGA
* * *
15909512 TCACCGTCACTTAGCCTGCTAGGTTTATAACCTGATTC-AGATCACCGGCACTTAGCCTGCTAGA
1 TCACCGGCACTTAGCCTACTAGGCTTATAACCTGATTCTA-ATCACCGGCACTTAGCCTGCTAGA
* ** *
15909576 CGTA-AAGTCTGAATT-ATTTCACCGGC-CTTAAGCCTGTTAGGTTTTAAACCTGA
65 CGTATAA-CCTG-ATTCAGATCACCGGCACTT-AGCCTGCTAGGTTTTAAACCTGA
15909629 AAATTTCAAT
Statistics
Matches: 101, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
122 6 0.06
123 88 0.87
124 7 0.07
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (123 bp):
TCACCGGCACTTAGCCTACTAGGCTTATAACCTGATTCTAATCACCGGCACTTAGCCTGCTAGAC
GTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGGTTTTAAACCTGATTCAGA
Found at i:15922614 original size:26 final size:26
Alignment explanation
Indices: 15922576--15922626 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
15922566 CTTGTTGCGT
*
15922576 CCTCAGAATGACACCAATATGACTTG
1 CCTCAGAACGACACCAATATGACTTG
* * *
15922602 CCTCGGAACGACACCATTGTGACTT
1 CCTCAGAACGACACCAATATGACTT
15922627 TCCTTGAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (26 bp):
CCTCAGAACGACACCAATATGACTTG
Found at i:15925648 original size:16 final size:17
Alignment explanation
Indices: 15925627--15925658 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
15925617 AAATATGCAA
15925627 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
15925643 TCACATAACTTCATAT
1 TCACATAACTTCATAT
15925659 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:15925885 original size:43 final size:43
Alignment explanation
Indices: 15925819--15925989 Score: 158
Period size: 43 Copynumber: 4.0 Consensus size: 43
15925809 GACTCGTACA
* *
15925819 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAATCACATATCG
1 ATGCC-ACTGTCCCAGACAG-GGTCTTACATGAAAACACATATCG
* * * *
15925862 ATGCCACTGTCTCAGACAGGGTCTTACA-CAAATCAAATA-CG
1 ATGCCACTGTCCCAGACAGGGTCTTACATGAAAACACATATCG
* * * *
15925903 ATGCCAATGTCCCAAACATGGTCTTACATGTAAACACA-AGTCG
1 ATGCCACTGTCCCAGACAGGGTCTTACATGAAAACACATA-TCG
15925946 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAAACACATATCG
1 ATGCC-ACTGTCCCAGACAG-GGTCTTACATGAAAACACATATCG
15925989 A
1 A
15925990 AATCCTATGT
Statistics
Matches: 104, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
41 27 0.26
42 15 0.14
43 59 0.57
44 3 0.03
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACAGGGTCTTACATGAAAACACATATCG
Found at i:15925962 original size:84 final size:84
Alignment explanation
Indices: 15925819--15925973 Score: 217
Period size: 84 Copynumber: 1.8 Consensus size: 84
15925809 GACTCGTACA
* * * *
15925819 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACTGTCTCAGACAG-GG
1 ATGCCAACGTCCCAAACATGGTCTTACATGTAAACACATATCGATGCCACTGTCCCAGAC-GTGG
15925883 TCTTACACAAATCAAATACG
65 TCTTACACAAATCAAATACG
*
15925903 ATGCCAATGTCCCAAACATGGTCTTACATGTAAACACA-AGTCGATGCCAAC-GTCCCAGACGTG
1 ATGCCAACGTCCCAAACATGGTCTTACATGTAAACACATA-TCGATGCC-ACTGTCCCAGACGTG
15925966 GTCTTACA
64 GTCTTACA
15925974 TGAAAACACA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
83 2 0.03
84 59 0.94
85 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (84 bp):
ATGCCAACGTCCCAAACATGGTCTTACATGTAAACACATATCGATGCCACTGTCCCAGACGTGGT
CTTACACAAATCAAATACG
Found at i:15931155 original size:35 final size:35
Alignment explanation
Indices: 15931109--15931182 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
15931099 ACAAGGAGAG
15931109 AAAGAAAAAAATTAGGGTTCATGCTATTATTTTGT
1 AAAGAAAAAAATTAGGGTTCATGCTATTATTTTGT
15931144 AAAGAAAAAAATTAGGGTTCATGCTATTATTTTGT
1 AAAGAAAAAAATTAGGGTTCATGCTATTATTTTGT
15931179 AAAG
1 AAAG
15931183 CTTCAATTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (35 bp):
AAAGAAAAAAATTAGGGTTCATGCTATTATTTTGT
Found at i:15931921 original size:22 final size:22
Alignment explanation
Indices: 15931896--15931969 Score: 103
Period size: 22 Copynumber: 3.4 Consensus size: 22
15931886 TAGTGCCTAG
* * *
15931896 CAGGATTAGTGTCGGTTTTATT
1 CAGGCTTAATGTCGGTGTTATT
*
15931918 CAGGCTTAATGCCGGTGTTATT
1 CAGGCTTAATGTCGGTGTTATT
*
15931940 CAGTCTTAATGTCGGTGTTATT
1 CAGGCTTAATGTCGGTGTTATT
15931962 CAGGCTTA
1 CAGGCTTA
15931970 GTGCCTAGCA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.41
Consensus pattern (22 bp):
CAGGCTTAATGTCGGTGTTATT
Found at i:15932270 original size:43 final size:43
Alignment explanation
Indices: 15932223--15932366 Score: 200
Period size: 43 Copynumber: 3.3 Consensus size: 43
15932213 TGTGAAAAAA
*
15932223 CGCTATAGAACATGATCTTTAGTGGCGCTTTTATCACAAACGC
1 CGCTAAAGAACATGATCTTTAGTGGCGCTTTTATCACAAACGC
* *
15932266 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGC
1 CGCTAAAGAACATGATCTTTAGTGGCGCTTTTATCACAAACGC
* * *
15932309 CGCTAAAATAACATGATCTTTGGTGGCG-TTTTACCCACAAACGC
1 CGCT-AAAGAACATGATCTTTAGTGGCGCTTTTA-TCACAAACGC
*
15932353 CGCTAAAGATCATG
1 CGCTAAAGAACATG
15932367 CCTTTTAGCG
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
43 57 0.64
44 32 0.36
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (43 bp):
CGCTAAAGAACATGATCTTTAGTGGCGCTTTTATCACAAACGC
Found at i:15933639 original size:7 final size:7
Alignment explanation
Indices: 15933627--15933745 Score: 53
Period size: 7 Copynumber: 16.7 Consensus size: 7
15933617 ACTAATTAAT
15933627 CTAAACC
1 CTAAACC
15933634 CTAAACCC
1 CTAAA-CC
*
15933642 CTAACCC
1 CTAAACC
15933649 CTAATA-C
1 CTAA-ACC
* *
15933656 TTAACCC
1 CTAAACC
*
15933663 CTAAATC
1 CTAAACC
* *
15933670 TTGAACC
1 CTAAACC
*
15933677 C-CAACC
1 CTAAACC
15933683 CTTAAACC
1 C-TAAACC
*
15933691 GTAAACC
1 CTAAACC
*
15933698 ATAAACC
1 CTAAACC
* *
15933705 ATAAATC
1 CTAAACC
*
15933712 ATAAACC
1 CTAAACC
15933719 CTAAACC
1 CTAAACC
*
15933726 CATAATCC
1 C-TAAACC
*
15933734 ATAAACC
1 CTAAACC
*
15933741 TTAAA
1 CTAAA
15933746 ATAACATCTT
Statistics
Matches: 84, Mismatches: 22, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
6 5 0.06
7 64 0.76
8 15 0.18
ACGTcount: A:0.43, C:0.35, G:0.02, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:15933702 original size:14 final size:14
Alignment explanation
Indices: 15933685--15933745 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 14
15933675 CCCCAACCCT
*
15933685 TAAACCGTAAACCA
1 TAAACCATAAACCA
*
15933699 TAAACCATAAATCA
1 TAAACCATAAACCA
*
15933713 TAAACCCTAAACCCA
1 TAAACCATAAA-CCA
* *
15933728 TAATCCATAAACCT
1 TAAACCATAAACCA
15933742 TAAA
1 TAAA
15933746 ATAACATCTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 27 0.71
15 11 0.29
ACGTcount: A:0.51, C:0.28, G:0.02, T:0.20
Consensus pattern (14 bp):
TAAACCATAAACCA
Found at i:15933709 original size:21 final size:22
Alignment explanation
Indices: 15933679--15933745 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
15933669 CTTGAACCCC
* *
15933679 AACCCTTAAACCGTAAACCATA
1 AACCCATAAACCATAAACCATA
* *
15933701 AA-CCATAAATCATAAACCCTA
1 AACCCATAAACCATAAACCATA
* *
15933722 AACCCATAATCCATAAACCTTA
1 AACCCATAAACCATAAACCATA
15933744 AA
1 AA
15933746 ATAACATCTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
21 17 0.46
22 20 0.54
ACGTcount: A:0.49, C:0.30, G:0.01, T:0.19
Consensus pattern (22 bp):
AACCCATAAACCATAAACCATA
Found at i:15933803 original size:14 final size:14
Alignment explanation
Indices: 15933679--15933808 Score: 66
Period size: 14 Copynumber: 9.1 Consensus size: 14
15933669 CTTGAACCCC
*
15933679 AACCCTTAAACCGTA
1 AACCC-TAAACCATA
*
15933694 AACCATAAACCATA
1 AACCCTAAACCATA
* * *
15933708 AATCATAAACCCTA
1 AACCCTAAACCATA
*
15933722 AACCCATAATCCATA
1 AACCC-TAAACCATA
*
15933737 AACCTTAAA--ATA
1 AACCCTAAACCATA
** **
15933749 ACATCTTTTAAACTTTA
1 A-A-C-CCTAAACCATA
*
15933766 AACCCTAAAACATA
1 AACCCTAAACCATA
* *
15933780 TACCCCAAACCATA
1 AACCCTAAACCATA
*
15933794 AACCCTAAACTATA
1 AACCCTAAACCATA
15933808 A
1 A
15933809 TGATAATTAA
Statistics
Matches: 86, Mismatches: 23, Indels: 13
0.70 0.19 0.11
Matches are distributed among these distances:
12 4 0.05
13 1 0.01
14 56 0.65
15 21 0.24
16 1 0.01
17 3 0.03
ACGTcount: A:0.48, C:0.28, G:0.01, T:0.22
Consensus pattern (14 bp):
AACCCTAAACCATA
Found at i:15933951 original size:7 final size:7
Alignment explanation
Indices: 15933941--15934000 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
15933931 CCTAAATCAC
*
15933941 TAACTCT
1 TAACCCT
15933948 TAACCCT
1 TAACCCT
15933955 TAA-CCT
1 TAACCCT
*
15933961 CTAACCCC
1 -TAACCCT
15933969 TAACCCAT
1 TAACCC-T
* *
15933977 AAACCCA
1 TAACCCT
15933984 TAACCCT
1 TAACCCT
*
15933991 TAAACCT
1 TAACCCT
15933998 TAA
1 TAA
15934001 ATCCTAGCCT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
6 3 0.07
7 32 0.76
8 7 0.17
ACGTcount: A:0.37, C:0.38, G:0.00, T:0.25
Consensus pattern (7 bp):
TAACCCT
Found at i:15933981 original size:15 final size:15
Alignment explanation
Indices: 15933963--15933996 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
15933953 CTTAACCTCT
*
15933963 AACCCCTAACCCATA
1 AACCCATAACCCATA
*
15933978 AACCCATAACCCTTA
1 AACCCATAACCCATA
15933993 AACC
1 AACC
15933997 TTAAATCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (15 bp):
AACCCATAACCCATA
Found at i:15934028 original size:14 final size:14
Alignment explanation
Indices: 15934011--15934045 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
15934001 ATCCTAGCCT
15934011 CTAAACCATAATCC
1 CTAAACCATAATCC
* *
15934025 CTAATCCATACTCC
1 CTAAACCATAATCC
15934039 CTAAACC
1 CTAAACC
15934046 TTAAAATACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.37, C:0.40, G:0.00, T:0.23
Consensus pattern (14 bp):
CTAAACCATAATCC
Found at i:15934521 original size:41 final size:41
Alignment explanation
Indices: 15934386--15934527 Score: 203
Period size: 41 Copynumber: 3.5 Consensus size: 41
15934376 TAAAATGTTT
* * *
15934386 TTAGAGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCCAGCA
1 TTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCACCAGCA
*
15934427 TTAGCGGCGTTTTCTCAAAAACGCCGCTAAAGCCACCAGCA
1 TTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCACCAGCA
* * *
15934468 TTAGTGACGCTTTCTCAAAAATGCCGCTAAAGCCACCAGCA
1 TTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCACCAGCA
* *
15934509 TTAGCGGTGCTTTTTCAAA
1 TTAGCGGCGCTTTCTCAAA
15934528 TACTTGGTTC
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (41 bp):
TTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCACCAGCA
Found at i:15941232 original size:29 final size:30
Alignment explanation
Indices: 15941173--15941230 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
15941163 TCCGAGCCTT
**
15941173 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATAAAAAAGTTTA
* *
15941203 GGGGCAAAATTGTAATTTTAAAAAAGTT
1 GGGGCAAAAATGTAATTATAAAAAAGTT
15941231 AGAGTCGAGG
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:0.03, G:0.22, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATAAAAAAGTTTA
Found at i:15941461 original size:13 final size:13
Alignment explanation
Indices: 15941443--15941473 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
15941433 TTCCAGCAAC
15941443 TATGAATTTATTT
1 TATGAATTTATTT
15941456 TATGAATTTATTT
1 TATGAATTTATTT
*
15941469 GATGA
1 TATGA
15941474 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:15941682 original size:50 final size:50
Alignment explanation
Indices: 15941568--15941809 Score: 286
Period size: 50 Copynumber: 4.7 Consensus size: 50
15941558 ATTTGGGTAA
* * *
15941568 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--AAGA-C--G
* *
15941624 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
15941674 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
15941724 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
15941774 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
15941810 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 92 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:15941760 original size:100 final size:103
Alignment explanation
Indices: 15941568--15941817 Score: 353
Period size: 100 Copynumber: 2.4 Consensus size: 103
15941558 ATTTGGGTAA
15941568 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATAAGAGGTCCC
* * *
15941633 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * * *
15941674 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
*
15941736 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
15941774 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
15941818 GTTATTATCA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 50 0.38
101 39 0.30
105 2 0.02
106 40 0.31
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:15949430 original size:9 final size:9
Alignment explanation
Indices: 15949416--15949446 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
15949406 GTTAAACGAA
15949416 TCGAGTTAT
1 TCGAGTTAT
*
15949425 TCGAGTTAA
1 TCGAGTTAT
15949434 TCGAGTTAT
1 TCGAGTTAT
15949443 TCGA
1 TCGA
15949447 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:15950559 original size:5 final size:5
Alignment explanation
Indices: 15950549--15950574 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
15950539 CTCGAAAATT
15950549 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
15950575 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:15955122 original size:17 final size:17
Alignment explanation
Indices: 15955100--15955133 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
15955090 GTGATGTGCC
15955100 AAAGTATTAGTATTCTT
1 AAAGTATTAGTATTCTT
15955117 AAAGTATTAGTATTCTT
1 AAAGTATTAGTATTCTT
15955134 TGTTGTTGCC
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:0.12, T:0.47
Consensus pattern (17 bp):
AAAGTATTAGTATTCTT
Found at i:15966985 original size:45 final size:47
Alignment explanation
Indices: 15966934--15967026 Score: 118
Period size: 49 Copynumber: 2.0 Consensus size: 47
15966924 CATATAGAAC
* * * *
15966934 TATACTTCTTTTATTT-TATT-TTAGAATAAGGTTTTTCAATCTTAT
1 TATACTTCATCTATTTATATTATTAGAATAAGGTGTTTCAACCTTAT
15966979 TATACTTCATCTATTTGATATTGATTAGAATAAGGTGTTTCAACCTTA
1 TATACTTCATCTATTT-ATATT-ATTAGAATAAGGTGTTTCAACCTTA
15967027 CTACACTCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
45 14 0.35
47 4 0.10
49 22 0.55
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.51
Consensus pattern (47 bp):
TATACTTCATCTATTTATATTATTAGAATAAGGTGTTTCAACCTTAT
Found at i:15973443 original size:13 final size:13
Alignment explanation
Indices: 15973427--15973492 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
15973417 TTTAAACCAA
15973427 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
15973440 ACTTATCAAAAGC
1 ACTTTTCAAAAGC
* *
15973453 ACTTCTCAAAAAC
1 ACTTTTCAAAAGC
*
15973466 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
*
15973479 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
15973492 A
1 A
15973493 TTGCCAAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
12 3 0.07
13 37 0.84
14 4 0.09
ACGTcount: A:0.41, C:0.26, G:0.05, T:0.29
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:15974455 original size:25 final size:25
Alignment explanation
Indices: 15974421--15974472 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
15974411 CTTGATGATG
*
15974421 GAAGATTCCACTTATAATTTTTAAT
1 GAAGATTCCACTTATAATTGTTAAT
15974446 GAAGATTCCACTTATAATTGTTAAT
1 GAAGATTCCACTTATAATTGTTAAT
15974471 GA
1 GA
15974473 TGGATTAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (25 bp):
GAAGATTCCACTTATAATTGTTAAT
Found at i:15975667 original size:30 final size:30
Alignment explanation
Indices: 15975629--15975743 Score: 140
Period size: 30 Copynumber: 3.8 Consensus size: 30
15975619 GGGTAATCTC
*
15975629 GATATAATGTCATCTTGTGTGAGCAACCTG
1 GATATAATGTCAGCTTGTGTGAGCAACCTG
* *
15975659 GTTATAATGTCAGCTTGTGTGAGCAACCTT
1 GATATAATGTCAGCTTGTGTGAGCAACCTG
* * * *
15975689 GAAATATTGTCAGCTTATGTGAGCAACCTT
1 GATATAATGTCAGCTTGTGTGAGCAACCTG
* * *
15975719 GAAATATTGTCAGCTTATGTGAGCA
1 GATATAATGTCAGCTTGTGTGAGCA
15975744 TTTCATTCTC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 78 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34
Consensus pattern (30 bp):
GATATAATGTCAGCTTGTGTGAGCAACCTG
Found at i:15980987 original size:28 final size:28
Alignment explanation
Indices: 15980955--15981009 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
15980945 ATGGTTTGAA
*
15980955 TTATTTTTA-ACTAAGTTTTCTGGATTTT
1 TTATTTTTAGACTAAGCTTT-TGGATTTT
15980983 TTATTTTTAGACTAAGCTTTTGGATTT
1 TTATTTTTAGACTAAGCTTTTGGATTT
15981010 GATTTTGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.22, C:0.07, G:0.13, T:0.58
Consensus pattern (28 bp):
TTATTTTTAGACTAAGCTTTTGGATTTT
Found at i:15990417 original size:20 final size:20
Alignment explanation
Indices: 15990392--15990431 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
15990382 CCTAAAATGA
*
15990392 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
15990412 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
15990432 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:15990555 original size:20 final size:20
Alignment explanation
Indices: 15990530--15990568 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
15990520 GTTTTTACAT
15990530 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
15990550 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
15990569 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:15993492 original size:14 final size:14
Alignment explanation
Indices: 15993475--15993505 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
15993465 GTGGAGGACC
15993475 GGAGGTGGACCGGT
1 GGAGGTGGACCGGT
*
15993489 GGAGGTGGATCGGT
1 GGAGGTGGACCGGT
15993503 GGA
1 GGA
15993506 AGACGGAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.10, G:0.58, T:0.16
Consensus pattern (14 bp):
GGAGGTGGACCGGT
Found at i:15998009 original size:11 final size:11
Alignment explanation
Indices: 15997983--15998053 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
15997973 TAATCCCCTT
*
15997983 TCAATTATTTTC
1 TCAATT-TTCTC
15997995 TCAATTTTCTC
1 TCAATTTTCTC
* *
15998006 TCAATTTGCTT
1 TCAATTTTCTC
* *
15998017 TCAAGTTGCTC
1 TCAATTTTCTC
*
15998028 TCAATTTCCT-
1 TCAATTTTCTC
*
15998038 TCTAAATTTCTC
1 TC-AATTTTCTC
15998050 TCAA
1 TCAA
15998054 ATTCATATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
10 2 0.04
11 38 0.79
12 8 0.17
ACGTcount: A:0.23, C:0.24, G:0.04, T:0.49
Consensus pattern (11 bp):
TCAATTTTCTC
Found at i:15998050 original size:22 final size:22
Alignment explanation
Indices: 15997995--15998053 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
15997985 AATTATTTTC
* *
15997995 TCAATTTTCTCTCAATTTGCTT
1 TCAAATTTCTCTCAATTTCCTT
* *
15998017 TCAAGTTGCTCTCAATTTCC-T
1 TCAAATTTCTCTCAATTTCCTT
15998038 TCTAAATTTCTCTCAA
1 TC-AAATTTCTCTCAA
15998054 ATTCATATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.22, C:0.25, G:0.05, T:0.47
Consensus pattern (22 bp):
TCAAATTTCTCTCAATTTCCTT
Found at i:15999254 original size:7 final size:7
Alignment explanation
Indices: 15999242--15999267 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
15999232 TAGTCGATTG
15999242 GTATTTA
1 GTATTTA
15999249 GTATTTA
1 GTATTTA
15999256 GTATTTA
1 GTATTTA
15999263 GTATT
1 GTATT
15999268 ACGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:16000493 original size:8 final size:8
Alignment explanation
Indices: 16000480--16000521 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
16000470 AATTTATTAA
16000480 AAATTTAT
1 AAATTTAT
16000488 AAATTTAT
1 AAATTTAT
16000496 AAATTATAATT
1 AAATT-T-A-T
16000507 AAATTTAT
1 AAATTTAT
16000515 -AATTTAT
1 AAATTTAT
16000522 TTGACAAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 7 0.23
8 14 0.45
9 2 0.06
10 2 0.06
11 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AAATTTAT
Found at i:16000496 original size:98 final size:97
Alignment explanation
Indices: 16000382--16000560 Score: 263
Period size: 98 Copynumber: 1.8 Consensus size: 97
16000372 AATAAAATAG
* *
16000382 AAATTTATAAATTTATAATTTATAATTAAATTT-TGATATTAATTGACAAATACAAAAACCCT-A
1 AAATTTATAAATTTATAAATTATAATTAAATTTATAAT-TTAATTGAC-AA-ACAAAAACCCTAA
16000445 ACCCTTAACTTAAAAACCCTAAACTAATTTATTAA
63 ACCCTTAACTTAAAAACCCTAAACTAATTTATTAA
* ***
16000480 AAATTTATAAATTTATAAATTATAATTAAATTTATAATTTATTTGACAAACCTTAACCCTAAACC
1 AAATTTATAAATTTATAAATTATAATTAAATTTATAATTTAATTGACAAACAAAAACCCTAAACC
16000545 CTTAACTTAAAAACCC
66 CTTAACTTAAAAACCC
16000561 CAACCCTTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
96 8 0.11
97 22 0.30
98 40 0.55
99 3 0.04
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.37
Consensus pattern (97 bp):
AAATTTATAAATTTATAAATTATAATTAAATTTATAATTTAATTGACAAACAAAAACCCTAAACC
CTTAACTTAAAAACCCTAAACTAATTTATTAA
Found at i:16000566 original size:21 final size:21
Alignment explanation
Indices: 16000541--16000583 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
16000531 CTTAACCCTA
*
16000541 AACCCTTAACTTAAAAACCCC
1 AACCCTTAACATAAAAACCCC
16000562 AACCCTTAACATAAAAACCCC
1 AACCCTTAACATAAAAACCCC
16000583 A
1 A
16000584 TAATCCTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.16
Consensus pattern (21 bp):
AACCCTTAACATAAAAACCCC
Found at i:16004131 original size:126 final size:125
Alignment explanation
Indices: 16003741--16004172 Score: 704
Period size: 126 Copynumber: 3.5 Consensus size: 125
16003731 CATGCTACTG
* * * * *
16003741 TAGCAAAAGGGCGTCCACGAGGGCGCGATTTCATAAATTCTTCTGATAAAGCATCATACTTGAAG
1 TAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTTGAAG
* *
16003806 CGTTTTTTATACTATTCGCTCAGAAACGTGAACTCGAAATTA-TTTTTCAGGACCAACTG
66 CGTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTA
*
16003865 TAGCAAAAGCGCGTCCACGTAGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTTGAAG
1 TAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTTGAAG
* *
16003930 CGTTTTTTATACTATTCGCTCAGAAACGTCAACTTGAAATTATTTTTTTAGGACCAACTA
66 CGTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTA
* * *
16003990 TAGCAAAAGCACGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATTAAGCATCCTGCTTGAAG
1 TAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTTGAAG
**
16004055 CGTTTTTTTATACTATTTTCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTA
66 CG-TTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTA
*
16004116 TAGCAAAAGCTCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCT
1 TAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCT
16004173 ACTTTGATTT
Statistics
Matches: 285, Mismatches: 21, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
124 99 0.35
125 78 0.27
126 108 0.38
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (125 bp):
TAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTTGAAG
CGTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTA
Found at i:16004208 original size:126 final size:122
Alignment explanation
Indices: 16003741--16004172 Score: 496
Period size: 124 Copynumber: 3.5 Consensus size: 122
16003731 CATGCTACTG
** * * * *
16003741 TAGCAAAAGGGCGTCCACGAGGGCGCGATTTCATAAATTCTTCTGATAAAGCATCATACTTGAAG
1 TAGCAAAAGCACGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTTGAA-
* * * * *
16003806 CGTTTTTTATACTATTCGCTCA-GAAACGTGAACTCGAAATTA-TTTTTCAGGACCAACTG
65 -GTTTTTTA-AATA-CCACTCACGAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTA
* *
16003865 TAGCAAAAGCGCGTCCACGTAGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTTGAAG
1 TAGCAAAAGCACGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTTGAA-
* * * * *
16003930 CGTTTTTTATACTATTCGCTCA-GAAACGTCAACTTGAAATTATTTTTTTAGGACCAACTA
65 -GTTTTTTA-AATA-CCACTCACGAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTA
* *
16003990 TAGCAAAAGCACGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATTAAGCATCCTGCTTGAAG
1 TAGCAAAAGCACGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTTGAA-
* *
16004055 CGTTTTTT-TATACTATTTTCTCA-GAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTA
65 -GTTTTTTAAATACCA----CTCACGAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTA
*
16004116 TAGCAAAAGCTCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCT
1 TAGCAAAAGCACGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCT
16004173 ACTTTGATTT
Statistics
Matches: 279, Mismatches: 24, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
123 2 0.01
124 99 0.35
125 84 0.30
126 94 0.34
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (122 bp):
TAGCAAAAGCACGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTTGAAG
TTTTTTAAATACCACTCACGAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTA
Found at i:16007346 original size:6 final size:6
Alignment explanation
Indices: 16007335--16007403 Score: 97
Period size: 6 Copynumber: 11.5 Consensus size: 6
16007325 TTTTGGTACA
*
16007335 TAGATG TAGATG TAGATG TAGATG TAGATG TAGATG TAGATG TAAATG
1 TAGATG TAGATG TAGATG TAGATG TAGATG TAGATG TAGATG TAGATG
16007383 T-GATTTG TAGATG TA-ATG TAG
1 TAGA--TG TAGATG TAGATG TAG
16007404 GGGATGGATG
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
5 6 0.11
6 46 0.81
7 3 0.05
8 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.36
Consensus pattern (6 bp):
TAGATG
Found at i:16007495 original size:10 final size:10
Alignment explanation
Indices: 16007480--16007505 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
16007470 ATATTGTTAT
16007480 CATTTTATAC
1 CATTTTATAC
16007490 CATTTTATAC
1 CATTTTATAC
16007500 CATTTT
1 CATTTT
16007506 GTTAGTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (10 bp):
CATTTTATAC
Found at i:16013311 original size:40 final size:39
Alignment explanation
Indices: 16013257--16013411 Score: 238
Period size: 40 Copynumber: 3.8 Consensus size: 39
16013247 AATAAATATA
* *
16013257 TTAATTTTTTTAATTTTAAAATATTTTTTACATACTTTT
1 TTAATTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
16013296 TTAATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
1 TTAA-TTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
16013336 TTAAATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
1 TT-AATTTTTTTAATTTTAAAATATTTTTAAAATAC---TTTT
*
16013379 TTAATTTTTTTATTTTTAAAATATTTTTAAAAT
1 TTAATTTTTTTAATTTTAAAATATTTTTAAAAT
16013412 TTTTAAAATA
Statistics
Matches: 108, Mismatches: 3, Indels: 7
0.92 0.03 0.06
Matches are distributed among these distances:
39 4 0.04
40 66 0.61
41 2 0.02
42 30 0.28
43 6 0.06
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (39 bp):
TTAATTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
Found at i:16013324 original size:11 final size:11
Alignment explanation
Indices: 16013310--16013421 Score: 68
Period size: 11 Copynumber: 10.9 Consensus size: 11
16013300 TTTTTTTTAA
16013310 TTTTAAAATAT
1 TTTTAAAATAT
16013321 TTTTAAAATACT
1 TTTTAAAATA-T
*
16013333 TTTTTAAAT-T
1 TTTTAAAATAT
*
16013343 TTTT----TAA
1 TTTTAAAATAT
16013350 TTTTAAAATAT
1 TTTTAAAATAT
16013361 TTTTAAAATACTTT
1 TTTTAAAATA---T
**
16013375 TTTTTTAAT-T
1 TTTTAAAATAT
16013385 TTTT----TAT
1 TTTTAAAATAT
16013392 TTTTAAAATAT
1 TTTTAAAATAT
16013403 TTTT-AAA-AT
1 TTTTAAAATAT
16013412 TTTTAAAATA
1 TTTTAAAATA
16013422 AAAATGAGCC
Statistics
Matches: 80, Mismatches: 5, Indels: 32
0.68 0.04 0.27
Matches are distributed among these distances:
6 2 0.03
7 9 0.11
9 6 0.08
10 16 0.20
11 30 0.38
12 9 0.11
14 8 0.10
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:16013903 original size:34 final size:35
Alignment explanation
Indices: 16013859--16013925 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
16013849 CAGTAAAATA
*
16013859 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
16013893 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
16013926 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:16014336 original size:21 final size:21
Alignment explanation
Indices: 16014312--16014363 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
16014302 AAGGGTAAGA
16014312 CATTTTCCCTAAAATGTAACC
1 CATTTTCCCTAAAATGTAACC
16014333 CATTTTCCCTAAAATGTAACC
1 CATTTTCCCTAAAATGTAACC
16014354 CATTTTCCCT
1 CATTTTCCCT
16014364 TGTTTTGGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.31, G:0.04, T:0.37
Consensus pattern (21 bp):
CATTTTCCCTAAAATGTAACC
Found at i:16018231 original size:29 final size:27
Alignment explanation
Indices: 16018190--16018275 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 27
16018180 CTTTTAAAAA
* *
16018190 TTAAAAATATAAAAAATTAATAATTAATT
1 TTAAAATTTTAAAAAATTAATAATT--TT
**
16018219 TTAAAATTTTAAAATATATTTTTTAATTTT
1 TTAAAATTTTAAAA-A-A-TTAATAATTTT
16018249 TTAAAATTTTAAAAAAATTAATTAATT
1 TTAAAATTTT-AAAAAATTAA-TAATT
16018276 CATGGCGTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
28 2 0.04
29 18 0.39
30 14 0.30
31 5 0.11
32 7 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TTAAAATTTTAAAAAATTAATAATTTT
Found at i:16023368 original size:26 final size:26
Alignment explanation
Indices: 16023291--16023373 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 26
16023281 TATATTAATG
*
16023291 TTTTAAAAATAATTTATTATTAGATTTAA
1 TTTTATAAATAATTTA-TATT-GA-TTAA
* ** *
16023320 GTTT-TAAATTTTTTATGTATGATTAA
1 TTTTATAAATAATTTATAT-TGATTAA
16023346 TTTTATAAATAATTTATATTGATTAA
1 TTTTATAAATAATTTATATTGATTAA
16023372 TT
1 TT
16023374 AAAAGGTATG
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
26 16 0.37
27 15 0.35
28 9 0.21
29 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (26 bp):
TTTTATAAATAATTTATATTGATTAA
Found at i:16025312 original size:22 final size:22
Alignment explanation
Indices: 16025287--16025330 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
16025277 AATAATATTT
16025287 TTTCTTTCTTCGCATTCTTTTG
1 TTTCTTTCTTCGCATTCTTTTG
16025309 TTTCTTTCTTCGCATTCTTTTG
1 TTTCTTTCTTCGCATTCTTTTG
16025331 GCAATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.05, C:0.23, G:0.09, T:0.64
Consensus pattern (22 bp):
TTTCTTTCTTCGCATTCTTTTG
Found at i:16033477 original size:2 final size:2
Alignment explanation
Indices: 16033470--16033499 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16033460 TATTTCACAA
16033470 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16033500 TCTGTTCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16036635 original size:20 final size:19
Alignment explanation
Indices: 16036607--16036681 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
16036597 TTTTAAAATT
*
16036607 AAGTGAAAATGATTTTAACC
1 AAGTCAAAATGATTTTAA-C
* *
16036627 AAGTCAAAATGATTTCCATC
1 AAGTCAAAATGATTT-TAAC
* *
16036647 AAGTTAAAATCATTTTAAC
1 AAGTCAAAATGATTTTAAC
16036666 ACA-TCAAAATGATTTT
1 A-AGTCAAAATGATTTT
16036682 CAAACAAGCC
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
19 14 0.32
20 29 0.66
21 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.33
Consensus pattern (19 bp):
AAGTCAAAATGATTTTAAC
Found at i:16039649 original size:2 final size:2
Alignment explanation
Indices: 16039642--16039681 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
16039632 ATAGGATAGA
16039642 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16039682 GGTGCATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16044240 original size:162 final size:165
Alignment explanation
Indices: 16044040--16044366 Score: 473
Period size: 162 Copynumber: 2.0 Consensus size: 165
16044030 AATTGACACA
* * * *
16044040 GACACTACGAGTTTCTAGTAATGTCGTTTGGGCTAACCAA-TGCCCCATCTGCTTTTATGGATCT
1 GACACTACGAGTTTCTAGTAATATCATTTGGACTAACCAACT-CCCCATCTACTTTTATGGATCT
* *
16044104 GATGAACATAAATTTTCATTTATAT-TTG-TAGGAAT-TTGTTGTGTTCATAGATGATATATTGA
65 GATGAACATAAATTTTAATTTATATCTGGATAGGAATGTTGTTGTGTTCATAGATGATATATTGA
16044166 TCTACTCAAAAAATGAAAATGATCATCATCAACATC
130 TCTACTCAAAAAATGAAAATGATCATCATCAACATC
*
16044202 GACACTATGAGTTTCTAGTAATATCATTTGGACTAACCAACTCCCCATCTACTTTTATGGATCTG
1 GACACTACGAGTTTCTAGTAATATCATTTGGACTAACCAACTCCCCATCTACTTTTATGGATCTG
* * ** * *
16044267 ATGAACATAATTTTTAATTTATATCTGGATTGGTTTGTTGTTGTTTTCATAGATGATCTATTGAT
66 ATGAACATAAATTTTAATTTATATCTGGATAGGAATGTTGTTGTGTTCATAGATGATATATTGAT
* * *
16044332 CTACTCGAAAAATGAAAATGATCATGATTAACATC
131 CTACTCAAAAAATGAAAATGATCATCATCAACATC
16044367 TGAGAATTTT
Statistics
Matches: 145, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
162 80 0.55
163 3 0.02
164 4 0.03
165 58 0.40
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (165 bp):
GACACTACGAGTTTCTAGTAATATCATTTGGACTAACCAACTCCCCATCTACTTTTATGGATCTG
ATGAACATAAATTTTAATTTATATCTGGATAGGAATGTTGTTGTGTTCATAGATGATATATTGAT
CTACTCAAAAAATGAAAATGATCATCATCAACATC
Found at i:16051005 original size:2 final size:2
Alignment explanation
Indices: 16050998--16051049 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
16050988 GTATATTCGG
16050998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16051040 AT AT AT AT AT
1 AT AT AT AT AT
16051050 GATAGTATGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16068074 original size:17 final size:17
Alignment explanation
Indices: 16068052--16068087 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
16068042 ATAGAAAGTC
16068052 AAAGATATGGGTATCAA
1 AAAGATATGGGTATCAA
16068069 AAAGATATGGGTATCAA
1 AAAGATATGGGTATCAA
16068086 AA
1 AA
16068088 TCTGGGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (17 bp):
AAAGATATGGGTATCAA
Found at i:16071869 original size:17 final size:18
Alignment explanation
Indices: 16071832--16071874 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
16071822 TTCATGTTTT
* *
16071832 TAAAAATATTAATTATTA
1 TAAAAATATTAAGTATAA
16071850 TAAAAATATT-AGTATAA
1 TAAAAATATTAAGTATAA
16071867 TAAAAATA
1 TAAAAATA
16071875 ATTTCTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
TAAAAATATTAAGTATAA
Found at i:16082285 original size:19 final size:20
Alignment explanation
Indices: 16082252--16082290 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
16082242 AAAAGTTAGT
16082252 TTTTTTTTGAAAGTT-AATA
1 TTTTTTTTGAAAGTTGAATA
**
16082271 TTTTTTTTGGTAGTTGAATA
1 TTTTTTTTGAAAGTTGAATA
16082291 AATTTGTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (20 bp):
TTTTTTTTGAAAGTTGAATA
Found at i:16082290 original size:20 final size:19
Alignment explanation
Indices: 16082243--16082279 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16082233 TGATTTATGA
*
16082243 AAAGTTAGT-TTTTTTTTG
1 AAAGTTAATATTTTTTTTG
16082261 AAAGTTAATATTTTTTTTG
1 AAAGTTAATATTTTTTTTG
16082280 GTAGTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (19 bp):
AAAGTTAATATTTTTTTTG
Found at i:16085463 original size:22 final size:24
Alignment explanation
Indices: 16085438--16085482 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
16085428 ATATGGCAAA
16085438 GAATTAAG-TAGAAAAG-AAGTAC
1 GAATTAAGTTAGAAAAGTAAGTAC
16085460 GAATTAAGTTAGAAAAGTAAGTA
1 GAATTAAGTTAGAAAAGTAAGTA
16085483 AACTTAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
23 8 0.38
24 5 0.24
ACGTcount: A:0.53, C:0.02, G:0.22, T:0.22
Consensus pattern (24 bp):
GAATTAAGTTAGAAAAGTAAGTAC
Found at i:16085766 original size:3 final size:3
Alignment explanation
Indices: 16085758--16085823 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
16085748 GAGGTAAGTG
16085758 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16085806 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
16085824 AGATGAGTGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16101322 original size:4 final size:4
Alignment explanation
Indices: 16101305--16101394 Score: 171
Period size: 4 Copynumber: 22.5 Consensus size: 4
16101295 CCTACTTTCT
*
16101305 CATA CATG CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
16101353 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
16101395 CTTCAGCTAG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 84 1.00
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:16105482 original size:25 final size:24
Alignment explanation
Indices: 16105401--16105482 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 24
16105391 GGACTCACCA
*
16105401 CAGCTTGTATGAGCTTACCGATTT
1 CAGCTCGTATGAGCTTACCGATTT
*
16105425 GCAGCTCATGA-GAGCTTACCGATTCT
1 -CAGCTCGT-ATGAGCTTACCGATT-T
16105451 CAGCTCGTATGAGCTTACCGTATTT
1 CAGCTCGTATGAGCTTACCG-ATTT
*
16105476 TAGCTCG
1 CAGCTCG
16105483 GAATAGTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
24 1 0.02
25 43 0.88
26 5 0.10
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (24 bp):
CAGCTCGTATGAGCTTACCGATTT
Found at i:16107449 original size:25 final size:24
Alignment explanation
Indices: 16107348--16107473 Score: 127
Period size: 22 Copynumber: 5.3 Consensus size: 24
16107338 CACTAATGAA
* *
16107348 CAGAGAGCACTAAAGTGCTAT-A-
1 CAGAGAGCACCAACGTGCTATAAT
*
16107370 CAGAGAGCA-CAGATGTGCTA-AA-
1 CAGAGAGCACCA-ACGTGCTATAAT
** *
16107392 CAGAGAGCACTGACGTGCTAAAAT
1 CAGAGAGCACCAACGTGCTATAAT
*
16107416 CAGAGAGCACCAACGTGCTAGTAGT
1 CAGAGAGCACCAACGTGCTA-TAAT
16107441 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCT-ATAAT
16107466 CAGAGAGC
1 CAGAGAGC
16107474 GCGCTAAAGT
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
21 1 0.01
22 33 0.38
23 2 0.02
24 18 0.21
25 32 0.37
26 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.15
Consensus pattern (24 bp):
CAGAGAGCACCAACGTGCTATAAT
Found at i:16108748 original size:5 final size:5
Alignment explanation
Indices: 16108730--16108815 Score: 56
Period size: 5 Copynumber: 17.2 Consensus size: 5
16108720 TGTTTTATGT
* * *
16108730 ATATA ATAATA ATATA ATATT ATAATA ATATA ATATA ATA-A CT-TA CTTATTA
1 ATATA AT-ATA ATATA ATATA AT-ATA ATATA ATATA ATATA ATATA -ATA-TA
*
16108782 AT-TA A-ATA ACATA ATATA ATAT- ATATA TATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA -ATATA A
16108816 CTTAAATTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
4 13 0.20
5 35 0.54
6 15 0.23
7 2 0.03
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:16108754 original size:16 final size:16
Alignment explanation
Indices: 16108730--16108770 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
16108720 TGTTTTATGT
16108730 ATATAATAATAATATA
1 ATATAATAATAATATA
*
16108746 ATATTATAATAATATA
1 ATATAATAATAATATA
16108762 ATATAATAA
1 ATATAATAA
16108771 CTTACTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAATAATAATATA
Found at i:16108770 original size:8 final size:8
Alignment explanation
Indices: 16108735--16108764 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
16108725 TATGTATATA
16108735 ATAATAAT
1 ATAATAAT
*
16108743 ATAATATT
1 ATAATAAT
16108751 ATAATAAT
1 ATAATAAT
16108759 ATAATA
1 ATAATA
16108765 TAATAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATAAT
Found at i:16110149 original size:24 final size:24
Alignment explanation
Indices: 16110117--16110171 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
16110107 TCTTCCAGTT
16110117 AAACTCTGTTTATTTATTTCAATC
1 AAACTCTGTTTATTTATTTCAATC
* *
16110141 AAACTCTGTTTATTTGTTTTAATC
1 AAACTCTGTTTATTTATTTCAATC
16110165 AAACTCT
1 AAACTCT
16110172 AATTAGTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTATTTATTTCAATC
Found at i:16112618 original size:15 final size:15
Alignment explanation
Indices: 16112598--16112663 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
16112588 ACTACAAAAC
16112598 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
16112613 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
16112632 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
16112647 A-TTAATATTAA-AT
1 ATTTATTATTAATAT
16112660 ATTT
1 ATTT
16112664 TTCAATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 10 0.24
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:16128450 original size:40 final size:41
Alignment explanation
Indices: 16128406--16128518 Score: 124
Period size: 40 Copynumber: 2.8 Consensus size: 41
16128396 CGTTTGAACA
*
16128406 AAAAACGCCTCTAAAAATCAAGCATTAGCGGCG-CTTTAGG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTCTTTAGG
* * * * * *
16128446 AAAAACACCGCTAAAGATCCAGTATTAGCGGCGTTTTTTGG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTCTTTAGG
* *
16128487 -AAAACGCCGCTAAAAATGAA-CATTAGTGGCGT
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGT
16128519 TTTTCAAAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
39 10 0.17
40 44 0.75
41 5 0.08
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.22
Consensus pattern (41 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTCTTTAGG
Found at i:16128645 original size:41 final size:40
Alignment explanation
Indices: 16128580--16128812 Score: 326
Period size: 41 Copynumber: 5.7 Consensus size: 40
16128570 TTTTTCAGGG
16128580 CTTTAGCGGCGTTTTTCGAAAAGCGCCGCTAATGCTCGGGT
1 CTTTAGCGGCGTTTTT-GAAAAGCGCCGCTAATGCTCGGGT
16128621 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGT
1 CTTTAGCGGCGTTTTTGAA-AAGCGCCGCTAATGCTCGGGT
* *
16128662 CTTTAACGGCGATTTTGAAGAAGCGCCGCTAATGCTCGGGT
1 CTTTAGCGGCGTTTTTGAA-AAGCGCCGCTAATGCTCGGGT
*
16128703 CTTTAGCGGCGTTTCTT-AAGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTT-TTGAA-AAGCGCCGCTAATGCTCGGGT
* **
16128744 CTTTAGTGGCGTTTTTGATAAAGCGCCGCTAATGCTC-TAT
1 CTTTAGCGGCGTTTTTGA-AAAGCGCCGCTAATGCTCGGGT
*
16128784 TTTTAGCGGCGTTTTTTGAAAAGCGCCGC
1 CTTTAGCGGCG-TTTTTGAAAAGCGCCGC
16128813 AAAAAATATT
Statistics
Matches: 177, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
40 25 0.14
41 149 0.84
42 3 0.02
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.31
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTTGAAAAGCGCCGCTAATGCTCGGGT
Found at i:16129913 original size:21 final size:21
Alignment explanation
Indices: 16129879--16129981 Score: 79
Period size: 21 Copynumber: 5.0 Consensus size: 21
16129869 TATAGATTTA
*
16129879 GGGA-TTATGGTTTAAGGGTT
1 GGGATTTAGGGTTTAAGGGTT
* *
16129899 GGGATTTAAGGTTTAGGGGTT
1 GGGATTTAGGGTTTAAGGGTT
** * * *
16129920 ATGAGTTAGGGGTTAAGAGTT
1 GGGATTTAGGGTTTAAGGGTT
*
16129941 AGGGATTTAGGGTTTCAAGGGTC
1 -GGGATTTAGGGTTT-AAGGGTT
16129964 GGG--TTAGGGTTT-AGGGTT
1 GGGATTTAGGGTTTAAGGGTT
16129982 TAGATTAATT
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
18 5 0.08
20 13 0.20
21 28 0.44
22 13 0.20
23 5 0.08
ACGTcount: A:0.20, C:0.02, G:0.42, T:0.36
Consensus pattern (21 bp):
GGGATTTAGGGTTTAAGGGTT
Found at i:16129928 original size:14 final size:14
Alignment explanation
Indices: 16129911--16129944 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
16129901 GATTTAAGGT
*
16129911 TTAGGGGTTATGAG
1 TTAGGGGTTAAGAG
16129925 TTAGGGGTTAAGAG
1 TTAGGGGTTAAGAG
16129939 TTAGGG
1 TTAGGG
16129945 ATTTAGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (14 bp):
TTAGGGGTTAAGAG
Found at i:16133409 original size:43 final size:43
Alignment explanation
Indices: 16133356--16133604 Score: 333
Period size: 43 Copynumber: 5.8 Consensus size: 43
16133346 AAGACATATT
* * * * *
16133356 TTTAGTGGCGTTTGTTTGAAGAGCGCCGCTAAAAGCCATGGTC
1 TTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
16133399 TTTAGCGGCGTTTG-TGGTAAAAGCGCCGCTAATGGTCATAGTC
1 TTTAGCGGCGTTTGTTGG-AAAAGCGCCGCTAAAGGTCATGGTC
*
16133442 TTTAGCGGCGTTTG-TGGTAAAAGCGCCACTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTTGG-AAAAGCGCCGCTAAAGGTCATGGTC
* *
16133485 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
16133528 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGGTC
*
16133571 TTTAGCGGCGTTT-ATGGAAAAAGCGCCGCTAAAG
1 TTTAGCGGCGTTTGTTGG-AAAAGCGCCGCTAAAG
16133605 TTAGCGATGC
Statistics
Matches: 188, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
42 4 0.02
43 182 0.97
44 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:16133593 original size:129 final size:129
Alignment explanation
Indices: 16133356--16133604 Score: 372
Period size: 129 Copynumber: 1.9 Consensus size: 129
16133346 AAGACATATT
* ** * *
16133356 TTTAGTGGCGTTTGTTTGAAGAGCGCCGCTAAAAGCCATGGTCTTTAGCGGCGTTTGTGGTAAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGCCATGGTCTTTAGCGGCGTTTGTGGGAAAA
* * *
16133421 GCGCCGCTAATGGTCATAGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCACTAAAGGTCATGGTC
66 GCGCCGCTAAAGGTCATAGTCTTTAGCGGCGTTTATGGAAAAAGCGCCACTAAAGGTCATGGTC
* * *
16133485 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGCCATGGTCTTTAGCGGCGTTTGTGGGAAAA
* * *
16133550 GCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTATGGAAAAAGCGCCGCTAAAG
66 GCGCCGCTAAAGGTCATAGTCTTTAGCGGCGTTTATGGAAAAAGCGCCACTAAAG
16133605 TTAGCGATGC
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
129 106 1.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (129 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGCCATGGTCTTTAGCGGCGTTTGTGGGAAAA
GCGCCGCTAAAGGTCATAGTCTTTAGCGGCGTTTATGGAAAAAGCGCCACTAAAGGTCATGGTC
Found at i:16135585 original size:2 final size:2
Alignment explanation
Indices: 16135578--16135603 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16135568 AAAAGAAAGA
16135578 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
16135604 GAAGGCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16136027 original size:22 final size:22
Alignment explanation
Indices: 16135999--16136151 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
16135989 TTTATTGTTC
*
16135999 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
16136021 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
16136043 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
16136065 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
16136087 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
16136109 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
16136131 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
16136152 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:16138193 original size:15 final size:15
Alignment explanation
Indices: 16138173--16138201 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16138163 GTACCAGACA
16138173 TGGATAATGAAAAAT
1 TGGATAATGAAAAAT
16138188 TGGATAATGAAAAA
1 TGGATAATGAAAAA
16138202 CAAGTCACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (15 bp):
TGGATAATGAAAAAT
Found at i:16141299 original size:50 final size:50
Alignment explanation
Indices: 16141236--16141331 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
16141226 CAGCAAATAC
* * *
16141236 ATGGTCCAAAGAGCGAAACTTGGTTTCAAGTTACGGAAATAAGTCTCAAT
1 ATGGTCCAAAGAGCAAAACTTGGTTTCAAGTTACAGAAAGAAGTCTCAAT
* * *
16141286 ATGGTCCATAGAGCAAAATTTTGTTTCAAGTTACAGAAAGAAGTCT
1 ATGGTCCAAAGAGCAAAACTTGGTTTCAAGTTACAGAAAGAAGTCT
16141332 AAATTAAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (50 bp):
ATGGTCCAAAGAGCAAAACTTGGTTTCAAGTTACAGAAAGAAGTCTCAAT
Found at i:16146347 original size:19 final size:19
Alignment explanation
Indices: 16146316--16146359 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
16146306 CAAGCTTAAT
16146316 ATTAAATTAATTAAGATTTA
1 ATTAAATTAATTAAG-TTTA
*
16146336 GTTAAA-TAATTAAGTTTA
1 ATTAAATTAATTAAGTTTA
16146354 ATTAAA
1 ATTAAA
16146360 CGTTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 8 0.36
20 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (19 bp):
ATTAAATTAATTAAGTTTA
Found at i:16147671 original size:16 final size:17
Alignment explanation
Indices: 16147628--16147673 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
16147618 GAGTATAGTT
16147628 TAATA-GTATATG-TTA
1 TAATATGTATATGATTA
*
16147643 TAATATG-AAATGATTA
1 TAATATGTATATGATTA
16147659 T-ATATGTATATGATT
1 TAATATGTATATGATT
16147674 TTGGTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (17 bp):
TAATATGTATATGATTA
Done.