Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015020.1 Kokia drynarioides strain JFW-HI SEQ_130064, whole genome shotgun sequence
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: 1341705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 344 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:492666 original size:21 final size:21
Alignment explanation
Indices: 492642--492689 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
492632 ATGACCAGCT
492642 GAAGG-AAAAGAAAAAAAAAGA
1 GAAGGAAAAAG-AAAAAAAAGA
* *
492663 GAAGGAAAAAGAGAATAAAGA
1 GAAGGAAAAAGAAAAAAAAGA
492684 GAAGGA
1 GAAGGA
492690 CCCTACTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (21 bp):
GAAGGAAAAAGAAAAAAAAGA
Found at i:499893 original size:108 final size:107
Alignment explanation
Indices: 499738--499962 Score: 337
Period size: 108 Copynumber: 2.1 Consensus size: 107
499728 TCGAATCTTC
** *
499738 AAGAATAAAGAACATTTATTGATTTAAAATAGAATATTCGATTATTTAAGTTCAAAGAAAAATCA
1 AAGAATATTGAACATTTATTGATTTAAAAAAGAATATTCGATTATTTAAGTTCAAAGAAAAATCA
499803 TACCCAATACGTTTGAGCAT-AATTTTT-GAATTCCCTAAATAA
66 TACCCAATACGTTTGAGC-TCAATTTTTCGAATTCCCTAAA-AA
* *
499845 AAGAATATTGAACATTTGTTGATTTTAAAAAAGGATATTCGATTATTTAAGTTCAAAGAAAAATC
1 AAGAATATTGAACATTTATTGA-TTTAAAAAAGAATATTCGATTATTTAAGTTCAAAGAAAAATC
* *
499910 ATACCCAATATGTTTGAGCTCAATTTTTCGAATTCCTTAAAAA
65 ATACCCAATACGTTTGAGCTCAATTTTTCGAATTCCCTAAAAA
*
499953 AAGAACATTG
1 AAGAATATTG
499963 CCCTCTTTTT
Statistics
Matches: 107, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
107 20 0.19
108 76 0.71
109 11 0.10
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (107 bp):
AAGAATATTGAACATTTATTGATTTAAAAAAGAATATTCGATTATTTAAGTTCAAAGAAAAATCA
TACCCAATACGTTTGAGCTCAATTTTTCGAATTCCCTAAAAA
Found at i:500097 original size:22 final size:22
Alignment explanation
Indices: 500069--500113 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
500059 TAGTTTAAAA
500069 ATATACATGGATGAAGTAATGG
1 ATATACATGGATGAAGTAATGG
500091 ATATACATGGATGAAGTAATGG
1 ATATACATGGATGAAGTAATGG
500113 A
1 A
500114 GTGAGCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.27, T:0.27
Consensus pattern (22 bp):
ATATACATGGATGAAGTAATGG
Found at i:500299 original size:35 final size:35
Alignment explanation
Indices: 500233--500299 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
500223 TTTCATCTTT
* * *
500233 CTTGACTTTTAACCTTCCATCTTCTTTAACCTCCC
1 CTTGACCTTTAACCTTCCATCTTCCTCAACCTCCC
*
500268 CTTGACCTTTAACCTTCTATCTTCCTCAACCT
1 CTTGACCTTTAACCTTCCATCTTCCTCAACCT
500300 TTCATGTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.18, C:0.37, G:0.03, T:0.42
Consensus pattern (35 bp):
CTTGACCTTTAACCTTCCATCTTCCTCAACCTCCC
Found at i:500770 original size:30 final size:30
Alignment explanation
Indices: 500736--500795 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
500726 AAGACTTTGA
500736 ATAAGATTGAAGAATCAACAACTTGGATAT
1 ATAAGATTGAAGAATCAACAACTTGGATAT
*
500766 ATAAGATTGAAGTATCAACAACTTGGATAT
1 ATAAGATTGAAGAATCAACAACTTGGATAT
500796 TTTTACTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (30 bp):
ATAAGATTGAAGAATCAACAACTTGGATAT
Found at i:505682 original size:17 final size:17
Alignment explanation
Indices: 505662--505736 Score: 87
Period size: 17 Copynumber: 4.4 Consensus size: 17
505652 TTCCTTGACT
505662 TTTAACCTTCCATCTTC
1 TTTAACCTTCCATCTTC
505679 TTTAACCTTCCATCTTC
1 TTTAACCTTCCATCTTC
* *
505696 CTTAACCTCCCATCTTC
1 TTTAACCTTCCATCTTC
* * * *
505713 CTCAACCTTTCATATTC
1 TTTAACCTTCCATCTTC
505730 TTGTAAC
1 TT-TAAC
505737 TAGTTTTTCC
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
17 46 0.94
18 3 0.06
ACGTcount: A:0.20, C:0.36, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAACCTTCCATCTTC
Found at i:506177 original size:31 final size:32
Alignment explanation
Indices: 506133--506196 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
506123 AAACGGTAAT
506133 TTTTAAAAGAAATAAAAATAAAA-GAGTTAAA
1 TTTTAAAAGAAATAAAAATAAAATGAGTTAAA
* *
506164 TTTTAACAA-AAATACAAATAAAATGATTTAAA
1 TTTTAA-AAGAAATAAAAATAAAATGAGTTAAA
506196 T
1 T
506197 AAAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (32 bp):
TTTTAAAAGAAATAAAAATAAAATGAGTTAAA
Found at i:508358 original size:78 final size:78
Alignment explanation
Indices: 508114--508589 Score: 477
Period size: 78 Copynumber: 5.9 Consensus size: 78
508104 GAGATGATAG
* *
508114 CTTCAATCTGCCCCTCTTGATTTAGGTGTAAGAGATTGGATGGTGGCTTCAATCTGCCCCATGAT
1 CTTCAATCTG-CCCTC-TGA-TTAGG-GTAAAAGATCGGA---T-GCTTCAATCTGCCCCATGAT
* * *
508179 AGGTGTAAAAGATTGGATGATGT
58 CGGGGTAAGAGATTGG-TG-TGT
* * * * * * * *
508202 GTTCAATATGCCTTTTGATTAGGGTAAGAGATTGGATGGCTTCAA-CGTGCCCCATGGTTGGGGT
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATCGGAT-GCTTCAATC-TGCCCCATGATCGGGGT
* ***
508266 AAAAGATCAATGTGT
64 AAGAGATTGGTGTGT
* * * * * *
508281 CTTCATTCTACCTTCTAATTAGGGTAAAAGATCGGATGCTTCAATCTGCCTCATGATCGAGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATCGGATGCTTCAATCTGCCCCATGATCGGGGTAA
508346 GAGATTGGTGTGT
66 GAGATTGGTGTGT
* * * * *
508359 CCTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATGATTCAATCTGCCCCATGGTCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATCGGATGCTTCAATCTGCCCCATGATCGGGGTAA
508424 GAGATTGGATGATGT
66 GAGATTGG-TG-TGT
* * *
508439 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATCAGATGCTTCAATCTACCCCATGATCAGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATCGGATGCTTCAATCTGCCCCATGATCGGGGTAA
508504 GAGATTGGTGTGT
66 GAGATTGGTGTGT
* * * * *
508517 CTTCAATATGCCGTCTGATTAGGGTAAAAGATTGGGATGCTTTAATCTGCCTCATGATCGGGGTA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGA-TCGGATGCTTCAATCTGCCCCATGATCGGGGTA
*
508582 TGAGATTG
65 AGAGATTG
508590 TGGTAGCTTC
Statistics
Matches: 331, Mismatches: 52, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
78 127 0.38
79 71 0.21
80 71 0.21
81 30 0.09
84 13 0.04
85 5 0.02
86 3 0.01
87 3 0.01
88 8 0.02
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (78 bp):
CTTCAATCTGCCCTCTGATTAGGGTAAAAGATCGGATGCTTCAATCTGCCCCATGATCGGGGTAA
GAGATTGGTGTGT
Found at i:508477 original size:158 final size:157
Alignment explanation
Indices: 508159--508589 Score: 528
Period size: 158 Copynumber: 2.7 Consensus size: 157
508149 TTGGATGGTG
* * * * *
508159 GCTTCAATCTGCCCCATGATAG-GTGTAAAAGATTGGATGATGTGTTCAATATGCCTTTTGATTA
1 GCTTCAATCTGCCCCATGATCGAG-GTAAGAGATTGG-TG-TGTCTTCAATATGCCCTCTGATTA
* * * *
508223 GGGTAAGAGATTGGATGGCTTCAA-CGTGCCCCATGGTTGGGGTAAAAGA-TCAATGTGTCTTCA
63 GGGTAAAAGATTGGAT-GCTTCAATC-TGCCCCATGGTCGGGGTAAGAGATTGAATGTGTCTTCA
* * *
508286 TTCTACCTTCTAATTAGGGTAAAAGATCGGAT
126 ATCTACCCTCTAATTAGGGTAAAAGATCAGAT
* * * *
508318 GCTTCAATCTGCCTCATGATCGAGGTAAGAGATTGGTGTGTCCTCAATCTGCCCTCTAATTAGGG
1 GCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGGTGTGTCTTCAATATGCCCTCTGATTAGGG
* *
508383 TAAAAGATTGGATGATTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATCT
66 TAAAAGATTGGATGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATG-TGTCTTCAATCT
* *
508448 GCCCTCTGATTAGGGTAAAAGATCAGAT
130 ACCCTCTAATTAGGGTAAAAGATCAGAT
* *
508476 GCTTCAATCTACCCCATGATC-AGGGTAAGAGATTGGTGTGTCTTCAATATGCCGTCTGATTAGG
1 GCTTCAATCTGCCCCATGATCGA-GGTAAGAGATTGGTGTGTCTTCAATATGCCCTCTGATTAGG
* * * *
508540 GTAAAAGATTGGGATGCTTTAATCTGCCTCATGATCGGGGTATGAGATTG
65 GTAAAAGATT-GGATGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTG
508590 TGGTAGCTTC
Statistics
Matches: 235, Mismatches: 31, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
156 27 0.11
157 39 0.17
158 103 0.44
159 65 0.28
160 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (157 bp):
GCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGGTGTGTCTTCAATATGCCCTCTGATTAGGG
TAAAAGATTGGATGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGTGTCTTCAATCTA
CCCTCTAATTAGGGTAAAAGATCAGAT
Found at i:508576 original size:237 final size:237
Alignment explanation
Indices: 508161--508589 Score: 574
Period size: 237 Copynumber: 1.8 Consensus size: 237
508151 GGATGGTGGC
* * * *
508161 TTCAATCTGCCCCATGATAGGTGTAAAAGATTGGATGATGTGTTCAATATGCCTTTTGATTAGGG
1 TTCAATCTGCCCCATGATAGGGGTAAAAGATTGGATGATGTCTTCAATATGCCCTCTGATTAGGG
* ** * * ** * *
508226 TAAGAGATTGGATGGCTTCAACGTGCCCCATGGTTGGGGTAAAAGATCAATGTGTCTTCATTCTA
66 TAAAAGATCAGATGGCTTCAACGTACCCCATGATCAGGGTAAAAGATCAATGTGTCTTCAATATA
*
508291 CCTTCTAATTAGGGTAAAAGATCGGATGCTTCAATCTGCCTCATGATCGAGGTAAGAGATTGGTG
131 CCGTCTAATTAGGGTAAAAGATCGGATGCTTCAATCTGCCTCATGATCGAGGTAAGAGATTGGTG
508356 TGTCCTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATGA
196 TGTCCTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATGA
* * * *
508398 TTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCTCTGATTAGGG
1 TTCAATCTGCCCCATGATAGGGGTAAAAGATTGGATGATGTCTTCAATATGCCCTCTGATTAGGG
* ***
508463 TAAAAGATCAGAT-GCTTCAATC-TACCCCATGATCAGGGTAAGAGATTGGTGTGTCTTCAATAT
66 TAAAAGATCAGATGGCTTCAA-CGTACCCCATGATCAGGGTAAAAGATCAATGTGTCTTCAATAT
* * * * * *
508526 GCCGTCTGATTAGGGTAAAAGATTGGGATGCTTTAATCTGCCTCATGATCGGGGTATGAGATTG
130 ACCGTCTAATTAGGGTAAAAGA-TCGGATGCTTCAATCTGCCTCATGATCGAGGTAAGAGATTG
508590 TGGTAGCTTC
Statistics
Matches: 162, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
236 57 0.35
237 105 0.65
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (237 bp):
TTCAATCTGCCCCATGATAGGGGTAAAAGATTGGATGATGTCTTCAATATGCCCTCTGATTAGGG
TAAAAGATCAGATGGCTTCAACGTACCCCATGATCAGGGTAAAAGATCAATGTGTCTTCAATATA
CCGTCTAATTAGGGTAAAAGATCGGATGCTTCAATCTGCCTCATGATCGAGGTAAGAGATTGGTG
TGTCCTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATGA
Found at i:508900 original size:49 final size:49
Alignment explanation
Indices: 508847--508988 Score: 124
Period size: 49 Copynumber: 2.9 Consensus size: 49
508837 TGCTTTTCCT
* * * *
508847 CATCTTCATGGTATAAGATTTGTCGTTGCGGCCTGAATCTTTCCATTCA
1 CATCTTCATGGTATAAGATTCGTCGTTGCAGCCTCAACCTTTCCATTCA
* * * * *
508896 CATC-TCTAAGGTATAAGGTTCGTTGTTGCAGCTTCAACCTTTCCCTTCA
1 CATCTTC-ATGGTATAAGATTCGTCGTTGCAGCCTCAACCTTTCCATTCA
* * * * * * *
508945 TATCTCCATGGTACAAGATTCGTTGTTACAGCTTCAATCTTTCC
1 CATCTTCATGGTATAAGATTCGTCGTTGCAGCCTCAACCTTTCC
508989 CATCACGTCT
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
48 2 0.03
49 72 0.96
50 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (49 bp):
CATCTTCATGGTATAAGATTCGTCGTTGCAGCCTCAACCTTTCCATTCA
Found at i:509147 original size:49 final size:49
Alignment explanation
Indices: 508897--509153 Score: 187
Period size: 49 Copynumber: 5.2 Consensus size: 49
508887 TTCCATTCAC
* * * *
508897 ATCTCTAAGGTATAAGGTTCGTTGTTGCAGCTTCAACCTTTCCCTTCAT
1 ATCTCTAAGGTACAAGGTTTGTAGTTGCAGCTTCAACCTTTCCCTCCAT
* * * * * * * *
508946 ATCTCCATGGTACAAGATTCGTTGTTACAGCTTCAATCTTTCCCAT-CAC
1 ATCTCTAAGGTACAAGGTTTGTAGTTGCAGCTTCAACCTTTCCC-TCCAT
* * * * *
508995 GTCTCTAAGGTACAAGGTTTATCGTTAC-GACTTCAGCCTTTCCCTCCAT
1 ATCTCTAAGGTACAAGGTTTGTAGTTGCAG-CTTCAACCTTTCCCTCCAT
* ** * ** ** * *
509044 ATCTCTAGGGTATTA-GTTTTTCAGTTGTGGCTTCAATATTTCCCTTCAC
1 ATCTCTAAGGTACAAGGTTTGT-AGTTGCAGCTTCAACCTTTCCCTCCAT
* * *
509093 GTCTCTAAGGTACAAGGTTTGTAGTTGCAACTTCAACCTTTTCCTCCAT
1 ATCTCTAAGGTACAAGGTTTGTAGTTGCAGCTTCAACCTTTCCCTCCAT
*
509142 ATCTCTAGGGTA
1 ATCTCTAAGGTA
509154 TTAGATTTGT
Statistics
Matches: 157, Mismatches: 45, Indels: 12
0.73 0.21 0.06
Matches are distributed among these distances:
48 7 0.04
49 143 0.91
50 7 0.04
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (49 bp):
ATCTCTAAGGTACAAGGTTTGTAGTTGCAGCTTCAACCTTTCCCTCCAT
Found at i:509154 original size:98 final size:96
Alignment explanation
Indices: 508882--509186 Score: 330
Period size: 98 Copynumber: 3.1 Consensus size: 96
508872 TTGCGGCCTG
* * * * * * *
508882 AATCTTTCCATTCACATCTCTAAGGTATAAGGTTCGTTGTTGCAGCTTCAACCTTTCCCTTCATA
1 AATCTTTCCCTTCACGTCTCTAAGGTACAAGGTTTGTAGTTGCAACTTCAACCTTTCCCTCCATA
* * ** *
508947 TCTCCATGGTACAAG--ATTCGTTGTTACAGCTTC
66 TCTCTAGGGTATTAGTTTTTCGTTG-T---GCTTC
* * * * * *
508980 AATCTTTCCCATCACGTCTCTAAGGTACAAGGTTTATCGTTACGACTTCAGCCTTTCCCTCCATA
1 AATCTTTCCCTTCACGTCTCTAAGGTACAAGGTTTGTAGTTGCAACTTCAACCTTTCCCTCCATA
509045 TCTCTAGGGTATTAGTTTTTCAGTTGTGGCTTC
66 TCTCTAGGGTATTAGTTTTTC-GTTGT-GCTTC
* *
509078 AATATTTCCCTTCACGTCTCTAAGGTACAAGGTTTGTAGTTGCAACTTCAACCTTTTCCTCCATA
1 AATCTTTCCCTTCACGTCTCTAAGGTACAAGGTTTGTAGTTGCAACTTCAACCTTTCCCTCCATA
*
509143 TCTCTAGGGTATTAGATTTGTCGTT-T-CTTC
66 TCTCTAGGGTATTAG-TTTTTCGTTGTGCTTC
509173 AATCTTTCCCTTCA
1 AATCTTTCCCTTCA
509187 AACCTATAGA
Statistics
Matches: 175, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
95 17 0.10
97 1 0.01
98 144 0.82
99 5 0.03
100 4 0.02
101 4 0.02
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.39
Consensus pattern (96 bp):
AATCTTTCCCTTCACGTCTCTAAGGTACAAGGTTTGTAGTTGCAACTTCAACCTTTCCCTCCATA
TCTCTAGGGTATTAGTTTTTCGTTGTGCTTC
Found at i:510034 original size:2 final size:2
Alignment explanation
Indices: 510027--510051 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
510017 GTAGATTCAA
510027 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
510052 CATAAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:510499 original size:41 final size:43
Alignment explanation
Indices: 510441--510628 Score: 158
Period size: 41 Copynumber: 4.5 Consensus size: 43
510431 ACATTTAATA
* * *
510441 ACCGAGTCGTGAA-TCTTCCTTTTTAA-ATAATCTTATGCTC-T
1 ACCGAGTCAT-AAGTCTTCCTTTTAAACATAATCTCATGCTCAT
510482 ACCGAGTCATAAGTCTTCC-TTTAAACATAATCTCATGCTCAT
1 ACCGAGTCATAAGTCTTCCTTTTAAACATAATCTCATGCTCAT
** * *
510524 TTCGAGTCATGAGTCCTCC--TTAAACATAATCTCATGCTCAT
1 ACCGAGTCATAAGTCTTCCTTTTAAACATAATCTCATGCTCAT
** ** * *
510565 TTCGAGTCGCAAGTCTTCC--TAAAACAAAATCTCATGCTCAT
1 ACCGAGTCATAAGTCTTCCTTTTAAACATAATCTCATGCTCAT
* * **
510606 TCCGATTCACGAGTCTTCCTTTT
1 ACCGAGTCATAAGTCTTCCTTTT
510629 TCTTTTGAGT
Statistics
Matches: 124, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
40 7 0.06
41 100 0.81
42 16 0.13
43 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.36
Consensus pattern (43 bp):
ACCGAGTCATAAGTCTTCCTTTTAAACATAATCTCATGCTCAT
Found at i:514756 original size:83 final size:83
Alignment explanation
Indices: 514668--514838 Score: 288
Period size: 83 Copynumber: 2.1 Consensus size: 83
514658 AGACTACCGA
* *
514668 TACTTCTATGAGTAAAACTACCGATAGTTATCTTTCATCTATCAAAACAACACAAGTCAGTAACC
1 TACTTCTATGAGTAAAACTACCGATACTTATCTTTCATCTACCAAAACAACACAAGTCAGTAACC
*
514733 TACATCTCATTTCCTCTG
66 TACATCTCACTTCCTCTG
* *
514751 TACTTCTATGAGTAGAACTACCGATACTTATCTTTCATCTACCGAAACAACACAAGTCAGTAACC
1 TACTTCTATGAGTAAAACTACCGATACTTATCTTTCATCTACCAAAACAACACAAGTCAGTAACC
*
514816 TACATCTCACTTCCTTTG
66 TACATCTCACTTCCTCTG
514834 TACTT
1 TACTT
514839 TTACTGATAC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.33
Consensus pattern (83 bp):
TACTTCTATGAGTAAAACTACCGATACTTATCTTTCATCTACCAAAACAACACAAGTCAGTAACC
TACATCTCACTTCCTCTG
Found at i:515395 original size:41 final size:42
Alignment explanation
Indices: 515331--515561 Score: 223
Period size: 43 Copynumber: 5.5 Consensus size: 42
515321 TTATACTCTA
**
515331 CCGAGTCATAAGTCTTCCTTTAAACATAATCTCATGCTCATT
1 CCGAGTCACGAGTCTTCCTTTAAACATAATCTCATGCTCATT
** * * * *
515373 TTGAGTCACGAGTATTCC-TTAAACAAAATCTCATACTTATT
1 CCGAGTCACGAGTCTTCCTTTAAACATAATCTCATGCTCATT
* *
515414 CCAAGTCACGAGTCTTTC-TTAAACATAATCTCATGCTCATT
1 CCGAGTCACGAGTCTTCCTTTAAACATAATCTCATGCTCATT
* ** *
515455 CCGAGTCACGAGTCTTCCATTTATATTTAATCTCATGCTCATC
1 CCGAGTCACGAGTCTTCC-TTTAAACATAATCTCATGCTCATT
* ** * * * *
515498 CCGAGACGTGAGTCTTCTATTTATACATAATCTCATTCTCATC
1 CCGAGTCACGAGTCTTC-CTTTAAACATAATCTCATGCTCATT
* *
515541 CCGAGACATGAGTCTTCCTTT
1 CCGAGTCACGAGTCTTCCTTT
515562 TTCTTTTGAT
Statistics
Matches: 155, Mismatches: 31, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
41 69 0.45
42 16 0.10
43 70 0.45
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.36
Consensus pattern (42 bp):
CCGAGTCACGAGTCTTCCTTTAAACATAATCTCATGCTCATT
Found at i:518349 original size:19 final size:19
Alignment explanation
Indices: 518326--518370 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
518316 TTTCTTTTTC
518326 CTTTTTTT-CTTTTTATTT
1 CTTTTTTTCCTTTTTATTT
*
518344 CTTTTTTCCCTTTTTATTT
1 CTTTTTTTCCTTTTTATTT
*
518363 ATTTTTTT
1 CTTTTTTT
518371 GGGTGAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (19 bp):
CTTTTTTTCCTTTTTATTT
Found at i:525558 original size:108 final size:108
Alignment explanation
Indices: 525416--525626 Score: 325
Period size: 108 Copynumber: 2.0 Consensus size: 108
525406 AAGAATAAAG
* * *
525416 AACATTTATTGATTTAAAATAGGATATTCGATTATTTAAGTTCGAAGAAAAATCATACACAGTAC
1 AACATTTATTGATTTAAAATAGGATACTCGATTATTTAAGTTCAAAGAAAAATCATACACAATAC
525481 GTTTGAGCACAATTTTT-GAATTCCCTAAATAAAAGAATATCA
66 GTTTGAGCACAATTTTTCGAATTCCCTAAATAAAAGAATATCA
* * *
525523 AACATTTGTTGATTTTAAAGTAGGATACTCGATTATTTAAGTTCAAAGAAAAATCATACCCAATA
1 AACATTTATTGA-TTTAAAATAGGATACTCGATTATTTAAGTTCAAAGAAAAATCATACACAATA
* **
525588 TGTTTGAGCACAATTTTTCGAATTCTTTAAATAAAAGAA
65 CGTTTGAGCACAATTTTTCGAATTCCCTAAATAAAAGAA
525627 CATTGCCCTC
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 11 0.12
108 64 0.69
109 18 0.19
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (108 bp):
AACATTTATTGATTTAAAATAGGATACTCGATTATTTAAGTTCAAAGAAAAATCATACACAATAC
GTTTGAGCACAATTTTTCGAATTCCCTAAATAAAAGAATATCA
Found at i:526025 original size:19 final size:20
Alignment explanation
Indices: 525987--526027 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
525977 TAATTTTTTT
* *
525987 AAAAAGGATTTAATTAATAA
1 AAAAAGGATTAAAATAATAA
526007 AAAAAGGATTAAAAT-ATAA
1 AAAAAGGATTAAAATAATAA
526026 AA
1 AA
526028 GAAACATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (20 bp):
AAAAAGGATTAAAATAATAA
Found at i:526105 original size:25 final size:22
Alignment explanation
Indices: 526077--526121 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 22
526067 AGAGTTAAAT
526077 TTTAACAAAAATACAAATAAAAGGA
1 TTTAA-AAAAATA-AAA-AAAAGGA
*
526102 TTTAAATAAATAAAAAAAAG
1 TTTAAAAAAATAAAAAAAAG
526122 AACAGAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 3 0.16
24 6 0.32
25 5 0.26
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (22 bp):
TTTAAAAAAATAAAAAAAAGGA
Found at i:528455 original size:21 final size:22
Alignment explanation
Indices: 528426--528467 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
528416 CATGTAATGA
*
528426 TCTAATTTT-ATTTTTTTTTGC
1 TCTAATTTTAATTTGTTTTTGC
*
528447 TCTATTTTTAATTTGTTTTTG
1 TCTAATTTTAATTTGTTTTTG
528468 GATTCTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.71
Consensus pattern (22 bp):
TCTAATTTTAATTTGTTTTTGC
Found at i:529024 original size:60 final size:57
Alignment explanation
Indices: 528881--529150 Score: 301
Period size: 60 Copynumber: 4.6 Consensus size: 57
528871 TAAAAAAAAA
* * * * *
528881 TTGGTGTTGGCCAATGCTTGACCGACACCACCTTTTTTACCAGATAAGAAAAATATT
1 TTGGTGTTGGACAATGCTTGGCCGACACCACCTTTTTTATCAGATAAAAAAAATTTT
* *
528938 TTGGTGTTGGACAATGCTTGGCCGACACCACTTTTTTTATCATATAAAAAAGTAATTTTT
1 TTGGTGTTGGACAATGCTTGGCCGACACCACCTTTTTTATCAGATAAAAAA--AA-TTTT
* * * *
528998 TTGGTGTTGGTC-ATACATTGGCCGACACCACATTTTTTATCAGATAAGAAAAAAATTT
1 TTGGTGTTGGACAATGC-TTGGCCGACACCACCTTTTTTATCAGATAA-AAAAAATTTT
* *
529056 TTGGTGTTGGACAATGCTTGGCCGACACTACCTTTTTTATCTGATAAAAAAACAAATTTT
1 TTGGTGTTGGACAATGCTTGGCCGACACCACCTTTTTTATCAGAT--AAAAA-AAATTTT
* * *
529116 TTGGTGTTAG-CCATGCATTGGCCGACACCAACTTT
1 TTGGTGTTGGACAATGC-TTGGCCGACACCACCTTT
529151 CCCTCCTTTC
Statistics
Matches: 181, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
57 45 0.25
58 39 0.22
59 18 0.10
60 75 0.41
61 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (57 bp):
TTGGTGTTGGACAATGCTTGGCCGACACCACCTTTTTTATCAGATAAAAAAAATTTT
Found at i:529103 original size:118 final size:117
Alignment explanation
Indices: 528902--529145 Score: 364
Period size: 118 Copynumber: 2.1 Consensus size: 117
528892 CAATGCTTGA
* *
528902 CCGACACCACCTTTTTTACCAGATAAGAAAAATATTTTGGTGTTGGACAATGCTTGGCCGACACC
1 CCGACACCACATTTTTTACCAGATAAGAAAAAAATTTTGGTGTTGGACAATGCTTGGCCGACACC
* ** * * *
528967 ACTTTTTTTATCATATAAAAAAGTAATTTTTTTGGTGTTGGTCATACATTGG
66 ACCTTTTTTATCATATAAAAAAACAAATTTTTTGGTGTTAGCCATACATTGG
*
529019 CCGACACCACATTTTTTATCAGATAAGAAAAAAATTTTTGGTGTTGGACAATGCTTGGCCGACAC
1 CCGACACCACATTTTTTACCAGATAAGAAAAAAA-TTTTGGTGTTGGACAATGCTTGGCCGACAC
* *
529084 TACCTTTTTTATC-TGATAAAAAAACAAATTTTTTGGTGTTAGCCATGCATTGG
65 CACCTTTTTTATCAT-ATAAAAAAACAAATTTTTTGGTGTTAGCCATACATTGG
529137 CCGACACCA
1 CCGACACCA
529146 ACTTTCCCTC
Statistics
Matches: 114, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
117 32 0.28
118 82 0.72
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (117 bp):
CCGACACCACATTTTTTACCAGATAAGAAAAAAATTTTGGTGTTGGACAATGCTTGGCCGACACC
ACCTTTTTTATCATATAAAAAAACAAATTTTTTGGTGTTAGCCATACATTGG
Found at i:530013 original size:18 final size:18
Alignment explanation
Indices: 529992--530045 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
529982 AATTAGAAAT
529992 GAAATTTAAAATATAAAC
1 GAAATTTAAAATATAAAC
530010 GAAA-TTAGAAAT-T----
1 GAAATTTA-AAATATAAAC
530023 -AAATTTAAAATATAAAC
1 GAAATTTAAAATATAAAC
530040 GAAATT
1 GAAATT
530046 ACTAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
12 7 0.25
13 4 0.14
17 4 0.14
18 13 0.46
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (18 bp):
GAAATTTAAAATATAAAC
Found at i:530018 original size:30 final size:30
Alignment explanation
Indices: 529982--530073 Score: 148
Period size: 30 Copynumber: 3.1 Consensus size: 30
529972 AAAAAATAAT
*
529982 AATTAGAAATGAAATTTAAAATATAAACGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
530012 AATTAGAAATTAAATTTAAAATATAAACGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
** *
530042 AATTACTAATTAAATTTAAAAAATAAACGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
530072 AA
1 AA
530074 AATAATCAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (30 bp):
AATTAGAAATTAAATTTAAAATATAAACGA
Found at i:530577 original size:12 final size:12
Alignment explanation
Indices: 530529--530609 Score: 65
Period size: 12 Copynumber: 6.8 Consensus size: 12
530519 GGGTTGGTCT
*
530529 TCGGGCTGATCC
1 TCGGGCTCATCC
* *
530541 GC-GGCGTCATAC
1 TCGGGC-TCATCC
* *
530553 TCGAGCGCATCC
1 TCGGGCTCATCC
*
530565 TCGGGCTCGTCC
1 TCGGGCTCATCC
* *
530577 TCAGGCTCATTC
1 TCGGGCTCATCC
530589 TCGGGCTCATCC
1 TCGGGCTCATCC
*
530601 TCGAGCTCA
1 TCGGGCTCA
530610 AAATCTGAAT
Statistics
Matches: 51, Mismatches: 16, Indels: 4
0.72 0.23 0.06
Matches are distributed among these distances:
11 3 0.06
12 46 0.90
13 2 0.04
ACGTcount: A:0.12, C:0.37, G:0.27, T:0.23
Consensus pattern (12 bp):
TCGGGCTCATCC
Found at i:530608 original size:24 final size:24
Alignment explanation
Indices: 530547--530609 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
530537 ATCCGCGGCG
* *
530547 TCATACTCGAGCGCATCCTCGGGC
1 TCATCCTCGAGCTCATCCTCGGGC
* *
530571 TCGTCCTC-AGGCTCATTCTCGGGC
1 TCATCCTCGA-GCTCATCCTCGGGC
530595 TCATCCTCGAGCTCA
1 TCATCCTCGAGCTCA
530610 AAATCTGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
23 1 0.03
24 30 0.94
25 1 0.03
ACGTcount: A:0.14, C:0.38, G:0.22, T:0.25
Consensus pattern (24 bp):
TCATCCTCGAGCTCATCCTCGGGC
Found at i:532399 original size:51 final size:50
Alignment explanation
Indices: 532344--532493 Score: 122
Period size: 51 Copynumber: 3.1 Consensus size: 50
532334 TAATTTGGTA
532344 AATAATGTATTATCAAATCAACACATTATTTTATATAAATTAAAATATTAT
1 AATAATGTATT-TCAAATCAACACATTATTTTATATAAATTAAAATATTAT
* ** * **
532395 AATAA--TCTTT--AATTTA-A-A-TAATTT-TA-AAATTTGAAT-TTGAT
1 AATAATGTATTTCAAATCAACACATTATTTTATATAAATTAAAATATT-AT
* *
532436 AAATAATGTATTGTCAAATCAACACATTATTTGATATAAATTGAAATATTAT
1 -AATAATGTATT-TCAAATCAACACATTATTTTATATAAATTAAAATATTAT
532488 AATAAT
1 AATAAT
532494 CTTTAATTTA
Statistics
Matches: 73, Mismatches: 13, Indels: 26
0.65 0.12 0.23
Matches are distributed among these distances:
40 2 0.03
41 10 0.14
42 7 0.10
43 5 0.07
44 4 0.05
45 2 0.03
46 4 0.05
47 4 0.05
48 2 0.03
49 4 0.05
50 4 0.05
51 13 0.18
52 10 0.14
53 2 0.03
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (50 bp):
AATAATGTATTTCAAATCAACACATTATTTTATATAAATTAAAATATTAT
Found at i:532455 original size:93 final size:93
Alignment explanation
Indices: 532289--533038 Score: 652
Period size: 93 Copynumber: 8.2 Consensus size: 93
532279 GACTAAGGGT
* * *
532289 AATATTATAATAATCATTTTTAATTTAAATAATTTTAAATTTTTTTAATTTGGTAAATAATGTAT
1 AATATTATAATAATC---TTTAATTTAAATAATTTTAAA--ATTTAAATTTGATAAATAATGTAT
* *
532354 TATCAAATCAACACATTATTTTATATAAATTAA
61 TGTCAAATCAACACATTATTTTATATAAATTGA
*
532387 AATATTATAATAATCTTTAATTTAAATAATTTTAAAATTTGAATTTGATAAATAATGTATTGTCA
1 AATATTATAATAATCTTTAATTTAAATAATTTTAAAATTTAAATTTGATAAATAATGTATTGTCA
*
532452 AATCAACACATTATTTGATATAAATTGA
66 AATCAACACATTATTTTATATAAATTGA
* * * *
532480 AATATTATAATAATCTTTAATTTAAATAATTTGAAATTTTGAATTTGATAAATAATGTGTTGTCT
1 AATATTATAATAATCTTTAATTTAAATAATTTTAAAATTTAAATTTGATAAATAATGTATTGTC-
** * * **
532545 AAATTGA-A-A-TATTATA-ATAATTTTT
65 AAATCAACACATTATTTTATATAAATTGA
* * **
532570 ACT-TTA-AATAAT-TTTGAATTT---TGAATTTGATAAA--TAATATATTG-TCAAATCAACAT
1 AATATTATAATAATCTTT-AATTTAAAT-AATTTTA-AAATTTAA-AT-TTGAT-AAAT-AATGT
* ** **
532626 ATTATTTAAT-ATA-A-ATTGA-AATAT-TATAA-T--
59 ATTGTCAAATCA-ACACATT-ATTTTATATA-AATTGA
* * *
532656 AATCATT-T-TTAA--TTTAA-ATAAATTTAATTTT----TTT-AATTCCG-TAAATAATGTATT
1 AAT-ATTATAATAATCTTTAATTTAAA--TAATTTTAAAATTTAAATT-TGATAAATAATGTATT
*
532710 GTCACATCAACA-ATTATTTTATATAAATTGA
62 GTCAAATCAACACATTATTTTATATAAATTGA
* *
532741 AATATTATAATAATCGTTTTTAATTTAAATAA-TTTAAATTTTTAATTTGATAAATAATGTATTG
1 AATATTATAATAATC---TTTAATTTAAATAATTTTAAAATTTAAATTTGATAAATAATGTATTG
532805 TCAAATCAACACATTATTTTATATAAATTGA
63 TCAAATCAACACATTATTTTATATAAATTGA
* *
532836 AATATTATAATAATCATTTTTACTTTAAATAATTTT-AAATTTAAATTTGGTAAATAATGTATTG
1 AATATTATAATAATC---TTTAATTTAAATAATTTTAAAATTTAAATTTGATAAATAATGTATTG
* * * *
532900 TCAAATCAATATATTATTTGATATAAATTAA
63 TCAAATCAACACATTATTTTATATAAATTGA
* *
532931 AATATTATAATAATTTTTAATTTAAATAATTTTAAAATGTAAATTTGATAAATAATGTATTGTCA
1 AATATTATAATAATCTTTAATTTAAATAATTTTAAAATTTAAATTTGATAAATAATGTATTGTCA
*
532996 AATCAACACATTATTTGATATAAATTGA
66 AATCAACACATTATTTTATATAAATTGA
533024 AATATTATAATAATC
1 AATATTATAATAATC
533039 AATTTTAAAT
Statistics
Matches: 542, Mismatches: 62, Indels: 101
0.77 0.09 0.14
Matches are distributed among these distances:
81 11 0.02
82 15 0.03
83 7 0.01
84 5 0.01
85 10 0.02
86 18 0.03
87 21 0.04
88 31 0.06
89 9 0.02
90 11 0.02
91 10 0.02
92 22 0.04
93 185 0.34
94 33 0.06
95 136 0.25
96 3 0.01
98 15 0.03
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (93 bp):
AATATTATAATAATCTTTAATTTAAATAATTTTAAAATTTAAATTTGATAAATAATGTATTGTCA
AATCAACACATTATTTTATATAAATTGA
Found at i:532552 original size:72 final size:72
Alignment explanation
Indices: 532472--532607 Score: 238
Period size: 72 Copynumber: 1.9 Consensus size: 72
532462 TTATTTGATA
532472 TAAATTGAAATATTATAATAATCTTTAATTTAAATAA-TTTGAAATTTTGAATTTGATAAATAAT
1 TAAATTGAAATATTATAATAATCTTTAATTTAAATAATTTTG-AATTTTGAATTTGATAAATAAT
532536 GTGTTGTC
65 GTGTTGTC
* *
532544 TAAATTGAAATATTATAATAATTTTTACTTTAAATAATTTTGAATTTTGAATTTGATAAATAAT
1 TAAATTGAAATATTATAATAATCTTTAATTTAAATAATTTTGAATTTTGAATTTGATAAATAAT
532608 ATATTGTCAA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
72 57 0.93
73 4 0.07
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (72 bp):
TAAATTGAAATATTATAATAATCTTTAATTTAAATAATTTTGAATTTTGAATTTGATAAATAATG
TGTTGTC
Found at i:532797 original size:191 final size:188
Alignment explanation
Indices: 532544--533046 Score: 758
Period size: 191 Copynumber: 2.7 Consensus size: 188
532534 ATGTGTTGTC
* * * *
532544 TAAATTGAAATATTATAATAATTTTTACTTTAAATAATTTTGAATTTTGAATTTGATAAATAATA
1 TAAATTGAAATATTATAATAATTTTTAATTTAAATAATTTTAAATTTTAAATTTGATAAATAATG
*
532609 TATTGTCAAATCAACATATTATTTAATATAAATTGAAATATTATAATAATCATTTTTAATTTAAA
66 TATTGTCAAATCAACACATTATTTAATATAAATTGAAATATTATAATAATCATTTTTAATTTAAA
* * * *
532674 TAAATTTAATTTTTTTAATTCCGTAAATAATGTATTGTCACATCAACA-ATTATTTTATA
131 TAAATTTAA--ATTTAAATTCCGTAAATAATGTATTGTCAAATCAACATATTATTTGATA
*
532733 TAAATTGAAATATTATAATAATCGTTTTTAATTTAAATAA-TTTAAATTTTTAATTTGATAAATA
1 TAAATTGAAATATTATAATAA---TTTTTAATTTAAATAATTTTAAATTTTAAATTTGATAAATA
* *
532797 ATGTATTGTCAAATCAACACATTATTTTATATAAATTGAAATATTATAATAATCATTTTTACTTT
63 ATGTATTGTCAAATCAACACATTATTTAATATAAATTGAAATATTATAATAATCATTTTTAATTT
* ** *
532862 AAATAATTTTAAATTTAAATTTGGTAAATAATGTATTGTCAAATCAATATATTATTTGATA
128 AAATAAATTTAAATTTAAATTCCGTAAATAATGTATTGTCAAATCAACATATTATTTGATA
* * *
532923 TAAATTAAAATATTATAATAATTTTTAATTTAAATAATTTTAAAATGTAAATTTGATAAATAATG
1 TAAATTGAAATATTATAATAATTTTTAATTTAAATAATTTTAAATTTTAAATTTGATAAATAATG
* *
532988 TATTGTCAAATCAACACATTATTTGATATAAATTGAAATATTATAATAATCAATTTTAA
66 TATTGTCAAATCAACACATTATTTAATATAAATTGAAATATTATAATAATCATTTTTAA
533047 ATTTGAATTT
Statistics
Matches: 287, Mismatches: 22, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
187 16 0.06
188 80 0.28
189 52 0.18
190 30 0.10
191 94 0.33
192 15 0.05
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (188 bp):
TAAATTGAAATATTATAATAATTTTTAATTTAAATAATTTTAAATTTTAAATTTGATAAATAATG
TATTGTCAAATCAACACATTATTTAATATAAATTGAAATATTATAATAATCATTTTTAATTTAAA
TAAATTTAAATTTAAATTCCGTAAATAATGTATTGTCAAATCAACATATTATTTGATA
Found at i:532840 original size:95 final size:95
Alignment explanation
Indices: 532544--533038 Score: 700
Period size: 95 Copynumber: 5.2 Consensus size: 95
532534 ATGTGTTGTC
* * *
532544 TAAATTGAAATATTATAATAA--TTTTTACTTTAAATAATTTTGAATTTTGAATTTGATAAATAA
1 TAAATTGAAATATTATAATAATCTTTTTAATTTAAATAATTTTAAATTTTAAATTTGATAAATAA
* * *
532607 TATATTGTCAAATCAACATATTATTTAATA
66 TGTATTGTCAAATCAACACATTATTTGATA
* * * *
532637 TAAATTGAAATATTATAATAATCATTTTTAATTTAAATAAATTTAATTTTTTTAATTCCG-TAAA
1 TAAATTGAAATATTATAATAATC-TTTTTAATTTAAATAATTTTAA-ATTTTAAATT-TGATAAA
* *
532701 TAATGTATTGTCACATCAACA-ATTATTTTATA
63 TAATGTATTGTCAAATCAACACATTATTTGATA
*
532733 TAAATTGAAATATTATAATAATCGTTTTTAATTTAAATAA-TTTAAATTTTTAATTTGATAAATA
1 TAAATTGAAATATTATAATAATC-TTTTTAATTTAAATAATTTTAAATTTTAAATTTGATAAATA
*
532797 ATGTATTGTCAAATCAACACATTATTTTATA
65 ATGTATTGTCAAATCAACACATTATTTGATA
* *
532828 TAAATTGAAATATTATAATAATCATTTTTACTTTAAATAATTTTAAA-TTTAAATTTGGTAAATA
1 TAAATTGAAATATTATAATAATC-TTTTTAATTTAAATAATTTTAAATTTTAAATTTGATAAATA
* *
532892 ATGTATTGTCAAATCAATATATTATTTGATA
65 ATGTATTGTCAAATCAACACATTATTTGATA
* * *
532923 TAAATTAAAATATTATAATAA--TTTTTAATTTAAATAATTTTAAAATGTAAATTTGATAAATAA
1 TAAATTGAAATATTATAATAATCTTTTTAATTTAAATAATTTTAAATTTTAAATTTGATAAATAA
532986 TGTATTGTCAAATCAACACATTATTTGATA
66 TGTATTGTCAAATCAACACATTATTTGATA
533016 TAAATTGAAATATTATAATAATC
1 TAAATTGAAATATTATAATAATC
533039 AATTTTAAAT
Statistics
Matches: 364, Mismatches: 27, Indels: 20
0.89 0.07 0.05
Matches are distributed among these distances:
92 22 0.06
93 86 0.24
94 33 0.09
95 117 0.32
96 74 0.20
97 31 0.09
98 1 0.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.45
Consensus pattern (95 bp):
TAAATTGAAATATTATAATAATCTTTTTAATTTAAATAATTTTAAATTTTAAATTTGATAAATAA
TGTATTGTCAAATCAACACATTATTTGATA
Found at i:533128 original size:24 final size:24
Alignment explanation
Indices: 533080--533128 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
533070 TTGTCAAATC
* *
533080 AAGTTAATTTTCAATTTAGATTTT
1 AAGTTAATTTTCAATTTACAATTT
*
533104 AAGTTAATTTTCAATTTTCAATTT
1 AAGTTAATTTTCAATTTACAATTT
533128 A
1 A
533129 TTTTTGGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (24 bp):
AAGTTAATTTTCAATTTACAATTT
Found at i:533224 original size:6 final size:6
Alignment explanation
Indices: 533148--533274 Score: 57
Period size: 6 Copynumber: 21.5 Consensus size: 6
533138 TTTTAAATAT
* * * * * * * *
533148 TTTAAA -TTAAA TTTCAA CTTAAT TTTCAA TTTAGA TTTTAA GTT-CA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
533194 TTTAAA ATT-CA TTTGAAA ATTAAA TTTAAA TTT-AA TTGAAA TTTCAA
1 TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
533241 TTT-AA TTTAAAA TTGTAAG TTTAAA ATTAAA TTT
1 TTTAAA TTT-AAA TT-TAAA TTTAAA TTTAAA TTT
533275 TTTACTTATT
Statistics
Matches: 85, Mismatches: 28, Indels: 16
0.66 0.22 0.12
Matches are distributed among these distances:
5 20 0.24
6 53 0.62
7 11 0.13
8 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:533235 original size:17 final size:16
Alignment explanation
Indices: 533211--533247 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
533201 TTCATTTGAA
533211 AATTAAATTTAAATTT
1 AATTAAATTTAAATTT
*
533227 AATTGAAATTTCAATTT
1 AATT-AAATTTAAATTT
533244 AATT
1 AATT
533248 TAAAATTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (16 bp):
AATTAAATTTAAATTT
Found at i:533348 original size:12 final size:11
Alignment explanation
Indices: 533331--533401 Score: 63
Period size: 12 Copynumber: 6.1 Consensus size: 11
533321 TTTAAACTTC
533331 ATTTCAACTTTA
1 ATTTCAA-TTTA
*
533343 ATTTCAATTTC
1 ATTTCAATTTA
533354 ATTT-AATCTTA
1 ATTTCAAT-TTA
*
533365 ATTTCAAATGTA
1 ATTTC-AATTTA
*
533377 ATTTTAATTTTA
1 ATTTCAA-TTTA
533389 ATTTCAAATTTA
1 ATTTC-AATTTA
533401 A
1 A
533402 ACTATAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
10 3 0.06
11 15 0.31
12 25 0.52
13 5 0.10
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.52
Consensus pattern (11 bp):
ATTTCAATTTA
Found at i:533369 original size:34 final size:34
Alignment explanation
Indices: 533321--533386 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
533311 TAAATTAAAG
* * *
533321 TTTAAACTTCATTTCAACTTTAATTTCAATTTCA
1 TTTAAACTTAATTTCAAATGTAATTTCAATTTCA
* *
533355 TTTAATCTTAATTTCAAATGTAATTTTAATTT
1 TTTAAACTTAATTTCAAATGTAATTTCAATTT
533387 TAATTTCAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (34 bp):
TTTAAACTTAATTTCAAATGTAATTTCAATTTCA
Found at i:533415 original size:25 final size:25
Alignment explanation
Indices: 533357--533446 Score: 137
Period size: 25 Copynumber: 3.6 Consensus size: 25
533347 CAATTTCATT
* * * *
533357 TAATCTTAATTTCAAATGT-AATTT
1 TAATTTTAATTTCAAATTTAAACTA
533381 TAATTTTAATTTCAAATTTAAACTA
1 TAATTTTAATTTCAAATTTAAACTA
533406 TAATTTTAATTTCAAATTTAAACTA
1 TAATTTTAATTTCAAATTTAAACTA
533431 TAATTTTAATTTCAAA
1 TAATTTTAATTTCAAA
533447 CTAGTATTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
24 17 0.28
25 44 0.72
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (25 bp):
TAATTTTAATTTCAAATTTAAACTA
Found at i:533436 original size:19 final size:19
Alignment explanation
Indices: 533412--533483 Score: 53
Period size: 19 Copynumber: 3.9 Consensus size: 19
533402 ACTATAATTT
533412 TAATTTCAAATTT-AAACTA
1 TAATTT-AAATTTCAAACTA
*
533431 TAATTTTAATTTCAAACTA
1 TAATTTAAATTTCAAACTA
* * **
533450 GT-ATTTTAATTTGAAGTTA
1 -TAATTTAAATTTCAAACTA
533469 -AATTTAAATTT-AAAC
1 TAATTTAAATTTCAAAC
533484 ATGTATTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
17 2 0.05
18 14 0.33
19 26 0.60
20 1 0.02
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (19 bp):
TAATTTAAATTTCAAACTA
Found at i:533461 original size:6 final size:6
Alignment explanation
Indices: 533355--533442 Score: 50
Period size: 6 Copynumber: 14.3 Consensus size: 6
533345 TTCAATTTCA
* * * * * * *
533355 TTTAAT CTTAAT TTCAAA TGTAAT TTTAAT TTTAAT TTCAAAT TTAAAC
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TT-TAAT TTTAAT
* * * * *
533404 TATAAT TTTAAT TTCAAAT TTAAAC TATAAT TTTAAT TT
1 TTTAAT TTTAAT TT-TAAT TTTAAT TTTAAT TTTAAT TT
533443 CAAACTAGTA
Statistics
Matches: 60, Mismatches: 20, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
6 50 0.83
7 10 0.17
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAT
Found at i:533461 original size:25 final size:25
Alignment explanation
Indices: 533339--533446 Score: 134
Period size: 25 Copynumber: 4.5 Consensus size: 25
533329 TCATTTCAAC
*
533339 TTTAATTTC-AATTT-CA-TTTAAT
1 TTTAATTTCAAATTTAAACTTTAAT
* * *
533361 CTTAATTTCAAATGT-AATTTTAAT
1 TTTAATTTCAAATTTAAACTTTAAT
*
533385 TTTAATTTCAAATTTAAACTATAAT
1 TTTAATTTCAAATTTAAACTTTAAT
*
533410 TTTAATTTCAAATTTAAACTATAAT
1 TTTAATTTCAAATTTAAACTTTAAT
533435 TTTAATTTCAAA
1 TTTAATTTCAAA
533447 CTAGTATTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
22 8 0.11
23 5 0.07
24 19 0.25
25 44 0.58
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (25 bp):
TTTAATTTCAAATTTAAACTTTAAT
Found at i:533490 original size:36 final size:38
Alignment explanation
Indices: 533432--533512 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
533422 TTTAAACTAT
* *
533432 AATTTTAATTTCAAACTAGTATTTTAA-TTTGAAGTTA
1 AATTTAAATTTCAAACTAGTATTTTAATTTTGAAATTA
533469 AATTTAAATTT-AAAC-ATGTATTTTAATTTTGAAATTA
1 AATTTAAATTTCAAACTA-GTATTTTAATTTTGAAATTA
*
533506 ATTTTAA
1 AATTTAA
533513 CTTAATTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
35 1 0.03
36 13 0.33
37 25 0.64
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (38 bp):
AATTTAAATTTCAAACTAGTATTTTAATTTTGAAATTA
Found at i:533509 original size:18 final size:17
Alignment explanation
Indices: 533431--533526 Score: 61
Period size: 18 Copynumber: 5.4 Consensus size: 17
533421 ATTTAAACTA
* *
533431 TAATTTTAATTTCAAAC
1 TAATTTTAATTTGAAAT
*
533448 TAGTATTTTAATTTGAAGT
1 TA--ATTTTAATTTGAAAT
* *
533467 TAAATTTAAATTTAAACAT
1 T-AATTTTAATTTGAA-AT
533486 GT-ATTTTAATTTTGAAAT
1 -TAATTTTAA-TTTGAAAT
* *
533504 TAATTTTAACTT-AATT
1 TAATTTTAATTTGAAAT
533520 TAATTTT
1 TAATTTT
533527 CAAATTAATT
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
16 10 0.16
17 5 0.08
18 26 0.42
19 19 0.31
20 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (17 bp):
TAATTTTAATTTGAAAT
Found at i:533536 original size:17 final size:16
Alignment explanation
Indices: 533503--533537 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
533493 AATTTTGAAA
*
533503 TTAATTTTAACTTAAT
1 TTAATTTTAAATTAAT
533519 TTAATTTTCAAATTAAT
1 TTAATTTT-AAATTAAT
533536 TT
1 TT
533538 CAACATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAATTTTAAATTAAT
Found at i:535273 original size:46 final size:46
Alignment explanation
Indices: 535206--535300 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
535196 AGTGGGGACG
535206 CTTTCATCATAGGCATGATGTAGTTGCATATGGTCTTTGCATCTAA
1 CTTTCATCATAGGCATGATGTAGTTGCATATGGTCTTTGCATCTAA
535252 CTTTCATCATAGGCATGATGTAGTTGCATATGGTCTTTGCATCTAA
1 CTTTCATCATAGGCATGATGTAGTTGCATATGGTCTTTGCATCTAA
535298 CTT
1 CTT
535301 CCAATGGTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (46 bp):
CTTTCATCATAGGCATGATGTAGTTGCATATGGTCTTTGCATCTAA
Found at i:537634 original size:60 final size:58
Alignment explanation
Indices: 537553--538175 Score: 313
Period size: 60 Copynumber: 10.9 Consensus size: 58
537543 TCGGCCAAAA
* * *
537553 CATGGCCAACACCAAAAAAATTTGTTTTTTATTTGATAAAAAAGATGGTGTCGGCAATG
1 CATGACCAACACAAAAAAAATTT-TTTTTTATCTGATAAAAAAGATGGTGTCGGCAATG
* *
537612 CATGACCAACACAAAAAAAAATTATTTTTTCTCTGATAAAAAAGATGGTGTCGGCCAATG
1 CATGACCAACAC-AAAAAAAATTTTTTTTTATCTGATAAAAAAGATGGTGTCGG-CAATG
* * **
537672 CATGACCAACACTAAAAAATTTATTTTTTTATCAAATAAAAAA-AGTGGTGTCGGTCAA-G
1 CATGACCAACACAAAAAAAATT-TTTTTTTATCTGATAAAAAAGA-TGGTGTCGG-CAATG
* * * * * * *
537731 CATTGACCAACAC---CAAAATTTTTTTTTATTTGGTAAAAATG-TGGTGCCAGCAAACG
1 CA-TGACCAACACAAAAAAAATTTTTTTTTATCTGATAAAAAAGATGGTGTCGGC-AATG
* * * * * * *
537787 CATTATCAATACCAAAAAAAATTATTTTTTTATCAGATTAAAAAAAATGGTGTTGACCAA-G
1 CATGACCAACA-CAAAAAAAATT-TTTTTTTATCTGA-TAAAAAAGATGGTGTCG-GCAATG
* * * * * *
537848 CATTATCCAACAC---CAAATTTTTTTTCTTATCTAATAAAAAAGGTGGTGTCGACCAATG
1 CATGA-CCAACACAAAAAAAATTTTTTT-TTATCTGATAAAAAAGATGGTGTCG-GCAATG
* ** * *
537906 TATGGTCAACACAAAAAAAAAATTATATTTTTA-CTTGAT-AAAAAGGTGGTGTCGGCCAATG
1 CATGACCAACAC--AAAAAAAATT-TTTTTTTATC-TGATAAAAAAGATGGTGTCGG-CAATG
* * * *
537967 CATGATCAACAC---CAAAA--TTTTTTT-TCTGATAAAAAAGGTGGTGTCGGCAAAG
1 CATGACCAACACAAAAAAAATTTTTTTTTATCTGATAAAAAAGATGGTGTCGGCAATG
* * * * * *
538019 CATTGGCCAACAC--CAAAAA-TTTTTTTAATCTAATAAAAAATGCTGGTGTCGACCAATG
1 CA-TGACCAACACAAAAAAAATTTTTTTTTATCTGATAAAAAA-GATGGTGTCG-GCAATG
* * * * *
538077 AATGGCCAACAC----CAAA-TTTTTTTT-TCTAATAAAAAAGATGGTGTCGACCAA-G
1 CATGACCAACACAAAAAAAATTTTTTTTTATCTGATAAAAAAGATGGTGTCG-GCAATG
* * * *
538129 CATTGATCAACAC---CAAAA--TTTTTTTATCTGATCAAAAAGGTGGTGTC
1 CA-TGACCAACACAAAAAAAATTTTTTTTTATCTGATAAAAAAGATGGTGTC
538176 AGCCAAGCAT
Statistics
Matches: 450, Mismatches: 76, Indels: 81
0.74 0.13 0.13
Matches are distributed among these distances:
52 12 0.03
53 60 0.13
54 38 0.08
55 31 0.07
56 34 0.08
57 54 0.12
58 19 0.04
59 57 0.13
60 74 0.16
61 44 0.10
62 22 0.05
63 5 0.01
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (58 bp):
CATGACCAACACAAAAAAAATTTTTTTTTATCTGATAAAAAAGATGGTGTCGGCAATG
Found at i:537640 original size:59 final size:58
Alignment explanation
Indices: 537553--538175 Score: 304
Period size: 59 Copynumber: 10.9 Consensus size: 58
537543 TCGGCCAAAA
* * * *
537553 CATGGCCAACACCAAAAAAATTTGTTTTTTATTTGATAAAAAAGATGGTGTCGGCAATG
1 CATGACCAACA-CAAAAAAAATTATTTTTTATCTGATAAAAAAGATGGTGTCGGCAATG
*
537612 CATGACCAACACAAAAAAAAATTATTTTTTCTCTGATAAAAAAGATGGTGTCGGCCAATG
1 CATGACCAACAC-AAAAAAAATTATTTTTTATCTGATAAAAAAGATGGTGTCGG-CAATG
* * **
537672 CATGACCAACACTAAAAAATTTATTTTTTTATCAAATAAAAAA-AGTGGTGTCGGTCAA-G
1 CATGACCAACACAAAAAAAATTA-TTTTTTATCTGATAAAAAAGA-TGGTGTCGG-CAATG
* * * * * * * *
537731 CATTGACCAACAC---CAAAATTTTTTTTTATTTGGTAAAAATG-TGGTGCCAGCAAACG
1 CA-TGACCAACACAAAAAAAATTATTTTTTATCTGATAAAAAAGATGGTGTCGGC-AATG
* * * * * * *
537787 CATTATCAATACCAAAAAAAATTATTTTTTTATCAGATTAAAAAAAATGGTGTTGACCAA-G
1 CATGACCAACA-CAAAAAAAATTA-TTTTTTATCTGA-TAAAAAAGATGGTGTCG-GCAATG
* * * * * * *
537848 CATTATCCAACAC---CAAATTTTTTTTCTTATCTAATAAAAAAGGTGGTGTCGACCAATG
1 CATGA-CCAACACAAAAAAAATTATTTT-TTATCTGATAAAAAAGATGGTGTCG-GCAATG
* ** *
537906 TATGGTCAACACAAAAAAAAAATTATATTTTTA-CTTGAT-AAAAAGGTGGTGTCGGCCAATG
1 CATGACCAACAC--AAAAAAAATTAT-TTTTTATC-TGATAAAAAAGATGGTGTCGG-CAATG
* * * *
537967 CATGATCAACAC---CAAAA-T-TTTTTT-TCTGATAAAAAAGGTGGTGTCGGCAAAG
1 CATGACCAACACAAAAAAAATTATTTTTTATCTGATAAAAAAGATGGTGTCGGCAATG
* * * * * *
538019 CATTGGCCAACAC--CAAAAATT-TTTTTAATCTAATAAAAAATGCTGGTGTCGACCAATG
1 CA-TGACCAACACAAAAAAAATTATTTTTTATCTGATAAAAAA-GATGGTGTCG-GCAATG
* * * * *
538077 AATGGCCAACAC----CAAATT-TTTTTT-TCTAATAAAAAAGATGGTGTCGACCAA-G
1 CATGACCAACACAAAAAAAATTATTTTTTATCTGATAAAAAAGATGGTGTCG-GCAATG
* * * *
538129 CATTGATCAACAC---CAAAA-T-TTTTTTATCTGATCAAAAAGGTGGTGTC
1 CA-TGACCAACACAAAAAAAATTATTTTTTATCTGATAAAAAAGATGGTGTC
538176 AGCCAAGCAT
Statistics
Matches: 449, Mismatches: 77, Indels: 81
0.74 0.13 0.13
Matches are distributed among these distances:
52 12 0.03
53 59 0.13
54 39 0.09
55 32 0.07
56 33 0.07
57 53 0.12
58 20 0.04
59 66 0.15
60 64 0.14
61 44 0.10
62 23 0.05
63 4 0.01
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (58 bp):
CATGACCAACACAAAAAAAATTATTTTTTATCTGATAAAAAAGATGGTGTCGGCAATG
Found at i:537682 original size:119 final size:112
Alignment explanation
Indices: 537541--538209 Score: 444
Period size: 119 Copynumber: 5.9 Consensus size: 112
537531 GGAAAGTTGA
* * *
537541 TGTCGGCCAAAACATGGCCAACACCAAAAAAATTTGTTTTTTATTTGATAAAAAAGATGGTGTCG
1 TGTCGGCCAAAGCATGACCAACACCAAAAAAATTT-TTTTTTATCTGATAAAAAAGATGGTGTCG
*
537606 GCAATGCATGACCAACACAAAAAAAAATTATTTTTTCTCTGATAAAAAAGATGG
65 GCAATGCATGACCAACAC----CAAAATT-TTTTTT-TCTGATAAAAAAGATGG
* * * **
537660 TGTCGGCCAATGCATGACCAACACTAAAAAATTTATTTTTTTATCAAATAAAAAA-AGTGGTGTC
1 TGTCGGCCAAAGCATGACCAACACCAAAAAAATT-TTTTTTTATCTGATAAAAAAGA-TGGTGTC
* * *
537724 GGTCAA-GCATTGACCAACACCAAAATTTTTTTTTATTTGGTAAAAATG-TGG
64 GG-CAATGCA-TGACCAACACCAAAA-TTTTTTTT-TCTGATAAAAAAGATGG
* * * * * * *
537775 TGCCAG-CAAACGCATTATCAATACCAAAAAAAATTATTTTTTTATCAGATTAAAAAAAATGGTG
1 TGTCGGCCAAA-GCATGACCAACACC-AAAAAAATT-TTTTTTTATCTGA-TAAAAAAGATGGTG
* * * * * *
537839 TTGACCAA-GCATTATCCAACACCAAATTTTTTTTCTTATCTAATAAAAAAGGTGG
62 TCG-GCAATGCATGA-CCAACACCAAA-ATTTTTT-TT-TCTGATAAAAAAGATGG
* * * ** * * *
537894 TGTCGACCAATGTATGGTCAACACAAAAAAAAAATTATATTTTTA-CTTGAT-AAAAAGGTGGTG
1 TGTCGGCCAAAGCATGACCAACAC--CAAAAAAATT-TTTTTTTATC-TGATAAAAAAGATGGTG
* *
537957 TCGGCCAATGCATGATCAACACCAAAA-TTTTTTTTCTGATAAAAAAGGTGG
62 TCGG-CAATGCATGACCAACACCAAAATTTTTTTTTCTGATAAAAAAGATGG
* * * *
538008 TGTCGG-CAAAGCATTGGCCAACACC--AAAAA-TTTTTTTAATCTAATAAAAAATGCTGGTGTC
1 TGTCGGCCAAAGCA-TGACCAACACCAAAAAAATTTTTTTTTATCTGATAAAAAA-GATGGTGTC
* * * *
538069 GACCAATGAATGGCCAACACC-AAATTTTTTTTTCTAATAAAAAAGATGG
64 G-GCAATGCATGACCAACACCAAAATTTTTTTTTCTGATAAAAAAGATGG
* * * *
538118 TGTCGACC-AAGCATTGATCAACACC---AAAA--TTTTTTTATCTGATCAAAAAGGTGGTGTCA
1 TGTCGGCCAAAGCA-TGACCAACACCAAAAAAATTTTTTTTTATCTGATAAAAAAGATGGTGTC-
* **
538177 GCCAA-GCATTGGTCAACACC-AAATTTTTTTTTC
64 GGCAATGCA-TGACCAACACCAAAATTTTTTTTTC
538210 AAAATCTCGT
Statistics
Matches: 448, Mismatches: 73, Indels: 70
0.76 0.12 0.12
Matches are distributed among these distances:
106 2 0.00
107 35 0.08
108 27 0.06
109 14 0.03
110 71 0.16
111 1 0.00
113 5 0.01
114 33 0.07
115 19 0.04
116 48 0.11
117 39 0.09
118 39 0.09
119 79 0.18
120 36 0.08
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (112 bp):
TGTCGGCCAAAGCATGACCAACACCAAAAAAATTTTTTTTTATCTGATAAAAAAGATGGTGTCGG
CAATGCATGACCAACACCAAAATTTTTTTTTCTGATAAAAAAGATGG
Found at i:538007 original size:53 final size:53
Alignment explanation
Indices: 537810--538207 Score: 320
Period size: 54 Copynumber: 7.2 Consensus size: 53
537800 AAAAAAAATT
* ** * **
537810 ATTTTTTTATCAGATTAAAAAAAATGGTGTTGACCAAGCATTATCCAACACCAAA
1 ATTTTTTTATCTGA-TAAAAAAGGTGGTGTCGACCAAGCATGGT-CAACACCAAA
* * * *
537865 TTTTTTTTCTTATCTAATAAAAAAGGTGGTGTCGACCAATGTATGGTCAACACAAAAAAAAA
1 --ATTTTT-TTATCTGATAAAAAAGGTGGTGTCGACCAA-GCATGGTCAACAC-----CAAA
* *
537927 ATTATATTTT-TACTTGAT-AAAAAGGTGGTGTCGGCCAATGCATGATCAACACCAAA
1 ATT-T-TTTTAT-C-TGATAAAAAAGGTGGTGTCGACCAA-GCATGGTCAACACCAAA
* * *
537983 ATTTTTTT-TCTGATAAAAAAGGTGGTGTCGGCAAAGCATTGGCCAACACCAAAA
1 ATTTTTTTATCTGATAAAAAAGGTGGTGTCGACCAAGCA-TGGTCAACACC-AAA
* * * *
538037 ATTTTTTTAATCTAATAAAAAATGCTGGTGTCGACCAATGAATGGCCAACACC-AA
1 ATTTTTTT-ATCTGATAAAAAA-GGTGGTGTCGACCAA-GCATGGTCAACACCAAA
* * * *
538092 ATTTTTTTTTCTAATAAAAAAGATGGTGTCGACCAAGCATTGATCAACACCAAA
1 ATTTTTTTATCTGATAAAAAAGGTGGTGTCGACCAAGCA-TGGTCAACACCAAA
*
538146 ATTTTTTTATCTGATCAAAAAGGTGGTGTC-AGCCAAGCATTGGTCAACACCAAA
1 ATTTTTTTATCTGATAAAAAAGGTGGTGTCGA-CCAAGCA-TGGTCAACACCAAA
*
538200 TTTTTTTT
1 ATTTTTTT
538208 TCAAAATCTC
Statistics
Matches: 285, Mismatches: 35, Indels: 45
0.78 0.10 0.12
Matches are distributed among these distances:
52 9 0.03
53 53 0.19
54 84 0.29
55 11 0.04
56 17 0.06
57 53 0.19
58 12 0.04
60 3 0.01
61 35 0.12
62 8 0.03
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (53 bp):
ATTTTTTTATCTGATAAAAAAGGTGGTGTCGACCAAGCATGGTCAACACCAAA
Found at i:538044 original size:54 final size:55
Alignment explanation
Indices: 537577--538208 Score: 315
Period size: 54 Copynumber: 11.1 Consensus size: 55
537567 AAAAAATTTG
* * * *
537577 TTTTTTATTTGATAAAAAAGATGGTGTCGGCAATGCA-TGACCAACACAAAAAAAAATT
1 TTTTTTATCTGATAAAAAAGGTGGTGTCGGCAAAGCATTGACCAACAC---CAAAAA-T
* * * *
537635 ATTTTTTCTCTGATAAAAAAGATGGTGTCGGCCAATGCA-TGACCAACACTAAAAAATTTAT
1 -TTTTTTATCTGATAAAAAAGGTGGTGTCGG-CAAAGCATTGACCAACAC--CAAAA---AT
** * *
537696 TTTTTTATCAAATAAAAAAAGTGGTGTCGGTC-AAGCATTGACCAACACCAAAATTT
1 TTTTTTATCTGATAAAAAAGGTGGTGTCGG-CAAAGCATTGACCAACACCAAAA-AT
* * * * * * *
537752 TTTTTTATTTGGT-AAAAATGTGGTGCCAGCAAACGCATT-ATCAATACCAAAAAAAATTAT
1 TTTTTTATCTGATAAAAAAGGTGGTGTCGGCAAA-GCATTGACCAACACC----AAAA--AT
* ** * * * **
537812 TTTTTTATCAGATTAAAAAAAATGGTGTTGACCAAGCATT-ATCCAACACCAAATTTT
1 TTTTTTATCTGA-TAAAAAAGGTGGTGTCGGCAAAGCATTGA-CCAACACCAAA-AAT
* * * * * **
537869 TTTTCTTATCTAATAAAAAAGGTGGTGTCGACCAATGTATGGTCAACACAA-AAAAAAAAT
1 TTTT-TTATCTGATAAAAAAGGTGGTGTCG-GCAAAGCAT--T-GAC-CAACACCAAAAAT
* *
537929 TATATTTT-TACTTGAT-AAAAAGGTGGTGTCGGCCAATGCA-TGATCAACACC-AAAAT
1 T-T-TTTTAT-C-TGATAAAAAAGGTGGTGTCGG-CAAAGCATTGACCAACACCAAAAAT
*
537985 TTTTTT-TCTGATAAAAAAGGTGGTGTCGGCAAAGCATTGGCCAACACCAAAAAT
1 TTTTTTATCTGATAAAAAAGGTGGTGTCGGCAAAGCATTGACCAACACCAAAAAT
* * * * * *
538039 TTTTTTAATCTAATAAAAAATGCTGGTGTCGACCAATG-AATGGCCAACACC--AAAT
1 TTTTTT-ATCTGATAAAAAA-GGTGGTGTCG-GCAAAGCATTGACCAACACCAAAAAT
* * * * * *
538094 TTTTTTTTCTAATAAAAAAGATGGTGTCGACCAAGCATTGATCAACACC-AAAAT
1 TTTTTTATCTGATAAAAAAGGTGGTGTCGGCAAAGCATTGACCAACACCAAAAAT
* * * ** **
538148 TTTTTTATCTGATCAAAAAGGTGGTGTCAGCCAAGCATTGGTCAACACCAAATTT
1 TTTTTTATCTGATAAAAAAGGTGGTGTCGGCAAAGCATTGACCAACACCAAAAAT
538203 TTTTTT
1 TTTTTT
538209 CAAAATCTCG
Statistics
Matches: 453, Mismatches: 81, Indels: 82
0.74 0.13 0.13
Matches are distributed among these distances:
52 13 0.03
53 45 0.10
54 75 0.17
55 42 0.09
56 36 0.08
57 42 0.09
58 23 0.05
59 42 0.09
60 68 0.15
61 38 0.08
62 29 0.06
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (55 bp):
TTTTTTATCTGATAAAAAAGGTGGTGTCGGCAAAGCATTGACCAACACCAAAAAT
Found at i:538090 original size:110 final size:107
Alignment explanation
Indices: 537945--538209 Score: 327
Period size: 110 Copynumber: 2.4 Consensus size: 107
537935 TTTACTTGAT
* * * * * * *
537945 AAAAAGGTGGTGTCGGCCAATGCATGATCAACACCAAAATTTTTTTTCTGATAAAAAAGGTGGTG
1 AAAAAGCTGGTGTCGACCAATGAATGGTCAACACCAAATTTTTTTTTCTAATAAAAAAGATGGTG
* *
538010 TCGGCAAAGCATTGGCCAACACCAAAAATTTTTTTAATCTAATA
66 TCGACAAAGCATTGACCAACACC-AAAATTTTTTT-ATCTAATA
*
538054 AAAAATGCTGGTGTCGACCAATGAATGGCCAACACCAAATTTTTTTTTCTAATAAAAAAGATGGT
1 AAAAA-GCTGGTGTCGACCAATGAATGGTCAACACCAAATTTTTTTTTCTAATAAAAAAGATGGT
* * * *
538119 GTCGACCAAGCATTGATCAACACCAAAATTTTTTTATCTGATC
65 GTCGACAAAGCATTGACCAACACCAAAATTTTTTTATCTAATA
* *
538162 AAAAAGGTGGTGTC-AGCCAA-GCATTGGTCAACACCAAATTTTTTTTTC
1 AAAAAGCTGGTGTCGA-CCAATG-AATGGTCAACACCAAATTTTTTTTTC
538210 AAAATCTCGT
Statistics
Matches: 136, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
106 2 0.01
107 36 0.26
108 11 0.08
109 16 0.12
110 71 0.52
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (107 bp):
AAAAAGCTGGTGTCGACCAATGAATGGTCAACACCAAATTTTTTTTTCTAATAAAAAAGATGGTG
TCGACAAAGCATTGACCAACACCAAAATTTTTTTATCTAATA
Found at i:539400 original size:18 final size:18
Alignment explanation
Indices: 539378--539420 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
539368 TTTTTTTTCA
*
539378 ATTTTTTGAGT-TTTTAT
1 ATTTTTTGAGTATTATAT
539395 ATTTTTTGAGTATTATAT
1 ATTTTTTGAGTATTATAT
539413 ATTATTTT
1 ATT-TTTT
539421 ATAAAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.48
18 8 0.35
19 4 0.17
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.67
Consensus pattern (18 bp):
ATTTTTTGAGTATTATAT
Found at i:539471 original size:20 final size:19
Alignment explanation
Indices: 539446--539517 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 19
539436 TTTGTTAGAA
539446 TTTAAATGATTTTCAATTT
1 TTTAAATGATTTTCAATTT
* * *
539465 TTATAAATAAGTTTAAATTTT
1 TT-TAAATGATTTTCAA-TTT
* *
539486 TTTATAT-TTTTTCAATTT
1 TTTAAATGATTTTCAATTT
* *
539504 CTTAAATGGTTTTC
1 TTTAAATGATTTTC
539518 TTTTAATTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
18 8 0.20
19 12 0.30
20 15 0.38
21 5 0.12
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (19 bp):
TTTAAATGATTTTCAATTT
Found at i:546182 original size:14 final size:14
Alignment explanation
Indices: 546163--546189 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
546153 AATAACCCTA
546163 AACCAAAATATGTT
1 AACCAAAATATGTT
546177 AACCAAAATATGT
1 AACCAAAATATGT
546190 GATTATCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (14 bp):
AACCAAAATATGTT
Found at i:546291 original size:6 final size:6
Alignment explanation
Indices: 546280--546314 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
546270 CCTAAATAAA
* *
546280 AAATCC AAATCC AAATCC AAATCT AAATCA AAATC
1 AAATCC AAATCC AAATCC AAATCC AAATCC AAATC
546315 GAATAAACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATCC
Found at i:546746 original size:64 final size:64
Alignment explanation
Indices: 546645--546773 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 64
546635 AACAATCTGA
* * * *
546645 TTTTAGGGTTAAACAACATAATCCATTTGATTTCAATGACTGTTTTGTTACTTTTCGATAACGT
1 TTTTAAGGTTAAACAACATAACCCAATTGATTTCAATGACTGTTTTGTCACTTTTCGATAACGT
546709 TTTTAAGGTTAAACAACATAACCCAATTGATTTCAATGACTGTTTTGTCACTTTTCGATAACGT
1 TTTTAAGGTTAAACAACATAACCCAATTGATTTCAATGACTGTTTTGTCACTTTTCGATAACGT
546773 T
1 T
546774 AGTGACTATT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (64 bp):
TTTTAAGGTTAAACAACATAACCCAATTGATTTCAATGACTGTTTTGTCACTTTTCGATAACGT
Found at i:550526 original size:15 final size:15
Alignment explanation
Indices: 550505--550546 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
550495 TAAGCACATC
550505 AATCAAGAATTAATA
1 AATCAAGAATTAATA
* *
550520 TATCAAGAA-TACTA
1 AATCAAGAATTAATA
550534 AATCAAGAATTAA
1 AATCAAGAATTAA
550547 GCACACATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (15 bp):
AATCAAGAATTAATA
Found at i:550953 original size:25 final size:23
Alignment explanation
Indices: 550925--550970 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
550915 TTTGGATCCA
550925 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
550950 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
550971 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:551062 original size:13 final size:13
Alignment explanation
Indices: 551041--551074 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
551031 ACAATATAAC
551041 AATAATAATCCTA
1 AATAATAATCCTA
*
551054 AATATTAATCCTA
1 AATAATAATCCTA
*
551067 AAAAATAA
1 AATAATAA
551075 AAATTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:553361 original size:2 final size:2
Alignment explanation
Indices: 553354--553383 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
553344 GAAGATTAAA
553354 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
553384 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:553388 original size:2 final size:2
Alignment explanation
Indices: 553383--553413 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
553373 TCTCTCTCTC
553383 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
553414 CTCCTTATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:555268 original size:6 final size:7
Alignment explanation
Indices: 555243--555267 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
555233 TAATTAAATA
555243 AAAAAGG
1 AAAAAGG
555250 AAAAAGG
1 AAAAAGG
555257 AAAAAGG
1 AAAAAGG
555264 AAAA
1 AAAA
555268 GAAATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:558337 original size:22 final size:22
Alignment explanation
Indices: 558312--558357 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
558302 GCTATCCCCT
*
558312 TTTTTAGAATCTGTTTCTTATG
1 TTTTTAGAATCTGTTTCTAATG
** *
558334 TTTTTTTAATTTGTTTCTAATG
1 TTTTTAGAATCTGTTTCTAATG
558356 TT
1 TT
558358 ATCTTTGTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.17, C:0.07, G:0.11, T:0.65
Consensus pattern (22 bp):
TTTTTAGAATCTGTTTCTAATG
Found at i:559688 original size:125 final size:122
Alignment explanation
Indices: 559466--559787 Score: 349
Period size: 125 Copynumber: 2.6 Consensus size: 122
559456 GCTTCATCTC
* ** * *
559466 TTGGTCTACTTCTCTGTATCTCATCAGGAATATGACCATTTTATTGTTTCGA-CTCACTTCTTTG
1 TTGGTCTACTTCTCTGTATCTCATCA-GAAGATGACCGCTTCATTGTTT-GATC-CACTTCTCTG
* * * * * ** * *
559530 TATCTCATCAGGAAGATAGGGATTTGGAGTTTCATTTGCATTGAACTTTGCTTCATTTGAT
63 TATCTCATAAAGAAGATAGGGATTCGAAGTTTCACTCACATTGAACTTCGCTTCA-TCGAT
* * *
559591 TTGGTCTACTTCTCTATATCTCATCAGAAAGATGACCGCTTCATTATTGTGATCCACTTCTCTAT
1 TTGGTCTACTTCTCTGTATCTCATCAG-AAGATGACCGCTTCATTGTT-TGATCCACTTCTCTGT
* *
559656 ATCTCATAAAGAAGATGGGGGTTCGAAGTTTCACTCACATTGAACTTCGCTTCATCGAT
64 ATCTCATAAAGAAGATAGGGATTCGAAGTTTCACTCACATTGAACTTCGCTTCATCGAT
* * * *
559715 TTGGTCTACTTCTTTGTATCTCATCATGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTG
1 TTGGTCTACTTCTCTGTATCTCATCA-GAAGATGACCGCTTCA-TTG-TTTGATCCACTTCTCTG
559780 TATCTCAT
63 TATCTCAT
559788 CAGGAAGACG
Statistics
Matches: 165, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
124 43 0.26
125 118 0.72
126 4 0.02
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (122 bp):
TTGGTCTACTTCTCTGTATCTCATCAGAAGATGACCGCTTCATTGTTTGATCCACTTCTCTGTAT
CTCATAAAGAAGATAGGGATTCGAAGTTTCACTCACATTGAACTTCGCTTCATCGAT
Found at i:559882 original size:210 final size:209
Alignment explanation
Indices: 559588--560184 Score: 849
Period size: 210 Copynumber: 2.8 Consensus size: 209
559578 TGCTTCATTT
* * * * * *
559588 GATTTGGTCTACTTCTCTATATCTCA-TCAGAAAGATGACCGCTTCATTATTGTGATCCACTTCT
1 GATTTGGTCTACTTCTCTGTATCTCATTAAG-AAGACGACCGCTTTATTCTT-TGACCCACTTCT
* * *
559652 CTATATCTCATAAAGAAGATGGGGGTTCGAAGTTTCACTCACATTGAACTTCGCTTCATCGATTT
64 CTGTATCTCATAAGGAAGATGGGGGTTCGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTT
* * *
559717 GGTCTACTTCTTTGTATCTCATCATGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTA
129 GGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTA
559782 TCTCATCAGGAAGACG
194 TCTCATCAGGAAGACG
* *
559798 GATTTGGTCTTCTTCTTTGTATCTCATTAAGAAGACGACCGCTTTATTGCTTTGACCCACTTCTC
1 GATTTGGTCTACTTCTCTGTATCTCATTAAGAAGACGACCGCTTTATT-CTTTGACCCACTTCTC
* *
559863 TGTATCTCATTAGGAAGATGGGGGTTCGAAGTTTCACTCATATTGAGCTTCGCTTCATCGATTTG
65 TGTATCTCATAAGGAAGATGGGGGTTCGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTG
* *
559928 GTCTACTTCTCTATATCTCATTAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTAT
130 GTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTAT
559993 CTCATCAGGAAGACG
195 CTCATCAGGAAGACG
* * * * *
560008 GATTTGGT-TCACTTCTCTGTGTCTTATTAGGAAGACGATCGCGTTATTACTTTGACCCACTTCT
1 GATTTGGTCT-ACTTCTCTGTATCTCATTAAGAAGACGACCGCTTTATT-CTTTGACCCACTTCT
* * * * * * *
560072 TTGTATCTCATCAGAAAGATGGGGGTTCAAAGTTTCACTCACATTGAGTTTTGTTTCATCGATTT
64 CTGTATCTCATAAGGAAGATGGGGGTTCGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTT
*
560137 GGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCAC-TGTTTT
129 GGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTT
560185 GATGTTTCAC
Statistics
Matches: 347, Mismatches: 37, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
209 7 0.02
210 335 0.97
211 5 0.01
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (209 bp):
GATTTGGTCTACTTCTCTGTATCTCATTAAGAAGACGACCGCTTTATTCTTTGACCCACTTCTCT
GTATCTCATAAGGAAGATGGGGGTTCGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTGG
TCTACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATC
TCATCAGGAAGACG
Found at i:561114 original size:38 final size:38
Alignment explanation
Indices: 561072--561144 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
561062 TCATTTCGAA
* * * *
561072 TTCGAGTCGCCATTTGTGGGTTTTCATTTCGATTTTTT
1 TTCGAGACACCATTTGCGAGTTTTCATTTCGATTTTTT
*
561110 TTCGAGACACCCTTTGCGAGTTTTCATTTCGATTT
1 TTCGAGACACCATTTGCGAGTTTTCATTTCGATTT
561145 CCCTTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.48
Consensus pattern (38 bp):
TTCGAGACACCATTTGCGAGTTTTCATTTCGATTTTTT
Found at i:572039 original size:29 final size:29
Alignment explanation
Indices: 572007--572261 Score: 176
Period size: 29 Copynumber: 8.8 Consensus size: 29
571997 TTGAGGGTTG
* * *
572007 AAATGTGATTTTGGGAAAGTTCAAGGTCA
1 AAATGTAATTTTGGAAAAGTTTAAGGTCA
* * * *
572036 AAATGTAATTTTTGAAATGTTTAGGGTTA
1 AAATGTAATTTTGGAAAAGTTTAAGGTCA
* * * * *
572065 AAATATTATTTTAGAAAAATTTAAGGCCA
1 AAATGTAATTTTGGAAAAGTTTAAGGTCA
* * ** *
572094 AAATATGATTTTAGGAAAA-TTTGGGGGACA
1 AAATGTAATTTT-GGAAAAGTTT-AAGGTCA
**
572124 AAATGTAATTTTGGAAAAGTTTGGGGTC-
1 AAATGTAATTTTGGAAAAGTTTAAGGTCA
* *
572152 AAATGTAATTTTGGAAAA-ATTAAGGGTTA
1 AAATGTAATTTTGGAAAAGTTTAA-GGTCA
* * * *
572181 AAATGTGATTTTGG-GAAGTTCAAGGGTTA
1 AAATGTAATTTTGGAAAAGTTTAA-GGTCA
* * *
572210 AAATGTAATTTTAGAAAAGTTTGAGGGTTA
1 AAATGTAATTTTGGAAAAGTTT-AAGGTCA
*
572240 AAATGTGATTTTGGAAAAGTTT
1 AAATGTAATTTTGGAAAAGTTT
572262 GGAGGTAAAA
Statistics
Matches: 180, Mismatches: 38, Indels: 15
0.77 0.16 0.06
Matches are distributed among these distances:
27 2 0.01
28 23 0.13
29 102 0.57
30 52 0.29
31 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
AAATGTAATTTTGGAAAAGTTTAAGGTCA
Found at i:572044 original size:58 final size:58
Alignment explanation
Indices: 571977--572260 Score: 250
Period size: 59 Copynumber: 4.9 Consensus size: 58
571967 TTGGGGGTAA
* * * *
571977 AAAATGTAATTTGGGGAAGTTTGAGGGTTGAAATGTGATTTTGGGAAAGTTCAAGGTC
1 AAAATGTAATTTAGGAAAGTTTGAGGGTTAAAATGTGATTTTGGAAAAGTTCAAGGTC
** * * * * * *
572035 AAAATGTAATTTTTGAAATGTTT-AGGGTTAAAATATTATTTTAGAAAAATTTAAGGCC
1 AAAATGTAATTTAGGAAA-GTTTGAGGGTTAAAATGTGATTTTGGAAAAGTTCAAGGTC
* * * * ** * ***
572093 AAAATATGATTTTAGGAAAATTTGGGGGACAAAATGTAATTTTGGAAAAGTTTGGGGTC
1 AAAATGT-AATTTAGGAAAGTTTGAGGGTTAAAATGTGATTTTGGAAAAGTTCAAGGTC
* ** * * *
572152 -AAATGTAATTTTGGAAAAATTAAGGGTTAAAATGTGATTTTGG-GAAGTTCAAGGGTT
1 AAAATGTAATTTAGGAAAGTTTGAGGGTTAAAATGTGATTTTGGAAAAGTTCAA-GGTC
*
572209 AAAATGTAATTTTAGAAAAGTTTGAGGGTTAAAATGTGATTTTGGAAAAGTT
1 AAAATGTAA-TTTAGGAAAGTTTGAGGGTTAAAATGTGATTTTGGAAAAGTT
572261 TGGAGGTAAA
Statistics
Matches: 173, Mismatches: 46, Indels: 12
0.75 0.20 0.05
Matches are distributed among these distances:
56 5 0.03
57 32 0.18
58 64 0.37
59 67 0.39
60 5 0.03
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.35
Consensus pattern (58 bp):
AAAATGTAATTTAGGAAAGTTTGAGGGTTAAAATGTGATTTTGGAAAAGTTCAAGGTC
Found at i:572192 original size:116 final size:117
Alignment explanation
Indices: 571993--572273 Score: 280
Period size: 116 Copynumber: 2.4 Consensus size: 117
571983 TAATTTGGGG
*** * *** * ** *
571993 AAGTTTGAGGGTTGAAATGTGATTTTGGGAAAGTTCAAGGTCAAAATGTAATTTTTGAAATGTTT
1 AAGTTTGAGGGACAAAATGTGATTTTGGAAAAGTTTGGGGTCAAAATGTAATTTTGGAAAAATTA
* * *
572058 AGGGTTAAAATATTATTTTAGAAAAATTTAA-GGCCAAAATATGATTTTAGGAA
66 AGGGTTAAAATATGATTTT-GAAAAATTCAAGGGCCAAAATATAATTTTA-GAA
* *
572111 AA-TTTGGGGGACAAAATGTAATTTTGGAAAAGTTTGGGGTC-AAATGTAATTTTGGAAAAATTA
1 AAGTTTGAGGGACAAAATGTGATTTTGGAAAAGTTTGGGGTCAAAATGTAATTTTGGAAAAATTA
* ** * ** *
572174 AGGGTTAAAATGTGATTTTGGGAAGTTCAAGGGTTAAAATGTAATTTTAGAA
66 AGGGTTAAAATATGATTTTGAAAAATTCAAGGGCCAAAATATAATTTTAGAA
** *
572226 AAGTTTGAGGGTTAAAATGTGATTTTGGAAAAGTTTGGAGGTAAAAAT
1 AAGTTTGAGGGACAAAATGTGATTTTGGAAAAGTTTGG-GGTCAAAAT
572274 ATGATTTTTA
Statistics
Matches: 131, Mismatches: 28, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
115 12 0.09
116 80 0.61
117 33 0.25
118 6 0.05
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (117 bp):
AAGTTTGAGGGACAAAATGTGATTTTGGAAAAGTTTGGGGTCAAAATGTAATTTTGGAAAAATTA
AGGGTTAAAATATGATTTTGAAAAATTCAAGGGCCAAAATATAATTTTAGAA
Found at i:572273 original size:30 final size:30
Alignment explanation
Indices: 571955--572281 Score: 174
Period size: 29 Copynumber: 11.1 Consensus size: 30
571945 GTCAAAAAAT
* * *
571955 TTTTGGAAAAGCTTGGGGGTAAAAAATGT-A
1 TTTTGGAAAAGTTTGGAGGT-TAAAATGTGA
* ** *
571985 ATTTGGGGAAGTTT-GAGGGTTGAAATGTGA
1 TTTTGGAAAAGTTTGGA-GGTTAAAATGTGA
* ** * *
572015 TTTTGGGAAAG-TTCAAGGTCAAAATGTAA
1 TTTTGGAAAAGTTTGGAGGTTAAAATGTGA
* * * * *
572044 TTTTTGAAATGTTTAG-GGTTAAAATATTA
1 TTTTGGAAAAGTTTGGAGGTTAAAATGTGA
* * * ** *
572073 TTTTAGAAAAATTT-AAGGCCAAAATATGA
1 TTTTGGAAAAGTTTGGAGGTTAAAATGTGA
* ** *
572102 TTTTAGGAAAA-TTTGGGGGACAAAATGTAA
1 TTTT-GGAAAAGTTTGGAGGTTAAAATGTGA
* *
572132 TTTTGGAAAAGTTTGG-GG-TCAAATGTAA
1 TTTTGGAAAAGTTTGGAGGTTAAAATGTGA
* **
572160 TTTTGGAAAAATTAAG-GGTTAAAATGTGA
1 TTTTGGAAAAGTTTGGAGGTTAAAATGTGA
* ** *
572189 TTTTGG-GAAG-TTCAAGGGTTAAAATGTAA
1 TTTTGGAAAAGTTTGGA-GGTTAAAATGTGA
*
572218 TTTTAGAAAAGTTT-GAGGGTTAAAATGTGA
1 TTTTGGAAAAGTTTGGA-GGTTAAAATGTGA
* *
572248 TTTTGGAAAAGTTTGGAGGTAAAAATATGA
1 TTTTGGAAAAGTTTGGAGGTTAAAATGTGA
572278 TTTT
1 TTTT
572282 TAAATAAAAT
Statistics
Matches: 229, Mismatches: 54, Indels: 28
0.74 0.17 0.09
Matches are distributed among these distances:
27 1 0.00
28 25 0.11
29 104 0.45
30 95 0.41
31 4 0.02
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (30 bp):
TTTTGGAAAAGTTTGGAGGTTAAAATGTGA
Found at i:572823 original size:30 final size:29
Alignment explanation
Indices: 572767--572891 Score: 135
Period size: 30 Copynumber: 4.2 Consensus size: 29
572757 CACAGCAGTC
** * *
572767 GATTTTGGAAAAATTAGGGGTCAAAATGT
1 GATTTTGGAAAGTTTAAGGGTTAAAATGT
572796 GATTTTAGGAAAGTTTAAGGGTTAAAATGT
1 GATTTT-GGAAAGTTTAAGGGTTAAAATGT
*
572826 AATTTTGGAAAAGTTTAAGGGTTAAAATGT
1 GATTTTGG-AAAGTTTAAGGGTTAAAATGT
* * *
572856 GATTTTGAAAAAGTTT-GGGGTTAAAAATAT
1 GATTTTG-GAAAGTTTAAGGGTT-AAAATGT
572886 GATTTT
1 GATTTT
572892 TAAATAAAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
29 13 0.16
30 70 0.84
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.37
Consensus pattern (29 bp):
GATTTTGGAAAGTTTAAGGGTTAAAATGT
Found at i:572883 original size:60 final size:59
Alignment explanation
Indices: 572768--572881 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 59
572758 ACAGCAGTCG
* *
572768 ATTTTGGAAAAATTAGGGGTCAAAATGTGATTTTAGGAAAGTTTAAGGGTTAAAATGTA
1 ATTTTGGAAAAATTAAGGGTCAAAATGTGATTTTAGAAAAGTTTAAGGGTTAAAATGTA
* * *
572827 ATTTTGGAAAAGTTTAAGGGTTAAAATGTGATTTT-GAAAAAGTTT-GGGGTTAAAA
1 ATTTTGGAAAA-ATTAAGGGTCAAAATGTGATTTTAG-AAAAGTTTAAGGGTTAAAA
572882 ATATGATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 21 0.44
60 27 0.56
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.35
Consensus pattern (59 bp):
ATTTTGGAAAAATTAAGGGTCAAAATGTGATTTTAGAAAAGTTTAAGGGTTAAAATGTA
Found at i:574435 original size:14 final size:13
Alignment explanation
Indices: 574400--574434 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
574390 ATTTGGACAT
*
574400 TTTTAATTTAAAA
1 TTTTATTTTAAAA
574413 TTTTATTTTAAAA
1 TTTTATTTTAAAA
574426 TTTTATTTT
1 TTTTATTTT
574435 TTAGGTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTATTTTAAAA
Found at i:578890 original size:20 final size:19
Alignment explanation
Indices: 578865--578914 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
578855 CAGTATTTGG
*
578865 TATCGATACCAATTAAAAAA
1 TATCGATACCAA-GAAAAAA
*
578885 TATCGATACTCGAGAAAAAA
1 TATCGATAC-CAAGAAAAAA
578905 TATCGATACC
1 TATCGATACC
578915 TCTAGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 1 0.04
20 24 0.89
21 2 0.07
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.24
Consensus pattern (19 bp):
TATCGATACCAAGAAAAAA
Found at i:585760 original size:18 final size:18
Alignment explanation
Indices: 585735--585786 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
585725 TATAAAAATT
*
585735 AAAT-TTATAATAATATA
1 AAATATTATAATAATAAA
* *
585752 TAATATTATTATAATAAA
1 AAATATTATAATAATAAA
585770 AAATATTAATAA-AATAA
1 AAATATT-ATAATAATAA
585787 CTAAATATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 3 0.11
18 22 0.79
19 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATTATAATAATAAA
Found at i:585838 original size:26 final size:24
Alignment explanation
Indices: 585764--585830 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 24
585754 ATATTATTAT
* * *
585764 AATAAAAAATATTAATAAAATAACTA
1 AATATAAAATTTTAAT-AAATAA-AA
585790 AATATAAAATTTTAATAAATAAAA
1 AATATAAAATTTTAATAAATAAAA
585814 AATATATAAATTGTTAA
1 AATATA-AAATT-TTAA
585831 ATATTAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 7 0.19
25 11 0.31
26 18 0.50
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (24 bp):
AATATAAAATTTTAATAAATAAAA
Found at i:589348 original size:173 final size:174
Alignment explanation
Indices: 589059--589409 Score: 641
Period size: 173 Copynumber: 2.0 Consensus size: 174
589049 TCTGGCATGG
*
589059 AGAATTCATATTGCTCTCTTGATCTTGTCTTTGGCTAGTTTCAATTTTTTGAATTAATAAGCTGC
1 AGAATTCATATTGCTCTCTTGATCTTGTCTTTGGCTAGTTTCAATGTTTTGAATTAATAAGCTGC
589124 TGGAGATAGGCGGATTCATCTAGCACCAATGCTTTAGGGTCTAGGAATGTTTTTGTTCTGATATC
66 TGGAGATAGGCGGATTCATCTAGCACCAATGCTTTAGGGTCTAGGAATGTTTTTGTTCTGATATC
*
589189 TTAATTCATG-ACATGCATTTTCTAAAAAAAATTGTTTGTCATA
131 TTAATTCATGAACATGCATATTCTAAAAAAAATTGTTTGTCATA
*
589232 AGAATTCATATTGCTCTCTTGATCTTGTCTTTGGCTGGTTTCAATGTTTTGAATTAATAAGCTGC
1 AGAATTCATATTGCTCTCTTGATCTTGTCTTTGGCTAGTTTCAATGTTTTGAATTAATAAGCTGC
*
589297 TGGAGATAGGCGGATTCATCTAGCACCAATGCTTTAGGGTTTAGGAATGTTTTTGTTCTGATATC
66 TGGAGATAGGCGGATTCATCTAGCACCAATGCTTTAGGGTCTAGGAATGTTTTTGTTCTGATATC
* *
589362 TTAATTCATGAACCTGCATATTCTAAAAAAATTTGTTTGTCATA
131 TTAATTCATGAACATGCATATTCTAAAAAAAATTGTTTGTCATA
589406 AGAA
1 AGAA
589410 GGTTTATCTA
Statistics
Matches: 171, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
173 137 0.80
174 34 0.20
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (174 bp):
AGAATTCATATTGCTCTCTTGATCTTGTCTTTGGCTAGTTTCAATGTTTTGAATTAATAAGCTGC
TGGAGATAGGCGGATTCATCTAGCACCAATGCTTTAGGGTCTAGGAATGTTTTTGTTCTGATATC
TTAATTCATGAACATGCATATTCTAAAAAAAATTGTTTGTCATA
Found at i:589573 original size:5 final size:5
Alignment explanation
Indices: 589559--589589 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
589549 GAGGTATTCA
*
589559 TGGGT CGGGT TGGGT TGGGT TGGGT TGGGT T
1 TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT T
589590 TAGATCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.03, G:0.58, T:0.39
Consensus pattern (5 bp):
TGGGT
Found at i:589782 original size:27 final size:27
Alignment explanation
Indices: 589751--589843 Score: 68
Period size: 26 Copynumber: 3.5 Consensus size: 27
589741 TTAAAAAAAT
589751 ATATTTATATTATATTATATTATTTTA
1 ATATTTATATTATATTATATTATTTTA
* * *
589778 ATATTTA-A-TAAATTTTATACATTTT-
1 ATATTTATATTATATTATAT-TATTTTA
* * * *
589803 TTATATAT-TTATCTTAACATTATTTTA
1 ATATTTATATTATATT-ATATTATTTTA
*
589830 ATATTTACATTATA
1 ATATTTATATTATA
589844 GTGGTATTAT
Statistics
Matches: 46, Mismatches: 14, Indels: 11
0.65 0.20 0.15
Matches are distributed among these distances:
25 13 0.28
26 15 0.33
27 14 0.30
28 4 0.09
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (27 bp):
ATATTTATATTATATTATATTATTTTA
Found at i:590654 original size:17 final size:17
Alignment explanation
Indices: 590629--590697 Score: 50
Period size: 17 Copynumber: 3.9 Consensus size: 17
590619 AGAAGTTTTG
*
590629 ATAATTATAATTTAAAA
1 ATAACTATAATTTAAAA
* *
590646 ATAACTATAGTTTAATTATG
1 ATAACTATAATTTAA--A-A
*
590666 ATAACTACACATTTAAAA
1 ATAACTATA-ATTTAAAA
*
590684 TTAAC-ATAATTTAA
1 ATAACTATAATTTAA
590698 TTTACTATTA
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
16 6 0.15
17 15 0.38
18 4 0.10
19 2 0.05
20 8 0.20
21 5 0.12
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (17 bp):
ATAACTATAATTTAAAA
Found at i:597617 original size:19 final size:20
Alignment explanation
Indices: 597578--597617 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
597568 GTCTTCTAGT
* *
597578 GAAATAACTCTTGCGATCTA
1 GAAATAACTCTTACGAGCTA
597598 GAAAT-ACTCTTACGAGCTA
1 GAAATAACTCTTACGAGCTA
597617 G
1 G
597618 TATGCTACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (20 bp):
GAAATAACTCTTACGAGCTA
Found at i:601827 original size:21 final size:21
Alignment explanation
Indices: 601800--601859 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
601790 ATCAGCATAC
*
601800 TCAGATGCATCCACAACA-AA
1 TCAGATGCAGCCACAACAGAA
*
601820 TCCAGATGCAGCCACACCAGAA
1 T-CAGATGCAGCCACAACAGAA
*
601842 TCAGATGCAGCTACAACA
1 TCAGATGCAGCCACAACA
601860 CTCTTCAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.03
21 30 0.88
22 3 0.09
ACGTcount: A:0.40, C:0.32, G:0.15, T:0.13
Consensus pattern (21 bp):
TCAGATGCAGCCACAACAGAA
Found at i:607879 original size:12 final size:12
Alignment explanation
Indices: 607862--607886 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
607852 TCGTGTGAAG
607862 GAAGAAAAAGAT
1 GAAGAAAAAGAT
607874 GAAGAAAAAGAT
1 GAAGAAAAAGAT
607886 G
1 G
607887 TCGAGGGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (12 bp):
GAAGAAAAAGAT
Found at i:623790 original size:23 final size:23
Alignment explanation
Indices: 623764--623828 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
623754 TCTAATTAGT
623764 AAATATATATTTTAAAATTTAAA
1 AAATATATATTTTAAAATTTAAA
*
623787 AAATATATTTTTTAATGAA-TTAAA
1 AAATATATATTTTAA--AATTTAAA
* *
623811 AAATAAATA-TATAAAATT
1 AAATATATATTTTAAAATT
623829 ACGAGCAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
21 2 0.06
22 1 0.03
23 18 0.51
24 12 0.34
25 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
AAATATATATTTTAAAATTTAAA
Found at i:629265 original size:20 final size:20
Alignment explanation
Indices: 629235--629287 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
629225 AAGGCTTTTT
629235 TTATGTATTTTATAAAATTTA
1 TTAT-TATTTTATAAAATTTA
* ** *
629256 TTATTATTTTTTCTAATTTT
1 TTATTATTTTATAAAATTTA
629276 TTATT-TTTTATA
1 TTATTATTTTATA
629288 TTTTTATTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 5 0.19
20 17 0.65
21 4 0.15
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TTATTATTTTATAAAATTTA
Found at i:629292 original size:17 final size:17
Alignment explanation
Indices: 629259--629331 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 17
629249 AAATTTATTA
*
629259 TTATTTTTTCTAATTTT
1 TTATTTTTTATAATTTT
*
629276 TTATTTTTTATATTTTT
1 TTATTTTTTATAATTTT
** *
629293 ATTAAAATTTAATAAATTTT
1 -TT-ATTTTTTAT-AATTTT
* *
629313 ATATTTTTAATAATTTT
1 TTATTTTTTATAATTTT
629330 TT
1 TT
629332 GCCACATTTC
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
17 22 0.51
18 9 0.21
19 7 0.16
20 5 0.12
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTTTTTATAATTTT
Found at i:630724 original size:21 final size:22
Alignment explanation
Indices: 630685--630730 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
630675 TTTATATTTT
*
630685 TTAAAGTTAAAAGTCAAAATTA
1 TTAAAGTTAAAAGTCAAAACTA
630707 TTAAA-TTAAAAGGT-AAAACTA
1 TTAAAGTTAAAA-GTCAAAACTA
630728 TTA
1 TTA
630731 TATTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (22 bp):
TTAAAGTTAAAAGTCAAAACTA
Found at i:632544 original size:11 final size:11
Alignment explanation
Indices: 632518--632614 Score: 95
Period size: 11 Copynumber: 8.8 Consensus size: 11
632508 ACCGTCAACT
*
632518 GTCAATGGTCG
1 GTCAACGGTCG
*
632529 GTCAACGGTTG
1 GTCAACGGTCG
* * *
632540 ATCAATGGTTG
1 GTCAACGGTCG
632551 GTCAACGGTCG
1 GTCAACGGTCG
*
632562 GTCAATGGTCG
1 GTCAACGGTCG
* *
632573 ATCAACGGTTG
1 GTCAACGGTCG
* *
632584 GTCAATGATCG
1 GTCAACGGTCG
632595 GTCAACGGTCG
1 GTCAACGGTCG
*
632606 ATCAACGGT
1 GTCAACGGT
632615 TTGACTTGGT
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 68 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.26
Consensus pattern (11 bp):
GTCAACGGTCG
Found at i:632546 original size:22 final size:22
Alignment explanation
Indices: 632519--632610 Score: 121
Period size: 22 Copynumber: 4.2 Consensus size: 22
632509 CCGTCAACTG
*
632519 TCAATGGTCGGTCAACGGTTGA
1 TCAATGGTCGGTCAACGGTCGA
* *
632541 TCAATGGTTGGTCAACGGTCGG
1 TCAATGGTCGGTCAACGGTCGA
* * *
632563 TCAATGGTCGATCAACGGTTGG
1 TCAATGGTCGGTCAACGGTCGA
*
632585 TCAATGATCGGTCAACGGTCGA
1 TCAATGGTCGGTCAACGGTCGA
632607 TCAA
1 TCAA
632611 CGGTTTGACT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (22 bp):
TCAATGGTCGGTCAACGGTCGA
Found at i:632555 original size:33 final size:33
Alignment explanation
Indices: 632518--632615 Score: 151
Period size: 33 Copynumber: 3.0 Consensus size: 33
632508 ACCGTCAACT
* *
632518 GTCAATGGTCGGTCAACGGTTGATCAATGGTTG
1 GTCAATGGTCGGTCAACGGTCGATCAACGGTTG
* *
632551 GTCAACGGTCGGTCAATGGTCGATCAACGGTTG
1 GTCAATGGTCGGTCAACGGTCGATCAACGGTTG
*
632584 GTCAATGATCGGTCAACGGTCGATCAACGGTT
1 GTCAATGGTCGGTCAACGGTCGATCAACGGTT
632616 TGACTTGGTT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (33 bp):
GTCAATGGTCGGTCAACGGTCGATCAACGGTTG
Found at i:632655 original size:15 final size:16
Alignment explanation
Indices: 632637--632673 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
632627 GGGTTTGGAC
632637 TTGGTTCA-ATTGGGT
1 TTGGTTCACATTGGGT
*
632652 TTGGTTCACTTTGGGT
1 TTGGTTCACATTGGGT
632668 TTGGTT
1 TTGGTT
632674 TTAATAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.08, C:0.08, G:0.32, T:0.51
Consensus pattern (16 bp):
TTGGTTCACATTGGGT
Found at i:632733 original size:26 final size:26
Alignment explanation
Indices: 632697--632750 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
632687 GCTTAAAGTT
*
632697 TTTTAAAAGGTTTATAA-GG-TTTGGG
1 TTTTAAAAGG-TAATAAGGGTTTTGGG
632722 TTTTAAATAGGTAATAAGGGTTTTGGG
1 TTTTAAA-AGGTAATAAGGGTTTTGGG
632749 TT
1 TT
632751 AGGTTGGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 12 0.48
26 5 0.20
27 8 0.32
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (26 bp):
TTTTAAAAGGTAATAAGGGTTTTGGG
Found at i:638230 original size:2 final size:2
Alignment explanation
Indices: 638223--638268 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
638213 TAGAATAAAT
638223 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
638265 CA CA
1 CA CA
638269 TATATATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:639742 original size:21 final size:21
Alignment explanation
Indices: 639696--639774 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
639686 TGTCGAAAAA
639696 AGTCAACGTGTCAATC--TCAA-
1 AGTCAACG-GTCAA-CGGTCAAC
*
639716 AGTCAACGATCAACGGTCAAC
1 AGTCAACGGTCAACGGTCAAC
**
639737 AGTCAACGGTCAACTATCAAC
1 AGTCAACGGTCAACGGTCAAC
639758 AGTCAACGGTCAACGGT
1 AGTCAACGGTCAACGGT
639775 TGGTTAATGG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
18 1 0.02
19 4 0.08
20 12 0.24
21 33 0.66
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (21 bp):
AGTCAACGGTCAACGGTCAAC
Found at i:639773 original size:7 final size:7
Alignment explanation
Indices: 639717--639774 Score: 71
Period size: 7 Copynumber: 8.3 Consensus size: 7
639707 CAATCTCAAA
639717 GTCAACG
1 GTCAACG
*
639724 ATCAACG
1 GTCAACG
*
639731 GTCAACA
1 GTCAACG
639738 GTCAACG
1 GTCAACG
*
639745 GTCAACT
1 GTCAACG
* *
639752 ATCAACA
1 GTCAACG
639759 GTCAACG
1 GTCAACG
639766 GTCAACG
1 GTCAACG
639773 GT
1 GT
639775 TGGTTAATGG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:639792 original size:22 final size:22
Alignment explanation
Indices: 639764--639815 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
639754 CAACAGTCAA
* *
639764 CGGTCAACGGTTGGTTAATGGT
1 CGGTCAACGGTTGGTCAAAGGT
639786 CGGTCAACGGTTGGTCAAAGGT
1 CGGTCAACGGTTGGTCAAAGGT
*
639808 TGGTCAAC
1 CGGTCAAC
639816 AGTCGATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.21, C:0.17, G:0.35, T:0.27
Consensus pattern (22 bp):
CGGTCAACGGTTGGTCAAAGGT
Found at i:639803 original size:11 final size:11
Alignment explanation
Indices: 639765--639815 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
639755 AACAGTCAAC
639765 GGTCAACGGTT
1 GGTCAACGGTT
* * *
639776 GGTTAATGGTC
1 GGTCAACGGTT
639787 GGTCAACGGTT
1 GGTCAACGGTT
*
639798 GGTCAAAGGTT
1 GGTCAACGGTT
639809 GGTCAAC
1 GGTCAAC
639816 AGTCGATCAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.22, C:0.16, G:0.35, T:0.27
Consensus pattern (11 bp):
GGTCAACGGTT
Found at i:640452 original size:20 final size:20
Alignment explanation
Indices: 640416--640453 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
640406 TCGGCAGAGC
640416 AAAGAACAAAAAGGAAAAGA
1 AAAGAACAAAAAGGAAAAGA
640436 AAAG-ACAAAAAGAGAAAA
1 AAAGAACAAAAAG-GAAAA
640454 TAAGGTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.76, C:0.05, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAGAACAAAAAGGAAAAGA
Found at i:641830 original size:12 final size:12
Alignment explanation
Indices: 641813--641837 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
641803 TTTGAAAGCG
641813 AAAAGAGTGAAA
1 AAAAGAGTGAAA
641825 AAAAGAGTGAAA
1 AAAAGAGTGAAA
641837 A
1 A
641838 TCGAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (12 bp):
AAAAGAGTGAAA
Found at i:641903 original size:30 final size:30
Alignment explanation
Indices: 641862--641936 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
641852 CAGATTTTAG
* **
641862 GAGCAACACGGGTTGGGCACACAGTCATGT
1 GAGCCACACGGGTTGGGCACACAACCATGT
*
641892 GAGCCACACGGGCTGGGCACACAACCATGT
1 GAGCCACACGGGTTGGGCACACAACCATGT
641922 GAGCCACACGGGTTG
1 GAGCCACACGGGTTG
641937 CCATATAGCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.25, C:0.28, G:0.33, T:0.13
Consensus pattern (30 bp):
GAGCCACACGGGTTGGGCACACAACCATGT
Found at i:642952 original size:28 final size:27
Alignment explanation
Indices: 642921--642973 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
642911 TCACGAACCT
642921 TCTTTCCTTCAAAAAAATTCAGCAACTC
1 TCTTTCCTT-AAAAAAATTCAGCAACTC
* * *
642949 TCTTTGCTTTAAAAAATTCATCAAC
1 TCTTTCCTTAAAAAAATTCAGCAAC
642974 CCTTCCAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (27 bp):
TCTTTCCTTAAAAAAATTCAGCAACTC
Found at i:644465 original size:13 final size:12
Alignment explanation
Indices: 644447--644481 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
644437 CTTTTGAAAA
644447 TATGTTTATGAAG
1 TATGTTTATG-AG
644460 TATGTTTATGAG
1 TATGTTTATGAG
*
644472 TATATTTATG
1 TATGTTTATG
644482 TCGGATTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (12 bp):
TATGTTTATGAG
Found at i:646806 original size:3 final size:3
Alignment explanation
Indices: 646798--646841 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
646788 AGTAAAATTG
646798 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
646842 ATCATTACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:653624 original size:39 final size:40
Alignment explanation
Indices: 653570--653649 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
653560 TATGCACTCA
*
653570 ATGGACACCTTTTGAAGAGTCACAA-CCCTTTCAAATTGG
1 ATGGACACCTATTGAAGAGTCACAATCCCTTTCAAATTGG
* *
653609 ATGGACACCTATTGAAGAGTCACAATCCTTTTCATATTGG
1 ATGGACACCTATTGAAGAGTCACAATCCCTTTCAAATTGG
653649 A
1 A
653650 CATACCTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 24 0.65
40 13 0.35
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (40 bp):
ATGGACACCTATTGAAGAGTCACAATCCCTTTCAAATTGG
Found at i:653665 original size:39 final size:38
Alignment explanation
Indices: 653574--653666 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 38
653564 CACTCAATGG
* *
653574 ACACCTTTTGAAGAGTCACAACCCTTTCAAATTGGATGG
1 ACACCTATTGAAGAGTCACAACCCTTTCAAATTGGA-GC
* *
653613 ACACCTATTGAAGAGTCACAATCCTTTTCATATTGGA-C
1 ACACCTATTGAAGAGTCACAA-CCCTTTCAAATTGGAGC
* *
653651 ATACCTCTTGGAAGAG
1 ACACCTATT-GAAGAG
653667 ACTTGTCCCA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 7 0.15
39 26 0.57
40 13 0.28
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (38 bp):
ACACCTATTGAAGAGTCACAACCCTTTCAAATTGGAGC
Found at i:654620 original size:31 final size:31
Alignment explanation
Indices: 654559--654626 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 31
654549 TAAATTTAAG
** *
654559 TTAAAATGTTTTATTTTTTTTTTAATTA-TT
1 TTAAAATGTTTTATAATTTTATTAATTATTT
654589 TTAAAATGTATTTATGAATTTTATTAA-TATTT
1 TTAAAATGT-TTTAT-AATTTTATTAATTATTT
654621 TTAAAA
1 TTAAAA
654627 AAATAAATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 9 0.28
31 7 0.22
32 16 0.50
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (31 bp):
TTAAAATGTTTTATAATTTTATTAATTATTT
Found at i:660168 original size:27 final size:28
Alignment explanation
Indices: 660091--660169 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 28
660081 CAAATGATTT
* * * *
660091 TAAAGTTATAAAAATTATTTTTTTAAATA
1 TAAAATTATTAAAATTA-ATTTTAAAATA
660120 TAAAATTATTAAAATTAA-TTTAAAATAA
1 TAAAATTATTAAAATTAATTTTAAAAT-A
660148 TAAAATTATT-AAA-TAATTTTAA
1 TAAAATTATTAAAATTAATTTTAA
660170 TTTCTAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
26 3 0.07
27 15 0.34
28 11 0.25
29 15 0.34
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (28 bp):
TAAAATTATTAAAATTAATTTTAAAATA
Found at i:661099 original size:28 final size:30
Alignment explanation
Indices: 661067--661140 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
661057 AATGATGATG
661067 ATTTTAATATTTTTA-TATTTAAAAAAT-A
1 ATTTTAATATTTTTATTATTTAAAAAATAA
* *
661095 ATTTTAATAATTTAATATTTTTTAAAAAATAA
1 ATTTTAAT-ATTT-TTATTATTTAAAAAATAA
*
661127 ATTTT-ATAATTTTA
1 ATTTTAATATTTTTA
661141 AAATAATTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 8 0.21
29 6 0.16
30 5 0.13
31 13 0.34
32 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
ATTTTAATATTTTTATTATTTAAAAAATAA
Found at i:662754 original size:22 final size:22
Alignment explanation
Indices: 662725--662770 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
662715 TTTTGAATTA
662725 TTATGTTT-AATTCGGT-AAACT
1 TTATGTTTAAATTC-GTCAAACT
662746 TTATCGTTTAAATTCGTCAAACT
1 TTAT-GTTTAAATTCGTCAAACT
662769 TT
1 TT
662771 CTAAGCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 6 0.27
23 12 0.55
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (22 bp):
TTATGTTTAAATTCGTCAAACT
Found at i:668476 original size:35 final size:35
Alignment explanation
Indices: 668430--668498 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
668420 ACTCTGTTCG
668430 CGGATCTTGGGCAAAACGAAAAGATAAGTAACAAA
1 CGGATCTTGGGCAAAACGAAAAGATAAGTAACAAA
668465 CGGATCTTGGGCAAAACGAAAAGATAAGTAACAA
1 CGGATCTTGGGCAAAACGAAAAGATAAGTAACAA
668499 TCTTTCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.48, C:0.14, G:0.23, T:0.14
Consensus pattern (35 bp):
CGGATCTTGGGCAAAACGAAAAGATAAGTAACAAA
Found at i:678532 original size:12 final size:13
Alignment explanation
Indices: 678505--678534 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
678495 ACCCAGTCCT
678505 AACAAAAATAAGA
1 AACAAAAATAAGA
678518 AACAAAAATAA-A
1 AACAAAAATAAGA
678530 AACAA
1 AACAA
678535 GAGAGAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.80, C:0.10, G:0.03, T:0.07
Consensus pattern (13 bp):
AACAAAAATAAGA
Found at i:680194 original size:49 final size:49
Alignment explanation
Indices: 680117--680237 Score: 138
Period size: 49 Copynumber: 2.5 Consensus size: 49
680107 GTTCACGATT
* * *
680117 GTTATACAATCACGAGTTGAAGTATAACT-AGGACTCCC-AGTTAATAATG
1 GTTATGCAATCACGGGTTGAAGTATAACTCAGG--TCCCTAGTTAACAATG
* * *
680166 GTTATGCGATCACGGGTTGAAGTGTAACTCAGGTCCCTAGTTAACAGTG
1 GTTATGCAATCACGGGTTGAAGTATAACTCAGGTCCCTAGTTAACAATG
* *
680215 GTTATGCAATCATGGGTTCAAGT
1 GTTATGCAATCACGGGTTGAAGT
680238 TTCACGACAC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
48 4 0.07
49 54 0.89
50 3 0.05
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (49 bp):
GTTATGCAATCACGGGTTGAAGTATAACTCAGGTCCCTAGTTAACAATG
Found at i:681481 original size:72 final size:76
Alignment explanation
Indices: 681283--681483 Score: 230
Period size: 77 Copynumber: 2.7 Consensus size: 76
681273 TGCTTCTCAT
* * * *** *
681283 TTTTTGGTAAATTGTAAATATTGATATATTATTAATGTAAAATATGGTAGAATACAATATAAACA
1 TTTTTCGTAGATTGTAAATA-AGATATATTATTAATGTAAAATACAATAGAATACAATACAAACA
*
681348 AATTCTTTTTTA
65 AATTCTTTTATA
* * * * *
681360 TTTTTCGTAGATTCTAAATAAGAATATATTATTTATATGAAATACAATAGAATACAATACAAGC-
1 TTTTTCGTAGATTGTAAATAAG-ATATATTATTAATGTAAAATACAATAGAATACAATACAAACA
681424 AATT-TTTTAT-
65 AATTCTTTTATA
*
681434 TTTTTCTTAGATTGTAAATAAG-TATATTATTAATGTAAAATACAATAGAA
1 TTTTTCGTAGATTGTAAATAAGATATATTATTAATGTAAAATACAATAGAA
681484 CAACTTTTTT
Statistics
Matches: 105, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
72 25 0.24
74 20 0.19
75 5 0.05
76 5 0.05
77 50 0.48
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.42
Consensus pattern (76 bp):
TTTTTCGTAGATTGTAAATAAGATATATTATTAATGTAAAATACAATAGAATACAATACAAACAA
ATTCTTTTATA
Found at i:682812 original size:15 final size:15
Alignment explanation
Indices: 682792--682824 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
682782 ATATGTTATT
682792 TAAAAAATATAATAA
1 TAAAAAATATAATAA
*
682807 TAAAAAATATTATAA
1 TAAAAAATATAATAA
682822 TAA
1 TAA
682825 CTATAATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAAAATATAATAA
Found at i:694116 original size:102 final size:101
Alignment explanation
Indices: 693939--694186 Score: 302
Period size: 102 Copynumber: 2.4 Consensus size: 101
693929 AGATTAGTGA
* * * ** *
693939 AACACCAAATCATATATCCCTAAAGTTTCAGTGGATCAAATTAAAACTAACAGTAGTGGATTTCA
1 AACACCAAATCATATATCCCTAAAGTTTC-GTAGATCAGATTAAAACTAACAATAGCAGATCTCA
* * *
694004 ATATCTCTGAAGTTGTAGTGGAATGGAGTGAAGTTAC
65 ATATCTCTGAACTTGCAGTGGAATGGAGTGAAGCTAC
* * * *
694041 AACACCAAATCCTATATCCATGAAGTTGTCGTAGATCAGATTAAATCTAACAATAGCAGATCTCA
1 AACACCAAATCATATATCCCTAAAGTT-TCGTAGATCAGATTAAAACTAACAATAGCAGATCTCA
* *
694106 GTCT-TCCTGAACTTGCAGTGGAATGGAGTGAAGCTAC
65 ATATCT-CTGAACTTGCAGTGGAATGGAGTGAAGCTAC
*
694143 AACACCAAATCATATATCCCTAAAGTTAC-TAAGATCAGATTAAA
1 AACACCAAATCATATATCCCTAAAGTTTCGT-AGATCAGATTAAA
694187 GCTATAATAG
Statistics
Matches: 124, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
100 1 0.01
101 15 0.12
102 106 0.85
103 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (101 bp):
AACACCAAATCATATATCCCTAAAGTTTCGTAGATCAGATTAAAACTAACAATAGCAGATCTCAA
TATCTCTGAACTTGCAGTGGAATGGAGTGAAGCTAC
Found at i:694309 original size:100 final size:101
Alignment explanation
Indices: 694180--694518 Score: 348
Period size: 101 Copynumber: 3.4 Consensus size: 101
694170 ACTAAGATCA
* * * *
694180 GATTAAAGCTATAATAGCAAATCGTTATCTCTCTAAAGTTGAAGTAGAGCAAGATTAAGCTACCA
1 GATTAAAGCTACAAAAGCAAATCTTTATCTCTCTAAAGTTGAAGTAGAGCAAGATAAAGCTACCA
*
694245 CATCAAATCATATACTCCTGAAGTTGTAGTGGGTTA
66 CATCAAATCATATACTCCTGAAGTTGTAGTGGGTTG
* * * * * * * ** **
694281 GATTGAAGTTACAAAAGCAAAT-TTTATCTCCCTAAAGAT-ACAGTGGAGTAAGATGAATTTATG
1 GATTAAAGCTACAAAAGCAAATCTTTATCTCTCTAAAGTTGA-AGTAGAGCAAGATAAAGCTACC
* * * *
694344 AAATCAAATCCTATA-TCCCTGAAATTGTAGTGGATTG
65 ACATCAAATCATATACT-CCTGAAGTTGTAGTGGGTTG
** * * * *
694381 GATTAAAGCTACAGTAGCAAATCTTTATCTTTTTGAAGTTGCAGTAGAGCAAGATAAAGCTACCA
1 GATTAAAGCTACAAAAGCAAATCTTTATCTCTCTAAAGTTGAAGTAGAGCAAGATAAAGCTACCA
*
694446 CATCAAA-AATTATAC-CCTTGAAGTTGTAGTGGGTTG
66 CATCAAATCA-TATACTCC-TGAAGTTGTAGTGGGTTG
*
694482 GATTAAAGCTACAAAAGCAAATC-TTATCTATCTAAAG
1 GATTAAAGCTACAAAAGCAAATCTTTATCTCTCTAAAG
694519 ATACAATGGA
Statistics
Matches: 185, Mismatches: 46, Indels: 15
0.75 0.19 0.06
Matches are distributed among these distances:
99 2 0.01
100 90 0.49
101 93 0.50
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (101 bp):
GATTAAAGCTACAAAAGCAAATCTTTATCTCTCTAAAGTTGAAGTAGAGCAAGATAAAGCTACCA
CATCAAATCATATACTCCTGAAGTTGTAGTGGGTTG
Found at i:694429 original size:201 final size:201
Alignment explanation
Indices: 694175--694600 Score: 577
Period size: 201 Copynumber: 2.1 Consensus size: 201
694165 AAGTTACTAA
* * *
694175 GATCAGATTAAAGCTATAATAGCAAATCGTTATCTCTCTAAAGTTGAAGTAGAGCAAGATTAAGC
1 GATCGGATTAAAGCTACAATAGCAAATCGTTATCTCTCTAAAGTTGAAGTAGAGCAAGATAAAGC
* * *
694240 TACCACATCAAATCA-TATACTCC-TGAAGTTGTAGTGGGTTAGATTGAAGTTACAAAAGCAAAT
66 TACCACATCAAA-AATTATAC-CCTTGAAGTTGTAGTGGGTTAGATTAAAGCTACAAAAGCAAAT
* * * * * *
694303 TTTATCTCCCTAAAGATACAGTGGAGTAAGATGAATTTATGAAATCAAATCCTATATCCCTGAAA
129 CTTATCTACCTAAAGATACAATGGAGTAAGATGAAGTTACGAAATCAAATCCTATATCCCTAAAA
*
694368 TTGTAGTG
194 TTGCAGTG
* * * * * * *
694376 GATTGGATTAAAGCTACAGTAGCAAATCTTTATCTTTTTGAAGTTGCAGTAGAGCAAGATAAAGC
1 GATCGGATTAAAGCTACAATAGCAAATCGTTATCTCTCTAAAGTTGAAGTAGAGCAAGATAAAGC
*
694441 TACCACATCAAAAATTATACCCTTGAAGTTGTAGTGGGTTGGATTAAAGCTACAAAAGCAAATCT
66 TACCACATCAAAAATTATACCCTTGAAGTTGTAGTGGGTTAGATTAAAGCTACAAAAGCAAATCT
* * *
694506 TATCTATCTAAAGATACAATGGAGTAAGATGAAGTTACGACATTAAATCCTATATCCCTAAAATT
131 TATCTACCTAAAGATACAATGGAGTAAGATGAAGTTACGAAATCAAATCCTATATCCCTAAAATT
694571 GCAGTG
196 GCAGTG
* * *
694577 GATCGGATTAGAGTTACATTAGCA
1 GATCGGATTAAAGCTACAATAGCA
694601 GGCCCTATCT
Statistics
Matches: 195, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
200 3 0.02
201 192 0.98
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (201 bp):
GATCGGATTAAAGCTACAATAGCAAATCGTTATCTCTCTAAAGTTGAAGTAGAGCAAGATAAAGC
TACCACATCAAAAATTATACCCTTGAAGTTGTAGTGGGTTAGATTAAAGCTACAAAAGCAAATCT
TATCTACCTAAAGATACAATGGAGTAAGATGAAGTTACGAAATCAAATCCTATATCCCTAAAATT
GCAGTG
Found at i:695287 original size:15 final size:16
Alignment explanation
Indices: 695267--695296 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
695257 CAAGCTGCAA
695267 ACAG-AAAGAAAAAGG
1 ACAGAAAAGAAAAAGG
695282 ACAGAAAAGAAAAAG
1 ACAGAAAAGAAAAAG
695297 AAAATTGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.07, G:0.23, T:0.00
Consensus pattern (16 bp):
ACAGAAAAGAAAAAGG
Found at i:696442 original size:25 final size:24
Alignment explanation
Indices: 696401--696447 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
696391 TTTTACTTTA
696401 TTTTAATTCGATCCTTTATATTTGG
1 TTTTAATTCGATCCTTTA-ATTTGG
*
696426 TTTTAATT-TATCTCTTTAATTT
1 TTTTAATTCGATC-CTTTAATTT
696448 TTCTTAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.21, C:0.11, G:0.06, T:0.62
Consensus pattern (24 bp):
TTTTAATTCGATCCTTTAATTTGG
Done.