Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold324
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: 2336777
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 16 of 16
Found at i:2264269 original size:19 final size:18
Alignment explanation
Indices: 2264241--2264279 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
2264231 AAACTATTTT
2264241 AAATTTAAAAAATTCAAA
1 AAATTTAAAAAATTCAAA
2264259 AAATTTAAAAAAATTCAAA
1 AAATTT-AAAAAATTCAAA
2264278 AA
1 AA
2264280 TAAAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATTTAAAAAATTCAAA
Found at i:2266304 original size:11 final size:11
Alignment explanation
Indices: 2266287--2266328 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
2266277 ATTCATGTCA
2266287 TATTATATTTT
1 TATTATATTTT
*
2266298 TACTATATTTT
1 TATTATATTTT
*
2266309 AATTA-ATTTT
1 TATTATATTTT
2266319 TATTATATTT
1 TATTATATTT
2266329 AAACTCTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTATATTTT
Found at i:2266319 original size:21 final size:22
Alignment explanation
Indices: 2266288--2266328 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2266278 TTCATGTCAT
2266288 ATTATATTTTTACTATATTTTA
1 ATTATATTTTTACTATATTTTA
*
2266310 ATTA-ATTTTTATTATATTT
1 ATTATATTTTTACTATATTT
2266329 AAACTCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTATATTTTTACTATATTTTA
Found at i:2266533 original size:40 final size:40
Alignment explanation
Indices: 2266457--2266534 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
2266447 GTAATAGTAT
*
2266457 TTATAAGTTGGGTCATACCTGATTTAGGTTGAGTTTAAGCA
1 TTATAAGTTGGGTCATA-CTGATTTAGATTGAGTTTAAGCA
*
2266498 TTATAAGTTGGGTCATA-TGAATTTAGATTGGGTTTAA
1 TTATAAGTTGGGTCATACTG-ATTTAGATTGAGTTTAA
2266535 ATATAGTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 2 0.06
40 15 0.44
41 17 0.50
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.41
Consensus pattern (40 bp):
TTATAAGTTGGGTCATACTGATTTAGATTGAGTTTAAGCA
Found at i:2267812 original size:11 final size:10
Alignment explanation
Indices: 2267785--2267829 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
2267775 ATAAAATATA
*
2267785 TTTTTTATATA
1 TTTTTTAT-TC
2267796 TTTTTTATTC
1 TTTTTTATTC
2267806 TTCTTTTATTC
1 TT-TTTTATTC
*
2267817 TTTTTTTTTC
1 TTTTTTATTC
2267827 TTT
1 TTT
2267830 AACCAATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
10 13 0.42
11 18 0.58
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTATTC
Found at i:2267822 original size:21 final size:22
Alignment explanation
Indices: 2267787--2267828 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2267777 AAAATATATT
2267787 TTTTATATATTTTTTATTCTTC
1 TTTTATATATTTTTTATTCTTC
* *
2267809 TTTTAT-TCTTTTTTTTTCTT
1 TTTTATATATTTTTTATTCTT
2267829 TAACCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTATATATTTTTTATTCTTC
Found at i:2267991 original size:16 final size:16
Alignment explanation
Indices: 2267966--2268003 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2267956 TACTTGAATT
*
2267966 ATAATATAATTTAATA
1 ATAATTTAATTTAATA
2267982 ATAATTTAATTTAATA
1 ATAATTTAATTTAATA
*
2267998 GTAATT
1 ATAATT
2268004 AAAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAATTTAATTTAATA
Found at i:2267996 original size:26 final size:27
Alignment explanation
Indices: 2267962--2268014 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
2267952 CATGTACTTG
*
2267962 AATTATAATA-TAATTTAATAATAATTT
1 AATTATAATAGTAA-TTAAAAATAATTT
2267989 AATT-TAATAGTAATTAAAAATAATTT
1 AATTATAATAGTAATTAAAAATAATTT
2268015 TAAGATTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
AATTATAATAGTAATTAAAAATAATTT
Found at i:2268603 original size:14 final size:14
Alignment explanation
Indices: 2268584--2268610 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2268574 TTTGTTTTTT
2268584 TAATTTATTTTAAA
1 TAATTTATTTTAAA
2268598 TAATTTATTTTAA
1 TAATTTATTTTAA
2268611 CGAGGTTAGT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTTATTTTAAA
Found at i:2268980 original size:20 final size:20
Alignment explanation
Indices: 2268954--2269003 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2268944 TTTTTATTTT
*
2268954 TATATTTAAATTTTATATTAA
1 TATATTTAAATTTTA-AATAA
**
2268975 TA-ATTTATTTTTTAAATAA
1 TATATTTAAATTTTAAATAA
2268994 TATATTTAAA
1 TATATTTAAA
2269004 AGAGTTATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
19 6 0.26
20 15 0.65
21 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATTTAAATTTTAAATAA
Found at i:2272959 original size:16 final size:16
Alignment explanation
Indices: 2272930--2272963 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2272920 GCTGGTGTGG
*
2272930 ATAAACGAAACAATTA
1 ATAAAAGAAACAATTA
*
2272946 ATAAAAGAACCAATTA
1 ATAAAAGAAACAATTA
2272962 AT
1 AT
2272964 TTTTCTGCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.21
Consensus pattern (16 bp):
ATAAAAGAAACAATTA
Found at i:2275162 original size:33 final size:34
Alignment explanation
Indices: 2275104--2275172 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 34
2275094 TTTTATTTTA
* * *
2275104 AATTTATTAATATTAAAGACGAATATTATC-TCT
1 AATTTAATAATATTAAAGACAAATATAATCTTCT
* *
2275137 AATTTAATAGTATTAAAGATAAATATAATCTTCT
1 AATTTAATAATATTAAAGACAAATATAATCTTCT
2275171 AA
1 AA
2275173 ACCTTTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 25 0.83
34 5 0.17
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (34 bp):
AATTTAATAATATTAAAGACAAATATAATCTTCT
Found at i:2276866 original size:22 final size:22
Alignment explanation
Indices: 2276841--2276885 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2276831 TATATTTAAA
2276841 AAATAAATTTAAATAAA-AAATT
1 AAATAAATTTAAA-AAATAAATT
**
2276863 AAATTTATTTAAAAAATAAATT
1 AAATAAATTTAAAAAATAAATT
2276885 A
1 A
2276886 GATTTTGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATAAATTTAAAAAATAAATT
Found at i:2276890 original size:18 final size:18
Alignment explanation
Indices: 2276829--2276890 Score: 74
Period size: 18 Copynumber: 3.5 Consensus size: 18
2276819 GAATAAAAAT
2276829 ATTATATTTAAAAAATAA
1 ATTATATTTAAAAAATAA
**
2276847 ATT-TAAATAAAAAATTAA
1 ATTATATTTAAAAAA-TAA
2276865 ATT-TATTTAAAAAATAA
1 ATTATATTTAAAAAATAA
*
2276882 ATTAGATTT
1 ATTATATTT
2276891 TGACTCTCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 15 0.41
18 22 0.59
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATTATATTTAAAAAATAA
Found at i:2276890 original size:22 final size:22
Alignment explanation
Indices: 2276847--2276890 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2276837 TAAAAAATAA
2276847 ATTTAAATAAAAAATTAAATTT
1 ATTTAAATAAAAAATTAAATTT
*
2276869 ATTTAAA-AAATAAATTAGATTT
1 ATTTAAATAAA-AAATTAAATTT
2276891 TGACTCTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
ATTTAAATAAAAAATTAAATTT
Found at i:2277358 original size:21 final size:21
Alignment explanation
Indices: 2277332--2277373 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2277322 AAATAATCAC
2277332 ATTAACTCTCCATTAGACCTA
1 ATTAACTCTCCATTAGACCTA
2277353 ATTAACTCTCCATTAGACCTA
1 ATTAACTCTCCATTAGACCTA
2277374 CTCATGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (21 bp):
ATTAACTCTCCATTAGACCTA
Found at i:2277771 original size:25 final size:24
Alignment explanation
Indices: 2277723--2277807 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 24
2277713 ACCTTTCGTT
2277723 ATTTTTATTTTTAA-AAAATTTTAA
1 ATTTTTATTTTTAATAAAATTTT-A
**
2277747 GATTTTTATTTTTAATTTAA-TTTA
1 -ATTTTTATTTTTAATAAAATTTTA
*
2277771 ATTAATTTATTTTTAATATAAAATTTA
1 ATT--TTTATTTTTAATA-AAATTTTA
*
2277798 ATTATTATTT
1 ATTTTTATTT
2277808 AACATAAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
23 3 0.06
24 1 0.02
25 35 0.70
26 4 0.08
27 7 0.14
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (24 bp):
ATTTTTATTTTTAATAAAATTTTA
Found at i:2277808 original size:23 final size:23
Alignment explanation
Indices: 2277772--2277815 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2277762 TTTAATTTAA
*
2277772 TTAATTTATTTTTAATATAAAAT
1 TTAATTTATTTTTAACATAAAAT
2277795 TTAA-TTATTATTTAACATAAA
1 TTAATTTATT-TTTAACATAAA
2277816 CATAACTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAATTTATTTTTAACATAAAAT
Found at i:2280505 original size:37 final size:37
Alignment explanation
Indices: 2280458--2280540 Score: 157
Period size: 37 Copynumber: 2.2 Consensus size: 37
2280448 ATAATCTAAA
2280458 AATTCTATAATAGTACAAAAATAATTATAACTTTTATG
1 AATT-TATAATAGTACAAAAATAATTATAACTTTTATG
2280496 AATTTATAATAGTACAAAAATAATTATAACTTTTATG
1 AATTTATAATAGTACAAAAATAATTATAACTTTTATG
2280533 AATTTATA
1 AATTTATA
2280541 CTTTTGAGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 41 0.91
38 4 0.09
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (37 bp):
AATTTATAATAGTACAAAAATAATTATAACTTTTATG
Found at i:2280732 original size:3 final size:3
Alignment explanation
Indices: 2280724--2280767 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2280714 AGAAATGCAC
2280724 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2280768 CAAAGGTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2281431 original size:15 final size:15
Alignment explanation
Indices: 2281399--2281428 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2281389 AAAGTATTTG
2281399 ATAAAAAAGAAGAAA
1 ATAAAAAAGAAGAAA
2281414 ATAAAAAAG-AGAAA
1 ATAAAAAAGAAGAAA
2281428 A
1 A
2281429 ATATATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (15 bp):
ATAAAAAAGAAGAAA
Found at i:2281640 original size:23 final size:24
Alignment explanation
Indices: 2281598--2281653 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
2281588 AATATGTAAG
*
2281598 AATTAATTATTTCATTAATT-TTTA
1 AATT-ATTATTTCATTAATTGATTA
2281622 AATTATTATTT-ATTAAATTGATTA
1 AATTATTATTTCATT-AATTGATTA
2281646 AA-TATTAT
1 AATTATTAT
2281654 AAAAATGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.10
23 17 0.59
24 9 0.31
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
AATTATTATTTCATTAATTGATTA
Found at i:2282575 original size:20 final size:20
Alignment explanation
Indices: 2282543--2282581 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2282533 TATTACAAAA
*
2282543 AAATAATACAAATATAATAT
1 AAATAATACAAATAAAATAT
2282563 AAATATATA-AAATAAAATA
1 AAATA-ATACAAATAAAATA
2282582 ATTACACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATAATACAAATAAAATAT
Found at i:2282582 original size:18 final size:17
Alignment explanation
Indices: 2282539--2282598 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 17
2282529 TAATTATTAC
2282539 AAAA-AAATAATACAAAT
1 AAAATAAATAATA-AAAT
2282556 ATAATATAAATATATAAAAT
1 A-AA-ATAAATA-ATAAAAT
* *
2282576 AAAATAATTACACAAAAT
1 AAAATAAATA-ATAAAAT
2282594 AAAAT
1 AAAAT
2282599 TAAGAGCTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.03
18 19 0.53
19 3 0.08
20 10 0.28
21 3 0.08
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAATAAATAATAAAAT
Found at i:2282999 original size:17 final size:17
Alignment explanation
Indices: 2282975--2283031 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
2282965 TTGTAATTTT
2282975 TATTTAATAATAAATTAG
1 TATTTAATAATAAATT-G
*
2282993 T-TTTAAT--TAAATTT
1 TATTTAATAATAAATTG
* *
2283007 TATTTAATAATAATTTT
1 TATTTAATAATAAATTG
2283024 TATTTAAT
1 TATTTAAT
2283032 TTTTGTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 1 0.03
15 12 0.35
17 20 0.59
18 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTTAATAATAAATTG
Found at i:2283740 original size:15 final size:16
Alignment explanation
Indices: 2283720--2283756 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2283710 AATTTATCAT
2283720 TTAAAAAAAT-AAAAA
1 TTAAAAAAATAAAAAA
*
2283735 TT-AAAAATTAAAAAA
1 TTAAAAAAATAAAAAA
2283750 TTAAAAA
1 TTAAAAA
2283757 TAATTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.32
15 9 0.47
16 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
TTAAAAAAATAAAAAA
Found at i:2283992 original size:23 final size:23
Alignment explanation
Indices: 2283948--2284000 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2283938 TAATATTTAA
*
2283948 AATTAAAAAAATAAATTAAAAAT
1 AATTAATAAAATAAATTAAAAAT
2283971 AATTAATAAAAT-AATTAAAAAAT
1 AATTAATAAAATAAATT-AAAAAT
*
2283994 ATTTAAT
1 AATTAAT
2284001 TAATCTGATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AATTAATAAAATAAATTAAAAAT
Found at i:2283994 original size:11 final size:11
Alignment explanation
Indices: 2283948--2283999 Score: 61
Period size: 11 Copynumber: 4.5 Consensus size: 11
2283938 TAATATTTAA
2283948 AATTAAAAAAAT
1 AATT-AAAAAAT
2283960 AAATT-AAAAAT
1 -AATTAAAAAAT
2283971 AATTAATAAAAT
1 AATTAA-AAAAT
2283983 AATTAAAAAAT
1 AATTAAAAAAT
*
2283994 ATTTAA
1 AATTAA
2284000 TTAATCTGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
10 4 0.11
11 17 0.47
12 11 0.31
13 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AATTAAAAAAT
Found at i:2285767 original size:9 final size:9
Alignment explanation
Indices: 2285753--2285785 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
2285743 TTTCCCACAG
2285753 CAACAAGTC
1 CAACAAGTC
2285762 CAACAAGTC
1 CAACAAGTC
*
2285771 CATCAAGTC
1 CAACAAGTC
2285780 CAACAA
1 CAACAA
2285786 TAGCTCGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.45, C:0.33, G:0.09, T:0.12
Consensus pattern (9 bp):
CAACAAGTC
Found at i:2287075 original size:14 final size:14
Alignment explanation
Indices: 2287056--2287094 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2287046 AAAGCATATG
2287056 TTTCTTTTTTTCT-T
1 TTTCTTTTTTT-TGT
2287070 TTTCTTTTTTTTGT
1 TTTCTTTTTTTTGT
*
2287084 TTCCTTTTTTT
1 TTTCTTTTTTT
2287095 GTATCAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 1 0.04
14 22 0.96
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (14 bp):
TTTCTTTTTTTTGT
Found at i:2287079 original size:13 final size:13
Alignment explanation
Indices: 2287054--2287096 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
2287044 TGAAAGCATA
2287054 TGTTTCTTTTTTT
1 TGTTTCTTTTTTT
*
2287067 CTTTTTCTTTTTTT
1 -TGTTTCTTTTTTT
*
2287081 TGTTTCCTTTTTT
1 TGTTTCTTTTTTT
2287094 TGT
1 TGT
2287097 ATCAAGTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (13 bp):
TGTTTCTTTTTTT
Found at i:2289152 original size:19 final size:19
Alignment explanation
Indices: 2289112--2289154 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2289102 TACTAATTTT
*
2289112 TAATTATCTAATATTAAAA
1 TAATTATCTAACATTAAAA
*
2289131 TAATTATTTAACA-TAAATA
1 TAATTATCTAACATTAAA-A
2289150 TAATT
1 TAATT
2289155 TTATTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATTATCTAACATTAAAA
Found at i:2289171 original size:17 final size:17
Alignment explanation
Indices: 2289151--2289235 Score: 59
Period size: 17 Copynumber: 4.8 Consensus size: 17
2289141 ACATAAATAT
2289151 AATTTT-ATTAATTATCA
1 AATTTTAATTAA-TATCA
2289168 AATTTTAATTAATATCATA
1 AATTTTAATTAATATC--A
* * *
2289187 AATATTAAATAA-ATTTA
1 AATTTTAATTAATA-TCA
*
2289204 AATTTTTATTATATAT-A
1 AATTTTAATTA-ATATCA
2289221 AATTTTAATTTAATA
1 AATTTTAA-TTAATA
2289236 ATTTTTTTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
17 30 0.56
18 11 0.20
19 13 0.24
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTTAATTAATATCA
Found at i:2290808 original size:26 final size:25
Alignment explanation
Indices: 2290779--2290848 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 25
2290769 GTCAGATTTG
2290779 TTTTTTAGTTATATAATATATATTAA
1 TTTTTTA-TTATATAATATATATTAA
*
2290805 TTTTATATT-TAT-ATAT-TATATAA
1 TTTTTTATTATATAATATATAT-TAA
*
2290828 -TTTTTATTGTATAATATATAT
1 TTTTTTATTATATAATATATAT
2290849 ATATAATGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 10 0.26
23 10 0.26
24 7 0.18
25 5 0.13
26 6 0.16
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (25 bp):
TTTTTTATTATATAATATATATTAA
Found at i:2290820 original size:21 final size:22
Alignment explanation
Indices: 2290794--2290849 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
2290784 TAGTTATATA
2290794 ATATATAT-TAATTTTATATT-T
1 ATATATATATAATTTT-TATTGT
2290815 ATATATTATATAATTTTTATTGT
1 ATATA-TATATAATTTTTATTGT
2290838 ATAATATATATA
1 AT-ATATATATA
2290850 TATAATGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 5 0.16
22 7 0.23
23 16 0.52
24 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATATATATATAATTTTTATTGT
Found at i:2290860 original size:26 final size:28
Alignment explanation
Indices: 2290814--2290867 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
2290804 ATTTTATATT
* *
2290814 TATATATTATATAATTTTTATTGTATAA
1 TATATATTATATAATTGTTATAGTATAA
2290842 TATATA-TATATAA-TGTTATAGTATAA
1 TATATATTATATAATTGTTATAGTATAA
2290868 ACATTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 11 0.46
27 7 0.29
28 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (28 bp):
TATATATTATATAATTGTTATAGTATAA
Found at i:2291133 original size:19 final size:20
Alignment explanation
Indices: 2291106--2291147 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
2291096 TAAACACCTA
2291106 TTATAATTTTATAAAAT-TAT
1 TTATAATTTTA-AAAATATAT
2291126 TTAT-ATTTTAAAAATATAT
1 TTATAATTTTAAAAATATAT
2291145 TTA
1 TTA
2291148 AAGTACTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 12 0.57
20 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATAATTTTAAAAATATAT
Found at i:2292440 original size:16 final size:16
Alignment explanation
Indices: 2292421--2292460 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2292411 TTTGATATTC
2292421 AAGTTATTTAAAGTTT
1 AAGTTATTTAAAGTTT
**
2292437 AAGTTATTTCGAGTTT
1 AAGTTATTTAAAGTTT
*
2292453 GAGTTATT
1 AAGTTATT
2292461 CTGATTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (16 bp):
AAGTTATTTAAAGTTT
Found at i:2292485 original size:16 final size:17
Alignment explanation
Indices: 2292466--2292500 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2292456 TTATTCTGAT
2292466 TTTAGATT-ATTTCAAA
1 TTTAGATTGATTTCAAA
*
2292482 TTTAGATTGTTTTCAAA
1 TTTAGATTGATTTCAAA
2292499 TT
1 TT
2292501 GATCAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.54
Consensus pattern (17 bp):
TTTAGATTGATTTCAAA
Found at i:2294422 original size:11 final size:11
Alignment explanation
Indices: 2294398--2294484 Score: 52
Period size: 12 Copynumber: 7.2 Consensus size: 11
2294388 ATGTGAGTAC
*
2294398 AAATACATAAAA
1 AAATA-ATATAA
2294410 AATATAAT-TAA
1 AA-ATAATATAA
2294421 AACATAATATAA
1 AA-ATAATATAA
2294433 AAATAATATGAA
1 AAATAATAT-AA
*
2294445 TACAATATAAATAA
1 -A-AATA-ATATAA
2294459 ATAA-ACATATAA
1 A-AATA-ATATAA
2294471 AAATATATATAA
1 AAATA-ATATAA
2294483 AA
1 AA
2294485 TAAATTATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
11 18 0.30
12 27 0.44
13 7 0.11
14 6 0.10
15 3 0.05
ACGTcount: A:0.68, C:0.05, G:0.01, T:0.26
Consensus pattern (11 bp):
AAATAATATAA
Found at i:2294476 original size:156 final size:157
Alignment explanation
Indices: 2294245--2294562 Score: 423
Period size: 156 Copynumber: 2.0 Consensus size: 157
2294235 TTAATACAAT
* ** * *
2294245 ATAAGAAAAATAATTAAAACATAATATGAAAAATAACTTTAATATGACAAGAATAAATCAACATG
1 ATAAGAAAAATAATTAAAACATAATATGAAAAATAACTTGAATACAACAAGAATAAATAAACATA
2294310 TCAAAAAATATATATAAAATAAATTATTAACATATAAAAATTTATAAAAAATTAAAAAC-CTTTA
66 T-AAAAAATATATATAAAATAAATTATTAACATATAAAAATTTATAAAAAATTAAAAACTCTTTA
*
2294374 AGCACAAAAAATTAATGTGAGTACAAATAC
130 AACACAAAAAA--AATGTGAGTACAAATAC
*
2294404 ATAA-AAAATATAATTAAAACATAATAT-AAAAATAA-TATGAATACAATATA-AATAAATAAAC
1 ATAAGAAAA-ATAATTAAAACATAATATGAAAAATAACT-TGAATACAACA-AGAATAAATAAAC
* * * * *
2294465 ATAT-AAAAATATATATAAAATAAATTATTAATATATAAAAATTTATATAAATTTCAAAACTTTT
63 ATATAAAAAATATATATAAAATAAATTATTAACATATAAAAATTTATAAAAAATTAAAAACTCTT
*
2294529 TAAACACAAAAAAATTGTGAGTACAAATAC
128 TAAACACAAAAAAAATGTGAGTACAAATAC
2294559 ATAA
1 ATAA
2294563 CTTTGTTTCT
Statistics
Matches: 142, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
155 20 0.14
156 52 0.37
157 15 0.11
158 32 0.23
159 23 0.16
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (157 bp):
ATAAGAAAAATAATTAAAACATAATATGAAAAATAACTTGAATACAACAAGAATAAATAAACATA
TAAAAAATATATATAAAATAAATTATTAACATATAAAAATTTATAAAAAATTAAAAACTCTTTAA
ACACAAAAAAAATGTGAGTACAAATAC
Found at i:2294743 original size:13 final size:13
Alignment explanation
Indices: 2294725--2294749 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2294715 TAATTGTGTA
2294725 CCTACTTTATCTG
1 CCTACTTTATCTG
2294738 CCTACTTTATCT
1 CCTACTTTATCT
2294750 TTTCATATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.04, T:0.48
Consensus pattern (13 bp):
CCTACTTTATCTG
Found at i:2297978 original size:2 final size:2
Alignment explanation
Indices: 2297940--2297968 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2297930 AATTGATCTG
2297940 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2297969 GACTTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2299223 original size:30 final size:31
Alignment explanation
Indices: 2299196--2299258 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 31
2299186 CTTAATTTGA
2299196 TAAAAAAGTAAA-A-AAAA-AAATTAAATTT
1 TAAAAAAGTAAATATAAAATAAATTAAATTT
* *
2299224 TAAAAAATTAAATATAAAATAATTTAAA-TT
1 TAAAAAAGTAAATATAAAATAAATTAAATTT
2299254 TAAAA
1 TAAAA
2299259 TTATCTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 11 0.37
29 1 0.03
30 11 0.37
31 7 0.23
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (31 bp):
TAAAAAAGTAAATATAAAATAAATTAAATTT
Found at i:2299230 original size:16 final size:15
Alignment explanation
Indices: 2299209--2299258 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
2299199 AAAAGTAAAA
2299209 AAAAAAATTAAATTT
1 AAAAAAATTAAATTT
* *
2299224 TAAAAAATTAAATAT
1 AAAAAAATTAAATTT
*
2299239 AAAATAATTTAAATTT
1 AAAA-AAATTAAATTT
2299255 AAAA
1 AAAA
2299259 TTATCTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAAAATTAAATTT
Found at i:2299259 original size:16 final size:16
Alignment explanation
Indices: 2299216--2299275 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
2299206 AAAAAAAAAA
2299216 TTAAATTTTAAAA-AA-
1 TTAAA-TTTAAAATAAT
*
2299231 TTAAATATAAAATAAT
1 TTAAATTTAAAATAAT
*
2299247 TTAAATTTAAAATTAT
1 TTAAATTTAAAATAAT
*
2299263 CTAAATCTTAAAA
1 TTAAAT-TTAAAA
2299276 ACTTCAACCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
14 6 0.16
15 7 0.18
16 19 0.50
17 6 0.16
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAATTTAAAATAAT
Found at i:2299403 original size:15 final size:17
Alignment explanation
Indices: 2299385--2299425 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 17
2299375 AATTTATTCG
2299385 AATTTAAAATGA-TTT-
1 AATTTAAAATGAGTTTA
2299400 AA-TTAAAAT-AGTTTA
1 AATTTAAAATGAGTTTA
2299415 AATTTAAAATG
1 AATTTAAAATG
2299426 TTCAAAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.05
14 10 0.45
15 4 0.18
16 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (17 bp):
AATTTAAAATGAGTTTA
Found at i:2299970 original size:5 final size:5
Alignment explanation
Indices: 2299962--2300060 Score: 51
Period size: 5 Copynumber: 19.4 Consensus size: 5
2299952 TTTTATGAAG
* * ** * * *
2299962 AAAGA AAAGA AAAGA AAAAA AAAGG GGA-A AAAGT AAAGA TAATAGA GAGGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA -AA-AGA AAAGA
* *
2300013 AAAG- AAAGA GAATGA GAAAGA AAAGA AAGGA AAA-A AAAGA AGAAGA
1 AAAGA AAAGA -AAAGA -AAAGA AAAGA AAAGA AAAGA AAAGA A-AAGA
2300059 AA
1 AA
2300061 GATTCATAAG
Statistics
Matches: 69, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
4 9 0.13
5 40 0.58
6 17 0.25
7 3 0.04
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:2300071 original size:29 final size:29
Alignment explanation
Indices: 2300039--2300097 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2300029 AAAGAAAAGA
2300039 AAGGAAAAAAAAGAAGAAGAAAGATTCAT
1 AAGGAAAAAAAAGAAGAAGAAAGATTCAT
2300068 AAGGAAAAAAAAGAAGAAGAAAGATTCAT
1 AAGGAAAAAAAAGAAGAAGAAAGATTCAT
2300097 A
1 A
2300098 TATTTGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.20, T:0.10
Consensus pattern (29 bp):
AAGGAAAAAAAAGAAGAAGAAAGATTCAT
Found at i:2300877 original size:13 final size:13
Alignment explanation
Indices: 2300859--2300884 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2300849 CTGTGGCAGA
2300859 TTAAAACAATTAT
1 TTAAAACAATTAT
2300872 TTAAAACAATTAT
1 TTAAAACAATTAT
2300885 AGAGTACAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAACAATTAT
Found at i:2301112 original size:16 final size:16
Alignment explanation
Indices: 2301093--2301123 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2301083 AAATAAACTT
*
2301093 TTATTTATTAAAAATG
1 TTATTTATCAAAAATG
2301109 TTATTTATCAAAAAT
1 TTATTTATCAAAAAT
2301124 AATTTTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
TTATTTATCAAAAATG
Found at i:2301212 original size:18 final size:18
Alignment explanation
Indices: 2301191--2301227 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2301181 ATATTTCATT
*
2301191 AATAACGATAATTTTGTA
1 AATAACGATAATTTAGTA
*
2301209 AATAATGATAATTTAGTA
1 AATAACGATAATTTAGTA
2301227 A
1 A
2301228 TAAAGTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.38
Consensus pattern (18 bp):
AATAACGATAATTTAGTA
Found at i:2301524 original size:23 final size:24
Alignment explanation
Indices: 2301497--2301542 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
2301487 CTAATAATTA
*
2301497 ATATTAATTGTA-TATTTTTATTC
1 ATATTAATTGTATTATTATTATTC
2301520 ATATTAATTGTATTATTATTATT
1 ATATTAATTGTATTATTATTATT
2301543 TGTATGGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (24 bp):
ATATTAATTGTATTATTATTATTC
Found at i:2302574 original size:20 final size:20
Alignment explanation
Indices: 2302500--2302574 Score: 50
Period size: 20 Copynumber: 3.8 Consensus size: 20
2302490 TTAAATTATC
2302500 ATTATAAATA-TTTT-ATTATT
1 ATTA-AAATATTTTTAATT-TT
*
2302520 AATAAAAT-TTATTTAA-TTT
1 ATTAAAATATT-TTTAATTTT
* **
2302539 ATAAATAATAAATTTAATTTT
1 ATTAA-AATATTTTTAATTTT
2302560 ATTAAAATATTTTTA
1 ATTAAAATATTTTTA
2302575 TTAAATAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
19 10 0.24
20 23 0.56
21 8 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTAAAATATTTTTAATTTT
Found at i:2307604 original size:20 final size:20
Alignment explanation
Indices: 2307576--2307650 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
2307566 TCATACCCTG
2307576 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
2307596 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
2307616 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
2307636 ATGTATCGATACATT
1 ATGTATCGATACATT
2307651 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2307643 original size:40 final size:39
Alignment explanation
Indices: 2307576--2307653 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
2307566 TCATACCCTG
* *
2307576 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
2307616 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
2307654 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:2308588 original size:23 final size:23
Alignment explanation
Indices: 2308561--2308617 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
2308551 AGCCTTTGAC
2308561 CATGCATTTTTTTTATTATATTT
1 CATGCATTTTTTTTATTATATTT
*
2308584 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATATTT
2308607 CATGCATTTTT
1 CATGCATTTTT
2308618 AACATGTCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.19, C:0.11, G:0.07, T:0.63
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATATTT
Found at i:2316162 original size:27 final size:27
Alignment explanation
Indices: 2316122--2316349 Score: 242
Period size: 27 Copynumber: 8.2 Consensus size: 27
2316112 AGTGGCATTT
* * *
2316122 TCTTTTAAACTCCACAACTCTGTGGCA
1 TCTTTTTAAGTCCACAACTCCGTGGCA
*
2316149 TCTTTTTAAGTCCACAACTCTGTGGCA
1 TCTTTTTAAGTCCACAACTCCGTGGCA
* *
2316176 CCCTTTTAAAGTCCACAACTCCGTGGCA
1 -TCTTTTTAAGTCCACAACTCCGTGGCA
*
2316204 CCCTTTTT-AGTCCACAACTCCGTGGCA
1 -TCTTTTTAAGTCCACAACTCCGTGGCA
* *
2316231 CCCTTTTAAGTCCACAACTCCGTGGCA
1 TCTTTTTAAGTCCACAACTCCGTGGCA
* *
2316258 CCCTTTTAAGTCCACAACTCCGTGGCA
1 TCTTTTTAAGTCCACAACTCCGTGGCA
* *
2316285 TCCCTTTTAAGTCCACAACTCCATGGCA
1 T-CTTTTTAAGTCCACAACTCCGTGGCA
* * *
2316313 TCTCTTTTCAAAGCCCACAAATCAGTGGCA
1 TCT-TTTT--AAGTCCACAACTCCGTGGCA
2316343 CTCTTTT
1 -TCTTTT
2316350 CAAAGCCCAC
Statistics
Matches: 180, Mismatches: 14, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
26 6 0.03
27 91 0.51
28 61 0.34
30 19 0.11
31 3 0.02
ACGTcount: A:0.23, C:0.33, G:0.13, T:0.30
Consensus pattern (27 bp):
TCTTTTTAAGTCCACAACTCCGTGGCA
Found at i:2316181 original size:28 final size:28
Alignment explanation
Indices: 2316160--2317871 Score: 2230
Period size: 28 Copynumber: 59.9 Consensus size: 28
2316150 CTTTTTAAGT
* * * *
2316160 CCACAACTCTGTGGCACCCTTTTAAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * ** *
2316188 CCACAACTCCGTGGCACCCTTT-TTAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * *
2316215 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * *
2316242 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * *
2316269 CCACAACTCCGTGGCATCCCTTT-TAAGT
1 CCACAAGTCAGTGGCA-CCCTTTCAAAGC
* *
2316297 CCACAACTCCA-TGGCATCTCTTTTCAAAGC
1 CCACAAGT-CAGTGGCA-C-CCTTTCAAAGC
* *
2316327 CCACAAATCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
*
2316356 CCACAAGTTAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
2316384 CCACAAGTCAGTGGCACTCCTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
*
2316413 CCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
* * *
2316442 CCACAAATCAATAGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
2316470 CCACAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
2316498 CCACAAGTCAGTGGCACTCCTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
*
2316527 CCACAAGTTAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * *
2316555 CCATAAATCAGTGACACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
2316584 CCACAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
2316612 CCACAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* *
2316640 CCACAAGTTAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
2316669 CCACAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
2316697 CTACAAGTCAGTGGCACTCCTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
*
2316726 CCACAAGTTAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
2316754 CCACAAGTCAGTGGCACTCCTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
* *
2316783 TCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
*
2316812 CCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
2316841 CCACAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
2316869 CCACAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
2316897 CCACAAGTCAGTGGCACTCCTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
* *
2316926 CCACAAATCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
2316955 CCACAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
2316983 CCACAAGTCAGTGGCACCCTTTGAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
2317011 CCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
*
2317040 CCACAAGTCAGTGGCACCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
2317068 CCACAAGTCAGTGGCGCTCCTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
* *
2317097 CCATAAGTCAGTGGCACCCTTTCAAAAC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
2317125 CCACAAGTCAGTGGCACTCCTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
*
2317154 CCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
* *
2317183 CCACAAATCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
* *
2317212 CCACAAATCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
2317241 CCACAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
2317269 CCAC-AGCTCAGTGGCACCCTTTCAAAGC
1 CCACAAG-TCAGTGGCACCCTTTCAAAGC
2317297 CCACAAGTCAGTGGCACTCCTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
* *
2317326 CCACAAGTTAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
* * *
2317355 CCACAAATCAGTGGCACTCTTTTCAAAAC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
*
2317384 CCACAAGTTAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
2317412 CCACAAGTCAGTGGCACTCCTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
*
2317441 CCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
* *
2317470 CCACAAATCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
*
2317499 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * *
2317527 CCACAAGTTAGTGGCACCCTTGCAGAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
**
2317555 CCACAAGTCAGTGGCACCCTTTTGAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * *
2317583 CCACAAGTCAGTGGCACCATTGCGAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* *
2317611 CCACAATTCAGTGGCACTCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
2317639 CCACAAGTCAGTGGCACCCTTTTAAAGCC
1 CCACAAGTCAGTGGCACCCTTTCAAAG-C
*
2317668 CACACAAGTCAGTGGCACTCCTTTTAAAGC
1 C-CACAAGTCAGTGGCAC-CCTTTCAAAGC
* * *
2317698 TCACGCAAGTCAGTGGTACCTTTTCAAAGC
1 -C-CACAAGTCAGTGGCACCCTTTCAAAGC
*
2317728 CCACAAGTCAGTGGCACTCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
2317756 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * **
2317784 CCACGAGTTAGTGGCATTCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
2317812 CCACGCAAGTCAGTGGCACCCTTTTAAAGC
1 CCA--CAAGTCAGTGGCACCCTTTCAAAGC
*
2317842 CCATGCAAGTCAATGGCAACCCTTTTCAAA
1 CCA--CAAGTCAGTGGC-ACCC-TTTCAAA
2317872 TCACCACTGT
Statistics
Matches: 1540, Mismatches: 117, Indels: 50
0.90 0.07 0.03
Matches are distributed among these distances:
27 74 0.05
28 698 0.45
29 656 0.43
30 76 0.05
31 30 0.02
32 6 0.00
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (28 bp):
CCACAAGTCAGTGGCACCCTTTCAAAGC
Found at i:2316381 original size:57 final size:57
Alignment explanation
Indices: 2316094--2317871 Score: 2254
Period size: 57 Copynumber: 31.1 Consensus size: 57
2316084 ACTGTGACCT
* * * * * * * *
2316094 TTTCAAAGCCCACGACTCAGTGGCATTTTCTTTTAAA-CTCCACAACTCTGTGGCA-TC
1 TTTCAAAGCCCACAAGTCAGTGGCA-CTCCTTTCAAAGC-CCACAAGTCAGTGGCACCC
** * * * * * * *
2316151 TTTTTAAGTCCACAACTCTGTGGCAC-CCTTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
** * * * * * * *
2316207 TTT-TTAGTCCACAACTCCGTGGCAC-CCTTT-TAAGTCCACAACTCCGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* * * * * * * *
2316261 TTT-TAAGTCCACAACTCCGTGGCA-TCCCTTT-TAAGTCCACAACTCCA-TGGCATCTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACT-CCTTTCAAAGCCCACAAGT-CAGTGGCA-C-CC
* * *
2316318 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
*
2316375 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CC
* * *
2316433 TTTCAAAGCCCACAAATCAATAGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
*
2316489 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* * * *
2316546 TTTCAAAGCCCATAAATCAGTGACACTCTTTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* *
2316603 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CC
*
2316660 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCTACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CC
*
2316717 TTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CC
* * *
2316774 TTTCAAAGCTCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CC
2316832 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* *
2316888 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CC
2316946 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* * *
2317002 TTTGAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* *
2317059 TTTCAAAGCCCACAAGTCAGTGGCGCTCCTTTCAAAGCCCATAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* *
2317116 TTTCAAAACCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CC
* * * *
2317174 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CC
2317232 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCAC-AGCTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAG-TCAGTGGCACCC
* *
2317288 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CC
* * * *
2317346 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAACCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
*
2317403 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CC
* * *
2317461 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* * *
2317518 TTTCAAAGCCCACAAGTTAGTGGCAC-CCTTGCAGAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
** * * * * *
2317574 TTTTGAAGCCCACAAGTCAGTGGCAC-CATTGCGAAGCCCACAATTCAGTGGCACTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
*
2317630 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTTAAAGCCCACACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG-CC-CACAAGTCAGTGGCAC-CC
* * * * *
2317689 TTTTAAAGCTCACGCAAGTCAGTGGTAC-CTTTTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTCAAAGC-C-CACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* * **
2317747 TTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGAGTTAGTGGCATTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* *
2317803 TTTCAAAGCCCACGCAAGTCAGTGGCAC-CCTTTTAAAGCCCATGCAAGTCAATGGCAACCC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGC-ACCC
2317864 TTTTCAAA
1 -TTTCAAA
2317872 TCACCACTGT
Statistics
Matches: 1543, Mismatches: 141, Indels: 69
0.88 0.08 0.04
Matches are distributed among these distances:
54 46 0.03
55 71 0.05
56 292 0.19
57 684 0.44
58 366 0.24
59 41 0.03
60 12 0.01
61 24 0.02
62 7 0.00
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (57 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCC
Found at i:2318413 original size:20 final size:20
Alignment explanation
Indices: 2318385--2318464 Score: 88
Period size: 20 Copynumber: 4.0 Consensus size: 20
2318375 TCATACCCTG
2318385 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
2318405 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
2318425 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
2318445 ATGTATCGATACATTATTTC
1 ATGTATCGATACATT-TTTC
2318465 TTTTTACCTA
Statistics
Matches: 45, Mismatches: 14, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2319396 original size:22 final size:22
Alignment explanation
Indices: 2319370--2319424 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
2319360 AGCCTTTGAC
2319370 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
2319392 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
2319414 CATGCATTTTT
1 CATGCATTTTT
2319425 AACATGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:2319431 original size:20 final size:21
Alignment explanation
Indices: 2319370--2319431 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
2319360 AGCCTTTGAC
**
2319370 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
**
2319392 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
2319414 CATGCA-TTTTTAACATGT
1 CATGCATTTTTTAACATGT
2319432 CCAGCATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.26
22 28 0.74
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.58
Consensus pattern (21 bp):
CATGCATTTTTTAACATGTTT
Found at i:2322123 original size:19 final size:19
Alignment explanation
Indices: 2322101--2322144 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
2322091 GAATTTATAA
*
2322101 ATATAATAATTATTTATTT
1 ATATAATAATTATATATTT
* *
2322120 ATATCATATTTATATATTT
1 ATATAATAATTATATATTT
2322139 -TATAAT
1 ATATAAT
2322145 TTTATAATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATAATAATTATATATTT
Found at i:2322392 original size:17 final size:16
Alignment explanation
Indices: 2322365--2322396 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2322355 ATATTTTAGT
2322365 TATTTTATAAATATTA
1 TATTTTATAAATATTA
2322381 TATTTATATAAATATT
1 TATTT-TATAAATATT
2322397 TTTAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTTATAAATATTA
Found at i:2322743 original size:17 final size:17
Alignment explanation
Indices: 2322721--2322753 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2322711 TTAATGATTT
*
2322721 TAAATTAAATATAAAAA
1 TAAATTAAAAATAAAAA
2322738 TAAATTAAAAATAAAA
1 TAAATTAAAAATAAAA
2322754 TCATTTGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATTAAAAATAAAAA
Found at i:2326488 original size:12 final size:13
Alignment explanation
Indices: 2326465--2326493 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2326455 AGTGAGATTA
2326465 TAAATATTTGAAT
1 TAAATATTTGAAT
2326478 TAAAT-TTTGAAT
1 TAAATATTTGAAT
2326490 TAAA
1 TAAA
2326494 AAATATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (13 bp):
TAAATATTTGAAT
Found at i:2328632 original size:14 final size:15
Alignment explanation
Indices: 2328613--2328649 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
2328603 CATGAATCTC
2328613 ATTTTTTATTT-AAT
1 ATTTTTTATTTCAAT
2328627 ATTTTTTATTTCAAT
1 ATTTTTTATTTCAAT
*
2328642 TTTTTTTA
1 ATTTTTTA
2328650 AAATATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTTTTATTTCAAT
Found at i:2329087 original size:15 final size:15
Alignment explanation
Indices: 2329063--2329092 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2329053 TAAAATCCAG
*
2329063 ATATTTTATTTTAAA
1 ATATTATATTTTAAA
2329078 ATATTATATTTTAAA
1 ATATTATATTTTAAA
2329093 TTAAAATAAT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATTATATTTTAAA
Found at i:2329088 original size:20 final size:20
Alignment explanation
Indices: 2329063--2329100 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2329053 TAAAATCCAG
**
2329063 ATATTTTATTTTAAAATATT
1 ATATTTTAAATTAAAATATT
2329083 ATATTTTAAATTAAAATA
1 ATATTTTAAATTAAAATA
2329101 ATAAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTTTAAATTAAAATATT
Found at i:2331889 original size:22 final size:22
Alignment explanation
Indices: 2331861--2331915 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
2331851 TGGACATGTT
2331861 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
2331883 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
2331905 AAAAATGCATG
1 AAAAATGCATG
2331916 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:2332876 original size:20 final size:20
Alignment explanation
Indices: 2332829--2332903 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
2332819 AAAAAGACAT
*
2332829 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
2332848 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
2332869 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
2332889 AATGTATCGATACAT
1 AATGTATCGATACAT
2332904 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:2332897 original size:40 final size:39
Alignment explanation
Indices: 2332826--2332903 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
2332816 GGTAAAAAGA
* *
2332826 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
2332865 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
2332904 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:2333725 original size:57 final size:57
Alignment explanation
Indices: 2333511--2334154 Score: 929
Period size: 57 Copynumber: 11.2 Consensus size: 57
2333501 CACTGACACA
** *
2333511 TGTGGGCTTTGAAAAGAGTGTTACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
2333570 TGCGTGGGCTTTGAAAGGA-TGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACT
1 T--GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
2333628 TGTGGGCTTTG-AAA-AGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
2333683 CGTGGGCTTTGAAAAGATTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACT
* *
2333741 TGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
*
2333797 TGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACT
* *
2333855 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2333912 TGTGGGCTTTGAGAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
2333969 TGTGGGTTTTGAAAAGAGTGCCACCGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
2334026 TGTGGGCTTTGAAATG-GTGCCACTGACTTGTGGGTTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
2334083 TGTGGGCTTTGAAAAGAGTGCCACTGATTTGTTGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACT
2334141 TGTGGGCTTTGAAA
1 TGTGGGCTTTGAAA
2334155 GGGATGAACA
Statistics
Matches: 527, Mismatches: 47, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
54 1 0.00
55 48 0.09
56 56 0.11
57 251 0.48
58 146 0.28
59 2 0.00
60 8 0.02
61 15 0.03
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (57 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:2334155 original size:29 final size:29
Alignment explanation
Indices: 2333465--2334156 Score: 924
Period size: 29 Copynumber: 24.0 Consensus size: 29
2333455 AAAAAAAAAT
**
2333465 GTGCCACT-AGCTTGTGTAGGCTTTGAAAAAA
1 GTGCCACTGA-CTTGTG--GGCTTTGAAAGGA
* *
2333496 GTTGCCACTGACACATGTGGGCTTTGAAAAGA
1 G-TGCCACTG--ACTTGTGGGCTTTGAAAGGA
** *
2333528 GTGTTACTGACTTGTGTGGGCTTTAAAAGG-
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGGA
2333558 GTGCCACTGACTTGCGTGGGCTTTGAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAGGA
*
2333589 -TGCCACTGACTCGTGGGCTTTGAAA-GA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
2333616 GTGCCACTGACTTGTGGGCTTTGAAA--A
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
2333643 GTGCCACTGACTCGTGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
2333671 GTACCACTGACTCGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
2333700 TTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
2333729 GTGCCACTAACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
2333757 GTGCCACTAACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
2333785 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
2333814 GTGCCACTGATTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
2333843 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
2333872 GTGCCACTGACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
2333900 GTGCCACTAACTTGTGGGCTTTGAGAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
2333929 GTGCCACTGACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
2333957 GTGCCACTGACTTGTGGGTTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
2333986 GTGCCACCGACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
2334014 GTGCCACTAACTTGTGGGCTTTGAAATG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
2334042 GTGCCACTGACTTGTGGGTTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
2334071 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
2334100 GTGCCACTGATTTGTTGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
2334129 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
2334157 GATGAACATT
Statistics
Matches: 598, Mismatches: 46, Indels: 36
0.88 0.07 0.05
Matches are distributed among these distances:
27 28 0.05
28 221 0.37
29 268 0.45
30 34 0.06
31 21 0.04
32 20 0.03
34 5 0.01
35 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:2334244 original size:257 final size:254
Alignment explanation
Indices: 2333511--2334157 Score: 685
Period size: 257 Copynumber: 2.5 Consensus size: 254
2333501 CACTGACACA
* ** * *
2333511 TGTGGGCTTTGAAAAGAGTGTTACTGACTTGTGTGGGCTTT-AAAAGGGTGCCACTGACTTGCGT
1 TGTGGGCTTTG-AAAGGGTGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTGCCACTGA-TT-TGT
* *
2333575 GGGCTTTGAAAGGA-TGCCACTGACTCGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTT
61 GGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTT
* * * * ** * * *** *
2333638 GAAA-AGTGCCACTGACTCGTGGGCTTTGAAAAGG--TACCACTGACTCGTGGGCTTTGAAAAGA
126 GAAAGGGTGACACTAACTAGAAGGCTTT-AAGAGGAATGCCACTGACAAATGGGC--T-AAAAGG
* * * ** ** * *
2333700 TTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACT
187 GTGCCACTAACATGTAAG-TAAGAAAAGAGTGCCACCAACTTGTGGGCTTTGAAAGGGTGCCACT
2333765 AACT
251 AACT
2333769 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCT
*
2333834 TTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAG
66 TTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAG
* * ** * * *** *
2333899 GGTGCCACTAACTTGTGGGCTTTGAGAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
131 GGTGACACTAACTAGAAGGCTTTAAGAGGAATGCCACTGACAAATGGGC--TAAAAGGGTGCCAC
* * ** ** *
2333964 TGACTTGTGGGTTTTGAAAAGAGTGCCACCGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
194 TAACATGTAAG-TAAGAAAAGAGTGCCACCAACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* *
2334026 TGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGTTTTGAAAAGAGTGCCACTGATTTGTGGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCT
* *
2334091 TTGAAAAGAGTGCCACTGATTTGTTGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAG
66 TTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAG
2334156 GG
131 GG
2334158 ATGAACATTC
Statistics
Matches: 358, Mismatches: 25, Indels: 13
0.90 0.06 0.03
Matches are distributed among these distances:
254 16 0.04
255 36 0.10
256 48 0.13
257 228 0.64
258 30 0.08
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (254 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCT
TTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAG
GGTGACACTAACTAGAAGGCTTTAAGAGGAATGCCACTGACAAATGGGCTAAAAGGGTGCCACTA
ACATGTAAGTAAGAAAAGAGTGCCACCAACTTGTGGGCTTTGAAAGGGTGCCACTAACT
Found at i:2336726 original size:13 final size:13
Alignment explanation
Indices: 2336676--2336725 Score: 84
Period size: 13 Copynumber: 3.8 Consensus size: 13
2336666 TCTTACACCC
2336676 AAAAAAAAAAACA
1 AAAAAAAAAAACA
2336689 AAAAAAAAAAACA
1 AAAAAAAAAAACA
2336702 AAAAAAAAAAA-A
1 AAAAAAAAAAACA
2336714 AAAAAAGAAAAA
1 AAAAAA-AAAAA
2336726 ATAGCAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.19
13 29 0.81
ACGTcount: A:0.94, C:0.04, G:0.02, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACA
Found at i:2336736 original size:1 final size:1
Alignment explanation
Indices: 2336676--2336726 Score: 75
Period size: 1 Copynumber: 51.0 Consensus size: 1
2336666 TCTTACACCC
* * *
2336676 AAAAAAAAAAACAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2336727 TAGCAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.94, C:0.04, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Done.