Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 179 of 230
Found at i:53532923 original size:3 final size:3
Alignment explanation
Indices: 53532910--53532951 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
53532900 TTAATTAATC
* * *
53532910 TAT TGT TAT TAT TAT TAT TAT TAT TAT TAG TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53532952 ATGTTTATAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:53533425 original size:3 final size:3
Alignment explanation
Indices: 53533417--53533444 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
53533407 ATATATTGAT
53533417 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
53533445 CATCTTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:53534492 original size:20 final size:21
Alignment explanation
Indices: 53534467--53534505 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
53534457 AATTTGTTGA
53534467 TTAAATATTTATG-ATTATTT
1 TTAAATATTTATGAATTATTT
*
53534487 TTAAATTTTTATGAATTAT
1 TTAAATATTTATGAATTAT
53534506 ACATGGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
TTAAATATTTATGAATTATTT
Found at i:53548145 original size:24 final size:24
Alignment explanation
Indices: 53548118--53548164 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
53548108 ATGACCCTCC
*
53548118 AATTTTAAAATATATGTTTTTTTT
1 AATTTTAAAATATATATTTTTTTT
* *
53548142 AATTTTTAAATTTATATTTTTTT
1 AATTTTAAAATATATATTTTTTT
53548165 ATCAAATCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
AATTTTAAAATATATATTTTTTTT
Found at i:53559011 original size:17 final size:16
Alignment explanation
Indices: 53558969--53559036 Score: 55
Period size: 16 Copynumber: 4.0 Consensus size: 16
53558959 CAGAAGAATA
*
53558969 TGCCAAACCACAAATCT
1 TGCCAAAACACAAAT-T
* *
53558986 CGCCAAAAACATAGAATT
1 TGCC-AAAACACA-AATT
53559004 TGCCAAAACACAAATT
1 TGCCAAAACACAAATT
* *
53559020 TGTCAAATCACATAATT
1 TGCCAAAACACA-AATT
53559037 CACCAATCAG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
16 14 0.34
17 14 0.34
18 10 0.24
19 3 0.07
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.22
Consensus pattern (16 bp):
TGCCAAAACACAAATT
Found at i:53559778 original size:15 final size:15
Alignment explanation
Indices: 53559758--53559789 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
53559748 CATTTCACTA
*
53559758 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
53559773 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
53559788 TT
1 TT
53559790 TACATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:53561448 original size:37 final size:36
Alignment explanation
Indices: 53561395--53561470 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
53561385 ATTCTAAAAA
*
53561395 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATCTTAATAGTATT-ATATT-AATTTAATAT
*
53561431 TAATATTTATCTTAATAGTATTTTATTAATTTAATAT
1 TAATA-TTATCTTAATAGTATTATATTAATTTAATAT
53561468 TAA
1 TAA
53561471 AGTGATTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 13 0.37
37 20 0.57
38 2 0.06
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (36 bp):
TAATATTATCTTAATAGTATTATATTAATTTAATAT
Found at i:53561470 original size:11 final size:11
Alignment explanation
Indices: 53561395--53561470 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
53561385 ATTCTAAAAA
*
53561395 TAATATTATTT
1 TAATATTAATT
53561406 TAATAGTTTAATAT
1 TAATA--TTAAT-T
53561420 TAA-ATTTAATT
1 TAATA-TTAATT
*
53561431 TAATATTTATCT
1 TAATATTAAT-T
*
53561443 TAATAGT-ATT
1 TAATATTAATT
53561453 T--TATTAATT
1 TAATATTAATT
53561462 TAATATTAA
1 TAATATTAA
53561471 AGTGATTAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 2 0.04
11 21 0.40
12 14 0.26
13 5 0.09
14 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:53568699 original size:46 final size:46
Alignment explanation
Indices: 53568630--53568718 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
53568620 GTCTACTATC
*
53568630 TTTAAACTCAATACAACAGGTGATTTAAGTCATATCACATCCTGTT
1 TTTAAACTCAATACAACAAGTGATTTAAGTCATATCACATCCTGTT
* * *
53568676 TTTAAACTCAATATAACAAGTGATTTAAGTCCTATCAGATCCT
1 TTTAAACTCAATACAACAAGTGATTTAAGTCATATCACATCCT
53568719 AATGTAGCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (46 bp):
TTTAAACTCAATACAACAAGTGATTTAAGTCATATCACATCCTGTT
Found at i:53576307 original size:13 final size:13
Alignment explanation
Indices: 53576291--53576320 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
53576281 ATTGTCATGT
*
53576291 AATTGTTTTTCTG
1 AATTGATTTTCTG
53576304 AATTGATTTTCTG
1 AATTGATTTTCTG
53576317 AATT
1 AATT
53576321 TAGCTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (13 bp):
AATTGATTTTCTG
Found at i:53577099 original size:18 final size:17
Alignment explanation
Indices: 53577071--53577105 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53577061 ATTATTAAGA
*
53577071 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
53577088 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
53577106 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:53577362 original size:16 final size:16
Alignment explanation
Indices: 53577341--53577408 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
53577331 GATTTGCTAT
53577341 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
53577357 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
53577373 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
53577389 TACACCTCTAATCTAA
1 TACACCTCTAATCCAA
53577405 TACA
1 TACA
53577409 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:53579032 original size:20 final size:20
Alignment explanation
Indices: 53579007--53579045 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
53578997 GCAGGGTTTC
53579007 GGAGTTAT-ATGATGTTACTT
1 GGAGTTATAAT-ATGTTACTT
*
53579027 GGAGTTTTAATATGTTACT
1 GGAGTTATAATATGTTACT
53579046 CTATGGTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.26, C:0.05, G:0.23, T:0.46
Consensus pattern (20 bp):
GGAGTTATAATATGTTACTT
Found at i:53582724 original size:26 final size:26
Alignment explanation
Indices: 53582681--53582733 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
53582671 ACCTTCACAC
* * * *
53582681 TAATATTGCATCATAGCTGCCAGTAG
1 TAATAATGCAGCAGAGCTGCCAATAG
53582707 TAATAATGCAGCAGAGCTGCCAATAG
1 TAATAATGCAGCAGAGCTGCCAATAG
53582733 T
1 T
53582734 CAGAATGGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (26 bp):
TAATAATGCAGCAGAGCTGCCAATAG
Found at i:53582860 original size:32 final size:32
Alignment explanation
Indices: 53582810--53583029 Score: 223
Period size: 32 Copynumber: 6.8 Consensus size: 32
53582800 TACAATAATG
*
53582810 TGATTGGCACAAAGCCATCAGTAGCAGTGATA
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATA
* * * * *
53582842 TGATCGACACACAA-CCATCAGTAACGGTAACA
1 TGATCGGCACA-AAGCCATCAGTAGCAGTGATA
53582874 TGATCGGCACAAAGCCATCAGTAGCAGTGATA
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATA
* * * *
53582906 AGATCGGCACACAGCTATCAGTAACAGTGAAATA
1 TGATCGGCACAAAGCCATCAGTAGCAGTG--ATA
*
53582940 TGATCGGCACAAAGCCATCAGTAAC-GAT-ACTA
1 TGATCGGCACAAAGCCATCAGTAGCAG-TGA-TA
* * *
53582972 TGAACGACACAAAGCCATCAGTAGCGGT-ACTA
1 TGATCGGCACAAAGCCATCAGTAGCAGTGA-TA
*
53583004 TGATTGGCACAAAGCCATCAGTAGCA
1 TGATCGGCACAAAGCCATCAGTAGCA
53583030 TCGCAGCAAA
Statistics
Matches: 156, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
31 3 0.02
32 123 0.79
33 4 0.03
34 26 0.17
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.18
Consensus pattern (32 bp):
TGATCGGCACAAAGCCATCAGTAGCAGTGATA
Found at i:53582917 original size:64 final size:64
Alignment explanation
Indices: 53582810--53583029 Score: 259
Period size: 64 Copynumber: 3.4 Consensus size: 64
53582800 TACAATAATG
*
53582810 TGATTGGCACAAAGCCATCAGTAGCAGTGATATGATCGACACACAACCATCAGTAACGGTAACA
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGACACACAACCATCAGTAACGGTAACA
* * * * * *
53582874 TGATCGGCACAAAGCCATCAGTAGCAGTGATAAGATCGGCACACAGCTATCAGTAACAGTGAAAT
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGACACACAACCATCAGTAAC-G-GTAAC
53582939 A
64 A
* * *
53582940 TGATCGGCACAAAGCCATCAGTAAC-GAT-ACTATGAACGACACA-AAGCCATCAGTAGCGGT-A
1 TGATCGGCACAAAGCCATCAGTAGCAG-TGA-TATGATCGACACACAA-CCATCAGTAACGGTAA
53583001 CTA
63 C-A
*
53583004 TGATTGGCACAAAGCCATCAGTAGCA
1 TGATCGGCACAAAGCCATCAGTAGCA
53583030 TCGCAGCAAA
Statistics
Matches: 131, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
63 1 0.01
64 77 0.59
65 5 0.04
66 48 0.37
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.18
Consensus pattern (64 bp):
TGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGACACACAACCATCAGTAACGGTAACA
Found at i:53582983 original size:98 final size:96
Alignment explanation
Indices: 53582815--53583026 Score: 268
Period size: 98 Copynumber: 2.2 Consensus size: 96
53582805 TAATGTGATT
* * *
53582815 GGCACAAAGCCATCAGTAGCAGTGATATGATCGACACACAACCATCAGTAACGGTAACATGATCG
1 GGCACAAAGCCATCAGTAACAGTGATATGATCGACACACAACCATCAGTAACGATAACATGAACG
*
53582880 GCACAAAGCCATCAGTAGCAGTGATAAGATC
66 ACACAAAGCCATCAGTAGCAGTGATAAGATC
* * *
53582911 GGCACACAGCTATCAGTAACAGTGAAATATGATCGGCACA-AAGCCATCAGTAACGAT-ACTATG
1 GGCACAAAGCCATCAGTAACAGTG--ATATGATCGACACACAA-CCATCAGTAACGATAAC-ATG
* * *
53582974 AACGACACAAAGCCATCAGTAGCGGT-ACTATGATT
62 AACGACACAAAGCCATCAGTAGCAGTGA-TAAGATC
53583009 GGCACAAAGCCATCAGTA
1 GGCACAAAGCCATCAGTA
53583027 GCATCGCAGC
Statistics
Matches: 99, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
96 21 0.21
97 5 0.05
98 73 0.74
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (96 bp):
GGCACAAAGCCATCAGTAACAGTGATATGATCGACACACAACCATCAGTAACGATAACATGAACG
ACACAAAGCCATCAGTAGCAGTGATAAGATC
Found at i:53583058 original size:26 final size:26
Alignment explanation
Indices: 53583029--53583082 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
53583019 CATCAGTAGC
53583029 ATCGCAGCAAAGTTGCCAGCAACAGT
1 ATCGCAGCAAAGTTGCCAGCAACAGT
* * *
53583055 ATCGCAGCAGAGTTGCCAGTAATAGT
1 ATCGCAGCAAAGTTGCCAGCAACAGT
53583081 AT
1 AT
53583083 ATGTGGCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.20
Consensus pattern (26 bp):
ATCGCAGCAAAGTTGCCAGCAACAGT
Found at i:53584720 original size:20 final size:20
Alignment explanation
Indices: 53584695--53584732 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53584685 AAAGCATAAA
*
53584695 ATACCAAGTATCAACAAAAT
1 ATACCAAATATCAACAAAAT
53584715 ATACCAAATATCAACAAA
1 ATACCAAATATCAACAAA
53584733 GTGCATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.21, G:0.03, T:0.18
Consensus pattern (20 bp):
ATACCAAATATCAACAAAAT
Found at i:53587537 original size:28 final size:28
Alignment explanation
Indices: 53587481--53587538 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
53587471 AAAAATAATA
**
53587481 AAAATTAAATATTTTCATAATTTGAATG
1 AAAATTAAATATTTTCATAATTAAAATG
*
53587509 AAAATTAATTATTTT-ATAATTAAATATG
1 AAAATTAAATATTTTCATAATTAAA-ATG
53587537 AA
1 AA
53587539 TTTTGACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (28 bp):
AAAATTAAATATTTTCATAATTAAAATG
Found at i:53588622 original size:12 final size:12
Alignment explanation
Indices: 53588605--53588631 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53588595 TAATTTACAA
53588605 CCACGTGAGAAT
1 CCACGTGAGAAT
53588617 CCACGTGAGAAT
1 CCACGTGAGAAT
53588629 CCA
1 CCA
53588632 TTGTTCGACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.30, G:0.22, T:0.15
Consensus pattern (12 bp):
CCACGTGAGAAT
Found at i:53590012 original size:38 final size:39
Alignment explanation
Indices: 53589934--53590021 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 39
53589924 GTAGAAAACG
* * *
53589934 GTTGTACTTCGGTACTCCTGATCGCACTTACGTGCCCCT
1 GTTGTACTTCAGTACCCCTCATCGCACTTACGTGCCCCT
* * *
53589973 GTTGTACTT-AGTACCCCTCATCGTACTTATGTGCTCCT
1 GTTGTACTTCAGTACCCCTCATCGCACTTACGTGCCCCT
*
53590011 GTTGTATTTCA
1 GTTGTACTTCA
53590022 ATTCTCCTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 31 0.76
39 10 0.24
ACGTcount: A:0.15, C:0.28, G:0.18, T:0.39
Consensus pattern (39 bp):
GTTGTACTTCAGTACCCCTCATCGCACTTACGTGCCCCT
Found at i:53596354 original size:22 final size:20
Alignment explanation
Indices: 53596301--53596357 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
53596291 TTATATACAT
*
53596301 ATATATACATACATTTTTATA
1 ATATATACATA-TTTTTTATA
53596322 ATATACGTACATATTTTTTATA
1 ATATA--TACATATTTTTTATA
53596344 ACTTATATACATAT
1 A--TATATACATAT
53596358 ATACATACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.16
22 16 0.52
23 6 0.19
24 4 0.13
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATATACATATTTTTTATA
Found at i:53605159 original size:50 final size:50
Alignment explanation
Indices: 53605052--53605449 Score: 472
Period size: 50 Copynumber: 7.8 Consensus size: 50
53605042 ATTTGGGTAA
* **
53605052 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ACCGAG---ATG
*
53605108 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
53605158 AGAGGTCTCATGTAAGACCATGTCTGGGACATAGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
53605208 ACAGGTACCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
53605258 AGAGGTCCCATTTAAGACCATGTTTGGGACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * * *
53605308 GGAGGTCCTATGTAAGACCATGTCTCGGACATGACGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
53605358 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATAGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
53605408 AGAACTCTCATGTAAGACCATATCTGGGATATGACATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
53605450 GTACAAGAAA
Statistics
Matches: 296, Mismatches: 46, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
50 253 0.85
53 4 0.01
56 39 0.13
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:53605288 original size:150 final size:149
Alignment explanation
Indices: 53605059--53605498 Score: 508
Period size: 150 Copynumber: 2.9 Consensus size: 149
53605049 TAAAGAGATC
*
53605059 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGATTATGAGAGGTCCCATGTAAG
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGC---ATCGAG---ATGAGAGGTCCCATGTAAG
*
53605124 ACCATGTCTAGGACATGGCATTGGCACCGAGATGAGAGGTCTCATGTAAGACCATGTCTGGGACA
60 ACCATGTCTGGGACATGGCATTGGCA-CGAGATGAGAGGTCTCATGTAAGACCATGTCTGGGACA
*
53605189 TAGCGTTGGCACCGAGATGACAGGTA
124 TAGCGTTGGCACCAAGATGACAGGTA
*
53605215 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGGTCCCATTTAAGACCATG
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGGTCCCATGTAAGACCATG
* * * *
53605280 TTTGGGACATGGCGTTGGCACTGAGATGGGAGGTC-CTATGTAAGACCATGTCTCGGACAT-GAC
66 TCTGGGACATGGCATTGGCAC-GAGATGAGAGGTCTC-ATGTAAGACCATGTCTGGGACATAG-C
* *
53605343 GTTGGCACCAAGATGAGAGGTC
128 GTTGGCACCAAGATGACAGGTA
* * * * * ** * *
53605365 CCCTGTAAGACCATGTCTGGGACATGGCATAGGCACCTATATGAGAACTCTCATGTAAGACCATA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGGTCCCATGTAAGACCATG
* * * * * ** * *
53605430 TCTGGGATATGACATTGGCA-GTACAAGAAACATCTCATGTAAGACTATGTCTGGGACATAGCTT
66 TCTGGGACATGGCATTGGCACG-AGATGAGAGGTCTCATGTAAGACCATGTCTGGGACATAGCGT
53605494 TGGCA
130 TGGCA
53605499 TGTTATATTC
Statistics
Matches: 245, Mismatches: 33, Indels: 19
0.82 0.11 0.06
Matches are distributed among these distances:
148 1 0.00
149 37 0.15
150 168 0.69
153 5 0.02
156 34 0.14
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (149 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGGTCCCATGTAAGACCATG
TCTGGGACATGGCATTGGCACGAGATGAGAGGTCTCATGTAAGACCATGTCTGGGACATAGCGTT
GGCACCAAGATGACAGGTA
Found at i:53605497 original size:49 final size:49
Alignment explanation
Indices: 53605116--53605498 Score: 218
Period size: 50 Copynumber: 7.7 Consensus size: 49
53605106 TGAGAGGTCC
* * * * **
53605116 CATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACAT-GCATTGGCACCTACAAGAGAACTCT
* * * * * **
53605166 CATGTAAGACCATGTCTGGGACATAGCGTTGGCACCGAGATGACAGGTAC-
1 CATGTAAGACCATGTCTGGGACAT-GCATTGGCACCTACAAGAGAACT-CT
* * * * ** *
53605216 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACAT-GCATTGGCACCTACAAGAGAACTCT
* * * * * * **
53605266 CATTTAAGACCATGTTTGGGACATGGCGTTGGCA-CTGAGATGGGAGGTC-
1 CATGTAAGACCATGTCTGGGACAT-GCATTGGCACCT-ACAAGAGAACTCT
* * * * * ** *
53605315 CTATGTAAGACCATGTCTCGGACATGACGTTGGCACCAAGATGAGAGGTCC
1 C-ATGTAAGACCATGTCTGGGACATG-CATTGGCACCTACAAGAGAACTCT
* * * *
53605366 CCTGTAAGACCATGTCTGGGACATGGCATAGGCACCTATATGAGAACTCT
1 CATGTAAGACCATGTCTGGGACAT-GCATTGGCACCTACAAGAGAACTCT
* * *
53605416 CATGTAAGACCATATCTGGGATATGACATTGGCA-GTACAAGA-AACATCT
1 CATGTAAGACCATGTCTGGGACATG-CATTGGCACCTACAAGAGAAC-TCT
* *
53605465 CATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACAT-GCATTGGCA
53605499 TGTTATATTC
Statistics
Matches: 284, Mismatches: 38, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
48 3 0.01
49 41 0.14
50 236 0.83
51 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (49 bp):
CATGTAAGACCATGTCTGGGACATGCATTGGCACCTACAAGAGAACTCT
Found at i:53616346 original size:28 final size:28
Alignment explanation
Indices: 53616295--53616348 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
53616285 ACTGTTCTAA
*
53616295 AATATTTATAAAAAAGGCATCTAATTTT
1 AATATTTATAAAAAAGGCAACTAATTTT
*
53616323 AATATTTA-CAAAAAGGACAACTAATT
1 AATATTTATAAAAAAGG-CAACTAATT
53616349 ATTGAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.33
Consensus pattern (28 bp):
AATATTTATAAAAAAGGCAACTAATTTT
Found at i:53621756 original size:17 final size:16
Alignment explanation
Indices: 53621725--53621764 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
53621715 CCTTCGTTCC
53621725 TCTTCTTTCTTTTTCT
1 TCTTCTTTCTTTTTCT
*
53621741 TCTTCATTTGTTTTTCT
1 TCTTC-TTTCTTTTTCT
53621758 T-TTCTTT
1 TCTTCTTT
53621765 TAATTTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 8 0.36
17 11 0.50
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.75
Consensus pattern (16 bp):
TCTTCTTTCTTTTTCT
Found at i:53622533 original size:104 final size:105
Alignment explanation
Indices: 53622415--53622658 Score: 312
Period size: 104 Copynumber: 2.3 Consensus size: 105
53622405 AGTGTAGGGT
* * * * *
53622415 TCACACGGGAAAGGACACGGGCGTGTGTCTAGGCCGTGTAACTCACTATTTGTGACTT-AGAACC
1 TCACACGGGAAAGGACATGGGCGTGTGTCCAAGCCATGTAACTCACTATTTATG-CTTGAGAACC
* * * *
53622479 ACATGGTC-AGGGACATGGGTGTGTGTCCAGGCCATGTGAG
65 ACATGGGCAAAGGACATAGGTGTGTGTCCAAGCCATGTGAG
* * *
53622519 TCACACGGGCAAGGACATGGGCGTGTGTCCAAGCCATGTAACTCACTATTTATGTTTGAGAACCG
1 TCACACGGGAAAGGACATGGGCGTGTGTCCAAGCCATGTAACTCACTATTTATGCTTGAGAACCA
*
53622584 CATGGGCAAAGGACATAGGTGTGTGTCCAAGCCGTGTGAG
66 CATGGGCAAAGGACATAGGTGTGTGTCCAAGCCATGTGAG
* * * *
53622624 CCACACGGGTAAGGACATGGGCGTCTGCCCAAGCC
1 TCACACGGGAAAGGACATGGGCGTGTGTCCAAGCC
53622659 GTGTGGCATA
Statistics
Matches: 121, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
103 2 0.02
104 60 0.50
105 59 0.49
ACGTcount: A:0.24, C:0.23, G:0.32, T:0.21
Consensus pattern (105 bp):
TCACACGGGAAAGGACATGGGCGTGTGTCCAAGCCATGTAACTCACTATTTATGCTTGAGAACCA
CATGGGCAAAGGACATAGGTGTGTGTCCAAGCCATGTGAG
Found at i:53627940 original size:21 final size:21
Alignment explanation
Indices: 53627916--53627956 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
53627906 AAGCCCGAGG
* *
53627916 GCTACACAGAAGCACATAAGT
1 GCTAAACAGAAACACATAAGT
*
53627937 GCTAAACAGAAACCCATAAG
1 GCTAAACAGAAACACATAAG
53627957 GGTTGAACGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.12
Consensus pattern (21 bp):
GCTAAACAGAAACACATAAGT
Found at i:53627975 original size:21 final size:21
Alignment explanation
Indices: 53627945--53628002 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
53627935 GTGCTAAACA
53627945 GAAACCCATAAGGGTTGAACG
1 GAAACCCATAAGGGTTGAACG
** * * *
53627966 GAGGCTCATAAGAGCTGAACG
1 GAAACCCATAAGGGTTGAACG
53627987 GAAACCCATAAGGGTT
1 GAAACCCATAAGGGTT
53628003 AAACAGAAGC
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.16
Consensus pattern (21 bp):
GAAACCCATAAGGGTTGAACG
Found at i:53627991 original size:42 final size:41
Alignment explanation
Indices: 53627921--53628068 Score: 143
Period size: 42 Copynumber: 3.5 Consensus size: 41
53627911 CGAGGGCTAC
* * *
53627921 ACAGAAGCACATAAGTGCTAAACAGAAACCCATAAGGGTTGA
1 ACAGAAGCTCATAAGAGCT-AACGGAAACCCATAAGGGTTGA
* * *
53627963 ACGGAGGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTAA
1 ACAGAAGCTCATAAGAGCT-AACGGAAACCCATAAGGGTTGA
* * * *
53628005 ACAGAAGCTTAAAAGAGCTAATTGGAAACCCATTAGGGTTGA
1 ACAGAAGCTCATAAGAGCTAA-CGGAAACCCATAAGGGTTGA
* * * *
53628047 ACAAAAACTCATATGAGTTAAC
1 ACAGAAGCTCATAAGAGCTAAC
53628069 AGAAGCTCAT
Statistics
Matches: 84, Mismatches: 21, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
41 2 0.02
42 82 0.98
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.18
Consensus pattern (41 bp):
ACAGAAGCTCATAAGAGCTAACGGAAACCCATAAGGGTTGA
Found at i:53628586 original size:38 final size:38
Alignment explanation
Indices: 53628543--53628616 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 38
53628533 ATTAATATTA
53628543 AAATAAGCTA-TTTTTCTCAATTAATATTTTAGTCTACC
1 AAATAAGCTATTTTTTCTCAATTAATATTTTA-TCTACC
53628581 AAATAAGCTATTTTTTCTCAATTAATATTTTATCTA
1 AAATAAGCTATTTTTTCTCAATTAATATTTTATCTA
53628617 AATATTCTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 14 0.40
39 21 0.60
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.47
Consensus pattern (38 bp):
AAATAAGCTATTTTTTCTCAATTAATATTTTATCTACC
Found at i:53628611 original size:17 final size:17
Alignment explanation
Indices: 53628553--53628611 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
53628543 AAATAAGCTA
53628553 TTTTTCTCAATTAATAT
1 TTTTTCTCAATTAATAT
* *
53628570 TTTAGTCTACCAAATAAGCTAT
1 TTT-TTCT--CAATTAA--TAT
53628592 TTTTTCTCAATTAATAT
1 TTTTTCTCAATTAATAT
53628609 TTT
1 TTT
53628612 ATCTAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
17 9 0.27
18 3 0.09
19 6 0.18
20 6 0.18
21 3 0.09
22 6 0.18
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTTTCTCAATTAATAT
Found at i:53635540 original size:21 final size:21
Alignment explanation
Indices: 53635489--53635582 Score: 71
Period size: 21 Copynumber: 4.5 Consensus size: 21
53635479 AGGCTACACA
** **
53635489 GAAGCTCATAAATGTTAAATA
1 GAAGCTCATAAGGGTTAAACG
* * *
53635510 GAAACCCATAAGGGTTGAACG
1 GAAGCTCATAAGGGTTAAACG
* *
53635531 GAAGCTCATAAGAGCTAAACG
1 GAAGCTCATAAGGGTTAAACG
* * * *
53635552 GAAACCCATAAAGGTTAAACA
1 GAAGCTCATAAGGGTTAAACG
53635573 GAAGCTCATA
1 GAAGCTCATA
53635583 TGAGTTAATA
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (21 bp):
GAAGCTCATAAGGGTTAAACG
Found at i:53635589 original size:21 final size:20
Alignment explanation
Indices: 53635486--53635612 Score: 58
Period size: 21 Copynumber: 6.1 Consensus size: 20
53635476 CAAAGGCTAC
*
53635486 ACAGAAGCTCATAAATGTTAA
1 ACAGAAGCTCATAGA-GTTAA
* * * * *
53635507 ATAGAAACCCATAAGGGTTGA
1 ACAGAAGCTCAT-AGAGTTAA
* *
53635528 ACGGAAGCTCATAAGAGCTAA
1 ACAGAAGCTCAT-AGAGTTAA
* * * *
53635549 ACGGAAACCCATAAAGGTTAA
1 ACAGAAGCTCATAGA-GTTAA
53635570 ACAGAAGCTCATATGAGTT-A
1 ACAGAAGCTCATA-GAGTTAA
* * *
53635590 ATAGAAGCTTATGAGAGCTAA
1 ACAGAAGCTCAT-AGAGTTAA
53635611 AC
1 AC
53635613 GGAAAGTAAA
Statistics
Matches: 76, Mismatches: 25, Indels: 10
0.68 0.23 0.09
Matches are distributed among these distances:
20 17 0.22
21 57 0.75
22 2 0.03
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (20 bp):
ACAGAAGCTCATAGAGTTAA
Found at i:53637853 original size:24 final size:26
Alignment explanation
Indices: 53637816--53637870 Score: 96
Period size: 24 Copynumber: 2.2 Consensus size: 26
53637806 TTCATCATTT
53637816 AATGGTAAGAACACCTAGCATTCATC
1 AATGGTAAGAACACCTAGCATTCATC
53637842 AATGG-AA-AACACCTAGCATTCATC
1 AATGGTAAGAACACCTAGCATTCATC
53637866 AATGG
1 AATGG
53637871 CAAGTTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 22 0.76
25 2 0.07
26 5 0.17
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (26 bp):
AATGGTAAGAACACCTAGCATTCATC
Found at i:53640453 original size:24 final size:24
Alignment explanation
Indices: 53640425--53640474 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
53640415 GAAACATTCT
53640425 AAATCATCTAAAAGAATTCCAGGC
1 AAATCATCTAAAAGAATTCCAGGC
53640449 AAATCATCTAAAAGAATTCCAGGC
1 AAATCATCTAAAAGAATTCCAGGC
53640473 AA
1 AA
53640475 CCATATTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (24 bp):
AAATCATCTAAAAGAATTCCAGGC
Found at i:53643124 original size:17 final size:16
Alignment explanation
Indices: 53643104--53643137 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
53643094 TTAATATTTT
*
53643104 ATTTCAATATTTATTAA
1 ATTTAAATATTT-TTAA
53643121 ATTTAAATATTTTTAA
1 ATTTAAATATTTTTAA
53643137 A
1 A
53643138 AATAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTAAATATTTTTAA
Found at i:53644817 original size:31 final size:31
Alignment explanation
Indices: 53644779--53644859 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
53644769 CAAACCTTTC
53644779 AAAGTGCTCAAATAAGGGCCAAAAGTTTTTG
1 AAAGTGCTCAAATAAGGGCCAAAAGTTTTTG
** **
53644810 AAAGTGCTCAAATAAAAGCCAAACTTTTTTG
1 AAAGTGCTCAAATAAGGGCCAAAAGTTTTTG
*
53644841 AAAGTACTCAAATAAGGGC
1 AAAGTGCTCAAATAAGGGC
53644860 TTCTCATATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (31 bp):
AAAGTGCTCAAATAAGGGCCAAAAGTTTTTG
Found at i:53645244 original size:17 final size:18
Alignment explanation
Indices: 53645222--53645255 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53645212 ATAATTGTAA
53645222 TTTAAAT-TGTAATTATT
1 TTTAAATATGTAATTATT
53645239 TTTAAATATGTAATTAT
1 TTTAAATATGTAATTAT
53645256 CATAATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAAATATGTAATTATT
Found at i:53655898 original size:13 final size:13
Alignment explanation
Indices: 53655882--53655913 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
53655872 TTTTTTAATA
53655882 CTCATTTTTTCTT
1 CTCATTTTTTCTT
53655895 CTCA-TTTTTCTT
1 CTCATTTTTTCTT
53655907 CTC-TTTT
1 CTCATTTT
53655914 CTCCTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (13 bp):
CTCATTTTTTCTT
Found at i:53657063 original size:19 final size:20
Alignment explanation
Indices: 53657033--53657070 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
53657023 TGGTAGGACT
53657033 GTTTTCACAAAATCTGCATC
1 GTTTTCACAAAATCTGCATC
*
53657053 GTTTT-ACAAAATGTGCAT
1 GTTTTCACAAAATCTGCAT
53657071 TAACATGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (20 bp):
GTTTTCACAAAATCTGCATC
Found at i:53669342 original size:19 final size:19
Alignment explanation
Indices: 53669318--53669359 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
53669308 ACATATATAT
53669318 TACACATTTATTACATGTA
1 TACACATTTATTACATGTA
53669337 TACACATTTATTACATGTA
1 TACACATTTATTACATGTA
53669356 TACA
1 TACA
53669360 ATTGCACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (19 bp):
TACACATTTATTACATGTA
Found at i:53679952 original size:28 final size:27
Alignment explanation
Indices: 53679904--53679974 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 27
53679894 TTATGAAAAT
* *
53679904 TTATTATAAAAATAAT-T-AAAATTCAA
1 TTATTTTAAAATTAATGTGAAAATT-AA
*
53679930 -TATTTTAATAATTTATGTGAAAATTAA
1 TTATTTTAA-AATTAATGTGAAAATTAA
53679957 TTATTTTAAAATTAATGT
1 TTATTTTAAAATTAATGT
53679975 ATGAATTTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
25 7 0.19
26 5 0.14
27 11 0.30
28 14 0.38
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (27 bp):
TTATTTTAAAATTAATGTGAAAATTAA
Found at i:53701504 original size:15 final size:15
Alignment explanation
Indices: 53701484--53701514 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53701474 GTTATGTAAG
53701484 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
*
53701499 TGAAAGGTTAAGAGT
1 TGAAAGGTCAAGAGT
53701514 T
1 T
53701515 ATGTTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:53708173 original size:51 final size:49
Alignment explanation
Indices: 53708048--53708233 Score: 219
Period size: 51 Copynumber: 3.7 Consensus size: 49
53708038 GTGAAAGTGA
* * *
53708048 TGGTCACTTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-T
* * * *
53708098 TGGTCGCATGTGTAGTACTATGTGCTGGCTACTATGCGTACCGGATAGCT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-T
* * * *
53708148 TCGATCACGTGTTTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGT
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT
*
53708198 GATGGTCACATGTGTAGTACTATGTGTAGGCTACTA
1 --TGGTCACATGTGTAGTACTATGTGCAGGCTACTA
53708234 TGTGAACCAG
Statistics
Matches: 113, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
50 44 0.39
51 68 0.60
52 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (49 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT
Found at i:53708235 original size:102 final size:101
Alignment explanation
Indices: 53708051--53708235 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 101
53708041 AAAGTGATGG
* *
53708051 TCACTTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGATTGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGATTGGTCACATGTGTAGTAC
53708116 TATGTGCTGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCTGGCTACTATGCGTACCGGATAGCTTCGA
* * * *
53708152 TCACGTGTTTAGTACTATGTGCAGGCTACTACGTGTATCGGATAG-TGATGGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGAT--TGGTCACATGTGTAGT
53708216 ACTATGTG-TAGGCTACTATG
64 ACTATGTGCT-GGCTACTATG
53708236 TGAACCAGTA
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
100 1 0.01
101 41 0.55
102 33 0.44
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGATTGGTCACATGTGTAGTAC
TATGTGCTGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:53708506 original size:37 final size:38
Alignment explanation
Indices: 53708437--53708509 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
53708427 ATGTGTGGAA
* * **
53708437 TTGAATTGAATATTGACTTGAAAATGGCAAAGTGAATT
1 TTGAATTAAATAGTGACTTGAAAATGAAAAAGTGAATT
*
53708475 TTGAATTAAATAGTGA-TTGAAATTGAAAAAGTGAA
1 TTGAATTAAATAGTGACTTGAAAATGAAAAAGTGAA
53708510 ATTATGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 16 0.53
38 14 0.47
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.33
Consensus pattern (38 bp):
TTGAATTAAATAGTGACTTGAAAATGAAAAAGTGAATT
Found at i:53711696 original size:178 final size:179
Alignment explanation
Indices: 53711397--53711735 Score: 608
Period size: 178 Copynumber: 1.9 Consensus size: 179
53711387 TGATTTCATC
*
53711397 AAAACTTGAAGGTGGATTATGGCATTTTTTAGAGAAAATGGAGAATATGCAAGAGAAAATGAAAA
1 AAAACTTGAAGGTGGATTATGGCATTTTTTAGAGAAAATGGAGAATATGCAAGAAAAAATGAAAA
*
53711462 AAGAAGAATATAGAGGCCATGGGGGAGCTGGCCAACTAGTTCTTAGCTGAATGGTGAG-GGGGGT
66 AAGAAGAACATAGAGGCCATGGGGGAGCTGGCCAACTAGTTCTTAGCTGAATGGTGAGCGGGGGT
*
53711526 TCCCCATTCTTCATTTTAAATACAACAAAAATGAATATAGAGAAAATGG
131 TCCCCATTCTTCATTTTAAATACAAAAAAAATGAATATAGAGAAAATGG
* *
53711575 AAAACTTGAAGGTGGATTATGGCATTTTTTAGAGAAAATGTAGAATATGCAAGAAAAAATGGAAA
1 AAAACTTGAAGGTGGATTATGGCATTTTTTAGAGAAAATGGAGAATATGCAAGAAAAAATGAAAA
* *
53711640 AAGAAGAACATAGAGGCCATGGGGGAGCTGGCCAACTAGTTCTTAGTTGAATGGTGAGCGGGGTT
66 AAGAAGAACATAGAGGCCATGGGGGAGCTGGCCAACTAGTTCTTAGCTGAATGGTGAGCGGGGGT
53711705 TCCCCATTCTTCATTTTAAATACAAAAAAAA
131 TCCCCATTCTTCATTTTAAATACAAAAAAAA
53711736 ATAGGCTCAA
Statistics
Matches: 153, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
178 118 0.77
179 35 0.23
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (179 bp):
AAAACTTGAAGGTGGATTATGGCATTTTTTAGAGAAAATGGAGAATATGCAAGAAAAAATGAAAA
AAGAAGAACATAGAGGCCATGGGGGAGCTGGCCAACTAGTTCTTAGCTGAATGGTGAGCGGGGGT
TCCCCATTCTTCATTTTAAATACAAAAAAAATGAATATAGAGAAAATGG
Found at i:53716269 original size:45 final size:45
Alignment explanation
Indices: 53716232--53716350 Score: 220
Period size: 45 Copynumber: 2.6 Consensus size: 45
53716222 TTTCAGCCAC
*
53716232 GGTCTTATTTATTTTCAACATTATGCCATAGTGTCTTTCAACTAT
1 GGTCTTATTTATTTTCGACATTATGCCATAGTGTCTTTCAACTAT
*
53716277 GGTCTTTTTTATTTTCGACATTATGCCATAGTGTCTTTCAACTAT
1 GGTCTTATTTATTTTCGACATTATGCCATAGTGTCTTTCAACTAT
53716322 GGTCTTATTTATTTTCGACATTATGCCAT
1 GGTCTTATTTATTTTCGACATTATGCCAT
53716351 TTCCATCATG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.48
Consensus pattern (45 bp):
GGTCTTATTTATTTTCGACATTATGCCATAGTGTCTTTCAACTAT
Found at i:53728441 original size:22 final size:22
Alignment explanation
Indices: 53728403--53728446 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53728393 GTGGATGTCA
53728403 TGACTTTGGTGGCCCAATGTTG
1 TGACTTTGGTGGCCCAATGTTG
*
53728425 TGACTTTGG-GTCTCCAATGTTG
1 TGACTTTGGTGGC-CCAATGTTG
53728447 CAACTTTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.14, C:0.18, G:0.30, T:0.39
Consensus pattern (22 bp):
TGACTTTGGTGGCCCAATGTTG
Found at i:53729767 original size:6 final size:6
Alignment explanation
Indices: 53729756--53729791 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
53729746 GGTTTTCTCC
*
53729756 AAAATG AAAATG AAAGTG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
53729792 GGGAAATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:53729816 original size:75 final size:76
Alignment explanation
Indices: 53729710--53729864 Score: 233
Period size: 75 Copynumber: 2.0 Consensus size: 76
53729700 CATAAATGGT
* *
53729710 AAAATGGAGAAATAGGAAACATTTGGAAATGATTATGGTTTTCTCCAAAATGAAAATGAAAGTGA
1 AAAATGGAGAAATA-GAAACATTTGGAAATGAATATGGTTTTCTCCAAAATGAAAATGAAAATGA
53729775 AAATG-AAAATG
65 AAATGAAAAATG
* **
53729786 AAAATGGGGAAAT-GAAATCATTTGGAAATGAATATGGTTTTCTGTAAAATGAAAATGAAAATGA
1 AAAATGGAGAAATAGAAA-CATTTGGAAATGAATATGGTTTTCTCCAAAATGAAAATGAAAATGA
53729850 AAATGAAAAATG
65 AAATGAAAAATG
53729862 AAA
1 AAA
53729865 TTGACCTGGA
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
74 4 0.06
75 47 0.65
76 21 0.29
ACGTcount: A:0.50, C:0.04, G:0.21, T:0.25
Consensus pattern (76 bp):
AAAATGGAGAAATAGAAACATTTGGAAATGAATATGGTTTTCTCCAAAATGAAAATGAAAATGAA
AATGAAAAATG
Found at i:53729842 original size:6 final size:6
Alignment explanation
Indices: 53729831--53729864 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
53729821 GGTTTTCTGT
53729831 AAAATG AAAATG AAAATG AAAATG AAAAATG AAA
1 AAAATG AAAATG AAAATG AAAATG -AAAATG AAA
53729865 TTGACCTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:53736207 original size:6 final size:6
Alignment explanation
Indices: 53736196--53736241 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
53736186 AGGAAAATTT
53736196 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCT
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCT
53736242 ATCCTTGACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CCCTTC
Found at i:53750385 original size:24 final size:24
Alignment explanation
Indices: 53750333--53750424 Score: 114
Period size: 24 Copynumber: 3.8 Consensus size: 24
53750323 TCATGTACAT
*
53750333 GTATGCTCAT-ACGAGCTATGAATTG
1 GTATGCTC-TCACGAGCTGT-AATTG
53750358 GTATGCTCTCACGAGCTGTAATTG
1 GTATGCTCTCACGAGCTGTAATTG
* *
53750382 GTATGCTCCCACGAGCTGTAATCG
1 GTATGCTCTCACGAGCTGTAATTG
* *
53750406 GTCTACTCTCACGAGCTGT
1 GTATGCTCTCACGAGCTGT
53750425 GGGTTGGAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
24 44 0.73
25 16 0.27
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (24 bp):
GTATGCTCTCACGAGCTGTAATTG
Found at i:53760863 original size:19 final size:21
Alignment explanation
Indices: 53760823--53760863 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
53760813 TGATAATAAC
*
53760823 TAGTATATAATTATATTTTTA
1 TAGTATATAATTATATTATTA
53760844 TAGTATAT-ATTA-ATTATTA
1 TAGTATATAATTATATTATTA
53760863 T
1 T
53760864 CAACTTTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
TAGTATATAATTATATTATTA
Found at i:53761446 original size:8 final size:8
Alignment explanation
Indices: 53761433--53761458 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
53761423 AATTTCAATT
53761433 TTATTTAA
1 TTATTTAA
53761441 TTATTTAA
1 TTATTTAA
53761449 TTATTTAA
1 TTATTTAA
53761457 TT
1 TT
53761459 TATTGAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTATTTAA
Found at i:53762335 original size:3 final size:3
Alignment explanation
Indices: 53762327--53762358 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
53762317 CAAAGATCCC
53762327 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
53762359 TCCCACAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:53765177 original size:19 final size:19
Alignment explanation
Indices: 53765146--53765260 Score: 149
Period size: 19 Copynumber: 5.8 Consensus size: 19
53765136 AATCTTCAAG
*
53765146 GATATGCAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
53765165 GATTTGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
53765184 GATATGCAATCTTAGATAT
1 GATATGTAATCTTAGATAT
53765203 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
53765222 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTT---AGATAT
*
53765244 GATTTTGTAATCTTAGA
1 GA-TATGTAATCTTAGA
53765261 GATTTAATTT
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
19 64 0.76
20 3 0.04
22 8 0.10
23 9 0.11
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.40
Consensus pattern (19 bp):
GATATGTAATCTTAGATAT
Found at i:53765190 original size:38 final size:38
Alignment explanation
Indices: 53765146--53765260 Score: 185
Period size: 38 Copynumber: 2.9 Consensus size: 38
53765136 AATCTTCAAG
53765146 GATATGCAATCTTAGATATGATTTGTAATCTTAGATAT
1 GATATGCAATCTTAGATATGATTTGTAATCTTAGATAT
*
53765184 GATATGCAATCTTAGATATGATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATATGATTTGTAATCTTAGATAT
53765222 GATATGCAATCTTAGAAGATATGATTTTGTAATCTTAGA
1 GATATGCAATCTT---AGATATGA-TTTGTAATCTTAGA
53765261 GATTTAATTT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
38 50 0.70
41 8 0.11
42 13 0.18
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.40
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATTTGTAATCTTAGATAT
Found at i:53765668 original size:15 final size:16
Alignment explanation
Indices: 53765650--53765681 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
53765640 TAATCCTCTA
53765650 TTTTTTATT-TTAAAT
1 TTTTTTATTATTAAAT
53765665 TTTTTTATTATTAAAT
1 TTTTTTATTATTAAAT
53765681 T
1 T
53765682 AATTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTATTATTAAAT
Found at i:53770853 original size:21 final size:23
Alignment explanation
Indices: 53770829--53770872 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53770819 AGATATAAAA
53770829 AAAAGAA-AAA-AAAATAGAGAG
1 AAAAGAAGAAAGAAAATAGAGAG
*
53770850 AAAAGAAGAAAGAAAATGGAGAG
1 AAAAGAAGAAAGAAAATAGAGAG
53770873 GCCAAGGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 3 0.15
23 10 0.50
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAGAAGAAAGAAAATAGAGAG
Found at i:53772463 original size:88 final size:88
Alignment explanation
Indices: 53772070--53772454 Score: 502
Period size: 88 Copynumber: 4.4 Consensus size: 88
53772060 TTCCTTCTTG
* * * * *
53772070 CACCGACAGCGAAGCAAATCGAAGACACCAACCTTGCCTCCCTGGGTTGTAGCGGAGTAGGCTAA
1 CACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCGAAGCAGGTTAA
* *
53772135 AAATAGAAGATCTTGTCTTCCTA
66 AAATAGCAGATCTTGCCTTCCTA
* * * * *
53772158 CACTGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTAAA
1 CACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCGAAGCAGGTTAA
* *
53772223 AAATAGCAGATCTTGCCTTCTTG
66 AAATAGCAGATCTTGCCTTCCTA
* *
53772246 CACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGATTGTAGC-AGAGCAGGTTA
1 CACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCGA-AGCAGGTTA
* * *
53772310 AAAATAGCAAATCTTACCTTCCTG
65 AAAATAGCAGATCTTGCCTTCCTA
* * * * *
53772334 TACCAACAACGAAGCAGATCGAAGACACCAGTCTTGCCTCCCTGGGTTGTAGTGAAGCAGGTTAA
1 CACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCGAAGCAGGTTAA
53772399 AAATAGCAGATCTTGCCTTCCTA
66 AAATAGCAGATCTTGCCTTCCTA
* * * *
53772422 CACCGATAGCGAAGCAAATCGATGACCCCAGCC
1 CACCGACAGCGAAGCAGATCGAAGACACCAGCC
53772455 CTATCTCCCA
Statistics
Matches: 255, Mismatches: 40, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
88 254 1.00
89 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (88 bp):
CACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCGAAGCAGGTTAA
AAATAGCAGATCTTGCCTTCCTA
Found at i:53772571 original size:44 final size:44
Alignment explanation
Indices: 53772472--53772575 Score: 131
Period size: 44 Copynumber: 2.4 Consensus size: 44
53772462 CCATGACAGT
*
53772472 AGTGGAATAGGTTGAAGATTATAAGTCCTATCTCCCTGGTCAGC
1 AGTGGAATAGGTTGAAGATTATAAGTCCTATCTCCCTGGTCAAC
* * *
53772516 AATGGAATAGGTTGAAGATTGTGAA-TCCTATCTCCTTGAG-CAAC
1 AGTGGAATAGGTTGAAGATTAT-AAGTCCTATCTCCCTG-GTCAAC
*
53772560 AGTGGAGTAGGTTGAA
1 AGTGGAATAGGTTGAA
53772576 AATAGCAGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 49 0.94
45 3 0.06
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (44 bp):
AGTGGAATAGGTTGAAGATTATAAGTCCTATCTCCCTGGTCAAC
Found at i:53773312 original size:217 final size:218
Alignment explanation
Indices: 53772924--53773457 Score: 688
Period size: 217 Copynumber: 2.5 Consensus size: 218
53772914 GCAATTTAAA
* * * *
53772924 AGACTAAAGATAA-CGAATCTTATCTCCCTGAAGTTACAGTGGAACAGATTAAAGCCAATAATCA
1 AGACTCAAGA-AACCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCC
* * *
53772988 TATCTCCCTAAAGTCGTAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAG
65 TATCTCCCTAAAGTTGTAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAAAG
* * *
53773053 ACCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGA-CTAAGTAAGCAAGCCTT
130 ACCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAAGCCTT
*
53773117 ATC-CTCCTGAAATTGTAGT-GAGGC
195 ATCTC-CCTGAAATTGCAGTGGA-GC
* **
53773141 AGACTGAAGATGCCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
1 AGACTCAAGAAACCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
* * *
53773206 ATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACATATCTTATCTCTCTGAAGTTGCAAAGA
66 ATCTCCCTAAAGTTGTAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAAAGA
* * *
53773271 GCAGATCGCATC-AGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCGAGTCTT
131 CCAGATCGCATCTAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAAGCCTT
*
53773335 ATCTCCCTGAAGTTGCAGTGGAGC
195 ATCTCCCTGAAATTGCAGTGGAGC
* * * * ** *
53773359 AGACTCAAGAAATC-AAGTCTTATC-CCCTGAAATTGCAGTGGGGCAGACTAAA-TAAACAAATC
1 AGACTCAAGAAACCGAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA-TAATC
* *
53773421 CCATCTCCCTAAAGTTGTAGTGGAGTGGATTAGAATC
64 CTATCTCCCTAAAGTTGTAGTGGAGTGGATTAAAATC
53773458 TCTCTAAAAT
Statistics
Matches: 276, Mismatches: 34, Indels: 14
0.85 0.10 0.04
Matches are distributed among these distances:
216 4 0.01
217 222 0.80
218 47 0.17
219 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (218 bp):
AGACTCAAGAAACCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
ATCTCCCTAAAGTTGTAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAAAGA
CCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAAGCCTTA
TCTCCCTGAAATTGCAGTGGAGC
Found at i:53773405 original size:44 final size:45
Alignment explanation
Indices: 53773067--53773445 Score: 256
Period size: 44 Copynumber: 8.6 Consensus size: 45
53773057 GATCGCATCT
* *
53773067 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACT-AAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * * * *
53773111 AGCCTTATC-CTCCTGAAATTGTAGT-GAGGCAGACTGAAG-ATGCCGA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTCAAGAAAG-C-A
* * * *
53773157 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA-TA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAG-AAAGCA
* ** *
53773201 A-TCCTATCTCCCTGAAGTTGCAGTGGAGTGGA-TTAA-AATCA-CA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAA--AGCA
* ** * *
53773244 TA-TCTTATCTCTCTGAAGTTGCA-AAGAGCAGA-TC--G-CATC-
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* *
53773283 AGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCG
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
*
53773329 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * * *
53773374 AGTCTTATC-CCCTGAAATTGCAGTGGGGCAGACTAAATAAA-CA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* ** * *
53773417 AATCCCATCTCCCTAAAGTTGTAGTGGAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
53773446 TGGATTAGAA
Statistics
Matches: 268, Mismatches: 44, Indels: 46
0.75 0.12 0.13
Matches are distributed among these distances:
38 1 0.00
39 1 0.00
40 21 0.08
41 8 0.03
42 1 0.00
43 22 0.08
44 124 0.46
45 82 0.31
46 7 0.03
47 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
Found at i:53781167 original size:17 final size:19
Alignment explanation
Indices: 53781141--53781175 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
53781131 AAAAAACATG
53781141 AAGCATTAAAA-TAGTTTC
1 AAGCATTAAAAGTAGTTTC
53781159 AAGCA-TAAAAGTAGTTT
1 AAGCATTAAAAGTAGTTT
53781176 GGCACGTCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (19 bp):
AAGCATTAAAAGTAGTTTC
Found at i:53794748 original size:14 final size:14
Alignment explanation
Indices: 53794729--53794755 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53794719 AAGAATAGTT
53794729 TAATATTTTTATTA
1 TAATATTTTTATTA
53794743 TAATATTTTTATT
1 TAATATTTTTATT
53794756 GTTAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TAATATTTTTATTA
Found at i:53798358 original size:22 final size:21
Alignment explanation
Indices: 53798304--53798360 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 21
53798294 AATATATGTT
*
53798304 ATAATTTTTTTATTTTTAAAA
1 ATAATTTTTTTATTTTAAAAA
*
53798325 ATAGTTTTTTTTTATTTTAAAAA
1 ATA--ATTTTTTTATTTTAAAAA
*
53798348 ATAATTGTTTTAT
1 ATAATTTTTTTAT
53798361 GGCATCCACA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 11 0.37
23 19 0.63
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (21 bp):
ATAATTTTTTTATTTTAAAAA
Found at i:53798358 original size:23 final size:23
Alignment explanation
Indices: 53798309--53798358 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
53798299 ATGTTATAAT
* * *
53798309 TTTTTTATTTTTAAAAATAGTTT
1 TTTTTTATTTTAAAAAATAATTG
53798332 TTTTTTATTTTAAAAAATAATTG
1 TTTTTTATTTTAAAAAATAATTG
53798355 TTTT
1 TTTT
53798359 ATGGCATCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (23 bp):
TTTTTTATTTTAAAAAATAATTG
Found at i:53803448 original size:6 final size:6
Alignment explanation
Indices: 53803439--53803493 Score: 74
Period size: 6 Copynumber: 9.0 Consensus size: 6
53803429 AAATAAAATT
* *
53803439 CTAAAA CTAAAA CTAAAA CTACAA CTAAAA CTAAAA CTAAAGT CTAAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAA-A CTAAAA
*
53803488 ATAAAA
1 CTAAAA
53803494 AACATATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
6 38 0.88
7 5 0.12
ACGTcount: A:0.64, C:0.16, G:0.02, T:0.18
Consensus pattern (6 bp):
CTAAAA
Found at i:53803537 original size:9 final size:9
Alignment explanation
Indices: 53803500--53803567 Score: 82
Period size: 9 Copynumber: 7.6 Consensus size: 9
53803490 AAAAAACATA
*
53803500 TAATTCAGG
1 TAATTCAGT
* *
53803509 TAATCCAGG
1 TAATTCAGT
*
53803518 TAATTCGGT
1 TAATTCAGT
*
53803527 TAGTTCAGT
1 TAATTCAGT
*
53803536 TAATTCAGG
1 TAATTCAGT
53803545 TAATTCAGT
1 TAATTCAGT
53803554 TAATTCAGT
1 TAATTCAGT
53803563 TAATT
1 TAATT
53803568 TTTAACCAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.40
Consensus pattern (9 bp):
TAATTCAGT
Found at i:53803544 original size:27 final size:27
Alignment explanation
Indices: 53803500--53803567 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
53803490 AAAAAACATA
* * *
53803500 TAATTCAGGTAATCCAGGTAATTCGGT
1 TAATTCAGTTAATTCAGGTAATTCAGT
*
53803527 TAGTTCAGTTAATTCAGGTAATTCAGT
1 TAATTCAGTTAATTCAGGTAATTCAGT
53803554 TAATTCAGTTAATT
1 TAATTCAGTTAATT
53803568 TTTAACCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.40
Consensus pattern (27 bp):
TAATTCAGTTAATTCAGGTAATTCAGT
Found at i:53804165 original size:30 final size:30
Alignment explanation
Indices: 53804072--53804267 Score: 189
Period size: 30 Copynumber: 6.6 Consensus size: 30
53804062 GTAAGTAGGT
* * *
53804072 GCCTTTGTGGCTA-CTTAAAGTTCTGTGGAC
1 GCCTTTGTGGCTATC-TGATGTTATGTGGAC
* * * * *
53804102 GCCCTTGTGGCTATCT-AAGTCAAGTGGAA
1 GCCTTTGTGGCTATCTGATGTTATGTGGAC
* * *
53804131 GCCTTCGTGGCTATCTGATGTTGTGTGGAT
1 GCCTTTGTGGCTATCTGATGTTATGTGGAC
* ** *
53804161 GCCTTTGTGGCTATTTGATGTTACATGGAT
1 GCCTTTGTGGCTATCTGATGTTATGTGGAC
* * *
53804191 GCCTTCGTGACTATTTGATGTTATGTGGAC
1 GCCTTTGTGGCTATCTGATGTTATGTGGAC
*
53804221 GCCTTTGTGGCTATCTAATGTTATGTGGAC
1 GCCTTTGTGGCTATCTGATGTTATGTGGAC
*
53804251 GCCTTTGTAGCTATCTG
1 GCCTTTGTGGCTATCTG
53804268 TCTATTATGC
Statistics
Matches: 136, Mismatches: 28, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
29 23 0.17
30 112 0.82
31 1 0.01
ACGTcount: A:0.16, C:0.18, G:0.28, T:0.38
Consensus pattern (30 bp):
GCCTTTGTGGCTATCTGATGTTATGTGGAC
Found at i:53806223 original size:9 final size:9
Alignment explanation
Indices: 53806209--53806237 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
53806199 TGGATACGAA
53806209 TTTAAAGGT
1 TTTAAAGGT
53806218 TTTAAAGGT
1 TTTAAAGGT
53806227 TTTAAAGGT
1 TTTAAAGGT
53806236 TT
1 TT
53806238 CAAGTGAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (9 bp):
TTTAAAGGT
Found at i:53819702 original size:83 final size:84
Alignment explanation
Indices: 53819506--53819816 Score: 232
Period size: 83 Copynumber: 3.7 Consensus size: 84
53819496 TCCACAAGGT
* * * * * *
53819506 CTTCATTTAACTGAGATAGCCACAAAGACATCTTTTTAACAGAGATAGCCAT-AAAGACTT-CGT
1 CTTCCTTTAACAGAGATAGCCACAAAGGCTTC-CTTTAACAGAGATAGCCATAAAAG-CTTACCT
* * * *
53819569 TATAACAGAGGTCA-TCAC-AAAGG
64 T-T-ACAAAGAT-AGCCACGAAA-A
* * *
53819592 CTTCCTTATAACAGAGATCA-CCACAAAGGCTTCCTTATAACAGAGAT-TCCA-ACAAAGTTTTC
1 CTTCCTT-TAACAGAGAT-AGCCACAAAGGCTTCCTT-TAACAGAGATAGCCATA-AAAGCTTAC
**
53819654 CTTTACAGGGATAGCCAC-AAAGGA
62 CTTTACAAAGATAGCCACGAAA--A
* * * * *
53819678 -TT-TTTTAACAGAGATAGCCACAAAGGCTTCCTTTAATAGTGATAGCCATAAAGGCTTACTTTT
1 CTTCCTTTAACAGAGATAGCCACAAAGGCTTCCTTTAACAGAGATAGCCATAAAAGCTTACCTTT
53819741 ACAAAGATAGCCACGAAAA
66 ACAAAGATAGCCACGAAAA
* *
53819760 CTTCCTTTAACAGAGATAGCCACAAAGGCTTCCTTT--CAGAGATAGCCACAAAGGCTT
1 CTTCCTTTAACAGAGATAGCCACAAAGGCTTCCTTTAACAGAGATAGCCATAAAAGCTT
53819817 CCATTTAGAG
Statistics
Matches: 185, Mismatches: 26, Indels: 32
0.76 0.11 0.13
Matches are distributed among these distances:
82 28 0.15
83 52 0.28
84 38 0.21
85 14 0.08
86 15 0.08
87 37 0.20
88 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (84 bp):
CTTCCTTTAACAGAGATAGCCACAAAGGCTTCCTTTAACAGAGATAGCCATAAAAGCTTACCTTT
ACAAAGATAGCCACGAAAA
Found at i:53819721 original size:28 final size:28
Alignment explanation
Indices: 53819473--53819842 Score: 314
Period size: 29 Copynumber: 13.2 Consensus size: 28
53819463 TCTCGCCAGG
* * **
53819473 AAGGCATCCTTTTAACAAAGATTTCCAC-
1 AAGGCTTCC-TTTAACAGAGATAGCCACA
* *
53819501 AAGGTCTTCATTTAACTGAGATAGCCACA
1 AAGG-CTTCCTTTAACAGAGATAGCCACA
* * * *
53819530 AAGACATCTTTTTAACAGAGATAGCCATA
1 AAGGCTTC-CTTTAACAGAGATAGCCACA
* * * *
53819559 AAGACTTCGTTATAACAGAGGTCA-TCACA
1 AAGGCTTCCTT-TAACAGAGAT-AGCCACA
53819588 AAGGCTTCCTTATAACAGAGATCA-CCACA
1 AAGGCTTCCTT-TAACAGAGAT-AGCCACA
*
53819617 AAGGCTTCCTTATAACAGAGAT-TCCAACA
1 AAGGCTTCCTT-TAACAGAGATAGCC-ACA
** *
53819646 AAGTTTTCCTTT-ACAGGGATAGCCACA
1 AAGGCTTCCTTTAACAGAGATAGCCACA
* *
53819673 AAGGATT-TTTTAACAGAGATAGCCACA
1 AAGGCTTCCTTTAACAGAGATAGCCACA
* * *
53819700 AAGGCTTCCTTTAATAGTGATAGCCATA
1 AAGGCTTCCTTTAACAGAGATAGCCACA
* * *
53819728 AAGGCTTACTTTTACAAAGATAGCCACGA
1 AAGGCTTCCTTTAACAGAGATAGCCAC-A
*
53819757 AA-ACTTCCTTTAACAGAGATAGCCACA
1 AAGGCTTCCTTTAACAGAGATAGCCACA
53819784 AAGGCTTCCTTT--CAGAGATAGCCACA
1 AAGGCTTCCTTTAACAGAGATAGCCACA
53819810 AAGGCTTCCATTT---AGAGATAGCCACA
1 AAGGCTTCC-TTTAACAGAGATAGCCACA
53819836 AAGGCTT
1 AAGGCTT
53819843 GCTTAGATTG
Statistics
Matches: 285, Mismatches: 44, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
26 46 0.16
27 41 0.14
28 93 0.33
29 104 0.36
30 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (28 bp):
AAGGCTTCCTTTAACAGAGATAGCCACA
Found at i:53819806 original size:26 final size:27
Alignment explanation
Indices: 53819411--53819842 Score: 263
Period size: 28 Copynumber: 15.5 Consensus size: 27
53819401 TTCAAATTTT
* *
53819411 GCCACAAAGGCGTTCCTTTCCAAAGATA
1 GCCACAAAGGC-TTCCTTTACAGAGATA
* * * * *
53819439 GCCACAGAGGTTTTCCTTT-TAGAGTCTC
1 GCCACAAAGG-CTTCCTTTACAGAG-ATA
** * * *
53819467 GCCAGGAAGGCATCCTTTTAACAAAGATT
1 GCCACAAAGGCTTCC-TTT-ACAGAGATA
* * *
53819496 TCCAC-AAGGTCTTCATTTAACTGAGATA
1 GCCACAAAGG-CTTCCTTT-ACAGAGATA
* * *
53819524 GCCACAAAGACATCTTTTTAACAGAGATA
1 GCCACAAAGGCTTC-CTTT-ACAGAGATA
* * * *
53819553 GCCATAAAGACTTCGTTATAACAGAGGTCA
1 GCCACAAAGGCTTCCTT-T-ACAGAGAT-A
*
53819583 -TCACAAAGGCTTCCTTATAACAGAGATCA
1 GCCACAAAGGCTTCCTT-T-ACAGAGAT-A
53819612 -CCACAAAGGCTTCCTTATAACAGAGAT-
1 GCCACAAAGGCTTCCTT-T-ACAGAGATA
* ** *
53819639 TCCAACAAAGTTTTCCTTTACAGGGATA
1 GCC-ACAAAGGCTTCCTTTACAGAGATA
* *
53819667 GCCACAAAGGATT-TTTTAACAGAGATA
1 GCCACAAAGGCTTCCTTT-ACAGAGATA
* *
53819694 GCCACAAAGGCTTCCTTTAATAGTGATA
1 GCCACAAAGGCTTCCTTT-ACAGAGATA
* * *
53819722 GCCATAAAGGCTTACTTTTACAAAGATA
1 GCCACAAAGGCTT-CCTTTACAGAGATA
*
53819750 GCCACGAAA-ACTTCCTTTAACAGAGATA
1 GCCAC-AAAGGCTTCCTTT-ACAGAGATA
53819778 GCCACAAAGGCTTCCTTT-CAGAGATA
1 GCCACAAAGGCTTCCTTTACAGAGATA
53819804 GCCACAAAGGCTTCCATTT--AGAGATA
1 GCCACAAAGGCTTCC-TTTACAGAGATA
53819830 GCCACAAAGGCTT
1 GCCACAAAGGCTT
53819843 GCTTAGATTG
Statistics
Matches: 325, Mismatches: 59, Indels: 42
0.76 0.14 0.10
Matches are distributed among these distances:
26 46 0.14
27 51 0.16
28 112 0.34
29 112 0.34
30 4 0.01
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (27 bp):
GCCACAAAGGCTTCCTTTACAGAGATA
Found at i:53838781 original size:21 final size:20
Alignment explanation
Indices: 53838732--53838791 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
53838722 GGTGAACCGG
53838732 TTTTTA-TAAATTTTTAATA
1 TTTTTATTAAATTTTTAATA
53838751 TATTTT-TTAAATCTTTT-ATGA
1 T-TTTTATTAAAT-TTTTAAT-A
*
53838772 TTTTTATTAATTTATTTAAT
1 TTTTTATTAAATT-TTTAAT
53838792 TTAAAATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
19 1 0.03
20 16 0.48
21 14 0.42
22 2 0.06
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTATTAAATTTTTAATA
Found at i:53839516 original size:18 final size:18
Alignment explanation
Indices: 53839493--53839533 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
53839483 TTACAAAATA
**
53839493 AAAATATATAACCTTTTT
1 AAAATATATAAAATTTTT
53839511 AAAATATATAAAATTTTT
1 AAAATATATAAAATTTTT
53839529 AAAAT
1 AAAAT
53839534 TTTCAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATATATAAAATTTTT
Found at i:53842656 original size:6 final size:6
Alignment explanation
Indices: 53842647--53842743 Score: 59
Period size: 6 Copynumber: 15.7 Consensus size: 6
53842637 TAATGAAATC
* ** * * **
53842647 GAAAAA GAAAAC GAAAAA GAAAAA GAAATT GCAAAA GAATAA GAAATC
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
** * * *
53842695 GAAAAA GTGAGA GAAAAA GAAAAT GATGAAAA GAAAATT GAAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GA--AAAA GAAAA-A GAAAAA GAAA
53842744 TTGAGATTGA
Statistics
Matches: 64, Mismatches: 24, Indels: 6
0.68 0.26 0.06
Matches are distributed among these distances:
6 54 0.84
7 5 0.08
8 5 0.08
ACGTcount: A:0.68, C:0.03, G:0.20, T:0.09
Consensus pattern (6 bp):
GAAAAA
Found at i:53842668 original size:18 final size:18
Alignment explanation
Indices: 53842647--53842743 Score: 68
Period size: 18 Copynumber: 5.2 Consensus size: 18
53842637 TAATGAAATC
53842647 GAAAAAGAAAACGAAAAA
1 GAAAAAGAAAACGAAAAA
** *
53842665 GAAAAAGAAATTGCAAAA
1 GAAAAAGAAAACGAAAAA
* *
53842683 GAATAAGAAATCGAAAAA
1 GAAAAAGAAAACGAAAAA
** * * *
53842701 GTGAGAGAAAAAGAAAAT
1 GAAAAAGAAAACGAAAAA
*
53842719 GATGAAAAGAAAATTGAAAAA
1 GA--AAAAGAAAA-CGAAAAA
53842740 GAAA
1 GAAA
53842744 TTGAGATTGA
Statistics
Matches: 58, Mismatches: 18, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
18 42 0.72
19 2 0.03
20 7 0.12
21 7 0.12
ACGTcount: A:0.68, C:0.03, G:0.20, T:0.09
Consensus pattern (18 bp):
GAAAAAGAAAACGAAAAA
Found at i:53842752 original size:18 final size:18
Alignment explanation
Indices: 53842731--53842765 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53842721 TGAAAAGAAA
53842731 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
53842749 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
53842766 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:53842774 original size:16 final size:18
Alignment explanation
Indices: 53842753--53842791 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
53842743 ATTGAGATTG
53842753 AGAAAAA-A-ATTGAAAA
1 AGAAAAAGATATTGAAAA
*
53842769 AGAAAAAGATGTTGAAAA
1 AGAAAAAGATATTGAAAA
53842787 AGAAA
1 AGAAA
53842792 CGAGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (18 bp):
AGAAAAAGATATTGAAAA
Found at i:53844987 original size:20 final size:20
Alignment explanation
Indices: 53844962--53845025 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
53844952 CAGCTCCTTT
*
53844962 AGCTCATTTCAGCTCCAA-TC
1 AGCTCATTTAAGCT-CAATTC
53844982 AGCTCATTTAAGCTCAATTC
1 AGCTCATTTAAGCTCAATTC
** *
53845002 AGCTCATTCGAGCTCAATTT
1 AGCTCATTTAAGCTCAATTC
53845022 AGCT
1 AGCT
53845026 TTCTTCCAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.08
20 36 0.92
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.33
Consensus pattern (20 bp):
AGCTCATTTAAGCTCAATTC
Found at i:53845015 original size:10 final size:9
Alignment explanation
Indices: 53844952--53845017 Score: 51
Period size: 10 Copynumber: 6.8 Consensus size: 9
53844942 AGCTTAATTC
*
53844952 CAGCTCCTT
1 CAGCTCATT
*
53844961 TAGCTCATTT
1 CAGCTCA-TT
*
53844971 CAGCTCCAAT
1 CAGCT-CATT
53844981 CAGCTCATTT
1 CAGCTCA-TT
*
53844991 AAGCTCAATT
1 CAGCTC-ATT
53845001 CAGCTCATT
1 CAGCTCATT
53845010 CGAGCTCA
1 C-AGCTCA
53845018 ATTTAGCTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
9 11 0.24
10 31 0.69
11 3 0.07
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (9 bp):
CAGCTCATT
Found at i:53850804 original size:15 final size:14
Alignment explanation
Indices: 53850783--53850818 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
53850773 ATAATCTTTA
*
53850783 ATAATTATCTTAAT
1 ATAATTATCCTAAT
53850797 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
53850812 ATAATTA
1 ATAATTA
53850819 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:53855537 original size:17 final size:16
Alignment explanation
Indices: 53855514--53855590 Score: 61
Period size: 17 Copynumber: 4.7 Consensus size: 16
53855504 ACACAATTCT
53855514 AATAATAAAAAAAT-A
1 AATAATAAAAAAATAA
**
53855529 AAT-ATAATACTAATAA
1 AATAATAA-AAAAATAA
*
53855545 CAATAATAAAATAAATAT
1 -AATAATAAAA-AAATAA
53855563 AATAATAAATAAAAT-A
1 AATAATAAA-AAAATAA
53855579 AATAAATAAAAA
1 AAT-AATAAAAA
53855591 GGAAGGATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
14 4 0.08
15 7 0.14
16 6 0.12
17 23 0.47
18 9 0.18
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.25
Consensus pattern (16 bp):
AATAATAAAAAAATAA
Found at i:53855550 original size:29 final size:29
Alignment explanation
Indices: 53855517--53855588 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
53855507 CAATTCTAAT
*
53855517 AATAAAAAAATAAATATAATACT-AATAA
1 AATAAAAAAATAAATATAATAATAAATAA
*
53855545 CAATAATAAAATAAATATAATAATAAATAA
1 -AATAAAAAAATAAATATAATAATAAATAA
*
53855575 AATAAATAAATAAA
1 AATAAAAAAATAAA
53855589 AAGGAAGGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 33 0.87
30 5 0.13
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (29 bp):
AATAAAAAAATAAATATAATAATAAATAA
Found at i:53855551 original size:9 final size:8
Alignment explanation
Indices: 53855514--53855589 Score: 50
Period size: 9 Copynumber: 9.2 Consensus size: 8
53855504 ACACAATTCT
53855514 AATAATAA
1 AATAATAA
*
53855522 AAAAAT-A
1 AATAATAA
53855529 AAT-ATAA
1 AATAATAA
*
53855536 TACTAATAA
1 -AATAATAA
53855545 CAATAATAA
1 -AATAATAA
*
53855554 AATAAATAT
1 AAT-AATAA
53855563 AATAAT-A
1 AATAATAA
*
53855570 AATAAAATA
1 AATAATA-A
53855579 AATAAATAA
1 AAT-AATAA
53855588 AA
1 AA
53855590 AGGAAGGATA
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
6 2 0.04
7 9 0.17
8 13 0.25
9 25 0.48
10 3 0.06
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (8 bp):
AATAATAA
Found at i:53855561 original size:12 final size:12
Alignment explanation
Indices: 53855546--53855587 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
53855536 TACTAATAAC
53855546 AATAATAAAATA
1 AATAATAAAATA
53855558 AAT-ATAATAATA
1 AATAATAA-AATA
*
53855570 AATAAAATAAATA
1 AATAATA-AAATA
53855583 AATAA
1 AATAA
53855588 AAAGGAAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 4 0.15
12 10 0.38
13 11 0.42
14 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAATAAAATA
Found at i:53859397 original size:20 final size:20
Alignment explanation
Indices: 53859368--53859411 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
53859358 ATTAAAATGT
* *
53859368 AAAA-ATTAAATTAGAAACA
1 AAAATATTAAAATAAAAACA
*
53859387 AAAATATTAAAATAAAAATA
1 AAAATATTAAAATAAAAACA
53859407 AAAAT
1 AAAAT
53859412 GGCTAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAATATTAAAATAAAAACA
Found at i:53861668 original size:33 final size:35
Alignment explanation
Indices: 53861613--53861677 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 35
53861603 TATCTGTTTC
***
53861613 GTGTTTACTATCCCAGTGGACTT-A-CTCTATTTT
1 GTGTTTACTATCCCAACAGACTTCATCTCTATTTT
*
53861646 GTGTTTACTGTCCCAACAGACTTCATCTCTAT
1 GTGTTTACTATCCCAACAGACTTCATCTCTAT
53861678 GGATGCCATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 19 0.73
34 1 0.04
35 6 0.23
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.42
Consensus pattern (35 bp):
GTGTTTACTATCCCAACAGACTTCATCTCTATTTT
Found at i:53879599 original size:14 final size:13
Alignment explanation
Indices: 53879561--53879600 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
53879551 AAGTGATGTG
*
53879561 GAAAATGAAAAGAT
1 GAAATTGAAAA-AT
53879575 GAAATTGAAAAAT
1 GAAATTGAAAAAT
53879588 GAAATTGTAAAAA
1 GAAATTG-AAAAA
53879601 CGGAGAGGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (13 bp):
GAAATTGAAAAAT
Found at i:53881127 original size:132 final size:132
Alignment explanation
Indices: 53880951--53882242 Score: 1797
Period size: 132 Copynumber: 9.9 Consensus size: 132
53880941 TAGATAGCGA
* * *
53880951 AGCAGATCGAAGATGG-TGAATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAA
1 AGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
* *
53881015 TTCTACTTCCCTAGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
65 TTCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
53881080 TGG
130 TGG
* * *
53881083 AGCAGATCGAATG-TGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACAATGAAGCCAGCAA
1 AGCAGATC-AAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
*
53881147 TTCTACTTCCCT-GAGTAGCAGTGG---A-A-T--AGATTTCAGATCTT-TCCTCCCTAAGCAGT
65 TTCTACTTCCCTAG-GCAGCAGTGGAATAGATTGAAGATTTCAGATCTTAT-CTCCCTAAGCAGT
53881203 AGTGG
128 AGTGG
* * *
53881208 AGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
53881273 TCTA-TCTCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATATTACCTCCCTAAGCAGTAG
66 TCTACT-TCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
53881337 TGG
130 TGG
* * ** * *
53881340 AGTAGATCAAGGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
53881405 TCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
66 TCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
53881470 GG
131 GG
* *
53881472 GGCAGATCAAAGATGG-TGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
1 AGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
*
53881536 TTCTA-TCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTA
65 TTCTACT-TCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
53881600 GTGG
129 GTGG
*
53881604 AGCAGATCAAAGATGGCAGATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* **
53881669 TCTACTTCCCTAGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
66 TCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
53881734 GG
131 GG
* * *
53881736 AGCAGATCGAATG-TGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACAATGAAGCCAGCAA
1 AGCAGATC-AAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
* *
53881800 TTCTACTTCCCTAAGTAGCAGTGG---A-A-T--AGATTTCAGATCTT-TCCTCCCTAAGCAGTA
65 TTCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTAT-CTCCCTAAGCAGTA
53881857 GTGG
129 GTGG
* * *
53881861 AGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
53881926 TCTA-TCTCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATATTACCTCCCTAAGCAGTAG
66 TCTACT-TCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
53881990 TGG
130 TGG
* * * *
53881993 AGCAGATCAAGGATGGCGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
53882058 TCTACTTCCTTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
66 TCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
53882123 GG
131 GG
* *
53882125 GGCAGATCAAAGATGG-TGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
1 AGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * *
53882189 TTCTACTTTCCTAGGCAGCAGTGGAATAGATTAAAGATTGCAGATCTTATCTCC
65 TTCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCC
53882243 TTGAAGTTGC
Statistics
Matches: 1040, Mismatches: 86, Indels: 68
0.87 0.07 0.06
Matches are distributed among these distances:
124 9 0.01
125 208 0.20
126 1 0.00
127 2 0.00
128 4 0.00
129 4 0.00
130 2 0.00
131 4 0.00
132 796 0.77
133 10 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (132 bp):
AGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
GG
Found at i:53881854 original size:389 final size:388
Alignment explanation
Indices: 53880951--53882220 Score: 1807
Period size: 389 Copynumber: 3.2 Consensus size: 388
53880941 TAGATAGCGA
* * *
53880951 AGCAGATCGAAGATGGTGAATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
53881016 TCTACTTCCCTAGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
65 TCTACTTCCCTAGGCAGCAGT-G----GAAT-AAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
* * *
53881081 GGAGCAGATCGAATG-TGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACAATGAAGCCAGC
124 GGAGCAGATC-AAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGT
* *
53881145 AATTCTA-CTTCCCTGAGTAGCAGTGG---A-A-T--AGATTTCAGATCTTTCCTCCCTAAGCAG
188 AATTCTATC-TCCCTG-GCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAG
* *
53881202 TAGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCT
251 TAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCC
* * *
53881267 AGTAATTCTA-TCTCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATATTACCTCCCTAAG
316 AGTAATTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAG
53881331 CAGTAGTGG
380 CAGTAGTGG
* * * * *
53881340 AGTAGATCAAGGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGG-AGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
53881405 TCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
65 TCTACTTCCCTAGGCAGCAGTGG---A-A-T-AAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
* *
53881470 GGGGCAGATCAAAGATGG-TGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGT
124 GGAGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGT
53881534 AATTCTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGT
188 AATTCTATCTCCCT-GGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGT
53881599 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCT-ATGGTTACAGTGGAGTACATTGAAGCC
252 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGA-GGTTACAGTGGAGTACATTGAAGCC
* *
53881663 AGTAATTCTACTTCCCTAGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGC
316 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGC
53881728 AGTAGTGG
381 AGTAGTGG
* * *
53881736 AGCAGATCGAATG-TGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACAATGAAGCCAGCAA
1 AGCAGATC-AAAGATGG-AGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
* *
53881800 TTCTACTTCCCTAAGTAGCAGTGGAAT-AGATTTCAGATCTT-TCCTCCCTAAGCAGTAGTGGAG
64 TTCTACTTCCCTAGGCAGCAGTGGAATAAGATTTCAGATCTTGT-CTCCCTAAGCAGTAGTGGAG
* * *
53881863 CAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAGTAATTC
128 CAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* *
53881928 TATCTCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATATTACCTCCCTAAGCAGTAGTGG
193 TATCTCCCT-GGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTAGTGG
* * *
53881993 AGCAGATCAAGGATGGCGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAT
257 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
53882058 TCTACTTCCTTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
322 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
53882123 GG
387 GG
* *
53882125 GGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
53882190 TCTACTTTCCTAGGCAGCAGTGGAAT-AGATT
65 TCTACTTCCCTAGGCAGCAGTGGAATAAGATT
53882221 AAAGATTGCA
Statistics
Matches: 797, Mismatches: 59, Indels: 50
0.88 0.07 0.06
Matches are distributed among these distances:
384 1 0.00
387 1 0.00
388 10 0.01
389 542 0.68
390 5 0.01
391 1 0.00
392 2 0.00
393 2 0.00
394 1 0.00
395 1 0.00
396 227 0.28
397 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (388 bp):
AGCAGATCAAAGATGGAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATT
CTACTTCCCTAGGCAGCAGTGGAATAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAG
ATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
CTCCCTGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTAGTGGAGCA
GATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
CTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGG
Found at i:53881938 original size:521 final size:523
Alignment explanation
Indices: 53880951--53882236 Score: 1893
Period size: 521 Copynumber: 2.5 Consensus size: 523
53880941 TAGATAGCGA
* *
53880951 AGCAGATCGAAGATGGTGAATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
53881016 TCTACTTCCCTAGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
66 TCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
* * *
53881081 GGAGCAGATCGAATG-TGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACAATGAAGCCAGC
131 GGAGCAGATC-AAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGT
* * *
53881145 AATTCTACTTCCCT-GAGTAGCAGTG----GAAT-AGATTTCAGATCTTTCCTCCCTAAGCAGTA
195 AATTCTACTTCCCTAG-GCAGCAGTGAATAGATTAAGATTTCAGATCTTGCCTCCCTAAGCAGTA
* *
53881204 GTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAG
259 GTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACAATGAAGCCAG
* **
53881269 TAATTCTATCTCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATATTACCTCCCTAAGCAG
324 CAATTCTATCTCCCTAAGCAGCAATGG-A-AGATT-AAGATTTCAGATATTACCTCCCTAAGCAG
* * *** *
53881334 TAGTGGAGTAGATCAAGGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCC
386 TAGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCC
* * **
53881399 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGC
451 AGTAATTCTACTTCCCTGGGCAGCAATGGAATAGATTAAAGATTTCAGATATTACCTCCCTAAGC
53881464 AGTAGTGG
516 AGTAGTGG
*
53881472 GGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
**
53881537 TCTA-TCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTAG
66 TCTACT-TCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
*
53881601 TGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGT
130 TGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGT
53881666 AATTCTACTTCCCTAGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGT
195 AATTCTACTTCCCTAGGCAGCAGT-GAATAGATT-AAGATTTCAGATCTTGCCTCCCTAAGCAGT
* * *
53881731 AGTGGAGCAGATCGAATG-TGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACAATGAAGCC
258 AGTGGAGCAGATC-AAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACAATGAAGCC
* * * *
53881795 AGCAATTCTA-CTTCCCTAAGTAGCAGTGG-A-A-T-AGATTTCAGATCTTTCCTCCCTAAGCAG
322 AGCAATTCTATC-TCCCTAAGCAGCAATGGAAGATTAAGATTTCAGATATTACCTCCCTAAGCAG
*
53881855 TAGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCT
386 TAGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCC
*
53881920 AGTAATTCTA-TCTCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATATTACCTCCCTAAG
451 AGTAATTCTACT-TCCCTGGGCAGCAATGGAATAGATTAAAGATTTCAGATATTACCTCCCTAAG
53881984 CAGTAGTGG
515 CAGTAGTGG
* * * * *
53881993 AGCAGATCAAGGATGGCGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
53882058 TCTACTTCCTTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
66 TCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
* *
53882123 GGGGCAGATCAAAGATGG-TGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGT
131 GGAGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGT
* *
53882187 AATTCTACTTTCCTAGGCAGCAGTGGAATAGATTAAAGATTGCAGATCTT
195 AATTCTACTTCCCTAGGCAGCAGT-GAATAGATT-AAGATTTCAGATCTT
53882237 ATCTCCTTGA
Statistics
Matches: 695, Mismatches: 55, Indels: 30
0.89 0.07 0.04
Matches are distributed among these distances:
520 6 0.01
521 571 0.82
522 3 0.00
523 1 0.00
524 1 0.00
525 1 0.00
526 3 0.00
527 1 0.00
528 105 0.15
529 3 0.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (523 bp):
AGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
GGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
ATTCTACTTCCCTAGGCAGCAGTGAATAGATTAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
GGAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACAATGAAGCCAGCA
ATTCTATCTCCCTAAGCAGCAATGGAAGATTAAGATTTCAGATATTACCTCCCTAAGCAGTAGTG
GAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
TTCTACTTCCCTGGGCAGCAATGGAATAGATTAAAGATTTCAGATATTACCTCCCTAAGCAGTAG
TGG
Found at i:53882204 original size:653 final size:653
Alignment explanation
Indices: 53880951--53882242 Score: 2453
Period size: 653 Copynumber: 2.0 Consensus size: 653
53880941 TAGATAGCGA
* *
53880951 AGCAGATCGAAGATGGTGAATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGAGAATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
53881016 TCTACTTCCCTAGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
66 TCTACTTCCCTAGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
53881081 GGAGCAGATCGAATGTGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACAATGAAGCCAGCA
131 GGAGCAGATCGAATGTGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACAATGAAGCCAGCA
*
53881146 ATTCTACTTCCCTGAGTAGCAGTGGAATAGATTTCAGATCTTTCCTCCCTAAGCAGTAGTGGAGC
196 ATTCTACTTCCCTAAGTAGCAGTGGAATAGATTTCAGATCTTTCCTCCCTAAGCAGTAGTGGAGC
53881211 AGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAGTAATTCT
261 AGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAGTAATTCT
53881276 ATCTCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATATTACCTCCCTAAGCAGTAGTGGA
326 ATCTCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATATTACCTCCCTAAGCAGTAGTGGA
* *
53881341 GTAGATCAAGGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATT
391 GCAGATCAAGGATGGCGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATT
53881406 CTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTG
456 CTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTG
53881471 GGGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
521 GGGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
* *
53881536 TTCTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTAG
586 TTCTATCTCCCTAGGCAGCAGTGGAATAGATTAAAGATTGCAGATCTTACCTCCCTAAGCAGTAG
53881601 TGG
651 TGG
53881604 AGCAGATCAAAGATGGCAG-ATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAA
1 AGCAGATCAAAGATGG-AGAATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAA
53881668 TTCTACTTCCCTAGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAG
65 TTCTACTTCCCTAGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAG
53881733 TGGAGCAGATCGAATGTGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACAATGAAGCCAGC
130 TGGAGCAGATCGAATGTGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACAATGAAGCCAGC
53881798 AATTCTACTTCCCTAAGTAGCAGTGGAATAGATTTCAGATCTTTCCTCCCTAAGCAGTAGTGGAG
195 AATTCTACTTCCCTAAGTAGCAGTGGAATAGATTTCAGATCTTTCCTCCCTAAGCAGTAGTGGAG
53881863 CAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAGTAATTC
260 CAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAGTAATTC
53881928 TATCTCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATATTACCTCCCTAAGCAGTAGTGG
325 TATCTCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATATTACCTCCCTAAGCAGTAGTGG
53881993 AGCAGATCAAGGATGGCGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAT
390 AGCAGATCAAGGATGGCGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAT
*
53882058 TCTACTTCCTTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
455 TCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
53882123 GGGGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
520 GGGGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
* *
53882188 ATTCTA-CTTTCCTAGGCAGCAGTGGAATAGATTAAAGATTGCAGATCTTATCTCC
585 ATTCTATC-TCCCTAGGCAGCAGTGGAATAGATTAAAGATTGCAGATCTTACCTCC
53882243 TTGAAGTTGC
Statistics
Matches: 626, Mismatches: 11, Indels: 4
0.98 0.02 0.01
Matches are distributed among these distances:
652 1 0.00
653 624 1.00
654 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (653 bp):
AGCAGATCAAAGATGGAGAATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTAGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
GGAGCAGATCGAATGTGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACAATGAAGCCAGCA
ATTCTACTTCCCTAAGTAGCAGTGGAATAGATTTCAGATCTTTCCTCCCTAAGCAGTAGTGGAGC
AGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAGTAATTCT
ATCTCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATATTACCTCCCTAAGCAGTAGTGGA
GCAGATCAAGGATGGCGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATT
CTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTG
GGGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
TTCTATCTCCCTAGGCAGCAGTGGAATAGATTAAAGATTGCAGATCTTACCTCCCTAAGCAGTAG
TGG
Found at i:53884609 original size:210 final size:210
Alignment explanation
Indices: 53884247--53884724 Score: 856
Period size: 210 Copynumber: 2.3 Consensus size: 210
53884237 AAGTTTTTTG
** *
53884247 AATAAAAGCAATATTCAAAGTTTGAGATTTTCAAGGAAAATTGAGCCCTAACGTATTGGGTTCTG
1 AATAAAAGTGATATTCAAAGTTTGGGATTTTCAAGGAAAATTGAGCCCTAACGTATTGGGTTCTG
53884312 ATTTTCTTTGATGATCTTAAATGGCCGAGGATATTCTTTATTCAAAATGCATGAGTATAAAAATC
66 ATTTTCTTTGATGATCTTAAATGGCCGAGGATATTCTTTATTCAAAATGCATGAGTATAAAAATC
*
53884377 ATTTTTGGGAACTTAACTTGTTGTGTCCTAACGTATTGGGTGTGGCATGTTACCTTCTCAAAATG
131 ATTTTTGGAAACTTAACTTGTTGTGTCCTAACGTATTGGGTGTGGCATGTTACCTTCTCAAAATG
53884442 AAGATTTTCACATAA
196 AAGATTTTCACATAA
53884457 AATAAAAGTGATATTCAAAGTTTGGGATTTTCAAGGAAAATTGAGCCCTAACGTATTGGGTTCTG
1 AATAAAAGTGATATTCAAAGTTTGGGATTTTCAAGGAAAATTGAGCCCTAACGTATTGGGTTCTG
53884522 ATTTTCTTTGATGATCTTAAATGGCCGAGGATATTCTTTATTCAAAATGCATGAGTATAAAAATC
66 ATTTTCTTTGATGATCTTAAATGGCCGAGGATATTCTTTATTCAAAATGCATGAGTATAAAAATC
53884587 ATTTTTGGAAACTTAACTTGTTGTGTCCTAACGTATTGGGTGTGGCATGTTACCTTCTCAAAATG
131 ATTTTTGGAAACTTAACTTGTTGTGTCCTAACGTATTGGGTGTGGCATGTTACCTTCTCAAAATG
53884652 AAGATTTTCACATAA
196 AAGATTTTCACATAA
* *
53884667 AATAAAAGTGATATTCAAAGTTCGGGGATTTT-GAGG--AATTGTA-CCCTAACGTATTGGG
1 AATAAAAGTGATATTCAAAGTT-TGGGATTTTCAAGGAAAATTG-AGCCCTAACGTATTGGG
53884725 ACTCGATTTC
Statistics
Matches: 260, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
208 20 0.08
209 1 0.00
210 231 0.89
211 8 0.03
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.36
Consensus pattern (210 bp):
AATAAAAGTGATATTCAAAGTTTGGGATTTTCAAGGAAAATTGAGCCCTAACGTATTGGGTTCTG
ATTTTCTTTGATGATCTTAAATGGCCGAGGATATTCTTTATTCAAAATGCATGAGTATAAAAATC
ATTTTTGGAAACTTAACTTGTTGTGTCCTAACGTATTGGGTGTGGCATGTTACCTTCTCAAAATG
AAGATTTTCACATAA
Found at i:53885709 original size:32 final size:32
Alignment explanation
Indices: 53885673--53885736 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
53885663 AAACTTTATC
53885673 AATCTATCAACTATCACCCAAATTGAATTCTT
1 AATCTATCAACTATCACCCAAATTGAATTCTT
53885705 AATCTATCAACTATCACCCAAATTGAATTCTT
1 AATCTATCAACTATCACCCAAATTGAATTCTT
53885737 CTTTCTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (32 bp):
AATCTATCAACTATCACCCAAATTGAATTCTT
Found at i:53890497 original size:41 final size:42
Alignment explanation
Indices: 53890440--53890541 Score: 138
Period size: 41 Copynumber: 2.5 Consensus size: 42
53890430 CCTTTCGGGT
*
53890440 CTTTAGCGGCGTTTTTAAAAAAGCGTC-GCTAATGCT-GGTGA
1 CTTTAGCGGCGTTTTTAAAAAAGCG-CAGCTAATGCTGGGGGA
*
53890481 CTTTAGCGGCGTTTTTAAGAAAGCGCAGCTAATGCTGGGGGA
1 CTTTAGCGGCGTTTTTAAAAAAGCGCAGCTAATGCTGGGGGA
* *
53890523 -TTTAGCAGCGTTTTGAAAA
1 CTTTAGCGGCGTTTTTAAAA
53890542 GGCGCCGCTA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 1 0.02
41 49 0.91
42 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTAAAAAAGCGCAGCTAATGCTGGGGGA
Found at i:53890914 original size:14 final size:14
Alignment explanation
Indices: 53890895--53890928 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
53890885 ATTTTAAGGT
53890895 TTAGGGAGTATGGA
1 TTAGGGAGTATGGA
* *
53890909 TTAGGGATTATGGT
1 TTAGGGAGTATGGA
53890923 TTAGGG
1 TTAGGG
53890929 GTTGGGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (14 bp):
TTAGGGAGTATGGA
Found at i:53890961 original size:15 final size:15
Alignment explanation
Indices: 53890941--53890988 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
53890931 TGGGATTTAA
53890941 GGTTTAGGGGTTATG
1 GGTTTAGGGGTTATG
*
53890956 GGTTTATGGGTTA-G
1 GGTTTAGGGGTTATG
* **
53890970 GGGTTAGACGTTATG
1 GGTTTAGGGGTTATG
53890985 GGTT
1 GGTT
53890989 AAAAGTTAGG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.15, C:0.02, G:0.44, T:0.40
Consensus pattern (15 bp):
GGTTTAGGGGTTATG
Found at i:53891222 original size:15 final size:15
Alignment explanation
Indices: 53891198--53891232 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
53891188 CTATTTAAAG
*
53891198 GTTTATGGATTATGA
1 GTTTAGGGATTATGA
53891213 GTTTAGGGATTATGA
1 GTTTAGGGATTATGA
53891228 GTTTA
1 GTTTA
53891233 AGGTTTAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.46
Consensus pattern (15 bp):
GTTTAGGGATTATGA
Found at i:53891260 original size:28 final size:28
Alignment explanation
Indices: 53891222--53891303 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
53891212 AGTTTAGGGA
*
53891222 TTATGAGTTTAAGGTTTAGGGTTTATGAT
1 TTATG-GTTTAAGGTTTAGGGTTTAAGAT
* * *
53891251 TTATGGTTTAAGGGTTGGGGTTCAAGAT
1 TTATGGTTTAAGGTTTAGGGTTTAAGAT
* * *
53891279 TTAAGGGTTAGGGGTTTAGGGTTTA
1 TTATGGTTTA-AGGTTTAGGGTTTA
53891304 GTTTAATTAG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
28 27 0.64
29 15 0.36
ACGTcount: A:0.22, C:0.01, G:0.34, T:0.43
Consensus pattern (28 bp):
TTATGGTTTAAGGTTTAGGGTTTAAGAT
Found at i:53891264 original size:22 final size:21
Alignment explanation
Indices: 53891197--53891266 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 21
53891187 GCTATTTAAA
53891197 GGTTTATGGA-TTATGAGTTTAG
1 GGTTTAT-GATTTATG-GTTTAG
* *
53891219 GGATTATGAGTTTAAGGTTTAG
1 GGTTTATGA-TTTATGGTTTAG
53891241 GGTTTATGATTTATGGTTTAAG
1 GGTTTATGATTTATGGTTT-AG
53891263 GGTT
1 GGTT
53891267 GGGGTTCAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 11 0.27
22 26 0.63
23 4 0.10
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (21 bp):
GGTTTATGATTTATGGTTTAG
Found at i:53893586 original size:193 final size:191
Alignment explanation
Indices: 53893284--53893639 Score: 459
Period size: 193 Copynumber: 1.9 Consensus size: 191
53893274 ATCTATAATG
* * * **
53893284 GGTTTAAGTCATGGTTTTCATTTGGAGCTTTGTGATTAAAACACTATTATTACTTGAATGGAAAT
1 GGTTCAAGTCATGGTTTTCATTTGGAACTTTGTGATTAAAACACAACAATTACTTGAATGGAAAT
* * * * * * * * *
53893349 GCATTTGCATTTGTGTATCCTGCAATGCTTTTTAATTGAACTTTGGGGTTGGAATTGTTATTAGG
66 GCACTTGCATTTGTATATCCTACAAAGCTTCTTAAGTCAACTTTGGAGTTGAAATTGTTATTAGG
*
53893414 AAGTAATTGATG-TTTTTATGTTGATGTTAATGAATACAATAGACTAAGTTGAATTTTTTATA
131 AAGTAATTGATGATTTTT-T-ATGATGTTAATGAATACAATAGACTAAGTTGAATTTTTTATA
*
53893476 GGTTCAAGTCATTGGTTTTCATTT-GAACTTTGTGATTACAACACAACAATTTACTTGAATGGAA
1 GGTTCAAGTCA-TGGTTTTCATTTGGAACTTTGTGATTAAAACACAACAA-TTACTTGAATGGAA
**
53893540 ATGCACTTGTGTTT-TCATATCCTACAAAGCTTCCTT-AGTCAACTTTGGAGTTGAAATTGTTAT
64 ATGCACTTGCATTTGT-ATATCCTACAAAGCTT-CTTAAGTCAACTTTGGAGTTGAAATTGTTAT
*
53893603 TAGGATGTAATTGATGATTTTTTATGATGTTAATGAA
127 TAGGAAGTAATTGATGATTTTTTATGATGTTAATGAA
53893640 CATAATAATA
Statistics
Matches: 140, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
192 44 0.31
193 89 0.64
194 7 0.05
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (191 bp):
GGTTCAAGTCATGGTTTTCATTTGGAACTTTGTGATTAAAACACAACAATTACTTGAATGGAAAT
GCACTTGCATTTGTATATCCTACAAAGCTTCTTAAGTCAACTTTGGAGTTGAAATTGTTATTAGG
AAGTAATTGATGATTTTTTATGATGTTAATGAATACAATAGACTAAGTTGAATTTTTTATA
Found at i:53894829 original size:87 final size:86
Alignment explanation
Indices: 53894669--53894904 Score: 258
Period size: 87 Copynumber: 2.7 Consensus size: 86
53894659 CGCTAAAGGA
* * * * * * *
53894669 CATGATCTTTAGCGACGTTTG-AGATAAAAGCGCCACTAAAGGTAATGATCTTTAGCGGCATTTG
1 CATGTTCTTTAGCGGCGTTTGTA-ATAAAAGCGCCGCTAAAGATCATGTTCTTTAGCAGCATTTG
* *
53894733 TGGGCAAAGCGCCGCCAAAGAT
65 TGAGAAAAGCGCCGCCAAAGAT
* * *
53894755 CATGTTATTTTAGCGGCGTTTGTAATAAAAGCGCTGCTAAAGATCATGTTCTTTAGCAGCGTTTG
1 CATGTT-CTTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGATCATGTTCTTTAGCAGCATTTG
* ** *
53894820 TGATAAAAGCGCCGTTAAAGGT
65 TGAGAAAAGCGCCGCCAAAGAT
* * * * *
53894842 CATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGTTAATGATCATGTTCTATAGCGGCATTT
1 CATGTTCTTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGATCATGTTCTTTAGCAGCATTT
53894905 TCCACATAAA
Statistics
Matches: 124, Mismatches: 24, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
86 54 0.44
87 69 0.56
88 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (86 bp):
CATGTTCTTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGATCATGTTCTTTAGCAGCATTTGT
GAGAAAAGCGCCGCCAAAGAT
Found at i:53894877 original size:43 final size:43
Alignment explanation
Indices: 53894659--53894900 Score: 270
Period size: 43 Copynumber: 5.6 Consensus size: 43
53894649 TTGTTAACGT
* * *
53894659 CGCTAAAGGA-CATGATCTTTAGCGACGTTTGAGATAAAAGCGC
1 CGCTAAA-GATCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGC
* * * * * ***
53894702 CACTAAAGGTAATGATCTTTAGCGGCATTTGTGGGCAAAGCGC
1 CGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGC
* * *
53894745 CGCCAAAGATCATGTTATTTTAGCGGCGTTTGTAATAAAAGCGC
1 CGCTAAAGATCATGTT-CTTTAGCGGCGTTTGTGATAAAAGCGC
* *
53894789 TGCTAAAGATCATGTTCTTTAGCAGCGTTTGTGATAAAAGCGC
1 CGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGC
* *
53894832 CGTTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGC
1 CGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGC
* * *
53894875 CGTTAATGATCATGTTCTATAGCGGC
1 CGCTAAAGATCATGTTCTTTAGCGGC
53894901 ATTTTCCACA
Statistics
Matches: 165, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
42 1 0.01
43 129 0.78
44 35 0.21
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (43 bp):
CGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGC
Found at i:53905689 original size:4 final size:5
Alignment explanation
Indices: 53905660--53905709 Score: 59
Period size: 5 Copynumber: 10.0 Consensus size: 5
53905650 AAAGAAACAG
*
53905660 AGAAA AGAAA ACGAAA GGCAAA AG-AA AG-AA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA A-GAAA AG-AAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
53905710 TAAAACGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
4 8 0.20
5 24 0.60
6 8 0.20
ACGTcount: A:0.74, C:0.04, G:0.22, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:53905694 original size:19 final size:19
Alignment explanation
Indices: 53905660--53905714 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
53905650 AAAGAAACAG
*
53905660 AGAAAAGAAAACGAAAGGCAAA
1 AGAAAAG-AAA-GAAAAG-AAA
53905682 AG-AAAGAAAGAAAAGAAA
1 AGAAAAGAAAGAAAAGAAA
*
53905700 AGAAAAGAAATAAAA
1 AGAAAAGAAAGAAAA
53905715 CGTAAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 5 0.17
19 16 0.53
20 3 0.10
21 4 0.13
22 2 0.07
ACGTcount: A:0.75, C:0.04, G:0.20, T:0.02
Consensus pattern (19 bp):
AGAAAAGAAAGAAAAGAAA
Found at i:53910442 original size:27 final size:28
Alignment explanation
Indices: 53910389--53910448 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
53910379 AAAATAATTA
*
53910389 AAATTCAATATTTTAATAATTTAAGTAT
1 AAATTCAATATTTTAATAATTAAAGTAT
53910417 AAATT-AATTATTTT-ATAATTAAAGTAT
1 AAATTCAA-TATTTTAATAATTAAAGTAT
*
53910444 GAATT
1 AAATT
53910449 TCGACAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (28 bp):
AAATTCAATATTTTAATAATTAAAGTAT
Found at i:53910891 original size:21 final size:21
Alignment explanation
Indices: 53910867--53910922 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
53910857 ACAAGTCACA
53910867 TGGATGGTTTGGGCATGCATG
1 TGGATGGTTTGGGCATGCATG
*
53910888 TGGATGGTTTAGGCATGCATG
1 TGGATGGTTTGGGCATGCATG
*
53910909 TGGATGATTTGGGC
1 TGGATGGTTTGGGC
53910923 TCCTTTAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.16, C:0.09, G:0.41, T:0.34
Consensus pattern (21 bp):
TGGATGGTTTGGGCATGCATG
Found at i:53912098 original size:16 final size:18
Alignment explanation
Indices: 53912071--53912103 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53912061 TAGAATTGGG
53912071 TTGAGAAAATTA-TTTAA
1 TTGAGAAAATTAGTTTAA
53912088 TTGAG-AAATTAGTTTA
1 TTGAGAAAATTAGTTTA
53912104 TTTAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAGTTTAA
Found at i:53918368 original size:13 final size:13
Alignment explanation
Indices: 53918343--53918380 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
53918333 TATTTGTTTC
53918343 TTTAATTTATTTTA
1 TTTAATTT-TTTTA
53918357 GTTTAATTTTTTTA
1 -TTTAATTTTTTTA
53918371 TTTAATTTTT
1 TTTAATTTTT
53918381 CACATAACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.43
14 5 0.22
15 8 0.35
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTAATTTTTTTA
Found at i:53922354 original size:29 final size:28
Alignment explanation
Indices: 53922305--53922377 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
53922295 TATCAAATAC
*
53922305 GAAAAGAAAGGAAA-TAAAAAAAAAGAAAG
1 GAAAAGAAA-GAAACT-AAAAAAAAGAAAA
* *
53922334 GGAAAGAAAGAAACTAGAAAAAAGAAAA
1 GAAAAGAAAGAAACTAAAAAAAAGAAAA
53922362 GAAAAGAAA-AAACTAA
1 GAAAAGAAAGAAACTAA
53922378 TGTGAGCAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
27 6 0.16
28 23 0.61
29 9 0.24
ACGTcount: A:0.74, C:0.03, G:0.19, T:0.04
Consensus pattern (28 bp):
GAAAAGAAAGAAACTAAAAAAAAGAAAA
Found at i:53922359 original size:18 final size:17
Alignment explanation
Indices: 53922336--53922373 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
53922326 AAAGAAAGGG
53922336 AAAG-AAAGAAACTAGAAA
1 AAAGAAAAGAAA--AGAAA
53922354 AAAGAAAAGAAAAGAAA
1 AAAGAAAAGAAAAGAAA
53922371 AAA
1 AAA
53922374 CTAATGTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (17 bp):
AAAGAAAAGAAAAGAAA
Found at i:53923123 original size:71 final size:71
Alignment explanation
Indices: 53923007--53923144 Score: 267
Period size: 71 Copynumber: 1.9 Consensus size: 71
53922997 CCACAAATGA
53923007 ATAAATCCATAAATAGATTCAAGATCCATTCTTCTTGGGTCTAGTAGATGTATTGACATTCTAGT
1 ATAAATCCATAAATAGATTCAAGATCCATTCTTCTTGGGTCTAGTAGATGTATTGACATTCTAGT
53923072 CAATAC
66 CAATAC
*
53923078 ATAAATCCATAAATAGATTCAAGATCTATTCTTCTTGGGTCTAGTAGATGTATTGACATTCTAGT
1 ATAAATCCATAAATAGATTCAAGATCCATTCTTCTTGGGTCTAGTAGATGTATTGACATTCTAGT
53923143 CA
66 CA
53923145 GTCACATCCA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (71 bp):
ATAAATCCATAAATAGATTCAAGATCCATTCTTCTTGGGTCTAGTAGATGTATTGACATTCTAGT
CAATAC
Done.