Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 120 of 235
Found at i:40841733 original size:75 final size:74
Alignment explanation
Indices: 40841642--40841907 Score: 351
Period size: 77 Copynumber: 3.6 Consensus size: 74
40841632 CGACGTGTGG
* *
40841642 CCCGAGACTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTAAAAAGCAAAAATTGAAAATAC
1 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAA-CAAAAATTGAAAATAC
40841707 CTCAGCGTGT
65 CTCAGCGTGT
* *
40841717 CCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGATAAAA-ATAGAATTTGAAAA
1 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT-A-AAAACA-A-AAATTGAAAA
*
40841781 TATCTCAGCGTGT
62 TACCTCAGCGTGT
* * * *
40841794 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGACAAACAAAAATTGAAATTACC
1 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAAAAATTGAAAATACC
40841858 TCAGC--GT
66 TCAGCGTGT
** *
40841865 CTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTT
1 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
40841908 TTGAAACATA
Statistics
Matches: 170, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
71 36 0.21
72 5 0.03
73 16 0.09
74 4 0.02
75 43 0.25
76 7 0.04
77 59 0.35
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (74 bp):
CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAAAAATTGAAAATACC
TCAGCGTGT
Found at i:40841805 original size:77 final size:77
Alignment explanation
Indices: 40841608--40841907 Score: 350
Period size: 77 Copynumber: 4.0 Consensus size: 77
40841598 AAAAAGAAAT
** *
40841608 TAAAAATAGAATTTGAAAGGACCTC-GACGTGTGGCCCGAGACTCAACTCACCTCTCGCAATATG
1 TAAAAATAGAATTTGAAAATACCTCAG-CGTGT--CCCGAGGCTCAACTCACCTCTCGCAATATG
*
40841672 AGTTGATTCTTTT-A
63 AGTTGATTTTTTTGA
** * * *
40841686 -AAAAGCAAAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCACAATATGAGT
1 TAAAAATAGAATTTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGT
40841750 TGATTTTTTTGA
66 TGATTTTTTTGA
* *
40841762 TAAAAATAGAATTTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 TAAAAATAGAATTTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGT
40841827 TGA--TTTTTGA
66 TGATTTTTTTGA
* * ** *
40841837 CAAACAA-A-AA-TTGAAATTACCTCAGC--GTCTTGAGGCTCAACTCACTTCTCGCAATATGAG
1 TAAA-AATAGAATTTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
40841897 TTGATTTTTTT
65 TTGATTTTTTT
40841908 TTGAAACATA
Statistics
Matches: 195, Mismatches: 21, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
71 36 0.18
73 19 0.10
74 2 0.01
75 51 0.26
76 3 0.02
77 83 0.43
78 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (77 bp):
TAAAAATAGAATTTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTTGA
Found at i:40841871 original size:417 final size:418
Alignment explanation
Indices: 40841229--40841986 Score: 1007
Period size: 417 Copynumber: 1.8 Consensus size: 418
40841219 TAAGCCAAGG
* * *
40841229 CTCAACTCACCTTTCGCAATATGAGTTGATTTTTTGAAAAATAGAAATTGAAAACACCTCAGCAT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAAAAATTGAAAACACCTCAGCAT
*
40841294 GTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAGCAGAAATT
66 GTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACATAAATT--G-AGAAATT
* * **
40841359 GAAAATACCTCAACGGGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATGA
128 GAAAATACCTCAACGGGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAACA
* * *
40841424 TAAATTGAAAATACCTCAATGTGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTT
193 AAAATTGAAAATACCTCAATGCGACTTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTT
* * * *
40841489 TGAATTAAAACAGAAATTGAAAATA-G-AAATGGAAAACACCTCAGC-GTCTTGAGGTTCAACTC
258 T--ATTAAAACAGAAATTAAAAAAACGAAAATGGAAAACACCTCAGCGGTCCTGAGGCTCAACTC
40841551 ACCTCTCGCAATATGAGCTGATTTTTTTGAAACACATAAATTAAAAAAAAAAGAAATTAAAAATA
321 ACCTCTCGCAATATGAGCTGATTTTTTTGAAACACATAAATTAAAAAAAAAAGAAATTAAAAATA
40841616 GAATTTGAAAGGACCTCGACGTGTGGCCCGAGA
386 GAATTTGAAAGGACCTCGACGTGTGGCCCGAGA
*
40841649 CTCAACTCACCTCTCGCAATATGAGTTGATTCTTTT-AAAAAGCAAAAATTGAAAATACCTCAGC
1 CTCAACTCACCTCTCGCAATATGAGTTGATT-TTTTGAAAAA-CAAAAATTGAAAACACCTCAGC
* *** * *
40841713 GTGTCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGATA-A-AAA-T-AGAAT
64 ATGT---GAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACATAAATTGAGAAA
* * *
40841774 TTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAC
126 TTGAAAATACCTCAACGGGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG--
* * * *
40841838 AAACAAAAATTGAAATTACCTC-A-GCGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGA
189 -AACAAAAATTGAAAATACCTCAATGCGACTTGAGGCTCAACTCACCTCTCACAATATGAGTTGA
* * * * *
40841901 TTTTTTTTTGAAACATAAATTAAAAAAACGAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCA
253 TTTTTTATTAAAACAGAAATTAAAAAAACGAAAATGGAAAACACCTCAGCG-GTCCTGAGGCTCA
40841966 ACTCACCTCTCGCAATATGAG
317 ACTCACCTCTCGCAATATGAG
40841987 TTGAAATTAA
Statistics
Matches: 292, Mismatches: 34, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
415 17 0.06
416 7 0.02
417 113 0.39
418 1 0.00
419 49 0.17
420 35 0.12
421 27 0.09
422 3 0.01
423 1 0.00
424 39 0.13
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (418 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAAAAATTGAAAACACCTCAGCAT
GTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACATAAATTGAGAAATTGAA
AATACCTCAACGGGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAACAAAA
ATTGAAAATACCTCAATGCGACTTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTAT
TAAAACAGAAATTAAAAAAACGAAAATGGAAAACACCTCAGCGGTCCTGAGGCTCAACTCACCTC
TCGCAATATGAGCTGATTTTTTTGAAACACATAAATTAAAAAAAAAAGAAATTAAAAATAGAATT
TGAAAGGACCTCGACGTGTGGCCCGAGA
Found at i:40841971 original size:161 final size:161
Alignment explanation
Indices: 40841774--40842066 Score: 455
Period size: 161 Copynumber: 1.8 Consensus size: 161
40841764 AAAATAGAAT
* ** *
40841774 TTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA
1 TTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-AATT-AAA
* ** * *
40841839 A-ACAAAAATTGAAATTACCTCAGCGT-CTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
64 ACACAAAAATTGAAAATACCTCAGCGTCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
40841902 TTTTTTTTGAAACATAAATTAAAAAAACGAAAA
129 TTTTTTTTGAAACATAAATTAAAAAAACGAAAA
40841935 TTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAAC
1 TTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAAC
*
40842000 ACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATT
66 ACAAAAATTGAAAATACCTCAGCGT-CCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATT
40842065 TT
130 TT
40842067 GAAAAAGTAG
Statistics
Matches: 119, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
159 3 0.03
160 26 0.22
161 55 0.46
162 35 0.29
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (161 bp):
TTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAAC
ACAAAAATTGAAAATACCTCAGCGTCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTT
TTTTTTGAAACATAAATTAAAAAAACGAAAA
Found at i:40842035 original size:72 final size:73
Alignment explanation
Indices: 40841917--40842058 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 73
40841907 TTTGAAACAT
* * *
40841917 AAATTAAAAAAACGAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
1 AAATTAAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAAT
40841982 ATGAGTTG
66 ATGAGTTG
* *
40841990 AAATT-AAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAAT
1 AAATTAAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAAT
40842054 ATGAG
66 ATGAG
40842059 CTGATTTTGA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
72 59 0.92
73 5 0.08
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (73 bp):
AAATTAAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAAT
ATGAGTTG
Found at i:40842510 original size:77 final size:76
Alignment explanation
Indices: 40842212--40842553 Score: 442
Period size: 72 Copynumber: 4.5 Consensus size: 76
40842202 AGTGTGTAAT
* *
40842212 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAACAGAAATTGAAAATAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATAC
*
40842277 CTCAGCATGTGAAC
66 CTCAGC--GTG-TC
*
40842291 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATAC
*
40842355 CTCAACGTGTC
66 CTCAGCGTGTC
* * ** * * *
40842366 TTAAGGCTCAACTCATTTCTCGCAATATAAGTTGA----ATTTTGAAAACAGAAATTGAAATTAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATAC
40842427 CTCAGCGTGTC
66 CTCAGCGTGTC
** * * *
40842438 CTGAGGCTCAACTCATTTCTCGCAATATGAGTGGATTTTTTTTTTAACAACAGAAATTGAAATTA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAA-AACAGAAATTGAAAATA
40842503 CCTCAGCGTGTC
65 CCTCAGCGTGTC
* *
40842515 CTGAGGCTCAACTCACATCTAGCAATATGAGTTGATTTT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
40842554 GAAAAAAAAA
Statistics
Matches: 235, Mismatches: 22, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
72 65 0.28
75 1 0.00
76 39 0.17
77 64 0.27
78 65 0.28
79 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (76 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATAC
CTCAGCGTGTC
Found at i:40842513 original size:149 final size:148
Alignment explanation
Indices: 40842252--40842558 Score: 420
Period size: 149 Copynumber: 2.1 Consensus size: 148
40842242 GTTGATTTTT
*
40842252 TTTTTAAAACAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATA
1 TTTTGAAAACAGAAATTGAAAATACCTCAGCA-GTGAACCGAGGCTCAACTCACCTCTCGCAATA
* * *
40842317 TAAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTAAGGCTCAACTCAT
65 TAAGTGGATTTTTTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCCTAAGGCTCAACTCAC
* *
40842382 TTCTCGCAATATAAGTTGAA
130 ATCTAGCAATATAAGTTG-A
* * **
40842402 TTTTGAAAACAGAAATTGAAATTACCTCAGC-GTG-TCCTGAGGCTCAACTCATTTCTCGCAATA
1 TTTTGAAAACAGAAATTGAAAATACCTCAGCAGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
* * * * *
40842465 TGAGTGGATTTTTTTTTTAACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCA
65 TAAGTGGATTTTTTTTTGAA-AACAGAAATTGAAAATACCTCAACGTGTCCTAAGGCTCAACTCA
*
40842530 CATCTAGCAATATGAGTTGA
129 CATCTAGCAATATAAGTTGA
40842550 TTTTGAAAA
1 TTTTGAAAA
40842559 AAAAAATTAA
Statistics
Matches: 139, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
147 2 0.01
148 53 0.38
149 55 0.40
150 29 0.21
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (148 bp):
TTTTGAAAACAGAAATTGAAAATACCTCAGCAGTGAACCGAGGCTCAACTCACCTCTCGCAATAT
AAGTGGATTTTTTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCCTAAGGCTCAACTCACA
TCTAGCAATATAAGTTGA
Found at i:40842718 original size:71 final size:70
Alignment explanation
Indices: 40842570--40842745 Score: 212
Period size: 71 Copynumber: 2.5 Consensus size: 70
40842560 AAAAATTAAA
* * * * * * **
40842570 AGGCTTAACTCACCTCTCGCAATATGAG-TAAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAAAAAAAACTAAAAATACCTCAACGTG
40842634 CCCCG
66 CCCCG
*
40842639 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAAAAAAAACTAAAAATACCTCAACGT
* **
40842704 GTCTTG
65 GCCCCG
40842710 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
40842746 CCTTGGAAAG
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
69 26 0.28
70 6 0.07
71 60 0.65
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAAAAAAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:40850303 original size:14 final size:15
Alignment explanation
Indices: 40850273--40850305 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40850263 AAACTAAACC
*
40850273 AAAATTAAAACCATA
1 AAAATTAAAAACATA
40850288 AAAATTAAAAAC-TA
1 AAAATTAAAAACATA
40850302 AAAA
1 AAAA
40850306 ACAACCAAAT
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:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATTAAAAACATA
Found at i:40853663 original size:24 final size:23
Alignment explanation
Indices: 40853634--40853719 Score: 77
Period size: 24 Copynumber: 3.6 Consensus size: 23
40853624 GCGTCAACCT
40853634 CCATATCCACCACCGCCACCGCCG
1 CCATATCCACCACCGCC-CCGCCG
* *
40853658 CCATATCCGCCACCG--CCTCCG
1 CCATATCCACCACCGCCCCGCCG
40853679 CCATATCCGCCACCACCGCCTCCGCCG
1 CCATAT---CCACCACCGCC-CCGCCG
* *
40853706 TCATATCCTCCACC
1 CCATATCCACCACC
40853720 ATTCCCGAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
21 11 0.22
24 29 0.58
27 10 0.20
ACGTcount: A:0.17, C:0.57, G:0.12, T:0.14
Consensus pattern (23 bp):
CCATATCCACCACCGCCCCGCCG
Found at i:40853669 original size:18 final size:18
Alignment explanation
Indices: 40853646--40853698 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 18
40853636 ATATCCACCA
40853646 CCGCCACCGCCGCCATAT
1 CCGCCACCGCCGCCATAT
40853664 CCGCCACCGCCTCCGCCATAT
1 CCGCCACCG---CCGCCATAT
*
40853685 CCGCCACCACCGCC
1 CCGCCACCGCCGCC
40853699 TCCGCCGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 14 0.45
21 17 0.55
ACGTcount: A:0.15, C:0.60, G:0.15, T:0.09
Consensus pattern (18 bp):
CCGCCACCGCCGCCATAT
Found at i:40856275 original size:17 final size:18
Alignment explanation
Indices: 40856245--40856278 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40856235 AAACAAGTGT
40856245 AAAACTATAAAAAAATAG
1 AAAACTATAAAAAAATAG
*
40856263 AAAA-TATACAAAAATA
1 AAAACTATAAAAAAATA
40856279 TTAATAATTA
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:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAACTATAAAAAAATAG
Found at i:40856376 original size:9 final size:9
Alignment explanation
Indices: 40856362--40856388 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
40856352 TGCAAATATG
40856362 AAAAAAAAT
1 AAAAAAAAT
40856371 AAAAAAAAT
1 AAAAAAAAT
40856380 AAAAAAAAT
1 AAAAAAAAT
40856389 TAAATAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:40856497 original size:9 final size:9
Alignment explanation
Indices: 40856475--40856549 Score: 53
Period size: 9 Copynumber: 7.9 Consensus size: 9
40856465 GAAAACAGGG
*
40856475 TTTATAGTT
1 TTTATAATT
*
40856484 CTTATAATT
1 TTTATAATT
40856493 TTTATATCTATT
1 TTTATA---ATT
*
40856505 TTTAGAATT
1 TTTATAATT
*
40856514 ATTAATATATT
1 -TTTATA-ATT
40856525 TTTATAATT
1 TTTATAATT
40856534 TTTA-AATT
1 TTTATAATT
*
40856542 TTTTTAAT
1 TTTATAAT
40856550 AGTTTTGCAC
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
8 7 0.13
9 25 0.48
10 9 0.17
11 3 0.06
12 8 0.15
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTATAATT
Found at i:40856526 original size:20 final size:19
Alignment explanation
Indices: 40856501--40856547 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
40856491 TTTTTATATC
40856501 TATTTTTAGAATTATTAATA
1 TATTTTTAGAATTATTAA-A
* *
40856521 TATTTTTATAATTTTTAAA
1 TATTTTTAGAATTATTAAA
*
40856540 TTTTTTTA
1 TATTTTTA
40856548 ATAGTTTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTTTTAGAATTATTAAA
Found at i:40856746 original size:19 final size:17
Alignment explanation
Indices: 40856724--40856759 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
40856714 GAATTTTTAA
40856724 ATAATTATTTATATTTTTT
1 ATAATT-TTTA-ATTTTTT
40856743 ATAATTTTTAATTTTTT
1 ATAATTTTTAATTTTTT
40856760 TTTATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 4 0.24
19 6 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATAATTTTTAATTTTTT
Found at i:40856751 original size:10 final size:10
Alignment explanation
Indices: 40856704--40856770 Score: 55
Period size: 10 Copynumber: 6.7 Consensus size: 10
40856694 TTTCATATTT
*
40856704 TAATTTCTTA
1 TAATTTTTTA
* *
40856714 GAATTTTTAAA
1 TAATTTTT-TA
*
40856725 TAATTATTTA
1 TAATTTTTTA
40856735 T-ATTTTTTA
1 TAATTTTTTA
*
40856744 TAATTTTTAA
1 TAATTTTTTA
**
40856754 TTTTTTTTTA
1 TAATTTTTTA
40856764 TAATTTT
1 TAATTTT
40856771 AGACTCATCT
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
9 8 0.19
10 27 0.64
11 7 0.17
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:40856770 original size:30 final size:31
Alignment explanation
Indices: 40856699--40856770 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
40856689 ATGCTTTTCA
*
40856699 TATTT-TAATTTCTTAGAATTTTTAAATAAT
1 TATTTATAATTTTTTAGAATTTTTAAATAAT
* **
40856729 TATTTAT-ATTTTTTATAATTTTT-AATTTT
1 TATTTATAATTTTTTAGAATTTTTAAATAAT
*
40856758 TTTTTATAATTTT
1 TATTTATAATTTT
40856771 AGACTCATCT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 10 0.29
30 24 0.69
31 1 0.03
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (31 bp):
TATTTATAATTTTTTAGAATTTTTAAATAAT
Found at i:40858427 original size:27 final size:25
Alignment explanation
Indices: 40858397--40858464 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 25
40858387 GAACAATTCA
40858397 AAATGAATAAATAAAAAAATCTCAAA-T
1 AAAT-AATAAATAAAAAAAT-T-AAAGT
40858424 AAATAATATATATAAAAAAATTAAAGT
1 AAATAATA-A-ATAAAAAAATTAAAGT
40858451 AAATAAT-AATAAAA
1 AAATAATAAATAAAA
40858465 CAGTTTGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
24 6 0.16
25 1 0.03
26 7 0.18
27 14 0.37
28 10 0.26
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (25 bp):
AAATAATAAATAAAAAAATTAAAGT
Found at i:40858440 original size:26 final size:25
Alignment explanation
Indices: 40858366--40858632 Score: 209
Period size: 26 Copynumber: 10.4 Consensus size: 25
40858356 TAAATAATGG
*
40858366 TTTAAAATAAATAATGTATAAGAACAA
1 TTTAAAATAAATAATATATAA-AA-AA
* *
40858393 TTCAAAATGAATAA-ATA-AAAAAA
1 TTTAAAATAAATAATATATAAAAAA
* *
40858416 TCTCAAATAAATAATATATATAAAAAA
1 TTTAAAATAAAT-A-ATATATAAAAAA
* * *
40858443 ATTAAAGTAAATAATA-ATAAAACAG
1 TTTAAAATAAATAATATATAAAA-AA
* *
40858468 TTTGAAATAAACAATATATAAAAGAA
1 TTTAAAATAAATAATATATAAAA-AA
* *
40858494 TTTTAAAATAAATAACATATAAAATAG
1 -TTTAAAATAAATAATATATAAAA-AA
* * * *
40858521 TTTGAACTACATAACATATATAAAAA
1 TTTAAAATAAATAATATATA-AAAAA
* * *
40858547 TTTAAAATATATAATATGT-AAAAT
1 TTTAAAATAAATAATATATAAAAAA
*
40858571 TTTAAAATAAATAGTATATATAAAAA
1 TTTAAAATAAATAATATATA-AAAAA
**
40858597 CGTAAAATAAATAATATATAAAATAA
1 TTTAAAATAAATAATATATAAAA-AA
40858623 TTTAAAATAA
1 TTTAAAATAA
40858633 TATGTAATAA
Statistics
Matches: 187, Mismatches: 42, Indels: 23
0.74 0.17 0.09
Matches are distributed among these distances:
23 10 0.05
24 29 0.16
25 22 0.12
26 76 0.41
27 50 0.27
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (25 bp):
TTTAAAATAAATAATATATAAAAAA
Found at i:40858620 original size:50 final size:51
Alignment explanation
Indices: 40858366--40858632 Score: 231
Period size: 50 Copynumber: 5.2 Consensus size: 51
40858356 TAAATAATGG
* * * *
40858366 TTTAAAATAAATAATGTATA-AGAACAATTCAAAATGAATAA-ATA-AAAAAA
1 TTTAAAATAAATAATATATATA-AA-AATTTAAAATAAATAATATATAAAATA
* * * * *
40858416 TCTCAAATAAATAATATATATAAAAAAATTAAAGTAAATAATA-ATAAAACA
1 TTTAAAATAAATAATATATAT-AAAAATTTAAAATAAATAATATATAAAATA
* * *
40858467 GTTTGAAATAAACAATATATA-AAAGAATTTTAAAATAAATAACATATAAAATA
1 -TTTAAAATAAATAATATATATAAA-AA-TTTAAAATAAATAATATATAAAATA
* * * * * *
40858520 GTTTGAACTACATAACATATATAAAAATTTAAAATATATAATATGTAAAAT-
1 -TTTAAAATAAATAATATATATAAAAATTTAAAATAAATAATATATAAAATA
* **
40858571 TTTAAAATAAATAGTATATATAAAAACGTAAAATAAATAATATATAAAATAA
1 TTTAAAATAAATAATATATATAAAAATTTAAAATAAATAATATATAAAAT-A
40858623 TTTAAAATAA
1 TTTAAAATAA
40858633 TATGTAATAA
Statistics
Matches: 175, Mismatches: 31, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
50 74 0.42
51 10 0.06
52 62 0.35
53 26 0.15
54 3 0.02
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (51 bp):
TTTAAAATAAATAATATATATAAAAATTTAAAATAAATAATATATAAAATA
Found at i:40858717 original size:24 final size:24
Alignment explanation
Indices: 40858690--40858735 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40858680 TTAAAATAAT
40858690 ATACAATAAAACAATTTGAAATGA
1 ATACAATAAAACAATTTGAAATGA
* * *
40858714 ATACCATAAATCAATTTTAAAT
1 ATACAATAAAACAATTTGAAAT
40858736 AAATGATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.30
Consensus pattern (24 bp):
ATACAATAAAACAATTTGAAATGA
Found at i:40860802 original size:21 final size:22
Alignment explanation
Indices: 40860778--40860827 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
40860768 ATCTTGTTCT
40860778 TTTTTTTC-TTTTGTTTTCAAA
1 TTTTTTTCTTTTTGTTTTCAAA
* *
40860799 TTTTTCTCTTTTTTTTTTCAAA
1 TTTTTTTCTTTTTGTTTTCAAA
40860821 TTTTTTT
1 TTTTTTT
40860828 ACGAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTTTTCTTTTTGTTTTCAAA
Found at i:40860979 original size:19 final size:20
Alignment explanation
Indices: 40860942--40860979 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
40860932 CAGATAAATA
* *
40860942 ATGCAAGACATTAATTAAAG
1 ATGCAAGACATAAACTAAAG
40860962 ATGCAA-ACATAAACTAAA
1 ATGCAAGACATAAACTAAA
40860980 CTAAAACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.21
Consensus pattern (20 bp):
ATGCAAGACATAAACTAAAG
Found at i:40863244 original size:20 final size:20
Alignment explanation
Indices: 40863221--40863259 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40863211 ATTTTCACTT
* *
40863221 ATTTATTTTCTTTTTTTATC
1 ATTTATTTTATTGTTTTATC
40863241 ATTTATTTTATTGTTTTAT
1 ATTTATTTTATTGTTTTAT
40863260 TAATTATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (20 bp):
ATTTATTTTATTGTTTTATC
Found at i:40863266 original size:20 final size:20
Alignment explanation
Indices: 40863223--40863266 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
40863213 TTTCACTTAT
* * *
40863223 TTATTTTCTTTTTTTATCAT
1 TTATTTTATTGTTTTATCAA
*
40863243 TTATTTTATTGTTTTATTAA
1 TTATTTTATTGTTTTATCAA
40863263 TTAT
1 TTAT
40863267 CATATTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (20 bp):
TTATTTTATTGTTTTATCAA
Found at i:40863936 original size:30 final size:30
Alignment explanation
Indices: 40863902--40863966 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
40863892 ATTCTCGTTT
40863902 CGAGAATTTGAAGCATTGTGTCCTAACTTA
1 CGAGAATTTGAAGCATTGTGTCCTAACTTA
40863932 CGAGAATTTGAAGCATTGTGTCCTAACTTA
1 CGAGAATTTGAAGCATTGTGTCCTAACTTA
40863962 CGAGA
1 CGAGA
40863967 TGCAATTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (30 bp):
CGAGAATTTGAAGCATTGTGTCCTAACTTA
Found at i:40875229 original size:44 final size:44
Alignment explanation
Indices: 40875155--40875269 Score: 126
Period size: 44 Copynumber: 2.6 Consensus size: 44
40875145 GTTATCATGG
* * *
40875155 CGAATCTTATCTC-CCAGAAATTACAATGGAGTAGATTGA-AACCA
1 CGAATCTTATCTCACC-GAAGTTGCAGTGGAGTAGATTGAGAA-CA
* ** *
40875199 CTAATCTTATCTCATTGAAGTTGCAGTGGAGTAGATTGAGAATA
1 CGAATCTTATCTCACCGAAGTTGCAGTGGAGTAGATTGAGAACA
*
40875243 CGAATCTTATTTCACCGAAGTTGCAGT
1 CGAATCTTATCTCACCGAAGTTGCAGT
40875270 AGAATGGATT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
44 56 0.97
45 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (44 bp):
CGAATCTTATCTCACCGAAGTTGCAGTGGAGTAGATTGAGAACA
Found at i:40875413 original size:44 final size:44
Alignment explanation
Indices: 40875349--40875451 Score: 136
Period size: 44 Copynumber: 2.3 Consensus size: 44
40875339 CATGACAAAT
* * * *
40875349 CTTATCTCCCGGAAGTTGCAGTGGAGCAAACTAAAGCCATAAAC
1 CTTATCTTCCTGAAGATGCAGTGGAGCAAACTAAAACCATAAAC
* *
40875393 CTTATCTTCCTGAAGATGCAGTGGAGCAGACTAAAACCATAAAT
1 CTTATCTTCCTGAAGATGCAGTGGAGCAAACTAAAACCATAAAC
40875437 CTTATC-TCTCTGAAG
1 CTTATCTTC-CTGAAG
40875452 TTGAAGTGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 2 0.04
44 50 0.96
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (44 bp):
CTTATCTTCCTGAAGATGCAGTGGAGCAAACTAAAACCATAAAC
Found at i:40875607 original size:51 final size:50
Alignment explanation
Indices: 40875523--40875666 Score: 147
Period size: 44 Copynumber: 3.0 Consensus size: 50
40875513 GAAGATAGCG
* * * * * *
40875523 AATCTTATTTTCCTGAAGTTGCAATGGAACAGATTAAAGCTACAAATTACA
1 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGCTACAAA-TACA
40875574 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGC--C----ACA
1 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGCTACAAATACA
* * *
40875618 GATCTTATCTCCCTAAAGTTGTAGTGGAGTAGATTAAAGATAGCAAATA
1 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGCTA-CAAATA
40875667 TTATCTCTCT
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
44 40 0.52
47 1 0.01
49 1 0.01
51 35 0.45
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (50 bp):
AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGCTACAAATACA
Found at i:40875638 original size:44 final size:44
Alignment explanation
Indices: 40875570--40876062 Score: 247
Period size: 44 Copynumber: 11.0 Consensus size: 44
40875560 AGCTACAAAT
40875570 TACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGC
1 TACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGC
* * * *
40875614 CACAGATCTTATCTCCCTAAAGTTGTAGTGGAGTAGATTAAAGA
1 TACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGC
* * * * *
40875658 TAGCAAATATTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGC
1 TA-CAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGC
* * * * * * * * *
40875703 TATAAACCTTATCTCTCTGAAGTTGTAGTAGAGTAGGTTGAAGT
1 TACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGC
* * * ** *
40875747 TACGAGTCTTATTTCCCTAAAGTTACAGTGGAGTAG-TCTAAAGAC
1 TACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGAT-TAAAG-C
* * ** * * * * *
40875792 -AGCGAATCTTATTTTTCTGAAGTTGCAGTGGAACAAATCAAAGCTAC
1 TA-CAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAG---C
* * * *
40875839 AAATTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCATATTGAAGA
1 ----TACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGC
* * * ** * *
40875887 TAGCAAACCTTATCTCTCTAAAGTTGCAGTAAAG-AGGTTGAAA-T
1 TA-CAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATT-AAAGC
* * * * * * *
40875931 TACAAGTCTTATCTCCCTAAGGTTGCAGTGGGGTAGACTAAAGA
1 TACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGC
** * * ** *
40875975 TACCGATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAGC
1 TACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGC
* * * * * * * *
40876019 TTCTAATCCTATCTCCCTGAAGTTGCAATGGAGCGGGTTAAAGC
1 TACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGC
40876063 GAAAAATCCT
Statistics
Matches: 343, Mismatches: 90, Indels: 32
0.74 0.19 0.07
Matches are distributed among these distances:
43 28 0.08
44 184 0.54
45 95 0.28
46 1 0.00
47 2 0.01
51 32 0.09
52 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (44 bp):
TACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGC
Found at i:40875685 original size:140 final size:139
Alignment explanation
Indices: 40875478--40875877 Score: 458
Period size: 133 Copynumber: 2.9 Consensus size: 139
40875468 TGAAATGACA
* * * *
40875478 AGTCTTATCTCACTAAAGTTACAGTGGAGCAGACTGAAGATAGCGAATCTTATTTTCCTGAAGTT
1 AGTCTTATCTCCCTAAAGTTACAGTGGAGTAGATTAAAGATAGCGAATCTTATTTT-CTGAAGTT
*
40875543 GCAATGGAACAGATTAAAGCTACAAATTACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGAT
65 GCAGTGGAACAGATTAAAGCTACAAATTACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGAT
40875608 TAAAGCCAC-
130 TAAAGCCACG
** * * *
40875617 AGATCTTATCTCCCTAAAGTTGTAGTGGAGTAGATTAAAGATAGCAAATATTATCTCTCTGAAGT
1 AG-TCTTATCTCCCTAAAGTTACAGTGGAGTAGATTAAAGATAGCGAATCTTAT-TTTCTGAAGT
* * * * * * * *
40875682 TGCAGTAGAGCAGATTAAAGCT----A-T--AAACCTTATCTCTCTGAAGTTGTAGTAGAGTAGG
64 TGCAGTGGAACAGATTAAAGCTACAAATTACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGA
* **
40875740 TTGAAGTTACG
129 TTAAAGCCACG
* *
40875751 AGTCTTATTTCCCTAAAGTTACAGTGGAGTAG-TCTAAAGACAGCGAATCTTATTTTTCTGAAGT
1 AGTCTTATCTCCCTAAAGTTACAGTGGAGTAGAT-TAAAGATAGCGAATCTTA-TTTTCTGAAGT
* * *
40875815 TGCAGTGGAACAAATCAAAGCTACAAATTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCA
64 TGCAGTGGAACAGATTAAAGCTACAAATTACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCA
40875878 TATTGAAGAT
Statistics
Matches: 211, Mismatches: 38, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
132 1 0.00
133 104 0.49
134 3 0.01
135 1 0.00
136 1 0.00
137 1 0.00
138 1 0.00
139 2 0.01
140 95 0.45
141 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (139 bp):
AGTCTTATCTCCCTAAAGTTACAGTGGAGTAGATTAAAGATAGCGAATCTTATTTTCTGAAGTTG
CAGTGGAACAGATTAAAGCTACAAATTACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATT
AAAGCCACG
Found at i:40875693 original size:89 final size:89
Alignment explanation
Indices: 40875572--40875738 Score: 226
Period size: 89 Copynumber: 1.9 Consensus size: 89
40875562 CTACAAATTA
* * * * *
40875572 CAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGCCACAGATCTTATCTCCCTAAAGT
1 CAAATATTATCTCCCTAAAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCCTAAAGT
*
40875637 TGTAGTGGAGTAGATTAAAGATAG
66 TGTAGTAGAGTAGATTAAAGATAG
* * * * * *
40875661 CAAATATTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCTCTGAAGT
1 CAAATATTATCTCCCTAAAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCCTAAAGT
40875726 TGTAGTAGAGTAG
66 TGTAGTAGAGTAG
40875739 GTTGAAGTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
89 66 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (89 bp):
CAAATATTATCTCCCTAAAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCCTAAAGT
TGTAGTAGAGTAGATTAAAGATAG
Found at i:40875777 original size:133 final size:132
Alignment explanation
Indices: 40875393--40875842 Score: 424
Period size: 133 Copynumber: 3.3 Consensus size: 132
40875383 AGCCATAAAC
* * * * *
40875393 CTTATC-TTCCTGAAGATGCAGTGGAGCAGACTAAAACCATAAATCTTATCTCTCTGAAGTTGAA
1 CTTATCTTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCTCTGAAGTTGTA
* * * * * * *
40875457 GTGAGGCAAGTTGAAATGACAAGTCTTATCTCACTAAAGTTACAGTGGAGCAGACTGAAGATAGC
66 GTGA-GCAGGTTGAAGTCAC-AGTCTTATCTCCCTAAAGTTACAGTGGAGTAGATTAAAGATAGC
40875522 GAAT
129 GAAT
* * * *
40875526 CTTAT-TTTCCTGAAGTTGCAATGGAACAGATTAAAGCTACAAATTACAAATCTTATCTCCCTAA
1 CTTATCTTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCT----A-T--AAATCTTATCTCTCTGA
* * * **
40875590 AGTTGTAGTGGAGCAGATTAAAGCCACAGATCTTATCTCCCTAAAGTTGTAGTGGAGTAGATTAA
59 AGTTGTAGT-GAGCAGGTTGAAGTCACAG-TCTTATCTCCCTAAAGTTACAGTGGAGTAGATTAA
*
40875655 AGATAGCAAAT
122 AGATAGCGAAT
* * * *
40875666 ATTATCTCT-CTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCTCTGAAGTTGTA
1 CTTATCTTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCTCTGAAGTTGTA
* * * *
40875730 GTAGAGTAGGTTGAAGTTACGAGTCTTATTTCCCTAAAGTTACAGTGGAGTAG-TCTAAAGACAG
66 GT-GAGCAGGTTGAAGTCAC-AGTCTTATCTCCCTAAAGTTACAGTGGAGTAGAT-TAAAGATAG
40875794 CGAAT
128 CGAAT
* * * * *
40875799 CTTAT-TTTTCTGAAGTTGCAGTGGAACAAATCAAAGCTACAAAT
1 CTTATCTTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAAT
40875843 TACAAATCTT
Statistics
Matches: 254, Mismatches: 49, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
132 3 0.01
133 138 0.54
134 2 0.01
135 1 0.00
136 1 0.00
137 1 0.00
138 1 0.00
139 2 0.01
140 101 0.40
141 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (132 bp):
CTTATCTTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCTCTGAAGTTGTA
GTGAGCAGGTTGAAGTCACAGTCTTATCTCCCTAAAGTTACAGTGGAGTAGATTAAAGATAGCGA
AT
Found at i:40875868 original size:184 final size:183
Alignment explanation
Indices: 40875566--40876007 Score: 477
Period size: 184 Copynumber: 2.4 Consensus size: 183
40875556 TTAAAGCTAC
* ** * * * *
40875566 AAATTACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGCCACAGATCTTATCTCCC
1 AAATTACAAGTCTTATCTCCCTAAAGTTACAGTGGAGTAGACTAAAGACACCGATCTTATCTCCC
* * ** * * * *
40875631 TAAAGTTGTAGTGGAGTAGATTAAAG------A-TAGCAAATATTATCTCTCTGAAGTTGCAGTA
66 TGAAGTTGCAGTGGAACAAATCAAAGCTACAAATTA-CAAATATTATCTCCCTAAAGTTGCAGTA
* * * * *
40875689 GAGCAGATTAAAGCTA-TAAACCTTATCTCTCTGAAGTTGTAGTAGAGTAGGTTG
130 GAGCAGATTAAAGATAGCAAACCTTATCTCTCTAAAGTTGCAGTAAAG-AGGTTG
* * * * * * **
40875743 AAGTTACGAGTCTTATTTCCCTAAAGTTACAGTGGAGTAGTCTAAAGACAGCGAATCTTATTTTT
1 AAATTACAAGTCTTATCTCCCTAAAGTTACAGTGGAGTAGACTAAAGACACCG-ATCTTATCTCC
* *
40875808 CTGAAGTTGCAGTGGAACAAATCAAAGCTACAAATTACAAATCTTATCTCCCTAAAGTTGCAGTG
65 CTGAAGTTGCAGTGGAACAAATCAAAGCTACAAATTACAAATATTATCTCCCTAAAGTTGCAGTA
* *
40875873 GAGCATATTGAAGATAGCAAACCTTATCTCTCTAAAGTTGCAGTAAAGAGGTTG
130 GAGCAGATTAAAGATAGCAAACCTTATCTCTCTAAAGTTGCAGTAAAGAGGTTG
* * * *
40875927 AAATTACAAGTCTTATCTCCCTAAGGTTGCAGTGGGGTAGACTAAAGATACCGATCTTATCTCCC
1 AAATTACAAGTCTTATCTCCCTAAAGTTACAGTGGAGTAGACTAAAGACACCGATCTTATCTCCC
40875992 TGAAGTTGCAGTGGAA
66 TGAAGTTGCAGTGGAA
40876008 TAGATTGAAG
Statistics
Matches: 212, Mismatches: 44, Indels: 12
0.79 0.16 0.04
Matches are distributed among these distances:
177 41 0.19
178 29 0.14
183 25 0.12
184 88 0.42
185 29 0.14
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (183 bp):
AAATTACAAGTCTTATCTCCCTAAAGTTACAGTGGAGTAGACTAAAGACACCGATCTTATCTCCC
TGAAGTTGCAGTGGAACAAATCAAAGCTACAAATTACAAATATTATCTCCCTAAAGTTGCAGTAG
AGCAGATTAAAGATAGCAAACCTTATCTCTCTAAAGTTGCAGTAAAGAGGTTG
Found at i:40875943 original size:43 final size:44
Alignment explanation
Indices: 40875839--40875959 Score: 138
Period size: 45 Copynumber: 2.8 Consensus size: 44
40875829 TCAAAGCTAC
** *
40875839 AAATTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCATATTG
1 AAATTACAAATCTTATCTCCCTAAAGTTGCAGTAAAGCAGATTG
* * *
40875883 AAGA-TAGCAAACCTTATCTCTCTAAAGTTGCAGTAAAG-AGGTTG
1 AA-ATTA-CAAATCTTATCTCCCTAAAGTTGCAGTAAAGCAGATTG
* *
40875927 AAATTACAAGTCTTATCTCCCTAAGGTTGCAGT
1 AAATTACAAATCTTATCTCCCTAAAGTTGCAGT
40875960 GGGGTAGACT
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
43 24 0.38
44 12 0.19
45 28 0.44
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (44 bp):
AAATTACAAATCTTATCTCCCTAAAGTTGCAGTAAAGCAGATTG
Found at i:40877730 original size:23 final size:22
Alignment explanation
Indices: 40877686--40877745 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
40877676 TTTAGATTAT
*
40877686 TTATTATT-TTATTATTACTAA
1 TTATTATTCTTATTTTTACTAA
40877707 -TATTATTCTTATTTTTCACTTAA
1 TTATTATTCTTATTTTT-AC-TAA
40877730 TTATT-TTCTT-TTTTTA
1 TTATTATTCTTATTTTTA
40877746 TCATTTCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 7 0.21
23 8 0.24
24 4 0.12
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATTATTCTTATTTTTACTAA
Found at i:40880513 original size:14 final size:13
Alignment explanation
Indices: 40880484--40880522 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
40880474 AAAAGTTTAA
*
40880484 TAAATAAAAATGT
1 TAAATAAAAATAT
40880497 TAAATAATAAATAT
1 TAAATAA-AAATAT
*
40880511 TAAATTAAAATA
1 TAAATAAAAATA
40880523 ACATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
TAAATAAAAATAT
Found at i:40880808 original size:31 final size:31
Alignment explanation
Indices: 40880770--40880831 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
40880760 ACTCCTTTTT
* *
40880770 TTTTTTTTTTTTCCTTATTCTCTCATTTATG
1 TTTTTTTTTGTTCCTTATTCTATCATTTATG
40880801 TTTTTTTTTGTTCCTTATTCTATCATTTATG
1 TTTTTTTTTGTTCCTTATTCTATCATTTATG
40880832 ACAATTTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.11, C:0.15, G:0.05, T:0.69
Consensus pattern (31 bp):
TTTTTTTTTGTTCCTTATTCTATCATTTATG
Found at i:40884563 original size:26 final size:26
Alignment explanation
Indices: 40884527--40885000 Score: 786
Period size: 26 Copynumber: 18.2 Consensus size: 26
40884517 TGATACAAAT
*
40884527 TGATAAAAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884553 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884579 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884605 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884631 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884657 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884683 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884709 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884735 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884761 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884787 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884813 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884839 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884865 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884891 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884917 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884943 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40884969 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
40884995 TGATAA
1 TGATAA
40885001 GAATTTCATG
Statistics
Matches: 416, Mismatches: 32, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 416 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:40884591 original size:52 final size:52
Alignment explanation
Indices: 40884535--40885000 Score: 914
Period size: 52 Copynumber: 9.0 Consensus size: 52
40884525 ATTGATAAAA
40884535 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
1 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
40884587 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
1 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
40884639 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
1 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
40884691 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
1 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
40884743 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
1 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
40884795 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
1 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
40884847 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
1 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
40884899 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
1 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
* *
40884951 GGTTAGGTAAATGTTTCATGATAATGGGTTAGGTAAATGTTTCATGATAA
1 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAA
40885001 GAATTTCATG
Statistics
Matches: 412, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 412 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.37
Consensus pattern (52 bp):
GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATG
Found at i:40890529 original size:25 final size:25
Alignment explanation
Indices: 40890495--40890542 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
40890485 AACGAAGTTT
40890495 GTAGGGAAATGTCTGACATGCCAAC
1 GTAGGGAAATGTCTGACATGCCAAC
40890520 GTAGGGAAATGTCTGACATGCCA
1 GTAGGGAAATGTCTGACATGCCA
40890543 GCAAGTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (25 bp):
GTAGGGAAATGTCTGACATGCCAAC
Found at i:40891952 original size:26 final size:26
Alignment explanation
Indices: 40891916--40892025 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
40891906 TGATACAAAT
*
40891916 TGATAAAAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40891942 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40891968 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
40891994 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
40892020 TGATAA
1 TGATAA
40892026 GAATTTCATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:40893562 original size:26 final size:26
Alignment explanation
Indices: 40893510--40893562 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
40893500 TTTACAGTTT
*
40893510 TACCCCTAGGAGATAAATTATCGAAA
1 TACCCCTAGGAGATAAATTACCGAAA
* *
40893536 TACCCCTAGG-GTTAAATTGACCTAAA
1 TACCCCTAGGAGATAAATT-ACCGAAA
40893562 T
1 T
40893563 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGAGATAAATTACCGAAA
Found at i:40898997 original size:15 final size:15
Alignment explanation
Indices: 40898979--40899008 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40898969 TAATATATAA
*
40898979 AAATTTAAAGAAAAT
1 AAATTTAAACAAAAT
40898994 AAATTTAAACAAAAT
1 AAATTTAAACAAAAT
40899009 GTATGAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (15 bp):
AAATTTAAACAAAAT
Found at i:40906702 original size:21 final size:21
Alignment explanation
Indices: 40906672--40906740 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
40906662 AAAGCTTAAA
40906672 AGCTGAACAGAAGCTCATAAG
1 AGCTGAACAGAAGCTCATAAG
40906693 AGCTTG-ACAGAAGCTCATAAG
1 AGC-TGAACAGAAGCTCATAAG
* * *
40906714 AGCTGAACAGAAGGTCGTAAA
1 AGCTGAACAGAAGCTCATAAG
40906735 AGCTGA
1 AGCTGA
40906741 TCCACCCAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 2 0.05
21 39 0.91
22 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.26, T:0.16
Consensus pattern (21 bp):
AGCTGAACAGAAGCTCATAAG
Found at i:40909653 original size:24 final size:25
Alignment explanation
Indices: 40909612--40909661 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
40909602 TAATTCAATT
* * *
40909612 AAAATTATTTACTATCATTTTGATA
1 AAAATTATTAAATATCATTTTCATA
40909637 AAAATTATTAAAT-TCATTTTCATA
1 AAAATTATTAAATATCATTTTCATA
40909661 A
1 A
40909662 TTCCTGTGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (25 bp):
AAAATTATTAAATATCATTTTCATA
Found at i:40927279 original size:21 final size:23
Alignment explanation
Indices: 40927255--40927296 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
40927245 TTTAAAAATA
*
40927255 AAATAAC-ATATAAAT-AATATG
1 AAATAACTAAATAAATGAATATG
40927276 AAATAACTAAATAAATGAATA
1 AAATAACTAAATAAATGAATA
40927297 GCTACTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (23 bp):
AAATAACTAAATAAATGAATATG
Found at i:40933739 original size:25 final size:25
Alignment explanation
Indices: 40933705--40933755 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
40933695 TTTTGTTAGT
40933705 AATTCAATTGTTG-GTGACAAAAAA
1 AATTCAATTGTTGAGTGACAAAAAA
*
40933729 AATTCGAATTGTTGAGTGACCAAAAA
1 AATTC-AATTGTTGAGTGACAAAAAA
40933755 A
1 A
40933756 GAAATTTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.21
25 8 0.33
26 11 0.46
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (25 bp):
AATTCAATTGTTGAGTGACAAAAAA
Found at i:40933753 original size:24 final size:23
Alignment explanation
Indices: 40933705--40933755 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
40933695 TTTTGTTAGT
40933705 AATTCAATTGTTGGTGACAAAAAA
1 AATTCAATTGTTGGTGAC-AAAAA
*
40933729 AATTCGAATTGTTGAGTGACCAAAA
1 AATTC-AATTGTTG-GTGACAAAAA
40933754 AA
1 AA
40933756 GAAATTTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 5 0.21
25 14 0.58
26 5 0.21
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (23 bp):
AATTCAATTGTTGGTGACAAAAA
Found at i:40933922 original size:18 final size:19
Alignment explanation
Indices: 40933901--40933937 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
40933891 TTTCTTTGTG
40933901 TTAATGCTA-ATTTT-TTTA
1 TTAATG-TATATTTTATTTA
40933919 TTAATGTATATTTTATTTA
1 TTAATGTATATTTTATTTA
40933938 ATAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.12
18 11 0.65
19 4 0.24
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
TTAATGTATATTTTATTTA
Found at i:40935210 original size:21 final size:21
Alignment explanation
Indices: 40935184--40935246 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
40935174 AAAACTGTTG
40935184 TTTTTTTTTTACTATTCTTGC
1 TTTTTTTTTTACTATTCTTGC
*
40935205 TTTTTTTTTCTA-TTTTCTTG-
1 TTTTTTTTT-TACTATTCTTGC
* *
40935225 TTATTATTTTCACTATT-TTGC
1 TT-TTTTTTTTACTATTCTTGC
40935246 T
1 T
40935247 ATCATTTCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 6 0.18
21 26 0.76
22 2 0.06
ACGTcount: A:0.11, C:0.13, G:0.05, T:0.71
Consensus pattern (21 bp):
TTTTTTTTTTACTATTCTTGC
Found at i:40938696 original size:17 final size:18
Alignment explanation
Indices: 40938676--40938710 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40938666 ATACCTTCAC
40938676 AGCTTGG-CGACCTTGAT
1 AGCTTGGTCGACCTTGAT
*
40938693 AGCTTGGTGGACCTTGAT
1 AGCTTGGTCGACCTTGAT
40938711 CTCAGCAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.17, C:0.20, G:0.31, T:0.31
Consensus pattern (18 bp):
AGCTTGGTCGACCTTGAT
Found at i:40950266 original size:16 final size:16
Alignment explanation
Indices: 40950245--40950313 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
40950235 TTTGGTTCGC
40950245 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40950261 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40950277 TGTATTAGGATTAGAGG
1 TGTATT-GGATTAGAGG
40950294 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40950310 TGTA
1 TGTA
40950314 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:40950289 original size:33 final size:32
Alignment explanation
Indices: 40950245--40950313 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
40950235 TTTGGTTCGC
40950245 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
40950277 TGTATTAGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
40950310 TGTA
1 TGTA
40950314 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:40954967 original size:22 final size:21
Alignment explanation
Indices: 40954942--40954986 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40954932 TGAATAAAAT
40954942 AACACAAAATCAATAGAGAAGA
1 AACACAAAAT-AATAGAGAAGA
* * *
40954964 AACACTAAATATTTGAGAAGA
1 AACACAAAATAATAGAGAAGA
40954985 AA
1 AA
40954987 AAGAAATGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.60, C:0.11, G:0.13, T:0.16
Consensus pattern (21 bp):
AACACAAAATAATAGAGAAGA
Found at i:40960811 original size:39 final size:38
Alignment explanation
Indices: 40960767--40960915 Score: 190
Period size: 39 Copynumber: 3.9 Consensus size: 38
40960757 ATAAAGTATG
* *
40960767 GTTTTAATTAATAATAAAACAAAATGGTATGAGGAAGTA
1 GTTTTAATTAACAATAAAACAAAATAGTATG-GGAAGTA
*
40960806 GTTTTAATTAACAAGAAAACAAAATAGTATGGGAAAGTA
1 GTTTTAATTAACAATAAAACAAAATAGTATGGG-AAGTA
* * *
40960845 GTTTTAATTAACAATAAAACAAAATAGCATGGGGAGTG
1 GTTTTAATTAACAATAAAACAAAATAGTATGGGAAGTA
* * * *
40960883 GTTTTGATTAATAATAAAACAAAGTAGCATGGG
1 GTTTTAATTAACAATAAAACAAAATAGTATGGG
40960916 GGAGTGGAAT
Statistics
Matches: 99, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
38 35 0.35
39 64 0.65
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.28
Consensus pattern (38 bp):
GTTTTAATTAACAATAAAACAAAATAGTATGGGAAGTA
Found at i:40960861 original size:78 final size:77
Alignment explanation
Indices: 40960767--40960915 Score: 199
Period size: 77 Copynumber: 1.9 Consensus size: 77
40960757 ATAAAGTATG
* * *
40960767 GTTTTAATTAATAATAAAACAAAATGGTATGAGGAAGTAGTTTTAATTAACAAGAAAACAAAATA
1 GTTTTAATTAACAATAAAACAAAATAGCATG-GGAAGTAGTTTTAATTAACAAGAAAACAAAATA
*
40960832 GTATGGGAAAGTA
65 GCATGGGAAAGTA
* * * * * *
40960845 GTTTTAATTAACAATAAAACAAAATAGCATGGGGAGTGGTTTTGATTAATAATAAAACAAAGTAG
1 GTTTTAATTAACAATAAAACAAAATAGCATGGGAAGTAGTTTTAATTAACAAGAAAACAAAATAG
40960910 CATGGG
66 CATGGG
40960916 GGAGTGGAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
77 33 0.54
78 28 0.46
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.28
Consensus pattern (77 bp):
GTTTTAATTAACAATAAAACAAAATAGCATGGGAAGTAGTTTTAATTAACAAGAAAACAAAATAG
CATGGGAAAGTA
Found at i:40961452 original size:24 final size:24
Alignment explanation
Indices: 40961407--40961473 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
40961397 TTTATTTTTT
* * *
40961407 ACATTATTATGTAAATACCATGTAA
1 ACATT-TTATATATATATCATGTAA
* *
40961432 ATATTTTA-ATATTATATCATGTAT
1 ACATTTTATATA-TATATCATGTAA
40961456 ACATTTTATATATATATC
1 ACATTTTATATATATATC
40961474 TTTTAATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
23 2 0.06
24 25 0.74
25 7 0.21
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.46
Consensus pattern (24 bp):
ACATTTTATATATATATCATGTAA
Found at i:40963979 original size:13 final size:13
Alignment explanation
Indices: 40963961--40964010 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
40963951 TCCTCGTTAC
*
40963961 TTTTAAAAAGTAT
1 TTTTAAAAAGTGT
*
40963974 TTTTAAAAAATGT
1 TTTTAAAAAGTGT
* *
40963987 TATAAAAAAGTGT
1 TTTTAAAAAGTGT
40964000 TTTTAAAAAGT
1 TTTTAAAAAGT
40964011 TTAGTTTAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (13 bp):
TTTTAAAAAGTGT
Found at i:40970603 original size:93 final size:93
Alignment explanation
Indices: 40970488--40970658 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
40970478 CGCCCATAAC
* * * * *
40970488 CGAACTCGGACTTAATTCAACGAGCTCGGGCGTTCGCATCCATAAGTAAACTCGGACTCAACTCA
1 CGAACTAGGACTCAACTCAACGAGCTCAGACGTTCGCATCCATAAGTAAACTCGGACTCAACTCA
40970553 ACGAGTTCGGATGCTTAGTTACATTTCA
66 ACGAGTTCGGATGCTTAGTTACATTTCA
* *
40970581 CGAACTAGGACTCAACTCAACGAGTTCAGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTAGGACTCAACTCAACGAGCTCAGACGTTCGCATCCATAAGTAAACTCGGACTCAACTCA
*
40970646 ACGAGTTTGGATG
66 ACGAGTTCGGATG
40970659 TTCGCATCCA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (93 bp):
CGAACTAGGACTCAACTCAACGAGCTCAGACGTTCGCATCCATAAGTAAACTCGGACTCAACTCA
ACGAGTTCGGATGCTTAGTTACATTTCA
Found at i:40970704 original size:46 final size:46
Alignment explanation
Indices: 40970489--40970704 Score: 238
Period size: 46 Copynumber: 4.7 Consensus size: 46
40970479 GCCCATAACC
* * * **
40970489 GAACTCGGACTTAATTCAACGAGCTCGGGCGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGT
* * * * * *
40970535 AAACTCGGACTCAACTCAACGAGTTCGGATGCTTAG-TTACATTTCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATG-TTCGCATCCA--TAAGT
* * *
40970582 GAACTAGGACTCAACTCAACGAGTTCAGACGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGT
*
40970628 GAACTCGGACTCAACTCAACGAGTTTGGATGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGT
* *
40970674 GAACTCAGACTCAACTCAACGAGGTCGGATG
1 GAACTCGGACTCAACTCAACGAGTTCGGATG
40970705 CCTAAATATC
Statistics
Matches: 138, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
45 2 0.01
46 101 0.73
47 33 0.24
48 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGT
Found at i:40972724 original size:35 final size:35
Alignment explanation
Indices: 40972685--40972753 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
40972675 ACTTGCCTCT
40972685 TCCCACTCTCCCATGCTGTCTGCCACCAGCACCAC
1 TCCCACTCTCCCATGCTGTCTGCCACCAGCACCAC
40972720 TCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
1 TCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
40972754 TCACACACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.17, C:0.51, G:0.12, T:0.20
Consensus pattern (35 bp):
TCCCACTCTCCCATGCTGTCTGCCACCAGCACCAC
Found at i:40973791 original size:3 final size:3
Alignment explanation
Indices: 40973783--40973808 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40973773 CTGTTTTTAA
40973783 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
40973809 ATATCCTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:40973865 original size:14 final size:14
Alignment explanation
Indices: 40973846--40973872 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40973836 ATATTACTAT
40973846 TTTTAATACCTTTA
1 TTTTAATACCTTTA
40973860 TTTTAATACCTTT
1 TTTTAATACCTTT
40973873 TGGGCCAAGA
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:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTAATACCTTTA
Found at i:40974906 original size:46 final size:46
Alignment explanation
Indices: 40974838--40974928 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
40974828 AATAAAAGAA
40974838 GAAGTCAAGAAGCAATTGGATGCTGGCTTCCTACAAGCCTCCAAAG
1 GAAGTCAAGAAGCAATTGGATGCTGGCTTCCTACAAGCCTCCAAAG
*
40974884 GAAGTCAAGAAGCAATTTGATGCTGGCTTCCTACAAGCCTCCAAA
1 GAAGTCAAGAAGCAATTGGATGCTGGCTTCCTACAAGCCTCCAAA
40974929 TATCCAGAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (46 bp):
GAAGTCAAGAAGCAATTGGATGCTGGCTTCCTACAAGCCTCCAAAG
Found at i:40993474 original size:93 final size:93
Alignment explanation
Indices: 40993366--40993536 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
40993356 CGCCCATAAG
* * ***
40993366 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTTGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCACATCCATAAGTGAACCAAGACTCAACTCA
*
40993431 ACGAGTTCGGATGCCTAGTTACACTTCA
66 ACAAGTTCGGATGCCTAGTTACACTTCA
* *
40993459 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACATCCATAAGTGAACCAAGATTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCACATCCATAAGTGAACCAAGACTCAACTCA
40993524 ACAAGTTCGGATG
66 ACAAGTTCGGATG
40993537 TTTGCATCCA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCACATCCATAAGTGAACCAAGACTCAACTCA
ACAAGTTCGGATGCCTAGTTACACTTCA
Found at i:40993581 original size:46 final size:46
Alignment explanation
Indices: 40993359--40993582 Score: 222
Period size: 46 Copynumber: 4.8 Consensus size: 46
40993349 TGTAACCCGC
* * ** *
40993359 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACAT
* *
40993405 CCATAAGTGAACTTGGACTCAACTCAACGAGTTCGGATGCCTAGTTACA-
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG--T--TCACAT
* * * *
40993454 -CTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACAT
* * * **
40993498 CCATAAGTGAAC-CAAGATTCAACTCAACAAGTTCGGATGTTTGCAT
1 CCATAAGTGAACTC-GGACTCAACTCAACGAGTTCGGATGTTCACAT
*
40993544 CCATAAGTGAACTCGGACTCAACTCAACGAGGTCGGATG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
40993583 CCCAAATATC
Statistics
Matches: 143, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
43 4 0.03
45 5 0.03
46 97 0.68
47 30 0.21
48 4 0.03
50 3 0.02
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACAT
Found at i:40996502 original size:40 final size:40
Alignment explanation
Indices: 40996458--40996577 Score: 204
Period size: 40 Copynumber: 3.0 Consensus size: 40
40996448 GAACATGATA
*
40996458 AAATTTTGACATTTTGATAACATGTTAAATGATGTAACAT
1 AAATTTTGACATTTTGATAACATGTTAAATGACGTAACAT
40996498 AAATTTTGACATTTTGATAACATGTTAAATGACGTAACAT
1 AAATTTTGACATTTTGATAACATGTTAAATGACGTAACAT
* * *
40996538 AAATTTTGATATTTTGATAACGTGTTAAATGACCTAACAT
1 AAATTTTGACATTTTGATAACATGTTAAATGACGTAACAT
40996578 TAGAGGCAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (40 bp):
AAATTTTGACATTTTGATAACATGTTAAATGACGTAACAT
Found at i:40997103 original size:44 final size:44
Alignment explanation
Indices: 40997029--40997124 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
40997019 TATTAAACTC
* * * * *
40997029 TAATTTTAGTTTCTCACTTAAACTTAAATTAGTGTAGGTTATTT
1 TAATATTAGTTACCCACTTAAACTTAAATTAGAGTAAGTTATTT
40997073 TAATATTAGTTACCCACTTAAACTCT-AATTAGAGTAAGTTATTT
1 TAATATTAGTTACCCACTTAAACT-TAAATTAGAGTAAGTTATTT
40997117 TAATATTA
1 TAATATTA
40997125 TTTGACCTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 45 0.98
45 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.46
Consensus pattern (44 bp):
TAATATTAGTTACCCACTTAAACTTAAATTAGAGTAAGTTATTT
Found at i:41007939 original size:69 final size:68
Alignment explanation
Indices: 41007824--41008223 Score: 363
Period size: 69 Copynumber: 5.8 Consensus size: 68
41007814 AAATTATCGT
* ** * * * *
41007824 CTGTAAAATTAAGGTTCACAATTGAAGGGCTGCGACCTCTACCACAGTTAGCAAGAGCAATGTTT
1 CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCACCACAGTTAGCGAGAGCAATG-CT
41007889 CCAG
65 CCAG
* *
41007893 CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCAGCACAGTTAGCGAGAGCAATGGTC
1 CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCACCACAGTTAGCGAGAGCAATGCTC
41007958 TCAG
66 -CAG
* * * * * * *
41007962 CTGTAAAATTAAGGTTCGCAGGCAAAGAGCTGTGACCTCCATCATAGTTAGTGAGAGCAATACTC
1 CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCACCACAGTTAGCGAGAGCAATGCTC
*
41008027 CTAA
66 C-AG
** * * * * *
41008031 CTGTAAAATTAAGGTTCATAGGCGAAGAGCCGCAACCTTCACCACAGTTAGCGAGAGCAAAGCTC
1 CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCACCACAGTTAGCGAGAGCAATGCTC
41008096 CTAG
66 C-AG
** * * * ** * * * *
41008100 CTAAAAAATTAAGGTTTGCAGGCTAAGAGCCACGACCTCTAGCACAATTAGCGAGAGCAAAGCTC
1 CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCACCACAGTTAGCGAGAGCAATGCTC
*
41008165 TCAA
66 -CAG
* * * *
41008169 CTATAAAATTAAGGTTCG-TAGACGAAGAG-TCGCGACCTCCAACATAGTTAGCGAG
1 CTGTAAAATTAAGGTTCGCAAG-CGAAGAGCT-GCGACCTCCACCACAGTTAGCGAG
41008224 GGTAAACCTC
Statistics
Matches: 272, Mismatches: 54, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
68 4 0.01
69 267 0.98
70 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (68 bp):
CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCACCACAGTTAGCGAGAGCAATGCTC
CAG
Found at i:41008179 original size:207 final size:207
Alignment explanation
Indices: 41007824--41008219 Score: 492
Period size: 207 Copynumber: 1.9 Consensus size: 207
41007814 AAATTATCGT
** * * * * *
41007824 CTGTAAAATTAAGGTTCACAATTGAAGGGCTGCGACCTCTACCACAGTTAGCAAGAGCAATGTTT
1 CTGTAAAATTAAGGTTCACAAGCGAAGAGCCGCAACCTCTACCACAGTTAGCAAGAGCAAAGTCT
** ** * *
41007889 CCAGCTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCAGCACAGTTAGCGAGAGCAAT
66 CCAGCTAAAAAATTAAGGTTCGCAAGCGAAGAGCCACGACCTCCAGCACAATTAGCGAGAGCAAA
* * * * * *
41007954 GGTCTCAGCTGTAAAATTAAGGTTCGCAGGCAAAGAG-CTGTGACCTCCATCATAGTTAGTGAGA
131 GCTCTCAACTATAAAATTAAGGTTCGCAGACAAAGAGTC-GCGACCTCCAACATAGTTAGTGAGA
41008018 GCAATACTCCTAA
195 GCAATACTCCTAA
* * *
41008031 CTGTAAAATTAAGGTTCATAGGCGAAGAGCCGCAACCT-TCACCACAGTTAGCGAGAGCAAAG-C
1 CTGTAAAATTAAGGTTCACAAGCGAAGAGCCGCAACCTCT-ACCACAGTTAGCAAGAGCAAAGTC
* * * *
41008094 TCCTAGCTAAAAAATTAAGGTTTGCAGGCTAAGAGCCACGACCTCTAGCACAATTAGCGAGAGCA
65 TCC-AGCTAAAAAATTAAGGTTCGCAAGCGAAGAGCCACGACCTCCAGCACAATTAGCGAGAGCA
* *
41008159 AAGCTCTCAACTATAAAATTAAGGTTCGTAGACGAAGAGTCGCGACCTCCAACATAGTTAG
129 AAGCTCTCAACTATAAAATTAAGGTTCGCAGACAAAGAGTCGCGACCTCCAACATAGTTAG
41008220 CGAGGGTAAA
Statistics
Matches: 158, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
206 4 0.03
207 153 0.97
208 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (207 bp):
CTGTAAAATTAAGGTTCACAAGCGAAGAGCCGCAACCTCTACCACAGTTAGCAAGAGCAAAGTCT
CCAGCTAAAAAATTAAGGTTCGCAAGCGAAGAGCCACGACCTCCAGCACAATTAGCGAGAGCAAA
GCTCTCAACTATAAAATTAAGGTTCGCAGACAAAGAGTCGCGACCTCCAACATAGTTAGTGAGAG
CAATACTCCTAA
Found at i:41014682 original size:21 final size:21
Alignment explanation
Indices: 41014656--41014696 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
41014646 TGCTTTCTGT
*
41014656 TTTCTTTTCTTTGTTCTTTTG
1 TTTCTTTTCTTTATTCTTTTG
41014677 TTTCTTTTCTTTATTCTTTT
1 TTTCTTTTCTTTATTCTTTT
41014697 TCTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTCTTTTCTTTATTCTTTTG
Found at i:41014827 original size:8 final size:7
Alignment explanation
Indices: 41014800--41014826 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
41014790 ACATTTGTAT
41014800 TTTTTTA
1 TTTTTTA
41014807 TTTTTTA
1 TTTTTTA
41014814 TTTTTTA
1 TTTTTTA
41014821 TTTTTT
1 TTTTTT
41014827 TTAACATCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:41020818 original size:69 final size:69
Alignment explanation
Indices: 41020707--41021128 Score: 345
Period size: 69 Copynumber: 6.1 Consensus size: 69
41020697 CAAACCTTGG
* * * * * * * *
41020707 TTTTACAGTTGAGAGGTTTACCCTCGCTAACTATGTTGGAGGTCGCGACTCTTCGTCTACGAACC
1 TTTTACAGCTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGCGACTCTTCGCCTGCGAACC
41020772 TTAA
66 TTAA
* * * * * * * *
41020776 TTTTATAGTTGAGAGCTTTGCTCTCGCTAATTGTGCTAGAGGTCGTGGCTCTTAGCCTGCAAACC
1 TTTTACAGCTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGCGACTCTTCGCCTGCGAACC
41020841 TTAA
66 TTAA
** * * * * **
41020845 TTTTTTAGCT-AGGAGCTTTGCTCTCGCTAACTGTGGTGAAGGTTGCGGCTCTTCGCCTATGAAC
1 TTTTACAGCTGA-GAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGCGACTCTTCGCCTGCGAAC
41020909 CTTAA
65 CTTAA
* * * * * *
41020914 TTTTACAG-TTAGGAG-TATTGCTCTCACTAACTATGATGGAGGTCAC-AGCTCTTTGCCTGCGA
1 TTTTACAGCTGA-GAGCT-TTGCTCTCGCTAACTGTGCTGGAGGTCGCGA-CTCTTCGCCTGCGA
41020976 ACCTTAA
63 ACCTTAA
* * *
41020983 TTTTACAGCTGAGACCATTGCTCTCGCTAACTGTGCTGGAGGTCGC-AGCTCTTCGCTTGCGAAC
1 TTTTACAGCTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGCGA-CTCTTCGCCTGCGAAC
41021047 CTTAA
65 CTTAA
* * * * * * *** *
41021052 TTTTACAGCTG-GAAACATTGCTCTTGCTAACTGTGGTAGAGGTCGC-AGCCCTTCAATTGTGAA
1 TTTTACAGCTGAG-AGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGCGA-CTCTTCGCCTGCGAA
41021115 CCTTAA
64 CCTTAA
41021121 TTTTACAG
1 TTTTACAG
41021129 ACGATAATTT
Statistics
Matches: 291, Mismatches: 55, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
68 4 0.01
69 285 0.98
70 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (69 bp):
TTTTACAGCTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGCGACTCTTCGCCTGCGAACC
TTAA
Found at i:41020956 original size:138 final size:138
Alignment explanation
Indices: 41020729--41021059 Score: 380
Period size: 138 Copynumber: 2.4 Consensus size: 138
41020719 GAGGTTTACC
* * * * *
41020729 CTCGCTAACTATGTTGGAGGTCGCGACTCTTCGTCTACGAACCTTAATTTTATAGTTGAGAGCTT
1 CTCGCTAACTGTGCTGGAGGTCGCGGCTCTTCGCCTACGAACCTTAATTTTACAGTTGAGAGCTT
* * * * *** **
41020794 TGCTCTCGCTAATTGTGCTAGAGGTCGTGGCTCTTAGCCTGCAAACCTTAATTTTTTAGCT-AGG
66 TGCTCTCACTAACTATGATAGAGGTCACAGCTCTTAGCCTGCAAACCTTAATTTTACAGCTGA-G
* *
41020858 AGCTTTGCT
130 ACCATTGCT
* * * *
41020867 CTCGCTAACTGTGGTGAAGGTTGCGGCTCTTCGCCTATGAACCTTAATTTTACAGTT-AGGAG-T
1 CTCGCTAACTGTGCTGGAGGTCGCGGCTCTTCGCCTACGAACCTTAATTTTACAGTTGA-GAGCT
* * *
41020930 ATTGCTCTCACTAACTATGATGGAGGTCACAGCTCTTTGCCTGCGAACCTTAATTTTACAGCTGA
65 -TTGCTCTCACTAACTATGATAGAGGTCACAGCTCTTAGCCTGCAAACCTTAATTTTACAGCTGA
41020995 GACCATTGCT
129 GACCATTGCT
* * *
41021005 CTCGCTAACTGTGCTGGAGGTCGCAGCTCTTCGCTTGCGAACCTTAATTTTACAG
1 CTCGCTAACTGTGCTGGAGGTCGCGGCTCTTCGCCTACGAACCTTAATTTTACAG
41021060 CTGGAAACAT
Statistics
Matches: 161, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
137 2 0.01
138 158 0.98
139 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (138 bp):
CTCGCTAACTGTGCTGGAGGTCGCGGCTCTTCGCCTACGAACCTTAATTTTACAGTTGAGAGCTT
TGCTCTCACTAACTATGATAGAGGTCACAGCTCTTAGCCTGCAAACCTTAATTTTACAGCTGAGA
CCATTGCT
Found at i:41021075 original size:207 final size:207
Alignment explanation
Indices: 41020733--41021128 Score: 492
Period size: 207 Copynumber: 1.9 Consensus size: 207
41020723 TTTACCCTCG
* * * * * * *
41020733 CTAACTATGTTGGAGGTCGCGACTCTTCGTCTACGAACCTTAATTTTATAGTTGAGAGCTTTGCT
1 CTAACTATGATGGAGGTCACGACTCTTCGCCTACGAACCTTAATTTTACAGCTGAGACCATTGCT
* ** ** * *
41020798 CTCGCTAATTGTGCTAGAGGTCGTGGCTCTTAGCCTGCAAACCTTAATTTTTTAGCTAGGAGCTT
66 CTCGCTAACTGTGCTAGAGGTCGCAGCTCTTAGCCTGCAAACCTTAATTTTACAGCTAGGAACAT
* * * **
41020863 TGCTCTCGCTAACTGTGGT-GAAGGTTGCGGCTCTTCGCCTATGAACCTTAATTTTACAGTTAGG
131 TGCTCTCGCTAACTGTGGTAG-AGGTCGCAGCCCTTCAACTATGAACCTTAATTTTACAGTTAGG
41020927 AGTATTGCTCTCA
195 AGTATTGCTCTCA
* *
41020940 CTAACTATGATGGAGGTCAC-AGCTCTTTGCCTGCGAACCTTAATTTTACAGCTGAGACCATTGC
1 CTAACTATGATGGAGGTCACGA-CTCTTCGCCTACGAACCTTAATTTTACAGCTGAGACCATTGC
* * * *
41021004 TCTCGCTAACTGTGCTGGAGGTCGCAGCTCTTCGCTTGCGAACCTTAATTTTACAGCT-GGAAAC
65 TCTCGCTAACTGTGCTAGAGGTCGCAGCTCTTAGCCTGCAAACCTTAATTTTACAGCTAGG-AAC
* * *
41021068 ATTGCTCTTGCTAACTGTGGTAGAGGTCGCAGCCCTTCAATTGTGAACCTTAATTTTACAG
129 ATTGCTCTCGCTAACTGTGGTAGAGGTCGCAGCCCTTCAACTATGAACCTTAATTTTACAG
41021129 ACGATAATTT
Statistics
Matches: 158, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
206 3 0.02
207 154 0.97
208 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (207 bp):
CTAACTATGATGGAGGTCACGACTCTTCGCCTACGAACCTTAATTTTACAGCTGAGACCATTGCT
CTCGCTAACTGTGCTAGAGGTCGCAGCTCTTAGCCTGCAAACCTTAATTTTACAGCTAGGAACAT
TGCTCTCGCTAACTGTGGTAGAGGTCGCAGCCCTTCAACTATGAACCTTAATTTTACAGTTAGGA
GTATTGCTCTCA
Found at i:41031393 original size:28 final size:28
Alignment explanation
Indices: 41031355--41031411 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
41031345 GAGAATCCTT
*
41031355 AAAACATTTCACTACCAATATAAAAATA
1 AAAACATTTCAATACCAATATAAAAATA
*
41031383 AAAACATTTCAATAGCAATATAAAAATA
1 AAAACATTTCAATACCAATATAAAAATA
41031411 A
1 A
41031412 TGATTGGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.25
Consensus pattern (28 bp):
AAAACATTTCAATACCAATATAAAAATA
Found at i:41034670 original size:15 final size:16
Alignment explanation
Indices: 41034650--41034689 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
41034640 ATTACCAACA
*
41034650 AATGTAGTAGCAA-TC
1 AATGTAGCAGCAATTC
*
41034665 AATGTAGCAGTAATTC
1 AATGTAGCAGCAATTC
41034681 AATGTAGCA
1 AATGTAGCA
41034690 ATTGGCAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (16 bp):
AATGTAGCAGCAATTC
Found at i:41034836 original size:44 final size:44
Alignment explanation
Indices: 41034786--41034872 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
41034776 GGGTTATGTA
41034786 AGTAAGGTACGGTTACGCAAAAGGGTTGAGAACAAGTGAATATG
1 AGTAAGGTACGGTTACGCAAAAGGGTTGAGAACAAGTGAATATG
41034830 AGTAAGGTACGGTTACGCAAAAGGGTTGAGAACAAGTGAATAT
1 AGTAAGGTACGGTTACGCAAAAGGGTTGAGAACAAGTGAATAT
41034873 TGAATAGGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.39, C:0.09, G:0.31, T:0.21
Consensus pattern (44 bp):
AGTAAGGTACGGTTACGCAAAAGGGTTGAGAACAAGTGAATATG
Found at i:41047719 original size:44 final size:44
Alignment explanation
Indices: 41047655--41047744 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
41047645 CCTACATACC
41047655 TTCTTCTTACATCCCAATCTATTCTCAAATAATAATATTTTTAT
1 TTCTTCTTACATCCCAATCTATTCTCAAATAATAATATTTTTAT
*
41047699 TTCTTCTTACATCCCGATCTATTCTCAAATAATAATATTTTTAT
1 TTCTTCTTACATCCCAATCTATTCTCAAATAATAATATTTTTAT
41047743 TT
1 TT
41047745 TTATTAAATG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.30, C:0.20, G:0.01, T:0.49
Consensus pattern (44 bp):
TTCTTCTTACATCCCAATCTATTCTCAAATAATAATATTTTTAT
Found at i:41048422 original size:31 final size:29
Alignment explanation
Indices: 41048387--41048444 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
41048377 ACTTTCATTA
*
41048387 AAGTATTTTTGTAAAGGTTAAGCCCTTATAT
1 AAGTA-TTTTGAAAAGGTTAA-CCCTTATAT
*
41048418 AAGTATTTTGAAAAGTTTAACCCTTAT
1 AAGTATTTTGAAAAGGTTAACCCTTAT
41048445 GGGTTGGGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 13 0.52
31 5 0.20
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (29 bp):
AAGTATTTTGAAAAGGTTAACCCTTATAT
Found at i:41049640 original size:19 final size:18
Alignment explanation
Indices: 41049618--41049665 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
41049608 AAAATAAAGA
41049618 TAAAGAAATAATGT-AAAAT
1 TAAA-AAATAAT-TAAAAAT
41049637 TAAAAAACTAAATTAAAAAT
1 TAAAAAA-T-AATTAAAAAT
41049657 TAAAAAATA
1 TAAAAAATA
41049666 TTTTTGATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 7 0.27
20 15 0.58
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (18 bp):
TAAAAAATAATTAAAAAT
Found at i:41052097 original size:2 final size:2
Alignment explanation
Indices: 41052092--41052121 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41052082 AATATATATA
41052092 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
41052122 GTTATTAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:41064344 original size:11 final size:11
Alignment explanation
Indices: 41064328--41064380 Score: 63
Period size: 11 Copynumber: 4.6 Consensus size: 11
41064318 CTTCAAAAAT
41064328 AAATAAAAGTA
1 AAATAAAAGTA
41064339 AAATAAAAGTA
1 AAATAAAAGTA
*
41064350 AAATTAAAAAGAA
1 AAA-T-AAAAGTA
41064363 AAATAATAA-TA
1 AAATAA-AAGTA
41064374 AAATAAA
1 AAATAAA
41064381 TGGACTCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 1 0.03
11 23 0.62
12 4 0.11
13 9 0.24
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (11 bp):
AAATAAAAGTA
Found at i:41064365 original size:24 final size:24
Alignment explanation
Indices: 41064332--41064377 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41064322 AAAAATAAAT
*
41064332 AAAAGTAAAATAA-AAGTAAAATTA
1 AAAAGAAAAATAATAA-TAAAATTA
41064356 AAAAGAAAAATAATAATAAAAT
1 AAAAGAAAAATAATAATAAAAT
41064378 AAATGGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (24 bp):
AAAAGAAAAATAATAATAAAATTA
Found at i:41064376 original size:12 final size:11
Alignment explanation
Indices: 41064322--41064380 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
41064312 ATAAGTCTTC
41064322 AAAAAT-AAAT
1 AAAAATAAAAT
*
41064332 AAAAGTAAAAT
1 AAAAATAAAAT
*
41064343 AAAAGTAAAATT
1 AAAAATAAAA-T
*
41064355 AAAAAGAAAAAT
1 AAAAA-TAAAAT
*
41064367 AATAATAAAAT
1 AAAAATAAAAT
41064378 AAA
1 AAA
41064381 TGGACTCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 5 0.12
11 21 0.52
12 10 0.25
13 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:41072018 original size:24 final size:23
Alignment explanation
Indices: 41071983--41072031 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
41071973 ACAAGGTCTT
*
41071983 ATTTTCTTGCTT-GAGTTCTAGAA
1 ATTTTCTTGCTTCGAG-TCTAAAA
*
41072006 ATTTTTTTCGCTTCGAGTCTAAAA
1 ATTTTCTT-GCTTCGAGTCTAAAA
41072030 AT
1 AT
41072032 CTTTGACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 7 0.32
24 12 0.55
25 3 0.14
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (23 bp):
ATTTTCTTGCTTCGAGTCTAAAA
Found at i:41083376 original size:13 final size:14
Alignment explanation
Indices: 41083353--41083382 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
41083343 GACTTGTTCG
41083353 TATTAATTTTTTTA
1 TATTAATTTTTTTA
41083367 TATT-ATTTTTTTA
1 TATTAATTTTTTTA
41083380 TAT
1 TAT
41083383 AAAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTAATTTTTTTA
Found at i:41089136 original size:12 final size:12
Alignment explanation
Indices: 41089119--41089143 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41089109 TTACAGCTAG
41089119 TCTAGGAGTATT
1 TCTAGGAGTATT
41089131 TCTAGGAGTATT
1 TCTAGGAGTATT
41089143 T
1 T
41089144 TGGTGATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (12 bp):
TCTAGGAGTATT
Found at i:41092760 original size:126 final size:126
Alignment explanation
Indices: 41092488--41092924 Score: 562
Period size: 122 Copynumber: 3.5 Consensus size: 126
41092478 TTAAGTTCAT
* * * *
41092488 TGCATCCTGCTTGAAGCATTTTTAACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTC
1 TGCATTCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTC
* * *
41092553 AGGAACTA-TGTAGAAAAAGAGCGTCCACGTGGGAGTTTTTTTCTACAATTTTGTTGACAA
66 AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTATAATTTTGTTGACAG
* *
41092613 TGCA-TCTTGCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTT
1 TGCATTC-TACTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTT
* * * **
41092677 CATGAACTACTATAGAAAAAGAGTGTCCACGTGATAGCTTTTTTCTATAATTTTGTTGACAG
65 CAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTATAATTTTGTTGACAG
* * **
41092739 TGTATTCTACTTGAAGCGTTTTTGACACTA----TTCATAAATGTCTTCTCAAAATTATTTTTTC
1 TGCATTCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTC
* * * * * * *
41092800 AGGAACTACTGTAGAAAAAGAACATCCACGTGGGAGCTTTTTTTTGTATTTTTGCTGATAG
66 AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTATAATTTTGTTGACAG
* * **
41092861 TGCATCCTACTTGAAGCGTTTTTGATACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTT
1 TGCATTCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTT
41092925 GGGGGTAAAA
Statistics
Matches: 271, Mismatches: 34, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
122 104 0.38
124 1 0.00
125 66 0.24
126 98 0.36
127 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (126 bp):
TGCATTCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTC
AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTATAATTTTGTTGACAG
Found at i:41093058 original size:30 final size:28
Alignment explanation
Indices: 41093013--41093216 Score: 114
Period size: 34 Copynumber: 6.7 Consensus size: 28
41093003 ATTTAACCAT
41093013 AAACCCTAAACCCTAATTTAATTTATTTA
1 AAACCCTAAA-CCTAATTTAATTTATTTA
41093042 AAACCCTAGAATCCTAAATTACTTAATTTATTTAA
1 AAACCCTA-AA-CCT-AA-T--TTAATTTATTT-A
*
41093077 AAACCATAAACTCTAATTTAATTTATTTA
1 AAACCCTAAAC-CTAATTTAATTTATTTA
*
41093106 AAA-CCT-----TATTTTAATTTATTTA
1 AAACCCTAAACCTAATTTAATTTATTTA
* *
41093128 AAACCTATAAACCTTAAACCTTAATTTATTTA
1 AAACC-CTAAACC-T-AA-TTTAATTTATTTA
*
41093160 AAACCTTAAAAACCCTAATTTATTTAATTTATTTAA
1 AAACCCT--AAA-CCT-A---ATTTAATTTATTT-A
*
41093196 AAACCATAAACCCTAATTTAA
1 AAACCCTAAA-CCTAATTTAA
41093217 ATAATTTTTA
Statistics
Matches: 141, Mismatches: 10, Indels: 47
0.71 0.05 0.24
Matches are distributed among these distances:
22 18 0.13
23 1 0.01
24 1 0.01
28 2 0.01
29 12 0.09
30 23 0.16
31 4 0.03
32 19 0.13
33 10 0.07
34 24 0.17
35 19 0.13
36 8 0.06
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (28 bp):
AAACCCTAAACCTAATTTAATTTATTTA
Found at i:41093121 original size:52 final size:54
Alignment explanation
Indices: 41093064--41093167 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
41093054 CCTAAATTAC
*
41093064 TTAATTTATTTAAAAACC-ATAAA-CTCT-AA-TTTAATTTATTTAAAACCTTATT
1 TTAATTTATTT-AAAACCTATAAACCT-TAAACCTTAATTTATTTAAAACCTTATT
41093116 TTAATTTATTTAAAACCTATAAACCTTAAACCTTAATTTATTTAAAACCTTA
1 TTAATTTATTTAAAACCTATAAACCTTAAACCTTAATTTATTTAAAACCTTA
41093168 AAAACCCTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
51 6 0.13
52 17 0.36
53 4 0.09
54 20 0.43
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (54 bp):
TTAATTTATTTAAAACCTATAAACCTTAAACCTTAATTTATTTAAAACCTTATT
Found at i:41093222 original size:34 final size:35
Alignment explanation
Indices: 41093149--41093231 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 35
41093139 CCTTAAACCT
**
41093149 TAATTTATTT-AAAACCTTAAAAACCCTAATTTATT
1 TAATTTATTTAAAAACC-TAAAAACCCTAATTTAAA
*
41093184 TAATTTATTTAAAAACC-ATAAACCCTAATTTAAA
1 TAATTTATTTAAAAACCTAAAAACCCTAATTTAAA
41093218 TAATTT-TTATAAAA
1 TAATTTATT-TAAAA
41093232 TAACACCAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 2 0.05
34 25 0.58
35 10 0.23
36 6 0.14
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (35 bp):
TAATTTATTTAAAAACCTAAAAACCCTAATTTAAA
Found at i:41104266 original size:18 final size:20
Alignment explanation
Indices: 41104224--41104260 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41104214 ATATTTTATG
*
41104224 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
41104243 ATTATTTTAATGAGATAT
1 ATTATTTTAATGAGATAT
41104261 TTTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:41106466 original size:46 final size:46
Alignment explanation
Indices: 41106414--41106734 Score: 426
Period size: 46 Copynumber: 7.0 Consensus size: 46
41106404 AGTGTGCTCT
41106414 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
41106460 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
41106506 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
41106552 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** *** *
41106598 ATGACGGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
41106644 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * ** * * * *
41106690 ATGACAAAAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGA-TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
41106735 TCATGTCAAA
Statistics
Matches: 249, Mismatches: 25, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
46 216 0.87
47 33 0.13
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:41109298 original size:24 final size:25
Alignment explanation
Indices: 41109271--41109318 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
41109261 CCTGAATTAC
41109271 AAATAGAAAATAAAAC-TAAGTAAG
1 AAATAGAAAATAAAACTTAAGTAAG
*
41109295 AAATGGAAAATAAAACTTAAGTAA
1 AAATAGAAAATAAAACTTAAGTAA
41109319 AAACTATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.19
Consensus pattern (25 bp):
AAATAGAAAATAAAACTTAAGTAAG
Found at i:41111791 original size:53 final size:53
Alignment explanation
Indices: 41111650--41111864 Score: 216
Period size: 53 Copynumber: 4.2 Consensus size: 53
41111640 TGTGCGCCCT
* ** *
41111650 TATAAGACCATAGTTGGGCTATGGCATCTGTGCAATGTGAT-ACGTG-TTCCCG
1 TATAAGACCATAGTTGGGCTATGGCATCAGTGTGATGTGATAATGTGATT-CCG
* * * *
41111702 TATAAGACCATAGTTGGGCTATGGCTTCGGTATGATGTGATAATGTGATTCCA
1 TATAAGACCATAGTTGGGCTATGGCATCAGTGTGATGTGATAATGTGATTCCG
* * *
41111755 TATAAGACCATAGCTGGGCTATAGCGTCAGTGTGATGTGATAATGTGATTCCG
1 TATAAGACCATAGTTGGGCTATGGCATCAGTGTGATGTGATAATGTGATTCCG
* *
41111808 TATAAAACCATA-TATGGGATATGGCATC-G-GT-AT-T-AT-ATGTGA-TCCG
1 TATAAGACCATAGT-TGGGCTATGGCATCAGTGTGATGTGATAATGTGATTCCG
*
41111854 TGTAAGACCAT
1 TATAAGACCAT
41111865 GGGATGGATA
Statistics
Matches: 140, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
46 13 0.09
47 6 0.04
48 2 0.01
49 1 0.01
50 2 0.01
51 2 0.01
52 37 0.26
53 75 0.54
54 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (53 bp):
TATAAGACCATAGTTGGGCTATGGCATCAGTGTGATGTGATAATGTGATTCCG
Found at i:41112757 original size:37 final size:37
Alignment explanation
Indices: 41112705--41112778 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
41112695 TGGCTTAGCC
*
41112705 ACATGGGCGTATGCCTAGGCCATGTGCCGCTCTGATA
1 ACATGGGCGTATGCCTAGGCCATGTGCCCCTCTGATA
* * *
41112742 ACATGGGTGTGTGCCTAGGCCGTGTGCCCCTCTGATA
1 ACATGGGCGTATGCCTAGGCCATGTGCCCCTCTGATA
41112779 CTTAAGAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.16, C:0.27, G:0.31, T:0.26
Consensus pattern (37 bp):
ACATGGGCGTATGCCTAGGCCATGTGCCCCTCTGATA
Found at i:41113380 original size:22 final size:22
Alignment explanation
Indices: 41113352--41113406 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
41113342 TTCTTCTTTG
41113352 TTTTCTCCTTTTCTCCAAAATT
1 TTTTCTCCTTTTCTCCAAAATT
*
41113374 TTTTCTCCTCTTCTCCAAAATT
1 TTTTCTCCTTTTCTCCAAAATT
*
41113396 TATT-TCCTTTT
1 TTTTCTCCTTTT
41113407 TCCTTATCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTCTCCTTTTCTCCAAAATT
Found at i:41123987 original size:16 final size:14
Alignment explanation
Indices: 41123964--41124003 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 14
41123954 CGTCTTTCCC
41123964 TCTTTCTTTTCTCAT
1 TCTTTCTTTTCTC-T
41123979 TCTTTTCTTTTTCTCT
1 TC-TTTC-TTTTCTCT
41123995 TCTTTCTTT
1 TCTTTCTTT
41124004 AACCAAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.13
15 6 0.26
16 7 0.30
17 7 0.30
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (14 bp):
TCTTTCTTTTCTCT
Found at i:41125001 original size:21 final size:21
Alignment explanation
Indices: 41124972--41125014 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
41124962 ATAAACAATA
*
41124972 TAATTGTTTTG-CTTTTTAACT
1 TAATGGTTTTGAC-TTTTAACT
41124993 TAATGGTTTTGACTTTTAACT
1 TAATGGTTTTGACTTTTAACT
41125014 T
1 T
41125015 TAGAAAAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (21 bp):
TAATGGTTTTGACTTTTAACT
Found at i:41126289 original size:10 final size:10
Alignment explanation
Indices: 41126257--41126298 Score: 50
Period size: 9 Copynumber: 4.0 Consensus size: 10
41126247 GTCTGATTAA
41126257 TTTTAATTTT
1 TTTTAATTTT
41126267 AATTTTAAATTTT
1 --TTTT-AATTTT
41126280 TTTT-ATTTT
1 TTTTAATTTT
41126289 TTTTAATTTT
1 TTTTAATTTT
41126299 CCAAAACTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 9 0.32
10 5 0.18
11 4 0.14
12 4 0.14
13 6 0.21
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTAATTTT
Found at i:41127839 original size:42 final size:42
Alignment explanation
Indices: 41127776--41127902 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
41127766 CTTCGTTTTC
** * *
41127776 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
41127819 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
41127860 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
41127901 TC
1 TC
41127903 TCACTGATGC
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
41 10 0.13
42 64 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:41127964 original size:47 final size:46
Alignment explanation
Indices: 41127861--41127982 Score: 163
Period size: 47 Copynumber: 2.6 Consensus size: 46
41127851 ATTCATATAT
* * * * *
41127861 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
41127907 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
41127954 CGATGCCATATCCCAGATATGGTCTTATA
1 CGATGCCATATCCCAGATATGGTCTTATA
41127983 TGGAAATCAC
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
46 26 0.39
47 40 0.61
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:41128051 original size:31 final size:31
Alignment explanation
Indices: 41128016--41128156 Score: 219
Period size: 31 Copynumber: 4.5 Consensus size: 31
41128006 CTTGTAGCGA
* *
41128016 AGCTACCACTATTCACTGATAAGGTAGCCGG
1 AGCTACCACTTTTCACTGATCAGGTAGCCGG
*
41128047 AGCTACCATTTTTCACTGATCAGGTAGCCGG
1 AGCTACCACTTTTCACTGATCAGGTAGCCGG
41128078 AGCTACCACTTTTCACTGATCAGGTAGCCGG
1 AGCTACCACTTTTCACTGATCAGGTAGCCGG
* ** *
41128109 AACTACCACTTTTCACTGATCAGGTAGTTGA
1 AGCTACCACTTTTCACTGATCAGGTAGCCGG
41128140 AGCTACCACTTTTCACT
1 AGCTACCACTTTTCACT
41128157 TGTCATTTGT
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 101 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (31 bp):
AGCTACCACTTTTCACTGATCAGGTAGCCGG
Found at i:41128236 original size:50 final size:50
Alignment explanation
Indices: 41128138--41128358 Score: 390
Period size: 50 Copynumber: 4.4 Consensus size: 50
41128128 TCAGGTAGTT
* * *
41128138 GAAGCTACCACTTTTCACTTGTCA-TTTGTCATTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGTGTAGCC
41128189 GAAGCTATCACTTATCACTTTCACTTTTCCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTTCACTTTTCCTTGATCAGATAAGTGTAGCC
41128239 GAAGCTATCACTTATCACTTTCACTTTTCCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTTCACTTTTCCTTGATCAGATAAGTGTAGCC
41128289 GAAGCTATCACTTATCACTTTCACTTTTCCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTTCACTTTTCCTTGATCAGATAAGTGTAGCC
41128339 GAAGCTATCACTTATCACTT
1 GAAGCTATCACTTATCACTT
41128359 GTTGCCATGG
Statistics
Matches: 166, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
50 145 0.87
51 21 0.13
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (50 bp):
GAAGCTATCACTTATCACTTTCACTTTTCCTTGATCAGATAAGTGTAGCC
Found at i:41128495 original size:14 final size:15
Alignment explanation
Indices: 41128476--41128504 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41128466 TTTTATCATC
41128476 AACACAT-ATGAAAT
1 AACACATCATGAAAT
41128490 AACACATCATGAAAT
1 AACACATCATGAAAT
41128505 TCATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (15 bp):
AACACATCATGAAAT
Found at i:41138878 original size:41 final size:41
Alignment explanation
Indices: 41138754--41139060 Score: 386
Period size: 41 Copynumber: 7.5 Consensus size: 41
41138744 ATAACGGCAT
* * * * *
41138754 TTTTAGTAAGACGCCGCTAAA-AACAGAGCAATAGCGGTG-
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
* * * * *
41138793 TTTTAGTAAAAAGCACCGCTAAA-AACAAAGCATTAGTGGCGC
1 TTTTGGT-AAAA-CGCCGCTAAAGACCAGAGCATTAGCGGCGC
* *
41138835 TTTTGGTAAAACGCCGCTAAAGACCAGAGTATTATCGGCGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
** *
41138876 TTTTATTAAAACGCCGTTAAAGACCAGAGCATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
*
41138917 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGACGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
41138958 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
** * *
41138999 TTTTATTAAAACGACGCTAAAGACCAGAACATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
*
41139040 TTTTGGTAAAACACCGCTAAA
1 TTTTGGTAAAACGCCGCTAAA
41139061 AGTCATATAA
Statistics
Matches: 233, Mismatches: 31, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
39 7 0.03
40 12 0.05
41 208 0.89
42 6 0.03
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (41 bp):
TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
Found at i:41138959 original size:123 final size:122
Alignment explanation
Indices: 41138754--41139061 Score: 431
Period size: 123 Copynumber: 2.5 Consensus size: 122
41138744 ATAACGGCAT
* * * * * *
41138754 TTTTAGTAAGACGCCGCTAAA-AACAGAGCAATAGCGGTG-TTTTAGTAAAAAGCACCGCTAAAA
1 TTTTATTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGT-AAAA-CACCGCTAAAA
* * * *
41138817 ACAAAGCATTAGTGGCGCTTTTGGTAAAACGCCGCTAAAGACCAGAGTATTATCGGCGC
64 ACAAAGCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
* * *
41138876 TTTTATTAAAACGCCGTTAAAGACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAGAC
1 TTTTATTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTAAAACACCGCTAAA-AA
*
41138941 CAGAGCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
65 CAAAGCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
* *
41138999 TTTTATTAAAACGACGCTAAAGACCAGAACATTAGCGGCGCTTTTGGTAAAACACCGCTAAAA
1 TTTTATTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTAAAACACCGCTAAAA
41139062 GTCATATAAC
Statistics
Matches: 165, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
122 28 0.17
123 131 0.79
124 6 0.04
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (122 bp):
TTTTATTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTAAAACACCGCTAAAAAC
AAAGCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
Found at i:41139300 original size:21 final size:21
Alignment explanation
Indices: 41139223--41139300 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
41139213 TTATCATTGT
41139223 AGTTTAAG-GTTTATGGTTTAA
1 AGTTTAAGAGTTTATGGTTT-A
*
41139244 AGTTTATGAGTTAACTATGGTTTA
1 AGTTTAAGAGTT---TATGGTTTA
* * *
41139268 AG-ATATATAGTTTAGGGTTTA
1 AGTTTA-AGAGTTTATGGTTTA
41139289 AGTTTAAGAGTT
1 AGTTTAAGAGTT
41139301 AACTAGTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
21 22 0.50
22 5 0.11
23 2 0.05
24 7 0.16
25 8 0.18
ACGTcount: A:0.31, C:0.01, G:0.23, T:0.45
Consensus pattern (21 bp):
AGTTTAAGAGTTTATGGTTTA
Found at i:41139609 original size:21 final size:21
Alignment explanation
Indices: 41139585--41139630 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
41139575 TGATTTAATT
* *
41139585 TTTAAGGTTTGGAGATTAGGG
1 TTTAAGGTTTAGAGATTAGGC
* *
41139606 TTTAGGGTTTAGAGTTTAGGC
1 TTTAAGGTTTAGAGATTAGGC
41139627 TTTA
1 TTTA
41139631 TAATTTAGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.02, G:0.33, T:0.43
Consensus pattern (21 bp):
TTTAAGGTTTAGAGATTAGGC
Found at i:41145169 original size:9 final size:9
Alignment explanation
Indices: 41145152--41145207 Score: 58
Period size: 9 Copynumber: 5.9 Consensus size: 9
41145142 CTTCTCTCAT
41145152 ATAACTTAC
1 ATAACTTAC
*
41145161 ATAATTTAC
1 ATAACTTAC
*
41145170 ATAACTCAC
1 ATAACTTAC
*
41145179 ATAACGTAC
1 ATAACTTAC
41145188 ATAACAACTTAC
1 AT---AACTTAC
41145200 ATAACTTA
1 ATAACTTA
41145208 ACTAATACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 30 0.79
12 8 0.21
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.30
Consensus pattern (9 bp):
ATAACTTAC
Found at i:41150780 original size:21 final size:21
Alignment explanation
Indices: 41150754--41150801 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
41150744 TCAACTCAGA
41150754 GCGGAGGCAGCAGCGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
*
41150775 GCGGAGGCAGCAGTGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
*
41150796 GAGGAG
1 GCGGAG
41150802 CAGAACAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.58, T:0.02
Consensus pattern (21 bp):
GCGGAGGCAGCAGCGAGGGAG
Found at i:41151226 original size:43 final size:43
Alignment explanation
Indices: 41151094--41151276 Score: 158
Period size: 43 Copynumber: 4.3 Consensus size: 43
41151084 ACTGGGCAAA
* * * *
41151094 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTA-AAGACCAAGACTT
1 TTAGCGGCGTTTTTTAAAAATGCGCCGCTATAAGTCCTAGTC-T
* * * * ** * *
41151137 TTAGTGGCGCTGTTTTAAAAA-ACGCCACTA-AAGAACAAGACTT
1 TTAGCGGCG-TTTTTTAAAAATGCGCCGCTATAAGTCCTAGTC-T
* * * *
41151180 TTAGCGACGTTTTTTATATAA-GCGTCGCTATAAGTCCTGGTCT
1 TTAGCGGCGTTTTTTA-AAAATGCGCCGCTATAAGTCCTAGTCT
41151223 TTAGCGGCGTTTTTTAAAAATGCGCCGCTATAAGTCCTAGTCT
1 TTAGCGGCGTTTTTTAAAAATGCGCCGCTATAAGTCCTAGTCT
41151266 TTAGCGGCGTT
1 TTAGCGGCGTT
41151277 ACATATAGCG
Statistics
Matches: 115, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
42 9 0.08
43 90 0.78
44 16 0.14
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (43 bp):
TTAGCGGCGTTTTTTAAAAATGCGCCGCTATAAGTCCTAGTCT
Found at i:41161571 original size:18 final size:19
Alignment explanation
Indices: 41161545--41161580 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
41161535 GAAGATATTA
*
41161545 TTTTGTTTTATT-ATTTAT
1 TTTTATTTTATTAATTTAT
41161563 TTTTATTTTATTAATTTA
1 TTTTATTTTATTAATTTA
41161581 GGATTAAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTTATTTTATTAATTTAT
Found at i:41166650 original size:21 final size:21
Alignment explanation
Indices: 41166625--41166693 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
41166615 TATAATGATT
41166625 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
41166646 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
41166666 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
41166686 ATTATTAT
1 ATTATTAT
41166694 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:41166706 original size:15 final size:14
Alignment explanation
Indices: 41166680--41166710 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
41166670 TATGGTTTTA
41166680 TATTAGATTATTAT
1 TATTAGATTATTAT
41166694 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
41166709 TA
1 TA
41166711 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:41176893 original size:21 final size:19
Alignment explanation
Indices: 41176859--41176923 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 19
41176849 GCTTTCACAT
*
41176859 TAAAAAAATAATAAATAAA
1 TAAATAAATAATAAATAAA
*
41176878 TAAAT-AATAA-CAATAAA
1 TAAATAAATAATAAATAAA
41176895 -ATAATAAAT-ATAAATATAA
1 TA-AATAAATAATAAATA-AA
41176914 T-AATAAATAA
1 TAAATAAATAA
41176924 AATTTAAGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
16 1 0.03
17 10 0.27
18 19 0.51
19 7 0.19
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAATAAATAATAAATAAA
Found at i:41176896 original size:18 final size:16
Alignment explanation
Indices: 41176859--41176926 Score: 72
Period size: 15 Copynumber: 4.4 Consensus size: 16
41176849 GCTTTCACAT
41176859 TAAAA-AAATAATAAA
1 TAAAATAAATAATAAA
41176874 T-AAATAAATAAT-AA
1 TAAAATAAATAATAAA
* *
41176888 CAATA-AAATAATAAA
1 TAAAATAAATAATAAA
41176903 TATAAATATAATAATAAA
1 TA-AAATA-AATAATAAA
41176921 TAAAAT
1 TAAAAT
41176927 TTAAGACGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 12 0.28
15 13 0.30
16 2 0.05
17 5 0.12
18 11 0.26
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAATAAATAATAAA
Done.