Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 168 of 279
Found at i:55794653 original size:46 final size:46
Alignment explanation
Indices: 55794586--55794752 Score: 208
Period size: 46 Copynumber: 3.6 Consensus size: 46
55794576 GCTCTCTGAA
**
55794586 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * * * *
55794632 ATGAAAAGAATAAGACCATGGTTGAGAGATACCATAGCAACATGGC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
** * * *
55794678 GGGAAGTGAATAAGACCATGGTTGAAAGATACCATGGCAGCGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
**
55794724 ATGAAATGTGTAAGACCATGGTTGAAAGA
1 ATGAAATGAATAAGACCATGGTTGAAAGA
55794753 GACAATGGTT
Statistics
Matches: 99, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 99 1.00
ACGTcount: A:0.39, C:0.13, G:0.28, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
Found at i:55794760 original size:16 final size:16
Alignment explanation
Indices: 55794736--55794768 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
55794726 GAAATGTGTA
*
55794736 AGACCATGGTTGAAAG
1 AGACAATGGTTGAAAG
55794752 AGACAATGGTTGAAAG
1 AGACAATGGTTGAAAG
55794768 A
1 A
55794769 TACCATAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.30, T:0.18
Consensus pattern (16 bp):
AGACAATGGTTGAAAG
Found at i:55794761 original size:62 final size:62
Alignment explanation
Indices: 55794690--55794814 Score: 169
Period size: 62 Copynumber: 2.0 Consensus size: 62
55794680 GAAGTGAATA
* * * * ****
55794690 AGACCATGGTTGAAAGATACCATGGCAGCGTGATATGAAATGTGTAAGACCATGGTTGAAAG
1 AGACAATGGTTGAAAGATACCATAGCAACGTGACATGAAAAAAATAAGACCATGGTTGAAAG
*
55794752 AGACAATGGTTGAAAGATACCATAGCAATGTGACATGAAAAAAATAAGACCATGGTTGAAAG
1 AGACAATGGTTGAAAGATACCATAGCAACGTGACATGAAAAAAATAAGACCATGGTTGAAAG
55794814 A
1 A
55794815 TACCATGGCA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.21
Consensus pattern (62 bp):
AGACAATGGTTGAAAGATACCATAGCAACGTGACATGAAAAAAATAAGACCATGGTTGAAAG
Found at i:55794809 original size:46 final size:45
Alignment explanation
Indices: 55794752--55794859 Score: 135
Period size: 46 Copynumber: 2.4 Consensus size: 45
55794742 TGGTTGAAAG
* **
55794752 AGACAATGGTTGAAAGATACCATAGCAATGTGACATGAAAAAAATA
1 AGACCATGGTTGAAAGATACCATAGCAACATGACA-GAAAAAAATA
* ***
55794798 AGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGGTA
1 AGACCATGGTTGAAAGATACCATAGCAACATGACAGAAAAAAATA
*
55794843 AGACCATAGTTGAAAGA
1 AGACCATGGTTGAAAGA
55794860 CATTATGGCA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
45 23 0.43
46 31 0.57
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.19
Consensus pattern (45 bp):
AGACCATGGTTGAAAGATACCATAGCAACATGACAGAAAAAAATA
Found at i:55799516 original size:18 final size:18
Alignment explanation
Indices: 55799489--55799528 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
55799479 TACATCATTC
*
55799489 TATTTGTTTTATT-TTTCA
1 TATTTATTTTATTATTT-A
55799507 TATTTATTTTATTATTTA
1 TATTTATTTTATTATTTA
55799525 TATT
1 TATT
55799529 CCAAGTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
TATTTATTTTATTATTTA
Found at i:55806267 original size:14 final size:14
Alignment explanation
Indices: 55806248--55806277 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55806238 TTATATCAAG
55806248 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
55806262 ACCAATCCAATTCA
1 ACCAATCCAAATCA
55806276 AC
1 AC
55806278 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:55817728 original size:12 final size:12
Alignment explanation
Indices: 55817713--55817743 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
55817703 TTCTCTTTTA
55817713 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
55817725 TTTTTCTTTCTC
1 TTTTTCTTTCCC
55817737 TTTTTCT
1 TTTTTCT
55817744 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:55817844 original size:16 final size:16
Alignment explanation
Indices: 55817823--55817853 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55817813 TTTATTATTT
55817823 TATTAACATAATATAA
1 TATTAACATAATATAA
*
55817839 TATTAATATAATATA
1 TATTAACATAATATA
55817854 TTAAAATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:55819028 original size:40 final size:41
Alignment explanation
Indices: 55818978--55819062 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
55818968 TATAACCACT
*
55818978 TTTTATTATA-TTTTCAATTTGTGTCTTGTTTTAAGAATTG
1 TTTTAGTATATTTTTCAATTTGTGTCTTGTTTTAAGAATTG
** * * *
55819018 TTTTAGTATATTTTTTTATTTGTTTCTTGTTTTAATATTTG
1 TTTTAGTATATTTTTCAATTTGTGTCTTGTTTTAAGAATTG
55819059 TTTT
1 TTTT
55819063 TATGTTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
40 9 0.24
41 29 0.76
ACGTcount: A:0.19, C:0.04, G:0.11, T:0.67
Consensus pattern (41 bp):
TTTTAGTATATTTTTCAATTTGTGTCTTGTTTTAAGAATTG
Found at i:55819594 original size:31 final size:31
Alignment explanation
Indices: 55819558--55819638 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 31
55819548 TCAAAAAGCC
55819558 TAATTAATCTTCTGAATTTTTTTTAAAACTT
1 TAATTAATCTTCTGAATTTTTTTTAAAACTT
* ** *
55819589 TAATTAGAAC-TCT-AA-AATTTTTAAAATTT
1 TAATTA-ATCTTCTGAATTTTTTTTAAAACTT
55819618 TAATTAATCTCTTCTGAATTT
1 TAATTAA--TCTTCTGAATTT
55819639 AATGATATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
28 1 0.03
29 17 0.46
30 3 0.08
31 12 0.32
32 4 0.11
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.51
Consensus pattern (31 bp):
TAATTAATCTTCTGAATTTTTTTTAAAACTT
Found at i:55834225 original size:47 final size:47
Alignment explanation
Indices: 55833918--55834224 Score: 492
Period size: 47 Copynumber: 6.5 Consensus size: 47
55833908 ATTTCCGTAC
*
55833918 AAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTTTAT
1 AAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTAT
55833965 AAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTAT
1 AAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTAT
55834012 AAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTAT
1 AAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTAT
*
55834059 AAGACCATATCTGGGATATGGCATCGGTGTGTTATATGCTACTGTAT
1 AAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTAT
*
55834106 AAGACCATATCTGGGATATGGCATCGGTGTGTTATATGCTACTGTAT
1 AAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTAT
* * * * * *
55834153 AAGACCATATCTGGGATATGACATCAGTGAGATATGTGATTAC-GTGT
1 AAGACCATATCTGGGATATGGCATCGGTGTGATATATG-CTACTGTAT
*
55834200 AAGACCATAGT-TGGGCTATGGCATC
1 AAGACCATA-TCTGGGATATGGCATC
55834225 ATTATGTAAA
Statistics
Matches: 247, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
47 243 0.98
48 4 0.02
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (47 bp):
AAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTAT
Found at i:55841163 original size:61 final size:62
Alignment explanation
Indices: 55841067--55841183 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 62
55841057 CAGAAAAAAC
* *
55841067 AATAAACTGTTTTAAATACTTACCACATGTCTATCAAAGATCAAAATACATGTCGATTGTCG
1 AATAAACTGTTTTAAATACTTACCACATGCCTATCAAAGAACAAAATACATGTCGATTGTCG
* * * * *
55841129 AATAAATTG-TTTAAATACTTACTACGTGCCTATCAAGGAACTAAATACATGTCGA
1 AATAAACTGTTTTAAATACTTACCACATGCCTATCAAAGAACAAAATACATGTCGA
55841184 ACATATATTC
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
61 40 0.83
62 8 0.17
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (62 bp):
AATAAACTGTTTTAAATACTTACCACATGCCTATCAAAGAACAAAATACATGTCGATTGTCG
Found at i:55841773 original size:76 final size:78
Alignment explanation
Indices: 55841643--55841793 Score: 207
Period size: 76 Copynumber: 2.0 Consensus size: 78
55841633 AAAGAAAAAA
* *
55841643 CAAATTTTTATAAGCAGAAATTATAAATTTTTACAAACAAATTATGTTAATTTTTTATTATATAA
1 CAAATTTTTATAAACAAAAATTATAAATTTTTACAAACAAATTATGTTAATTTTTTATTATATAA
55841708 ATATTATTTATCT
66 ATATTATTTATCT
* * * **
55841721 CAAATTTTTATAAATAAAAATTAT-TA-TTTTACAAACAAATTATTTTGTTTTTTTATTATATAA
1 CAAATTTTTATAAACAAAAATTATAAATTTTTACAAACAAATTATGTTAATTTTTTATTATATAA
* *
55841784 TTGTTATTTA
66 ATATTATTTA
55841794 CCTCTCAATA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 42 0.66
77 1 0.02
78 21 0.33
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.50
Consensus pattern (78 bp):
CAAATTTTTATAAACAAAAATTATAAATTTTTACAAACAAATTATGTTAATTTTTTATTATATAA
ATATTATTTATCT
Found at i:55841976 original size:21 final size:21
Alignment explanation
Indices: 55841946--55841993 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
55841936 AATTATATAA
55841946 AAATAT-TTTAAAATTTA-ATT
1 AAATATATTT-AAATTTATATT
*
55841966 AAATATATTTATATTTATATT
1 AAATATATTTAAATTTATATT
55841987 AAATATA
1 AAATATA
55841994 AAAATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATATATTTAAATTTATATT
Found at i:55843306 original size:48 final size:48
Alignment explanation
Indices: 55843214--55843306 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
55843204 AATGATAGCC
* ** *
55843214 TCATAAATCTTAGTTTGGCTTTCACTATTCAAAAGGTATTGTGGTAGT
1 TCATAAATCTTAGTTTGACTTTCACTATTCAAAAACTATGGTGGTAGT
* * *
55843262 TCATAAATCTTGGTTTGACTTTCACTATTGAAAAACTGTGGTGGT
1 TCATAAATCTTAGTTTGACTTTCACTATTCAAAAACTATGGTGGT
55843307 TCAAAAGGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (48 bp):
TCATAAATCTTAGTTTGACTTTCACTATTCAAAAACTATGGTGGTAGT
Found at i:55843490 original size:21 final size:21
Alignment explanation
Indices: 55843466--55843505 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55843456 TCAACAATTT
*
55843466 AATATTGATATTAAAATTAAA
1 AATATTAATATTAAAATTAAA
*
55843487 AATATTAATATTATAATTA
1 AATATTAATATTAAAATTA
55843506 CAAAGAATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
AATATTAATATTAAAATTAAA
Found at i:55843700 original size:12 final size:12
Alignment explanation
Indices: 55843683--55843714 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
55843673 AACGTGAACC
55843683 AATGAAAACAAA
1 AATGAAAACAAA
*
55843695 AATGAAAACATA
1 AATGAAAACAAA
55843707 AATGAAAA
1 AATGAAAA
55843715 GTACCTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.12
Consensus pattern (12 bp):
AATGAAAACAAA
Found at i:55846014 original size:87 final size:87
Alignment explanation
Indices: 55845868--55846089 Score: 297
Period size: 87 Copynumber: 2.6 Consensus size: 87
55845858 CGCTTTCTCT
*
55845868 TGCCAGTAATCAGGA-TATCAGTTTCCAATACCTT-GATCTCCCTCATTGCTGATAGATCCATCT
1 TGCCAGTAATC-GGAGTATCAGTTTCCAAT-CCTTCGATCTCCCTCACTGCTGATAGATCCATCT
55845931 T-TCCAGTGACACAAAGGTTATCAG
64 TAT-CAGTGACACAAAGGTTATCAG
* * *
55845955 TGCCAGTAATCGGAGTATCAGTTTCCAATGCTTCAATCTCCCTCACTGCTGATATATCCATCTTA
1 TGCCAGTAATCGGAGTATCAGTTTCCAATCCTTCGATCTCCCTCACTGCTGATAGATCCATCTTA
**
55846020 TCAGTGACACAAAGGTTATCTT
66 TCAGTGACACAAAGGTTATCAG
* * * * *
55846042 TGCCAGTAATCAGAGCATCAGTTTCCCATTCTTCGATCTCCCCCACTG
1 TGCCAGTAATCGGAGTATCAGTTTCCAATCCTTCGATCTCCCTCACTG
55846090 TTTTATCAAT
Statistics
Matches: 120, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
86 6 0.05
87 113 0.94
88 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (87 bp):
TGCCAGTAATCGGAGTATCAGTTTCCAATCCTTCGATCTCCCTCACTGCTGATAGATCCATCTTA
TCAGTGACACAAAGGTTATCAG
Found at i:55846155 original size:75 final size:75
Alignment explanation
Indices: 55846017--55846158 Score: 167
Period size: 75 Copynumber: 1.9 Consensus size: 75
55846007 TATATCCATC
* * ** * * *
55846017 TTATCAGTGACACAAAGGTTATCTTTGCCAGTAATCAGAGCATCAGTTTCCCATTCTTCGATCTC
1 TTATCAATGACACAAAGATTATCAGTGCCAGTAATCAGAGCATAAGTTTCCAATACTTCGATCTC
55846082 CCCCACTGTT
66 CCCCACTGTT
* ** * * *
55846092 TTATCAATTACACAAAGATTATCAGTGCCAGTAATTGGGGCATAAGTTTCTAATACTTTGATCTC
1 TTATCAATGACACAAAGATTATCAGTGCCAGTAATCAGAGCATAAGTTTCCAATACTTCGATCTC
55846157 CC
66 CC
55846159 TCATTGCTGA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
75 54 1.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (75 bp):
TTATCAATGACACAAAGATTATCAGTGCCAGTAATCAGAGCATAAGTTTCCAATACTTCGATCTC
CCCCACTGTT
Found at i:55847066 original size:39 final size:39
Alignment explanation
Indices: 55847023--55847107 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
55847013 TTCGCAGCTA
55847023 CAAGCTTTGGTTTCTTTT-CCTTGACTAGCTTTGGAGTTG
1 CAAGCTTTGGTTTCTTTTCCCTT-ACTAGCTTTGGAGTTG
* *
55847062 CAAGCCTTGGTTTCTTTTCCCTTACTTGCTTTGGAGTTG
1 CAAGCTTTGGTTTCTTTTCCCTTACTAGCTTTGGAGTTG
55847101 CAAGCTT
1 CAAGCTT
55847108 CAGTGTGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
39 38 0.90
40 4 0.10
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (39 bp):
CAAGCTTTGGTTTCTTTTCCCTTACTAGCTTTGGAGTTG
Found at i:55857569 original size:18 final size:18
Alignment explanation
Indices: 55857528--55857574 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
55857518 TAAAAAGAAA
* *
55857528 CCTCATCAGACTCGTCAT
1 CCTCATCAGAATCATCAT
* *
55857546 CGTCATCAGAATCATCTT
1 CCTCATCAGAATCATCAT
55857564 CCTCATCAGAA
1 CCTCATCAGAA
55857575 CCACTCTCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.34, G:0.11, T:0.28
Consensus pattern (18 bp):
CCTCATCAGAATCATCAT
Found at i:55870213 original size:31 final size:31
Alignment explanation
Indices: 55870176--55870241 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
55870166 TAAAATATAC
*
55870176 ACATGAAACATTGATTGTAG-TTCAACCATAT
1 ACATGAAACATTAATT-TAGATTCAACCATAT
* * *
55870207 ACATGAAACTTTAATTTTGATTCAATCATAT
1 ACATGAAACATTAATTTAGATTCAACCATAT
55870238 ACAT
1 ACAT
55870242 TTAAAGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.36
Consensus pattern (31 bp):
ACATGAAACATTAATTTAGATTCAACCATAT
Found at i:55870292 original size:21 final size:21
Alignment explanation
Indices: 55870266--55870341 Score: 73
Period size: 21 Copynumber: 3.3 Consensus size: 21
55870256 ACGTTAATTT
55870266 ATTATTTGTTAAATAAATATA
1 ATTATTTGTTAAATAAATATA
*
55870287 ATTATTTTTGTATGCAATATATAAT-TT
1 ATTA--TTTGT-T--AA-ATA-AATATA
55870314 ATTATTTGTTAAATAAATATA
1 ATTATTTGTTAAATAAATATA
55870335 ATTATTT
1 ATTATTT
55870342 TTGTATGCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
20 3 0.07
21 15 0.33
22 2 0.04
23 5 0.11
24 2 0.04
25 5 0.11
26 2 0.04
27 8 0.18
28 3 0.07
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (21 bp):
ATTATTTGTTAAATAAATATA
Found at i:55870305 original size:25 final size:25
Alignment explanation
Indices: 55870277--55870360 Score: 104
Period size: 25 Copynumber: 3.4 Consensus size: 25
55870267 TTATTTGTTA
55870277 AATAAATATAATTATTTTTGTATGC
1 AATAAATATAATTATTTTTGTATGC
*
55870302 AAT--ATATAATTTATTATTTGT-T-A
1 AATAAATATAA-TTATT-TTTGTATGC
55870325 AATAAATATAATTATTTTTGTATGC
1 AATAAATATAATTATTTTTGTATGC
*
55870350 AATATATATAA
1 AATAAATATAA
55870361 AATATAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
23 14 0.28
24 12 0.24
25 24 0.48
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (25 bp):
AATAAATATAATTATTTTTGTATGC
Found at i:55870308 original size:23 final size:23
Alignment explanation
Indices: 55870282--55870357 Score: 93
Period size: 23 Copynumber: 3.2 Consensus size: 23
55870272 TGTTAAATAA
55870282 ATATAATTATTTTTGTATGCAAT
1 ATATAATTATTTTTGTATGCAAT
*
55870305 ATATAATTTATTATTTGT-T-AAAT
1 ATATAA-TTATT-TTTGTATGCAAT
55870328 AAATATAATTATTTTTGTATGCAAT
1 --ATATAATTATTTTTGTATGCAAT
55870353 ATATA
1 ATATA
55870358 TAAAATATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
23 19 0.42
24 12 0.27
25 14 0.31
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (23 bp):
ATATAATTATTTTTGTATGCAAT
Found at i:55870316 original size:48 final size:48
Alignment explanation
Indices: 55870260--55870357 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
55870250 ATAAATACGT
55870260 TAATTTATTATTTGTTAAATAAATATAATTATTTTTGTATGCAATATA
1 TAATTTATTATTTGTTAAATAAATATAATTATTTTTGTATGCAATATA
55870308 TAATTTATTATTTGTTAAATAAATATAATTATTTTTGTATGCAATATA
1 TAATTTATTATTTGTTAAATAAATATAATTATTTTTGTATGCAATATA
55870356 TA
1 TA
55870358 TAAAATATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (48 bp):
TAATTTATTATTTGTTAAATAAATATAATTATTTTTGTATGCAATATA
Found at i:55870318 original size:27 final size:28
Alignment explanation
Indices: 55870281--55870357 Score: 89
Period size: 21 Copynumber: 3.0 Consensus size: 28
55870271 TTGTTAAATA
55870281 AATATAATTATTTTTGTATGCAATATAT
1 AATATAATTATTTTTGTATGCAATATAT
*
55870309 AAT-TTATTA--TTTGT-T--AA-ATA-
1 AATATAATTATTTTTGTATGCAATATAT
55870329 AATATAATTATTTTTGTATGCAATATAT
1 AATATAATTATTTTTGTATGCAATATAT
55870357 A
1 A
55870358 TAAAATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 16
0.68 0.04 0.28
Matches are distributed among these distances:
20 3 0.08
21 8 0.21
22 2 0.05
23 5 0.13
24 2 0.05
25 5 0.13
26 2 0.05
27 8 0.21
28 4 0.10
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (28 bp):
AATATAATTATTTTTGTATGCAATATAT
Found at i:55871019 original size:16 final size:16
Alignment explanation
Indices: 55870988--55871035 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
55870978 TGAAAATTTT
*
55870988 AAAAATATTAAAAAAATA
1 AAAAATATT--AAAACTA
*
55871006 AAAATTTATTAAAACTA
1 AAAA-ATATTAAAACTA
55871023 AAAAATATTAAAA
1 AAAAATATTAAAA
55871036 AATAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 8 0.31
17 10 0.38
18 4 0.15
19 4 0.15
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAATATTAAAACTA
Found at i:55883761 original size:50 final size:50
Alignment explanation
Indices: 55883703--55883802 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
55883693 TATTATTCAG
* **
55883703 ATTCACAATTTAAATAGTCTTTAGTTTTAATTATAAAAACTTATATAAAC
1 ATTCACAATTTAAATAGTCTGTAACTTTAATTATAAAAACTTATATAAAC
55883753 ATTCACAATTTAAATAGTCTGTAACTTTAATTATAAAAACTTATATAAAC
1 ATTCACAATTTAAATAGTCTGTAACTTTAATTATAAAAACTTATATAAAC
55883803 TTAATTTAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (50 bp):
ATTCACAATTTAAATAGTCTGTAACTTTAATTATAAAAACTTATATAAAC
Found at i:55884112 original size:13 final size:13
Alignment explanation
Indices: 55884081--55884113 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
55884071 AATAAATATA
55884081 TTATAA-AATTTT
1 TTATAATAATTTT
55884093 TTA-AATAATTTT
1 TTATAATAATTTT
55884105 TTATAATAA
1 TTATAATAA
55884114 ACTTTTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 12 0.63
13 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATAATAATTTT
Found at i:55886587 original size:3 final size:3
Alignment explanation
Indices: 55886581--55886611 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
55886571 AAGCATGTTG
55886581 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
55886612 AATTTTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55892647 original size:22 final size:22
Alignment explanation
Indices: 55892622--55892666 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
55892612 TTTAATAAAA
55892622 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
55892644 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
55892666 A
1 A
55892667 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:55894472 original size:21 final size:21
Alignment explanation
Indices: 55894446--55894486 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
55894436 GGATATGTCT
*
55894446 TCTTTTTTTTGTGTAGACACA
1 TCTTTTTCTTGTGTAGACACA
55894467 TCTTTTTCTTGTGTAGACAC
1 TCTTTTTCTTGTGTAGACAC
55894487 GAAGCTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.51
Consensus pattern (21 bp):
TCTTTTTCTTGTGTAGACACA
Found at i:55895722 original size:13 final size:13
Alignment explanation
Indices: 55895706--55895749 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 13
55895696 TCCTAAAGGA
55895706 ATTCTGTAGGAAT
1 ATTCTGTAGGAAT
55895719 ATTCTGTA--AAT
1 ATTCTGTAGGAAT
55895730 ATT-T-TAGGAAT
1 ATTCTGTAGGAAT
*
55895741 ATTTTGTAG
1 ATTCTGTAG
55895750 ATATTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
9 2 0.07
10 1 0.04
11 12 0.44
12 1 0.04
13 11 0.41
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (13 bp):
ATTCTGTAGGAAT
Found at i:55895737 original size:22 final size:22
Alignment explanation
Indices: 55895712--55895756 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
55895702 AGGAATTCTG
55895712 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
55895734 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
55895756 T
1 T
55895757 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:55897402 original size:22 final size:22
Alignment explanation
Indices: 55897377--55897421 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
55897367 TTTAATAAAA
55897377 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
55897399 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
55897421 A
1 A
55897422 CACTTACTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:55904716 original size:3 final size:3
Alignment explanation
Indices: 55904708--55904737 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
55904698 TTGCAAAAGT
55904708 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
55904738 TTTCAGCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:55908319 original size:52 final size:48
Alignment explanation
Indices: 55908225--55908431 Score: 179
Period size: 47 Copynumber: 4.2 Consensus size: 48
55908215 CCATGGCAGC
* * * *
55908225 ATGTGAAATGTGATTTCCGTATAAGACCATAGT-TGGGCTATGGCTTCGGAG
1 ATGTGATATGTG-CTTCCGTATAAGACCATA-TCTGGGATATGGCCTC-G-G
* *
55908276 AAATGTGATATGTGCTTCCGTATAATACCATATCCGGGATATGGCCTCGG
1 --ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCCTCGG
* * * *
55908326 -TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCAG
1 ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCCTCGG
* * ** * *
55908373 -TGTGATATGTG-ATCCGTGTAAGACCATGGCTGGGCTATGGCCCCGG
1 ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCCTCGG
55908419 TATGTGATATGTG
1 -ATGTGATATGTG
55908432 ACTATGTGCA
Statistics
Matches: 129, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
46 25 0.19
47 52 0.40
48 11 0.09
50 1 0.01
51 2 0.02
52 27 0.21
53 11 0.09
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (48 bp):
ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCCTCGG
Found at i:55914715 original size:24 final size:23
Alignment explanation
Indices: 55914687--55914735 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
55914677 TAAATTATTA
*
55914687 ATTTTTATATTTT-TTTAATGATT
1 ATTTTT-TATTTTCTTGAATGATT
*
55914710 ATTTTTTATTTTCTTGAATTATT
1 ATTTTTTATTTTCTTGAATGATT
55914733 ATT
1 ATT
55914736 ATGATTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (23 bp):
ATTTTTTATTTTCTTGAATGATT
Found at i:55926946 original size:40 final size:39
Alignment explanation
Indices: 55926862--55926996 Score: 134
Period size: 40 Copynumber: 3.4 Consensus size: 39
55926852 CGTTTGAATA
* * * *
55926862 AAAAACACCGCTAAAAATC-AATCATTAGCGGCGCTATATA
1 AAAAACGCCGCTAAAAATCGAGT-ATTAGCGGCGCT-TTTC
*
55926902 AAAAACGCCGCTAAAGATCGAGTATTAGCGGCGCTTTTC
1 AAAAACGCCGCTAAAAATCGAGTATTAGCGGCGCTTTTC
* *
55926941 TAAAAACGCCACTAAAAAT-GAGCATTAGCGGCG-TTTTAC
1 -AAAAACGCCGCTAAAAATCGAGTATTAGCGGCGCTTTT-C
55926980 AAAAAGCGCCGC-AAAAA
1 AAAAA-CGCCGCTAAAAA
55926997 CCTAAACCTA
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
38 14 0.17
39 21 0.26
40 45 0.55
41 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATCGAGTATTAGCGGCGCTTTTC
Found at i:55927231 original size:41 final size:41
Alignment explanation
Indices: 55927036--55927231 Score: 311
Period size: 41 Copynumber: 4.8 Consensus size: 41
55927026 TTTTTAGCGA
* *
55927036 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTAGTC
1 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTC
* * * *
55927077 TTTAGCGGCGTTTTTGATGAAGCGCCACTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTC
* *
55927118 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAATCTCTGGTC
1 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTC
55927159 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTC
1 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTC
*
55927200 TTTAGGGGCGTTTTTTAAGAAGCGCCGCTAAA
1 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAA
55927232 AGCATTTTAT
Statistics
Matches: 144, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 144 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.33
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTC
Found at i:55927822 original size:15 final size:15
Alignment explanation
Indices: 55927802--55927833 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
55927792 TATTTTAATG
55927802 TTTAGGGAGTATGGA
1 TTTAGGGAGTATGGA
*
55927817 TTTAGGGATTATGGA
1 TTTAGGGAGTATGGA
55927832 TT
1 TT
55927834 AGCGTTTATG
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:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (15 bp):
TTTAGGGAGTATGGA
Found at i:55928594 original size:21 final size:21
Alignment explanation
Indices: 55928551--55928604 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
55928541 TAAATAAGGT
*
55928551 TTAGGGGTTAGTAGTCAGGGG
1 TTAGGGGTTAGTAGTCAGAGG
*
55928572 TTAGGGGTTA-TATGTTAGAGG
1 TTAGGGGTTAGTA-GTCAGAGG
* *
55928593 TTAAGAGTTAGT
1 TTAGGGGTTAGT
55928605 GATTTAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.07
21 24 0.89
22 1 0.04
ACGTcount: A:0.24, C:0.02, G:0.39, T:0.35
Consensus pattern (21 bp):
TTAGGGGTTAGTAGTCAGAGG
Found at i:55932110 original size:27 final size:26
Alignment explanation
Indices: 55932080--55932136 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
55932070 AATTTCGAGG
*
55932080 TTTACAATTTT-TAATTTTTATTAATT
1 TTTA-AATTTTCTAACTTTTATTAATT
* *
55932106 ATTTATATTTTCTCACTTTTATTAATT
1 -TTTAAATTTTCTAACTTTTATTAATT
55932133 TTTA
1 TTTA
55932137 TTATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTAAATTTTCTAACTTTTATTAATT
Found at i:55932487 original size:43 final size:43
Alignment explanation
Indices: 55932383--55932526 Score: 220
Period size: 43 Copynumber: 3.4 Consensus size: 43
55932373 GTTTGAGATA
* *
55932383 AAAAGCGTCGCTAAAGATCATGGTCTTTAGCGGC-ATTTGTGGG
1 AAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGA-TTGTGGG
55932426 -AAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGATTGTGGG
1 AAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGATTGTGGG
*
55932468 AAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGATTGTGGG
* *
55932511 AGAAGCGCCGCAAAAG
1 AAAAGCGCCGCTAAAG
55932527 TTAGCGACGT
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
42 38 0.40
43 56 0.60
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.22
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGATTGTGGG
Found at i:55932615 original size:22 final size:22
Alignment explanation
Indices: 55932587--55932630 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
55932577 TAGTGGCGCT
*
55932587 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
55932609 AAAAAGCGCCGCTAAAAGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
55932631 TTTTGGTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.27, G:0.20, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:55937561 original size:2 final size:2
Alignment explanation
Indices: 55937556--55937588 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
55937546 GAGAATCCAT
*
55937556 GA GA GA GA GA GA GT GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
55937589 TTAAGTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.52, T:0.03
Consensus pattern (2 bp):
GA
Found at i:55942586 original size:21 final size:21
Alignment explanation
Indices: 55942560--55942604 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
55942550 TTTAGTGGCG
*
55942560 CTAAAAAGCGCCGCTAAAGGC
1 CTAAAAAGCGCCGCTAAAAGC
*
55942581 CTAAAAAGCGCCTCTAAAAGC
1 CTAAAAAGCGCCGCTAAAAGC
55942602 CTA
1 CTA
55942605 TTTTGGTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.29, G:0.18, T:0.13
Consensus pattern (21 bp):
CTAAAAAGCGCCGCTAAAAGC
Found at i:55945397 original size:14 final size:14
Alignment explanation
Indices: 55945378--55945405 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55945368 GAAATAAAAT
55945378 TTAATTTATTCAGA
1 TTAATTTATTCAGA
55945392 TTAATTTATTCAGA
1 TTAATTTATTCAGA
55945406 ACAAACTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
TTAATTTATTCAGA
Found at i:55950215 original size:21 final size:21
Alignment explanation
Indices: 55950190--55950257 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
55950180 ATATTGTAGC
*
55950190 AAAATAGTGAGAAAACAATAA
1 AAAATAGTGAAAAAACAATAA
* * *
55950211 AAAATAGTAAAAAAATAGTAAA
1 AAAATAGTGAAAAAACAAT-AA
*
55950233 AAAATA-AGAAAAAACAA-AA
1 AAAATAGTGAAAAAACAATAA
55950252 AAAATA
1 AAAATA
55950258 ATAATTTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 8 0.21
21 22 0.58
22 8 0.21
ACGTcount: A:0.75, C:0.03, G:0.09, T:0.13
Consensus pattern (21 bp):
AAAATAGTGAAAAAACAATAA
Found at i:55950246 original size:11 final size:11
Alignment explanation
Indices: 55950209--55950238 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
55950199 AGAAAACAAT
55950209 AAAAAATAGTA
1 AAAAAATAGTA
55950220 AAAAAATAGTA
1 AAAAAATAGTA
55950231 AAAAAATA
1 AAAAAATA
55950239 AGAAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (11 bp):
AAAAAATAGTA
Found at i:55954824 original size:13 final size:13
Alignment explanation
Indices: 55954806--55954831 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55954796 CCAGAAACTG
55954806 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
55954819 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
55954832 TACCCATTTG
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:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ATTTGCAGAAAAC
Found at i:55958712 original size:21 final size:20
Alignment explanation
Indices: 55958597--55958715 Score: 63
Period size: 21 Copynumber: 6.0 Consensus size: 20
55958587 TTATATTTTC
* *
55958597 TATTA-AAAATTAATATAAA
1 TATTATAAAATTTATAAAAA
*
55958616 T-TTATAAAAAATTCATAAAAA
1 TATTAT--AAAATTTATAAAAA
* *
55958637 CA-TAT-AAATATTATACAAA
1 TATTATAAAAT-TTATAAAAA
* *
55958656 TACTA-ATAAA-TTATTAAAA
1 TATTATA-AAATTTATAAAAA
*
55958675 TATTATAAAATTAATAAAACA
1 TATTATAAAATTTATAAAA-A
55958696 TATT-TAAAATTTTATAAAAA
1 TATTATAAAA-TTTATAAAAA
55958716 CTCACCAAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
18 7 0.09
19 23 0.30
20 15 0.20
21 31 0.41
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
TATTATAAAATTTATAAAAA
Found at i:55959244 original size:3 final size:3
Alignment explanation
Indices: 55959236--55959363 Score: 256
Period size: 3 Copynumber: 42.7 Consensus size: 3
55959226 AAAAATTCAA
55959236 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55959284 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55959332 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
55959364 AATCCGATTC
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 125 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55966885 original size:29 final size:29
Alignment explanation
Indices: 55966848--55967024 Score: 229
Period size: 29 Copynumber: 6.1 Consensus size: 29
55966838 AAATATATAT
*
55966848 ATATGTAGTGTATTTTAAAAGTAAAAAAA
1 ATATGTAGTGTATTTTAAAAATAAAAAAA
55966877 ATATGTAGTGTATTTTAAAAATAAAAAATA
1 ATATGTAGTGTATTTTAAAAATAAAAAA-A
* *
55966907 TATATGTAGTGTATTTT--AAAT---ATAT
1 -ATATGTAGTGTATTTTAAAAATAAAAAAA
*
55966932 ATATGTAGTGTATTTTAAAAGTAAAAAAAA
1 ATATGTAGTGTATTTTAAAAAT-AAAAAAA
*
55966962 TATATGTAGTGTATTTTAAAAATAAAAAAT
1 -ATATGTAGTGTATTTTAAAAATAAAAAAA
*
55966992 ATATGTAGTGTATTTTAAAAATAAAAAAT
1 ATATGTAGTGTATTTTAAAAATAAAAAAA
55967021 ATAT
1 ATAT
55967025 AAAGTAGTCA
Statistics
Matches: 131, Mismatches: 8, Indels: 18
0.83 0.05 0.11
Matches are distributed among these distances:
24 16 0.12
26 5 0.04
29 64 0.49
30 9 0.07
31 37 0.28
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (29 bp):
ATATGTAGTGTATTTTAAAAATAAAAAAA
Found at i:55966929 original size:22 final size:23
Alignment explanation
Indices: 55966901--55966951 Score: 93
Period size: 24 Copynumber: 2.2 Consensus size: 23
55966891 TTAAAAATAA
55966901 AAAATATATATGTAGTGTATTTT
1 AAAATATATATGTAGTGTATTTT
55966924 AAATATATATATGTAGTGTATTTT
1 AAA-ATATATATGTAGTGTATTTT
55966948 AAAA
1 AAAA
55966952 GTAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (23 bp):
AAAATATATATGTAGTGTATTTT
Found at i:55966994 original size:84 final size:84
Alignment explanation
Indices: 55966842--55967010 Score: 306
Period size: 84 Copynumber: 2.0 Consensus size: 84
55966832 ATTTTAAAAT
55966842 ATATATATATGTAGTGTATTTTAAAAGTAAAAAAAATATGTAGTGTATTTTAAAAATAAAAAATA
1 ATATATATATGTAGTGTATTTTAAAAGTAAAAAAAATATGTAGTGTATTTTAAAAATAAAAAATA
55966907 TATATGTAGTGTATTTTAA
66 TATATGTAGTGTATTTTAA
55966926 ATATATATATGTAGTGTATTTTAAAAGTAAAAAAAATATATGTAGTGTATTTTAAAAAT-AAAAA
1 ATATATATATGTAGTGTATTTTAAAAGT-AAAAAAA-ATATGTAGTGTATTTTAAAAATAAAAAA
55966990 -ATATATGTAGTGTATTTTAA
64 TATATATGTAGTGTATTTTAA
55967010 A
1 A
55967011 AATAAAAAAT
Statistics
Matches: 83, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
84 49 0.59
85 12 0.14
86 22 0.27
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (84 bp):
ATATATATATGTAGTGTATTTTAAAAGTAAAAAAAATATGTAGTGTATTTTAAAAATAAAAAATA
TATATGTAGTGTATTTTAA
Found at i:55970564 original size:21 final size:21
Alignment explanation
Indices: 55970540--55970592 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
55970530 CATTATTTCT
* *
55970540 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAATAACC
*
55970561 AATCTCACCGCTACAATAACT
1 AATCTCACCGCTACAATAACC
55970582 AATCTCACCGC
1 AATCTCACCGC
55970593 CACCACTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.40, G:0.08, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:55974520 original size:30 final size:32
Alignment explanation
Indices: 55974460--55974521 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
55974450 AAAACAAATA
*
55974460 TATATATAATTGTATATCTTAATTATTCTATT
1 TATATATAATTGTATATCTAAATTATTCTATT
*
55974492 TATATATATTTGT-TA-CTAAAGTTA-TCTATT
1 TATATATAATTGTATATCTAAA-TTATTCTATT
55974522 GCTACTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 10 0.37
31 5 0.19
32 12 0.44
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (32 bp):
TATATATAATTGTATATCTAAATTATTCTATT
Found at i:55976223 original size:42 final size:42
Alignment explanation
Indices: 55976173--55976272 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
55976163 TTATATGAAC
55976173 GGCACTAAGTGTGCGAAACTAAAAT-GACGAGGTTGAATAAAG
1 GGCACTAAGTGTGCGAAACTAAAATAGA-GAGGTTGAATAAAG
* * *
55976215 GGCACTAAGTGTGCGAAATTAAAATAGAGATGTTGAATAATG
1 GGCACTAAGTGTGCGAAACTAAAATAGAGAGGTTGAATAAAG
55976257 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
55976273 TACCGAGAGC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
42 52 0.96
43 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.29, T:0.22
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAACTAAAATAGAGAGGTTGAATAAAG
Found at i:55979506 original size:29 final size:30
Alignment explanation
Indices: 55979473--55979543 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
55979463 AAATCAAAAT
55979473 TTCATGTATAAAATT-ACATAAAATTAAAG
1 TTCATGTATAAAATTAACATAAAATTAAAG
* * * * *
55979502 TTCATATGTACAATTACACATTAAATTACAG
1 TTCATGTATAAAATTA-ACATAAAATTAAAG
55979533 TTCATGTATAA
1 TTCATGTATAA
55979544 TTTTGAGATT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
29 12 0.38
31 20 0.62
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (30 bp):
TTCATGTATAAAATTAACATAAAATTAAAG
Found at i:55982733 original size:3 final size:3
Alignment explanation
Indices: 55982727--55982754 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
55982717 CCTCCTACTC
55982727 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
55982755 ATGAATTTTG
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:55995040 original size:18 final size:17
Alignment explanation
Indices: 55994999--55995065 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
55994989 AGCATGTTTC
55994999 GAACTTAAAGAAA-TTTT
1 GAACTT-AAGAAATTTTT
**
55995016 GGGCTTAAGCAAATTTTT
1 GAACTTAAG-AAATTTTT
*
55995034 GAACTTAA-ATATGTTTT
1 GAACTTAAGAAAT-TTTT
55995051 GAACTTAAGTAAATT
1 GAACTTAAG-AAATT
55995066 CTGAACTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
16 6 0.15
17 19 0.49
18 11 0.28
19 3 0.08
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (17 bp):
GAACTTAAGAAATTTTT
Found at i:55997242 original size:13 final size:13
Alignment explanation
Indices: 55997224--55997248 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55997214 TGTAAATCCG
55997224 AATTCATTTTAAA
1 AATTCATTTTAAA
55997237 AATTCATTTTAA
1 AATTCATTTTAA
55997249 CCAAATTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTCATTTTAAA
Found at i:56000215 original size:48 final size:48
Alignment explanation
Indices: 56000127--56000218 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
56000117 CCAAGTTTGC
* * * *
56000127 TTCTTTTCTCATTTCTATCTCGAATCCATTGACCCGTTTTATATTTAT
1 TTCTTTTCTCATTTCTATCTCAAATCCACTAACCCATTTTATATTTAT
* **
56000175 TTCTTTTCTCATTTCTATTTCAAATCCACTAATTCATTTTATAT
1 TTCTTTTCTCATTTCTATCTCAAATCCACTAACCCATTTTATAT
56000219 CCATATCAGC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.53
Consensus pattern (48 bp):
TTCTTTTCTCATTTCTATCTCAAATCCACTAACCCATTTTATATTTAT
Found at i:56000439 original size:28 final size:31
Alignment explanation
Indices: 56000390--56000450 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 31
56000380 ACATTTTTGT
56000390 TTGATCAATTTTAGCCTTTATACTTTT-AAA
1 TTGATCAATTTTAGCCTTTATACTTTTCAAA
56000420 TTGATC-A-TTTAGTCC-TTATACTTTTCAAA
1 TTGATCAATTTTAG-CCTTTATACTTTTCAAA
56000449 TT
1 TT
56000451 TTAAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 15 0.52
29 8 0.28
30 6 0.21
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.51
Consensus pattern (31 bp):
TTGATCAATTTTAGCCTTTATACTTTTCAAA
Found at i:56009348 original size:9 final size:9
Alignment explanation
Indices: 56009323--56009363 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
56009313 TTATTTATCG
56009323 AATTAATTA
1 AATTAATTA
* *
56009332 AATAAATTT
1 AATTAATTA
56009341 AATTAATTA
1 AATTAATTA
*
56009350 ACTTAATTA
1 AATTAATTA
56009359 AATTA
1 AATTA
56009364 TATTCTCAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTAATTA
Found at i:56021211 original size:17 final size:18
Alignment explanation
Indices: 56021163--56021199 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
56021153 CTCGCCTCAC
56021163 TCGAAAAAATTAAATTGT
1 TCGAAAAAATTAAATTGT
56021181 TCGAAAAAATTAAATTGT
1 TCGAAAAAATTAAATTGT
56021199 T
1 T
56021200 TTAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (18 bp):
TCGAAAAAATTAAATTGT
Found at i:56021537 original size:29 final size:30
Alignment explanation
Indices: 56021450--56021538 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 30
56021440 AACGGCTCAG
* * *
56021450 TGACTAAAATGTTACAACGTGATAACGTAAA
1 TGACTAAAATGTAAC-ATGTGATAACATAAA
* * *
56021481 TGACTAAAACGTAACATTTCA-AACATAAA
1 TGACTAAAATGTAACATGTGATAACATAAA
*
56021510 TGACTAAAATGTAACATGAGATAA-ATAAA
1 TGACTAAAATGTAACATGTGATAACATAAA
56021539 AATGACTTTG
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
29 29 0.62
30 5 0.11
31 13 0.28
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (30 bp):
TGACTAAAATGTAACATGTGATAACATAAA
Found at i:56021724 original size:21 final size:21
Alignment explanation
Indices: 56021700--56021740 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
56021690 AAAATTTAAG
56021700 ATTCA-AAAAATTATAAAAAAA
1 ATTCATAAAAATT-TAAAAAAA
56021721 ATTCATAAAAATTTAAAAAA
1 ATTCATAAAAATTTAAAAAA
56021741 CAGCATGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (21 bp):
ATTCATAAAAATTTAAAAAAA
Found at i:56022404 original size:21 final size:20
Alignment explanation
Indices: 56022382--56022460 Score: 61
Period size: 21 Copynumber: 3.9 Consensus size: 20
56022372 AAATCTTAGA
56022382 ATTTTATGAATTTTTTTAAG
1 ATTTTATGAATTTTTTTAAG
** *
56022402 AATTTTA-GGGTATTTTTGAAG
1 -ATTTTATGAAT-TTTTTTAAG
* * *
56022423 ATTTCAATGATTTTTTTTATG
1 ATTT-TATGAATTTTTTTAAG
*
56022444 TTTTTATGAATTTTTTT
1 ATTTTATGAATTTTTTT
56022461 TATATTTTCT
Statistics
Matches: 44, Mismatches: 11, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
20 17 0.39
21 25 0.57
22 2 0.05
ACGTcount: A:0.25, C:0.01, G:0.13, T:0.61
Consensus pattern (20 bp):
ATTTTATGAATTTTTTTAAG
Found at i:56026119 original size:41 final size:41
Alignment explanation
Indices: 56026074--56026271 Score: 238
Period size: 41 Copynumber: 4.8 Consensus size: 41
56026064 AAATTGTTCA
56026074 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
*
56026115 GACTATACGTCCAGCAGGCTAAGTGCCGGTGAATTGAATCG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
* * * *
56026156 GATTATATGTCCAGCAGGCTAAGTGCCGGTGAACTGAATCAG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATC-G
* * ** **
56026198 G-CTATAGGCCTAGCAGGCTAAGTGCCGGTGAACGGAATTA
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
* * *
56026238 GACTATAAGTCTATCAGG-TGAAGTGCCAGTGAAT
1 GACTATACGTCTAGCAGGCT-AAGTGCCGGTGAAT
56026272 CTGTTTAAAT
Statistics
Matches: 138, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 2 0.01
41 134 0.97
42 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.23
Consensus pattern (41 bp):
GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
Found at i:56032322 original size:25 final size:25
Alignment explanation
Indices: 56032260--56032368 Score: 101
Period size: 25 Copynumber: 4.4 Consensus size: 25
56032250 CGCTCTTATG
* *
56032260 AGCTTCCCGATATTTAACTCACATG
1 AGCTTCCCGATATTTAGCTCACATA
* * **
56032285 AGATTTCTAATATTTAGCTCACATA
1 AGCTTCCCGATATTTAGCTCACATA
*
56032310 AGCTTCCCGATATTTAGCTCATATA
1 AGCTTCCCGATATTTAGCTCACATA
** * * *
56032335 AGCTTTTCGATACTTAGCTCGCATG
1 AGCTTCCCGATATTTAGCTCACATA
*
56032360 AGTTTCCCG
1 AGCTTCCCG
56032369 TTATACAACT
Statistics
Matches: 64, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 64 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (25 bp):
AGCTTCCCGATATTTAGCTCACATA
Found at i:56032352 original size:50 final size:50
Alignment explanation
Indices: 56032260--56032368 Score: 121
Period size: 50 Copynumber: 2.2 Consensus size: 50
56032250 CGCTCTTATG
* *
56032260 AGCTTCCCGATATTTAACTCACATGAGATTTCTAATATTTAGCTCACATA
1 AGCTTCCCGATATTTAACTCACATAAGATTTCTAATACTTAGCTCACATA
* * * * * *
56032310 AGCTTCCCGATATTTAGCTCATATAAGCTTT-TCGATACTTAGCTCGCATG
1 AGCTTCCCGATATTTAACTCACATAAGATTTCT-AATACTTAGCTCACATA
*
56032360 AGTTTCCCG
1 AGCTTCCCG
56032369 TTATACAACT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 1 0.02
50 48 0.98
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (50 bp):
AGCTTCCCGATATTTAACTCACATAAGATTTCTAATACTTAGCTCACATA
Found at i:56035158 original size:38 final size:37
Alignment explanation
Indices: 56035089--56035161 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
56035079 TTTTCATAAT
* *
56035089 TTCACTTTTTCACTTTTAATCACTATTCAATTCAAAA
1 TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
56035126 TTCACTTTTCCA-TTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTTCCACTTTT-AA-TCAATATTCAATTCAA
56035162 TTCCACACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.45
Consensus pattern (37 bp):
TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
Found at i:56035192 original size:23 final size:22
Alignment explanation
Indices: 56035149--56035192 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
56035139 TTTCAAGTCA
56035149 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
56035172 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
56035193 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:56042685 original size:20 final size:20
Alignment explanation
Indices: 56042660--56042705 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
56042650 TATTTATTAA
56042660 GAAAGAATCACTAGACTTGT
1 GAAAGAATCACTAGACTTGT
56042680 GAAAGAATCACTAGACTTGT
1 GAAAGAATCACTAGACTTGT
56042700 GAAAGA
1 GAAAGA
56042706 TGACGCTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (20 bp):
GAAAGAATCACTAGACTTGT
Found at i:56044446 original size:19 final size:21
Alignment explanation
Indices: 56044408--56044448 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
56044398 TTTCCCAATA
*
56044408 CCTCAAACATTTTTATTTCTC
1 CCTCAAACATTTTTACTTCTC
56044429 CCTCAAA-A-TTTTACTTCTC
1 CCTCAAACATTTTTACTTCTC
56044448 C
1 C
56044449 AAAACCCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 1 0.05
21 7 0.37
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (21 bp):
CCTCAAACATTTTTACTTCTC
Found at i:56044512 original size:71 final size:72
Alignment explanation
Indices: 56044409--56044569 Score: 163
Period size: 72 Copynumber: 2.2 Consensus size: 72
56044399 TTCCCAATAC
* *
56044409 CTCAAACATTTTTATTT-CTCCCTCAAAATTTTACTTCTCCAAAACC-CTAAA-ATTTTTTTCCT
1 CTCAAA-ACTTTTATTTCCTCCCTCAAAATTTTAC--CTCCAAAACCTCAAAACATTTTTTTCCT
*
56044471 TT-CATTCTTA
63 TTAC-TTCCTA
* * *
56044481 TTCAAAACTTTTATTTCCT-CC-CAAATATTTTACCTCCCAAACCTTCAAAACATTTTTTTTCTT
1 CTCAAAACTTTTATTTCCTCCCTCAAA-ATTTTACCTCCAAAACC-TCAAAACATTTTTTTCCTT
*
56044544 TACTTCCTC
64 TACTTCCTA
56044553 CTCAAAACTTTTATTTC
1 CTCAAAACTTTTATTTC
56044570 TTCAAACCTC
Statistics
Matches: 75, Mismatches: 8, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
69 9 0.12
70 4 0.05
71 22 0.29
72 39 0.52
73 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.45
Consensus pattern (72 bp):
CTCAAAACTTTTATTTCCTCCCTCAAAATTTTACCTCCAAAACCTCAAAACATTTTTTTCCTTTA
CTTCCTA
Found at i:56047073 original size:21 final size:21
Alignment explanation
Indices: 56047019--56047078 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
56047009 ATCAGTATAT
56047019 GACACATAAGTGCCTG-TAAC
1 GACACATAAGTGCCTGATAAC
* *
56047039 GACACACGAGGTGCCTGAT-AC
1 GACACA-TAAGTGCCTGATAAC
56047060 GACACATAAAGTGCCTGAT
1 GACACAT-AAGTGCCTGAT
56047079 CGGCAAAGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 6 0.18
21 26 0.79
22 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.18
Consensus pattern (21 bp):
GACACATAAGTGCCTGATAAC
Found at i:56048281 original size:15 final size:16
Alignment explanation
Indices: 56048263--56048294 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56048253 TTAATTAATA
56048263 TAATTT-ATAATATTT
1 TAATTTAATAATATTT
56048278 TAATTTAATAATATTT
1 TAATTTAATAATATTT
56048294 T
1 T
56048295 TATAGTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTAATAATATTT
Found at i:56048921 original size:19 final size:21
Alignment explanation
Indices: 56048882--56048923 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
56048872 CTCGTGCTTT
*
56048882 TATATATATTATAAATTAAAA
1 TATATATATTATAAATAAAAA
*
56048903 TATATAT-TTATAAAAAAAAA
1 TATATATATTATAAATAAAAA
56048923 T
1 T
56048924 TTAAAACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATATATATTATAAATAAAAA
Found at i:56052803 original size:17 final size:15
Alignment explanation
Indices: 56052763--56052806 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
56052753 ATTATTGATT
*
56052763 AATTAATATTTTTAA
1 AATTAAAATTTTTAA
56052778 AATTTAAAATTTTATAGA
1 AA-TTAAAATTTT-TA-A
56052796 AATTAAAATTT
1 AATTAAAATTT
56052807 CTGGTCTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 2 0.08
16 9 0.36
17 11 0.44
18 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
AATTAAAATTTTTAA
Found at i:56067967 original size:13 final size:13
Alignment explanation
Indices: 56067949--56067974 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56067939 CTCTAAAGAA
56067949 GGTTCACAAATAT
1 GGTTCACAAATAT
56067962 GGTTCACAAATAT
1 GGTTCACAAATAT
56067975 ATATAAACGG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
GGTTCACAAATAT
Found at i:56080431 original size:97 final size:97
Alignment explanation
Indices: 56080265--56080460 Score: 365
Period size: 97 Copynumber: 2.0 Consensus size: 97
56080255 TTTCTTAAAA
* *
56080265 TATAACAGATTTTGTAGTAAGCTTTTGAGGGTAAACTACAAAAATAGTCACTTTTGTTTGCCTCA
1 TATAACAGATTTTGTAGTAAACTTTTAAGGGTAAACTACAAAAATAGTCACTTTTGTTTGCCTCA
56080330 GATTACATTTTAGTCACTTATGTTTGAAATGT
66 GATTACATTTTAGTCACTTATGTTTGAAATGT
*
56080362 TATAACAGATTTTGTAGTAAACTTTTAAGGGTAAACTACAAAAATAGTTACTTTTGTTTGCCTCA
1 TATAACAGATTTTGTAGTAAACTTTTAAGGGTAAACTACAAAAATAGTCACTTTTGTTTGCCTCA
56080427 GATTACATTTTAGTCACTTATGTTTGAAATGT
66 GATTACATTTTAGTCACTTATGTTTGAAATGT
56080459 TA
1 TA
56080461 GGTTTTAGTC
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 96 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (97 bp):
TATAACAGATTTTGTAGTAAACTTTTAAGGGTAAACTACAAAAATAGTCACTTTTGTTTGCCTCA
GATTACATTTTAGTCACTTATGTTTGAAATGT
Found at i:56080874 original size:23 final size:23
Alignment explanation
Indices: 56080840--56080883 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56080830 TTTATCCAAT
*
56080840 TTTTAATAAATAAATTTAATATA
1 TTTTAATAAATAAATATAATATA
* *
56080863 TTTTAATTAATATATATAATA
1 TTTTAATAAATAAATATAATA
56080884 CAAATAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTAATAAATAAATATAATATA
Found at i:56083237 original size:73 final size:73
Alignment explanation
Indices: 56083019--56083337 Score: 487
Period size: 73 Copynumber: 4.4 Consensus size: 73
56083009 AAAATAATCA
* ** ***
56083019 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACATCGTTTCCCGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
* *
56083083 TCGGGGAA
66 TCAGGGAT
* * *
56083091 TTAGCGGCGTTTCTGAGAAAGCGCCACAAAAAAACCATAAGCCCAACGACGCCGTTTTGTGAGCT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACC-TAAGCCCAACGACGCCGTTTTGTGAGCT
*
56083156 TTCGGGGAT
65 TTCAGGGAT
56083165 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
*
56083230 TTAGGGAT
66 TCAGGGAT
* *
56083238 TTAGCGGCGTTTTTAAGGAAGCGCCGCAAAAAAACCTAAGGCCAACGACGCCGTTTTGTGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
56083303 TCAGGGAT
66 TCAGGGAT
56083311 TTAGCGGCGTTTTTAAGAAAGCGCCGC
1 TTAGCGGCGTTTTTAAGAAAGCGCCGC
56083338 TAATGCTTTG
Statistics
Matches: 228, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
72 25 0.11
73 139 0.61
74 64 0.28
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (73 bp):
TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
TCAGGGAT
Found at i:56083379 original size:114 final size:114
Alignment explanation
Indices: 56083232--56083545 Score: 474
Period size: 114 Copynumber: 2.8 Consensus size: 114
56083222 GTGAGCTTTT
* * * *
56083232 AGGGATTTAGCGGCGTTTTTAAGG-AAGCGCCGCAAAAAAACCTAAGGCCAACGACGCCGTTTTG
1 AGGGCTTTAGCGGCGTTTTT-GGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTC
*
56083296 TGAGCTTTCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTT-
65 TGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATG-TTC
*
56083346 TGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCT
1 AGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCT
* *
56083411 GAGCTTTCGGGGATTTAACGACGTTTTTAAGAAAGCGCCGCTAATGTTC
66 GAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGTTC
* * *
56083460 AGGGCTTTAGCGGCGTTTTTGAGAAAGCGCTGCAAAAATTA--TAAGCCCAACGACGCCGTTTTC
1 AGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAA-AACCTAAGCCCAACGACGCCGTTTTC
56083523 TGAGCTTTCGGGGATTTAGCGGC
65 TGAGCTTTCGGGGATTTAGCGGC
56083546 CAAAAATGCT
Statistics
Matches: 183, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
113 47 0.26
114 135 0.74
115 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (114 bp):
AGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCT
GAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGTTC
Found at i:56083884 original size:14 final size:14
Alignment explanation
Indices: 56083865--56083896 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
56083855 AAGTATGGGT
56083865 TTAGGGATTATGGA
1 TTAGGGATTATGGA
56083879 TTAGGGATTATGGA
1 TTAGGGATTATGGA
56083893 TTAG
1 TTAG
56083897 AGGTTGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:56083924 original size:7 final size:7
Alignment explanation
Indices: 56083914--56083962 Score: 53
Period size: 7 Copynumber: 6.4 Consensus size: 7
56083904 GATTTAAGGT
56083914 TTAGGGG
1 TTAGGGG
56083921 TTAGAGGG
1 TTAG-GGG
56083929 TTAGGGG
1 TTAGGGG
56083936 TTTAGGGG
1 -TTAGGGG
*
56083944 TTAGACGTG
1 TTAG--GGG
56083953 TTAGGGG
1 TTAGGGG
56083960 TTA
1 TTA
56083963 AAAGTTAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
7 16 0.44
8 14 0.39
9 6 0.17
ACGTcount: A:0.18, C:0.02, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:56083934 original size:15 final size:15
Alignment explanation
Indices: 56083914--56083962 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
56083904 GATTTAAGGT
56083914 TTAGGGG-TTAGAGGG
1 TTAGGGGTTTAG-GGG
56083929 TTAGGGGTTTAGGGG
1 TTAGGGGTTTAGGGG
**
56083944 TTAGACGTGTTAGGGG
1 TTAGGGGT-TTAGGGG
56083960 TTA
1 TTA
56083963 AAAGTTAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 16 0.53
16 14 0.47
ACGTcount: A:0.18, C:0.02, G:0.47, T:0.33
Consensus pattern (15 bp):
TTAGGGGTTTAGGGG
Found at i:56083938 original size:23 final size:24
Alignment explanation
Indices: 56083911--56083961 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
56083901 TGGGATTTAA
56083911 GGTTTAGGGGTTAGA-GGGTTAGG
1 GGTTTAGGGGTTAGACGGGTTAGG
*
56083934 GGTTTAGGGGTTAGACGTGTTAGG
1 GGTTTAGGGGTTAGACGGGTTAGG
56083958 GGTT
1 GGTT
56083962 AAAAGTTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.16, C:0.02, G:0.49, T:0.33
Consensus pattern (24 bp):
GGTTTAGGGGTTAGACGGGTTAGG
Found at i:56084219 original size:21 final size:22
Alignment explanation
Indices: 56084189--56084229 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
56084179 AGGGATTATG
*
56084189 GTTTAAGGGTTGGGA-TTTAAT
1 GTTTAAGGGTTAGGAGTTTAAT
*
56084210 GTTTAGGGGTTAGGAGTTTA
1 GTTTAAGGGTTAGGAGTTTA
56084230 GGGGTTAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (22 bp):
GTTTAAGGGTTAGGAGTTTAAT
Found at i:56084246 original size:14 final size:13
Alignment explanation
Indices: 56084212--56084260 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
56084202 GATTTAATGT
56084212 TTAGGGGTTAGGAG
1 TTAGGGGTTA-GAG
56084226 TTTAGGGGTTAGATG
1 -TTAGGGGTTAGA-G
56084241 TTAGGGGTTAAGAG
1 TTAGGGGTT-AGAG
56084255 TTAGGG
1 TTAGGG
56084261 ATTTAAGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 18 0.56
15 14 0.44
ACGTcount: A:0.22, C:0.00, G:0.45, T:0.33
Consensus pattern (13 bp):
TTAGGGGTTAGAG
Found at i:56084370 original size:303 final size:299
Alignment explanation
Indices: 56083761--56084374 Score: 959
Period size: 303 Copynumber: 2.0 Consensus size: 299
56083751 AGAGATAATA
* *
56083761 ATAATAATAAATTTGTTTAGGGTTTTTGGTTTAGGGTATATGATTTATTTAAGATTTAAGGCCGA
1 ATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCGA
* * *
56083826 TTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGGTTTAGGGATTATGGATTAGGGATTATG
66 TTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGATTTAGGAATTATGAATTAGGGATTATG
*
56083891 GATTAGAGGTTGGGATTTAAGGTTTAGGGGTTAGAGGGTTAGGGGTTTAGGGGTTAGACGTGTTA
131 GATTAGAGGTTGGGATTTAAGGTTTAGGGGTTAGAGGGTTAGGGGTTTAGGGGTTAGACGAGTTA
* * *
56083956 GGGGTTAAAAGTTAGGGATTCAGGGGTCGAGTTAGGGTTTTGGGTTTAGATTAATTATTTTTTAA
196 GGGATTAAAAGTTAGGGATTCAGGGGTCGAGTTAAGGTTTTGAGTTTAGATTAATTATTTTTTAA
56084021 TTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAG
261 TTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAG
*
56084060 ATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCGG
1 ATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCGA
56084125 TTTAGGAGTTCATATTTTAAGGTTTAGGG-AGTATGGATTTAGGAATTATGAATTAGGGATTATG
66 TTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGATTTAGGAATTATGAATTAGGGATTATG
* * *
56084189 GTTTA-AGGGTTGGGATTTAATGTTTAGGGGTTAG-GAGTTTAGGGGTTAGATGTTAGGGGTTA-
131 GATTAGA-GGTTGGGATTTAAGGTTTAGGGGTTAGAG-GGTTA-GGG---G-T-TTAGGGGTTAG
* *
56084251 A-GAGTTAGGGATTTAAGGTTTAGGGATTCAGGGGTCGAGTTAAGGTTTTGAGTTTAGATTAATT
188 ACGAGTTAGGGATTAAAAG-TTAGGGATTCAGGGGTCGAGTTAAGGTTTTGAGTTTAGATTAATT
*
56084315 ATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAATAG
252 ATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAG
*
56084363 GTAATAATAAAT
1 ATAATAATAAAT
56084375 CAAATATATT
Statistics
Matches: 289, Mismatches: 17, Indels: 14
0.90 0.05 0.04
Matches are distributed among these distances:
297 2 0.01
298 66 0.23
299 94 0.33
302 14 0.05
303 103 0.36
304 10 0.03
ACGTcount: A:0.29, C:0.02, G:0.28, T:0.41
Consensus pattern (299 bp):
ATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCGA
TTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGATTTAGGAATTATGAATTAGGGATTATG
GATTAGAGGTTGGGATTTAAGGTTTAGGGGTTAGAGGGTTAGGGGTTTAGGGGTTAGACGAGTTA
GGGATTAAAAGTTAGGGATTCAGGGGTCGAGTTAAGGTTTTGAGTTTAGATTAATTATTTTTTAA
TTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAG
Found at i:56084578 original size:107 final size:106
Alignment explanation
Indices: 56084387--56084585 Score: 317
Period size: 106 Copynumber: 1.9 Consensus size: 106
56084377 AATATATTGA
* * *
56084387 TTTATAAAAAACGCCACAAAAAATTAATCAATTTATAAAAAAATAAAATAAAAATTTTTAGCATA
1 TTTATAAAAAACGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTAGCAGA
** *
56084452 GCAAAACGGCGTCATTTTGTTGAAAATTAAATAGCGGCATT
66 GCAAAACAACGTCATTTTGTTCAAAATTAAATAGCGGCATT
* *
56084493 TTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAATTAAAAAAATTTTAGCAG
1 TTTATAAAAAACGCCACAAAAAATAAATCAATTTATAAAAAAATAAAAT-AAAAAATTTTAGCAG
56084558 AGCAAAACAACGTCATTTTGTTCAAAAT
65 AGCAAAACAACGTCATTTTGTTCAAAAT
56084586 GAAAAAAAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
106 46 0.55
107 38 0.45
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (106 bp):
TTTATAAAAAACGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTAGCAGA
GCAAAACAACGTCATTTTGTTCAAAATTAAATAGCGGCATT
Found at i:56084767 original size:108 final size:104
Alignment explanation
Indices: 56084638--56084847 Score: 305
Period size: 103 Copynumber: 2.0 Consensus size: 104
56084628 GTAAGCAATA
*
56084638 GCGGCGTTTTTTTATAAAAACGCCGTAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAAA
1 GCGGCGTTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTAT---A-AAAT-AAATAAAAAA
* * *
56084703 AATTTAGCATAACAAAACGGCGTCATTTTGCTGAAAATGAAATT
61 AATTTAGCAGAACAAAACGACGTCATTTTGCTCAAAATGAAATT
*
56084747 GCGGCG-TTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAATAAATAAAAAAATTTT
1 GCGGCGTTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAATAAATAAAAAAAATTT
* *
56084811 AGCAGAGCAAAACGACGTCATTTTGTTCAAAATGAAA
66 AGCAGAACAAAACGACGTCATTTTGCTCAAAATGAAA
56084848 AAATTTTTGC
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
103 46 0.49
104 4 0.04
105 1 0.01
108 37 0.39
109 6 0.06
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (104 bp):
GCGGCGTTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAATAAATAAAAAAAATTT
AGCAGAACAAAACGACGTCATTTTGCTCAAAATGAAATT
Found at i:56084954 original size:241 final size:245
Alignment explanation
Indices: 56084387--56085044 Score: 927
Period size: 241 Copynumber: 2.6 Consensus size: 245
56084377 AATATATTGA
* *
56084387 TTTATAAAAAACGCCACAAAAAATTAATCAATTTATAAAA-AAATAAAATAAAAATTTTTAGCAT
1 TTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAATTTTTAGCAT
* *
56084451 AGCAAAACGGCGTCATTTTGTTGAAAATTAAATAGCGGC-ATTTTTATAAAAAACGCCGCAAAAA
66 AGCAAAACGGCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTTTAT-AAAAACGCCGCAAAAA
56084515 ATAAATCAATTTATAAAAAAATAAATTAAAAAAATTTTAGCAGAGCAAAACAACGTCATTTTGTT
130 ATAAATCAATTTAT---AAAATAAA-TAAAAAAATTTTAGCAGAGCAAAACAACGTCATTTTGTT
56084580 CAAAATGAAAAAAAATTTGCGGCGTTTTTATGAAAAACGCCGCTAAAGGTAAGCAATAGCGGCGT
191 CAAAATGAAAAAAAATTTGCGGCGTTTTTAT----AA-----CT--AGGTAAGCAATAGCGGCGT
56084645 T
245 T
* * **
56084646 TTTTTATAAAAACGCCGTAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAAAAATTTAGC
1 TTTATA-AAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAAT-AAAAATTTTTAGC
* * *
56084711 ATAACAAAACGGCGTCATTTTGCTGAAAATGAAATTGCGGCGTTTTTTATAAAAACGCCGCAAAA
64 ATAGCAAAACGGCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTTTATAAAAACGCCGCAAAA
*
56084776 AATAAATCAATTTATAAAATAAATAAAAAAATTTTAGCAGAGCAAAACGACGTCATTTTGTTCAA
129 AATAAATCAATTTATAAAATAAATAAAAAAATTTTAGCAGAGCAAAACAACGTCATTTTGTTCAA
**
56084841 AATGAAAAAATTTTTGCGGCG-TTTT-T-A-T-GGTAAGCAATAGCGGCGTT
194 AATGAAAAAAAATTTGCGGCGTTTTTATAACTAGGTAAGCAATAGCGGCGTT
*
56084888 TTTATAAAAAACACCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAATTTTTTAGCA
1 TTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAA-TTTTTAGCA
* *
56084953 TAGCAAAACAGCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTTATAAAAAAACGCCGCAAAA
65 TAGCAAAACGGCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTT-TATAAAAACGCCGCAAAA
56085018 AATAAATCAATTTATAAAA-AAATAAAA
129 AATAAATCAATTTATAAAATAAATAAAA
56085045 TATAAAATTT
Statistics
Matches: 369, Mismatches: 24, Indels: 30
0.87 0.06 0.07
Matches are distributed among these distances:
240 5 0.01
241 99 0.27
242 60 0.16
245 1 0.00
251 1 0.00
256 1 0.00
257 4 0.01
258 60 0.16
259 13 0.04
260 31 0.08
261 9 0.02
262 78 0.21
263 7 0.02
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (245 bp):
TTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAATTTTTAGCAT
AGCAAAACGGCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTTTATAAAAACGCCGCAAAAAA
TAAATCAATTTATAAAATAAATAAAAAAATTTTAGCAGAGCAAAACAACGTCATTTTGTTCAAAA
TGAAAAAAAATTTGCGGCGTTTTTATAACTAGGTAAGCAATAGCGGCGTT
Found at i:56086320 original size:30 final size:31
Alignment explanation
Indices: 56086259--56086323 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
56086249 ATCTCCAAAC
* *
56086259 TATATATGAACTTTGATTTTATGTATAATTT
1 TATATAGGAACTTTGATTTTATGAATAATTT
*
56086290 TATATAGGAAC-TTGATTTTGTGCAAT-ATTT
1 TATATAGGAACTTTGATTTTATG-AATAATTT
56086320 TATA
1 TATA
56086324 CTTGAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (31 bp):
TATATAGGAACTTTGATTTTATGAATAATTT
Found at i:56086496 original size:31 final size:31
Alignment explanation
Indices: 56086460--56086520 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
56086450 ATTTTTTTAA
*
56086460 ATGTATATAATTGAA-TCAAAATTAAAGTTTT
1 ATGTATACAATTGAACT-AAAATTAAAGTTTT
* *
56086491 ATGTATACATTTGAACTACAATTAAAGTTT
1 ATGTATACAATTGAACTAAAATTAAAGTTT
56086521 CACGTGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.41
Consensus pattern (31 bp):
ATGTATACAATTGAACTAAAATTAAAGTTTT
Found at i:56105369 original size:20 final size:21
Alignment explanation
Indices: 56105346--56105389 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
56105336 AAAAATTACA
56105346 AAAAAATT-AAAATAATTTTC
1 AAAAAATTCAAAATAATTTTC
*
56105366 -AAAAATTCAAAATAATTTTT
1 AAAAAATTCAAAATAATTTTC
56105386 AAAA
1 AAAA
56105390 TTGAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 11 0.52
21 3 0.14
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAAATTCAAAATAATTTTC
Found at i:56105371 original size:19 final size:19
Alignment explanation
Indices: 56105347--56105417 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
56105337 AAAATTACAA
56105347 AAAAATT-AAAATAATTTT
1 AAAAATTCAAAATAATTTT
56105365 CAAAAATTCAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
* *
56105385 TAAAATTGAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
56105404 AAAAATTCTAAAAT
1 AAAAATTC-AAAAT
56105418 TAAAGAAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
18 4 0.09
19 25 0.56
20 16 0.36
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:56105480 original size:9 final size:9
Alignment explanation
Indices: 56105468--56105497 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
56105458 TTTTTTGAAT
56105468 TTAAATAAG
1 TTAAATAAG
56105477 TT-AATAAG
1 TTAAATAAG
56105485 TTAAATAAG
1 TTAAATAAG
56105494 TTAA
1 TTAA
56105498 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (9 bp):
TTAAATAAG
Found at i:56108936 original size:20 final size:19
Alignment explanation
Indices: 56108913--56108980 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
56108903 TTACAAATAG
56108913 AATTTAAAATAATTTTCAAA
1 AATTTAAAATAATTTT-AAA
* *
56108933 AATTCAAAATAATTTTTAA
1 AATTTAAAATAATTTTAAA
*
56108952 AATTGAAAAT-ATTTGTAAA
1 AATTTAAAATAATTT-TAAA
56108971 AATTCTAAAA
1 AATT-TAAAA
56108981 ATTCTAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 4 0.10
19 18 0.44
20 19 0.46
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTTAAAATAATTTTAAA
Found at i:56108972 original size:19 final size:19
Alignment explanation
Indices: 56108913--56108990 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
56108903 TTACAAATAG
*
56108913 AATTTAAAATAATTTTCAAA
1 AATTCAAAATAATTTT-AAA
*
56108933 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTTAAA
*
56108952 AATTGAAAAT-ATTTGTAAA
1 AATTCAAAATAATTT-TAAA
* *
56108971 AATTCTAAA-AATTCTAAA
1 AATTCAAAATAATTTTAAA
56108989 AA
1 AA
56108991 AAAAAGAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
18 10 0.20
19 24 0.49
20 15 0.31
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:56112435 original size:40 final size:40
Alignment explanation
Indices: 56112384--56112461 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
56112374 AATTAGTAAA
**
56112384 TTGAATGAAATACTAATTTAGCTCAAGACT-GGGTGGAAAT
1 TTGAATGAAATACTAATTTAGAGCAAGA-TGGGGTGGAAAT
*
56112424 TTGAATGAAATATTAATTTAGAGCAAGATGGGGTGGAA
1 TTGAATGAAATACTAATTTAGAGCAAGATGGGGTGGAA
56112462 GTTCGAGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.03
40 33 0.97
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.29
Consensus pattern (40 bp):
TTGAATGAAATACTAATTTAGAGCAAGATGGGGTGGAAAT
Found at i:56126113 original size:6 final size:6
Alignment explanation
Indices: 56126102--56126212 Score: 156
Period size: 6 Copynumber: 19.0 Consensus size: 6
56126092 AAGATTACAC
*
56126102 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA A-TTTA TTTTTA ATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
* *
56126149 ATTTTT A-TAT- ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
* *
56126195 ATTTTT ATTTTT ATTTTA
1 ATTTTA ATTTTA ATTTTA
56126213 CATGTAGACA
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
4 1 0.01
5 8 0.08
6 86 0.91
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
ATTTTA
Found at i:56126169 original size:45 final size:46
Alignment explanation
Indices: 56126114--56126202 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
56126104 TTTAATTTTA
*
56126114 ATTTTAATTTTAATTTTAA-TTTATTTTTAATTTTAATTTTTATAT
1 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTATAT
56126159 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTAT
1 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTAT
56126203 TTTTATTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
45 19 0.45
46 23 0.55
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (46 bp):
ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTATAT
Found at i:56126174 original size:51 final size:52
Alignment explanation
Indices: 56126108--56126208 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 52
56126098 ACACATTTTA
*
56126108 ATTTTAATTTTAATTTTAATTTTAA-TTTATTTTTAATTTTAATTTTTATAT
1 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTATAT
*
56126159 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTATTTTTAT
1 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTAT
56126209 TTTACATGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 25 0.53
52 22 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (52 bp):
ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTATAT
Found at i:56135616 original size:47 final size:47
Alignment explanation
Indices: 56135557--56135863 Score: 483
Period size: 47 Copynumber: 6.6 Consensus size: 47
56135547 ATTCATGAAT
* ** **
56135557 TTGGTCAGCATATATAAAACAGTTTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
56135604 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
* *
56135651 TTGGACAGCAT-TATGTAACAAATTGGGCAGCTTTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
*
56135697 TTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
*
56135744 TTGGACAGCAT-TATGTAACAAATTGGGCAGCATTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
* * *
56135790 TTGGACAGCATAAATGTAATAAATTGGGCAGCATTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
*
56135837 TTGGACAGCATATATGTAATAAATTGG
1 TTGGACAGCATATATGTAACAAATTGG
56135864 TTCAACTCAT
Statistics
Matches: 243, Mismatches: 15, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
46 88 0.36
47 155 0.64
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (47 bp):
TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
Found at i:56135739 original size:93 final size:93
Alignment explanation
Indices: 56135580--56135863 Score: 505
Period size: 93 Copynumber: 3.0 Consensus size: 93
56135570 ATAAAACAGT
* *
56135580 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
56135645 TCAAAATTGGACAGCATTATGTAACAAA
66 TCAAAATTGGACAGCATTATGTAACAAA
*
56135673 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
56135738 TCAAAATTGGACAGCATTATGTAACAAA
66 TCAAAATTGGACAGCATTATGTAACAAA
* *
56135766 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATAAATGTAATAAATTGGGCAGCATTTATGCA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
*
56135831 TCAAAATTGGACAGCATATATGTAATAAA
66 TCAAAATTGGACAGCAT-TATGTAACAAA
56135860 TTGG
1 TTGG
56135864 TTCAACTCAT
Statistics
Matches: 183, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
93 169 0.92
94 14 0.08
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (93 bp):
TTGGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
TCAAAATTGGACAGCATTATGTAACAAA
Found at i:56135814 original size:140 final size:140
Alignment explanation
Indices: 56135580--56135863 Score: 516
Period size: 140 Copynumber: 2.0 Consensus size: 140
56135570 ATAAAACAGT
56135580 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
1 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
* *
56135645 TCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCTTTTATGCATCAAAATTGGACAGCATAT
66 TCAAAATTGGACAGCATAATGTAACAAATTGGGCAGCATTTATGCATCAAAATTGGACAGCATAT
56135710 ATGTAATAAA
131 ATGTAATAAA
*
56135720 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCAT-TATGTAACAAATTGGGCAGCATTTATGCA
1 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
*
56135784 TCAAAATTGGACAGCATAAATGTAATAAATTGGGCAGCATTTATGCATCAAAATTGGACAGCATA
66 TCAAAATTGGACAGCAT-AATGTAACAAATTGGGCAGCATTTATGCATCAAAATTGGACAGCATA
56135849 TATGTAATAAA
130 TATGTAATAAA
56135860 TTGG
1 TTGG
56135864 TTCAACTCAT
Statistics
Matches: 139, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
139 45 0.32
140 94 0.68
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (140 bp):
TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
TCAAAATTGGACAGCATAATGTAACAAATTGGGCAGCATTTATGCATCAAAATTGGACAGCATAT
ATGTAATAAA
Found at i:56136813 original size:43 final size:43
Alignment explanation
Indices: 56136704--56136819 Score: 141
Period size: 43 Copynumber: 2.7 Consensus size: 43
56136694 AACTCGTACA
*
56136704 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
56136747 ATGCC-ACTGTCCCAGACAG-GGTCTTAGACGTTAA-CACA-AGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACG-TAATCACATA-TCG
*
56136790 ATGCCAACGTCCCAAACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
56136820 ATGATTAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
42 4 0.06
43 53 0.84
44 6 0.10
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:56141881 original size:15 final size:16
Alignment explanation
Indices: 56141849--56141881 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
56141839 AGTGGGAGAA
56141849 TATTATGGGATTTATTT
1 TATTATGGGA-TTATTT
56141866 TATTATGGGA-TATTT
1 TATTATGGGATTATTT
56141881 T
1 T
56141882 TTTCCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TATTATGGGATTATTT
Found at i:56142243 original size:83 final size:83
Alignment explanation
Indices: 56142104--56142266 Score: 308
Period size: 83 Copynumber: 2.0 Consensus size: 83
56142094 TCAACTTTTC
56142104 ACAAATTTATTTATTGTCTTTAGTTTCTTTAACTTTCAATTCCTAAAACTTCCAGCTTGTTACTA
1 ACAAATTTATTTATTGTCTTTAGTTTCTTTAACTTTCAATTCCTAAAACTTCCAGCTTGTTACTA
56142169 CTTACCATTTACAACTCT
66 CTTACCATTTACAACTCT
56142187 ACAAATTTATTTATTGTCTTTAGTTTCTTTAACTTTCAATTCCTAAAACTTCCAGCTTGTTACTA
1 ACAAATTTATTTATTGTCTTTAGTTTCTTTAACTTTCAATTCCTAAAACTTCCAGCTTGTTACTA
* *
56142252 GTTGCCATTTACAAC
66 CTTACCATTTACAAC
56142267 CTTTTTTTTT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.45
Consensus pattern (83 bp):
ACAAATTTATTTATTGTCTTTAGTTTCTTTAACTTTCAATTCCTAAAACTTCCAGCTTGTTACTA
CTTACCATTTACAACTCT
Found at i:56162417 original size:16 final size:17
Alignment explanation
Indices: 56162378--56162430 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
56162368 TTTTTAAAAA
* *
56162378 AATATTTTAAAAAATAT
1 AATATTTTTACAAATAT
56162395 AATATTTTTACAAATAT
1 AATATTTTTACAAATAT
*
56162412 -ATATTTTTACAAAGAT
1 AATATTTTTACAAATAT
56162428 AAT
1 AAT
56162431 GAATTTTGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 15 0.47
17 17 0.53
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
AATATTTTTACAAATAT
Found at i:56162419 original size:17 final size:16
Alignment explanation
Indices: 56162389--56162429 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
56162379 ATATTTTAAA
56162389 AAATATAATATTTTTAC
1 AAATATAA-ATTTTTAC
*
56162406 AAATATATATTTTTAC
1 AAATATAAATTTTTAC
*
56162422 AAAGATAA
1 AAATATAA
56162430 TGAATTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (16 bp):
AAATATAAATTTTTAC
Found at i:56162484 original size:3 final size:3
Alignment explanation
Indices: 56162476--56162501 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
56162466 CCCCTTTAAA
56162476 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
56162502 TATTTATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:56164916 original size:18 final size:17
Alignment explanation
Indices: 56164890--56164927 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
56164880 CACTCTAGAC
*
56164890 ATATTTTTTAATATTTTT
1 ATATATTTTAA-ATTTTT
56164908 ATATATTTTAAATTTTT
1 ATATATTTTAAATTTTT
56164925 ATA
1 ATA
56164928 ACATATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATATTTTAAATTTTT
Found at i:56165192 original size:9 final size:9
Alignment explanation
Indices: 56165180--56165217 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
56165170 GTGTTATACG
56165180 TTTTATATA
1 TTTTATATA
*
56165189 TTTT-TAGA
1 TTTTATATA
*
56165197 TTTTATTTA
1 TTTTATATA
56165206 TTTTATATA
1 TTTTATATA
56165215 TTT
1 TTT
56165218 GGACAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (9 bp):
TTTTATATA
Done.