Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 60 of 235
Found at i:20367568 original size:14 final size:14
Alignment explanation
Indices: 20367549--20367578 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20367539 ATGGCATATT
20367549 GGTTAGTTGAATTA
1 GGTTAGTTGAATTA
20367563 GGTTAGTTGAATTA
1 GGTTAGTTGAATTA
20367577 GG
1 GG
20367579 GTATTGGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.40
Consensus pattern (14 bp):
GGTTAGTTGAATTA
Found at i:20370099 original size:19 final size:20
Alignment explanation
Indices: 20370056--20370101 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20370046 ATTGGGCATT
20370056 GCCCATATTAACACAGTTGG
1 GCCCATATTAACACAGTTGG
* *
20370076 GCCCATTTTAATACAGTT-G
1 GCCCATATTAACACAGTTGG
20370095 GCCCATA
1 GCCCATA
20370102 ACAAAATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (20 bp):
GCCCATATTAACACAGTTGG
Found at i:20375812 original size:24 final size:24
Alignment explanation
Indices: 20375785--20375832 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
20375775 TAGTGAATAT
20375785 ATATATGAG-GTTATAATATGGTTA
1 ATATATGAGTGTT-TAATATGGTTA
* *
20375809 ATATATGTGTGTTTGATATGGTTA
1 ATATATGAGTGTTTAATATGGTTA
20375833 TATTGAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (24 bp):
ATATATGAGTGTTTAATATGGTTA
Found at i:20381678 original size:27 final size:27
Alignment explanation
Indices: 20381648--20381825 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
20381638 ATATTGAGTC
* * * *
20381648 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
20381675 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
20381702 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
20381730 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
20381757 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
20381784 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
20381811 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20381826 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:20381787 original size:82 final size:81
Alignment explanation
Indices: 20381669--20381824 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
20381659 TGCTATATAA
* *
20381669 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
20381734 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
20381751 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
20381815 CACTTAGTGC
65 CACTTAGTGC
20381825 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:20389742 original size:27 final size:27
Alignment explanation
Indices: 20389712--20389889 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
20389702 ATATTGAGCC
* * * *
20389712 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
20389739 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
20389766 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
20389794 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
20389821 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
20389848 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
20389875 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20389890 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:20389851 original size:82 final size:81
Alignment explanation
Indices: 20389733--20389888 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
20389723 TGCTATATAA
* *
20389733 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
20389798 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
20389815 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
20389879 CACTTAGTGC
65 CACTTAGTGC
20389889 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:20415551 original size:36 final size:36
Alignment explanation
Indices: 20415504--20415577 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
20415494 TTGAATCAGT
20415504 ATCCTGGGATATCAAAACAAGAATTAAGAACACATA
1 ATCCTGGGATATCAAAACAAGAATTAAGAACACATA
20415540 ATCCTGGGATATCAAAACAAGAATTAAGAACACATA
1 ATCCTGGGATATCAAAACAAGAATTAAGAACACATA
20415576 AT
1 AT
20415578 TAAGAACAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (36 bp):
ATCCTGGGATATCAAAACAAGAATTAAGAACACATA
Found at i:20418831 original size:21 final size:21
Alignment explanation
Indices: 20418805--20418844 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20418795 TAATATAAAC
20418805 AATAATAGTAATAGATAAATG
1 AATAATAGTAATAGATAAATG
* *
20418826 AATAATAGTGATAGGTAAA
1 AATAATAGTAATAGATAAA
20418845 CAAATTCGAA
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:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (21 bp):
AATAATAGTAATAGATAAATG
Found at i:20419943 original size:40 final size:39
Alignment explanation
Indices: 20419888--20420046 Score: 212
Period size: 40 Copynumber: 4.0 Consensus size: 39
20419878 CCGAATCCAG
* * *
20419888 TTACTAGCACAAAGCCTGCGGGACTTTAGGCCCGGATATA-
1 TTACCAGCACGAAGCCTGCGGGA-TTTA-ACCCGGATATAC
* *
20419928 GTACCAGCACTAAGCCTGCGGGATTTAACCCGGATATAC
1 TTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAC
*
20419967 TTTACCAGCACGAAGCCTGCGGGCTTTAACCCGGATATAC
1 -TTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAC
*
20420007 TTTACCAGCACGAAGCCTGCAGGATTTAACCCGGATATAC
1 -TTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAC
20420047 AATATAGCGA
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
38 10 0.09
39 4 0.04
40 94 0.87
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.22
Consensus pattern (39 bp):
TTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAC
Found at i:20422515 original size:13 final size:13
Alignment explanation
Indices: 20422497--20422521 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20422487 TGTGGGTGCA
20422497 CACGGCCATGTCG
1 CACGGCCATGTCG
20422510 CACGGCCATGTC
1 CACGGCCATGTC
20422522 TGGCGTTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.28, T:0.16
Consensus pattern (13 bp):
CACGGCCATGTCG
Found at i:20428917 original size:42 final size:42
Alignment explanation
Indices: 20428856--20429022 Score: 226
Period size: 42 Copynumber: 4.0 Consensus size: 42
20428846 GAAAATATTT
*
20428856 GAGATAGCTTCGACTATGCATTGGCACTTAGTGTGCAAGATC
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGATC
* *
20428898 GGGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCGAGATC
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGATC
* * * ** *
20428940 AAGATAGCTTCAGCTATGCATTGGCACTTAGTATGCGTGATT
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGATC
* * *
20428982 GAGTTAGCTTCGGCTACGTATTGGCACTTAGTGTGCAAGAT
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGAT
20429023 TCCCGAGTAA
Statistics
Matches: 108, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 108 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (42 bp):
GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGATC
Found at i:20429154 original size:32 final size:32
Alignment explanation
Indices: 20429092--20429154 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
20429082 TATGAGATTG
* * *
20429092 GTACGATATGGTACAAGTATGTATGGAAATTT
1 GTACGAGATGGTACAAGTATGTACGAAAATTT
*
20429124 GTACGAGATGGTACAGGTATGTACGAAAATT
1 GTACGAGATGGTACAAGTATGTACGAAAATT
20429155 CAATTGAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (32 bp):
GTACGAGATGGTACAAGTATGTACGAAAATTT
Found at i:20432863 original size:19 final size:20
Alignment explanation
Indices: 20432836--20432875 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
20432826 ATGATTATGT
*
20432836 CAATGCATATTTTGT-AAAA
1 CAATACATATTTTGTGAAAA
20432855 CAATACATATTTTGTGAAAA
1 CAATACATATTTTGTGAAAA
20432875 C
1 C
20432876 GGACCTACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (20 bp):
CAATACATATTTTGTGAAAA
Found at i:20433074 original size:49 final size:51
Alignment explanation
Indices: 20432941--20433081 Score: 196
Period size: 51 Copynumber: 2.8 Consensus size: 51
20432931 CTAAACACCA
* *
20432941 TTTGTGGACAAGCTACCACTGATTTGCAGATAAATTGCCAGTGATAACACT
1 TTTGTGGACAAGCTACCACTGATTTGCAGATATATTGCCACTGATAACACT
* * * *
20432992 TTTGTAGACAAGCCACCATTGATATGCAGATATATTGCCACTGATAA-A-T
1 TTTGTGGACAAGCTACCACTGATTTGCAGATATATTGCCACTGATAACACT
* *
20433041 TTTGTGGACAAGCTACCACTGATTTGCAAATATACTGCCAC
1 TTTGTGGACAAGCTACCACTGATTTGCAGATATATTGCCAC
20433082 AGCTTCAACC
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 36 0.46
50 1 0.01
51 41 0.53
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (51 bp):
TTTGTGGACAAGCTACCACTGATTTGCAGATATATTGCCACTGATAACACT
Found at i:20436559 original size:46 final size:46
Alignment explanation
Indices: 20436391--20436568 Score: 157
Period size: 46 Copynumber: 3.8 Consensus size: 46
20436381 TGTAACCCAC
* * *
20436391 CCATAAGCGAACTCAGACTCAACTCAATGAGATCGGGTGTTCCCA-T
1 CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGATGTT-CCATT
* *
20436437 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATG--CCTAGTT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGATGTTCC-A-TT
* * * * * *
20436483 ACATCTCA-CAAACTCGGACTCAACTCAACGAGTTCGGACGTTCGATT
1 CCA--TAAGCGAACTCAGACTCAACTCAACGAGTTCGGATGTTCCATT
* * *
20436530 CCATAAGTGAACTCGGACTCAACTCAACGAGTTAGGATG
1 CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGATG
20436569 CCCAAATATC
Statistics
Matches: 106, Mismatches: 18, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
43 2 0.02
44 1 0.01
45 2 0.02
46 66 0.62
47 31 0.29
48 3 0.03
49 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGATGTTCCATT
Found at i:20436559 original size:93 final size:93
Alignment explanation
Indices: 20436400--20436570 Score: 245
Period size: 93 Copynumber: 1.8 Consensus size: 93
20436390 CCCATAAGCG
* **
20436400 AACTCAGACTCAACTCAATGAGATCGGGTGTTCCCATCCATAAGTGAACTCAGACTCAACTCAAC
1 AACTCAGACTCAACTCAACGAGATCGGACGTTCCCATCCATAAGTGAACTCAGACTCAACTCAAC
*
20436465 GAGCTCGGATGCCTAGTTACATCTCACA
66 GAGCTAGGATGCCTAGTTACATCTCACA
* * * *
20436493 AACTCGGACTCAACTCAACGAGTTCGGACGTT-CGATTCCATAAGTGAACTCGGACTCAACTCAA
1 AACTCAGACTCAACTCAACGAGATCGGACGTTCCCA-TCCATAAGTGAACTCAGACTCAACTCAA
*
20436557 CGAGTTAGGATGCC
65 CGAGCTAGGATGCC
20436571 CAAATATCCG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
92 2 0.03
93 66 0.97
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (93 bp):
AACTCAGACTCAACTCAACGAGATCGGACGTTCCCATCCATAAGTGAACTCAGACTCAACTCAAC
GAGCTAGGATGCCTAGTTACATCTCACA
Found at i:20439347 original size:15 final size:15
Alignment explanation
Indices: 20439299--20439367 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 15
20439289 TAAAGATAAC
*
20439299 AAGAAAACC-GAATA
1 AAGAAACCCAGAATA
* *
20439313 AAGAAATCCA-AGATT
1 AAGAAACCCAGA-ATA
*
20439328 GAGAAACCCAGAATA
1 AAGAAACCCAGAATA
*
20439343 AAGAAATCCAGAATA
1 AAGAAACCCAGAATA
20439358 AAGAAACCCA
1 AAGAAACCCA
20439368 AGATACGATA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
14 9 0.20
15 34 0.77
16 1 0.02
ACGTcount: A:0.58, C:0.17, G:0.14, T:0.10
Consensus pattern (15 bp):
AAGAAACCCAGAATA
Found at i:20439363 original size:30 final size:30
Alignment explanation
Indices: 20439299--20439367 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
20439289 TAAAGATAAC
* *
20439299 AAGAAAACC-GAATAAAGAAATCCAAGATT
1 AAGAAACCCAGAATAAAGAAATCCAAGATA
*
20439328 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAACCCAGAATAAAGAAATCCAAG-ATA
20439358 AAGAAACCCA
1 AAGAAACCCA
20439368 AGATACGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.26
30 25 0.74
ACGTcount: A:0.58, C:0.17, G:0.14, T:0.10
Consensus pattern (30 bp):
AAGAAACCCAGAATAAAGAAATCCAAGATA
Found at i:20454793 original size:20 final size:19
Alignment explanation
Indices: 20454747--20454784 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
20454737 ATATTAATAC
20454747 ATTTTTATATAAAATTTAA
1 ATTTTTATATAAAATTTAA
20454766 ATATTTTA-ACTAAAATTTA
1 AT-TTTTATA-TAAAATTTA
20454785 TTATTTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTTATATAAAATTTAA
Found at i:20458604 original size:3 final size:3
Alignment explanation
Indices: 20458596--20458625 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
20458586 TATGAGTGGT
20458596 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20458626 GAAAAACTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20459780 original size:3 final size:3
Alignment explanation
Indices: 20459774--20459807 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
20459764 CTCTATTTTT
20459774 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20459808 GAGATAAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20462200 original size:16 final size:16
Alignment explanation
Indices: 20462179--20462215 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
20462169 ATAGTGAATG
20462179 AATGCTCATAGTTATA
1 AATGCTCATAGTTATA
20462195 AATGCTCATAGTTATA
1 AATGCTCATAGTTATA
20462211 AATGC
1 AATGC
20462216 ATTTGTAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (16 bp):
AATGCTCATAGTTATA
Found at i:20473224 original size:30 final size:30
Alignment explanation
Indices: 20473190--20473250 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
20473180 TCCTTAACTC
20473190 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
20473220 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
20473250 A
1 A
20473251 GGCTTGGGAA
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:20481398 original size:61 final size:61
Alignment explanation
Indices: 20481303--20481505 Score: 358
Period size: 61 Copynumber: 3.4 Consensus size: 61
20481293 GAAAATGGTT
20481303 TTAATTTGATTGAACCACTTATAATTAACATGTCTTGTATCAATCTCATACATATCCATAA
1 TTAATTTGATTGAACCACTTATAATTAACATGTCTTGTATCAATCTCATACATATCCATAA
20481364 TTAATTTGATTGAACCACTTATAATTAACATGTCTTGTATCAATCTCATACATATCCATAA
1 TTAATTTGATTGAACCACTTATAATTAACATGTCTTGTATCAATCTCATACATATCCATAA
* * *
20481425 TTAATTTGATTGAACCACTTATAATTAACATGTCTTGTATCAATCTCATACACAT--GT-T
1 TTAATTTGATTGAACCACTTATAATTAACATGTCTTGTATCAATCTCATACATATCCATAA
20481483 TTAATTTGATTGAACCACTTATA
1 TTAATTTGATTGAACCACTTATA
20481506 TGATTCAACC
Statistics
Matches: 139, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
58 23 0.17
59 1 0.01
61 115 0.83
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (61 bp):
TTAATTTGATTGAACCACTTATAATTAACATGTCTTGTATCAATCTCATACATATCCATAA
Found at i:20485760 original size:11 final size:11
Alignment explanation
Indices: 20485744--20485769 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20485734 ACAAATAATA
20485744 TAAATAAGTTT
1 TAAATAAGTTT
20485755 TAAATAAGTTT
1 TAAATAAGTTT
20485766 TAAA
1 TAAA
20485770 ATACTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (11 bp):
TAAATAAGTTT
Found at i:20486243 original size:40 final size:40
Alignment explanation
Indices: 20486090--20486305 Score: 200
Period size: 40 Copynumber: 5.4 Consensus size: 40
20486080 ACATACTAGT
* * * * *
20486090 TTGTGGACAAGCCACCAGTGTTGTAGATAAACTACCAAAA
1 TTGTGGACAAGCCACCAGTATTGCAAATAAACTGCCAGAA
* * * * *
20486130 ATGTGGACAAGCCACCAGTGTTGTAAATAAACTACAAGAA
1 TTGTGGACAAGCCACCAGTATTGCAAATAAACTGCCAGAA
* * * * *
20486170 ATGTGGACAATCCACCAGTATTGCAAATAAACTGTCGGTA
1 TTGTGGACAAGCCACCAGTATTGCAAATAAACTGCCAGAA
*
20486210 TTGTGGACAAGCCACCAGTATTGCAAATAAACTGCCAGTA
1 TTGTGGACAAGCCACCAGTATTGCAAATAAACTGCCAGAA
* * ** * * *
20486250 TTGTGGATAAGCTATTAGTATTGTAAACAAGCTGCCAGTAA
1 TTGTGGACAAGCCACCAGTATTGCAAATAAACTGCCAG-AA
*
20486291 -TGTGAACAAGCCACC
1 TTGTGGACAAGCCACC
20486306 GGCGTTGCAG
Statistics
Matches: 146, Mismatches: 29, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
40 145 0.99
41 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (40 bp):
TTGTGGACAAGCCACCAGTATTGCAAATAAACTGCCAGAA
Found at i:20486289 original size:20 final size:20
Alignment explanation
Indices: 20486224--20486301 Score: 57
Period size: 20 Copynumber: 3.9 Consensus size: 20
20486214 GGACAAGCCA
* * *
20486224 CCAGTATTGCAAATAAACTG
1 CCAGTATTGTAAACAAGCTG
** * *
20486244 CCAGTATTGTGGATAAGCTA
1 CCAGTATTGTAAACAAGCTG
**
20486264 TTAGTATTGTAAACAAGCTG
1 CCAGTATTGTAAACAAGCTG
* *
20486284 CCAGTAATGTGAACAAGC
1 CCAGTATTGTAAACAAGC
20486302 CACCGGCGTT
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (20 bp):
CCAGTATTGTAAACAAGCTG
Found at i:20489931 original size:40 final size:40
Alignment explanation
Indices: 20489850--20489991 Score: 198
Period size: 40 Copynumber: 3.6 Consensus size: 40
20489840 CAACCAAGTA
** * *
20489850 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
20489889 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
20489929 CCTTCGGGACTTAGCCCGGTTATCGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
20489969 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
20489992 CATCCGAATA
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
39 13 0.14
40 80 0.86
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:20499743 original size:40 final size:40
Alignment explanation
Indices: 20499699--20499870 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
20499689 GGACTAAGAT
*
20499699 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
*
20499739 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * *
20499779 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
20499819 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
20499858 CCGAAGGCATTTG
1 CCGAAGGCATTTG
20499871 AACGAGGAGC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 34 0.29
40 81 0.69
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:20499784 original size:80 final size:79
Alignment explanation
Indices: 20499699--20499870 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
20499689 GGACTAAGAT
*
20499699 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
20499763 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
20499779 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
20499844 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
20499858 CCGAAGGCATTTG
1 CCGAAGGCATTTG
20499871 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:20499888 original size:79 final size:80
Alignment explanation
Indices: 20499726--20499903 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
20499716 AGATACAAAT
* * * *
20499726 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
20499791 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
20499806 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
20499870 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
20499885 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
20499904 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:20504219 original size:41 final size:41
Alignment explanation
Indices: 20504162--20504239 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
20504152 GTAAGACCTG
20504162 GATGTCGAACACAAAGGAACTAAAAGTACTAGTATTAACTT
1 GATGTCGAACACAAAGGAACTAAAAGTACTAGTATTAACTT
* *
20504203 GATGTCGAACCCAAAGGAACTAAAAGTACTATTATTA
1 GATGTCGAACACAAAGGAACTAAAAGTACTAGTATTA
20504240 GCTTTCTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (41 bp):
GATGTCGAACACAAAGGAACTAAAAGTACTAGTATTAACTT
Found at i:20512270 original size:28 final size:28
Alignment explanation
Indices: 20512205--20512436 Score: 231
Period size: 27 Copynumber: 8.4 Consensus size: 28
20512195 GAGATTGGCG
* * * *
20512205 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
20512234 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
20512262 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
** *
20512290 CTAAGTGTGCGA-AATGAATATGAT-GCA
1 CTAAGTGTGCGAGTTTGATTAT-ATAGCA
** ** ***
20512317 CTAAGTGTGCGA-ACTGACCATGCGGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
20512344 CTAAGTGTGCGAGTTTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
**
20512372 CTAAGTGTGCGA-TTTGATTACGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
20512399 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
20512426 CTGAGTGTGCG
1 CTAAGTGTGCG
20512437 GACTCAATAT
Statistics
Matches: 175, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
27 89 0.51
28 71 0.41
29 15 0.09
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:20512319 original size:27 final size:27
Alignment explanation
Indices: 20512230--20512436 Score: 236
Period size: 27 Copynumber: 7.6 Consensus size: 27
20512220 TAAATTGTAC
*
20512230 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-TTTGATTATGT
20512258 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGATTATGT
** *
20512286 AGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
** ** *
20512312 ATGCACTAAGTGTGCGAACTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* *
20512340 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGATTATGT
*
20512368 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* *
20512395 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
20512422 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
20512437 GACTCAATAT
Statistics
Matches: 157, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
26 1 0.01
27 91 0.58
28 65 0.41
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:20512427 original size:82 final size:81
Alignment explanation
Indices: 20512230--20512436 Score: 270
Period size: 82 Copynumber: 2.5 Consensus size: 81
20512220 TAAATTGTAC
*
20512230 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAG
1 AGCACTAAGTGTGCGAG-TTGATTATATAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAG
*
20512295 TGTGCGAAATGAATATG
65 TGTGCGAAATGAATACG
** ** ***
20512312 ATGCACTAAGTGTGCGAACTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAG
1 A-GCACTAAGTGTGCGAGTTGATTATATAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAG
** *
20512377 TGTGCGATTTGATTACG
65 TGTGCGAAATGAATACG
*
20512394 TAGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 -AGCACTAAGTGTGCGAGTTGATTATATAGCACTAAGTGTGCG
20512437 GACTCAATAT
Statistics
Matches: 103, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
82 87 0.84
83 16 0.16
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (81 bp):
AGCACTAAGTGTGCGAGTTGATTATATAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGT
GTGCGAAATGAATACG
Found at i:20520350 original size:27 final size:27
Alignment explanation
Indices: 20520319--20520496 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
20520309 TAAATTGTAC
20520319 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
20520346 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
** * *
20520372 ATGCACTAAGTGTGCGAACTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
20520400 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
20520428 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
20520455 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
20520482 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
20520497 GACTCAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 106 0.83
28 22 0.17
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:20520433 original size:82 final size:81
Alignment explanation
Indices: 20520320--20520470 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 81
20520310 AAATTGTACA
* *
20520320 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
20520384 TGCGAACTGACCATGCG
65 TGCGAACTGACCATGCG
** *
20520401 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
20520466 TGCGA
65 TGCGA
20520471 GTTGATTATA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.24
82 47 0.75
83 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAACTGACCATGCG
Found at i:20523904 original size:21 final size:21
Alignment explanation
Indices: 20523852--20523907 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
20523842 TCTCCAGTTT
*
20523852 CCACATGCCCATGTCACTTAC
1 CCACATGCCCGTGTCACTTAC
*
20523873 CCACACGCCCGTGTCACTTAC
1 CCACATGCCCGTGTCACTTAC
20523894 CCACATGCCCGTGT
1 CCACATGCCCGTGT
20523908 GTAAACCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.45, G:0.14, T:0.21
Consensus pattern (21 bp):
CCACATGCCCGTGTCACTTAC
Found at i:20532306 original size:42 final size:43
Alignment explanation
Indices: 20532251--20532356 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 43
20532241 AATTTGAGAT
* * *
20532251 TTACATATAAGACCATGTCTGAGACATTGGAATC-GTATTTGA
1 TTACATGTAAGACCATGTCTGAGACAATGGAATCAATATTTGA
* * * * * *
20532293 TTTCGTGTAAGACCCTATCTGGGACAATGGCATCAATATTTGA
1 TTACATGTAAGACCATGTCTGAGACAATGGAATCAATATTTGA
*
20532336 TTACATGTAAGACCACGTCTG
1 TTACATGTAAGACCATGTCTG
20532357 GGATGTTGGC
Statistics
Matches: 49, Mismatches: 14, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
42 26 0.53
43 23 0.47
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (43 bp):
TTACATGTAAGACCATGTCTGAGACAATGGAATCAATATTTGA
Found at i:20532357 original size:43 final size:43
Alignment explanation
Indices: 20532197--20532368 Score: 127
Period size: 43 Copynumber: 4.0 Consensus size: 43
20532187 ATAGGATTTC
* * * *
20532197 CAATATGTGATTTCATGTAAGATCACGTCTGAGG-CGTTGGCAT
1 CAATATTTGATTACATGTAAGACCACGTCTG-GGACATTGGCAT
* * * * * *
20532240 TAAT-TTGAGATTTACATATAAGACCATGTCTGAGACATTGGAAT
1 CAATATT-TGA-TTACATGTAAGACCACGTCTGGGACATTGGCAT
* * * * *
20532284 C-GTATTTGATTTCGTGTAAGACC-CTATCTGGGACAATGGCAT
1 CAATATTTGATTACATGTAAGACCAC-GTCTGGGACATTGGCAT
**
20532326 CAATATTTGATTACATGTAAGACCACGTCTGGGATGTTGGCAT
1 CAATATTTGATTACATGTAAGACCACGTCTGGGACATTGGCAT
20532369 TGTACGAGCT
Statistics
Matches: 94, Mismatches: 28, Indels: 14
0.69 0.21 0.10
Matches are distributed among these distances:
42 26 0.28
43 41 0.44
44 27 0.29
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (43 bp):
CAATATTTGATTACATGTAAGACCACGTCTGGGACATTGGCAT
Found at i:20533973 original size:22 final size:22
Alignment explanation
Indices: 20533948--20534000 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
20533938 AGGCTCACAC
20533948 GCCCGTGTGGTCCAAGAGACAT
1 GCCCGTGTGGTCCAAGAGACAT
*
20533970 GCCCGTGTGGTCCAAGGGACAT
1 GCCCGTGTGGTCCAAGAGACAT
*
20533992 GCTCGTGTG
1 GCCCGTGTG
20534001 ACCTTATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.26, G:0.36, T:0.21
Consensus pattern (22 bp):
GCCCGTGTGGTCCAAGAGACAT
Found at i:20538764 original size:40 final size:40
Alignment explanation
Indices: 20538625--20538767 Score: 155
Period size: 40 Copynumber: 3.6 Consensus size: 40
20538615 GCTACTCGTT
* * * *
20538625 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCAGATATAGTAACTAGCA
* * * *
20538665 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCAGATATAGTAACTAGCA
* * *
20538705 CAAATGCCTTC-GGATCTTAGTCCAGATATGGTCAGCTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCAGATATAGT-AACTAGCA
20538746 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
20538768 GGACATCATT
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 3 0.03
40 72 0.82
41 13 0.15
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCAGATATAGTAACTAGCA
Found at i:20543439 original size:13 final size:13
Alignment explanation
Indices: 20543421--20543445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20543411 CCAAGCACAC
20543421 GCTCGTGTCCCTA
1 GCTCGTGTCCCTA
20543434 GCTCGTGTCCCT
1 GCTCGTGTCCCT
20543446 CACACGGCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.40, G:0.24, T:0.32
Consensus pattern (13 bp):
GCTCGTGTCCCTA
Found at i:20554835 original size:292 final size:292
Alignment explanation
Indices: 20554311--20554895 Score: 1152
Period size: 292 Copynumber: 2.0 Consensus size: 292
20554301 TCCCACGCCC
20554311 GTGTCTCACCCCTGTTCTCCACCGTCAACGCCACCAGCTCCGACCACGATCCTTCGACGACCGGC
1 GTGTCTCACCCCTGTTCTCCACCGTCAACGCCACCAGCTCCGACCACGATCCTTCGACGACCGGC
20554376 CACCACCACCGTCGGTCACACCCTCTTTACCAAATCCTCCATCATTTTCATTATTTATTTTTATT
66 CACCACCACCGTCGGTCACACCCTCTTTACCAAATCCTCCATCATTTTCATTATTTATTTTTATT
20554441 TTTATATTTTTTTGTTATCATTGTTATTATTATTAGAAGTATTATGCCATGCCTTTTATTCATCT
131 TTTATATTTTTTTGTTATCATTGTTATTATTATTAGAAGTATTATGCCATGCCTTTTATTCATCT
20554506 TTTGTTCTTACTTTAGCCTTATTTTTTTATGTCATTGAGTTCATGTTGATGTTGCTAGTTAGTTT
196 TTTGTTCTTACTTTAGCCTTATTTTTTTATGTCATTGAGTTCATGTTGATGTTGCTAGTTAGTTT
20554571 AGGATCATTCTGTTAAGTCTGTTATTTTCTTA
261 AGGATCATTCTGTTAAGTCTGTTATTTTCTTA
* *
20554603 GTGTCTCCCCCCTGTTCTCCACCGTCAACGCCCCCAGCTCCGACCACGATCCTTCGACGACCGGC
1 GTGTCTCACCCCTGTTCTCCACCGTCAACGCCACCAGCTCCGACCACGATCCTTCGACGACCGGC
20554668 CACCACCACCGTCGGTCACACCCTCTTTACCAAATCCTCCATCATTTTCATTATTTATTTTTATT
66 CACCACCACCGTCGGTCACACCCTCTTTACCAAATCCTCCATCATTTTCATTATTTATTTTTATT
20554733 TTTATATTTTTTTGTTATCATTGTTATTATTATTAGAAGTATTATGCCATGCCTTTTATTCATCT
131 TTTATATTTTTTTGTTATCATTGTTATTATTATTAGAAGTATTATGCCATGCCTTTTATTCATCT
20554798 TTTGTTCTTACTTTAGCCTTATTTTTTTATGTCATTGAGTTCATGTTGATGTTGCTAGTTAGTTT
196 TTTGTTCTTACTTTAGCCTTATTTTTTTATGTCATTGAGTTCATGTTGATGTTGCTAGTTAGTTT
20554863 AGGATCATTCTGTTAAGTCTGTTATTTTCTTA
261 AGGATCATTCTGTTAAGTCTGTTATTTTCTTA
20554895 G
1 G
20554896 AAGCCCCATA
Statistics
Matches: 291, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
292 291 1.00
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.43
Consensus pattern (292 bp):
GTGTCTCACCCCTGTTCTCCACCGTCAACGCCACCAGCTCCGACCACGATCCTTCGACGACCGGC
CACCACCACCGTCGGTCACACCCTCTTTACCAAATCCTCCATCATTTTCATTATTTATTTTTATT
TTTATATTTTTTTGTTATCATTGTTATTATTATTAGAAGTATTATGCCATGCCTTTTATTCATCT
TTTGTTCTTACTTTAGCCTTATTTTTTTATGTCATTGAGTTCATGTTGATGTTGCTAGTTAGTTT
AGGATCATTCTGTTAAGTCTGTTATTTTCTTA
Found at i:20556193 original size:27 final size:27
Alignment explanation
Indices: 20556163--20556217 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
20556153 GTGCTTTGAG
20556163 CGATTCAACAGCATCGACGCCACTCTC
1 CGATTCAACAGCATCGACGCCACTCTC
** * * *
20556190 CGATTTGATAGCATTGAGGCCACTCTC
1 CGATTCAACAGCATCGACGCCACTCTC
20556217 C
1 C
20556218 AATAGATTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (27 bp):
CGATTCAACAGCATCGACGCCACTCTC
Found at i:20556319 original size:17 final size:17
Alignment explanation
Indices: 20556297--20556337 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
20556287 TTTGAGTCCC
20556297 TTTATTTTACTATTATT
1 TTTATTTTACTATTATT
* *
20556314 TTTATTTTTCTTTTATT
1 TTTATTTTACTATTATT
20556331 TTTATTT
1 TTTATTT
20556338 AAACTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTTACTATTATT
Found at i:20564236 original size:43 final size:43
Alignment explanation
Indices: 20564170--20564298 Score: 156
Period size: 43 Copynumber: 3.0 Consensus size: 43
20564160 AGCTCGTACA
* *
20564170 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCACTGTCCCAGACGTGGTCTTACATGAAATCACATATCG
* * * *
20564213 ATGCCACTGTCCCAGACAG-GGTCTTTCACGCAAATCACAAATTG
1 ATGCCACTGTCCCAGAC-GTGGTCTTACATG-AAATCACATATCG
20564257 ATGCCAAC-GTCCCAG-CGTGGTCTTACATGAAATCACATATCG
1 ATGCC-ACTGTCCCAGACGTGGTCTTACATGAAATCACATATCG
20564299 GAATCCTATG
Statistics
Matches: 72, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
42 12 0.17
43 35 0.49
44 23 0.32
45 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACGTGGTCTTACATGAAATCACATATCG
Found at i:20570559 original size:28 final size:29
Alignment explanation
Indices: 20570510--20570565 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
20570500 ATTCCTTCCC
20570510 AGATGCCATTTTTTTTAGGAACGTAGTGT
1 AGATGCCATTTTTTTTAGGAACGTAGTGT
*
20570539 AGATGCCA-TTTTTTTAGGAACTTAGTG
1 AGATGCCATTTTTTTTAGGAACGTAGTG
20570566 GCGCCACCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (29 bp):
AGATGCCATTTTTTTTAGGAACGTAGTGT
Found at i:20579332 original size:22 final size:22
Alignment explanation
Indices: 20579307--20579350 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
20579297 TTCGATGAAT
*
20579307 TTGACATAATTCCGGGAATGGA
1 TTGACATAATTCCGAGAATGGA
*
20579329 TTGACATAATTCTGAGAATGGA
1 TTGACATAATTCCGAGAATGGA
20579351 CTGGTTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (22 bp):
TTGACATAATTCCGAGAATGGA
Found at i:20583704 original size:43 final size:42
Alignment explanation
Indices: 20583639--20583789 Score: 162
Period size: 43 Copynumber: 3.5 Consensus size: 42
20583629 TTTCAGACAT
* *
20583639 CGTGTAAGACCGTGTCTGGGACACAGGCCTCGATTTAGATTTA
1 CGTGTAAGACCATGTCTGGGACACAGGCATCGATTT-GATTTA
* *
20583682 CGTATAAGACCATGTCTGGGACATC-GGCATCGTATCTGATTT-
1 CGTGTAAGACCATGTCTGGGACA-CAGGCATCG-ATTTGATTTA
* * *
20583724 CGTGTAAGACCCTGTCTGGGACAGAGGCATCGATATTGAATTA
1 CGTGTAAGACCATGTCTGGGACACAGGCATCGAT-TTGATTTA
* * *
20583767 CATGTAAGACCATATCCGGGACA
1 CGTGTAAGACCATGTCTGGGACA
20583790 TTGGCATTAT
Statistics
Matches: 90, Mismatches: 13, Indels: 10
0.80 0.12 0.09
Matches are distributed among these distances:
41 2 0.02
42 33 0.37
43 51 0.57
44 4 0.04
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTGGGACACAGGCATCGATTTGATTTA
Found at i:20583788 original size:85 final size:85
Alignment explanation
Indices: 20583638--20583796 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 85
20583628 GTTTCAGACA
* * * * * *
20583638 TCGTGTAAGACCGTGTCTGGGACACAGGCCTCGATTTAGATTTACGTATAAGACCATGTCTGGGA
1 TCGTGTAAGACCCTGTCTGGGACACAGGCATCGATTTAGAATTACATATAAGACCATATCCGGGA
20583703 CATCGGCATCGTATCTGATT
66 CATCGGCATCGTATCTGATT
* *
20583723 TCGTGTAAGACCCTGTCTGGGACAGAGGCATCGATATT-GAATTACATGTAAGACCATATCCGGG
1 TCGTGTAAGACCCTGTCTGGGACACAGGCATCGAT-TTAGAATTACATATAAGACCATATCCGGG
*
20583787 ACATTGGCAT
65 ACATCGGCAT
20583797 TATACTTGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
85 62 0.97
86 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (85 bp):
TCGTGTAAGACCCTGTCTGGGACACAGGCATCGATTTAGAATTACATATAAGACCATATCCGGGA
CATCGGCATCGTATCTGATT
Found at i:20585187 original size:24 final size:24
Alignment explanation
Indices: 20585158--20585228 Score: 115
Period size: 24 Copynumber: 2.9 Consensus size: 24
20585148 CTGTCAGGAA
20585158 AAGATTTAGGAGCTGATAAGGGAG
1 AAGATTTAGGAGCTGATAAGGGAG
* *
20585182 AGGATTTAGGAGCTGATAAAGGAG
1 AAGATTTAGGAGCTGATAAGGGAG
20585206 AAGATTTAGGAGCTGATCAAGGG
1 AAGATTTAGGAGCTGAT-AAGGG
20585229 GCAGGAGTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 38 0.90
25 4 0.10
ACGTcount: A:0.37, C:0.06, G:0.37, T:0.21
Consensus pattern (24 bp):
AAGATTTAGGAGCTGATAAGGGAG
Found at i:20585409 original size:24 final size:24
Alignment explanation
Indices: 20585381--20585455 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
20585371 AAAGGCTGTC
20585381 AGGAGAAGATTTAGGAGCTGATAA
1 AGGAGAAGATTTAGGAGCTGATAA
* *
20585405 GGGAGAGGATTTAGGAGCTGATAA
1 AGGAGAAGATTTAGGAGCTGATAA
20585429 AGGAGAAGATTTAGGAGCTGATCAA
1 AGGAGAAGATTTAGGAGCTGAT-AA
20585454 AG
1 AG
20585456 AACAAGAGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
24 42 0.91
25 4 0.09
ACGTcount: A:0.39, C:0.05, G:0.36, T:0.20
Consensus pattern (24 bp):
AGGAGAAGATTTAGGAGCTGATAA
Found at i:20587154 original size:33 final size:34
Alignment explanation
Indices: 20587077--20587157 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
20587067 TATAGGCCAT
*
20587077 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTC
* * **
20587111 AATGTAATCTGAA-AA-GGGCTCTGGCCCAGTATC
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGT-TC
20587144 ACTGTTATCTGAAT
1 ACTGTTATCTGAAT
20587158 GAGCTTAGGC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
32 13 0.34
33 14 0.37
34 11 0.29
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (34 bp):
ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTC
Found at i:20587295 original size:39 final size:39
Alignment explanation
Indices: 20587241--20587318 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
20587231 CACCCCTTCT
* *
20587241 TTAACCTTGTAGGTGGGCCTCGATGTGGATGTCTTGGAG
1 TTAACCTTGCAGGTGGGCCTCGATGTGGATGTCTGGGAG
* *
20587280 TTAACCTTGCAGGTGGGCCTTGATGTGGGTGTCTGGGAG
1 TTAACCTTGCAGGTGGGCCTCGATGTGGATGTCTGGGAG
20587319 CCGGAGGGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.14, C:0.15, G:0.38, T:0.32
Consensus pattern (39 bp):
TTAACCTTGCAGGTGGGCCTCGATGTGGATGTCTGGGAG
Found at i:20593314 original size:24 final size:24
Alignment explanation
Indices: 20593287--20593361 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
20593277 AAGGCTGTCA
20593287 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* *
20593311 GGAGAGGATTTAGGAGCTGATAAA
1 GGAGAAGATTTAGGAGCTGATAAG
20593335 GGAGAAGATTTAGGAGCTGATCAAG
1 GGAGAAGATTTAGGAGCTGAT-AAG
20593360 GG
1 GG
20593362 GCAGGAGTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
24 42 0.91
25 4 0.09
ACGTcount: A:0.36, C:0.05, G:0.39, T:0.20
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:20593497 original size:22 final size:21
Alignment explanation
Indices: 20593471--20593520 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
20593461 GACCATTCTC
20593471 CTCTTCTTTCTTTTCTCCTTTT
1 CTCTTCTTTCTTTT-TCCTTTT
**
20593493 CTCTTC-AACTTTTTCCTTTT
1 CTCTTCTTTCTTTTTCCTTTT
20593513 -TCTTCTTT
1 CTCTTCTTT
20593521 TCCTCCATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
19 5 0.22
20 7 0.30
21 5 0.22
22 6 0.26
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.66
Consensus pattern (21 bp):
CTCTTCTTTCTTTTTCCTTTT
Found at i:20596201 original size:27 final size:27
Alignment explanation
Indices: 20596148--20596201 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
20596138 TTTTATTCAT
** * *
20596148 ATAACCTTTATTAATTCATTTACTAAA
1 ATAACCTTTATTAAAACATATAATAAA
20596175 ATAACCTTTATTAAAACATATAATAAA
1 ATAACCTTTATTAAAACATATAATAAA
20596202 CATATAATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (27 bp):
ATAACCTTTATTAAAACATATAATAAA
Found at i:20601549 original size:48 final size:48
Alignment explanation
Indices: 20601486--20601755 Score: 231
Period size: 48 Copynumber: 5.8 Consensus size: 48
20601476 CACATGGTAA
** * *
20601486 GATGCCAATGCCATATCCCAGTTATGGTTTTACATGGGATCACATATT
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
* ** **
20601534 GATGCCAATGCCATATCCCAGACATGGTCTTACATTGGATCGTAGGTC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
* *** * *
20601582 GATGCCAATGCCATGTGTTAGGCATGGTTTTACATGGGATCACATATC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
* *
20601630 AATGCC---G--ATAGCCCAG-CTATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATATCCCAGAC-ATGGTCTTACATGGGATCACATATC
* * **
20601673 GATGCC---G--ATAGCCCAG-CTATGGTCTTACACGAAATCACATATC
1 GATGCCAATGCCATATCCCAGAC-ATGGTCTTACATGGGATCACATATC
* *
20601716 GATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGAT
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGAT
20601756 TGTACATAAC
Statistics
Matches: 179, Mismatches: 36, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
42 1 0.01
43 73 0.41
45 1 0.01
46 1 0.01
48 102 0.57
49 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (48 bp):
GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
Found at i:20601658 original size:43 final size:43
Alignment explanation
Indices: 20601605--20601721 Score: 189
Period size: 43 Copynumber: 2.7 Consensus size: 43
20601595 TGTGTTAGGC
* *
20601605 ATGGTTTTACATGGGATCACATATCAATGCCGATAGCCCAGCT
1 ATGGTCTTACATGGGATCACATATCGATGCCGATAGCCCAGCT
20601648 ATGGTCTTACATGGGATCACATATCGATGCCGATAGCCCAGCT
1 ATGGTCTTACATGGGATCACATATCGATGCCGATAGCCCAGCT
* **
20601691 ATGGTCTTACACGAAATCACATATCGATGCC
1 ATGGTCTTACATGGGATCACATATCGATGCC
20601722 AAAGCCATGT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (43 bp):
ATGGTCTTACATGGGATCACATATCGATGCCGATAGCCCAGCT
Found at i:20609362 original size:48 final size:48
Alignment explanation
Indices: 20609287--20609436 Score: 185
Period size: 48 Copynumber: 3.1 Consensus size: 48
20609277 CACATGGTAG
** *
20609287 GATGCCAATGCCATA-TCCCGGAGATGGTCTTATATGGGATCACATATC
1 GATGCCAATGCCA-AGTCCCACACATGGTCTTATATGGGATCACATATC
** **
20609335 GATGCCAATGCCAAGTCCCACACATGGTCTTATATGGGATCGTAGGTC
1 GATGCCAATGCCAAGTCCCACACATGGTCTTATATGGGATCACATATC
* * * *
20609383 GATGCCAATGTCATGTCCCATACATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCAAGTCCCACACATGGTCTTATATGGGATCACATATC
20609431 GATGCC
1 GATGCC
20609437 GATAGCCTAG
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
47 1 0.01
48 85 0.99
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.27
Consensus pattern (48 bp):
GATGCCAATGCCAAGTCCCACACATGGTCTTATATGGGATCACATATC
Found at i:20615563 original size:22 final size:22
Alignment explanation
Indices: 20615538--20615580 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20615528 TTTTCCTATT
20615538 TTGCTACCATTTTATTATTATG
1 TTGCTACCATTTTATTATTATG
* *
20615560 TTGCTACTATTTTATTGTTAT
1 TTGCTACCATTTTATTATTAT
20615581 TGTTTGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (22 bp):
TTGCTACCATTTTATTATTATG
Found at i:20615776 original size:18 final size:20
Alignment explanation
Indices: 20615755--20615795 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
20615745 GAAATATTTA
*
20615755 TTTTGATGT-TTTTA-ATAT
1 TTTTGATGTATTATATATAT
20615773 TTTTGATGTATTATATATAT
1 TTTTGATGTATTATATATAT
20615793 TTT
1 TTT
20615796 AAAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 4 0.20
20 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (20 bp):
TTTTGATGTATTATATATAT
Found at i:20615826 original size:12 final size:12
Alignment explanation
Indices: 20615796--20615828 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
20615786 TATATATTTT
20615796 AAAATT-ATATA
1 AAAATTAATATA
20615807 AAAA-TAATATA
1 AAAATTAATATA
20615818 AAAATTAATAT
1 AAAATTAATAT
20615829 GGGCATGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:20621568 original size:25 final size:25
Alignment explanation
Indices: 20621537--20621586 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
20621527 TAGTGCAAAG
20621537 AATTATTTATTTCTAACATTTCCAA
1 AATTATTTATTTCTAACATTTCCAA
*
20621562 AATTATTTGTTTCTAACATTTCCAA
1 AATTATTTATTTCTAACATTTCCAA
20621587 GTCAAGGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (25 bp):
AATTATTTATTTCTAACATTTCCAA
Found at i:20629505 original size:27 final size:25
Alignment explanation
Indices: 20629442--20629510 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
20629432 TGTACATATA
* *
20629442 TGCTTACACGAGCTATGAATAAGTG
1 TGCTTACACGAGCTGTGAATAAGGG
*
20629467 TGCTCACACGAGCTGTGAA-AATGGG
1 TGCTTACACGAGCTGTGAATAA-GGG
20629492 CCTGCTTACACGAGCTGTG
1 --TGCTTACACGAGCTGTG
20629511 GAGTATCCGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.05
25 19 0.51
27 16 0.43
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (25 bp):
TGCTTACACGAGCTGTGAATAAGGG
Found at i:20631645 original size:45 final size:45
Alignment explanation
Indices: 20631567--20631667 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 45
20631557 ATCTGTATTA
** * * * *
20631567 TTTTGTTGTGTACCAATAACCATAGGTAGATTCCATTTATAGTGT
1 TTTTGTTGTGTACCAATAACCATAGACAAATTCCATCTACAATGT
* *
20631612 TTTTGTTGTGTACCCATAACCATAGACAAATTCCATCTGCAATGT
1 TTTTGTTGTGTACCAATAACCATAGACAAATTCCATCTACAATGT
20631657 TTTTGTTGTGT
1 TTTTGTTGTGT
20631668 GTCCATAGCC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.43
Consensus pattern (45 bp):
TTTTGTTGTGTACCAATAACCATAGACAAATTCCATCTACAATGT
Found at i:20634904 original size:26 final size:26
Alignment explanation
Indices: 20634875--20635215 Score: 151
Period size: 26 Copynumber: 13.5 Consensus size: 26
20634865 GGGAAAAAAA
*
20634875 TTAAAATAAATAATATGTAAAATAAT
1 TTAAAATAAATAATATATAAAATAAT
* **
20634901 TTAAGATAAATAATATAT-AAATGAGC
1 TTAAAATAAATAATATATAAAAT-AAT
* * *
20634927 TTAAAATAAATATTATGTAAAAAGAAAT
1 TTAAAATAAATAATATAT-AAAA-TAAT
* * *
20634955 TTAAAATAAGTAATATACAAAA-CAT
1 TTAAAATAAATAATATATAAAATAAT
* *
20634980 CTTAAAA-AAATAA-ATGGT-ATATAA-
1 -TTAAAATAAATAATAT-ATAAAATAAT
* *
20635004 --AAAATAGATAATACATATAAA-AAT
1 TTAAAATAAATAATATATA-AAATAAT
* ** * *
20635028 TTGAAATTGATAATATATGAAAAAAAA
1 TTAAAATAAATAATATAT-AAAATAAT
** *
20635055 TT--AATGTA-AATA-ATAAAACAAT
1 TTAAAATAAATAATATATAAAATAAT
* * *
20635077 TTAAAATGAATAATACATAAAACAAGT
1 TTAAAATAAATAATATATAAAATAA-T
* **
20635104 TTAAAATAAATAATGTATAAAGCAAT
1 TTAAAATAAATAATATATAAAATAAT
* * *
20635130 TTAAAGTATATAGTATATAAAATAAT
1 TTAAAATAAATAATATATAAAATAAT
* *
20635156 TTAAAAT-AAT-ATATCTAAAAAAAT
1 TTAAAATAAATAATATATAAAATAAT
* * * *
20635180 TTAAAA-CAGT-TTA-ATAAAACAAT
1 TTAAAATAAATAATATATAAAATAAT
20635203 TTAAAATAAATAA
1 TTAAAATAAATAA
20635216 AAAAAATCAA
Statistics
Matches: 236, Mismatches: 55, Indels: 49
0.69 0.16 0.14
Matches are distributed among these distances:
21 4 0.02
22 14 0.06
23 19 0.08
24 38 0.16
25 22 0.09
26 90 0.38
27 31 0.13
28 18 0.08
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAATAAT
Found at i:20634984 original size:54 final size:52
Alignment explanation
Indices: 20634875--20634992 Score: 139
Period size: 54 Copynumber: 2.2 Consensus size: 52
20634865 GGGAAAAAAA
* * * **
20634875 TTAAAATAAATAATATGTAAAATAATTTAAGATAAATAATATATAAATGAGC
1 TTAAAATAAATAATATGTAAAAAAATTTAAAATAAATAATATACAAAACAGC
* * *
20634927 TTAAAATAAATATTATGTAAAAAGAAATTTAAAATAAGTAATATACAAAACATC
1 TTAAAATAAATAATATGT-AAAA-AAATTTAAAATAAATAATATACAAAACAGC
20634981 TTAAAA-AAATAA
1 TTAAAATAAATAA
20634993 ATGGTATATA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
52 17 0.31
53 9 0.16
54 29 0.53
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (52 bp):
TTAAAATAAATAATATGTAAAAAAATTTAAAATAAATAATATACAAAACAGC
Found at i:20637845 original size:54 final size:54
Alignment explanation
Indices: 20637763--20637875 Score: 208
Period size: 54 Copynumber: 2.1 Consensus size: 54
20637753 ATCTCATGCC
20637763 TGCATCCAATATATATTGCTTAGGTTGACCAATTAACTCTGATTCATATATAGT
1 TGCATCCAATATATATTGCTTAGGTTGACCAATTAACTCTGATTCATATATAGT
* *
20637817 TGCATCCAATATATATTGTTTAGGTTGACCAATTAACTCTGATTCCTATATAGT
1 TGCATCCAATATATATTGCTTAGGTTGACCAATTAACTCTGATTCATATATAGT
20637871 TGCAT
1 TGCAT
20637876 TTGTCAAGTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (54 bp):
TGCATCCAATATATATTGCTTAGGTTGACCAATTAACTCTGATTCATATATAGT
Found at i:20639768 original size:21 final size:21
Alignment explanation
Indices: 20639732--20639788 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
20639722 CAAAAAATAT
20639732 ATATAAATACATAAATTAAAAAA
1 ATAT-AATA-ATAAATTAAAAAA
* *
20639755 ATATAATAATAAATTTAAAAT
1 ATATAATAATAAATTAAAAAA
*
20639776 ATATAAAAATAAA
1 ATATAATAATAAA
20639789 AATATCGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 23 0.74
22 4 0.13
23 4 0.13
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
ATATAATAATAAATTAAAAAA
Found at i:20639977 original size:39 final size:39
Alignment explanation
Indices: 20639919--20639996 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
20639909 AAAAAGAAAA
*
20639919 CCTCCTCATCCCGTTCCTCTCTCCCCCACCATCCCCCTT
1 CCTCCTCATCCCGTCCCTCTCTCCCCCACCATCCCCCTT
20639958 CCTCCTCATCCCGTCCCTCTCTCCCCCACCATCCCCCTT
1 CCTCCTCATCCCGTCCCTCTCTCCCCCACCATCCCCCTT
20639997 TCTACCTCCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.08, C:0.63, G:0.03, T:0.27
Consensus pattern (39 bp):
CCTCCTCATCCCGTCCCTCTCTCCCCCACCATCCCCCTT
Found at i:20657643 original size:28 final size:27
Alignment explanation
Indices: 20657579--20657758 Score: 279
Period size: 28 Copynumber: 6.6 Consensus size: 27
20657569 ATATTAAGTC
* *
20657579 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
20657606 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
20657634 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
20657661 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
20657689 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
20657717 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
20657744 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20657759 GCACAATTTA
Statistics
Matches: 143, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
27 66 0.46
28 76 0.53
29 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:20657663 original size:55 final size:55
Alignment explanation
Indices: 20657579--20657758 Score: 299
Period size: 55 Copynumber: 3.3 Consensus size: 55
20657569 ATATTAAGTC
* * *
20657579 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
20657634 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
* *
20657689 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATATTCA-ATT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAATCATACT
20657744 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20657759 GCACAATTTA
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
55 92 0.77
56 27 0.23
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.28
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
Found at i:20657718 original size:83 final size:82
Alignment explanation
Indices: 20657579--20657758 Score: 297
Period size: 83 Copynumber: 2.2 Consensus size: 82
20657569 ATATTAAGTC
* * *
20657579 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACTCGCACACTTA
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
20657644 GTGCTACATAGTCAACT
66 GTGCTACATAGTCAACT
*
20657661 CGCACACTTAGTGCTACATAATCATACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 CGCACACTTAGTGCTACATAATCA-ACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
* *
20657726 AGTGCTACATATTCAATT
65 AGTGCTACATAGTCAACT
20657744 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20657759 GCACAATTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 22 0.24
83 69 0.76
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.28
Consensus pattern (82 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAACT
Found at i:20664189 original size:37 final size:37
Alignment explanation
Indices: 20664139--20664217 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
20664129 TTATTACGAA
* * *
20664139 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
20664176 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
20664213 GTCTT
1 GTCTT
20664218 TAGAGCTCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:20664463 original size:49 final size:49
Alignment explanation
Indices: 20664336--20664700 Score: 625
Period size: 49 Copynumber: 7.6 Consensus size: 49
20664326 CCCTTCGGGA
* * * * *
20664336 CTTATCACAT-T-TATGCACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
20664383 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20664430 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20664479 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20664528 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20664577 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20664626 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20664675 CTTATCAC--ATATATACACTTTCACAT
1 CTTATCACATATATATACACTTTCACAT
20664701 ATGGGTTTAA
Statistics
Matches: 305, Mismatches: 9, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
46 1 0.00
47 61 0.20
49 243 0.80
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:20667436 original size:38 final size:38
Alignment explanation
Indices: 20667380--20667520 Score: 122
Period size: 38 Copynumber: 3.7 Consensus size: 38
20667370 CAAATAAAAC
* * *
20667380 ATCAAAAGATCATAATAGTTGATCCAACCAAAACATCA
1 ATCAGAAGCTCATAATAGTTGATCCAACCAAAACACCA
* * * *
20667418 AGT-AGAAGCTCATGATAGTTGATCGAACCGAAACGCCA
1 A-TCAGAAGCTCATAATAGTTGATCCAACCAAAACACCA
* * * * **
20667456 ATCAGAAGCTCATAAGAGCTGATCGAACCGAAATGCCA
1 ATCAGAAGCTCATAATAGTTGATCCAACCAAAACACCA
* * *
20667494 AACAGAAGCTCATAAGAGCTGATCCAA
1 ATCAGAAGCTCATAATAGTTGATCCAA
20667521 TCGAAACGCC
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
37 1 0.01
38 86 0.98
39 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.18
Consensus pattern (38 bp):
ATCAGAAGCTCATAATAGTTGATCCAACCAAAACACCA
Found at i:20667526 original size:38 final size:38
Alignment explanation
Indices: 20667421--20667538 Score: 164
Period size: 38 Copynumber: 3.1 Consensus size: 38
20667411 AACATCAAGT
* * * *
20667421 AGAAGCTCATGATAGTTGATCGAACCGAAACGCCAATC
1 AGAAGCTCATAAGAGCTGATCGAACCGAAACGCCAAAC
*
20667459 AGAAGCTCATAAGAGCTGATCGAACCGAAATGCCAAAC
1 AGAAGCTCATAAGAGCTGATCGAACCGAAACGCCAAAC
* * *
20667497 AGAAGCTCATAAGAGCTGATCCAATCGAAACGCCAAAT
1 AGAAGCTCATAAGAGCTGATCGAACCGAAACGCCAAAC
20667535 AGAA
1 AGAA
20667539 AGTATAACAC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 71 1.00
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (38 bp):
AGAAGCTCATAAGAGCTGATCGAACCGAAACGCCAAAC
Found at i:20673806 original size:46 final size:46
Alignment explanation
Indices: 20673753--20673965 Score: 191
Period size: 46 Copynumber: 4.6 Consensus size: 46
20673743 AGACTTGTGT
* * *
20673753 GCCAGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGA
* *
20673799 GCCAGTGTAAGACCATGTTTGGGACATGGGATCAG---CATTGA-GACGA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCACATT-ATGA-GA
* ** *
20673845 GGGCTAGTGTAAGACATGTCTGGGACATGCATCAGTAACAGTATGAGA
1 --GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGA
* * ** **
20673893 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGTTA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGA
* *
20673939 GCCAGTGTCAGATATGTCTGGGACATG
1 GCCAGTGTAAGACATGTCTGGGACATG
20673966 TGTTGGCTAC
Statistics
Matches: 137, Mismatches: 20, Indels: 20
0.77 0.11 0.11
Matches are distributed among these distances:
45 6 0.04
46 82 0.60
47 25 0.18
48 19 0.14
49 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGA
Found at i:20674005 original size:44 final size:46
Alignment explanation
Indices: 20673753--20674015 Score: 167
Period size: 46 Copynumber: 5.7 Consensus size: 46
20673743 AGACTTGTGT
* * * ** * *
20673753 GCCAGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGTATCGGCCTCAAGACGTTA
* * * * ** ***
20673799 GCCAGTGTAAGACCATGTTTGGGACATGGGATCAGCATTGAGACGAGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GTATCGGCCTCAAGACGTTA
* * * * * **
20673847 GCTAGTGTAAGACATGTCTGGGACATGCATCAG--TAACAGTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGTATCGGCCTCA-AG-ACGTTA
* *
20673893 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGTTA
1 GCCAGTGTAAGACATGTCTGGGACATGTATCGGCCTCAAGACGTTA
* * * * *
20673939 GCCAGTGTCAGATATGTCTGGGACATGTGTTGG-CTACGAGACG-T-
1 GCCAGTGTAAGACATGTCTGGGACATGTATCGGCCT-CAAGACGTTA
*
20673983 GCTAGTGTAAGACATGTCTGGGACATGTATCGG
1 GCCAGTGTAAGACATGTCTGGGACATGTATCGG
20674016 TACGGTTACA
Statistics
Matches: 173, Mismatches: 37, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
44 29 0.17
45 5 0.03
46 90 0.52
47 27 0.16
48 22 0.13
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGTATCGGCCTCAAGACGTTA
Found at i:20674048 original size:136 final size:140
Alignment explanation
Indices: 20673750--20674055 Score: 356
Period size: 136 Copynumber: 2.2 Consensus size: 140
20673740 ATGAGACTTG
* **
20673750 TGTGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATGATAGCCAGTGTAAGACCAT
1 TGTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGATAGCCAGTGTAAGACCAT
* *
20673815 GTTTGGGACATGGGATCAGCATTGAGACGAGGGCTAGTGTAAGACATGTCTGGGACATGCATCAG
66 GTCTGGGACATGGGATCAGCATCGAGAC-AGGGCTAGTGTAAGACATGTCTGGGACATGCATCAG
*
20673880 TAACAGTATGA
130 TAACAGTATCA
* * * * *
20673891 -GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGTTAGCCAGTGTCAGA-TAT
1 TGTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGATAGCCAGTGTAAGACCAT
* ** * * *
20673954 GTCTGGGACATGTG-TTGGC-TACGAGAC-GTGCTAGTGTAAGACATGTCTGGGACATGTATCGG
66 GTCTGGGACATGGGATCAGCAT-CGAGACAGGGCTAGTGTAAGACATGTCTGGGACATGCATCAG
*
20674016 T-ACGGT-TACA
130 TAACAGTAT-CA
* *
20674026 TGTGTCAGTGTAAGACCTGTCTGGGACATG
1 TGTGCCAGTGTAAGACATGTCTGGGACATG
20674056 GTTTCGACAC
Statistics
Matches: 141, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
134 1 0.01
135 5 0.04
136 59 0.42
137 1 0.01
138 8 0.06
139 14 0.10
140 53 0.38
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.25
Consensus pattern (140 bp):
TGTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGATAGCCAGTGTAAGACCAT
GTCTGGGACATGGGATCAGCATCGAGACAGGGCTAGTGTAAGACATGTCTGGGACATGCATCAGT
AACAGTATCA
Found at i:20682950 original size:12 final size:12
Alignment explanation
Indices: 20682933--20682958 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20682923 ATGTAAGTGA
20682933 TCTTGATGATTT
1 TCTTGATGATTT
20682945 TCTTGATGATTT
1 TCTTGATGATTT
20682957 TC
1 TC
20682959 ACATTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:20683769 original size:46 final size:46
Alignment explanation
Indices: 20683714--20683873 Score: 157
Period size: 46 Copynumber: 3.5 Consensus size: 46
20683704 CAAGGCTAGT
* *
20683714 GTAAAACATGTCTGGGACATGCTTCATCCATATTATGAGTGCCAGA
1 GTAAGACATGTCTGGGACATGCTTCACCCATATTATGAGTGCCAGA
* * * * *
20683760 GTAAGACATGTCTGGGACATGCATCGGCCTC-GA-CA-GAGATAGCCAGT
1 GTAAGACATGTCTGGGACATGCTTC-ACC-CATATTATGAG-T-GCCAGA
* *
20683807 GTAAGACGTGTTTGGGACATGCTTCACCCATATTATGAGTGCCAGA
1 GTAAGACATGTCTGGGACATGCTTCACCCATATTATGAGTGCCAGA
*
20683853 GCTTA-ACATGTCTGGGACATG
1 G-TAAGACATGTCTGGGACATG
20683874 GCATCGACAT
Statistics
Matches: 89, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
45 4 0.04
46 48 0.54
47 33 0.37
48 4 0.04
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (46 bp):
GTAAGACATGTCTGGGACATGCTTCACCCATATTATGAGTGCCAGA
Found at i:20683823 original size:93 final size:92
Alignment explanation
Indices: 20683660--20683916 Score: 295
Period size: 93 Copynumber: 2.8 Consensus size: 92
20683650 GTGATTTGTA
* *
20683660 TGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCAGACAAGGCTAGTGTAAAACATGT
1 TGCCAGAGTAAGA-CATGTCTGGGACATGGCATCGGCATCCAGACAAGGCCAGTGTAAAACATGT
*
20683725 CTGGGACATGCTTCATCCATATTATGAG
65 CTGGGACATGCTTCACCCATATTATGAG
* * * *
20683753 TGCCAGAGTAAGACATGTCTGGGACAT-GCATCGGCCTCGACAGAGATA-GCCAGTGTAAGACGT
1 TGCCAGAGTAAGACATGTCTGGGACATGGCATCGGCATC--CAGACA-AGGCCAGTGTAAAACAT
*
20683816 GTTTGGGACATGCTTCACCCATATTATGAG
63 GTCTGGGACATGCTTCACCCATATTATGAG
* * * * * * * *
20683846 TGCCAGAGCTTA-ACATGTCTGGGACATGGCATCGACATCTAGATGAGGGCTAGTGTAAGACGTG
1 TGCCAGAG-TAAGACATGTCTGGGACATGGCATCGGCATCCAGA-CAAGGCCAGTGTAAAACATG
20683910 TCTGGGA
64 TCTGGGA
20683917 TACGCATCGG
Statistics
Matches: 142, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
91 10 0.07
92 17 0.12
93 103 0.73
94 12 0.08
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (92 bp):
TGCCAGAGTAAGACATGTCTGGGACATGGCATCGGCATCCAGACAAGGCCAGTGTAAAACATGTC
TGGGACATGCTTCACCCATATTATGAG
Found at i:20690523 original size:12 final size:12
Alignment explanation
Indices: 20690506--20690531 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20690496 ATGTAAGTGA
20690506 TCTTGATGATTT
1 TCTTGATGATTT
20690518 TCTTGATGATTT
1 TCTTGATGATTT
20690530 TC
1 TC
20690532 ACATTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:20697159 original size:26 final size:26
Alignment explanation
Indices: 20697130--20697180 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
20697120 CATGTTTAAT
20697130 TACAATCA-TACATCACATAAGGGCAA
1 TACAATCATTACATCACAT-AGGGCAA
* *
20697156 TACAGTCATTTCATCACATAGGGCA
1 TACAATCATTACATCACATAGGGCA
20697181 TAACAACCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (26 bp):
TACAATCATTACATCACATAGGGCAA
Found at i:20697191 original size:26 final size:27
Alignment explanation
Indices: 20697140--20697192 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
20697130 TACAATCATA
**
20697140 CATCACATAAGGGCAATACAGTCATTT
1 CATCACATAAGGGCAATACAACCATTT
20697167 CATCACAT-AGGGC-ATAACAACCATTT
1 CATCACATAAGGGCAAT-ACAACCATTT
20697193 TTATCAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 2 0.09
26 13 0.57
27 8 0.35
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.25
Consensus pattern (27 bp):
CATCACATAAGGGCAATACAACCATTT
Found at i:20705184 original size:47 final size:47
Alignment explanation
Indices: 20705131--20705541 Score: 750
Period size: 47 Copynumber: 8.7 Consensus size: 47
20705121 TTAGGATTCT
20705131 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
20705178 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
20705225 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
20705272 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
20705319 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
20705366 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
20705413 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
20705460 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
20705507 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
20705542 TCCCGAAGGG
Statistics
Matches: 354, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 354 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:20705716 original size:37 final size:37
Alignment explanation
Indices: 20705660--20705738 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
20705650 CCGAGCTCTA
* * *
20705660 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
20705697 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
20705734 AAGAC
1 AAGAC
20705739 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:20710400 original size:20 final size:20
Alignment explanation
Indices: 20710375--20710415 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
20710365 AGGGGCATAC
20710375 GCCCGTGTGACCTAGGACAT
1 GCCCGTGTGACCTAGGACAT
* *
20710395 GCCCGTGTGGCTTAGGACAT
1 GCCCGTGTGACCTAGGACAT
20710415 G
1 G
20710416 GCCATGGGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.27, G:0.34, T:0.22
Consensus pattern (20 bp):
GCCCGTGTGACCTAGGACAT
Found at i:20719432 original size:46 final size:46
Alignment explanation
Indices: 20719377--20719552 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 46
20719367 TATTTGGGCA
20719377 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * * * * * *
20719423 TCTGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCGA-ACG
20719470 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
20719516 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20719553 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
45 1 0.01
46 69 0.65
47 35 0.33
48 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:20719483 original size:93 final size:93
Alignment explanation
Indices: 20719373--20719545 Score: 319
Period size: 93 Copynumber: 1.9 Consensus size: 93
20719363 CGGATATTTG
* *
20719373 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCTGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
20719438 TTGAGTCCGAGTTCGTGAAATGTAACTA
66 TTGAGTCCGAGTTCGTGAAATGTAACTA
*
20719466 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
20719531 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
20719546 CTTATGGGCG
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAAATGTAACTA
Found at i:20722149 original size:54 final size:54
Alignment explanation
Indices: 20722067--20722179 Score: 208
Period size: 54 Copynumber: 2.1 Consensus size: 54
20722057 ATCTCATGCC
20722067 TGCATCCAATATATATTGCTTAGGTTGACCAATTAACTCTGATTCATATATAGT
1 TGCATCCAATATATATTGCTTAGGTTGACCAATTAACTCTGATTCATATATAGT
* *
20722121 TGCATCCAATATATATTGTTTAGGTTGACCAATTAACTCTGATTCCTATATAGT
1 TGCATCCAATATATATTGCTTAGGTTGACCAATTAACTCTGATTCATATATAGT
20722175 TGCAT
1 TGCAT
20722180 ATGTCAAGTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (54 bp):
TGCATCCAATATATATTGCTTAGGTTGACCAATTAACTCTGATTCATATATAGT
Found at i:20724037 original size:21 final size:21
Alignment explanation
Indices: 20724001--20724057 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
20723991 CAAAAAATAT
20724001 ATATAAATACATAAATTCAAAAA
1 ATAT-AATA-ATAAATTCAAAAA
* **
20724024 ATATAATAATAAATTTAAAGT
1 ATATAATAATAAATTCAAAAA
*
20724045 ATATAAAAATAAA
1 ATATAATAATAAA
20724058 AATATCGTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 22 0.73
22 4 0.13
23 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (21 bp):
ATATAATAATAAATTCAAAAA
Found at i:20724089 original size:9 final size:9
Alignment explanation
Indices: 20724075--20724113 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
20724065 TAGACAAGAA
20724075 ATAAAATAT
1 ATAAAATAT
20724084 ATAAAAT-T
1 ATAAAATAT
*
20724092 TTAAAATAT
1 ATAAAATAT
*
20724101 ATAAAATAA
1 ATAAAATAT
20724110 ATAA
1 ATAA
20724114 TATTTTCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAAAATAT
Found at i:20725583 original size:93 final size:93
Alignment explanation
Indices: 20725471--20725641 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
20725461 GCCCATAAGT
* *
20725471 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
20725536 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
20725564 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
20725629 CGAGTTCGGATGC
66 CGAGTTCGGATGC
20725642 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:20725638 original size:46 final size:46
Alignment explanation
Indices: 20725463--20725638 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
20725453 TGTAACCCGC
* * *
20725463 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
20725509 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
20725559 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
20725602 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
20725639 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:20731613 original size:33 final size:33
Alignment explanation
Indices: 20731571--20731640 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
20731561 CGACACGTAG
* *
20731571 TCAAATTGGCCTCAAATGTATCACGTACCTTGT
1 TCAAATTGGCCACAAATGTATCACGTACCTCGT
20731604 TCAAATTGGCCACAAATGTATCACGTACCTCGT
1 TCAAATTGGCCACAAATGTATCACGTACCTCGT
20731637 TCAA
1 TCAA
20731641 TTGATTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (33 bp):
TCAAATTGGCCACAAATGTATCACGTACCTCGT
Found at i:20751657 original size:40 final size:40
Alignment explanation
Indices: 20751613--20751795 Score: 278
Period size: 40 Copynumber: 4.6 Consensus size: 40
20751603 GCCACTAGCT
* * *
20751613 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCA
20751653 CAAATGCCTTCGGGACTTAGCCCGG-TATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCA
*
20751692 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCA
* * * *
20751732 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGAA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCA
*
20751772 CGAATGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
20751796 AAATTAGCCA
Statistics
Matches: 134, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 37 0.28
40 97 0.72
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCA
Found at i:20751711 original size:79 final size:80
Alignment explanation
Indices: 20751613--20751795 Score: 278
Period size: 79 Copynumber: 2.3 Consensus size: 80
20751603 GCCACTAGCT
* * * *
20751613 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAACGCCTTCGGGACTTAGCCCGG
*
20751678 -TATAATAACTCGCA
66 ATATAATAACTCGAA
*
20751692 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGCACAAACGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAACGCCTTCGGGACTTAGCCCGG
* *
20751757 ATATAGTAGCTCGAA
66 ATATAATAACTCGAA
*
20751772 CGAATGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
20751796 AAATTAGCCA
Statistics
Matches: 94, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 60 0.64
80 34 0.36
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAACGCCTTCGGGACTTAGCCCGG
ATATAATAACTCGAA
Found at i:20751818 original size:40 final size:38
Alignment explanation
Indices: 20751613--20751835 Score: 189
Period size: 40 Copynumber: 5.6 Consensus size: 38
20751603 GCCACTAGCT
** *
20751613 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGAAT-TAG-AACTCGCA
* * *
20751653 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GAATTAGAACTCGCA
*
20751692 CAAATGCCTTCGGGACTTAGCCCGGATATA-ATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGAAT-TAGA-A-CTCGCA
* * * *
20751732 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGAA
1 CAAATGCCTTCGGGACTTAGCCCGAAT-TAG-AACTCGCA
* * * *
20751772 CGAATGCCTTCGGGACTTAGCCCGAAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCG-AATTAG-AACTCGCA
*
20751812 CAAATG-CTCTCGAGACTTAGCCCG
1 CAAATGCCT-TCGGGACTTAGCCCG
20751836 GTTATCATCC
Statistics
Matches: 154, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
38 4 0.03
39 34 0.22
40 111 0.72
41 4 0.03
42 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (38 bp):
CAAATGCCTTCGGGACTTAGCCCGAATTAGAACTCGCA
Found at i:20755184 original size:46 final size:46
Alignment explanation
Indices: 20755114--20755213 Score: 173
Period size: 46 Copynumber: 2.2 Consensus size: 46
20755104 GAAAGTCACA
*
20755114 TAGCCATAAAATTTGTTTCGTTTAAATCTAGACTCAATAAGGAATC
1 TAGCCATAAAATTTGTTTCCTTTAAATCTAGACTCAATAAGGAATC
*
20755160 TAGCCATAAAATTTTTTTCCTTTAAATCTAGACTCAATAAGGAATC
1 TAGCCATAAAATTTGTTTCCTTTAAATCTAGACTCAATAAGGAATC
*
20755206 TAGGCATA
1 TAGCCATA
20755214 TAAACTATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (46 bp):
TAGCCATAAAATTTGTTTCCTTTAAATCTAGACTCAATAAGGAATC
Found at i:20762228 original size:19 final size:21
Alignment explanation
Indices: 20762189--20762228 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20762179 ACTATATTTC
*
20762189 TTAATTATTTTTGTACAATGT
1 TTAATGATTTTTGTACAATGT
20762210 TTAATGATTTTT-T-CAATGT
1 TTAATGATTTTTGTACAATGT
20762229 CAGAACAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.57
Consensus pattern (21 bp):
TTAATGATTTTTGTACAATGT
Found at i:20763747 original size:85 final size:85
Alignment explanation
Indices: 20763604--20763782 Score: 358
Period size: 85 Copynumber: 2.1 Consensus size: 85
20763594 GGCCGGCCAT
20763604 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
20763669 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
20763689 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
20763754 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
20763774 GAGCATGGG
1 GAGCATGGG
20763783 CAATAAAATA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:20766013 original size:47 final size:47
Alignment explanation
Indices: 20765962--20766184 Score: 331
Period size: 47 Copynumber: 4.7 Consensus size: 47
20765952 TTAGGATTCT
* * *
20765962 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
20766009 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
20766056 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
20766103 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
20766150 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
20766185 TCCCGAAGGG
Statistics
Matches: 162, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 1 0.01
47 161 0.99
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:20766037 original size:25 final size:25
Alignment explanation
Indices: 20766009--20766087 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
20765999 CTAATGGCCG
20766009 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ****
20766034 ATGTGAT-AAGGCCTAA-TG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
20766056 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
20766081 ATGTGAT
1 ATGTGAT
20766088 AAGGCCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 7 0.20
25 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:20766359 original size:37 final size:37
Alignment explanation
Indices: 20766303--20766381 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
20766293 CCGAGCTCTA
* * *
20766303 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
20766340 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
20766377 AAGAC
1 AAGAC
20766382 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:20769482 original size:13 final size:13
Alignment explanation
Indices: 20769464--20769490 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20769454 CCAACCAATG
20769464 AATTGGAGCTAGC
1 AATTGGAGCTAGC
20769477 AATTGGAGCTAGC
1 AATTGGAGCTAGC
20769490 A
1 A
20769491 GCGGTGGTTT
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:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (13 bp):
AATTGGAGCTAGC
Found at i:20772680 original size:28 final size:29
Alignment explanation
Indices: 20772638--20772703 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 29
20772628 AGCATGACTG
* *
20772638 TAAATGTGATTTGGGCCTAGT-GGCCATA
1 TAAATGTGATTTGGGCCTAATGGGCCACA
*
20772666 TGAATGTGATTTGGGCCTAATGGGCCACA
1 TAAATGTGATTTGGGCCTAATGGGCCACA
20772695 TAAATGTGA
1 TAAATGTGA
20772704 AAGAACCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 19 0.58
29 14 0.42
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (29 bp):
TAAATGTGATTTGGGCCTAATGGGCCACA
Found at i:20772740 original size:28 final size:28
Alignment explanation
Indices: 20772643--20772751 Score: 87
Period size: 28 Copynumber: 3.9 Consensus size: 28
20772633 GACTGTAAAT
* *
20772643 GTGATTTGGGCCTAGT-GGCCATATGAAT
1 GTGA-TTGGGCCTAATGGGCCATATGAAA
*
20772671 GTGATTTGGGCCTAATGGGCCACAT-AAA
1 GTGA-TTGGGCCTAATGGGCCATATGAAA
** **
20772699 TGTGAAAGAACCTAATGGGCCATATGAAA
1 -GTGATTGGGCCTAATGGGCCATATGAAA
* * *
20772728 GAGATTGGGCCTAGTGGGCTATAT
1 GTGATTGGGCCTAATGGGCCATAT
20772752 ATGTATGTGG
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
28 49 0.78
29 14 0.22
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (28 bp):
GTGATTGGGCCTAATGGGCCATATGAAA
Found at i:20781270 original size:42 final size:43
Alignment explanation
Indices: 20781182--20781283 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 43
20781172 CCGACGTCCC
* * *
20781182 AGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCT
1 AGACGTGGTCTTACACGAAATCAAATATCGATGCCACTATCCT
*
20781225 AGACAG-GGTTTTACACGAAATCAAATAT-GATGCCAAC-ATCCT
1 AGAC-GTGGTCTTACACGAAATCAAATATCGATGCC-ACTATCCT
20781267 AGACGTGGTCTTACACG
1 AGACGTGGTCTTACACG
20781284 TAAAACATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
41 1 0.02
42 24 0.47
43 25 0.49
44 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (43 bp):
AGACGTGGTCTTACACGAAATCAAATATCGATGCCACTATCCT
Found at i:20797002 original size:24 final size:23
Alignment explanation
Indices: 20796957--20797030 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 23
20796947 GATCAATTGA
20796957 AATTGAAAGAAAAAGTACAAGAAAAAG
1 AATTG-AA-AAAAAG-A-AAGAAAAAG
20796984 AGATTGAAAAAAAGAAAGATAAGAA-
1 A-ATTGAAAAAAAGAAAGA-AA-AAG
*
20797009 AATTGAAAAAAA-AAGGAAAAAG
1 AATTGAAAAAAAGAAAGAAAAAG
20797031 TGAGAGAGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 4 0.10
24 15 0.36
25 4 0.10
26 8 0.19
27 3 0.07
28 4 0.10
ACGTcount: A:0.69, C:0.01, G:0.19, T:0.11
Consensus pattern (23 bp):
AATTGAAAAAAAGAAAGAAAAAG
Found at i:20799322 original size:34 final size:34
Alignment explanation
Indices: 20799239--20799324 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 34
20799229 CAGTATCGAG
* *
20799239 CAGTCTGGGCCTAAGCCCATATCAGTAACAATAT
1 CAGTGTGGGCCTTAGCCCATATCAGTAACAATAT
* * *
20799273 CAGTGT-GGCCTTAGCCTATCA-CAGTAGCAGTAT
1 CAGTGTGGGCCTTAGCCCAT-ATCAGTAACAATAT
20799306 CAGTGTGGGCCTTAGCCCA
1 CAGTGTGGGCCTTAGCCCA
20799325 AATTAGTATA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
33 27 0.61
34 17 0.39
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (34 bp):
CAGTGTGGGCCTTAGCCCATATCAGTAACAATAT
Found at i:20803089 original size:19 final size:18
Alignment explanation
Indices: 20803060--20803099 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
20803050 TTAAGTTAAG
* *
20803060 TGTTTAATGTGTTTTATA
1 TGTTTAATGTGATTAATA
20803078 TGTTTAAATGTGATTAATA
1 TGTTT-AATGTGATTAATA
20803097 TGT
1 TGT
20803100 CTATTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (18 bp):
TGTTTAATGTGATTAATA
Found at i:20803266 original size:22 final size:22
Alignment explanation
Indices: 20803203--20803278 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 22
20803193 ATTTCGGTTA
*
20803203 CATTCAAAGGGAAGCATTATTC-TT
1 CATT-AAAGGG-AGCATTA-TCATC
* *
20803227 CATTAAAAGGAACTATTATCATC
1 CATTAAAGGGAGC-ATTATCATC
20803250 CATTAAAGGGAGCATTATACATC
1 CATTAAAGGGAGCATTAT-CATC
20803273 C-TTAAA
1 CATTAAA
20803279 TTTGCCAGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 14 0.32
23 26 0.59
24 4 0.09
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.30
Consensus pattern (22 bp):
CATTAAAGGGAGCATTATCATC
Found at i:20806171 original size:15 final size:16
Alignment explanation
Indices: 20806144--20806205 Score: 76
Period size: 15 Copynumber: 4.0 Consensus size: 16
20806134 CAAGGAAACC
20806144 GAATAAAAGAAATCCAA
1 GAAT-AAAGAAATCCAA
*
20806161 G-ATAGAGAAATCC-A
1 GAATAAAGAAATCCAA
20806175 GAATAAAGAAATCC-A
1 GAATAAAGAAATCCAA
*
20806190 GAATAAAGAAACCCAA
1 GAATAAAGAAATCCAA
20806206 TATACGATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
14 2 0.05
15 34 0.85
16 3 0.08
17 1 0.03
ACGTcount: A:0.60, C:0.15, G:0.15, T:0.11
Consensus pattern (16 bp):
GAATAAAGAAATCCAA
Found at i:20811276 original size:27 final size:27
Alignment explanation
Indices: 20811246--20811297 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
20811236 GACCAAAATA
20811246 CCCCTAAAGGGTAAAATGACT-ATTTTG
1 CCCCTAAAGGGT-AAATGACTGATTTTG
**
20811273 CCCCTCGAGGGTAAATGACTGATTT
1 CCCCTAAAGGGTAAATGACTGATTT
20811298 GTCTGTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (27 bp):
CCCCTAAAGGGTAAATGACTGATTTTG
Found at i:20815297 original size:47 final size:47
Alignment explanation
Indices: 20815228--20815326 Score: 189
Period size: 47 Copynumber: 2.1 Consensus size: 47
20815218 GTGTGTATAC
20815228 GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAAT
*
20815275 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAAT
20815322 GTGAA
1 GTGAA
20815327 CGTGATGGAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAAT
Done.