Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 104 of 120
Found at i:30078382 original size:34 final size:35
Alignment explanation
Indices: 30078351--30078435 Score: 88
Period size: 34 Copynumber: 2.5 Consensus size: 35
30078341 TTTTTAAATT
30078351 TAAAATT-AAGTTAAGAAGAATTTTAAA-TTAAAAA
1 TAAAATTAAAGTTAA-AAGAATTTTAAACTTAAAAA
* * *
30078385 TAAATTTAAATTTAAAATAATTTTAAACTT-AAAA
1 TAAAATTAAAGTTAAAAGAATTTTAAACTTAAAAA
*
30078419 TAAATTTTAAA-TTAAAA
1 TAAA-ATTAAAGTTAAAA
30078436 ATTGGGTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 31 0.69
35 14 0.31
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.38
Consensus pattern (35 bp):
TAAAATTAAAGTTAAAAGAATTTTAAACTTAAAAA
Found at i:30078436 original size:18 final size:18
Alignment explanation
Indices: 30078369--30078437 Score: 99
Period size: 17 Copynumber: 3.9 Consensus size: 18
30078359 AGTTAAGAAG
30078369 AATTTTAAATTAAAAATA
1 AATTTTAAATTAAAAATA
*
30078387 AA-TTTAAATTTAAAAT-
1 AATTTTAAATTAAAAATA
30078403 AATTTTAAACTT-AAAATA
1 AATTTTAAA-TTAAAAATA
30078421 AATTTTAAATTAAAAAT
1 AATTTTAAATTAAAAAT
30078438 TGGGTTTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
16 2 0.04
17 26 0.57
18 18 0.39
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTTTAAATTAAAAATA
Found at i:30078979 original size:39 final size:39
Alignment explanation
Indices: 30078845--30079220 Score: 178
Period size: 39 Copynumber: 9.7 Consensus size: 39
30078835 AATGACTGCC
* * *
30078845 ATCTGCCCCATGATCGGGGTAAGAGA-TTAGTTGAT-AGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTA-ATGATGA-TG
* * ** *
30078884 ATCTGCCCCAAGCTTGGGGTAAGAGATCAAATG--GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTAATGATGATG
* * * * *
30078921 CAATTTGCCTCATGATCGGGGTAAGAGATTTACTGATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTTAATGATGATG
* * ** * **
30078962 ATCTGCCCCAGGCTCGGGATAAGAAATCGAATAGCT-ACA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTAAT-GATGATG
* * ** *
30079001 ATCTGCCCCAAGATCGGGGTAAGAGATTTGCTGATGATA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTAATGATGATG
* * * * * *
30079040 ATCTGCCCTAGGCTCGGGGTAAGAAAATGAATAGCT-ATA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTAAT-GATGATG
* * *
30079079 ATCTGCCCTAGGCTCGGAGTAAGAGATTTACTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTAATGATGATG
* ** * ** *
30079118 ATTTGCCCCAAACTCAGGGTAAGAGATCGAAT-A-GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTAATGATGATG
* * * **
30079155 CAATCTGTCTCAGGCTCGAGGTAAGAGATTTGCTGATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTTAATGATGATG
* *
30079196 ATCTGCCTCA-ACTC-GGGTAAGAGAT
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT
30079221 CGGATAACTG
Statistics
Matches: 244, Mismatches: 79, Indels: 30
0.69 0.22 0.08
Matches are distributed among these distances:
37 15 0.06
38 8 0.03
39 209 0.86
40 6 0.02
41 6 0.02
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTTAATGATGATG
Found at i:30078985 original size:78 final size:77
Alignment explanation
Indices: 30078845--30079260 Score: 417
Period size: 78 Copynumber: 5.4 Consensus size: 77
30078835 AATGACTGCC
* * *
30078845 ATCTGCCCCATGATCGGGGTAAGAGA-TTAGTTGAT-AGTGATCTGCCCCAAGCTTGGGGTAAGA
1 ATCTGCCCCAGGATCGGGGTAAGAGATTTA-CTGATGA-TGATCTGCCCCAAGC-TCGGGTAAGA
* * *
30078908 GATCAAATGGCTGCA
63 GATCGAATAGCTACA
* * * * *
30078923 ATTTGCCTCATGATCGGGGTAAGAGATTTACTGATGATGATCTGCCCCAGGCTCGGGATAAGAAA
1 ATCTGCCCCAGGATCGGGGTAAGAGATTTACTGATGATGATCTGCCCCAAGCTCGGG-TAAGAGA
30078988 TCGAATAGCTACA
65 TCGAATAGCTACA
* * * * * *
30079001 ATCTGCCCCAAGATCGGGGTAAGAGATTTGCTGATGATAATCTGCCCTAGGCTCGGGGTAAGAAA
1 ATCTGCCCCAGGATCGGGGTAAGAGATTTACTGATGATGATCTGCCCCAAGCTC-GGGTAAG-AG
*
30079066 AT-GAATAGCTATA
64 ATCGAATAGCTACA
* * * * *
30079079 ATCTGCCCTAGGCTCGGAGTAAGAGATTTACTGATGATGATTTGCCCCAAACTCAGGGTAAGAGA
1 ATCTGCCCCAGGATCGGGGTAAGAGATTTACTGATGATGATCTGCCCCAAGCTC-GGGTAAGAGA
*
30079144 TCGAATAGCTGCA
65 TCGAATAGCTACA
* * * * * *
30079157 ATCTGTCTCAGGCTCGAGGTAAGAGATTTGCTGATGATGATCTGCCTCAA-CTCGGGTAAGAGAT
1 ATCTGCCCCAGGATCGGGGTAAGAGATTTACTGATGATGATCTGCCCCAAGCTCGGGTAAGAGAT
* * *
30079221 CGGATAACTGCA
66 CGAATAGCTACA
* * *
30079233 ATCTGCCCCAAGCTCGAGGTAAGAGATT
1 ATCTGCCCCAGGATCGGGGTAAGAGATT
30079261 GGCTGGTGAT
Statistics
Matches: 289, Mismatches: 43, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
76 46 0.16
77 10 0.03
78 222 0.77
79 11 0.04
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.25
Consensus pattern (77 bp):
ATCTGCCCCAGGATCGGGGTAAGAGATTTACTGATGATGATCTGCCCCAAGCTCGGGTAAGAGAT
CGAATAGCTACA
Found at i:30079257 original size:39 final size:39
Alignment explanation
Indices: 30079121--30079259 Score: 119
Period size: 39 Copynumber: 3.6 Consensus size: 39
30079111 GATGATGATT
* * *
30079121 TGCCCCAAACTC-AGGGTAAGAGATCGAATAGCTGCAATC
1 TGCCCCAAGCTCGA-GGTAAGAGATCGGATAACTGCAATC
* * * * *
30079160 TGTCTCAGGCTCGAGGTAAGAGATTTGCTGATGA-TG--ATC
1 TGCCCCAAGCTCGAGGTAAGAGA--T-CGGATAACTGCAATC
*
30079199 TGCCTCAA-CTCG-GGTAAGAGATCGGATAACTGCAATC
1 TGCCCCAAGCTCGAGGTAAGAGATCGGATAACTGCAATC
30079236 TGCCCCAAGCTCGAGGTAAGAGAT
1 TGCCCCAAGCTCGAGGTAAGAGAT
30079260 TGGCTGGTGA
Statistics
Matches: 78, Mismatches: 13, Indels: 18
0.72 0.12 0.17
Matches are distributed among these distances:
34 5 0.06
35 3 0.04
37 19 0.24
38 8 0.10
39 36 0.46
40 1 0.01
41 3 0.04
42 3 0.04
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (39 bp):
TGCCCCAAGCTCGAGGTAAGAGATCGGATAACTGCAATC
Found at i:30084592 original size:23 final size:23
Alignment explanation
Indices: 30084566--30084686 Score: 163
Period size: 23 Copynumber: 5.2 Consensus size: 23
30084556 ACACTAGCGC
30084566 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
30084589 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
30084612 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
* *
30084637 TCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
30084660 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
30084683 GCTC
1 GCTC
30084687 AGTACTTTGT
Statistics
Matches: 87, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
22 3 0.03
23 65 0.75
25 16 0.18
26 3 0.03
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:30084635 original size:48 final size:46
Alignment explanation
Indices: 30084566--30084686 Score: 163
Period size: 48 Copynumber: 2.6 Consensus size: 46
30084556 ACACTAGCGC
*
30084566 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCT-CGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCAC-TCTGCGT
* * *
30084612 GCTCTCTGTTATTAGCACTGTGTGTTCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACTCTGCGT
*
30084660 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
30084687 AGTACTTTGT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
46 25 0.38
47 2 0.03
48 39 0.59
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTCTGCGT
Found at i:30084705 original size:39 final size:39
Alignment explanation
Indices: 30084651--30084725 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
30084641 TCTGATTAGC
*
30084651 ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTTGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
*
30084690 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTTGTGTACTCTCTGATTAGCACTTTGTGTGCTC
30084726 TCTGTTCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (39 bp):
ACTTTGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:30084720 original size:23 final size:23
Alignment explanation
Indices: 30084690--30084754 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
30084680 TGTGCTCAGT
30084690 ACTTTGTGTACTCTCTGTTTAGC
1 ACTTTGTGTACTCTCTGTTTAGC
* * *
30084713 ACTTTGTGTGCTCTCTGTTCAGT
1 ACTTTGTGTACTCTCTGTTTAGC
* *
30084736 ACTTCG-GTACTCTCCGTTT
1 ACTTTGTGTACTCTCTGTTT
30084755 GTTCCGTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
22 10 0.29
23 25 0.71
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.46
Consensus pattern (23 bp):
ACTTTGTGTACTCTCTGTTTAGC
Found at i:30093675 original size:67 final size:67
Alignment explanation
Indices: 30093564--30093706 Score: 243
Period size: 67 Copynumber: 2.1 Consensus size: 67
30093554 TACGAAACAA
30093564 AATAATTAAGCAGATAAATATATACAGAAAAATTAAACATAAAATATTAGAATACAAAATACGAA
1 AATAATTAAGCAGATAAATATATACAGAAAAATTAAACATAAAATATTAGAATACAAAATACGAA
30093629 AG
66 AG
* * *
30093631 AATAATTAAGTAGATAAATATATACA-CAAAATTAAACATAAAAATATTAGAATACAAAATATGA
1 AATAATTAAGCAGATAAATATATACAGAAAAATTAAACAT-AAAATATTAGAATACAAAATACGA
30093695 AAG
65 AAG
30093698 AATAATTAA
1 AATAATTAA
30093707 ATTCTATGTA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
66 12 0.17
67 60 0.83
ACGTcount: A:0.62, C:0.06, G:0.08, T:0.24
Consensus pattern (67 bp):
AATAATTAAGCAGATAAATATATACAGAAAAATTAAACATAAAATATTAGAATACAAAATACGAA
AG
Found at i:30093954 original size:30 final size:30
Alignment explanation
Indices: 30093869--30094113 Score: 238
Period size: 30 Copynumber: 8.3 Consensus size: 30
30093859 GGAAAATTAG
*
30093869 GGGT-AAAATGGTGATTTTTG-GAAGTTTGA
1 GGGTAAAAAT-GTAATTTTTGAGAAGTTTGA
* * *
30093898 GGGCAAAAATGTGATTTTTG-GAAGTTCGA
1 GGGTAAAAATGTAATTTTTGAGAAGTTTGA
*
30093927 GGGTAAAAATGTAATTTTTGAGAAGTTCGA
1 GGGTAAAAATGTAATTTTTGAGAAGTTTGA
*
30093957 GGGTAAAAATGTAATCTTTGAGAAGTTT-A
1 GGGTAAAAATGTAATTTTTGAGAAGTTTGA
* * *
30093986 GGGTTAAAATATAATTTTTG-GAAAGTTTAA
1 GGGTAAAAATGTAATTTTTGAG-AAGTTTGA
* *
30094016 GGGTTAAAAA-GTAATTTTTGAAAAGTTTAA
1 GGG-TAAAAATGTAATTTTTGAGAAGTTTGA
* *
30094046 GGGT-TAAATGTAATTTTT-AGAAAGTTTGG
1 GGGTAAAAATGTAATTTTTGAG-AAGTTTGA
* *
30094075 GGGTTAAAATGTAATTTTTG-GAGAGTTTGG
1 GGGTAAAAATGTAATTTTTGAGA-AGTTTGA
*
30094105 GGGTCAAAA
1 GGGTAAAAA
30094114 CATGATTTAT
Statistics
Matches: 187, Mismatches: 18, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
28 5 0.03
29 84 0.45
30 93 0.50
31 5 0.03
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (30 bp):
GGGTAAAAATGTAATTTTTGAGAAGTTTGA
Found at i:30093965 original size:59 final size:58
Alignment explanation
Indices: 30093869--30094094 Score: 235
Period size: 59 Copynumber: 3.8 Consensus size: 58
30093859 GGAAAATTAG
* * * *
30093869 GGGTAAAATGGTGATTTTTGG-AAGTTTGAGGGCAAAAATGTGATTTTTG-GAAGTTCGA
1 GGGTAAAAT-GTAATTTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGAGAAGTT-AA
* * *
30093927 GGGTAAAAATGTAATTTTT-GAGAAGTTCGAGGGTAAAAATGTAATCTTTGAGAAGTTTA
1 GGGT-AAAATGTAATTTTTGGA-AAGTTTGAGGGTAAAAATGTAATTTTTGAGAAGTTAA
* * *
30093986 GGGTTAAAATATAATTTTTGGAAAGTTTAAGGGTTAAAAA-GTAATTTTTGAAAAGTTTAA
1 GGG-TAAAATGTAATTTTTGGAAAGTTTGAGGG-TAAAAATGTAATTTTTGAGAAG-TTAA
* * * *
30094046 GGGTTAAATGTAATTTTTAGAAAGTTTGGGGGTTAAAATGTAATTTTTG
1 GGGTAAAATGTAATTTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTG
30094095 GAGAGTTTGG
Statistics
Matches: 141, Mismatches: 18, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
57 1 0.01
58 17 0.12
59 102 0.72
60 21 0.15
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (58 bp):
GGGTAAAATGTAATTTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGAGAAGTTAA
Found at i:30093989 original size:29 final size:29
Alignment explanation
Indices: 30093855--30094102 Score: 216
Period size: 29 Copynumber: 8.4 Consensus size: 29
30093845 AAAGTCAAAC
** * *
30093855 TTTTGGAAAATTAGGGGT-AAAATGGTGAT
1 TTTTGGAAGTTTAAGGGTAAAAAT-GTAAT
* * *
30093884 TTTTGGAAGTTTGAGGGCAAAAATGTGAT
1 TTTTGGAAGTTTAAGGGTAAAAATGTAAT
**
30093913 TTTTGGAAGTTCGAGGGTAAAAATGTAAT
1 TTTTGGAAGTTTAAGGGTAAAAATGTAAT
**
30093942 TTTTGAGAAGTTCGAGGGTAAAAATGTAAT
1 TTTTG-GAAGTTTAAGGGTAAAAATGTAAT
* * *
30093972 CTTTGAGAAGTTT-AGGGTTAAAATATAAT
1 TTTTG-GAAGTTTAAGGGTAAAAATGTAAT
30094001 TTTTGGAAAGTTTAAGGGTTAAAAA-GTAAT
1 TTTTGG-AAGTTTAAGGG-TAAAAATGTAAT
* *
30094031 TTTTGAAAAGTTTAAGGGT-TAAATGTAAT
1 TTTTG-GAAGTTTAAGGGTAAAAATGTAAT
* ** *
30094060 TTTTAGAAAGTTTGGGGGTTAAAATGTAAT
1 TTTT-GGAAGTTTAAGGGTAAAAATGTAAT
30094090 TTTTGGAGAGTTT
1 TTTTGGA-AGTTT
30094103 GGGGGTCAAA
Statistics
Matches: 188, Mismatches: 21, Indels: 19
0.82 0.09 0.08
Matches are distributed among these distances:
28 4 0.02
29 96 0.51
30 83 0.44
31 5 0.03
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.38
Consensus pattern (29 bp):
TTTTGGAAGTTTAAGGGTAAAAATGTAAT
Found at i:30094127 original size:89 final size:86
Alignment explanation
Indices: 30093885--30094134 Score: 236
Period size: 89 Copynumber: 2.8 Consensus size: 86
30093875 AATGGTGATT
** * * *
30093885 TTTG-GAAGTTTGAGGGCAAAAATGTGATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAG
1 TTTGAGAAGTTT-AGGGTTAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATG--ATTTTTGAA
*
30093949 AAGTTCGAGGGTAAAAATGTAATC
63 AAGTTCAAGGGTAAAAATGTAATC
* * *
30093973 TTTGAGAAGTTTAGGGTTAAAATATAATTTTTGGAAAGTTTAAGGGTTAAAAAGTAATTTTTGAA
1 TTTGAGAAGTTTAGGGTTAAAATGTAATTTTTGG-AAGTTTGAGGG-TAAAAA-TGATTTTTGAA
* *
30094038 AAGTTTAAGGGT-TAAATGTAAT-
63 AAGTTCAAGGGTAAAAATGTAATC
* * * *
30094060 TTTTAGAAAGTTTGGGGGTTAAAATGTAATTTTTGGAGAGTTTGGGGGTCAAAACATGATTTATG
1 TTTGAG-AAGTTT-AGGGTTAAAATGTAATTTTTGGA-AGTTTGAGGGT-AAAA-ATGATTTTTG
*
30094125 AAAAATTCAA
61 AAAAGTTCAA
30094135 TGACCTTCTA
Statistics
Matches: 133, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
87 5 0.04
88 39 0.29
89 81 0.61
90 7 0.05
91 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (86 bp):
TTTGAGAAGTTTAGGGTTAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGATTTTTGAAAAG
TTCAAGGGTAAAAATGTAATC
Found at i:30095886 original size:17 final size:17
Alignment explanation
Indices: 30095864--30095929 Score: 105
Period size: 17 Copynumber: 3.8 Consensus size: 17
30095854 TTTAGAAAAT
30095864 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
30095881 TTTAAATTTAAAATAAT
1 TTTAAATTTAAAATAAA
*
30095898 TTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAA
30095915 TTTAAAATTTAAAAT
1 TTT-AAATTTAAAAT
30095930 TAGGTTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
17 34 0.77
18 10 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:30095910 original size:34 final size:34
Alignment explanation
Indices: 30095844--30095929 Score: 120
Period size: 34 Copynumber: 2.5 Consensus size: 34
30095834 TTTTTAAATT
* * * *
30095844 TAAAATTAAGTTTAGAA-AATTTTAAATTTAAAA
1 TAAATTTAAATTTAAAATAATTTTAAACTTAAAA
30095877 TAAATTTAAATTTAAAATAATTTTAAACTTAAAA
1 TAAATTTAAATTTAAAATAATTTTAAACTTAAAA
30095911 TAAATTTAAAATTTAAAAT
1 TAAATTT-AAATTTAAAAT
30095930 TAGGTTTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
33 14 0.30
34 22 0.47
35 11 0.23
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (34 bp):
TAAATTTAAATTTAAAATAATTTTAAACTTAAAA
Found at i:30102952 original size:45 final size:46
Alignment explanation
Indices: 30102903--30103014 Score: 131
Period size: 46 Copynumber: 2.5 Consensus size: 46
30102893 TTGCGATTGC
* * *
30102903 AAGATACTCTGGCATCGTATTCGATATG-TATAAGACCGC-AGTTGA
1 AAGATACTCTGGCATCATATCCAATATGCTATAAGACC-CTAGTTGA
* *
30102948 AAGATACTAC-GACATCATATCCAATATGCTATAAGACCCTATTTGA
1 AAGATACT-CTGGCATCATATCCAATATGCTATAAGACCCTAGTTGA
*
30102994 AAGATACTATGGCATCATATC
1 AAGATACTCTGGCATCATATC
30103015 GGTAATGAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
45 23 0.41
46 33 0.59
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (46 bp):
AAGATACTCTGGCATCATATCCAATATGCTATAAGACCCTAGTTGA
Found at i:30114701 original size:6 final size:6
Alignment explanation
Indices: 30114690--30114715 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
30114680 GTTTCTTAGA
30114690 AAAGTC AAAGTC AAAGTC AAAGTC AA
1 AAAGTC AAAGTC AAAGTC AAAGTC AA
30114716 CGGGTCTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAGTC
Found at i:30118636 original size:14 final size:14
Alignment explanation
Indices: 30118617--30118644 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30118607 GAAATTTCTA
30118617 CCGATACAAGTCAT
1 CCGATACAAGTCAT
30118631 CCGATACAAGTCAT
1 CCGATACAAGTCAT
30118645 GCATCTACCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (14 bp):
CCGATACAAGTCAT
Found at i:30119432 original size:51 final size:51
Alignment explanation
Indices: 30119356--30119643 Score: 389
Period size: 51 Copynumber: 5.6 Consensus size: 51
30119346 TTTCATTTAA
* * * * * * *
30119356 TACTCACGATGACATATTA-TCATCGGACCATTAATTCATCATGGATTCACT
1 TACTCACGATGACA-CTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
30119407 TACTCAAGATGACACTTAGTCATCGGACCTTTAATCCCTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
30119458 TACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTTATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
30119509 TACTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * * *
30119560 TACTCACGATGACATTTAGTCATCAGACCTTTAATCCGTAATGGATTCAAT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
30119611 TAATCACAATGACACTTAGTCATCGGACTCTTT
1 TACTCACGATGACACTTAGTCATCGGAC-CTTT
30119644 CGTTTATAGC
Statistics
Matches: 212, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
50 3 0.01
51 205 0.97
52 4 0.02
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:30127360 original size:2 final size:2
Alignment explanation
Indices: 30127353--30127381 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30127343 GACTAAACAT
30127353 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
30127382 TATAAGGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30146398 original size:2 final size:2
Alignment explanation
Indices: 30146391--30146421 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30146381 ACAAAATTTA
30146391 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
30146422 CTAAAAATTA
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:30149899 original size:29 final size:30
Alignment explanation
Indices: 30149867--30149925 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
30149857 TATGGTCTAA
* *
30149867 TGTGTAATTGTATACAT-AAACTTTGATTT
1 TGTGCAATTATATACATGAAACTTTGATTT
*
30149896 TGTGCAATTATATACATGAAATTTTGATTT
1 TGTGCAATTATATACATGAAACTTTGATTT
30149926 GATCAAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (30 bp):
TGTGCAATTATATACATGAAACTTTGATTT
Found at i:30150098 original size:31 final size:31
Alignment explanation
Indices: 30150053--30150137 Score: 75
Period size: 31 Copynumber: 2.7 Consensus size: 31
30150043 TCTTTAAATG
* *
30150053 TGTATGATTAAATCAAAATTAAAGTTTCA-A
1 TGTATAATTGAATCAAAATTAAAGTTTCACA
* * *
30150083 -GTATACATTTGAATCACAATCAGAGTTTCACA
1 TGTATA-A-TTGAATCAAAATTAAAGTTTCACA
* *
30150115 TGTATAATTGCACCAAAATTAAA
1 TGTATAATTGAATCAAAATTAAA
30150138 ATTCATGTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
29 4 0.10
30 1 0.02
31 29 0.71
32 2 0.05
33 5 0.12
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.33
Consensus pattern (31 bp):
TGTATAATTGAATCAAAATTAAAGTTTCACA
Found at i:30150153 original size:30 final size:30
Alignment explanation
Indices: 30150117--30150179 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
30150107 GTTTCACATG
* *
30150117 TATAATTGCACCA-AAATTAAAATTCATGTA
1 TATAATTACA-CATAAATCAAAATTCATGTA
30150147 TATAATTACACATTAAATCAAAATTCATGTA
1 TATAATTACACA-TAAATCAAAATTCATGTA
30150178 TA
1 TA
30150180 CTTTTGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 2 0.07
30 9 0.31
31 18 0.62
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.35
Consensus pattern (30 bp):
TATAATTACACATAAATCAAAATTCATGTA
Found at i:30153417 original size:30 final size:30
Alignment explanation
Indices: 30153378--30153460 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 30
30153368 TAACCATTAA
30153378 ACTATAATTTTAAAATCTAAAAAATAAAAAG
1 ACTA-AATTTTAAAATCTAAAAAATAAAAAG
* * *
30153409 ACTAAATTTTTAAAA-AT-AAAAGTAAAATG
1 ACTAAA-TTTTAAAATCTAAAAAATAAAAAG
30153438 ACTAAATTTT-AAATCTACAAAAA
1 ACTAAATTTTAAAATCTA-AAAAA
30153461 ATACATCGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 3 0.07
28 5 0.12
29 16 0.37
30 7 0.16
31 12 0.28
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (30 bp):
ACTAAATTTTAAAATCTAAAAAATAAAAAG
Found at i:30153552 original size:18 final size:18
Alignment explanation
Indices: 30153526--30153560 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30153516 TAGTTTTTAT
30153526 ATAGGTGGTTATGTATTA
1 ATAGGTGGTTATGTATTA
* *
30153544 ATAGTTGGTTATTTATT
1 ATAGGTGGTTATGTATT
30153561 CAACATCAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (18 bp):
ATAGGTGGTTATGTATTA
Found at i:30155980 original size:31 final size:31
Alignment explanation
Indices: 30155936--30156028 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
30155926 TATTTATCCA
* *
30155936 ATATGATTGAACCACAATCAAAGTTTTGTGT
1 ATATAATTGAACCACAATCAAAGTTTCGTGT
*
30155967 ATATATTTGAACCACAATCAAAGTTTCGTGT
1 ATATAATTGAACCACAATCAAAGTTTCGTGT
* *
30155998 GTATAATT-ACACCA-AATCAAA-TTTCATGT
1 ATATAATTGA-ACCACAATCAAAGTTTCGTGT
30156027 AT
1 AT
30156029 TAAATTGCAG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.15
30 8 0.15
31 38 0.70
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (31 bp):
ATATAATTGAACCACAATCAAAGTTTCGTGT
Found at i:30176638 original size:31 final size:31
Alignment explanation
Indices: 30176597--30176655 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
30176587 AGATCAAGTT
*
30176597 TCAATGTGAAAATAATTGTCAAGTTTAATCC
1 TCAATATGAAAATAATTGTCAAGTTTAATCC
*
30176628 TCAATATGAAAATTATTGTCAAGTTTAA
1 TCAATATGAAAATAATTGTCAAGTTTAA
30176656 AGACTAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (31 bp):
TCAATATGAAAATAATTGTCAAGTTTAATCC
Found at i:30177003 original size:17 final size:17
Alignment explanation
Indices: 30176981--30177040 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
30176971 AAGAATATGA
*
30176981 AAGGTTGAGGAAGATGG
1 AAGGTTAAGGAAGATGG
*
30176998 AAGGTTAAAGGTCA-ATAGG
1 AAGGTT-AAGG-AAGAT-GG
30177017 -AGGTTAAGGAAGATGG
1 AAGGTTAAGGAAGATGG
30177033 AAGGTTAA
1 AAGGTTAA
30177041 AAGTCAAGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
16 3 0.09
17 19 0.54
18 10 0.29
19 3 0.09
ACGTcount: A:0.40, C:0.02, G:0.38, T:0.20
Consensus pattern (17 bp):
AAGGTTAAGGAAGATGG
Found at i:30182425 original size:35 final size:34
Alignment explanation
Indices: 30182379--30182450 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 34
30182369 AATAATATGA
* *
30182379 AAGGTTGAGGAAAATGAAAGGTTAAAGGTCAACGG
1 AAGGTTAAGGAAAATGAAAGGTTAAAAGTCAA-GG
*
30182414 AAGGTTAAGGAAGATGAAAGGTTAAAAGTCAAGG
1 AAGGTTAAGGAAAATGAAAGGTTAAAAGTCAAGG
30182448 AAG
1 AAG
30182451 ATAAAAGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 5 0.15
35 29 0.85
ACGTcount: A:0.46, C:0.04, G:0.33, T:0.17
Consensus pattern (34 bp):
AAGGTTAAGGAAAATGAAAGGTTAAAAGTCAAGG
Found at i:30182434 original size:17 final size:16
Alignment explanation
Indices: 30182375--30182438 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
30182365 TTACAATAAT
*
30182375 ATGAAAGGTTGAGGAAA
1 ATGAAAGGTTAAGG-AA
*
30182392 ATGAAAGGTTAAAGGTCA
1 ATGAAAGGTT-AAGG-AA
* *
30182410 ACGGAAGGTTAAGGAA
1 ATGAAAGGTTAAGGAA
30182426 GATGAAAGGTTAA
1 -ATGAAAGGTTAA
30182439 AAGTCAAGGA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
16 1 0.03
17 24 0.65
18 12 0.32
ACGTcount: A:0.45, C:0.03, G:0.33, T:0.19
Consensus pattern (16 bp):
ATGAAAGGTTAAGGAA
Found at i:30186909 original size:24 final size:26
Alignment explanation
Indices: 30186871--30186918 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
30186861 TCTACATGGG
30186871 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
30186897 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
30186919 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:30198313 original size:27 final size:27
Alignment explanation
Indices: 30198263--30198314 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
30198253 AAAAAACTCA
* *
30198263 ATGCGTGAAAGATGAAATACCAAAGAC
1 ATGCATGAAAGAGGAAATACCAAAGAC
* *
30198290 ATGCATGAAAGAGGAGATATCAAAG
1 ATGCATGAAAGAGGAAATACCAAAG
30198315 TCATAAGCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.48, C:0.12, G:0.25, T:0.15
Consensus pattern (27 bp):
ATGCATGAAAGAGGAAATACCAAAGAC
Found at i:30218924 original size:19 final size:18
Alignment explanation
Indices: 30218895--30218930 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30218885 TTTCTTCGAG
*
30218895 GAAGTTCCGCCGCCGCTC
1 GAAGTTCCGCCACCGCTC
30218913 GAAGTATCCGCCACCGCT
1 GAAGT-TCCGCCACCGCT
30218931 TCCGCCGCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.17, C:0.42, G:0.25, T:0.17
Consensus pattern (18 bp):
GAAGTTCCGCCACCGCTC
Found at i:30227033 original size:15 final size:15
Alignment explanation
Indices: 30226984--30227034 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
30226974 TTGTCTCAAG
*
30226984 TTATATTTTAGTCAC
1 TTATGTTTTAGTCAC
* *
30226999 TTATGTTTGAAAT-A-
1 TTATGTTT-TAGTCAC
30227013 TTATGTTTTAGTCAC
1 TTATGTTTTAGTCAC
30227028 TTATGTT
1 TTATGTT
30227035 AGTAGTTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 15 0.54
16 2 0.07
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.55
Consensus pattern (15 bp):
TTATGTTTTAGTCAC
Found at i:30236326 original size:6 final size:6
Alignment explanation
Indices: 30236315--30236356 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
30236305 TACACATACC
* *
30236315 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAC ATGTCT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
30236357 GTTTAAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (6 bp):
ATGTAT
Found at i:30236879 original size:42 final size:42
Alignment explanation
Indices: 30236795--30236886 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
30236785 ATGATCCAAG
* * * *
30236795 GGAAAGCTAACGGTGTTTGGAGGCCTCGGCGTCATCCAAAAT
1 GGAAAGCTAACGGTGTTTGGAAGCCGCGCCGCCATCCAAAAT
* ***
30236837 GGAAAGCTAACGGTGTTTGGAAGTCGCGCCGCCATTGGAAAT
1 GGAAAGCTAACGGTGTTTGGAAGCCGCGCCGCCATCCAAAAT
30236879 GGAAAGCT
1 GGAAAGCT
30236887 GCTGAGTGCT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.21
Consensus pattern (42 bp):
GGAAAGCTAACGGTGTTTGGAAGCCGCGCCGCCATCCAAAAT
Found at i:30237419 original size:23 final size:23
Alignment explanation
Indices: 30237386--30237430 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
30237376 ATTATTCGAG
*
30237386 TTGATATCTATTGAATAATTATA
1 TTGATACCTATTGAATAATTATA
30237409 TTGATACCTATTGAATAATTAT
1 TTGATACCTATTGAATAATTAT
30237431 GTATACATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (23 bp):
TTGATACCTATTGAATAATTATA
Found at i:30241232 original size:20 final size:21
Alignment explanation
Indices: 30241202--30241242 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
30241192 CAGCTTGCTG
30241202 AGAGCTTGCTTCTAACATCAA
1 AGAGCTTGCTTCTAACATCAA
* *
30241223 AGAG-TTGCTTTTGACATCAA
1 AGAGCTTGCTTCTAACATCAA
30241243 TAAGTGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (21 bp):
AGAGCTTGCTTCTAACATCAA
Found at i:30245791 original size:29 final size:30
Alignment explanation
Indices: 30245759--30245817 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
30245749 TATGGTTTAA
*
30245759 TGTGTAATTATATACAT-AAATTTTGATTT
1 TGTGTAATTATATACATGAAAATTTGATTT
*
30245788 TGTGTAATTTTATACATGAAAATTTGATTT
1 TGTGTAATTATATACATGAAAATTTGATTT
30245818 GATCCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.51
Consensus pattern (30 bp):
TGTGTAATTATATACATGAAAATTTGATTT
Found at i:30247081 original size:15 final size:15
Alignment explanation
Indices: 30247061--30247099 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
30247051 CAAATGAGTC
30247061 CAAAAAATTTTCTAT
1 CAAAAAATTTTCTAT
*
30247076 CAAAAAATATTTTTAT
1 CAAAAAAT-TTTCTAT
30247092 -AAAAAATT
1 CAAAAAATT
30247100 CAATTCTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 15 0.68
16 6 0.27
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (15 bp):
CAAAAAATTTTCTAT
Found at i:30250121 original size:21 final size:21
Alignment explanation
Indices: 30250097--30250139 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
30250087 CTCATATTGT
* *
30250097 TTTTAATATTTATTTATTTTA
1 TTTTAATATTTAATAATTTTA
*
30250118 TTTTAGTATTTAATAATTTTA
1 TTTTAATATTTAATAATTTTA
30250139 T
1 T
30250140 ATACTTTCTA
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:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTAATATTTAATAATTTTA
Found at i:30250274 original size:18 final size:20
Alignment explanation
Indices: 30250248--30250286 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
30250238 AATGTGTTTT
*
30250248 AAATTACATA-AT-ATATAA
1 AAATAACATATATAATATAA
30250266 AAATAACATATATAATATAA
1 AAATAACATATATAATATAA
30250286 A
1 A
30250287 TTATTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATAACATATATAATATAA
Found at i:30251322 original size:17 final size:17
Alignment explanation
Indices: 30251300--30251341 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
30251290 TCCAAAACTA
30251300 TTTTAATTTAATT-TAAT
1 TTTTAATTT-ATTCTAAT
*
30251317 TTTTAATATATTCTAAT
1 TTTTAATTTATTCTAAT
*
30251334 TATTAATT
1 TTTTAATT
30251342 CGATTATCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAATTTATTCTAAT
Found at i:30252750 original size:27 final size:26
Alignment explanation
Indices: 30252713--30252780 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
30252703 CTTTATTTCC
30252713 TTTTTTATTTTATTTA-CCCTCCACTTT
1 TTTTTTATTTTATTTATCCC-CC-CTTT
* *
30252740 TTTTTTCTTTTCTTTATTCCCCCCTTT
1 TTTTTTATTTTATTTA-TCCCCCCTTT
*
30252767 TTTTTAATTTTATT
1 TTTTTTATTTTATT
30252781 CCATTTCGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 29 0.85
28 2 0.06
29 3 0.09
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTTTATTTTATTTATCCCCCCTTT
Found at i:30262239 original size:7 final size:7
Alignment explanation
Indices: 30262227--30262251 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30262217 TCTCATTCAT
30262227 AAAAAGA
1 AAAAAGA
30262234 AAAAAGA
1 AAAAAGA
30262241 AAAAAGA
1 AAAAAGA
30262248 AAAA
1 AAAA
30262252 TCAAACTCCA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:30264104 original size:18 final size:19
Alignment explanation
Indices: 30264063--30264110 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
30264053 GAGGAGAAAA
30264063 AAAAAAGAAAACGTTAGTG
1 AAAAAAGAAAACGTTAGTG
30264082 AAAAAAGAAAACGTTAGTG
1 AAAAAAGAAAACGTTAGTG
30264101 AAAAAA-AAAA
1 AAAAAAGAAAA
30264111 AAAGTGGGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 4 0.14
19 25 0.86
ACGTcount: A:0.67, C:0.04, G:0.17, T:0.12
Consensus pattern (19 bp):
AAAAAAGAAAACGTTAGTG
Found at i:30270199 original size:6 final size:6
Alignment explanation
Indices: 30270188--30270224 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
30270178 AGTAATAGGA
30270188 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
30270225 ATATTCTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:30272796 original size:2 final size:2
Alignment explanation
Indices: 30272789--30272820 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30272779 TGAAGTAGCA
30272789 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
30272821 TTACCCCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30294296 original size:33 final size:32
Alignment explanation
Indices: 30294258--30294323 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 32
30294248 AAATAGGGAG
* *
30294258 TTATTAATATTTATAATTA-AAATTTAAATAAAT
1 TTATTAATAGTTAT--TTATAAATTTAAAAAAAT
30294291 TTATTAATAGTTATTTATAAATTTAAAAAAAT
1 TTATTAATAGTTATTTATAAATTTAAAAAAAT
30294323 T
1 T
30294324 ATTTAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 3 0.10
32 14 0.47
33 13 0.43
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (32 bp):
TTATTAATAGTTATTTATAAATTTAAAAAAAT
Found at i:30301151 original size:16 final size:16
Alignment explanation
Indices: 30301132--30301178 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
30301122 AATTTTCAAT
30301132 AAATAAAAAATATATA
1 AAATAAAAAATATATA
**
30301148 AAATTATTAAATAT-TA
1 AAA-TAAAAAATATATA
30301164 AAATAAAACAATATA
1 AAATAAAA-AATATA
30301179 AATATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 13 0.54
17 8 0.33
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:30301160 original size:28 final size:27
Alignment explanation
Indices: 30301114--30301205 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 27
30301104 TTAAGATGAC
*
30301114 TATATAAAAATTTTCAATAAATAAAAAA
1 TATAT-AAAATTTTAAATAAATAAAAAA
30301142 TATATAAAATTATTAAATATTAAAATAAAACAA
1 TATATAAAATT-TT-AA-A-T-AAATAAAA-AA
* *
30301175 TATA-AATATTTTTAAAAAAATAAAAAA
1 TATATAA-AATTTTAAATAAATAAAAAA
30301202 -ATAT
1 TATAT
30301206 GAGCAAATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
26 3 0.06
27 8 0.15
28 15 0.28
29 1 0.02
30 2 0.04
31 3 0.06
32 12 0.23
33 9 0.17
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
TATATAAAATTTTAAATAAATAAAAAA
Found at i:30301199 original size:33 final size:32
Alignment explanation
Indices: 30301132--30301199 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
30301122 AATTTTCAAT
* *
30301132 AAATAAAAAATATATAAAATTATTAAATATTA
1 AAATAAAAAATATATAAAATTATTAAAAAATA
* *
30301164 AAATAAAACAATATA-AATATTTTTAAAAAAATA
1 AAATAAAA-AATATATAAAATTATT-AAAAAATA
30301197 AAA
1 AAA
30301200 AAATATGAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (32 bp):
AAATAAAAAATATATAAAATTATTAAAAAATA
Found at i:30301752 original size:3 final size:3
Alignment explanation
Indices: 30301744--30301771 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
30301734 ATACGAATGA
30301744 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
30301772 TTGACGGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:30303631 original size:44 final size:43
Alignment explanation
Indices: 30303578--30303686 Score: 166
Period size: 44 Copynumber: 2.5 Consensus size: 43
30303568 GAGTAAGTAG
30303578 AATCATTGTTGAATTAGAGATGTTTATTTCAACTAGAAAAACGA
1 AATCATTGTTGAATTAGAGATGTTTATTTCAACTAG-AAAACGA
* *
30303622 AATCTTTGTTGAATTAGAGAAGTTTATTTCAACTAGAAAACGA
1 AATCATTGTTGAATTAGAGATGTTTATTTCAACTAGAAAACGA
* *
30303665 AATCCTAGTTGAATTAG-GATGT
1 AATCATTGTTGAATTAGAGATGT
30303687 AGGGCGCGAC
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 4 0.07
43 22 0.37
44 34 0.57
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (43 bp):
AATCATTGTTGAATTAGAGATGTTTATTTCAACTAGAAAACGA
Found at i:30304133 original size:63 final size:63
Alignment explanation
Indices: 30304066--30304186 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
30304056 GTTTTTCAAG
* * * * *
30304066 TCATTTTCATTTTGAAGAAAACCACATTT-ATTTTCAAATGATTTTATTTTTTCATTTTTGTTT
1 TCATTTTAATTTTGAAGAAAACCAC-TTTCATTTCCAAATGATTTAATTTCTCCATTTTTGTTT
* *
30304129 TCATTTTAATTTTGGAGAAAACCACTTTCATTTCCAAATTATTTAATTTCTCCATTTT
1 TCATTTTAATTTTGAAGAAAACCACTTTCATTTCCAAATGATTTAATTTCTCCATTTT
30304187 CATTTTGGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 3 0.06
63 47 0.94
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.52
Consensus pattern (63 bp):
TCATTTTAATTTTGAAGAAAACCACTTTCATTTCCAAATGATTTAATTTCTCCATTTTTGTTT
Found at i:30308974 original size:114 final size:114
Alignment explanation
Indices: 30308770--30309098 Score: 419
Period size: 114 Copynumber: 2.8 Consensus size: 114
30308760 ATAGCAATCT
*
30308770 ATACCGAACAAGAAGCACAGGCAGAGAAGCAAACTCACATGAATAACATTTTAAAACCAAACTTA
1 ATACCGAACAAGAAGCACAGGCAGAGAAGCAAACTCACATGAATAACATTTTAAAA-CGAACTTA
* *
30308835 TCTCGGAAGCTAAAGATTGTTCAAACATGTAATCAG-C-TAGAGTAAGCAA
65 TCTCGAAAACTAAAGATTGTTCAAACATGTAATC-GCCTTAGAGTAAGCAA
* *** * * *
30308884 ATATCGAACAAGAAGCATTTGCAGAGATGCAAACTCGCATGCATAACATTTTAAAATCGAACTTA
1 ATACCGAACAAGAAGCACAGGCAGAGAAGCAAACTCACATGAATAACATTTTAAAA-CGAACTTA
*
30308949 TCTCAAAAACTAAAGATTGTTCAAACATGTAATCGCCTCAATTTTAGAGTAAGCAA
65 TCTCGAAAACTAAAGATTGTTCAAACATGTAATCG-C-C----TTAGAGTAAGCAA
* *
30309005 ATACCGAACAAGAAGCACAGGCAGAGAAGCAAACTCACATGTATAACATTTTAAGAAGGAACTTA
1 ATACCGAACAAGAAGCACAGGCAGAGAAGCAAACTCACATGAATAACATTTTAA-AACGAACTTA
*
30309070 TCTCGAAAACTAAAAGATTATTCAAACAT
65 TCTCGAAAACT-AAAGATTGTTCAAACAT
30309099 TACCTTGATT
Statistics
Matches: 183, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
113 1 0.01
114 87 0.48
116 1 0.01
121 76 0.42
122 18 0.10
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (114 bp):
ATACCGAACAAGAAGCACAGGCAGAGAAGCAAACTCACATGAATAACATTTTAAAACGAACTTAT
CTCGAAAACTAAAGATTGTTCAAACATGTAATCGCCTTAGAGTAAGCAA
Found at i:30318434 original size:2 final size:2
Alignment explanation
Indices: 30318427--30318469 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
30318417 GTTAATTTTA
30318427 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
30318469 A
1 A
30318470 ATTCAATAAT
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:30320349 original size:29 final size:30
Alignment explanation
Indices: 30320317--30320373 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
30320307 GAATCAAAAC
* * *
30320317 TAATCTATTTATTATTAAATAG-ATCAATT
1 TAATCCATATATTATTAAAAAGAATCAATT
*
30320346 TAATCCCTATATTATTAAAAAGAATCAA
1 TAATCCATATATTATTAAAAAGAATCAA
30320374 ATAAACCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.40
Consensus pattern (30 bp):
TAATCCATATATTATTAAAAAGAATCAATT
Found at i:30323955 original size:28 final size:29
Alignment explanation
Indices: 30323912--30323979 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
30323902 CAAAAGTTAA
*
30323912 TAAAAACAATAAATTT-GGGCCTTTAAAAAC
1 TAAAAA-AA-AAATTTGGGGCCCTTAAAAAC
*
30323942 TAAAAAAAAAATTTGGGGCCCTTAAAAAT
1 TAAAAAAAAAATTTGGGGCCCTTAAAAAC
30323971 TAAAAAAAA
1 TAAAAAAAA
30323980 TATAAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 6 0.17
29 23 0.66
30 6 0.17
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.24
Consensus pattern (29 bp):
TAAAAAAAAAATTTGGGGCCCTTAAAAAC
Found at i:30326409 original size:61 final size:61
Alignment explanation
Indices: 30326308--30326426 Score: 154
Period size: 61 Copynumber: 2.0 Consensus size: 61
30326298 TTGACCTCTT
* *
30326308 CAAAATTTTGAAAAATTTTGATTTTCTGTTTGAATGTTTTAGAATATTTTAATTAGGTTTC
1 CAAAATTTTGAAAAATTTTGATTTTCTGTTTGAATGTTTTAGAAAATTTCAATTAGGTTTC
* *
30326369 CAAAATTTTTG-AAAATTTTTATTTT-TTTCTTGAA-GTTTTTAGAAAATTTCAATTAGGT
1 CAAAA-TTTTGAAAAATTTTGATTTTCTGT-TTGAATG-TTTTAGAAAATTTCAATTAGGT
30326427 CCCCTCAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
60 3 0.06
61 43 0.84
62 5 0.10
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (61 bp):
CAAAATTTTGAAAAATTTTGATTTTCTGTTTGAATGTTTTAGAAAATTTCAATTAGGTTTC
Found at i:30328825 original size:30 final size:31
Alignment explanation
Indices: 30328791--30328853 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
30328781 CATTTAACAC
30328791 AATAGACACTCAAC-TT-T-GAAAATGTGACAA
1 AATAGACACT-AACGTTATCGAAAA-GTGACAA
*
30328821 AATAGTCACTAACGTTATCGAAAAGTGACAA
1 AATAGACACTAACGTTATCGAAAAGTGACAA
30328852 AA
1 AA
30328854 CAATCACTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 3 0.10
30 11 0.38
31 10 0.34
32 5 0.17
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (31 bp):
AATAGACACTAACGTTATCGAAAAGTGACAA
Found at i:30329499 original size:30 final size:31
Alignment explanation
Indices: 30329432--30329502 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
30329422 ACTGTTAATC
*
30329432 AGTGATTGTTTTGGCACTTTTCGATAACGTT
1 AGTGACTGTTTTGGCACTTTTCGATAACGTT
*
30329463 AGTGACTGTTTTGTCACATTTTC-A-AA-GTT
1 AGTGACTGTTTTGGCAC-TTTTCGATAACGTT
30329492 GAGTGACTGTT
1 -AGTGACTGTT
30329503 GTGTTAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 3 0.08
30 12 0.33
31 16 0.44
32 5 0.14
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.44
Consensus pattern (31 bp):
AGTGACTGTTTTGGCACTTTTCGATAACGTT
Found at i:30345743 original size:15 final size:15
Alignment explanation
Indices: 30345723--30345752 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30345713 TTTCTACCCA
30345723 AAAAAAAAAGGATAT
1 AAAAAAAAAGGATAT
*
30345738 AAAAAAAGAGGATAT
1 AAAAAAAAAGGATAT
30345753 TGTTTAAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAAAAAAAGGATAT
Found at i:30345932 original size:24 final size:24
Alignment explanation
Indices: 30345903--30345963 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
30345893 TTTAAACCAT
*
30345903 TTAT-AATTTATAAAATTTTAAAA
1 TTATAAATTTATAAAATATTAAAA
* *
30345926 GTTATAAATATATAAACTATTAAAA
1 -TTATAAATTTATAAAATATTAAAA
*
30345951 TAATAAATTTATA
1 TTATAAATTTATA
30345964 TTTTTACTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 15 0.48
25 16 0.52
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
TTATAAATTTATAAAATATTAAAA
Found at i:30350071 original size:3 final size:3
Alignment explanation
Indices: 30350063--30350112 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
30350053 TCCTGATGCT
*
30350063 TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30350111 TT
1 TT
30350113 TTCCTAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:30355141 original size:48 final size:48
Alignment explanation
Indices: 30355070--30355213 Score: 279
Period size: 48 Copynumber: 3.0 Consensus size: 48
30355060 TATTTTGACA
30355070 GCTAATTGGATCAAACTTGCTAATCCTCTAACCTTTGTATATGTGATT
1 GCTAATTGGATCAAACTTGCTAATCCTCTAACCTTTGTATATGTGATT
30355118 GCTAATTGGATCAAACTTGCTAATCCTCTAACCTTTGTATATGTGATT
1 GCTAATTGGATCAAACTTGCTAATCCTCTAACCTTTGTATATGTGATT
*
30355166 GCTAATTGGATCAAACTTGCTAATCCTTTAACCTTTGTATATGTGATT
1 GCTAATTGGATCAAACTTGCTAATCCTCTAACCTTTGTATATGTGATT
30355214 AATAGAAATT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 95 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (48 bp):
GCTAATTGGATCAAACTTGCTAATCCTCTAACCTTTGTATATGTGATT
Found at i:30365831 original size:16 final size:14
Alignment explanation
Indices: 30365799--30365839 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
30365789 TATTTTATTT
30365799 CTTTAAACATTATC
1 CTTTAAACATTATC
30365813 CTTTAAACACTTCATC
1 CTTTAAACA-TT-ATC
30365829 C-TTAAA-ATTAT
1 CTTTAAACATTAT
30365840 AAAATCAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 2 0.08
13 2 0.08
14 10 0.40
15 7 0.28
16 4 0.16
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (14 bp):
CTTTAAACATTATC
Found at i:30382069 original size:6 final size:6
Alignment explanation
Indices: 30382054--30382090 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
30382044 ACATACCATA
* *
30382054 TATATT TATATG TATATG TATATG TATATG TGTATG T
1 TATATG TATATG TATATG TATATG TATATG TATATG T
30382091 TTAAAGAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (6 bp):
TATATG
Found at i:30382700 original size:42 final size:42
Alignment explanation
Indices: 30382617--30382707 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
30382607 TGATCCAATC
* *
30382617 GAAAGCTAACGGTGTTTGGAGGCCTCGGCGTCATCGAAAATG
1 GAAAGCTAACGGTGTTTGGAGGCCTCGCCGCCATCGAAAATG
* * * *
30382659 GAAATCTAACGGTGTTTGGAGGGCTCGCCGCCATTGGAAATG
1 GAAAGCTAACGGTGTTTGGAGGCCTCGCCGCCATCGAAAATG
*
30382701 GGAAGCT
1 GAAAGCT
30382708 GTTGAGTGCT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.22
Consensus pattern (42 bp):
GAAAGCTAACGGTGTTTGGAGGCCTCGCCGCCATCGAAAATG
Found at i:30383543 original size:20 final size:21
Alignment explanation
Indices: 30383520--30383562 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
30383510 GATTATTAAA
30383520 TTTT-TTAATTTATTGAATTT
1 TTTTATTAATTTATTGAATTT
* *
30383540 TTTTATTATTTTGTTGAATTT
1 TTTTATTAATTTATTGAATTT
30383561 TT
1 TT
30383563 ATCAACTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (21 bp):
TTTTATTAATTTATTGAATTT
Found at i:30386964 original size:29 final size:30
Alignment explanation
Indices: 30386911--30386969 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
30386901 CATGGTTTAA
*
30386911 TGTGCAATTGTATACAAGAACTTTT-ATTT
1 TGTGCAATTGTATACAAGAAATTTTGATTT
*
30386940 TGTGCAATTTTATACATA-AAATTTTGATTT
1 TGTGCAATTGTATACA-AGAAATTTTGATTT
30386970 GATTCAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.47
Consensus pattern (30 bp):
TGTGCAATTGTATACAAGAAATTTTGATTT
Found at i:30388914 original size:16 final size:16
Alignment explanation
Indices: 30388889--30388921 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
30388879 CGATCATTTT
30388889 TTATAATATTTTTATA
1 TTATAATATTTTTATA
*
30388905 TTATATTATTTTTATA
1 TTATAATATTTTTATA
30388921 T
1 T
30388922 ATTATGCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATAATATTTTTATA
Found at i:30389748 original size:13 final size:13
Alignment explanation
Indices: 30389730--30389757 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
30389720 TTAGGTTTGA
30389730 AAAAGAATTCAAT
1 AAAAGAATTCAAT
30389743 AAAAGAATTCAAT
1 AAAAGAATTCAAT
30389756 AA
1 AA
30389758 GTGGCTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AAAAGAATTCAAT
Found at i:30400416 original size:19 final size:19
Alignment explanation
Indices: 30400385--30400426 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
30400375 ATTAAATAAA
*
30400385 TTTT-ATAACTTTTATGTTT
1 TTTTAATAACTTTTA-GTAT
30400404 TTTTAATAA-TTTTAGTAT
1 TTTTAATAACTTTTAGTAT
30400422 TTTTA
1 TTTTA
30400427 TTTTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTAATAACTTTTAGTAT
Found at i:30406054 original size:17 final size:15
Alignment explanation
Indices: 30406032--30406066 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 15
30406022 AGCTTTCAAG
30406032 TTTGAATTTTATTTTTA
1 TTTGAA-TTT-TTTTTA
30406049 TTTGAATTTTTTTTA
1 TTTGAATTTTTTTTA
30406064 TTT
1 TTT
30406067 AAGTTTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 3 0.17
17 6 0.33
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTGAATTTTTTTTA
Found at i:30406251 original size:16 final size:18
Alignment explanation
Indices: 30406220--30406256 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
30406210 ATTTTTCATT
*
30406220 TAAAATCTTTATAATTTA
1 TAAAATCTTTATAATTAA
30406238 TAAAAT-TTTA-AATTAA
1 TAAAATCTTTATAATTAA
30406254 TAA
1 TAA
30406257 TAATAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 4 0.22
18 6 0.33
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAATCTTTATAATTAA
Found at i:30406399 original size:27 final size:27
Alignment explanation
Indices: 30406342--30406429 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
30406332 TTATTAAAAT
* *
30406342 AAAAAAATTATAATTTTTTTGATGA-ACA
1 AAAAAAATTAT-ATTTTTATGATCATA-A
30406370 AAAAAAATTATATTTTTATGATCATAA
1 AAAAAAATTATATTTTTATGATCATAA
* *
30406397 AAATAAA-TA-A-TTTAATTGATCATAA
1 AAAAAAATTATATTTTTA-TGATCATAA
*
30406422 AAATAAAT
1 AAAAAAAT
30406430 AATTTAATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
24 4 0.08
25 17 0.32
26 2 0.04
27 18 0.34
28 12 0.23
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (27 bp):
AAAAAAATTATATTTTTATGATCATAA
Found at i:30406409 original size:25 final size:26
Alignment explanation
Indices: 30406388--30406438 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
30406378 TATATTTTTA
30406388 TGATCATAAAAATAAATAA-TTTAAT
1 TGATCATAAAAATAAATAATTTTAAT
30406413 TGATCATAAAAATAAATAA-TTTAAT
1 TGATCATAAAAATAAATAATTTTAAT
30406438 T
1 T
30406439 TTAACCCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (26 bp):
TGATCATAAAAATAAATAATTTTAAT
Found at i:30408499 original size:21 final size:20
Alignment explanation
Indices: 30408470--30408518 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
30408460 TTTAACGATT
* *
30408470 TTTTTAATATTATTTGGTAAA
1 TTTTAAATATT-TTTGATAAA
*
30408491 TTTTAAATATTTTTTATAAA
1 TTTTAAATATTTTTGATAAA
30408511 TATTTAAA
1 T-TTTAAA
30408519 AAAAATCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
TTTTAAATATTTTTGATAAA
Found at i:30410264 original size:21 final size:19
Alignment explanation
Indices: 30410240--30410278 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
30410230 ATACTGTTTA
30410240 TATATTGCATACATATATAAT
1 TATATT-CATACA-ATATAAT
*
30410261 TATATTTATACAATATAA
1 TATATTCATACAATATAA
30410279 AAATAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (19 bp):
TATATTCATACAATATAAT
Found at i:30412420 original size:23 final size:25
Alignment explanation
Indices: 30412394--30412448 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 25
30412384 AAAATTTTAA
30412394 AAATATTAACTCTTTTAA-AC-AGT
1 AAATATTAACTCTTTTAACACTAGT
*
30412417 AAATA-T-ACTTTTTTAACACTAGT
1 AAATATTAACTCTTTTAACACTAGT
30412440 AAATATTAA
1 AAATATTAA
30412449 ATCTATTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 9 0.33
22 3 0.11
23 13 0.48
24 1 0.04
25 1 0.04
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (25 bp):
AAATATTAACTCTTTTAACACTAGT
Found at i:30412929 original size:29 final size:30
Alignment explanation
Indices: 30412897--30412955 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
30412887 TATGATTTAA
*
30412897 TATGTAATTATATATAT-AAATTTTAATTT
1 TATGTAATTATATACATGAAATTTTAATTT
* *
30412926 TATGTAATTTTATACATGAAATTTTGATTT
1 TATGTAATTATATACATGAAATTTTAATTT
30412956 GATCAAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (30 bp):
TATGTAATTATATACATGAAATTTTAATTT
Found at i:30413181 original size:29 final size:30
Alignment explanation
Indices: 30413097--30413185 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 30
30413087 GATTAAATCA
* * *
30413097 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCATGTATACAATTGCACC
* *
30413127 ATAAATAAAGTTTCACATGTAT--AATTGCATC
1 A-AATTAAAGTTT--CATGTATACAATTGCACC
30413158 AAATTAAA-TTTCATGTATACAATTGCAC
1 AAATTAAAGTTTCATGTATACAATTGCAC
30413186 ATTAAATCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
27 7 0.15
29 10 0.21
30 7 0.15
31 17 0.36
33 6 0.13
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (30 bp):
AAATTAAAGTTTCATGTATACAATTGCACC
Found at i:30413661 original size:30 final size:30
Alignment explanation
Indices: 30413622--30413700 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
30413612 ATATAATATG
30413622 GTAATTAAATTAAATTAATTATTATATAAT
1 GTAATTAAATTAAATTAATTATTATATAAT
* * * * *
30413652 GTGATTAAATAAAATAAAATATTATATGAT
1 GTAATTAAATTAAATTAATTATTATATAAT
*
30413682 GTAATTACATTAAATTAAT
1 GTAATTAAATTAAATTAAT
30413701 AATGAAGTTC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (30 bp):
GTAATTAAATTAAATTAATTATTATATAAT
Found at i:30418826 original size:31 final size:31
Alignment explanation
Indices: 30418786--30418847 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
30418776 ACGTTTTAAC
*
30418786 TATTAAACTATTTGAAAATTTTTATTTAAGT
1 TATTAAACTATTTGAAAAGTTTTATTTAAGT
* **
30418817 TATTGAACTATTTGAATGGTTTTATTTAAGT
1 TATTAAACTATTTGAAAAGTTTTATTTAAGT
30418848 AGTTGGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (31 bp):
TATTAAACTATTTGAAAAGTTTTATTTAAGT
Found at i:30420058 original size:24 final size:24
Alignment explanation
Indices: 30420001--30420100 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
30419991 CGGTGTTTCC
*
30420001 GGTGAAGGTGGCTTCACGATAGGA
1 GGTGAAGGTGGCTTCACAATAGGA
* **
30420025 GGCGTTGGTGGCTTCACAATAGGA
1 GGTGAAGGTGGCTTCACAATAGGA
* * * *
30420049 GGTGAAGGTGGCGGT-AGAATCGGC
1 GGTGAAGGTGGC-TTCACAATAGGA
** *
30420073 GGTGTTGGTGGATTCACAATAGGA
1 GGTGAAGGTGGCTTCACAATAGGA
30420097 GGTG
1 GGTG
30420101 GCAGAATCGG
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 54 0.96
25 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.43, T:0.23
Consensus pattern (24 bp):
GGTGAAGGTGGCTTCACAATAGGA
Found at i:30420111 original size:39 final size:39
Alignment explanation
Indices: 30420064--30420206 Score: 241
Period size: 39 Copynumber: 3.7 Consensus size: 39
30420054 AGGTGGCGGT
*
30420064 AGAATCGGCGGTGTTGGTGGATTCACAATAGGAGGTGGC
1 AGAATCGGCGGTATTGGTGGATTCACAATAGGAGGTGGC
* *
30420103 AGAATCGGCGGTGTTGGTGGATTCACAATAGGAGGTGGA
1 AGAATCGGCGGTATTGGTGGATTCACAATAGGAGGTGGC
*
30420142 AGAATCGGCGGTATTGGTGGGTTCACAATAGGAGGTGGC
1 AGAATCGGCGGTATTGGTGGATTCACAATAGGAGGTGGC
*
30420181 AGAATCGGCGGTATTGGTGGGTTCAC
1 AGAATCGGCGGTATTGGTGGATTCAC
30420207 TATTGGTGGA
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 100 1.00
ACGTcount: A:0.23, C:0.13, G:0.41, T:0.24
Consensus pattern (39 bp):
AGAATCGGCGGTATTGGTGGATTCACAATAGGAGGTGGC
Found at i:30420346 original size:33 final size:33
Alignment explanation
Indices: 30420304--30420431 Score: 130
Period size: 33 Copynumber: 3.8 Consensus size: 33
30420294 TGTATGTGGC
*
30420304 GGAGGCTTCACAACAGGTGGTTTGGGTGTATAT
1 GGAGGCTTCACAACAGGTGGTTTGGGTGCATAT
*
30420337 GGAGGCTTCACAACCGGTGGTTTGGGTGCATACGGT
1 GGAGGCTTCACAACAGGTGGTTTGGGTGCATA---T
* * * * * * *
30420373 GGAGGCTTTACAATAGGAGGCTTAGGTACATAG
1 GGAGGCTTCACAACAGGTGGTTTGGGTGCATAT
* *
30420406 GGAGGCTTTACAGCAGGTGGTTTGGG
1 GGAGGCTTCACAACAGGTGGTTTGGG
30420432 AGGATGCGGT
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
33 51 0.66
36 26 0.34
ACGTcount: A:0.21, C:0.14, G:0.38, T:0.27
Consensus pattern (33 bp):
GGAGGCTTCACAACAGGTGGTTTGGGTGCATAT
Found at i:30420510 original size:42 final size:42
Alignment explanation
Indices: 30420451--30420581 Score: 174
Period size: 42 Copynumber: 3.1 Consensus size: 42
30420441 TGGTTGTTTT
30420451 GGTGGTTTAGGGTGATACGGGGGTTTCACCACCGGAGGCTTA
1 GGTGGTTTAGGGTGATACGGGGGTTTCACCACCGGAGGCTTA
* * * *
30420493 GGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGTGGCTTC
1 GGTGGTTTAGGGTGATACGGGGGTTTCACCACCGGAGGCTTA
* * * *
30420535 GGCGGTTTAGGGTGATATGGGGGGTTT-ACAACTGGAGGCTTA
1 GGTGGTTTAGGGTGATA-CGGGGGTTTCACCACCGGAGGCTTA
30420577 GGTGG
1 GGTGG
30420582 CTTTGGAGGA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
42 69 0.92
43 6 0.08
ACGTcount: A:0.15, C:0.15, G:0.42, T:0.27
Consensus pattern (42 bp):
GGTGGTTTAGGGTGATACGGGGGTTTCACCACCGGAGGCTTA
Found at i:30420622 original size:108 final size:108
Alignment explanation
Indices: 30420493--30420734 Score: 439
Period size: 108 Copynumber: 2.2 Consensus size: 108
30420483 CGGAGGCTTA
30420493 GGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGTGGCTTCGGCGGTTTAGGGTGATATGGGGG
1 GGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGTGGCTTCGGCGGTTTAGGGTGATATGGGGG
30420558 GTTTACAACTGGAGGCTTAGGTGGCTTTGGAGGATGATGTATT
66 GTTTACAACTGGAGGCTTAGGTGGCTTTGGAGGATGATGTATT
* *
30420601 GGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGTGGCTTCGGTGGTTTAGGGTGATATGGTGG
1 GGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGTGGCTTCGGCGGTTTAGGGTGATATGGGGG
* *
30420666 GTTTACCACTGGAGGCTTAGGTGGCTTTGGAGGATGATGTTTT
66 GTTTACAACTGGAGGCTTAGGTGGCTTTGGAGGATGATGTATT
*
30420709 GGTGGTTTAGGGTGATAGGGTGGCTT
1 GGTGGTTTAGGGTGATACGGTGGCTT
30420735 AACAATGGGA
Statistics
Matches: 129, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 129 1.00
ACGTcount: A:0.14, C:0.12, G:0.41, T:0.32
Consensus pattern (108 bp):
GGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGTGGCTTCGGCGGTTTAGGGTGATATGGGGG
GTTTACAACTGGAGGCTTAGGTGGCTTTGGAGGATGATGTATT
Found at i:30420647 original size:42 final size:42
Alignment explanation
Indices: 30420601--30420689 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
30420591 ATGATGTATT
* *
30420601 GGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGTGGCTTC
1 GGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGAGGCTTA
* * * *
30420643 GGTGGTTTAGGGTGATATGGTGGGTTTACCACTGGAGGCTTA
1 GGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGAGGCTTA
30420685 GGTGG
1 GGTGG
30420690 CTTTGGAGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.13, C:0.15, G:0.42, T:0.30
Consensus pattern (42 bp):
GGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGAGGCTTA
Found at i:30421426 original size:15 final size:15
Alignment explanation
Indices: 30421406--30421454 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
30421396 TTGTGTCATA
30421406 TTATATTTTAATCAC
1 TTATATTTTAATCAC
*
30421421 TTATA-TTTAAT-ATA
1 TTATATTTTAATCA-C
*
30421435 TTAAATTTTAATCAC
1 TTATATTTTAATCAC
30421450 TTATA
1 TTATA
30421455 CTATCGTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 1 0.04
14 10 0.37
15 15 0.56
16 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATATTTTAATCAC
Found at i:30426647 original size:31 final size:31
Alignment explanation
Indices: 30426588--30426647 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
30426578 GAAAACTCTA
* *
30426588 AAGTTCAAGCGCCAATGTGATAACAATTACC
1 AAGTTCAAGCGCCAATATGAAAACAATTACC
*
30426619 AAGTTCATA-CGCCAATATGAAAATAATTA
1 AAGTTCA-AGCGCCAATATGAAAACAATTA
30426648 TTAAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.25
Consensus pattern (31 bp):
AAGTTCAAGCGCCAATATGAAAACAATTACC
Found at i:30427845 original size:18 final size:17
Alignment explanation
Indices: 30427824--30427869 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
30427814 TTGTCGTCAC
30427824 TAAATAATTTTAAAATAA
1 TAAA-AATTTTAAAATAA
*
30427842 TAAAAATATTTGAAATAA
1 TAAAAAT-TTTAAAATAA
30427860 TAAAAATTTT
1 TAAAAATTTT
30427870 CCAAATTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAAAATTTTAAAATAA
Found at i:30427875 original size:18 final size:18
Alignment explanation
Indices: 30427836--30427875 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
30427826 AATAATTTTA
*
30427836 AAATAATAAAAATATTTG
1 AAATAATAAAAATATTTC
30427854 AAATAATAAAAAT-TTTCC
1 AAATAATAAAAATATTT-C
30427872 AAAT
1 AAAT
30427876 TTCAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (18 bp):
AAATAATAAAAATATTTC
Found at i:30438685 original size:27 final size:24
Alignment explanation
Indices: 30438657--30438702 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
30438647 CATTGGAAAT
*
30438657 GATGATAAGAAGAATGTACAGGAA
1 GATGATAAGAAGAATATACAGGAA
30438681 GATGATAAGAAGAATATACAGG
1 GATGATAAGAAGAATATACAGG
30438703 TATGCATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.04, G:0.28, T:0.17
Consensus pattern (24 bp):
GATGATAAGAAGAATATACAGGAA
Found at i:30440453 original size:42 final size:42
Alignment explanation
Indices: 30440394--30440478 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
30440384 TAGATTAAAT
*
30440394 CTAAAACTATACACATAGTACAAGACTAATAATAAAATTTAA
1 CTAAAACTATAAACATAGTACAAGACTAATAATAAAATTTAA
* * *
30440436 CTAAAACTGTAAACATAGTACGAGACTAATAATCAAATTTAA
1 CTAAAACTATAAACATAGTACAAGACTAATAATAAAATTTAA
30440478 C
1 C
30440479 CAAGTAGAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (42 bp):
CTAAAACTATAAACATAGTACAAGACTAATAATAAAATTTAA
Found at i:30440848 original size:23 final size:22
Alignment explanation
Indices: 30440821--30440871 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
30440811 TTATTTTTTA
*
30440821 AATTTTTAATAAAATATTTATAT
1 AATTTTGAATAAAATATTTA-AT
* **
30440844 TATTTTGAATTTAATATTTAAT
1 AATTTTGAATAAAATATTTAAT
30440866 AATTTT
1 AATTTT
30440872 ATATATTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
AATTTTGAATAAAATATTTAAT
Found at i:30449024 original size:10 final size:8
Alignment explanation
Indices: 30448997--30449025 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
30448987 AATTAGAGGG
30448997 ATATGAAT
1 ATATGAAT
30449005 ATATGAAT
1 ATATGAAT
30449013 ATATGAAT
1 ATATGAAT
30449021 ATATG
1 ATATG
30449026 CCAAGGCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (8 bp):
ATATGAAT
Found at i:30460178 original size:2 final size:2
Alignment explanation
Indices: 30460171--30460234 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
30460161 TAAAATGAAA
30460171 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
30460213 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
30460235 TTAAGTTTTC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30460401 original size:5 final size:5
Alignment explanation
Indices: 30460391--30460419 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
30460381 TTGGTGTCTC
30460391 TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
30460420 CTATCAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:30460516 original size:25 final size:24
Alignment explanation
Indices: 30460486--30460542 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
30460476 AATTTAGTGC
*
30460486 TTAGTATTTATATCTTTTTA-TCAAT
1 TTAGTATTTAT-T-TTTTTACTAAAT
30460511 TTAGTATTTATTTTTTTAGCTAAAT
1 TTAGTATTTATTTTTTTA-CTAAAT
30460536 TTAGTAT
1 TTAGTAT
30460543 CAATCTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 6 0.21
24 1 0.03
25 22 0.76
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (24 bp):
TTAGTATTTATTTTTTTACTAAAT
Found at i:30461417 original size:40 final size:40
Alignment explanation
Indices: 30461333--30461417 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
30461323 TCGTTGACCT
* * * * * * *
30461333 AAAAATCGATAGTTTACTGATTTATATGTAAGGAATCAGC
1 AAAAATCAATAGATTAATAATTTATATGTAAGAAAACAGA
*
30461373 AAAAATCAATAGATTAATAATTTATATGTAATAAAACAGA
1 AAAAATCAATAGATTAATAATTTATATGTAAGAAAACAGA
30461413 AAAAA
1 AAAAA
30461418 AAAAAAAGCA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (40 bp):
AAAAATCAATAGATTAATAATTTATATGTAAGAAAACAGA
Found at i:30468642 original size:22 final size:22
Alignment explanation
Indices: 30468614--30468658 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
30468604 TAACATATAT
30468614 TAGGTTTAAGTCGATTTGACGA
1 TAGGTTTAAGTCGATTTGACGA
30468636 TAGGTTTAAGTCGATTTGACGA
1 TAGGTTTAAGTCGATTTGACGA
30468658 T
1 T
30468659 TAATGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.38
Consensus pattern (22 bp):
TAGGTTTAAGTCGATTTGACGA
Found at i:30469811 original size:13 final size:13
Alignment explanation
Indices: 30469793--30469817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30469783 TCAAATTATC
30469793 TTAAAAAGTGTTT
1 TTAAAAAGTGTTT
30469806 TTAAAAAGTGTT
1 TTAAAAAGTGTT
30469818 GTGCAAAACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
TTAAAAAGTGTTT
Found at i:30470321 original size:20 final size:21
Alignment explanation
Indices: 30470296--30470335 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
30470286 ATATATTATT
*
30470296 TATAAATCTTAATTT-TAATA
1 TATAAATCATAATTTATAATA
30470316 TATAAATCATAATTTATAAT
1 TATAAATCATAATTTATAAT
30470336 TTATGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
TATAAATCATAATTTATAATA
Found at i:30473347 original size:2 final size:2
Alignment explanation
Indices: 30473340--30473365 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30473330 CAATCCAAGT
30473340 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
30473366 GTTACAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30491125 original size:17 final size:19
Alignment explanation
Indices: 30491103--30491137 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
30491093 GAAAAAAGTC
30491103 TTCT-AAAATAT-TAATTA
1 TTCTAAAAATATATAATTA
30491120 TTCTAAAAATATATAATT
1 TTCTAAAAATATATAATT
30491138 TACTTTACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (19 bp):
TTCTAAAAATATATAATTA
Found at i:30496762 original size:21 final size:22
Alignment explanation
Indices: 30496738--30496780 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
30496728 TTAAATATTT
30496738 TTTAAAAAAATT-AATAAATTA
1 TTTAAAAAAATTGAATAAATTA
**
30496759 TTTAATCAAATTGAATAAATTA
1 TTTAAAAAAATTGAATAAATTA
30496781 ATTGAATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
TTTAAAAAAATTGAATAAATTA
Found at i:30509208 original size:28 final size:28
Alignment explanation
Indices: 30509146--30509209 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
30509136 AAACTATTCA
* *
30509146 AAGTTTTCATTTAAGTCATTGAGCTATT
1 AAGTTTTTATTTAAGTCATCGAGCTATT
* * *
30509174 CATTTTTTATTTAAGTCACTCG-GCTGTT
1 AAGTTTTTATTTAAGTCA-TCGAGCTATT
30509202 AAGTTTTT
1 AAGTTTTT
30509210 TAATTTATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
28 26 0.93
29 2 0.07
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.50
Consensus pattern (28 bp):
AAGTTTTTATTTAAGTCATCGAGCTATT
Found at i:30509548 original size:23 final size:22
Alignment explanation
Indices: 30509520--30509574 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
30509510 TATCGAATAA
30509520 TTTATTT-TTAGATTAATTTTAAT
1 TTTATTTATTAGATTAA-TTT-AT
*
30509543 TTTATTTTATTCGATTAATTTAT
1 TTTA-TTTATTAGATTAATTTAT
30509566 TTTATTTAT
1 TTTATTTAT
30509575 ATTTTTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.17
23 10 0.34
24 6 0.21
25 8 0.28
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTATTTATTAGATTAATTTAT
Found at i:30509929 original size:31 final size:29
Alignment explanation
Indices: 30509893--30509972 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
30509883 ATCCCAAAAC
30509893 TATACAT-AAATTATGATTTAATGTGTAATTA
1 TATACATGAAATT-TGATTT--TGTGTAATTA
* *
30509924 TATACATGAACTTTGATTTTGTGTAATTT
1 TATACATGAAATTTGATTTTGTGTAATTA
*
30509953 TATGCATGAAATTTTGATTT
1 TATACATGAAA-TTTGATTT
30509973 GATCCAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
29 18 0.42
30 8 0.19
31 13 0.30
32 4 0.09
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (29 bp):
TATACATGAAATTTGATTTTGTGTAATTA
Found at i:30510199 original size:29 final size:30
Alignment explanation
Indices: 30510165--30510226 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
30510155 ATTTTACGTG
30510165 TATAATTACAC-CAAATCAAAATTCATGTA
1 TATAATTACACACAAATCAAAATTCATGTA
* *
30510194 TATAATTACACATTAAATCAAAATTTATGTA
1 TATAATTACACA-CAAATCAAAATTCATGTA
30510225 TA
1 TA
30510227 ATTTTAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 11 0.38
31 18 0.62
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.35
Consensus pattern (30 bp):
TATAATTACACACAAATCAAAATTCATGTA
Found at i:30510227 original size:29 final size:27
Alignment explanation
Indices: 30510163--30510229 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 27
30510153 AAATTTTACG
30510163 TGTATAATTACACCAAATCAAAATTCA
1 TGTATAATTACACCAAATCAAAATTCA
* *
30510190 TGTATATAATTACACATTAAATCAAAATTTA
1 TG--TATAATTACAC--CAAATCAAAATTCA
30510221 TGTATAATT
1 TGTATAATT
30510230 TTAAGATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 2 0.06
29 18 0.53
31 14 0.41
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.37
Consensus pattern (27 bp):
TGTATAATTACACCAAATCAAAATTCA
Found at i:30511927 original size:46 final size:46
Alignment explanation
Indices: 30511875--30511969 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
30511865 ACAACAATGA
30511875 TTTATTTTATTCTTTCTTTTTACATTTTCCTTTATCGATTTAATTT
1 TTTATTTTATTCTTTCTTTTTACATTTTCCTTTATCGATTTAATTT
30511921 TTTATTTTATTCTTTCTTTTTACATTTTCCTTTATCGATTTAATTT
1 TTTATTTTATTCTTTCTTTTTACATTTTCCTTTATCGATTTAATTT
30511967 TTT
1 TTT
30511970 TTATACATGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.68
Consensus pattern (46 bp):
TTTATTTTATTCTTTCTTTTTACATTTTCCTTTATCGATTTAATTT
Found at i:30511967 original size:26 final size:26
Alignment explanation
Indices: 30511892--30511967 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
30511882 TATTCTTTCT
30511892 TTTTACATTTTCCTTTATCGATTTAA
1 TTTTACATTTTCCTTTATCGATTTAA
* **
30511918 TTTT---TTAT--TTTATTC--TTTCT
1 TTTTACATTTTCCTTTA-TCGATTTAA
30511938 TTTTACATTTTCCTTTATCGATTTAA
1 TTTTACATTTTCCTTTATCGATTTAA
30511964 TTTT
1 TTTT
30511968 TTTTATACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
20 7 0.19
21 4 0.11
22 2 0.06
23 6 0.17
24 2 0.06
25 4 0.11
26 11 0.31
ACGTcount: A:0.18, C:0.13, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTTACATTTTCCTTTATCGATTTAA
Found at i:30514164 original size:13 final size:13
Alignment explanation
Indices: 30514146--30514170 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30514136 ATAAAATTAA
30514146 TTTTTATTTTATT
1 TTTTTATTTTATT
30514159 TTTTTATTTTAT
1 TTTTTATTTTAT
30514171 GTGTACCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:30515527 original size:6 final size:6
Alignment explanation
Indices: 30515506--30515547 Score: 66
Period size: 6 Copynumber: 6.7 Consensus size: 6
30515496 TAAAGTGTAA
30515506 AAGATTG AATGATG AAGATG AAGATG AAGATG AAGATG AAGA
1 AAGA-TG AA-GATG AAGATG AAGATG AAGATG AAGATG AAGA
30515548 GTTTGATGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 26 0.76
7 6 0.18
8 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (6 bp):
AAGATG
Done.