Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 126 of 230
Found at i:36636853 original size:10 final size:9
Alignment explanation
Indices: 36636828--36636852 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
36636818 TGCAATGATC
36636828 TAAAAAACA
1 TAAAAAACA
36636837 TAAAAAACA
1 TAAAAAACA
36636846 TAAAAAA
1 TAAAAAA
36636853 ATGAAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (9 bp):
TAAAAAACA
Found at i:36642343 original size:17 final size:17
Alignment explanation
Indices: 36642316--36642372 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
36642306 TTGCATGCCC
36642316 ATGTGGGCCCACAAGCCT
1 ATGT-GGCCCACAAGCCT
36642334 ATGTGG-CC-C-A---T
1 ATGTGGCCCACAAGCCT
36642345 ATG-GGCCCACAAGCCT
1 ATGTGGCCCACAAGCCT
36642361 ATGTGGCCCACA
1 ATGTGGCCCACA
36642373 CGGCCCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 15
0.68 0.00 0.32
Matches are distributed among these distances:
10 2 0.06
11 6 0.19
12 1 0.03
13 1 0.03
14 1 0.03
15 1 0.03
16 6 0.19
17 10 0.31
18 4 0.12
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (17 bp):
ATGTGGCCCACAAGCCT
Found at i:36642349 original size:27 final size:27
Alignment explanation
Indices: 36642312--36642370 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
36642302 CATGTTGCAT
*
36642312 GCCCATGTGGGCCCACAAGCCTATGTG
1 GCCCATATGGGCCCACAAGCCTATGTG
36642339 GCCCATATGGGCCCACAAGCCTATGTG
1 GCCCATATGGGCCCACAAGCCTATGTG
36642366 GCCCA
1 GCCCA
36642371 CACGGCCCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.20, C:0.36, G:0.27, T:0.17
Consensus pattern (27 bp):
GCCCATATGGGCCCACAAGCCTATGTG
Found at i:36651815 original size:94 final size:94
Alignment explanation
Indices: 36651705--36651880 Score: 334
Period size: 94 Copynumber: 1.9 Consensus size: 94
36651695 GATAAAAAGG
*
36651705 GGATTTGATATATTCCTTATCAGATAAGGAAATATAATTTAATTATTATTTAAAAGAGTTTTAAA
1 GGATTTGATATATTCCTTATCAGATAAGAAAATATAATTTAATTATTATTTAAAAGAGTTTTAAA
36651770 TAAATAATAATTAAAATTCAAAATCAAAA
66 TAAATAATAATTAAAATTCAAAATCAAAA
*
36651799 GGATTTGATATATTCCTTATCAGATAAGAAAATATAATTTAATTATTATTTAAAAGAGTTTTAGA
1 GGATTTGATATATTCCTTATCAGATAAGAAAATATAATTTAATTATTATTTAAAAGAGTTTTAAA
36651864 TAAATAATAATTAAAAT
66 TAAATAATAATTAAAAT
36651881 AGAATTTAAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 80 1.00
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.39
Consensus pattern (94 bp):
GGATTTGATATATTCCTTATCAGATAAGAAAATATAATTTAATTATTATTTAAAAGAGTTTTAAA
TAAATAATAATTAAAATTCAAAATCAAAA
Found at i:36668066 original size:13 final size:13
Alignment explanation
Indices: 36668048--36668099 Score: 68
Period size: 13 Copynumber: 3.8 Consensus size: 13
36668038 ACTAGCTCTC
36668048 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
36668061 TTTTTTTTTCACAAT
1 TTTTTTTTT--CAAT
*
36668076 TTTTTTTTTCAAA
1 TTTTTTTTTCAAT
*
36668089 ATTTTTTTTCA
1 TTTTTTTTTCA
36668100 CAACTTGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 22 0.63
15 13 0.37
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:36668068 original size:15 final size:15
Alignment explanation
Indices: 36668048--36668097 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
36668038 ACTAGCTCTC
36668048 TTTTTTTTT--CAAT
1 TTTTTTTTTCACAAT
36668061 TTTTTTTTTCACAAT
1 TTTTTTTTTCACAAT
*
36668076 TTTTTTTTTCAAAAT
1 TTTTTTTTTCACAAT
36668091 TTTTTTT
1 TTTTTTT
36668098 CACAACTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
13 9 0.26
15 25 0.74
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTTTTCACAAT
Found at i:36668093 original size:28 final size:28
Alignment explanation
Indices: 36668048--36668102 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
36668038 ACTAGCTCTC
**
36668048 TTTTTTTTTCAATTTTTTTTTTCACAAT
1 TTTTTTTTTCAAAATTTTTTTTCACAAT
36668076 TTTTTTTTTCAAAATTTTTTTTCACAA
1 TTTTTTTTTCAAAATTTTTTTTCACAA
36668103 CTTGATATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTTTTTTCAAAATTTTTTTTCACAAT
Found at i:36668156 original size:11 final size:11
Alignment explanation
Indices: 36668140--36668178 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
36668130 TGGAAACTAG
36668140 TTTTTTTTGAA
1 TTTTTTTTGAA
36668151 TTTTTTTT-AA
1 TTTTTTTTGAA
*
36668161 TTTTTTTTGAG
1 TTTTTTTTGAA
36668172 TTTTTTT
1 TTTTTTT
36668179 CGAGAAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:36670782 original size:25 final size:25
Alignment explanation
Indices: 36670746--36670813 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
36670736 AGAGAGCAGA
36670746 ATTT-TCT-TTGAGTTTTCTCCAAG
1 ATTTCTCTCTTGAGTTTTCTCCAAG
36670769 ATTTCTCTCTTGAGTTTTCTCCAAG
1 ATTTCTCTCTTGAGTTTTCTCCAAG
36670794 ATTTCTCTCTTGAGTTTTCT
1 ATTTCTCTCTTGAGTTTTCT
36670814 TTAGAAGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.09
24 3 0.07
25 36 0.84
ACGTcount: A:0.15, C:0.21, G:0.12, T:0.53
Consensus pattern (25 bp):
ATTTCTCTCTTGAGTTTTCTCCAAG
Found at i:36670996 original size:28 final size:29
Alignment explanation
Indices: 36670959--36671020 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
36670949 GGACTTATCT
36670959 TTTA-TTCTTGCTG-TTCAATTTCT-TTTC
1 TTTATTTCTTGCTGTTTC-ATTTCTATTTC
* *
36670986 TTTATTTCTTGTTGTTTCATTTTTATTTC
1 TTTATTTCTTGCTGTTTCATTTCTATTTC
36671015 TTTATT
1 TTTATT
36671021 CCTACTTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 4 0.13
28 13 0.43
29 13 0.43
ACGTcount: A:0.11, C:0.13, G:0.06, T:0.69
Consensus pattern (29 bp):
TTTATTTCTTGCTGTTTCATTTCTATTTC
Found at i:36678275 original size:13 final size:13
Alignment explanation
Indices: 36678257--36678291 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
36678247 TTGGAGTAAC
36678257 AAAAAAAATCAAA
1 AAAAAAAATCAAA
* *
36678270 AAAAAAATTCGAA
1 AAAAAAAATCAAA
36678283 AAAAAAAAT
1 AAAAAAAAT
36678292 TGATTGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.80, C:0.06, G:0.03, T:0.11
Consensus pattern (13 bp):
AAAAAAAATCAAA
Found at i:36678313 original size:12 final size:13
Alignment explanation
Indices: 36678257--36678317 Score: 70
Period size: 14 Copynumber: 4.5 Consensus size: 13
36678247 TTGGAGTAAC
36678257 AAAAAAAA-TCAA
1 AAAAAAAATTCAA
36678269 AAAAAAAATTCGAA
1 AAAAAAAATTC-AA
*
36678283 AAAAAAAATTGATTGA
1 AAAAAAAATTCA---A
36678299 AAAAAAAATTCAA
1 AAAAAAAATTCAA
36678312 AAAAAA
1 AAAAAA
36678318 GTGAAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
12 8 0.19
13 10 0.24
14 12 0.29
16 12 0.29
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:36678343 original size:17 final size:17
Alignment explanation
Indices: 36678321--36678360 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
36678311 AAAAAAAGTG
36678321 AAAAAAA-ATCGAGCAAA
1 AAAAAAAGAT-GAGCAAA
*
36678338 AAAAAAAGGTGAGCAAA
1 AAAAAAAGATGAGCAAA
36678355 AAAAAA
1 AAAAAA
36678361 TCAAGTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.72, C:0.07, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAAAAAGATGAGCAAA
Found at i:36679432 original size:17 final size:18
Alignment explanation
Indices: 36679400--36679433 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36679390 AAAAGAGAGT
*
36679400 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
36679418 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
36679434 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:36684892 original size:21 final size:21
Alignment explanation
Indices: 36684867--36684907 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
36684857 ACATTCCATA
*
36684867 ACCAAACCTAAACCATATTCG
1 ACCAAACCTAAACCAAATTCG
* *
36684888 ACCAATCTTAAACCAAATTC
1 ACCAAACCTAAACCAAATTC
36684908 CTTCTATCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.22
Consensus pattern (21 bp):
ACCAAACCTAAACCAAATTCG
Found at i:36687717 original size:43 final size:43
Alignment explanation
Indices: 36687657--36687773 Score: 110
Period size: 54 Copynumber: 2.5 Consensus size: 43
36687647 AATCACTTAT
* *
36687657 TTATTAAAC-AAAGATGAGTTGAATAAATGTTCGGCAACTCAA
1 TTATTTAACTAAAGATGAGTTGAATAAATGTTCAGCAACTCAA
36687699 TTATTTAACTAAAGATGAGTTTCTTTAAAGTTGAATAAATGTTCAGCAACTCAA
1 TTATTTAACTAAAGAT--G---------AGTTGAATAAATGTTCAGCAACTCAA
36687753 TTATTTAACTAAAGATGAGTT
1 TTATTTAACTAAAGATGAGTT
36687774 TTTTTAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 23
0.71 0.02 0.27
Matches are distributed among these distances:
42 8 0.13
43 10 0.16
45 1 0.02
52 1 0.02
54 41 0.67
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (43 bp):
TTATTTAACTAAAGATGAGTTGAATAAATGTTCAGCAACTCAA
Found at i:36687755 original size:54 final size:54
Alignment explanation
Indices: 36687673--36687781 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
36687663 AACAAAGATG
*
36687673 AGTTGAATAAATGTTCGGCAACTCAATTATTTAACTAAAGATGAGTTTCTTTAA
1 AGTTGAATAAATGTTCAGCAACTCAATTATTTAACTAAAGATGAGTTTCTTTAA
*
36687727 AGTTGAATAAATGTTCAGCAACTCAATTATTTAACTAAAGATGAGTTTTTTTAA
1 AGTTGAATAAATGTTCAGCAACTCAATTATTTAACTAAAGATGAGTTTCTTTAA
36687781 A
1 A
36687782 ATTTCAGTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (54 bp):
AGTTGAATAAATGTTCAGCAACTCAATTATTTAACTAAAGATGAGTTTCTTTAA
Found at i:36688073 original size:13 final size:13
Alignment explanation
Indices: 36688045--36688085 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
36688035 TTGTAAATTG
36688045 AAAAAATTTAGAAA
1 AAAAAATTT-GAAA
*
36688059 AAGAAATTTGAAA
1 AAAAAATTTGAAA
36688072 AAAAAATTGTGAAA
1 AAAAAATT-TGAAA
36688086 TCAAGTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (13 bp):
AAAAAATTTGAAA
Found at i:36688138 original size:11 final size:10
Alignment explanation
Indices: 36688122--36688149 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
36688112 TTGTGATTTT
36688122 AAAAAAATTC
1 AAAAAAATTC
36688132 AAAAAAATTC
1 AAAAAAATTC
36688142 AAAAAAAT
1 AAAAAAAT
36688150 GTGAAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:36697781 original size:54 final size:54
Alignment explanation
Indices: 36697718--36697826 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
36697708 AACAAAGATG
*
36697718 AGTTGAATAAATGTTCAGCAACTCAATTATTTAACTAAAGATGAGTTTCTTTAA
1 AGTTGAATAAATGTTCAACAACTCAATTATTTAACTAAAGATGAGTTTCTTTAA
36697772 AGTTGAATAAATGTTCAACAACTCAATTATTTAACTAAAGATGAGTTTCTTTAA
1 AGTTGAATAAATGTTCAACAACTCAATTATTTAACTAAAGATGAGTTTCTTTAA
36697826 A
1 A
36697827 CTTTCAATTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (54 bp):
AGTTGAATAAATGTTCAACAACTCAATTATTTAACTAAAGATGAGTTTCTTTAA
Found at i:36701289 original size:20 final size:20
Alignment explanation
Indices: 36701266--36701319 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
36701256 AGTTTTTCCC
*
36701266 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
36701286 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
36701306 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
36701320 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:36701301 original size:30 final size:30
Alignment explanation
Indices: 36701266--36701339 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
36701256 AGTTTTTCCC
36701266 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
36701296 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
36701326 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
36701340 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:36701329 original size:20 final size:20
Alignment explanation
Indices: 36701266--36701330 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
36701256 AGTTTTTCCC
* * * *
36701266 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
36701286 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
36701305 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
36701326 AGCTC
1 AGCTC
36701331 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:36708448 original size:17 final size:18
Alignment explanation
Indices: 36708425--36708486 Score: 76
Period size: 17 Copynumber: 3.6 Consensus size: 18
36708415 AGATTGAGAA
36708425 TGAAAAAGAAATAGAGTT
1 TGAAAAAGAAATAGAGTT
*
36708443 TG-AAAAGAAATCGAG--
1 TGAAAAAGAAATAGAGTT
*
36708458 TGAAAAAGAAAAAGAGTT
1 TGAAAAAGAAATAGAGTT
*
36708476 TGCAAAAGAAA
1 TGAAAAAGAAA
36708487 CGAGTGAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
15 2 0.05
16 11 0.30
17 12 0.32
18 12 0.32
ACGTcount: A:0.58, C:0.03, G:0.23, T:0.16
Consensus pattern (18 bp):
TGAAAAAGAAATAGAGTT
Found at i:36708462 original size:33 final size:33
Alignment explanation
Indices: 36708425--36708499 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 33
36708415 AGATTGAGAA
*
36708425 TGAAAAAGAAATAGAGTTTG-AAAAGAAATCGAG
1 TGAAAAAGAAAAAGAGTTTGCAAAAGAAA-CGAG
36708458 TGAAAAAGAAAAAGAGTTTGCAAAAGAAACGAG
1 TGAAAAAGAAAAAGAGTTTGCAAAAGAAACGAG
36708491 TGAAGAAAG
1 TGAA-AAAG
36708500 TAATCAAGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
33 27 0.69
34 12 0.31
ACGTcount: A:0.56, C:0.04, G:0.25, T:0.15
Consensus pattern (33 bp):
TGAAAAAGAAAAAGAGTTTGCAAAAGAAACGAG
Found at i:36711788 original size:22 final size:22
Alignment explanation
Indices: 36711760--36711801 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
36711750 TATTTGGGAA
36711760 TTGGTACGAAATGGCAATGGAT
1 TTGGTACGAAATGGCAATGGAT
*
36711782 TTGGTACGAAATGGTAATGG
1 TTGGTACGAAATGGCAATGG
36711802 TTCAAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.07, G:0.33, T:0.29
Consensus pattern (22 bp):
TTGGTACGAAATGGCAATGGAT
Found at i:36712621 original size:31 final size:30
Alignment explanation
Indices: 36712586--36712645 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
36712576 ATCATGCATG
36712586 CACCTAGCTAAATGAATCTCC-ACATTCGGCT
1 CACCTAGCTAAATGAA-C-CCTACATTCGGCT
* *
36712617 CACCTTGGTAAATGAACCCTACATTCGGC
1 CACCTAGCTAAATGAACCCTACATTCGGC
36712646 CAACCTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 2 0.08
30 10 0.38
31 14 0.54
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (30 bp):
CACCTAGCTAAATGAACCCTACATTCGGCT
Found at i:36712982 original size:30 final size:30
Alignment explanation
Indices: 36712924--36712982 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
36712914 TTGAAAATGT
* *
36712924 TTGAGCTGAAGTTGAGATAATTCGAGCTCA
1 TTGAGCTGAAATGGAGATAATTCGAGCTCA
*
36712954 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGATAATTCGAGCTC
36712983 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGATAATTCGAGCTCA
Found at i:36714694 original size:20 final size:19
Alignment explanation
Indices: 36714662--36714699 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
36714652 GAGCTAATAA
36714662 TGAGCTCAATGAGCTGAAT
1 TGAGCTCAATGAGCTGAAT
*
36714681 TGAGCTCAGGTGAGCTGAA
1 TGAGCTCA-ATGAGCTGAA
36714700 ATAACTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.24
Consensus pattern (19 bp):
TGAGCTCAATGAGCTGAAT
Found at i:36717667 original size:20 final size:19
Alignment explanation
Indices: 36717644--36717708 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
36717634 AAGCTCAAAC
36717644 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
36717664 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
36717684 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
36717704 GAGCT
1 GAGCT
36717709 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:36718996 original size:17 final size:18
Alignment explanation
Indices: 36718974--36719007 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36718964 ACAATACTCC
*
36718974 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
36718991 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
36719008 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:36720061 original size:29 final size:27
Alignment explanation
Indices: 36720029--36720097 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
36720019 GCAAGACTTT
*
36720029 TCACTTTTTTTTTAACTTGAATTTTTTGG
1 TCACTTTTTTTTTAAC-TCAATTTTTT-G
** *
36720058 TCACCTTTTTTTTTTGCTCAATTTTTTT
1 TCA-CTTTTTTTTTAACTCAATTTTTTG
36720086 TCACTTTTTTTT
1 TCACTTTTTTTT
36720098 GAATATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 9 0.26
28 3 0.09
29 12 0.34
30 11 0.31
ACGTcount: A:0.13, C:0.14, G:0.06, T:0.67
Consensus pattern (27 bp):
TCACTTTTTTTTTAACTCAATTTTTTG
Found at i:36721783 original size:20 final size:19
Alignment explanation
Indices: 36721760--36721824 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
36721750 AAGCTCAAAC
36721760 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
36721780 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
36721800 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
36721820 GAGCT
1 GAGCT
36721825 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:36722860 original size:111 final size:111
Alignment explanation
Indices: 36722666--36722887 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
36722656 TTCCAATGGA
36722666 GAATGTGATCATTGCTTGCTTGGTAACCTTTAATTTGACCCATTCGTTGAGCAATTACAATTTAT
1 GAATGTGATCATTGCTTGCTTGGTAACCTTTAATTTGACCCATTCGTTGAGCAATTACAATTTAT
**
36722731 ATGGGCTCGGGTGCTTGATAGTCGGCAAGGCAAGTTTTTCCACCAT
66 ATGGGCTCGGGTGCTTGATAGTCAACAAGGCAAGTTTTTCCACCAT
* * * *
36722777 GAATGTGATCATTGCTTGCTTGGTAACCTTTAATTTGACCCCTTCGTTGAGCCATTTCCATTTAT
1 GAATGTGATCATTGCTTGCTTGGTAACCTTTAATTTGACCCATTCGTTGAGCAATTACAATTTAT
36722842 ATGGGCTCGGGTGCTTGATAGTCAACAAGGCAAGTTTTTCCACCAT
66 ATGGGCTCGGGTGCTTGATAGTCAACAAGGCAAGTTTTTCCACCAT
36722888 ATACGTGCTT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (111 bp):
GAATGTGATCATTGCTTGCTTGGTAACCTTTAATTTGACCCATTCGTTGAGCAATTACAATTTAT
ATGGGCTCGGGTGCTTGATAGTCAACAAGGCAAGTTTTTCCACCAT
Found at i:36729022 original size:20 final size:20
Alignment explanation
Indices: 36728978--36729052 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
36728968 GAGCTAATAA
*
36728978 TGAGCTC-AATGAGCTGAA-T
1 TGAGCTCGAGTGAGCT-AACT
* *
36728997 TCAGCTCGTGTGAGCTAACT
1 TGAGCTCGAGTGAGCTAACT
* *
36729017 TGAGCTCGAATGAACTAACT
1 TGAGCTCGAGTGAGCTAACT
36729037 TGAGCTCGAGTGAGCT
1 TGAGCTCGAGTGAGCT
36729053 GAACCACATG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 8 0.18
20 37 0.82
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (20 bp):
TGAGCTCGAGTGAGCTAACT
Found at i:36731980 original size:122 final size:122
Alignment explanation
Indices: 36731763--36732010 Score: 487
Period size: 122 Copynumber: 2.0 Consensus size: 122
36731753 CATTCTGGAG
36731763 CAACCAAAGAGTTTAGAAAGAGCTTTAAATTCCCCATTGGACAGCCGAATAGACACCATGGAGAA
1 CAACCAAAGAGTTTAGAAAGAGCTTTAAATTCCCCATTGGACAGCCGAATAGACACCATGGAGAA
*
36731828 GAAGAATAAACGGCCAAATTTTAAAATATGTATAAATCTTTCCTTTAAATGACATAA
66 GAAGAATAAAAGGCCAAATTTTAAAATATGTATAAATCTTTCCTTTAAATGACATAA
36731885 CAACCAAAGAGTTTAGAAAGAGCTTTAAATTCCCCATTGGACAGCCGAATAGACACCATGGAGAA
1 CAACCAAAGAGTTTAGAAAGAGCTTTAAATTCCCCATTGGACAGCCGAATAGACACCATGGAGAA
36731950 GAAGAATAAAAGGCCAAATTTTAAAATATGTATAAATCTTTCCTTTAAATGACATAA
66 GAAGAATAAAAGGCCAAATTTTAAAATATGTATAAATCTTTCCTTTAAATGACATAA
36732007 CAAC
1 CAAC
36732011 TCCTTTAAAT
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 125 1.00
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.24
Consensus pattern (122 bp):
CAACCAAAGAGTTTAGAAAGAGCTTTAAATTCCCCATTGGACAGCCGAATAGACACCATGGAGAA
GAAGAATAAAAGGCCAAATTTTAAAATATGTATAAATCTTTCCTTTAAATGACATAA
Found at i:36732121 original size:55 final size:55
Alignment explanation
Indices: 36732047--36732171 Score: 200
Period size: 55 Copynumber: 2.3 Consensus size: 55
36732037 CTTTAATTGA
* *
36732047 TGTAACAACCCTTTATATGTAACCGATTCCAACTG-GTTAGTCACATTTAACACTT
1 TGTAACAACCCCTTGTATGTAACCGATTCCAACTGAG-TAGTCACATTTAACACTT
36732102 TGTAACAACCCCTTGTATGTAACCGATTCCAACTGAGTAGTCACATTTAACACTT
1 TGTAACAACCCCTTGTATGTAACCGATTCCAACTGAGTAGTCACATTTAACACTT
*
36732157 TGTAAC-AGCCCTTGT
1 TGTAACAACCCCTTGT
36732172 TCATAATTTA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
54 8 0.12
55 57 0.86
56 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.33
Consensus pattern (55 bp):
TGTAACAACCCCTTGTATGTAACCGATTCCAACTGAGTAGTCACATTTAACACTT
Found at i:36732232 original size:10 final size:10
Alignment explanation
Indices: 36732210--36732243 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
36732200 CCTACAATCA
36732210 AAACACA-TT
1 AAACACATTT
36732219 AAACACATTT
1 AAACACATTT
36732229 AAACACATATT
1 AAACACAT-TT
36732240 AAAC
1 AAAC
36732244 TTAATAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 7 0.30
10 10 0.43
11 6 0.26
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.24
Consensus pattern (10 bp):
AAACACATTT
Found at i:36740653 original size:11 final size:10
Alignment explanation
Indices: 36740628--36740688 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
36740618 ACCAATAAAA
36740628 TAAA-TGAGC
1 TAAATTGAGC
*
36740637 TGAATTGTAGC
1 TAAATTG-AGC
36740648 TAAATTGAGC
1 TAAATTGAGC
**
36740658 TCGATTGAGC
1 TAAATTGAGC
36740668 TGAAA-TGAGC
1 T-AAATTGAGC
*
36740678 TCAATTGAGC
1 TAAATTGAGC
36740688 T
1 T
36740689 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:36740689 original size:20 final size:20
Alignment explanation
Indices: 36740629--36740689 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
36740619 CCAATAAAAT
*
36740629 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
36740649 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
36740670 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
36740690 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:36742747 original size:33 final size:33
Alignment explanation
Indices: 36742709--36742771 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
36742699 GATTACTCAC
36742709 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
36742742 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
36742772 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:36745262 original size:11 final size:10
Alignment explanation
Indices: 36745237--36745297 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
36745227 ACCAATAAAA
36745237 TAAA-TGAGC
1 TAAATTGAGC
*
36745246 TGAATTGTAGC
1 TAAATTG-AGC
36745257 TAAATTGAGC
1 TAAATTGAGC
**
36745267 TCGATTGAGC
1 TAAATTGAGC
36745277 TGAAA-TGAGC
1 T-AAATTGAGC
*
36745287 TCAATTGAGC
1 TAAATTGAGC
36745297 T
1 T
36745298 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:36745298 original size:20 final size:20
Alignment explanation
Indices: 36745238--36745298 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
36745228 CCAATAAAAT
*
36745238 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
36745258 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
36745279 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
36745299 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:36747114 original size:21 final size:21
Alignment explanation
Indices: 36747088--36747150 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
36747078 TTGGTATTTG
36747088 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
36747109 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
36747130 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
36747151 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:36750539 original size:46 final size:46
Alignment explanation
Indices: 36750472--36750565 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
36750462 ATTGTGTGGC
*
36750472 GTTCATCATATACCAAGGTTCCTACCATCCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTACCATCCTTGATAGTGGGACGAG
* *
36750518 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGACGAG
1 GTTCATCATATACCAAGGTTCCTACCATCCTTGATAGTGGGACGAG
36750564 GT
1 GT
36750566 CTTTTCTTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.32
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTACCATCCTTGATAGTGGGACGAG
Found at i:36750943 original size:21 final size:21
Alignment explanation
Indices: 36750909--36750976 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
36750899 ACTGTCGAAT
* *
36750909 TTTAAAGGACGTAACAGCTCC
1 TTTAAATGATGTAACAGCTCC
*
36750930 TTTAAATGATGTAAAATGCTCTCC
1 TTTAAATGATGTAACA-G--CTCC
* *
36750954 TTTAATTGATGTAACAGCCCC
1 TTTAAATGATGTAACAGCTCC
36750975 TT
1 TT
36750977 GTATGTAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 18 0.47
22 1 0.03
23 1 0.03
24 18 0.47
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.34
Consensus pattern (21 bp):
TTTAAATGATGTAACAGCTCC
Found at i:36752631 original size:33 final size:33
Alignment explanation
Indices: 36752594--36752689 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 33
36752584 TGAGTTAATG
*
36752594 CATGACTTAATTTAATGATGCAAACTTTACTAA
1 CATGACTTAATTTAATGATGCAAACTTAACTAA
*
36752627 CATGA---AATTT-A-CAT---AA-TTAAACTAA
1 CATGACTTAATTTAATGATGCAAACTT-AACTAA
36752652 CATGACTTAATTTAATGATGCAAACTTAACTAA
1 CATGACTTAATTTAATGATGCAAACTTAACTAA
36752685 CATGA
1 CATGA
36752690 AAGTTACATA
Statistics
Matches: 50, Mismatches: 3, Indels: 20
0.68 0.04 0.27
Matches are distributed among these distances:
24 2 0.04
25 12 0.24
28 7 0.14
29 2 0.04
30 7 0.14
33 18 0.36
34 2 0.04
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (33 bp):
CATGACTTAATTTAATGATGCAAACTTAACTAA
Found at i:36758362 original size:58 final size:58
Alignment explanation
Indices: 36758272--36758389 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
36758262 TCATCCGATT
36758272 TAGCCTTATGCCTAGCTCACATAGGACTACAATCTCATTAGAGTGAATGGTCTTATCA
1 TAGCCTTATGCCTAGCTCACATAGGACTACAATCTCATTAGAGTGAATGGTCTTATCA
36758330 TAGCCTTATGCCTAGCTCACATAGGACTACAATCTCATTAGAGTGAATGGTCTTATCA
1 TAGCCTTATGCCTAGCTCACATAGGACTACAATCTCATTAGAGTGAATGGTCTTATCA
36758388 TA
1 TA
36758390 CTCGATTTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (58 bp):
TAGCCTTATGCCTAGCTCACATAGGACTACAATCTCATTAGAGTGAATGGTCTTATCA
Found at i:36777342 original size:20 final size:20
Alignment explanation
Indices: 36777317--36777371 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
36777307 TGTGGTTCAA
*
36777317 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
36777337 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
36777357 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
36777372 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:36780216 original size:10 final size:10
Alignment explanation
Indices: 36780203--36780240 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
36780193 ATCTCACTTG
*
36780203 AGCTCAAGTC
1 AGCTCAATTC
36780213 AGCTC-ATTC
1 AGCTCAATTC
36780222 GAGCTCAATTC
1 -AGCTCAATTC
36780233 AGCTCAAT
1 AGCTCAAT
36780241 CTTAACCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.72
11 4 0.16
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:36781789 original size:13 final size:14
Alignment explanation
Indices: 36781773--36781801 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
36781763 CAAAAAAATC
36781773 AAAATTC-AAAAAA
1 AAAATTCGAAAAAA
36781786 AAAATTCGAAAAAA
1 AAAATTCGAAAAAA
36781800 AA
1 AA
36781802 TAAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.76, C:0.07, G:0.03, T:0.14
Consensus pattern (14 bp):
AAAATTCGAAAAAA
Found at i:36782929 original size:15 final size:15
Alignment explanation
Indices: 36782904--36782950 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
36782894 AGAAAATAAT
36782904 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
36782920 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
36782935 AAA-AATATGAAAATG
1 AAAGAA-ATGAAAATG
36782950 A
1 A
36782951 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:36783021 original size:15 final size:15
Alignment explanation
Indices: 36783003--36783036 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
36782993 AAAAGAAATT
36783003 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
36783018 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
36783033 GAAA
1 GAAA
36783037 TTGAAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:36787873 original size:20 final size:20
Alignment explanation
Indices: 36787848--36787893 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
36787838 ATCATGATCT
36787848 TTACTTCTTTACTTACTCT-C
1 TTACTTCTTTACTTACT-TGC
*
36787868 TTACTTGTTTACTTACTTGC
1 TTACTTCTTTACTTACTTGC
36787888 TTACTT
1 TTACTT
36787894 AAATAACTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.15, C:0.24, G:0.04, T:0.57
Consensus pattern (20 bp):
TTACTTCTTTACTTACTTGC
Found at i:36794610 original size:24 final size:25
Alignment explanation
Indices: 36794583--36794636 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
36794573 ATGAGTGATA
*
36794583 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
36794607 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
36794631 AAAAAA
1 AAAAAA
36794637 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:36805828 original size:28 final size:28
Alignment explanation
Indices: 36805779--36805834 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
36805769 AAATCGTAGC
*
36805779 TTCGAAAAAAAAAAGTTAAAAAAAAAGT
1 TTCGAAAAAAAAAAGTCAAAAAAAAAGT
36805807 TTCGAAAAAAAAAA-TCCGAAAAAAAAAG
1 TTCGAAAAAAAAAAGT-C-AAAAAAAAAG
36805835 AAGAAGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 1 0.04
28 14 0.56
29 10 0.40
ACGTcount: A:0.68, C:0.07, G:0.11, T:0.14
Consensus pattern (28 bp):
TTCGAAAAAAAAAAGTCAAAAAAAAAGT
Found at i:36805859 original size:14 final size:14
Alignment explanation
Indices: 36805842--36805868 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36805832 AAGAAGAAGG
36805842 AAAAAAAATTGCAA
1 AAAAAAAATTGCAA
36805856 AAAAAAAATTGCA
1 AAAAAAAATTGCA
36805869 TACGGTCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAAAAAATTGCAA
Found at i:36806618 original size:15 final size:15
Alignment explanation
Indices: 36806586--36806619 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
36806576 GCTCAACGAA
*
36806586 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
36806601 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
36806616 GAGG
1 GAGG
36806620 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:36813586 original size:24 final size:23
Alignment explanation
Indices: 36813532--36813588 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
36813522 GGATAATTAA
**
36813532 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
36813555 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
36813579 GAAATGGTAT
1 GAAATGGTAT
36813589 GAATAGAATG
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.42
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:36813590 original size:92 final size:92
Alignment explanation
Indices: 36813486--36813681 Score: 392
Period size: 92 Copynumber: 2.1 Consensus size: 92
36813476 TGGTTTTAGT
36813486 CGAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAAGAAATGGTATTTGGTTTTG
1 CGAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAAGAAATGGTATTTGGTTTTG
36813551 GTACGTTTTGGTATTTGGGAATTGGTA
66 GTACGTTTTGGTATTTGGGAATTGGTA
36813578 CGAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAAGAAATGGTATTTGGTTTTG
1 CGAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAAGAAATGGTATTTGGTTTTG
36813643 GTACGTTTTGGTATTTGGGAATTGGTA
66 GTACGTTTTGGTATTTGGGAATTGGTA
36813670 CGAAATGGTATG
1 CGAAATGGTATG
36813682 GATTTGGTAT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 104 1.00
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.36
Consensus pattern (92 bp):
CGAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAAGAAATGGTATTTGGTTTTG
GTACGTTTTGGTATTTGGGAATTGGTA
Found at i:36813633 original size:45 final size:45
Alignment explanation
Indices: 36813487--36813633 Score: 122
Period size: 45 Copynumber: 3.2 Consensus size: 45
36813477 GGTTTTAGTC
36813487 GAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAA
1 GAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAA
* * ** * * * * * *
36813532 GAAATGGTAT--TTGGTTTTGGTACG-TTTTGGTATTTGGGA-ATTGGTAC
1 GAAATGGTATGAATAG-AATGG-AAGAGTTCGG--TTTAGGATAAT--TAA
36813579 GAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAA
1 GAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAA
36813624 GAAATGGTAT
1 GAAATGGTAT
36813634 TTGGTTTTGG
Statistics
Matches: 72, Mismatches: 20, Indels: 20
0.64 0.18 0.18
Matches are distributed among these distances:
43 2 0.03
44 7 0.10
45 26 0.36
46 12 0.17
47 16 0.22
48 7 0.10
49 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (45 bp):
GAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAA
Found at i:36813690 original size:21 final size:22
Alignment explanation
Indices: 36813664--36813727 Score: 94
Period size: 21 Copynumber: 2.9 Consensus size: 22
36813654 TATTTGGGAA
36813664 TTGGTACGAAATGGTATGG-AT
1 TTGGTACGAAATGGTATGGTAT
*
36813685 TTGGTATGAAATGGTATGGTAT
1 TTGGTACGAAATGGTATGGTAT
*
36813707 TTGGTACGAATTGGTAATGGT
1 TTGGTACGAAATGGT-ATGGT
36813728 TCGAAGAGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 18 0.47
22 15 0.39
23 5 0.13
ACGTcount: A:0.27, C:0.03, G:0.33, T:0.38
Consensus pattern (22 bp):
TTGGTACGAAATGGTATGGTAT
Found at i:36819176 original size:14 final size:15
Alignment explanation
Indices: 36819157--36819189 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
36819147 AAATGAAGGC
36819157 AAAAGA-ACAAAAAG
1 AAAAGATACAAAAAG
*
36819171 AAAAGATAGAAAAAG
1 AAAAGATACAAAAAG
36819186 AAAA
1 AAAA
36819190 AAAGAGTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAAGATACAAAAAG
Found at i:36819181 original size:18 final size:20
Alignment explanation
Indices: 36819160--36819220 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 20
36819150 TGAAGGCAAA
36819160 AGAACAAAAAGAAAAGA-T-
1 AGAACAAAAAGAAAAGAGTG
*
36819178 AGAA-AAAGAAAAAAAGAGTG
1 AGAACAAA-AAGAAAAGAGTG
36819198 AGAAAACAAAAAGAAAA-AGTG
1 AG--AACAAAAAGAAAAGAGTG
36819219 AG
1 AG
36819221 TTGAAATTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 3 0.09
18 12 0.34
19 1 0.03
20 2 0.06
21 6 0.17
22 8 0.23
23 3 0.09
ACGTcount: A:0.70, C:0.03, G:0.21, T:0.05
Consensus pattern (20 bp):
AGAACAAAAAGAAAAGAGTG
Found at i:36819220 original size:21 final size:21
Alignment explanation
Indices: 36819162--36819220 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
36819152 AAGGCAAAAG
36819162 AACAAAAAG-AAAAGAT-AGAA
1 AACAAAAAGAAAAAG-TGAGAA
*
36819182 AA-AGAAAA-AAAGAGTGAGAA
1 AACA-AAAAGAAAAAGTGAGAA
36819202 AACAAAAAGAAAAAGTGAG
1 AACAAAAAGAAAAAGTGAG
36819221 TTGAAATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 2 0.06
20 20 0.62
21 10 0.31
ACGTcount: A:0.71, C:0.03, G:0.20, T:0.05
Consensus pattern (21 bp):
AACAAAAAGAAAAAGTGAGAA
Found at i:36827515 original size:20 final size:20
Alignment explanation
Indices: 36827490--36827528 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
36827480 TTACTTCTTC
36827490 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
36827510 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
36827529 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:36829031 original size:42 final size:43
Alignment explanation
Indices: 36828984--36829069 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 43
36828974 TTTCGAGGTG
* *
36828984 TGATTTCATGTAAGACCTTATCTAGGACATTGGCATCG-TATA
1 TGATTTCATGTAAGACCCTATCTAGGACAGTGGCATCGATATA
* * *
36829026 TGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATA
1 TGATTTCATGTAAGACCCTATCTAGGACAGTGGCATCGATATA
36829069 T
1 T
36829070 TATAACATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 33 0.87
43 5 0.13
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (43 bp):
TGATTTCATGTAAGACCCTATCTAGGACAGTGGCATCGATATA
Found at i:36832517 original size:22 final size:22
Alignment explanation
Indices: 36832486--36832550 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
36832476 ACCTTTTTGA
*
36832486 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
* *
36832509 ACCATACCATTTCATACCAACT
1 ACCATACCATTTCGTACCAAAT
* *
36832531 TCCATACCATTTTGTACCAA
1 ACCATACCATTTCGTACCAA
36832551 TTCCCAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 32 0.89
23 4 0.11
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.29
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:36832898 original size:18 final size:17
Alignment explanation
Indices: 36832854--36832914 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
36832844 ATAGGTACGT
* * *
36832854 AAAAAAAAGAGTTCAAA
1 AAAAAAAAAAATTGAAA
36832871 AAAATCAAAAAAATTGAAA
1 AAAA--AAAAAAATTGAAA
36832890 AGAAAAAAAAAATTGAAA
1 A-AAAAAAAAAATTGAAA
36832908 AAAAAAA
1 AAAAAAA
36832915 TTTGCATACG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
17 10 0.26
18 14 0.37
19 11 0.29
20 3 0.08
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.11
Consensus pattern (17 bp):
AAAAAAAAAAATTGAAA
Found at i:36832907 original size:13 final size:13
Alignment explanation
Indices: 36832891--36832916 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36832881 AAATTGAAAA
36832891 GAAAAAAAAAATT
1 GAAAAAAAAAATT
36832904 GAAAAAAAAAATT
1 GAAAAAAAAAATT
36832917 TGCATACGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
GAAAAAAAAAATT
Found at i:36835400 original size:23 final size:22
Alignment explanation
Indices: 36835349--36835400 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
36835339 CCTCGTCTTT
*
36835349 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
36835371 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
36835394 TTCTTTT
1 TTCTTTT
36835401 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:36842841 original size:22 final size:22
Alignment explanation
Indices: 36842810--36842874 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
36842800 ACCTTATTGA
*
36842810 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
* *
36842833 ACCATACCATTTCATACCAACT
1 ACCATACCATTTCGTACCAAAT
*
36842855 TCCATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
36842875 TTCCCAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 33 0.89
23 4 0.11
ACGTcount: A:0.35, C:0.34, G:0.03, T:0.28
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:36844999 original size:21 final size:22
Alignment explanation
Indices: 36844953--36844999 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
36844943 CATTTTTCTT
*
36844953 TTCTTTTTCACTCTCTCTCAAT
1 TTCTTTTTCACTCTCTCTCAAA
* *
36844975 TTCTTTTTCAGT-TCTTTCAAA
1 TTCTTTTTCACTCTCTCTCAAA
36844996 TTCT
1 TTCT
36845000 CCAAAGATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.15, C:0.26, G:0.02, T:0.57
Consensus pattern (22 bp):
TTCTTTTTCACTCTCTCTCAAA
Found at i:36847216 original size:17 final size:16
Alignment explanation
Indices: 36847194--36847233 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 16
36847184 CCGTATACAA
36847194 TTTTTTTTCTTTTCAAT
1 TTTTTTTTC-TTTCAAT
36847211 TTTTTTTTCTTTCAAT
1 TTTTTTTTCTTTCAAT
36847227 TTTTTTT
1 TTTTTTT
36847234 AAATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTTTCTTTCAAT
Found at i:36848040 original size:13 final size:13
Alignment explanation
Indices: 36848022--36848046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36848012 GTATTGATCA
36848022 TGTGTTCACACCT
1 TGTGTTCACACCT
36848035 TGTGTTCACACC
1 TGTGTTCACACC
36848047 ATGATGACCA
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:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:36849052 original size:22 final size:22
Alignment explanation
Indices: 36849022--36849065 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
36849012 TTTGGTATTT
*
36849022 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACAAAATGGTAA
*
36849044 GGGATTTGGTACAAAATGGTAA
1 GGGAATTGGTACAAAATGGTAA
36849066 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.34, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACAAAATGGTAA
Found at i:36855744 original size:21 final size:22
Alignment explanation
Indices: 36855701--36855749 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
36855691 TCTTTTTGGA
36855701 TTTCTTTTCTTTTTCAATCTCTT
1 TTTCTTTTC-TTTTCAATCTCTT
* *
36855724 TTTCTTTTC-TTTCGATTTCTT
1 TTTCTTTTCTTTTCAATCTCTT
36855745 TTTCT
1 TTTCT
36855750 CGCTCGTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 15 0.62
23 9 0.38
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTCTTTTCTTTTCAATCTCTT
Found at i:36856699 original size:30 final size:30
Alignment explanation
Indices: 36856658--36856714 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
36856648 GCAAGACTTT
* *
36856658 TCACTTTTTTTTAACTTGATTTTTTTTTGC
1 TCACCTTTTTTTAACTCGATTTTTTTTTGC
**
36856688 TCACCTTTTTTTTGCTCGATTTTTTTT
1 TCACCTTTTTTTAACTCGATTTTTTTT
36856715 CACTTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.07, T:0.67
Consensus pattern (30 bp):
TCACCTTTTTTTAACTCGATTTTTTTTTGC
Found at i:36856710 original size:14 final size:14
Alignment explanation
Indices: 36856678--36856725 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
36856668 TTAACTTGAT
36856678 TTTTTTTTGCTCACC
1 TTTTTTTTGCTCA-C
36856693 TTTTTTTTGCTCGA-
1 TTTTTTTTGCTC-AC
36856707 -TTTTTTT--TCAC
1 TTTTTTTTGCTCAC
36856718 TTTTTTTT
1 TTTTTTTT
36856726 TGAATTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
10 1 0.03
11 2 0.07
12 7 0.23
13 7 0.23
15 12 0.40
16 1 0.03
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTTTTTTGCTCAC
Found at i:36856711 original size:15 final size:15
Alignment explanation
Indices: 36856675--36856714 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
36856665 TTTTTAACTT
36856675 GATTTTTTTTTGCTC
1 GATTTTTTTTTGCTC
*
36856690 -ACCTTTTTTTTGCTC
1 GA-TTTTTTTTTGCTC
36856705 GATTTTTTTT
1 GATTTTTTTT
36856715 CACTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.07, C:0.15, G:0.10, T:0.68
Consensus pattern (15 bp):
GATTTTTTTTTGCTC
Found at i:36856771 original size:12 final size:12
Alignment explanation
Indices: 36856707--36856772 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 12
36856697 TTTTGCTCGA
* *
36856707 TTTTTTTTCACT
1 TTTTTTTTGAAT
36856719 TTTTTTTTGAA-
1 TTTTTTTTGAAT
*
36856730 TTTTTTTTCAAT
1 TTTTTTTTGAAT
*
36856742 CAATTTTTTTCGAAT
1 ---TTTTTTTTGAAT
36856757 TTTTTTTTG-AT
1 TTTTTTTTGAAT
36856768 TTTTT
1 TTTTT
36856773 GTTACTCCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
11 17 0.39
12 17 0.39
15 10 0.23
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.73
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:36859627 original size:15 final size:17
Alignment explanation
Indices: 36859607--36859648 Score: 61
Period size: 15 Copynumber: 2.5 Consensus size: 17
36859597 TGAAAAGAAG
36859607 TTAAAAAAAG-TTTG-A
1 TTAAAAAAAGTTTTGAA
36859622 TTAAAAAAAGTTTTGAA
1 TTAAAAAAAGTTTTGAA
36859639 TATAAAAAAA
1 T-TAAAAAAA
36859649 AGTGTTGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.42
16 4 0.17
17 2 0.08
18 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (17 bp):
TTAAAAAAAGTTTTGAA
Found at i:36861064 original size:92 final size:92
Alignment explanation
Indices: 36860957--36861160 Score: 302
Period size: 92 Copynumber: 2.2 Consensus size: 92
36860947 TAATGTGGAG
* *
36860957 CATGCACCCGATTGTGCATGAATGTCGAGAGCTAGTTTTT-AGCTGGACATTCATGTATCTTCCG
1 CATGCACCCGATTGTGCATGAATGTCGAGAGCTA-TTTTTCAGCTGGACATACATGTATCTTCCA
* *
36861021 GATTCAATGAAGCTACTTTAATGAAGAA
65 GATTCAATGAAGCTAATTTAAAGAAGAA
** * * * *
36861049 CATGCACCTTATTGTGCATGAATGTTGGGAGCTATTTTTCAGCTGGATATAGATGTATCTTCCAG
1 CATGCACCCGATTGTGCATGAATGTCGAGAGCTATTTTTCAGCTGGACATACATGTATCTTCCAG
36861114 ATTCAATGAAGCTAATTTAAAGAAGAA
66 ATTCAATGAAGCTAATTTAAAGAAGAA
36861141 CATGCACCCGATTGTGCATG
1 CATGCACCCGATTGTGCATG
36861161 TATTTTGAGA
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
91 5 0.05
92 94 0.95
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (92 bp):
CATGCACCCGATTGTGCATGAATGTCGAGAGCTATTTTTCAGCTGGACATACATGTATCTTCCAG
ATTCAATGAAGCTAATTTAAAGAAGAA
Found at i:36866000 original size:33 final size:33
Alignment explanation
Indices: 36865962--36866024 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
36865952 GATTACTCAC
36865962 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
36865995 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
36866025 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:36866051 original size:21 final size:21
Alignment explanation
Indices: 36866022--36866077 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
36866012 CAAGCTCTCT
*
36866022 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
36866043 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
36866064 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
36866078 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:36866051 original size:27 final size:26
Alignment explanation
Indices: 36866021--36866146 Score: 78
Period size: 28 Copynumber: 4.6 Consensus size: 26
36866011 TCAAGCTCTC
36866021 TTTCAATTTCTTTTTTCGCTTTTTCTT
1 TTTCAATTTCTTTTTTC-CTTTTTCTT
* *
36866048 TTTCAATTTTCTTTTCTTCATTTTCTTTT
1 TTTCAA-TTTCTTTT-TTCCTTTT-TCTT
* *
36866077 TCTCTCACTTT-TTCGATTT-CTTTTTCTT
1 T-T-TCAATTTCTT--TTTTCCTTTTTCTT
* * *
36866105 TTGCAATTTC-TTTTTCTTTTTGTTTT
1 TTTCAATTTCTTTTTTCCTTTT-TCTT
36866131 CTTTCAATTTCTTTTT
1 -TTTCAATTTCTTTTT
36866147 CAATCTCTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
24 3 0.04
25 4 0.05
26 9 0.12
27 16 0.21
28 20 0.27
29 13 0.17
30 6 0.08
31 4 0.05
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (26 bp):
TTTCAATTTCTTTTTTCCTTTTTCTT
Found at i:36866070 original size:14 final size:14
Alignment explanation
Indices: 36866021--36866077 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
36866011 TCAAGCTCTC
36866021 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
36866034 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
36866048 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
36866062 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
36866076 TT
1 TT
36866078 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:36866105 original size:18 final size:18
Alignment explanation
Indices: 36866084--36866134 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
36866074 TTTTCTCTCA
36866084 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
36866102 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
36866120 CTTTTT-GTTTTCTTT
1 CTTTTTCGATTTCTTT
36866135 CAATTTCTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.06, C:0.16, G:0.06, T:0.73
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:36866147 original size:6 final size:6
Alignment explanation
Indices: 36866039--36866134 Score: 59
Period size: 6 Copynumber: 15.7 Consensus size: 6
36866029 TCTTTTTTCG
* * * **
36866039 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
36866090 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
36866135 CAATTTCTTT
Statistics
Matches: 64, Mismatches: 23, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
5 4 0.06
6 48 0.75
7 9 0.14
8 3 0.05
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:36867186 original size:16 final size:16
Alignment explanation
Indices: 36867167--36867210 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
36867157 TTAAACTTGA
36867167 TTTTTTTTGCTCACCT
1 TTTTTTTTGCTCACCT
* ***
36867183 TTTTTTTTTCTTTTCT
1 TTTTTTTTGCTCACCT
36867199 TTTTTTTTGCTC
1 TTTTTTTTGCTC
36867211 GATTTTTTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (16 bp):
TTTTTTTTGCTCACCT
Found at i:36867228 original size:12 final size:12
Alignment explanation
Indices: 36867213--36867248 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
36867203 TTTTGCTCGA
*
36867213 TTTTTTTTCACT
1 TTTTTTTTCAAT
*
36867225 TTTTTTTTGAAT
1 TTTTTTTTCAAT
36867237 TTTTTTTTCAAT
1 TTTTTTTTCAAT
36867249 CAAATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:36867241 original size:14 final size:14
Alignment explanation
Indices: 36867224--36867275 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
36867214 TTTTTTTCAC
36867224 TTTTTTTTT-GAAT
1 TTTTTTTTTCGAAT
*
36867237 TTTTTTTTCAATCAAAT
1 TTTTTTTT---TCGAAT
36867254 TTTTTTTTTCGAAT
1 TTTTTTTTTCGAAT
36867268 TTTTTTTT
1 TTTTTTTT
36867276 ATTTTTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 8 0.24
14 13 0.39
16 1 0.03
17 11 0.33
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTCGAAT
Found at i:36876558 original size:23 final size:22
Alignment explanation
Indices: 36876506--36876558 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
36876496 TCCACGTCTT
*
36876506 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
36876528 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
36876551 TTTCTTTT
1 TTTCTTTT
36876559 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:36880987 original size:44 final size:44
Alignment explanation
Indices: 36880938--36881078 Score: 110
Period size: 43 Copynumber: 3.2 Consensus size: 44
36880928 ATTTTCTTGA
36880938 TTCTTGAAATTGCTCCGAACAGCAAAATTGGGCCAAGATTCGAT
1 TTCTTGAAATTGCTCCGAACAGCAAAATTGGGCCAAGATTCGAT
* * * * * *** **
36880982 TTCTTG-ATTTTCT-TGAA-AACAAGAAAGTGAATCTTGATTTTCTTGA-
1 TTCTTGAAATTGCTCCGAACAGC-A-AAATTGGGCCAAGA--TTC--GAT
36881028 TTCTTGAAATTGCTCCGAACAGCAAAATTGGGCCAAGATTCGAT
1 TTCTTGAAATTGCTCCGAACAGCAAAATTGGGCCAAGATTCGAT
36881072 TTCTTGA
1 TTCTTGA
36881079 TTTTCTTAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 20
0.63 0.19 0.19
Matches are distributed among these distances:
41 2 0.03
42 4 0.06
43 15 0.22
44 13 0.19
45 6 0.09
46 6 0.09
47 15 0.22
48 4 0.06
49 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (44 bp):
TTCTTGAAATTGCTCCGAACAGCAAAATTGGGCCAAGATTCGAT
Found at i:36881034 original size:90 final size:90
Alignment explanation
Indices: 36880921--36881119 Score: 380
Period size: 90 Copynumber: 2.2 Consensus size: 90
36880911 CAAGATTTGA
36880921 AATCTTGATTTTCTTGATTCTTGAAATTGCTCCGAACAGCAAAATTGGGCCAAGATTCGATTTCT
1 AATCTTGATTTTCTTGATTCTTGAAATTGCTCCGAACAGCAAAATTGGGCCAAGATTCGATTTCT
*
36880986 TGATTTTCTTGAAAACAAGAAAGTG
66 TGATTTTCTTAAAAACAAGAAAGTG
36881011 AATCTTGATTTTCTTGATTCTTGAAATTGCTCCGAACAGCAAAATTGGGCCAAGATTCGATTTCT
1 AATCTTGATTTTCTTGATTCTTGAAATTGCTCCGAACAGCAAAATTGGGCCAAGATTCGATTTCT
36881076 TGATTTTCTTAAAAACAAGAAAGTG
66 TGATTTTCTTAAAAACAAGAAAGTG
*
36881101 GATCTTGATTTTCTTGATT
1 AATCTTGATTTTCTTGATT
36881120 TGAGCCCATC
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 107 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (90 bp):
AATCTTGATTTTCTTGATTCTTGAAATTGCTCCGAACAGCAAAATTGGGCCAAGATTCGATTTCT
TGATTTTCTTAAAAACAAGAAAGTG
Found at i:36886783 original size:55 final size:54
Alignment explanation
Indices: 36886688--36886837 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
36886678 CTACTTTGTT
* ** * *
36886688 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
36886742 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
36886797 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
36886838 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:36886800 original size:27 final size:27
Alignment explanation
Indices: 36886660--36886837 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
36886650 TAAATTGTAC
36886660 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
36886687 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
36886713 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
36886741 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
36886769 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
36886796 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
36886823 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
36886838 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:36886801 original size:82 final size:81
Alignment explanation
Indices: 36886661--36886816 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
36886651 AAATTGTACA
* * * *
36886661 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
36886726 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
36886742 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
36886805 TGTGCGAGTTGA
63 TGTGCGAATTGA
36886817 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:36894763 original size:55 final size:54
Alignment explanation
Indices: 36894668--36894817 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
36894658 CTACTTTGTT
* ** * *
36894668 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
36894722 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
36894777 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
36894818 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:36894780 original size:27 final size:27
Alignment explanation
Indices: 36894640--36894817 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
36894630 TAAATTGTAC
36894640 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
36894667 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
36894693 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
36894721 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
36894749 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
36894776 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
36894803 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
36894818 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:36894781 original size:82 final size:81
Alignment explanation
Indices: 36894641--36894796 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
36894631 AAATTGTACA
* * * *
36894641 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
36894706 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
36894722 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
36894785 TGTGCGAGTTGA
63 TGTGCGAATTGA
36894797 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:36912816 original size:40 final size:40
Alignment explanation
Indices: 36912786--36912995 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
36912776 GGACTAAGAT
* * * **
36912786 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
36912826 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
36912866 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
36912906 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
* ** * * *
36912946 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
36912985 CCGAAGGCATT
1 CCGAAGGCATT
36912996 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 33 0.21
40 126 0.79
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
Found at i:36919778 original size:40 final size:40
Alignment explanation
Indices: 36919748--36919957 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
36919738 GGACTAAGAT
* * * **
36919748 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
36919788 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
36919828 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
36919868 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
* ** * * *
36919908 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
36919947 CCGAAGGCATT
1 CCGAAGGCATT
36919958 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 33 0.21
40 126 0.79
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
Found at i:36924115 original size:18 final size:18
Alignment explanation
Indices: 36924074--36924109 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
36924064 CATTCCGAAG
*
36924074 TATATATATATATACATA
1 TATATGTATATATACATA
36924092 TATATGTATATATACATA
1 TATATGTATATATACATA
36924110 AGTATGCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (18 bp):
TATATGTATATATACATA
Found at i:36924598 original size:28 final size:28
Alignment explanation
Indices: 36924558--36924707 Score: 248
Period size: 28 Copynumber: 5.4 Consensus size: 28
36924548 GAGATTGGCG
36924558 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGCTTGATTATGTAGCA
36924586 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGCTTGATTATGTAGCA
36924614 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGCTTGATTATGTAGCA
* * *
36924642 CTAAGTGTGAGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGCTTGATTATGTAGCA
*
36924670 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGCTTGATTATGTAGCA
*
36924697 CTGAGTGTGCG
1 CTAAGTGTGCG
36924708 GACTTAATAT
Statistics
Matches: 117, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 24 0.21
28 93 0.79
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGCTTGATTATGTAGCA
Found at i:36927280 original size:20 final size:20
Alignment explanation
Indices: 36927257--36927303 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
36927247 GGGTTAAGAT
*
36927257 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
36927277 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
36927297 TGAGCTG
1 TGAGCTG
36927304 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:36928546 original size:18 final size:18
Alignment explanation
Indices: 36928525--36928584 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
36928515 GACCTCACTC
36928525 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** *
36928543 TCTTTTTCAATCTCTTTT
1 TCTTTTTTGATTTCTTTT
36928561 TCTTTTCTTTTGATTTCTTTT
1 TC--TT-TTTTGATTTCTTTT
36928582 TCT
1 TCT
36928585 CGCTCGCACT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 17 0.52
19 1 0.03
20 2 0.06
21 13 0.39
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:36929526 original size:13 final size:12
Alignment explanation
Indices: 36929510--36929543 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
36929500 TATACTTCAA
36929510 AATTATTTTTTTG
1 AATT-TTTTTTTG
36929523 AA-TTTTTTTTG
1 AATTTTTTTTTG
36929534 AATTTTTTTT
1 AATTTTTTTT
36929544 CAAATTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 10 0.50
12 8 0.40
13 2 0.10
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:36929531 original size:11 final size:11
Alignment explanation
Indices: 36929515--36929543 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
36929505 TTCAAAATTA
36929515 TTTTTTTGAAT
1 TTTTTTTGAAT
36929526 TTTTTTTGAAT
1 TTTTTTTGAAT
36929537 TTTTTTT
1 TTTTTTT
36929544 CAAATTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:36930799 original size:72 final size:73
Alignment explanation
Indices: 36930716--36930863 Score: 192
Period size: 72 Copynumber: 2.0 Consensus size: 73
36930706 TTTAATGCTA
* * *
36930716 TCCCAAGTCCCATGCACACACTAAATTCGGCTG-GTTGGGAAAATACAACAG-CAACTTTCGCTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTT-GCTT
36930779 TAAATGCCG
65 TAAATGCCG
* * * * * *
36930788 TCCCAAGTCCCATGCACTCAATAAATTCGGCAGCTTTGGAAAAATGCAGCAGCCACCTTTTCTTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
36930853 AAATGCCG
66 AAATGCCG
36930861 TCC
1 TCC
36930864 ATGTACCTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 30 0.46
73 29 0.45
74 6 0.09
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (73 bp):
TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
AAATGCCG
Found at i:36931071 original size:16 final size:16
Alignment explanation
Indices: 36931050--36931081 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
36931040 CATTCTGTAT
36931050 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
36931066 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
36931082 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:36941812 original size:14 final size:14
Alignment explanation
Indices: 36941793--36941823 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
36941783 CGGTCAATGT
36941793 ATATTAATACCTGC
1 ATATTAATACCTGC
36941807 ATATTAATACCTGC
1 ATATTAATACCTGC
36941821 ATA
1 ATA
36941824 CGAGTCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (14 bp):
ATATTAATACCTGC
Found at i:36947694 original size:22 final size:22
Alignment explanation
Indices: 36947666--36947729 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
36947656 CCTTTTTGAA
*
36947666 CCATTACCATTTCGAACCAAAT
1 CCATTACCATTTCGTACCAAAT
* **
36947688 CCATTACCATTTTGTGTCAAAT
1 CCATTACCATTTCGTACCAAAT
*
36947710 CCTTTACCATTTCGTACCAA
1 CCATTACCATTTCGTACCAA
36947730 TTCCCAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:36955512 original size:15 final size:15
Alignment explanation
Indices: 36955492--36955526 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
36955482 TTGTCCATTC
36955492 GGCTACTAGTAGAAA
1 GGCTACTAGTAGAAA
36955507 GGCTACTAGTAGAAA
1 GGCTACTAGTAGAAA
36955522 GGCTA
1 GGCTA
36955527 ATTTTGCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20
Consensus pattern (15 bp):
GGCTACTAGTAGAAA
Found at i:36956032 original size:17 final size:16
Alignment explanation
Indices: 36956010--36956053 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
36956000 AATTGTAGTT
36956010 TCGAAAAAAAAAAGAAA
1 TCGAAAAAAAAAA-AAA
36956027 TCGAAAAGAAAAAAAAA
1 TCGAAAA-AAAAAAAAA
*
36956044 TTGAAAAAAA
1 TCGAAAAAAA
36956054 TTGTATACGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 3 0.12
17 16 0.64
18 6 0.24
ACGTcount: A:0.75, C:0.05, G:0.11, T:0.09
Consensus pattern (16 bp):
TCGAAAAAAAAAAAAA
Found at i:36967403 original size:5 final size:5
Alignment explanation
Indices: 36967393--36967417 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
36967383 ATAATTTTCA
36967393 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
36967418 ATAGATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:36973073 original size:25 final size:25
Alignment explanation
Indices: 36972978--36973061 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
36972968 AGTGGTAAGA
* * *
36972978 TACTTTGATGTTTATAATGAAGAAT
1 TACTTTGATTTTTGTAATGAGGAAT
** *
36973003 TACTTTGATTCTTCTACGTTTTTAGGAAT
1 TACTTTGATT-TT-T--GTAATGAGGAAT
36973032 TACTTTGATTTTTGTAATGAGGAAT
1 TACTTTGATTTTTGTAATGAGGAAT
36973057 TACTT
1 TACTT
36973062 GTTTAATTGT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
25 23 0.50
26 2 0.04
27 2 0.04
28 2 0.04
29 17 0.37
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.49
Consensus pattern (25 bp):
TACTTTGATTTTTGTAATGAGGAAT
Found at i:36973954 original size:31 final size:30
Alignment explanation
Indices: 36973910--36973985 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 30
36973900 ATTTTGTTCT
**
36973910 ATTATTTAAATTTTATTTT-ATCTATATTATA
1 ATTATTTTTATTTTATTTTGATCTATA-TA-A
*
36973941 ATTATTTTTATTTTTATTTTGATGTATATAA
1 ATTATTTTTA-TTTTATTTTGATCTATATAA
36973972 A-TATTTTTATTTTA
1 ATTATTTTTATTTTA
36973986 AAAAATATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 5 0.12
30 8 0.20
31 10 0.25
32 11 0.28
33 6 0.15
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (30 bp):
ATTATTTTTATTTTATTTTGATCTATATAA
Found at i:36982297 original size:22 final size:22
Alignment explanation
Indices: 36982261--36982320 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
36982251 TTTTTTTTAA
* *
36982261 TTTTTATTTGATTTTGTCTTTTTT
1 TTTTTATTT--TTTTGACTTTTTC
36982285 TTTTTATTTTTTTGACTTTTTC
1 TTTTTATTTTTTTGACTTTTTC
* *
36982307 TATTGATTTTTTTG
1 TTTTTATTTTTTTG
36982321 CGGGAAATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 23 0.72
24 9 0.28
ACGTcount: A:0.10, C:0.05, G:0.08, T:0.77
Consensus pattern (22 bp):
TTTTTATTTTTTTGACTTTTTC
Found at i:36985242 original size:45 final size:45
Alignment explanation
Indices: 36985191--36985277 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
36985181 GATGAGTCTC
*
36985191 GATCCTATTGAAGTGGAGTTAGGGGAAGGATTACCTAGTAATCTT
1 GATCCTATTGAAATGGAGTTAGGGGAAGGATTACCTAGTAATCTT
*
36985236 GATCCTATTGAAATGGAGTTGGGGGAAGGATTACCTAGTAAT
1 GATCCTATTGAAATGGAGTTAGGGGAAGGATTACCTAGTAAT
36985278 GTGATAGATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (45 bp):
GATCCTATTGAAATGGAGTTAGGGGAAGGATTACCTAGTAATCTT
Done.