Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 192 of 199
Found at i:55587530 original size:16 final size:16
Alignment explanation
Indices: 55587511--55587544 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
55587501 AATACATTGG
55587511 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
55587527 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
55587543 AA
1 AA
55587545 ATATAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATATTAAAAATAAAA
Found at i:55588987 original size:20 final size:20
Alignment explanation
Indices: 55588962--55589005 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
55588952 CATAGAACAC
55588962 AAAAGAAGGGCCAAGTAGAA
1 AAAAGAAGGGCCAAGTAGAA
55588982 AAAAGAAGGGCCAAGTAGAA
1 AAAAGAAGGGCCAAGTAGAA
55589002 AAAA
1 AAAA
55589006 ATCATCCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.59, C:0.09, G:0.27, T:0.05
Consensus pattern (20 bp):
AAAAGAAGGGCCAAGTAGAA
Found at i:55589100 original size:12 final size:12
Alignment explanation
Indices: 55589080--55589109 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
55589070 GAGATAAAGG
*
55589080 AAACGCTATATT
1 AAACTCTATATT
55589092 AAACTCTATATT
1 AAACTCTATATT
55589104 AAACTC
1 AAACTC
55589110 AGCAAGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.33
Consensus pattern (12 bp):
AAACTCTATATT
Found at i:55590876 original size:13 final size:13
Alignment explanation
Indices: 55590858--55590892 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
55590848 TGATTTTGTG
55590858 AAAATTTCGTTAA
1 AAAATTTCGTTAA
* *
55590871 AAAATTTCATTCA
1 AAAATTTCGTTAA
55590884 AAAATTTCG
1 AAAATTTCG
55590893 AAGTTTGGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (13 bp):
AAAATTTCGTTAA
Found at i:55593721 original size:41 final size:40
Alignment explanation
Indices: 55593671--55593845 Score: 147
Period size: 41 Copynumber: 4.3 Consensus size: 40
55593661 ATTTATAGAA
* **
55593671 CATAGAGCCTTGTATAAAACACCGGCATAAAGCCTGCTAGG
1 CATAAAGCC-TGTATAATTCACCGGCATAAAGCCTGCTAGG
* * *
55593712 CACAAAGCCTG-ATACATTTCACCGGCACAAAGCCTGCTAGA
1 CATAAAGCCTGTATA-A-TTCACCGGCATAAAGCCTGCTAGG
* * *
55593753 CATAAAGTCTGATATAATTCACTGGCACT-GAGCCTGCTAGG
1 CATAAAGCCTG-TATAATTCACCGGCA-TAAAGCCTGCTAGG
* * * * *
55593794 CATAAAGCCTGATGTAATCCACCGACATCAAGTCTGCTAGG
1 CATAAAGCCTG-TATAATTCACCGGCATAAAGCCTGCTAGG
*
55593835 CATTAAGCCTG
1 CATAAAGCCTG
55593846 AAAATCTCAA
Statistics
Matches: 108, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
39 3 0.03
40 4 0.04
41 97 0.90
42 1 0.01
43 3 0.03
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (40 bp):
CATAAAGCCTGTATAATTCACCGGCATAAAGCCTGCTAGG
Found at i:55602046 original size:41 final size:40
Alignment explanation
Indices: 55601996--55602170 Score: 147
Period size: 41 Copynumber: 4.3 Consensus size: 40
55601986 ATTTATAGAA
* **
55601996 CATAGAGCCTTGTATAAAACACCGGCATAAAGCCTGCTAGG
1 CATAAAGCC-TGTATAATTCACCGGCATAAAGCCTGCTAGG
* * *
55602037 CACAAAGCCTG-ATACATTTCACCGGCACAAAGCCTGCTAGA
1 CATAAAGCCTGTATA-A-TTCACCGGCATAAAGCCTGCTAGG
* * *
55602078 CATAAAGTCTGATATAATTCACTGGCACT-GAGCCTGCTAGG
1 CATAAAGCCTG-TATAATTCACCGGCA-TAAAGCCTGCTAGG
* * * * *
55602119 CATAAAGCCTGATGTAATCCACCGACATCAAGTCTGCTAGG
1 CATAAAGCCTG-TATAATTCACCGGCATAAAGCCTGCTAGG
*
55602160 CATTAAGCCTG
1 CATAAAGCCTG
55602171 AAAATCTCAA
Statistics
Matches: 108, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
39 3 0.03
40 4 0.04
41 97 0.90
42 1 0.01
43 3 0.03
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (40 bp):
CATAAAGCCTGTATAATTCACCGGCATAAAGCCTGCTAGG
Found at i:55603938 original size:50 final size:50
Alignment explanation
Indices: 55603861--55604053 Score: 269
Period size: 50 Copynumber: 3.9 Consensus size: 50
55603851 CCTTGAGATC
*
55603861 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* *
55603911 ACGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * * *
55603961 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCATCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* ** * *
55604011 ATTAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
55604054 TAGTTTAAAA
Statistics
Matches: 125, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 125 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
Found at i:55611717 original size:19 final size:19
Alignment explanation
Indices: 55611653--55611717 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 19
55611643 CAAAAAATAA
* *
55611653 ATTTTTTTATAAAATGACTT
1 ATTTTTTGA-AAAATAACTT
*
55611673 ATTATTTTGAAAAATAGAAATT
1 ATT-TTTTGAAAAAT--AACTT
*
55611695 ATTTTTTGAAAAATAACTC
1 ATTTTTTGAAAAATAACTT
55611714 ATTT
1 ATTT
55611718 ATAAATAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 7 0.19
20 8 0.22
21 16 0.43
22 6 0.16
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (19 bp):
ATTTTTTGAAAAATAACTT
Found at i:55611843 original size:22 final size:22
Alignment explanation
Indices: 55611791--55611844 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
55611781 ATAATTTTTT
55611791 AATTTTAAT-TAAAAATATTAA
1 AATTTTAATATAAAAATATTAA
*
55611812 AAATTTAATAT-AAAATATTATA
1 AATTTTAATATAAAAATATTA-A
*
55611834 ATTTTTAATAT
1 AATTTTAATAT
55611845 TATTAAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTTTAATATAAAAATATTAA
Found at i:55611941 original size:31 final size:30
Alignment explanation
Indices: 55611883--55611948 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
55611873 TTTAATAATA
**
55611883 TAATAAATTATTAATATAATTTATTTATTG
1 TAATAAATTATTAATATAAAATATTTATTG
*
55611913 TAATAAATTATTCAATATTAAAAT-TTTATTT
1 TAATAAATTATT-AATA-TAAAATATTTATTG
55611944 TAATA
1 TAATA
55611949 GTAAATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 12 0.39
31 15 0.48
32 4 0.13
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
TAATAAATTATTAATATAAAATATTTATTG
Found at i:55619761 original size:27 final size:28
Alignment explanation
Indices: 55619730--55619794 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
55619720 TAACAAATAA
*
55619730 TTTAAAAATTATAAAAAAAAT-TCAAAT
1 TTTAAAAATTATAAAAAAAATATAAAAT
**
55619757 TTTAAAAATT-TTTAAAAAATATAAAAT
1 TTTAAAAATTATAAAAAAAATATAAAAT
*
55619784 ATTAAAAATTA
1 TTTAAAAATTA
55619795 AAATTAGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 8 0.25
27 24 0.75
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
TTTAAAAATTATAAAAAAAATATAAAAT
Found at i:55620970 original size:14 final size:15
Alignment explanation
Indices: 55620948--55620976 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55620938 TTAGATTAAT
55620948 TTTTATTTAAAATTA
1 TTTTATTTAAAATTA
55620963 TTTT-TTTAAAATTA
1 TTTTATTTAAAATTA
55620977 CATATATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTATTTAAAATTA
Found at i:55627184 original size:20 final size:21
Alignment explanation
Indices: 55627155--55627194 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
55627145 CTAAACATTT
*
55627155 ACTTTTTTTTCTT-AATTTGG
1 ACTTTATTTTCTTAAATTTGG
*
55627175 ACTTTATTTTGTTAAATTTG
1 ACTTTATTTTCTTAAATTTG
55627195 ACCTTCAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.62
Consensus pattern (21 bp):
ACTTTATTTTCTTAAATTTGG
Found at i:55627224 original size:31 final size:32
Alignment explanation
Indices: 55627189--55627255 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
55627179 TATTTTGTTA
**
55627189 AATTTGACCTTCA-ACATTTTAAAAAGACTTG
1 AATTTGACCACCAGACATTTTAAAAAGACTTG
* * *
55627220 AATTTGACCACCAGCCTTTTTAAAAAGAGTTG
1 AATTTGACCACCAGACATTTTAAAAAGACTTG
55627252 AATT
1 AATT
55627256 GTTTTCGTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (32 bp):
AATTTGACCACCAGACATTTTAAAAAGACTTG
Found at i:55627817 original size:13 final size:15
Alignment explanation
Indices: 55627799--55627830 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
55627789 TTTTACTTTA
55627799 AAAAAAT-TAAAT-T
1 AAAAAATATAAATAT
55627812 AAAAAATATAAATAT
1 AAAAAATATAAATAT
55627827 AAAA
1 AAAA
55627831 GAGTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAAAATATAAATAT
Found at i:55630516 original size:32 final size:33
Alignment explanation
Indices: 55630472--55630585 Score: 124
Period size: 32 Copynumber: 3.2 Consensus size: 33
55630462 CCAAAATTTT
55630472 TTTTAAAAATTAAAATAAAAATTAAAAAAAGTA
1 TTTTAAAAATTAAAATAAAAATTAAAAAAAGTA
*
55630505 TTTT-AAAATTAAAA-AAAATTTTAAAAAAAGTA
1 TTTTAAAAATTAAAATAAAA-ATTAAAAAAAGTA
55630537 TTTTAAAAAAATTTTAAAATTAAAAAAATTTAAAAAAAGTA
1 TTTT--AAAAA--TTAAAA-T--AAAAA-TTAAAAAAAGTA
55630578 TTTTAAAA
1 TTTTAAAA
55630586 GTATTTTAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
31 4 0.06
32 26 0.38
33 4 0.06
35 4 0.06
37 6 0.09
39 4 0.06
41 20 0.29
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (33 bp):
TTTTAAAAATTAAAATAAAAATTAAAAAAAGTA
Found at i:55630525 original size:18 final size:19
Alignment explanation
Indices: 55630489--55630530 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
55630479 AATTAAAATA
55630489 AAAATTAAAAAAAGTATTTT
1 AAAATTAAAAAAAG-ATTTT
55630509 AAAATTAAAAAAA-ATTTT
1 AAAATTAAAAAAAGATTTT
55630527 AAAA
1 AAAA
55630531 AAAGTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTAAAAAAAGATTTT
Found at i:55630530 original size:11 final size:11
Alignment explanation
Indices: 55630516--55630596 Score: 55
Period size: 11 Copynumber: 7.4 Consensus size: 11
55630506 TTTAAAATTA
55630516 AAAAAAATTTT
1 AAAAAAATTTT
55630527 AAAAAAAGTATTTT
1 -AAAAAA--ATTTT
55630541 AAAAAAATTTT
1 AAAAAAATTTT
55630552 ---AAAA--TT
1 AAAAAAATTTT
*
55630558 AAAAAAATTTA
1 AAAAAAATTTT
55630569 AAAAAAGTATTTT
1 AAAAAA--ATTTT
**
55630582 AAAAGTATTTT
1 AAAAAAATTTT
55630593 AAAA
1 AAAA
55630597 TTAAAAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
6 2 0.04
8 4 0.07
9 4 0.07
11 21 0.38
12 6 0.11
13 14 0.25
14 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (11 bp):
AAAAAAATTTT
Found at i:55630533 original size:41 final size:42
Alignment explanation
Indices: 55630476--55630605 Score: 135
Period size: 42 Copynumber: 3.1 Consensus size: 42
55630466 AATTTTTTTT
* *
55630476 AAAAA-TTAAAATAAAAATTAAAAAAAGTATTTTAAAATTAAA
1 AAAAATTTAAAA-AAAAGTTTAAAAAAGTATTTTAAAATTAAA
*
55630518 AAAAATTTTAAAAAAAGTATTTTAAAAAA--ATTTTAAAATT-AA
1 AAAAA-TTTAAAAAAA--AGTTTAAAAAAGTATTTTAAAATTAAA
**
55630560 AAAAATTT-AAAAAAAGTATTTTAAAAGTATTTTAAAATTAAA
1 AAAAATTTAAAAAAAAGT-TTAAAAAAGTATTTTAAAATTAAA
55630602 AAAA
1 AAAA
55630606 TAAAAAAAAT
Statistics
Matches: 75, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
38 2 0.03
39 6 0.08
40 6 0.08
41 14 0.19
42 18 0.24
43 14 0.19
44 6 0.08
45 9 0.12
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (42 bp):
AAAAATTTAAAAAAAAGTTTAAAAAAGTATTTTAAAATTAAA
Found at i:55630572 original size:17 final size:17
Alignment explanation
Indices: 55630539--55630572 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55630529 AAAAAGTATT
*
55630539 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTAAAAA
55630556 TTAAAAAAATTTAAAAA
1 TTAAAAAAATTTAAAAA
55630573 AAGTATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAA
Found at i:55630606 original size:41 final size:41
Alignment explanation
Indices: 55630498--55630614 Score: 182
Period size: 41 Copynumber: 2.8 Consensus size: 41
55630488 AAAAATTAAA
55630498 AAAAGTATTTTAAAATTAAAAAAAATTTTAAAAAAAGTATTTT
1 AAAAGTATTTTAAAATT-AAAAAAA-TTTAAAAAAAGTATTTT
**
55630541 AAAAAAATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTT
1 AAAAGTATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTT
*
55630582 AAAAGTATTTTAAAATTAAAAAAA-TAAAAAAAA
1 AAAAGTATTTTAAAATTAAAAAAATTTAAAAAAA
55630615 TAAATATTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
40 8 0.12
41 39 0.57
42 7 0.10
43 15 0.22
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (41 bp):
AAAAGTATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTT
Found at i:55633766 original size:19 final size:19
Alignment explanation
Indices: 55633742--55633779 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
55633732 CATCCAAACA
55633742 CTAGAAAAATAAATCATTT
1 CTAGAAAAATAAATCATTT
*
55633761 CTAGAAAAGTAAATCATTT
1 CTAGAAAAATAAATCATTT
55633780 TCCAGAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (19 bp):
CTAGAAAAATAAATCATTT
Found at i:55633786 original size:20 final size:19
Alignment explanation
Indices: 55633744--55633787 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
55633734 TCCAAACACT
*
55633744 AGAAAAATAAATCATTTCT
1 AGAAAAATAAATCATTTCC
*
55633763 AGAAAAGTAAATCATTTTCC
1 AGAAAAATAAATCA-TTTCC
55633783 AGAAA
1 AGAAA
55633788 TCATTTTCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.27
Consensus pattern (19 bp):
AGAAAAATAAATCATTTCC
Found at i:55633790 original size:14 final size:14
Alignment explanation
Indices: 55633771--55633808 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
55633761 CTAGAAAAGT
55633771 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
55633785 AAATCATTTTCCGG
1 AAATCATTTTCCAG
*
55633799 AAAACATTTT
1 AAATCATTTT
55633809 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:55636614 original size:37 final size:36
Alignment explanation
Indices: 55636567--55636636 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
55636557 GATTTATTTA
*
55636567 TAATAAATAAA-TCATTGCAATATGTGTAAAAACAATT
1 TAATAAATAAATTCATT--AATATATGTAAAAACAATT
* *
55636604 TAATATATAAATTTATTAATATATGTAAAAACA
1 TAATAAATAAATTCATTAATATATGTAAAAACA
55636637 GCTTTTCCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 15 0.52
37 10 0.34
38 4 0.14
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (36 bp):
TAATAAATAAATTCATTAATATATGTAAAAACAATT
Found at i:55644559 original size:32 final size:32
Alignment explanation
Indices: 55644517--55644585 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
55644507 CAAATTGGAA
55644517 GAAAA-AGAATAATTTCTCTTAAATTCCAAAT
1 GAAAATAGAATAATTTCTCTTAAATTCCAAAT
55644548 GAAAATAGAATAATTTCTCTTAAATTCCAAAT
1 GAAAATAGAATAATTTCTCTTAAATTCCAAAT
55644580 GAAAAT
1 GAAAAT
55644586 CAAATTCGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 5 0.14
32 32 0.86
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (32 bp):
GAAAATAGAATAATTTCTCTTAAATTCCAAAT
Found at i:55646181 original size:26 final size:25
Alignment explanation
Indices: 55646090--55646182 Score: 71
Period size: 26 Copynumber: 3.6 Consensus size: 25
55646080 TATGTAAATT
* * * *
55646090 ATAAAAATTAAAAAAAATTGAAAAT
1 ATAAATATTCAAAAAAATTAAAAAG
* *
55646115 ATATATAATCAAAAAAA-TAAAATAG
1 ATAAATATTCAAAAAAATTAAAA-AG
* * *
55646140 TTAAATTTTTCTAAAAAATTAAAAAG
1 ATAAA-TATTCAAAAAAATTAAAAAG
55646166 AATAAATATTCAAAAAA
1 -ATAAATATTCAAAAAA
55646183 TTGGCCGACA
Statistics
Matches: 50, Mismatches: 14, Indels: 7
0.70 0.20 0.10
Matches are distributed among these distances:
24 4 0.08
25 17 0.34
26 20 0.40
27 9 0.18
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (25 bp):
ATAAATATTCAAAAAAATTAAAAAG
Found at i:55654347 original size:17 final size:18
Alignment explanation
Indices: 55654315--55654349 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
55654305 TAAAAATTTA
*
55654315 TAAAATTTATTTAAAAAG
1 TAAAAATTATTTAAAAAG
55654333 TAAAAATTA-TTAAAAAG
1 TAAAAATTATTTAAAAAG
55654350 GTATAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
TAAAAATTATTTAAAAAG
Found at i:55657371 original size:21 final size:19
Alignment explanation
Indices: 55657346--55657387 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
55657336 TATATAATAT
*
55657346 AAAATTTTAGAAATTATTAAA
1 AAAATATTAGAAA-TA-TAAA
55657367 AAAATATTAGAAATATAAA
1 AAAATATTAGAAATATAAA
55657386 AA
1 AA
55657388 TGGTAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AAAATATTAGAAATATAAA
Found at i:55661190 original size:18 final size:20
Alignment explanation
Indices: 55661169--55661205 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
55661159 GATCATTAAT
55661169 TTGTA-ATTTAAA-AATTTA
1 TTGTAGATTTAAATAATTTA
*
55661187 TTGTAGTTTTAAATAATTT
1 TTGTAGATTTAAATAATTT
55661206 CAAATGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 6 0.38
20 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
TTGTAGATTTAAATAATTTA
Found at i:55665096 original size:29 final size:30
Alignment explanation
Indices: 55665044--55665110 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
55665034 TTCTACTTTT
*
55665044 TTTTTTGAATTTTTATAAACTTTTTATATA
1 TTTTTTGAATTTTTATAAACTTTTAATATA
* *
55665074 TTTTTTGAATTTTTA-AAAGTTTTAATTTA
1 TTTTTTGAATTTTTATAAACTTTTAATATA
*
55665103 TTTGTTGA
1 TTTTTTGA
55665111 TGACACATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.28, C:0.01, G:0.07, T:0.63
Consensus pattern (30 bp):
TTTTTTGAATTTTTATAAACTTTTAATATA
Found at i:55668533 original size:21 final size:22
Alignment explanation
Indices: 55668501--55668542 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
55668491 ATATTTAATA
55668501 ATATTAAATATTATAATATTTG
1 ATATTAAATATTATAATATTTG
*
55668523 ATATT-AATATTTTAATATTT
1 ATATTAAATATTATAATATTT
55668543 TTAGAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATATTAAATATTATAATATTTG
Found at i:55671367 original size:19 final size:19
Alignment explanation
Indices: 55671343--55671380 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
55671333 GGCGAGAGTG
55671343 GATGTTATTAAATCCATCA
1 GATGTTATTAAATCCATCA
*
55671362 GATGTTATTGAATCCATCA
1 GATGTTATTAAATCCATCA
55671381 CCACTCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (19 bp):
GATGTTATTAAATCCATCA
Found at i:55675325 original size:642 final size:642
Alignment explanation
Indices: 55674102--55675388 Score: 2574
Period size: 642 Copynumber: 2.0 Consensus size: 642
55674092 CCAATCATCA
55674102 TGTTCGTTTATGTTACTACTAGGAGGGGGGGAGGAGGTGCTATACTCTTTTGGCCAAGTCGTTTT
1 TGTTCGTTTATGTTACTACTAGGAGGGGGGGAGGAGGTGCTATACTCTTTTGGCCAAGTCGTTTT
55674167 TATATAAGATCAAAAAGTACAACTGAAATTTGGGTTTACTTGGGTTAGAAGCCTCATCAACTTTT
66 TATATAAGATCAAAAAGTACAACTGAAATTTGGGTTTACTTGGGTTAGAAGCCTCATCAACTTTT
55674232 CCAAGCATTTTCCTTTTTATTTTTATTTTCAATCCAACTTTTTTGGCTTTTGAAAATTCAGTCCT
131 CCAAGCATTTTCCTTTTTATTTTTATTTTCAATCCAACTTTTTTGGCTTTTGAAAATTCAGTCCT
55674297 AAGTTCTCATTACTTTGGAAACTTTTGGTTTAGTGAAATGGATGCATATGTATAGTGGGTTTTTT
196 AAGTTCTCATTACTTTGGAAACTTTTGGTTTAGTGAAATGGATGCATATGTATAGTGGGTTTTTT
55674362 CATATTATATTCATGAACTTTTGTTCTAATAATTTATATTGTTGTTCATATTTGTTTTTGTATAA
261 CATATTATATTCATGAACTTTTGTTCTAATAATTTATATTGTTGTTCATATTTGTTTTTGTATAA
55674427 TCTATAGGTGTATATATTTGACCATATTTTCCTGTATTCATTCAATAAGAAAAAGATGCCGACAT
326 TCTATAGGTGTATATATTTGACCATATTTTCCTGTATTCATTCAATAAGAAAAAGATGCCGACAT
55674492 GAGCTTTGCATGGGACAGAAAACCATTTAAAAGGGATGGCCTTTTTTTCATGTAAATCAGATTAG
391 GAGCTTTGCATGGGACAGAAAACCATTTAAAAGGGATGGCCTTTTTTTCATGTAAATCAGATTAG
55674557 TGAACAAATTGTGCTTAAATCATTTTTGAAATTACTTAAATTTTATGAAATAGTAAAAATTATTT
456 TGAACAAATTGTGCTTAAATCATTTTTGAAATTACTTAAATTTTATGAAATAGTAAAAATTATTT
55674622 ATTTTTGTAAATGAATTCGACCGATAAATTAGCATAATTAAATAAATTTAAACATTTTAGTATTC
521 ATTTTTGTAAATGAATTCGACCGATAAATTAGCATAATTAAATAAATTTAAACATTTTAGTATTC
55674687 AAATAGCCAGTTCGATTATTAATCTAGCTGAATTAGCATTAACCAAATTAATCGAAC
586 AAATAGCCAGTTCGATTATTAATCTAGCTGAATTAGCATTAACCAAATTAATCGAAC
55674744 TGTTCGTTTATGTTACTACTAGGAGGGGGGGAGGAGGTGCTATACTCTTTTGGCCAAGTCGTTTT
1 TGTTCGTTTATGTTACTACTAGGAGGGGGGGAGGAGGTGCTATACTCTTTTGGCCAAGTCGTTTT
55674809 TATATAAGATCAAAAAGTACAACTGAAATTTGGGTTTACTTGGGTTAGAAGCCTCATCAACTTTT
66 TATATAAGATCAAAAAGTACAACTGAAATTTGGGTTTACTTGGGTTAGAAGCCTCATCAACTTTT
55674874 CCAAGCATTTTCCTTTTTATTTTTATTTTCAATCCAACTTTTTTGGCTTTTGAAAATTCAGTCCT
131 CCAAGCATTTTCCTTTTTATTTTTATTTTCAATCCAACTTTTTTGGCTTTTGAAAATTCAGTCCT
55674939 AAGTTCTCATTACTTTGGAAACTTTTGGTTTAGTGAAATGGATGCATATGTATAGTGGGTTTTTT
196 AAGTTCTCATTACTTTGGAAACTTTTGGTTTAGTGAAATGGATGCATATGTATAGTGGGTTTTTT
55675004 CATATTATATTCATGAACTTTTGTTCTAATAATTTATATTGTTGTTCATATTTGTTTTTGTATAA
261 CATATTATATTCATGAACTTTTGTTCTAATAATTTATATTGTTGTTCATATTTGTTTTTGTATAA
55675069 TCTATAGGTGTATATATTTGACCATATTTTCCTGTATTCATTCAATAAGAAAAAGATGCCGACAT
326 TCTATAGGTGTATATATTTGACCATATTTTCCTGTATTCATTCAATAAGAAAAAGATGCCGACAT
55675134 GAGCTTTGCATGGGACAGAAAACCATTTAAAAGGGATGGCCTTTTTTTCATGTAAATCAGATTAG
391 GAGCTTTGCATGGGACAGAAAACCATTTAAAAGGGATGGCCTTTTTTTCATGTAAATCAGATTAG
55675199 TGAACAAATTGTGCTTAAATCATTTTTGAAATTACTTAAATTTTATGAAATAGTAAAAATTATTT
456 TGAACAAATTGTGCTTAAATCATTTTTGAAATTACTTAAATTTTATGAAATAGTAAAAATTATTT
55675264 ATTTTTGTAAATGAATTCGACCGATAAATTAGCATAATTAAATAAATTTAAACATTTTAGTATTC
521 ATTTTTGTAAATGAATTCGACCGATAAATTAGCATAATTAAATAAATTTAAACATTTTAGTATTC
55675329 AAATAGCCAGTTCGATTATTAATCTAGCTGAATTAGCATTAACCAAATTAATCGAAC
586 AAATAGCCAGTTCGATTATTAATCTAGCTGAATTAGCATTAACCAAATTAATCGAAC
55675386 TGT
1 TGT
55675389 ATAATCCTTT
Statistics
Matches: 645, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
642 645 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.40
Consensus pattern (642 bp):
TGTTCGTTTATGTTACTACTAGGAGGGGGGGAGGAGGTGCTATACTCTTTTGGCCAAGTCGTTTT
TATATAAGATCAAAAAGTACAACTGAAATTTGGGTTTACTTGGGTTAGAAGCCTCATCAACTTTT
CCAAGCATTTTCCTTTTTATTTTTATTTTCAATCCAACTTTTTTGGCTTTTGAAAATTCAGTCCT
AAGTTCTCATTACTTTGGAAACTTTTGGTTTAGTGAAATGGATGCATATGTATAGTGGGTTTTTT
CATATTATATTCATGAACTTTTGTTCTAATAATTTATATTGTTGTTCATATTTGTTTTTGTATAA
TCTATAGGTGTATATATTTGACCATATTTTCCTGTATTCATTCAATAAGAAAAAGATGCCGACAT
GAGCTTTGCATGGGACAGAAAACCATTTAAAAGGGATGGCCTTTTTTTCATGTAAATCAGATTAG
TGAACAAATTGTGCTTAAATCATTTTTGAAATTACTTAAATTTTATGAAATAGTAAAAATTATTT
ATTTTTGTAAATGAATTCGACCGATAAATTAGCATAATTAAATAAATTTAAACATTTTAGTATTC
AAATAGCCAGTTCGATTATTAATCTAGCTGAATTAGCATTAACCAAATTAATCGAAC
Found at i:55676112 original size:17 final size:18
Alignment explanation
Indices: 55676092--55676125 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55676082 TAATTAATTT
55676092 TTTA-TATTTTTTAAATC
1 TTTATTATTTTTTAAATC
55676109 TTTATTATTTTTTAAAT
1 TTTATTATTTTTTAAAT
55676126 AATTTTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTATTTTTTAAATC
Found at i:55676769 original size:5 final size:5
Alignment explanation
Indices: 55676759--55676790 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
55676749 ACAAGATTAC
55676759 ATCAA ATCAA ATCAA ATCAA ATCAA ATCAA AT
1 ATCAA ATCAA ATCAA ATCAA ATCAA ATCAA AT
55676791 TTTTACAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (5 bp):
ATCAA
Found at i:55680038 original size:5 final size:5
Alignment explanation
Indices: 55680028--55680075 Score: 96
Period size: 5 Copynumber: 9.6 Consensus size: 5
55680018 AATTATTTTC
55680028 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
55680076 TAATAATCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:55681697 original size:17 final size:17
Alignment explanation
Indices: 55681675--55681714 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
55681665 ATTATGAAAT
55681675 GTAATTAAATTTGAGCC
1 GTAATTAAATTTGAGCC
55681692 GTAATTAAATTTGAGCC
1 GTAATTAAATTTGAGCC
*
55681709 TTAATT
1 GTAATT
55681715 GAGCGTACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (17 bp):
GTAATTAAATTTGAGCC
Found at i:55685717 original size:41 final size:41
Alignment explanation
Indices: 55685671--55685856 Score: 277
Period size: 41 Copynumber: 4.5 Consensus size: 41
55685661 CACCGCACTT
*
55685671 AGCCTGCTAGACATATAGTCTGAAATGTATCACCGGCATTA
1 AGCCTGCTAGACATAAAGTCTGAAATGTATCACCGGCATTA
*
55685712 AGCCTGCTAGACATATAGTCTGAAATGTATCACCGGCATTA
1 AGCCTGCTAGACATAAAGTCTGAAATGTATCACCGGCATTA
* *
55685753 AGCCTGCTAGACTTAAAGTCTGAAATGTATCACCGGCATTT
1 AGCCTGCTAGACATAAAGTCTGAAATGTATCACCGGCATTA
*
55685794 AGCCTGCTAGACTTAAAGTCTG-AAT-TACTTCACCGGCATTA
1 AGCCTGCTAGACATAAAGTCTGAAATGTA--TCACCGGCATTA
* *
55685835 AGCCTGCTAGACGTAACGTCTG
1 AGCCTGCTAGACATAAAGTCTG
55685857 TATTATATTC
Statistics
Matches: 137, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
39 2 0.01
40 3 0.02
41 132 0.96
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCTGAAATGTATCACCGGCATTA
Found at i:55693337 original size:41 final size:41
Alignment explanation
Indices: 55693292--55693487 Score: 265
Period size: 41 Copynumber: 4.8 Consensus size: 41
55693282 TGATTCAGTA
*
55693292 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCA-TTAAGCCTGCTAGACATAAAGTCTGAAATGTAT
*
55693333 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATGTAT
* *
55693374 CACCGGCATTAAGCCTGCTAGACTTAAAGTTTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATGTAT
* *
55693415 CACCGGCATTTAGCCTGCTAGACTTAAAGTCTG-AAT-TACTT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATGTA--T
* *
55693456 CA-CGGCATTAAGCCTGCTAGACGTAACGTCTG
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTG
55693488 TATTATATTC
Statistics
Matches: 144, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
39 2 0.01
40 32 0.22
41 110 0.76
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATGTAT
Found at i:55693389 original size:82 final size:81
Alignment explanation
Indices: 55693250--55693487 Score: 268
Period size: 82 Copynumber: 2.9 Consensus size: 81
55693240 TTAAACAGAT
** * * * *
55693250 TCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTG-ATTCAGTACACCGGCACTT-AGCCTGCTAG
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAATT-ACT-CACCGGCA-TTAAGCCTGCTAG
*
55693313 ACATATAGTCTGAAATGTA
63 ACATAAAGTCTGAAATGTA
*
55693332 TCACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA-TCACCGGCATTAAGCCTGCTAGA
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTG-AAT-TACTCACCGGCATTAAGCCTGCTAGA
* *
55693396 CTTAAAGTTTGAAATGTA
64 CATAAAGTCTGAAATGTA
* *
55693414 TCACCGGCATTTAGCCTGCTAGACTTAAAGTCTGAATTACTTCA-CGGCATTAAGCCTGCTAGAC
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAATTAC-TCACCGGCATTAAGCCTGCTAGAC
* *
55693478 GTAACGTCTG
65 ATAAAGTCTG
55693488 TATTATATTC
Statistics
Matches: 135, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
80 2 0.01
81 32 0.24
82 96 0.71
83 1 0.01
84 3 0.02
85 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (81 bp):
TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAATTACTCACCGGCATTAAGCCTGCTAGACA
TAAAGTCTGAAATGTA
Found at i:55696290 original size:15 final size:16
Alignment explanation
Indices: 55696262--55696291 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55696252 GTTGGACTAA
55696262 ATTGAATATGAGTTAT
1 ATTGAATATGAGTTAT
55696278 ATTGAAT-TGAGTTA
1 ATTGAATATGAGTTA
55696292 AATTCATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (16 bp):
ATTGAATATGAGTTAT
Found at i:55696689 original size:25 final size:25
Alignment explanation
Indices: 55696607--55696679 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
55696597 CACAACTTAT
* *
55696607 ATGAGCTTCTCGTTATACAGCTCGC
1 ATGAGCTTCCCGTTATTCAGCTCGC
* * *
55696632 ATGAGCTTCCCGTTACTCAGGTCGT
1 ATGAGCTTCCCGTTATTCAGCTCGC
55696657 ATGAGCTTCCCGTTATTCAGCTC
1 ATGAGCTTCCCGTTATTCAGCTC
55696680 TGAAGAGCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.18, C:0.29, G:0.21, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATTCAGCTCGC
Found at i:55698408 original size:627 final size:627
Alignment explanation
Indices: 55697215--55699088 Score: 3658
Period size: 627 Copynumber: 3.0 Consensus size: 627
55697205 TATAATTGTT
55697215 TTGTTGATACTAGCCACTTGAATGACTTGTGTTTGGTATATTTTGATGTGTTTATATATGTGGCC
1 TTGTTGATACTAGCCACTTGAATGACTTGTGTTTGGTATATTTTGATGTGTTTATATATGTGGCC
55697280 TTATCATATTTAATGTGTATTTGATATGGTTGAATGATGGAAAAATTATAGGTATATTTGGTACC
66 TTATCATATTTAATGTGTATTTGATATGGTTGAATGATGGAAAAATTATAGGTATATTTGGTACC
55697345 ATTAAGCATATATGCATTTGGTTATCTAGGTAAATATGGATATTTGGTTGACATGTTATTAATTT
131 ATTAAGCATATATGCATTTGGTTATCTAGGTAAATATGGATATTTGGTTGACATGTTATTAATTT
55697410 GTCATTTGAGGTGCCTAAGGGCATATTGGTTATATGTTGTGATAATACATGTTTAAGACTTGATT
196 GTCATTTGAGGTGCCTAAGGGCATATTGGTTATATGTTGTGATAATACATGTTTAAGACTTGATT
55697475 TTAGCTTGATTTGGATGCCTAGTTATGGCTTGTTGATGTGCAAATTGTTCTGTTTAGGTTGGTAC
261 TTAGCTTGATTTGGATGCCTAGTTATGGCTTGTTGATGTGCAAATTGTTCTGTTTAGGTTGGTAC
* *
55697540 CGAATTGGGTGAGAAATGTGGCTTGGAAAATGACTTATTTTCATCCAAATGGGCAAAGACATGGG
326 CAAATTGGGTGAGAAATGTGGCTTGGAAAATGACTTATTTTCATCCAAATGGGCAAAGACACGGG
*
55697605 CATGCGTCTCAGCCGTGTGTGACACACGGCCAGGTGGCATGGCTGTGTGTTCCCTGTATCTTTAA
391 CGTGCGTCTCAGCCGTGTGTGACACACGGCCAGGTGGCATGGCTGTGTGTTCCCTGTATCTTTAA
55697670 AATTGCACAAGTCAGTATGCTCAACACGGCCTAGCACATAGGTGTGTGACTTGGTCGTGTGACCC
456 AATTGCACAAGTCAGTATGCTCAACACGGCCTAGCACATAGGTGTGTGACTTGGTCGTGTGACCC
55697735 AAGTTAGAGAGTTACACGGGCAAGGACACGGGCTGGGACACGGCCGTGTGTCCCTATTTCGAATG
521 AAGTTAGAGAGTTACACGGGCAAGGACACGGGCTGGGACACGGCCGTGTGTCCCTATTTCGAATG
55697800 CCCACACGGCCTGGCCACACGACCGTGTGTCCCCTGAATGAC
586 CCCACACGGCCTGGCCACACGACCGTGTGTCCCCTGAATGAC
55697842 TTGTTGATACTAGCCACTTGAATGACTTGTGTTTGGTATATTTTGATGTGTTTATATATGTGGCC
1 TTGTTGATACTAGCCACTTGAATGACTTGTGTTTGGTATATTTTGATGTGTTTATATATGTGGCC
55697907 TTATCATATTTAATGTGTATTTGATATGGTTGAATGATGGAAAAATTATAGGTATATTTGGTACC
66 TTATCATATTTAATGTGTATTTGATATGGTTGAATGATGGAAAAATTATAGGTATATTTGGTACC
55697972 ATTAAGCATATATGCATTTGGTTATCTAGGTAAATATGGATATTTGGTTGACATGTTATTAATTT
131 ATTAAGCATATATGCATTTGGTTATCTAGGTAAATATGGATATTTGGTTGACATGTTATTAATTT
55698037 GTCATTTGAGGTGCCTAAGGGCATATTGGTTATATGTTGTGATAATACATGTTTAAGACTTGATT
196 GTCATTTGAGGTGCCTAAGGGCATATTGGTTATATGTTGTGATAATACATGTTTAAGACTTGATT
55698102 TTAGCTTGATTTGGATGCCTAGTTATGGCTTGTTGATGTGCAAATTGTTCTGTTTAGGTTGGTAC
261 TTAGCTTGATTTGGATGCCTAGTTATGGCTTGTTGATGTGCAAATTGTTCTGTTTAGGTTGGTAC
55698167 CAAATTGGGTGAGAAATGTGGCTTGGAAAATGACTTATTTTCATCCAAATGGGCAAAGACACGGG
326 CAAATTGGGTGAGAAATGTGGCTTGGAAAATGACTTATTTTCATCCAAATGGGCAAAGACACGGG
55698232 CGTGCGTCTCAGCCGTGTGTGACACACGGCCAGGTGGCATGGCTGTGTGTTCCCTGTATCTTTAA
391 CGTGCGTCTCAGCCGTGTGTGACACACGGCCAGGTGGCATGGCTGTGTGTTCCCTGTATCTTTAA
55698297 AATTGCACAAGTCAGTATGCTCAACACGGCCTAGCACATAGGTGTGTGACTTGGTCGTGTGACCC
456 AATTGCACAAGTCAGTATGCTCAACACGGCCTAGCACATAGGTGTGTGACTTGGTCGTGTGACCC
55698362 AAGTTAGAGAGTTACACGGGCAAGGACACGGGCTGGGACACGGCCGTGTGTCCCTATTTCGAATG
521 AAGTTAGAGAGTTACACGGGCAAGGACACGGGCTGGGACACGGCCGTGTGTCCCTATTTCGAATG
55698427 CCCACACGGCCTGGCCACACGACCGTGTGTCCCCTGAATGAC
586 CCCACACGGCCTGGCCACACGACCGTGTGTCCCCTGAATGAC
55698469 TTGTTGATACTAGCCACTTGAATGACTTGTGTTTGGTATATTTTGATGTGTTTATATATGTGGCC
1 TTGTTGATACTAGCCACTTGAATGACTTGTGTTTGGTATATTTTGATGTGTTTATATATGTGGCC
55698534 TTATCATATTTAATGTGTATTTGATATGGTTGAATGATGGAAAAATTATAGGTATATTTGGTACC
66 TTATCATATTTAATGTGTATTTGATATGGTTGAATGATGGAAAAATTATAGGTATATTTGGTACC
55698599 ATTAAGCATATATGCATTTGGTTATCTAGGTAAATATGGATATTTGGTTGACATGTTATTAATTT
131 ATTAAGCATATATGCATTTGGTTATCTAGGTAAATATGGATATTTGGTTGACATGTTATTAATTT
55698664 GTCATTTGAGGTGCCTAAGGGCATATTGGTTATATGTTGTGATAATACATGTTTAAGACTTGATT
196 GTCATTTGAGGTGCCTAAGGGCATATTGGTTATATGTTGTGATAATACATGTTTAAGACTTGATT
55698729 TTAGCTTGATTTGGATGCCTAGTTATGGCTTGTTGATGTGCAAATTGTTCTGTTTAGGTTGGTAC
261 TTAGCTTGATTTGGATGCCTAGTTATGGCTTGTTGATGTGCAAATTGTTCTGTTTAGGTTGGTAC
*
55698794 CAAATTGGGTGAGAAATGTGGCTTGGAAAATGACCTATTTTCATCCAAATGGGCAAAGACACGGG
326 CAAATTGGGTGAGAAATGTGGCTTGGAAAATGACTTATTTTCATCCAAATGGGCAAAGACACGGG
*
55698859 CGTGCGTCTCAGCCGTGTGTGACACACGGCCAGGTGACATGGCTGTGTGTTCCCTGTATCTTTAA
391 CGTGCGTCTCAGCCGTGTGTGACACACGGCCAGGTGGCATGGCTGTGTGTTCCCTGTATCTTTAA
* *
55698924 AATTGCACAAGTTAGTATGCTCAACACGGCCTAGCACATAGGTGTGTGACTTGGTCATGTGACCC
456 AATTGCACAAGTCAGTATGCTCAACACGGCCTAGCACATAGGTGTGTGACTTGGTCGTGTGACCC
* *
55698989 AAGTCAGAGAGTTACACGGGCACGGACACGGGCTGGGACACGGCCGTGTGTCCCTATTTCGAATG
521 AAGTTAGAGAGTTACACGGGCAAGGACACGGGCTGGGACACGGCCGTGTGTCCCTATTTCGAATG
*
55699054 CCCACACGGCCTGGCCACACGGCCGTGTGTCCCCT
586 CCCACACGGCCTGGCCACACGACCGTGTGTCCCCT
55699089 ATAGCTTTGA
Statistics
Matches: 1237, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
627 1237 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (627 bp):
TTGTTGATACTAGCCACTTGAATGACTTGTGTTTGGTATATTTTGATGTGTTTATATATGTGGCC
TTATCATATTTAATGTGTATTTGATATGGTTGAATGATGGAAAAATTATAGGTATATTTGGTACC
ATTAAGCATATATGCATTTGGTTATCTAGGTAAATATGGATATTTGGTTGACATGTTATTAATTT
GTCATTTGAGGTGCCTAAGGGCATATTGGTTATATGTTGTGATAATACATGTTTAAGACTTGATT
TTAGCTTGATTTGGATGCCTAGTTATGGCTTGTTGATGTGCAAATTGTTCTGTTTAGGTTGGTAC
CAAATTGGGTGAGAAATGTGGCTTGGAAAATGACTTATTTTCATCCAAATGGGCAAAGACACGGG
CGTGCGTCTCAGCCGTGTGTGACACACGGCCAGGTGGCATGGCTGTGTGTTCCCTGTATCTTTAA
AATTGCACAAGTCAGTATGCTCAACACGGCCTAGCACATAGGTGTGTGACTTGGTCGTGTGACCC
AAGTTAGAGAGTTACACGGGCAAGGACACGGGCTGGGACACGGCCGTGTGTCCCTATTTCGAATG
CCCACACGGCCTGGCCACACGACCGTGTGTCCCCTGAATGAC
Found at i:55700358 original size:11 final size:11
Alignment explanation
Indices: 55700342--55700368 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
55700332 AAACATTCAA
55700342 GGCCCGAGCTT
1 GGCCCGAGCTT
55700353 GGCCCGAGCTT
1 GGCCCGAGCTT
55700364 GGCCC
1 GGCCC
55700369 AGATTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.41, G:0.37, T:0.15
Consensus pattern (11 bp):
GGCCCGAGCTT
Found at i:55703383 original size:24 final size:26
Alignment explanation
Indices: 55703345--55703410 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 26
55703335 TACTATTATC
*
55703345 ATTATTTATT-TTTATGTTATTCAT-A
1 ATTATTTATTACTTATGTTATT-ATAA
55703370 A-TATTT-TTACTTATG-TATTATAA
1 ATTATTTATTACTTATGTTATTATAA
55703393 ATTATTTATTAC-TATGTT
1 ATTATTTATTACTTATGTT
55703411 TACCTCTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
22 2 0.06
23 8 0.23
24 19 0.54
25 6 0.17
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (26 bp):
ATTATTTATTACTTATGTTATTATAA
Found at i:55703640 original size:18 final size:19
Alignment explanation
Indices: 55703617--55703653 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
55703607 ATTATGGTAT
55703617 TTAATC-AATAAAAT-ATAA
1 TTAATCTAA-AAAATGATAA
55703635 TTAATCTAAAAAATGATAA
1 TTAATCTAAAAAATGATAA
55703654 GATATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (19 bp):
TTAATCTAAAAAATGATAA
Found at i:55703745 original size:45 final size:41
Alignment explanation
Indices: 55703694--55703782 Score: 117
Period size: 41 Copynumber: 2.1 Consensus size: 41
55703684 ATTTGCTCCT
55703694 AAAATACTACAAAACAAAATTA-AAATAATTTGTATAATTCCATGA
1 AAAATACTACAAAACAAAA--AGAAA-AA--TGTATAATTCCATGA
*
55703739 AAAATACTACAAAGCAAAAAGAAAAATGTATAATTCCATGA
1 AAAATACTACAAAACAAAAAGAAAAATGTATAATTCCATGA
55703780 AAA
1 AAA
55703783 GCCCCTGTAC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
41 18 0.43
43 3 0.07
44 3 0.07
45 18 0.43
ACGTcount: A:0.58, C:0.11, G:0.07, T:0.24
Consensus pattern (41 bp):
AAAATACTACAAAACAAAAAGAAAAATGTATAATTCCATGA
Found at i:55707697 original size:16 final size:16
Alignment explanation
Indices: 55707672--55707707 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
55707662 CATCAACAAA
55707672 TTTTTTTATATAT-AT
1 TTTTTTTATATATAAT
55707687 TTTTCTTTATATATAAT
1 TTTT-TTTATATATAAT
55707704 TTTT
1 TTTT
55707708 ATATGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 9 0.47
17 6 0.32
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTTATATATAAT
Found at i:55710338 original size:85 final size:86
Alignment explanation
Indices: 55710184--55710344 Score: 227
Period size: 85 Copynumber: 1.9 Consensus size: 86
55710174 TAGTTGCCCA
* *
55710184 TCCACAAAACCCAGTGACAGTTTGTTTAATCTGCGAATATGTTGTGCACTCACAACAAGTGACAA
1 TCCACAAAACCCAGTGACAGTTTGTTTAATCTGCAAACATGTTGTGCACTCACAACAAGTGACAA
*
55710249 TAACTGTAAATATGTGGTTCG
66 TAACTGCAAATATGTGGTTCG
* * * *
55710270 TCCAC-AAACCTAGTGGCAGTTTGTTTAATCTG-AAACCATGTTGTGCACTCATAACAAGTGGCA
1 TCCACAAAACCCAGTGACAGTTTGTTTAATCTGCAAA-CATGTTGTGCACTCACAACAAGTGACA
*
55710333 GTAACTGCAAAT
65 ATAACTGCAAAT
55710345 GTTTTTATCT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
84 2 0.03
85 59 0.89
86 5 0.08
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (86 bp):
TCCACAAAACCCAGTGACAGTTTGTTTAATCTGCAAACATGTTGTGCACTCACAACAAGTGACAA
TAACTGCAAATATGTGGTTCG
Found at i:55712321 original size:29 final size:30
Alignment explanation
Indices: 55712254--55712331 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
55712244 AAACTATATT
*
55712254 TTAGGAGCTCAATTGATTGCCAACTTTCAA
1 TTAGGGGCTCAATTGATTGCCAACTTTCAA
** *
55712284 TTAATGGCTCAATTGATTG-CAATTTTCAA
1 TTAGGGGCTCAATTGATTGCCAACTTTCAA
*
55712313 TTAGGGGCTTAATTGATTG
1 TTAGGGGCTCAATTGATTG
55712332 TATTCTTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 25 0.61
30 16 0.39
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.38
Consensus pattern (30 bp):
TTAGGGGCTCAATTGATTGCCAACTTTCAA
Found at i:55719298 original size:20 final size:20
Alignment explanation
Indices: 55719260--55719308 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
55719250 TTTTTAAACT
* *
55719260 TTTAACTTTTAAAATTTATA
1 TTTAATTTTTAAAACTTATA
*
55719280 TTTAATTTTTATAACTTATA
1 TTTAATTTTTAAAACTTATA
*
55719300 ATT-ATTTTT
1 TTTAATTTTT
55719309 TTCTCATCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTAATTTTTAAAACTTATA
Found at i:55721720 original size:20 final size:20
Alignment explanation
Indices: 55721695--55721736 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
55721685 TGCTTTCCGT
55721695 TTATCTC-TCATGAGCTTCAG
1 TTATCTCAT-ATGAGCTTCAG
*
55721715 TTATCTCATATGAGTTTCAG
1 TTATCTCATATGAGCTTCAG
55721735 TT
1 TT
55721737 TAACCCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.45
Consensus pattern (20 bp):
TTATCTCATATGAGCTTCAG
Found at i:55721780 original size:42 final size:42
Alignment explanation
Indices: 55721723--55721828 Score: 135
Period size: 42 Copynumber: 2.5 Consensus size: 42
55721713 AGTTATCTCA
* * *
55721723 TATGAGTTTCAGTTTAACCCTTCTGGG-TTTCAGTTCAGCTATT
1 TATGAGCTGCAGTTTAACCCTTATGGGTTTTC-GTTCAGCT-TT
55721766 T-TGAGCTGCAGTTTAACCCTTATGGGTTTTCGTTCAGCTTT
1 TATGAGCTGCAGTTTAACCCTTATGGGTTTTCGTTCAGCTTT
* *
55721807 TATGAGCTTCCGTTTAACCCTT
1 TATGAGCTGCAGTTTAACCCTT
55721829 GCAGGTTTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
41 3 0.05
42 48 0.86
43 5 0.09
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (42 bp):
TATGAGCTGCAGTTTAACCCTTATGGGTTTTCGTTCAGCTTT
Found at i:55727786 original size:14 final size:14
Alignment explanation
Indices: 55727767--55727796 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
55727757 CCATACCTTC
55727767 ATTCTCATTTTCTA
1 ATTCTCATTTTCTA
55727781 ATTCTCATTTTCTA
1 ATTCTCATTTTCTA
55727795 AT
1 AT
55727797 AGGCATATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTCTCATTTTCTA
Found at i:55729004 original size:21 final size:20
Alignment explanation
Indices: 55728970--55729010 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
55728960 TTTGTTATTG
*
55728970 AAATTTATTTCAAATATATA
1 AAATTTATTCCAAATATATA
*
55728990 AAATTATATTCCAAATTTATA
1 AAATT-TATTCCAAATATATA
55729011 TTTCATATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTTATTCCAAATATATA
Found at i:55733893 original size:21 final size:21
Alignment explanation
Indices: 55733859--55733899 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
55733849 AGACGAGCAA
* *
55733859 TACTCCACAGCAGGTAGAGTG
1 TACTCCAAAACAGGTAGAGTG
*
55733880 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTAGAGT
55733900 TTGAGCAGAT
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:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTAGAGTG
Found at i:55737908 original size:17 final size:17
Alignment explanation
Indices: 55737886--55737949 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
55737876 AATCTTAAAG
55737886 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
55737903 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
*
55737922 TTCAAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
55737939 TTTTAATTGTA
1 TTCTAATTGTA
55737950 GCCCTTGATG
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
16 1 0.03
17 20 0.56
18 4 0.11
19 10 0.28
20 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.45
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:55737918 original size:36 final size:36
Alignment explanation
Indices: 55737878--55737948 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
55737868 GATTATGTAA
*
55737878 TCTTAAAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAAAGTTCAAATTGTATACAGCTTCTAATTGTG
* *
55737914 TCTTAGAGTTCAAATTGTATACAGCTTTTAATTGT
1 TCTTAAAGTTCAAATTGTATACAGCTTCTAATTGT
55737949 AGCCCTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (36 bp):
TCTTAAAGTTCAAATTGTATACAGCTTCTAATTGTG
Found at i:55738308 original size:15 final size:16
Alignment explanation
Indices: 55738272--55738305 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
55738262 AGCACTTCCC
55738272 TTTGAAGATTGGATTT
1 TTTGAAGATTGGATTT
55738288 TTTGAAGATTGGATTT
1 TTTGAAGATTGGATTT
55738304 TT
1 TT
55738306 GAAAGTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (16 bp):
TTTGAAGATTGGATTT
Found at i:55743169 original size:90 final size:89
Alignment explanation
Indices: 55743066--55743260 Score: 234
Period size: 90 Copynumber: 2.2 Consensus size: 89
55743056 GTAGTGTCAC
* *
55743066 AGTATCTTTCAACTATGGTATTGA-TCATTATCCA-TGTGA-TGCCATAATATCTTTCAACTATG
1 AGTATCTTTCAACTATGGTATT-ACACATT-TCCAGT-TGAGTGCCATAATATCTTTCAACTATA
* *
55743128 GTCTTATTCGTATCAGATTTAATGCCAT
63 GTCTTATTCAT-TCAGATTTAATACCAT
* * * * *
55743156 AGTATCTTTCAACTACGGTCTTACACATTTCCAGTTTAGTGCCGTAGTATCTTTCAACTATAGTC
1 AGTATCTTTCAACTATGGTATTACACATTTCCAGTTGAGTGCCATAATATCTTTCAACTATAGTC
* *
55743221 TTATTCATTCCGATTTAATATCAT
66 TTATTCATTCAGATTTAATACCAT
55743245 AGTATCTTTCAACTAT
1 AGTATCTTTCAACTAT
55743261 AGTCTTTCTC
Statistics
Matches: 90, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
89 35 0.39
90 55 0.61
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (89 bp):
AGTATCTTTCAACTATGGTATTACACATTTCCAGTTGAGTGCCATAATATCTTTCAACTATAGTC
TTATTCATTCAGATTTAATACCAT
Found at i:55743273 original size:44 final size:44
Alignment explanation
Indices: 55743104--55743266 Score: 184
Period size: 45 Copynumber: 3.7 Consensus size: 44
55743094 TATCCATGTG
* * * *
55743104 ATGCCATAATATCTTTCAACTATGGTCTTATTCGTATCAGATTTA
1 ATGCCATAGTATCTTTCAACTATAGTCTTATTCAT-TCCGATTTA
** **
55743149 ATGCCATAGTATCTTTCAACTACGGTCTTACACATTTCC-AGTTTA
1 ATGCCATAGTATCTTTCAACTATAGTCTTATTCA-TTCCGA-TTTA
* *
55743194 GTGCCGTAGTATCTTTCAACTATAGTCTTATTCATTCCGATTTA
1 ATGCCATAGTATCTTTCAACTATAGTCTTATTCATTCCGATTTA
**
55743238 ATATCATAGTATCTTTCAACTATAGTCTT
1 ATGCCATAGTATCTTTCAACTATAGTCTT
55743267 TCTCATTTCG
Statistics
Matches: 99, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
44 34 0.34
45 64 0.65
46 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (44 bp):
ATGCCATAGTATCTTTCAACTATAGTCTTATTCATTCCGATTTA
Found at i:55743311 original size:89 final size:90
Alignment explanation
Indices: 55743103--55743311 Score: 228
Period size: 89 Copynumber: 2.3 Consensus size: 90
55743093 TTATCCATGT
* *
55743103 GATGCCATAATATCTTTCAACTATGGTCTTATTCGTATCAGATTTAATGCCATAGTATCTTTCAA
1 GATGCCAT-ATATCTTTCAACTATGGTCTTATTCATATCAGATTTAATACCATAGTATCTTTCAA
* * *
55743168 CTACGGTCTTACACATTTCCAGTTTA
65 CTACAGTCTTACACATTTCCAGGTAA
* * * *
55743194 G-TGCCGTAGTATCTTTCAACTATAGTCTTATTCAT-TCCGATTTAATATCATAGTATCTTTCAA
1 GATGCCATA-TATCTTTCAACTATGGTCTTATTCATATCAGATTTAATACCATAGTATCTTTCAA
* * * *
55743257 CTATAGTCTTTCTCATTT-CGGGTAA
65 CTACAGTCTTACACATTTCCAGGTAA
*
55743282 GATGCCATGATATGTTTCAA-TCATGGTCTT
1 GATGCCAT-ATATCTTTCAACT-ATGGTCTT
55743312 TCTCGTTTCT
Statistics
Matches: 98, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
88 6 0.06
89 61 0.62
90 30 0.31
91 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (90 bp):
GATGCCATATATCTTTCAACTATGGTCTTATTCATATCAGATTTAATACCATAGTATCTTTCAAC
TACAGTCTTACACATTTCCAGGTAA
Found at i:55757266 original size:3 final size:3
Alignment explanation
Indices: 55757258--55757287 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
55757248 TGTTGAAATC
55757258 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
55757288 AGTTGAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:55760337 original size:6 final size:6
Alignment explanation
Indices: 55760326--55760354 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
55760316 ACCCCATAGT
55760326 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
55760355 TATGTCCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:55761910 original size:77 final size:77
Alignment explanation
Indices: 55761782--55761937 Score: 242
Period size: 77 Copynumber: 2.0 Consensus size: 77
55761772 ATATAATTTA
* * *
55761782 ATTTTATCAATGAAGCCTTGGTTGTGTTTACAAGGTTAAGGCCCTCAAACTTTCATAGTCTATAT
1 ATTTTATCAATGAAGCATTAGTTGTGTTTACAAGATTAAGGCCCTCAAACTTTCATAGTCTATAT
55761847 TTGAGGCTCGCC
66 TTGAGGCTCGCC
* *
55761859 ATTTTATCAATGATGCATTAGTTGTGTTTACAAGATTAAGGCCC-CGTAACTTTCATAGTCTATA
1 ATTTTATCAATGAAGCATTAGTTGTGTTTACAAGATTAAGGCCCTC-AAACTTTCATAGTCTATA
*
55761923 TTTGAGTCTCGCC
65 TTTGAGGCTCGCC
55761936 AT
1 AT
55761938 GCACAAATGA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
76 1 0.01
77 71 0.99
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (77 bp):
ATTTTATCAATGAAGCATTAGTTGTGTTTACAAGATTAAGGCCCTCAAACTTTCATAGTCTATAT
TTGAGGCTCGCC
Found at i:55772952 original size:11 final size:11
Alignment explanation
Indices: 55772919--55772962 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
55772909 TAAAATGTCT
*
55772919 TAATAAAATAT
1 TAATAAAATAA
*
55772930 TATCTAAAATAA
1 TA-ATAAAATAA
*
55772942 TAATTAAATAA
1 TAATAAAATAA
55772953 TAATAAAATA
1 TAATAAAATA
55772963 TCACCAACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:55777448 original size:26 final size:25
Alignment explanation
Indices: 55777402--55777451 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
55777392 AGAGATACTA
*
55777402 CAAACTTTATTTTGGGAAAGGATGG
1 CAAACTTGATTTTGGGAAAGGATGG
55777427 CAAACTTCGATTTATGGG-AAGGATG
1 CAAACTT-GATTT-TGGGAAAGGATG
55777452 TATGTTCCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 11 0.50
27 4 0.18
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.30
Consensus pattern (25 bp):
CAAACTTGATTTTGGGAAAGGATGG
Found at i:55781509 original size:20 final size:20
Alignment explanation
Indices: 55781484--55781527 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
55781474 TCTCTCGTAG
55781484 GCATGAGTTCTTTCAATCCA
1 GCATGAGTTCTTTCAATCCA
55781504 GCATGAGTTCTTTCAATCCA
1 GCATGAGTTCTTTCAATCCA
55781524 GCAT
1 GCAT
55781528 AAGTGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (20 bp):
GCATGAGTTCTTTCAATCCA
Found at i:55787862 original size:31 final size:32
Alignment explanation
Indices: 55787827--55787892 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 32
55787817 TATATTTTGA
* * *
55787827 TCACTGAATTATTTAAAAA-TTTTTATTTAAG
1 TCACTAAACTATTCAAAAATTTTTTATTTAAG
55787858 TCACTAAACTATTCAAAAATTGTTTTTATTTAAG
1 TCACTAAACTATTCAAAAA-T-TTTTTATTTAAG
55787892 T
1 T
55787893 TATTGAGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 16 0.55
34 13 0.45
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (32 bp):
TCACTAAACTATTCAAAAATTTTTTATTTAAG
Found at i:55795574 original size:52 final size:53
Alignment explanation
Indices: 55795495--55795710 Score: 217
Period size: 52 Copynumber: 4.0 Consensus size: 53
55795485 ATAAATTTGA
* *
55795495 AAAAAAAGTTTTTGGGGTTCGGAGGAAGTAAAAGTTTT-GGGAGAAAGCAAAAGG
1 AAAAAAA--TTTTGGGGTTTGGGGGAAGTAAAAGTTTTAGGGAGAAAGCAAAAGG
* *
55795549 AAAAAAAATTTGGGAGTTT-GGGGAAGTAAAAGTTTTAGGGAGAAAGTAAAAGG
1 AAAAAAATTTTGGG-GTTTGGGGGAAGTAAAAGTTTTAGGGAGAAAGCAAAAGG
* * * *
55795602 -AAAAATTTTTAGGGGTTTGGGGGAAGTAAAACTTTT-GAGG-GAAATCAAAAAG
1 AAAAAAATTTT-GGGGTTTGGGGGAAGTAAAAGTTTTAG-GGAGAAAGCAAAAGG
** * *
55795654 AAAAAAAGTTTTTGGGGATTTGGGGGAAGTAAATTTTTTAGGGAAAAAGTAAAAGG
1 AAAAAAA--TTTTGGGG-TTTGGGGGAAGTAAAAGTTTTAGGGAGAAAGCAAAAGG
55795710 A
1 A
55795711 TTTGAGGGGT
Statistics
Matches: 134, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
52 44 0.33
53 44 0.33
54 11 0.08
55 25 0.19
56 10 0.07
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.25
Consensus pattern (53 bp):
AAAAAAATTTTGGGGTTTGGGGGAAGTAAAAGTTTTAGGGAGAAAGCAAAAGG
Found at i:55797189 original size:15 final size:16
Alignment explanation
Indices: 55797169--55797214 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
55797159 AAAATATCAA
55797169 TTAAAA-ATATAATTT
1 TTAAAATATATAATTT
* *
55797184 TTAAAATTTATTATTT
1 TTAAAATATATAATTT
55797200 TTAAAATAGTATAAT
1 TTAAAATA-TATAAT
55797215 GGGTTTTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 6 0.24
16 14 0.56
17 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTAAAATATATAATTT
Found at i:55798400 original size:21 final size:21
Alignment explanation
Indices: 55798342--55798403 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
55798332 ATTTGTATAG
* *
55798342 TATTTTTAAGTTATTTAAAAT
1 TATTTTGAATTTATTTAAAAT
* ** *
55798363 GATTATTGAATAAATTTAAATT
1 TATT-TTGAATTTATTTAAAAT
55798385 TATTTTGAATTTATTTAAA
1 TATTTTGAATTTATTTAAA
55798404 GTTAATTATT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (21 bp):
TATTTTGAATTTATTTAAAAT
Found at i:55801601 original size:21 final size:21
Alignment explanation
Indices: 55801575--55801615 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
55801565 ATCTGCTCAA
* *
55801575 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
*
55801596 ACTCCATCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
55801616 TAGCTCGTCT
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:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:55804966 original size:19 final size:20
Alignment explanation
Indices: 55804907--55804968 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
55804897 ATTTTTTAAA
*
55804907 ATTTTAAAATTTATTATTATT
1 ATTTTAAAATTTTTTA-TATT
*
55804928 ATTTTAATTTAATATTTTATATT
1 ATTTTAA---AATTTTTTATATT
55804951 -TTTTAAAATTTTTTATAT
1 ATTTTAAAATTTTTTATAT
55804969 AGTCATCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 11 0.31
21 7 0.20
22 6 0.17
23 4 0.11
24 7 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTAAAATTTTTTATATT
Found at i:55815247 original size:18 final size:18
Alignment explanation
Indices: 55815213--55815247 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55815203 CATGGTGGAA
*
55815213 TAAATTTTATATGTTTTC
1 TAAATTTTATATATTTTC
*
55815231 TAAATTTTATGTATTTT
1 TAAATTTTATATATTTT
55815248 TTATTTTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (18 bp):
TAAATTTTATATATTTTC
Found at i:55825473 original size:17 final size:18
Alignment explanation
Indices: 55825453--55825487 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
55825443 TATGTTTCTA
55825453 AATAAATTT-TAAAATAC
1 AATAAATTTATAAAATAC
*
55825470 AATAATTTTATAAAATAC
1 AATAAATTTATAAAATAC
55825488 TCTAACATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAATTTATAAAATAC
Found at i:55825966 original size:22 final size:21
Alignment explanation
Indices: 55825914--55825953 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
55825904 GGCAAAGAGT
55825914 AAATTAATC-ATTTTTATTAA
1 AAATTAATCTATTTTTATTAA
*
55825934 AAATTTCATCTATTTTTATT
1 AAA-TTAATCTATTTTTATT
55825954 GTAAAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 5 0.29
22 9 0.53
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
AAATTAATCTATTTTTATTAA
Found at i:55831517 original size:21 final size:22
Alignment explanation
Indices: 55831486--55831527 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
55831476 TGAATTCGTA
* *
55831486 AGAATATAATAGGAAGATATAC
1 AGAATATAATAGAAAAATATAC
55831508 AGAAT-TAATAGAAAAATATA
1 AGAATATAATAGAAAAATATA
55831528 TTAATTATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.60, C:0.02, G:0.14, T:0.24
Consensus pattern (22 bp):
AGAATATAATAGAAAAATATAC
Found at i:55832791 original size:21 final size:20
Alignment explanation
Indices: 55832766--55832822 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
55832756 ATTAAAATAG
55832766 AAAAATTAT-AAATAATCATTA
1 AAAAATTATAAAATAAT-A-TA
*
55832787 AAAAATTCTAAAATAATAT-
1 AAAAATTATAAAATAATATA
*
55832806 AAAAATTACAAAA-AATA
1 AAAAATTATAAAATAATA
55832823 CACATTCAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 4 0.12
19 11 0.34
20 1 0.03
21 9 0.28
22 7 0.22
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATTATAAAATAATATA
Found at i:55832800 original size:22 final size:19
Alignment explanation
Indices: 55832766--55832810 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 19
55832756 ATTAAAATAG
55832766 AAAAATTATAAATAATCATTA
1 AAAAATTATAAATAAT-A-TA
*
55832787 AAAAATTCTAAAATAATATA
1 AAAAATTAT-AAATAATATA
55832807 AAAA
1 AAAA
55832811 TTACAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 9 0.41
22 7 0.32
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATTATAAATAATATA
Found at i:55838475 original size:13 final size:13
Alignment explanation
Indices: 55838457--55838484 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55838447 ATAAAATTGG
55838457 AAAGATGAAAAAT
1 AAAGATGAAAAAT
55838470 AAAGATGAAAAAT
1 AAAGATGAAAAAT
55838483 AA
1 AA
55838485 TAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAGATGAAAAAT
Found at i:55839527 original size:26 final size:26
Alignment explanation
Indices: 55839497--55839571 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
55839487 ACAGTTCTTA
*
55839497 TGAGCATCCCGA-TATATGGCTCTTCG
1 TGAGCATCCCGATTA-AAGGCTCTTCG
* *
55839523 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCATCCCGATTAAAGGCTCTTCG
* ** *
55839549 TGAGCTTCTTGATTAATGGCTCT
1 TGAGCATCCCGATTAAAGGCTCT
55839572 CCGGAGCTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 40 0.95
27 2 0.05
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36
Consensus pattern (26 bp):
TGAGCATCCCGATTAAAGGCTCTTCG
Found at i:55842722 original size:18 final size:17
Alignment explanation
Indices: 55842699--55842732 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
55842689 TATTTCGATA
55842699 TTTTAATAAAATGTAATC
1 TTTTAA-AAAATGTAATC
*
55842717 TTTTAAACAATGTAAT
1 TTTTAAAAAATGTAAT
55842733 GTGATTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (17 bp):
TTTTAAAAAATGTAATC
Found at i:55842812 original size:11 final size:11
Alignment explanation
Indices: 55842794--55842826 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
55842784 TACACCAATG
55842794 AATAACAAACA
1 AATAACAAACA
*
55842805 ATTAACAAACA
1 AATAACAAACA
55842816 AAT-ACAAACA
1 AATAACAAACA
55842826 A
1 A
55842827 GCATAGCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.70, C:0.18, G:0.00, T:0.12
Consensus pattern (11 bp):
AATAACAAACA
Found at i:55850322 original size:2 final size:2
Alignment explanation
Indices: 55850315--55850344 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
55850305 CATGGTTCCA
55850315 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55850345 AAGTTGCAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55850336 original size:13 final size:13
Alignment explanation
Indices: 55850318--55850343 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55850308 GGTTCCAATA
55850318 TATATATATATAT
1 TATATATATATAT
55850331 TATATATATATAT
1 TATATATATATAT
55850344 AAAGTTGCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:55850336 original size:15 final size:15
Alignment explanation
Indices: 55850316--55850344 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55850306 ATGGTTCCAA
55850316 TATATATATATATAT
1 TATATATATATATAT
55850331 TATATATATATATA
1 TATATATATATATA
55850345 AAGTTGCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:55855255 original size:32 final size:30
Alignment explanation
Indices: 55855215--55855275 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 30
55855205 TTTAATTAAT
55855215 TTTTTAAAT-TATTTTAAAATCATAAAAAAATA
1 TTTTTAAATAT-TTTTAAAAT--TAAAAAAATA
55855247 TTTTTAAATATTTTTAAAATTAAAAAAAT
1 TTTTTAAATATTTTTAAAATTAAAAAAAT
55855276 TTAGTAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 9 0.32
32 18 0.64
33 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (30 bp):
TTTTTAAATATTTTTAAAATTAAAAAAATA
Found at i:55859929 original size:18 final size:17
Alignment explanation
Indices: 55859902--55859946 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
55859892 ATATTTAGTT
*
55859902 ATTTATTTTTTTAATTTA
1 ATTTAATTTTTT-ATTTA
*
55859920 ATTTAATTTTTTATTTT
1 ATTTAATTTTTTATTTA
55859937 ATTT-ATTTTT
1 ATTTAATTTTT
55859947 ATACATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 6 0.24
17 8 0.32
18 11 0.44
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTAATTTTTTATTTA
Found at i:55861780 original size:43 final size:43
Alignment explanation
Indices: 55861672--55861811 Score: 113
Period size: 43 Copynumber: 3.3 Consensus size: 43
55861662 TTTGGTTTAT
* * * * * *
55861672 CCGATGATGCACTATGCATGCCAATATAATTGGCCT-GGTTTGT
1 CCGATGATGCACTATGTATGCTAGTATAATT-GCTTCAGTTTGC
* * *
55861715 CCAATGATGCACCT-CGTGTGCTAGTATAATTGCTTCAGTTTGC
1 CCGATGATGCA-CTATGTATGCTAGTATAATTGCTTCAGTTTGC
* ** * * *
55861758 CCGATGATGCACTATGTTTGCTAGTATCTTTCCTTCAGTATAC
1 CCGATGATGCACTATGTATGCTAGTATAATTGCTTCAGTTTGC
55861801 CCGATGATGCA
1 CCGATGATGCA
55861812 TTGCAATTCC
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
42 5 0.06
43 70 0.91
44 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (43 bp):
CCGATGATGCACTATGTATGCTAGTATAATTGCTTCAGTTTGC
Found at i:55863846 original size:18 final size:18
Alignment explanation
Indices: 55863823--55863863 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
55863813 AGTTTAGAGT
55863823 TTATTTTTCTACAT-TTGC
1 TTATTTTTCTACATGTT-C
*
55863841 TTATTTTTCTTCATGTTC
1 TTATTTTTCTACATGTTC
55863859 TTATT
1 TTATT
55863864 GTTAGTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (18 bp):
TTATTTTTCTACATGTTC
Found at i:55869819 original size:48 final size:48
Alignment explanation
Indices: 55869763--55869856 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
55869753 AGGGAATTCT
* *
55869763 GTTGAATCCTTTATTGTTGCG-AGTT-GAGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCTTTATCGGTG-GAAGTTAG-GCTGACTTAGGCGTTTTTACG
55869811 GTTGAATCCTTTATCGGTGGAAGTTAGGCTGACTTAGGCGTTTTTA
1 GTTGAATCCTTTATCGGTGGAAGTTAGGCTGACTTAGGCGTTTTTA
55869857 AGCCAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 1 0.02
48 40 0.95
49 1 0.02
ACGTcount: A:0.18, C:0.14, G:0.28, T:0.40
Consensus pattern (48 bp):
GTTGAATCCTTTATCGGTGGAAGTTAGGCTGACTTAGGCGTTTTTACG
Found at i:55872566 original size:132 final size:132
Alignment explanation
Indices: 55872327--55872845 Score: 582
Period size: 132 Copynumber: 3.9 Consensus size: 132
55872317 ACTTTATTTT
* * * * * **
55872327 ATGAACAAATTTTATTTGAGTTAGCTGATCTCATATTGCAAC-TCTTAATAGCTCGCTGGTTTAA
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAGATCGCAACTTC-AAACAGCTCGCTAATTTAA
* ** ** * *
55872391 TATTGCAACTGATATTGTTAAGGTTCGTTAATTTAATATTGCAACCTAAGTTCATTCGGTTTAAG
65 GATCACAACTGATATTGTTAAGGTTCACTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAG
55872456 ATC
130 ATC
* *
55872459 AAGAACAAATTTTATTTGAGTTAGTTGATC-CAAGATCGCAACTTCAAACAGCTTGCTAATTTAA
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTC-AGATCGCAACTTCAAACAGCTCGCTAATTTAA
* *
55872523 GATCGCAACTGATATTGTTAAGGTTCACTGATTTAAGATTGCAACCTAAGTTCATTCGATTTAAG
65 GATCACAACTGATATTGTTAAGGTTCACTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAG
*
55872588 ACC
130 ATC
* * * * *
55872591 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAGATCGCAACTCCGAACAACTTGCTAATTTAAT
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAGATCGCAACTTCAAACAGCTCGCTAATTTAAG
* * * *
55872656 ATCACAGCTGATGTTGTTAAGGTT-AGCTGATTTAATATCGCAACCTAAGTTCATTCAATTTAAG
66 ATCACAACTGATATTGTTAAGGTTCA-CTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAG
*
55872720 ATT
130 ATC
* * * *
55872723 GTGAACAAATTTTATTTGAGTTAGTTGATCTTAGATCGCAACTCTGAATA-A-CTCACTAATTTA
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAGATCGCAACT-TCAA-ACAGCTCGCTAATTTA
* * * * * * *
55872786 AGATCATAGCTAATATTGTTAAGGTTCGA-TGATTTAAGATCGTAACCTAAGCTCATTCGA
64 AGATCACAACTGATATTGTTAAGGTTC-ACTGATTTAATATTGCAACCTAAGTTCATTCGA
55872846 AATTTTATTT
Statistics
Matches: 334, Mismatches: 45, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
131 2 0.01
132 325 0.97
133 5 0.01
134 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (132 bp):
ATGAACAAATTTTATTTGAGTTAGTTGATCTCAGATCGCAACTTCAAACAGCTCGCTAATTTAAG
ATCACAACTGATATTGTTAAGGTTCACTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAGA
TC
Found at i:55872804 original size:264 final size:253
Alignment explanation
Indices: 55872327--55872993 Score: 769
Period size: 264 Copynumber: 2.6 Consensus size: 253
55872317 ACTTTATTTT
* * * ** * *
55872327 ATGAACAAATTTTATTTGAGTTAGCTGATCTCATATTGCAACTCTTAATAGCTCGCTGGTTTAAT
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAATCGCAACTCCAAACAGCTCGCTGATTTAAT
** * * *
55872392 ATTGCAACTGATATTGTTAAGGTTCGTTAATTTAATATTGCAACCTAAGTTCATTCGGTTTAAGA
66 ATCACAACTGATATTGTTAAGGTTCGCTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAGA
* **
55872457 TCAAGAACAAATTTTATTTGAGTTAGTTGATCCAAGATCGCAACTTCAAACAGCTTGCTAATTTA
131 TCATGAACAAATTTTATTTGAGTTAGTTGATCCAAGATCGCAACTTCAAACAGCTCACTAATTTA
* * *
55872522 AGATCGCAACTGATATTGTTAAGGTTC-ACTGATTTAAGATTGCAACCTAAGTTCATTCGATTTA
196 AGATCACAACTAATATTGTTAAGGTTCGA-TGATTTAAGATCGCAACCTAAG--C--TC-A-TT-
55872586 AGACC
253 ----C
* * * * *
55872591 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAGATCGCAACTCCGAACAACTTGCTAATTTAAT
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAATCGCAACTCCAAACAGCTCGCTGATTTAAT
* * * * *
55872656 ATCACAGCTGATGTTGTTAAGGTTAGCTGATTTAATATCGCAACCTAAGTTCATTCAATTTAAGA
66 ATCACAACTGATATTGTTAAGGTTCGCTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAGA
** ** *
55872721 TTGTGAACAAATTTTATTTGAGTTAGTTGATCTTAGATCGCAACTCTGAATA-A-CTCACTAATT
131 TCATGAACAAATTTTATTTGAGTTAGTTGATCCAAGATCGCAACT-TCAA-ACAGCTCACTAATT
* * *
55872784 TAAGATCATAGCTAATATTGTTAAGGTTCGATGATTTAAGATCGTAACCTAAGCTCATTC
194 TAAGATCACAACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTC
55872844 --G---AAATTTTATTTGAGTTAGTTGATCTCAAATC-CTAACTCCAAACAGCTCGCTGATTTAA
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAATCGC-AACTCCAAACAGCTCGCTGATTTAA
* * *
55872903 GATCATAACTGATATTGTTAAGTTTCGCTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAG
65 TATCACAACTGATATTGTTAAGGTTCGCTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAG
*
55872968 ATCATGATCAAA-TTTATTTGAGTTAG
130 ATCATGAACAAATTTTATTTGAGTTAG
55872994 CTAATTTAAT
Statistics
Matches: 349, Mismatches: 50, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
247 15 0.04
248 117 0.34
251 1 0.00
253 1 0.00
258 2 0.01
259 1 0.00
260 2 0.01
262 1 0.00
264 203 0.58
265 5 0.01
266 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (253 bp):
ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAATCGCAACTCCAAACAGCTCGCTGATTTAAT
ATCACAACTGATATTGTTAAGGTTCGCTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAGA
TCATGAACAAATTTTATTTGAGTTAGTTGATCCAAGATCGCAACTTCAAACAGCTCACTAATTTA
AGATCACAACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTC
Found at i:55872935 original size:116 final size:116
Alignment explanation
Indices: 55872729--55872961 Score: 306
Period size: 116 Copynumber: 2.0 Consensus size: 116
55872719 GATTGTGAAC
* * ** *
55872729 AAATTTTATTTGAGTTAGTTGATCTTAGATCGCAACTCTGAATAACTCACTAATTTAAGATCATA
1 AAATTTTATTTGAGTTAGTTGATCTCAAATCGCAACTCCAAACAACTCACTAATTTAAGATCATA
* *
55872794 GCTAATATTGTTAAGGTTCGATGATTTAAGATCGTAACCTAAGCTCATTCG
66 ACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTCG
* * *
55872845 AAATTTTATTTGAGTTAGTTGATCTCAAATC-CTAACTCCAAACAGCTCGCTGATTTAAGATCAT
1 AAATTTTATTTGAGTTAGTTGATCTCAAATCGC-AACTCCAAACAACTCACTAATTTAAGATCAT
* * * * * *
55872909 AACTGATATTGTTAAGTTTCGCTGATTTAATATTGCAACCTAAGTTCATTCG
65 AACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTCG
55872961 A
1 A
55872962 TTTAAGATCA
Statistics
Matches: 100, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
115 1 0.01
116 99 0.99
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (116 bp):
AAATTTTATTTGAGTTAGTTGATCTCAAATCGCAACTCCAAACAACTCACTAATTTAAGATCATA
ACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTCG
Found at i:55880984 original size:46 final size:46
Alignment explanation
Indices: 55880909--55881173 Score: 260
Period size: 46 Copynumber: 5.7 Consensus size: 46
55880899 TACCCTGTTT
55880909 TGGACAGCATTTATACATCAAATTGGACAGCATTAATATGCTCAAAA
1 TGGACAGCA-TTATACATCAAATTGGACAGCATTAATATGCTCAAAA
* * *
55880956 TGGATAGCATTATACATCAAATTAGACAGCATCAATATGCTCAAAA
1 TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAA
* *
55881002 TGGACAGCATTATACATCAAATTGGACAGCTTTAATATGCTCAAAT
1 TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAA
* *
55881048 TGGACAGCTTTAATATGC-TCAAATTGGACAGCATT-ATA--CATCAAAT
1 TGGACAGCATT-ATA--CATCAAATTGGACAGCATTAATATGC-TCAAAA
* * *
55881094 TGGACAGCATCAATATGC-TCAAAATGGACAGCATT-ATA--CATCAAAT
1 TGGACAGCAT---TATACATCAAATTGGACAGCATTAATATGC-TCAAAA
*
55881140 TGGACAGCATTAATATGC-TCAAATTAGACAGCAT
1 TGGACAGCATT-ATA--CATCAAATTGGACAGCAT
55881174 CATAACATAT
Statistics
Matches: 192, Mismatches: 16, Indels: 21
0.84 0.07 0.09
Matches are distributed among these distances:
43 1 0.01
44 2 0.01
45 1 0.01
46 154 0.80
47 14 0.07
48 18 0.09
49 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.28
Consensus pattern (46 bp):
TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAA
Found at i:55881068 original size:116 final size:116
Alignment explanation
Indices: 55880908--55881173 Score: 446
Period size: 116 Copynumber: 2.3 Consensus size: 116
55880898 CTACCCTGTT
* *
55880908 TTGGACAGCATT--TATACATCAAATTGGACAGCATTAATATGCTCAAAATGGATAGCATTATAC
1 TTGGACAGCATTAATATGC-TCAAATTGGACAGCATTAATATGCTCAAAATGGACAGCATTATAC
55880971 ATCAAATTAGACAGCATCAATATGCTCAAAATGGACAGCATTATACATCAAA
65 ATCAAATTAGACAGCATCAATATGCTCAAAATGGACAGCATTATACATCAAA
* * *
55881023 TTGGACAGCTTTAATATGCTCAAATTGGACAGCTTTAATATGCTCAAATTGGACAGCATTATACA
1 TTGGACAGCATTAATATGCTCAAATTGGACAGCATTAATATGCTCAAAATGGACAGCATTATACA
*
55881088 TCAAATTGGACAGCATCAATATGCTCAAAATGGACAGCATTATACATCAAA
66 TCAAATTAGACAGCATCAATATGCTCAAAATGGACAGCATTATACATCAAA
*
55881139 TTGGACAGCATTAATATGCTCAAATTAGACAGCAT
1 TTGGACAGCATTAATATGCTCAAATTGGACAGCAT
55881174 CATAACATAT
Statistics
Matches: 140, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
115 11 0.08
116 125 0.89
117 4 0.03
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (116 bp):
TTGGACAGCATTAATATGCTCAAATTGGACAGCATTAATATGCTCAAAATGGACAGCATTATACA
TCAAATTAGACAGCATCAATATGCTCAAAATGGACAGCATTATACATCAAA
Found at i:55881174 original size:70 final size:67
Alignment explanation
Indices: 55880908--55881175 Score: 258
Period size: 70 Copynumber: 3.8 Consensus size: 67
55880898 CTACCCTGTT
* *
55880908 TTGGACAGCATTTATACATCAAATTGGACAGCATTAATATGC-TCAAAATGGATAGCAT---TAT
1 TTGGACAGCA-TTATAC-TCAAATTGGACAGCATT-ATA--CATCAAATTGGACAGCATCAATAT
*
55880969 ACATCAAA
61 GC-TCAAA
* * * * *
55880977 TTAGACAGCATCAATATGCTCAAAATGGACAGCATTATACATCAAATTGGACAGCTTTAATATGC
1 TTGGACAGCAT---TATACTCAAATTGGACAGCATTATACATCAAATTGGACAGCATCAATATGC
55881042 TCAAA
63 TCAAA
*
55881047 TTGGACAGCTTTAATATGCTCAAATTGGACAGCATTATACATCAAATTGGACAGCATCAATATGC
1 TTGGACAGCATT-ATA--CTCAAATTGGACAGCATTATACATCAAATTGGACAGCATCAATATGC
55881112 TCAAA
63 TCAAA
* *
55881117 ATGGACAGCATTATACATCAAATTGGACAGCATTAATATGC-TCAAATTAGACAGCATCA
1 TTGGACAGCATTATAC-TCAAATTGGACAGCATT-ATA--CATCAAATTGGACAGCATCA
55881176 TAACATATAA
Statistics
Matches: 169, Mismatches: 16, Indels: 27
0.80 0.08 0.13
Matches are distributed among these distances:
67 3 0.02
68 33 0.20
69 18 0.11
70 106 0.63
71 9 0.05
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.28
Consensus pattern (67 bp):
TTGGACAGCATTATACTCAAATTGGACAGCATTATACATCAAATTGGACAGCATCAATATGCTCA
AA
Found at i:55881356 original size:16 final size:18
Alignment explanation
Indices: 55881321--55881358 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
55881311 TGGACATCTT
55881321 TATTATCACACAATTATA
1 TATTATCACACAATTATA
55881339 TATTATCACACAATTATA
1 TATTATCACACAATTATA
55881357 TA
1 TA
55881359 CTATATAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (18 bp):
TATTATCACACAATTATA
Found at i:55881935 original size:41 final size:40
Alignment explanation
Indices: 55881865--55882014 Score: 124
Period size: 41 Copynumber: 3.7 Consensus size: 40
55881855 CAATGTTTTG
* * *
55881865 TACACTAATTGCCATTGCATAGCCGAAGCTATTATAATCTCA
1 TACACTAAGTGCC-TTACATAGCCGAAGCTATT-CAATCTCA
* * *
55881907 TACACTAAGTGCCTTACATAACCGAAGCTATCTCAGTCTCG
1 TACACTAAGTGCCTTACATAGCCGAAGCTAT-TCAATCTCA
* * * *
55881948 CACACTAAGTGCCATATATAGCCGAAGCTATTCCAAATCGC-
1 TACACTAAGTGCCTTACATAGCCGAAGCTATT-C-AATCTCA
** *
55881989 -ACACTAAGTGCAATAAATAGCCGAAG
1 TACACTAAGTGCCTTACATAGCCGAAG
55882015 TCTCGTGTAT
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 25 0.27
41 49 0.54
42 17 0.19
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.25
Consensus pattern (40 bp):
TACACTAAGTGCCTTACATAGCCGAAGCTATTCAATCTCA
Found at i:55885252 original size:12 final size:12
Alignment explanation
Indices: 55885249--55885281 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
55885239 TTTTATCTTG
55885249 TTTTATTTTATT
1 TTTTATTTTATT
55885261 TTTTATTTTATT
1 TTTTATTTTATT
55885273 TTTTATTTT
1 TTTTATTTT
55885282 TAAACTAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:55885269 original size:17 final size:17
Alignment explanation
Indices: 55885237--55885281 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
55885227 TTTTTTTTGT
* *
55885237 TTTTTTATCTTGTTTTA
1 TTTTTTATTTTATTTTA
55885254 TTTTATT-TTTTATTTTA
1 TTTT-TTATTTTATTTTA
55885271 TTTTTTATTTT
1 TTTTTTATTTT
55885282 TAAACTAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTTTTATTTTATTTTA
Found at i:55886137 original size:26 final size:24
Alignment explanation
Indices: 55886107--55886165 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
55886097 TACATCCTTG
55886107 ATATATAC-TTTATAATTTATATATAC
1 ATATATACATTT-TAA-TT-TATATAC
* *
55886133 ATATACACATTTTAATTTATGTAC
1 ATATATACATTTTAATTTATATAC
55886157 ATATATACA
1 ATATATACA
55886166 CATATTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 14 0.48
25 2 0.07
26 10 0.34
27 3 0.10
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (24 bp):
ATATATACATTTTAATTTATATAC
Found at i:55886166 original size:26 final size:26
Alignment explanation
Indices: 55886119--55886168 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
55886109 ATATACTTTA
*
55886119 TAATTTATATATACATATACACATTT
1 TAATTTATATACACATATACACATTT
* *
55886145 TAATTTATGTACATATATACACAT
1 TAATTTATATACACATATACACAT
55886169 ATTTTCATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATTTATATACACATATACACATTT
Found at i:55886259 original size:22 final size:21
Alignment explanation
Indices: 55886234--55886282 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
55886224 AATCCATAAT
*
55886234 TTTCTTATGTATATATTTTATA
1 TTTCTTATATATAT-TTTTATA
*
55886256 TTTCATATATATATTTTTATA
1 TTTCTTATATATATTTTTATA
55886277 TATTCT
1 T-TTCT
55886283 ACAATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTCTTATATATATTTTTATA
Found at i:55886289 original size:22 final size:22
Alignment explanation
Indices: 55886243--55886293 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
55886233 TTTTCTTATG
*
55886243 TATATATTTTATATTTCATATA
1 TATATATTTTATATTTCATAAA
55886265 TATAT-TTTTATATATTC-TACAA
1 TATATATTTTATAT-TTCATA-AA
55886287 TATATAT
1 TATATAT
55886294 ATACATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 10 0.40
22 14 0.56
23 1 0.04
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATATTTTATATTTCATAAA
Found at i:55888929 original size:20 final size:20
Alignment explanation
Indices: 55888904--55888945 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
55888894 TAGTGGCATT
55888904 TCGCGATATTCATTTTAACA
1 TCGCGATATTCATTTTAACA
55888924 TCGCGATATTCATTTTAACA
1 TCGCGATATTCATTTTAACA
55888944 TC
1 TC
55888946 CGTTTTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (20 bp):
TCGCGATATTCATTTTAACA
Found at i:55891276 original size:10 final size:10
Alignment explanation
Indices: 55891261--55891331 Score: 60
Period size: 10 Copynumber: 7.2 Consensus size: 10
55891251 AAAAAATAAG
55891261 AAGAAAAAGA
1 AAGAAAAAGA
*
55891271 AAGAAAAACA
1 AAGAAAAAGA
*
55891281 AGGAAAAA-A
1 AAGAAAAAGA
55891290 GAA-AAAAAGA
1 -AAGAAAAAGA
55891300 AA-AGAAAAG-
1 AAGA-AAAAGA
55891309 AAGAAAAAGAA
1 AAGAAAAAG-A
*
55891320 AAGAAAAGGA
1 AAGAAAAAGA
55891330 AA
1 AA
55891332 AAGGAGAGGC
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
9 16 0.31
10 27 0.53
11 8 0.16
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:55891302 original size:5 final size:5
Alignment explanation
Indices: 55891286--55891332 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
55891276 AAACAAGGAA
*
55891286 AAAAG -AAA- AAAAG AAAAG AAAAG AAGA- AAAAG AAAAG AAAAGG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA-G AAAA
55891333 AGGAGAGGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
4 9 0.25
5 22 0.61
6 5 0.14
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:55891317 original size:19 final size:18
Alignment explanation
Indices: 55891265--55891333 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 18
55891255 AATAAGAAGA
55891265 AAAAG-AAAGAAAAACAAG
1 AAAAGAAAAGAAAAA-AAG
*
55891283 -GAA-AAAAGAAAAAAAG
1 AAAAGAAAAGAAAAAAAG
55891299 AAAAGAAAAGAAGAAAAAG
1 AAAAGAAAAGAA-AAAAAG
55891318 AAAAGAAAAGGAAAAA
1 AAAAGAAAA-GAAAAA
55891334 GGAGAGGCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.07
17 13 0.30
18 7 0.16
19 18 0.41
20 3 0.07
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAAAAAAG
Found at i:55891322 original size:14 final size:14
Alignment explanation
Indices: 55891285--55891324 Score: 64
Period size: 13 Copynumber: 2.9 Consensus size: 14
55891275 AAAACAAGGA
*
55891285 AAAAAGAAAAAAAG
1 AAAAAGAAAAGAAG
55891299 -AAAAGAAAAGAAG
1 AAAAAGAAAAGAAG
55891312 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
55891325 AAGGAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAGAAG
Found at i:55891768 original size:97 final size:97
Alignment explanation
Indices: 55891602--55891889 Score: 445
Period size: 97 Copynumber: 3.0 Consensus size: 97
55891592 ATTCATTTCG
*
55891602 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGTTGTGCTCTCAATAAAATTT
* *
55891667 CATCTTATCTATTGTAATAATCTTTTTCATCT
66 CATCTTATCCATTGTGATAATCTTTTTCATCT
*
55891699 TATCTTAGCAAAATTTGCTATCTTGATTGATTTATTCATTTCGAGTTGTGCTCTCAATAAAATTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGTTGTGCTCTCAATAAAATTT
55891764 CATCTTATCCATTGTGATAATCTTTTTCATCT
66 CATCTTATCCATTGTGATAATCTTTTTCATCT
* * * ** *
55891796 TAT-TCTAGAAAAATTTACTATCTTCATTAATTTATTCATTTTAAGCTT-TGTTCTCAATAAAAT
1 TATCT-TAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAG-TTGTGCTCTCAATAAAAT
*
55891859 TTCATCTTGTCCATTGTGATAATCTTTTTCA
64 TTCATCTTATCCATTGTGATAATCTTTTTCA
55891890 AGCATTTTTC
Statistics
Matches: 177, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
96 1 0.01
97 174 0.98
98 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (97 bp):
TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGTTGTGCTCTCAATAAAATTT
CATCTTATCCATTGTGATAATCTTTTTCATCT
Found at i:55892736 original size:44 final size:44
Alignment explanation
Indices: 55892667--55892758 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
55892657 ACAGATCAAC
* * * *
55892667 GAAGTCACAAACCTTGTCTCTCTGAAGTTACAGTGGAGCAGGTT
1 GAAGTCACAAACCTTATCCCCCTGAAGTTACAGTGGAGCAAGTT
* ** *
55892711 GAAGTCACTAACCTTATCCCCCTGAAGTTGTAGTGGGGCAAGTT
1 GAAGTCACAAACCTTATCCCCCTGAAGTTACAGTGGAGCAAGTT
55892755 GAAG
1 GAAG
55892759 ATATGAGTCT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (44 bp):
GAAGTCACAAACCTTATCCCCCTGAAGTTACAGTGGAGCAAGTT
Found at i:55893025 original size:44 final size:44
Alignment explanation
Indices: 55892955--55893059 Score: 113
Period size: 44 Copynumber: 2.4 Consensus size: 44
55892945 TAGAAGCTAT
* * * *
55892955 AAATTACAAACCTTATCTCTTCAAAGTCGTAGTAGAGTAGGTTG
1 AAATAACAAACCTTATCTCTTCAAAGTCGCAGTAAAGCAGGTTG
* *
55892999 AAATAACAAACCTTGTCTC-TCTAAAGTTGCAGTAAAGCAGGTTG
1 AAATAACAAACCTTATCTCTTC-AAAGTCGCAGTAAAGCAGGTTG
* * *
55893043 AAGTCACTAACCTTATC
1 AAATAACAAACCTTATC
55893060 CCCCTGAAGT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 2 0.04
44 48 0.96
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (44 bp):
AAATAACAAACCTTATCTCTTCAAAGTCGCAGTAAAGCAGGTTG
Found at i:55893272 original size:139 final size:137
Alignment explanation
Indices: 55893101--55893381 Score: 366
Period size: 139 Copynumber: 2.0 Consensus size: 137
55893091 TATGAGTCCG
* ** * * * *
55893101 ATCTCCCTGAAGTTGTAGTGGAGCGGGTCAAAATGATGGATCTTATCCCTCTAAAGTTGCAGTAA
1 ATCTCCCTGAAGATGTAGTGGAGCGGACCAAAATAATGAATCCTATACCTCTAAAGTTGCAGTAA
* *
55893166 GTTGGATTAAATTTACCATGACAAGTCTTATCTCCCTAAAGTTGCAGTGGAACAGACTGAAGATA
66 GTTGGATTAAATTCACCATGACAAG--TTATCTCCCTAAAGTTGCAGTGGAACAGACTGAACATA
*
55893231 GCAGACCTT
129 GCAAACCTT
55893240 ATCTCCCTGACA-ATGTAGTGGAGCGGACCAAAATAATGAATCCTATACCTCTAAAGTTGCAGTA
1 ATCTCCCTGA-AGATGTAGTGGAGCGGACCAAAATAATGAATCCTATACCTCTAAAGTTGCAGTA
* * * * * * * *
55893304 GGTTGGATTAAATTCACCATGACAAGTTATCTCTCTGAAGTTGTAGTGGAGCAGATTGATCATAT
65 AGTTGGATTAAATTCACCATGACAAGTTATCTCCCTAAAGTTGCAGTGGAACAGACTGAACATAG
55893369 CAAACCTT
130 CAAACCTT
55893377 ATCTC
1 ATCTC
55893382 ACTAAGGTTG
Statistics
Matches: 123, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
137 43 0.35
139 79 0.64
140 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (137 bp):
ATCTCCCTGAAGATGTAGTGGAGCGGACCAAAATAATGAATCCTATACCTCTAAAGTTGCAGTAA
GTTGGATTAAATTCACCATGACAAGTTATCTCCCTAAAGTTGCAGTGGAACAGACTGAACATAGC
AAACCTT
Found at i:55894863 original size:16 final size:16
Alignment explanation
Indices: 55894842--55894878 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
55894832 TTCAAGACCG
55894842 TATGGGTTATTTGCGC
1 TATGGGTTATTTGCGC
55894858 TATGGGTTATTTGCGC
1 TATGGGTTATTTGCGC
55894874 TATGG
1 TATGG
55894879 ATCCCTCCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.14, C:0.11, G:0.32, T:0.43
Consensus pattern (16 bp):
TATGGGTTATTTGCGC
Found at i:55895133 original size:3 final size:3
Alignment explanation
Indices: 55895125--55895170 Score: 67
Period size: 3 Copynumber: 15.0 Consensus size: 3
55895115 TTTTGCTATC
55895125 ATT ATT ATT ATT ATT ATT ATT ATT ATT GA-T ATT ATT ATT ACTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT A-TT ATT
55895171 TATTTATACC
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 1 0.03
3 35 0.88
4 4 0.10
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:55895270 original size:26 final size:24
Alignment explanation
Indices: 55895241--55895299 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
55895231 CACTTTTTTT
55895241 ATATATAC-TTTATAATTTATATATAC
1 ATATATACATTT-TAA-TT-TATATAC
* *
55895267 ATATACACATTTTAATTTATGTAC
1 ATATATACATTTTAATTTATATAC
55895291 ATATATACA
1 ATATATACA
55895300 CATATTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 14 0.48
25 2 0.07
26 10 0.34
27 3 0.10
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (24 bp):
ATATATACATTTTAATTTATATAC
Found at i:55895300 original size:26 final size:27
Alignment explanation
Indices: 55895240--55895302 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
55895230 CCACTTTTTT
* *
55895240 TATATATAC-TTTATAATTTATATATA
1 TATATACACATTTATAATTTATATACA
* *
55895266 CATATACACATTT-TAATTTATGTACA
1 TATATACACATTTATAATTTATATACA
55895292 TATATACACAT
1 TATATACACAT
55895303 ATTTTCATAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 28 0.90
27 3 0.10
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (27 bp):
TATATACACATTTATAATTTATATACA
Done.