Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 31 of 106
Found at i:12114602 original size:26 final size:24
Alignment explanation
Indices: 12114555--12114603 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
12114545 AGGAAAGCTT
*
12114555 TGAGAGTAGCCAAAATTTTGAAAG
1 TGAGAGTAGCCAAAATTCTGAAAG
*
12114579 TGAGAGTAGCTCCAATATTCTGAAA
1 TGAGAGTAG--CCAAAATTCTGAAA
12114604 ACTGAAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
26 12 0.57
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (24 bp):
TGAGAGTAGCCAAAATTCTGAAAG
Found at i:12118401 original size:20 final size:20
Alignment explanation
Indices: 12118356--12118393 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
12118346 TTTTGGCCCT
12118356 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
12118376 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
12118394 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:12119642 original size:13 final size:13
Alignment explanation
Indices: 12119624--12119648 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12119614 AGAGAAATTG
12119624 TGATTTTATAAAA
1 TGATTTTATAAAA
12119637 TGATTTTATAAA
1 TGATTTTATAAA
12119649 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:12121920 original size:10 final size:11
Alignment explanation
Indices: 12121902--12121930 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
12121892 CTCCTACAAA
12121902 AACATAAAAAT
1 AACATAAAAAT
12121913 AA-ATAAAAAT
1 AACATAAAAAT
12121923 AACATAAA
1 AACATAAA
12121931 TTTAACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (11 bp):
AACATAAAAAT
Found at i:12121974 original size:19 final size:20
Alignment explanation
Indices: 12121923--12121974 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
12121913 AAATAAAAAT
* *
12121923 AACATAAATTTAACATTATT
1 AACATAAATTAAACATTATA
* *
12121943 AACTTAAAATAAACATT-TA
1 AACATAAATTAAACATTATA
12121962 AACATAAATTAAA
1 AACATAAATTAAA
12121975 ATAAACTAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
AACATAAATTAAACATTATA
Found at i:12121987 original size:24 final size:23
Alignment explanation
Indices: 12121946--12121991 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
12121936 CATTATTAAC
*
12121946 TTAAAATAAACATTTAAACATAAA
1 TTAAAATAAACATATAAA-ATAAA
12121970 TTAAAATAAAC-TAATAAAATAA
1 TTAAAATAAACAT-ATAAAATAA
12121992 CTAAAAACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (23 bp):
TTAAAATAAACATATAAAATAAA
Found at i:12155287 original size:19 final size:19
Alignment explanation
Indices: 12155249--12155287 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12155239 CCCATGTCTA
*
12155249 TTAAAGACATTTGTAGTTT
1 TTAAAGACATTTGGAGTTT
12155268 TTAAAGACATGTTGGA-TTT
1 TTAAAGACAT-TTGGAGTTT
12155287 T
1 T
12155288 ATAGGAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (19 bp):
TTAAAGACATTTGGAGTTT
Found at i:12156890 original size:25 final size:25
Alignment explanation
Indices: 12156856--12156908 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
12156846 ACTTAATGAG
*
12156856 ATGGATGAACTTCGCCAAGAAGCAT
1 ATGGATGAACTTCACCAAGAAGCAT
* *
12156881 ATGGATGAACTTCATCACGAAGCAT
1 ATGGATGAACTTCACCAAGAAGCAT
12156906 ATG
1 ATG
12156909 AGAGTGCACG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (25 bp):
ATGGATGAACTTCACCAAGAAGCAT
Found at i:12159637 original size:20 final size:20
Alignment explanation
Indices: 12159612--12159657 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
12159602 CTTTTAAACC
12159612 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
12159632 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
12159652 TCAAAT
1 TCAAAT
12159658 GGTGCAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:12164446 original size:23 final size:23
Alignment explanation
Indices: 12164420--12164467 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
12164410 TTAGAAAAGG
12164420 TTTATACTAATGTAAATTTTAGA
1 TTTATACTAATGTAAATTTTAGA
12164443 TTTATACTAATGTAAATTTTAGA
1 TTTATACTAATGTAAATTTTAGA
12164466 TT
1 TT
12164468 ATATCAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (23 bp):
TTTATACTAATGTAAATTTTAGA
Found at i:12168563 original size:78 final size:80
Alignment explanation
Indices: 12168427--12168640 Score: 261
Period size: 82 Copynumber: 2.7 Consensus size: 80
12168417 AATGTTAAAC
* * * * * * *
12168427 TTACATATTGGCACCATTATACCTTCATGCATAATAAGAATGCCACATGCCCACCTAT-CA-CAT
1 TTACATATTGACATCATTATACCTTAATGTATAATAGGAATGCCACATGTCCATCTATACAGCAT
12168490 GGACCTTGATGGTAT
66 GGACCTTGATGGTAT
* * *
12168505 TTTCATATTGACATCGTTATACCTTAATGTACAATAGGAATGCCACATGTCCATCTATCACATGC
1 TTACATATTGACATCATTATACCTTAATGTATAATAGGAATGCCACATGTCCATCTAT-ACA-GC
*
12168570 ATGGATCTTGATGGTAT
64 ATGGACCTTGATGGTAT
* * **
12168587 TTACATATTGACATCATTATACTTTGATGTATAATAGGAATATCACATGTCCAT
1 TTACATATTGACATCATTATACCTTAATGTATAATAGGAATGCCACATGTCCAT
12168641 GCCTTGTGTC
Statistics
Matches: 114, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
78 48 0.42
80 2 0.02
82 64 0.56
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (80 bp):
TTACATATTGACATCATTATACCTTAATGTATAATAGGAATGCCACATGTCCATCTATACAGCAT
GGACCTTGATGGTAT
Found at i:12171657 original size:17 final size:16
Alignment explanation
Indices: 12171594--12171653 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 16
12171584 AAATTATAAA
12171594 TAAAATATTAATATTT
1 TAAAATATTAATATTT
*
12171610 TAAAAATATTAAT-GTT
1 T-AAAATATTAATATTT
*
12171626 TAAATTATTAAATATTT
1 TAAAATATT-AATATTT
*
12171643 TAAAATTTTAA
1 TAAAATATTAA
12171654 ATATAAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 7 0.19
16 9 0.25
17 20 0.56
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:12171664 original size:43 final size:43
Alignment explanation
Indices: 12171542--12171664 Score: 125
Period size: 43 Copynumber: 2.9 Consensus size: 43
12171532 AGTAAAAAAN
12171542 ATAAATTATT-AATATTTTAATATTTT-AATCAT-AA-TAATGT
1 ATAAATTATTAAATATTTTAATATTTTAAAT-ATAAATTAATGT
* *
12171582 ATAAATTA-TAAATAAAATATTAATATTTTAAA-A-ATATTAATGT
1 ATAAATTATTAAAT---ATTTTAATATTTTAAATATAAATTAATGT
* *
12171625 TTAAATTATTAAATATTTTAAAATTTTAAATATAAATTAA
1 ATAAATTATTAAATATTTTAATATTTTAAATATAAATTAA
12171665 AATGAAAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
39 1 0.01
40 11 0.16
41 14 0.21
42 3 0.04
43 31 0.46
44 7 0.10
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (43 bp):
ATAAATTATTAAATATTTTAATATTTTAAATATAAATTAATGT
Found at i:12172059 original size:27 final size:28
Alignment explanation
Indices: 12172014--12172072 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
12172004 TGTTAATATT
12172014 TAAATTATAAATTACTAATATTTT-AAA
1 TAAATTATAAATTACTAATATTTTAAAA
* * *
12172041 TAAATTATGATTTATTAATATTTTAAAA
1 TAAATTATAAATTACTAATATTTTAAAA
12172069 TAAA
1 TAAA
12172073 ATAACATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (28 bp):
TAAATTATAAATTACTAATATTTTAAAA
Found at i:12172122 original size:37 final size:38
Alignment explanation
Indices: 12172081--12172161 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 38
12172071 AAATAACATA
12172081 AAATAATTATATATTATAATAAAAGTATTTTT-TTATC
1 AAATAATTATATATTATAATAAAAGTATTTTTATTATC
* * * ** *
12172118 AAATATTTTTTTATTATTCTAAAATTATTTTTACTTATC
1 AAATAATTATATATTATAATAAAAGTATTTTTA-TTATC
12172157 AAATA
1 AAATA
12172162 TTGCAATAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
37 26 0.72
39 10 0.28
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.52
Consensus pattern (38 bp):
AAATAATTATATATTATAATAAAAGTATTTTTATTATC
Found at i:12173892 original size:28 final size:28
Alignment explanation
Indices: 12173860--12173916 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
12173850 TTCATCAGAT
*
12173860 AGTTTATTTTGCATCTAATTATAAATTA
1 AGTTTATTTTACATCTAATTATAAATTA
12173888 AGTTTATTTTACATCTAATTATAAATTA
1 AGTTTATTTTACATCTAATTATAAATTA
12173916 A
1 A
12173917 AATAATCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (28 bp):
AGTTTATTTTACATCTAATTATAAATTA
Found at i:12176121 original size:27 final size:27
Alignment explanation
Indices: 12176063--12176131 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
12176053 CAATTTAATT
* * *
12176063 AATTAATTAATAT-TTTTATAAAATAA
1 AATTAATTAATTTATTTTAAAAAAAAA
**
12176089 TTTTAATTAATTTATTTTAAAAAAAAA
1 AATTAATTAATTTATTTTAAAAAAAAA
*
12176116 AATTAATCAATTTATT
1 AATTAATTAATTTATT
12176132 AAGAATAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
26 10 0.29
27 24 0.71
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (27 bp):
AATTAATTAATTTATTTTAAAAAAAAA
Found at i:12184320 original size:90 final size:90
Alignment explanation
Indices: 12184167--12184350 Score: 359
Period size: 90 Copynumber: 2.0 Consensus size: 90
12184157 CTGTCGAAAA
*
12184167 TAATAAAAAATTAAGATTAATTGACACGGGTAACATGGTTGTTATATTCCTCTGGAATATTTGAT
1 TAATAAAAAATTAAGATTAATTGACACGGGTAACATGGTTGTTATATGCCTCTGGAATATTTGAT
12184232 TTAATTTGCATACGACAATATGCAT
66 TTAATTTGCATACGACAATATGCAT
12184257 TAATAAAAAATTAAGATTAATTGACACGGGTAACATGGTTGTTATATGCCTCTGGAATATTTGAT
1 TAATAAAAAATTAAGATTAATTGACACGGGTAACATGGTTGTTATATGCCTCTGGAATATTTGAT
12184322 TTAATTTGCATACGACAATATGCAT
66 TTAATTTGCATACGACAATATGCAT
12184347 TAAT
1 TAAT
12184351 TAATAGCGTG
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 93 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (90 bp):
TAATAAAAAATTAAGATTAATTGACACGGGTAACATGGTTGTTATATGCCTCTGGAATATTTGAT
TTAATTTGCATACGACAATATGCAT
Found at i:12191216 original size:29 final size:28
Alignment explanation
Indices: 12191184--12191262 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 28
12191174 GAATATTATG
*
12191184 TGCTAGTTATTATGGATATTCAATTATCT
1 TGCTAGCTATTATGGATATTCAA-TATCT
* * **
12191213 TGCTTAGCTACTATAGATATTGTATATCT
1 TGC-TAGCTATTATGGATATTCAATATCT
*
12191242 TGTTTAGCTATTATGGATATT
1 TG-CTAGCTATTATGGATATT
12191263 ATAAATATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.48
Consensus pattern (28 bp):
TGCTAGCTATTATGGATATTCAATATCT
Found at i:12192701 original size:24 final size:22
Alignment explanation
Indices: 12192670--12192732 Score: 56
Period size: 24 Copynumber: 2.7 Consensus size: 22
12192660 TTAAGTGAGA
12192670 TTTATTTAATA-TTTAATTTTAGT
1 TTTATTTAATAGTTTAATTTT--T
*
12192693 TTTAGTTTATTAGTTTTAATTTTT
1 TTTA-TTTAATAG-TTTAATTTTT
*
12192717 TTTATTTTAATTGTTT
1 TTTA-TTTAATAGTTT
12192733 GGATAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 7 0.21
24 17 0.52
26 9 0.27
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (22 bp):
TTTATTTAATAGTTTAATTTTT
Found at i:12193011 original size:28 final size:28
Alignment explanation
Indices: 12192980--12193042 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
12192970 ATTTTTTTAA
12192980 TTTATATTATT-ATTT-TAATTTATATTTG
1 TTTATATTATTCATTTCT-ATTT-TATTTG
* *
12193008 TTTATTTTTTTCATTTCTATTTTATTTG
1 TTTATATTATTCATTTCTATTTTATTTG
*
12193036 TTCATAT
1 TTTATAT
12193043 GTTATAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 20 0.69
29 8 0.28
30 1 0.03
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (28 bp):
TTTATATTATTCATTTCTATTTTATTTG
Found at i:12193012 original size:23 final size:23
Alignment explanation
Indices: 12192986--12193029 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12192976 TTAATTTATA
12192986 TTATTATTTTAATTTATATTTGT
1 TTATTATTTTAATTTATATTTGT
* * *
12193009 TTATTTTTTTCATTTCTATTT
1 TTATTATTTTAATTTATATTT
12193030 TATTTGTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (23 bp):
TTATTATTTTAATTTATATTTGT
Found at i:12195294 original size:40 final size:40
Alignment explanation
Indices: 12195250--12195329 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
12195240 CTACATTAAC
12195250 TTTTATTTATTTTCTTTTTGTAGT-AAAAAAAATCCTCCT
1 TTTTATTTATTTTCTTTTTGTAGTAAAAAAAAATCCTCCT
12195289 NTTTTATTTATTTTCTTTTTGTAGTAAAAAAAAATCCTCCT
1 -TTTTATTTATTTTCTTTTTGTAGTAAAAAAAAATCCTCCT
12195330 AAAAAGTGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
40 24 0.62
41 15 0.38
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.53
Consensus pattern (40 bp):
TTTTATTTATTTTCTTTTTGTAGTAAAAAAAAATCCTCCT
Found at i:12199344 original size:19 final size:20
Alignment explanation
Indices: 12199322--12199370 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
12199312 AAATTTTTAT
12199322 ATATTAAAATTT-TTAACAA
1 ATATTAAAATTTATTAACAA
12199341 ATA-TAACAATTTCATTAACAA
1 ATATTAA-AATTT-ATTAACAA
12199362 ATATTAAAA
1 ATATTAAAA
12199371 ATATCTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 8 0.31
21 12 0.46
22 3 0.12
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATTAAAATTTATTAACAA
Found at i:12199379 original size:21 final size:20
Alignment explanation
Indices: 12199322--12199379 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
12199312 AAATTTTTAT
*
12199322 ATATT-AAAATTTTTAACAA
1 ATATTAAAAATTCTTAACAA
*
12199341 ATA-TAACAATTTCATTAACAA
1 ATATTAA-AAATTC-TTAACAA
12199362 ATATTAAAAATATCTTAA
1 ATATTAAAAAT-TCTTAA
12199380 GACACCATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 1 0.03
19 4 0.13
20 4 0.13
21 17 0.55
22 5 0.16
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATTAAAAATTCTTAACAA
Found at i:12200139 original size:30 final size:30
Alignment explanation
Indices: 12200103--12200170 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
12200093 TTGATCTTCA
*
12200103 TCTTCATTTTCATCTCCTTCCATGTCATCT
1 TCTTCATCTTCATCTCCTTCCATGTCATCT
* *
12200133 TCTTCATCTTCATCTCTTTGCATGTCATCT
1 TCTTCATCTTCATCTCCTTCCATGTCATCT
*
12200163 TTTTCATC
1 TCTTCATC
12200171 CTCAATCAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.13, C:0.31, G:0.04, T:0.51
Consensus pattern (30 bp):
TCTTCATCTTCATCTCCTTCCATGTCATCT
Found at i:12206700 original size:13 final size:13
Alignment explanation
Indices: 12206660--12206700 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
12206650 ACAGAAAATT
12206660 TTTCATTGAAAAA
1 TTTCATTGAAAAA
* *
12206673 TTTCGTTG-GAAA
1 TTTCATTGAAAAA
12206685 TTTCATTGAAAAA
1 TTTCATTGAAAAA
12206698 TTT
1 TTT
12206701 GGTGGGAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (13 bp):
TTTCATTGAAAAA
Found at i:12215693 original size:31 final size:29
Alignment explanation
Indices: 12215656--12215728 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
12215646 TGCTAGTTAT
12215656 TATGGATATTCAATATATCTTGCTTAGCTAC
1 TATGGATATT--ATATATCTTGCTTAGCTAC
* * * *
12215687 TGTGGATATTGTATATCTTGTTTAGCTAT
1 TATGGATATTATATATCTTGCTTAGCTAC
12215716 TATGGATATTATA
1 TATGGATATTATA
12215729 AATATTTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 27 0.75
31 9 0.25
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (29 bp):
TATGGATATTATATATCTTGCTTAGCTAC
Found at i:12219550 original size:200 final size:199
Alignment explanation
Indices: 12219203--12219596 Score: 578
Period size: 200 Copynumber: 2.0 Consensus size: 199
12219193 GCATGTTATA
* *
12219203 TTATTGTCAGATGTAGTTGCCTTAGTCATTTCCTTTTTGGACTTCTAGAGTACAACTTTCACCTA
1 TTATTGTCAGATGTAGTTGCCTTAGTCATTT-CTTTTTAGACTTCTAGAGTACAACTTTAACCTA
*
12219268 CACGCTCTTGTTTCTCTTTTTCTACTTTCTGCCCCCTTTGAACTAGTCAAACCCCATTGCACTTA
65 CAAGCTCTTGTTTCTCTTTTTCTACTTTCTGCCCCCTTTGAACTAGTCAAACCCCATTGCACTTA
* * *
12219333 ACGTCTTCCCCTGGAGTTTTACTCTTTTTTTCTTCTTTAATATAATGGGATTTGATTCCACCCTG
130 ACGCCTTCCCCTGGAGTTATACTCGTTTTTTCTTCTTTAATATAATGGGATTTGATTCCACCCTG
12219398 CTATG
195 CTATG
* *
12219403 TTATTGTCAGATGTAGTTGCCTTAGT-AGTCTT-TTTCTTAGACTT-TCGGAGTACAGCTTTAAC
1 TTATTGTCAGATGTAGTTGCCTTAGTCA-T-TTCTTT-TTAGACTTCT-AGAGTACAACTTTAAC
** **
12219465 CTACAAGCTCTTGTTTCTCTTTTTCTACTTTCTGCCCCCTTTGAACTAGTCGGACCGTATTGCAC
62 CTACAAGCTCTTGTTTCTCTTTTTCTACTTTCTGCCCCCTTTGAACTAGTCAAACCCCATTGCAC
* * * *
12219530 TTAATGCCTTCCCTTGGAGTTATACTCGTTTTTTCTTCTTTAATTTAATGGGATTTTATTCCACC
127 TTAACGCCTTCCCCTGGAGTTATACTCGTTTTTTCTTCTTTAATATAATGGGATTTGATTCCACC
12219595 CT
192 CT
12219597 CCGTAGAGTC
Statistics
Matches: 174, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
199 5 0.03
200 167 0.96
201 2 0.01
ACGTcount: A:0.18, C:0.24, G:0.14, T:0.44
Consensus pattern (199 bp):
TTATTGTCAGATGTAGTTGCCTTAGTCATTTCTTTTTAGACTTCTAGAGTACAACTTTAACCTAC
AAGCTCTTGTTTCTCTTTTTCTACTTTCTGCCCCCTTTGAACTAGTCAAACCCCATTGCACTTAA
CGCCTTCCCCTGGAGTTATACTCGTTTTTTCTTCTTTAATATAATGGGATTTGATTCCACCCTGC
TATG
Found at i:12228156 original size:69 final size:73
Alignment explanation
Indices: 12228045--12228182 Score: 180
Period size: 69 Copynumber: 1.9 Consensus size: 73
12228035 AATATTCAAC
12228045 TATTTTTCCTATTTCCAATCAACTAACTATAATATATATTTAATC-TC-C-AATAGCT-TTTTTT
1 TATTTTTCCTATTTCCAATCAACTAACTATAATATATATTTAATCATCTCTAATAGCTATTTTTT
12228106 TTCTCATA
66 TTCTCATA
* * * *
12228114 TATTTTT-CTAATTTTCAATCAACTAA-TGGTAATATGTATTTAATCATCTCTAGTAGCTATTTT
1 TATTTTTCCT-ATTTCCAATCAACTAACT-ATAATATATATTTAATCATCTCTAATAGCTATTTT
12228177 TTTTCT
64 TTTTCT
12228183 TGTATATAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
68 3 0.05
69 37 0.63
70 2 0.03
71 1 0.02
72 6 0.10
73 10 0.17
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (73 bp):
TATTTTTCCTATTTCCAATCAACTAACTATAATATATATTTAATCATCTCTAATAGCTATTTTTT
TTCTCATA
Found at i:12228479 original size:14 final size:14
Alignment explanation
Indices: 12228462--12228493 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
12228452 TGAAAAAAAT
*
12228462 ATTATAAAAATTTG
1 ATTATAAAAATTTA
12228476 ATTATAAAAATTTA
1 ATTATAAAAATTTA
12228490 ATTA
1 ATTA
12228494 GAAATTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
ATTATAAAAATTTA
Found at i:12237772 original size:22 final size:21
Alignment explanation
Indices: 12237747--12237801 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
12237737 AGTTTTTAGG
*
12237747 TATTGCGTGACTGATTTTTATA
1 TATTGCGTGACTG-TTGTTATA
*
12237769 TATTACGTGACCTGTTGTTATA
1 TATTGCGTGA-CTGTTGTTATA
12237791 TATTGCGTGAC
1 TATTGCGTGAC
12237802 ATTGGGCCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 25 0.86
23 3 0.10
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.45
Consensus pattern (21 bp):
TATTGCGTGACTGTTGTTATA
Found at i:12237934 original size:207 final size:205
Alignment explanation
Indices: 12237568--12238156 Score: 797
Period size: 207 Copynumber: 2.9 Consensus size: 205
12237558 TATGTATTTG
* * * **
12237568 GTGACTTGTTGTTATGTATTGCGTGACGTTGGGCCAATACGTGATTGGTTATGTTGGCATAACAT
1 GTGACCTGTTGTTATGTATTGCGTGACATTGGGCCAATACGTGACTGGTTATGTTGGCATAATGT
* * * *
12237633 GAGTGGATATTAGGCATCGAGCGACTTATTATTAGGTATTGCGAGACTGGTGGTGCGTGACTAAC
66 GAGTGGATATTAGGCATTGAGTGACTTATTATTAGGTATTGCAAGACTGGTGGTGCGT-ACTGAC
* * *
12237698 TTGTGCAATTCACCTCTTGTTTGGAGGCTTTGGTTCACTAGTTTTTAGGTATTGCGTGACTGATT
130 TTGTGCAATTCA-CTCTTGTTTTGAGGCTTTTGTTCACTAGTTTTTAGGCATTGCGTGACTGATT
12237763 TTTATATATTAC
194 TTTATATATTAC
* ** *
12237775 GTGACCTGTTGTTATATATTGCGTGACATTGGGCCAGCATGTGACTGGTTATGTTGGCATAATGT
1 GTGACCTGTTGTTATGTATTGCGTGACATTGGGCCAATACGTGACTGGTTATGTTGGCATAATGT
* * * * * * *
12237840 GACTGGGTATAAGGCATTGAGTGACTTATTCTTAGGTATTGCAAGACTAGCGGTGCGTCACTGAG
66 GAGTGGATATTAGGCATTGAGTGACTTATTATTAGGTATTGCAAGACTGGTGGTGCGT-ACTGAC
* * *
12237905 TTGTGCAATTCATCTGTTGTTTTGAGGCTTTTATTCACTAGATTTTAGGCATTGCGTGACTGATT
130 TTGTGCAATTCA-CTCTTGTTTTGAGGCTTTTGTTCACTAGTTTTTAGGCATTGCGTGACTGATT
*
12237970 TTTATATATTGC
194 TTTATATATTAC
* * *
12237982 GTCACCTGTTGTTATGTATTGCGTGACATTGGGCCATTACGTGACTGGTTATGTTGGCGTAATGT
1 GTGACCTGTTGTTATGTATTGCGTGACATTGGGCCAATACGTGACTGGTTATGTTGGCATAATGT
* * * *
12238047 GAGTGGATATTACGCATTAAGTGACTTATTATTAGGTATTTCAAGATTGGTGGTGCG---TGACT
66 GAGTGGATATTAGGCATTGAGTGACTTATTATTAGGTATTGCAAGACTGGTGGTGCGTACTGACT
*
12238109 TGTGTAATTCACGTCTTGTTTTGAGGCTTTTGTTCACTAGTTTTTAGG
131 TGTGCAATTCAC-TCTTGTTTTGAGGCTTTTGTTCACTAGTTTTTAGG
12238157 GTTTGCATGA
Statistics
Matches: 331, Mismatches: 50, Indels: 6
0.86 0.13 0.02
Matches are distributed among these distances:
202 1 0.00
203 46 0.14
207 284 0.86
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.39
Consensus pattern (205 bp):
GTGACCTGTTGTTATGTATTGCGTGACATTGGGCCAATACGTGACTGGTTATGTTGGCATAATGT
GAGTGGATATTAGGCATTGAGTGACTTATTATTAGGTATTGCAAGACTGGTGGTGCGTACTGACT
TGTGCAATTCACTCTTGTTTTGAGGCTTTTGTTCACTAGTTTTTAGGCATTGCGTGACTGATTTT
TATATATTAC
Found at i:12237980 original size:22 final size:21
Alignment explanation
Indices: 12237955--12238008 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
12237945 GATTTTAGGC
*
12237955 ATTGCGTGACTGATTTTTATAT
1 ATTGCGTGACTG-TTGTTATAT
* *
12237977 ATTGCGTCACCTGTTGTTATGT
1 ATTGCGTGA-CTGTTGTTATAT
12237999 ATTGCGTGAC
1 ATTGCGTGAC
12238009 ATTGGGCCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.04
22 23 0.85
23 3 0.11
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.44
Consensus pattern (21 bp):
ATTGCGTGACTGTTGTTATAT
Found at i:12242258 original size:23 final size:23
Alignment explanation
Indices: 12242217--12242304 Score: 79
Period size: 23 Copynumber: 3.8 Consensus size: 23
12242207 GAACCAATCC
* *
12242217 CGCGATTCCATAATAACTAGTCA
1 CGCGACTCCATATTAACTAGTCA
* *
12242240 CG-GCACTCCATATTTACTACTCA
1 CGCG-ACTCCATATTAACTAGTCA
* * * *
12242263 CGCGACTCAAGATCAAATAGTCA
1 CGCGACTCCATATTAACTAGTCA
*
12242286 CGCGACTCCATATTTACTA
1 CGCGACTCCATATTAACTA
12242305 CCTCAGTTGA
Statistics
Matches: 48, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
22 1 0.02
23 46 0.96
24 1 0.02
ACGTcount: A:0.32, C:0.30, G:0.12, T:0.26
Consensus pattern (23 bp):
CGCGACTCCATATTAACTAGTCA
Found at i:12243385 original size:15 final size:15
Alignment explanation
Indices: 12243361--12243395 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
12243351 TTCGCTCTGA
*
12243361 ACTTGTTTTTATGGT
1 ACTTGCTTTTATGGT
12243376 ACTTGCTTTTATGGT
1 ACTTGCTTTTATGGT
12243391 ACTTG
1 ACTTG
12243396 TTCTTAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.54
Consensus pattern (15 bp):
ACTTGCTTTTATGGT
Found at i:12245355 original size:184 final size:182
Alignment explanation
Indices: 12245044--12245522 Score: 715
Period size: 184 Copynumber: 2.6 Consensus size: 182
12245034 ATCTATGAGT
* * * *
12245044 GAAATATCTATTGATAGATTTTACATATATCGATAGATACCGTATCATCTTTCAAGCATACGAAA
1 GAAATATCTATCGATAGATTTTAAATATATCGATAGATGCCGTTTCATC-TTCAAGCATACGAAA
12245109 TATCTATCAATAGATTTTAAATATATCGATAGATGTCGTTTCATCTTCCAAGCATACGAAATATC
65 TATCTATCAATAGATTTTAAATATATCGATAGATGTCGTTTCATCTTCCAAGCATACGAAATATC
* * ** * *
12245174 TATTGATAGATTTTAAATATATCGATAAGATGCTGTTTCATCTTTCAAGCATAC
130 TATCGATAGATGTTAAATATATCGAT-AGATGCCCTTTCACCTTCCAAGCATAC
*
12245228 GAAATATCTATCGATAGATTTTAAATATATCGATAGATGTCGTTTCATCTTCCAAGCATACGAAA
1 GAAATATCTATCGATAGATTTTAAATATATCGATAGATGCCGTTTCATCTT-CAAGCATACGAAA
** * *
12245293 TATCTATTGATAGATTTTAAATATATCGATAGATGCCGTTTCATCTTCCAAGCATGCGAAATATC
65 TATCTATCAATAGATTTTAAATATATCGATAGATGTCGTTTCATCTTCCAAGCATACGAAATATC
* *
12245358 TATCGATAGATGTTAAATATATTGATAGATGCCCTTTCACCTTCCAAGCATAT
130 TATCGATAGATGTTAAATATATCGATAGATGCCCTTTCACCTTCCAAGCATAC
* **
12245411 GAAATATCTATCGATAGATTTTAAATATATCGATAGATGCCCTTTCATCTTCAAGCATACGCCTA
1 GAAATATCTATCGATAGATTTTAAATATATCGATAGATGCCGTTTCATCTTCAAGCATACG-AAA
* * *
12245476 CAACTATCAATAGATTTTAAATATATTGATAGATGTCGTTTCATCTT
65 TATCTATCAATAGATTTTAAATATATCGATAGATGTCGTTTCATCTT
12245523 TTAGCAAATG
Statistics
Matches: 266, Mismatches: 27, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
182 10 0.04
183 115 0.43
184 141 0.53
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (182 bp):
GAAATATCTATCGATAGATTTTAAATATATCGATAGATGCCGTTTCATCTTCAAGCATACGAAAT
ATCTATCAATAGATTTTAAATATATCGATAGATGTCGTTTCATCTTCCAAGCATACGAAATATCT
ATCGATAGATGTTAAATATATCGATAGATGCCCTTTCACCTTCCAAGCATAC
Found at i:12245554 original size:61 final size:61
Alignment explanation
Indices: 12245044--12245522 Score: 699
Period size: 61 Copynumber: 7.8 Consensus size: 61
12245034 ATCTATGAGT
* * * * *
12245044 GAAATATCTATTGATAGATTTTACATATATCGATAGATACCGTATCATCTTTCAAGCATAC
1 GAAATATCTATCGATAGATTTTAAATATATCGATAGATGCCGTTTCATCTTCCAAGCATAC
* *
12245105 GAAATATCTATCAATAGATTTTAAATATATCGATAGATGTCGTTTCATCTTCCAAGCATAC
1 GAAATATCTATCGATAGATTTTAAATATATCGATAGATGCCGTTTCATCTTCCAAGCATAC
* * *
12245166 GAAATATCTATTGATAGATTTTAAATATATCGATAAGATGCTGTTTCATCTTTCAAGCATAC
1 GAAATATCTATCGATAGATTTTAAATATATCGAT-AGATGCCGTTTCATCTTCCAAGCATAC
*
12245228 GAAATATCTATCGATAGATTTTAAATATATCGATAGATGTCGTTTCATCTTCCAAGCATAC
1 GAAATATCTATCGATAGATTTTAAATATATCGATAGATGCCGTTTCATCTTCCAAGCATAC
* *
12245289 GAAATATCTATTGATAGATTTTAAATATATCGATAGATGCCGTTTCATCTTCCAAGCATGC
1 GAAATATCTATCGATAGATTTTAAATATATCGATAGATGCCGTTTCATCTTCCAAGCATAC
* * * * *
12245350 GAAATATCTATCGATAGATGTTAAATATATTGATAGATGCCCTTTCACCTTCCAAGCATAT
1 GAAATATCTATCGATAGATTTTAAATATATCGATAGATGCCGTTTCATCTTCCAAGCATAC
*
12245411 GAAATATCTATCGATAGATTTTAAATATATCGATAGATGCCCTTTCATCTT-CAAGCATAC
1 GAAATATCTATCGATAGATTTTAAATATATCGATAGATGCCGTTTCATCTTCCAAGCATAC
** * * * * *
12245471 GCCTACAACTATCAATAGATTTTAAATATATTGATAGATGTCGTTTCATCTT
1 G-AAATATCTATCGATAGATTTTAAATATATCGATAGATGCCGTTTCATCTT
12245523 TTAGCAAATG
Statistics
Matches: 378, Mismatches: 38, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
60 9 0.02
61 312 0.83
62 57 0.15
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (61 bp):
GAAATATCTATCGATAGATTTTAAATATATCGATAGATGCCGTTTCATCTTCCAAGCATAC
Found at i:12247781 original size:23 final size:23
Alignment explanation
Indices: 12247755--12247806 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
12247745 ATAATAAATG
12247755 AGTCATGCAATCCCATATCAACT
1 AGTCATGCAATCCCATATCAACT
* * *
12247778 AGTCACGCGATTCCATATCAACT
1 AGTCATGCAATCCCATATCAACT
12247801 AGTCAT
1 AGTCAT
12247807 TCGATTCCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.27
Consensus pattern (23 bp):
AGTCATGCAATCCCATATCAACT
Found at i:12247811 original size:23 final size:23
Alignment explanation
Indices: 12247767--12247817 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
12247757 TCATGCAATC
12247767 CCATATCAACTAGTCACGCGATT
1 CCATATCAACTAGTCACGCGATT
**
12247790 CCATATCAACTAGTCATTCGATT
1 CCATATCAACTAGTCACGCGATT
12247813 CCATA
1 CCATA
12247818 ACAAGTGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.29
Consensus pattern (23 bp):
CCATATCAACTAGTCACGCGATT
Found at i:12248030 original size:23 final size:23
Alignment explanation
Indices: 12248004--12248070 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
12247994 ACTCAATATC
*
12248004 AACTAGTAACGCGATTCCATAAT
1 AACTAGTAACACGATTCCATAAT
* *
12248027 AACTAGTCACATGATTCCATAAT
1 AACTAGTAACACGATTCCATAAT
* * *
12248050 AACTACTAACACCACTCCATA
1 AACTAGTAACACGATTCCATA
12248071 TTTACTACTC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.25
Consensus pattern (23 bp):
AACTAGTAACACGATTCCATAAT
Found at i:12250422 original size:12 final size:12
Alignment explanation
Indices: 12250405--12250482 Score: 59
Period size: 12 Copynumber: 6.5 Consensus size: 12
12250395 TAAGGATGAG
12250405 GAGGAGCAGCAT
1 GAGGAGCAGCAT
12250417 GAGGAGTCA-CAT
1 GAGGAG-CAGCAT
* * * * *
12250429 TAGTAGTAGTAA
1 GAGGAGCAGCAT
12250441 GAGGAGCAGCAT
1 GAGGAGCAGCAT
* *
12250453 GAGAAACAGCAT
1 GAGGAGCAGCAT
* *
12250465 GAAGAGCCGCAT
1 GAGGAGCAGCAT
12250477 GAGGAG
1 GAGGAG
12250483 AATCAGGCTC
Statistics
Matches: 47, Mismatches: 17, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
11 1 0.02
12 44 0.94
13 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.36, T:0.13
Consensus pattern (12 bp):
GAGGAGCAGCAT
Found at i:12251908 original size:20 final size:17
Alignment explanation
Indices: 12251884--12251932 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 17
12251874 GTTACTTTTC
12251884 AGTTAGTTATTTTAATTTT
1 AGTTA-TTATTTTAA-TTT
*
12251903 ATGTTATTCCTTTTAATTT
1 A-GTTATT-ATTTTAATTT
12251922 AGTTATTATTT
1 AGTTATTATTT
12251933 ATTAGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 3 0.12
18 6 0.23
19 7 0.27
20 10 0.38
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.63
Consensus pattern (17 bp):
AGTTATTATTTTAATTT
Found at i:12253779 original size:23 final size:23
Alignment explanation
Indices: 12253753--12253821 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
12253743 TCACACAATA
* *
12253753 ACCTATAAACCAGTCACGCAAAG
1 ACCTATCAATCAGTCACGCAAAG
* *
12253776 ACCTATCAATTAGTCACGTAAAG
1 ACCTATCAATCAGTCACGCAAAG
* *
12253799 ATCTATCAATCAGTCACACAAAG
1 ACCTATCAATCAGTCACGCAAAG
12253822 TTTAACCTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.20
Consensus pattern (23 bp):
ACCTATCAATCAGTCACGCAAAG
Found at i:12269002 original size:22 final size:22
Alignment explanation
Indices: 12268949--12269005 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
12268939 TTTACTGTAA
12268949 TTAATAATATTTTCATCAAAAT
1 TTAATAATATTTTCATCAAAAT
** * *
12268971 ACAA-ATATATTTTCATTATAAT
1 TTAATA-ATATTTTCATCAAAAT
12268993 TTAATAATATTTT
1 TTAATAATATTTT
12269006 GTATTAGAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAATAATATTTTCATCAAAAT
Found at i:12269634 original size:22 final size:20
Alignment explanation
Indices: 12269595--12269656 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
12269585 TCTTTTAATA
*
12269595 TAATTTTTTAATATTTATTT
1 TAATTTTTTAATATTTATAT
*
12269615 TAATTTTTTACCTATATTATA-
1 TAATTTTTTA-ATAT-TTATAT
*
12269636 TAA-ATTTTAATATCTTATAT
1 TAATTTTTTAATAT-TTATAT
12269656 T
1 T
12269657 TTATTTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 8 0.24
20 16 0.47
21 6 0.18
22 4 0.12
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
TAATTTTTTAATATTTATAT
Found at i:12269663 original size:5 final size:5
Alignment explanation
Indices: 12269653--12269711 Score: 52
Period size: 5 Copynumber: 12.4 Consensus size: 5
12269643 TAATATCTTA
* * * * *
12269653 TATTT TATTT TATTT TAATT TAATT T-TTA TATAT TA-TA TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
12269701 T-TTT TATTT TA
1 TATTT TATTT TA
12269712 ATTATAATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
4 8 0.19
5 35 0.81
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (5 bp):
TATTT
Found at i:12269690 original size:36 final size:37
Alignment explanation
Indices: 12269638--12269721 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
12269628 ATATTATATA
*
12269638 AATTTTAATAT-CT-TATATTTTATTTTATTTTAATTT
1 AATTTTAATATATTATATATTTTATTTT-TTTTAATTT
* *
12269674 AATTTTTATATATTATATATTTTATTTTTTTTATTTT
1 AATTTTAATATATTATATATTTTATTTTTTTTAATTT
*
12269711 AATTATAATAT
1 AATTTTAATAT
12269722 TACAAAATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 10 0.24
37 18 0.44
38 13 0.32
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (37 bp):
AATTTTAATATATTATATATTTTATTTTTTTTAATTT
Found at i:12269732 original size:38 final size:38
Alignment explanation
Indices: 12269652--12269734 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 38
12269642 TTAATATCTT
* * ** *
12269652 ATATTTTATTTTATTTTAATTTAATTTTTATATATTAT
1 ATATTTTATTTTATTTTAATTTAATTATAATATACAAA
*
12269690 ATATTTTATTTT-TTTTATTTTAATTATAATATTACAAA
1 ATATTTTATTTTATTTTAATTTAATTATAATA-TACAAA
12269728 ATATTTT
1 ATATTTT
12269735 TAACAAAGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 16 0.42
38 22 0.58
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (38 bp):
ATATTTTATTTTATTTTAATTTAATTATAATATACAAA
Found at i:12273735 original size:2 final size:2
Alignment explanation
Indices: 12273728--12273755 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12273718 AGACACTTAA
12273728 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12273756 AGTGTGTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:12282386 original size:92 final size:92
Alignment explanation
Indices: 12282226--12282408 Score: 330
Period size: 92 Copynumber: 2.0 Consensus size: 92
12282216 TGGATTACTC
*
12282226 AATCCAAGGCATTTGTGAGAGTATAGGACTTCAATTTAGCATATTTAGTAGCAACTTGGAAGGCA
1 AATCCAAGGCATTTGTGAGAGTATAGGACTTCAATTTAGCATATTTAGTAGCAACTTGGAAGGAA
*
12282291 AATATGACCTCCAACCACCTTGATAAT
66 AATATGACCTCCAACCACCTCGATAAT
* *
12282318 AATCCAAGGCATTTGTGATAGTATAGGACTTCAATTTAGCGTATTTAGTAGCAACTTGGAAGGAA
1 AATCCAAGGCATTTGTGAGAGTATAGGACTTCAATTTAGCATATTTAGTAGCAACTTGGAAGGAA
12282383 AATATGACCTCCAACCACCTCGATAA
66 AATATGACCTCCAACCACCTCGATAA
12282409 CATCTTTCAA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 87 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (92 bp):
AATCCAAGGCATTTGTGAGAGTATAGGACTTCAATTTAGCATATTTAGTAGCAACTTGGAAGGAA
AATATGACCTCCAACCACCTCGATAAT
Found at i:12289285 original size:36 final size:37
Alignment explanation
Indices: 12289236--12289305 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
12289226 CAAACAGCTC
* *
12289236 AATACAATACC-TTTTATGGATCAAGCATAACCATAT
1 AATACAATACCTTTTTATGGATAAAGCACAACCATAT
* *
12289272 AATACAATGCCTTTTTATGGTTAAAGCACAACCA
1 AATACAATACCTTTTTATGGATAAAGCACAACCA
12289306 CTCTACCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 10 0.34
37 19 0.66
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (37 bp):
AATACAATACCTTTTTATGGATAAAGCACAACCATAT
Found at i:12289326 original size:32 final size:30
Alignment explanation
Indices: 12289281--12289339 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
12289271 TAATACAATG
12289281 CCTTTTTATGGTTAAAGCACAACCACTCTA
1 CCTTTTTATGGTTAAAGCACAACCACTCTA
* *
12289311 CCTTTTCTATTGGTTAAAGTATAACCACT
1 CCTTTT-TA-TGGTTAAAGCACAACCACT
12289340 TGAGCAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 2 0.08
32 17 0.68
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (30 bp):
CCTTTTTATGGTTAAAGCACAACCACTCTA
Found at i:12289889 original size:21 final size:20
Alignment explanation
Indices: 12289852--12289895 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
12289842 GACCATTTTG
*
12289852 TTAAAAATATATTGATACAT
1 TTAAAAATATATCGATACAT
* *
12289872 TTAAGAAATGTATCGATACTT
1 TTAA-AAATATATCGATACAT
12289893 TTA
1 TTA
12289896 GGTCAGTCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (20 bp):
TTAAAAATATATCGATACAT
Found at i:12296622 original size:12 final size:11
Alignment explanation
Indices: 12296600--12296637 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
12296590 TTTAAATTAA
12296600 AATATTAAAAAT
1 AATA-TAAAAAT
12296612 AATGATAAAAAT
1 AAT-ATAAAAAT
12296624 AATA-AAAAAT
1 AATATAAAAAT
12296634 AATA
1 AATA
12296638 AATTTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.40
11 1 0.04
12 13 0.52
13 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:12296633 original size:10 final size:10
Alignment explanation
Indices: 12296606--12296639 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
12296596 TTAAAATATT
12296606 AAAAATAATGA
1 AAAAATAAT-A
12296617 TAAAAATAATA
1 -AAAAATAATA
12296628 AAAAATAATA
1 AAAAATAATA
12296638 AA
1 AA
12296640 TTTAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 1 0.05
12 9 0.41
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (10 bp):
AAAAATAATA
Found at i:12296766 original size:18 final size:18
Alignment explanation
Indices: 12296734--12296768 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12296724 ATGAACTTCA
*
12296734 TTCAACTTCTTTTGATGT
1 TTCAACTTCTCTTGATGT
*
12296752 TTCAACTTGTCTTGATG
1 TTCAACTTCTCTTGATG
12296769 CTTAAGGATT
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:0.17, C:0.17, G:0.14, T:0.51
Consensus pattern (18 bp):
TTCAACTTCTCTTGATGT
Found at i:12302753 original size:2 final size:2
Alignment explanation
Indices: 12302746--12302777 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
12302736 CTACTCCAAT
12302746 TA TA TA TA TA TA TA TA -A T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12302778 ATTATCCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12302766 original size:18 final size:18
Alignment explanation
Indices: 12302743--12302777 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
12302733 TGTCTACTCC
12302743 AATTATATATATATATAT
1 AATTATATATATATATAT
12302761 AATTATATATATATATA
1 AATTATATATATATATA
12302778 ATTATCCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTATATATATATATAT
Found at i:12302769 original size:16 final size:16
Alignment explanation
Indices: 12302748--12302782 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
12302738 ACTCCAATTA
12302748 TATATATATATATAAT
1 TATATATATATATAAT
12302764 TATATATATATATAAT
1 TATATATATATATAAT
12302780 TAT
1 TAT
12302783 CCAATCATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATATATATATATAAT
Found at i:12309290 original size:31 final size:32
Alignment explanation
Indices: 12309233--12309296 Score: 105
Period size: 31 Copynumber: 2.0 Consensus size: 32
12309223 CACAACTTTA
12309233 TGAAGATAATAAAAAAACAGACTTGTATATTC
1 TGAAGATAATAAAAAAACAGACTTGTATATTC
12309265 NTGAAGATAAT-AAAAAACAGA-TTGTATATTC
1 -TGAAGATAATAAAAAAACAGACTTGTATATTC
12309296 T
1 T
12309297 TTGGAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 1 0.03
31 10 0.32
32 10 0.32
33 10 0.32
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.30
Consensus pattern (32 bp):
TGAAGATAATAAAAAAACAGACTTGTATATTC
Found at i:12309651 original size:17 final size:16
Alignment explanation
Indices: 12309629--12309673 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
12309619 TTTTATTAAT
*
12309629 TATTTTTTACTTTTCTA
1 TATTTTTTAATTTT-TA
12309646 TATTTTTTAATTTTTA
1 TATTTTTTAATTTTTA
12309662 TATATTTTTAAT
1 TAT-TTTTTAAT
12309674 ATAATTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTTTAATTTTTA
Found at i:12309660 original size:18 final size:17
Alignment explanation
Indices: 12309629--12309670 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
12309619 TTTTATTAAT
*
12309629 TATTTTTTACTTTTCTA
1 TATTTTTTACTTTTATA
*
12309646 TATTTTTTAATTTTTATA
1 TATTTTTT-ACTTTTATA
12309664 TATTTTT
1 TATTTTT
12309671 AATATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTTTTACTTTTATA
Found at i:12313661 original size:3 final size:3
Alignment explanation
Indices: 12313647--12313684 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
12313637 TATGGATCTA
*
12313647 AAT AAA AAT AAT AAT AAT AAAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
12313685 ATAAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:12313670 original size:13 final size:13
Alignment explanation
Indices: 12313647--12313680 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
12313637 TATGGATCTA
12313647 AATAA-AAATAAT
1 AATAATAAATAAT
12313659 AATAATAAATAAT
1 AATAATAAATAAT
12313672 AATAATAAA
1 AATAATAAA
12313681 ATAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:12313678 original size:22 final size:22
Alignment explanation
Indices: 12313647--12313692 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
12313637 TATGGATCTA
12313647 AATAAAAATAATAAT-AATAAAT
1 AATAAAAATAA-AATAAATAAAT
*
12313669 AATAATAATAAAATAAATAAAT
1 AATAAAAATAAAATAAATAAAT
12313691 AA
1 AA
12313693 ATTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (22 bp):
AATAAAAATAAAATAAATAAAT
Found at i:12313691 original size:16 final size:18
Alignment explanation
Indices: 12313645--12313724 Score: 69
Period size: 19 Copynumber: 4.4 Consensus size: 18
12313635 GATATGGATC
12313645 TAAATAAAAATAATAATAA
1 TAAAT-AAAATAATAATAA
12313664 TAAATAATAATAATAA-AA
1 TAAATAA-AATAATAATAA
*
12313682 TAAAT-AAATAA-ATTTAA
1 TAAATAAAATAATA-ATAA
*
12313699 AAAATAACAA-AATAATATA
1 TAAATAA-AATAATAATA-A
12313718 TAAATAA
1 TAAATAA
12313725 GGTGATAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
15 1 0.02
16 5 0.10
17 7 0.14
18 14 0.28
19 23 0.46
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAATAAAATAATAATAA
Found at i:12327217 original size:3 final size:3
Alignment explanation
Indices: 12327203--12327240 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
12327193 TATGGATCTA
*
12327203 AAT AAA AAT AAT AAT AAT AAAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
12327241 ATAAATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:12327226 original size:13 final size:13
Alignment explanation
Indices: 12327203--12327236 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
12327193 TATGGATCTA
12327203 AATAA-AAATAAT
1 AATAATAAATAAT
12327215 AATAATAAATAAT
1 AATAATAAATAAT
12327228 AATAATAAA
1 AATAATAAA
12327237 ATAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:12327234 original size:22 final size:22
Alignment explanation
Indices: 12327203--12327249 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
12327193 TATGGATCTA
12327203 AATAAAAATAATAAT-AATAAAT
1 AATAAAAATAA-AATAAATAAAT
*
12327225 AATAATAATAAAATAAATAAAT
1 AATAAAAATAAAATAAATAAAT
12327247 AAT
1 AAT
12327250 TCAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
AATAAAAATAAAATAAATAAAT
Found at i:12327247 original size:19 final size:20
Alignment explanation
Indices: 12327201--12327249 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
12327191 GATATGGATC
12327201 TAAATAAA-AATAATAATAA
1 TAAATAAATAATAATAATAA
12327220 TAAAT-AATAATAATAA-AA
1 TAAATAAATAATAATAATAA
12327238 TAAATAAATAAT
1 TAAATAAATAAT
12327250 TCAAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAATAAATAATAATAATAA
Found at i:12333904 original size:21 final size:21
Alignment explanation
Indices: 12333867--12333923 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
12333857 ATGCAAAGAA
* *
12333867 CCTCATCGAGTAGCTGACTAT
1 CCTCATCAAGCAGCTGACTAT
** *
12333888 CCTTGTCAAGCAGCTGACTGT
1 CCTCATCAAGCAGCTGACTAT
12333909 CCTCATCAAGCAGCT
1 CCTCATCAAGCAGCT
12333924 CTCAGTGCGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (21 bp):
CCTCATCAAGCAGCTGACTAT
Found at i:12336758 original size:17 final size:18
Alignment explanation
Indices: 12336727--12336760 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12336717 ATATAAGTTA
12336727 ATTATTAATTGATATTTG
1 ATTATTAATTGATATTTG
*
12336745 ATTA-TAATTTATATTT
1 ATTATTAATTGATATTT
12336761 ATTTTCAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (18 bp):
ATTATTAATTGATATTTG
Found at i:12340586 original size:7 final size:7
Alignment explanation
Indices: 12340569--12340754 Score: 77
Period size: 7 Copynumber: 27.4 Consensus size: 7
12340559 ATGTCATATA
12340569 TTTTA-T
1 TTTTATT
12340575 TTTTATT
1 TTTTATT
12340582 TTTTA-T
1 TTTTATT
* *
12340588 TATAATT
1 TTTTATT
* *
12340595 TTATATA
1 TTTTATT
12340602 TTTTA-T
1 TTTTATT
12340608 TTTTATT
1 TTTTATT
*
12340615 TTTT-TAA
1 TTTTAT-T
* *
12340622 TATAATT
1 TTTTATT
*
12340629 TTTTATA
1 TTTTATT
*
12340636 TTTTATA
1 TTTTATT
12340643 TTTTA-T
1 TTTTATT
*
12340649 ATTTATT
1 TTTTATT
12340656 TTTTA-T
1 TTTTATT
* *
12340662 CTATATT
1 TTTTATT
* * *
12340669 ATATAAAT
1 -TTTTATT
*
12340677 TTTAATT
1 TTTTATT
*
12340684 TTTTATA
1 TTTTATT
12340691 TTTTA--
1 TTTTATT
12340696 TTTTA-T
1 TTTTATT
*
12340702 TTTAATT
1 TTTTATT
12340709 TTTTA-T
1 TTTTATT
*
12340715 TTTTATA
1 TTTTATT
*
12340722 TTATATAT
1 TTTTAT-T
12340730 TTTTATT
1 TTTTATT
*
12340737 TTAATATT
1 TT-TTATT
12340745 TTTTATT
1 TTTTATT
12340752 TTT
1 TTT
12340755 ATTATAACGT
Statistics
Matches: 130, Mismatches: 37, Indels: 25
0.68 0.19 0.13
Matches are distributed among these distances:
5 5 0.04
6 33 0.25
7 78 0.60
8 14 0.11
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTATT
Found at i:12340601 original size:10 final size:9
Alignment explanation
Indices: 12340572--12340756 Score: 60
Period size: 8 Copynumber: 20.9 Consensus size: 9
12340562 TCATATATTT
12340572 TATTTT-TA
1 TATTTTATA
*
12340580 TTTTTTATTA
1 TATTTTA-TA
12340590 TAATTTTATA
1 T-ATTTTATA
12340600 TA-TTT-TA
1 TATTTTATA
12340607 T-TTTTAT-
1 TATTTTATA
*
12340614 TTTTTTAATA
1 TATTTT-ATA
*
12340624 TAATTTTTTA
1 T-ATTTTATA
12340634 TATTTTATA
1 TATTTTATA
12340643 T-TTTATATTTA
1 TATTT-TA--TA
*
12340654 TTTTTTATCTA
1 TATTTTA--TA
*
12340665 TATTATATA
1 TATTTTATA
*
12340674 AATTTTA-A
1 TATTTTATA
12340682 T-TTTT-TA
1 TATTTTATA
*
12340689 TATTTTATTT
1 TATTTTA-TA
12340699 TATTTTA-A
1 TATTTTATA
12340707 T-TTTT-TA
1 TATTTTATA
12340714 T-TTTTATA
1 TATTTTATA
*
12340722 TTATATATT-TT
1 -TAT-T-TTATA
12340733 TATTTTA-A
1 TATTTTATA
*
12340741 TATTTTTTA
1 TATTTTATA
12340750 T-TTTTAT
1 TATTTTAT
12340757 TATAACGTTA
Statistics
Matches: 135, Mismatches: 17, Indels: 50
0.67 0.08 0.25
Matches are distributed among these distances:
7 23 0.17
8 37 0.27
9 24 0.18
10 22 0.16
11 24 0.18
12 5 0.04
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.72
Consensus pattern (9 bp):
TATTTTATA
Found at i:12340626 original size:34 final size:34
Alignment explanation
Indices: 12340564--12340648 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 34
12340554 TTTTAATGTC
*
12340564 ATATATTTTATTTTTA-TTTTTTATTATAATTTT
1 ATATATTTTATTTTTATTTTTTTAATATAATTTT
12340597 ATATATTTTATTTTTATTTTTTTAATATAATTTT
1 ATATATTTTATTTTTATTTTTTTAATATAATTTT
*
12340631 TTATATTTTATATTTTAT
1 ATATATTTTAT-TTTTAT
12340649 ATTTATTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 16 0.33
34 26 0.54
35 6 0.12
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (34 bp):
ATATATTTTATTTTTATTTTTTTAATATAATTTT
Found at i:12340646 original size:74 final size:73
Alignment explanation
Indices: 12340502--12340738 Score: 207
Period size: 74 Copynumber: 3.2 Consensus size: 73
12340492 AAATTTAATA
* * * * * *
12340502 TATTTATATTTTTTATTATTAATTTT-TATA---TAATATCATTTTTTAAATAT-ATTTTTAATG
1 TATTTTTATTTTTTATTA-TAATTTTATATATTTTATTTTTATTTTTTTAATATAATTTTTTAT-
**
12340562 TCATATATTT
64 TTTTATATTT
12340572 TATTTTTATTTTTTATTATAATTTTATATATTTTATTTTTATTTTTTTAATATAATTTTTTATAT
1 TATTTTTATTTTTTATTATAATTTTATATATTTTATTTTTATTTTTTTAATATAATTTTTTAT-T
12340637 TTTATATTT
65 TTTATATTT
* * * * *
12340646 TATATTTATTTTTTATCTAT-ATTATATAAATTTTAATTTTTTATATTTTATTTTATTTTAATTT
1 TATTTTTATTTTTTAT-TATAATTTTATATATTTT-A--TTTT-TA-TTT-TTTTAATATAATTT
12340710 TTTATTTTTATATTAT
59 TTTATTTTTATATT-T
12340726 ATATTTTTATTTT
1 -TATTTTTATTTT
12340739 AATATTTTTT
Statistics
Matches: 138, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
69 7 0.05
70 21 0.15
73 16 0.12
74 43 0.31
75 4 0.03
77 4 0.03
78 2 0.01
79 12 0.09
80 18 0.13
81 11 0.08
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (73 bp):
TATTTTTATTTTTTATTATAATTTTATATATTTTATTTTTATTTTTTTAATATAATTTTTTATTT
TTATATTT
Found at i:12340650 original size:48 final size:48
Alignment explanation
Indices: 12340598--12340757 Score: 134
Period size: 48 Copynumber: 3.4 Consensus size: 48
12340588 TATAATTTTA
12340598 TATATTTTATTTTTATTTTTTTAATATAATTTTTTATATTTTATATTT
1 TATATTTTATTTTTATTTTTTTAATATAATTTTTTATATTTTATATTT
* * * * *
12340646 TATA-TTTATTTTTTATCTATATT-ATATAAATTTTAATTTTTTATA-TT
1 TATATTTTA-TTTTTAT-TTTTTTAATATAATTTTTTATATTTTATATTT
* * * * * *
12340693 T-TATTTTA-TTTTAATTTTTTATTTTTATATTATATATTTT-TATTT
1 TATATTTTATTTTTATTTTTTTAATATAATTTTTTATATTTTATATTT
12340738 TAATATTTTTTATTTTTATT
1 T-ATA--TTTTATTTTTATT
12340758 ATAACGTTAT
Statistics
Matches: 85, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
44 6 0.07
45 19 0.22
46 2 0.02
47 13 0.15
48 30 0.35
49 9 0.11
50 6 0.07
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.72
Consensus pattern (48 bp):
TATATTTTATTTTTATTTTTTTAATATAATTTTTTATATTTTATATTT
Found at i:12340667 original size:114 final size:113
Alignment explanation
Indices: 12340507--12340757 Score: 242
Period size: 114 Copynumber: 2.2 Consensus size: 113
12340497 TAATATATTT
* *
12340507 ATATTTTTTATTATTAATTTTTATATAATATCATTTTTTAAATATATT-T-TTAATGTCATATAT
1 ATATTTTTTATT-TTTA-TTTTATAT--T-T-ATTTTTTAAATATATTATATAAATGTCA-ATAT
* *
12340570 TTTAT-TTTTATTTTTTATTATAATTTTATATATTTTAT-TTTTATTTTTTTAATATA
59 TTTATATTTTA--TTTTATTATAATTTTATAT-TTTTATATTATATATTTTTAATATA
** * * *
12340626 AT-TTTTTATATTTTATATTTTATATTTATTTTTTATCTATATTATATAAATTTTAATTTTTTAT
1 ATATTTTT-TATTTT-TATTTTATATTTATTTTTTAAATATATTATATAAATGTCAATATTTTAT
* * * *
12340690 ATTTTATTTTATTTTAATTTTTTATTTTTATATTATATATTTTTATTTTA
64 ATTTTATTTTATTATAATTTTATATTTTTATATTATATATTTTTAATATA
12340740 ATATTTTTTATTTTTATT
1 ATATTTTTTATTTTTATT
12340758 ATAACGTTAT
Statistics
Matches: 112, Mismatches: 13, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
113 10 0.09
114 53 0.47
115 15 0.13
116 12 0.11
118 15 0.13
119 7 0.06
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (113 bp):
ATATTTTTTATTTTTATTTTATATTTATTTTTTAAATATATTATATAAATGTCAATATTTTATAT
TTTATTTTATTATAATTTTATATTTTTATATTATATATTTTTAATATA
Found at i:12340695 original size:55 final size:54
Alignment explanation
Indices: 12340624--12340757 Score: 154
Period size: 53 Copynumber: 2.5 Consensus size: 54
12340614 TTTTTTAATA
12340624 TAATTTTTTATATTTTATATTTTATATTT-ATTTTTTA-TCTATATTATATAAATTT
1 TAATTTTTTATATTTT-TATTTTATATTTAATTTTTTATTCTATATTATAT--ATTT
*
12340679 TAATTTTTTATA-TTTTATTTTAT-TTTAATTTTTTATTTTTATATTATATATTT
1 TAATTTTTTATATTTTTATTTTATATTTAATTTTTTA-TTCTATATTATATATTT
* *
12340732 TTA-TTTTAATATTTTTTATTTT-TATT
1 TAATTTTTTATA-TTTTTATTTTATATT
12340758 ATAACGTTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 13
0.81 0.03 0.15
Matches are distributed among these distances:
52 10 0.14
53 23 0.33
54 14 0.20
55 23 0.33
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.72
Consensus pattern (54 bp):
TAATTTTTTATATTTTTATTTTATATTTAATTTTTTATTCTATATTATATATTT
Found at i:12340739 original size:34 final size:35
Alignment explanation
Indices: 12340551--12340755 Score: 93
Period size: 34 Copynumber: 6.2 Consensus size: 35
12340541 TTTTTAAATA
* **
12340551 TATTTTTAATGTCATATATTTTATTTT-TAT-TTTT
1 TATTTTTAATTTTTTAT-TTTTATTTTATATATTTT
* * *
12340585 TA-TTATAATTTTATATATTTTATTTT-TATTTTTT
1 TATTTTTAATTTTTTAT-TTTTATTTTATATATTTT
* *
12340619 TA-ATATAATTTTTTA----TA-TTT-TATA-TTT
1 TATTTTTAATTTTTTATTTTTATTTTATATATTTT
* * * * *
12340646 TATATTT-ATTTTTTATCTATATTATATAAATTTT
1 TATTTTTAATTTTTTATTTTTATTTTATATATTTT
* * *
12340680 AATTTTTTATATTTTA-TTTTATTTTA-AT-TTTT
1 TATTTTTAATTTTTTATTTTTATTTTATATATTTT
* *
12340712 TATTTTTATATTATATATTTTTATTTTA-ATATTTTT
1 TATTTTTA-ATTTTTTATTTTTATTTTATATA-TTTT
12340748 TATTTTTA
1 TATTTTTA
12340756 TTATAACGTT
Statistics
Matches: 136, Mismatches: 21, Indels: 26
0.74 0.11 0.14
Matches are distributed among these distances:
27 13 0.10
28 9 0.07
29 2 0.01
31 2 0.01
32 12 0.09
33 33 0.24
34 46 0.34
35 7 0.05
36 12 0.09
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (35 bp):
TATTTTTAATTTTTTATTTTTATTTTATATATTTT
Found at i:12340758 original size:34 final size:33
Alignment explanation
Indices: 12340574--12340760 Score: 118
Period size: 34 Copynumber: 5.5 Consensus size: 33
12340564 ATATATTTTA
12340574 TTTTTATTTTTTATTATA-ATTTTATATATTT-TA-
1 TTTTTA-TTTTTATTATATATTTT-TAT-TTTATAT
12340607 TTTTTATTTTT-TTAATATAATTTTTTATATTT-TAT
1 TTTTTATTTTTATT-ATAT-A-TTTTTAT-TTTATAT
* * * * * * * *
12340642 ATTTTATATTTATTTTTTATCTATATTATATAA
1 TTTTTATTTTTATTATATATTTTTATTTTATAT
* * *
12340675 ATTTTAATTTT-TTATATTTTATTTTATTTTA-AT
1 TTTTTATTTTTATTATA-TAT-TTTTATTTTATAT
12340708 TTTTTATTTTTATATTATATATTTTTATTTTAATAT
1 TTTTTA-TTTT-TATTATATATTTTTATTTT-ATAT
12340744 TTTTTATTTTTATTATA
1 TTTTTATTTTTATTATA
12340761 ACGTTATAAA
Statistics
Matches: 120, Mismatches: 20, Indels: 27
0.72 0.12 0.16
Matches are distributed among these distances:
31 2 0.02
32 13 0.11
33 30 0.25
34 37 0.31
35 23 0.19
36 15 0.12
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.72
Consensus pattern (33 bp):
TTTTTATTTTTATTATATATTTTTATTTTATAT
Found at i:12346619 original size:22 final size:22
Alignment explanation
Indices: 12346526--12346623 Score: 63
Period size: 22 Copynumber: 4.4 Consensus size: 22
12346516 AGATTTATAT
*
12346526 ATTTTTATTTTAGATTAAATAA
1 ATTTTTATTTTAAATTAAATAA
* * **
12346548 ATTTTTATAATTAATAATAAATTT
1 ATTTTTAT-TTTAA-ATTAAATAA
* * *** *
12346572 ATTATTATTTGT-TATTTTTTAT
1 ATTTTTATTT-TAAATTAAATAA
12346594 ATTTTTATTTTAAATTAAATAA
1 ATTTTTATTTTAAATTAAATAA
12346616 ATTTTTAT
1 ATTTTTAT
12346624 AACTAACAAT
Statistics
Matches: 53, Mismatches: 19, Indels: 8
0.66 0.24 0.10
Matches are distributed among these distances:
21 1 0.02
22 34 0.64
23 4 0.08
24 14 0.26
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTTTATTTTAAATTAAATAA
Found at i:12346642 original size:83 final size:84
Alignment explanation
Indices: 12346555--12346726 Score: 197
Period size: 83 Copynumber: 2.1 Consensus size: 84
12346545 TAAATTTTTA
** * * * *
12346555 TAATTAATAATAAAT-TTATTATTATTTGTTATTTTTTATATTTTTATTTTAAATTAAATAAATT
1 TAATTAATAATAAATCAAAATATTATTTATTATTTTATATATTTTTATTTCAAATTAAATAAATT
12346619 TTTATAACTAAC-AATAGAT
66 TTTATAACTAACGAATA-AT
** ***
12346638 TAATT-ATCTTTTGTCAAAATATTATTTATTATTTTATATATTTTTATTTCAAATTAAATAAATT
1 TAATTAATAATAAATCAAAATATTATTTATTATTTTATATATTTTTATTTCAAATTAAATAAATT
* *
12346702 TTTATAATTAACGATTAAT
66 TTTATAACTAACGAATAAT
12346721 TAATTA
1 TAATTA
12346727 TTATTTGTCA
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
82 4 0.05
83 66 0.90
84 3 0.04
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.54
Consensus pattern (84 bp):
TAATTAATAATAAATCAAAATATTATTTATTATTTTATATATTTTTATTTCAAATTAAATAAATT
TTTATAACTAACGAATAAT
Found at i:12346670 original size:68 final size:66
Alignment explanation
Indices: 12346525--12346673 Score: 165
Period size: 68 Copynumber: 2.2 Consensus size: 66
12346515 AAGATTTATA
* * * * ***
12346525 TATTTTTATTTTAGATTAAATAAATTTTTATAATTAATAATAAATTTATTATTATTTGTTATTTT
1 TATTTTTATTTTAAATTAAATAAATTTTTATAACTAACAATAAATTAATTATTATTTG-TAAAAT
*
12346590 TT
65 AT
*
12346592 ATATTTTTATTTTAAATTAAATAAATTTTTATAACTAACAATAGATTAATTATCT-TTTGTCAAA
1 -TATTTTTATTTTAAATTAAATAAATTTTTATAACTAACAATAAATTAATTAT-TATTTGT-AAA
12346656 ATAT
63 ATAT
12346660 TATTTATTATTTTA
1 TATTT-TTATTTTA
12346674 TATATTTTTA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
67 6 0.09
68 62 0.90
69 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (66 bp):
TATTTTTATTTTAAATTAAATAAATTTTTATAACTAACAATAAATTAATTATTATTTGTAAAATA
T
Found at i:12346727 original size:83 final size:83
Alignment explanation
Indices: 12346574--12346740 Score: 257
Period size: 83 Copynumber: 2.0 Consensus size: 83
12346564 ATAAATTTAT
* * *
12346574 TATTATTTGTTATTTTTTATATTTTTATTTTAAATTAAATAAATTTTTATAACTAACAATAGATT
1 TATTATTTATTATTTTATATATTTTTATTTCAAATTAAATAAATTTTTATAACTAACAATAGATT
12346639 AATTATCT-TTTGTCAAAA
66 AATTAT-TATTTGTCAAAA
* *
12346657 TATTATTTATTATTTTATATATTTTTATTTCAAATTAAATAAATTTTTATAATTAACGATTA-AT
1 TATTATTTATTATTTTATATATTTTTATTTCAAATTAAATAAATTTTTATAACTAAC-AATAGAT
12346721 TAATTATTATTTGTCAAAA
65 TAATTATTATTTGTCAAAA
12346740 T
1 T
12346741 GTCTCTTATT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
82 1 0.01
83 73 0.95
84 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (83 bp):
TATTATTTATTATTTTATATATTTTTATTTCAAATTAAATAAATTTTTATAACTAACAATAGATT
AATTATTATTTGTCAAAA
Found at i:12360999 original size:15 final size:16
Alignment explanation
Indices: 12360979--12361012 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12360969 TGTTATGTGG
*
12360979 ATTTT-ATTTTTAATA
1 ATTTTAATTTTTAAAA
12360994 ATTTTAATTTTTAAAA
1 ATTTTAATTTTTAAAA
12361010 ATT
1 ATT
12361013 AAAATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAATTTTTAAAA
Found at i:12361698 original size:23 final size:23
Alignment explanation
Indices: 12361668--12361711 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
12361658 AATTAGGAAG
12361668 TATGCATATCAATGCTGAATTCC
1 TATGCATATCAATGCTGAATTCC
12361691 TATGCATATCAATGCTGAATT
1 TATGCATATCAATGCTGAATT
12361712 GCTCATCAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (23 bp):
TATGCATATCAATGCTGAATTCC
Found at i:12372034 original size:26 final size:26
Alignment explanation
Indices: 12371982--12372035 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
12371972 TAATTAGAAC
* * *
12371982 AAGTGAAGAGCTACTTCACGCAGAAT
1 AAGTGAAGAGCTACTTAAAGCAAAAT
12372008 AAGTGAAGTA-CTACTTAAAGCAAAAT
1 AAGTGAAG-AGCTACTTAAAGCAAAAT
12372034 AA
1 AA
12372036 TTAGAAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.20
Consensus pattern (26 bp):
AAGTGAAGAGCTACTTAAAGCAAAAT
Found at i:12372314 original size:29 final size:28
Alignment explanation
Indices: 12372281--12372362 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 28
12372271 TCTTATCTTG
* *
12372281 TTCTCGTGTACTTATTCATGTACAGCTTA
1 TTCTCTTGTACCTATTC-TGTACAGCTTA
*
12372310 TTCTCTTGTACCTATTCTCGTACAGCTTC
1 TTCTCTTGTACCTATTCT-GTACAGCTTA
12372339 TTCTCTTGTACCTATTCTTGTACA
1 TTCTCTTGTACCTATTC-TGTACA
12372363 CCTCTTTTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
28 1 0.02
29 46 0.96
30 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.11, T:0.46
Consensus pattern (28 bp):
TTCTCTTGTACCTATTCTGTACAGCTTA
Found at i:12384537 original size:3 final size:3
Alignment explanation
Indices: 12384529--12384577 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
12384519 AATTATAAAT
*
12384529 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT- TTA TT- TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12384574 TTA T
1 TTA T
12384578 ATGCAATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 5 0.12
3 36 0.88
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12385670 original size:41 final size:41
Alignment explanation
Indices: 12385625--12385762 Score: 135
Period size: 41 Copynumber: 3.5 Consensus size: 41
12385615 GTTTTTATGA
* *
12385625 AAAAGATATTAAATATTATTGCATAATCAGTAAAATATTAC
1 AAAAGATATTAAATATTATTGCATAATCAATCAAATATTAC
* * *
12385666 AAAAGATATTGACATA--A---AAAAATGCAATCAAATATTAC
1 AAAAGATATT-AAATATTATTGCATAAT-CAATCAAATATTAC
* * *
12385704 GAAAGATATTAAATATTATTGCATAATTAATCATATATTAC
1 AAAAGATATTAAATATTATTGCATAATCAATCAAATATTAC
*
12385745 AAAAGATATT-GATATTAT
1 AAAAGATATTAAATATTAT
12385763 AAAAAAATAT
Statistics
Matches: 77, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
37 8 0.10
38 21 0.27
39 1 0.01
40 8 0.10
41 31 0.40
42 8 0.10
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.33
Consensus pattern (41 bp):
AAAAGATATTAAATATTATTGCATAATCAATCAAATATTAC
Found at i:12385761 original size:18 final size:18
Alignment explanation
Indices: 12385738--12385782 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
12385728 AATTAATCAT
*
12385738 ATATTACAAAAGATATTG
1 ATATTACAAAAAATATTG
*
12385756 ATATTATAAAAAAATATTG
1 ATATTA-CAAAAAATATTG
*
12385775 GTATTACA
1 ATATTACA
12385783 CCTTACACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (18 bp):
ATATTACAAAAAATATTG
Found at i:12386070 original size:26 final size:26
Alignment explanation
Indices: 12386041--12386161 Score: 89
Period size: 26 Copynumber: 4.3 Consensus size: 26
12386031 ACAAAACGAC
12386041 CAAAATAAGTGAAGTGCTACTTCACG
1 CAAAATAAGTGAAGTGCTACTTCACG
*
12386067 CAAAATAATTAGAACAAGTGAAGAGCTACTTCACG
1 CAAAATAAGT-G---AAGT-----GCTACTTCACG
* * *
12386102 CAGAACAAGTGAAGCGCTACTTCACG
1 CAAAATAAGTGAAGTGCTACTTCACG
* * * *
12386128 CAGAATAAGTGAAGTACTACTTAAAG
1 CAAAATAAGTGAAGTGCTACTTCACG
12386154 CAAAATAA
1 CAAAATAA
12386162 TTAGAAAAAG
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
26 48 0.64
27 1 0.01
30 4 0.05
31 3 0.04
34 1 0.01
35 18 0.24
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (26 bp):
CAAAATAAGTGAAGTGCTACTTCACG
Found at i:12386451 original size:29 final size:29
Alignment explanation
Indices: 12386430--12386488 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
12386420 ATTCATGTAT
*
12386430 AGCTTATTCTCTTGTACCTATTTTCGTAC
1 AGCTTATTCTCTTGTACCTATTATCGTAC
* *
12386459 AGCTTCTTCTCTTGTACCTATTATTGTAC
1 AGCTTATTCTCTTGTACCTATTATCGTAC
12386488 A
1 A
12386489 CCCCTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.24, G:0.10, T:0.47
Consensus pattern (29 bp):
AGCTTATTCTCTTGTACCTATTATCGTAC
Found at i:12386726 original size:13 final size:13
Alignment explanation
Indices: 12386708--12386732 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12386698 ACTTGAGAGC
12386708 TTCTCTCTCTAAA
1 TTCTCTCTCTAAA
12386721 TTCTCTCTCTAA
1 TTCTCTCTCTAA
12386733 TTATCTTGTA
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:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCTCTCTCTAAA
Found at i:12389713 original size:26 final size:26
Alignment explanation
Indices: 12389659--12389713 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
12389649 ATGTGACTGG
*
12389659 TTTTTTAGATATGTTTCATAATTGGT
1 TTTTTTAGATATGTTTCATAATTGAT
* *
12389685 TTTTTTAGATATGTTTCATTATTTAT
1 TTTTTTAGATATGTTTCATAATTGAT
12389711 TTT
1 TTT
12389714 ACAGTTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.04, G:0.11, T:0.64
Consensus pattern (26 bp):
TTTTTTAGATATGTTTCATAATTGAT
Found at i:12392654 original size:15 final size:15
Alignment explanation
Indices: 12392620--12392654 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12392610 AATTACTATT
*
12392620 ATATATATACTTTTA
1 ATATATATACTTTAA
*
12392635 GTATATATACTTTAA
1 ATATATATACTTTAA
12392650 ATATA
1 ATATA
12392655 AAAATATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (15 bp):
ATATATATACTTTAA
Found at i:12392903 original size:33 final size:35
Alignment explanation
Indices: 12392854--12392926 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 35
12392844 ATTTGTAATG
* *
12392854 TTTAAGTTGTTGTTTGA-ATA-TT-GTTTTTAGTTA
1 TTTAAGTTGATATTTGAGATATTTAGTTTTTA-TTA
*
12392887 TTTAAGTTGATATTTGAGATATTTATTTTTTATTA
1 TTTAAGTTGATATTTGAGATATTTAGTTTTTATTA
12392922 TTTAA
1 TTTAA
12392927 ATCTAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 15 0.44
34 3 0.09
35 10 0.29
36 6 0.18
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (35 bp):
TTTAAGTTGATATTTGAGATATTTAGTTTTTATTA
Found at i:12394893 original size:35 final size:35
Alignment explanation
Indices: 12394847--12394982 Score: 200
Period size: 35 Copynumber: 3.9 Consensus size: 35
12394837 GAACAACCAG
12394847 AACAAGTGAAGTGCTACTTCACGCAGAATAAGTAA
1 AACAAGTGAAGTGCTACTTCACGCAGAATAAGTAA
* *
12394882 AACAAGTGAAGTGCTACTTCACGTAGAATAAGTAG
1 AACAAGTGAAGTGCTACTTCACGCAGAATAAGTAA
* * * *
12394917 AACAAGTGAAGCGCTACTTCACGCAAAACAACTAA
1 AACAAGTGAAGTGCTACTTCACGCAGAATAAGTAA
* *
12394952 AACAAGTGAAGTGCTACTTAACGTAGAATAA
1 AACAAGTGAAGTGCTACTTCACGCAGAATAA
12394983 CTAGAATAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 88 1.00
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (35 bp):
AACAAGTGAAGTGCTACTTCACGCAGAATAAGTAA
Found at i:12394933 original size:70 final size:70
Alignment explanation
Indices: 12394836--12394988 Score: 234
Period size: 70 Copynumber: 2.2 Consensus size: 70
12394826 TGTTGTACAG
* * * * * *
12394836 AGAACAACCAGAACAAGTGAAGTGCTACTTCACGCAGAATAAGTAAAACAAGTGAAGTGCTACTT
1 AGAATAACTAGAACAAGTGAAGCGCTACTTCACGCAAAACAACTAAAACAAGTGAAGTGCTACTT
*
12394901 CACGT
66 AACGT
*
12394906 AGAATAAGTAGAACAAGTGAAGCGCTACTTCACGCAAAACAACTAAAACAAGTGAAGTGCTACTT
1 AGAATAACTAGAACAAGTGAAGCGCTACTTCACGCAAAACAACTAAAACAAGTGAAGTGCTACTT
12394971 AACGT
66 AACGT
12394976 AGAATAACTAGAA
1 AGAATAACTAGAA
12394989 TAAATAGAAC
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 74 1.00
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.18
Consensus pattern (70 bp):
AGAATAACTAGAACAAGTGAAGCGCTACTTCACGCAAAACAACTAAAACAAGTGAAGTGCTACTT
AACGT
Found at i:12395049 original size:18 final size:18
Alignment explanation
Indices: 12394990--12395061 Score: 56
Period size: 18 Copynumber: 4.1 Consensus size: 18
12394980 TAACTAGAAT
*
12394990 AAATAGAAC-ACTACTCC
1 AAATAGAACAACTACTTC
* * * * *
12395007 ATATGGAACAATTAATGC
1 AAATAGAACAACTACTTC
*
12395025 AAGTAGAACAACTACTTC
1 AAATAGAACAACTACTTC
* *
12395043 AAATAGAATAACCACTTC
1 AAATAGAACAACTACTTC
12395061 A
1 A
12395062 CTTGGATGAC
Statistics
Matches: 40, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
17 7 0.17
18 33 0.82
ACGTcount: A:0.47, C:0.21, G:0.10, T:0.22
Consensus pattern (18 bp):
AAATAGAACAACTACTTC
Found at i:12395272 original size:29 final size:28
Alignment explanation
Indices: 12395240--12395309 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 28
12395230 CTCGTATACT
12395240 TATTCATGTACAACTTATTCTCTTGTACC
1 TATTC-TGTACAACTTATTCTCTTGTACC
* *
12395269 TATTCTCGTACAGCTTCTTCTCTTGTACC
1 TATTCT-GTACAACTTATTCTCTTGTACC
12395298 TATTCTTGTACA
1 TATTC-TGTACA
12395310 CCTCTTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 1 0.03
29 35 0.95
30 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.09, T:0.46
Consensus pattern (28 bp):
TATTCTGTACAACTTATTCTCTTGTACC
Found at i:12396189 original size:102 final size:101
Alignment explanation
Indices: 12396048--12396329 Score: 343
Period size: 102 Copynumber: 2.8 Consensus size: 101
12396038 AAAAAAAAAT
* * * * * *
12396048 TTCATATTCAGCCGCTAGCTTTATCGCTTATATTTTGGCTGTAATTATATTATACTATTGGTCAC
1 TTCACATTCAGCCGCTAGCTTTATCGCTCATATTTTGGCTGTAATGATGTTATGCTATTGGTCGC
*
12396113 AAGCTTTATCGCTTATTCTTTGACCAT-AGTTCATCA
66 AAGCTTTATCGCTTATTCTTTGACCATAAGTTAAT-A
* * * * *
12396149 TTCTTAC-TTCAGCCGCAAGCTTTACCGCTCATATTTTGGCTGCAATGATGTTCTGCTTTTGGTC
1 TTC--ACATTCAGCCGCTAGCTTTATCGCTCATATTTTGGCTGTAATGATGTTATGCTATTGGTC
* *
12396213 GCGAGCTTTATCGCTTATTCTTTGACCATAATTTAATA
64 GCAAGCTTTATCGCTTATTCTTTGACCATAAGTTAATA
* * * *
12396251 TTCACATTCCAGTCGCTAGCTTTATCGCTCATAATTTGACTGTAATGATGTTATGCTATTGGCCG
1 TTCACATT-CAGCCGCTAGCTTTATCGCTCATATTTTGGCTGTAATGATGTTATGCTATTGGTCG
*
12396316 CTAGCTTTATCGCT
65 CAAGCTTTATCGCT
12396330 CATTTCTTGG
Statistics
Matches: 152, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
100 2 0.01
101 5 0.03
102 139 0.91
103 6 0.04
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (101 bp):
TTCACATTCAGCCGCTAGCTTTATCGCTCATATTTTGGCTGTAATGATGTTATGCTATTGGTCGC
AAGCTTTATCGCTTATTCTTTGACCATAAGTTAATA
Found at i:12396437 original size:26 final size:27
Alignment explanation
Indices: 12396401--12396455 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
12396391 AAGGGTTGAA
*
12396401 TTAATCTCCTTCATATCAAGTT-AGAG
1 TTAATCTCCTTCATATAAAGTTGAGAG
* *
12396427 TTAATCTCCTTGATGTAAAGTTGAGAG
1 TTAATCTCCTTCATATAAAGTTGAGAG
12396454 TT
1 TT
12396456 CCCTTTTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (27 bp):
TTAATCTCCTTCATATAAAGTTGAGAG
Found at i:12398144 original size:15 final size:14
Alignment explanation
Indices: 12398118--12398174 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
12398108 AGTGAAGTCC
12398118 ATATAAAAAATAAT
1 ATATAAAAAATAAT
12398132 ATATAATAAAATAAT
1 ATATAA-AAAATAAT
12398147 A-ATAAAATAAATAAT
1 ATAT-AAA-AAATAAT
*
12398162 AAATAAACAAATA
1 ATATAAA-AAATA
12398175 TAAATGATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
14 9 0.24
15 27 0.71
16 2 0.05
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (14 bp):
ATATAAAAAATAAT
Found at i:12398150 original size:11 final size:11
Alignment explanation
Indices: 12398129--12398164 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 11
12398119 TATAAAAAAT
12398129 AATATATAATAA
1 AATA-ATAATAA
12398141 AATAATAATAA
1 AATAATAATAA
12398152 AATAAATAATAA
1 AAT-AATAATAA
12398164 A
1 A
12398165 TAAACAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAATAATAA
Found at i:12398865 original size:17 final size:16
Alignment explanation
Indices: 12398845--12398915 Score: 83
Period size: 15 Copynumber: 4.4 Consensus size: 16
12398835 AATAATAAGG
12398845 AATAAAATAAAAAATAT
1 AATAAAAT-AAAAATAT
*
12398862 AATAATA-AAAAATAT
1 AATAAAATAAAAATAT
12398877 AATAAAATAAAAATAAT
1 AATAAAATAAAAAT-AT
* *
12398894 AATTAAATAATAATA-
1 AATAAAATAAAAATAT
12398909 AATAAAA
1 AATAAAA
12398916 AATAGATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
15 20 0.43
16 7 0.15
17 20 0.43
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AATAAAATAAAAATAT
Found at i:12398868 original size:3 final size:3
Alignment explanation
Indices: 12398835--12398909 Score: 51
Period size: 3 Copynumber: 27.7 Consensus size: 3
12398825 AGGTATAAAA
*
12398835 AAT AAT AAGG AAT AA- AAT AA- AA- AAT -AT AAT AAT AA- AA- AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
12398875 -AT AAT AA- AAT AAA AAT AAT AAT TA- AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12398910 ATAAAAAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
2 17 0.29
3 39 0.67
4 2 0.03
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:12398870 original size:37 final size:35
Alignment explanation
Indices: 12398829--12398919 Score: 96
Period size: 38 Copynumber: 2.5 Consensus size: 35
12398819 AATGTAAGGT
12398829 ATAAAAAATAATAAGGAAT-AAAATAAAAAATATAATA
1 ATAAAAAATAATAA--AATAAAAATAAAAAATA-AATA
* *
12398866 ATAAAAAATATAATAAAATAAAAATAATAATTAAATA
1 AT-AAAAA-ATAATAAAATAAAAATAAAAAATAAATA
*
12398903 ATAATAAATAA-AAAATA
1 ATAAAAAATAATAAAATA
12398920 GATAATTGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
34 6 0.12
35 4 0.08
36 4 0.08
37 11 0.23
38 16 0.33
39 7 0.15
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (35 bp):
ATAAAAAATAATAAAATAAAAATAAAAAATAAATA
Found at i:12398871 original size:14 final size:14
Alignment explanation
Indices: 12398854--12398925 Score: 60
Period size: 14 Copynumber: 5.0 Consensus size: 14
12398844 GAATAAAATA
12398854 AAAAATATAATAAT
1 AAAAATATAATAAT
12398868 AAAAAATATAATAA-
1 -AAAAATATAATAAT
*
12398882 AATAAAAATAATAAT
1 AA-AAATATAATAAT
*
12398897 -TAAATAATAATAAAT
1 AAAAAT-ATAAT-AAT
12398912 AAAAA-ATAGATAAT
1 AAAAATATA-ATAAT
12398926 TGCATTAGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
13 5 0.11
14 21 0.45
15 18 0.38
16 3 0.06
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.26
Consensus pattern (14 bp):
AAAAATATAATAAT
Found at i:12398881 original size:32 final size:31
Alignment explanation
Indices: 12398845--12398919 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
12398835 AATAATAAGG
12398845 AATAAAATAAAAAATATAATAATAAAAAATAT
1 AATAAAATAAAAAATATAATAATAAAAAA-AT
* *
12398877 AATAAAAT--AAAA-ATAATAATTAAATAAT
1 AATAAAATAAAAAATATAATAATAAAAAAAT
12398905 AAT-AAATAAAAAATA
1 AATAAAATAAAAAATA
12398920 GATAATTGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 4 0.11
28 5 0.13
29 16 0.42
30 5 0.13
32 8 0.21
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (31 bp):
AATAAAATAAAAAATATAATAATAAAAAAAT
Found at i:12398918 original size:17 final size:17
Alignment explanation
Indices: 12398849--12398925 Score: 66
Period size: 15 Copynumber: 5.0 Consensus size: 17
12398839 ATAAGGAATA
12398849 AAATAAAAAAT-ATAAT
1 AAATAAAAAATAATAAT
12398865 -AATAAAAAAT-ATAAT
1 AAATAAAAAATAATAAT
12398880 AAA-ATAAAAATAATAAT
1 AAATA-AAAAATAATAAT
12398897 ---T---AAATAATAAT
1 AAATAAAAAATAATAAT
12398908 AAATAAAAAATAGATAAT
1 AAATAAAAAATA-ATAAT
12398926 TGCATTAGCA
Statistics
Matches: 50, Mismatches: 0, Indels: 20
0.71 0.00 0.29
Matches are distributed among these distances:
11 10 0.20
14 1 0.02
15 16 0.32
16 8 0.16
17 10 0.20
18 5 0.10
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.26
Consensus pattern (17 bp):
AAATAAAAAATAATAAT
Found at i:12398925 original size:32 final size:29
Alignment explanation
Indices: 12398835--12398925 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 29
12398825 AGGTATAAAA
**
12398835 AATAATAAGGAATA-AAATAAAAAAT-AT
1 AATAATAAAAAATATAAATAAAAAATAAT
*
12398862 AATAATAAAAAATAT-AATAAAATAAAAAT
1 AATAATAAAAAATATAAATAAAA-AATAAT
*
12398891 AATAATTAAATAATAATAAATAAAAAATAGAT
1 AATAA-TAAAAAAT-ATAAATAAAAAATA-AT
12398923 AAT
1 AAT
12398926 TGCATTAGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
27 19 0.37
28 2 0.04
29 7 0.13
30 7 0.13
31 5 0.10
32 12 0.23
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (29 bp):
AATAATAAAAAATATAAATAAAAAATAAT
Found at i:12398960 original size:30 final size:30
Alignment explanation
Indices: 12398924--12398986 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
12398914 AAAATAGATA
* *
12398924 ATTGCATTA-GCATAGCATATATATATATAT
1 ATTGCATCATGCATAGCAT-TATATATAAAT
* *
12398954 ATTGCATCATGCATATCATTGTATATAAAT
1 ATTGCATCATGCATAGCATTATATATAAAT
12398984 ATT
1 ATT
12398987 TCTGTTTTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (30 bp):
ATTGCATCATGCATAGCATTATATATAAAT
Found at i:12401586 original size:16 final size:16
Alignment explanation
Indices: 12401565--12401601 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
12401555 TCTTATATAA
12401565 GGAGCTTAAATATAGT
1 GGAGCTTAAATATAGT
12401581 GGAGCTTAAATATAGT
1 GGAGCTTAAATATAGT
12401597 GGAGC
1 GGAGC
12401602 AAGAGGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.08, G:0.30, T:0.27
Consensus pattern (16 bp):
GGAGCTTAAATATAGT
Found at i:12403216 original size:65 final size:64
Alignment explanation
Indices: 12403108--12403231 Score: 212
Period size: 65 Copynumber: 1.9 Consensus size: 64
12403098 AAGCCACATT
* *
12403108 GAATCAAGGTTTTTATGGAAAATATATTAAATATTATTACATAATCAATAAAATATTACGAATA
1 GAATCAAGGTTTTTATGAAAAAGATATTAAATATTATTACATAATCAATAAAATATTACGAATA
*
12403172 GAATCAAGGTTTTTTATGAAAAAGATATTAAATATTATTGCATAATCAATAAAATATTAC
1 GAATCAAGG-TTTTTATGAAAAAGATATTAAATATTATTACATAATCAATAAAATATTAC
12403232 AAAAGATATT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
64 9 0.16
65 47 0.84
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (64 bp):
GAATCAAGGTTTTTATGAAAAAGATATTAAATATTATTACATAATCAATAAAATATTACGAATA
Found at i:12403239 original size:41 final size:41
Alignment explanation
Indices: 12403191--12403322 Score: 153
Period size: 41 Copynumber: 3.2 Consensus size: 41
12403181 TTTTTTATGA
*
12403191 AAAAGATATTAAATATTATTGCATAATCAATAAAATATTAC
1 AAAAGATATTAAATATTATTGCATAATCAATCAAATATTAC
* ** * *
12403232 AAAAGATATTGAA-ATTA--AAAAAATACAATCAAATATTAT
1 AAAAGATATTAAATATTATTGCATAAT-CAATCAAATATTAC
* *
12403271 GAAAGACATTAAATATTATTGCATAATCAATCAAATATTAC
1 AAAAGATATTAAATATTATTGCATAATCAATCAAATATTAC
12403312 AAAAAGATATT
1 -AAAAGATATT
12403323 GACATTACAA
Statistics
Matches: 71, Mismatches: 15, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
38 4 0.06
39 22 0.31
40 8 0.11
41 25 0.35
42 12 0.17
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (41 bp):
AAAAGATATTAAATATTATTGCATAATCAATCAAATATTAC
Found at i:12403654 original size:35 final size:35
Alignment explanation
Indices: 12403606--12403749 Score: 207
Period size: 35 Copynumber: 4.1 Consensus size: 35
12403596 GAGAACAACC
*
12403606 AGAACAAGTGAAGTGCTACTTCACGCAGAATAAGT
1 AGAACAAGTGAAGTGCTACTTCACGCAAAATAAGT
* *
12403641 AAAACAAGTGAAGTGCTACTTCACGTAAAATAAGT
1 AGAACAAGTGAAGTGCTACTTCACGCAAAATAAGT
* * *
12403676 AGAACAAGTGAAGCGCTACTTCACGCAAAACAACT
1 AGAACAAGTGAAGTGCTACTTCACGCAAAATAAGT
* * *
12403711 AGAACAAGTGAAGTGCTACTTAACGCAGAATAACT
1 AGAACAAGTGAAGTGCTACTTCACGCAAAATAAGT
12403746 AGAA
1 AGAA
12403750 TAAATAGAAC
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 97 1.00
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (35 bp):
AGAACAAGTGAAGTGCTACTTCACGCAAAATAAGT
Found at i:12403765 original size:70 final size:70
Alignment explanation
Indices: 12403606--12403768 Score: 184
Period size: 70 Copynumber: 2.3 Consensus size: 70
12403596 GAGAACAACC
* ** * * * * *
12403606 AGAACAAGTGAAGTGCTACTTCACGCAGAATAAGTAAAACAAGTGAAGTGCTACTTCACGTAAAA
1 AGAACAAATGAAGCACTACTTCACGCAAAACAACTAAAACAAGTGAAGTGCTACTTAACGCAAAA
*
12403671 TAAGT
66 TAACT
* * * *
12403676 AGAACAAGTGAAGCGCTACTTCACGCAAAACAACTAGAACAAGTGAAGTGCTACTTAACGCAGAA
1 AGAACAAATGAAGCACTACTTCACGCAAAACAACTAAAACAAGTGAAGTGCTACTTAACGCAAAA
12403741 TAACT
66 TAACT
*
12403746 AGAATAAATAGAA-CACTACTTCA
1 AGAACAAAT-GAAGCACTACTTCA
12403769 TATGGAATAA
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
70 77 0.96
71 3 0.04
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (70 bp):
AGAACAAATGAAGCACTACTTCACGCAAAACAACTAAAACAAGTGAAGTGCTACTTAACGCAAAA
TAACT
Done.