Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 176 of 284
Found at i:59239165 original size:9 final size:9
Alignment explanation
Indices: 59239151--59239254 Score: 120
Period size: 9 Copynumber: 11.6 Consensus size: 9
59239141 TTTATACAAA
59239151 TAATTCGGT
1 TAATTCGGT
59239160 TAATTCGGT
1 TAATTCGGT
*
59239169 TAACTCGGT
1 TAATTCGGT
59239178 TAATTCGGT
1 TAATTCGGT
* *
59239187 TAATTTGGG
1 TAATTCGGT
59239196 TAATTCAGG-
1 TAATTC-GGT
* *
59239205 TAATTTGGG
1 TAATTCGGT
*
59239214 TAATTCAGT
1 TAATTCGGT
* *
59239223 TAATTTGAT
1 TAATTCGGT
59239232 TAATTCGGT
1 TAATTCGGT
59239241 TAATTCGGT
1 TAATTCGGT
59239250 TAATT
1 TAATT
59239255 TTATACTTAT
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
8 2 0.03
9 75 0.95
10 2 0.03
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:59241558 original size:93 final size:93
Alignment explanation
Indices: 59241446--59241616 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
59241436 GCCCATAAGT
* *
59241446 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
59241511 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
59241539 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
59241604 CGAGTTCGGATGC
66 CGAGTTCGGATGC
59241617 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:59241613 original size:46 final size:46
Alignment explanation
Indices: 59241438--59241613 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
59241428 TGTAACCCGC
* * *
59241438 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
59241484 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
59241534 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
59241577 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
59241614 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:59244048 original size:30 final size:30
Alignment explanation
Indices: 59244004--59244092 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
59243994 CAAAGATAAC
59244004 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
59244033 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * *
59244063 AAGAGATCCAGAATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
59244093 CGATACTATG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 9 0.18
30 40 0.78
31 2 0.04
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:59244052 original size:15 final size:15
Alignment explanation
Indices: 59244004--59244083 Score: 101
Period size: 15 Copynumber: 5.4 Consensus size: 15
59243994 CAAAGATAAC
*
59244004 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
59244018 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
59244033 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
59244048 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
*
59244063 AAGAGATCCAGAATA
1 AAGAAATCCAGAATA
59244078 AAGAAA
1 AAGAAA
59244084 CCCAAGATAC
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
14 9 0.16
15 46 0.82
16 1 0.02
ACGTcount: A:0.60, C:0.14, G:0.16, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:59247113 original size:93 final size:93
Alignment explanation
Indices: 59247001--59247171 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
59246991 GCCCATAAGT
* *
59247001 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
59247066 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
59247094 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
59247159 CGAGTTCGGATGC
66 CGAGCTCGGATGC
59247172 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:59247168 original size:46 final size:46
Alignment explanation
Indices: 59246993--59247168 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
59246983 TGTAACCCGC
* *
59246993 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
59247039 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
59247085 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
59247132 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
59247169 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:59249603 original size:30 final size:30
Alignment explanation
Indices: 59249559--59249647 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
59249549 CAAAGATAAC
59249559 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
59249588 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
59249618 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
59249648 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:59249607 original size:15 final size:15
Alignment explanation
Indices: 59249559--59249638 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
59249549 CAAAGATAAC
*
59249559 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
59249573 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
59249588 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
59249603 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
59249618 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
59249633 AAGAAA
1 AAGAAA
59249639 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:59249647 original size:15 final size:15
Alignment explanation
Indices: 59249570--59249647 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
59249560 AGAAAACCGA
59249570 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
59249585 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
59249599 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
59249614 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
59249630 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
59249645 ATA
1 ATA
59249648 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:59252682 original size:93 final size:93
Alignment explanation
Indices: 59252570--59252740 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
59252560 GCCCATAAGT
* *
59252570 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
59252635 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
59252663 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
59252728 CGAGTTCGGATGC
66 CGAGTTCGGATGC
59252741 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:59252737 original size:46 final size:46
Alignment explanation
Indices: 59252562--59252737 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
59252552 TGTAACCCGC
* * *
59252562 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
59252608 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
59252658 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
59252701 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
59252738 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:59257450 original size:5 final size:5
Alignment explanation
Indices: 59257440--59257482 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
59257430 TGCTCATGAA
59257440 AAAAG AAAAG AAAAG AAAAG AAAAAG AACAA- AAAA- AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG -AAAAG AA-AAG AAAAG AAAAG AAA
59257483 GCATATGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 6 0.17
5 22 0.63
6 7 0.20
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:59261658 original size:27 final size:26
Alignment explanation
Indices: 59261641--59261710 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
59261631 ATATTAAGTC
59261641 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
59261668 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
59261696 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
59261711 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:59261704 original size:28 final size:28
Alignment explanation
Indices: 59261641--59261738 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
59261631 ATATTAAGTC
*
59261641 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
59261668 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
59261696 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
59261725 CGCACACTTAGTGC
1 CGCACACTTAGTGC
59261739 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:59262196 original size:2 final size:2
Alignment explanation
Indices: 59262189--59262218 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
59262179 CATACTTATG
*
59262189 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59262219 CTTCGGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59267121 original size:21 final size:22
Alignment explanation
Indices: 59267088--59267128 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
59267078 TTCCTTTATG
*
59267088 TTTCATTGGCACATA-ATCATA
1 TTTCATTGCCACATACATCATA
*
59267109 TTTCATTTCCACATACATCA
1 TTTCATTGCCACATACATCA
59267129 CAATACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (22 bp):
TTTCATTGCCACATACATCATA
Found at i:59271834 original size:21 final size:22
Alignment explanation
Indices: 59271801--59271841 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
59271791 TTCCTTTATG
*
59271801 TTTCATTGGCACATA-ATCATA
1 TTTCATTGCCACATACATCATA
*
59271822 TTTCATTTCCACATACATCA
1 TTTCATTGCCACATACATCA
59271842 CAATACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (22 bp):
TTTCATTGCCACATACATCATA
Found at i:59275911 original size:27 final size:27
Alignment explanation
Indices: 59275880--59275965 Score: 104
Period size: 27 Copynumber: 3.1 Consensus size: 27
59275870 AACACGTCAA
*
59275880 GAAATGAAATCCTTTATGGTGAA-TCAT
1 GAAATGAAATCCTTTGTGGTGAAGT-AT
59275907 GAAATGAAAGT-CTTTGTGGTGAAGTAT
1 GAAATGAAA-TCCTTTGTGGTGAAGTAT
* *
59275934 GAAAAGAATAGCCTTTGTGGTGAAGTAT
1 GAAATGAA-ATCCTTTGTGGTGAAGTAT
59275962 GAAA
1 GAAA
59275966 AGAACAGCCT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 29 0.56
28 23 0.44
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (27 bp):
GAAATGAAATCCTTTGTGGTGAAGTAT
Found at i:59275956 original size:28 final size:27
Alignment explanation
Indices: 59275880--59275975 Score: 113
Period size: 28 Copynumber: 3.5 Consensus size: 27
59275870 AACACGTCAA
* * *
59275880 GAAATGAAATCCTTTATGGTGAA-TCAT
1 GAAAAGAAAGCCTTTGTGGTGAAGT-AT
* *
59275907 GAAATGAAAGTCTTTGTGGTGAAGTAT
1 GAAAAGAAAGCCTTTGTGGTGAAGTAT
59275934 GAAAAGAATAGCCTTTGTGGTGAAGTAT
1 GAAAAGAA-AGCCTTTGTGGTGAAGTAT
59275962 GAAAAGAACAGCCT
1 GAAAAGAA-AGCCT
59275976 CTATGGCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
27 29 0.48
28 32 0.52
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (27 bp):
GAAAAGAAAGCCTTTGTGGTGAAGTAT
Found at i:59284303 original size:8 final size:8
Alignment explanation
Indices: 59284290--59284315 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
59284280 TAAACCATAT
59284290 TTTTAAAA
1 TTTTAAAA
59284298 TTTTAAAA
1 TTTTAAAA
59284306 TTTTAAAA
1 TTTTAAAA
59284314 TT
1 TT
59284316 ATTTATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTTAAAA
Found at i:59284757 original size:15 final size:16
Alignment explanation
Indices: 59284737--59284766 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
59284727 TAAATTTTGA
59284737 AAATAAA-GTAAATTT
1 AAATAAAGGTAAATTT
59284752 AAATAAAGGTAAATT
1 AAATAAAGGTAAATT
59284767 ATGAAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (16 bp):
AAATAAAGGTAAATTT
Found at i:59289701 original size:43 final size:42
Alignment explanation
Indices: 59289631--59289774 Score: 141
Period size: 43 Copynumber: 3.4 Consensus size: 42
59289621 TGTTCTCGTA
* * *
59289631 TAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGTG
1 TAAGACCATGTCTGGGAC-ATGACATCGATATGTGATTACGTG
* *
59289674 TAAGACCATGCCTGGGACATCGACATCG-TATTTGATT-CGTG
1 TAAGACCATGTCTGGGACAT-GACATCGATATGTGATTACGTG
* * *
59289715 TAAGACCCTGTCTGGGATAGTGACATCGATATGTGA-TAGCATG
1 TAAGACCATGTCTGGGACA-TGACATCGATATGTGATTA-CGTG
* *
59289758 TAAGACCACGTTTGGGA
1 TAAGACCATGTCTGGGA
59289775 TGTTGGCATT
Statistics
Matches: 83, Mismatches: 13, Indels: 10
0.78 0.12 0.09
Matches are distributed among these distances:
41 28 0.34
42 16 0.19
43 39 0.47
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACATGACATCGATATGTGATTACGTG
Found at i:59289730 original size:41 final size:42
Alignment explanation
Indices: 59289626--59289751 Score: 132
Period size: 41 Copynumber: 3.0 Consensus size: 42
59289616 GATAGTGTTC
* * * *
59289626 TCGTATAAGACCAC-GTCTGGGACGTTGGCATCGATATGTGAT
1 TCGTGTAAGACC-CTGTCTGGGACATCGACATCGATATGTGAT
* * *
59289668 TACGTGTAAGACCATGCCTGGGACATCGACATCG-TATTTGAT
1 T-CGTGTAAGACCCTGTCTGGGACATCGACATCGATATGTGAT
*
59289710 TCGTGTAAGACCCTGTCTGGGATAGT-GACATCGATATGTGAT
1 TCGTGTAAGACCCTGTCTGGGACA-TCGACATCGATATGTGAT
59289752 AGCATGTAAG
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
41 27 0.39
42 17 0.25
43 25 0.36
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (42 bp):
TCGTGTAAGACCCTGTCTGGGACATCGACATCGATATGTGAT
Found at i:59296329 original size:18 final size:18
Alignment explanation
Indices: 59296302--59296337 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
59296292 AAATGAGGTC
*
59296302 AGGTATATTTATATGTTT
1 AGGTAAATTTATATGTTT
*
59296320 AGGTAAATTTGTATGTTT
1 AGGTAAATTTATATGTTT
59296338 TCTTTTAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (18 bp):
AGGTAAATTTATATGTTT
Found at i:59296609 original size:84 final size:84
Alignment explanation
Indices: 59296468--59296634 Score: 289
Period size: 84 Copynumber: 2.0 Consensus size: 84
59296458 TACATGCTTG
59296468 ATTTGGTGATGAAAATGGCTTGATTTTTGGCCAATTTCATGTCCACAAAGCATGAGACACGGACG
1 ATTTGGTGATGAAAATGGCTTGATTTTTGGCCAATTTCATGTCCACAAAGCATGAGACACGGACG
59296533 TGTGAATCAGTCGTGTGTT
66 TGTGAATCAGTCGTGTGTT
* * * *
59296552 ATTTGGTGATGGAAATGGCTTGATTTTTGGCCAATTTCATGTCCACACAGCCTGAGACATGGACG
1 ATTTGGTGATGAAAATGGCTTGATTTTTGGCCAATTTCATGTCCACAAAGCATGAGACACGGACG
*
59296617 TGTGACTCAGTCGTGTGT
66 TGTGAATCAGTCGTGTGT
59296635 GACACACGAT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (84 bp):
ATTTGGTGATGAAAATGGCTTGATTTTTGGCCAATTTCATGTCCACAAAGCATGAGACACGGACG
TGTGAATCAGTCGTGTGTT
Found at i:59302191 original size:12 final size:12
Alignment explanation
Indices: 59302172--59302203 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
59302162 ATTCTCACAT
59302172 GCCCGTGTGCTA
1 GCCCGTGTGCTA
*
59302184 GGCCGTGTGCTA
1 GCCCGTGTGCTA
59302196 GCCCGTGT
1 GCCCGTGT
59302204 AACAACCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.31, G:0.38, T:0.25
Consensus pattern (12 bp):
GCCCGTGTGCTA
Found at i:59308724 original size:27 final size:27
Alignment explanation
Indices: 59308692--59309234 Score: 713
Period size: 27 Copynumber: 20.2 Consensus size: 27
59308682 AAAGTACTCC
* *
59308692 CGATTTATAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * * *
59308719 CAATTTATAGAATTATCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
59308746 CGATTTATAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
59308773 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
59308800 CGATTTATAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
59308827 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
59308854 C-AGTTTACAGAATTACCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
59308881 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
59308908 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
59308935 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
59308962 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
59308989 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
59309016 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
59309043 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
59309070 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
59309097 CGATTTACAGAATTA-CGGTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** * *
59309123 CGATTTGTAAAATTACCG-TTTACCAT
1 CGATTTACAGAATTACCGTTTTACCCT
* * * *
59309149 TGATTTACAAAATTACTGGTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
59309176 C-AGTTTACAAAATTATCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
59309203 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
59309230 CGATT
1 CGATT
59309235 GTGAAATTAC
Statistics
Matches: 458, Mismatches: 46, Indels: 24
0.87 0.09 0.05
Matches are distributed among these distances:
26 46 0.10
27 407 0.89
28 5 0.01
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.39
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:59309425 original size:27 final size:27
Alignment explanation
Indices: 59309239--59309434 Score: 221
Period size: 27 Copynumber: 7.3 Consensus size: 27
59309229 TCGATTGTGA
* *
59309239 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
59309266 AATTTTCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
59309293 AATTACTGAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
59309320 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
59309347 AACTATCGAAATACACTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
59309374 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
59309401 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
59309428 AATTACC
1 AATTACC
59309435 ATTTTGCCCC
Statistics
Matches: 142, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 142 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:59309671 original size:27 final size:26
Alignment explanation
Indices: 59309633--59309715 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
59309623 CGGAGGAAGC
*
59309633 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
59309660 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
59309686 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
59309713 GTT
1 GTT
59309716 GACCGATCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.20
27 41 0.80
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:59310039 original size:25 final size:26
Alignment explanation
Indices: 59310011--59310067 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
59310001 TGCCACGTAT
* * *
59310011 TCTGTT-AGGTGGGTTTGCCACATTA
1 TCTGTTCAGGTGGCTATGCCACAATA
*
59310036 TCTGATTCTGGTGGCTATGCCACAATA
1 TCTG-TTCAGGTGGCTATGCCACAATA
59310063 TCTGT
1 TCTGT
59310068 ATCTGGTGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 4 0.15
26 3 0.12
27 19 0.73
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.39
Consensus pattern (26 bp):
TCTGTTCAGGTGGCTATGCCACAATA
Found at i:59310224 original size:6 final size:6
Alignment explanation
Indices: 59310215--59310291 Score: 97
Period size: 6 Copynumber: 12.8 Consensus size: 6
59310205 TTGCATTCAC
*
59310215 ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG
59310263 ATTCTG -TTACTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATT-CTG ATTCTG ATTCTG ATTCT
59310292 CATTTTGGTT
Statistics
Matches: 63, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
5 5 0.08
6 54 0.86
7 3 0.05
8 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (6 bp):
ATTCTG
Found at i:59310312 original size:30 final size:30
Alignment explanation
Indices: 59310215--59310291 Score: 129
Period size: 30 Copynumber: 2.6 Consensus size: 30
59310205 TTGCATTCAC
59310215 ATTCTGATTCTGATTCTGATTCTGTTACTA
1 ATTCTGATTCTGATTCTGATTCTGTTACTA
*
59310245 ATAT-TGATTCTGATTCTGATTCTGTTACTG
1 AT-TCTGATTCTGATTCTGATTCTGTTACTA
59310275 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
59310292 CATTTTGGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
29 1 0.02
30 42 0.95
31 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTGATTCTGTTACTA
Found at i:59316040 original size:48 final size:48
Alignment explanation
Indices: 59315982--59316158 Score: 136
Period size: 48 Copynumber: 3.8 Consensus size: 48
59315972 TGATTAATGA
* * * * *
59315982 GATCCTGTGTAATACCATGTCTGAGACATGGCATCGGTATCGA-TACGT
1 GATCCCGTGTAAGACCATGTCTGGGACATGGCATCGGCATC-ATTAAGT
* * *
59316030 GATCCCGTGTAAGACCATAT-TAGGGATATGGCTTCGGCATCATTAAGT
1 GATCCCGTGTAAGACCATGTCT-GGGACATGGCATCGGCATCATTAAGT
** * * *
59316078 GATTTCGTATAAGACCATGTCTGGGACATGGCATC-G-AT--GTGAG-
1 GATCCCGTGTAAGACCATGTCTGGGACATGGCATCGGCATCATTAAGT
* * *
59316121 G-TCCCGTATAAGACCATGTCTGGGGCATGGCAGCGGCA
1 GATCCCGTGTAAGACCATGTCTGGGACATGGCATCGGCA
59316159 CTGATTCAAG
Statistics
Matches: 104, Mismatches: 20, Indels: 14
0.75 0.14 0.10
Matches are distributed among these distances:
42 29 0.28
43 2 0.02
44 4 0.04
46 2 0.02
47 3 0.03
48 63 0.61
49 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (48 bp):
GATCCCGTGTAAGACCATGTCTGGGACATGGCATCGGCATCATTAAGT
Found at i:59321854 original size:13 final size:13
Alignment explanation
Indices: 59321836--59321862 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59321826 GAAGTAATAG
59321836 CACACGGGCGTGT
1 CACACGGGCGTGT
59321849 CACACGGGCGTGT
1 CACACGGGCGTGT
59321862 C
1 C
59321863 CTTGCCGAGC
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:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:59332778 original size:19 final size:19
Alignment explanation
Indices: 59332754--59332814 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
59332744 GGACATGTGT
59332754 GTGTCCCATGCACACAGGC
1 GTGTCCCATGCACACAGGC
*
59332773 GTGTCCCATGCACAC-GAGT
1 GTGTCCCATGCACACAG-GC
59332792 GTGTCCCATGCACACAGGC
1 GTGTCCCATGCACACAGGC
59332811 GTGT
1 GTGT
59332815 GCATTGCCCC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.03
19 36 0.95
20 1 0.03
ACGTcount: A:0.20, C:0.33, G:0.28, T:0.20
Consensus pattern (19 bp):
GTGTCCCATGCACACAGGC
Found at i:59333251 original size:13 final size:13
Alignment explanation
Indices: 59333233--59333258 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59333223 GGAACTTAAC
59333233 CTTATGTATTGGG
1 CTTATGTATTGGG
59333246 CTTATGTATTGGG
1 CTTATGTATTGGG
59333259 ATTTCATCTT
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:0.15, C:0.08, G:0.31, T:0.46
Consensus pattern (13 bp):
CTTATGTATTGGG
Found at i:59340771 original size:16 final size:16
Alignment explanation
Indices: 59340750--59340802 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
59340740 TTGAATTGAG
59340750 AAAATTATTTAATTAA
1 AAAATTATTTAATTAA
*
59340766 AAAATTAATTAATTAA
1 AAAATTATTTAATTAA
* *
59340782 ATAA-TATTTATTTTAA
1 AAAATTATTTA-ATTAA
59340798 AAAAT
1 AAAAT
59340803 AGAAAAACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 5 0.17
16 25 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATTATTTAATTAA
Found at i:59366282 original size:16 final size:16
Alignment explanation
Indices: 59366261--59366301 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
59366251 TTTTGTATTA
59366261 TTTTAATATTAAATAT
1 TTTTAATATTAAATAT
*
59366277 TTTTAAAATTAAATAT
1 TTTTAATATTAAATAT
*
59366293 TATTAATAT
1 TTTTAATAT
59366302 AACTTATTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTAATATTAAATAT
Found at i:59367487 original size:16 final size:16
Alignment explanation
Indices: 59367466--59367497 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
59367456 CTTAAAGAAT
59367466 GGAAATAATAATGATA
1 GGAAATAATAATGATA
59367482 GGAAATAATAATGATA
1 GGAAATAATAATGATA
59367498 AAAAATCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (16 bp):
GGAAATAATAATGATA
Found at i:59367503 original size:16 final size:16
Alignment explanation
Indices: 59367468--59367503 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
59367458 TAAAGAATGG
**
59367468 AAATAATAATGATAGG
1 AAATAATAATGATAAA
59367484 AAATAATAATGATAAA
1 AAATAATAATGATAAA
59367500 AAAT
1 AAAT
59367504 CTAACAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (16 bp):
AAATAATAATGATAAA
Found at i:59368389 original size:8 final size:8
Alignment explanation
Indices: 59368374--59368403 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
59368364 ACAAAAGTAC
59368374 ACATTTCA
1 ACATTTCA
*
59368382 AGATTTCA
1 ACATTTCA
59368390 ACATTTCA
1 ACATTTCA
59368398 ACATTT
1 ACATTT
59368404 TTTGACAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (8 bp):
ACATTTCA
Found at i:59379813 original size:18 final size:18
Alignment explanation
Indices: 59379790--59379827 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
59379780 TTCGTAAGTC
59379790 ATGTCGGACTAAATTTCA
1 ATGTCGGACTAAATTTCA
*
59379808 ATGTCGGACTGAATTTCA
1 ATGTCGGACTAAATTTCA
59379826 AT
1 AT
59379828 CTCAGATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (18 bp):
ATGTCGGACTAAATTTCA
Found at i:59388317 original size:35 final size:35
Alignment explanation
Indices: 59388271--59388342 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
59388261 TGTATTCGAG
*
59388271 TAAAAAAATATTTAAATATTATTTTCTGTGTTTAT
1 TAAAAAAATATTTAAATATTATTTTCCGTGTTTAT
59388306 TAAAAAAATATTTAAATATTATTTTCCGTGTTTAT
1 TAAAAAAATATTTAAATATTATTTTCCGTGTTTAT
59388341 TA
1 TA
59388343 TATGTGAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (35 bp):
TAAAAAAATATTTAAATATTATTTTCCGTGTTTAT
Found at i:59389824 original size:35 final size:36
Alignment explanation
Indices: 59389774--59389867 Score: 111
Period size: 35 Copynumber: 2.6 Consensus size: 36
59389764 CATAGGTAAG
*
59389774 TACATGTAAGCTTATATTGAACTAGTA-TATTCGAC
1 TACATGTGAGCTTATATTGAACTAGTAGTATTCGAC
* * ** *
59389809 TGCATGTGAGATTATATTGAA-TTTTAGTATTCGAT
1 TACATGTGAGCTTATATTGAACTAGTAGTATTCGAC
59389844 TACATGTGAGCTTATATTTGAACT
1 TACATGTGAGCTTATA-TTGAACT
59389868 TGCATACTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
34 3 0.06
35 39 0.81
36 5 0.10
37 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (36 bp):
TACATGTGAGCTTATATTGAACTAGTAGTATTCGAC
Found at i:59392303 original size:67 final size:66
Alignment explanation
Indices: 59392173--59392308 Score: 150
Period size: 67 Copynumber: 2.0 Consensus size: 66
59392163 GCTAATTTAA
** **
59392173 TTTGTCCAGCCGCATGACATAAATTGCATTGGTTTGAATGTTGCTGAATTTAATTTGTCTTAACA
1 TTTGTCCAGCCGCATGACATAAATTAAATTGGTTTG-ATGTTGCTGAATTTAATGAGTCTTAACA
59392238 CT
65 CT
* * *
59392240 TTTGTCTAGCCGCATGACATGAATTAAATTGGTTTG-T-TTGCTGTCAATTTTAATGAGTTTTAA
1 TTTGTCCAGCCGCATGACATAAATTAAATTGGTTTGATGTTGCTG--AA-TTTAATGAGTCTTAA
*
59392303 CCCT
63 CACT
59392307 TT
1 TT
59392309 AATTGCTGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
64 6 0.10
65 1 0.02
66 2 0.03
67 49 0.84
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (66 bp):
TTTGTCCAGCCGCATGACATAAATTAAATTGGTTTGATGTTGCTGAATTTAATGAGTCTTAACAC
T
Found at i:59393402 original size:23 final size:23
Alignment explanation
Indices: 59393328--59393400 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 23
59393318 TCAGTGAAAA
* *
59393328 AAATTGTACAAAAAAAGGAATAT
1 AAATAGTAAAAAAAAAGGAATAT
* *
59393351 ATATAGTAAAAAAAAAGAGAGGT-T
1 AAATAGTAAAAAAAAAG-GA-ATAT
*
59393375 GAAATA-TTAAAAAAAAGGAATAT
1 -AAATAGTAAAAAAAAAGGAATAT
59393398 AAA
1 AAA
59393401 ATTCAAAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
22 4 0.10
23 17 0.44
24 13 0.33
25 5 0.13
ACGTcount: A:0.63, C:0.01, G:0.15, T:0.21
Consensus pattern (23 bp):
AAATAGTAAAAAAAAAGGAATAT
Found at i:59395547 original size:18 final size:20
Alignment explanation
Indices: 59395506--59395551 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
59395496 AAAAAGAAAA
59395506 AAAAAGTG-GAAAAGAGAGG
1 AAAAAGTGAGAAAAGAGAGG
*
59395525 AAAAAGTGAGAAAAGTGA-G
1 AAAAAGTGAGAAAAGAGAGG
59395544 -AAAAGTGA
1 AAAAAGTGA
59395552 TTCAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 8 0.32
ACGTcount: A:0.59, C:0.00, G:0.33, T:0.09
Consensus pattern (20 bp):
AAAAAGTGAGAAAAGAGAGG
Found at i:59395548 original size:9 final size:9
Alignment explanation
Indices: 59395507--59395551 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
59395497 AAAAGAAAAA
59395507 AAAAGTG-G
1 AAAAGTGAG
*
59395515 AAAAGAGAGG
1 AAAAGTGA-G
59395525 AAAAAGTGAG
1 -AAAAGTGAG
59395535 AAAAGTGAG
1 AAAAGTGAG
59395544 AAAAGTGA
1 AAAAGTGA
59395552 TTCAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 6 0.19
9 17 0.53
10 2 0.06
11 7 0.22
ACGTcount: A:0.58, C:0.00, G:0.33, T:0.09
Consensus pattern (9 bp):
AAAAGTGAG
Found at i:59398922 original size:67 final size:67
Alignment explanation
Indices: 59398840--59398971 Score: 183
Period size: 67 Copynumber: 2.0 Consensus size: 67
59398830 GCTAATTTAA
* * *
59398840 TTTGTCCAGCTGCATGACATAAATTACATTGGTTTGAATGCTGCCGAATTTAATGAGTCTTAACC
1 TTTGTCCAGCCGCATGACATAAATCAAATTGGTTTGAATGCTGCCGAATTTAATGAGTCTTAACC
59398905 AT
66 AT
* ** * * *
59398907 TTTGTCCAGCCGCATGACATGAATCAAATTGGTTTGTCTGCTGCCGATTTTAATGTGTTTTAACC
1 TTTGTCCAGCCGCATGACATAAATCAAATTGGTTTGAATGCTGCCGAATTTAATGAGTCTTAACC
59398972 CTTTAATTGT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
67 56 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (67 bp):
TTTGTCCAGCCGCATGACATAAATCAAATTGGTTTGAATGCTGCCGAATTTAATGAGTCTTAACC
AT
Found at i:59400896 original size:56 final size:56
Alignment explanation
Indices: 59400810--59400929 Score: 240
Period size: 56 Copynumber: 2.1 Consensus size: 56
59400800 ACAAGGGATG
59400810 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
59400866 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
59400922 ATGGGCAA
1 ATGGGCAA
59400930 TAAACTAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:59402247 original size:40 final size:39
Alignment explanation
Indices: 59402057--59402240 Score: 185
Period size: 40 Copynumber: 4.6 Consensus size: 39
59402047 CGAATGATGT
* * * *
59402057 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
* * * *
59402097 CCAGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
* *
59402137 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAATTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
59402175 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
59402216 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
59402241 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
39 33 0.28
40 77 0.64
41 10 0.08
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:59402262 original size:79 final size:79
Alignment explanation
Indices: 59402109--59402273 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
59402099 AGACTAAGAT
* ** *
59402109 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAATTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAAGTACTAA
*
59402174 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
59402188 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACG-AGTAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAAGTA-C
* *
59402251 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
59402267 CCGAAGG
1 CCGAAGG
59402274 TACGTGATTC
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.67
80 22 0.30
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAAGTACTAA
ATCCGGGTTAAATC
Found at i:59403853 original size:13 final size:14
Alignment explanation
Indices: 59403823--59403853 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
59403813 TTTCTTATGA
59403823 TTTTTAAAAGTAGT
1 TTTTTAAAAGTAGT
59403837 TTTTTAAAAGTAGT
1 TTTTTAAAAGTAGT
59403851 TTT
1 TTT
59403854 CTTCTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (14 bp):
TTTTTAAAAGTAGT
Found at i:59405933 original size:9 final size:9
Alignment explanation
Indices: 59405919--59405966 Score: 64
Period size: 10 Copynumber: 5.3 Consensus size: 9
59405909 AGATAGTGTG
59405919 TTAATATTT
1 TTAATATTT
59405928 TTAATATTTT
1 TTAATA-TTT
59405938 TTAATATTTT
1 TTAATA-TTT
59405948 TTAATA-TT
1 TTAATATTT
59405956 TT-ATATTT
1 TTAATATTT
59405964 TTA
1 TTA
59405967 GATACCTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 3 0.08
8 8 0.22
9 6 0.17
10 19 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTAATATTT
Found at i:59405940 original size:10 final size:10
Alignment explanation
Indices: 59405919--59405957 Score: 71
Period size: 10 Copynumber: 4.0 Consensus size: 10
59405909 AGATAGTGTG
59405919 TTAATA-TTT
1 TTAATATTTT
59405928 TTAATATTTT
1 TTAATATTTT
59405938 TTAATATTTT
1 TTAATATTTT
59405948 TTAATATTTT
1 TTAATATTTT
59405958 ATATTTTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 6 0.21
10 23 0.79
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTAATATTTT
Found at i:59413565 original size:137 final size:137
Alignment explanation
Indices: 59413319--59413592 Score: 523
Period size: 137 Copynumber: 2.0 Consensus size: 137
59413309 TATACTTATC
59413319 TGTAATTTCATATTTTGAAAAGAAGCTCTGTTGTATGCAAGTGAAGATTAACTCTTTTTCTAGTT
1 TGTAATTTCATATTTTGAAAAGAAGCTCTGTTGTATGCAAGTGAAGATTAACTCTTTTTCTAGTT
*
59413384 AGGCAATTTTTCAATTTAATCTCGATTCTAACCCTTTCTTTCAGCTTGTGACCACACCCCC-TAA
66 AGGCAATTTTTCAATTTAATCTCGATTCTAACCCTTTATTTCAGCTTGTGACCAC-CCCCCTTAA
59413448 CCAAGCCT
130 CCAAGCCT
59413456 TGTAATTTCATATTTTGAAAAGAAGCTCTGTTGTATGCAAGTGAAGATTAACTCTTTTTCTAGTT
1 TGTAATTTCATATTTTGAAAAGAAGCTCTGTTGTATGCAAGTGAAGATTAACTCTTTTTCTAGTT
59413521 AGGCAATTTTTCAATTTAATCTCGATTCTAACCCTTTATTTCAGCTTGTGACCACCCCCCTTAAC
66 AGGCAATTTTTCAATTTAATCTCGATTCTAACCCTTTATTTCAGCTTGTGACCACCCCCCTTAAC
59413586 CAAGCCT
131 CAAGCCT
59413593 CACTACAACC
Statistics
Matches: 135, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
136 5 0.04
137 130 0.96
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (137 bp):
TGTAATTTCATATTTTGAAAAGAAGCTCTGTTGTATGCAAGTGAAGATTAACTCTTTTTCTAGTT
AGGCAATTTTTCAATTTAATCTCGATTCTAACCCTTTATTTCAGCTTGTGACCACCCCCCTTAAC
CAAGCCT
Found at i:59418829 original size:20 final size:21
Alignment explanation
Indices: 59418804--59418843 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
59418794 TCTTAAAAAC
59418804 AGGGC-ACACGCCCGTGTGGA
1 AGGGCAACACGCCCGTGTGGA
59418824 AGGGCAACACGCCCGTGTGG
1 AGGGCAACACGCCCGTGTGG
59418844 CCATTAGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.20, C:0.30, G:0.40, T:0.10
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTGGA
Found at i:59419033 original size:28 final size:28
Alignment explanation
Indices: 59418993--59419057 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
59418983 CGTGTCCATG
59418993 GCCCGTGTCCCTTACACAGCCATGACAC
1 GCCCGTGTCCCTTACACAGCCATGACAC
* *
59419021 GCCCGTGTCCCTTACACGGCCATGACAT
1 GCCCGTGTCCCTTACACAGCCATGACAC
59419049 GCCCGTGTC
1 GCCCGTGTC
59419058 TTAGCCGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.17, C:0.42, G:0.22, T:0.20
Consensus pattern (28 bp):
GCCCGTGTCCCTTACACAGCCATGACAC
Found at i:59425094 original size:28 final size:29
Alignment explanation
Indices: 59425057--59425115 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
59425047 ATTTTTTTAA
*
59425057 ATTTTAAATTCTTAATTTTAA-TTTAATT
1 ATTTTAAATTATTAATTTTAAGTTTAATT
* *
59425085 ATTTTTAATTATTGATTTTAATGTTTAATT
1 ATTTTAAATTATTAATTTTAA-GTTTAATT
59425115 A
1 A
59425116 GGTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 18 0.69
30 8 0.31
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (29 bp):
ATTTTAAATTATTAATTTTAAGTTTAATT
Found at i:59428076 original size:14 final size:14
Alignment explanation
Indices: 59428057--59428087 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
59428047 AAGAGAGAAT
59428057 GATGATGGATGAGG
1 GATGATGGATGAGG
*
59428071 GATGATTGATGAGG
1 GATGATGGATGAGG
59428085 GAT
1 GAT
59428088 CAAATGAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.26
Consensus pattern (14 bp):
GATGATGGATGAGG
Found at i:59433591 original size:18 final size:18
Alignment explanation
Indices: 59433551--59433602 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
59433541 AATAAGTATA
* *
59433551 AAATTAATCGAATTAATT
1 AAATTAACCGAATTAATC
* *
59433569 GAATTAACCGAATTACTC
1 AAATTAACCGAATTAATC
* *
59433587 AAATTACCCAAATTAA
1 AAATTAACCGAATTAA
59433603 CCGAATTATT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (18 bp):
AAATTAACCGAATTAATC
Found at i:59433591 original size:27 final size:27
Alignment explanation
Indices: 59433552--59433610 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
59433542 ATAAGTATAA
* ***
59433552 AATTAATCGAATTAATTGAATTAACCG
1 AATTAATCAAATTAACCAAATTAACCG
* *
59433579 AATTACTCAAATTACCCAAATTAACCG
1 AATTAATCAAATTAACCAAATTAACCG
59433606 AATTA
1 AATTA
59433611 TTTGTATAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.31
Consensus pattern (27 bp):
AATTAATCAAATTAACCAAATTAACCG
Found at i:59449561 original size:21 final size:21
Alignment explanation
Indices: 59449537--59449583 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
59449527 GGAGAAGTGT
* * *
59449537 GGGATAGTGGGAGTATTTTGA
1 GGGATAGGGGGAGTAATTAGA
*
59449558 GGGATTGGGGGAGTAATTAGA
1 GGGATAGGGGGAGTAATTAGA
59449579 GGGAT
1 GGGAT
59449584 TTGGAGAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.47, T:0.28
Consensus pattern (21 bp):
GGGATAGGGGGAGTAATTAGA
Found at i:59449584 original size:21 final size:21
Alignment explanation
Indices: 59449545--59449584 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59449535 GTGGGATAGT
* *
59449545 GGGAGTATTTTGAGGGATTGG
1 GGGAGTAATTAGAGGGATTGG
59449566 GGGAGTAATTAGAGGGATT
1 GGGAGTAATTAGAGGGATT
59449585 TGGAGAGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.45, T:0.30
Consensus pattern (21 bp):
GGGAGTAATTAGAGGGATTGG
Found at i:59468176 original size:40 final size:40
Alignment explanation
Indices: 59468121--59468378 Score: 387
Period size: 40 Copynumber: 6.5 Consensus size: 40
59468111 TGGATGATAA
* * *
59468121 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
59468161 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
59468201 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
59468241 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
59468281 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
59468321 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
59468361 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
59468379 TACTTGGCTT
Statistics
Matches: 205, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
39 16 0.08
40 189 0.92
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:59471171 original size:26 final size:26
Alignment explanation
Indices: 59471135--59471218 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
59471125 CATGAAATTC
59471135 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
59471161 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
59471187 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
59471213 TTATCA
1 TTATCA
59471219 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:59486899 original size:19 final size:20
Alignment explanation
Indices: 59486862--59486899 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
59486852 ATAAGGTGGT
59486862 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
59486882 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
59486900 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:59490223 original size:43 final size:42
Alignment explanation
Indices: 59490158--59490241 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 42
59490148 GAAATTTGAG
** * *
59490158 CTTGTTGAGCGGTCTGATTTCGTGATATATGTGAGAATCCGAA
1 CTTGTTGAGCGGTCCAACTTCGTAATATATGTG-GAATCCGAA
* *
59490201 CTTGTTGAGTGGTCCAACTTCGTAATATATGTGGCATCCGA
1 CTTGTTGAGCGGTCCAACTTCGTAATATATGTGGAATCCGA
59490242 GCCCGTTGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
42 7 0.20
43 28 0.80
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.35
Consensus pattern (42 bp):
CTTGTTGAGCGGTCCAACTTCGTAATATATGTGGAATCCGAA
Found at i:59505043 original size:43 final size:43
Alignment explanation
Indices: 59504995--59505078 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
59504985 ATATTAACGA
* * *
59504995 TATGTGATTATGTGTAAGACCATGTC-TGGGGCATTGGCATCAT
1 TATGTGATTATGTATAAGACCATG-CATGGGACATCGGCATCAT
59505038 TATGTGATTATGTATAAGACCATGCATGGGACATCGGCATC
1 TATGTGATTATGTATAAGACCATGCATGGGACATCGGCATC
59505079 GTTAATTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 36 0.97
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (43 bp):
TATGTGATTATGTATAAGACCATGCATGGGACATCGGCATCAT
Found at i:59508477 original size:8 final size:8
Alignment explanation
Indices: 59508459--59508488 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
59508449 ATGAAAATTA
59508459 TGTGTATTT
1 TGTG-ATTT
59508468 TGTGATTT
1 TGTGATTT
59508476 TGTGATTT
1 TGTGATTT
59508484 TGTGA
1 TGTGA
59508489 ATTAGGGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (8 bp):
TGTGATTT
Found at i:59508947 original size:44 final size:42
Alignment explanation
Indices: 59508897--59509056 Score: 182
Period size: 44 Copynumber: 3.7 Consensus size: 42
59508887 ATATGGGTTA
59508897 TCATGTAAGACCACGTCTGGGACATTGGCATCGACTTATGATTT
1 TCATGTAAGACCACGTCTGGGACATTGGCATCGA-TT-TGATTT
*
59508941 TCATGTAAGACCATGTCTGGGACATTGGCATCGTATTTGA-TT
1 TCATGTAAGACCACGTCTGGGACATTGGCATCG-ATTTGATTT
* * * *
59508983 TCATGTAAAACC-CTGTCTAGGACAGTGGCATCGATATTTGATTA
1 TCATGTAAGACCAC-GTCTGGGACATTGGCATCG--ATTTGATTT
* *
59509027 T-ATGTAAGACCATGTCTGGGACCTTGGCAT
1 TCATGTAAGACCACGTCTGGGACATTGGCAT
59509057 TGTATGAGCT
Statistics
Matches: 100, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
42 30 0.30
43 33 0.33
44 36 0.36
45 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (42 bp):
TCATGTAAGACCACGTCTGGGACATTGGCATCGATTTGATTT
Found at i:59509021 original size:43 final size:43
Alignment explanation
Indices: 59508897--59509056 Score: 209
Period size: 43 Copynumber: 3.7 Consensus size: 43
59508887 ATATGGGTTA
* *
59508897 TCATGTAAGACCACGTCTGGGACATTGGCATCGACT-TATGATTT
1 TCATGTAAGACCATGTCTGGGACATTGGCATCGA-TATTTGA-TT
59508941 TCATGTAAGACCATGTCTGGGACATTGGCATCG-TATTTGATT
1 TCATGTAAGACCATGTCTGGGACATTGGCATCGATATTTGATT
* * * *
59508983 TCATGTAAAACCCTGTCTAGGACAGTGGCATCGATATTTGATT
1 TCATGTAAGACCATGTCTGGGACATTGGCATCGATATTTGATT
*
59509026 AT-ATGTAAGACCATGTCTGGGACCTTGGCAT
1 -TCATGTAAGACCATGTCTGGGACATTGGCAT
59509057 TGTATGAGCT
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
42 32 0.31
43 37 0.36
44 33 0.32
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (43 bp):
TCATGTAAGACCATGTCTGGGACATTGGCATCGATATTTGATT
Found at i:59516639 original size:43 final size:43
Alignment explanation
Indices: 59516540--59516666 Score: 132
Period size: 42 Copynumber: 3.0 Consensus size: 43
59516530 TTTGGAACGT
* * *
59516540 TGGCATCAACT-TATGATTTTCGTGTAAGACCATGTCTGGGGCAT
1 TGGCATCAA-TATTTGA-TTTCGTGTAAGACCATGTCTGGGACAG
* *
59516584 TGGCATC-GTATTTGATTTCGTGTAAGACCCTGTCTGGGACAG
1 TGGCATCAATATTTGATTTCGTGTAAGACCATGTCTGGGACAG
* * * * *
59516626 TGGCATCAATATTTGACTACATGTAAGACCACGTTTGGGAC
1 TGGCATCAATATTTGATTTCGTGTAAGACCATGTCTGGGAC
59516667 CTTGGCATTG
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
42 32 0.46
43 30 0.43
44 7 0.10
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (43 bp):
TGGCATCAATATTTGATTTCGTGTAAGACCATGTCTGGGACAG
Found at i:59516673 original size:43 final size:43
Alignment explanation
Indices: 59516515--59516674 Score: 137
Period size: 43 Copynumber: 3.7 Consensus size: 43
59516505 ATATGTGTCA
* * * * *
59516515 TCATGTAAGACCACATTTGGAACGTTGGCATCAACT-TATGATTT
1 TCATGTAAGACCACGTCTGGGACATTGGCATCAA-TATTTGA-TT
* * * *
59516559 TCGTGTAAGACCATGTCTGGGGCATTGGCATC-GTATTTGATT
1 TCATGTAAGACCACGTCTGGGACATTGGCATCAATATTTGATT
* * *
59516601 TCGTGTAAGACC-CTGTCTGGGACAGTGGCATCAATATTTGACT
1 TCATGTAAGACCAC-GTCTGGGACATTGGCATCAATATTTGATT
* * *
59516644 ACATGTAAGACCACGTTTGGGACCTTGGCAT
1 TCATGTAAGACCACGTCTGGGACATTGGCAT
59516675 TGTATAGCTT
Statistics
Matches: 93, Mismatches: 19, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
42 31 0.33
43 36 0.39
44 26 0.28
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (43 bp):
TCATGTAAGACCACGTCTGGGACATTGGCATCAATATTTGATT
Found at i:59523318 original size:49 final size:51
Alignment explanation
Indices: 59523238--59523368 Score: 160
Period size: 49 Copynumber: 2.6 Consensus size: 51
59523228 TGTCACTAGT
*
59523238 GACT-CAAGTGTGGTACTATGTGAAGACCACTTTGAGAAG-AGATAGCTTG
1 GACTACAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAGAAGATAGCTTG
* * * * *
59523287 GTC-ACAAGTGTGGTACTATGTGAAGGTCACTTTGTGAAGAAGCTAGCTTT
1 GACTACAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAGAAGATAGCTTG
* * *
59523337 GACTACATGGGTGGTACTATGTGCAGGCCACT
1 GACTACAAGTGTGGTACTATGTGAAGGCCACT
59523369 AGGTATCCGT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
49 34 0.50
50 10 0.15
51 24 0.35
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (51 bp):
GACTACAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAGAAGATAGCTTG
Found at i:59525913 original size:43 final size:43
Alignment explanation
Indices: 59525852--59525933 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
59525842 TATTAACGAG
* *
59525852 ATGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCATT
1 ATGTGATTATGTATAAGACCATGTCTGGGAAATTGGCATCATT
59525895 ATGTGATTATGTATAAGACCATGTCTGGGAAATTGGCAT
1 ATGTGATTATGTATAAGACCATGTCTGGGAAATTGGCAT
59525934 TGTTAATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (43 bp):
ATGTGATTATGTATAAGACCATGTCTGGGAAATTGGCATCATT
Found at i:59525955 original size:43 final size:43
Alignment explanation
Indices: 59525852--59525959 Score: 130
Period size: 43 Copynumber: 2.5 Consensus size: 43
59525842 TATTAACGAG
* *
59525852 ATGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCATT
1 ATGTAATTATGTGTAAGACCATGTCTGGGAAATTGGCATCATT
* * **
59525895 ATGTGATTATGTATAAGACCATGTCTGGGAAATTGGCATTGTT
1 ATGTAATTATGTGTAAGACCATGTCTGGGAAATTGGCATCATT
59525938 AAT-TAATT-TCGTGTAAGACCAT
1 -ATGTAATTAT-GTGTAAGACCAT
59525960 AGCTAGGCTA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
42 1 0.02
43 54 0.95
44 2 0.04
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (43 bp):
ATGTAATTATGTGTAAGACCATGTCTGGGAAATTGGCATCATT
Found at i:59532869 original size:23 final size:23
Alignment explanation
Indices: 59532839--59532896 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
59532829 AACAATTAAT
59532839 TAAT-TTTTTAAAAAATTTAAAA
1 TAATATTTTTAAAAAATTTAAAA
* * **
59532861 TATTATTTTTATAATTTTTAAAA
1 TAATATTTTTAAAAAATTTAAAA
*
59532884 TAATATTTATAAA
1 TAATATTTTTAAA
59532897 TTTTTCAATT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 3 0.11
23 25 0.89
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATATTTTTAAAAAATTTAAAA
Found at i:59532876 original size:21 final size:20
Alignment explanation
Indices: 59532851--59532899 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
59532841 ATTTTTTAAA
*
59532851 AAATTTAAAATATTATTTTTAT
1 AAATTTAAAATA--ATATTTAT
*
59532873 AATTTTTAAAATAATATTTAT
1 AA-ATTTAAAATAATATTTAT
59532894 AAATTT
1 AAATTT
59532900 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 3 0.13
21 9 0.39
22 2 0.09
23 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTTAAAATAATATTTAT
Found at i:59532901 original size:23 final size:23
Alignment explanation
Indices: 59532854--59532901 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
59532844 TTTTAAAAAA
* *
59532854 TTTAAAATATTATTTTTATAATT
1 TTTAAAATAATATTTATATAATT
59532877 TTTAAAATAATATTTATA-AATT
1 TTTAAAATAATATTTATATAATT
59532899 TTT
1 TTT
59532902 CAATTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTAAAATAATATTTATATAATT
Found at i:59533507 original size:29 final size:30
Alignment explanation
Indices: 59533447--59533512 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
59533437 ATTGGATTTG
* *
59533447 AATTTTAAAATATAAAAAATAGACAGATTA
1 AATTTTAAAATATAAAAAATAAACAGACTA
*
59533477 AATTTCTAAAA-AT-AAAAATAAATAGACTA
1 AATTT-TAAAATATAAAAAATAAACAGACTA
59533506 AATTTTA
1 AATTTTA
59533513 TATACGTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 2 0.06
29 18 0.56
30 7 0.22
31 5 0.16
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (30 bp):
AATTTTAAAATATAAAAAATAAACAGACTA
Found at i:59544161 original size:30 final size:29
Alignment explanation
Indices: 59544125--59544185 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
59544115 AAATGGAAGT
*
59544125 TTTGGCACTATGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGCGATTT-AACTAGC
59544155 TTTGGCACTAAGTGTGCGATTTAACTAGC
1 TTTGGCACTAAGTGTGCGATTTAACTAGC
59544184 TT
1 TT
59544186 CAGCTATTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (29 bp):
TTTGGCACTAAGTGTGCGATTTAACTAGC
Found at i:59556761 original size:19 final size:19
Alignment explanation
Indices: 59556737--59556778 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
59556727 CAATTATGAT
*
59556737 TAAAATCAGCT-ACAATACA
1 TAAAATAAGCTGA-AATACA
59556756 TAAAATAAGCTGAAATACA
1 TAAAATAAGCTGAAATACA
59556775 -AAAA
1 TAAAA
59556779 CATAATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 16 0.76
20 1 0.05
ACGTcount: A:0.60, C:0.14, G:0.07, T:0.19
Consensus pattern (19 bp):
TAAAATAAGCTGAAATACA
Found at i:59557141 original size:30 final size:30
Alignment explanation
Indices: 59557107--59557167 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
59557097 TCCTTAACTC
59557107 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
59557137 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
59557167 A
1 A
59557168 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:59566593 original size:59 final size:59
Alignment explanation
Indices: 59566501--59566616 Score: 214
Period size: 59 Copynumber: 2.0 Consensus size: 59
59566491 TTTATCGAAA
*
59566501 ATAAGCAAACCGATTGAAAGACTAATATGTCACCTATCAATTCCAATTGGGAAGATTCT
1 ATAAGCAAACCGATTAAAAGACTAATATGTCACCTATCAATTCCAATTGGGAAGATTCT
*
59566560 ATAAGCAATCCGATTAAAAGACTAATATGTCACCTATCAATTCCAATTGGGAAGATT
1 ATAAGCAAACCGATTAAAAGACTAATATGTCACCTATCAATTCCAATTGGGAAGATT
59566617 TTTTGTTCTG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.28
Consensus pattern (59 bp):
ATAAGCAAACCGATTAAAAGACTAATATGTCACCTATCAATTCCAATTGGGAAGATTCT
Found at i:59568853 original size:93 final size:93
Alignment explanation
Indices: 59568741--59568911 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
59568731 GCCCATAAGT
* *
59568741 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
59568806 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
59568834 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
59568899 CGAGTTCGGATGC
66 CGAGCTCGGATGC
59568912 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:59568908 original size:46 final size:46
Alignment explanation
Indices: 59568733--59568908 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
59568723 TGTAACCCGC
* *
59568733 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
59568779 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
59568825 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
59568872 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
59568909 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:59572499 original size:27 final size:26
Alignment explanation
Indices: 59572443--59572499 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
59572433 CAACCTTAAC
* * *
59572443 CCTAGGGGTATATCAGTAATTTTGCT
1 CCTAGGGGTAAATCAGTAATTTTCCA
*
59572469 CCTAGGGGTAAATCTGTAAATTTTCCA
1 CCTAGGGGTAAATCAGT-AATTTTCCA
59572496 CCTA
1 CCTA
59572500 TAAAGGTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (26 bp):
CCTAGGGGTAAATCAGTAATTTTCCA
Found at i:59579516 original size:19 final size:18
Alignment explanation
Indices: 59579492--59579561 Score: 88
Period size: 19 Copynumber: 3.8 Consensus size: 18
59579482 TAAGAATATT
59579492 CAATCTTAGATATGACATG
1 CAATCTTAGATATGA-ATG
*
59579511 CAATCTTAGATGTGATATG
1 CAATCTTAGATATGA-ATG
* *
59579530 AAATCTTAGATATG-ATA
1 CAATCTTAGATATGAATG
59579547 CAATCTTAGATATGA
1 CAATCTTAGATATGA
59579562 TATGATATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
17 15 0.34
19 29 0.66
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (18 bp):
CAATCTTAGATATGAATG
Found at i:59579543 original size:14 final size:15
Alignment explanation
Indices: 59579524--59579561 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
59579514 TCTTAGATGT
59579524 GATATGA-AATCTTA
1 GATATGACAATCTTA
59579538 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
59579555 GATATGA
1 GATATGA
59579562 TATGATATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 1 0.05
16 1 0.05
17 13 0.62
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:59579551 original size:36 final size:37
Alignment explanation
Indices: 59579493--59579566 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 37
59579483 AAGAATATTC
* *
59579493 AATCTTAGATATGACATGCAATCTTAGATGTGATATGA
1 AATCTTAGATATGA-ATACAATCTTAGATATGATATGA
59579531 AATCTTAGATATG-ATACAATCTTAGATATGATATGA
1 AATCTTAGATATGAATACAATCTTAGATATGATATGA
59579567 TATGATATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 21 0.62
38 13 0.38
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (37 bp):
AATCTTAGATATGAATACAATCTTAGATATGATATGA
Found at i:59579563 original size:5 final size:5
Alignment explanation
Indices: 59579555--59579580 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
59579545 TACAATCTTA
59579555 GATAT GATAT GATAT GATAT GATAT G
1 GATAT GATAT GATAT GATAT GATAT G
59579581 CAATCTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (5 bp):
GATAT
Found at i:59589088 original size:8 final size:8
Alignment explanation
Indices: 59589050--59589114 Score: 60
Period size: 8 Copynumber: 7.6 Consensus size: 8
59589040 TTCTATTTCA
59589050 AAAAAAAG
1 AAAAAAAG
*
59589058 GAAAAAAG
1 AAAAAAAG
59589066 TAAAAAAAG
1 -AAAAAAAG
59589075 AGAGAAAAA-
1 A-A-AAAAAG
*
59589084 AAGAAAAAT
1 AA-AAAAAG
59589093 AAAAAAGAG
1 AAAAAA-AG
59589102 AAAAAAAG
1 AAAAAAAG
59589110 AAAAA
1 AAAAA
59589115 TGGAGAGGCC
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
8 26 0.53
9 18 0.37
10 5 0.10
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:59589096 original size:23 final size:23
Alignment explanation
Indices: 59589069--59589115 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
59589059 AAAAAAGTAA
59589069 AAAAAGAGAGAAAAAAAGAAAAAT
1 AAAAA-AGAGAAAAAAAGAAAAAT
59589093 AAAAAAGAGAAAAAAAGAAAAAT
1 AAAAAAGAGAAAAAAAGAAAAAT
59589116 GGAGAGGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (23 bp):
AAAAAAGAGAAAAAAAGAAAAAT
Found at i:59590161 original size:41 final size:41
Alignment explanation
Indices: 59590115--59590751 Score: 174
Period size: 41 Copynumber: 15.3 Consensus size: 41
59590105 ATCTTATCTA
*
59590115 CCTAAGTAGTAGTGGAGCAGATCGAAGAATCGCCTTAATCC
1 CCTAAGCAGTAGTGGAGCAGATCGAAGAATCGCCTTAATCC
* * **
59590156 CCTAAGCAGTAG-GGTAACAGGTTAAATTTGTAAAT---CTT-ATCTC
1 CCTAAGCAGTAGTGG-AGCAGATCGAA---G--AATCGCCTTAATC-C
*
59590199 CCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCC
1 CCTAAGCAGTAGTGGAGCAGATCGAAGAATCGCCTTAATCC
* * * * *
59590240 CCTAAGCAGTAG-GGTAACAGGT-TAA-ATTTGCAGATCTT-ATCTC
1 CCTAAGCAGTAGTGG-AGCAGATCGAAGA-AT-C-G-CCTTAATC-C
* *
59590283 CCTAAGCAGCAGTGGAGCAGATCGAAGACTCGCCTTAATCC
1 CCTAAGCAGTAGTGGAGCAGATCGAAGAATCGCCTTAATCC
** * *
59590324 CCTAAATAGTAG-GGTAAG-AGGTTCGCAG-AT---CTT-ATCTC
1 CCTAAGCAGTAGTGG--AGCA-GATCGAAGAATCGCCTTAATC-C
* * *
59590362 CCTAAGCAGTAGCGGAGTAGATCGACGACGACTCGCCTTAATCC
1 CCTAAGCAGTAGTGGAGCAGATCGA--A-GAATCGCCTTAATCC
* * * * * *
59590406 CCTAAGTAGTAG-GGTAACAGGT-TAA-ATTTGCAGATCTT-ATCTC
1 CCTAAGCAGTAGTGG-AGCAGATCGAAGA-AT-C-G-CCTTAATC-C
**
59590449 CCTAAGCAGTAGTGGAGCAGATCGAAGACCCGCCTTAATCC
1 CCTAAGCAGTAGTGGAGCAGATCGAAGAATCGCCTTAATCC
* * * * * * *
59590490 CTTAAGCGGTAG-GGTAACAGGT-TAA-ATTTGCAGATCTT-ATCTC
1 CCTAAGCAGTAGTGG-AGCAGATCGAAGA-AT-C-G-CCTTAATC-C
*
59590533 CCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCC
1 CCTAAGCAGTAGTGGAGCAGATCGAAGAATCGCCTTAATCC
* * * *
59590574 CCTAAGCAGTAAG-GTAACAGGTTCGCAG-AT---CTT-ATCTC
1 CCTAAGCAGT-AGTGGAGCA-GATCGAAGAATCGCCTTAATC-C
** *
59590612 CCTAAGCAGTAGCAGAGCAGATCGACGACGACTCGCCTTAATCC
1 CCTAAGCAGTAGTGGAGCAGATCGA--A-GAATCGCCTTAATCC
* * ** *
59590656 CCTAAGCAGTAG-GGTAACAGGTTAAATTTGAA--G-ATCTAATCTC
1 CCTAAGCAGTAGTGG-AGCAGATCGAA---GAATCGCCT-TAATC-C
* *
59590699 CCTAAGCAGTAGTGGAGCAAATCGAAG-ATGCGCCTTAACCC
1 CCTAAGCAGTAGTGGAGCAGATCGAAGAAT-CGCCTTAATCC
59590740 CCTAAGCAGTAG
1 CCTAAGCAGTAG
59590752 GGTAAAAGGT
Statistics
Matches: 431, Mismatches: 87, Indels: 156
0.64 0.13 0.23
Matches are distributed among these distances:
37 18 0.04
38 34 0.08
39 8 0.02
40 18 0.04
41 112 0.26
42 58 0.13
43 109 0.25
44 62 0.14
45 9 0.02
46 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (41 bp):
CCTAAGCAGTAGTGGAGCAGATCGAAGAATCGCCTTAATCC
Found at i:59590202 original size:43 final size:42
Alignment explanation
Indices: 59590071--59590291 Score: 122
Period size: 43 Copynumber: 5.2 Consensus size: 42
59590061 CGCCTTAATC
* *
59590071 CCCTAAGCAGTAAGGTAACAGGTTAAATTTGTAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTG-AAATCTTATCT
* * * * **
59590114 ACCTAAGTAGTAGTGG-AGCAGATCGAA---G-AATCGCCTTAATC-
1 CCCTAAGCAGTAG-GGTAACAGGTTAAATTTGAAAT---CTT-ATCT
59590155 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGTAAATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTG-AAATCTTATCT
* * * * * *
59590198 CCCTAAGCAGTAGTGG-AGCAGATCGAAGACTCG---CCTTAATC-
1 CCCTAAGCAGTAG-GGTAACAGGT-TAA-ATTTGAAATCTT-ATCT
*
59590239 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTG-AAATCTTATCT
59590282 CCCTAAGCAG
1 CCCTAAGCAG
59590292 CAGTGGAGCA
Statistics
Matches: 130, Mismatches: 26, Indels: 44
0.65 0.13 0.22
Matches are distributed among these distances:
38 2 0.02
39 3 0.02
40 7 0.05
41 42 0.32
42 12 0.09
43 51 0.39
44 7 0.05
45 3 0.02
46 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (42 bp):
CCCTAAGCAGTAGGGTAACAGGTTAAATTTGAAATCTTATCT
Found at i:59590203 original size:84 final size:84
Alignment explanation
Indices: 59590061--59590765 Score: 1027
Period size: 84 Copynumber: 8.4 Consensus size: 84
59590051 CAAAATTCAG
* * * *
59590061 CGCCTTAATCCCCTAAGCAGTAAGGTAACAGGTTAAATTTGTAGATCTTATCTACCTAAGTAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
59590126 GTGGAGCAGATCGAAGAAT
66 GTGGAGCAGATCGAAGACT
* *
59590145 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGTAAATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
59590210 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
*
59590229 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGCA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
59590294 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
** * *
59590313 CGCCTTAATCCCCTAAATAGTAGGGTAAGAGG-----TTCGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
* *
59590373 GCGGAGTAGATCGACGACGACT
66 GTGGAGCAGATCGA--A-GACT
*
59590395 CGCCTTAATCCCCTAAGTAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
59590460 GTGGAGCAGATCGAAGACC
66 GTGGAGCAGATCGAAGACT
* *
59590479 CGCCTTAATCCCTTAAGCGGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
59590544 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
* *
59590563 CGCCTTAATCCCCTAAGCAGTAAGGTAACAGG-----TTCGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
**
59590623 GCAGAGCAGATCGACGACGACT
66 GTGGAGCAGATCGA--A-GACT
* *
59590645 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGAAGATCTAATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
59590710 GTGGAGCAAATCGAAGA-T
66 GTGGAGCAGATCGAAGACT
* *
59590728 GCGCCTTAACCCCCTAAGCAGTAGGGTAAAAGGTTAAA
1 -CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAA
59590766 GTATAGCAGA
Statistics
Matches: 564, Mismatches: 40, Indels: 34
0.88 0.06 0.05
Matches are distributed among these distances:
79 77 0.14
81 2 0.00
82 69 0.12
83 1 0.00
84 338 0.60
85 2 0.00
87 75 0.13
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (84 bp):
CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
GTGGAGCAGATCGAAGACT
Found at i:59590460 original size:43 final size:43
Alignment explanation
Indices: 59590405--59590544 Score: 126
Period size: 43 Copynumber: 3.3 Consensus size: 43
59590395 CGCCTTAATC
*
59590405 CCCTAAGTAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCT
* * ** *** * *
59590448 CCCTAAGCAGTAGTGG-AGCAGATCGAA-GACCCG-CCTTAATC-
1 CCCTAAGCAGTAG-GGTAACAGGTTAAATTTGCAGATCTT-ATCT
* *
59590489 CCTTAAGCGGTAGGGTAACAGGTTAAATTTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCT
59590532 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
59590545 TGGAGCAGAT
Statistics
Matches: 68, Mismatches: 23, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
40 2 0.03
41 21 0.31
42 10 0.15
43 33 0.49
44 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCT
Found at i:59590598 original size:250 final size:250
Alignment explanation
Indices: 59590061--59590765 Score: 1112
Period size: 250 Copynumber: 2.8 Consensus size: 250
59590051 CAAAATTCAG
* * * *
59590061 CGCCTTAATCCCCTAAGCAGTAAGGTAACAGGTTAAATTTGTAGATCTTATCTACCTAAGTAGTA
1 CGCCTTAATCCCCTAAGCAGTAAGGTAACAGG-----TTCGCAGATCTTATCTCCCTAAGCAGTA
* *
59590126 GTGGAGCAGATCGA--A-GAATCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGTA
61 GCGGAGCAGATCGACGACGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTG-A
*
59590188 A-ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAGTAG
125 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCGCCTTAATCCCCTAAGCAGTAG
59590252 GGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACT
190 GGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACT
** * *
59590313 CGCCTTAATCCCCTAAATAGTAGGGTAAGAGGTTCGCAGATCTTATCTCCCTAAGCAGTAGCGGA
1 CGCCTTAATCCCCTAAGCAGTAAGGTAACAGGTTCGCAGATCTTATCTCCCTAAGCAGTAGCGGA
* * *
59590378 GTAGATCGACGACGACTCGCCTTAATCCCCTAAGTAGTAGGGTAACAGGTTAAATTTGCAGATCT
66 GCAGATCGACGACGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGAAGATCT
* *
59590443 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCGCCTTAATCCCTTAAGCGGTAGGGTAAC
131 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCGCCTTAATCCCCTAAGCAGTAGGGTAAC
*
59590508 AGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACT
196 AGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACT
*
59590563 CGCCTTAATCCCCTAAGCAGTAAGGTAACAGGTTCGCAGATCTTATCTCCCTAAGCAGTAGCAGA
1 CGCCTTAATCCCCTAAGCAGTAAGGTAACAGGTTCGCAGATCTTATCTCCCTAAGCAGTAGCGGA
59590628 GCAGATCGACGACGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGAAGATCT
66 GCAGATCGACGACGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGAAGATCT
* * ** * *
59590693 AATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGATGCGCCTTAACCCCCTAAGCAGTAGGGTAAA
131 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCGCCTTAATCCCCTAAGCAGTAGGGTAAC
59590758 AGGTTAAA
196 AGGTTAAA
59590766 GTATAGCAGA
Statistics
Matches: 416, Mismatches: 33, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
247 36 0.09
249 2 0.00
250 350 0.84
252 28 0.07
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (250 bp):
CGCCTTAATCCCCTAAGCAGTAAGGTAACAGGTTCGCAGATCTTATCTCCCTAAGCAGTAGCGGA
GCAGATCGACGACGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGAAGATCT
TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCGCCTTAATCCCCTAAGCAGTAGGGTAAC
AGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACT
Found at i:59590735 original size:334 final size:330
Alignment explanation
Indices: 59590060--59590765 Score: 1017
Period size: 334 Copynumber: 2.1 Consensus size: 330
59590050 ACAAAATTCA
* * *
59590060 GCGCCTTAATCCCCTAAGCAGTAAGGTAACAGGTTAAATTTGTAGATCTTATCTACCTAAGTAGT
1 GCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTACCTAAGCAGT
* *
59590125 AGTGGAGCAGATCGAAGAATCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGTAAA
66 AGTGGAGCAGATCGAAGAACCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAAA
*
59590190 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAGTAGGGT
131 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAGTAAGGT
* **
59590255 AACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACTCGCCTTA
196 AACAGG----ATTCGCAGATCTTATCTCCCTAAGCAGCAGCAGAGCAGATCGAAGACTCGCCTTA
* * * * * *
59590320 ATCCCCTAAATAGTAGGGTAAGAGGTTCGCAGATCTTATCTCCCTAAGCAGTAGCGGAGTAGATC
257 ATCCCCTAAACAGTAGGGTAACAGGTTCGAAGATCTAATCTCCCTAAGCAGTAGCGGAGCAAATC
59590385 GACGACGACT
322 GAC-ACGACT
* *
59590395 -CGCCTTAATCCCCTAAGTAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGT
1 GCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTACCTAAGCAGT
* * * *
59590459 AGTGGAGCAGATCGAAGACCCGCCTTAATCCCTTAAGCGGTAGGGTAACAGGTTAAATTTGCAGA
66 AGTGGAGCAGATCGAAGAACCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAAA
59590524 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAGTAAGGT
131 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAGTAAGGT
*
59590589 AACAGG-TTCGCAGATCTTATCTCCCTAAGCAGTAGCAGAGCAGATCGACGACGACTCGCCTTAA
196 AACAGGATTCGCAGATCTTATCTCCCTAAGCAGCAGCAGAGCAGATCGA--A-GACTCGCCTTAA
* * *
59590653 TCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGAAGATCTAATCTCCCTAAGCAGTAGTGGAGCA
258 TCCCCTAAACAGTAGGGTAACAGG-----TTCGAAGATCTAATCTCCCTAAGCAGTAGCGGAGCA
59590718 AATCGA-A-GA-T
318 AATCGACACGACT
* *
59590728 GCGCCTTAACCCCCTAAGCAGTAGGGTAAAAGGTTAAA
1 GCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAA
59590766 GTATAGCAGA
Statistics
Matches: 334, Mismatches: 28, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
329 38 0.11
331 1 0.00
332 33 0.10
333 1 0.00
334 224 0.67
335 1 0.00
337 36 0.11
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (330 bp):
GCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTACCTAAGCAGT
AGTGGAGCAGATCGAAGAACCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAAA
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAGTAAGGT
AACAGGATTCGCAGATCTTATCTCCCTAAGCAGCAGCAGAGCAGATCGAAGACTCGCCTTAATCC
CCTAAACAGTAGGGTAACAGGTTCGAAGATCTAATCTCCCTAAGCAGTAGCGGAGCAAATCGACA
CGACT
Found at i:59590986 original size:81 final size:79
Alignment explanation
Indices: 59590884--59591031 Score: 197
Period size: 81 Copynumber: 1.8 Consensus size: 79
59590874 ATTTGACGGA
* * * * *
59590884 GAGCAGATCAAAGACATAGCAGATCTGACCTTCAGATATTTTCACATTGAAGTAGATCCAAGATG
1 GAGCAAATCAAAGACATAGCAGATCTAACCTTCAGAT-GTTT-ACACTGAAGCAGATCCAAGATG
59590949 ATTTAGCGTTTACAAG
64 ATTTAGCGTTTACAAG
* * * *
59590965 GAGCAAATCGAAGACATAGCAGATCTAACCTTTAGGTGTTTACGCTGAAGCAGATCCAAGATGAT
1 GAGCAAATCAAAGACATAGCAGATCTAACCTTCAGATGTTTACACTGAAGCAGATCCAAGATGAT
59591030 TT
66 TT
59591032 GGCAACCCTG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
79 23 0.40
80 3 0.05
81 32 0.55
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (79 bp):
GAGCAAATCAAAGACATAGCAGATCTAACCTTCAGATGTTTACACTGAAGCAGATCCAAGATGAT
TTAGCGTTTACAAG
Found at i:59591685 original size:19 final size:19
Alignment explanation
Indices: 59591661--59591740 Score: 128
Period size: 19 Copynumber: 4.3 Consensus size: 19
59591651 AATCTTTAAG
*
59591661 GATATGCAACCTTAGATAT
1 GATATGCAATCTTAGATAT
*
59591680 GATATGCAATCTTAGATGT
1 GATATGCAATCTTAGATAT
59591699 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
59591718 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
59591735 GATATG
1 GATATG
59591741 ATATGATATG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
17 17 0.30
19 39 0.70
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:59591718 original size:14 final size:15
Alignment explanation
Indices: 59591699--59591736 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
59591689 TCTTAGATGT
59591699 GATATG-CAATCTTA
1 GATATGACAATCTTA
59591713 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
59591730 GATATGA
1 GATATGA
59591737 TATGATATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 1 0.05
17 14 0.67
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:59591766 original size:21 final size:22
Alignment explanation
Indices: 59591740--59591785 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
59591730 GATATGATAT
59591740 GATATGA-TATGTAATCTTGAA
1 GATATGATTATGTAATCTTGAA
* *
59591761 GATATGATTTTGTAATCTTGGA
1 GATATGATTATGTAATCTTGAA
59591783 GAT
1 GAT
59591786 TTAATTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (22 bp):
GATATGATTATGTAATCTTGAA
Found at i:59591792 original size:22 final size:22
Alignment explanation
Indices: 59591749--59591792 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
59591739 TGATATGATA
*
59591749 TGTAATCTTGAAGATATGATTT
1 TGTAATCTTGAAGATATAATTT
* *
59591771 TGTAATCTTGGAGATTTAATTT
1 TGTAATCTTGAAGATATAATTT
59591793 GTAGATATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.48
Consensus pattern (22 bp):
TGTAATCTTGAAGATATAATTT
Found at i:59596055 original size:22 final size:22
Alignment explanation
Indices: 59596021--59596064 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
59596011 CAAATTTGTG
* *
59596021 AAAATTTATTATAAAAATAATT
1 AAAATTAAATATAAAAATAATT
**
59596043 AAAATTAAATATATTAATAATT
1 AAAATTAAATATAAAAATAATT
59596065 TAAGTGCAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTAAATATAAAAATAATT
Found at i:59598559 original size:43 final size:41
Alignment explanation
Indices: 59598491--59598587 Score: 104
Period size: 43 Copynumber: 2.3 Consensus size: 41
59598481 ATGAGTTTAC
* * * * *
59598491 GTGTAAGACCATATCCAGTATATGGCATCGTTATGAAAATTTT
1 GTGTAAGACCATATCCAGGACATGGCACCGATATGAAAA--TA
* * *
59598534 GTGTAAGACCATGTCTAGGACATGGCACCGATATGAGAATA
1 GTGTAAGACCATATCCAGGACATGGCACCGATATGAAAATA
59598575 GTGTAAGACCATA
1 GTGTAAGACCATA
59598588 GTGAGCTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 13 0.29
43 32 0.71
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (41 bp):
GTGTAAGACCATATCCAGGACATGGCACCGATATGAAAATA
Found at i:59599741 original size:13 final size:13
Alignment explanation
Indices: 59599719--59599749 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
59599709 ATCGAGAGTT
*
59599719 ACACGGGCTGAGA
1 ACACGAGCTGAGA
59599732 ACACGAGCTGAGA
1 ACACGAGCTGAGA
59599745 ACACG
1 ACACG
59599750 GGCGTGTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.26, G:0.32, T:0.06
Consensus pattern (13 bp):
ACACGAGCTGAGA
Found at i:59605784 original size:11 final size:11
Alignment explanation
Indices: 59605768--59605792 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59605758 GCTTTATCAA
59605768 TCTATATATAG
1 TCTATATATAG
59605779 TCTATATATAG
1 TCTATATATAG
59605790 TCT
1 TCT
59605793 TTATCAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (11 bp):
TCTATATATAG
Found at i:59608383 original size:70 final size:70
Alignment explanation
Indices: 59608270--59608419 Score: 282
Period size: 70 Copynumber: 2.1 Consensus size: 70
59608260 CATGATTTTC
*
59608270 TTTCTTCAGATACCTTTTTCTTCTTTCCTTTCTGGAAAAAGAAAAATCAAATTTCTTCCTCCTTC
1 TTTCTTCAAATACCTTTTTCTTCTTTCCTTTCTGGAAAAAGAAAAATCAAATTTCTTCCTCCTTC
59608335 AGTTA
66 AGTTA
*
59608340 TTTCTTCAAATACCTTTTTCTTCTTTCCTTTCTGGAAAAAGAAAAATCAATTTTCTTCCTCCTTC
1 TTTCTTCAAATACCTTTTTCTTCTTTCCTTTCTGGAAAAAGAAAAATCAAATTTCTTCCTCCTTC
59608405 AGTTA
66 AGTTA
59608410 TTTCTTCAAA
1 TTTCTTCAAA
59608420 CCATTATTAT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
70 78 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (70 bp):
TTTCTTCAAATACCTTTTTCTTCTTTCCTTTCTGGAAAAAGAAAAATCAAATTTCTTCCTCCTTC
AGTTA
Found at i:59610297 original size:12 final size:12
Alignment explanation
Indices: 59610280--59610320 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
59610270 GGGTGCCTGA
59610280 AAAGGTACTTGT
1 AAAGGTACTTGT
59610292 AAAGGTACTTGT
1 AAAGGTACTTGT
*
59610304 AAAGGTAATTGT
1 AAAGGTACTTGT
59610316 AAAGG
1 AAAGG
59610321 GAAACTAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.39, C:0.05, G:0.27, T:0.29
Consensus pattern (12 bp):
AAAGGTACTTGT
Found at i:59611560 original size:21 final size:21
Alignment explanation
Indices: 59611534--59611573 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
59611524 CTACTAGAAA
59611534 ACAATT-TTTTGCTTGATTTCC
1 ACAATTGTTTT-CTTGATTTCC
*
59611555 ACAATTGTTTTCTTTATTT
1 ACAATTGTTTTCTTGATTT
59611574 GAGGCTAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (21 bp):
ACAATTGTTTTCTTGATTTCC
Found at i:59613655 original size:336 final size:337
Alignment explanation
Indices: 59613030--59613704 Score: 1102
Period size: 336 Copynumber: 2.0 Consensus size: 337
59613020 TGGTACTAGA
* * *
59613030 TAAGAGTTCAACCTATGTATATACCAAACCTATAGGAGACAACACTTAAAGAATTTGTACTTACT
1 TAAGAGCTCAACCTATGTATATACCAAACCTATAGGAGACAACACTTAAAGAATTTATACCTACT
*
59613095 CTTCAAACTTTGATAAGGTGATGAAATCTCCTGAAGTGGGCATGGGTTCTATTGGAACATCGATA
66 CTTCAAACTTTGATAAGGTGATAAAATCTCCTGAAGTGGGCATGGGTTCTATTGGAACATCGATA
*
59613160 TGCCTCCTGGCACAGCGAAAAAATAATTTCGGTGATCACAACCCATGGTATAAGCAAGTGACATA
131 TGCCTCCTGGCACAACGAAAAAATAATTTCGGTGATCACAACCCATGGTATAAGCAAGTGACATA
* *
59613225 TTAAGAATATGAGCACCACCATAATGTAATACTAAACCCACAATCAAGCCTTCATCCCAACAAGA
196 TTAAGAATACGAGCACCACCATAAGGTAATACTAAACCCACAATCAAGCCTTCATCCCAACAAGA
* *
59613290 ACCATCAACACTCAATAGCTCACTGAACTCCATATCTTTCAGCCCATCCAATGGAACCAAGTCAA
261 ACCATCAACACTCAATAGCTCACTGAACTCCATATCTTCCAGCCCATCCAACGGAACCAAGTCAA
59613355 CC-AAAAATTGT
326 CCAAAAAATTGT
*
59613366 TAAGAGCTCAACCTATGTATATACCAAACCTATAGGAGACAACACTTAAAGAATTTATACCTATT
1 TAAGAGCTCAACCTATGTATATACCAAACCTATAGGAGACAACACTTAAAGAATTTATACCTACT
* * * * * * * *
59613431 CTTCAAGCTTTGCTGAGGTGATAAAATGTCTTGCAGTGGGCATGGGTTCTATTGGAATATCGGTA
66 CTTCAAACTTTGATAAGGTGATAAAATCTCCTGAAGTGGGCATGGGTTCTATTGGAACATCGATA
* * *
59613496 TGCCTCGTGGCACAACGATAAAATAA-TTCTGGTGATCATAACCCATGGTATAAGCAAGTGACAT
131 TGCCTCCTGGCACAACGAAAAAATAATTTC-GGTGATCACAACCCATGGTATAAGCAAGTGACAT
* *
59613560 ATTAAGAATACGAGCACCACCATAAGGTAATAGTAAACCCACAATCAAGCCTTCATCCTAACAAG
195 ATTAAGAATACGAGCACCACCATAAGGTAATACTAAACCCACAATCAAGCCTTCATCCCAACAAG
* *
59613625 AACCATCAACACTCAATAGCTCATTGAACTCCATATCTTCCAGCCTATCCAACGGAACCAAGTCA
260 AACCATCAACACTCAATAGCTCACTGAACTCCATATCTTCCAGCCCATCCAACGGAACCAAGTCA
59613690 ACCAAAAAATTGT
325 ACCAAAAAATTGT
59613703 TA
1 TA
59613705 TCACAAAAAA
Statistics
Matches: 312, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
335 3 0.01
336 298 0.96
337 11 0.04
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (337 bp):
TAAGAGCTCAACCTATGTATATACCAAACCTATAGGAGACAACACTTAAAGAATTTATACCTACT
CTTCAAACTTTGATAAGGTGATAAAATCTCCTGAAGTGGGCATGGGTTCTATTGGAACATCGATA
TGCCTCCTGGCACAACGAAAAAATAATTTCGGTGATCACAACCCATGGTATAAGCAAGTGACATA
TTAAGAATACGAGCACCACCATAAGGTAATACTAAACCCACAATCAAGCCTTCATCCCAACAAGA
ACCATCAACACTCAATAGCTCACTGAACTCCATATCTTCCAGCCCATCCAACGGAACCAAGTCAA
CCAAAAAATTGT
Found at i:59614839 original size:20 final size:20
Alignment explanation
Indices: 59614814--59614852 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59614804 CTCAATTTAG
**
59614814 GATAATTAATTATTTAATTA
1 GATAATTAAAGATTTAATTA
59614834 GATAATTAAAGATTTAATT
1 GATAATTAAAGATTTAATT
59614853 GATCATAGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (20 bp):
GATAATTAAAGATTTAATTA
Found at i:59615312 original size:17 final size:17
Alignment explanation
Indices: 59615290--59615323 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
59615280 TCTACCTTTA
59615290 TCTACTTTAAGAAAAAC
1 TCTACTTTAAGAAAAAC
59615307 TCTACTTTAAGAAAAAC
1 TCTACTTTAAGAAAAAC
59615324 ACACTTAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (17 bp):
TCTACTTTAAGAAAAAC
Found at i:59615329 original size:16 final size:17
Alignment explanation
Indices: 59615291--59615329 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
59615281 CTACCTTTAT
*
59615291 CTACTTTAAGAAAAACT
1 CTACTTTAAGAAAAACA
59615308 CTACTTTAAGAAAAACA
1 CTACTTTAAGAAAAACA
59615325 C-ACTT
1 CTACTT
59615330 AGGGAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.46, C:0.21, G:0.05, T:0.28
Consensus pattern (17 bp):
CTACTTTAAGAAAAACA
Found at i:59620263 original size:11 final size:11
Alignment explanation
Indices: 59620247--59620276 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
59620237 AAATGAGCCT
*
59620247 TTTACCACAAG
1 TTTACCAAAAG
59620258 TTTACCAAAAG
1 TTTACCAAAAG
59620269 TTTACCAA
1 TTTACCAA
59620277 CCCTGCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (11 bp):
TTTACCAAAAG
Found at i:59622082 original size:5 final size:5
Alignment explanation
Indices: 59622074--59622126 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
59622064 CTTTATGTTT
59622074 TATTA TATTA TATTA TATTA T-TATA TTATTA TATTA -A-TA TATTA -A-TA
1 TATTA TATTA TATTA TATTA TAT-TA -TATTA TATTA TATTA TATTA TATTA
59622121 TATTA T
1 TATTA T
59622127 TATAATGTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
3 4 0.10
4 5 0.12
5 28 0.68
6 3 0.07
7 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:59622095 original size:8 final size:8
Alignment explanation
Indices: 59622073--59622130 Score: 80
Period size: 8 Copynumber: 7.0 Consensus size: 8
59622063 ACTTTATGTT
59622073 TTATTATA
1 TTATTATA
59622081 TTATATTATA
1 -T-TATTATA
59622091 TTATTATA
1 TTATTATA
59622099 TTATTATA
1 TTATTATA
*
59622107 TTAATATA
1 TTATTATA
*
59622115 TTAATATA
1 TTATTATA
59622123 TTATTATA
1 TTATTATA
59622131 ATGTATATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
8 37 0.80
9 2 0.04
10 7 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATTATA
Done.