Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 26 of 109
Found at i:4463631 original size:25 final size:25
Alignment explanation
Indices: 4463541--4463633 Score: 80
Period size: 25 Copynumber: 3.5 Consensus size: 25
4463531 TATGATAATT
*
4463541 ATTAAATAAATATCATAATTAAATA
1 ATTAAAAAAATATCATAATTAAATA
*
4463566 TTTAAAATAATTTATAT-ATGATATTAAATA
1 ATTAAAA-AA---ATATCAT-A-ATTAAATA
** *
4463596 ATTAATTAAATATCATAATTAAAAA
1 ATTAAAAAAATATCATAATTAAATA
4463621 ATTAAAAAAATAT
1 ATTAAAAAAATAT
4463634 TTATATATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
25 23 0.43
26 7 0.13
27 2 0.04
28 2 0.04
29 7 0.13
30 12 0.23
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (25 bp):
ATTAAAAAAATATCATAATTAAATA
Found at i:4464807 original size:24 final size:24
Alignment explanation
Indices: 4464773--4464820 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
4464763 TGGAGTTCGG
*
4464773 GGGCTGATTTTTTTGGCATAGATT
1 GGGCTGATTTTTTTGGCAGAGATT
*
4464797 GGGCTGGTTTTTTTGGCAGAGATT
1 GGGCTGATTTTTTTGGCAGAGATT
4464821 AGGTAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.08, G:0.33, T:0.44
Consensus pattern (24 bp):
GGGCTGATTTTTTTGGCAGAGATT
Found at i:4465764 original size:16 final size:17
Alignment explanation
Indices: 4465732--4465765 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4465722 TATATACATT
4465732 TAAATTTATTTAGTAAA
1 TAAATTTATTTAGTAAA
*
4465749 TAAATTT-TTTATTAAA
1 TAAATTTATTTAGTAAA
4465765 T
1 T
4465766 GATATAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TAAATTTATTTAGTAAA
Found at i:4465833 original size:14 final size:14
Alignment explanation
Indices: 4465814--4465853 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
4465804 ATATTTATTG
4465814 AAAATATATATTAA
1 AAAATATATATTAA
*
4465828 AAAATATTTA-TAA
1 AAAATATATATTAA
4465841 AAAAT-TAT-TTAA
1 AAAATATATATTAA
4465853 A
1 A
4465854 TATACAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 6 0.26
13 8 0.35
14 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATATATATTAA
Found at i:4465844 original size:27 final size:25
Alignment explanation
Indices: 4465804--4465853 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
4465794 AAATTAATAT
**
4465804 ATATTTATTGAAAATATATATTAAAAA
1 ATATTTATAAAAAAT-TAT-TTAAAAA
4465831 ATATTTATAAAAAATTATTTAAA
1 ATATTTATAAAAAATTATTTAAA
4465854 TATACAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 3 0.14
27 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
ATATTTATAAAAAATTATTTAAAAA
Found at i:4467197 original size:20 final size:20
Alignment explanation
Indices: 4467174--4467237 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
4467164 GATTTATGAA
4467174 TTTAATTAAAATTTTA-TAT
1 TTTAATTAAAATTTTATTAT
* * *
4467193 TTTTATATATATTTTTATTAT
1 TTTAAT-TAAAATTTTATTAT
4467214 TTTAATTCAAAA-TTTATTAT
1 TTTAATT-AAAATTTTATTAT
4467234 TTTA
1 TTTA
4467238 TTTTTATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
19 5 0.14
20 21 0.58
21 10 0.28
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAATTAAAATTTTATTAT
Found at i:4469648 original size:17 final size:17
Alignment explanation
Indices: 4469595--4469648 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
4469585 TTTAATTTTC
*
4469595 TAATTTTTTTATATATAT
1 TAATATTTTTATATAT-T
* *
4469613 TATTATTTTTGT-TATTT
1 TAATATTTTTATATA-TT
4469630 TAATATTTTTATATATT
1 TAATATTTTTATATATT
4469647 TA
1 TA
4469649 TGCATGATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TAATATTTTTATATATT
Found at i:4475035 original size:45 final size:45
Alignment explanation
Indices: 4474966--4475080 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
4474956 AAAGGCCCCA
* * *
4474966 TTACTGTCCCTCCCATTGTTAAACCCCCAATCA-ACTTGCCACCAG
1 TTACTGTCCCTCCAATTGTAAAACCCCCAATCACAC-TCCCACCAG
* * *
4475011 TTACTGTCCCTCCAATTGTAAAACCCCCAGTGACACTCCCTCCAG
1 TTACTGTCCCTCCAATTGTAAAACCCCCAATCACACTCCCACCAG
*
4475056 TTACTGTTCCTCCAATTGTAAAACC
1 TTACTGTCCCTCCAATTGTAAAACC
4475081 ACCGGTTACA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 60 0.97
46 2 0.03
ACGTcount: A:0.25, C:0.37, G:0.10, T:0.28
Consensus pattern (45 bp):
TTACTGTCCCTCCAATTGTAAAACCCCCAATCACACTCCCACCAG
Found at i:4475083 original size:75 final size:75
Alignment explanation
Indices: 4475004--4475144 Score: 176
Period size: 75 Copynumber: 1.9 Consensus size: 75
4474994 AATCAACTTG
* * * *
4475004 CCACCAGTTACTGTCCCTCCAATTGTAAAACCCCCAGTG-ACACTCCCTCCAGTTACTGTTCCTC
1 CCACCAGTTACAGTCCCTCCAATTGTAAAACCACCAATGAAC-CTCCCTCCAGTGACTGTTCCTC
4475068 CAATTGTAAAA
65 CAATTGTAAAA
* * * * * *
4475079 CCACCGGTTACAGTTCCTCCAATTGTGAAGCCACCAATTAACCTCCCTCCTGTGACTGTTCCTCC
1 CCACCAGTTACAGTCCCTCCAATTGTAAAACCACCAATGAACCTCCCTCCAGTGACTGTTCCTCC
4475144 A
66 A
4475145 GTGACTGTCA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
75 53 0.96
76 2 0.04
ACGTcount: A:0.24, C:0.37, G:0.12, T:0.27
Consensus pattern (75 bp):
CCACCAGTTACAGTCCCTCCAATTGTAAAACCACCAATGAACCTCCCTCCAGTGACTGTTCCTCC
AATTGTAAAA
Found at i:4475095 original size:30 final size:30
Alignment explanation
Indices: 4475055--4475113 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
4475045 ACTCCCTCCA
*
4475055 GTTACTGTTCCTCCAATTGTAAAACCACCG
1 GTTACAGTTCCTCCAATTGTAAAACCACCG
* *
4475085 GTTACAGTTCCTCCAATTGTGAAGCCACC
1 GTTACAGTTCCTCCAATTGTAAAACCACC
4475114 AATTAACCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (30 bp):
GTTACAGTTCCTCCAATTGTAAAACCACCG
Found at i:4475219 original size:60 final size:59
Alignment explanation
Indices: 4475082--4475220 Score: 188
Period size: 60 Copynumber: 2.3 Consensus size: 59
4475072 TGTAAAACCA
* * * *
4475082 CCGGTTACAGTTCCTCCAATTGTGAAGCCACCAATTAACCTCCCTCCTGTGACTGTTCCT
1 CCGGTGACAG-TCCTCCAATTGTGAAGCCACCAATTAACCTCCCTCCAGTGACAGGTCCT
* * *
4475142 CCAGTGACTGTCACTCCAATTGTGAAGCCACCCATTAACCTCCCTCCAGTGACAGGTCCT
1 CCGGTGACAGTC-CTCCAATTGTGAAGCCACCAATTAACCTCCCTCCAGTGACAGGTCCT
4475202 CCGGTGACAGTGCCTCCAA
1 CCGGTGACAGT-CCTCCAA
4475221 CTACTAATCC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 2 0.03
60 65 0.96
61 1 0.01
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (59 bp):
CCGGTGACAGTCCTCCAATTGTGAAGCCACCAATTAACCTCCCTCCAGTGACAGGTCCT
Found at i:4478903 original size:17 final size:17
Alignment explanation
Indices: 4478855--4478894 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
4478845 TGATTTTACA
*
4478855 AGTAATAAGATTATTTT
1 AGTAATAAGATTACTTT
4478872 AGTAATAAGATTACTTT
1 AGTAATAAGATTACTTT
4478889 AGTAAT
1 AGTAAT
4478895 TATATTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (17 bp):
AGTAATAAGATTACTTT
Found at i:4485422 original size:15 final size:15
Alignment explanation
Indices: 4485402--4485432 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4485392 CCAAGTAATC
4485402 ACACTACAAATATTT
1 ACACTACAAATATTT
4485417 ACACTACAAATATTT
1 ACACTACAAATATTT
4485432 A
1 A
4485433 GAACTTACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (15 bp):
ACACTACAAATATTT
Found at i:4492264 original size:2 final size:2
Alignment explanation
Indices: 4492257--4492283 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4492247 ACAACTCAAA
4492257 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
4492284 AGCCCCTTTG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4496660 original size:2 final size:2
Alignment explanation
Indices: 4496653--4496686 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4496643 TACTTCTTGC
4496653 AT AT AT AT A- AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4496687 GTAGATAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4496675 original size:17 final size:17
Alignment explanation
Indices: 4496653--4496686 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4496643 TACTTCTTGC
4496653 ATATATATAATATATAT
1 ATATATATAATATATAT
*
4496670 ATATATATATTATATAT
1 ATATATATAATATATAT
4496687 GTAGATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATATAATATATAT
Found at i:4497682 original size:32 final size:31
Alignment explanation
Indices: 4497629--4497750 Score: 93
Period size: 32 Copynumber: 3.9 Consensus size: 31
4497619 AATAATTTTT
**
4497629 TAAAAATTCTATATCTTTTTAAAAAATTAAA
1 TAAAAATTCTATATCGGTTTAAAAAATTAAA
* *
4497660 TAAAAATTTTTATATCGGTTTAAGAAATTAAA
1 TAAAAA-TTCTATATCGGTTTAAAAAATTAAA
* * * * **
4497692 TAAAAACTCCATAT-GATTTTAAAATATTATG
1 TAAAAATTCTATATCG-GTTTAAAAAATTAAA
* **
4497723 TAAAAATTTTCATATCATTTTAAAAAAT
1 TAAAAATTCT-ATATCGGTTTAAAAAAT
4497751 ATTTTTATTA
Statistics
Matches: 70, Mismatches: 17, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
30 1 0.01
31 28 0.40
32 41 0.59
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (31 bp):
TAAAAATTCTATATCGGTTTAAAAAATTAAA
Found at i:4498050 original size:22 final size:20
Alignment explanation
Indices: 4498008--4498046 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4497998 GAAAATATAC
* *
4498008 ATTTTTTAAAAATGTATTGA
1 ATTTTTTAAAAAGGAATTGA
4498028 ATTTTTTAAAAAAGGAATT
1 ATTTTTT-AAAAAGGAATT
4498047 TGAAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (20 bp):
ATTTTTTAAAAAGGAATTGA
Found at i:4498481 original size:2 final size:2
Alignment explanation
Indices: 4498476--4498500 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4498466 AAAATTAACC
4498476 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4498501 AAGAAACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4498716 original size:20 final size:20
Alignment explanation
Indices: 4498662--4498718 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
4498652 TGGAGTTTGA
* **
4498662 AAAAGAGAAGCTGGGGGTTG
1 AAAAGAGGAGCTAAGGGTTG
* *
4498682 AAAACAAGGAACTAAGGGTTG
1 AAAA-GAGGAGCTAAGGGTTG
4498703 AAAAGAGGAGCTAAGG
1 AAAAGAGGAGCTAAGG
4498719 CTCGAAAGAG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.44, C:0.07, G:0.37, T:0.12
Consensus pattern (20 bp):
AAAAGAGGAGCTAAGGGTTG
Found at i:4501686 original size:15 final size:15
Alignment explanation
Indices: 4501666--4501723 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
4501656 TTGTGTGCTA
*
4501666 ATTTTAGAGTTTAAG
1 ATTTTAGATTTTAAG
* **
4501681 ATTTTAGAATTTGGG
1 ATTTTAGATTTTAAG
*
4501696 ATTTTGGATTTTAAG
1 ATTTTAGATTTTAAG
*
4501711 GTTTTAGATTTTA
1 ATTTTAGATTTTA
4501724 GGGTTTTAAG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
ATTTTAGATTTTAAG
Found at i:4501728 original size:15 final size:15
Alignment explanation
Indices: 4501667--4501731 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
4501657 TGTGTGCTAA
* *
4501667 TTTTAGAGTTTAAGA
1 TTTTAGATTTTAAGG
* *
4501682 TTTTAGAATTT-GGG
1 TTTTAGATTTTAAGG
*
4501696 ATTTTGGATTTTAAGG
1 -TTTTAGATTTTAAGG
*
4501712 TTTTAGATTTTAGGG
1 TTTTAGATTTTAAGG
4501727 TTTTA
1 TTTTA
4501732 AGGATCTATG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 1 0.03
15 37 0.93
16 2 0.05
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (15 bp):
TTTTAGATTTTAAGG
Found at i:4501843 original size:15 final size:14
Alignment explanation
Indices: 4501825--4501900 Score: 57
Period size: 14 Copynumber: 5.4 Consensus size: 14
4501815 TAATTTTTGG
4501825 GGTTTGGGATTTTAA
1 GGTTT-GGATTTTAA
* *
4501840 GGTTT-CAATTTAA
1 GGTTTGGATTTTAA
*
4501853 GAGTTTGGGTTTTAA
1 G-GTTTGGATTTTAA
*
4501868 GGGTTTGG-TTTTAG
1 -GGTTTGGATTTTAA
* *
4501882 GGTTTCGATTTTAG
1 GGTTTGGATTTTAA
4501896 GGTTT
1 GGTTT
4501901 AGTGTTTAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
13 13 0.26
14 20 0.40
15 16 0.32
16 1 0.02
ACGTcount: A:0.17, C:0.03, G:0.32, T:0.49
Consensus pattern (14 bp):
GGTTTGGATTTTAA
Found at i:4501877 original size:14 final size:14
Alignment explanation
Indices: 4501855--4501914 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
4501845 CAATTTAAGA
*
4501855 GTTTGGGTTTTAAGG
1 GTTTCGGTTTT-AGG
4501870 GTTT-GGTTTTAGG
1 GTTTCGGTTTTAGG
*
4501883 GTTTCGATTTTAGG
1 GTTTCGGTTTTAGG
*
4501897 GTTT-AGTGTTTAGG
1 GTTTCGGT-TTTAGG
4501911 GTTT
1 GTTT
4501915 TAGATTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
13 8 0.20
14 28 0.70
15 4 0.10
ACGTcount: A:0.12, C:0.02, G:0.35, T:0.52
Consensus pattern (14 bp):
GTTTCGGTTTTAGG
Found at i:4501886 original size:28 final size:28
Alignment explanation
Indices: 4501819--4501914 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 28
4501809 ATTTTTTAAT
* *
4501819 TTTTGGGGTTTGGGATTTTAA-GGTTTCAA
1 TTTTAGGGTTTGGG-TTTTAAGGGTTT-AG
* * *
4501848 TTTAAGAGTTTGGGTTTTAAGGGTTTGG
1 TTTTAGGGTTTGGGTTTTAAGGGTTTAG
* *
4501876 TTTTAGGGTTTCGATTTT-AGGGTTTAG
1 TTTTAGGGTTTGGGTTTTAAGGGTTTAG
4501903 TGTTTAGGGTTT
1 T-TTTAGGGTTT
4501915 TAGATTTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
27 9 0.16
28 30 0.55
29 16 0.29
ACGTcount: A:0.16, C:0.02, G:0.32, T:0.50
Consensus pattern (28 bp):
TTTTAGGGTTTGGGTTTTAAGGGTTTAG
Found at i:4502052 original size:22 final size:22
Alignment explanation
Indices: 4502027--4502069 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4502017 AAAAAATTTT
4502027 ATATGAAAATTTA-TTATTAATA
1 ATAT-AAAATTTATTTATTAATA
**
4502049 ATATTTAATTTATTTATTAAT
1 ATATAAAATTTATTTATTAAT
4502070 TTTGTATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATAAAATTTATTTATTAATA
Found at i:4509386 original size:14 final size:12
Alignment explanation
Indices: 4509344--4509386 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
4509334 AAAAATGATT
*
4509344 AAATAAAAATTAA
1 AAATCAAAATT-A
4509357 AAATCAAAATTA
1 AAATCAAAATTA
4509369 AAATCGATAAATTA
1 AAATC-A-AAATTA
4509383 AAAT
1 AAAT
4509387 ATCTCATTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 6 0.22
13 11 0.41
14 10 0.37
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (12 bp):
AAATCAAAATTA
Found at i:4509462 original size:14 final size:16
Alignment explanation
Indices: 4509437--4509468 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4509427 TTTTATACAT
4509437 TTTTTAGAT-AAAATA
1 TTTTTAGATAAAAATA
4509452 TTTTTAG-TAAAAATA
1 TTTTTAGATAAAAATA
4509467 TT
1 TT
4509469 GATAGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 1 0.06
15 15 0.94
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTTTAGATAAAAATA
Found at i:4509665 original size:24 final size:23
Alignment explanation
Indices: 4509615--4509669 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
4509605 TATTAAATTA
* * *
4509615 TTTTTTTAAAAAATTTTACAAAT
1 TTTTCTTAAAAAATTTCACAAAG
*
4509638 TTTTCTTAAAAAATTTCACATAGG
1 TTTTCTTAAAAAATTTCACA-AAG
4509662 TTTTCTTA
1 TTTTCTTA
4509670 TATAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (23 bp):
TTTTCTTAAAAAATTTCACAAAG
Found at i:4510018 original size:21 final size:21
Alignment explanation
Indices: 4509992--4510034 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4509982 TATAATTAAG
4509992 ATTATTAAAAATTAAAAATTA
1 ATTATTAAAAATTAAAAATTA
* * *
4510013 ATTATTGAAATTTAAAATTTA
1 ATTATTAAAAATTAAAAATTA
4510034 A
1 A
4510035 AATTATATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
ATTATTAAAAATTAAAAATTA
Found at i:4517362 original size:70 final size:70
Alignment explanation
Indices: 4517285--4517419 Score: 180
Period size: 70 Copynumber: 1.9 Consensus size: 70
4517275 CTTTAGCATC
* * * * * * *
4517285 ATAAAATCTTAAATTTATATCTTACGATTTATGAGTTTATTTTAATTTTATGTTGAACTTATTTA
1 ATAAAATCTTAAATTTAAATCTCACGATGTATGAATTTATTTCAATTTTATATTAAACTTATTTA
4517350 GAACT
66 GAACT
* * *
4517355 ATAAAATCTTAAATTTAAATCTCATGGTGTATGAATTTATTTCAATTTTATATTAAATTTATTTA
1 ATAAAATCTTAAATTTAAATCTCACGATGTATGAATTTATTTCAATTTTATATTAAACTTATTTA
4517420 ATTATATTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
70 55 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (70 bp):
ATAAAATCTTAAATTTAAATCTCACGATGTATGAATTTATTTCAATTTTATATTAAACTTATTTA
GAACT
Found at i:4517448 original size:31 final size:31
Alignment explanation
Indices: 4517411--4517469 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
4517401 TTTATATTAA
**
4517411 ATTTATTTAATTATATTTTAATTAATTAATT
1 ATTTATTTAATTATATAATAATTAATTAATT
*
4517442 ATTTATTTATTTATATAATAATTAATTA
1 ATTTATTTAATTATATAATAATTAATTA
4517470 TAATTATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
ATTTATTTAATTATATAATAATTAATTAATT
Found at i:4517557 original size:3 final size:3
Alignment explanation
Indices: 4517549--4517598 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
4517539 CAGATCCTAA
4517549 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4517597 AT
1 AT
4517599 AACAAAATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4521182 original size:2 final size:2
Alignment explanation
Indices: 4521175--4521205 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4521165 TTTGTTCTTA
4521175 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 A
4521206 AATCTGTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4526186 original size:29 final size:27
Alignment explanation
Indices: 4526136--4526237 Score: 78
Period size: 29 Copynumber: 3.5 Consensus size: 27
4526126 AAAAGTTTAA
* *
4526136 AAAAATTTTTAAAATATTAAAACATTCTT
1 AAAAATTTAT-AAATATTAAAAAATT-TT
*
4526165 AAAAATTTATAAATAGTCAAAAAAATTTT
1 AAAAATTTATAAATA-T-TAAAAAATTTT
* * *
4526194 AAAAATTCAAAACATATTTAAAATATTTTT
1 AAAAATTTATAA-ATA-TTAAAA-AATTTT
*
4526224 AAAAATTTCTAAAT
1 AAAAATTTATAAAT
4526238 TTCTTTTCAA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
28 5 0.09
29 28 0.48
30 25 0.43
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (27 bp):
AAAAATTTATAAATATTAAAAAATTTT
Found at i:4526188 original size:20 final size:20
Alignment explanation
Indices: 4526165--4526218 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
4526155 AAACATTCTT
4526165 AAAAATTTATAAATAGTCAA
1 AAAAATTTATAAATAGTCAA
* *
4526185 AAAAATTT-TAAAAATTCAA
1 AAAAATTTATAAATAGTCAA
*
4526204 AACATATTTA-AAATA
1 AA-AAATTTATAAATA
4526219 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAATTTATAAATAGTCAA
Found at i:4526199 original size:9 final size:9
Alignment explanation
Indices: 4526185--4526280 Score: 52
Period size: 9 Copynumber: 10.0 Consensus size: 9
4526175 AAATAGTCAA
4526185 AAAAATTTT
1 AAAAATTTT
*
4526194 AAAAA-TTC
1 AAAAATTTT
4526202 AAAACATATTT
1 AAAA-AT-TTT
4526213 AAAATATTTTT
1 AAAA-A-TTTT
4526224 AAAAATTTCT
1 AAAAATTT-T
**
4526234 AAATTTCTTTT
1 AAA--AATTTT
*
4526245 CAAAATTTTT
1 -AAAAATTTT
* *
4526255 AAAAGTTCT
1 AAAAATTTT
4526264 AAAAATTTT
1 AAAAATTTT
4526273 -AAAATTTT
1 AAAAATTTT
4526281 TTTAATTTTA
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
8 14 0.21
9 23 0.34
10 9 0.13
11 15 0.22
12 7 0.10
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (9 bp):
AAAAATTTT
Found at i:4526263 original size:22 final size:21
Alignment explanation
Indices: 4526220--4526263 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4526210 TTTAAAATAT
*
4526220 TTTTAAAAATTTCTAAATTTC
1 TTTTAAAAATTTCTAAAGTTC
* *
4526241 TTTTCAAAATTTTTAAAAGTTC
1 TTTTAAAAATTTCT-AAAGTTC
4526263 T
1 T
4526264 AAAAATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTTAAAAATTTCTAAAGTTC
Found at i:4526412 original size:27 final size:27
Alignment explanation
Indices: 4526380--4526441 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
4526370 ATAAAAAATT
4526380 AAAATTTTCAA-TATTTTTAAAATTAT-
1 AAAATTTT-AATTATTTTTAAAATTATC
* *
4526406 AATAATTTTAATTTTTTTTTAAATTATC
1 AA-AATTTTAATTATTTTTAAAATTATC
4526434 AAAATTTT
1 AAAATTTT
4526442 TTAAAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.13
27 25 0.81
28 2 0.06
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (27 bp):
AAAATTTTAATTATTTTTAAAATTATC
Found at i:4526414 original size:17 final size:18
Alignment explanation
Indices: 4526378--4526416 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
4526368 TTATAAAAAA
* *
4526378 TTAAAATTTTCAATATTT
1 TTAAAATTATCAATAATT
4526396 TTAAAATTAT-AATAATT
1 TTAAAATTATCAATAATT
4526413 TTAA
1 TTAA
4526417 TTTTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAAAATTATCAATAATT
Found at i:4526486 original size:16 final size:16
Alignment explanation
Indices: 4526435--4526492 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
4526425 TAAATTATCA
*
4526435 AAATTTTTTAAAAATT
1 AAATTTTATAAAAATT
* *
4526451 AAAAATTTCAAAACAAATT
1 --AAATTTTATAA-AAATT
4526470 AAATTTTATAAAAATT
1 AAATTTTATAAAAATT
4526486 AAATTTT
1 AAATTTT
4526493 CTTCAAGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 12 0.35
17 9 0.26
18 8 0.24
19 5 0.15
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTTTATAAAAATT
Found at i:4526534 original size:24 final size:24
Alignment explanation
Indices: 4526506--4526553 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4526496 CAAGTTTAAA
* * *
4526506 CAAAATCACAAAACTTTAAAAATT
1 CAAAATAACAAAAATCTAAAAATT
*
4526530 CAAAATAAGAAAAATCTAAAAATT
1 CAAAATAACAAAAATCTAAAAATT
4526554 TTTCAAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.23
Consensus pattern (24 bp):
CAAAATAACAAAAATCTAAAAATT
Found at i:4526874 original size:19 final size:17
Alignment explanation
Indices: 4526846--4526973 Score: 89
Period size: 19 Copynumber: 7.1 Consensus size: 17
4526836 CCTTAATTCC
4526846 TTTT-GAATTTTTAACAA
1 TTTTAGAATTTTTAA-AA
*
4526863 TTTCTAGAATTTTTAGAAC
1 TTT-TAGAATTTTTA-AAA
4526882 TTTTAGAATTTTTAAAA
1 TTTTAGAATTTTTAAAA
** * *
4526899 TTTTTTAATATGTTAATAT
1 TTTTAGAAT-TTTTAA-AA
4526918 TATTTA-ATATTTTTAAAA
1 T-TTTAGA-ATTTTTAAAA
*
4526936 TTTTAAAATTTTTAAAA
1 TTTTAGAATTTTTAAAA
*
4526953 GGTTTTAGAACTTTTCAAAA
1 --TTTTAGAA-TTTTTAAAA
4526973 T
1 T
4526974 ATTTCAAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 21
0.74 0.09 0.17
Matches are distributed among these distances:
17 26 0.29
18 21 0.24
19 28 0.31
20 14 0.16
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (17 bp):
TTTTAGAATTTTTAAAA
Found at i:4526903 original size:10 final size:10
Alignment explanation
Indices: 4526890--4527162 Score: 76
Period size: 10 Copynumber: 27.5 Consensus size: 10
4526880 ACTTTTAGAA
4526890 TTTTTAAAAT
1 TTTTTAAAAT
4526900 TTTTT--AAT
1 TTTTTAAAAT
* * *
4526908 ATGTTAATAT
1 TTTTTAAAAT
* *
4526918 TATTTAATA-
1 TTTTTAAAAT
4526927 TTTTTAAAA-
1 TTTTTAAAAT
4526936 -TTTTAAAA-
1 TTTTTAAAAT
*
4526944 TTTTTAAAAG
1 TTTTTAAAAT
* * *
4526954 GTTTTAGAAC
1 TTTTTAAAAT
*
4526964 TTTTCAAAAT
1 TTTTTAAAAT
* * *
4526974 ATTTCAAAAA
1 TTTTTAAAAT
*
4526984 TTTTT-AACT
1 TTTTTAAAAT
**
4526993 TTTTTTGAAT
1 TTTTTAAAAT
* *
4527003 TTGTTAAAAAA
1 TT-TTTAAAAT
* *
4527014 ATTTTGAAAT
1 TTTTTAAAAT
*
4527024 TATTTTAGAAT
1 T-TTTTAAAAT
*
4527035 TTTTAAAAAT
1 TTTTTAAAAT
* * *
4527045 ATGTTAGAATT
1 TTTTTA-AAAT
*
4527056 TTTTTTAAAT
1 TTTTTAAAAT
*
4527066 GTTTTAAAAT
1 TTTTTAAAAT
*
4527076 TTTCTAAAATT
1 TTTTTAAAA-T
**
4527087 TTTGTTTGAA-
1 TTT-TTAAAAT
*
4527097 TTTTTCAAAT
1 TTTTTAAAAT
**
4527107 TTTTTTGAAT
1 TTTTTAAAAT
*
4527117 TTTTTAAAAAA
1 TTTTT-AAAAT
* *
4527128 ATTTTAGAAT
1 TTTTTAAAAT
* *
4527138 TTTTTGAACT
1 TTTTTAAAAT
* *
4527148 TTTCTGAAAT
1 TTTTTAAAAT
4527158 TTTTT
1 TTTTT
4527163 TTTTAAAATG
Statistics
Matches: 183, Mismatches: 68, Indels: 24
0.67 0.25 0.09
Matches are distributed among these distances:
8 14 0.08
9 26 0.14
10 111 0.61
11 29 0.16
12 3 0.02
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (10 bp):
TTTTTAAAAT
Found at i:4526941 original size:8 final size:9
Alignment explanation
Indices: 4526851--4527089 Score: 95
Period size: 9 Copynumber: 24.8 Consensus size: 9
4526841 ATTCCTTTTG
4526851 AATTTTTAA
1 AATTTTTAA
* *
4526860 CAATTTCTAG
1 -AATTTTTAA
*
4526870 AATTTTTAG
1 AATTTTTAA
* *
4526879 AACTTTTAG
1 AATTTTTAA
4526888 AATTTTTAA
1 AATTTTTAA
*
4526897 AATTTTT-T
1 AATTTTTAA
*
4526905 AATATGTTAA
1 AAT-TTTTAA
*
4526915 TATTATTTAA
1 AATT-TTTAA
*
4526925 TATTTTTAA
1 AATTTTTAA
4526934 AA-TTTTAA
1 AATTTTTAA
4526942 AATTTTTAA
1 AATTTTTAA
*
4526951 AAGGTTTTAGA
1 AA-TTTTTA-A
* *
4526962 ACTTTTCAA
1 AATTTTTAA
*
4526971 AATATTTCAAA
1 AAT-TTT-TAA
4526982 AATTTTTAA
1 AATTTTTAA
** **
4526991 CTTTTTTTG
1 AATTTTTAA
4527000 AATTTGTTAAAAA
1 AATTT-TT---AA
*
4527013 AATTTTGAA
1 AATTTTTAA
* *
4527022 ATTATTTTAG
1 AAT-TTTTAA
4527032 AATTTTTAAA
1 AATTTTT-AA
*
4527042 AATATGTTAGA
1 AAT-TTTTA-A
* *
4527053 ATTTTTTTTA
1 A-ATTTTTAA
4527063 AATGTTTTAA
1 AAT-TTTTAA
4527073 AATTTTCTAA
1 AATTTT-TAA
4527083 AATTTTT
1 AATTTTT
4527090 GTTTGAATTT
Statistics
Matches: 171, Mismatches: 39, Indels: 39
0.69 0.16 0.16
Matches are distributed among these distances:
8 11 0.06
9 74 0.43
10 64 0.37
11 15 0.09
12 2 0.01
13 5 0.03
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.52
Consensus pattern (9 bp):
AATTTTTAA
Found at i:4527017 original size:31 final size:31
Alignment explanation
Indices: 4526979--4527074 Score: 88
Period size: 32 Copynumber: 3.1 Consensus size: 31
4526969 AAAATATTTC
* * *
4526979 AAAAATTTTTAACTT-TTTTTGAATTTGTTAA
1 AAAAATTTTGAAATTATTTTAGAATTT-TTAA
4527010 AAAAATTTTGAAATTATTTTAGAATTTTTAA
1 AAAAATTTTGAAATTATTTTAGAATTTTTAA
* * * *
4527041 AAATATGTTAGAATTTTTTTTA-AATGTTTTAA
1 AAAAAT-TTTGAAATTATTTTAGAAT-TTTTAA
4527073 AA
1 AA
4527075 TTTTCTAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
31 25 0.45
32 30 0.55
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (31 bp):
AAAAATTTTGAAATTATTTTAGAATTTTTAA
Found at i:4527038 original size:20 final size:20
Alignment explanation
Indices: 4527015--4527141 Score: 87
Period size: 20 Copynumber: 6.2 Consensus size: 20
4527005 GTTAAAAAAA
*
4527015 TTTTGAAATTATTTTAGAAT
1 TTTTAAAATTATTTTAGAAT
* *
4527035 TTTTAAAAATATGTTAGAATTT
1 TTTTAAAATTATTTTAGAA--T
* * *
4527057 TTTTTAAA-TGTTTTAAAAT
1 TTTTAAAATTATTTTAGAAT
* *
4527076 TTTCTAAAATTTTTGTTTGAAT
1 TTT-TAAAATTATT-TTAGAAT
* *
4527098 TTTTCAAATT-TTTTTGAATT
1 TTTTAAAATTATTTTAGAA-T
**
4527118 TTTTAAAAAAATTTTAGAAT
1 TTTTAAAATTATTTTAGAAT
4527138 TTTT
1 TTTT
4527142 TGAACTTTTC
Statistics
Matches: 84, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
19 10 0.12
20 35 0.42
21 23 0.27
22 16 0.19
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTAAAATTATTTTAGAAT
Found at i:4527062 original size:32 final size:31
Alignment explanation
Indices: 4526992--4527074 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
4526982 AATTTTTAAC
*
4526992 TTTTTTT-GAATTTGTTAAAAAAATTTTGAAA
1 TTTTTTTAGAATTT-TTAAAAAAATTTAGAAA
* * *
4527023 TTATTTTAGAATTTTTAAAAATATGTTAGAAT
1 TTTTTTTAGAATTTTTAAAAAAAT-TTAGAAA
4527055 TTTTTTTA-AATGTTTTAAAA
1 TTTTTTTAGAAT-TTTTAAAA
4527075 TTTTCTAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
31 18 0.41
32 26 0.59
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (31 bp):
TTTTTTTAGAATTTTTAAAAAAATTTAGAAA
Found at i:4527118 original size:31 final size:31
Alignment explanation
Indices: 4527049--4527121 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
4527039 AAAAATATGT
4527049 TAGAATTTTTTTTAAATGTTTTAAAATTTTC
1 TAGAATTTTTTTTAAATGTTTTAAAATTTTC
* * * *
4527080 TAAAATTTTTGTTTGAAT-TTTTCAAATTTTT
1 TAGAATTTTT-TTTAAATGTTTTAAAATTTTC
*
4527111 TTGAATTTTTT
1 TAGAATTTTTT
4527122 AAAAAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
30 1 0.03
31 28 0.80
32 6 0.17
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.62
Consensus pattern (31 bp):
TAGAATTTTTTTTAAATGTTTTAAAATTTTC
Found at i:4527770 original size:68 final size:68
Alignment explanation
Indices: 4527682--4527812 Score: 156
Period size: 68 Copynumber: 1.9 Consensus size: 68
4527672 TAAGTTTCGC
* * * * * * *
4527682 AAGGTTCTCAAAATTTCATTTTC-ATAAGCCTTTTAAAGTTTACAGATATCTATTTTTGTAAGCT
1 AAGGCTCTCAAAATTGCATTTTCGAGAAGCC-TTTAAAGCTTACAGAAATCCATTTCTGTAAGCT
4527746 TTAA
65 TTAA
* * *
4527750 AAGGCTCTCGAAATTGCATTTTCGAGAAGTCTTTGAAGCTTACAGAAATCCATTTCTGTAAGC
1 AAGGCTCTCAAAATTGCATTTTCGAGAAGCCTTTAAAGCTTACAGAAATCCATTTCTGTAAGC
4527813 CATTCAGAGC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
68 47 0.90
69 5 0.10
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (68 bp):
AAGGCTCTCAAAATTGCATTTTCGAGAAGCCTTTAAAGCTTACAGAAATCCATTTCTGTAAGCTT
TAA
Found at i:4528357 original size:12 final size:12
Alignment explanation
Indices: 4528322--4528364 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
4528312 TAGTTGATGT
*
4528322 TGTTGTTTTTTA
1 TGTTGTTATTTA
* * *
4528334 TGATATTGTTTA
1 TGTTGTTATTTA
4528346 TGTTGTTATTTA
1 TGTTGTTATTTA
4528358 TGTTGTT
1 TGTTGTT
4528365 GATATTATTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.14, C:0.00, G:0.19, T:0.67
Consensus pattern (12 bp):
TGTTGTTATTTA
Found at i:4528390 original size:18 final size:18
Alignment explanation
Indices: 4528315--4528392 Score: 61
Period size: 18 Copynumber: 4.2 Consensus size: 18
4528305 AATGAATTAG
*
4528315 TTGATGTTGTTGTTTTT-
1 TTGATGTTGTTATTTTTA
*
4528332 TATGATATTGTTTATGTTGTTA
1 T-TGATGTTG-TTAT-TT-TTA
* *
4528354 TTTATGTTGTTGA-TATTA
1 TTGATGTTGTT-ATTTTTA
4528372 TTGATGTTGTTATTTTTA
1 TTGATGTTGTTATTTTTA
4528390 TTG
1 TTG
4528393 TTACAAAAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
17 2 0.04
18 27 0.57
19 4 0.09
20 4 0.09
21 9 0.19
22 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.19, T:0.64
Consensus pattern (18 bp):
TTGATGTTGTTATTTTTA
Found at i:4528394 original size:30 final size:29
Alignment explanation
Indices: 4528310--4528394 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 29
4528300 TTTAAAATGA
* *
4528310 ATTAGTTGATGTTGTT-GTTTTTT-ATGAT
1 ATTA-TTGATGTTGTTATTTTTTTGTTGAT
* * *
4528338 ATTGTTTATGTTGTTATTTATGTTGTTGAT
1 ATTATTGATGTTGTTATTT-TTTTGTTGAT
4528368 ATTATTGATGTTGTTATTTTTATTGTT
1 ATTATTGATGTTGTTATTTTT-TTGTT
4528395 ACAAAAACGA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
27 10 0.22
28 5 0.11
29 4 0.09
30 26 0.58
ACGTcount: A:0.18, C:0.00, G:0.19, T:0.64
Consensus pattern (29 bp):
ATTATTGATGTTGTTATTTTTTTGTTGAT
Found at i:4531072 original size:30 final size:30
Alignment explanation
Indices: 4531019--4531077 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
4531009 TATTTAGTAA
* *
4531019 ATTATGTTTATAAAACAATCATTATATTAT
1 ATTATATTTATAAAACAATCATTAGATTAT
4531049 ATTATATTTATAAAAC-ATCCATTAGATTA
1 ATTATATTTATAAAACAAT-CATTAGATTA
4531078 CTTGTTCGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (30 bp):
ATTATATTTATAAAACAATCATTAGATTAT
Found at i:4531102 original size:31 final size:31
Alignment explanation
Indices: 4531067--4531132 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
4531057 TATAAAACAT
* *
4531067 CCATTAGATTAC-TTGTTCGACATAACATATC
1 CCATTAGATAACATT-TTCAACATAACATATC
* *
4531098 CCATTAGGTAACATTTTCAATATAACATATC
1 CCATTAGATAACATTTTCAACATAACATATC
4531129 CCAT
1 CCAT
4531133 AACATATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (31 bp):
CCATTAGATAACATTTTCAACATAACATATC
Found at i:4534266 original size:58 final size:58
Alignment explanation
Indices: 4534190--4534458 Score: 175
Period size: 59 Copynumber: 4.5 Consensus size: 58
4534180 TTCATACATT
*
4534190 TATTCAAGGAAAATTGATA-TTTTAACTTTTTCTAAAAAAACATTTTTCAAAATTTTTA
1 TATTTAAGGAAAATTGATACTTTTAACTTTTTCTAAAAAAACATTTTT-AAAATTTTTA
* ** * * * *
4534248 TATTTAAGAAAAATTGATACGCTCAACTTTTTCT-CAAAATCATCTTTTGAAATTTTTA
1 TATTTAAGGAAAATTGATACTTTTAACTTTTTCTAAAAAAACAT-TTTTAAAATTTTTA
* * * * * * ** * * *
4534306 TTTTTTTAGGACAATTGATAC-TCTAAATCTTTCCCCAAAAAATATCTTTAAAAATTTTCA
1 -TATTTAAGGAAAATTGATACTTTTAACT-TTTTCTAAAAAAACAT-TTTTAAAATTTTTA
* * * * *** *
4534366 TGTTAAAGAAAAATTGATACTTTTAACTTTTCTTTAAAGTAAATTTTTGTTTGAAATTTTTA
1 TATTTAAGGAAAATTGATACTTTTAACTTTT-TCTAAA--AAAACATT-TTTAAAATTTTTA
* *
4534428 TTTTTAAGGAAAATTGATACTTTCAACTTTT
1 TATTTAAGGAAAATTGATACTTTTAACTTTT
4534459 CCTTAAAGTA
Statistics
Matches: 157, Mismatches: 44, Indels: 16
0.72 0.20 0.07
Matches are distributed among these distances:
58 36 0.23
59 53 0.34
60 25 0.16
61 1 0.01
62 42 0.27
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (58 bp):
TATTTAAGGAAAATTGATACTTTTAACTTTTTCTAAAAAAACATTTTTAAAATTTTTA
Found at i:4534441 original size:62 final size:63
Alignment explanation
Indices: 4534356--4534589 Score: 250
Period size: 63 Copynumber: 3.8 Consensus size: 63
4534346 AATATCTTTA
* * * *
4534356 AAAATTTTCATGTTAAAGAAAAATTGATACTTTTAACTTTTCTTTAAAGTA-AATTTTTGTTT
1 AAAATTTTTATTTTAAAGAAAAATTGATACTTTCAACTTTTCCTTAAAGTATAATTTTTGTTT
* * * **
4534418 GAAATTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTTAAAGTATTTTTTTTGTTT
1 AAAATTTTTATTTTAAAGAAAAATTGATACTTTCAACTTTTCCTTAAAGTATAATTTTTGTTT
* * * *
4534481 AAAATTTTTATTTTCAAGAAAAATTGATACTATCAAATTTTTCTTAAAG--T-A--TTT-TTT
1 AAAATTTTTATTTTAAAGAAAAATTGATACTTTCAACTTTTCCTTAAAGTATAATTTTTGTTT
* * * *
4534538 AAAA-TTTGATCTTCAAAAAAAAATTGATACTTTCAACTTTTTCTTAAAGTAT
1 AAAATTTTTAT-TTTAAAGAAAAATTGATACTTTCAACTTTTCCTTAAAGTAT
4534590 TTTTGAAATT
Statistics
Matches: 146, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
56 5 0.03
57 40 0.27
58 3 0.02
59 1 0.01
61 1 0.01
62 44 0.30
63 52 0.36
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.48
Consensus pattern (63 bp):
AAAATTTTTATTTTAAAGAAAAATTGATACTTTCAACTTTTCCTTAAAGTATAATTTTTGTTT
Found at i:4534539 original size:57 final size:57
Alignment explanation
Indices: 4534231--4534607 Score: 224
Period size: 63 Copynumber: 6.4 Consensus size: 57
4534221 CTAAAAAAAC
* * * * *
4534231 ATTTTTCAAAATTTTTATATTT-AAGAAAAATTGATACGCTCAACTTTTTCTCAAAAT
1 ATTTTTTAAAATTTTTAT-TTTCAAGAAAAATTGATACTCTCAAATTTTTCTTAAAGT
* * ** * * * ** *
4534288 CATCTTTTGAAATTTTTATTTTTTTAGGACAATTGATACTCT-AAATCTTTCCCCAAAAAAT
1 -ATTTTTTAAAATTTTTA-TTTTCAAGAAAAATTGATACTCTCAAAT-TTT--TCTTAAAGT
* * * * * ** *
4534349 ATCTTTAAAAATTTTCATGTTAAAGAAAAATTGATACT-TTTAACTTTTCTTTAAAGT
1 ATTTTTTAAAATTTTTATTTTCAAGAAAAATTGATACTCTCAAATTTTTC-TTAAAGT
* * * * * *
4534406 AAATTTTTGTTTGAAATTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTTAAAGT
1 --A--TTT-TTTAAAATTTTTATTTTCAAGAAAAATTGATACTCTCAAATTTTTCTTAAAGT
*
4534468 ATTTTTTTTGTTTAAAATTTTTATTTTCAAGAAAAATTGATACTATCAAATTTTTCTTAAAGT
1 A-----TTT-TTTAAAATTTTTATTTTCAAGAAAAATTGATACTCTCAAATTTTTCTTAAAGT
* * * * *
4534531 ATTTTTTAAAA-TTTGATCTTCAAAAAAAAATTGATACTTTCAACTTTTTCTTAAAGT
1 ATTTTTTAAAATTTTTATTTTC-AAGAAAAATTGATACTCTCAAATTTTTCTTAAAGT
*
4534588 A-TTTTTGAAATTTTTATTTT
1 ATTTTTTAAAATTTTTATTTT
4534608 TATTTTTTAT
Statistics
Matches: 250, Mismatches: 51, Indels: 37
0.74 0.15 0.11
Matches are distributed among these distances:
56 17 0.07
57 51 0.20
58 27 0.11
59 37 0.15
60 15 0.06
61 8 0.03
62 35 0.14
63 60 0.24
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (57 bp):
ATTTTTTAAAATTTTTATTTTCAAGAAAAATTGATACTCTCAAATTTTTCTTAAAGT
Found at i:4536045 original size:26 final size:26
Alignment explanation
Indices: 4536016--4536069 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
4536006 ATTGGATGTG
4536016 AGGCTAGATTGATTGCAATGGAATTT
1 AGGCTAGATTGATTGCAATGGAATTT
*
4536042 AGGCTAGATTGTTTGCAATGGAATTT
1 AGGCTAGATTGATTGCAATGGAATTT
4536068 AG
1 AG
4536070 TAATAGAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (26 bp):
AGGCTAGATTGATTGCAATGGAATTT
Found at i:4537146 original size:15 final size:14
Alignment explanation
Indices: 4537126--4537155 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4537116 ACTCAAGTGG
4537126 AAGGAAGAAAAAAAA
1 AAGGAA-AAAAAAAA
4537141 AAGGAAAAAAAAAA
1 AAGGAAAAAAAAAA
4537155 A
1 A
4537156 GAGAAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAGGAAAAAAAAAA
Found at i:4537918 original size:2 final size:2
Alignment explanation
Indices: 4537906--4537940 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4537896 CCTCTCCCCC
*
4537906 AT AT GT 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 A
4537941 AACCTAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4540078 original size:29 final size:29
Alignment explanation
Indices: 4540015--4540072 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
4540005 TTTATAATTC
* *
4540015 AAATTTTATCAATATTTATTTAAAAATAA
1 AAATTTTATCAAAATTTATCTAAAAATAA
4540044 AAATTTTATCAAAATTT-TACTAAAAATAA
1 AAATTTTATCAAAATTTAT-CTAAAAATAA
4540073 TTATTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (29 bp):
AAATTTTATCAAAATTTATCTAAAAATAA
Found at i:4540635 original size:22 final size:23
Alignment explanation
Indices: 4540610--4540655 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
4540600 TTTTTATCTC
*
4540610 ATATAT-TTATATTT-TTTTATAA
1 ATATATATTA-ATTTGTTTAATAA
4540632 ATATATATTAATTTGTTTAATAA
1 ATATATATTAATTTGTTTAATAA
4540655 A
1 A
4540656 AATACATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATATATATTAATTTGTTTAATAA
Found at i:4541394 original size:25 final size:22
Alignment explanation
Indices: 4541342--4541408 Score: 84
Period size: 24 Copynumber: 3.0 Consensus size: 22
4541332 TGTCTCAAAA
4541342 TTATTTTTTA-ATCT-AAAATTT
1 TTATTTTTTATAT-TAAAAATTT
4541363 TTATTTTTTATATTTTAAAAATTT
1 TTATTTTTTATA--TTAAAAATTT
4541387 TTACTTTTTTATATTAAAAATT
1 TTA-TTTTTTATATTAAAAATT
4541409 ATAAAACCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
21 10 0.24
22 1 0.02
23 10 0.24
24 11 0.27
25 9 0.22
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATTTTTTATATTAAAAATTT
Found at i:4541460 original size:15 final size:15
Alignment explanation
Indices: 4541438--4541474 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
4541428 ATAAAAATTT
*
4541438 AAATTTTAATATTAA
1 AAATTTTAACATTAA
*
4541453 ATATTTTAACATTAA
1 AAATTTTAACATTAA
4541468 AAATTTT
1 AAATTTT
4541475 CTTAAATTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATTTTAACATTAA
Found at i:4548311 original size:10 final size:10
Alignment explanation
Indices: 4548296--4548320 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4548286 TATAAGCATA
4548296 TTAAATATAT
1 TTAAATATAT
4548306 TTAAATATAT
1 TTAAATATAT
4548316 TTAAA
1 TTAAA
4548321 AAATAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TTAAATATAT
Found at i:4548519 original size:23 final size:23
Alignment explanation
Indices: 4548487--4548533 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4548477 GAACTCTGGC
* *
4548487 TACATGTGACAATCATCGTTATA
1 TACATATGACAATCATCATTATA
*
4548510 TACATATGACGATCATCATTATA
1 TACATATGACAATCATCATTATA
4548533 T
1 T
4548534 TGCAACTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (23 bp):
TACATATGACAATCATCATTATA
Found at i:4554002 original size:2 final size:2
Alignment explanation
Indices: 4553995--4554019 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4553985 CCCCAAAGGA
4553995 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
4554020 TATGGGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4554352 original size:30 final size:30
Alignment explanation
Indices: 4554238--4554389 Score: 122
Period size: 30 Copynumber: 5.2 Consensus size: 30
4554228 TAAAAAATAT
* *
4554238 TTTAAATTTTATCATTT-TATTTAAATAAATT
1 TTTAAATTTTA--ATTTATATATAAATAAATC
*
4554269 TTTAAATTTT-A-TTATAT-TCAAATACATC
1 TTTAAATTTTAATTTATATAT-AAATAAATC
* *
4554297 TTTAACATTTT--TTTACATCA-AAATAAACC
1 TTTAA-ATTTTAATTTATAT-ATAAATAAATC
4554326 TTTAAATTTTAATTTATATATAAATAAATC
1 TTTAAATTTTAATTTATATATAAATAAATC
* * * *
4554356 TATAATTTTTAATTTATATCTCAATAAA-C
1 TTTAAATTTTAATTTATATATAAATAAATC
4554385 TTTAA
1 TTTAA
4554390 CATAAATTAA
Statistics
Matches: 100, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
27 3 0.03
28 21 0.21
29 28 0.28
30 38 0.38
31 10 0.10
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (30 bp):
TTTAAATTTTAATTTATATATAAATAAATC
Found at i:4554448 original size:27 final size:28
Alignment explanation
Indices: 4554410--4554470 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
4554400 TTTTTTATTT
4554410 AAAATAATAA-TTTATTTAGATATA-AATA
1 AAAATAATAATTTTATTTA-A-ATACAATA
4554438 AAAATAA-AATTTTATTTAAATACAATA
1 AAAATAATAATTTTATTTAAATACAATA
4554465 AAAATA
1 AAAATA
4554471 TAAAAACTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 3 0.10
27 13 0.42
28 15 0.48
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (28 bp):
AAAATAATAATTTTATTTAAATACAATA
Found at i:4557079 original size:35 final size:37
Alignment explanation
Indices: 4557040--4557113 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 37
4557030 AAGGATTAAC
**
4557040 AACTTTCTATGGTTCAA-AAAA-ACCAAAAAAAAAAA
1 AACTTTCTATGAATCAACAAAATACCAAAAAAAAAAA
* *
4557075 AACTTTCTATTAATCAACAAAATATCAAAAAAAAAAA
1 AACTTTCTATGAATCAACAAAATACCAAAAAAAAAAA
4557112 AA
1 AA
4557114 AAAGAACCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 14 0.42
36 4 0.12
37 15 0.45
ACGTcount: A:0.62, C:0.14, G:0.03, T:0.22
Consensus pattern (37 bp):
AACTTTCTATGAATCAACAAAATACCAAAAAAAAAAA
Found at i:4557568 original size:2 final size:2
Alignment explanation
Indices: 4557561--4557591 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4557551 CTCTAAAAGA
4557561 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 A
4557592 GAATGAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4563932 original size:4 final size:4
Alignment explanation
Indices: 4563923--4563958 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
4563913 AGCCAAAAGC
4563923 CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
4563959 AGATGTCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:4569131 original size:2 final size:2
Alignment explanation
Indices: 4569124--4569162 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4569114 TCTTTAATTT
4569124 TC TC 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 TC TC T
4569163 TTTTTAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4575817 original size:31 final size:31
Alignment explanation
Indices: 4575781--4575856 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 31
4575771 ATACGATTGA
*
4575781 ATTAAATTTTTAAAAAAATAATAATACAATG
1 ATTAAATTTTTAAAAAAATAATAATAAAATG
** * *
4575812 ATTAAA-TTTT-ATTAAATTATATTAAAATG
1 ATTAAATTTTTAAAAAAATAATAATAAAATG
4575841 ATTAAAATTTTTAAAA
1 ATT-AAATTTTTAAAA
4575857 TTTGATAAGC
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
29 17 0.49
30 7 0.20
31 10 0.29
32 1 0.03
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTAAATTTTTAAAAAAATAATAATAAAATG
Found at i:4577393 original size:19 final size:21
Alignment explanation
Indices: 4577350--4577396 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
4577340 ATTTTCAAGT
4577350 AATAAAAATATTACTATAAAAA
1 AATAAAAATATTA-TATAAAAA
*
4577372 AATAAAAATATT-T-TAAATA
1 AATAAAAATATTATATAAAAA
4577391 AATAAA
1 AATAAA
4577397 TTGTATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 11 0.46
20 1 0.04
22 12 0.50
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AATAAAAATATTATATAAAAA
Found at i:4584034 original size:23 final size:25
Alignment explanation
Indices: 4583979--4584036 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
4583969 AAAGGGTTCG
* * *
4583979 GCAATGAAGGCCTAAACAGGATTCG
1 GCAATGAAGGCCTAAACAGAAGTCA
4584004 GCAATGAAGGCCTAAA-A-AAGTCA
1 GCAATGAAGGCCTAAACAGAAGTCA
4584027 GCAATGAAGG
1 GCAATGAAGG
4584037 TTGAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 13 0.43
24 1 0.03
25 16 0.53
ACGTcount: A:0.41, C:0.17, G:0.28, T:0.14
Consensus pattern (25 bp):
GCAATGAAGGCCTAAACAGAAGTCA
Found at i:4587505 original size:19 final size:20
Alignment explanation
Indices: 4587468--4587507 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4587458 TGTCTGGATC
*
4587468 TAGCAGATAGATTTAGTATG
1 TAGCAAATAGATTTAGTATG
*
4587488 TAGCAAATA-ATTTTGTATG
1 TAGCAAATAGATTTAGTATG
4587507 T
1 T
4587508 TCATTAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (20 bp):
TAGCAAATAGATTTAGTATG
Found at i:4593052 original size:20 final size:20
Alignment explanation
Indices: 4593029--4593072 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
4593019 ATCTCATTTA
4593029 GCATATACTTTTCTCGATGT
1 GCATATACTTTTCTCGATGT
*
4593049 GCATATACTTTTCTTGATGT
1 GCATATACTTTTCTCGATGT
4593069 GCAT
1 GCAT
4593073 GTACCTCTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (20 bp):
GCATATACTTTTCTCGATGT
Found at i:4597460 original size:2 final size:2
Alignment explanation
Indices: 4597453--4597487 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4597443 CTCCCCAGTC
4597453 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4597488 ACACACACAC
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:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:4600162 original size:8 final size:8
Alignment explanation
Indices: 4600149--4600178 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
4600139 AGATAAATGT
4600149 AAATTTTA
1 AAATTTTA
4600157 AAATTTTA
1 AAATTTTA
*
4600165 AAATTTAA
1 AAATTTTA
4600173 AAATTT
1 AAATTT
4600179 GAATAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
AAATTTTA
Found at i:4605389 original size:18 final size:18
Alignment explanation
Indices: 4605363--4605405 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
4605353 TATAATAGAG
*
4605363 TTATATATTTTTATTAATTT
1 TTATAT-TTTTTA-AAATTT
4605383 TTATATTTTTTAAAATTT
1 TTATATTTTTTAAAATTT
4605401 TTATA
1 TTATA
4605406 AACTAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 6 0.27
20 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATATTTTTTAAAATTT
Found at i:4605392 original size:9 final size:9
Alignment explanation
Indices: 4605363--4605406 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
4605353 TATAATAGAG
4605363 TTATATATTT
1 TTATA-ATTT
4605373 TTATTAATTT
1 TTA-TAATTT
*
4605383 TTATATTTT
1 TTATAATTT
*
4605392 TTAAAATTT
1 TTATAATTT
4605401 TTATAA
1 TTATAA
4605407 ACTAATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 17 0.59
10 10 0.34
11 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTATAATTT
Found at i:4605492 original size:14 final size:15
Alignment explanation
Indices: 4605439--4605502 Score: 50
Period size: 15 Copynumber: 4.6 Consensus size: 15
4605429 CAAATTTATT
*
4605439 TTAATACATTAAAAA
1 TTAATAAATTAAAAA
4605454 TT-AT--ATT-AAAA
1 TTAATAAATTAAAAA
* *
4605465 -TAATATATCAAAAAA
1 TTAATAAAT-TAAAAA
4605480 TTAA-AAATTAAAAA
1 TTAATAAATTAAAAA
4605494 TTAATAAAT
1 TTAATAAAT
4605503 CAAATTAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
10 1 0.03
11 6 0.15
12 3 0.08
13 2 0.05
14 11 0.28
15 13 0.33
16 3 0.08
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAATAAATTAAAAA
Found at i:4605505 original size:30 final size:32
Alignment explanation
Indices: 4605446--4605506 Score: 81
Period size: 30 Copynumber: 1.9 Consensus size: 32
4605436 ATTTTAATAC
*
4605446 ATTAAAAATTATATTAAAATAATATATCAAAAA
1 ATTAAAAATTATA-TAAAATAATAAATCAAAAA
*
4605479 ATTAAAAATTA-A-AAATTAATAAATCAAA
1 ATTAAAAATTATATAAAATAATAAATCAAA
4605507 TTAAACCGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 14 0.54
32 1 0.04
33 11 0.42
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (32 bp):
ATTAAAAATTATATAAAATAATAAATCAAAAA
Found at i:4606611 original size:12 final size:12
Alignment explanation
Indices: 4606594--4606618 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4606584 ATCATACATT
4606594 ATTAAATAATAA
1 ATTAAATAATAA
4606606 ATTAAATAATAA
1 ATTAAATAATAA
4606618 A
1 A
4606619 ATAAGTATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAAATAATAA
Found at i:4611372 original size:8 final size:8
Alignment explanation
Indices: 4611359--4611396 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
4611349 AATATTAAAT
4611359 TTTATTAA
1 TTTATTAA
4611367 TTTATTAA
1 TTTATTAA
*
4611375 TTAATT-A
1 TTTATTAA
*
4611382 TTTATTAG
1 TTTATTAA
4611390 TTTATTA
1 TTTATTA
4611397 TAGTAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (8 bp):
TTTATTAA
Found at i:4611396 original size:15 final size:15
Alignment explanation
Indices: 4611359--4611397 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4611349 AATATTAAAT
4611359 TTTATTAATTTATTAA
1 TTTATT-ATTTATTAA
* *
4611375 TTAATTATTTATTAG
1 TTTATTATTTATTAA
4611390 TTTATTAT
1 TTTATTAT
4611398 AGTAAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
TTTATTATTTATTAA
Found at i:4612063 original size:16 final size:15
Alignment explanation
Indices: 4612012--4612071 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 15
4612002 TAAATTTGAC
*
4612012 TATAATAAACTAATA
1 TATAATAAATTAATA
* *
4612027 TATAAACAAACTAATA
1 TAT-AATAAATTAATA
*
4612043 AATAATAAATTAATGA
1 TATAATAAATTAAT-A
4612059 TATAATAAATTAA
1 TATAATAAATTAA
4612072 AATTTTAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
15 12 0.32
16 26 0.68
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (15 bp):
TATAATAAATTAATA
Found at i:4612523 original size:21 final size:21
Alignment explanation
Indices: 4612499--4612545 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
4612489 GTCTAACTAA
*
4612499 CATAACTTTATTCTCAAACTT
1 CATAACTTCATTCTCAAACTT
**
4612520 CATAGGTTCATTCTCAAACTT
1 CATAACTTCATTCTCAAACTT
4612541 CATAA
1 CATAA
4612546 TAATAGAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.38
Consensus pattern (21 bp):
CATAACTTCATTCTCAAACTT
Found at i:4613236 original size:2 final size:2
Alignment explanation
Indices: 4613229--4613264 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4613219 GATACGTCTT
4613229 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
4613265 AGATATTGAA
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:4613501 original size:3 final size:3
Alignment explanation
Indices: 4613493--4613530 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
4613483 TAATAAATAT
4613493 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4613531 TGATGCATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4614712 original size:29 final size:30
Alignment explanation
Indices: 4614652--4614724 Score: 103
Period size: 29 Copynumber: 2.4 Consensus size: 30
4614642 TAGGTACGTT
*
4614652 TTTAAATTATAATAAAATATTTAATATAATA
1 TTTAAATTATAA-AAAAAATTTAATATAATA
* *
4614683 TTTAAATT-TAAAAAAAATTTAATTTGATA
1 TTTAAATTATAAAAAAAATTTAATATAATA
4614712 TTTAAATTATAAA
1 TTTAAATTATAAA
4614725 TATATTAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.61
30 7 0.18
31 8 0.21
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (30 bp):
TTTAAATTATAAAAAAAATTTAATATAATA
Found at i:4615742 original size:20 final size:24
Alignment explanation
Indices: 4615698--4615743 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 24
4615688 TTTATTTTAT
4615698 TTTTATATATTATGTTAATATAAA
1 TTTTATATATTATGTTAATATAAA
4615722 TTTTA-ATA-TAT-TTAA-ATAAA
1 TTTTATATATTATGTTAATATAAA
4615742 TT
1 TT
4615744 CAAATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 3 0.14
23 3 0.14
24 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTTATATATTATGTTAATATAAA
Found at i:4615749 original size:20 final size:21
Alignment explanation
Indices: 4615712--4615751 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
4615702 ATATATTATG
**
4615712 TTAATATAAATTTTAATATAT
1 TTAATATAAATTCAAATATAT
4615733 TTAA-ATAAATTCAAATATA
1 TTAATATAAATTCAAATATA
4615752 AAATAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAATATAAATTCAAATATAT
Found at i:4615798 original size:17 final size:18
Alignment explanation
Indices: 4615769--4615807 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
4615759 TATTTTATTT
4615769 TATAAAAATTTAAAAAAA
1 TATAAAAATTTAAAAAAA
*
4615787 TATAAAAA-TTAATAAAA
1 TATAAAAATTTAAAAAAA
4615804 TATA
1 TATA
4615808 TCATTCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TATAAAAATTTAAAAAAA
Found at i:4625970 original size:3 final size:3
Alignment explanation
Indices: 4625964--4626004 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
4625954 ATGATAATAA
*
4625964 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4626005 AGTACGAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4626918 original size:10 final size:10
Alignment explanation
Indices: 4626901--4627000 Score: 75
Period size: 10 Copynumber: 10.3 Consensus size: 10
4626891 AAGTTTTTTT
4626901 AAATTCTAAA
1 AAATTCTAAA
*
4626911 ACATTCTAAA
1 AAATTCTAAA
4626921 AAATTCT-AA
1 AAATTCTAAA
* * *
4626930 AATTTTTTAA
1 AAATTCTAAA
* *
4626940 AATTTTTATAA
1 AAATTCTA-AA
4626951 AAATTCTAAA
1 AAATTCTAAA
*
4626961 AAATTTTAAA
1 AAATTCTAAA
4626971 AAA---TAAA
1 AAATTCTAAA
4626978 AAATATCT-AA
1 AAAT-TCTAAA
*
4626988 AAATTGTAAA
1 AAATTCTAAA
4626998 AAA
1 AAA
4627001 AATTTAAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
7 7 0.09
9 9 0.12
10 49 0.66
11 9 0.12
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.35
Consensus pattern (10 bp):
AAATTCTAAA
Found at i:4626989 original size:27 final size:27
Alignment explanation
Indices: 4626949--4627000 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
4626939 AAATTTTTAT
*
4626949 AAAAATTCTAAAAAATTTTAAAAAATA
1 AAAAATTCTAAAAAATTGTAAAAAATA
4626976 AAAAATATCT-AAAAATTGTAAAAAA
1 AAAAAT-TCTAAAAAATTGTAAAAAA
4627001 AATTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (27 bp):
AAAAATTCTAAAAAATTGTAAAAAATA
Found at i:4627295 original size:12 final size:13
Alignment explanation
Indices: 4627269--4627298 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
4627259 TAGACCTTGG
4627269 AAAATCAATTAAA
1 AAAATCAATTAAA
4627282 AAAATCAATTAAA
1 AAAATCAATTAAA
4627295 AAAA
1 AAAA
4627299 AAGGCAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATCAATTAAA
Found at i:4628103 original size:10 final size:10
Alignment explanation
Indices: 4628090--4628257 Score: 87
Period size: 11 Copynumber: 16.6 Consensus size: 10
4628080 ATTTTTTTTT
4628090 AATTTTTAAA
1 AATTTTTAAA
4628100 AATTTTTAAGA
1 AATTTTTAA-A
4628111 AA-TTTT--A
1 AATTTTTAAA
*
4628118 AATTTTT-AG
1 AATTTTTAAA
*
4628127 AATTTTAAAAA
1 AATTTT-TAAA
*
4628138 AATTTTTAAG
1 AATTTTTAAA
***
4628148 AATTTTTTTC
1 AATTTTTAAA
*
4628158 CATTTTTAAA
1 AATTTTTAAA
4628168 TAA-TTTTAAA
1 -AATTTTTAAA
* *
4628178 AATTTTTTGAG
1 AA-TTTTTAAA
4628189 AATTTTTCAAA
1 AATTTTT-AAA
* *
4628200 AGTTTTT-AT
1 AATTTTTAAA
*
4628209 AATTTTTAATT
1 AATTTTTAA-A
*
4628220 ATTTTTTAAA
1 AATTTTTAAA
*
4628230 AATATTTTTAA
1 AAT-TTTTAAA
*
4628241 ATTTTTTAAAA
1 AATTTTT-AAA
4628252 AATTTT
1 AATTTT
4628258 CTTTTTATAC
Statistics
Matches: 118, Mismatches: 27, Indels: 25
0.69 0.16 0.15
Matches are distributed among these distances:
7 3 0.03
8 4 0.03
9 15 0.13
10 47 0.40
11 49 0.42
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:4628116 original size:20 final size:20
Alignment explanation
Indices: 4628093--4628257 Score: 81
Period size: 20 Copynumber: 8.2 Consensus size: 20
4628083 TTTTTTTAAT
4628093 TTTTAAAAATTTTTAAGAAA
1 TTTTAAAAATTTTTAAGAAA
4628113 TTTT--AAATTTTT-AG-AA
1 TTTTAAAAATTTTTAAGAAA
*
4628129 TTTTAAAAAAATTTTTAAGAAT
1 TTTT--AAAAATTTTTAAGAAA
****
4628151 TTTTTTCCATTTTTAA-ATAA
1 TTTTAAAAATTTTTAAGA-AA
* *
4628171 TTTTAAAAATTTTTTGAGAAT
1 TTTTAAAAA-TTTTTAAGAAA
* * *
4628192 TTTTCAAAAGTTTTT-ATAAT
1 TTTT-AAAAATTTTTAAGAAA
* * *
4628212 TTTTAATTATTTTTTAAAAATA
1 TTTTAA-AAATTTTTAAGAA-A
* * *
4628234 TTTTTAAATTTTTTAAAAAA
1 TTTTAAAAATTTTTAAGAAA
4628254 TTTT
1 TTTT
4628258 CTTTTTATAC
Statistics
Matches: 112, Mismatches: 20, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
16 6 0.05
17 2 0.02
18 8 0.07
19 3 0.03
20 45 0.40
21 33 0.29
22 15 0.13
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTAAAAATTTTTAAGAAA
Found at i:4628116 original size:27 final size:27
Alignment explanation
Indices: 4628085--4628143 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
4628075 TTTTGATTTT
* * *
4628085 TTTTTAATTTTTAAAAATTTTTAAGAAA
1 TTTTAAATTTTT-AAAATTTTAAAAAAA
*
4628113 TTTTAAATTTTTAGAATTTTAAAAAAA
1 TTTTAAATTTTTAAAATTTTAAAAAAA
4628140 TTTT
1 TTTT
4628144 TAAGAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (27 bp):
TTTTAAATTTTTAAAATTTTAAAAAAA
Found at i:4628132 original size:16 final size:18
Alignment explanation
Indices: 4628099--4628135 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
4628089 TAATTTTTAA
4628099 AAATTTTTAAGAAATTTT
1 AAATTTTTAAGAAATTTT
4628117 AAATTTTT-AG-AATTTT
1 AAATTTTTAAGAAATTTT
4628133 AAA
1 AAA
4628136 AAAATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 2 0.11
18 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
AAATTTTTAAGAAATTTT
Found at i:4638425 original size:3 final size:3
Alignment explanation
Indices: 4638419--4638453 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
4638409 CAGAAGAATG
* *
4638419 ATT ATT ATT GTT GTT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4638454 CCGTACTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4639903 original size:160 final size:160
Alignment explanation
Indices: 4639703--4640025 Score: 646
Period size: 160 Copynumber: 2.0 Consensus size: 160
4639693 CAAAAAAACA
4639703 AAATCAAAAGTTCTTTCTCCAAATCACCCCCCAACTAATTTATTTCTTACCTTAATTAACCCTTT
1 AAATCAAAAGTTCTTTCTCCAAATCACCCCCCAACTAATTTATTTCTTACCTTAATTAACCCTTT
4639768 AATTATTTTTTATATCTCATCTTAAATGTCTTTAAAAAATTTTGACATATTATAGGTAGTGATGT
66 AATTATTTTTTATATCTCATCTTAAATGTCTTTAAAAAATTTTGACATATTATAGGTAGTGATGT
4639833 GATTAATTTTTATTTACATTTTCTAAATGG
131 GATTAATTTTTATTTACATTTTCTAAATGG
4639863 AAATCAAAAGTTCTTTCTCCAAATCACCCCCCAACTAATTTATTTCTTACCTTAATTAACCCTTT
1 AAATCAAAAGTTCTTTCTCCAAATCACCCCCCAACTAATTTATTTCTTACCTTAATTAACCCTTT
4639928 AATTATTTTTTATATCTCATCTTAAATGTCTTTAAAAAATTTTGACATATTATAGGTAGTGATGT
66 AATTATTTTTTATATCTCATCTTAAATGTCTTTAAAAAATTTTGACATATTATAGGTAGTGATGT
4639993 GATTAATTTTTATTTACATTTTCTAAATGG
131 GATTAATTTTTATTTACATTTTCTAAATGG
4640023 AAA
1 AAA
4640026 ATGGTGATTT
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 163 1.00
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (160 bp):
AAATCAAAAGTTCTTTCTCCAAATCACCCCCCAACTAATTTATTTCTTACCTTAATTAACCCTTT
AATTATTTTTTATATCTCATCTTAAATGTCTTTAAAAAATTTTGACATATTATAGGTAGTGATGT
GATTAATTTTTATTTACATTTTCTAAATGG
Found at i:4662417 original size:27 final size:27
Alignment explanation
Indices: 4662379--4662435 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
4662369 CATGAAGCTA
4662379 CACATTTCCTTTTGGCATTGAGCAGGC
1 CACATTTCCTTTTGGCATTGAGCAGGC
*
4662406 CACATTTCCTTTTGGCATTGAGCGGGC
1 CACATTTCCTTTTGGCATTGAGCAGGC
4662433 CAC
1 CAC
4662436 TTGATTCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.32
Consensus pattern (27 bp):
CACATTTCCTTTTGGCATTGAGCAGGC
Found at i:4666314 original size:35 final size:33
Alignment explanation
Indices: 4666266--4666338 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 33
4666256 AAAATTTTGC
4666266 AAAA-ATTTTAAATATGAT-TTTTTATTTTTTTAA
1 AAAATATTTTAAATAT-ATATTTTTA-TTTTTTAA
*
4666299 AAAATATTTATAAATATTTATTTTTATTTTTTAA
1 AAAATATTT-TAAATATATATTTTTATTTTTTAA
*
4666333 ACAATA
1 AAAATA
4666339 AATCTAATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 4 0.11
34 18 0.51
35 13 0.37
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (33 bp):
AAAATATTTTAAATATATATTTTTATTTTTTAA
Found at i:4666799 original size:17 final size:17
Alignment explanation
Indices: 4666763--4666798 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
4666753 CGACGGATGC
*
4666763 AAATATTAAAGATTAAA
1 AAATAATAAAGATTAAA
4666780 AAATAATAAA-ATTAAA
1 AAATAATAAAGATTAAA
4666796 AAA
1 AAA
4666799 ACTTATTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
AAATAATAAAGATTAAA
Found at i:4667113 original size:16 final size:16
Alignment explanation
Indices: 4667094--4667128 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4667084 ATCAAAATTT
* *
4667094 TAATTGAAATATAACA
1 TAATTCAAATATAAAA
4667110 TAATTCAAATATAAAA
1 TAATTCAAATATAAAA
4667126 TAA
1 TAA
4667129 AAAATACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (16 bp):
TAATTCAAATATAAAA
Found at i:4667363 original size:5 final size:5
Alignment explanation
Indices: 4667353--4667403 Score: 59
Period size: 5 Copynumber: 10.0 Consensus size: 5
4667343 AAAATTGATA
**
4667353 AATTT AATTT AATTAAT AAAAT AATTT AATTT AATTT AA-TT AATTT AATTT
1 AATTT AATTT AATT--T AATTT AATTT AATTT AATTT AATTT AATTT AATTT
4667404 TAAATAATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 4 0.10
5 32 0.82
7 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (5 bp):
AATTT
Found at i:4667368 original size:9 final size:9
Alignment explanation
Indices: 4667356--4667402 Score: 60
Period size: 9 Copynumber: 5.2 Consensus size: 9
4667346 ATTGATAAAT
4667356 TTAATTTAA
1 TTAATTTAA
*
4667365 TTAA-TAAA
1 TTAATTTAA
*
4667373 ATAATTTAA
1 TTAATTTAA
4667382 TTTAATTTAA
1 -TTAATTTAA
4667392 TTAATTTAA
1 TTAATTTAA
4667401 TT
1 TT
4667403 TTAAATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 6 0.19
9 18 0.56
10 8 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTAATTTAA
Found at i:4667405 original size:15 final size:15
Alignment explanation
Indices: 4667378--4667417 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4667368 ATAAAATAAT
4667378 TTAATTTAA-TTTAA
1 TTAATTTAATTTTAA
4667392 TTAATTTAATTTTAA
1 TTAATTTAATTTTAA
* *
4667407 ATAATTCAATT
1 TTAATTTAATT
4667418 CAAAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATTTAATTTTAA
Found at i:4667411 original size:19 final size:19
Alignment explanation
Indices: 4667356--4667417 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
4667346 ATTGATAAAT
4667356 TTAATTTAA-TTAATA-AA
1 TTAATTTAATTTAATATAA
* *
4667373 ATAATTTAATTTAATTTAA
1 TTAATTTAATTTAATATAA
4667392 TTAATTTAATTTTAA-ATAA
1 TTAATTTAA-TTTAATATAA
4667411 TTCAATT
1 TT-AATT
4667418 CAAAATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 8 0.22
18 5 0.14
19 15 0.41
20 9 0.24
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAATTTAATTTAATATAA
Found at i:4669181 original size:24 final size:24
Alignment explanation
Indices: 4669147--4669213 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
4669137 TTTTGAAAAA
*
4669147 ATATAATTAAATCATTATTAATACT
1 ATATAAATAAATCATTATTAATA-T
*
4669172 AT-TAAATAAATCATTATCAATAT
1 ATATAAATAAATCATTATTAATAT
* *
4669195 ATATAATTAAATAATTATT
1 ATATAAATAAATCATTATT
4669214 TAACTAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 3 0.08
24 31 0.86
25 2 0.06
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATAAATAAATCATTATTAATAT
Found at i:4669806 original size:6 final size:6
Alignment explanation
Indices: 4669791--4669825 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
4669781 CTCTCTCTTA
*
4669791 GGGCAT GGGCAC GGGCAC GGGCAC GGGCAC GGGCA
1 GGGCAC GGGCAC GGGCAC GGGCAC GGGCAC GGGCA
4669826 TCGAGAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.29, G:0.51, T:0.03
Consensus pattern (6 bp):
GGGCAC
Found at i:4669936 original size:22 final size:22
Alignment explanation
Indices: 4669895--4669937 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4669885 AATTTTTAAA
* **
4669895 AAATTTTAATTTTGGGTTAATT
1 AAATTTAAATTTTGAATTAATT
4669917 AAATTTAAATTTTGAATTAAT
1 AAATTTAAATTTTGAATTAAT
4669938 CAAAATTGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
AAATTTAAATTTTGAATTAATT
Found at i:4670857 original size:13 final size:14
Alignment explanation
Indices: 4670827--4670859 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
4670817 ATTGTTAATG
4670827 TTTTATTATATTAA
1 TTTTATTATATTAA
4670841 -TTTATTA-ATTAA
1 TTTTATTATATTAA
4670853 TTTTATT
1 TTTTATT
4670860 TAAATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATTATATTAA
Found at i:4677436 original size:21 final size:23
Alignment explanation
Indices: 4677401--4677447 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
4677391 TGTTTTTGTT
*
4677401 TTTTTATATATTATTTTAATAAA
1 TTTTTATATATTATTTAAATAAA
*
4677424 TTTTTA-ATA-TATTTAAATATA
1 TTTTTATATATTATTTAAATAAA
4677445 TTT
1 TTT
4677448 AAGTATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.59
22 3 0.14
23 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTTATATATTATTTAAATAAA
Found at i:4677487 original size:9 final size:10
Alignment explanation
Indices: 4677468--4677507 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
4677458 TAATTATTTT
4677468 AATTTATAAA
1 AATTTATAAA
4677478 AATTTA-AAA
1 AATTTATAAA
*
4677487 AATATATAAA
1 AATTTATAAA
*
4677497 AATTAATAAA
1 AATTTATAAA
4677507 A
1 A
4677508 GTATATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AATTTATAAA
Done.