Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 26
Found at i:3851657 original size:72 final size:72
Alignment explanation
Indices: 3851502--3851657 Score: 192
Period size: 72 Copynumber: 2.2 Consensus size: 72
3851492 AAACGGATAT
* * *
3851502 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCATGTCAAGTATCAGATCAG
1 ATCAAAAATCAGATCATAATCCACGTCAAGTATCAGATCAAAATCCATGTCAAGTATCAGATCAG
3851567 AATCCAA
66 AATCCAA
* ** * *
3851574 GTCAAGTATCAGATCATAATCCATGTC-AGATATCAGATCAGAATCCATGTCAAGTATCAGATCA
1 ATCAAAAATCAGATCATAATCCACGTCAAG-TATCAGATCAAAATCCATGTCAAGTATCAGATCA
3851638 GAAAT-CAA
65 G-AATCCAA
3851646 AT-AGAAAATCAG
1 ATCA-AAAATCAG
3851658 GTAAAATATT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
71 3 0.04
72 64 0.91
73 3 0.04
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.24
Consensus pattern (72 bp):
ATCAAAAATCAGATCATAATCCACGTCAAGTATCAGATCAAAATCCATGTCAAGTATCAGATCAG
AATCCAA
Found at i:3853793 original size:13 final size:13
Alignment explanation
Indices: 3853751--3853780 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3853741 TTTTGTCAAC
*
3853751 GGTCAACGGGTCG
1 GGTCAACGGATCG
3853764 GGTCAACGGATCG
1 GGTCAACGGATCG
3853777 GGTC
1 GGTC
3853781 GGGTCAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACGGATCG
Found at i:3855951 original size:24 final size:24
Alignment explanation
Indices: 3855898--3856018 Score: 104
Period size: 24 Copynumber: 5.0 Consensus size: 24
3855888 CATAATTCAC
* * *
3855898 GTCAAGTATCATATCAAAATC-TA
1 GTCAAGTATCAGATCAGAATCAAA
*
3855921 TTGCAAGTATCAGATCAGAATCAAA
1 GT-CAAGTATCAGATCAGAATCAAA
* *
3855946 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCAAA
* *
3855970 GTC-AGATATTAGATCAGAATCCATA
1 GTCAAG-TATCAGATCAGAAT-CAAA
*
3855995 -TCAAGTAACAGATCAGAAATCAAA
1 GTCAAGTATCAGATCAG-AATCAAA
3856019 TCGAAAATCA
Statistics
Matches: 78, Mismatches: 14, Indels: 11
0.76 0.14 0.11
Matches are distributed among these distances:
23 3 0.04
24 67 0.86
25 8 0.10
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCAAA
Found at i:3855984 original size:48 final size:49
Alignment explanation
Indices: 3855898--3856012 Score: 130
Period size: 48 Copynumber: 2.4 Consensus size: 49
3855888 CATAATTCAC
* * *
3855898 GTCAAGTATCATATCAAAATCTATTGCAAGTATCAGATCAGAAT-CAAA
1 GTCAAGTATCAGATCAGAATCCATTGCAAGTATCAGATCAGAATCCAAA
* *
3855946 GTCAAGTATCAGATCAGAATCCA-TGTC-AGATATTAGATCAGAATCCATA
1 GTCAAGTATCAGATCAGAATCCATTG-CAAG-TATCAGATCAGAATCCAAA
*
3855995 -TCAAGTAACAGATCAGAA
1 GTCAAGTATCAGATCAGAA
3856013 ATCAAATCGA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
47 4 0.07
48 51 0.88
49 3 0.05
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (49 bp):
GTCAAGTATCAGATCAGAATCCATTGCAAGTATCAGATCAGAATCCAAA
Found at i:3859729 original size:13 final size:13
Alignment explanation
Indices: 3859711--3859771 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
3859701 AGTCAATAGT
3859711 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3859724 GGTCAACGGATTGGGTCG
1 GGTCAAC-----GGGTCG
*
3859742 GGTCAAAGGGTCG
1 GGTCAACGGGTCG
*
3859755 AGTCAACGGGTCG
1 GGTCAACGGGTCG
3859768 GGTC
1 GGTC
3859772 GGGTTGTGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 27 0.69
18 12 0.31
ACGTcount: A:0.18, C:0.20, G:0.44, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3859747 original size:31 final size:31
Alignment explanation
Indices: 3859711--3859775 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
3859701 AGTCAATAGT
* * *
3859711 GGTCAACGGGTCGGGTCAACGGATTGGGTCG
1 GGTCAAAGGGTCGAGTCAACGGATCGGGTCG
*
3859742 GGTCAAAGGGTCGAGTCAACGGGTCGGGTCG
1 GGTCAAAGGGTCGAGTCAACGGATCGGGTCG
3859773 GGT
1 GGT
3859776 TGTGACCGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.17, C:0.18, G:0.46, T:0.18
Consensus pattern (31 bp):
GGTCAAAGGGTCGAGTCAACGGATCGGGTCG
Found at i:3861679 original size:2 final size:2
Alignment explanation
Indices: 3861672--3861712 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3861662 ATCTTTTAAA
3861672 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
3861713 CCCTCATCCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3861936 original size:24 final size:24
Alignment explanation
Indices: 3861926--3862043 Score: 148
Period size: 24 Copynumber: 4.9 Consensus size: 24
3861916 CATAATTCAC
* *
3861926 GTCAAGTATCATATTAAAATCCAT
1 GTCAAGTATCAGATCAAAATCCAT
* *
3861950 GTCAAGTATTAGATCAAAATCCAA
1 GTCAAGTATCAGATCAAAATCCAT
*
3861974 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAT
* *
3861998 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAT
3862022 GTCAAGTATCAGATCAGAAATC
1 GTCAAGTATCAGATCA-AAATC
3862044 AAATTGAAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
23 2 0.02
24 73 0.90
25 6 0.07
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAT
Found at i:3862057 original size:72 final size:71
Alignment explanation
Indices: 3861906--3862057 Score: 171
Period size: 72 Copynumber: 2.1 Consensus size: 71
3861896 GGATATATCA
* * * * *
3861906 AAAATCAAATCATAATTCACGTCAAGTATCATATTAAAATCCATGTCAAGTATTAGATCAAAATC
1 AAAATCAGATCAGAATCCACGTCAAGTATCATATCAAAATCCATGTCAAGTATCAGATCAAAATC
*
3861971 CAAGTC
66 AAAGTC
* * *
3861977 AAGTATCAGATCAGAATCCATGTC-AGATATCATATCAGAATCCATGTCAAGTATCAGATCAGAA
1 AA-AATCAGATCAGAATCCACGTCAAG-TATCATATCAAAATCCATGTCAAGTATCAGATCA-AA
* *
3862041 ATCAAATTG
63 ATCAAAGTC
3862050 AAAATCAG
1 AAAATCAG
3862058 GTAAAATATT
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
71 4 0.06
72 52 0.79
73 10 0.15
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (71 bp):
AAAATCAGATCAGAATCCACGTCAAGTATCATATCAAAATCCATGTCAAGTATCAGATCAAAATC
AAAGTC
Found at i:3864491 original size:13 final size:13
Alignment explanation
Indices: 3864473--3864532 Score: 66
Period size: 13 Copynumber: 4.2 Consensus size: 13
3864463 ACGGTTCATA
3864473 GTCAACGGGTCGG
1 GTCAACGGGTCGG
3864486 GTCAACGGATCAGGTCGG
1 GTCAAC-G----GGTCGG
*
3864504 GTCAAAGGGTCGG
1 GTCAACGGGTCGG
3864517 GTCAACGGGTCGG
1 GTCAACGGGTCGG
3864530 GTC
1 GTC
3864533 GGGTTGTGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 27 0.68
14 1 0.03
17 1 0.03
18 11 0.28
ACGTcount: A:0.18, C:0.22, G:0.43, T:0.17
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:3864514 original size:31 final size:31
Alignment explanation
Indices: 3864473--3864536 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
3864463 ACGGTTCATA
*
3864473 GTCAACGGGTCGGGTCAACGGATCAGGTCGG
1 GTCAAAGGGTCGGGTCAACGGATCAGGTCGG
* *
3864504 GTCAAAGGGTCGGGTCAACGGGTCGGGTCGG
1 GTCAAAGGGTCGGGTCAACGGATCAGGTCGG
3864535 GT
1 GT
3864537 TGTGACCGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.17, C:0.20, G:0.45, T:0.17
Consensus pattern (31 bp):
GTCAAAGGGTCGGGTCAACGGATCAGGTCGG
Found at i:3864536 original size:18 final size:18
Alignment explanation
Indices: 3864478--3864519 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3864468 TCATAGTCAA
*
3864478 CGGGTCGGGTCAACGGAT
1 CGGGTCGGGTCAAAGGAT
* *
3864496 CAGGTCGGGTCAAAGGGT
1 CGGGTCGGGTCAAAGGAT
3864514 CGGGTC
1 CGGGTC
3864520 AACGGGTCGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAAAGGAT
Found at i:3866096 original size:67 final size:67
Alignment explanation
Indices: 3866018--3866145 Score: 211
Period size: 67 Copynumber: 1.9 Consensus size: 67
3866008 AAAAGATTAA
* * *
3866018 AGGCCTAACTGTGCATTTGATAGAAAGGTTTCAATTATGCCAGTTAGATGAAAGGCTAAGTTCTT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCACTTAGATGAAAGGCTAAGTTCTT
3866083 TG
66 TG
* *
3866085 AGGCCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCACTTAGATGAAAGGTTAAGT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCACTTAGATGAAAGGCTAAGT
3866146 ACCATTGTGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 56 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (67 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCACTTAGATGAAAGGCTAAGTTCTT
TG
Found at i:3866224 original size:81 final size:81
Alignment explanation
Indices: 3866086--3866647 Score: 687
Period size: 81 Copynumber: 6.9 Consensus size: 81
3866076 AGTTCTTTGA
* * * *
3866086 GGCCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCACTTAGATGAAAGGTTAAGTACCAT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
* * *
3866151 TGTGTAAAAGTATACT
66 TGAGTAAAAGAATAAT
* * * * * * * *
3866167 AGTCTAACTGTGCATTTGATAGAAACGTTTCAATTATGCCATTTAGATGAATTGTTAATTACCGT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
3866232 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
3866248 GGCCTAACTGTGCATTTGACA-AAAGGGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCG
1 GGCCTAACTGTGCATTTGACAGAAA-GGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCG
*
3866312 TTGAGTAAAAGACTAAT
65 TTGAGTAAAAGAATAAT
* * * * *** *
3866329 GGCTTAACTGTGCATCTGACAAAAAGGTGTCAATTATACCAGTTAGATGAACATTTAAGTACTGT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
3866394 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * * * * *
3866410 GGCCTAGCTATACATTTGATAGAAATGTGTCAATGATGCCAGTTAGATGAATGGTTAAGTACCAT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
3866475 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
** * * * * *
3866491 GGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCGAGTTAGATCAACT-GATAAGTACTG
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA-TGGTTAAGTACCG
3866555 TTGAGTAAAAGAATAAT
65 TTGAGTAAAAGAATAAT
* * * * ** *
3866572 GGCCTAACTGTGCATTTGACATAAAGGTATCAATTATGCCAGTTAGAGGAACGGTTAAACACTGT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
3866637 TGAGTAAAAGA
66 TGAGTAAAAGA
3866648 TGAACAGTTA
Statistics
Matches: 410, Mismatches: 67, Indels: 8
0.85 0.14 0.02
Matches are distributed among these distances:
80 3 0.01
81 403 0.98
82 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (81 bp):
GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
TGAGTAAAAGAATAAT
Found at i:3869167 original size:2 final size:2
Alignment explanation
Indices: 3869160--3869202 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3869150 ATGATGTCAG
3869160 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
3869202 A
1 A
3869203 GCTTTTATGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3871502 original size:81 final size:81
Alignment explanation
Indices: 3871366--3871909 Score: 793
Period size: 81 Copynumber: 6.7 Consensus size: 81
3871356 GTGCCTTTGA
*
3871366 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAATTAGATGAACGGTTAAGTACCGT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
*
3871431 TGTGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * *
3871447 AGCCTAACTGTGCATTTGACATAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCAT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
3871512 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * *
3871528 GGCCTAACTGTGCATTTGACAGAAATGTGTCAATTATGTCAGTTAGATGAACGGTTAATTATCGT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
*
3871593 CGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * *
3871609 GACCTAACTGTACATTTGACAGAAAGGTGTCAATTATACCAGTTAGATGAATGGTTAAGTACCGT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
3871674 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
** * *
3871690 GGCCTAGTTGTGCATTTAACTGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
3871755 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * * *
3871771 GGCCT-ACGTGCGCATTTGACAGAAAGATGTCAATTATGCTAGTTAGATGAACGATTAAGTACCA
1 GGCCTAAC-TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCG
3871835 TTGAGTAAAAGAATAAT
65 TTGAGTAAAAGAATAAT
* ** * * * *
3871852 GACCTAACAATACATTTGACAGAAAGGTGTCAATTATTCCAGTGAGAGGAACGGTTAA
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAA
3871910 ACACGATTGA
Statistics
Matches: 411, Mismatches: 50, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
81 409 1.00
82 2 0.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.28
Consensus pattern (81 bp):
GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
TGAGTAAAAGAATAAT
Found at i:3873757 original size:134 final size:134
Alignment explanation
Indices: 3873517--3874067 Score: 640
Period size: 134 Copynumber: 4.1 Consensus size: 134
3873507 GTTTTTCCAT
* * *
3873517 GGGAGATCAGACTCGAGAAAATTTTGATCCACTTCGCTGCTCTTCAGGGAAGGTTGAATCGAACT
1 GGGAGATCAGACTCGAGAAAATTTTGATCCACTTCGCTTCTCTTCAGGGAAGATTGAATCGAACA
* * *
3873582 TGATTTGCTTCACTACTCTTTAGGAAGACCAAATCTGAAAGAAAAAGAATCTACTCCATTACTCT
66 TGATTTGCTTCGCTACTCTTTAGGAAGACCAAATCTAAAAGAAAAAGAATCTACTCCACTACTCT
3873647 TTAG
131 TTAG
*
3873651 GGGAGATCATACTCGAGAAAATTTTGATCCACTTCAG-TTCTCTTCAGGGAAGATTGAATCGAAC
1 GGGAGATCAGACTCGAGAAAATTTTGATCCACTTC-GCTTCTCTTCAGGGAAGATTGAATCGAAC
* * * * ** * *
3873715 ATGATTTGCTACGTTGCTCTTTAGGAAGACCAAATCTGAAAGAAGGAGAAGCTGCTCCACTACTC
65 ATGATTTGCTTCGCTACTCTTTAGGAAGACCAAATCTAAAAGAAAAAGAATCTACTCCACTACTC
*
3873780 TTTTG
130 TTTAG
* * * * *
3873785 GGGAGACCAGACTCGAGAAAATTTTGATCCACTTCCCTGT-TGTTCAGGGAAGATTAAATTGAAC
1 GGGAGATCAGACTCGAGAAAATTTTGATCCACTTCGCT-TCTCTTCAGGGAAGATTGAATCGAAC
* * * * * * *
3873849 ATGATTTGCTTTGCTGCTCTTCAGGAAGACGAAATCTAAAAGAAGAAGAATCTACTTCACTGCTC
65 ATGATTTGCTTCGCTACTCTTTAGGAAGACCAAATCTAAAAGAAAAAGAATCTACTCCACTACTC
*
3873914 TTTAT
130 TTTAG
* * ** * *
3873919 GGGAGATCAGACTCGAGAAAAGTTTGATCCACTTCGCTACTCACCAGGGAAGACTGAATCGAACT
1 GGGAGATCAGACTCGAGAAAATTTTGATCCACTTCGCTTCTCTTCAGGGAAGATTGAATCGAACA
* * * * * *
3873984 TGATTTACTTCGTTACT-TTTCAAGAATATCAAATCTAAAAGAAAAACGAGGATCTTCTCCACTA
66 TGATTTGCTTCGCTACTCTTT-AGGAAGACCAAATCTAAAAGAAAAA-GA--ATCTACTCCACTA
3874048 CTCTTTAG
127 CTCTTTAG
* *
3874056 GGAAGACCAGAC
1 GGGAGATCAGAC
3874068 CTTTCAAAGG
Statistics
Matches: 349, Mismatches: 60, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
133 2 0.01
134 316 0.91
135 4 0.01
137 27 0.08
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (134 bp):
GGGAGATCAGACTCGAGAAAATTTTGATCCACTTCGCTTCTCTTCAGGGAAGATTGAATCGAACA
TGATTTGCTTCGCTACTCTTTAGGAAGACCAAATCTAAAAGAAAAAGAATCTACTCCACTACTCT
TTAG
Found at i:3875809 original size:38 final size:38
Alignment explanation
Indices: 3875692--3876135 Score: 345
Period size: 38 Copynumber: 11.3 Consensus size: 38
3875682 AGGTTCACAT
* * * *
3875692 CAAAGATTGACTCCTCTTCATGAGAAAGTTAAGAATAA
1 CAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAA
* * *
3875730 CATTGAAATATTGACTCCTCTTCACAAGGGAA-TCAAGAATAA
1 C----AAAGATTGACTTCTCTTCACGA-GGAAGTCAAGAATAA
* * * *
3875772 CAAAGATTGACTTCTTTTCATGAGTAAGTCAATAATAA
1 CAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAA
* * *
3875810 TAAGGATTGACTTCTATTCACGAGGAAGTCAAGAATAA
1 CAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAA
** * * *
3875848 CAAAGATCAACTTCTCTTTAGGAGAAAG-CTAAGAATAA
1 CAAAGATTGACTTCTCTTCACGAGGAAGTC-AAGAATAA
* * *
3875886 AAAAGATCGACTTCTCTTCACGAGGAAGTCGAGAATAA
1 CAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAA
* ** * *
3875924 AAAAGATCAAATTCTCTTCAGGAGGAAGTCAAGAATAA
1 CAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAA
* *
3875962 CATTGAAAGATTGACTCCACTTCACGAGGAAGTCAAGAATAA
1 C----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAA
** * *
3876004 CATTGAAAGATTGACTTCTCATT-GTGAGGGAGTCAGGAATAA
1 C----AAAGATTGACTTCTC-TTCACGAGGAAGTCAAGAATAA
* * *
3876046 CAAAGATTGACTTCTGTTTACGAGGAAGCCAAGAATAA
1 CAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAA
* * *
3876084 CATTGAAATATTGACTCCTCTTCATGAGGAAGTCAAGAATAA
1 C----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAA
3876126 CAAAGATTGA
1 CAAAGATTGA
3876136 AGTTTCAAGG
Statistics
Matches: 326, Mismatches: 62, Indels: 36
0.77 0.15 0.08
Matches are distributed among these distances:
37 6 0.02
38 188 0.58
39 1 0.00
42 126 0.39
43 5 0.02
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (38 bp):
CAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAA
Found at i:3875850 original size:76 final size:76
Alignment explanation
Indices: 3875692--3876135 Score: 365
Period size: 80 Copynumber: 5.6 Consensus size: 76
3875682 AGGTTCACAT
* * * * * * *
3875692 CAAAGATTGACTCCTCTTCATGAGAAAGTTAAGAATAACATTGAAATATTGACTCCTCTTCACAA
1 CAAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAAC----AAAGATTGACTTCTATTCACGA
3875757 GGGAA-TCAAGAATAA
62 -GGAAGTCAAGAATAA
* * * * *
3875772 CAAAGATTGACTTCTTTTCATGAGTAAGTCAATAATAATAAGGATTGACTTCTATTCACGAGGAA
1 CAAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTTCTATTCACGAGGAA
3875837 GTCAAGAATAA
66 GTCAAGAATAA
** * * * * * *
3875848 CAAAGATCAACTTCTCTTTAGGAGAAAG-CTAAGAATAAAAAAGATCGACTTCTCTTCACGAGGA
1 CAAAGATTGACTTCTCTTCATGAGGAAGTC-AAGAATAACAAAGATTGACTTCTATTCACGAGGA
*
3875912 AGTCGAGAATAA
65 AGTCAAGAATAA
* ** * * *
3875924 AAAAGATCAAATTCTCTTCAGGAGGAAGTCAAGAATAACATTGAAAGATTGAC-TCCACTTCACG
1 CAAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAAC----AAAGATTGACTTCTA-TTCACG
3875988 AGGAAGTCAAGAATAA
61 AGGAAGTCAAGAATAA
* * * * *
3876004 CATTGAAAGATTGACTTCTCATT-GTGAGGGAGTCAGGAATAACAAAGATTGACTTCTGTTTACG
1 C----AAAGATTGACTTCTC-TTCATGAGGAAGTCAAGAATAACAAAGATTGACTTCTATTCACG
*
3876068 AGGAAGCCAAGAATAA
61 AGGAAGTCAAGAATAA
* *
3876084 CATTGAAATATTGACTCCTCTTCATGAGGAAGTCAAGAATAACAAAGATTGA
1 C----AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAAGATTGA
3876136 AGTTTCAAGG
Statistics
Matches: 300, Mismatches: 49, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
75 5 0.02
76 121 0.40
77 1 0.00
79 4 0.01
80 137 0.46
81 2 0.01
84 28 0.09
85 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (76 bp):
CAAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTTCTATTCACGAGGAA
GTCAAGAATAA
Found at i:3876021 original size:37 final size:38
Alignment explanation
Indices: 3875939--3876021 Score: 114
Period size: 42 Copynumber: 2.1 Consensus size: 38
3875929 ATCAAATTCT
*
3875939 CTTCAGGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCA
1 CTTCACGAGGAAGTCAAGAATAACATTGAAAGATTG----CA
3875981 CTTCACGAGGAAGTCAAGAATAACATTGAAAGATTG-A
1 CTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGCA
3876018 CTTC
1 CTTC
3876022 TCATTGTGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
37 5 0.12
42 35 0.88
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (38 bp):
CTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGCA
Found at i:3876554 original size:65 final size:65
Alignment explanation
Indices: 3876450--3876577 Score: 168
Period size: 65 Copynumber: 2.0 Consensus size: 65
3876440 ATTGGCTTTC
* * * * * *
3876450 CTGAACTTGTGTAGACATCCAATAGATCTTTCATCTTTGAAAAGATGATCTACTATCTTTGGAGA
1 CTGAACTTGTGTAGACATCCAATAGAGCATTCATCTTTGAAAAAAGGATCTACCATATTTGGAGA
**
3876515 CTGAACTTGTGTAGA-ACTTTAATAGAGCATTCATCTTTGAAAAAAGGATCTACCATATTTGGA
1 CTGAACTTGTGTAGACA-TCCAATAGAGCATTCATCTTTGAAAAAAGGATCTACCATATTTGGA
3876578 AATTGTGTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
64 1 0.02
65 53 0.98
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (65 bp):
CTGAACTTGTGTAGACATCCAATAGAGCATTCATCTTTGAAAAAAGGATCTACCATATTTGGAGA
Found at i:3881323 original size:20 final size:20
Alignment explanation
Indices: 3881291--3881329 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3881281 CATATATATA
3881291 TATATATCCTTCATATCACT
1 TATATATCCTTCATATCACT
3881311 TATAT-TCCATTCATATCAC
1 TATATATCC-TTCATATCAC
3881330 ATTTAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.44
Consensus pattern (20 bp):
TATATATCCTTCATATCACT
Found at i:3881541 original size:81 final size:81
Alignment explanation
Indices: 3881467--3881734 Score: 346
Period size: 81 Copynumber: 3.3 Consensus size: 81
3881457 CTAACTTGCG
* * * * * *
3881467 TAATTGGCACCTATCTACCAATTACAAACTTTGTCCATTATTATTTTCCTCAACGATATTTAACC
1 TAATTGGTACCTTTCTACCAATTGCAAACTTTGGCCATTATTCTTTTACTCAACGATATTTAACC
3881532 GTTCATCTAATTAGCA
66 GTTCATCTAATTAGCA
* *
3881548 TAATTGGTACCTTTCTACCAATTGCACAA-TTAGGCCATTATTCTTTTACTCAACGGTATTTAAC
1 TAATTGGTACCTTTCTACCAATTGCA-AACTTTGGCCATTATTCTTTTACTCAACGATATTTAAC
* *
3881612 CGTTAATCTAATTGGCA
65 CGTTCATCTAATTAGCA
* *
3881629 TAATTGGTACATTTATACCAATTGC--ACTATTAGGCCATT-TTCTTTTACTCAACGATATTTAA
1 TAATTGGTACCTTTCTACCAATTGCAAACT-TT-GGCCATTATTCTTTTACTCAACGATATTTAA
*
3881691 CCGTTCATCTAACTAGCA
64 CCGTTCATCTAATTAGCA
* *
3881709 TAATTGGTACCTTTTTACCAACTGCA
1 TAATTGGTACCTTTCTACCAATTGCA
3881735 CAATTAGTCC
Statistics
Matches: 162, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
78 1 0.01
79 1 0.01
80 60 0.37
81 98 0.60
82 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38
Consensus pattern (81 bp):
TAATTGGTACCTTTCTACCAATTGCAAACTTTGGCCATTATTCTTTTACTCAACGATATTTAACC
GTTCATCTAATTAGCA
Found at i:3881710 original size:80 final size:81
Alignment explanation
Indices: 3881501--3881741 Score: 376
Period size: 81 Copynumber: 3.0 Consensus size: 81
3881491 CAAACTTTGT
* * *
3881501 CCATTATTATTTTCCTCAACGATATTTAACCGTTCATCTAATTAGCATAATTGGTACCTTTCTAC
1 CCATTATTCTTTTACTCAACGATATTTAACCGTTCATCTAATTAGCATAATTGGTACCTTTATAC
3881566 CAATTGCACAATTAGG
66 CAATTGCACAATTAGG
* * * *
3881582 CCATTATTCTTTTACTCAACGGTATTTAACCGTTAATCTAATTGGCATAATTGGTACATTTATAC
1 CCATTATTCTTTTACTCAACGATATTTAACCGTTCATCTAATTAGCATAATTGGTACCTTTATAC
*
3881647 CAATTGCACTATTAGG
66 CAATTGCACAATTAGG
* *
3881663 CCATT-TTCTTTTACTCAACGATATTTAACCGTTCATCTAACTAGCATAATTGGTACCTTTTTAC
1 CCATTATTCTTTTACTCAACGATATTTAACCGTTCATCTAATTAGCATAATTGGTACCTTTATAC
*
3881727 CAACTGCACAATTAG
66 CAATTGCACAATTAG
3881742 TCCTCAAAGG
Statistics
Matches: 144, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 66 0.46
81 78 0.54
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (81 bp):
CCATTATTCTTTTACTCAACGATATTTAACCGTTCATCTAATTAGCATAATTGGTACCTTTATAC
CAATTGCACAATTAGG
Found at i:3885393 original size:21 final size:20
Alignment explanation
Indices: 3885363--3885402 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3885353 TTATTTAAGT
3885363 AATAAATAATAATAATAATA
1 AATAAATAATAATAATAATA
*
3885383 AATAAGATAATAATATTAAT
1 AATAA-ATAATAATAATAAT
3885403 TAAAACCCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AATAAATAATAATAATAATA
Found at i:3886310 original size:45 final size:47
Alignment explanation
Indices: 3886193--3886318 Score: 136
Period size: 45 Copynumber: 2.8 Consensus size: 47
3886183 TATAAAATCT
* * *
3886193 CTTACCAT-TTATCCCATAAACTC-TAAGCTTA-TTTTACCAAAATA
1 CTTACCATCTAATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
* *
3886237 CTTACCATCTAAATTCCATAAGCTCATAAGCTTATTTTTTCCAATATA
1 CTTACCATCT-AATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
* * *
3886285 CTTGCCAT-T-ATTCCGTAATCTCATAAGCTTATTT
1 CTTACCATCTAATTCCATAAGCTCATAAGCTTATTT
3886319 GCATGGTTAC
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
44 8 0.11
45 24 0.34
46 11 0.16
47 9 0.13
48 18 0.26
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.40
Consensus pattern (47 bp):
CTTACCATCTAATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
Found at i:3886467 original size:40 final size:40
Alignment explanation
Indices: 3886423--3886584 Score: 279
Period size: 40 Copynumber: 4.0 Consensus size: 40
3886413 ACCGTAGTGC
3886423 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
3886463 TACACATAAGGTCGTGCCCACCATACACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
3886503 TACATATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
3886543 TACACATAAGGTCGTGACCATCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
3886583 TA
1 TA
3886585 TAAACCTGCA
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 114 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:3892958 original size:13 final size:13
Alignment explanation
Indices: 3892940--3892969 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3892930 ACGAATAGTC
*
3892940 AACAGTACCTGTG
1 AACAGTACCCGTG
3892953 AACAGTACCCGTG
1 AACAGTACCCGTG
3892966 AACA
1 AACA
3892970 ATGTGGGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.17
Consensus pattern (13 bp):
AACAGTACCCGTG
Found at i:3893523 original size:47 final size:45
Alignment explanation
Indices: 3893453--3893578 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
3893443 TATAAAATCT
*
3893453 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
3893498 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
3893545 CTTGCCA-TTATTCCGTAAGCTCATAAGTTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
3893579 GTATGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 38 0.53
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:3893727 original size:40 final size:40
Alignment explanation
Indices: 3893683--3893804 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
3893673 ACCGTAGTGC
*
3893683 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
3893723 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
3893763 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
3893803 TA
1 TA
3893805 TAAACCTGCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:3899269 original size:36 final size:38
Alignment explanation
Indices: 3899196--3899275 Score: 137
Period size: 36 Copynumber: 2.2 Consensus size: 38
3899186 GATCGAACTT
*
3899196 TTGATCTGATATTGCTTCACTACTCTTTTTGTGAAGGC
1 TTGATTTGATATTGCTTCACTACTCTTTTTGTGAAGGC
3899234 TTGATTTG-TATTGCTTCACTACTC-TTTTGTGAAGGC
1 TTGATTTGATATTGCTTCACTACTCTTTTTGTGAAGGC
3899270 TTGATT
1 TTGATT
3899276 GAGAAGAATC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 18 0.44
37 16 0.39
38 7 0.17
ACGTcount: A:0.17, C:0.16, G:0.19, T:0.47
Consensus pattern (38 bp):
TTGATTTGATATTGCTTCACTACTCTTTTTGTGAAGGC
Found at i:3910739 original size:39 final size:41
Alignment explanation
Indices: 3910634--3911089 Score: 474
Period size: 41 Copynumber: 11.1 Consensus size: 41
3910624 TAGCGACATT
* * * ** *
3910634 TTTAGCGGCGTTTTTAGAACAAACGCCGCTAAATACTTGTAT
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGACTCATAC
*
3910676 TTTAGTGGTG-TTTTATACAAACGCCGCTAAAGAC-CAT-C
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
*
3910714 GTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-AT-C
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
* *
3910753 GTTAGTGGCGTTTTGATACAAACGCCGCTAAAGACT-ATAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
** * * * *
3910793 TTTAGCAGCATTTTTAGAACAAACACCGCTAAAGACTCATTC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGACTCATAC
* * * * *
3910835 TTTAGTGGCATTTTTAATACAAACACCGCTATATACTCATAT
1 TTTAGTGGCGTTTTT-ATACAAACGCCGCTAAAGACTCATAC
* *
3910877 TTTAGTGGCATTTTTATACAAACGTCGCTAAAGACTCATAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
* * * *
3910918 TTTAGTGGTGTTTTTATATAAACGCCGCTATAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
* *
3910959 TTTAGTGGCGTTTTTATACAAACGTCGCTATAGACTCATAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
* * ** *
3911000 TTTAGTGGCGTTTTTTTTTACAAACACCGCTGTAGACTCATGC
1 TTTAGTGGCG--TTTTTATACAAACGCCGCTAAAGACTCATAC
* * * * *
3911043 TTTAGTAGCATTTTTATACAAACGCCGCTATAGACTCGTTC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
3911084 TTTAGT
1 TTTAGT
3911090 TGGAGCCCCT
Statistics
Matches: 354, Mismatches: 52, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
38 8 0.02
39 65 0.18
40 29 0.08
41 158 0.45
42 59 0.17
43 35 0.10
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
Found at i:3910982 original size:82 final size:82
Alignment explanation
Indices: 3910634--3911089 Score: 474
Period size: 84 Copynumber: 5.6 Consensus size: 82
3910624 TAGCGACATT
* * * * ** *
3910634 TTTAGCGGCGTTTTTAGAACAAACGCCGCTAAATACTTGTATTTTAGTGGTG-TTTTATACAAAC
1 TTTAGTGGCATTTTTA-TACAAACGCCGCTAAAGACTCATACTTTAGTGGTGTTTTTATACAAAC
*
3910698 GCCGCTAAAGAC-CAT-C
65 GCCGCTATAGACTCATAC
* * * * *
3910714 GTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-AT-CGTTAGTGGCGTTTTGATACAAACG
1 TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGTGTTTTTATACAAACG
*
3910777 CCGCTAAAGACT-ATAC
66 CCGCTATAGACTCATAC
** * * * **
3910793 TTTAGCAGCATTTTTAGAACAAACACCGCTAAAGACTCATTCTTTAGTGGCATTTTTAATACAAA
1 TTTAGTGGCATTTTTA-TACAAACGCCGCTAAAGACTCATACTTTAGTGGTGTTTTT-ATACAAA
* * *
3910858 CACCGCTATATACTCATAT
64 CGCCGCTATAGACTCATAC
* *
3910877 TTTAGTGGCATTTTTATACAAACGTCGCTAAAGACTCATACTTTAGTGGTGTTTTTATATAAACG
1 TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGTGTTTTTATACAAACG
*
3910942 CCGCTATAGACTCGTAC
66 CCGCTATAGACTCATAC
* * * * *
3910959 TTTAGTGGCGTTTTTATACAAACGTCGCTATAGACTCATACTTTAGTGGCGTTTTTTTTTACAAA
1 TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCATACTTTAGT-G-GTGTTTTTATACAAA
* * *
3911024 CACCGCTGTAGACTCATGC
64 CGCCGCTATAGACTCATAC
* * * *
3911043 TTTAGTAGCATTTTTATACAAACGCCGCTATAGACTCGTTCTTTAGT
1 TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCATACTTTAGT
3911090 TGGAGCCCCT
Statistics
Matches: 317, Mismatches: 49, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
77 8 0.03
78 26 0.08
79 31 0.10
80 32 0.10
81 2 0.01
82 79 0.25
83 53 0.17
84 86 0.27
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (82 bp):
TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGTGTTTTTATACAAACG
CCGCTATAGACTCATAC
Found at i:3911046 original size:125 final size:123
Alignment explanation
Indices: 3910634--3911089 Score: 494
Period size: 125 Copynumber: 3.7 Consensus size: 123
3910624 TAGCGACATT
* * * ** * *
3910634 TTTAGCGGCGTTTTTAGAACAAACGCCGCTAAATACTTGTATTTTAGT-G-GTGTTTTATACAAA
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGACTCATACTTTAGTAGCAT-TTTTATACAAA
* *
3910697 CGCCGCTAAAGAC-CA-TCGTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-AT-C
64 CGCCGCTAAAGACTCATTCTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCATAC
* * * *
3910753 GTTAGTGGCGTTTTGATACAAACGCCGCTAAAGACT-ATACTTTAGCAGCATTTTTAGAACAAAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTAGCATTTTTA-TACAAAC
* * * * *
3910817 ACCGCTAAAGACTCATTCTTTAGTGGCATTTTTAATACAAACACCGCTATATACTCATAT
65 GCCGCTAAAGACTCATTCTTTAGTGGCGTTTTT-ATACAAACGCCGCTATAGACTCATAC
* * * ** *
3910877 TTTAGTGGCATTTTTATACAAACGTCGCTAAAGACTCATACTTTAGTGGTGTTTTTATATAAACG
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTAGCATTTTTATACAAACG
* * * *
3910942 CCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAACGTCGCTATAGACTCATAC
66 CCGCTAAAGACTCATTCTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCATAC
* * ** *
3911000 TTTAGTGGCGTTTTTTTTTACAAACACCGCTGTAGACTCATGCTTTAGTAGCATTTTTATACAAA
1 TTTAGTGGCG--TTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTAGCATTTTTATACAAA
* *
3911065 CGCCGCTATAGACTCGTTCTTTAGT
64 CGCCGCTAAAGACTCATTCTTTAGT
3911090 TGGAGCCCCT
Statistics
Matches: 278, Mismatches: 48, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
117 7 0.03
118 24 0.09
119 31 0.11
120 2 0.01
121 15 0.05
122 18 0.06
123 33 0.12
124 65 0.23
125 83 0.30
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (123 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTAGCATTTTTATACAAACG
CCGCTAAAGACTCATTCTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCATAC
Found at i:3913698 original size:2 final size:2
Alignment explanation
Indices: 3913691--3913717 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3913681 TATTACGATA
3913691 AT 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 AT A
3913718 ATGTAGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3913912 original size:16 final size:16
Alignment explanation
Indices: 3913891--3913927 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
3913881 TGATCTTATT
3913891 GCATGTGGTTAATGTA
1 GCATGTGGTTAATGTA
*
3913907 GCATGTGGTTGATGTA
1 GCATGTGGTTAATGTA
3913923 GCATG
1 GCATG
3913928 CAATTTTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.08, G:0.35, T:0.35
Consensus pattern (16 bp):
GCATGTGGTTAATGTA
Found at i:3915081 original size:43 final size:44
Alignment explanation
Indices: 3915024--3915232 Score: 205
Period size: 43 Copynumber: 4.9 Consensus size: 44
3915014 GCGTTTTTGA
** * * *
3915024 AAAAACGCTGCTATAGATCT-AACTTTTTGCGGCGTTTGTATCT
1 AAAAACGCCACTATAGATCTCGACCTTTTGCGGCGTTTGTATCC
* * * * **
3915067 AAAAATGACACTATAGATCT-GGCCTTTTACGATGTTTGTATCC
1 AAAAACGCCACTATAGATCTCGACCTTTTGCGGCGTTTGTATCC
*
3915110 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGC-TTT-TATTCC
1 AAAAACGCCACTATAGATCTCGACCTTTTGCGGCGTTTGTA-TCC
*
3915153 -AAAACGCCACTATAGATATCGACCTTTTGCGGCGTTTGT-TCC
1 AAAAACGCCACTATAGATCTCGACCTTTTGCGGCGTTTGTATCC
* * * * *
3915195 AAAAACGCCGCGATAGATATTGACCTATTGCGGCGTTT
1 AAAAACGCCACTATAGATCTCGACCTTTTGCGGCGTTT
3915233 TTTGTTCTCA
Statistics
Matches: 137, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
42 36 0.26
43 91 0.66
44 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (44 bp):
AAAAACGCCACTATAGATCTCGACCTTTTGCGGCGTTTGTATCC
Found at i:3915175 original size:42 final size:43
Alignment explanation
Indices: 3915107--3915233 Score: 175
Period size: 42 Copynumber: 3.0 Consensus size: 43
3915097 GATGTTTGTA
*
3915107 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCTTTTAT
1 TCCAAAAACGCCGCTATAGATATCGACCTTTTGCGGCTTTTAT
* * *
3915150 TCC-AAAACGCCACTATAGATATCGACCTTTTGCGGCGTTTGT
1 TCCAAAAACGCCGCTATAGATATCGACCTTTTGCGGCTTTTAT
* * *
3915192 TCCAAAAACGCCGCGATAGATATTGACCTATTGCGGCGTTTT
1 TCCAAAAACGCCGCTATAGATATCGACCTTTTGCGGC-TTTT
3915234 TTGTTCTCAA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
42 38 0.52
43 32 0.44
44 3 0.04
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (43 bp):
TCCAAAAACGCCGCTATAGATATCGACCTTTTGCGGCTTTTAT
Found at i:3915204 original size:85 final size:84
Alignment explanation
Indices: 3915011--3915233 Score: 227
Period size: 85 Copynumber: 2.6 Consensus size: 84
3915001 GAGGTAATTA
** * * * *
3915011 GCGGCGTTT-TTGAAAAAACGCTGCTATAGATCTAACTTTTTGCGGCGTTTGTATCTAAAAATGA
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTT-TATCTAAAAACGA
* *
3915075 CACTATAGATCTGGCCTTTT
65 CACTATAGATATGACCTTTT
* ** *
3915095 ACGATGTTTGTATCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGC-TTTTAT-TCCAAAAC
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTTATCT-AAAAAC
*
3915158 GCCACTATAGATATCGACCTTTT
63 GACACTATAGATAT-GACCTTTT
* * *
3915181 GCGGCGTTTGTTCCAAAAACGCCGCGATAGATATTGACCTATTGCGGCGTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGAT-CTGACCTTTTGCGGCGTTTT
3915234 TTGTTCTCAA
Statistics
Matches: 113, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
84 7 0.06
85 52 0.46
86 43 0.38
87 11 0.10
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (84 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTTATCTAAAAACGAC
ACTATAGATATGACCTTTT
Found at i:3919989 original size:20 final size:21
Alignment explanation
Indices: 3919951--3919990 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3919941 TATTGGACAC
*
3919951 AAAATATTGAATAAAAATATA
1 AAAATATTGAAGAAAAATATA
*
3919972 AAAATATT-AAGAATAATAT
1 AAAATATTGAAGAAAAATAT
3919991 TTTAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAATATTGAAGAAAAATATA
Found at i:3921048 original size:35 final size:35
Alignment explanation
Indices: 3920998--3921077 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
3920988 ACAAGATTTG
**
3920998 GTGGTGGTAGAACTTGTTACTGGCGATGACTTGAT
1 GTGGTGGTAGAACTTGTTACTGGCGAAAACTTGAT
* * *
3921033 GTGGTGGTAGTACTTGTTATTGGCGAAAACTTGTT
1 GTGGTGGTAGAACTTGTTACTGGCGAAAACTTGAT
3921068 GTGGTGGTAG
1 GTGGTGGTAG
3921078 CAATTTTTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.19, C:0.09, G:0.36, T:0.36
Consensus pattern (35 bp):
GTGGTGGTAGAACTTGTTACTGGCGAAAACTTGAT
Found at i:3921334 original size:17 final size:17
Alignment explanation
Indices: 3921312--3921348 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3921302 AAACTTAATT
*
3921312 TATTTATCATAAGTATA
1 TATTTATCATAAATATA
3921329 TATTTATCATAAATATA
1 TATTTATCATAAATATA
3921346 TAT
1 TAT
3921349 CGATATTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (17 bp):
TATTTATCATAAATATA
Found at i:3929918 original size:26 final size:26
Alignment explanation
Indices: 3929875--3929942 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
3929865 AATGAACCAC
*
3929875 ATGCAAGGCACATGGGGGCTGATCAT
1 ATGCAAAGCACATGGGGGCTGATCAT
*
3929901 ATGTAAAGCACATGGGGGCTGATCAT
1 ATGCAAAGCACATGGGGGCTGATCAT
3929927 ATGCAAAGCACATGGG
1 ATGCAAAGCACATGGG
3929943 TGTTCTAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.32, T:0.19
Consensus pattern (26 bp):
ATGCAAAGCACATGGGGGCTGATCAT
Found at i:3940025 original size:18 final size:17
Alignment explanation
Indices: 3940002--3940036 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3939992 AACAATCATG
*
3940002 AATGGCTCTTTTGGCGTC
1 AATGGCCCTTTT-GCGTC
3940020 AATGGCCCTTTTGCGTC
1 AATGGCCCTTTTGCGTC
3940037 CAAATCATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.11, C:0.26, G:0.26, T:0.37
Consensus pattern (17 bp):
AATGGCCCTTTTGCGTC
Found at i:3942713 original size:21 final size:22
Alignment explanation
Indices: 3942688--3942738 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
3942678 CTGAAGTGCC
3942688 ACATA-ATTGTCCCGAAAGACA
1 ACATAGATTGTCCCGAAAGACA
* *
3942709 ACATATGTTTGTCCCGAAAGACC
1 ACATA-GATTGTCCCGAAAGACA
3942732 ACATAGA
1 ACATAGA
3942739 ACCCTCGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.20
22 1 0.04
23 19 0.76
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.22
Consensus pattern (22 bp):
ACATAGATTGTCCCGAAAGACA
Found at i:3949611 original size:23 final size:23
Alignment explanation
Indices: 3949574--3949637 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
3949564 CATATAATTA
* *
3949574 TCCCGAATGAGCACATAGGTTTG
1 TCCCGAAAGACCACATAGGTTTG
3949597 -CCTC-AAAGGACCACATAGGTTTG
1 TCC-CGAAA-GACCACATAGGTTTG
3949620 TCCCGAAAGACCACATAG
1 TCCCGAAAGACCACATAG
3949638 AACCCTCGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
22 4 0.11
23 26 0.74
24 5 0.14
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (23 bp):
TCCCGAAAGACCACATAGGTTTG
Found at i:3950134 original size:20 final size:19
Alignment explanation
Indices: 3950097--3950148 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
3950087 TACCTCTACA
3950097 GTACCGATACTTCCCCTTTATG
1 GTACCGATAC--CCCC-TTATG
* *
3950119 GTATCGATACCCCCTTCTG
1 GTACCGATACCCCCTTATG
3950138 GTACCGATACC
1 GTACCGATACC
3950149 ATTTTGGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 14 0.52
20 4 0.15
22 9 0.33
ACGTcount: A:0.19, C:0.35, G:0.15, T:0.31
Consensus pattern (19 bp):
GTACCGATACCCCCTTATG
Found at i:3953688 original size:22 final size:21
Alignment explanation
Indices: 3953660--3953701 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3953650 TTTAAATATA
*
3953660 TTAAAGGAAGTATCGATACTCG
1 TTAAAGG-AGTACCGATACTCG
*
3953682 TTAAAGGGGTACCGATACTC
1 TTAAAGGAGTACCGATACTC
3953702 CCTGTACTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (21 bp):
TTAAAGGAGTACCGATACTCG
Found at i:3957103 original size:29 final size:30
Alignment explanation
Indices: 3957071--3957127 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3957061 TATGTCAATT
*
3957071 TTATTTATTT-TTTCTATTTTTATTTTTGG
1 TTATTCATTTATTTCTATTTTTATTTTTGG
* *
3957100 TTATTCATTTATTTTTCTTTTTATTTTT
1 TTATTCATTTATTTCTATTTTTATTTTT
3957128 AGGTACCCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.77
Consensus pattern (30 bp):
TTATTCATTTATTTCTATTTTTATTTTTGG
Found at i:3957128 original size:18 final size:17
Alignment explanation
Indices: 3957069--3957128 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 17
3957059 TTTATGTCAA
3957069 TTTTATTTATTTTTTCTAT
1 TTTTATTT-TTTTTT-TAT
**
3957088 TTTTA-TTTTTGGTTAT
1 TTTTATTTTTTTTTTAT
3957104 TCATTTATTTTTCTTTTTAT
1 T--TTTATTTTT-TTTTTAT
3957124 TTTTA
1 TTTTA
3957129 GGTACCCCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
16 4 0.12
17 4 0.12
18 10 0.30
19 9 0.27
20 6 0.18
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTATTTTTTTTTTAT
Found at i:3958299 original size:11 final size:11
Alignment explanation
Indices: 3958285--3958311 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3958275 AAAAGGAAAA
3958285 GAGAAAAGAGT
1 GAGAAAAGAGT
3958296 GAGAAAAGAGT
1 GAGAAAAGAGT
3958307 GAGAA
1 GAGAA
3958312 GAGTGAGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.07
Consensus pattern (11 bp):
GAGAAAAGAGT
Found at i:3963887 original size:20 final size:20
Alignment explanation
Indices: 3963864--3963904 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3963854 TTTTTCATAC
*
3963864 TTATAATATTTATATATATA
1 TTATAATAATTATATATATA
*
3963884 TTATATTAATTATATATATA
1 TTATAATAATTATATATATA
3963904 T
1 T
3963905 ATTTATTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATAATAATTATATATATA
Found at i:3965046 original size:2 final size:2
Alignment explanation
Indices: 3965039--3965074 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3965029 TTATCCCTTT
3965039 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3965075 CTATTATTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3965110 original size:15 final size:14
Alignment explanation
Indices: 3965076--3965223 Score: 53
Period size: 15 Copynumber: 10.4 Consensus size: 14
3965066 ATATATATAC
*
3965076 TATTATTTCCTTTTTT
1 TATTATTT--TTTCTT
3965092 TATTATTTTATTCTT
1 TATTATTTT-TTCTT
3965107 TATTATTTTTTCTAT
1 TATTATTTTTTCT-T
* * *
3965122 TTTTCTTATTTTCAT
1 TATTATT-TTTTCTT
*
3965137 TATCT-TTATTTCATT
1 TAT-TATTTTTTC-TT
3965152 T-TT-TTATTTTCTT
1 TATTATT-TTTTCTT
3965165 TA-TATTTATTT-TAT
1 TATTATTT-TTTCT-T
*
3965179 T-TTA-TTTAT-TT
1 TATTATTTTTTCTT
3965190 TATTATTTTCTTCTT
1 TATTATTTT-TTCTT
* * *
3965205 GATT-TTATTTATT
1 TATTATTTTTTCTT
3965218 TATTAT
1 TATTAT
3965224 ATGTATATAT
Statistics
Matches: 102, Mismatches: 14, Indels: 34
0.68 0.09 0.23
Matches are distributed among these distances:
11 2 0.02
12 6 0.06
13 21 0.21
14 28 0.27
15 31 0.30
16 14 0.14
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (14 bp):
TATTATTTTTTCTT
Found at i:3965130 original size:18 final size:16
Alignment explanation
Indices: 3965086--3965221 Score: 83
Period size: 18 Copynumber: 7.6 Consensus size: 16
3965076 TATTATTTCC
*
3965086 TTTTTTTATTATTTTA
1 TTTTTTTATTTTTTTA
3965102 TTCTTTATTATTTTTTCTA
1 TT-TTT-TTATTTTTT-TA
*
3965121 TTTTTCTTATTTTCATTA
1 TTTTT-TTATTTT-TTTA
3965139 TCTTTATTTCATTTTTTTA
1 T-TTT-TTT-ATTTTTTTA
3965158 TTTTCTTTATATTTATTTTA
1 -TTT-TTT-TATTT-TTTTA
*
3965178 TTTTATTTATTTTATTA
1 TTTT-TTTATTTTTTTA
* * *
3965195 TTTTCTTCTTGATTTTA
1 TTTTTTTATT-TTTTTA
*
3965212 TTTATTTATT
1 TTTTTTTATT
3965222 ATATGTATAT
Statistics
Matches: 95, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
16 6 0.06
17 22 0.23
18 27 0.28
19 26 0.27
20 14 0.15
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.75
Consensus pattern (16 bp):
TTTTTTTATTTTTTTA
Found at i:3965130 original size:28 final size:25
Alignment explanation
Indices: 3965086--3965198 Score: 102
Period size: 28 Copynumber: 4.2 Consensus size: 25
3965076 TATTATTTCC
*
3965086 TTTTTTTATTATTTTATTCTTTATTA
1 TTTTTTTATTTTTTTATT-TTTATTA
*
3965112 TTTTTTCTATTTTTCTTATTTTCATTA
1 TTTTTT-TATTTTT-TTATTTTTATTA
*
3965139 TCTTTATTTCATTTTTTTATTTTCTTTATA
1 T-TTT-TTT-ATTTTTTTATTTT-TAT-TA
3965169 TTTATTTTATTTTATTTA-TTTTATTA
1 TTT-TTTTATTTT-TTTATTTTTATTA
3965195 TTTT
1 TTTT
3965199 CTTCTTGATT
Statistics
Matches: 73, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
25 1 0.01
26 11 0.15
27 15 0.21
28 24 0.33
29 18 0.25
30 4 0.05
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTTTTTATTTTTTTATTTTTATTA
Found at i:3965139 original size:9 final size:8
Alignment explanation
Indices: 3965089--3965198 Score: 69
Period size: 8 Copynumber: 12.5 Consensus size: 8
3965079 TATTTCCTTT
3965089 TTTTATTA
1 TTTTATTA
3965097 TTTTATT-
1 TTTTATTA
*
3965104 CTTTATTA
1 TTTTATTA
*
3965112 TTTTTTCTA
1 TTTTAT-TA
*
3965121 TTTTTCTTA
1 -TTTTATTA
3965130 TTTTCATTA
1 TTTT-ATTA
3965139 TCTTTATTTCA
1 T-TTTA-TT-A
*
3965150 TTTTTTTA
1 TTTTATTA
*
3965158 TTTTCTTTA
1 TTTT-ATTA
3965167 TATTTATTTTA
1 T-TTTA--TTA
3965178 TTTTATTTA
1 TTTTA-TTA
3965187 TTTTATTA
1 TTTTATTA
3965195 TTTT
1 TTTT
3965199 CTTCTTGATT
Statistics
Matches: 84, Mismatches: 7, Indels: 22
0.74 0.06 0.19
Matches are distributed among these distances:
7 6 0.07
8 27 0.32
9 25 0.30
10 20 0.24
11 6 0.07
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTATTA
Found at i:3965148 original size:14 final size:14
Alignment explanation
Indices: 3965131--3965225 Score: 61
Period size: 14 Copynumber: 6.8 Consensus size: 14
3965121 TTTTTCTTAT
*
3965131 TTTCATTATCTTTA
1 TTTCATTATATTTA
*
3965145 TTTCATT-TTTTTA
1 TTTCATTATATTTA
*
3965158 TTTTCTTTATATTTA
1 -TTTCATTATATTTA
* *
3965173 TTTTATTTTATTTA
1 TTTCATTATATTTA
* *
3965187 TTTTATTAT-TTTCT
1 TTTCATTATATTT-A
* *
3965201 TCTTGATTTTATTTA
1 T-TTCATTATATTTA
3965216 TTT-ATTATAT
1 TTTCATTATAT
3965226 GTATATATTA
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
13 14 0.22
14 35 0.55
15 12 0.19
16 3 0.05
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73
Consensus pattern (14 bp):
TTTCATTATATTTA
Found at i:3965172 original size:6 final size:5
Alignment explanation
Indices: 3965094--3965218 Score: 58
Period size: 5 Copynumber: 26.2 Consensus size: 5
3965084 CCTTTTTTTA
* * *
3965094 TTATT TTATT CTT-TA TTATT TT-TT CTATT TT-TC TTATT TTCA-- TTATCT
1 TTATT TTATT -TTATT TTATT TTATT TTATT TTATT TTATT TT-ATT TTAT-T
* *
3965142 TTATT TCA-T TT-TT TTATT TT-CT TTATAT TTATT TTATT TTA-T TTATT
1 TTATT TTATT TTATT TTATT TTATT TTAT-T TTATT TTATT TTATT TTATT
*
3965189 TTA-- TTATT TTCTT CTTGATT TTA-T TTATT T
1 TTATT TTATT TTATT -TT-ATT TTATT TTATT T
3965219 ATTATATGTA
Statistics
Matches: 90, Mismatches: 12, Indels: 36
0.65 0.09 0.26
Matches are distributed among these distances:
3 4 0.04
4 26 0.29
5 42 0.47
6 16 0.18
7 2 0.02
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:3965190 original size:37 final size:36
Alignment explanation
Indices: 3965094--3965221 Score: 108
Period size: 37 Copynumber: 3.5 Consensus size: 36
3965084 CCTTTTTTTA
3965094 TTATTTTATTCTT-TATTATTTTTTCTATTTT-TCTTATT
1 TTATTTTATT-TTAT-TTATTTTTT-TATTTTCT-TTATT
3965132 TTCA--TTATCTTTATTTCATTTTTTTATTTTCTTTATAT
1 TT-ATTTTAT-TTTATTT-ATTTTTTTATTTTCTTTAT-T
* *
3965170 TTATTTTATTTTATTTATTTTATTATTTTC-TT-CT
1 TTATTTTATTTTATTTATTTTTTTATTTTCTTTATT
*
3965204 TGATTTTA-TTTATTTATT
1 TTATTTTATTTTATTTATT
3965222 ATATGTATAT
Statistics
Matches: 79, Mismatches: 3, Indels: 21
0.77 0.03 0.20
Matches are distributed among these distances:
33 10 0.13
34 8 0.10
36 2 0.03
37 32 0.41
38 22 0.28
39 5 0.06
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (36 bp):
TTATTTTATTTTATTTATTTTTTTATTTTCTTTATT
Found at i:3965294 original size:16 final size:16
Alignment explanation
Indices: 3965270--3965309 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3965260 TTTTATATTT
3965270 TTTCATTTTGTTTTTG
1 TTTCATTTTGTTTTTG
*
3965286 TTTCTTTTTGTTTTTG
1 TTTCATTTTGTTTTTG
*
3965302 TTTTATTT
1 TTTCATTT
3965310 CTATTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.05, C:0.05, G:0.10, T:0.80
Consensus pattern (16 bp):
TTTCATTTTGTTTTTG
Found at i:3965316 original size:22 final size:22
Alignment explanation
Indices: 3965275--3965316 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
3965265 TATTTTTTCA
*
3965275 TTTTGTTTTTGTTTCTTTTTGT
1 TTTTGTTTTTATTTCTTTTTGT
3965297 TTTTG-TTTTATTTCTATTTT
1 TTTTGTTTTTATTTCT-TTTT
3965317 TATTTCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.05, C:0.05, G:0.10, T:0.81
Consensus pattern (22 bp):
TTTTGTTTTTATTTCTTTTTGT
Found at i:3965347 original size:13 final size:14
Alignment explanation
Indices: 3965323--3965356 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3965313 TTTTTATTTC
3965323 TTTATTTAATTTTG
1 TTTATTTAATTTTG
3965337 TTTATTT-ATTTTG
1 TTTATTTAATTTTG
*
3965350 GTTATTT
1 TTTATTT
3965357 TTTATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (14 bp):
TTTATTTAATTTTG
Found at i:3967853 original size:3 final size:3
Alignment explanation
Indices: 3967845--3967879 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
3967835 CCAGTTTAAA
3967845 ATT ATT ATT ATT ATT ATT ATAT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT A
3967880 AATAAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3967888 original size:22 final size:20
Alignment explanation
Indices: 3967843--3967879 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3967833 TTCCAGTTTA
3967843 AAAT-TATTATTATTATTAT
1 AAATATATTATTATTATTAT
*
3967862 -TATATATTATTATTATTA
1 AAATATATTATTATTATTA
3967880 AATAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 2 0.12
19 14 0.88
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
AAATATATTATTATTATTAT
Found at i:3969311 original size:18 final size:19
Alignment explanation
Indices: 3969274--3969312 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3969264 TATTTTAAAA
*
3969274 ATAAAAAAATATCATGTTT
1 ATAAAAAAATATCATATTT
*
3969293 ATAAAAATATAT-ATATTT
1 ATAAAAAAATATCATATTT
3969311 AT
1 AT
3969313 TTTATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (19 bp):
ATAAAAAAATATCATATTT
Found at i:3970889 original size:36 final size:36
Alignment explanation
Indices: 3970838--3970909 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
3970828 GAGCTATGCA
*
3970838 CACAAAGATCATGTTAGATTGATACCAAAAGTATTC
1 CACAAAGATCATGTTAGATTGATACCAAAAGCATTC
* *
3970874 CACAAAGATCCTGTTAGATTGGTACCAAAAGCATTC
1 CACAAAGATCATGTTAGATTGATACCAAAAGCATTC
3970910 TACGGTAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.26
Consensus pattern (36 bp):
CACAAAGATCATGTTAGATTGATACCAAAAGCATTC
Found at i:3971577 original size:21 final size:21
Alignment explanation
Indices: 3971537--3971577 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3971527 TTTTCATACA
**
3971537 TGCATTTGCATTTTGCATCTT
1 TGCATTTGCATTTTAAATCTT
*
3971558 TGCATTTTCATTTTAAATCT
1 TGCATTTGCATTTTAAATCT
3971578 ACATTTTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.54
Consensus pattern (21 bp):
TGCATTTGCATTTTAAATCTT
Found at i:3971600 original size:20 final size:19
Alignment explanation
Indices: 3971577--3971629 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
3971567 ATTTTAAATC
3971577 TACATTTTTGCATTTGTATT
1 TACA-TTTTGCATTTGTATT
3971597 TACA-TTTGCATCTTTGTATT
1 TACATTTTGCA--TTTGTATT
*
3971617 TTCATTTTGCATT
1 TACATTTTGCATT
3971630 CGTACTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 2 0.07
20 15 0.52
21 6 0.21
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.58
Consensus pattern (19 bp):
TACATTTTGCATTTGTATT
Found at i:3976816 original size:75 final size:75
Alignment explanation
Indices: 3976637--3976816 Score: 211
Period size: 75 Copynumber: 2.4 Consensus size: 75
3976627 ATTAGCAAGA
* *
3976637 AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTAACGCATTTTGAA
1 AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATAGGAATATTAACGAATTTTGAA
*
3976702 CGATTGTATC
66 CGATTATATC
* * * * **
3976712 AGCAAATGCTGGGGCATACTGAAATCCCATTTCAATTAG-AATAAGGAATGTTGGCGAATTTTGA
1 AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAAT-AGGAATATTAACGAATTTTGA
*
3976776 ACG-TCTATATT
65 ACGAT-TATATC
* * *
3976787 AGCAAATGTTGGGGCATGTTGAAGGCCCAT
1 AGCAAATGCTGGGGCATGCTGAAAGCCCAT
3976817 ATCATCTTTT
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
74 4 0.05
75 84 0.95
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (75 bp):
AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATAGGAATATTAACGAATTTTGAA
CGATTATATC
Found at i:3978130 original size:20 final size:22
Alignment explanation
Indices: 3978063--3978141 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
3978053 ACATCTACAT
* *
3978063 TCTTCAAAGATAATAGATT-TAT
1 TCTTCAAAGATGATAGATTCT-C
3978085 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
3978107 TCTTCAAATATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
3978129 TTTTCAAAGATGA
1 TCTTCAAAGATGA
3978142 AAGTTTTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 50 0.98
23 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:3978841 original size:42 final size:42
Alignment explanation
Indices: 3978777--3979013 Score: 285
Period size: 42 Copynumber: 5.5 Consensus size: 42
3978767 CCCACATCTG
*
3978777 TAAGACCTCCAGTGCAAGATGTTAAATCCTCCAGGTCATCCA
1 TAAGACCTCCAGTGCAAGATGTTAAATCCTCCGGGTCATCCA
* * * **
3978819 TAAGGCCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTG
1 TAAGACCTCCAGTGCAAGATG-TT-AAATCCTCCGGGTCATCCA
*
3978863 TAAGACCTCCAGTGCAAGATATTAAATCCTCCGGGTCATCCA
1 TAAGACCTCCAGTGCAAGATGTTAAATCCTCCGGGTCATCCA
* ** ****
3978905 TAAGACCTCCAGTGCAGGATGTTTAAAATCCTTAGGGTCAAATG
1 TAAGACCTCCAGTGCAAGATG-TT-AAATCCTCCGGGTCATCCA
* *
3978949 TAAGACCTCCAGTGCAAGATGTAAAATCCTCTGGGTCATCCA
1 TAAGACCTCCAGTGCAAGATGTTAAATCCTCCGGGTCATCCA
*
3978991 TAAGACCTCCAGTGCAGGATGTT
1 TAAGACCTCCAGTGCAAGATGTT
3979014 TTTTTAGTCC
Statistics
Matches: 161, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
42 88 0.55
43 7 0.04
44 66 0.41
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (42 bp):
TAAGACCTCCAGTGCAAGATGTTAAATCCTCCGGGTCATCCA
Found at i:3978916 original size:86 final size:86
Alignment explanation
Indices: 3978771--3979014 Score: 416
Period size: 86 Copynumber: 2.8 Consensus size: 86
3978761 CTATTTCCCA
* *
3978771 CATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTCCAGGTCATCCATAAGGCCTCCAGTGCAG
1 CATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTCCGGGTCATCCATAAGACCTCCAGTGCAG
*
3978836 GATGTTTAAAATCCTTCGGGT
66 GATGTTTAAAATCCTTAGGGT
*
3978857 CATCTGTAAGACCTCCAGTGCAAGATATTAAATCCTCCGGGTCATCCATAAGACCTCCAGTGCAG
1 CATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTCCGGGTCATCCATAAGACCTCCAGTGCAG
3978922 GATGTTTAAAATCCTTAGGGT
66 GATGTTTAAAATCCTTAGGGT
** * *
3978943 CAAATGTAAGACCTCCAGTGCAAGATGTAAAATCCTCTGGGTCATCCATAAGACCTCCAGTGCAG
1 CATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTCCGGGTCATCCATAAGACCTCCAGTGCAG
3979008 GATGTTT
66 GATGTTT
3979015 TTTTAGTCCT
Statistics
Matches: 149, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 149 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (86 bp):
CATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTCCGGGTCATCCATAAGACCTCCAGTGCAG
GATGTTTAAAATCCTTAGGGT
Found at i:3979197 original size:3 final size:3
Alignment explanation
Indices: 3979189--3979238 Score: 91
Period size: 3 Copynumber: 16.3 Consensus size: 3
3979179 CCAGTTTAAA
3979189 ATT ATT ATT ATT ATT ATAT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
3979235 ATT A
1 ATT A
3979239 AATAAATATT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3979680 original size:12 final size:12
Alignment explanation
Indices: 3979663--3979691 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3979653 ACAGCAAGAT
3979663 ACAACCAACAAC
1 ACAACCAACAAC
3979675 ACAACCAACAAC
1 ACAACCAACAAC
3979687 ACAAC
1 ACAAC
3979692 ATCCAGTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (12 bp):
ACAACCAACAAC
Found at i:3983954 original size:64 final size:64
Alignment explanation
Indices: 3983874--3984040 Score: 266
Period size: 64 Copynumber: 2.6 Consensus size: 64
3983864 TGCAGCTTTT
* * *
3983874 AGAGTTAATTTCAACTTCACATCGAAGGATATAGGACTCAACAAACAAC-TTTCTAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTTC-AGTTTCATTC
3983938 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTTCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTTCAGTTTCATTC
*
3984002 AAAGTCAATTTCAACTTCA-AAGCGAAGGATATTGGACTC
1 AGAGTCAATTTCAACTTCACAA-CGAAGGATATTGGACTC
3984041 GAAGCAACAC
Statistics
Matches: 97, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
63 2 0.02
64 91 0.94
65 4 0.04
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTTCAGTTTCATTC
Found at i:3984268 original size:109 final size:109
Alignment explanation
Indices: 3984127--3984467 Score: 520
Period size: 109 Copynumber: 3.1 Consensus size: 109
3984117 ACGATACTTG
** * *
3984127 GATTTCAACTTCAAAACGAAGGATATCGTGCCAACAATCCTTGGATTTCAACTTCGCAATGAAGG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCAACAATCCTTGGATTTCAACTTCACAACGAAGG
* *
3984192 ATATCCAATTCAAATCTCAACTTCACAATGAATGAGCCATCCAC
66 ATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
* *
3984236 GATTTCAACTTCACGACGAAGGATATCATGCCAACAATCCTTGGATTTTAACTTCACAACGAAGG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCAACAATCCTTGGATTTCAACTTCACAACGAAGG
* *
3984301 ATATCCAATTCAAAGCTCAACTTCACAACGAATCAACCATCCAC
66 ATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
* * * * * *
3984345 AATTTCAACTTTACGATGAAGGATATCGTGCCAACAATCCTTGGAATTCAACTTTACGACGAAGG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCAACAATCCTTGGATTTCAACTTCACAACGAAGG
* *
3984410 ATATCCAATTCCAAGCTCAACTTCACAACGAATGAGCCATCTAC
66 ATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
3984454 GATTTCAACTTCAC
1 GATTTCAACTTCAC
3984468 AGTAAATGAT
Statistics
Matches: 208, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
109 208 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (109 bp):
GATTTCAACTTCACGACGAAGGATATCGTGCCAACAATCCTTGGATTTCAACTTCACAACGAAGG
ATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
Found at i:3985168 original size:2 final size:2
Alignment explanation
Indices: 3985159--3985206 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
3985149 TTTTAACACT
3985159 TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- TA T- TGA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
3985198 TA TA TA TA T
1 TA TA TA TA T
3985207 TTATTACTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.10
2 36 0.88
3 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3986340 original size:18 final size:19
Alignment explanation
Indices: 3986309--3986344 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3986299 TTAATCTGTT
3986309 ATTATTATTATTATATATA
1 ATTATTATTATTATATATA
*
3986328 ATTA-TATTTTTATATAT
1 ATTATTATTATTATATAT
3986345 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTATTATTATTATATATA
Found at i:3986351 original size:19 final size:19
Alignment explanation
Indices: 3986329--3986369 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3986319 TTATATATAA
3986329 TTATATTTTTATATATTTT
1 TTATATTTTTATATATTTT
* * *
3986348 TTATTTTTTTCTTTATTTT
1 TTATATTTTTATATATTTT
3986367 TTA
1 TTA
3986370 CTTGTTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (19 bp):
TTATATTTTTATATATTTT
Found at i:3986407 original size:2 final size:2
Alignment explanation
Indices: 3986400--3986434 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3986390 TTTCCTTCTT
3986400 TA TA TA TA TA 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 TA TA TA TA TA T
3986435 TATTTTTATT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3986551 original size:9 final size:8
Alignment explanation
Indices: 3986537--3986641 Score: 59
Period size: 9 Copynumber: 11.6 Consensus size: 8
3986527 TATTATTTCC
3986537 TTTTTTTA
1 TTTTTTTA
3986545 TTCTTTTGT-
1 TT-TTTT-TA
3986554 TTTTTTTA
1 TTTTTTTA
*
3986562 TTATATTTA
1 TT-TTTTTA
3986571 TTTTTCTTA
1 TTTTT-TTA
*
3986580 TTTTCATTA
1 TTTT-TTTA
3986589 TCTTTATTTCA
1 T-TTT-TTT-A
3986600 TTTGTTTTA
1 TTT-TTTTA
3986609 TTTTCTTTATA
1 -TTT-TTT-TA
3986620 TTTATTTTA
1 TTT-TTTTA
*
3986629 TTTATTTA
1 TTTTTTTA
3986637 TTTTT
1 TTTTT
3986642 ATTTTCTTCT
Statistics
Matches: 77, Mismatches: 9, Indels: 22
0.71 0.08 0.20
Matches are distributed among these distances:
7 1 0.01
8 18 0.23
9 30 0.39
10 23 0.30
11 5 0.06
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (8 bp):
TTTTTTTA
Found at i:3986595 original size:15 final size:14
Alignment explanation
Indices: 3986577--3986645 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
3986567 TTTATTTTTC
*
3986577 TTATTTTCATTATCT
1 TTATTTTCATT-TAT
*
3986592 TTA-TTTCATTTGTT
1 TTATTTTCATTT-AT
*
3986606 TTATTTTCTTTATAT
1 TTATTTTCATT-TAT
3986621 TTATTTT-ATTTAT
1 TTATTTTCATTTAT
*
3986634 TTATTTTTATTT
1 TTATTTTCATTT
3986646 TCTTCTTGCT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
13 11 0.24
14 17 0.37
15 17 0.37
16 1 0.02
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (14 bp):
TTATTTTCATTTAT
Found at i:3986602 original size:29 final size:27
Alignment explanation
Indices: 3986565--3986649 Score: 89
Period size: 29 Copynumber: 3.0 Consensus size: 27
3986555 TTTTTTATTA
3986565 TATTTATTTTTCTTATTTTCATTATCTT
1 TATTTATTTTT-TTATTTTCATTATCTT
* *
3986593 TATTTCATTTGTTTTATTTTCTTTATATT
1 TATTT-ATTT-TTTTATTTTCATTATCTT
* * *
3986622 TATTTTATTTATTTATTTTTATTTTCTT
1 TA-TTTATTTTTTTATTTTCATTATCTT
3986650 CTTGCTTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
28 18 0.38
29 24 0.51
30 5 0.11
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (27 bp):
TATTTATTTTTTTATTTTCATTATCTT
Found at i:3986626 original size:24 final size:23
Alignment explanation
Indices: 3986554--3986635 Score: 67
Period size: 24 Copynumber: 3.5 Consensus size: 23
3986544 ATTCTTTTGT
* * * *
3986554 TTTTTTTATTATATTTATTTTTC
1 TTTTTTTATTTTCTTTATATTTA
* * *
3986577 TTATTTTCATTATCTTTAT-TTCA
1 TT-TTTTTATTTTCTTTATATTTA
3986600 TTTGTTTTATTTTCTTTATATTTA
1 TTT-TTTTATTTTCTTTATATTTA
3986624 TTTTATTTATTT
1 TTTT-TTTATTT
3986636 ATTTTTATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
22 1 0.02
23 20 0.42
24 27 0.56
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.74
Consensus pattern (23 bp):
TTTTTTTATTTTCTTTATATTTA
Found at i:3986643 original size:14 final size:14
Alignment explanation
Indices: 3986539--3986645 Score: 55
Period size: 14 Copynumber: 7.6 Consensus size: 14
3986529 TTATTTCCTT
*
3986539 TTTTTATTCT-TTTG
1 TTTTTATT-TATTTA
3986553 TTTTT-TTTA-TTA
1 TTTTTATTTATTTA
* *
3986565 TATTTATTTTTCTTA
1 TTTTTATTTAT-TTA
* *
3986580 TTTTCATTATCTTTA
1 TTTTTATT-TATTTA
* *
3986595 -TTTCATTTGTTTTA
1 TTTTTATTT-ATTTA
3986609 TTTTCT-TTATATTTA
1 TTTT-TATT-TATTTA
3986624 -TTTTATTTATTTA
1 TTTTTATTTATTTA
3986637 TTTTTATTT
1 TTTTTATTT
3986646 TCTTCTTGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
12 7 0.10
13 13 0.18
14 29 0.40
15 21 0.29
16 3 0.04
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTTTATTTATTTA
Found at i:3986733 original size:16 final size:16
Alignment explanation
Indices: 3986714--3986764 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
3986704 TTTCTTTTCA
3986714 TTTTTTTTATTTTTAT
1 TTTTTTTTATTTTTAT
* *
3986730 TTTTGTTTCTTTTTAT
1 TTTTTTTTATTTTTAT
*
3986746 TTTTGTTTTATTTCTAT
1 TTTT-TTTTATTTTTAT
3986763 TT
1 TT
3986765 CTATTTTCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 18 0.62
17 11 0.38
ACGTcount: A:0.10, C:0.04, G:0.04, T:0.82
Consensus pattern (16 bp):
TTTTTTTTATTTTTAT
Found at i:3986733 original size:22 final size:22
Alignment explanation
Indices: 3986694--3986777 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 22
3986684 TTCGCATTCT
* *
3986694 TTTTCTATATTTTCTTTTCATTT-
1 TTTT-TAT-TTTTATTTTTATTTC
*
3986717 TTTTTATTTTTATTTTTGTTTC
1 TTTTTATTTTTATTTTTATTTC
*
3986739 TTTTTATTTTT-GTTTTATTTC
1 TTTTTATTTTTATTTTTATTTC
3986760 TATTTCTATTTTCTATTT
1 T-TTT-TATTTT-TATTT
3986778 CATTTGTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
21 20 0.40
22 17 0.34
23 10 0.20
24 1 0.02
25 2 0.04
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTTATTTTTATTTTTATTTC
Found at i:3986784 original size:33 final size:31
Alignment explanation
Indices: 3986701--3986791 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 31
3986691 TCTTTTTCTA
* *
3986701 TATTTTCTTTTCATTTTTTTTATTTTTATTT
1 TATTTTCTTTTCATTTGTTTTATTTCTATTT
*
3986732 T-TGTTTCTTTTTATTTTTGTTTTATTTCTATTT
1 TAT-TTTCTTTTCA--TTTGTTTTATTTCTATTT
*
3986765 CTATTTTCTATTTCATTTGTTTAATTT
1 -TATTTTCT-TTTCATTTGTTTTATTT
3986792 ATTTTGTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
30 1 0.02
31 10 0.20
33 27 0.55
34 6 0.12
35 5 0.10
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.76
Consensus pattern (31 bp):
TATTTTCTTTTCATTTGTTTTATTTCTATTT
Found at i:3988853 original size:32 final size:32
Alignment explanation
Indices: 3988812--3988877 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
3988802 GACACCCAAG
* *
3988812 TTACTTTAGCAAATAACTGTAATATCTTAATT
1 TTACTTTAGCAAATAACTATAATACCTTAATT
3988844 TTACTTTAGCAAATAACTATAATACCTTAATT
1 TTACTTTAGCAAATAACTATAATACCTTAATT
3988876 TT
1 TT
3988878 GTCCGAGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.44
Consensus pattern (32 bp):
TTACTTTAGCAAATAACTATAATACCTTAATT
Found at i:3990486 original size:22 final size:23
Alignment explanation
Indices: 3990443--3990487 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
3990433 AAAGTCTAAT
*
3990443 TTAACCACTAACTTTGCTAATTTA
1 TTAACCACTAAC-TCGCTAATTTA
3990467 TTAACCACTAA-TCGCTAATTT
1 TTAACCACTAACTCGCTAATTT
3990488 TTTATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
24 11 0.55
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.40
Consensus pattern (23 bp):
TTAACCACTAACTCGCTAATTTA
Found at i:3990676 original size:28 final size:28
Alignment explanation
Indices: 3990597--3990676 Score: 70
Period size: 29 Copynumber: 2.8 Consensus size: 28
3990587 CTAACTCTAA
* *
3990597 TTATATTTCATTCACTTTAATTTCTATCAT
1 TTATATTT--TTCCCTTTAATTTATATCAT
* ** * *
3990627 TTACATTTTTTCCCTTCCATTTATGTTAT
1 TTATA-TTTTTCCCTTTAATTTATATCAT
3990656 TTATATTTTTCCCTTTAATTT
1 TTATATTTTTCCCTTTAATTT
3990677 CCCTTGTATG
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
28 14 0.36
29 18 0.46
30 4 0.10
31 3 0.08
ACGTcount: A:0.21, C:0.17, G:0.01, T:0.60
Consensus pattern (28 bp):
TTATATTTTTCCCTTTAATTTATATCAT
Found at i:3998954 original size:35 final size:35
Alignment explanation
Indices: 3998908--3999046 Score: 136
Period size: 35 Copynumber: 3.9 Consensus size: 35
3998898 CATAGATCTG
* *
3998908 TAAGGAATTACCAACTTGATCGATATGAACCTATA
1 TAAGGAATTACCAATTTGATCGATCTGAACCTATA
* * *
3998943 TAAGGAATTACCAATTTGA-CTGAGCTGAACATGTCA
1 TAAGGAATTACCAATTTGATC-GATCTGAACCTAT-A
* * * *
3998979 TAAGGAATTCCCAGTTTGATTGGTCTGAACCTATA
1 TAAGGAATTACCAATTTGATCGATCTGAACCTATA
* * * *
3999014 TAAGGAATTACTAGTTTGATCGAGCTAAACCTA
1 TAAGGAATTACCAATTTGATCGATCTGAACCTA
3999047 CAAAGACTTC
Statistics
Matches: 83, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
34 1 0.01
35 55 0.66
36 27 0.33
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (35 bp):
TAAGGAATTACCAATTTGATCGATCTGAACCTATA
Found at i:3998997 original size:36 final size:35
Alignment explanation
Indices: 3998933--3999032 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 35
3998923 TTGATCGATA
* *
3998933 TGAACCTATATAAGGAATTACCAATTTGACTGAG-C
1 TGAACATATATAAGGAATTACCAGTTTGACTG-GTC
* * *
3998968 TGAACATGTCATAAGGAATTCCCAGTTTGATTGGTC
1 TGAACATAT-ATAAGGAATTACCAGTTTGACTGGTC
* *
3999004 TGAACCTATATAAGGAATTACTAGTTTGA
1 TGAACATATATAAGGAATTACCAGTTTGA
3999033 TCGAGCTAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
35 26 0.48
36 28 0.52
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (35 bp):
TGAACATATATAAGGAATTACCAGTTTGACTGGTC
Found at i:4000143 original size:26 final size:27
Alignment explanation
Indices: 4000090--4000142 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
4000080 TTTTTACGAA
* *
4000090 ATAAGGGTATTTTTGTAATTTTACCCC
1 ATAAGGGAATTTTCGTAATTTTACCCC
4000117 ATAAGGGAATTTTCGTAATTTTACCC
1 ATAAGGGAATTTTCGTAATTTTACCC
4000143 AACCAAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (27 bp):
ATAAGGGAATTTTCGTAATTTTACCCC
Found at i:4003169 original size:35 final size:34
Alignment explanation
Indices: 4003033--4003169 Score: 98
Period size: 35 Copynumber: 3.9 Consensus size: 34
4003023 CATTGGATCC
* *
4003033 ATAAGGAATTACCAACTTGATCGATTTGAATCTAT
1 ATAAGGAATTACCAATTTGATCGAGTTGAA-CTAT
* * ** *
4003068 ATAAGGAAATACCAATTTGACCGAACTGAACCTACC
1 ATAAGGAATTACCAATTTGATCGAGTTGAA-CTA-T
* ** *
4003104 GTAAGGAATTA-CAAGTTCAATTG-GTCTGAACATAT
1 ATAAGGAATTACCAA-TTTGATCGAGT-TGAAC-TAT
*
4003139 ATAAGGAATTACCAGTTTGATCGAGTTGAAC
1 ATAAGGAATTACCAATTTGATCGAGTTGAAC
4003170 CTGCAGAGAC
Statistics
Matches: 75, Mismatches: 21, Indels: 12
0.69 0.19 0.11
Matches are distributed among these distances:
35 52 0.69
36 23 0.31
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (34 bp):
ATAAGGAATTACCAATTTGATCGAGTTGAACTAT
Found at i:4007239 original size:35 final size:35
Alignment explanation
Indices: 4007200--4007312 Score: 111
Period size: 35 Copynumber: 3.2 Consensus size: 35
4007190 TCTATCGGTC
* *
4007200 TGAACCTATATAAGGAAATACCAATTTGACCGAGT
1 TGAACCTATATAAGGAAATACCAGTTTGATCGAGT
** * * *
4007235 TGAACCTGCCATAAGTAATTACCAGTTCGATCG-GT
1 TGAACCT-ATATAAGGAAATACCAGTTTGATCGAGT
* **
4007270 CTGAACCTATATAAGGAACTAATAGTTTGATCGAGT
1 -TGAACCTATATAAGGAAATACCAGTTTGATCGAGT
4007306 TGAACCT
1 TGAACCT
4007313 GCATAGACTT
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
35 34 0.56
36 27 0.44
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (35 bp):
TGAACCTATATAAGGAAATACCAGTTTGATCGAGT
Found at i:4007299 original size:71 final size:71
Alignment explanation
Indices: 4007175--4007314 Score: 199
Period size: 71 Copynumber: 2.0 Consensus size: 71
4007165 CTTAGATCCG
* * *
4007175 TAAGGAATTACTAGCTCTATCGGTCTGAACCTATATAAGGAAATACCAATTTGACCGAGTTGAAC
1 TAAGGAATTACCAGCTCGATCGGTCTGAACCTATATAAGGAAATAACAATTTGACCGAGTTGAAC
4007240 CTGCCA
66 CTGCCA
* * * * * *
4007246 TAAGTAATTACCAGTTCGATCGGTCTGAACCTATATAAGGAACTAATAGTTTGATCGAGTTGAAC
1 TAAGGAATTACCAGCTCGATCGGTCTGAACCTATATAAGGAAATAACAATTTGACCGAGTTGAAC
4007311 CTGC
66 CTGC
4007315 ATAGACTTCA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (71 bp):
TAAGGAATTACCAGCTCGATCGGTCTGAACCTATATAAGGAAATAACAATTTGACCGAGTTGAAC
CTGCCA
Found at i:4010981 original size:33 final size:33
Alignment explanation
Indices: 4010943--4011008 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
4010933 AAAAACTCAT
4010943 GTTCGAGCAAGAAATACTTTGTTCTCGTTAGGG
1 GTTCGAGCAAGAAATACTTTGTTCTCGTTAGGG
4010976 GTTCGAGCAAGAAATACTTTGTTCTCGTTAGGG
1 GTTCGAGCAAGAAATACTTTGTTCTCGTTAGGG
4011009 TTGAAGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.33
Consensus pattern (33 bp):
GTTCGAGCAAGAAATACTTTGTTCTCGTTAGGG
Found at i:4015249 original size:27 final size:27
Alignment explanation
Indices: 4015219--4015282 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
4015209 GATAATTATT
4015219 TTTTA-CCACATAAGGGTATTTTCATAA
1 TTTTACCCA-ATAAGGGTATTTTCATAA
*
4015246 TTTTACCCAATAAGGGTATTTTCGTAA
1 TTTTACCCAATAAGGGTATTTTCATAA
4015273 TTTTACCCAA
1 TTTTACCCAA
4015283 CCAAACTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 32 0.91
28 3 0.09
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (27 bp):
TTTTACCCAATAAGGGTATTTTCATAA
Found at i:4015292 original size:27 final size:27
Alignment explanation
Indices: 4015235--4015302 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
4015225 CACATAAGGG
* **
4015235 TATTTTCATAATTTTACCCAATAAGGG
1 TATTTTCATAATTTTACCCAACAAGAC
*
4015262 TATTTTCGTAATTTTACCCAACCAA-AC
1 TATTTTCATAATTTTACCCAA-CAAGAC
**
4015289 TATTACCATAATTT
1 TATTTTCATAATTT
4015303 CTCATCTAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
27 31 0.94
28 2 0.06
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (27 bp):
TATTTTCATAATTTTACCCAACAAGAC
Found at i:4015877 original size:19 final size:19
Alignment explanation
Indices: 4015853--4015889 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4015843 TAACTTTTTT
*
4015853 GTCAAATTCAACGGGTCAG
1 GTCAAAGTCAACGGGTCAG
4015872 GTCAAAGTCAACGGGTCA
1 GTCAAAGTCAACGGGTCA
4015890 AGTCTGGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (19 bp):
GTCAAAGTCAACGGGTCAG
Found at i:4018401 original size:2 final size:2
Alignment explanation
Indices: 4018394--4018464 Score: 115
Period size: 2 Copynumber: 35.5 Consensus size: 2
4018384 TTTTATACGC
4018394 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
4018436 TA TA TA TA TA GA TA TA TA TT TA TC TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4018465 GAATCTTTCT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4019579 original size:107 final size:107
Alignment explanation
Indices: 4019425--4019638 Score: 428
Period size: 107 Copynumber: 2.0 Consensus size: 107
4019415 GCCACTAGAA
4019425 TGCTCATTTAGTGAATGCATATAATATAATACAATTATCAGTGAGGCTCTAGGCTCGTAAGCTCA
1 TGCTCATTTAGTGAATGCATATAATATAATACAATTATCAGTGAGGCTCTAGGCTCGTAAGCTCA
4019490 GCGTTCAAATTTTTTTTTCCGTGCACAGGTTCTTAGGTGACC
66 GCGTTCAAATTTTTTTTTCCGTGCACAGGTTCTTAGGTGACC
4019532 TGCTCATTTAGTGAATGCATATAATATAATACAATTATCAGTGAGGCTCTAGGCTCGTAAGCTCA
1 TGCTCATTTAGTGAATGCATATAATATAATACAATTATCAGTGAGGCTCTAGGCTCGTAAGCTCA
4019597 GCGTTCAAATTTTTTTTTCCGTGCACAGGTTCTTAGGTGACC
66 GCGTTCAAATTTTTTTTTCCGTGCACAGGTTCTTAGGTGACC
4019639 AGTCAAGGAG
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (107 bp):
TGCTCATTTAGTGAATGCATATAATATAATACAATTATCAGTGAGGCTCTAGGCTCGTAAGCTCA
GCGTTCAAATTTTTTTTTCCGTGCACAGGTTCTTAGGTGACC
Found at i:4021708 original size:27 final size:27
Alignment explanation
Indices: 4021661--4021729 Score: 120
Period size: 27 Copynumber: 2.5 Consensus size: 27
4021651 TTGAACTATA
4021661 AAATGACCAAAAAATGCCCCTAGAGTGT
1 AAATGACC-AAAAATGCCCCTAGAGTGT
4021689 AAATGACCAAAAATGCCCCTAGAGTGT
1 AAATGACCAAAAATGCCCCTAGAGTGT
*
4021716 AAATGACCTAAAAT
1 AAATGACCAAAAAT
4021730 ACCCTCAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 32 0.80
28 8 0.20
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.19
Consensus pattern (27 bp):
AAATGACCAAAAATGCCCCTAGAGTGT
Found at i:4022593 original size:35 final size:36
Alignment explanation
Indices: 4022515--4022654 Score: 119
Period size: 35 Copynumber: 4.0 Consensus size: 36
4022505 GAAGTATCTG
* *
4022515 CAGGTTCAACTCTGATCAAGCTGGTTATTTCTTATA
1 CAGGTTCAACTCTGATCAAGCTGGTAATTCCTTATA
* *
4022551 TAGGTTCAACTCTCG-TCAAG-TTGTAATTCCTTATA
1 CAGGTTCAACTCT-GATCAAGCTGGTAATTCCTTATA
* * * * * *
4022586 CATGTTCAGCACCGATC-GGTTGGTAATTCCTTATA
1 CAGGTTCAACTCTGATCAAGCTGGTAATTCCTTATA
* *
4022621 TAGGTTCAA-TACTGCTC-AGCTGGTAATTCCTTAT
1 CAGGTTCAACT-CTGATCAAGCTGGTAATTCCTTAT
4022655 GGATCTAAGG
Statistics
Matches: 81, Mismatches: 19, Indels: 9
0.74 0.17 0.08
Matches are distributed among these distances:
34 2 0.02
35 61 0.75
36 17 0.21
37 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (36 bp):
CAGGTTCAACTCTGATCAAGCTGGTAATTCCTTATA
Found at i:4026795 original size:36 final size:36
Alignment explanation
Indices: 4026754--4026884 Score: 142
Period size: 35 Copynumber: 3.7 Consensus size: 36
4026744 CATGTTTAGC
* *
4026754 TCTGATCGAGCTGGTAATTCCTTATATAGGCTCAGT
1 TCTGATCGAGCTGGTAATTCCTTATATAGGTTCAAT
* * * * *
4026790 TCTGATCAAGCTGGTAATTCTTTATATAAGTTAAAC
1 TCTGATCGAGCTGGTAATTCCTTATATAGGTTCAAT
* *
4026826 ACTGATCGA-TTGGTAATTCCTTATATAGGTTCAAT
1 TCTGATCGAGCTGGTAATTCCTTATATAGGTTCAAT
*
4026861 AT-TGATC-AGTTGGTAATTCCTTAT
1 -TCTGATCGAGCTGGTAATTCCTTAT
4026885 GGATCTAAGG
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
34 1 0.01
35 41 0.53
36 36 0.46
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (36 bp):
TCTGATCGAGCTGGTAATTCCTTATATAGGTTCAAT
Found at i:4028353 original size:20 final size:21
Alignment explanation
Indices: 4028309--4028356 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
4028299 TTAAAATTGT
4028309 TCTAATAATTACTGCAAAGATA
1 TCTAA-AATTACTGCAAAGATA
*
4028331 TCTAAAATTACTG-AAATATA
1 TCTAAAATTACTGCAAAGATA
4028351 TCTAAA
1 TCTAAA
4028357 GTTAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 12 0.48
21 8 0.32
22 5 0.20
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (21 bp):
TCTAAAATTACTGCAAAGATA
Found at i:4029820 original size:115 final size:115
Alignment explanation
Indices: 4029618--4029847 Score: 415
Period size: 115 Copynumber: 2.0 Consensus size: 115
4029608 TGAATAAATC
4029618 AAATAAGGTAGACGATATAGGTTCAGTGAGCCCCATATCACGCTCTTGATTGAGAGTGATGTTGC
1 AAATAAGGTAGACGATATAGGTTCAGTGAGCCCCATATCACGCTCTTGATTGAGAGTGATGTTGC
* *
4029683 ACTCTAACATTCACTATGGCTCGAAGGATCTCTTATCCAAGAGTATTTAT
66 ACTCTAACATTCACTATGGCTCGAAGGATCTATCATCCAAGAGTATTTAT
* *
4029733 AAATAAGGTAGACGATTTAGGTTCGGTGAGCCCCATATCACGCTCTTGATTGAGAGTGATGTTGC
1 AAATAAGGTAGACGATATAGGTTCAGTGAGCCCCATATCACGCTCTTGATTGAGAGTGATGTTGC
*
4029798 ACTCTAACATTCGCTATGGCTCGAAGGATCTATCATCCAAGAGTATTTAT
66 ACTCTAACATTCACTATGGCTCGAAGGATCTATCATCCAAGAGTATTTAT
4029848 GGCTTTCAAA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
115 110 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (115 bp):
AAATAAGGTAGACGATATAGGTTCAGTGAGCCCCATATCACGCTCTTGATTGAGAGTGATGTTGC
ACTCTAACATTCACTATGGCTCGAAGGATCTATCATCCAAGAGTATTTAT
Found at i:4033735 original size:17 final size:16
Alignment explanation
Indices: 4033715--4033756 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
4033705 TAATTATGTG
4033715 AATTAAACAAATGACTAA
1 AATTAAACAAATG-C-AA
*
4033733 ATTTAAA-AAATGCAA
1 AATTAAACAAATGCAA
4033748 AATTAAACA
1 AATTAAACA
4033757 TACAATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 8 0.38
16 2 0.10
17 5 0.24
18 6 0.29
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.24
Consensus pattern (16 bp):
AATTAAACAAATGCAA
Found at i:4036324 original size:7 final size:7
Alignment explanation
Indices: 4036312--4036336 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4036302 TTATTAAGTA
4036312 TAAACTT
1 TAAACTT
4036319 TAAACTT
1 TAAACTT
4036326 TAAACTT
1 TAAACTT
4036333 TAAA
1 TAAA
4036337 TACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAACTT
Found at i:4040600 original size:16 final size:16
Alignment explanation
Indices: 4040581--4040632 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
4040571 AAATATGCGG
4040581 TAAATCAGATATCACA
1 TAAATCAGATATCACA
*
4040597 TAAA-CAG-TATTCCAAA
1 TAAATCAGATA-T-CACA
*
4040613 CAAATCAGATATCACA
1 TAAATCAGATATCACA
4040629 TAAA
1 TAAA
4040633 CAGTATTCCG
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 2 0.07
15 4 0.14
16 16 0.57
17 4 0.14
18 2 0.07
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (16 bp):
TAAATCAGATATCACA
Found at i:4040623 original size:32 final size:32
Alignment explanation
Indices: 4040582--4040646 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
4040572 AATATGCGGT
4040582 AAATCAGATATCACATAAACAGTATTCCAAAC
1 AAATCAGATATCACATAAACAGTATTCCAAAC
*
4040614 AAATCAGATATCACATAAACAGTATTCCGAAC
1 AAATCAGATATCACATAAACAGTATTCCAAAC
4040646 A
1 A
4040647 TCGGATATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.49, C:0.22, G:0.08, T:0.22
Consensus pattern (32 bp):
AAATCAGATATCACATAAACAGTATTCCAAAC
Found at i:4041277 original size:18 final size:18
Alignment explanation
Indices: 4041196--4041261 Score: 123
Period size: 18 Copynumber: 3.7 Consensus size: 18
4041186 TTTTGGTCAA
*
4041196 AGTCAACGGTCAACAATT
1 AGTCAACGGTCAACAATC
4041214 AGTCAACGGTCAACAATC
1 AGTCAACGGTCAACAATC
4041232 AGTCAACGGTCAACAATC
1 AGTCAACGGTCAACAATC
4041250 AGTCAACGGTCA
1 AGTCAACGGTCA
4041262 GTCATCGGTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (18 bp):
AGTCAACGGTCAACAATC
Found at i:4041352 original size:16 final size:15
Alignment explanation
Indices: 4041322--4041365 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
4041312 TTCAAGTCAG
*
4041322 CAGGTCGGACAGATA
1 CAGGTCGGTCAGATA
4041337 CAGGTCGAGTCAGATA
1 CAGGTCG-GTCAGATA
*
4041353 CGGGTCGGGTCAG
1 CAGGTC-GGTCAG
4041366 GTCAACAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 17 0.68
17 1 0.04
ACGTcount: A:0.25, C:0.20, G:0.39, T:0.16
Consensus pattern (15 bp):
CAGGTCGGTCAGATA
Found at i:4046895 original size:32 final size:32
Alignment explanation
Indices: 4046850--4046914 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
4046840 AATATGTGGT
* *
4046850 AAATCATACATCACATAAACAGTATTCCGAAC
1 AAATCAGACATCACATAAACAATATTCCGAAC
*
4046882 AAATCAGATATCACATAAACAATATTCCGAAC
1 AAATCAGACATCACATAAACAATATTCCGAAC
4046914 A
1 A
4046915 TTGGATATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.22
Consensus pattern (32 bp):
AAATCAGACATCACATAAACAATATTCCGAAC
Found at i:4048848 original size:23 final size:23
Alignment explanation
Indices: 4048818--4048880 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
4048808 ACTGCCTGCT
4048818 ACCGCGTGTTTAACCCACTTGCC
1 ACCGCGTGTTTAACCCACTTGCC
4048841 ACCGCGTGTTTAACCCACTTGCC
1 ACCGCGTGTTTAACCCACTTGCC
*
4048864 ACCGCGTGCTTAACCCA
1 ACCGCGTGTTTAACCCA
4048881 TTTCCTTGTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.17, T:0.24
Consensus pattern (23 bp):
ACCGCGTGTTTAACCCACTTGCC
Found at i:4049252 original size:24 final size:24
Alignment explanation
Indices: 4049225--4049294 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
4049215 CGTTCATTTA
4049225 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
4049249 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * *
4049273 CGTTCGGTTATGTTCGCTTATG
1 CGTTCGGTAACGTTCGGTTATG
4049295 CTCATTCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 39 0.95
25 2 0.05
ACGTcount: A:0.10, C:0.16, G:0.27, T:0.47
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:4049254 original size:14 final size:14
Alignment explanation
Indices: 4049235--4049288 Score: 80
Period size: 14 Copynumber: 4.1 Consensus size: 14
4049225 CGTTCGTGAA
4049235 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
4049249 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
4049263 CG-T---TTATGTT
1 CGTTCGGTTATGTT
4049273 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
4049287 CG
1 CG
4049289 CTTATGCTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 1 0.03
14 25 0.69
ACGTcount: A:0.07, C:0.15, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:4049307 original size:24 final size:24
Alignment explanation
Indices: 4049236--4049310 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
4049226 GTTCGTGAAC
* * * *
4049236 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGCTTATGCTCATTCAGTTAT
* * * *
4049260 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGCTTATGCTCATTCAGTTAT
*
4049284 GTTCGCTTATGCTCATTCATTTAT
1 GTTCGCTTATGCTCATTCAGTTAT
4049308 GTT
1 GTT
4049311 TAACCCAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.11, C:0.15, G:0.23, T:0.52
Consensus pattern (24 bp):
GTTCGCTTATGCTCATTCAGTTAT
Done.