Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 186 of 189
Found at i:55556766 original size:31 final size:30
Alignment explanation
Indices: 55556735--55556792 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
55556725 CCACTCAACT
55556735 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
55556765 TTTTGCATAATTACATTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
55556793 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:55559272 original size:41 final size:41
Alignment explanation
Indices: 55559117--55559262 Score: 226
Period size: 41 Copynumber: 3.6 Consensus size: 41
55559107 TGATTCAGTA
55559117 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCA-TTAAGCCTGCTAGACATATAGTCTGAAATGTAT
55559158 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
* *
55559199 CACCGGCATTAAGCCTGCTAGACTTAAAGTCTG-AAT-TACTT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA--T
55559240 CACCGGCATTAAGCCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGAC
55559263 GTAACGTCTG
Statistics
Matches: 100, Mismatches: 2, Indels: 6
0.93 0.02 0.06
Matches are distributed among these distances:
39 2 0.02
40 5 0.05
41 93 0.93
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
Found at i:55559278 original size:41 final size:40
Alignment explanation
Indices: 55559117--55559283 Score: 182
Period size: 41 Copynumber: 4.0 Consensus size: 40
55559107 TGATTCAGTA
55559117 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTA--T
1 CACCGGCA-TTAAGCCTGCTAGACATA-AGTCTG-AAT-TACTT
55559158 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA--T
1 CACCGGCATTAAGCCTGCTAGACATA-AGTCTG-AAT-TACTT
*
55559199 CACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTACTT
1 CACCGGCATTAAGCCTGCTAGACAT-AAGTCTGAATTACTT
* *
55559240 CACCGGCATTAAGCCTGCTAGACGTAACGTCTGTATTACATT
1 CACCGGCATTAAGCCTGCTAGACATAA-GTCTGAATTAC-TT
55559282 CA
1 CA
55559284 ATCACTTTAT
Statistics
Matches: 117, Mismatches: 3, Indels: 11
0.89 0.02 0.08
Matches are distributed among these distances:
39 2 0.02
40 7 0.06
41 103 0.88
42 5 0.04
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACATAAGTCTGAATTACTT
Found at i:55561886 original size:7 final size:7
Alignment explanation
Indices: 55561876--55561942 Score: 64
Period size: 7 Copynumber: 9.7 Consensus size: 7
55561866 CATAAATTTG
55561876 AAACTCA
1 AAACTCA
55561883 AAACTCA
1 AAACTCA
* **
55561890 AAAATTG
1 AAACTCA
55561897 AAACTCA
1 AAACTCA
* *
55561904 AAACCCT
1 AAACTCA
55561911 AAACTCA
1 AAACTCA
*
55561918 AAACTCC
1 AAACTCA
*
55561925 AAATTCA
1 AAACTCA
55561932 AAAC-CA
1 AAACTCA
55561938 AAACT
1 AAACT
55561943 TGAAGCCCTA
Statistics
Matches: 45, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
6 6 0.13
7 39 0.87
ACGTcount: A:0.55, C:0.27, G:0.01, T:0.16
Consensus pattern (7 bp):
AAACTCA
Found at i:55561921 original size:21 final size:20
Alignment explanation
Indices: 55561897--55561975 Score: 59
Period size: 21 Copynumber: 3.9 Consensus size: 20
55561887 TCAAAAATTG
55561897 AAACTCAAAACCCTAAACTCA
1 AAACTCAAAACCCTAAAC-CA
* ** *
55561918 AAACTCCAAATTCAAAACCA
1 AAACTCAAAACCCTAAACCA
** * *
55561938 AAACTTGAAGCCCTAAACCTT
1 AAACTCAAAACCCTAAACC-A
*
55561959 AAACCCAAAACCCTAAA
1 AAACTCAAAACCCTAAA
55561976 ATCAACCCAA
Statistics
Matches: 42, Mismatches: 15, Indels: 2
0.71 0.25 0.03
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.51, C:0.32, G:0.03, T:0.15
Consensus pattern (20 bp):
AAACTCAAAACCCTAAACCA
Found at i:55561932 original size:28 final size:28
Alignment explanation
Indices: 55561883--55561936 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
55561873 TTGAAACTCA
**
55561883 AAACTCAAAAATTGAAACTCAAAACCCT
1 AAACTCAAAAATCCAAACTCAAAACCCT
* *
55561911 AAACTCAAAACTCCAAATTCAAAACC
1 AAACTCAAAAATCCAAACTCAAAACC
55561937 AAAACTTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.54, C:0.28, G:0.02, T:0.17
Consensus pattern (28 bp):
AAACTCAAAAATCCAAACTCAAAACCCT
Found at i:55561956 original size:48 final size:48
Alignment explanation
Indices: 55561880--55561990 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 48
55561870 AATTTGAAAC
* * * *
55561880 TCAAAACTCAAAAATTGAAACTCAAAACCCTAAACTCAAAACTCC-AAAT
1 TCAAAAC-CAAAACTTGAAACCCAAAACCCTAAACCCAAAAC-CCTAAAA
* * *
55561929 TCAAAACCAAAACTTGAAGCCCTAAACCTTAAACCCAAAACCCTAAAA
1 TCAAAACCAAAACTTGAAACCCAAAACCCTAAACCCAAAACCCTAAAA
*
55561977 TC-AACCCAAAACTT
1 TCAAAACCAAAACTT
55561991 TAGATCGTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
47 13 0.25
48 33 0.62
49 7 0.13
ACGTcount: A:0.50, C:0.30, G:0.03, T:0.17
Consensus pattern (48 bp):
TCAAAACCAAAACTTGAAACCCAAAACCCTAAACCCAAAACCCTAAAA
Found at i:55569023 original size:10 final size:11
Alignment explanation
Indices: 55568994--55569026 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
55568984 ATTGTGAACA
55568994 TACCGTTTCAT
1 TACCGTTTCAT
*
55569005 TACCTTTTC-T
1 TACCGTTTCAT
55569015 TACCGTTTCAT
1 TACCGTTTCAT
55569026 T
1 T
55569027 TGTATAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.15, C:0.27, G:0.06, T:0.52
Consensus pattern (11 bp):
TACCGTTTCAT
Found at i:55569496 original size:34 final size:34
Alignment explanation
Indices: 55569453--55569536 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 34
55569443 AGTCCAACCA
55569453 AACACACCAGATGCTCACACAAGTCAATCCCTCC
1 AACACACCAGATGCTCACACAAGTCAATCCCTCC
* *
55569487 AACACACCAGATGCTCACACGAGTTAATCCCTCC
1 AACACACCAGATGCTCACACAAGTCAATCCCTCC
55569521 AACACACCA-ATGCTCA
1 AACACACCAGATGCTCA
55569537 TAAGAGCTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 7 0.15
34 41 0.85
ACGTcount: A:0.36, C:0.39, G:0.10, T:0.15
Consensus pattern (34 bp):
AACACACCAGATGCTCACACAAGTCAATCCCTCC
Found at i:55569548 original size:33 final size:33
Alignment explanation
Indices: 55569453--55569548 Score: 124
Period size: 34 Copynumber: 2.8 Consensus size: 33
55569443 AGTCCAACCA
55569453 AACACACCAGATGCTCACACA-AGTCAATCCCTCC
1 AACACACCAGATGCTCACA-AGAGT-AATCCCTCC
*
55569487 AACACACCAGATGCTCACACGAGTTAATCCCTCC
1 AACACACCAGATGCTCACAAGAG-TAATCCCTCC
*
55569521 AACACACCA-ATGCTCATAAGAGCTAATC
1 AACACACCAGATGCTCACAAGAG-TAATC
55569549 TAACCAATAC
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
33 16 0.29
34 39 0.70
35 1 0.02
ACGTcount: A:0.36, C:0.36, G:0.10, T:0.17
Consensus pattern (33 bp):
AACACACCAGATGCTCACAAGAGTAATCCCTCC
Found at i:55572478 original size:3 final size:3
Alignment explanation
Indices: 55572470--55572511 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
55572460 TTCATTTCAT
55572470 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55572512 ACACTTATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:55577788 original size:27 final size:27
Alignment explanation
Indices: 55577758--55577811 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
55577748 TTTGCATGTA
55577758 AGGATTTTTAGGTTCTGTTTATTTGGT
1 AGGATTTTTAGGTTCTGTTTATTTGGT
55577785 AGGATTTTTAGGTTCTGTTTATTTGGT
1 AGGATTTTTAGGTTCTGTTTATTTGGT
55577812 CACCTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.04, G:0.26, T:0.56
Consensus pattern (27 bp):
AGGATTTTTAGGTTCTGTTTATTTGGT
Found at i:55585162 original size:19 final size:20
Alignment explanation
Indices: 55585124--55585164 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
55585114 TTAGTTTTTT
55585124 TATAAAAATACATAAGATTA
1 TATAAAAATACATAAGATTA
55585144 TATAAAATATACA-AA-ATTA
1 TATAAAA-ATACATAAGATTA
55585163 TA
1 TA
55585165 CCTTTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 9 0.45
21 5 0.25
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (20 bp):
TATAAAAATACATAAGATTA
Found at i:55588138 original size:42 final size:42
Alignment explanation
Indices: 55588040--55588140 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
55588030 AGACACATGC
* * * *
55588040 TCGTGTCTCAGGCCGTGTAACAATCGAAATAGGGACACACGG
1 TCGTGTCCCAGCCCGTGTAACAATCGAAATAGAGACACACAG
*** * * *
55588082 TCGTGTCGTTGCCCGTGTAACATTCGAACTAGAGACATACAG
1 TCGTGTCCCAGCCCGTGTAACAATCGAAATAGAGACACACAG
55588124 TCGTGTCCCAGCCCGTG
1 TCGTGTCCCAGCCCGTG
55588141 CCTCTGCCCG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.23
Consensus pattern (42 bp):
TCGTGTCCCAGCCCGTGTAACAATCGAAATAGAGACACACAG
Found at i:55593343 original size:21 final size:21
Alignment explanation
Indices: 55593318--55593376 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
55593308 CTTCAGTGGG
* *
55593318 ATCGCGGTATCCCCTTTTGGT
1 ATCGCGATATCCCCTTTAGGT
*
55593339 ATCGCGATATCCTCTTTAGGT
1 ATCGCGATATCCCCTTTAGGT
55593360 ATCGCGATATCCACCTT
1 ATCGCGATATCC-CCTT
55593377 CTAAGGAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
21 30 0.91
22 3 0.09
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.36
Consensus pattern (21 bp):
ATCGCGATATCCCCTTTAGGT
Found at i:55600187 original size:21 final size:21
Alignment explanation
Indices: 55600163--55600202 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55600153 TATGTCGAAA
* *
55600163 TTTAGTCTCTTTATTTTTATT
1 TTTAGTCTATTTACTTTTATT
55600184 TTTAGTCTATTTACTTTTA
1 TTTAGTCTATTTACTTTTA
55600203 AGATTTACAT
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:0.17, C:0.10, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTAGTCTATTTACTTTTATT
Found at i:55618483 original size:27 final size:27
Alignment explanation
Indices: 55618448--55618515 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
55618438 ATAACGTAAA
* *
55618448 GCAT-ACAGTCATTTTATAATATAGGG
1 GCATAACAGTCATTTTACAACATAGGG
* * * *
55618474 GCATAACAGTTATTTTACCACGTGGGG
1 GCATAACAGTCATTTTACAACATAGGG
55618501 GCATAACAGTCATTT
1 GCATAACAGTCATTT
55618516 CATATCAGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 4 0.12
27 30 0.88
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (27 bp):
GCATAACAGTCATTTTACAACATAGGG
Found at i:55638133 original size:46 final size:46
Alignment explanation
Indices: 55638059--55638156 Score: 135
Period size: 46 Copynumber: 2.1 Consensus size: 46
55638049 ATCCATGGAA
* *
55638059 AGTTATGAAAAGTAGGTATGGTGCTTCAGTGAAGAAAA-TCATACTG
1 AGTTATGAAAAGCAGGTATGGTACTTCAGTGAAGAAAACT-ATACTG
* * *
55638105 AGTTGTGAAAAGCAGGTATGGTATTTCAGTGAAGGAAACTATACTG
1 AGTTATGAAAAGCAGGTATGGTACTTCAGTGAAGAAAACTATACTG
55638151 AGTTAT
1 AGTTAT
55638157 AGCATTGTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.27, T:0.30
Consensus pattern (46 bp):
AGTTATGAAAAGCAGGTATGGTACTTCAGTGAAGAAAACTATACTG
Found at i:55642889 original size:13 final size:13
Alignment explanation
Indices: 55642871--55642913 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
55642861 AGTGGCATAG
55642871 AAATAATATAAAT
1 AAATAATATAAAT
*
55642884 AAATAAAATAAAT
1 AAATAATATAAAT
*
55642897 ATACATAATAAAAAT
1 A-A-ATAATATAAAT
55642912 AA
1 AA
55642914 TCACATACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 13 0.52
14 2 0.08
15 10 0.40
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (13 bp):
AAATAATATAAAT
Found at i:55642913 original size:19 final size:19
Alignment explanation
Indices: 55642871--55642909 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
55642861 AGTGGCATAG
55642871 AAAT-AATATAAATAAATA
1 AAATAAATATAAATAAATA
*
55642889 AAATAAATATACAT-AATA
1 AAATAAATATAAATAAATA
55642907 AAA
1 AAA
55642910 ATAATCACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATAAATATAAATAAATA
Found at i:55643413 original size:22 final size:21
Alignment explanation
Indices: 55643388--55643462 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 21
55643378 ACATATATTT
*
55643388 AAAAAATAATAATTAAATATGAA
1 AAAAAATAATAATTAAAAAT--A
55643411 AAAGAAATAATAA--AAAAATA
1 AAA-AAATAATAATTAAAAATA
*
55643431 AAAAACTAATTAATTAAAAATA
1 AAAAAATAA-TAATTAAAAATA
55643453 AAGAAAATAA
1 AA-AAAATAA
55643463 AAAAAGCTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
19 5 0.11
20 7 0.16
22 14 0.32
23 9 0.20
24 9 0.20
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAAATAATAATTAAAAATA
Found at i:55643466 original size:40 final size:42
Alignment explanation
Indices: 55643387--55643467 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
55643377 TACATATATT
*
55643387 TAAAAAATAATAATTAAATATGAAAAAGAAATAATAAAAAAA
1 TAAAAAATAATAATTAAAAATGAAAAAGAAATAATAAAAAAA
*
55643429 TAAAAAACTAATTAATTAAAAAT-AAAGA-AAATAA-AAAAA
1 TAAAAAA-TAA-TAATTAAAAATGAAAAAGAAATAATAAAAA
55643468 GCTAATTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 5 0.14
42 13 0.37
43 7 0.20
44 10 0.29
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (42 bp):
TAAAAAATAATAATTAAAAATGAAAAAGAAATAATAAAAAAA
Found at i:55644013 original size:19 final size:19
Alignment explanation
Indices: 55643989--55644044 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 19
55643979 AATCACATCT
55643989 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
55644008 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
55644029 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
55644045 CTCGAAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.44
21 18 0.56
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:55644026 original size:21 final size:21
Alignment explanation
Indices: 55644000--55644043 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
55643990 CTAAGATTAC
55644000 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
55644021 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
55644042 AT
1 AT
55644044 CCTCGAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:55645895 original size:54 final size:54
Alignment explanation
Indices: 55645836--55645952 Score: 145
Period size: 49 Copynumber: 2.2 Consensus size: 54
55645826 GTAATCTAAT
* *
55645836 TATTTATTTTCAATACATAAGATAATATTTATTTTAAAACAAATCC-AAAAATAA
1 TATTTATTTTC-ATACATAAGATAATATTTACTTTAAAACAAACCCAAAAAATAA
* * *
55645890 TATTTA--TT--TACATTAGATAATATTTACTTTGAAGCAAACCCAAAAAATAA
1 TATTTATTTTCATACATAAGATAATATTTACTTTAAAACAAACCCAAAAAATAA
55645940 TATTTATTTTCAT
1 TATTTATTTTCAT
55645953 TTAAAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
49 28 0.53
50 14 0.26
52 4 0.08
54 7 0.13
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.41
Consensus pattern (54 bp):
TATTTATTTTCATACATAAGATAATATTTACTTTAAAACAAACCCAAAAAATAA
Found at i:55645913 original size:49 final size:50
Alignment explanation
Indices: 55645849--55645953 Score: 149
Period size: 49 Copynumber: 2.1 Consensus size: 50
55645839 TTATTTTCAA
* * *
55645849 TACATAAGATAATATTTATTTTAAAACAAATCC-AAAAATAATATTTATT
1 TACATTAGATAATATTTACTTTAAAACAAACCCAAAAAATAATATTTATT
* *
55645898 TACATTAGATAATATTTACTTTGAAGCAAACCCAAAAAATAATATTTATT
1 TACATTAGATAATATTTACTTTAAAACAAACCCAAAAAATAATATTTATT
*
55645948 TTCATT
1 TACATT
55645954 TAAAAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
49 28 0.57
50 21 0.43
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (50 bp):
TACATTAGATAATATTTACTTTAAAACAAACCCAAAAAATAATATTTATT
Found at i:55648384 original size:16 final size:16
Alignment explanation
Indices: 55648363--55648401 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
55648353 AATTAAATTG
55648363 TAATTTTTTATTTTAA
1 TAATTTTTTATTTTAA
* *
55648379 TAA-TTTATATTTTTA
1 TAATTTTTTATTTTAA
55648394 TAATTTTT
1 TAATTTTT
55648402 AAAAGATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TAATTTTTTATTTTAA
Found at i:55649964 original size:26 final size:25
Alignment explanation
Indices: 55649872--55649999 Score: 89
Period size: 26 Copynumber: 4.9 Consensus size: 25
55649862 TTTTAAAGAA
* *
55649872 AAAATTATAGGAAACTTTTAAAATGATTT
1 AAAATTAT--GAAAATTTTAAAA--AATT
*
55649901 AAAATTAT-AAAATTATTTAAAAATT
1 AAAATTATGAAAATT-TTAAAAAATT
* *
55649926 CAATATT-TTAAAATTTTTAAAAAATT
1 -AAAATTATGAAAA-TTTTAAAAAATT
**
55649952 AAAATTATGAAAATTCAAAAAATATT
1 AAAATTATGAAAATTTTAAAAA-ATT
* *
55649978 AAAATTATTAAAAATTTAAAAA
1 AAAATTATGAAAATTTTAAAAA
55650000 CATATAATTT
Statistics
Matches: 80, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
25 16 0.20
26 49 0.61
27 7 0.09
29 8 0.10
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (25 bp):
AAAATTATGAAAATTTTAAAAAATT
Found at i:55649996 original size:17 final size:17
Alignment explanation
Indices: 55649888--55649998 Score: 70
Period size: 17 Copynumber: 6.4 Consensus size: 17
55649878 ATAGGAAACT
* *
55649888 TTTAAAATGATTTAAAA
1 TTTAAAATTATTAAAAA
55649905 TTATAAAATTATTTAAAAA
1 TT-TAAAATTA-TTAAAAA
* * *
55649924 TTCAATATT-TTAAAATT
1 TTTAAAATTATTAAAA-A
*
55649941 TTTAAAA-AATT-AAAA
1 TTTAAAATTATTAAAAA
55649956 TTATGAAAATTCA--AAAAA
1 TT-T-AAAATT-ATTAAAAA
55649974 TATTAAAATTATTAAAAA
1 T-TTAAAATTATTAAAAA
55649992 TTTAAAA
1 TTTAAAA
55649999 ACATATAATT
Statistics
Matches: 72, Mismatches: 10, Indels: 24
0.68 0.09 0.23
Matches are distributed among these distances:
15 2 0.03
16 11 0.15
17 25 0.35
18 24 0.33
19 10 0.14
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTAAAATTATTAAAAA
Found at i:55650052 original size:37 final size:37
Alignment explanation
Indices: 55649952--55650053 Score: 93
Period size: 37 Copynumber: 2.8 Consensus size: 37
55649942 TTAAAAAATT
* *
55649952 AAAATTATGAAAAT-TCAAAAAATATTAAAATTATTA
1 AAAATTATAAAAATATAAAAAAATATTAAAATTATTA
* **** *
55649988 AAAATT-TAAAAACATATAATTTTTATTAAAATTGTTA
1 AAAATTATAAAAATATA-AAAAAATATTAAAATTATTA
55650025 AAAATTAT-AAAATATAAAAAGAATATTAA
1 AAAATTATAAAAATATAAAAA-AATATTAA
55650054 TTATATTTTC
Statistics
Matches: 49, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
35 5 0.10
36 9 0.18
37 34 0.69
38 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (37 bp):
AAAATTATAAAAATATAAAAAAATATTAAAATTATTA
Found at i:55654905 original size:25 final size:24
Alignment explanation
Indices: 55654860--55654911 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
55654850 GTCATTAGGG
* *
55654860 TTACCGATTCCAGCTCTTATGAGC
1 TTACCGATACCAGCTCATATGAGC
55654884 TTACCGATACTCAGCTCATATGAGC
1 TTACCGATAC-CAGCTCATATGAGC
55654909 TTA
1 TTA
55654912 TCGTTATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (24 bp):
TTACCGATACCAGCTCATATGAGC
Found at i:55654942 original size:25 final size:25
Alignment explanation
Indices: 55654914--55654962 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
55654904 TGAGCTTATC
55654914 GTTATTCAACTCGAAAGAACTTACT
1 GTTATTCAACTCGAAAGAACTTACT
* * *
55654939 GTTATTCAGCTCGGAAGAGCTTAC
1 GTTATTCAACTCGAAAGAACTTAC
55654963 CGTTTATAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (25 bp):
GTTATTCAACTCGAAAGAACTTACT
Found at i:55655191 original size:31 final size:31
Alignment explanation
Indices: 55655132--55655191 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
55655122 TATACATGAA
*
55655132 ATATATAGAAATGATGGTACATGATATATTG
1 ATATATAGAAATGATGATACATGATATATTG
* *
55655163 ATATATTGAAATGGATGATATATG-TATAT
1 ATATATAGAAAT-GATGATACATGATATAT
55655192 GATGAAACGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (31 bp):
ATATATAGAAATGATGATACATGATATATTG
Found at i:55658552 original size:29 final size:30
Alignment explanation
Indices: 55658510--55658581 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 30
55658500 AAAATAATAT
*
55658510 TTACATTTTGGCCCC-CACTATTTT-TAAAA
1 TTACATTTTAGCCCCTCACT-TTTTCTAAAA
55658539 TTACATTTTAGCCCCTCACTTTTTCTAAAA
1 TTACATTTTAGCCCCTCACTTTTTCTAAAA
55658569 TTACATTTTAGCC
1 TTACATTTTAGCC
55658582 TCGGGAGTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
29 18 0.45
30 22 0.55
ACGTcount: A:0.26, C:0.25, G:0.06, T:0.43
Consensus pattern (30 bp):
TTACATTTTAGCCCCTCACTTTTTCTAAAA
Found at i:55659184 original size:32 final size:32
Alignment explanation
Indices: 55659121--55659222 Score: 102
Period size: 32 Copynumber: 3.2 Consensus size: 32
55659111 GAAAAGAAAT
* * *
55659121 AAAG-AAAAAGAAAAAACAAGAG-AAAGGAGA
1 AAAGAAAAAAGAAGAGAGAAGAGAAAAGGAGA
*
55659151 AAAGAAAAAAGAAGAGAGGAGAGAAAAGGAGA
1 AAAGAAAAAAGAAGAGAGAAGAGAAAAGGAGA
* *
55659183 AACGAAGAAAGAAGAGAGAAGGAGAAGAGAGGA-A
1 AAAGAAAAAAGAAGAGAGAA-GAGAA-A-AGGAGA
55659217 AAAGAA
1 AAAGAA
55659223 CACTAGCGGC
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
30 4 0.07
31 14 0.24
32 25 0.42
33 5 0.08
34 7 0.12
35 4 0.07
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (32 bp):
AAAGAAAAAAGAAGAGAGAAGAGAAAAGGAGA
Found at i:55659198 original size:25 final size:25
Alignment explanation
Indices: 55659147--55659221 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 25
55659137 CAAGAGAAAG
* * *
55659147 GAGAAAA-GAAAAAAGAAGAGAGGA
1 GAGAAAAGGAGAAAAGAAGAAAGAA
*
55659171 GAGAAAAGGAGAAACGAAGAAAGAA
1 GAGAAAAGGAGAAAAGAAGAAAGAA
* * *
55659196 GAGAGAAGGAGAAGAGAGGAAA-AA
1 GAGAAAAGGAGAAAAGAAGAAAGAA
55659220 GA
1 GA
55659222 ACACTAGCGG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 11 0.26
25 31 0.74
ACGTcount: A:0.63, C:0.01, G:0.36, T:0.00
Consensus pattern (25 bp):
GAGAAAAGGAGAAAAGAAGAAAGAA
Found at i:55662019 original size:29 final size:29
Alignment explanation
Indices: 55661967--55662048 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
55661957 GCTTACAAAA
*
55661967 AAAAAATTCAAAATAATT-TTTA-TTTTTT
1 AAAAAATTCAAAA-AATTATATATTTTTTT
55661995 ATAAAAATTCAAAAAATTATATATTTTTTT
1 A-AAAAATTCAAAAAATTATATATTTTTTT
*
55662025 AAAAAATTCTAAATAATATATATA
1 AAAAAATTC-AAAAAAT-TATATA
55662049 GAAAGTTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
28 5 0.11
29 23 0.49
30 13 0.28
31 6 0.13
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAAAATTCAAAAAATTATATATTTTTTT
Found at i:55662099 original size:40 final size:38
Alignment explanation
Indices: 55662021--55662099 Score: 88
Period size: 40 Copynumber: 2.0 Consensus size: 38
55662011 TTATATATTT
**
55662021 TTTTAAAAAATTCTAAATAATATATATAGAAAGTTAAA
1 TTTTAAAAAATTCTAAATAATATATATAGAAACCTAAA
* *
55662059 TTTTAAAAAATTTCTAAAATAATA-ATTTTGAAGACCTAAA
1 TTTTAAAAAA-TTCT-AAATAATATATATAGAA-ACCTAAA
55662099 T
1 T
55662100 AAGTTAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
38 10 0.29
39 10 0.29
40 14 0.41
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (38 bp):
TTTTAAAAAATTCTAAATAATATATATAGAAACCTAAA
Found at i:55663499 original size:27 final size:25
Alignment explanation
Indices: 55663454--55663529 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 25
55663444 AGAAAATCTC
* *
55663454 AAAAAATATAAAATCATAAAAAAATTTAG
1 AAAAAATTTAAAA--ATAAAAAAA--TAA
*
55663483 AAAAATTTTAAAAATAACAAAAATAA
1 AAAAAATTTAAAAATAA-AAAAATAA
55663509 AAAAAATTTAAAAACTAAAAA
1 AAAAAATTTAAAAA-TAAAAA
55663530 TTTTTTTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
26 18 0.44
27 7 0.17
28 5 0.12
29 11 0.27
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.22
Consensus pattern (25 bp):
AAAAAATTTAAAAATAAAAAAATAA
Found at i:55667618 original size:22 final size:23
Alignment explanation
Indices: 55667592--55667644 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
55667582 TAAATAATAA
55667592 AATATTAAAAATATTTT-TAATT
1 AATATTAAAAATATTTTATAATT
* *
55667614 AATATT-TATATATTTTATAATT
1 AATATTAAAAATATTTTATAATT
55667636 AA-ATTAAAA
1 AATATTAAAA
55667645 TTTTAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATATTAAAAATATTTTATAATT
Found at i:55670569 original size:31 final size:32
Alignment explanation
Indices: 55670527--55670586 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
55670517 CTTAACAACC
*
55670527 TAGTGACTTAAATG-AAAACTTTTGAATAAAT
1 TAGTAACTTAAATGAAAAACTTTTGAATAAAT
*
55670558 TAGTAACTTAAATGAAAAATTTTTGAATA
1 TAGTAACTTAAATGAAAAACTTTTGAATA
55670587 GCTCAATGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (32 bp):
TAGTAACTTAAATGAAAAACTTTTGAATAAAT
Found at i:55671613 original size:6 final size:6
Alignment explanation
Indices: 55671604--55671640 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
55671594 GCTCAGTCGA
55671604 AAGCTC AAGCTC AAGCTC AAGCTC AAGCTC AAGCTC A
1 AAGCTC AAGCTC AAGCTC AAGCTC AAGCTC AAGCTC A
55671641 TGCCCAACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
AAGCTC
Found at i:55671655 original size:18 final size:18
Alignment explanation
Indices: 55671604--55671647 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
55671594 GCTCAGTCGA
*
55671604 AAGCTCAAGCTCAAGCTC
1 AAGCCCAAGCTCAAGCTC
*
55671622 AAGCTCAAGCTCAAGCTC
1 AAGCCCAAGCTCAAGCTC
*
55671640 ATGCCCAA
1 AAGCCCAA
55671648 CTCCAAGCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.34, C:0.34, G:0.16, T:0.16
Consensus pattern (18 bp):
AAGCCCAAGCTCAAGCTC
Found at i:55676499 original size:24 final size:22
Alignment explanation
Indices: 55676468--55676523 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
55676458 CAAGAGAATC
*
55676468 ATAAATAAACA-TATTTATTAGAT
1 ATAAATAAACAGCATTTA-TA-AT
55676491 ATAAAATAATACAGCATTTATAAT
1 AT-AAATAA-ACAGCATTTATAAT
55676515 ATAAATAAA
1 ATAAATAAA
55676524 TGAATTGAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 1 0.03
23 8 0.28
24 10 0.34
25 5 0.17
26 5 0.17
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (22 bp):
ATAAATAAACAGCATTTATAAT
Found at i:55677662 original size:18 final size:19
Alignment explanation
Indices: 55677634--55677683 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 19
55677624 TACTTTAATG
* *
55677634 TAAATTAAAAAATGTT-GAC
1 TAAA-TAAAAAATGTTCCAA
55677653 TAAAT-AAAAAT-TTCCAA
1 TAAATAAAAAATGTTCCAA
55677670 TAAATAAAAAATGT
1 TAAATAAAAAATGT
55677684 ATAAAATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 2 0.08
17 12 0.46
18 7 0.27
19 5 0.19
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (19 bp):
TAAATAAAAAATGTTCCAA
Found at i:55684243 original size:106 final size:105
Alignment explanation
Indices: 55683929--55684352 Score: 609
Period size: 106 Copynumber: 4.0 Consensus size: 105
55683919 TGGATTGAGA
* * * * ** *
55683929 TTTAAGAGGATATTTGGCTATTTAGTCAAATGAGAAATTGAAACCCAGCATGTTAGGGCACGTTT
1 TTTAA-AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCACATTT
*
55683994 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAATT
65 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
* *
55684035 TTTAATAGGATATTTGGCTATTTGGTTGAACGAAAAAATCGAAACCCAGCACATTAGGGCACATT
1 TTTAA-AGGATATTTGGCTATTTGGTCGAACG-AGAAATCGAAACCCAGCACATTAGGGCACATT
*
55684100 TTCTCGAATTTCCAAAAGCAAAATATTGTCC-TACTTTGAAAT
64 TTCTCGAATTTCCAAACGCAAAATATTG-CCTTACTTTGAAAT
* * *
55684142 TTTAGAAGGATATTTGGCTATTTGGTCGAACGAGAAATTGAAACCCAGCACATTAGGACACGTTT
1 TTTA-AAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCACATTT
*
55684207 TCTCGAATTTCCAAACGCAAAATATTGCCTTCCTTTGAAAT
65 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
55684248 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCACATTT
1 TTT-AAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCACATTT
* * *
55684313 TATCGAATTTCCAAACACAAAATATTGTCTTA-TTTAGAAA
65 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTT-GAAA
55684353 AAAAAATTCT
Statistics
Matches: 286, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
105 5 0.02
106 184 0.64
107 94 0.33
108 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (105 bp):
TTTAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCACATTTT
CTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
Found at i:55684423 original size:20 final size:21
Alignment explanation
Indices: 55684380--55684424 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
55684370 GTATGATGTT
*
55684380 AATATGCATAATGGAACAATA
1 AATATGCATAATGAAACAATA
55684401 AATATG-ATAATGTAAACAA-A
1 AATATGCATAATG-AAACAATA
55684421 AATA
1 AATA
55684425 ATATGAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.58, C:0.07, G:0.11, T:0.24
Consensus pattern (21 bp):
AATATGCATAATGAAACAATA
Found at i:55684778 original size:42 final size:40
Alignment explanation
Indices: 55684694--55684780 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 40
55684684 TTTAAAATGT
* * *
55684694 AATATATATAAGTGTGTATATAAATTTATGAAACATAGAA
1 AATATATAAAAGTGTGTATATAAATTTATGAAAAATAAAA
*
55684734 AATATATAAAAGTATGTGTATATATATTTAT-AAAAATTAAAA
1 AATATATAAAAG--TGTGTATATAAATTTATGAAAAA-TAAAA
55684776 AATAT
1 AATAT
55684781 GTTCGTACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
40 11 0.28
41 4 0.10
42 25 0.62
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (40 bp):
AATATATAAAAGTGTGTATATAAATTTATGAAAAATAAAA
Found at i:55686624 original size:42 final size:42
Alignment explanation
Indices: 55686532--55686650 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
55686522 GTTTTAATTC
* * *
55686532 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCT
1 GCTCCACTACAACTTTAGGGAGATAAGACT--TATCTTCAACCT
* * **
55686576 GGTCCACTACAACTTTAGGGAGATAAGGCTTATCTTCAGTCT
1 GCTCCACTACAACTTTAGGGAGATAAGACTTATCTTCAACCT
* *
55686618 GCTCCACTTCAACTCTAGGGAGATAAGACTTAT
1 GCTCCACTACAACTTTAGGGAGATAAGACTTAT
55686651 TATGGTGCGA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 39 0.61
44 25 0.39
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (42 bp):
GCTCCACTACAACTTTAGGGAGATAAGACTTATCTTCAACCT
Found at i:55686722 original size:176 final size:179
Alignment explanation
Indices: 55686433--55686778 Score: 416
Period size: 176 Copynumber: 1.9 Consensus size: 179
55686423 TAGTGGTTTT
55686433 AGTCTGCTCCACTACAACATCAGGGAGATAAGACTTATCATGGTGGATTTAATCCAACTTACTAC
1 AGTCTGCTCCACTACAACATCAGGGAGATAAGACTTATCATGGTGGA-TTAATCCAACTTACTAC
* * * * * *
55686498 AACTTCAGAGGTATAGGATTTATCGTTTTAATTCGCTCCACTGCAACTTCAGGGAGATAAGATTG
65 AACTTCAGAGGTATAAGATTCATCGTTTTAATCCACTCCACTGCAACTTCAAGGAGATAAGATTA
* * * *
55686563 GTATCTTCAACCTGGTCCACTACAACTTTAGGGAGATAAGGCTTATCTTC
130 ATAGCTTCAACCTGCTCCACTACAACTTCAGGGAGATAAGGCTTATCTTC
* * * * * *
55686613 AGTCTGCTCCACTTCAAC-TCTAGGGAGATAAGACTTATTATGGTGCGA-T-CTGC-TC-TACTG
1 AGTCTGCTCCACTACAACATC-AGGGAGATAAGACTTATCATGGTG-GATTAATCCAACTTACTA
* * *
55686673 CAACTTCAGAGAG-ATAAGATTCATCGTTTTAATCCACTCCATTGCAACTTCAATGAGATAGGAT
64 CAACTTCAGAG-GTATAAGATTCATCGTTTTAATCCACTCCACTGCAACTTCAAGGAGATAAGAT
** *
55686737 TAATAGCTTCAATTTGCTCCACTATAACTTCAGGGAGATAAG
128 TAATAGCTTCAACCTGCTCCACTACAACTTCAGGGAGATAAG
55686779 ACTGGATGCG
Statistics
Matches: 141, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
176 92 0.65
177 2 0.01
178 2 0.01
179 3 0.02
180 40 0.28
181 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (179 bp):
AGTCTGCTCCACTACAACATCAGGGAGATAAGACTTATCATGGTGGATTAATCCAACTTACTACA
ACTTCAGAGGTATAAGATTCATCGTTTTAATCCACTCCACTGCAACTTCAAGGAGATAAGATTAA
TAGCTTCAACCTGCTCCACTACAACTTCAGGGAGATAAGGCTTATCTTC
Found at i:55686808 original size:41 final size:41
Alignment explanation
Indices: 55686751--55686950 Score: 132
Period size: 41 Copynumber: 4.7 Consensus size: 41
55686741 AGCTTCAATT
** *
55686751 TGCTCCACTATAACTTCAGGGAGATAAGACTGGATGCGATC
1 TGCTCCACTGCAACTTCAGAGAGATAAGACTGGATGCGATC
* * * *** *
55686792 TGCTCTACTGCAACTTCAGAGAGATAATATCTGTAGTTTTAACC
1 TGCTCCACTGCAACTTCAGAGAGATAAGA-CTG--GATGCGATC
* ** * * * *
55686836 TGCTCCACTGTAACTTTTGTAGAGATAGGATTGGCTTCTTCTG-TC
1 TGCTCCACTGCAACTTCAG-AGAGATAAGACTGG---ATGC-GATC
* *
55686881 TGCTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATC
1 TGCTCCACTGCAACTTCAGAGAGATAAGACTGGATGCGATC
* *
55686922 TGCTCTACTGCAACTTCAGATAGATAAGA
1 TGCTCCACTGCAACTTCAGAGAGATAAGA
55686951 TCTGTGATTT
Statistics
Matches: 119, Mismatches: 31, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
40 1 0.01
41 54 0.45
42 4 0.03
44 33 0.28
45 27 0.23
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (41 bp):
TGCTCCACTGCAACTTCAGAGAGATAAGACTGGATGCGATC
Found at i:55686923 original size:130 final size:128
Alignment explanation
Indices: 55686606--55686965 Score: 388
Period size: 130 Copynumber: 2.7 Consensus size: 128
55686596 AGATAAGGCT
*
55686606 TATCTTCAGTCTGCTCCACTTCAAC-TCTAGGGAGATAAGACTTATTATGG-TGCGATCTGCTCT
1 TATCTTCAGTCTGCTCCACTACAACTTC-AGGGAGATAAG----A-T-TGGATGCGATCTGCTCT
* *
55686669 ACTGCAACTTCAGAGAGATAAGATTCAT-CGTTTTAATCCACTCCATTGCAACTTCAATGAGATA
59 ACTGCAACTTCAGAGAGATAAGA-TC-TGTGTTTTAATCCACTCCACTGCAACTTCAATGAGATA
55686733 GGATTAA
122 GGATTAA
* * * * *
55686740 TAGCTTCAATTTGCTCCACTATAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAA
1 TATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAA
* * * ***
55686805 CTTCAGAGAGATAATATCTGTAGTTTTAA-CCTGCTCCACTGTAACTTTTGTAGAGATAGGATTG
66 CTTCAGAGAGATAAGATCTGT-GTTTTAATCC-ACTCCACTGCAACTTCAAT-GAGATAGGATT-
**
55686869 GC
127 AA
* *
55686871 T-TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAA
1 TATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAA
*
55686935 CTTCAGATAGATAAGATCTGTGATTTTAATC
66 CTTCAGAGAGATAAGATCTGTG-TTTTAATC
55686966 TATTCTACTA
Statistics
Matches: 192, Mismatches: 25, Indels: 21
0.81 0.11 0.09
Matches are distributed among these distances:
127 1 0.01
128 7 0.04
129 56 0.29
130 93 0.48
131 2 0.01
134 31 0.16
135 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (128 bp):
TATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAA
CTTCAGAGAGATAAGATCTGTGTTTTAATCCACTCCACTGCAACTTCAATGAGATAGGATTAA
Found at i:55687094 original size:44 final size:44
Alignment explanation
Indices: 55687046--55687377 Score: 146
Period size: 44 Copynumber: 7.5 Consensus size: 44
55687036 AGATTCGTCG
* *
55687046 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTGCAA
1 TCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCTACAA
* * * * *
55687090 TCTTCAACCTACTCCACTGCTGCTCAGGGGGATAGGA-CT--AA
1 TCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCTACAA
** * * * **
55687131 TGGCTTAAAT-TAGCTTCC-CTACTACCTT-GAGAAGATAAGAT-TCACCG
1 T--CTTCGATCTA-C-TCCACTACT-GCTTAG-GGAGATAGGATCT-ACAA
55687178 TCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCTACAA
1 TCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCTACAA
* * * * ****
55687222 TCTTCGACCTACTCCACTGCTGCTCAGAGAGATAAGG--CTGGTG
1 TCTTCGATCTACTCCACTACTGCTTAGGGAGAT-AGGATCTACAA
* ** ** * * * * **
55687265 GCTTAAATCTGTTTCC-CTACTACATT-GGGAAGATAAGACCCACCG
1 TCTTCGATCT-ACTCCACTACTGC-TTAGGG-AGATAGGATCTACAA
* * *
55687310 TCTTCGATTTGCTCCACTACTGCTTAGGGAGACAGGATCTACAA
1 TCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCTACAA
* *
55687354 TCTTCGACCTACTCCACTGCTGCT
1 TCTTCGATCTACTCCACTACTGCT
55687378 CAAGAAGATA
Statistics
Matches: 203, Mismatches: 63, Indels: 44
0.65 0.20 0.14
Matches are distributed among these distances:
41 3 0.01
42 2 0.01
43 30 0.15
44 132 0.65
45 33 0.16
46 2 0.01
47 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (44 bp):
TCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCTACAA
Found at i:55687116 original size:132 final size:132
Alignment explanation
Indices: 55686980--55687479 Score: 686
Period size: 132 Copynumber: 3.8 Consensus size: 132
55686970 CTACTACAAT
* * * **
55686980 CTCAGGGAGAT-AGGATTTGTGGCTTAAATATGTTTCCCTACTACCTTGGAAAGATAAGATTCGT
1 CTCAGGGAGATAAGG-CTTGTGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCAC
* * *
55687044 CGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTGCAATCTTCAACCTACTCCACTG
65 CGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCGACCTACTCCACTG
55687109 CTG
130 CTG
* **
55687112 CTCAGGGGGAT-AGGACTAATGGCTTAAAT-TAGCTTCCCTACTACCTT-GAGAAGATAAGATTC
1 CTCAGGGAGATAAGG-CTTGTGGCTTAAATCT-GCTTCCCTACTACCTTGGA-AAGATAAGATTC
* *
55687174 ACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCGACCTACTCCAC
63 ACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCGACCTACTCCAC
55687239 TGCTG
128 TGCTG
* * * * * **
55687244 CTCAGAGAGATAAGGCTGGTGGCTTAAATCTGTTTCCCTACTACATTGGGAAGATAAGACCCACC
1 CTCAGGGAGATAAGGCTTGTGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACC
*
55687309 GTCTTCGATTTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCGACCTACTCCACTGC
66 GTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCGACCTACTCCACTGC
55687374 TG
131 TG
* * * *
55687376 CTCAAGAAGATAAGGC-TGATAGCTTAAATCTGCTTCTCTACTACCTTGGAAAGATAAGATTCAC
1 CTCAGGGAGATAAGGCTTG-TGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCAC
*
55687440 CGTCTTCAATCTGCTCCACTACTGCTTAGGGAGACAGGAT
65 CGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGAT
55687480 TAGGGGTGAG
Statistics
Matches: 327, Mismatches: 35, Indels: 12
0.87 0.09 0.03
Matches are distributed among these distances:
131 4 0.01
132 318 0.97
133 5 0.02
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (132 bp):
CTCAGGGAGATAAGGCTTGTGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACC
GTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCGACCTACTCCACTGC
TG
Found at i:55688562 original size:9 final size:9
Alignment explanation
Indices: 55688548--55688584 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
55688538 TATAGTTTGA
55688548 TATTCGAAT
1 TATTCGAAT
55688557 TATTCGAAT
1 TATTCGAAT
*
55688566 TATTCGAGT
1 TATTCGAAT
55688575 TATTCGAAT
1 TATTCGAAT
55688584 T
1 T
55688585 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:55688655 original size:9 final size:9
Alignment explanation
Indices: 55688638--55688668 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
55688628 TCGAGTTGAT
55688638 TCGAATAAC
1 TCGAATAAC
*
55688647 TCGATTAAC
1 TCGAATAAC
55688656 TCGAATAAC
1 TCGAATAAC
55688665 TCGA
1 TCGA
55688669 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:55689323 original size:24 final size:24
Alignment explanation
Indices: 55689275--55689332 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
55689265 CGGATTGCCC
55689275 CCACTGTAATCTTCAAAGTCAAAT
1 CCACTGTAATCTTCAAAGTCAAAT
* *
55689299 CTACTGTAATCTTCAAGATTC-AAT
1 CCACTGTAATCTTCAA-AGTCAAAT
*
55689323 CCACTATAAT
1 CCACTGTAAT
55689333 TTTGGGACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (24 bp):
CCACTGTAATCTTCAAAGTCAAAT
Found at i:55689940 original size:57 final size:57
Alignment explanation
Indices: 55689870--55690040 Score: 141
Period size: 57 Copynumber: 3.1 Consensus size: 57
55689860 CCAAAATAGA
*
55689870 AAATTTTGCTAAGACGAACTGAATAAGATGAAAAAGATTATCACAATGGACAACATG
1 AAATTTTACTAAGACGAACTGAATAAGATGAAAAAGATTATCACAATGGACAACATG
* * * * *
55689927 AAATTTTATTAAGAGCAAAGCTCG---AA-ATGAATAA-ATTAATCA-AA---ATAGC---
1 AAATTTTACTAAGA-CGAA-CT-GAATAAGATGAAAAAGATT-ATCACAATGGACAACATG
* *
55689976 AAATTTTGCTAAGACGAACTGAATAAGATGAAAAAGATTATCACAATGGACAAGATG
1 AAATTTTACTAAGACGAACTGAATAAGATGAAAAAGATTATCACAATGGACAACATG
*
55690033 GAATTTTA
1 AAATTTTA
55690041 TTGAGAGCAA
Statistics
Matches: 83, Mismatches: 15, Indels: 32
0.64 0.12 0.25
Matches are distributed among these distances:
46 1 0.01
47 2 0.02
48 3 0.04
49 14 0.17
50 11 0.13
51 5 0.06
52 3 0.04
54 2 0.02
55 5 0.06
56 11 0.13
57 20 0.24
58 3 0.04
59 2 0.02
60 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (57 bp):
AAATTTTACTAAGACGAACTGAATAAGATGAAAAAGATTATCACAATGGACAACATG
Found at i:55689980 original size:106 final size:106
Alignment explanation
Indices: 55689791--55690117 Score: 546
Period size: 106 Copynumber: 3.1 Consensus size: 106
55689781 AGTTATTTCA
* * **
55689791 ATGAAAAATATTATCACAATGGACAAGATAAAATTTTATTGAGAATAAAGCTCGAAATGAATAAA
1 ATGAAAAAGATTATCACAATGGACAAGATGAAATTTTATTGAGAGCAAAGCTCGAAATGAATAAA
*
55689856 TTAACCAAAATAGAAAATTTTGCTAAGACGAACTGAATAAG
66 TTAATCAAAATAGAAAATTTTGCTAAGACGAACTGAATAAG
* *
55689897 ATGAAAAAGATTATCACAATGGACAACATGAAATTTTATTAAGAGCAAAGCTCGAAATGAATAAA
1 ATGAAAAAGATTATCACAATGGACAAGATGAAATTTTATTGAGAGCAAAGCTCGAAATGAATAAA
*
55689962 TTAATCAAAATAGCAAATTTTGCTAAGACGAACTGAATAAG
66 TTAATCAAAATAGAAAATTTTGCTAAGACGAACTGAATAAG
*
55690003 ATGAAAAAGATTATCACAATGGACAAGATGGAATTTTATTGAGAGCAAAGCTCGAAATGAATAAA
1 ATGAAAAAGATTATCACAATGGACAAGATGAAATTTTATTGAGAGCAAAGCTCGAAATGAATAAA
*
55690068 TTAATCAAAATAGAAAATTTTGCTAAGATCCGAAATGAATAAG
66 TTAATCAAAATAGAAAATTTTGCTAAGA--CGAACTGAATAAG
55690111 ATGAAAA
1 ATGAAAA
55690118 CAAGTACCCA
Statistics
Matches: 206, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
106 187 0.91
108 19 0.09
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.25
Consensus pattern (106 bp):
ATGAAAAAGATTATCACAATGGACAAGATGAAATTTTATTGAGAGCAAAGCTCGAAATGAATAAA
TTAATCAAAATAGAAAATTTTGCTAAGACGAACTGAATAAG
Found at i:55690405 original size:20 final size:20
Alignment explanation
Indices: 55690377--55690426 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
55690367 CACCTTGGCC
*
55690377 TCTCCTTTTCCTTTTTCTTT
1 TCTCTTTTTCCTTTTTCTTT
**
55690397 TCTCTTTTTTGTTTTTCTTT
1 TCTCTTTTTCCTTTTTCTTT
*
55690417 TCTTTTTTTC
1 TCTCTTTTTC
55690427 GTCTTTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (20 bp):
TCTCTTTTTCCTTTTTCTTT
Found at i:55690437 original size:20 final size:20
Alignment explanation
Indices: 55690388--55690425 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
55690378 CTCCTTTTCC
55690388 TTTTTCTTTTCTCTTTTTTG
1 TTTTTCTTTTCTCTTTTTTG
55690408 TTTTTCTTTTCT-TTTTTT
1 TTTTTCTTTTCTCTTTTTT
55690426 CGTCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (20 bp):
TTTTTCTTTTCTCTTTTTTG
Found at i:55695223 original size:107 final size:107
Alignment explanation
Indices: 55695036--55695395 Score: 521
Period size: 106 Copynumber: 3.4 Consensus size: 107
55695026 GAGATTTAAG
* * * *
55695036 AGGATATTTGGTTATTTGGTCAAACGAGAAATCGAAACCCAACACGTTAGGGCATGTTTTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACATTAGGGCACGTTTTCTCGA
* *
55695101 ATTTCCAGACACAAAATATTGCCTTACTTTGAAATTTTA-AT
66 ATTTCTAAACACAAAATATTGCCTTACTTTGAAATTTTAGAT
* *
55695142 AGGATATTTGGCTATTTGGTTGAACGAAAAAATCGAAACCCAACACATTAGGGCACGTTTTCTCG
1 AGGATATTTGGCTATTTGGTCGAACG-AGAAATCGAAACCCAACACATTAGGGCACGTTTTCTCG
* * * *
55695207 AATTTCTAAACGCAAAATATTGCTTTATTTTTAAATTTTAGAT
65 AATTTCTAAACACAAAATATTGCCTTACTTTGAAATTTTAGAT
* * *
55695250 -GGATATTTGGCTATTTGGTCGAACGAGAAATTGAAACCCAGCACATTAGGACACGTTTTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACATTAGGGCACGTTTTCTCGA
* *
55695314 ATTT-TCAAACTCAAAATATTGTCTTACTTTGAAATTTTAGA-
66 ATTTCT-AAACACAAAATATTGCCTTACTTTGAAATTTTAGAT
55695355 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCA
55695396 GTAAAAAAAT
Statistics
Matches: 227, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
105 1 0.00
106 131 0.58
107 93 0.41
108 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (107 bp):
AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACATTAGGGCACGTTTTCTCGA
ATTTCTAAACACAAAATATTGCCTTACTTTGAAATTTTAGAT
Found at i:55695512 original size:4 final size:4
Alignment explanation
Indices: 55695505--55695544 Score: 53
Period size: 4 Copynumber: 9.2 Consensus size: 4
55695495 TTATGGACAT
55695505 ATAA ATAA ATAA ATAA ATAA ATAA ATGAA CATAA AGTAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA AT-AA -ATAA A-TAA A
55695545 ACAATAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
4 23 0.70
5 8 0.24
6 2 0.06
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:55695573 original size:22 final size:21
Alignment explanation
Indices: 55695505--55695577 Score: 53
Period size: 22 Copynumber: 3.4 Consensus size: 21
55695495 TTATGGACAT
*
55695505 ATAAATAAATAAA-TAAATA-A
1 ATAAAAAAATAAAGTAAA-ACA
*
55695525 ATAAATGAACATAAAGTAAAACA
1 ATAAA--AAAATAAAGTAAAACA
*
55695548 ATAATAAAAATAAAG-AAAATA
1 ATAA-AAAAATAAAGTAAAACA
55695569 GATAAAAAA
1 -ATAAAAAA
55695578 TTATAAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
20 5 0.12
21 9 0.21
22 19 0.44
23 9 0.21
24 1 0.02
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (21 bp):
ATAAAAAAATAAAGTAAAACA
Found at i:55695601 original size:19 final size:18
Alignment explanation
Indices: 55695547--55695601 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
55695537 AAAGTAAAAC
* *
55695547 AATAATAAAAATAAAGAA
1 AATAATAAAAATATATAA
55695565 AATAGATAAAAA-ATTATAA
1 AATA-ATAAAAATA-TATAA
55695584 AATATATAAAAATATATA
1 AATA-ATAAAAATATATA
55695602 TATGTACATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 5 0.16
19 25 0.81
20 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (18 bp):
AATAATAAAAATATATAA
Found at i:55695627 original size:23 final size:22
Alignment explanation
Indices: 55695587--55695630 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
55695577 ATTATAAAAT
*
55695587 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
55695609 ATATAAGAAAAATATATATGTA
1 ATATAA-AAAAATATATATGTA
55695631 TGTGAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:55695803 original size:12 final size:12
Alignment explanation
Indices: 55695786--55695817 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
55695776 GGCAACCAAT
55695786 AATAATAATAAC
1 AATAATAATAAC
55695798 AATAATAATAAC
1 AATAATAATAAC
*
55695810 CATAATAA
1 AATAATAA
55695818 AACCTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:55711309 original size:17 final size:17
Alignment explanation
Indices: 55711279--55711311 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
55711269 CGTCGATATG
55711279 TTTATATTTAATAATTT
1 TTTATATTTAATAATTT
55711296 TTTAT-TTTATATAATT
1 TTTATATTTA-ATAATT
55711312 AATTTAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTTAATAATTT
Found at i:55714955 original size:4 final size:4
Alignment explanation
Indices: 55714946--55714976 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
55714936 TTTGAACTTC
55714946 AATT AATT AATT AATT AATT AATT AA-T AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT
55714977 CGAAAAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:55716575 original size:39 final size:37
Alignment explanation
Indices: 55716508--55716600 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
55716498 ACCAGAATGG
* *
55716508 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
55716547 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
55716584 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
55716601 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:55716964 original size:3 final size:3
Alignment explanation
Indices: 55716956--55716982 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55716946 ATTCCCACTC
55716956 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
55716983 CTTACCTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55717720 original size:5 final size:5
Alignment explanation
Indices: 55717710--55717766 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
55717700 TTACTTATTT
* *
55717710 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
55717758 ATAT- ATATA
1 ATATA ATATA
55717767 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:55717726 original size:12 final size:12
Alignment explanation
Indices: 55717709--55717764 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
55717699 TTTACTTATT
55717709 TATATAATATAA
1 TATATAATATAA
55717721 TATATAATATAATA
1 TATATAATAT-A-A
55717735 TACTATAATATAA
1 TA-TATAATATAA
*
55717748 TA-ATAATTTAA
1 TATATAATATAA
55717759 TATATA
1 TATATA
55717765 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:55717779 original size:26 final size:26
Alignment explanation
Indices: 55717711--55717766 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
55717701 TACTTATTTA
*
55717711 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
55717738 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
55717763 TATA
1 TATA
55717767 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:55720188 original size:36 final size:36
Alignment explanation
Indices: 55720140--55720212 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
55720130 TAAATTCGCC
* *
55720140 TAAGTCAGCCTATGTAACACCCTTTACCCTACTTGA
1 TAAGTCAACCTATGTAACACCCCTTACCCTACTTGA
*
55720176 TAAGTCAACCTATGTAACACCCCTTACTCTACTTGA
1 TAAGTCAACCTATGTAACACCCCTTACCCTACTTGA
55720212 T
1 T
55720213 CGTTGGGTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.30, G:0.10, T:0.32
Consensus pattern (36 bp):
TAAGTCAACCTATGTAACACCCCTTACCCTACTTGA
Found at i:55732363 original size:27 final size:27
Alignment explanation
Indices: 55732319--55732382 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
55732309 ACATACAAAA
55732319 GAAATTTCAAATCTAATTACCAAATTAT
1 GAAA-TTCAAATCTAATTACCAAATTAT
55732347 GAAATTCAACATC-AATTACCAAATTAT
1 GAAATTCAA-ATCTAATTACCAAATTAT
55732374 -AAATTCAAA
1 GAAATTCAAA
55732383 CTTAATCCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
25 1 0.03
26 8 0.23
27 19 0.54
28 7 0.20
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.31
Consensus pattern (27 bp):
GAAATTCAAATCTAATTACCAAATTAT
Found at i:55735877 original size:17 final size:18
Alignment explanation
Indices: 55735843--55735888 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
55735833 CCGTTATGTC
55735843 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
55735858 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
55735875 CGCGACCGCGACCG
1 CGCGACCGCGACCG
55735889 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:55736576 original size:21 final size:21
Alignment explanation
Indices: 55736551--55736599 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
55736541 TAAGAAAATG
55736551 AAAAT-ATATAAAATTATCATA
1 AAAATAAT-TAAAATTATCATA
* *
55736572 AAAATAATTAATATTATCATT
1 AAAATAATTAAAATTATCATA
55736593 AAAATAA
1 AAAATAA
55736600 ATATTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATAATTAAAATTATCATA
Found at i:55736629 original size:25 final size:26
Alignment explanation
Indices: 55736584--55736634 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
55736574 AATAATTAAT
55736584 ATTATCATTAAAATAAATATT-TTTA
1 ATTATCATTAAAATAAATATTATTTA
*
55736609 ATTATCATTAAGAA-AATTATTATTTA
1 ATTATCATTAA-AATAAATATTATTTA
55736635 TCTTAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (26 bp):
ATTATCATTAAAATAAATATTATTTA
Found at i:55739541 original size:104 final size:105
Alignment explanation
Indices: 55739361--55739595 Score: 361
Period size: 105 Copynumber: 2.2 Consensus size: 105
55739351 ATTACATATA
*
55739361 GAGGGGTTGCTAAGTGCTGATTCCCCTACTTATTGGTGGTTGCTAAGTGCTGAGTCCACCGTATT
1 GAGGGGTTGCTAAGTGCTGATTCCCCTACTTATTGGTGGTTGCTAAGTGCTGAGTCCACCATATT
*
55739426 TTTAAATGTG-AAAGGGGGTTGCTATGTGCTGATTCCCCC
66 TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCC
** *
55739465 GAGGGGTTGCTAAGTGCTGATTCCCC-GGTTCATTGGTGG-TGCTATGTGCGTGA-TCCACCATA
1 GAGGGGTTGCTAAGTGCTGATTCCCCTACTT-ATTGGTGGTTGCTAAGTGC-TGAGTCCACCATA
55739527 TCTTTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCC
64 T-TTTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
55739570 AAGGGGTTGCTAAGTGCTGATTCCCC
1 GAGGGGTTGCTAAGTGCTGATTCCCC
55739596 CAAGGGGTTG
Statistics
Matches: 121, Mismatches: 6, Indels: 7
0.90 0.04 0.05
Matches are distributed among these distances:
103 20 0.17
104 47 0.39
105 54 0.45
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.32
Consensus pattern (105 bp):
GAGGGGTTGCTAAGTGCTGATTCCCCTACTTATTGGTGGTTGCTAAGTGCTGAGTCCACCATATT
TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:55739581 original size:27 final size:27
Alignment explanation
Indices: 55739545--55739622 Score: 147
Period size: 27 Copynumber: 2.9 Consensus size: 27
55739535 ATGTGAAAAG
*
55739545 GGGGTTGCTATGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
55739572 GGGGTTGCTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
55739599 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
55739623 GGTTCATTGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.15, C:0.26, G:0.31, T:0.28
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:55739756 original size:103 final size:103
Alignment explanation
Indices: 55739572--55739758 Score: 329
Period size: 103 Copynumber: 1.8 Consensus size: 103
55739562 ATTCCCCCAA
* *
55739572 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGT
*
55739637 GCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAAG
66 GCTAAGTGCGAGATCCACCGTATCTTTGAAATGAAAAG
* *
55739675 GGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGT
55739740 GCTAAGTGCGAGATCCACC
66 GCTAAGTGCGAGATCCACC
55739759 AATAACGGTT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 79 1.00
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (103 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGT
GCTAAGTGCGAGATCCACCGTATCTTTGAAATGAAAAG
Found at i:55743254 original size:16 final size:16
Alignment explanation
Indices: 55743233--55743263 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
55743223 AAATAAAGTA
55743233 TAATAAAAGAAATAGG
1 TAATAAAAGAAATAGG
55743249 TAATAAAAGAAATAG
1 TAATAAAAGAAATAG
55743264 AAAGCCATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (16 bp):
TAATAAAAGAAATAGG
Found at i:55744080 original size:16 final size:16
Alignment explanation
Indices: 55744055--55744088 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55744045 ATGAATATAT
* *
55744055 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
55744071 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
55744087 AT
1 AT
55744089 TGGATATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:55745881 original size:9 final size:9
Alignment explanation
Indices: 55745862--55745898 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
55745852 TGAATTTTCA
*
55745862 AATTTGAAT
1 AATTCGAAT
*
55745871 AACTCGAAT
1 AATTCGAAT
55745880 AATTCGAAT
1 AATTCGAAT
55745889 AATTCGAAT
1 AATTCGAAT
55745898 A
1 A
55745899 TAAGCTATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:55746040 original size:14 final size:14
Alignment explanation
Indices: 55746021--55746055 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
55746011 CGAGAATCTT
55746021 CACCTCCACCAATC
1 CACCTCCACCAATC
**
55746035 CACCTCCACCGGTC
1 CACCTCCACCAATC
55746049 CACCTCC
1 CACCTCC
55746056 GGTCCTCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.60, G:0.06, T:0.14
Consensus pattern (14 bp):
CACCTCCACCAATC
Found at i:55746794 original size:72 final size:72
Alignment explanation
Indices: 55746677--55746940 Score: 332
Period size: 72 Copynumber: 3.7 Consensus size: 72
55746667 GTTACTCAGC
* * * *
55746677 TTGATCTTTCAGAAAATCAATTAAACGACCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTTG
1 TTGATGTTTCAAAAAATCAATTAAACGGCCAAATTCCATTGTCTATAGGGCAGTTGTCATCTTTG
55746742 GAGGAGT
66 GAGGAGT
* * * * *
55746749 TTGATGTTTCAAAAAATAAATTAAATGGTCAAATTCCATTTTCTATAGAGG-AGTTATCATCTTT
1 TTGATGTTTCAAAAAATCAATTAAACGGCCAAATTCCATTGTCTATAG-GGCAGTTGTCATCTTT
* **
55746813 GAAGTTGT
65 GGAGGAGT
* * * *
55746821 TTGATGTTTCAAAAAATCAGTTAAACGGCCAAATTCCCTTGTCTATAAGGCAGTTGTCATATTTG
1 TTGATGTTTCAAAAAATCAATTAAACGGCCAAATTCCATTGTCTATAGGGCAGTTGTCATCTTTG
55746886 GAGGAGT
66 GAGGAGT
* * * *
55746893 TTGATGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGCCTATAG
1 TTGATGTTTCAAAAAATCAATTAAACGGCCAAATTCCATTGTCTATAG
55746941 TCCAATAATA
Statistics
Matches: 159, Mismatches: 31, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
71 2 0.01
72 155 0.97
73 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (72 bp):
TTGATGTTTCAAAAAATCAATTAAACGGCCAAATTCCATTGTCTATAGGGCAGTTGTCATCTTTG
GAGGAGT
Found at i:55746939 original size:144 final size:144
Alignment explanation
Indices: 55746677--55746940 Score: 438
Period size: 144 Copynumber: 1.8 Consensus size: 144
55746667 GTTACTCAGC
* * *
55746677 TTGATCTTTCAGAAAATCAATTAAACGACCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTTG
1 TTGATCTTTCAAAAAATCAATTAAACGACCAAATTCCCTTGTCTATAAGGCAGTTGTCATATTTG
**
55746742 GAGGAGTTTGATGTTTCAAAAAATAAATTAAATGGTCAAATTCCATTTTCTATAGAGGAGTTATC
66 GAGGAGTTTGATGTTTCAAAAAATAAATTAAATGGTCAAATTCCATTGCCTATAGAGGAGTTATC
55746807 ATCTTTGAAGTTGT
131 ATCTTTGAAGTTGT
* * *
55746821 TTGATGTTTCAAAAAATCAGTTAAACGGCCAAATTCCCTTGTCTATAAGGCAGTTGTCATATTTG
1 TTGATCTTTCAAAAAATCAATTAAACGACCAAATTCCCTTGTCTATAAGGCAGTTGTCATATTTG
* *
55746886 GAGGAGTTTGATGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGCCTATAG
66 GAGGAGTTTGATGTTTCAAAAAATAAATTAAATGGTCAAATTCCATTGCCTATAG
55746941 TCCAATAATA
Statistics
Matches: 110, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
144 110 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (144 bp):
TTGATCTTTCAAAAAATCAATTAAACGACCAAATTCCCTTGTCTATAAGGCAGTTGTCATATTTG
GAGGAGTTTGATGTTTCAAAAAATAAATTAAATGGTCAAATTCCATTGCCTATAGAGGAGTTATC
ATCTTTGAAGTTGT
Found at i:55751348 original size:44 final size:44
Alignment explanation
Indices: 55751279--55751440 Score: 166
Period size: 44 Copynumber: 3.7 Consensus size: 44
55751269 GATTTGGCAA
** * *
55751279 CTTGTCTGTGAATTTGGTGGTTTCATCCAAAACCTACATGGTAG
1 CTTGTCTGCAAATTTGGTGGCTTCATCCACAACCTACATGGTAG
*
55751323 CTTGTCTGCAAATTTGGTAGCTTCATCCACAACCTACATGGTAG
1 CTTGTCTGCAAATTTGGTGGCTTCATCCACAACCTACATGGTAG
* * *** * * **
55751367 CTTATATATTAATTTGGTTG-TTTATCCACAACCTACATGACAG
1 CTTGTCTGCAAATTTGGTGGCTTCATCCACAACCTACATGGTAG
*
55751410 TTTGTCTGCAAATTTGGTGGCTT-AGTCCACA
1 CTTGTCTGCAAATTTGGTGGCTTCA-TCCACA
55751441 TATATATTGG
Statistics
Matches: 95, Mismatches: 21, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
43 34 0.36
44 61 0.64
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (44 bp):
CTTGTCTGCAAATTTGGTGGCTTCATCCACAACCTACATGGTAG
Found at i:55753812 original size:76 final size:76
Alignment explanation
Indices: 55753722--55753917 Score: 356
Period size: 76 Copynumber: 2.6 Consensus size: 76
55753712 GATATTGTAA
** *
55753722 GTATCCCCTTCTGTCTTCCTTTTTTGGTAGCTTGCATGTGGTTATGTTGAATTGGGAATTTTTAT
1 GTATCCCCTTCTGTCTTCCCCTTCTGGTAGCTTGCATGTGGTTATGTTGAATTGGGAATTTTTAT
55753787 TGTTCTTTCTG
66 TGTTCTTTCTG
55753798 GTATCCCCTTCTGTCTTCCCCTTCTGGTAGCTTGCATGTGGTTATGTTGAATTGGGAATTTTTAT
1 GTATCCCCTTCTGTCTTCCCCTTCTGGTAGCTTGCATGTGGTTATGTTGAATTGGGAATTTTTAT
55753863 TGTTCTTTCTG
66 TGTTCTTTCTG
*
55753874 GTATCCCTTTCTGTCTTCCCCTTCTGGTAGCTTGCATGTGGTTA
1 GTATCCCCTTCTGTCTTCCCCTTCTGGTAGCTTGCATGTGGTTA
55753918 AGTCCTTTCA
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 116 1.00
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (76 bp):
GTATCCCCTTCTGTCTTCCCCTTCTGGTAGCTTGCATGTGGTTATGTTGAATTGGGAATTTTTAT
TGTTCTTTCTG
Found at i:55754985 original size:20 final size:20
Alignment explanation
Indices: 55754960--55754999 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
55754950 TATGTTCTCA
55754960 ATGCTAAACGGGGTATGAAT
1 ATGCTAAACGGGGTATGAAT
55754980 ATGCTAAACGGGGTATGAAT
1 ATGCTAAACGGGGTATGAAT
55755000 TGTATCTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (20 bp):
ATGCTAAACGGGGTATGAAT
Found at i:55757524 original size:32 final size:32
Alignment explanation
Indices: 55757485--55757577 Score: 168
Period size: 32 Copynumber: 2.9 Consensus size: 32
55757475 TTAGATATTG
*
55757485 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
55757517 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
*
55757549 ATTGTGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTTGGATATTGAA
55757578 ATGATTGACA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTGGATATTGAATTT
Found at i:55757535 original size:59 final size:62
Alignment explanation
Indices: 55757440--55757579 Score: 171
Period size: 59 Copynumber: 2.3 Consensus size: 62
55757430 CCATTTTAGT
* *
55757440 TTGTTGGATTTTGAAATTATTATGTCTTGAATTTGTTAGATATTG-A-TTA-TGTTTTAAGC
1 TTGTTGGATATTGAAATTATTATGTCTTGAACTTGTTAGATATTGAATTTATTGTTTTAAGC
* * * *
55757499 TTGTTAGATATTGAATTTATTATGT-TTTAAGCTTGTTGGATATTGAATTTATTGTGTTTTAAGC
1 TTGTTGGATATTGAAATTATTATGTCTTGAA-CTTGTTAGATATTGAATTTA-T-TGTTTTAAGC
55757563 TTGTTGGATATTGAAAT
1 TTGTTGGATATTGAAAT
55757580 GATTGACAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
58 4 0.06
59 34 0.51
60 1 0.01
61 3 0.04
64 25 0.37
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (62 bp):
TTGTTGGATATTGAAATTATTATGTCTTGAACTTGTTAGATATTGAATTTATTGTTTTAAGC
Found at i:55758851 original size:20 final size:20
Alignment explanation
Indices: 55758826--55758863 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55758816 AAAATTTAAA
*
55758826 ATATAAATTTATTAATATGT
1 ATATAAATATATTAATATGT
55758846 ATATAAATATATTAATAT
1 ATATAAATATATTAATAT
55758864 ATGTAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
ATATAAATATATTAATATGT
Found at i:55758973 original size:20 final size:20
Alignment explanation
Indices: 55758946--55758992 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
55758936 CATTCAAACA
55758946 CCAGAAAAGTAAATCATTTT
1 CCAGAAAAGTAAATCATTTT
* *
55758966 CTAGAAAAGTAAATTATTTT
1 CCAGAAAAGTAAATCATTTT
55758986 CCAGAAA
1 CCAGAAA
55758993 TCATTTTCCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.30
Consensus pattern (20 bp):
CCAGAAAAGTAAATCATTTT
Found at i:55761271 original size:18 final size:18
Alignment explanation
Indices: 55761248--55761291 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
55761238 CAAAATGAAT
*
55761248 GAAATGAATAGAAATAAA
1 GAAATGAATAGAAACAAA
55761266 GAAATGAATAGAAACAAA
1 GAAATGAATAGAAACAAA
55761284 GAAATGAA
1 GAAATGAA
55761292 AAGTATTCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.66, C:0.02, G:0.18, T:0.14
Consensus pattern (18 bp):
GAAATGAATAGAAACAAA
Found at i:55771761 original size:24 final size:20
Alignment explanation
Indices: 55771707--55771750 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
55771697 TTAAACCTCT
55771707 TAGGACTCTCATTTTATAGA
1 TAGGACTCTCATTTTATAGA
*
55771727 TAGGACTCTCATTTTGTAGA
1 TAGGACTCTCATTTTATAGA
55771747 TAGG
1 TAGG
55771751 CACTAATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (20 bp):
TAGGACTCTCATTTTATAGA
Found at i:55772948 original size:19 final size:19
Alignment explanation
Indices: 55772924--55772962 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
55772914 ATTGAATGAA
55772924 AAAGAAAGAAAATAAGTTG
1 AAAGAAAGAAAATAAGTTG
*
55772943 AAAGAAAGAATATAAGTTG
1 AAAGAAAGAAAATAAGTTG
55772962 A
1 A
55772963 GTAGATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (19 bp):
AAAGAAAGAAAATAAGTTG
Found at i:55774222 original size:12 final size:12
Alignment explanation
Indices: 55774205--55774237 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
55774195 ACATTTTTAA
55774205 AAAAAATTATAT
1 AAAAAATTATAT
*
55774217 AAAAAATGATAT
1 AAAAAATTATAT
55774229 AAAAAATTA
1 AAAAAATTA
55774238 ATACAGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (12 bp):
AAAAAATTATAT
Found at i:55793759 original size:24 final size:22
Alignment explanation
Indices: 55793713--55793759 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 22
55793703 AGATAAATTG
*
55793713 TAAAAATATACATGAATTTTAA
1 TAAAAATATACATAAATTTTAA
55793735 TAAAAATATACAAATAAATTTTAA
1 TAAAAATATAC--ATAAATTTTAA
55793759 T
1 T
55793760 TTTATGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
24 11 0.50
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAAAATATACATAAATTTTAA
Found at i:55798268 original size:24 final size:24
Alignment explanation
Indices: 55798240--55798291 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
55798230 TTAGTAAGTC
* *
55798240 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
55798264 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
55798288 AAAT
1 AAAT
55798292 CTTCTACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:55802854 original size:82 final size:82
Alignment explanation
Indices: 55802712--55802875 Score: 292
Period size: 82 Copynumber: 2.0 Consensus size: 82
55802702 TTCCACTCCA
* *
55802712 GTGGTCAATCTTTTCAAAGTATCCCATGAAACGTTCCTCTCCTGGACATATGTGGAACCATAGAA
1 GTGGCCAATCTTTTCAAAGTATCCCATGAAACGTTCCTCTCCTGGACATATGGGGAACCATAGAA
55802777 TCCTGTGAATCTCCATT
66 TCCTGTGAATCTCCATT
* *
55802794 GTGGCCAATCTTTTCAAAGTATCCCATGAAATGTTCCTGTCCTGGACATATGGGGAACCATAGAA
1 GTGGCCAATCTTTTCAAAGTATCCCATGAAACGTTCCTCTCCTGGACATATGGGGAACCATAGAA
55802859 TCCTGTGAATCTCCATT
66 TCCTGTGAATCTCCATT
55802876 TCACACCTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (82 bp):
GTGGCCAATCTTTTCAAAGTATCCCATGAAACGTTCCTCTCCTGGACATATGGGGAACCATAGAA
TCCTGTGAATCTCCATT
Found at i:55804375 original size:25 final size:25
Alignment explanation
Indices: 55804339--55804388 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
55804329 TTTAAACCTA
55804339 AGAACCCATGCCAGAGACGGCAGAC
1 AGAACCCATGCCAGAGACGGCAGAC
*
55804364 AGAACCCGTGCCAGAGACGGCAGAC
1 AGAACCCATGCCAGAGACGGCAGAC
55804389 TTTTTTTGAA
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:0.32, G:0.30, T:0.04
Consensus pattern (25 bp):
AGAACCCATGCCAGAGACGGCAGAC
Found at i:55811398 original size:17 final size:17
Alignment explanation
Indices: 55811376--55811413 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
55811366 TTAAAAACAA
55811376 CATAACTCTTGACCTTT
1 CATAACTCTTGACCTTT
55811393 CATAACTCTTGACCTTT
1 CATAACTCTTGACCTTT
55811410 CATA
1 CATA
55811414 TAACATAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.29, G:0.05, T:0.39
Consensus pattern (17 bp):
CATAACTCTTGACCTTT
Found at i:55814989 original size:73 final size:73
Alignment explanation
Indices: 55814870--55815186 Score: 447
Period size: 73 Copynumber: 4.3 Consensus size: 73
55814860 TGCTCAGCGC
* * * * *
55814870 TTTAGCGGCGTTTTTGAGAAAGCACTGCAAAGAACATAAGCCAAAACGACATCATTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCTGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
55814935 TTGGGGGA
66 TTGGGGGA
* *
55814943 TTTAGCGACGTTTTTAAAAAAGCG-TCGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCT-GCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGC
55815007 TTTGGGGGA
65 TTTGGGGGA
55815016 TTTAGCGGCGTTTTTAAGAAAGCGCTGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCTGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
55815081 TTGGGGGA
66 TTGGGGGA
* * * * * * * * *
55815089 TTTAGCGGCGTCTTTGAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGATTTATAAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCTGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
*
55815154 TTCGGGGA
66 TTGGGGGA
* *
55815162 TTTAGCGGCATTTTTAGGAAAGCGC
1 TTTAGCGGCGTTTTTAAGAAAGCGC
55815187 CGCTAATGCT
Statistics
Matches: 218, Mismatches: 24, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
72 1 0.00
73 216 0.99
74 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCTGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
TTGGGGGA
Found at i:55815396 original size:187 final size:188
Alignment explanation
Indices: 55815203--55815679 Score: 611
Period size: 187 Copynumber: 2.5 Consensus size: 188
55815193 TGCTCAGGGC
* * * * *
55815203 TTTAGCGACGTTTTTGAGAAAGCGCCGTAAAAAACTTAAGCCAAAACAACGCCATTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGTAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGCT
* * *
55815268 TTCGGGGATTTAGCGGCGTTTTTATGAATGTGCCGCTAATGCTCAAGGCTTTAGCGGTAATTTTT
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGG-AATTTTT
* * *
55815333 GA-AAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCG-TTTTGTGAGCTTTGGGGGA
130 GAGAAAGCGCCGCAAAAAACCTAAGCCAAAACAACGCCGTTTTTGTGAGCTTTCGGGGA
* * *
55815390 TTTAGCGGCGTTTTCGATG-AAGCGCCGCAAAAAACCTAAGGCAAAACGACGCCGTTTTATGAGC
1 TTTAGCGGCGTTTTTGA-GAAAGCGCCGTAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGC
* * * **
55815454 TTTCGGGGATTTAGCGGTGTTTTTAAGAAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTT
65 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGGAATTTTT
* * *
55815519 TAGAAAGCGCCGCAAAAAACTTAGGCCAAAACAACGCCGTTTTTGTGAGCTTTCGGGGA
130 GAGAAAGCGCCGCAAAAAACCTAAGCCAAAACAACGCCGTTTTTGTGAGCTTTCGGGGA
* * * *
55815578 TTTAGCGGCGTTTTTTAAGAAAGCGCCGCT-AAGAACCTAAGCCAAAACGACGTCGTTTTTTGAG
1 TTTAGCGGCG-TTTTTGAGAAAGCGCCG-TAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAG
* * * * *
55815642 CTTTGGGGGATTTAGTGGCGTTTATGAGGAAGCGCCGC
64 CTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
55815680 AAAAAAACCT
Statistics
Matches: 249, Mismatches: 35, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
186 6 0.02
187 138 0.55
188 30 0.12
189 75 0.30
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (188 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGTAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGGAATTTTTG
AGAAAGCGCCGCAAAAAACCTAAGCCAAAACAACGCCGTTTTTGTGAGCTTTCGGGGA
Found at i:55815417 original size:114 final size:113
Alignment explanation
Indices: 55815101--55815417 Score: 431
Period size: 114 Copynumber: 2.8 Consensus size: 113
55815091 TAGCGGCGTC
* * * *
55815101 TTTGAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGATTTATAAGCTTTCGGGGATTTA
1 TTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCTTTCGGGGATTTA
* * * *
55815166 GCGGCATTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGACGTT
66 GCGGCGTTTTTATG-AAGCGCCGCTAATGCTCAAGGCTTTAGCGACATT
* * * *
55815215 TTTGAGAAAGCGCCGTAAAAAACTTAAGCCAAAACAACGCCATTTTGTGAGCTTTCGGGGATTTA
1 TTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCTTTCGGGGATTTA
*
55815280 GCGGCGTTTTTATGAATGTGCCGCTAATGCTCAAGGCTTTAGCGGTA-ATT
66 GCGGCGTTTTTATGAA-GCGCCGCTAATGCTCAAGGCTTTAGC-G-ACATT
* *
55815330 TTTGA-AAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTGTGAGCTTTGGGGGATTTA
1 TTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCTTTCGGGGATTTA
*
55815394 GCGGCGTTTTCGATGAAGCGCCGC
66 GCGGCGTTTT-TATGAAGCGCCGC
55815418 AAAAAACCTA
Statistics
Matches: 178, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
113 2 0.01
114 162 0.91
115 13 0.07
116 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (113 bp):
TTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCTTTCGGGGATTTA
GCGGCGTTTTTATGAAGCGCCGCTAATGCTCAAGGCTTTAGCGACATT
Found at i:55815436 original size:73 final size:73
Alignment explanation
Indices: 55815336--55815476 Score: 237
Period size: 73 Copynumber: 1.9 Consensus size: 73
55815326 AATTTTTGAA
* * *
55815336 AAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTGTGAGCTTTGGGGGATTTAGCGGCGT
1 AAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGCTTTCGGGGATTTAGCGGCGT
55815401 TTTCGATG
66 TTTCGATG
* *
55815409 AAGCGCCGCAAAAAACCTAAGGCAAAACGACGCCGTTTTATGAGCTTTCGGGGATTTAGCGGTGT
1 AAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGCTTTCGGGGATTTAGCGGCGT
55815474 TTT
66 TTT
55815477 TAAGAAAGCG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (73 bp):
AAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGCTTTCGGGGATTTAGCGGCGT
TTTCGATG
Found at i:55815486 original size:73 final size:73
Alignment explanation
Indices: 55815317--55815490 Score: 235
Period size: 73 Copynumber: 2.4 Consensus size: 73
55815307 TGCTCAAGGC
* * * *
55815317 TTTAGCGGTAATTTTTGA-AAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTGTGAGC
1 TTTAGCGGT-GTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGC
*
55815381 TTTGGGGGA
65 TTTCGGGGA
* * * *
55815390 TTTAGCGGCGTTTTCGATG-AAGCGCCGCAAAAAACCTAAGGCAAAACGACGCCGTTTTATGAGC
1 TTTAGCGGTGTTTT-TAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGC
55815454 TTTCGGGGA
65 TTTCGGGGA
55815463 TTTAGCGGTGTTTTTAAGAAAGCGCCGC
1 TTTAGCGGTGTTTTTAAGAAAGCGCCGC
55815491 TAATGCTTAG
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
72 6 0.07
73 80 0.93
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (73 bp):
TTTAGCGGTGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGCT
TTCGGGGA
Found at i:55815515 original size:114 final size:116
Alignment explanation
Indices: 55815390--55815609 Score: 340
Period size: 114 Copynumber: 1.9 Consensus size: 116
55815380 CTTTGGGGGA
*
55815390 TTTAGCGGCGTTTTCGATG-AAGCGCCGCAAAAAACCTAAGG-CAAAACGACGCCG-TTTTATGA
1 TTTAGCGGCGTTTTCGA-GAAAGCGCCGCAAAAAA-CTAAGGCCAAAACAACGCCGTTTTTATGA
*
55815452 GCTTTCGGGGATTTAGCGGTG-TTTTTAAGAAAGCGCCGCTAATGCTTAGGGC
64 GCTTTCGGGGATTTAGCGGCGTTTTTTAAGAAAGCGCCGCTAATGCTTAGGGC
** * *
55815504 TTTAGCGGCGTTTTTTAGAAAGCGCCGCAAAAAACTTAGGCCAAAACAACGCCGTTTTTGTGAGC
1 TTTAGCGGCGTTTTCGAGAAAGCGCCGCAAAAAACTAAGGCCAAAACAACGCCGTTTTTATGAGC
55815569 TTTCGGGGATTTAGCGGCGTTTTTTAAGAAAGCGCCGCTAA
66 TTTCGGGGATTTAGCGGCGTTTTTTAAGAAAGCGCCGCTAA
55815610 GAACCTAAGC
Statistics
Matches: 96, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
113 6 0.06
114 42 0.44
115 27 0.28
116 21 0.22
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (116 bp):
TTTAGCGGCGTTTTCGAGAAAGCGCCGCAAAAAACTAAGGCCAAAACAACGCCGTTTTTATGAGC
TTTCGGGGATTTAGCGGCGTTTTTTAAGAAAGCGCCGCTAATGCTTAGGGC
Found at i:55815542 original size:42 final size:41
Alignment explanation
Indices: 55815463--55815543 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
55815453 CTTTCGGGGA
* * **
55815463 TTTAGCGGTGTTTTTAAGAAAGCGCCGCTAATGCTTAGGGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAACTTAGGGC
*
55815504 TTTAGCGGCGTTTTTTAGAAAGCGCCGCAAAAAACTTAGG
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGC-AAAAACTTAGG
55815544 CCAAAACAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 26 0.76
42 8 0.24
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAACTTAGGGC
Found at i:55815651 original size:74 final size:74
Alignment explanation
Indices: 55815504--55815752 Score: 299
Period size: 73 Copynumber: 3.4 Consensus size: 74
55815494 TGCTTAGGGC
* * * *
55815504 TTTAGCGGCGTTTTTT-AGAAAGCGCCGCAAAAAACTTAGGCCAAAACAACGCCGTTTTTGTGAG
1 TTTAGCGGCGTTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTT-TGAG
55815568 CTTTCGGGGA
65 CTTTCGGGGA
* *
55815578 TTTAGCGGCGTTTTTTAAGAAAGCGCCGCTAAGAACCTAAGCCAAAACGACGTCGTTTTTTGAGC
1 TTTAGCGGCGTTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTTTGAGC
*
55815643 TTTGGGGGA
66 TTTCGGGGA
* * * * * * * *
55815652 TTTAGTGGCG-TTTATGAGGAAGCGCCGCAAAAAAACCT-ATCCAAAATGGCGTCGTTTTATGAG
1 TTTAGCGGCGTTTTTTAAGAAAGCGCCGC-AAAAAACCTAAGCCAAAACGACGTCGTTTTTTGAG
55815715 CTTTCGGGGA
65 CTTTCGGGGA
* *
55815725 TTTAGCGGC-ATTTTTAGGAAAGCGCCGC
1 TTTAGCGGCGTTTTTTAAGAAAGCGCCGC
55815753 TAATGCTTAG
Statistics
Matches: 149, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
73 67 0.45
74 45 0.30
75 37 0.25
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (74 bp):
TTTAGCGGCGTTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTTTGAGC
TTTCGGGGA
Found at i:55815967 original size:14 final size:14
Alignment explanation
Indices: 55815931--55815984 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
55815921 TTAAATATCA
55815931 TTATAGTTTAGGGT
1 TTATAGTTTAGGGT
* *
55815945 TTTTGGTTTAGGGT
1 TTATAGTTTAGGGT
* *
55815959 ATATAGTTTAGAGT
1 TTATAGTTTAGGGT
*
55815973 TTAAAGTTTAGG
1 TTATAGTTTAGG
55815985 TGTTACCATT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (14 bp):
TTATAGTTTAGGGT
Found at i:55816019 original size:22 final size:21
Alignment explanation
Indices: 55815994--55816046 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
55815984 GTGTTACCAT
*
55815994 TTTAAGGTTTATTGATTATGGG
1 TTTAAGGTTTATGGATTAT-GG
* *
55816016 TTTAAGGGTTATGGTTTATGG
1 TTTAAGGTTTATGGATTATGG
55816037 TTTAAAGGTT
1 TTT-AAGGTT
55816047 GGGGTTTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (21 bp):
TTTAAGGTTTATGGATTATGG
Found at i:55816040 original size:21 final size:21
Alignment explanation
Indices: 55815994--55816122 Score: 70
Period size: 21 Copynumber: 6.2 Consensus size: 21
55815984 GTGTTACCAT
* * *
55815994 TTTAAGGTTTATTGATTATGGG
1 TTTAAGGGTTATGGTTTAT-GG
55816016 TTTAAGGGTTATGGTTTATGG
1 TTTAAGGGTTATGGTTTATGG
* ** *
55816037 TTTAAAGGTTGGGGTTTAAGG
1 TTTAAGGGTTATGGTTTATGG
**
55816058 TTT-AGAGGTTAT-GTGCAT-G
1 TTTAAG-GGTTATGGTTTATGG
*
55816077 -TTAAGGGGTTATGGTTTTAGGG
1 TTTAA-GGGTTATGG-TTTATGG
* * *
55816099 TTT-ATGTTTATGGTTTAGGG
1 TTTAAGGGTTATGGTTTATGG
55816119 TTTA
1 TTTA
55816123 GATTAACTAG
Statistics
Matches: 81, Mismatches: 18, Indels: 17
0.70 0.16 0.15
Matches are distributed among these distances:
18 2 0.02
19 8 0.10
20 16 0.20
21 35 0.43
22 18 0.22
23 2 0.02
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.47
Consensus pattern (21 bp):
TTTAAGGGTTATGGTTTATGG
Found at i:55816437 original size:21 final size:21
Alignment explanation
Indices: 55816413--55816453 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
55816403 ATTTAAAGGT
55816413 TTAGGGGTT-AGTAGTTAGGGG
1 TTAGGGGTTAAG-AGTTAGGGG
55816434 TTAGGGGTTAAGAGTTAGGG
1 TTAGGGGTTAAGAGTTAGGG
55816454 ATTTACGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.22, C:0.00, G:0.46, T:0.32
Consensus pattern (21 bp):
TTAGGGGTTAAGAGTTAGGGG
Found at i:55816763 original size:29 final size:29
Alignment explanation
Indices: 55816730--55816803 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 29
55816720 TATTTTTCGT
55816730 GATTTAAAATTTTAAAATAAATTTT-AAAA
1 GATTTAAAATTTTAAAA-AAATTTTAAAAA
*
55816759 GATTTCAAAATTTTTAAAAAATTTTAAAAA
1 GATTT-AAAATTTTAAAAAAATTTTAAAAA
*
55816789 GAATTTAAACTTTTA
1 G-ATTTAAAATTTTA
55816804 TTTTTATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 12 0.31
30 23 0.59
31 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (29 bp):
GATTTAAAATTTTAAAAAAATTTTAAAAA
Found at i:55816775 original size:19 final size:19
Alignment explanation
Indices: 55816751--55816787 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55816741 TTAAAATAAA
*
55816751 TTTTAAAAGATTTCAAAAT
1 TTTTAAAAAATTTCAAAAT
*
55816770 TTTTAAAAAATTTTAAAA
1 TTTTAAAAAATTTCAAAA
55816788 AGAATTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (19 bp):
TTTTAAAAAATTTCAAAAT
Found at i:55816778 original size:10 final size:10
Alignment explanation
Indices: 55816735--55816788 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
55816725 TTCGTGATTT
55816735 AAAATTTTAAA
1 AAAATTTT-AA
55816746 ATAAATTTTAA
1 A-AAATTTTAA
* *
55816757 AAGA-TTTCA
1 AAAATTTTAA
*
55816766 AAATTTTTAA
1 AAAATTTTAA
55816776 AAAATTTTAA
1 AAAATTTTAA
55816786 AAA
1 AAA
55816789 GAATTTAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
9 6 0.17
10 18 0.51
11 4 0.11
12 7 0.20
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:55817328 original size:68 final size:69
Alignment explanation
Indices: 55817251--55817389 Score: 244
Period size: 68 Copynumber: 2.0 Consensus size: 69
55817241 TTTGATACAG
55817251 AAATTTAATTTTTAGCAAAAATTATACAATTAGTGCCG-TTTTTTATAAGCGCCACAAATATTTA
1 AAATTTAATTTTTAGCAAAAATTATACAATTAGTGCCGTTTTTTTATAAGCGCCACAAATATTTA
55817315 CAAT
66 CAAT
* *
55817319 AAATTTAATTTTTAGCAAAAATTATACAATTAGTGGCGTTTTTTTTTTAAGCGCCACAAATATTT
1 AAATTTAATTTTTAGCAAAAATTATACAATTAGTGCCG-TTTTTTTATAAGCGCCACAAATATTT
55817384 ACAAT
65 ACAAT
55817389 A
1 A
55817390 CCAAAATGGC
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 37 0.55
70 30 0.45
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (69 bp):
AAATTTAATTTTTAGCAAAAATTATACAATTAGTGCCGTTTTTTTATAAGCGCCACAAATATTTA
CAAT
Done.