Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 64 of 167
Found at i:20120952 original size:3 final size:3
Alignment explanation
Indices: 20120944--20120972 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20120934 GATGAAAGGC
20120944 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
20120973 GTTATTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:20121593 original size:6 final size:7
Alignment explanation
Indices: 20121578--20121602 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20121568 TAAGGTTGAA
20121578 TTTTCTT
1 TTTTCTT
20121585 TTTTCTT
1 TTTTCTT
20121592 TTTTCTT
1 TTTTCTT
20121599 TTTT
1 TTTT
20121603 GAAAAATTGG
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:20121946 original size:70 final size:70
Alignment explanation
Indices: 20121866--20122011 Score: 276
Period size: 70 Copynumber: 2.1 Consensus size: 70
20121856 TTGGGTCGAG
20121866 TCAA-GTCTCCTATTAAATTTCAGGTTCGAGCAAGTTTTAATTTTAAGAGTTTGTGTCGGGTTGG
1 TCAAGGTCTCCTATTAAATTTCAGGTTCGAGCAAGTTTTAATTTTAAGAGTTTGTGTCGGGTTGG
*
20121930 ATTCC
66 ATTCA
20121935 TCAAGGTCTCCTATTAAATTTCAGGTTCGAGCAAGTTTTAATTTTAAGAGTTTGTGTCGGGTTGG
1 TCAAGGTCTCCTATTAAATTTCAGGTTCGAGCAAGTTTTAATTTTAAGAGTTTGTGTCGGGTTGG
20122000 ATTCA
66 ATTCA
20122005 TCAAGGT
1 TCAAGGT
20122012 TCTAGTTAGG
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 4 0.05
70 71 0.95
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.40
Consensus pattern (70 bp):
TCAAGGTCTCCTATTAAATTTCAGGTTCGAGCAAGTTTTAATTTTAAGAGTTTGTGTCGGGTTGG
ATTCA
Found at i:20126077 original size:13 final size:13
Alignment explanation
Indices: 20126061--20126086 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20126051 AATTGAATAA
20126061 ACAAATTTAACAT
1 ACAAATTTAACAT
20126074 ACAAATTTAACAT
1 ACAAATTTAACAT
20126087 GGAAAAACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
ACAAATTTAACAT
Found at i:20130057 original size:6 final size:7
Alignment explanation
Indices: 20130036--20130062 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
20130026 ATTTTTGCAG
20130036 AAAGAAA
1 AAAGAAA
20130043 AAAGAAA
1 AAAGAAA
20130050 AAAGAAA
1 AAAGAAA
20130057 AAAGAA
1 AAAGAA
20130063 TTACAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:20132453 original size:5 final size:5
Alignment explanation
Indices: 20132443--20132481 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
20132433 AAAAATCTGT
*
20132443 TTTTA TTTTA TTTTA TTATA TTTT- TGTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTT
20132482 CTCTATCAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 1 0.03
5 28 0.93
6 1 0.03
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:20134508 original size:20 final size:20
Alignment explanation
Indices: 20134471--20134510 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20134461 AAATGTATTA
* *
20134471 TAAAATCTAAACCCTAAACT
1 TAAAATCTAAAACATAAACT
*
20134491 TAAAATCTAAAATATAAACT
1 TAAAATCTAAAACATAAACT
20134511 CGAAATTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAATCTAAAACATAAACT
Found at i:20139544 original size:37 final size:38
Alignment explanation
Indices: 20139503--20139577 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
20139493 ATGATGATAC
*
20139503 ATGGTAGTGGAATCC-AAAAATGATAATTTGTATGACT
1 ATGGTAGTGGAATCCAAAAAATGATAATTTGTAAGACT
20139540 ATGGTAGTGGAATCCAAAAAATGATAATTTGTAAGACT
1 ATGGTAGTGGAATCCAAAAAATGATAATTTGTAAGACT
20139578 TCCCTTTTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 15 0.42
38 21 0.58
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (38 bp):
ATGGTAGTGGAATCCAAAAAATGATAATTTGTAAGACT
Found at i:20141629 original size:50 final size:50
Alignment explanation
Indices: 20141554--20141793 Score: 296
Period size: 50 Copynumber: 4.9 Consensus size: 50
20141544 TGATGCTAGG
*
20141554 GAGATATGAGAGCTAGTGCAAGACCATGTCTGGGACATGGCATCGGCCTC
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
*
20141604 GAGATATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCT-
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
* * *
20141653 --GATATGTG-TC-AGTGTAAGACCATGTTTGGGACATGGCATCGGCAC-C
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTC
* * * *
20141699 GATAGATGAGAGCTAGTGTAAGACCATGTATGGGACATGGCATCAGCCTC
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
* * **
20141749 GATATACGAGAG-TCAGTGTAAGATAATGTCTGGGACATGGCATCG
1 GAGATATGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCG
20141794 ACTTTGATAT
Statistics
Matches: 166, Mismatches: 16, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
45 33 0.20
46 2 0.01
47 7 0.04
48 5 0.03
49 3 0.02
50 116 0.70
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (50 bp):
GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
Found at i:20141736 original size:95 final size:97
Alignment explanation
Indices: 20141568--20141793 Score: 314
Period size: 95 Copynumber: 2.3 Consensus size: 97
20141558 TATGAGAGCT
* *
20141568 AGTGCAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAGAGCTAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAGATGAGAGCTAGTGTAAGACCATGT
* * *
20141633 TTGGGACATGGCATCGGCCT-GATAT-GTGTC
66 ATGGGACATGGCATCAGCCTCGATATAGAGTC
* *
20141663 AGTGTAAGACCATGTTTGGGACATGGCATCGGCAC-CGATAGATGAGAGCTAGTGTAAGACCATG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGAGAGATGAGAGCTAGTGTAAGACCATG
20141727 TATGGGACATGGCATCAGCCTCGATATACGAGAGTC
65 TATGGGACATGGCATCAGCCTCGATAT---AGAGTC
**
20141763 AGTGTAAGATAATGTCTGGGACATGGCATCG
1 AGTGTAAGACCATGTCTGGGACATGGCATCG
20141794 ACTTTGATAT
Statistics
Matches: 115, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
95 77 0.67
96 6 0.05
100 32 0.28
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (97 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAGATGAGAGCTAGTGTAAGACCATGT
ATGGGACATGGCATCAGCCTCGATATAGAGTC
Found at i:20141803 original size:50 final size:49
Alignment explanation
Indices: 20141556--20141876 Score: 232
Period size: 50 Copynumber: 6.8 Consensus size: 49
20141546 ATGCTAGGGA
* *
20141556 GATAT-GAGAG-CTAGTGCAAGACCATGTCTGGGACATGGCATCGGCCTC
1 GATATAGAGAGTC-AGTGTAAGACCATGTCTGGGACATGGCATCGACCTC
* * *
20141604 GAGATATGAGAG-CTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCT-
1 GATATA-GAGAGTC-AGTGTAAGACCATGTCTGGGACATGGCATCGACCTC
* * *
20141653 GATAT---GTGTCAGTGTAAGACCATGTTTGGGACATGGCATCGGCAC-C
1 GATATAGAGAGTCAGTGTAAGACCATGTCTGGGACATGGCATCGAC-CTC
* *
20141699 GATAGATGAGAG-CTAGTGTAAGACCATGTATGGGACATGGCATC-AGCCTC
1 GATATA-GAGAGTC-AGTGTAAGACCATGTCTGGGACATGGCATCGA-CCTC
**
20141749 GATATACGAGAGTCAGTGTAAGATAATGTCTGGGACATGGCATCGA-CT-
1 GATATA-GAGAGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACCTC
* ** * * *
20141797 --T-T-GATA-T--GTGTAAGATAATGTCTGAGACATGGCATCGACTTT
1 GATATAGAGAGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACCTC
* ** *
20141839 GATAT-GTGAACCAGTGTAAGACCATGTCTGAGACATGG
1 GATATAGAGAGTCAGTGTAAGACCATGTCTGGGACATGG
20141877 TGTTGGCACT
Statistics
Matches: 229, Mismatches: 22, Indels: 44
0.78 0.07 0.15
Matches are distributed among these distances:
40 30 0.13
41 1 0.00
42 1 0.00
43 3 0.01
44 1 0.00
45 39 0.17
46 7 0.03
48 27 0.12
49 8 0.03
50 110 0.48
51 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (49 bp):
GATATAGAGAGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACCTC
Found at i:20141819 original size:40 final size:40
Alignment explanation
Indices: 20141764--20141846 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
20141754 ACGAGAGTCA
*
20141764 GTGTAAGATAATGTCTGGGACATGGCATCGACTTTGATAT
1 GTGTAAGATAATGTCTGAGACATGGCATCGACTTTGATAT
20141804 GTGTAAGATAATGTCTGAGACATGGCATCGACTTTGATAT
1 GTGTAAGATAATGTCTGAGACATGGCATCGACTTTGATAT
20141844 GTG
1 GTG
20141847 AACCAGTGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (40 bp):
GTGTAAGATAATGTCTGAGACATGGCATCGACTTTGATAT
Found at i:20147134 original size:48 final size:45
Alignment explanation
Indices: 20146969--20147190 Score: 164
Period size: 48 Copynumber: 4.7 Consensus size: 45
20146959 GGTGTAATGT
* *
20146969 CGATGCCATGTCCCAGACATGGTCTTACACTGATTATCGAAATCGA-G-GT
1 CGATGCCATGTCCCAGACATGGTCTTACACTG---A-C-ACATC-ACGTGC
* * * * * *
20147018 CGACGCCATGTCCTAGCCATGGTCTTACACTAGCTCTCACATCTCTATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACT-G---ACACATCAC-GTGC
* *
20147068 CAATGCCATGTCCCAGACATGGTCTTACACTGACACCTCTATACGTGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACACATC---ACGTGC
* *
20147116 CGATGCCATGTCCGAGACATGGTCTTACACTGACACATCCCGTAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACACATCACGT-GC
*
20147162 CGATG-CATGTCCTAGACAT-GTCTTACACT
1 CGATGCCATGTCCCAGACATGGTCTTACACT
20147191 AGCTCTTGTT
Statistics
Matches: 142, Mismatches: 23, Indels: 21
0.76 0.12 0.11
Matches are distributed among these distances:
44 10 0.07
45 16 0.11
46 12 0.08
48 43 0.30
49 31 0.22
50 30 0.21
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (45 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACACATCACGTGC
Found at i:20147226 original size:92 final size:94
Alignment explanation
Indices: 20147113--20147287 Score: 237
Period size: 94 Copynumber: 1.9 Consensus size: 94
20147103 CCTCTATACG
* * * **
20147113 TGCCGATGCCATGTCCGAGACATGGTCTTACACT-G-ACACATCCCGTAGCCGATGCATGTCCTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAATGGCACACATAACGTAGCCGATGCATGTCCTA
20147176 GACATGTCTTACACTAGCTCTTGTTTCAA
66 GACATGTCTTACACTAGCTCTTGTTTCAA
* * * * **
20147205 TGCCAATGCCATGTCCCAGACATGGTCTTACAATGGCTCTCATAATGTGGTTGATGCATGTCCTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAATGGCACACATAACGTAGCCGATGCATGTCCTA
20147270 GACATGTCTTACACTAGC
66 GACATGTCTTACACTAGC
20147288 GCACAAATGA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
92 31 0.44
93 1 0.01
94 38 0.54
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (94 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAATGGCACACATAACGTAGCCGATGCATGTCCTA
GACATGTCTTACACTAGCTCTTGTTTCAA
Found at i:20147261 original size:140 final size:140
Alignment explanation
Indices: 20147024--20147284 Score: 341
Period size: 140 Copynumber: 1.9 Consensus size: 140
20147014 AGGTCGACGC
* *
20147024 CATGTCCTAGCCATGGTCTTACACTAGCTCTCACATCTCTATGCCAATGCCATGTCCCAGACATG
1 CATGTCCTAGACATGGTCTTACACTAGCTCT-ACATCTCAATGCCAATGCCATGTCCCAGACATG
*
20147089 GTCTTACACTGACACCTCTATACGTGCCGATGCCATGTCCGAGACATGGTCTTACACTGACACAT
65 GTCTTACAATGACACCTCTATACGTGCCGATG-CATGTCCGAGACAT-GTCTTACACTGACACAT
20147154 CCCGTAGCCGATG
128 CCCGTAGCCGATG
** *
20147167 CATGTCCTAGACAT-GTCTTACACTAGCTCT-TGTTTCAATGCCAATGCCATGTCCCAGACATGG
1 CATGTCCTAGACATGGTCTTACACTAGCTCTACATCTCAATGCCAATGCCATGTCCCAGACATGG
* * * ** *
20147230 TCTTACAATGGC-TCTC-ATAATGTGGTTGATGCATGTCCTAGACATGTCTTACACT
66 TCTTACAATGACACCTCTAT-ACGT-GCCGATGCATGTCCGAGACATGTCTTACACT
20147285 AGCGCACAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
138 12 0.12
139 19 0.18
140 44 0.42
142 16 0.15
143 13 0.12
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (140 bp):
CATGTCCTAGACATGGTCTTACACTAGCTCTACATCTCAATGCCAATGCCATGTCCCAGACATGG
TCTTACAATGACACCTCTATACGTGCCGATGCATGTCCGAGACATGTCTTACACTGACACATCCC
GTAGCCGATG
Found at i:20152492 original size:17 final size:18
Alignment explanation
Indices: 20152470--20152503 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20152460 TTATTTTCAA
20152470 AGAAAA-AAAGAAGAGAT
1 AGAAAATAAAGAAGAGAT
*
20152487 AGAAAATAAATAAGAGA
1 AGAAAATAAAGAAGAGA
20152504 AAATTAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.09
Consensus pattern (18 bp):
AGAAAATAAAGAAGAGAT
Found at i:20155674 original size:51 final size:51
Alignment explanation
Indices: 20155598--20155714 Score: 191
Period size: 51 Copynumber: 2.3 Consensus size: 51
20155588 CTGATCACAT
20155598 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAG-AAGAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCAA-AAGCTACCAC
* * *
20155649 TTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACTAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCAAAAGCTACCAC
20155700 TTATCACTTGTCACT
1 TTATCACTTGTCACT
20155715 GATCAGAAGT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
51 60 0.98
52 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCAAAAGCTACCAC
Found at i:20156790 original size:16 final size:16
Alignment explanation
Indices: 20156769--20156810 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
20156759 TATAAGTTAT
20156769 TTCAGAATTTTTTAAA
1 TTCAGAATTTTTTAAA
20156785 TTCAGAATTTTTTAAA
1 TTCAGAATTTTTTAAA
20156801 TTCAGAATTT
1 TTCAGAATTT
20156811 CTACATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (16 bp):
TTCAGAATTTTTTAAA
Found at i:20160973 original size:25 final size:25
Alignment explanation
Indices: 20160939--20160989 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
20160929 AAATAGAACT
20160939 TAATGAATCCAATGAAACAAAAACA
1 TAATGAATCCAATGAAACAAAAACA
*
20160964 TAATGAATCCGATGAAACAAAAACA
1 TAATGAATCCAATGAAACAAAAACA
20160989 T
1 T
20160990 CCAAGTCCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.57, C:0.16, G:0.10, T:0.18
Consensus pattern (25 bp):
TAATGAATCCAATGAAACAAAAACA
Found at i:20168237 original size:150 final size:150
Alignment explanation
Indices: 20167966--20168266 Score: 557
Period size: 150 Copynumber: 2.0 Consensus size: 150
20167956 AGTGTTAACG
*
20167966 AGCGATAACTCCAAGCTCACGTCCGAGTGGATCCTAGATTCGGGATGTTCTTTCCACATGTGTCC
1 AGCGATAACTCCAAGCTCACATCCGAGTGGATCCTAGATTCGGGATGTTCTTTCCACATGTGTCC
20168031 CAATAGAGAATAGTTCTTCACATACAGTTCAGTTGAAAGTGAAGTTGTGCGCATGGGAAATTATT
66 CAATAGAGAATAGTTCTTCACATACAGTTCAGTTGAAAGTGAAGTTGTGCGCATGGGAAATTATT
20168096 CATCTAGCAAGGTAATTGGT
131 CATCTAGCAAGGTAATTGGT
* *
20168116 AGCGATAACTCTAAGCTCACATTCGAGTGGATCCTAGATTCGGGATGTTCTTTCCACATGTGTCC
1 AGCGATAACTCCAAGCTCACATCCGAGTGGATCCTAGATTCGGGATGTTCTTTCCACATGTGTCC
*
20168181 CAATAGAGAATAGTTCTTCACATACAGTTCAGTTGAAGGTGAAGTTGTGCGCATGGGAAATTATT
66 CAATAGAGAATAGTTCTTCACATACAGTTCAGTTGAAAGTGAAGTTGTGCGCATGGGAAATTATT
*
20168246 CATCTAGTAAGGTAATTGGT
131 CATCTAGCAAGGTAATTGGT
20168266 A
1 A
20168267 TTGGTACTGT
Statistics
Matches: 146, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
150 146 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (150 bp):
AGCGATAACTCCAAGCTCACATCCGAGTGGATCCTAGATTCGGGATGTTCTTTCCACATGTGTCC
CAATAGAGAATAGTTCTTCACATACAGTTCAGTTGAAAGTGAAGTTGTGCGCATGGGAAATTATT
CATCTAGCAAGGTAATTGGT
Found at i:20170699 original size:25 final size:25
Alignment explanation
Indices: 20170671--20170754 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 25
20170661 AGTTAAATTT
20170671 AATTATTAACCTTTTAAAAAGAGTC
1 AATTATTAACCTTTTAAAAAGAGTC
*
20170696 AATTCACTT-A-CTTTTAATTAATA-AGCTATT
1 AATT-A-TTAACCTTTTAA--AA-AGAG---TC
20170726 AATTATTAACCTTTTAAAAAGAGTC
1 AATTATTAACCTTTTAAAAAGAGTC
20170751 AATT
1 AATT
20170755 CACTTACTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 22
0.66 0.03 0.31
Matches are distributed among these distances:
25 16 0.35
26 2 0.04
27 7 0.15
28 7 0.15
29 2 0.04
30 12 0.26
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (25 bp):
AATTATTAACCTTTTAAAAAGAGTC
Found at i:20170753 original size:55 final size:56
Alignment explanation
Indices: 20170669--20170783 Score: 214
Period size: 55 Copynumber: 2.1 Consensus size: 56
20170659 TTAGTTAAAT
*
20170669 TTAATTATTAACCTTTTAAAAAGAGTCAATTCACTTACTTTTAATTAATAAGCT-A
1 TTAATTATTAACCTTTTAAAAAGAGTCAATTCACTTACTTTTAATAAATAAGCTAA
20170724 TTAATTATTAACCTTTTAAAAAGAGTCAATTCACTTACTTTTAATAAATAAGCTAA
1 TTAATTATTAACCTTTTAAAAAGAGTCAATTCACTTACTTTTAATAAATAAGCTAA
20170780 TTAA
1 TTAA
20170784 AACATTAATT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
55 53 0.91
56 5 0.09
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (56 bp):
TTAATTATTAACCTTTTAAAAAGAGTCAATTCACTTACTTTTAATAAATAAGCTAA
Found at i:20170764 original size:25 final size:25
Alignment explanation
Indices: 20170681--20170767 Score: 72
Period size: 25 Copynumber: 3.3 Consensus size: 25
20170671 AATTATTAAC
20170681 CTTTTAAAAAGAGTCAATTCACTTA
1 CTTTTAAAAAGAGTCAATTCACTTA
*
20170706 CTTTTAATTAATA-AGCTATTAATT-A-TTAA
1 CTTTTAA--AA-AGAG---TCAATTCACTT-A
20170735 CCTTTTAAAAAGAGTCAATTCACTTA
1 -CTTTTAAAAAGAGTCAATTCACTTA
20170761 CTTTTAA
1 CTTTTAA
20170768 TAAATAAGCT
Statistics
Matches: 49, Mismatches: 2, Indels: 22
0.67 0.03 0.30
Matches are distributed among these distances:
25 19 0.39
26 2 0.04
27 7 0.14
28 7 0.14
29 2 0.04
30 12 0.24
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (25 bp):
CTTTTAAAAAGAGTCAATTCACTTA
Found at i:20170928 original size:29 final size:29
Alignment explanation
Indices: 20170892--20170962 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
20170882 AAAATAATTT
**
20170892 AAAATTTATAAAAATATTCAAA-TAAATA
1 AAAATTTATAAAAATATAAAAAGTAAATA
*
20170920 AATAATTTA-AAAATATATAAAAAGTTAATA
1 AA-AATTTATAAAA-ATATAAAAAGTAAATA
20170950 AAAATTT-TAAAAA
1 AAAATTTATAAAAA
20170963 ATAGTATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
28 7 0.19
29 22 0.61
30 7 0.19
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAATTTATAAAAATATAAAAAGTAAATA
Found at i:20170939 original size:19 final size:18
Alignment explanation
Indices: 20170883--20170940 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
20170873 TGTCATAAAA
*
20170883 AAATAATTTAAAATTTAT
1 AAATAATTTAAAATATAT
* *
20170901 AAA-AATATTCAAATAAAT
1 AAATAAT-TTAAAATATAT
20170919 AAATAATTTAAAAATATAT
1 AAATAATTT-AAAATATAT
20170938 AAA
1 AAA
20170941 AAGTTAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.09
18 16 0.50
19 13 0.41
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATAATTTAAAATATAT
Found at i:20171597 original size:20 final size:20
Alignment explanation
Indices: 20171572--20171617 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
20171562 CTGATAAGTC
20171572 CATTTTTACTCACATTTTTA
1 CATTTTTACTCACATTTTTA
20171592 CA-TTTTACTCACATTTTTA
1 CATTTTTACTCACATTTTTA
20171611 CATTTTT
1 CATTTTT
20171618 TAATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.57
Consensus pattern (20 bp):
CATTTTTACTCACATTTTTA
Found at i:20172781 original size:23 final size:25
Alignment explanation
Indices: 20172755--20172800 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
20172745 AATTAACTCG
*
20172755 TAAATCAAGAAAA-ATA-ATATACA
1 TAAATAAAGAAAATATATATATACA
20172778 TAAATAAAGAAAATATATATATA
1 TAAATAAAGAAAATATATATATA
20172801 AAATATTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 3 0.15
25 5 0.25
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.26
Consensus pattern (25 bp):
TAAATAAAGAAAATATATATATACA
Found at i:20174841 original size:77 final size:78
Alignment explanation
Indices: 20174709--20174857 Score: 210
Period size: 77 Copynumber: 1.9 Consensus size: 78
20174699 ATGTGTAACC
* * * * *
20174709 GTGTAATACCATGTTTGGGACATGGCATCAGCATTGTTACATGAGCCGGTGTAAGACTATGTCTG
1 GTGTAAGACCATGTCTGGGACATGGCATCAGCATTGTTACATGAGCCAGTATAAGACCATGTCTG
20174774 GGACATGACATTG
66 GGACATGACATTG
* * **
20174787 GTGTAAGACCATGTCT-GGACATGGTATCGGCATTGTTATGTGAGCCAGTATAAGACCATGTCTG
1 GTGTAAGACCATGTCTGGGACATGGCATCAGCATTGTTACATGAGCCAGTATAAGACCATGTCTG
20174851 GGACATG
66 GGACATG
20174858 GCATCGGCAT
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
77 48 0.77
78 14 0.23
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (78 bp):
GTGTAAGACCATGTCTGGGACATGGCATCAGCATTGTTACATGAGCCAGTATAAGACCATGTCTG
GGACATGACATTG
Found at i:20174866 original size:48 final size:48
Alignment explanation
Indices: 20174790--20174973 Score: 217
Period size: 48 Copynumber: 3.6 Consensus size: 48
20174780 GACATTGGTG
*
20174790 TAAGACCATGTCT-GGACATGGTATCGGCATTGTTATGTGAGCCAGTA
1 TAAGACCATGTCTGGGACATGGCATCGGCATTGTTATGTGAGCCAGTA
*
20174837 TAAGACCATGTCTGGGACATGGCATCGGCATTGTTACGTGAGCTTACGTGAGCTA
1 TAAGACCATGTCTGGGACATGGCATCGGCATTGTTATGTGAGC---C---AG-TA
* * *
20174892 GTGTAAGACTATGTCTGGGACATGACATCGGCATTGTTATGTGAGCCAGTG
1 ---TAAGACCATGTCTGGGACATGGCATCGGCATTGTTATGTGAGCCAGTA
*
20174943 TAAGACCATGTCTGAGACATGGCATCGGCAT
1 TAAGACCATGTCTGGGACATGGCATCGGCAT
20174974 GAGGCATCGT
Statistics
Matches: 117, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
47 13 0.11
48 55 0.47
51 2 0.02
52 2 0.02
54 2 0.02
55 3 0.03
58 40 0.34
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCATCGGCATTGTTATGTGAGCCAGTA
Found at i:20174921 original size:58 final size:58
Alignment explanation
Indices: 20174826--20174937 Score: 179
Period size: 58 Copynumber: 1.9 Consensus size: 58
20174816 GCATTGTTAT
*
20174826 GTGAGCCAGTATAAGACCATGTCTGGGACATGGCATCGGCATTGTTACGTGAGCTTAC
1 GTGAGCCAGTATAAGACCATGTCTGGGACATGACATCGGCATTGTTACGTGAGCTTAC
* * * *
20174884 GTGAGCTAGTGTAAGACTATGTCTGGGACATGACATCGGCATTGTTATGTGAGC
1 GTGAGCCAGTATAAGACCATGTCTGGGACATGACATCGGCATTGTTACGTGAGC
20174938 CAGTGTAAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (58 bp):
GTGAGCCAGTATAAGACCATGTCTGGGACATGACATCGGCATTGTTACGTGAGCTTAC
Found at i:20182410 original size:20 final size:20
Alignment explanation
Indices: 20182385--20182424 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
20182375 AAAAAGAAAT
20182385 AATTTTTAAAGCTCAAACAG
1 AATTTTTAAAGCTCAAACAG
*
20182405 AATTTTTAGAGCTCAAACAG
1 AATTTTTAAAGCTCAAACAG
20182425 GGGAATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (20 bp):
AATTTTTAAAGCTCAAACAG
Found at i:20188276 original size:44 final size:45
Alignment explanation
Indices: 20188210--20188382 Score: 153
Period size: 45 Copynumber: 3.9 Consensus size: 45
20188200 TTTTCTCAAA
* * * *
20188210 TCACCGGCATT-TCGCCTGCTAGGAC-CG-AGGCCCGATTA-TCATT
1 TCACCGGCATTATAGCCTGCTAGG-CTCGAAAGCCCGAATAGT-ATC
* *
20188253 TCATCGGCATTATATCCTGCTAGGCTCGAAAGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAAGCCCGAATAGTATC
* *
20188298 TCACCGGCATTATAGCCTGCTAGGC-CCAAAGGCCCGAATAGTGTC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAA-GCCCGAATAGTATC
* * *
20188343 TCATCGGCA-TACTAGTCTGCTAGGCTC-AAAGGCTCGAATA
1 TCACCGGCATTA-TAGCCTGCTAGGCTCGAAA-GCCCGAATA
20188383 TAATAGCAGC
Statistics
Matches: 110, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
43 11 0.10
44 18 0.16
45 79 0.72
46 2 0.02
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAAGCCCGAATAGTATC
Found at i:20188306 original size:45 final size:45
Alignment explanation
Indices: 20188257--20188382 Score: 159
Period size: 45 Copynumber: 2.8 Consensus size: 45
20188247 ATCATTTCAT
20188257 CGGCATTATATCCTGCTAGGCTCGAAA-GCCCGAATAGTATCTCAC
1 CGGCATTATATCCTGCTAGGCTC-AAAGGCCCGAATAGTATCTCAC
* * * *
20188302 CGGCATTATAGCCTGCTAGGCCCAAAGGCCCGAATAGTGTCTCAT
1 CGGCATTATATCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCAC
*
20188347 CGGCA-TACTAGT-CTGCTAGGCTCAAAGGCTCGAATA
1 CGGCATTA-TA-TCCTGCTAGGCTCAAAGGCCCGAATA
20188383 TAATAGCAGC
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
44 5 0.07
45 66 0.93
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (45 bp):
CGGCATTATATCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCAC
Found at i:20188347 original size:90 final size:88
Alignment explanation
Indices: 20188210--20188382 Score: 201
Period size: 90 Copynumber: 1.9 Consensus size: 88
20188200 TTTTCTCAAA
* * * *
20188210 TCACCGGCATTTCGCCTGCTAGGACCGAGGCCCGATTATCATTTCATCGGCATTA-TA-TCCTGC
1 TCACCGGCATTTAGCCTGCTAGGACCAAGGCCCGAATATCATCTCATCGGCA-TACTAGT-CTGC
20188273 TAGGCTCGAAA-GCCCGAATAGTATC
64 TAGGCTC-AAAGGCCCGAATAGTATC
* *
20188298 TCACCGGCATTATAGCCTGCTAGGCCCAAAGGCCCGAATAGT-GTCTCATCGGCATACTAGTCTG
1 TCACCGGCATT-TAGCCTGCTAGGACC-AAGGCCCGAATA-TCATCTCATCGGCATACTAGTCTG
*
20188362 CTAGGCTCAAAGGCTCGAATA
63 CTAGGCTCAAAGGCCCGAATA
20188383 TAATAGCAGC
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
88 11 0.15
89 18 0.25
90 41 0.57
91 2 0.03
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (88 bp):
TCACCGGCATTTAGCCTGCTAGGACCAAGGCCCGAATATCATCTCATCGGCATACTAGTCTGCTA
GGCTCAAAGGCCCGAATAGTATC
Found at i:20188431 original size:38 final size:38
Alignment explanation
Indices: 20188380--20188534 Score: 204
Period size: 38 Copynumber: 4.1 Consensus size: 38
20188370 AAAGGCTCGA
* *
20188380 ATATAATAGCAGCACTAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
20188418 ATATAATACCAGCACGAAGCCTGCGGGAATTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* *
20188456 ATATATTACCAGCACGAAGCCTGCGGGATTTACCCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* * ** *
20188494 ATATAATTCCAGCA-TATAGCCTGCGGTCTTTAAGCCGG
1 ATATAATACCAGCACGA-AGCCTGCGGGATTTAACCCGG
20188532 ATA
1 ATA
20188535 CAAATATCAT
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
37 1 0.01
38 102 0.99
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:20200302 original size:230 final size:230
Alignment explanation
Indices: 20199899--20200359 Score: 922
Period size: 230 Copynumber: 2.0 Consensus size: 230
20199889 AAATTGGACA
20199899 CTGTAGAACAATCATCAATTGTGTCAAGAAATCGTAGAGACTTAAAAATGTCAAATGTTACTTGA
1 CTGTAGAACAATCATCAATTGTGTCAAGAAATCGTAGAGACTTAAAAATGTCAAATGTTACTTGA
20199964 TCATCCTGAACACGCATAGTAAGCTTGCCCTTCTGCACATCAATAAGGGTCCTTTCGATTGCTGA
66 TCATCCTGAACACGCATAGTAAGCTTGCCCTTCTGCACATCAATAAGGGTCCTTTCGATTGCTGA
20200029 GAATAGTCTTAGTAGGATGATTGGCACCTCTTTGTCTGCTTCAAAGTCTAGAATCACAAAGTCAG
131 GAATAGTCTTAGTAGGATGATTGGCACCTCTTTGTCTGCTTCAAAGTCTAGAATCACAAAGTCAG
20200094 TAGGAAAGATAAATTTGTCTACACGTACCAATACG
196 TAGGAAAGATAAATTTGTCTACACGTACCAATACG
20200129 CTGTAGAACAATCATCAATTGTGTCAAGAAATCGTAGAGACTTAAAAATGTCAAATGTTACTTGA
1 CTGTAGAACAATCATCAATTGTGTCAAGAAATCGTAGAGACTTAAAAATGTCAAATGTTACTTGA
20200194 TCATCCTGAACACGCATAGTAAGCTTGCCCTTCTGCACATCAATAAGGGTCCTTTCGATTGCTGA
66 TCATCCTGAACACGCATAGTAAGCTTGCCCTTCTGCACATCAATAAGGGTCCTTTCGATTGCTGA
20200259 GAATAGTCTTAGTAGGATGATTGGCACCTCTTTGTCTGCTTCAAAGTCTAGAATCACAAAGTCAG
131 GAATAGTCTTAGTAGGATGATTGGCACCTCTTTGTCTGCTTCAAAGTCTAGAATCACAAAGTCAG
20200324 TAGGAAAGATAAATTTGTCTACACGTACCAATACG
196 TAGGAAAGATAAATTTGTCTACACGTACCAATACG
20200359 C
1 C
20200360 CCTCGATTTT
Statistics
Matches: 231, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
230 231 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (230 bp):
CTGTAGAACAATCATCAATTGTGTCAAGAAATCGTAGAGACTTAAAAATGTCAAATGTTACTTGA
TCATCCTGAACACGCATAGTAAGCTTGCCCTTCTGCACATCAATAAGGGTCCTTTCGATTGCTGA
GAATAGTCTTAGTAGGATGATTGGCACCTCTTTGTCTGCTTCAAAGTCTAGAATCACAAAGTCAG
TAGGAAAGATAAATTTGTCTACACGTACCAATACG
Found at i:20202312 original size:40 final size:40
Alignment explanation
Indices: 20202240--20202616 Score: 625
Period size: 40 Copynumber: 9.5 Consensus size: 40
20202230 CCCAAGTACA
* *
20202240 TTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGCC
1 TTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCC
*
20202279 TTCGGGACTTAGCCCGGATATAGTCACTAGCACAAACGCC
1 TTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCC
*
20202319 TTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATGCC
1 TTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCC
*
20202359 TTCGGGACTTAGCCCGGATATAGTCACTAGCACAAACGCC
1 TTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCC
*
20202399 TTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATGCC
1 TTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCC
*
20202439 TTCGGGACTTAGCCCGGATATAGTCACTAGCACAAACGCC
1 TTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCC
*
20202479 TTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATGCC
1 TTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCC
*
20202519 TTCGGGACTTAGCCCGGATATAGTCACTAGCACAACTGCC
1 TTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCC
* *
20202559 TTTGGGACTTAGCCCGGATATAGTCACTAGCAC-CATGCC
1 TTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCC
20202598 TTCGGGACTTAGCCCGGAT
1 TTCGGGACTTAGCCCGGAT
20202617 GTCATCCGAA
Statistics
Matches: 317, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
39 33 0.10
40 283 0.89
41 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (40 bp):
TTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCC
Found at i:20211417 original size:43 final size:44
Alignment explanation
Indices: 20211356--20211448 Score: 104
Period size: 44 Copynumber: 2.1 Consensus size: 44
20211346 TATTGCACAC
*
20211356 AGTGCCATTTATTCAGCCA-ACGCT-GTT-TTAATCTCGCACACTT
1 AGTGCCATTTAGTCAGCCATA-GCTAGTTCTTAAT-TCGCACACTT
* *
20211399 AGTGCCATTTTAGT-AGCCATAGCTATTTCTTTATTCGCACACTT
1 AGTGCCA-TTTAGTCAGCCATAGCTAGTTCTTAATTCGCACACTT
20211443 AGTGCC
1 AGTGCC
20211449 TCATATATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
43 15 0.35
44 24 0.56
45 4 0.09
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.37
Consensus pattern (44 bp):
AGTGCCATTTAGTCAGCCATAGCTAGTTCTTAATTCGCACACTT
Found at i:20218038 original size:47 final size:47
Alignment explanation
Indices: 20217956--20218056 Score: 109
Period size: 47 Copynumber: 2.2 Consensus size: 47
20217946 TGAGAGCTAA
** **
20217956 TGTAAGA-CATGTATGGGACATGCGTCGGCTATGAGATGAT-AGTTAG
1 TGTAAGACCATGTATGGGACATGCGTCAACTATGAGAT-ATAAGCCAG
* *
20218002 TGTAAGACCATGTTTGGGACATGGCTTCAACT-TGAGATATAAGCCAG
1 TGTAAGACCATGTATGGGACAT-GCGTCAACTATGAGATATAAGCCAG
20218049 TGTAAGAC
1 TGTAAGAC
20218057 TGTGTCTGGG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
46 9 0.20
47 31 0.67
48 6 0.13
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.28
Consensus pattern (47 bp):
TGTAAGACCATGTATGGGACATGCGTCAACTATGAGATATAAGCCAG
Found at i:20225201 original size:47 final size:45
Alignment explanation
Indices: 20225128--20225340 Score: 148
Period size: 46 Copynumber: 4.6 Consensus size: 45
20225118 AATTGTGAGA
*
20225128 GCTAGTGTAAGACCATGTCTAGGACATGGCATCAACATTGAGACTAGT
1 GCTAGTGTAAGACCATGTCTGGGACAT-GCATCAACATTGAGA-TA-T
** * * *
20225176 GCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCCTCGAGACGTAA
1 GCTAGTGTAAGACCATGTCTGGGACATGCATCAACATTGAGA--TAT
* * * *
20225222 GCGAGTGTAAGA-CATGTCTGGGACATACATCAGC-TATAAGATGAT
1 GCTAGTGTAAGACCATGTCTGGGACATGCATCAACAT-TGAGAT-AT
* * *
20225267 AG-TCAGTGTAAGACCATGTTTGGGACATGGCTTCGAC-TTGAGATAT
1 -GCT-AGTGTAAGACCATGTCTGGGACAT-GCATCAACATTGAGATAT
* *
20225313 AAGCCAGTGTAAGATCATGTCTGGGACA
1 --GCTAGTGTAAGACCATGTCTGGGACA
20225341 CAGCATCAGT
Statistics
Matches: 133, Mismatches: 23, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
44 1 0.01
45 2 0.02
46 57 0.43
47 56 0.42
48 17 0.13
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.25
Consensus pattern (45 bp):
GCTAGTGTAAGACCATGTCTGGGACATGCATCAACATTGAGATAT
Found at i:20225291 original size:93 final size:94
Alignment explanation
Indices: 20225179--20225349 Score: 231
Period size: 93 Copynumber: 1.8 Consensus size: 94
20225169 GACTAGTGCT
* * *
20225179 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCGAGACGTAAGCGAGTGTAAGA-CATGTCTG
1 AGTGTAAGACATGTCTGGGACATGGCATC-GACTCGAGACATAAGCCAGTGTAAGATCATGTCTG
*
20225242 GGACATA-CATCAGCTATAAGATGATAGTC
65 GGACACAGCATCAGCTATAAGATGATAGTC
* * * *
20225271 AGTGTAAGACCATGTTTGGGACATGGCTTCGACTTGAGATATAAGCCAGTGTAAGATCATGTCTG
1 AGTGTAAGA-CATGTCTGGGACATGGCATCGACTCGAGACATAAGCCAGTGTAAGATCATGTCTG
20225336 GGACACAGCATCAG
65 GGACACAGCATCAG
20225350 TATCTTACCC
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
92 9 0.13
93 34 0.51
94 18 0.27
95 6 0.09
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATGGCATCGACTCGAGACATAAGCCAGTGTAAGATCATGTCTGG
GACACAGCATCAGCTATAAGATGATAGTC
Found at i:20232324 original size:22 final size:21
Alignment explanation
Indices: 20232299--20232340 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
20232289 TTGGAATGGT
20232299 CACACGGGCGTGTTGCCCCTGC
1 CACACGGGCGTG-TGCCCCTGC
* *
20232321 CACATGGGTGTGTGCCCCTG
1 CACACGGGCGTGTGCCCCTG
20232341 TGTCAAGTGA
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:0.10, C:0.36, G:0.33, T:0.21
Consensus pattern (21 bp):
CACACGGGCGTGTGCCCCTGC
Found at i:20235457 original size:93 final size:93
Alignment explanation
Indices: 20235349--20235519 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
20235339 GCCCCTAAGT
* * *
20235349 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
20235414 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
20235442 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
20235507 CGAGTTCGGATGC
66 CGAGTTCGGATGC
20235520 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:20235516 original size:46 final size:46
Alignment explanation
Indices: 20235344--20235516 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
20235334 AACCCGCCCC
* * * *
20235344 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
20235390 TAAGTGAACTCGAACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
20235438 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
20235483 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
20235517 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 59 0.57
47 28 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:20235973 original size:30 final size:30
Alignment explanation
Indices: 20235939--20235998 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
20235929 ATTTAATACG
20235939 AACTTTTGAAAAATTACACTTTTGCCCCTA
1 AACTTTTGAAAAATTACACTTTTGCCCCTA
* *
20235969 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTTGAAAAATTACACTTTTGCCCCTA
20235999 GGCTCGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTTGAAAAATTACACTTTTGCCCCTA
Found at i:20237792 original size:46 final size:47
Alignment explanation
Indices: 20237740--20237890 Score: 133
Period size: 48 Copynumber: 3.2 Consensus size: 47
20237730 CACATTTGGT
* *
20237740 CATTCGGC-CACAATATACACACATCTCCTACATATTTCACACTAGC
1 CATTCGGCTCACAACATACACACATCTCCTACATATTTCACACTAAC
* * * * *
20237786 CATTCGGCTTTACCACATATACATATCTCGTACATATTTCACACTAAC
1 CATTCGGC-TCACAACATACACACATCTCCTACATATTTCACACTAAC
* * * * * ** * *
20237834 CATTCGGCTTTACCACATATACATATCTCATATGTATTTCACATTAGC
1 CATTCGGC-TCACAACATACACACATCTCCTACATATTTCACACTAAC
20237882 CATTCGGCT
1 CATTCGGCT
20237891 TTACCACATA
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
46 8 0.09
47 1 0.01
48 82 0.90
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CATTCGGCTCACAACATACACACATCTCCTACATATTTCACACTAAC
Found at i:20237820 original size:48 final size:48
Alignment explanation
Indices: 20237762--20237913 Score: 250
Period size: 48 Copynumber: 3.2 Consensus size: 48
20237752 ATATACACAC
*
20237762 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
20237810 ATCTCGTACATATTTCACACTAACCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
** *
20237858 ATCTCATATGTATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
20237906 ATCTCATA
1 ATCTCATA
20237914 TATCAATTTC
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 97 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:20256696 original size:40 final size:40
Alignment explanation
Indices: 20256622--20256698 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
20256612 TCAATGCCAC
*
20256622 ATATAGCCGAAGCTATTCCAATTCACACACTGAGTGCTTT
1 ATATAGCCGAAGCTATTCCAAATCACACACTGAGTGCTTT
* * *
20256662 ATATAGCCGAAGCTATTTCAAATCGCACATTGAGTGC
1 ATATAGCCGAAGCTATTCCAAATCACACACTGAGTGC
20256699 CAAACATAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (40 bp):
ATATAGCCGAAGCTATTCCAAATCACACACTGAGTGCTTT
Found at i:20261822 original size:30 final size:30
Alignment explanation
Indices: 20261765--20261822 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
20261755 TTTTTGGGCT
* ***
20261765 TAGGGGTAAAATGGTCATTTTGTCAAAGTC
1 TAGGGGCAAAATGGTCATTTCACCAAAGTC
20261795 TAGGGGCAAAATGGTCATTTCACCAAAG
1 TAGGGGCAAAATGGTCATTTCACCAAAG
20261823 ATATGAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTCACCAAAGTC
Found at i:20262342 original size:46 final size:45
Alignment explanation
Indices: 20262165--20262380 Score: 217
Period size: 46 Copynumber: 4.7 Consensus size: 45
20262155 TGTGTGAGGT
* * *
20262165 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACA-GACGAGAGCC
* *
20262211 AGTGTAAGACCATGTCTGGGACATGGCATTGGCATTA-AGACGAGTGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC--TACAGACGAGAGCC
20262259 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CTAC-AGACG-AGAGCC
* *
20262305 AGTGTAAGACATGTCTGGGACATGCATCGGCTAC-GA-GATGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACAGACGA-GAGCC
* *
20262349 AGTGTAAGACCCTGTCTAGGACATGGCATCGG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG
20262381 GATAGATATG
Statistics
Matches: 146, Mismatches: 11, Indels: 26
0.80 0.06 0.14
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 13 0.09
45 15 0.10
46 61 0.42
47 30 0.21
48 23 0.16
49 1 0.01
50 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACAGACGAGAGCC
Found at i:20264746 original size:32 final size:32
Alignment explanation
Indices: 20264700--20264763 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
20264690 TGTGTGTCTG
*
20264700 GAAGTTGAAACTAAAGGCTTATCCTTTGAGTT
1 GAAGCTGAAACTAAAGGCTTATCCTTTGAGTT
20264732 GAAGCTGAAACTAAAGGCTTATCCTTTGAGTT
1 GAAGCTGAAACTAAAGGCTTATCCTTTGAGTT
20264764 AATCTTGAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (32 bp):
GAAGCTGAAACTAAAGGCTTATCCTTTGAGTT
Found at i:20271412 original size:123 final size:123
Alignment explanation
Indices: 20271193--20271414 Score: 417
Period size: 123 Copynumber: 1.8 Consensus size: 123
20271183 AAGGAGATCT
*
20271193 ATTCTAGGACTACCGTAATACGTCCGGGTCTAGCTATACATGCCGATAAGTGTTTATTTGATAGT
1 ATTCTAAGACTACCGTAATACGTCCGGGTCTAGCTATACATGCCGATAAGTGTTTATTTGATAGT
*
20271258 GTGGAGATTTTTGACAGTTAAAAATGTGTTTATTGGTATCAGAGCTACGGTTTAGTCG
66 GTGGAGATTTCTGACAGTTAAAAATGTGTTTATTGGTATCAGAGCTACGGTTTAGTCG
*
20271316 ATTCTAAGACTACCGTAATACGTCCGGGTCTAGCTATACATGCCGATATGTGTTTATTTGATAGT
1 ATTCTAAGACTACCGTAATACGTCCGGGTCTAGCTATACATGCCGATAAGTGTTTATTTGATAGT
20271381 GTGGAGATTTCTGACAGTTAAAAATGTGTTTATT
66 GTGGAGATTTCTGACAGTTAAAAATGTGTTTATT
20271415 TATAGTAATG
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 96 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (123 bp):
ATTCTAAGACTACCGTAATACGTCCGGGTCTAGCTATACATGCCGATAAGTGTTTATTTGATAGT
GTGGAGATTTCTGACAGTTAAAAATGTGTTTATTGGTATCAGAGCTACGGTTTAGTCG
Found at i:20277765 original size:40 final size:40
Alignment explanation
Indices: 20277710--20277861 Score: 236
Period size: 40 Copynumber: 3.8 Consensus size: 40
20277700 CGGATGGTAA
* *
20277710 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
20277750 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-T
*
20277790 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATT
*
20277831 -CGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
20277862 AGCTATATCC
Statistics
Matches: 104, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
39 2 0.02
40 99 0.95
41 1 0.01
42 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
Found at i:20277843 original size:80 final size:80
Alignment explanation
Indices: 20277710--20277887 Score: 263
Period size: 80 Copynumber: 2.2 Consensus size: 80
20277700 CGGATGGTAA
* *
20277710 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
*
20277775 TGCGAGTTA-CTATAT
66 AGCGAG-TAGCTATAT
*
20277790 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATATT-CGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTGACTA-ATTCCGGGCTAAGTCCCGAAGGCATTT
20277854 GAGCGAGTAGCTATAT
65 GAGCGAGTAGCTATAT
* *
20277870 CC-AGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
20277888 TACTTGGTTT
Statistics
Matches: 90, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
79 16 0.18
80 71 0.79
81 3 0.03
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
AGCGAGTAGCTATAT
Found at i:20277868 original size:40 final size:40
Alignment explanation
Indices: 20277711--20277887 Score: 227
Period size: 40 Copynumber: 4.5 Consensus size: 40
20277701 GGATGGTAAC
* * *
20277711 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATATT
* *
20277750 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 -CGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATATT
20277791 CGGGCTAAGTCCCGAAGGCATTTGTA-CGAGTTACTATATT
1 CGGGCTAAGTCCCGAAGGCATTTG-AGCGAGTTACTATATT
20277831 CGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATA-T
1 CGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTA-CTATATT
** *
20277870 CCAGCTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
20277888 TACTTGGTTT
Statistics
Matches: 125, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
39 19 0.15
40 104 0.83
41 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATATT
Found at i:20283265 original size:14 final size:15
Alignment explanation
Indices: 20283246--20283282 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
20283236 ATAATTAAAA
20283246 ATATAATAATAAT-G
1 ATATAATAATAATAG
20283260 ATATAAT-ATAATAG
1 ATATAATAATAATAG
*
20283274 TTATAATAA
1 ATATAATAA
20283283 ATAAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 14 0.70
15 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
ATATAATAATAATAG
Found at i:20283362 original size:17 final size:16
Alignment explanation
Indices: 20283340--20283376 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
20283330 AGCAGGGAAA
*
20283340 GAAAGAAGAAGAAAAAG
1 GAAAGAAAAAG-AAAAG
20283357 GAAAGAAAAAGAAAAG
1 GAAAGAAAAAGAAAAG
20283373 GAAA
1 GAAA
20283377 ATTTAGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAAGAAAAG
Found at i:20284321 original size:31 final size:31
Alignment explanation
Indices: 20284278--20284363 Score: 147
Period size: 31 Copynumber: 2.8 Consensus size: 31
20284268 TCAATCTCAG
20284278 CATAT-ACTGGGCCGAAGCCTTTACATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
* *
20284308 CATGTCACTGGGCCGAAGCCTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
20284339 CATATCACTGGGCCGAAGCCTTTAC
1 CATATCACTGGGCCGAAGCCTTTAC
20284364 TGTAAACGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 4 0.08
31 47 0.92
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTACATTATT
Found at i:20284620 original size:25 final size:25
Alignment explanation
Indices: 20284583--20284652 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
20284573 CTCTTTTAAT
*
20284583 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
* * *
20284608 AATTGGGGCAAAGCTCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
20284633 AACTAGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
20284653 AGCACTTCCT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:20284966 original size:26 final size:27
Alignment explanation
Indices: 20284855--20284987 Score: 151
Period size: 27 Copynumber: 5.0 Consensus size: 27
20284845 GGGGCAAAAT
* * * * *
20284855 GGTAATTTTACCCCACAAGGATATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
20284882 GATAATTATACCCTATATGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
20284909 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
20284936 GGTAATTCTACCCTACA-GGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
20284962 AGTAATTCTACCCTACAGGGGTATTT
1 GGTAATTCTACCCTACAGGGGTATTT
20284988 TGATATTTTA
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 25 0.27
27 66 0.73
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:20284975 original size:53 final size:54
Alignment explanation
Indices: 20284856--20284992 Score: 168
Period size: 53 Copynumber: 2.6 Consensus size: 54
20284846 GGGCAAAATG
* * * * * *
20284856 GTAATTTTACCCCACAAGGATATCTCGATAATTATACCCTATATGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCGATAATTATACCCTACATGGGTATTTCA
* * *
20284910 GTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACA-GGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGATAATTATACCCTACATGGGTATTTCA
* *
20284963 GTAATTCTACCCTACAGGGGTATTTTGATA
1 GTAATTCTACCCTACAAGGGTATTTCGATA
20284993 TTTTACAAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
53 35 0.50
54 35 0.50
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (54 bp):
GTAATTCTACCCTACAAGGGTATTTCGATAATTATACCCTACATGGGTATTTCA
Found at i:20285030 original size:27 final size:27
Alignment explanation
Indices: 20284980--20285228 Score: 171
Period size: 27 Copynumber: 9.2 Consensus size: 27
20284970 TACCCTACAG
*
20284980 GGGTATTTTGAT-ATTTTACAAATCGA
1 GGGTATTTTGGTAATTTTACAAATCGA
* * * *
20285006 GAGTATTTTGATAATTTCACAAATCAA
1 GGGTATTTTGGTAATTTTACAAATCGA
* *
20285033 GGGTATTTTGGTAATTTTAC-AAGCTA
1 GGGTATTTTGGTAATTTTACAAATCGA
20285059 GGGGTATTTTGGTAATTTTACAAATC-A
1 -GGGTATTTTGGTAATTTTACAAATCGA
**
20285086 GGGGTATTTTGGTAATTTTACTGATCGA
1 -GGGTATTTTGGTAATTTTACAAATCGA
** ** * *
20285114 GGGTATTTTTATTAAATTTTGTAAACCAA
1 GGGTA-TTTTGGT-AATTTTACAAATCGA
* **
20285143 GGGTATTTTAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAATCGA
* **** * *
20285170 GTGTAAAACGGTAATTCTATAAATCGA
1 GGGTATTTTGGTAATTTTACAAATCGA
**** *
20285197 GGGTAAAACGGTAATTTTATAAATCGA
1 GGGTATTTTGGTAATTTTACAAATCGA
20285224 GGGTA
1 GGGTA
20285229 AAACGGTAAT
Statistics
Matches: 185, Mismatches: 32, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
26 15 0.08
27 141 0.76
28 15 0.08
29 14 0.08
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCGA
Found at i:20285229 original size:27 final size:27
Alignment explanation
Indices: 20285153--20285280 Score: 186
Period size: 27 Copynumber: 4.7 Consensus size: 27
20285143 GGGTATTTTA
* *
20285153 GTAATTTTGTAAATCGAGTGTAAAACG
1 GTAATTTTATAAATCGAGGGTAAAACG
*
20285180 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTTTATAAATCGAGGGTAAAACG
20285207 GTAATTTTATAAATCGAGGGTAAAACG
1 GTAATTTTATAAATCGAGGGTAAAACG
*
20285234 GTAATTCTT-TAAATCGAGGGTAAAACA
1 GTAATT-TTATAAATCGAGGGTAAAACG
* *
20285261 GTAATTTTACAAATTGAGGG
1 GTAATTTTATAAATCGAGGG
20285281 CATTTCAGTA
Statistics
Matches: 92, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
26 2 0.02
27 88 0.96
28 2 0.02
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (27 bp):
GTAATTTTATAAATCGAGGGTAAAACG
Found at i:20292153 original size:39 final size:38
Alignment explanation
Indices: 20292099--20292244 Score: 202
Period size: 39 Copynumber: 3.8 Consensus size: 38
20292089 TGTTTATCCA
* *
20292099 GACTTAGGGTCCGCAGGCTATGTGCTAGAATTATACCCG
1 GACTTAAGGTCCGCAGGCTATGTGCTGGAATTATA-CCG
* *
20292138 GACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCTG
1 GACTTAAGGTCCGCAGGCTATGTGCTGGAATTATA-CCG
** *
20292177 GACTTAAGGTTTGCAGGCTATATGCTGGAATTATACCG
1 GACTTAAGGTCCGCAGGCTATGTGCTGGAATTATACCG
*
20292215 GACTTAAGGTCCGCAGGCTACGTGCTGGAA
1 GACTTAAGGTCCGCAGGCTATGTGCTGGAA
20292245 ATATGTCCGA
Statistics
Matches: 95, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
38 28 0.29
39 67 0.71
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27
Consensus pattern (38 bp):
GACTTAAGGTCCGCAGGCTATGTGCTGGAATTATACCG
Found at i:20292272 original size:77 final size:78
Alignment explanation
Indices: 20292093--20292253 Score: 198
Period size: 77 Copynumber: 2.1 Consensus size: 78
20292083 CAGTGATGTT
* ** * *
20292093 TATCCAGACTTAGGGTCCGCAGGCTATGTGCTAGAATTATACCCGGACTTAGGGTCCGCAGGCTA
1 TATCCGGACTTAAAGTCCGCAGGCTATATGCTAGAATTATACCCGGACTTAAGGTCCGCAGGCTA
* *
20292158 TGTGCTGGAATTA
66 CGTGCTGGAAATA
* * ** *
20292171 TATCTGGACTTAAGGTTTGCAGGCTATATGCTGGAATTATA-CCGGACTTAAGGTCCGCAGGCTA
1 TATCCGGACTTAAAGTCCGCAGGCTATATGCTAGAATTATACCCGGACTTAAGGTCCGCAGGCTA
20292235 CGTGCTGGAAATA
66 CGTGCTGGAAATA
*
20292248 TGTCCG
1 TATCCG
20292254 AGCTAAAGTC
Statistics
Matches: 71, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
77 37 0.52
78 34 0.48
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (78 bp):
TATCCGGACTTAAAGTCCGCAGGCTATATGCTAGAATTATACCCGGACTTAAGGTCCGCAGGCTA
CGTGCTGGAAATA
Found at i:20293625 original size:28 final size:28
Alignment explanation
Indices: 20293594--20293658 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
20293584 TAAGCCCCTG
* *
20293594 TATGCGAAGCCCTATAAGTGAGCCTCTA
1 TATGCGAACCCCTATAAGCGAGCCTCTA
* * *
20293622 TATGTGAACCCCTATAGGCGAGCCTCTG
1 TATGCGAACCCCTATAAGCGAGCCTCTA
*
20293650 TATACGAAC
1 TATGCGAAC
20293659 TGTAACACCC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25
Consensus pattern (28 bp):
TATGCGAACCCCTATAAGCGAGCCTCTA
Found at i:20294899 original size:35 final size:35
Alignment explanation
Indices: 20294813--20294945 Score: 144
Period size: 35 Copynumber: 3.8 Consensus size: 35
20294803 TGATTCACAA
* * * * *
20294813 CTCAATATGGTTAATACCATACCTACGT-TTCACAA
1 CTCAGTATGGATAATATCATACCTACGTATT-ATAG
* **
20294848 CTCGGTATAGGA-AATATTGTACCTACGTATTATAG
1 CTCAGTAT-GGATAATATCATACCTACGTATTATAG
*
20294883 CTTAGTATGGATAATATCATACCTACGTATTATAG
1 CTCAGTATGGATAATATCATACCTACGTATTATAG
*
20294918 CTCAGTATGGATAATACCATACCTACGT
1 CTCAGTATGGATAATATCATACCTACGT
20294946 GTCATAACTT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
34 3 0.04
35 74 0.91
36 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (35 bp):
CTCAGTATGGATAATATCATACCTACGTATTATAG
Found at i:20295918 original size:12 final size:13
Alignment explanation
Indices: 20295890--20295922 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
20295880 TTATTTCTTT
20295890 TTCTCCATCTACC
1 TTCTCCATCTACC
*
20295903 TTCTCC-TCTTCC
1 TTCTCCATCTACC
20295915 TTCTCCAT
1 TTCTCCAT
20295923 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:20297023 original size:28 final size:28
Alignment explanation
Indices: 20296991--20297055 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
20296981 ATTTACTAGA
*
20296991 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
20297019 ATACCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
20297047 ATACCCCTA
1 ATACCCCTA
20297056 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:20297219 original size:27 final size:28
Alignment explanation
Indices: 20297161--20297250 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
20297151 AGGAAGCGTC
*
20297161 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
20297189 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
20297216 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
20297245 CTGGTG
1 CTGGTG
20297251 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:20297261 original size:29 final size:28
Alignment explanation
Indices: 20297171--20297261 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
20297161 CTGGTGGCTA
* * *
20297171 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
20297199 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
20297226 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
20297255 TGTCACA
1 TGCCACA
20297262 TTTTCTGTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 23 0.44
28 14 0.27
29 15 0.29
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:20297269 original size:55 final size:56
Alignment explanation
Indices: 20297161--20297275 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
20297151 AGGAAGCGTC
* * *
20297161 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
20297216 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
20297272 CTGG
1 CTGG
20297276 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:20298372 original size:12 final size:11
Alignment explanation
Indices: 20298338--20298378 Score: 57
Period size: 10 Copynumber: 3.6 Consensus size: 11
20298328 AGCCTGTAAG
20298338 TATTCTGAATA
1 TATTCTGAATA
20298349 -ATTCTGAATA
1 TATTCTGAATA
20298359 TATTCTGAAATA
1 TATTCTG-AATA
20298371 TATGTCTG
1 TAT-TCTG
20298379 TACTGAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.37
11 6 0.22
12 7 0.26
13 4 0.15
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (11 bp):
TATTCTGAATA
Found at i:20305273 original size:40 final size:39
Alignment explanation
Indices: 20305229--20305453 Score: 281
Period size: 40 Copynumber: 5.7 Consensus size: 39
20305219 GCCACTAGCT
*
20305229 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
*
20305269 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* * *
20305308 CAAATGCCTTTGGGACTTAGCCCGGATATAATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* *
20305348 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * ** * *
20305388 CGAATGCCTTCGGGACTTAGCCCGGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
20305428 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
20305454 TATCATCCGA
Statistics
Matches: 165, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 39 0.24
40 126 0.76
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:20309083 original size:28 final size:28
Alignment explanation
Indices: 20309051--20309115 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
20309041 ATTTACTAGA
*
20309051 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
20309079 ATACCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
20309107 ATACCCCTA
1 ATACCCCTA
20309116 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:20309279 original size:27 final size:28
Alignment explanation
Indices: 20309221--20309310 Score: 105
Period size: 28 Copynumber: 3.2 Consensus size: 28
20309211 AGGAAGCGTC
*
20309221 CTGGTGGCTA-TGCCACAAAGTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
**
20309249 CTGGTGGC-CTTGCCAC-GTATATCTGTT
1 CTGGTGGCAC-TGCCACAAAATATCTGTT
20309276 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
20309305 CTGGTG
1 CTGGTG
20309311 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
27 22 0.42
28 23 0.44
29 7 0.13
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:20309321 original size:29 final size:28
Alignment explanation
Indices: 20309231--20309321 Score: 87
Period size: 27 Copynumber: 3.2 Consensus size: 28
20309221 CTGGTGGCTA
* *
20309231 TGCCACAAAGTATCTGTTCTGGTGGC-C
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
20309258 TTGCCAC-GTATATCTGTTCTGGTGGCAC
1 -TGCCACAAAATATCTGTTCTGGTGACAC
*
20309286 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
20309315 TGTCACA
1 TGCCACA
20309322 TTTTCTGTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 22 0.42
28 15 0.29
29 15 0.29
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:20309329 original size:55 final size:56
Alignment explanation
Indices: 20309221--20309335 Score: 130
Period size: 55 Copynumber: 2.1 Consensus size: 56
20309211 AGGAAGCGTC
* * *
20309221 CTGGTGGCTATGCCACAAAGTATCTGTTCTGGTGGCCTTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCTTGCCACATATATCTGTAT
* *
20309276 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGA-CTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCT-TGCCACATATATCTGTAT
20309332 CTGG
1 CTGG
20309336 CAGCCAGGCT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
54 1 0.02
55 32 0.63
56 18 0.35
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCTTGCCACATATATCTGTAT
Found at i:20311556 original size:28 final size:28
Alignment explanation
Indices: 20311505--20311577 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
20311495 TATATGAATA
* *
20311505 TGCAAACCCATATATGTGAAAACCTCTGGG
1 TGCAAACCC--ATATGTGAAAACCACTAGG
20311535 TGCAAACCCATATGT-AACAACCACTAGG
1 TGCAAACCCATATGTGAA-AACCACTAGG
*
20311563 TGCGAA-CCATATGTG
1 TGCAAACCCATATGTG
20311578 CTAACCCTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 10 0.26
28 19 0.50
30 9 0.24
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (28 bp):
TGCAAACCCATATGTGAAAACCACTAGG
Found at i:20312429 original size:27 final size:28
Alignment explanation
Indices: 20312382--20312438 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
20312372 ACAACATTTG
*
20312382 TTAAGAGATTTTTGGTAAAAT-TGTCAA
1 TTAAGAGATTTTTGGTAAAATGTGTAAA
* *
20312409 TTAAG-GATTTATTTGTGAAATGTGTAAA
1 TTAAGAGATTT-TTGGTAAAATGTGTAAA
20312437 TT
1 TT
20312439 TTGTGGTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 5 0.20
27 13 0.52
28 7 0.28
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (28 bp):
TTAAGAGATTTTTGGTAAAATGTGTAAA
Found at i:20316211 original size:55 final size:55
Alignment explanation
Indices: 20316114--20316244 Score: 156
Period size: 55 Copynumber: 2.4 Consensus size: 55
20316104 TTAAAATTTT
* * * * *
20316114 AAGTCATTGTTGTATACGGGCAGGCAACACGGGCGTGTGCCATGGT-CGTGTATTA
1 AAGTCAGTATTGTACACGGGCAGGCAACACGGGCGTGCGCCAT-GTCCATGTATTA
* * *
20316169 AAGTTAGTATTGTACACGGGCAGGCCACACGGGCGTGCGCCATGTCCATGTTTTA
1 AAGTCAGTATTGTACACGGGCAGGCAACACGGGCGTGCGCCATGTCCATGTATTA
* *
20316224 AAGTCAGTGTTGCACACGGGC
1 AAGTCAGTATTGTACACGGGC
20316245 TACGGGCACG
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 2 0.03
55 62 0.97
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.25
Consensus pattern (55 bp):
AAGTCAGTATTGTACACGGGCAGGCAACACGGGCGTGCGCCATGTCCATGTATTA
Found at i:20319765 original size:39 final size:39
Alignment explanation
Indices: 20319721--20319914 Score: 298
Period size: 39 Copynumber: 5.0 Consensus size: 39
20319711 ATATTACCAG
*
20319721 CACAAAGCCTGCGGGTCTTTAGCCCGGATACATTTCCAA
1 CACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAA
*
20319760 CACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAG
1 CACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAA
* *
20319799 CACAAAGCCTGCGGGACTTTAGCCTGGATACACTTCCAA
1 CACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAA
** *
20319838 CAGGAAGCCTGTGGGACTTTAGCCCGGATACATTTCCAA
1 CACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAA
** *
20319877 CATGAAGCCTGCGGTACTTTAGCCCGGATACATTTCCA
1 CACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCA
20319915 GCGTCTTGAA
Statistics
Matches: 142, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 142 1.00
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (39 bp):
CACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAA
Found at i:20325281 original size:19 final size:20
Alignment explanation
Indices: 20325239--20325287 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
20325229 TCATGCTTTC
* *
20325239 TATTCATATTTTCATATTCA
1 TATTCACATTTTCATAATCA
20325259 -ATTCACATTTTCA-AATCA
1 TATTCACATTTTCATAATCA
20325277 TATTCCACATT
1 TATT-CACATT
20325288 CACGTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 4 0.16
19 15 0.60
20 6 0.24
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTCACATTTTCATAATCA
Found at i:20325567 original size:33 final size:33
Alignment explanation
Indices: 20325525--20325602 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 33
20325515 ATTCATTTTC
* *
20325525 TCAATTCAATATCAC-TTTCAATTCATTTACAAA
1 TCAATTCAATATCACTTTTC-ATTAATATACAAA
* *
20325558 TCAATTCAATTTCACTTTTCATTAATATACAAT
1 TCAATTCAATATCACTTTTCATTAATATACAAA
20325591 TCAATATCAATA
1 TCAAT-TCAATA
20325603 CTTATCCATC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.41
Consensus pattern (33 bp):
TCAATTCAATATCACTTTTCATTAATATACAAA
Found at i:20326631 original size:102 final size:102
Alignment explanation
Indices: 20326455--20326656 Score: 370
Period size: 102 Copynumber: 2.0 Consensus size: 102
20326445 CTAGGGTAAA
*
20326455 ATTGTAAATTAGCCAAAATGAATGTGTTAGGCTAAATTGAATTGAATGAAAGTTTGAATGAGTTA
1 ATTGTAAATTAGCCAAAATGAATGTGTTAGGCTAAATTGAATTGAATGAAAGTTTGAATAAGTTA
20326520 ATTTGATATTATATAGATCAAGATAAGCAAATATCAG
66 ATTTGATATTATATAGATCAAGATAAGCAAATATCAG
*
20326557 ATTGTAAATTAGCCAAAATGAATGTGTTTA-GCTAATTTGAATTGAATGAAAGTTTGAATAAGTT
1 ATTGTAAATTAGCCAAAATGAATGTG-TTAGGCTAAATTGAATTGAATGAAAGTTTGAATAAGTT
20326621 AATTTGATATTATATAGATCAAGATAAGCAAATATC
65 AATTTGATATTATATAGATCAAGATAAGCAAATATC
20326657 GAAACTAGAT
Statistics
Matches: 97, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
102 94 0.97
103 3 0.03
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (102 bp):
ATTGTAAATTAGCCAAAATGAATGTGTTAGGCTAAATTGAATTGAATGAAAGTTTGAATAAGTTA
ATTTGATATTATATAGATCAAGATAAGCAAATATCAG
Found at i:20327004 original size:22 final size:22
Alignment explanation
Indices: 20326963--20327046 Score: 100
Period size: 22 Copynumber: 3.7 Consensus size: 22
20326953 TTTAGCTCAT
20326963 TAGAGCTTACCGT-TTCAGCTCGA
1 TAGAGCTTA-C-TATTCAGCTCGA
20326986 TAGAGCTTACTATTCAGCTCGA
1 TAGAGCTTACTATTCAGCTCGA
*
20327008 TAGAGCTTACTGTTTCAGCTC-A
1 TAGAGCTTACT-ATTCAGCTCGA
*
20327030 TTAGAGTTTACTATTCA
1 -TAGAGCTTACTATTCA
20327047 TCAGCTCAGG
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
21 1 0.02
22 27 0.49
23 27 0.49
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (22 bp):
TAGAGCTTACTATTCAGCTCGA
Found at i:20327034 original size:23 final size:23
Alignment explanation
Indices: 20326931--20327068 Score: 120
Period size: 23 Copynumber: 5.9 Consensus size: 23
20326921 GGACTCACCA
* *
20326931 CAGCTCGTAAGAGCTTACTGTTTT
1 CAGCTCATTAGAGCTTACTG-TTT
* *
20326955 TAGCTCATTAGAGCTTACCGTTT
1 CAGCTCATTAGAGCTTACTGTTT
*
20326978 CAGCTCGA-TAGAGCTTACT-ATT
1 CAGCTC-ATTAGAGCTTACTGTTT
20327000 CAGCTCGA-TAGAGCTTACTGTTT
1 CAGCTC-ATTAGAGCTTACTGTTT
* *
20327023 CAGCTCATTAGAGTTTACTATTCAT
1 CAGCTCATTAGAGCTTACTGTT--T
**
20327048 CAGCTCAGGAGGAGCTTACTG
1 CAGCTCATTA-GAGCTTACTG
20327069 ATCATGGCTC
Statistics
Matches: 94, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
22 22 0.23
23 38 0.40
24 17 0.18
25 9 0.10
26 8 0.09
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (23 bp):
CAGCTCATTAGAGCTTACTGTTT
Found at i:20331016 original size:46 final size:46
Alignment explanation
Indices: 20330963--20331135 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
20330953 TATTTGGGCA
20330963 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
20331009 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
* * *
20331054 CATCCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
20331102 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
20331136 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 61 0.57
47 27 0.25
48 2 0.02
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:20331069 original size:93 final size:93
Alignment explanation
Indices: 20330959--20331130 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
20330949 CAGATATTTG
* **
20330959 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAG
20331024 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
20331052 GGCATCCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAG
20331117 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
20331131 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:20337188 original size:23 final size:23
Alignment explanation
Indices: 20337106--20337189 Score: 66
Period size: 23 Copynumber: 3.7 Consensus size: 23
20337096 AACTGTTTTT
* *
20337106 AGCTCATTGGAGCTTACCGTTTC
1 AGCTCATTAGAGCTTATCGTTTC
* *
20337129 AGCTC-GTATGAGCTTATTG-TTC
1 AGCTCATTA-GAGCTTATCGTTTC
** *
20337151 AAATCGA-TAGAGCTTATCGTTTT
1 AGCTC-ATTAGAGCTTATCGTTTC
20337174 AGCTCATTAGAGCTTA
1 AGCTCATTAGAGCTTA
20337190 CTGTTCATCA
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
22 17 0.37
23 29 0.63
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (23 bp):
AGCTCATTAGAGCTTATCGTTTC
Found at i:20356388 original size:26 final size:26
Alignment explanation
Indices: 20356352--20356419 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
20356342 ACTCGAAAAA
20356352 GCTCACACGAGTTGTGAAATGAGCCT
1 GCTCACACGAGTTGTGAAATGAGCCT
*
20356378 GCTCACACGAGTTGTGAAATGGGCCT
1 GCTCACACGAGTTGTGAAATGAGCCT
20356404 GCTCACACGAGTTGTG
1 GCTCACACGAGTTGTG
20356420 GGTCAAAATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (26 bp):
GCTCACACGAGTTGTGAAATGAGCCT
Found at i:20360010 original size:15 final size:15
Alignment explanation
Indices: 20359965--20360072 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
20359955 CCAATATCTC
20359965 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
20359980 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
20359995 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
20360010 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
20360025 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
20360040 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
20360055 GATACCCATATCTTT
1 GATACCCATATCTTT
20360070 GAT
1 GAT
20360073 TTTCCATAAA
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:20360079 original size:30 final size:30
Alignment explanation
Indices: 20359955--20360078 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
20359945 TTTTATTATG
*
20359955 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
20359986 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
20360016 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
20360046 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
20360076 CCA
1 CCA
20360079 TAAATATGGA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 83 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.25, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:20364695 original size:30 final size:30
Alignment explanation
Indices: 20364649--20364772 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
20364639 TTTTATTATG
*
20364649 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
20364680 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
20364710 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
** * *
20364740 TTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
20364770 CCA
1 CCA
20364773 TAAATATGGA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
30 79 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:20364704 original size:15 final size:15
Alignment explanation
Indices: 20364659--20364766 Score: 69
Period size: 15 Copynumber: 7.2 Consensus size: 15
20364649 CCAATATCTC
20364659 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
20364674 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
20364689 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
20364704 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
20364719 GATACCCATATCTTT
1 GATACCCATATCTTT
**** *
20364734 GACTTTTTAT-TATTT
1 GA-TACCCATATCTTT
20364749 GATACCCATATCTTT
1 GATACCCATATCTTT
20364764 GAT
1 GAT
20364767 TTTCCATAAA
Statistics
Matches: 65, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
14 11 0.17
15 43 0.66
16 11 0.17
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:20365462 original size:27 final size:28
Alignment explanation
Indices: 20365418--20365476 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
20365408 TTGTACTTTT
*
20365418 TTTAATTAATAACATTATTTTATTTTAA
1 TTTAATTAATAAAATTATTTTATTTTAA
*
20365446 TTTAATT-ATAAAATTATTTTATTTTAT
1 TTTAATTAATAAAATTATTTTATTTTAA
20365473 TTTA
1 TTTA
20365477 TGAAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTAATTAATAAAATTATTTTATTTTAA
Found at i:20365465 original size:22 final size:22
Alignment explanation
Indices: 20365437--20365510 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
20365427 TAACATTATT
20365437 TTATTTTAATTTAATTATAAAA
1 TTATTTTAATTTAATTATAAAA
* * *
20365459 TTATTTTATTTTATTTTATGAAA
1 TTATTTTAATTTA-ATTATAAAA
*
20365482 TTA-TTTAATTT-ATT-TTAAA
1 TTATTTTAATTTAATTATAAAA
*
20365501 TTATATTAAT
1 TTATTTTAAT
20365511 GTGGAGAGCT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 7 0.16
20 7 0.16
22 19 0.44
23 10 0.23
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (22 bp):
TTATTTTAATTTAATTATAAAA
Found at i:20366088 original size:28 final size:28
Alignment explanation
Indices: 20366030--20366088 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
20366020 ATTATTAATG
** *
20366030 ATAAAATTATATTTTAATCTTTAAAATA
1 ATAAAATTATATTTTAATCGATAAAAAA
*
20366058 ATAAAATTATATTTTTA-CGATAATAAAA
1 ATAAAATTATATTTTAATCGATAA-AAAA
20366086 ATA
1 ATA
20366089 TATAATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (28 bp):
ATAAAATTATATTTTAATCGATAAAAAA
Found at i:20366447 original size:4 final size:4
Alignment explanation
Indices: 20366438--20366464 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20366428 TGCTCCAAGG
20366438 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
20366465 TGTTAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:20372008 original size:19 final size:19
Alignment explanation
Indices: 20371984--20372020 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20371974 CAAATTTAAC
*
20371984 AATTAAGCTTAATTAAATA
1 AATTAAGATTAATTAAATA
*
20372003 AATTAAGATTGATTAAAT
1 AATTAAGATTAATTAAAT
20372021 CTAAAACATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (19 bp):
AATTAAGATTAATTAAATA
Found at i:20372258 original size:13 final size:14
Alignment explanation
Indices: 20372228--20372261 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
20372218 AAAAGTAAGT
*
20372228 CATTTTCTAGAAAT
1 CATTTTCTAGAAAC
20372242 CATTTTCT-GAAAC
1 CATTTTCTAGAAAC
20372255 CATTTTC
1 CATTTTC
20372262 AGTGAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (14 bp):
CATTTTCTAGAAAC
Found at i:20377821 original size:144 final size:144
Alignment explanation
Indices: 20377447--20377825 Score: 508
Period size: 144 Copynumber: 2.6 Consensus size: 144
20377437 GTGAATTACC
* * * * *
20377447 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCTGATGCCATGTCCCAGAC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGGCTGATGCCATGTTCCAAAC
* * *** * *
20377512 ATGGTCTTACACTAGCTCTCGCCTCATTGTCGATGCCATGTCCCAGACATGGTCTTACACTAGCT
66 ATGGTCTTACACTAGCACACATATCAATGTCGATGCCATGTCCCAAACATGGTCTTACACTAGCT
* ** *
20377577 CTCATAATGTGGCT
131 CTCACAACATCGCT
*
20377591 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAAT-GTGGCCGATGCCATGTTCCAAA
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCAT-ATCGTGGCTGATGCCATGTTCCAAA
* ** * *
20377655 CATGCTCTTACACTAGTGCACATATCAATGTCGATGCCATGTCCCAAATATGGTCTTACACTGGC
65 CATGGTCTTACACTAGCACACATATCAATGTCGATGCCATGTCCCAAACATGGTCTTACACTAGC
20377720 TCTCACAACATCGCT
130 TCTCACAACATCGCT
* *
20377735 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCGTGGCTAATGCCATGTTCCAAAC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGGCTGATGCCATGTTCCAAAC
* *
20377800 ATGGTCTTAAACTGGCACACATATCA
66 ATGGTCTTACACTAGCACACATATCA
20377826 CCCAAATGTC
Statistics
Matches: 204, Mismatches: 29, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
143 2 0.01
144 201 0.99
145 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (144 bp):
GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGGCTGATGCCATGTTCCAAAC
ATGGTCTTACACTAGCACACATATCAATGTCGATGCCATGTCCCAAACATGGTCTTACACTAGCT
CTCACAACATCGCT
Found at i:20377824 original size:48 final size:48
Alignment explanation
Indices: 20377447--20377808 Score: 401
Period size: 48 Copynumber: 7.5 Consensus size: 48
20377437 GTGAATTACC
* * * *
20377447 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCT
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCGTGGCT
* * *** * *
20377495 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCCTCATTG-T
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCGTGGCT
* *
20377542 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAT-GTGGCT
1 -GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCAT-ATCGTGGCT
* *
20377591 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAAT-GTGGCC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCAT-ATCGTGGCT
* * * *
20377639 GATGCCATGTTCCAAACATGCTCTTACACTAG-TGCACATATCAATGTC-
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCT-CTCATATC-GTGGCT
* * * * * * *
20377687 GATGCCATGTCCCAAATATGGTCTTACACTGGCTCTCACAACATCGCT
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCGTGGCT
20377735 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCGTGGCT
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCGTGGCT
*
20377783 AATGCCATGTTCCAAACATGGTCTTA
1 GATGCCATGTTCCAAACATGGTCTTA
20377809 AACTGGCACA
Statistics
Matches: 265, Mismatches: 41, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
47 7 0.03
48 252 0.95
49 6 0.02
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (48 bp):
GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCGTGGCT
Found at i:20380668 original size:20 final size:18
Alignment explanation
Indices: 20380638--20380681 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
20380628 TTTGTAACGT
*
20380638 TTGTAAAATAAGTTGTAAA
1 TTGTGAAATAAGTTG-AAA
*
20380657 TGTGTGAAATAATTTGAAA
1 T-TGTGAAATAAGTTGAAA
20380676 TTGTGA
1 TTGTGA
20380682 GTTACTATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 5 0.23
20 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (18 bp):
TTGTGAAATAAGTTGAAA
Found at i:20381371 original size:46 final size:46
Alignment explanation
Indices: 20381315--20381481 Score: 171
Period size: 46 Copynumber: 3.6 Consensus size: 46
20381305 TATGTGTGCT
20381315 AGTGTAAGACATGTCTGGGACATGCATCGACCACATATTGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCACATATTGAGAGCC
* * * * *
20381361 AGAGTAAGACATGTTTGGGACATGCATCGACCTCGAAATAT-ACAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCAC-ATAT-TGA-GAGCC
* * ** *
20381409 AGTGTAAGACATGTCTGGG-CATGTATC-AGCAC-TGAGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGACCACAT-A-TTGAGAGCC
20381454 AGTGTAAGACATGTCTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
20381482 AGTCTCGAGA
Statistics
Matches: 98, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
45 23 0.23
46 42 0.43
47 11 0.11
48 22 0.22
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACCACATATTGAGAGCC
Found at i:20381422 original size:48 final size:47
Alignment explanation
Indices: 20381315--20381525 Score: 184
Period size: 48 Copynumber: 4.5 Consensus size: 47
20381305 TATGTGTGCT
* * *
20381315 AGTGTAAGACATGTCTGGGACATGCATC-GAC-C-ACATATTGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATA-T-AAAGCC
* * *
20381361 AGAGTAAGACATGTTTGGGACATGCATC-GACCTCGAAATATACAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAG-CCTCGAGATATA-AAGCC
* ** * *
20381409 AGTGTAAGACATGTCTGGG-CATGTATCAGCACT-GAGA-CGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGC-CTCGAGATATAAAGCC
* *
20381454 AGTGTAAGACATGTCTGGGACATGCATCAGTCTCGAGATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATA-AAGCC
* *
20381502 AGTGTAAGACCTATCTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
20381526 GCACCGACAC
Statistics
Matches: 135, Mismatches: 20, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
45 24 0.18
46 41 0.30
47 14 0.10
48 52 0.39
49 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATAAAGCC
Found at i:20381475 original size:93 final size:94
Alignment explanation
Indices: 20381315--20381525 Score: 259
Period size: 93 Copynumber: 2.3 Consensus size: 94
20381305 TATGTGTGCT
** *
20381315 AGTGTAAGACATGTCTGGGACATGCATCGACCACATATTGAGAGCCAGAGTAAGACATGTTTGGG
1 AGTGTAAGACATGTCTGGGACATGCATCGACCACATAACGAGAGCCAGAGTAAGACATGTCTGGG
20381380 ACATGCATC-GACCTCGAAATATACAAGCC
66 ACATGCATCAG-CCTCGAAATATACAAGCC
* * * *
20381409 AGTGTAAGACATGTCTGGG-CATGTATC-AGCAC-TGAGACGAGAGCTAGTGTAAGACATGTCTG
1 AGTGTAAGACATGTCTGGGACATGCATCGACCACAT-A-ACGAGAGCCAGAGTAAGACATGTCTG
* * *
20381471 GGACATGCATCAGTCTCGAGATATACAAGCT
64 GGACATGCATCAGCCTCGAAATATACAAGCC
* *
20381502 AGTGTAAGACCTATCTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
20381526 GCACCGACAC
Statistics
Matches: 101, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
91 1 0.01
92 5 0.05
93 71 0.70
94 24 0.24
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACCACATAACGAGAGCCAGAGTAAGACATGTCTGGG
ACATGCATCAGCCTCGAAATATACAAGCC
Found at i:20388083 original size:40 final size:40
Alignment explanation
Indices: 20388052--20388301 Score: 292
Period size: 40 Copynumber: 6.3 Consensus size: 40
20388042 GGACTAAGAT
* *
20388052 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATATCAAA-TCCGGGTTAAGTC
* *
20388092 CCGAAGGCCTTTGTGCGAGATA-CTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATC-AAATCCGGGTTAAGTC
* *
20388132 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATCAAATCCGGGTTAAGTC
* *
20388172 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATCAAATCCGGGTTAAGTC
* * * *
20388212 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATATCAAATCCGGGTTAAGTC
* * * * *
20388252 CCGAAGGCATT-GTGTGAGTTA-CTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATATC-AAATCCGGGTTAAGTC
20388291 CCGAAGGCATT
1 CCGAAGGCATT
20388302 TGAACGAGGA
Statistics
Matches: 194, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
39 33 0.17
40 158 0.81
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATATCAAATCCGGGTTAAGTC
Found at i:20388136 original size:80 final size:79
Alignment explanation
Indices: 20387999--20388301 Score: 342
Period size: 80 Copynumber: 3.8 Consensus size: 79
20387989 TTGAATGCTG
* * * * * **
20387999 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
* * *
20388062 TTGTGCGAGATACAAA
64 TCGTGCGAGTTATAAA
* *
20388078 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
20388143 CGTGCGAGTTATTAAA
65 CGTGCGAGTTA-TAAA
* * *
20388159 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
*
20388224 GTGCGAGTTGTTAAA
66 GTGCGAGTT-ATAAA
* * * * * *
20388239 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
20388302 TGAACGAGGA
Statistics
Matches: 192, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
79 36 0.19
80 145 0.76
81 11 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
GTGCGAGTTATAAA
Found at i:20388215 original size:120 final size:119
Alignment explanation
Indices: 20387999--20388301 Score: 358
Period size: 120 Copynumber: 2.5 Consensus size: 119
20387989 TTGAATGCTG
* * * * * *
20387999 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGCTAAG-TCCCGAAGGCATT
* * *
20388063 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
64 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTAAA
* *
20388119 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTC
* * * * **
20388184 GTGCGAGTTATTAAA-TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
65 GTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTAAA
* * * * *
20388239 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATT
20388302 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
119 35 0.22
120 115 0.73
121 7 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTAAA
Found at i:20394526 original size:40 final size:40
Alignment explanation
Indices: 20394482--20394705 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 40
20394472 AAGTGAATAT
* * * * **
20394482 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTGTTAA
20394522 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
20394562 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
20394602 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * **
20394642 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * *
20394681 AACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATT
20394706 TGAACGAGGA
Statistics
Matches: 171, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.20
40 136 0.80
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
Found at i:20394580 original size:80 final size:80
Alignment explanation
Indices: 20394443--20394705 Score: 318
Period size: 80 Copynumber: 3.3 Consensus size: 80
20394433 TTGAATGCTG
* * * * *
20394443 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGAATATATCCGGATTAAGAT-CCGAAGGCC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCC
*
20394505 TTTGTGCGAGATACTAAA
63 TTTGTGCGAGTTACTAAA
* * *
20394523 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
**
20394588 GTGCGAGTTGTTAAA
66 GTGCGAGTTACTAAA
* * *
20394603 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGG-CATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
*
20394667 GTGTGAGTTACTAAA
66 GTGCGAGTTACTAAA
* *
20394682 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
20394706 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
79 35 0.22
80 116 0.73
81 8 0.05
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
GTGCGAGTTACTAAA
Found at i:20394657 original size:120 final size:120
Alignment explanation
Indices: 20394443--20394705 Score: 318
Period size: 120 Copynumber: 2.2 Consensus size: 120
20394433 TTGAATGCTG
* * *
20394443 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
* **
20394507 TGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
66 CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* * * *
20394563 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAG-TGAATAAATCCGGATTAAGAT-CCGAAGGCA
* ** * *
20394625 TTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
64 TTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
20394682 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
20394706 TGAACGAGGA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 34 0.28
120 80 0.66
121 8 0.07
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:20409276 original size:48 final size:48
Alignment explanation
Indices: 20409203--20409582 Score: 383
Period size: 48 Copynumber: 7.9 Consensus size: 48
20409193 TTTAAAATAA
* *
20409203 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAGG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGAGG
* * * * * * *
20409251 CTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTC-ATTG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGA-GG
* * * * *
20409299 CCGATGCCATGTCCCAGAGATGGTCTTACACTAGCTCTCATAAT-GTGG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCAT-ATCGAGG
* *
20409347 CCGATGCCATGTTTCAAACATGGTCTTACACTGGCTCTCATAAT-GTGG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCAT-ATCGAGG
* * * * * * *
20409395 CTGATGCCATGTTCCAAACATTGTCTTACACTAGCGCACATATCAATG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGAGG
* * * * *
20409443 CCGATGCCATG-TCCTAGACATGGGCTTACACTGGCTCTCACAAC-ATCG
1 CCGATGCCATGTTCC-AAACATGGTCTTACACTGGCTCTCATATCGA-GG
* *
20409491 CCGATGTCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGAGG
* * *
20409539 TCGATGCCATGTTCCAAACATGGTCTTACACTGGCACACATATC
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATC
20409583 ACCCAAATGT
Statistics
Matches: 275, Mismatches: 49, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
47 7 0.03
48 264 0.96
49 4 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (48 bp):
CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGAGG
Found at i:20409471 original size:144 final size:144
Alignment explanation
Indices: 20409203--20409583 Score: 523
Period size: 144 Copynumber: 2.6 Consensus size: 144
20409193 TTTAAAATAA
* * * * *
20409203 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCTGATGCCATGTCCCAG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGGCTGATGCCATGTTCCAA
* * * * * * *
20409268 ACATGGTCTTACACTAGCTCTCGTCTCATTGCCGATGCCATGTCCCAGAGATGGTCTTACACTAG
66 ACATGGTCTTACACTAGCACACATATCAATGCCGATGCCATGTCCCAGACATGGGCTTACACTAG
* ** *
20409333 CTCTCATAATGTGG
131 CTCTCACAACATCG
*
20409347 CCGATGCCATGTTTCAAACATGGTCTTACACTGGCTCTCATAAT-GTGGCTGATGCCATGTTCCA
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCAT-ATCGTGGCTGATGCCATGTTCCA
* * * *
20409411 AACATTGTCTTACACTAGCGCACATATCAATGCCGATGCCATGTCCTAGACATGGGCTTACACTG
65 AACATGGTCTTACACTAGCACACATATCAATGCCGATGCCATGTCCCAGACATGGGCTTACACTA
20409476 GCTCTCACAACATCG
130 GCTCTCACAACATCG
*
20409491 CCGATGTCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGG-TCGATGCCATGTTCCA
1 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGGCT-GATGCCATGTTCCA
*
20409555 AACATGGTCTTACACTGGCACACATATCA
65 AACATGGTCTTACACTAGCACACATATCA
20409584 CCCAAATGTC
Statistics
Matches: 209, Mismatches: 25, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
143 3 0.01
144 205 0.98
145 1 0.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28
Consensus pattern (144 bp):
CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGGCTGATGCCATGTTCCAA
ACATGGTCTTACACTAGCACACATATCAATGCCGATGCCATGTCCCAGACATGGGCTTACACTAG
CTCTCACAACATCG
Found at i:20412346 original size:18 final size:17
Alignment explanation
Indices: 20412306--20412347 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
20412296 ATCATTTCAT
20412306 TTCTTTATCTTTCTTTC
1 TTCTTTATCTTTCTTTC
*
20412323 TCTCTTTATCTTTGTATTC
1 T-TCTTTATCTTTCT-TTC
20412342 TTCTTT
1 TTCTTT
20412348 TAGTTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 17 0.77
19 4 0.18
ACGTcount: A:0.07, C:0.21, G:0.02, T:0.69
Consensus pattern (17 bp):
TTCTTTATCTTTCTTTC
Found at i:20426817 original size:289 final size:289
Alignment explanation
Indices: 20426298--20426875 Score: 1156
Period size: 289 Copynumber: 2.0 Consensus size: 289
20426288 AAGACGTTAA
20426298 GTTTGAATGGATAGAGAAGTGCCAGCAGAGTTTCGAAAAGTTGAAGACATTGCTGACTGAAGCTC
1 GTTTGAATGGATAGAGAAGTGCCAGCAGAGTTTCGAAAAGTTGAAGACATTGCTGACTGAAGCTC
20426363 CAGTTTTAGTATTGCCTGAGCTGGGAAAAGAGTTTGTGGTCTATAGTGATGCATCCTTAAATGGA
66 CAGTTTTAGTATTGCCTGAGCTGGGAAAAGAGTTTGTGGTCTATAGTGATGCATCCTTAAATGGA
20426428 TTGGGTTGTGTACTTATGGAAGATGACAAGGTGATAGCCTATGCTTCGCGGCAGTTGAAACCAAA
131 TTGGGTTGTGTACTTATGGAAGATGACAAGGTGATAGCCTATGCTTCGCGGCAGTTGAAACCAAA
20426493 CGAGAAGAATTATCCGACGCATGACTTAGAGCTTGCCGCCATTGTTTTTGCTTTGAAAATCCAGA
196 CGAGAAGAATTATCCGACGCATGACTTAGAGCTTGCCGCCATTGTTTTTGCTTTGAAAATCCAGA
20426558 GGCATTACTTATATAGTGAGACTTGTCGG
261 GGCATTACTTATATAGTGAGACTTGTCGG
20426587 GTTTGAATGGATAGAGAAGTGCCAGCAGAGTTTCGAAAAGTTGAAGACATTGCTGACTGAAGCTC
1 GTTTGAATGGATAGAGAAGTGCCAGCAGAGTTTCGAAAAGTTGAAGACATTGCTGACTGAAGCTC
20426652 CAGTTTTAGTATTGCCTGAGCTGGGAAAAGAGTTTGTGGTCTATAGTGATGCATCCTTAAATGGA
66 CAGTTTTAGTATTGCCTGAGCTGGGAAAAGAGTTTGTGGTCTATAGTGATGCATCCTTAAATGGA
20426717 TTGGGTTGTGTACTTATGGAAGATGACAAGGTGATAGCCTATGCTTCGCGGCAGTTGAAACCAAA
131 TTGGGTTGTGTACTTATGGAAGATGACAAGGTGATAGCCTATGCTTCGCGGCAGTTGAAACCAAA
20426782 CGAGAAGAATTATCCGACGCATGACTTAGAGCTTGCCGCCATTGTTTTTGCTTTGAAAATCCAGA
196 CGAGAAGAATTATCCGACGCATGACTTAGAGCTTGCCGCCATTGTTTTTGCTTTGAAAATCCAGA
20426847 GGCATTACTTATATAGTGAGACTTGTCGG
261 GGCATTACTTATATAGTGAGACTTGTCGG
20426876 ATATTCACAG
Statistics
Matches: 289, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
289 289 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (289 bp):
GTTTGAATGGATAGAGAAGTGCCAGCAGAGTTTCGAAAAGTTGAAGACATTGCTGACTGAAGCTC
CAGTTTTAGTATTGCCTGAGCTGGGAAAAGAGTTTGTGGTCTATAGTGATGCATCCTTAAATGGA
TTGGGTTGTGTACTTATGGAAGATGACAAGGTGATAGCCTATGCTTCGCGGCAGTTGAAACCAAA
CGAGAAGAATTATCCGACGCATGACTTAGAGCTTGCCGCCATTGTTTTTGCTTTGAAAATCCAGA
GGCATTACTTATATAGTGAGACTTGTCGG
Found at i:20432256 original size:27 final size:26
Alignment explanation
Indices: 20432221--20432271 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
20432211 AGCATGCATA
* *
20432221 AAACATATCTTTAAAATCATAGTTTAT
1 AAACATATCTTGAAAA-CAGAGTTTAT
20432248 AAACATATCTTGAAAACAGAGTTT
1 AAACATATCTTGAAAACAGAGTTT
20432272 CAGAACTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (26 bp):
AAACATATCTTGAAAACAGAGTTTAT
Found at i:20433734 original size:19 final size:17
Alignment explanation
Indices: 20433693--20433736 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 17
20433683 ATCCTTGTCA
20433693 AAAAATAATTAAATATT
1 AAAAATAATTAAATATT
20433710 ATAAAATAATTAAATTATGT
1 A-AAAATAATTAAA-TAT-T
20433730 AAAAATA
1 AAAAATA
20433737 TGAACATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.04
18 12 0.50
19 9 0.38
20 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAAATAATTAAATATT
Found at i:20434370 original size:323 final size:323
Alignment explanation
Indices: 20433782--20434427 Score: 1267
Period size: 323 Copynumber: 2.0 Consensus size: 323
20433772 TTTTGATTAA
*
20433782 ATTTGGTTATTTTTGACAGAATTACACAATTGGAGAAAAATGGCTCGGTGAACACTGTGAGAAGA
1 ATTTGGTTATTTTTGACAGAATTACACAATTGGAGAAAAAGGGCTCGGTGAACACTGTGAGAAGA
20433847 ACAAAACCGAGAGTAATTTGAAGTATCGAGGCCAATTAGTTTCCAGCCCAAGACGGTCCAGAAAT
66 ACAAAACCGAGAGTAATTTGAAGTATCGAGGCCAATTAGTTTCCAGCCCAAGACGGTCCAGAAAT
20433912 GTGTATTAATTCATAATTAAATTAATTTTAAATTATTTCCTATTCAATTTAGGTTAAATGAATTA
131 GTGTATTAATTCATAATTAAATTAATTTTAAATTATTTCCTATTCAATTTAGGTTAAATGAATTA
20433977 ATTTTAATTAATTATGAAGAAATGGCCTAGTAAACCGCACTGGTTGAACCGAATGGAGTGAGCCG
196 ATTTTAATTAATTATGAAGAAATGGCCTAGTAAACCGCACTGGTTGAACCGAATGGAGTGAGCCG
20434042 GACCAGCCACTAATTGTGCTGACCAGAACTGTCCATTGGCTGACCCAAAAAATAAAATTAGCT
261 GACCAGCCACTAATTGTGCTGACCAGAACTGTCCATTGGCTGACCCAAAAAATAAAATTAGCT
20434105 ATTTGGTTATTTTTGACAGAATTACACAATTGGAGAAAAAGGGC-CTGGTGAACACTGTGAGAAG
1 ATTTGGTTATTTTTGACAGAATTACACAATTGGAGAAAAAGGGCTC-GGTGAACACTGTGAGAAG
20434169 AACAAAACCGAGAGTAATTTGAAGTATCGAGGCCAATTAGTTTCCAGCCCAAGACGGTCCAGAAA
65 AACAAAACCGAGAGTAATTTGAAGTATCGAGGCCAATTAGTTTCCAGCCCAAGACGGTCCAGAAA
20434234 TGTGTATTAATTCATAATTAAATTAATTTTAAATTATTTCCTATTCAATTTAGGTTAAATGAATT
130 TGTGTATTAATTCATAATTAAATTAATTTTAAATTATTTCCTATTCAATTTAGGTTAAATGAATT
20434299 AATTTTAATTAATTATGAAGAAATGGCCTAGTAAACCGCACTGGTTGAACCGAATGGAGTGAGCC
195 AATTTTAATTAATTATGAAGAAATGGCCTAGTAAACCGCACTGGTTGAACCGAATGGAGTGAGCC
20434364 GGACCAGCCACTAATTGTGCTGACCAGAACTGTCCATTGGCTGACCCAAAAAATAAAATTAGCT
260 GGACCAGCCACTAATTGTGCTGACCAGAACTGTCCATTGGCTGACCCAAAAAATAAAATTAGCT
20434428 GATAAAATAT
Statistics
Matches: 321, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
322 1 0.00
323 320 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (323 bp):
ATTTGGTTATTTTTGACAGAATTACACAATTGGAGAAAAAGGGCTCGGTGAACACTGTGAGAAGA
ACAAAACCGAGAGTAATTTGAAGTATCGAGGCCAATTAGTTTCCAGCCCAAGACGGTCCAGAAAT
GTGTATTAATTCATAATTAAATTAATTTTAAATTATTTCCTATTCAATTTAGGTTAAATGAATTA
ATTTTAATTAATTATGAAGAAATGGCCTAGTAAACCGCACTGGTTGAACCGAATGGAGTGAGCCG
GACCAGCCACTAATTGTGCTGACCAGAACTGTCCATTGGCTGACCCAAAAAATAAAATTAGCT
Done.