Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 47 of 145
Found at i:16528119 original size:9 final size:9
Alignment explanation
Indices: 16528102--16528138 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
16528092 TAAGTTTTCG
16528102 AATTCGAAT
1 AATTCGAAT
*
16528111 AACTCGAAT
1 AATTCGAAT
16528120 AATTCGAAT
1 AATTCGAAT
16528129 AATTCGAAT
1 AATTCGAAT
16528138 A
1 A
16528139 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:16528990 original size:8 final size:8
Alignment explanation
Indices: 16528977--16529006 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
16528967 AGCTCATTTT
16528977 ATCACATC
1 ATCACATC
16528985 ATCACATC
1 ATCACATC
16528993 ATCACATC
1 ATCACATC
16529001 ATCACA
1 ATCACA
16529007 AAACATATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (8 bp):
ATCACATC
Found at i:16529920 original size:15 final size:15
Alignment explanation
Indices: 16529873--16529921 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 15
16529863 TATGTTTCCT
*
16529873 TTATTTTAA-TGTTA
1 TTATTTTAATTTTTA
16529887 TTATTTTAACCTTTATTA
1 TTATTTTAA--TTT-TTA
16529905 TTATTTTAATTTTTA
1 TTATTTTAATTTTTA
16529920 TT
1 TT
16529922 TAATATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 9 0.30
15 5 0.17
16 3 0.10
17 1 0.03
18 12 0.40
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATTTTAATTTTTA
Found at i:16531473 original size:4 final size:4
Alignment explanation
Indices: 16531464--16531493 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
16531454 TTAGTAGACT
16531464 TAAC TAAC TAAC TAAC TAAC TAAC TTAAC T
1 TAAC TAAC TAAC TAAC TAAC TAAC -TAAC T
16531494 TAAACCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (4 bp):
TAAC
Found at i:16531481 original size:12 final size:13
Alignment explanation
Indices: 16531461--16531493 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
16531451 CGCTTAGTAG
16531461 ACTTAACTAACTA
1 ACTTAACTAACTA
16531474 AC-TAACTAACTA
1 ACTTAACTAACTA
16531486 ACTTAACT
1 ACTTAACT
16531494 TAAACCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (13 bp):
ACTTAACTAACTA
Found at i:16544496 original size:25 final size:25
Alignment explanation
Indices: 16544478--16544525 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
16544468 CCACATAGTC
*
16544478 TTTACAGGTAACCTACCACAAAGAA
1 TTTACAGATAACCTACCACAAAGAA
16544503 TTTACAGATAACCTACCACAAAG
1 TTTACAGATAACCTACCACAAAG
16544526 GCTTACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.21
Consensus pattern (25 bp):
TTTACAGATAACCTACCACAAAGAA
Found at i:16544538 original size:25 final size:25
Alignment explanation
Indices: 16544486--16544538 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
16544476 TCTTTACAGG
* *
16544486 TAACCTACCACAAAGAATTTACAGA
1 TAACCTACCACAAAGAACTTACAAA
*
16544511 TAACCTACCACAAAG-GCTTACCAAA
1 TAACCTACCACAAAGAACTTA-CAAA
16544536 TAA
1 TAA
16544539 ATCGCCACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.47, C:0.26, G:0.08, T:0.19
Consensus pattern (25 bp):
TAACCTACCACAAAGAACTTACAAA
Found at i:16558614 original size:9 final size:9
Alignment explanation
Indices: 16558585--16558614 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
16558575 TTCGCATCAT
16558585 TTTCTCTTA
1 TTTCTCTTA
*
16558594 TTGCTCTTA
1 TTTCTCTTA
16558603 TTTCTCTTA
1 TTTCTCTTA
16558612 TTT
1 TTT
16558615 AGCGACAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.67
Consensus pattern (9 bp):
TTTCTCTTA
Found at i:16562140 original size:43 final size:43
Alignment explanation
Indices: 16562079--16562321 Score: 291
Period size: 43 Copynumber: 5.7 Consensus size: 43
16562069 GATATGATTT
*
16562079 CGTGTAAGACCACGTCTGGGACGTTGGCATCAACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
*
16562122 CGTGTAAGACCACGTCTGGGACATTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
*
16562165 CGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
* * * *
16562208 CGTGTAAGACCATGTCAGGGACATTGGCATCGTA-TT-TGATT-
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCG-ACTTGTGTTTA
* * * * *
16562249 CGTATAAGACC-CTGTCTGGGACAG-TGGAATTGA-TATATGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGTTTA
*
16562292 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
16562322 TGTACGAGAT
Statistics
Matches: 174, Mismatches: 18, Indels: 16
0.84 0.09 0.08
Matches are distributed among these distances:
40 2 0.01
41 25 0.14
42 10 0.06
43 135 0.78
44 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
Found at i:16562310 original size:127 final size:129
Alignment explanation
Indices: 16562079--16562321 Score: 307
Period size: 127 Copynumber: 1.9 Consensus size: 129
16562069 GATATGATTT
* * * *
16562079 CGTGTAAGACCACGTCTGGGACGTTGGCATCAACTTGTGTTTACGTGTAAGACCACGTCTGGGAC
1 CGTGTAAGACCACGTCAGGGACATTGGCATCAACTTGTGATTACGTATAAGACCACGTCTGGGAC
* * * * *
16562144 ATTGGCATCGACTTGTGTTTACGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
66 AGTGGAATCGACTTATGATTACATGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
* *
16562208 CGTGTAAGACCATGTCAGGGACATTGGCATCGTA-TT-TGATT-CGTATAAGACC-CTGTCTGGG
1 CGTGTAAGACCACGTCAGGGACATTGGCATC-AACTTGTGATTACGTATAAGACCAC-GTCTGGG
* *
16562269 ACAGTGGAATTGA-TATATGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
64 ACAGTGGAATCGACT-TATGATTACATGTAAGACCACATCTGGGACGTTGGCAT
16562322 TGTACGAGAT
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
126 2 0.02
127 61 0.62
128 4 0.04
129 30 0.31
130 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (129 bp):
CGTGTAAGACCACGTCAGGGACATTGGCATCAACTTGTGATTACGTATAAGACCACGTCTGGGAC
AGTGGAATCGACTTATGATTACATGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
Found at i:16566043 original size:49 final size:47
Alignment explanation
Indices: 16565958--16566061 Score: 126
Period size: 49 Copynumber: 2.2 Consensus size: 47
16565948 TGCTCTCCCA
16565958 TCCCTCT--CCCTCTTCTCCACCATTCCTCCCCCTACTCTGATTCTCT
1 TCCCTCTCCCCCTCTTCTCCACCATTCCTCCCCCTACTCTGATTCT-T
* *
16566004 CTCCCTCTCCCCCTCTTC-CCTACCA-TCACTCCTCTTACTCTGATTCTT
1 -TCCCTCTCCCCCTCTTCTCC-ACCATTC-CTCCCCCTACTCTGATTCTT
16566052 TCCCTCTCCC
1 TCCCTCTCCC
16566062 ACACCGTCCC
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
47 17 0.33
48 5 0.10
49 29 0.57
ACGTcount: A:0.09, C:0.53, G:0.02, T:0.37
Consensus pattern (47 bp):
TCCCTCTCCCCCTCTTCTCCACCATTCCTCCCCCTACTCTGATTCTT
Found at i:16568017 original size:29 final size:30
Alignment explanation
Indices: 16567960--16568016 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
16567950 TTCAATAAAA
16567960 ATATAAGAAAATAATATTATTAATATTTTG
1 ATATAAGAAAATAATATTATTAATATTTTG
*
16567990 ATATATGAAATATAAT-TT-TTAA-ATTTT
1 ATATAAGAAA-ATAATATTATTAATATTTT
16568017 TAAGCAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 4 0.16
30 11 0.44
31 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (30 bp):
ATATAAGAAAATAATATTATTAATATTTTG
Found at i:16568504 original size:9 final size:9
Alignment explanation
Indices: 16568492--16568524 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
16568482 GTTAATCGAA
16568492 TCGAGTTAT
1 TCGAGTTAT
16568501 TCGAGTTAT
1 TCGAGTTAT
*
16568510 TCGAATTAT
1 TCGAGTTAT
16568519 TCGAGT
1 TCGAGT
16568525 CAAATCAAAT
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:0.24, C:0.12, G:0.21, T:0.42
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:16575288 original size:21 final size:21
Alignment explanation
Indices: 16575248--16575288 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16575238 AATAACTACC
*
16575248 CAGCTAACAACCAACTAACTT
1 CAGCTAACAACCAACAAACTT
* *
16575269 CAGCTAACTACTAACAAACT
1 CAGCTAACAACCAACAAACT
16575289 AACTGACTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.32, G:0.05, T:0.20
Consensus pattern (21 bp):
CAGCTAACAACCAACAAACTT
Found at i:16576015 original size:18 final size:18
Alignment explanation
Indices: 16575992--16576029 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
16575982 AATATATCAA
16575992 AAAGACTCTTTCACCATT
1 AAAGACTCTTTCACCATT
16576010 AAAGACTCTTTCACCATT
1 AAAGACTCTTTCACCATT
16576028 AA
1 AA
16576030 CTTTAATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (18 bp):
AAAGACTCTTTCACCATT
Found at i:16576146 original size:9 final size:9
Alignment explanation
Indices: 16576120--16576151 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
16576110 GATATGACAA
16576120 AAAAATTAT
1 AAAAATTAT
16576129 AAAAA--AT
1 AAAAATTAT
16576136 AAAAATTAT
1 AAAAATTAT
16576145 AAAAATT
1 AAAAATT
16576152 TTTTATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.33
9 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:16576737 original size:90 final size:89
Alignment explanation
Indices: 16576582--16576745 Score: 197
Period size: 90 Copynumber: 1.8 Consensus size: 89
16576572 CGGTCAAATA
** * * *
16576582 GTCTTTTTGATGCATTTTGGCAGTTTAAGTACCAAATTGAATGCAAAAAAAAAACACCGGTTTAA
1 GTCTTTTTGATGCATTTTGAAAGTTCAACTACCAAATTGAATGCAAAAAAAAAACACCGGCTTAA
16576647 TTGCCTTTTTTGAAAAAGTTTTAGT
66 TTG-CTTTTTTGAAAAAGTTTTAGT
* * * **
16576672 GTCTTTTTTATGCATTTTGAAAGTTCAACTACTC-AATTGAGTG-AAAAAAAAAAGTAGGGGCTT
1 GTCTTTTTGATGCATTTTGAAAGTTCAACTAC-CAAATTGAATGCAAAAAAAAAA-CACCGGCTT
16576735 AATTGCTTTTT
64 AATTGCTTTTT
16576746 AAAAAAAATT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
89 16 0.26
90 45 0.73
91 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (89 bp):
GTCTTTTTGATGCATTTTGAAAGTTCAACTACCAAATTGAATGCAAAAAAAAAACACCGGCTTAA
TTGCTTTTTTGAAAAAGTTTTAGT
Found at i:16578746 original size:15 final size:16
Alignment explanation
Indices: 16578728--16578758 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
16578718 CTCCCAATCC
16578728 CTCTTCTCTTC-CTTT
1 CTCTTCTCTTCTCTTT
16578743 CTCTTCTCTTCTCTTT
1 CTCTTCTCTTCTCTTT
16578759 TTCATGGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
CTCTTCTCTTCTCTTT
Found at i:16583629 original size:6 final size:6
Alignment explanation
Indices: 16583618--16583674 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
16583608 ATATTGCAAG
*
16583618 TTTCCA TTTCCA TTTTCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA
16583666 TTTCCA TTT
1 TTTCCA TTT
16583675 TTTGGAAACC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.16, C:0.30, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTCCA
Found at i:16592445 original size:14 final size:13
Alignment explanation
Indices: 16592425--16592456 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
16592415 TATAAATACT
16592425 AAATAAAATAATA
1 AAATAAAATAATA
16592438 ATAATAAAATAATA
1 A-AATAAAATAATA
16592452 AAATA
1 AAATA
16592457 TCATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAATAAAATAATA
Found at i:16594684 original size:27 final size:27
Alignment explanation
Indices: 16594625--16594692 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
16594615 ATTTAACCCA
** *
16594625 TGTTTAATGTCCTGGCAGACTATCCCG
1 TGTTTAATGTCCCAGCAGACTACCCCG
* *
16594652 TATTTAATGTCCCAGCAGACTACCCCT
1 TGTTTAATGTCCCAGCAGACTACCCCG
*
16594679 TGTTTATTGTCCCA
1 TGTTTAATGTCCCA
16594693 ATGAACTATA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (27 bp):
TGTTTAATGTCCCAGCAGACTACCCCG
Found at i:16597304 original size:13 final size:13
Alignment explanation
Indices: 16597286--16597312 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16597276 AAAGTCAACC
16597286 ATATAAGAAGTTA
1 ATATAAGAAGTTA
16597299 ATATAAGAAGTTA
1 ATATAAGAAGTTA
16597312 A
1 A
16597313 AATCAAGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (13 bp):
ATATAAGAAGTTA
Found at i:16597945 original size:20 final size:20
Alignment explanation
Indices: 16597912--16597963 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
16597902 CAACCCAATC
16597912 ATAAAAA-AATAATT-TAATAA
1 ATAAAAATAA-AATTCTAA-AA
16597932 ATAAAAATAAAATTCTAAAA
1 ATAAAAATAAAATTCTAAAA
* *
16597952 CTAAAACTAAAA
1 ATAAAAATAAAA
16597964 CTAAAACTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (20 bp):
ATAAAAATAAAATTCTAAAA
Found at i:16597955 original size:6 final size:6
Alignment explanation
Indices: 16597946--16597974 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
16597936 AAATAAAATT
16597946 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
16597975 GTAGATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:16598002 original size:9 final size:9
Alignment explanation
Indices: 16597988--16598039 Score: 86
Period size: 9 Copynumber: 5.8 Consensus size: 9
16597978 GATTCAATTA
16597988 GTTAATTCG
1 GTTAATTCG
16597997 GTTAATTCG
1 GTTAATTCG
*
16598006 GGTAATTCG
1 GTTAATTCG
16598015 GTTAATTCG
1 GTTAATTCG
*
16598024 GGTAATTCG
1 GTTAATTCG
16598033 GTTAATT
1 GTTAATT
16598040 TTTAACCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (9 bp):
GTTAATTCG
Found at i:16598013 original size:18 final size:18
Alignment explanation
Indices: 16597990--16598039 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
16597980 TTCAATTAGT
16597990 TAATTCGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
16598008 TAATTCGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
16598026 TAATTCGGTTAATT
1 TAATTCGGTTAATT
16598040 TTTAACCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (18 bp):
TAATTCGGTTAATTCGGG
Found at i:16603084 original size:6 final size:6
Alignment explanation
Indices: 16603075--16603119 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
16603065 TTCTTGGTAT
16603075 TGGGAA TGGGAA TGGGAA TGGGAA TGGGAA TGGGAA TGGGAA TGG
1 TGGGAA TGGGAA TGGGAA TGGGAA TGGGAA TGGGAA TGGGAA TGG
16603120 AGTTGAGGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.31, C:0.00, G:0.51, T:0.18
Consensus pattern (6 bp):
TGGGAA
Found at i:16604615 original size:16 final size:16
Alignment explanation
Indices: 16604596--16604630 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
16604586 TAATTGAAAT
16604596 GTGTTAGAATTTTAGG
1 GTGTTAGAATTTTAGG
16604612 GTGTTAGAATTTTAGG
1 GTGTTAGAATTTTAGG
16604628 GTG
1 GTG
16604631 GTGCCACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.43
Consensus pattern (16 bp):
GTGTTAGAATTTTAGG
Found at i:16604880 original size:18 final size:18
Alignment explanation
Indices: 16604857--16604893 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
16604847 TAACAAAGTG
16604857 TGTATAATAAA-ATTAAAA
1 TGTATAA-AAATATTAAAA
16604875 TGTATAAAAATATTAAAA
1 TGTATAAAAATATTAAAA
16604893 T
1 T
16604894 AAAAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
TGTATAAAAATATTAAAA
Found at i:16606755 original size:8 final size:8
Alignment explanation
Indices: 16606737--16606785 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
16606727 TTTTTAAAAT
16606737 ATTTA-AA
1 ATTTATAA
16606744 ATTTATAA
1 ATTTATAA
16606752 ATTTATGAA
1 ATTTAT-AA
* *
16606761 AATTAAAA
1 ATTTATAA
16606769 ATTTATAA
1 ATTTATAA
*
16606777 ATATATAA
1 ATTTATAA
16606785 A
1 A
16606786 AGAACTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
7 5 0.14
8 24 0.69
9 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (8 bp):
ATTTATAA
Found at i:16613407 original size:16 final size:16
Alignment explanation
Indices: 16613383--16613454 Score: 72
Period size: 16 Copynumber: 4.5 Consensus size: 16
16613373 CGTTTGGTTC
*
16613383 ATTGGAATGGAATAGA
1 ATTGTAATGGAATAGA
*
16613399 ATTGTAATGGAATAGG
1 ATTGTAATGGAATAGA
* *
16613415 ACTGTAATGGAATAAA
1 ATTGTAATGGAATAGA
* * *
16613431 ACTGTGATGGGATAGA
1 ATTGTAATGGAATAGA
*
16613447 GTTGTAAT
1 ATTGTAAT
16613455 CAGTGATTCA
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.39, C:0.03, G:0.29, T:0.29
Consensus pattern (16 bp):
ATTGTAATGGAATAGA
Found at i:16613514 original size:62 final size:62
Alignment explanation
Indices: 16613417--16613559 Score: 277
Period size: 62 Copynumber: 2.3 Consensus size: 62
16613407 GGAATAGGAC
16613417 TGTAATGGAATAAAACTGTGATGGGATAGAGTTGTAATCAGTGATTCAATTGTTTGGTTGAA
1 TGTAATGGAATAAAACTGTGATGGGATAGAGTTGTAATCAGTGATTCAATTGTTTGGTTGAA
16613479 TGTAATGGAATAAAACTGTGATGGGATAGAGTTGTAATCAGTGATTCAATTGTTTGGTTGAA
1 TGTAATGGAATAAAACTGTGATGGGATAGAGTTGTAATCAGTGATTCAATTGTTTGGTTGAA
*
16613541 TGTAATGGAATAGAACTGT
1 TGTAATGGAATAAAACTGT
16613560 AATAGTATTA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 80 1.00
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (62 bp):
TGTAATGGAATAAAACTGTGATGGGATAGAGTTGTAATCAGTGATTCAATTGTTTGGTTGAA
Found at i:16617907 original size:9 final size:9
Alignment explanation
Indices: 16617893--16617960 Score: 84
Period size: 9 Copynumber: 7.4 Consensus size: 9
16617883 TTTGGTTAAA
16617893 AATTACCCG
1 AATTACCCG
16617902 AATTACCCG
1 AATTACCCG
16617911 AATTACCCG
1 AATTACCCG
* *
16617920 AATTAACCA
1 AATTACCCG
16617929 AATTA-CCG
1 AATTACCCG
*
16617937 AAAAATACCCG
1 --AATTACCCG
16617948 AATTACCCG
1 AATTACCCG
16617957 AATT
1 AATT
16617961 TTTTTTTTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
8 2 0.04
9 42 0.82
10 4 0.08
11 3 0.06
ACGTcount: A:0.41, C:0.28, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:16622357 original size:194 final size:193
Alignment explanation
Indices: 16622029--16622416 Score: 740
Period size: 194 Copynumber: 2.0 Consensus size: 193
16622019 CCTGCGTCAT
16622029 CAAATCCCACTGCTTCATGCCGCTCCTTTTTTGGGATAAAGACATCCACAATACTACTTGGAACA
1 CAAATCCCACTGCTTCATGCCGCTCCTTTTTTGGGATAAAGACATCCACAATACTACTTGGAACA
*
16622094 ACTTCCTCTCTTTGCCATCTGTTCGTACTACTTTTTACATTATGTTCTACTCTAATAAAATATAT
66 ACTTCCTCTCTTTGCCATCTGTTCCTACTACTTTTTACATTATGTTCTACTCTAATAAAATATAT
*
16622159 ATATTTTTTATATTTAAAAGTAAAACATTATTTTAATGGTAATATTCACGCTTTCATTTTTGG
131 ATATTTTTTATATTTAAAAGTAAAACATTATTTTAATAGTAATATTCACGCTTTCATTTTTGG
16622222 CAAATCCCACTGCTTCATGCCGCTCCTTTTTTCGGGATAAAGACATCCACAATACTACTTGGAAC
1 CAAATCCCACTGCTTCATGCCGCTCCTTTTTT-GGGATAAAGACATCCACAATACTACTTGGAAC
*
16622287 AACTTCCTCTCTTTGTCATCTGTTCCTACTACTTTTTACATTATGTTCTACTCTAATAAAATATA
65 AACTTCCTCTCTTTGCCATCTGTTCCTACTACTTTTTACATTATGTTCTACTCTAATAAAATATA
16622352 TATATTTTTTATATTTAAAAGTAAAACATTATTTTAATAGTAATATTCACGCTTTCATTTTTGG
130 TATATTTTTTATATTTAAAAGTAAAACATTATTTTAATAGTAATATTCACGCTTTCATTTTTGG
16622416 C
1 C
16622417 CTCAAATTTT
Statistics
Matches: 191, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
193 32 0.17
194 159 0.83
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (193 bp):
CAAATCCCACTGCTTCATGCCGCTCCTTTTTTGGGATAAAGACATCCACAATACTACTTGGAACA
ACTTCCTCTCTTTGCCATCTGTTCCTACTACTTTTTACATTATGTTCTACTCTAATAAAATATAT
ATATTTTTTATATTTAAAAGTAAAACATTATTTTAATAGTAATATTCACGCTTTCATTTTTGG
Found at i:16623203 original size:18 final size:18
Alignment explanation
Indices: 16623180--16623256 Score: 88
Period size: 18 Copynumber: 4.4 Consensus size: 18
16623170 CAAGGTCACG
*
16623180 ATCAATAGCGTCACTATC
1 ATCAATAACGTCACTATC
* *
16623198 ATCAATAATGTCACTAGC
1 ATCAATAACGTCACTATC
*
16623216 ATCAATATCGTCACTATC
1 ATCAATAACGTCACTATC
*
16623234 ATCAATATCG--A-TATC
1 ATCAATAACGTCACTATC
16623249 ATCAATAA
1 ATCAATAA
16623257 GAAAACCCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
15 11 0.21
16 1 0.02
18 40 0.77
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (18 bp):
ATCAATAACGTCACTATC
Found at i:16625752 original size:24 final size:21
Alignment explanation
Indices: 16625689--16625760 Score: 99
Period size: 21 Copynumber: 3.3 Consensus size: 21
16625679 AACTGAGTTA
*
16625689 GACAAAAAGAGAAGCAACTTG
1 GACAAAAAGAGAAGTAACTTG
16625710 GACAAAAAGAGAAGTAACTTG
1 GACAAAAAGAGAAGTAACTTG
*
16625731 GACAAAAAGAAACGAAGTAACTTC
1 GACAAAAAG--A-GAAGTAACTTG
16625755 GACAAA
1 GACAAA
16625761 TCTTTTTTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
21 29 0.63
23 1 0.02
24 16 0.35
ACGTcount: A:0.54, C:0.14, G:0.21, T:0.11
Consensus pattern (21 bp):
GACAAAAAGAGAAGTAACTTG
Found at i:16628525 original size:7 final size:7
Alignment explanation
Indices: 16628513--16628538 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16628503 TATTGAATAA
16628513 TATTTTG
1 TATTTTG
16628520 TATTTTG
1 TATTTTG
16628527 TATTTTG
1 TATTTTG
16628534 TATTT
1 TATTT
16628539 AATTATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (7 bp):
TATTTTG
Found at i:16636549 original size:12 final size:12
Alignment explanation
Indices: 16636526--16636559 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
16636516 TATATATTTT
16636526 AAAATT-ATATA
1 AAAATTAATATA
16636537 AAAATTAATATA
1 AAAATTAATATA
*
16636549 AAAAGTAATAT
1 AAAATTAATAT
16636560 GGGTGGGCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:16643315 original size:30 final size:30
Alignment explanation
Indices: 16643281--16643339 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
16643271 TACGAGCTTT
16643281 GGGGCAAAAGTGTAAATATGCAAAAGTTTA
1 GGGGCAAAAGTGTAAATATGCAAAAGTTTA
* * *
16643311 GGGGCAAAATTGTAAATTTGCCAAAGTTT
1 GGGGCAAAAGTGTAAATATGCAAAAGTTT
16643340 GAGTCAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.27
Consensus pattern (30 bp):
GGGGCAAAAGTGTAAATATGCAAAAGTTTA
Found at i:16643811 original size:23 final size:23
Alignment explanation
Indices: 16643781--16643825 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
16643771 GTGTTATTGA
*
16643781 TCAGTGGTAGTTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
16643804 TCAGTGGTAGCTTCGGCTACAT
1 TCAGTGGTAGCTTCGGCTACAT
16643826 ATAAGTGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.36
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:16643832 original size:23 final size:23
Alignment explanation
Indices: 16643783--16643832 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
16643773 GTTATTGATC
* * *
16643783 AGTGGTAGTTTCGGCTACATTTC
1 AGTGGTAGCTTCGGCTACATATA
16643806 AGTGGTAGCTTCGGCTACATATA
1 AGTGGTAGCTTCGGCTACATATA
16643829 AGTG
1 AGTG
16643833 TGGCACTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (23 bp):
AGTGGTAGCTTCGGCTACATATA
Found at i:16663353 original size:5 final size:5
Alignment explanation
Indices: 16663343--16663373 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
16663333 CTTTTTTTAT
16663343 TTAAA TTAAA TTAAA TT-AA TTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TT
16663374 GTAAATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
TTAAA
Found at i:16663365 original size:14 final size:14
Alignment explanation
Indices: 16663346--16663373 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16663336 TTTTTATTTA
16663346 AATTAAATTAAATT
1 AATTAAATTAAATT
16663360 AATTAAATTAAATT
1 AATTAAATTAAATT
16663374 GTAAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTAAATTAAATT
Found at i:16666415 original size:8 final size:8
Alignment explanation
Indices: 16666402--16666438 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
16666392 AAAGTGCTGG
*
16666402 AAATAATA
1 AAATAAAA
16666410 AAATAAAA
1 AAATAAAA
16666418 AAAT-AAA
1 AAATAAAA
16666425 AAATAAAA
1 AAATAAAA
16666433 AAATAA
1 AAATAA
16666439 GTAGGCAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (8 bp):
AAATAAAA
Found at i:16666429 original size:15 final size:16
Alignment explanation
Indices: 16666402--16666438 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
16666392 AAAGTGCTGG
16666402 AAATAATAAAATAAAA
1 AAATAATAAAATAAAA
16666418 AAATAA-AAAATAAAA
1 AAATAATAAAATAAAA
16666433 AAATAA
1 AAATAA
16666439 GTAGGCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAATAATAAAATAAAA
Found at i:16677965 original size:27 final size:27
Alignment explanation
Indices: 16677931--16677994 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
16677921 CATTTCAATT
16677931 CCTA-GGGGTGTA-ACAG-TCATTTTAC
1 CCTATGGGG-GTATACAGATCATTTTAC
* *
16677956 CCTATGGGGGTATTCGGATCATTTTAC
1 CCTATGGGGGTATACAGATCATTTTAC
16677983 CCTATGGGGGTA
1 CCTATGGGGGTA
16677995 CTTTGGTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 7 0.21
26 6 0.18
27 21 0.62
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (27 bp):
CCTATGGGGGTATACAGATCATTTTAC
Found at i:16680738 original size:17 final size:16
Alignment explanation
Indices: 16680672--16680738 Score: 55
Period size: 17 Copynumber: 4.1 Consensus size: 16
16680662 CATTCATAGT
*
16680672 TCACAATTAATATAGC
1 TCACAATTAATAGAGC
*
16680688 TCACAATTCAACAGAGC
1 TCACAATT-AATAGAGC
* *
16680705 TCACACA-TAGTATAGC
1 TCACA-ATTAATAGAGC
*
16680721 TCACAATTCAGTAGAGC
1 TCACAATT-AATAGAGC
16680738 T
1 T
16680739 AGCATAGTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
15 1 0.02
16 19 0.46
17 20 0.49
18 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (16 bp):
TCACAATTAATAGAGC
Found at i:16692050 original size:17 final size:18
Alignment explanation
Indices: 16692018--16692051 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16692008 GGAAGTGTTG
16692018 TGCTTTGTTGGATGATGT
1 TGCTTTGTTGGATGATGT
*
16692036 TGCTTT-TTTGATGATG
1 TGCTTTGTTGGATGATG
16692052 AATATTTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.12, C:0.06, G:0.29, T:0.53
Consensus pattern (18 bp):
TGCTTTGTTGGATGATGT
Found at i:16693942 original size:26 final size:26
Alignment explanation
Indices: 16693908--16693959 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
16693898 TGATTGAAAC
*
16693908 ACATTAATTACAACACAATTCAAAAT
1 ACATGAATTACAACACAATTCAAAAT
16693934 ACATGAATTACAACACAATTCAAAAT
1 ACATGAATTACAACACAATTCAAAAT
16693960 TAAACATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.54, C:0.19, G:0.02, T:0.25
Consensus pattern (26 bp):
ACATGAATTACAACACAATTCAAAAT
Found at i:16705726 original size:30 final size:31
Alignment explanation
Indices: 16705671--16705791 Score: 122
Period size: 30 Copynumber: 4.0 Consensus size: 31
16705661 CAGATTTTAT
*
16705671 TATGCCAATATCTCGATATCCATATCTTTGA-
1 TATGCCAATA-CTCGATACCCATATCTTTGAC
*
16705702 TATGCCAATACTCGTTACCCATATCTTTGAC
1 TATGCCAATACTCGATACCCATATCTTTGAC
* * *
16705733 T-TTCCAATATTTGATACCCATATCTTTGAC
1 TATGCCAATACTCGATACCCATATCTTTGAC
* * * * *
16705763 T-TTCTATTATTTGATACCCATATCTTTGA
1 TATGCCAATACTCGATACCCATATCTTTGA
16705792 ATTTCCATAA
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
30 70 0.86
31 11 0.14
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.42
Consensus pattern (31 bp):
TATGCCAATACTCGATACCCATATCTTTGAC
Found at i:16705760 original size:15 final size:16
Alignment explanation
Indices: 16705717--16705791 Score: 59
Period size: 15 Copynumber: 4.9 Consensus size: 16
16705707 CAATACTCGT
16705717 TACCCATATCTTTGAC
1 TACCCATATCTTTGAC
** *
16705733 TTTCCA-ATATTTGA-
1 TACCCATATCTTTGAC
16705747 TACCCATATCTTTGAC
1 TACCCATATCTTTGAC
** * *
16705763 TTTCTAT-TATTTGA-
1 TACCCATATCTTTGAC
16705777 TACCCATATCTTTGA
1 TACCCATATCTTTGA
16705792 ATTTCCATAA
Statistics
Matches: 42, Mismatches: 14, Indels: 7
0.67 0.22 0.11
Matches are distributed among these distances:
14 8 0.19
15 26 0.62
16 8 0.19
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (16 bp):
TACCCATATCTTTGAC
Found at i:16714174 original size:72 final size:72
Alignment explanation
Indices: 16714057--16714220 Score: 215
Period size: 72 Copynumber: 2.3 Consensus size: 72
16714047 CGAAGTATGT
* * * * *
16714057 TTTTATCAATAGTTATTTATGCTTGGTTTTTGGATATTGAATTTATGTTTTACTTATTTATGT-G
1 TTTTATCAATAGTTGTTTATGCTTGGTCTTTAGATATTGAATTTATGTTCTACTTATTT-TGTAC
16714121 T-AATCTAG
65 TAAAT-TAG
* * * *
16714129 TTTTATTAATAGTTGTTTGTGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTATTTTTTACT
1 TTTTATCAATAGTTGTTTATGCTTGGTCTTTAGATATTGAATTTATGTTCTACTTATTTTGTACT
16714194 AAATTAG
66 AAATTAG
16714201 TTTTATCAATAGTTGTTTAT
1 TTTTATCAATAGTTGTTTAT
16714221 ATGTGATTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
71 2 0.03
72 74 0.94
73 3 0.04
ACGTcount: A:0.24, C:0.05, G:0.14, T:0.57
Consensus pattern (72 bp):
TTTTATCAATAGTTGTTTATGCTTGGTCTTTAGATATTGAATTTATGTTCTACTTATTTTGTACT
AAATTAG
Found at i:16715819 original size:13 final size:13
Alignment explanation
Indices: 16715798--16715846 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
16715788 ACACTCAAAA
16715798 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
16715811 TTCTCAAAACCAC
1 TTTTCAAAAGCAC
* *
16715824 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
16715837 TTTTCAAAAG
1 TTTTCAAAAG
16715847 TAAGGAAGAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:16721996 original size:31 final size:31
Alignment explanation
Indices: 16721942--16722003 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
16721932 AATAACAATC
* *
16721942 CAATGACTTCAATAAAAACTTTTGAATAGTT
1 CAATAACTTAAATAAAAACTTTTGAATAGTT
* *
16721973 CAATAACTTAAATCAAAATTTTTGAATAGTT
1 CAATAACTTAAATAAAAACTTTTGAATAGTT
16722004 TAATGACCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (31 bp):
CAATAACTTAAATAAAAACTTTTGAATAGTT
Found at i:16722022 original size:31 final size:32
Alignment explanation
Indices: 16721955--16722024 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
16721945 TGACTTCAAT
* * *
16721955 AAAAACTTTTGAATAGTTCAATAACTTAAATC
1 AAAAATTTTTGAATAGTTCAATAACTCAAAAC
* *
16721987 -AAAATTTTTGAATAGTTTAATGAC-CAAAAC
1 AAAAATTTTTGAATAGTTCAATAACTCAAAAC
16722017 AAAAATTT
1 AAAAATTT
16722025 ATAATTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (32 bp):
AAAAATTTTTGAATAGTTCAATAACTCAAAAC
Found at i:16723344 original size:19 final size:19
Alignment explanation
Indices: 16723320--16723366 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
16723310 CTAACCAAAA
16723320 TTTTACAACATTT-TTTTTC
1 TTTTACAAC-TTTATTTTTC
*
16723339 TTTTACAACTTTATTTTTT
1 TTTTACAACTTTATTTTTC
16723358 TTCTTACAA
1 TT-TTACAA
16723367 AAATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 3 0.12
19 16 0.64
20 6 0.24
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTACAACTTTATTTTTC
Found at i:16726608 original size:26 final size:25
Alignment explanation
Indices: 16726565--16726622 Score: 89
Period size: 26 Copynumber: 2.3 Consensus size: 25
16726555 CTCACCCCAG
*
16726565 TTTTACCCCAGTAAAATTTTTATAA
1 TTTTACCCCAGTAAAATTTTGATAA
*
16726590 TTTTACCCCTAGTAAAATTTTGATGA
1 TTTTACCCC-AGTAAAATTTTGATAA
16726616 TTTTACC
1 TTTTACC
16726623 ATCGATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 9 0.30
26 21 0.70
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (25 bp):
TTTTACCCCAGTAAAATTTTGATAA
Found at i:16726631 original size:26 final size:26
Alignment explanation
Indices: 16726565--16726635 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
16726555 CTCACCCCAG
*
16726565 TTTTACCCC-AGTAAAATTTTTATAA
1 TTTTACCCCGAGTAAAATTTTGATAA
* *
16726590 TTTTACCCCTAGTAAAATTTTGATGA
1 TTTTACCCCGAGTAAAATTTTGATAA
*
16726616 TTTTACCATCGA-TAAAATTT
1 TTTTACC-CCGAGTAAAATTT
16726636 AGAGAAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 9 0.22
26 29 0.73
27 2 0.05
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (26 bp):
TTTTACCCCGAGTAAAATTTTGATAA
Found at i:16730987 original size:73 final size:73
Alignment explanation
Indices: 16730876--16731038 Score: 204
Period size: 73 Copynumber: 2.2 Consensus size: 73
16730866 ACTAAAATTA
* * * *
16730876 CTCAAACGAGTAATGTCTACTGATTCC-ATTGAAAGTGCTCAAACGAGAAATATCTACTGATTCT
1 CTCAAACGAGCAATATCGACT-AATCCTATTGAAAGTGCTCAAACGAGAAATATCTACTGATTCT
16730940 ACTGAAAGTG
65 ACTG-AAGTG
* * * * * *
16730950 TTC-AATGAGCAATATCGACTAATCCTATTGAATGTGCTCAAATGAGCAATGTCTACTGATTCTA
1 CTCAAACGAGCAATATCGACTAATCCTATTGAAAGTGCTCAAACGAGAAATATCTACTGATTCTA
16731014 CTGAAGTG
66 CTGAAGTG
16731022 CTCAAACGAGCAATATC
1 CTCAAACGAGCAATATC
16731039 TACTGCTACT
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
72 11 0.15
73 62 0.83
74 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (73 bp):
CTCAAACGAGCAATATCGACTAATCCTATTGAAAGTGCTCAAACGAGAAATATCTACTGATTCTA
CTGAAGTG
Found at i:16731033 original size:36 final size:36
Alignment explanation
Indices: 16730876--16731223 Score: 223
Period size: 37 Copynumber: 9.7 Consensus size: 36
16730866 ACTAAAATTA
* * * *
16730876 CTCAAACGAGTAATGTCTACTGATTCCATTGAAAGTG
1 CTCAAACGAGCAATATCTACTGATTCTACTG-AAGTG
*
16730913 CTCAAACGAGAAATATCTACTGATTCTACTGAAAGTG
1 CTCAAACGAGCAATATCTACTGATTCTACTG-AAGTG
* * * * * *
16730950 TTC-AATGAGCAATATCGACTAATCCTATTGAATGTG
1 CTCAAACGAGCAATATCTACTGATTCTACTGAA-GTG
* *
16730986 CTCAAATGAGCAATGTCTACTGATTCTACTGAAGTG
1 CTCAAACGAGCAATATCTACTGATTCTACTGAAGTG
16731022 CTCAAACGAGCAATATCTACTG---CTACTGAAAGTG
1 CTCAAACGAGCAATATCTACTGATTCTACTG-AAGTG
* * * *
16731056 CT-TAACAAGCAGTATCTACTGATCCTACTGAA-T-
1 CTCAAACGAGCAATATCTACTGATTCTACTGAAGTG
* * * * * * *
16731089 CT---GCTAGCAATGTCTATTGATTCGAATG-CGTG
1 CTCAAACGAGCAATATCTACTGATTCTACTGAAGTG
* ** * *
16731121 CTCAAACAAGCGGTATCTATTGATTCTATTGCATAGTTG
1 CTCAAACGAGCAATATCTACTGATTCTACTG-A-AG-TG
* * *
16731160 CTTAAACGAGCAATATCCACTGATTATACTGAATGCTTG
1 CTCAAACGAGCAATATCTACTGATTCTACTGAA-G--TG
* *
16731199 CTCAAACGAGCATTATCCACTGATT
1 CTCAAACGAGCAATATCTACTGATT
16731224 ATATTGAATA
Statistics
Matches: 245, Mismatches: 49, Indels: 32
0.75 0.15 0.10
Matches are distributed among these distances:
31 19 0.08
32 2 0.01
33 24 0.10
34 8 0.03
35 23 0.09
36 55 0.22
37 60 0.24
38 3 0.01
39 51 0.21
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (36 bp):
CTCAAACGAGCAATATCTACTGATTCTACTGAAGTG
Found at i:16731072 original size:33 final size:33
Alignment explanation
Indices: 16730978--16731076 Score: 92
Period size: 36 Copynumber: 2.9 Consensus size: 33
16730968 CTAATCCTAT
** *
16730978 TGAATGTGCTCAAATGAGCAATGTCTACTGATTCTAC
1 TGAA-GTGCTCAAACAAGCAATATCTACTG---CTAC
*
16731015 TGAAGTGCTCAAACGAGCAATATCTACTGCTAC
1 TGAAGTGCTCAAACAAGCAATATCTACTGCTAC
* *
16731048 TGAAAGTGCT-TAACAAGCAGTATCTACTG
1 TG-AAGTGCTCAAACAAGCAATATCTACTG
16731077 ATCCTACTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
33 22 0.39
34 7 0.12
36 23 0.41
37 4 0.07
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (33 bp):
TGAAGTGCTCAAACAAGCAATATCTACTGCTAC
Found at i:16731200 original size:39 final size:39
Alignment explanation
Indices: 16731157--16731232 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
16731147 TATTGCATAG
*
16731157 TTGCTTAAACGAGCAATATCCACTGATTATACTGAATGC
1 TTGCTCAAACGAGCAATATCCACTGATTATACTGAATGC
* *
16731196 TTGCTCAAACGAGCATTATCCACTGATTATATTGAAT
1 TTGCTCAAACGAGCAATATCCACTGATTATACTGAAT
16731233 AAGATTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (39 bp):
TTGCTCAAACGAGCAATATCCACTGATTATACTGAATGC
Found at i:16739750 original size:54 final size:54
Alignment explanation
Indices: 16739690--16739795 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
16739680 AGCCCACACG
*
16739690 GGCGTGTGAACCAAGTCAGTGAGTCACACGGGCT-AGCACACGGGTT-GACACATC
1 GGCGTGTGAACCAAGTCAATGAGTCACACGGG-TGAGCACAC-GGTTGGACACATC
* *
16739744 GGCGTGTGAACTAAGTCAATGAGTTACACGGGTGAGCACACGGTTGGACACA
1 GGCGTGTGAACCAAGTCAATGAGTCACACGGGTGAGCACACGGTTGGACACA
16739796 CGGGTATGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
53 5 0.11
54 42 0.89
ACGTcount: A:0.27, C:0.23, G:0.32, T:0.18
Consensus pattern (54 bp):
GGCGTGTGAACCAAGTCAATGAGTCACACGGGTGAGCACACGGTTGGACACATC
Found at i:16739854 original size:19 final size:19
Alignment explanation
Indices: 16739832--16739870 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
16739822 ATGTTAGAGC
*
16739832 CACACAGTCTAGGCTCTGT
1 CACACAGCCTAGGCTCTGT
* *
16739851 CACACGGCCTGGGCTCTGT
1 CACACAGCCTAGGCTCTGT
16739870 C
1 C
16739871 TTACGGCCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.36, G:0.26, T:0.23
Consensus pattern (19 bp):
CACACAGCCTAGGCTCTGT
Found at i:16742214 original size:20 final size:20
Alignment explanation
Indices: 16742171--16742218 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
16742161 AAAAAGTATT
*
16742171 TTTTGTTAAAATATAAATTC
1 TTTTGTTAAAATATAAATTA
16742191 TTTTGTTAAAA-AT-AATTA
1 TTTTGTTAAAATATAAATTA
*
16742209 TATT-TTAAAA
1 TTTTGTTAAAA
16742219 GAAATAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 6 0.23
18 7 0.27
19 2 0.08
20 11 0.42
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (20 bp):
TTTTGTTAAAATATAAATTA
Found at i:16746607 original size:39 final size:39
Alignment explanation
Indices: 16746553--16746711 Score: 318
Period size: 39 Copynumber: 4.1 Consensus size: 39
16746543 TCACAAAAAC
16746553 AAAGTTAAATAAATTAGGGTGTTACAACTCTACCCCTCT
1 AAAGTTAAATAAATTAGGGTGTTACAACTCTACCCCTCT
16746592 AAAGTTAAATAAATTAGGGTGTTACAACTCTACCCCTCT
1 AAAGTTAAATAAATTAGGGTGTTACAACTCTACCCCTCT
16746631 AAAGTTAAATAAATTAGGGTGTTACAACTCTACCCCTCT
1 AAAGTTAAATAAATTAGGGTGTTACAACTCTACCCCTCT
16746670 AAAGTTAAATAAATTAGGGTGTTACAACTCTACCCCTCT
1 AAAGTTAAATAAATTAGGGTGTTACAACTCTACCCCTCT
16746709 AAA
1 AAA
16746712 AGAAATTTCA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 120 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (39 bp):
AAAGTTAAATAAATTAGGGTGTTACAACTCTACCCCTCT
Found at i:16748173 original size:412 final size:414
Alignment explanation
Indices: 16747407--16748231 Score: 1456
Period size: 412 Copynumber: 2.0 Consensus size: 414
16747397 GACTAACTAT
* * *
16747407 AGAAAATCCTCCTAACTCCTTCGGAAATCAATCGCACAACTCCAAAGCATATCCTCCAGTATTTT
1 AGAAAATCCTCCTAACTCCCTCGGAAATCAATCGCACAACTCCAAAGCATATCCTCCAGTATCTG
16747472 AATCACCCTTTCAGATTAACTATCGGTCTGAGGATGGAATGCAGTACTAAAGCCCAATCTCGAAC
66 AATCACCCTTTCAGATTAACTATCGGTCTGAGGATGGAATGCAGTACTAAAGCCCAATCTCGAAC
16747537 CCAAAGTCTCATGAAGTTTTTTTCCAAAACCGAGAAGTGAAACGAGGATCTCTATCAGAAATTAT
131 CCAAAGTCTCATGAAGTTTTTTTCCAAAACCGAGAAGTGAAACGAGGATCTCTATCAGAAATTAT
** * * *
16747602 CAAAATTGGAACCCCGTGAAGCTTTACAATCTCAGAAATGTAGAGCTTGGCCAACTTTTGCAGTA
196 CAAAACCGGAACCCCGTGAAGCCTTACAATCTCAGAAATATAGAGCTTGGCCAACTTTTACAGTA
16747667 AATAATTTGTCCAAACTGGAATGAAATGGGTGGACTTGGTTAACTGATCCACGATGACCCAAACA
261 AATAATTTGTCCAAACTGGAATGAAATGGGTGGACTTGGTTAACTGATCCACGATGACCCAAACA
16747732 AAATCCTTCTTAGTAGGTGTTAAAGGCAACCCACTAACGAAGTCCATAGTTACATGTTCCCATTT
326 AAATCCTTCTTAGTAGGTGTTAAAGGCAACCCACTAACGAAGTCCATAGTTACATGTTCCCATTT
16747797 CCATAAGGGAATCTTAACGAGTTA
391 CCATAAGGGAATCTTAACGAGTTA
*
16747821 AGAAAATTCTCCTAACTCCCTCGGAAATCAATCGCACAACTCCAAAGCATATCCTCCAGTATCTG
1 AGAAAATCCTCCTAACTCCCTCGGAAATCAATCGCACAACTCCAAAGCATATCCTCCAGTATCTG
* * * *
16747886 AATCACCCTTTTAGATTGATTATCGGTCTGAGGATGGAATG-AGTACTAAAGTCCAATCTCGAAC
66 AATCACCCTTTCAGATTAACTATCGGTCTGAGGATGGAATGCAGTACTAAAGCCCAATCTCGAAC
*
16747950 CCAAAGTCTCATGAAG-TTTTTTCCAAAATCGAGAAGTGAAACGAGGATCTCTATCAGAAATTAT
131 CCAAAGTCTCATGAAGTTTTTTTCCAAAACCGAGAAGTGAAACGAGGATCTCTATCAGAAATTAT
* *
16748014 CAAAACCGGAACCCCGTGAAGCCTTACAATCTCAGAAATATAGAGCTTGTCCAACTTTTACAGTG
196 CAAAACCGGAACCCCGTGAAGCCTTACAATCTCAGAAATATAGAGCTTGGCCAACTTTTACAGTA
* *
16748079 AATAATTTGTTCGAACTGGAATGAAATGGGTGGACTTGGTTAACTGATCCACGATGACCCAAACA
261 AATAATTTGTCCAAACTGGAATGAAATGGGTGGACTTGGTTAACTGATCCACGATGACCCAAACA
*
16748144 AAATCCTTCTTAGTAGGTGTTAAAGGCAACCCACTAACGAAGTCTATAGTTACATGTTCCCATTT
326 AAATCCTTCTTAGTAGGTGTTAAAGGCAACCCACTAACGAAGTCCATAGTTACATGTTCCCATTT
*
16748209 TCATAAGGGAATCTTAACGAGTT
391 CCATAAGGGAATCTTAACGAGTT
16748232 GGAGCAAACC
Statistics
Matches: 391, Mismatches: 20, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
412 254 0.65
413 38 0.10
414 99 0.25
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (414 bp):
AGAAAATCCTCCTAACTCCCTCGGAAATCAATCGCACAACTCCAAAGCATATCCTCCAGTATCTG
AATCACCCTTTCAGATTAACTATCGGTCTGAGGATGGAATGCAGTACTAAAGCCCAATCTCGAAC
CCAAAGTCTCATGAAGTTTTTTTCCAAAACCGAGAAGTGAAACGAGGATCTCTATCAGAAATTAT
CAAAACCGGAACCCCGTGAAGCCTTACAATCTCAGAAATATAGAGCTTGGCCAACTTTTACAGTA
AATAATTTGTCCAAACTGGAATGAAATGGGTGGACTTGGTTAACTGATCCACGATGACCCAAACA
AAATCCTTCTTAGTAGGTGTTAAAGGCAACCCACTAACGAAGTCCATAGTTACATGTTCCCATTT
CCATAAGGGAATCTTAACGAGTTA
Found at i:16750693 original size:12 final size:11
Alignment explanation
Indices: 16750675--16750706 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
16750665 TATTCTTGCC
16750675 TAAATCTTGAG
1 TAAATCTTGAG
16750686 TAAAATCTTGAG
1 T-AAATCTTGAG
16750698 TAAATCTTG
1 TAAATCTTG
16750707 TCAATCTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (11 bp):
TAAATCTTGAG
Found at i:16751622 original size:91 final size:91
Alignment explanation
Indices: 16751513--16751685 Score: 301
Period size: 91 Copynumber: 1.9 Consensus size: 91
16751503 TGCAAACATT
*
16751513 GGTGATTTATCCACAAATTTACTAGCAGCTTTTATTTGCAAACCCATTGTGCATTCACAACCTAT
1 GGTGATTTATCCACAAATTTACTAGCAGCTTTTATCTGCAAACCCATTGTGCATTCACAACCTAT
16751578 TGGCAACATATTAACCTACAAACACA
66 TGGCAACATATTAACCTACAAACACA
* * *
16751604 GGTGGTTTATCCATAAATTTACTAGCAGCTTTTATCTGCAAACCCATTGTGCATTCATAACCTAT
1 GGTGATTTATCCACAAATTTACTAGCAGCTTTTATCTGCAAACCCATTGTGCATTCACAACCTAT
*
16751669 TGGCAGCATATTAACCT
66 TGGCAACATATTAACCT
16751686 GCAACACTAA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (91 bp):
GGTGATTTATCCACAAATTTACTAGCAGCTTTTATCTGCAAACCCATTGTGCATTCACAACCTAT
TGGCAACATATTAACCTACAAACACA
Found at i:16751688 original size:45 final size:45
Alignment explanation
Indices: 16751549--16751689 Score: 115
Period size: 45 Copynumber: 3.1 Consensus size: 45
16751539 AGCTTTTATT
* *
16751549 TGCAAACCCATTGTGCATTCACAACCTATTGGCAACATATTAACC
1 TGCAAACCCATTGTGCATTCATAACCTATTGGCAGCATATTAACC
* * * ** * ** * * * *
16751594 TACAAACACAGGTGGTTTATCCATAAATTTACTAGCAGC-T-TTTATC
1 TGCAAACCCA--TTGTGCATTCAT-AACCTATTGGCAGCATATTAACC
16751640 TGCAAACCCATTGTGCATTCATAACCTATTGGCAGCATATTAACC
1 TGCAAACCCATTGTGCATTCATAACCTATTGGCAGCATATTAACC
16751685 TGCAA
1 TGCAA
16751690 CACTAATGGT
Statistics
Matches: 65, Mismatches: 26, Indels: 10
0.64 0.26 0.10
Matches are distributed among these distances:
43 10 0.15
44 9 0.14
45 17 0.26
46 12 0.18
47 8 0.12
48 9 0.14
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.30
Consensus pattern (45 bp):
TGCAAACCCATTGTGCATTCATAACCTATTGGCAGCATATTAACC
Found at i:16752971 original size:34 final size:34
Alignment explanation
Indices: 16752928--16752993 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
16752918 CAGTAAAATA
*
16752928 TTTTCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
*
16752961 TTTTCTGTAAAATTATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACTGGAAAATATTTT
16752994 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 11 0.38
35 13 0.45
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:16755707 original size:29 final size:30
Alignment explanation
Indices: 16755675--16755738 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
16755665 ATTAAAAAGA
* *
16755675 TAAA-ATAAGTGACCAAAATGAAAATTTAC
1 TAAAGATAAGTGACCAAAATAAAAAATTAC
* * *
16755704 TAAAGTTAGGTGACCGAAATAAAAAATTAC
1 TAAAGATAAGTGACCAAAATAAAAAATTAC
16755734 TAAAG
1 TAAAG
16755739 TTGGGTGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.23
Consensus pattern (30 bp):
TAAAGATAAGTGACCAAAATAAAAAATTAC
Found at i:16755734 original size:30 final size:30
Alignment explanation
Indices: 16755683--16755753 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
16755673 GATAAAATAA
* *
16755683 GTGACCAAAATGAAAATTTACTAAAGTTAG
1 GTGACCAAAATAAAAAATTACTAAAGTTAG
* *
16755713 GTGACCGAAATAAAAAATTACTAAAGTTGG
1 GTGACCAAAATAAAAAATTACTAAAGTTAG
*
16755743 GTGACTAAAAT
1 GTGACCAAAAT
16755754 GAAAGTACAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.25
Consensus pattern (30 bp):
GTGACCAAAATAAAAAATTACTAAAGTTAG
Found at i:16757853 original size:19 final size:20
Alignment explanation
Indices: 16757829--16757883 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
16757819 ATGTGGTATA
16757829 TTTTTACATTTTTA-TAATT
1 TTTTTACATTTTTATTAATT
* *
16757848 TTTTTA-AATTTTATTTATT
1 TTTTTACATTTTTATTAATT
* *
16757867 TATTTACATTTTCATTA
1 TTTTTACATTTTTATTA
16757884 TTATCTTGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 6 0.21
19 15 0.54
20 7 0.25
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTACATTTTTATTAATT
Found at i:16758515 original size:43 final size:43
Alignment explanation
Indices: 16758467--16758588 Score: 190
Period size: 43 Copynumber: 2.8 Consensus size: 43
16758457 TTTTAGGAAT
*
16758467 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * **
16758510 AAACGCCGCTATAGATCAAGAGCTTTAACGGAGCTTTTTGCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
16758553 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT
16758589 GACGTTACAT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:16758683 original size:17 final size:18
Alignment explanation
Indices: 16758650--16758704 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
16758640 AAATTCAAAA
*
16758650 AAAAATGTAAAAGTTATTT
1 AAAAAT-TAAAAATTATTT
16758669 AAAAA-TAAAAATTA-TT
1 AAAAATTAAAAATTATTT
16758685 AAAAATTCTAAAAATTATTT
1 AAAAA-T-TAAAAATTATTT
16758705 TGTTAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 7 0.23
17 8 0.26
19 14 0.45
20 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (18 bp):
AAAAATTAAAAATTATTT
Found at i:16759839 original size:43 final size:43
Alignment explanation
Indices: 16759791--16760170 Score: 463
Period size: 43 Copynumber: 8.8 Consensus size: 43
16759781 TTTTAGGAAT
*
16759791 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * **
16759834 AAACGCCGCTATAGATCAAGAGCTTTAACGGAGCTTTTTGCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
16759877 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTCTCCCAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * ** **
16759920 AAATGTCGCTATAGATCAAGAGCTTTAGCTACGCTTTTTGCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
16759963 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTCTCCCAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * ** **
16760006 AAATGTCGCTATAGATCAAGAGCTTTAGCTACGCTTTTTGCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
16760049 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTCCCCAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
16760092 AAACGCCGCTATAGCTCGAGGCCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
16760135 AAACGCCGCTATAGCTCGAGACCTTTAGCGACGCTT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT
16760171 CTCGTAAAAA
Statistics
Matches: 281, Mismatches: 56, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 281 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:16759893 original size:86 final size:86
Alignment explanation
Indices: 16759791--16760184 Score: 569
Period size: 86 Copynumber: 4.6 Consensus size: 86
16759781 TTTTAGGAAT
* * *
16759791 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAG
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTCTCCCAAAAACGCCGCTATAGATCAAGAG
*
16759856 CTTTAACGGA-GCTTTTTGCAC
66 CTTTAGC-GACGCTTTTTGCAC
* *
16759877 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTCTCCCAAAAATGTCGCTATAGATCAAGAG
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTCTCCCAAAAACGCCGCTATAGATCAAGAG
*
16759942 CTTTAGCTACGCTTTTTGCAC
66 CTTTAGCGACGCTTTTTGCAC
* *
16759963 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTCTCCCAAAAATGTCGCTATAGATCAAGAG
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTCTCCCAAAAACGCCGCTATAGATCAAGAG
*
16760028 CTTTAGCTACGCTTTTTGCAC
66 CTTTAGCGACGCTTTTTGCAC
* *
16760049 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT-TCCCCAAAAACGCCGCTATAGCTCGAG-
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTCT-CCCAAAAACGCCGCTATAGATCAAGA
**
16760112 GCCTTTAGCGACGCTTTTCCCAC
65 G-CTTTAGCGACGCTTTTTGCAC
* * * **
16760135 AAACGCCGCTATAGCTCGAGACCTTTAGCGACGCTTCTCGTAAAAACGCC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTCTCCCAAAAACGCC
16760185 ACTAAAAACA
Statistics
Matches: 285, Mismatches: 19, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
85 3 0.01
86 281 0.99
87 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (86 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTCTCCCAAAAACGCCGCTATAGATCAAGAG
CTTTAGCGACGCTTTTTGCAC
Found at i:16763601 original size:14 final size:14
Alignment explanation
Indices: 16763582--16763630 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
16763572 AACCTTAAAT
16763582 CCCTAACTCTTAAC
1 CCCTAACTCTTAAC
16763596 CCCTAACGTC-TAAC
1 CCCTAAC-TCTTAAC
*
16763610 CCCTAAACCCTTAAC
1 CCCT-AACTCTTAAC
*
16763625 CACTAA
1 CCCTAA
16763631 ACCTTAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.33, C:0.43, G:0.02, T:0.22
Consensus pattern (14 bp):
CCCTAACTCTTAAC
Found at i:16763670 original size:14 final size:14
Alignment explanation
Indices: 16763653--16763697 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
16763643 AACCCTTAAA
16763653 CCATAATCCCTAAT
1 CCATAATCCCTAAT
16763667 CCATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
16763682 CCATACTCCCTAAT
1 CCATAATCCCTAAT
16763696 CC
1 CC
16763698 TTAAAATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.27
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:16763682 original size:15 final size:15
Alignment explanation
Indices: 16763649--16763694 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
16763639 TCCCAACCCT
16763649 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
16763663 T-AATCCATAATCCC
1 TAAATCCATAATCCC
*
16763677 TAAATCCATACTCCC
1 TAAATCCATAATCCC
16763692 TAA
1 TAA
16763695 TCCTTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 2 0.07
14 12 0.41
15 15 0.52
ACGTcount: A:0.39, C:0.35, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:16763982 original size:298 final size:302
Alignment explanation
Indices: 16763469--16764405 Score: 1101
Period size: 298 Copynumber: 3.1 Consensus size: 302
16763459 AATATATTTG
* * *
16763469 ATTTATTATTATCTATTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAA-TAAT
1 ATTTATTATTATCTCTTTTACAATCATATAAGAACATATTCAAAATATAAATTAAAAAAATTAAT
* * * * *
16763533 -TAATCTACTCAAAACCTTAACCCGGCCCCTGAATCCTTAAACCTTAAATCCCTAA--CTCTTAA
66 CTAAAC--CCCAAAACCCTAA--C--CACCTGAA-CC----ACCCTAAATCCCTAACTCTCTTAA
* * *
16763595 CCCCTAACGTCTAACCCCT--A-----AACCCT-TAACCACTAAACCTTAAATCCCAACCCTTAA
120 CCCCTAACATCTAACCCCTAAACCCCTAACCCTCTAACCCCTAAACCTTAAATCCTAACCCTTAA
* *
16763652 ACCATAATCCCTAATCCATAATCCCTAAATCCATACTCCCTAATCCTTAAAATATGAGCTCCTAA
185 A-CATAATCCCTAATCCATAATCCCTAAATCCATACTCCCTAAACCTTAAAATATGAACTCCTAA
* *
16763717 ACCGGCCTTAAATCTTAAATTAATCATATACCCTAAACTAAAAACCCTAAACAA
249 ACCGGCCTTAAATCTTAAATAAATCATATACCCTAAACCAAAAACCCTAAACAA
16763771 ATTTATTATTATCTCTTTTACAATCATATAAGAACATATTCAAAATATAAATTAAAAAATAATTA
1 ATTTATTATTATCTCTTTTACAATCATATAAGAACATATTCAAAATATAAATT-AAAAA-AATTA
*
16763836 ATCTAAA-CCCAAAACCCTAA-C-CC-G-A-C-CCCTGAATCCCTAACT-T-TTAACCCCTAATG
64 ATCTAAACCCCAAAACCCTAACCACCTGAACCACCCTAAATCCCTAACTCTCTTAACCCCTAA--
** *
16763892 TGTCTAACCCCTAAACCCCTAACCATCTAACCCCTAAACCTTAAATCCTAACCCTTAAATCATAA
127 CATCTAACCCCTAAACCCCTAACCCTCTAACCCCTAAACCTTAAATCCTAACCCTTAAA-CATAA
* * * * *
16763957 TCCATAATCCATAATCCCTAAATCCATACTCTCTAAACCTTAAAATATGAACTCTTAAATCGACC
191 TCCCTAATCCATAATCCCTAAATCCATACTCCCTAAACCTTAAAATATGAACTCCTAAACCGGCC
16764022 TTAAATCTTAAATAAATCATATACCCTAAACCAAAAACCCTAAACAA
256 TTAAATCTTAAATAAATCATATACCCTAAACCAAAAACCCTAAACAA
* * * *
16764069 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATGAATTTAAAAAATTAAT
1 ATTTATTATTATCTCTTTTACAATCATATAAGAACATATTCAAAATATAAATTAAAAAAATTAAT
*
16764134 CTAAACGCCCAAAATCCTAACTCGACCTTTGAATCCCTAAACCCTAAATCCCTAACTCTCTTAAC
66 CTAAAC-CCCAAAACCCTAAC-C-ACC--TGAA--CC---ACCCTAAATCCCTAACTCTCTTAAC
* ** *
16764199 CCCTAACATCTAACCCCTAAACCCTTAACCCTCTAACCCCTAAACCCTTAACCCTCTAACCCCTA
121 CCCTAACATCTAACCCCTAAACCCCTAACCCTCTAACCCCTAAA-CCTTAAATC-CTAACCCTTA
* * * *
16764264 AACCTTA-CCCTAATCTATAATCCCTAAACCCATACTCCCTAAACCTTAAAATA-GTAACTCCTA
184 AACATAATCCCTAATCCATAATCCCTAAATCCATACTCCCTAAACCTTAAAATATG-AACTCCTA
*
16764327 AACTGGCCTTAAATCTTAAATAAATCATATACCCTAAACCAAAAACCCTAAACAA
248 AACCGGCCTTAAATCTTAAATAAATCATATACCCTAAACCAAAAACCCTAAACAA
16764382 ATTTATTATTATCTCTTTTACAAT
1 ATTTATTATTATCTCTTTTACAAT
16764406 TATTTTAAAT
Statistics
Matches: 552, Mismatches: 45, Indels: 65
0.83 0.07 0.10
Matches are distributed among these distances:
288 23 0.04
289 1 0.00
290 11 0.02
292 1 0.00
293 1 0.00
295 1 0.00
296 13 0.02
297 11 0.02
298 201 0.36
300 1 0.00
302 52 0.09
303 16 0.03
304 2 0.00
305 5 0.01
306 4 0.01
309 1 0.00
312 1 0.00
313 174 0.32
314 11 0.02
315 22 0.04
ACGTcount: A:0.40, C:0.28, G:0.03, T:0.29
Consensus pattern (302 bp):
ATTTATTATTATCTCTTTTACAATCATATAAGAACATATTCAAAATATAAATTAAAAAAATTAAT
CTAAACCCCAAAACCCTAACCACCTGAACCACCCTAAATCCCTAACTCTCTTAACCCCTAACATC
TAACCCCTAAACCCCTAACCCTCTAACCCCTAAACCTTAAATCCTAACCCTTAAACATAATCCCT
AATCCATAATCCCTAAATCCATACTCCCTAAACCTTAAAATATGAACTCCTAAACCGGCCTTAAA
TCTTAAATAAATCATATACCCTAAACCAAAAACCCTAAACAA
Found at i:16763993 original size:15 final size:15
Alignment explanation
Indices: 16763933--16763984 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 15
16763923 CCCTAAACCT
16763933 TAAATCC-TAA-CCC
1 TAAATCCATAATCCC
*
16763946 TTAAAT-CATAATCCA
1 -TAAATCCATAATCCC
16763961 T-AATCCATAATCCC
1 TAAATCCATAATCCC
16763975 TAAATCCATA
1 TAAATCCATA
16763985 CTCTCTAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 4 0.12
14 18 0.56
15 10 0.31
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:16764000 original size:22 final size:22
Alignment explanation
Indices: 16763925--16764000 Score: 52
Period size: 22 Copynumber: 3.5 Consensus size: 22
16763915 CATCTAACCC
*
16763925 CTAAACCTTAAATCC-TAACCCT
1 CTAAACCTTAAATCCAT-ACTCT
* * *
16763947 -TAAATCAT-AATCCATAATC-
1 CTAAACCTTAAATCCATACTCT
* *
16763966 CATAATCCCTAAATCCATACTCT
1 C-TAAACCTTAAATCCATACTCT
16763989 CTAAACCTTAAA
1 CTAAACCTTAAA
16764001 ATATGAACTC
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
20 7 0.18
21 12 0.31
22 19 0.49
23 1 0.03
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.29
Consensus pattern (22 bp):
CTAAACCTTAAATCCATACTCT
Found at i:16764229 original size:15 final size:14
Alignment explanation
Indices: 16764168--16764270 Score: 73
Period size: 15 Copynumber: 6.9 Consensus size: 14
16764158 ACCTTTGAAT
* *
16764168 CCCTAAACCCTAAAT
1 CCCT-AACCCTTAAC
16764183 CCCTAACTCTCTTAAC
1 CCCTAAC-C-CTTAAC
*
16764199 CCCTAA-CATCTAAC
1 CCCTAACCCT-TAAC
16764213 CCCTAAACCCTTAAC
1 CCCT-AACCCTTAAC
*
16764228 CCTCTAACCCCTAAAC
1 CC-CTAA-CCCTTAAC
*
16764244 CCTTAACCCTCTAAC
1 CCCTAACCCT-TAAC
*
16764259 CCCTAAACCTTA
1 CCCTAACCCTTA
16764271 CCCTAATCTA
Statistics
Matches: 71, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
13 1 0.01
14 18 0.25
15 29 0.41
16 23 0.32
ACGTcount: A:0.32, C:0.45, G:0.00, T:0.23
Consensus pattern (14 bp):
CCCTAACCCTTAAC
Found at i:16764233 original size:23 final size:23
Alignment explanation
Indices: 16764207--16764274 Score: 122
Period size: 23 Copynumber: 3.0 Consensus size: 23
16764197 ACCCCTAACA
16764207 TCTAACCCCTAAACCCTTAACCC
1 TCTAACCCCTAAACCCTTAACCC
16764230 TCTAACCCCTAAACCCTTAACCC
1 TCTAACCCCTAAACCCTTAACCC
16764253 TCTAACCCCTAAA-CCTT-ACCC
1 TCTAACCCCTAAACCCTTAACCC
16764274 T
1 T
16764275 AATCTATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.11
22 4 0.09
23 36 0.80
ACGTcount: A:0.29, C:0.47, G:0.00, T:0.24
Consensus pattern (23 bp):
TCTAACCCCTAAACCCTTAACCC
Found at i:16764590 original size:84 final size:86
Alignment explanation
Indices: 16764494--16764665 Score: 269
Period size: 88 Copynumber: 2.0 Consensus size: 86
16764484 GATTTTACAT
*
16764494 ATTCAATTAGAAATAAATTGAATTTTA-T-TTAATATGAATAAACCAATTAAGATAAAATATTTT
1 ATTCAATTAGAAATAAATTGAATTTTATTATTAATATAAATAAACCAATTAAGATAAAATATTTT
16764557 TAGCGGCACTTTT-TCAAAAAC
66 TAGCGGCACTTTTCT-AAAAAC
*
16764578 ATTCAATTAGAAATAAATTGAATTTTATTTAATTAATATAAATAAACCAATTAAGATAAAATGTT
1 ATTCAATTAGAAATAAATTGAATTTTA-TT-ATTAATATAAATAAACCAATTAAGATAAAATATT
*
16764643 TTTAGCGGCGCTTTTCTAAAAAC
64 TTTAGCGGCACTTTTCTAAAAAC
16764666 GCCGCTAAAG
Statistics
Matches: 80, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
84 27 0.34
86 1 0.01
88 51 0.64
89 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (86 bp):
ATTCAATTAGAAATAAATTGAATTTTATTATTAATATAAATAAACCAATTAAGATAAAATATTTT
TAGCGGCACTTTTCTAAAAAC
Found at i:16764705 original size:41 final size:41
Alignment explanation
Indices: 16764644--16764804 Score: 279
Period size: 41 Copynumber: 3.9 Consensus size: 41
16764634 TAAAATGTTT
16764644 TTAGCGGCGCTT-TTCTAAAAACGCCGCTAAAGGCCCCAGCA
1 TTAGCGGCGCTTCTTC-AAAAACGCCGCTAAAGGCCCCAGCA
16764685 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCCAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCCAGCA
* *
16764726 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCCAGCA
*
16764767 TTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCCCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCCA
16764805 AAAACTCAGA
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
41 111 0.97
42 3 0.03
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.19
Consensus pattern (41 bp):
TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCCAGCA
Found at i:16771749 original size:27 final size:27
Alignment explanation
Indices: 16771719--16771773 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
16771709 ATTATCAAAA
*
16771719 TTAATTAAAATTCAA-TATTTTAATAAT
1 TTAAGTAAAATTCAATTATTTT-ATAAT
* *
16771746 TTAAGTACAATTTAATTATTTTATAAT
1 TTAAGTAAAATTCAATTATTTTATAAT
16771773 T
1 T
16771774 ATATTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (27 bp):
TTAAGTAAAATTCAATTATTTTATAAT
Found at i:16775933 original size:9 final size:9
Alignment explanation
Indices: 16775916--16775952 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
16775906 TGAGTTTTCG
16775916 AATTCGAAT
1 AATTCGAAT
*
16775925 AACTCGAAT
1 AATTCGAAT
16775934 AATTCGAAT
1 AATTCGAAT
16775943 AATTCGAAT
1 AATTCGAAT
16775952 A
1 A
16775953 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:16781045 original size:20 final size:20
Alignment explanation
Indices: 16781022--16781059 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16781012 TTACTAATTT
* *
16781022 ATTTTACATTAAACATAAAC
1 ATTTGACATCAAACATAAAC
16781042 ATTTGACATCAAACATAA
1 ATTTGACATCAAACATAA
16781060 GGAAAACCTA
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:0.50, C:0.16, G:0.03, T:0.32
Consensus pattern (20 bp):
ATTTGACATCAAACATAAAC
Found at i:16781436 original size:5 final size:4
Alignment explanation
Indices: 16781385--16781452 Score: 57
Period size: 4 Copynumber: 15.8 Consensus size: 4
16781375 AAATTTTTGT
* *
16781385 TTTC TTTC TTTC TTTC TTT- TTGTT TTTC TCTTC TCTTC TCTTA TTTC
1 TTTC TTTC TTTC TTTC TTTC TT-TC TTTC T-TTC T-TTC T-TTC TTTC
16781432 TTTTC TTTC TTTCC TTTC TTT
1 -TTTC TTTC TTT-C TTTC TTT
16781453 TTCAGCTGCT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
3 2 0.04
4 31 0.55
5 23 0.41
ACGTcount: A:0.01, C:0.24, G:0.01, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:16784310 original size:22 final size:20
Alignment explanation
Indices: 16784285--16784333 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
16784275 ATAAAATATT
*
16784285 TTTATATTTACTTTTTAAAATC
1 TTTATATTTA-TATTT-AAATC
*
16784307 TTTATAATTTATATTTAAATT
1 TTTAT-ATTTATATTTAAATC
16784328 TTTATA
1 TTTATA
16784334 ATTTTCTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 9 0.38
22 9 0.38
23 5 0.21
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTATATTTATATTTAAATC
Found at i:16784343 original size:22 final size:22
Alignment explanation
Indices: 16784282--16784345 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
16784272 AATATAAAAT
* *
16784282 ATTTTTAT-ATTTACTTTTTAAA
1 ATTTTTATAATTTTCTATTT-AA
* *
16784304 ATCTTTATAA-TTTATATTTAA
1 ATTTTTATAATTTTCTATTTAA
16784325 ATTTTTATAATTTTCTATTTA
1 ATTTTTATAATTTTCTATTTA
16784346 CTTTTTTTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 11 0.32
22 22 0.65
23 1 0.03
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTTTATAATTTTCTATTTAA
Found at i:16785120 original size:30 final size:28
Alignment explanation
Indices: 16785084--16785164 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 28
16785074 TTAAAATATT
*
16785084 TTTATATTTTCTTTTTAGAAATTTTTTAAA
1 TTTATATTTACTTTTTA-AAA-TTTTTAAA
16785114 TTTATATTTACTTTTTAAAATTTTTAAA
1 TTTATATTTACTTTTTAAAATTTTTAAA
* *
16785142 TATTCT-TTTGACTTTTTATAATT
1 T-TTATATTT-ACTTTTTAAAATT
16785165 AGAACTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
28 12 0.26
29 18 0.39
30 16 0.35
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTATATTTACTTTTTAAAATTTTTAAA
Found at i:16785157 original size:28 final size:30
Alignment explanation
Indices: 16785084--16785159 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
16785074 TTAAAATATT
*
16785084 TTTATATTTTCTTTTTAGAAATTTTTTAAA
1 TTTATATTTACTTTTTAGAAATTTTTTAAA
16785114 TTTATATTTACTTTTTA-AAA-TTTTTAAA
1 TTTATATTTACTTTTTAGAAATTTTTTAAA
*
16785142 TATTCT-TTTGACTTTTTA
1 T-TTATATTT-ACTTTTTA
16785160 TAATTAGAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 12 0.29
29 14 0.33
30 16 0.38
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (30 bp):
TTTATATTTACTTTTTAGAAATTTTTTAAA
Found at i:16785404 original size:29 final size:30
Alignment explanation
Indices: 16785360--16785418 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
16785350 CAAAAGCTTG
* *
16785360 AGTGACTAAAACAAAA-AAAATTAATAGTT
1 AGTGACCAAAACAAAATAAAATGAATAGTT
* *
16785389 AGTGACCAAAATAAAATAAACTGAATAGTT
1 AGTGACCAAAACAAAATAAAATGAATAGTT
16785419 GGGTGACTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (30 bp):
AGTGACCAAAACAAAATAAAATGAATAGTT
Found at i:16785876 original size:27 final size:27
Alignment explanation
Indices: 16785846--16785908 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
16785836 AAAAAACCTG
*
16785846 TGGCGGCACCAAAGGTGCCAAAGTGAT
1 TGGCGGCACCAAAGGTGCCAAAGAGAT
16785873 TGGCGGCACCAAAGGTGCCAAAGAGAT
1 TGGCGGCACCAAAGGTGCCAAAGAGAT
16785900 TGGCGGCAC
1 TGGCGGCAC
16785909 AGAACTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.24, G:0.35, T:0.13
Consensus pattern (27 bp):
TGGCGGCACCAAAGGTGCCAAAGAGAT
Found at i:16788633 original size:28 final size:27
Alignment explanation
Indices: 16788575--16788637 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
16788565 TTTTTAGTAT
* ** *
16788575 ATTTTGATAAATAAAAAAAATTATAAT
1 ATTTTGGTAAATAAAAAAAAAGATAAC
16788602 ATTTTGGTAAATAATAAAAAAAGATAAC
1 ATTTTGGTAAATAA-AAAAAAAGATAAC
16788630 ATTTTGGT
1 ATTTTGGT
16788638 TATTTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.37
Consensus pattern (27 bp):
ATTTTGGTAAATAAAAAAAAAGATAAC
Found at i:16790698 original size:10 final size:10
Alignment explanation
Indices: 16790671--16790703 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
16790661 TAATATTCAT
*
16790671 AAAAATTATA
1 AAAAATTCTA
16790681 AAAAATTCTA
1 AAAAATTCTA
16790691 AAAAATTC-A
1 AAAAATTCTA
16790700 AAAA
1 AAAA
16790704 TATAAAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 5 0.23
10 17 0.77
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATTCTA
Found at i:16791224 original size:28 final size:29
Alignment explanation
Indices: 16791168--16791229 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
16791158 TGTATATTTG
* ***
16791168 GAATTTAATCTCTAATTTTTTATTTTTAA
1 GAATTTAATCTATAATTTTTTAAAATTAA
16791197 GAATTTAATCTAT-ATTTTTTAAAATTAA
1 GAATTTAATCTATAATTTTTTAAAATTAA
*
16791225 AAATT
1 GAATT
16791230 CAAATCCAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (29 bp):
GAATTTAATCTATAATTTTTTAAAATTAA
Found at i:16802444 original size:46 final size:44
Alignment explanation
Indices: 16802375--16802463 Score: 160
Period size: 46 Copynumber: 2.0 Consensus size: 44
16802365 GGTATCAGAG
16802375 CCAGGTTGTAAATCGGCTGTAGATTATGGGTTTTATAAAAAAAA
1 CCAGGTTGTAAATCGGCTGTAGATTATGGGTTTTATAAAAAAAA
16802419 CCAGGTTGTAAAATTCGGCTGTAGATTATGGGTTTTATAAAAAAA
1 CCAGGTTGT-AAA-TCGGCTGTAGATTATGGGTTTTATAAAAAAA
16802464 TTTGGCTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 9 0.21
45 3 0.07
46 31 0.72
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (44 bp):
CCAGGTTGTAAATCGGCTGTAGATTATGGGTTTTATAAAAAAAA
Found at i:16812203 original size:3 final size:3
Alignment explanation
Indices: 16812195--16812227 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
16812185 ACATGTTTCC
16812195 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16812228 TACATATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:16819601 original size:26 final size:25
Alignment explanation
Indices: 16819556--16819604 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
16819546 AAATGTCAAA
16819556 AAAAGTAGAAAGGCCAAAATTTGGG
1 AAAAGTAGAAAGGCCAAAATTTGGG
*
16819581 AAAAGTATGAGAA-GCCGAAATTTG
1 AAAAGTA-GA-AAGGCCAAAATTTG
16819605 AAAAAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 12 0.57
27 2 0.10
ACGTcount: A:0.47, C:0.08, G:0.27, T:0.18
Consensus pattern (25 bp):
AAAAGTAGAAAGGCCAAAATTTGGG
Found at i:16819610 original size:26 final size:25
Alignment explanation
Indices: 16819554--16819610 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
16819544 CAAAATGTCA
16819554 AAAAAAGTAGAAAGGCCAAAATTTG
1 AAAAAAGTAGAAAGGCCAAAATTTG
** *
16819579 GGAAAAGTATGAGAA-GCCGAAATTTG
1 AAAAAAGTA-GA-AAGGCCAAAATTTG
16819605 AAAAAA
1 AAAAAA
16819611 AAAGATAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 7 0.28
26 16 0.64
27 2 0.08
ACGTcount: A:0.54, C:0.07, G:0.23, T:0.16
Consensus pattern (25 bp):
AAAAAAGTAGAAAGGCCAAAATTTG
Found at i:16824182 original size:25 final size:24
Alignment explanation
Indices: 16824115--16824175 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
16824105 GGATGATATA
*
16824115 TCGA-CTTTTCATTGAGATCCTTT
1 TCGACCTTTTCATTGATATCCTTT
* *
16824138 TAGACTTTTTCATTGATATCCTTT
1 TCGACCTTTTCATTGATATCCTTT
16824162 TCGACCTTTTCATT
1 TCGACCTTTTCATT
16824176 TGTTATCTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 3 0.09
24 29 0.91
ACGTcount: A:0.18, C:0.21, G:0.10, T:0.51
Consensus pattern (24 bp):
TCGACCTTTTCATTGATATCCTTT
Found at i:16824187 original size:40 final size:40
Alignment explanation
Indices: 16824142--16824255 Score: 131
Period size: 40 Copynumber: 2.9 Consensus size: 40
16824132 TCCTTTTAGA
* * * *
16824142 CTTTTTCATTGATATCCTTTTCGACCTTTTCATTTGTTAT
1 CTTTTTCAATGACATCCTGTTCAACCTTTTCATTTGTTAT
*
16824182 CTTTTTGAATGACATCCTGTTCAACCTTTTCATTTGTTAT
1 CTTTTTCAATGACATCCTGTTCAACCTTTTCATTTGTTAT
* * * *
16824222 C-CTTTCGGATAACATCCTTTTCAACCTTTTCATT
1 CTTTTTC-AATGACATCCTGTTCAACCTTTTCATT
16824256 GGTTCAAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 3 0.05
40 60 0.95
ACGTcount: A:0.18, C:0.23, G:0.08, T:0.51
Consensus pattern (40 bp):
CTTTTTCAATGACATCCTGTTCAACCTTTTCATTTGTTAT
Found at i:16833229 original size:3 final size:3
Alignment explanation
Indices: 16833221--16833273 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
16833211 GCAGAAATAT
16833221 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
16833269 ATG AT
1 ATG AT
16833274 AAACAATCAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:16835925 original size:65 final size:65
Alignment explanation
Indices: 16835850--16835985 Score: 272
Period size: 65 Copynumber: 2.1 Consensus size: 65
16835840 TGCAAGTTAT
16835850 TTAACATCACAAATATATATCTATTGCTAGAATTGTATAAATCCTTTTGAAAAGATAGGACATCA
1 TTAACATCACAAATATATATCTATTGCTAGAATTGTATAAATCCTTTTGAAAAGATAGGACATCA
16835915 TTAACATCACAAATATATATCTATTGCTAGAATTGTATAAATCCTTTTGAAAAGATAGGACATCA
1 TTAACATCACAAATATATATCTATTGCTAGAATTGTATAAATCCTTTTGAAAAGATAGGACATCA
16835980 TTAACA
1 TTAACA
16835986 CAATTACTCG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 71 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (65 bp):
TTAACATCACAAATATATATCTATTGCTAGAATTGTATAAATCCTTTTGAAAAGATAGGACATCA
Found at i:16837766 original size:3 final size:3
Alignment explanation
Indices: 16837760--16837785 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16837750 TCTTTTTCCT
16837760 TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TC
16837786 TTCTTCTAGT
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:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
TCC
Found at i:16840565 original size:23 final size:23
Alignment explanation
Indices: 16840518--16840564 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
16840508 TATGGTTTAA
*
16840518 TTATTATATTTTTTATTGTTATT
1 TTATTATATTTTTTATTCTTATT
16840541 TTATTA-AGTTTTTTATTC-TATT
1 TTATTATA-TTTTTTATTCTTATT
16840563 TT
1 TT
16840565 TGCAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (23 bp):
TTATTATATTTTTTATTCTTATT
Found at i:16843352 original size:66 final size:66
Alignment explanation
Indices: 16843230--16843353 Score: 144
Period size: 66 Copynumber: 1.9 Consensus size: 66
16843220 TGTGATTATG
* **
16843230 TATTGAATTTTCATTATTGTATTAACTTAAATTATTTACATATATTTGCATTATATTTCTATTTT
1 TATTGAATTTTCATTATTGTATTAACTTAAATTATTTACATATACTTGCAAAATATTTCTATTTT
16843295 T
66 T
* * * * *
16843296 TATTGAATTTTCATTCTTGT-TTCAATTTCAATTATTTAGATGA-ACTTGTAAAATATTT
1 TATTGAATTTTCATTATTGTATT-AACTTAAATTATTTACAT-ATACTTGCAAAATATTT
16843354 GAATGAACTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
65 2 0.04
66 45 0.94
67 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.55
Consensus pattern (66 bp):
TATTGAATTTTCATTATTGTATTAACTTAAATTATTTACATATACTTGCAAAATATTTCTATTTT
T
Found at i:16843986 original size:30 final size:30
Alignment explanation
Indices: 16843952--16844014 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
16843942 ACTTATTTTA
*
16843952 TTGTTAATTTTGTTATTATTTTAAAGACGT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
16843982 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
16844012 TTG
1 TTG
16844015 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:16858361 original size:14 final size:14
Alignment explanation
Indices: 16858342--16858387 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
16858332 TTTTTTTATT
16858342 ATAATAATAATTTA
1 ATAATAATAATTTA
*
16858356 ATAATACTAATTTA
1 ATAATAATAATTTA
16858370 ATAATAATAATTTA
1 ATAATAATAATTTA
16858384 ATAA
1 ATAA
16858388 CATTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:16858397 original size:28 final size:28
Alignment explanation
Indices: 16858332--16858398 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
16858322 TTTGTCAACT
*
16858332 TTTTTTTATTATAATAATAATTTAATAATA
1 TTTTTTTA--ATAATAATAATTTAATAACA
* **
16858362 CTAATTTAATAATAATAATTTAATAACA
1 TTTTTTTAATAATAATAATTTAATAACA
16858390 TTTTTTTAA
1 TTTTTTTAA
16858399 CACATAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
28 25 0.83
30 5 0.17
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTTTTTAATAATAATAATTTAATAACA
Found at i:16865226 original size:25 final size:25
Alignment explanation
Indices: 16865189--16865304 Score: 83
Period size: 25 Copynumber: 4.7 Consensus size: 25
16865179 TCATATTCAT
16865189 GTATGCTCATACGAGCTATGAATCA
1 GTATGCTCATACGAGCTATGAATCA
* * *
16865214 GTATGCTCTTACGAGCTTTGAATCG
1 GTATGCTCATACGAGCTATGAATCA
* * * * *
16865239 GGAAGCTCATATGAGC--TGCAGTCG
1 GTATGCTCATACGAGCTATG-AATCA
* * * *
16865263 GGAAGCTCATACGAGCTATAAATCG
1 GTATGCTCATACGAGCTATGAATCA
* *
16865288 GGAAGCTCATACGAGCT
1 GTATGCTCATACGAGCT
16865305 GTGGTGTGTT
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.03
24 19 0.25
25 55 0.71
26 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATGAATCA
Found at i:16865268 original size:24 final size:24
Alignment explanation
Indices: 16865234--16865305 Score: 99
Period size: 25 Copynumber: 3.0 Consensus size: 24
16865224 ACGAGCTTTG
* *
16865234 AATCGGGAAGCTCATATGAGCTGC
1 AATCGGGAAGCTCATACGAGCTGA
* *
16865258 AGTCGGGAAGCTCATACGAGCTATA
1 AATCGGGAAGCTCATACGAGCT-GA
16865283 AATCGGGAAGCTCATACGAGCTG
1 AATCGGGAAGCTCATACGAGCTG
16865306 TGGTGTGTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 20 0.49
25 21 0.51
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (24 bp):
AATCGGGAAGCTCATACGAGCTGA
Found at i:16866736 original size:18 final size:18
Alignment explanation
Indices: 16866700--16866784 Score: 59
Period size: 18 Copynumber: 4.5 Consensus size: 18
16866690 AAAAAAAATT
*
16866700 AATTATTAAAATTTATAA
1 AATTATTAAAAGTTATAA
*
16866718 AATTATTAAAAGTTGTAA
1 AATTATTAAAAGTTATAA
16866736 ATATGT-TTAAAAAGTTATTAA
1 A-AT-TATT-AAAAGTTA-TAA
*
16866757 CAATGTCA--AAAAATTATAA
1 -AAT-T-ATTAAAAGTTATAA
16866776 AATTATTAA
1 AATTATTAA
16866785 TTATTAGAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
16 1 0.02
17 1 0.02
18 22 0.41
19 7 0.13
20 15 0.28
21 7 0.13
22 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (18 bp):
AATTATTAAAAGTTATAA
Found at i:16875442 original size:21 final size:21
Alignment explanation
Indices: 16875416--16875474 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
16875406 CATGGTTTGC
*
16875416 CCACACGACTGTGTATCTCAG
1 CCACACGACTGTGTACCTCAG
* * *
16875437 CCACACGGCCGTGTCCCTCAG
1 CCACACGACTGTGTACCTCAG
*
16875458 CCATACGACTGTGTACC
1 CCACACGACTGTGTACC
16875475 CCGGTCACAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.20
Consensus pattern (21 bp):
CCACACGACTGTGTACCTCAG
Found at i:16882831 original size:20 final size:20
Alignment explanation
Indices: 16882785--16882832 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
16882775 TGAACTAAAC
*
16882785 TTTAATTTAATTTTTGAGTAT
1 TTTAA-TTAATTTTGGAGTAT
*
16882806 TGTAATTAATTTTGGA-TAAT
1 TTTAATTAATTTTGGAGT-AT
16882826 TTTAATT
1 TTTAATT
16882833 TTTATCGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 18 0.78
21 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.58
Consensus pattern (20 bp):
TTTAATTAATTTTGGAGTAT
Done.