Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold15
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: 4011073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11440 characters in sequence are not A, C, G, or T
File 10 of 25
Found at i:1530889 original size:13 final size:13
Alignment explanation
Indices: 1530871--1530896 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1530861 CACACAAATA
1530871 TGTATCGATACAC
1 TGTATCGATACAC
1530884 TGTATCGATACAC
1 TGTATCGATACAC
1530897 ACAAATACGT
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:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1530983 original size:22 final size:22
Alignment explanation
Indices: 1530928--1530983 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
1530918 ACAGTGACCT
* *
1530928 ATGAACAATGATGTATTGATAC
1 ATGAACAGTGATGTATCGATAC
1530950 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
1530971 ATGAACAGTGATG
1 ATGAACAGTGATG
1530984 AATAGTGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:1531089 original size:53 final size:53
Alignment explanation
Indices: 1531025--1531161 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
1531015 CTACTTCCAA
1531025 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
1531078 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1531131 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
1531162 TATGCAATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:1531194 original size:20 final size:20
Alignment explanation
Indices: 1531131--1531201 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1531121 GCCAATGTCC
**
1531131 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
1531151 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
1531171 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1531191 TGTATCGATAC
1 TGTATCGATAC
1531202 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1532141 original size:46 final size:46
Alignment explanation
Indices: 1532088--1532190 Score: 206
Period size: 46 Copynumber: 2.2 Consensus size: 46
1532078 TTTATACAAA
1532088 CTCTCCCCCTTAATACGTTGTCACCCTTAAACCAATAAACAATAAT
1 CTCTCCCCCTTAATACGTTGTCACCCTTAAACCAATAAACAATAAT
1532134 CTCTCCCCCTTAATACGTTGTCACCCTTAAACCAATAAACAATAAT
1 CTCTCCCCCTTAATACGTTGTCACCCTTAAACCAATAAACAATAAT
1532180 CTCTCCCCCTT
1 CTCTCCCCCTT
1532191 TTTGGTTCAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (46 bp):
CTCTCCCCCTTAATACGTTGTCACCCTTAAACCAATAAACAATAAT
Found at i:1538629 original size:13 final size:13
Alignment explanation
Indices: 1538611--1538635 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1538601 AATTTTTTTA
1538611 TGTATCGATACAT
1 TGTATCGATACAT
1538624 TGTATCGATACA
1 TGTATCGATACA
1538636 ATTTTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1538633 original size:34 final size:34
Alignment explanation
Indices: 1538590--1538669 Score: 142
Period size: 34 Copynumber: 2.4 Consensus size: 34
1538580 TACAAGCTAA
1538590 TGTATCGATACAATTTTTTTATGTATCGATACAT
1 TGTATCGATACAATTTTTTTATGTATCGATACAT
*
1538624 TGTATCGATACAATTTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTTTTTTATGTATCGATACAT
*
1538658 TTTATCGATACA
1 TGTATCGATACA
1538670 TACTTTGTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (34 bp):
TGTATCGATACAATTTTTTTATGTATCGATACAT
Found at i:1538682 original size:32 final size:34
Alignment explanation
Indices: 1538590--1538688 Score: 130
Period size: 34 Copynumber: 3.0 Consensus size: 34
1538580 TACAAGCTAA
** *
1538590 TGTATCGATACAATTTTTTTATGTATCGATACAT
1 TGTATCGATACAATTACTTTGTGTATCGATACAT
**
1538624 TGTATCGATACAATTTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTACTTTGTGTATCGATACAT
*
1538658 TTTATCGATAC-A-TACTTTGTGTATCGATACA
1 TGTATCGATACAATTACTTTGTGTATCGATACA
1538689 AGTTTGGCTA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.28
33 1 0.02
34 43 0.70
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.45
Consensus pattern (34 bp):
TGTATCGATACAATTACTTTGTGTATCGATACAT
Found at i:1540014 original size:28 final size:28
Alignment explanation
Indices: 1539975--1540434 Score: 465
Period size: 28 Copynumber: 16.5 Consensus size: 28
1539965 ACATTCATCT
*
1539975 CTTT-AAAGCCCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
1540002 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1540030 CTTTCAAAGCTCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* *
1540059 TTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1540087 CTTTCAAAGCCCACGAGTCGGTGGCAACTC
1 CTTTCAAAGCCCACAAGTCAGTGGC-AC-C
* ***
1540117 TTTTCAAAGCTGGCAA--C--T-----C
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
1540136 TTTTTAAAGCCCATAAGTCAATGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
1540164 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* * * *
1540193 TTTTCAAAGCCTATAAGTCAATGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1540221 CTTTCAAAGCCCATAAGTTAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * **
1540249 CTTTCAAAGCCCACAATTCAATGGCATT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1540277 CTTTCAAAGCCCACGAGTCGGTGGCAACTC
1 CTTTCAAAGCCCACAAGTCAGTGGC-AC-C
* *
1540307 TTTTCAAAGCCCACAAGTCAGTGGTACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1540335 CTTTCAAAGCCCACAAGTCAGTGGCGCC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1540363 CTTTCAAAGACCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1540391 TTTTCAAAGCCCACAAGTC-GATGGCACTC
1 CTTTCAAAGCCCACAAGTCAG-TGGCAC-C
*
1540420 TTTTCAAAGCCCACA
1 CTTTCAAAGCCCACA
1540435 TGAGTCGGTG
Statistics
Matches: 359, Mismatches: 56, Indels: 34
0.80 0.12 0.08
Matches are distributed among these distances:
19 12 0.03
21 1 0.00
23 1 0.00
26 1 0.00
27 5 0.01
28 237 0.66
29 69 0.19
30 33 0.09
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:1540079 original size:57 final size:56
Alignment explanation
Indices: 1539975--1540434 Score: 467
Period size: 57 Copynumber: 8.3 Consensus size: 56
1539965 ACATTCATCT
*
1539975 CTTT-AAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1540030 CTTTCAAAGCTCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
1540087 CTTTCAAAGCCCACGAGTCGGTGGCAACTCTTT------TCA-AAG-C--TGGCAACTC
1 CTTTCAAAGCCCACAAGTCAGTGGC-ACCCTTTCAAAGCCCACAAGTCAGTGGC-AC-C
* * * *
1540136 TTTTTAAAGCCCATAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-C
* * * * * * *
1540193 TTTTCAAAGCCTATAAGTCAATGGCACCCTTTCAAAGCCCATAAGTTAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
* * ** * *
1540249 CTTTCAAAGCCCACAATTCAATGGCATTCTTTCAAAGCCCACGAGTCGGTGGCAACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC-AC-C
* * *
1540307 TTTTCAAAGCCCACAAGTCAGTGGTACCCTTTCAAAGCCCACAAGTCAGTGGCGCC
1 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1540363 CTTTCAAAGACCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTC-GATGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAG-TGGCAC-C
*
1540420 TTTTCAAAGCCCACA
1 CTTTCAAAGCCCACA
1540435 TGAGTCGGTG
Statistics
Matches: 334, Mismatches: 52, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
47 4 0.01
48 7 0.02
49 21 0.06
50 3 0.01
51 2 0.01
54 2 0.01
55 8 0.02
56 113 0.34
57 122 0.37
58 52 0.16
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (56 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:1540083 original size:85 final size:84
Alignment explanation
Indices: 1539979--1540434 Score: 504
Period size: 85 Copynumber: 5.5 Consensus size: 84
1539969 TCATCTCTTT
*
1539979 AAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCTCAC
1 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC-CAC
1540044 AAGTCAGTGGCACTCTTTTC
65 AAGTCAGTGGCACTCTTTTC
* * * * *
1540064 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCGGTGGCAACTCTTT-----TCA-
1 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC-ACCCTTTCAAAGCCAC
*
1540123 AAG-C--TGGCAACTCTTTTT
65 AAGTCAGTGGC-ACTCTTTTC
* * *
1540141 AAAGCCCATAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCTA
1 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCC-A
* * *
1540206 TAAGTCAATGGCAC-CCTTTC
64 CAAGTCAGTGGCACTCTTTTC
* * * * * **
1540226 AAAGCCCATAAGTTAGTGGCATCCTTTCAAAGCCCACAATTCAATGGCATTCTTTCAAAGCCCAC
1 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CCAC
* *
1540291 GAGTCGGTGGCAACTCTTTTC
65 AAGTCAGTGGC-ACTCTTTTC
* *
1540312 AAAGCCCACAAGTCAGTGGTACCCTTTCAAAGCCCACAAGTCAGTGGCGCCCTTTCAAAGACCAC
1 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CCAC
*
1540377 AAGTTAGTGGCAC-CTTTTC
65 AAGTCAGTGGCACTCTTTTC
*
1540396 AAAGCCCACAAGTC-GATGGCACTCTTTTCAAAGCCCACA
1 AAAGCCCACAAGTCAG-TGGCAC-CCTTTCAAAGCCCACA
1540435 TGAGTCGGTG
Statistics
Matches: 308, Mismatches: 45, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
76 6 0.02
77 54 0.18
78 1 0.00
79 3 0.01
80 2 0.01
82 1 0.00
83 2 0.01
84 45 0.15
85 114 0.37
86 76 0.25
87 4 0.01
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (84 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCACA
AGTCAGTGGCACTCTTTTC
Found at i:1540132 original size:19 final size:19
Alignment explanation
Indices: 1540108--1540145 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1540098 CACGAGTCGG
1540108 TGGCAACTCTTTTCAAAGC
1 TGGCAACTCTTTTCAAAGC
*
1540127 TGGCAACTCTTTTTAAAGC
1 TGGCAACTCTTTTCAAAGC
1540146 CCATAAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (19 bp):
TGGCAACTCTTTTCAAAGC
Found at i:1540347 original size:114 final size:111
Alignment explanation
Indices: 1540141--1540484 Score: 393
Period size: 114 Copynumber: 3.0 Consensus size: 111
1540131 AACTCTTTTT
* * * *
1540141 AAAGCCCATAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCTA
1 AAAGCCCACAATTCAATGGCA-CCTTTCAAAGCCCACAAGTCGGTGGCACTCTTTTCAAAGCCCA
* * *
1540206 TAAGTCAATGGCACCCTTTCAAAGCCCATAAGTTAGTGGCATCCTTTC
65 CAAGTCAGTGGAACCCTTTCAAAGCCCATAAGTTAGTGGCA-CCTTTC
* *
1540254 AAAGCCCACAATTCAATGGCATTCTTTCAAAGCCCACGAGTCGGTGGCAACTCTTTTCAAAGCCC
1 AAAGCCCACAATTCAATGGCA-CCTTTCAAAGCCCACAAGTCGGTGGC-ACTCTTTTCAAAGCCC
* * * *
1540319 ACAAGTCAGTGGTACCCTTTCAAAGCCCACAAGTCAGTGGCGCCCTTTC
64 ACAAGTCAGTGGAACCCTTTCAAAGCCCATAAGTTAGTGGC-ACCTTTC
* * *
1540368 AAAGACCACAAGTT-AGTGGCACCTTTTCAAAGCCCACAAGTCGATGGCACTCTTTTCAAAGCCC
1 AAAGCCCACAA-TTCAATGGCACC-TTTCAAAGCCCACAAGTCGGTGGCACTCTTTTCAAAGCCC
* * *
1540432 ACATGAGTCGGTGGCAACTCTTTTCAATGTCCACATAAGTTAGTGGCACCTTT
64 ACA--AGTCAGTGG-AAC-CCTTTCAAAG-CC-CATAAGTTAGTGGCACCTTT
1540485 TTTAAAAAGA
Statistics
Matches: 196, Mismatches: 25, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
113 62 0.32
114 95 0.48
115 10 0.05
116 2 0.01
117 8 0.04
118 7 0.04
119 12 0.06
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (111 bp):
AAAGCCCACAATTCAATGGCACCTTTCAAAGCCCACAAGTCGGTGGCACTCTTTTCAAAGCCCAC
AAGTCAGTGGAACCCTTTCAAAGCCCATAAGTTAGTGGCACCTTTC
Found at i:1540478 original size:32 final size:32
Alignment explanation
Indices: 1540127--1540479 Score: 222
Period size: 28 Copynumber: 12.2 Consensus size: 32
1540117 TTTTCAAAGC
* *
1540127 TGGCAACTCTTTTTAAAG-CC-CATAAGTCAA
1 TGGCAACTCTTTTCAAAGCCCACATAAGTCAG
*
1540157 TGGC-AC-CCTTTCAAAGCCCAC--AAGTCAG
1 TGGCAACTCTTTTCAAAGCCCACATAAGTCAG
* *
1540185 TGGC-ACTCTTTTCAAAG-CC-TATAAGTCAA
1 TGGCAACTCTTTTCAAAGCCCACATAAGTCAG
* *
1540214 TGGC-AC-CCTTTCAAAG-CC-CATAAGTTAG
1 TGGCAACTCTTTTCAAAGCCCACATAAGTCAG
* * *
1540242 TGGC-A-TCCTTTCAAAGCCCAC--AATTCAA
1 TGGCAACTCTTTTCAAAGCCCACATAAGTCAG
* * *
1540270 TGGC-ATTC-TTTCAAAGCCCAC--GAGTCGG
1 TGGCAACTCTTTTCAAAGCCCACATAAGTCAG
1540298 TGGCAACTCTTTTCAAAGCCCAC--AAGTCAG
1 TGGCAACTCTTTTCAAAGCCCACATAAGTCAG
* *
1540328 TGG-TAC-CCTTTCAAAGCCCAC--AAGTCAG
1 TGGCAACTCTTTTCAAAGCCCACATAAGTCAG
* * * *
1540356 TGGC-GC-CCTTTCAAAGACCAC--AAGTTAG
1 TGGCAACTCTTTTCAAAGCCCACATAAGTCAG
1540384 TGGC-AC-CTTTTCAAAGCCCAC--AAGTC-G
1 TGGCAACTCTTTTCAAAGCCCACATAAGTCAG
* *
1540411 ATGGC-ACTCTTTTCAAAGCCCACATGAGTCGG
1 -TGGCAACTCTTTTCAAAGCCCACATAAGTCAG
* * *
1540443 TGGCAACTCTTTTCAATGTCCACATAAGTTAG
1 TGGCAACTCTTTTCAAAGCCCACATAAGTCAG
1540475 TGGCA
1 TGGCA
1540480 CCTTTTTTAA
Statistics
Matches: 270, Mismatches: 35, Indels: 34
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.00
28 157 0.58
29 49 0.18
30 27 0.10
31 8 0.03
32 28 0.10
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (32 bp):
TGGCAACTCTTTTCAAAGCCCACATAAGTCAG
Found at i:1541398 original size:20 final size:20
Alignment explanation
Indices: 1541373--1541449 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
1541363 AAAGCACCAG
*
1541373 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
* * *
1541393 ATGTATCGATACATGCATGA
1 ATGTATCGATACATTCTTCA
*
1541413 ATGTATCGATGCATTCTTCA
1 ATGTATCGATACATTCTTCA
*
1541433 ATGTATCGAAACATTCT
1 ATGTATCGATACATTCT
1541450 GTCTTTTTAC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1545140 original size:30 final size:30
Alignment explanation
Indices: 1545106--1545198 Score: 132
Period size: 30 Copynumber: 3.1 Consensus size: 30
1545096 ATTTAAAGTA
*
1545106 GATAGTAGTGCACTAGTCCTTAATCTAAGG
1 GATAGTGGTGCACTAGTCCTTAATCTAAGG
* * *
1545136 GATAGTGGTGCACTAGTCTTTAATCCAAGA
1 GATAGTGGTGCACTAGTCCTTAATCTAAGG
* *
1545166 GAGAGTGGTGCATTAGTCCTTAATCTAAGG
1 GATAGTGGTGCACTAGTCCTTAATCTAAGG
1545196 GAT
1 GAT
1545199 TTAAATTGAT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (30 bp):
GATAGTGGTGCACTAGTCCTTAATCTAAGG
Found at i:1550325 original size:26 final size:26
Alignment explanation
Indices: 1550251--1550326 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 26
1550241 TGATGAATTT
*
1550251 AAGAATGGGGTTGGAGTATCCCCTCAG
1 AAGAAT-GGGTTGGAGTATCCTCTCAG
*
1550278 AAGAATGGAGTTGGAGTATCCTCTCGG
1 AAGAATGG-GTTGGAGTATCCTCTCAG
*
1550305 AAGAATGGGTTAGAGTATCCTC
1 AAGAATGGGTTGGAGTATCCTC
1550327 GTGAATAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 15 0.33
27 30 0.67
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.25
Consensus pattern (26 bp):
AAGAATGGGTTGGAGTATCCTCTCAG
Found at i:1552784 original size:52 final size:51
Alignment explanation
Indices: 1552642--1552805 Score: 206
Period size: 51 Copynumber: 3.2 Consensus size: 51
1552632 ATTGGATACA
*
1552642 TCGATACATTTAGG-TCAAAACTCAAAATGTATCGATACAATAAAGAATGTG
1 TCGATACATTT-GGATCAAAACCCAAAATGTATCGATACAATAAAGAATGTG
* * * * * *
1552693 TCAATGCATTTGGATGAAAACCCAGAATGTATTGATACAATGAAGAATGTG
1 TCGATACATTTGGATCAAAACCCAAAATGTATCGATACAATAAAGAATGTG
* *
1552744 TCGATACATTTGGATCAAAAACCCAAAATGTATCGATACAATAAA-AACGTA
1 TCGATACATTTGGATC-AAAACCCAAAATGTATCGATACAATAAAGAATGTG
*
1552795 TCAATACATTT
1 TCGATACATTT
1552806 TCTTTCCAGA
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
50 2 0.02
51 68 0.72
52 25 0.26
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (51 bp):
TCGATACATTTGGATCAAAACCCAAAATGTATCGATACAATAAAGAATGTG
Found at i:1552870 original size:20 final size:20
Alignment explanation
Indices: 1552845--1552889 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1552835 AAGGTCCAGT
* *
1552845 ATACATTGACTTATGCATCG
1 ATACATTCACTTAAGCATCG
*
1552865 ATACATTCACTTAAGTATCG
1 ATACATTCACTTAAGCATCG
1552885 ATACA
1 ATACA
1552890 AATTGTAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (20 bp):
ATACATTCACTTAAGCATCG
Found at i:1558106 original size:13 final size:13
Alignment explanation
Indices: 1558088--1558144 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1558078 CATAAAGTGT
1558088 TGTATCGATACAA
1 TGTATCGATACAA
1558101 TGTATCGATACATAA
1 TGTATCGATAC--AA
1558116 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
1558133 TGTATCGATACA
1 TGTATCGATACA
1558145 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1558125 original size:19 final size:19
Alignment explanation
Indices: 1558066--1558163 Score: 94
Period size: 19 Copynumber: 5.7 Consensus size: 19
1558056 ATTTCAACGA
1558066 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACAT-AAGT
*
1558086 GTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1558101 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1558118 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1558133 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1558150 TTTGTATCGATACA
1 TTTGTATCGATACA
1558164 ATATAAGCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 25
0.71 0.01 0.27
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 23 0.35
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1558128 original size:32 final size:32
Alignment explanation
Indices: 1558068--1558165 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
1558058 TTCAACGATT
*
1558068 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1558101 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
1558133 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
1558165 T
1 T
1558166 ATAAGCTACT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:1558224 original size:13 final size:13
Alignment explanation
Indices: 1558206--1558230 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1558196 ACTACCCAAA
1558206 TGTATCGATACAT
1 TGTATCGATACAT
1558219 TGTATCGATACA
1 TGTATCGATACA
1558231 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1558282 original size:52 final size:51
Alignment explanation
Indices: 1558219--1558367 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
1558209 ATCGATACAT
*** *
1558219 TGTATCGATACACTGATCTTTGTATCGATACAAGCAGGCAAATTTGCCAAGA
1 TGTATCGATACACT-ATAAATGTATCGATACATGCAGGCAAATTTGCCAAGA
* *
1558271 TGTATCGATACACTATAAAATGTATCGATACATGTAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-AAATGTATCGATACATGCAGGCAAATTTGCCAAGA
1558323 TGTATCGATACACTAATAAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACT-ATAAATGTATCGATACATGCAGGCAAATTT
1558368 TCATATTTCT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATAAATGTATCGATACATGCAGGCAAATTTGCCAAGA
Found at i:1572213 original size:37 final size:37
Alignment explanation
Indices: 1572172--1572253 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
1572162 TGCCACAATC
* *
1572172 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACACTCATAACATTTCATTTTGCATA
1572209 ATGCATTTGTGACACTCATAACATTTCATTTTGCATA
1 ATGCATTTGTGACACTCATAACATTTCATTTTGCATA
1572246 ATGCATTT
1 ATGCATTT
1572254 ATGCTTCATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (37 bp):
ATGCATTTGTGACACTCATAACATTTCATTTTGCATA
Found at i:1572651 original size:28 final size:28
Alignment explanation
Indices: 1572619--1573030 Score: 428
Period size: 28 Copynumber: 14.5 Consensus size: 28
1572609 TCTCACCTTT
*
1572619 TTCAAAAGCCCACATGTCAGTGGCAACC
1 TTCAAAAGCCCACAAGTCAGTGGCAACC
* * *
1572647 TTCAAAAGCCCACAAGTTAGTGGCATCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAAC-C
*
1572676 TTCAAAAGCCCACAAGTTAGTGGC-ACC
1 TTCAAAAGCCCACAAGTCAGTGGCAACC
*
1572703 TTTTC-AAAGTCCACAAGTCAGTGGCAACC
1 --TTCAAAAGCCCACAAGTCAGTGGCAACC
1572732 TTCAAAAGCCCACAAGTCAGTGGCAACC
1 TTCAAAAGCCCACAAGTCAGTGGCAACC
*
1572760 TTCAAAAGCCCACAAGTTAGTGGC-ACC
1 TTCAAAAGCCCACAAGTCAGTGGCAACC
1572787 TTTTC-AAAGCCCACAAGTCAGTGGCAACC
1 --TTCAAAAGCCCACAAGTCAGTGGCAACC
* * *
1572816 TTTAAAAGCCCACAAGTCGGTGGCACCTC
1 TTCAAAAGCCCACAAGTCAGTGGCAAC-C
1572845 TTTC-AAAGCCCACAAGTCAGTGGC-ACC
1 -TTCAAAAGCCCACAAGTCAGTGGCAACC
***
1572872 TTCCAAAAGCCCACAAGTCAGTGGCATTTT
1 TT-CAAAAGCCCACAAGTCAGTGGCA-ACC
*
1572902 TTGCAAAAGCCCACAAGTTAGTGGC-ACC
1 TT-CAAAAGCCCACAAGTCAGTGGCAACC
* * * *
1572930 TTTTCAGAAGCCCATAAGTCAATGGCACCTC
1 --TTCAAAAGCCCACAAGTCAGTGGCAAC-C
*
1572961 TTC-AAAGCCCACAAGACAGTGGCAACC
1 TTCAAAAGCCCACAAGTCAGTGGCAACC
* **
1572988 TTCAAAAGCACACAAGTTGGT-GCAACTC
1 TTCAAAAGCCCACAAGTCAGTGGCAAC-C
1573016 ATTCAAAAGCCCACA
1 -TTCAAAAGCCCACA
1573031 CAAGTTGGTG
Statistics
Matches: 322, Mismatches: 40, Indels: 43
0.80 0.10 0.11
Matches are distributed among these distances:
26 2 0.01
27 19 0.06
28 182 0.57
29 90 0.28
30 28 0.09
31 1 0.00
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.20
Consensus pattern (28 bp):
TTCAAAAGCCCACAAGTCAGTGGCAACC
Found at i:1572717 original size:57 final size:58
Alignment explanation
Indices: 1572612--1573030 Score: 488
Period size: 57 Copynumber: 7.3 Consensus size: 58
1572602 TAGACATTCT
* *
1572612 CACCTTTTTCAAAAGCCCACATGTCAGTGGCAACC-TTCAAAAGCCCACAAGTTAGTGG
1 CACC-TTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCCACAAGTCAGTGG
* * *
1572670 CATCTTTTCAAAAGCCCACAAGTTAGTGGC-ACCTTTTC-AAAGTCCACAAGTCAGTGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGGCAACC-TTTCAAAAGCCCACAAGTCAGTGG
*
1572727 CAACC--TTCAAAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCCCACAAGTTAGTGG
1 C-ACCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCCACAAGTCAGTGG
*
1572783 CACCTTTTC-AAAGCCCACAAGTCAGTGGCAACCTTT-AAAAGCCCACAAGTCGGTGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCCACAAGTCAGTGG
*
1572839 CACCTCTTTC-AAAGCCCACAAGTCAGTGGC-ACCTTCCAAAAGCCCACAAGTCAGTGG
1 CACCT-TTTCAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCCACAAGTCAGTGG
** * * * *
1572896 CATTTTTTGCAAAAGCCCACAAGTTAGTGGC-ACCTTTTCAGAAGCCCATAAGTCAATGG
1 CACCTTTT-CAAAAGCCCACAAGTCAGTGGCAACC-TTTCAAAAGCCCACAAGTCAGTGG
* * * **
1572955 CACCTCTTC-AAAGCCCACAAGACAGTGGCAACC-TTCAAAAGCACACAAGTTGGT-G
1 CACCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCCACAAGTCAGTGG
* *
1573010 CAACTCATTCAAAAGCCCACA
1 CACCT-TTTCAAAAGCCCACA
1573031 CAAGTTGGTG
Statistics
Matches: 312, Mismatches: 33, Indels: 33
0.83 0.09 0.09
Matches are distributed among these distances:
55 11 0.04
56 117 0.38
57 125 0.40
58 34 0.11
59 25 0.08
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (58 bp):
CACCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCCACAAGTCAGTGG
Found at i:1572727 original size:85 final size:85
Alignment explanation
Indices: 1572612--1573030 Score: 531
Period size: 85 Copynumber: 4.9 Consensus size: 85
1572602 TAGACATTCT
* *
1572612 CACCTTTTTCAAAAGCCCACATGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCATCTTT
1 CACC-TTTTC-AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCAACTTT
1572677 TCAAAAGCCCACAAGTTAGTGG
64 TCAAAAGCCCACAAGTTAGTGG
* * *
1572699 CACCTTTTCAAAGTCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAAC-CTTC
1 CACCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCAACTTTTC
1572763 AAAAGCCCACAAGTTAGTGG
66 AAAAGCCCACAAGTTAGTGG
* ** *
1572783 CACCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCGGTGGCACCTCTTT
1 CACCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCAACT-TTT
*
1572848 C-AAAGCCCACAAGTCAGTGG
65 CAAAAGCCCACAAGTTAGTGG
* *** *
1572868 CACC-TTCCAAAAGCCCACAAGTCAGTGGCATTTTTTGCAAAAGCCCACAAGTTAGTGGCACCTT
1 CACCTTTTC-AAAGCCCACAAGTCAGTGGCA-ACCTT-CAAAAGCCCACAAGTTAGTGGCAACTT
* * * *
1572932 TTCAGAAGCCCATAAGTCAATGG
63 TTCAAAAGCCCACAAGTTAGTGG
* * * * *
1572955 CACCTCTTCAAAGCCCACAAGACAGTGGCAACCTTCAAAAGCACACAAGTTGGT-GCAACTCATT
1 CACCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCAACT-TTT
1573019 CAAAAGCCCACA
65 CAAAAGCCCACA
1573031 CAAGTTGGTG
Statistics
Matches: 291, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
84 87 0.30
85 119 0.41
86 16 0.05
87 67 0.23
88 2 0.01
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (85 bp):
CACCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCAACTTTTC
AAAAGCCCACAAGTTAGTGG
Found at i:1572817 original size:113 final size:113
Alignment explanation
Indices: 1572623--1573030 Score: 574
Period size: 113 Copynumber: 3.6 Consensus size: 113
1572613 ACCTTTTTCA
*
1572623 AAAGCCCACATGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCATCTTTTCAAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCATCTTTTCAAAAGCCCA
* *
1572688 CAAGTTAGTGGCACCTTTTCAAAGTCCACAAGTCAGTGGCAAC-CTTC
66 CAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCTCTTC
*
1572735 AAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCACCTTTTC-AAAGCCC
1 -AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCATCTTTTCAAAAGCCC
* * *
1572799 ACAAGTCAGTGGCAACC-TTTAAAAGCCCACAAGTCGGTGGCACCTCTTTC
65 ACAAGTTAGTGGC-ACCTTTTCAAAGCCCACAAGTCAGTGGCACCTC-TTC
* *
1572849 AAAGCCCACAAGTCAGTGGC-ACCTTCCAAAAGCCCACAAGTCAGTGGCATTTTTTGCAAAAGCC
1 AAAGCCCACAAGTCAGTGGCAACCTT-CAAAAGCCCACAAGTTAGTGGCATCTTTT-CAAAAGCC
* *
1572913 CACAAGTTAGTGGCACCTTTTCAGAAGCCCATAAGTCAATGGCACCTCTTC
64 CACAAGTTAGTGGCACCTTTTCA-AAGCCCACAAGTCAGTGGCACCTCTTC
* * * * *
1572964 AAAGCCCACAAGACAGTGGCAACCTTCAAAAGCACACAAGTTGGT-GCAACTCATTCAAAAGCCC
1 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCATCT-TTTCAAAAGCCC
1573028 ACA
65 ACA
1573031 CAAGTTGGTG
Statistics
Matches: 263, Mismatches: 22, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
112 47 0.18
113 104 0.40
114 23 0.09
115 63 0.24
116 26 0.10
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.20
Consensus pattern (113 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCATCTTTTCAAAAGCCCA
CAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCTCTTC
Found at i:1573133 original size:42 final size:43
Alignment explanation
Indices: 1573052--1573133 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 43
1573042 CATCTTCTTC
* *
1573052 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATCGGCACCTT
* * *
1573095 TAAGTCCAATGTTGCT-GCCTTGAATTAGCACATCGGCAC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATCGGCAC
1573134 TTTCATCTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 20 0.59
43 14 0.41
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (43 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCACATCGGCACCTT
Found at i:1573231 original size:52 final size:49
Alignment explanation
Indices: 1573052--1573328 Score: 190
Period size: 49 Copynumber: 5.7 Consensus size: 49
1573042 CATCTTCTTC
* * *
1573052 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG------CACCTT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTT
* * * * * *
1573095 TAAGTCCAATGTTGCT-GCCTTGAATTAGCACATCGGCACTTTCATCTT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTT
* * * * * * * *
1573143 TAAGCCCAATATCACTAGCCATGAATCAGCATATTGGCGCCTTAACCATCTT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT---CACCTT
* * * *
1573195 TAAGACCGATGTCGTTGGCCTTGAATTAGCACATTGGCATCTTCACCTT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTT
* * ** **
1573244 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCATATTCTTCTT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTT
* * * * *
1573293 CAAGTCTAATGTCGCTGACCATGAATCAGCACATTG
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTG
1573329 TCATTCTTCG
Statistics
Matches: 183, Mismatches: 41, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
42 17 0.09
43 14 0.08
48 17 0.09
49 97 0.53
52 38 0.21
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTT
Found at i:1573263 original size:49 final size:49
Alignment explanation
Indices: 1573092--1573337 Score: 217
Period size: 49 Copynumber: 5.0 Consensus size: 49
1573082 ATATTGGCAC
* * *
1573092 CTTTAAGTCCAATGTTGCT-GCCTTGAATTAGCACATCGGCA-CTTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATC-TTCAT
* * * * * * **
1573140 CTTTAAGCCCAATATCACTAGCCATGAATCAGCATATTGGCGCCTTAACCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTT---CAT
* * * * *
1573192 CTTTAAGACCGATGTCGTTGGCCTTGAATTAGCACATTGGCATCTTCAC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
* * *
1573241 CTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCATATTCTT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
* * * * *
1573290 CTTCAAGTCTAATGTCGCTGACCATGAATCAGCACATTGTCATTCTTC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-TCTTC
1573338 GCATCTTCGA
Statistics
Matches: 156, Mismatches: 36, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
48 15 0.10
49 98 0.63
50 5 0.03
52 38 0.24
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (49 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
Found at i:1573854 original size:13 final size:13
Alignment explanation
Indices: 1573836--1573864 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1573826 TTCGACAATT
1573836 TAGGCCTAGCTAA
1 TAGGCCTAGCTAA
1573849 TAGGCCTAGCTAA
1 TAGGCCTAGCTAA
1573862 TAG
1 TAG
1573865 ATTATCATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (13 bp):
TAGGCCTAGCTAA
Found at i:1577323 original size:20 final size:19
Alignment explanation
Indices: 1577298--1577381 Score: 90
Period size: 19 Copynumber: 4.7 Consensus size: 19
1577288 TTTCAACGAT
1577298 TTGTATCGATACATAAAGTA
1 TTGTATCGATACAT-AAGTA
*
1577318 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTA
1577337 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
*
1577351 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTA
*
1577369 TTGCATCGATACA
1 TTGTATCGATACA
1577382 ATATAAGCTA
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
13 11 0.20
16 2 0.04
19 27 0.50
20 14 0.26
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:1577356 original size:13 final size:13
Alignment explanation
Indices: 1577338--1577362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1577328 ACATAAGTGT
1577338 TGTATCGATACAA
1 TGTATCGATACAA
1577351 TGTATCGATACA
1 TGTATCGATACA
1577363 TAAGTTTTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1577360 original size:32 final size:32
Alignment explanation
Indices: 1577319--1577383 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
1577309 CATAAAGTAT
*
1577319 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGCATCGATACAA
*
1577351 TGTATCGATACATAAGTTTTGCATCGATACAA
1 TGTATCGATACATAAGTGTTGCATCGATACAA
1577383 T
1 T
1577384 ATAAGCTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGCATCGATACAA
Found at i:1577442 original size:13 final size:13
Alignment explanation
Indices: 1577424--1577448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1577414 ATTACTCAAA
1577424 TGTATCGATACAT
1 TGTATCGATACAT
1577437 TGTATCGATACA
1 TGTATCGATACA
1577449 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1577501 original size:52 final size:52
Alignment explanation
Indices: 1577457--1577585 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1577447 CACTGATCTT
*
1577457 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1577509 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1577561 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1577586 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1580941 original size:324 final size:325
Alignment explanation
Indices: 1580352--1580998 Score: 1055
Period size: 324 Copynumber: 2.0 Consensus size: 325
1580342 TACCTTTTTG
* *
1580352 CGCGTAATCAACTCCCGAACCCAACCGGCGAATCTCTAAAGTACGCAGACCACGGGATCGATGCT
1 CGCGTAACCAACTCCCGAACCCAACCGGCGAATCTCTAAAGTACACAGACCACGGGATCGATGCT
* *
1580417 TTGAGTTTCGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCTCGAAATGATC
66 TTGAGTTTCGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGATCGAAATAATC
* * *
1580482 GGTGGCGACTCCAAAATCTCGGTCACTTTGTAGTGACCATTAAAGATCAATTAGATGGGCGATTC
131 GGTGGCGACTCCAAAATCTCAGTCACTTCGTAGTGACCATTAAAGATCAATTAGATGGGAGATTC
** * *
1580547 ATCTACTGATCTTCCCTCTTTAATCAGCACACTTCCCATCATGCCATAGAAATCCCCAATCACGA
196 ATCTACCAATCTTCCCCCTTTAATCAACACACTTCCCATCATGCCATAGAAATCCCCAATCACGA
* *
1580612 GGGATATTAAGTCGAGTGTGCCTCAT-T-TGCCCTATCGCCGGGGTCGAGCGCACGTTACGACAT
261 GGGATATTAAGTAGAGCGTGCCTCATCTAT-CCCTATCGCCGGGGTCGAGCGCACGTTACGACAT
1580675 A
325 A
* * * *
1580676 CGCGTAACCAACTCCCGAACCCAACCGGCGAATCTCTAAATTACATAGACCACGGGATTGATGTT
1 CGCGTAACCAACTCCCGAACCCAACCGGCGAATCTCTAAAGTACACAGACCACGGGATCGATGCT
1580741 TTGAGTTTCGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGATCGAAATAATC
66 TTGAGTTTCGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGATCGAAATAATC
* *
1580806 GGTGGCGACTCCAAAATTTCAGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGAGATTC
131 GGTGGCGACTCCAAAATCTCAGTCACTTCGTAGTGACCATTAAAGATCAATTAGATGGGAGATTC
* * *
1580871 ATTTACCAATCTTCCCCCTTTAATCAACATACTTCCCATCATGCCATAGAAATCCCCAATCGCGA
196 ATCTACCAATCTTCCCCCTTTAATCAACACACTTCCCATCATGCCATAGAAATCCCCAATCACGA
* *
1580936 GGGATATTAAGTAGGGCGTGCCTCATCTATCCCTATCGCCGGGGTCGAGCGCACGTTGCGACA
261 GGGATATTAAGTAGAGCGTGCCTCATCTATCCCTATCGCCGGGGTCGAGCGCACGTTACGACA
1580999 ACCACCTCCT
Statistics
Matches: 297, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
324 263 0.89
325 33 0.11
326 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (325 bp):
CGCGTAACCAACTCCCGAACCCAACCGGCGAATCTCTAAAGTACACAGACCACGGGATCGATGCT
TTGAGTTTCGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGATCGAAATAATC
GGTGGCGACTCCAAAATCTCAGTCACTTCGTAGTGACCATTAAAGATCAATTAGATGGGAGATTC
ATCTACCAATCTTCCCCCTTTAATCAACACACTTCCCATCATGCCATAGAAATCCCCAATCACGA
GGGATATTAAGTAGAGCGTGCCTCATCTATCCCTATCGCCGGGGTCGAGCGCACGTTACGACATA
Found at i:1586839 original size:16 final size:14
Alignment explanation
Indices: 1586798--1586836 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
1586788 TTAATCCGAC
*
1586798 TATTGTATAATGATA
1 TATT-TATAATTATA
1586813 TATTTATAATTATA
1 TATTTATAATTATA
1586827 TATGTTATAA
1 TAT-TTATAA
1586837 ATTTGTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (14 bp):
TATTTATAATTATA
Found at i:1589897 original size:13 final size:13
Alignment explanation
Indices: 1589879--1589905 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1589869 TACCAAGATC
1589879 ATGTATCGATACA
1 ATGTATCGATACA
1589892 ATGTATCGATACA
1 ATGTATCGATACA
1589905 A
1 A
1589906 AGCAATATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1590572 original size:21 final size:21
Alignment explanation
Indices: 1590532--1590594 Score: 90
Period size: 21 Copynumber: 2.9 Consensus size: 21
1590522 CAAATTAAAA
1590532 CTCCCTCTTAATTAAAAATTTTT
1 CTCCCTCTTAA-T-AAAATTTTT
*
1590555 CTCCCTCTCAATAAAATTTTT
1 CTCCCTCTTAATAAAATTTTT
*
1590576 CTCCCCCTTAATAAAATTT
1 CTCCCTCTTAATAAAATTT
1590595 CTTCCCATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 26 0.70
22 1 0.03
23 10 0.27
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (21 bp):
CTCCCTCTTAATAAAATTTTT
Found at i:1593221 original size:13 final size:13
Alignment explanation
Indices: 1593203--1593229 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1593193 ACATTATGCT
1593203 TTGTATCGATACA
1 TTGTATCGATACA
1593216 TTGTATCGATACA
1 TTGTATCGATACA
1593229 T
1 T
1593230 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1593259 original size:20 final size:19
Alignment explanation
Indices: 1593213--1593269 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
1593203 TTGTATCGAT
*
1593213 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
1593232 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
1593251 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1593270 AAATTGGTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1595668 original size:13 final size:13
Alignment explanation
Indices: 1595650--1595675 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1595640 TATTTTATGG
1595650 TGTATCGATACAT
1 TGTATCGATACAT
1595663 TGTATCGATACAT
1 TGTATCGATACAT
1595676 ACTGTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1595773 original size:20 final size:20
Alignment explanation
Indices: 1595748--1595813 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
1595738 TCTTTTTCAA
1595748 GTATCGATACAATGCAACAT
1 GTATCGATACAATGCAACAT
1595768 GTATCGATAC-AT------T
1 GTATCGATACAATGCAACAT
**
1595781 GTATCGATACTGTGCAACAT
1 GTATCGATACAATGCAACAT
1595801 GTATCGATACAAT
1 GTATCGATACAAT
1595814 TAAATGTGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 14
0.68 0.06 0.26
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
19 2 0.06
20 22 0.61
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATGCAACAT
Found at i:1595785 original size:33 final size:33
Alignment explanation
Indices: 1595748--1595811 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
1595738 TCTTTTTCAA
1595748 GTATCGATACAATGCAACATGTATCGATACATT
1 GTATCGATACAATGCAACATGTATCGATACATT
**
1595781 GTATCGATACTGTGCAACATGTATCGATACA
1 GTATCGATACAATGCAACATGTATCGATACA
1595812 ATTAAATGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (33 bp):
GTATCGATACAATGCAACATGTATCGATACATT
Found at i:1596572 original size:139 final size:139
Alignment explanation
Indices: 1596322--1596590 Score: 493
Period size: 139 Copynumber: 1.9 Consensus size: 139
1596312 AGATTTCAAA
* *
1596322 AATCAAGATTTTACATTTTTCTTTTCTTTCCCCCTTAATCAAACATTTCTCCCCTTTAATAAGGT
1 AATCAAGATTTTACATTTTTCTTTTCATTCCCCCTTAATCAAACATTTCTCCCCCTTAATAAGGT
*
1596387 AACTTTAACAAATTTGCATTCTCCTCCTTAATCATAAGCAATTATCTCTTTCTCCCCCTTAATCA
66 AACTTTAACAAATTCGCATTCTCCTCCTTAATCATAAGCAATTATCTCTTTCTCCCCCTTAATCA
1596452 TAAGCACTT
131 TAAGCACTT
1596461 AATCAAGATTTTACATTTTTCTTTTCATTCCCCCTTAATCAAACATTTCTCCCCCTTAATAAGGT
1 AATCAAGATTTTACATTTTTCTTTTCATTCCCCCTTAATCAAACATTTCTCCCCCTTAATAAGGT
* *
1596526 AATTTTAACAAATTCGCATTCTCCTCCTTAATCATAAGCACTTATCTCTTTCTCCCCCTTAATCA
66 AACTTTAACAAATTCGCATTCTCCTCCTTAATCATAAGCAATTATCTCTTTCTCCCCCTTAATCA
1596591 AAAATTTATT
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
139 125 1.00
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.41
Consensus pattern (139 bp):
AATCAAGATTTTACATTTTTCTTTTCATTCCCCCTTAATCAAACATTTCTCCCCCTTAATAAGGT
AACTTTAACAAATTCGCATTCTCCTCCTTAATCATAAGCAATTATCTCTTTCTCCCCCTTAATCA
TAAGCACTT
Found at i:1596583 original size:68 final size:68
Alignment explanation
Indices: 1596367--1596588 Score: 186
Period size: 68 Copynumber: 3.2 Consensus size: 68
1596357 TAATCAAACA
* * *
1596367 TTTCTCCCCTTTAATAAGGTAACTTTAACAAATTTGCATTCTCCTCCTTAATCATAAGCAATTAT
1 TTTCTCCCCCTTAATAAGGTAAATTTAACAAATTTGCATTCTCCTCCTTAATCATAAGCACTTAT
1596432 CTC
66 CTC
* * * * * *** *
1596435 TTTCTCCCCCTTAATCA--TAAGCACTTAATCAAGATTTTACATT-T--TTCTT-TTCATTCCCC
1 TTTCTCCCCCTTAATAAGGTAA--ATTTAA-CAA-A-TTTGCATTCTCCTCCTTAATCATAAGCA
*
1596494 CTTAATCAAAC
61 CTT-ATC--TC
* *
1596505 ATTTCTCCCCCTTAATAAGGTAATTTTAACAAATTCGCATTCTCCTCCTTAATCATAAGCACTTA
1 -TTTCTCCCCCTTAATAAGGTAAATTTAACAAATTTGCATTCTCCTCCTTAATCATAAGCACTTA
1596570 TCTC
65 TCTC
1596574 TTTCTCCCCCTTAAT
1 TTTCTCCCCCTTAAT
1596589 CAAAAATTTA
Statistics
Matches: 114, Mismatches: 25, Indels: 30
0.67 0.15 0.18
Matches are distributed among these distances:
66 3 0.03
67 7 0.06
68 47 0.41
69 6 0.05
70 6 0.05
71 34 0.30
72 8 0.07
73 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTCTCCCCCTTAATAAGGTAAATTTAACAAATTTGCATTCTCCTCCTTAATCATAAGCACTTAT
CTC
Found at i:1598200 original size:22 final size:23
Alignment explanation
Indices: 1598175--1598228 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
1598165 ACTTGTTTTT
1598175 GAAGATGATTTTG-A-TGAAAAAC
1 GAAGAT-ATTTTGAAGTGAAAAAC
1598197 GAAG-TATTTTGAAGTGAAAAAC
1 GAAGATATTTTGAAGTGAAAAAC
1598219 -AAGA-ATTTTG
1 GAAGATATTTTG
1598229 CAAAAGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 6 0.21
21 11 0.38
22 12 0.41
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (23 bp):
GAAGATATTTTGAAGTGAAAAAC
Found at i:1598207 original size:20 final size:21
Alignment explanation
Indices: 1598182--1598228 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1598172 TTTGAAGATG
*
1598182 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGA
1598202 ATTTTGAAGTGAAAAACAAGA
1 ATTTTGAAGTGAAAAACAAGA
1598223 ATTTTG
1 ATTTTG
1598229 CAAAAGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 6 0.25
21 10 0.42
22 8 0.33
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGA
Found at i:1598559 original size:8 final size:8
Alignment explanation
Indices: 1598543--1598576 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1598533 AACATCATTC
*
1598543 ATCATAAA
1 ATCACAAA
1598551 ATCACAAA
1 ATCACAAA
*
1598559 ATCATAAA
1 ATCACAAA
1598567 ATCACAAA
1 ATCACAAA
1598575 AT
1 AT
1598577 TTAATCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.62, C:0.18, G:0.00, T:0.21
Consensus pattern (8 bp):
ATCACAAA
Found at i:1598564 original size:16 final size:16
Alignment explanation
Indices: 1598543--1598576 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1598533 AACATCATTC
1598543 ATCATAAAATCACAAA
1 ATCATAAAATCACAAA
1598559 ATCATAAAATCACAAA
1 ATCATAAAATCACAAA
1598575 AT
1 AT
1598577 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.62, C:0.18, G:0.00, T:0.21
Consensus pattern (16 bp):
ATCATAAAATCACAAA
Found at i:1604553 original size:13 final size:13
Alignment explanation
Indices: 1604535--1604560 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1604525 CATTTTATGG
1604535 TGTATCGATACAT
1 TGTATCGATACAT
1604548 TGTATCGATACAT
1 TGTATCGATACAT
1604561 ACTGTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1604557 original size:33 final size:32
Alignment explanation
Indices: 1604515--1604578 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
1604505 TACAAGCCAA
**
1604515 TGTATCGATACATTTTATGGTGTATCGATACAT
1 TGTATCGATACATACTAT-GTGTATCGATACAT
*
1604548 TGTATCGATACATACTGTGTGTATCGATACA
1 TGTATCGATACATACTATGTGTATCGATACA
1604579 AGTTTAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATACTATGTGTATCGATACAT
Found at i:1604669 original size:13 final size:13
Alignment explanation
Indices: 1604651--1604675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1604641 ACAATGCAAC
1604651 ATGTATCGATACA
1 ATGTATCGATACA
1604664 ATGTATCGATAC
1 ATGTATCGATAC
1604676 TGTGCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1604670 original size:33 final size:33
Alignment explanation
Indices: 1604633--1604698 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1604623 TCTTTTTCAA
1604633 GTATCGATACAATGCAACATGTATCGATACAAT
1 GTATCGATACAATGCAACATGTATCGATACAAT
**
1604666 GTATCGATACTGTGCAACATGTATCGATACAAT
1 GTATCGATACAATGCAACATGTATCGATACAAT
1604699 TAAATGTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (33 bp):
GTATCGATACAATGCAACATGTATCGATACAAT
Found at i:1605638 original size:21 final size:20
Alignment explanation
Indices: 1605598--1605646 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1605588 AGATGATATT
*
1605598 AAGAAGTTAGCTAATGAAAAT
1 AAGAA-TTAGCTAATGAAAAC
1605619 AATGAATTAGCTAA-GAAAAAC
1 AA-GAATTAGCTAATG-AAAAC
1605640 AAGAATT
1 AAGAATT
1605647 TGCATGATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.24
21 16 0.64
22 3 0.12
ACGTcount: A:0.55, C:0.06, G:0.16, T:0.22
Consensus pattern (20 bp):
AAGAATTAGCTAATGAAAAC
Found at i:1605645 original size:20 final size:21
Alignment explanation
Indices: 1605598--1605646 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
1605588 AGATGATATT
1605598 AAGAAGTTAGCTAATGAAAATA
1 AAGAA-TTAGCTAATGAAAATA
*
1605620 ATGAATTAGCTAA-GAAAA-A
1 AAGAATTAGCTAATGAAAATA
1605639 CAAGAATT
1 -AAGAATT
1605647 TGCATGATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 11 0.46
21 8 0.33
22 4 0.17
ACGTcount: A:0.55, C:0.06, G:0.16, T:0.22
Consensus pattern (21 bp):
AAGAATTAGCTAATGAAAATA
Found at i:1609288 original size:10 final size:10
Alignment explanation
Indices: 1609273--1609316 Score: 63
Period size: 10 Copynumber: 4.3 Consensus size: 10
1609263 AAATGACATT
1609273 TTTTTACAAA
1 TTTTTACAAA
1609283 TTTTTACAAA
1 TTTTTACAAA
1609293 TTTCTT-CAAA
1 TTT-TTACAAA
1609303 TCTTTTACAAA
1 T-TTTTACAAA
1609314 TTT
1 TTT
1609317 CTTGTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 22 0.71
11 9 0.29
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (10 bp):
TTTTTACAAA
Found at i:1609310 original size:21 final size:20
Alignment explanation
Indices: 1609279--1609319 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
1609269 CATTTTTTTA
1609279 CAAATTTTTACAAATTTCTT
1 CAAATTTTTACAAATTTCTT
1609299 CAAATCTTTTACAAATTTCTT
1 CAAAT-TTTTACAAATTTCTT
1609320 GTTTTTCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (20 bp):
CAAATTTTTACAAATTTCTT
Found at i:1611078 original size:22 final size:22
Alignment explanation
Indices: 1611060--1611115 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
1611050 AGATTTGACA
1611060 AAGGGGGAGAAATACTTTGATT
1 AAGGGGGAGAAATACTTTGATT
* *
1611082 AAGGGGGAGAAATTCTTTAATT
1 AAGGGGGAGAAATACTTTGATT
1611104 AAGGGGGAGAAA
1 AAGGGGGAGAAA
1611116 AACGAAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.39, C:0.04, G:0.34, T:0.23
Consensus pattern (22 bp):
AAGGGGGAGAAATACTTTGATT
Found at i:1611714 original size:20 final size:19
Alignment explanation
Indices: 1611668--1611724 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1611658 TTGTATTGAT
*
1611668 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
1611687 TCATTGTATCGAAACATGG
1 ACATTGTATCGATACATGG
1611706 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1611725 AAATTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1611790 original size:13 final size:13
Alignment explanation
Indices: 1611769--1611799 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1611759 CTATACATGG
*
1611769 TACAATGTATCGA
1 TACATTGTATCGA
1611782 TACATTGTATCGA
1 TACATTGTATCGA
1611795 TACAT
1 TACAT
1611800 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1614617 original size:34 final size:34
Alignment explanation
Indices: 1614574--1614639 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
1614564 TTCGGGCTAG
1614574 GCATGATCGGATGCCTATTGAAACCTACGTCTAA
1 GCATGATCGGATGCCTATTGAAACCTACGTCTAA
*
1614608 GCATGATCGGATGCCTATTGAAACCTATGTCT
1 GCATGATCGGATGCCTATTGAAACCTACGTCT
1614640 TGAGTTACGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (34 bp):
GCATGATCGGATGCCTATTGAAACCTACGTCTAA
Found at i:1616357 original size:130 final size:129
Alignment explanation
Indices: 1616159--1616455 Score: 325
Period size: 130 Copynumber: 2.3 Consensus size: 129
1616149 AATGGGGTTA
* * * *
1616159 GAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCGATTGTGAAAAATCGATGATTTAGAAA
1 GAGTATCCCCTCGAAAATAAAGGG-TTGGAGTATCCCCAATTATGAAAAATCAATGATTTAGAAA
* *
1616224 TAAGGCAAGGGTTGAAGTGTCCCCGATTAT-AGAAAAT-AGATGTTTCAAAAATAAAATCGGAAT
65 TAAGGCAAGGGTTGAAGTATCCCCGATTATGAG-AAATCA-ATATTTCAAAAATAAAATCGGAAT
1616287 TG
128 TG
* *
1616289 GAGTATCCCCGT-GAAAATAATAGGGTTGGAGTATCCCTAATTATGAGAAATCAAT-ATTTTAGA
1 GAGTATCCCC-TCGAAAATAA-AGGGTTGGAGTATCCCCAATTATGAAAAATCAATGA-TTTAGA
** * * *** * *
1616352 AATAAGGCCGGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAATAAAGTCGGGAT
63 AATAAGGCAAGGGTTGAAGTATCCCCGATTATGAGAAATCAATATTTCAAAAATAAAATCGGAAT
1616417 TG
128 TG
* *
1616419 GAGTA-CCCCTCGGAAATAACGGGGTTGGAGTATCCCC
1 GAGTATCCCCTCGAAAATAA-AGGGTTGGAGTATCCCC
1616456 GATGAAATAA
Statistics
Matches: 140, Mismatches: 21, Indels: 13
0.80 0.12 0.07
Matches are distributed among these distances:
128 1 0.01
129 27 0.19
130 105 0.75
131 7 0.05
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (129 bp):
GAGTATCCCCTCGAAAATAAAGGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTTAGAAAT
AAGGCAAGGGTTGAAGTATCCCCGATTATGAGAAATCAATATTTCAAAAATAAAATCGGAATTG
Found at i:1616376 original size:51 final size:51
Alignment explanation
Indices: 1616311--1616407 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
1616301 GAAAATAATA
*
1616311 GGGTTGGAGTATCCCTAATTATGAGAAATCAATATTTTAGAAATAAGGCCG
1 GGGTTGAAGTATCCCTAATTATGAGAAATCAATATTTTAGAAATAAGGCCG
* * *
1616362 GGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAATAA
1 GGGTTGAAGTATCCCTAATTATGAGAAATCAATATTTTAGAAATAA
1616408 AGTCGGGATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (51 bp):
GGGTTGAAGTATCCCTAATTATGAGAAATCAATATTTTAGAAATAAGGCCG
Found at i:1616446 original size:27 final size:27
Alignment explanation
Indices: 1616411--1616485 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
1616401 GAAATAAAGT
*
1616411 CGGGATTGGAGTACCCCTCG-GAAATAA
1 CGGGGTTGGAGTACCCC-CGAGAAATAA
*
1616438 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTACCCCCGA-GAAATAA
* * *
1616466 CAGGGTTGGATTATCCCCGA
1 CGGGGTTGGAGTACCCCCGA
1616486 TTGTGAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 2 0.05
27 15 0.36
28 25 0.60
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (27 bp):
CGGGGTTGGAGTACCCCCGAGAAATAA
Found at i:1616464 original size:28 final size:28
Alignment explanation
Indices: 1616431--1616486 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
1616421 GTACCCCTCG
*
1616431 GAAATAACGGGGTTGGAGTATCCCCGAT
1 GAAATAACAGGGTTGGAGTATCCCCGAT
*
1616459 GAAATAACAGGGTTGGATTATCCCCGAT
1 GAAATAACAGGGTTGGAGTATCCCCGAT
1616487 TGTGAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (28 bp):
GAAATAACAGGGTTGGAGTATCCCCGAT
Found at i:1616532 original size:51 final size:51
Alignment explanation
Indices: 1616470--1616614 Score: 163
Period size: 51 Copynumber: 2.9 Consensus size: 51
1616460 AAATAACAGG
* * *
1616470 GTTGGATTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGAA
1 GTTGGAATATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCGAA
* * * **
1616521 GTTGGAATATCCCCAATTATGGAGAATTAGTGTTTTAGAAATAAAATCGGG
1 GTTGGAATATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCGAA
* *
1616572 GTTGGAGTATCCCCG---ATGAAAAATT-GATGTTTTAAAAATAAAA
1 GTTGGAATATCCCCGATTATGAAAAATTAG-TGTTTTAGAAATAAAA
1616615 CTGGGTTGGA
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
47 1 0.01
48 23 0.29
51 56 0.70
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (51 bp):
GTTGGAATATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCGAA
Found at i:1616647 original size:75 final size:76
Alignment explanation
Indices: 1616568--1616739 Score: 271
Period size: 76 Copynumber: 2.3 Consensus size: 76
1616558 GAAATAAAAT
1616568 CGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTA-AAAATAAAA-CTGG-GTTGGAGTGTC
1 CGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTAGAAAA-AAAATC-GGAGTTGGAGTGTC
*
1616630 CCTTC-GAAAATAA
64 CCCTCAG-AAATAA
*
1616643 CGGGGTTAGAGTATCCCCGATGAAAAATTGATGTTTTAGAAAAAAAATCGGAGTTGGAGTGTCCC
1 CGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTAGAAAAAAAATCGGAGTTGGAGTGTCCC
1616708 CTCAGAAATAA
66 CTCAGAAATAA
1616719 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1616740 TGTGAAAAGT
Statistics
Matches: 90, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
75 43 0.48
76 46 0.51
77 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (76 bp):
CGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTAGAAAAAAAATCGGAGTTGGAGTGTCCC
CTCAGAAATAA
Found at i:1616859 original size:51 final size:51
Alignment explanation
Indices: 1616723--1616888 Score: 185
Period size: 51 Copynumber: 3.3 Consensus size: 51
1616713 AAATAACGGG
* * *
1616723 GTTGGAGTATCCCCGATTGTGA-AAAGTCGGTGTTTTGGAAATAAAATTGAA
1 GTTGGAGTATCCCCGATTATGAGAAA-TCGGTGTTTTGGAAATAAAATAGGA
* *
1616774 GTTGGAGTATCCCCGATTATG-GAAAATGGGTGTTTTAGAAATAAAATAGGA
1 GTTGGAGTATCCCCGATTATGAG-AAATCGGTGTTTTGGAAATAAAATAGGA
* * * * **
1616825 GTTGGAGTATCCCCGATTAAGAGAAATTGATGTTTTGGAAATGAAA-CCGA
1 GTTGGAGTATCCCCGATTATGAGAAATCGGTGTTTTGGAAATAAAATAGGA
1616875 GATTGGAGTATCCC
1 G-TTGGAGTATCCC
1616889 GAGATGAAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
50 3 0.03
51 92 0.93
52 4 0.04
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAGAAATCGGTGTTTTGGAAATAAAATAGGA
Found at i:1619252 original size:33 final size:33
Alignment explanation
Indices: 1619210--1619279 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
1619200 TACATTGTAA
1619210 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
1619243 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
1619276 AATG
1 AATG
1619280 CAAAATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAATGAGCAATGTATCGATAC
Found at i:1619252 original size:53 final size:53
Alignment explanation
Indices: 1619190--1619296 Score: 146
Period size: 53 Copynumber: 2.0 Consensus size: 53
1619180 AAAATGCGTG
* *
1619190 AATGTATCGATACATTGTA-AAATGTATCGATACAATG-AGCAATGTATCGATAC
1 AATGTATCGATACAATG-AGAAATGTATCGATACAATGCA-AAATGTATCGATAC
* *
1619243 AATGTATCGATACAATGAGCAATGTATCGATACAATGCAAAATGTATTGATAC
1 AATGTATCGATACAATGAGAAATGTATCGATACAATGCAAAATGTATCGATAC
1619296 A
1 A
1619297 TCTGGGTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
52 1 0.02
53 46 0.96
54 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (53 bp):
AATGTATCGATACAATGAGAAATGTATCGATACAATGCAAAATGTATCGATAC
Found at i:1619265 original size:20 final size:19
Alignment explanation
Indices: 1619190--1619296 Score: 100
Period size: 20 Copynumber: 5.7 Consensus size: 19
1619180 AAAATGCGTG
* *
1619190 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AC
1619210 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
1619230 AATGTATCG-----AT-AC
1 AATGTATCGATACAATGAC
1619243 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
*
1619263 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AC
*
1619283 AATGTATTGATACA
1 AATGTATCGATACA
1619297 TCTGGGTAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
13 10 0.14
14 1 0.01
15 2 0.03
18 2 0.03
19 2 0.03
20 56 0.76
21 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (19 bp):
AATGTATCGATACAATGAC
Found at i:1619278 original size:13 final size:13
Alignment explanation
Indices: 1619229--1619259 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1619219 ATACAATGAG
1619229 CAATGTATCGATA
1 CAATGTATCGATA
1619242 CAATGTATCGATA
1 CAATGTATCGATA
1619255 CAATG
1 CAATG
1619260 AGCAATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1619330 original size:13 final size:13
Alignment explanation
Indices: 1619312--1619374 Score: 66
Period size: 13 Copynumber: 5.3 Consensus size: 13
1619302 GTAAACCCAG
1619312 AATGTATCGATAC
1 AATGTATCGATAC
*
1619325 AATGTATTGATAC
1 AATGTATCGATAC
1619338 -A---AT-GA-AC
1 AATGTATCGATAC
*
1619345 AATATATCGATAC
1 AATGTATCGATAC
1619358 AATGTATCGATAC
1 AATGTATCGATAC
1619371 AATG
1 AATG
1619375 AACAATATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 2 0.05
8 3 0.07
9 2 0.05
11 2 0.05
12 3 0.07
13 30 0.71
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1619356 original size:20 final size:20
Alignment explanation
Indices: 1619323--1619412 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
1619313 ATGTATCGAT
* *
1619323 ACAATGTATTGATACAATGA
1 ACAATATATCGATACAATGA
1619343 ACAATATATCGATACAATG-
1 ACAATATATCGATACAATGA
1619362 ------TATCGATACAATGA
1 ACAATATATCGATACAATGA
*
1619376 ACAATATATCGACACAATGA
1 ACAATATATCGATACAATGA
*
1619396 ACAATGTATCGATACAA
1 ACAATATATCGATACAA
1619413 ATTGTGAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
13 13 0.22
20 45 0.78
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.26
Consensus pattern (20 bp):
ACAATATATCGATACAATGA
Found at i:1619358 original size:33 final size:33
Alignment explanation
Indices: 1619316--1619394 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
1619306 ACCCAGAATG
*
1619316 TATCGATACAATGTATTGATACAATGAACAATA
1 TATCGATACAATGTATCGATACAATGAACAATA
1619349 TATCGATACAATGTATCGATACAATGAACAATA
1 TATCGATACAATGTATCGATACAATGAACAATA
*
1619382 TATCGACACAATG
1 TATCGATACAATG
1619395 AACAATGTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (33 bp):
TATCGATACAATGTATCGATACAATGAACAATA
Found at i:1626514 original size:20 final size:20
Alignment explanation
Indices: 1626491--1626553 Score: 99
Period size: 20 Copynumber: 3.0 Consensus size: 20
1626481 CAAAGCAATA
*
1626491 TGTATGGATACTTCTGGGTT
1 TGTATCGATACTTCTGGGTT
1626511 TGTATCGATACTTCTGGGTT
1 TGTATCGATACTTCTGGGTT
1626531 TGTATCGATACTTTCTAGGGTT
1 TGTATCGATAC-TTCT-GGGTT
1626553 T
1 T
1626554 TGACCTTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 30 0.75
21 4 0.10
22 6 0.15
ACGTcount: A:0.16, C:0.13, G:0.25, T:0.46
Consensus pattern (20 bp):
TGTATCGATACTTCTGGGTT
Found at i:1627533 original size:47 final size:47
Alignment explanation
Indices: 1627463--1627565 Score: 161
Period size: 47 Copynumber: 2.2 Consensus size: 47
1627453 TTGAGTGACT
* * *
1627463 TTAAAGCATATCGCCTACTTTGATGTTCGATGTTCTAGGTCAGGTCAG
1 TTAAAG-ATATCACCTACTTTGATGTTCGATGTTCTAGGTCAAGTCAC
*
1627511 TTAAAGATATCACCTACTTTGATGTTTGATGTTCTAGGTCAAGTCAC
1 TTAAAGATATCACCTACTTTGATGTTCGATGTTCTAGGTCAAGTCAC
1627558 TTAAAGAT
1 TTAAAGAT
1627566 TTGTTATTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 45 0.88
48 6 0.12
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (47 bp):
TTAAAGATATCACCTACTTTGATGTTCGATGTTCTAGGTCAAGTCAC
Found at i:1629114 original size:34 final size:33
Alignment explanation
Indices: 1629048--1629117 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
1629038 CTATCACTAT
**
1629048 TTGTATCGATAAATGGGACAATGTATTGATACA
1 TTGTATCGATAAATGGGACAATGTATCAATACA
*
1629081 TTGTATCGATAAATGATGA-AATTGTATCAATACA
1 TTGTATCGATAAATG-GGACAA-TGTATCAATACA
1629115 TTG
1 TTG
1629118 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 17 0.53
34 15 0.47
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATAAATGGGACAATGTATCAATACA
Found at i:1635196 original size:13 final size:13
Alignment explanation
Indices: 1635178--1635206 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1635168 ATAACATTCC
1635178 TTGTATCGATACA
1 TTGTATCGATACA
1635191 TTGTATCGATACA
1 TTGTATCGATACA
1635204 TTG
1 TTG
1635207 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1637700 original size:20 final size:19
Alignment explanation
Indices: 1637677--1637750 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
1637667 CACTCCCAGA
* *
1637677 TGTATCGATACATTATGCTT
1 TGTATCGATACATGAT-CAT
*
1637697 TGTATCGATACATGCTCAT
1 TGTATCGATACATGATCAT
1637716 TGTATCGATACATAGA-CAAT
1 TGTATCGATACAT-GATC-AT
1637736 TGTATCGATACATGA
1 TGTATCGATACATGA
1637751 GATTGGCAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 18 0.38
20 30 0.62
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATGATCAT
Found at i:1637822 original size:33 final size:34
Alignment explanation
Indices: 1637778--1637847 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
1637768 CTATCACTAT
1637778 TTGTATCGATACATG-GGACAA-TGCATCGATACA
1 TTGTATCGATACATGAGGA-AATTGCATCGATACA
* * *
1637811 TTGTATTGATACATGATGAAATTGTATCGATACA
1 TTGTATCGATACATGAGGAAATTGCATCGATACA
1637845 TTG
1 TTG
1637848 CTTGTAATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 16 0.50
34 16 0.50
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (34 bp):
TTGTATCGATACATGAGGAAATTGCATCGATACA
Found at i:1642355 original size:20 final size:20
Alignment explanation
Indices: 1642332--1642406 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
1642322 TACATTTTTC
1642332 AATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
* *
1642352 AATGTATCGATACATTCATA
1 AATGTATCGATACATTGAAA
*
1642372 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
*
1642392 AATGTGTCGATACAT
1 AATGTATCGATACAT
1642407 CTGGGTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:1645608 original size:128 final size:126
Alignment explanation
Indices: 1645363--1645610 Score: 361
Period size: 127 Copynumber: 2.0 Consensus size: 126
1645353 CATTTAATAA
* * * *
1645363 TGTTAGGATCTTGGTTTTGACAAACAAAGTATGAATAAAACTGAAAAAATATTTAAAAAATCGTA
1 TGTTAGAATCTTGGTTTTGACAAACAAAGTATGAATAAAACCGAAAAAAGATTTAAAAAACCGTA
***
1645428 AACAAGCTTTATTCATTAAAAATACTCTAAAACCTTGTTCTAAATGATTTTCAATCTTAGC
66 AACAAGCTTTATTCATTAAAAATACTCTAAAACCGCATTCTAAATGATTTTCAATCTTAGC
* * * *
1645489 TGTTAGAATCTTGGTTTTGATATAATAAAGTATGAATAAAACCGAAAAAAGATTTGAGAAACCGT
1 TGTTAGAATCTTGGTTTTGACA-AACAAAGTATGAATAAAACCGAAAAAAGATTTAAAAAACCGT
* *
1645554 AAACAAGTTTTATTCTATTAAAAATACTCTAAAACCGCATTCTAAGTGATTTTCAAT
65 AAACAAGCTTTATTC-ATTAAAAATACTCTAAAACCGCATTCTAAATGATTTTCAAT
1645611 ATCAATAATG
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
126 20 0.19
127 50 0.47
128 37 0.35
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (126 bp):
TGTTAGAATCTTGGTTTTGACAAACAAAGTATGAATAAAACCGAAAAAAGATTTAAAAAACCGTA
AACAAGCTTTATTCATTAAAAATACTCTAAAACCGCATTCTAAATGATTTTCAATCTTAGC
Found at i:1645852 original size:20 final size:19
Alignment explanation
Indices: 1645806--1645860 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
1645796 TGTATCGATA
* * *
1645806 CATTATATCGATAAATGCT
1 CATTGTATCGATACATACT
1645825 CATTGTATCGATACATACT
1 CATTGTATCGATACATACT
1645844 CACTTGTATCGATACAT
1 CA-TTGTATCGATACAT
1645861 GAAACTCGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:1653327 original size:21 final size:21
Alignment explanation
Indices: 1653302--1653345 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1653292 AACCCTAACA
1653302 AATTCTTTCTTC-AATTTCTTC
1 AATTCTTT-TTCGAATTTCTTC
1653323 AATTCTTTTTCGAATTTCTTC
1 AATTCTTTTTCGAATTTCTTC
1653344 AA
1 AA
1653346 ATACTCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.23, C:0.20, G:0.02, T:0.55
Consensus pattern (21 bp):
AATTCTTTTTCGAATTTCTTC
Found at i:1655476 original size:20 final size:22
Alignment explanation
Indices: 1655451--1655493 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
1655441 TTTTCTTTTC
*
1655451 TCTCCCCCTTAA-AAAA-AATT
1 TCTCCCCCATAATAAAATAATT
1655471 TCTCCCCCATAATAAAATAATT
1 TCTCCCCCATAATAAAATAATT
1655493 T
1 T
1655494 AACAAATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 4 0.20
22 5 0.25
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.33
Consensus pattern (22 bp):
TCTCCCCCATAATAAAATAATT
Found at i:1655526 original size:42 final size:42
Alignment explanation
Indices: 1655463--1655547 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
1655453 TCCCCCTTAA
1655463 AAAAAATTTCTCCCCCATAATAAAATAATTTAACAAATTCGC
1 AAAAAATTTCTCCCCCATAATAAAATAATTTAACAAATTCGC
* *
1655505 AAAAAATTTCTCCCCCTTAATAAAATAATTTAACAATTTCGC
1 AAAAAATTTCTCCCCCATAATAAAATAATTTAACAAATTCGC
1655547 A
1 A
1655548 CATTAACAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (42 bp):
AAAAAATTTCTCCCCCATAATAAAATAATTTAACAAATTCGC
Found at i:1656959 original size:21 final size:20
Alignment explanation
Indices: 1656920--1656961 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1656910 GGGTCTGCCC
* *
1656920 GGTTGCGACTTGGGGGTGCT
1 GGTTGAGACCTGGGGGTGCT
1656940 GGTTGAGACCTGGTGGGTGCT
1 GGTTGAGACCTGG-GGGTGCT
1656961 G
1 G
1656962 CCTAGAGGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.07, C:0.14, G:0.50, T:0.29
Consensus pattern (20 bp):
GGTTGAGACCTGGGGGTGCT
Found at i:1657411 original size:13 final size:13
Alignment explanation
Indices: 1657393--1657430 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1657383 ATAAACCCTT
*
1657393 TGTATCGATACAC
1 TGTATCGATACAA
1657406 TGTATCGATACAA
1 TGTATCGATACAA
1657419 TGTATCGATACA
1 TGTATCGATACA
1657431 GAGAATGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1657475 original size:47 final size:50
Alignment explanation
Indices: 1657418--1657515 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 50
1657408 TATCGATACA
*
1657418 ATGTATCGATACA-GAGAATGCTGTATCGATAC-TTCT-GAA-TTTTCCAG
1 ATGTATCGATACATGAGAA-CCTGTATCGATACATTCTGGAATTTTTCCAG
**
1657465 ATGTATCGATACATTTGAACCTGTATCGATACATTCTGGAATTTTTCCAG
1 ATGTATCGATACATGAGAACCTGTATCGATACATTCTGGAATTTTTCCAG
1657515 A
1 A
1657516 ATTTGACCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
47 25 0.57
48 7 0.16
49 3 0.07
50 9 0.20
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (50 bp):
ATGTATCGATACATGAGAACCTGTATCGATACATTCTGGAATTTTTCCAG
Found at i:1657646 original size:8 final size:8
Alignment explanation
Indices: 1657633--1657658 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1657623 AACATCATTC
1657633 ATCACAAA
1 ATCACAAA
1657641 ATCACAAA
1 ATCACAAA
1657649 ATCACAAA
1 ATCACAAA
1657657 AT
1 AT
1657659 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:1663602 original size:13 final size:13
Alignment explanation
Indices: 1663584--1663640 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
1663574 ACATTTTAGG
1663584 ATGTATCGATAGA
1 ATGTATCGATAGA
*
1663597 ATGTATCGATA-T
1 ATGTATCGATAGA
*
1663609 AT-T-T---TAGG
1 ATGTATCGATAGA
1663617 ATGTATCGATAGA
1 ATGTATCGATAGA
1663630 ATGTATCGATA
1 ATGTATCGATA
1663641 CATATTGTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
7 2 0.06
8 2 0.06
9 1 0.03
10 2 0.06
11 1 0.03
12 2 0.06
13 25 0.71
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (13 bp):
ATGTATCGATAGA
Found at i:1663605 original size:33 final size:33
Alignment explanation
Indices: 1663563--1663659 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
1663553 GTTACAAGCC
1663563 AATGTATCGATACATTTTAGGATGTATCGATAG
1 AATGTATCGATACATTTTAGGATGTATCGATAG
*
1663596 AATGTATCGATATATTTTAGGATGTATCGATAG
1 AATGTATCGATACATTTTAGGATGTATCGATAG
*
1663629 AATGTATCGATACATATT-GTG-TGTATCGATA
1 AATGTATCGATACATTTTAG-GATGTATCGATA
1663660 CAAACAGTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
32 11 0.18
33 49 0.82
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (33 bp):
AATGTATCGATACATTTTAGGATGTATCGATAG
Found at i:1663750 original size:20 final size:21
Alignment explanation
Indices: 1663703--1663755 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1663693 GCCAATGACC
**
1663703 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
1663724 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
1663744 TGTATCGATACA
1 TGTATCGATACA
1663756 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:1663761 original size:13 final size:13
Alignment explanation
Indices: 1663743--1663767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1663733 ACATTTGGTC
1663743 ATGTATCGATACA
1 ATGTATCGATACA
1663756 ATGTATCGATAC
1 ATGTATCGATAC
1663768 TGTGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1665230 original size:20 final size:20
Alignment explanation
Indices: 1665205--1665243 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1665195 AGAGAGCCTT
1665205 AAAATTTTATCAAGGGGAAA
1 AAAATTTTATCAAGGGGAAA
*
1665225 AAAATTTTATTAAGGGGAA
1 AAAATTTTATCAAGGGGAA
1665244 GTTTTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.21, T:0.28
Consensus pattern (20 bp):
AAAATTTTATCAAGGGGAAA
Found at i:1665878 original size:20 final size:19
Alignment explanation
Indices: 1665855--1665927 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
1665845 CAAATCTAGA
*
1665855 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
1665875 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
1665894 TGTATCGATACATACTCAAT
1 TGTATCGATACATGTTC-AT
1665914 TGTATCGATACATG
1 TGTATCGATACATG
1665928 AAACTGGTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.36
20 29 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:1667559 original size:28 final size:28
Alignment explanation
Indices: 1667519--1667590 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
1667509 GAAATAAAGC
** *
1667519 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1667547 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1667575 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1667591 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1667648 original size:52 final size:52
Alignment explanation
Indices: 1667579--1667916 Score: 180
Period size: 52 Copynumber: 6.4 Consensus size: 52
1667569 AAATAACGAG
*
1667579 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
1667631 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * * *
1667684 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGG
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
**** * * *
1667735 GTTGGAGTAT-CCC--TTCG-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATT-GTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
1667790 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATT-G-GTATTTTTGGAAATAAAATCGGA
* * * * *
1667845 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
*
1667896 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
1667917 GAGAATTGAT
Statistics
Matches: 216, Mismatches: 40, Indels: 60
0.68 0.13 0.19
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
50 1 0.00
51 40 0.19
52 75 0.35
53 20 0.09
54 17 0.08
55 39 0.18
56 5 0.02
57 3 0.01
58 7 0.03
59 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:1667794 original size:27 final size:28
Alignment explanation
Indices: 1667731--1667806 Score: 104
Period size: 27 Copynumber: 2.8 Consensus size: 28
1667721 GCGATAAAAC
1667731 CGGGGTTGGAGTATCCCTTCG--GAAATAA
1 CGGGGTTGGAGTATCCC--CGATGAAATAA
*
1667759 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1667786 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1667807 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 2 0.04
27 25 0.56
28 18 0.40
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1670288 original size:13 final size:13
Alignment explanation
Indices: 1670270--1670295 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1670260 ACAAAGATCC
1670270 ATGTATCGATACA
1 ATGTATCGATACA
1670283 ATGTATCGATACA
1 ATGTATCGATACA
1670296 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1670291 original size:33 final size:33
Alignment explanation
Indices: 1670249--1670315 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1670239 AAAATTTCCA
***
1670249 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1670282 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1670315 A
1 A
1670316 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1670907 original size:55 final size:55
Alignment explanation
Indices: 1670823--1671610 Score: 1134
Period size: 55 Copynumber: 14.3 Consensus size: 55
1670813 ATAAACTGTA
* * * * *
1670823 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
1670878 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AAGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
1670933 TCCTGCTCTTTGGGGAAT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
1670988 TCCTGCTCTTTGAGGACTGGAAAATGCCACTAACCTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
1671043 TCCTGTTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGTCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
1671098 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
1671153 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1671208 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
1671263 TCCTGCTCTTTGAGGAC-CGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * * *
1671318 TCCTGCTCTTTGGGGA-TTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1671373 TCCTGCTCGTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1671428 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1671483 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1671538 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1671593 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
1671611 AAAAAGCGGA
Statistics
Matches: 681, Mismatches: 36, Indels: 32
0.91 0.05 0.04
Matches are distributed among these distances:
54 18 0.03
55 642 0.94
56 21 0.03
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:1671177 original size:26 final size:26
Alignment explanation
Indices: 1671093--1671178 Score: 77
Period size: 26 Copynumber: 3.2 Consensus size: 26
1671083 GGTCTTTAAG
1671093 AGGTGTCCTGCTCTTTGGGGACTGAA
1 AGGTGTCCTGCTCTTTGGGGACTGAA
** * *
1671119 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA
1671147 GAGGTGTCCTGCTCTTTGGGGACTGAA
1 -AGGTGTCCTGCTCTTTGGGGACTGAA
1671174 AGGTG
1 AGGTG
1671179 CCACCAACTT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 13 0.29
27 9 0.20
28 9 0.20
29 8 0.18
30 3 0.07
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGGGGACTGAA
Found at i:1671450 original size:27 final size:27
Alignment explanation
Indices: 1671420--1671560 Score: 65
Period size: 27 Copynumber: 5.1 Consensus size: 27
1671410 TGTGGGCTTT
1671420 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
1671447 GAAA-ATG-CCACCAACTTGTGTGGGCTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGACTG
*
1671474 TAAGAGGTGTCCTGCTCTTTGAGGACTG
1 GAA-AGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
1671502 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
1671530 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
1671557 GAAA
1 GAAA
1671561 ATGCCACCAA
Statistics
Matches: 74, Mismatches: 30, Indels: 20
0.60 0.24 0.16
Matches are distributed among these distances:
25 6 0.08
26 10 0.14
27 23 0.31
28 19 0.26
29 10 0.14
30 6 0.08
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:1672596 original size:1 final size:1
Alignment explanation
Indices: 1672592--1672657 Score: 60
Period size: 1 Copynumber: 66.0 Consensus size: 1
1672582 CTTTTCTCTC
* * * * * ** *
1672592 TTTTTCTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTTTTTTGCTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1672657 T
1 T
1672658 GAAGAGAAGG
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.88
Consensus pattern (1 bp):
T
Found at i:1672610 original size:8 final size:8
Alignment explanation
Indices: 1672599--1672643 Score: 83
Period size: 8 Copynumber: 5.8 Consensus size: 8
1672589 CTCTTTTTCT
1672599 TTTTTTTG
1 TTTTTTTG
1672607 TTTTTTTG
1 TTTTTTTG
1672615 TTTTTTTG
1 TTTTTTTG
1672623 TTTTTTTG
1 TTTTTTTG
1672631 TTTTTTT-
1 TTTTTTTG
1672638 TTTTTT
1 TTTTTT
1672644 GCTCTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 6 0.16
8 31 0.84
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1672610 original size:15 final size:16
Alignment explanation
Indices: 1672592--1672654 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 16
1672582 CTTTTCTCTC
1672592 TTTTTCT-TTTTTTTG
1 TTTTTCTGTTTTTTTG
*
1672607 TTTTTTTGTTTTTTTG
1 TTTTTCTGTTTTTTTG
* *
1672623 TTTTTTTGTTTTTTTT
1 TTTTTCTGTTTTTTTG
*
1672639 TTTTTGCTCTTTTTTT
1 TTTTT-CTGTTTTTTT
1672655 TTTGAAGAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.14
16 28 0.67
17 8 0.19
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (16 bp):
TTTTTCTGTTTTTTTG
Found at i:1672651 original size:16 final size:15
Alignment explanation
Indices: 1672600--1672658 Score: 77
Period size: 14 Copynumber: 4.0 Consensus size: 15
1672590 TCTTTTTCTT
1672600 TTTTTTGTTTTTTTG
1 TTTTTTGTTTTTTTG
1672615 TTTTTTTGTTTTTTTG
1 -TTTTTTGTTTTTTTG
1672631 TTTTTT-TTTTTTTG
1 TTTTTTGTTTTTTTG
* *
1672645 CTCTTT-TTTTTTTG
1 TTTTTTGTTTTTTTG
1672659 AAGAGAAGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
14 20 0.49
15 6 0.15
16 15 0.37
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.86
Consensus pattern (15 bp):
TTTTTTGTTTTTTTG
Found at i:1685178 original size:28 final size:28
Alignment explanation
Indices: 1685138--1685209 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
1685128 GAAATAAAGC
** *
1685138 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1685166 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1685194 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1685210 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1685267 original size:52 final size:52
Alignment explanation
Indices: 1685198--1685535 Score: 180
Period size: 52 Copynumber: 6.4 Consensus size: 52
1685188 AAATAACGAG
*
1685198 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
1685250 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * * *
1685303 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGG
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
**** * * *
1685354 GTTGGAGTAT-CCC--TTCG-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATT-GTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
1685409 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATT-G-GTATTTTTGGAAATAAAATCGGA
* * * * *
1685464 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
*
1685515 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
1685536 GAGAATTGAT
Statistics
Matches: 216, Mismatches: 40, Indels: 60
0.68 0.13 0.19
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
50 1 0.00
51 40 0.19
52 75 0.35
53 20 0.09
54 17 0.08
55 39 0.18
56 5 0.02
57 3 0.01
58 7 0.03
59 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:1685413 original size:27 final size:28
Alignment explanation
Indices: 1685350--1685425 Score: 104
Period size: 27 Copynumber: 2.8 Consensus size: 28
1685340 GCGATAAAAC
1685350 CGGGGTTGGAGTATCCCTTCG--GAAATAA
1 CGGGGTTGGAGTATCCC--CGATGAAATAA
*
1685378 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1685405 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1685426 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 2 0.04
27 25 0.56
28 18 0.40
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1687907 original size:13 final size:13
Alignment explanation
Indices: 1687889--1687914 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1687879 ACAAAGATCC
1687889 ATGTATCGATACA
1 ATGTATCGATACA
1687902 ATGTATCGATACA
1 ATGTATCGATACA
1687915 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1687910 original size:33 final size:33
Alignment explanation
Indices: 1687868--1687934 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1687858 AAAATTTCCA
***
1687868 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1687901 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1687934 A
1 A
1687935 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1695307 original size:13 final size:13
Alignment explanation
Indices: 1695289--1695314 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1695279 TACAGCAAGT
1695289 ATGTATCGATACA
1 ATGTATCGATACA
1695302 ATGTATCGATACA
1 ATGTATCGATACA
1695315 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1697570 original size:21 final size:21
Alignment explanation
Indices: 1697537--1697581 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1697527 TTGCAAGTTG
*
1697537 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1697559 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1697579 AAA
1 AAA
1697582 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Done.