Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 180 of 204
Found at i:53395826 original size:25 final size:27
Alignment explanation
Indices: 53395784--53395840 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 27
53395774 AAATAATTTT
* *
53395784 TAAAATTTTAAATATTTATAAAAATTC
1 TAAAATTTTAAATATTTAAAAAAATTA
*
53395811 TAAAA-TTTATAT-TTTAAAAAAATTA
1 TAAAATTTTAAATATTTAAAAAAATTA
53395836 TAAAA
1 TAAAA
53395841 ACTAAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 16 0.59
26 6 0.22
27 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAAATTTTAAATATTTAAAAAAATTA
Found at i:53400890 original size:27 final size:27
Alignment explanation
Indices: 53400852--53400911 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
53400842 GATATTTATA
*
53400852 TATGCTAAGAGAACATTGTAAAGTTCT
1 TATGCTAAGAGAACATTATAAAGTTCT
53400879 TATGCTAAGAGAACATTATAAAGTTCT
1 TATGCTAAGAGAACATTATAAAGTTCT
53400906 TATGCT
1 TATGCT
53400912 TGTTTAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (27 bp):
TATGCTAAGAGAACATTATAAAGTTCT
Found at i:53403602 original size:34 final size:35
Alignment explanation
Indices: 53403562--53403635 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 35
53403552 AGCATATATT
* *
53403562 TATACTTATCAAT-TACATGTGCCGAATGCA-CATA
1 TATACTTAT-AATCCACATATGCCGAATGCAGCATA
53403596 TATACTTATAATCCACATATGCCGAATGCATGCATA
1 TATACTTATAATCCACATATGCCGAATGCA-GCATA
53403632 TATA
1 TATA
53403636 TATCCAACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 3 0.09
34 24 0.69
36 8 0.23
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.32
Consensus pattern (35 bp):
TATACTTATAATCCACATATGCCGAATGCAGCATA
Found at i:53403852 original size:41 final size:41
Alignment explanation
Indices: 53403802--53404039 Score: 309
Period size: 41 Copynumber: 5.8 Consensus size: 41
53403792 TTAATTTAAA
*
53403802 CAGATTCACCGGCACTTAGCCTGTTAGGCTTAAAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
*
53403844 CAGATCACCGACACTTAGCCTGCTAGGCTTATAA-CCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTA-AAGCCTGATT
* *
53403885 CAGATCACCGGCACTTAGCCTGTTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
* * *
53403926 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCTTGGTT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
* *
53403967 CAGATCACCGGCACTTAGCCTGCTAGGTTTTAAAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGG-CTTAAAGCCTGATT
* ** *
53404009 TAG-TACACCGGCTTTTAGCCTGCTAGACTTA
1 CAGAT-CACCGGCACTTAGCCTGCTAGGCTTA
53404040 TAGTCCGAAA
Statistics
Matches: 174, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
40 1 0.01
41 137 0.79
42 36 0.21
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
Found at i:53404324 original size:23 final size:23
Alignment explanation
Indices: 53404294--53404340 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
53404284 GATCCAACCA
53404294 AACACATTTATATATAACTTCAT
1 AACACATTTATATATAACTTCAT
53404317 AACACATTTATATATAACTTCAT
1 AACACATTTATATATAACTTCAT
53404340 A
1 A
53404341 CTTTAGATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (23 bp):
AACACATTTATATATAACTTCAT
Found at i:53404895 original size:74 final size:74
Alignment explanation
Indices: 53404768--53405114 Score: 480
Period size: 74 Copynumber: 4.5 Consensus size: 74
53404758 ACATTCAACA
*
53404768 TTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATAT----ATATATCCGAACTTTATATATATAAATAT
53404832 AACATACATACTT
62 AACATACATACTT
53404845 TTAACTAAATTCAAGAATTTATTCATGTATATATATATCCGAACTTTATATATATAAATATAACA
1 TTAACTAAATTCAAGAATTTATTCATGTATATATATATCCGAACTTTATATATATAAATATAACA
*
53404910 TACATAATT
66 TACATACTT
53404919 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATATCCGAACTTTATATATATAAAT
1 TTAACTAAATTCAAGAATTTATTCATG----T--ATATATATATCCGAACTTTATATATATAAAT
53404984 ATAACATACATACTT
60 ATAACATACATACTT
* * *
53404999 TTAACTAAATTCAAGAACTTATACATCTATATACATATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAA-TT-TA-TTC-ATGTATATATATATCCGAACTTTATATATATAAATAT
53405064 AACATACATACTT
62 AACATACATACTT
* * * *
53405077 TTAACTAAATTCAAGAACTTATACATCTATATACATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATATATAT
53405115 ATTATCCACT
Statistics
Matches: 247, Mismatches: 12, Indels: 25
0.87 0.04 0.09
Matches are distributed among these distances:
74 79 0.32
75 1 0.00
76 2 0.01
77 15 0.06
78 79 0.32
80 63 0.26
81 2 0.01
82 2 0.01
83 2 0.01
84 2 0.01
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (74 bp):
TTAACTAAATTCAAGAATTTATTCATGTATATATATATCCGAACTTTATATATATAAATATAACA
TACATACTT
Found at i:53405052 original size:78 final size:78
Alignment explanation
Indices: 53404667--53405121 Score: 563
Period size: 78 Copynumber: 5.9 Consensus size: 78
53404657 TATATTACAC
* * * * * *
53404667 ATATATATATGTAACATCCATACTTTTAA-TAAAATCCAAGAATTTATAC-TCATATATACATAC
1 ATATATAAATATAACATACATACTTTTAACT-AAATTCAAGAACTTATACATC-TATATACATAT
* * *
53404730 CTATTCGAACCTCTTGT
64 ATATCCGAA-CT-TTAT
* * * * * * *
53404747 A-A-ACATATATAACATTCA-AC-ATTAACTAAATTCAA-AACTTATTCATGTATATACACATAT
1 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATCTATATACATATAT
53404807 ATCCGAACTTTAT
66 ATCCGAACTTTAT
* * *
53404820 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAA-TT-TA-TTC-ATGTATATATAT
1 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATCTATATACATATAT
53404881 ATCCGAACTTTAT
66 ATCCGAACTTTAT
* * * *
53404894 ATATATAAATATAACATACATAATTTTAACTAAATTCAAGAATTTATTCATGTATATACATATAT
1 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATCTATATAC--ATAT
53404959 ATATCCGAACTTTAT
64 ATATCCGAACTTTAT
53404974 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATCTATATACATATAT
1 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATCTATATACATATAT
53405039 ATCCGAACTTTAT
66 ATCCGAACTTTAT
53405052 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATCTATATACATATAT
1 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATCTATATACATATA-
53405117 TATCC
65 TATCC
53405122 ACTATTAGTT
Statistics
Matches: 328, Mismatches: 33, Indels: 29
0.84 0.08 0.07
Matches are distributed among these distances:
73 4 0.01
74 66 0.20
75 39 0.12
76 16 0.05
77 20 0.06
78 102 0.31
79 6 0.02
80 75 0.23
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (78 bp):
ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATCTATATACATATAT
ATCCGAACTTTAT
Found at i:53425271 original size:15 final size:17
Alignment explanation
Indices: 53425251--53425287 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
53425241 ATATCAAAAA
53425251 ATAATA-TTAAA-AATC
1 ATAATACTTAAATAATC
*
53425266 ATAATACTTAAATAATT
1 ATAATACTTAAATAATC
53425283 ATAAT
1 ATAAT
53425288 TCCATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 8 0.42
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATACTTAAATAATC
Found at i:53427285 original size:19 final size:19
Alignment explanation
Indices: 53427245--53427286 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
53427235 AAATTTTATA
*
53427245 TTTAATTTATTATTTTAAT
1 TTTAATTTATTATTATAAT
*
53427264 TTTAATTTGA-TATTATATT
1 TTTAATTT-ATTATTATAAT
53427283 TTTA
1 TTTA
53427287 TAATGTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTAATTTATTATTATAAT
Found at i:53427286 original size:25 final size:25
Alignment explanation
Indices: 53427236--53427284 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
53427226 AATATGTCAA
53427236 AATTTTATATTTAATTTATTATTTT
1 AATTTTATATTTAATTTATTATTTT
*
53427261 AATTTTA-ATTTGATATTA-TATTTT
1 AATTTTATATTTAAT-TTATTATTTT
53427285 TATAATGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
AATTTTATATTTAATTTATTATTTT
Found at i:53431496 original size:33 final size:32
Alignment explanation
Indices: 53431452--53431627 Score: 120
Period size: 27 Copynumber: 5.4 Consensus size: 32
53431442 CGGTGGGATT
53431452 AGCACTTAGCAACCACCAATGAGTCGGGGAATC
1 AGCACTTAGCAACCACCAATGA-TCGGGGAATC
* *
53431485 AACACTTAGCAACC-CC--T--TGGGGGAATC
1 AGCACTTAGCAACCACCAATGATCGGGGAATC
* *
53431512 AGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATC
1 AGCACTTAGCAA-CCAC--CA-A--T--GAT-CGG-GGAATC
*
53431554 AGCACTTAGCAACCACCAATGATTCGGGAAATC
1 AGCACTTAGCAACCACCAATGA-TCGGGGAATC
*
53431587 AGCACTTAGCAACC-CC--T--TGGGGGAATC
1 AGCACTTAGCAACCACCAATGATCGGGGAATC
53431614 AGCACTTAGCAACC
1 AGCACTTAGCAACC
53431628 CCCTTTATAT
Statistics
Matches: 118, Mismatches: 9, Indels: 38
0.72 0.05 0.23
Matches are distributed among these distances:
27 42 0.36
28 2 0.02
29 1 0.01
30 2 0.02
31 1 0.01
32 4 0.03
33 32 0.27
34 4 0.03
35 1 0.01
36 2 0.02
38 1 0.01
39 2 0.02
40 1 0.01
41 5 0.04
42 18 0.15
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (32 bp):
AGCACTTAGCAACCACCAATGATCGGGGAATC
Found at i:53431581 original size:102 final size:102
Alignment explanation
Indices: 53431402--53431632 Score: 390
Period size: 102 Copynumber: 2.3 Consensus size: 102
53431392 CCAGTGATTC
* * * * *
53431402 GGGGAATCAGCACTGAGCAACCCCTTTCACATTTAAGATACGGTGGGATTAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
*
53431467 CCAATGAGTCGGGGAATCAACACTTAGCAACCCCTTG
66 CCAATGAGTCGGGAAATCAACACTTAGCAACCCCTTG
53431504 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
* *
53431569 CCAATGATTCGGGAAATCAGCACTTAGCAACCCCTTG
66 CCAATGAGTCGGGAAATCAACACTTAGCAACCCCTTG
53431606 GGGGAATCAGCACTTAGCAACCCCCTT
1 GGGGAATCAGCACTTAGCAACCCCCTT
53431633 TATATTCAAT
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 121 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAGTCGGGAAATCAACACTTAGCAACCCCTTG
Found at i:53433341 original size:57 final size:57
Alignment explanation
Indices: 53433253--53433366 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
53433243 TAGAGTAGCA
*
53433253 GAACGGAAACATCGACATATTGTTGAGGTCAGTTTTATGCTTTTTGCTCAAGCAAAT
1 GAACGGAAACAACGACATATTGTTGAGGTCAGTTTTATGCTTTTTGCTCAAGCAAAT
53433310 GAACGGAAACAACGACATATTGTTGAGGTCAGTTTTATGCTTTTTGCTCAAGCAAAT
1 GAACGGAAACAACGACATATTGTTGAGGTCAGTTTTATGCTTTTTGCTCAAGCAAAT
53433367 CTGCCATTGA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (57 bp):
GAACGGAAACAACGACATATTGTTGAGGTCAGTTTTATGCTTTTTGCTCAAGCAAAT
Found at i:53442581 original size:20 final size:19
Alignment explanation
Indices: 53442556--53442596 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
53442546 AAATTAAGAG
53442556 TTATTT-TTTAATTTCATGTA
1 TTATTTATTT-ATTTCAT-TA
53442576 TTATTTATTTATTTCATTA
1 TTATTTATTTATTTCATTA
53442595 TT
1 TT
53442597 TTTCACATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 13 0.65
21 3 0.15
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (19 bp):
TTATTTATTTATTTCATTA
Found at i:53443329 original size:19 final size:17
Alignment explanation
Indices: 53443305--53443366 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 17
53443295 TAAAGGCTGA
53443305 GAAATAAAAGTTTTGGGGG
1 GAAATAAAAGTTTT--GGG
53443324 GAAATAAAAAGTTTTGGG
1 GAAAT-AAAAGTTTTGGG
53443342 G-AATAAAAG-TTTGAGG
1 GAAATAAAAGTTTTG-GG
53443358 GAAAGTAAA
1 GAAA-TAAA
53443367 TAGGGGGAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.10
16 8 0.21
17 5 0.13
18 8 0.21
19 5 0.13
20 9 0.23
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (17 bp):
GAAATAAAAGTTTTGGG
Found at i:53443335 original size:20 final size:19
Alignment explanation
Indices: 53443305--53443353 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
53443295 TAAAGGCTGA
53443305 GAAATAAAAGTTTTGGGGG
1 GAAATAAAAGTTTTGGGGG
53443324 GAAATAAAAAGTTTT--GGG
1 GAAAT-AAAAGTTTTGGGGG
53443342 G-AATAAAAGTTT
1 GAAATAAAAGTTT
53443354 GAGGGAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.28
17 3 0.10
18 4 0.14
19 5 0.17
20 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (19 bp):
GAAATAAAAGTTTTGGGGG
Found at i:53443485 original size:30 final size:31
Alignment explanation
Indices: 53443446--53443505 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
53443436 AGAGGTGGGA
*
53443446 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
53443477 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
53443506 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:53445838 original size:46 final size:46
Alignment explanation
Indices: 53445782--53445874 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
53445772 TATAAGTGTA
* *
53445782 TAGATATGGCTTAGTATTTGATATCAATGAAACTTTTATATATGTG
1 TAGATATGGCTTAGTATTTAATATCAATAAAACTTTTATATATGTG
53445828 TAGATATGGCTTAGTATTTAATATCAATAAAACTTTTATATATGTG
1 TAGATATGGCTTAGTATTTAATATCAATAAAACTTTTATATATGTG
53445874 T
1 T
53445875 TGATGTGTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.44
Consensus pattern (46 bp):
TAGATATGGCTTAGTATTTAATATCAATAAAACTTTTATATATGTG
Found at i:53446949 original size:5 final size:5
Alignment explanation
Indices: 53446941--53446969 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
53446931 TCAAGTCAAG
53446941 TCGAA TCGAA TCGAA TCGAA TCGAA TCGA
1 TCGAA TCGAA TCGAA TCGAA TCGAA TCGA
53446970 GTGAAATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (5 bp):
TCGAA
Found at i:53453113 original size:2 final size:2
Alignment explanation
Indices: 53453106--53453131 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53453096 TCTCCTTACC
53453106 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
53453132 TTGTAACGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53453951 original size:27 final size:27
Alignment explanation
Indices: 53453913--53453986 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
53453903 ACTGGGTCAG
*
53453913 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAATACCATTGGCGGCACCAATGGT
*
53453940 GCCAATACCATTAGCGGCACCAATGGT
1 GCCAATACCATTGGCGGCACCAATGGT
*
53453967 GCC-ATACTGATTGGCGGCAC
1 GCCAATAC-CATTGGCGGCAC
53453987 TACTCGTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.10
27 38 0.90
ACGTcount: A:0.24, C:0.30, G:0.27, T:0.19
Consensus pattern (27 bp):
GCCAATACCATTGGCGGCACCAATGGT
Found at i:53454232 original size:3 final size:3
Alignment explanation
Indices: 53454226--53454254 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
53454216 ATTATTATTA
53454226 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
53454255 AGTATTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:53460464 original size:24 final size:25
Alignment explanation
Indices: 53460437--53460523 Score: 83
Period size: 26 Copynumber: 3.4 Consensus size: 25
53460427 ATGTACATAT
53460437 CATAACA-AAAATACGTATAATGTA
1 CATAACATAAAATACGTATAATGTA
53460461 CATAACATCAAAATA--TAT-ATGCTA
1 CATAACAT-AAAATACGTATAATG-TA
* *
53460485 AATAAAATATTAAAATACGTATAATGTA
1 CAT--AACA-TAAAATACGTATAATGTA
53460513 CATAACATAAA
1 CATAACATAAA
53460524 TTTTTAACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
23 3 0.06
24 14 0.28
25 4 0.08
26 18 0.36
27 1 0.02
28 7 0.14
29 3 0.06
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (25 bp):
CATAACATAAAATACGTATAATGTA
Found at i:53460637 original size:10 final size:9
Alignment explanation
Indices: 53460595--53460838 Score: 74
Period size: 10 Copynumber: 26.3 Consensus size: 9
53460585 TGCTTCCCTC
53460595 TTCTTCTTCT
1 TTCTT-TTCT
53460605 TT-TTTT-T
1 TTCTTTTCT
53460612 TTCTCTTCTCCT
1 TTCT-TT-T-CT
53460624 TTCCTTTTCT
1 TT-CTTTTCT
53460634 TTCCTTCTT-T
1 TT-CTT-TTCT
53460644 TTC-TTTC-
1 TTCTTTTCT
53460651 TT-TTTTCT
1 TTCTTTTCT
*
53460659 TCTCCTTTCCT
1 T-T-CTTTTCT
53460670 CTTCTTCTTCT
1 -TTCTT-TTCT
53460681 TTCTTTT-T
1 TTCTTTTCT
53460689 TT-TTTCTCCT
1 TTCTTT-T-CT
53460699 TTCCTTTTCT
1 TT-CTTTTCT
53460709 TTCCTTCTT-T
1 TT-CTT-TTCT
53460719 TTC-TTTC-
1 TTCTTTTCT
53460726 TT-TTTTCT
1 TTCTTTTCT
*
53460734 TCTCCTTTCCT
1 T-T-CTTTTCT
53460745 CTTCTTCTTCT
1 -TTCTT-TTCT
53460756 TTCTTTT-T
1 TTCTTTTCT
53460764 TT-TTTCTCCT
1 TTCTTT-T-CT
53460774 TTCCTTTTCT
1 TT-CTTTTCT
53460784 TTCCTTCTT-T
1 TT-CTT-TTCT
53460794 TTC-TTTCT
1 TTCTTTTCT
* * *
53460802 TTCCTCTCC
1 TTCTTTTCT
* *
53460811 TTCCTTCCT
1 TTCTTTTCT
53460820 TTC-TTTCT
1 TTCTTTTCT
53460828 TTC-TTTCT
1 TTCTTTTCT
53460836 TTC
1 TTC
53460839 CCTCTCCTTC
Statistics
Matches: 187, Mismatches: 10, Indels: 76
0.68 0.04 0.28
Matches are distributed among these distances:
7 27 0.14
8 35 0.19
9 25 0.13
10 58 0.31
11 27 0.14
12 13 0.07
13 2 0.01
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (9 bp):
TTCTTTTCT
Found at i:53460643 original size:13 final size:13
Alignment explanation
Indices: 53460627--53460839 Score: 86
Period size: 14 Copynumber: 16.8 Consensus size: 13
53460617 TTCTCCTTTC
53460627 CTTTTCTTTCCTT
1 CTTTTCTTTCCTT
53460640 CTTTTTCTTT-CTT
1 C-TTTTCTTTCCTT
53460653 -TTTTCTTCTCCTTT
1 CTTTTCTT-TCC-TT
*
53460667 CCTCTTC-TT-CTT
1 -CTTTTCTTTCCTT
53460679 C-TTTCTTT--TT
1 CTTTTCTTTCCTT
*
53460689 -TTTT-TCTCCTTT
1 CTTTTCTTTCC-TT
53460701 CCTTTTCTTTCCTT
1 -CTTTTCTTTCCTT
53460715 CTTTTTCTTT-CTT
1 C-TTTTCTTTCCTT
53460728 -TTTTCTTCTCCTTT
1 CTTTTCTT-TCC-TT
*
53460742 CCTCTTC-TT-CTT
1 -CTTTTCTTTCCTT
53460754 C-TTTCTTT--TT
1 CTTTTCTTTCCTT
*
53460764 -TTTT-TCTCCTTT
1 CTTTTCTTTCC-TT
53460776 CCTTTTCTTTCCTT
1 -CTTTTCTTTCCTT
*
53460790 CTTTTTCTTTCTTT
1 C-TTTTCTTTCCTT
* * *
53460804 CCTCTCCTTCCTT
1 CTTTTCTTTCCTT
* *
53460817 CCTTTCTTTCTTT
1 CTTTTCTTTCCTT
53460830 C-TTTCTTTCC
1 CTTTTCTTTCC
53460840 CTCTCCTTCT
Statistics
Matches: 154, Mismatches: 17, Indels: 59
0.67 0.07 0.26
Matches are distributed among these distances:
9 4 0.03
10 16 0.10
11 20 0.13
12 18 0.12
13 32 0.21
14 46 0.30
15 10 0.06
16 8 0.05
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
CTTTTCTTTCCTT
Found at i:53460650 original size:4 final size:4
Alignment explanation
Indices: 53460629--53460838 Score: 92
Period size: 4 Copynumber: 53.0 Consensus size: 4
53460619 CTCCTTTCCT
*
53460629 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC
* * *
53460674 -TTC -TTC TTTC TTT- TTTT TTTC -TCC TTTCC TTTTC TTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C -TTTC TTTC TTTC TTTC
53460718 TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC -TTC -TTC TTTC TTT-
1 TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC TTTC TTTC TTTC TTTC
* * * *
53460762 TTTT TTTC -TCC TTTCC TTTTC TTTC CTTC -TT- TTTC TTTC TTTCC TCTCC
1 TTTC TTTC TTTC TTT-C -TTTC TTTC TTTC TTTC TTTC TTTC TTT-C T-TTC
* *
53460811 TTCC TTCC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
53460839 CCTCTCCTTC
Statistics
Matches: 169, Mismatches: 11, Indels: 52
0.73 0.05 0.22
Matches are distributed among these distances:
3 40 0.24
4 92 0.54
5 20 0.12
6 17 0.10
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:53460707 original size:75 final size:75
Alignment explanation
Indices: 53460591--53460837 Score: 401
Period size: 75 Copynumber: 3.3 Consensus size: 75
53460581 TCCTTGCTTC
53460591 CCTCTTCTTCTTCTTT-TTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTT
1 CCTCTTCTTCTTCTTTCTTTTTTT-T-TTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTT
53460655 TTCTTCTCCTTT
64 TTCTTCTCCTTT
53460667 CCTCTTCTTCTTCTTTCTTTTTTTTTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTT
1 CCTCTTCTTCTTCTTTCTTTTTTTTTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTT
53460732 CTTCTCCTTT
66 CTTCTCCTTT
**
53460742 CCTCTTCTTCTTCTTTCTTTTTTTTTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCT
1 CCTCTTCTTCTTCTTTCTTTTTTTTTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTT
*
53460807 CTCCTTCC-TT
66 CTTC-TCCTTT
53460817 CCT-TTCTTTCTTTCTTTCTTT
1 CCTCTTC-TTC-TTCTTTCTTT
53460838 CCCTCTCCTT
Statistics
Matches: 164, Mismatches: 3, Indels: 8
0.94 0.02 0.05
Matches are distributed among these distances:
74 3 0.02
75 124 0.76
76 30 0.18
77 7 0.04
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (75 bp):
CCTCTTCTTCTTCTTTCTTTTTTTTTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTT
CTTCTCCTTT
Found at i:53460729 original size:42 final size:42
Alignment explanation
Indices: 53460670--53460803 Score: 187
Period size: 42 Copynumber: 3.4 Consensus size: 42
53460660 CTCCTTTCCT
*
53460670 CTTCTTCTTCTTTCTTTTTTTTTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTTTTTTTTCTCCTTTCCTTTTCTTTC
*
53460712 CTTCTTTTTCTTTC-TTTTTTCTTCTCCTTTCC---TC-TT-
1 CTTCTTTTTCTTTCTTTTTTTTTTCTCCTTTCCTTTTCTTTC
53460748 CTTC---TTCTTTCTTTTTTTTTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTTTTTTTTCTCCTTTCCTTTTCTTTC
53460787 CTTCTTTTTCTTTCTTT
1 CTTCTTTTTCTTTCTTT
53460804 CCTCTCCTTC
Statistics
Matches: 80, Mismatches: 3, Indels: 18
0.79 0.03 0.18
Matches are distributed among these distances:
33 7 0.09
34 17 0.21
36 4 0.05
37 4 0.05
38 4 0.05
39 4 0.05
41 17 0.21
42 23 0.29
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (42 bp):
CTTCTTTTTCTTTCTTTTTTTTTTCTCCTTTCCTTTTCTTTC
Found at i:53461026 original size:23 final size:24
Alignment explanation
Indices: 53461000--53461062 Score: 92
Period size: 26 Copynumber: 2.6 Consensus size: 24
53460990 TTTTTTTGGT
53461000 ATATTTTGGTAATTAAAAAA-ATA
1 ATATTTTGGTAATTAAAAAAGATA
*
53461023 ATATTTTGGTAAATAAAAAAAGGATA
1 ATATTTTGGT-AATTAAAAAA-GATA
53461049 ATATTTTGGTAATT
1 ATATTTTGGTAATT
53461063 TTAATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 10 0.29
24 9 0.26
25 3 0.09
26 13 0.37
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.40
Consensus pattern (24 bp):
ATATTTTGGTAATTAAAAAAGATA
Found at i:53467156 original size:34 final size:34
Alignment explanation
Indices: 53467117--53467189 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
53467107 CAAATGATAG
53467117 TGTTAATTATTTCCATTAATACATGACATGTATA
1 TGTTAATTATTTCCATTAATACATGACATGTATA
53467151 TGTTAATTATTTCCATTAATACATGACATGTATA
1 TGTTAATTATTTCCATTAATACATGACATGTATA
53467185 TGTTA
1 TGTTA
53467190 TAAACTAGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (34 bp):
TGTTAATTATTTCCATTAATACATGACATGTATA
Found at i:53471509 original size:28 final size:28
Alignment explanation
Indices: 53471469--53471546 Score: 138
Period size: 28 Copynumber: 2.8 Consensus size: 28
53471459 CTCACTCATT
*
53471469 TGTTAGAAAGAGTACGGAATCTAAGGAA
1 TGTTAGAAAGAGTACAGAATCTAAGGAA
53471497 TGTTAGAAAGAGTACAGAATCTAAGGAA
1 TGTTAGAAAGAGTACAGAATCTAAGGAA
*
53471525 TGTTAGAAAGAGTACACAATCT
1 TGTTAGAAAGAGTACAGAATCT
53471547 GTAAATAGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (28 bp):
TGTTAGAAAGAGTACAGAATCTAAGGAA
Found at i:53471783 original size:138 final size:138
Alignment explanation
Indices: 53471532--53471809 Score: 538
Period size: 138 Copynumber: 2.0 Consensus size: 138
53471522 GAATGTTAGA
53471532 AAGAGTACACAATCTGTAAATAGATACAATTTCTGCTCTGCTATGGTTTCTATCCTTGCAGCTAA
1 AAGAGTACACAATCTGTAAATAGATACAATTTCTGCTCTGCTATGGTTTCTATCCTTGCAGCTAA
*
53471597 AAAGGATAACTTTTAGTTATTTCCCTCTCACATTTCTAAAGTTAACGTTTTCATCACTTATTTTT
66 AAAGGATAACTTTTAGTTATTTCCCTCTCACATTTCTAAAATTAACGTTTTCATCACTTATTTTT
53471662 GTCAAGTT
131 GTCAAGTT
53471670 AAGAGTACACAATCTGTAAATAGATACAATTTCTGCTCTGCTATGGTTTCTATCCTTGCAGCTAA
1 AAGAGTACACAATCTGTAAATAGATACAATTTCTGCTCTGCTATGGTTTCTATCCTTGCAGCTAA
*
53471735 AAAGGATAACTTTTAGTTATTTCCCTCTCACATTTCTAAAATTTACGTTTTCATCACTTATTTTT
66 AAAGGATAACTTTTAGTTATTTCCCTCTCACATTTCTAAAATTAACGTTTTCATCACTTATTTTT
53471800 GTCAAGTT
131 GTCAAGTT
53471808 AA
1 AA
53471810 CGTTTTCATC
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 138 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (138 bp):
AAGAGTACACAATCTGTAAATAGATACAATTTCTGCTCTGCTATGGTTTCTATCCTTGCAGCTAA
AAAGGATAACTTTTAGTTATTTCCCTCTCACATTTCTAAAATTAACGTTTTCATCACTTATTTTT
GTCAAGTT
Found at i:53479883 original size:23 final size:21
Alignment explanation
Indices: 53479857--53479901 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
53479847 AAATTGAAGG
*
53479857 ACCAAACTCTAATAAATTTTTAT
1 ACCAAA-TCT-ATAAATATTTAT
*
53479880 ACCAAATCTGTAAATATTTAT
1 ACCAAATCTATAAATATTTAT
53479901 A
1 A
53479902 TTTAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 3 0.15
23 6 0.30
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (21 bp):
ACCAAATCTATAAATATTTAT
Found at i:53480026 original size:48 final size:48
Alignment explanation
Indices: 53479950--53480045 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
53479940 CAAAACCACC
53479950 TTTCCTGATACCACTAGAAATCGAGTTGTTACAACGATAACTTTTCTT
1 TTTCCTGATACCACTAGAAATCGAGTTGTTACAACGATAACTTTTCTT
*
53479998 TTTCCTGATACCACTAGAAATCGGGTTGTTACAACGATAACTTTTCTT
1 TTTCCTGATACCACTAGAAATCGAGTTGTTACAACGATAACTTTTCTT
53480046 ATCAAGTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (48 bp):
TTTCCTGATACCACTAGAAATCGAGTTGTTACAACGATAACTTTTCTT
Found at i:53481419 original size:19 final size:19
Alignment explanation
Indices: 53481344--53481420 Score: 50
Period size: 19 Copynumber: 3.8 Consensus size: 19
53481334 TAAATTAGTT
53481344 AATTAAAATATGTTTTAAAAA
1 AATTAAAAT-TG-TTTAAAAA
* *
53481365 AATTATAA-CG-TTAATATTAA
1 AATTAAAATTGTTTAA-A--AA
* *
53481385 AATTTAAAAATATTTAAAAA
1 AA-TTAAAATTGTTTAAAAA
53481405 AATTAAAATTGTTTAA
1 AATTAAAATTGTTTAA
53481421 TTTTCAATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 13 0.30
20 8 0.19
21 12 0.28
22 1 0.02
23 4 0.09
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (19 bp):
AATTAAAATTGTTTAAAAA
Found at i:53482195 original size:45 final size:45
Alignment explanation
Indices: 53482144--53482234 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 45
53482134 AGGGAGTACC
*
53482144 ACAAGTAAAG-TTAAAGGGTTAACAAGTGT-TATATAGGG-TATAATA
1 ACAAGT-AAGTTTAAA-AGTTAACAAGTGTAT-TATAGGGTTATAATA
*
53482189 ACAAGTAGGTTTAAAAGTTAACAAGTGTATTATAGGGTTATAATA
1 ACAAGTAAGTTTAAAAGTTAACAAGTGTATTATAGGGTTATAATA
53482234 A
1 A
53482235 ATAATAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
44 21 0.51
45 20 0.49
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.31
Consensus pattern (45 bp):
ACAAGTAAGTTTAAAAGTTAACAAGTGTATTATAGGGTTATAATA
Found at i:53486464 original size:24 final size:24
Alignment explanation
Indices: 53486435--53486483 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
53486425 GGTAAACAAA
* *
53486435 TTGAAGCTAGAAGTTGAAATGATG
1 TTGAAGCTAGAAGCTGAAATAATG
*
53486459 TTGAAGCTTGAAGCTGAAATAATG
1 TTGAAGCTAGAAGCTGAAATAATG
53486483 T
1 T
53486484 AGCTGTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.31
Consensus pattern (24 bp):
TTGAAGCTAGAAGCTGAAATAATG
Found at i:53489457 original size:24 final size:22
Alignment explanation
Indices: 53489408--53489451 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
53489398 ACCCTTTCCA
53489408 TTATCAAATTTGCTATATATGC
1 TTATCAAATTTGCTATATATGC
53489430 TTATCAAATTTGCTATATATGC
1 TTATCAAATTTGCTATATATGC
53489452 ACTTATTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (22 bp):
TTATCAAATTTGCTATATATGC
Found at i:53493105 original size:6 final size:6
Alignment explanation
Indices: 53493094--53493119 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
53493084 AGGTGGGATG
53493094 GTGATT GTGATT GTGATT GTGATT GT
1 GTGATT GTGATT GTGATT GTGATT GT
53493120 TATTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (6 bp):
GTGATT
Found at i:53494393 original size:299 final size:301
Alignment explanation
Indices: 53493853--53494436 Score: 861
Period size: 299 Copynumber: 1.9 Consensus size: 301
53493843 ATAGGCCTTC
53493853 TCCAAATCTATCTTAATAACCATCCATATTTTGTGTTTGCTTCTCATGGAATAAATAACTTCTTG
1 TCCAAATCTATCTTAATAACCATCCATATTTTGTGTTTGCTTCTCATGGAATAAATAACTTCTTG
* * * *
53493918 GACGACTATGATATTGTTAGTGATGTTCCTTCCAGCAAAAAAACCCACCTGTTCTAGGTCAATGA
66 GACGACTATGATATTGTTAGTGATATTACTTCCAGCAAAAAAACCCACATGTTCTAGGCCAATGA
* * * * * *
53493983 TTCTAGGAAAAACAACCTTATATTTGTTCGGAATGGTATTTATGACTTGCATGTAAAGAACTGAA
131 TTCTAGGAAAAACAACCTTATATCTATTCAGAATGATATTTAGGACCTGCATGTAAAGAACTGAA
* * *
53494048 CACAAGTTTATTGGGCAAAATTGTGCAAAGTTTGTGCAATTAAAGGGTAGAAGGGATATATTAGA
196 CACAAATTTATTGGGCAAAATTGTGCAAAGTTTGTGCAATTAAAGGGTAGAAGGGATATATCAAA
53494113 GGGTACTTTATTGTCATGGAATTAAGAGGCATAATAGCTTA
261 GGGTACTTTATTGTCATGGAATTAAGAGGCATAATAGCTTA
* ** * *
53494154 TCCAAATCTATCTTGATGGCCATCCATCTTTTGTGTTTGC-TCTCATGG-ATGAATAACTTCTTG
1 TCCAAATCTATCTTAATAACCATCCATATTTTGTGTTTGCTTCTCATGGAATAAATAACTTCTTG
** * * * *
53494217 GGTGATTATGATATTGTTAGTGATATTACTTCCAG-AAATAAAACCCGCATTTTCTGGGCCAATG
66 GACGACTATGATATTGTTAGTGATATTACTTCCAGCAAA-AAAACCCACATGTTCTAGGCCAATG
* *
53494281 ATTCTAGGAAAAACAACCTTATATCTATTCAGAATGATCTTTAGGACCTGCTTGTAAAGAACTGA
130 ATTCTAGGAAAAACAACCTTATATCTATTCAGAATGATATTTAGGACCTGCATGTAAAGAACTGA
**
53494346 ACACAAATTTATTGGGTGAAATTGTGCAAAGTTCT-TGCAATTAAAGGGTAGAAGGGATATATCA
195 ACACAAATTTATTGGGCAAAATTGTGCAAAGTT-TGTGCAATTAAAGGGTAGAAGGGATATATCA
*
53494410 AAGGGTATTTTATTGTCATGGAATTAA
259 AAGGGTACTTTATTGTCATGGAATTAA
53494437 AAGGTAGAAT
Statistics
Matches: 252, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
298 3 0.01
299 204 0.81
300 9 0.04
301 36 0.14
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (301 bp):
TCCAAATCTATCTTAATAACCATCCATATTTTGTGTTTGCTTCTCATGGAATAAATAACTTCTTG
GACGACTATGATATTGTTAGTGATATTACTTCCAGCAAAAAAACCCACATGTTCTAGGCCAATGA
TTCTAGGAAAAACAACCTTATATCTATTCAGAATGATATTTAGGACCTGCATGTAAAGAACTGAA
CACAAATTTATTGGGCAAAATTGTGCAAAGTTTGTGCAATTAAAGGGTAGAAGGGATATATCAAA
GGGTACTTTATTGTCATGGAATTAAGAGGCATAATAGCTTA
Found at i:53494846 original size:25 final size:25
Alignment explanation
Indices: 53494806--53494854 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
53494796 TGCACACCAA
* *
53494806 ACAATTTTTCTTTATCATTTTTTTT
1 ACAATTTCTCTCTATCATTTTTTTT
53494831 ACAATTTCTCTCTATCATTTTTTT
1 ACAATTTCTCTCTATCATTTTTTT
53494855 GTACCCTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.63
Consensus pattern (25 bp):
ACAATTTCTCTCTATCATTTTTTTT
Found at i:53499249 original size:50 final size:50
Alignment explanation
Indices: 53499136--53499371 Score: 283
Period size: 50 Copynumber: 4.7 Consensus size: 50
53499126 ACATGTCAAA
** * *
53499136 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAAT
* ** *
53499187 GCCATGTCCCAGACATGATCTTACGGGGGACCTCTCGTCTCGGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
** *
53499237 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTGGTCTCGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
* ** * * * * *
53499287 GCCATGTTCCAGTTATGGTCTTTCATGAGAGCTCCCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
*
53499337 GCCGTGTCCCAGACATGGTCTTACATGGGACCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
53499372 TTACCCAAAT
Statistics
Matches: 153, Mismatches: 32, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
50 126 0.82
51 27 0.18
ACGTcount: A:0.18, C:0.30, G:0.25, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
Found at i:53499743 original size:30 final size:30
Alignment explanation
Indices: 53499709--53499766 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
53499699 CCTCGACTCT
53499709 AACTTTGTA-AAAATTACAATTTTGCCCCTA
1 AACTTT-TACAAAATTACAATTTTGCCCCTA
* *
53499739 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
53499767 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:53502485 original size:3 final size:3
Alignment explanation
Indices: 53502473--53502564 Score: 73
Period size: 3 Copynumber: 30.7 Consensus size: 3
53502463 AAGAGAAATG
* *
53502473 ATA ATAA ATA ATA ATA A-A GTA AGTA ATA ATA ATA GAT- ACA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA A-TA ATA ATA ATA -ATA ATA ATA ATA
* ** * *
53502519 GTA ATA GCA ATA TTA A-A ATA TTA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
53502565 GATAGTACTA
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
2 4 0.06
3 57 0.83
4 8 0.12
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:53503376 original size:16 final size:16
Alignment explanation
Indices: 53503355--53503385 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53503345 TTTATACTGA
*
53503355 AAATAATCATAATAAT
1 AAATAATAATAATAAT
53503371 AAATAATAATAATAA
1 AAATAATAATAATAA
53503386 ATCCTATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAATAATAAT
Found at i:53503381 original size:13 final size:13
Alignment explanation
Indices: 53503363--53503387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53503353 GAAAATAATC
53503363 ATAATAATAAATA
1 ATAATAATAAATA
53503376 ATAATAATAAAT
1 ATAATAATAAAT
53503388 CCTATATCTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATAATAAATA
Found at i:53503510 original size:36 final size:36
Alignment explanation
Indices: 53503463--53503543 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
53503453 AGGGCGACTT
*
53503463 GCTGCAACGTTCGCGGAGTTGCTGTGCATGGGTGAG
1 GCTGCTACGTTCGCGGAGTTGCTGTGCATGGGTGAG
*
53503499 GCTGCTACGTTCGCGGAGTTGCTGTGCGTGGGTGAG
1 GCTGCTACGTTCGCGGAGTTGCTGTGCATGGGTGAG
53503535 GCTGCTACG
1 GCTGCTACG
53503544 ACAGAGGCGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.11, C:0.21, G:0.42, T:0.26
Consensus pattern (36 bp):
GCTGCTACGTTCGCGGAGTTGCTGTGCATGGGTGAG
Found at i:53505818 original size:22 final size:22
Alignment explanation
Indices: 53505790--53505839 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
53505780 AAAATTTTTT
53505790 TAAAAAATTAAATTAAAAAAAA
1 TAAAAAATTAAATTAAAAAAAA
* * **
53505812 TAAAAAATTTATTTAAAAAGTA
1 TAAAAAATTAAATTAAAAAAAA
53505834 TAAAAA
1 TAAAAA
53505840 TTATAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (22 bp):
TAAAAAATTAAATTAAAAAAAA
Found at i:53505861 original size:12 final size:12
Alignment explanation
Indices: 53505846--53505871 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53505836 AAAATTATAA
53505846 AAAAATATTTTT
1 AAAAATATTTTT
53505858 AAAAATATTTTT
1 AAAAATATTTTT
53505870 AA
1 AA
53505872 TTTAAAAAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAAAATATTTTT
Found at i:53509808 original size:6 final size:6
Alignment explanation
Indices: 53509801--53509837 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
53509791 AAAACAAAAA
*
53509801 AAACAA AAACCAG AAACAG AAACAG AAACAG AAACAG
1 AAACAG AAA-CAG AAACAG AAACAG AAACAG AAACAG
53509838 GGAAGATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.68, C:0.19, G:0.14, T:0.00
Consensus pattern (6 bp):
AAACAG
Found at i:53517044 original size:24 final size:24
Alignment explanation
Indices: 53517012--53517060 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
53517002 ATAATGCCTT
53517012 AAACTCGTATTCTTAATTCGTTAA
1 AAACTCGTATTCTTAATTCGTTAA
53517036 AAACTCGTATTCTTAATTCGTTAA
1 AAACTCGTATTCTTAATTCGTTAA
53517060 A
1 A
53517061 CTGATGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (24 bp):
AAACTCGTATTCTTAATTCGTTAA
Found at i:53524318 original size:12 final size:11
Alignment explanation
Indices: 53524296--53524325 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
53524286 TAAAATTAGT
53524296 TAAATAATAAA
1 TAAATAATAAA
53524307 TAAATGAATAAA
1 TAAAT-AATAAA
53524319 TAAATAA
1 TAAATAA
53524326 AAAGGATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (11 bp):
TAAATAATAAA
Found at i:53524719 original size:31 final size:31
Alignment explanation
Indices: 53524626--53524721 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
53524616 GGCAAATTAC
*
53524626 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
53524657 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
53524689 AAGGGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
53524720 AA
1 AA
53524722 ATTATCTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:53527865 original size:14 final size:14
Alignment explanation
Indices: 53527846--53527896 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
53527836 AAGGTAGGAA
53527846 CTTTTTTTTTTGCG
1 CTTTTTTTTTTGCG
*
53527860 CTTTTTTGCTTTTTGCT
1 C-TTTTT--TTTTTGCG
*
53527877 TTTTTTTTTTTGCG
1 CTTTTTTTTTTGCG
53527891 CTTTTT
1 CTTTTT
53527897 ACTCTCTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 13 0.43
15 5 0.17
16 5 0.17
17 7 0.23
ACGTcount: A:0.00, C:0.14, G:0.12, T:0.75
Consensus pattern (14 bp):
CTTTTTTTTTTGCG
Found at i:53527887 original size:15 final size:15
Alignment explanation
Indices: 53527847--53527896 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
53527837 AGGTAGGAAC
*
53527847 TTTTTTTTTTGCGCT
1 TTTTTTTTTTTCGCT
*
53527862 TTTTTGCTTTTT-GCT
1 TTTTT-TTTTTTCGCT
53527877 TTTTTTTTTTTGCGCT
1 TTTTTTTTTTT-CGCT
53527893 TTTT
1 TTTT
53527897 ACTCTCTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 5 0.17
15 13 0.45
16 11 0.38
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.76
Consensus pattern (15 bp):
TTTTTTTTTTTCGCT
Found at i:53527930 original size:9 final size:9
Alignment explanation
Indices: 53527918--53528010 Score: 54
Period size: 9 Copynumber: 10.4 Consensus size: 9
53527908 TTTTGCGCTT
53527918 TTTTTTTGC
1 TTTTTTTGC
53527927 TTTTTTTG-
1 TTTTTTTGC
53527935 -TTTTTT--
1 TTTTTTTGC
**
53527941 TTTTTGCGC
1 TTTTTTTGC
53527950 TTTTTACTCT-C
1 TTTTT--T-TGC
53527961 TTTTTTTGC
1 TTTTTTTGC
* *
53527970 GCTTTTTTGTT
1 -TTTTTTTG-C
53527981 TTTTTTTG-
1 TTTTTTTGC
53527989 TTTTTTTGC
1 TTTTTTTGC
*
53527998 TGTTTTTGC
1 TTTTTTTGC
53528007 TTTT
1 TTTT
53528011 ATTTAAAGAA
Statistics
Matches: 65, Mismatches: 9, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
7 10 0.15
8 9 0.14
9 26 0.40
10 14 0.22
11 6 0.09
ACGTcount: A:0.01, C:0.11, G:0.12, T:0.76
Consensus pattern (9 bp):
TTTTTTTGC
Found at i:53527930 original size:10 final size:10
Alignment explanation
Indices: 53527917--53528010 Score: 52
Period size: 10 Copynumber: 9.4 Consensus size: 10
53527907 TTTTTGCGCT
53527917 TTTTTTTTGC
1 TTTTTTTTGC
**
53527927 TTTTTTTGTTT
1 TTTTTTT-TGC
53527938 TTTTTTTTGCGC
1 TTTTTTTT--GC
**
53527950 TTTTTACT-C
1 TTTTTTTTGC
53527959 TCTTTTTTTGC
1 T-TTTTTTTGC
** *
53527970 GCTTTTTTGT
1 TTTTTTTTGC
53527980 TTTTTTTTG-
1 TTTTTTTTGC
53527989 -TTTTTTTGC
1 TTTTTTTTGC
*
53527998 -TGTTTTTGC
1 TTTTTTTTGC
53528007 TTTT
1 TTTT
53528011 ATTTAAAGAA
Statistics
Matches: 62, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
8 8 0.13
9 10 0.16
10 29 0.47
11 9 0.15
12 6 0.10
ACGTcount: A:0.01, C:0.11, G:0.12, T:0.77
Consensus pattern (10 bp):
TTTTTTTTGC
Found at i:53527939 original size:58 final size:56
Alignment explanation
Indices: 53527850--53527995 Score: 205
Period size: 58 Copynumber: 2.7 Consensus size: 56
53527840 TAGGAACTTT
*
53527850 TTTTTTTGCGC---TTTTTTGCTTTTTGCT-TTTTTTTTTTTGCGCTTTTTACTCTCTC
1 TTTTTTTGCGCTTTTTTTTTGCTTTTT-TTGTTTTTTTTTTTGCGCTTTTTA--CTCTC
53527905 TTTTTTTGCGCTTTTTTTTTGCTTTTTTTGTTTTTTTTTTTGCGCTTTTTACTCTC
1 TTTTTTTGCGCTTTTTTTTTGCTTTTTTTGTTTTTTTTTTTGCGCTTTTTACTCTC
*
53527961 TTTTTTTGCGCTTTTTTGTT--TTTTTTTGTTTTTTT
1 TTTTTTTGCGCTTTTTTTTTGCTTTTTTTGTTTTTTT
53527996 GCTGTTTTTG
Statistics
Matches: 85, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
54 15 0.18
55 11 0.13
56 24 0.28
57 1 0.01
58 34 0.40
ACGTcount: A:0.01, C:0.14, G:0.11, T:0.74
Consensus pattern (56 bp):
TTTTTTTGCGCTTTTTTTTTGCTTTTTTTGTTTTTTTTTTTGCGCTTTTTACTCTC
Found at i:53527976 original size:34 final size:34
Alignment explanation
Indices: 53527905--53527977 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
53527895 TTACTCTCTC
* * ***
53527905 TTTTTTTGCGCTTTTTTTTTGCTTTTTTTGTTTT
1 TTTTTTTGCGCTTTTTCTCTGCTTTTTTTGCGCT
53527939 TTTTTTTGCGCTTTTTACTCT-CTTTTTTTGCGCT
1 TTTTTTTGCGCTTTTT-CTCTGCTTTTTTTGCGCT
53527973 TTTTT
1 TTTTT
53527978 GTTTTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 31 0.94
35 2 0.06
ACGTcount: A:0.01, C:0.14, G:0.11, T:0.74
Consensus pattern (34 bp):
TTTTTTTGCGCTTTTTCTCTGCTTTTTTTGCGCT
Found at i:53528011 original size:56 final size:56
Alignment explanation
Indices: 53527850--53528011 Score: 160
Period size: 56 Copynumber: 2.9 Consensus size: 56
53527840 TAGGAACTTT
* *
53527850 TTTTTTTGCGCTTTTTTGCTTTTTGCTTTTTTTTTTTTGC-GCTTTTTAC---T-CTCTC
1 TTTTTTTGCGCTTTTTTG-TTTTT--TTTTGTTTTTTTGCTG-TTTTTGCTTTTACTCTC
* **
53527905 TTTTTTTGCGCTTTTTTTTTGCTTTTTTTGTTTTTTT--T-TTTGCGCTTTTTACTCTC
1 TTTTTTTGCGCTTTTTTGTT--TTTTTTTGTTTTTTTGCTGTTTTTGC-TTTTACTCTC
53527961 TTTTTTTGCGCTTTTTTGTTTTTTTTTGTTTTTTTGCTGTTTTTGCTTTTA
1 TTTTTTTGCGCTTTTTTGTTTTTTTTTGTTTTTTTGCTGTTTTTGCTTTTA
53528012 TTTAAAGAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 21
0.75 0.07 0.18
Matches are distributed among these distances:
51 4 0.05
54 28 0.32
55 18 0.20
56 33 0.38
57 5 0.06
ACGTcount: A:0.02, C:0.14, G:0.12, T:0.73
Consensus pattern (56 bp):
TTTTTTTGCGCTTTTTTGTTTTTTTTTGTTTTTTTGCTGTTTTTGCTTTTACTCTC
Found at i:53528242 original size:4 final size:4
Alignment explanation
Indices: 53528230--53528260 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
53528220 TAAAATTAGT
53528230 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
53528261 AAGGATAGAT
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:53528652 original size:31 final size:31
Alignment explanation
Indices: 53528559--53528654 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
53528549 GGCAAATTAC
*
53528559 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
53528590 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
53528622 AAGGGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
53528653 AA
1 AA
53528655 ATTATCTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:53537259 original size:11 final size:11
Alignment explanation
Indices: 53537215--53537259 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
53537205 TATTTTTTAA
*
53537215 TTTTAAAATAC
1 TTTTAAAATAT
53537226 TTTTAAAATAT
1 TTTTAAAATAT
*
53537237 TTTT---TTAT
1 TTTTAAAATAT
53537245 TTTTAAAATAT
1 TTTTAAAATAT
53537256 TTTT
1 TTTT
53537260 TGTGTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
8 7 0.25
11 21 0.75
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:53540934 original size:17 final size:18
Alignment explanation
Indices: 53540912--53540948 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
53540902 ATAAATTTAG
53540912 TTTTTAAT-ATTTAATTT
1 TTTTTAATAATTTAATTT
*
53540929 TTTTTATTAATTTAATTT
1 TTTTTAATAATTTAATTT
53540947 TT
1 TT
53540949 AATCTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTAATAATTTAATTT
Found at i:53541229 original size:30 final size:29
Alignment explanation
Indices: 53541195--53541342 Score: 136
Period size: 30 Copynumber: 5.0 Consensus size: 29
53541185 CTGTACGTTT
53541195 TAAAATTTACATTTTGACCCCAAAATTTTC
1 TAAAA-TTACATTTTGACCCCAAAATTTTC
** *
53541225 TAAAATTACATTTCAACCCCAAAACTTTC
1 TAAAATTACATTTTGACCCCAAAATTTTC
* * *
53541254 TCAAAATTACACTTTGACCCCTAAACTTTC
1 T-AAAATTACATTTTGACCCCAAAATTTTC
* * * *
53541284 TAAAAATTACATATTGA-CTCTATATTTTCC
1 T-AAAATTACATTTTGACCCCAAAATTTT-C
* *
53541314 CAAAATTACATTTTTACCCCAAATATTTT
1 TAAAATTACATTTTGACCCCAAA-ATTTT
53541343 GTGTCTTCTA
Statistics
Matches: 95, Mismatches: 19, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
29 43 0.45
30 47 0.49
31 5 0.05
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (29 bp):
TAAAATTACATTTTGACCCCAAAATTTTC
Found at i:53542282 original size:17 final size:17
Alignment explanation
Indices: 53542235--53542284 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
53542225 GGCCAGCCCA
53542235 AAAAAAAGGAAAAATGAAG
1 AAAAAAA-GAAAAA-GAAG
*
53542254 AAAGAGAA-AAAAAGAAG
1 AAA-AAAAGAAAAAGAAG
53542271 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
53542285 GCCCAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 3 0.11
17 13 0.48
18 5 0.19
19 3 0.11
20 3 0.11
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAAAAAGAAAAAGAAG
Found at i:53542283 original size:8 final size:9
Alignment explanation
Indices: 53542243--53542284 Score: 52
Period size: 8 Copynumber: 4.8 Consensus size: 9
53542233 CAAAAAAAAG
53542243 GAAAAATGAA
1 GAAAAA-GAA
*
53542253 GAAAGAGAA
1 GAAAAAGAA
53542262 -AAAAAGAA
1 GAAAAAGAA
53542270 GAAAAA-AA
1 GAAAAAGAA
53542278 GAAAAAG
1 GAAAAAG
53542285 GCCCAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 15 0.54
9 8 0.29
10 5 0.18
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (9 bp):
GAAAAAGAA
Found at i:53542811 original size:30 final size:29
Alignment explanation
Indices: 53542775--53542831 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
53542765 TCATGTTTCC
53542775 AAAATTTCCCGTGTTTCAAAAAATAATAAT
1 AAAATTTCCCGTGTTTCAAAAAA-AATAAT
**
53542805 AAAATTTCTTGTGTTTCAAAAAAAATA
1 AAAATTTCCCGTGTTTCAAAAAAAATA
53542832 TATTCGTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (29 bp):
AAAATTTCCCGTGTTTCAAAAAAAATAAT
Found at i:53542841 original size:22 final size:24
Alignment explanation
Indices: 53542818--53542872 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
53542808 ATTTCTTGTG
53542818 TTTCAAAAAAAAT-ATATTCGTGT
1 TTTCAAAAAAAATAATATTCGTGT
* *
53542841 TTTTAAAAAAAATAATTTTCGTGT
1 TTTCAAAAAAAATAATATTCGTGT
53542865 TTTCAAAA
1 TTTCAAAA
53542873 TTTCTCGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (24 bp):
TTTCAAAAAAAATAATATTCGTGT
Found at i:53542894 original size:27 final size:26
Alignment explanation
Indices: 53542864--53542918 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
53542854 AATTTTCGTG
*
53542864 TTTTCAAAATTTCTCGTGTTTTAAAAA
1 TTTTCAAAATTTCTCGT-TTTCAAAAA
* **
53542891 TTTTCGATTTTTCTCGTTTTCAAAAA
1 TTTTCAAAATTTCTCGTTTTCAAAAA
53542917 TT
1 TT
53542919 GTCGTGTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (26 bp):
TTTTCAAAATTTCTCGTTTTCAAAAA
Found at i:53542902 original size:17 final size:17
Alignment explanation
Indices: 53542854--53542896 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 17
53542844 TAAAAAAAAT
*
53542854 AATTTTCGTGTTTTCAA
1 AATTTTCGTGTTTTAAA
53542871 AATTTCTCGTGTTTTAAA
1 AATTT-TCGTGTTTTAAA
53542889 AATTTTCG
1 AATTTTCG
53542897 ATTTTTCTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.51
Consensus pattern (17 bp):
AATTTTCGTGTTTTAAA
Found at i:53542933 original size:18 final size:17
Alignment explanation
Indices: 53542906--53542986 Score: 60
Period size: 18 Copynumber: 4.6 Consensus size: 17
53542896 GATTTTTCTC
*
53542906 GTTTTCAAAAATTGTCGT
1 GTTTTAAAAAATT-TCGT
*
53542924 GTTTTAAAAAAAATTCGT
1 GTTTT-AAAAAATTTCGT
*
53542942 GTTTCT--AAAATTCTTGT
1 GTTT-TAAAAAATT-TCGT
*
53542959 ATTTTAAAAAA-TTCGT
1 GTTTTAAAAAATTTCGT
53542975 GTTTTCAAAAAA
1 GTTTT-AAAAAA
53542987 GGAAAAAGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
16 13 0.26
17 13 0.26
18 17 0.34
19 7 0.14
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (17 bp):
GTTTTAAAAAATTTCGT
Found at i:53542947 original size:43 final size:43
Alignment explanation
Indices: 53542863--53542947 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
53542853 TAATTTTCGT
* ** *
53542863 GTTTTCAAAATTTCTCGTGTTTTAAAAATTTTCGATTTTTCTC
1 GTTTTCAAAAATTCTCGTGTTTTAAAAAAATTCGATGTTTCTC
*
53542906 GTTTTCAAAAATTGTCGTGTTTTAAAAAAAATTCG-TGTTTCT
1 GTTTTCAAAAATTCTCGTGTTTT-AAAAAAATTCGATGTTTCT
53542948 AAAATTCTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 27 0.75
44 9 0.25
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (43 bp):
GTTTTCAAAAATTCTCGTGTTTTAAAAAAATTCGATGTTTCTC
Found at i:53542953 original size:15 final size:16
Alignment explanation
Indices: 53542932--53542978 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
53542922 GTGTTTTAAA
53542932 AAAAATTCGTGTTTCT
1 AAAAATTCGTGTTTCT
* *
53542948 -AAAATTCTTGTATTTT
1 AAAAATTCGTGT-TTCT
53542964 AAAAAATTCGTGTTT
1 -AAAAATTCGTGTTT
53542979 TCAAAAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 10 0.40
16 3 0.12
17 2 0.08
18 10 0.40
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.47
Consensus pattern (16 bp):
AAAAATTCGTGTTTCT
Found at i:53547552 original size:30 final size:30
Alignment explanation
Indices: 53547504--53547648 Score: 128
Period size: 30 Copynumber: 4.8 Consensus size: 30
53547494 TTTCTCAATT
* *
53547504 GTCGGCTCTTCTGTGGCTTCTGCATGGACA
1 GTCGGCACTTCTGCGGCTTCTGCATGGACA
** * * *
53547534 GTCGGTGCTTTTGCGGCTTCGGCATGGATA
1 GTCGGCACTTCTGCGGCTTCTGCATGGACA
*
53547564 GTCGGCACTTCTGCGGCTTTTGCATGGACA
1 GTCGGCACTTCTGCGGCTTCTGCATGGACA
* * * * * * *
53547594 GTCGACATTTCTACGGCTTTTGTATGGTCC
1 GTCGGCACTTCTGCGGCTTCTGCATGGACA
** *
53547624 GTCGGTGCTTCTGTGGCTTCTGCAT
1 GTCGGCACTTCTGCGGCTTCTGCAT
53547649 AAACCGTGGG
Statistics
Matches: 89, Mismatches: 26, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 89 1.00
ACGTcount: A:0.10, C:0.24, G:0.30, T:0.35
Consensus pattern (30 bp):
GTCGGCACTTCTGCGGCTTCTGCATGGACA
Found at i:53548736 original size:30 final size:30
Alignment explanation
Indices: 53548702--53548789 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
53548692 CAGCTTTGGT
* *
53548702 ATGGACAGTCGGCACTTCTACGGCTTCTCC
1 ATGGACAGTCGGCACTTCTGCGGCTTCTAC
** *
53548732 ATGGACAGTCAACATTTCTGCGGCTTCTAC
1 ATGGACAGTCGGCACTTCTGCGGCTTCTAC
* * *
53548762 ATGGTCCGTCGGCACTTCTGTGGCTTCT
1 ATGGACAGTCGGCACTTCTGCGGCTTCT
53548790 GCATTAATCG
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.16, C:0.30, G:0.24, T:0.31
Consensus pattern (30 bp):
ATGGACAGTCGGCACTTCTGCGGCTTCTAC
Found at i:53550265 original size:98 final size:98
Alignment explanation
Indices: 53550093--53550287 Score: 363
Period size: 98 Copynumber: 2.0 Consensus size: 98
53550083 ACAATAAAAT
*
53550093 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
53550158 TCTAGAATCCCAAACTCGGAATATTTCCTTTAC
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
53550191 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
53550256 TTTAAAATCCCAAACTCGGAATATTTCCTTTA
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTA
53550288 TTGTTTTTAG
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
Found at i:53551144 original size:3 final size:3
Alignment explanation
Indices: 53551136--53551181 Score: 51
Period size: 3 Copynumber: 15.0 Consensus size: 3
53551126 ATATAGCTAA
53551136 AAT AAT AAT AATT ACAT -AT GAA- AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T A-AT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
53551182 TACATTAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
2 4 0.11
3 29 0.76
4 4 0.11
5 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:53551772 original size:19 final size:19
Alignment explanation
Indices: 53551748--53551879 Score: 219
Period size: 19 Copynumber: 6.8 Consensus size: 19
53551738 AATCATATAT
53551748 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
53551767 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
53551786 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
53551805 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
53551826 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
53551845 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
53551864 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
53551880 CTCAAAAATT
Statistics
Matches: 105, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
19 86 0.82
21 19 0.18
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:53551832 original size:59 final size:59
Alignment explanation
Indices: 53551741--53551878 Score: 221
Period size: 59 Copynumber: 2.4 Consensus size: 59
53551731 ATTACAAAAT
*
53551741 CATAT-AT-TCTAAGATTGC--ATATCATATCTAAGATTATATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTG
* *
53551796 CATATCATATCTAAGATTGCATATATCATATCTAAGATTGCATATCATATCTAGGATTG
1 CATATCATATCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTG
53551855 CATATCATATCTAAGATTGCATAT
1 CATATCATATCTAAGATTGCATAT
53551879 CCTCAAAAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
55 5 0.07
56 2 0.03
57 11 0.14
59 58 0.76
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (59 bp):
CATATCATATCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTG
Found at i:53552304 original size:89 final size:88
Alignment explanation
Indices: 53552066--53552565 Score: 315
Period size: 89 Copynumber: 5.8 Consensus size: 88
53552056 GTCTGCCTCG
* * * * * *
53552066 CTGCAACTTCA-GGAGGATAAGACTTGCTTATTTAGTATGCTTCACTGCAACTTCAGGGAAATAA
1 CTGCAACTTCAGGGA-GATAAGACTTGCATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* * *** *
53552130 GACTA---GATGCGATCTGCT-CT
65 GATTATCGGCTTTAATCTGCTCCA
* * * * * *
53552150 CTGCAACTTCAGAGAGATAAGATCTAAG-GT-TTTAATCCGCTCCACTGCAACTTCAGGGAGATA
1 CTGCAACTTCAGGGAGATAAGA-CT-TGCATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATA
53552213 AGATTATCGGCTTTAATCTGCTCCA
64 AGATTATCGGCTTTAATCTGCTCCA
53552238 CTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGC-CCTACTGCAACTTCA-GGAGGAT
1 CTGCAACTTCAGGGAGATAAGACTTG-CATCTTCAGTCTGCTCC-ACTGCAACTTCAGGGA-GAT
* *
53552301 AAGACT-T--GCTTACTTAGTCTGCTCCA
63 AAGATTATCGGC-T--TTAATCTGCTCCA
* * * * *
53552327 CTGCAACTTCAGGGAGATAAGATTTG-A--TGC-GATCTGCT-CTCTGTAACTTCAGAGAGATAA
1 CTGCAACTTCAGGGAGATAAGACTTGCATCTTCAG-TCTGCTCCACTGCAACTTCAGGGAGATAA
* *
53552387 GATCTA-AGGTTTTAAT-TCGCTCCA
65 GAT-TATCGGCTTTAATCT-GCTCCA
* * ** * *
53552411 CTGCAACTTCAGGGAGATAGGA-TTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
1 CTGCAACTTCAGGGAGATAAGACTT-GCATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
** ** * * * *
53552475 GACTTGCCATCTTCAGTTTGCCCCA
65 GA-TTATCGGCTTTAATCTGCTCCA
* *
53552500 CTACAACTTCA-GGAGGATAAGACTTGCTTACTT-AGTCTGCTCCACTGCAACTTCAGGGAGATA
1 CTGCAACTTCAGGGA-GATAAGACTTGCAT-CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATA
53552563 AGA
64 AGA
53552566 CTAGATGCGA
Statistics
Matches: 328, Mismatches: 53, Indels: 65
0.74 0.12 0.15
Matches are distributed among these distances:
83 3 0.01
84 100 0.30
85 16 0.05
86 5 0.02
87 21 0.06
88 54 0.16
89 123 0.38
90 6 0.02
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (88 bp):
CTGCAACTTCAGGGAGATAAGACTTGCATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
ATTATCGGCTTTAATCTGCTCCA
Found at i:53552377 original size:173 final size:173
Alignment explanation
Indices: 53552198--53552521 Score: 410
Period size: 173 Copynumber: 1.9 Consensus size: 173
53552188 GCTCCACTGC
* *
53552198 AACTTCAGGGAGATAAGAT-TATCGGCTTTAA-TCTGCTCCACTGCAACTTCAGGGAGATAAGAC
1 AACTTCAGAGAGATAAGATCTA-AGGCTTTAATTC-GCTCCACTGCAACTTCAGGGAGATAAGA-
* * * *
53552261 TTGCCATCTTCAGTCTGC-CCTACTGCAACTTCA-GGAGGATAAGACTTG-CTTACTT-AGTCTG
63 TTACCAGCTTCAATCTGCTCC-ACTGCAACTTCAGGGA-GATAAGACTTGCCAT-CTTCAGTCTG
* *
53552322 CTCCACTGCAACTTCAGG-GAGATAAGATTTGATGCGATCTGCTCTCTGT
125 CCCCACTACAACTTCAGGAG-GATAAGATTTGATGCGATCTGCTCTCTGT
* *
53552371 AACTTCAGAGAGATAAGATCTAAGGTTTTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTA
1 AACTTCAGAGAGATAAGATCTAAGGCTTTAATTCGCTCCACTGCAACTTCAGGGAGATAAGATTA
* * * *
53552436 TCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTTTGCCCCAC
66 CCAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCAC
53552501 TACAACTTCAGGAGGATAAGA
131 TACAACTTCAGGAGGATAAGA
53552522 CTTGCTTACT
Statistics
Matches: 130, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
172 38 0.29
173 87 0.67
174 5 0.04
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (173 bp):
AACTTCAGAGAGATAAGATCTAAGGCTTTAATTCGCTCCACTGCAACTTCAGGGAGATAAGATTA
CCAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCAC
TACAACTTCAGGAGGATAAGATTTGATGCGATCTGCTCTCTGT
Found at i:53552652 original size:44 final size:43
Alignment explanation
Indices: 53552103--53552653 Score: 366
Period size: 44 Copynumber: 12.8 Consensus size: 43
53552093 TTATTTAGTA
* * * ***
53552103 TGCTTCACTGCAACTTCAGGGAAATAAGA-CTA-GATGCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTAGGTTTTAATC
* *
53552144 TGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCT-AGGTTTTAATC
* *
53552187 CGCTCCACTGCAACTTCAGGGAGATAAGAT-TATCGGCTTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTA--GGTTTTAATC
* * * *
53552231 TGCTCCACTGCAACTTCAGGGAGATAAGA-CTTGCCATCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTAG--GT-TTTAATC
* * *
53552276 TGC-CCTACTGCAACTTCA-GGAGGATAAGA-CTTGCTTACTTAGTC
1 TGCTCC-ACTGCAACTTCAGGGA-GATAAGATCTAGGTT--TTAATC
* * ***
53552320 TGCTCCACTGCAACTTCAGGGAGATAAGAT-T-TGATGCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTAGGTTTTAATC
* * *
53552361 TGCT-CTCTGTAACTTCAGAGAGATAAGATCTAAGGTTTTAAT-
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCT-AGGTTTTAATC
* *
53552403 TCGCTCCACTGCAACTTCAGGGAGATAGGAT-TATCGGCTTTAATC
1 T-GCTCCACTGCAACTTCAGGGAGATAAGATCTA--GGTTTTAATC
* * * * *
53552448 TGCTCCACTGCAACTTCAGGGAGATAAGA-CTTGCCATCTTCAGTT
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTAG--GT-TTTAATC
* * * * *
53552493 TGCCCCACTACAACTTCA-GGAGGATAAGA-CTTGCTTACTTAGTC
1 TGCTCCACTGCAACTTCAGGGA-GATAAGATCTAGGTT--TTAATC
* ***
53552537 TGCTCCACTGCAACTTCAGGGAGATAAGA-CTA-GATGCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTAGGTTTTAATC
* *
53552578 TGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCT-AGGTTTTAATC
** *
53552621 CACTCCACTGCAACTTCAGGGAGATAGGATCTA
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTA
53552654 CAATCTTCAA
Statistics
Matches: 402, Mismatches: 71, Indels: 72
0.74 0.13 0.13
Matches are distributed among these distances:
40 65 0.16
41 21 0.05
42 9 0.02
43 29 0.07
44 207 0.51
45 71 0.18
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (43 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGATCTAGGTTTTAATC
Found at i:53552688 original size:217 final size:217
Alignment explanation
Indices: 53552045--53552650 Score: 1068
Period size: 217 Copynumber: 2.8 Consensus size: 217
53552035 TAGGAATTAG
* * * * * *
53552045 TGCCTTCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGTATGCTTCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
*
53552110 CTGCAACTTCAGGGAAATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
*
53552175 AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTGCTCCACT
131 AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
53552240 GCAACTTCAGGGAGATAAGACT
196 GCAACTTCAGGGAGATAAGACT
*
53552262 TGCCATCTTCAGTCTGCCCTACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
* * *
53552327 CTGCAACTTCAGGGAGATAAGATTTGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
*
53552392 AAGGTTTTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
131 AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
53552457 GCAACTTCAGGGAGATAAGACT
196 GCAACTTCAGGGAGATAAGACT
* *
53552479 TGCCATCTTCAGTTTGCCCCACTACAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
53552544 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
*
53552609 AAGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGAT
131 AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT
53552651 CTACAATCTT
Statistics
Matches: 368, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
217 368 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (217 bp):
TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
GCAACTTCAGGGAGATAAGACT
Found at i:53552777 original size:132 final size:132
Alignment explanation
Indices: 53552640--53553026 Score: 675
Period size: 132 Copynumber: 2.9 Consensus size: 132
53552630 GCAACTTCAG
*
53552640 GGAGATAGGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGCTT
1 GGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGCTT
* *
53552705 AAATCTGCTTCCCACTATCTTGGAAAAATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTT
66 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATCTGCCGTCTTCGATCTGCTCCACTACTGCTT
53552770 AA
131 AA
* *
53552772 GGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGGGACAAAGCTTGGTGGCTT
1 GGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGCTT
*
53552837 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATCCGCCGTCTTCGATCTGCTCCACTACTGCTT
66 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATCTGCCGTCTTCGATCTGCTCCACTACTGCTT
*
53552902 AG
131 AA
* *
53552904 GGAGATAAGATCTACAATCTTCAACCTTCTTCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTT
1 GGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGCTT
* *
53552969 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGACCTGCTCCACT
66 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATCTGCCGTCTTCGATCTGCTCCACT
53553027 GTCAATGCAG
Statistics
Matches: 241, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 241 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (132 bp):
GGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGCTT
AAATCTGCTTCCCACTATCTTGGAAAGATAAGATCTGCCGTCTTCGATCTGCTCCACTACTGCTT
AA
Found at i:53552925 original size:44 final size:44
Alignment explanation
Indices: 53552732--53552927 Score: 114
Period size: 44 Copynumber: 4.5 Consensus size: 44
53552722 TCTTGGAAAA
* * * *
53552732 ATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTTAAGGAG
1 ATAAGATCTACAATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * * * * *
53552776 ATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGGG
1 ATAAGATCTACAATCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * *** * *
53552820 ACAA-AGCT-TGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAAAG
1 ATAAGATCTACAAT--CTTCAATCTGC-T-CCACTACTGCTTAGG-GAG
** ** *
53552864 ATAAGATCCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 ATAAGATCTACAATCTTCAATCTGCTCCACTACTGCTTAGGGAG
53552908 ATAAGATCTACAATCTTCAA
1 ATAAGATCTACAATCTTCAA
53552928 CCTTCTTCGC
Statistics
Matches: 106, Mismatches: 36, Indels: 20
0.65 0.22 0.12
Matches are distributed among these distances:
42 7 0.07
43 7 0.07
44 80 0.75
45 6 0.06
46 6 0.06
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (44 bp):
ATAAGATCTACAATCTTCAATCTGCTCCACTACTGCTTAGGGAG
Found at i:53554310 original size:8 final size:8
Alignment explanation
Indices: 53554297--53554332 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
53554287 TTCACTTTTA
53554297 TTTTTTGT
1 TTTTTTGT
53554305 TTTTTTG-
1 TTTTTTGT
53554312 -TTTTTGT
1 TTTTTTGT
53554319 TTTTTTGT
1 TTTTTTGT
53554327 TTTTTT
1 TTTTTT
53554333 AATCTGAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.23
8 20 0.77
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTTTGT
Found at i:53554315 original size:14 final size:14
Alignment explanation
Indices: 53554298--53554330 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
53554288 TCACTTTTAT
53554298 TTTTTGTTTTTTTG
1 TTTTTGTTTTTTTG
53554312 TTTTTGTTTTTTTG
1 TTTTTGTTTTTTTG
53554326 TTTTT
1 TTTTT
53554331 TTAATCTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (14 bp):
TTTTTGTTTTTTTG
Found at i:53560400 original size:19 final size:19
Alignment explanation
Indices: 53560376--53560488 Score: 165
Period size: 19 Copynumber: 5.8 Consensus size: 19
53560366 AATCATATAT
53560376 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
53560395 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
53560414 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
53560435 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
53560454 TCT-AGAATTGCATATCATA
1 TCTAAG-ATTGCATATCATA
53560473 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
53560489 CTCAAAAATT
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
18 2 0.02
19 62 0.74
20 2 0.02
21 18 0.21
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:53560441 original size:40 final size:38
Alignment explanation
Indices: 53560350--53560487 Score: 161
Period size: 38 Copynumber: 3.5 Consensus size: 38
53560340 TACAAATTAA
*
53560350 ATATCTAAGATTACAAAATCATATATTCTAAGATTGCATATC
1 ATATCTAAGATTAC-ATAT--TATA-TCTAAGATTGCATATC
*
53560392 ATATCTAAGATTATATATTATATCTAAGATTGCATATATC
1 ATATCTAAGATTACATATTATATCTAAGATTGC--ATATC
* *
53560432 ATATCTAAGATTGCATATCATATCT-AGAATTGCATATC
1 ATATCTAAGATTACATATTATATCTAAG-ATTGCATATC
*
53560470 ATATCTAAGATTGCATAT
1 ATATCTAAGATTACATAT
53560488 CCTCAAAAAT
Statistics
Matches: 88, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
38 34 0.39
39 6 0.07
40 32 0.36
41 3 0.03
42 13 0.15
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (38 bp):
ATATCTAAGATTACATATTATATCTAAGATTGCATATC
Found at i:53560446 original size:59 final size:61
Alignment explanation
Indices: 53560350--53560487 Score: 185
Period size: 59 Copynumber: 2.3 Consensus size: 61
53560340 TACAAATTAA
* * * *
53560350 ATATCTAAGATTACA-AAATCATATATTCTAAGATTGCATATCATATCTA-AGATTATATATT
1 ATATCTAAGATTGCATATATCA-ATATTCTAAGATTGCATATCATATCTAGA-ATTACATATC
*
53560411 ATATCTAAGATTGCATATATC-ATA-TCTAAGATTGCATATCATATCTAGAATTGCATATC
1 ATATCTAAGATTGCATATATCAATATTCTAAGATTGCATATCATATCTAGAATTACATATC
53560470 ATATCTAAGATTGCATAT
1 ATATCTAAGATTGCATAT
53560488 CCTCAAAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
59 48 0.69
60 4 0.06
61 14 0.20
62 4 0.06
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (61 bp):
ATATCTAAGATTGCATATATCAATATTCTAAGATTGCATATCATATCTAGAATTACATATC
Found at i:53561204 original size:23 final size:22
Alignment explanation
Indices: 53561168--53561216 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
53561158 TCCTTTTTTT
53561168 TTTTCTTTCTATTTTCGTT-TCTC
1 TTTTCTTTCTA-TTTCGTTCT-TC
53561191 TTTTCTTTAC-ATTTCGTTCTTC
1 TTTTCTTT-CTATTTCGTTCTTC
53561213 TTTT
1 TTTT
53561217 TATTTGGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.54
23 10 0.42
24 1 0.04
ACGTcount: A:0.06, C:0.20, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTCTTTCTATTTCGTTCTTC
Found at i:53561996 original size:30 final size:30
Alignment explanation
Indices: 53561858--53562001 Score: 132
Period size: 30 Copynumber: 4.8 Consensus size: 30
53561848 TTCCCCAATT
* * * *
53561858 GTCGGCTCTTTTGTGGCTTCTCCATGGACG
1 GTCGGCGCTTTTGCGGCTTCTGCATGGACA
53561888 GTCGGCGCTTTTGCGGCTT-TCGCATGGACA
1 GTCGGCGCTTTTGCGGCTTCT-GCATGGACA
** *
53561918 GTCGGAACTTCTGCGGCTT-TGCATGGACA
1 GTCGGCGCTTTTGCGGCTTCTGCATGGACA
* * * *
53561947 ATCGACGTTTTTACGGCTTCTGCATGGA-A
1 GTCGGCGCTTTTGCGGCTTCTGCATGGACA
* *
53561976 CGTCGGCGCTTCTGTGGCTTCTGCAT
1 -GTCGGCGCTTTTGCGGCTTCTGCAT
53562002 AAACCGTGGG
Statistics
Matches: 91, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
29 23 0.25
30 68 0.75
ACGTcount: A:0.12, C:0.26, G:0.30, T:0.33
Consensus pattern (30 bp):
GTCGGCGCTTTTGCGGCTTCTGCATGGACA
Found at i:53562025 original size:30 final size:30
Alignment explanation
Indices: 53561952--53562027 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
53561942 GGACAATCGA
*
53561952 CGTTTTT-ACGGCTTCTGCATGGAACGTCGG
1 CGTTTTTGA-GGCTTCTGCATGAAACGTCGG
* * * *
53561982 CGCTTCTGTGGCTTCTGCAT-AAACCGTGGG
1 CGTTTTTGAGGCTTCTGCATGAAA-CGTCGG
53562012 CGTTTTTGAGGCTTCT
1 CGTTTTTGAGGCTTCT
53562028 AGTTCTCTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
29 2 0.06
30 34 0.94
ACGTcount: A:0.12, C:0.24, G:0.29, T:0.36
Consensus pattern (30 bp):
CGTTTTTGAGGCTTCTGCATGAAACGTCGG
Found at i:53562905 original size:104 final size:104
Alignment explanation
Indices: 53562698--53562973 Score: 285
Period size: 105 Copynumber: 2.6 Consensus size: 104
53562688 TCCTCTTTTT
*
53562698 ATTTTGTATAAAGTGGGTGCCGGCCATTGCCAGGCCACCCCTAA-TTTTTTTTTACTTTTTTCTT
1 ATTTTGTATAAAG-GGGTGCC-GCCATTGCCAGGCCACCCC-AATTTTTTTTTTACTTTTTTCGT
* ** * *
53562762 ATACCGGTGTCGGCAATTGTCACACCAAAAGT-AAAAAAAAA
63 ATACCGGTGCCACCAATTGACACAACAAAAGTAAAAAAAAAA
53562803 A-TTTGTATAAAGGGGTTGCCTGCCATTGCCAGGCCACCCCAATTGTTTTTTTTACTTTTTTCGT
1 ATTTTGTATAAAGGGG-TGCC-GCCATTGCCAGGCCACCCCAATT-TTTTTTTTACTTTTTTCGT
* * * **
53562867 ATGCTGGTGCCAACCAATT-ACACAACAAAATTTTAAAAAAAA
63 ATACCGGTGCC-ACCAATTGACACAACAAAAGTAAAAAAAAAA
* ** *
53562909 ATTATTGTAGGATGGGGGTGTCGACCATTGCCAGGCCA--CCAATTTTTTTTTTACTTTTTTCGT
1 ATT-TTGTA-TAAAGGGGTGCCG-CCATTGCCAGGCCACCCCAATTTTTTTTTTACTTTTTTCGT
53562972 AT
63 AT
53562974 TTTGGTGCTG
Statistics
Matches: 147, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
103 5 0.03
104 35 0.24
105 58 0.39
106 20 0.14
107 2 0.01
108 22 0.15
109 5 0.03
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (104 bp):
ATTTTGTATAAAGGGGTGCCGCCATTGCCAGGCCACCCCAATTTTTTTTTTACTTTTTTCGTATA
CCGGTGCCACCAATTGACACAACAAAAGTAAAAAAAAAA
Found at i:53564860 original size:30 final size:30
Alignment explanation
Indices: 53564788--53564918 Score: 111
Period size: 30 Copynumber: 4.4 Consensus size: 30
53564778 GCTCTTTTGT
*
53564788 GGCTTCTGCATGGACAGTCGGCACTTCTGC
1 GGCTTCTGCATGGACAGTCGCCACTTCTGC
*
53564818 GGCTT-TGGCATGGATAGTCGCCACTTCTGC
1 GGCTTCT-GCATGGACAGTCGCCACTTCTGC
* * * ** **
53564848 GGCTTCTCCATGGACAATCGACGTTTCTAT
1 GGCTTCTGCATGGACAGTCGCCACTTCTGC
* * * * *
53564878 GGCTTCTGCATGGTCCGTCGGCGCTTCTGT
1 GGCTTCTGCATGGACAGTCGCCACTTCTGC
*
53564908 TGCTTCTGCAT
1 GGCTTCTGCAT
53564919 AAACCGTGGG
Statistics
Matches: 81, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
29 1 0.01
30 79 0.98
31 1 0.01
ACGTcount: A:0.12, C:0.28, G:0.27, T:0.32
Consensus pattern (30 bp):
GGCTTCTGCATGGACAGTCGCCACTTCTGC
Found at i:53565555 original size:9 final size:9
Alignment explanation
Indices: 53565541--53565567 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
53565531 AAAAAAATTT
53565541 TGATTCCTC
1 TGATTCCTC
53565550 TGATTCCTC
1 TGATTCCTC
53565559 TGATTCCTC
1 TGATTCCTC
53565568 CAGTCCCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.33, G:0.11, T:0.44
Consensus pattern (9 bp):
TGATTCCTC
Found at i:53565815 original size:104 final size:101
Alignment explanation
Indices: 53565622--53566097 Score: 421
Period size: 104 Copynumber: 4.5 Consensus size: 101
53565612 TCTTTCTATT
* * *
53565622 TTGTATAAAGTCGGTGCCGGCCATTGCCAGGCCACCCCTAA-TTTTTTTTACTTTTTTCGTATAC
1 TTGTATAAAG-GGGTGCC-GCTATTGCCAGGCCA-CCCAAATTTTTTTTTACTTTTTTCGTATAC
* * *
53565686 TGGTGCCGGCAATTGTCACTCCAAAAGTAAAAAAAATTTA
63 TGGTGCTGGCAATTGACACACCAAAAGTAAAAAAAA-TTA
* **
53565726 TCGTATAAAGGGGTGCCTGCTATTTTCAGGCCACCCCAAATTTTTTTTTACTTTTTTCGTATACT
1 TTGTATAAAGGGGTGCC-GCTATTGCCAGGCCA-CCCAAATTTTTTTTTACTTTTTTCGTATACT
* * *
53565791 GGTGCTGGCCATTGACAGAGCAAAAGTAAAAAAAA--A
64 GGTGCTGGCAATTGACACACCAAAAGTAAAAAAAATTA
* *
53565827 TTGTATAAATGGGGTGCCGGCCATTGCCAGGCCACCCAAATTTTTTTTTACTTTTTTCGTATGCT
1 TTGTATAAA-GGGGTGCC-GCTATTGCCAGGCCACCCAAATTTTTTTTTACTTTTTTCGTATACT
53565892 GGTG-TCGGCTAATT-ACACACCAAAAGTAAAAAAAAATTA
64 GGTGCT-GGC-AATTGACACACCAAAAGT-AAAAAAAATTA
** * ** * *
53565931 TTGTAGGAAGTGGGTGTCGACTATTGCCAAACCA-CCAATTTTTTTTTTTTACTTTTTTCGTATT
1 TTGTATAAAG-GGGTGCCG-CTATTGCCAGGCCACCCAA--ATTTTTTTTTACTTTTTTCGTATA
*
53565995 CTGGTGCTGGCAATTGACAAATCCACATCCCAA--AAAAAAAATT-
62 CTGGTGCTGGCAATTGACACA-CCA-A----AAGTAAAAAAAATTA
* * * *
53566038 TCCGTATAAAGGGGTGCCGTCCATTGACAGGCTAGCACCCAAATTTTTTTTTCCTTTTTT
1 T-TGTATAAAGGGGTGCCG-CTATTGCCAGGC---CACCCAAATTTTTTTTTACTTTTTT
53566098 TCTAGTTTTC
Statistics
Matches: 306, Mismatches: 42, Indels: 43
0.78 0.11 0.11
Matches are distributed among these distances:
100 1 0.00
101 57 0.19
102 31 0.10
103 30 0.10
104 91 0.30
105 35 0.11
106 4 0.01
107 17 0.06
108 16 0.05
109 16 0.05
110 2 0.01
111 6 0.02
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (101 bp):
TTGTATAAAGGGGTGCCGCTATTGCCAGGCCACCCAAATTTTTTTTTACTTTTTTCGTATACTGG
TGCTGGCAATTGACACACCAAAAGTAAAAAAAATTA
Found at i:53565977 original size:205 final size:206
Alignment explanation
Indices: 53565619--53566097 Score: 524
Period size: 205 Copynumber: 2.3 Consensus size: 206
53565609 TCTTCTTTCT
* * *
53565619 ATTTTGTATAAAGTCGGTGCCGGCCATTGCCAGGCCACCCCTAA-TTTTTTTTACTTTTTTCGTA
1 ATTTCGTATAAAG-GGGTGCCGGCCATTGCCAGGCCA-CCCAAATTTTTTTTTACTTTTTTCGTA
* * * *
53565683 TACTGGTGCCGGCAATTGTCACTCCAAAAGTAAAAAAAATTTATCGTATAAAGGGGTGCCTGCTA
64 TACTGGTGCCGGCAATTGACACACCAAAAGTAAAAAAAAATTATCGTAGAAAGGGGTGCCTGCTA
** ** * *
53565748 TTTTCAGGCCACCCCAA-ATTTTTTTTTACTTTTTTCGTATACTGGTGCTGGCCATTGACAGAGC
129 TTGCCAAACCA-CCCAATATTTTTTTTTACTTTTTTCGTATACTGGTGCTGGCAATTGACAAAGC
53565812 AAAAGT-AAAAAAAA
193 AAAA-TCAAAAAAAA
53565826 A-TT-GTATAAATGGGGTGCCGGCCATTGCCAGGCCACCCAAATTTTTTTTTACTTTTTTCGTAT
1 ATTTCGTATAAA-GGGGTGCCGGCCATTGCCAGGCCACCCAAATTTTTTTTTACTTTTTTCGTAT
* * * * *
53565889 GCTGGTGTCGGCTAATT-ACACACCAAAAGTAAAAAAAAATTATTGTAGGAAGTGGGTGTC-GAC
65 ACTGGTGCCGGC-AATTGACACACCAAAAGTAAAAAAAAATTATCGTAGAAAG-GGGTGCCTG-C
* *
53565952 TATTGCCAAACCA-CCAATTTTTTTTTTTTACTTTTTTCGTATTCTGGTGCTGGCAATTGACAAA
127 TATTGCCAAACCACCCAA-TATTTTTTTTTACTTTTTTCGTATACTGGTGCTGGCAATTGACAAA
* * *
53566016 TCCACATCCCAAAAAAAAA
191 GCAAAAT--C-AAAAAAAA
* * *
53566035 ATTTCCGTATAAAGGGGTGCCGTCCATTGACAGGCTAGCACCCAAATTTTTTTTTCCTTTTTT
1 ATTT-CGTATAAAGGGGTGCCGGCCATTGCCAGGC---CACCCAAATTTTTTTTTACTTTTTT
53566098 TCTAGTTTTC
Statistics
Matches: 230, Mismatches: 25, Indels: 27
0.82 0.09 0.10
Matches are distributed among these distances:
204 9 0.04
205 91 0.40
206 67 0.29
207 1 0.00
209 9 0.04
210 2 0.01
211 20 0.09
212 7 0.03
214 24 0.10
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (206 bp):
ATTTCGTATAAAGGGGTGCCGGCCATTGCCAGGCCACCCAAATTTTTTTTTACTTTTTTCGTATA
CTGGTGCCGGCAATTGACACACCAAAAGTAAAAAAAAATTATCGTAGAAAGGGGTGCCTGCTATT
GCCAAACCACCCAATATTTTTTTTTACTTTTTTCGTATACTGGTGCTGGCAATTGACAAAGCAAA
ATCAAAAAAAA
Found at i:53566587 original size:52 final size:53
Alignment explanation
Indices: 53566481--53566594 Score: 194
Period size: 52 Copynumber: 2.2 Consensus size: 53
53566471 TTACTGGCCA
* *
53566481 GTCAATGGTCGGCGCCACCTTTATACGAAAATTTTTTTTTCGGGTGTTATTCT
1 GTCAATGGCCGACGCCACCTTTATACGAAAATTTTTTTTTCGGGTGTTATTCT
*
53566534 GTCAATGGCCGACGCCTCCTTTATACG-AAATTTTTTTTTCGGGTGTTATTCT
1 GTCAATGGCCGACGCCACCTTTATACGAAAATTTTTTTTTCGGGTGTTATTCT
53566586 GTCAATGGC
1 GTCAATGGC
53566595 TGGCACCAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 34 0.59
53 24 0.41
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.40
Consensus pattern (53 bp):
GTCAATGGCCGACGCCACCTTTATACGAAAATTTTTTTTTCGGGTGTTATTCT
Found at i:53566617 original size:52 final size:52
Alignment explanation
Indices: 53566503--53566613 Score: 147
Period size: 52 Copynumber: 2.2 Consensus size: 52
53566493 CGCCACCTTT
* ***
53566503 ATACGAAAATTTTTTTTTCGGGTGTTATTCTGTCAATGGCCGACGCCTCCTTT
1 ATACGAAAATTTTTTTTTCGGGTGTTATTCTGTCAATGGCCGA-GCCACCAGA
*
53566556 ATACG-AAATTTTTTTTTCGGGTGTTATTCTGTCAATGGCTG-G-CACCAGA
1 ATACGAAAATTTTTTTTTCGGGTGTTATTCTGTCAATGGCCGAGCCACCAGA
53566605 ATACGAAAA
1 ATACGAAAA
53566614 AATTAAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
49 8 0.15
50 4 0.08
52 35 0.67
53 5 0.10
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (52 bp):
ATACGAAAATTTTTTTTTCGGGTGTTATTCTGTCAATGGCCGAGCCACCAGA
Found at i:53566710 original size:110 final size:104
Alignment explanation
Indices: 53566587--53566867 Score: 269
Period size: 108 Copynumber: 2.6 Consensus size: 104
53566577 TGTTATTCTG
* *
53566587 TCAATGGCTGGCACCAGAATACGAAAAAATTAAAAAAAAATTTTGGGGTGGCTTGGCAATGGCCG
1 TCAATGGCCGGCACCAGAATACGAAAAAATTAAAAAAAAATTTTGGGGTGGCCTGGCAATGGCCG
* * *
53566652 GCACCCCCTTTCTACAATAATATATATATTTTTACTTTTGGTGTA
66 GCA-CCCCTTTCTA-AACAAT-T-T-T-TTTTTACTTTTAGTCTA
* * * * * *
53566697 TCAATGGCCGGCACCAGCATATGAAAAAAGTAAAAAAACAAAAATTTTTGGGTGGCCTAGCAATA
1 TCAATGGCCGGCACCAGAATACGAAAAAA-T--TAAAA-AAAAATTTTGGGGTGGCCTGGCAATG
* * * * * *
53566762 GCCAGCACCCTTTTTTATACAATTTTTTTTTACTTTTATTCTG
62 GCCGGCACCCCTTTCTAAACAATTTTTTTTTACTTTTAGTCTA
* ** *
53566805 TCAATAGCCGGCACCAGTGTACGAAAAAAGTAAAAAAAAA--TTGGGGTGGCCTGGCAATGGCCG
1 TCAATGGCCGGCACCAGAATACGAAAAAATTAAAAAAAAATTTTGGGGTGGCCTGGCAATGGCCG
53566868 ACATCCTTTT
Statistics
Matches: 140, Mismatches: 27, Indels: 16
0.77 0.15 0.09
Matches are distributed among these distances:
102 19 0.14
104 5 0.04
105 4 0.03
108 38 0.27
109 1 0.01
110 27 0.19
111 2 0.01
112 4 0.03
113 12 0.09
114 28 0.20
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (104 bp):
TCAATGGCCGGCACCAGAATACGAAAAAATTAAAAAAAAATTTTGGGGTGGCCTGGCAATGGCCG
GCACCCCTTTCTAAACAATTTTTTTTTACTTTTAGTCTA
Found at i:53568249 original size:30 final size:30
Alignment explanation
Indices: 53568215--53568324 Score: 130
Period size: 30 Copynumber: 3.7 Consensus size: 30
53568205 ATTGTCGGCT
* *
53568215 CTTCTGTGGCTTTTGCATGGACAGTCGACG
1 CTTCTGCGGCTTCTGCATGGACAGTCGACG
* * *
53568245 CTTCTGCGGCTTCAGCATGGACAGTCGGCA
1 CTTCTGCGGCTTCTGCATGGACAGTCGACG
** *
53568275 CTTCTGTAGCTTCTGCATGGACAGTCGATG
1 CTTCTGCGGCTTCTGCATGGACAGTCGACG
* *
53568305 TTTCTGCGGCTTCTACATGG
1 CTTCTGCGGCTTCTGCATGG
53568325 TCTTTCGGCG
Statistics
Matches: 65, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.15, C:0.25, G:0.28, T:0.32
Consensus pattern (30 bp):
CTTCTGCGGCTTCTGCATGGACAGTCGACG
Found at i:53568333 original size:60 final size:60
Alignment explanation
Indices: 53568208--53568348 Score: 176
Period size: 60 Copynumber: 2.4 Consensus size: 60
53568198 TTTCTCAATT
* *
53568208 GTCGGCTCTTCTGTGGCTTTTGCATGGACAGTCGACGCTTCTGCGGCTTCAGCATGGACA
1 GTCGGCACTTCTGTGGCTTCTGCATGGACAGTCGACGCTTCTGCGGCTTCAGCATGGACA
* * * * *
53568268 GTCGGCACTTCTGTAGCTTCTGCATGGACAGTCGATGTTTCTGCGGCTTCTA-CATGGTCT
1 GTCGGCACTTCTGTGGCTTCTGCATGGACAGTCGACGCTTCTGCGGCTTC-AGCATGGACA
* * *
53568328 TTCGGCGCTTCTATGGCTTCT
1 GTCGGCACTTCTGTGGCTTCT
53568349 ACATAAACTG
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
60 68 0.99
61 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.28, T:0.34
Consensus pattern (60 bp):
GTCGGCACTTCTGTGGCTTCTGCATGGACAGTCGACGCTTCTGCGGCTTCAGCATGGACA
Found at i:53570761 original size:37 final size:37
Alignment explanation
Indices: 53570710--53570857 Score: 251
Period size: 37 Copynumber: 4.0 Consensus size: 37
53570700 TAGCTAGGCT
****
53570710 ACCACTTATCACTTTACCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
53570747 GCCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
53570784 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
53570821 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
53570858 GCTAAAACTA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 105 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:53578080 original size:37 final size:37
Alignment explanation
Indices: 53578029--53578176 Score: 251
Period size: 37 Copynumber: 4.0 Consensus size: 37
53578019 TAGCTAGGCT
****
53578029 ACCACTTATCACTTTACCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
53578066 GCCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
53578103 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
53578140 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
53578177 GCTAAAACTA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 105 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:53587580 original size:21 final size:21
Alignment explanation
Indices: 53587529--53587580 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
53587519 ACCATTGTTT
*
53587529 CTAATCTCACTGCTACAGTAT
1 CTAATCTCACTGCTACAGTAA
*
53587550 CCAATCTCACTGCTACAGTAA
1 CTAATCTCACTGCTACAGTAA
*
53587571 CTAATGTCAC
1 CTAATCTCAC
53587581 CGCCACCGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.29
Consensus pattern (21 bp):
CTAATCTCACTGCTACAGTAA
Found at i:53587915 original size:154 final size:154
Alignment explanation
Indices: 53587635--53587932 Score: 506
Period size: 154 Copynumber: 1.9 Consensus size: 154
53587625 ATCCAAACTA
* *
53587635 AGGGTGAGTTTGGATGGGCGGTGCGTTTACCTGCGGTTAGTGTAAAAACAGCAGTGGTGGTGAGA
1 AGGGTGAGTTTGGATCGGCGGTGCGTTTACCTGCGGTTAGTGTAAAAACAGCAGTGGCGGTGAGA
* ** * *
53587700 TTAGATACTGTAGGGATACTGTAGCGTGAGACAAAAAGTAAGTTAAACGCACCGCACCCAATCGC
66 TTAAATACTGTAGCAATACTGTAGCGTGAGACAAAAAATAAGCTAAACGCACCGCACCCAATCGC
53587765 CCATCCAAACCCACACTAAGCCTT
131 CCATCCAAACCCACACTAAGCCTT
* *
53587789 AGGGTGAGTTTGGATCGGCGGTGCGTTTACCTGCGGTTAGTGTAAAAATAGCGGTGGCGGTGAGA
1 AGGGTGAGTTTGGATCGGCGGTGCGTTTACCTGCGGTTAGTGTAAAAACAGCAGTGGCGGTGAGA
*
53587854 TTAAATACTGTAGCAATACTGTAGCGTGAGACAAAAAATAGGCTAAACGCACCGCACCCAATCGC
66 TTAAATACTGTAGCAATACTGTAGCGTGAGACAAAAAATAAGCTAAACGCACCGCACCCAATCGC
53587919 CCATCCAAACCCAC
131 CCATCCAAACCCAC
53587933 CTTAGTCCAC
Statistics
Matches: 134, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
154 134 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (154 bp):
AGGGTGAGTTTGGATCGGCGGTGCGTTTACCTGCGGTTAGTGTAAAAACAGCAGTGGCGGTGAGA
TTAAATACTGTAGCAATACTGTAGCGTGAGACAAAAAATAAGCTAAACGCACCGCACCCAATCGC
CCATCCAAACCCACACTAAGCCTT
Found at i:53596186 original size:44 final size:44
Alignment explanation
Indices: 53596136--53596225 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
53596126 ACCATTTTTA
*
53596136 GAAAGAGCCGCTAAATCAAGTTCTCAGCTAGGTGAATGAAGTAT
1 GAAAGAGCCGCTAAATCAAGTTCTCAGCTAGGTGAATAAAGTAT
*
53596180 GAAAGAGCTGCTAAATCAAGTTCTCAGCTAGGTGAATAAAGTAT
1 GAAAGAGCCGCTAAATCAAGTTCTCAGCTAGGTGAATAAAGTAT
53596224 GA
1 GA
53596226 CTGTTTTACC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.23
Consensus pattern (44 bp):
GAAAGAGCCGCTAAATCAAGTTCTCAGCTAGGTGAATAAAGTAT
Found at i:53601261 original size:46 final size:46
Alignment explanation
Indices: 53601177--53601543 Score: 309
Period size: 46 Copynumber: 7.6 Consensus size: 46
53601167 TTTGAGTACT
* * *
53601177 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCT-TTAGCTACACTTA
1 TCTGATCAAGTGA-CAAGTGATAAGTGATAGCTATCAGCTACACTTA
* * *
53601223 TCTGATCAAGTGACAAGTGGA-AAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAGT-GATAAGTGAT-AG--CTA---TCAGCTACACTTA
* * * *
53601275 TCTGATCAAGTGATAAAGTGATAACTGATAGCT-TCGGCTATACTTA
1 TCTGATCAAGTGA-CAAGTGATAAGTGATAGCTATCAGCTACACTTA
53601321 TCTGATCAAGTGACAAAGTGATAAGTGATAGCT-TCAGCTACACTTA
1 TCTGATCAAGTGAC-AAGTGATAAGTGATAGCTATCAGCTACACTTA
*
53601367 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCT-TCGGCTACACTTA
1 TCTGATCAAGTGAC-------AAGTGATAAGTGATAGCTATCAGCTACACTTA
* *
53601419 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCT-TCGGCTATACTTA
1 TCTGATCAAGTGAC-------AAGTGATAAGTGATAGCTATCAGCTACACTTA
* *
53601471 TCTGATCAAGAGACAAAGTGATAAGTGATAGCT-TTAGCTACACTTA
1 TCTGATCAAGTGAC-AAGTGATAAGTGATAGCTATCAGCTACACTTA
*
53601517 TCTGATC-AGGGACAAGTGATAAGTGAT
1 TCTGATCAAGTGACAAGTGATAAGTGAT
53601544 CATACGTAAG
Statistics
Matches: 283, Mismatches: 21, Indels: 36
0.83 0.06 0.11
Matches are distributed among these distances:
44 14 0.05
45 15 0.05
46 121 0.43
48 1 0.00
50 1 0.00
52 121 0.43
53 10 0.04
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAGTGATAAGTGATAGCTATCAGCTACACTTA
Found at i:53601262 original size:52 final size:50
Alignment explanation
Indices: 53601190--53601543 Score: 428
Period size: 52 Copynumber: 7.2 Consensus size: 50
53601180 GATCAAGTGA
* **
53601190 TAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAG
1 TAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAG
* *
53601240 TGGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTG---A-
1 T--AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAG
* *
53601288 TAAAGTGATAACTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC---
1 TAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAG
*
53601335 -AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAG
1 TAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAG
53601384 TGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAG
1 T--AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAG
* *
53601436 TGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC---
1 T--AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAG
** *
53601485 -AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATC-AGGGACAAG
1 TAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAG
53601533 TGATAAGTGAT
1 T-A-AAGTGAT
53601544 CATACGTAAG
Statistics
Matches: 270, Mismatches: 18, Indels: 31
0.85 0.06 0.10
Matches are distributed among these distances:
45 5 0.02
46 121 0.45
48 1 0.00
49 1 0.00
50 2 0.01
51 7 0.03
52 133 0.49
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (50 bp):
TAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAG
Found at i:53601297 original size:98 final size:97
Alignment explanation
Indices: 53601177--53601543 Score: 494
Period size: 98 Copynumber: 3.8 Consensus size: 97
53601167 TTTGAGTACT
* *
53601177 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
53601242 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * *
53601275 TCTGATCAAGTGATAAAGTGATAACTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
53601335 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
53601367 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
53601432 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * * *
53601471 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATC-AGGGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
53601535 ATAAGTGAT
66 A-AAGTGAT
53601544 CATACGTAAG
Statistics
Matches: 239, Mismatches: 17, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
92 41 0.17
95 1 0.00
96 2 0.01
97 17 0.07
98 136 0.57
101 1 0.00
104 41 0.17
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:53607404 original size:31 final size:32
Alignment explanation
Indices: 53607345--53607409 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
53607335 GGCAAATTAC
53607345 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
53607377 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
53607408 AA
1 AA
53607410 ATTATCTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:53611779 original size:14 final size:14
Alignment explanation
Indices: 53611760--53611790 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
53611750 GAGGGATAGG
53611760 ACCTCGTTCTATAA
1 ACCTCGTTCTATAA
*
53611774 ACCTCGTTTTATAA
1 ACCTCGTTCTATAA
53611788 ACC
1 ACC
53611791 GAGCCGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (14 bp):
ACCTCGTTCTATAA
Found at i:53638244 original size:18 final size:19
Alignment explanation
Indices: 53638221--53638259 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
53638211 TTCGGGGGGC
*
53638221 TTGACTTTGA-TTTTGATT
1 TTGACTTTGACTTTTAATT
53638239 TTGACTTTGACTTTTAATT
1 TTGACTTTGACTTTTAATT
53638258 TT
1 TT
53638260 TATTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.18, C:0.08, G:0.13, T:0.62
Consensus pattern (19 bp):
TTGACTTTGACTTTTAATT
Found at i:53639340 original size:9 final size:9
Alignment explanation
Indices: 53639326--53639376 Score: 77
Period size: 9 Copynumber: 5.7 Consensus size: 9
53639316 TTTGGTTAAA
53639326 AATTAACCG
1 AATTAACCG
53639335 AATTAACCG
1 AATTAACCG
*
53639344 AATTACCCG
1 AATTAACCG
53639353 AATTAACCG
1 AATTAACCG
53639362 AATT-ACCTG
1 AATTAACC-G
53639371 AATTAA
1 AATTAA
53639377 ATCACTACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
8 3 0.08
9 34 0.89
10 1 0.03
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:53641973 original size:3 final size:3
Alignment explanation
Indices: 53641965--53641990 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53641955 ACTAGTTACC
53641965 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
53641991 TGGGGCAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:53642978 original size:3 final size:3
Alignment explanation
Indices: 53642970--53642998 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
53642960 AAAAGCCTTA
53642970 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53642999 AAGAACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:53644149 original size:90 final size:93
Alignment explanation
Indices: 53644031--53644284 Score: 239
Period size: 95 Copynumber: 2.7 Consensus size: 93
53644021 CTTCAAGGAG
* * * *
53644031 ATAAGACTTGTAACTTCAATTTGCTCCACTGCAACTTT-A-AG-TAGA-TTTGTAACTTGTAGCT
1 ATAAGATTTGTAACTTCAATCTGCTCCACTGCAA-TTTCAGAGATAAAGTTTATAACTTGTAGCT
* *
53644092 TTAACCTGTTCCACTACAACTTTAGGAAA
65 TTAACCTATTCCACTACAACTTCAGGAAA
* *
53644121 ATAAGATTTGTAGCTTTAATCTGCTCCACTGCAATTTCAGGGAGATAAAGTTTATAACTTGTAGC
1 ATAAGATTTGTAACTTCAATCTGCTCCACTGCAATTTCA--GAGATAAAGTTTATAACTTGTAGC
* *
53644186 TTTAATCTATTCCACTACAACTTCAGGGAA
64 TTTAACCTATTCCACTACAACTTCAGGAAA
* ** * * * * * *
53644216 ATATGATTCACTATCTTCAATCTGATCCAGTGCAACTTCAGGGAGAT-AAGATTTGTATCTTGTA
1 ATAAGATT-TGTAACTTCAATCTGCTCCACTGCAATTTCA--GAGATAAAG-TTTATAACTTGTA
53644280 GCTTT
62 GCTTT
53644285 GTATTTTGTC
Statistics
Matches: 136, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
89 3 0.02
90 31 0.23
93 2 0.01
94 3 0.02
95 50 0.37
96 47 0.35
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (93 bp):
ATAAGATTTGTAACTTCAATCTGCTCCACTGCAATTTCAGAGATAAAGTTTATAACTTGTAGCTT
TAACCTATTCCACTACAACTTCAGGAAA
Found at i:53644279 original size:96 final size:95
Alignment explanation
Indices: 53644073--53644284 Score: 273
Period size: 96 Copynumber: 2.2 Consensus size: 95
53644063 AACTTTAAGT
* * ** *
53644073 AGATTTGTAACTTGTAGCTTTAACCTGTTCCACTACAACTTTAGGAAAATAAGATTTGTAGCTTT
1 AGATTTGTAACTTGTAGCTTTAACCTATTCCACTACAACTTCAGGAAAATAAGATTACTAGCTTC
* *
53644138 AATCTGCTCCACTGCAATTTCAGGGAGATA
66 AATCTGATCCACTGCAACTTCAGGGAGATA
* * * * *
53644168 A-AGTTTATAACTTGTAGCTTTAATCTATTCCACTACAACTTCAGGGAAATATGATTCACTATCT
1 AGA-TTTGTAACTTGTAGCTTTAACCTATTCCACTACAACTTCAGGAAAATAAGATT-ACTAGCT
*
53644232 TCAATCTGATCCAGTGCAACTTCAGGGAGATA
64 TCAATCTGATCCACTGCAACTTCAGGGAGATA
*
53644264 AGATTTGTATCTTGTAGCTTT
1 AGATTTGTAACTTGTAGCTTT
53644285 GTATTTTGTC
Statistics
Matches: 99, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
94 1 0.01
95 48 0.48
96 49 0.49
97 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (95 bp):
AGATTTGTAACTTGTAGCTTTAACCTATTCCACTACAACTTCAGGAAAATAAGATTACTAGCTTC
AATCTGATCCACTGCAACTTCAGGGAGATA
Done.